BioPerl-1.007002000755000766000024 013155576322 13360 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/.travis.yml000444000766000024 424213155576320 15626 0ustar00cjfieldsstaff000000000000language: perl perl: - "5.26" - "5.24" - "5.20" - "5.18" - "5.16" matrix: include: - perl: 5.18 env: COVERAGE=1 TEST_PARTITION=1 - perl: 5.18 env: COVERAGE=1 TEST_PARTITION=2 - perl: 5.18 env: COVERAGE=1 TEST_PARTITION=3 - perl: 5.18 env: COVERAGE=1 TEST_PARTITION=4 - perl: 5.18 env: COVERAGE=1 TEST_PARTITION=5 - perl: 5.18 env: COVERAGE=1 TEST_PARTITION=6 sudo: false env: global: - PERL_CPANM_OPT="--notest --force --skip-satisfied" - BIOPERL_NETWORK_TESTING=0 # disables the network tests - TEST_PARTITIONS=6 addons: apt: packages: - libdb-dev - graphviz - libgd2-xpm-dev - libxml2-dev before_install: - export BRANCH=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_BRANCH; else echo $TRAVIS_PULL_REQUEST_BRANCH; fi) - git clone git://github.com/travis-perl/helpers ~/travis-perl-helpers - source ~/travis-perl-helpers/init - build-perl - perl -V - cpanm DBD::mysql DBD::Pg DBD::SQLite 2>&1 | tail -n 1 - cpanm Test::Pod 2>&1 | tail -n 1 - cpanm Bio::ASN1::EntrezGene 2>&1 | tail -n 1 - if [ "$TRAVIS_EVENT_TYPE" = "cron" -a "$BRANCH" = "network-cron-master" ]; then export BIOPERL_NETWORK_TESTING=1; git fetch origin master:master; git checkout master; fi - if [ "$BIOPERL_NETWORK_TESTING" = "1" ]; then export TRAVIS_AUTHOR_TESTING=1; export TRAVIS_RELEASE_TESTING=1; cpanm LWP::UserAgent LWP::Protocol::https 2>&1 | tail -n 1; fi - build-dist - cd $BUILD_DIR install: - cpan-install --deps - cpan-install --coverage before_script: - coverage-setup script: - export AUTHOR_TESTING=${TRAVIS_AUTHOR_TESTING:=0} - export RELEASE_TESTING=${TRAVIS_RELEASE_TESTING:=0} - prove -l -j$(test-jobs) $(test-files) after_success: - coverage-report - ./travis_scripts/trigger-dockerhub.sh #TODO - send emails to bioperl-guts-l notifications: email: recipients: - bioperl-guts-l@lists.open-bio.org - cjfields1@gmail.com on_success: change on_failure: change # whitelist branches branches: only: - master - /^release-[1-9]*-[0-9]*-[0-9]*$/ - network-cron-master BioPerl-1.007002/AUTHORS000444000766000024 1450413155576320 14607 0ustar00cjfieldsstaff000000000000=head1 PRIMARY AUTHORS AND MAJOR CONTRIBUTORS TO BIOPERL =head2 Releases co-ordinated and submitted by bioperl core devs. =over =item * Sendu Bala =item * Chris Dagdigian =item * Christopher Fields =item * Mark Jensen =item * Hilmar Lapp =item * Heikki Lehväslaiho =item * Aaron Mackey =item * Brian Osborne =item * Francisco J. Ossandon =item * Jason Stajich =item * Lincoln Stein =back =head2 Previous Bioperl Coordinators: =over =item * Ewan Birney =item * Steven Brenner =item * Georg Fuellen =item * Steve Chervitz =back =head2 Major Contributors (Feel free to add descriptions of which modules you are responsible for if you see fit) =over =item * Richard Adams =item * Shuly Avraham - Bio::Graphics::Glyph =item * Peter Blaiklock =item * Benjamin Berman =item * Matthew Betts =item * David Block =item * Kris Boulez =item * Tim Bunce - code optimizations =item * Scott Cain - Bio::Graphics::Glyph, Bio::DB::GFF::Adaptor::dbi::pg, GFF related tools and scripts =item * Yee Man Chan - Bio::Tools::dpAlign =item * Brad Chapman =item * Roy R. Chaudhuri - Bio::SeqUtils Bio::Align::Utilities =item * Michele Clamp =item * Malcolm Cook =item * Tony Cox =item * James Cuff =item * Andrew Dalke =item * Allen Day =item * Jared Fox - Bio::SeqIO::interpro =item * Brian O'Connor - Bio::TreeIO::svggraph =item * James Diggans =item * Peter Dimitrov - Bio::Ontology =item * Rich Dobson - Bio::PopGen::IO::hapmap,phase =item * Paul Edlefsen =item * Rob Edwards - Bio::Restriction =item * Arne Elofsson =item * David Evans =item * Mark Fiers =item * The Fugu Team =item * Luc Gauthier =item * James Gilbert =item * Nat Goodman =item * Ed Green =item * Matthew Hahn =item * Roger Hall =item * Todd Harris - SVG support in Bio::Graphics =item * Mauricio Herrera Cuadra =item * Ian Holmes =item * Shawn Hoon =item * Robert Hubley =item * Joseph Insana - Bio::LiveSeq =item * Donald Jackson - SiRNA =item * Keith James - Bio::Tools::Geneid =item * Mark A. Jensen - Bio::DB::HIVQuery, Bio::Search::Tiling =item * Nicolas Joly =item * Ian Korf =item * Dan Kortschak =item * Arek Kasprzyk =item * Andreas Kähäri =item * Charles C. Kim =item * Stefan Kirov - Bio::Matrix::PSM =item * Balamurugan Kumarasamy =item * Josh Lauricha - Bio::SeqIO::tigr =item * Eckhard Lehmann =item * Catherine Letondal =item * Philip Lijnzaad =item * Brad Marshall =item * Chad Matsalla =item * Andrew Macgregor =item * Sheldon McKay =item * Dave Messina - Deobfuscator, judicious meddling =item * Chase Miller - Bio::Nexml and related IO modules =item * Juha Muilu =item * Chris Mungall =item * Giri Narasimhan =item * Xiaokang Pan - Bio::Graphics::Glyph =item * Jong Park =item * Matthew Pocock =item * Lorenz Pollack -- BPlite porting =item * Richard Resnick -- original Bio::Seq =item * Todd Richmond =item * Peter Schattner =item * Torsten Seemann -- Bio::Tools::Run::StandaloneBlast =item * Martin Senger -- Bio::Biblio =item * Nigam Shah =item * Shengqiang Shu - Bio::Graphics::Glyph =item * Allen Smith -- Bio::Matrix and Bio::SimpleAlign fixes =item * Marc Sohrmann =item * Robson Francisco de Souza - Bio::Assembly =item * Mark Southern =item * Will Spooner =item * Arne Stabenau =item * Elia Stupka =item * Gert Thijs =item * James Thompson - Bio::Matrix::PSM protein-related modules. =item * Charles Tilford =item * Anthony Underwood =item * Paul-Christophe Varoutas =item * Andrew G. Walsh =item * Kai Wang =item * Gary Williams =item * Mark Wilkinson =item * Helge Weissig =item * Juguang Xiao =item * Alex Zelensky - Bioperl-DB =item * Peili Zhang =item * Christian M. Zmasek - Bio::Phenotype & Bio::Ontology =back BioPerl-1.007002/BUGS000444000766000024 1255213155576320 14223 0ustar00cjfieldsstaff000000000000# $Id: BUGS,v 1.7 2006-11-16 10:51:50 sendu Exp $ Known Bugs Bugs are tracked at this URL: https://github.com/bioperl/bioperl-live/issues Bioperl 1.6 series ============= Though a stable release, some bugs and enhancements remain for this series that will be addressed in future point releases. For a full list please see: https://github.com/bioperl/bioperl-live/issues Bug Summary (additional info) 2247 Have Bio::SearchIO::blast methods available for other BLAST parsers (enhancement request) 2332 Software for analysis of redundant fragments of affys human mitochip v2 (API hasn't stabilized, may appear in a 1.6 point release) 2439 multiple results HTMLResultWriter.pm and non-redundant entries in SearchIO (partially implemented) 2463 bp_seqconvert.pl & Bio::SeqIO code cleanup and user friendly interface (enhancement request) 2476 "Undefined sub-sequence" when processing tblastx output (related to HSP tiling) 2482 paml4 mlc file fails to parse (may require refactoring Bio::Tools::Phylo::PAML) 2492 Method "pi" in package Bio::PopGen::Statistics (awaiting comment from Jason) 2513 creating a Bio::SeqFeature::Annotation object downloads the entire so.obo (should allow local copies) 2594 Bio::Species memory leak (fix implemented, but additional leaks likely remain) 2673 original fields not inherited by seq objects in alignment slices (request for bequest/bequeath behavior for attribute carryover) 2686 WU-BLAST XML support (partially implemented, but issues remain) 2691 Bio::Microarray::Tools::ReseqChip depends on CPAN module Statistics::Frequency (related to bug 2332 above) 2696 global verbosity does not propagate to new objects post-set (requires more specific implementation details) 2700 Refactor Build.PL (some of the behind-the-scenes stuff is a little klunky) 2702 Scripts recopied upon each call to './Build test' (minor bug) 2703 Bio::Tools::GuessSeqFormat guesses SELEX as PHYLIP (minor bug that mistakes format) 2707 Bio::Tools::Run::StandAloneBlast does not quote shell metacharacters in filenames, but Bio::SearchIO::blast does (bug within StandAloneBlast) 2715 LocatableSeq symbols are globally set (bug related to sequence symbol issues; rarely surfaces but needs addressing) Bioperl 1.5.2 ============= There are no known installation bugs in 1.5.2 per se, but issues with external programs may cause problems. See the following URL for details: http://www.bioperl.org/wiki/Release_1.5.2#Notes Bioperl 1.2 =========== * The StandAloneBlast.t test is failing on cygwin installations (and nowhere else). We suspect something to do with temporary file opening. Fixed in 1.4 (set TMPDIR). Bioperl 0.9.0 ============= * Bio::Tools::Blast continues to cause problems for some people. As it is not actively maintained there are a slew of reported bugs for it that have not been fixed. * Bio::Tools::Run::Alignment::TCoffee - t_coffee binary does not get all parameters it needs when aligning (two) two DNA sequences (jitterbug #966). * Bio::Tools::Run::ClustalW and t/ClustalW will report errors for clustalw versions 1.8x due to a bug in clustalw. * Bio::DB::GenBank continues to have intermittent errors. Bio::DB::GDB is also unreliable at times and one can safely ignore errors from these during a make test. Bio::DB::GenBank is unable to download whole contig files as well as NCBI ref seqs like NT_* numbers unless the -format flag is passed in and specified as 'fasta' in the constructor. get_Stream_by_batch() also has intermittent errors which are being tracked down. Bioperl 0.7.2 ============= * NCBI has changed some of the cgi scripts for retrieving sequences online which as resulted in some of the DB methods from not working consistently. We are addressing these in the 0.9.x and 1.0 series of releases. We recommend using the Bio::DB::EMBL object that is part of the later releases. Additionally RefSeq Contigs are not properly downloaded, please see the bioperl list archives for information about potential workarounds and ongoing development effort to address these. Bioperl 0.7.1 ============= * Bio::Tools::BPlite does not parse and set frame properly for tblastx reports (Jitterbug bug # 978). * Bio::Tools::BPlite interface needs to be updated to fix parsing more than bl2seq report report (Jitterbug bug #940), this has been fixed on the main code trunk and will be part of the next major bioperl release. * If File::Temp is not installed, tempdirs are not cleaned up properly. This is fixed on main code trunk with the introduction of rmtree method in Bio::Root::IO, however, it is best to install File::Temp when running 0.7 branch code. * Bio::Tools::Blast does not allow users to run blast, instead use Bio::Tools::Run::StandAloneBlast to run local blasts. To submit jobs to a remote blast server like NCBI a module Bio::Tools::Run::RemoteBlast has been written but is part of the main trunk code and must be obtained through CVS until the next major bioperl release. Bioperl 0.7 =========== * Bio::Tools::BPlite doc error lists code synopsis code as my $parser = new BPlite(\*FH); should be my $parser = new Bio::Tools::BPlite(\*FH); BioPerl-1.007002/BioPerl.pm000444000766000024 1474513155576320 15440 0ustar00cjfieldsstaff000000000000package BioPerl; use strict; # At some future point, when we break the current core into more maintainable # bits, this will have a direct VERSION number, but for now we will be using # the root version for everything use Bio::Root::Version; our $VERSION = $Bio::Root::Version::VERSION; eval $VERSION; 1; __END__ =head1 NAME BioPerl - Perl Modules for Biology =head1 SYNOPSIS If you're new to BioPerl, you should start reading the BioPerl HOWTO's: L =head2 References for Individual Modules For ease of maintenance and coordination amongst contributors, BioPerl code is maintained in a modular form, as is the documentation. Refer to the documentation for individual modules by using perldoc, i.e. C to get documentation for the Bio::Seq object. =head1 DESCRIPTION BioPerl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. These objects not only do what they are advertised to do in the documentation, but they also interact - Alignment objects are made from the Sequence objects, Sequence objects have access to Annotation and SeqFeature objects and databases, Blast objects can be converted to Alignment objects, and so on. This means that the objects provide a coordinated and extensible framework to do computational biology. BioPerl development focuses on Perl classes, or code that is used to create objects representing biological entities. There are scripts provided in the scripts/ and examples/ directories but scripts are not the main focus of the BioPerl developers. Of course, as the objects do most of the hard work for you, all you have to do is combine a number of objects together sensibly to make useful scripts. The intent of the BioPerl development effort is to make reusable tools that aid people in creating their own sites or job-specific applications. The BioPerl website at L also attempts to maintain links and archives of standalone bio-related Perl tools that are not affiliated or related to the core BioPerl effort. Check the site for useful code ideas and contribute your own if possible. =head1 INSTALLATION The BioPerl modules are distributed as a tar file that expands into a standard perl CPAN distribution. Detailed installation directions can be found in the distribution INSTALL file. Installing on windows using ActiveState Perl is covered in the INSTALL.WIN file. We highly suggest reading the installation instructions on the BioPerl website: L Note that only the following are supported at this time with the current API: =over 3 =item BioPerl-db =item BioPerl-network =item BioPerl-run =item BioPerl-pedigree =item Bio::Graphics =back =head1 GETTING STARTED The distribution I directory has working scripts for use with BioPerl, check the self-described I directory as well. You are more than welcome to contribute your script! If you have installed BioPerl in the standard way, as detailed in the INSTALL in the distribution, these scripts should work by just running them. If you have not installed it in a standard way you will have to change the 'use lib' to point to your installation (see INSTALL for details). =head1 GETTING INVOLVED BioPerl is a completely open community of developers. We are not funded and we don't have a mission statement. We encourage collaborative code, in particular in Perl. You can help us in many different ways, from just a simple statement about how you have used BioPerl to doing something interesting to contributing a whole new object hierarchy. See L for more information. Here are some ways of helping us: =head2 Asking questions and telling us you used it We are very interested to hear how you experienced using BioPerl. Did it install cleanly? Did you understand the documentation? Could you get the objects to do what you wanted them to do? If BioPerl was useless we want to know why, and if it was great - that too. Post a message to B, the BioPerl mailing list, where all the developers are. Only by getting people's feedback do we know whether we are providing anything useful. =head2 Writing a script that uses it By writing a good script that uses BioPerl you both show that BioPerl is useful and probably save someone elsewhere writing it. If you contribute it to the 'script central' at L then other people can view and use it. Don't be nervous if you've never done this sort of work, advice is freely given and all are welcome! =head2 Find bugs! We know that there are bugs in this code. If you find something which you are pretty sure is a problem, post a bug report using our Bugzilla tracking system: L Please read the main bug tracking (L) for an overview of what we expect in a bug report. Specifically, having a code and data example where appropriate helps tremendously. We gladly accept all patches after a quick code review. =head2 Suggest new functionality You can suggest areas where the objects are not ideally written and could be done better. The best way is to find the main developer of the module (each module was written principally by one person, except for Seq.pm). Talk to him or her and suggest changes. =head2 Make your own objects If you can make a useful object we will happily include it into the core. Probably you will want to read a lot of the documentation in L and talk to people on the BioPerl mailing list, B. =head2 Writing documentation We appreciate good documentation. It's what tells the world what's in BioPerl, it's what instructs the user, it's what describes the rationale and inner workings of the package. Feel free to contribute. =head1 ACKNOWLEDGEMENTS For a more detailed history of the BioPerl project, we recommend the History of BioPerl: L =head1 COPYRIGHT Copyright (c) 1996-2009 Georg Fuellen, Richard Resnick, Steven E. Brenner, Chris Dagdigian, Steve Chervitz, Ewan Birney, James Gilbert, Elia Stupka, and others. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Build.PL000444000766000024 4046613155576320 15041 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl # This is a Module::Build script for Bioperl installation. # See http://search.cpan.org/~kwilliams/Module-Build/lib/Module/Build.pm # Uses a custom subclass of Module::Build called Bio::Root::Build # In the future developers may need to alter the requires and recommends # sections of Bio::Root::Build->new() below, but otherwise nothing else here is # likely to need changing. use strict; use lib '.'; use Bio::Root::Build; # XML::SAX::RTF doesn't work with BioPerl, at all, nada, zilch. # # Since we're running into this now on CPAN Testers, catch it up front and # deal with it. # # See: https://rt.cpan.org/Ticket/Display.html?id=5943 # https://redmine.open-bio.org/issues/2975 { eval { require XML::SAX; 1; }; unless ($@) { if ( grep { $_->{Name} =~ 'XML::SAX::RTF' } @{ XML::SAX->parsers() } ) { warn < [0, # 'Access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace'], 'Algorithm::Munkres' => [ 0, 'Phylogenetic Networks/Bio::PhyloNetwork' ], 'Array::Compare' => [ 0, 'Phylogenetic Networks/Bio::PhyloNetwork' ], # this won't actually install due to circular dep, but we have no way of # doing a post-install the [circular dependency!] specifies it is only # installed on explicit request for this specific module, not when simply # choosing to install 'all' modules #'Bio::ASN1::EntrezGene' => [0, # 'Parsing entrezgene/Bio::SeqIO::entrezgene [circular dependency!]'], 'Bio::Phylo' => [ 0, 'NeXML related modules/Bio::AlignIO::nexml,Bio::Nexml::Factory,' . 'Bio::SeqIO::nexml,Bio::TreeIO::nexml' ], 'CGI' => [ 0, 'CGI-y things/Bio::DB::Query::HIVQuery' ], 'Clone' => [ 0, 'Cloning objects/Bio::Root::Root,Bio::Tools::Primer3' ], 'Convert::Binary::C' => [ 0, 'Strider functionality/Bio::SeqIO::strider' ], 'DB_File' => [ 0, 'Database functionality/Bio::Assemby,Bio::DB' ], 'Error' => [ 0, 'OO-based exception handling (very optional)/Bio::Root::Exception' ], 'GD' => [ 0, 'Alignment graphic output/Bio::Align::Graphics' ], 'Graph' => [ 0.50, 'Phylogenetic Networks, ontology engine implementation, contig analysis' . '/Bio::PhyloNetwork,Bio::Ontology::SimpleGOEngine::GraphAdaptor,' . 'Bio::Assembly::Tools::ContigSpectrum' ], 'GraphViz' => [ 0, 'Phylogenetic Network Visualization/Bio::PhyloNetwork::GraphViz' ], 'HTML::Entities' => [ 0, 'Remote analysis POST submissions/Bio::SearchIO::blastxml' ], 'HTML::HeadParser' => [ 3, 'Parsing section of HTML docs/Bio::Tools::Analysis::DNA::ESEfinder' ], 'HTML::TableExtract' => [ 0, 'Parsing HTML tables/Bio::DB::SeqVersion::gi' ], 'HTTP::Request::Common' => [ 0, 'GenBank+GenPept sequence retrieval, remote http Blast jobs' . '/Bio::DB::*,Bio::Tools::Run::RemoteBlast,' . 'Bio::Tools::Analysis::Protein*,Bio::Tools::Analysis::DNA*' ], 'Inline::C' => [ 0.67, 'Speeding up code like Fasta Bio::DB::Fasta' ], 'IO::Scalar' => [ 0, 'Deal with non-seekable filehandles/Bio::Tools::GuessSeqFormat' ], 'List::MoreUtils' => [ 0, 'Back- or reverse-translation of sequences/' . 'Bio::Tools::SeqPattern,Bio::Tools::SeqPattern::BackTranslate' ], 'LWP::UserAgent' => [ 0, 'Remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::WebAgent' ], 'PostScript::TextBlock' => [ 0, 'EPS output/Bio::Tree::Draw::Cladogram' ], 'Set::Scalar' => [ 0, 'Proper operation/Bio::Tree::Compatible' ], 'Sort::Naturally' => [ 0, 'Sort lexically, but sort numeral parts numerically/' . 'Bio::Assembly::IO::ace,Bio::Assembly::IO::tigr' ], 'Spreadsheet::ParseExcel' => [ 0, 'Parsing Excel files/Bio::SeqIO::excel' ], 'Storable' => [ 2.05, 'Storing sequence objects in local file cache/' . 'Bio::DB::FileCache,Bio::SeqFeature::Collection,Bio::PopGen::HtSNP,' . 'Bio::PopGen::TagHaplotype,Bio::DB::GFF::Adaptor::berkeleydb,Bio::Root::Root' ], 'SVG' => [ 2.26, 'Creating SVG images/Bio::Draw::Pictogram' ], 'SVG::Graph' => [ 0.01, 'Creating SVG images/Bio::TreeIO::svggraph' ], 'Text::ParseWords' => [ 0, 'Test scripts/Bio::DB::SeqFeature::Store::FeatureFileLoader' ], 'XML::DOM' => [ 0, 'Parsing XML/Bio::SeqIO::bsml,Bio::SeqIO::interpro' ], 'XML::DOM::XPath' => [ 0, 'Parsing XML/Bio::SeqIO::interpro' ], 'XML::LibXML' => [ 0, 'Parsing XML/Bio::SeqIO::seqxml,Bio::TreeIO::phyloxml' ], 'XML::Parser' => [ 0, 'Parsing XML/Bio::OntologyIO::InterProParser' ], 'XML::Parser::PerlSAX' => [ 0, 'Parsing XML/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,', 'Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp' ], 'XML::SAX' => [ 0.15, 'Parsing XML/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax' ], 'XML::SAX::Writer' => [ 0, 'Writing XML/Bio::SeqIO::tigrxml' ], 'XML::Simple' => [ 0, 'Reading custom XML/Bio::Tools::EUtilities,Bio::DB::HIV,Bio::DB::Query::HIVQuery' ], 'XML::Twig' => [ 0, 'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez' ], 'XML::Writer' => [ 0.4, 'Parsing and writing XML/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,' . 'Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,' . 'Bio::SearchIO::Writer::BSMLResultWriter' ], 'YAML' => [ 0, 'GenBank->GFF3/bp_genbank2gff3.pl' ], ); my $mysql_ok = 0; my @drivers = available_drivers(); # Set up the Bio::Root::Build object my $build = Bio::Root::Build->new( module_name => 'Bio', dist_name => 'BioPerl', dist_version => $Bio::Root::Version::VERSION, dist_author => 'BioPerl Team ', dist_abstract => 'Bioinformatics Toolkit', license => 'perl', requires => { 'perl' => '5.6.1', 'IO::String' => 0, # why is this required? 'Data::Stag' => 0.11, # Bio::SeqIO::swiss, we can change to 'recommend' if needed 'Scalar::Util' => 0, # not in Perl 5.6.1, arrived in core in 5.7.3 'ExtUtils::Manifest' => '1.52', # allows spaces in file names }, configure_requires => { 'Module::Build' => 0.42, }, build_requires => { 'Module::Build' => 0.42, 'CPAN' => 1.81, 'Test::Harness' => 2.62, 'Test::Most' => 0, 'URI::Escape' => 0 }, recommends => { # reverted to a simple Module::Build-compatible hash, but we keep # additional data in the %recommends hash above. May be converted to # something simpler if there aren't complaints down the line. map { $_ => $recommends{$_}[0] } sort keys %recommends }, get_options => { accept => {}, network => {} # say 'perl Build.PL --network' to manually request network tests }, auto_features => { 'EntrezGene' => { description => "Presence of Bio::ASN1::EntrezGene", requires => { 'Bio::ASN1::EntrezGene' => 0 } # feature_requires is like requires, except that it doesn't trigger installation }, 'DB_File Tests' => { description => "BDB tests for Bio::DB::SeqFeature::Store", requires => { 'DB_File' => 0 } # feature_requires is like requires, except that it doesn't trigger installation }, 'Bio::DB::GFF Tests' => { description => "Bio::DB::GFF database tests (will need to answer questions before really enabling)", requires => { 'DBI' => 0 }, }, 'MySQL Tests' => { description => "MySQL-related tests for Bio::DB::SeqFeature::Store", requires => { 'DBI' => 0, 'DBD::mysql' => 0 }, }, 'Pg Tests' => { description => "PostgreSQL-related tests for Bio::DB::SeqFeature::Store", requires => { 'DBI' => 0, 'DBD::Pg' => 0 }, }, 'SQLite Tests' => { description => "SQLite-related tests for Bio::DB::SeqFeature::Store", requires => { 'DBI' => 0, 'DBD::SQLite' => 0 }, }, 'Network Tests' => { description => "Enable tests that need an internet connection", requires => { 'LWP::UserAgent' => 0 }, } }, dynamic_config => 1, recursive_test_files => 1, # Extra files needed for BioPerl modules xml_files => { './Bio/DB/HIV/lanl-schema.xml' => 'lib/Bio/DB/HIV/lanl-schema.xml' }, #pm_files => {} # modules in Bio are treated as if they were in lib and auto-installed #script_files => [] # scripts in scripts directory are installed on-demand ); my $accept = $build->args('accept'); my $proceed = prompt_for_biodb($accept) if $build->feature('Bio::DB::GFF') || $build->feature('MySQL Tests') || $build->feature('Pg Tests') || $build->feature('SQLite Tests'); # Handle auto features if ( $proceed && $build->feature('DB_File Tests') ) { # will return without doing anything if user chose not to run tests during make_bdb_test(); } if ($proceed && ( $build->feature('MySQL Tests') || $build->feature('Pg Tests') || $build->feature('SQLite Tests') ) ) { make_dbi_test(); } # Ask questions $build->choose_scripts($accept); if ( $build->args('network') ) { if ( $build->feature('Network Tests') ) { $build->notes( network => 1 ); $build->log_info(" - will run internet-requiring tests\n"); } else { $build->notes( network => 0 ); $build->log_info( " - Missing LWP::UserAgent, can't run network tests\n"); } } else { $build->prompt_for_network($accept) if $build->feature('Network Tests'); } # Add additional files here $build->add_build_element('xml'); if ( ! -e 'MANIFEST' ) { $build->ACTION_manifest(); } # Create the build script and exit $build->create_build_script(); exit; ########################## Helper subs ########################## sub make_bdb_test { my $path0 = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature.t' ); my $path = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature_BDB.t' ); unlink($path) if ( -e $path ); open my $F, '>', $path or die "Could not write test file '$path': $!\n"; print $F <add_to_cleanup($path); #$build->add_to_manifest_skip($path); } sub available_drivers { eval { require DBI; 1; }; # if not installed, this sub won't actually be called return if $@; @drivers = DBI->available_drivers; unless ( grep {/mysql|Pg|SQLite/i} @drivers ) { $mysql_ok = 0; return "Only MySQL, Postgres and SQLite DBI drivers supported for Bio::DB::SeqFeature RDMS tests"; } $mysql_ok = 1; return @drivers; } sub make_dbi_test { my $dsn = $build->notes('test_dsn') || return; my $path0 = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature.t' ); my $driver = $build->notes('dbd_driver'); my $path = File::Spec->catfile( 't', 'LocalDB', ( $driver eq 'mysql' ) ? 'SeqFeature_mysql.t' : ( $driver eq 'SQLite' ) ? 'SeqFeature_SQLite.t' : 'SeqFeature_Pg.t' ); my $test_db = $build->notes('test_db'); my $user = $build->notes('test_user'); my $pass = $build->notes('test_pass'); open my $F, '>', $path or die "Could not write file '$path' for DBI test: $!\n"; my $str = "$path0 -adaptor DBI::$driver -create 1 -temp 1 -dsn \"$dsn\""; $str .= " -user $user" if $user; $str .= " -password $pass" if $pass; print $F <add_to_cleanup($path); $build->add_to_cleanup($test_db) if $driver eq 'SQLite'; #$build->add_to_manifest_skip($path); } sub test_biodbgff { eval { require DBI; }; # if not installed, this sub won't actually be called return if $@; @drivers = DBI->available_drivers; unless ( grep {/mysql|Pg|Oracle/i} @drivers ) { return "MySQL, Pg nor Oracle DBI drivers are installed"; } return; } sub prompt_for_biodb { my $accept = shift; my $proceed = $accept ? 0 : $build->y_n( "Do you want to run the Bio::DB::GFF or " . "Bio::DB::SeqFeature::Store live database tests? " . "y/n", 'n' ); if ($proceed) { my @driver_choices; foreach my $poss ( 'SQLite', 'mysql', 'Pg', 'Oracle' ) { if ( grep {/$poss/i} @drivers ) { my $choice = $poss; $choice =~ s/^(.)/[$1]/; push( @driver_choices, $choice ); } } my $driver; if ( @driver_choices > 1 ) { my ($default) = $driver_choices[0] =~ /\[(.)/; $driver = $build->prompt( "Which database driver should be used? " . join( " ", @driver_choices ), $default ); } else { ($driver) = $driver_choices[0] =~ /\[(.)/; } if ( $driver =~ /^[mM]/ ) { $driver = 'mysql'; } elsif ( $driver =~ /^[pP]/ ) { $driver = 'Pg'; } elsif ( $driver =~ /^[oO]/ ) { $driver = 'Oracle'; } elsif ( $driver =~ /^[sS]/ ) { $driver = 'SQLite'; } my $test_db = $build->prompt( "Which database should I use for testing the $driver driver?\n" . "This database should already be present but doesn't have to " . "be preloaded for any schema", 'test' ); my $test_host = $build->prompt( "On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost' ); my $test_user = $build->prompt( "User name for connecting to database '$test_db'?", 'undef' ); my $test_pass = $build->prompt( "Password for connecting to database '$test_db'?", 'undef' ); my $use_host = 1; if ( $test_host eq 'undef' || $test_host eq 'localhost' ) { $use_host = 0; } my $test_dsn; if ( $driver eq 'Pg' || $driver eq 'SQLite' ) { $test_dsn = "dbi:$driver:dbname=$test_db"; $mysql_ok = 0; } else { $test_dsn = "dbi:$driver:database=$test_db"; $mysql_ok = 0; } if ($use_host) { $test_dsn .= ";host=$test_host"; } $build->notes( dbd_driver => $driver ); $build->notes( test_db => $test_db ); $build->notes( test_host => $test_host ); $build->notes( test_user => $test_user eq 'undef' ? undef : $test_user ); $build->notes( test_pass => $test_pass eq 'undef' ? undef : $test_pass ); $build->notes( test_dsn => $test_dsn ); $build->log_info( " - will run tests with database driver '$driver' and these settings:\n", " Database $test_db\n", " Host $test_host\n", " DSN $test_dsn\n", " User $test_user\n", " Password $test_pass\n" ); $build->log_info( " - will not run the BioDBSeqFeature live " . "database tests (requires MySQL or Pg driver)\n" ) unless ( $driver eq 'mysql' or $driver eq 'Pg' ); } else { $build->log_info( " - will not run the BioDBGFF or BioDBSeqFeature live database tests\n" ); } $build->log_info("\n"); return $proceed; } BioPerl-1.007002/Changes000444000766000024 24572513155576320 15065 0ustar00cjfieldsstaff000000000000--------------------------------------------------------- Revision history for BioPerl core modules --------------------------------------------------------- The comprehensive history and ongoing development of BioPerl: http://github.com/bioperl/bioperl-live Some of that history is also highlighted on our wiki: http://www.bioperl.org/wiki/Change_log http://www.bioperl.org/wiki/History_of_BioPerl Bugs and requested features list: https://github.com/bioperl/bioperl-live/issues CPAN releases are branched from 'master'. --------------------------------------------------------- Philosophy for 1.7.x: In order to reduce the number of dependencies, we are actively encouraging developers wanting to submit new code with additional dependencies to release code in a separate repository and release it on CPAN. We can help assist in this process and can also place this under the 'bioperl' Github organization (and similarly under the bioperl umbrella account in CPAN), though this is not required. We will also be moving additonal code to other repositories and will release them separately on CPAN. Modules considered obsolute (relies on a dead web service or utilizes strict dependencies that are also considered obsolete) will be removed. 1.7.2 - "Entebbe" [Bugs] * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks] * #245 - Code coverage fixes [zmughal,cjfields] * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne] * #238 - Use a Travis cron job for network tests [zmughal,cjfields] * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne] * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne] * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields] * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields] * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne] * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne] * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields] * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp] [Code changes] * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug] 1.7.1 - "Election" [Bugs] * Minor release to incorporate fix for CPAN indexing, which prevented proper updates [cjfields] * Fix problem in managing Target attribute for gff3 [Jukes34] * Minor bug fixes related to NCBI HTTPS support [cjfields] 1.7.0 - "Disney" [New site] * We have migrated to Github Pages. This was actually planned, but the recent OBF server compromise forced our hand. Brian Osborne [bosborne] took this under his wing to move docs and has done a tremendous amount of work formatting the site and working out some of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul Cantalupo and Franscison Ossandon also helped. Kudos!! * Similarly, the official issue tracker is now Github Issues. This has been updated in the relevant documentation bits (we hope!) [Code changes] * Previously deprecated modules removed * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif * Bio::DB::SeqHound has been removed due to the service no longer being available * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security reasons due to the server no longer having a valid cert * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN * Bio::Coordinate, Bio::SearchIO::blastxml, Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be added on CPAN [New features] * Docker instances of tagged releases are available! [hlapp] * NCBI HTTPS support [mjohnson and others] * Bio::SearchIO::infernal - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo] * Bio::Search::HSP::ModelHSP - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH reports [pcantalupo] * Bio::Search::Result::INFERNALResult - Added new module to represent features of Infernal reports [pcantalupo] * Bio::DB::Taxonomy SQLite option [cjfields] * WrapperBase quoted option values [majensen] * Various documentation fixes and updates [bosborne] [Bug Fixes] * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields] * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne] * NeXML parser fixes [fjossandon] * Bug fix for Bio::DB::SeqFeature memory adapter [lstein] * RT 103272 : SeqFeature database deletion skipped features with a decimal - Joshua Fortriede (Xenbase) * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon] * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon] * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon] * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields] * Issue #84: EMBL format wrapping problem [nyamned] * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon] * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex or compiled C code (when Inline::C is installed) [rocky] * Fix various Bio::Tools::Analysis remote server config problems [cjfields] * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon] * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon] * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef to be consistent with "$hit->bits" behaviour [fjossandon] * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF aminoacids made "next_seq" confused and broke the parser [fjossandon] * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table Definition, so now "join(complement(C..D),complement(A..B))" is equivalent to "complement(join(A..B,C..D))" [fjossandon] * For the many many many fixes that weren't mentioned - blame the release guy! 1.6.924 [Significant changes] * Bug/feature issue tracking has moved to GitHub Issues: https://github.com/bioperl/bioperl-live/issues * DB_File has been demoted from "required" to "recommended", which should make easier for Windows users to install BioPerl if they don't need that module. [New features] * Bio::Search::HSP::GenericHSP - Bug #3370, added a "posterior_string" method to retrieve the posterior probability lines (PP) from HMMER3 reports [fjossandon] - Added a "consensus_string" method to retrieve the consensus structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon] * Bio::SearchIO::hmmer2 - The number of identical and conserved residues are now calculated directly from the homology line [fjossandon] - Now the Query Length and Hit Length are reported when the alignment runs until the end of the sequence/model ('.]' or '[]') [fjossandon] - Implemented the capture of the consensus structure lines [fjossandon] * Bio::SearchIO::hmmer3 - The number of identical and conserved residues are now calculated directly from the homology line [fjossandon] - Now the Hit Length is reported when the alignment runs until the end of the sequence/model ('.]' or '[]') [fjossandon] - Implemented the capture of the consensus structure lines [fjossandon] - Implemented the capture of the posterior probability lines [fjossandon] - Completed the development of NHMMER parsing, including alignments [fjossandon] * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder - Feature #2615, moved "_init_parse_params", "max_significance, "signif", "min_score", "min_bits, and "hit_filter" methods from 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'. This means that the Bio::SearchIO->new() parameters '-signif', '-score', '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats besides Blast, instead of being ignored. Added tests for all moved methods using HMMER outputs and run the full test suite and everything pass [fjossandon] * Bio::SeqIO::MultiFile - Autodetection of file format [fangly] * Bio::Tools::GuessSeqFormat: - Format detection from non-seekable filehandles such as STDIN [fangly] [Bug fixes] * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley] * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley] * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks] * Abstract: Fixed ActivePerl incapability of removing temporary files because of problems closing tied filehandles [fjossandon] * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing because ActivePerl were producing a ".index.pag" and ".index.dir" files instead of a single ".index" file (like Strawberry Perl). Now those temporary files are correctly considered and deleted. [fjossandon] * Test files: Added missing module requirements (DB_File and Data::Stag) to several tests files that were failing because those modules were not present. Now those test files are correctly skipped instead. [fjossandon] * Blast: Added support to changes in bl2seq from BLAST+ output, which now uses "Subject=" instead of ">" to start hit lines [yschensandiego] * Phylip: Return undef in "next_aln" at file end to avoid an infinite loop [yschensandiego] * HMMER3: When a hit description is too long, it is truncated in the Scores table. In those cases, the more complete description from the Annotation line (>>) will be used [fjossandon] * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN), since it is now used by HMMER3 format in alignments [fjossandon] * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit" to return undef if the query/hit length is unknown (like in some HMMER outputs), to avoid division by 0 crashes. Also "query_length" now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon] * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs, added support to multi-query reports, reduced code redundancy, and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon] * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon] * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon] * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne] * Fixed some Bio::Root::Utilities subroutines [fjossandon] * Double-quotes on paths are needed in some places [fjossandon] * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon] * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon] * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml with the latest changes made in their own repositories [fjossandon] * General synching of files with the master branch [fjossandon] * Fixed tests failing in Windows because of using Linux commands [fjossandon] * Closed many open filehandles that prevented temporary files deletion [fjossandon] * Fixed broken MeSH parser [fjossandon] * Fixed missing detection of format in SeqIO when given a -string [fangly] 1.6.923 * Major Windows support updates! [fjossandon] * MAKER update to allow for stricter standard codon table [cjfields] * Better support for circular sequences [fjossandon] * Fixes for some complex location types [fjossandon] * Address CONTIG bug in GenBank format, bug #3448 [cjfields] * Fix bug #2978 related to BLAST report type [fjossandon] * Deobfuscator fixes [DaveMessina] 1.6.922 * Address CPAN test failures [cjfields] * Add BIOPROJECT support for Genbank files [hyphaltip] * Better regex support for HMMER3 output [bosborne] 1.6.921 * Minor update to address CPAN test failures 1.6.920 * Remove Bio::Biblio and related files [carandraug] - this cause version clashes with an independently-released version of Bio::Biblio 1.6.910 [New features] * Hash randomization fixes for perl 5.18.x - Note: at least one module (Bio::Map::Physical) still has a failing test; this is documented in bug #3446 and has been TODO'd; we will be pulling Bio::Map and similar modules out of core into separate distributions in the 1.7.x release series [cjfields] [New features] * Bio::Seq::SimulatedRead - New module to represent reads taken from other sequences [fangly] * Bio::Root::Root - Support of Clone::Fast as a faster cloning alternative [fangly] * Bio::Root::IO - Moved the format() and variant() methods from Bio::*IO modules to Bio::Root::IO [fangly] - Can now use format() to get the type of IO format in use [fangly] * Bio::Tools::IUPAC - New regexp() method to create regular expressions from IUPAC sequences [fangly] * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq: - Code refresh [fangly] * Bio::DB::Taxonomy - Added support for the Greengenes and Silva taxonomies [fangly] * Bio::Tree::TreeFunctionsI - get_lineage_string() represents a lineage as a string [fangly] - add_trait() returns instead of reporting an error when the column number is exceeded in add_trait() [fangly] - Option to support tree leaves without trait [fangly] - Allow ID of 0 in trait files [fangly] * Bio::DB::Taxonomy::list - Misc optimizations [fangly] - Option -names of get_taxon() to help with ambiguous taxa [fangly] * Bio::DB::Taxonomy::* - get_num_taxa() returns the number of taxa in the database [fangly] * Bio::DB::Fasta and Bio::DB::Qual - support indexing an arbitrary list of files [fangly] - user can supply an arbitrary index file name [fangly] - new option to remove index file at the end [fangly] * Bio::DB::Fasta - now handles IUPAC degenerate residues [fangly] * Bio::PrimarySeq and Bio::PrimarySeqI - speed improvements for large sequences [Ben Woodcroft, fangly] * Bio::PrimaryQual - tightened and optimized quality string validation [fangly] * Bio::SeqIO::fasta - new method and option 'block', to create FASTA output with space intervaled blocks (similar to genbank or EMBL) has been implemented. - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed in favour of the methods 'width' and 'preferred_id_type` respectively. * Bio::FeatureIO::* - moved from bioperl-live into the separate distribution Bio-FeatureIO * Bio::SeqFeature::Annotated - moved from bioperl-live into the separate distribution Bio-FeatureIO * Bio::Cluster::SequenceFamily - improved performance when using get_members with overlapping multiple criteria * Bio::SearchIO::hmmer3 - now supports nhmmer [bosborne] [Bug fixes] * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo] * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo] * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version information was lost in a multi-result blast file [Paul Cantalupo] * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate total gaps [Paul Cantalupo] * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo] * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case when end of domain indicator is split across lines [Paul Cantalupo] * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web, cjfields] * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches instances where blank lines are within sequences [cjfields] * Bio::DB::Fasta reports correct alphabet for files with multiple sequence types [fangly] * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly] * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard, cjfields] * Various fixes for Stockholm file indexing and processing [bosborne] * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0 breaks parsing [cjfields] * Fix case where Bio::Seq::Meta* objects with no meta information could not be reverse-complemented [fangly] * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly] * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically when unsure that values will be numerical [fangly] * Fix undef warnings in Bio::SeqIO::embl [fangly] * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly] * Fix Bio::Tools::IUPAC should accept any sequence object [fangly] * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier Sallou] * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag, source_tag and display_name must return a string, not undef [fangly] * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI add_SeqFeature takes a single argument [fangly] * Use cross-platform filenames and temporary directory in Bio::DB::Taxonomy::flatfile [fangly] * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not properly identified as existing taxa in the database [fangly] * Fix issue where a Bio::DB::Taxonomy::list object could not be created without also passing a lineage to store [fangly] * Prevent passing a directory to the gi2taxid option (-g) of bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning [fangly] * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly] * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly] * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species object before trying to access, and no longer returns repeated sequences. 1.6.901 May 18, 2011 [Notes] * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and modules using Ace will also be deprecated [lds, cjfields] * Minor bug fix release * Bio::SeqIO::gbxml tests require XML::SAX [hartzell] * Address Build.PL issues when DBI is not present [hartzell] * Skip gbxml.t and Interpro tests when modules not installed [cjfields] * Remove deprecated code for perl 5.14.0 compat [cjfields] * Due to schema changes and lack of support for older versions, support for NeXML 0.9 is only (very) partially implemented. See: https://redmine.open-bio.org/issues/3207 [Bug fixes] * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with docs [genehack, cjfields] * $VERSION for CPAN/cpanm-based installs was broken; force setting of module version from dist_version (probably not the best way to do this, but it seems to work) [rbuels, cjfields] 1.6.900 April 14, 201 [Notes] * This will probably be the last release to add significant features to core modules; subsequent releases will be for bug fixes alone. We are planning on a restructuring of core for summer 2011, potentially as part of the Google Summer of Code. This may become BioPerl 2.0. * Version bump represents 'just prior to v 1.7'. We may have point releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc. This code essentially is what is on the github master branch. [New features] * Core code updated for perl 5.12.x [cjfields, Charle Tilford] * Bio::Tree refactor - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs - removal of Scalar::Util::weaken code, which was causing odd headaches with premature GC, memory leaks with perl 5.10.0, etc [cjfields] * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain, many others] * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs [Warren Kretzschmar] * Bio::SeqIO::gbxml - bug 2515 - new contribution [Ryan Golhar, jhannah] * Bio::Assembly::IO - support for reading Maq, Sam and Bowtie files [maj] - support for reading 454 GS Assembler (Newbler) ACE files [fangly] - bug 2483: support for writing ACE files [Joshua Udall, fangly] - bug 2599: support DBLINK annotation in GenBank files [cjfields] - bug 2726: reading/writing granularity: whole scaffold or one contig at a time [Joshua Udall, fangly] * Bio::OntologyIO - Added parsing of xrefs to OBO files, which are stored as secondary dbxrefs of the cvterm [Naama Menda] - General Interpro-related code refactors [dukeleto, rbuels, cjfields] * PAML code updated to work with PAML 4.4d [DaveMessina] [Bug fixes] * [3198] - sort tabular BLAST hits by score [DaveMessina] * [3196] - fix invalid metadata produced by latest Module::Build [cjfields] * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields] * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW [cjfields] * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields] * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields] * [3164] - TreeFunctionsI syntax bug [gjuggler] * [3163] - AssemblyIO speedup [fangly] * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo, hyphaltip] * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip] * [3158] - fix EMBL file mis-parsing [cjfields] * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry, cjfields] * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields] * [3148] - URL change for UniProt [cjfields] * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields] * [3136] - HMMer3 parser fixes [kblin] * [3126] - catch description [Toshihiko Akiba] * [3122] - Catch instances where non-seekable filehandles were being seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri] * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file [dukeleto, rbuels, cjfields] * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann, jhannah] * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford] * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser, cjfields] * [3107] - BLAST alignment column_from_residue_number() [cjfields] * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields] * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields] * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields] * [3086] - EMBL misparsing long tags [kblin, cjfields] * [3085] - CommandExts and array of files [maj, hyphaltip] * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates for alignment slices [Ha X. Dang, cjfields] * [3076] - XMFA alignment strand wrong [Ha X., cjfields] * [3073] - fix parsing of GenBank files from RDP [cjfields] * [3068] - FASTQ parse failure with trailing 0 [cjfields] * [3064] - All-gap midline BLAST report issues [cjfields] * [3063] - BLASt report RID [Razi Khaja, cjfields] * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields] * [3053] - LOCUS line formatting [M. Wayne, cjfields] * [3039] - correct Newick output root node branch length [gjuggler, DaveMessina] * [3038] - SELEX alignment error [Bernd, cjfields] * [3033] - PrimarySeq ID setting [Bernd, maj] * [3032] - Fgenesh errors [Wes Barris, hyphaltip] * [3034] - AlignIO::clustal output [Bernd, DaveMessina] * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields] * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields] * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields] * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with PAML 4.4d [DaveMessina] * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon, DaveMessina] * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields] * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields] * [3017] - using threads with Bio::DB::GenBank [cjfields] * [3012] - Bio::Root::HTTPget fixes [maj, cjfields] * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields] * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields] * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj] * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney, cjfields] * [2983] - fix score/percent ID mixup [Alexie Papanicolaou] * [2977] - TreeIO issues [DaveMessina] * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj] * [2944] - Bio::Tools::GFF score [cjfields] * [2942] - correct MapTiling output [maj] * [2939] - PDB residue insertion codes [John May, maj] * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj] * [2928] - GuessSeqFormat raw [maj] * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields] * [2922] - open() directive issue [cjfields] * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields] * [2901] - DNAStatistics div by zero error [Janet Young, cjfields] * [2899] - SeqFeature::Store host issues [lstein, dbolser] * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser, cjfields] * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields] * [2876] - CDD search with RemoteBlast [Malcolm Cook] * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina] * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields] * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields] * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields] * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields] * [2758] - Bio::AssemblyIO ace problems [fangly] * [2744] - Bio::LocatableSeq::end [Bernd, cjfields] * [2726] - ace file IO [Josh, fangly] * [2700] - Refactor Build.PL [cjfields] * [2673] - addition of simple Root-based clone() method [cjfields] * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly] * [2599] - support for DBLINK annotation in GenBank files [cjfields] * [2594] - Bio::Species memory leak [cjfields] * [2515] - GenBank XML parser [jhannah] * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip] * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly] * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly, cjfields] * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip] [Deprecated] * Bio::Expression modules - these were originally designed to go with the bioperl-microarray suite of tools, however they have never been completed and so have been removed from the distribution. The original code has been moved into the inactive bioperl-microarray suite. [cjfields] [Other] * Repository moved from Subversion (SVN) to http://github.com/bioperl/bioperl-live [cjfields] * Bug database has moved to Redmine (https://redmine.open-bio.org) * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian Thieme have been moved to their own distribution (Bio-Microarray). [cjfields] 1.6.1 Sept. 29, 2009 (point release) * No change from last alpha except VERSION and doc updates [cjfields] 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha) * Fix for silent OBDA bug related to FASTA validation [cjfields] 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha) * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields] * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS [cjfields] * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields] 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha) * WinXP test fixes [cjfields, maj] * BioPerl.pod added for descriptive information, fixes CPAN indexing [cjfields] * Minor doc fixes [cjfields] 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha) * Fix tests failing due to merging issues [cjfields] * More documentation updates for POD parsing [cjfields] 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha) * Bio::Root::Build - fix YAML meta data generation [cjfields] 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha) * Bio::Align::DNAStatistics - fix divide by zero problem [jason] * Bio::AlignIO::* - bug 2813 - fix faulty logic to detect end-of-stream [cjfields] * Bio::AlignIO::stockholm - bug 2796 - fix faulty logic to detect end-of-stream [cjfields] * Bio::Assembly::Tools::ContigSpectrum - function to score contig spectrum [fangly] * Bio::DB::EUtilities - small updates [cjfields] * Bio::DB::Fasta - berkeleydb database now autoindexes wig files and locks correctly [lstein] * Bio::DB::HIV - various small updates for stability; tracking changes to LANL database interface [maj] * Bio::DB::SeqFeature (lots of updates and changes) - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain] - bug 2835 - patch [Dan Bolser] - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham] * Bio::DB::SwissProt - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders] * Bio::Factory::FTLocationFactory - mailing list bug fix [cjfields] * Bio::LocatableSeq - performance work on column_from_residue_number [hartzell] * Bio::Matrix::IO::phylip - bug 2800 - patch to fix phylip parsing [Wei Zou] * Bio::Nexml - Google Summer of Code project from Chase Miller - parsers for Nexml file format [maj, chmille4] * Bio::PopGen - Make Individual, Population, Marker objects AnnotatableI [maj] - simplify LD code [jason] * Bio::RangeI - deal with empty intersection [jason] * Bio::Restriction - significant overhaul of Bio::Restriction system: complete support for external and non-palindromic cutters. [maj] * Bio::Root::Build - CPANPLUS support, no automatic installation [sendu] * Bio::Root::IO - allow IO::String (regression fix) [cjfields] - catch unintentional undef values [cjfields] - throw if non-fh is passed to -fh [maj] * Bio::Root::Root/RootI - small debugging and core fixes [cjfields] * Bio::Root::Test - bug RT 48813 - fix for Strawberry Perl bug [kmx] * Bio::Root::Utilities - bug 2737 - better warnings [cjfields] * Bio::Search - tiling completely refactored, HOWTO added [maj] NOTE : Bio::Search::Hit::* classes do not use this code directly; we will deprecate usage of the older tiling code in the next BioPerl release - small fixes [cjfields] * Bio::SearchIO - Infernal 1.0 output now parsed [cjfields] - new parser for gmap -f9 output [hartzell] - bug 2852 - fix infinite loop in some output [cjfields] - blastxml output now passes all TODO tests [cjfields] - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon] - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day] - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields] * Bio::Seq::LargePrimarySeq - delete tempdirs [cjfields] - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon] * Bio::Seq::Quality - extract regions based on quality threshold value [Dan Bolser, heikki] - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi) * Bio::SeqFeature::Lite - various Bio::DB::SeqFeature-related fixes [lstein] * Bio::SeqFeature::Tools::TypeMapper - additional terms for GenBank to SO map [scain] * Bio::SeqIO::chadoxml - bug 2785 - patch to get this working for bp_seqconvert [cjfields] * Bio::SeqIO::embl - support for CDS records [dave_messina, Sylvia] * Bio::SeqIO::fastq - complete refactoring to handle all FASTQ variants, perform validation, write output. API now conforms with other Bio* parsers and the rest of Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output). [cjfields] * Bio::SeqIO::genbank - bug 2784 - fix DBSOURCE issue [Phillip Garland] - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields] * Bio::SeqIO::largefasta - parser returns a Bio::Seq::LargePrimarySeq [jhannah] * Bio::SeqIO::raw - add option for 'single' and 'multiple' * Bio::SeqIO::scf - bug 2881 - fix scf round-tripping [Adam Søgren] * Bio::SeqUtils - bug 2766, 2810 - copy over tags from features, doc fixes [David Jackson] * Bio::SimpleAlign - bug 2793 - patch for add_seq index issue [jhannah, maj] - bug 2801 - throw if args are required [cjfields] - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types [Tristan Lefebure, maj] - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi] - fix POD and add get_SeqFeatures filter [maj] * Bio::Tools::dpAlign - add support for LocatableSeq [ymc] - to be moved to a separate distribution [cjfields, rbuels] * Bio::Tools::EUtilities - fix for two bugs from mail list [Adam Whitney, cjfields] - add generic ItemContainerI interface for containing same methods [cjfields] * Bio::Tools::HMM - fix up code, add more warnings [cjfields] - to be moved to a separate distribution [cjfields, rbuels] * Bio::Tools::Primer3 - bug 2862 - fenceposting issue fixed [maj] * Bio::Tools::Run::RemoteBlast - tests for remote RPS-BLAST [mcook] * Bio::Tools::SeqPattern - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi] * Bio::Tools::tRNAscanSE - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason] * Bio::Tree::* - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj] * Bio::Tree::Statistics - several methods for calculating Fitch-based score, internal trait values, statratio(), sum of leaf distances [heikki] * Bio::Tree::Tree - bug 2869 - add docs indicating edge case where nodes can be prematurely garbage-collected [cjfields] - add as_text() function to create Tree as a string in specified format [maj] * Bio::Tree::TreeFunctionsI - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan Lefebure, maj] * Bio::TreeIO::newick - fix small semicolon issue [cjfields] * scripts - update to bp_seqfeature_load for SQLite [lstein] - hivq.pl - commmand-line interface to Bio::DB::HIV [maj] - fastam9_to_table - fix for MPI output [jason] - gccalc - total stats [jason] * General Stuff - POD cleanup re: FEEDBACK section [maj, cjfields] - cleanup or fix dead links [cjfields] - Use of no_* methods (indicating 'number of something') is deprecated in favor of num_* [cjfields] - lots of new tests for the above bugs and refactors [everyone!] - new template for Komodo text editor [cjfields] 1.6.0 Winter 2009 * Feature/Annotation rollback - Problematic changes introduced prior to the 1.5 release have been rolled back. These changes led to subtle bugs involving operator overloading and interface methods. - Behavior is very similar to that for BioPerl 1.4, with tag values being stored generically as simple scalars. Results in a modest speedup. * Bio::Graphics - Split into a separate distribution on CPAN, primarily so development isn't reliant on a complete BioPerl release. - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but is only available via Subversion (via bioperl-live main trunk) * Bio::Root::Test - Common test bed for all BioPerl modules * Bio::Root::Build - Common Module::Build-based subclass for all BioPerl modules * Bio::DB::EUtilities - Complete refactoring to split up parsing (Bio::Tools::EUtilities), parameter handling (Bio::Tools::EUtilities::EUtilParameters), and user agent request posting and retrieval * Test implementation and reorganization - Tests have been reorganized into groups based on classes or use cases. - Automated test coverage is now online: http://www.bioperl.org/wiki/Test_Coverage - After this release, untested modules will be moved into a separate developer distribution until tests can be derived. Also, new modules to be added are expected to have a test suite and adequate test coverage. 1.5.2 Developer release Full details of changes since 1.5.1 are available online at: http://www.bioperl.org/wiki/Change_log The following represents a brief overview of the most important changes. o Bio::Map - Overhaul. Brand new system fully allows markers to have multiple positions on multiple maps, and to have relative positions. Should be backward compatible. o Bio::Taxonomy - This module and all the modules in the Taxonomy directory now deprecated in favour of Bio::Taxon and Bio::Tree::Tree o Bio::DB::Taxonomy - Taxonomy.pm * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon(). * New methods ancestor(), each_Descendent() and _handle_internal_id(). * Allows for different database modules to create Bio::Taxon objects with the same internal id when the same taxon is requested from each. - flatfile.pm * get_Children_Taxids() is deprecated, superceded by each_Descendent(). * No longer includes the fake root node 'root'; there are multiple roots now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm - entrez.pm * get_node() has new option -full * Caches data retrieved from website o Bio::Species - Now a Bio::Taxon. Carries out the species name -> specific name munging that Bio::DB::Taxonomy modules and SeqIO modules used to do, for backward compatability in species() method. o Bio::Search and Bio::SearchIO - Overhaul. The existing system has been sped up via some minor changes (mostly gain-of-function to the API). Bio::PullParserI is introduced as a potential eventual replacment for the existing system, though as yet only a Hmmpfam parser exists written using it. 1.5.1 Developer release o Major problem with how Annotations were written out with Bio::Seq is fixed by reverting to old behavior for Bio::Annotation objects. o Bio::SeqIO - genbank.pm * bug #1871; REFLOOP' parsing loop, I changed the pattern to expect at l east 9 spaces at the beginning of a line to indicate line wrapping. * Treat multi-line SOURCE sections correctly, this defect broke both common_name() and classification() * parse swissprot fields in genpept file * parse WGS genbank records - embl.pm * Changed regexp for ID line. The capturing parentheses are the same, the difference is an optional repeated-not-semi- colon expression following the captured \S+. This means the regexp works when the division looks like /PRO;/ or when the division looks like /ANG ;/ - the latter is from EMBL repbase * fix ID line parsing: the molecule string can have spaces in it. Like: "genomic DNA" - swiss.pm: bugs #1727, #1734 - entrezgene.pm * Added parser for entrezgene ASN1 (text format) files. Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN) o Bio::AlignIO - maf.pm coordinate problem fixed o Bio::Taxonomy and Bio::DB::Taxonomy - Parse NCBI XML now so that nearly all the taxonomy up-and-down can be done via Web without downloading all the sequence. o Bio::Tools::Run::RemoteBlast supports more options and complies to changes to the NCBI interface. It is reccomended that you retrieve the data in XML instead of plain-text BLAST report to insure proper parsing and retrieval of all information as NCBI fully expects to change things in the future. o Bio::Tree and Bio::TreeIO - Fixes so that re-rooting a tree works properly - Writing out nhx format from a newick/nexus file will properly output bootstrap information. The use must move the internal node labels over to bootstraps. for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) { $node->bootstrap($node->id); $node->id(''); } - Nexus parsing is much more flexible now, does not care about LF. - Cladogram drawing module in Bio::Tree::Draw - Node height and depth now properly calculated - fix tree pruning algorithm so that node with 1 child gets merged o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized bugs and improvements were added, see Gbrowse mailing list for most of these. o Bio::DB::GFF partially supports GFF3. See information about gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl. o Better location parsing in Bio::Factory::FTLocationFactory - this is part of the engine for parsing EMBL/GenBank feature table locations. Nested join/order-by/complement are allowed now o Bio::PrimarySeqI->translate now takes named parameters o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence reconstruction) is now supported. Parsing different models and branch specific parametes are now supported. o Bio::Factory::FTLocationFactory - parse hierarchical locations (joins of joins) o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays for getter/setter functions o Bio::SearchIO - blast bug #1739; match scientific notation in score and possible e+ values - blast.pm reads more WU-BLAST parameters and parameters, match a full database pathname, - Handle NCBI WEB and newer BLAST formats specifically (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct). - psl off-by-one error fixed - exonerate parsing much improved, CIGAR and VULGAR can be parsed and HSPs can be constructed from them. - HSPs query/hit now have a seqdesc field filled out (this was always available via $hit->description and $result->query_description - hmmer.pm can parse -A0 hmmpfam files - Writer::GbrowseGFF more customizeable. o Bio::Tools::Hmmpfam make e-value default score displayed in gff, rather than raw score allow parse of multiple records 1.5 Developer release o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics provide Jukes-Cantor and Kimura pairwise distance methods, respectively. o Bio::AlignIO support for "po" format of POA, and "maf"; Bio::AlignIO::largemultifasta is a new alternative to Bio::AlignIO::fasta for temporary file-based manipulation of particularly large multiple sequence alignments. o Bio::Assembly::Singlet allows orphan, unassembled sequences to be treated similarly as an assembled contig. o Bio::CodonUsage provides new rare_codon() and probable_codons() methods for identifying particular codons that encode a given amino acid. o Bio::Coordinate::Utils provides new from_align() method to build a Bio::Coordinate pair directly from a Bio::Align::AlignI-conforming object. o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils. Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's web service using standard Pubmed query syntax, and retrieve results as XML. o Bio::DB::GFF has various sundry bug fixes. o Bio::FeatureIO is a new SeqIO-style subsystem for writing/reading genomic features to/from files. I/O classes exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO classes only read/write Bio::SeqFeature::Annotated objects. Notably, the GFF v3 class requires features to be typed into the Sequence Ontology. o Bio::Graph namespace contains new modules for manipulation and analysis of protein interaction graphs. o Bio::Graphics has many bug fixes and shiny new glyphs. o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file indexing for HMMER reports and FASTA qual files, respectively. o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are new objects that can be placed within a Bio::Map::MapI-compliant genetic/physical map; Bio::Map::Physical provides a new physical map type; Bio::MapIO::fpc provides finger-printed clone mapping import. o Bio::Matrix::PSM provide new support for postion-specific (scoring) matrices (e.g. profiles, or "possums"). o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now be instantiated without explicitly using Bio::OntologyIO. This is possible through changes to Bio::Ontology::OntologyStore to download ontology files from the web as necessary. Locations of ontology files are hard-coded into Bio::Ontology::DocumentRegistry. o Bio::PopGen includes many new methods and data types for population genetics analyses. o New constructor to Bio::Range, unions(). Given a list of ranges, returns another list of "flattened" ranges -- overlapping ranges are merged into a single range with the mininum and maximum coordinates of the entire overlapping group. o Bio::Root::IO now supports -url, in addition to -file and -fh. The new -url argument allows one to specify the network address of a file for input. -url currently only works for GET requests, and thus is read-only. o Bio::SearchIO::hmmer now returns individual Hit objects for each domain alignment (thus containing only one HSP); previously separate alignments would be merged into one hit if the domain involved in the alignments was the same, but this only worked when the repeated domain occured without interruption by any other domain, leading to a confusing mixture of Hit and HSP objects. o Bio::Search::Result::ResultI-compliant report objects now implement the "get_statistics" method to access Bio::Search::StatisticsI objects that encapsulate any statistical parameters associated with the search (e.g. Karlin's lambda for BLAST/FASTA). o Bio::Seq::LargeLocatableSeq combines the functionality already found in Bio::Seq::LargeSeq and Bio::LocatableSeq. o Bio::SeqFeature::Annotated is a replacement for Bio::SeqFeature::Generic. It breaks compliance with the Bio::SeqFeatureI interface because the author was sick of dealing with untyped annotation tags. All Bio::SeqFeature::Annotated annotations are Bio::AnnotationI compliant, and accessible through Bio::Annotation::Collection. o Bio::SeqFeature::Primer implements a Tm() method for primer melting point predictions. o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML, InterProScan-XML, TIGR-XML, and NCBI TinySeq formats. o Bio::Taxonomy::Node now implements the methods necessary for Bio::Species interoperability. o Bio::Tools::CodonTable has new reverse_translate_all() and make_iupac_string() methods. o Bio::Tools::dpAlign now provides sequence profile alignments. o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF). o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report parsers. o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl) for designing small inhibitory RNA. o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building methods based on a distance matrix. o Bio::Tree::Statistics provides an assess_bootstrap() method to calculate bootstrap support values on a guide tree topology, based on provided bootstrap tree topologies. o Bio::TreeIO now supports the Pagel (PAG) tree format. 1.4 branch 1.4.1 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files o Bio::Graphics will work with gd1 or gd2 o Bio::SearchIO - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs (RF lines alone) - blast.pm Parse multi-line query fields properly - small speed improvements to blasttable.pm and others o Bio::DB::Taxonomy has better support for hierarchy traversal so that Bio::Taxonomy::Node can be as simple as Bio::Species object while still supporting more complex queries 1.4. Stable major release Since initial 1.2.0, 3000 separate changes have been made to make this release. o installable scripts o global module version from Bio::Root:Version o Bio::Graphics - major improvements; SVG support o Bio::Popgen - population genetics - support several population genetics types of questions. - Tests for statistical neutrality of mutations (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics. Tests of population structure (Wright's F-statistic: Fst) is in Bio::PopGen::PopStats. Calculating composite linkage disequilibrium (LD) is available in Bio::PopGen::Statistics as well. - Bio::PopGen::IO for reading in prettybase (SeattleSNPs) and csv (comma delimited formatted) data. - a directory for implementing population simulations has been added Bio::PopGen::Simulation and 2 simulations - a Coalescent and a simple single-locus multi-allele genetic drift simulation have been provided. This replaces the code in Bio::Tree::RandomTree which has been deprecated until proper methods for generating random phylogenetic trees are implemented. o Bio::Restriction - new restrion analysis modules o Bio::Tools::Analysis - web based DNA and Protein analysis framework and several implementations o Bio::Seq::Meta - per residue annotable sequences o Bio::Matrix - Bio::Matrix::PSM - Position Scoring Matrix - Bio::Matrix::IO has been added for generalized parsing of matrix data. Matrix::IO::scoring and Matrix::IO::phylip are initial implementations for parsing BLOSUM/PAM and Phylip Distance matricies respectively. A generic matrix implementation for general use was added in Bio::Matrix::Generic. o Bio::Ontology - major changes o Bio:Tree o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA - small inhibitory RNA o Bio::SeqFeature::Tools - seqFeature mapping tools - Bio::SeqFeature::Tools::Unflattener.pm -- deal with mapping GenBank feature collections into Chado/GFF3 processable feature sets (with SO term mappings) o Bio::Tools::dpAlign - pure perl dynamic programming sequence alignment - needs Bioperl-ext o new Bio::SearchIO formats - axt and psl: UCSC formats. - blasttable: NCBI -m 8 or -m 9 format from blastall o new Bio::SeqIO formats - chado, tab, kegg, tigr, game - important fixes for old modules o Bio::AlignIO: maf o improved Bio::Tools::Genewise o Bio::SeqIO now can recongnize sequence formats automatically from stream o new parsers in Bio::Tools: Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan, o Bio::DB::Registry bugs fixed - BerkeleyDB-indexed flat files can be used by the OBDA system - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all used by the OBDA system o several new HOWTOs - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat Databases o hundreds of new and improved files o o Bio::Tree::AlleleNode has been updated to be a container of an Bio::PopGen::Individual object for use in the Coalescent simulations. 1.2 Branch 1.2.3 Stable release update o Bug #1475 - Fix and add speedup to spliced_seq for remote location handling. o Bug #1477 - Sel --> Sec abbreviation fixed o Fix bug #1487 where paring in-between locations when end < start caused the FTLocationFactory logic to fail. o Fix bug #1489 which was not dealing with keywords as an arrayref properly (this is fixed on the main trunk because keywords returns a string and the array is accessible via get_keywords). o Bio::Tree::Tree memory leak (bug #1480) fixed Added a new initialization option -nodelete which won't try and cleanup the containing nodes if this is true. o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed this was only present on the branch for the 1.2.1 and 1.2.2 series - Also merged main trunk changes to the branch which make newick -> nhx round tripping more effective (storing branch length and bootstrap values in same locate for NodeNHX and Node implementations.) Fixes to TreeIO parsing for labeled internal also required small changes to TreeIO::nhx. Improved tests for this module as well. o Bio::SearchIO - Fixed bugs in BLAST parsing which couldn't parse NCBI gapped blast properly (was losing hit significance values due to the extra unexpeted column). - Parsing of blastcl3 (netblast from NCBI) now can handle case of integer overflow (# of letters in nt seq dbs is > MAX_INT) although doesn't try to correct it - will get the negative number for you. Added a test for this as well. - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report has no top-level family classification scores but does have scores and alignments for individual domains. - Parsing FASTA reports where ungapped percent ID is < 10 and the regular expression to match the line was missing the possibility of an extra space. This is rare, which is why we probably did not catch it before. - BLAST parsing picks up more of the statistics/parameter fields at the bottom of reports. Still not fully complete. - SearchIO::Writer::HTMLResultWriter and TextResultWriter were fixed to include many improvements and added flexiblity in outputting the files. Bug #1495 was also fixed in the process. o Bio::DB::GFF - Update for GFF3 compatibility. - Added scripts for importing from UCSC and GenBank. - Added a 1.2003 version number. o Bio::Graphics - Updated tutorial. - Added a 1.2003 version number. o SeqIO::swiss Bug #1504 fixed with swiss writing which was not properly writing keywords out. o Bio::SeqIO::genbank - Fixed bug/enhancement #1513 where dates of the form D-MMM-YYYY were not parsed. Even though this is invalid format we can handle it - and also cleanup the date string so it is properly formatted. - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed and written with Genbank format. Similarly bug #1515 is fixed to parse in the ORIGIN text. o Bio::SeqIO::fasta, a new method called preferred_id_type allows you to specify the ID type, one of (accession accession.version display primary). See Bio::SeqIO::preferred_id_type method documentation for more information. o Unigene parsing updated to handle file format changes by NCBI 1.2.2 Stable release update o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers: - auto-discover ontology name - bug in parsing relationships when certain characters are in the term - fixed hard-coded prefix for term identifiers - various smaller issues o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all of Bio::Ontology::TermI o brought the OBDA Registry code up to latest specs o Bio::DB::GenBank - eutils URL change - accession number retrieval fixed o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458, #1459 which now properly report alignment start/end info for translated BLAST/FASTA searches. o Bio::TreeIO::newick can parse labeled internal nodes o Bio::Tools::BPbl2seq can properly report strand info for HSPs for BLASTX if if you provide -report_type => 'BLASTX' when initializing a BPbl2seq object. Bioperl 1.3 will have better support for bl2seq in the SearchIO system. o Bio::Root::IO support a -noclose boolean flag which will not close a filehandle upon object cleanup - useful when sharing a filehandle among objects. Additionally code added s.t. STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup. o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction o Bio::SeqIO::genbank - bug #1456 fixed which generated extra sequence lines - write moltype correctly for genpept 1.2.1 Stable release update o Inclusion of WrapperBase, a needed component for StandAloneBlast o Addition from main trunk of Ontology objects, principly to allow BioSQL releases against 1.2.1 o Fixes and cleanup of Bio::Coordinate modules o A fix to Bio::Index::EMBL allowing retrieval of entries using the primary accession number o Other bug fixes, including bpindex GenBank fix o Bio::SeqIO::genbank bug #1389 fixed 1.2 Stable major release o More functionality added to Bio::Perl, the newbie module o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2 Support for New Hampshire Extended (NHX) format parsing. o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome, Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight Hmmpfam parser. o New ontology parsing Bio::Ontology o Bug fixes in Bio::SearchIO for HMMer parsing, support for multi-report (mlib) fasta reports, support for waba and exonerate. o Bio::ClusterIO for parsing Unigene clusters o Bio::Assembly added for representing phrap and ace assembly clusters. o Rudimentary support for writing Chado XML (see GMOD project: www.gmod.org for more information) o Bio::Coordinate for mapping between different coordinate systems such as protein -> cDNA -> Exon -> DNA and back. Useful for mapping features into different coordinate systems. o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries with the get_Stream_by_query method and supports the latest NCBI eutils interface. o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast object for extracting subsets of features : currently only supports extraction by location. 1.1.1 Developer release o Deprecated modules are now listed in the DEPRECATED file o New HowTo documents located in doc/howto describing a domain of Bioperl. o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/ and all old bugs are searchable through the bugzilla interface. o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign have been addressed. o Support for Genewise parsing in Bio::Tools::Genewise o Start of Ontology framework with Bio::Ontology o Speedup to the Bio::Root::Root object method _rearrange. A global _load_module method was implemented to simplify the dynamic loading of modules ala Bio::SeqIO::genbank. This method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO, etc). o Several performance improvements to sequence parsing in Bio::SeqIO. Attempt to speedup by reducing object creation overhead. o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved method for sequence retrieval with their E-utils CGI scripts. More work to support Entrez queries to their fullest is planned before 1.2 release. o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot) 1.1 Developer release o Bio::Tools::Run has been broken off into a new pkg bioperl-run, this separation removes some of the complexity in our test suite and separates the core modules in bioperl from those that need external programs to run. o With latest ExtUtils::MakeMaker module installed SGI/IRIX should not run into trouble running the makefile o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly read,create,and write locations for grouped/split locations (like mRNA features on genomic sequence). o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml) and PAML (codeml,aaml, etc) parsing. o Bio::Tree:: objects expanded to handle testing monophyly, paraphyly, least common ancestor, etc. o Bio::Coordinate for mapping locations from different coordinate spaces o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer added for parsing hmmpfam and hmmsearch output. o Bio::SearchIO::Writer::TextResultWriter for outputting a pseudo-blast textfile format 1.0.2 Bug fix release o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided in this release will not work after December 2002 when NCBI shuts off the old Entrez cgi scripts. We have already fixed on our main development branch and the functionality will be available in the next stable bioperl release (1.2) slated for Fall 2002. o Numerous parsing bugs in Bio::SearchIO::fasta found through testset by Robin Emig. These were fixed as was the get_aln method in Bio::Search::HSP::GenericHSP to handle the extra context sequence that is provided with a FastA alignment. o Migrating differences between Bio::Search::XX::BlastXX to Bio::Search::XX::GenericXX objects. This included mechanism to retrieve whole list of HSPs from Hits and whole list of Hits from Results in addition to the current next_XX iterator methods that are available. Added seq_inds() method to GenericHSP which identifies indexes in the query or hit sequences where conserved,identical,gaps, or mismatch residues are located (adapted from Steve Chervitz's implementation in BlastHSP). o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release. Bio::DB::GFF::RelSegment is now Bio::SeqI compliant. o Bio::Graphics glyph set improved and extended for GBrowse release o Bio::Tree::Tree get_nodes implementation improvement thanks to Howard Ross notice performance problem when writing out unbalanced trees. o Bio::Location::Fuzzy::new named parameter -loc_type became -location_type, Bio::Location::Simple::new named parameter -seqid becamse -seq_id. o Fixed major Bio::AlignIO::emboss parsing bug on needle output, was mis-detecting that gaps should be placed at the beginning of the alignment when the best alignment starts internally in the sequence. 1.0.1 Bug fix release o Minor bug fixes to Bio::DB:GFF. Glyph sets improved. o Parser fixes in SearchIO blast, fasta for more complete WU BLAST and mixed (3.3 - 3.4) versions of FASTA. o Small API change to add methods for completeness across implementations of Bio::Search objects. These new methods in the interface are implemented by the GenericXX object as well as the BlastXX objects. * Bio::Search::Result::ResultI - hits() method returns list of all Hits (next_hit is an iterator method) * Bio::Search::Hit::HitI - hsps() method returns list of all HSPs (next_hsp is an iterator method) o The Bio::SearchIO::Writer classes have been fixed to handle results created from either psiblast (Search::BlastXX objects) or blast|fasta|blastxml objects (Search::GenericXX objects). More work has to be done here to make it work properly and will nee major API changes. o Bugs in Bio::Tools::HMMER fixed, including * #1178 - Root::IO destructor wasn't being called * #1034 - filter_on_cutoff now behaves properly o Bio::SeqFeature::Computation initialization args fixed and tests added. o Tests are somewhat cleaner, flat.t now properly cleans up after itsself, o Updated FAQ with more example based answers to typical questions o Bug #1202 was fixed which would improperly join together qual values parsed by Bio::SeqIO::qual when a trailing space was not present before the newline. 1.0.0 Major Stable Release This represents a major release of bioperl with significant improvements over the 0.7.x series of releases. o Bio::Tools::Blast is officially deprecated. Please see Bio::SearchIO for BLAST and FastA parsing. o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts Bio::LocationI objects as well as start/end. o Bio::Biblio contains modules for Bibliographic data. Bio::DB::Biblio contains the query modules. Additionally one can parse medlinexml from the ebi bibliographic query service (BQS) system and Pubmed xml from NCBI. See Martin Senger's documentation in Bio::Biblio for more information. o Bio::DB::Registry is a sequence database registry part of Open Bioinformatics Database Access. See http://obda.open-bio.org for more information. o File-based and In-Memory Sequence caching is provided by Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a local database. o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has been added by Lincoln Stein. o XEMBL SOAP service access in provided in Bio::DB::XEMBL. o A FAQ has been started and is included in the release to provide a starting point for frequent questions and issues. 0.9.3 Developer's release o Event based parsing system improved (SearchIO). With parsers for XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta). Additionally a lazy parsing system for text and html blast reports was added and is called psiblast (name subject to change in future releases). o Bio::Search objects improved and standardized with associated Interfaces written. The concept of a search "Hit" was standardized to be called "hit" consistently and the use of "subject" was deprecated in all active modules. o Bio::Structure added (since 0.9.1) for Protein structure objects and PDB parser to retrieve and write these structures from data files. o Several important Bio::DB::GFF bug fixes for handling features that are mapped to multiple reference points. Updated mysql adaptor so as to be able to store large (>100 megabase) chunks of DNA into Bio::DB::GFF databases. 0.9.2 Developer's release o Bio::Search and Bio::SearchIO system introduced for event based parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST in text and XML and FASTA reports in standard output format. o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree generator is included in Bio::TreeIO::RandomTrees and a statistics module for evaluating. o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB server for DAS servers. o Bio::Tools::BPlite is provides more robust parsing of BLAST files. The entire BPlite system migrated to using Bio::Root::IO for the data stream. o Bio::Tools::Alignment for Consed and sequence Trimming functionality. o Bio::Structure for Protein structure information and parsing o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez cgi-bin entry point which should be more reliable. o Bio::Map and Bio::MapIO for biological map navigation and a framework afor parsing them in. Only preliminary work here. o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS Future work will integrate Pise and allow submission of analysis on remote servers. o Bio::AnnotationCollectionI and Bio::Annotation::Collection introduced as new objects for handling Sequence Annotation information (dblinks, references, etc) and is more robust that previous system. o Bio::Tools::FASTAParser introduced. o Scripts from the bioperl script submission project and new scripts from bioperl authors are included in "scripts" directory. o Factory objects and interfaces are being introduced and are more strictly enforced. o Bio::Root::Root introduced as the base object while Bio::Root::RootI is now simply an interface. o Bio::DB::RefSeq provides database access to copy of the NCBI RefSeq database using the EBI dbfetch script. 0.9.0 Developer's release o perl version at least 5.005 is now required instead of perl 5.004 o Bio::Tools::Run::RemoteBlast is available for running remote blast jobs at NCBI. o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs. o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene. Also added are related modules UTR3, UTR5, Exon, Intron, Promotor, PolyA and Transcript. o Speedup of translate method in PrimarySeq o Bio::SimpleAlign has new methods: location_from_column(), slice(), select(), dot(), get_seq_by_pos(), column_from_residue_number() o Various fixes to Variation toolkit o Bio::DB::EMBL provides database access to EMBL sequence data. Bio::DB::Universal provides a central way to point to indexes and dbs in a single interface. o Bio::DB::GFF - a database suitable for running DAS servers locally. o Bio::Factory::EMBOSS is still in design phase as is Bio::Factory::ApplicationFactoryI o Dia models for bioperl design are provided in the models/ directory 0.7.2 Bug fix release o documentation fixes in many modules - SYNOPSIS code verified to be runnable in many (but not all modules) o corrected MANIFEST file from 0.7.1 release o Bug fix in Bio::SeqIO::FTHelper to properly handle split locations o Bio::SeqIO::genbank * Correct parsing and writing of genbank format with protein data * moltype and molecule separation o Bio::SeqIO::largefasta fix to avoid inifinite loops o Bio::SimpleAlign fixed to correctly handle consensus sequence calculation o Bio::Tools::HMMER supports hmmer 2.2g o Bio::Tools::BPlite to support report type specific parsing. Most major changes are not on the 0.7 branch. o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works with File::Spec o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles in several types of mutations: 1.) AA level: deletion, complex 2.) AA level: complex, inframe 3.) RNA level: silent o BPbl2seq parsing of empty reports will not die, but will return a valid, empty, Bio::SeqFeature::SimilarityFeature for $report->query() and $report->subject() methods. So an easy way to test if report was empty is to see if $report->query->seqname is undefined. 0.7.1 Bug fix release o Better parsing of genbank/EMBL files especially fixing bugs related to Feature table parsing and locations on remote sequences. Additionally, species name parsing was better. o Bio::SeqIO::genbank can parse now NCBI produced genbank database which include a number of header lines. o More strict genbank and EMBL format writing (corrected number of spaces where appropriate). o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS for related BPlite BUGS that are unresolved in this release. o Bio::DB::GenBank, Bio::DB::GenPept have less problems downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can use expasy mirrors or EBI dbfetch cgi-script. o A moderate number of documentation improvements were made as well to provide a better code synopsis in each module. 0.7 Large number of changes, including refactoring of the Object system, new parsers, new functionality and all round better system. Highlights are: o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI; Bio::Root::IO for I/O and file/handle capabilities. o Imported BPlite modules from Ian Korf for BLAST parsing. This is considered the supported BLAST parser; Bio::Tools::Blast.pm will eventually phase out due to lack of support. o Improved Sequence Feature model. Added complete location modelling (with fuzzy and compound locations). See Bio::LocationI and the modules under Bio/Location. Added support in Genbank/EMBL format parsing to completely parse feature tables for complex locations. o Moved special support for databanks etc to specialized modules under Bio/Seq/. One of these supports very large sequences through a temporary file as a backend. o Explicit Gene, Transcript and Exon SeqFeature objects, supporting CDS retrieval and exon shuffling. o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and DB/GDB (the latter has platform-specific limitations). o New analysis parser framework for HT sequence annotation (see Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory) o New Alignment IO framework o New Index modules (Swissprot) o New modules for running Blast within perl (Bio::Tools::Run::StandAloneBlast). Added modules for running Multiple Sequence Alignment tools ClustalW and TCoffee (Bio::Tools::Run::Alignment). o New Cookbook-style tutorial (see bptutorial.pl). Improved documentation across the package. o Much improved cross platform support. Many known incompatibilities have been fixed; however, NT and Mac do not work across the entire setup (see PLATFORMS). o Many bug fixes, code restructuring, etc. Overall stability and maintainability benefit a lot. o A total of 957 automatic tests 0.6.2 There are very few functionality changes but a large number of software improvements/bug fixes across the package. o The EMBL/GenBank parsing are improved. o The Swissprot reading is improved. Swissprot writing is disabled as it doesn't work at all. This needs to wait for 0.7 release o BLAST reports with no hits are correctly parsed. o Several other bugs of the BLAST parser (regular expressions, ...) fixed. o Old syntax calls have been replaced with more modern syntax o Modules that did not work at all, in particular the Sim4 set have been removed o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair have improved compliance with interface specs and documentation o Mailing list documentation updated throughout the distribution o Most minor bug fixes have happened. o The scripts in /examples now work and have the modern syntax rather than the deprecated syntax 0.6.1 Sun April 2 2000 o Sequences can have Sequence Features attached to them - The sequence features can be read from or written to EMBL and GenBank style flat files o Objects for Annotation, including References (but not full medline abstracts), Database links and Comments are provided o A Species object to represent nodes on a taxonomy tree is provided o The ability to parse HMMER and Sim4 output has been added o The Blast parsing has been improved, with better PSI-BLAST support and better overall behaviour. o Flat file indexed databases provide both random access and sequential access to their component sequences. o A CodonTable object has been written with all known CodonTables accessible. o A number of new lightweight analysis tools have been added, such as molecular weight determination. The 0.6 release also has improved software engineering o The sequence objects have been rewritten, providing more maintainable and easier to implement objects. These objects are backwardly compatible with the 0.05.1 objects o Many objects are defined in terms of interfaces and then a Perl implementation has been provided. The interfaces are found in the 'I' files (module names ending in 'I'). This means that it is possible to wrap C/CORBA/SQL access as true "bioperl" objects, compatible with the rest of bioperl. o The SeqIO system has been overhauled to provide better processing and perl-like automatic interpretation of <> over arguments. o Many more tests have been added (a total of 172 automatic tests are now run before release). 0.05.1 Tue Jun 29 05:30:44 1999 - Central distribution now requires Perl 5.004. This was done to get around 5.003-based problems in Bio/Index/* and SimpleAlign. - Various bug fixes in the Bio::Tools::Blast modules including better exception handling and PSI-Blast support. See Bio/Tools/Blast/CHANGES for more. - Fixed the Parse mechanism in Seq.pm to use readseq. Follow the instructions in README for how to install it (basically, you have to edit Parse.pm). - Improved documentation of Seq.pm, indicating where objects are returned and where strings are returned. - Fixed uninitialized warnings in Bio::Root::Object.pm and Bio::Tools::SeqPattern.pm. - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52. 0.05 Sun Apr 25 01:14:11 1999 - Bio::Tools::Blast modules have less memory problems and faster parsing. Webblast uses LWP and supports more functionality. See Bio/Tools/Blast/CHANGES for more. - The Bio::SeqIO system has been started, moving the sequence reformatting code out of the sequence object - The Bio::Index:: system has been started, providing generic index capabilities and specifically works for Fasta formatted databases and EMBL .dat formatted databases - The Bio::DB:: system started, providing access to databases, both via flat file + index (see above) and via http to NCBI - The scripts/ directory, where industrial strength scripts are put has been started. - Many changes - a better distribution all round. 0.04.4 Wed Feb 17 02:20:13 1999 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl (see Bio::Tools::Blast::CHANGES). - Fixed a bug in Bio::Tools::Fasta::num_seqs(). - Beefed up the t/Fasta.t test script. - Small fix in Bio::Seq::type() (now always returns a string). - Changed Bio::Root::Utilities::get_newline_char() to get_newline() since it could return more than one char. - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global. - Changed default timeout to 20 seconds (was 3). - Moved lengthy modification notes to the bottom of some files. - Fixed SimpleAlign write_fasta bug. - Beefed up SimpleAlign.t test 0.04.3 Thu Feb 4 07:48:53 1999 - Bio::Root::Object.pm and Global.pm now detect when script is run as a CGI and suppress output that is only appropriate when running interactively. - Bio::Root::Err::_set_context() adds name of script ($0). - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm regarding the use of the static objects via the qw(:obj) tag. - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to CORE::reverse, avoiding Perl warnings. - Bug fixes in Bio::Tools::Blast modules (version 0.074) and example scripts (see Bio::Tools::Blast::CHANGES). - examples/seq/seqtools.pl no longer always warns about using -prot or -nucl command-line arguments; only when using the -debug argument. - Methods added to Bio::Root::Utilities: create_filehandle(), get_newline_char(), and taste_file() to generalize filehandle creation and autodetect newline characters in files/streams (see bug report #19). - Bio::Root::IOManager::read() now handles timeouts and uses Utilities::create_filehandle(). - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead of hardwiring in "\n". - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW 0.04.2 Wed Dec 30 02:27:36 1998 - Bug fixes in Bio::Tools::Blast modules, version 0.073 (see Bio::Tools::Blast::CHANGES). - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm to CORE::reverse (prevents ambiguous warnings with 5.005). - Appending '.tmp.bioperl' to temporary files created by Bio::Root::Utilities::compress() or uncompress() to make it easy to identify & cleanup these files as needed. - Developers: Created CVS branch release-0-04-bug from release-0-04-1. Before making bug fixes to the 0.04.1 release, be sure to cvs checkout this branch into a clean area. 0.04.1 Wed Dec 16 05:39:15 1998 - Bug fixes in Bio::Tools::Blast modules, version 0.072 (see Bio::Tools::Blast::CHANGES). - Compile/SW/Makefile.PL now removes *.o and *.a files with make clean. 0.04 Tue Dec 8 07:49:19 1998 - Lots of new modules added including: * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm, and Bio/Compile directory containing XS-linked C code for creating Smith-Waterman sequence alignments from within Perl. * Steve Chervitz's Blast distribution has been incorporated. * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects. - Bio/examples directory for demo scripts for all included modules. - Bio/t directory containing test suit for all included modules. - For changes specific to the Blast-related modules prior to incorporation in this central distribution, see the CHANGES file in the Bio/Tools/Blast directory. 0.01 Tue Sep 8 14:23:22 1998 - original version from central CVS tree; created by h2xs 1.18 BioPerl-1.007002/DEPENDENCIES000444000766000024 13522613155576320 15335 0ustar00cjfieldsstaff000000000000BioPerl Dependencies NOTE : This file was auto-generated by the helper script maintenance/dependencies.pl. Do not edit directly! The following packages are used by BioPerl. While not all are required for BioPerl to operate properly, some functionality will be missing without them. You can easily choose to install all of these during the normal installation process. Note that the PPM version of the BioPerl packages always tries to install all dependencies. The DBD::mysql, DB_File and XML::Parser modules require other applications or databases: MySQL, Berkeley DB, and expat respectively. NB: This list of packages is not authoritative. See the 'requires', 'build_requires' and 'recommends' sections of Build.PL instead. ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | AcePerl | * Ace - NA | None | | | * Ace::Sequence::Homol - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::Ace - Ace | | * Bio::DB::GFF::Adaptor::ace - Ace | | * Bio::DB::GFF::Adaptor::dbi::mysqlace - Ace::Sequence::Homol | | * Bio::DB::GFF::Adaptor::dbi::oracleace - Ace::Sequence::Homol | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Algorithm-Munkres | * Algorithm::Munkres - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::PhyloNetwork - Algorithm::Munkres | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Archive-Tar | * Archive::Tar - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Root::Build - Archive::Tar | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Array-Compare | * Array::Compare - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::PhyloNetwork - Array::Compare | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Bio-ASN1-EntrezGene | * Bio::ASN1::EntrezGene - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::SeqIO::entrezgene - Bio::ASN1::EntrezGene | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Bio-FeatureIO | * Bio::SeqFeature::Annotated - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Tools::Phylo::Gumby - Bio::SeqFeature::Annotated | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Bio-Graphics | * Bio::Graphics::Wiggle::Loader - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::SeqFeature::Store::berkeleydb - Bio::Graphics::Wiggle::Loader | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Bio-Phylo | * Bio::Phylo - NA | None | | | * Bio::Phylo::Factory - NA | | | | * Bio::Phylo::Forest::Tree - NA | | | | * Bio::Phylo::IO - NA | | | | * Bio::Phylo::Matrices - NA | | | | * Bio::Phylo::Matrices::Datum - NA | | | | * Bio::Phylo::Matrices::Matrix - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Nexml::Factory - Bio::Phylo | | * Bio::Nexml::Factory - Bio::Phylo::Factory | | * Bio::Nexml::Factory - Bio::Phylo::Forest::Tree | | * Bio::Nexml::Factory - Bio::Phylo::IO | | * Bio::Nexml::Factory - Bio::Phylo::Matrices | | * Bio::Nexml::Factory - Bio::Phylo::Matrices::Datum | | * Bio::Nexml::Factory - Bio::Phylo::Matrices::Matrix | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Bio-SamTools | * Bio::DB::Sam - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Assembly::IO::sam - Bio::DB::Sam | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | BioPerl-Run | * Bio::Tools::Run::Bowtie - NA | None | | | * Bio::Tools::Run::Samtools - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Assembly::IO::bowtie - Bio::Tools::Run::Bowtie | | * Bio::Assembly::IO::bowtie - Bio::Tools::Run::Samtools | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Convert-Binary-C | * Convert::Binary::C - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::SeqIO::strider - Convert::Binary::C | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | DBD-SQLite | * DBD::SQLite - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::SeqFeature::Store::DBI::SQLite - DBD::SQLite | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | DBI | * DBI - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::GFF::Adaptor::dbi - DBI | | * Bio::DB::GFF::Adaptor::dbi::caching_handle - DBI | | * Bio::DB::SeqFeature::Store::DBI::mysql - DBI | | * Bio::DB::SeqFeature::Store::DBI::Pg - DBI | | * Bio::DB::Taxonomy::sqlite - DBI | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Data-Stag | * Data::Stag - NA | None | | | * Data::Stag::XMLWriter - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Annotation::TagTree - Data::Stag | | * Bio::SeqIO::chaosxml - Data::Stag::XMLWriter | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Digest-MD5 | * Digest::MD5 - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::IndexedBase - Digest::MD5 | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Encode | * Encode - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::SeqVersion::gi - Encode | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Error | * Error - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Root::Root - Error | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | GD | * GD - NA | None | | | * GD::Simple - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Align::Graphics - GD | | * Bio::Align::Graphics - GD::Simple | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Graph | * Graph::Directed - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::PhyloNetwork - Graph::Directed | | * Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph::Directed | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | HTML-Parser | * HTML::HeadParser - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Tools::Analysis::DNA::ESEfinder - HTML::HeadParser | | * Bio::Tools::Analysis::Protein::ELM - HTML::HeadParser | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | HTML-TableExtract | * HTML::TableExtract - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::SeqVersion::gi - HTML::TableExtract | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | HTTP-Message | * HTTP::Request::Common - NA | None | | | * HTTP::Response - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::DBFetch - HTTP::Request::Common | | * Bio::DB::HIV - HTTP::Request::Common | | * Bio::DB::NCBIHelper - HTTP::Request::Common | | * Bio::DB::SwissProt - HTTP::Request::Common | | * Bio::DB::WebDBSeqI - HTTP::Request::Common | | * Bio::DB::Query::WebQuery - HTTP::Request::Common | | * Bio::Tools::Run::RemoteBlast - HTTP::Request::Common | | * Bio::DB::WebDBSeqI - HTTP::Response | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | IO-Compress | * Compress::Zlib - NA | None | | | * IO::Uncompress::Gunzip - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::SeqFeature::Store - Compress::Zlib | | * Bio::Assembly::IO::bowtie - IO::Uncompress::Gunzip | | * Bio::Assembly::IO::sam - IO::Uncompress::Gunzip | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | IO-String | * IO::String - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::PhyloNetwork - IO::String | | * Bio::DB::CUTG - IO::String | | * Bio::DB::WebDBSeqI - IO::String | | * Bio::Index::Blast - IO::String | | * Bio::Index::BlastTable - IO::String | | * Bio::Index::Hmmer - IO::String | | * Bio::SeqIO::game::gameWriter - IO::String | | * Bio::Tools::Analysis::DNA::ESEfinder - IO::String | | * Bio::Tools::Analysis::Protein::Domcut - IO::String | | * Bio::Tools::Analysis::Protein::ELM - IO::String | | * Bio::Tools::Analysis::Protein::GOR4 - IO::String | | * Bio::Tools::Analysis::Protein::HNN - IO::String | | * Bio::Tools::Analysis::Protein::NetPhos - IO::String | | * Bio::Tools::Analysis::Protein::Scansite - IO::String | | * Bio::Tools::Analysis::Protein::Sopma - IO::String | | * Bio::Tools::Phylo::Molphy - IO::String | | * Bio::Tools::Phylo::PAML - IO::String | | * Bio::Tools::Phylo::PAML::Codeml - IO::String | | * Bio::Tools::Run::RemoteBlast - IO::String | | * Bio::TreeIO::cluster - IO::String | | * Bio::TreeIO::nexml - IO::String | | * Bio::TreeIO::nexus - IO::String | | * Bio::Variation::IO::xml - IO::String | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | MIME-Base64 | * MIME::Base64 - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::SeqFeature::Store::DBI::Pg - MIME::Base64 | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Memoize | * Memoize - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::SeqFeature::Store::DBI::mysql - Memoize | | * Bio::DB::SeqFeature::Store::DBI::Pg - Memoize | | * Bio::DB::SeqFeature::Store::DBI::SQLite - Memoize | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Module-Build | * Module::Build - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Root::Test - Module::Build | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | PostScript | * PostScript::TextBlock - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Tree::Draw::Cladogram - PostScript::TextBlock | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | SVG | * SVG - NA | 2.26 | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Draw::Pictogram - SVG | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | SVG-Graph | * SVG::Graph - NA | None | | | * SVG::Graph::Data - NA | | | | * SVG::Graph::Data::Node - NA | | | | * SVG::Graph::Data::Tree - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::TreeIO::svggraph - SVG::Graph | | * Bio::TreeIO::svggraph - SVG::Graph::Data | | * Bio::TreeIO::svggraph - SVG::Graph::Data::Node | | * Bio::TreeIO::svggraph - SVG::Graph::Data::Tree | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Set-Scalar | * Set::Scalar - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Tree::Compatible - Set::Scalar | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Spreadsheet-ParseExcel | * Spreadsheet::ParseExcel - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::SeqIO::excel - Spreadsheet::ParseExcel | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Storable | * Storable - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::SeqFeature::Store - Storable | | * Bio::Restriction::Enzyme - Storable | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Test-Most | * Test::Most - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Root::Test - Test::Most | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Test-Simple | * Test::Builder - NA | None | | | * Test::Builder::Module - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Root::Test - Test::Builder | | * Bio::Root::Test - Test::Builder::Module | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Tie-Cacher | * Tie::Cacher - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::SeqFeature::Store - Tie::Cacher | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Time-HiRes | * Time::HiRes - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::GenericWebAgent - Time::HiRes | | * Bio::DB::SeqFeature::Store::Loader - Time::HiRes | | * Bio::DB::SeqFeature::Store::DBI::mysql - Time::HiRes | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Tree-DAG_Node | * Tree::DAG_Node - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::TreeIO::svggraph - Tree::DAG_Node | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | URI | * URI - NA | None | | | * URI::Escape - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::NCBIHelper - URI | | * Bio::DB::Query::WebQuery - URI | | * Bio::DB::CUTG - URI::Escape | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | WWW-Mechanize | * WWW::Mechanize - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::MeSH - WWW::Mechanize | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Win32 | * Win32 - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::GFF - Win32 | | * Bio::DB::IndexedBase - Win32 | | * Bio::Root::IO - Win32 | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-DOM | * XML::DOM - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::SeqIO::bsml - XML::DOM | | * Bio::SeqIO::interpro - XML::DOM | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-DOM-XPath | * XML::DOM::XPath - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::SeqIO::interpro - XML::DOM::XPath | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-LibXML | * XML::LibXML - NA | None | | | * XML::LibXML::Reader - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::SeqIO::seqxml - XML::LibXML | | * Bio::TreeIO::phyloxml - XML::LibXML | | * Bio::SeqIO::seqxml - XML::LibXML::Reader | | * Bio::TreeIO::phyloxml - XML::LibXML::Reader | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-SAX | * XML::SAX - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::ClusterIO::dbsnp - XML::SAX | | * Bio::SeqIO::bsml_sax - XML::SAX | | * Bio::SeqIO::gbxml - XML::SAX | | * Bio::SeqIO::tigrxml - XML::SAX | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-SAX-Writer | * XML::SAX::Writer - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::SeqIO::tigrxml - XML::SAX::Writer | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-Simple | * XML::Simple - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::HIV::HIVQueryHelper - XML::Simple | | * Bio::DB::Query::HIVQuery - XML::Simple | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-Twig | * XML::Twig - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::Taxonomy::entrez - XML::Twig | | * Bio::Variation::IO::xml - XML::Twig | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-Writer | * XML::Writer - NA | 0.4 | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::SeqIO::agave - XML::Writer | | * Bio::SeqIO::chadoxml - XML::Writer | | * Bio::SeqIO::seqxml - XML::Writer | | * Bio::SeqIO::tinyseq - XML::Writer | | * Bio::SeqIO::game::gameWriter - XML::Writer | | * Bio::Variation::IO::xml - XML::Writer | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | libwww-perl | * LWP - NA | 5.64 | | | * LWP::UserAgent - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Tools::Protparam - LWP | | * Bio::Tools::Run::RemoteBlast - LWP | | * Bio::DB::GenericWebAgent - LWP::UserAgent | | * Bio::DB::MeSH - LWP::UserAgent | | * Bio::DB::WebDBSeqI - LWP::UserAgent | | * Bio::DB::Query::WebQuery - LWP::UserAgent | | * Bio::Root::Build - LWP::UserAgent | | * Bio::Root::IO - LWP::UserAgent | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | libxml-perl | * XML::Parser::PerlSAX - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::OntologyIO::InterProParser - XML::Parser::PerlSAX | | * Bio::SeqIO::tinyseq - XML::Parser::PerlSAX | | * Bio::SeqIO::game::gameSubs - XML::Parser::PerlSAX | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | mod_perl | * Apache2::SubProcess - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::WebDBSeqI - Apache2::SubProcess | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | version | * version - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::SeqIO::mbsout - version | | * Bio::SeqIO::msout - version | ============================================================================== BioPerl-1.007002/DEPRECATED000444000766000024 612213155576320 15037 0ustar00cjfieldsstaff000000000000# These are modules which are deprecated and later removed from the toolkit # See http://www.bioperl.org/wiki/Deprecated_modules for the latest details Version Version Deprecated Modules Deprecated Removed Comment -------------------------------------------------------------------------------- Bio::Annotation 1.0 1.1 use Bio::Annotation::Collection Bio::Tools::Blast 1.0 1.1 use Bio::SearchIO Bio::Tools::Blast::HSP 1.0 1.1 use Bio::Search::HSP::GenericHSP Bio::Tools::Blast::Sbjct 1.0 1.1 use Bio::Search::Hit::GenericHit Bio::Tools::Blast::HTML 1.0 1.1 use Bio::SearchIO::Writer::HTMLWriter Bio::Tools::SeqAnal 1.0 1.1 used only by deprecated Bio::Tools::Blast Bio::UnivAln 1.0 1.1 use Bio::SimpleAlign Bio::Tools::WWW 1.1 1.1.1 Just a collection of links Bio::Root::Err 1.5.2 1.5.2 Bio::Root* redundant classes Bio::Root::Global 1.5.2 1.5.2 Bio::Root* redundant classes Bio::Root::IOManager 1.5.2 1.5.2 Bio::Root* redundant classes Bio::Root::Object 1.5.2 1.5.2 Bio::Root* redundant classes Bio::Root::Vector 1.5.2 1.5.2 Bio::Root* redundant classes Bio::Root::Xref 1.5.2 1.5.2 Bio::Root* redundant classes Bio::Tools::RestrictionEnzyme 1.5 1.6 use Bio::Restriction Bio::Tools::BPlite 1.5 1.6 use Bio::SearchIO Bio::Tools::BPpsilite 1.5 1.6 use Bio::SearchIO Bio::Tools::BPbl2seq 1.5 1.6 use Bio::SearchIO Bio::Ontology::SimpleGOEngine 1.5.1 1.6 use Bio::Ontology::OBOEngine Bio::Factory::ResultFactoryI 1.5.2 1.6 Superseded by Bio::Factory::ObjectFactory Bio::Factory::HitFactoryI 1.5.2 1.6 Superseded by Bio::Factory::ObjectFactory Bio::Graph 1.5.2 1.6 Superseded by bioperl-network Bio::Tools::WebBlat 1.5.2 1.6 Requested that this not be maintained Bio::DB::XEMBL 1.5.2 1.6 Service no longer available; use DBFetch Bio::DB::XEMBLService 1.5.2 1.6 Service no longer available; use DBFetch Bio::Taxonomy 1.5.1 1.7 use Bio::Taxon & Bio::Tree::Tree Bio::Taxonomy::Node 1.5.1 1.7 renamed Bio::Taxon Bio::Taxonomy::Taxon 1.5.1 1.7 use Bio::Taxon Bio::Taxonomy::Tree 1.5.1 1.7 use Bio::Taxon & Bio::Tree::Tree Bio::Taxonomy::FactoryI 1.5.1 1.7 Redundant, no implementors Bio::Search::Processor 1.5.1 1.7 Superseded by Bio::SearchIO Bio::Tools::RNAMotif 1.5.2 1.7 Superseded by Bio::SearchIO::rnamotif Bio::Tools::Infernal 1.5.2 1.7 Superseded by Bio::SearchIO::infernal Bio::Tools::ERPIN 1.5.2 1.7 Superseded by Bio::SearchIO::erpin Bio::Seq::SeqWithQuality 1.5.1 1.7 Superceded by Bio::Seq::Quality Bio::DB::GDB 1.6 1.6 Service no longer available Bio::Expression - - Moved to inactive bioperl-microarray BioPerl-1.007002/INSTALL-WIN.md000444000766000024 1535013155576320 15622 0ustar00cjfieldsstaff000000000000# Installing BioPerl on Windows # Introduction This installation guide was written by Barry Moore, Nathan Haigh and other BioPerl authors based on the original work of Paul Boutros. The guide has been updated by Paul Cantalupo and Francisco Ossandon. *Note* For Windows it is recommended to install BioPerl version 1.6.924 or newer, since many Windows-specific bugs from previous versions were fixed. Please report problems and/or fixes to the BioPerl mailing list. # Perl Options There are a couple of ways of installing Perl on a Windows machine. One is to get the most recent build from [Strawberry Perl](http://strawberryperl.com/) and the other is to get it from [ActiveState](http://www.activestate.com/). Both are software companies that provide free builds of Perl for Windows users. Strawberry Perl is recommended since is more CPAN-friendly and because it includes a compiler (gcc), related tools and other external libraries. These installation steps were verified on December 2015 using ActivePerl 5.20.2.2002 (5.22 has been released but the MinGW package is not available for it yet) and Strawberry Perl 5.22.0.1 from a clean install. *Note* Only ActivePerl **5.18 or greater** is supported by the BioPerl team. This is because the necessary MinGW package needed for CPAN installations is only available for both 32-bit and 64-bit Windows since this version (32-bit was available on previous versions but only in the Business edition, see [ActivePerl MinGW PPM webpage](http://www.activestate.com/activeperl/downloads)). *Note* Support for installation through ActivePerl Perl Package Manager has been dropped in favor of CPAN. # Installing Perl on Windows 1. Download the [Strawberry Perl MSI](http://strawberryperl.com/releases.html) or [ActivePerl MSI](http://www.activestate.com/activeperl/downloads). 2. Run the Installer (accepting all defaults is fine). You can also build Perl yourself (which requires a C compiler). The Perl source for building it yourself is available from [CPAN](http://www.cpan.org/). This approach is not recommended unless you have specific reasons for doing so and know what you're doing. [Cygwin](http://en.wikipedia.org/wiki/Cygwin) is a [UNIX](http://en.wikipedia.org/wiki/UNIX) emulation environment for Windows and comes with its own copy of Perl. Information on Cygwin and BioPerl is found below. ### Installation using the ActiveState Perl Package Manager This installation is not supported nor recommended anymore, because the last BioPerl package produced for it was the old version 1.6.1 (2009) and many Windows-specific bugs were fixed in more recent versions 1.6.923 and 1.6.924. Please install using the CPAN instructions below. # CPAN for Strawberry Perl and ActivePerl Both CPAN and manual methods ultimately need the accessory compiling program MinGW, which incorporates the necessary tools like `dmake` and `gcc`. MinGW comes by default with Strawberry Perl, but must it be installed through PPM for ActivePerl (CPAN will display a warning if not present). Also, CPAN need to be upgraded to >= v1.81, [Module::Build](https://metacpan.org/pod/Module::Build) to be upgraded (>= v0.2805) and [Test::Harness](https://metacpan.org/pod/Test::Harness) to be upgraded to >= v2.62. ### Dmake for ActivePerl 1) Install MinGW package through PPM: Using a cmd window type `ppm install MinGW`. It is `important` to check if ActiveState provides the [MinGW package](http://code.activestate.com/ppm/MinGW/) for your ActivePerl version, since each version have to wait its own release. For example, although MinGW has been available since ActivePerl version 5.18, the release for newest version 5.22 it's still not available (December 2015). ### Start the install with CPAN 1. Open a cmd window by going to `Start >> Run` and typing `cmd` into the box and pressing return. 2. Type `cpan` to enter the CPAN shell. 3. At the `cpan>` prompt, type `install CPAN` to upgrade to the latest version. 4. Quit (by typing 'q') and reload CPAN. You may be asked some configuration questions; accepting defaults is fine. 5. At the `cpan>` prompt, type `o conf prefer_installer MB` to tell CPAN to prefer to use `Build.PL` scripts for installation, and the type `o conf commit` to save that choice. 6. At the `cpan>` prompt, type `install Module::Build`. 7. At the `cpan>` prompt, type `install Test::Harness`. 8. At the `cpan>` prompt, type `install Test::Most`. ### Finish the install with CPAN You can now follow the instructions INSTALLING BioPerl THE EASY WAY USING CPAN in the INSTALL file. ### Finish the install with BioPerl from GitHub For the bleeding edge version install manually using a ZIP file from the GitHub repository: 1. Go to [GitHub](https://github.com/BioPerl/BioPerl-live) and press the `Download ZIP` button. 2. Extract the archive in the normal way. 3. In a cmd window `cd` to the directory you extracted to. Eg. if you extracted to directory 'BioPerl-live', `cd BioPerl-live` 4. Type `perl Build.PL` and answer the questions appropriately. 5. Type `perl Build test`. All the tests should pass, but if they don't, [let us know](https://github.com/BioPerl/BioPerl-live/issues). Your usage of BioPerl may not be affected by the failure, so you can choose to continue anyway. 6. Type `perl Build install` to install BioPerl. # BioPerl in Cygwin Cygwin is a Unix emulator and shell environment available free at http://www.cygwin.com. Some users claim that installation of BioPerl is easier within Cygwin than within Windows, but these may be users with UNIX backgrounds. A note on Cygwin: it doesn't write to your Registry, it doesn't alter your system or your existing files in any way, it doesn't create partitions, it simply creates a `cygwin/` directory and writes all of its files to that directory. To uninstall Cygwin just delete that directory. To get BioPerl running first install the basic Cygwin package as well as the Cygwin `perl`, `make`, `binutils`, and `gcc` packages. Clicking the View button in the upper right of the installer window enables you to see details on the various packages. Then start up Cygwin and follow the BioPerl installation instructions for UNIX in BioPerl's `INSTALL` file. ## Cygwin paths If you're trying to use some application or resource outside of the Cygwin directory and you're having a problem remember that Cygwin's path syntax may not be the correct one. Cygwin understands `/home/jacky` or `/cygdrive/e/cygwin/home/jacky` (when referring to the E: drive) but the external resource may want `E:/cygwin/home/jacky`. So your `*rc` files may end up with paths written in these different syntaxes, depending. For example, here's how to set the environmental variable TMPDIR, programs like BLAST and clustalw need a place to create temporary files: ``` setenv TMPDIR e:/cygwin/tmp # csh, tcsh export TMPDIR=e:/cygwin/tmp # sh, bash ``` BioPerl-1.007002/INSTALL.SKIP000444000766000024 2113155576320 15242 0ustar00cjfieldsstaff000000000000ConfigData\.\S+$ BioPerl-1.007002/INSTALL.md000444000766000024 2004713155576320 15166 0ustar00cjfieldsstaff000000000000# BioPerl Installation There are two principle ways to get BioPerl onto your system. One (and the still most common) is to install it locally on your machine. To do this, refer to and follow the instructions below for installing BioPerl on Unix, Linux, and Mac OS X. For installing BioPerl on Windows, please read INSTALL.WIN. The other way is to use a Docker image with a BioPerl build, whether one we support or one you build yourself. # Installing BioPerl locally Note that this documentation is for Unix, Linux, and MacOSX. For installing BioPerl on Windows, please read INSTALL.WIN. ## System Requirments * `Perl 5.6.1 or higher` Version 5.10 or higher is highly recommended. Modules are tested against version 5.14 and above. * `make` For Mac OS X, this requires installing the Xcode Developer Tools. ## Preliminary Preparation These are optional, but regardless of your subsequent choice of installation method, it will help to carry out the following steps. They will increase the likelihood of installation success (especially of the optional dependencies). * Upgrade CPAN: ``` perl -MCPAN -e shell ``` * Install or upgrade `Module::Build`, and make it your preferred installer: ``` cpan>install Module::Build cpan>o conf prefer_installer MB cpan>o conf commit ``` * Install the `expat` library by whatever method is appropriate for your system (e.g. `apt`, `yum`, `homebrew`). ## Installing BioPerl the Easy Way We highly recommend using [cpanminus](https://metacpan.org/pod/distribution/App-cpanminus/bin/cpanm) for installing BioPerl and its dependencies. We also highly recommend (if possible) using a tool like [perlbrew](https://perlbrew.pl) to locally install a modern version of perl (a version that is higher than perl 5.16). The linked pages describe how to install each tool; make sure if you install perlbrew that you follow up with installing `cpanm`: ``` perlbrew install-cpanm ``` Then, you can install BioPerl: ``` cpanm Bio::Perl ``` You can also use the older CPAN shell to install BioPerl. For example: ``` perl -MCPAN -e shell ``` Or you might have the `cpan` alias installed: ``` cpan ``` Then find the name of the latest BioPerl package: ``` cpan>d /bioperl/ .... Distribution C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz Distribution C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz Distribution C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz ``` And install the most recent: ``` cpan>install C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz ``` If you've installed everything perfectly and all the network connections are working then you will pass all the tests run in the `./Build test` phase. Sometimes you may see a failed test. Remember that there are over 900 modules in BioPerl and the test suite is running more than 12000 individual tests, a failed test may not affect your usage of BioPerl. If there's a failed test and you think that the failed test will not affect how you intend to use BioPerl then do: ``` cpan>force install C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz ``` If you're concerned about a failed test and need assistance or advice then contact bioperl-l@bioperl.org, and provide us the detailed results of the failed install. ## Installing BioPerl from Github **NOTE:** We generally do not recommend installing the latest code from Github unless you absolutely need the latest bug fixes. The very latest version of Bioperl is at github.com. If you want this version then download it from https://github.com/bioperl/bioperl-live as a `tar.gz` or `zip` file, or retrieve it using the command line: ``` git clone https://github.com/bioperl/bioperl-live.git cd bioperl-live ``` ### Using cpanm If you have `cpanm`, you can install within the checkout directory by simply using: ``` cpanm --interactive . ``` to run interative installation, or you can leave out the `--interactive` flag to accept the defaults. ### Using the Installation Script Issue the build commands: ``` perl Build.PL ``` You will be asked a few questions about installing BioPerl scripts and running various test suites, hit `return` to accept the defaults. Test: ``` ./Build test ``` Install: ``` ./Build install ``` You may need root permissions in order to run `./Build install`, so you will want to talk to your systems manager if you don't have the necessary privileges. Or you can install the package in your own home directory, see INSTALLING BIOPERL USING `local::lib`. ## Installing Bioperl using `local::lib` If you lack permission to install Perl modules into the standard system directories you can install them in your home directory using [local::lib](https://metacpan.org/pod/local::lib). The instructions for first installing `local::lib` are found in the link. Once `local::lib` is installed you can install BioPerl using a command like this: ``` perl -MCPAN -Mlocal::lib -e 'CPAN::install(C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz)' ``` ## Installing BioPerl Scripts BioPerl comes with a set of production-quality scripts that are kept in the scripts/ directory. You can install these scripts if you'd like, simply answer the questions during `perl Build.PL`. The installation directory can be specified by: ``` perl Build.PL ./Build install --install_path script=/foo/scripts ``` By default they install to `/usr/bin` or similar, depending on platform. ## The Test System The BioPerl test system is located in the `t/` directory and is automatically run whenever you execute the `./Build test` command. The tests have been organized into groups based upon the specific task or class the module being tested belongs to. If you want to investigate the behavior of a specific test such as the Seq test you would type: ``` ./Build test --test_files t/Seq/Seq.t --verbose ``` The `--test_files` argument can be used multiple times to try a set of test scripts in one go. The `--verbose` arguement outputs the detailed test results, instead of just the summary you see during `./Build test`. The `--test-files` argument can also work as a glob. For instance, to run tests on all SearchIO modules, use the following: ``` ./Build test --test_files t/SearchIO* --verbose ``` You can also use the command-line tool `prove` to run tests as well, which is quite useful if you are developing code: ``` prove -lrv t/SearchIO* ``` If you are trying to learn how to use a module, often the test suite is a good place to look. All good extreme programmers try and write a test BEFORE they write the module to insure that their module behaves the way they expect. You'll notice some `ok` and `skip` commands in a test, this is part of the Perl test suite that signifies a passed test with an 'ok N', where N is the test number. Alternatively you can tell Perl to skip tests. This is useful when, for example, your test detects that the network is not present and thus should skip, not fail, any tests that require a network connection. The core developers have indicated that future releases of BioPerl will require that new modules come with a test suite with some minimal tests. Modules that lack adequate tests or could otherwise be considered 'unstable' will be moved into a separate developer distribution until adequate tests are added and the API stablizes. [how to install Docker]: https://docs.docker.com/engine/installation/ [bioperl/bioperl]: https://hub.docker.com/r/bioperl/bioperl/ [bioperl/bioperl-deps]: https://hub.docker.com/r/bioperl/bioperl-deps/ # Using BioPerl via Docker If you don't have Docker installed already, instructions for [how to install Docker] on Linux, MacOSX, and Windows are available online. We officially support several builds (latest, stable, and releases) hosted in the [bioperl/bioperl] repo on Docker Hub. These images do not have a pre-defined entrypoint. If you have a BioPerl script in the current directory, you can run it as simple as this: ``` docker run -t --rm -v `pwd`:/work -w /work bioperl/bioperl perl my-script.pl ``` Or run an interactive shell: ``` docker run -ti --rm -v `pwd`:/work -w /work bioperl/bioperl bash ``` You can also build your own Docker image of BioPerl, using the same base image and pre-built dependencies that we use. Simply build off of the [bioperl/bioperl-deps] image. BioPerl-1.007002/LICENSE000444000766000024 12127013155576320 14563 0ustar00cjfieldsstaff000000000000BioPerl is licensed under the same terms as Perl itself, which means it is dually-licensed under either the Artistic or GPL licenses. Below are details of the Artistic License and, following it, the GPL. 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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 17. Interpretation of Sections 15 and 16. If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read . BioPerl-1.007002/MANIFEST000444000766000024 14712113155576320 14712 0ustar00cjfieldsstaff000000000000.travis.yml AUTHORS Bio/Align/AlignI.pm Bio/Align/DNAStatistics.pm Bio/Align/Graphics.pm Bio/Align/PairwiseStatistics.pm Bio/Align/ProteinStatistics.pm Bio/Align/StatisticsI.pm Bio/Align/Utilities.pm Bio/AlignIO.pm Bio/AlignIO/arp.pm Bio/AlignIO/bl2seq.pm Bio/AlignIO/clustalw.pm Bio/AlignIO/emboss.pm Bio/AlignIO/fasta.pm Bio/AlignIO/Handler/GenericAlignHandler.pm Bio/AlignIO/largemultifasta.pm Bio/AlignIO/maf.pm Bio/AlignIO/mase.pm Bio/AlignIO/mega.pm Bio/AlignIO/meme.pm Bio/AlignIO/metafasta.pm Bio/AlignIO/msf.pm Bio/AlignIO/nexml.pm Bio/AlignIO/nexus.pm Bio/AlignIO/pfam.pm Bio/AlignIO/phylip.pm Bio/AlignIO/po.pm Bio/AlignIO/proda.pm Bio/AlignIO/prodom.pm Bio/AlignIO/psi.pm Bio/AlignIO/selex.pm Bio/AlignIO/stockholm.pm Bio/AlignIO/xmfa.pm Bio/AnalysisI.pm Bio/AnalysisParserI.pm Bio/AnalysisResultI.pm Bio/AnnotatableI.pm Bio/Annotation/AnnotationFactory.pm Bio/Annotation/Collection.pm 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Bio/Factory/SequenceProcessorI.pm Bio/Factory/SequenceStreamI.pm Bio/Factory/TreeFactoryI.pm Bio/FeatureHolderI.pm Bio/HandlerBaseI.pm Bio/IdCollectionI.pm Bio/IdentifiableI.pm Bio/Index/Abstract.pm Bio/Index/AbstractSeq.pm Bio/Index/Blast.pm Bio/Index/BlastTable.pm Bio/Index/EMBL.pm Bio/Index/Fasta.pm Bio/Index/Fastq.pm Bio/Index/GenBank.pm Bio/Index/Hmmer.pm Bio/Index/Qual.pm Bio/Index/Stockholm.pm Bio/Index/SwissPfam.pm Bio/Index/Swissprot.pm Bio/LiveSeq/AARange.pm Bio/LiveSeq/Chain.pm Bio/LiveSeq/ChainI.pm Bio/LiveSeq/DNA.pm Bio/LiveSeq/Exon.pm Bio/LiveSeq/Gene.pm Bio/LiveSeq/Intron.pm Bio/LiveSeq/IO/BioPerl.pm Bio/LiveSeq/IO/Loader.pm Bio/LiveSeq/IO/README Bio/LiveSeq/Mutation.pm Bio/LiveSeq/Mutator.pm Bio/LiveSeq/Prim_Transcript.pm Bio/LiveSeq/Range.pm Bio/LiveSeq/Repeat_Region.pm Bio/LiveSeq/Repeat_Unit.pm Bio/LiveSeq/SeqI.pm Bio/LiveSeq/Transcript.pm Bio/LiveSeq/Translation.pm Bio/LocatableSeq.pm Bio/Location/Atomic.pm Bio/Location/AvWithinCoordPolicy.pm Bio/Location/CoordinatePolicyI.pm Bio/Location/Fuzzy.pm Bio/Location/FuzzyLocationI.pm Bio/Location/NarrowestCoordPolicy.pm Bio/Location/Simple.pm Bio/Location/Split.pm Bio/Location/SplitLocationI.pm Bio/Location/WidestCoordPolicy.pm Bio/LocationI.pm Bio/Map/Clone.pm Bio/Map/Contig.pm Bio/Map/CytoMap.pm Bio/Map/CytoMarker.pm Bio/Map/CytoPosition.pm Bio/Map/EntityI.pm Bio/Map/FPCMarker.pm Bio/Map/Gene.pm Bio/Map/GeneMap.pm Bio/Map/GenePosition.pm Bio/Map/GeneRelative.pm Bio/Map/LinkageMap.pm Bio/Map/LinkagePosition.pm Bio/Map/MapI.pm Bio/Map/Mappable.pm Bio/Map/MappableI.pm Bio/Map/Marker.pm Bio/Map/MarkerI.pm Bio/Map/Microsatellite.pm Bio/Map/OrderedPosition.pm Bio/Map/OrderedPositionWithDistance.pm Bio/Map/Physical.pm Bio/Map/Position.pm Bio/Map/PositionHandler.pm Bio/Map/PositionHandlerI.pm Bio/Map/PositionI.pm Bio/Map/PositionWithSequence.pm Bio/Map/Prediction.pm Bio/Map/Relative.pm Bio/Map/RelativeI.pm Bio/Map/SimpleMap.pm Bio/Map/TranscriptionFactor.pm Bio/MapIO.pm Bio/MapIO/fpc.pm Bio/MapIO/mapmaker.pm Bio/Matrix/Generic.pm Bio/Matrix/IO.pm Bio/Matrix/IO/mlagan.pm Bio/Matrix/IO/phylip.pm Bio/Matrix/IO/scoring.pm Bio/Matrix/MatrixI.pm Bio/Matrix/Mlagan.pm Bio/Matrix/PhylipDist.pm Bio/Matrix/PSM/InstanceSite.pm Bio/Matrix/PSM/InstanceSiteI.pm Bio/Matrix/PSM/IO.pm Bio/Matrix/PSM/IO/mast.pm Bio/Matrix/PSM/IO/masta.pm Bio/Matrix/PSM/IO/meme.pm Bio/Matrix/PSM/IO/psiblast.pm Bio/Matrix/PSM/IO/transfac.pm Bio/Matrix/PSM/ProtMatrix.pm Bio/Matrix/PSM/ProtPsm.pm Bio/Matrix/PSM/Psm.pm Bio/Matrix/PSM/PsmHeader.pm Bio/Matrix/PSM/PsmHeaderI.pm Bio/Matrix/PSM/PsmI.pm Bio/Matrix/PSM/SiteMatrix.pm Bio/Matrix/PSM/SiteMatrixI.pm Bio/Matrix/Scoring.pm Bio/MolEvol/CodonModel.pm Bio/Nexml/Factory.pm Bio/NexmlIO.pm Bio/Ontology/DocumentRegistry.pm Bio/Ontology/GOterm.pm Bio/Ontology/InterProTerm.pm Bio/Ontology/OBOEngine.pm Bio/Ontology/OBOterm.pm Bio/Ontology/Ontology.pm Bio/Ontology/OntologyEngineI.pm Bio/Ontology/OntologyI.pm Bio/Ontology/OntologyStore.pm Bio/Ontology/Path.pm Bio/Ontology/PathI.pm Bio/Ontology/Relationship.pm Bio/Ontology/RelationshipFactory.pm Bio/Ontology/RelationshipI.pm Bio/Ontology/RelationshipType.pm Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm Bio/Ontology/SimpleOntologyEngine.pm Bio/Ontology/Term.pm Bio/Ontology/TermFactory.pm Bio/Ontology/TermI.pm Bio/OntologyIO.pm Bio/OntologyIO/dagflat.pm Bio/OntologyIO/goflat.pm Bio/OntologyIO/Handlers/BaseSAXHandler.pm Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm Bio/OntologyIO/Handlers/InterProHandler.pm Bio/OntologyIO/InterProParser.pm Bio/OntologyIO/obo.pm Bio/OntologyIO/simplehierarchy.pm Bio/OntologyIO/soflat.pm Bio/ParameterBaseI.pm Bio/Perl.pm Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/MeSH/Term.pm Bio/Phenotype/MeSH/Twig.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm Bio/Phenotype/Phenotype.pm Bio/Phenotype/PhenotypeI.pm Bio/PhyloNetwork.pm Bio/PhyloNetwork/Factory.pm Bio/PhyloNetwork/FactoryX.pm Bio/PhyloNetwork/GraphViz.pm Bio/PhyloNetwork/muVector.pm Bio/PhyloNetwork/RandomFactory.pm Bio/PhyloNetwork/TreeFactory.pm Bio/PhyloNetwork/TreeFactoryMulti.pm Bio/PhyloNetwork/TreeFactoryX.pm Bio/PopGen/Genotype.pm Bio/PopGen/GenotypeI.pm Bio/PopGen/HtSNP.pm Bio/PopGen/Individual.pm Bio/PopGen/IndividualI.pm Bio/PopGen/IO.pm Bio/PopGen/IO/csv.pm Bio/PopGen/IO/hapmap.pm Bio/PopGen/IO/phase.pm Bio/PopGen/IO/prettybase.pm Bio/PopGen/Marker.pm Bio/PopGen/MarkerI.pm Bio/PopGen/PopStats.pm Bio/PopGen/Population.pm Bio/PopGen/PopulationI.pm Bio/PopGen/Simulation/Coalescent.pm Bio/PopGen/Simulation/GeneticDrift.pm Bio/PopGen/Statistics.pm Bio/PopGen/TagHaplotype.pm Bio/PopGen/Utilities.pm Bio/PrimarySeq.pm Bio/PrimarySeqI.pm Bio/PullParserI.pm Bio/Range.pm Bio/RangeI.pm Bio/Restriction/Analysis.pm Bio/Restriction/Enzyme.pm Bio/Restriction/Enzyme/MultiCut.pm Bio/Restriction/Enzyme/MultiSite.pm Bio/Restriction/EnzymeCollection.pm Bio/Restriction/EnzymeI.pm Bio/Restriction/IO.pm Bio/Restriction/IO/bairoch.pm Bio/Restriction/IO/base.pm Bio/Restriction/IO/itype2.pm Bio/Restriction/IO/prototype.pm Bio/Restriction/IO/withrefm.pm Bio/Root/Build.pm Bio/Root/Exception.pm Bio/Root/HTTPget.pm Bio/Root/IO.pm Bio/Root/Root.pm Bio/Root/RootI.pm Bio/Root/Storable.pm Bio/Root/Test.pm Bio/Root/TestObject.pm Bio/Root/Utilities.pm Bio/Root/Version.pm Bio/Search/BlastStatistics.pm Bio/Search/BlastUtils.pm Bio/Search/DatabaseI.pm Bio/Search/GenericDatabase.pm Bio/Search/GenericStatistics.pm Bio/Search/Hit/BlastHit.pm Bio/Search/Hit/BlastPullHit.pm Bio/Search/Hit/Fasta.pm Bio/Search/Hit/GenericHit.pm Bio/Search/Hit/HitFactory.pm Bio/Search/Hit/HitI.pm Bio/Search/Hit/hmmer3Hit.pm Bio/Search/Hit/HMMERHit.pm Bio/Search/Hit/HmmpfamHit.pm Bio/Search/Hit/ModelHit.pm Bio/Search/Hit/PsiBlastHit.pm Bio/Search/Hit/PullHitI.pm Bio/Search/HSP/BlastHSP.pm Bio/Search/HSP/BlastPullHSP.pm Bio/Search/HSP/FastaHSP.pm Bio/Search/HSP/GenericHSP.pm Bio/Search/HSP/HMMERHSP.pm Bio/Search/HSP/HmmpfamHSP.pm Bio/Search/HSP/HSPFactory.pm Bio/Search/HSP/HSPI.pm Bio/Search/HSP/ModelHSP.pm Bio/Search/HSP/PsiBlastHSP.pm Bio/Search/HSP/PSLHSP.pm Bio/Search/HSP/PullHSPI.pm Bio/Search/HSP/WABAHSP.pm Bio/Search/Iteration/GenericIteration.pm Bio/Search/Iteration/IterationI.pm Bio/Search/Processor.pm Bio/Search/Result/BlastPullResult.pm Bio/Search/Result/BlastResult.pm Bio/Search/Result/CrossMatchResult.pm Bio/Search/Result/GenericResult.pm Bio/Search/Result/hmmer3Result.pm Bio/Search/Result/HMMERResult.pm Bio/Search/Result/HmmpfamResult.pm Bio/Search/Result/INFERNALResult.pm Bio/Search/Result/PullResultI.pm Bio/Search/Result/ResultFactory.pm Bio/Search/Result/ResultI.pm Bio/Search/Result/WABAResult.pm Bio/Search/SearchUtils.pm Bio/Search/StatisticsI.pm Bio/Search/Tiling/MapTileUtils.pm Bio/Search/Tiling/MapTiling.pm Bio/Search/Tiling/TilingI.pm Bio/SearchDist.pm Bio/SearchIO.pm Bio/SearchIO/axt.pm Bio/SearchIO/blast.pm Bio/SearchIO/blast_pull.pm Bio/SearchIO/blasttable.pm Bio/SearchIO/cross_match.pm Bio/SearchIO/erpin.pm Bio/SearchIO/EventHandlerI.pm Bio/SearchIO/exonerate.pm Bio/SearchIO/fasta.pm Bio/SearchIO/FastHitEventBuilder.pm Bio/SearchIO/gmap_f9.pm Bio/SearchIO/hmmer.pm Bio/SearchIO/hmmer2.pm Bio/SearchIO/hmmer3.pm Bio/SearchIO/hmmer_pull.pm Bio/SearchIO/infernal.pm Bio/SearchIO/IteratedSearchResultEventBuilder.pm Bio/SearchIO/megablast.pm Bio/SearchIO/psl.pm Bio/SearchIO/rnamotif.pm Bio/SearchIO/SearchResultEventBuilder.pm Bio/SearchIO/SearchWriterI.pm Bio/SearchIO/sim4.pm Bio/SearchIO/waba.pm Bio/SearchIO/wise.pm Bio/SearchIO/Writer/GbrowseGFF.pm Bio/SearchIO/Writer/HitTableWriter.pm Bio/SearchIO/Writer/HSPTableWriter.pm Bio/SearchIO/Writer/HTMLResultWriter.pm Bio/SearchIO/Writer/ResultTableWriter.pm Bio/SearchIO/Writer/TextResultWriter.pm Bio/Seq.pm Bio/Seq/BaseSeqProcessor.pm Bio/Seq/EncodedSeq.pm Bio/Seq/LargeLocatableSeq.pm Bio/Seq/LargePrimarySeq.pm Bio/Seq/LargeSeq.pm Bio/Seq/LargeSeqI.pm Bio/Seq/Meta.pm Bio/Seq/Meta/Array.pm Bio/Seq/MetaI.pm Bio/Seq/PrimaryQual.pm Bio/Seq/PrimedSeq.pm Bio/Seq/QualI.pm Bio/Seq/Quality.pm Bio/Seq/RichSeq.pm Bio/Seq/RichSeqI.pm Bio/Seq/SeqBuilder.pm Bio/Seq/SeqFactory.pm Bio/Seq/SeqFastaSpeedFactory.pm Bio/Seq/SequenceTrace.pm Bio/Seq/SeqWithQuality.pm Bio/Seq/SimulatedRead.pm Bio/Seq/TraceI.pm Bio/SeqAnalysisParserI.pm Bio/SeqEvolution/DNAPoint.pm Bio/SeqEvolution/EvolutionI.pm Bio/SeqEvolution/Factory.pm Bio/SeqFeature/Amplicon.pm Bio/SeqFeature/AnnotationAdaptor.pm Bio/SeqFeature/Collection.pm Bio/SeqFeature/CollectionI.pm Bio/SeqFeature/Computation.pm Bio/SeqFeature/FeaturePair.pm Bio/SeqFeature/Gene/Exon.pm Bio/SeqFeature/Gene/ExonI.pm Bio/SeqFeature/Gene/GeneStructure.pm Bio/SeqFeature/Gene/GeneStructureI.pm Bio/SeqFeature/Gene/Intron.pm Bio/SeqFeature/Gene/NC_Feature.pm Bio/SeqFeature/Gene/Poly_A_site.pm Bio/SeqFeature/Gene/Promoter.pm Bio/SeqFeature/Gene/Transcript.pm Bio/SeqFeature/Gene/TranscriptI.pm Bio/SeqFeature/Gene/UTR.pm Bio/SeqFeature/Generic.pm Bio/SeqFeature/Lite.pm Bio/SeqFeature/PositionProxy.pm Bio/SeqFeature/Primer.pm Bio/SeqFeature/Similarity.pm Bio/SeqFeature/SimilarityPair.pm Bio/SeqFeature/SiRNA/Oligo.pm Bio/SeqFeature/SiRNA/Pair.pm Bio/SeqFeature/SubSeq.pm Bio/SeqFeature/Tools/FeatureNamer.pm Bio/SeqFeature/Tools/IDHandler.pm Bio/SeqFeature/Tools/TypeMapper.pm Bio/SeqFeature/Tools/Unflattener.pm Bio/SeqFeature/TypedSeqFeatureI.pm Bio/SeqFeatureI.pm Bio/SeqI.pm Bio/SeqIO.pm Bio/SeqIO/abi.pm Bio/SeqIO/ace.pm Bio/SeqIO/agave.pm Bio/SeqIO/alf.pm Bio/SeqIO/asciitree.pm Bio/SeqIO/bsml.pm Bio/SeqIO/bsml_sax.pm Bio/SeqIO/chadoxml.pm Bio/SeqIO/chaos.pm Bio/SeqIO/chaosxml.pm Bio/SeqIO/ctf.pm Bio/SeqIO/embl.pm Bio/SeqIO/embldriver.pm Bio/SeqIO/entrezgene.pm Bio/SeqIO/excel.pm Bio/SeqIO/exp.pm Bio/SeqIO/fasta.pm Bio/SeqIO/fastq.pm Bio/SeqIO/flybase_chadoxml.pm Bio/SeqIO/FTHelper.pm Bio/SeqIO/game.pm Bio/SeqIO/game/featHandler.pm Bio/SeqIO/game/gameHandler.pm Bio/SeqIO/game/gameSubs.pm Bio/SeqIO/game/gameWriter.pm Bio/SeqIO/game/seqHandler.pm Bio/SeqIO/gbdriver.pm Bio/SeqIO/gbxml.pm Bio/SeqIO/gcg.pm Bio/SeqIO/genbank.pm Bio/SeqIO/Handler/GenericRichSeqHandler.pm Bio/SeqIO/interpro.pm Bio/SeqIO/kegg.pm Bio/SeqIO/largefasta.pm Bio/SeqIO/lasergene.pm Bio/SeqIO/locuslink.pm Bio/SeqIO/mbsout.pm Bio/SeqIO/metafasta.pm Bio/SeqIO/msout.pm Bio/SeqIO/MultiFile.pm Bio/SeqIO/nexml.pm Bio/SeqIO/phd.pm Bio/SeqIO/pir.pm Bio/SeqIO/pln.pm Bio/SeqIO/qual.pm Bio/SeqIO/raw.pm Bio/SeqIO/scf.pm Bio/SeqIO/seqxml.pm Bio/SeqIO/strider.pm Bio/SeqIO/swiss.pm Bio/SeqIO/swissdriver.pm Bio/SeqIO/tab.pm Bio/SeqIO/table.pm Bio/SeqIO/tigr.pm Bio/SeqIO/tigrxml.pm Bio/SeqIO/tinyseq.pm Bio/SeqIO/tinyseq/tinyseqHandler.pm Bio/SeqIO/ztr.pm Bio/SeqUtils.pm Bio/SimpleAlign.pm Bio/SimpleAnalysisI.pm Bio/Species.pm Bio/Structure/Atom.pm Bio/Structure/Chain.pm Bio/Structure/Entry.pm Bio/Structure/IO.pm Bio/Structure/IO/pdb.pm Bio/Structure/Model.pm Bio/Structure/Residue.pm Bio/Structure/SecStr/DSSP/Res.pm Bio/Structure/SecStr/STRIDE/Res.pm Bio/Structure/StructureI.pm Bio/Symbol/Alphabet.pm Bio/Symbol/AlphabetI.pm Bio/Symbol/DNAAlphabet.pm Bio/Symbol/ProteinAlphabet.pm Bio/Symbol/README.Symbol Bio/Symbol/Symbol.pm Bio/Symbol/SymbolI.pm Bio/Taxon.pm Bio/Taxonomy.pm Bio/Taxonomy/FactoryI.pm Bio/Taxonomy/Node.pm Bio/Taxonomy/Taxon.pm Bio/Taxonomy/Tree.pm Bio/Tools/AlignFactory.pm Bio/Tools/Alignment/Consed.pm Bio/Tools/Alignment/Trim.pm Bio/Tools/AmpliconSearch.pm Bio/Tools/Analysis/DNA/ESEfinder.pm Bio/Tools/Analysis/Protein/Domcut.pm Bio/Tools/Analysis/Protein/ELM.pm Bio/Tools/Analysis/Protein/GOR4.pm Bio/Tools/Analysis/Protein/HNN.pm Bio/Tools/Analysis/Protein/NetPhos.pm Bio/Tools/Analysis/Protein/Scansite.pm Bio/Tools/Analysis/Protein/Sopma.pm Bio/Tools/Analysis/SimpleAnalysisBase.pm Bio/Tools/AnalysisResult.pm Bio/Tools/Blat.pm Bio/Tools/CodonTable.pm Bio/Tools/Coil.pm Bio/Tools/dpAlign.pm Bio/Tools/ECnumber.pm Bio/Tools/EMBOSS/Palindrome.pm Bio/Tools/EPCR.pm Bio/Tools/Eponine.pm Bio/Tools/Est2Genome.pm Bio/Tools/ESTScan.pm Bio/Tools/Fgenesh.pm Bio/Tools/FootPrinter.pm Bio/Tools/Gel.pm Bio/Tools/Geneid.pm Bio/Tools/Genemark.pm Bio/Tools/Genewise.pm Bio/Tools/Genomewise.pm Bio/Tools/Genscan.pm Bio/Tools/GFF.pm Bio/Tools/Glimmer.pm Bio/Tools/Grail.pm Bio/Tools/GuessSeqFormat.pm Bio/Tools/HMMER/Domain.pm Bio/Tools/HMMER/Results.pm Bio/Tools/HMMER/Set.pm Bio/Tools/Hmmpfam.pm Bio/Tools/ipcress.pm Bio/Tools/isPcr.pm Bio/Tools/IUPAC.pm Bio/Tools/Lucy.pm Bio/Tools/Match.pm Bio/Tools/MZEF.pm Bio/Tools/OddCodes.pm Bio/Tools/Phylo/Gerp.pm Bio/Tools/Phylo/Gumby.pm Bio/Tools/Phylo/Molphy.pm Bio/Tools/Phylo/Molphy/Result.pm Bio/Tools/Phylo/Phylip/ProtDist.pm Bio/Tools/pICalculator.pm Bio/Tools/Prediction/Exon.pm Bio/Tools/Prediction/Gene.pm Bio/Tools/Primer/Assessor/Base.pm Bio/Tools/Primer/AssessorI.pm Bio/Tools/Primer/Feature.pm Bio/Tools/Primer/Pair.pm Bio/Tools/Primer3.pm Bio/Tools/Prints.pm Bio/Tools/Profile.pm Bio/Tools/Promoterwise.pm Bio/Tools/PrositeScan.pm Bio/Tools/Protparam.pm Bio/Tools/Pseudowise.pm Bio/Tools/pSW.pm Bio/Tools/QRNA.pm Bio/Tools/RandomDistFunctions.pm Bio/Tools/RepeatMasker.pm Bio/Tools/Run/GenericParameters.pm Bio/Tools/Run/ParametersI.pm Bio/Tools/Run/README Bio/Tools/Run/RemoteBlast.pm Bio/Tools/Seg.pm Bio/Tools/SeqPattern.pm Bio/Tools/SeqPattern/Backtranslate.pm Bio/Tools/SeqStats.pm Bio/Tools/SeqWords.pm Bio/Tools/Sigcleave.pm Bio/Tools/Signalp.pm Bio/Tools/Signalp/ExtendedSignalp.pm Bio/Tools/Sim4/Exon.pm Bio/Tools/Sim4/Results.pm Bio/Tools/SiRNA.pm Bio/Tools/SiRNA/Ruleset/saigo.pm Bio/Tools/SiRNA/Ruleset/tuschl.pm Bio/Tools/Spidey/Exon.pm Bio/Tools/Spidey/Results.pm Bio/Tools/TandemRepeatsFinder.pm Bio/Tools/TargetP.pm Bio/Tools/Tmhmm.pm Bio/Tools/tRNAscanSE.pm Bio/Tree/AlleleNode.pm Bio/Tree/AnnotatableNode.pm Bio/Tree/Compatible.pm Bio/Tree/DistanceFactory.pm Bio/Tree/Draw/Cladogram.pm Bio/Tree/Node.pm Bio/Tree/NodeI.pm Bio/Tree/NodeNHX.pm Bio/Tree/RandomFactory.pm Bio/Tree/Statistics.pm Bio/Tree/Tree.pm Bio/Tree/TreeFunctionsI.pm Bio/Tree/TreeI.pm Bio/TreeIO.pm Bio/TreeIO/cluster.pm Bio/TreeIO/lintree.pm Bio/TreeIO/newick.pm Bio/TreeIO/NewickParser.pm Bio/TreeIO/nexml.pm Bio/TreeIO/nexus.pm Bio/TreeIO/nhx.pm Bio/TreeIO/pag.pm Bio/TreeIO/phyloxml.pm Bio/TreeIO/svggraph.pm Bio/TreeIO/tabtree.pm Bio/TreeIO/TreeEventBuilder.pm Bio/UpdateableSeqI.pm Bio/Variation/AAChange.pm Bio/Variation/AAReverseMutate.pm Bio/Variation/Allele.pm Bio/Variation/DNAMutation.pm Bio/Variation/IO.pm Bio/Variation/IO/flat.pm Bio/Variation/IO/xml.pm Bio/Variation/README Bio/Variation/RNAChange.pm Bio/Variation/SeqDiff.pm Bio/Variation/SNP.pm Bio/Variation/VariantI.pm Bio/WebAgent.pm BioPerl.pm BUGS Build.PL Changes deobfuscator/Deobfuscator/bin/deob_index.pl deobfuscator/Deobfuscator/bin/run-deobfuscator-update.pl deobfuscator/Deobfuscator/Build.PL deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi deobfuscator/Deobfuscator/cgi-bin/deob_flowchart.png deobfuscator/Deobfuscator/cgi-bin/deob_help.html deobfuscator/Deobfuscator/cgi-bin/deob_interface.cgi deobfuscator/Deobfuscator/Changes deobfuscator/Deobfuscator/excluded_modules.txt deobfuscator/Deobfuscator/lib/Deobfuscator.pm deobfuscator/Deobfuscator/LICENSE deobfuscator/Deobfuscator/Makefile.PL deobfuscator/Deobfuscator/MANIFEST deobfuscator/Deobfuscator/META.yml deobfuscator/Deobfuscator/README deobfuscator/Deobfuscator/t/00.load.t deobfuscator/Deobfuscator/t/pod.t deobfuscator/makedoc.PL DEPENDENCIES DEPRECATED examples/align/align_on_codons.pl examples/align/aligntutorial.pl examples/align/clustalw.pl examples/align/FastAlign.pl examples/align/simplealign.pl examples/Bio-DB-GFF/load_ucsc.pl examples/bioperl.pl examples/cluster/dbsnp.pl examples/contributed/nmrpdb_parse.pl examples/contributed/prosite2perl.pl examples/contributed/rebase2list.pl examples/db/dbfetch examples/db/est_tissue_query.pl examples/db/gb2features.pl examples/db/get_seqs.pl examples/db/getGenBank.pl examples/db/rfetch.pl examples/db/use_registry.pl examples/generate_random_seq.pl examples/liveseq/change_gene.pl examples/longorf.pl examples/make_primers.pl examples/popgen/parse_calc_stats.pl examples/quality/svgtrace.pl examples/rev_and_trans.pl examples/revcom_dir.pl examples/root/exceptions1.pl examples/root/exceptions2.pl examples/root/exceptions3.pl examples/root/exceptions4.pl examples/root/README examples/searchio/blast_example.pl examples/searchio/custom_writer.pl examples/searchio/hitwriter.pl examples/searchio/hspwriter.pl examples/searchio/htmlwriter.pl examples/searchio/psiblast_features.pl examples/searchio/psiblast_iterations.pl examples/searchio/rawwriter.pl examples/searchio/resultwriter.pl examples/searchio/waba2gff.pl examples/searchio/waba2gff3.pl examples/sirna/rnai_finder.cgi examples/sirna/TAG examples/structure/structure-io.pl examples/subsequence.cgi examples/tk/gsequence.pl examples/tk/hitdisplay.pl examples/tools/extract_genes.pl examples/tools/gb_to_gff.pl examples/tools/gff2ps.pl examples/tools/parse_codeml.pl examples/tools/psw.pl examples/tools/reverse-translate.pl examples/tools/run_genscan.pl examples/tools/run_primer3.pl examples/tools/seq_pattern.pl examples/tools/standaloneblast.pl examples/tree/paup2phylip.pl ide/bioperl-mode/dist/bioperl-mode-xemacs.tar ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5 ide/bioperl-mode/dist/bioperl-mode.tar ide/bioperl-mode/dist/bioperl-mode.tar.md5 ide/bioperl-mode/dist/Changes ide/bioperl-mode/dist/package-me ide/bioperl-mode/dist/SKIP ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm ide/bioperl-mode/etc/images/bpmode-tool.xpm ide/bioperl-mode/README ide/bioperl-mode/site-lisp/bioperl-init.el ide/bioperl-mode/site-lisp/bioperl-mode.el ide/bioperl-mode/site-lisp/bioperl-skel.el ide/bioperl-mode/site-lisp/pod.el ide/bioperl.komodo INSTALL-WIN.md INSTALL.md INSTALL.SKIP LICENSE maintenance/authors.pl maintenance/big_split/file_classification.csv maintenance/big_split/rbuels_notes.txt maintenance/check_NAME.pl maintenance/check_URLs.pl maintenance/cvs2cl_by_file.pl maintenance/dependencies.pl maintenance/deprecated.pl maintenance/find_mod_deps.pl maintenance/module_usage.pl maintenance/modules.pl maintenance/ncbi_blast_switches.pl maintenance/perltidy.conf maintenance/pod.pl maintenance/README maintenance/symlink_script.pl maintenance/version.pl MANIFEST This list of files models/biblio.dia models/bio_liveseq_variation.dia models/bio_map.dia models/bio_restriction.dia models/bioperl.dia models/coordinatemapper.dia models/map_proposal.txt models/maps_and_markers.dia models/popgen.dia models/population_proposal.txt models/README README.md scripts/Bio-DB-GFF/bp_bulk_load_gff.pl scripts/Bio-DB-GFF/bp_fast_load_gff.pl scripts/Bio-DB-GFF/bp_genbank2gff.pl scripts/Bio-DB-GFF/bp_genbank2gff3.pl scripts/Bio-DB-GFF/bp_generate_histogram.pl scripts/Bio-DB-GFF/bp_load_gff.pl scripts/Bio-DB-GFF/bp_meta_gff.pl scripts/Bio-DB-GFF/bp_process_gadfly.pl scripts/Bio-DB-GFF/bp_process_sgd.pl scripts/Bio-DB-GFF/bp_process_wormbase.pl scripts/Bio-DB-GFF/README scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl scripts/das/bp_das_server.pl scripts/das/README scripts/das/TAG scripts/DB-HIV/bp_hivq.pl scripts/DB/bp_biofetch_genbank_proxy.pl scripts/DB/bp_bioflat_index.pl scripts/DB/bp_biogetseq.pl scripts/DB/bp_flanks.pl scripts/DB/TAG scripts/index/bp_fetch.pl scripts/index/bp_index.pl scripts/index/bp_seqret.pl scripts/index/TAG scripts/popgen/bp_composite_LD.pl scripts/popgen/bp_heterogeneity_test.pl scripts/README scripts/searchio/bp_fastam9_to_table.pl scripts/searchio/bp_filter_search.pl scripts/searchio/bp_hmmer_to_table.pl scripts/searchio/bp_parse_hmmsearch.pl scripts/searchio/bp_search2table.pl scripts/searchio/README scripts/searchio/TAG scripts/seq/bp_extract_feature_seq.pl scripts/seq/bp_make_mrna_protein.pl scripts/seq/bp_seqconvert.pl scripts/seq/bp_seqcut.pl scripts/seq/bp_seqpart.pl scripts/seq/bp_seqretsplit.pl scripts/seq/bp_split_seq.pl scripts/seq/bp_translate_seq.pl scripts/seq/bp_unflatten_seq.pl scripts/seq/TAG scripts/seqstats/bp_aacomp.pl scripts/seqstats/bp_chaos_plot.pl scripts/seqstats/bp_gccalc.pl scripts/seqstats/bp_oligo_count.pl scripts/seqstats/TAG scripts/taxa/bp_classify_hits_kingdom.pl scripts/taxa/bp_local_taxonomydb_query.pl scripts/taxa/bp_query_entrez_taxa.pl scripts/taxa/bp_taxid4species.pl scripts/taxa/bp_taxonomy2tree.pl scripts/taxa/TAG scripts/tree/bp_blast2tree.pl scripts/tree/bp_nexus2nh.pl scripts/tree/bp_tree2pag.pl scripts/tree/TAG scripts/utilities/bp_dbsplit.pl scripts/utilities/bp_download_query_genbank.pl scripts/utilities/bp_find-blast-matches.pl scripts/utilities/bp_mask_by_search.pl scripts/utilities/bp_mrtrans.pl scripts/utilities/bp_mutate.pl scripts/utilities/bp_netinstall.pl scripts/utilities/bp_nrdb.pl scripts/utilities/bp_remote_blast.pl scripts/utilities/bp_revtrans-motif.pl scripts/utilities/bp_search2alnblocks.pl scripts/utilities/bp_search2gff.pl scripts/utilities/bp_search2tribe.pl scripts/utilities/bp_seq_length.pl scripts/utilities/bp_sreformat.pl scripts/utilities/README scripts/utilities/TAG t/Align/AlignStats.t t/Align/AlignUtil.t t/Align/Graphics.t t/Align/SimpleAlign.t t/Align/TreeBuild.t t/Align/Utilities.t t/AlignIO/AlignIO.t t/AlignIO/arp.t t/AlignIO/bl2seq.t t/AlignIO/clustalw.t t/AlignIO/emboss.t t/AlignIO/fasta.t t/AlignIO/largemultifasta.t t/AlignIO/maf.t t/AlignIO/mase.t t/AlignIO/mega.t t/AlignIO/meme.t t/AlignIO/metafasta.t t/AlignIO/msf.t t/AlignIO/nexml.t t/AlignIO/nexus.t t/AlignIO/pfam.t t/AlignIO/phylip.t t/AlignIO/po.t t/AlignIO/prodom.t t/AlignIO/psi.t t/AlignIO/selex.t t/AlignIO/stockholm.t t/AlignIO/xmfa.t t/Alphabet.t t/Annotation/Annotation.t 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"1.007002" }, "Bio::TreeIO::nhx" : { "file" : "Bio/TreeIO/nhx.pm", "version" : "1.007002" }, "Bio::TreeIO::pag" : { "file" : "Bio/TreeIO/pag.pm", "version" : "1.007002" }, "Bio::TreeIO::phyloxml" : { "file" : "Bio/TreeIO/phyloxml.pm", "version" : "1.007002" }, "Bio::TreeIO::svggraph" : { "file" : "Bio/TreeIO/svggraph.pm", "version" : "1.007002" }, "Bio::TreeIO::tabtree" : { "file" : "Bio/TreeIO/tabtree.pm", "version" : "1.007002" }, "Bio::UpdateableSeqI" : { "file" : "Bio/UpdateableSeqI.pm", "version" : "1.007002" }, "Bio::Variation::AAChange" : { "file" : "Bio/Variation/AAChange.pm", "version" : "1.007002" }, "Bio::Variation::AAReverseMutate" : { "file" : "Bio/Variation/AAReverseMutate.pm", "version" : "1.007002" }, "Bio::Variation::Allele" : { "file" : "Bio/Variation/Allele.pm", "version" : "1.007002" }, "Bio::Variation::DNAMutation" : { "file" : "Bio/Variation/DNAMutation.pm", "version" : "1.007002" }, "Bio::Variation::IO" : { "file" : "Bio/Variation/IO.pm", "version" : "1.007002" }, "Bio::Variation::IO::flat" : { "file" : "Bio/Variation/IO/flat.pm", "version" : "1.007002" }, "Bio::Variation::IO::xml" : { "file" : "Bio/Variation/IO/xml.pm", "version" : "1.007002" }, "Bio::Variation::RNAChange" : { "file" : "Bio/Variation/RNAChange.pm", "version" : "1.007002" }, "Bio::Variation::SNP" : { "file" : "Bio/Variation/SNP.pm", "version" : "1.007002" }, "Bio::Variation::SeqDiff" : { "file" : "Bio/Variation/SeqDiff.pm", "version" : "1.007002" }, "Bio::Variation::VariantI" : { "file" : "Bio/Variation/VariantI.pm", "version" : "1.007002" }, "Bio::WebAgent" : { "file" : "Bio/WebAgent.pm", "version" : "1.007002" }, "FeatureStore" : { "file" : "Bio/DB/GFF/Adaptor/berkeleydb.pm", "version" : "1.007002" } }, "release_status" : "stable", "resources" : { "license" : [ "http://dev.perl.org/licenses/" ] }, "version" : "1.007002", "x_serialization_backend" : "JSON::PP version 2.27300_01" } BioPerl-1.007002/META.yml000444000766000024 21413013155576320 15025 0ustar00cjfieldsstaff000000000000--- abstract: 'Bioinformatics Toolkit' author: - 'BioPerl Team ' build_requires: CPAN: '1.81' Module::Build: '0.42' Test::Harness: '2.62' Test::Most: '0' URI::Escape: '0' configure_requires: Module::Build: '0.42' dynamic_config: 1 generated_by: 'Module::Build version 0.4224, CPAN::Meta::Converter version 2.150005' license: perl meta-spec: url: http://module-build.sourceforge.net/META-spec-v1.4.html version: '1.4' name: BioPerl provides: Bio::Align::AlignI: file: Bio/Align/AlignI.pm version: '1.007002' Bio::Align::DNAStatistics: file: Bio/Align/DNAStatistics.pm version: '1.007002' Bio::Align::Graphics: file: Bio/Align/Graphics.pm version: '1.007002' Bio::Align::PairwiseStatistics: file: Bio/Align/PairwiseStatistics.pm version: '1.007002' Bio::Align::ProteinStatistics: file: Bio/Align/ProteinStatistics.pm version: '1.007002' Bio::Align::StatisticsI: file: Bio/Align/StatisticsI.pm version: '1.007002' Bio::Align::Utilities: file: Bio/Align/Utilities.pm 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Bio::Annotation::Target: file: Bio/Annotation/Target.pm version: '1.007002' Bio::Annotation::Tree: file: Bio/Annotation/Tree.pm version: '1.007002' Bio::Annotation::TypeManager: file: Bio/Annotation/TypeManager.pm version: '1.007002' Bio::AnnotationCollectionI: file: Bio/AnnotationCollectionI.pm version: '1.007002' Bio::AnnotationI: file: Bio/AnnotationI.pm version: '1.007002' Bio::Assembly::Contig: file: Bio/Assembly/Contig.pm version: '1.007002' Bio::Assembly::ContigAnalysis: file: Bio/Assembly/ContigAnalysis.pm version: '1.007002' Bio::Assembly::IO: file: Bio/Assembly/IO.pm version: '1.007002' Bio::Assembly::IO::ace: file: Bio/Assembly/IO/ace.pm version: '1.007002' Bio::Assembly::IO::bowtie: file: Bio/Assembly/IO/bowtie.pm version: '1.007002' Bio::Assembly::IO::maq: file: Bio/Assembly/IO/maq.pm version: '1.007002' Bio::Assembly::IO::phrap: file: Bio/Assembly/IO/phrap.pm version: '1.007002' Bio::Assembly::IO::sam: file: Bio/Assembly/IO/sam.pm version: '1.007002' 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Bio::Tools::GuessSeqFormat: file: Bio/Tools/GuessSeqFormat.pm version: '1.007002' Bio::Tools::HMMER::Domain: file: Bio/Tools/HMMER/Domain.pm version: '1.007002' Bio::Tools::HMMER::Results: file: Bio/Tools/HMMER/Results.pm version: '1.007002' Bio::Tools::HMMER::Set: file: Bio/Tools/HMMER/Set.pm version: '1.007002' Bio::Tools::Hmmpfam: file: Bio/Tools/Hmmpfam.pm version: '1.007002' Bio::Tools::IUPAC: file: Bio/Tools/IUPAC.pm version: '1.007002' Bio::Tools::Lucy: file: Bio/Tools/Lucy.pm version: '1.007002' Bio::Tools::MZEF: file: Bio/Tools/MZEF.pm version: '1.007002' Bio::Tools::Match: file: Bio/Tools/Match.pm version: '1.007002' Bio::Tools::OddCodes: file: Bio/Tools/OddCodes.pm version: '1.007002' Bio::Tools::Phylo::Gerp: file: Bio/Tools/Phylo/Gerp.pm version: '1.007002' Bio::Tools::Phylo::Gumby: file: Bio/Tools/Phylo/Gumby.pm version: '1.007002' Bio::Tools::Phylo::Molphy: file: Bio/Tools/Phylo/Molphy.pm version: '1.007002' Bio::Tools::Phylo::Molphy::Result: file: Bio/Tools/Phylo/Molphy/Result.pm version: '1.007002' Bio::Tools::Phylo::Phylip::ProtDist: file: Bio/Tools/Phylo/Phylip/ProtDist.pm version: '1.007002' Bio::Tools::Prediction::Exon: file: Bio/Tools/Prediction/Exon.pm version: '1.007002' Bio::Tools::Prediction::Gene: file: Bio/Tools/Prediction/Gene.pm version: '1.007002' Bio::Tools::Primer3: file: Bio/Tools/Primer3.pm version: '1.007002' Bio::Tools::Primer::Assessor::Base: file: Bio/Tools/Primer/Assessor/Base.pm version: '1.007002' Bio::Tools::Primer::AssessorI: file: Bio/Tools/Primer/AssessorI.pm version: '1.007002' Bio::Tools::Primer::Feature: file: Bio/Tools/Primer/Feature.pm version: '1.007002' Bio::Tools::Primer::Pair: file: Bio/Tools/Primer/Pair.pm version: '1.007002' Bio::Tools::Prints: file: Bio/Tools/Prints.pm version: '1.007002' Bio::Tools::Profile: file: Bio/Tools/Profile.pm version: '1.007002' Bio::Tools::Promoterwise: file: Bio/Tools/Promoterwise.pm version: '1.007002' Bio::Tools::PrositeScan: file: Bio/Tools/PrositeScan.pm 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Bio/Tools/SeqWords.pm version: '1.007002' Bio::Tools::SiRNA: file: Bio/Tools/SiRNA.pm version: '1.007002' Bio::Tools::SiRNA::Ruleset::saigo: file: Bio/Tools/SiRNA/Ruleset/saigo.pm version: '1.007002' Bio::Tools::SiRNA::Ruleset::tuschl: file: Bio/Tools/SiRNA/Ruleset/tuschl.pm version: '1.007002' Bio::Tools::Sigcleave: file: Bio/Tools/Sigcleave.pm version: '1.007002' Bio::Tools::Signalp: file: Bio/Tools/Signalp.pm version: '1.007002' Bio::Tools::Signalp::ExtendedSignalp: file: Bio/Tools/Signalp/ExtendedSignalp.pm version: '1.007002' Bio::Tools::Sim4::Exon: file: Bio/Tools/Sim4/Exon.pm version: '1.007002' Bio::Tools::Sim4::Results: file: Bio/Tools/Sim4/Results.pm version: '1.007002' Bio::Tools::Spidey::Exon: file: Bio/Tools/Spidey/Exon.pm version: '1.007002' Bio::Tools::Spidey::Results: file: Bio/Tools/Spidey/Results.pm version: '1.007002' Bio::Tools::TandemRepeatsFinder: file: Bio/Tools/TandemRepeatsFinder.pm version: '1.007002' Bio::Tools::TargetP: file: Bio/Tools/TargetP.pm version: '1.007002' Bio::Tools::Tmhmm: file: Bio/Tools/Tmhmm.pm version: '1.007002' Bio::Tools::dpAlign: file: Bio/Tools/dpAlign.pm version: '1.007002' Bio::Tools::ipcress: file: Bio/Tools/ipcress.pm version: '1.007002' Bio::Tools::isPcr: file: Bio/Tools/isPcr.pm version: '1.007002' Bio::Tools::pICalculator: file: Bio/Tools/pICalculator.pm version: '1.007002' Bio::Tools::pSW: file: Bio/Tools/pSW.pm version: '1.007002' Bio::Tools::tRNAscanSE: file: Bio/Tools/tRNAscanSE.pm version: '1.007002' Bio::Tree::AlleleNode: file: Bio/Tree/AlleleNode.pm version: '1.007002' Bio::Tree::AnnotatableNode: file: Bio/Tree/AnnotatableNode.pm version: '1.007002' Bio::Tree::Compatible: file: Bio/Tree/Compatible.pm version: '1.007002' Bio::Tree::DistanceFactory: file: Bio/Tree/DistanceFactory.pm version: '1.007002' Bio::Tree::Draw::Cladogram: file: Bio/Tree/Draw/Cladogram.pm version: '1.007002' Bio::Tree::Node: file: Bio/Tree/Node.pm version: '1.007002' Bio::Tree::NodeI: file: Bio/Tree/NodeI.pm version: '1.007002' Bio::Tree::NodeNHX: file: Bio/Tree/NodeNHX.pm version: '1.007002' Bio::Tree::RandomFactory: file: Bio/Tree/RandomFactory.pm version: '1.007002' Bio::Tree::Statistics: file: Bio/Tree/Statistics.pm version: '1.007002' Bio::Tree::Tree: file: Bio/Tree/Tree.pm version: '1.007002' Bio::Tree::TreeFunctionsI: file: Bio/Tree/TreeFunctionsI.pm version: '1.007002' Bio::Tree::TreeI: file: Bio/Tree/TreeI.pm version: '1.007002' Bio::TreeIO: file: Bio/TreeIO.pm version: '1.007002' Bio::TreeIO::NewickParser: file: Bio/TreeIO/NewickParser.pm version: '1.007002' Bio::TreeIO::TreeEventBuilder: file: Bio/TreeIO/TreeEventBuilder.pm version: '1.007002' Bio::TreeIO::cluster: file: Bio/TreeIO/cluster.pm version: '1.007002' Bio::TreeIO::lintree: file: Bio/TreeIO/lintree.pm version: '1.007002' Bio::TreeIO::newick: file: Bio/TreeIO/newick.pm version: '1.007002' Bio::TreeIO::nexml: file: Bio/TreeIO/nexml.pm version: '1.007002' Bio::TreeIO::nexus: file: Bio/TreeIO/nexus.pm version: '1.007002' Bio::TreeIO::nhx: file: Bio/TreeIO/nhx.pm version: '1.007002' Bio::TreeIO::pag: file: Bio/TreeIO/pag.pm version: '1.007002' Bio::TreeIO::phyloxml: file: Bio/TreeIO/phyloxml.pm version: '1.007002' Bio::TreeIO::svggraph: file: Bio/TreeIO/svggraph.pm version: '1.007002' Bio::TreeIO::tabtree: file: Bio/TreeIO/tabtree.pm version: '1.007002' Bio::UpdateableSeqI: file: Bio/UpdateableSeqI.pm version: '1.007002' Bio::Variation::AAChange: file: Bio/Variation/AAChange.pm version: '1.007002' Bio::Variation::AAReverseMutate: file: Bio/Variation/AAReverseMutate.pm version: '1.007002' Bio::Variation::Allele: file: Bio/Variation/Allele.pm version: '1.007002' Bio::Variation::DNAMutation: file: Bio/Variation/DNAMutation.pm version: '1.007002' Bio::Variation::IO: file: Bio/Variation/IO.pm version: '1.007002' Bio::Variation::IO::flat: file: Bio/Variation/IO/flat.pm version: '1.007002' Bio::Variation::IO::xml: file: Bio/Variation/IO/xml.pm version: '1.007002' Bio::Variation::RNAChange: file: Bio/Variation/RNAChange.pm version: '1.007002' Bio::Variation::SNP: file: Bio/Variation/SNP.pm version: '1.007002' Bio::Variation::SeqDiff: file: Bio/Variation/SeqDiff.pm version: '1.007002' Bio::Variation::VariantI: file: Bio/Variation/VariantI.pm version: '1.007002' Bio::WebAgent: file: Bio/WebAgent.pm version: '1.007002' FeatureStore: file: Bio/DB/GFF/Adaptor/berkeleydb.pm version: '1.007002' recommends: Algorithm::Munkres: '0' Array::Compare: '0' Bio::Phylo: '0' CGI: '0' Clone: '0' Convert::Binary::C: '0' DB_File: '0' Error: '0' GD: '0' Graph: '0.5' GraphViz: '0' HTML::Entities: '0' HTML::HeadParser: '3' HTML::TableExtract: '0' HTTP::Request::Common: '0' IO::Scalar: '0' Inline::C: '0.67' LWP::UserAgent: '0' List::MoreUtils: '0' PostScript::TextBlock: '0' SVG: '2.26' SVG::Graph: '0.01' Set::Scalar: '0' Sort::Naturally: '0' Spreadsheet::ParseExcel: '0' Storable: '2.05' Text::ParseWords: '0' XML::DOM: '0' XML::DOM::XPath: '0' XML::LibXML: '0' XML::Parser: '0' XML::Parser::PerlSAX: '0' XML::SAX: '0.15' XML::SAX::Writer: '0' XML::Simple: '0' XML::Twig: '0' XML::Writer: '0.4' YAML: '0' requires: Data::Stag: '0.11' ExtUtils::Manifest: '1.52' IO::String: '0' Scalar::Util: '0' perl: v5.6.1 resources: license: http://dev.perl.org/licenses/ version: '1.007002' x_serialization_backend: 'CPAN::Meta::YAML version 0.018' BioPerl-1.007002/README.md000444000766000024 2672213155576320 15023 0ustar00cjfieldsstaff000000000000[![Build Status](https://travis-ci.org/bioperl/bioperl-live.svg?branch=master)](https://travis-ci.org/bioperl/bioperl-live) [![Coverage Status](https://coveralls.io/repos/bioperl/bioperl-live/badge.png?branch=master)](https://coveralls.io/r/bioperl/bioperl-live?branch=master) [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.16344.svg)](http://dx.doi.org/10.5281/zenodo.16344) [![Documentation Status](https://readthedocs.org/projects/bioperl/badge/?version=latest)](https://readthedocs.org/projects/bioperl/?badge=latest) # Getting Started Please see the the [INSTALL](http://bioperl.org/INSTALL.html) or [INSTALL.WIN](http://bioperl.org/INSTALL.WIN.html) documents for installation instructions. # About BioPerl BioPerl is a package of public domain Perl tools for computational molecular biology. Our website (http://bioperl.org/) provides an online resource of modules, scripts, and web links for developers of Perl-based software for life science research. # Contact Information * BioPerl mailing list: bioperl-l@bioperl.org * Project website : http://bioperl.org/ * Bug reports : https://github.com/bioperl/bioperl-live/issues Please submit bugs, in particular about documentation which you think is unclear, or about problems in installation. We are also very interested in functions which don't work the way you think they do! # The Directory Structure The BioPerl directory structure is organized as follows: * **`Bio/`** - BioPerl modules * **`deobfuscator/`** - Code for tracing OOP relationships * **`examples/`** - Scripts demonstrating the many uses of BioPerl * **`ide/`** - Files for developing BioPerl using an IDE * **`maintenance/`** - BioPerl housekeeping scripts * **`models/`** - DIA drawing program generated OO UML for BioPerl classes (these are quite out-of-date) * **`scripts/`** - Useful production-quality scripts with POD documentation * **`t/`** - Perl built-in tests, tests are divided into subdirectories based on the specific classes being tested * **`t/data/`** - Data files used for the tests, provides good example data * **`travis_scripts/`** - script to customize Travis # Documentation For documentation on BioPerl see the **HOWTO** documents online at http://bioperl.org/howtos. Useful documentation in the form of example code can also be found in the **`examples/`** and **`scripts/`** directories. The current collection includes scripts that run BLAST, index flat files, parse PDB structure files, make primers, retrieve ESTs based on tissue, align protein to nucleotide sequence, run GENSCAN on multiple sequences, and much more! See `bioscripts.pod` for a complete listing. Individual `*.pm` modules have their own embedded POD documentation as well. A complete set of hyperlinked POD, or module, documentation is available at http://www.bioperl.org/. Remember that '`perldoc`' is your friend. You can use it to read any file containing POD formatted documentation without needing any type of translator (e.g. '`perldoc Bio::SeqIO`'). If you used the Build.PL installation, and depending on your platform, you may have documentation installed as man pages, which can be accessed in the usual way. # Releases BioPerl releases are always available from the website at http://www.bioperl.org/DIST or in CPAN. The latest code can be found at https://github.com/bioperl. * BioPerl currently uses a sematic numbering scheme to indicate stable release series vs. development release series. A release number is a three digit number like `1.2.0`. * The *first digit indicates the major release*, the idea being that all the API calls in a major release are reasonably consistent. * The *second number is the release series*. This is probably the most important number, and represents added functionality that is backwards-compatible. * The *third number is the point or patch release* and represents mainly bug fixes or additional code that doesn't add significant functionality to the code base. From the **1.0 release until the 1.6 release** even numbers (e.g. `1.4`) indicated stable releases. Stable releases were well tested and recommended for most uses. Odd numbers (e.g. `1.3`) were development releases which one would only use if one were interested in the latest features. The final number (e.g. in `1.2.1`) is the point or patch release. The higher the number the more bug fixes has been incorporated. In theory you can upgrade from one point or patch release to the next with no changes to your own code (for production cases, obviously check things out carefully before you switch over). The upcoming **1.7 release** will be the last release series to utilize the alternating 'stable'/'developer' convention. Starting immediately after the final 1.6 branch, we will start splitting BioPerl into several smaller easier-to-manage distributions. These will have independent versions, all likely starting with v1.7.0. **We do not anticipate major API changes in the 1.7.x release series, merely that the code will be restructured in a way to make maintenance more feasible.** We anticipate retaining semantic versioning until the 2.x release. # Caveats and Warnings When you run the tests with `./Build test` some tests may issue warnings messages or even fail. Sometimes this is because we didn't have anyone to test the test system on the combination of your operating system, version of perl, and associated libraries and other modules. Because BioPerl depends on several outside libraries we may not be able to test every single combination so if there are warnings you may find that the package is still perfectly useful. If you install the bioperl-run system and run tests when you don't have the program installed you'll get messages like `program XXX not found, skipping tests`. That's okay, BioPerl is doing what it is supposed to do. If you wanted to run the program you'd need to install it first. Not all scripts in the `examples/` directory are correct and up-to-date. If you find an issue with a script please submit a bug report to https://github.com/bioperl/bioperl-live/issues and consider helping out in their maintenance. If you are confused about what modules are appropriate when you try and solve a particular issue in bioinformatics we urge you to look at HOWTO documents first. # A simple module summary Here is a quick summary of many of the useful modules and how the toolkit is laid out: All modules are in the **`Bio/`** namespace, * **`Perl`** is for *new users*, and gives a functional interface to the main parts of the package. * **`Seq`** is for *Sequences* (protein and DNA). * `Bio::PrimarySeq` is a plain sequence (sequence data + identifiers) * `Bio::Seq` is a fancier `PrimarySeq`, in that it has annotation (via `Bio::Annotation::Collection`) and sequence features (via `Bio::SeqFeatureI` objects, attached via `Bio::FeatureHolderI`). * `Bio::Seq::RichSeq` is all of the above, plus it has slots for extra information specific to GenBank/EMBL/SwissProt files. * `Bio::Seq::LargeSeq` is for sequences which are too big for fitting into memory. * **`SeqIO`** is for *reading and writing Sequences*. It is a front end module for separate driver modules supporting the different sequence formats * **`SeqFeature`** represent *start/stop/strand-based localized annotations (features) of sequences* * **`Bio::SeqFeature::Generic`** is basic catchall * **`Bio::SeqFeature::Similarity`** a similarity sequence feature * **`Bio::SeqFeature::FeaturePair`** a sequence feature which is pairwise such as query/hit pairs * **`SearchIO`** is for *reading and writing pairwise alignment reports*, like BLAST or FASTA * **`Search`** is where the *alignment objects for `SearchIO` are defined* * **`Bio::Search::Result::GenericResult`** is the result object (a blast query is a `Result` object) * **`Bio::Search::Hit::GenericHit`** is the `Hit` object (a query will have 0 to many hits in a database) * **`Bio::Search::HSP::GenericHSP`** is the High-scoring Segment Pair object defining the alignment(s) of the query and hit. * **`SimpleAlign`** is for *multiple sequence alignments* * **`AlignIO`** is for *reading and writing multiple sequence alignment formats* * **`Assembly`** provides the start of an *infrastructure for assemblies* and **`Assembly::IO`** *IO converters* for them * **`DB`** is the namespace for *all the database query classes* * **`Bio::DB::GenBank/GenPept`** are two modules which query NCBI entrez for sequences * **`Bio::DB::SwissProt/EMBL`** query various EMBL and SwissProt repositories for a sequences * **`Bio::DB::GFF`** is Lincoln Stein's fast, lightweight feature and sequence database which is the backend to his GBrowse system (see www.gmod.org) * **`Bio::DB::Flat`** is a fast implementation of the OBDA flat-file indexing system (cross-language and cross-platform supported by O|B|F projects see http://obda.open-bio.org). * **`Bio::DB::BioFetch/DBFetch`** for OBDA, Web (HTTP) access to remote databases. * **`Bio::DB::InMemoryCache/FileCache`** (fast local caching of sequences from remote dbs to speed up your access). * **`Bio::DB::Registry`** interface to the OBDA specification for remote data sources * **`Bio::DB::Biblio`** for access to remote bibliographic databases. * **`Bio::DB::EUtilities`** is the initial set of modules used for generic queried using NCBI's eUtils. * **`Annotation`** collection of *annotation objects* (comments, DBlinks, References, and misc key/value pairs) * **`Coordinate`** is a system for *mapping between different coordinate systems* such as DNA to protein or between assemblies * **`Index`** is for *locally indexed flatfiles* with BerkeleyDB * **`Tools`** contains many *miscellaneous parsers and functions* for different bioinformatics needs * Gene prediction parser (Genscan, MZEF, Grail, Genemark) * Annotation format (GFF) * Enumerate codon tables and valid sequences symbols (CodonTable, IUPAC) * Phylogenetic program parsing (PAML, Molphy, Phylip) * **`Map`** represents *genetic and physical map representations* * **`Structure`** - parse and represent *protein structure data* * **`TreeIO`** is for reading and writing *Tree formats* * **`Tree`** is the namespace for **all associated Tree classes** * **`Bio::Tree::Tree`** is the basic tree object * **`Bio::Tree::Node`** are the nodes which make up the tree * **`Bio::Tree::Statistics`** is for computing statistics for a tree * **`Bio::Tree::TreeFunctionsI`** is where specific tree functions are implemented (like `is_monophyletic` and `lca`) * **`Bio::Biblio`** is where *bibliographic data and database access objects* are kept * **`Variation`** represent *sequences with mutations and variations* applied so one can compare and represent wild-type and mutation versions of a sequence. * **`Root`**, basic objects for the *internals of BioPerl* # Upgrading from an older version If you have a previously installed version of BioPerl on your system some of these notes may help you. * Some modules have been removed because they have been superceded by new development efforts. They are documented in the **`DEPRECATED`** file that is included in the release. * Some methods, or the Application Programming Interface (API), have changed or been removed. You may find that scripts which worked with BioPerl 1.4 may give you warnings or may not work at all (although we have tried very hard to minimize this!). Send an email to the list and we'll be happy to give you pointers. BioPerl-1.007002/Bio000755000766000024 013155576320 14067 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/AlignIO.pm000444000766000024 3631013155576320 16067 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO # # based on the Bio::SeqIO module # by Ewan Birney # and Lincoln Stein # # Copyright Peter Schattner # # You may distribute this module under the same terms as perl itself # # History # September, 2000 AlignIO written by Peter Schattner # POD documentation - main docs before the code =head1 NAME Bio::AlignIO - Handler for AlignIO Formats =head1 SYNOPSIS use Bio::AlignIO; $inputfilename = "testaln.fasta"; $in = Bio::AlignIO->new(-file => $inputfilename , -format => 'fasta'); $out = Bio::AlignIO->new(-file => ">out.aln.pfam" , -format => 'pfam'); while ( my $aln = $in->next_aln() ) { $out->write_aln($aln); } # OR use Bio::AlignIO; open MYIN, '<', 'testaln.fasta' or die "Could not read file 'testaln.fasta': $!\n"; $in = Bio::AlignIO->newFh(-fh => \*MYIN, -format => 'fasta'); open my $MYOUT, '>', 'testaln.pfam' or die "Could not write file 'testaln.pfam': $!\n"; $out = Bio::AlignIO->newFh(-fh => $MYOUT, -format => 'pfam'); # World's smallest Fasta<->pfam format converter: print $out $_ while <$in>; =head1 DESCRIPTION L is a handler module for the formats in the AlignIO set, for example, L. It is the officially sanctioned way of getting at the alignment objects. The resulting alignment is a L-compliant object. The idea is that you request an object for a particular format. All the objects have a notion of an internal file that is read from or written to. A particular AlignIO object instance is configured for either input or output, you can think of it as a stream object. Each object has functions: $stream->next_aln(); And: $stream->write_aln($aln); Also: $stream->type() # returns 'INPUT' or 'OUTPUT' As an added bonus, you can recover a filehandle that is tied to the AlignIO object, allowing you to use the standard EE and print operations to read and write alignment objects: use Bio::AlignIO; # read from standard input $stream = Bio::AlignIO->newFh(-format => 'Fasta'); while ( $aln = <$stream> ) { # do something with $aln } And: print $stream $aln; # when stream is in output mode L is patterned on the L module and shares most of its features. One significant difference is that L usually handles IO for only a single alignment at a time, whereas L handles IO for multiple sequences in a single stream. The principal reason for this is that whereas simultaneously handling multiple sequences is a common requirement, simultaneous handling of multiple alignments is not. The only current exception is format C which parses results of the BLAST C program and which may produce several alignment pairs. This set of alignment pairs can be read using multiple calls to L. =head1 CONSTRUCTORS =head2 Bio::AlignIO-Enew() $seqIO = Bio::AlignIO->new(-file => 'filename', -format=>$format); $seqIO = Bio::AlignIO->new(-fh => \*FILEHANDLE, -format=>$format); $seqIO = Bio::AlignIO->new(-format => $format); $seqIO = Bio::AlignIO->new(-fh => \*STDOUT, -format => $format); The L class method constructs a new L object. The returned object can be used to retrieve or print alignment objects. L accepts the following parameters: =over 4 =item -file A file path to be opened for reading or writing. The usual Perl conventions apply: 'file' # open file for reading '>file' # open file for writing '>>file' # open file for appending '+new(-fh => \*STDIN); Note that you must pass filehandles as references to globs. If neither a filehandle nor a filename is specified, then the module will read from the @ARGV array or STDIN, using the familiar EE semantics. =item -format Specify the format of the file. Supported formats include: bl2seq Bl2seq Blast output clustalw clustalw (.aln) format emboss EMBOSS water and needle format fasta FASTA format maf Multiple Alignment Format mase mase (seaview) format mega MEGA format meme MEME format msf msf (GCG) format nexus Swofford et al NEXUS format pfam Pfam sequence alignment format phylip Felsenstein PHYLIP format prodom prodom (protein domain) format psi PSI-BLAST format selex selex (hmmer) format stockholm stockholm format Currently only those formats which were implemented in L have been incorporated into L. Specifically, C, C and C have only been implemented for input. See the specific module (e.g. L) for notes on supported versions. If no format is specified and a filename is given, then the module will attempt to deduce it from the filename suffix. If this is unsuccessful, C format is assumed. The format name is case insensitive; C, C and C are all treated equivalently. =back =head2 Bio::AlignIO-EnewFh() $fh = Bio::AlignIO->newFh(-fh => \*FILEHANDLE, -format=>$format); # read from STDIN or use @ARGV: $fh = Bio::AlignIO->newFh(-format => $format); This constructor behaves like L, but returns a tied filehandle rather than a L object. You can read sequences from this object using the familiar EE operator, and write to it using L. The usual array and $_ semantics work. For example, you can read all sequence objects into an array like this: @sequences = <$fh>; Other operations, such as read(), sysread(), write(), close(), and printf() are not supported. =over 1 =item -flush By default, all files (or filehandles) opened for writing alignments will be flushed after each write_aln() making the file immediately usable. If you do not need this facility and would like to marginally improve the efficiency of writing multiple sequences to the same file (or filehandle), pass the -flush option '0' or any other value that evaluates as defined but false: my $clustal = Bio::AlignIO->new( -file => " "clustalw" ); my $msf = Bio::AlignIO->new(-file => ">prot.msf", -format => "msf", -flush => 0 ); # go as fast as we can! while($seq = $clustal->next_aln) { $msf->write_aln($seq) } =back =head1 OBJECT METHODS See below for more detailed summaries. The main methods are: =head2 $alignment = $AlignIO-Enext_aln() Fetch an alignment from a formatted file. =head2 $AlignIO-Ewrite_aln($aln) Write the specified alignment to a file.. =head2 TIEHANDLE(), READLINE(), PRINT() These provide the tie interface. See L for more details. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Peter Schattner Email: schattner@alum.mit.edu =head1 CONTRIBUTORS Jason Stajich, jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # 'Let the code begin... package Bio::AlignIO; use strict; use Bio::Seq; use Bio::LocatableSeq; use Bio::SimpleAlign; use Bio::Tools::GuessSeqFormat; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : $stream = Bio::AlignIO->new(-file => $filename, -format => 'Format') Function: Returns a new seqstream Returns : A Bio::AlignIO::Handler initialised with the appropriate format Args : -file => $filename -format => format -fh => filehandle to attach to -displayname_flat => 1 [optional] to force the displayname to not show start/end information =cut sub new { my ($caller,@args) = @_; my $class = ref($caller) || $caller; # or do we want to call SUPER on an object if $caller is an # object? if( $class =~ /Bio::AlignIO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $format = $param{'-format'} || $class->_guess_format( $param{-file} || $ARGV[0] ); unless ($format) { if ($param{-file}) { $format = Bio::Tools::GuessSeqFormat->new(-file => $param{-file}||$ARGV[0] )->guess; } elsif ($param{-fh}) { $format = Bio::Tools::GuessSeqFormat->new(-fh => $param{-fh}||$ARGV[0] )->guess; } } $format = "\L$format"; # normalize capitalization to lower case $class->throw("Unknown format given or could not determine it [$format]") unless $format; return unless( $class->_load_format_module($format) ); return "Bio::AlignIO::$format"->new(@args); } } =head2 newFh Title : newFh Usage : $fh = Bio::AlignIO->newFh(-file=>$filename,-format=>'Format') Function: does a new() followed by an fh() Example : $fh = Bio::AlignIO->newFh(-file=>$filename,-format=>'Format') $sequence = <$fh>; # read a sequence object print $fh $sequence; # write a sequence object Returns : filehandle tied to the Bio::AlignIO::Fh class Args : =cut sub newFh { my $class = shift; return unless my $self = $class->new(@_); return $self->fh; } =head2 fh Title : fh Usage : $obj->fh Function: Example : $fh = $obj->fh; # make a tied filehandle $sequence = <$fh>; # read a sequence object print $fh $sequence; # write a sequence object Returns : filehandle tied to the Bio::AlignIO::Fh class Args : =cut sub fh { my $self = shift; my $class = ref($self) || $self; my $s = Symbol::gensym; tie $$s,$class,$self; return $s; } =head2 format Title : format Usage : $format = $stream->format() Function: Get the alignment format Returns : alignment format Args : none =cut # format() method inherited from Bio::Root::IO # _initialize is where the heavy stuff will happen when new is called sub _initialize { my($self,@args) = @_; my ($flat,$alphabet,$width) = $self->_rearrange([qw(DISPLAYNAME_FLAT ALPHABET WIDTH)], @args); $self->force_displayname_flat($flat) if defined $flat; $self->alphabet($alphabet); $self->width($width) if defined $width; $self->_initialize_io(@args); 1; } =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL AlignIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($self,$format) = @_; my $module = "Bio::AlignIO::" . $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <next_aln Function: reads the next $aln object from the stream Returns : a Bio::Align::AlignI compliant object Args : =cut sub next_aln { my ($self,$aln) = @_; $self->throw("Sorry, you cannot read from a generic Bio::AlignIO object."); } =head2 write_aln Title : write_aln Usage : $stream->write_aln($aln) Function: writes the $aln object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object =cut sub write_aln { my ($self,$aln) = @_; $self->throw("Sorry, you cannot write to a generic Bio::AlignIO object."); } =head2 _guess_format Title : _guess_format Usage : $obj->_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args : =cut sub _guess_format { my $class = shift; return unless $_ = shift; return 'clustalw' if /\.aln$/i; return 'emboss' if /\.(water|needle)$/i; return 'metafasta' if /\.metafasta$/; return 'fasta' if /\.(fasta|fast|seq|fa|fsa|nt|aa)$/i; return 'maf' if /\.maf/i; return 'mega' if /\.(meg|mega)$/i; return 'meme' if /\.meme$/i; return 'msf' if /\.(msf|pileup|gcg)$/i; return 'nexus' if /\.(nexus|nex)$/i; return 'pfam' if /\.(pfam|pfm)$/i; return 'phylip' if /\.(phylip|phlp|phyl|phy|ph)$/i; return 'psi' if /\.psi$/i; return 'stockholm' if /\.stk$/i; return 'selex' if /\.(selex|slx|selx|slex|sx)$/i; return 'xmfa' if /\.xmfa$/i; } sub DESTROY { my $self = shift; $self->close(); } sub TIEHANDLE { my $class = shift; return bless {'alignio' => shift},$class; } sub READLINE { my $self = shift; return $self->{'alignio'}->next_aln() || undef unless wantarray; my (@list,$obj); push @list,$obj while $obj = $self->{'alignio'}->next_aln(); return @list; } sub PRINT { my $self = shift; $self->{'alignio'}->write_aln(@_); } =head2 force_displayname_flat Title : force_displayname_flat Usage : $obj->force_displayname_flat($newval) Function: Example : Returns : value of force_displayname_flat (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub force_displayname_flat{ my $self = shift; return $self->{'_force_displayname_flat'} = shift if @_; return $self->{'_force_displayname_flat'} || 0; } =head2 alphabet Title : alphabet Usage : $obj->alphabet($newval) Function: Get/Set alphabet for purpose of passing to Bio::LocatableSeq creation Example : $obj->alphabet('dna'); Returns : value of alphabet (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub alphabet { my $self = shift; my $value = shift; if ( defined $value ) { $self->throw("Invalid alphabet $value") unless $value eq 'rna' || $value eq 'protein' || $value eq 'dna'; $self->{'_alphabet'} = $value; } return $self->{'_alphabet'}; } 1; BioPerl-1.007002/Bio/AnalysisI.pm000444000766000024 5444013155576320 16505 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AnalysisI # # Please direct questions and support issues to # # Cared for by Martin Senger # For copyright and disclaimer see below. # # POD documentation - main docs before the code =head1 NAME Bio::AnalysisI - An interface to any (local or remote) analysis tool =head1 SYNOPSIS This is an interface module - you do not instantiate it. Use C module: use Bio::Tools::Run::Analysis; my $tool = Bio::Tools::Run::Analysis->new(@args); =head1 DESCRIPTION This interface contains all public methods for accessing and controlling local and remote analysis tools. It is meant to be used on the client side. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Martin Senger (martin.senger@gmail.com) =head1 COPYRIGHT Copyright (c) 2003, Martin Senger and EMBL-EBI. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 SEE ALSO http://www.ebi.ac.uk/Tools/webservices/soaplab/guide =head1 APPENDIX This is actually the main documentation... If you try to call any of these methods directly on this C object you will get a I error message. You need to call them on a C object instead. =cut # Let the code begin... package Bio::AnalysisI; use strict; use base qw(Bio::Root::RootI); # ----------------------------------------------------------------------------- =head2 analysis_name Usage : $tool->analysis_name; Returns : a name of this analysis Args : none =cut sub analysis_name { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 analysis_spec Usage : $tool->analysis_spec; Returns : a hash reference describing this analysis Args : none The returned hash reference uses the following keys (not all of them always present, perhaps others present as well): C, C, C, C, C, C. Here is an example output: Analysis 'edit.seqret': installation => EMBL-EBI description => Reads and writes (returns) sequences supplier => EMBOSS version => 2.6.0 type => edit name => seqret =cut sub analysis_spec { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 describe Usage : $tool->analysis_spec; Returns : an XML detailed description of this analysis Args : none The returned XML string contains metadata describing this analysis service. It includes also metadata returned (and easier used) by method C, C and C. The DTD used for returned metadata is based on the adopted standard (BSA specification for analysis engine): But the DTD may be extended by provider-specific metadata. For example, the EBI experimental SOAP-based service on top of EMBOSS uses DTD explained at C. =cut sub describe { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 input_spec Usage : $tool->input_spec; Returns : an array reference with hashes as elements Args : none The analysis input data are named, and can be also associated with a default value, with allowed values and with few other attributes. The names are important for feeding the service with the input data (the inputs are given to methods C, C, and/or C as name/value pairs). Here is a (slightly shortened) example of an input specification: $input_spec = [ { 'mandatory' => 'false', 'type' => 'String', 'name' => 'sequence_usa' }, { 'mandatory' => 'false', 'type' => 'String', 'name' => 'sequence_direct_data' }, { 'mandatory' => 'false', 'allowed_values' => [ 'gcg', 'gcg8', ... 'raw' ], 'type' => 'String', 'name' => 'sformat' }, { 'mandatory' => 'false', 'type' => 'String', 'name' => 'sbegin' }, { 'mandatory' => 'false', 'type' => 'String', 'name' => 'send' }, { 'mandatory' => 'false', 'type' => 'String', 'name' => 'sprotein' }, { 'mandatory' => 'false', 'type' => 'String', 'name' => 'snucleotide' }, { 'mandatory' => 'false', 'type' => 'String', 'name' => 'sreverse' }, { 'mandatory' => 'false', 'type' => 'String', 'name' => 'slower' }, { 'mandatory' => 'false', 'type' => 'String', 'name' => 'supper' }, { 'mandatory' => 'false', 'default' => 'false', 'type' => 'String', 'name' => 'firstonly' }, { 'mandatory' => 'false', 'default' => 'fasta', 'allowed_values' => [ 'gcg', 'gcg8', 'embl', ... 'raw' ], 'type' => 'String', 'name' => 'osformat' } ]; =cut sub input_spec { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 result_spec Usage : $tool->result_spec; Returns : a hash reference with result names as keys and result types as values Args : none The analysis results are named and can be retrieved using their names by methods C and C. Here is an example of the result specification (again for the service I): $result_spec = { 'outseq' => 'String', 'report' => 'String', 'detailed_status' => 'String' }; =cut sub result_spec { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 create_job Usage : $tool->create_job ( {'sequence'=>'tatat'} ) Returns : Bio::Tools::Run::Analysis::Job Args : data and parameters for this execution (in various formats) Create an object representing a single execution of this analysis tool. Call this method if you wish to "stage the scene" - to create a job with all input data but without actually running it. This method is called automatically from other methods (C and C) so usually you do not need to call it directly. The input data and prameters for this execution can be specified in various ways: =over =item array reference The array has scalar elements of the form name = [[@]value] where C is the name of an input data or input parameter (see method C for finding what names are recognized by this analysis) and C is a value for this data/parameter. If C is missing a 1 is assumed (which is convenient for the boolean options). If C starts with C<@> it is treated as a local filename, and its contents is used as the data/parameter value. =item hash reference The same as with the array reference but now there is no need to use an equal sign. The hash keys are input names and hash values their data. The values can again start with a C<@> sign indicating a local filename. =item scalar In this case, the parameter represents a job ID obtained in some previous invocation - such job already exists on the server side, and we are just re-creating it here using the same job ID. I =item undef Finally, if the parameter is undefined, ask server to create an empty job. The input data may be added later using C method(s) - see scripts/papplmaker.PLS for details. =back =cut sub create_job { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 run Usage : $tool->run ( ['sequence=@my.seq', 'osformat=embl'] ) Returns : Bio::Tools::Run::Analysis::Job, representing started job (an execution) Args : the same as for create_job Create a job and start it, but do not wait for its completion. =cut sub run { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 wait_for Usage : $tool->wait_for ( { 'sequence' => '@my,file' } ) Returns : Bio::Tools::Run::Analysis::Job, representing finished job Args : the same as for create_job Create a job, start it and wait for its completion. Note that this is a blocking method. It returns only after the executed job finishes, either normally or by an error. Usually, after this call, you ask for results of the finished job: $analysis->wait_for (...)->results; =cut sub wait_for { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- # # Bio::AnalysisI::JobI # # ----------------------------------------------------------------------------- package Bio::AnalysisI::JobI; =head1 Module Bio::AnalysisI::JobI An interface to the public methods provided by C objects. The C objects represent a created, running, or finished execution of an analysis tool. The factory for these objects is module C where the following methods return an C object: create_job (returning a prepared job) run (returning a running job) wait_for (returning a finished job) =cut use strict; use base qw(Bio::Root::RootI); # ----------------------------------------------------------------------------- =head2 id Usage : $job->id; Returns : this job ID Args : none Each job (an execution) is identifiable by this unique ID which can be used later to re-create the same job (in other words: to re-connect to the same job). It is useful in cases when a job takes long time to finish and your client program does not want to wait for it within the same session. =cut sub id { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 Bio::AnalysisI::JobI::run Usage : $job->run Returns : itself Args : none It starts previously created job. The job already must have all input data filled-in. This differs from the method of the same name of the C object where the C method creates also a new job allowing to set input data. =cut sub run { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 Bio::AnalysisI::JobI::wait_for Usage : $job->wait_for Returns : itself Args : none It waits until a previously started execution of this job finishes. =cut sub wait_for { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 terminate Usage : $job->terminate Returns : itself Args : none Stop the currently running job (represented by this object). This is a definitive stop, there is no way to resume it later. =cut sub terminate { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 last_event Usage : $job->last_event Returns : an XML string Args : none It returns a short XML document showing what happened last with this job. This is the used DTD: Here is an example what is returned after a job was created and started, but before it finishes (note that the example uses an analysis 'showdb' which does not need any input data): use Bio::Tools::Run::Analysis; print new Bio::Tools::Run::Analysis (-name => 'display.showdb') ->run ->last_event; It prints: Mar 3, 2003 5:14:46 PM (Europe/London) The same example but now after it finishes: use Bio::Tools::Run::Analysis; print new Bio::Tools::Run::Analysis (-name => 'display.showdb') ->wait_for ->last_event; Mar 3, 2003 5:17:14 PM (Europe/London) =cut sub last_event { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 status Usage : $job->status Returns : string describing the job status Args : none It returns one of the following strings (and perhaps more if a server implementation extended possible job states): CREATED RUNNING COMPLETED TERMINATED_BY_REQUEST TERMINATED_BY_ERROR =cut sub status { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 created Usage : $job->created (1) Returns : time when this job was created Args : optional Without any argument it returns a time of creation of this job in seconds, counting from the beginning of the UNIX epoch (1.1.1970). With a true argument it returns a formatted time, using rules described in C. =cut sub created { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 started Usage : $job->started (1) Returns : time when this job was started Args : optional See C. =cut sub started { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 ended Usage : $job->ended (1) Returns : time when this job was terminated Args : optional See C. =cut sub ended { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 elapsed Usage : $job->elapsed Returns : elapsed time of the execution of the given job (in milliseconds), or 0 of job was not yet started Args : none Note that some server implementations cannot count in millisecond - so the returned time may be rounded to seconds. =cut sub elapsed { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 times Usage : $job->times ('formatted') Returns : a hash reference with all time characteristics Args : optional It is a convenient method returning a hash reference with the following keys: created started ended elapsed See C for remarks on time formatting. An example - both for unformatted and formatted times: use Data::Dumper; use Bio::Tools::Run::Analysis; my $rh = Bio::Tools::Run::Analysis->new(-name => 'nucleic_cpg_islands.cpgplot') ->wait_for ( { 'sequence_usa' => 'embl:hsu52852' } ) ->times (1); print Data::Dumper->Dump ( [$rh], ['Times']); $rh = Bio::Tools::Run::Analysis->new(-name => 'nucleic_cpg_islands.cpgplot') ->wait_for ( { 'sequence_usa' => 'embl:AL499624' } ) ->times; print Data::Dumper->Dump ( [$rh], ['Times']); $Times = { 'ended' => 'Mon Mar 3 17:52:06 2003', 'started' => 'Mon Mar 3 17:52:05 2003', 'elapsed' => '1000', 'created' => 'Mon Mar 3 17:52:05 2003' }; $Times = { 'ended' => '1046713961', 'started' => '1046713926', 'elapsed' => '35000', 'created' => '1046713926' }; =cut sub times { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 results Usage : $job->results (...) Returns : one or more results created by this job Args : various, see belou This is a complex method trying to make sense for all kinds of results. Especially it tries to help to put binary results (such as images) into local files. Generally it deals with fhe following facts: =over =item * Each analysis tool may produce more results. =item * Some results may contain binary data not suitable for printing into a terminal window. =item * Some results may be split into variable number of parts (this is mainly true for the image results that can consist of more *.png files). =back Note also that results have names to distinguish if there are more of them. The names can be obtained by method C. Here are the rules how the method works: Retrieving NAMED results: ------------------------- results ('name1', ...) => return results as they are, no storing into files results ( { 'name1' => 'filename', ... } ) => store into 'filename', return 'filename' results ( 'name1=filename', ...) => ditto results ( { 'name1' => '-', ... } ) => send result to the STDOUT, do not return anything results ( 'name1=-', ...) => ditto results ( { 'name1' => '@', ... } ) => store into file whose name is invented by this method, perhaps using RESULT_NAME_TEMPLATE env results ( 'name1=@', ...) => ditto results ( { 'name1' => '?', ... } ) => find of what type is this result and then use {'name1'=>'@' for binary files, and a regular return for non-binary files results ( 'name=?', ...) => ditto Retrieving ALL results: ----------------------- results() => return all results as they are, no storing into files results ('@') => return all results, as if each of them given as {'name' => '@'} (see above) results ('?') => return all results, as if each of them given as {'name' => '?'} (see above) Misc: ----- * any result can be returned as a scalar value, or as an array reference (the latter is used for results consisting of more parts, such images); this applies regardless whether the returned result is the result itself or a filename created for the result * look in the documentation of the C script for examples (especially how to use various templates for inventing file names) =cut sub results { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 result Usage : $job->result (...) Returns : the first result Args : see 'results' =cut sub result { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 remove Usage : $job->remove Returns : 1 Args : none The job object is not actually removed in this time but it is marked (setting 1 to C<_destroy_on_exit> attribute) as ready for deletion when the client program ends (including a request to server to forget the job mirror object on the server side). =cut sub remove { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- 1; __END__ BioPerl-1.007002/Bio/AnalysisParserI.pm000444000766000024 1170613155576320 17660 0ustar00cjfieldsstaff000000000000#--------------------------------------------------------------- # # BioPerl module Bio::AnalysisParserI # # Please direct questions and support issues to # # Cared for by Steve Chervitz # # Derived from Bio::SeqAnalysisParserI by Jason Stajich, Hilmar Lapp. # # You may distribute this module under the same terms as perl itself #--------------------------------------------------------------- =head1 NAME Bio::AnalysisParserI - Generic analysis output parser interface =head1 SYNOPSIS # get a AnalysisParserI somehow. # Eventually, there may be an Bio::Factory::AnalysisParserFactory. # For now a SearchIO object, an implementation of AnalysisParserI, can be created # directly, as in the following: my $parser = Bio::SearchIO->new( '-file' => 'inputfile', '-format' => 'blast'); while( my $result = $parser->next_result() ) { print "Result: ", $result->analysis_method, ", Query: ", $result->query_name, "\n"; while( my $feature = $result->next_feature() ) { print "Feature from ", $feature->start, " to ", $feature->end, "\n"; } } =head1 DESCRIPTION AnalysisParserI is a interface for describing generic analysis result parsers. This module makes no assumption about the nature of analysis being parsed, only that zero or more result sets can be obtained from the input source. This module was derived from Bio::SeqAnalysisParserI, the differences being =over 4 =item 1. next_feature() was replaced with next_result(). Instead of flattening a stream containing potentially multiple analysis results into a single set of features, AnalysisParserI segments the stream in terms of analysis result sets (Bio::AnalysisResultI objects). Each AnalysisResultI can then be queried for its features (if any) as well as other information about the result =item 2. AnalysisParserI is a pure interface. It does not inherit from Bio::Root::RootI and does not provide a new() method. Implementations are free to choose how to implement it. =back =head2 Rationale (copied from Bio::SeqAnalysisParserI) The concept behind this interface is to have a generic interface in sequence annotation pipelines (as used e.g. in high-throughput automated sequence annotation). This interface enables plug-and-play for new analysis methods and their corresponding parsers without the necessity for modifying the core of the annotation pipeline. In this concept the annotation pipeline has to rely on only a list of methods for which to process the results, and a factory from which it can obtain the corresponding parser implementing this interface. =head2 TODO Create Bio::Factory::AnalysisParserFactoryI and Bio::Factory::AnalysisParserFactory for interface and an implementation. Note that this factory could return Bio::SearchIO-derived objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Steve Chervitz, Jason Stajich, Hilmar Lapp Email sac@bioperl.org Authors of Bio::SeqAnalysisParserI on which this module is based: Email jason@bioperl.org Email hlapp@gmx.net =head1 COPYRIGHT Copyright (c) 2001 Steve Chervitz. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::AnalysisParserI; use strict; use base qw(Bio::Root::RootI); =head2 next_result Title : next_result Usage : $result = $obj->next_result(); Function: Returns the next result available from the input, or undef if there are no more results. Example : Returns : A Bio::Search::Result::ResultI implementing object, or undef if there are no more results. Args : none =cut sub next_result { my ($self); $self->throw_not_implemented; } 1; __END__ NOTE (sac): My ten-month old son Russell added the following line. It doesn't look like it will compile so I'm putting it here: mt6 j7qa BioPerl-1.007002/Bio/AnalysisResultI.pm000444000766000024 1454313155576320 17704 0ustar00cjfieldsstaff000000000000#----------------------------------------------------------------- # # BioPerl module Bio::AnalysisResultI # # Please direct questions and support issues to # # Cared for by Steve Chervitz # # Derived from Bio::Tools::AnalysisResult by Hilmar Lapp # # You may distribute this module under the same terms as perl itself #----------------------------------------------------------------- # POD documentation - main docs before the code =head1 NAME Bio::AnalysisResultI - Interface for analysis result objects =head1 SYNOPSIS Bio::AnalysisResultI defines an interface that must be implemented by a subclass. So you cannot create Bio::AnalysisResultI objects, only objects that inherit from Bio::AnalysisResultI. =head1 DESCRIPTION The AnalysisResultI module provides an interface for modules encapsulating the result of an analysis that was carried out with a query sequence and an optional subject dataset. The notion of an analysis represented by this base class is that of a unary or binary operator, taking either one query or a query and a subject and producing a result. The query is e.g. a sequence, and a subject is either a sequence, too, or a database of sequences. This interface defines methods to access analysis result data and does not impose any constraints on how the analysis result data is acquired. Note that this module does not provide support for B an analysis. Rather, it is positioned in the subsequent parsing step (concerned with turning raw results into BioPerl objects). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Steve Chervitz, Hilmar Lapp Email sac@bioperl.org Email hlapp@gmx.net (author of Bio::Tools::AnalysisResult on which this module is based) =head1 COPYRIGHT Copyright (c) 2001 Steve Chervitz. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AnalysisResultI; use strict; use base qw(Bio::Root::RootI); =head2 analysis_query Usage : $query_obj = $result->analysis_query(); Purpose : Get a Bio::PrimarySeqI-compatible object representing the entity on which the analysis was performed. Lacks sequence information. Argument : n/a Returns : A Bio::PrimarySeqI-compatible object without sequence information. The sequence will have display_id, description, moltype, and length data. =cut #--------------------- sub analysis_query { #--------------------- my ($self) = @_; $self->throw_not_implemented; } =head2 analysis_subject Usage : $obj = $result->analyis_subject(); Purpose : Get the subject of the analysis against which it was performed. For similarity searches it will probably be a database, and for sequence feature predictions (exons, promoters, etc) it may be a collection of models or homologous sequences that were used, or undefined. Returns : An object of a type the depends on the implementation May also return undef for analyses that don\'t involve subjects. Argument : n/a Comments : Implementation of this method is optional. AnalysisResultI provides a default behavior of returning undef. =cut #--------------- sub analysis_subject { #--------------- my ($self) = @_; return; } =head2 analysis_subject_version Usage : $vers = $result->analyis_subject_version(); Purpose : Get the version string of the subject of the analysis. Returns : String or undef for analyses that don\'t involve subjects. Argument : n/a Comments : Implementation of this method is optional. AnalysisResultI provides a default behavior of returning undef. =cut #--------------- sub analysis_subject_version { #--------------- my ($self) = @_; return; } =head2 analysis_date Usage : $date = $result->analysis_date(); Purpose : Get the date on which the analysis was performed. Returns : String Argument : n/a =cut #--------------------- sub analysis_date { #--------------------- my ($self) = @_; $self->throw_not_implemented; } =head2 analysis_method Usage : $meth = $result->analysis_method(); Purpose : Get the name of the sequence analysis method that was used to produce this result (BLASTP, FASTA, etc.). May also be the actual name of a program. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self) = @_; $self->throw_not_implemented; } =head2 analysis_method_version Usage : $vers = $result->analysis_method_version(); Purpose : Get the version string of the analysis program. : (e.g., 1.4.9MP, 2.0a19MP-WashU). Returns : String Argument : n/a =cut #--------------------- sub analysis_method_version { #--------------------- my ($self) = @_; $self->throw_not_implemented; } =head2 next_feature Title : next_feature Usage : $seqfeature = $obj->next_feature(); Function: Returns the next feature available in the analysis result, or undef if there are no more features. Example : Returns : A Bio::SeqFeatureI implementing object, or undef if there are no more features. Args : none =cut #--------------------- sub next_feature { #--------------------- my ($self); $self->throw_not_implemented; } 1; BioPerl-1.007002/Bio/AnnotatableI.pm000444000766000024 544113155576320 17127 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AnnotatableI # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::AnnotatableI - the base interface an annotatable object must implement =head1 SYNOPSIS use Bio::SeqIO; # get an annotatable object somehow: for example, Bio::SeqI objects # are annotatable my $seqio = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank'); while (my $seq = $seqio->next_seq()) { # $seq is-a Bio::AnnotatableI, hence: my $ann_coll = $seq->annotation(); # $ann_coll is-a Bio::AnnotationCollectionI, hence: my @all_anns = $ann_coll->get_Annotations(); # do something with the annotation objects } =head1 DESCRIPTION This is the base interface that all annotatable objects must implement. A good example is Bio::Seq which is an AnnotableI object. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Hilmar Lapp Ehlapp@gmx.netE Allen Day Eallenday@ucla.eduE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AnnotatableI; use strict; use base qw(Bio::Root::RootI); =head2 annotation Title : annotation Usage : $obj->annotation($newval) Function: Get the annotation collection for this annotatable object. Example : Returns : a Bio::AnnotationCollectionI implementing object, or undef Args : on set, new value (a Bio::AnnotationCollectionI implementing object, optional) (an implementation may not support changing the annotation collection) See L =cut sub annotation{ shift->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/AnnotationCollectionI.pm000444000766000024 1457313155576320 21053 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AnnotationCollectionI # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::AnnotationCollectionI - Interface for annotation collections =head1 SYNOPSIS # get an AnnotationCollectionI somehow, eg $ac = $seq->annotation(); foreach $key ( $ac->get_all_annotation_keys() ) { @values = $ac->get_Annotations($key); foreach $value ( @values ) { # value is an Bio::AnnotationI, and defines a "as_text" method print "Annotation ",$key," stringified value ",$value->as_text,"\n"; # also defined hash_tree method, which allows data orientated # access into this object $hash = $value->hash_tree(); } } =head1 DESCRIPTION Annotation Collections are a way of storing a series of "interesting facts" about something. We call an "interesting fact" in Bioperl an Annotation (this differs from a Sequence Feature, which is called a Sequence Feature and may or may not have an Annotation Collection). A benefit of this approach is that all sorts of simple, interesting observations can be collected, the possibility is endless. The Bioperl approach is that the "interesting facts" are represented by Bio::AnnotationI objects. The interface Bio::AnnotationI guarantees two methods $obj->as_text(); # string formatted to display to users and $obj->hash_tree(); # hash with defined rules for data-orientated discovery The hash_tree method is designed to play well with XML output and other "nested-tag-of-data-values", think BoulderIO and/or Ace stuff. For more information see L. Annotations are stored in AnnotationCollections, each Annotation under a different "tag". The tags allow simple discovery of the available annotations, and in some cases (like the tag "gene_name") indicate how to interpret the data underneath the tag. The tag is only one tag deep and each tag can have an array of values. In addition, AnnotationCollections are guaranteed to maintain consistent types of objects under each tag - at least that each object complies to one interface. The "standard" AnnotationCollection insists the following rules are set up: Tag Object --- ------ comment Bio::Annotation::Comment dblink Bio::Annotation::DBLink description Bio::Annotation::SimpleValue gene_name Bio::Annotation::SimpleValue ontology_term Bio::Annotation::OntologyTerm reference Bio::Annotation::Reference These tags are the implict tags that the SeqIO system needs to round-trip GenBank/EMBL/Swissprot. However, you as a user and us collectively as a community can grow the "standard" tag mapping over time and specifically for a particular area. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AnnotationCollectionI; use strict; # Interface preamble - inherits from Bio::Root::RootI use base qw(Bio::Root::RootI); =head1 ACCESSOR METHODS Use these for Bio::AnnotationI object access. =cut =head2 get_all_annotation_keys() Usage : $ac->get_all_annotation_keys() Function: gives back a list of annotation keys, which are simple text strings Returns : list of strings Args : none =cut sub get_all_annotation_keys{ shift->throw_not_implemented(); } =head2 get_Annotations() Usage : my @annotations = $collection->get_Annotations('key') Function: Retrieves all the Bio::AnnotationI objects for a specific key Returns : list of Bio::AnnotationI - empty if no objects stored for a key Args : string which is key for annotations =cut sub get_Annotations{ shift->throw_not_implemented(); } =head2 add_Annotation() Usage : $self->add_Annotation('reference',$object); $self->add_Annotation($object,'Bio::MyInterface::DiseaseI'); $self->add_Annotation($object); $self->add_Annotation('disease',$object,'Bio::MyInterface::DiseaseI'); Function: Adds an annotation for a specific key. If the key is omitted, the object to be added must provide a value via its tagname(). If the archetype is provided, this and future objects added under that tag have to comply with the archetype and will be rejected otherwise. Returns : none Args : annotation key ('disease', 'dblink', ...) object to store (must be Bio::AnnotationI compliant) [optional] object archetype to map future storage of object of these types to =cut sub add_Annotation { shift->throw_not_implemented(); } =head2 remove_Annotations() Usage : Function: Remove the annotations for the specified key from this collection. Returns : an list of Bio::AnnotationI compliant objects which were stored under the given key(s) Args : the key(s) (tag name(s), one or more strings) for which to remove annotations (optional; if none given, flushes all annotations) =cut sub remove_Annotations{ shift->throw_not_implemented(); } =head2 get_num_of_annotations() Usage : my $count = $collection->get_num_of_annotations() Function: Returns the count of all annotations stored in this collection Returns : integer Args : none =cut sub get_num_of_annotations{ shift->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/AnnotationI.pm000444000766000024 1262613155576320 17034 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AnnotationI # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::AnnotationI - Annotation interface =head1 SYNOPSIS # generally you get AnnotationI's from AnnotationCollectionI's foreach $key ( $ac->get_all_annotation_keys() ) { @values = $ac->get_Annotations($key); foreach $value ( @values ) { # value is an Bio::AnnotationI, and defines a "as_text" method print "Annotation ",$key," stringified value ",$value->as_text,"\n"; # you can also use a generic hash_tree method for getting # stuff out say into XML format $hash_tree = $value->hash_tree(); } } =head1 DESCRIPTION Interface all annotations must support. There are two things that each annotation has to support. $annotation->as_text() Annotations have to support an "as_text" method. This should be a single text string, without newlines representing the annotation, mainly for human readability. It is not aimed at being able to store/represent the annotation. The second method allows annotations to at least attempt to represent themselves as pure data for storage/display/whatever. The method hash_tree should return an anonymous hash with "XML-like" formatting: $hash = $annotation->hash_tree(); The formatting is as follows. (1) For each key in the hash, if the value is a reference'd array - (2) For each element of the array if the value is a object - Assume the object has the method "hash_tree"; (3) else if the value is a reference to a hash Recurse again from point (1) (4) else Assume the value is a scalar, and handle it directly as text (5) else (if not an array) apply rules 2,3 and 4 to value The XML path in tags is represented by the keys taken in the hashes. When arrays are encountered they are all present in the path level of this tag This is a pretty "natural" representation of an object tree in an XML style, without forcing everything to inherit off some super-generic interface for representing things in the hash. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::AnnotationI; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::RootI); =head2 as_text Title : as_text Usage : Function: single text string, without newlines representing the annotation, mainly for human readability. It is not aimed at being able to store/represent the annotation. Example : Returns : a string Args : none =cut sub as_text{ shift->throw_not_implemented(); } =head2 display_text Title : display_text Usage : my $str = $ann->display_text(); Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for the specific implementation. Implementations should allow passing a callback as an argument which allows custom text generation; the callback will be passed the current implementation. Note that this is meant to be used as a simple representation of the annotation data but probably shouldn't be used in cases where more complex comparisons are needed or where data is stored. Example : Returns : a string Args : [optional] callback =cut sub display_text { shift->throw_not_implemented(); } =head2 hash_tree Title : hash_tree Usage : Function: should return an anonymous hash with "XML-like" formatting Example : Returns : a hash reference Args : none =cut sub hash_tree{ shift->throw_not_implemented(); } =head2 tagname Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to Bio::AnnotationCollectionI when adding this object. When obtaining an AnnotationI object from the collection, the collection will set the value to the tag under which it was stored unless the object has a tag stored already. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional) =cut sub tagname{ shift->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/ClusterI.pm000444000766000024 1011413155576320 16331 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::ClusterI # # Please direct questions and support issues to # # Cared for by Shawn Hoon # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::ClusterI - Cluster Interface =head1 SYNOPSIS # see the implementations of this interface for details my $cluster= $cluster->new(-description=>"POLYUBIQUITIN", -members =>[$seq1,$seq2]); my @members = $cluster->get_members(); my @sub_members = $cluster->get_members(-species=>"homo sapiens"); =head1 DESCRIPTION This interface is the basic structure for a cluster of bioperl objects. In this case it is up to the implementer to check arguments and initialize whatever new object the implementing class is designed for. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::ClusterI; use strict; use base qw(Bio::Root::RootI); =head1 Implementation Specific Functions These functions are the ones that a specific implementation must define. =head2 new We don't mandate but encourage implementors to support at least the following named parameters upon object initialization. Argument Description -------- ----------- -display_id the display ID or name for the cluster -description the consensus description or name of the cluster -members the array of objects belonging to the family =cut =head2 display_id Title : display_id Usage : Function: Get the display name or identifier for the cluster Returns : a string Args : =cut sub display_id{ shift->throw_not_implemented(); } =head2 description Title : description Usage : Bio::ClusterI->description("POLYUBIQUITIN") Function: get/set for the consensus description of the cluster Returns : the description string Args : Optional the description string =cut sub description{ shift->throw_not_implemented(); } =head2 size Title : size Usage : Bio::ClusterI->size(); Function: get/set for the size of the family, calculated from the number of members Returns : the size of the family Args : =cut sub size { shift->throw_not_implemented(); } =head2 cluster_score Title : cluster_score Usage : $cluster ->cluster_score(100); Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster. Returns : a number =cut sub cluster_score{ shift->throw_not_implemented(); } =head2 get_members Title : get_members Usage : Bio::ClusterI->get_members(($seq1, $seq2)); Function: retrieve the members of the family by some criteria, for example : $cluster->get_members(-species => 'homo sapiens'); Will return all members if no criteria are provided. Returns : the array of members Args : =cut sub get_members { shift->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/ClusterIO.pm000444000766000024 1745013155576320 16462 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::ClusterIO.pm # # Please direct questions and support issues to # # Cared for by Andrew Macgregor # # Copyright Andrew Macgregor, Jo-Ann Stanton, David Green # Molecular Embryology Group, Anatomy & Structural Biology, University of Otago # http://anatomy.otago.ac.nz/meg # # You may distribute this module under the same terms as perl itself # # _history # # May 7, 2002 - changed from UniGene.pm to more generic ClusterIO.pm # by Andrew Macgregor # # April 17, 2002 - Initial implementation by Andrew Macgregor # POD documentation - main docs before the code =head1 NAME Bio::ClusterIO - Handler for Cluster Formats =head1 SYNOPSIS #NB: This example is unigene specific use Bio::ClusterIO; $stream = Bio::ClusterIO->new('-file' => "Hs.data", '-format' => "unigene"); # note: we quote -format to keep older perl's from complaining. while ( my $in = $stream->next_cluster() ) { print $in->unigene_id() . "\n"; while ( my $sequence = $in->next_seq() ) { print $sequence->accession_number() . "\n"; } } # Parsing errors are printed to STDERR. =head1 DESCRIPTION The ClusterIO module works with the ClusterIO format module to read various cluster formats such as NCBI UniGene. =head1 CONSTRUCTORS =head2 Bio::ClusterIO-Enew() $str = Bio::ClusterIO->new(-file => 'filename', -format=>$format); The new() class method constructs a new Bio::ClusterIO object. The returned object can be used to retrieve or print cluster objects. new() accepts the following parameters: =over 4 =item -file A file path to be opened for reading. =item -format Specify the format of the file. Supported formats include: unigene *.data UniGene build files. dbsnp *.xml dbSNP XML files If no format is specified and a filename is given, then the module will attempt to deduce it from the filename. If this is unsuccessful, the main UniGene build format is assumed. The format name is case insensitive. 'UNIGENE', 'UniGene' and 'unigene' are all supported, as are dbSNP, dbsnp, and DBSNP =back =head1 OBJECT METHODS See below for more detailed summaries. The main methods are: =head2 $cluster = $str-Enext_cluster() Fetch the next cluster from the stream. =head2 TIEHANDLE(), READLINE(), PRINT() These I've left in here because they were in the SeqIO module. Feedback appreciated. There they provide the tie interface. See L for more details. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Andrew Macgregor Email andrew@anatomy.otago.ac.nz =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::ClusterIO; use strict; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : Bio::ClusterIO->new(-file => $filename, -format => 'format') Function: Returns a new cluster stream Returns : A Bio::ClusterIO::Handler initialised with the appropriate format Args : -file => $filename -format => format =cut my $entry = 0; sub new { my ($caller,@args) = @_; my $class = ref($caller) || $caller; # or do we want to call SUPER on an object if $caller is an # object? if( $class =~ /Bio::ClusterIO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $format = $param{'-format'} || $class->_guess_format( $param{-file} || $ARGV[0] ); $format = "\L$format"; # normalize capitalization to lower case return unless( $class->_load_format_module($format) ); return "Bio::ClusterIO::$format"->new(@args); } } =head2 format Title : format Usage : $format = $stream->format() Function: Get the cluster format Returns : cluster format Args : none =cut # format() method inherited from Bio::Root::IO # _initialize is chained for all ClusterIO classes sub _initialize { my($self, @args) = @_; # initialize the IO part $self->_initialize_io(@args); } =head2 next_cluster Title : next_cluster Usage : $cluster = $stream->next_cluster() Function: Reads the next cluster object from the stream and returns it. Returns : a L compliant object Args : none =cut sub next_cluster { my ($self, $seq) = @_; $self->throw("Sorry, you cannot read from a generic Bio::ClusterIO object."); } =head2 cluster_factory Title : cluster_factory Usage : $obj->cluster_factory($newval) Function: Get/set the object factory to use for creating the cluster objects. Example : Returns : a L compliant object Args : on set, new value (a L compliant object or undef, optional) =cut sub cluster_factory{ my $self = shift; return $self->{'cluster_factory'} = shift if @_; return $self->{'cluster_factory'}; } =head2 object_factory Title : object_factory Usage : $obj->object_factory($newval) Function: This is an alias to cluster_factory with a more generic name. Example : Returns : a L compliant object Args : on set, new value (a L compliant object or undef, optional) =cut sub object_factory{ return shift->cluster_factory(@_); } =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL ClusterIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($self,$format) = @_; my $module = "Bio::ClusterIO::" . $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <_guess_format($filename) Function: guess format based on file suffix Example : Returns : guessed format of filename (lower case) Args : Notes : formats that _filehandle() will guess include unigene and dbsnp =cut sub _guess_format { my $class = shift; return unless $_ = shift; return 'unigene' if /\.(data)$/i; return 'dbsnp' if /\.(xml)$/i; } sub DESTROY { my $self = shift; $self->close(); } # I need some direction on these!! The module works so I haven't fiddled with them! sub TIEHANDLE { my ($class,$val) = @_; return bless {'seqio' => $val}, $class; } sub READLINE { my $self = shift; return $self->{'seqio'}->next_seq() || undef unless wantarray; my (@list, $obj); push @list, $obj while $obj = $self->{'seqio'}->next_seq(); return @list; } sub PRINT { my $self = shift; $self->{'seqio'}->write_seq(@_); } 1; BioPerl-1.007002/Bio/DBLinkContainerI.pm000444000766000024 541113155576320 17642 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DBLinkContainerI # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DBLinkContainerI - Abstract interface for any object wanting to use database cross references =head1 SYNOPSIS # get an objects containing database cross reference foreach $obj ( @objs ) { if( $obj->isa('Bio::DBLinkContainerI') ) { foreach $dblink ( $obj->each_DBLink() ) { # do stuff } } } =head1 DESCRIPTION This interface defines the functions one can expect for any object wanting to use database cross-references. This class does not actually provide any implementation, it just provides the definitions of what methods one can call. The database cross-references are implemented as L objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DBLinkContainerI; use strict; use Carp; use base qw(Bio::Root::RootI); =head2 each_DBLink Title : each_DBLink Usage : foreach $ref ( $self->each_DBlink() ) Function: gets an array of DBlink of objects Example : Returns : an array of Bio::Annotation::DBLink objects Args : none =cut sub each_DBLink{ my ($self) = @_; my $class = ref($self) || $self; $self->throw("Class $class did not define method 'each_DBLink' for interface DBLinkContainerI"); } 1; BioPerl-1.007002/Bio/DasI.pm000444000766000024 3273013155576320 15427 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DasI # # Please direct questions and support issues to # # Cared for by Lincoln Stein # # Copyright Lincoln Stein # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DasI - DAS-style access to a feature database =head1 SYNOPSIS # Open up a feature database somehow... $db = Bio::DasI->new(@args); @segments = $db->segment(-name => 'NT_29921.4', -start => 1, -end => 1000000); # segments are Bio::Das::SegmentI - compliant objects # fetch a list of features @features = $db->features(-type=>['type1','type2','type3']); # invoke a callback over features $db->features(-type=>['type1','type2','type3'], -callback => sub { ... } ); $stream = $db->get_seq_stream(-type=>['type1','type2','type3']); while (my $feature = $stream->next_seq) { # each feature is a Bio::SeqFeatureI-compliant object } # get all feature types @types = $db->types; # count types %types = $db->types(-enumerate=>1); @feature = $db->get_feature_by_name($class=>$name); @feature = $db->get_feature_by_target($target_name); @feature = $db->get_feature_by_attribute($att1=>$value1,$att2=>$value2); $feature = $db->get_feature_by_id($id); $error = $db->error; =head1 DESCRIPTION Bio::DasI is a simplified alternative interface to sequence annotation databases used by the distributed annotation system (see L). In this scheme, the genome is represented as a series of features, a subset of which are named. Named features can be used as reference points for retrieving "segments" (see L), and these can, in turn, be used as the basis for exploring the genome further. In addition to a name, each feature has a "class", which is essentially a namespace qualifier and a "type", which describes what type of feature it is. Das uses the GO consortium's ontology of feature types, and so the type is actually an object of class Bio::Das::FeatureTypeI (see L). Bio::DasI provides methods for interrogating the database for the types it contains and the counts of each type. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Lincoln Stein Email lstein@cshl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::DasI; use strict; use Bio::Das::SegmentI; # Object preamble - inherits from Bio::Root::Root; use base qw(Bio::Root::RootI Bio::SeqFeature::CollectionI); =head2 new Title : new Usage : Bio::DasI->new(@args) Function: Create new Bio::DasI object Returns : a Bio::DasI object Args : see below The new() method creates a new object. The argument list is either a single argument consisting of a connection string, or the following list of -name=Evalue arguments: Argument Description -------- ----------- -dsn Connection string for database -adaptor Name of an adaptor class to use when connecting -aggregator Array ref containing list of aggregators "semantic mappers" to apply to database -user Authentication username -pass Authentication password Implementors of DasI may add other arguments. =cut sub new {shift->throw_not_implemented} =head2 types Title : types Usage : $db->types(@args) Function: return list of feature types in database Returns : a list of Bio::Das::FeatureTypeI objects Args : see below This routine returns a list of feature types known to the database. It is also possible to find out how many times each feature occurs. Arguments are -option=Evalue pairs as follows: -enumerate if true, count the features The returned value will be a list of Bio::Das::FeatureTypeI objects (see L. If -enumerate is true, then the function returns a hash (not a hash reference) in which the keys are the stringified versions of Bio::Das::FeatureTypeI and the values are the number of times each feature appears in the database. =cut sub types { shift->throw_not_implemented; } =head2 parse_types Title : parse_types Usage : $db->parse_types(@args) Function: parses list of types Returns : an array ref containing ['method','source'] pairs Args : a list of types in 'method:source' form Status : internal This method takes an array of type names in the format "method:source" and returns an array reference of ['method','source'] pairs. It will also accept a single argument consisting of an array reference with the list of type names. =cut # turn feature types in the format "method:source" into a list of [method,source] refs sub parse_types { my $self = shift; return [] if !@_ or !defined($_[0]); return $_[0] if ref $_[0] eq 'ARRAY' && ref $_[0][0]; my @types = ref($_[0]) ? @{$_[0]} : @_; my @type_list = map { [split(':',$_,2)] } @types; return \@type_list; } =head2 segment Title : segment Usage : $db->segment(@args); Function: create a segment object Returns : segment object(s) Args : see below This method generates a Bio::Das::SegmentI object (see L). The segment can be used to find overlapping features and the raw sequence. When making the segment() call, you specify the ID of a sequence landmark (e.g. an accession number, a clone or contig), and a positional range relative to the landmark. If no range is specified, then the entire region spanned by the landmark is used to generate the segment. Arguments are -option=Evalue pairs as follows: -name ID of the landmark sequence. -class A namespace qualifier. It is not necessary for the database to honor namespace qualifiers, but if it does, this is where the qualifier is indicated. -version Version number of the landmark. It is not necessary for the database to honor versions, but if it does, this is where the version is indicated. -start Start of the segment relative to landmark. Positions follow standard 1-based sequence rules. If not specified, defaults to the beginning of the landmark. -end End of the segment relative to the landmark. If not specified, defaults to the end of the landmark. The return value is a list of Bio::Das::SegmentI objects. If the method is called in a scalar context and there are no more than one segments that satisfy the request, then it is allowed to return the segment. Otherwise, the method must throw a "multiple segment exception". =cut #' sub segment { shift->throw_not_implemented } =head2 features Title : features Usage : $db->features(@args) Function: get all features, possibly filtered by type Returns : a list of Bio::SeqFeatureI objects Args : see below Status : public This routine will retrieve features in the database regardless of position. It can be used to return all features, or a subset based on their type Arguments are -option=Evalue pairs as follows: -types List of feature types to return. Argument is an array of Bio::Das::FeatureTypeI objects or a set of strings that can be converted into FeatureTypeI objects. -callback A callback to invoke on each feature. The subroutine will be passed each Bio::SeqFeatureI object in turn. -attributes A hash reference containing attributes to match. The -attributes argument is a hashref containing one or more attributes to match against: -attributes => { Gene => 'abc-1', Note => 'confirmed' } Attribute matching is simple exact string matching, and multiple attributes are ANDed together. See L for a more sophisticated take on this. If one provides a callback, it will be invoked on each feature in turn. If the callback returns a false value, iteration will be interrupted. When a callback is provided, the method returns undef. =cut sub features { shift->throw_not_implemented } =head2 get_feature_by_name Title : get_feature_by_name Usage : $db->get_feature_by_name(-class=>$class,-name=>$name) Function: fetch features by their name Returns : a list of Bio::SeqFeatureI objects Args : the class and name of the desired feature Status : public This method can be used to fetch named feature(s) from the database. The -class and -name arguments have the same meaning as in segment(), and the method also accepts the following short-cut forms: 1) one argument: the argument is treated as the feature name 2) two arguments: the arguments are treated as the class and name (note: this uses _rearrange() so the first argument must not begin with a hyphen or it will be interpreted as a named argument). This method may return zero, one, or several Bio::SeqFeatureI objects. The implementor may allow the name to contain wildcards, in which case standard C-shell glob semantics are expected. =cut sub get_feature_by_name { shift->throw_not_implemented(); } =head2 get_feature_by_target Title : get_feature_by_target Usage : $db->get_feature_by_target($class => $name) Function: fetch features by their similarity target Returns : a list of Bio::SeqFeatureI objects Args : the class and name of the desired feature Status : public This method can be used to fetch a named feature from the database based on its similarity hit. The arguments are the same as get_feature_by_name(). If this is not implemented, the interface defaults to using get_feature_by_name(). =cut sub get_feature_by_target { shift->get_feature_by_name(@_); } =head2 get_feature_by_id Title : get_feature_by_id Usage : $db->get_feature_by_target($id) Function: fetch a feature by its ID Returns : a Bio::SeqFeatureI objects Args : the ID of the feature Status : public If the database provides unique feature IDs, this can be used to retrieve a single feature from the database. If not overridden, this interface calls get_feature_by_name() and returns the first element. =cut sub get_feature_by_id { (shift->get_feature_by_name(@_))[0]; } =head2 get_feature_by_attribute Title : get_feature_by_attribute Usage : $db->get_feature_by_attribute(attribute1=>value1,attribute2=>value2) Function: fetch features by combinations of attribute values Returns : a list of Bio::SeqFeatureI objects Args : the class and name of the desired feature Status : public This method can be used to fetch a set of features from the database. Attributes are a list of name=Evalue pairs. They will be logically ANDed together. If an attribute value is an array reference, the list of values in the array is treated as an alternative set of values to be ORed together. =cut sub get_feature_by_attribute { shift->throw_not_implemented(); } =head2 search_notes Title : search_notes Usage : $db->search_notes($search_term,$max_results) Function: full-text search on features, ENSEMBL-style Returns : an array of [$name,$description,$score] Args : see below Status : public This routine performs a full-text search on feature attributes (which attributes depend on implementation) and returns a list of [$name,$description,$score], where $name is the feature ID, $description is a human-readable description such as a locus line, and $score is the match strength. Since this is a decidedly non-standard thing to do (but the generic genome browser uses it), the default method returns an empty list. You do not have to implement it. =cut sub search_notes { return } =head2 get_seq_stream Title : get_seq_stream Usage : $seqio = $db->get_seq_stream(@args) Function: Performs a query and returns an iterator over it Returns : a Bio::SeqIO stream capable of returning Bio::SeqFeatureI objects Args : As in features() Status : public This routine takes the same arguments as features(), but returns a Bio::SeqIO::Stream-compliant object. Use it like this: $stream = $db->get_seq_stream('exon'); while (my $exon = $stream->next_seq) { print $exon,"\n"; } NOTE: In the interface this method is aliased to get_feature_stream(), as the name is more descriptive. =cut sub get_seq_stream { shift->throw_not_implemented } sub get_feature_stream {shift->get_seq_stream(@_) } =head2 refclass Title : refclass Usage : $class = $db->refclass Function: returns the default class to use for segment() calls Returns : a string Args : none Status : public For data sources which use namespaces to distinguish reference sequence accessions, this returns the default namespace (or "class") to use. This interface defines a default of "Accession". =cut sub refclass { "Accession" } 1; BioPerl-1.007002/Bio/DescribableI.pm000444000766000024 567213155576320 17104 0ustar00cjfieldsstaff000000000000 # # This module is licensed under the same terms as Perl itself. You use, # modify, and redistribute it under the terms of the Perl Artistic License. # =head1 NAME Bio::DescribableI - interface for objects with human readable names and descriptions =head1 SYNOPSIS # to test this is a describable object $obj->isa("Bio::DescribableI") || $obj->throw("$obj does not implement the Bio::DescribableI interface"); # accessors $name = $obj->display_name(); $desc = $obj->description(); =head1 DESCRIPTION This interface describes methods expected on describable objects, ie ones which have human displayable names and descriptions =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@sanger.ac.uk =cut package Bio::DescribableI; use strict; use base qw(Bio::Root::RootI); =head1 Implementation Specific Functions These functions are the ones that a specific implementation must define. =head2 display_name Title : display_name Usage : $string = $obj->display_name() Function: A string which is what should be displayed to the user the string should have no spaces (ideally, though a cautious user of this interface would not assume this) and should be less than thirty characters (though again, double checking this is a good idea) Returns : A scalar Status : Virtual =cut sub display_name { my ($self) = @_; $self->throw_not_implemented(); } =head2 description Title : description Usage : $string = $obj->description() Function: A text string suitable for displaying to the user a description. This string is likely to have spaces, but should not have any newlines or formatting - just plain text. The string should not be greater than 255 characters and clients can feel justified at truncating strings at 255 characters for the purposes of display Returns : A scalar Status : Virtual =cut sub description { my ($self) = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/FeatureHolderI.pm000444000766000024 1614213155576320 17450 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::FeatureHolderI # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::FeatureHolderI - the base interface an object with features must implement =head1 SYNOPSIS use Bio::SeqIO; # get a feature-holding object somehow: for example, Bio::SeqI objects # have features my $seqio = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank'); while (my $seq = $seqio->next_seq()) { # $seq is-a Bio::FeatureHolderI, hence: my @feas = $seq->get_SeqFeatures(); # each element is-a Bio::SeqFeatureI foreach my $fea (@feas) { # do something with the feature objects } } =head1 DESCRIPTION This is the base interface that all feature-holding objects must implement. Popular feature-holders are for instance L objects. Since L defines a sub_SeqFeature() method, most Bio::SeqFeatureI implementations like L will implement the feature holder interface as well. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 CONTRIBUTORS Steffen Grossmann [SG], grossman-at-molgen.mpg.de Mark A. Jensen, maj -at- fortinbras -dot- us =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::FeatureHolderI; use strict; use Carp; use base qw(Bio::Root::RootI); =head2 get_SeqFeatures() Usage : @feats = $obj->get_SeqFeatures() Function: Get the feature objects held by this feature holder. Example : Returns : an array of Bio::SeqFeatureI implementing objects if tag specified, return features having that tag Args : [optional] scalar string (feature tag) =cut sub get_SeqFeatures { shift->throw_not_implemented(); } =head2 add_SeqFeature() Usage : $feat->add_SeqFeature($subfeat); $feat->add_SeqFeature($subfeat,'EXPAND') Function: Add a SeqFeature into the subSeqFeature array. with no 'EXPAND' qualifer, subfeat will be tested as to whether it lies inside the parent, and throw an exception if not. If EXPAND is used and the object implements Bio::RangeI (which is not guaranteed), the parent''s start/end/strand will be extended so that the new subFeature can be accomodated. Example : Returns : nothing Args : a Bio::SeqFeatureI object =cut sub add_SeqFeature { shift->throw_not_implemented(); } =head2 remove_SeqFeatures() Usage : $obj->remove_SeqFeatures Function: Removes all sub SeqFeatures. If you want to remove only a subset, remove that subset from the returned array, and add back the rest. Returns : The array of Bio::SeqFeatureI implementing sub-features that was deleted from this feature. Args : none =cut sub remove_SeqFeatures { shift->throw_not_implemented(); } =head2 feature_count Title : feature_count Usage : $obj->feature_count() Function: Return the number of SeqFeatures attached to a feature holder. This is before flattening a possible sub-feature tree. We provide a default implementation here that just counts the number of objects returned by get_SeqFeatures(). Implementors may want to override this with a more efficient implementation. Returns : integer representing the number of SeqFeatures Args : None At some day we may want to expand this method to allow for a feature filter to be passed in. Our default implementation allows for any number of additional arguments and will pass them on to get_SeqFeatures(). I.e., in order to support filter arguments, just support them in get_SeqFeatures(). =cut sub feature_count { return scalar(shift->get_SeqFeatures(@_)); } =head2 get_all_SeqFeatures Title : get_all_SeqFeatures Usage : Function: Get the flattened tree of feature objects held by this feature holder. The difference to get_SeqFeatures is that the entire tree of sub-features will be flattened out. We provide a default implementation here, so implementors don''t necessarily need to implement this method. Example : Returns : an array of Bio::SeqFeatureI implementing objects Args : none At some day we may want to expand this method to allow for a feature filter to be passed in. Our default implementation allows for any number of additional arguments and will pass them on to any invocation of get_SeqFeatures(), wherever a component of the tree implements FeatureHolderI. I.e., in order to support filter arguments, just support them in get_SeqFeatures(). =cut sub get_all_SeqFeatures{ my $self = shift; my @flatarr; foreach my $feat ( $self->get_SeqFeatures(@_) ){ push(@flatarr,$feat); &_add_flattened_SeqFeatures(\@flatarr,$feat,@_); } # needed to deal with subfeatures which appear more than once in the hierarchy [SG] my %seen = (); my @uniq_flatarr = (); foreach my $feat (@flatarr) { push(@uniq_flatarr, $feat) unless $seen{$feat}++; } return @uniq_flatarr; } sub _add_flattened_SeqFeatures { my ($arrayref,$feat,@args) = @_; my @subs = (); if($feat->isa("Bio::FeatureHolderI")) { @subs = $feat->get_SeqFeatures(@args); } elsif($feat->isa("Bio::SeqFeatureI")) { @subs = $feat->sub_SeqFeature(); } else { confess ref($feat)." is neither a FeatureHolderI nor a SeqFeatureI. ". "Don't know how to flatten."; } foreach my $sub (@subs) { push(@$arrayref,$sub); &_add_flattened_SeqFeatures($arrayref,$sub); } } sub set_ParentIDs_from_hierarchy(){ # DEPRECATED - use IDHandler my $self = shift; require "Bio/SeqFeature/Tools/IDHandler.pm"; Bio::SeqFeature::Tools::IDHandler->new->set_ParentIDs_from_hierarchy($self); } sub create_hierarchy_from_ParentIDs(){ # DEPRECATED - use IDHandler my $self = shift; require "Bio/SeqFeature/Tools/IDHandler.pm"; Bio::SeqFeature::Tools::IDHandler->new->create_hierarchy_from_ParentIDs($self); } 1; BioPerl-1.007002/Bio/HandlerBaseI.pm000444000766000024 1651413155576320 17072 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::HandlerI # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::HandlerBaseI - Interface class for handler methods which interact with any event-driven parsers (drivers). =head1 SYNOPSIS # MyHandler is a Bio::HandlerBaseI-derived class for dealing with GenBank # sequence data, derived from a GenBank event-driven parser # inside a parser (driver) constructor $self->seqhandler($handler || MyHandler->new(-format => 'genbank')); # in the driver parsing method ( such as next_seq() ) ... $handler = $self->seqhandler(); # roll data up into hashref chunks, pass off into Handler for processing... $hobj->data_handler($data); # or retrieve Handler methods and pass data directly to Handler methods my $hmeth = $hobj->handler_methods; if ($hmeth->{ $data->{NAME} }) { my $mth = $hmeth->{ $data->{NAME} }; # code ref $hobj->$mth($data); } =head1 DESCRIPTION This interface describes simple class methods used for processing data from an event-based parser (a driver). This is similar in theme to an XML SAX-based driver but differs in that one can optionally pass related data semi-intelligently as chunks (defined in a hash reference) vs. passing as single data elements in a stream. For instance, any reference-related and species-related data as well as individual sequence features could be passed as chunks of data to be processed in part or as a whole (from Data::Dumper output): Annotation Data (References): $VAR1 = { 'NAME' => 'REFERENCE', 'DATA' => '1 (bases 1 to 10001)' 'AUTHORS' => 'International Human Genome Sequencing Consortium.' 'TITLE' => 'The DNA sequence of Homo sapiens' 'JOURNAL' => 'Unpublished (2003)' }; Sequence features (source seqfeature): $VAR1 = { 'mol_type' => 'genomic DNA', 'LOCATION' => '<1..>10001', 'NAME' => 'FEATURES', 'FEATURE_KEY' => 'source', 'note' => 'Accession AL451081 sequenced by The Sanger Centre', 'db_xref' => 'taxon:9606', 'clone' => 'RP11-302I18', 'organism' => 'Homo sapiens' }; These would be 'handled' accordingly by methods specified in a HandlerI-based class. The data in a chunk is intentionally left vague here since this may vary from implementation to implementation and can be somewhat open to interpretation. A data chunk in a sequence record, for instance, will be different than a data chunk in a BLAST report. This also allows one the flexibility to pass data as more XML-like small bits, as huge chunks, or even as indexed locations in a file (such as when using a "pull" parser, like a Bio::PullParserI). For an sequence-based implementation see Bio::SeqIO::RichSeq::GenericRichSeqHandler, which handles any GenBank, UniProt, and EMBL data from their respective driver modules (Bio::SeqIO::gbdriver, Bio::SeqIO::swissdriver, and Bio::SeqIO::embldriver). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Fields Email cjfields at bioperl dot org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::HandlerBaseI; use strict; use warnings; use base qw(Bio::Root::RootI); my %HANDLERS = ('foo' => \&noop); =head2 data_handler Title : data_handler Usage : $handler->data_handler($data) Function: Centralized method which accepts all data chunks, then distributes to the appropriate methods for processing based on the chunk name from within the HandlerBaseI object. One can also use Returns : None Args : an hash ref containing a data chunk. =cut sub data_handler { shift->throw_not_implemented } =head2 handler_methods Title : handler_methods Usage : $handler->handler_methods('GenBank') %handlers = $handler->handler_methods(); Function: Retrieve the handler methods used for the current format() in the handler. This assumes the handler methods are already described in the HandlerI-implementing class. Returns : a hash reference with the data type handled and the code ref associated with it. Args : [optional] String representing the sequence format. If set here this will also set sequence_format() Throws : On unimplemented sequence format in %HANDLERS =cut sub handler_methods { shift->throw_not_implemented } =head2 format Title : format Usage : $handler->format('GenBank') $handler->format('BLAST') Function: Get/Set the format for the report/record being parsed. This can be used to set handlers in classes which are capable of processing similar data chunks from multiple driver modules. Returns : String with the sequence format Args : [optional] String with the sequence format Note : The format may be used to set the handlers (as in the current GenericRichSeqHandler implementation) =cut sub format { shift->throw_not_implemented } =head2 get_params Title : get_params Usage : $handler->get_params('-species') Function: Convenience method used to retrieve the specified parameters from the internal parameter cache Returns : Hash ref containing parameters requested and data as key-value pairs. Note that some parameter values may be objects, arrays, etc. Args : List (array) representing the parameters requested =cut sub get_params { shift->throw_not_implemented } =head2 set_params Title : set_params Usage : $handler->set_params({ '-species' => $species, '-accession_number' => $acc }); Function: Convenience method used to set specific parameters Returns : None Args : Hash ref containing the data to be passed as key-value pairs =cut sub set_params { shift->throw_not_implemented } =head2 reset_parameters Title : reset_parameters Usage : $handler->reset_parameters() Function: Resets the internal cache of data (normally object parameters for a builder or factory) Returns : None Args : None =cut sub reset_parameters { shift->throw_not_implemented } 1; BioPerl-1.007002/Bio/IdCollectionI.pm000444000766000024 514013155576320 17243 0ustar00cjfieldsstaff000000000000 # # This module is licensed under the same terms as Perl itself. You use, # modify, and redistribute it under the terms of the Perl Artistic License. # =head1 NAME Bio::IdCollectionI - interface for objects with multiple identifiers =head1 SYNOPSIS # to test this is an identifiable collection object $obj->isa("Bio::IdCollectionI") || $obj->throw("$obj does not implement the Bio::IdCollectionI interface"); # accessors @authorities = $obj->id_authorities(); @ids = $obj->ids(); $id = $obj->ids($authority); =head1 DESCRIPTION This interface describes methods expected on objects that have multiple identifiers, each of which is controlled by a different authority. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Lincoln Stein Email lstein@cshl.org =cut package Bio::IdCollectionI; use strict; use base qw(Bio::Root::RootI); =head1 Implementation Specific Functions These functions are the ones that a specific implementation must define. =head2 id_authorities Title : id_authorities Usage : @array = $obj->id_authorities() Function: Return the authorities which have names for this object. The authorities can then be used to select ids. Returns : An array Status : Virtual =cut sub id_authorities { my ($self) = @_; $self->throw_not_implemented(); } =head2 ids Title : ids Usage : @ids = $obj->ids([$authority1,$authority2...]) Function: return a list of Bio::IdentifiableI objects, optionally filtered by the list of authorities. Returns : A list of Bio::IdentifiableI objects. Status : Virtual =cut sub ids { my ($self) = @_; my @authorities = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/IdentifiableI.pm000444000766000024 1204713155576320 17276 0ustar00cjfieldsstaff000000000000# # This module is licensed under the same terms as Perl itself. You use, # modify, and redistribute it under the terms of the Perl Artistic License. # =head1 NAME Bio::IdentifiableI - interface for objects with identifiers =head1 SYNOPSIS # to test this is an identifiable object $obj->isa("Bio::IdentifiableI") || $obj->throw("$obj does not implement the Bio::IdentifiableI interface"); # Accessors $object_id = $obj->object_id(); $namespace = $obj->namespace(); $authority = $obj->authority(); $version = $obj->version(); # Gets authority:namespace:object_id $lsid = $obj->lsid_string(); # Gets namespace:object_id.version $ns_string = $obj->namespace_string(); =head1 DESCRIPTION This interface describes methods expected on identifiable objects, i.e. ones which have identifiers expected to make sense across a number of instances and/or domains. This interface is modeled after pretty much ubiquitous ideas for names in bioinformatics being databasename:object_id.version Example: swissprot:P012334.2 or: GO:0007048 The object will also work with LSID proposals which adds the concept of an authority, being the DNS name of the organisation assigning the namespace. See L. Helper functions are provided to make useful strings: lsid_string - string complying to the LSID standard namespace_string - string complying to the usual convention of namespace:object_id.version =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =cut package Bio::IdentifiableI; use strict; use base qw(Bio::Root::RootI); =head1 Implementation Specific Functions These functions are the ones that a specific implementation must define. =head2 object_id Title : object_id Usage : $string = $obj->object_id() Function: a string which represents the stable primary identifier in this namespace of this object. For DNA sequences this is its accession_number, similarly for protein sequences Returns : A scalar Status : Virtual =cut sub object_id { my ($self) = @_; $self->throw_not_implemented(); } =head2 version Title : version Usage : $version = $obj->version() Function: a number which differentiates between versions of the same object. Higher numbers are considered to be later and more relevant, but a single object described the same identifier should represent the same concept Returns : A number Status : Virtual =cut sub version { my ($self) = @_; $self->throw_not_implemented(); } =head2 authority Title : authority Usage : $authority = $obj->authority() Function: a string which represents the organisation which granted the namespace, written as the DNS name for organisation (eg, wormbase.org) Returns : A scalar Status : Virtual =cut sub authority { my ($self) = @_; $self->throw_not_implemented(); } =head2 namespace Title : namespace Usage : $string = $obj->namespace() Function: A string representing the name space this identifier is valid in, often the database name or the name describing the collection Returns : A scalar Status : Virtual =cut sub namespace { my ($self) = @_; $self->throw_not_implemented(); } =head1 Implementation optional functions These functions are helper functions that are provided by the interface but can be overridden if so wished =head2 lsid_string Title : lsid_string Usage : $string = $obj->lsid_string() Function: a string which gives the LSID standard notation for the identifier of interest Returns : A scalar =cut sub lsid_string { my ($self) = @_; return $self->authority.":".$self->namespace.":".$self->object_id; } =head2 namespace_string Title : namespace_string Usage : $string = $obj->namespace_string() Function: a string which gives the common notation of namespace:object_id.version Returns : A scalar =cut sub namespace_string { my ($self) = @_; return $self->namespace.":".$self->object_id . (defined($self->version()) ? ".".$self->version : ''); } 1; BioPerl-1.007002/Bio/LocatableSeq.pm000444000766000024 5216313155576320 17150 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::LocatableSeq # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::LocatableSeq - A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. =head1 SYNOPSIS use Bio::LocatableSeq; my $seq = Bio::LocatableSeq->new(-seq => "CAGT-GGT", -id => "seq1", -start => 1, -end => 7); # a normal sequence object $locseq->seq(); $locseq->id(); # has start,end points $locseq->start(); $locseq->end(); # inherits off RangeI, so range operations possible =head1 DESCRIPTION The LocatableSeq sequence object was developed mainly because the SimpleAlign object requires this functionality, and in the rewrite of the Sequence object we had to decide what to do with this. It is, to be honest, not well integrated with the rest of bioperl. For example, the trunc() function does not return a LocatableSeq object, as some might have thought. Also, the sequence is not a Bio::SeqI, so the location is simply inherited from Bio::RangeI and is not stored in a Bio::Location. There are all sorts of nasty gotcha's about interactions between coordinate systems when these sort of objects are used. Some mapping now occurs to deal with HSP data, however it can probably be integrated in better and most methods do not implement it correctly yet. Also, several PrimarySeqI methods (subseq(), trunc(), etc.) do not behave as expected and must be used with care. Due to this, LocatableSeq functionality is to be refactored in a future BioPerl release. However, for alignment functionality it works adequately for the time being. If you do not need alignment functionality, L-implementing modules may be a suitable alternative to L. For example, L and L provide methods to attach a sequence to a specific region of a parent sequence and to set other useful attributes. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::LocatableSeq; use strict; use Bio::Location::Simple; use Bio::Location::Fuzzy; use vars qw($GAP_SYMBOLS $OTHER_SYMBOLS $FRAMESHIFT_SYMBOLS $RESIDUE_SYMBOLS $MATCHPATTERN); # The following global variables contain symbols used to represent gaps, # frameshifts, residues, and other valid symbols. These are set at compile-time; # expect scoping errors when using 'local' and resetting $MATCHPATTERN (see # LocatableSeq.t) $GAP_SYMBOLS = '\-\.=~'; $FRAMESHIFT_SYMBOLS = '\\\/'; $OTHER_SYMBOLS = '\?'; $RESIDUE_SYMBOLS = '0-9A-Za-z\*'; $MATCHPATTERN = $RESIDUE_SYMBOLS.$GAP_SYMBOLS.$FRAMESHIFT_SYMBOLS.$OTHER_SYMBOLS; use base qw(Bio::PrimarySeq Bio::RangeI); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($start,$end,$strand, $mapping, $fs, $nse) = $self->_rearrange( [qw(START END STRAND MAPPING FRAMESHIFTS FORCE_NSE )], @args); $mapping ||= [1,1]; $self->mapping($mapping); $nse || 0; $self->force_nse($nse); defined $fs && $self->frameshifts($fs); defined $start && $self->start($start); defined $end && $self->end($end); defined $strand && $self->strand($strand); return $self; # success - we hope! } =head2 start Title : start Usage : $obj->start($newval) Function: Get/set the 1-based start position of this sequence in the original sequence. '0' means before the original sequence starts. Returns : value of start Args : newvalue (optional) =cut sub start { my $self = shift; if( @_ ) { my $value = shift; $self->{'start'} = $value; } return $self->{'start'} if defined $self->{'start'}; return 1 if $self->seq; return; } =head2 end Title : end Usage : $obj->end($newval) Function: Get/set the 1-based end position of this sequence in the original sequence. '0' means before the original sequence starts. Returns : value of end Args : newvalue (optional) Note : although this is a get/set, it checks passed values against the calculated end point ( derived from the sequence and based on $GAP_SYMBOLS and possible frameshifts() ). If there is no match, it will warn and set the proper value. Probably best used for debugging proper sequence calculations. =cut sub end { my $self = shift; if( @_ ) { my $value = shift; my $st = $self->start; # start of 0 usually means the sequence is all gaps but maps to # other sequences in an alignment if ($self->seq && $st != 0 ) { my $len = $self->_ungapped_len; my $calend = $st + $len - 1; my $id = $self->id || 'unknown'; if ($calend != $value) { $self->warn("In sequence $id residue count gives end value ". "$calend. \nOverriding value [$value] with value $calend for ". "Bio::LocatableSeq::end().\n".$self->seq); $value = $calend; } } $self->{'end'} = $value; } if (defined $self->{'end'}) { return $self->{'end'} } elsif ( my $len = $self->_ungapped_len) { return $len + $self->start - 1; } else { return; } } # changed 08.10.26 to return ungapped length, not the calculated end # of the sequence sub _ungapped_len { my $self = shift; return unless my $string = $self->seq; my ($map_res, $map_coord) = $self->mapping; my $offset = 0; if (my %data = $self->frameshifts) { map {$offset += $_} values %data; } $string =~ s{[$GAP_SYMBOLS$FRAMESHIFT_SYMBOLS]+}{}g; return CORE::length($string)/($map_res/$map_coord) + $offset/($map_coord/$map_res); } #sub length { # my $self = shift; # return unless my $string = $self->seq; # $string =~ s{[$GAP_SYMBOLS$FRAMESHIFT_SYMBOLS]+}{}g; # return CORE::length($string); #} =head2 strand Title : strand Usage : $obj->strand($newval) Function: return or set the strandedness Returns : the value of the strandedness (-1, 0 or 1) Args : the value of the strandedness (-1, 0 or 1) =cut sub strand { my $self = shift; if( @_ ) { my $value = shift; $self->{'strand'} = $value; } return $self->{'strand'}; } =head2 mapping Title : mapping Usage : $obj->mapping($newval) Function: return or set the mapping indices (indicates # symbols/positions in the source string mapping to # of coordinate positions) Returns : two-element array (# symbols => # coordinate pos) Args : two elements (# symbols => # coordinate pos); this can also be passed in as an array reference of the two elements (as might be passed upon Bio::LocatableSeq instantiation, for instance). =cut sub mapping { my $self = shift; if( @_ ) { my @mapping = (ref($_[0]) eq 'ARRAY') ? @{$_[0]} : @_; $self->throw("Must pass two values (# residues mapped to # positions)") if @mapping != 2; if ((grep {$_ != 1 && $_ != 3} @mapping) || ($mapping[0] == 3 && $mapping[1] == 3)) { $self->throw("Mapping values other than 1 or 3 are not currently supported") } $self->{'_mapping'} = \@mapping; } $self->throw('Mapping for LocatableSeq not set') if !exists $self->{'_mapping'}; return @{ $self->{'_mapping'} }; } =head2 frameshifts Title : frameshifts Usage : $obj->frameshifts($newval) Function: get/set the frameshift hash, which contains sequence positions as keys and the shift (-2, -1, 1, 2) as the value Returns : hash Args : hash or hash reference =cut sub frameshifts { my $self = shift; if( @_ ) { if (ref $_[0] eq 'HASH') { $self->{_frameshifts} = $_[0]; } else { # assume this is a full list to be converted to a hash $self->{_frameshifts} = \%{@_} # coerce into hash ref } } (defined $self->{_frameshifts} && ref $self->{_frameshifts} eq 'HASH') ? return %{$self->{_frameshifts}} : return (); } =head2 get_nse Title : get_nse Usage : Function: read-only name of form id/start-end Example : Returns : Args : =cut sub get_nse { my ($self,$char1,$char2) = @_; $char1 ||= "/"; $char2 ||= "-"; my ($id, $st, $end, $strand) = ($self->id(), $self->start(), $self->end(), $self->strand || 0); if ($self->force_nse) { $id ||= ''; $st ||= 0; $end ||= 0; } $self->throw("Attribute id not set") unless defined($id); $self->throw("Attribute start not set") unless defined($st); $self->throw("Attribute end not set") unless defined($end); if ($strand && $strand == -1) { ($st, $end) = ($end, $st); } #Stockholm Rfam includes version if present so it is optional my $v = $self->version ? '.'.$self->version : ''; return join('',$id, $v, $char1, $st, $char2, $end); } =head2 force_nse Title : force_nse Usage : $ls->force_nse() Function: Boolean which forces get_nse() to build an NSE, regardless of whether id(), start(), or end() is set Returns : Boolean value Args : (optional) Boolean (1 or 0) Note : This will convert any passed value evaluating as TRUE/FALSE to 1/0 respectively =cut sub force_nse { my ($self, $flag) = @_; if (defined $flag) { $flag ? (return $self->{'_force_nse'} = 1) : (return $self->{'_force_nse'} = 0); } return $self->{'_force_nse'}; } =head2 num_gaps Title : num_gaps Usage :$self->num_gaps('.') Function:Gets number of gaps in the sequence. The count excludes leading or trailing gap characters. Valid bioperl sequence characters are [A-Za-z\-\.\*]. Of these, '.' and '-' are counted as gap characters unless an optional argument specifies one of them. Returns : number of internal gaps in the sequence. Args : a gap character (optional) Status : Stable Note : replaces no_gaps =cut sub num_gaps { my ($self,$char) = @_; my ($seq, $count) = (undef, 0); # default gap characters $char ||= $GAP_SYMBOLS; $self->warn("I hope you know what you are doing setting gap to [$char]") unless $char =~ /[$GAP_SYMBOLS]/; $seq = $self->seq; return 0 unless $seq; # empty sequence does not have gaps $seq =~ s/^([$char]+)//; $seq =~ s/([$char]+)$//; while ( $seq =~ /[$char]+/g ) { $count++; } return $count; } =head2 column_from_residue_number Title : column_from_residue_number Usage : $col = $seq->column_from_residue_number($resnumber) Function: This function gives the position in the alignment (i.e. column number) of the given residue number in the sequence. For example, for the sequence Seq1/91-97 AC..DEF.GH column_from_residue_number(94) returns 6. An exception is thrown if the residue number would lie outside the length of the aligment (e.g. column_from_residue_number( "Seq2", 22 ) Returns : A column number for the position of the given residue in the given sequence (1 = first column) Args : A residue number in the whole sequence (not just that segment of it in the alignment) =cut sub column_from_residue_number { my ($self, $resnumber) = @_; $self->throw("Residue number has to be a positive integer, not [$resnumber]") unless $resnumber =~ /^\d+$/ and $resnumber > 0; if ($resnumber >= $self->start() and $resnumber <= $self->end()) { my @chunks; my $column_incr; my $current_column; my $current_residue = $self->start - 1; my $seq = $self->seq; my $strand = $self->strand || 0; if ($strand == -1) { #@chunks = reverse $seq =~ m/[^\.\-]+|[\.\-]+/go; @chunks = reverse $seq =~ m/[$RESIDUE_SYMBOLS]+|[$GAP_SYMBOLS]+/go; $column_incr = -1; $current_column = (CORE::length $seq) + 1; } else { #@chunks = $seq =~ m/[^\.\-]+|[\.\-]+/go; @chunks = $seq =~ m/[$RESIDUE_SYMBOLS]+|[$GAP_SYMBOLS]+/go; $column_incr = 1; $current_column = 0; } while (my $chunk = shift @chunks) { #if ($chunk =~ m|^[\.\-]|o) { if ($chunk =~ m|^[$GAP_SYMBOLS]|o) { $current_column += $column_incr * CORE::length($chunk); } else { if ($current_residue + CORE::length($chunk) < $resnumber) { $current_column += $column_incr * CORE::length($chunk); $current_residue += CORE::length($chunk); } else { if ($strand == -1) { $current_column -= $resnumber - $current_residue; } else { $current_column += $resnumber - $current_residue; } return $current_column; } } } } $self->throw("Could not find residue number $resnumber"); } =head2 location_from_column Title : location_from_column Usage : $loc = $ali->location_from_column($column_number) Function: This function gives the residue number for a given position in the alignment (i.e. column number) of the given. Gaps complicate this process and force the output to be a L where values can be undefined. For example, for the sequence: Seq/91-96 .AC..DEF.G. location_from_column( 3 ) position 92 location_from_column( 4 ) position 92^93 location_from_column( 9 ) position 95^96 location_from_column( 1 ) position undef An exact position returns a Bio::Location::Simple object where where location_type() returns 'EXACT', if a position is between bases location_type() returns 'IN-BETWEEN'. Column before the first residue returns undef. Note that if the position is after the last residue in the alignment, that there is no guarantee that the original sequence has residues after that position. An exception is thrown if the column number is not within the sequence. Returns : Bio::Location::Simple or undef Args : A column number Throws : If column is not within the sequence See L for more. =cut sub location_from_column { my ($self, $column) = @_; $self->throw("Column number has to be a positive integer, not [$column]") unless $column =~ /^\d+$/ and $column > 0; $self->throw("Column number [$column] is larger than". " sequence length [". $self->length. "]") unless $column <= $self->length; my ($loc); my $s = $self->subseq(1,$column); $s =~ s/[^a-zA-Z\*]//g; my $pos = CORE::length $s; my $start = $self->start || 0 ; my $strand = $self->strand() || 1; my $relative_pos = ($strand == -1) ? ($self->end - $pos + 1) : ($pos + $start - 1); if ($self->subseq($column, $column) =~ /[a-zA-Z\*]/ ) { $loc = Bio::Location::Simple->new (-start => $relative_pos, -end => $relative_pos, -strand => 1, ); } elsif ($pos == 0 and $self->start == 1) { } else { my ($start,$end) = ($relative_pos, $relative_pos + $strand); if ($strand == -1) { ($start,$end) = ($end,$start); } $loc = Bio::Location::Simple->new (-start => $start, -end => $end, -strand => 1, -location_type => 'IN-BETWEEN' ); } return $loc; } =head2 revcom Title : revcom Usage : $rev = $seq->revcom() Function: Produces a new Bio::LocatableSeq object which has the reversed complement of the sequence. For protein sequences this throws an exception of "Sequence is a protein. Cannot revcom" Returns : A new Bio::LocatableSeq object Args : none =cut sub revcom { my ($self) = @_; # since we don't know whether sequences without 1 => 1 correlation can be # revcom'd, kick back if (grep {$_ != 1} $self->mapping) { $self->warn('revcom() not supported for sequences with mapped values of > 1'); return; } my $new = $self->SUPER::revcom; $new->strand($self->strand * -1) if $self->strand; $new->start($self->start) if $self->start; $new->end($self->end) if $self->end; return $new; } =head2 trunc Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence, Returns : a fresh Bio::PrimarySeqI implementing object Args : Two integers denoting first and last columns of the sequence to be included into sub-sequence. =cut sub trunc { my ($self, $start, $end) = @_; my $new = $self->SUPER::trunc($start, $end); $new->strand($self->strand); # end will be automatically calculated $start = $end if $self->strand && $self->strand == -1; $start = $self->location_from_column($start); $start ? ($start = $start->end) : ($start = 1); $new->start($start) if $start; return $new; } =head2 validate_seq Title : validate_seq Usage : if(! $seqobj->validate_seq($seq_str) ) { print "sequence $seq_str is not valid for an object of alphabet ",$seqobj->alphabet, "\n"; } Function: Test that the given sequence is valid, i.e. contains only valid characters. The allowed characters are all letters (A-Z) and '-','.', '*','?','=' and '~'. Spaces are not valid. Note that this implementation does not take alphabet() into account. Returns : 1 if the supplied sequence string is valid, 0 otherwise. Args : - Sequence string to be validated - Boolean to throw an error if the sequence is invalid =cut sub validate_seq { my ($self, $seqstr, $throw) = @_; $seqstr = '' if not defined $seqstr; $throw = 0 if not defined $throw ; # 0 for backward compatibility if ( (CORE::length $seqstr > 0 ) && ($seqstr !~ /^([$MATCHPATTERN]+)$/) ) { if ($throw) { $self->throw("Failed validation of sequence '".(defined($self->id) || '[unidentified sequence]')."'. Invalid characters were: " . join('',($seqstr =~ /([^$MATCHPATTERN]+)/g))); } return 0; } return 1; } ################## DEPRECATED METHODS ################## =head2 no_gap Title : no_gaps Usage : $self->no_gaps('.') Function : Gets number of gaps in the sequence. The count excludes leading or trailing gap characters. Valid bioperl sequence characters are [A-Za-z\-\.\*]. Of these, '.' and '-' are counted as gap characters unless an optional argument specifies one of them. Returns : number of internal gaps in the sequence. Args : a gap character (optional) Status : Deprecated (in favor of num_gaps()) =cut sub no_gaps { my $self = shift; $self->deprecated( -warn_version => 1.0069, -throw_version => 1.0075, -message => 'Use of method no_gaps() is deprecated, use num_gaps() instead' ); return $self->num_gaps(@_); } =head2 no_sequences Title : no_sequences Usage : $gaps = $seq->no_sequences Function : number of sequence in the sequence alignment Returns : integer Argument : Status : Deprecated (in favor of num_sequences()) =cut sub no_sequences { my $self = shift; $self->deprecated( -warn_version => 1.0069, -throw_version => 1.0075, -message => 'Use of method no_sequences() is deprecated, use num_sequences() instead' ); return $self->num_sequences(@_); } 1; BioPerl-1.007002/Bio/LocationI.pm000444000766000024 3004013155576320 16460 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::LocationI # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::LocationI - Abstract interface of a Location on a Sequence =head1 SYNOPSIS # get a LocationI somehow printf( "start = %d, end = %d, strand = %s, seq_id = %s\n", $location->start, $location->end, $location->strand, $location->seq_id); print "location str is ", $location->to_FTstring(), "\n"; =head1 DESCRIPTION This Interface defines the methods for a Bio::LocationI, an object which encapsulates a location on a biological sequence. Locations need not be attached to actual sequences as they are stand alone objects. LocationI objects are used by L objects to manage and represent locations for a Sequence Feature. =head1 FEEDBACK User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::LocationI; use strict; use Carp; use base qw(Bio::RangeI); =head2 location_type Title : location_type Usage : my $location_type = $location->location_type(); Function: Get location type encoded as text Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN') Args : none =cut sub location_type { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 start Title : start Usage : $start = $location->start(); Function: Get the start coordinate of this location as defined by the currently active coordinate computation policy. In simple cases, this will return the same number as min_start() and max_start(), in more ambiguous cases like fuzzy locations the number may be equal to one or neither of both. We override this here from RangeI in order to delegate 'get' to a L implementing object. Implementing classes may also wish to provide 'set' functionality, in which case they *must* override this method. The implementation provided here will throw an exception if called with arguments. Returns : A positive integer value. Args : none See L for more information =cut sub start { my ($self,@args) = @_; # throw if @args means that we don't support updating information # in the interface but will delegate to the coordinate policy object # for interpreting the 'start' value $self->throw_not_implemented if @args; return $self->coordinate_policy()->start($self); } =head2 end Title : end Usage : $end = $location->end(); Function: Get the end coordinate of this location as defined by the currently active coordinate computation policy. In simple cases, this will return the same number as min_end() and max_end(), in more ambiguous cases like fuzzy locations the number may be equal to one or neither of both. We override this here from Bio::RangeI in order to delegate 'get' to a L implementing object. Implementing classes may also wish to provide 'set' functionality, in which case they *must* override this method. The implementation provided here will throw an exception if called with arguments. Returns : A positive integer value. Args : none See L and L for more information =cut sub end { my ($self,@args) = @_; # throw if @args means that we don't support updating information # in the interface but will delegate to the coordinate policy object # for interpreting the 'end' value $self->throw_not_implemented if @args; return $self->coordinate_policy()->end($self); } =head2 min_start Title : min_start Usage : my $minstart = $location->min_start(); Function: Get minimum starting point of feature. Note that an implementation must not call start() in this method. Returns : integer or undef if no minimum starting point. Args : none =cut sub min_start { my($self) = @_; $self->throw_not_implemented(); } =head2 max_start Title : max_start Usage : my $maxstart = $location->max_start(); Function: Get maximum starting point of feature. Note that an implementation must not call start() in this method unless start() is overridden such as not to delegate to the coordinate computation policy object. Returns : integer or undef if no maximum starting point. Args : none =cut sub max_start { my($self) = @_; $self->throw_not_implemented(); } =head2 start_pos_type Title : start_pos_type Usage : my $start_pos_type = $location->start_pos_type(); Function: Get start position type encoded as text Known valid values are 'BEFORE' (<5..100), 'AFTER' (>5..100), 'EXACT' (5..100), 'WITHIN' ((5.10)..100), 'BETWEEN', (5^6), with their meaning best explained by their GenBank/EMBL location string encoding in brackets. Returns : string ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none =cut sub start_pos_type { my($self) = @_; $self->throw_not_implemented(); } =head2 flip_strand Title : flip_strand Usage : $location->flip_strand(); Function: Flip-flop a strand to the opposite Returns : None Args : None =cut sub flip_strand { my $self= shift; $self->strand($self->strand * -1); } =head2 min_end Title : min_end Usage : my $minend = $location->min_end(); Function: Get minimum ending point of feature. Note that an implementation must not call end() in this method unless end() is overridden such as not to delegate to the coordinate computation policy object. Returns : integer or undef if no minimum ending point. Args : none =cut sub min_end { my($self) = @_; $self->throw_not_implemented(); } =head2 max_end Title : max_end Usage : my $maxend = $location->max_end(); Function: Get maximum ending point of feature. Note that an implementation must not call end() in this method unless end() is overridden such as not to delegate to the coordinate computation policy object. Returns : integer or undef if no maximum ending point. Args : none =cut sub max_end { my($self) = @_; $self->throw_not_implemented(); } =head2 end_pos_type Title : end_pos_type Usage : my $end_pos_type = $location->end_pos_type(); Function: Get end position encoded as text. Known valid values are 'BEFORE' (5..<100), 'AFTER' (5..>100), 'EXACT' (5..100), 'WITHIN' (5..(90.100)), 'BETWEEN', (5^6), with their meaning best explained by their GenBank/EMBL location string encoding in brackets. Returns : string ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none =cut sub end_pos_type { my($self) = @_; $self->throw_not_implemented(); } =head2 seq_id Title : seq_id Usage : my $seqid = $location->seq_id(); Function: Get/Set seq_id that location refers to Returns : seq_id (a string) Args : [optional] seq_id value to set =cut sub seq_id { my($self) = @_; $self->throw_not_implemented(); } =head2 is_remote Title : is_remote Usage : $is_remote_loc = $loc->is_remote() Function: Whether or not a location is a remote location. A location is said to be remote if it is on a different 'object' than the object which 'has' this location. Typically, features on a sequence will sometimes have a remote location, which means that the location of the feature is on a different sequence than the one that is attached to the feature. In such a case, $loc->seq_id will be different from $feat->seq_id (usually they will be the same). While this may sound weird, it reflects the location of the kind of AL445212.9:83662..166657 which can be found in GenBank/EMBL feature tables. Example : Returns : TRUE if the location is a remote location, and FALSE otherwise Args : Value to set to =cut sub is_remote{ shift->throw_not_implemented(); } =head2 coordinate_policy Title : coordinate_policy Usage : $policy = $location->coordinate_policy(); $location->coordinate_policy($mypolicy); # set may not be possible Function: Get the coordinate computing policy employed by this object. See L for documentation about the policy object and its use. The interface *does not* require implementing classes to accept setting of a different policy. The implementation provided here does, however, allow one to do so. Implementors of this interface are expected to initialize every new instance with a L object. The implementation provided here will return a default policy object if none has been set yet. To change this default policy object call this method as a class method with an appropriate argument. Note that in this case only subsequently created Location objects will be affected. Returns : A L implementing object. Args : On set, a L implementing object. See L for more information =cut sub coordinate_policy { shift->throw_not_implemented(); } =head2 to_FTstring Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none =cut sub to_FTstring { my($self) = @_; $self->throw_not_implemented(); } =head2 each_Location Title : each_Location Usage : @locations = $locObject->each_Location($order); Function: Conserved function call across Location:: modules - will return an array containing the component Location(s) in that object, regardless if the calling object is itself a single location or one containing sublocations. Returns : an array of Bio::LocationI implementing objects Args : Optional sort order to be passed to sub_Location() for Splits =cut sub each_Location { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 valid_Location Title : valid_Location Usage : if ($location->valid_location) {...}; Function: boolean method to determine whether location is considered valid (has minimum requirements for a specific LocationI implementation) Returns : Boolean value: true if location is valid, false otherwise Args : none =cut sub valid_Location { my ($self,@args) = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/MapIO.pm000444000766000024 1252413155576320 15553 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::MapIO # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::MapIO - A Map Factory object =head1 SYNOPSIS use Bio::MapIO; my $mapio = Bio::MapIO->new(-format => "mapmaker", -file => "mapfile.map"); while( my $map = $mapio->next_map ) { # get each map foreach my $marker ( $map->each_element ) { # loop through the markers associated with the map } } =head1 DESCRIPTION This is the Factory object for reading Maps from a data stream or file. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::MapIO; use strict; use base qw(Bio::Root::Root Bio::Root::IO Bio::Factory::MapFactoryI); =head2 new Title : new Usage : my $obj = Bio::MapIO->new(); Function: Builds a new Bio::MapIO object Returns : Bio::MapIO Args : =cut sub new { my($caller,@args) = @_; my $class = ref($caller) || $caller; # or do we want to call SUPER on an object if $caller is an # object? if( $class =~ /Bio::MapIO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $format = $param{'-format'} || $class->_guess_format( $param{'-file'} || $ARGV[0] ) || 'mapmaker'; $format = "\L$format"; # normalize capitalization to lower case # normalize capitalization return unless( $class->_load_format_module($format) ); return "Bio::MapIO::$format"->new(@args); } } =head2 format Title : format Usage : $format = $stream->format() Function: Get the map format Returns : map format Args : none =cut # format() method inherited from Bio::Root::IO =head2 Bio::Factory::MapFactoryI methods =cut =head2 next_map Title : next_tree Usage : my $map = $factory->next_map; Function: Get a map from the factory Returns : L Args : none =head2 write_map Title : write_tree Usage : $factory->write_map($map); Function: Write a map out through the factory Returns : none Args : L =cut =head2 attach_EventHandler Title : attach_EventHandler Usage : $parser->attatch_EventHandler($handler) Function: Adds an event handler to listen for events Returns : none Args : L =cut sub attach_EventHandler{ my ($self,$handler) = @_; return if( ! $handler ); if( ! $handler->isa('Bio::Event::EventHandlerI') ) { $self->warn("Ignoring request to attatch handler ".ref($handler). ' because it is not a Bio::Event::EventHandlerI'); } $self->{'_handler'} = $handler; return; } =head2 _eventHandler Title : _eventHandler Usage : private Function: Get the EventHandler Returns : L Args : none =cut sub _eventHandler{ my ($self) = @_; return $self->{'_handler'}; } sub _initialize { my($self, @args) = @_; $self->{'_handler'} = undef; # initialize the IO part $self->_initialize_io(@args); # $self->attach_EventHandler(Bio::MapIO::MapEventBuilder->new()); } =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL MapIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($self,$format) = @_; my $module = "Bio::MapIO::" . $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args : =cut sub _guess_format { my $class = shift; return unless $_ = shift; return 'mapmaker' if /\.(map)$/i; return 'mapxml' if /\.(xml)$/i; } sub DESTROY { my $self = shift; $self->close(); } 1; BioPerl-1.007002/Bio/NexmlIO.pm000444000766000024 3346013155576320 16123 0ustar00cjfieldsstaff000000000000# $Id: Nexml.pm 15889 2009-07-29 13:35:29Z chmille4 $ # BioPerl module for Bio::NexmlIO # # Please direct questions and support issues to # # Cared for by Chase Miller # # Copyright Chase Miller # # You may distribute this module under the same terms as perl itself # # _history # June 16, 2009 Largely rewritten by Chase Miller # POD documentation - main docs before the code =head1 NAME Bio::NexmlIO - stream handler for NeXML documents =head1 SYNOPSIS #Instantiate a Bio::Nexml object and link it to a file my $in_nexml = Bio::Nexml->new(-file => 'nexml_doc.xml', -format => 'Nexml'); #Read in some data my $bptree1 = $in_nexml->next_tree(); my $bpaln1 = $in_nexml->next_aln(); my $bpseq1 = $in_nexml->next_seq(); #Use/manipulate data ... #Write data to nexml file my $out_nexml = Bio::Nexml->new(-file => '>new_nexml_doc.xml', -format => 'Nexml'); $out_nexml->to_xml(); =head1 DESCRIPTION Bio::NexmlIO is an I/O handler for a NeXML document. A NeXML document can represent three different data types: simple sequences, alignments, and trees. NexmlIO has four main methods next_tree, next_seq, next_aln, and write. NexmlIO returns bioperl seq, tree, and aln objects which can be manipulated then passed to the write method of a new NexmlIO instance to allow the creation of a NeXML document. Each bioperl object contains all the information necessary to recreate a Bio::Phylo::Taxa object, so each time a bioperl object is converted to a biophylo object, the bioperl object is checked to see if its associated taxa has already been created (against a hash using the NexmlIO_ID and Taxa_ID to create a unique string). If not, it is created; if so, that taxa object is used to link the Bio::Phylo tree or matrix. For more information on the NeXML format, see L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chase Miller Email chmille4@gmail.com =head1 CONTRIBUTORS Mark A. Jensen, maj -at- fortinbras -dot- com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::NexmlIO; use strict; #TODO Change this use lib '..'; use Bio::SeqIO::nexml; use Bio::AlignIO::nexml; use Bio::TreeIO::nexml; use Bio::Nexml::Factory; use base qw(Bio::Root::IO); my $nexml_fac = Bio::Nexml::Factory->new(); =head1 CONSTRUCTOR =head2 new Title : new Usage : my $in_nexmlIO = Bio::NexmlIO->new(-file => 'data.nexml.xml'); Function: Creates a L object linked to a stream Returns : a L object Args : file name See L =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my %params = @args; my $file_string = $params{'-file'}; #create unique ID by creating a scalar and using the memory address my $ID = bless \(my $dummy), "UniqueID"; ($self->{'_ID'}) = sprintf("%s",\$ID) =~ /(0x[0-9a-fA-F]+)/; unless ($file_string =~ m/^\>/) { # Only pass filename if filehandle is not available, # or "Bio::Phylo" will create a new filehandle that ends # out of scope and can't be closed directly, leaving 2 open # filehandles for the same file (so file can't be deleted) my $file_arg; my $file_value; if ( exists $self->{'_filehandle'} and defined $self->{'_filehandle'} ) { $file_arg = '-handle'; $file_value = $self->{'_filehandle'}; } else { $file_arg = '-file'; $file_value = $self->{'_file'}; } $self->{'_doc'} = Bio::Phylo::IO->parse($file_arg => $file_value,, '-format' => 'nexml', '-as_project' => '1'); } return $self; } =head2 doc Title : doc Usage : my $nexml_doc = $in_nexmlIO->doc(); Function: returns a L object that contains all the Bio::Phylo data objects parsed from the stream Returns : a L object Args : none =cut sub doc { my $self = shift; return $self->{'_doc'}; } # Takes the Bio::Phylo::Project object and creats BioPerl trees, alns, and seqs from it sub _parse { my ($self) = @_; $self->{'_treeiter'} = 0; $self->{'_seqiter'} = 0; $self->{'_alniter'} = 0; $self->{_trees} = $nexml_fac->create_bperl_tree($self); $self->{_alns} = $nexml_fac->create_bperl_aln($self); $self->{_seqs} = $nexml_fac->create_bperl_seq($self); my $taxa_array = $self->doc->get_taxa(); $self->{'_parsed'} = 1; #success } =head1 ITERATORS =head2 next_tree Title : next_tree Usage : $tree = $stream->next_tree Function: Reads the next tree object from the stream and returns it. Returns : a L object Args : none See L, L =cut sub next_tree { my $self = shift; $self->_parse unless $self->{'_parsed'}; return $self->{'_trees'}->[ $self->{'_treeiter'}++ ]; } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq Function: Reads the next seq object from the stream and returns it. Returns : a L object Args : none See L, L =cut sub next_seq { my $self = shift; unless ( $self->{'_parsed'} ) { $self->_parse; } return $self->{'_seqs'}->[ $self->{'_seqiter'}++ ]; } =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln Function: Reads the next aln object from the stream and returns it. Returns : a L object Args : none See L, L =cut sub next_aln { my $self = shift; unless ( $self->{'_parsed'} ) { $self->_parse; } return $self->{'_alns'}->[ $self->{'_alniter'}++ ]; } sub _rewind { my $self = shift; my $elt = shift; $self->{"_${elt}iter"} = 0 if defined $self->{"_${elt}iter"}; return 1; } =head2 rewind_seq Title : rewind_seq Usage : $stream->rewind_seq Function: Resets the stream for seqs Returns : none Args : none See L, L =cut sub rewind_seq { shift->_rewind('seq'); } =head2 rewind_aln Title : rewind_aln Usage : $stream->rewind_aln Function: Resets the stream for alns Returns : none Args : none See L, L =cut sub rewind_aln { shift->_rewind('aln'); } =head2 rewind_tree Title : rewind_tree Usage : $stream->rewind_tree Function: Resets the stream for trees Returns : none Args : none See L, L =cut sub rewind_tree { shift->_rewind('tree'); } =head2 write Title : write Usage : $stream->write(-alns => $alns,-seqs => $seqs,-trees => $trees) Function: converts BioPerl seq, tree, and aln objects into Bio::Phylo seq, tree, and aln objects, constructs a Bio::Phylo::Project object made up of the newly created Bio::Phylo objects, and writes the Bio::Phylo:Project object to the stream as a valid nexml document Returns : none Args : \@L, \@L, \@L See L, L, L, L =cut sub write { my ($self, @args) = @_; my %params = @args; my ($trees, $alns, $seqs) = @params{qw( -trees -alns -seqs )}; my %taxa_hash = (); my %seq_matrices = (); my $proj_doc = Bio::Phylo::Factory->create_project(); #convert trees to bio::Phylo objects my $forest = Bio::Phylo::Factory->create_forest(); my @forests; my @taxa_array; my $ent; my $taxa_o; my $phylo_tree_o; foreach my $tree (@$trees) { my $nexml_id = $tree->get_tag_values('_NexmlIO_ID'); $taxa_o = undef; if ( defined $taxa_hash{$nexml_id} ) { $taxa_o = $taxa_hash{$nexml_id}; } else { ($taxa_o) = $nexml_fac->create_bphylo_taxa($tree); $forest->set_taxa($taxa_o) if defined $taxa_o; $taxa_hash{$nexml_id} = $taxa_o; } ($phylo_tree_o) = $nexml_fac->create_bphylo_tree($tree, $taxa_o); $forest->insert($phylo_tree_o); } #convert matrices to Bio::Phylo objects my $matrices = Bio::Phylo::Matrices->new(); my $phylo_matrix_o; foreach my $aln (@$alns) { $taxa_o = undef; if (defined $taxa_hash{ $aln->{_Nexml_ID} }) { $taxa_o = $taxa_hash{$aln->{_Nexml_ID}}; } else { ($taxa_o) = $nexml_fac->create_bphylo_taxa($aln); $taxa_hash{$aln->{_Nexml_ID}} = $taxa_o; } ($phylo_matrix_o) = $nexml_fac->create_bphylo_aln($aln, $taxa_o); $phylo_matrix_o->set_taxa($taxa_o) if defined $taxa_o; $matrices->insert($phylo_matrix_o); } my $seq_matrix_o; my $datum; #convert sequences to Bio::Phylo objects foreach my $seq (@$seqs) { $taxa_o = undef; #check if this Bio::Phylo::Taxa obj has already been created if (defined $taxa_hash{ $seq->{_Nexml_ID} }) { $taxa_o = $taxa_hash{$seq->{_Nexml_ID}}; } else { ($taxa_o) = $nexml_fac->create_bphylo_taxa($seq); $taxa_hash{$seq->{_Nexml_ID}} = $taxa_o; } $datum = $nexml_fac->create_bphylo_seq($seq, $taxa_o); #check if this Bio::Phylo::Matrices::Matrix obj has already been created if (defined $seq_matrices{ $seq->{_Nexml_matrix_ID} }) { $seq_matrix_o = $seq_matrices{$seq->{_Nexml_matrix_ID}}; my $taxon_name = $datum->get_taxon()->get_name(); $datum->unset_taxon(); $seq_matrix_o->insert($datum); $datum->set_taxon($seq_matrix_o->get_taxa()->get_by_name($taxon_name)); } else { $seq_matrix_o = Bio::Phylo::Factory->create_matrix('-type' => $datum->moltype); $seq_matrices{$seq->{_Nexml_matrix_ID}} = $seq_matrix_o; $seq_matrix_o->set_taxa($taxa_o) if defined $taxa_o; $seq_matrix_o->insert($datum); #get matrix label my $feat = ($seq->get_SeqFeatures())[0]; my $matrix_label = ($feat->get_tag_values('matrix_label'))[0] if $feat->has_tag('id'); $seq_matrix_o->set_name($matrix_label); $matrices->insert($seq_matrix_o); } } #Add matrices and forest objects to project object which represents a complete nexml document if($forest->first) { $proj_doc->insert($forest); } while(my $curr_matrix = $matrices->next) { $proj_doc->insert($curr_matrix); } #write nexml document to stream my $ret = $self->_print($proj_doc->to_xml(-compact=>1)); $self->flush; return($ret); } =head2 extract_seqs Title : extract_seqs Usage : $nexmlIO->extract_seqs(-file => ">$outfile", -format => $format) Function: converts BioPerl seqs stored in the NexmlIO object into the provided format and writes it to the provided file. Uses L to do the conversion and writing. Returns : none Args : file to write to, format to be converted to See L, L =cut sub extract_seqs { my $self = shift; unless ( $self->{'_parsed'} ) { $self->_parse; } my %params = @_; my $remove_spaces = 0; my $ret = 0; my ($format, $file) = @params{qw( -format -file)}; for ($format) { /^fasta$/i && do { # this is ok, flag so that the nexmlid gets converted; $remove_spaces = 1; last; }; # default do { $self->throw("Format '$format' not yet supported for extraction"); }; } my $seqIO = Bio::SeqIO->new(-format => $format, -file => $file); my $seqs = $self->{_seqs}; foreach my $seq (@$seqs) { if ($remove_spaces) { my $id = $seq->id; $id =~ s/ /_/; $seq->id($id); } $ret = $seqIO->write_seq($seq); } return $ret; } =head2 extract_alns Title : extract_alns Usage : $nexmlIO->extract_alns(-file => ">$outfile", -format => $format) Function: converts BioPerl alns stored in the NexmlIO object into the provided format and writes it to the provided file. Uses L to do the conversion and writing. Returns : none Args : file to write to, format to be converted to See L, L =cut sub extract_alns { my $self = shift; unless ( $self->{'_parsed'} ) { $self->_parse; } my $ret = 0; my %params = @_; my ($format, $file) = @params{qw( -format -file)}; my $alignIO = Bio::AlignIO->new(-format => $format, -file => $file); my $alns = $self->{_alns}; foreach my $aln (@$alns) { $ret = $alignIO->write_aln($aln); } return $ret; } =head2 extract_trees Title : extract_trees Usage : $nexmlIO->extract_trees(-file => ">$outfile", -format => $format) Function: converts BioPerl trees stored in the NexmlIO object into the provided format and writes it to the provided file. Uses L to do the conversion and writing. Returns : none Args : file to write to, format to be converted to See L, L =cut sub extract_trees { my $self = shift; unless ( $self->{'_parsed'} ) { $self->_parse; } my $ret = 0; my %params = @_; my ($format, $file) = @params{qw( -format -file)}; my $treeIO = Bio::TreeIO->new(-format => $format, -file => $file); my $trees = $self->{_trees}; foreach my $tree (@$trees) { $treeIO->write_tree($tree); $ret = 1; } return $ret; } 1; BioPerl-1.007002/Bio/OntologyIO.pm000444000766000024 2300313155576320 16642 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::OntologyIO # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2003. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::OntologyIO - Parser factory for Ontology formats =head1 SYNOPSIS use Bio::OntologyIO; my $parser = Bio::OntologyIO->new(-format => "go", -file=> $file); while(my $ont = $parser->next_ontology()) { print "read ontology ",$ont->name()," with ", scalar($ont->get_root_terms)," root terms, and ", scalar($ont->get_leaf_terms)," leaf terms\n"; } =head1 DESCRIPTION This is the parser factory for different ontology sources and formats. Conceptually, it is very similar to L, but the difference is that the chunk of data returned as an object is an entire ontology. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::OntologyIO; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root Bio::Root::IO); # # Maps from format name to driver suitable for the format. # my %format_driver_map = ( "go" => "goflat", "so" => "soflat", "interpro" => "InterProParser", "interprosax" => "Handlers::InterPro_BioSQL_Handler", "evoc" => "simplehierarchy", "obo" => "obo" ); =head2 new Title : new Usage : my $parser = Bio::OntologyIO->new(-format => 'go', @args); Function: Returns a stream of ontologies opened on the specified input for the specified format. Returns : An ontology parser (an instance of Bio::OntologyIO) initialized for the specified format. Args : Named parameters. Common parameters are -format - the format of the input; the following are presently supported: goflat: DAG-Edit Gene Ontology flat files go : synonymous to goflat soflat: DAG-Edit Sequence Ontology flat files so : synonymous to soflat simplehierarchy: text format with one term per line and indentation giving the hierarchy evoc : synonymous to simplehierarchy interpro: InterPro XML interprosax: InterPro XML - this is actually not a Bio::OntologyIO compliant parser; instead it persists terms as they are encountered. L obo : OBO format style from Gene Ontology Consortium -file - the file holding the data -fh - the stream providing the data (-file and -fh are mutually exclusive) -ontology_name - the name of the ontology -engine - the L object to be reused (will be created otherwise); note that every L will qualify as well since that one inherits from the former. -term_factory - the ontology term factory to use. Provide a value only if you know what you are doing. DAG-Edit flat file parsers will usually also accept the following parameters. -defs_file - the name of the file holding the term definitions -files - an array ref holding the file names (for GO, there will usually be 3 files: component.ontology, function.ontology, process.ontology) Other parameters are specific to the parsers. =cut sub new { my ($caller,@args) = @_; my $class = ref($caller) || $caller; # or do we want to call SUPER on an object if $caller is an # object? if( $class =~ /Bio::OntologyIO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $format = $class->_map_format($param{'-format'}); # normalize capitalization return unless( $class->_load_format_module($format) ); return "Bio::OntologyIO::$format"->new(@args); } } =head2 format Title : format Usage : $format = $parser->format() Function: Get the ontology format Returns : ontology format Args : none =cut # format() method inherited from Bio::Root::IO sub _initialize { my($self, @args) = @_; # initialize factories etc my ($eng,$fact,$ontname) = $self->_rearrange([qw(TERM_FACTORY) ], @args); # term object factory $self->term_factory($fact) if $fact; # initialize the Bio::Root::IO part $self->_initialize_io(@args); } =head2 next_ontology Title : next_ontology Usage : $ont = $stream->next_ontology() Function: Reads the next ontology object from the stream and returns it. Returns : a L compliant object, or undef at the end of the stream Args : none =cut sub next_ontology { shift->throw_not_implemented(); } =head2 term_factory Title : term_factory Usage : $obj->term_factory($newval) Function: Get/set the ontology term factory to use. As a user of this module it is not necessary to call this method as there will be default. In order to change the default, the easiest way is to instantiate L with the proper -type argument. Most if not all parsers will actually use this very implementation, so even easier than the aforementioned way is to simply call $ontio->term_factory->type("Bio::Ontology::MyTerm"). Example : Returns : value of term_factory (a Bio::Factory::ObjectFactoryI object) Args : on set, new value (a Bio::Factory::ObjectFactoryI object, optional) =cut sub term_factory{ my $self = shift; return $self->{'term_factory'} = shift if @_; return $self->{'term_factory'}; } =head1 Private Methods Some of these are actually 'protected' in OO speak, which means you may or will want to utilize them in a derived ontology parser, but you should not call them from outside. =cut =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL OntologyIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($self, $format) = @_; my $module = "Bio::OntologyIO::" . $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <close(); } sub _map_format { my $self = shift; my $format = shift; my $mod; if($format) { $mod = $format_driver_map{lc($format)}; $mod = lc($format) unless $mod; } else { $self->throw("unable to guess ontology format, specify -format"); } return $mod; } sub unescape { my( $self, $ref ) = @_; $ref =~ s/<\\;/\/g; $ref =~ s/&pct\\;/\%/g; $ref =~ s/\\n/\n/g; $ref =~ s/\\t/\t/g; return $ref; } 1; BioPerl-1.007002/Bio/ParameterBaseI.pm000444000766000024 1565713155576320 17444 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::ParameterBaseI # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::ParameterBaseI - Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends. =head1 SYNOPSIS # Bio::DB::MyParams implements Bio::ParameterBaseI @params = (-db => 'protein', -id => \@ids, -retmax => 10); $pobj->Bio::DB::MyDBParams->new(); # sets only parameters passed; results in a state change if any parameter # passed is new or differs from previously set value $pobj->set_params(@params); # reset all parameters (sets to undef); results in a state change $pobj->reset_params(); # resets parameters to those in %param (sets all others to undef); resets the # object state to indicate change. $pobj->reset_params(@params); # direct get/set; results in a state change if any parameter passed is new or # differs from previously set value $pobj->db('nucleotide'); @ids = $pobj->id(); # retrieve list containing set defined parameters %myparams = $pobj->get_parameters(); # checks whether the state of the object has changed (i.e. parameter has # changed, so on) if ($pobj->parameters_changed) { # run new search } else { # return cached search } # available parameters @params = $pobj->available_parameters(); # retrieve string (URI, query, etc); calling to* methods changes object state # to indicate data hasn't changed (so future calls to parameters_changed() # will return FALSE) $query = $pobj->to_string(); # returns raw string $uri = $pobj->to_uri(); # returns URI-based object $uri = $pobj->to_my_data_struct(); # returns implemenation-specific data structure ... =head1 DESCRIPTION This is a class interface which focuses on common parameter-related tasks such as building simple database queries, URI-related requests, program arguments, etc. Implementing classes use the following ways to set parameters: 1) Create a new instance of a ParameterBaseI-implementing object. $pobj->Bio::DB::MyParamClass->new(-db => 'local', -id => \@ids); 2) Pass the parameters as a hash or array to set_parameters(), which sets the parameters listed in the hash but leaves all others as is. $pobj->set_parameters(-retmax => 100, -retstart => 20); 3) Pass the parameters as a hash or array to reset_parameters(), which sets the parameters listed in the hash and resets everything else. $pobj->reset_parameters(-term => 'pyrimidine'); # sets db and id to undef 4) Pass values using specific getter/setters. $pobj->id(\@ids); # sets IDs There is no restriction on what one uses to set up individual parameter getter/setters, though there are some other options implemented in BioPerl (for instance, Bio::Root::RootI::_set_from_args()). A key requirement is there be a way to detect changes in the state of the ParameterBaseI object so that any object with a Bio::ParameterBaseI can decide whether to submit a new request or return cached data. State changes are revealed by the returned values of the parameters_changed() method, which is a simple boolean set to TRUE when the object is first instantiated or parameters have changed. When retrieving anything using the implementation-specific to_* methods (such as to_query, to_string, to_uri, to_request, etc), the ParameterBaseI object state is set to FALSE to indicate the data has been accessed and indicate reaccessing will retrieve the same value. The observing object can then independently decide whether to rerun the cached query or return a previously cached result. One can also use indiviual getter/setters to retrieve single parameter values as well as use parameter_hash() to retrieve all of the parameters in one go as a hash. To check which parameters are available use available_parameters(). Args passed to =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@lists.open-bio.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web. https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Email cjfields at bioperl dot org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::ParameterBaseI; use strict; use warnings; use base qw(Bio::Root::RootI); =head2 set_parameters Title : set_parameters Usage : $pobj->set_parameters(%params); Function: sets the parameters listed in the hash or array Returns : None Args : [optional] hash or array of parameter/values. =cut sub set_parameters { shift->throw_not_implemented; } =head2 reset_parameters Title : reset_parameters Usage : resets values Function: resets parameters to either undef or value in passed hash Returns : none Args : [optional] hash of parameter-value pairs =cut sub reset_parameters { shift->throw_not_implemented; } =head2 parameters_changed Title : parameters_changed Usage : if ($pobj->parameters_changed) {...} Function: Returns boolean true (1) if parameters have changed Returns : Boolean (0 or 1) Args : [optional] Boolean =cut sub parameters_changed { shift->throw_not_implemented; } =head2 available_parameters Title : available_parameters Usage : @params = $pobj->available_parameters() Function: Returns a list of the available parameters Returns : Array of parameters Args : [optional, implementation-dependent] string for returning subset of parameters =cut sub available_parameters { shift->throw_not_implemented; } =head2 get_parameters Title : get_parameters Usage : %params = $pobj->get_parameters; Function: Returns list of key-value pairs of parameter => value Returns : List of key-value pairs Args : [optional] A string is allowed if subsets are wanted or (if a parameter subset is default) 'all' to return all parameters =cut sub get_parameters { shift->throw_not_implemented; } =head1 to* methods All to_* methods are implementation-specific =cut 1; BioPerl-1.007002/Bio/Perl.pm000444000766000024 4340513155576320 15512 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Perl # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Perl - Functional access to BioPerl for people who don't know objects =head1 SYNOPSIS use Bio::Perl; # will guess file format from extension $seq_object = read_sequence($filename); # forces genbank format $seq_object = read_sequence($filename,'genbank'); # reads an array of sequences @seq_object_array = read_all_sequences($filename,'fasta'); # sequences are Bio::Seq objects, so the following methods work # for more info see Bio::Seq, or do 'perldoc Bio/Seq.pm' print "Sequence name is ",$seq_object->display_id,"\n"; print "Sequence acc is ",$seq_object->accession_number,"\n"; print "First 5 bases is ",$seq_object->subseq(1,5),"\n"; # get the whole sequence as a single string $sequence_as_a_string = $seq_object->seq(); # writing sequences write_sequence(">$filename",'genbank',$seq_object); write_sequence(">$filename",'genbank',@seq_object_array); # making a new sequence from just a string $seq_object = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA", "myname","AL12232"); # getting a sequence from a database (assumes internet connection) $seq_object = get_sequence('swissprot',"ROA1_HUMAN"); $seq_object = get_sequence('embl',"AI129902"); $seq_object = get_sequence('genbank',"AI129902"); # BLAST a sequence (assumes an internet connection) $blast_report = blast_sequence($seq_object); write_blast(">blast.out",$blast_report); =head1 DESCRIPTION Easy first time access to BioPerl via functions. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::Perl; use vars qw(@EXPORT @EXPORT_OK $DBOKAY); use strict; use Carp; use Bio::SeqIO; use Bio::Seq; use Bio::Root::Version '$VERSION'; BEGIN { eval { require Bio::DB::EMBL; require Bio::DB::GenBank; require Bio::DB::SwissProt; require Bio::DB::RefSeq; require Bio::DB::GenPept; }; if( $@ ) { $DBOKAY = 0; } else { $DBOKAY = 1; } } use base qw(Exporter); @EXPORT = qw(read_sequence read_all_sequences write_sequence new_sequence get_sequence translate translate_as_string reverse_complement revcom revcom_as_string reverse_complement_as_string blast_sequence write_blast); @EXPORT_OK = @EXPORT; =head2 read_sequence Title : read_sequence Usage : $seq = read_sequence('sequences.fa') $seq = read_sequence($filename,'genbank'); # pipes are fine $seq = read_sequence("my_fetching_program $id |",'fasta'); Function: Reads the top sequence from the file. If no format is given, it will try to guess the format from the filename. If a format is given, it forces that format. The filename can be any valid perl open() string - in particular, you can put in pipes Returns : A Bio::Seq object. A quick synopsis: $seq_object->display_id - name of the sequence $seq_object->seq - sequence as a string Args : Two strings, first the filename - any Perl open() string is ok Second string is the format, which is optional For more information on Seq objects see L. =cut sub read_sequence{ my ($filename,$format) = @_; if( !defined $filename ) { confess "read_sequence($filename) - usage incorrect"; } my $seqio; if( defined $format ) { $seqio = Bio::SeqIO->new( '-file' => $filename, '-format' => $format); } else { $seqio = Bio::SeqIO->new( '-file' => $filename); } my $seq = $seqio->next_seq(); return $seq; } =head2 read_all_sequences Title : read_all_sequences Usage : @seq_object_array = read_all_sequences($filename); @seq_object_array = read_all_sequences($filename,'genbank'); Function: Just as the function above, but reads all the sequences in the file and loads them into an array. For very large files, you will run out of memory. When this happens, you've got to use the SeqIO system directly (this is not so hard! Don't worry about it!). Returns : array of Bio::Seq objects Args : two strings, first the filename (any open() string is ok) second the format (which is optional) See L and L for more information =cut sub read_all_sequences{ my ($filename,$format) = @_; if( !defined $filename ) { confess "read_all_sequences($filename) - usage incorrect"; } my $seqio; if( defined $format ) { $seqio = Bio::SeqIO->new( '-file' => $filename, '-format' => $format); } else { $seqio = Bio::SeqIO->new( '-file' => $filename); } my @seq_array; while( my $seq = $seqio->next_seq() ) { push(@seq_array,$seq); } return @seq_array; } =head2 write_sequence Title : write_sequence Usage : write_sequence(">new_file.gb",'genbank',$seq) write_sequence(">new_file.gb",'genbank',@array_of_sequence_objects) Function: writes sequences in the specified format Returns : true Args : filename as a string, must provide an open() output file format as a string one or more sequence objects =cut sub write_sequence{ my ($filename,$format,@sequence_objects) = @_; if( scalar(@sequence_objects) == 0 ) { confess("write_sequence(filename,format,sequence_object)"); } my $error = 0; my $seqname = "sequence1"; # catch users who haven't passed us a filename we can open if( $filename !~ /^\>/ && $filename !~ /^|/ ) { $filename = ">".$filename; } my $seqio = Bio::SeqIO->new('-file' => $filename, '-format' => $format); foreach my $seq ( @sequence_objects ) { my $seq_obj; if( !ref $seq ) { if( length $seq > 50 ) { # odds are this is a sequence as a string, and someone has not figured out # how to make objects. Warn him/her and then make a sequence object # from this if( $error == 0 ) { carp("WARNING: You have put in a long string into write_sequence.\n". "I suspect this means that this is the actual sequence\n". "In the future try the\n". " new_sequence method of this module to make a new sequence object.\n". "Doing this for you here\n"); $error = 1; } $seq_obj = new_sequence($seq,$seqname); $seqname++; } else { confess("You have a non object [$seq] passed to write_sequence. It maybe that you". "want to use new_sequence to make this string into a sequence object?"); } } else { if( !$seq->isa("Bio::SeqI") ) { confess("object [$seq] is not a Bio::Seq object; can't write it out"); } $seq_obj = $seq; } # finally... we get to write out the sequence! $seqio->write_seq($seq_obj); } 1; } =head2 new_sequence Title : new_sequence Usage : $seq_obj = new_sequence("GATTACA", "kino-enzyme"); Function: Construct a sequency object from sequence string Returns : A Bio::Seq object Args : sequence string name string (optional, default "no-name-for-sequence") accession - accession number (optional, no default) =cut sub new_sequence{ my ($seq,$name,$accession) = @_; if( !defined $seq ) { confess("new_sequence(sequence_as_string) usage"); } $name ||= "no-name-for-sequence"; my $seq_object = Bio::Seq->new( -seq => $seq, -id => $name); $accession && $seq_object->accession_number($accession); return $seq_object; } =head2 blast_sequence Title : blast_sequence Usage : $blast_result = blast_sequence($seq) $blast_result = blast_sequence('MFVEGGTFASEDDDSASAEDE'); Function: If the computer has Internet accessibility, blasts the sequence using the NCBI BLAST server against nrdb. It chooses the flavour of BLAST on the basis of the sequence. This function uses Bio::Tools::Run::RemoteBlast, which itself use Bio::SearchIO - as soon as you want to know more, check out these modules Returns : Bio::Search::Result::GenericResult.pm Args : Either a string of protein letters or nucleotides, or a Bio::Seq object =cut sub blast_sequence { my ($seq,$verbose) = @_; if( !defined $verbose ) { $verbose = 1; } if( !ref $seq ) { $seq = Bio::Seq->new( -seq => $seq, -id => 'blast-sequence-temp-id'); } elsif ( !$seq->isa('Bio::PrimarySeqI') ) { croak("[$seq] is an object, but not a Bio::Seq object, cannot be blasted"); } require Bio::Tools::Run::RemoteBlast; my $prog = ( $seq->alphabet eq 'protein' ) ? 'blastp' : 'blastn'; my $e_val= '1e-10'; my @params = ( '-prog' => $prog, '-expect' => $e_val, '-readmethod' => 'SearchIO' ); my $factory = Bio::Tools::Run::RemoteBlast->new(@params); my $r = $factory->submit_blast($seq); if( $verbose ) { print STDERR "Submitted Blast for [".$seq->id."] "; } sleep 5; my $result; LOOP : while( my @rids = $factory->each_rid) { foreach my $rid ( @rids ) { my $rc = $factory->retrieve_blast($rid); if( !ref($rc) ) { if( $rc < 0 ) { $factory->remove_rid($rid); } if( $verbose ) { print STDERR "."; } sleep 10; } else { $result = $rc->next_result(); $factory->remove_rid($rid); last LOOP; } } } if( $verbose ) { print STDERR "\n"; } return $result; } =head2 write_blast Title : write_blast Usage : write_blast($filename,$blast_report); Function: Writes a BLAST result object (or more formally a SearchIO result object) out to a filename in BLAST-like format Returns : none Args : filename as a string Bio::SearchIO::Results object =cut sub write_blast { my ($filename,$blast) = @_; if( $filename !~ /^\>/ && $filename !~ /^|/ ) { $filename = ">".$filename; } my $output = Bio::SearchIO->new( -output_format => 'blast', -file => $filename); $output->write_result($blast); } =head2 get_sequence Title : get_sequence Usage : $seq_object = get_sequence('swiss',"ROA1_HUMAN"); Function: If the computer has Internet access this method gets the sequence from Internet accessible databases. Currently this supports Swissprot ('swiss'), EMBL ('embl'), GenBank ('genbank'), GenPept ('genpept'), and RefSeq ('refseq'). Swissprot and EMBL are more robust than GenBank fetching. If the user is trying to retrieve a RefSeq entry from GenBank/EMBL, the query is silently redirected. Returns : A Bio::Seq object Args : database type - one of swiss, embl, genbank, genpept, or refseq =cut my $genbank_db = undef; my $genpept_db = undef; my $embl_db = undef; my $swiss_db = undef; my $refseq_db = undef; sub get_sequence{ my ($db_type,$identifier) = @_; if( ! $DBOKAY ) { confess ("Your system does not have one of LWP, HTTP::Request::Common, IO::String\n". "installed so the DB retrieval method is not available.\n". "Full error message is:\n $!\n"); return; } $db_type = lc($db_type); my $db; if( $db_type =~ /genbank/ ) { if( !defined $genbank_db ) { $genbank_db = Bio::DB::GenBank->new(); } $db = $genbank_db; } if( $db_type =~ /genpept/ ) { if( !defined $genpept_db ) { $genpept_db = Bio::DB::GenPept->new(); } $db = $genpept_db; } if( $db_type =~ /swiss/ ) { if( !defined $swiss_db ) { $swiss_db = Bio::DB::SwissProt->new(); } $db = $swiss_db; } if( $db_type =~ /embl/ ) { if( !defined $embl_db ) { $embl_db = Bio::DB::EMBL->new(); } $db = $embl_db; } if( $db_type =~ /refseq/ or ($db_type !~ /swiss/ and $identifier =~ /^\s*N\S+_/)) { if( !defined $refseq_db ) { $refseq_db = Bio::DB::RefSeq->new(); } $db = $refseq_db; } my $seq; if( $identifier =~ /^\w+\d+$/ ) { $seq = $db->get_Seq_by_acc($identifier); } else { $seq = $db->get_Seq_by_id($identifier); } return $seq; } =head2 translate Title : translate Usage : $seqobj = translate($seq_or_string_scalar) Function: translates a DNA sequence object OR just a plain string of DNA to amino acids Returns : A Bio::Seq object Args : Either a sequence object or a string of just DNA sequence characters =cut sub translate { my ($scalar) = shift; my $obj; if( ref $scalar ) { if( !$scalar->isa("Bio::PrimarySeqI") ) { confess("Expecting a sequence object not a $scalar"); } else { $obj= $scalar; } } else { # check this looks vaguely like DNA my $n = ( $scalar =~ tr/ATGCNatgcn/ATGCNatgcn/ ); if( $n < length($scalar) * 0.85 ) { confess("Sequence [$scalar] is less than 85% ATGCN, which doesn't look very DNA to me"); } $obj = Bio::PrimarySeq->new(-id => 'internalbioperlseq',-seq => $scalar); } return $obj->translate(); } =head2 translate_as_string Title : translate_as_string Usage : $seqstring = translate_as_string($seq_or_string_scalar) Function: translates a DNA sequence object OR just a plain string of DNA to amino acids Returns : A string of just amino acids Args : Either a sequence object or a string of just DNA sequence characters =cut sub translate_as_string { my ($scalar) = shift; my $obj = Bio::Perl::translate($scalar); return $obj->seq; } =head2 reverse_complement Title : reverse_complement Usage : $seqobj = reverse_complement($seq_or_string_scalar) Function: reverse complements a string or sequence argument producing a Bio::Seq - if you want a string, you can use reverse_complement_as_string Returns : A Bio::Seq object Args : Either a sequence object or a string of just DNA sequence characters =cut sub reverse_complement { my ($scalar) = shift; my $obj; if( ref $scalar ) { if( !$scalar->isa("Bio::PrimarySeqI") ) { confess("Expecting a sequence object not a $scalar"); } else { $obj= $scalar; } } else { # check this looks vaguely like DNA my $n = ( $scalar =~ tr/ATGCNatgcn/ATGCNatgcn/ ); if( $n < length($scalar) * 0.85 ) { confess("Sequence [$scalar] is less than 85% ATGCN, which doesn't look very DNA to me"); } $obj = Bio::PrimarySeq->new(-id => 'internalbioperlseq',-seq => $scalar); } return $obj->revcom(); } =head2 revcom Title : revcom Usage : $seqobj = revcom($seq_or_string_scalar) Function: reverse complements a string or sequence argument producing a Bio::Seq - if you want a string, you can use reverse_complement_as_string This is an alias for reverse_complement Returns : A Bio::Seq object Args : Either a sequence object or a string of just DNA sequence characters =cut sub revcom { return &Bio::Perl::reverse_complement(@_); } =head2 reverse_complement_as_string Title : reverse_complement_as_string Usage : $string = reverse_complement_as_string($seq_or_string_scalar) Function: reverse complements a string or sequence argument producing a string Returns : A string of DNA letters Args : Either a sequence object or a string of just DNA sequence characters =cut sub reverse_complement_as_string { my ($scalar) = shift; my $obj = &Bio::Perl::reverse_complement($scalar); return $obj->seq; } =head2 revcom_as_string Title : revcom_as_string Usage : $string = revcom_as_string($seq_or_string_scalar) Function: reverse complements a string or sequence argument producing a string Returns : A string of DNA letters Args : Either a sequence object or a string of just DNA sequence characters =cut sub revcom_as_string { my ($scalar) = shift; my $obj = &Bio::Perl::reverse_complement($scalar); return $obj->seq; } 1; BioPerl-1.007002/Bio/PhyloNetwork.pm000444000766000024 12734513155576320 17303 0ustar00cjfieldsstaff000000000000# # Module for Bio::PhyloNetwork # # Please direct questions and support issues to # # Cared for by Gabriel Cardona # # Copyright Gabriel Cardona, Gabriel Valiente # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PhyloNetwork - Module to compute with Phylogenetic Networks =head1 SYNOPSIS use Bio::PhyloNetwork; # Create a PhyloNetwork object from a eNewick string my $net1=Bio::PhyloNetwork->new( -eNewick=>'t0:((H1,(H2,l2)),H2); H1:((H3,l1)); H2:((H3,(l3,H1))); H3:(l4);' ); # Print all available data print $net1; # Rebuild $net1 from its mu_data my %mudata=$net1->mudata(); my $net2=Bio::PhyloNetwork->new(-mudata=>\%mudata,-numleaves=>4); print $net2; print "d=".$net1->mu_distance($net2)."\n"; # Get another one and compute distance my $net3=Bio::PhyloNetwork->new( -eNewick=>'(l2,((l1,(H1,l4)),H1))r; (l3)H1;' ); print "d=".$net1->mu_distance($net3)."\n"; # ...and find an optimal alignment w.r.t. the Manhattan distance (default) my ($weight,%alignment)=$net1->optimal_alignment($net3); print "weight:$weight\n"; foreach my $node1 (keys %alignment) { print "$node1 => ".$alignment{$node1}."\n"; } # ...or the Hamming distance my ($weightH,%alignmentH)=$net1->optimal_alignment($net3,-metric=>'Hamming'); print "weight:$weightH\n"; foreach my $node1 (keys %alignmentH) { print "$node1 => ".$alignmentH{$node1}."\n"; } # Test for time consistency of $net1 if ($net1->is_time_consistent) { print "net1 is time consistent\n" } else { print "net1 is not time consistent\n" } # create a network from the list of edges my $net4=Bio::PhyloNetwork->new(-edges=> [qw(r s r t s u s c t c t v u b u l3 u b v b v l4 b l2 c l1)]); # Test for time consistency of $net3 if ($net4->is_time_consistent) { print "net4 is time consistent\n" } else { print "net4 is not time consistent\n" } # And print all information on net4 print $net4; # Compute some tripartitions my %triparts=$net1->tripartitions(); # Now these are stored print $net1; # And can compute the tripartition error print "dtr=".$net1->tripartition_error($net3)."\n"; =head1 DESCRIPTION =head2 Phylogenetic Networks This is a module to work with phylogenetic networks. Phylogenetic networks have been studied over the last years as a richer model of the evolutionary history of sets of organisms than phylogenetic trees, because they take not only mutation events but also recombination and horizontal gene transfer events into account. The natural model for describing the evolutionary history of a set of sequences under recombination events is a DAG, hence this package relies on the package Graph::Directed to represent the underlying graph of a phylogenetic network. We refer the reader to [CRV1,CRV2] for formal definitions related to phylogenetic networks. =head2 eNewick description With this package, phylogenetic networks can be given by its eNewick string. This description appeared in other packages related to phylogenetic networks (see [PhyloNet] and [NetGen]); in fact, these two packages use different descriptions. The Bio::PhyloNetwork package allows both of them, but uses the second one in its output. The first approach [PhyloNet] goes as follows: For each hybrid node H, say with parents u_1,u_2,...,u_k and children v_1,v_2,...v_l: split H in k+1 different nodes; let each of the first k copies be a child of one of the u_1,...,u_k (one for each) and have no children (hence we will have k extra leaves); as for the last copy, let it have no parents and have v_1,...,v_l be its children. This way we get a forest; each of the trees will be rooted at either one root of the phylogenetic network or a hybrid node of it; the set of leaves (of the whole forest) will be the set of leaves of the original network together with the set of hybrid nodes (each of them repeated as many times as its in-degree). Then, the eNewick representation of the phylogenetic network will be the Newick representation of all the trees in the obtained forest, each of them with its root labeled. The second approach [NetGen] goes as follows: For each hybrid node H, say with parents u_1,u_2,...,u_k and children v_1,v_2,...v_l: split H in k different nodes; let the first copy be a child of u_1 and have all v_1,v_2,...v_l as its children; let the other copies be child of u_2,...,u_k (one for each) and have no children. This way, we get a tree whose set of leaves is the set of leaves of the original network together with the set of hybrid nodes (possibly repeated). Then the Newick string of the obtained tree (note that some internal nodes will be labeled and some leaves will be repeated) is the eNewick string of the phylogenetic network. For example, consider the network depicted below: r / \ / \ U V / \ / \ 1 \ / 3 H | 2 If the first approach is taken, we get the forest: r / \ / \ U V / \ / \ 1 H H 3 | H | 2 Hence, the eNewick string is '((1,H),(H,3))r; (2)H;'. As for the second one, one gets the tree: r / \ / \ U V / \ / \ 1 H | 3 H | 2 Hence, the eNewick string is '((1,H),((2)H,3))r;'. Note: when rooting a tree, this package allows the notations '(subtree,subtree,...)root' as well as 'root:(subtree,subtree,...)', but the first one is used when writing eNewick strings. =head2 Tree-child phylogenetic networks Tree-child (TC) phylogenetic networks are a special class of phylogenetic networks for which a distance, called mu-distance, is defined [CRV2] based on certain data (mu-data) associated to every node. Moreover, this distance extends the Robinson-Foulds on phylogenetic trees. This package allows testing for a phylogenetic network if it is TC and computes mu-distances between networks over the same set of leaves. Moreover, the mu-data allows one to define the optimal (in some precise sense) alignment between networks over the same set of leaves. This package also computes this optimal alignment. =head2 Tripartitions Although tripartitions (see [CRV1] and the references therein) do not allow to define distances, this package outputs tripartitions and computes a weak form of the tripartition error. =head2 Time-consistency Another useful property of Phylogenetic Networks that appears in the literature is that of time-consistency or real-time hybrids [BSS]. Roughly speaking, a network admits a temporal representation if it can be drawn in such a way that tree arcs (those whose end is a tree node) are inclined downwards, while hybridization arcs (those whose end is a hybrid node) are horizontal. This package checks for time-consistency and, if so, a temporal representation is provided. =head1 AUTHOR Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es Gabriel Valiente, valiente(at)lsi(dot)upc(dot)edu =head1 SEE ALSO =over =item [CRV1] G. Cardona, F. Rossello, G. Valiente. Tripartitions do not always discriminate phylogenetic networks. arXiv:0707.2376v1 [q-bio.PE] =item [CRV2] G. Cardona, F. Rossello, G. Valiente. A Distance Measure for Tree-Child Phylogenetic Networks. Preprint. =item [NetGen] M.M. Morin, and B.M.E. Moret. NetGen: generating phylogenetic networks with diploid hybrids. Bioinformatics 22 (2006), 1921-1923 =item [PhyloNet] PhyloNet: "Phylogenetic Networks Toolkit". http://bioinfo.cs.rice.edu/phylonet =item [BSS] M. Baroni, C. Semple, and M. Steel. Hybrids in Real Time. Syst. Biol. 55(1):46-56, 2006 =back =head1 APPENDIX The rest of the documentation details each of the object methods. =cut package Bio::PhyloNetwork; use strict; use warnings; use base qw(Bio::Root::Root); use Bio::PhyloNetwork::muVector; use Graph::Directed; use Bio::TreeIO; use Bio::Tree::Node; use IO::String; use Array::Compare; use Algorithm::Munkres; # Creator =head2 new Title : new Usage : my $obj = new Bio::PhyloNetwork(); Function: Creates a new Bio::PhyloNetwork object Returns : Bio::PhyloNetwork Args : none OR -eNewick => string OR -graph => Graph::Directed object OR -edges => reference to an array OR -tree => Bio::Tree::Tree object OR -mudata => reference to a hash, -leaves => reference to an array OR -mudata => reference to a hash, -numleaves => integer Returns a Bio::PhyloNetwork object, created according to the data given: =over 3 =item new() creates an empty network. =item new(-eNewick =E $str) creates the network whose Extended Newick representation (see description above) is the string $str. =item new(-graph =E $graph) creates the network with underlying graph given by the Graph::Directed object $graph =item new(-tree =E $tree) creates a network as a copy of the Bio::Tree::Tree object in $tree =item new(-mudata =E \%mudata, -leaves =E \@leaves) creates the network by reconstructing it from its mu-data stored in \%mudata and with set of leaves in \@leaves. =item new(-mudata =E \%mudata, -numleaves =E $numleaves) creates the network by reconstructing it from its mu-data stored in \%mudata and with set of leaves in ("l1".."l$numleaves"). =back =cut sub new { my ($pkg,@args)=@_; my $self=$pkg->SUPER::new(@args); my ($eNewick,$edgesR,$leavesR,$numleaves,$graph,$tree,$mudataR)= $self->_rearrange([qw(ENEWICK EDGES LEAVES NUMLEAVES GRAPH TREE MUDATA)],@args); bless($self,$pkg); $self->build_from_eNewick($eNewick) if defined $eNewick; $self->build_from_edges(@$edgesR) if defined $edgesR; $self->build_from_graph($graph) if defined $graph; $self->build_from_tree($tree) if defined $tree; if ((! defined $leavesR) && (defined $numleaves)) { my @leaves=map {"l$_"} (1..$numleaves); $leavesR=\@leaves; } $self->build_from_mudata($mudataR,$leavesR) if ((defined $mudataR) && (defined $leavesR)); return $self; } # Builders sub build_from_edges { my ($self,@edges)=@_; my $graph=Graph::Directed->new(); $graph->add_edges(@edges); $self->{graph}=$graph; $self->recompute(); my $labels={}; foreach my $node ($self->nodes()) { $labels->{$node}=$node; } $self->{labels}=$labels; } sub build_from_graph { my ($self,$graph)=@_; my $graphcp=$graph->copy(); $self->{graph}=$graphcp; $self->recompute(); my $labels={}; foreach my $node ($self->nodes()) { $labels->{$node}=$node; } $self->{labels}=$labels; } my $_eN_index; sub build_from_eNewick { my ($self,$string)=@_; $_eN_index=0; my $graph=Graph::Directed->new(); my $labels={}; my @blocks=split(/; */,$string); foreach my $block (@blocks) { my ($rt,$str)=get_root_and_subtree($block); my ($rtlbl,$rttype,$rtid,$rtlng)=get_label_type_id_length($rt); process_block($graph,$labels,$block,$rtid); $labels->{$rtid}=$rtlbl.''; } $self->{graph}=$graph; $self->{labels}=$labels; $self->recompute(); } sub process_block { my ($graph,$labels,$block,$rtid)=@_; my ($rt,$str)=get_root_and_subtree($block); my @substrs=my_split($str); foreach my $substr (@substrs) { my ($subrt,$subblock)=get_root_and_subtree($substr); my ($subrtlbl,$subrttype,$subrtid,$subrtlng)= get_label_type_id_length($subrt); if (! $subrtlng eq '') { $graph->add_weighted_edges($rtid,$subrtid,$subrtlng); } else { $graph->add_edges($rtid,$subrtid); } if (! $subrttype eq '') { $graph->set_edge_attribute($rtid,$subrtid,'type',$subrttype); } $subrtlbl.=''; # if (! $subrtlbl eq '') { if ((! defined $labels->{$subrtid})||($labels->{$subrtid} eq '')){ $labels->{$subrtid}=$subrtlbl; } elsif (( $labels->{$subrtid} ne $subrtlbl )&&($subrtlbl ne '')) { # error die("Different labels for the same node (".$labels->{$subrtid}." and $subrtlbl)"); } # } if ($subblock ne "") { process_block($graph,$labels,$subblock,$subrtid); } } } sub get_root_and_subtree { my ($block)=@_; my ($rt,$str)=("",""); # ($rt,$str)=split(/:|=/,$block); ($rt,$str)=split(/=/,$block); if ($rt eq $block) { # try to look for root label at the end my $pos=length($rt)-1; while ((substr($rt,$pos,1) ne ")") && ($pos >=0)) { $pos--; } $rt=substr($block,$pos+1,length($block)-$pos); $str=substr($block,0,$pos+1); } $rt=trim($rt); $str=trim($str); return ($rt,$str); } sub get_label_type_id_length { my ($string) = @_; $string.=''; # print "$string\n"; if (index($string,'#')==-1) { # no hybrid my ($label,$length)=split(':',$string); $label.=''; my $id; if ((! defined $label) || ($label eq '')) { # create id $_eN_index++; $id="T$_eN_index"; } else { $id=$label; } return ($label,'',$id,$length); } else { # hybrid my ($label,$string2)=split('#',$string); my ($typeid,$length)=split(':',$string2); my $type=$typeid; $type =~ s/\d//g; my $id=$typeid; $id =~ s/\D//g; return ($label,$type,'#'.$id,$length); } } sub trim { my ($string) = @_; $string =~ s/^\s+//; $string =~ s/\s+$//; return $string; } sub my_split { my ( $string ) = @_; my $temp=""; my @substrings; my $level=1; for my $i ( 1 .. length( $string ) ) { my $char=substr($string,$i,1); if ($char eq "(") { $level++; } if ($char eq ")") { if ($level==1) { push @substrings, $temp; $temp=""; } $level--; } if (($char eq ",") && ($level==1)) { push @substrings, $temp; $temp=""; $char=""; } $temp = $temp.$char; } return @substrings; } sub build_from_mudata { my ($self,$mus,$leavesR)=@_; my $graph=Graph::Directed->new(); my @nodes=keys %{$mus}; my @leaves=@{$leavesR}; my %seen; my @internal; @seen{@leaves} = (); foreach my $node (@nodes) { push(@internal, $node) unless exists $seen{$node}; } @internal=sort {$mus->{$b} <=> $mus->{$a} } @internal; @nodes=(@internal,@leaves); my $numnodes=@nodes; for (my $i=0;$i<$numnodes;$i++) { my $mu=$mus->{$nodes[$i]}; my $j=$i+1; while ($mu->is_positive() && $j<$numnodes) { if ($mu->geq_poset($mus->{$nodes[$j]})) { $graph->add_edges(($nodes[$i],$nodes[$j])); $mu = $mu - $mus->{$nodes[$j]}; } $j++; } } $self->build_from_graph($graph); } # sub relabel_tree { # my ($tree)=@_; # my $i=1; # my $j=1; # my $root=$tree->get_root_node(); # foreach my $node ($tree->get_nodes()) { # if ($node == $root) { # $node->{'_id'}="r"; # } # elsif (! $node->is_Leaf) { # $node->{'_id'}="t$i"; # $i++; # } # else { # if ($node->{'_id'} eq "") { # $node->{'_id'}="l$j"; # $j++; # } # } # } # return $tree; # } # sub build_subtree { # my ($graph,$root)=@_; # foreach my $child ($root->each_Descendent) { # $graph->add_edge($root->id,$child->id); # $graph=build_subtree($graph,$child); # } # return $graph; # } sub build_from_tree { my ($self,$tree)=@_; # relabel_tree($tree); # my $treeroot=$tree->get_root_node; # my $graph=Graph::Directed->new(); # $graph=build_subtree($graph,$treeroot); # $self->build_from_graph($graph); my $str; my $io=IO::String->new($str); my $treeio=Bio::TreeIO->new(-format => 'newick', -fh => $io); $treeio->write_tree($tree); # print "intern: $str\n"; $self->build_from_eNewick($str); } sub recompute { my ($self)=@_; $self->throw("Graph is not DAG:".$self->{graph}) unless $self->{graph}->is_dag(); my @leaves=$self->{graph}->successorless_vertices(); @leaves=sort @leaves; my $numleaves=@leaves; my @roots=$self->{graph}->predecessorless_vertices(); my $numroots=@roots; #$self->throw("Graph is not rooted") unless ($numroots == 1); my @nodes=$self->{graph}->vertices(); @nodes=sort @nodes; my $numnodes=@nodes; foreach my $node (@nodes) { if (! defined $self->{labels}->{$node}) { $self->{labels}->{$node}=''; } } $self->{leaves}=\@leaves; $self->{numleaves}=$numleaves; $self->{roots}=\@roots; $self->{numroots}=$numroots; $self->{nodes}=\@nodes; $self->{numnodes}=$numnodes; $self->{mudata}={}; $self->{h}={}; $self->compute_height(); $self->compute_mu(); return $self; } # Hybridizing sub is_attackable { my ($self,$u1,$v1,$u2,$v2)=@_; if ( $self->is_hybrid_node($v1) || $self->is_hybrid_node($v2) || $self->graph->is_reachable($v2,$u1) || (($u1 eq $u2)&&($v1 eq $v2)) || (! scalar grep {($_ ne $v2) && ($self->is_tree_node($_))} $self->graph->successors($u2))) { return 0; } return 1; } sub do_attack { my ($self,$u1,$v1,$u2,$v2,$lbl)=@_; my $graph=$self->{graph}; $graph->delete_edge($u1,$v1); $graph->delete_edge($u2,$v2); $graph->add_edge($u1,"T$lbl"); $graph->add_edge("T$lbl",$v1); $graph->add_edge($u2,"#H$lbl"); $graph->add_edge("#H$lbl",$v2); $graph->add_edge("T$lbl","#H$lbl"); $self->build_from_graph($graph); } # Computation of mu-data sub compute_mu { my ($self)=@_; my $graph=$self->{graph}; my $mudata=$self->{mudata}; my @leaves=@{$self->{leaves}}; my $numleaves=$self->{numleaves}; for (my $i=0;$i<$numleaves;$i++) { my $vec=Bio::PhyloNetwork::muVector->new($numleaves); $vec->[$i]=1; $mudata->{$leaves[$i]}=$vec; } my $h=1; while (my @nodes=grep {$self->{h}->{$_} == $h} @{$self->{nodes}} ) { foreach my $u (@nodes) { my $vec=Bio::PhyloNetwork::muVector->new($numleaves); foreach my $son ($graph->successors($u)) { $vec+=$mudata->{$son}; } $mudata->{$u}=$vec; } $h++; } } sub compute_height { my ($self)=@_; my $graph=$self->{graph}; my @leaves=@{$self->{leaves}}; foreach my $leaf (@leaves) { $self->{h}->{$leaf}=0; } my $h=0; while (my @nodes=grep {(defined $self->{h}->{$_})&&($self->{h}->{$_} == $h)} @{$self->{nodes}} ) { foreach my $node (@nodes) { foreach my $parent ($graph->predecessors($node)) { $self->{h}->{$parent}=$h+1; } } $h++; } } # Tests =head2 is_leaf Title : is_leaf Usage : my $b=$net->is_leaf($u) Function: tests if $u is a leaf in $net Returns : boolean Args : scalar =cut sub is_leaf { my ($self,$node)=@_; if ($self->{graph}->out_degree($node) == 0) {return 1;} return 0; } =head2 is_root Title : is_root Usage : my $b=$net->is_root($u) Function: tests if $u is the root of $net Returns : boolean Args : scalar =cut sub is_root { my ($self,$node)=@_; if ($self->{graph}->in_degree($node) == 0) {return 1;} return 0; } =head2 is_tree_node Title : is_tree_node Usage : my $b=$net->is_tree_node($u) Function: tests if $u is a tree node in $net Returns : boolean Args : scalar =cut sub is_tree_node { my ($self,$node)=@_; if ($self->{graph}->in_degree($node) <= 1) {return 1;} return 0; } =head2 is_hybrid_node Title : is_hybrid_node Usage : my $b=$net->is_hybrid_node($u) Function: tests if $u is a hybrid node in $net Returns : boolean Args : scalar =cut sub is_hybrid_node { my ($self,$node)=@_; if ($self->{graph}->in_degree($node) > 1) {return 1;} return 0; } sub has_tree_child { # has_tree_child(g,u) returns 1 if u has a tree child in graph g # and 0 otherwise my $g=shift(@_); my $node=shift(@_); my @Sons=$g->successors($node); foreach my $son (@Sons) { if ($g->in_degree($son)==1) { return 1; } } return 0; } =head2 is_tree_child Title : is_tree_child Usage : my $b=$net->is_tree_child() Function: tests if $net is a Tree-Child phylogenetic network Returns : boolean Args : Bio::PhyloNetwork =cut sub is_tree_child { my ($self)=@_; if (defined $self->{is_tree_child}) { return $self->{is_tree_child}; } $self->{is_tree_child}=0; my $graph=$self->{graph}; foreach my $node (@{$self->{nodes}}) { return 0 unless ($graph->out_degree($node)==0 || has_tree_child($graph,$node)); } $self->{is_tree_child}=1; return 1; } # Accessors =head2 nodes Title : nodes Usage : my @nodes=$net->nodes() Function: returns the set of nodes of $net Returns : array Args : none =cut sub nodes { my ($self)=@_; return @{$self->{nodes}}; } =head2 leaves Title : leaves Usage : my @leaves=$net->leaves() Function: returns the set of leaves of $net Returns : array Args : none =cut sub leaves { my ($self)=@_; return @{$self->{leaves}}; } =head2 roots Title : roots Usage : my @roots=$net->roots() Function: returns the set of roots of $net Returns : array Args : none =cut sub roots { my ($self)=@_; return @{$self->{roots}}; } =head2 internal_nodes Title : internal_nodes Usage : my @internal_nodes=$net->internal_nodes() Function: returns the set of internal nodes of $net Returns : array Args : none =cut sub internal_nodes { my ($self)=@_; return grep {! $self->is_leaf($_)} $self->nodes(); } =head2 tree_nodes Title : tree_nodes Usage : my @tree_nodes=$net->tree_nodes() Function: returns the set of tree nodes of $net Returns : array Args : none =cut sub tree_nodes { my ($self)=@_; return grep {$self->is_tree_node($_)} $self->nodes(); } =head2 hybrid_nodes Title : hybrid_nodes Usage : my @hybrid_nodes=$net->hybrid_nodes() Function: returns the set of hybrid nodes of $net Returns : array Args : none =cut sub hybrid_nodes { my ($self)=@_; return grep {$self->is_hybrid_node($_)} $self->nodes(); } =head2 graph Title : graph Usage : my $graph=$net->graph() Function: returns the underlying graph of $net Returns : Graph::Directed Args : none =cut sub graph { my ($self)=@_; return $self->{graph}; } =head2 edges Title : edges Usage : my @edges=$net->edges() Function: returns the set of edges of $net Returns : array Args : none Each element in the array is an anonimous array whose first element is the head of the edge and the second one is the tail. =cut sub edges { my ($self)=@_; return $self->{graph}->edges(); } =head2 tree_edges Title : tree_edges Usage : my @tree_edges=$net->tree_edges() Function: returns the set of tree edges of $net (those whose tail is a tree node) Returns : array Args : none =cut sub tree_edges { my ($self)=@_; return grep {$self->is_tree_node($_->[1])} $self->edges(); } =head2 hybrid_edges Title : hybrid_edges Usage : my @hybrid_edges=$net->hybrid_edges() Function: returns the set of hybrid edges of $net (those whose tail is a hybrid node) Returns : array Args : none =cut sub hybrid_edges { my ($self)=@_; return grep {$self->is_hybrid_node($_->[1])} $self->edges(); } =head2 explode Title : explode Usage : my @trees=$net->explode() Function: returns the representation of $net by a set of Bio::Tree:Tree objects Returns : array Args : none =cut sub explode { my ($self)=@_; my @trees; $self->explode_rec(\@trees); return @trees; } sub explode_rec { my ($self,$trees)=@_; my @h = $self->hybrid_nodes; if (scalar @h) { my $v = shift @h; for my $u ($self->{graph}->predecessors($v)) { $self->{graph}->delete_edge($u,$v); $self->explode_rec($trees); $self->{graph}->add_edge($u,$v); } } else { my $io = IO::String->new($self->eNewick); my $treeio = Bio::TreeIO->new(-format => 'newick', -fh => $io); my $tree = $treeio->next_tree; $tree->contract_linear_paths; push @{$trees}, $tree; } } =head2 mudata Title : mudata Usage : my %mudata=$net->mudata() Function: returns the representation of $net by its mu-data Returns : hash Args : none $net-Emudata() returns a hash with keys the nodes of $net and each value is a muVector object holding its mu-vector. =cut sub mudata { my ($self)=@_; return %{$self->{mudata}}; } sub mudata_node { my ($self,$u)=@_; return $self->{mudata}{$u}; } =head2 heights Title : heights Usage : my %heights=$net->heights() Function: returns the heights of the nodes of $net Returns : hash Args : none $net-Eheights() returns a hash with keys the nodes of $net and each value is its height. =cut sub heights { my ($self)=@_; return %{$self->{h}}; } sub height_node { my ($self,$u)=@_; return $self->{h}{$u}; } =head2 mu_distance Title : mu_distance Usage : my $dist=$net1->mu_distance($net2) Function: Computes the mu-distance between the networks $net1 and $net2 on the same set of leaves Returns : scalar Args : Bio::PhyloNetwork =cut sub mu_distance { my ($net1,$net2)=@_; my @nodes1=$net1->nodes; my @nodes2=$net2->nodes; my $comp = Array::Compare->new; $net1->throw("Cannot compare phylogenetic networks on different set of leaves") unless $comp->compare($net1->{leaves},$net2->{leaves}); $net1->warn("Not a tree-child phylogenetic network") unless $net1->is_tree_child(); $net2->warn("Not a tree-child phylogenetic network") unless $net2->is_tree_child(); my @leaves=@{$net1->{leaves}}; my %matched1; my %matched2; OUTER: foreach my $node1 (@nodes1) { foreach my $node2 (@nodes2) { if ( (! exists $matched1{$node1}) && (! exists $matched2{$node2}) && ($net1->{mudata}{$node1} == $net2->{mudata}{$node2}) ) { $matched1{$node1}=$node2; $matched2{$node2}=$node1; next OUTER; } } } return (scalar @nodes1)+(scalar @nodes2)-2*(scalar keys %matched1); } =head2 mu_distance_generalized Title : mu_distance_generalized Usage : my $dist=$net1->mu_distance($net2) Function: Computes the mu-distance between the topological restrictions of networks $net1 and $net2 on its common set of leaves Returns : scalar Args : Bio::PhyloNetwork =cut sub mu_distance_generalized { my ($net1,$net2)=@_; my ($netr1,$netr2)=$net1->topological_restriction($net2); return $netr1->mu_distance($netr2); } # mudata_string (code mu_data in a string; useful for isomorphism testing) sub mudata_string_node { my ($self,$u)=@_; return $self->{mudata}->{$u}->display(); } sub mudata_string { my ($self)=@_; return $self->{mudata_string} if defined $self->{mudata_string}; my @internal=$self->internal_nodes; my $mus=$self->{mudata}; @internal=sort {$mus->{$b} <=> $mus->{$a} } @internal; my $str=""; foreach my $node (@internal) { $str=$str.$self->mudata_string_node($node); } $self->{mudata_string}=$str; return $str; } sub is_mu_isomorphic { my ($net1,$net2)=@_; return ($net1->mudata_string() eq $net2->mudata_string()); } # tripartitions sub compute_tripartition_node { my ($self,$u)=@_; $self->warn("Cannot compute tripartitions on unrooted networks. Will assume one at random") unless ($self->{numroots} == 1); my $root=$self->{roots}->[0]; my $graph=$self->{graph}; my $graphPruned=$graph->copy(); $graphPruned->delete_vertex($u); my $tripartition=""; foreach my $leaf (@{$self->{leaves}}) { my $type; if ($graph->is_reachable($u,$leaf)) { if ($graphPruned->is_reachable($root,$leaf)) {$type="B";} else {$type="A";} } else {$type="C";} $tripartition .= $type; } $self->{tripartitions}->{$u}=$tripartition; } sub compute_tripartitions { my ($self)=@_; foreach my $node (@{$self->{nodes}}) { $self->compute_tripartition_node($node); } } =head2 tripartitions Title : tripartitions Usage : my %tripartitions=$net->tripartitions() Function: returns the set of tripartitions of $net Returns : hash Args : none $net-Etripartitions() returns a hash with keys the nodes of $net and each value is a string representing the tripartition of the leaves induced by the node. A string "BCA..." associated with a node u (e.g.) means, the first leaf is in the set B(u), the second one in C(u), the third one in A(u), and so on. =cut sub tripartitions { my ($self)=@_; $self->compute_tripartitions() unless defined $self->{tripartitions}; return %{$self->{tripartitions}}; } # to do: change to tri_distance and test for TC and time-cons sub tripartition_error { my ($net1,$net2)=@_; my $comp = Array::Compare->new; $net1->throw("Cannot compare phylogenetic networks on different set of leaves") unless $comp->compare($net1->{leaves},$net2->{leaves}); $net1->warn("Not a tree-child phylogenetic network") unless $net1->is_tree_child(); $net2->warn("Not a tree-child phylogenetic network") unless $net2->is_tree_child(); $net1->warn("Not a time-consistent network") unless $net1->is_time_consistent(); $net2->warn("Not a time-consistent network") unless $net2->is_time_consistent(); $net1->compute_tripartitions() unless defined $net1->{tripartitions}; $net2->compute_tripartitions() unless defined $net2->{tripartitions}; my @edges1=$net1->{graph}->edges(); my @edges2=$net2->{graph}->edges(); my ($FN,$FP)=(0,0); foreach my $edge1 (@edges1) { my $matched=0; foreach my $edge2 (@edges2) { if ($net1->{tripartitions}->{$edge1->[1]} eq $net2->{tripartitions}->{$edge2->[1]}) { $matched=1; last; } } if (! $matched) {$FN++;} } foreach my $edge2 (@edges2) { my $matched=0; foreach my $edge1 (@edges1) { if ($net1->{tripartitions}->{$edge1->[1]} eq $net2->{tripartitions}->{$edge2->[1]}) { $matched=1; last; } } if (! $matched) {$FP++;} } return ($FN/(scalar @edges1)+$FP/(scalar @edges2))/2; } # Time-consistency # to do: add weak time consistency =head2 is_time_consistent Title : is_time_consistent Usage : my $b=$net->is_time_consistent() Function: tests if $net is (strong) time-consistent Returns : boolean Args : none =cut sub is_time_consistent { my ($self)=@_; $self->compute_temporal_representation() unless exists $self->{has_temporal_representation}; return $self->{has_temporal_representation}; } =head2 temporal_representation Title : temporal_representation Usage : my %time=$net->temporal_representation() Function: returns a hash containing a temporal representation of $net, or 0 if $net is not time-consistent Returns : hash Args : none =cut sub temporal_representation { my ($self)=@_; if ($self->is_time_consistent) { return %{$self->{temporal_representation}}; } return 0; } sub compute_temporal_representation { my ($self)=@_; my $quotient=Graph::Directed->new(); my $classes=find_classes($self); my %repr; map {$repr{$_}=$classes->{$_}[0]} $self->nodes(); foreach my $e ($self->tree_edges()) { $quotient->add_edge($repr{$e->[0]},$repr{$e->[1]}); } my %temp; my $depth=0; while ($quotient->vertices()) { if (my @svs=$quotient->predecessorless_vertices()) { foreach my $sv (@svs) { $temp{$sv}=$depth; } $quotient->delete_vertices(@svs); } else { return 0; } $depth++; } foreach my $node (@{$self->{nodes}}) { $temp{$node}=$temp{$repr{$node}} } $self->{temporal_representation}=\%temp; $self->{has_temporal_representation}=1; } sub find_classes { my ($self)=@_; my $classes={}; map {$classes->{$_}=[$_]} $self->nodes(); foreach my $e ($self->hybrid_edges()) { $classes=join_classes($classes,$e->[0],$e->[1]); } return $classes; } sub join_classes { my ($classes,$u,$v)=@_; my @clu=@{$classes->{$u}}; my @clv=@{$classes->{$v}}; my @cljoin=(@clu,@clv); map {$classes->{$_}=\@cljoin} @cljoin; return $classes; } # alignment =head2 contract_elementary Title : contract_elementary Usage : my ($contracted,$blocks)=$net->contract_elementary(); Function: Returns the network $contracted, obtained by contracting elementary paths of $net into edges. The reference $blocks points to a hash where, for each node of $contracted, gives the corresponding nodes of $net that have been deleted. Returns : Bio::PhyloNetwork,reference to hash Args : none =cut sub contract_elementary { my ($self)=@_; my $contracted=$self->graph->copy(); my @nodes=$self->nodes(); my $mus=$self->{mudata}; my $hs=$self->{h}; my %blocks; foreach my $u (@nodes) { $blocks{$u}=[$u]; } my @elementary=grep { $contracted->out_degree($_) == 1} $self->tree_nodes(); @elementary=sort {$mus->{$b} <=> $mus->{$a} || $hs->{$b} <=> $hs->{$a}} @elementary; foreach my $elem (@elementary) { my @children=$contracted->successors($elem); my $child=$children[0]; if ($contracted->in_degree($elem) == 1) { my @parents=$contracted->predecessors($elem); my $parent=$parents[0]; $contracted->add_edge($parent,$child); } $contracted->delete_vertex($elem); my @blch=@{$blocks{$child}}; my @blem=@{$blocks{$elem}}; $blocks{$child}=[@blem,@blch]; delete $blocks{$elem}; } my $contr=Bio::PhyloNetwork->new(-graph => $contracted); return $contr,\%blocks; } =head2 optimal_alignment Title : optimal_alignment Usage : my ($weight,$alignment,$wgts)=$net->optimal_alignment($net2) Function: returns the total weight of an optimal alignment, the alignment itself, and partial weights between the networks $net1 and $net2 on the same set of leaves. An optional argument allows one to use the Manhattan (default) or the Hamming distance between mu-vectors. Returns : scalar,reference to hash,reference to hash Args : Bio::PhyloNetwork, -metric => string (optional) Supported strings for the -metric parameter are 'Manhattan' or 'Hamming'. =cut sub optimal_alignment { my ($net1,$net2,%params)=@_; my ($net1cont,$blocks1)=contract_elementary($net1); my ($net2cont,$blocks2)=contract_elementary($net2); my ($wc,$alignc,$weightc)= optimal_alignment_noelementary($net1cont,$net2cont,%params); my %alignment=(); my $totalweigth=0; my %weigths=(); foreach my $u1 (keys %$alignc) { my $u2=$alignc->{$u1}; my @block1=@{$blocks1->{$u1}}; my @block2=@{$blocks2->{$u2}}; while (@block1 && @block2) { my $u1dc=pop @block1; my $u2dc=pop @block2; $alignment{$u1dc}=$u2dc; $weigths{$u1dc}=$weightc->{$u1}; $totalweigth+=$weigths{$u1dc}; } } return $totalweigth,\%alignment,\%weigths; } sub optimal_alignment_noelementary { my ($net1,$net2,%params)=@_; my $comp = Array::Compare->new; $net1->throw("Cannot align phylogenetic networks on different set of leaves") unless $comp->compare($net1->{leaves},$net2->{leaves}); my $distance; if ((defined $params{-metric})and ($params{-metric} eq 'Hamming')) { $distance='Hamming'; } else { $distance='Manhattan'; } my $numleaves=$net1->{numleaves}; my @nodes1=$net1->internal_nodes(); my @nodes2=$net2->internal_nodes(); my $numnodes1=@nodes1; my $numnodes2=@nodes2; my @matrix=(); for (my $i=0;$i<$numnodes1;$i++) { my @row=(); for (my $j=0;$j<$numnodes2;$j++) { push @row,weight($net1,$nodes1[$i],$net2,$nodes2[$j],$distance); } push @matrix,\@row; } my @alignment=(); Algorithm::Munkres::assign(\@matrix,\@alignment); my %alignmenthash; my %weighthash; my $totalw=0; foreach my $leaf (@{$net1->{leaves}}) { $alignmenthash{$leaf}=$leaf; $weighthash{$leaf}=0; } for (my $i=0;$i<$numnodes1;$i++) { if (defined $nodes2[$alignment[$i]]) { $alignmenthash{$nodes1[$i]}=$nodes2[$alignment[$i]]; $weighthash{$nodes1[$i]}=$matrix[$i][$alignment[$i]]; $totalw += $matrix[$i][$alignment[$i]]; } } return $totalw,\%alignmenthash,\%weighthash; } =head2 optimal_alignment_generalized Title : optimal_alignment_generalized Usage : my ($weight,%alignment)=$net->optimal_alignment_generalized($net2) Function: returns the wieght of an optimal alignment, and the alignment itself, between the topological restriction of the networks $net1 and $net2 on the set of common leaves. An optional argument allows one to use the Manhattan (default) or the Hamming distance between mu-vectors. Returns : scalar,hash Args : Bio::PhyloNetwork, -metric => string (optional) Supported strings for the -metric parameter are 'Manhattan' or 'Hamming'. =cut sub optimal_alignment_generalized { my ($net1,$net2,%params)=@_; my ($netr1,$netr2)=$net1->topological_restriction($net2); return $netr1->optimal_alignment($netr2,%params); } sub weight { my ($net1,$v1,$net2,$v2,$distance)=@_; my $w; if (! defined $distance) { $distance='Manhattan'; } if ($distance eq 'Hamming') { $w=$net1->{mudata}->{$v1}->hamming($net2->{mudata}->{$v2}); } else { $w=$net1->{mudata}->{$v1}->manhattan($net2->{mudata}->{$v2}); } if (($net1->is_tree_node($v1) && $net2->is_hybrid_node($v2)) || ($net2->is_tree_node($v2) && $net1->is_hybrid_node($v1)) ) { $w +=1/(2*$net1->{numleaves}); } return $w; } =head2 topological_restriction Title : topological_restriction Usage : my ($netr1,$netr2)=$net1->topological_restriction($net2) Function: returns the topological restriction of $net1 and $net2 on its common set of leaves Returns : Bio::PhyloNetwork, Bio::PhyloNetwork Args : Bio::PhyloNetwork =cut sub topological_restriction { my ($net1,$net2)=@_; my @leaves1=$net1->leaves(); my @leaves2=$net2->leaves(); my $numleaves1=scalar @leaves1; my $numleaves2=scalar @leaves2; my %position1; for (my $i=0; $i<$numleaves1; $i++) { $position1{$leaves1[$i]}=$i; } my %position2; my @commonleaves=(); for (my $j=0; $j<$numleaves2; $j++) { if (defined $position1{$leaves2[$j]}) { push @commonleaves,$leaves2[$j]; $position2{$leaves2[$j]}=$j; } } my $graphred1=$net1->{graph}->copy(); my $graphred2=$net2->{graph}->copy(); OUTER1: foreach my $u ($graphred1->vertices()) { my $mu=$net1->mudata_node($u); foreach my $leaf (@commonleaves) { if ($mu->[$position1{$leaf}]>0) { next OUTER1; } } $graphred1->delete_vertex($u); } OUTER2: foreach my $u ($graphred2->vertices()) { my $mu=$net2->mudata_node($u); foreach my $leaf (@commonleaves) { if ($mu->[$position2{$leaf}]>0) { next OUTER2; } } $graphred2->delete_vertex($u); } my $netr1=Bio::PhyloNetwork->new(-graph => $graphred1); my $netr2=Bio::PhyloNetwork->new(-graph => $graphred2); return ($netr1,$netr2); } # Functions for eNewick representation =head2 eNewick Title : eNewick Usage : my $str=$net->eNewick() Function: returns the eNewick representation of $net without labeling internal tree nodes Returns : string Args : none =cut sub eNewick { my ($self)=@_; my $str=""; my $seen={}; foreach my $root ($self->roots()) { $str=$str.$self->eNewick_aux($root,$seen,undef)."; "; } return $str; } sub eNewick_aux { my ($self,$node,$seen,$parent)=@_; my $str=''; if ($self->is_leaf($node) || (defined $seen->{$node}) ) { $str=make_label($self,$parent,$node); } else { $seen->{$node}=1; my @sons=$self->{graph}->successors($node); $str="("; foreach my $son (@sons) { $str=$str.$self->eNewick_aux($son,$seen,$node).","; } chop($str); $str.=")".make_label($self,$parent,$node); } return $str; } sub make_label { my ($self,$parent,$node)=@_; my $str=''; if ($self->is_hybrid_node($node)) { my $lbl=$self->{labels}->{$node}; if ($lbl =~ /#/) { $lbl=''; } $str.=$lbl; #$self->{labels}->{$node}; $str.='#'; if ((defined $parent) && ($self->graph->has_edge_attribute($parent,$node,'type'))) { $str.=$self->graph->get_edge_attribute($parent,$node,'type'); } $str.=substr $node,1; } else { $str.=$self->{labels}->{$node}; } if ((defined $parent) && ($self->graph->has_edge_weight($parent,$node))) { $str.=":".$self->graph->get_edge_weight($parent,$node); } return $str; } =head2 eNewick_full Title : eNewick_full Usage : my $str=$net->eNewick_full() Function: returns the eNewick representation of $net labeling internal tree nodes Returns : string Args : none =cut sub eNewick_full { my ($self)=@_; my $str=""; my $seen={}; foreach my $root ($self->roots()) { $str=$str.$self->eNewick_full_aux($root,$seen,undef)."; "; } return $str; } sub eNewick_full_aux { my ($self,$node,$seen,$parent)=@_; my $str=''; if ($self->is_leaf($node) || (defined $seen->{$node}) ) { $str=make_label_full($self,$parent,$node); } else { $seen->{$node}=1; my @sons=$self->{graph}->successors($node); $str="("; foreach my $son (@sons) { $str=$str.$self->eNewick_full_aux($son,$seen,$node).","; } chop($str); $str.=")".make_label_full($self,$parent,$node); } return $str; } sub make_label_full { my ($self,$parent,$node)=@_; my $str=''; if ($self->is_hybrid_node($node)) { my $lbl=$self->{labels}->{$node}; if ($lbl =~ /#/) { $lbl=''; } $str.=$lbl; #$self->{labels}->{$node}; $str.='#'; if ((defined $parent) && ($self->graph->has_edge_attribute($parent,$node,'type'))) { $str.=$self->graph->get_edge_attribute($parent,$node,'type'); } $str.=substr $node,1; } else { if ((defined $self->{labels}->{$node})&&($self->{labels}->{$node} ne '')) { $str.=$self->{labels}->{$node}; } else { $str.=$node; } } if ((defined $parent) && ($self->graph->has_edge_weight($parent,$node))) { $str.=":".$self->graph->get_edge_weight($parent,$node); } return $str; } # sub eNewick_full { # my ($self)=@_; # my $str=""; # my $seen={}; # foreach my $root ($self->roots()) { # $str=$str.$self->eNewick_full_aux($root,$seen,undef)."; "; # } # return $str; # } # sub eNewick_full_aux { # my ($self,$node,$seen,$parent)=@_; # my $str; # if ($self->is_leaf($node) || # (defined $seen->{$node}) ) # { # if ($self->is_hybrid_node($node)) { # my $tag=substr $node,1; # if ((defined $parent) && # ($self->graph->has_edge_attribute($parent,$node,'type'))) { # $str='#'.$self->graph->get_edge_attribute($parent,$node,'type').$tag; # } else { # $str=$node; # } # } else { # $str=$node; # } # } # else { # $seen->{$node}=1; # my @sons=$self->{graph}->successors($node); # $str="("; # foreach my $son (@sons) { # $str=$str.$self->eNewick_full_aux($son,$seen,$node).","; # } # chop($str); # if ($self->is_hybrid_node($node)) { # my $tag=substr $node,1; # if ((defined $parent) && # ($self->graph->has_edge_attribute($parent,$node,'type'))) { # $str.=')#'.$self->graph->get_edge_attribute($parent,$node,'type').$tag; # } else { # $str.=")$node"; # } # } else { # $str.=")$node"; # } # } # if ((defined $parent) && # ($self->graph->has_edge_weight($parent,$node))) { # $str.=":".$self->graph->get_edge_weight($parent,$node); # } # return $str; # } # displaying data use overload '""' => \&display; =head2 display Title : display Usage : my $str=$net->display() Function: returns a string containing all the available information on $net Returns : string Args : none =cut sub display { my ($self)=@_; my $str=""; my $graph=$self->{graph}; my @leaves=$self->leaves(); my @nodes=@{$self->{nodes}}; $str.= "Leaves:\t@leaves\n"; $str.= "Nodes:\t@nodes\n"; $str.= "Graph:\t$graph\n"; $str.= "eNewick:\t".$self->eNewick()."\n"; $str.= "Full eNewick:\t".$self->eNewick_full()."\n"; $str.= "Mu-data and heights:\n"; foreach my $node (@nodes) { $str.= "v=$node: "; if (exists $self->{labels}->{$node}) { $str.="\tlabel=".$self->{labels}->{$node}.","; } else { $str.="\tlabel=(none),"; } $str.= "\th=".$self->{h}->{$node}.", \tmu=".$self->{mudata}->{$node}."\n"; } if (exists $self->{has_temporal_representation}) { $str.= "Temporal representation:\n"; if ($self->{has_temporal_representation}) { foreach my $node (@nodes) { $str.= "v=$node; "; $str.= "\tt=".$self->{temporal_representation}->{$node}."\n"; } } else { $str.= "Does not exist.\n"; } } if (exists $self->{tripartitions}) { $str.= "Tripartitions:\n"; foreach my $node (@nodes) { $str.= "v=$node; "; $str.= "\ttheta=".$self->{tripartitions}->{$node}."\n"; } } return $str; } 1; BioPerl-1.007002/Bio/PrimarySeq.pm000444000766000024 7465013155576320 16712 0ustar00cjfieldsstaff000000000000# # bioperl module for Bio::PrimarySeq # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PrimarySeq - Bioperl lightweight sequence object =head1 SYNOPSIS # Bio::SeqIO for file reading, Bio::DB::GenBank for # database reading use Bio::Seq; use Bio::SeqIO; use Bio::DB::GenBank; # make from memory $seqobj = Bio::PrimarySeq->new ( -seq => 'ATGGGGTGGGCGGTGGGTGGTTTG', -id => 'GeneFragment-12', -accession_number => 'X78121', -alphabet => 'dna', -is_circular => 1, ); print "Sequence ", $seqobj->id(), " with accession ", $seqobj->accession_number, "\n"; # read from file $inputstream = Bio::SeqIO->new( -file => "myseq.fa", -format => 'Fasta', ); $seqobj = $inputstream->next_seq(); print "Sequence ", $seqobj->id(), " and desc ", $seqobj->desc, "\n"; # to get out parts of the sequence. print "Sequence ", $seqobj->id(), " with accession ", $seqobj->accession_number, " and desc ", $seqobj->desc, "\n"; $string = $seqobj->seq(); $string2 = $seqobj->subseq(1,40); =head1 DESCRIPTION PrimarySeq is a lightweight sequence object, storing the sequence, its name, a computer-useful unique name, and other fundamental attributes. It does not contain sequence features or other information. To have a sequence with sequence features you should use the Seq object which uses this object. Although new users will use Bio::PrimarySeq a lot, in general you will be using it from the Bio::Seq object. For more information on Bio::Seq see L. For interest you might like to know that Bio::Seq has-a Bio::PrimarySeq and forwards most of the function calls to do with sequence to it (the has-a relationship lets us get out of a otherwise nasty cyclical reference in Perl which would leak memory). Sequence objects are defined by the Bio::PrimarySeqI interface, and this object is a pure Perl implementation of the interface. If that's gibberish to you, don't worry. The take home message is that this object is the bioperl default sequence object, but other people can use their own objects as sequences if they so wish. If you are interested in wrapping your own objects as compliant Bioperl sequence objects, then you should read the Bio::PrimarySeqI documentation The documentation of this object is a merge of the Bio::PrimarySeq and Bio::PrimarySeqI documentation. This allows all the methods which you can call on sequence objects here. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::PrimarySeq; use strict; our $MATCHPATTERN = 'A-Za-z\-\.\*\?=~'; our $GAP_SYMBOLS = '-~'; use base qw(Bio::Root::Root Bio::PrimarySeqI Bio::IdentifiableI Bio::DescribableI); # Setup the allowed values for alphabet() my %valid_type = map {$_, 1} qw( dna rna protein ); =head2 new Title : new Usage : $seqobj = Bio::PrimarySeq->new( -seq => 'ATGGGGGTGGTGGTACCCT', -id => 'human_id', -accession_number => 'AL000012', ); Function: Returns a new primary seq object from basic constructors, being a string for the sequence and strings for id and accession_number. Note that you can provide an empty sequence string. However, in this case you MUST specify the type of sequence you wish to initialize by the parameter -alphabet. See alphabet() for possible values. Returns : a new Bio::PrimarySeq object Args : -seq => sequence string -ref_to_seq => ... or reference to a sequence string -display_id => display id of the sequence (locus name) -accession_number => accession number -primary_id => primary id (Genbank id) -version => version number -namespace => the namespace for the accession -authority => the authority for the namespace -description => description text -desc => alias for description -alphabet => skip alphabet guess and set it to dna, rna or protein -id => alias for display id -is_circular => boolean to indicate that sequence is circular -direct => boolean to directly set sequences. The next time -seq, seq() or -ref_to_seq is use, the sequence will not be validated. Be careful with this... -nowarnonempty => boolean to avoid warning when sequence is empty =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($seq, $id, $acc, $pid, $ns, $auth, $v, $oid, $desc, $description, $alphabet, $given_id, $is_circular, $direct, $ref_to_seq, $len, $nowarnonempty) = $self->_rearrange([qw(SEQ DISPLAY_ID ACCESSION_NUMBER PRIMARY_ID NAMESPACE AUTHORITY VERSION OBJECT_ID DESC DESCRIPTION ALPHABET ID IS_CIRCULAR DIRECT REF_TO_SEQ LENGTH NOWARNONEMPTY )], @args); # Private var _nowarnonempty, needs to be set before calling _guess_alphabet $self->{'_nowarnonempty'} = $nowarnonempty; $self->{'_direct'} = $direct; if( defined $id && defined $given_id ) { if( $id ne $given_id ) { $self->throw("Provided both id and display_id constructors: [$id] [$given_id]"); } } if( defined $given_id ) { $id = $given_id; } # Bernd's idea: set ids now for more informative invalid sequence messages defined $id && $self->display_id($id); $acc && $self->accession_number($acc); defined $pid && $self->primary_id($pid); # Set alphabet now to avoid guessing it later, when sequence is set $alphabet && $self->alphabet($alphabet); # Set the length before the seq. If there is a seq, length will be updated later $self->{'length'} = $len || 0; # Set the sequence (but also alphabet and length) if ($ref_to_seq) { $self->_set_seq_by_ref($ref_to_seq, $alphabet); } else { if (defined $seq) { # Note: the sequence string may be empty $self->seq($seq); } } $desc && $self->desc($desc); $description && $self->description($description); $ns && $self->namespace($ns); $auth && $self->authority($auth); # Any variable that can have a value "0" must be tested with defined # or it will fail to be added to the new object defined($v) && $self->version($v); defined($oid) && $self->object_id($oid); defined($is_circular) && $self->is_circular($is_circular); return $self; } =head2 seq Title : seq Usage : $string = $seqobj->seq(); Function: Get or set the sequence as a string of letters. The case of the letters is left up to the implementer. Suggested cases are upper case for proteins and lower case for DNA sequence (IUPAC standard), but you should not rely on this. An error is thrown if the sequence contains invalid characters: see validate_seq(). Returns : A scalar Args : - Optional new sequence value (a string) to set - Optional alphabet (it is guessed by default) =cut sub seq { my ($self, @args) = @_; if( scalar @args == 0 ) { return $self->{'seq'}; } my ($seq_str, $alphabet) = @args; if (@args) { $self->_set_seq_by_ref(\$seq_str, $alphabet); } return $self->{'seq'}; } sub _set_seq_by_ref { # Set a sequence by reference. A reference is used to avoid the cost of # copying the sequence (which can be very large) between functions. my ($self, $seq_str_ref, $alphabet) = @_; # Validate sequence if sequence is not empty and we are not in direct mode if ( (! $self->{'_direct'}) && (defined $$seq_str_ref) ) { $self->validate_seq($$seq_str_ref, 1); } delete $self->{'_direct'}; # next sequence will have to be validated # Record sequence length my $len = CORE::length($$seq_str_ref || ''); my $is_changed_seq = (exists $self->{'seq'}) && ($len > 0); # Note: if the new seq is empty or undef, this is not considered a change delete $self->{'_freeze_length'} if $is_changed_seq; $self->{'length'} = $len if not exists $self->{'_freeze_length'}; # Set sequence $self->{'seq'} = $$seq_str_ref; # Set or guess alphabet if ($alphabet) { # Alphabet specified, set it no matter what $self->alphabet($alphabet); } elsif ($is_changed_seq || (! defined($self->alphabet()))) { # If we changed a previous sequence to a new one or if there is no # alphabet yet at all, we need to guess the (possibly new) alphabet $self->_guess_alphabet(); } # else (seq not changed and alphabet was defined) do nothing return 1; } =head2 validate_seq Title : validate_seq Usage : if(! $seqobj->validate_seq($seq_str) ) { print "sequence $seq_str is not valid for an object of alphabet ",$seqobj->alphabet, "\n"; } Function: Test that the given sequence is valid, i.e. contains only valid characters. The allowed characters are all letters (A-Z) and '-','.', '*','?','=' and '~'. Spaces are not valid. Note that this implementation does not take alphabet() into account and that empty sequences are considered valid. Returns : 1 if the supplied sequence string is valid, 0 otherwise. Args : - Sequence string to be validated - Boolean to optionally throw an error if the sequence is invalid =cut sub validate_seq { my ($self, $seqstr, $throw) = @_; if ( (defined $seqstr ) && ($seqstr !~ /^[$MATCHPATTERN]*$/) ) { if ($throw) { $self->throw("Failed validation of sequence '".(defined($self->id) || '[unidentified sequence]')."'. Invalid characters were: " . join('',($seqstr =~ /[^$MATCHPATTERN]/g))); } return 0; } return 1; } =head2 subseq Title : subseq Usage : $substring = $seqobj->subseq(10,40); $substring = $seqobj->subseq(10,40,'nogap'); $substring = $seqobj->subseq(-start=>10, -end=>40, -replace_with=>'tga'); $substring = $seqobj->subseq($location_obj); $substring = $seqobj->subseq($location_obj, -nogap => 1); Function: Return the subseq from start to end, where the first sequence character has coordinate 1 number is inclusive, ie 1-2 are the first two characters of the sequence. The given start coordinate has to be larger than the end, even if the sequence is circular. Returns : a string Args : integer for start position integer for end position OR Bio::LocationI location for subseq (strand honored) Specify -NOGAP=>1 to return subseq with gap characters removed Specify -REPLACE_WITH=>$new_subseq to replace the subseq returned with $new_subseq in the sequence object =cut sub subseq { my $self = shift; my @args = @_; my ($start, $end, $nogap, $replace) = $self->_rearrange([qw(START END NOGAP REPLACE_WITH)], @args); # If -replace_with is specified, validate the replacement sequence if (defined $replace) { $self->validate_seq( $replace ) || $self->throw("Replacement sequence does not look valid"); } if( ref($start) && $start->isa('Bio::LocationI') ) { my $loc = $start; my $seq = ''; # For Split objects if Guide Strand is negative, # pass the sublocations in reverse my $order = 0; if ($loc->isa('Bio::Location::SplitLocationI')) { # guide_strand can return undef, so don't compare directly # to avoid 'uninitialized value' warning my $guide_strand = defined ($loc->guide_strand) ? ($loc->guide_strand) : 0; $order = ($guide_strand == -1) ? -1 : 0; } # Reversing order using ->each_Location(-1) does not work well for # cut by origin-splits (like "complement(join(1900..END,START..50))"), # so use "reverse" instead my @sublocs = ($order == -1) ? reverse $loc->each_Location(): $loc->each_Location; foreach my $subloc (@sublocs) { my $piece = $self->subseq(-start => $subloc->start(), -end => $subloc->end(), -replace_with => $replace, -nogap => $nogap); $piece =~ s/[$GAP_SYMBOLS]//g if $nogap; # strand can return undef, so don't compare directly # to avoid 'uninitialized value' warning my $strand = defined ($subloc->strand) ? ($subloc->strand) : 0; if ($strand < 0) { $piece = $self->_revcom_from_string($piece, $self->alphabet); } $seq .= $piece; } return $seq; } elsif( defined $start && defined $end ) { if( $start > $end ){ $self->throw("Bad start,end parameters. Start [$start] has to be ". "less than end [$end]"); } if( $start <= 0 ) { $self->throw("Bad start parameter ($start). Start must be positive."); } # Remove one from start, and then length is end-start $start--; my $seqstr; if (defined $replace) { $seqstr = substr $self->{seq}, $start, $end-$start, $replace; } else { $seqstr = substr $self->{seq}, $start, $end-$start; } if ($end > $self->length) { if ($self->is_circular) { my $start = 0; my $end = $end - $self->length; my $appendstr; if (defined $replace) { $appendstr = substr $self->{seq}, $start, $end-$start, $replace; } else { $appendstr = substr $self->{seq}, $start, $end-$start; } $seqstr .= $appendstr; } else { $self->throw("Bad end parameter ($end). End must be less than ". "the total length of sequence (total=".$self->length.")") } } $seqstr =~ s/[$GAP_SYMBOLS]//g if ($nogap); return $seqstr; } else { $self->warn("Incorrect parameters to subseq - must be two integers or ". "a Bio::LocationI object. Got:", $self,$start,$end,$replace,$nogap); return; } } =head2 length Title : length Usage : $len = $seqobj->length(); Function: Get the stored length of the sequence in number of symbols (bases or amino acids). In some circumstances, you can also set this attribute: 1. For empty sequences, you can set the length to anything you want: my $seqobj = Bio::PrimarySeq->new( -length => 123 ); my $len = $seqobj->len; # 123 2. To save memory when using very long sequences, you can set the length of the sequence to the length of the sequence (and nothing else): my $seqobj = Bio::PrimarySeq->new( -seq => 'ACGT...' ); # 1 Mbp sequence # process $seqobj... then after you're done with it $seqobj->length($seqobj->length); $seqobj->seq(undef); # free memory! my $len = $seqobj->len; # 1 Mbp Note that if you set seq() to a value other than undef at any time, the length attribute will be reset. Returns : integer representing the length of the sequence. Args : Optionally, the value on set =cut sub length { my ($self, $val) = @_; if (defined $val) { my $len = $self->{'length'}; if ($len && ($len != $val)) { $self->throw("Can not set the length to $val, current length value is $len"); } $self->{'length'} = $val; $self->{'_freeze_length'} = undef; } return $self->{'length'}; } =head2 display_id Title : display_id or display_name Usage : $id_string = $seqobj->display_id(); Function: Get or set the display id, aka the common name of the sequence object. The semantics of this is that it is the most likely string to be used as an identifier of the sequence, and likely to have "human" readability. The id is equivalent to the ID field of the GenBank/EMBL databanks and the id field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. With the new Bio::DescribeableI interface, display_name aliases to this method. Returns : A string for the display ID Args : Optional string for the display ID to set =cut sub display_id { my ($self, $value) = @_; if( defined $value) { $self->{'display_id'} = $value; } return $self->{'display_id'}; } =head2 accession_number Title : accession_number or object_id Usage : $unique_key = $seqobj->accession_number; Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". [Note this method name is likely to change in 1.3] With the new Bio::IdentifiableI interface, this is aliased to object_id Returns : A string Args : A string (optional) for setting =cut sub accession_number { my( $self, $acc ) = @_; if (defined $acc) { $self->{'accession_number'} = $acc; } else { $acc = $self->{'accession_number'}; $acc = 'unknown' unless defined $acc; } return $acc; } =head2 primary_id Title : primary_id Usage : $unique_key = $seqobj->primary_id; Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a way the implementation can control clients can expect one id to map to one object. For sequences with no natural primary id, this method should return a stringified memory location. Returns : A string Args : A string (optional, for setting) =cut sub primary_id { my $self = shift; if(@_) { $self->{'primary_id'} = shift; } if( ! defined($self->{'primary_id'}) ) { return "$self"; } return $self->{'primary_id'}; } =head2 alphabet Title : alphabet Usage : if( $seqobj->alphabet eq 'dna' ) { # Do something } Function: Get/set the alphabet of sequence, one of 'dna', 'rna' or 'protein'. This is case sensitive. This is not called because this would cause upgrade problems from the 0.5 and earlier Seq objects. Returns : a string either 'dna','rna','protein'. NB - the object must make a call of the type - if there is no alphabet specified it has to guess. Args : optional string to set : 'dna' | 'rna' | 'protein' =cut sub alphabet { my ($self,$value) = @_; if (defined $value) { $value = lc $value; unless ( $valid_type{$value} ) { $self->throw("Alphabet '$value' is not a valid alphabet (". join(',', map "'$_'", sort keys %valid_type) .") lowercase"); } $self->{'alphabet'} = $value; } return $self->{'alphabet'}; } =head2 desc Title : desc or description Usage : $seqobj->desc($newval); Function: Get/set description of the sequence. 'description' is an alias for this for compliance with the Bio::DescribeableI interface. Returns : value of desc (a string) Args : newvalue (a string or undef, optional) =cut sub desc{ my $self = shift; return $self->{'desc'} = shift if @_; return $self->{'desc'}; } =head2 can_call_new Title : can_call_new Usage : Function: Example : Returns : true Args : =cut sub can_call_new { my ($self) = @_; return 1; } =head2 id Title : id Usage : $id = $seqobj->id(); Function: This is mapped on display_id Example : Returns : Args : =cut sub id { return shift->display_id(@_); } =head2 is_circular Title : is_circular Usage : if( $seqobj->is_circular) { # Do something } Function: Returns true if the molecule is circular Returns : Boolean value Args : none =cut sub is_circular{ my $self = shift; return $self->{'is_circular'} = shift if @_; return $self->{'is_circular'}; } =head1 Methods for Bio::IdentifiableI compliance =head2 object_id Title : object_id Usage : $string = $seqobj->object_id(); Function: Get or set a string which represents the stable primary identifier in this namespace of this object. For DNA sequences this is its accession_number, similarly for protein sequences. This is aliased to accession_number(). Returns : A scalar Args : Optional object ID to set. =cut sub object_id { return shift->accession_number(@_); } =head2 version Title : version Usage : $version = $seqobj->version(); Function: Get or set a number which differentiates between versions of the same object. Higher numbers are considered to be later and more relevant, but a single object described the same identifier should represent the same concept. Returns : A number Args : Optional version to set. =cut sub version{ my ($self,$value) = @_; if( defined $value) { $self->{'_version'} = $value; } return $self->{'_version'}; } =head2 authority Title : authority Usage : $authority = $seqobj->authority(); Function: Get or set a string which represents the organisation which granted the namespace, written as the DNS name of the organisation (eg, wormbase.org). Returns : A scalar Args : Optional authority to set. =cut sub authority { my ($self, $value) = @_; if( defined $value) { $self->{'authority'} = $value; } return $self->{'authority'}; } =head2 namespace Title : namespace Usage : $string = $seqobj->namespace(); Function: Get or set a string representing the name space this identifier is valid in, often the database name or the name describing the collection. Returns : A scalar Args : Optional namespace to set. =cut sub namespace{ my ($self,$value) = @_; if( defined $value) { $self->{'namespace'} = $value; } return $self->{'namespace'} || ""; } =head1 Methods for Bio::DescribableI compliance This comprises of display_name and description. =head2 display_name Title : display_name Usage : $string = $seqobj->display_name(); Function: Get or set a string which is what should be displayed to the user. The string should have no spaces (ideally, though a cautious user of this interface would not assume this) and should be less than thirty characters (though again, double checking this is a good idea). This is aliased to display_id(). Returns : A string for the display name Args : Optional string for the display name to set. =cut sub display_name { return shift->display_id(@_); } =head2 description Title : description Usage : $string = $seqobj->description(); Function: Get or set a text string suitable for displaying to the user a description. This string is likely to have spaces, but should not have any newlines or formatting - just plain text. The string should not be greater than 255 characters and clients can feel justified at truncating strings at 255 characters for the purposes of display. This is aliased to desc(). Returns : A string for the description Args : Optional string for the description to set. =cut sub description { return shift->desc(@_); } =head1 Methods Inherited from Bio::PrimarySeqI These methods are available on Bio::PrimarySeq, although they are actually implemented on Bio::PrimarySeqI =head2 revcom Title : revcom Usage : $rev = $seqobj->revcom(); Function: Produces a new Bio::SeqI implementing object which is the reversed complement of the sequence. For protein sequences this throws an exception of "Sequence is a protein. Cannot revcom". The id is the same id as the original sequence, and the accession number is also identical. If someone wants to track that this sequence has be reversed, it needs to define its own extensions. To do an inplace edit of an object you can go: $seqobj = $seqobj->revcom(); This of course, causes Perl to handle the garbage collection of the old object, but it is roughly speaking as efficient as an inplace edit. Returns : A new (fresh) Bio::SeqI object Args : none =head2 trunc Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence, Returns : A fresh Bio::SeqI implementing object. Args : Numbers for the start and end positions =head1 Internal methods These are internal methods to PrimarySeq =head2 _guess_alphabet Title : _guess_alphabet Usage : Function: Automatically guess and set the type of sequence: dna, rna, protein or '' if the sequence was empty. This method first removes dots (.), dashes (-) and question marks (?) before guessing the alphabet using the IUPAC conventions for ambiguous residues. Since the DNA and RNA characters are also valid characters for proteins, there is no foolproof way of determining the right alphabet. This is our best guess only! Returns : string 'dna', 'rna', 'protein' or ''. Args : none =cut sub _guess_alphabet { my ($self) = @_; # Guess alphabet my $alphabet = $self->_guess_alphabet_from_string($self->seq, $self->{'_nowarnonempty'}); # Set alphabet unless it is unknown $self->alphabet($alphabet) if $alphabet; return $alphabet; } sub _guess_alphabet_from_string { # Get the alphabet from a sequence string my ($self, $str, $nowarnonempty) = @_; $nowarnonempty = 0 if not defined $nowarnonempty; # Remove chars that clearly don't denote nucleic or amino acids $str =~ s/[-.?]//gi; # Check for sequences without valid letters my $alphabet; my $total = CORE::length($str); if( $total == 0 ) { if (not $nowarnonempty) { $self->warn("Got a sequence without letters. Could not guess alphabet"); } $alphabet = ''; } # Determine alphabet now if (not defined $alphabet) { if ($str =~ m/[EFIJLOPQXZ]/i) { # Start with a safe method to find proteins. # Unambiguous IUPAC letters for proteins are: E,F,I,J,L,O,P,Q,X,Z $alphabet = 'protein'; } else { # Alphabet is unsure, could still be DNA, RNA or protein # DNA and RNA contain mostly A, T, U, G, C and N, but the other # letters they use are also among the 15 valid letters that a # protein sequence can contain at this stage. Make our best guess # based on sequence composition. If it contains over 70% of ACGTUN, # it is likely nucleic. if( ($str =~ tr/ATUGCNWSKMatugcnwskm//) / $total > 0.7 ) { if ( $str =~ m/U/i ) { $alphabet = 'rna'; } else { $alphabet = 'dna'; } } else { $alphabet = 'protein'; } } } return $alphabet; } ############################################################################ # aliases due to name changes or to compensate for our lack of consistency # ############################################################################ sub accession { my $self = shift; $self->warn(ref($self)."::accession is deprecated, ". "use accession_number() instead"); return $self->accession_number(@_); } 1; BioPerl-1.007002/Bio/PrimarySeqI.pm000444000766000024 7706013155576320 17021 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PrimarySeqI # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq =head1 SYNOPSIS # Bio::PrimarySeqI is the interface class for sequences. # If you are a newcomer to bioperl, you might want to start with # Bio::Seq documentation. # Test if this is a seq object $obj->isa("Bio::PrimarySeqI") || $obj->throw("$obj does not implement the Bio::PrimarySeqI interface"); # Accessors $string = $obj->seq(); $substring = $obj->subseq(12,50); $display = $obj->display_id(); # for human display $id = $obj->primary_id(); # unique id for this object, # implementation defined $unique_key= $obj->accession_number(); # unique biological id # Object manipulation eval { $rev = $obj->revcom(); }; if( $@ ) { $obj->throw( "Could not reverse complement. ". "Probably not DNA. Actual exception\n$@\n" ); } $trunc = $obj->trunc(12,50); # $rev and $trunc are Bio::PrimarySeqI compliant objects =head1 DESCRIPTION This object defines an abstract interface to basic sequence information - for most users of the package the documentation (and methods) in this class are not useful - this is a developers-only class which defines what methods have to be implemented by other Perl objects to comply to the Bio::PrimarySeqI interface. Go "perldoc Bio::Seq" or "man Bio::Seq" for more information on the main class for sequences. PrimarySeq is an object just for the sequence and its name(s), nothing more. Seq is the larger object complete with features. There is a pure perl implementation of this in L. If you just want to use L objects, then please read that module first. This module defines the interface, and is of more interest to people who want to wrap their own Perl Objects/RDBs/FileSystems etc in way that they "are" bioperl sequence objects, even though it is not using Perl to store the sequence etc. This interface defines what bioperl considers necessary to "be" a sequence, without providing an implementation of this, an implementation is provided in L. If you want to provide a Bio::PrimarySeq-compliant object which in fact wraps another object/database/out-of-perl experience, then this is the correct thing to wrap, generally by providing a wrapper class which would inherit from your object and this Bio::PrimarySeqI interface. The wrapper class then would have methods lists in the "Implementation Specific Functions" which would provide these methods for your object. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::PrimarySeqI; use strict; use Bio::Tools::CodonTable; use base qw(Bio::Root::RootI); =head1 Implementation-specific Functions These functions are the ones that a specific implementation must define. =head2 seq Title : seq Usage : $string = $obj->seq() Function: Returns the sequence as a string of letters. The case of the letters is left up to the implementer. Suggested cases are upper case for proteins and lower case for DNA sequence (IUPAC standard), but implementations are suggested to keep an open mind about case (some users... want mixed case!) Returns : A scalar Status : Virtual =cut sub seq { my ($self) = @_; $self->throw_not_implemented(); } =head2 subseq Title : subseq Usage : $substring = $obj->subseq(10,40); Function: Returns the subseq from start to end, where the first base is 1 and the number is inclusive, i.e. 1-2 are the first two bases of the sequence. Start cannot be larger than end but can be equal. Returns : A string Args : Status : Virtual =cut sub subseq { my ($self) = @_; $self->throw_not_implemented(); } =head2 display_id Title : display_id Usage : $id_string = $obj->display_id(); Function: Returns the display id, also known as the common name of the Sequence object. The semantics of this is that it is the most likely string to be used as an identifier of the sequence, and likely to have "human" readability. The id is equivalent to the ID field of the GenBank/EMBL databanks and the id field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. Notice that $seq->id() maps to this function, mainly for legacy/convenience reasons. Returns : A string Args : None Status : Virtual =cut sub display_id { my ($self) = @_; $self->throw_not_implemented(); } =head2 accession_number Title : accession_number Usage : $unique_biological_key = $obj->accession_number; Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". Returns : A string Args : None Status : Virtual =cut sub accession_number { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 primary_id Title : primary_id Usage : $unique_implementation_key = $obj->primary_id; Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a way the implementation can control clients can expect one id to map to one object. For sequences with no accession number, this method should return a stringified memory location. Returns : A string Args : None Status : Virtual =cut sub primary_id { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 can_call_new Title : can_call_new Usage : if( $obj->can_call_new ) { $newobj = $obj->new( %param ); } Function: Can_call_new returns 1 or 0 depending on whether an implementation allows new constructor to be called. If a new constructor is allowed, then it should take the followed hashed constructor list. $myobject->new( -seq => $sequence_as_string, -display_id => $id -accession_number => $accession -alphabet => 'dna', ); Returns : 1 or 0 Args : =cut sub can_call_new { my ($self,@args) = @_; # we default to 0 here return 0; } =head2 alphabet Title : alphabet Usage : if( $obj->alphabet eq 'dna' ) { /Do Something/ } Function: Returns the type of sequence being one of 'dna', 'rna' or 'protein'. This is case sensitive. This is not called "type" because this would cause upgrade problems from the 0.5 and earlier Seq objects. Returns : A string either 'dna','rna','protein'. NB - the object must make a call of the alphabet, if there is no alphabet specified it has to guess. Args : None Status : Virtual =cut sub alphabet { my ( $self ) = @_; $self->throw_not_implemented(); } =head2 moltype Title : moltype Usage : Deprecated. Use alphabet() instead. =cut sub moltype { my ($self,@args) = @_; $self->warn("moltype: pre v1.0 method. Calling alphabet() instead..."); return $self->alphabet(@args); } =head1 Implementation-optional Functions The following functions rely on the above functions. An implementing class does not need to provide these functions, as they will be provided by this class, but is free to override these functions. The revcom(), trunc(), and translate() methods create new sequence objects. They will call new() on the class of the sequence object instance passed as argument, unless can_call_new() returns FALSE. In the latter case a Bio::PrimarySeq object will be created. Implementors which really want to control how objects are created (eg, for object persistence over a database, or objects in a CORBA framework), they are encouraged to override these methods =head2 revcom Title : revcom Usage : $rev = $seq->revcom() Function: Produces a new Bio::PrimarySeqI implementing object which is the reversed complement of the sequence. For protein sequences this throws an exception of "Sequence is a protein. Cannot revcom". The id is the same id as the original sequence, and the accession number is also identical. If someone wants to track that this sequence has be reversed, it needs to define its own extensions. To do an inplace edit of an object you can go: $seq = $seq->revcom(); This of course, causes Perl to handle the garbage collection of the old object, but it is roughly speaking as efficient as an inplace edit. Returns : A new (fresh) Bio::PrimarySeqI object Args : None =cut sub revcom { my ($self) = @_; # Create a new fresh object if $self is 'Bio::Seq::LargePrimarySeq' # or 'Bio::Seq::LargeSeq', if not take advantage of # Bio::Root::clone to get an object copy my $out; if ( $self->isa('Bio::Seq::LargePrimarySeq') or $self->isa('Bio::Seq::LargeSeq') ) { my ($seqclass, $opts) = $self->_setup_class; $out = $seqclass->new( -seq => $self->_revcom_from_string($self->seq, $self->alphabet), -is_circular => $self->is_circular, -display_id => $self->display_id, -accession_number => $self->accession_number, -alphabet => $self->alphabet, -desc => $self->desc, -verbose => $self->verbose, %$opts, ); } else { $out = $self->clone; $out->seq( $out->_revcom_from_string($out->seq, $out->alphabet) ); } return $out; } sub _revcom_from_string { my ($self, $string, $alphabet) = @_; # Check that reverse-complementing makes sense if( $alphabet eq 'protein' ) { $self->throw("Sequence is a protein. Cannot revcom."); } if( $alphabet ne 'dna' && $alphabet ne 'rna' ) { my $msg = "Sequence is not dna or rna, but [$alphabet]. Attempting to revcom, ". "but unsure if this is right."; if( $self->can('warn') ) { $self->warn($msg); } else { warn("[$self] $msg"); } } # If sequence is RNA, map to DNA (then map back later) if( $alphabet eq 'rna' ) { $string =~ tr/uU/tT/; } # Reverse-complement now $string =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; $string = CORE::reverse $string; # Map back RNA to DNA if( $alphabet eq 'rna' ) { $string =~ tr/tT/uU/; } return $string; } =head2 trunc Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence. Returns : A fresh Bio::PrimarySeqI implementing object. Args : Two integers denoting first and last base of the sub-sequence. =cut sub trunc { my ($self,$start,$end) = @_; my $str; if( defined $start && ref($start) && $start->isa('Bio::LocationI') ) { $str = $self->subseq($start); # start is a location actually } elsif( !$end ) { $self->throw("trunc start,end -- there was no end for $start"); } elsif( $end < $start ) { my $msg = "start [$start] is greater than end [$end]. \n". "If you want to truncated and reverse complement, \n". "you must call trunc followed by revcom. Sorry."; $self->throw($msg); } else { $str = $self->subseq($start,$end); } # Create a new fresh object if $self is 'Bio::Seq::LargePrimarySeq' # or 'Bio::Seq::LargeSeq', if not take advantage of # Bio::Root::clone to get an object copy my $out; if ( $self->isa('Bio::Seq::LargePrimarySeq') or $self->isa('Bio::Seq::LargeSeq') or $self->isa('Bio::Seq::RichSeq') ) { my ($seqclass, $opts) = $self->_setup_class; $out = $seqclass->new( -seq => $str, -is_circular => $self->is_circular, -display_id => $self->display_id, -accession_number => $self->accession_number, -alphabet => $self->alphabet, -desc => $self->desc, -verbose => $self->verbose, %$opts, ); } else { $out = $self->clone; $out->seq($str); } return $out; } =head2 translate Title : translate Usage : $protein_seq_obj = $dna_seq_obj->translate Or if you expect a complete coding sequence (CDS) translation, with initiator at the beginning and terminator at the end: $protein_seq_obj = $cds_seq_obj->translate(-complete => 1); Or if you want translate() to find the first initiation codon and return the corresponding protein: $protein_seq_obj = $cds_seq_obj->translate(-orf => 1); Function: Provides the translation of the DNA sequence using full IUPAC ambiguities in DNA/RNA and amino acid codes. The complete CDS translation is identical to EMBL/TREMBL database translation. Note that the trailing terminator character is removed before returning the translated protein object. Note: if you set $dna_seq_obj->verbose(1) you will get a warning if the first codon is not a valid initiator. Returns : A Bio::PrimarySeqI implementing object Args : -terminator character for terminator, default '*' -unknown character for unknown, default 'X' -frame positive integer frame shift (in bases), default 0 -codontable_id integer codon table id, default 1 -complete boolean, if true, complete CDS is expected. default false -complete_codons boolean, if true, codons which are incomplete are translated if a suitable amino acid is found. For instance, if the incomplete codon is 'GG', the completed codon is 'GGN', which is glycine (G). Defaults to 'false'; setting '-complete' also makes this true. -throw boolean, throw exception if ORF not complete, default false -orf if 'longest', find longest ORF. other true value, find first ORF. default 0 -codontable optional L object to use for translation -start optional three-character string to force as initiation codon (e.g. 'atg'). If unset, start codons are determined by the CodonTable. Case insensitive. -offset optional positive integer offset for fuzzy locations. if set, must be either 1, 2, or 3 =head3 Notes The -start argument only applies when -orf is set to 1. By default all initiation codons found in the given codon table are used but when "start" is set to some codon this codon will be used exclusively as the initiation codon. Note that the default codon table (NCBI "Standard") has 3 initiation codons! By default translate() translates termination codons to the some character (default is *), both internal and trailing codons. Setting "-complete" to 1 tells translate() to remove the trailing character. -offset is used for seqfeatures which contain the the \codon_start tag and can be set to 1, 2, or 3. This is the offset by which the sequence translation starts relative to the first base of the feature For details on codon tables used by translate() see L. Deprecated argument set (v. 1.5.1 and prior versions) where each argument is an element in an array: 1: character for terminator (optional), defaults to '*'. 2: character for unknown amino acid (optional), defaults to 'X'. 3: frame (optional), valid values are 0, 1, 2, defaults to 0. 4: codon table id (optional), defaults to 1. 5: complete coding sequence expected, defaults to 0 (false). 6: boolean, throw exception if not complete coding sequence (true), defaults to warning (false) 7: codontable, a custom Bio::Tools::CodonTable object (optional). =cut sub translate { my ($self,@args) = @_; my ($terminator, $unknown, $frame, $codonTableId, $complete, $complete_codons, $throw, $codonTable, $orf, $start_codon, $offset); ## new API with named parameters, post 1.5.1 if ($args[0] && $args[0] =~ /^-[A-Z]+/i) { ($terminator, $unknown, $frame, $codonTableId, $complete, $complete_codons, $throw,$codonTable, $orf, $start_codon, $offset) = $self->_rearrange([qw(TERMINATOR UNKNOWN FRAME CODONTABLE_ID COMPLETE COMPLETE_CODONS THROW CODONTABLE ORF START OFFSET)], @args); ## old API, 1.5.1 and preceding versions } else { ($terminator, $unknown, $frame, $codonTableId, $complete, $throw, $codonTable, $offset) = @args; } ## Initialize termination codon, unknown codon, codon table id, frame $terminator = '*' unless (defined($terminator) and $terminator ne ''); $unknown = "X" unless (defined($unknown) and $unknown ne ''); $frame = 0 unless (defined($frame) and $frame ne ''); $codonTableId = 1 unless (defined($codonTableId) and $codonTableId ne ''); $complete_codons ||= $complete || 0; ## Get a CodonTable, error if custom CodonTable is invalid if ($codonTable) { $self->throw("Need a Bio::Tools::CodonTable object, not ". $codonTable) unless $codonTable->isa('Bio::Tools::CodonTable'); } else { # shouldn't this be cached? Seems wasteful to have a new instance # every time... $codonTable = Bio::Tools::CodonTable->new( -id => $codonTableId); } ## Error if alphabet is "protein" $self->throw("Can't translate an amino acid sequence.") if ($self->alphabet =~ /protein/i); ## Error if -start parameter isn't a valid codon if ($start_codon) { $self->throw("Invalid start codon: $start_codon.") if ( $start_codon !~ /^[A-Z]{3}$/i ); } my $seq; if ($offset) { $self->throw("Offset must be 1, 2, or 3.") if ( $offset !~ /^[123]$/ ); my ($start, $end) = ($offset, $self->length); ($seq) = $self->subseq($start, $end); } else { ($seq) = $self->seq(); } ## ignore frame if an ORF is supposed to be found if ( $orf ) { my ($orf_region) = $self->_find_orfs_nucleotide( $seq, $codonTable, $start_codon, $orf eq 'longest' ? 0 : 'first_only' ); $seq = $self->_orf_sequence( $seq, $orf_region ); } else { ## use frame, error if frame is not 0, 1 or 2 $self->throw("Valid values for frame are 0, 1, or 2, not $frame.") unless ($frame == 0 or $frame == 1 or $frame == 2); $seq = substr($seq,$frame); } ## Translate it my $output = $codonTable->translate($seq, $complete_codons); # Use user-input terminator/unknown $output =~ s/\*/$terminator/g; $output =~ s/X/$unknown/g; ## Only if we are expecting to translate a complete coding region if ($complete) { my $id = $self->display_id; # remove the terminator character if( substr($output,-1,1) eq $terminator ) { chop $output; } else { $throw && $self->throw("Seq [$id]: Not using a valid terminator codon!"); $self->warn("Seq [$id]: Not using a valid terminator codon!"); } # test if there are terminator characters inside the protein sequence! if ($output =~ /\Q$terminator\E/) { $id ||= ''; $throw && $self->throw("Seq [$id]: Terminator codon inside CDS!"); $self->warn("Seq [$id]: Terminator codon inside CDS!"); } # if the initiator codon is not ATG, the amino acid needs to be changed to M if ( substr($output,0,1) ne 'M' ) { if ($codonTable->is_start_codon(substr($seq, 0, 3)) ) { $output = 'M'. substr($output,1); } elsif ($throw) { $self->throw("Seq [$id]: Not using a valid initiator codon!"); } else { $self->warn("Seq [$id]: Not using a valid initiator codon!"); } } } # Create a new fresh object if $self is 'Bio::Seq::LargePrimarySeq' # or 'Bio::Seq::LargeSeq', if not take advantage of # Bio::Root::clone to get an object copy my $out; if ( $self->isa('Bio::Seq::LargePrimarySeq') or $self->isa('Bio::Seq::LargeSeq') ) { my ($seqclass, $opts) = $self->_setup_class; $out = $seqclass->new( -seq => $output, -is_circular => $self->is_circular, -display_id => $self->display_id, -accession_number => $self->accession_number, -alphabet => 'protein', -desc => $self->desc, -verbose => $self->verbose, %$opts, ); } else { $out = $self->clone; $out->seq($output); $out->alphabet('protein'); } return $out; } =head2 transcribe() Title : transcribe Usage : $xseq = $seq->transcribe Function: Convert base T to base U Returns : PrimarySeqI object of alphabet 'rna' or undef if $seq->alphabet ne 'dna' Args : =cut sub transcribe { my $self = shift; return unless $self->alphabet eq 'dna'; my $s = $self->seq; $s =~ tr/tT/uU/; my $desc = $self->desc || ''; # Create a new fresh object if $self is 'Bio::Seq::LargePrimarySeq' # or 'Bio::Seq::LargeSeq', if not take advantage of # Bio::Root::clone to get an object copy my $out; if ( $self->isa('Bio::Seq::LargePrimarySeq') or $self->isa('Bio::Seq::LargeSeq') ) { my ($seqclass, $opts) = $self->_setup_class; $out = $seqclass->new( -seq => $s, -is_circular => $self->is_circular, -display_id => $self->display_id, -accession_number => $self->accession_number, -alphabet => 'rna', -desc => "${desc}[TRANSCRIBED]", -verbose => $self->verbose, %$opts, ); } else { $out = $self->clone; $out->seq($s); $out->alphabet('rna'); $out->desc($desc . "[TRANSCRIBED]"); } return $out; } =head2 rev_transcribe() Title : rev_transcribe Usage : $rtseq = $seq->rev_transcribe Function: Convert base U to base T Returns : PrimarySeqI object of alphabet 'dna' or undef if $seq->alphabet ne 'rna' Args : =cut sub rev_transcribe { my $self = shift; return unless $self->alphabet eq 'rna'; my $s = $self->seq; $s =~ tr/uU/tT/; my $desc = $self->desc || ''; # Create a new fresh object if $self is 'Bio::Seq::LargePrimarySeq' # or 'Bio::Seq::LargeSeq', if not take advantage of # Bio::Root::clone to get an object copy my $out; if ( $self->isa('Bio::Seq::LargePrimarySeq') or $self->isa('Bio::Seq::LargeSeq') ) { my ($seqclass, $opts) = $self->_setup_class; $out = $seqclass->new( -seq => $s, -is_circular => $self->is_circular, -display_id => $self->display_id, -accession_number => $self->accession_number, -alphabet => 'dna', -desc => $self->desc . "[REVERSE TRANSCRIBED]", -verbose => $self->verbose, %$opts, ); } else { $out = $self->clone; $out->seq($s); $out->alphabet('dna'); $out->desc($desc . "[REVERSE TRANSCRIBED]"); } return $out; } =head2 id Title : id Usage : $id = $seq->id() Function: ID of the sequence. This should normally be (and actually is in the implementation provided here) just a synonym for display_id(). Returns : A string. Args : =cut sub id { my ($self)= @_; return $self->display_id(); } =head2 length Title : length Usage : $len = $seq->length() Function: Returns : Integer representing the length of the sequence. Args : =cut sub length { my ($self)= @_; $self->throw_not_implemented(); } =head2 desc Title : desc Usage : $seq->desc($newval); $description = $seq->desc(); Function: Get/set description text for a seq object Returns : Value of desc Args : newvalue (optional) =cut sub desc { shift->throw_not_implemented(); } =head2 is_circular Title : is_circular Usage : if( $obj->is_circular) { # Do something } Function: Returns true if the molecule is circular Returns : Boolean value Args : none =cut sub is_circular { shift->throw_not_implemented; } =head1 Private functions These are some private functions for the PrimarySeqI interface. You do not need to implement these functions =head2 _find_orfs_nucleotide Title : _find_orfs_nucleotide Usage : Function: Finds ORF starting at 1st initiation codon in nucleotide sequence. The ORF is not required to have a termination codon. Example : Returns : a list of string coordinates of ORF locations (0-based half-open), sorted descending by length (so that the longest is first) as: [ start, end, frame, length ], [ start, end, frame, length ], ... Args : Nucleotide sequence, CodonTable object, (optional) alternative initiation codon (e.g. 'ATA'), (optional) boolean that, if true, stops after finding the first available ORF =cut sub _find_orfs_nucleotide { my ( $self, $sequence, $codon_table, $start_codon, $first_only ) = @_; $sequence = uc $sequence; $start_codon = uc $start_codon if $start_codon; my $is_start = $start_codon ? sub { shift eq $start_codon } : sub { $codon_table->is_start_codon( shift ) }; # stores the begin index of the currently-running ORF in each # reading frame my @current_orf_start = (-1,-1,-1); #< stores coordinates of longest observed orf (so far) in each # reading frame my @orfs; # go through each base of the sequence, and each reading frame for each base my $seqlen = CORE::length $sequence; my @start_frame_order; for( my $j = 0; $j <= $seqlen-3; $j++ ) { my $frame = $j % 3; my $this_codon = substr( $sequence, $j, 3 ); # if in an orf and this is either a stop codon or the last in-frame codon in the string if ( $current_orf_start[$frame] >= 0 ) { if ( $codon_table->is_ter_codon( $this_codon ) ||( my $is_last_codon_in_frame = ($j >= $seqlen-5)) ) { # record ORF start, end (half-open), length, and frame my @this_orf = ( $current_orf_start[$frame], $j+3, undef, $frame ); my $this_orf_length = $this_orf[2] = ( $this_orf[1] - $this_orf[0] ); if ($first_only && $frame == $start_frame_order[0]) { $self->warn( "Translating partial ORF " .$self->_truncate_seq( $self->_orf_sequence( $sequence, \@this_orf )) .' from end of nucleotide sequence' ) if $is_last_codon_in_frame; return \@this_orf; } push @orfs, \@this_orf; $current_orf_start[$frame] = -1; } } # if this is a start codon elsif ( $is_start->($this_codon) ) { $current_orf_start[$frame] = $j; push @start_frame_order, $frame; } } return sort { $b->[2] <=> $a->[2] } @orfs; } sub _truncate_seq { my ($self, $seq) = @_; return CORE::length($seq) > 200 ? substr($seq,0,50).'...'.substr($seq,-50) : $seq; } sub _orf_sequence { my ($self, $seq, $orf ) = @_; return '' unless $orf; return substr( $seq, $orf->[0], $orf->[2] ) } =head2 _attempt_to_load_Seq Title : _attempt_to_load_Seq Usage : Function: Example : Returns : Args : =cut sub _attempt_to_load_Seq { my ($self) = @_; if( $main::{'Bio::PrimarySeq'} ) { return 1; } else { eval { require Bio::PrimarySeq; }; if( $@ ) { my $text = "Bio::PrimarySeq could not be loaded for [$self]\n". "This indicates that you are using Bio::PrimarySeqI ". "without Bio::PrimarySeq loaded or without providing a ". "complete implementation.\nThe most likely problem is that there ". "has been a misconfiguration of the bioperl environment\n". "Actual exception:\n\n"; $self->throw("$text$@\n"); return 0; } return 1; } } sub _setup_class { # Return name of class and setup some default parameters my ($self) = @_; my $seqclass; if ($self->can_call_new()) { $seqclass = ref($self); } else { $seqclass = 'Bio::PrimarySeq'; $self->_attempt_to_load_Seq(); } my %opts; if ($seqclass eq 'Bio::PrimarySeq') { # Since sequence is in a Seq object, it has already been validated. # We do not need to validate its trunc(), revcom(), etc $opts{ -direct } = 1; } return $seqclass, \%opts; } 1; BioPerl-1.007002/Bio/PullParserI.pm000444000766000024 4707013155576320 17014 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PullParserI # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PullParserI - A base module for fast 'pull' parsing =head1 SYNOPSIS # do not use this class, it is intended for parser module # writers only =head1 DESCRIPTION If you are writing a module to parse some new format, you may wish to use a 'pull' approach whereby you only do work (reading file data, parsing it, turning the parsed data in an object) when absolutely necessary. PullParserI provides a system for doing exactly that. As a PullParser you need a chunk. A chunk is just a Bio::Root::IO that contains all the raw data you would want to parse. You can use the chunk() method to create a chunk from a filename, existing filehandle or even a string. If you make a chunk from a large file, but actually only want your chunk to be some portion of the whole file, supply start and end amounts in bytes to chunk() at the same time. The methods _chunk_seek() and _chunk_tell() provide seeks and tells that are relative to the start and end of your chunk, not the whole file. The other thing you will need to decide when making a chunk is how to handle piped input. A PullParser typically needs seekable data to parse, so if your data is piped in and unseekable, you must decide between creating a temp file or reading the input into memory, which will be done before the chunk becomes usable and you can begin any parsing. Alternatively you can choose to force a sequential read, in which case you can make use of _dependencies() to define the linear order of methods that would result in the file being read sequentially. The return value of _sequential() is also useful here, if you would need to cache some data or otherwise behave differently during a sequential read. The main method in the system is get_field(). This method relies on the existence of a private hash reference accessible to it with the method _fields(). That hash ref should have as keys all the sorts of data you will want to parse (eg. 'score'), and prior to parsing the values would be undefined. A user of your module can then call either $module-Eget_field('score') or $module-Escore and get_field will either return the answer from $self-E_fields-E{score} if it is defined, or call a method _discover_score() first if not. So for the system to work you need to define a _discover_*() method for every field in the fields hash, and ensure that the method stores an answer in the fields hash. How you implement your _discover_* methods is up to you, though you should never call a _discover_* method directly yourself; always use get_field(), since get_field() will deal with calling dependent methods for you if a forced sequenctial read is in progress due to piped input. You will almost certainly want to make use of the various chunk-related methods of this class (that are denoted private by the leading '_'; this means you can use them as the author of a parser class, but users of your parser should not). Primary amongst them is _*_chunk_by_end() to which you provide text that represents the end of your desired chunk and it does a readline with your argument as $/. The chunk knows about its line-endings, so if you want your end definition to include a new line, just always use "\n" and PullParserI will do any necessary conversion for you. If your input data is hierarchical (eg. report-Emany results-Emany hits-Emany hsps), and you want an object at the leaf of the hierarchy to have access to information that is shared amongst all of them (is parsed in the root), you don't have to copy the data to each leaf object; simply by defining parent(), when you call get_field() and the requested field isn't in your leaf's fields hash, the leaf's parent will be asked for the field instead, and so on till root. See Bio::SearchIO::hmmer_pull for an example of implementing a parser using PullParserI. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 CONTRIBUTORS Inspired by a posting by Aaron J. Mackey =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PullParserI; use vars qw($AUTOLOAD $FORCE_TEMP_FILE); use strict; use Bio::Root::IO; use base qw(Bio::Root::RootI); BEGIN { # chunk() needs perl 5.8 feature for modes other than temp_file, so will # workaround by forcing temp_file mode in <5.8. Could also rewrite using # IO::String, but don't want to. if ($] < 5.008) { $FORCE_TEMP_FILE = 1; } } =head2 _fields Title : _fields Usage : $obj->_fields( { field1 => undef } ); my $fields_ref = $obj->_fields; Function: Get/set the hash reference containing all the fields for this parser Returns : hash ref Args : none to get, OR hash ref to set =cut sub _fields { my $self = shift; if (@_) { $self->{_fields} = shift; } unless (defined $self->{_fields}) { $self->{_fields} = { }; } return $self->{_fields}; } =head2 has_field Title : has_field Usage : if ($obj->has_field('field_name') {...} Function: Ask if a particular object has a given field (doesn't ask ancestors) Returns : boolean Args : string (the field name to test) =cut sub has_field { my ($self, $desired) = @_; $desired || return; return exists $self->_fields->{$desired}; } =head2 get_field Title : get_field Usage : my $field_value = $obj->get_field('field_name'); Function: Get the value of a given field. If this $obj doesn't have the field, it's parent() will be asked, and so on until there are no more parents. Returns : scalar, warns if a value for the field couldn't be found and returns undef. Args : string (the field to get) =cut sub get_field { my $self = shift; my $desired = shift || return keys %{$self->_fields}; if (exists $self->_fields->{$desired}) { unless (defined $self->_fields->{$desired}) { my $method = '_discover_'.$desired; my $dependency = $self->_dependencies($desired); if ($dependency && ! defined $self->_fields->{$dependency}) { $self->get_field($dependency); } # it might exist now $self->$method unless defined $self->_fields->{$desired}; } return $self->_fields->{$desired}; } # is it a field of our parent? (checks all ancestors) if (my $parent = $self->parent) { return $parent->get_field($desired); } $desired =~ s/_discover_//; $self->warn("This report does not hold information about '$desired'"); return; } =head2 parent Title : parent Usage : $obj->parent($parent_obj); my $parent_obj = $obj->parent; Function: Get/set the parent object of this one. Returns : Bio::PullParserI Args : none to get, OR Bio::PullParserI to set =cut sub parent { my $self = shift; if (@_) { $self->{parent} = shift } return $self->{parent} || return; } =head2 chunk Title : chunk Usage : $obj->chunk($filename); my $chunk = $obj->chunk; Function: Get/set the chunk of this parser. Returns : Bio:Root::IO Args : none to get, OR First argument of a GLOB reference, filename string, string data to treat as the chunk, or Bio::Root::IO. Optionally, also provide: -start => int : the byte position within the thing described by the first argument to consider as the start of this chunk (default 0) -end => int : the byte position to consider as the end (default true end) -piped_behaviour => 'memory'|'temp_file'|'sequential_read' The last option comes into effect when the first argument is something that cannot be seeked (eg. piped input filehandle). 'memory' means read all the piped input into a string first, then set the chunk to that string. 'temp_file' means read all the piped input and output it to a temp file, then set the chunk to that temp file. 'sequential_read' means that the piped input should be read sequentially and your parsing code must cope with not being able to seek. 'memory' is the fastest but uses the most memory. 'temp_file' and 'sequential_read' can be slow, with 'temp_file' being the most memory efficient but requiring disc space. The default is 'sequential_read'. Note that in versions of perl earlier than 5.8 only temp_file works and will be used regardless of what value is supplied here. =cut sub chunk { my $self = shift; if (@_) { my $thing = shift || $self->throw("Trying to set chunk() to an undefined value"); if (ref($thing) eq 'GLOB') { $self->{_chunk} = Bio::Root::IO->new(-fh => $thing); } elsif (ref(\$thing) eq 'SCALAR') { if ($thing !~ /\n/ && -e $thing) { $self->{_chunk} = Bio::Root::IO->new(-file => $thing); } else { unless ($FORCE_TEMP_FILE) { # treat a string as a filehandle open my $fake_fh, "+<", \$thing or $self->throw("Could not open file '$thing': $!"); # requires perl 5.8 $self->{_chunk} = Bio::Root::IO->new(-fh => $fake_fh); } else { my ($handle) = $self->{_chunk}->tempfile(); print $handle $thing; $self->{_chunk} = Bio::Root::IO->new(-fh => $handle); } } } elsif ($thing->isa('Bio::Root::IO')) { $self->{_chunk} = $thing; } else { $self->throw("Unknown input into chunk()"); } my ($piped_behaviour, $start, $end); if (@_) { ($piped_behaviour, $start, $end) = $self->_rearrange([qw(PIPED_BEHAVIOUR START END)], @_); } $piped_behaviour ||= 'sequential_read'; $FORCE_TEMP_FILE && ($piped_behaviour = 'temp_file'); $start ||= 0; $self->_chunk_true_start($start); $self->_chunk_true_end($end); # determine if the chunk is seekable my $fh = $self->{_chunk}->_fh; seek($fh, 0, 0); my $first_line = <$fh>; seek($fh, 0, 0); my $seekable = tell($fh) == 0; unless ($seekable) { if ($piped_behaviour eq 'memory') { my $string = $first_line; while (<$fh>) { $string .= $_; } $self->chunk($string); } elsif ($piped_behaviour eq 'temp_file') { my ($handle) = $self->{_chunk}->tempfile(); print $handle $first_line; while (<$fh>) { print $handle $_; } seek($handle, 0, 0); $self->chunk($handle); } elsif ($piped_behaviour eq 'sequential_read') { $self->{_chunk}->_pushback($first_line); $self->_sequential(1); } else { $self->throw("Unknown piped behaviour type '$piped_behaviour'"); } } # determine our line ending if ($first_line =~ /\r\n/) { $self->_line_ending("\r\n"); } elsif ($first_line =~ /\r/) { $self->_line_ending("\r"); } else { $self->_line_ending("\n"); } } return $self->{_chunk} || return; } =head2 _sequential Title : _sequential Usage : if ($obj->_sequential) {...} Function: Ask if we have to do operations such that the input is read sequentially. Returns : boolean Args : none to get, OR boolean to set (typically, you should never set this yourself) =cut sub _sequential { my $self = shift; if (@_) { $self->{_sequential} = shift; } return $self->{_sequential} || 0; } =head2 _dependencies Title : _dependencies Usage : $obj->_dependencies( { field1 => field2 } ); my $dependancy = $obj->_dependencies('field_name'); Function: Set the fields that are dependent on each other, or get the field than another is dependent upon. Returns : string (a field name) Args : string (a field name) to get, OR hash ref to initially set, with field names as keys and values, key field being dependent upon value field. =cut sub _dependencies { my ($self, $thing) = @_; $thing || return; if (ref($thing) eq 'HASH') { $self->{_dependencies} = $thing; } else { return $self->{_dependencies}->{$thing}; } } =head2 _chunk_true_start Title : _chunk_true_start Usage : my $true_start = $obj->_chunk_true_start; Function: Get/set the true start position of the chunk within the filehandle it is part of. Returns : int Args : none to get, OR int to set (typically, you won't set this yourself) =cut sub _chunk_true_start { my $self = shift; if (@_) { $self->{_chunk_start} = shift; } return $self->{_chunk_start} || 0; } =head2 _chunk_true_end Title : _chunk_true_end Usage : my $true_end = $obj->_chunk_true_end; Function: Get/set for the true end position of the chunk within the filehandle it is part of. Returns : int Args : none to get, OR int to set (typically, you won't set this yourself) =cut sub _chunk_true_end { my $self = shift; if (@_) { $self->{_chunk_end} = shift; } return $self->{_chunk_end}; } =head2 _line_ending Title : _line_ending Usage : my $line_ending = $obj->_line_ending; Function: Get/set for the line ending for the chunk. Returns : string Args : none to get, OR string to set (typically, you won't set this yourself) =cut sub _line_ending { my $self = shift; if (@_) { $self->{_chunk_line_ending} = shift; } return $self->{_chunk_line_ending}; } =head2 _chunk_seek Title : _chunk_seek Usage : $obj->_chunk_seek($pos); Function: seek() the chunk to the provided position in bytes, relative to the defined start of the chunk within its filehandle. In _sequential() mode, this function does nothing. Returns : n/a Args : int =cut sub _chunk_seek { my ($self, $pos) = @_; $self->throw("Undefined position passed") unless defined $pos; return if $self->_sequential; my $fh = $self->chunk->_fh; # seek to the defined start seek($fh, $self->_chunk_true_start, 0); # now seek to desired position relative to defined start seek($fh, $pos, 1); } =head2 _chunk_tell Title : _chunk_seek Usage : my $pos = $obj->_chunk_tell; Function: Get the current tell() position within the chunk, relative to the defined start of the chunk within its filehandle. In _sequential() mode, this function does nothing. Returns : int Args : none =cut sub _chunk_tell { my $self = shift; return if $self->_sequential; my $fh = $self->chunk->_fh; return tell($fh) - $self->_chunk_true_start; } =head2 _get_chunk_by_nol Title : _chunk_seek Usage : my $string = $obj->_get_chunk_by_nol; Function: Get a chunk of chunk() from the current position onward for the given number of lines. Returns : string Args : int (number of lines you want) =cut sub _get_chunk_by_nol { my ($self, $nol) = @_; $nol > 0 || $self->throw("Can't request a chunk of fewer than 1 lines"); # hope that $/ is \n my ($line, $count); while (defined($_ = $self->chunk->_readline)) { $line .= $_; $count++; last if $count == $nol; } my $current = $self->_chunk_tell; my $end = ($current || 0) + $self->_chunk_true_start; if (! $current || ($self->_chunk_true_end ? $end <= $self->_chunk_true_end : 1)) { return $line; } return; } =head2 _get_chunk_by_end Title : _get_chunk_by_end Usage : my $string = $obj->_get_chunk_by_end; Function: Get a chunk of chunk() from the current position onward till the end of the line, as defined by the supplied argument. Returns : string Args : string (line ending - if you want the line ending to include a new line, always use \n) =cut sub _get_chunk_by_end { my ($self, $chunk_ending) = @_; my $start = $self->_chunk_tell; my $line_ending = $self->_line_ending; $chunk_ending =~ s/\n/$line_ending/g; local $/ = $chunk_ending || ''; my $line = $self->chunk->_readline; my $current = $self->_chunk_tell; my $end = ($current || 0) + $self->_chunk_true_start; if (! $current || ($self->_chunk_true_end ? $end <= $self->_chunk_true_end : 1)) { return $line; } $self->_chunk_seek($start); return; } =head2 _find_chunk_by_end Title : _find_chunk_by_end Usage : my $string = $obj->_find_chunk_by_end; Function: Get the start and end of what would be a chunk of chunk() from the current position onward till the end of the line, as defined by the supplied argument. In _sequential() mode, this function does nothing. Returns : _chunk_tell values for start and end in 2 element list Args : string (line ending - if you want the line ending to include a new line, always use \n) =cut sub _find_chunk_by_end { my ($self, $chunk_ending) = @_; return if $self->_sequential; my $line_ending = $self->_line_ending; $chunk_ending =~ s/\n/$line_ending/g; local $/ = $chunk_ending || ''; my $start = $self->_chunk_tell; $self->chunk->_readline; my $end = $self->_chunk_tell; my $comp_end = $end + $self->_chunk_true_start; if ($self->_chunk_true_end ? $comp_end <= $self->_chunk_true_end : 1) { return ($start, $end); } $self->_chunk_seek($start); return; } =head2 AUTOLOAD Title : AUTOLOAD Usage : n/a Function: Assumes that any unknown method called should be treated as get_field($method_name). Returns : n/a Args : n/a =cut sub AUTOLOAD { my $self = shift; ref($self) || return; my $name = $AUTOLOAD; $name =~ s/.*://; # strip fully-qualified portion # is it one of our fields? return $self->get_field($name); } 1; BioPerl-1.007002/Bio/Range.pm000444000766000024 2121413155576320 15636 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Range # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho # # Copywright Matthew Pocock # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code # =head1 NAME Bio::Range - Pure perl RangeI implementation =head1 SYNOPSIS $range = Bio::Range->new(-start=>10, -end=>30, -strand=>+1); $r2 = Bio::Range->new(-start=>15, -end=>200, -strand=>+1); print join(', ', $range->union($r2)), "\n"; print join(', ', $range->intersection($r2)), "\n"; print $range->overlaps($r2), "\n"; print $range->contains($r2), "\n"; =head1 DESCRIPTION This provides a pure perl implementation of the BioPerl range interface. Ranges are modeled as having (start, end, length, strand). They use Bio-coordinates - all points E= start and E= end are within the range. End is always greater-than or equal-to start, and length is greather than or equal to 1. The behaviour of a range is undefined if ranges with negative numbers or zero are used. So, in summary: length = end - start + 1 end >= start strand = (-1 | 0 | +1) =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Range; use strict; use Carp; use integer; use base qw(Bio::Root::Root Bio::RangeI); =head1 Constructors =head2 new Title : new Usage : $range = Bio::Range->new(-start => 100, -end=> 200, -strand = +1); Function: generates a new Bio::Range Returns : a new range Args : -strand (defaults to 0) and any two of (-start, -end, -length), the third will be calculated =cut sub new { my ($caller, @args) = @_; my $self = $caller->SUPER::new(@args); my ($strand, $start, $end, $length) = $self->_rearrange([qw(STRAND START END LENGTH )],@args); $self->strand($strand || 0); if(defined $start ) { $self->start($start); if(defined $end) { $self->end($end); } elsif(defined $length) { $self->end($self->start()+ $length - 1); } } elsif(defined $end && defined $length ) { $self->end($end); $self->start($self->end() - $length + 1); } return $self; } =head2 unions Title : unions Usage : @unions = Bio::Range->unions(@ranges); Function: generate a list of non-intersecting Bio::Range objects from a list of Bio::Range objects which may intersect Returns : a list of Bio::Range objects Args : a list of Bio::Range objects =cut sub unions { my ($class,@i) = @_; my $i = 0; my %i = map { $i++ => $_ } @i; my $lastsize = scalar(keys %i); do { foreach my $j (sort { $i{$a}->start <=> $i{$b}->start } keys %i){ foreach my $k (sort { $i{$a}->start <=> $i{$b}->start } keys %i){ #it may have been replaced by a union under the key of #the overlapping range, we are altering the hash in-place next unless $i{$j}; next if $i{$k}->end < $i{$j}->start; last if $i{$k}->start > $i{$j}->end; if($i{$j}->overlaps($i{$k})){ my($start,$end,$strand) = $i{$j}->union($i{$k}); delete($i{$k}); $i{$j} = Bio::Range->new( -start => $start , -end => $end , -strand => $strand ); } } } goto DONE if scalar(keys %i) == $lastsize; $lastsize = scalar(keys %i); #warn $lastsize; } while(1); DONE: return values %i; } =head1 Member variable access These methods let you get at and set the member variables =head2 start Title : start Function : return or set the start co-ordinate Example : $s = $range->start(); $range->start(7); Returns : the value of the start co-ordinate Args : optionally, the new start co-ordinate Overrides: Bio::RangeI::start =cut sub start { my ($self,$value) = @_; if( defined $value) { $self->throw("'$value' is not an integer.\n") unless $value =~ /^[-+]?\d+$/; $self->{'start'} = $value; } return $self->{'start'}; } =head2 end Title : end Function : return or set the end co-ordinate Example : $e = $range->end(); $range->end(2000); Returns : the value of the end co-ordinate Args : optionally, the new end co-ordinate Overrides: Bio::RangeI::end =cut sub end { my ($self,$value) = @_; if( defined $value) { $self->throw("'$value' is not an integer.\n") unless $value =~ /^[-+]?\d+$/; $self->{'end'} = $value; } return $self->{'end'}; } =head2 strand Title : strand Function : return or set the strandedness Example : $st = $range->strand(); $range->strand(-1); Returns : the value of the strandedness (-1, 0 or 1) Args : optionally, the new strand - (-1, 0, 1) or (-, ., +). Overrides: Bio::RangeI::strand =cut { my %VALID_STRAND = ( -1 => -1, 0 => 0, 1 => 1, '+' => 1, '-' => -1, '.' => 0 ); sub strand { my $self = shift; if(@_) { my $val = shift; if (exists $VALID_STRAND{$val}) { $self->{'strand'} = $VALID_STRAND{$val}; } else { $self->throw("Invalid strand: $val"); } } return $self->{'strand'}; } } =head2 length Title : length Function : returns the length of this range Example : $length = $range->length(); Returns : the length of this range, equal to end - start + 1 Args : if you attempt to set the length an exception will be thrown Overrides: Bio::RangeI::Length =cut sub length { my $self = shift; if(@_) { confess ref($self), "->length() is read-only"; } return $self->end() - $self->start() + 1; } =head2 toString Title : toString Function: stringifies this range Example : print $range->toString(), "\n"; Returns : a string representation of this range =cut sub toString { my $self = shift; return "(${\$self->start}, ${\$self->end}) strand=${\$self->strand}"; } =head1 Boolean Methods These methods return true or false. $range->overlaps($otherRange) && print "Ranges overlap\n"; =head2 overlaps Title : overlaps Usage : if($r1->overlaps($r2)) { do stuff } Function : tests if $r2 overlaps $r1 Args : a range to test for overlap with Returns : true if the ranges overlap, false otherwise Inherited: Bio::RangeI =head2 contains Title : contains Usage : if($r1->contains($r2) { do stuff } Function : tests whether $r1 totally contains $r2 Args : a range to test for being contained Returns : true if the argument is totally contained within this range Inherited: Bio::RangeI =head2 equals Title : equals Usage : if($r1->equals($r2)) Function : test whether $r1 has the same start, end, length as $r2 Args : a range to test for equality Returns : true if they are describing the same range Inherited: Bio::RangeI =head1 Geometrical methods These methods do things to the geometry of ranges, and return triplets (start, end, strand) from which new ranges could be built. =head2 intersection Title : intersection Usage : ($start, $stop, $strand) = $r1->intersection($r2) Function : gives the range that is contained by both ranges Args : a range to compare this one to Returns : nothing if they do not overlap, or the range that they do overlap Inherited: Bio::RangeI::intersection =cut =head2 union Title : union Usage : ($start, $stop, $strand) = $r1->union($r2); : ($start, $stop, $strand) = Bio::Range->union(@ranges); Function : finds the minimal range that contains all of the ranges Args : a range or list of ranges Returns : the range containing all of the ranges Inherited: Bio::RangeI::union =cut 1; BioPerl-1.007002/Bio/RangeI.pm000444000766000024 4664013155576320 15761 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::RangeI # # Please direct questions and support issues to # # Cared for by Lehvaslaiho # # Copyright Matthew Pocock # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::RangeI - Range interface =head1 SYNOPSIS #Do not run this module directly =head1 DESCRIPTION This provides a standard BioPerl range interface that should be implemented by any object that wants to be treated as a range. This serves purely as an abstract base class for implementers and can not be instantiated. Ranges are modeled as having (start, end, length, strand). They use Bio-coordinates - all points E= start and E= end are within the range. End is always greater-than or equal-to start, and length is greater than or equal to 1. The behaviour of a range is undefined if ranges with negative numbers or zero are used. So, in summary: length = end - start + 1 end >= start strand = (-1 | 0 | +1) =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 CONTRIBUTORS Juha Muilu (muilu@ebi.ac.uk) Sendu Bala (bix@sendu.me.uk) Malcolm Cook (mec@stowers-institute.org) Stephen Montgomery (sm8 at sanger.ac.uk) =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::RangeI; use strict; use Carp; use integer; use vars qw(%STRAND_OPTIONS); use base qw(Bio::Root::RootI); BEGIN { # STRAND_OPTIONS contains the legal values for the strand-testing options %STRAND_OPTIONS = map { $_, '_' . $_ } ( 'strong', # ranges must have the same strand 'weak', # ranges must have the same strand or no strand 'ignore', # ignore strand information ); } # utility methods # # returns true if strands are equal and non-zero sub _strong { my ($r1, $r2) = @_; my ($s1, $s2) = ($r1->strand(), $r2->strand()); return 1 if $s1 != 0 && $s1 == $s2; } # returns true if strands are equal or either is zero sub _weak { my ($r1, $r2) = @_; my ($s1, $s2) = ($r1->strand(), $r2->strand()); return 1 if $s1 == 0 || $s2 == 0 || $s1 == $s2; } # returns true for any strandedness sub _ignore { return 1; } # works out what test to use for the strictness and returns true/false # e.g. $r1->_testStrand($r2, 'strong') sub _testStrand() { my ($r1, $r2, $comp) = @_; return 1 unless $comp; my $func = $STRAND_OPTIONS{$comp}; return $r1->$func($r2); } =head1 Abstract methods These methods must be implemented in all subclasses. =head2 start Title : start Usage : $start = $range->start(); Function: get/set the start of this range Returns : the start of this range Args : optionally allows the start to be set using $range->start($start) =cut sub start { shift->throw_not_implemented(); } =head2 end Title : end Usage : $end = $range->end(); Function: get/set the end of this range Returns : the end of this range Args : optionally allows the end to be set using $range->end($end) =cut sub end { shift->throw_not_implemented(); } =head2 length Title : length Usage : $length = $range->length(); Function: get/set the length of this range Returns : the length of this range Args : optionally allows the length to be set using $range->length($length) =cut sub length { shift->throw_not_implemented(); } =head2 strand Title : strand Usage : $strand = $range->strand(); Function: get/set the strand of this range Returns : the strandedness (-1, 0, +1) Args : optionally allows the strand to be set using $range->strand($strand) =cut sub strand { shift->throw_not_implemented(); } =head1 Boolean Methods These methods return true or false. They throw an error if start and end are not defined. $range->overlaps($otherRange) && print "Ranges overlap\n"; =head2 overlaps Title : overlaps Usage : if($r1->overlaps($r2)) { do stuff } Function: tests if $r2 overlaps $r1 Args : arg #1 = a range to compare this one to (mandatory) arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore') Returns : true if the ranges overlap, false otherwise =cut sub overlaps { my ($self, $other, $so) = @_; $self->throw("start is undefined") unless defined $self->start; $self->throw("end is undefined") unless defined $self->end; $self->throw("not a Bio::RangeI object") unless defined $other && $other->isa('Bio::RangeI'); $other->throw("start is undefined") unless defined $other->start; $other->throw("end is undefined") unless defined $other->end; return ($self->_testStrand($other, $so) and not ( ($self->start() > $other->end() or $self->end() < $other->start() ) )); } =head2 contains Title : contains Usage : if($r1->contains($r2) { do stuff } Function: tests whether $r1 totally contains $r2 Args : arg #1 = a range to compare this one to (mandatory) alternatively, integer scalar to test arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore') Returns : true if the argument is totally contained within this range =cut sub contains { my ($self, $other, $so) = @_; $self->throw("start is undefined") unless defined $self->start; $self->throw("end is undefined") unless defined $self->end; if(defined $other && ref $other) { # a range object? $other->throw("Not a Bio::RangeI object: $other") unless $other->isa('Bio::RangeI'); $other->throw("start is undefined") unless defined $other->start; $other->throw("end is undefined") unless defined $other->end; return ($self->_testStrand($other, $so) and $other->start() >= $self->start() and $other->end() <= $self->end()); } else { # a scalar? $self->throw("'$other' is not an integer.\n") unless $other =~ /^[-+]?\d+$/; return ($other >= $self->start() and $other <= $self->end()); } } =head2 equals Title : equals Usage : if($r1->equals($r2)) Function: test whether $r1 has the same start, end, length as $r2 Args : arg #1 = a range to compare this one to (mandatory) arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore') Returns : true if they are describing the same range =cut sub equals { my ($self, $other, $so) = @_; $self->throw("start is undefined") unless defined $self->start; $self->throw("end is undefined") unless defined $self->end; $other->throw("Not a Bio::RangeI object") unless $other->isa('Bio::RangeI'); $other->throw("start is undefined") unless defined $other->start; $other->throw("end is undefined") unless defined $other->end; return ($self->_testStrand($other, $so) and $self->start() == $other->start() and $self->end() == $other->end() ); } =head1 Geometrical methods These methods do things to the geometry of ranges, and return Bio::RangeI compliant objects or triplets (start, stop, strand) from which new ranges could be built. =head2 intersection Title : intersection Usage : ($start, $end, $strand) = $r1->intersection($r2); OR ($start, $end, $strand) = Bio::Range->intersection(\@ranges); OR my $containing_range = $r1->intersection($r2); OR my $containing_range = Bio::Range->intersection(\@ranges); Function: gives the range that is contained by all ranges Returns : undef if they do not overlap or if @ranges has only a single range, else returns the range that they do overlap. In scalar contex, the return value is an object of the same class as the calling one. In array context the return value is a three element array. Args : arg #1 = [REQUIRED] a Bio::RangeI to compare this one to, or an array ref of ranges arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore') =cut sub intersection { my ($self, $given, $so) = @_; $self->throw("missing arg: you need to pass in another feature") unless $given; my @ranges; if ($self eq "Bio::RangeI") { $self = "Bio::Range"; $self->warn("calling static methods of an interface is deprecated; use $self instead"); } if (ref $self) { push(@ranges, $self); } ref($given) eq 'ARRAY' ? push(@ranges, @{$given}) : push(@ranges, $given); #$self->throw("Need at least 2 ranges") unless @ranges >= 2; # Rather than the above, I think the following is more consistent return undef unless @ranges >= 2; my $intersect; while (@ranges > 0) { unless ($intersect) { $intersect = shift(@ranges); $self->throw("Not an object: $intersect") unless ref($intersect); $self->throw("Not a Bio::RangeI object: $intersect") unless $intersect->isa('Bio::RangeI'); $self->throw("start is undefined") unless defined $intersect->start; $self->throw("end is undefined") unless defined $intersect->end; } my $compare = shift(@ranges); $self->throw("Not an object: $compare") unless ref($compare); $self->throw("Not a Bio::RangeI object: $compare") unless $compare->isa('Bio::RangeI'); $self->throw("start is undefined") unless defined $compare->start; $self->throw("end is undefined") unless defined $compare->end; return unless $compare->_testStrand($intersect, $so); my @starts = sort {$a <=> $b} ($intersect->start(), $compare->start()); my @ends = sort {$a <=> $b} ($intersect->end(), $compare->end()); my $start = pop @starts; # larger of the 2 starts my $end = shift @ends; # smaller of the 2 ends my $intersect_strand; # strand for the intersection if (defined($intersect->strand) && defined($compare->strand) && $intersect->strand == $compare->strand) { $intersect_strand = $compare->strand; } else { $intersect_strand = 0; } if ($start > $end) { return; } else { $intersect = $self->new(-start => $start, -end => $end, -strand => $intersect_strand); } } if (wantarray()) { return ($intersect->start, $intersect->end, $intersect->strand); } else { return $intersect; } } =head2 union Title : union Usage : ($start, $end, $strand) = $r1->union($r2); : ($start, $end, $strand) = Bio::Range->union(@ranges); my $newrange = Bio::Range->union(@ranges); Function: finds the minimal Range that contains all of the Ranges Args : a Range or list of Range objects Returns : the range containing all of the range. In scalar contex, the return value is an object of the same class as the calling one. In array context the return value is a three element array. =cut sub union { my $self = shift; my @ranges = @_; if ($self eq "Bio::RangeI") { $self = "Bio::Range"; $self->warn("calling static methods of an interface is deprecated; use $self instead"); } if(ref $self) { unshift @ranges, $self; } my @start = sort {$a<=>$b} map( { $_->start() } @ranges); my @end = sort {$a<=>$b} map( { $_->end() } @ranges); my $start = shift @start; while( !defined $start ) { $start = shift @start; } my $end = pop @end; my $union_strand; # Strand for the union range object. foreach(@ranges) { if(! defined $union_strand) { $union_strand = $_->strand; next; } else { if(not defined $_->strand or $union_strand ne $_->strand) { $union_strand = 0; last; } } } return unless $start or $end; if( wantarray() ) { return ( $start,$end,$union_strand); } else { return $self->new('-start' => $start, '-end' => $end, '-strand' => $union_strand ); } } =head2 overlap_extent Title : overlap_extent Usage : ($a_unique,$common,$b_unique) = $a->overlap_extent($b) Function: Provides actual amount of overlap between two different ranges Example : Returns : array of values containing the length unique to the calling range, the length common to both, and the length unique to the argument range Args : a range =cut sub overlap_extent{ my ($a,$b) = @_; $a->throw("start is undefined") unless defined $a->start; $a->throw("end is undefined") unless defined $a->end; $b->throw("Not a Bio::RangeI object") unless $b->isa('Bio::RangeI'); $b->throw("start is undefined") unless defined $b->start; $b->throw("end is undefined") unless defined $b->end; if( ! $a->overlaps($b) ) { return ($a->length,0,$b->length); } my ($au,$bu) = (0, 0); if( $a->start < $b->start ) { $au = $b->start - $a->start; } else { $bu = $a->start - $b->start; } if( $a->end > $b->end ) { $au += $a->end - $b->end; } else { $bu += $b->end - $a->end; } my $intersect = $a->intersection($b); if( ! $intersect ) { warn("no intersection\n"); return ($au, 0, $bu); } else { my $ie = $intersect->end; my $is = $intersect->start; return ($au,$ie-$is+1,$bu); } } =head2 disconnected_ranges Title : disconnected_ranges Usage : my @disc_ranges = Bio::Range->disconnected_ranges(@ranges); Function: finds the minimal set of ranges such that each input range is fully contained by at least one output range, and none of the output ranges overlap Args : a list of ranges Returns : a list of objects of the same type as the input (conforms to RangeI) =cut sub disconnected_ranges { my $self = shift; if ($self eq "Bio::RangeI") { $self = "Bio::Range"; $self->warn("calling static methods of an interface is deprecated; use $self instead"); } my @inranges = @_; if(ref $self) { unshift @inranges, $self; } my @outranges = (); # disconnected ranges # iterate through all input ranges $inrange, # adding each input range to the set of output ranges @outranges, # provided $inrange does not overlap ANY range in @outranges # - if it does overlap an outrange, then merge it foreach my $inrange (@inranges) { my $intersects = 0; my @outranges_new = (); my @intersecting_ranges = (); # iterate through all @outranges, testing if it intersects # current $inrange; if it does, merge and add to list # of @intersecting_ranges, otherwise add $outrange to # the new list of outranges that do NOT intersect for (my $i=0; $i<@outranges; $i++) { my $outrange = $outranges[$i]; my $intersection = $inrange->intersection($outrange); if ($intersection) { $intersects = 1; my $union = $inrange->union($outrange); push(@intersecting_ranges, $union); } else { push(@outranges_new, $outrange); } } @outranges = @outranges_new; # @outranges now contains a list of non-overlapping ranges # that do not intersect the current $inrange if (@intersecting_ranges) { if (@intersecting_ranges > 1) { # this sf intersected > 1 range, which means that # all the ranges it intersects should be joined # together in a new range my $merged_range = $self->union(@intersecting_ranges); push(@outranges, $merged_range); } else { # exactly 1 intersecting range push(@outranges, @intersecting_ranges); } } else { # no intersections found - new range push(@outranges, $self->new('-start'=>$inrange->start, '-end'=>$inrange->end, '-strand'=>$inrange->strand, )); } } return @outranges; } =head2 offsetStranded Title : offsetStranded Usage : $rnge->ofsetStranded($fiveprime_offset, $threeprime_offset) Function : destructively modifies RangeI implementing object to offset its start and stop coordinates by values $fiveprime_offset and $threeprime_offset (positive values being in the strand direction). Args : two integer offsets: $fiveprime_offset and $threeprime_offset Returns : $self, offset accordingly. =cut sub offsetStranded { my ($self, $offset_fiveprime, $offset_threeprime) = @_; my ($offset_start, $offset_end) = $self->strand() eq -1 ? (- $offset_threeprime, - $offset_fiveprime) : ($offset_fiveprime, $offset_threeprime); $self->start($self->start + $offset_start); $self->end($self->end + $offset_end); return $self; }; =head2 subtract Title : subtract Usage : my @subtracted = $r1->subtract($r2) Function: Subtract range r2 from range r1 Args : arg #1 = a range to subtract from this one (mandatory) arg #2 = strand option ('strong', 'weak', 'ignore') (optional) Returns : undef if they do not overlap or r2 contains this RangeI, or an arrayref of Range objects (this is an array since some instances where the subtract range is enclosed within this range will result in the creation of two new disjoint ranges) =cut sub subtract() { my ($self, $range, $so) = @_; $self->throw("missing arg: you need to pass in another feature") unless $range; return unless $self->_testStrand($range, $so); if ($self eq "Bio::RangeI") { $self = "Bio::Range"; $self->warn("calling static methods of an interface is deprecated; use $self instead"); } $range->throw("Input a Bio::RangeI object") unless $range->isa('Bio::RangeI'); my @sub_locations; if ($self->location->isa('Bio::Location::SplitLocationI') ) { @sub_locations = $self->location->sub_Location; } else { @sub_locations = $self; } my @outranges; foreach my $sl (@sub_locations) { if (!$sl->overlaps($range)) { push(@outranges, $self->new('-start' =>$sl->start, '-end' =>$sl->end, '-strand'=>$sl->strand, )); next; } ##Subtracts everything if ($range->contains($sl)) { next; } my ($start, $end, $strand) = $sl->intersection($range, $so); ##Subtract intersection from $self range if ($sl->start < $start) { push(@outranges, $self->new('-start' =>$sl->start, '-end' =>$start - 1, '-strand'=>$sl->strand, )); } if ($sl->end > $end) { push(@outranges, $self->new('-start' =>$end + 1, '-end' =>$sl->end, '-strand'=>$sl->strand, )); } } if (@outranges) { return \@outranges; } return; } 1; BioPerl-1.007002/Bio/SearchDist.pm000444000766000024 1260413155576320 16636 0ustar00cjfieldsstaff000000000000 # # BioPerl module for Bio::SearchDist # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchDist - A perl wrapper around Sean Eddy's histogram object =head1 SYNOPSIS $dis = Bio::SearchDist->new(); foreach $score ( @scores ) { $dis->add_score($score); } if( $dis->fit_evd() ) { foreach $score ( @scores ) { $evalue = $dis->evalue($score); print "Score $score had an evalue of $evalue\n"; } } else { warn("Could not fit histogram to an EVD!"); } =head1 DESCRIPTION The Bio::SearchDist object is a wrapper around Sean Eddy's excellent histogram object. The histogram object can bascially take in a number of scores which are sensibly distributed somewhere around 0 that come from a supposed Extreme Value Distribution. Having add all the scores from a database search via the add_score method you can then fit a extreme value distribution using fit_evd(). Once fitted you can then get out the evalue for each score (or a new score) using evalue($score). The fitting procedure is better described in Sean Eddy's own code (available from http://hmmer.janelia.org/, or in the histogram.h header file in Compile/SW). Bascially it fits a EVD via a maximum likelhood method with pruning of the top end of the distribution so that real positives are discarded in the fitting procedure. This comes from an originally idea of Richard Mott's and the likelhood fitting is from a book by Lawless [should ref here]. The object relies on the fact that the scores are sensibly distributed around about 0 and that integer bins are sensible for the histogram. Scores based on bits are often ideal for this (bits based scoring mechanisms is what this histogram object was originally designed for). =head1 CONTACT The original code this was based on comes from the histogram module as part of the HMMer2 package. Look at http://hmmer.janelia.org/ Its use in Bioperl is via the Compiled XS extension which is cared for by Ewan Birney (birney@ebi.ac.uk). Please contact Ewan first about the use of this module =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchDist; use strict; BEGIN { eval { require Bio::Ext::Align; }; if ( $@ ) { print $@; print STDERR ("\nThe C-compiled engine for histogram object (Bio::Ext::Align) has not been installed.\n Please install the bioperl-ext package\n\n"); exit(1); } } use base qw(Bio::Root::Root); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my($min, $max, $lump) = $self->_rearrange([qw(MIN MAX LUMP)], @args); if( ! $min ) { $min = -100; } if( ! $max ) { $max = +100; } if( ! $lump ) { $lump = 50; } $self->_engine(&Bio::Ext::Align::new_Histogram($min,$max,$lump)); return $self; } =head2 add_score Title : add_score Usage : $dis->add_score(300); Function: Adds a single score to the distribution Returns : nothing Args : =cut sub add_score{ my ($self,$score) = @_; my ($eng); $eng = $self->_engine(); #$eng->AddToHistogram($score); $eng->add($score); } =head2 fit_evd Title : fit_evd Usage : $dis->fit_evd(); Function: fits an evd to the current distribution Returns : 1 if it fits successfully, 0 if not Args : =cut sub fit_evd{ my ($self,@args) = @_; return $self->_engine()->fit_EVD(10000,1); } =head2 fit_Gaussian Title : fit_Gaussian Usage : Function: Example : Returns : Args : =cut sub fit_Gaussian{ my ($self,$high) = @_; if( ! defined $high ) { $high = 10000; } return $self->_engine()->fit_Gaussian($high); } =head2 evalue Title : evalue Usage : $eval = $dis->evalue($score) Function: Returns the evalue of this score Returns : float Args : =cut sub evalue{ my ($self,$score) = @_; return $self->_engine()->evalue($score); } =head2 _engine Title : _engine Usage : $obj->_engine($newval) Function: underlyine bp_sw:: histogram engine Returns : value of _engine Args : newvalue (optional) =cut sub _engine{ my ($self,$value) = @_; if( defined $value) { $self->{'_engine'} = $value; } return $self->{'_engine'}; } ## End of Package 1; __END__ BioPerl-1.007002/Bio/SearchIO.pm000444000766000024 5351013155576320 16243 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...) =head1 SYNOPSIS use Bio::SearchIO; # format can be 'fasta', 'blast', 'exonerate', ... my $searchio = Bio::SearchIO->new( -format => 'blastxml', -file => 'blastout.xml' ); while ( my $result = $searchio->next_result() ) { while( my $hit = $result->next_hit ) { # process the Bio::Search::Hit::HitI object while( my $hsp = $hit->next_hsp ) { # process the Bio::Search::HSP::HSPI object } } } =head1 DESCRIPTION This is a driver for instantiating a parser for report files from sequence database searches. This object serves as a wrapper for the format parsers in Bio::SearchIO::* - you should not need to ever use those format parsers directly. (For people used to the SeqIO system it, we are deliberately using the same pattern). Once you get a SearchIO object, calling next_result() gives you back a L compliant object, which is an object that represents one Blast/Fasta/HMMER whatever report. A list of module names and formats is below: blast BLAST (WUBLAST, NCBIBLAST,bl2seq) fasta FASTA -m9 and -m0 blasttable BLAST -m9 or -m8 output (both NCBI and WUBLAST tabular) megablast MEGABLAST psl UCSC PSL format waba WABA output axt AXT format sim4 Sim4 hmmer HMMER2 hmmpfam and hmmsearch or HMMER3 hmmscan and hmmsearch exonerate Exonerate CIGAR and VULGAR format blastxml NCBI BLAST XML wise Genewise -genesf format Also see the SearchIO HOWTO: http://bioperl.org/howtos/SearchIO_HOWTO.html =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich & Steve Chervitz Email jason-at-bioperl.org Email sac-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO; use strict; use warnings; # Object preamble - inherits from Bio::Root::IO use Bio::SearchIO::SearchResultEventBuilder; # Special exception class for exceptions during parsing. # End users should not ever see these. # For an example of usage, see blast.pm. @Bio::SearchIO::InternalParserError::ISA = qw(Bio::Root::Exception); use Symbol; use base qw(Bio::Root::IO Bio::Event::EventGeneratorI Bio::AnalysisParserI); =head2 new Title : new Usage : my $obj = Bio::SearchIO->new(); Function: Builds a new Bio::SearchIO object Returns : Bio::SearchIO initialized with the correct format Args : -file => $filename -format => format -fh => filehandle to attach to -result_factory => object implementing Bio::Factory::ObjectFactoryI -hit_factory => object implementing Bio::Factory::ObjectFactoryI -hsp_factory => object implementing Bio::Factory::ObjectFactoryI -writer => object implementing Bio::SearchIO::SearchWriterI -output_format => output format, which will dynamically load writer -inclusion_threshold => e-value threshold for inclusion in the PSI-BLAST score matrix model -signif => float or scientific notation number to be used as a P- or Expect value cutoff -check_all_hits => boolean. Check all hits for significance against significance criteria. Default = false. If false, stops processing hits after the first non-significant hit or the first hit that fails the hit_filter call. This speeds parsing, taking advantage of the fact that the hits are processed in the order they appear in the report. -min_query_len => integer to be used as a minimum for query sequence length. Reports with query sequences below this length will not be processed. default = no minimum length. -best => boolean. Only process the best hit of each report; default = false. See L, L Any factory objects in the arguments are passed along to the SearchResultEventBuilder object which holds these factories and sets default ones if none are supplied as arguments. =cut # TODO: The below don't seem to be implemented (e.g. in Bio::SearchIO::blast) # # -score => integer or scientific notation number to be used # as a blast score value cutoff # -bits => integer or scientific notation number to be used # as a bit score value cutoff # -overlap => integer. The amount of overlap to permit between # adjacent HSPs when tiling HSPs. A reasonable value is 2. # default = $Bio::SearchIO::blast::MAX_HSP_OVERLAP. sub new { my($caller,@args) = @_; my $class = ref($caller) || $caller; # or do we want to call SUPER on an object if $caller is an # object? if( $class =~ /Bio::SearchIO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $format = $param{'-format'} || $class->_guess_format( $param{'-file'} || $ARGV[0] ) || 'blast'; my $output_format = $param{'-output_format'}; my $writer = undef; if( defined $output_format ) { if( defined $param{'-writer'} ) { my $dummy = Bio::Root::Root->new(); $dummy->throw("Both writer and output format specified - not good"); } if( $output_format =~ /^blast$/i ) { $output_format = 'TextResultWriter'; } my $output_module = "Bio::SearchIO::Writer::".$output_format; $class->_load_module($output_module); $writer = $output_module->new(@args); push(@args,"-writer",$writer); } # normalize capitalization to lower case $format = "\L$format"; return unless( $class->_load_format_module($format) ); return "Bio::SearchIO::${format}"->new(@args); } } sub _initialize { my($self, @args) = @_; $self->{'_handler'} = undef; # not really necessary unless we put more in RootI #$self->SUPER::_initialize(@args); # initialize the IO part $self->_initialize_io(@args); $self->attach_EventHandler(Bio::SearchIO::SearchResultEventBuilder->new(@args)); $self->{'_reporttype'} = ''; $self->{_notfirsttime} = 0; my ($min_qlen, $check_all, $overlap, $best, $it, $writer ) = $self->_rearrange([qw( MIN_LENGTH CHECK_ALL_HITS OVERLAP BEST INCLUSION_THRESHOLD WRITER)], @args); # note: $overlap isn't used for some reason $writer && $self->writer( $writer ); defined $it && $self->inclusion_threshold($it); defined $min_qlen && $self->min_query_length($min_qlen); defined $best && $self->best_hit_only($best); defined $check_all && $self->check_all_hits($check_all); } =head2 newFh Title : newFh Usage : $fh = Bio::SearchIO->newFh(-file=>$filename, -format=>'Format') Function: does a new() followed by an fh() Example : $fh = Bio::SearchIO->newFh(-file=>$filename, -format=>'Format') $result = <$fh>; # read a ResultI object print $fh $result; # write a ResultI object Returns : filehandle tied to the Bio::SearchIO::Fh class Args : =cut sub newFh { my $class = shift; return unless my $self = $class->new(@_); return $self->fh; } =head2 fh Title : fh Usage : $obj->fh Function: Example : $fh = $obj->fh; # make a tied filehandle $result = <$fh>; # read a ResultI object print $fh $result; # write a ResultI object Returns : filehandle tied to the Bio::SearchIO::Fh class Args : =cut sub fh { my $self = shift; my $class = ref($self) || $self; my $s = Symbol::gensym; tie $$s,$class,$self; return $s; } =head2 format Title : format Usage : $format = $obj->format() Function: Get the search format Returns : search format Args : none =cut # format() method inherited from Bio::Root::IO =head2 attach_EventHandler Title : attach_EventHandler Usage : $parser->attatch_EventHandler($handler) Function: Adds an event handler to listen for events Returns : none Args : Bio::SearchIO::EventHandlerI See L =cut sub attach_EventHandler{ my ($self,$handler) = @_; return if( ! $handler ); if( ! $handler->isa('Bio::SearchIO::EventHandlerI') ) { $self->warn("Ignoring request to attatch handler ".ref($handler). ' because it is not a Bio::SearchIO::EventHandlerI'); } $self->{'_handler'} = $handler; return; } =head2 _eventHandler Title : _eventHandler Usage : private Function: Get the EventHandler Returns : Bio::SearchIO::EventHandlerI Args : none See L =cut sub _eventHandler{ my ($self) = @_; return $self->{'_handler'}; } =head2 next_result Title : next_result Usage : $result = stream->next_result Function: Reads the next ResultI object from the stream and returns it. Certain driver modules may encounter entries in the stream that are either misformatted or that use syntax not yet understood by the driver. If such an incident is recoverable, e.g., by dismissing a feature of a feature table or some other non-mandatory part of an entry, the driver will issue a warning. In the case of a non-recoverable situation an exception will be thrown. Do not assume that you can resume parsing the same stream after catching the exception. Note that you can always turn recoverable errors into exceptions by calling $stream->verbose(2) (see Bio::Root::RootI POD page). Returns : A Bio::Search::Result::ResultI object Args : n/a See L =cut sub next_result { my ($self) = @_; $self->throw_not_implemented; } =head2 write_result Title : write_result Usage : $stream->write_result($result_result, @other_args) Function: Writes data from the $result_result object into the stream. : Delegates to the to_string() method of the associated : WriterI object. Returns : 1 for success and 0 for error Args : Bio::Search:Result::ResultI object, : plus any other arguments for the Writer Throws : Bio::Root::Exception if a Writer has not been set. See L =cut sub write_result { my ($self, $result, @args) = @_; if( not ref($self->{'_result_writer'}) ) { $self->throw("ResultWriter not defined."); } @args = $self->{'_notfirsttime'} unless( @args ); my $str = $self->writer->to_string( $result, @args); $self->{'_notfirsttime'} = 1; $self->_print( "$str" ) if defined $str; $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 write_report Title : write_report Usage : $stream->write_report(SearchIO stream, @other_args) Function: Writes data directly from the SearchIO stream object into the : writer. This is mainly useful if one has multiple ResultI objects : in a SearchIO stream and you don't want to reiterate header/footer : between each call. Returns : 1 for success and 0 for error Args : Bio::SearchIO stream object, : plus any other arguments for the Writer Throws : Bio::Root::Exception if a Writer has not been set. See L =cut sub write_report { my ($self, $result, @args) = @_; if( not ref($self->{'_result_writer'}) ) { $self->throw("ResultWriter not defined."); } @args = $self->{'_notfirsttime'} unless( @args ); my $str = $self->writer->to_string( $result, @args); $self->{'_notfirsttime'} = 1; $self->_print( "$str" ) if defined $str; $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 writer Title : writer Usage : $writer = $stream->writer; Function: Sets/Gets a SearchWriterI object to be used for this searchIO. Returns : 1 for success and 0 for error Args : Bio::SearchIO::SearchWriterI object (when setting) Throws : Bio::Root::Exception if a non-Bio::SearchIO::SearchWriterI object is passed in. =cut sub writer { my ($self, $writer) = @_; if( ref($writer) and $writer->isa( 'Bio::SearchIO::SearchWriterI' )) { $self->{'_result_writer'} = $writer; } elsif( defined $writer ) { $self->throw("Can't set ResultWriter. Not a Bio::SearchIO::SearchWriterI: $writer"); } return $self->{'_result_writer'}; } =head2 result_count Title : result_count Usage : $num = $stream->result_count; Function: Gets the number of Blast results that have been successfully parsed at the point of the method call. This is not the total # of results in the file. Returns : integer Args : none Throws : none =cut sub result_count { my $self = shift; $self->throw_not_implemented; } =head2 inclusion_threshold Title : inclusion_threshold Usage : my $incl_thresh = $isreb->inclusion_threshold; : $isreb->inclusion_threshold(1e-5); Function: Get/Set the e-value threshold for inclusion in the PSI-BLAST score matrix model (blastpgp) that was used for generating the reports being parsed. Returns : number (real) Default value: $Bio::SearchIO::IteratedSearchResultEventBuilder::DEFAULT_INCLUSION_THRESHOLD Args : number (real) (e.g., 0.0001 or 1e-4 ) =cut # Delegates to the event handler. sub inclusion_threshold { shift->_eventHandler->inclusion_threshold(@_); } =head2 max_significance Usage : $obj->max_significance(); Purpose : Set/Get the P or Expect value used as significance screening cutoff. This is the value of the -signif parameter supplied to new(). Hits with P or E-value above this are skipped. Returns : Scientific notation number with this format: 1.0e-05. Argument : Scientific notation number or float (when setting) Comments : Screening of significant hits uses the data provided on the : description line. For NCBI BLAST1 and WU-BLAST, this data : is P-value. for NCBI BLAST2 it is an Expect value. =cut sub max_significance { shift->{'_handler_cache'}->max_significance(@_) } =head2 signif Synonym for L =cut sub signif { shift->max_significance(@_) } =head2 min_score Usage : $obj->min_score(); Purpose : Set/Get the Blast score used as screening cutoff. This is the value of the -score parameter supplied to new(). Hits with scores below this are skipped. Returns : Integer or scientific notation number. Argument : Integer or scientific notation number (when setting) Comments : Screening of significant hits uses the data provided on the : description line. =cut sub min_score { shift->{'_handler_cache'}->min_score(@_) } =head2 min_query_length Usage : $obj->min_query_length(); Purpose : Gets the query sequence length used as screening criteria. This is the value of the -min_query_len parameter supplied to new(). Hits with sequence length below this are skipped. Returns : Integer Argument : n/a =cut sub min_query_length { my $self = shift; if (@_) { my $min_qlen = shift; if ( $min_qlen =~ /\D/ or $min_qlen <= 0 ) { $self->throw( -class => 'Bio::Root::BadParameter', -text => "Invalid minimum query length value: $min_qlen\n" . "Value must be an integer > 0. Value not set.", -value => $min_qlen ); } $self->{'_confirm_qlength'} = 1; $self->{'_min_query_length'} = $min_qlen; } return $self->{'_min_query_length'}; } =head2 best_hit_only Title : best_hit_only Usage : print "only getting best hit.\n" if $obj->best_hit_only; Purpose : Set/Get the indicator for whether or not to process only : the best BlastHit. Returns : Boolean (1 | 0) Argument : Boolean (1 | 0) (when setting) =cut sub best_hit_only { my $self = shift; if (@_) { $self->{'_best'} = shift; } $self->{'_best'}; } =head2 check_all_hits Title : check_all_hits Usage : print "checking all hits.\n" if $obj->check_all_hits; Purpose : Set/Get the indicator for whether or not to process all hits. : If false, the parser will stop processing hits after the : the first non-significance hit or the first hit that fails : any hit filter. Returns : Boolean (1 | 0) Argument : Boolean (1 | 0) (when setting) =cut sub check_all_hits { my $self = shift; if (@_) { $self->{'_check_all'} = shift; } $self->{'_check_all'}; } =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL SearchIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($self,$format) = @_; my $module = "Bio::SearchIO::" . $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args : =cut sub _guess_format { my $class = shift; return unless $_ = shift; return 'blast' if (/\.(blast|t?bl\w)$/i ); return 'fasta' if (/\. (?: t? fas (?:ta)? | m\d+ | (?: t? (?: fa | fx | fy | ff | fs ) ) | (?: (?:ss | os | ps) (?:earch)? )) $/ix ); return 'blastxml' if ( /\.(blast)?xml$/i); return 'exonerate' if ( /\.exon(erate)?/i ); } sub close { my $self = shift; if( $self->writer ) { $self->_print($self->writer->end_report()); $self->{'_result_writer'}= undef; } $self->SUPER::close(@_); } sub DESTROY { my $self = shift; $self->close() if defined $self->_fh; $self->SUPER::DESTROY; } sub TIEHANDLE { my $class = shift; return bless {processor => shift}, $class; } sub READLINE { my $self = shift; return $self->{'processor'}->next_result() || undef unless wantarray; my (@list, $obj); push @list, $obj while $obj = $self->{'processor'}->next_result(); return @list; } sub PRINT { my $self = shift; $self->{'processor'}->write_result(@_); } 1; __END__ BioPerl-1.007002/Bio/Seq.pm000444000766000024 12031313155576320 15352 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Seq # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq - Sequence object, with features =head1 SYNOPSIS # This is the main sequence object in Bioperl # gets a sequence from a file $seqio = Bio::SeqIO->new( '-format' => 'embl' , -file => 'myfile.dat'); $seqobj = $seqio->next_seq(); # SeqIO can both read and write sequences; see Bio::SeqIO # for more information and examples # get from database $db = Bio::DB::GenBank->new(); $seqobj = $db->get_Seq_by_acc('X78121'); # make from strings in script $seqobj = Bio::Seq->new( -display_id => 'my_id', -seq => $sequence_as_string); # gets sequence as a string from sequence object $seqstr = $seqobj->seq(); # actual sequence as a string $seqstr = $seqobj->subseq(10,50); # slice in biological coordinates # retrieves information from the sequence # features must implement Bio::SeqFeatureI interface @features = $seqobj->get_SeqFeatures(); # just top level foreach my $feat ( @features ) { print "Feature ",$feat->primary_tag," starts ",$feat->start," ends ", $feat->end," strand ",$feat->strand,"\n"; # features retain link to underlying sequence object print "Feature sequence is ",$feat->seq->seq(),"\n" } # sequences may have a species if( defined $seq->species ) { print "Sequence is from ",$species->binomial," [",$species->common_name,"]\n"; } # annotation objects are Bio::AnnotationCollectionI's $ann = $seqobj->annotation(); # annotation object # references is one type of annotations to get. Also get # comment and dblink. Look at Bio::AnnotationCollection for # more information foreach my $ref ( $ann->get_Annotations('reference') ) { print "Reference ",$ref->title,"\n"; } # you can get truncations, translations and reverse complements, these # all give back Bio::Seq objects themselves, though currently with no # features transferred my $trunc = $seqobj->trunc(100,200); my $rev = $seqobj->revcom(); # there are many options to translate - check out the docs my $trans = $seqobj->translate(); # these functions can be chained together my $trans_trunc_rev = $seqobj->trunc(100,200)->revcom->translate(); =head1 DESCRIPTION A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently Bio::PrimarySeq - just the sequence and its names, nothing else. Bio::SeqFeatureI - a feature on a sequence, potentially with a sequence and a location and annotation. Bio::Seq - A sequence and a collection of sequence features (an aggregate) with its own annotation. Although Bioperl is not tied heavily to file formats these distinctions do map to file formats sensibly and for some bioinformaticians this might help Bio::PrimarySeq - Fasta file of a sequence Bio::SeqFeatureI - A single entry in an EMBL/GenBank/DDBJ feature table Bio::Seq - A single EMBL/GenBank/DDBJ entry By having this split we avoid a lot of nasty circular references (sequence features can hold a reference to a sequence without the sequence holding a reference to the sequence feature). See L and L for more information. Ian Korf really helped in the design of the Seq and SeqFeature system. =head2 Examples A simple and fundamental block of code: use Bio::SeqIO; my $seqIOobj = Bio::SeqIO->new(-file=>"1.fa"); # create a SeqIO object my $seqobj = $seqIOobj->next_seq; # get a Seq object With the Seq object in hand one has access to a powerful set of Bioperl methods and related Bioperl objects. This next script will take a file of sequences in EMBL format and create a file of the reverse-complemented sequences in Fasta format using Seq objects. It also prints out details about the exons it finds as sequence features in Genbank Flat File format. use Bio::Seq; use Bio::SeqIO; $seqin = Bio::SeqIO->new( -format => 'EMBL' , -file => 'myfile.dat'); $seqout= Bio::SeqIO->new( -format => 'Fasta', -file => '>output.fa'); while((my $seqobj = $seqin->next_seq())) { print "Seen sequence ",$seqobj->display_id,", start of seq ", substr($seqobj->seq,1,10),"\n"; if( $seqobj->alphabet eq 'dna') { $rev = $seqobj->revcom; $id = $seqobj->display_id(); $id = "$id.rev"; $rev->display_id($id); $seqout->write_seq($rev); } foreach $feat ( $seqobj->get_SeqFeatures() ) { if( $feat->primary_tag eq 'exon' ) { print STDOUT "Location ",$feat->start,":", $feat->end," GFF[",$feat->gff_string,"]\n"; } } } Let's examine the script. The lines below import the Bioperl modules. Seq is the main Bioperl sequence object and SeqIO is the Bioperl support for reading sequences from files and to files use Bio::Seq; use Bio::SeqIO; These two lines create two SeqIO streams: one for reading in sequences and one for outputting sequences: $seqin = Bio::SeqIO->new( -format => 'EMBL' , -file => 'myfile.dat'); $seqout= Bio::SeqIO->new( -format => 'Fasta', -file => '>output.fa'); Notice that in the "$seqout" case there is a greater-than sign, indicating the file is being opened for writing. Using the '-argument' => value syntax is common in Bioperl. The file argument is like an argument to open() . You can also pass in filehandles or FileHandle objects by using the -fh argument (see L documentation for details). Many formats in Bioperl are handled, including Fasta, EMBL, GenBank, Swissprot (swiss), PIR, and GCG. $seqin = Bio::SeqIO->new( -format => 'EMBL' , -file => 'myfile.dat'); $seqout= Bio::SeqIO->new( -format => 'Fasta', -file => '>output.fa'); This is the main loop which will loop progressively through sequences in a file, and each call to $seqio-Enext_seq() provides a new Seq object from the file: while((my $seqobj = $seqio->next_seq())) { This print line below accesses fields in the Seq object directly. The $seqobj-Edisplay_id is the way to access the display_id attribute of the Seq object. The $seqobj-Eseq method gets the actual sequence out as string. Then you can do manipulation of this if you want to (there are however easy ways of doing truncation, reverse-complement and translation). print "Seen sequence ",$seqobj->display_id,", start of seq ", substr($seqobj->seq,1,10),"\n"; Bioperl has to guess the alphabet of the sequence, being either 'dna', 'rna', or 'protein'. The alphabet attribute is one of these three possibilities. if( $seqobj->alphabet eq 'dna') { The $seqobj-Erevcom method provides the reverse complement of the Seq object as another Seq object. Thus, the $rev variable is a reference to another Seq object. For example, one could repeat the above print line for this Seq object (putting $rev in place of $seqobj). In this case we are going to output the object into the file stream we built earlier on. $rev = $seqobj->revcom; When we output it, we want the id of the outputted object to be changed to "$id.rev", ie, with .rev on the end of the name. The following lines retrieve the id of the sequence object, add .rev to this and then set the display_id of the rev sequence object to this. Notice that to set the display_id attribute you just need call the same method, display_id(), with the new value as an argument. Getting and setting values with the same method is common in Bioperl. $id = $seqobj->display_id(); $id = "$id.rev"; $rev->display_id($id); The write_seq method on the SeqIO output object, $seqout, writes the $rev object to the filestream we built at the top of the script. The filestream knows that it is outputting in fasta format, and so it provides fasta output. $seqout->write_seq($rev); This block of code loops over sequence features in the sequence object, trying to find ones who have been tagged as 'exon'. Features have start and end attributes and can be outputted in Genbank Flat File format, GFF, a standarized format for sequence features. foreach $feat ( $seqobj->get_SeqFeatures() ) { if( $feat->primary_tag eq 'exon' ) { print STDOUT "Location ",$feat->start,":", $feat->end," GFF[",$feat->gff_string,"]\n"; } } The code above shows how a few Bio::Seq methods suffice to read, parse, reformat and analyze sequences from a file. A full list of methods available to Bio::Seq objects is shown below. Bear in mind that some of these methods come from PrimarySeq objects, which are simpler than Seq objects, stripped of features (see L for more information). # these methods return strings, and accept strings in some cases: $seqobj->seq(); # string of sequence $seqobj->subseq(5,10); # part of the sequence as a string $seqobj->accession_number(); # when there, the accession number $seqobj->alphabet(); # one of 'dna','rna',or 'protein' $seqobj->version() # when there, the version $seqobj->keywords(); # when there, the Keywords line $seqobj->length() # length $seqobj->desc(); # description $seqobj->primary_id(); # a unique id for this sequence regardless # of its display_id or accession number $seqobj->display_id(); # the human readable id of the sequence Some of these values map to fields in common formats. For example, The display_id() method returns the LOCUS name of a Genbank entry, the (\S+) following the E character in a Fasta file, the ID from a SwissProt file, and so on. The desc() method will return the DEFINITION line of a Genbank file, the description following the display_id in a Fasta file, and the DE field in a SwissProt file. # the following methods return new Seq objects, but # do not transfer features across to the new object: $seqobj->trunc(5,10) # truncation from 5 to 10 as new object $seqobj->revcom # reverse complements sequence $seqobj->translate # translation of the sequence # if new() can be called this method returns 1, else 0 $seqobj->can_call_new # the following method determines if the given string will be accepted # by the seq() method - if the string is acceptable then validate() # returns 1, or 0 if not $seqobj->validate_seq($string) # the following method returns or accepts a Species object: $seqobj->species(); Please see L for more information on this object. # the following method returns or accepts an Annotation object # which in turn allows access to Annotation::Reference # and Annotation::Comment objects: $seqobj->annotation(); These annotations typically refer to entire sequences, unlike features. See L, L, L, and L for details. It is also important to be able to describe defined portions of a sequence. The combination of some description and the corresponding sub-sequence is called a feature - an exon and its coordinates within a gene is an example of a feature, or a domain within a protein. # the following methods return an array of SeqFeatureI objects: $seqobj->get_SeqFeatures # The 'top level' sequence features $seqobj->get_all_SeqFeatures # All sequence features, including sub-seq # features, such as features in an exon # to find out the number of features use: $seqobj->feature_count Here are just some of the methods available to SeqFeatureI objects: # these methods return numbers: $feat->start # start position (1 is the first base) $feat->end # end position (2 is the second base) $feat->strand # 1 means forward, -1 reverse, 0 not relevant # these methods return or accept strings: $feat->primary_tag # the name of the sequence feature, eg # 'exon', 'glycoslyation site', 'TM domain' $feat->source_tag # where the feature comes from, eg, 'EMBL_GenBank', # or 'BLAST' # this method returns the more austere PrimarySeq object, not a # Seq object - the main difference is that PrimarySeq objects do not # themselves contain sequence features $feat->seq # the sequence between start,end on the # correct strand of the sequence See L for more details on PrimarySeq objects. # useful methods for feature comparisons, for start/end points $feat->overlaps($other) # do $feat and $other overlap? $feat->contains($other) # is $other completely within $feat? $feat->equals($other) # do $feat and $other completely agree? # one can also add features $seqobj->add_SeqFeature($feat) # returns 1 if successful # sub features. For complex join() statements, the feature # is one sequence feature with many sub SeqFeatures $feat->sub_SeqFeature # returns array of sub seq features Please see L and L, for more information on sequence features. It is worth mentioning that one can also retrieve the start and end positions of a feature using a Bio::LocationI object: $location = $feat->location # $location is a Bio::LocationI object $location->start; # start position $location->end; # end position This is useful because one needs a Bio::Location::SplitLocationI object in order to retrieve the coordinates inside the Genbank or EMBL join() statements (e.g. "CDS join(51..142,273..495,1346..1474)"): if ( $feat->location->isa('Bio::Location::SplitLocationI') && $feat->primary_tag eq 'CDS' ) { foreach $loc ( $feat->location->sub_Location ) { print $loc->start . ".." . $loc->end . "\n"; } } See L and L for more information. =head1 Implemented Interfaces This class implements the following interfaces. =over 4 =item Bio::SeqI Note that this includes implementing Bio::PrimarySeqI. =item Bio::IdentifiableI =item Bio::DescribableI =item Bio::AnnotatableI =item Bio::FeatureHolderI =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney, inspired by Ian Korf objects Email birney@ebi.ac.uk =head1 CONTRIBUTORS Jason Stajich Ejason@bioperl.orgE Mark A. Jensen maj -at- fortinbras -dot- us =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_". =cut #' # Let the code begin... package Bio::Seq; use strict; use Bio::Annotation::Collection; use Bio::PrimarySeq; use base qw(Bio::Root::Root Bio::SeqI Bio::IdentifiableI Bio::DescribableI Bio::AnnotatableI Bio::FeatureHolderI Bio::AnnotationCollectionI); =head2 new Title : new Usage : $seq = Bio::Seq->new( -seq => 'ATGGGGGTGGTGGTACCCT', -id => 'human_id', -accession_number => 'AL000012', ); Function: Returns a new Seq object from basic constructors, being a string for the sequence and strings for id and accession_number Returns : a new Bio::Seq object =cut sub new { my($caller,@args) = @_; if( $caller ne 'Bio::Seq') { $caller = ref($caller) if ref($caller); } # we know our inherietance hierarchy my $self = Bio::Root::Root->new(@args); bless $self,$caller; # this is way too sneaky probably. We delegate the construction of # the Seq object onto PrimarySeq and then pop primary_seq into # our primary_seq slot my $pseq = Bio::PrimarySeq->new(@args); # as we have just made this, we know it is ok to set hash directly # rather than going through the method $self->{'primary_seq'} = $pseq; # setting this array is now delayed until the final # moment, again speed ups for non feature containing things # $self->{'_as_feat'} = []; my ($ann, $pid,$feat,$species) = &Bio::Root::RootI::_rearrange($self,[qw(ANNOTATION PRIMARY_ID FEATURES SPECIES)], @args); # for a number of cases - reading fasta files - these are never set. This # gives a quick optimisation around testing things later on if( defined $ann || defined $pid || defined $feat || defined $species ) { $pid && $self->primary_id($pid); $species && $self->species($species); $ann && $self->annotation($ann); if( defined $feat ) { if( ref($feat) !~ /ARRAY/i ) { if( ref($feat) && $feat->isa('Bio::SeqFeatureI') ) { $self->add_SeqFeature($feat); } else { $self->warn("Must specify a valid Bio::SeqFeatureI or ArrayRef of Bio::SeqFeatureI's with the -features init parameter for ".ref($self)); } } else { foreach my $feature ( @$feat ) { $self->add_SeqFeature($feature); } } } } return $self; } =head1 PrimarySeq interface The PrimarySeq interface provides the basic sequence getting and setting methods for on all sequences. These methods implement the Bio::PrimarySeq interface by delegating to the primary_seq inside the object. This means that you can use a Seq object wherever there is a PrimarySeq, and of course, you are free to use these functions anyway. =cut =head2 seq Title : seq Usage : $string = $obj->seq() Function: Get/Set the sequence as a string of letters. The case of the letters is left up to the implementer. Suggested cases are upper case for proteins and lower case for DNA sequence (IUPAC standard), but implementations are suggested to keep an open mind about case (some users... want mixed case!) Returns : A scalar Args : Optionally on set the new value (a string). An optional second argument presets the alphabet (otherwise it will be guessed). Both parameters may also be given in named parameter style with -seq and -alphabet being the names. =cut sub seq { return shift->primary_seq()->seq(@_); } =head2 validate_seq Title : validate_seq Usage : if(! $seqobj->validate_seq($seq_str) ) { print "sequence $seq_str is not valid for an object of alphabet ",$seqobj->alphabet, "\n"; } Function: Test that the given sequence is valid, i.e. contains only valid characters. The allowed characters are all letters (A-Z) and '-','.', '*','?','=' and '~'. Spaces are not valid. Note that this implementation does not take alphabet() into account. Returns : 1 if the supplied sequence string is valid, 0 otherwise. Args : - Sequence string to be validated - Boolean to throw an error if the sequence is invalid =cut sub validate_seq { return shift->primary_seq()->validate_seq(@_); } =head2 length Title : length Usage : $len = $seq->length() Function: Example : Returns : Integer representing the length of the sequence. Args : None =cut sub length { return shift->primary_seq()->length(@_); } =head1 Methods from the Bio::PrimarySeqI interface =head2 subseq Title : subseq Usage : $substring = $obj->subseq(10,40); Function: Returns the subseq from start to end, where the first base is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence Start cannot be larger than end but can be equal Returns : A string Args : 2 integers =cut sub subseq { return shift->primary_seq()->subseq(@_); } =head2 display_id Title : display_id Usage : $id = $obj->display_id or $obj->display_id($newid); Function: Gets or sets the display id, also known as the common name of the Seq object. The semantics of this is that it is the most likely string to be used as an identifier of the sequence, and likely to have "human" readability. The id is equivalent to the LOCUS field of the GenBank/EMBL databanks and the ID field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. Notice that $seq->id() maps to this function, mainly for legacy/convenience issues. Returns : A string Args : None or a new id =cut sub display_id { return shift->primary_seq->display_id(@_); } =head2 accession_number Title : accession_number Usage : $unique_biological_key = $obj->accession_number; Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". Can also be used to set the accession number. Example : $key = $seq->accession_number or $seq->accession_number($key) Returns : A string Args : None or an accession number =cut sub accession_number { return shift->primary_seq->accession_number(@_); } =head2 desc Title : desc Usage : $seqobj->desc($string) or $seqobj->desc() Function: Sets or gets the description of the sequence Example : Returns : The description Args : The description or none =cut sub desc { return shift->primary_seq->desc(@_); } =head2 primary_id Title : primary_id Usage : $unique_implementation_key = $obj->primary_id; Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a way the implementation can control clients can expect one id to map to one object. For sequences with no natural id, this method should return a stringified memory location. Can also be used to set the primary_id (or unset to undef). [Note this method name is likely to change in 1.3] Example : $id = $seq->primary_id or $seq->primary_id($id) Returns : A string Args : None or an id, or undef to unset the primary id. =cut sub primary_id { # Note: this used to not delegate to the primary seq. This is # really bad in very subtle ways. E.g., if you created the object # with a primary id given to the constructor and then later you # change the primary id, if this method wouldn't delegate you'd # have different values for primary id in the PrimarySeq object # compared to this instance. Not good. # I can't remember why not delegating was ever deemed # advantageous, but I hereby claim that its problems far outweigh # its advantages, if there are any. Convince me otherwise if you # disagree. HL 2004/08/05 return shift->primary_seq->primary_id(@_); } =head2 can_call_new Title : can_call_new Usage : if ( $obj->can_call_new ) { $newobj = $obj->new( %param ); } Function: can_call_new returns 1 or 0 depending on whether an implementation allows new constructor to be called. If a new constructor is allowed, then it should take the followed hashed constructor list. $myobject->new( -seq => $sequence_as_string, -display_id => $id -accession_number => $accession -alphabet => 'dna', ); Example : Returns : 1 or 0 Args : None =cut sub can_call_new { return 1; } =head2 alphabet Title : alphabet Usage : if ( $obj->alphabet eq 'dna' ) { /Do Something/ } Function: Get/Set the type of sequence being one of 'dna', 'rna' or 'protein'. This is case sensitive. This is not called because this would cause upgrade problems from the 0.5 and earlier Seq objects. Returns : A string either 'dna','rna','protein'. NB - the object must make a call of the type - if there is no type specified it has to guess. Args : optional string to set : 'dna' | 'rna' | 'protein' =cut sub alphabet { my $self = shift; return $self->primary_seq->alphabet(@_) if @_ && defined $_[0]; return $self->primary_seq->alphabet(); } =head2 is_circular Title : is_circular Usage : if( $obj->is_circular) { /Do Something/ } Function: Returns true if the molecule is circular Returns : Boolean value Args : none =cut sub is_circular { return shift->primary_seq()->is_circular(@_); } =head1 Methods for Bio::IdentifiableI compliance =head2 object_id Title : object_id Usage : $string = $obj->object_id() Function: a string which represents the stable primary identifier in this namespace of this object. For DNA sequences this is its accession_number, similarly for protein sequences This is aliased to accession_number(). Returns : A scalar =cut sub object_id { return shift->accession_number(@_); } =head2 version Title : version Usage : $version = $obj->version() Function: a number which differentiates between versions of the same object. Higher numbers are considered to be later and more relevant, but a single object described the same identifier should represent the same concept Returns : A number =cut sub version{ return shift->primary_seq->version(@_); } =head2 authority Title : authority Usage : $authority = $obj->authority() Function: a string which represents the organisation which granted the namespace, written as the DNS name for organisation (eg, wormbase.org) Returns : A scalar =cut sub authority { return shift->primary_seq()->authority(@_); } =head2 namespace Title : namespace Usage : $string = $obj->namespace() Function: A string representing the name space this identifier is valid in, often the database name or the name describing the collection Returns : A scalar =cut sub namespace{ return shift->primary_seq()->namespace(@_); } =head1 Methods for Bio::DescribableI compliance =head2 display_name Title : display_name Usage : $string = $obj->display_name() Function: A string which is what should be displayed to the user the string should have no spaces (ideally, though a cautious user of this interface would not assume this) and should be less than thirty characters (though again, double checking this is a good idea) This is aliased to display_id(). Returns : A scalar =cut sub display_name { return shift->display_id(@_); } =head2 description Title : description Usage : $string = $obj->description() Function: A text string suitable for displaying to the user a description. This string is likely to have spaces, but should not have any newlines or formatting - just plain text. The string should not be greater than 255 characters and clients can feel justified at truncating strings at 255 characters for the purposes of display This is aliased to desc(). Returns : A scalar =cut sub description { return shift->desc(@_); } =head1 Methods for implementing Bio::AnnotatableI =head2 annotation Title : annotation Usage : $ann = $seq->annotation or $seq->annotation($ann) Function: Gets or sets the annotation Returns : Bio::AnnotationCollectionI object Args : None or Bio::AnnotationCollectionI object See L and L for more information =cut sub annotation { my ($obj,$value) = @_; if( defined $value ) { $obj->throw("object of class ".ref($value)." does not implement ". "Bio::AnnotationCollectionI. Too bad.") unless $value->isa("Bio::AnnotationCollectionI"); $obj->{'_annotation'} = $value; } elsif( ! defined $obj->{'_annotation'}) { $obj->{'_annotation'} = Bio::Annotation::Collection->new(); } return $obj->{'_annotation'}; } =head1 Methods for delegating Bio::AnnotationCollectionI =head2 get_Annotations() Usage : my @annotations = $seq->get_Annotations('key') Function: Retrieves all the Bio::AnnotationI objects for a specific key for this object Returns : list of Bio::AnnotationI - empty if no objects stored for a key Args : string which is key for annotations =cut sub get_Annotations { shift->annotation->get_Annotations(@_); } =head2 add_Annotation() Usage : $seq->add_Annotation('reference',$object); $seq->add_Annotation($object,'Bio::MyInterface::DiseaseI'); $seq->add_Annotation($object); $seq->add_Annotation('disease',$object,'Bio::MyInterface::DiseaseI'); Function: Adds an annotation for a specific key for this sequence object. If the key is omitted, the object to be added must provide a value via its tagname(). If the archetype is provided, this and future objects added under that tag have to comply with the archetype and will be rejected otherwise. Returns : none Args : annotation key ('disease', 'dblink', ...) object to store (must be Bio::AnnotationI compliant) [optional] object archetype to map future storage of object of these types to =cut sub add_Annotation { shift->annotation->add_Annotation(@_) } =head2 remove_Annotations() Usage : $seq->remove_Annotations() Function: Remove the annotations for the specified key from this sequence object Returns : an list of Bio::AnnotationI compliant objects which were stored under the given key(s) for this sequence object Args : the key(s) (tag name(s), one or more strings) for which to remove annotations (optional; if none given, flushes all annotations) =cut sub remove_Annotations { shift->annotation->remove_Annotations(@_) } =head2 get_num_of_annotations() Usage : my $count = $seq->get_num_of_annotations() Alias : num_Annotations Function: Returns the count of all annotations stored for this sequence object Returns : integer Args : none =cut sub get_num_of_annotations { shift->annotation->get_num_of_annotations(@_) } sub num_Annotations { shift->get_num_of_annotations }; #DWYM =head1 Methods to implement Bio::FeatureHolderI This includes methods for retrieving, adding, and removing features. =cut =head2 get_SeqFeatures Title : get_SeqFeatures Usage : Function: Get the feature objects held by this feature holder. Features which are not top-level are subfeatures of one or more of the returned feature objects, which means that you must traverse the subfeature arrays of each top-level feature object in order to traverse all features associated with this sequence. Specific features can be obtained by primary tag, specified in the argument. Use get_all_SeqFeatures() if you want the feature tree flattened into one single array. Example : my @feats = $seq->get_SeqFeatures or my @genefeats = $seq->get_SeqFeatures('gene') Returns : an array of Bio::SeqFeatureI implementing objects Args : [optional] string (feature tag) =cut sub get_SeqFeatures{ my $self = shift; my $tag = shift; if( !defined $self->{'_as_feat'} ) { $self->{'_as_feat'} = []; } if ($tag) { return map { $_->primary_tag eq $tag ? $_ : () } @{$self->{'_as_feat'}}; } else { return @{$self->{'_as_feat'}}; } } =head2 get_all_SeqFeatures Title : get_all_SeqFeatures Usage : @feat_ary = $seq->get_all_SeqFeatures(); Function: Returns the tree of feature objects attached to this sequence object flattened into one single array. Top-level features will still contain their subfeature-arrays, which means that you will encounter subfeatures twice if you traverse the subfeature tree of the returned objects. Use get_SeqFeatures() if you want the array to contain only the top-level features. Returns : An array of Bio::SeqFeatureI implementing objects. Args : None =cut # this implementation is inherited from FeatureHolderI =head2 feature_count Title : feature_count Usage : $seq->feature_count() Function: Return the number of SeqFeatures attached to a sequence Returns : integer representing the number of SeqFeatures Args : None =cut sub feature_count { my ($self) = @_; if (defined($self->{'_as_feat'})) { return ($#{$self->{'_as_feat'}} + 1); } else { return 0; } } =head2 add_SeqFeature Title : add_SeqFeature Usage : $seq->add_SeqFeature($feat); Function: Adds the given feature object to the feature array of this sequence. The object passed is required to implement the Bio::SeqFeatureI interface. The 'EXPAND' qualifier (see L) is supported, but has no effect, Returns : 1 on success Args : A Bio::SeqFeatureI implementing object. =cut sub add_SeqFeature { my ($self, @feat) = @_; $self->{'_as_feat'} = [] unless $self->{'_as_feat'}; if (scalar @feat > 1) { $self->deprecated( -message => 'Providing an array of features to Bio::Seq add_SeqFeature()'. ' is deprecated and will be removed in a future version. '. 'Add a single feature at a time instead.', -warn_version => 1.007, -throw_version => 1.009, ); } for my $feat ( @feat ) { next if $feat eq 'EXPAND'; # Need to support it for FeatureHolderI compliance if( !$feat->isa("Bio::SeqFeatureI") ) { $self->throw("Expected a Bio::SeqFeatureI object, but got a $feat."); } # make sure we attach ourselves to the feature if the feature wants it my $aseq = $self->primary_seq; $feat->attach_seq($aseq) if $aseq; push(@{$self->{'_as_feat'}},$feat); } return 1; } =head2 remove_SeqFeatures Title : remove_SeqFeatures Usage : $seq->remove_SeqFeatures(); Function: Removes all attached SeqFeatureI objects or those with the specified primary tag Example : my @gene_feats = $seq->remove_seqFeatures('gene') or my @feats = $seq->remove_seqFeatures() Returns : The array of Bio::SeqFeatureI objects removed from the sequence Args : None, or a feature primary tag =cut sub remove_SeqFeatures { my ( $self, $tag ) = @_; return () unless $self->{'_as_feat'}; if ( $tag ) { my @selected_feats = grep { $_->primary_tag eq $tag } @{ $self->{'_as_feat'} }; my @unselected_feats = grep { $_->primary_tag ne $tag } @{ $self->{'_as_feat'} }; $self->{'_as_feat'} = \@unselected_feats; return @selected_feats; } else { my @all_feats = @{ $self->{'_as_feat'} }; $self->{'_as_feat'} = []; return @all_feats; } } =head1 Methods provided in the Bio::PrimarySeqI interface These methods are inherited from the PrimarySeq interface and work as one expects, building new Bio::Seq objects or other information as expected. See L for more information. Sequence Features are B transferred to the new objects. To reverse complement and include the features use L. =head2 revcom Title : revcom Usage : $rev = $seq->revcom() Function: Produces a new Bio::Seq object which is the reversed complement of the sequence. For protein sequences this throws an exception of "Sequence is a protein. Cannot revcom" The id is the same id as the original sequence, and the accession number is also identical. If someone wants to track that this sequence has be reversed, it needs to define its own extensions To do an in-place edit of an object you can go: $seq = $seq->revcom(); This of course, causes Perl to handle the garbage collection of the old object, but it is roughly speaking as efficient as an in-place edit. Returns : A new (fresh) Bio::Seq object Args : None =head2 trunc Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence Example : Returns : A fresh Seq object Args : A Seq object =head2 id Title : id Usage : $id = $seq->id() Function: This is mapped on display_id Returns : value of display_id() Args : [optional] value to update display_id =cut sub id { return shift->display_id(@_); } =head1 Seq only methods These methods are specific to the Bio::Seq object, and not found on the Bio::PrimarySeq object =head2 primary_seq Title : primary_seq Usage : $seq->primary_seq or $seq->primary_seq($newval) Function: Get or set a PrimarySeq object Example : Returns : PrimarySeq object Args : None or PrimarySeq object =cut sub primary_seq { my ($obj,$value) = @_; if( defined $value) { if( ! ref $value || ! $value->isa('Bio::PrimarySeqI') ) { $obj->throw("$value is not a Bio::PrimarySeq compliant object"); } $obj->{'primary_seq'} = $value; # descend down over all seqfeature objects, seeing whether they # want an attached seq. foreach my $sf ( $obj->get_SeqFeatures() ) { $sf->attach_seq($value); } } return $obj->{'primary_seq'}; } =head2 species Title : species Usage : $species = $seq->species() or $seq->species($species) Function: Gets or sets the species Returns : L object Args : None or L object See L for more information =cut sub species { my ($self, $species) = @_; if ($species) { $self->{'species'} = $species; } else { return $self->{'species'}; } } # Internal methods follow... # keep AUTOLOAD happy sub DESTROY { } ############################################################################ # aliases due to name changes or to compensate for our lack of consistency # ############################################################################ # in all other modules we use the object in the singular -- # lack of consistency sucks *flush_SeqFeature = \&remove_SeqFeatures; *flush_SeqFeatures = \&remove_SeqFeatures; # this is now get_SeqFeatures() (from FeatureHolderI) *top_SeqFeatures = \&get_SeqFeatures; # this is now get_all_SeqFeatures() in FeatureHolderI sub all_SeqFeatures{ return shift->get_all_SeqFeatures(@_); } sub accession { my $self = shift; $self->warn(ref($self)."::accession is deprecated, ". "use accession_number() instead"); return $self->accession_number(@_); } 1; BioPerl-1.007002/Bio/SeqAnalysisParserI.pm000444000766000024 667213155576320 20317 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SeqAnalysisParserI # # Please direct questions and support issues to # # Cared for by Jason Stajich , # and Hilmar Lapp # # Copyright Jason Stajich, Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqAnalysisParserI - Sequence analysis output parser interface =head1 SYNOPSIS # get a SeqAnalysisParserI somehow, e.g. by my $parser = Bio::Factory::SeqAnalysisParserFactory->get_parser( '-input' => 'inputfile', '-method' => 'genscan'); while( my $feature = $parser->next_feature() ) { print "Feature from ", $feature->start, " to ", $feature->end, "\n"; } =head1 DESCRIPTION SeqAnalysisParserI is a generic interface for describing sequence analysis result parsers. Sequence analysis in this sense is a search for similarities or the identification of features on the sequence, like a databank search or a a gene prediction result. The concept behind this interface is to have a generic interface in sequence annotation pipelines (as used e.g. in high-throughput automated sequence annotation). This interface enables plug-and-play for new analysis methods and their corresponding parsers without the necessity for modifying the core of the annotation pipeline. In this concept the annotation pipeline has to rely on only a list of methods for which to process the results, and a factory from which it can obtain the corresponding parser implementing this interface. See Bio::Factory::SeqAnalysisParserFactoryI and Bio::Factory::SeqAnalysisParserFactory for interface and an implementation of the corresponding factory. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp, Jason Stajich Email Hilmar Lapp Ehlapp@gmx.netE, Jason Stajich Ejason@bioperl.orgE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqAnalysisParserI; use strict; use Carp; use base qw(Bio::Root::RootI); =head2 next_feature Title : next_feature Usage : $seqfeature = $obj->next_feature(); Function: Returns the next feature available in the analysis result, or undef if there are no more features. Example : Returns : A Bio::SeqFeatureI implementing object, or undef if there are no more features. Args : none =cut sub next_feature { my ($self) = shift; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/SeqFeatureI.pm000444000766000024 6131313155576320 16763 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SeqFeatureI # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeatureI - Abstract interface of a Sequence Feature =head1 SYNOPSIS # get a seqfeature somehow, eg, from a Sequence with Features attached foreach $feat ( $seq->get_SeqFeatures() ) { print "Feature from ", $feat->start, "to ", $feat->end, " Primary tag ", $feat->primary_tag, ", produced by ", $feat->source_tag(), "\n"; if ( $feat->strand == 0 ) { print "Feature applicable to either strand\n"; } else { print "Feature on strand ", $feat->strand,"\n"; # -1,1 } print "feature location is ",$feat->start, "..", $feat->end, " on strand ", $feat->strand, "\n"; print "easy utility to print locations in GenBank/EMBL way ", $feat->location->to_FTstring(), "\n"; foreach $tag ( $feat->get_all_tags() ) { print "Feature has tag ", $tag, " with values, ", join(' ',$feat->get_tag_values($tag)), "\n"; } print "new feature\n" if $feat->has_tag('new'); # features can have sub features my @subfeat = $feat->get_SeqFeatures(); } =head1 DESCRIPTION This interface is the functions one can expect for any Sequence Feature, whatever its implementation or whether it is a more complex type (eg, a Gene). This object does not actually provide any implementation, it just provides the definitions of what methods one can call. See Bio::SeqFeature::Generic for a good standard implementation of this object =head1 FEEDBACK User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeatureI; use vars qw($HasInMemory); use strict; BEGIN { eval { require Bio::DB::InMemoryCache }; if( $@ ) { $HasInMemory = 0 } else { $HasInMemory = 1 } } use Bio::Seq; use Carp; use base qw(Bio::RangeI); =head1 Bio::SeqFeatureI specific methods New method interfaces. =cut =head2 get_SeqFeatures Title : get_SeqFeatures Usage : @feats = $feat->get_SeqFeatures(); Function: Returns an array of sub Sequence Features Returns : An array Args : none =cut sub get_SeqFeatures{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 display_name Title : display_name Usage : $name = $feat->display_name() Function: Returns the human-readable name of the feature for displays. Returns : a string Args : none =cut sub display_name { shift->throw_not_implemented(); } =head2 primary_tag Title : primary_tag Usage : $tag = $feat->primary_tag() Function: Returns the primary tag for a feature, eg 'exon' Returns : a string Args : none =cut sub primary_tag{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 source_tag Title : source_tag Usage : $tag = $feat->source_tag() Function: Returns the source tag for a feature, eg, 'genscan' Returns : a string Args : none =cut sub source_tag{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 has_tag Title : has_tag Usage : $tag_exists = $self->has_tag('some_tag') Function: Returns : TRUE if the specified tag exists, and FALSE otherwise Args : =cut sub has_tag{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_tag_values Title : get_tag_values Usage : @values = $self->get_tag_values('some_tag') Function: Returns : An array comprising the values of the specified tag. Args : a string throws an exception if there is no such tag =cut sub get_tag_values { shift->throw_not_implemented(); } =head2 get_tagset_values Title : get_tagset_values Usage : @values = $self->get_tagset_values(qw(label transcript_id product)) Function: Returns : An array comprising the values of the specified tags, in order of tags Args : An array of strings does NOT throw an exception if none of the tags are not present this method is useful for getting a human-readable label for a SeqFeatureI; not all tags can be assumed to be present, so a list of possible tags in preferential order is provided =cut # interface + abstract method sub get_tagset_values { my ($self, @args) = @_; my @vals = (); foreach my $arg (@args) { if ($self->has_tag($arg)) { push(@vals, $self->get_tag_values($arg)); } } return @vals; } =head2 get_all_tags Title : get_all_tags Usage : @tags = $feat->get_all_tags() Function: gives all tags for this feature Returns : an array of strings Args : none =cut sub get_all_tags{ shift->throw_not_implemented(); } =head2 attach_seq Title : attach_seq Usage : $sf->attach_seq($seq) Function: Attaches a Bio::Seq object to this feature. This Bio::Seq object is for the *entire* sequence: ie from 1 to 10000 Note that it is not guaranteed that if you obtain a feature from an object in bioperl, it will have a sequence attached. Also, implementors of this interface can choose to provide an empty implementation of this method. I.e., there is also no guarantee that if you do attach a sequence, seq() or entire_seq() will not return undef. The reason that this method is here on the interface is to enable you to call it on every SeqFeatureI compliant object, and that it will be implemented in a useful way and set to a useful value for the great majority of use cases. Implementors who choose to ignore the call are encouraged to specifically state this in their documentation. Example : Returns : TRUE on success Args : a Bio::PrimarySeqI compliant object =cut sub attach_seq { shift->throw_not_implemented(); } =head2 seq Title : seq Usage : $tseq = $sf->seq() Function: returns the truncated sequence (if there is a sequence attached) for this feature Example : Returns : sub seq (a Bio::PrimarySeqI compliant object) on attached sequence bounded by start & end, or undef if there is no sequence attached. If the strand is defined and set to -1, the returned sequence is the reverse-complement of the region Args : none =cut sub seq { shift->throw_not_implemented(); } =head2 entire_seq Title : entire_seq Usage : $whole_seq = $sf->entire_seq() Function: gives the entire sequence that this seqfeature is attached to Example : Returns : a Bio::PrimarySeqI compliant object, or undef if there is no sequence attached Args : none =cut sub entire_seq { shift->throw_not_implemented(); } =head2 seq_id Title : seq_id Usage : $obj->seq_id($newval) Function: There are many cases when you make a feature that you do know the sequence name, but do not know its actual sequence. This is an attribute such that you can store the ID (e.g., display_id) of the sequence. This attribute should *not* be used in GFF dumping, as that should come from the collection in which the seq feature was found. Returns : value of seq_id Args : newvalue (optional) =cut sub seq_id { shift->throw_not_implemented(); } =head2 gff_string Title : gff_string Usage : $str = $feat->gff_string; $str = $feat->gff_string($gff_formatter); Function: Provides the feature information in GFF format. The implementation provided here returns GFF2 by default. If you want a different version, supply an object implementing a method gff_string() accepting a SeqFeatureI object as argument. E.g., to obtain GFF1 format, do the following: my $gffio = Bio::Tools::GFF->new(-gff_version => 1); $gff1str = $feat->gff_string($gff1io); Returns : A string Args : Optionally, an object implementing gff_string(). =cut sub gff_string{ my ($self,$formatter) = @_; $formatter = $self->_static_gff_formatter unless $formatter; return $formatter->gff_string($self); } my $static_gff_formatter = undef; =head2 _static_gff_formatter Title : _static_gff_formatter Usage : Function: Example : Returns : Args : =cut sub _static_gff_formatter{ my ($self,@args) = @_; require Bio::Tools::GFF; # on the fly inclusion -- is this better? if( !defined $static_gff_formatter ) { $static_gff_formatter = Bio::Tools::GFF->new('-gff_version' => 2); } return $static_gff_formatter; } =head1 Decorating methods These methods have an implementation provided by Bio::SeqFeatureI, but can be validly overwritten by subclasses =head2 spliced_seq Title : spliced_seq Usage : $seq = $feature->spliced_seq() $seq = $feature_with_remote_locations->spliced_seq($db_for_seqs) Function: Provides a sequence of the feature which is the most semantically "relevant" feature for this sequence. A default implementation is provided which for simple cases returns just the sequence, but for split cases, loops over the split location to return the sequence. In the case of split locations with remote locations, eg join(AB000123:5567-5589,80..1144) in the case when a database object is passed in, it will attempt to retrieve the sequence from the database object, and "Do the right thing", however if no database object is provided, it will generate the correct number of N's (DNA) or X's (protein, though this is unlikely). This function is deliberately "magical" attempting to second guess what a user wants as "the" sequence for this feature. Implementing classes are free to override this method with their own magic if they have a better idea what the user wants. Args : [optional] -db A L compliant object if one needs to retrieve remote seqs. -nosort boolean if the locations should not be sorted by start location. This may occur, for instance, in a circular sequence where a gene span starts before the end of the sequence and ends after the sequence start. Example : join(15685..16260,1..207) (default = if sequence is_circular(), 1, otherwise 0) -phase truncates the returned sequence based on the intron phase (0,1,2). Returns : A L object =cut sub spliced_seq { my $self = shift; my @args = @_; my ($db, $nosort, $phase) = $self->_rearrange([qw(DB NOSORT PHASE)], @args); # set no_sort based on the parent sequence status if ($self->entire_seq->is_circular) { $nosort = 1; } # (added 7/7/06 to allow use old API (with warnings) my $old_api = (!(grep {$_ =~ /(?:nosort|db|phase)/} @args)) ? 1 : 0; if (@args && $old_api) { $self->warn( q(API has changed; please use '-db' or '-nosort' ) . qq(for args. See POD for more details.)); $db = shift @args if @args; $nosort = shift @args if @args; $phase = shift @args if @args; }; if (defined($phase) && ($phase < 0 || $phase > 2)) { $self->warn("Phase must be 0,1, or 2. Setting phase to 0..."); $phase = 0; } if ( $db && ref($db) && ! $db->isa('Bio::DB::RandomAccessI') ) { $self->warn( "Must pass in a valid Bio::DB::RandomAccessI object" . " for access to remote locations for spliced_seq"); $db = undef; } elsif ( defined $db && $HasInMemory && $db->isa('Bio::DB::InMemoryCache') ) { $db = Bio::DB::InMemoryCache->new(-seqdb => $db); } if ( not $self->location->isa("Bio::Location::SplitLocationI") ) { if ($phase) { $self->debug("Subseq start: ",$phase+1,"\tend: ",$self->end,"\n"); my $seqstr = substr($self->seq->seq, $phase); my $out = Bio::Seq->new( -id => $self->entire_seq->display_id . "_spliced_feat", -seq => $seqstr); return $out; } else { return $self->seq(); # nice and easy! } } # redundant test, but the above ISA is probably not ideal. if ( not $self->location->isa("Bio::Location::SplitLocationI") ) { $self->throw("not atomic, not split, yikes, in trouble!"); } my $seqstr = ''; my $seqid = $self->entire_seq->display_id; # This is to deal with reverse strand features # so we are really sorting features 5' -> 3' on their strand # i.e. rev strand features will be sorted largest to smallest # as this how revcom CDSes seem to be annotated in genbank. # Might need to eventually allow this to be programable? # (can I mention how much fun this is NOT! --jason) my ($mixed,$mixedloc, $fstrand) = (0); if ( $self->isa('Bio::Das::SegmentI') and not $self->absolute ) { $self->warn( "Calling spliced_seq with a Bio::Das::SegmentI which " . "does have absolute set to 1 -- be warned you may not " . "be getting things on the correct strand"); } my @locset = $self->location->each_Location; my @locs; if ( not $nosort ) { # @locs = map { $_->[0] } # sort so that most negative is first basically to order # the features on the opposite strand 5'->3' on their strand # rather than they way most are input which is on the fwd strand # sort { $a->[1] <=> $b->[1] } # Yes Tim, Schwartzian transformation my @proc_locs = map { $fstrand = $_->strand unless defined $fstrand; $mixed = 1 if defined $_->strand && $fstrand != $_->strand; if( defined $_->seq_id ) { $mixedloc = 1 if( $_->seq_id ne $seqid ); } [ $_, $_->start * ($_->strand || 1) ]; } @locset; my @sort_locs; if ( $fstrand == 1 ) { @sort_locs = sort { $a->[1] <=> $b->[1] } @proc_locs; # Yes Tim, Schwartzian transformation }elsif ( $fstrand == -1 ){ @sort_locs = sort { $b->[1] <=> $a->[1] } @proc_locs; # Yes Tim, Schwartzian transformation } else { @sort_locs = @proc_locs; } @locs = map { $_->[0] } @sort_locs; if ( $mixed ) { $self->warn( "Mixed strand locations, spliced seq using the " . "input order rather than trying to sort"); @locs = @locset; } } else { # use the original order instead of trying to sort @locs = @locset; $fstrand = $locs[0]->strand; } my $last_id = undef; my $called_seq = undef; # This will be left as undefined if 1) db is remote or 2)seq_id is undefined. # In that case, old code is used to make exon sequence my $called_seq_seq = undef; my $called_seq_len = undef; foreach my $loc ( @locs ) { if ( not $loc->isa("Bio::Location::Atomic") ) { $self->throw("Can only deal with one level deep locations"); } if ( $fstrand != $loc->strand ) { $self->warn("feature strand is different from location strand!"); } my $loc_seq_id; if ( defined $loc->seq_id ) { $loc_seq_id = $loc->seq_id; # deal with remote sequences if ($loc_seq_id ne $seqid ) { # might be too big to download whole sequence $called_seq_seq = undef; if ( defined $db ) { my $sid = $loc_seq_id; $sid =~ s/\.\d+$//g; eval { $called_seq = $db->get_Seq_by_acc($sid); }; if( $@ ) { $self->warn( "In attempting to join a remote location, sequence $sid " . "was not in database. Will provide padding N's. Full exception \n\n$@"); $called_seq = undef; } } else { $self->warn( "cannot get remote location for ".$loc_seq_id ." without a valid " . "Bio::DB::RandomAccessI database handle (like Bio::DB::GenBank)"); $called_seq = undef; } if ( !defined $called_seq ) { $seqstr .= 'N' x $loc->length; next; } } # have local sequence available else { # don't have to pull out source sequence again if it's local unless # it's the first exon or different from previous exon unless (defined(($last_id) && $last_id eq $loc_seq_id )){ $called_seq = $self->entire_seq; $called_seq_seq = $called_seq->seq(); # this is slow } } } #undefined $loc->seq->id else { $called_seq = $self->entire_seq; $called_seq_seq = undef; } my ($start,$end) = ($loc->start,$loc->end); # does the called sequence make sense? Bug 1780 my $called_seq_len; # can avoid a seq() call on called_seq if (defined($called_seq_seq)) { $called_seq_len = length($called_seq_seq); } # can't avoid a seq() call on called_seq else { $called_seq_len = $called_seq->length # this is slow } if ($called_seq_len < $loc->end) { my $accession = $called_seq->accession; my $orig_id = $self->seq_id; # originating sequence my ($locus) = $self->get_tagset_values("locus_tag"); $self->throw( "Location end ($end) exceeds length ($called_seq_len) of " . "called sequence $accession.\nCheck sequence version used in " . "$locus locus-tagged SeqFeature in $orig_id."); } if ( $self->isa('Bio::Das::SegmentI') ) { # $called_seq is Bio::DB::GFF::RelSegment, as well as its subseq(); # Bio::DB::GFF::RelSegment::seq() returns a Bio::PrimarySeq, and using seq() # in turn returns a string. Confused? $seqstr .= $called_seq->subseq($start,$end)->seq()->seq(); # this is slow } else { my $exon_seq; if (defined ($called_seq_seq)){ $exon_seq = substr($called_seq_seq, $start-1, $end-$start+1); # this is quick } else { $exon_seq = $called_seq->subseq($loc->start,$loc->end); # this is slow } # If guide_strand is defined, assemble the sequence first and revcom later if needed, # if its not defined, apply revcom immediately to proper locations if (defined $self->location->guide_strand) { $seqstr .= $exon_seq; } else { my $strand = defined ($loc->strand) ? ($loc->strand) : 0; # revcomp $exon_seq if ($strand == -1) { $exon_seq = reverse($exon_seq); $exon_seq =~ tr/ABCDGHKMNRSTUVWXYabcdghkmnrstuvwxy/TVGHCDMKNYSAABWXRtvghcdmknysaabwxr/; $seqstr .= $exon_seq; } else { $seqstr .= $exon_seq; } } } $last_id = $loc_seq_id if (defined($loc_seq_id)); } #next $loc # Use revcom only after the whole sequence has been assembled my $guide_strand = defined ($self->location->guide_strand) ? ($self->location->guide_strand) : 0; if ($guide_strand == -1) { my $seqstr_obj = Bio::Seq->new(-seq => $seqstr); $seqstr = $seqstr_obj->revcom->seq; } if (defined($phase)) { $seqstr = substr($seqstr, $phase); } my $out = Bio::Seq->new( -id => $self->entire_seq->display_id . "_spliced_feat", -seq => $seqstr); return $out; } =head2 location Title : location Usage : my $location = $seqfeature->location() Function: returns a location object suitable for identifying location of feature on sequence or parent feature Returns : Bio::LocationI object Args : none =cut sub location { my ($self) = @_; $self->throw_not_implemented(); } =head2 primary_id Title : primary_id Usage : $obj->primary_id($newval) Function: Example : Returns : value of primary_id (a scalar) Args : on set, new value (a scalar or undef, optional) Primary ID is a synonym for the tag 'ID' =cut sub primary_id{ my $self = shift; # note from cjm@fruitfly.org: # I have commented out the following 2 lines: #return $self->{'primary_id'} = shift if @_; #return $self->{'primary_id'}; #... and replaced it with the following; see # http://bioperl.org/pipermail/bioperl-l/2003-December/014150.html # for the discussion that lead to this change if (@_) { if ($self->has_tag('ID')) { $self->remove_tag('ID'); } $self->add_tag_value('ID', shift); } my ($id) = $self->get_tagset_values('ID'); return $id; } sub generate_unique_persistent_id { # DEPRECATED - us IDHandler my $self = shift; require Bio::SeqFeature::Tools::IDHandler; Bio::SeqFeature::Tools::IDHandler->new->generate_unique_persistent_id($self); } =head2 phase Title : phase Usage : $obj->phase($newval) Function: get/set this feature's phase. Example : Returns : undef if no phase is set, otherwise 0, 1, or 2 (the only valid values for phase) Args : on set, the new value Most features do not have or need a defined phase. For features representing a CDS, the phase indicates where the feature begins with reference to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon. In other words, a phase of "0" indicates that the next codon begins at the first base of the region described by the current line, a phase of "1" indicates that the next codon begins at the second base of this region, and a phase of "2" indicates that the codon begins at the third base of this region. This is NOT to be confused with the frame, which is simply start modulo 3. For forward strand features, phase is counted from the start field. For reverse strand features, phase is counted from the end field. =cut sub phase { my $self = shift; if( @_ ) { $self->remove_tag('phase') if $self->has_tag('phase'); my $newphase = shift; $self->throw("illegal phase value '$newphase', phase must be either undef, 0, 1, or 2") unless !defined $newphase || $newphase == 0 || $newphase == 1 || $newphase == 2; $self->add_tag_value('phase', $newphase ); return $newphase; } return $self->has_tag('phase') ? ($self->get_tag_values('phase'))[0] : undef; } =head1 Bio::RangeI methods These methods are inherited from RangeI and can be used directly from a SeqFeatureI interface. Remember that a SeqFeature is-a RangeI, and so wherever you see RangeI you can use a feature ($r in the below documentation). =cut =head2 start() See L =head2 end() See L =head2 strand() See L =head2 overlaps() See L =head2 contains() See L =head2 equals() See L =head2 intersection() See L =head2 union() See L =cut 1; BioPerl-1.007002/Bio/SeqI.pm000444000766000024 1462113155576320 15447 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SeqI # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqI - [Developers] Abstract Interface of Sequence (with features) =head1 SYNOPSIS # Bio::SeqI is the interface class for sequences. # If you are a newcomer to bioperl, you should # start with Bio::Seq documentation. This # documentation is mainly for developers using # Bioperl. # Bio::SeqI implements Bio::PrimarySeqI $seq = $seqobj->seq(); # actual sequence as a string $seqstr = $seqobj->subseq(10,50); # Bio::SeqI has annotationcollections $ann = $seqobj->annotation(); # annotation object # Bio::SeqI has sequence features # features must implement Bio::SeqFeatureI @features = $seqobj->get_SeqFeatures(); # just top level @features = $seqobj->get_all_SeqFeatures(); # descend into sub features =head1 DESCRIPTION Bio::SeqI is the abstract interface of annotated Sequences. These methods are those which you can be guaranteed to get for any Bio::SeqI. For most users of the package the documentation (and methods) in this class are not at useful - this is a developers only class which defines what methods have to be implemented by other Perl objects to comply to the Bio::SeqI interface. Go "perldoc Bio::Seq" or "man Bio::Seq" for more information. There aren't many method here, because too many complicated functions here would prevent implementations which are just wrappers around a database or similar delayed mechanisms. Most of the clever stuff happens inside the SeqFeatureI system. A good reference implementation is Bio::Seq which is a pure perl implementation of this class with a lot of extra pieces for extra manipulation. However, if you want to be able to use any sequence object in your analysis, if you can do it just using these methods, then you know you will be future proof and compatible with other implementations of Seq. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::SeqI; use strict; # Object preamble - inherits from Bio::PrimarySeqI use base qw(Bio::PrimarySeqI Bio::AnnotatableI Bio::FeatureHolderI); =head2 get_SeqFeatures Title : get_SeqFeatures Usage : my @feats = $seq->get_SeqFeatures(); Function: retrieve just the toplevel sequence features attached to this seq Returns : array of Bio::SeqFeatureI objects Args : none This method comes through extension of Bio::FeatureHolderI. See L and L for more information. =head2 get_all_SeqFeatures Title : get_all_SeqFeatures Usage : my @feats = $seq->get_all_SeqFeatures(); Function: returns all SeqFeatures, including sub SeqFeatures Returns : an array of Bio::SeqFeatureI objects Args : none This method comes through extension of Bio::FeatureHolderI. See L and L for more information. =head2 feature_count Title : feature_count Usage : my $count = $seq->feature_count(); Function: Return the number of SeqFeatures attached to a sequence Returns : integer representing the number of SeqFeatures Args : none This method comes through extension of Bio::FeatureHolderI. See L for more information. =head2 seq Title : seq Usage : my $string = $seq->seq(); Function: Retrieves the sequence string for the sequence object Returns : string Args : none =cut sub seq { my ($self) = @_; $self->throw_not_implemented(); } =head2 write_GFF Title : write_GFF Usage : $seq->write_GFF(\*FILEHANDLE); Function: Convenience method to write out all the sequence features in GFF format to the provided filehandle (STDOUT by default) Returns : none Args : [optional] filehandle to write to (default is STDOUT) =cut sub write_GFF { my ($self,$fh) = @_; $fh || do { $fh = \*STDOUT; }; foreach my $sf ( $self->get_all_SeqFeatures() ) { print $fh $sf->gff_string, "\n"; } } =head2 annotation Title : annotation Usage : my $ann = $seq->annotation($seq_obj); Function: retrieve the attached annotation object Returns : Bio::AnnotationCollectionI or none; See L and L for more information. This method comes through extension from L. =head2 species Title : species Usage : Function: Gets or sets the species Example : my $species = $seq->species(); Returns : Bio::Species object Args : Bio::Species object or none; See L for more information =cut sub species { my ($self) = @_; $self->throw_not_implemented(); } =head2 primary_seq Title : primary_seq Usage : my $primaryseq = $seq->primary_seq($newval) Function: Retrieve the underlying Bio::PrimarySeqI object if available. This is in the event one has a sequence with lots of features but want to be able to narrow the object to just one with the basics of a sequence (no features or annotations). Returns : Bio::PrimarySeqI Args : Bio::PrimarySeqI or none; See L for more information =cut sub primary_seq { my ($self) = @_; $self->throw_not_implemented; } 1; BioPerl-1.007002/Bio/SeqIO.pm000444000766000024 6125013155576320 15566 0ustar00cjfieldsstaff000000000000# BioPerl module for Bio::SeqIO # # Please direct questions and support issues to # # Cared for by Ewan Birney # and Lincoln Stein # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # # _history # October 18, 1999 Largely rewritten by Lincoln Stein # POD documentation - main docs before the code =head1 NAME Bio::SeqIO - Handler for SeqIO Formats =head1 SYNOPSIS use Bio::SeqIO; $in = Bio::SeqIO->new(-file => "inputfilename" , -format => 'Fasta'); $out = Bio::SeqIO->new(-file => ">outputfilename" , -format => 'EMBL'); while ( my $seq = $in->next_seq() ) { $out->write_seq($seq); } # Now, to actually get at the sequence object, use the standard Bio::Seq # methods (look at Bio::Seq if you don't know what they are) use Bio::SeqIO; $in = Bio::SeqIO->new(-file => "inputfilename" , -format => 'genbank'); while ( my $seq = $in->next_seq() ) { print "Sequence ",$seq->id, " first 10 bases ", $seq->subseq(1,10), "\n"; } # The SeqIO system does have a filehandle binding. Most people find this # a little confusing, but it does mean you can write the world's # smallest reformatter use Bio::SeqIO; $in = Bio::SeqIO->newFh(-file => "inputfilename" , -format => 'Fasta'); $out = Bio::SeqIO->newFh(-format => 'EMBL'); # World's shortest Fasta<->EMBL format converter: print $out $_ while <$in>; =head1 DESCRIPTION Bio::SeqIO is a handler module for the formats in the SeqIO set (eg, Bio::SeqIO::fasta). It is the officially sanctioned way of getting at the format objects, which most people should use. The Bio::SeqIO system can be thought of like biological file handles. They are attached to filehandles with smart formatting rules (eg, genbank format, or EMBL format, or binary trace file format) and can either read or write sequence objects (Bio::Seq objects, or more correctly, Bio::SeqI implementing objects, of which Bio::Seq is one such object). If you want to know what to do with a Bio::Seq object, read L. The idea is that you request a stream object for a particular format. All the stream objects have a notion of an internal file that is read from or written to. A particular SeqIO object instance is configured for either input or output. A specific example of a stream object is the Bio::SeqIO::fasta object. Each stream object has functions $stream->next_seq(); and $stream->write_seq($seq); As an added bonus, you can recover a filehandle that is tied to the SeqIO object, allowing you to use the standard EE and print operations to read and write sequence objects: use Bio::SeqIO; $stream = Bio::SeqIO->newFh(-format => 'Fasta', -fh => \*ARGV); # read from standard input or the input filenames while ( $seq = <$stream> ) { # do something with $seq } and print $stream $seq; # when stream is in output mode This makes the simplest ever reformatter #!/usr/bin/perl use strict; my $format1 = shift; my $format2 = shift || die "Usage: reformat format1 format2 < input > output"; use Bio::SeqIO; my $in = Bio::SeqIO->newFh(-format => $format1, -fh => \*ARGV ); my $out = Bio::SeqIO->newFh(-format => $format2 ); # Note: you might want to quote -format to keep older # perl's from complaining. print $out $_ while <$in>; =head1 CONSTRUCTORS =head2 Bio::SeqIO-Enew() $seqIO = Bio::SeqIO->new(-file => 'seqs.fasta', -format => $format); $seqIO = Bio::SeqIO->new(-fh => \*FILEHANDLE, -format => $format); $seqIO = Bio::SeqIO->new(-string => $string , -format => $format); $seqIO = Bio::SeqIO->new(-format => $format); The new() class method constructs a new Bio::SeqIO object. The returned object can be used to retrieve or print Seq objects. new() accepts the following parameters: =over 5 =item -file A file path to be opened for reading or writing. The usual Perl conventions apply: 'file' # open file for reading '>file' # open file for writing '>>file' # open file for appending '+new(-fh => \*STDIN); A string filehandle is handy if you want to modify the output in the memory, before printing it out. The following program reads in EMBL formatted entries from a file and prints them out in fasta format with some HTML tags: use Bio::SeqIO; use IO::String; my $in = Bio::SeqIO->new(-file => "emblfile", -format => 'EMBL'); while ( my $seq = $in->next_seq() ) { # the output handle is reset for every file my $stringio = IO::String->new($string); my $out = Bio::SeqIO->new(-fh => $stringio, -format => 'fasta'); # output goes into $string $out->write_seq($seq); # modify $string $string =~ s|(>)(\w+)|$1$2|g; # print into STDOUT print $string; } Filehandles can also be used to read from or write to a piped command: use Bio::SeqIO; #convert .fastq.gz to .fasta open my $zcat, 'zcat seq.fastq.gz |' or die $!; my $in=Bio::SeqIO->new(-fh=>$zcat, -format=>'fastq'); my $out=Bio::SeqIO->new(-file=>'>seq.fasta', -format=>'fasta'); while (my $seq=$in->next_seq) { $out->write_seq($seq) } =item -string A string to read the sequences from. For example: my $string = ">seq1\nACGCTAGCTAGC\n"; my $seqIO = Bio::SeqIO->new(-string => $string); =item -format Specify the format of the file. Supported formats include fasta, genbank, embl, swiss (SwissProt), Entrez Gene and tracefile formats such as abi (ABI) and scf. There are many more, for a complete listing see the SeqIO HOWTO (L). If no format is specified and a filename is given then the module will attempt to deduce the format from the filename suffix. If there is no suffix that Bioperl understands then it will attempt to guess the format based on file content. If this is unsuccessful then SeqIO will throw a fatal error. The format name is case-insensitive: 'FASTA', 'Fasta' and 'fasta' are all valid. Currently, the tracefile formats (except for SCF) require installation of the external Staden "io_lib" package, as well as the Bio::SeqIO::staden::read package available from the bioperl-ext repository. =item -alphabet Sets the alphabet ('dna', 'rna', or 'protein'). When the alphabet is set then Bioperl will not attempt to guess what the alphabet is. This may be important because Bioperl does not always guess correctly. =item -flush By default, all files (or filehandles) opened for writing sequences will be flushed after each write_seq() (making the file immediately usable). If you do not need this facility and would like to marginally improve the efficiency of writing multiple sequences to the same file (or filehandle), pass the -flush option '0' or any other value that evaluates as defined but false: my $gb = Bio::SeqIO->new(-file => " "gb"); my $fa = Bio::SeqIO->new(-file => ">gball.fa", -format => "fasta", -flush => 0); # go as fast as we can! while($seq = $gb->next_seq) { $fa->write_seq($seq) } =item -seqfactory Provide a Bio::Factory::SequenceFactoryI object. See the sequence_factory() method. =item -locfactory Provide a Bio::Factory::LocationFactoryI object. See the location_factory() method. =item -objbuilder Provide a Bio::Factory::ObjectBuilderI object. See the object_builder() method. =back =head2 Bio::SeqIO-EnewFh() $fh = Bio::SeqIO->newFh(-fh => \*FILEHANDLE, -format=>$format); $fh = Bio::SeqIO->newFh(-format => $format); # etc. This constructor behaves like new(), but returns a tied filehandle rather than a Bio::SeqIO object. You can read sequences from this object using the familiar EE operator, and write to it using print(). The usual array and $_ semantics work. For example, you can read all sequence objects into an array like this: @sequences = <$fh>; Other operations, such as read(), sysread(), write(), close(), and printf() are not supported. =head1 OBJECT METHODS See below for more detailed summaries. The main methods are: =head2 $sequence = $seqIO-Enext_seq() Fetch the next sequence from the stream, or nothing if no more. =head2 $seqIO-Ewrite_seq($sequence [,$another_sequence,...]) Write the specified sequence(s) to the stream. =head2 TIEHANDLE(), READLINE(), PRINT() These provide the tie interface. See L for more details. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and responsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney, Lincoln Stein Email birney@ebi.ac.uk lstein@cshl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' Let the code begin... package Bio::SeqIO; use strict; use warnings; use Bio::Factory::FTLocationFactory; use Bio::Seq::SeqBuilder; use Bio::Tools::GuessSeqFormat; use Symbol; use parent qw(Bio::Root::Root Bio::Root::IO Bio::Factory::SequenceStreamI); my %valid_alphabet_cache; =head2 new Title : new Usage : $stream = Bio::SeqIO->new(-file => 'sequences.fasta', -format => 'fasta'); Function: Returns a new sequence stream Returns : A Bio::SeqIO stream initialised with the appropriate format Args : Named parameters indicating where to read the sequences from or to write them to: -file => filename, OR -fh => filehandle to attach to, OR -string => string Additional arguments, all with reasonable defaults: -format => format of the sequences, usually auto-detected -alphabet => 'dna', 'rna', or 'protein' -flush => 0 or 1 (default: flush filehandles after each write) -seqfactory => sequence factory -locfactory => location factory -objbuilder => object builder See L =cut my $entry = 0; sub new { my ($caller, @args) = @_; my $class = ref($caller) || $caller; # or do we want to call SUPER on an object if $caller is an # object? if( $class =~ /Bio::SeqIO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %params = @args; @params{ map { lc $_ } keys %params } = values %params; # lowercase keys unless( defined $params{-file} || defined $params{-fh} || defined $params{-string} ) { $class->throw("file argument provided, but with an undefined value") if exists $params{'-file'}; $class->throw("fh argument provided, but with an undefined value") if exists $params{'-fh'}; $class->throw("string argument provided, but with an undefined value") if exists($params{'-string'}); # $class->throw("No file, fh, or string argument provided"); # neither defined } # Determine or guess sequence format and variant my $format = $params{'-format'}; if (! $format ) { if ($params{-file}) { # Guess from filename extension, and then from file content $format = $class->_guess_format( $params{-file} ) || Bio::Tools::GuessSeqFormat->new(-file => $params{-file} )->guess; } elsif ($params{-fh}) { # Guess from filehandle content $format = Bio::Tools::GuessSeqFormat->new(-fh => $params{-fh} )->guess; } elsif ($params{-string}) { # Guess from string content $format = Bio::Tools::GuessSeqFormat->new(-text => $params{-string})->guess; } } # changed 1-3-11; no need to print out an empty string (only way this # exception is triggered) - cjfields $class->throw("Could not guess format from file, filehandle or string") if not $format; $format = "\L$format"; # normalize capitalization to lower case if ($format =~ /-/) { ($format, my $variant) = split('-', $format, 2); $params{-variant} = $variant; } return unless( $class->_load_format_module($format) ); return "Bio::SeqIO::$format"->new(%params); } } =head2 newFh Title : newFh Usage : $fh = Bio::SeqIO->newFh(-file=>$filename,-format=>'Format') Function: Does a new() followed by an fh() Example : $fh = Bio::SeqIO->newFh(-file=>$filename,-format=>'Format') $sequence = <$fh>; # read a sequence object print $fh $sequence; # write a sequence object Returns : filehandle tied to the Bio::SeqIO::Fh class Args : See L =cut sub newFh { my $class = shift; return unless my $self = $class->new(@_); return $self->fh; } =head2 fh Title : fh Usage : $obj->fh Function: Get or set the IO filehandle Example : $fh = $obj->fh; # make a tied filehandle $sequence = <$fh>; # read a sequence object print $fh $sequence; # write a sequence object Returns : filehandle tied to Bio::SeqIO class Args : none =cut sub fh { my $self = shift; my $class = ref($self) || $self; my $s = Symbol::gensym; tie $$s,$class,$self; return $s; } # _initialize is chained for all SeqIO classes sub _initialize { my($self, @args) = @_; # flush is initialized by the Root::IO init my ($seqfact,$locfact,$objbuilder, $alphabet) = $self->_rearrange([qw(SEQFACTORY LOCFACTORY OBJBUILDER ALPHABET) ], @args); $locfact = Bio::Factory::FTLocationFactory->new(-verbose => $self->verbose) if ! $locfact; $objbuilder = Bio::Seq::SeqBuilder->new(-verbose => $self->verbose) unless $objbuilder; $self->sequence_builder($objbuilder); $self->location_factory($locfact); # note that this should come last because it propagates the sequence # factory to the sequence builder $seqfact && $self->sequence_factory($seqfact); #bug 2160 $alphabet && $self->alphabet($alphabet); # initialize the IO part $self->_initialize_io(@args); } =head2 next_seq Title : next_seq Usage : $seq = stream->next_seq Function: Reads the next sequence object from the stream and returns it. Certain driver modules may encounter entries in the stream that are either misformatted or that use syntax not yet understood by the driver. If such an incident is recoverable, e.g., by dismissing a feature of a feature table or some other non-mandatory part of an entry, the driver will issue a warning. In the case of a non-recoverable situation an exception will be thrown. Do not assume that you can resume parsing the same stream after catching the exception. Note that you can always turn recoverable errors into exceptions by calling $stream->verbose(2). Returns : a Bio::Seq sequence object, or nothing if no more sequences are available Args : none See L, L, L =cut sub next_seq { my ($self, $seq) = @_; $self->throw("Sorry, you cannot read from a generic Bio::SeqIO object."); } =head2 write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object =cut sub write_seq { my ($self, $seq) = @_; $self->throw("Sorry, you cannot write to a generic Bio::SeqIO object."); } =head2 format Title : format Usage : $format = $stream->format() Function: Get the sequence format Returns : sequence format, e.g. fasta, fastq Args : none =cut # format() method inherited from Bio::Root::IO =head2 alphabet Title : alphabet Usage : $self->alphabet($newval) Function: Set/get the molecule type for the Seq objects to be created. Example : $seqio->alphabet('protein') Returns : value of alphabet: 'dna', 'rna', or 'protein' Args : newvalue (optional) Throws : Exception if the argument is not one of 'dna', 'rna', or 'protein' =cut sub alphabet { my ($self, $value) = @_; if ( defined $value) { $value = lc $value; unless ($valid_alphabet_cache{$value}) { # instead of hard-coding the allowed values once more, we check by # creating a dummy sequence object eval { require Bio::PrimarySeq; my $seq = Bio::PrimarySeq->new( -verbose => $self->verbose, -alphabet => $value ); }; if ($@) { $self->throw("Invalid alphabet: $value\n. See Bio::PrimarySeq for allowed values."); } $valid_alphabet_cache{$value} = 1; } $self->{'alphabet'} = $value; } return $self->{'alphabet'}; } =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL SeqIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($self, $format) = @_; my $module = "Bio::SeqIO::" . $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <_filehandle($newval) Function: This method is deprecated. Call _fh() instead. Example : Returns : value of _filehandle Args : newvalue (optional) =cut sub _filehandle { my ($self,@args) = @_; return $self->_fh(@args); } =head2 _guess_format Title : _guess_format Usage : $obj->_guess_format($filename) Function: guess format based on file suffix Example : Returns : guessed format of filename (lower case) Args : Notes : formats that _filehandle() will guess include fasta, genbank, scf, pir, embl, raw, gcg, ace, bsml, swissprot, fastq and phd/phred =cut sub _guess_format { my $class = shift; return unless $_ = shift; return 'abi' if /\.ab[i1]$/i; return 'ace' if /\.ace$/i; return 'alf' if /\.alf$/i; return 'bsml' if /\.(bsm|bsml)$/i; return 'ctf' if /\.ctf$/i; return 'embl' if /\.(embl|ebl|emb|dat)$/i; return 'entrezgene' if /\.asn$/i; return 'exp' if /\.exp$/i; return 'fasta' if /\.(fasta|fast|fas|seq|fa|fsa|nt|aa|fna|faa)$/i; return 'fastq' if /\.fastq$/i; return 'gcg' if /\.gcg$/i; return 'genbank' if /\.(gb|gbank|genbank|gbk|gbs)$/i; return 'phd' if /\.(phd|phred)$/i; return 'pir' if /\.pir$/i; return 'pln' if /\.pln$/i; return 'qual' if /\.qual$/i; return 'raw' if /\.txt$/i; return 'scf' if /\.scf$/i; # from Strider 1.4 Release Notes: The file name extensions used by # Strider 1.4 are ".xdna", ".xdgn", ".xrna" and ".xprt" for DNA, # DNA Degenerate, RNA and Protein Sequence Files, respectively return 'strider' if /\.(xdna|xdgn|xrna|xprt)$/i; return 'swiss' if /\.(swiss|sp)$/i; return 'ztr' if /\.ztr$/i; } sub DESTROY { my $self = shift; $self->close(); } sub TIEHANDLE { my ($class,$val) = @_; return bless {'seqio' => $val}, $class; } sub READLINE { my $self = shift; return $self->{'seqio'}->next_seq() || undef unless wantarray; my (@list, $obj); push @list, $obj while $obj = $self->{'seqio'}->next_seq(); return @list; } sub PRINT { my $self = shift; $self->{'seqio'}->write_seq(@_); } =head2 sequence_factory Title : sequence_factory Usage : $seqio->sequence_factory($seqfactory) Function: Get/Set the Bio::Factory::SequenceFactoryI Returns : Bio::Factory::SequenceFactoryI Args : [optional] Bio::Factory::SequenceFactoryI =cut sub sequence_factory { my ($self, $obj) = @_; if( defined $obj ) { if( ! ref($obj) || ! $obj->isa('Bio::Factory::SequenceFactoryI') ) { $self->throw("Must provide a valid Bio::Factory::SequenceFactoryI object to ".ref($self)."::sequence_factory()"); } $self->{'_seqio_seqfactory'} = $obj; my $builder = $self->sequence_builder(); if($builder && $builder->can('sequence_factory') && (! $builder->sequence_factory())) { $builder->sequence_factory($obj); } } $self->{'_seqio_seqfactory'}; } =head2 object_factory Title : object_factory Usage : $obj->object_factory($newval) Function: This is an alias to sequence_factory with a more generic name. Example : Returns : value of object_factory (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub object_factory{ return shift->sequence_factory(@_); } =head2 sequence_builder Title : sequence_builder Usage : $seqio->sequence_builder($seqfactory) Function: Get/Set the Bio::Factory::ObjectBuilderI used to build sequence objects. This applies to rich sequence formats only, e.g. genbank but not fasta. If you do not set the sequence object builder yourself, it will in fact be an instance of L, and you may use all methods documented there to configure it. Returns : a Bio::Factory::ObjectBuilderI compliant object Args : [optional] a Bio::Factory::ObjectBuilderI compliant object =cut sub sequence_builder { my ($self, $obj) = @_; if( defined $obj ) { if( ! ref($obj) || ! $obj->isa('Bio::Factory::ObjectBuilderI') ) { $self->throw("Must provide a valid Bio::Factory::ObjectBuilderI object to ".ref($self)."::sequence_builder()"); } $self->{'_object_builder'} = $obj; } $self->{'_object_builder'}; } =head2 location_factory Title : location_factory Usage : $seqio->location_factory($locfactory) Function: Get/Set the Bio::Factory::LocationFactoryI object to be used for location string parsing Returns : a Bio::Factory::LocationFactoryI implementing object Args : [optional] on set, a Bio::Factory::LocationFactoryI implementing object. =cut sub location_factory { my ($self,$obj) = @_; if( defined $obj ) { if( ! ref($obj) || ! $obj->isa('Bio::Factory::LocationFactoryI') ) { $self->throw("Must provide a valid Bio::Factory::LocationFactoryI" . " object to ".ref($self)."->location_factory()"); } $self->{'_seqio_locfactory'} = $obj; } $self->{'_seqio_locfactory'}; } 1; BioPerl-1.007002/Bio/SeqUtils.pm000444000766000024 16167413155576320 16412 0ustar00cjfieldsstaff000000000000# BioPerl module for Bio::SeqUtils # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqUtils - Additional methods for PrimarySeq objects =head1 SYNOPSIS use Bio::SeqUtils; # get a Bio::PrimarySeqI compliant object, $seq, somehow $util = Bio::SeqUtils->new(); $polypeptide_3char = $util->seq3($seq); # or $polypeptide_3char = Bio::SeqUtils->seq3($seq); # set the sequence string (stored in one char code in the object) Bio::SeqUtils->seq3($seq, $polypeptide_3char); # translate a sequence in all six frames @seqs = Bio::SeqUtils->translate_6frames($seq); # inplace editing of the sequence Bio::SeqUtils->mutate($seq, Bio::LiveSeq::Mutation->new(-seq => 'c', -pos => 3 )); # mutate a sequence to desired similarity% $newseq = Bio::SeqUtils-> evolve ($seq, $similarity, $transition_transversion_rate); # concatenate two or more sequences with annotations and features, # the first sequence will be modified Bio::SeqUtils->cat(@seqs); my $catseq=$seqs[0]; # truncate a sequence, retaining features and adjusting their # coordinates if necessary my $truncseq = Bio::SeqUtils->trunc_with_features($seq, 100, 200); # reverse complement a sequence and its features my $revcomseq = Bio::SeqUtils->revcom_with_features($seq); # simulate cloning of a fragment into a vector. Cut the vector at # positions 1000 and 1100 (deleting positions 1001 to 1099) and # "ligate" a fragment into the sites. The fragment is # reverse-complemented in this example (option "flip"). # All features of the vector and fragment are preserved and # features that are affected by the deletion/insertion are # modified accordingly. # $vector and $fragment must be Bio::SeqI compliant objects my $new_molecule = Bio::Sequtils->ligate( -vector => $vector, -fragment => $fragment, -left => 1000, -right => 1100, -flip => 1 ); # delete a segment of a sequence (from pos 1000 to 1100, inclusive), # again preserving features and annotations my $new_molecule = Bio::SeqUtils->cut( $seq, 1000, 1100 ); # insert a fragment into a recipient between positions 1000 and # 1001. $recipient is a Bio::SeqI compliant object my $new_molecule = Bio::SeqUtils::PbrTools->insert( $recipient_seq, $fragment_seq, 1000 ); =head1 DESCRIPTION This class is a holder of methods that work on Bio::PrimarySeqI- compliant sequence objects, e.g. Bio::PrimarySeq and Bio::Seq. These methods are not part of the Bio::PrimarySeqI interface and should in general not be essential to the primary function of sequence objects. If you are thinking of adding essential functions, it might be better to create your own sequence class. See L, L, and L for more. The methods take as their first argument a sequence object. It is possible to use methods without first creating a SeqUtils object, i.e. use it as an anonymous hash. The first two methods, seq3() and seq3in(), give out or read in protein sequences coded in three letter IUPAC amino acid codes. The next two methods, translate_3frames() and translate_6frames(), wrap around the standard translate method to give back an array of three forward or all six frame translations. The mutate() method mutates the sequence string with a mutation description object. The cat() method concatenates two or more sequences. The first sequence is modified by addition of the remaining sequences. All annotations and sequence features will be transferred. The revcom_with_features() and trunc_with_features() methods are similar to the revcom() and trunc() methods from Bio::Seq, but also adjust any features associated with the sequence as appropriate. There are also methods that simulate molecular cloning with rich sequence objects. The delete() method cuts a segment out of a sequence and re-joins the left and right fragments (like splicing or digesting and re-ligating a molecule). Positions (and types) of sequence features are adjusted accordingly: Features that span the deleted segment are converted to split featuress to indicate the disruption. (Sub)Features that extend into the deleted segment are truncated. A new molecule is created and returned. The insert() method inserts a fragment (which can be a rich Bio::Seq object) into another sequence object adding all annotations and features to the final product. Features that span the insertion site are converted to split features to indicate the disruption. A new feature is added to indicate the inserted fragment itself. A new molecule is created and returned. The ligate() method simulates digesting a recipient (vector) and ligating a fragment into it, which can also be flipped if needed. It is simply a combination of a deletion and an insertion step and returns a new molecule. The rules for modifying feature locations outlined above are also used here, e.g. features that span the cut sites are converted to split features with truncated sub-locations. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 CONTRIBUTORS Roy R. Chaudhuri - roy.chaudhuri at gmail.com Frank Schwach - frank.schwach@sanger.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqUtils; use strict; use warnings; use Scalar::Util qw(blessed); use parent qw(Bio::Root::Root); # new inherited from RootI our %ONECODE = ( 'Ala' => 'A', 'Asx' => 'B', 'Cys' => 'C', 'Asp' => 'D', 'Glu' => 'E', 'Phe' => 'F', 'Gly' => 'G', 'His' => 'H', 'Ile' => 'I', 'Lys' => 'K', 'Leu' => 'L', 'Met' => 'M', 'Asn' => 'N', 'Pro' => 'P', 'Gln' => 'Q', 'Arg' => 'R', 'Ser' => 'S', 'Thr' => 'T', 'Val' => 'V', 'Trp' => 'W', 'Xaa' => 'X', 'Tyr' => 'Y', 'Glx' => 'Z', 'Ter' => '*', 'Sec' => 'U', 'Pyl' => 'O', 'Xle' => 'J' ); our %THREECODE = ( 'A' => 'Ala', 'B' => 'Asx', 'C' => 'Cys', 'D' => 'Asp', 'E' => 'Glu', 'F' => 'Phe', 'G' => 'Gly', 'H' => 'His', 'I' => 'Ile', 'K' => 'Lys', 'L' => 'Leu', 'M' => 'Met', 'N' => 'Asn', 'P' => 'Pro', 'Q' => 'Gln', 'R' => 'Arg', 'S' => 'Ser', 'T' => 'Thr', 'V' => 'Val', 'W' => 'Trp', 'Y' => 'Tyr', 'Z' => 'Glx', 'X' => 'Xaa', '*' => 'Ter', 'U' => 'Sec', 'O' => 'Pyl', 'J' => 'Xle' ); =head2 seq3 Title : seq3 Usage : $string = Bio::SeqUtils->seq3($seq) Function: Read only method that returns the amino acid sequence as a string of three letter codes. alphabet has to be 'protein'. Output follows the IUPAC standard plus 'Ter' for terminator. Any unknown character, including the default unknown character 'X', is changed into 'Xaa'. A noncoded aminoacid selenocystein is recognized (Sec, U). Returns : A scalar Args : character used for stop in the protein sequence optional, defaults to '*' string used to separate the output amino acid codes, optional, defaults to '' =cut sub seq3 { my ( $self, $seq, $stop, $sep ) = @_; $seq->isa('Bio::PrimarySeqI') || $self->throw('Not a Bio::PrimarySeqI object but [$self]'); $seq->alphabet eq 'protein' || $self->throw('Not a protein sequence'); if ( defined $stop ) { length $stop != 1 and $self->throw('One character stop needed, not [$stop]'); $THREECODE{$stop} = "Ter"; } $sep ||= ''; my $aa3s; foreach my $aa ( split //, uc $seq->seq ) { $THREECODE{$aa} and $aa3s .= $THREECODE{$aa} . $sep, next; $aa3s .= 'Xaa' . $sep; } $sep and substr( $aa3s, -( length $sep ), length $sep ) = ''; return $aa3s; } =head2 seq3in Title : seq3in Usage : $seq = Bio::SeqUtils->seq3in($seq, 'MetGlyTer') Function: Method for changing of the sequence of a Bio::PrimarySeqI sequence object. The three letter amino acid input string is converted into one letter code. Any unknown character triplet, including the default 'Xaa', is converted into 'X'. Returns : Bio::PrimarySeq object Args : sequence string optional character to be used for stop in the protein sequence, defaults to '*' optional character to be used for unknown in the protein sequence, defaults to 'X' =cut sub seq3in { my ( $self, $seq, $string, $stop, $unknown ) = @_; $seq->isa('Bio::PrimarySeqI') || $self->throw("Not a Bio::PrimarySeqI object but [$self]"); $seq->alphabet eq 'protein' || $self->throw('Not a protein sequence'); if ( defined $stop ) { length $stop != 1 and $self->throw("One character stop needed, not [$stop]"); $ONECODE{'Ter'} = $stop; } if ( defined $unknown ) { length $unknown != 1 and $self->throw("One character stop needed, not [$unknown]"); $ONECODE{'Xaa'} = $unknown; } my ( $aas, $aa3 ); my $length = ( length $string ) - 2; for ( my $i = 0 ; $i < $length ; $i += 3 ) { $aa3 = substr( $string, $i, 3 ); $aa3 = ucfirst( lc($aa3) ); $ONECODE{$aa3} and $aas .= $ONECODE{$aa3}, next; $aas .= $ONECODE{'Xaa'}; } $seq->seq($aas); return $seq; } =head2 translate_3frames Title : translate_3frames Usage : @prots = Bio::SeqUtils->translate_3frames($seq) Function: Translate a nucleotide sequence in three forward frames. The IDs of the sequences are appended with '-0F', '-1F', '-2F'. Returns : An array of seq objects Args : sequence object same arguments as to Bio::PrimarySeqI::translate =cut sub translate_3frames { my ( $self, $seq, @args ) = @_; $self->throw( 'Object [$seq] ' . 'of class [' . ref($seq) . '] can not be translated.' ) unless $seq->can('translate'); my ( $stop, $unknown, $frame, $tableid, $fullCDS, $throw ) = @args; my @seqs; my $f = 0; while ( $f != 3 ) { my $translation = $seq->translate( $stop, $unknown, $f, $tableid, $fullCDS, $throw ); $translation->id( $seq->id . "-" . $f . "F" ); push @seqs, $translation; $f++; } return @seqs; } =head2 translate_6frames Title : translate_6frames Usage : @prots = Bio::SeqUtils->translate_6frames($seq) Function: translate a nucleotide sequence in all six frames The IDs of the sequences are appended with '-0F', '-1F', '-2F', '-0R', '-1R', '-2R'. Returns : An array of seq objects Args : sequence object same arguments as to Bio::PrimarySeqI::translate =cut sub translate_6frames { my ( $self, $seq, @args ) = @_; my @seqs = $self->translate_3frames( $seq, @args ); my @seqs2 = $self->translate_3frames( $seq->revcom, @args ); foreach my $seq2 (@seqs2) { my ($tmp) = $seq2->id; $tmp =~ s/F$/R/g; $seq2->id($tmp); } return @seqs, @seqs2; } =head2 valid_aa Title : valid_aa Usage : my @aa = $table->valid_aa Function: Retrieves a list of the valid amino acid codes. The list is ordered so that first 21 codes are for unique amino acids. The rest are ['B', 'Z', 'X', '*']. Returns : array of all the valid amino acid codes Args : [optional] $code => [0 -> return list of 1 letter aa codes, 1 -> return list of 3 letter aa codes, 2 -> return associative array of both ] =cut sub valid_aa { my ( $self, $code ) = @_; if ( !$code ) { my @codes; foreach my $c ( sort values %ONECODE ) { push @codes, $c unless ( $c =~ /[BZX\*]/ ); } push @codes, qw(B Z X *); # so they are in correct order ? return @codes; } elsif ( $code == 1 ) { my @codes; foreach my $c ( sort keys %ONECODE ) { push @codes, $c unless ( $c =~ /(Asx|Glx|Xaa|Ter)/ ); } push @codes, ( 'Asx', 'Glx', 'Xaa', 'Ter' ); return @codes; } elsif ( $code == 2 ) { my %codes = %ONECODE; foreach my $c ( keys %ONECODE ) { my $aa = $ONECODE{$c}; $codes{$aa} = $c; } return %codes; } else { $self->warn( "unrecognized code in " . ref($self) . " method valid_aa()" ); return (); } } =head2 mutate Title : mutate Usage : Bio::SeqUtils->mutate($seq,$mutation1, $mutation2); Function: Inplace editing of the sequence. The second argument can be a Bio::LiveSeq::Mutation object or an array of them. The mutations are applied sequentially checking only that their position is within the current sequence. Insertions are inserted before the given position. Returns : boolean Args : sequence object mutation, a Bio::LiveSeq::Mutation object, or an array of them See L. =cut sub mutate { my ( $self, $seq, @mutations ) = @_; $self->throw( 'Object [$seq] ' . 'of class [' . ref($seq) . '] should be a Bio::PrimarySeqI ' ) unless $seq->isa('Bio::PrimarySeqI'); $self->throw( 'Object [$mutations[0]] ' . 'of class [' . ref( $mutations[0] ) . '] should be a Bio::LiveSeq::Mutation' ) unless $mutations[0]->isa('Bio::LiveSeq::Mutation'); foreach my $mutation (@mutations) { $self->throw('Attempting to mutate sequence beyond its length') unless $mutation->pos - 1 <= $seq->length; my $string = $seq->seq; substr $string, $mutation->pos - 1, $mutation->len, $mutation->seq; $seq->seq($string); } 1; } =head2 cat Title : cat Usage : Bio::SeqUtils->cat(@seqs); my $catseq=$seqs[0]; Function: Concatenates a list of Bio::Seq objects, adding them all on to the end of the first sequence. Annotations and sequence features are copied over from any additional objects, and the coordinates of any copied features are adjusted appropriately. Returns : a boolean Args : array of sequence objects Note that annotations have no sequence locations. If you concatenate sequences with the same annotations they will all be added. =cut sub cat { my ( $self, $seq, @seqs ) = @_; $self->throw( 'Object [$seq] ' . 'of class [' . ref($seq) . '] should be a Bio::PrimarySeqI ' ) unless $seq->isa('Bio::PrimarySeqI'); for my $catseq (@seqs) { $self->throw( 'Object [$catseq] ' . 'of class [' . ref($catseq) . '] should be a Bio::PrimarySeqI ' ) unless $catseq->isa('Bio::PrimarySeqI'); $self->throw( 'Trying to concatenate sequences with different alphabets: ' . $seq->display_id . '(' . $seq->alphabet . ') and ' . $catseq->display_id . '(' . $catseq->alphabet . ')' ) unless $catseq->alphabet eq $seq->alphabet; my $length = $seq->length; $seq->seq( $seq->seq . $catseq->seq ); # move annotations if ( $seq->isa("Bio::AnnotatableI") and $catseq->isa("Bio::AnnotatableI") ) { foreach my $key ( $catseq->annotation->get_all_annotation_keys() ) { foreach my $value ( $catseq->annotation->get_Annotations($key) ) { $seq->annotation->add_Annotation( $key, $value ); } } } # move SeqFeatures if ( $seq->isa('Bio::SeqI') and $catseq->isa('Bio::SeqI') ) { for my $feat ( $catseq->get_SeqFeatures ) { $seq->add_SeqFeature( $self->_coord_adjust( $feat, $length ) ); } } } 1; } =head2 trunc_with_features Title : trunc_with_features Usage : $trunc=Bio::SeqUtils->trunc_with_features($seq, $start, $end); Function: Like Bio::Seq::trunc, but keeps features (adjusting coordinates where necessary. Features that partially overlap the region have their location changed to a Bio::Location::Fuzzy. Returns : A new sequence object Args : A sequence object, start coordinate, end coordinate (inclusive) =cut sub trunc_with_features { use Bio::Range; my ( $self, $seq, $start, $end ) = @_; $self->throw( 'Object [$seq] ' . 'of class [' . ref($seq) . '] should be a Bio::SeqI ' ) unless $seq->isa('Bio::SeqI'); my $trunc = $seq->trunc( $start, $end ); my $truncrange = Bio::Range->new( -start => $start, -end => $end, -strand => 0 ); # make sure that there is no annotation or features in $trunc # (->trunc() now clone objects except for Bio::Seq::LargePrimarySeq) $trunc->annotation->remove_Annotations; $trunc->remove_SeqFeatures; # move annotations foreach my $key ( $seq->annotation->get_all_annotation_keys() ) { foreach my $value ( $seq->annotation->get_Annotations($key) ) { $trunc->annotation->add_Annotation( $key, $value ); } } # move features foreach ( grep { $_ = $self->_coord_adjust( $_, 1 - $start, $end + 1 - $start ) if $_->overlaps($truncrange) } $seq->get_SeqFeatures ) { $trunc->add_SeqFeature($_); } return $trunc; } =head2 delete Title : delete Function: cuts a segment out of a sequence and re-joins the left and right fragments (like splicing or digesting and re-ligating a molecule). Positions (and types) of sequence features are adjusted accordingly: Features that span the cut site are converted to split featuress to indicate the disruption. Features that extend into the cut-out fragment are truncated. A new molecule is created and returned. Usage : my $cutseq = Bio::SeqUtils::PbrTools->cut( $seq, 1000, 1100 ); Args : a Bio::PrimarySeqI compliant object to cut, first nt of the segment to be deleted last nt of the segment to be deleted optional: hash-ref of options: clone_obj: if true, clone the input sequence object rather than calling "new" on the object's class Returns : a new Bio::Seq object =cut sub delete { my $self = shift; my ( $seq, $left, $right, $opts_ref ) = @_; $self->throw( 'was expecting 3-4 paramters but got ' . @_ ) unless @_ == 3 || @_ == 4; $self->throw( 'Object of class [' . ref($seq) . '] should be a Bio::PrimarySeqI ' ) unless blessed($seq) && $seq->isa('Bio::PrimarySeqI'); $self->throw("Left coordinate ($left) must be >= 1") if $left < 1; if ( $right > $seq->length ) { $self->throw( "Right coordinate ($right) must be less than " . 'sequence length (' . $seq->length . ')' ); } # piece together the sequence string of the remaining fragments my $left_seq = $seq->subseq( 1, $left - 1 ); my $right_seq = $seq->subseq( $right + 1, $seq->length ); if ( !$left_seq || !$right_seq ) { $self->throw( 'could not assemble sequences. At least one of the fragments is empty' ); } my $seq_str = $left_seq . $right_seq; # create the new seq object with the same class as the recipient # or (if requested), make a clone of the existing object. In the # latter case we need to remove sequence features from the cloned # object instead of copying them my $product; if ( $opts_ref->{clone_obj} ) { $product = $self->_new_seq_via_clone( $seq, $seq_str ); } else { $product = $self->_new_seq_from_old( $seq, { seq => $seq_str } ); } # move sequence features if ( $product->isa('Bio::SeqI') && $seq->isa('Bio::SeqI') ) { for my $feat ( $seq->get_SeqFeatures ) { my $adjfeat = $self->_coord_adjust_deletion( $feat, $left, $right ); $product->add_SeqFeature($adjfeat) if $adjfeat; } } # add a feature to annotatde the deletion my $deletion_feature = Bio::SeqFeature::Generic->new( -primary_tag => 'misc_feature', -tag => { note => 'deletion of ' . ( $right - $left + 1 ) . 'bp' }, -location => Bio::Location::Simple->new( -start => $left - 1, -end => $left, -location_type => 'IN-BETWEEN' ) ); $product->add_SeqFeature($deletion_feature); return $product; } =head2 insert Title : insert Function: inserts a fragment (a Bio::Seq object) into a nother sequence object adding all annotations and features to the final product. Features that span the insertion site are converted to split features to indicate the disruption. A new feature is added to indicate the inserted fragment itself. A new molecule is created and returned. Usage : # insert a fragment after pos 1000 my $insert_seq = Bio::SeqUtils::PbrTools->insert( $recipient_seq, $fragment_seq, 1000 ); Args : recipient sequence (a Bio::PrimarySeqI compliant object), a fragmetn to insert (Bio::PrimarySeqI compliant object), insertion position (fragment is inserted to the right of this pos) pos=0 will prepend the fragment to the recipient optional: hash-ref of options: clone_obj: if true, clone the input sequence object rather than calling "new" on the object's class Returns : a new Bio::Seq object =cut sub insert { my $self = shift; my ( $recipient, $fragment, $insert_pos, $opts_ref ) = @_; $self->throw( 'was expecting 3-4 paramters but got ' . @_ ) unless @_ == 3 || @_ == 4; $self->throw( 'Recipient object of class [' . ref($recipient) . '] should be a Bio::PrimarySeqI ' ) unless blessed($recipient) && $recipient->isa('Bio::PrimarySeqI'); $self->throw( 'Fragment object of class [' . ref($fragment) . '] should be a Bio::PrimarySeqI ' ) unless blessed($fragment) && $fragment->isa('Bio::PrimarySeqI'); $self->throw( 'Can\'t concatenate sequences with different alphabets: ' . 'recipient is ' . $recipient->alphabet . ' and fragment is ' . $fragment->alphabet ) unless $recipient->alphabet eq $fragment->alphabet; if ( $insert_pos < 0 or $insert_pos > $recipient->length ) { $self->throw( "insertion position ($insert_pos) must be between 0 and " . 'recipient sequence length (' . $recipient->length . ')' ); } if ( $fragment->can('is_circular') && $fragment->is_circular ) { $self->throw('Can\'t insert circular fragments'); } if ( !$recipient->seq ) { $self->throw( 'Recipient has no sequence, can not insert into this object'); } # construct raw sequence of the new molecule my $left_seq = $insert_pos > 0 ? $recipient->subseq( 1, $insert_pos ) : ''; my $mid_seq = $fragment->seq; my $right_seq = $insert_pos < $recipient->length ? $recipient->subseq( $insert_pos + 1, $recipient->length ) : ''; my $seq_str = $left_seq . $mid_seq . $right_seq; # create the new seq object with the same class as the recipient # or (if requested), make a clone of the existing object. In the # latter case we need to remove sequence features from the cloned # object instead of copying them my $product; if ( $opts_ref->{clone_obj} ) { $product = $self->_new_seq_via_clone( $recipient, $seq_str ); } else { my @desc; push @desc, 'Inserted fragment: ' . $fragment->desc if defined $fragment->desc; push @desc, 'Recipient: ' . $recipient->desc if defined $recipient->desc; $product = $self->_new_seq_from_old( $recipient, { seq => $seq_str, display_id => $recipient->display_id, accession_number => $recipient->accession_number || '', alphabet => $recipient->alphabet, desc => join( '; ', @desc ), verbose => $recipient->verbose || $fragment->verbose, is_circular => $recipient->is_circular || 0, } ); } # if clone_obj # move annotations from fragment to product if ( $product->isa("Bio::AnnotatableI") && $fragment->isa("Bio::AnnotatableI") ) { foreach my $key ( $fragment->annotation->get_all_annotation_keys ) { foreach my $value ( $fragment->annotation->get_Annotations($key) ) { $product->annotation->add_Annotation( $key, $value ); } } } # move sequence features to product with adjusted coordinates if ( $product->isa('Bio::SeqI') ) { # for the fragment, just shift the features to new position if ( $fragment->isa('Bio::SeqI') ) { for my $feat ( $fragment->get_SeqFeatures ) { my $adjfeat = $self->_coord_adjust( $feat, $insert_pos ); $product->add_SeqFeature($adjfeat) if $adjfeat; } } # for recipient, shift and modify features according to insertion. if ( $recipient->isa('Bio::SeqI') ) { for my $feat ( $recipient->get_SeqFeatures ) { my $adjfeat = $self->_coord_adjust_insertion( $feat, $insert_pos, $fragment->length ); $product->add_SeqFeature($adjfeat) if $adjfeat; } } } # add a feature to annotate the insertion my $insertion_feature = Bio::SeqFeature::Generic->new( -start => $insert_pos + 1, -end => $insert_pos + $fragment->length, -primary_tag => 'misc_feature', -tag => { note => 'inserted fragment' }, ); $product->add_SeqFeature($insertion_feature); return $product; } =head2 ligate title : ligate function: pastes a fragment (which can also have features) into a recipient sequence between two "cut" sites, preserving features and adjusting their locations. This is a shortcut for deleting a segment from a sequence object followed by an insertion of a fragmnet and is supposed to be used to simulate in-vitro cloning where a recipient (a vector) is digested and a fragment is then ligated into the recipient molecule. The fragment can be flipped (reverse-complemented with all its features). A new sequence object is returned to represent the product of the reaction. Features and annotations are transferred from the insert to the product and features on the recipient are adjusted according to the methods L amd L: Features spanning the insertion site will be split up into two sub-locations. (Sub-)features in the deleted region are themselves deleted. (Sub-)features that extend into the deleted region are truncated. The class of the product object depends on the class of the recipient (vector) sequence object. if it is not possible to instantiate a new object of that class, a Bio::Primaryseq object is created instead. usage : # insert the flipped fragment between positions 1000 and 1100 of the # vector, i.e. everything between these two positions is deleted and # replaced by the fragment my $new_molecule = Bio::Sequtils::Pbrtools->ligate( -recipient => $vector, -fragment => $fragment, -left => 1000, -right => 1100, -flip => 1, -clone_obj => 1 ); args : recipient: the recipient/vector molecule fragment: molecule that is to be ligated into the vector left: left cut site (fragment will be inserted to the right of this position) optional: right: right cut site (fragment will be inseterted to the left of this position). defaults to left+1 flip: boolean, if true, the fragment is reverse-complemented (including features) before inserting clone_obj: if true, clone the recipient object to create the product instead of calling "new" on its class returns : a new Bio::Seq object of the ligated fragments =cut sub ligate { my $self = shift; my ( $recipient, $fragment, $left, $right, $flip, $clone_obj ) = $self->_rearrange( [qw(RECIPIENT FRAGMENT LEFT RIGHT FLIP CLONE_OBJ )], @_ ); $self->throw("missing required parameter 'recipient'") unless $recipient; $self->throw("missing required parameter 'fragment'") unless $fragment; $self->throw("missing required parameter 'left'") unless defined $left; $right ||= $left + 1; $self->throw( "Fragment must be a Bio::PrimarySeqI compliant object but it is a " . ref($fragment) ) unless blessed($fragment) && $fragment->isa('Bio::PrimarySeqI'); $fragment = $self->revcom_with_features($fragment) if $flip; my $opts_ref = {}; $opts_ref->{clone_obj} = 1 if $clone_obj; # clone in two steps: first delete between the insertion sites, # then insert the fragment. Step 1 is skipped if insert positions # are adjacent (no deletion) my ( $product1, $product2 ); eval { if ( $right == $left + 1 ) { $product1 = $recipient; } else { $product1 = $self->delete( $recipient, $left + 1, $right - 1, $opts_ref ); } }; $self->throw( "Failed in step 1 (cut recipient): " . $@ ) if $@; eval { $product2 = $self->insert( $product1, $fragment, $left, $opts_ref ) }; $self->throw( "Failed in step 2 (insert fragment): " . $@ ) if $@; return $product2; } =head2 _coord_adjust_deletion title : _coord_adjust_deletion function: recursively adjusts coordinates of seqfeatures on a molecule where a segment has been deleted. (sub)features that span the deletion site become split features. (sub)features that extend into the deletion site are truncated. A note is added to the feature to inform about the size and position of the deletion. usage : my $adjusted_feature = Bio::Sequtils::_coord_adjust_deletion( $feature, $start, $end ); args : a Bio::SeqFeatureI compliant object, start (inclusive) position of the deletion site, end (inclusive) position of the deletion site returns : a Bio::SeqFeatureI compliant object =cut sub _coord_adjust_deletion { my ( $self, $feat, $left, $right ) = @_; $self->throw( 'object [$feat] ' . 'of class [' . ref($feat) . '] should be a Bio::SeqFeatureI ' ) unless $feat->isa('Bio::SeqFeatureI'); $self->throw('missing coordinates: need a left and a right position') unless defined $left && defined $right; if ( $left > $right ) { if ( $feat->can('is_circular') && $feat->is_circular ) { # todo handle circular molecules $self->throw( 'can not yet handle deletions in circular molecules if deletion spans origin' ); } else { $self->throw( "left coordinate ($left) must be less than right ($right)" . " but it was greater" ); } } my $deletion = Bio::Location::Simple->new( -start => $left, -end => $right, ); my $del_length = $right - $left + 1; my @adjsubfeat; for my $subfeat ( $feat->get_SeqFeatures ) { my $adjsubfeat = $self->_coord_adjust_deletion( $subfeat, $left, $right ); push @adjsubfeat, $adjsubfeat if $adjsubfeat; } my @loc; my $note; for ( $feat->location->each_Location ) { next if $deletion->contains($_); # this location will be deleted; my $strand = $_->strand; my $type = $_->location_type; my $start = $_->start; my $start_type = $_->can('start_pos_type') ? $_->start_pos_type : undef; my $end = $_->end; my $end_type = $_->can('end_pos_type') ? $_->end_pos_type : undef; my @newcoords = (); if ( $start < $deletion->start && $end > $deletion->end ) { # split the feature @newcoords = ( [ $start, ( $deletion->start - 1 ), $start_type, $end_type ], [ ( $deletion->start ), $end - $del_length, $start_type, $end_type ] ); $note = $del_length . 'bp internal deletion between pos ' . ( $deletion->start - 1 ) . ' and ' . $deletion->start; } elsif ( $_->start < $deletion->start && $_->end >= $deletion->start ) { # truncate feature end @newcoords = ( [ $start, ( $deletion->start - 1 ), $start_type, $end_type ] ); $note = ( $end - $deletion->start + 1 ) . 'bp deleted from feature '; if ( $feat->strand ) { $note .= $feat->strand == 1 ? "3' " : "5' "; } $note .= 'end'; } elsif ( $_->start <= $deletion->end && $_->end > $deletion->end ) { # truncate feature start and shift end @newcoords = ( [ ( $deletion->start ), $end - $del_length, $start_type, $end_type ] ); $note = ( $deletion->end - $start + 1 ) . 'bp deleted from feature '; if ( $feat->strand ) { $note .= $feat->strand == 1 ? "5' end" : "3' end"; } else { $note .= 'start'; } } elsif ( $start >= $deletion->end ) { # just shift entire location @newcoords = ( [ $start - $del_length, $end - $del_length, $start_type, $end_type ] ); } else { # not affected by deletion @newcoords = ( [ $start, $end, $start_type, $end_type ] ); } # if we have no coordinates, we return nothing # the feature is deleted return unless @newcoords; my @subloc = $self->_location_objects_from_coordinate_list( \@newcoords, $strand, $type ); push @loc, $self->_single_loc_object_from_collection(@subloc); } # each location # create new feature based on original one and move annotation across my $newfeat = Bio::SeqFeature::Generic->new( -primary => $feat->primary_tag ); foreach my $key ( $feat->annotation->get_all_annotation_keys() ) { foreach my $value ( $feat->annotation->get_Annotations($key) ) { $newfeat->annotation->add_Annotation( $key, $value ); } } foreach my $key ( $feat->get_all_tags() ) { $newfeat->add_tag_value( $key, $feat->get_tag_values($key) ); } # If we have a note about the deleted bases, add it if ($note) { $newfeat->add_tag_value( 'note', $note ); } # set modified location(s) for the new feature and # add its subfeatures if any my $loc = $self->_single_loc_object_from_collection(@loc); $loc ? $newfeat->location($loc) : return; $newfeat->add_SeqFeature($_) for @adjsubfeat; return $newfeat; } =head2 _coord_adjust_insertion title : _coord_adjust_insertion function: recursively adjusts coordinates of seqfeatures on a molecule where another sequence has been inserted. (sub)features that span the insertion site become split features and a note is added about the size and positin of the insertion. Features with an IN-BETWEEN location at the insertion site are lost (such features can only exist between adjacent bases) usage : my $adjusted_feature = Bio::Sequtils::_coord_adjust_insertion( $feature, $insert_pos, $insert_length ); args : a Bio::SeqFeatureI compliant object, insertion position (insert to the right of this position) length of inserted fragment returns : a Bio::SeqFeatureI compliant object =cut sub _coord_adjust_insertion { my ( $self, $feat, $insert_pos, $insert_len ) = @_; $self->throw( 'object [$feat] ' . 'of class [' . ref($feat) . '] should be a Bio::SeqFeatureI ' ) unless $feat->isa('Bio::SeqFeatureI'); $self->throw('missing insert position') unless defined $insert_pos; $self->throw('missing insert length') unless defined $insert_len; my @adjsubfeat; for my $subfeat ( $feat->get_SeqFeatures ) { push @adjsubfeat, $self->_coord_adjust_insertion( $subfeat, $insert_pos, $insert_len ); } my @loc; my $note; for ( $feat->location->each_Location ) { # loose IN-BETWEEN features at the insertion site next if ( $_->location_type eq 'IN-BETWEEN' && $_->start == $insert_pos ); my $strand = $_->strand; my $type = $_->location_type; my $start = $_->start; my $start_type = $_->can('start_pos_type') ? $_->start_pos_type : undef; my $end = $_->end; my $end_type = $_->can('end_pos_type') ? $_->end_pos_type : undef; my @newcoords = (); if ( $start <= $insert_pos && $end > $insert_pos ) { # split the feature @newcoords = ( [ $start, $insert_pos, $start_type, $end_type ], [ ( $insert_pos + 1 + $insert_len ), $end + $insert_len, $start_type, $end_type ] ); $note = $insert_len . 'bp internal insertion between pos ' . $insert_pos . ' and ' . ( $insert_pos + $insert_len + 1 ); } elsif ( $start > $insert_pos ) { # just shift entire location @newcoords = ( [ $start + $insert_len, $end + $insert_len, $start_type, $end_type ] ); } else { # not affected @newcoords = ( [ $start, $end, $start_type, $end_type ] ); } # if we have deleted all coordinates, return nothing # (possible if all locations are IN-BETWEEN) return unless @newcoords; my @subloc = $self->_location_objects_from_coordinate_list( \@newcoords, $strand, $type ); # put together final location which could be a split now push @loc, $self->_single_loc_object_from_collection(@subloc); } # each location # create new feature based on original one and move annotation across my $newfeat = Bio::SeqFeature::Generic->new( -primary => $feat->primary_tag ); foreach my $key ( $feat->annotation->get_all_annotation_keys() ) { foreach my $value ( $feat->annotation->get_Annotations($key) ) { $newfeat->annotation->add_Annotation( $key, $value ); } } foreach my $key ( $feat->get_all_tags() ) { $newfeat->add_tag_value( $key, $feat->get_tag_values($key) ); } # If we have a note about the inserted bases, add it if ($note) { $newfeat->add_tag_value( 'note', $note ); } # set modified location(s) for the new feature and # add its subfeatures if any my $loc = $self->_single_loc_object_from_collection(@loc); $loc ? $newfeat->location($loc) : return; $newfeat->add_SeqFeature($_) for @adjsubfeat; return $newfeat; } =head2 _single_loc_object_from_collection Title : _single_loc_object_from_collection Function: takes an array of location objects. Returns either a split location object if there are more than one locations in the array or returns the single location if there is only one Usage : my $loc = _single_loc_object_from_collection( @sublocs ); Args : array of Bio::Location objects Returns : a single Bio:;Location object containing all locations =cut sub _single_loc_object_from_collection { my ( $self, @locs ) = @_; my $loc; if ( @locs > 1 ) { $loc = Bio::Location::Split->new; $loc->add_sub_Location(@locs); } elsif ( @locs == 1 ) { $loc = shift @locs; } return $loc; } # _single_loc_object_from_collection =head2 _location_objects_from_coordinate_list Title : _location_objects_from_coordinate_list Function: takes an array-ref of start/end coordinates, a strand and a type and returns a list of Bio::Location objects (Fuzzy by default, Simple in case of in-between coordinates). If location type is not "IN-BETWEEN", individual types may be passed in for start and end location as per Bio::Location::Fuzzy documentation. Usage : my @loc_objs = $self->_location_objects_from_coordinate_list( \@coords, $strand, $type ); Args : array-ref of array-refs each containing: start, end [, start-type, end-type] where types are optional. If given, must be a one of ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') strand (all locations must be on same strand) location-type (EXACT, IN-BETWEEN etc) Returns : list of Bio::Location objects =cut sub _location_objects_from_coordinate_list { my $self = shift; my ( $coords_ref, $strand, $type ) = @_; $self->throw( 'expected 3 parameters but got ' . @_ ) unless @_ == 3; $self->throw('first argument must be an ARRAY reference#') unless ref($coords_ref) eq 'ARRAY'; my @loc; foreach my $coords_set (@$coords_ref) { my ( $start, $end, $start_type, $end_type ) = @$coords_set; # taken from Bio::SeqUtils::_coord_adjust if ( $type ne 'IN-BETWEEN' ) { my $loc = Bio::Location::Fuzzy->new( -start => $start, -end => $end, -strand => $strand, -location_type => $type ); $loc->start_pos_type($start_type) if $start_type; $loc->end_pos_type($end_type) if $end_type; push @loc, $loc; } else { push @loc, Bio::Location::Simple->new( -start => $start, -end => $end, -strand => $strand, -location_type => $type ); } } # each coords_set return @loc; } # _location_objects_from_coordinate_list =head2 _new_seq_via_clone Title : _new_seq_via_clone Function: clone a sequence object using Bio::Root::Root::clone and set the new sequence string sequence features are removed. Usage : my $new_seq = $self->_new_seq_via_clone( $seq_obj, $seq_str ); Args : original seq object [, new sequence string] Returns : a clone of the original sequence object, optionally with new sequence string =cut sub _new_seq_via_clone { my ( $self, $in_seq_obj, $seq_str ) = @_; my $out_seq_obj = $in_seq_obj->clone; $out_seq_obj->remove_SeqFeatures if $out_seq_obj->can('remove_SeqFeatures'); if ( blessed $out_seq_obj->seq && $out_seq_obj->seq->isa('Bio::PrimarySeq') ) { $out_seq_obj->seq->seq($seq_str); } else { $out_seq_obj->seq($seq_str); } return $out_seq_obj; } # _new_seq_via_clone =head2 _new_seq_from_old Title : _new_seq_from_old Function: creates a new sequence obejct, if possible of the same class as the old and adds attributes to it. Also copies annotation across to the new object. Usage : my $new_seq = $self->_new_seq_from_old( $seq_obj, { seq => $seq_str, display_id => 'some_ID'}); Args : old sequence object hashref of attributes for the new sequence (sequence string etc.) Returns : a new Bio::Seq object =cut sub _new_seq_from_old { my ( $self, $in_seq_obj, $attr ) = @_; $self->throw('attributes must be a hashref') if $attr && ref($attr) ne 'HASH'; my $seqclass; if ( $in_seq_obj->can_call_new ) { $seqclass = ref($in_seq_obj); } else { $seqclass = 'Bio::Primaryseq'; $self->_attempt_to_load_seq; } my $out_seq_obj = $seqclass->new( -seq => $attr->{seq} || $in_seq_obj->seq, -display_id => $attr->{display_id} || $in_seq_obj->display_id, -accession_number => $attr->{accession_number} || $in_seq_obj->accession_number || '', -alphabet => $in_seq_obj->alphabet, -desc => $attr->{desc} || $in_seq_obj->desc, -verbose => $attr->{verbose} || $in_seq_obj->verbose, -is_circular => $attr->{is_circular} || $in_seq_obj->is_circular || 0, ); # move the annotation across to the product if ( $out_seq_obj->isa("Bio::AnnotatableI") && $in_seq_obj->isa("Bio::AnnotatableI") ) { foreach my $key ( $in_seq_obj->annotation->get_all_annotation_keys ) { foreach my $value ( $in_seq_obj->annotation->get_Annotations($key) ) { $out_seq_obj->annotation->add_Annotation( $key, $value ); } } } return $out_seq_obj; } # _new_seq_from_old =head2 _coord_adjust Title : _coord_adjust Usage : my $newfeat=Bio::SeqUtils->_coord_adjust($feature, 100, $seq->length); Function: Recursive subroutine to adjust the coordinates of a feature and all its subfeatures. If a sequence length is specified, then any adjusted features that have locations beyond the boundaries of the sequence are converted to Bio::Location::Fuzzy objects. Returns : A Bio::SeqFeatureI compliant object. Args : A Bio::SeqFeatureI compliant object, the number of bases to add to the coordinates (optional) the length of the parent sequence =cut sub _coord_adjust { my ( $self, $feat, $add, $length ) = @_; $self->throw( 'Object [$feat] ' . 'of class [' . ref($feat) . '] should be a Bio::SeqFeatureI ' ) unless $feat->isa('Bio::SeqFeatureI'); my @adjsubfeat; for my $subfeat ( $feat->get_SeqFeatures ) { push @adjsubfeat, $self->_coord_adjust( $subfeat, $add, $length ); } my @loc; for ( $feat->location->each_Location ) { my @coords = ( $_->start, $_->end ); my $strand = $_->strand; my $type = $_->location_type; foreach (@coords) { $self->throw("can not handle negative feature positions (got: $_)") if $_ < 0; if ( $add + $_ < 1 ) { $_ = '<1'; } elsif ( defined $length and $add + $_ > $length ) { $_ = ">$length"; } else { $_ = $add + $_; } } push @loc, $self->_location_objects_from_coordinate_list( [ \@coords ], $strand, $type ); } my $newfeat = Bio::SeqFeature::Generic->new( -primary => $feat->primary_tag ); foreach my $key ( $feat->annotation->get_all_annotation_keys() ) { foreach my $value ( $feat->annotation->get_Annotations($key) ) { $newfeat->annotation->add_Annotation( $key, $value ); } } foreach my $key ( $feat->get_all_tags() ) { $newfeat->add_tag_value( $key, $feat->get_tag_values($key) ); } my $loc = $self->_single_loc_object_from_collection(@loc); $loc ? $newfeat->location($loc) : return; $newfeat->add_SeqFeature($_) for @adjsubfeat; return $newfeat; } =head2 revcom_with_features Title : revcom_with_features Usage : $revcom=Bio::SeqUtils->revcom_with_features($seq); Function: Like Bio::Seq::revcom, but keeps features (adjusting coordinates as appropriate. Returns : A new sequence object Args : A sequence object =cut sub revcom_with_features { my ( $self, $seq ) = @_; $self->throw( 'Object [$seq] ' . 'of class [' . ref($seq) . '] should be a Bio::SeqI ' ) unless $seq->isa('Bio::SeqI'); my $revcom = $seq->revcom; # make sure that there is no annotation or features in $trunc # (->revcom() now clone objects except for Bio::Seq::LargePrimarySeq) $revcom->annotation->remove_Annotations; $revcom->remove_SeqFeatures; #move annotations foreach my $key ( $seq->annotation->get_all_annotation_keys() ) { foreach my $value ( $seq->annotation->get_Annotations($key) ) { $revcom->annotation->add_Annotation( $key, $value ); } } #move features for ( map { $self->_feature_revcom( $_, $seq->length ) } reverse $seq->get_SeqFeatures ) { $revcom->add_SeqFeature($_); } return $revcom; } =head2 _feature_revcom Title : _feature_revcom Usage : my $newfeat=Bio::SeqUtils->_feature_revcom($feature, $seq->length); Function: Recursive subroutine to reverse complement a feature and all its subfeatures. The length of the parent sequence must be specified. Returns : A Bio::SeqFeatureI compliant object. Args : A Bio::SeqFeatureI compliant object, the length of the parent sequence =cut sub _feature_revcom { my ( $self, $feat, $length ) = @_; $self->throw( 'Object [$feat] ' . 'of class [' . ref($feat) . '] should be a Bio::SeqFeatureI ' ) unless $feat->isa('Bio::SeqFeatureI'); my @adjsubfeat; for my $subfeat ( $feat->get_SeqFeatures ) { push @adjsubfeat, $self->_feature_revcom( $subfeat, $length ); } my @loc; for ( $feat->location->each_Location ) { my $type = $_->location_type; my $strand; if ( $_->strand == -1 ) { $strand = 1 } elsif ( $_->strand == 1 ) { $strand = -1 } else { $strand = $_->strand } my $newend = $self->_coord_revcom( $_->start, $_->start_pos_type, $length ); my $newstart = $self->_coord_revcom( $_->end, $_->end_pos_type, $length ); my $newstart_type = $_->end_pos_type; $newstart_type = 'BEFORE' if $_->end_pos_type eq 'AFTER'; $newstart_type = 'AFTER' if $_->end_pos_type eq 'BEFORE'; my $newend_type = $_->start_pos_type; $newend_type = 'BEFORE' if $_->start_pos_type eq 'AFTER'; $newend_type = 'AFTER' if $_->start_pos_type eq 'BEFORE'; push @loc, $self->_location_objects_from_coordinate_list( [ [ $newstart, $newend, $newstart_type, $newend_type ] ], $strand, $type ); } my $newfeat = Bio::SeqFeature::Generic->new( -primary => $feat->primary_tag ); foreach my $key ( $feat->annotation->get_all_annotation_keys() ) { foreach my $value ( $feat->annotation->get_Annotations($key) ) { $newfeat->annotation->add_Annotation( $key, $value ); } } foreach my $key ( $feat->get_all_tags() ) { $newfeat->add_tag_value( $key, $feat->get_tag_values($key) ); } my $loc = $self->_single_loc_object_from_collection(@loc); $loc ? $newfeat->location($loc) : return; $newfeat->add_SeqFeature($_) for @adjsubfeat; return $newfeat; } sub _coord_revcom { my ( $self, $coord, $type, $length ) = @_; if ( $type eq 'BETWEEN' or $type eq 'WITHIN' ) { $coord =~ s/(\d+)(\D*)(\d+)/$length+1-$3.$2.$length+1-$1/ge; } else { $coord =~ s/(\d+)/$length+1-$1/ge; $coord =~ tr/<>/>' . $coord if $type eq 'BEFORE' and substr( $coord, 0, 1 ) ne '>'; $coord = '<' . $coord if $type eq 'AFTER' and substr( $coord, 0, 1 ) ne '<'; } return $coord; } =head2 evolve Title : evolve Usage : my $newseq = Bio::SeqUtils-> evolve($seq, $similarity, $transition_transversion_rate); Function: Mutates the sequence by point mutations until the similarity of the new sequence has decreased to the required level. Transition/transversion rate is adjustable. Returns : A new Bio::PrimarySeq object Args : sequence object percentage similarity (e.g. 80) tr/tv rate, optional, defaults to 1 (= 1:1) Set the verbosity of the Bio::SeqUtils object to positive integer to see the mutations as they happen. This method works only on nucleotide sequences. It prints a warning if you set the target similarity to be less than 25%. Transition/transversion ratio is an observed attribute of an sequence comparison. We are dealing here with the transition/transversion rate that we set for our model of sequence evolution. =cut sub evolve { my ( $self, $seq, $sim, $rate ) = @_; $rate ||= 1; $self->throw( 'Object [$seq] ' . 'of class [' . ref($seq) . '] should be a Bio::PrimarySeqI ' ) unless $seq->isa('Bio::PrimarySeqI'); $self->throw( "[$sim] " . ' should be a positive integer or float under 100' ) unless $sim =~ /^[+\d.]+$/ and $sim <= 100; $self->warn( "Nucleotide sequences are 25% similar by chance. Do you really want to set similarity to [$sim]%?\n" ) unless $sim > 25; $self->throw('Only nucleotide sequences are supported') if $seq->alphabet eq 'protein'; # arrays of possible changes have transitions as first items my %changes; $changes{'a'} = [ 't', 'c', 'g' ]; $changes{'t'} = [ 'a', 'c', 'g' ]; $changes{'c'} = [ 'g', 'a', 't' ]; $changes{'g'} = [ 'c', 'a', 't' ]; # given the desired rate, find out where cut off points need to be # when random numbers are generated from 0 to 100 # we are ignoring identical mutations (e.g. A->A) to speed things up my $bin_size = 100 / ( $rate + 2 ); my $transition = 100 - ( 2 * $bin_size ); my $first_transversion = $transition + $bin_size; # unify the look of sequence strings my $string = lc $seq->seq; # lower case $string =~ s/u/t/; # simplyfy our life; modules should deal with the change anyway # store the original sequence string my $oristring = $string; my $length = $seq->length; # stop evolving if the limit has been reached until ( $self->_get_similarity( $oristring, $string ) <= $sim ) { # find the location in the string to change my $loc = int( rand $length ) + 1; # nucleotide to change my $oldnuc = substr $string, $loc - 1, 1; my $newnuc; # nucleotide it is changed to my $choose = rand(100); if ( $choose < $transition ) { $newnuc = $changes{$oldnuc}[0]; } elsif ( $choose < $first_transversion ) { $newnuc = $changes{$oldnuc}[1]; } else { $newnuc = $changes{$oldnuc}[2]; } # do the change substr $string, $loc - 1, 1, $newnuc; $self->debug("$loc$oldnuc>$newnuc\n"); } return new Bio::PrimarySeq( -id => $seq->id . "-$sim", -description => $seq->description, -seq => $string ); } sub _get_similarity { my ( $self, $oriseq, $seq ) = @_; my $len = length($oriseq); my $c; for ( my $i = 0 ; $i < $len ; $i++ ) { $c++ if substr( $oriseq, $i, 1 ) eq substr( $seq, $i, 1 ); } return 100 * $c / $len; } 1; BioPerl-1.007002/Bio/SimpleAlign.pm000444000766000024 26756013155576320 17046 0ustar00cjfieldsstaff000000000000package Bio::SimpleAlign; use strict; use warnings; use Bio::LocatableSeq; # uses Seq's as list use Bio::Seq; use Bio::SeqFeature::Generic; use parent qw(Bio::Root::Root Bio::Align::AlignI Bio::AnnotatableI Bio::FeatureHolderI); # BioPerl module for SimpleAlign # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code # # History: # 11/3/00 Added threshold feature to consensus and consensus_aa - PS # May 2001 major rewrite - Heikki Lehvaslaiho =head1 NAME Bio::SimpleAlign - Multiple alignments held as a set of sequences =head1 SYNOPSIS # Use Bio::AlignIO to read in the alignment $str = Bio::AlignIO->new(-file => 't/data/testaln.pfam'); $aln = $str->next_aln(); # Describe print $aln->length; print $aln->num_residues; print $aln->is_flush; print $aln->num_sequences; print $aln->score; print $aln->percentage_identity; print $aln->consensus_string(50); # Find the position in the alignment for a sequence location $pos = $aln->column_from_residue_number('1433_LYCES', 14); # = 6; # Extract sequences and check values for the alignment column $pos foreach $seq ($aln->each_seq) { $res = $seq->subseq($pos, $pos); $count{$res}++; } foreach $res (keys %count) { printf "Res: %s Count: %2d\n", $res, $count{$res}; } # Manipulate $aln->remove_seq($seq); $mini_aln = $aln->slice(20,30); # get a block of columns $mini_aln = $aln->select_noncont(1,3,5,7,11); # select certain sequences $new_aln = $aln->remove_columns([20,30]); # remove by position $new_aln = $aln->remove_columns(['mismatch']); # remove by property # Analyze $str = $aln->consensus_string($threshold_percent); $str = $aln->match_line(); $str = $aln->cigar_line(); $id = $aln->percentage_identity; # See the module documentation for details and more methods. =head1 DESCRIPTION SimpleAlign is an object that handles a multiple sequence alignment (MSA). It is very permissive of types (it does not insist on sequences being all same length, for example). Think of it as a set of sequences with a whole series of built-in manipulations and methods for reading and writing alignments. SimpleAlign uses L, a subclass of L, to store its sequences. These are subsequences with a start and end positions in the parent reference sequence. Each sequence in the SimpleAlign object is a Bio::LocatableSeq. SimpleAlign expects the combination of name, start, and end for a given sequence to be unique in the alignment, and this is the key for the internal hashes (name, start, end are abbreviated C in the code). However, in some cases people do not want the name/start-end to be displayed: either multiple names in an alignment or names specific to the alignment (ROA1_HUMAN_1, ROA1_HUMAN_2 etc). These names are called C, and generally is what is used to print out the alignment. They default to name/start-end. The SimpleAlign Module is derived from the Align module by Ewan Birney. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Ewan Birney, birney@ebi.ac.uk =head1 CONTRIBUTORS Allen Day, allenday-at-ucla.edu, Richard Adams, Richard.Adams-at-ed.ac.uk, David J. Evans, David.Evans-at-vir.gla.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org, Allen Smith, allens-at-cpan.org, Jason Stajich, jason-at-bioperl.org, Anthony Underwood, aunderwood-at-phls.org.uk, Xintao Wei & Giri Narasimhan, giri-at-cs.fiu.edu Brian Osborne, bosborne at alum.mit.edu Weigang Qiu, Weigang at GENECTR-HUNTER-CUNY-EDU Hongyu Zhang, forward at hongyu.org Jay Hannah, jay at jays.net Alexandr Bezginov, albezg at gmail.com =head1 SEE ALSO L =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut ## This data should probably be in a more centralized module... ## it is taken from Clustalw documentation. ## These are all the positively scoring groups that occur in the ## Gonnet Pam250 matrix. The strong and weak groups are ## defined as strong score >0.5 and weak score =<0.5 respectively. our %CONSERVATION_GROUPS = ( 'strong' => [qw(STA NEQK NHQK NDEQ QHRK MILV MILF HY FYW )], 'weak' => [qw(CSA ATV SAG STNK STPA SGND SNDEQK NDEQHK NEQHRK FVLIM HFY)], ); =head2 new Title : new Usage : my $aln = Bio::SimpleAlign->new(); Function : Creates a new simple align object Returns : Bio::SimpleAlign Args : -source => string representing the source program where this alignment came from -annotation => Bio::AnnotationCollectionI -seq_annotation => Bio::AnnotationCollectionI for sequences (requires -annotation also be set) -seqs => array ref containing Bio::LocatableSeq or Bio::Seq::Meta -consensus => consensus string -consensus_meta => Bio::Seq::Meta object containing consensus met information (kludge) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($src, $score, $id, $acc, $desc, $seqs, $feats, $coll, $sa, $con, $cmeta) = $self->_rearrange([qw( SOURCE SCORE ID ACCESSION DESCRIPTION SEQS FEATURES ANNOTATION SEQ_ANNOTATION CONSENSUS CONSENSUS_META )], @args); $src && $self->source($src); defined $score && $self->score($score); # we need to set up internal hashs first! $self->{'_seq'} = {}; $self->{'_order'} = {}; $self->{'_start_end_lists'} = {}; $self->{'_dis_name'} = {}; $self->{'_id'} = 'NoName'; # maybe we should automatically read in from args. Hmmm... $id && $self->id($id); $acc && $self->accession($acc); $desc && $self->description($desc); $coll && $self->annotation($coll); # sequence annotation is layered into a provided annotation collection (or dies) if ($sa) { $self->throw("Must supply an alignment-based annotation collection (-annotation) ". "with a sequence annotation collection") if !$coll; $coll->add_Annotation('seq_annotation', $sa); } if ($feats && ref $feats eq 'ARRAY') { for my $feat (@$feats) { $self->add_SeqFeature($feat); } } $con && $self->consensus($con); $cmeta && $self->consensus_meta($cmeta); # assumes these are in correct alignment order if ($seqs && ref($seqs) eq 'ARRAY') { for my $seq (@$seqs) { $self->add_seq($seq); } } return $self; # success - we hope! } =head1 Modifier methods These methods modify the MSA by adding, removing or shuffling complete sequences. =head2 add_seq Title : add_seq Usage : $myalign->add_seq($newseq); $myalign->add_seq(-SEQ=>$newseq, -ORDER=>5); Function : Adds another sequence to the alignment. *Does not* align it - just adds it to the hashes. If -ORDER is specified, the sequence is inserted at the the position spec'd by -ORDER, and existing sequences are pushed down the storage array. Returns : nothing Args : A Bio::LocatableSeq object Positive integer for the sequence position (optional) See L for more information =cut sub addSeq { my $self = shift; $self->deprecated("addSeq - deprecated method. Use add_seq() instead."); $self->add_seq(@_); } sub add_seq { my $self = shift; my @args = @_; my ($seq, $order) = $self->_rearrange([qw(SEQ ORDER)], @args); my ($name,$id,$start,$end); unless ($seq) { $self->throw("LocatableSeq argument required"); } if( ! ref $seq || ! $seq->isa('Bio::LocatableSeq') ) { $self->throw("Unable to process non locatable sequences [". ref($seq). "]"); } !defined($order) and $order = 1 + keys %{$self->{'_seq'}}; # default $order--; # jay's patch (user-specified order is 1-origin) if ($order < 0) { $self->throw("User-specified value for ORDER must be >= 1"); } $id = $seq->id() ||$seq->display_id || $seq->primary_id; # build the symbol list for this sequence, # will prune out the gap and missing/match chars # when actually asked for the symbol list in the # symbol_chars # map { $self->{'_symbols'}->{$_} = 1; } split(//,$seq->seq) if $seq->seq; $name = $seq->get_nse; if( $self->{'_seq'}->{$name} ) { $self->warn("Replacing one sequence [$name]\n") unless $self->verbose < 0; } else { $self->debug( "Assigning $name to $order\n"); my $ordh = $self->{'_order'}; if ($ordh->{$order}) { # make space to insert # $c->() returns (in reverse order) the first subsequence # of consecutive integers; i.e., $c->(1,2,3,5,6,7) returns # (3,2,1), and $c->(2,4,5) returns (2). my $c; $c = sub { return (($_[1]-$_[0] == 1) ? ($c->(@_[1..$#_]),$_[0]) : $_[0]); }; map { $ordh->{$_+1} = $ordh->{$_} } $c->(sort {$a <=> $b} grep {$_ >= $order} keys %{$ordh}); } $ordh->{$order} = $name; unless( exists( $self->{'_start_end_lists'}->{$id})) { $self->{'_start_end_lists'}->{$id} = []; } push @{$self->{'_start_end_lists'}->{$id}}, $seq; } $self->{'_seq'}->{$name} = $seq; } =head2 remove_seq Title : remove_seq Usage : $aln->remove_seq($seq); Function : Removes a single sequence from an alignment Returns : Argument : a Bio::LocatableSeq object =cut sub removeSeq { my $self = shift; $self->deprecated("removeSeq - deprecated method. Use remove_seq() instead."); $self->remove_seq(@_); } sub remove_seq { my $self = shift; my $seq = shift; my ($name,$id); $self->throw("Need Bio::Locatable seq argument ") unless ref $seq && $seq->isa( 'Bio::LocatableSeq'); $id = $seq->id(); $name = $seq->get_nse; if( !exists $self->{'_seq'}->{$name} ) { $self->throw("Sequence $name does not exist in the alignment to remove!"); } delete $self->{'_seq'}->{$name}; # we need to remove this seq from the start_end_lists hash if (exists $self->{'_start_end_lists'}->{$id}) { # we need to find the sequence in the array. my ($i, $found);; for ($i=0; $i < @{$self->{'_start_end_lists'}->{$id}}; $i++) { if (${$self->{'_start_end_lists'}->{$id}}[$i] eq $seq) { $found = 1; last; } } if ($found) { splice @{$self->{'_start_end_lists'}->{$id}}, $i, 1; } else { $self->throw("Could not find the sequence to remoce from the start-end list"); } } else { $self->throw("There is no seq list for the name $id"); } # we need to shift order hash my %rev_order = reverse %{$self->{'_order'}}; my $no = $rev_order{$name}; my $num_sequences = $self->num_sequences; for (; $no < $num_sequences; $no++) { $self->{'_order'}->{$no} = $self->{'_order'}->{$no+1}; } delete $self->{'_order'}->{$no}; return 1; } =head2 purge Title : purge Usage : $aln->purge(0.7); Function: Removes sequences above given sequence similarity This function will grind on large alignments. Beware! Example : Returns : An array of the removed sequences Args : float, threshold for similarity =cut sub purge { my ($self,$perc) = @_; my (%duplicate, @dups); my @seqs = $self->each_seq(); for (my $i=0;$i< @seqs - 1;$i++ ) { #for each seq in alignment my $seq = $seqs[$i]; #skip if already in duplicate hash next if exists $duplicate{$seq->display_id} ; my $one = $seq->seq(); my @one = split '', $one; #split to get 1aa per array element for (my $j=$i+1;$j < @seqs;$j++) { my $seq2 = $seqs[$j]; #skip if already in duplicate hash next if exists $duplicate{$seq2->display_id} ; my $two = $seq2->seq(); my @two = split '', $two; my $count = 0; my $res = 0; for (my $k=0;$k<@one;$k++) { if ( $one[$k] ne '.' && $one[$k] ne '-' && defined($two[$k]) && $one[$k] eq $two[$k]) { $count++; } if ( $one[$k] ne '.' && $one[$k] ne '-' && defined($two[$k]) && $two[$k] ne '.' && $two[$k] ne '-' ) { $res++; } } my $ratio = 0; $ratio = $count/$res unless $res == 0; # if above threshold put in duplicate hash and push onto # duplicate array for returning to get_unique if ( $ratio > $perc ) { $self->warn("duplicate: ", $seq2->display_id) if $self->verbose > 0; $duplicate{$seq2->display_id} = 1; push @dups, $seq2; } } } foreach my $seq (@dups) { $self->remove_seq($seq); } return @dups; } =head2 sort_alphabetically Title : sort_alphabetically Usage : $ali->sort_alphabetically Function : Changes the order of the alignment to alphabetical on name followed by numerical by number. Returns : Argument : =cut sub sort_alphabetically { my $self = shift; my ($seq,$nse,@arr,%hash,$count); foreach $seq ( $self->each_seq() ) { $nse = $seq->get_nse; $hash{$nse} = $seq; } $count = 0; %{$self->{'_order'}} = (); # reset the hash; foreach $nse ( sort _alpha_startend keys %hash) { $self->{'_order'}->{$count} = $nse; $count++; } 1; } =head2 sort_by_list Title : sort_by_list Usage : $aln_ordered=$aln->sort_by_list($list_file) Function : Arbitrarily order sequences in an alignment Returns : A new Bio::SimpleAlign object Argument : a file listing sequence names in intended order (one name per line) =cut sub sort_by_list { my ($self, $list) = @_; my (@seq, @ids, %order); foreach my $seq ( $self->each_seq() ) { push @seq, $seq; push @ids, $seq->display_id; } my $ct=1; open my $listfh, '<', $list or $self->throw("Could not read file '$list': $!"); while (<$listfh>) { chomp; my $name=$_; $self->throw("Not found in alignment: $name") unless &_in_aln($name, \@ids); $order{$name}=$ct++; } close($listfh); # use the map-sort-map idiom: my @sorted= map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [$order{$_->id()}, $_] } @seq; my $aln = $self->new; foreach (@sorted) { $aln->add_seq($_) } return $aln; } =head2 set_new_reference Title : set_new_reference Usage : $aln->set_new_reference(3 or 'B31'): Select the 3rd sequence, or the sequence whoes name is "B31" (full, exact, and case-sensitive), as the reference (1st) sequence Function : Change/Set a new reference (i.e., the first) sequence Returns : a new Bio::SimpleAlign object. Throws an exception if designated sequence not found Argument : a positive integer of sequence order, or a sequence name in the original alignment =cut sub set_new_reference { my ($self, $seqid) = @_; my $aln = $self->new; my (@seq, @ids, @new_seq); my $is_num=0; foreach my $seq ( $self->each_seq() ) { push @seq, $seq; push @ids, $seq->display_id; } if ($seqid =~ /^\d+$/) { # argument is seq position $is_num=1; $self->throw("The new reference sequence number has to be a positive integer >1 and <= num_sequences ") if ($seqid <= 1 || $seqid > $self->num_sequences); } else { # argument is a seq name $self->throw("The new reference sequence not in alignment ") unless &_in_aln($seqid, \@ids); } for (my $i=0; $i<=$#seq; $i++) { my $pos=$i+1; if ( ($is_num && $pos == $seqid) || ($seqid eq $seq[$i]->display_id) ) { unshift @new_seq, $seq[$i]; } else { push @new_seq, $seq[$i]; } } foreach (@new_seq) { $aln->add_seq($_); } return $aln; } sub _in_aln { # check if input name exists in the alignment my ($str, $ref) = @_; foreach (@$ref) { return 1 if $str eq $_; } return 0; } =head2 uniq_seq Title : uniq_seq Usage : $aln->uniq_seq(): Remove identical sequences in in the alignment. Ambiguous base ("N", "n") and leading and ending gaps ("-") are NOT counted as differences. Function : Make a new alignment of unique sequence types (STs) Returns : 1a. if called in a scalar context, a new Bio::SimpleAlign object (all sequences renamed as "ST") 1b. if called in an array context, a new Bio::SimpleAlign object, and a hashref whose keys are sequence types, and whose values are arrayrefs to lists of sequence ids within the corresponding sequence type 2. if $aln->verbose > 0, ST of each sequence is sent to STDERR (in a tabular format) Argument : None =cut sub uniq_seq { my ($self, $seqid) = @_; my $aln = $self->new; my (%member, %order, @seq, @uniq_str, $st); my $order=0; my $len = $self->length(); $st = {}; foreach my $seq ( $self->each_seq() ) { my $str = $seq->seq(); # it's necessary to ignore "n", "N", leading gaps and ending gaps in # comparing two sequence strings # 1st, convert "n", "N" to "?" (for DNA sequence only): $str =~ s/n/\?/gi if $str =~ /^[atcgn-]+$/i; # 2nd, convert leading and ending gaps to "?": $str = &_convert_leading_ending_gaps($str, '-', '?'); # Note that '?' also can mean unknown residue. # I don't like making global class member changes like this, too # prone to errors... -- cjfields 08-11-18 local $Bio::LocatableSeq::GAP_SYMBOLS = '-\?'; my $new = Bio::LocatableSeq->new( -id => $seq->id(), -alphabet=> $seq->alphabet, -seq => $str, -start => $seq->start, -end => $seq->end ); push @seq, $new; } foreach my $seq (@seq) { my $str = $seq->seq(); my ($seen, $key) = &_check_uniq($str, \@uniq_str, $len); if ($seen) { # seen before my @memb = @{$member{$key}}; push @memb, $seq; $member{$key} = \@memb; } else { # not seen push @uniq_str, $key; $order++; $member{$key} = [ ($seq) ]; $order{$key} = $order; } } foreach my $str (sort {$order{$a} <=> $order{$b}} keys %order) { # sort by input order # convert leading/ending "?" back into "-" ("?" throws errors by SimpleAlign): my $str2 = &_convert_leading_ending_gaps($str, '?', '-'); # convert middle "?" back into "N" ("?" throws errors by SimpleAlign): $str2 =~ s/\?/N/g if $str2 =~ /^[atcg\-\?]+$/i; my $gap='-'; my $end= CORE::length($str2); $end -= CORE::length($1) while $str2 =~ m/($gap+)/g; my $new = Bio::LocatableSeq->new(-id =>"ST".$order{$str}, -seq =>$str2, -start=>1, -end =>$end ); $aln->add_seq($new); foreach (@{$member{$str}}) { push @{$$st{$order{$str}}}, $_->id(); # per Tristan's patch/Bug #2805 $self->debug($_->id(), "\t", "ST", $order{$str}, "\n"); } } return wantarray ? ($aln, $st) : $aln; } sub _check_uniq { # check if same seq exists in the alignment my ($str1, $ref, $length) = @_; my @char1=split //, $str1; my @array=@$ref; return (0, $str1) if @array==0; # not seen (1st sequence) foreach my $str2 (@array) { my $diff=0; my @char2=split //, $str2; for (my $i=0; $i<=$length-1; $i++) { next if $char1[$i] eq '?'; next if $char2[$i] eq '?'; $diff++ if $char1[$i] ne $char2[$i]; } return (1, $str2) if $diff == 0; # seen before } return (0, $str1); # not seen } sub _convert_leading_ending_gaps { my $s=shift; my $sym1=shift; my $sym2=shift; my @array=split //, $s; # convert leading char: for (my $i=0; $i<=$#array; $i++) { ($array[$i] eq $sym1) ? ($array[$i] = $sym2):(last); } # convert ending char: for (my $i = $#array; $i>= 0; $i--) { ($array[$i] eq $sym1) ? ($array[$i] = $sym2):(last); } my $s_new=join '', @array; return $s_new; } =head1 Sequence selection methods Methods returning one or more sequences objects. =head2 each_seq Title : each_seq Usage : foreach $seq ( $align->each_seq() ) Function : Gets a Seq object from the alignment Returns : Seq object Argument : =cut sub eachSeq { my $self = shift; $self->deprecated("eachSeq - deprecated method. Use each_seq() instead."); $self->each_seq(); } sub each_seq { my $self = shift; my (@arr,$order); foreach $order ( sort { $a <=> $b } keys %{$self->{'_order'}} ) { if( exists $self->{'_seq'}->{$self->{'_order'}->{$order}} ) { push(@arr,$self->{'_seq'}->{$self->{'_order'}->{$order}}); } } return @arr; } =head2 each_alphabetically Title : each_alphabetically Usage : foreach $seq ( $ali->each_alphabetically() ) Function : Returns a sequence object, but the objects are returned in alphabetically sorted order. Does not change the order of the alignment. Returns : Seq object Argument : =cut sub each_alphabetically { my $self = shift; my ($seq,$nse,@arr,%hash,$count); foreach $seq ( $self->each_seq() ) { $nse = $seq->get_nse; $hash{$nse} = $seq; } foreach $nse ( sort _alpha_startend keys %hash) { push(@arr,$hash{$nse}); } return @arr; } sub _alpha_startend { my ($aname,$astart,$bname,$bstart); ($aname,$astart) = split (/-/,$a); ($bname,$bstart) = split (/-/,$b); if( $aname eq $bname ) { return $astart <=> $bstart; } else { return $aname cmp $bname; } } =head2 each_seq_with_id Title : each_seq_with_id Usage : foreach $seq ( $align->each_seq_with_id() ) Function : Gets a Seq objects from the alignment, the contents being those sequences with the given name (there may be more than one) Returns : Seq object Argument : a seq name =cut sub eachSeqWithId { my $self = shift; $self->deprecated("eachSeqWithId - deprecated method. Use each_seq_with_id() instead."); $self->each_seq_with_id(@_); } sub each_seq_with_id { my $self = shift; my $id = shift; $self->throw("Method each_seq_with_id needs a sequence name argument") unless defined $id; my (@arr, $seq); if (exists($self->{'_start_end_lists'}->{$id})) { @arr = @{$self->{'_start_end_lists'}->{$id}}; } return @arr; } =head2 get_seq_by_pos Title : get_seq_by_pos Usage : $seq = $aln->get_seq_by_pos(3) # third sequence from the alignment Function : Gets a sequence based on its position in the alignment. Numbering starts from 1. Sequence positions larger than num_sequences() will throw an error. Returns : a Bio::LocatableSeq object Args : positive integer for the sequence position =cut sub get_seq_by_pos { my $self = shift; my ($pos) = @_; $self->throw("Sequence position has to be a positive integer, not [$pos]") unless $pos =~ /^\d+$/ and $pos > 0; $self->throw("No sequence at position [$pos]") unless $pos <= $self->num_sequences ; my $nse = $self->{'_order'}->{--$pos}; return $self->{'_seq'}->{$nse}; } =head2 get_seq_by_id Title : get_seq_by_id Usage : $seq = $aln->get_seq_by_id($name) # seq named $name Function : Gets a sequence based on its name. Sequences that do not exist will warn and return undef Returns : a Bio::LocatableSeq object Args : string for sequence name =cut sub get_seq_by_id { my ($self,$name) = @_; unless( defined $name ) { $self->warn("Must provide a sequence name"); return; } for my $seq ( values %{$self->{'_seq'}} ) { if ( $seq->id eq $name) { return $seq; } } return; } =head2 seq_with_features Title : seq_with_features Usage : $seq = $aln->seq_with_features(-pos => 1, -consensus => 60 -mask => sub { my $consensus = shift; for my $i (1..5){ my $n = 'N' x $i; my $q = '\?' x $i; while($consensus =~ /[^?]$q[^?]/){ $consensus =~ s/([^?])$q([^?])/$1$n$2/; } } return $consensus; } ); Function: produces a Bio::Seq object by first splicing gaps from -pos (by means of a splice_by_seq_pos() call), then creating features using non-? chars (by means of a consensus_string() call with stringency -consensus). Returns : a Bio::Seq object Args : -pos : required. sequence from which to build the Bio::Seq object -consensus : optional, defaults to consensus_string()'s default cutoff value -mask : optional, a coderef to apply to consensus_string()'s output before building features. this may be useful for closing gaps of 1 bp by masking over them with N, for instance =cut sub seq_with_features{ my ($self,%arg) = @_; #first do the preparatory splice $self->throw("must provide a -pos argument") unless $arg{-pos}; $self->splice_by_seq_pos($arg{-pos}); my $consensus_string = $self->consensus_string($arg{-consensus}); $consensus_string = $arg{-mask}->($consensus_string) if defined($arg{-mask}); my(@bs,@es); push @bs, 1 if $consensus_string =~ /^[^?]/; while($consensus_string =~ /\?[^?]/g){ push @bs, pos($consensus_string); } while($consensus_string =~ /[^?]\?/g){ push @es, pos($consensus_string); } push @es, CORE::length($consensus_string) if $consensus_string =~ /[^?]$/; my $seq = Bio::Seq->new(); # my $rootfeature = Bio::SeqFeature::Generic->new( # -source_tag => 'location', # -start => $self->get_seq_by_pos($arg{-pos})->start, # -end => $self->get_seq_by_pos($arg{-pos})->end, # ); # $seq->add_SeqFeature($rootfeature); while(my $b = shift @bs){ my $e = shift @es; $seq->add_SeqFeature( Bio::SeqFeature::Generic->new( -start => $b - 1 + $self->get_seq_by_pos($arg{-pos})->start, -end => $e - 1 + $self->get_seq_by_pos($arg{-pos})->start, -source_tag => $self->source || 'MSA', ) ); } return $seq; } =head1 Create new alignments The result of these methods are horizontal or vertical subsets of the current MSA. =head2 select Title : select Usage : $aln2 = $aln->select(1, 3) # three first sequences Function : Creates a new alignment from a continuous subset of sequences. Numbering starts from 1. Sequence positions larger than num_sequences() will throw an error. Returns : a Bio::SimpleAlign object Args : positive integer for the first sequence positive integer for the last sequence to include (optional) =cut sub select { my $self = shift; my ($start, $end) = @_; $self->throw("Select start has to be a positive integer, not [$start]") unless $start =~ /^\d+$/ and $start > 0; $self->throw("Select end has to be a positive integer, not [$end]") unless $end =~ /^\d+$/ and $end > 0; $self->throw("Select $start [$start] has to be smaller than or equal to end [$end]") unless $start <= $end; my $aln = $self->new; foreach my $pos ($start .. $end) { $aln->add_seq($self->get_seq_by_pos($pos)); } $aln->id($self->id); # fix for meta, sf, ann return $aln; } =head2 select_noncont Title : select_noncont Usage : # 1st and 3rd sequences, sorted $aln2 = $aln->select_noncont(1, 3) # 1st and 3rd sequences, sorted (same as first) $aln2 = $aln->select_noncont(3, 1) # 1st and 3rd sequences, unsorted $aln2 = $aln->select_noncont('nosort',3, 1) Function : Creates a new alignment from a subset of sequences. Numbering starts from 1. Sequence positions larger than num_sequences() will throw an error. Sorts the order added to new alignment by default, to prevent sorting pass 'nosort' as the first argument in the list. Returns : a Bio::SimpleAlign object Args : array of integers for the sequences. If the string 'nosort' is passed as the first argument, the sequences will not be sorted in the new alignment but will appear in the order listed. =cut sub select_noncont { my $self = shift; my $nosort = 0; my (@pos) = @_; if ($pos[0] !~ m{^\d+$}) { my $sortcmd = shift @pos; if ($sortcmd eq 'nosort') { $nosort = 1; } else { $self->throw("Command not recognized: $sortcmd. Only 'nosort' implemented at this time."); } } my $end = $self->num_sequences; foreach ( @pos ) { $self->throw("position must be a positive integer, > 0 and <= $end not [$_]") unless( /^\d+$/ && $_ > 0 && $_ <= $end ); } @pos = sort {$a <=> $b} @pos unless $nosort; my $aln = $self->new; foreach my $p (@pos) { $aln->add_seq($self->get_seq_by_pos($p)); } $aln->id($self->id); # fix for meta, sf, ann return $aln; } =head2 select_noncont_by_name Title : select_noncont_by_name Usage : my $aln2 = $aln->select_noncont_by_name('A123', 'B456'); Function : Creates a new alignment from a subset of sequences which are selected by name (sequence ID). Returns : a Bio::SimpleAlign object Args : array of names (i.e., identifiers) for the sequences. =cut sub select_noncont_by_name { my ($self, @names) = @_; my $aln = $self->new; foreach my $name (@names) { $aln->add_seq($self->get_seq_by_id($name)); } $aln->id($self->id); return $aln; } =head2 slice Title : slice Usage : $aln2 = $aln->slice(20,30) Function : Creates a slice from the alignment inclusive of start and end columns, and the first column in the alignment is denoted 1. Sequences with no residues in the slice are excluded from the new alignment and a warning is printed. Slice beyond the length of the sequence does not do padding. Returns : A Bio::SimpleAlign object Args : Positive integer for start column, positive integer for end column, optional boolean which if true will keep gap-only columns in the newly created slice. Example: $aln2 = $aln->slice(20,30,1) =cut sub slice { my $self = shift; my ($start, $end, $keep_gap_only) = @_; $self->throw("Slice start has to be a positive integer, not [$start]") unless $start =~ /^\d+$/ and $start > 0; $self->throw("Slice end has to be a positive integer, not [$end]") unless $end =~ /^\d+$/ and $end > 0; $self->throw("Slice start [$start] has to be smaller than or equal to end [$end]") unless $start <= $end; $self->throw("This alignment has only ". $self->length . " residues. Slice start " . "[$start] is too big.") if $start > $self->length; my $cons_meta = $self->consensus_meta; my $aln = $self->new; $aln->id($self->id); foreach my $seq ( $self->each_seq() ) { my $new_seq = $seq->isa('Bio::Seq::MetaI') ? Bio::Seq::Meta->new (-id => $seq->id, -alphabet => $seq->alphabet, -strand => $seq->strand, -verbose => $self->verbose) : Bio::LocatableSeq->new (-id => $seq->id, -alphabet => $seq->alphabet, -strand => $seq->strand, -verbose => $self->verbose); # seq my $seq_end = $end; $seq_end = $seq->length if( $end > $seq->length ); my $slice_seq = $seq->subseq($start, $seq_end); $new_seq->seq( $slice_seq ); # Allowed extra characters in string my $allowed_chars = ''; if (exists $self->{_mask_char}) { $allowed_chars = $self->{_mask_char}; $allowed_chars = quotemeta $allowed_chars; } $slice_seq =~ s/[^\w$allowed_chars]//g; if ($start > 1) { my $pre_start_seq = $seq->subseq(1, $start - 1); $pre_start_seq =~ s/[^\w$allowed_chars]//g; if (!defined($seq->strand)) { $new_seq->start( $seq->start + CORE::length($pre_start_seq) ); } elsif ($seq->strand < 0){ $new_seq->start( $seq->end - CORE::length($pre_start_seq) - CORE::length($slice_seq) + 1); } else { $new_seq->start( $seq->start + CORE::length($pre_start_seq) ); } } else { if ((defined $seq->strand)&&($seq->strand < 0)){ $new_seq->start( $seq->end - CORE::length($slice_seq) + 1); } else { $new_seq->start( $seq->start); } } if ($new_seq->isa('Bio::Seq::MetaI')) { for my $meta_name ($seq->meta_names) { $new_seq->named_meta($meta_name, $seq->named_submeta($meta_name, $start, $end)); } } $new_seq->end( $new_seq->start + CORE::length($slice_seq) - 1 ); if ($new_seq->start and $new_seq->end >= $new_seq->start) { $aln->add_seq($new_seq); } else { if( $keep_gap_only ) { $aln->add_seq($new_seq); } else { my $nse = $seq->get_nse(); $self->warn("Slice [$start-$end] of sequence [$nse] contains no residues.". " Sequence excluded from the new alignment."); } } } if ($cons_meta) { my $new = Bio::Seq::Meta->new(); for my $meta_name ($cons_meta->meta_names) { $new->named_meta($meta_name, $cons_meta->named_submeta($meta_name, $start, $end)); } $aln->consensus_meta($new); } $aln->annotation($self->annotation); # fix for meta, sf, ann return $aln; } =head2 remove_columns Title : remove_columns Usage : $aln2 = $aln->remove_columns(['mismatch','weak']) or $aln2 = $aln->remove_columns([0,0],[6,8]) Function : Creates an aligment with columns removed corresponding to the specified type or by specifying the columns by number. Returns : Bio::SimpleAlign object Args : Array ref of types ('match'|'weak'|'strong'|'mismatch'|'gaps'| 'all_gaps_columns') or array ref where the referenced array contains a pair of integers that specify a range. The first column is 0 =cut sub remove_columns { my ($self,@args) = @_; @args || $self->throw("Must supply column ranges or column types"); my $aln; if ($args[0][0] =~ /^[a-z_]+$/i) { $aln = $self->_remove_columns_by_type($args[0]); } elsif ($args[0][0] =~ /^\d+$/) { $aln = $self->_remove_columns_by_num(\@args); } else { $self->throw("You must pass array references to remove_columns(), not @args"); } # fix for meta, sf, ann $aln; } =head2 remove_gaps Title : remove_gaps Usage : $aln2 = $aln->remove_gaps Function : Creates an aligment with gaps removed Returns : a Bio::SimpleAlign object Args : a gap character(optional) if none specified taken from $self->gap_char, [optional] $all_gaps_columns flag (1 or 0, default is 0) indicates that only all-gaps columns should be deleted Used from method L in most cases. Set gap character using L. =cut sub remove_gaps { my ($self,$gapchar,$all_gaps_columns) = @_; my $gap_line; if ($all_gaps_columns) { $gap_line = $self->all_gap_line($gapchar); } else { $gap_line = $self->gap_line($gapchar); } my $aln = $self->new; my @remove; my $length = 0; my $del_char = $gapchar || $self->gap_char; # Do the matching to get the segments to remove while ($gap_line =~ m/[$del_char]/g) { my $start = pos($gap_line)-1; $gap_line =~ m/\G[$del_char]+/gc; my $end = pos($gap_line)-1; #have to offset the start and end for subsequent removes $start-=$length; $end -=$length; $length += ($end-$start+1); push @remove, [$start,$end]; } #remove the segments $aln = $#remove >= 0 ? $self->_remove_col($aln,\@remove) : $self; # fix for meta, sf, ann return $aln; } sub _remove_col { my ($self,$aln,$remove) = @_; my @new; my $gap = $self->gap_char; # splice out the segments and create new seq foreach my $seq($self->each_seq){ my $new_seq = Bio::LocatableSeq->new( -id => $seq->id, -alphabet=> $seq->alphabet, -strand => $seq->strand, -verbose => $self->verbose); my $sequence = $seq->seq; foreach my $pair(@{$remove}){ my $start = $pair->[0]; my $end = $pair->[1]; $sequence = $seq->seq unless $sequence; my $orig = $sequence; my $head = $start > 0 ? substr($sequence, 0, $start) : ''; my $tail = ($end + 1) >= CORE::length($sequence) ? '' : substr($sequence, $end + 1); $sequence = $head.$tail; # start unless (defined $new_seq->start) { if ($start == 0) { my $start_adjust = () = substr($orig, 0, $end + 1) =~ /$gap/g; $new_seq->start($seq->start + $end + 1 - $start_adjust); } else { my $start_adjust = $orig =~ /^$gap+/; if ($start_adjust) { $start_adjust = $+[0] == $start; } $new_seq->start($seq->start + $start_adjust); } } # end if (($end + 1) >= CORE::length($orig)) { my $end_adjust = () = substr($orig, $start) =~ /$gap/g; $new_seq->end($seq->end - (CORE::length($orig) - $start) + $end_adjust); } else { $new_seq->end($seq->end); } } if ($new_seq->end < $new_seq->start) { # we removed all columns except for gaps: set to 0 to indicate no # sequence $new_seq->start(0); $new_seq->end(0); } $new_seq->seq($sequence) if $sequence; push @new, $new_seq; } # add the new seqs to the alignment foreach my $new(@new){ $aln->add_seq($new); } # fix for meta, sf, ann return $aln; } sub _remove_columns_by_type { my ($self,$type) = @_; my $aln = $self->new; my @remove; my $gap = $self->gap_char if (grep { $_ eq 'gaps'} @{$type}); my $all_gaps_columns = $self->gap_char if (grep /all_gaps_columns/,@{$type}); my %matchchars = ( 'match' => '\*', 'weak' => '\.', 'strong' => ':', 'mismatch' => ' ', 'gaps' => '', 'all_gaps_columns' => '' ); # get the characters to delete against my $del_char; foreach my $type (@{$type}){ $del_char.= $matchchars{$type}; } my $length = 0; my $match_line = $self->match_line; # do the matching to get the segments to remove if($del_char){ while($match_line =~ m/[$del_char]/g ){ my $start = pos($match_line)-1; $match_line=~/\G[$del_char]+/gc; my $end = pos($match_line)-1; #have to offset the start and end for subsequent removes $start-=$length; $end -=$length; $length += ($end-$start+1); push @remove, [$start,$end]; } } # remove the segments $aln = $#remove >= 0 ? $self->_remove_col($aln,\@remove) : $self; $aln = $aln->remove_gaps() if $gap; $aln = $aln->remove_gaps('', 1) if $all_gaps_columns; # fix for meta, sf, ann $aln; } sub _remove_columns_by_num { my ($self,$positions) = @_; my $aln = $self->new; # sort the positions @$positions = sort { $a->[0] <=> $b->[0] } @$positions; my @remove; my $length = 0; foreach my $pos (@{$positions}) { my ($start, $end) = @{$pos}; #have to offset the start and end for subsequent removes $start-=$length; $end -=$length; $length += ($end-$start+1); push @remove, [$start,$end]; } #remove the segments $aln = $#remove >= 0 ? $self->_remove_col($aln,\@remove) : $self; # fix for meta, sf, ann $aln; } =head1 Change sequences within the MSA These methods affect characters in all sequences without changing the alignment. =head2 splice_by_seq_pos Title : splice_by_seq_pos Usage : $status = splice_by_seq_pos(1); Function: splices all aligned sequences where the specified sequence has gaps. Example : Returns : 1 on success Args : position of sequence to splice by =cut sub splice_by_seq_pos{ my ($self,$pos) = @_; my $guide = $self->get_seq_by_pos($pos); my $guide_seq = $guide->seq; $guide_seq =~ s/\./\-/g; my @gaps = (); $pos = -1; while(($pos = index($guide_seq, '-', $pos)) > -1 ){ unshift @gaps, $pos; $pos++; } foreach my $seq ($self->each_seq){ my @bases = split '', $seq->seq; splice(@bases, $_, 1) foreach @gaps; $seq->seq(join('', @bases)); } 1; } =head2 map_chars Title : map_chars Usage : $ali->map_chars('\.','-') Function : Does a s/$arg1/$arg2/ on the sequences. Useful for gap characters. Note that the first argument is interpreted as a regexp so be careful and escape any wild card characters (e.g. do $ali->map_chars('\.','-') to replace periods with dashes. Returns : 1 on success Argument : A regexp and a string =cut sub map_chars { my $self = shift; my $from = shift; my $to = shift; my ( $seq, $temp ); $self->throw("Need two arguments: a regexp and a string") unless defined $from and defined $to; foreach $seq ( $self->each_seq() ) { $temp = $seq->seq(); $temp =~ s/$from/$to/g; $seq->seq($temp); } return 1; } =head2 uppercase Title : uppercase() Usage : $ali->uppercase() Function : Sets all the sequences to uppercase Returns : 1 on success Argument : =cut sub uppercase { my $self = shift; my $seq; my $temp; foreach $seq ( $self->each_seq() ) { $temp = $seq->seq(); $temp =~ tr/[a-z]/[A-Z]/; $seq->seq($temp); } return 1; } =head2 cigar_line Title : cigar_line() Usage : %cigars = $align->cigar_line() Function : Generates a "cigar" (Compact Idiosyncratic Gapped Alignment Report) line for each sequence in the alignment. Examples are "1,60" or "5,10:12,58", where the numbers refer to conserved positions within the alignment. The keys of the hash are the NSEs (name/start/end) assigned to each sequence. Args : threshold (optional, defaults to 100) Returns : Hash of strings (cigar lines) =cut sub cigar_line { my $self = shift; my $thr=shift||100; my %cigars; my @consensus = split "",($self->consensus_string($thr)); my $len = $self->length; my $gapchar = $self->gap_char; # create a precursor, something like (1,4,5,6,7,33,45), # where each number corresponds to a conserved position foreach my $seq ( $self->each_seq ) { my @seq = split "", uc ($seq->seq); my $pos = 1; for (my $x = 0 ; $x < $len ; $x++ ) { if ($seq[$x] eq $consensus[$x]) { push @{$cigars{$seq->get_nse}},$pos; $pos++; } elsif ($seq[$x] ne $gapchar) { $pos++; } } } # duplicate numbers - (1,4,5,6,7,33,45) becomes (1,1,4,5,6,7,33,33,45,45) for my $name (keys %cigars) { splice @{$cigars{$name}}, 1, 0, ${$cigars{$name}}[0] if ( ${$cigars{$name}}[0] + 1 < ${$cigars{$name}}[1] ); push @{$cigars{$name}}, ${$cigars{$name}}[$#{$cigars{$name}}] if ( ${$cigars{$name}}[($#{$cigars{$name}} - 1)] + 1 < ${$cigars{$name}}[$#{$cigars{$name}}] ); for ( my $x = 1 ; $x < $#{$cigars{$name}} - 1 ; $x++) { if (${$cigars{$name}}[$x - 1] + 1 < ${$cigars{$name}}[$x] && ${$cigars{$name}}[$x + 1] > ${$cigars{$name}}[$x] + 1) { splice @{$cigars{$name}}, $x, 0, ${$cigars{$name}}[$x]; } } } # collapse series - (1,1,4,5,6,7,33,33,45,45) becomes (1,1,4,7,33,33,45,45) for my $name (keys %cigars) { my @remove; for ( my $x = 0 ; $x < $#{$cigars{$name}} ; $x++) { if ( ${$cigars{$name}}[$x] == ${$cigars{$name}}[($x - 1)] + 1 && ${$cigars{$name}}[$x] == ${$cigars{$name}}[($x + 1)] - 1 ) { unshift @remove,$x; } } for my $pos (@remove) { splice @{$cigars{$name}}, $pos, 1; } } # join and punctuate for my $name (keys %cigars) { my ($start,$end,$str) = ""; while ( ($start,$end) = splice @{$cigars{$name}}, 0, 2 ) { $str .= ($start . "," . $end . ":"); } $str =~ s/:$//; $cigars{$name} = $str; } %cigars; } =head2 match_line Title : match_line() Usage : $line = $align->match_line() Function : Generates a match line - much like consensus string except that a line indicating the '*' for a match. Args : (optional) Match line characters ('*' by default) (optional) Strong match char (':' by default) (optional) Weak match char ('.' by default) Returns : String =cut sub match_line { my ($self,$matchlinechar, $strong, $weak) = @_; my %matchchars = ('match' => $matchlinechar || '*', 'weak' => $weak || '.', 'strong' => $strong || ':', 'mismatch' => ' ', ); my @seqchars; my $alphabet; foreach my $seq ( $self->each_seq ) { push @seqchars, [ split(//, uc ($seq->seq)) ]; $alphabet = $seq->alphabet unless defined $alphabet; } my $refseq = shift @seqchars; # let's just march down the columns my $matchline; POS: foreach my $pos ( 0..$self->length ) { my $refchar = $refseq->[$pos]; my $char = $matchchars{'mismatch'}; unless( defined $refchar ) { last if $pos == $self->length; # short circuit on last residue # this in place to handle jason's soon-to-be-committed # intron mapping code goto bottom; } my %col = ($refchar => 1); my $dash = ($refchar eq '-' || $refchar eq '.' || $refchar eq ' '); foreach my $seq ( @seqchars ) { next if $pos >= scalar @$seq; $dash = 1 if( $seq->[$pos] eq '-' || $seq->[$pos] eq '.' || $seq->[$pos] eq ' ' ); $col{$seq->[$pos]}++ if defined $seq->[$pos]; } my @colresidues = sort keys %col; # if all the values are the same if( $dash ) { $char = $matchchars{'mismatch'} } elsif( @colresidues == 1 ) { $char = $matchchars{'match'} } elsif( $alphabet eq 'protein' ) { # only try to do weak/strong # matches for protein seqs TYPE: foreach my $type ( qw(strong weak) ) { # iterate through categories my %groups; # iterate through each of the aa in the col # look to see which groups it is in foreach my $c ( @colresidues ) { foreach my $f ( grep { index($_,$c) >= 0 } @{$CONSERVATION_GROUPS{$type}} ) { push @{$groups{$f}},$c; } } GRP: foreach my $cols ( values %groups ) { @$cols = sort @$cols; # now we are just testing to see if two arrays # are identical w/o changing either one # have to be same len next if( scalar @$cols != scalar @colresidues ); # walk down the length and check each slot for($_=0;$_ < (scalar @$cols);$_++ ) { next GRP if( $cols->[$_] ne $colresidues[$_] ); } $char = $matchchars{$type}; last TYPE; } } } bottom: $matchline .= $char; } return $matchline; } =head2 gap_line Title : gap_line() Usage : $line = $align->gap_line() Function : Generates a gap line - much like consensus string except that a line where '-' represents gap Args : (optional) gap line characters ('-' by default) Returns : string =cut sub gap_line { my ($self,$gapchar) = @_; $gapchar = $gapchar || $self->gap_char; my %gap_hsh; # column gaps vector foreach my $seq ( $self->each_seq ) { my $i = 0; map {$gap_hsh{$_->[0]} = undef} grep {$_->[1] =~ m/[$gapchar]/} map {[$i++, $_]} split(//, uc ($seq->seq)); } my $gap_line; foreach my $pos ( 0..$self->length-1 ) { $gap_line .= (exists $gap_hsh{$pos}) ? $self->gap_char:'.'; } return $gap_line; } =head2 all_gap_line Title : all_gap_line() Usage : $line = $align->all_gap_line() Function : Generates a gap line - much like consensus string except that a line where '-' represents all-gap column Args : (optional) gap line characters ('-' by default) Returns : string =cut sub all_gap_line { my ($self,$gapchar) = @_; $gapchar = $gapchar || $self->gap_char; my %gap_hsh; # column gaps counter hash my @seqs = $self->each_seq; foreach my $seq ( @seqs ) { my $i = 0; map {$gap_hsh{$_->[0]}++} grep {$_->[1] =~ m/[$gapchar]/} map {[$i++, $_]} split(//, uc ($seq->seq)); } my $gap_line; foreach my $pos ( 0..$self->length-1 ) { if (exists $gap_hsh{$pos} && $gap_hsh{$pos} == scalar @seqs) { # gaps column $gap_line .= $self->gap_char; } else { $gap_line .= '.'; } } return $gap_line; } =head2 gap_col_matrix Title : gap_col_matrix() Usage : my $cols = $align->gap_col_matrix() Function : Generates an array where each element in the array is a hash reference with a key of the sequence name and a value of 1 if the sequence has a gap at that column Returns : Reference to an array Args : Optional: gap line character ($aln->gap_char or '-' by default) =cut sub gap_col_matrix { my ( $self, $gapchar ) = @_; $gapchar = $gapchar || $self->gap_char; my %gap_hsh; # column gaps vector my @cols; foreach my $seq ( $self->each_seq ) { my $i = 0; my $str = $seq->seq; my $len = $seq->length; my $ch; my $id = $seq->display_id; while ( $i < $len ) { $ch = substr( $str, $i, 1 ); $cols[ $i++ ]->{$id} = ( $ch =~ m/[$gapchar]/ ); } } return \@cols; } =head2 match Title : match() Usage : $ali->match() Function : Goes through all columns and changes residues that are identical to residue in first sequence to match '.' character. Sets match_char. USE WITH CARE: Most MSA formats do not support match characters in sequences, so this is mostly for output only. NEXUS format (Bio::AlignIO::nexus) can handle it. Returns : 1 on success Argument : a match character, optional, defaults to '.' =cut sub match { my ( $self, $match ) = @_; $match ||= '.'; my ($matching_char) = $match; $matching_char = "\\$match" if $match =~ /[\^.$|()\[\]]/; #'; $self->map_chars( $matching_char, '-' ); my @seqs = $self->each_seq(); return 1 unless scalar @seqs > 1; my $refseq = shift @seqs; my @refseq = split //, $refseq->seq; my $gapchar = $self->gap_char; foreach my $seq (@seqs) { my @varseq = split //, $seq->seq(); for ( my $i = 0; $i < scalar @varseq; $i++ ) { $varseq[$i] = $match if defined $refseq[$i] && ( $refseq[$i] =~ /[A-Za-z\*]/ || $refseq[$i] =~ /$gapchar/ ) && $refseq[$i] eq $varseq[$i]; } $seq->seq( join '', @varseq ); } $self->match_char($match); return 1; } =head2 unmatch Title : unmatch() Usage : $ali->unmatch() Function : Undoes the effect of method match. Unsets match_char. Returns : 1 on success Argument : a match character, optional, defaults to '.' See L and L =cut sub unmatch { my ( $self, $match ) = @_; $match ||= '.'; my @seqs = $self->each_seq(); return 1 unless scalar @seqs > 1; my $refseq = shift @seqs; my @refseq = split //, $refseq->seq; my $gapchar = $self->gap_char; foreach my $seq (@seqs) { my @varseq = split //, $seq->seq(); for ( my $i = 0; $i < scalar @varseq; $i++ ) { $varseq[$i] = $refseq[$i] if defined $refseq[$i] && ( $refseq[$i] =~ /[A-Za-z\*]/ || $refseq[$i] =~ /$gapchar/ ) && $varseq[$i] eq $match; } $seq->seq( join '', @varseq ); } $self->match_char(''); return 1; } =head1 MSA attributes Methods for setting and reading the MSA attributes. Note that the methods defining character semantics depend on the user to set them sensibly. They are needed only by certain input/output methods. Unset them by setting to an empty string (''). =head2 id Title : id Usage : $myalign->id("Ig") Function : Gets/sets the id field of the alignment Returns : An id string Argument : An id string (optional) =cut sub id { my ( $self, $name ) = @_; if ( defined($name) ) { $self->{'_id'} = $name; } return $self->{'_id'}; } =head2 accession Title : accession Usage : $myalign->accession("PF00244") Function : Gets/sets the accession field of the alignment Returns : An acc string Argument : An acc string (optional) =cut sub accession { my ( $self, $acc ) = @_; if ( defined($acc) ) { $self->{'_accession'} = $acc; } return $self->{'_accession'}; } =head2 description Title : description Usage : $myalign->description("14-3-3 proteins") Function : Gets/sets the description field of the alignment Returns : An description string Argument : An description string (optional) =cut sub description { my ( $self, $name ) = @_; if ( defined($name) ) { $self->{'_description'} = $name; } return $self->{'_description'}; } =head2 missing_char Title : missing_char Usage : $myalign->missing_char("?") Function : Gets/sets the missing_char attribute of the alignment It is generally recommended to set it to 'n' or 'N' for nucleotides and to 'X' for protein. Returns : An missing_char string, Argument : An missing_char string (optional) =cut sub missing_char { my ( $self, $char ) = @_; if ( defined $char ) { $self->throw("Single missing character, not [$char]!") if CORE::length($char) > 1; $self->{'_missing_char'} = $char; } return $self->{'_missing_char'}; } =head2 match_char Title : match_char Usage : $myalign->match_char('.') Function : Gets/sets the match_char attribute of the alignment Returns : An match_char string, Argument : An match_char string (optional) =cut sub match_char { my ( $self, $char ) = @_; if ( defined $char ) { $self->throw("Single match character, not [$char]!") if CORE::length($char) > 1; $self->{'_match_char'} = $char; } return $self->{'_match_char'}; } =head2 gap_char Title : gap_char Usage : $myalign->gap_char('-') Function : Gets/sets the gap_char attribute of the alignment Returns : An gap_char string, defaults to '-' Argument : An gap_char string (optional) =cut sub gap_char { my ( $self, $char ) = @_; if ( defined $char || !defined $self->{'_gap_char'} ) { $char = '-' unless defined $char; $self->throw("Single gap character, not [$char]!") if CORE::length($char) > 1; $self->{'_gap_char'} = $char; } return $self->{'_gap_char'}; } =head2 symbol_chars Title : symbol_chars Usage : my @symbolchars = $aln->symbol_chars; Function: Returns all the seen symbols (other than gaps) Returns : array of characters that are the seen symbols Args : boolean to include the gap/missing/match characters =cut sub symbol_chars{ my ($self,$includeextra) = @_; unless ($self->{'_symbols'}) { foreach my $seq ($self->each_seq) { map { $self->{'_symbols'}->{$_} = 1; } split(//,$seq->seq); } } my %copy = %{$self->{'_symbols'}}; if( ! $includeextra ) { foreach my $char ( $self->gap_char, $self->match_char, $self->missing_char) { delete $copy{$char} if( defined $char ); } } return keys %copy; } =head1 Alignment descriptors These read only methods describe the MSA in various ways. =head2 score Title : score Usage : $str = $ali->score() Function : get/set a score of the alignment Returns : a score for the alignment Argument : an optional score to set =cut sub score { my $self = shift; $self->{score} = shift if @_; return $self->{score}; } =head2 consensus_string Title : consensus_string Usage : $str = $ali->consensus_string($threshold_percent) Function : Makes a strict consensus Returns : Consensus string Argument : Optional threshold ranging from 0 to 100. The consensus residue has to appear at least threshold % of the sequences at a given location, otherwise a '?' character will be placed at that location. (Default value = 0%) =cut sub consensus_string { my $self = shift; my $threshold = shift; my $out = ""; my $len = $self->length - 1; foreach ( 0 .. $len ) { $out .= $self->_consensus_aa( $_, $threshold ); } return $out; } =head2 consensus_conservation Title : consensus_conservation Usage : @conservation = $ali->consensus_conservation(); Function : Conservation (as a percent) of each position of alignment Returns : Array of percentages [0-100]. Gap columns are 0% conserved. Argument : =cut sub consensus_conservation { my $self = shift; my @cons; my $num_sequences = $self->num_sequences; foreach my $point (0..$self->length-1) { my %hash = $self->_consensus_counts($point); # max frequency of a non-gap letter my $max = (sort {$b<=>$a} values %hash )[0]; push @cons, 100 * $max / $num_sequences; } return @cons; } sub _consensus_aa { my $self = shift; my $point = shift; my $threshold_percent = shift || -1 ; my ($seq,%hash,$count,$letter,$key); my $gapchar = $self->gap_char; %hash = $self->_consensus_counts($point); my $number_of_sequences = $self->num_sequences(); my $threshold = $number_of_sequences * $threshold_percent / 100. ; $count = -1; $letter = '?'; foreach $key ( sort keys %hash ) { # print "Now at $key $hash{$key}\n"; if( $hash{$key} > $count && $hash{$key} >= $threshold) { $letter = $key; $count = $hash{$key}; } } return $letter; } # Frequency of each letter in one column sub _consensus_counts { my $self = shift; my $point = shift; my %hash; my $gapchar = $self->gap_char; foreach my $seq ( $self->each_seq() ) { my $letter = substr($seq->seq,$point,1); $self->throw("--$point-----------") if $letter eq ''; ($letter eq $gapchar || $letter =~ /\./) && next; $hash{$letter}++; } return %hash; } =head2 consensus_iupac Title : consensus_iupac Usage : $str = $ali->consensus_iupac() Function : Makes a consensus using IUPAC ambiguity codes from DNA and RNA. The output is in upper case except when gaps in a column force output to be in lower case. Note that if your alignment sequences contain a lot of IUPAC ambiquity codes you often have to manually set alphabet. Bio::PrimarySeq::_guess_type thinks they indicate a protein sequence. Returns : consensus string Argument : none Throws : on protein sequences =cut sub consensus_iupac { my $self = shift; my $out = ""; my $len = $self->length - 1; # only DNA and RNA sequences are valid foreach my $seq ( $self->each_seq() ) { $self->throw( "Seq [" . $seq->get_nse . "] is a protein" ) if $seq->alphabet eq 'protein'; } # loop over the alignment columns foreach my $count ( 0 .. $len ) { $out .= $self->_consensus_iupac($count); } return $out; } sub _consensus_iupac { my ($self, $column) = @_; my ($string, $char, $rna); #determine all residues in a column foreach my $seq ( $self->each_seq() ) { $string .= substr($seq->seq, $column, 1); } $string = uc $string; # quick exit if there's an N in the string if ($string =~ /N/) { $string =~ /\W/ ? return 'n' : return 'N'; } # ... or if there are only gap characters return '-' if $string =~ /^\W+$/; # treat RNA as DNA in regexps if ($string =~ /U/) { $string =~ s/U/T/; $rna = 1; } # the following s///'s only need to be done to the _first_ ambiguity code # as we only need to see the _range_ of characters in $string if ($string =~ /[VDHB]/) { $string =~ s/V/AGC/; $string =~ s/D/AGT/; $string =~ s/H/ACT/; $string =~ s/B/CTG/; } if ($string =~ /[SKYRWM]/) { $string =~ s/S/GC/; $string =~ s/K/GT/; $string =~ s/Y/CT/; $string =~ s/R/AG/; $string =~ s/W/AT/; $string =~ s/M/AC/; } # and now the guts of the thing if ($string =~ /A/) { $char = 'A'; # A A if ($string =~ /G/) { $char = 'R'; # A and G (purines) R if ($string =~ /C/) { $char = 'V'; # A and G and C V if ($string =~ /T/) { $char = 'N'; # A and G and C and T N } } elsif ($string =~ /T/) { $char = 'D'; # A and G and T D } } elsif ($string =~ /C/) { $char = 'M'; # A and C M if ($string =~ /T/) { $char = 'H'; # A and C and T H } } elsif ($string =~ /T/) { $char = 'W'; # A and T W } } elsif ($string =~ /C/) { $char = 'C'; # C C if ($string =~ /T/) { $char = 'Y'; # C and T (pyrimidines) Y if ($string =~ /G/) { $char = 'B'; # C and T and G B } } elsif ($string =~ /G/) { $char = 'S'; # C and G S } } elsif ($string =~ /G/) { $char = 'G'; # G G if ($string =~ /C/) { $char = 'S'; # G and C S } elsif ($string =~ /T/) { $char = 'K'; # G and T K } } elsif ($string =~ /T/) { $char = 'T'; # T T } $char = 'U' if $rna and $char eq 'T'; $char = lc $char if $string =~ /\W/; return $char; } =head2 consensus_meta Title : consensus_meta Usage : $seqmeta = $ali->consensus_meta() Function : Returns a Bio::Seq::Meta object containing the consensus strings derived from meta data analysis. Returns : Bio::Seq::Meta Argument : Bio::Seq::Meta Throws : non-MetaI object =cut sub consensus_meta { my ($self, $meta) = @_; if ($meta && (!ref $meta || !$meta->isa('Bio::Seq::MetaI'))) { $self->throw('Not a Bio::Seq::MetaI object'); } return $self->{'_aln_meta'} = $meta if $meta; return $self->{'_aln_meta'} } =head2 is_flush Title : is_flush Usage : if ( $ali->is_flush() ) Function : Tells you whether the alignment : is flush, i.e. all of the same length Returns : 1 or 0 Argument : =cut sub is_flush { my ( $self, $report ) = @_; my $seq; my $length = (-1); my $temp; foreach $seq ( $self->each_seq() ) { if ( $length == (-1) ) { $length = CORE::length( $seq->seq() ); next; } $temp = CORE::length( $seq->seq() ); if ( $temp != $length ) { $self->warn( "expecting $length not $temp from " . $seq->display_id ) if ($report); $self->debug( "expecting $length not $temp from " . $seq->display_id ); $self->debug( $seq->seq() . "\n" ); return 0; } } return 1; } =head2 length Title : length() Usage : $len = $ali->length() Function : Returns the maximum length of the alignment. To be sure the alignment is a block, use is_flush Returns : Integer Argument : =cut sub length_aln { my $self = shift; $self->deprecated("length_aln - deprecated method. Use length() instead."); $self->length(@_); } sub length { my $self = shift; my $seq; my $length = -1; my $temp; foreach $seq ( $self->each_seq() ) { $temp = $seq->length(); if( $temp > $length ) { $length = $temp; } } return $length; } =head2 maxdisplayname_length Title : maxdisplayname_length Usage : $ali->maxdisplayname_length() Function : Gets the maximum length of the displayname in the alignment. Used in writing out various MSA formats. Returns : integer Argument : =cut sub maxname_length { my $self = shift; $self->deprecated("maxname_length - deprecated method.". " Use maxdisplayname_length() instead."); $self->maxdisplayname_length(); } sub maxnse_length { my $self = shift; $self->deprecated("maxnse_length - deprecated method.". " Use maxnse_length() instead."); $self->maxdisplayname_length(); } sub maxdisplayname_length { my $self = shift; my $maxname = (-1); my ( $seq, $len ); foreach $seq ( $self->each_seq() ) { $len = CORE::length $self->displayname( $seq->get_nse() ); if ( $len > $maxname ) { $maxname = $len; } } return $maxname; } =head2 max_metaname_length Title : max_metaname_length Usage : $ali->max_metaname_length() Function : Gets the maximum length of the meta name tags in the alignment for the sequences and for the alignment. Used in writing out various MSA formats. Returns : integer Argument : None =cut sub max_metaname_length { my $self = shift; my $maxname = (-1); my ($seq,$len); # check seq meta first for $seq ( $self->each_seq() ) { next if !$seq->isa('Bio::Seq::MetaI' || !$seq->meta_names); for my $mtag ($seq->meta_names) { $len = CORE::length $mtag; if( $len > $maxname ) { $maxname = $len; } } } # alignment meta for my $meta ($self->consensus_meta) { next unless $meta; for my $name ($meta->meta_names) { $len = CORE::length $name; if( $len > $maxname ) { $maxname = $len; } } } return $maxname; } =head2 num_residues Title : num_residues Usage : $no = $ali->num_residues Function : number of residues in total in the alignment Returns : integer Argument : Note : replaces no_residues() =cut sub num_residues { my $self = shift; my $count = 0; foreach my $seq ( $self->each_seq ) { my $str = $seq->seq(); $count += ( $str =~ s/[A-Za-z]//g ); } return $count; } =head2 num_sequences Title : num_sequences Usage : $depth = $ali->num_sequences Function : number of sequence in the sequence alignment Returns : integer Argument : none Note : replaces no_sequences() =cut sub num_sequences { my $self = shift; return scalar($self->each_seq); } =head2 average_percentage_identity Title : average_percentage_identity Usage : $id = $align->average_percentage_identity Function: The function uses a fast method to calculate the average percentage identity of the alignment Returns : The average percentage identity of the alignment Args : None Notes : This method implemented by Kevin Howe calculates a figure that is designed to be similar to the average pairwise identity of the alignment (identical in the absence of gaps), without having to explicitly calculate pairwise identities proposed by Richard Durbin. Validated by Ewan Birney ad Alex Bateman. =cut sub average_percentage_identity{ my ($self,@args) = @_; my @alphabet = ('A','B','C','D','E','F','G','H','I','J','K','L','M', 'N','O','P','Q','R','S','T','U','V','W','X','Y','Z'); my ($len, $total, $subtotal, $divisor, $subdivisor, @seqs, @countHashes); if (! $self->is_flush()) { $self->throw("All sequences in the alignment must be the same length"); } @seqs = $self->each_seq(); $len = $self->length(); # load the each hash with correct keys for existence checks for( my $index=0; $index < $len; $index++) { foreach my $letter (@alphabet) { $countHashes[$index]->{$letter} = 0; } } foreach my $seq (@seqs) { my @seqChars = split //, $seq->seq(); for( my $column=0; $column < @seqChars; $column++ ) { my $char = uc($seqChars[$column]); if (exists $countHashes[$column]->{$char}) { $countHashes[$column]->{$char}++; } } } $total = 0; $divisor = 0; for(my $column =0; $column < $len; $column++) { my %hash = %{$countHashes[$column]}; $subdivisor = 0; foreach my $res (keys %hash) { $total += $hash{$res}*($hash{$res} - 1); $subdivisor += $hash{$res}; } $divisor += $subdivisor * ($subdivisor - 1); } return $divisor > 0 ? ($total / $divisor )*100.0 : 0; } =head2 percentage_identity Title : percentage_identity Usage : $id = $align->percentage_identity Function: The function calculates the average percentage identity (aliased to average_percentage_identity) Returns : The average percentage identity Args : None =cut sub percentage_identity { my $self = shift; return $self->average_percentage_identity(); } =head2 overall_percentage_identity Title : overall_percentage_identity Usage : $id = $align->overall_percentage_identity $id = $align->overall_percentage_identity('short') Function: The function calculates the percentage identity of the conserved columns Returns : The percentage identity of the conserved columns Args : length value to use, optional defaults to alignment length possible values: 'align', 'short', 'long' The argument values 'short' and 'long' refer to shortest and longest sequence in the alignment. Method modification code by Hongyu Zhang. =cut sub overall_percentage_identity{ my ($self, $length_measure) = @_; my %alphabet = map {$_ => undef} qw (A C G T U B D E F H I J K L M N O P Q R S V W X Y Z); my %enum = map {$_ => undef} qw (align short long); $self->throw("Unknown argument [$length_measure]") if $length_measure and not exists $enum{$length_measure}; $length_measure ||= 'align'; if (! $self->is_flush()) { $self->throw("All sequences in the alignment must be the same length"); } # Count the residues seen at each position my $len; my $total = 0; # number of positions with identical residues my @countHashes; my @seqs = $self->each_seq; my $nof_seqs = scalar @seqs; my $aln_len = $self->length(); for my $seq (@seqs) { my $seqstr = $seq->seq; # Count residues for given sequence for my $column (0 .. $aln_len-1) { my $char = uc( substr($seqstr, $column, 1) ); if ( exists $alphabet{$char} ) { # This is a valid char if ( defined $countHashes[$column]->{$char} ) { $countHashes[$column]->{$char}++; } else { $countHashes[$column]->{$char} = 1; } if ( $countHashes[$column]->{$char} == $nof_seqs ) { # All sequences have this same residue $total++; } } } # Sequence length if ($length_measure eq 'short' || $length_measure eq 'long') { my $seq_len = $seqstr =~ tr/[A-Za-z]//; if ($length_measure eq 'short') { if ( (not defined $len) || ($seq_len < $len) ) { $len = $seq_len; } } elsif ($length_measure eq 'long') { if ( (not defined $len) || ($seq_len > $len) ) { $len = $seq_len; } } } } if ($length_measure eq 'align') { $len = $aln_len; } return ($total / $len ) * 100.0; } =head1 Alignment positions Methods to map a sequence position into an alignment column and back. column_from_residue_number() does the former. The latter is really a property of the sequence object and can done using L: # select somehow a sequence from the alignment, e.g. my $seq = $aln->get_seq_by_pos(1); #$loc is undef or Bio::LocationI object my $loc = $seq->location_from_column(5); =head2 column_from_residue_number Title : column_from_residue_number Usage : $col = $ali->column_from_residue_number( $seqname, $resnumber) Function: This function gives the position in the alignment (i.e. column number) of the given residue number in the sequence with the given name. For example, for the alignment Seq1/91-97 AC..DEF.GH. Seq2/24-30 ACGG.RTY... Seq3/43-51 AC.DDEF.GHI column_from_residue_number( "Seq1", 94 ) returns 6. column_from_residue_number( "Seq2", 25 ) returns 2. column_from_residue_number( "Seq3", 50 ) returns 10. An exception is thrown if the residue number would lie outside the length of the aligment (e.g. column_from_residue_number( "Seq2", 22 ) Note: If the the parent sequence is represented by more than one alignment sequence and the residue number is present in them, this method finds only the first one. Returns : A column number for the position in the alignment of the given residue in the given sequence (1 = first column) Args : A sequence id/name (not a name/start-end) A residue number in the whole sequence (not just that segment of it in the alignment) =cut sub column_from_residue_number { my ( $self, $name, $resnumber ) = @_; $self->throw("No sequence with name [$name]") unless $self->{'_start_end_lists'}->{$name}; $self->throw("Second argument residue number missing") unless $resnumber; foreach my $seq ( $self->each_seq_with_id($name) ) { my $col; eval { $col = $seq->column_from_residue_number($resnumber); }; next if $@; return $col; } $self->throw( "Could not find a sequence segment in $name " . "containing residue number $resnumber" ); } =head1 Sequence names Methods to manipulate the display name. The default name based on the sequence id and subsequence positions can be overridden in various ways. =head2 displayname Title : displayname Usage : $myalign->displayname("Ig", "IgA") Function : Gets/sets the display name of a sequence in the alignment Returns : A display name string Argument : name of the sequence displayname of the sequence (optional) =cut sub displayname { my ( $self, $name, $disname ) = @_; $self->throw("No sequence with name [$name]") unless defined $self->{'_seq'}->{$name}; if ( $disname and $name ) { $self->{'_dis_name'}->{$name} = $disname; return $disname; } elsif ( defined $self->{'_dis_name'}->{$name} ) { return $self->{'_dis_name'}->{$name}; } else { return $name; } } sub get_displayname { my $self = shift; $self->deprecated("get_displayname - deprecated method. Use displayname() instead."); $self->displayname(@_); } sub set_displayname { my $self = shift; $self->deprecated("set_displayname - deprecated method. Use displayname() instead."); $self->displayname(@_); } =head2 set_displayname_count Title : set_displayname_count Usage : $ali->set_displayname_count Function : Sets the names to be name_# where # is the number of times this name has been used. Returns : 1, on success Argument : =cut sub set_displayname_count { my $self= shift; my (@arr,$name,$seq,$count,$temp,$nse); foreach $seq ( $self->each_alphabetically() ) { $nse = $seq->get_nse(); #name will be set when this is the second #time (or greater) is has been seen if( defined $name and $name eq ($seq->id()) ) { $temp = sprintf("%s_%s",$name,$count); $self->displayname($nse,$temp); $count++; } else { $count = 1; $name = $seq->id(); $temp = sprintf("%s_%s",$name,$count); $self->displayname($nse,$temp); $count++; } } return 1; } =head2 set_displayname_flat Title : set_displayname_flat Usage : $ali->set_displayname_flat() Function : Makes all the sequences be displayed as just their name, not name/start-end (NSE) Returns : 1 Argument : =cut sub set_displayname_flat { my $self = shift; my ( $nse, $seq ); foreach $seq ( $self->each_seq() ) { $nse = $seq->get_nse(); $self->displayname( $nse, $seq->id() ); } return 1; } =head2 set_displayname_normal Title : set_displayname_normal Usage : $ali->set_displayname_normal() Function : Makes all the sequences be displayed as name/start-end (NSE) Returns : 1, on success Argument : =cut sub set_displayname_normal { my $self = shift; my ( $nse, $seq ); foreach $seq ( $self->each_seq() ) { $nse = $seq->get_nse(); $self->displayname( $nse, $nse ); } return 1; } =head2 source Title : source Usage : $obj->source($newval) Function: sets the Alignment source program Example : Returns : value of source Args : newvalue (optional) =cut sub source { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_source'} = $value; } return $self->{'_source'}; } =head2 set_displayname_safe Title : set_displayname_safe Usage : ($new_aln, $ref_name)=$ali->set_displayname_safe(4) Function : Assign machine-generated serial names to sequences in input order. Designed to protect names during PHYLIP runs. Assign 10-char string in the form of "S000000001" to "S999999999". Restore the original names using "restore_displayname". Returns : 1. a new $aln with system names; 2. a hash ref for restoring names Argument : Number for id length (default 10) =cut sub set_displayname_safe { my $self = shift; my $idlength = shift || 10; my ( $seq, %phylip_name ); my $ct = 0; my $new = Bio::SimpleAlign->new(); foreach $seq ( $self->each_seq() ) { $ct++; my $pname = "S" . sprintf "%0" . ( $idlength - 1 ) . "s", $ct; $phylip_name{$pname} = $seq->id(); my $new_seq = Bio::LocatableSeq->new( -id => $pname, -seq => $seq->seq(), -alphabet => $seq->alphabet, -start => $seq->{_start}, -end => $seq->{_end} ); $new->add_seq($new_seq); } $self->debug( "$ct seq names changed. Restore names by using restore_displayname."); return ( $new, \%phylip_name ); } =head2 restore_displayname Title : restore_displayname Usage : $aln_name_restored=$ali->restore_displayname($hash_ref) Function : Restore original sequence names (after running $ali->set_displayname_safe) Returns : a new $aln with names restored. Argument : a hash reference of names from "set_displayname_safe". =cut sub restore_displayname { my $self = shift; my $ref=shift; my %name=%$ref; my $new=Bio::SimpleAlign->new(); foreach my $seq ( $self->each_seq() ) { $self->throw("No sequence with name") unless defined $name{$seq->id()}; my $new_seq= Bio::LocatableSeq->new(-id => $name{$seq->id()}, -seq => $seq->seq(), -alphabet => $seq->alphabet, -start => $seq->{_start}, -end => $seq->{_end} ); $new->add_seq($new_seq); } return $new; } =head2 sort_by_start Title : sort_by_start Usage : $ali->sort_by_start Function : Changes the order of the alignment to the start position of each subalignment Returns : 1 on success Argument : =cut sub sort_by_start { my $self = shift; my ($seq,$nse,@arr,%hash,$count); foreach $seq ( $self->each_seq() ) { $nse = $seq->get_nse; $hash{$nse} = $seq; } $count = 0; %{$self->{'_order'}} = (); # reset the hash; foreach $nse ( sort _startend keys %hash) { $self->{'_order'}->{$count} = $nse; $count++; } 1; } sub _startend { my ($aname,$arange) = split (/[\/]/,$a); my ($bname,$brange) = split (/[\/]/,$b); my ($astart,$aend) = split(/\-/,$arange); my ($bstart,$bend) = split(/\-/,$brange); return $astart <=> $bstart; } =head2 bracket_string Title : bracket_string Usage : my @params = (-refseq => 'testseq', -allele1 => 'allele1', -allele2 => 'allele2', -delimiters => '{}', -separator => '/'); $str = $aln->bracket_string(@params) Function : When supplied with a list of parameters (see below), returns a string in BIC format. This is used for allelic comparisons. Briefly, if either allele contains a base change when compared to the refseq, the base or gap for each allele is represented in brackets in the order present in the 'alleles' parameter. For the following data: >testseq GGATCCATTGCTACT >allele1 GGATCCATTCCTACT >allele2 GGAT--ATTCCTCCT the returned string with parameters 'refseq => testseq' and 'alleles => [qw(allele1 allele2)]' would be: GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT Returns : BIC-formatted string Argument : Required args refseq : string (ID) of the reference sequence used as basis for comparison allele1 : string (ID) of the first allele allele2 : string (ID) of the second allele Optional args delimiters: two symbol string of left and right delimiters. Only the first two symbols are used default = '[]' separator : string used as a separator. Only the first symbol is used default = '/' Throws : On no refseq/alleles, or invalid refseq/alleles. =cut sub bracket_string { my ($self, @args) = @_; my ($ref, $a1, $a2, $delim, $sep) = $self->_rearrange([qw(refseq allele1 allele2 delimiters separator)], @args); $self->throw('Missing refseq/allele1/allele2') if (!$a1 || !$a2 || !$ref); my ($ld, $rd); ($ld, $rd) = split('', $delim, 2) if $delim; $ld ||= '['; $rd ||= ']'; $sep ||= '/'; my ($refseq, $allele1, $allele2) = map {( $self->each_seq_with_id($_) )} ($ref, $a1, $a2); if (!$refseq || !$allele1 || !$allele2) { $self->throw("One of your refseq/allele IDs is invalid!"); } my $len = $self->length-1; my $bic = ''; # loop over the alignment columns for my $column ( 0 .. $len ) { my $string; my ($compres, $res1, $res2) = map{substr($_->seq, $column, 1)} ($refseq, $allele1, $allele2); # are any of the allele symbols different from the refseq? $string = ($compres eq $res1 && $compres eq $res2) ? $compres : $ld.$res1.$sep.$res2.$rd; $bic .= $string; } return $bic; } =head2 methods implementing Bio::FeatureHolderI FeatureHolderI implementation to support labeled character sets like one would get from NEXUS represented data. =head2 get_SeqFeatures Usage : @features = $aln->get_SeqFeatures Function: Get the feature objects held by this feature holder. Example : Returns : an array of Bio::SeqFeatureI implementing objects Args : optional filter coderef, taking a Bio::SeqFeatureI : as argument, returning TRUE if wanted, FALSE if : unwanted =cut sub get_SeqFeatures { my $self = shift; my $filter_cb = shift; $self->throw("Arg (filter callback) must be a coderef") unless !defined($filter_cb) or ref($filter_cb) eq 'CODE'; if ( !defined $self->{'_as_feat'} ) { $self->{'_as_feat'} = []; } if ($filter_cb) { return grep { $filter_cb->($_) } @{ $self->{'_as_feat'} }; } return @{ $self->{'_as_feat'} }; } =head2 add_SeqFeature Usage : $aln->add_SeqFeature($subfeat); Function: Adds a SeqFeature into the SeqFeature array. The 'EXPAND' qualifier (see L) is supported, but has no effect. Example : Returns : 1 on success Args : a Bio::SeqFeatureI object =cut sub add_SeqFeature { my ($self, @feat) = @_; $self->{'_as_feat'} = [] unless $self->{'_as_feat'}; if (scalar @feat > 1) { $self->deprecated( -message => 'Providing an array of features to Bio::SimpleAlign add_SeqFeature()'. ' is deprecated and will be removed in a future version. '. 'Add a single feature at a time instead.', -warn_version => 1.007, -throw_version => 1.009, ); } for my $feat ( @feat ) { next if $feat eq 'EXPAND'; # Need to support it for FeatureHolderI compliance if( !$feat->isa("Bio::SeqFeatureI") ) { $self->throw("Expected a Bio::SeqFeatureI object, but got a $feat."); } push @{$self->{'_as_feat'}}, $feat; } return 1; } =head2 remove_SeqFeatures Usage : $obj->remove_SeqFeatures Function: Removes all SeqFeatures. If you want to remove only a subset, remove that subset from the returned array, and add back the rest. Returns : The array of Bio::SeqFeatureI features that was deleted from this alignment. Args : none =cut sub remove_SeqFeatures { my $self = shift; return () unless $self->{'_as_feat'}; my @feats = @{$self->{'_as_feat'}}; $self->{'_as_feat'} = []; return @feats; } =head2 feature_count Title : feature_count Usage : $obj->feature_count() Function: Return the number of SeqFeatures attached to the alignment Returns : integer representing the number of SeqFeatures Args : None =cut sub feature_count { my ($self) = @_; if (defined($self->{'_as_feat'})) { return ($#{$self->{'_as_feat'}} + 1); } else { return 0; } } =head2 get_all_SeqFeatures Title : get_all_SeqFeatures Usage : Function: Get all SeqFeatures. Example : Returns : an array of Bio::SeqFeatureI implementing objects Args : none Note : Falls through to Bio::FeatureHolderI implementation. =cut =head2 methods for Bio::AnnotatableI AnnotatableI implementation to support sequence alignments which contain annotation (NEXUS, Stockholm). =head2 annotation Title : annotation Usage : $ann = $aln->annotation or $aln->annotation($ann) Function: Gets or sets the annotation Returns : Bio::AnnotationCollectionI object Args : None or Bio::AnnotationCollectionI object See L and L for more information =cut sub annotation { my ($obj,$value) = @_; if( defined $value ) { $obj->throw("object of class ".ref($value)." does not implement ". "Bio::AnnotationCollectionI. Too bad.") unless $value->isa("Bio::AnnotationCollectionI"); $obj->{'_annotation'} = $value; } elsif( ! defined $obj->{'_annotation'}) { $obj->{'_annotation'} = Bio::Annotation::Collection->new(); } return $obj->{'_annotation'}; } =head1 Deprecated methods =cut =head2 no_residues Title : no_residues Usage : $no = $ali->no_residues Function : number of residues in total in the alignment Returns : integer Argument : Note : deprecated in favor of num_residues() =cut sub no_residues { my $self = shift; $self->deprecated(-warn_version => 1.0069, -throw_version => 1.0075, -message => 'Use of method no_residues() is deprecated, use num_residues() instead'); $self->num_residues(@_); } =head2 no_sequences Title : no_sequences Usage : $depth = $ali->no_sequences Function : number of sequence in the sequence alignment Returns : integer Argument : Note : deprecated in favor of num_sequences() =cut sub no_sequences { my $self = shift; $self->deprecated(-warn_version => 1.0069, -throw_version => 1.0075, -message => 'Use of method no_sequences() is deprecated, use num_sequences() instead'); $self->num_sequences(@_); } =head2 mask_columns Title : mask_columns Usage : $aln2 = $aln->mask_columns(20,30) Function : Masks a slice of the alignment inclusive of start and end columns, and the first column in the alignment is denoted 1. Mask beyond the length of the sequence does not do padding. Returns : A Bio::SimpleAlign object Args : Positive integer for start column, positive integer for end column, optional string value use for the mask. Example: $aln2 = $aln->mask_columns(20,30,'?') Note : Masking must use a character that is not used for gaps or frameshifts. These can be adjusted using the relevant global variables, but be aware these may be (uncontrollably) modified elsewhere within BioPerl (see bug 2715) =cut sub mask_columns { #based on slice(), but did not include the Bio::Seq::Meta sections as I was not sure what it is doing my $self = shift; my $nonres = $Bio::LocatableSeq::GAP_SYMBOLS. $Bio::LocatableSeq::FRAMESHIFT_SYMBOLS; # coordinates are alignment-based, not sequence-based my ($start, $end, $mask_char) = @_; unless (defined $mask_char) { $mask_char = 'N' } $self->throw("Mask start has to be a positive integer and less than ". "alignment length, not [$start]") unless $start =~ /^\d+$/ && $start > 0 && $start <= $self->length; $self->throw("Mask end has to be a positive integer and less than ". "alignment length, not [$end]") unless $end =~ /^\d+$/ && $end > 0 && $end <= $self->length; $self->throw("Mask start [$start] has to be smaller than or equal to ". "end [$end]") unless $start <= $end; $self->throw("Mask character $mask_char has to be a single character ". "and not a gap or frameshift symbol") unless CORE::length($mask_char) == 1 && $mask_char !~ m{$nonres}; my $aln = $self->new; $aln->id($self->id); foreach my $seq ( $self->each_seq() ) { my $new_seq = Bio::LocatableSeq->new(-id => $seq->id, -alphabet => $seq->alphabet, -strand => $seq->strand, -verbose => $self->verbose); # convert from 1-based alignment coords! my $masked_string = substr($seq->seq, $start - 1, $end - $start + 1); $masked_string =~ s{[^$nonres]}{$mask_char}g; my $new_dna_string = substr($seq->seq,0,$start-1) . $masked_string . substr($seq->seq,$end); $new_seq->seq($new_dna_string); $aln->add_seq($new_seq); } # Preserve chosen mask character, it may be need later (like in 'slice') $aln->{_mask_char} = $mask_char; return $aln; } 1; BioPerl-1.007002/Bio/SimpleAnalysisI.pm000444000766000024 1704713155576320 17661 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SimpleAnalysisI # # Please direct questions and support issues to # # Cared for by Martin Senger # For copyright and disclaimer see below. # # POD documentation - main docs before the code =head1 NAME Bio::SimpleAnalysisI - A simple interface to any (local or remote) analysis tool =head1 SYNOPSIS This is an interface module - you do not instantiate it. Use other modules instead (those that implement this interface). =head1 DESCRIPTION This interface contains public methods for accessing and controlling local and remote analysis tools. It is meant to be used on the client side. The interface consists only of a necessary set of methods for synchronous invocation of analysis tools. For more complex set, including an asynchronous access, see interface C (which inherits from this one, by the way). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Martin Senger (martin.senger@gmail.com) =head1 COPYRIGHT Copyright (c) 2003, Martin Senger and EMBL-EBI. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 SEE ALSO =over =item * http://www.ebi.ac.uk/Tools/webservices/soaplab/guide =back =head1 APPENDIX This is actually the main documentation... If you try to call any of these methods directly on this C object you will get a I error message. =cut # Let the code begin... package Bio::SimpleAnalysisI; use strict; use base qw(Bio::Root::RootI); # ----------------------------------------------------------------------------- =head2 analysis_name Usage : $tool->analysis_name; Returns : a name of this analysis Args : none =cut sub analysis_name { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 analysis_spec Usage : $tool->analysis_spec; Returns : a hash reference describing this analysis Args : none The returned hash reference uses the following keys (not all of them always present, perhaps others present as well): C, C, C, C, C, C. =cut sub analysis_spec { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 input_spec Usage : $tool->input_spec; Returns : an array reference with hashes as elements Args : none The analysis input data are named, and can be also associated with a default value, with allowed values and with few other attributes. The names are important for feeding the analysis with the input data (the inputs are given to methods C and C as name/value pairs). =cut sub input_spec { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 result_spec Usage : $tool->result_spec; Returns : a hash reference with result names as keys and result types as values Args : none An analysis can produce several results, or the same result in several different formats. All such results are named and can be retrieved using their names by metod C. Here is an example of the result specification: $result_spec = { 'outseq' => 'String', 'report' => 'String', 'detailed_status' => 'String' }; =cut sub result_spec { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 run Usage : $tool->run ( ['sequence=@my.seq', 'osformat=embl'] ) Returns : $self Args : data and parameters for this execution (in various formats) Create a job, start it, and wait for its completion. The method is identical to the method C. Why there are two methods doing the same? Because it is expected that the sub-classes may implement them differently (an example is an interface C which uses method C for an asynchronous execution and method C for a synchronous one. Usually, after this call, you ask for results of the finished job: $analysis->run (...)->result; The input data and prameters for this execution can be specified in various ways: =over =item array reference The array has scalar elements of the form name = [[@]value] where C is the name of an input data or input parameter (see method C for finding what names are recognized by this analysis) and C is a value for this data/parameter. If C is missing a 1 is assumed (which is convenient for the boolean options). If C starts with C<@> it is treated as a local filename, and its contents is used as the data/parameter value. =item hash reference The same as with the array reference but now there is no need to use an equal sign. The hash keys are input names and hash values their data. The values can again start with a C<@> sign indicating a local filename. =back =cut sub run { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 wait_for Usage : $tool->wait_for ( { 'sequence' => '@my,file' } ) Returns : $self Args : the same as for method 'run' Create a job, start it and wait for its completion. The method is identical to the method C. See details in the C method. =cut sub wait_for { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 status Usage : $tool->status Returns : string describing a status of the execution Args : none It returns one of the following strings (and perhaps more if a server implementation extended possible job states): CREATED (not run yet) COMPLETED (run and finished normally) TERMINATED_BY_ERROR (run and finished with an error or a signal) =cut sub status { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 result Usage : $job->result (...) Returns : a result created by running an analysis Args : none (but an implementation may choose to add arguments for instructions how to process the raw result) The method returns a scalar representing a result of an executed job. If the job was terminated by an error the result may contain an error message instead of the real data (or both, depending on the implementation). =cut sub result { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- 1; __END__ BioPerl-1.007002/Bio/Species.pm000444000766000024 4621713155576320 16207 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Species # # Please direct questions and support issues to # # Cared for by James Gilbert # Reimplemented by Sendu Bala # Re-reimplemented by Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Species - Generic species object. =head1 SYNOPSIS $species = Bio::Species->new(-classification => [@classification]); # Can also pass classification # array to new as below $species->classification(qw( sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia Vertebrata Chordata Metazoa Eukaryota )); $genus = $species->genus(); $bi = $species->binomial(); # $bi is now "Homo sapiens" # For storing common name $species->common_name("human"); # For storing subspecies $species->sub_species("accountant"); =head1 DESCRIPTION B Provides a very simple object for storing phylogenetic information. The classification is stored in an array, which is a list of nodes in a phylogenetic tree. Access to getting and setting species and genus is provided, but not to any of the other node types (eg: "phylum", "class", "order", "family"). There's plenty of scope for making the model more sophisticated, if this is ever needed. A methods are also provided for storing common names, and subspecies. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR James Gilbert email B =head1 CONTRIBUTORS Sendu Bala, bix@sendu.me.uk Chris Fields, cjfields at bioperl dot org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' Let the code begin... package Bio::Species; use strict; use warnings; use Bio::DB::Taxonomy; use Bio::Tree::Tree; use Bio::Taxon; use base qw(Bio::Root::Root Bio::Tree::NodeI); =head2 new Title : new Usage : my $obj = Bio::Species->new(-classification => \@class) Function: Build a new Species object Returns : Bio::Species object Args : -ncbi_taxid => NCBI taxonomic ID (optional) -classification => arrayref of classification =cut sub new { my($class, @args) = @_; my $self = $class->SUPER::new(@args); # Bio::Species is now just a proxy object that just observes the NodeI # interface methods but delegates them to the proper classes (Bio::Taxon and # Bio::Tree::Tree). This will be surplanted by the much simpler # Bio::Taxon/Bio::DB::Taxonomy modules in the future. # Using a proxy allows proper GC w/o using weaken(). This just wraps the # older instances, which have no reciprocal refs (thus no circular refs). # This can then run proper cleanup $self->taxon(Bio::Taxon->new(@args)); my ($org, $sp, $var, $classification) = $self->_rearrange([qw(ORGANELLE SUB_SPECIES VARIANT CLASSIFICATION)], @args); if (defined $classification && ref($classification) eq "ARRAY" && @{$classification}) { $self->classification(@$classification); } else { $self->tree(Bio::Tree::Tree->new()); } defined $org && $self->organelle($org); defined $sp && $self->sub_species($sp); defined $var && $self->variant($var); return $self; } =head2 classification Title : classification Usage : $self->classification(@class_array); @classification = $self->classification(); Function: Get/set the lineage of this species. The array provided must be in the order ... ---> SPECIES, GENUS ---> KINGDOM ---> etc. Example : $obj->classification(qw( 'Homo sapiens' Homo Hominidae Catarrhini Primates Eutheria Mammalia Vertebrata Chordata Metazoa Eukaryota)); Returns : Classification array Args : Classification array OR A reference to the classification array. In the latter case if there is a second argument and it evaluates to true, names will not be validated. NB: in any case, names are never validated anyway. =cut sub classification { my ($self, @vals) = @_; my $taxon = $self->taxon; if (@vals) { if (ref($vals[0]) eq 'ARRAY') { @vals = @{$vals[0]}; } $vals[1] ||= ''; # make sure the lineage contains us as first or second element # (lineage may have subspecies, species, genus ...) my $name = $taxon->node_name; my ($genus, $species) = (quotemeta($vals[1]), quotemeta($vals[0])); if ($name && ($name !~ m{$species}i && $name !~ m{$genus}i) && $name !~ m{$genus $species}i) { if ($name =~ /^$genus $species\s*(.+)/) { # just assume the problem is someone tried to make a Bio::Species starting at subspecies #*** no idea if this is appropriate! just a possible fix related to bug 2092 $self->sub_species($1); $name = $taxon->node_name("$vals[1] $vals[0]"); } else { $self->warn("The supplied lineage does not start near '$name' (I was supplied '".join(" | ", @vals)."')"); } } # create a lineage for ourselves my $db = Bio::DB::Taxonomy->new(-source => 'list', -names => [reverse @vals]); unless ($taxon->scientific_name) { # assume we're supposed to be the leaf of the supplied lineage $self->taxon->scientific_name($vals[0]); } unless ($taxon->rank) { # and that we are rank species $taxon->rank('species'); } $taxon->db_handle($db); $self->tree(Bio::Tree::Tree->new(-node => $taxon)); } @vals = (); foreach my $node ($self->tree->get_lineage_nodes($taxon), $taxon) { unshift(@vals, $node->scientific_name || next); } return @vals; } =head2 ncbi_taxid Title : ncbi_taxid Usage : $obj->ncbi_taxid($newval) Function: Get/set the NCBI Taxon ID Returns : the NCBI Taxon ID as a string Args : newvalue to set or undef to unset (optional) =cut =head2 common_name Title : common_name Usage : $self->common_name( $common_name ); $common_name = $self->common_name(); Function: Get or set the common name of the species Example : $self->common_name('human') Returns : The common name in a string Args : String, which is the common name (optional) =cut =head2 division Title : division Usage : $obj->division($newval) Function: Genbank Division for a species Returns : value of division (a scalar) Args : value of division (a scalar) =cut =head2 species Title : species Usage : $self->species( $species ); $species = $self->species(); Function: Get or set the species name. Note that this is NOT genus and species -- use $self->binomial() for that. Example : $self->species('sapiens'); Returns : species name as string (NOT genus and species) Args : species name as string (NOT genus and species) =cut sub species { my ($self, $species) = @_; if ($species) { $self->{_species} = $species; } unless (defined $self->{_species}) { # work it out from our nodes my $species_taxon = $self->tree->find_node(-rank => 'species'); unless ($species_taxon) { # just assume we are rank species $species_taxon = $self->taxon; } $species = $species_taxon->scientific_name; # # munge it like the Bio::SeqIO modules used to do # (more or less copy/pasted from old Bio::SeqIO::genbank, hence comments # referring to 'ORGANISM' etc.) # my $root = $self->tree->get_root_node; unless ($root) { $self->tree(Bio::Tree::Tree->new(-node => $species_taxon)); $root = $self->tree->get_root_node; } my @spflds = split(' ', $species); if (@spflds > 1 && $root->node_name ne 'Viruses') { $species = undef; # does the next term start with uppercase? # yes: valid genus; no then unconventional # e.g. leaf litter basidiomycete sp. Collb2-39 my $genus; if ($spflds[0] =~ m/^[A-Z]/) { $genus = shift(@spflds); } else { undef $genus; } my $sub_species; if (@spflds) { while (my $fld = shift @spflds) { $species .= "$fld "; # does it have subspecies or varieties? last if ($fld =~ m/(sp\.|var\.)/); } chop $species; # last space $sub_species = join ' ',@spflds if(@spflds); } else { $species = 'sp.'; } # does ORGANISM start with any words which make its genus undefined? # these are in @unkn_genus # this in case species starts with uppercase so isn't caught above. # alter common name if required my $unconv = 0; # is it unconventional species name? my @unkn_genus = ('unknown','unclassified','uncultured','unidentified'); foreach (@unkn_genus) { if ($genus && $genus =~ m/$_/i) { $species = $genus . " " . $species; undef $genus; $unconv = 1; last; } elsif ($species =~ m/$_/i) { $unconv = 1; last; } } if (!$unconv && !$sub_species && $species =~ s/^(\w+)\s(\w+)$/$1/) { # need to extract subspecies from conventional ORGANISM format. # Will the 'word' in a two element species name # e.g. $species = 'thummi thummi' => $species='thummi' & # $sub_species='thummi' $sub_species = $2; } $self->genus($genus) if $genus; $self->sub_species($sub_species) if $sub_species; } $self->{_species} = $species; } return $self->{_species}; } =head2 genus Title : genus Usage : $self->genus( $genus ); $genus = $self->genus(); Function: Get or set the scientific genus name. Example : $self->genus('Homo'); Returns : Scientific genus name as string Args : Scientific genus name as string =cut sub genus { my ($self, $genus) = @_; # TODO: instead of caching the raw name, cache the actual node instance. if ($genus) { $self->{_genus} = $genus; } unless (defined $self->{_genus}) { my $genus_taxon = $self->tree->find_node(-rank => 'genus'); unless ($genus_taxon) { # just assume our ancestor is rank genus $genus_taxon = $self->taxon->ancestor; } $self->{_genus} = $genus_taxon->scientific_name if $genus_taxon; } return $self->{_genus}; } =head2 sub_species Title : sub_species Usage : $obj->sub_species($newval) Function: Get or set the scientific subspecies name. Returns : value of sub_species Args : newvalue (optional) =cut sub sub_species { my ($self, $sub) = @_; # TODO: instead of caching the raw name, cache the actual node instance. if (!defined $self->{'_sub_species'}) { my $ss_taxon = $self->tree->find_node(-rank => 'subspecies'); if ($ss_taxon) { if ($sub) { $ss_taxon->scientific_name($sub); # *** weakening ref to our root node in species() to solve a # memory leak means that we have a subspecies taxon to set # during the first call to species(), but it has vanished by # the time a user subsequently calls sub_species() to get the # value. So we 'cheat' and just store the subspecies name in # our self hash, instead of the tree. Is this a problem for # a Species object? Can't decide --sendu # This can now be changed to deal with this information on the # fly. For now, the caching remains, but maybe we should just # let these things deal with mutable data as needed? -- cjfields $self->{'_sub_species'} = $sub; } return $ss_taxon->scientific_name; } else { # should we create a node here to be added to the tree? } } # fall back to direct storage on self $self->{'_sub_species'} = $sub if $sub; return $self->{'_sub_species'}; } =head2 variant Title : variant Usage : $obj->variant($newval) Function: Get/set variant information for this species object (strain, isolate, etc). Example : Returns : value of variant (a scalar) Args : new value (a scalar or undef, optional) =cut sub variant{ my ($self, $var) = @_; # TODO: instead of caching the raw name, cache the actual node instance. if (!defined $self->{'_variant'}) { my $var_taxon = $self->tree->find_node(-rank => 'variant'); if ($var_taxon) { if ($var) { $var_taxon->scientific_name($var); } return $var_taxon->scientific_name; } else { # should we create a node here to be added to the tree? } } # fall back to direct storage on self $self->{'_variant'} = $var if $var; return $self->{'_variant'}; } =head2 binomial Title : binomial Usage : $binomial = $self->binomial(); $binomial = $self->binomial('FULL'); Function: Returns a string "Genus species", or "Genus species subspecies", if the first argument is 'FULL' (and the species has a subspecies). Args : Optionally the string 'FULL' to get the full name including the subspecies. Note : This is just munged from the taxon() name =cut sub binomial { my ($self, $full) = @_; my $rank = $self->taxon->rank || 'no rank'; my ($species, $genus) = ($self->species, $self->genus); unless (defined $species) { $species = 'sp.'; $self->warn("requested binomial but classification was not set"); } $genus = '' unless( defined $genus); $species =~ s/$genus\s+//; my $bi = "$genus $species"; if (defined($full) && $full =~ /full/i) { my $ssp = $self->sub_species; if ($ssp) { $ssp =~ s/$bi\s+//; $ssp =~ s/$species\s+//; $bi .= " $ssp"; } } return $bi; } =head2 validate_species_name Title : validate_species_name Usage : $result = $self->validate_species_name($string); Function: Validate the species portion of the binomial Args : string Notes : The string following the "genus name" in the NCBI binomial is so variable that it's not clear that this is a useful function. Consider the binomials "Simian 11 rotavirus (serotype 3 / strain SA11-Patton)", or "St. Thomas 3 rotavirus", straight from GenBank. This is particularly problematic in microbes and viruses. As such, this isn't actually used automatically by any Bio::Species method. =cut sub validate_species_name { my( $self, $string ) = @_; return 1 if $string eq "sp."; return 1 if $string =~ /strain/; return 1 if $string =~ /^[a-z][\w\s-]+$/i; $self->throw("Invalid species name '$string'"); } sub validate_name { return 1; } =head2 organelle Title : organelle Usage : $self->organelle( $organelle ); $organelle = $self->organelle(); Function: Get or set the organelle name Example : $self->organelle('Chloroplast') Returns : The organelle name in a string Args : String, which is the organelle name Note : TODO: We currently do not know where the organelle definition will eventually go. This is stored in the source seqfeature, though, so the information isn't lost. =cut sub organelle { my($self) = shift; return $self->{'_organelle'} = shift if @_; return $self->{'_organelle'}; } =head2 Delegation The following methods delegate to the internal Bio::Taxon instance. This is mainly to allow code continue using older methods, with the mind to migrate to using Bio::Taxon and related methods when this class is deprecated. =cut sub node_name {shift->taxon->node_name(@_)} sub scientific_name {shift->taxon->node_name(@_)} sub id {shift->taxon->id(@_)} sub object_id {shift->taxon->id(@_)} sub ncbi_taxid {shift->taxon->ncbi_taxid(@_)} sub rank {shift->taxon->rank(@_)} sub division {shift->taxon->division(@_)} sub common_names {shift->taxon->common_names(@_)} sub common_name {shift->taxon->common_names(@_)} sub genetic_code {shift->taxon->genetic_code(@_)} sub mitochondrial_genetic_code {shift->taxon->mitochondrial_genetic_code(@_)} sub create_date { shift->taxon->create_date(@_)} sub pub_date { shift->taxon->pub_date(@_)} sub update_date { shift->taxon->update_date(@_)} sub db_handle { shift->taxon->db_handle(@_)} sub parent_id { shift->taxon->parent_id(@_)} sub parent_taxon_id { shift->taxon->parent_id(@_)} sub version { shift->taxon->version(@_)} sub authority { shift->taxon->authority(@_)} sub namespace { shift->taxon->namespace(@_)} sub ancestor { shift->taxon->ancestor(@_)} sub get_Parent_Node { shift->taxon->get_Parent_Node(@_)} sub each_Descendent { shift->taxon->each_Descendent(@_)} sub get_Children_Nodes { shift->taxon->get_Children_Nodes(@_)} sub remove_Descendant { shift->taxon->remove_Descendant(@_)} sub name { shift->taxon->name(@_)} =head2 taxon Title : taxon Usage : $obj->taxon Function : retrieve the internal Bio::Taxon instance Returns : A Bio::Taxon. If one is not previously set, an instance is created lazily Args : Bio::Taxon (optional) =cut sub taxon { my ($self, $taxon) = @_; if (!$self->{taxon} || $taxon) { $taxon ||= Bio::Taxon->new(); $self->{taxon} = $taxon; } $self->{taxon}; } =head2 tree Title : tree Usage : $obj->tree Function : Returns a Bio::Tree::Tree object Returns : A Bio::Tree::Tree. If one is not previously set, an instance is created lazily Args : Bio::Tree::Tree (optional) =cut sub tree { my ($self, $tree) = @_; if (!$self->{tree} || $tree) { $tree ||= Bio::Tree::Tree->new(); delete $tree->{_root_cleanup_methods}; $self->{tree} = $tree; } $self->{tree}; } sub DESTROY { my $self = shift; $self->tree->cleanup_tree; delete $self->{tree}; $self->taxon->node_cleanup; } 1; BioPerl-1.007002/Bio/Taxon.pm000444000766000024 6005413155576320 15700 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Taxon # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala, based heavily on a module by Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Taxon - A node in a represented taxonomy =head1 SYNOPSIS use Bio::Taxon; # Typically you will get a Taxon from a Bio::DB::Taxonomy object # but here is how you initialize one my $taxon = Bio::Taxon->new(-name => $name, -id => $id, -rank => $rank, -division => $div); # Get one from a database my $dbh = Bio::DB::Taxonomy->new(-source => 'flatfile', -directory=> '/tmp', -nodesfile=> '/path/to/nodes.dmp', -namesfile=> '/path/to/names.dmp'); my $human = $dbh->get_taxon(-name => 'Homo sapiens'); $human = $dbh->get_taxon(-taxonid => '9606'); print "id is ", $human->id, "\n"; # 9606 print "rank is ", $human->rank, "\n"; # species print "scientific name is ", $human->scientific_name, "\n"; # Homo sapiens print "division is ", $human->division, "\n"; # Primates my $mouse = $dbh->get_taxon(-name => 'Mus musculus'); # You can quickly make your own lineages with the list database my @ranks = qw(superkingdom class genus species); my @h_lineage = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens'); my $list_dbh = Bio::DB::Taxonomy->new(-source => 'list', -names => \@h_lineage, -ranks => \@ranks); $human = $list_dbh->get_taxon(-name => 'Homo sapiens'); my @names = $human->common_names; # @names is empty $human->common_names('woman'); @names = $human->common_names; # @names contains woman # You can switch to another database when you need more information my $entrez_dbh = Bio::DB::Taxonomy->new(-source => 'entrez'); $human->db_handle($entrez_dbh); @names = $human->common_names; # @names contains woman, human, man # Since Bio::Taxon implements Bio::Tree::NodeI, we have access to those # methods (and can manually create our own taxa and taxonomy without the use # of any database) my $homo = $human->ancestor; # Though be careful with each_Descendent - unless you add_Descendent() # yourself, you won't get an answer because unlike for ancestor(), Bio::Taxon # does not ask the database for the answer. You can ask the database yourself # using the same method: ($human) = $homo->db_handle->each_Descendent($homo); # We can also take advantage of Bio::Tree::Tree* methods: # a) some methods are available with just an empty tree object use Bio::Tree::Tree; my $tree_functions = Bio::Tree::Tree->new(); my @lineage = $tree_functions->get_lineage_nodes($human); my $lineage = $tree_functions->get_lineage_string($human); my $lca = $tree_functions->get_lca($human, $mouse); # b) for other methods, create a tree using your Taxon object my $tree = Bio::Tree::Tree->new(-node => $human); my @taxa = $tree->get_nodes; $homo = $tree->find_node(-rank => 'genus'); # Normally you can't get the lca of a list-database derived Taxon and an # entrez or flatfile-derived one because the two different databases might # have different roots and different numbers of ranks between the root and the # taxa of interest. To solve this, make a tree of the Taxon with the more # detailed lineage and splice out all the taxa that won't be in the lineage of # your other Taxon: my $entrez_mouse = $entrez_dbh->get_taxon(-name => 'Mus musculus'); my $list_human = $list_dbh->get_taxon(-name => 'Homo sapiens'); my $mouse_tree = Bio::Tree::Tree->new(-node => $entrez_mouse); $mouse_tree->splice(-keep_rank => \@ranks); $lca = $mouse_tree->get_lca($entrez_mouse, $list_human); =head1 DESCRIPTION This is the next generation (for Bioperl) of representing Taxonomy information. Previously all information was managed by a single object called Bio::Species. This new implementation allows representation of the intermediate nodes not just the species nodes and can relate their connections. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 CONTRIBUTORS Jason Stajich, jason-at-bioperl-dot-org (original Bio::Taxonomy::Node) Juguang Xiao, juguang@tll.org.sg Gabriel Valiente, valiente@lsi.upc.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Taxon; use strict; use Scalar::Util qw(blessed); use Bio::DB::Taxonomy; use base qw(Bio::Tree::Node Bio::IdentifiableI); =head2 new Title : new Usage : my $obj = Bio::Taxonomy::Node->new(); Function: Builds a new Bio::Taxonomy::Node object Returns : an instance of Bio::Taxonomy::Node Args : -dbh => a reference to a Bio::DB::Taxonomy object [no default] -name => a string representing the taxon name (scientific name) -id => human readable id - typically NCBI taxid -ncbi_taxid => same as -id, but explicitly say that it is an NCBI taxid -rank => node rank (one of 'species', 'genus', etc) -common_names => array ref of all common names -division => 'Primates', 'Rodents', etc -genetic_code => genetic code table number -mito_genetic_code => mitochondrial genetic code table number -create_date => date created in database -update_date => date last updated in database -pub_date => date published in database =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($name, $id, $objid, $rank, $div, $dbh, $ncbitaxid, $commonname, $commonnames, $gcode, $mitocode, $createdate, $updatedate, $pubdate, $parent_id) = $self->_rearrange([qw(NAME ID OBJECT_ID RANK DIVISION DBH NCBI_TAXID COMMON_NAME COMMON_NAMES GENETIC_CODE MITO_GENETIC_CODE CREATE_DATE UPDATE_DATE PUB_DATE PARENT_ID)], @args); if (defined $id && (defined $ncbitaxid && $ncbitaxid ne $id || defined $objid && $objid ne $id)) { $self->warn("Only provide one of -id, -object_id or -ncbi_taxid, using $id\n"); } elsif(!defined $id) { $id = $objid || $ncbitaxid; } defined $id && $self->id($id); $self->{_ncbi_tax_id_provided} = 1 if $ncbitaxid; defined $rank && $self->rank($rank); defined $name && $self->node_name($name); my @common_names; if ($commonnames) { $self->throw("-common_names takes only an array reference") unless $commonnames && ref($commonnames) eq 'ARRAY'; @common_names = @{$commonnames}; } if ($commonname) { my %c_names = map { $_ => 1 } @common_names; unless (exists $c_names{$commonname}) { unshift(@common_names, $commonname); } } @common_names > 0 && $self->common_names(@common_names); defined $gcode && $self->genetic_code($gcode); defined $mitocode && $self->mitochondrial_genetic_code($mitocode); defined $createdate && $self->create_date($createdate); defined $updatedate && $self->update_date($updatedate); defined $pubdate && $self->pub_date($pubdate); defined $div && $self->division($div); defined $dbh && $self->db_handle($dbh); # Making an administrative decision to override this behavior, particularly # for optimization reasons (if it works to cache it up front, why not? # Please trust your implementations to get it right) # Original note: # deprecated and will issue a warning when method called, # eventually to be removed completely as option defined $parent_id && $self->parent_id($parent_id); # some things want to freeze/thaw Bio::Species objects, but # _root_cleanup_methods contains a CODE ref, delete it. delete $self->{_root_cleanup_methods}; return $self; } =head1 Bio::IdentifiableI interface Also see L =head2 version Title : version Usage : $taxon->version($newval) Returns : value of version (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub version { my $self = shift; return $self->{'version'} = shift if @_; return $self->{'version'}; } =head2 authority Title : authority Usage : $taxon->authority($newval) Returns : value of authority (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub authority { my $self = shift; return $self->{'authority'} = shift if @_; return $self->{'authority'}; } =head2 namespace Title : namespace Usage : $taxon->namespace($newval) Returns : value of namespace (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub namespace { my $self = shift; return $self->{'namespace'} = shift if @_; return $self->{'namespace'}; } =head1 Bio::Taxonomy::Node implementation =head2 db_handle Title : db_handle Usage : $taxon->db_handle($newval) Function: Get/Set Bio::DB::Taxonomy Handle Returns : value of db_handle (a scalar) (Bio::DB::Taxonomy object) Args : on set, new value (a scalar, optional) Bio::DB::Taxonomy object Also see L =cut sub db_handle { my $self = shift; if (@_) { my $db = shift; if (! ref($db) || ! $db->isa('Bio::DB::Taxonomy')) { $self->throw("Must provide a valid Bio::DB::Taxonomy object to db_handle()"); } if (!$self->{'db_handle'} || ($self->{'db_handle'} && $self->{'db_handle'} ne $db)) { my $new_self = $self->_get_similar_taxon_from_db($self, $db); $self->_merge_taxa($new_self) if $new_self; } # NB: The Bio::DB::Taxonomy modules access this data member directly # to avoid calling this method and going infinite $self->{'db_handle'} = $db; } return $self->{'db_handle'}; } =head2 rank Title : rank Usage : $taxon->rank($newval) Function: Get/set rank of this Taxon, 'species', 'genus', 'order', etc... Returns : value of rank (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub rank { my $self = shift; return $self->{'rank'} = shift if @_; return $self->{'rank'}; } =head2 id Title : id Usage : $taxon->id($newval) Function: Get/Set id (NCBI Taxonomy ID in most cases); object_id() and ncbi_taxid() are synonyms of this method. Returns : id (a scalar) Args : none to get, OR scalar to set =cut sub id { my $self = shift; return $self->SUPER::id(@_); } *object_id = \&id; =head2 ncbi_taxid Title : ncbi_taxid Usage : $taxon->ncbi_taxid($newval) Function: Get/Set the NCBI Taxonomy ID; This actually sets the id() but only returns an id when ncbi_taxid has been explictely set with this method. Returns : id (a scalar) Args : none to get, OR scalar to set =cut sub ncbi_taxid { my ($self, $id) = @_; if ($id) { $self->{_ncbi_tax_id_provided} = 1; return $self->SUPER::id($id); } if ($self->{_ncbi_tax_id_provided}) { return $self->SUPER::id; } return; } =head2 parent_id Title : parent_id Usage : $taxon->parent_id() Function: Get parent ID, (NCBI Taxonomy ID in most cases); parent_taxon_id() is a synonym of this method. Returns : value of parent_id (a scalar) Args : none =cut sub parent_id { my $self = shift; if (@_) { $self->{parent_id} = shift; } if (defined $self->{parent_id}) { return $self->{parent_id} } my $ancestor = $self->ancestor() || return; return $ancestor->id; } *parent_taxon_id = \&parent_id; =head2 trusted_parent_id Title : trusted_parent_id Usage : $taxon->trusted_parent_id() Function: If the parent_id is explicitly set, trust it Returns : simple boolean value (whether or not it has been set) Args : none Notes : Previously, the parent_id method was to be deprecated in favor of using ancestor(). However this removes one key optimization point, namely when an implementation has direct access to the taxon's parent ID when retrieving the information for the taxon ID. This method is in place so implementations can choose to (1) check whether the parent_id is set and (2) trust that the implementation (whether it is self or another implementation) set the parent_id correctly. =cut sub trusted_parent_id { return defined $_[0]->{parent_id}; } =head2 genetic_code Title : genetic_code Usage : $taxon->genetic_code($newval) Function: Get/set genetic code table Returns : value of genetic_code (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub genetic_code { my $self = shift; return $self->{'genetic_code'} = shift if @_; return $self->{'genetic_code'}; } =head2 mitochondrial_genetic_code Title : mitochondrial_genetic_code Usage : $taxon->mitochondrial_genetic_code($newval) Function: Get/set mitochondrial genetic code table Returns : value of mitochondrial_genetic_code (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub mitochondrial_genetic_code { my $self = shift; return $self->{'mitochondrial_genetic_code'} = shift if @_; return $self->{'mitochondrial_genetic_code'}; } =head2 create_date Title : create_date Usage : $taxon->create_date($newval) Function: Get/Set Date this node was created (in the database) Returns : value of create_date (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub create_date { my $self = shift; return $self->{'create_date'} = shift if @_; return $self->{'create_date'}; } =head2 update_date Title : update_date Usage : $taxon->update_date($newval) Function: Get/Set Date this node was updated (in the database) Returns : value of update_date (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub update_date { my $self = shift; return $self->{'update_date'} = shift if @_; return $self->{'update_date'}; } =head2 pub_date Title : pub_date Usage : $taxon->pub_date($newval) Function: Get/Set Date this node was published (in the database) Returns : value of pub_date (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub pub_date { my $self = shift; return $self->{'pub_date'} = shift if @_; return $self->{'pub_date'}; } =head2 ancestor Title : ancestor Usage : my $ancestor_taxon = $taxon->ancestor() Function: Retrieve the ancestor taxon. Normally the database is asked what the ancestor is. If you manually set the ancestor (or you make a Bio::Tree::Tree with this object as an argument to new()), the database (if any) will not be used for the purposes of this method. To restore normal database behaviour, call ancestor(undef) (which would remove this object from the tree), or request this taxon again as a new Taxon object from the database. Returns : Bio::Taxon Args : none =cut sub ancestor { my $self = shift; my $ancestor = $self->SUPER::ancestor(@_); if ($ancestor) { return $ancestor; } my $dbh = $self->db_handle; #*** could avoid the db lookup if we knew our current id was definitely # information from the db... my $definitely_from_dbh = $self->_get_similar_taxon_from_db($self); return $dbh->ancestor($definitely_from_dbh); } =head2 get_Parent_Node Title : get_Parent_Node Function: Synonym of ancestor() Status : deprecated =cut sub get_Parent_Node { my $self = shift; $self->warn("get_Parent_Node is deprecated, use ancestor() instead"); return $self->ancestor(@_); } =head2 each_Descendent Title : each_Descendent Usage : my @taxa = $taxon->each_Descendent(); Function: Get all the descendents for this Taxon (but not their descendents, ie. not a recursive fetchall). get_Children_Nodes() is a synonym of this method. Note that this method never asks the database for the descendents; it will only return objects you have manually set with add_Descendent(), or where this was done for you by making a Bio::Tree::Tree with this object as an argument to new(). To get the database descendents use $taxon->db_handle->each_Descendent($taxon). Returns : Array of Bio::Taxon objects Args : optionally, when you have set your own descendents, the string "height", "creation", "alpha", "revalpha", or coderef to be used to sort the order of children nodes. =cut # implemented by Bio::Tree::Node =head2 get_Children_Nodes Title : get_Children_Nodes Function: Synonym of each_Descendent() Status : deprecated =cut sub get_Children_Nodes { my $self = shift; $self->warn("get_Children_Nodes is deprecated, use each_Descendent() instead"); return $self->each_Descendent(@_); } =head2 name Title: name Usage: $taxon->name('scientific', 'Homo sapiens'); $taxon->name('common', 'human', 'man'); my @names = @{$taxon->name('common')}; Function: Get/set the names. node_name(), scientific_name() and common_names() are shorthands to name('scientific'), name('scientific') and name('common') respectively. Returns: names (a array reference) Args: Arg1 => the name_class. You can assign any text, but the words 'scientific' and 'common' have the special meaning, as scientific name and common name, respectively. 'scientific' and 'division' are treated specially, allowing only the first value in the Arg2 list to be set. Arg2 ... => list of names =cut sub name { my ($self, $name_class, @names) = @_; $self->throw('No name class specified') unless defined $name_class; if (@names) { if ($name_class =~ /scientific|division/i) { delete $self->{'_names_hash'}->{$name_class}; @names = (shift(@names)); } push @{$self->{'_names_hash'}->{$name_class}}, @names; } return $self->{'_names_hash'}->{$name_class} || return; } =head2 node_name Title : node_name Usage : $taxon->node_name($newval) Function: Get/set the name of this taxon (node), typically the scientific name of the taxon, eg. 'Primate' or 'Homo'; scientific_name() is a synonym of this method. Returns : value of node_name (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub node_name { my $self = shift; my @v = @{$self->name('scientific', @_) || []}; return pop @v; } *scientific_name = \&node_name; =head2 common_names Title : common_names Usage : $taxon->common_names($newval) Function: Get/add the other names of this taxon, typically the genbank common name and others, eg. 'Human' and 'man'. common_name() is a synonym of this method. Returns : array of names in list context, one of those names in scalar context Args : on add, new list of names (scalars, optional) =cut sub common_names { my $self = shift; my @v = @{$self->name('common', @_) || []}; return ( wantarray ) ? @v : pop @v; } *common_name = \&common_names; =head2 division Title : division Usage : $taxon->division($newval) Function: Get/set the division this taxon belongs to, eg. 'Primates' or 'Bacteria'. Returns : value of division (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub division { my $self = shift; my @v = @{$self->name('division',@_) || []}; return pop @v; } # get a node from the database that is like the supplied node sub _get_similar_taxon_from_db { #*** not really happy with this having to be called so much; there must be # a better way... my ($self, $taxon, $db) = @_; $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa("Bio::Taxon"); ($self->id || $self->node_name) || return; $db ||= $self->db_handle || return; if (!blessed($db) || !$db->isa('Bio::DB::Taxonomy')) { $self->throw("DB handle is not a Bio::DB::Taxonomy: got $db in node ".$self->node_name) } my $db_taxon = $db->get_taxon(-taxonid => $taxon->id) if $taxon->id; unless ($db_taxon) { my @try_ids = $db->get_taxonids($taxon->node_name) if $taxon->node_name; my $own_rank = $taxon->rank || 'no rank'; foreach my $try_id (@try_ids) { my $try = $db->get_taxon(-taxonid => $try_id); my $try_rank = $try->rank || 'no rank'; if ($own_rank eq 'no rank' || $try_rank eq 'no rank' || $own_rank eq $try_rank) { $db_taxon = $try; last; } } } return $db_taxon; } # merge data from supplied Taxon into self sub _merge_taxa { my ($self, $taxon) = @_; $self->throw("Must supply a Bio::Taxon object") unless ref($taxon) && $taxon->isa('Bio::Taxon'); return if ($taxon eq $self); foreach my $attrib (qw(scientific_name version authority namespace genetic_code mitochondrial_genetic_code create_date update_date pub_date division id)) { my $own = $self->$attrib(); my $his = $taxon->$attrib(); if (!$own && $his) { $self->$attrib($his); } } my $own = $self->rank || 'no rank'; my $his = $taxon->rank || 'no rank'; if ($own eq 'no rank' && $his ne 'no rank') { $self->rank($his); } my %own_cnames = map { $_ => 1 } $self->common_names; my %his_cnames = map { $_ => 1 } $taxon->common_names; foreach (keys %his_cnames) { unless (exists $own_cnames{$_}) { $self->common_names($_); } } #*** haven't merged the other things in names() hash, could do above much easier with direct access to object data } =head2 remove_Descendent Title : remove_Descendent Usage : $node->remove_Descedent($node_foo); Function: Removes a specific node from being a Descendent of this node Returns : nothing Args : An array of Bio::Node::NodeI objects which have been previously passed to the add_Descendent call of this object. =cut sub remove_Descendent { # need to override this method from Bio::Tree::Node since it casually # throws away nodes if they don't branch my ($self,@nodes) = @_; my $c= 0; foreach my $n ( @nodes ) { if ($self->{'_desc'}->{$n->internal_id}) { $self->{_removing_descendent} = 1; $n->ancestor(undef); $self->{_removing_descendent} = 0; $self->{'_desc'}->{$n->internal_id}->ancestor(undef); delete $self->{'_desc'}->{$n->internal_id}; $c++; } } return $c; } 1; BioPerl-1.007002/Bio/Taxonomy.pm000444000766000024 2707413155576320 16432 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Taxonomy # # Please direct questions and support issues to # # Cared for by Juguang Xiao # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Taxonomy - representing Taxonomy. =head1 SYNOPSIS # NB: This module is deprecated. Use Bio::Taxon in combination with # Bio::Tree::Tree methods instead. use Bio::Taxonomy; # CREATION: You can either create an instance by assigning it, # or fetch it through factory. # Create the nodes first. See Bio::Taxonomy::Node for details. my $node_species_sapiens = Bio::Taxonomy::Node->new( -object_id => 9606, # or -ncbi_taxid. Requird tag -names => { 'scientific' => ['sapiens'], 'common_name' => ['human'] }, -rank => 'species' # Required tag ); my $node_genus_Homo = Bio::Taxonomy::Node->new( -object_id => 9605, -names => { 'scientific' => ['Homo'] }, -rank => 'genus' ); my $node_class_Mammalia = Bio::Taxonomy::Node->new( -object_id => 40674, -names => { 'scientific' => ['Mammalia'], 'common' => ['mammals'] }, -rank => 'class' ); my $taxonomy = Bio::Taxonomy->new; $taxonomy->add_node($node_class_Mammalia); $taxonomy->add_node($node_species_sapiens); $taxonomy->add_node($node_genus_Homo); # OR you can fetch it through a factory implementing # Bio::Taxonomy::FactoryI my $factory; my $taxonomy = $factory->fetch_by_ncbi_taxid(40674); # USAGE # In this case, binomial returns a defined value. my $binomial = $taxonomy->binomial; # 'common_names' refers to the lowest-rank node's common names, in # array. my @common_names = $taxonomy->common_names; # 'get_node', will return undef if the rank is no defined in # taxonomy object. It will throw error if the rank string is not # defined, say 'species lah'. my $node = $taxonomy->get_node('class'); my @nodes = $taxonomy->get_all_nodes; # Also, you can search for parent and children nodes, if taxonomy # comes with factory. my $parent_taxonomy = $taxonomy->get_parent =head1 DESCRIPTION Bio::Taxonomy object represents any rank-level in taxonomy system, rather than Bio::Species which is able to represent only species-level. There are two ways to create Taxonomy object, e.g. 1) instantiate an object and assign all nodes on your own code; and 2) fetch an object by factory. =head2 Creation by instantiation The abstraction of Taxonomy is actually a hash in data structure term. The keys of the hash are the rank names, such as 'genus' and 'species', and the values are the instances of Bio::Taxonomy::Node. =head2 Creation by Factory fetching NCBI Taxonomy system is well accepted as the standard. The Taxonomy Factories in bioperl access this system, through HTTP to NCBI Entrez, dump file, and advanced biosql database. Bio::Taxonomy::FactoryI defines all methods that all implementations must obey. $factory-Efetch is a general method to fetch Taxonomy by either NCBI taxid or any types of names. $factory-Efetch_parent($taxonomy), returns a Taxonomy that is one-step higher rank of the taxonomy specified as argument. $factory-Efetch_children($taxonomy), reports an array of Taxonomy those are one-step lower rank of the taxonomy specified as the argument. =head2 Usage of Taxonomy object ## =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 CONTACT Juguang Xiao, juguang@tll.org.sg =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # code begins... package Bio::Taxonomy; use strict; use base qw(Bio::Root::Root); =head2 new Title : new Usage : my $obj = Bio::Taxonomy->new(); Function: Builds a new Bio::Taxonomy object Returns : Bio::Taxonomy Args : -method -> method used to decide classification (none|trust|lookup) -ranks -> what ranks are there =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->warn("Bio::Taxonomy is deprecated. Use Bio::Taxon in combination with Bio::Tree::Tree instead."); $self->{'_method'}='none'; $self->{'_ranks'}=[]; $self->{'_rank_hash'}={}; $self->{_hierarchy} = {}; # used to store the nodes, with ranks as keys. my ($method,$ranks,$order) = $self->_rearrange([qw(METHOD RANKS ORDER)], @args); if ($method) { $self->method($method); } if (defined $ranks && (ref($ranks) eq "ARRAY") ) { $self->ranks(@$ranks); } else { # default ranks # I think these are in the right order, but not sure: # some parvorder|suborder and varietas|subspecies seem # to be at the same level - any taxonomists? # I don't expect that these will actually be used except as a way # to find what ranks there are in taxonomic use $self->ranks(('root', 'superkingdom', 'kingdom', 'superphylum', 'phylum', 'subphylum', 'superclass', 'class', 'subclass', 'infraclass', 'superorder', 'order', 'suborder', 'parvorder', 'infraorder', 'superfamily', 'family', 'subfamily', 'tribe', 'subtribe', 'genus', 'subgenus', 'species group', 'species subgroup', 'species', 'subspecies', 'varietas', 'forma', 'no rank')); } return $self; } =head2 method Title : method Usage : $obj = taxonomy->method($method); Function: set or return the method used to decide classification Returns : $obj Args : $obj =cut sub method { my ($self,$value) = @_; if (defined $value && $value=~/none|trust|lookup/) { $self->{'_method'} = $value; } return $self->{'_method'}; } =head2 classify Title : classify Usage : @obj[][0-1] = taxonomy->classify($species); Function: return a ranked classification Returns : @obj of taxa and ranks as word pairs separated by "@" Args : Bio::Species object =cut sub classify { my ($self,$value) = @_; my @ranks; if (! $value->isa('Bio::Species') ) { $self->throw("Trying to classify $value which is not a Bio::Species object"); } my @classes=reverse($value->classification); if ($self->method eq 'none') { for (my $i=0; $i < @classes-2; $i++) { ($ranks[$i][0],$ranks[$i][1])=($classes[$i],'no rank'); } push @ranks,[$classes[-2],'genus']; push @ranks,[$value->binomial,'species']; } elsif ($self->method eq 'trust') { if (scalar(@classes)==scalar($self->ranks)) { for (my $i=0; $i < @classes; $i++) { if ($self->rank_of_number($i) eq 'species') { push @ranks,[$value->binomial,$self->rank_of_number($i)]; } else { push @ranks,[$classes[$i],$self->rank_of_number($i)]; } } } else { $self->throw("Species object and taxonomy object cannot be reconciled"); } } elsif ($self->method eq 'lookup') { # this will lookup a DB for the rank of a taxon name # I imagine that some kind of Bio::DB class will be need to # be given to the taxonomy object to act as an DB interface # (I'm not sure how useful this is though - if you have a DB of # taxonomy - why would you be doing things this way?) $self->throw_not_implemented(); } return @ranks; } =head2 level_of_rank Title : level_of_rank Usage : $obj = taxonomy->level_of_rank($obj); Function: returns the level of a rank name Returns : $obj Args : $obj =cut sub level_of { my ($self,$value) = @_; return $self->{'_rank_hash'}{$value}; } =head2 rank_of_number Title : rank_of_number Usage : $obj = taxonomy->rank_of_number($obj); Function: returns the rank name of a rank level Returns : $obj Args : $obj =cut sub rank_of_number { my ($self,$value) = @_; return ${$self->{'_ranks'}}[$value]; } =head2 ranks Title : ranks Usage : @obj = taxonomy->ranks(@obj); Function: set or return all ranks Returns : @obj Args : @obj =cut sub ranks { my ($self,@value) = @_; # currently this makes no uniqueness sanity check (this should be done) # I am think that adding a way of converting multiple 'no rank' ranks # to unique 'no rank #' ranks so that the level of a 'no rank' is # abstracted way from the user - I'm not sure of the value of this if (@value) { $self->{'_ranks'}=\@value; } for (my $i=0; $i <= @{$self->{'_ranks'}}-1; $i++) { $self->{'_rank_hash'}{$self->{'_ranks'}[$i]}=$i unless $self->{'_ranks'}[$i] eq 'no rank'; } return @{$self->{'_ranks'}}; } =head2 add_node Title: add_node Usage: $obj->add_node($node[, $node2, ...]); Function: add one or more Bio::Taxonomy::Node objects Returns: None Args: any number of Bio::Taxonomy::Node(s) =cut sub add_node { my ($self, @nodes) = @_; foreach(@nodes){ $self->throw("A Bio::Taxonomy::Node object needed") unless($_->isa('Bio::Taxonomy::Node')); my ($node, $rank) = ($_, $_->rank); if(exists $self->{_hierarchy}->{$rank}){ # $self->throw("$rank has been defined"); # print STDERR "RANK:$rank\n"; # return; } $self->{_hierarchy}->{$rank} = $node; } } =head2 binomial Title : binomial Usage : my $val = $obj->binomial; Function: returns the binomial name if this taxonomy reaches species level Returns : the binomial name OR undef if taxonmy does not reach species level Args : [No arguments] =cut sub binomial { my $self = shift; return $self->get_node('species')->scientific_name; my $genus = $self->get_node('genus'); my $species = $self->get_node('species'); return ($species && $genus) ? "$species $genus" : undef; } =head2 get_node Title : get_node Usage : $node = $taxonomy->get_node('species'); Function: get a Bio::Taxonomy::Node object according to rank name Returns : a Bio::Taxonomy::Node object or undef if null Args : a valid rank name =cut sub get_node { my ($self, $rank) = @_; unless(grep /$rank/, keys %{$self->{_hierarchy}}){ $self->throw("'$rank' is not in the rank list"); } return (exists $self->{_hierarchy}->{$rank})? $self->{_hierarchy}->{$rank} : undef; } =head2 classification Title : classification Usage : @names = $taxonomy->classification; Function: get the classification names of one taxonomy Returns : array of names Args : [No arguments] =cut sub classification { my $self = shift; my %rank_hash = %{$self->{_rank_hash}}; my %hierarchy = %{$self->{_hierarchy}}; my @ordered_nodes = sort { ($rank_hash{$a} <=> $rank_hash{$b}) } keys %hierarchy; return map {$hierarchy{$_}->scientific_name} @ordered_nodes; } 1; BioPerl-1.007002/Bio/TreeIO.pm000444000766000024 2032713155576320 15735 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::TreeIO # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::TreeIO - Parser for Tree files =head1 SYNOPSIS { use Bio::TreeIO; my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'globin.dnd'); while( my $tree = $treeio->next_tree ) { print "Tree is ", $tree->number_nodes, "\n"; } } =head1 DESCRIPTION This is the driver module for Tree reading from data streams and flatfiles. This is intended to be able to create Bio::Tree::TreeI objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 CONTRIBUTORS Allen Day Eallenday@ucla.eduE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::TreeIO; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::TreeIO::TreeEventBuilder; use base qw(Bio::Root::Root Bio::Root::IO Bio::Event::EventGeneratorI Bio::Factory::TreeFactoryI); =head2 new Title : new Usage : my $obj = Bio::TreeIO->new(); Function: Builds a new Bio::TreeIO object Returns : Bio::TreeIO Args : a hash. useful keys: -format : Specify the format of the file. Supported formats: newick Newick tree format nexus Nexus tree format nhx NHX tree format svggraph SVG graphical representation of tree tabtree ASCII text representation of tree lintree lintree output format =cut sub new { my($caller,@args) = @_; my $class = ref($caller) || $caller; # or do we want to call SUPER on an object if $caller is an # object?n my $obj; if( $class =~ /Bio::TreeIO::(\S+)/ ) { $obj = $class->SUPER::new(@args); $obj->_initialize(@args); } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $format = $param{'-format'} || $class->_guess_format( $param{'-file'} || $ARGV[0] ) || 'newick'; $format = "\L$format"; # normalize capitalization to lower case # normalize capitalization return undef unless( $class->_load_format_module($format) ); $obj = "Bio::TreeIO::$format"->new(@args); } return $obj; } =head2 format Title : format Usage : $format = $obj->format() Function: Get the tree format Returns : tree format Args : none =cut # format() method inherited from Bio::Root::IO =head2 next_tree Title : next_tree Usage : my $tree = $treeio->next_tree; Function: Gets the next tree off the stream Returns : Bio::Tree::TreeI or undef if no more trees Args : none =cut sub next_tree{ my ($self) = @_; $self->throw("Cannot call method next_tree on Bio::TreeIO object must use a subclass"); } =head2 write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Writes a tree onto the stream Returns : none Args : Bio::Tree::TreeI =cut sub write_tree{ my ($self,$tree) = @_; $self->throw("Cannot call method write_tree on Bio::TreeIO object must use a subclass"); } =head2 attach_EventHandler Title : attach_EventHandler Usage : $parser->attatch_EventHandler($handler) Function: Adds an event handler to listen for events Returns : none Args : Bio::Event::EventHandlerI =cut sub attach_EventHandler{ my ($self,$handler) = @_; return if( ! $handler ); if( ! $handler->isa('Bio::Event::EventHandlerI') ) { $self->warn("Ignoring request to attach handler ".ref($handler). ' because it is not a Bio::Event::EventHandlerI'); } $self->{'_handler'} = $handler; return; } =head2 _eventHandler Title : _eventHandler Usage : private Function: Get the EventHandler Returns : Bio::Event::EventHandlerI Args : none =cut sub _eventHandler{ my ($self) = @_; return $self->{'_handler'}; } sub _initialize { my($self, @args) = @_; $self->{'_handler'} = undef; $self->get_params; # Initialize the default parameters. my ($nen,$ini) = $self->_rearrange ([qw(NEWLINE_EACH_NODE INTERNAL_NODE_ID)],@args); $self->set_param('newline_each_node',$nen); $self->set_param('internal_node_id',$ini); $self->attach_EventHandler(Bio::TreeIO::TreeEventBuilder->new (-verbose => $self->verbose(), @args)); $self->_initialize_io(@args); #$self->debug_params; } =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL TreeIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($self,$format) = @_; my $module = "Bio::TreeIO::" . $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <get_params->{$param} = $value; } return $self->get_params->{$param}; } sub set_param { my $self = shift; my $param = shift; my $value = shift; #print STDERR "[$param] -> [undef]\n" if (!defined $value); return unless (defined $value); #print STDERR "[$param] -> [$value]\n"; $self->get_params->{$param} = $value; return $self->param($param); } sub params { my $self = shift; return $self->get_params; } sub get_params { my $self = shift; if (!defined $self->{_params}) { $self->{_params} = $self->get_default_params; } return $self->{_params}; } sub set_params { my $self = shift; my $params = shift; # Apply all the passed parameters to our internal parm hashref. my $cur_params = $self->get_params; $self->{_params} = { %$cur_params, %$params }; return $self->get_params; } sub get_default_params { my $self = shift; return {}; } sub debug_params { my $self = shift; my $params = $self->get_params; print STDERR "{\n"; foreach my $param (keys %$params) { my $value = $params->{$param}; print STDERR " [$param] -> [$value]\n"; } print STDERR "}\n"; } =head2 _guess_format Title : _guess_format Usage : $obj->_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args : =cut sub _guess_format { my $class = shift; return unless $_ = shift; return 'newick' if /\.(dnd|newick|nh)$/i; return 'nhx' if /\.(nhx)$/i; return 'phyloxml' if /\.(xml)$/i; return 'svggraph' if /\.svg$/i; return 'lintree' if( /\.(lin|lintree)$/i ); } sub DESTROY { my $self = shift; $self->close(); } sub TIEHANDLE { my $class = shift; return bless {'treeio' => shift},$class; } sub READLINE { my $self = shift; return $self->{'treeio'}->next_tree() || undef unless wantarray; my (@list,$obj); push @list,$obj while $obj = $self->{'treeio'}->next_tree(); return @list; } sub PRINT { my $self = shift; $self->{'treeio'}->write_tree(@_); } 1; BioPerl-1.007002/Bio/UpdateableSeqI.pm000444000766000024 662413155576320 17422 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::UpdateableSeqI # # Please direct questions and support issues to # # Cared for by David Block # # Copyright David Block # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates =head1 SYNOPSIS See Bio::SeqI for most of the documentation. See the documentation of the methods for further details. =head1 DESCRIPTION Bio::UpdateableSeqI is an interface for Sequence objects which are expected to allow users to perform basic editing functions (update/delete) on their component SeqFeatures. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - David Block Email dblock@gene.pbi.nrc.ca =head1 CONTRIBUTORS Ewan Birney forced me to this... =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::UpdateableSeqI; use strict; use Carp; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::SeqI); =head2 delete_feature Title : delete_feature Usage : my $orphanlist=$self->delete_feature($feature,$transcript,$gene); Function: deletes the specified $feature from the given transcript, if $transcript is sent and exists and $feature is a feature of $transcript, or from $gene if the $feature is a feature of $gene, or from $self if $transcript and $gene are not sent. Keeps track of the features of the $gene object that may be left as orphans and returns them as a listref. Example : I want to delete transcript 'abc' of gene 'def', with three exons, leaving only transcript 'ghi' with two exons. This will leave exons 1 and 3 part of 'ghi', but exon 2 will become an orphan. my $orphanlist=$seq->delete_feature($transcript{'abc'},undef,$gene{'def'}); $orphanlist is a reference to a list containing $exon{'2'}; Returns : a listref of orphaned features after the deletion of $feature (optional) Args : $feature - the feature to be deleted $transcript - the transcript containing the $feature, so that a $feature can be removed from only one transcript when there are multiple transcripts in a gene. $gene - the gene containing the $transcript and/or the $feature =cut sub delete_feature{ my ($self,$feature,$transcript,$gene) = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/WebAgent.pm000444000766000024 1204313155576320 16276 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::WebAgent # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho, heikki-at-bioperl-dot-org # For copyright and disclaimer see below. # # POD documentation - main docs before the code =head1 NAME Bio::WebAgent - A base class for Web (any protocol) access =head1 SYNOPSIS # This is a abstract superclass for bioperl modules accessing web # resources - normally you do not instantiate it but one of its # subclasess. =head1 DESCRIPTION This abstract superclass is a subclass of L which allows protocol independent access of remote locations over the Net. It takes care of error handling, proxies and various net protocols. BioPerl classes accessing the net should inherit from it. For details, see L. The interface is still evolving. For now, two public methods have been copied from Bio::DB::WebDBSeqI: delay() and delay_policy. These are used to prevent overwhelming the server by rapidly repeated . Ideally there should be a common abstract superclass with these. See L. =head1 SEE ALSO L, L, =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 COPYRIGHT Copyright (c) 2003, Heikki Lehvaslaiho and EMBL-EBI. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::WebAgent; use vars qw($LAST_INVOCATION_TIME); use strict; use base qw(LWP::UserAgent Bio::Root::Root); sub new { my $class = shift; # We make env_proxy the default here, but it can be # over-ridden by $self->env_proxy later, # or by new(env_proxy=>0) at constructor time my $self = $class->SUPER::new(env_proxy => 1); while( @_ ) { my $key = shift; $key =~ s/^-//; my $value = shift; $self->can($key) || next; $self->$key($value); } return $self; # success - we hope! } # ----------------------------------------------------------------------------- =head2 url Usage : $agent->url Returns : URL to reach out to Net Args : string =cut sub url { my ($self,$value) = @_; if( defined $value) { $self->{'_url'} = $value; } return $self->{'_url'}; } =head2 delay Title : delay Usage : $secs = $self->delay([$secs]) Function: get/set number of seconds to delay between fetches Returns : number of seconds to delay Args : new value NOTE: the default is to use the value specified by delay_policy(). This can be overridden by calling this method, or by passing the -delay argument to new(). =cut sub delay { my ($self, $value) = @_; if ($value) { $self->throw("Need a positive integer, not [$value]") unless $value >= 0; $self->{'_delay'} = int $value; } return $self->{'_delay'} || $self->delay_policy; } =head2 delay_policy Title : delay_policy Usage : $secs = $self->delay_policy Function: return number of seconds to delay between calls to remote db Returns : number of seconds to delay Args : none NOTE: The default delay policy is 3s. Override in subclasses to implement other delays. The timer has only second resolution, so the delay will actually be +/- 1s. =cut sub delay_policy { my $self = shift; return 3; } =head2 sleep Title : sleep Usage : $self->sleep Function: sleep for a number of seconds indicated by the delay policy Returns : none Args : none NOTE: This method keeps track of the last time it was called and only imposes a sleep if it was called more recently than the delay_policy() allows. =cut sub sleep { my $self = shift; $LAST_INVOCATION_TIME ||= 0; if (time - $LAST_INVOCATION_TIME < $self->delay) { my $delay = $self->delay - (time - $LAST_INVOCATION_TIME); $self->debug("sleeping for $delay seconds\n"); sleep $delay; } $LAST_INVOCATION_TIME = time; } 1; __END__ BioPerl-1.007002/Bio/Align000755000766000024 013155576320 15121 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Align/AlignI.pm000444000766000024 4706413155576320 17012 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Align::AlignI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Align::AlignI - An interface for describing sequence alignments. =head1 SYNOPSIS # get a Bio::Align::AlignI somehow - typically using Bio::AlignIO system # some descriptors print $aln->length, "\n"; print $aln->num_residues, "\n"; print $aln->is_flush, "\n"; print $aln->num_sequences, "\n"; print $aln->percentage_identity, "\n"; print $aln->consensus_string(50), "\n"; # find the position in the alignment for a sequence location $pos = $aln->column_from_residue_number('1433_LYCES', 14); # = 6; # extract sequences and check values for the alignment column $pos foreach $seq ($aln->each_seq) { $res = $seq->subseq($pos, $pos); $count{$res}++; } foreach $res (keys %count) { printf "Res: %s Count: %2d\n", $res, $count{$res}; } =head1 DESCRIPTION This interface describes the basis for alignment objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 CONTRIBUTORS Ewan Birney, birney@ebi.ac.uk Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Align::AlignI; use strict; use base qw(Bio::Root::RootI); =head1 Modifier methods These methods modify the MSE by adding, removing or shuffling complete sequences. =head2 add_seq Title : add_seq Usage : $myalign->add_seq($newseq); Function : Adds another sequence to the alignment. *Does not* align it - just adds it to the hashes. Returns : None Argument : a Bio::LocatableSeq object order (optional) See L for more information. =cut sub add_seq { my ($self) = @_; $self->throw_not_implemented(); } =head2 remove_seq Title : remove_seq Usage : $aln->remove_seq($seq); Function : Removes a single sequence from an alignment Returns : Argument : a Bio::LocatableSeq object =cut sub remove_seq { my ($self) = @_; $self->throw_not_implemented(); } =head2 purge Title : purge Usage : $aln->purge(0.7); Function: Removes sequences above whatever %id. This function will grind on large alignments. Beware! (perhaps not ideally implemented) Example : Returns : An array of the removed sequences Argument: =cut sub purge { my ($self) = @_; $self->throw_not_implemented(); } =head2 sort_alphabetically Title : sort_alphabetically Usage : $ali->sort_alphabetically Function : Changes the order of the alignment to alphabetical on name followed by numerical by number. Returns : an array Argument : =cut sub sort_alphabetically { my ($self) = @_; $self->throw_not_implemented(); } =head1 Sequence selection methods Methods returning one or more sequences objects. =head2 each_seq Title : each_seq Usage : foreach $seq ( $align->each_seq() ) Function : Gets an array of Seq objects from the alignment Returns : an array Argument : =cut sub each_seq { my ($self) = @_; $self->throw_not_implemented(); } =head2 each_alphabetically Title : each_alphabetically Usage : foreach $seq ( $ali->each_alphabetically() ) Function : Returns an array of sequence object sorted alphabetically by name and then by start point. Does not change the order of the alignment Returns : Argument : =cut sub each_alphabetically { my($self) = @_; $self->throw_not_implemented(); } =head2 each_seq_with_id Title : each_seq_with_id Usage : foreach $seq ( $align->each_seq_with_id() ) Function : Gets an array of Seq objects from the alignment, the contents being those sequences with the given name (there may be more than one) Returns : an array Argument : a seq name =cut sub each_seq_with_id { my ($self) = @_; $self->throw_not_implemented(); } =head2 get_seq_by_pos Title : get_seq_by_pos Usage : $seq = $aln->get_seq_by_pos(3) # third sequence from the alignment Function : Gets a sequence based on its position in the alignment. Numbering starts from 1. Sequence positions larger than num_sequences() will throw an error. Returns : a Bio::LocatableSeq object Argument : positive integer for the sequence position =cut sub get_seq_by_pos { my ($self) = @_; $self->throw_not_implemented(); } =head1 Create new alignments The result of these methods are horizontal or vertical subsets of the current MSE. =head2 select Title : select Usage : $aln2 = $aln->select(1, 3) # three first sequences Function : Creates a new alignment from a continuous subset of sequences. Numbering starts from 1. Sequence positions larger than num_sequences() will throw an error. Returns : a Bio::SimpleAlign object Argument : positive integer for the first sequence positive integer for the last sequence to include (optional) =cut sub select { my ($self) = @_; $self->throw_not_implemented(); } =head2 select_noncont Title : select_noncont Usage : $aln2 = $aln->select_noncont(1, 3) # first and 3rd sequences Function : Creates a new alignment from a subset of sequences. Numbering starts from 1. Sequence positions larger than num_sequences() will throw an error. Returns : a Bio::SimpleAlign object Args : array of integers for the sequences =cut sub select_noncont { my ($self) = @_; $self->throw_not_implemented(); } =head2 slice Title : slice Usage : $aln2 = $aln->slice(20, 30) Function : Creates a slice from the alignment inclusive of start and end columns. Sequences with no residues in the slice are excluded from the new alignment and a warning is printed. Slice beyond the length of the sequence does not do padding. Returns : a Bio::SimpleAlign object Argument : positive integer for start column positive integer for end column =cut sub slice { my ($self) = @_; $self->throw_not_implemented(); } =head1 Change sequences within the MSE These methods affect characters in all sequences without changing the alignment. =head2 map_chars Title : map_chars Usage : $ali->map_chars('\.','-') Function : Does a s/$arg1/$arg2/ on the sequences. Useful for gap characters Notice that the "from" (arg1) is interpreted as a regex, so be careful about quoting meta characters (e.g. $ali->map_chars('.', '-') won't do what you want) Returns : None Argument : 'from' rexexp 'to' string =cut sub map_chars { my ($self) = @_; $self->throw_not_implemented(); } =head2 uppercase Title : uppercase() Usage : $ali->uppercase() Function : Sets all the sequences to uppercase Returns : Argument : =cut sub uppercase { my ($self) = @_; $self->throw_not_implemented(); } =head2 match_line Title : match_line() Usage : $align->match_line() Function : Generates a match line - much like consensus string except that a line indicating the '*' for a match. Argument : (optional) Match line characters ('*' by default) (optional) Strong match char (':' by default) (optional) Weak match char ('.' by default) =cut sub match_line { my ($self) = @_; $self->throw_not_implemented(); } =head2 match Title : match() Usage : $ali->match() Function : Goes through all columns and changes residues that are identical to residue in first sequence to match '.' character. Sets match_char. USE WITH CARE: Most MSE formats do not support match characters in sequences, so this is mostly for output only. NEXUS format (Bio::AlignIO::nexus) can handle it. Returns : 1 Argument : a match character, optional, defaults to '.' =cut sub match { my ($self) = @_; $self->throw_not_implemented(); } =head2 unmatch Title : unmatch() Usage : $ali->unmatch() Function : Undoes the effect of method match. Unsets match_char. Returns : 1 Argument : a match character, optional, defaults to '.' =cut sub unmatch { my ($self) = @_; $self->throw_not_implemented(); } =head1 MSE attibutes Methods for setting and reading the MSE attributes. Note that the methods defining character semantics depend on the user to set them sensibly. They are needed only by certain input/output methods. Unset them by setting to an empty string (''). =head2 id Title : id Usage : $myalign->id("Ig") Function : Gets/sets the id field of the alignment Returns : An id string Argument : An id string (optional) =cut sub id { my ($self) = @_; $self->throw_not_implemented(); } =head2 missing_char Title : missing_char Usage : $myalign->missing_char("?") Function : Gets/sets the missing_char attribute of the alignment It is generally recommended to set it to 'n' or 'N' for nucleotides and to 'X' for protein. Returns : An missing_char string, Argument : An missing_char string (optional) =cut sub missing_char { my ($self) = @_; $self->throw_not_implemented(); } =head2 match_char Title : match_char Usage : $myalign->match_char('.') Function : Gets/sets the match_char attribute of the alignment Returns : An match_char string, Argument : An match_char string (optional) =cut sub match_char { my ($self) = @_; $self->throw_not_implemented(); } =head2 gap_char Title : gap_char Usage : $myalign->gap_char('-') Function : Gets/sets the gap_char attribute of the alignment Returns : An gap_char string, defaults to '-' Argument : An gap_char string (optional) =cut sub gap_char { my ($self) = @_; $self->throw_not_implemented(); } =head2 symbol_chars Title : symbol_chars Usage : my @symbolchars = $aln->symbol_chars; Function: Returns all the seen symbols (other than gaps) Returns : array of characters that are the seen symbols Argument: boolean to include the gap/missing/match characters =cut sub symbol_chars{ my ($self) = @_; $self->throw_not_implemented(); } =head1 Alignment descriptors These read only methods describe the MSE in various ways. =head2 consensus_string Title : consensus_string Usage : $str = $ali->consensus_string($threshold_percent) Function : Makes a strict consensus Returns : consensus string Argument : Optional threshold ranging from 0 to 100. The consensus residue has to appear at least threshold % of the sequences at a given location, otherwise a '?' character will be placed at that location. (Default value = 0%) =cut sub consensus_string { my ($self) = @_; $self->throw_not_implemented(); } =head2 consensus_iupac Title : consensus_iupac Usage : $str = $ali->consensus_iupac() Function : Makes a consensus using IUPAC ambiguity codes from DNA and RNA. The output is in upper case except when gaps in a column force output to be in lower case. Note that if your alignment sequences contain a lot of IUPAC ambiquity codes you often have to manually set alphabet. Bio::PrimarySeq::_guess_type thinks they indicate a protein sequence. Returns : consensus string Argument : none Throws : on protein sequences =cut sub consensus_iupac { my ($self) = @_; $self->throw_not_implemented(); } =head2 is_flush Title : is_flush Usage : if( $ali->is_flush() ) : : Function : Tells you whether the alignment : is flush, ie all of the same length : : Returns : 1 or 0 Argument : =cut sub is_flush { my ($self) = @_; $self->throw_not_implemented(); } =head2 length Title : length() Usage : $len = $ali->length() Function : Returns the maximum length of the alignment. To be sure the alignment is a block, use is_flush Returns : integer Argument : =cut sub length { my ($self) = @_; $self->throw_not_implemented(); } =head2 maxname_length Title : maxname_length Usage : $ali->maxname_length() Function : Gets the maximum length of the displayname in the alignment. Used in writing out various MSE formats. Returns : integer Argument : =cut sub maxname_length { my ($self) = @_; $self->throw_not_implemented(); } =head2 num_residues Title : num_residues Usage : $no = $ali->num_residues Function : number of residues in total in the alignment Returns : integer Argument : Note : replaces no_residues =cut sub num_residues { my ($self) = @_; $self->throw_not_implemented(); } =head2 num_sequences Title : num_sequences Usage : $depth = $ali->num_sequences Function : number of sequence in the sequence alignment Returns : integer Argument : None Note : replaces no_sequences =cut sub num_sequences { my ($self) = @_; $self->throw_not_implemented(); } =head2 percentage_identity Title : percentage_identity Usage : $id = $align->percentage_identity Function: The function calculates the percentage identity of the alignment Returns : The percentage identity of the alignment (as defined by the implementation) Argument: None =cut sub percentage_identity{ my ($self) = @_; $self->throw_not_implemented(); } =head2 overall_percentage_identity Title : overall_percentage_identity Usage : $id = $align->overall_percentage_identity Function: The function calculates the percentage identity of the conserved columns Returns : The percentage identity of the conserved columns Args : None =cut sub overall_percentage_identity{ my ($self) = @_; $self->throw_not_implemented(); } =head2 average_percentage_identity Title : average_percentage_identity Usage : $id = $align->average_percentage_identity Function: The function uses a fast method to calculate the average percentage identity of the alignment Returns : The average percentage identity of the alignment Args : None =cut sub average_percentage_identity{ my ($self) = @_; $self->throw_not_implemented(); } =head1 Alignment positions Methods to map a sequence position into an alignment column and back. column_from_residue_number() does the former. The latter is really a property of the sequence object and can done using L: # select somehow a sequence from the alignment, e.g. my $seq = $aln->get_seq_by_pos(1); #$loc is undef or Bio::LocationI object my $loc = $seq->location_from_column(5); =head2 column_from_residue_number Title : column_from_residue_number Usage : $col = $ali->column_from_residue_number( $seqname, $resnumber) Function: This function gives the position in the alignment (i.e. column number) of the given residue number in the sequence with the given name. For example, for the alignment Seq1/91-97 AC..DEF.GH Seq2/24-30 ACGG.RTY.. Seq3/43-51 AC.DDEFGHI column_from_residue_number( "Seq1", 94 ) returns 6. column_from_residue_number( "Seq2", 25 ) returns 2. column_from_residue_number( "Seq3", 50 ) returns 9. An exception is thrown if the residue number would lie outside the length of the alignment (e.g. column_from_residue_number( "Seq2", 22 ) Note: If the parent sequence is represented by more than one alignment sequence and the residue number is present in them, this method finds only the first one. Returns : A column number for the position in the alignment of the given residue in the given sequence (1 = first column) Args : A sequence id/name (not a name/start-end) A residue number in the whole sequence (not just that segment of it in the alignment) =cut sub column_from_residue_number { my ($self) = @_; $self->throw_not_implemented(); } =head1 Sequence names Methods to manipulate the display name. The default name based on the sequence id and subsequence positions can be overridden in various ways. =head2 displayname Title : displayname Usage : $myalign->displayname("Ig", "IgA") Function : Gets/sets the display name of a sequence in the alignment : Returns : A display name string Argument : name of the sequence displayname of the sequence (optional) =cut sub displayname { my ($self) = @_; $self->throw_not_implemented(); } =head2 set_displayname_count Title : set_displayname_count Usage : $ali->set_displayname_count Function : Sets the names to be name_# where # is the number of times this name has been used. Returns : None Argument : None =cut sub set_displayname_count { my ($self) = @_; $self->throw_not_implemented(); } =head2 set_displayname_flat Title : set_displayname_flat Usage : $ali->set_displayname_flat() Function : Makes all the sequences be displayed as just their name, not name/start-end Returns : 1 Argument : None =cut sub set_displayname_flat { my ($self) = @_; $self->throw_not_implemented(); } =head2 set_displayname_normal Title : set_displayname_normal Usage : $ali->set_displayname_normal() Function : Makes all the sequences be displayed as name/start-end Returns : None Argument : None =cut sub set_displayname_normal { my ($self) = @_; $self->throw_not_implemented(); } =head1 Deprecated methods =head2 no_residues Title : no_residues Usage : $no = $ali->no_residues Function : number of residues in total in the alignment Returns : integer Argument : Note : deprecated in favor of num_residues() =cut sub no_residues { # immediate deprecation shift->deprecated(); } =head2 no_sequences Title : no_sequences Usage : $depth = $ali->no_sequences Function : number of sequence in the sequence alignment Returns : integer Argument : None Note : deprecated in favor of num_sequences() =cut sub no_sequences { # immediate deprecation shift->deprecated(); } 1; BioPerl-1.007002/Bio/Align/DNAStatistics.pm000444000766000024 14366513155576320 20350 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Align::DNAStatistics # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Align::DNAStatistics - Calculate some statistics for a DNA alignment =head1 SYNOPSIS use Bio::AlignIO; use Bio::Align::DNAStatistics; my $stats = Bio::Align::DNAStatistics->new(); my $alignin = Bio::AlignIO->new(-format => 'emboss', -file => 't/data/insulin.water'); my $aln = $alignin->next_aln; my $jcmatrix = $stats->distance(-align => $aln, -method => 'Jukes-Cantor'); print $jcmatrix->print_matrix; ## and for measurements of synonymous /nonsynonymous substitutions ## my $in = Bio::AlignIO->new(-format => 'fasta', -file => 't/data/nei_gojobori_test.aln'); my $alnobj = $in->next_aln; my ($seq1id,$seq2id) = map { $_->display_id } $alnobj->each_seq; my $results = $stats->calc_KaKs_pair($alnobj, $seq1id, $seq2id); print "comparing ".$results->[0]{'Seq1'}." and ".$results->[0]{'Seq2'}."\n"; for (sort keys %{$results->[0]} ){ next if /Seq/; printf("%-9s %.4f \n",$_ , $results->[0]{$_}); } my $results2 = $stats->calc_all_KaKs_pairs($alnobj); for my $an (@$results2){ print "comparing ". $an->{'Seq1'}." and ". $an->{'Seq2'}. " \n"; for (sort keys %$an ){ next if /Seq/; printf("%-9s %.4f \n",$_ , $an->{$_}); } print "\n\n"; } my $result3 = $stats->calc_average_KaKs($alnobj, 1000); for (sort keys %$result3 ){ next if /Seq/; printf("%-9s %.4f \n",$_ , $result3->{$_}); } =head1 DESCRIPTION This object contains routines for calculating various statistics and distances for DNA alignments. The routines are not well tested and do contain errors at this point. Work is underway to correct them, but do not expect this code to give you the right answer currently! Use dnadist/distmat in the PHLYIP or EMBOSS packages to calculate the distances. Several different distance method calculations are supported. Listed in brackets are the pattern which will match =over 3 =item * JukesCantor [jc|jukes|jukescantor|jukes-cantor] =item * Uncorrected [jcuncor|uncorrected] =item * F81 [f81|felsenstein] =item * Kimura [k2|k2p|k80|kimura] =item * Tamura [t92|tamura|tamura92] =item * F84 [f84|felsenstein84] =item * TajimaNei [tajimanei|tajima\-nei] =item * JinNei [jinnei|jin\-nei] (not implemented) =back There are also three methods to calculate the ratio of synonymous to non-synonymous mutations. All are implementations of the Nei-Gojobori evolutionary pathway method and use the Jukes-Cantor method of nucleotide substitution. This method works well so long as the nucleotide frequencies are roughly equal and there is no significant transition/transversion bias. In order to use these methods there are several pre-requisites for the alignment. =over 3 =item 1 DNA alignment must be based on protein alignment. Use the subroutine L to achieve this. =item 2 Therefore alignment gaps must be in multiples of 3 (representing an aa deletion/insertion) and at present must be indicated by a '-' symbol. =item 3 Alignment must be solely of coding region and be in reading frame 0 to achieve meaningful results =item 4 Alignment must therefore be a multiple of 3 nucleotides long. =item 5 All sequences must be the same length (including gaps). This should be the case anyway if the sequences have been automatically aligned using a program like Clustal. =item 6 Only the standard codon alphabet is supported at present. =back calc_KaKs_pair() calculates a number of statistics for a named pair of sequences in the alignment. calc_all_KaKs_pairs() calculates these statistics for all pairwise comparisons in an MSA. The statistics returned are: =over 3 =item * S_d - Number of synonymous mutations between the 2 sequences. =item * N_d - Number of non-synonymous mutations between the 2 sequences. =item * S - Mean number of synonymous sites in both sequences. =item * N - mean number of synonymous sites in both sequences. =item * P_s - proportion of synonymous differences in both sequences given by P_s = S_d/S. =item * P_n - proportion of non-synonymous differences in both sequences given by P_n = S_n/S. =item * D_s - estimation of synonymous mutations per synonymous site (by Jukes-Cantor). =item * D_n - estimation of non-synonymous mutations per non-synonymous site (by Jukes-Cantor). =item * D_n_var - estimation of variance of D_n . =item * D_s_var - estimation of variance of S_n. =item * z_value - calculation of z value.Positive value indicates D_n E D_s, negative value indicates D_s E D_n. =back The statistics returned by calc_average_KaKs are: =over 3 =item * D_s - Average number of synonymous mutations/synonymous site. =item * D_n - Average number of non-synonymous mutations/non-synonymous site. =item * D_s_var - Estimated variance of Ds from bootstrapped alignments. =item * D_n_var - Estimated variance of Dn from bootstrapped alignments. =item * z_score - calculation of z value. Positive value indicates D_n ED_s, negative values vice versa. =back The design of the code is based around the explanation of the Nei-Gojobori algorithm in the excellent book "Molecular Evolution and Phylogenetics" by Nei and Kumar, published by Oxford University Press. The methods have been tested using the worked example 4.1 in the book, and reproduce those results. If people like having this sort of analysis in BioPerl other methods for estimating Ds and Dn can be provided later. Much of the DNA distance code is based on implementations in EMBOSS (Rice et al, www.emboss.org) [distmat.c] and PHYLIP (J. Felsenstein et al) [dnadist.c]. Insight also gained from Eddy, Durbin, Krogh, & Mitchison. =head1 REFERENCES =over 3 =item * D_JukesCantor "Phylogenetic Inference", Swoffrod, Olsen, Waddell and Hillis, in Mol. Systematics, 2nd ed, 1996, Ch 11. Derived from "Evolution of Protein Molecules", Jukes & Cantor, in Mammalian Prot. Metab., III, 1969, pp. 21-132. =item * D_Tamura K Tamura, Mol. Biol. Evol. 1992, 9, 678. =item * D_Kimura M Kimura, J. Mol. Evol., 1980, 16, 111. =item * JinNei Jin and Nei, Mol. Biol. Evol. 82, 7, 1990. =item * D_TajimaNei Tajima and Nei, Mol. Biol. Evol. 1984, 1, 269. =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-AT-bioperl.org =head1 CONTRIBUTORS Richard Adams, richard.adams@ed.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Align::DNAStatistics; use vars qw(%DNAChanges @Nucleotides %NucleotideIndexes $GapChars $SeqCount $DefaultGapPenalty %DistanceMethods $CODONS %synchanges $synsites $Precision $GCChhars); use strict; use Bio::Align::PairwiseStatistics; use Bio::Matrix::PhylipDist; use Bio::Tools::IUPAC; BEGIN { $GapChars = '[\.\-]'; $GCChhars = '[GCS]'; @Nucleotides = qw(A G T C); $SeqCount = 2; $Precision = 5; # these values come from EMBOSS distmat implementation %NucleotideIndexes = ( 'A' => 0, 'T' => 1, 'C' => 2, 'G' => 3, 'AT' => 0, 'AC' => 1, 'AG' => 2, 'CT' => 3, 'GT' => 4, 'CG' => 5, # these are wrong now # 'S' => [ 1, 3], # 'W' => [ 0, 4], # 'Y' => [ 2, 3], # 'R' => [ 0, 1], # 'M' => [ 0, 3], # 'K' => [ 1, 2], # 'B' => [ 1, 2, 3], # 'H' => [ 0, 2, 3], # 'V' => [ 0, 1, 3], # 'D' => [ 0, 1, 2], ); $DefaultGapPenalty = 0; # could put ambiguities here? %DNAChanges = ( 'Transversions' => { 'A' => [ 'T', 'C'], 'T' => [ 'A', 'G'], 'C' => [ 'A', 'G'], 'G' => [ 'C', 'T'], }, 'Transitions' => { 'A' => [ 'G' ], 'G' => [ 'A' ], 'C' => [ 'T' ], 'T' => [ 'C' ], }, ); %DistanceMethods = ( 'jc|jukes|jukescantor|jukes\-cantor' => 'JukesCantor', 'jcuncor|uncorrected' => 'Uncorrected', 'f81|felsenstein81' => 'F81', 'k2|k2p|k80|kimura' => 'Kimura', 't92|tamura|tamura92' => 'Tamura', 'f84|felsenstein84' => 'F84', 'tajimanei|tajima\-nei' => 'TajimaNei', 'jinnei|jin\-nei' => 'JinNei'); } use base qw(Bio::Root::Root Bio::Align::StatisticsI); ## generate look up hashes for Nei_Gojobori methods## $CODONS = get_codons(); my @t = split '', "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"; #create look up hash of number of possible synonymous mutations per codon $synsites = get_syn_sites(); #create reference look up hash of single basechanges in codons %synchanges = get_syn_changes(); =head2 new Title : new Usage : my $obj = Bio::Align::DNAStatistics->new(); Function: Builds a new Bio::Align::DNAStatistics object Returns : Bio::Align::DNAStatistics Args : none =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->pairwise_stats( Bio::Align::PairwiseStatistics->new()); return $self; } =head2 distance Title : distance Usage : my $distance_mat = $stats->distance(-align => $aln, -method => $method); Function: Calculates a distance matrix for all pairwise distances of sequences in an alignment. Returns : L object Args : -align => Bio::Align::AlignI object -method => String specifying specific distance method (implementing class may assume a default) See also: L =cut sub distance{ my ($self,@args) = @_; my ($aln,$method) = $self->_rearrange([qw(ALIGN METHOD)],@args); if( ! defined $aln || ! ref ($aln) || ! $aln->isa('Bio::Align::AlignI') ) { $self->throw("Must supply a valid Bio::Align::AlignI for the -align parameter in distance"); } $method ||= 'JukesCantor'; foreach my $m ( keys %DistanceMethods ) { if(defined $m && $method =~ /$m/i ) { my $mtd = "D_$DistanceMethods{$m}"; return $self->$mtd($aln); } } $self->warn("Unrecognized distance method $method must be one of [". join(',',$self->available_distance_methods())."]"); return; } =head2 available_distance_methods Title : available_distance_methods Usage : my @methods = $stats->available_distance_methods(); Function: Enumerates the possible distance methods Returns : Array of strings Args : none =cut sub available_distance_methods{ my ($self,@args) = @_; return values %DistanceMethods; } =head2 D - distance methods =cut =head2 D_JukesCantor Title : D_JukesCantor Usage : my $d = $stat->D_JukesCantor($aln) Function: Calculates D (pairwise distance) between 2 sequences in an alignment using the Jukes-Cantor 1 parameter model. Returns : L Args : L of DNA sequences double - gap penalty =cut sub D_JukesCantor{ my ($self,$aln,$gappenalty) = @_; return 0 unless $self->_check_arg($aln); $gappenalty = $DefaultGapPenalty unless defined $gappenalty; # ambiguities ignored at this point my (@seqs,@names,@values,%dist); my $seqct = 0; foreach my $seq ( $aln->each_seq) { push @names, $seq->display_id; push @seqs, uc $seq->seq(); $seqct++; } my $precisionstr = "%.$Precision"."f"; for(my $i = 0; $i < $seqct-1; $i++ ) { # (diagonals) distance is 0 for same sequence $dist{$names[$i]}->{$names[$i]} = [$i,$i]; $values[$i][$i] = sprintf($precisionstr,0); for( my $j = $i+1; $j < $seqct; $j++ ) { my ($matrix,$pfreq,$gaps) = $self->_build_nt_matrix($seqs[$i], $seqs[$j]); # just want diagonals my $m = ( $matrix->[0]->[0] + $matrix->[1]->[1] + $matrix->[2]->[2] + $matrix->[3]->[3] ); my $D = 1 - ( $m / ($aln->length - $gaps + ( $gaps * $gappenalty))); my $d = (- 3 / 4) * log ( 1 - (4 * $D/ 3)); # fwd and rev lookup $dist{$names[$i]}->{$names[$j]} = [$i,$j]; $dist{$names[$j]}->{$names[$i]} = [$i,$j]; $values[$j][$i] = $values[$i][$j] = sprintf($precisionstr,$d); # (diagonals) distance is 0 for same sequence $dist{$names[$j]}->{$names[$j]} = [$j,$j]; $values[$j][$j] = sprintf($precisionstr,0); } } return Bio::Matrix::PhylipDist->new(-program => 'bioperl_DNAstats', -matrix => \%dist, -names => \@names, -values => \@values); } =head2 D_F81 Title : D_F81 Usage : my $d = $stat->D_F81($aln) Function: Calculates D (pairwise distance) between 2 sequences in an alignment using the Felsenstein 1981 distance model. Relaxes the assumption of equal base frequencies that is in JC. Returns : L Args : L of DNA sequences =cut sub D_F81{ my ($self,$aln,$gappenalty) = @_; return 0 unless $self->_check_arg($aln); $gappenalty = $DefaultGapPenalty unless defined $gappenalty; # ambiguities ignored at this point my (@seqs,@names,@values,%dist); my $seqct = 0; foreach my $seq ( $aln->each_seq) { push @names, $seq->display_id;; push @seqs, uc $seq->seq(); $seqct++; } my $precisionstr = "%.$Precision"."f"; for(my $i = 0; $i < $seqct-1; $i++ ) { # (diagonals) distance is 0 for same sequence $dist{$names[$i]}->{$names[$i]} = [$i,$i]; $values[$i][$i] = sprintf($precisionstr,0); for( my $j = $i+1; $j < $seqct; $j++ ) { my ($matrix,$pfreq,$gaps) = $self->_build_nt_matrix($seqs[$i], $seqs[$j]); # just want diagonals my $m = ( $matrix->[0]->[0] + $matrix->[1]->[1] + $matrix->[2]->[2] + $matrix->[3]->[3] ); my $D = 1 - ( $m / ($aln->length - $gaps + ( $gaps * $gappenalty))); my $d = (- 3 / 4) * log ( 1 - (4 * $D/ 3)); # fwd and rev lookup $dist{$names[$i]}->{$names[$j]} = [$i,$j]; $dist{$names[$j]}->{$names[$i]} = [$i,$j]; $values[$j][$i] = $values[$i][$j] = sprintf($precisionstr,$d); # (diagonals) distance is 0 for same sequence $dist{$names[$j]}->{$names[$j]} = [$j,$j]; $values[$j][$j] = sprintf($precisionstr,0); } } return Bio::Matrix::PhylipDist->new(-program => 'bioperl_DNAstats', -matrix => \%dist, -names => \@names, -values => \@values); } =head2 D_Uncorrected Title : D_Uncorrected Usage : my $d = $stats->D_Uncorrected($aln) Function: Calculate a distance D, no correction for multiple substitutions is used. In rare cases where sequences may not overlap, 'NA' is substituted for the distance. Returns : L Args : L (DNA Alignment) [optional] gap penalty =cut sub D_Uncorrected { my ($self,$aln,$gappenalty) = @_; $gappenalty = $DefaultGapPenalty unless defined $gappenalty; return 0 unless $self->_check_arg($aln); # ambiguities ignored at this point my (@seqs,@names,@values,%dist); my $seqct = 0; foreach my $seq ( $aln->each_seq) { push @names, $seq->display_id; push @seqs, uc $seq->seq(); $seqct++; } my $precisionstr = "%.$Precision"."f"; my $len = $aln->length; for( my $i = 0; $i < $seqct-1; $i++ ) { # (diagonals) distance is 0 for same sequence $dist{$names[$i]}->{$names[$i]} = [$i,$i]; $values[$i][$i] = sprintf($precisionstr,0); for( my $j = $i+1; $j < $seqct; $j++ ) { my ($matrix,$pfreq,$gaps) = $self->_build_nt_matrix($seqs[$i], $seqs[$j]); my $m = ( $matrix->[0]->[0] + $matrix->[1]->[1] + $matrix->[2]->[2] + $matrix->[3]->[3] ); my $denom = ( $len - $gaps + ( $gaps * $gappenalty)); $self->warn("No distance calculated between $names[$i] and $names[$j], inserting -1") unless $denom; my $D = $denom ? 1 - ( $m / $denom) : -1; # fwd and rev lookup $dist{$names[$i]}->{$names[$j]} = [$i,$j]; $dist{$names[$j]}->{$names[$i]} = [$i,$j]; $values[$j][$i] = $values[$i][$j] = $denom ? sprintf($precisionstr,$D) : sprintf("%-*s", $Precision + 2, $D); # (diagonals) distance is 0 for same sequence $dist{$names[$j]}->{$names[$j]} = [$j,$j]; $values[$j][$j] = sprintf($precisionstr,0); } } return Bio::Matrix::PhylipDist->new(-program => 'bioperl_DNAstats', -matrix => \%dist, -names => \@names, -values => \@values); } # M Kimura, J. Mol. Evol., 1980, 16, 111. =head2 D_Kimura Title : D_Kimura Usage : my $d = $stat->D_Kimura($aln) Function: Calculates D (pairwise distance) between all pairs of sequences in an alignment using the Kimura 2 parameter model. Returns : L Args : L of DNA sequences =cut sub D_Kimura { my ($self,$aln) = @_; return 0 unless $self->_check_arg($aln); # ambiguities ignored at this point my (@names,@values,%dist); my $seqct = 0; foreach my $seq ( $aln->each_seq) { push @names, $seq->display_id; $seqct++; } my $precisionstr = "%.$Precision"."f"; for( my $i = 0; $i < $seqct-1; $i++ ) { # (diagonals) distance is 0 for same sequence $dist{$names[$i]}->{$names[$i]} = [$i,$i]; $values[$i][$i] = sprintf($precisionstr,0); for( my $j = $i+1; $j < $seqct; $j++ ) { my $pairwise = $aln->select_noncont($i+1,$j+1); my $L = $self->pairwise_stats->number_of_comparable_bases($pairwise); unless( $L ) { $L = 1; } my $P = $self->transitions($pairwise) / $L; my $Q = $self->transversions($pairwise) / $L; my $K = 0; my $denom = ( 1 - (2 * $P) - $Q); if( $denom == 0 ) { $self->throw("cannot find distance for ",$i+1, ",",$j+1," $P, $Q\n"); } my $a = 1 / ( 1 - (2 * $P) - $Q); my $b = 1 / ( 1 - 2 * $Q ); if( $a < 0 || $b < 0 ) { $K = -1; } else{ $K = (1/2) * log ( $a ) + (1/4) * log($b); } # fwd and rev lookup $dist{$names[$i]}->{$names[$j]} = [$i,$j]; $dist{$names[$j]}->{$names[$i]} = [$i,$j]; $values[$j][$i] = $values[$i][$j] = sprintf($precisionstr,$K); # (diagonals) distance is 0 for same sequence $dist{$names[$j]}->{$names[$j]} = [$j,$j]; $values[$j][$j] = sprintf($precisionstr,0); } } return Bio::Matrix::PhylipDist->new(-program => 'bioperl_DNAstats', -matrix => \%dist, -names => \@names, -values => \@values); } =head2 D_Kimura_variance Title : D_Kimura Usage : my $d = $stat->D_Kimura_variance($aln) Function: Calculates D (pairwise distance) between all pairs of sequences in an alignment using the Kimura 2 parameter model. Returns : array of 2 L, the first is the Kimura distance and the second is a matrix of variance V(K) Args : L of DNA sequences =cut sub D_Kimura_variance { my ($self,$aln) = @_; return 0 unless $self->_check_arg($aln); # ambiguities ignored at this point my (@names,@values,%dist,@var); my $seqct = 0; foreach my $seq ( $aln->each_seq) { push @names, $seq->display_id; $seqct++; } my $precisionstr = "%.$Precision"."f"; for( my $i = 0; $i < $seqct-1; $i++ ) { # (diagonals) distance is 0 for same sequence $dist{$names[$i]}->{$names[$i]} = [$i,$i]; $values[$i][$i] = sprintf($precisionstr,0); for( my $j = $i+1; $j < $seqct; $j++ ) { my $pairwise = $aln->select_noncont($i+1,$j+1); my $L = $self->pairwise_stats->number_of_comparable_bases($pairwise); unless( $L ) { $L = 1; } my $P = $self->transitions($pairwise) / $L; my $Q = $self->transversions($pairwise) / $L; my ($a,$b,$K,$var_k); my $a_denom = ( 1 - (2 * $P) - $Q); my $b_denom = 1 - 2 * $Q; unless( $a_denom > 0 && $b_denom > 0 ) { $a = 1; $b = 1; $K = -1; $var_k = -1; } else { $a = 1 / $a_denom; $b = 1 / $b_denom; $K = (1/2) * log ( $a ) + (1/4) * log($b); # from Wu and Li 1985 which in turn is from Kimura 1980 my $c = ( $a - $b ) / 2; my $d = ( $a + $b ) / 2; $var_k = ( $a**2 * $P + $d**2 * $Q - ( $a * $P + $d * $Q)**2 ) / $L; } # fwd and rev lookup $dist{$names[$i]}->{$names[$j]} = [$i,$j]; $dist{$names[$j]}->{$names[$i]} = [$i,$j]; $values[$j][$i] = $values[$i][$j] = sprintf($precisionstr,$K); # (diagonals) distance is 0 for same sequence $dist{$names[$j]}->{$names[$j]} = [$j,$j]; $values[$j]->[$j] = sprintf($precisionstr,0); $var[$j]->[$i] = $var[$i]->[$j] = sprintf($precisionstr,$var_k); $var[$j]->[$j] = $values[$j]->[$j]; } } return ( Bio::Matrix::PhylipDist->new(-program => 'bioperl_DNAstats', -matrix => \%dist, -names => \@names, -values => \@values), Bio::Matrix::PhylipDist->new(-program => 'bioperl_DNAstats', -matrix => \%dist, -names => \@names, -values => \@var) ); } # K Tamura, Mol. Biol. Evol. 1992, 9, 678. =head2 D_Tamura Title : D_Tamura Usage : Calculates D (pairwise distance) between 2 sequences in an alignment using Tamura 1992 distance model. Returns : L Args : L of DNA sequences =cut sub D_Tamura { my ($self,$aln) = @_; return 0 unless $self->_check_arg($aln); # ambiguities ignored at this point my (@seqs,@names,@values,%dist,$i,$j); my $seqct = 0; my $length = $aln->length; foreach my $seq ( $aln->each_seq) { push @names, $seq->display_id;; push @seqs, uc $seq->seq(); $seqct++; } my $precisionstr = "%.$Precision"."f"; my (@gap,@gc,@trans,@tranv,@score); $i = 0; for my $t1 ( @seqs ) { $j = 0; for my $t2 ( @seqs ) { $gap[$i][$j] = 0; for( my $k = 0; $k < $length; $k++ ) { my ($c1,$c2) = ( substr($seqs[$i],$k,1), substr($seqs[$j],$k,1) ); if( $c1 =~ /^$GapChars$/ || $c2 =~ /^$GapChars$/ ) { $gap[$i][$j]++; } elsif( $c2 =~ /^$GCChhars$/i ) { $gc[$i][$j]++; } } $gc[$i][$j] = ( $gc[$i][$j] / ($length - $gap[$i][$j]) ); $j++; } $i++; } for( $i = 0; $i < $seqct-1; $i++ ) { # (diagonals) distance is 0 for same sequence $dist{$names[$i]}->{$names[$i]} = [$i,$i]; $values[$i][$i] = sprintf($precisionstr,0); for( $j = $i+1; $j < $seqct; $j++ ) { my $pairwise = $aln->select_noncont($i+1,$j+1); my $L = $self->pairwise_stats->number_of_comparable_bases($pairwise); my $P = $self->transitions($pairwise) / $L; my $Q = $self->transversions($pairwise) / $L; my $C = $gc[$i][$j] + $gc[$j][$i]- ( 2 * $gc[$i][$j] * $gc[$j][$i] ); if( $P ) { $P = $P / $C; } my $d = -($C * log(1- $P - $Q)) -(0.5* ( 1 - $C) * log(1 - 2 * $Q)); # fwd and rev lookup $dist{$names[$i]}->{$names[$j]} = [$i,$j]; $dist{$names[$j]}->{$names[$i]} = [$i,$j]; $values[$j][$i] = $values[$i][$j] = sprintf($precisionstr,$d); # (diagonals) distance is 0 for same sequence $dist{$names[$j]}->{$names[$j]} = [$j,$j]; $values[$j][$j] = sprintf($precisionstr,0); } } return Bio::Matrix::PhylipDist->new(-program => 'bioperl_DNAstats', -matrix => \%dist, -names => \@names, -values => \@values); } =head2 D_F84 Title : D_F84 Usage : my $d = $stat->D_F84($aln) Function: Calculates D (pairwise distance) between 2 sequences in an alignment using the Felsenstein 1984 distance model. Returns : L Args : L of DNA sequences [optional] double - gap penalty =cut sub D_F84 { my ($self,$aln,$gappenalty) = @_; return 0 unless $self->_check_arg($aln); $self->throw_not_implemented(); # ambiguities ignored at this point my (@seqs,@names,@values,%dist); my $seqct = 0; foreach my $seq ( $aln->each_seq) { # if there is no name, my $id = $seq->display_id; if( ! length($id) || # deal with empty names $id =~ /^\s+$/ ) { $id = $seqct+1; } push @names, $id; push @seqs, uc $seq->seq(); $seqct++; } my $precisionstr = "%.$Precision"."f"; for( my $i = 0; $i < $seqct-1; $i++ ) { # (diagonals) distance is 0 for same sequence $dist{$names[$i]}->{$names[$i]} = [$i,$i]; $values[$i][$i] = sprintf($precisionstr,0); for( my $j = $i+1; $j < $seqct; $j++ ) { } } } # Tajima and Nei, Mol. Biol. Evol. 1984, 1, 269. # Tajima-Nei correction used for multiple substitutions in the calc # of the distance matrix. Nucleic acids only. # # D = p-distance = 1 - (matches/(posns_scored + gaps) # # distance = -b * ln(1-D/b) # =head2 D_TajimaNei Title : D_TajimaNei Usage : my $d = $stat->D_TajimaNei($aln) Function: Calculates D (pairwise distance) between 2 sequences in an alignment using the TajimaNei 1984 distance model. Returns : L Args : Bio::Align::AlignI of DNA sequences =cut sub D_TajimaNei{ my ($self,$aln) = @_; return 0 unless $self->_check_arg($aln); # ambiguities ignored at this point my (@seqs,@names,@values,%dist); my $seqct = 0; foreach my $seq ( $aln->each_seq) { # if there is no name, push @names, $seq->display_id; push @seqs, uc $seq->seq(); $seqct++; } my $precisionstr = "%.$Precision"."f"; my ($i,$j,$bs); # pairwise for( $i =0; $i < $seqct -1; $i++ ) { $dist{$names[$i]}->{$names[$i]} = [$i,$i]; $values[$i][$i] = sprintf($precisionstr,0); for ( $j = $i+1; $j <$seqct;$j++ ) { my ($matrix,$pfreq,$gaps) = $self->_build_nt_matrix($seqs[$i], $seqs[$j]); my $pairwise = $aln->select_noncont($i+1,$j+1); my $slen = $self->pairwise_stats->number_of_comparable_bases($pairwise); my $fij2 = 0; for( $bs = 0; $bs < 4; $bs++ ) { my $fi = 0; map {$fi += $matrix->[$bs]->[$_] } 0..3; my $fj = 0; # summation map { $fj += $matrix->[$_]->[$bs] } 0..3; my $fij = ( $fi && $fj ) ? ($fi + $fj) /( 2 * $slen) : 0; $fij2 += $fij**2; } my ($pair,$h) = (0,0); for( $bs = 0; $bs < 3; $bs++ ) { for(my $bs1 = $bs+1; $bs1 <= 3; $bs1++ ) { my $fij = $pfreq->[$pair++] / $slen; if( $fij ) { my ($ci1,$ci2,$cj1,$cj2) = (0,0,0,0); map { $ci1 += $matrix->[$_]->[$bs] } 0..3; map { $cj1 += $matrix->[$bs]->[$_] } 0..3; map { $ci2 += $matrix->[$_]->[$bs1] } 0..3; map { $cj2 += $matrix->[$bs1]->[$_] } 0..3; if( $fij ) { $h += ( ($fij**2) / 2 ) / ( ( ( $ci1 + $cj1 ) / (2 * $slen) ) * ( ( $ci2 + $cj2 ) / (2 * $slen) ) ); } $self->debug( "slen is $slen h is $h fij = $fij ci1 =$ci1 cj1=$cj1 ci2=$ci2 cj2=$cj2\n"); } } } # just want diagonals which are matches (A matched A, C -> C) my $m = ( $matrix->[0]->[0] + $matrix->[1]->[1] + $matrix->[2]->[2] + $matrix->[3]->[3] ); my $D = 1 - ( $m / $slen); my $d; if( $h == 0 ) { $d = -1; } else { my $b = (1 - $fij2 + (($D**2)/$h)) / 2; my $c = 1- $D/ $b; if( $c < 0 ) { $d = -1; } else { $d = (-1 * $b) * log ( $c); } } # fwd and rev lookup $dist{$names[$i]}->{$names[$j]} = [$i,$j]; $dist{$names[$j]}->{$names[$i]} = [$i,$j]; $values[$j][$i] = $values[$i][$j] = sprintf($precisionstr,$d); # (diagonals) distance is 0 for same sequence $dist{$names[$j]}->{$names[$j]} = [$j,$j]; $values[$j][$j] = sprintf($precisionstr,0); } } return Bio::Matrix::PhylipDist->new(-program => 'bioperl_DNAstats', -matrix => \%dist, -names => \@names, -values => \@values); } # Jin and Nei, Mol. Biol. Evol. 82, 7, 1990. =head2 D_JinNei Title : D_JinNei Usage : my $d = $stat->D_JinNei($aln) Function: Calculates D (pairwise distance) between 2 sequences in an alignment using the Jin-Nei 1990 distance model. Returns : L Args : L of DNA sequences =cut sub D_JinNei{ my ($self,@args) = @_; $self->warn("JinNei implementation not completed"); return; } =head2 transversions Title : transversions Usage : my $transversions = $stats->transversion($aln); Function: Calculates the number of transversions between two sequences in an alignment Returns : integer Args : Bio::Align::AlignI =cut sub transversions{ my ($self,$aln) = @_; return $self->_trans_count_helper($aln, $DNAChanges{'Transversions'}); } =head2 transitions Title : transitions Usage : my $transitions = Bio::Align::DNAStatistics->transitions($aln); Function: Calculates the number of transitions in a given DNA alignment Returns : integer representing the number of transitions Args : Bio::Align::AlignI object =cut sub transitions{ my ($self,$aln) = @_; return $self->_trans_count_helper($aln, $DNAChanges{'Transitions'}); } sub _trans_count_helper { my ($self,$aln,$type) = @_; return 0 unless( $self->_check_arg($aln) ); if( ! $aln->is_flush ) { $self->throw("must be flush") } my (@tcount); my ($first,$second) = ( uc $aln->get_seq_by_pos(1)->seq(), uc $aln->get_seq_by_pos(2)->seq() ); my $alen = $aln->length; for (my $i = 0;$i<$alen; $i++ ) { my ($c1,$c2) = ( substr($first,$i,1), substr($second,$i,1) ); if( $c1 ne $c2 ) { foreach my $nt ( @{$type->{$c1}} ) { if( $nt eq $c2) { $tcount[$i]++; } } } } my $sum = 0; map { if( $_) { $sum += $_} } @tcount; return $sum; } # this will generate a matrix which records across the row, the number # of DNA subst # sub _build_nt_matrix { my ($self,$seqa,$seqb) = @_; my $basect_matrix = [ [ qw(0 0 0 0) ], # number of bases that match [ qw(0 0 0 0) ], [ qw(0 0 0 0) ], [ qw(0 0 0 0) ] ]; my $gaps = 0; # number of gaps my $pfreq = [ qw( 0 0 0 0 0 0)]; # matrix for pair frequency my $len_a = length($seqa); for( my $i = 0; $i < $len_a; $i++) { my ($ti,$tj) = (substr($seqa,$i,1),substr($seqb,$i,1)); $ti =~ tr/U/T/; $tj =~ tr/U/T/; if( $ti =~ /^$GapChars$/) { $gaps++; next; } if( $tj =~ /^$GapChars$/) { $gaps++; next } my $ti_index = $NucleotideIndexes{$ti}; my $tj_index = $NucleotideIndexes{$tj}; if( ! defined $ti_index ) { $self->warn("ti_index not defined for $ti\n"); next; } $basect_matrix->[$ti_index]->[$tj_index]++; if( $ti ne $tj ) { $pfreq->[$NucleotideIndexes{join('',sort ($ti,$tj))}]++; } } return ($basect_matrix,$pfreq,$gaps); } sub _check_ambiguity_nucleotide { my ($base1,$base2) = @_; my %iub = Bio::Tools::IUPAC->iupac_iub(); my @amb1 = @{ $iub{uc($base1)} }; my @amb2 = @{ $iub{uc($base2)} }; my ($pmatch) = (0); for my $amb ( @amb1 ) { if( grep { $amb eq $_ } @amb2 ) { $pmatch = 1; last; } } if( $pmatch ) { return (1 / scalar @amb1) * (1 / scalar @amb2); } else { return 0; } } sub _check_arg { my($self,$aln ) = @_; if( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->warn("Must provide a Bio::Align::AlignI compliant object to Bio::Align::DNAStatistics"); return 0; } elsif( $aln->get_seq_by_pos(1)->alphabet ne 'dna' ) { $self->warn("Must provide a DNA alignment to Bio::Align::DNAStatistics, you provided a " . $aln->get_seq_by_pos(1)->alphabet); return 0; } return 1; } =head2 Data Methods =cut =head2 pairwise_stats Title : pairwise_stats Usage : $obj->pairwise_stats($newval) Function: Returns : value of pairwise_stats Args : newvalue (optional) =cut sub pairwise_stats{ my ($self,$value) = @_; if( defined $value) { $self->{'_pairwise_stats'} = $value; } return $self->{'_pairwise_stats'}; } =head2 calc_KaKs_pair Title : calc_KaKs_pair Useage : my $results = $stats->calc_KaKs_pair($alnobj, $name1, $name2). Function : calculates Nei-Gojobori statistics for pairwise comparison. Args : A Bio::Align::AlignI compliant object such as a Bio::SimpleAlign object, and 2 sequence name strings. Returns : a reference to a hash of statistics with keys as listed in Description. =cut sub calc_KaKs_pair { my ( $self, $aln, $seq1_id, $seq2_id) = @_; $self->throw("Needs 3 arguments - an alignment object, and 2 sequence ids") if @_!= 4; $self->throw ("This calculation needs a Bio::Align::AlignI compatible object, not a [ " . ref($aln) . " ]object") unless $aln->isa('Bio::Align::AlignI'); my @seqs = ( #{id => $seq1_id, seq =>($aln->each_seq_with_id($seq1_id))[0]->seq}, #{id => $seq2_id, seq =>($aln->each_seq_with_id($seq2_id))[0]->seq} {id => $seq1_id, seq => uc(($aln->each_seq_with_id($seq1_id))[0]->seq)}, {id => $seq2_id, seq => uc(($aln->each_seq_with_id($seq2_id))[0]->seq)} ) ; if (length($seqs[0]{'seq'}) != length($seqs[1]{'seq'})) { $self->throw(" aligned sequences must be of equal length!"); } my $results = []; $self->_get_av_ds_dn(\@seqs, $results); return $results; } =head2 calc_all_KaKs_pairs Title : calc_all_KaKs_pairs Useage : my $results2 = $stats->calc_KaKs_pair($alnobj). Function : Calculates Nei_gojobori statistics for all pairwise combinations in sequence. Arguments: A Bio::Align::ALignI compliant object such as a Bio::SimpleAlign object. Returns : A reference to an array of hashes of statistics of all pairwise comparisons in the alignment. =cut sub calc_all_KaKs_pairs { #returns a multi_element_array with all pairwise comparisons my ($self,$aln) = @_; $self->throw ("This calculation needs a Bio::Align::AlignI compatible object, not a [ " . ref($aln) . " ]object") unless $aln->isa('Bio::Align::AlignI'); my @seqs; for my $seq ($aln->each_seq) { push @seqs, {id => $seq->display_id, seq=>$seq->seq}; } my $results ; $results = $self->_get_av_ds_dn(\@seqs, $results); return $results; } =head2 calc_average_KaKs Title : calc_average_KaKs. Useage : my $res= $stats->calc_average_KaKs($alnobj, 1000). Function : calculates Nei_Gojobori stats for average of all sequences in the alignment. Args : A Bio::Align::AlignI compliant object such as a Bio::SimpleAlign object, number of bootstrap iterations (default 1000). Returns : A reference to a hash of statistics as listed in Description. =cut sub calc_average_KaKs { #calculates global value for sequences in alignment using bootstrapping #this is quite slow (~10 seconds per 3 X 200nt seqs); my ($self, $aln, $bootstrap_rpt) = @_; $bootstrap_rpt ||= 1000; $self->throw ("This calculation needs a Bio::Align::AlignI compatible object, not a [ " . ref($aln) . " ]object") unless $aln->isa('Bio::Align::AlignI'); my @seqs; for my $seq ($aln->each_seq) { push @seqs, {id => $seq->display_id, seq=>$seq->seq}; } my $results ; my ($ds_orig, $dn_orig) = $self->_get_av_ds_dn(\@seqs); #print "ds = $ds_orig, dn = $dn_orig\n"; $results = {D_s => $ds_orig, D_n => $dn_orig}; $self->_run_bootstrap(\@seqs, $results, $bootstrap_rpt); return $results; } ############## primary internal subs for alignment comparisons ######################## sub _run_bootstrap { ### generates sampled sequences, calculates Ds and Dn values, ### then calculates variance of sampled sequences and add results to results hash ### my ($self,$seq_ref, $results, $bootstrap_rpt) = @_; my @seqs = @$seq_ref; my @btstrp_aoa; # to hold array of array of nucleotides for resampling my %bootstrap_values = (ds => [], dn =>[]); # to hold list of av values #1st make alternative array of codons; my $c = 0; while ($c < length $seqs[0]{'seq'}) { for (0..$#seqs) { push @{$btstrp_aoa[$_]}, substr ($seqs[$_]{'seq'}, $c, 3); } $c+=3; } for (1..$bootstrap_rpt) { my $sampled = _resample (\@btstrp_aoa); my ($ds, $dn) = $self->_get_av_ds_dn ($sampled) ; # is array ref push @{$bootstrap_values{'ds'}}, $ds; push @{$bootstrap_values{'dn'}}, $dn; } $results->{'D_s_var'} = sampling_variance($bootstrap_values{'ds'}); $results->{'D_n_var'} = sampling_variance($bootstrap_values{'dn'}); $results->{'z_score'} = ($results->{'D_n'} - $results->{'D_s'}) / sqrt($results->{'D_s_var'} + $results->{'D_n_var'} ); #print "bootstrapped var_syn = $results->{'D_s_var'} \n" ; #print "bootstrapped var_nc = $results->{'D_n_var'} \n"; #print "z is $results->{'z_score'}\n"; ### end of global set up of/perm look up data } sub _resample { my $ref = shift; my $codon_num = scalar (@{$ref->[0]}); my @altered; for (0..$codon_num -1) { #for each codon my $rand = int (rand ($codon_num)); for (0..$#$ref) { push @{$altered[$_]}, $ref->[$_][$rand]; } } my @stringed = map {join '', @$_}@altered; my @return; #now out in random name to keep other subs happy for (@stringed) { push @return, {id=>'1', seq=> $_}; } return \@return; } sub _get_av_ds_dn { # takes array of hashes of sequence strings and ids # my $self = shift; my $seq_ref = shift; my $result = shift if @_; my @caller = caller(1); my @seqarray = @$seq_ref; my $bootstrap_score_list; #for a multiple alignment considers all pairwise combinations# my %dsfor_average = (ds => [], dn => []); for (my $i = 0; $i < scalar @seqarray; $i++) { for (my $j = $i +1; $jwarn(" aligned sequences must be of equal length!"); next; } my $syn_site_count = count_syn_sites($seqarray[$i]{'seq'}, $synsites); my $syn_site_count2 = count_syn_sites($seqarray[$j]{'seq'}, $synsites); # print "syn 1 is $syn_site_count , syn2 is $syn_site_count2\n"; my ($syn_count, $non_syn_count, $gap_cnt) = analyse_mutations($seqarray[$i]{'seq'}, $seqarray[$j]{'seq'}); #get averages my $av_s_site = ($syn_site_count + $syn_site_count2)/2; my $av_ns_syn_site = length($seqarray[$i]{'seq'}) - $gap_cnt- $av_s_site ; #calculate ps and pn (p54) my $syn_prop = $syn_count / $av_s_site; my $nc_prop = $non_syn_count / $av_ns_syn_site ; #now use jukes/cantor to calculate D_s and D_n, would alter here if needed a different method my $d_syn = $self->jk($syn_prop); my $d_nc = $self->jk($nc_prop); #JK calculation must succeed for continuation of calculation #ret_value = -1 if error next unless $d_nc >=0 && $d_syn >=0; push @{$dsfor_average{'ds'}}, $d_syn; push @{$dsfor_average{'dn'}}, $d_nc; #if not doing bootstrap, calculate the pairwise comparisin stats if ($caller[3] =~ /calc_KaKs_pair/ || $caller[3] =~ /calc_all_KaKs_pairs/) { #now calculate variances assuming large sample my $d_syn_var = jk_var($syn_prop, length($seqarray[$i]{'seq'}) - $gap_cnt ); my $d_nc_var = jk_var($nc_prop, length ($seqarray[$i]{'seq'}) - $gap_cnt); #now calculate z_value #print "d_syn_var is $d_syn_var,and d_nc_var is $d_nc_var\n"; #my $z = ($d_nc - $d_syn) / sqrt($d_syn_var + $d_nc_var); my $z = ($d_syn_var + $d_nc_var) ? ($d_nc - $d_syn) / sqrt($d_syn_var + $d_nc_var) : 0; # print "z is $z\n"; push @$result , {S => $av_s_site, N=>$av_ns_syn_site, S_d => $syn_count, N_d =>$non_syn_count, P_s => $syn_prop, P_n=>$nc_prop, D_s => @{$dsfor_average{'ds'}}[-1], D_n => @{$dsfor_average{'dn'}}[-1], D_n_var =>$d_nc_var, D_s_var => $d_syn_var, Seq1 => $seqarray[$i]{'id'}, Seq2 => $seqarray[$j]{'id'}, z_score => $z, }; $self->warn (" number of mutations too small to justify normal test for $seqarray[$i]{'id'} and $seqarray[$j]{'id'}\n- use Fisher's exact, or bootstrap a MSA") if ($syn_count < 10 || $non_syn_count < 10 ) && $self->verbose > -1 ; }#endif } } #warn of failure if no results hashes are present #will fail if Jukes Cantor has failed for all pairwise combinations #$self->warn("calculation failed!") if scalar @$result ==0; #return results unless bootstrapping return $result if $caller[3]=~ /calc_all_KaKs/ || $caller[3] =~ /calc_KaKs_pair/; #else if getting average for bootstrap return( mean ($dsfor_average{'ds'}),mean ($dsfor_average{'dn'})) ; } sub jk { my ($self, $p) = @_; if ($p > 0.75) { $self->warn( " Jukes Cantor won't work -too divergent!"); return -1; } return -1 * (3/4) * (log(1 - (4/3) * $p)); } #works for large value of n (50?100?) sub jk_var { my ($p, $n) = @_; return (9 * $p * (1 -$p))/(((3 - 4 *$p) **2) * $n); } # compares 2 sequences to find the number of synonymous/non # synonymous mutations between them sub analyse_mutations { my ($seq1, $seq2) = @_; my %mutator = ( 2=> {0=>[[1,2], # codon positions to be altered [2,1]], # depend on which is the same 1=>[[0,2], [2,0]], 2=>[[0,1], [1,0]], }, 3=> [ [0,1,2], # all need to be altered [1,0,2], [0,2,1], [1,2,0], [2,0,1], [2,1,0] ], ); my $TOTAL = 0; # total synonymous changes my $TOTAL_n = 0; # total non-synonymous changes my $gap_cnt = 0; my %input; my $seqlen = length($seq1); for (my $j=0; $j< $seqlen; $j+=3) { $input{'cod1'} = substr($seq1, $j,3); $input{'cod2'} = substr($seq2, $j,3); #ignore codon if beeing compared with gaps! if ($input{'cod1'} =~ /\-/ || $input{'cod2'} =~ /\-/){ $gap_cnt += 3; #just increments once if there is a pair of gaps next; } my ($diff_cnt, $same) = count_diffs(\%input); #ignore if codons are identical next if $diff_cnt == 0 ; if ($diff_cnt == 1) { $TOTAL += $synchanges{$input{'cod1'}}{$input{'cod2'}}; $TOTAL_n += 1 - $synchanges{$input{'cod1'}}{$input{'cod2'}}; #print " \nfordiff is 1 , total now $TOTAL, total n now $TOTAL_n\n\n" } elsif ($diff_cnt ==2) { my $s_cnt = 0; my $n_cnt = 0; my $tot_muts = 4; #will stay 4 unless there are stop codons at intervening point OUTER:for my $perm (@{$mutator{'2'}{$same}}) { my $altered = $input{'cod1'}; my $prev= $altered; # print "$prev -> (", $t[$CODONS->{$altered}], ")"; for my $mut_i (@$perm) { #index of codon mutated substr($altered, $mut_i,1) = substr($input{'cod2'}, $mut_i, 1); if ($t[$CODONS->{$altered}] eq '*') { $tot_muts -=2; #print "changes to stop codon!!\n"; next OUTER; } else { $s_cnt += $synchanges{$prev}{$altered}; # print "$altered ->(", $t[$CODONS->{$altered}], ") "; } $prev = $altered; } # print "\n"; } if ($tot_muts != 0) { $TOTAL += ($s_cnt/($tot_muts/2)); $TOTAL_n += ($tot_muts - $s_cnt)/ ($tot_muts / 2); } } elsif ($diff_cnt ==3 ) { my $s_cnt = 0; my $n_cnt = 0; my $tot_muts = 18; #potential number of mutations OUTER: for my $perm (@{$mutator{'3'}}) { my $altered = $input{'cod1'}; my $prev= $altered; # print "$prev -> (", $t[$CODONS->{$altered}], ")"; for my $mut_i (@$perm) { #index of codon mutated substr($altered, $mut_i,1) = substr($input{'cod2'}, $mut_i, 1); if ($t[$CODONS->{$altered}] eq '*') { $tot_muts -=3; # print "changes to stop codon!!\n"; next OUTER; } else { $s_cnt += $synchanges{$prev}{$altered}; # print "$altered ->(", $t[$CODONS->{$altered}], ") "; } $prev = $altered; } # print "\n"; }#end OUTER loop #calculate number of synonymous/non synonymous mutations for that codon # and add to total if ($tot_muts != 0) { $TOTAL += ($s_cnt / ($tot_muts /3)); $TOTAL_n += 3 - ($s_cnt / ($tot_muts /3)); } } #endif $diffcnt = 3 } #end of sequencetraversal return ($TOTAL, $TOTAL_n, $gap_cnt); } sub count_diffs { #counts the number of nucleotide differences between 2 codons # returns this value plus the codon index of which nucleotide is the same when 2 #nucleotides are different. This is so analyse_mutations() knows which nucleotides # to change. my $ref = shift; my $cnt = 0; my $same= undef; #just for 2 differences for (0..2) { if (substr($ref->{'cod1'}, $_,1) ne substr($ref->{'cod2'}, $_, 1)){ $cnt++; } else { $same = $_; } } return ($cnt, $same); } =head2 get_syn_changes Title : get_syn_changes Usage : Bio::Align::DNAStatitics->get_syn_changes Function: Generate a hashref of all pairwise combinations of codns differing by 1 Returns : Symetic matrix using hashes First key is codon and each codon points to a hashref of codons the values of which describe type of change. my $type = $hash{$codon1}->{$codon2}; values are : 1 synonymous 0 non-syn -1 either codon is a stop codon Args : none =cut sub get_syn_changes { #hash of all pairwise combinations of codons differing by 1 # 1 = syn, 0 = non-syn, -1 = stop my %results; my @codons = _make_codons (); my $arr_len = scalar @codons; for (my $i = 0; $i < $arr_len -1; $i++) { my $cod1 = $codons[$i]; for (my $j = $i +1; $j < $arr_len; $j++) { my $diff_cnt = 0; for my $pos(0..2) { $diff_cnt++ if substr($cod1, $pos, 1) ne substr($codons[$j], $pos, 1); } next if $diff_cnt !=1; #synon change if($t[$CODONS->{$cod1}] eq $t[$CODONS->{$codons[$j]}]) { $results{$cod1}{$codons[$j]} =1; $results{$codons[$j]}{$cod1} = 1; } #stop codon elsif ($t[$CODONS->{$cod1}] eq '*' or $t[$CODONS->{$codons[$j]}] eq '*') { $results{$cod1}{$codons[$j]} = -1; $results{$codons[$j]}{$cod1} = -1; } # nc change else { $results{$cod1}{$codons[$j]} = 0; $results{$codons[$j]}{$cod1} = 0; } } } return %results; } =head2 dnds_pattern_number Title : dnds_pattern_number Usage : my $patterns = $stats->dnds_pattern_number($alnobj); Function: Counts the number of codons with no gaps in the MSA Returns : Number of codons with no gaps ('patterns' in PAML notation) Args : A Bio::Align::AlignI compliant object such as a Bio::SimpleAlign object. =cut sub dnds_pattern_number{ my ($self, $aln) = @_; return ($aln->remove_gaps->length)/3; } sub count_syn_sites { #counts the number of possible synonymous changes for sequence my ($seq, $synsite) = @_; __PACKAGE__->throw("not integral number of codons") if length($seq) % 3 != 0; my $S = 0; for (my $i = 0; $i< length($seq); $i+=3) { my $cod = substr($seq, $i, 3); next if $cod =~ /\-/; #deal with alignment gaps $S += $synsite->{$cod}{'s'}; } #print "S is $S\n"; return $S; } sub get_syn_sites { #sub to generate lookup hash for the number of synonymous changes per codon my @nucs = qw(T C A G); my %raw_results; for my $i (@nucs) { for my $j (@nucs) { for my $k (@nucs) { # for each possible codon my $cod = "$i$j$k"; my $aa = $t[$CODONS->{$cod}]; #calculate number of synonymous mutations vs non syn mutations for my $i (qw(0 1 2)){ my $s = 0; my $n = 3; for my $nuc (qw(A T C G)) { next if substr ($cod, $i,1) eq $nuc; my $test = $cod; substr($test, $i, 1) = $nuc ; if ($t[$CODONS->{$test}] eq $aa) { $s++; } if ($t[$CODONS->{$test}] eq '*') { $n--; } } $raw_results{$cod}[$i] = {'s' => $s , 'n' => $n }; } } #end analysis of single codon } } #end analysis of all codons my %final_results; for my $cod (sort keys %raw_results) { my $t = 0; map{$t += ($_->{'s'} /$_->{'n'})} @{$raw_results{$cod}}; $final_results{$cod} = { 's'=>$t, 'n' => 3 -$t}; } return \%final_results; } sub _make_codons { #makes all codon combinations, returns array of them my @nucs = qw(T C A G); my @codons; for my $i (@nucs) { for my $j (@nucs) { for my $k (@nucs) { push @codons, "$i$j$k"; } } } return @codons; } sub get_codons { #generates codon translation look up table# my $x = 0; my $CODONS = {}; for my $codon (_make_codons) { $CODONS->{$codon} = $x; $x++; } return $CODONS; } #########stats subs, can go in another module? Here for speed. ### sub mean { my $ref = shift; my $el_num = scalar @$ref; my $tot = 0; map{$tot += $_}@$ref; return ($tot/$el_num); } sub variance { my $ref = shift; my $mean = mean($ref); my $sum_of_squares = 0; map{$sum_of_squares += ($_ - $mean) **2}@$ref; return $sum_of_squares; } sub sampling_variance { my $ref = shift; return variance($ref) / (scalar @$ref -1); } 1; BioPerl-1.007002/Bio/Align/Graphics.pm000444000766000024 11164613155576320 17425 0ustar00cjfieldsstaff000000000000#Author: William McCaig #Date: 06/16/2006 #Purpose: To print visual images of alignments # #Requires: An alignment file # #Produces: An image file # #Revision History: #09/01/2006 - WDM - Introduction of "wrap" flag, allowing alignment to be # wrapped at a set base and stacked vertically # Addition of internal members y_num and y_size for tracking # of number of vertical panels and size of panels, # respectively # #09/06/2006 - WDM - Introduction of "p_legend" flag, for printing of an optional # colored legend when protein coloring is selected # #09/24/2008 - WDM - Test file created for the module # #03/01/2009 - YH - Introduction of "show_nonsynonymous" flag which enables # highlighting of nonsynonymous mutations in nucleotide # alignments. Addition of internal members codon_table and # missense_pos for translating codons -> amino acids and for # keeping track of missense mutation positions respectively. # #03/05/2009 - YH - Swapped names of subroutines x_label and y_label to match # both documentation and intuition. Finalized implementation # of show_nonsynonymous functionality. # docs after the code! package Bio::Align::Graphics; use vars qw( @PRINT_PARAMS %OK_FIELD); use 5.008003; use strict; use warnings; use GD; use GD::Simple; use Bio::AlignIO; use Data::Dumper; use POSIX qw(ceil floor); require Exporter; our @ISA = qw(Exporter); # Items to export into callers namespace by default. Note: do not export # names by default without a very good reason. Use EXPORT_OK instead. # Do not simply export all your public functions/methods/constants. # This allows declaration use PrintAlignment ':all'; # If you do not need this, moving things directly into @EXPORT or @EXPORT_OK # will save memory. our %EXPORT_TAGS = ( 'all' => [ qw( ) ] ); our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } ); our @EXPORT = qw( ); # Preloaded methods go here. our %FONT_TABLE = (1 => gdTinyFont, 2 => gdSmallFont, 3 => gdMediumBoldFont, 4 => gdLargeFont, 5 => gdGiantFont ); our %PROTEIN_COLORS = ('Q' => [255, 0, 204], 'E' => [255, 0, 102], 'D' => [255, 0, 0] , 'S' => [255, 51, 0] , 'T' => [255, 102, 0 ], 'G' => [255, 153, 0] , 'P' => [255, 204, 0] , 'C' => [255, 255, 0] , 'A' => [204, 255, 0] , 'V' => [153, 255, 0], 'I' => [102, 255, 0] , 'L' => [51 , 255, 0] , 'M' => [0, 255, 0] , 'F' => [0 , 255, 102] , 'Y' => [0 , 255, 204], 'W' => [0, 204, 255] , 'H' => [0, 102, 255] , 'R' => [0, 0, 255] , 'K' => [102, 0, 255] , 'N' => [204, 0, 255] ); ################################################################# #New sub new { my $class = shift; my %options = @_; my $self = { #####OPTIONS##### #Display Defaults font => defined($options{font}) ? $FONT_TABLE{$options{font}} : $FONT_TABLE{2}, x_label => defined($options{x_label}) ? $options{x_label} : 1, y_label => defined($options{y_label}) ? $options{y_label} : 1, #Colors bg_color => $options{bg_color} || 'white', fg_color => $options{font_color} || 'black', x_label_color => $options{x_label_color} || 'blue', y_label_color => $options{y_label_color} || 'red', p_color => $options{p_color} || undef, p_legend => $options{p_legend} || undef, p_color_table => undef, #Sequence Defaults reference => $options{reference} || undef, reference_id => $options{reference_id} || undef, match_char => $options{match_char} || ".", block_size => defined($options{block_size}) ? $options{block_size} : 10, block_space => defined ($options{block_space}) ? ($options{block_space} * ($options{font} ? $FONT_TABLE{$options{font}}->width : $FONT_TABLE{2}->width)) : ( ($options{font} ? ($FONT_TABLE{$options{font}}->width * 2 ) : ($FONT_TABLE{2}->width * 2)) ), wrap => $options{wrap} || 80, show_nonsynonymous => $options{show_nonsynonymous} || undef, # If turned on, will highlight nonsynonymous (missense) mutations. Valid only for nucleotide alignments #Padding pad_left => $options{pad_left} || 5, #space between x label and border pad_right => $options{pad_right} || 5, #space between end of sequences and border pad_top => $options{pad_top} || 5, #space between y label and border pad_bottom => $options{pad_bottom} || 5, #space between bottom of sequences and border x_label_space => $options{x_label_space} || 1, #space between x label and sequences y_label_space => $options{y_label_space} || 1, #space between y label and sequences #Labels labels => $options{labels} || undef, dm_labels => $options{dm_labels} || undef, dm_label_start => $options{dml_start} || undef, dm_label_end => $options{dml_end} || undef, dm_label_color => $options{dml_color} || undef, domain_start => $options{dm_start} || undef, domain_end => $options{dm_end} || undef, domain_color => $options{dm_color} || undef, #File Defaults align => $options{align} || undef, output => $options{output} || undef, out_format => $options{out_format} || undef, ####PRIVATE VALUES##### image => $options{image} || undef, seq_format => undef, #X and Y size of char x_char_size => ($options{font} ? $FONT_TABLE{$options{font}}->width : $FONT_TABLE{2}->width), y_char_size => ($options{font} ? $FONT_TABLE{$options{font}}->height : $FONT_TABLE{2}->height), #Image W & H width => undef, #overall width of the image height => undef, #overall height of image #Sequences sequences => undef, seq_ids => undef, ref_sequence => undef, id_length => 0, seq_length => $options{align}->length() || 0, no_sequences => $options{align}->num_sequences() || 0, seq_start_x => undef, seq_start_y => undef, start => $options{start} || 1, end => $options{end} || $options{align}->length(), y_num => undef, y_size => undef, footer_size => 110, footer_start => undef }; bless ($self, $class); die "new:Must supply alignment for drawing!\n" unless defined ($self->{align}); foreach my $seq ($self->{align}->each_seq) { $self->{id_length} = ( length($seq->id()) > $self->{id_length} ) ? length($seq->id()) : $self->{id_length}; if( $self->{reference_id} && ($seq->id() eq $self->{reference_id}) ) { @{$self->{ref_sequence}} = split //, $seq->seq; unshift @{$self->{sequences}}, $seq->seq; unshift @{$self->{seq_ids}}, $seq->id(); }else { push @{$self->{sequences}}, $seq->seq; push @{$self->{seq_ids}}, $seq->id(); } if(!defined($self->{seq_format})) { $self->{seq_format} = $seq->alphabet; } } if(!($self->{reference_id}) ) { @{$self->{ref_sequence}} = split //, ${$self->{sequences}}[0]; $self->{reference_id} = ${$self->{seq_ids}}[0]; } $self->{y_num} = ($self->{seq_length} > $self->{wrap}) ? ( sprintf( "%.0f", ( ($self->{seq_length} / $self->{wrap}) + .5) ) ) : 1; $self->{y_size} = ( ($self->{no_sequences} + $self->{pad_bottom}) * $self->{y_char_size}); $self->{seq_start_x} = ($self->{pad_left} + $self->{id_length} + $self->{x_label_space}) * $self->{x_char_size}; if( defined($self->{show_nonsynonymous}) ) # Extra column changes dimensions { $self->{seq_length_aa} = ($self->{seq_length} / 3) + $self->{seq_length}; # Consider length of sequence plus extra column every 3 nucleotides $self->{seq_start_y} = ($self->{pad_top} + length($self->{seq_length_aa}) + $self->{y_label_space}) * $self->{y_char_size}; $self->{width} = $self->{seq_start_x} + ((( $self->{wrap} / $self->{block_size}) + 1) * $self->{block_space}) + ( ($self->{wrap} + $self->{pad_right}) * ($self->{x_char_size} + 1.2) ) + ( ($self->{seq_length} / 3) * 2); # Needed to add this for width to fit whole sequence on one line }else { $self->{seq_start_y} = ($self->{pad_top} + length($self->{seq_length}) + $self->{y_label_space}) * $self->{y_char_size}; $self->{width} = $self->{seq_start_x} + ((( $self->{wrap} / $self->{block_size}) + 1) * $self->{block_space}) + ($self->{wrap} + $self->{pad_right}) * $self->{x_char_size}; } $self->{footer_start} = $self->{seq_start_y} + $self->{y_size} * $self->{y_num}; if(defined($self->{p_color}) && defined($self->{p_legend}) && $self->{p_legend}){ $self->{height} = $self->{seq_start_y} + $self->{footer_size} + $self->{y_size} * $self->{y_num}; }else{ $self->{height} = $self->{seq_start_y} + $self->{y_size} * $self->{y_num}; } $self->{image} = GD::Simple->new($self->{width},$self->{height}); $self->{image}->alphaBlending(1); $self->{image}->saveAlpha(1); $self->{image}->bgcolor($self->{bg_color}); $self->{image}->fgcolor($self->{fg_color}); $self->{image}->rectangle(0,0,$self->{width}-1, $self->{height} - 1); return $self; } #End new Subroutine######################################################### sub draw{ my $self = shift; die "draw:Must supply alignment for drawing!\n" unless defined ($self->{align}); if(defined($self->{x_label}) && $self->{x_label}) { $self->x_label(); } if(defined($self->{y_label}) && $self->{y_label}) { $self->y_label(); } if(defined($self->{domain_start}) && defined($self->{domain_end}) && not defined($self->{p_color}) ) { $self->_draw_domain(); } # if( defined($self->{show_nonsynonymous}) && ( $self->{seq_format} eq "protein" ) ) { die "draw:Option show_nonsynonymous only works with Nucleotide alignments!\n"; }elsif ( defined($self->{show_nonsynonymous}) ) { $self->{codon_table} = Bio::Tools::CodonTable->new(); $self->{missense_pos} = {}; # print STDERR "You are using option show_nonsynonymous. Option works best if wrap value is a multiple of 4.\n" } if(defined($self->{p_color}) && $self->{seq_format} eq "protein") { $self->_draw_colored_sequences(); if(defined($self->{p_legend}) && $self->{p_legend}) { $self->_draw_legend(); } }elsif(defined($self->{p_color}) && ($self->{seq_format} ne "protein")) { die "draw:Option p_color only works with Protein alignments!\n"; }else { $self->_draw_sequences(); } if(defined($self->{dm_label_start})) { $self->_domain_label(); } if($self->{output}) { open my $OUTPUT, '>', $self->{output} or die "Could not read file '$self->{output}': $!\n"; binmode $OUTPUT; if(defined($self->{out_format})) { SWITCH: { if($self->{out_format} eq "png") {print $OUTPUT $self->{image}->png; last SWITCH;} if($self->{out_format} eq "jpeg") {print $OUTPUT $self->{image}->jpeg; last SWITCH;} if($self->{out_format} eq "gif") {print $OUTPUT $self->{image}->gif; last SWITCH;} if($self->{out_format} eq "gd") {print $OUTPUT $self->{image}->gd; last SWITCH;} } }else { print $OUTPUT $self->{image}->png; } close $OUTPUT; }else { binmode STDOUT; if(defined($self->{out_format})) { SWITCH: { if($self->{out_format} eq "png") {print STDOUT $self->{image}->png; last SWITCH;} if($self->{out_format} eq "jpeg") {print STDOUT $self->{image}->jpeg; last SWITCH;} if($self->{out_format} eq "gif") {print STDOUT $self->{image}->gif; last SWITCH;} if($self->{out_format} eq "gd") {print STDOUT $self->{image}->gd; last SWITCH;} } }else { print STDOUT $self->{image}->png; } }#End Output if/else #print "Left\tRight\tTop\tBottom\n"; #print $self->{pad_left}, "\t", $self->{pad_right}, "\t", $self->{pad_top}, "\t", $self->{pad_bottom}, "\n"; }; ########################################## #Draws Sequences sub _draw_sequences{ my $self = shift; my $block_num = 0; my $block_total = 0; my $print_char; $self->{image}->fgcolor($self->{fg_color}); for (my $i=0; $i < $self->{no_sequences}; $i++) { my @letters = split //, ${$self->{sequences}}[$i]; my $y_num = $self->{y_num}; #sprintf( "%.0f", ( ($self->{seq_length} / $self->{wrap}) + .5) ) - 1; my $y_char = $self->{y_size}; #( ($self->{no_sequences} + $self->{pad_bottom}) * $self->{y_char_size}); for(my $k=0; $k<=$y_num; $k++) { my $x_char = $k * $self->{wrap}; for (my $j=$x_char; $j <= ( ($x_char + $self->{wrap}) - 1); $j++) { last unless defined($letters[$j]); # If show_nonsynonymous is on, and this is the 3rd nucleotide, # save the codon and amino acid for comparison my ($codon, $aa); if ((defined($self->{show_nonsynonymous})) && ((($j+1) % 3) == 0)) { $codon = $letters[$j-2] . $letters[$j-1] . $letters[$j]; $aa = $self->{codon_table}->translate($codon); } if( $self->{reference} ) { if(${$self->{seq_ids}}[$i] eq $self->{reference_id}) { $print_char = $letters[$j]; }else { if($letters[$j] eq ${$self->{ref_sequence}}[$j]) { $print_char = $self->{match_char}; }else { $print_char = $letters[$j]; } } }else { $print_char = $letters[$j]; } if( ( ($j + 1) % ($self->{block_size})) == 0) { $block_num = $self->{block_space}; }else { $block_num = 0; } #print "J is: $j\n"; #print "Char is: $print_char\n"; my $new_x_pos = $self->{seq_start_x} + ( ($j - $x_char) * $self->{x_char_size}) + $block_total; my $new_y_pos = $self->{seq_start_y} + ($i * $self->{y_char_size}) + ($k * $y_char); $new_x_pos += ( ( floor( ($j-$x_char)/3 ) * $self->{x_char_size} ) + ( ( floor( ($j-$x_char)/3 ) ) * 6 )) if ( defined($self->{show_nonsynonymous}) ); $self->{image}->moveTo( $new_x_pos, $new_y_pos ); $self->{image}->font($self->{font}); $self->{image}->string($print_char); if ( (defined($self->{show_nonsynonymous})) && ((($j+1) % 3) == 0) ) { $new_x_pos += ($self->{x_char_size} + 3); $self->{image}->moveTo( $new_x_pos, $new_y_pos ); # If show_nonsynonymous is on, and this is the 3rd nucleotide # on reference, print the amino acid after the nucleotide if(($self->{reference}) && (${$self->{seq_ids}}[$i] eq $self->{reference_id})) { $self->{image}->font(gdMediumBoldFont); $self->{image}->string($aa); $self->{image}->font($self->{font}); }elsif ( ( $self->{reference} ) && ( ${$self->{seq_ids}}[$i] ne $self->{reference_id} ) ) { # In case current sequence is not reference my $ref_codon = ${$self->{ref_sequence}}[$j-2] . ${$self->{ref_sequence}}[$j-1] . ${$self->{ref_sequence}}[$j]; my $ref_aa = $self->{codon_table}->translate($ref_codon); if ( $ref_aa eq $aa ) # Synonymous mutation { $self->{image}->string($self->{match_char}); }else # Nonsynonymous mutation { $self->{image}->font(gdMediumBoldFont); $self->{image}->string($aa); $self->{image}->font($self->{font}); # Highlight nonsynonymous mutations by drawing a rectangle around them if ( ( ${$self->{seq_ids}}[$i] ne $self->{reference_id} ) && !( ${$self->{missense_pos}}{$j} ) ) { ${$self->{missense_pos}}{$j} = 1; $self->{image}->bgcolor(undef); $self->{image}->rectangle( $new_x_pos - 2, ( $new_y_pos - ( ( $self->{y_char_size} * ($i+1)) ) ) - 2, ( $new_x_pos + ( $self->{x_char_size} + 1) ), ( $new_y_pos + ( $self->{y_char_size} * ( $self->{no_sequences} - ( $i+1 ) ) ) ) + 2); $self->{image}->bgcolor($self->{bg_color}); } } }else # No reference sequence defined { $self->{image}->string($aa); } } if( defined($self->{labels}) && $i == ($self->{no_sequences} - 1)) { if(${$self->{labels}}{$j + 1}) { my $label = ${$self->{labels}}{$j + 1}; my $offset = defined($self->{dm_label_start}) ? 3 : 0; $self->{image}->moveTo($self->{seq_start_x} + ( ( ($j - $x_char) + 1.25) * $self->{x_char_size}) + $block_total, $self->{seq_start_y} + (($self->{no_sequences}) * $self->{y_char_size}) + ($k * $y_char) + ( (length($label) + $offset) * ($self->{x_char_size}) ) ); $self->{image}->font($self->{font}); $self->{image}->angle(-90); $self->{image}->string($label); $self->{image}->angle(0); } } $block_total += $block_num; } $block_total = 0; } } } # WARNING YH - This function has not been modified to work with show_nonsynonymous: needs test data to make sure it will work! ############################################## #Draw Domain Label sub _domain_label{ my $self = shift; my $start_block_total = 0; my $end_block_total = 0; my $wrap_block_total = 0; my $y_char = $self->{y_size};# ( ($self->{no_sequences} + $self->{pad_bottom}) * $self->{y_char_size}); for(my $i = 0; $i <= $#{$self->{dm_label_start}}; $i++) { my $start = ${$self->{dm_label_start}}[$i]; my $end = ${$self->{dm_label_end}}[$i]; my $y_num_start = int( $start / $self->{wrap}); my $y_num_end = int( $end / $self->{wrap}); my $x_num_start; if($start >= $self->{wrap}) { $x_num_start = ($start % $self->{wrap}) - 1; }else { $x_num_start = $start - 1; } my $x_num_end; if($end >= $self->{wrap}) { $x_num_end = ($end % $self->{wrap}); }else { $x_num_end = $end; } my $label = ${$self->{dm_labels}}[$i]; my $color = ${$self->{dm_label_color}}[$i] || ${$self->{dm_label_color}}[-1] || "silver"; my $label_x = (($x_num_end - $x_num_start) / 2) - (length($label) / 2); my $label_x_start = (($self->{wrap} - $x_num_start) / 2) - (length($label) / 2); my $label_x_end = ($x_num_end / 2) - (length($label) / 2); $start_block_total = ( ($x_num_start - ($x_num_start % $self->{block_size}) ) / $self->{block_size} ) * $self->{block_space}; $end_block_total = ( ($x_num_end - ($x_num_end % $self->{block_size}) ) / $self->{block_size} ) * $self->{block_space}; $wrap_block_total = ( ($self->{wrap} - ( ($self->{wrap} - 1) % $self->{block_size}) ) / $self->{block_size} ) * $self->{block_space}; $self->{image}->bgcolor($color); $self->{image}->fgcolor($color); if($y_num_start == $y_num_end) #if the label does not cross the wrap line { $self->{image}->rectangle( $self->{seq_start_x} + ( ($x_num_start) * $self->{x_char_size} ) + $start_block_total, $self->{seq_start_y} + (($self->{no_sequences}) * $self->{y_char_size}) + ($y_num_start * $y_char), $self->{seq_start_x} + (($x_num_end) * $self->{x_char_size}) + $end_block_total, $self->{seq_start_y} + (($self->{no_sequences} + 1) * $self->{y_char_size}) + ($y_num_start * $y_char)); $self->{image}->fgcolor($self->{fg_color}); $self->{image}->bgcolor($self->{bg_color}); $self->{image}->moveTo( $self->{seq_start_x} + ( ($x_num_start + $label_x) * $self->{x_char_size}) + $start_block_total, $self->{seq_start_y} + (($self->{no_sequences} + 1) * $self->{y_char_size}) + ($y_num_start * $y_char) ); $self->{image}->font($self->{font}); $self->{image}->string($label); }else { $self->{image}->rectangle( $self->{seq_start_x} + ( ($x_num_start) * $self->{x_char_size} ) + $start_block_total, $self->{seq_start_y} + (($self->{no_sequences}) * $self->{y_char_size}) + ($y_num_start * $y_char), $self->{seq_start_x} + (($self->{wrap}) * $self->{x_char_size}) + $wrap_block_total, $self->{seq_start_y} + (($self->{no_sequences} + 1) * $self->{y_char_size}) + ($y_num_start * $y_char)); $self->{image}->rectangle( $self->{seq_start_x} , $self->{seq_start_y} + (($self->{no_sequences}) * $self->{y_char_size}) + ($y_num_end * $y_char), $self->{seq_start_x} + (($x_num_end) * $self->{x_char_size}) + $end_block_total, $self->{seq_start_y} + (($self->{no_sequences} + 1) * $self->{y_char_size}) + ($y_num_end * $y_char)); $self->{image}->fgcolor($self->{fg_color}); $self->{image}->bgcolor($self->{bg_color}); $self->{image}->moveTo( $self->{seq_start_x} + ( ($x_num_start + $label_x_start) * $self->{x_char_size}) + $start_block_total, $self->{seq_start_y} + (($self->{no_sequences} + 1) * $self->{y_char_size}) + ($y_num_start * $y_char) ); $self->{image}->font($self->{font}); $self->{image}->string($label); $self->{image}->moveTo( $self->{seq_start_x} + ( $label_x_end * $self->{x_char_size}), $self->{seq_start_y} + (($self->{no_sequences} + 1) * $self->{y_char_size}) + ($y_num_end * $y_char) ); $self->{image}->font($self->{font}); $self->{image}->string($label); } } } ############################################## #Draw Y Label sub y_label{ my $self = shift; $self->{image}->fgcolor($self->{y_label_color}); my $y_num = $self->{y_num}; #sprintf( "%.0f" , (($self->{seq_length} / $self->{wrap}) + .5)) - 1; my $y_char = $self->{y_size}; # ( ($self->{no_sequences} + $self->{pad_bottom}) * $self->{y_char_size}); for(my $k=0; $k<$y_num; $k++) { for (my $i=0; $i< $self->{no_sequences}; $i++) { $self->{image}->moveTo($self->{pad_left}, $self->{seq_start_y} + ($i * $self->{y_char_size}) + ($k * $y_char) ); $self->{image}->font($self->{font}); $self->{image}->string(${$self->{seq_ids}}[$i]); } } } ##################################################### #Draw X Label sub x_label{ my $self = shift; my $block_num = 0; my $block_total = 0; $self->{image}->fgcolor($self->{x_label_color}); my $y_char = $self->{y_size}; # ( ($self->{no_sequences} + $self->{pad_bottom}) * $self->{y_char_size}); for (my $i=1; $i<= $self->{seq_length}; $i++) { my $y_num = floor( $i / $self->{wrap}); # Used to be int(), but perl documentation advises against this my $x_num; if($i >= $self->{wrap}) { $x_num = ($i % $self->{wrap}); }else { $x_num = $i; } my @digits = split //, reverse($i); if( ($i % $self->{block_size}) == 0) { $block_num = $self->{block_space}; }else { $block_num = 0; } if( (($i - 1) % $self->{block_size}) == 0) { for (my $j=0; $j<=$#digits; $j++) { if ( defined($self->{show_nonsynonymous}) ) { $self->{image}->moveTo($self->{seq_start_x} + $block_total + ( ($x_num-1) * $self->{x_char_size}) + ( ( floor( ($x_num-1)/3 ) * $self->{x_char_size} ) + ( ( floor( ($x_num-1)/3 ) ) * 6 )), ($self->{pad_top} + length($self->{seq_length_aa}) - $j) * $self->{y_char_size} + ($y_num * $y_char)); }else { $self->{image}->moveTo($self->{seq_start_x} + $block_total + ( ($x_num-1) * $self->{x_char_size}), ($self->{pad_top} + length($self->{seq_length}) - $j) * $self->{y_char_size} + ($y_num * $y_char)); } $self->{image}->font($self->{font}); $self->{image}->string($digits[$j]); } } if($x_num == 0) { $block_total = 0; }else { $block_total += $block_num; } } } #################################################### #Domain Highlighting sub _draw_domain{ my $self = shift; my $block_total = 0; my ($start, $end, $block_num); my $y_char = $self->{y_size}; # ( ($self->{no_sequences} + $self->{pad_bottom}) * $self->{y_char_size}); for (my $k=0; $k <= $#{$self->{domain_start}}; $k++) { #print STDERR join "\n", GD::Simple->color_names; my $dmc = $self->{domain_color}[$k] || $self->{domain_color}[-1] || "silver"; $start = ${$self->{domain_start}}[$k] - 1; $end = ${$self->{domain_end}}[$k] - 1; for (my $i=0; $i < $self->{no_sequences}; $i++) { for (my $j = $start; $j <= $end; $j++) { my $y_num = int( $j / $self->{wrap}); my $x_num; if($j >= $self->{wrap}) { $x_num = ($j % $self->{wrap}); }else { $x_num = $j; } #print "J: $j\nXNUM: $x_num\nYNUM: $y_num\n"; $block_total = ( ($x_num - ($x_num % $self->{block_size}) ) / $self->{block_size} ) * $self->{block_space}; $self->{image}->bgcolor($dmc); $self->{image}->fgcolor($dmc); if ( defined($self->{show_nonsynonymous}) ) { # NOTE To shade amino acids as well, change $x_num HERE and HERE to $x_num + 1 $self->{image}->rectangle( $self->{seq_start_x} + ( ($x_num ) * $self->{x_char_size} ) + $block_total - 1 + ( ( floor( $x_num / 3 ) * $self->{x_char_size} ) + ( ( floor( $x_num / 3 ) ) * 6 )), $self->{seq_start_y} + ( $i * $self->{y_char_size} ) - $self->{y_char_size} + ($y_num * $y_char) , $self->{seq_start_x} + (($x_num + 1) * $self->{x_char_size}) + $block_total - 1 + ( ( floor( ($x_num)/3 ) * $self->{x_char_size} ) + ( ( floor( ($x_num)/3 ) ) * 6 )), $self->{seq_start_y} + ( $i * $self->{y_char_size}) + ($y_num * $y_char)); }else { $self->{image}->rectangle( $self->{seq_start_x} + ( ($x_num ) * $self->{x_char_size} ) + $block_total - 1, $self->{seq_start_y} + ( $i * $self->{y_char_size} ) - $self->{y_char_size} + ($y_num * $y_char) , $self->{seq_start_x} + (($x_num + 1) * $self->{x_char_size}) + $block_total - 1, $self->{seq_start_y} + ( $i * $self->{y_char_size}) + ($y_num * $y_char)); } #$self->{image}->rectangle( $self->{seq_start_x} + ( ($j) * $self->{x_char_size} ) + $block_total, $self->{seq_start_y} + ($i - 1 * $self->{y_char_size}), $self->{seq_start_x} + (($j + 1) * $self->{x_char_size}) + $block_total , $self->{seq_start_y} + ( ($i) * $self->{y_char_size})); $self->{image}->fgcolor($self->{fg_color}); $self->{image}->bgcolor($self->{bg_color}); } $block_total = 0; } } } sub _draw_colored_sequences{ my $self = shift; my $block_num = 0; my $block_total = 0; my $print_char; my %colors; for my $values ( keys %PROTEIN_COLORS) { #print STDERR "$values : @{ $PROTEIN_COLORS{$values} }\n"; $colors{$values} = $self->{image}->colorAllocate(@{ $PROTEIN_COLORS{$values} }); } $self->{p_color_table} = \%colors; $self->{image}->fgcolor($self->{fg_color}); for (my $i=0; $i < $self->{no_sequences}; $i++) { my @letters = split //, ${$self->{sequences}}[$i]; my $y_num = $self->{y_num}; #sprintf( "%.0f", ( ($self->{seq_length} / $self->{wrap}) + .5) ) - 1; my $y_char = $self->{y_size}; #( ($self->{no_sequences} + $self->{pad_bottom}) * $self->{y_char_size}); for(my $k=0; $k<=$y_num; $k++) { my $x_char = $k * $self->{wrap}; for (my $j=$x_char; $j <= ( ($x_char + $self->{wrap}) - 1); $j++) { last unless defined($letters[$j]); $print_char = $letters[$j]; if( ( ($j + 1) % ($self->{block_size})) == 0) { $block_num = $self->{block_space}; }else { $block_num = 0; } #print "Chunk Space: $chunk_space\n"; $self->{image}->bgcolor($colors{$print_char}); $self->{image}->fgcolor($colors{$print_char}); $self->{image}->rectangle( $self->{seq_start_x} + ( ($j - $x_char) * $self->{x_char_size} ) + $block_total - 1 , $self->{seq_start_y} + ( $i * $self->{y_char_size} ) + ($k * $y_char) - $self->{y_char_size} , $self->{seq_start_x} + (($j - $x_char + 1) * $self->{x_char_size}) + $block_total - 1 , $self->{seq_start_y} + ($k * $y_char) + ( $i * $self->{y_char_size})); $self->{image}->moveTo($self->{seq_start_x} + ( ($j - $x_char) * $self->{x_char_size}) + $block_total, $self->{seq_start_y} + ($k * $y_char) + ($i * $self->{y_char_size}) ); $self->{image}->fgcolor($self->{fg_color}); $self->{image}->font($self->{font}); $self->{image}->string($print_char); if( defined($self->{labels}) && $i == ($self->{no_sequences} - 1)) { if(${$self->{labels}}{$j + 1}) { my $label = ${$self->{labels}}{$j + 1}; my $offset = defined($self->{dm_label_start}) ? 3 : 0; $self->{image}->moveTo($self->{seq_start_x} + ( ( ($j - $x_char) + 1.25) * $self->{x_char_size}) + $block_total, $self->{seq_start_y} + (($self->{no_sequences}) * $self->{y_char_size}) + ($k * $y_char) + ( (length($label) + $offset) * ($self->{x_char_size}) ) ); $self->{image}->font($self->{font}); $self->{image}->angle(-90); $self->{image}->string($label); $self->{image}->angle(0); } } $block_total += $block_num; } $block_total = 0; } } } sub _draw_legend{ my $self = shift; my $title_font = $FONT_TABLE{3}; my @l_order = ("Negatively Charged", "Positively Charged", "Hydrophobic", "Aromatic", "Found in Loops", "Large Polar Acids"); my %legend = ("Negatively Charged" => ["D" , "E"] , "Positively Charged" => ["K", "R"] , "Hydrophobic" => ["A","F","I","L","M","V","W","Y"] , "Aromatic" => ["F", "H", "W", "Y"] , "Found in Loops" => ["D", "G", "P", "S", "T"] , "Large Polar Acids" => ["H", "K", "N", "Q", "R"]); my $x1 = 2; my $x2 = 42; my $colors = $self->{p_color_table}; my $y_start = $self->{footer_start}; my $label = "Protein Color Legend"; $self->{image}->bgcolor($self->{bg_color}); $self->{image}->fgcolor($self->{fg_color}); $self->{image}->rectangle(1,$y_start, 70 * $self->{x_char_size}, $self->{height} - 2); $self->{image}->moveTo((35 - (length($label) / 2) ) * $self->{x_char_size} , $y_start + $self->{y_char_size}); $self->{image}->font($title_font); $self->{image}->string($label); my $count = 3; foreach my $c_label (@l_order) { if( ($count % 2) == 0) { $self->{image}->moveTo( $x2 * $self->{x_char_size}, $y_start + ( ($count - 1) * $self->{y_char_size})); $self->{image}->font($self->{font}); $self->{image}->string($c_label); my $i = 0; foreach my $chars(@{$legend{$c_label}}) { $self->{image}->bgcolor($$colors{$chars}); $self->{image}->fgcolor($$colors{$chars}); $self->{image}->rectangle( ($x2 + 20 + $i) * $self->{x_char_size}, $y_start + ( ($count - 2) * $self->{y_char_size}), ($x2 + 20 + $i + 1) * $self->{x_char_size}, $y_start + ( ($count -1) * $self->{y_char_size})); $self->{image}->bgcolor($self->{bg_color}); $self->{image}->fgcolor($self->{fg_color}); $i++; } }else { $self->{image}->moveTo($x1 * $self->{x_char_size} , $y_start + ($count * $self->{y_char_size})); $self->{image}->font($self->{font}); $self->{image}->string($c_label); my $i = 0; foreach my $chars(@{$legend{$c_label}}) { $self->{image}->bgcolor($$colors{$chars}); $self->{image}->fgcolor($$colors{$chars}); $self->{image}->rectangle( ($x1 + 20 + $i) * $self->{x_char_size}, $y_start + ( ($count - 1) * $self->{y_char_size}), ($x1 + 20 + $i + 1) * $self->{x_char_size}, $y_start + ( ($count) * $self->{y_char_size})); $self->{image}->bgcolor($self->{bg_color}); $self->{image}->fgcolor($self->{fg_color}); $i++; } } $count += 1; } } ######################################## #####ACCESSORS##### sub width{ my $self = shift; return $self->{image}->width if exists $self->{image}; } sub height{ my $self = shift; return $self->{image}->height if exists $self->{image}; } sub aln_length{ my $self = shift; return $self->{seq_length} if exists $self->{seq_length}; } sub aln_format{ my $self = shift; return $self->{seq_format} if exists $self->{seq_format}; } sub no_sequences{ my $self = shift; return $self->{no_sequences} if exists $self->{no_sequences}; } 1; __END__ =head1 NAME Bio::Align::Graphics - Graphic Rendering of Bio::Align::AlignI Objects =head1 SYNOPSIS use Bio::Align::Graphics; #Get an AlignI object, usually by using Bio::AlignIO my $file=shift @ARGV; my $in=new Bio::AlignIO(-file=>$file, -format=>'clustalw'); my $aln=$in->next_aln(); #Create a new Graphics object my $print_align = new Bio::Align::Graphics(align => $aln); #Draw the alignment $print_align->draw(); =head1 DESCRIPTION Bio::Align::Graphics is a module designed to create image files out of Bio::Align::AlignI objects. An alignment may be manipulated with various formatting and highlighting options. An example: #!/usr/bin/perl -w use Bio::AlignIO; use Bio::Align::Graphics; use strict; #Get an alignment file my $file = shift @ARGV; #Create an AlignI object using AlignIO my $in=new Bio::AlignIO(-file=>$file, -format=>'clustalw'); #Read the alignment my $aln=$in->next_aln(); #Create some domains for highlighting my @domain_start = ( 25 , 50, 80 ); my @domain_end = ( 40 , 60 , 100 ); my @domain_color = ( 'red' , 'cyan' , 'green' ); #Create Labels for the domains my @dml = ("CARD", "Proline Rich", "Transmembrane"); my @dml_start = (25, 50, 80); my @dml_end = (40, 60, 100); my @dml_color = ("lightpink", "lightblue", "lightgreen"); #Create individual labels my %labels = ( 145 => "Hep-c target"); my $print_align = new Bio::Align::Graphics( align => $aln, pad_bottom => 5, domain_start => \@domain_start, domain_end => \@domain_end, dm_color => \@domain_color, dm_labels => \@dml, dm_label_start => \@dml_start, dm_label_end => \@dml_end, dm_label_color => \@dml_color, labels => \%labels, out_format => "png"); $print_align->draw(); =head1 METHODS This section describes the class and object methods for Bio::Align::Graphics. Typically you will begin by creating a Bio::Align::Graphics object, passing it an alignment object created using Bio::AlignIO. The Bio::Align::Graphics-Enew() method has a number of configuration variables that allow you to control the appearance of the final image. You will then call the draw() method to output the final image. =head1 CONSTRUCTORS new() is the constructor for Bio::Align::Graphics: =over 4 =item $print_align = Bio::Align::Graphics-Enew(@options) The new() method creates a new graphics object. The options are a set of tag/value pairs as follows: Option Value Default ------ ----- ------- align Bio::AlignI object None, must be supplied to draw an alignment output Filename to print image to STDOUT out_format png, jpeg, gif, gd png font Size of font, ranging from 1 to 5 2 and equal to the standard GD fonts ranging from gdTinyFont to gdGiantFont x_label Draws a scale numbering alignment true bases along top of image, every x bases are numbered, where x is the block_size option y_label Draws sequence ids of alignment true along left side of image bg_color Background color of the image white font_color Color of the font used for drawing black the alignment characters x_label_color Color of the font used for drawing red the base scale characters y_label_color Color of the font used for drawing blue the sequence id characters p_color Colors protein bases according to false a coloring scheme proposed by W.R. Taylor(Protein Engineering, vol 10 no 7, 1997), only works with protein alignments pad_top Additional whitespace characters 5 between top of image and x-label pad_bottom Additional whitespace characters 5 between bottom of image and alignment pad_left Additional whitespace characters 5 between left side of image and y-label pad_right Additional whitespace characters 5 between right side of image and alignment x_label_space Additional whitespace characters 1 between x_label and alignment y_label_space Additional whitespace characters 1 between y_label and alignment reference Characters which are identical to false the reference sequence are replaced with the match character reference_id Sequence id of the sequence to use First sequence as the reference supplied in alignment match_char Character to replace identical bases . in aligned sequences block_size Number of bases to group together 10 when printing alignment, groups are separated by whitespace block_space Amount of character whitespace to 2 separate groups of bases by labels A hash containing labels to be none printed beneath the alignment, where the keys are the bases to print the values at dm_start An array containing start bases none for highlighting of segments of the alignment, paired with dm_end option dm_end An array containing end bases none for highlighting of segments of the alignment, paired with dm_start options dm_color An array containing colors for silver highlighting segments of bases denoted by the coordinates located in the dm_start and dm_end options dml_start An array containing start bases none for addition of domain labels underneath the alignment, paired with dml_end dml_end An array containing end bases none for addition of domain labels underneath the alignment, paired with dml_start dml_color An array containing colors for silver the domain labels denoted by the coordinates located in the dml_start and dml_end options dm_labels An array containing labels to be none printed underneath specified domains, each label should correspond with the base position located in the dml_start option show_nonsynonymous Boolean value to turn option false on or off. If 0 (or undef), option is off. If 1 (or non-0), option is on. Only valid for nucleotide alignments. Output images are wider with this option on. Note that all arrays and hashes must be passed by reference. =back =head1 OBJECT METHODS =over 4 =item $draw_align-Edraw(); The draw() method draws the image with the options that were specified with new(). =item $draw_align-Ewidth(); Get the width of the image created with new(), in pixels. =item $draw_align-Eheight(); Get the height of the image created with new(), in pixels. =item $draw_align-Ealn_length(); Get the length of the alignment submitted to new(). =item $draw_align-Ealn_format(); Get the format of the alignment submitted to new(). =item $draw_align-Eno_sequences(); Get the number of sequences in the alignment submitted to new(). =back =head1 AUTHORS AND CONTRIBUTORS William McCaig, Ewmccaig@gmail.comE Mikhail Bekarev, Embekarev@hunter.cuny.eduE YE<246>zen HernE<225>ndez, Eyzhernand@gmail.comE Weigang Qiu (Corresponding Developer), Eweigang@genectr.hunter.cuny.eduE =head1 COPYRIGHT AND LICENSE Copyright (C) 2006-2008 by William McCaig This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.3 or, at your option, any later version of Perl 5 you may have available. =head1 SEE ALSO L, L, L, L =cut BioPerl-1.007002/Bio/Align/PairwiseStatistics.pm000444000766000024 1630213155576320 21474 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Align::PairwiseStatistics # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments =head1 SYNOPSIS use strict; my $stats = Bio::Align::PairwiseStatistics->new(); # get alignment object of two sequences somehow my $pwaln; print $stats->number_of_comparable_bases($pwaln); my $score = $stats->score_nuc($pwaln); =head1 DESCRIPTION Calculate pairwise statistics. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Align::PairwiseStatistics; use vars qw($GapChars); use strict; BEGIN { $GapChars = '(\.|\-)'; } use base qw(Bio::Root::Root Bio::Align::StatisticsI); =head2 number_of_comparable_bases Title : number_of_comparable_bases Usage : my $bases = $stat->number_of_comparable_bases($aln); Function: Returns the count of the number of bases that can be compared (L) in this alignment ( length - gaps) Returns : integer Args : L =cut sub number_of_comparable_bases{ my ($self,$aln) = @_; if ( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->throw("Must provide a Bio::Align::AlignI compliant object to ". "Bio::Align::PairwiseStatistics"); return 0; } elsif ( $aln->num_sequences != 2 ) { $self->throw("Only pairwise calculations supported. Found ". $aln->num_sequences." sequences in alignment\n"); } my $L = $aln->length - $self->number_of_gaps($aln); return $L; } =head2 number_of_differences Title : number_of_differences Usage : my $nd = $stat->number_of_distances($aln); Function: Returns the number of differences between two sequences Returns : integer Args : L =cut sub number_of_differences{ my ($self,$aln) = @_; if( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->throw("Must provide a Bio::Align::AlignI compliant object to ". "Bio::Align::PairwiseStatistics"); } elsif ( $aln->num_sequences != 2 ) { $self->throw("Only pairwise calculations supported. Found ". $aln->num_sequences." sequences in alignment\n"); } my (@seqs); foreach my $seq ( $aln->each_seq ) { push @seqs, [ split(//,$seq->seq())]; } my $firstseq = shift @seqs; #my $secondseq = shift @seqs; my $diffcount = 0; for (my $i = 0;$i<$aln->length; $i++ ) { next if ( $firstseq->[$i] =~ /^$GapChars$/ ); foreach my $seq ( @seqs ) { next if ( $seq->[$i] =~ /^$GapChars$/ ); if( $firstseq->[$i] ne $seq->[$i] ) { $diffcount++; } } } return $diffcount; } =head2 number_of_gaps Title : number_of_gaps Usage : my $nd = $stat->number_of_gaps($aln); Function: Returns the number of gapped positions among sequences in alignment Returns : integer Args : L =cut sub number_of_gaps{ my ($self,$aln) = @_; if ( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->throw("Must provide a Bio::Align::AlignI compliant object to ". "Bio::Align::PairwiseStatistics"); } elsif ( $aln->num_sequences != 2 ) { $self->throw("Only pairwise calculations supported. Found ". $aln->num_sequences." sequences in alignment\n"); } my $gapline = $aln->gap_line; # this will count the number of '-' characters return $gapline =~ tr/-/-/; } =head2 score_nuc Title : score_nuc Usage : my $score = $stat->score_nuc($aln); or my $score = $stat->score_nuc( -aln =>$aln, -match => 1, -mismatch => -1, -gap_open => -1, -gap_ext => -1 ); Function: Calculate the score of an alignment of 2 nucleic acid sequences. The scoring parameters can be specified. Otherwise the blastn default parameters are used: match = 2, mismatch = -3, gap opening = -5, gap extension = -2 Returns : alignment score (number) Args : L match score [optional] mismatch score [optional] gap opening score [optional] gap extension score [optional] =cut sub score_nuc { my ($self, @args) = @_; my ( $aln, $match, $mismatch, $gap_open, $gap_ext) = $self->_rearrange( [qw( ALN MATCH MISMATCH GAP_OPEN GAP_EXT)], @args ); if ( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->throw("Must provide a Bio::Align::AlignI compliant object to ". "Bio::Align::PairwiseStatistics"); } elsif ( $aln->num_sequences != 2 ) { $self->throw("Only pairwise calculations supported. Found ". $aln->num_sequences." sequences in alignment\n"); } my $seq1 = $aln->get_seq_by_pos(1); my $seq2 = $aln->get_seq_by_pos(2); if (! ( ($seq1->alphabet eq 'dna' || $seq1->alphabet eq 'rna') && ($seq2->alphabet eq 'dna' || $seq2->alphabet eq 'rna') )) { $self->throw("Can only score nucleic acid alignments"); } $match ||= 2; # Blastn scoring defaults $mismatch ||= -3; $gap_open ||= -5; $gap_ext ||= -2; my $score = 0; my $prevres1 = '-'; my $prevres2 = '-'; for (my $pos = 1 ; $pos <= $aln->length ; $pos++) { my $res1 = $seq1->subseq($pos, $pos); my $res2 = $seq2->subseq($pos, $pos); if (!($res1 eq '-' || $res2 eq '-')) { # no gap if ($res1 eq $res2) { # same residue $score += $match; } else { # other residue $score += $mismatch; } } else { # open or ext gap? my $open = 0; if (!($res1 eq '-' && $res2 eq '-')) { # exactly one gap my $prevres = $prevres1; $prevres = $prevres2 if $res2 eq '-'; $open = 1 unless $prevres eq '-'; } else { # 2 gaps $open = 1 unless $prevres1 eq '-' && $prevres2 eq '-'; } if ($open) { $score += $gap_open; # gap opening } else { $score += $gap_ext; # gap extension } } $prevres1 = $res1; $prevres2 = $res2; } return $score; } 1; BioPerl-1.007002/Bio/Align/ProteinStatistics.pm000444000766000024 2052613155576320 21334 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Align::ProteinStatistics # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Align::ProteinStatistics - Calculate Protein Alignment statistics (mostly distances) =head1 SYNOPSIS use Bio::Align::ProteinStatistics; use Bio::AlignIO; my $in = Bio::AlignIO->new(-format => 'fasta', -file => 'pep-104.fasaln'); my $aln = $in->next_aln; my $pepstats = Bio::Align::ProteinStatistics->new(); $kimura = $protstats->distance(-align => $aln, -method => 'Kimura'); print $kimura->print_matrix; =head1 DESCRIPTION This object is for generating various statistics from a protein alignment. Mostly it is where pairwise protein distances can be calculated. =head1 REFERENCES D_Kimura - Kimura, M. 1983. The Neutral Theory of Molecular Evolution. CUP, Cambridge. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Align::ProteinStatistics; use vars qw(%DistanceMethods $Precision $DefaultGapPenalty); use strict; use Bio::Align::PairwiseStatistics; use Bio::Matrix::PhylipDist; %DistanceMethods = ('kimura|k' => 'Kimura', ); $Precision = 5; $DefaultGapPenalty = 0; use base qw(Bio::Root::Root Bio::Align::StatisticsI); =head2 new Title : new Usage : my $obj = Bio::Align::ProteinStatistics->new(); Function: Builds a new Bio::Align::ProteinStatistics object Returns : an instance of Bio::Align::ProteinStatistics Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->pairwise_stats( Bio::Align::PairwiseStatistics->new()); return $self; } =head2 distance Title : distance Usage : my $distance_mat = $stats->distance(-align => $aln, -method => $method); Function: Calculates a distance matrix for all pairwise distances of sequences in an alignment. Returns : L object Args : -align => Bio::Align::AlignI object -method => String specifying specific distance method (implementing class may assume a default) =cut sub distance{ my ($self,@args) = @_; my ($aln,$method) = $self->_rearrange([qw(ALIGN METHOD)],@args); if( ! defined $aln || ! ref ($aln) || ! $aln->isa('Bio::Align::AlignI') ) { $self->throw("Must supply a valid Bio::Align::AlignI for the -align parameter in distance"); } $method ||= 'Kimura'; foreach my $m ( keys %DistanceMethods ) { if(defined $m && $method =~ /$m/i ) { my $mtd = "D_$DistanceMethods{$m}"; return $self->$mtd($aln); } } $self->warn("Unrecognized distance method $method must be one of [". join(',',$self->available_distance_methods())."]"); return; } =head2 available_distance_methods Title : available_distance_methods Usage : my @methods = $stats->available_distance_methods(); Function: Enumerates the possible distance methods Returns : Array of strings Args : none =cut sub available_distance_methods{ my ($self,@args) = @_; return values %DistanceMethods; } =head2 D - distance methods =cut =head2 D_Kimura Title : D_Kimura Usage : my $matrix = $pepstats->D_Kimura($aln); Function: Calculate Kimura protein distance (Kimura 1983) which approximates PAM distance D = -ln ( 1 - p - 0.2 * p^2 ) Returns : L Args : L =cut # Kimura, M. 1983. The Neutral Theory of Molecular Evolution. CUP, Cambridge. sub D_Kimura{ my ($self,$aln) = @_; return 0 unless $self->_check_arg($aln); # ambiguities ignored at this point my (@seqs,@names,@values,%dist); my $seqct = 0; foreach my $seq ( $aln->each_seq) { push @names, $seq->display_id; push @seqs, uc $seq->seq(); $seqct++; } my $len = $aln->length; my $precisionstr = "%.$Precision"."f"; for( my $i = 0; $i < $seqct-1; $i++ ) { # (diagonals) distance is 0 for same sequence $dist{$names[$i]}->{$names[$i]} = [$i,$i]; $values[$i][$i] = sprintf($precisionstr,0); for( my $j = $i+1; $j < $seqct; $j++ ) { my ($scored,$match) = (0,0); for( my $k=0; $k < $len; $k++ ) { my $m1 = substr($seqs[$i],$k,1); my $m2 = substr($seqs[$j],$k,1); if( $m1 ne '-' && $m2 ne '-' ) { # score is number of scored bases (alignable bases) # it could have also come from # my $L = $self->pairwise_stats->number_of_comparable_bases($pairwise); # match is number of matches weighting ambiguity bases # as well $match += _check_ambiguity_protein($m1,$m2); $scored++; } } # From Felsenstein's PHYLIP documentation: # This is very quick to do but has some obvious # limitations. It does not take into account which amino # acids differ or to what amino acids they change, so some # information is lost. The units of the distance measure # are fraction of amino acids differing, as also in the # case of the PAM distance. If the fraction of amino acids # differing gets larger than 0.8541 the distance becomes # infinite. my $D = 1 - ( $match / $scored ); if( $D < 0.8541 ) { $D = - log ( 1 - $D - (0.2 * ($D ** 2))); $values[$j][$i] = $values[$i][$j] = sprintf($precisionstr,$D); } else { $values[$j][$i] = $values[$i][$j] = ' NaN'; } # fwd and rev lookup $dist{$names[$i]}->{$names[$j]} = [$i,$j]; $dist{$names[$j]}->{$names[$i]} = [$i,$j]; # (diagonals) distance is 0 for same sequence $dist{$names[$j]}->{$names[$j]} = [$j,$j]; $values[$j][$j] = sprintf($precisionstr,0); } } return Bio::Matrix::PhylipDist->new(-program => 'bioperl_PEPstats', -matrix => \%dist, -names => \@names, -values => \@values); } # some methods from EMBOSS distmat sub _check_ambiguity_protein { my ($t1,$t2) = @_; my $n = 0; if( $t1 ne 'X' && $t1 eq $t2 ) { $n = 1.0; } elsif( (($t1 eq 'B' && $t2 =~ /[DN]/ ) || ($t2 eq 'B' && $t1 =~ /[DN]/ )) || (($t1 eq 'Z' && $t2 =~ /[EQ]/) || ($t2 eq 'Z' && $t1 =~ /[EQ]/ ))) { $n = 0.5; } elsif ( $t1 eq 'X' && $t2 eq 'X' ) { $n = 0.0025; } elsif( $t1 eq 'X' || $t2 eq 'X' ) { $n = 0.05; } return $n; } =head2 Data Methods =cut =head2 pairwise_stats Title : pairwise_stats Usage : $obj->pairwise_stats($newval) Function: Returns : value of pairwise_stats Args : newvalue (optional) =cut sub pairwise_stats{ my ($self,$value) = @_; if( defined $value) { $self->{'_pairwise_stats'} = $value; } return $self->{'_pairwise_stats'}; } sub _check_arg { my($self,$aln ) = @_; if( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->warn("Must provide a Bio::Align::AlignI compliant object to Bio::Align::DNAStatistics"); return 0; } elsif( $aln->get_seq_by_pos(1)->alphabet ne 'protein' ) { $self->warn("Must provide a protein alignment to Bio::Align::ProteinStatistics, you provided a " . $aln->get_seq_by_pos(1)->alphabet); return 0; } return 1; } 1; BioPerl-1.007002/Bio/Align/StatisticsI.pm000444000766000024 506713155576320 20067 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Align::StatisticsI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Align::StatisticsI - Calculate some statistics for an alignment =head1 SYNOPSIS Give standard usage here =head1 DESCRIPTION Describe the interface here =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Align::StatisticsI; use strict; use base qw(Bio::Root::RootI); =head2 distance Title : distance Usage : my $distance_mat = $stats->distance(-align => $aln, -method => $method); Function: Calculates a distance matrix for all pairwise distances of sequences in an alignment. Returns : Array ref Args : -align => Bio::Align::AlignI object -method => String specifying specific distance method (implementing class may assume a default) =cut sub distance{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 available_distance_methods Title : available_distance_methods Usage : my @methods = $stats->available_distance_methods(); Function: Enumerates the possible distance methods Returns : Array of strings Args : none =cut sub available_distance_methods{ my ($self,@args) = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Align/Utilities.pm000444000766000024 4470413155576320 17620 0ustar00cjfieldsstaff000000000000package Bio::Align::Utilities; use strict; use warnings; use Carp; use Bio::Root::Version; use Exporter 'import'; our @EXPORT_OK = qw( aa_to_dna_aln bootstrap_replicates cat bootstrap_replicates_codons dna_to_aa_aln most_common_sequences ); our %EXPORT_TAGS = (all => \@EXPORT_OK); # # BioPerl module for Bio::Align::Utilities # # Please direct questions and support issues to # # Cared for by Jason Stajich and Brian Osborne # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Align::Utilities - A collection of utilities regarding converting and manipulating alignment objects =head1 SYNOPSIS use Bio::Align::Utilities qw(:all); # Even if the protein alignments are local make sure the start/end # stored in the LocatableSeq objects are to the full length protein. # The coding sequence that is passed in should still be the full # length CDS as the nt alignment will be generated. # %dnaseqs is a hash of CDS sequences (spliced) my $dna_aln = aa_to_dna_aln($aa_aln,\%dnaseqs); # The reverse, which is simpler. The input alignment has to be # translate-able, with gap lengths and an overall length divisible by 3 my $aa_aln = dna_to_aa_aln($dna_al); # Generate bootstraps my $replicates = bootstrap_replicates($aln,$count); =head1 DESCRIPTION This module contains utility methods for manipulating sequence alignments (L) objects. The B utility is essentially the same as the B program by Bill Pearson available at ftp://ftp.virginia.edu/pub/fasta/other/mrtrans.shar. Of course this is a pure-Perl implementation, but just to mention that if anything seems odd you can check the alignments generated against Bill's program. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut use constant CODONSIZE => 3; our $GAP = '-'; our $CODONGAP = $GAP x CODONSIZE; =head2 aa_to_dna_aln Title : aa_to_dna_aln Usage : my $dnaaln = aa_to_dna_aln($aa_aln, \%seqs); Function: Will convert an AA alignment to DNA space given the corresponding DNA sequences. Note that this method expects the DNA sequences to be in frame +1 (GFF frame 0) as it will start to project into coordinates starting at the first base of the DNA sequence, if this alignment represents a different frame for the cDNA you will need to edit the DNA sequences to remove the 1st or 2nd bases (and revcom if things should be). Returns : Bio::Align::AlignI object Args : 2 arguments, the alignment and a hashref. Alignment is a Bio::Align::AlignI of amino acid sequences. The hash reference should have keys which are the display_ids for the aa sequences in the alignment and the values are a Bio::PrimarySeqI object for the corresponding spliced cDNA sequence. See also: L, L, L =cut sub aa_to_dna_aln { my ( $aln, $dnaseqs ) = @_; unless ( defined $aln && ref($aln) && $aln->isa('Bio::Align::AlignI') ) { croak( 'Must provide a valid Bio::Align::AlignI object as the first argument to aa_to_dna_aln, see the documentation for proper usage and the method signature' ); } my $alnlen = $aln->length; my $dnaalign = Bio::SimpleAlign->new(); $aln->map_chars( '\.', $GAP ); foreach my $seq ( $aln->each_seq ) { my $aa_seqstr = $seq->seq(); my $pepid = $seq->display_id; my $dnaseq = $dnaseqs->{$pepid} || $aln->throw( "cannot find " . $seq->display_id ); my $start_offset = ( $seq->start - 1 ) * CODONSIZE; $dnaseq = $dnaseq->seq(); my $dnalen = $dnaseqs->{$pepid}->length; my $dnaid = $dnaseqs->{$pepid}->display_id || $pepid; # try to use DNAseq obj ID (issue #137) my $nt_seqstr; my $j = 0; for ( my $i = 0 ; $i < $alnlen ; $i++ ) { my $char = substr( $aa_seqstr, $i + $start_offset, 1 ); if ( $char eq $GAP || $j >= $dnalen ) { $nt_seqstr .= $CODONGAP; } else { $nt_seqstr .= substr( $dnaseq, $j, CODONSIZE ); $j += CODONSIZE; } } $nt_seqstr .= $GAP x ( ( $alnlen * 3 ) - length($nt_seqstr) ); my $newdna = Bio::LocatableSeq->new( -display_id => $dnaid, -alphabet => 'dna', -start => $start_offset + 1, -end => ( $seq->end * CODONSIZE ), -strand => 1, -seq => $nt_seqstr ); $dnaalign->add_seq($newdna); } return $dnaalign; } =head2 dna_to_aa_aln Title : dna_to_aa_aln Usage : my $aa_aln = dna_to_aa_aln($dna_aln); Function: Convert a DNA alignment to an amino acid alignment where the length of all alignment strings and the lengths of any gaps must be divisible by 3 Returns : Bio::Align::AlignI object Args : the DNA alignment, a Bio::Align::AlignI of DNA sequences See also: L, L, L =cut sub dna_to_aa_aln { my $dna_aln = shift; unless ( defined $dna_aln && ref($dna_aln) && $dna_aln->isa('Bio::Align::AlignI') ) { croak( 'Must provide a valid Bio::Align::AlignI object as the argument to dna_to_aa_aln' ); } my $codon_table = Bio::Tools::CodonTable->new; my $aa_aln = Bio::SimpleAlign->new; for my $seq ( $dna_aln->each_seq ) { my ($aa_str, $aa_len); my @aln_str = split '', $seq->seq; croak("All lines in the alignment must have lengths divisible by 3") if ( scalar(@aln_str) % CODONSIZE ); while ( @aln_str ) { my $triplet = join '', (splice( @aln_str, 0, CODONSIZE )); if ( $triplet =~ /^[GATC]+$/i ) { $aa_str .= $codon_table->translate($triplet); $aa_len++; } elsif ( $triplet =~ /^[$Bio::LocatableSeq::GAP_SYMBOLS]+$/ ) { $aa_str .= $GAP; } else { croak("The triplet '$triplet' is neither a valid codon nor all gaps"); } } my $new_aa = Bio::LocatableSeq->new( -display_id => $seq->display_id, -alphabet => 'protein', -start => 1, -end => $aa_len, -strand => 1, -seq => $aa_str ); $aa_aln->add_seq($new_aa); } $aa_aln; } =head2 bootstrap_replicates Title : bootstrap_replicates Usage : my $alns = &bootstrap_replicates($aln,100); Function: Generate a pseudo-replicate of the data by randomly sampling, with replacement, the columns from an alignment for the non-parametric bootstrap. Returns : Arrayref of L objects Args : L object Number of replicates to generate =cut sub bootstrap_replicates { my ( $aln, $count ) = @_; $count ||= 1; my $alen = $aln->length; my ( @seqs, @nm ); $aln->set_displayname_flat(1); for my $s ( $aln->each_seq ) { push @seqs, $s->seq(); push @nm, $s->id; } my ( @alns, $i ); while ( $count-- > 0 ) { my @newseqs; for ( $i = 0 ; $i < $alen ; $i++ ) { my $index = int( rand($alen) ); my $c = 0; for (@seqs) { $newseqs[ $c++ ] .= substr( $_, $index, 1 ); } } my $newaln = Bio::SimpleAlign->new(); my $i = 0; for my $s (@newseqs) { ( my $tmp = $s ) =~ s/[$Bio::LocatableSeq::GAP_SYMBOLS]+//g; $newaln->add_seq( Bio::LocatableSeq->new( -start => 1, -end => length($tmp), -display_id => $nm[ $i++ ], -seq => $s ) ); } push @alns, $newaln; } return \@alns; } =head2 bootstrap_replicates_codons Title : bootstrap_replicates_codons Usage : my $alns = &bootstrap_replicates_codons($aln,100); Function: Generate a pseudo-replicate of the data by randomly sampling, with replacement, the columns from a codon alignment for the non-parametric bootstrap. The alignment is assumed to start on the first position of a codon. Returns : Arrayref of L objects Args : L object Number of replicates to generate =cut sub bootstrap_replicates_codons { my ( $aln, $count ) = @_; $count ||= 1; my $alen = $aln->length; my $ncodon = int( $alen / 3 ); my ( @seqs, @nm ); $aln->set_displayname_flat(1); for my $s ( $aln->each_seq ) { push @seqs, $s->seq(); push @nm, $s->id; } my ( @alns, $i ); while ( $count-- > 0 ) { my @newseqs; for ( $i = 0 ; $i < $ncodon ; $i++ ) { my $index = int( rand($ncodon) ); my $seqpos = $index * 3; my $c = 0; for (@seqs) { $newseqs[ $c++ ] .= substr( $_, $seqpos, 3 ); } } my $newaln = Bio::SimpleAlign->new(); my $i = 0; for my $s (@newseqs) { ( my $tmp = $s ) =~ s{[$Bio::LocatableSeq::GAP_SYMBOLS]+}{}g; $newaln->add_seq( Bio::LocatableSeq->new( -start => 1, -end => length($tmp), -display_id => $nm[ $i++ ], -seq => $s ) ); } push @alns, $newaln; } return \@alns; } =head2 cat Title : cat Usage : $aln123 = cat($aln1, $aln2, $aln3) Function : Concatenates alignment objects. Sequences are identified by id. An error will be thrown if the sequence ids are not unique in the first alignment. If any ids are not present or not unique in any of the additional alignments then those sequences are omitted from the concatenated alignment, and a warning is issued. An error will be thrown if any of the alignments are not flush, since concatenating such alignments is unlikely to make biological sense. Returns : A new Bio::SimpleAlign object Args : A list of Bio::SimpleAlign objects =cut sub cat { my ( $self, @aln ) = @_; $self->throw("cat method called with no arguments") unless $self; for ( $self, @aln ) { $self->throw( $_->id . " is not a Bio::Align::AlignI object" ) unless $_->isa('Bio::Align::AlignI'); $self->throw( $_->id . " is not flush" ) unless $_->is_flush; } my $aln = $self->new; $aln->id( $self->id ); $aln->annotation( $self->annotation ); my %unique; SEQ: foreach my $seq ( $self->each_seq() ) { throw( "ID: ", $seq->id, " is not unique in initial alignment." ) if exists $unique{ $seq->id }; $unique{ $seq->id } = 1; # Can be Bio::LocatableSeq, Bio::Seq::Meta or Bio::Seq::Meta::Array my $new_seq = $seq->new( -id => $seq->id, -strand => $seq->strand, -verbose => $self->verbose ); $new_seq->seq( $seq->seq ); $new_seq->start( $seq->start ); $new_seq->end( $seq->end ); if ( $new_seq->isa('Bio::Seq::MetaI') ) { for my $meta_name ( $seq->meta_names ) { $new_seq->named_submeta( $meta_name, $new_seq->start, $new_seq->end, $seq->named_meta($meta_name) ); } } for my $cat_aln (@aln) { my @cat_seq = $cat_aln->each_seq_with_id( $seq->id ); if ( @cat_seq == 0 ) { $self->warn( $seq->id . " not found in alignment " . $cat_aln->id . ", skipping this sequence." ); next SEQ; } if ( @cat_seq > 1 ) { $self->warn( $seq->id . " found multiple times in alignment " . $cat_aln->id . ", skipping this sequence." ); next SEQ; } my $cat_seq = $cat_seq[0]; my $old_end = $new_seq->end; $new_seq->seq( $new_seq->seq . $cat_seq->seq ); # Not sure if this is a sensible way to deal with end coordinates $new_seq->end( $new_seq->end + $cat_seq->end + 1 - $cat_seq->start ); if ( $cat_seq->isa('Bio::Seq::Meta::Array') ) { unless ( $new_seq->isa('Bio::Seq::Meta::Array') ) { my $meta_seq = Bio::Seq::Meta::Array->new; $meta_seq->seq( $new_seq->seq ); $meta_seq->start( $new_seq->start ); $meta_seq->end( $new_seq->end ); if ( $new_seq->isa('Bio::Seq::Meta') ) { for my $meta_name ( $new_seq->meta_names ) { $meta_seq->named_submeta( $meta_name, $new_seq->start, $old_end, [ split( //, $new_seq->named_meta($meta_name) ) ] ); } } $new_seq = $meta_seq; } for my $meta_name ( $cat_seq->meta_names ) { $new_seq->named_submeta( $meta_name, $old_end + 1, $new_seq->end, $cat_seq->named_meta($meta_name) ); } } elsif ( $cat_seq->isa('Bio::Seq::Meta') ) { if ( $new_seq->isa('Bio::Seq::Meta::Array') ) { for my $meta_name ( $cat_seq->meta_names ) { $new_seq->named_submeta( $meta_name, $old_end + 1, $new_seq->end, [ split( //, $cat_seq->named_meta($meta_name) ) ] ); } } else { unless ( $new_seq->isa('Bio::Seq::Meta') ) { my $meta_seq = Bio::Seq::Meta::Array->new; $meta_seq->seq( $new_seq->seq ); $meta_seq->start( $new_seq->start ); $meta_seq->end( $new_seq->end ); $new_seq = $meta_seq; } for my $meta_name ( $cat_seq->meta_names ) { $new_seq->named_submeta( $meta_name, $old_end + 1, $new_seq->end, $cat_seq->named_meta($meta_name) ); } } } } $aln->add_seq($new_seq); } my $cons_meta = $self->consensus_meta; my $new_cons_meta; if ($cons_meta) { $new_cons_meta = Bio::Seq::Meta->new(); for my $meta_name ( $cons_meta->meta_names ) { $new_cons_meta->named_submeta( $meta_name, 1, $self->length, $cons_meta->$meta_name ); } } my $end = $self->length; for my $cat_aln (@aln) { my $cat_cons_meta = $cat_aln->consensus_meta; if ($cat_cons_meta) { $new_cons_meta = Bio::Seq::Meta->new() if !$new_cons_meta; for my $meta_name ( $cat_cons_meta->meta_names ) { $new_cons_meta->named_submeta( $meta_name, $end + 1, $end + $cat_aln->length, $cat_cons_meta->$meta_name ); } } $end += $cat_aln->length; } $aln->consensus_meta($new_cons_meta) if $new_cons_meta; return $aln; } =head2 most_common_sequences Title : most_common_sequences Usage : @common = most_common_sequences ($align, $case_sensitivity) Function : Returns an array of the sequences that appear most often in the alignment (although this probably makes more sense when there is only a single most common sequence). Sequences are compared after removing any "-" (gap characters), and ambiguous units (e.g., R for purines) are only compared to themselves. The returned sequence is also missing the "-" since they don't actually make part of the sequence. Returns : Array of text strings. Arguments : Optional argument defining whether the comparison between sequences to find the most common should be case sensitive. Defaults to false, i.e, not case sensitive. =cut sub most_common_sequences { my $align = shift or croak ("Must provide Bio::AlignI object to Bio::Align::Utilities::most_common_sequences"); my $case_sensitive = shift; # defaults to false (we get undef if nothing) ## We keep track of the max on this loop. Saves us having to ## transverse the hash table later to find the maximum value. my $max = 0; my %counts; foreach ($align->each_seq) { (my $seq = $_->seq) =~ tr/-//d; $seq = uc ($seq) unless $case_sensitive; $max++ if (++$counts{$seq} > $max); } my @common = grep ($counts{$_} == $max, keys %counts); return @common; } 1; BioPerl-1.007002/Bio/AlignIO000755000766000024 013155576320 15351 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/AlignIO/arp.pm000444000766000024 2153013155576320 16647 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::arp # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::arp - ARP MSA Sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L class. =head1 DESCRIPTION This object can create L objects from ARP flat files. These are typically configuration-like data files for the program Arlequin. For more information, see: http://lgb.unige.ch/arlequin/ For the moment, this retains the allele sequence data in the DATA section and inserts them into SimpleAlign objects. ARP files that contain other data (RFLP, etc.) are not expected to parse properly. Also, if the DNA data is actually SNP data, then the LocatableSeq object instantiation will throw an error. This is now set up as a generic parser (i.e. it parses everything) and collects as much data as possible into the SimpleAlign object. The following in a general mapping of where data can be found: Tag SimpleAlign Method ---------------------------------------------------------------------- Title description SampleName id ---------------------------------------------------------------------- Tag Bio::Annotation TagName Bio::Annotation Class Parameters ---------------------------------------------------------------------- NE SimpleValue pfam_family_accession value NL SimpleValue sequence_start_stop value SS SimpleValue sec_structure_source value BM SimpleValue build_model value RN Reference reference * ---------------------------------------------------------------------- * RN is generated based on the number of Bio::Annotation::Reference objects In addition, the number of samples found in the alignment is retained in a Bio::Annotation::TagTree object in the annotation collection and is accessible via: ($samples) = $aln->annotation->get_Annotations('Samples'); say $samples->display_text; # or use other relevant TagTree methods to retrieve data =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Chris Fields (cjfields) =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::arp; use strict; use base qw(Bio::AlignIO); use Data::Dumper; use Bio::Annotation::AnnotationFactory; =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln Function: returns the next alignment in the stream. Returns : Bio::Align::AlignI object - returns 0 on end of file or on error Args : -width => optional argument to specify the width sequence will be written (60 chars by default) See L =cut sub next_aln { my $self = shift; my $aln = Bio::SimpleAlign->new(-source => 'arp'); my ($data, $cur_block, $cur_type, $cur_data); SCAN: while (defined ($data = $self->_readline) ) { next if $data =~ m{^\s*$}xms; if ($data =~ m{\[{1,2}(\w+)\]{1,2}}xms) { $self->{state}->{current_block} = $1; next SCAN; } elsif ($data =~ m{^\s*(\w+)=\s?(\S[^\n]*$)}xms) { ($cur_type, $cur_data) = ($1, $2); if ($cur_data =~ m{^\s*\{\s*$}) { $self->throw("Curly block must be embedded in a named Block") if !exists($self->{state}->{current_block}); $self->{state}->{in_curly_block} = 1; next SCAN; } $cur_data =~ s{[\"\']}{}g; $cur_data =~ s{\s*$}{}; # per alignment annotation data (i.e. Sample Blocks) or # annotation data retained for each alignment? $self->{state}->{current_block} eq 'Samples' ? push @{$self->{state}->{SampleAnnotation}->{$cur_type}}, $cur_data : push @{$self->{state}->{Annotation}->{$cur_type}}, $cur_data; } elsif ($data =~ m{^\s*\}\s*$}xms) { $self->throw("Unmatched bracket in ARP file:\n$data") if !exists($self->{state}->{in_curly_block}); if ($self->{state}->{current_block} eq 'Samples') {; my $ac = $self->_process_annotation($aln); delete $self->{state}->{SampleAnnotation}; } else { # process other data at a later point } delete $self->{state}->{blockdata}; $self->{state}->{in_curly_block} = 0; last SCAN; } else { # all other data should be in a curly block and have a block title $self->throw("Data found outside of proper block:\n$data") if !exists($self->{state}->{current_block}) && !$self->{state}->{in_curly_block}; # bypass commented stuff (but we may want to process it at a later # point, so turn back here) next if $data =~ m{^\s*\#}xms; if ($self->{state}->{current_block} eq 'Samples') { chomp $data; # we have two possible ways to deal with sample number, either # clone the LocatableSeq (in which case we need to deal with ID # duplication), or store as annotation data. I chose the latter # route using a Bio::Annotation::TagTree. YMMV - cjfields 10-15-08 my ($ls, $samples) = $self->_process_sequence($data); my $id = $ls->id; push @{ $self->{state}->{SampleAnnotation}->{Samples} }, [$id => $samples]; $aln->add_seq($ls); } else { # add elsif's for further processing #$self->debug('Unmatched data in block '. # $self->{state}->{current_block}. # ":\n$data\n"); $self->{state}->{blockdata} .= $data; } } } # alignments only returned if they contain sequences return $aln if $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in xmfa format Returns : 1 for success and 0 for error Args : L object See L =cut sub write_aln { my ($self,@aln) = @_; $self->throw_not_implemented; } ################ PRIVATE SUBS ################ sub _process_sequence { my ($self, $raw) = @_; return unless defined $raw; $raw =~ s{(?:^\s+|\s+$)}{}g; my ($id, $samples, $seq) = split(' ', $raw); my $ls = Bio::LocatableSeq->new('-seq' => $seq, '-start' => 1, '-display_id' => $id, '-alphabet' => $self->alphabet); return($ls, $samples); } sub _process_annotation { my ($self, $aln) = @_; my $coll = Bio::Annotation::Collection->new(); my $factory = Bio::Annotation::AnnotationFactory->new(-type => 'Bio::Annotation::SimpleValue'); for my $anntype (qw(SampleAnnotation Annotation)) { for my $key (keys %{ $self->{state}->{$anntype} }) { if ($key eq 'Title') { $aln->description($self->{state}->{$anntype}->{$key}[0]); } elsif ($key eq 'Samples') { $factory->type('Bio::Annotation::TagTree'); $coll->add_Annotation($key, $factory->create_object( -value => [$key => $self->{state}->{$anntype}->{$key}])); $factory->type('Bio::Annotation::SimpleValue'); } elsif ($key eq 'SampleName') { $aln->id($self->{state}->{$anntype}->{$key}[0]); } else { $self->throw('Expecting an array reference') unless ref $self->{state}->{$anntype}->{$key} eq 'ARRAY'; for my $a (@{ $self->{state}->{$anntype}->{$key} }) { $coll->add_Annotation($key, $factory->create_object( -value => $a) ); } } } } #$self->debug("Collection:".Dumper($coll)."\n"); $aln->annotation($coll); } 1; BioPerl-1.007002/Bio/AlignIO/bl2seq.pm000444000766000024 1312013155576320 17251 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::bl2seq # based on the Bio::SeqIO modules # by Ewan Birney # and Lincoln Stein # # the Bio::Tools::BPlite modules by # Ian Korf (ifkorf at ucdavis.edu, http://www.bioperl.org/wiki/Ian_Korf), # Lorenz Pollak (lorenz@ist.org, bioperl port) # # and the SimpleAlign.pm module of Ewan Birney # # Copyright Peter Schattner # # You may distribute this module under the same terms as perl itself # _history # September 5, 2000 # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::bl2seq - bl2seq sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L class, as in: use Bio::AlignIO; $in = Bio::AlignIO->new(-file => "inputfilename" , -format => "bl2seq", -report_type => "blastn"); $aln = $in->next_aln(); =head1 DESCRIPTION This object can create L sequence alignment objects (of two sequences) from C BLAST reports. A nice feature of this module is that - in combination with L or a remote BLAST - it can be used to align two sequences and make a L object from them which can then be manipulated using any L methods, eg: # Get two sequences $str = Bio::SeqIO->new(-file=>'t/amino.fa' , '-format' => 'Fasta', ); my $seq3 = $str->next_seq(); my $seq4 = $str->next_seq(); # Run bl2seq on them $factory = Bio::Tools::StandAloneBlast->new('program' => 'blastp', 'outfile' => 'bl2seq.out'); my $bl2seq_report = $factory->bl2seq($seq3, $seq4); # Note that report is a Bio::SearchIO object # Use AlignIO.pm to create a SimpleAlign object from the bl2seq report $str = Bio::AlignIO->new(-file=> 'bl2seq.out','-format' => 'bl2seq'); $aln = $str->next_aln(); =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Peter Schattner Email: schattner@alum.mit.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::bl2seq; use strict; use Bio::SearchIO; use base qw(Bio::AlignIO); =head2 new Title : new Usage : my $alignio = Bio::SimpleAlign->new(-format => 'bl2seq', -file => 'filename', -report_type => 'blastx'); Function: Get a L Returns : L object Args : -report_type => report type (blastn,blastx,tblastx,tblastn,blastp) =cut sub _initialize { my ($self, @args) = @_; $self->SUPER::_initialize(@args); my ($rt) = $self->_rearrange([qw(REPORT_TYPE)],@args); defined $rt && $self->report_type($rt); } =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Returns : L object on success, undef on error or end of file Args : none =cut sub next_aln { my $self = shift; unless (exists $self->{'_searchio'}) { $self->{'_searchio'} = Bio::SearchIO->new(-fh => $self->_fh, -format => 'blast', -report_type => $self->report_type); } while (1) { if (!exists $self->{'_result'}) { $self->{'_result'} = $self->{'_searchio'}->next_result; } return if !defined $self->{'_result'}; if (!exists $self->{'_hit'}) { $self->{'_hit'} = $self->{'_result'}->next_hit; } # out of hits for this result? if (!defined $self->{'_hit'}) { delete $self->{'_result'}; next; } my $hsp = $self->{'_hit'}->next_hsp; # out of hsps for this hit? if (!defined $hsp) { delete $self->{'_hit'}; next; } $hsp ? return $hsp->get_aln: return; } } =head2 write_aln (NOT IMPLEMENTED) Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in bl2seq format Returns : 1 for success and 0 for error Args : L object =cut sub write_aln { my ($self,@aln) = @_; $self->throw_not_implemented(); } =head2 report_type Title : report_type Usage : $obj->report_type($newval) Function: Sets the report type (blastn, blastp...) Returns : value of report_type (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub report_type{ my $self = shift; return $self->{'report_type'} = shift if @_; return $self->{'report_type'}; } 1; BioPerl-1.007002/Bio/AlignIO/clustalw.pm000444000766000024 2431313155576320 17725 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::clustalw # # based on the Bio::SeqIO modules # by Ewan Birney # and Lincoln Stein # and the Bio::SimpleAlign module of Ewan Birney # # Copyright Peter Schattner # # You may distribute this module under the same terms as perl itself # History # September 5, 2000 # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::clustalw - clustalw sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. =head1 DESCRIPTION This object can transform Bio::Align::AlignI objects to and from clustalw files. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Peter Schattner Email: schattner@alum.mit.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::clustalw; use vars qw($LINELENGTH $CLUSTALPRINTVERSION); use strict; $LINELENGTH = 60; $CLUSTALPRINTVERSION = '1.81'; use base qw(Bio::AlignIO); =head2 new Title : new Usage : $alignio = Bio::AlignIO->new(-format => 'clustalw', -file => 'filename'); Function: returns a new Bio::AlignIO object to handle clustalw files Returns : Bio::AlignIO::clustalw object Args : -verbose => verbosity setting (-1, 0, 1, 2) -file => name of file to read in or to write, with ">" -fh => alternative to -file param - provide a filehandle to read from or write to -format => alignment format to process or produce -percentages => display a percentage of identity in each line of the alignment (clustalw only) -linelength=> alignment output line length (default 60) =cut sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); my ( $percentages, $ll ) = $self->_rearrange( [qw(PERCENTAGES LINELENGTH)], @args ); defined $percentages && $self->percentages($percentages); $self->line_length( $ll || $LINELENGTH ); } =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream Returns : Bio::Align::AlignI object Args : NONE See L for details =cut sub next_aln { my ($self) = @_; my $first_line; while ( $first_line = $self->_readline ) { last if $first_line !~ /^$/; } $self->_pushback($first_line); if ( defined( $first_line = $self->_readline ) && $first_line !~ /CLUSTAL/ ) { $self->throw( "trying to parse a file which does not start with a CLUSTAL header" ); } my %alignments; my $aln = Bio::SimpleAlign->new( -source => 'clustalw', -verbose => $self->verbose ); my $order = 0; my %order; $self->{_lastline} = ''; my ($first_block, $seen_block) = (0,0); while ( defined( $_ = $self->_readline ) ) { next if (/^\s+$/ && !$first_block); if (/^\s$/) { # line contains no description $seen_block = 1; next; } $first_block = 1; # break the loop if we come to the end of the current alignment # and push back the CLUSTAL header if (/CLUSTAL/) { $self->_pushback($_); last; } my ( $seqname, $aln_line ) = ( '', '' ); if (/^\s*(\S+)\s*\/\s*(\d+)-(\d+)\s+(\S+)\s*$/ox) { # clustal 1.4 format ( $seqname, $aln_line ) = ( "$1:$2-$3", $4 ); # } elsif( /^\s*(\S+)\s+(\S+)\s*$/ox ) { without trailing numbers } elsif (/^\s*(\S+)\s+(\S+)\s*\d*\s*$/ox) { # with numbers ( $seqname, $aln_line ) = ( $1, $2 ); if ( $seqname =~ /^[\*\.\+\:]+$/ ) { $self->{_lastline} = $_; next; } } else { $self->{_lastline} = $_; next; } if ( !$seen_block ) { if (exists $order{$seqname}) { $self->warn("Duplicate sequence : $seqname\n". "Can't guarantee alignment quality"); } else { $order{$seqname} = $order++; } } $alignments{$seqname} .= $aln_line; } my ( $sname, $start, $end ); foreach my $name ( sort { $order{$a} <=> $order{$b} } keys %alignments ) { if ( $name =~ /(\S+):(\d+)-(\d+)/ ) { ( $sname, $start, $end ) = ( $1, $2, $3 ); } else { ( $sname, $start ) = ( $name, 1 ); my $str = $alignments{$name}; $str =~ s/[^A-Za-z]//g; $end = length($str); } my $seq = Bio::LocatableSeq->new ( '-seq' => $alignments{$name}, '-display_id' => $sname, '-start' => $start, '-end' => $end, '-alphabet' => $self->alphabet, ); $aln->add_seq($seq); } # not sure if this should be a default option - or we can pass in # an option to do this in the future? --jason stajich # $aln->map_chars('\.','-'); # no sequences added, so just return return $aln if $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the clustalw-format object (.aln) into the stream Returns : 1 for success and 0 for error Args : Bio::Align::AlignI object =cut sub write_aln { my ( $self, @aln ) = @_; my ( $count, $length, $seq, @seq, $tempcount, $line_len ); $line_len = $self->line_length || $LINELENGTH; foreach my $aln (@aln) { if ( !$aln || !$aln->isa('Bio::Align::AlignI') ) { $self->warn( "Must provide a Bio::Align::AlignI object when calling write_aln" ); next; } my $matchline = $aln->match_line; if ( $self->force_displayname_flat ) { $aln->set_displayname_flat(1); } $self->_print( sprintf( "CLUSTAL W (%s) multiple sequence alignment\n\n\n", $CLUSTALPRINTVERSION ) ) or return; $length = $aln->length(); $count = $tempcount = 0; @seq = $aln->each_seq(); my $max = 22; foreach $seq (@seq) { $max = length( $aln->displayname( $seq->get_nse() ) ) if ( length( $aln->displayname( $seq->get_nse() ) ) > $max ); } while ( $count < $length ) { my ( $linesubstr, $first ) = ( '', 1 ); foreach $seq (@seq) { # # Following lines are to suppress warnings # if some sequences in the alignment are much longer than others. my ($substring); my $seqchars = $seq->seq(); SWITCH: { if ( length($seqchars) >= ( $count + $line_len ) ) { $substring = substr( $seqchars, $count, $line_len ); if ($first) { $linesubstr = substr( $matchline, $count, $line_len ); $first = 0; } last SWITCH; } elsif ( length($seqchars) >= $count ) { $substring = substr( $seqchars, $count ); if ($first) { $linesubstr = substr( $matchline, $count ); $first = 0; } last SWITCH; } $substring = ""; } $self->_print( sprintf( "%-" . $max . "s %s\n", $aln->displayname( $seq->get_nse() ), $substring ) ) or return; } my $percentages = ''; if ( $self->percentages ) { my ($strcpy) = ($linesubstr); my $count = ( $strcpy =~ tr/\*// ); $percentages = sprintf( "\t%d%%", 100 * ( $count / length($linesubstr) ) ); } $self->_print( sprintf( "%-" . $max . "s %s%s\n", '', $linesubstr, $percentages ) ); $self->_print( sprintf("\n\n") ) or return; $count += $line_len; } } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 percentages Title : percentages Usage : $obj->percentages($newval) Function: Set the percentages flag - whether or not to show percentages in each output line Returns : value of percentages Args : newvalue (optional) =cut sub percentages { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_percentages'} = $value; } return $self->{'_percentages'}; } =head2 line_length Title : line_length Usage : $obj->line_length($newval) Function: Set the alignment output line length Returns : value of line_length Args : newvalue (optional) =cut sub line_length { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_line_length'} = $value; } return $self->{'_line_length'}; } 1; BioPerl-1.007002/Bio/AlignIO/emboss.pm000444000766000024 1513413155576320 17360 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::emboss # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle) =head1 SYNOPSIS # do not use the object directly use Bio::AlignIO; # read in an alignment from the EMBOSS program water my $in = Bio::AlignIO->new(-format => 'emboss', -file => 'seq.water'); while( my $aln = $in->next_aln ) { # do something with the alignment } =head1 DESCRIPTION This object handles parsing and writing pairwise sequence alignments from the EMBOSS suite. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::emboss; use vars qw($EMBOSSTitleLen $EMBOSSLineLen); use strict; use Bio::LocatableSeq; use base qw(Bio::AlignIO); BEGIN { $EMBOSSTitleLen = 13; $EMBOSSLineLen = 50; } sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); $self->{'_type'} = undef; } =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Returns : L object - returns 0 on end of file or on error Args : NONE =cut sub next_aln { my ($self) = @_; my $seenbegin = 0; my %data = ( 'seq1' => { 'start'=> undef, 'end'=> undef, 'name' => '', 'data' => '' }, 'seq2' => { 'start'=> undef, 'end'=> undef, 'name' => '', 'data' => '' }, 'align' => '', 'type' => $self->{'_type'}, # to restore type from # previous aln if possible ); my %names; while( defined($_ = $self->_readline) ) { next if( /^\#?\s+$/ || /^\#+\s*$/ ); if( /^\#(\=|\-)+\s*$/) { last if( $seenbegin); } elsif( /(Local|Global):\s*(\S+)\s+vs\s+(\S+)/ || /^\#\s+Program:\s+(\S+)/ ) { my ($name1,$name2) = ($2,$3); if( ! defined $name1 ) { # Handle EMBOSS 2.2.X $data{'type'} = $1; $name1 = $name2 = ''; } else { $data{'type'} = $1 eq 'Local' ? 'water' : 'needle'; } $data{'seq1'}->{'name'} = $name1; $data{'seq2'}->{'name'} = $name2; $self->{'_type'} = $data{'type'}; } elsif( /Score:\s+(\S+)/ ) { $data{'score'} = $1; } elsif( /^\#\s+(1|2):\s+(\S+)/ && ! $data{"seq$1"}->{'name'} ) { my $nm = $2; $nm = substr($nm,0,$EMBOSSTitleLen); # emboss has a max seq length if( $names{$nm} ) { $nm .= "-". $names{$nm}; } $names{$nm}++; $data{"seq$1"}->{'name'} = $nm; } elsif( $data{'seq1'}->{'name'} && /^\Q$data{'seq1'}->{'name'}/ ) { my $count = 0; $seenbegin = 1; my @current; while( defined ($_) ) { my $align_other = ''; my $delayed; if($count == 0 || $count == 2 ) { my @l = split; my ($seq,$align,$start,$end); if( $count == 2 && $data{'seq2'}->{'name'} eq '' ) { # weird boundary condition ($start,$align,$end) = @l; } elsif( @l == 3 ) { $align = ''; ($seq,$start,$end) = @l } else { ($seq,$start,$align,$end) = @l; } my $seqname = sprintf("seq%d", ($count == 0) ? '1' : '2'); $data{$seqname}->{'data'} .= $align; $data{$seqname}->{'start'} ||= $start; $data{$seqname}->{'end'} = $end; $current[$count] = [ $start,$align || '']; } else { s/^\s+//; s/\s+$//; $data{'align'} .= $_; } BOTTOM: last if( $count++ == 2); $_ = $self->_readline(); } if( $data{'type'} eq 'needle' ) { # which ever one is shorter we want to bring it up to # length. Man this stinks. my ($s1,$s2) = ($data{'seq1'}, $data{'seq2'}); my $d = length($current[0]->[1]) - length($current[2]->[1]); if( $d < 0 ) { # s1 is smaller, need to add some # compare the starting points for this alignment line if( $current[0]->[0] <= 1 ) { $s1->{'data'} = ('-' x abs($d)) . $s1->{'data'}; $data{'align'} = (' 'x abs($d)).$data{'align'}; } else { $s1->{'data'} .= '-' x abs($d); $data{'align'} .= ' 'x abs($d); } } elsif( $d > 0) { # s2 is smaller, need to add some if( $current[2]->[0] <= 1 ) { $s2->{'data'} = ('-' x abs($d)) . $s2->{'data'}; $data{'align'} = (' 'x abs($d)).$data{'align'}; } else { $s2->{'data'} .= '-' x abs($d); $data{'align'} .= ' 'x abs($d); } } } } } return unless $seenbegin; my $aln = Bio::SimpleAlign->new(-verbose => $self->verbose(), -score => $data{'score'}, -source => "EMBOSS-".$data{'type'}); foreach my $seqname ( qw(seq1 seq2) ) { return unless ( defined $data{$seqname} ); $data{$seqname}->{'name'} ||= $seqname; my $seq = Bio::LocatableSeq->new ('-seq' => $data{$seqname}->{'data'}, '-display_id' => $data{$seqname}->{'name'}, '-start' => $data{$seqname}->{'start'}, '-end' => $data{$seqname}->{'end'}, '-alphabet' => $self->alphabet, ); $aln->add_seq($seq); } return $aln; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in emboss format Returns : 1 for success and 0 for error Args : L object =cut sub write_aln { my ($self,@aln) = @_; $self->throw("Sorry: writing emboss output is not currently available! \n"); } 1; BioPerl-1.007002/Bio/AlignIO/fasta.pm000444000766000024 1511613155576320 17166 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::fasta # # Copyright Peter Schattner # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::fasta - fasta MSA Sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L class. =head1 DESCRIPTION This object can transform L objects to and from fasta flat files. This is for the fasta alignment format, not for the FastA sequence analysis program. To process the alignments from FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module. =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Peter Schattner =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::fasta; use strict; use base qw(Bio::AlignIO); our $WIDTH = 60; use Bio::LocatableSeq; =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln Function: returns the next alignment in the stream. Returns : Bio::Align::AlignI object - returns 0 on end of file or on error Args : -width => optional argument to specify the width sequence will be written (60 chars by default) See L =cut sub next_aln { my $self = shift; my ($width) = $self->_rearrange( [qw(WIDTH)], @_ ); $self->width( $width || $WIDTH ); my ($start, $end, $name, $seqname, $seq, $seqchar, $entry, $tempname, $tempdesc, %align, $desc, $maxlen ); my $aln = Bio::SimpleAlign->new(); while ( defined( $entry = $self->_readline ) ) { chomp $entry; if ( $entry =~ s/^>\s*(\S+)\s*// ) { $tempname = $1; chomp($entry); $tempdesc = $entry; if ( defined $name ) { $seqchar =~ s/\s//g; $seqname = $name; $start = 1; $end = $self->_get_len($seqchar); $seq = Bio::LocatableSeq->new( -seq => $seqchar, -display_id => $seqname, -description => $desc, -start => $start, -end => $end, -alphabet => $self->alphabet, ); $aln->add_seq($seq); $self->debug("Reading $seqname\n"); } $desc = $tempdesc; $name = $tempname; $desc = $entry; $seqchar = ""; next; } # removed redundant symbol validation # this is already done in Bio::PrimarySeq $seqchar .= $entry; } # Next two lines are to silence warnings that # otherwise occur at EOF when using <$fh> $name = "" if ( !defined $name ); $seqchar = "" if ( !defined $seqchar ); $seqchar =~ s/\s//g; # Put away last name and sequence if ( $name =~ /(\S+\/(\d+)-(\d+))$/ ) { $seqname = $1; $start = $2; $end = $3; } else { $seqname = $name; $start = 1; $end = $self->_get_len($seqchar); } # This logic now also reads empty lines at the # end of the file. Skip this is seqchar and seqname is null unless ( length($seqchar) == 0 && length($seqname) == 0 ) { $seq = Bio::LocatableSeq->new( -seq => $seqchar, -display_id => $seqname, -description => $desc, -start => $start, -end => $end, -alphabet => $self->alphabet, ); $aln->add_seq($seq); $self->debug("Reading $seqname\n"); } my $alnlen = $aln->length; foreach my $seq ( $aln->each_seq ) { if ( $seq->length < $alnlen ) { my ($diff) = ( $alnlen - $seq->length ); $seq->seq( $seq->seq() . "-" x $diff ); } } # no sequences means empty alignment (possible EOF) return $aln if $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in fasta format Returns : 1 for success and 0 for error Args : L object See L =cut sub write_aln { my ($self,@aln) = @_; my $width = $self->width; my ($seq,$desc,$rseq,$name,$count,$length,$seqsub); foreach my $aln (@aln) { if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln"); next; } if( $self->force_displayname_flat ) { $aln->set_displayname_flat(1); } foreach $rseq ( $aln->each_seq() ) { $name = $aln->displayname($rseq->get_nse()); $seq = $rseq->seq(); $desc = $rseq->description || ''; $desc = ' '.$desc if $desc; $self->_print (">$name$desc\n") or return; $count = 0; $length = length($seq); if(defined $seq && $length > 0) { $seq =~ s/(.{1,$width})/$1\n/g; } else { $seq = "\n"; } $self->_print($seq); } } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 _get_len Title : _get_len Usage : Function: determine number of alphabetic chars Returns : integer Args : sequence string =cut sub _get_len { my ($self,$seq) = @_; my $chars = $Bio::LocatableSeq::GAP_SYMBOLS.$Bio::LocatableSeq::FRAMESHIFT_SYMBOLS; $seq =~ s{[$chars]+}{}gi; return CORE::length($seq); } =head2 width Title : width Usage : $obj->width($newwidth) $width = $obj->width; Function: Get/set width of alignment Returns : integer value of width Args : on set, new value (a scalar or undef, optional) =cut sub width{ my $self = shift; return $self->{'_width'} = shift if @_; return $self->{'_width'} || $WIDTH; } 1; BioPerl-1.007002/Bio/AlignIO/largemultifasta.pm000444000766000024 1255513155576320 21260 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::largemultifasta # based on the Bio::SeqIO::largefasta module # by Ewan Birney # and Lincoln Stein # # and the SimpleAlign.pm module of Ewan Birney # # Copyright Albert Vilella # # You may distribute this module under the same terms as perl itself # _history # January 20, 2004 # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::largemultifasta - Largemultifasta MSA Sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L class. =head1 DESCRIPTION This object can transform L objects to and from largemultifasta flat file databases. This is for the fasta sequence format NOT FastA analysis program. To process the pairwise alignments from a FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module. Reimplementation of Bio::AlignIO::fasta modules so that creates temporary files instead of keeping the whole sequences in memory. =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Albert Vilella, Heikki Lehvaslaiho Email: avilella-at-gmail-dot-com, heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::largemultifasta; use strict; use Bio::Seq::LargeLocatableSeq; use Bio::Seq::SeqFactory; use base qw(Bio::AlignIO Bio::SeqIO Bio::SimpleAlign); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new( -verbose => $self->verbose(), -type => 'Bio::Seq::LargeLocatableSeq' )); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream while taking care of the length Returns : Bio::Seq object Args : NONE =cut sub next_seq { my ($self) = @_; my $largeseq = $self->sequence_factory->create(-alphabet=>$self->alphabet); my ($id,$fulldesc,$entry); my $count = 0; my $seen = 0; while( defined ($entry = $self->_readline) ) { if( $seen == 1 && $entry =~ /^\s*>/ ) { $self->_pushback($entry); return $largeseq; } if ( $entry eq '>' ) { $seen = 1; next; } elsif( $entry =~ /\s*>(.+?)$/ ) { $seen = 1; ($id,$fulldesc) = ($1 =~ /^\s*(\S+)\s*(.*)$/) or $self->warn("Can't parse fasta header"); $largeseq->display_id($id); $largeseq->primary_id($id); $largeseq->desc($fulldesc); } else { $entry =~ s/\s+//g; $largeseq->add_sequence_as_string($entry); } (++$count % 1000 == 0 && $self->verbose() > 0) && print "line $count\n"; } if( ! $seen ) { return; } return $largeseq; } =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Returns : L object - returns 0 on end of file or on error Args : NONE =cut sub next_aln { my $self = shift; my $largeseq; my $aln = Bio::SimpleAlign->new(); while (defined ($largeseq = $self->next_seq) ) { $aln->add_seq($largeseq); $self->debug("sequence readed\n"); } my $alnlen = $aln->length; foreach my $largeseq ( $aln->each_seq ) { if( $largeseq->length < $alnlen ) { my ($diff) = ($alnlen - $largeseq->length); $largeseq->seq("-" x $diff); } } return $aln if $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in largemultifasta format Returns : 1 for success and 0 for error Args : L object =cut sub write_aln { my ($self,@aln) = @_; my ($seq,$desc,$rseq,$name,$count,$length,$seqsub); foreach my $aln (@aln) { if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln"); next; } foreach $rseq ( $aln->each_seq() ) { $name = $aln->displayname($rseq->get_nse()); $seq = $rseq->seq(); $desc = $rseq->description || ''; $self->_print (">$name $desc\n") or return ; $count =0; $length = length($seq); while( ($count * 60 ) < $length ) { $seqsub = substr($seq,$count*60,60); $self->_print ("$seqsub\n") or return ; $count++; } } } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; BioPerl-1.007002/Bio/AlignIO/maf.pm000444000766000024 1030513155576320 16626 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::maf # # Copyright Allen Day # =head1 NAME Bio::AlignIO::maf - Multiple Alignment Format sequence input stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. use Bio::AlignIO; my $alignio = Bio::AlignIO->new(-fh => \*STDIN, -format => 'maf'); while(my $aln = $alignio->next_aln()){ my $match_line = $aln->match_line; print $aln, "\n"; print $aln->length, "\n"; print $aln->num_residues, "\n"; print $aln->is_flush, "\n"; print $aln->num_sequences, "\n"; $aln->splice_by_seq_pos(1); print $aln->consensus_string(60), "\n"; print $aln->get_seq_by_pos(1)->seq, "\n"; print $aln->match_line(), "\n"; print "\n"; } =head1 DESCRIPTION This class constructs Bio::SimpleAlign objects from an MAF-format multiple alignment file. Writing in MAF format is currently unimplemented. Spec of MAF format is here: http://genome.ucsc.edu/FAQ/FAQformat =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Allen Day Email: allenday@ucla.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::maf; use strict; use Bio::SimpleAlign; use base qw(Bio::AlignIO); =head2 new Title : new Usage : my $alignio = Bio::AlignIO->new(-format => 'maf' -file => '>file', -idlength => 10, -idlinebreak => 1); Function: Initialize a new L reader Returns : L object Args : =cut sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); 1; } =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Throws an exception if trying to read in PHYLIP sequential format. Returns : L object Args : =cut sub next_aln { my $self = shift; # check beginning of file for proper header if(!$self->{seen_header}){ my $line = $self->_readline; $self->throw("This doesn't look like a MAF file. First line should start with ##maf, but it was: ".$line) unless $line =~ /^##maf/; $self->{seen_header} = 1; # keep in case we parse this later $self->_pushback($line); } my $aln = Bio::SimpleAlign->new(-source => 'maf'); my($aline, @slines, $seen_aline); while(my $line = $self->_readline()){ if ($line =~ /^a\s/xms) { # next block? if ($seen_aline) { $self->_pushback($line); last; } $aline = $line; $seen_aline++; } elsif ($line =~ /^s\s/xms) { push @slines, $line; } else { # missed lines $self->debug($line); } } # all MAF starts with 'a' line return unless $aline; my($kvs) = $aline =~ /^a\s+(.+)$/; my @kvs = split /\s+/, $kvs if $kvs; my %kv; foreach my $kv (@kvs){ my($k,$v) = $kv =~ /(.+)=(.+)/; $kv{$k} = $v; } $aln->score($kv{score}); foreach my $sline (@slines){ my($s,$src,$start,$size,$strand,$srcsize,$text) = split /\s+/, $sline; # adjust coordinates to be one-based inclusive $start = $start + 1; $strand = $strand eq '+' ? 1 : $strand eq '-' ? -1 : 0; my $seq = Bio::LocatableSeq->new('-seq' => $text, '-display_id' => $src, '-start' => $strand > 0 ? $start : ($srcsize-($start+$size-2)), '-end' => $strand > 0 ? ($start + $size - 1) : ($srcsize-($start-1)) , '-strand' => $strand, '-alphabet' => $self->alphabet, ); $aln->add_seq($seq); } return $aln if $aln->num_sequences; return; } sub write_aln { shift->throw_not_implemented } 1; BioPerl-1.007002/Bio/AlignIO/mase.pm000444000766000024 632713155576320 17001 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::mase # based on the Bio::SeqIO::mase module # by Ewan Birney # and Lincoln Stein # # and the SimpleAlign.pm module of Ewan Birney # # Copyright Peter Schattner # # You may distribute this module under the same terms as perl itself # _history # September 5, 2000 # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::mase - mase sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L class. =head1 DESCRIPTION This object can transform L objects to and from mase flat file databases. =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Peter Schattner Email: schattner@alum.mit.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::mase; use strict; use base qw(Bio::AlignIO); =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Returns : L object Args : NONE =cut sub next_aln { my $self = shift; my $entry; my $name; my $start; my $end; my $seq; my $add; my $count = 0; my $seq_residues; my $aln = Bio::SimpleAlign->new(-source => 'mase'); while( $entry = $self->_readline) { $entry =~ /^;/ && next; if( $entry =~ /^(\S+)\/(\d+)-(\d+)/ ) { $name = $1; $start = $2; $end = $3; } else { $entry =~ s/\s//g; $name = $entry; $end = -1; } $seq = ""; while( $entry = $self->_readline) { $entry =~ /^;/ && last; $entry =~ s/[^A-Za-z\.\-]//g; $seq .= $entry; } if( $end == -1) { $start = 1; $seq_residues = $seq; $seq_residues =~ s/\W//g; $end = length($seq_residues); } $add = Bio::LocatableSeq->new('-seq' => $seq, '-display_id' => $name, '-start' => $start, '-end' => $end, '-alphabet' => $self->alphabet, ); $aln->add_seq($add); # If $end <= 0, we have either reached the end of # file in <> or we have encountered some other error # if ($end <= 0) { undef $aln;} } return $aln if $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in mase format ###Not yet implemented!### Returns : 1 for success and 0 for error Args : L object =cut sub write_aln { my ($self,@aln) = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/AlignIO/mega.pm000444000766000024 1445513155576320 17006 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::mega # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::mega - Parse and Create MEGA format data files =head1 SYNOPSIS use Bio::AlignIO; my $alignio = Bio::AlignIO->new(-format => 'mega', -file => 't/data/hemoglobinA.meg'); while( my $aln = $alignio->next_aln ) { # process each alignment or convert to another format like NEXUS } =head1 DESCRIPTION This object handles reading and writing data streams in the MEGA format (Kumar and Nei). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::mega; use vars qw($MEGANAMELEN %VALID_TYPES $LINELEN $BLOCKLEN); use strict; use Bio::SimpleAlign; use Bio::LocatableSeq; # symbols are changed due to MEGA's use of '.' for redundant sequences BEGIN { $MEGANAMELEN = 10; $LINELEN = 60; $BLOCKLEN = 10; %VALID_TYPES = map {$_, 1} qw( dna rna protein standard); } use base qw(Bio::AlignIO); =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Supports the following MEGA format features: - The file has to start with '#mega' - Reads in the name of the alignment from a comment (anything after '!TITLE: ') . - Reads in the format parameters datatype Returns : L object - returns 0 on end of file or on error Args : NONE =cut sub next_aln{ my ($self) = @_; my $entry; my ($alphabet,%seqs); local $Bio::LocatableSeq::OTHER_SYMBOLS = '\*\?\.'; local $Bio::LocatableSeq::GAP_SYMBOLS = '\-'; my $aln = Bio::SimpleAlign->new(-source => 'mega'); while( defined($entry = $self->_readline()) && ($entry =~ /^\s+$/) ) {} $self->throw("Not a valid MEGA file! [#mega] not starting the file!") unless $entry =~ /^#mega/i; while( defined($entry = $self->_readline() ) ) { local($_) = $entry; if(/\!Title:\s*([^\;]+)\s*/i) { $aln->id($1)} elsif( s/\!Format\s+([^\;]+)\s*/$1/ ) { my (@fields) = split(/\s+/,$1); foreach my $f ( @fields ) { my ($name,$value) = split(/\=/,$f); if( $name eq 'datatype' ) { $alphabet = $value; } elsif( $name eq 'identical' ) { $aln->match_char($value); } elsif( $name eq 'indel' ) { $aln->gap_char($value); } } } elsif( /^\#/ ) { last; } } my @order; while( defined($entry) ) { if( $entry !~ /^\s+$/ ) { # this is to skip the leading '#' my $seqname = substr($entry,1,$MEGANAMELEN-1); $seqname =~ s/(\S+)\s+$/$1/g; my $line = substr($entry,$MEGANAMELEN); $line =~ s/\s+//g; if( ! defined $seqs{$seqname} ) {push @order, $seqname; } $seqs{$seqname} .= $line; } $entry = $self->_readline(); } foreach my $seqname ( @order ) { my $s = $seqs{$seqname}; $s =~ s/[$Bio::LocatableSeq::GAP_SYMBOLS]+//g; my $end = length($s); my $seq = Bio::LocatableSeq->new('-alphabet' => $alphabet, '-display_id' => $seqname, '-seq' => $seqs{$seqname}, '-start' => 1, '-end' => $end); $aln->add_seq($seq); } $aln->unmatch; return $aln if $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in MEGA format Returns : 1 for success and 0 for error Args : L object =cut sub write_aln{ my ($self,@aln) = @_; my $count = 0; my $wrapped = 0; my $maxname; foreach my $aln ( @aln ) { if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln"); return 0; } elsif( ! $aln->is_flush($self->verbose) ) { $self->warn("All Sequences in the alignment must be the same length"); return 0; } $aln->match(); my $len = $aln->length(); my $format = sprintf('datatype=%s identical=%s indel=%s;', $aln->get_seq_by_pos(1)->alphabet(), $aln->match_char, $aln->gap_char); $self->_print(sprintf("#mega\n!Title: %s;\n!Format %s\n\n\n", $aln->id, $format)); my ($count, $blockcount,$length) = ( 0,0,$aln->length()); $aln->set_displayname_flat(); while( $count < $length ) { foreach my $seq ( $aln->each_seq ) { my $seqchars = $seq->seq(); $blockcount = 0; my $substring = substr($seqchars, $count, $LINELEN); my @blocks; while( $blockcount < length($substring) ) { push @blocks, substr($substring, $blockcount,$BLOCKLEN); $blockcount += $BLOCKLEN; } $self->_print(sprintf("#%-".($MEGANAMELEN-1)."s%s\n", substr($aln->displayname($seq->get_nse()), 0,$MEGANAMELEN-2), join(' ', @blocks))); } $self->_print("\n"); $count += $LINELEN; } } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; BioPerl-1.007002/Bio/AlignIO/meme.pm000444000766000024 1547313155576320 17021 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::meme # Based on the Bio::SeqIO modules # by Ewan Birney # and Lincoln Stein # and the SimpleAlign.pm module of Ewan Birney # # Copyright Benjamin Berman # # You may distribute this module under the same terms as perl itself =head1 NAME Bio::AlignIO::meme - meme sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. use Bio::AlignIO; # read in an alignment from meme my $in = Bio::AlignIO->new(-format => 'meme', -file => 'meme.out'); while( my $aln = $in->next_aln ) { # do something with the alignment } =head1 DESCRIPTION This object transforms the "sites sorted by position p-value" sections of a meme (text) output file into a series of Bio::SimpleAlign objects. Each SimpleAlign object contains Bio::LocatableSeq objects which represent the individual aligned sites as defined by the central portion of the "site" field in the meme file. The start and end coordinates are derived from the "Start" field. See L and L for more information. This module can only parse MEME version 3 and 4. Previous versions have output formats that are more difficult to parse correctly. If the meme output file is not version 3.0 or greater we signal an error. =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Benjamin Berman Bbased on the Bio::SeqIO modules by Ewan Birney and others Email: benb@fruitfly.berkeley.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with an underscore. =cut # Let the code begin... package Bio::AlignIO::meme; use strict; use Bio::LocatableSeq; use base qw(Bio::AlignIO); # Constants my $MEME_VERS_ERR = "MEME output file must be generated by version 3.0 or higher"; my $MEME_NO_HEADER_ERR = "MEME output file contains no header line (ex: MEME version 3.0)"; my $HTML_VERS_ERR = "MEME output file must be generated with the -text option"; =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream Returns : Bio::SimpleAlign object with the score() set to the evalue of the motif. Args : NONE =cut sub next_aln { my ($self) = @_; my $aln = Bio::SimpleAlign->new( -source => 'meme' ); my $line; my $good_align_sec = 0; my $in_align_sec = 0; my $evalue; while ( !$good_align_sec && defined( $line = $self->_readline() ) ) { if ( !$in_align_sec ) { # Check for the meme header if ( $line =~ /^\s*MEME\s+version\s+(\S+)/ ) { $self->{'meme_vers'} = $1; my ($vers) = $self->{'meme_vers'} =~ /^(\d)/; $self->throw($MEME_VERS_ERR) unless ( $vers >= 3 ); $self->{'seen_header'} = 1; } # Check if they've output the HTML version if ( $line =~ /\/i ) { $self->throw($HTML_VERS_ERR); } # Grab the evalue if ( $line =~ /MOTIF\s+\d+\s+width.+E-value = (\S+)/ ) { $self->throw($MEME_NO_HEADER_ERR) unless ( $self->{'seen_header'} ); $evalue = $1; } # Check if we're going into an alignment section if ( $line =~ /sites sorted by position/ ) { $self->throw($MEME_NO_HEADER_ERR) unless ( $self->{'seen_header'} ); $in_align_sec = 1; } } # The first regexp is for version 3, the second is for version 4 elsif ( $line =~ /^(\S+)\s+([+-]?)\s+(\d+)\s+ \S+\s+[.A-Z\-]*\s+([A-Z\-]+)\s+ ([.A-Z\-]*)/xi || $line =~ /^(\S+)\s+([+-]?)\s+(\d+)\s+ \S+\s+\.\s+([A-Z\-]+)/xi ) { # Got a sequence line my $seq_name = $1; my $strand = ( $2 eq '-' ) ? -1 : 1; my $start_pos = $3; my $central = uc($4); # my $p_val = $4; # my $left_flank = uc($5); # my $right_flank = uc($7); # Info about the flanking sequence # my $start_len = ($strand > 0) ? length($left_flank) : # length($right_flank); # my $end_len = ($strand > 0) ? length($right_flank) : # length($left_flank); # Make the sequence. Meme gives the start coordinate at the left # hand side of the motif relative to the INPUT sequence. my $end_pos = $start_pos + length($central) - 1; my $seq = Bio::LocatableSeq->new( -seq => $central, -display_id => $seq_name, -start => $start_pos, -end => $end_pos, -strand => $strand, -alphabet => $self->alphabet, ); # Add the sequence motif to the alignment $aln->add_seq($seq); } elsif ( ( $line =~ /^\-/ ) || ( $line =~ /Sequence name/ ) ) { # These are acceptable things to be in the site section } elsif ( $line =~ /^\s*$/ ) { # This ends the site section $in_align_sec = 0; $good_align_sec = 1; } else { $self->warn("Unrecognized format:\n$line"); return; } } # Signal an error if we didn't find a header section $self->throw($MEME_NO_HEADER_ERR) unless ( $self->{'seen_header'} ); if ($good_align_sec) { $aln->score($evalue); return $aln; } return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: Not implemented Returns : 1 for success and 0 for error Args : Bio::SimpleAlign object =cut sub write_aln { my ( $self, @aln ) = @_; $self->throw_not_implemented(); } # ---------------------------------------- # - Private methods # ---------------------------------------- sub _initialize { my ( $self, @args ) = @_; # Call into our base version $self->SUPER::_initialize(@args); # Then initialize our data variables $self->{'seen_header'} = 0; } 1; BioPerl-1.007002/Bio/AlignIO/metafasta.pm000444000766000024 1304513155576320 20034 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::metafasta # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::metafasta - Metafasta MSA Sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L class. =head1 DESCRIPTION This object can transform L objects to and from metafasta flat file databases. The format of a metafasta file is >test/1-25 ABCDEFHIJKLMNOPQRSTUVWXYZ &charge NBNAANCNJCNNNONNCNNUNNXNZ &chemical LBSAARCLJCLSMOIMCHHULRXRZ where the sequence block is followed by one or several meta blocks. Each meta block starts with the ampersand character '&' in the first column and is immediately followed by the name of the meta data which continues until the new line. The meta data follows it. All characters, except new line, are important in meta data. =head1 SEE ALSO L =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::metafasta; use vars qw($WIDTH); use strict; use Bio::SimpleAlign; use Bio::Seq::Meta; use Bio::Seq::SeqFactory; use Bio::Seq::SeqFastaSpeedFactory; use base qw(Bio::AlignIO); BEGIN { $WIDTH = 60} sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); my ($width) = $self->_rearrange([qw(WIDTH)], @args); $width && $self->width($width); } =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Returns : L object - returns 0 on end of file or on error Args : NONE =cut sub next_aln { my( $self ) = @_; my $seq; my $alphabet; local $/ = "\n>"; my $aln = Bio::SimpleAlign->new(); while(defined (my $entry = $self->_readline)) { chomp($entry); if ($entry =~ m/\A\s*\Z/s) { # very first one return unless $entry = $self->_readline; chomp($entry); } $entry =~ s/^>//; my ($top,$sequence) = split(/\n/,$entry,2); defined $sequence && $sequence =~ s/>//g; my @metas; ($sequence, @metas) = split /\n&/, $sequence; my ($id, $start, $end); if ( $top =~ /(\S+)\/(\d+)-(\d+)/ ) { $id = $1; $start = $2; $end = $3; } elsif ($top =~ /(\S+)/) { $id = $1; $start = 1; $end = length($sequence); } defined $sequence && $sequence =~ s/\s//g; # Remove whitespace $seq = Bio::Seq::Meta->new('-seq' => $sequence, '-display_id' => $id, '-start' => $start, '-end' => $end, '-alphabet' => $self->alphabet, ); foreach my $meta (@metas) { my ($name,$string) = split /\n/, $meta; $string =~ s/\n//g; # Remove newlines, spaces are important $seq->named_meta($name, $string); } $aln->add_seq($seq); # alignment needs seqs all the same length, pad with gaps my $alnlen = $aln->length; foreach my $seq ( $aln->each_seq ) { if ( $seq->length < $alnlen ) { my ($diff) = ($alnlen - $seq->length); $seq->seq( $seq->seq() . "-" x $diff); } } } return $aln if $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in fasta format Returns : 1 for success and 0 for error Args : L object =cut sub write_aln { my ($self,@aln) = @_; my $width = $self->width; foreach my $aln (@aln) { if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln"); next; } foreach my $seq ( $aln->each_seq() ) { my $name = $aln->displayname($seq->get_nse); my $str = $seq->seq(); if(length($str) > 0) { $str =~ s/(.{1,$width})/$1\n/g; } else { $str = "\n"; } $self->_print (">",$name,"\n",$str) or return; if ($seq->isa('Bio::Seq::MetaI')) { foreach my $meta ($seq->meta_names) { my $str = $seq->named_meta($meta); $str =~ s/(.{1,$width})/$1\n/g; $self->_print ("&",$meta,"\n",$str); } } } } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 width Title : width Usage : $obj->width($newval) Function: Get/Set the line width for METAFASTA output Returns : value of width Args : newvalue (optional) =cut sub width{ my ($self,$value) = @_; if( defined $value) { $self->{'width'} = $value; } return $self->{'width'} || $WIDTH; } 1; BioPerl-1.007002/Bio/AlignIO/msf.pm000444000766000024 1412513155576320 16654 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::msf # based on the Bio::SeqIO::msf module # by Ewan Birney # and Lincoln Stein # # and the SimpleAlign.pm module of Ewan Birney # # Copyright Peter Schattner # # You may distribute this module under the same terms as perl itself # _history # September 5, 2000 # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::msf - msf sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L class. =head1 DESCRIPTION This object can transform L objects to and from msf flat file databases. =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Peter Schattner Email: schattner@alum.mit.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::msf; use vars qw(%valid_type); use strict; use Bio::SeqIO::gcg; # for GCG_checksum() use Bio::SimpleAlign; use base qw(Bio::AlignIO); BEGIN { %valid_type = qw( dna N rna N protein P ); } =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Tries to read *all* MSF It reads all non whitespace characters in the alignment area. For MSFs with weird gaps (eg ~~~) map them by using $aln->map_chars('~','-') Returns : Bio::Align::AlignI object Args : NONE =cut sub next_aln { my $self = shift; my $entry; my (%hash,$name,$str,@names,$seqname,$start,$end,$count,$seq); my $aln = Bio::SimpleAlign->new(-source => 'gcg' ); while( $entry = $self->_readline) { $entry =~ m{//} && last; # move to alignment section $entry =~ /Name:\s+(\S+)/ && do { $name = $1; $hash{$name} = ""; # blank line push(@names,$name); # we need it ordered! }; # otherwise - skip } # alignment section while( $entry = $self->_readline) { next if ( $entry =~ /^\s+(\d+)/ ) ; $entry =~ /^\s*(\S+)\s+(.*)$/ && do { $name = $1; $str = $2; if( ! exists $hash{$name} ) { $self->throw("$name exists as an alignment line but not in the header. Not confident of what is going on!"); } $str =~ s/\s//g; $str =~ s/~/-/g; $hash{$name} .= $str; }; } return if @names < 1; # now got this as a name - sequence hash. Let's make some sequences! for $name ( @names ) { if( $name =~ m{(\S+)/(\d+)-(\d+)} ) { $seqname = $1; $start = $2; $end = $3; } else { $seqname = $name; $start = 1; $str = $hash{$name}; $str =~ s/[^0-9A-Za-z$Bio::LocatableSeq::OTHER_SYMBOLS]//g; $end = length($str); } $seq = Bio::LocatableSeq->new('-seq' => $hash{$name}, '-display_id' => $seqname, '-start' => $start, '-end' => $end, '-alphabet' => $self->alphabet, ); $aln->add_seq($seq); # If $end <= 0, we have either reached the end of # file in <> or we have encountered some other error } return $aln if $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in MSF format Sequence type of the alignment is determined by the first sequence. Returns : 1 for success and 0 for error Args : Bio::Align::AlignI object =cut sub write_aln { my ($self,@aln) = @_; my $msftag; my $type; my $count = 0; my $maxname; my ($length,$date,$name,$seq,$miss,$pad,%hash,@arr,$tempcount,$index); foreach my $aln (@aln) { if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln"); next; } $date = localtime(time); $msftag = "MSF"; $type = $valid_type{$aln->get_seq_by_pos(1)->alphabet}; $maxname = $aln->maxdisplayname_length(); $length = $aln->length(); $name = $aln->id(); if( !defined $name ) { $name = "Align"; } $self->_print (sprintf("\n%s MSF: %d Type: %s %s Check: 00 ..\n\n", $name, $aln->num_sequences, $type, $date)); my $seqCountFormat = "%".($maxname > 20 ? $maxname + 2: 22)."s%-27d%27d\n"; my $seqNameFormat = "%-".($maxname > 20 ? $maxname : 20)."s "; foreach $seq ( $aln->each_seq() ) { $name = $aln->displayname($seq->get_nse()); $miss = $maxname - length ($name); $miss += 2; $pad = " " x $miss; $self->_print (sprintf(" Name: %s%sLen: %d Check: %d Weight: 1.00\n",$name,$pad,length $seq->seq(), Bio::SeqIO::gcg->GCG_checksum($seq))); $hash{$name} = $seq->seq(); push(@arr,$name); } # ok - heavy handed, but there you go. # $self->_print ("\n//\n\n\n"); while( $count < $length ) { # there is another block to go! $self->_print (sprintf($seqCountFormat,' ',$count+1,$count+50)); foreach $name ( @arr ) { $self->_print (sprintf($seqNameFormat,$name)); $tempcount = $count; $index = 0; while( ($tempcount + 10 < $length) && ($index < 5) ) { $self->_print (sprintf("%s ",substr($hash{$name}, $tempcount,10))); $tempcount += 10; $index++; } # # ok, could be the very last guy ;) # if( $index < 5) { # space to print! # $self->_print (sprintf("%s ",substr($hash{$name},$tempcount))); $tempcount += 10; } $self->_print ("\n"); } $self->_print ("\n\n"); $count = $tempcount; } } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; BioPerl-1.007002/Bio/AlignIO/nexml.pm000444000766000024 1041113155576320 17204 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::nexml # # Copyright Chase Miller # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::nexml - NeXML format sequence alignment input/output stream driver =head1 SYNOPSIS Do not use this module directly. Use it via the L class. =head1 DESCRIPTION This object can transform L objects to and from NeXML format. For more information on NeXML, visit L. =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Chase Miller =head1 CONTRIBUTORS Mark Jensen, maj@fortinbras.us Rutger Vos, rutgeraldo@gmail.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::nexml; use strict; use lib '../..'; use Bio::Nexml::Factory; use Bio::Phylo::IO qw(parse unparse); use base qw(Bio::AlignIO); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); $self->{_doc} = undef; } =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln Function: returns the next alignment in the stream. Returns : Bio::Align::AlignI object - returns 0 on end of file or on error Args : See L =cut sub next_aln { my ($self) = @_; unless ( $self->{'_parsed'} ) { #use a parse function to load all the alignment objects found in the nexml file at once $self->_parse; } return $self->{'_alns'}->[ $self->{'_alnsiter'}++ ]; } =head2 rewind Title : rewind Usage : $alnio->rewind Function: Resets the stream Returns : none Args : none =cut sub rewind { my $self = shift; $self->{'_alniter'} = 0; } =head2 doc Title : doc Usage : $treeio->doc Function: Returns the biophylo nexml document object Returns : Bio::Phylo::Project Args : none or Bio::Phylo::Project object =cut sub doc { my ($obj,$value) = @_; if( defined $value) { $obj->{'_doc'} = $value; } return $obj->{'_doc'}; } sub _parse { my ($self) = @_; $self->{'_parsed'} = 1; $self->{'_alnsiter'} = 0; my $fac = Bio::Nexml::Factory->new(); # Only pass filename if filehandle is not available, # or "Bio::Phylo" will create a new filehandle that ends # out of scope and can't be closed directly, leaving 2 open # filehandles for the same file (so file can't be deleted) my $file_arg; my $file_value; if ( exists $self->{'_filehandle'} and defined $self->{'_filehandle'} ) { $file_arg = '-handle'; $file_value = $self->{'_filehandle'}; } else { $file_arg = '-file'; $file_value = $self->{'_file'}; } $self->doc(parse( $file_arg => $file_value, '-format' => 'nexml', '-as_project' => '1' ) ); $self->{'_alns'} = $fac->create_bperl_aln($self); if(@{ $self->{'_alns'} } == 0) { self->debug("no seqs in $self->{_file}"); } } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in nexml format Returns : 1 for success and 0 for error Args : L object See L =cut sub write_aln { my ($self, $aln) = @_; my $fac = Bio::Nexml::Factory->new(); my $taxa = $fac->create_bphylo_taxa($aln); my ($matrix) = $fac->create_bphylo_aln($aln, $taxa); $matrix->set_taxa($taxa); $self->doc(Bio::Phylo::Factory->create_project()); $self->doc->insert($matrix); my $ret = $self->_print($self->doc->to_xml()); $self->flush; return $ret; } 1; BioPerl-1.007002/Bio/AlignIO/nexus.pm000444000766000024 3355713155576320 17243 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::nexus # # Copyright Heikki Lehvaslaiho # =head1 NAME Bio::AlignIO::nexus - NEXUS format sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L class. use Bio::AlignIO; my $in = Bio::AlignIO->new(-format => 'nexus', -file => 'aln.nexus'); while( my $aln = $in->next_aln ) { # do something with the alignment } =head1 DESCRIPTION This object can transform L objects to and from NEXUS data blocks. See method documentation for supported NEXUS features. =head1 ACKNOWLEDGEMENTS Will Fisher has written an excellent standalone NEXUS format parser in Perl, readnexus. A number of tricks were adapted from it. =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::nexus; use vars qw(%valid_type); use strict; no strict "refs"; use base qw(Bio::AlignIO); BEGIN { %valid_type = map {$_, 1} qw( dna rna protein standard ); # standard throws error: inherited from Bio::PrimarySeq } =head2 new Title : new Usage : $alignio = Bio::AlignIO->new(-format => 'nexus', -file => 'filename'); Function: returns a new Bio::AlignIO object to handle clustalw files Returns : Bio::AlignIO::clustalw object Args : -verbose => verbosity setting (-1,0,1,2) -file => name of file to read in or with ">" - writeout -fh => alternative to -file param - provide a filehandle to read from/write to -format => type of Alignment Format to process or produce Customization of nexus flavor output -show_symbols => print the symbols="ATGC" in the data definition (MrBayes does not like this) boolean [default is 1] -show_endblock => print an 'endblock;' at the end of the data (MyBayes does not like this) boolean [default is 1] =cut sub _initialize { my ($self, @args) = @_; $self->SUPER::_initialize(@args); my ($show_symbols, $endblock) = $self->_rearrange([qw(SHOW_SYMBOLS SHOW_ENDBLOCK)], @args); my @names = qw(symbols endblock); for my $v ( $show_symbols, $endblock ) { $v = 1 unless defined $v; # default value is 1 my $n = shift @names; $self->flag($n, $v); } } =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: Returns the next alignment in the stream. Supports the following NEXUS format features: - The file has to start with '#NEXUS' - Reads in the name of the alignment from a comment (anything after 'TITLE: ') . - Sequence names can be given in a taxa block, too. - If matchchar notation is used, converts them back to sequence characters. - Does character conversions specified in the NEXUS equate command. - Sequence names of type 'Homo sapiens' and Homo_sapiens are treated identically. Returns : L object Args : =cut sub next_aln { my $self = shift; my $entry; my ($aln_name, $seqcount, $residuecount, %hash, $alphabet, $match, $gap, $missing, $equate, $interleave, $name,$str,@names,$seqname,$start,$end,$count,$seq); local $Bio::LocatableSeq::OTHER_SYMBOLS = '\*\?\.'; local $Bio::LocatableSeq::GAP_SYMBOLS = '\-'; my $aln = Bio::SimpleAlign->new(-source => 'nexus'); # file starts with '#NEXUS' but we allow white space only lines before it $entry = $self->_readline; $entry = $self->_readline while defined $entry && $entry =~ /^\s+$/; return unless $entry; $self->throw("Not a valid interleaved NEXUS file! [#NEXUS] not starting the file\n$entry") unless ($entry && $entry =~ /^#NEXUS/i); # skip anything before either the taxa or data block # but read in the optional title in a comment while (defined($entry = $self->_readline)) { local ($_) = $entry; /\[TITLE. *([^\]]+)]\s+/i and $aln_name = $1; last if /^begin +data/i || /^begin +taxa/i; } $aln_name =~ s/\s/_/g and $aln->id($aln_name) if $aln_name; # data and taxa blocks my $incomment; while (defined ($entry = $self->_readline)) { local ($_) = $entry; next if s/\[[^\]]+\]//g; # remove comments if( s/\[[^\]]+$// ) { $incomment = 1; # skip line if it is now empty or contains only whitespace next if /^\s*$/; } elsif($incomment) { if( s/^[^\]]*\]// ) { $incomment = 0; } else { next; } } elsif( /taxlabels/i ) { # doesn't deal with taxlabels adequately and can mess things up! # @names = $self->_read_taxlabels; } else { /ntax\s*=\s*(\d+)/i and $seqcount = $1; /nchar\s*=\s*(\d+)/i and $residuecount = $1; /matchchar\s*=\s*(.)/i and $match = $1; /gap\s*=\s*(.)/i and $gap = $1; /missing\s*=\s*(.)/i and $missing = $1; /equate\s*=\s*\"([^\"]+)/i and $equate = $1; # "e.g. equate="T=C G=A"; /datatype\s*=\s*(\w+)/i and $alphabet = lc $1; /interleave/i and $interleave = 1 ; last if /matrix/io; } } $self->throw("Not a valid NEXUS sequence file. Datatype not specified.") unless $alphabet; $self->throw("Not a valid NEXUS sequence file. Datatype should not be [$alphabet]") unless $valid_type{$alphabet}; $self->throw("\"$gap\" is not a valid gap character. For compatability, gap char can not be one of: ()[]{}/\,;:=*'`\"<>^") if $gap && $gap =~ /[\(\)\[\]\{\}\/\\\,\;\:\=\*\'\`\<\>\^]/; $self->throw("\"$missing\" is not a valid missing character. For compatability, missing char can not be one of: ()[]{}/\,;:=*'`\"<>^") if $missing && $missing =~ /[\(\)\[\]\{\}\/\\\,\;\:\=\*\'\`\<\>\^]/; $aln->gap_char($gap); $aln->missing_char($missing); # # if data is not right after the matrix line # read the empty lines out # while ($entry = $self->_readline) { unless ($entry =~ /^\s+$/) { $self->_pushback($entry); last; } } # # matrix command # # first alignment section if (@names == 0) { # taxa block did not exist while ($entry = $self->_readline) { local ($_) = $entry; if( s/\[[^\]]+\]//g ) { #] remove comments next if /^\s*$/; # skip line if it is now empty or contains only whitespace } if ($interleave && defined$count && ($count <= $seqcount)) { /^\s+$/ and last; } else { /^\s+$/ and next; } /^\s*;/ and last; # stop if colon at end of matrix is on it's own line #/^\s*;\s*$/ and last; if ( /^\s*([\"\'](.+?)[\"\']|(\S+))\s+(.*)\s*$/ ) { # get single and double quoted names, or all the first # nonwhite word as the name, and remained is seq #if (/^\s*('([^']*?)'|([^']\S*))\s+(.*)$/) { #' $name = ($2 || $3); if ($4) { # seq is on same line as name # this is the usual NEXUS format $str = $4; } else { # otherwise get seq from following lines. No comments allowed # a less common matrix format, usually used for very long seqs $str=''; while (local ($_) = $self->_readline) { my $str_tmp = $_; $str_tmp =~ s/[\s;]//g; $str .= $str_tmp; last if length$str == $residuecount; } } $name =~ s/ /_/g; push @names, $name; $str =~ s/[\s;]//g; $count = @names; $hash{$count} = $str; } $self->throw("Not a valid interleaved NEXUS file! seqcount [$count] > predeclared [$seqcount] in the first section") if $count > $seqcount; /;/ and last; # stop if colon at end of matrix is on the same line as the last seq } } # interleaved sections $count = 0; if ( $interleave ) { # only read next section if file is interleaved while( $entry = $self->_readline) { local ($_) = $entry; if( s/\[[^\]]+\]//g ) { #] remove comments next if /^\s*$/; # skip line if it is now empty or contains only whitespace } /^\s*;/ and last; # stop if colon at end of matrix is on it's own line $count = 0, next if $entry =~ /^\s*$/; if (/^\s*(\'([^\']*?)\'|([^\']\S*))\s+(.*)$/) { $str = $4; $str =~ s/[\s;]//g; $count++; $hash{$count} .= $str; }; $self->throw("Not a valid interleaved NEXUS file! seqcount [$count] > predeclared [$seqcount] ") if $count > $seqcount; /;/ and last; # stop if colon at end of matrix is on the same line as the last seq } } return if @names < 1; # sequence creation $count = 0; foreach $name ( @names ) { $count++; if( $name =~ /(\S+)\/(\d+)-(\d+)/ ) { ($seqname,$start,$end) = ($1,$2,$3); } else { ($seqname,$start,$str) = ($name,1,$hash{$count}); $str =~ s/[$Bio::LocatableSeq::GAP_SYMBOLS]//g; $end = length($str); } # consistency test $self->throw("Length of sequence [$seqname] is not [$residuecount]; got".CORE::length($hash{$count})) unless CORE::length($hash{$count}) == $residuecount; $seq = Bio::LocatableSeq->new('-seq' => $hash{$count}, '-display_id' => $seqname, '-start' => $start, '-end' => $end, '-alphabet' => $alphabet ); $aln->add_seq($seq); } # if matchchar is used $aln->unmatch($match) if $match; # if equate ( e.g. equate="T=C G=A") is used if ($equate) { $aln->map_chars($1, $2) while $equate =~ /(\S)=(\S)/g; } while (defined $entry && $entry !~ /endblock/i) { $entry = $self->_readline; } return $aln if $aln->num_sequences; return; } sub _read_taxlabels { my ($self) = @_; my ($name, @names); while (my $entry = $self->_readline) { last if $entry =~ m/^\s*(END)?;/i; if( $entry =~ m/\s*(\S+)\s+/ ) { ($name) = ($1); $name =~ s/\[[^\[]+\]//g; $name =~ s/\W/_/g; push @names, $name; } } return @names; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: Writes the $aln object into the stream in interleaved NEXUS format. Everything is written into a data block. SimpleAlign methods match_char, missing_char and gap_char must be set if you want to see them in the output. Returns : 1 for success and 0 for error Args : L object =cut sub write_aln { my ($self,@aln) = @_; my $count = 0; my $wrapped = 0; my $maxname; my ($length,$date,$name,$seq,$miss,$pad,%hash,@arr,$tempcount,$index ); my ($match, $missing, $gap,$symbols) = ('', '', '',''); foreach my $aln (@aln) { if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln"); next; } $self->throw("All sequences in the alignment must be the same length") unless $aln->is_flush($self->verbose); $length = $aln->length(); $self->_print (sprintf("#NEXUS\n[TITLE: %s]\n\nbegin data;\ndimensions ntax=%s nchar=%s;\n", $aln->id, $aln->num_sequences, $length)); $match = "match=". $aln->match_char if $aln->match_char; $missing = "missing=". $aln->missing_char if $aln->missing_char; $gap = "gap=". $aln->gap_char if $aln->gap_char; $symbols = 'symbols="'.join('',$aln->symbol_chars). '"' if( $self->flag('symbols') && $aln->symbol_chars); $self->_print (sprintf("format interleave datatype=%s %s %s %s %s;\n\nmatrix\n", $aln->get_seq_by_pos(1)->alphabet, $match, $missing, $gap, $symbols)); # account for single quotes round names my $indent = $aln->maxdisplayname_length+2; $aln->set_displayname_flat(); foreach $seq ( $aln->each_seq() ) { my $nmid = $aln->displayname($seq->get_nse()); if( $nmid =~ /[^\w\d\.]/ ) { # put name in single quotes incase it contains any of # the following chars: ()[]{}/\,;:=*'"`+-<> that are not # allowed in PAUP* and possible other software $name = sprintf("%-${indent}s", "\'" . $nmid . "\'"); } else { $name = sprintf("%-${indent}s", $nmid); } $hash{$name} = $seq->seq; push(@arr,$name); } while( $count < $length ) { # there is another block to go! foreach $name ( @arr ) { my $dispname = $name; # $dispname = '' if $wrapped; $self->_print (sprintf("%${indent}s ",$dispname)); $tempcount = $count; $index = 0; while( ($tempcount + 10 < $length) && ($index < 5) ) { $self->_print (sprintf("%s ",substr($hash{$name},$tempcount,10))); $tempcount += 10; $index++; } # last if( $index < 5) { # space to print! $self->_print (sprintf("%s ",substr($hash{$name},$tempcount))); $tempcount += 10; } $self->_print ("\n"); } $self->_print ("\n\n"); $count = $tempcount; $wrapped = 1; } if( $self->flag('endblock') ) { $self->_print (";\n\nendblock;\n"); } else { $self->_print (";\n\nend;\n"); } } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 flag Title : flag Usage : $obj->flag($name,$value) Function: Get/Set a flag value Returns : value of flag (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub flag{ my ($self,$name,$val) = @_; return $self->{'flag'}->{$name} = $val if defined $val; return $self->{'flag'}->{$name}; } 1; BioPerl-1.007002/Bio/AlignIO/pfam.pm000444000766000024 713013155576320 16770 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::pfam # based on the Bio::SeqIO:: modules # by Ewan Birney # and Lincoln Stein # # and the SimpleAlign.pm module of Ewan Birney # # Copyright Peter Schattner # # You may distribute this module under the same terms as perl itself # _history # September 5, 2000 # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::pfam - pfam sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L class. =head1 DESCRIPTION This object can transform Bio::SimpleAlign objects to and from pfam flat file databases. =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Peter Schattner Email: schattner@alum.mit.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::pfam; use strict; use Bio::SimpleAlign; use base qw(Bio::AlignIO); =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream Returns : L object Args : NONE =cut sub next_aln { my $self = shift; my $entry; my $name; my $start; my $end; my $seq; my $add; my $acc; my %names; my $aln = Bio::SimpleAlign->new(-source => 'pfam'); while( $entry = $self->_readline) { chomp $entry; $entry =~ m{^//} && last; if($entry !~ m{^(\S+)/(\d+)-(\d+)\s+(\S+)\s*} ) { $self->throw("Found a bad line [$_] in the pfam format alignment"); next; } $name = $1; $start = $2; $end = $3; $seq = $4; $add = Bio::LocatableSeq->new('-seq' => $seq, '-display_id' => $name, '-start' => $start, '-end' => $end, '-alphabet' => $self->alphabet, ); $aln->add_seq($add); } # If $end <= 0, we have either reached the end of # file in <> or we have encountered some other error # return $aln if $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream Returns : 1 for success and 0 for error Args : L object =cut sub write_aln { my ($self,@aln) = @_; if( @aln > 1 ) { $self->warn("Only the 1st pfam alignment will be output since the format does not support multiple alignments in the same file"); } my $aln = shift @aln; if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln"); next; } my ($namestr,$seq,$add); my ($maxn); $maxn = $aln->maxdisplayname_length(); foreach $seq ( $aln->each_seq() ) { $namestr = $aln->displayname($seq->get_nse()); $add = $maxn - length($namestr) + 2; $namestr .= " " x $add; $self->_print (sprintf("%s %s\n",$namestr,$seq->seq())) or return; } $self->flush() if $self->_flush_on_write && defined $self->_fh; return 1; } 1; BioPerl-1.007002/Bio/AlignIO/phylip.pm000444000766000024 4560513155576320 17403 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::phylip # # Copyright Heikki Lehvaslaiho # =head1 NAME Bio::AlignIO::phylip - PHYLIP format sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. This example shows how to write to phylip format: use Bio::AlignIO; use Bio::SimpleAlign; # Use -idlength to set the name length to something other than # the default 10 if you need longer ids. my $phylipstream = Bio::AlignIO->new(-format => 'phylip', -fh => \*STDOUT, -idlength => 30); # Convert data from one format to another my $gcgstream = Bio::AlignIO->new(-format => 'msf', -file => 't/data/cysprot1a.msf'); while( my $aln = $gcgstream->next_aln ) { $phylipstream->write_aln($aln); } # With phylip sequential format format $phylipstream->interleaved(0); # Or initialize the object like this $phylipstream = Bio::AlignIO->new(-interleaved => 0, -format => 'phylip', -fh => \*STDOUT, -idlength => 20 ); $gcgstream = Bio::AlignIO->new(-format => 'msf', -file => 't/data/cysprot1a.msf'); while( my $aln = $gcgstream->next_aln ) { $phylipstream->write_aln($aln); } This example shows how to read phylip format: my $in = Bio::AlignIO->new( -file => $inFile, -format => 'phylip', -interleaved => 0, -longid => 1 ); my $out = Bio::AlignIO->new( -file => ">$outFile", -format => 'fasta' ); while ( my $aln = $in->next_aln() ) { $out->write_aln($aln); } The -longid argument is required if the input phylip format file has ids with lengths greater then 10 characters. =head1 DESCRIPTION This object can transform Bio::SimpleAlign objects to and from PHYLIP format. By default it works with the interleaved format. By specifying the flag -interleaved =E 0 in the initialization the module can read or write data in sequential format. Reading phylip format with long IDs up to 50 characters is supported by the flag -longid =E1. ID strings can be surrounded by single quotes. They are mandatory only if the IDs contain spaces. =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Heikki Lehvaslaiho and Jason Stajich Email: heikki at ebi.ac.uk Email: jason at bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::phylip; use vars qw($DEFAULTIDLENGTH $DEFAULTLINELEN $DEFAULTTAGLEN); use strict; use Bio::SimpleAlign; use POSIX; # for the rounding call use base qw(Bio::AlignIO); BEGIN { $DEFAULTIDLENGTH = 10; $DEFAULTLINELEN = 60; $DEFAULTTAGLEN = 10; } =head2 new Title : new Usage : my $alignio = Bio::AlignIO->new(-format => 'phylip' -file => '>file', -idlength => 10, -idlinebreak => 1); Function: Initialize a new L reader or writer Returns : L object Args : [specific for writing of phylip format files] -idlength => integer - length of the id (will pad w/ spaces if needed) when writing phylip -interleaved => boolean - whether interleaved or sequential format required -line_length => integer of how long a sequence lines should be -idlinebreak => insert a line break after the sequence id so that sequence starts on the next line -flag_SI => whether or not write a "S" or "I" just after the num.seq. and line len., in the first line -tag_length => integer of how long the tags have to be in each line between the space separator. set it to 0 to have 1 tag only. -wrap_sequential => boolean for whether or not sequential format should be broken up or a single line default is false (single line) -longid => boolean to read arbitrary long IDs (default is false) =cut sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); my ( $interleave, $linelen, $idlinebreak, $idlength, $flag_SI, $tag_length, $ws, $longid ) = $self->_rearrange( [ qw(INTERLEAVED LINE_LENGTH IDLINEBREAK IDLENGTH FLAG_SI TAG_LENGTH WRAP_SEQUENTIAL LONGID) ], @args ); $self->interleaved( $interleave ? 1 : 0 ) if defined $interleave; $self->idlength( $idlength || $DEFAULTIDLENGTH ); $self->id_linebreak(1) if ($idlinebreak); $self->line_length($linelen) if defined $linelen && $linelen > 0; $self->flag_SI(1) if ($flag_SI); $self->tag_length($tag_length) if ( $tag_length || $DEFAULTTAGLEN ); $self->wrap_sequential( $ws ? 1 : 0 ); $self->longid( $longid ? 1 : 0 ); 1; } =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Throws an exception if trying to read in PHYLIP sequential format. Returns : L object Args : =cut sub next_aln { my $self = shift; my $entry; my ($seqcount, $residuecount, %hash, $name, $str, @names, $seqname, $start, $end, $count, $seq ); my $aln = Bio::SimpleAlign->new( -source => 'phylip' ); # First, parse up through the header. # If we see a non-blank line that isn't the seqcount and residuecount line # then bail out of next_aln (return) while ( $entry = $self->_readline ) { if ( $entry =~ /^\s?$/ ) { next; } elsif ( $entry =~ /\s*(\d+)\s+(\d+)/ ) { ( $seqcount, $residuecount ) = ( $1, $2 ); last; } else { $self->warn( "Failed to parse PHYLIP: Did not see a sequence count and residue count." ); return; } } return unless $seqcount and $residuecount; # First alignment section. We expect to see a name and (part of) a sequence. my $idlen = $self->idlength; $count = 0; while ( $entry = $self->_readline ) { if ( $entry =~ /^\s?$/ ) { # eat the newlines next; } # Names can be in a few different formats: # 1. they can be traditional phylip: 10 chars long, period. If this is the case, that name can have spaces. # 2. they can be hacked with a long ID, as passed in with the flag -longid. # 3. if there is a long ID, the name can have spaces as long as it is wrapped in single quotes. if ( $self->longid() ) { # 2 or 3 if ( $entry =~ /^'(.+)'\s+(.+)$/ ) { # 3. name has single quotes. $name = $1; $str = $2; } else { # 2. name does not have single quotes, so should not have spaces. # therefore, the first part of the line is the name and the rest is the seq. # make sure that the line does not lead with extra spaces. $entry =~ s/^\s+//; ( $name, $str ) = split( /\s+/, $entry, 2 ); } } else { # 1. traditional phylip. $entry =~ /^(.{1,10})\s(.+)$/; $name = $1; $str = $2; $name =~ s/\s+$//; # eat any trailing spaces $name =~ s/\s+/_/g; } push @names, $name; #clean sequence of spaces: $str =~ s/\s+//g; # are we sequential? If so, we should keep adding to the sequence until we've got all the residues. if ( ( $self->interleaved ) == 0 ) { while ( length($str) < $residuecount ) { $entry = $self->_readline; $str .= $entry; $str =~ s/\s+//g; if ( $entry =~ /^\s*$/ ) { # we ran into a newline before we got a complete sequence: bail! $self->warn( "Failed to parse PHYLIP: Sequence $name was shorter than expected: " . length($str) . " instead of $residuecount." ); last; } } } $hash{$count} = $str; $count++; # if we've read as many seqs as we're supposed to, move on. if ( $count == $seqcount ) { last; } } # if we are interleaved, we're going to keep seeing chunks of sequence until we get all of it. if ( $self->interleaved ) { while ( length( $hash{ $seqcount - 1 } ) < $residuecount ) { $count = 0; while ( $entry = $self->_readline ) { if ( $entry =~ /^\s*$/ ) { # eat newlines if ( $count != 0 ) { # there was a newline at an unexpected place! $self->warn( "Failed to parse PHYLIP: Interleaved file is missing a segment: saw $count, expected $seqcount." ); return; } next; } else { # start taking in chunks $entry =~ s/\s//g; $hash{$count} .= $entry; $count++; } if ( $count >= $seqcount ) { # we've read all of the sequences for this chunk, so move on. last; } } } } if ( ( scalar @names ) != $seqcount ) { $self->warn( "Failed to parse PHYLIP: Did not see the correct number of seqs: saw " . scalar(@names) . ", expected $seqcount." ); return; } for ( $count = 0; $count < $seqcount; $count++ ) { $str = $hash{$count}; my $seqname = $names[$count]; if ( length($str) != $residuecount ) { $self->warn( "Failed to parse PHYLIP: Sequence $seqname was the wrong length: " . length($str) . " instead of $residuecount." ); } $seq = Bio::LocatableSeq->new( '-seq' => $hash{$count}, '-display_id' => $seqname ); $aln->add_seq($seq); } return $aln; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in phylip format Returns : 1 for success and 0 for error Args : L object =cut sub write_aln { my ( $self, @aln ) = @_; my $count = 0; my $wrapped = 0; my $maxname; my $width = $self->line_length(); my ($length, $date, $name, $seq, $miss, $pad, %hash, @arr, $tempcount, $index, $idlength, $flag_SI, $line_length, $tag_length ); foreach my $aln (@aln) { if ( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->warn( "Must provide a Bio::Align::AlignI object when calling write_aln" ); next; } $self->throw("All sequences in the alignment must be the same length") unless $aln->is_flush(1); $flag_SI = $self->flag_SI(); $aln->set_displayname_flat(); # plain $length = $aln->length(); if ($flag_SI) { if ( $self->interleaved() ) { $self->_print( sprintf( " %s %s I\n", $aln->num_sequences, $aln->length ) ); } else { $self->_print( sprintf( " %s %s S\n", $aln->num_sequences, $aln->length ) ); } } else { $self->_print( sprintf( " %s %s\n", $aln->num_sequences, $aln->length ) ); } $idlength = $self->idlength(); $line_length = $self->line_length(); $tag_length = $self->tag_length(); foreach $seq ( $aln->each_seq() ) { $name = $aln->displayname( $seq->get_nse ); if ( $self->longid ) { $self->warn( "The length of the name is over 50 chars long [$name]") if length($name) > 50; $name = "'$name' "; } else { $name = substr( $name, 0, $idlength ) if length($name) > $idlength; $name = sprintf( "%-" . $idlength . "s", $name ); if ( $self->interleaved() ) { $name .= ' '; } elsif ( $self->id_linebreak ) { $name .= "\n"; } } #phylip needs dashes not dots my $seq = $seq->seq(); $seq =~ s/\./-/g; $hash{$name} = $seq; push( @arr, $name ); } if ( $self->interleaved() ) { my $numtags; if ( $tag_length <= $line_length ) { $numtags = floor( $line_length / $tag_length ); $line_length = $tag_length * $numtags; } else { $numtags = 1; } while ( $count < $length ) { # there is another block to go! foreach $name (@arr) { my $dispname = $name; $dispname = '' if $wrapped; $self->_print( sprintf( "%" . ( $idlength + 3 ) . "s", $dispname ) ); $tempcount = $count; $index = 0; $self->debug("residue count: $count\n") if ( $count % 100000 == 0 ); while (( $tempcount + $tag_length < $length ) && ( $index < $numtags ) ) { $self->_print( sprintf( "%s ", substr( $hash{$name}, $tempcount, $tag_length ) ) ); $tempcount += $tag_length; $index++; } # last if ( $index < $numtags ) { # space to print! $self->_print( sprintf( "%s", substr( $hash{$name}, $tempcount ) ) ); $tempcount += $tag_length; } $self->_print("\n"); } $self->_print("\n"); $count = $tempcount; $wrapped = 1; } } else { foreach $name (@arr) { my $dispname = $name; my $line = sprintf( "%s%s\n", $dispname, $hash{$name} ); if ( $self->wrap_sequential ) { $line =~ s/(.{1,$width})/$1\n/g; } $self->_print($line); } } } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 interleaved Title : interleaved Usage : my $interleaved = $obj->interleaved Function: Get/Set Interleaved status Returns : boolean Args : boolean =cut sub interleaved { my ( $self, $value ) = @_; if ( defined $value ) { if ($value) { $self->{'_interleaved'} = 1 } else { $self->{'_interleaved'} = 0 } } return 1 unless defined $self->{'_interleaved'}; return $self->{'_interleaved'}; } =head2 flag_SI Title : flag_SI Usage : my $flag = $obj->flag_SI Function: Get/Set if the Sequential/Interleaved flag has to be shown after the number of sequences and sequence length Example : Returns : boolean Args : boolean =cut sub flag_SI { my ( $self, $value ) = @_; my $previous = $self->{'_flag_SI'}; if ( defined $value ) { $self->{'_flag_SI'} = $value; } return $previous; } =head2 idlength Title : idlength Usage : my $idlength = $obj->idlength Function: Get/Set value of id length Returns : string Args : string =cut sub idlength { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_idlength'} = $value; } return $self->{'_idlength'}; } =head2 line_length Title : line_length Usage : $obj->line_length($newval) Function: Returns : value of line_length Args : newvalue (optional) =cut sub line_length { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_line_length'} = $value; } return $self->{'_line_length'} || $DEFAULTLINELEN; } =head2 tag_length Title : tag_length Usage : $obj->tag_length($newval) Function: Example : my $tag_length = $obj->tag_length Returns : value of the length for each space-separated tag in a line Args : newvalue (optional) - set to zero to have one tag per line =cut sub tag_length { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_tag_length'} = $value; } return $self->{'_tag_length'} || $DEFAULTTAGLEN; } =head2 id_linebreak Title : id_linebreak Usage : $obj->id_linebreak($newval) Function: Returns : value of id_linebreak Args : newvalue (optional) =cut sub id_linebreak { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_id_linebreak'} = $value; } return $self->{'_id_linebreak'} || 0; } =head2 wrap_sequential Title : wrap_sequential Usage : $obj->wrap_sequential($newval) Function: Returns : value of wrap_sequential Args : newvalue (optional) =cut sub wrap_sequential { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_wrap_sequential'} = $value; } return $self->{'_wrap_sequential'} || 0; } =head2 longid Title : longid Usage : $obj->longid($newval) Function: Returns : value of longid Args : newvalue (optional) =cut sub longid { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_longid'} = $value; } return $self->{'_longid'} || 0; } 1; BioPerl-1.007002/Bio/AlignIO/po.pm000444000766000024 2137313155576320 16510 0ustar00cjfieldsstaff000000000000# $Id: po.pm # # BioPerl module for Bio::AlignIO::po # based on the Bio::AlignIO::fasta module # by Peter Schattner (and others?) # # and the SimpleAlign.pm module of Ewan Birney # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::po - po MSA Sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L class. =head1 DESCRIPTION This object can transform L objects to and from 'po' format flat file databases. 'po' format is the native format of the POA alignment program (Lee C, Grasso C, Sharlow MF, 'Multiple sequence alignment using partial order graphs', Bioinformatics (2002), 18(3):452-64). =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Matthew Betts Email: matthew.betts@ii.uib.no =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::po; use strict; use Bio::SimpleAlign; use base qw(Bio::AlignIO); =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Returns : L object - returns undef on end of file or on error Args : NONE =cut sub next_aln { my $self = shift; my $aln; my $entry; my $name; my $seqs; my $seq; my $nodes; my $list; my $node; my @chars; my $s; my $a; $aln = Bio::SimpleAlign->new(); # get to the first 'VERSION' line while(defined($entry = $self->_readline)) { if($entry =~ /^VERSION=(\S+)/) { $aln->source($1); if(defined($entry = $self->_readline) and $entry =~ /^NAME=(\S+)/) { $aln->id($1); } last; } } # read in the sequence names and node data, up to the end of # the file or the next 'VERSION' line, whichever comes first $seqs = []; $nodes = []; while(defined($entry = $self->_readline)) { if($entry =~ /^VERSION/) { # start of a new alignment, so... $self->_pushback($entry); last; } elsif($entry =~ /^SOURCENAME=(\S+)/) { $name = $1; if($name =~ /(\S+)\/(\d+)-(\d+)/) { $seq = Bio::LocatableSeq->new( '-display_id' => $1, '-start' => $2, '-end' => $3, '-alphabet' => $self->alphabet, ); } else { $seq = Bio::LocatableSeq->new('-display_id'=> $name, '-alphabet' => $self->alphabet); } # store sequences in a list initially, because can't guarantee # that will get them back from SimpleAlign object in the order # they were read, and also can't add them to the SimpleAlign # object here because their sequences are currently unknown push @{$seqs}, { 'seq' => $seq, 'str' => '', }; } elsif($entry =~ /^SOURCEINFO=(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(.*)/) { $seq->desc($5); } elsif($entry =~ /^(\S):(\S+)/) { $node = { 'aa' => $1, 'L' => [], 'S' => [], 'A' => [], 'status' => 'unvisited', }; $list = $2; if($list =~ /^([L\d]*)([S\d]*)([A\d]*)/) { push(@{$node->{'L'}}, split(/L/, $1)); push(@{$node->{'S'}}, split(/S/, $2)); push(@{$node->{'A'}}, split(/A/, $3)); (@{$node->{'L'}} > 0) and shift @{$node->{'L'}}; (@{$node->{'S'}} > 0) and shift @{$node->{'S'}}; (@{$node->{'A'}} > 0) and shift @{$node->{'A'}}; } push @{$nodes}, $node; } } # process the nodes foreach $node (@{$nodes}) { ($node->{'status'} ne 'unvisited') and next; @chars = ($aln->gap_char) x @{$seqs}; # char for each seq defaults to a gap # set the character for each sequence represented by this node foreach $s (@{$node->{'S'}}) { $chars[$s] = $node->{'aa'}; } $node->{'status'} = 'visited'; # do the same for each node in the same align ring while(defined($a = $node->{'A'}->[0])) { $node = $nodes->[$a]; ($node->{'status'} ne 'unvisited') and last; foreach $s (@{$node->{'S'}}) { $chars[$s] = $node->{'aa'}; } $node->{'status'} = 'visited'; } # update the sequences foreach $seq (@{$seqs}) { $seq->{'str'} .= shift @chars; } } # set the sequences of the bioperl objects # and add them to the alignment foreach $seq (@{$seqs}) { $seq->{'seq'}->seq($seq->{'str'}); $aln->add_seq($seq->{'seq'}); } # has an alignment been read?... return $aln if $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in po format Returns : 1 for success and 0 for error Args : L object =cut sub write_aln { my $self = shift; my @alns = @_; my $aln; my $seqs; my $nodes; my $seq; my $node; my $col; my $ring; my $i; my $char; foreach $aln (@alns) { if(!$aln or !$aln->isa('Bio::Align::AlignI')) { $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln"); next; } # store the seqs on a list, because po format # refers to them by position on this list $seqs = []; foreach $seq ($aln->each_seq()) { push @{$seqs}, { 'seq' => $seq, 'n_nodes' => 0, 'first' => undef, 'previous' => undef, }; } # go through each column in the alignment and construct # the nodes for the equivalent poa alignment ring $nodes = []; for($col = 0; $col < $aln->length; $col++) { $ring = { 'nodes' => {}, 'first' => scalar @{$nodes}, 'last' => scalar @{$nodes}, }; for($i = 0; $i < @{$seqs}; $i++) { $seq = $seqs->[$i]; $char = $seq->{'seq'}->subseq($col + 1, $col + 1); ($char eq $aln->gap_char) and next; if(!defined($node = $ring->{'nodes'}->{$char})) { $node = { 'n' => scalar @{$nodes}, 'aa' => $char, 'L' => {}, 'S' => [], 'A' => [], }; # update the ring $ring->{'nodes'}->{$char} = $node; $ring->{'last'} = $node->{'n'}; # add the node to the node list push @{$nodes}, $node; } # add the sequence to the node push @{$node->{'S'}}, $i; # add the node to the sequence defined($seq->{'first'}) or ($seq->{'first'} = $node); $seq->{'n_nodes'}++; # add an edge from the previous node in the sequence to this one. # Then set the previous node to the current one, ready for the next # residue in this sequence defined($seq->{'previous'}) and ($node->{'L'}->{$seq->{'previous'}->{'n'}} = $seq->{'previous'}); $seq->{'previous'} = $node; } # set the 'next node in ring' field for each node in the ring if($ring->{'first'} < $ring->{'last'}) { for($i = $ring->{'first'}; $i < $ring->{'last'}; $i++) { push @{$nodes->[$i]->{'A'}}, $i + 1; } push @{$nodes->[$ring->{'last'}]->{'A'}}, $ring->{'first'}; } } # print header information $self->_print( 'VERSION=', ($aln->source and ($aln->source !~ /\A\s*\Z/)) ? $aln->source : 'bioperl', "\n", 'NAME=', $aln->id, "\n", 'TITLE=', ($seqs->[0]->{'seq'}->description or $aln->id), "\n", 'LENGTH=', scalar @{$nodes}, "\n", 'SOURCECOUNT=', scalar @{$seqs}, "\n", ); # print sequence information foreach $seq (@{$seqs}) { $self->_print( 'SOURCENAME=', $seq->{'seq'}->display_id, "\n", 'SOURCEINFO=', $seq->{'n_nodes'}, ' ', # number of nodes in the sequence $seq->{'first'}->{'n'}, ' ', # index of first node containing the sequence 0, ' ', # FIXME - sequence weight? -1, ' ', # FIXME - index of bundle containing sequence? ($seq->{'seq'}->description or 'untitled'), "\n", ); } # print node information foreach $node (@{$nodes}) { $self->_print($node->{'aa'}, ':'); (keys %{$node->{'L'}} > 0) and $self->_print('L', join('L', sort {$a <=> $b} keys %{$node->{'L'}})); (@{$node->{'S'}} > 0) and $self->_print('S', join('S', @{$node->{'S'}})); (@{$node->{'A'}} > 0) and $self->_print('A', join('A', @{$node->{'A'}})); $self->_print("\n"); } } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; BioPerl-1.007002/Bio/AlignIO/proda.pm000444000766000024 2003213155576320 17166 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::proda # # based on the Bio::SeqIO modules # by Ewan Birney # and Lincoln Stein # and the Bio::SimpleAlign module of Ewan Birney # # Copyright Albert Vilella # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::proda - proda sequence input/output stream This provides the basic capabilities to parse the output alignments from the ProDA multiple sequence alignment program (http://proda.stanford.edu) =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. =head1 DESCRIPTION This object can transform Bio::Align::AlignI objects to and from proda files. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Albert Vilella Email: avilella-at-gmail-dot-com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::proda; use vars qw($LINELENGTH); use strict; $LINELENGTH = 60; use base qw(Bio::AlignIO); =head2 new Title : new Usage : $alignio = Bio::AlignIO->new(-format => 'proda', -file => 'filename'); Function: returns a new Bio::AlignIO object to handle proda files Returns : Bio::AlignIO::proda object Args : -verbose => verbosity setting (-1, 0, 1, 2) -file => name of file to read in or to write, with ">" -fh => alternative to -file param - provide a filehandle to read from or write to -format => alignment format to process or produce -percentages => display a percentage of identity in each line of the alignment (proda only) -linelength=> alignment output line length (default 60) =cut sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); my ( $percentages, $ll ) = $self->_rearrange( [qw(PERCENTAGES LINELENGTH)], @args ); defined $percentages && $self->percentages($percentages); $self->line_length( $ll || $LINELENGTH ); } =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream Returns : Bio::Align::AlignI object Args : NONE See L for details =cut sub next_aln { my ($self) = @_; my $first_line; while ( $first_line = $self->_readline ) { last if $first_line !~ /^$/; } $self->_pushback($first_line); if ( defined( $first_line = $self->_readline ) && $first_line !~ /\(/ ) { $self->throw( "trying to parse a file which does not start with proda headers" ); } else { # use it inside the loop $self->_pushback($first_line); } my %alignments; my $aln = Bio::SimpleAlign->new( -source => 'proda', -verbose => $self->verbose ); my $order = 0; my %order; $self->{_lastline} = ''; my ($first_block, $seen_block, $seen_header) = (0,0,0); my @ids; my @ids_copy; while ( defined( $_ = $self->_readline ) ) { next if (/^\s+$/ && !$first_block); if (/^\s$/) { # line contains no description $seen_block = 1; next; } $first_block = 1; # break the loop if we come to the end of the current alignment # and push back the proda header if (/\(/ && $seen_header) { $self->_pushback($_); last; } if (/\(/ && !$seen_header) { @ids = split(' ', $_); $seen_header = 1; next; } my ( $seqname, $aln_line ) = ( '', '' ); if (/^\s*(\S+)\s*\/\s*(\d+)-(\d+)\s+(\S+)\s*$/ox) { # clustal 1.4 format ( $seqname, $aln_line ) = ( "$1:$2-$3", $4 ); # } elsif( /^\s*(\S+)\s+(\S+)\s*$/ox ) { without trailing numbers } elsif (/^\s*(\S+)\s+(\S+)\s*\d*\s*$/ox) { # with numbers ( $seqname, $aln_line ) = ( $1, $2 ); if ( $seqname =~ /^[\*\.\+\:]+$/ ) { $self->{_lastline} = $_; next; } } else { $self->{_lastline} = $_; next; } # we ended up the first block and now are on the second @ids_copy = @ids unless(defined($ids_copy[0])); #FIXME - hacky my $seqname_with_coords = shift(@ids_copy); if ($seqname_with_coords !~ /$seqname/) { { $self->throw("header and body of the alignment dont match"); } } $alignments{$seqname_with_coords} .= $aln_line; if ( !$seen_block ) { if (exists $order{$seqname_with_coords}) { $self->warn("Duplicate sequence : $seqname\n". "Can't guarantee alignment quality"); } else { $order{$seqname_with_coords} = $order++; } } } my ( $sname, $start, $end ); foreach my $name ( sort { $order{$a} <=> $order{$b} } keys %alignments ) { if ( $name =~ /(\S+):(\d+)-(\d+)/ ) { ( $sname, $start, $end ) = ( $1, $2, $3 ); } else { ( $sname, $start ) = ( $name, 1 ); my $str = $alignments{$name}; $str =~ s/[^A-Za-z]//g; $end = length($str); } my $seq = Bio::LocatableSeq->new( -seq => $alignments{$name}, -id => $sname, -start => $start, -end => $end, -alphabet => $self->alphabet, ); $aln->add_seq($seq); } return $aln if $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the proda-format object (.aln) into the stream Returns : 1 for success and 0 for error Args : Bio::Align::AlignI object =cut sub write_aln { my ($self,@aln) = @_; $self->throw_not_implemented(); } =head2 percentages Title : percentages Usage : $obj->percentages($newval) Function: Set the percentages flag - whether or not to show percentages in each output line Returns : value of percentages Args : newvalue (optional) =cut sub percentages { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_percentages'} = $value; } return $self->{'_percentages'}; } =head2 line_length Title : line_length Usage : $obj->line_length($newval) Function: Set the alignment output line length Returns : value of line_length Args : newvalue (optional) =cut sub line_length { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_line_length'} = $value; } return $self->{'_line_length'}; } =head2 no_header Title : no_header Usage : $obj->no_header($newval) Function: Set if the alignment input has a CLUSTAL header or not Returns : value of no_header Args : newvalue (optional) =cut sub no_header { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_no_header'} = $value; } return $self->{'_no_header'}; } 1; BioPerl-1.007002/Bio/AlignIO/prodom.pm000444000766000024 600213155576320 17342 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::prodom # based on the Bio::SeqIO::prodom module # by Ewan Birney # and Lincoln Stein # # and the SimpleAlign.pm module of Ewan Birney # # Copyright Peter Schattner # # You may distribute this module under the same terms as perl itself # _history # September 5, 2000 # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::prodom - prodom sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L class. =head1 DESCRIPTION This object can transform L objects to and from prodom flat file databases. =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Peter Schattner Email: schattner@alum.mit.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::prodom; use strict; use base qw(Bio::AlignIO); =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Returns : L object Args : NONE =cut sub next_aln { my $self = shift; my $entry; my ($acc, $fake_id, $start, $end, $seq, $add, %names); my $aln = Bio::SimpleAlign->new(-source => 'prodom'); while( $entry = $self->_readline) { if ($entry =~ /^AC\s+(\S+)\s*$/) { #ps 9/12/00 $aln->id( $1 ); } elsif ($entry =~ /^AL\s+(\S+)\|(\S+)\s+(\d+)\s+(\d+)\s+\S+\s+(\S+)\s*$/){ #ps 9/12/00 $acc=$1; $fake_id=$2; # Accessions have _species appended $start=$3; $end=$4; $seq=$5; $names{'fake_id'} = $fake_id; $add = Bio::LocatableSeq->new('-seq' => $seq, '-id' => $acc, '-start' => $start, '-end' => $end, '-alphabet' => $self->alphabet, ); $aln->add_seq($add); } elsif ($entry =~ /^CO/) { # the consensus line marks the end of the alignment part of the entry last; } } return $aln if $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in prodom format ###Not yet implemented!### Returns : 1 for success and 0 for error Args : L object =cut sub write_aln { my ($self,@aln) = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/AlignIO/psi.pm000444000766000024 766613155576320 16656 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::psi # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files =head1 SYNOPSIS This module will parse PSI-BLAST output of the format seqid XXXX =head1 DESCRIPTION This is a parser for psi-blast blocks. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::psi; use vars qw($BlockLen $IdLength); use strict; $BlockLen = 100; $IdLength = 13; # Object preamble - inherits from Bio::Root::Root use Bio::SimpleAlign; use Bio::LocatableSeq; use base qw(Bio::AlignIO); =head2 new Title : new Usage : my $obj = Bio::AlignIO::psi->new(); Function: Builds a new Bio::AlignIO::psi object Returns : Bio::AlignIO::psi Args : =cut =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream Returns : Bio::Align::AlignI object Args : NONE See L =cut sub next_aln { my ($self) = @_; my $aln; my %seqs; my @order; while( defined ($_ = $self->_readline ) ) { next if( /^\s+$/); if( !defined $aln ) { $aln = Bio::SimpleAlign->new(); } my ($id,$s) = split; push @order, $id if( ! defined $seqs{$id}); $seqs{$id} .= $s; } foreach my $id ( @order) { my $gaps = $seqs{$id} =~ tr/-/-/; my $seq = Bio::LocatableSeq->new(-seq => $seqs{$id}, -id => $id, -start => 1, -end => length($seqs{$id}) - $gaps, -alphabet => $self->alphabet, ); $aln->add_seq($seq); } return $aln if defined $aln && $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the NCBI psi-format object (.aln) into the stream Returns : 1 for success and 0 for error Args : Bio::Align::AlignI object L =cut sub write_aln { my ($self,$aln) = @_; unless( defined $aln && ref($aln) && $aln->isa('Bio::Align::AlignI') ) { $self->warn("Must provide a valid Bio::Align::AlignI to write_aln"); return 0; } my $ct = 0; my @seqs = $aln->each_seq; my $len = 1; my $alnlen = $aln->length; my $idlen = $IdLength; my @ids = map { substr($_->display_id,0,$idlen) } @seqs; while( $len < ($alnlen + 1) ) { my $start = $len; my $end = $len + $BlockLen; $end = $alnlen if ( $end > $alnlen ); my $c = 0; foreach my $seq ( @seqs ) { $self->_print(sprintf("%-".$idlen."s %s\n", $ids[$c++], $seq->subseq($start,$end))); } $self->_print("\n"); $len += $BlockLen+1; } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; BioPerl-1.007002/Bio/AlignIO/selex.pm000444000766000024 1060313155576320 17204 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::selex # based on the Bio::SeqIO::selex module # by Ewan Birney # and Lincoln Stein # # and the SimpleAlign.pm module of Ewan Birney # # Copyright Peter Schattner # # You may distribute this module under the same terms as perl itself # _history # September 5, 2000 # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::selex - selex sequence input/output stream =head1 SYNOPSIS # Do not use this module directly. Use it via the L class. use Bio::AlignIO; use strict; my $in = Bio::AlignIO->new(-format => 'selex', -file => 't/data/testaln.selex'); while( my $aln = $in->next_aln ) { } =head1 DESCRIPTION This object can transform L objects to and from selex flat file databases. =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Peter Schattner Email: schattner@alum.mit.edu =head1 CONTRIBUTORS Jason Stajich, jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::selex; use strict; use base qw(Bio::AlignIO); =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Tries to read *all* selex It reads all non whitespace characters in the alignment area. For selexs with weird gaps (eg ~~~) map them by using $al->map_chars('~','-') Returns : L object Args : NONE =cut sub next_aln { my $self = shift; my $entry; my ($start,$end,%align,$name,$seqname,%hash,@c2name, %accession,%desc); my $aln = Bio::SimpleAlign->new(-source => 'selex'); # in selex format, every non-blank line that does not start # with '#=' is an alignment segment; the '#=' lines are mark up lines. # Of particular interest are the '#=GF AC ' # lines, which give accession numbers for each segment while( $entry = $self->_readline) { if( $entry =~ /^\#=GS\s+(\S+)\s+AC\s+(\S+)/ ) { $accession{ $1 } = $2; next; } elsif( $entry =~ /^\#=GS\s+(\S+)\s+DE\s+(.+)\s*$/ ) { $desc{$1} .= $2; } elsif ( $entry =~ /^([^\#]\S+)\s+([A-Za-z\.\-\*]+)\s*/ ) { my ($name,$seq) = ($1,$2); if( ! defined $align{$name} ) { push @c2name, $name; } $align{$name} .= $seq; } } # ok... now we can make the sequences foreach my $name ( @c2name ) { if( $name =~ /(\S+)\/(\d+)-(\d+)/ ) { $seqname = $1; $start = $2; $end = $3; } else { $seqname=$name; $start = 1; $end = length($align{$name}); } my $seq = Bio::LocatableSeq->new ('-seq' => $align{$name}, '-display_id' => $seqname, '-start' => $start, '-end' => $end, '-description' => $desc{$name}, '-accession_number' => $accession{$name}, '-alphabet' => $self->alphabet, ); $aln->add_seq($seq); } return $aln if $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in selex format Returns : 1 for success and 0 for error Args : L object =cut sub write_aln { my ($self,@aln) = @_; my ($namestr,$seq,$add); my ($maxn); foreach my $aln (@aln) { $maxn = $aln->maxdisplayname_length(); foreach $seq ( $aln->each_seq() ) { $namestr = $aln->displayname($seq->get_nse()); $add = $maxn - length($namestr) + 2; $namestr .= " " x $add; $self->_print (sprintf("%s %s\n",$namestr,$seq->seq())) or return; } } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; BioPerl-1.007002/Bio/AlignIO/stockholm.pm000444000766000024 6423513155576320 20101 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::stockholm # # Based on the Bio::SeqIO::stockholm module # by Ewan Birney # and Lincoln Stein # # and the SimpleAlign.pm module of Ewan Birney # # Copyright Peter Schattner, Chris Fields # # You may distribute this module under the same terms as perl itself # _history # September 5, 2000 # November 6, 2006 - completely refactor read_aln(), add write_aln() # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::stockholm - stockholm sequence input/output stream =head1 SYNOPSIS # Do not use this module directly. Use it via the L class. use Bio::AlignIO; use strict; my $in = Bio::AlignIO->new(-format => 'stockholm', -file => 't/data/testaln.stockholm'); while( my $aln = $in->next_aln ) { } =head1 DESCRIPTION This object can transform L objects to and from stockholm flat file databases. This has been completely refactored from the original stockholm parser to handle annotation data and now includes a write_aln() method for (almost) complete stockholm format output. Stockholm alignment records normally contain additional sequence-based and alignment-based annotation GF Lines (alignment feature/annotation): #=GF Placed above the alignment GC Lines (Alignment consensus) #=GC Placed below the alignment GS Lines (Sequence annotations) #=GS GR Lines (Sequence meta data) #=GR Currently, sequence annotations (those designated with GS tags) are parsed only for accession numbers and descriptions. It is intended that full parsing will be added at some point in the near future along with a builder option for optionally parsing alignment annotation and meta data. The following methods/tags are currently used for storing and writing the alignment annotation data. Tag SimpleAlign Method ---------------------------------------------------------------------- AC accession ID id DE description ---------------------------------------------------------------------- Tag Bio::Annotation TagName Parameters Class ---------------------------------------------------------------------- AU SimpleValue record_authors value SE SimpleValue seed_source value GA SimpleValue gathering_threshold value NC SimpleValue noise_cutoff value TC SimpleValue trusted_cutoff value TP SimpleValue entry_type value SQ SimpleValue num_sequences value PI SimpleValue previous_ids value DC Comment database_comment comment CC Comment alignment_comment comment DR Target dblink database primary_id comment AM SimpleValue build_method value NE SimpleValue pfam_family_accession value NL SimpleValue sequence_start_stop value SS SimpleValue sec_structure_source value BM SimpleValue build_model value RN Reference reference * RC Reference reference comment RM Reference reference pubmed RT Reference reference title RA Reference reference authors RL Reference reference location ---------------------------------------------------------------------- * RN is generated based on the number of Bio::Annotation::Reference objects =head2 Custom annotation Some users may want to add custom annotation beyond those mapped above. Currently there are two methods to do so; however, the methods used for adding such annotation may change in the future, particularly if alignment Writer classes are introduced. In particular, do not rely on changing the global variables @WRITEORDER or %WRITEMAP as these may be made private at some point. 1) Use (and abuse) the 'custom' tag. The tagname for the object can differ from the tagname used to store the object in the AnnotationCollection. # AnnotationCollection from the SimpleAlign object my $coll = $aln->annotation; my $factory = Bio::Annotation::AnnotationFactory->new(-type => Bio::Annotation::SimpleValue'); my $rfann = $factory->create_object(-value => $str, -tagname => 'mytag'); $coll->add_Annotation('custom', $rfann); $rfann = $factory->create_object(-value => 'foo', -tagname => 'bar'); $coll->add_Annotation('custom', $rfann); OUTPUT: # STOCKHOLM 1.0 #=GF ID myID12345 #=GF mytag katnayygqelggvnhdyddlakfyfgaglealdffnnkeaaakiinwvaEDTTRGKIQDLV?? #=GF mytag TPtd~????LDPETQALLV???????????????????????NAIYFKGRWE?????????~?? #=GF mytag ??HEF?A?EMDTKPY??DFQH?TNen?????GRI??????V???KVAM??MF?????????N?? #=GF mytag ???DD?VFGYAEL????DE???????L??D??????A??TALELAY?????????????????? #=GF mytag ?????????????KG??????Sa???TSMLILLP???????????????D?????????????? #=GF mytag ???????????EGTr?????AGLGKLLQ??QL????????SREef??DLNK??L???AH????R #=GF mytag ????????????L????????????????????????????????????????R?????????R #=GF mytag ??QQ???????V???????AVRLPKFSFefefdlkeplknlgmhqafdpnsdvfklmdqavlvi #=GF mytag gdlqhayafkvd???????????????????????????????????????????????????? #=GF mytag ???????????????????????????????????????????????????????????????? #=GF mytag ???????????????????????????????????????????????????????????????? #=GF mytag ???????????????????????????????????????????????????????????????? #=GF mytag ?????????????INVDEAG?TEAAAATAAKFVPLSLppkt??????????????????PIEFV #=GF mytag ADRPFAFAIR??????E?PAT?G????SILFIGHVEDPTP?msv? #=GF bar foo ... 2) Modify the global @WRITEORDER and %WRITEMAP. # AnnotationCollection from the SimpleAlign object my $coll = $aln->annotation; # add to WRITEORDER my @order = @Bio::AlignIO::stockholm::WRITEORDER; push @order, 'my_stuff'; @Bio::AlignIO::stockholm::WRITEORDER = @order; # make sure new tag maps to something $Bio::AlignIO::stockholm::WRITEMAP{my_stuff} = 'Hobbit/SimpleValue'; my $rfann = $factory->create_object(-value => 'Frodo', -tagname => 'Hobbit'); $coll->add_Annotation('my_stuff', $rfann); $rfann = $factory->create_object(-value => 'Bilbo', -tagname => 'Hobbit'); $coll->add_Annotation('my_stuff', $rfann); OUTPUT: # STOCKHOLM 1.0 #=GF ID myID12345 #=GF Hobbit Frodo #=GF Hobbit Bilbo .... =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Chris Fields, Peter Schattner Email: cjfields-at-uiuc-dot-edu, schattner@alum.mit.edu =head1 CONTRIBUTORS Andreas Kahari, ak-at-ebi.ac.uk Jason Stajich, jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::stockholm; use strict; use Bio::Seq::Meta; use Bio::AlignIO::Handler::GenericAlignHandler; use Text::Wrap qw(wrap); use base qw(Bio::AlignIO); my $STKVERSION = 'STOCKHOLM 1.0'; # This maps the two-letter annotation key to a Annotation/parameter/tagname # combination. Some data is stored using get/set methods ('Methods') The rest # is mapped to Annotation objects using the parameter for the parsed data # and the tagname for, well, the Annotation tagname. A few are treated differently # based on the type of data stored (Reference data in particular). my %MAPPING = ( 'AC' => 'ACCESSION', 'ID' => 'ID', 'DE' => ['DESCRIPTION' => 'DESCRIPTION'], 'AU' => ['RECORD_AUTHORS' => 'RECORD_AUTHORS'], 'SE' => 'SEED_SOURCE', 'BM' => 'BUILD_COMMAND', 'GA' => 'GATHERING_THRESHOLD', 'NC' => 'NOISE_CUTOFF', 'TC' => 'TRUSTED_CUTOFF', 'TP' => 'ENTRY_TYPE', 'SQ' => 'NUM_SEQUENCES', 'PI' => 'PREVIOUS_IDS', 'DC' => ['DATABASE_COMMENT' => 'DATABASE_COMMENT'], 'DR' => 'DBLINK', 'RN' => ['REFERENCE' => 'REFERENCE'], 'RC' => ['REFERENCE' => 'COMMENT'], 'RM' => ['REFERENCE' => 'PUBMED'], 'RT' => ['REFERENCE' => 'TITLE'], 'RA' => ['REFERENCE' => 'AUTHORS'], 'RL' => ['REFERENCE' => 'JOURNAL'], 'CC' => ['ALIGNMENT_COMMENT' => 'ALIGNMENT_COMMENT'], #Pfam-specific 'AM' => 'BUILD_METHOD', 'NE' => 'PFAM_FAMILY_ACCESSION', 'NL' => 'SEQ_START_STOP', # Rfam-specific GF lines #'SS' => 'SEC_STRUCTURE_SOURCE', 'SEQUENCE' => 'SEQUENCE' ); # this is the order that annotations are written our @WRITEORDER = qw(accession id description previous_ids record_authors seed_source sec_structure_source gathering_threshold trusted_cutoff noise_cutoff entry_type build_command build_method pfam_family_accession seq_start_stop reference database_comment custom dblink alignment_comment num_sequences seq_annotation ); # This maps the tagname back to a tagname-annotation value combination. # Some data is stored using get/set methods ('Methods'), others # are mapped b/c of more complex annotation types. our %WRITEMAP = ( 'accession' => 'AC/Method', 'id' => 'ID/Method', 'description' => 'DE/Method', 'record_authors' => 'AU/SimpleValue', 'seed_source' => 'SE/SimpleValue', 'build_command' => 'BM/SimpleValue', 'gathering_threshold' => 'GA/SimpleValue', 'noise_cutoff' => 'NC/SimpleValue', 'trusted_cutoff' => 'TC/SimpleValue', 'entry_type' => 'TP/SimpleValue', 'num_sequences' => 'SQ/SimpleValue', 'previous_ids' => 'PI/SimpleValue', 'database_comment' => 'DC/SimpleValue', 'dblink' => 'DR/DBLink', 'reference' => 'RX/Reference', 'ref_number' => 'RN/number', 'ref_comment' => 'RC/comment', 'ref_pubmed' => 'RM/pubmed', 'ref_title' => 'RT/title', 'ref_authors' => 'RA/authors', 'ref_location' => 'RL/location', 'alignment_comment' => 'CC/Comment', 'seq_annotation' => 'DR/Collection', #Pfam-specific 'build_method' => 'AM/SimpleValue', 'pfam_family_accession' => 'NE/SimpleValue', 'seq_start_stop' => 'NL/SimpleValue', # Rfam-specific GF lines 'sec_structure_source' => 'SS/SimpleValue', # custom; this is used to carry over anything from the input alignment # not mapped to LocatableSeqs or SimpleAlign in a meaningful way 'custom' => 'XX/SimpleValue' ); # This maps the tagname back to a tagname-annotation value combination. # Some data is stored using get/set methods ('Methods'), others # are mapped b/c of more complex annotation types. =head2 new Title : new Usage : my $alignio = Bio::AlignIO->new(-format => 'stockholm' -file => '>file'); Function: Initialize a new L reader or writer Returns : L object Args : -line_length : length of the line for the alignment block -alphabet : symbol alphabet to set the sequences to. If not set, the parser will try to guess based on the alignment accession (if present), defaulting to 'dna'. -spaces : (optional, def = 1) boolean to add a space in between the "# STOCKHOLM 1.0" header and the annotation and the annotation and the alignment. =cut sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); my ($handler, $linelength, $spaces) = $self->_rearrange([qw(HANDLER LINE_LENGTH SPACES)],@args); $spaces = defined $spaces ? $spaces : 1; $self->spaces($spaces); # hash for functions for decoding keys. $handler ? $self->alignhandler($handler) : $self->alignhandler(Bio::AlignIO::Handler::GenericAlignHandler->new( -format => 'stockholm', -verbose => $self->verbose, )); $linelength && $self->line_length($linelength); } =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Returns : L object Args : NONE =cut sub next_aln { my $self = shift; my $handler = $self->alignhandler; # advance to alignment header while( defined(my $line = $self->_readline) ) { if ($line =~ m{^\#\s*STOCKHOLM\s+}xmso) { last; } } $self->{block_line} = 0; # go into main body of alignment my ($data_chunk, $isa_primary, $name, $alphabet); my $last_feat = ''; while( defined(my $line = $self->_readline) ) { # only blank lines are in between blocks, so reset block line my ($primary_tag, $secondary_tag, $data, $nse, $feat, $align, $concat); if ($line =~ m{^\s*$}xmso) { $self->{block_line} &&= 0; next; } # End of Record if (index($line, '//') == 0) { # fencepost $handler->data_handler($data_chunk); undef $data_chunk; $handler->data_handler({ALIGNMENT => 1, NAME => 'ALPHABET', DATA => $self->alphabet}) if $self->alphabet; last; } elsif ($line =~ m{^\#=([A-Z]{2})\s+([^\n]+?)\s*$}xmso) { ($primary_tag, $data) = ($1, $2); if ($primary_tag eq 'GS' || $primary_tag eq 'GR') { ($nse, $feat, $data) = split(/\s+/, $data, 3); } else { ($feat, $data) = split(/\s+/, $data, 2); } $align = ($primary_tag eq 'GF' || $primary_tag eq 'GR') ? 1 : 0; } elsif ($line =~ m{^(\S+)\s+([^\s]+)\s*}) { $self->{block_line}++; ($feat, $nse, $data) = ('SEQUENCE', $1, $2); } else { $self->debug("Missed line : $line\n"); } $primary_tag ||= ''; # when no #= line is present $align ||= 0; # array refs where the two values are equal indicate the start of a # primary chunk of data, otherwise it is to be folded into the last # data chunk under a secondary tag. These are also concatenated # to previous values if the if (exists($MAPPING{$feat}) && ref $MAPPING{$feat} eq 'ARRAY') { ($name, $secondary_tag, $isa_primary) = ( $MAPPING{$feat}->[0] eq $MAPPING{$feat}->[1] ) ? ($MAPPING{$feat}->[0], 'DATA', 1) : (@{ $MAPPING{$feat} }, 0) ; $concat = $last_feat eq $feat ? 1 : 0; } elsif (exists($MAPPING{$feat})) { ($name, $secondary_tag, $isa_primary) = ($MAPPING{$feat}, 'DATA', 1); # catch alphabet here if possible if ($align && $name eq 'ACCESSION' && !$self->alphabet) { if ($data =~ m{^(P|R)F}) { $self->alphabet($1 eq 'R' ? 'rna' : $1 eq 'P' ? 'protein' : undef ); } } } else { $name = ($primary_tag eq 'GR') ? 'NAMED_META' : ($primary_tag eq 'GC') ? 'CONSENSUS_META' : 'CUSTOM'; ($secondary_tag, $isa_primary) = ('DATA', 1); } # Since we can't determine whether data should be passed into the # Handler until the next round (due to concatenation and combining # data), we always check for the presence of the last chunk when the # occasion calls for it (i.e. when the current data string needs to go # into a new data chunk). If the data needs to be concatenated it is # flagged above and checked below (and passed by if the conditions # warrant it). # We run into a bit of a fencepost problem, (one chunk left over at # the end); that is taken care of above when the end of the record is # found. if ($isa_primary && defined $data_chunk && !$concat) { $handler->data_handler($data_chunk); undef $data_chunk; } $data_chunk->{NAME} = $name; # used for the handler $data_chunk->{ALIGNMENT} = $align; # flag that determines chunk destination $data_chunk->{$secondary_tag} .= (defined($data_chunk->{$secondary_tag})) ? ' '.$data : $data; $data_chunk->{NSE} = $nse if $nse; if ($name eq 'SEQUENCE' || $name eq 'NAMED_META' || $name eq 'CONSENSUS_META') { $data_chunk->{BLOCK_LINE} = $self->{block_line}; $data_chunk->{META_TAG} = $feat if ($name ne 'SEQUENCE'); } $last_feat = $feat; } my $aln = $handler->build_alignment; $handler->reset_parameters; return $aln; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in stockholm format Returns : 1 for success and 0 for error Args : L object =cut { my %LINK_CB = ( 'PDB' => sub {join('; ',($_[0]->database, $_[0]->primary_id.' '. ($_[0]->optional_id || ''), $_[0]->start, $_[0]->end)).';'}, 'SCOP' => sub {join('; ',($_[0]->database, $_[0]->primary_id || '', $_[0]->optional_id)).';'}, '_DEFAULT_' => sub {join('; ',($_[0]->database, $_[0]->primary_id)).';'}, ); sub write_aln { # enable array of SimpleAlign objects as well (see clustalw write_aln()) my ($self, @aln) = @_; for my $aln (@aln) { $self->throw('Need Bio::Align::AlignI object') if (!$aln || !($aln->isa('Bio::Align::AlignI'))); my $coll = $aln->annotation; my ($aln_ann, $seq_ann) = ('#=GF ', '#=GS '); $self->_print("# $STKVERSION\n") || return 0; $self->spaces && $self->_print("\n"); # annotations first #=GF XX .... for my $param (@WRITEORDER) { my @anns; # no point in going through this if there is no annotation! last if !$coll; # alignment annotations my $ct = 1; $self->throw("Bad parameter: $param") if !exists $WRITEMAP{$param}; # get the data, act on it based on the tag my ($tag, $key) = split q(/), $WRITEMAP{$param}; if ($key eq 'Method') { push @anns, $aln->$param; } else { @anns = $coll->get_Annotations($param); } my $rn = 1; ANNOTATIONS: for my $ann (@anns) { # using Text::Wrap::wrap() for word wrap my ($text, $alntag, $data); if ($tag eq 'RX') { REFS: for my $rkey (qw(ref_comment ref_number ref_pubmed ref_title ref_authors ref_location)) { my ($newtag, $method) = split q(/), $WRITEMAP{$rkey}; $alntag = sprintf('%-10s',$aln_ann.$newtag); if ($rkey eq 'ref_number') { $data = "[$rn]"; } else { $data = $ann->$method; } next REFS unless $data; $text = wrap($alntag, $alntag, $data); $self->_print("$text\n") or return 0; } $rn++; next ANNOTATIONS; } elsif ($tag eq 'XX') { # custom my $newtag = $ann->tagname; my $tmp = $aln_ann.$newtag; $alntag = sprintf('%-*s',length($tmp) + 1, $tmp); $data = $ann->display_text; } elsif ($tag eq 'SQ') { # use the actual number, not the stored Annotation data my $tmp = $aln_ann.$tag; $alntag = sprintf('%-*s',length($tmp) + 1, $tmp); $data = $aln->num_sequences; } elsif ($tag eq 'DR') { my $tmp = $aln_ann.$tag; $alntag = sprintf('%-*s',length($tmp) + 1, $tmp); my $db = uc $ann->database; my $cb = exists $LINK_CB{$db} ? $LINK_CB{$db} : $LINK_CB{_DEFAULT_}; $data = $ann->display_text($cb); } else { my $tmp = $aln_ann.$tag; $alntag = sprintf('%-*s',length($tmp) + 1, $tmp); $data = ref $ann ? $ann->display_text : $ann; } next unless $data; $text = wrap($alntag, $alntag, $data); $self->_print("$text\n") || return 0; } } #=GS AC xxxxxx my $tag = 'AC'; for my $seq ($aln->each_seq) { if (my $acc = $seq->accession_number) { my $text = sprintf("%-4s%-22s %-3s%s\n",$seq_ann, $aln->displayname($seq->get_nse), $tag, $acc); $self->_print($text) || return 0; } } #=GS DR xxxxxx $tag = 'DR'; for my $sf ($aln->get_SeqFeatures) { if (my @links = $sf->annotation->get_Annotations('dblink')) { for my $link (@links) { my $db = uc $link->database; my $cb = exists $LINK_CB{$db} ? $LINK_CB{$db} : $LINK_CB{_DEFAULT_}; my $text = sprintf("%-4s%-22s%-3s%s\n",$seq_ann, $aln->displayname($sf->entire_seq->get_nse), $tag, $link->display_text($cb)); $self->_print($text) || return 0; } } } $self->spaces && $self->_print("\n"); # now the sequences... my $blocklen = $self->line_length; my $maxlen = $aln->maxdisplayname_length() + 3; my $metalen = $aln->max_metaname_length() || 0; if ($blocklen) { my $blockstart = 1; my $alnlen = $aln->length; while ($blockstart < $alnlen) { my $subaln = $aln->slice($blockstart, $blockstart+$blocklen-1 ,1); $self->_print_seqs($subaln,$maxlen,$metalen); $blockstart += $blocklen; $self->_print("\n") unless $blockstart >= $alnlen; } } else { $self->_print_seqs($aln,$maxlen,$metalen); } $self->_print("//\n") || return 0; } $self->flush() if $self->_flush_on_write && defined $self->_fh; return 1; } } =head2 line_length Title : line_length Usage : $obj->line_length($newval) Function: Set the alignment output line length Returns : value of line_length Args : newvalue (optional) =cut sub line_length { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_line_length'} = $value; } return $self->{'_line_length'}; } =head2 spaces Title : spaces Usage : $obj->spaces(1) Function: Set the 'spaces' flag, which prints extra newlines between the header and the annotation and the annotation and the alignment Returns : sequence data type Args : newvalue (optional) =cut sub spaces { my $self = shift; return $self->{'_spaces'} = shift if @_; return $self->{'_spaces'}; }; =head2 alignhandler Title : alignhandler Usage : $stream->alignhandler($handler) Function: Get/Set the Bio::HandlerBaseI object Returns : Bio::HandlerBaseI Args : Bio::HandlerBaseI =cut sub alignhandler { my ($self, $handler) = @_; if ($handler) { $self->throw("Not a Bio::HandlerBaseI") unless ref($handler) && $handler->isa("Bio::HandlerBaseI"); $self->{'_alignhandler'} = $handler; } return $self->{'_alignhandler'}; } ############# PRIVATE INIT/HANDLER METHODS ############# sub _print_seqs { my ($self, $aln, $maxlen, $metalen) = @_; my ($seq_meta, $aln_meta) = ('#=GR','#=GC'); # modified (significantly) from AlignIO::pfam my ($namestr,$seq,$add); # pad extra for meta lines for $seq ( $aln->each_seq() ) { my ($s, $e, $str) = ($seq->start, $seq->end, $seq->strand); $namestr = $aln->displayname($seq->get_nse()); $self->_print(sprintf("%-*s%s\n",$maxlen+$metalen, $namestr, $seq->seq())) || return 0; if ($seq->isa('Bio::Seq::MetaI')) { for my $mname ($seq->meta_names) { $self->_print(sprintf("%-*s%s\n",$maxlen+$metalen, $seq_meta.' '.$namestr.' '.$mname, $seq->named_meta($mname))) || return 0; } } } # alignment consensus my $ameta = $aln->consensus_meta; if ($ameta) { for my $mname ($ameta->meta_names) { $self->_print(sprintf("%-*s%s\n",$maxlen+$metalen, $aln_meta.' '.$mname, $ameta->named_meta($mname))) || return 0; } } } 1; BioPerl-1.007002/Bio/AlignIO/xmfa.pm000444000766000024 1464113155576320 17025 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::AlignIO::xmfa # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::xmfa - XMFA MSA Sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L class. =head1 DESCRIPTION This object can transform L objects from XMFA flat file databases. For more information, see: http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-output-file-formats.html This module is based on the AlignIO::fasta parser written by Peter Schattner =head1 TODO Finish write_aln(), clean up code, allow LargeLocatableSeq (e.g. for very large sequences from Mauve). =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Chris Fields =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::xmfa; use strict; use base qw(Bio::AlignIO); our $WIDTH = 60; =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln Function: returns the next alignment in the stream. Returns : Bio::Align::AlignI object - returns 0 on end of file or on error Args : -width => optional argument to specify the width sequence will be written (60 chars by default) See L =cut sub next_aln { my $self = shift; my ($width) = $self->_rearrange([qw(WIDTH)],@_); $self->width($width || $WIDTH); my ($name, $tempname, $seqchar); my $aln = Bio::SimpleAlign->new(); my $seqs = 0; # alignments while (defined (my $entry = $self->_readline) ) { chomp $entry; if ( index($entry, '=') == 0 ) { if (defined $name && $seqchar) { my $seq = $self->_process_seq($name, $seqchar); $aln->add_seq($seq); } if ($aln && $entry =~ m{score\s*=\s*(\d+)}) { $aln->score($1); } $seqchar = ''; undef $name; last; } elsif ( $entry =~ m{^>.+$}xms) { if ( defined $name ) { my $seq = $self->_process_seq($name, $seqchar); $aln->add_seq($seq); } $seqchar = ''; $name = $entry; } else { $seqchar .= $entry; } } # this catches last sequence if '=' is not present (Mauve) if ( defined $name ) { my $seq = $self->_process_seq($name, $seqchar); $aln->add_seq($seq); } $aln->num_sequences ? return $aln : return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in xmfa format Returns : 1 for success and 0 for error Args : L object See L =cut sub write_aln { my ($self,@aln) = @_; my $width = $self->width; my ($seq,$desc,$rseq,$name,$count,$length,$seqsub,$start,$end,$strand,$id); foreach my $aln (@aln) { if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) { $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln"); next; } #if( $self->force_displayname_flat ) { # $aln->set_displayname_flat(1); #} my $seqct = 1; foreach $rseq ( $aln->each_seq() ) { ($start, $end, $strand, $id) = ($rseq->start, $rseq->end, $rseq->strand || 0, $rseq->display_id); $strand = ($strand == 1) ? '+' : ($strand == -1) ? '-' : ''; $name = sprintf("%d:%d-%d %s %s",$seqct,$start,$end,$strand,$id); $seq = $rseq->seq(); $desc = $rseq->description || ''; $self->_print (">$name $desc\n") or return ; $count = 0; $length = length($seq); if(defined $seq && $length > 0) { $seq =~ s/(.{1,$width})/$1\n/g; } else { $seq = "\n"; } $self->_print($seq) || return 0; $seqct++; } my $alndesc = ''; $alndesc = "score = ".$aln->score if ($aln->score); $self->_print("= $alndesc\n") || return 0; } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 _get_len Title : _get_len Usage : Function: determine number of alphabetic chars Returns : integer Args : sequence string =cut sub _get_len { my ($self,$seq) = @_; $seq =~ s/[^A-Z]//gi; return CORE::length($seq); } =head2 width Title : width Usage : $obj->width($newwidth) $width = $obj->width; Function: Get/set width of alignment Returns : integer value of width Args : on set, new value (a scalar or undef, optional) =cut sub width{ my $self = shift; return $self->{'_width'} = shift if @_; return $self->{'_width'} || $WIDTH; } ####### PRIVATE ####### sub _process_seq { my ($self, $entry, $seq) = @_; my ($start, $end, $strand, $seqname, $desc, $all); # put away last name and sequence if ( $entry =~ m{^>\s*\d+:(\d+)-(\d+)\s+([+-]{1})(?:\s+(\S+)\s*(\S\.*)?)?} ) { ($start, $end, $seqname, $desc) = ($1, $2, $4, $5); $strand = ($3 eq '+') ? 1 : -1; } elsif ( $entry !~ /^>\s*\d+:/ ) { $self->throw("First field after '>' must be a number:\n$entry"); } else { $self->throw("Line does not comform to XMFA format:\n$entry"); } my $seqobj = Bio::LocatableSeq->new( -nowarnonempty => 1, -strand => $strand, -seq => $seq, -display_id => $seqname, -description => $desc || $all, -start => $start, -end => $end, -alphabet => $self->alphabet, ); $self->debug("Reading $seqname\n"); return $seqobj; } 1; BioPerl-1.007002/Bio/AlignIO/Handler000755000766000024 013155576320 16726 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/AlignIO/Handler/GenericAlignHandler.pm000444000766000024 5720713155576320 23301 0ustar00cjfieldsstaff000000000000# Let the code begin... package Bio::AlignIO::Handler::GenericAlignHandler; use strict; use warnings; use Bio::Annotation::Collection; use Bio::Annotation::Comment; use Bio::Annotation::SimpleValue; use Bio::Annotation::Target; use Bio::Annotation::DBLink; use Bio::Annotation::Reference; use Bio::SimpleAlign; use Data::Dumper; use base qw(Bio::Root::Root Bio::HandlerBaseI); # only stockholm is defined for now... my %HANDLERS = ( # stockholm has sequence and alignment specific annotation; this 'stockholm' => { 'CONSENSUS_META' => \&_generic_consensus_meta, 'SEQUENCE' => \&_generic_metaseq, 'NAMED_META' => \&_generic_metaseq, 'ACCESSION' => \&_generic_store, 'ALPHABET' => \&_generic_store, 'ID' => \&_generic_store, 'DESCRIPTION' => \&_generic_store, 'REFERENCE' => \&_generic_reference, 'DBLINK' => \&_stockholm_target, 'DATABASE_COMMENT' => \&_generic_comment, 'ALIGNMENT_COMMENT' => \&_generic_comment, '_DEFAULT_' => \&_generic_simplevalue }, ); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($format, $verbose) = $self->_rearrange([qw(FORMAT VERBOSE)], @args); $self->throw("Must define alignment record format") if !$format; $verbose && $self->verbose($verbose); $self->format($format); $self->handler_methods(); # if we intend at a later point we can add a Builder #$builder && $self->alignbuilder($builder); return $self; } sub handler_methods { my $self = shift; if (!($self->{'handlers'})) { $self->throw("No handlers defined for alignment format ",$self->format) unless exists $HANDLERS{$self->format}; $self->{'handlers'} = $HANDLERS{$self->format}; } return ($self->{'handlers'}); } sub data_handler { my ($self, $data) = @_; my $nm = $data->{NAME} || $self->throw("No name tag defined!"); # this should handle data on the fly w/o caching; any caching should be # done in the driver! my $method = (exists $self->{'handlers'}->{$nm}) ? ($self->{'handlers'}->{$nm}) : (exists $self->{'handlers'}->{'_DEFAULT_'}) ? ($self->{'handlers'}->{'_DEFAULT_'}) : undef; if (!$method) { $self->debug("No handler defined for $nm\n"); return; }; $self->$method($data); } sub reset_parameters { my $self = shift; $self->{'_params'} = undef; $self->{'_nse_cache'} = undef; $self->{'_features'} = undef; } sub format { my $self = shift; if (@_) { my $format = lc shift; $self->throw("Format $format not supported") unless exists $HANDLERS{$format}; $self->{'_alignformat'} = $format; }; return $self->{'_alignformat'}; } sub get_params { my ($self, @ids) = @_; my $data; if (scalar(@ids)) { for my $id (@ids) { if (!index($id, '-')==0) { $id = '-'.$id ; } $data->{$id} = $self->{'_params'}->{$id} if (exists $self->{'_params'}->{$id}); } $data ||= {}; } else { $data = $self->{'_params'}; } return $data; } sub set_params { shift->throw('Not implemented yet!'); } sub build_alignment { my $self = shift; my %init; $self->process_seqs; my $param = $self->get_params; if (defined $param->{-seqs}) { return Bio::SimpleAlign->new(%$param, -source => $self->format); } return; } sub annotation_collection { my ($self, $coll) = @_; if ($coll) { $self->throw("Must have Bio::AnnotationCollectionI ". "when explicitly setting annotation_collection()") unless (ref($coll) && $coll->isa('Bio::AnnotationCollectionI')); $self->{'_params'}->{'-annotation'} = $coll; } elsif (!exists($self->{'_params'}->{'-annotation'})) { $self->{'_params'}->{'-annotation'} = Bio::Annotation::Collection->new() } return $self->{'_params'}->{'-annotation'}; } sub seq_annotation_collection { my ($self, $coll) = @_; if ($coll) { $self->throw("Must have Bio::AnnotationCollectionI ". "when explicitly setting seq_annotation_collection()") unless (ref($coll) && $coll->isa('Bio::AnnotationCollectionI')); $self->{'_params'}->{'-seq_annotation'} = $coll; } elsif (!exists($self->{'_params'}->{'-seq_annotation'})) { $self->{'_params'}->{'-seq_annotation'} = Bio::Annotation::Collection->new() } return $self->{'_params'}->{'-seq_annotation'}; } sub process_seqs { my $self = shift; my $data = $self->get_params(qw(-seqs -seq_class -consensus_meta)); my $class = $data->{-seq_class} || 'Bio::LocatableSeq'; # cache classes loaded already if (!exists($self->{'_loaded_modules'}->{$class})) { $self->_load_module($class); $self->{'_loaded_modules'}->{$class}++; } # process any meta sequence data if ( $data->{-consensus_meta} && !UNIVERSAL::isa($data->{-consensus_meta},'Bio::Seq::Meta')) { my $ref = $data->{-consensus_meta}; if (!exists($self->{'_loaded_modules'}->{'Bio::Seq::Meta'})) { $self->_load_module('Bio::Seq::Meta'); $self->{'_loaded_modules'}->{'Bio::Seq::Meta'}++; } my $ms = Bio::Seq::Meta->new(); for my $tag (sort keys %{$ref}) { $ms->named_meta($tag, $ref->{$tag}); } $self->{'_params'}->{'-consensus_meta'} = $ms; } # this should always be an array ref! for my $seq (@{$data->{-seqs}}) { next if (UNIVERSAL::isa($seq,'Bio::LocatableI')); # process anything else $self->_from_nse($seq) if $seq->{NSE}; if (UNIVERSAL::isa($seq,'HASH')) { my %param; for my $p (keys %$seq) { $param{'-'.lc $p} = $seq->{$p} if exists $seq->{$p}; } my $ls = $class->new(%param); # a little switcheroo to attach the sequence # (though using it to get seq() doesn't work correctly yet!) if (defined $seq->{NSE} && exists $self->{'_features'} && exists $self->{'_features'}->{ $seq->{NSE} }) { for my $feat (@{ $self->{'_features'}->{ $seq->{NSE} } }) { push @{ $self->{'_params'}->{'-features'} }, $feat; $feat->attach_seq($ls); } } $seq = $ls; } } } ####################### SEQUENCE HANDLERS ####################### # any sequence data for a Bio::Seq::Meta sub _generic_metaseq { my ($self, $data) = @_; return unless $data; $self->throw("No alignment position passed") if !exists($data->{BLOCK_LINE}); $self->throw("Alignment position must be an index greater than 0") if $data->{BLOCK_LINE} < 1; $self->{'_params'}->{'-seq_class'} = 'Bio::Seq::Meta'; my $index = $data->{BLOCK_LINE} - 1; if (my $nse = $self->{'_params'}->{'-seqs'}->[$index]->{NSE}) { $self->throw("NSE in passed data doesn't match stored data in same position: $nse") unless $nse eq $data->{NSE}; } else { $self->{'_params'}->{'-seqs'}->[$index]->{NSE} = $data->{NSE}; } if ($data->{NAME} eq 'SEQUENCE') { $self->{'_params'}->{'-seqs'}->[$index]->{SEQ} .= $data->{DATA}; } elsif ($data->{NAME} eq 'NAMED_META') { $self->{'_params'}->{'-seqs'}->[$index]->{NAMED_META}->{$data->{META_TAG}} .= $data->{DATA}; } } sub _generic_consensus_meta { my ($self, $data) = @_; return unless $data; if ($data->{NAME} eq 'CONSENSUS_META') { $self->{'_params'}->{'-consensus_meta'}->{$data->{META_TAG}} .= $data->{DATA}; } } # any sequence data for a Bio::LocatableSeq sub _generic_locatableseq { my ($self, $data) = @_; return unless $data; $self->throw("No alignment position passed") if !exists($data->{BLOCK_LINE}); $self->throw("Alignment position must be an index greater than 0") if $data->{BLOCK_LINE} < 1; my $index = $data->{BLOCK_LINE} - 1; if (my $nse = $self->{'_params'}->{'-seqs'}->[$index]->{NSE}) { $self->throw("NSE in passed data doesn't match stored data in same position: $nse") if $nse ne $data->{NSE}; } else { $self->{'_params'}->{'-seqs'}->[$index]->{NSE} = $data->{NSE}; } if ($data->{NAME} eq 'SEQUENCE') { $self->{'_params'}->{'-seqs'}->[$index]->{SEQ} .= $data->{DATA}; } } ####################### RAW DATA HANDLERS ####################### # store by data name (ACCESSION, ID, etc), which can be mapped to the # appropriate alignment or sequence parameter sub _generic_store { my ($self, $data) = @_; return unless $data; if ($data->{ALIGNMENT}) { $self->{'_params'}->{'-'.lc $data->{NAME}} = $data->{DATA}; } else { $self->{'_params'}->{'-seq_'.lc $data->{NAME}}->{$data->{NSE}} = $data->{DATA} } } sub _generic_reference { my ($self, $data) = @_; my $ref = Bio::Annotation::Reference->new(-title => $data->{TITLE}, -authors => $data->{AUTHORS}, -pubmed => $data->{PUBMED}, -location => $data->{JOURNAL}, -tagname => lc $data->{NAME}); $self->annotation_collection->add_Annotation($ref); } sub _generic_simplevalue { my ($self, $data) = @_; my $sv = Bio::Annotation::SimpleValue->new(-value => $data->{DATA}, -tagname => lc $data->{NAME}); $self->annotation_collection->add_Annotation($sv); } sub _generic_comment { my ($self, $data) = @_; my $comment = Bio::Annotation::Comment->new(-type => lc $data->{NAME}, -text => $data->{DATA}, -tagname => lc $data->{NAME}); $self->annotation_collection->add_Annotation($comment); } # Some DBLinks in Stockholm format are unique, so a unique handler for them sub _stockholm_target { my ($self, $data) = @_; # process database info $self->_from_stk_dblink($data); my $comment; # Bio::Annotation::Target is now a DBLink, but has additional (RangeI) # capabilities (for PDB data) my $dblink = Bio::Annotation::Target->new( -database => $data->{DBLINK_DB}, -primary_id => $data->{DBLINK_ACC}, -optional_id => $data->{DBLINK_OPT}, -start => $data->{DBLINK_START}, -end => $data->{DBLINK_END}, -strand => $data->{DBLINK_STRAND}, -comment => $comment, -tagname => 'dblink', ); if ($data->{ALIGNMENT}) { # Alignment-specific DBLinks $self->annotation_collection->add_Annotation($dblink); } else { # Sequence-specific DBLinks # These should come with identifying information of some sort # (ID/START/END/STRAND). Make into a SeqFeature (SimpleAlign is # FeatureHolderI) spanning the length acc. to the NSE. Add the DBLink as # Annotation specific to that SeqFeature, store in an internal hash by # NSE so we can tie the LocatableSeq to the proper Features $self->_from_nse($data) if $data->{NSE}; $self->throw("Must supply an sequence DISPLAY_ID or NSE for sequence-related DBLinks") unless $data->{ACCESSION_NUMBER} || $data->{DISPLAY_ID}; my $sf = Bio::SeqFeature::Generic->new(-seq_id => $data->{DISPLAY_ID}, -accession_number => $data->{ACCESSION_NUMBER}, -start => $data->{START}, -end => $data->{END}, -strand => $data->{STRAND} ); $sf->annotation->add_Annotation($dblink); # index by NSE push @{ $self->{'_features'}->{ $data->{NSE} } }, $sf; #$self->seq_annotation_collection->add_Annotation($dblink); } } ####################### HELPER METHODS ####################### # returns ACCESSION VERSION START END STRAND ALPHABET # cached for multiple lookups, should reset in between uses sub _from_nse { my ($self, $data) = @_; return unless my $nse = $data->{NSE}; $data->{ALPHABET} = $self->get_params('-alphabet')->{'-alphabet'} || 'protein'; # grab any accessions if present, switch out with ACCESSION from NSE # (move that to primary_id) my $new_acc; if (exists $self->{'_params'}->{'-seq_accession'}) { $new_acc = $self->{'_params'}->{'-seq_accession'}->{$data->{NSE}}; } if ($nse =~ m{(\S+?)(?:\.(\d+))?/(\d+)-(\d+)}xmso) { my $strand = $data->{ALPHABET} eq 'dna' || $data->{ALPHABET} eq 'rna' ? 1 : undef; my ($start, $end) = ($3, $4); if ($start > $end) { ($start, $end, $strand) = ($end, $start, -1); } $data->{ACCESSION_NUMBER} = $new_acc || $1; $data->{DISPLAY_ID} = $1; $data->{VERSION} = $2; $data->{START} = $start; $data->{END} = $end; $data->{STRAND} = $strand; } else { # we can parse for version here if needed $data->{DISPLAY_ID} = $data->{NSE}; } } # this will probably be split up into subhandlers based on Record/DB sub _from_stk_dblink { my ($self, $data) = @_; return unless my $raw = $data->{DATA}; my @rawdata = split(m{\s*;\s*}, $raw); my %dblink_data; if ($rawdata[0] eq 'PDB') { # fix for older Stockholm PDB range format if (scalar(@rawdata) == 3 && $rawdata[2] =~ m{-}) { @rawdata[2,3] = split('-',$rawdata[2],2); } $self->throw("Not standard PDB form: ".$data->{DATA}) if scalar(@rawdata) != 4; my ($main, $chain) = split(m{\s+}, $rawdata[1]); %dblink_data = ( DBLINK_DB => $rawdata[0], DBLINK_ACC => $main, DBLINK_OPT => $chain || '', DBLINK_START => $rawdata[2], DBLINK_END => $rawdata[3] ); } elsif ($rawdata[0] eq 'SCOP') { $self->throw("Not standard SCOP form: ".$data->{DATA}) if scalar(@rawdata) != 3; %dblink_data = ( DBLINK_DB => $rawdata[0], DBLINK_ACC => $rawdata[1], DBLINK_OPT => $rawdata[2], ); } else { $self->warn("Some data missed: ".$data->{DATA}) if scalar(@rawdata) > 2; %dblink_data = ( DBLINK_DB => $rawdata[0], DBLINK_ACC => $rawdata[1], ); } while (my ($k, $v) = each %dblink_data) { $data->{$k} = $v if $v; } } 1; __END__ # $Id: GenericAlignHandler.pm 14816 2008-08-21 16:00:12Z cjfields $ # # BioPerl module for Bio::AlignIO::Handler::GenericAlignHandler # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code # # Documentation after the __END__ marker =head1 NAME Bio::AlignIO::Handler::GenericAlignHandler - Bio::HandlerI-based generic data handler class for alignment-based data =head1 SYNOPSIS # MyHandler is a GenericAlignHandler object. # inside a parser (driver) constructor.... $self->alignhandler($handler || MyHandler->new(-format => 'stockholm')); # in next_aln() in driver... $hobj = $self->alignhandler(); # roll data up into hashref chunks, pass off into Handler for processing... $hobj->data_handler($data); # or retrieve Handler methods and pass data directly to Handler methods... my $hmeth = $hobj->handler_methods; if ($hmeth->{ $data->{NAME} }) { my $mth = $hmeth->{ $data->{NAME} }; $hobj->$mth($data); } =head1 DESCRIPTION This is an experimental implementation of a alignment-based HandlerBaseI parser and may change over time. It is possible that the way handler methods are set up will change over development to allow more flexibility. Standard Developer caveats: Here thar be dragoons... Consider yourself warned! =head2 NOTES As in the SeqIO Handler object (still in development), data is passed in as chunks. The Annotation and SeqFeatures are essentially the same as the SeqIO parser; the significant difference is that data hash being passed could pertain to either the alignment or to a specific sequence, so an extra tag may be needed to disambiguate between the two in some cases. Here I use the ALIGNMENT tag as a boolean flag: it must be present and set to 0 for the data to be tagged for Bio::LocatableSeq or similar (in all other cases it is assumed to be for the alignment). In some cases this will not matter (the actual sequence data, for instance) but it is highly recommmended adding this tag in to prevent possible ambiguities. This is the current Annotation data chunk (via Data::Dumper): $VAR1 = { 'NAME' => 'REFERENCE', 'DATA' => '1 (bases 1 to 10001)' 'AUTHORS' => 'International Human Genome Sequencing Consortium.' 'TITLE' => 'The DNA sequence of Homo sapiens' 'JOURNAL' => 'Unpublished (2003)' 'ALIGNMENT' => 1, }; In the case of LocatableSeqs, one can pass them in as follows for simplicity (note the block line): $VAR1 = { 'NAME' => 'SEQUENCE', 'BLOCK_LINE' => 0, 'NSE' => 'Q7WNI7_BORBR/113-292', 'ALPHABET' => 'protein', 'DATA' => 'VALILGVYRRL...CYVNREM..RAG....QW', 'ALIGNMENT' => 0 }; This can be done as the parser parses each block instead of parsing all the blocks and then passing them in one at a time; the handler will store the sequence data by the block line in an internal hash, concatenating them along the way. This behaviour is b/c the alignment building step requires that the sequence be checked for start/end/strand, possible meta sequence, optional accession, etc. Similarly, a Meta sequence line can be passed in as follows: $VAR1 = { 'NAME' => 'NAMED_META', 'BLOCK_LINE' => 0, 'NSE' => 'Q7WNI7_BORBR/113-292', 'META_KEY' => 'pAS', 'DATA' => '................................', 'ALIGNMENT' => 0 }; The meta sequence will be checked against the NSE for the block position and stored based on the meta tag. A meta sequence does not have to correspond to a real sequence. At this time, unique meta sequence tags must be used for each sequence or they will be overwritten (this may change). An alignment consensus string: $VAR1 = { 'NAME' => 'CONSENSUS', 'DATA' => 'VALILGVYRRL...CYVNREM..RAG....QW', 'ALIGNMENT' => 1 }; A consensus meta sequence: $VAR1 = { 'NAME' => 'CONSENSUS_META', 'META_KEY' => 'pAS', 'DATA' => '................................', 'ALIGNMENT' => 1 }; =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Fields Email cjfields at bioperl dot org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut =head2 new Title : new Usage : Function: Returns : Args : -format Sequence format to be mapped for handler methods -builder Bio::Seq::SeqBuilder object (normally defined in SequenceStreamI object implementation constructor) Throws : On undefined '-format' sequence format parameter Note : Still under heavy development =cut =head1 L implementing methods =head2 handler_methods Title : handler_methods Usage : $handler->handler_methods('GenBank') %handlers = $handler->handler_methods(); Function: Retrieve the handler methods used for the current format() in the handler. This assumes the handler methods are already described in the HandlerI-implementing class. Returns : a hash reference with the data type handled and the code ref associated with it. Args : [optional] String representing the sequence format. If set here this will also set sequence_format() Throws : On unimplemented sequence format in %HANDLERS =cut =head2 data_handler Title : data_handler Usage : $handler->data_handler($data) Function: Centralized method which accepts all data chunks, then distributes to the appropriate methods for processing based on the chunk name from within the HandlerBaseI object. One can also use Returns : None Args : an hash ref containing a data chunk. =cut =head2 reset_parameters Title : reset_parameters Usage : $handler->reset_parameters() Function: Resets the internal cache of data (normally object parameters for a builder or factory) Returns : None Args : None =cut =head2 format Title : format Usage : $handler->format('GenBank') Function: Get/Set the format for the report/record being parsed. This can be used to set handlers in classes which are capable of processing similar data chunks from multiple driver modules. Returns : String with the sequence format Args : [optional] String with the sequence format Note : The format may be used to set the handlers (as in the current GenericRichSeqHandler implementation) =cut =head2 get_params Title : get_params Usage : $handler->get_params('-species') Function: Convenience method used to retrieve the specified parameters from the internal parameter cache Returns : Hash ref containing parameters requested and data as key-value pairs. Note that some parameter values may be objects, arrays, etc. Args : List (array) representing the parameters requested =cut =head2 set_params Title : set_params Usage : $handler->set_param({'-seqs' => $seqs}) Function: Convenience method used to set specific parameters Returns : None Args : Hash ref containing the data to be passed as key-value pairs =cut =head1 Methods unique to this implementation =head2 build_alignment Title : build_alignment Usage : Function: Returns : a Bio::SimpleAlign Args : Throws : Note : This may be replaced by a Builder object at some point =cut =head2 annotation_collection Title : annotation_collection Usage : Function: Returns : Args : Throws : Note : =cut =head2 seq_annotation_collection Title : seq_annotation_collection Usage : Function: Returns : Args : Throws : Note : =cut =head2 process_seqs Title : process_seqs Usage : $handler->process_seqs; Function: checks internal sequences to ensure they are converted over to the proper Bio::AlignI-compatible sequence class Returns : 1 if successful Args : none =cut BioPerl-1.007002/Bio/Annotation000755000766000024 013155576320 16201 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Annotation/AnnotationFactory.pm000444000766000024 1624713155576320 22370 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Annotation::AnnotationFactory # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Annotation::AnnotationFactory - Instantiates a new Bio::AnnotationI (or derived class) through a factory =head1 SYNOPSIS use Bio::Annotation::AnnotationFactory; # my $factory = Bio::Annotation::AnnotationFactory->new( -type => 'Bio::Annotation::SimpleValue'); my $ann = $factory->create_object(-value => 'peroxisome', -tagname => 'cellular component'); =head1 DESCRIPTION This object will build L objects generically. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 CONTRIBUTORS This is mostly copy-and-paste with subsequent adaptation from Bio::Seq::SeqFactory by Jason Stajich. Most credits should in fact go to him. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Annotation::AnnotationFactory; use strict; use base qw(Bio::Root::Root Bio::Factory::ObjectFactoryI); =head2 new Title : new Usage : my $obj = Bio::Annotation::AnnotationFactory->new(); Function: Builds a new Bio::Annotation::AnnotationFactory object Returns : Bio::Annotation::AnnotationFactory Args : -type => string, name of a L derived class. If type is not set the module guesses it based on arguments passed to method L. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($type) = $self->_rearrange([qw(TYPE)], @args); $self->{'_loaded_types'} = {}; $self->type($type) if $type; return $self; } =head2 create_object Title : create_object Usage : my $seq = $factory->create_object(); Function: Instantiates new Bio::AnnotationI (or one of its child classes) This object allows us to genericize the instantiation of cluster objects. Returns : L compliant object The return type is configurable using new(-type =>"..."). Args : initialization parameters specific to the type of annotation object we want. =cut sub create_object { my ($self,@args) = @_; my $type = $self->type; if(! $type) { # we need to guess this $type = $self->_guess_type(@args); if(! $type) { $self->throw("No annotation type set and unable to guess."); } # load dynamically if it hasn't been loaded yet if(! $self->{'_loaded_types'}->{$type}) { eval { $self->_load_module($type); $self->{'_loaded_types'}->{$type} = 1; }; if($@) { $self->throw("Bio::AnnotationI implementation $type ". "failed to load: ".$@); } } } return $type->new(-verbose => $self->verbose, @args); } =head2 type Title : type Usage : $obj->type($newval) Function: Get/set the type of L object to be created. This may be changed at any time during the lifetime of this factory. Returns : value of type Args : newvalue (optional) =cut sub type{ my $self = shift; if(@_) { my $type = shift; if($type && (! $self->{'_loaded_types'}->{$type})) { eval { $self->_load_module($type); }; if( $@ ) { $self->throw("Annotation class '$type' failed to load: ". $@); } my $a = bless {},$type; if( ! $a->isa('Bio::AnnotationI') ) { $self->throw("'$type' does not implement Bio::AnnotationI. ". "Too bad."); } $self->{'_loaded_types'}->{$type} = 1; } return $self->{'type'} = $type; } return $self->{'type'}; } =head2 _guess_type Title : _guess_type Usage : Function: Guesses the right type of L implementation based on initialization parameters for the prospective object. Example : Returns : the type (a string, the module name) Args : initialization parameters to be passed to the prospective cluster object =cut sub _guess_type{ my ($self,@args) = @_; my $type; # we can only guess from a certain number of arguments my ($val, $db, $text, $name, $authors, $start, $tree, $node) = $self->_rearrange([qw(VALUE DATABASE TEXT NAME AUTHORS START TREE_OBJ NODE )], @args); SWITCH: { $val && do { $type = ref($val) ? "TagTree" : "SimpleValue"; last SWITCH; }; $authors && do { $type = "Reference"; last SWITCH; }; $db && do { $type = "DBLink"; last SWITCH; }; $text && do { $type = "Comment"; last SWITCH; }; $name && do { $type = "OntologyTerm"; last SWITCH; }; $start && do { $type = "Target"; last SWITCH; }; $tree && do { $type = "Tree"; last SWITCH; }; $node && do { $type = "TagTree"; last SWITCH; }; # what else could we look for? } $type = "Bio::Annotation::".$type; return $type; } ##################################################################### # aliases for naming consistency or other reasons # ##################################################################### *create = \&create_object; 1; BioPerl-1.007002/Bio/Annotation/Collection.pm000444000766000024 4460613155576320 21021 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Annotation::Collection.pm # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Annotation::Collection - Default Perl implementation of AnnotationCollectionI =head1 SYNOPSIS # get an AnnotationCollectionI somehow, eg $ac = $seq->annotation(); foreach $key ( $ac->get_all_annotation_keys() ) { @values = $ac->get_Annotations($key); foreach $value ( @values ) { # value is an Bio::AnnotationI, and defines a "as_text" method print "Annotation ",$key," stringified value ",$value->as_text,"\n"; # also defined hash_tree method, which allows data orientated # access into this object $hash = $value->hash_tree(); } } =head1 DESCRIPTION Bioperl implementation for Bio::AnnotationCollectionI =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Annotation::Collection; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Annotation::TypeManager; use Bio::Annotation::SimpleValue; use base qw(Bio::Root::Root Bio::AnnotationCollectionI Bio::AnnotationI); =head2 new Title : new Usage : $coll = Bio::Annotation::Collection->new() Function: Makes a new Annotation::Collection object. Returns : Bio::Annotation::Collection Args : none =cut sub new{ my ($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_annotation'} = {}; $self->_typemap(Bio::Annotation::TypeManager->new()); return $self; } =head1 L implementing methods =cut =head2 get_all_annotation_keys Title : get_all_annotation_keys Usage : $ac->get_all_annotation_keys() Function: gives back a list of annotation keys, which are simple text strings Returns : list of strings Args : none =cut sub get_all_annotation_keys{ my ($self) = @_; return keys %{$self->{'_annotation'}}; } =head2 get_Annotations Title : get_Annotations Usage : my @annotations = $collection->get_Annotations('key') Function: Retrieves all the Bio::AnnotationI objects for one or more specific key(s). If no key is given, returns all annotation objects. The returned objects will have their tagname() attribute set to the key under which they were attached, unless the tagname was already set. Returns : list of Bio::AnnotationI - empty if no objects stored for a key Args : keys (list of strings) for annotations (optional) =cut sub get_Annotations{ my ($self,@keys) = @_; my @anns = (); @keys = $self->get_all_annotation_keys() unless @keys; foreach my $key (@keys) { if(exists($self->{'_annotation'}->{$key})) { push(@anns, map { $_->tagname($key) if ! $_->tagname(); $_; } @{$self->{'_annotation'}->{$key}}); } } return @anns; } =head2 get_nested_Annotations Title : get_nested_Annotations Usage : my @annotations = $collection->get_nested_Annotations( '-key' => \@keys, '-recursive => 1); Function: Retrieves all the Bio::AnnotationI objects for one or more specific key(s). If -recursive is set to true, traverses the nested annotation collections recursively and returns all annotations matching the key(s). If no key is given, returns all annotation objects. The returned objects will have their tagname() attribute set to the key under which they were attached, unless the tagname was already set. Returns : list of Bio::AnnotationI - empty if no objects stored for a key Args : -keys => arrayref of keys to search for (optional) -recursive => boolean, whether or not to recursively traverse the nested annotations and return annotations with matching keys. =cut sub get_nested_Annotations { my ($self, @args) = @_; my ($keys, $recursive) = $self->_rearrange([qw(KEYS RECURSIVE)], @args); $self->verbose(1); my @anns = (); # if not recursive behave exactly like get_Annotations() if (!$recursive) { my @keys = $keys? @$keys : $self->get_all_annotation_keys(); foreach my $key (@keys) { if(exists($self->{'_annotation'}->{$key})) { push(@anns, map { $_->tagname($key) if ! $_->tagname(); $_; } @{$self->{'_annotation'}->{$key}}); } } } # if recursive search for keys recursively else { my @allkeys = $self->get_all_annotation_keys(); foreach my $key (@allkeys) { my $keymatch = 0; foreach my $searchkey (@$keys) { if ($key eq $searchkey) { $keymatch = 1;} } if ($keymatch) { if(exists($self->{'_annotation'}->{$key})) { push(@anns, map { $_->tagname($key) if ! $_->tagname(); $_; } @{$self->{'_annotation'}->{$key}}); } } else { my @annotations = @{$self->{'_annotation'}->{$key}}; foreach (@annotations) { if ($_->isa("Bio::AnnotationCollectionI")) { push (@anns, $_->get_nested_Annotations('-keys' => $keys, '-recursive' => 1) ); } } } } } return @anns; } =head2 get_all_Annotations Title : get_all_Annotations Usage : Function: Similar to get_Annotations, but traverses and flattens nested annotation collections. This means that collections in the tree will be replaced by their components. Keys will not be passed on to nested collections. I.e., if the tag name of a nested collection matches the key, it will be flattened in its entirety. Hence, for un-nested annotation collections this will be identical to get_Annotations. Example : Returns : an array of L compliant objects Args : keys (list of strings) for annotations (optional) =cut sub get_all_Annotations{ my ($self,@keys) = @_; return map { $_->isa("Bio::AnnotationCollectionI") ? $_->get_all_Annotations() : $_; } $self->get_Annotations(@keys); } =head2 get_num_of_annotations Title : get_num_of_annotations Usage : my $count = $collection->get_num_of_annotations() Function: Returns the count of all annotations stored in this collection Returns : integer Args : none =cut sub get_num_of_annotations{ my ($self) = @_; my $count = 0; map { $count += scalar @$_ } values %{$self->{'_annotation'}}; return $count; } =head1 Implementation specific functions - mainly for adding =cut =head2 add_Annotation Title : add_Annotation Usage : $self->add_Annotation('reference',$object); $self->add_Annotation($object,'Bio::MyInterface::DiseaseI'); $self->add_Annotation($object); $self->add_Annotation('disease',$object,'Bio::MyInterface::DiseaseI'); Function: Adds an annotation for a specific key. If the key is omitted, the object to be added must provide a value via its tagname(). If the archetype is provided, this and future objects added under that tag have to comply with the archetype and will be rejected otherwise. Returns : none Args : annotation key ('disease', 'dblink', ...) object to store (must be Bio::AnnotationI compliant) [optional] object archetype to map future storage of object of these types to =cut sub add_Annotation{ my ($self,$key,$object,$archetype) = @_; # if there's no key we use the tagname() as key if(ref($key) && $key->isa("Bio::AnnotationI") && (!ref($object))) { $archetype = $object if defined($object); $object = $key; $key = $object->tagname(); $key = $key->name() if ref($key); # OntologyTermI $self->throw("Annotation object must have a tagname if key omitted") unless $key; } if( !defined $object ) { $self->throw("Must have at least key and object in add_Annotation"); } if( !ref $object ) { $self->throw("Must add an object. Use Bio::Annotation::{Comment,SimpleValue,OntologyTerm} for simple text additions"); } if( !$object->isa("Bio::AnnotationI") ) { $self->throw("object must be AnnotationI compliant, otherwise we won't add it!"); } # ok, now we are ready! If we don't have an archetype, set it # from the type of the object if( !defined $archetype ) { $archetype = ref $object; } # check typemap, storing if needed. my $stored_map = $self->_typemap->type_for_key($key); if( defined $stored_map ) { # check validity, irregardless of archetype. A little cheeky # this means isa stuff is executed correctly if( !$self->_typemap()->is_valid($key,$object) ) { $self->throw("Object $object was not valid with key $key. ". "If you were adding new keys in, perhaps you want to make use\n". "of the archetype method to allow registration to a more basic type"); } } else { $self->_typemap->_add_type_map($key,$archetype); } # we are ok to store if( !defined $self->{'_annotation'}->{$key} ) { $self->{'_annotation'}->{$key} = []; } push(@{$self->{'_annotation'}->{$key}},$object); return 1; } =head2 remove_Annotations Title : remove_Annotations Usage : Function: Remove the annotations for the specified key from this collection. Example : Returns : an array Bio::AnnotationI compliant objects which were stored under the given key(s) Args : the key(s) (tag name(s), one or more strings) for which to remove annotations (optional; if none given, flushes all annotations) =cut sub remove_Annotations{ my ($self, @keys) = @_; @keys = $self->get_all_annotation_keys() unless @keys; my @anns = $self->get_Annotations(@keys); # flush foreach my $key (@keys) { delete $self->{'_annotation'}->{$key}; delete $self->{'_typemap'}->{'_type'}->{$key}; } return @anns; } =head2 flatten_Annotations Title : flatten_Annotations Usage : Function: Flattens part or all of the annotations in this collection. This is a convenience method for getting the flattened annotation for the given keys, removing the annotation for those keys, and adding back the flattened array. This should not change anything for un-nested collections. Example : Returns : an array Bio::AnnotationI compliant objects which were stored under the given key(s) Args : list of keys (strings) the annotation for which to flatten, defaults to all keys if not given =cut sub flatten_Annotations{ my ($self,@keys) = @_; my @anns = $self->get_all_Annotations(@keys); my @origanns = $self->remove_Annotations(@keys); foreach (@anns) { $self->add_Annotation($_); } return @origanns; } =head1 Bio::AnnotationI methods implementations This is to allow nested annotation: you can use a collection as an annotation object for an annotation collection. =cut =head2 as_text Title : as_text Usage : Function: See L Example : Returns : a string Args : none =cut sub as_text{ my $self = shift; my $txt = "Collection consisting of "; my @texts = (); foreach my $ann ($self->get_Annotations()) { push(@texts, $ann->as_text()); } if(@texts) { $txt .= join(", ", map { '['.$_.']'; } @texts); } else { $txt .= "no elements"; } return $txt; } =head2 display_text Title : display_text Usage : my $str = $ann->display_text(); Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for te specific implementation. One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned Example : Returns : a string Args : [optional] callback =cut { # this just calls the default display_text output for # any AnnotationI my $DEFAULT_CB = sub { my $obj = shift; my $txt; foreach my $ann ($obj->get_Annotations()) { $txt .= $ann->display_text()."\n"; } return $txt; }; sub display_text { my ($self, $cb) = @_; $cb ||= $DEFAULT_CB; $self->throw("") if ref $cb ne 'CODE'; return $cb->($self); } } =head2 hash_tree Title : hash_tree Usage : Function: See L Example : Returns : a hash reference Args : none =cut sub hash_tree{ my $self = shift; my $tree = {}; foreach my $key ($self->get_all_annotation_keys()) { # all contained objects will support hash_tree() # (they are AnnotationIs) $tree->{$key} = [$self->get_Annotations($key)]; } return $tree; } =head2 tagname Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to Bio::AnnotationCollectionI when adding this object. When obtaining an AnnotationI object from the collection, the collection will set the value to the tag under which it was stored unless the object has a tag stored already. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional) =cut sub tagname{ my $self = shift; return $self->{'tagname'} = shift if @_; return $self->{'tagname'}; } =head1 Backward compatible functions Functions put in for backward compatibility with old Bio::Annotation.pm stuff =cut =head2 description Title : description Usage : Function: Example : Returns : Args : =cut sub description{ my ($self,$value) = @_; $self->deprecated("Using old style annotation call on new Annotation::Collection object"); if( defined $value ) { my $val = Bio::Annotation::SimpleValue->new(); $val->value($value); $self->add_Annotation('description',$val); } my ($desc) = $self->get_Annotations('description'); # If no description tag exists, do not attempt to call value on undef: return $desc ? $desc->value : undef; } =head2 add_gene_name Title : add_gene_name Usage : Function: Example : Returns : Args : =cut sub add_gene_name{ my ($self,$value) = @_; $self->deprecated("Old style add_gene_name called on new style Annotation::Collection"); my $val = Bio::Annotation::SimpleValue->new(); $val->value($value); $self->add_Annotation('gene_name',$val); } =head2 each_gene_name Title : each_gene_name Usage : Function: Example : Returns : Args : =cut sub each_gene_name{ my ($self) = @_; $self->deprecated("Old style each_gene_name called on new style Annotation::Collection"); my @out; my @gene = $self->get_Annotations('gene_name'); foreach my $g ( @gene ) { push(@out,$g->value); } return @out; } =head2 add_Reference Title : add_Reference Usage : Function: Example : Returns : Args : =cut sub add_Reference{ my ($self, @values) = @_; $self->deprecated("add_Reference (old style Annotation) on new style Annotation::Collection"); # Allow multiple (or no) references to be passed, as per old method foreach my $value (@values) { $self->add_Annotation('reference',$value); } } =head2 each_Reference Title : each_Reference Usage : Function: Example : Returns : Args : =cut sub each_Reference{ my ($self) = @_; $self->deprecated("each_Reference (old style Annotation) on new style Annotation::Collection"); return $self->get_Annotations('reference'); } =head2 add_Comment Title : add_Comment Usage : Function: Example : Returns : Args : =cut sub add_Comment{ my ($self,$value) = @_; $self->deprecated("add_Comment (old style Annotation) on new style Annotation::Collection"); $self->add_Annotation('comment',$value); } =head2 each_Comment Title : each_Comment Usage : Function: Example : Returns : Args : =cut sub each_Comment{ my ($self) = @_; $self->deprecated("each_Comment (old style Annotation) on new style Annotation::Collection"); return $self->get_Annotations('comment'); } =head2 add_DBLink Title : add_DBLink Usage : Function: Example : Returns : Args : =cut sub add_DBLink{ my ($self,$value) = @_; $self->deprecated("add_DBLink (old style Annotation) on new style Annotation::Collection"); $self->add_Annotation('dblink',$value); } =head2 each_DBLink Title : each_DBLink Usage : Function: Example : Returns : Args : =cut sub each_DBLink{ my ($self) = @_; $self->deprecated("each_DBLink (old style Annotation) on new style Annotation::Collection - use get_Annotations('dblink')"); return $self->get_Annotations('dblink'); } =head1 Implementation management functions =cut =head2 _typemap Title : _typemap Usage : $obj->_typemap($newval) Function: Example : Returns : value of _typemap Args : newvalue (optional) =cut sub _typemap{ my ($self,$value) = @_; if( defined $value) { $self->{'_typemap'} = $value; } return $self->{'_typemap'}; } 1; BioPerl-1.007002/Bio/Annotation/Comment.pm000444000766000024 1101113155576320 20310 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Annotation::Comment # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Annotation::Comment - A comment object, holding text =head1 SYNOPSIS $comment = Bio::Annotation::Comment->new(); $comment->text("This is the text of this comment"); $annotation->add_Annotation('comment', $comment); =head1 DESCRIPTION A holder for comments in annotations, just plain text. This is a very simple object, and justifiably so. =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Annotation::Comment; use strict; use base qw(Bio::Root::Root Bio::AnnotationI); =head2 new Title : new Usage : $comment = Bio::Annotation::Comment->new( '-text' => 'some text for this comment'); Function: This returns a new comment object, optionally with text filed Example : Returns : a Bio::Annotation::Comment object Args : a hash with -text optionally set =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($text,$tag, $type) = $self->_rearrange([qw(TEXT TAGNAME TYPE)], @args); defined $text && $self->text($text); defined $tag && $self->tagname($tag); defined $type && $self->type($type); return $self; } =head1 AnnotationI implementing functions =cut =head2 as_text Title : as_text Usage : Function: Example : Returns : Args : =cut sub as_text{ my ($self) = @_; return "Comment: ".$self->text; } =head2 display_text Title : display_text Usage : my $str = $ann->display_text(); Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for te specific implementation. One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned Example : Returns : a string Args : [optional] callback =cut { my $DEFAULT_CB = sub {$_[0]->text || ''}; sub display_text { my ($self, $cb) = @_; $cb ||= $DEFAULT_CB; $self->throw("Callback must be a code reference") if ref $cb ne 'CODE'; return $cb->($self); } } =head2 hash_tree Title : hash_tree Usage : Function: Example : Returns : Args : =cut sub hash_tree{ my $self = shift; my $h = {}; $h->{'text'} = $self->text; return $h; } =head2 tagname Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to Bio::AnnotationCollectionI when adding this object. When obtaining an AnnotationI object from the collection, the collection will set the value to the tag under which it was stored unless the object has a tag stored already. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional) =cut sub tagname{ my ($self,$value) = @_; if( defined $value) { $self->{'tagname'} = $value; } return $self->{'tagname'}; } =head1 Specific accessors for Comments =cut =head2 text Title : text Usage : $value = $self->text($newval) Function: get/set for the text field. A comment object just holds a single string which is accessible through this method Example : Returns : value of text Args : newvalue (optional) =cut sub text{ my ($self,$value) = @_; if( defined $value) { $self->{'text'} = $value; } return $self->{'text'}; } =head2 value Title : value Usage : $value = $self->value($newval) Function: Alias of the 'text' method Example : Returns : value of text Args : newvalue (optional) =cut *value = \&text; =head2 type Title : type Usage : $value = $self->type($newval) Function: get/set for the comment type field. The comment type is normally found as a subfield within comment sections in some files, such as SwissProt Example : Returns : value of text Args : newvalue (optional) =cut sub type { my ($self,$type) = @_; if( defined $type) { $self->{'type'} = $type; } return $self->{'type'}; } 1; BioPerl-1.007002/Bio/Annotation/DBLink.pm000444000766000024 2456013155576320 20026 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Annotation::DBLink # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Annotation::DBLink - untyped links between databases =head1 SYNOPSIS $link1 = Bio::Annotation::DBLink->new(-database => 'TSC', -primary_id => 'TSC0000030' ); #or $link2 = Bio::Annotation::DBLink->new(); $link2->database('dbSNP'); $link2->primary_id('2367'); # DBLink is-a Bio::AnnotationI object, can be added to annotation # collections, e.g. the one on features or seqs $feat->annotation->add_Annotation('dblink', $link2); =head1 DESCRIPTION Provides an object which represents a link from one object to something in another database without prescribing what is in the other database. Aside from L, this class also implements L. =head1 AUTHOR - Ewan Birney Ewan Birney - birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Annotation::DBLink; use strict; use base qw(Bio::Root::Root Bio::AnnotationI Bio::IdentifiableI); =head2 new Title : new Usage : $dblink = Bio::Annotation::DBLink->new(-database =>"GenBank", -primary_id => "M123456"); Function: Creates a new instance of this class. Example : Returns : A new instance of Bio::Annotation::DBLink. Args : Named parameters. At present, the following parameters are recognized. -database the name of the database referenced by the xref -primary_id the primary (main) id of the referenced entry (usually this will be an accession number) -optional_id a secondary ID under which the referenced entry is known in the same database -comment comment text for the dbxref -tagname the name of the tag under which to add this instance to an annotation bundle (usually 'dblink') -type the type of information in the referenced entry (e.g. protein, mRNA, structure) -namespace synonymous with -database (also overrides) -version version of the referenced entry -authority attribute of the Bio::IdentifiableI interface -url attribute of the Bio::IdentifiableI interface =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($database,$primary_id,$optional_id,$comment,$tag,$type,$ns,$auth,$v,$url) = $self->_rearrange([qw(DATABASE PRIMARY_ID OPTIONAL_ID COMMENT TAGNAME TYPE NAMESPACE AUTHORITY VERSION URL )], @args); $database && $self->database($database); $primary_id && $self->primary_id($primary_id); $optional_id && $self->optional_id($optional_id); $comment && $self->comment($comment); $tag && $self->tagname($tag); $type && $self->type($type); # Bio::IdentifiableI parameters: $ns && $self->namespace($ns); # this will override $database $auth && $self->authority($auth); defined($v) && $self->version($v); defined($url) && $self->url($url); return $self; } =head1 AnnotationI implementing functions =cut =head2 as_text Title : as_text Usage : Function: Example : Returns : Args : =cut sub as_text{ my ($self) = @_; return "Direct database link to ".$self->primary_id .($self->version ? ".".$self->version : "") .($self->optional_id ? " (".$self->optional_id.")" : "") ." in database ".$self->database; } =head2 display_text Title : display_text Usage : my $str = $ann->display_text(); Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for te specific implementation. One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned Example : Returns : a string Args : [optional] callback =cut { my $DEFAULT_CB = sub { (($_[0]->database ? $_[0]->database . ':' : '' ) . ($_[0]->primary_id ? $_[0]->primary_id : '') . ($_[0]->version ? '.' . $_[0]->version : '')) || '' }; sub display_text { my ($self, $cb) = @_; $cb ||= $DEFAULT_CB; $self->throw("Callback must be a code reference") if ref $cb ne 'CODE'; return $cb->($self); } } =head2 hash_tree Title : hash_tree Usage : Function: Example : Returns : Args : =cut sub hash_tree{ my ($self) = @_; my $h = {}; $h->{'database'} = $self->database; $h->{'primary_id'} = $self->primary_id; if( defined $self->optional_id ) { $h->{'optional_id'} = $self->optional_id; } if( defined $self->comment ) { # we know that comments have hash_tree methods $h->{'comment'} = $self->comment; } return $h; } =head2 tagname Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to Bio::AnnotationCollectionI when adding this object. When obtaining an AnnotationI object from the collection, the collection will set the value to the tag under which it was stored unless the object has a tag stored already. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional) =cut sub tagname{ my $self = shift; return $self->{'tagname'} = shift if @_; return $self->{'tagname'}; } =head1 Specific accessors for DBLinks =cut =head2 database Title : database Usage : $self->database($newval) Function: set/get on the database string. Databases are just a string here which can then be interpreted elsewhere Example : Returns : value of database Args : newvalue (optional) =cut sub database{ my $self = shift; return $self->{'database'} = shift if @_; return $self->{'database'}; } =head2 primary_id Title : primary_id Usage : $self->primary_id($newval) Function: set/get on the primary id (a string) The primary id is the main identifier used for this object in the database. Good examples would be accession numbers. The id is meant to be the main, stable identifier for this object Example : Returns : value of primary_id Args : newvalue (optional) =cut sub primary_id{ my $self = shift; return $self->{'primary_id'} = shift if @_; return $self->{'primary_id'}; } =head2 optional_id Title : optional_id Usage : $self->optional_id($newval) Function: get/set for the optional_id (a string) optional id is a slot for people to use as they wish. The main issue is that some databases do not have a clean single string identifier scheme. It is hoped that the primary_id can behave like a reasonably sane "single string identifier" of objects, and people can use/abuse optional ids to their heart's content to provide precise mappings. Example : Returns : value of optional_id Args : newvalue (optional) =cut #' sub optional_id{ my $self = shift; return $self->{'optional_id'} = shift if @_; return $self->{'optional_id'}; } =head2 comment Title : comment Usage : $self->comment($newval) Function: get/set of comments (comment object) Sets or gets comments of this dblink, which is sometimes relevant Example : Returns : value of comment (Bio::Annotation::Comment) Args : newvalue (optional) =cut sub comment{ my $self = shift; return $self->{'comment'} = shift if @_; return $self->{'comment'}; } =head2 type Title : type Usage : $self->type($newval) Function: get/set of type Sets or gets the type of this dblink. Example : $self->type('protein') Returns : value of type Args : newvalue (optional) =cut sub type { my $self = shift; return $self->{'type'} = shift if @_; return $self->{'type'}; } =head1 Methods for Bio::IdentifiableI compliance =head2 object_id Title : object_id Usage : $string = $obj->object_id() Function: a string which represents the stable primary identifier in this namespace of this object. For DNA sequences this is its accession_number, similarly for protein sequences This is aliased to primary_id(). Returns : A scalar =cut sub object_id { return shift->primary_id(@_); } =head2 version Title : version Usage : $version = $obj->version() Function: a number which differentiates between versions of the same object. Higher numbers are considered to be later and more relevant, but a single object described the same identifier should represent the same concept Returns : A number =cut sub version{ my $self = shift; return $self->{'version'} = shift if @_; return $self->{'version'}; } =head2 url Title : url Usage : $url = $obj->url() Function: URL which is associated with this DB link Returns : string, full URL descriptor =cut sub url { my $self = shift; return $self->{'url'} = shift if @_; return $self->{'url'}; } =head2 authority Title : authority Usage : $authority = $obj->authority() Function: a string which represents the organisation which granted the namespace, written as the DNS name for organisation (eg, wormbase.org) Returns : A scalar =cut sub authority{ my $self = shift; return $self->{'authority'} = shift if @_; return $self->{'authority'}; } =head2 namespace Title : namespace Usage : $string = $obj->namespace() Function: A string representing the name space this identifier is valid in, often the database name or the name describing the collection For DBLink this is the same as database(). Returns : A scalar =cut sub namespace{ return shift->database(@_); } 1; BioPerl-1.007002/Bio/Annotation/OntologyTerm.pm000444000766000024 3444713155576320 21372 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Annotation::OntologyTerm # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI =head1 SYNOPSIS use Bio::Annotation::OntologyTerm; use Bio::Annotation::Collection; use Bio::Ontology::Term; my $coll = Bio::Annotation::Collection->new(); # this also implements a tag/value pair, where tag _and_ value are treated # as ontology terms my $annterm = Bio::Annotation::OntologyTerm->new(-label => 'ABC1', -tagname => 'Gene Name'); # ontology terms can be added directly - they implicitly have a tag $coll->add_Annotation($annterm); # implementation is by composition - you can get/set the term object # e.g. my $term = $annterm->term(); # term is-a Bio::Ontology::TermI print "ontology term ",$term->name()," (ID ",$term->identifier(), "), ontology ",$term->ontology()->name(),"\n"; $term = Bio::Ontology::Term->new(-name => 'ABC2', -ontology => 'Gene Name'); $annterm->term($term); =head1 DESCRIPTION Ontology term annotation object =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Annotation::OntologyTerm; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Ontology::Term; use base qw(Bio::Root::Root Bio::AnnotationI Bio::Ontology::TermI); =head2 new Title : new Usage : my $sv = Bio::Annotation::OntologyTerm->new(); Function: Instantiate a new OntologyTerm object Returns : Bio::Annotation::OntologyTerm object Args : -term => $term to initialize the term data field [optional] Most named arguments that Bio::Ontology::Term accepts will work here too. -label is a synonym for -name, -tagname is a synonym for -ontology. =cut sub new{ my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($term,$name,$label,$identifier,$definition,$ont,$tag) = $self->_rearrange([qw(TERM NAME LABEL IDENTIFIER DEFINITION ONTOLOGY TAGNAME)], @args); if($term) { $self->term($term); } else { $self->name($name || $label) if $name || $label; $self->identifier($identifier) if $identifier; $self->definition($definition) if $definition; } $self->ontology($ont || $tag) if $ont || $tag; return $self; } =head1 AnnotationI implementing functions =cut =head2 as_text Title : as_text Usage : my $text = $obj->as_text Function: Returns a textual representation of the annotation that this object holds. Presently, it is tag name, name of the term, and the is_obsolete attribute concatenated togather with a delimiter (|). Returns : string Args : none =cut sub as_text{ my ($self) = @_; return $self->tagname()."|".$self->name()."|".($self->is_obsolete()||''); } =head2 display_text Title : display_text Usage : my $str = $ann->display_text(); Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for te specific implementation. One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned Example : Returns : a string Args : [optional] callback =cut { my $DEFAULT_CB = sub { $_[0]->identifier || ''}; sub display_text { my ($self, $cb) = @_; $cb ||= $DEFAULT_CB; $self->throw("Callback must be a code reference") if ref $cb ne 'CODE'; return $cb->($self); } } =head2 hash_tree Title : hash_tree Usage : my $hashtree = $value->hash_tree Function: For supporting the AnnotationI interface just returns the value as a hashref with the key 'value' pointing to the value Returns : hashrf Args : none =cut sub hash_tree{ my ($self) = @_; my $h = {}; $h->{'name'} = $self->name(); $h->{'identifier'} = $self->identifier(); $h->{'definition'} = $self->definition(); $h->{'synonyms'} = [$self->get_synonyms()]; } =head2 tagname Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to AnnotationCollection when adding this object. This is aliased to ontology() here. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional) =cut sub tagname{ my $self = shift; return $self->ontology(@_) if @_; # if in get mode we need to get the name from the ontology my $ont = $self->ontology(); return ref($ont) ? $ont->name() : $ont; } =head1 Methods for Bio::Ontology::TermI compliance =cut =head2 term Title : term Usage : $obj->term($newval) Function: Get/set the Bio::Ontology::TermI implementing object. We implement TermI by composition, and this method sets/gets the object we delegate to. Example : Returns : value of term (a Bio::Ontology::TermI compliant object) Args : new value (a Bio::Ontology::TermI compliant object, optional) =cut sub term{ my ($self,$value) = @_; if( defined $value) { $self->{'term'} = $value; } if(! exists($self->{'term'})) { $self->{'term'} = Bio::Ontology::Term->new(); } return $self->{'term'}; } =head2 identifier Title : identifier Usage : $term->identifier( "0003947" ); or print $term->identifier(); Function: Set/get for the identifier of this Term. Returns : The identifier [scalar]. Args : The identifier [scalar] (optional). =cut sub identifier { return shift->term()->identifier(@_); } # identifier =head2 name Title : name Usage : $term->name( "N-acetylgalactosaminyltransferase" ); or print $term->name(); Function: Set/get for the name of this Term. Returns : The name [scalar]. Args : The name [scalar] (optional). =cut sub name { return shift->term()->name(@_); } # name =head2 definition Title : definition Usage : $term->definition( "Catalysis of ..." ); or print $term->definition(); Function: Set/get for the definition of this Term. Returns : The definition [scalar]. Args : The definition [scalar] (optional). =cut sub definition { return shift->term()->definition(@_); } # definition =head2 ontology Title : ontology Usage : $term->ontology( $top ); or $top = $term->ontology(); Function: Set/get for a relationship between this Term and another Term (e.g. the top level of the ontology). Returns : The ontology of this Term [TermI]. Args : The ontology of this Term [TermI or scalar -- which becomes the name of the category term] (optional). =cut sub ontology { return shift->term()->ontology(@_); } =head2 is_obsolete Title : is_obsolete Usage : $term->is_obsolete( 1 ); or if ( $term->is_obsolete() ) Function: Set/get for the obsoleteness of this Term. Returns : the obsoleteness [0 or 1]. Args : the obsoleteness [0 or 1] (optional). =cut sub is_obsolete { return shift->term()->is_obsolete(@_); } # is_obsolete =head2 comment Title : comment Usage : $term->comment( "Consider the term ..." ); or print $term->comment(); Function: Set/get for an arbitrary comment about this Term. Returns : A comment. Args : A comment (optional). =cut sub comment { return shift->term()->comment(@_); } # comment =head2 get_synonyms Title : get_synonyms() Usage : @aliases = $term->get_synonyms(); Function: Returns a list of aliases of this Term. Returns : A list of aliases [array of [scalar]]. Args : =cut sub get_synonyms { return shift->term()->get_synonyms(@_); } # get_synonyms =head2 add_synonym Title : add_synonym Usage : $term->add_synonym( @asynonyms ); or $term->add_synonym( $synonym ); Function: Pushes one or more synonyms into the list of synonyms. Returns : Args : One synonym [scalar] or a list of synonyms [array of [scalar]]. =cut sub add_synonym { return shift->term()->add_synonym(@_); } # add_synonym =head2 remove_synonyms Title : remove_synonyms() Usage : $term->remove_synonyms(); Function: Deletes (and returns) the synonyms of this Term. Returns : A list of synonyms [array of [scalar]]. Args : =cut sub remove_synonyms { return shift->term()->remove_synonyms(@_); } # remove_synonyms =head2 get_dblinks Title : get_dblinks() Usage : @ds = $term->get_dblinks(); Function: Returns a list of each dblinks of this GO term. Returns : A list of dblinks [array of [scalars]]. Args : Note : this is deprecated in favor of get_dbxrefs(), which works with strings or L instances =cut sub get_dblinks { my $self = shift; $self->deprecated('get_dblinks() is deprecated; use get_dbxrefs()'); return $self->term->get_dbxrefs(@_); } # get_dblinks =head2 get_dbxrefs Title : get_dbxrefs() Usage : @ds = $term->get_dbxrefs(); Function: Returns a list of each dblinks of this GO term. Returns : A list of dblinks [array of [scalars] or Bio::Annotation::DBLink instances]. Args : =cut sub get_dbxrefs { return shift->term->get_dbxrefs(@_); } # get_dblinks =head2 add_dblink Title : add_dblink Usage : $term->add_dblink( @dbls ); or $term->add_dblink( $dbl ); Function: Pushes one or more dblinks into the list of dblinks. Returns : Args : One dblink [scalar] or a list of dblinks [array of [scalars]]. Note : this is deprecated in favor of add_dbxref(), which works with strings or L instances =cut sub add_dblink { my $self = shift; $self->deprecated('add_dblink() is deprecated; use add_dbxref()'); return $self->term->add_dbxref(@_); } # add_dblink =head2 add_dbxref Title : add_dbxref Usage : $term->add_dbxref( @dbls ); or $term->add_dbxref( $dbl ); Function: Pushes one or more dblinks into the list of dblinks. Returns : Args : =cut sub add_dbxref { return shift->term->add_dbxref(@_); } =head2 remove_dblinks Title : remove_dblinks() Usage : $term->remove_dblinks(); Function: Deletes (and returns) the definition references of this GO term. Returns : A list of definition references [array of [scalars]]. Args : Note : this is deprecated in favor of remove_dbxrefs(), which works with strings or L instances =cut sub remove_dblinks { my $self = shift; $self->deprecated('remove_dblinks() is deprecated; use remove_dbxrefs()'); return $self->term->remove_dbxrefs(@_); } # remove_dblinks =head2 remove_dbxrefs Title : remove_dbxrefs() Usage : $term->remove_dbxrefs(); Function: Deletes (and returns) the definition references of this GO term. Returns : A list of definition references [array of [scalars]]. Args : =cut sub remove_dbxrefs { return shift->term->remove_dbxrefs(@_); } =head2 get_secondary_ids Title : get_secondary_ids Usage : @ids = $term->get_secondary_ids(); Function: Returns a list of secondary identifiers of this Term. Secondary identifiers mostly originate from merging terms, or possibly also from splitting terms. Returns : A list of secondary identifiers [array of [scalar]] Args : =cut sub get_secondary_ids { return shift->term->get_secondary_ids(@_); } # get_secondary_ids =head2 add_secondary_id Title : add_secondary_id Usage : $term->add_secondary_id( @ids ); or $term->add_secondary_id( $id ); Function: Adds one or more secondary identifiers to this term. Returns : Args : One or more secondary identifiers [scalars] =cut sub add_secondary_id { return shift->term->add_secondary_id(@_); } # add_secondary_id =head2 remove_secondary_ids Title : remove_secondary_ids Usage : $term->remove_secondary_ids(); Function: Deletes (and returns) the secondary identifiers of this Term. Returns : The previous list of secondary identifiers [array of [scalars]] Args : =cut sub remove_secondary_ids { return shift->term->remove_secondary_ids(@_); } # remove_secondary_ids 1; BioPerl-1.007002/Bio/Annotation/Reference.pm000444000766000024 3074113155576320 20617 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Annotation::Reference # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Annotation::Reference - Specialised DBLink object for Literature References =head1 SYNOPSIS $reg = Bio::Annotation::Reference->new( -title => 'title line', -location => 'location line', -authors => 'author line', -medline => 998122 ); =head1 DESCRIPTION Object which presents a literature reference. This is considered to be a specialised form of database link. The additional methods provided are all set/get methods to store strings commonly associated with references, in particular title, location (ie, journal page) and authors line. There is no attempt to do anything more than store these things as strings for processing elsewhere. This is mainly because parsing these things suck and generally are specific to the specific format one is using. To provide an easy route to go format --E object --E format without losing data, we keep them as strings. Feel free to post the list for a better solution, but in general this gets very messy very fast... =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Annotation::Reference; use strict; use base qw(Bio::Annotation::DBLink); =head2 new Title : new Usage : $ref = Bio::Annotation::Reference->new( -title => 'title line', -authors => 'author line', -location => 'location line', -medline => 9988812); Function: Example : Returns : a new Bio::Annotation::Reference object Args : a hash with optional title, authors, location, medline, pubmed, start, end, consortium, rp and rg attributes =cut sub new{ my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($start,$end,$authors,$consortium,$location,$title,$medline, $pubmed,$rp,$rg,$doi) = $self->_rearrange([qw(START END AUTHORS CONSORTIUM LOCATION TITLE MEDLINE PUBMED RP RG DOI )],@args); defined $start && $self->start($start); defined $end && $self->end($end); defined $authors && $self->authors($authors); defined $consortium && $self->consortium($consortium); defined $location && $self->location($location); defined $title && $self->title($title); defined $medline && $self->medline($medline); defined $pubmed && $self->pubmed($pubmed); defined $rp && $self->rp($rp); defined $rg && $self->rg($rg); defined $doi && $self->doi($doi); return $self; } =head1 AnnotationI implementing functions =cut =head2 as_text Title : as_text Usage : Function: Example : Returns : Args : =cut sub as_text{ my ($self) = @_; # this could get out of hand! return "Reference: ".$self->title; } =head2 display_text Title : display_text Usage : my $str = $ann->display_text(); Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for te specific implementation. One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned Example : Returns : a string Args : [optional] callback =cut { my $DEFAULT_CB = sub { $_[0]->title || ''}; sub display_text { my ($self, $cb) = @_; $cb ||= $DEFAULT_CB; $self->throw("Callback must be a code reference") if ref $cb ne 'CODE'; return $cb->($self); } } =head2 hash_tree Title : hash_tree Usage : Function: Example : Returns : Args : =cut sub hash_tree{ my ($self) = @_; my $h = {}; $h->{'title'} = $self->title; $h->{'authors'} = $self->authors; $h->{'location'} = $self->location; if (defined $self->start) { $h->{'start'} = $self->start; } if (defined $self->end) { $h->{'end'} = $self->end; } $h->{'medline'} = $self->medline; if (defined $self->pubmed) { $h->{'pubmed'} = $self->pubmed; } return $h; } =head2 tagname Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to Bio::AnnotationCollectionI when adding this object. When obtaining an AnnotationI object from the collection, the collection will set the value to the tag under which it was stored unless the object has a tag stored already. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional) =cut =head1 Specific accessors for References =cut =head2 start Title : start Usage : $self->start($newval) Function: Gives the reference start base Example : Returns : value of start Args : newvalue (optional) =cut sub start { my ($self,$value) = @_; if( defined $value) { $self->{'start'} = $value; } return $self->{'start'}; } =head2 end Title : end Usage : $self->end($newval) Function: Gives the reference end base Example : Returns : value of end Args : newvalue (optional) =cut sub end { my ($self,$value) = @_; if( defined $value) { $self->{'end'} = $value; } return $self->{'end'}; } =head2 rp Title : rp Usage : $self->rp($newval) Function: Gives the RP line. No attempt is made to parse this line. Example : Returns : value of rp Args : newvalue (optional) =cut sub rp{ my ($self,$value) = @_; if( defined $value) { $self->{'rp'} = $value; } return $self->{'rp'}; } =head2 rg Title : rg Usage : $obj->rg($newval) Function: Gives the RG line. This is Swissprot/Uniprot specific, and if set will usually be identical to the authors attribute, but the swissprot manual does allow both RG and RA (author) to be present for the same reference. Example : Returns : value of rg (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub rg{ my $self = shift; return $self->{'rg'} = shift if @_; return $self->{'rg'}; } =head2 authors Title : authors Usage : $self->authors($newval) Function: Gives the author line. No attempt is made to parse the author line Example : Returns : value of authors Args : newvalue (optional) =cut sub authors{ my ($self,$value) = @_; if( defined $value) { $self->{'authors'} = $value; } return $self->{'authors'}; } =head2 location Title : location Usage : $self->location($newval) Function: Gives the location line. No attempt is made to parse the location line Example : Returns : value of location Args : newvalue (optional) =cut sub location{ my ($self,$value) = @_; if( defined $value) { $self->{'location'} = $value; } return $self->{'location'}; } =head2 title Title : title Usage : $self->title($newval) Function: Gives the title line (if exists) Example : Returns : value of title Args : newvalue (optional) =cut sub title{ my ($self,$value) = @_; if( defined $value) { $self->{'title'} = $value; } return $self->{'title'}; } =head2 medline Title : medline Usage : $self->medline($newval) Function: Gives the medline number Example : Returns : value of medline Args : newvalue (optional) =cut sub medline{ my ($self,$value) = @_; if( defined $value) { $self->{'medline'} = $value; } return $self->{'medline'}; } =head2 pubmed Title : pubmed Usage : $refobj->pubmed($newval) Function: Get/Set the PubMed number, if it is different from the MedLine number. Example : Returns : value of medline Args : newvalue (optional) =cut sub pubmed { my ($self,$value) = @_; if( defined $value) { $self->{'pubmed'} = $value; } return $self->{'pubmed'}; } =head2 database Title : database Usage : Function: Overrides DBLink database to be hard coded to 'MEDLINE' (or 'PUBMED' if only pubmed id has been supplied), unless the database has been set explicitly before. Example : Returns : Args : =cut sub database{ my ($self, @args) = @_; my $default = 'MEDLINE'; if (! defined $self->medline && defined $self->pubmed) { $default = 'PUBMED'; } return $self->SUPER::database(@args) || $default; } =head2 primary_id Title : primary_id Usage : Function: Overrides DBLink primary_id to provide medline number, or pubmed number if only that has been defined Example : Returns : Args : =cut sub primary_id{ my ($self, @args) = @_; if (@args) { $self->medline(@args); } if (! defined $self->medline && defined $self->pubmed) { return $self->pubmed; } return $self->medline; } =head2 optional_id Title : optional_id Usage : Function: Overrides DBLink optional_id to provide the PubMed number. Example : Returns : Args : =cut sub optional_id{ my ($self, @args) = @_; return $self->pubmed(@args); } =head2 publisher Title : publisher Usage : $self->publisher($newval) Function: Gives the publisher line. No attempt is made to parse the publisher line Example : Returns : value of publisher Args : newvalue (optional) =cut sub publisher { my ($self,$value) = @_; if( defined $value) { $self->{'publisher'} = $value; } return $self->{'publisher'}; } =head2 editors Title : editors Usage : $self->editors($newval) Function: Gives the editors line. No attempt is made to parse the editors line Example : Returns : value of editors Args : newvalue (optional) =cut sub editors { my ($self,$value) = @_; if( defined $value) { $self->{'editors'} = $value; } return $self->{'editors'}; } =head2 encoded_ref Title : encoded_ref Usage : $self->encoded_ref($newval) Function: Gives the encoded_ref line. No attempt is made to parse the encoded_ref line (this is added for reading PDB records (REFN record), where this contains ISBN/ISSN/ASTM code) Example : Returns : value of encoded_ref Args : newvalue (optional) =cut sub encoded_ref { my ($self,$value) = @_; if( defined $value) { $self->{'encoded_ref'} = $value; } return $self->{'encoded_ref'}; } =head2 doi Title : doi Usage : $self->doi($newval) Function: Gives the DOI (Digital Object Identifier) from the International DOI Foundation (http://www.doi.org/), which can be used to resolve URL links for the full-text documents using: http://dx.doi.org/ Example : Returns : value of doi Args : newvalue (optional) =cut sub doi { my ($self,$value) = @_; if( defined $value) { $self->{'doi'} = $value; } return $self->{'doi'}; } =head2 consortium Title : consortium Usage : $self->consortium($newval) Function: Gives the consortium line. No attempt is made to parse the consortium line Example : Returns : value of consortium Args : newvalue (optional) =cut sub consortium{ my ($self,$value) = @_; if( defined $value) { $self->{'consortium'} = $value; } return $self->{'consortium'}; } =head2 gb_reference Title : gb_reference Usage : $obj->gb_reference($newval) Function: Gives the generic GenBank REFERENCE line. This is GenBank-specific. If set, this includes everything on the reference line except the REFERENCE tag and the reference count. This is mainly a fallback for the few instances when REFERENCE lines have unusual additional information such as split sequence locations, feature references, etc. See Bug 2020 in Bugzilla for more information. Example : Returns : value of gb_reference (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub gb_reference{ my ($self,$value) = @_; if( defined $value) { $self->{'gb_reference'} = $value; } return $self->{'gb_reference'}; } 1; BioPerl-1.007002/Bio/Annotation/Relation.pm000444000766000024 1675413155576320 20506 0ustar00cjfieldsstaff000000000000# $Id: Relation.pm 14708 2008-06-10 00:08:17Z heikki $ # # BioPerl module for Bio::Annotation::Relation # # Please direct questions and support issues to # # Cared for by bioperl # # Copyright bioperl # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Annotation::Relation - Relationship (pairwise) with other objects SeqI and NodeI; =head1 SYNOPSIS use Bio::Annotation::Relation; use Bio::Annotation::Collection; my $col = Bio::Annotation::Collection->new(); my $sv = Bio::Annotation::Relation->new(-type => "paralogy" -to => "someSeqI"); $col->add_Annotation('tagname', $sv); =head1 DESCRIPTION Scalar value annotation object =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Mira Han Email mirhan@indiana.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Annotation::Relation; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root Bio::AnnotationI); =head2 new Title : new Usage : my $sv = Bio::Annotation::Relation->new(); Function: Instantiate a new Relation object Returns : Bio::Annotation::Relation object Args : -type => $type of relation [optional] -to => $obj which $self is in relation to [optional] -tagname => $tag to initialize the tagname [optional] -tag_term => ontology term representation of the tag [optional] =cut sub new{ my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($type, $to, $tag, $term) = $self->_rearrange([qw(TYPE TO TAGNAME TAG_TERM)], @args); # set the term first defined $term && $self->tag_term($term); defined $type && $self->type($type); defined $to && $self->to($to); defined $tag && $self->tagname($tag); return $self; } =head1 AnnotationI implementing functions =cut =head2 as_text Title : as_text Usage : my $text = $obj->as_text Function: return the string "Value: $v" where $v is the value Returns : string Args : none =cut sub as_text{ my ($self) = @_; return $self->type." to ".$self->to->id; } =head2 display_text Title : display_text Usage : my $str = $ann->display_text(); Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for te specific implementation. One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned Example : Returns : a string Args : [optional] callback =cut { my $DEFAULT_CB = sub { return $_[0]->type." to ".$_[0]->to->id }; #my $DEFAULT_CB = sub { $_[0]->value}; sub display_text { my ($self, $cb) = @_; $cb ||= $DEFAULT_CB; $self->throw("Callback must be a code reference") if ref $cb ne 'CODE'; return $cb->($self); } } =head2 hash_tree Title : hash_tree Usage : my $hashtree = $value->hash_tree Function: For supporting the AnnotationI interface just returns the value as a hashref with the key 'value' pointing to the value Returns : hashrf Args : none =cut sub hash_tree{ my $self = shift; my $h = {}; $h->{'type'} = $self->type; $h->{'to'} = $self->to; return $h; } =head2 tagname Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to AnnotationCollection when adding this object. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional) =cut sub tagname{ my $self = shift; # check for presence of an ontology term if($self->{'_tag_term'}) { # keep a copy in case the term is removed later $self->{'tagname'} = $_[0] if @_; # delegate to the ontology term object return $self->tag_term->name(@_); } return $self->{'tagname'} = shift if @_; return $self->{'tagname'}; } =head1 Specific accessors for Relation =cut =head2 type Title : type Usage : $obj->type($newval) Function: Get/Set the type Returns : type of relation Args : newtype (optional) =cut sub type{ my ($self,$type) = @_; if( defined $type) { $self->{'type'} = $type; } return $self->{'type'}; } =head2 to Title : to Usage : $obj->to($newval) Function: Get/Set the object which $self is in relation to Returns : the object which the relation applies to Args : new target object (optional) =cut sub to{ my ($self,$to) = @_; if( defined $to) { $self->{'to'} = $to; } return $self->{'to'}; } =head2 confidence Title : confidence Usage : $self->confidence($newval) Function: Gives the confidence value. Example : Returns : value of confidence Args : newvalue (optional) =cut sub confidence{ my ($self,$value) = @_; if( defined $value) { $self->{'confidence'} = $value; } return $self->{'confidence'}; } =head2 confidence_type Title : confidence_type Usage : $self->confidence_type($newtype) Function: Gives the confidence type. Example : Returns : type of confidence Args : newtype (optional) =cut sub confidence_type{ my ($self,$type) = @_; if( defined $type) { $self->{'confidence_type'} = $type; } return $self->{'confidence_type'}; } =head2 tag_term Title : tag_term Usage : $obj->tag_term($newval) Function: Get/set the L object representing the tag name. This is so you can specifically relate the tag of this annotation to an entry in an ontology. You may want to do this to associate an identifier with the tag, or a particular category, such that you can better match the tag against a controlled vocabulary. This accessor will return undef if it has never been set before in order to allow this annotation to stay light-weight if an ontology term representation of the tag is not needed. Once it is set to a valid value, tagname() will actually delegate to the name() of this term. Example : Returns : a L compliant object, or undef Args : on set, new value (a L compliant object or undef, optional) =cut sub tag_term{ my $self = shift; return $self->{'_tag_term'} = shift if @_; return $self->{'_tag_term'}; } 1; BioPerl-1.007002/Bio/Annotation/SimpleValue.pm000444000766000024 1435713155576320 21154 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Annotation::SimpleValue # # Please direct questions and support issues to # # Cared for by bioperl # # Copyright bioperl # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Annotation::SimpleValue - A simple scalar =head1 SYNOPSIS use Bio::Annotation::SimpleValue; use Bio::Annotation::Collection; my $col = Bio::Annotation::Collection->new(); my $sv = Bio::Annotation::SimpleValue->new(-value => 'someval'); $col->add_Annotation('tagname', $sv); =head1 DESCRIPTION Scalar value annotation object =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Annotation::SimpleValue; use strict; # Object preamble - inherits from Bio::Root::Root #use Bio::Ontology::TermI; use base qw(Bio::Root::Root Bio::AnnotationI); =head2 new Title : new Usage : my $sv = Bio::Annotation::SimpleValue->new(); Function: Instantiate a new SimpleValue object Returns : Bio::Annotation::SimpleValue object Args : -value => $value to initialize the object data field [optional] -tagname => $tag to initialize the tagname [optional] -tag_term => ontology term representation of the tag [optional] =cut sub new{ my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($value,$tag,$term) = $self->_rearrange([qw(VALUE TAGNAME TAG_TERM)], @args); # set the term first defined $term && $self->tag_term($term); defined $value && $self->value($value); defined $tag && $self->tagname($tag); return $self; } =head1 AnnotationI implementing functions =cut =head2 as_text Title : as_text Usage : my $text = $obj->as_text Function: return the string "Value: $v" where $v is the value Returns : string Args : none =cut sub as_text{ my ($self) = @_; return "Value: ".$self->value; } =head2 display_text Title : display_text Usage : my $str = $ann->display_text(); Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for te specific implementation. One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned Example : Returns : a string Args : [optional] callback =cut { my $DEFAULT_CB = sub { $_[0]->value}; sub display_text { my ($self, $cb) = @_; $cb ||= $DEFAULT_CB; $self->throw("Callback must be a code reference") if ref $cb ne 'CODE'; return $cb->($self); } } =head2 hash_tree Title : hash_tree Usage : my $hashtree = $value->hash_tree Function: For supporting the AnnotationI interface just returns the value as a hashref with the key 'value' pointing to the value Returns : hashrf Args : none =cut sub hash_tree{ my $self = shift; my $h = {}; $h->{'value'} = $self->value; return $h; } =head2 tagname Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to AnnotationCollection when adding this object. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional) =cut sub tagname{ my $self = shift; # check for presence of an ontology term if($self->{'_tag_term'}) { # keep a copy in case the term is removed later $self->{'tagname'} = $_[0] if @_; # delegate to the ontology term object return $self->tag_term->name(@_); } return $self->{'tagname'} = shift if @_; return $self->{'tagname'}; } =head1 Specific accessors for SimpleValue =cut =head2 value Title : value Usage : $obj->value($newval) Function: Get/Set the value for simplevalue Returns : value of value Args : newvalue (optional) =cut sub value{ my ($self,$value) = @_; if( defined $value) { $self->{'value'} = $value; } return $self->{'value'}; } =head2 tag_term Title : tag_term Usage : $obj->tag_term($newval) Function: Get/set the L object representing the tag name. This is so you can specifically relate the tag of this annotation to an entry in an ontology. You may want to do this to associate an identifier with the tag, or a particular category, such that you can better match the tag against a controlled vocabulary. This accessor will return undef if it has never been set before in order to allow this annotation to stay light-weight if an ontology term representation of the tag is not needed. Once it is set to a valid value, tagname() will actually delegate to the name() of this term. Example : Returns : a L compliant object, or undef Args : on set, new value (a L compliant object or undef, optional) =cut sub tag_term{ my $self = shift; return $self->{'_tag_term'} = shift if @_; return $self->{'_tag_term'}; } 1; BioPerl-1.007002/Bio/Annotation/StructuredValue.pm000444000766000024 2340313155576320 22057 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Annotation::StructuredValue # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # (c) Hilmar Lapp, hlapp at gmx.net, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Annotation::StructuredValue - A scalar with embedded structured information =head1 SYNOPSIS use Bio::Annotation::StructuredValue; use Bio::Annotation::Collection; my $col = Bio::Annotation::Collection->new(); my $sv = Bio::Annotation::StructuredValue->new(-value => 'someval'); $col->add_Annotation('tagname', $sv); =head1 DESCRIPTION Scalar value annotation object. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp-at-gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Annotation::StructuredValue; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Annotation::SimpleValue); =head2 new Title : new Usage : my $sv = Bio::Annotation::StructuredValue->new(); Function: Instantiate a new StructuredValue object Returns : Bio::Annotation::StructuredValue object Args : -value => $value to initialize the object data field [optional] -tagname => $tag to initialize the tagname [optional] =cut sub new{ my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($value,$tag) = $self->_rearrange([qw(VALUE TAGNAME)], @args); $self->{'values'} = []; defined $value && $self->value($value); defined $tag && $self->tagname($tag); return $self; } =head1 AnnotationI implementing functions =cut =head2 as_text Title : as_text Usage : my $text = $obj->as_text Function: return the string "Value: $v" where $v is the value Returns : string Args : none =cut sub as_text{ my ($self) = @_; return "Value: ".$self->value; } =head2 display_text Title : display_text Usage : my $str = $ann->display_text(); Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for te specific implementation. One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned Example : Returns : a string Args : [optional] callback =cut { my $DEFAULT_CB = sub { $_[0]->value || ''}; sub display_text { my ($self, $cb) = @_; $cb ||= $DEFAULT_CB; $self->throw("Callback must be a code reference") if ref $cb ne 'CODE'; return $cb->($self); } } =head2 hash_tree Title : hash_tree Usage : my $hashtree = $value->hash_tree Function: For supporting the AnnotationI interface just returns the value as a hashref with the key 'value' pointing to the value Returns : hashrf Args : none =cut sub hash_tree{ my ($self) = @_; my $h = {}; $h->{'value'} = $self->value; } =head2 tagname Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to AnnotationCollection when adding this object. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional) =cut sub tagname{ my ($self,$value) = @_; if( defined $value) { $self->{'tagname'} = $value; } return $self->{'tagname'}; } =head1 Specific accessors for StructuredValue =cut =head2 value Title : value Usage : $obj->value($newval) Function: Get/set the value for this annotation. Set mode is here only to retain compatibility with SimpleValue. It is equivalent to calling add_value([0], $newval). In get mode, this implementation allows one to pass additional parameters that control how the structured annotation components will be joined together to form a string. Recognized are presently -joins a reference to an array of join strings, the elements at index i applying to joining annotations at dimension i. The last element will be re-used for dimensions higher than i. Defaults to ['; ']. -brackets a reference to an array of two strings denoting the opening and closing brackets for the elements of one dimension, if there is more than one element in the dimension. Defaults to ['(',')']. Returns : value of value Args : newvalue (optional) =cut sub value{ my ($self,$value,@args) = @_; # set mode? return $self->add_value([0], $value) if defined($value) && (@args == 0); # no, get mode # determine joins and brackets unshift(@args, $value); my ($joins, $brackets) = $self->_rearrange([qw(JOINS BRACKETS)], @args); $joins = ['; '] unless $joins; $brackets = ['(', ')'] unless $brackets; my $txt = &_to_text($self->{'values'}, $joins, $brackets); # if there's only brackets at the start and end, remove them if((@{$self->{'values'}} == 1) && (length($brackets->[0]) == 1) && (length($brackets->[1]) == 1)) { my $re = '\\'.$brackets->[0]. '([^\\'.$brackets->[1].']*)\\'.$brackets->[1]; $txt =~ s/^$re$/$1/; } return $txt; } sub _to_text{ my ($arr, $joins, $brackets, $rec_n) = @_; $rec_n = 0 unless defined($rec_n); my $i = $rec_n >= @$joins ? @$joins-1 : $rec_n; my $txt = join($joins->[$i], map { ref($_) ? (ref($_) eq "ARRAY" ? &_to_text($_, $joins, $brackets, $rec_n+1) : $_->value()) : $_; } @$arr); if($rec_n && (@$arr > 1)) { $txt = $brackets->[0] . $txt . $brackets->[1]; } return $txt; } =head2 get_values Title : get_values Usage : Function: Get the top-level array of values. Each of the elements will recursively be a reference to an array or a scalar, depending on the depth of this structured value annotation. Example : Returns : an array Args : none =cut sub get_values{ my $self = shift; return @{$self->{'values'}}; } =head2 get_all_values Title : get_all_values Usage : Function: Flattens all values in this structured annotation and returns them as an array. Example : Returns : the (flat) array of values Args : none =cut sub get_all_values{ my ($self) = @_; # we code lazy here and just take advantage of value() my $txt = $self->value(-joins => ['@!@'], -brackets => ['','']); return split(/\@!\@/, $txt); } =head2 add_value Title : add_value Usage : Function: Adds the given value to the structured annotation at the given index. The index is multi-dimensional, with the first dimension applying to the first level, and so forth. If a particular dimension or a particular index does not exist yet, it will be created. If it does exist and adding the value would mean replacing a scalar with an array reference, we throw an exception to prevent unintended damage. An index of -1 at any dimension means append. If an array of values is to be added, it will create an additional dimension at the index specified, unless the last index value is -1, in which case they will all be appended to the last dimension. Example : Returns : none Args : the index at which to add (a reference to an array) the value(s) to add =cut sub add_value{ my ($self,$index,@values) = @_; my $tree = $self->{'values'}; my $lastidx = pop(@$index); foreach my $i (@$index) { if($i < 0) { my $subtree = []; push(@$tree, $subtree); $tree = $subtree; } elsif((! $tree->[$i]) || (ref($tree->[$i]) eq "ARRAY")) { $tree->[$i] = [] unless ref($tree->[$i]) eq "ARRAY"; $tree = $tree->[$i]; } else { $self->throw("element $i is a scalar but not in last dimension"); } } if($lastidx < 0) { push(@$tree, @values); } elsif(@values < 2) { $tree->[$lastidx] = shift(@values); } else { $tree->[$lastidx] = [@values]; } } 1; BioPerl-1.007002/Bio/Annotation/TagTree.pm000444000766000024 4507413155576320 20261 0ustar00cjfieldsstaff000000000000# $Id: TagTree.pm 11693 2007-09-17 20:54:04Z cjfields $ # # BioPerl module for Bio::Annotation::TagTree # # Cared for Chris Fields # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Annotation::TagTree - AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text. =head1 SYNOPSIS use Bio::Annotation::TagTree; use Bio::Annotation::Collection; my $col = Bio::Annotation::Collection->new(); # data structure can be an array reference with a data structure # corresponding to that defined by Data::Stag: my $sv = Bio::Annotation::TagTree->new(-tagname => 'mytag1', -value => $data_structure); $col->add_Annotation($sv); # regular text passed is parsed based on the tagformat(). my $sv2 = Bio::Annotation::TagTree->new(-tagname => 'mytag2', -tagformat => 'xml', -value => $xmltext); $col->add_Annotation($sv2); =head1 DESCRIPTION This takes tagged data values and stores them in a hierarchal structured element-value hierarchy (complements of Chris Mungall's Data::Stag module). Data can then be represented as text using a variety of output formats (indention, itext, xml, spxr). Furthermore, the data structure can be queried using various means. See L for details. Data passed in using value() or the '-value' parameter upon instantiation can either be: 1) an array reference corresponding to the data structure for Data::Stag; 2) a text string in 'xml', 'itext', 'spxr', or 'indent' format. The default format is 'xml'; this can be changed using tagformat() prior to using value() or by passing in the proper format using '-tagformat' upon instantiation; 3) another Bio::Annotation::TagTree or Data::Stag node instance. In both cases a deep copy (duplicate) of the instance is generated. Beyond checking for an array reference no format guessing occurs (so, for roundtrip tests ensure that the IO formats correspond). For now, we recommend when using text input to set tagformat() to one of these formats prior to data loading to ensure the proper Data::Stag parser is selected. After data loading, the tagformat() can be changed to change the text string format returned by value(). (this may be rectified in the future) This Annotation type is fully BioSQL compatible and could be considered a temporary replacement for nested Bio::Annotation::Collections, at least until BioSQL and bioperl-db can support nested annotation collections. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Chris Fields =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Annotation::TagTree; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Annotation::SimpleValue); use Data::Stag; =head2 new Title : new Usage : my $sv = Bio::Annotation::TagTree->new(); Function: Instantiate a new TagTree object Returns : Bio::Annotation::TagTree object Args : -value => $value to initialize the object data field [optional] -tagname => $tag to initialize the tagname [optional] -tagformat => format for output [optional] (types 'xml', 'itext', 'sxpr', 'indent', default = 'itext') -node => Data::Stag node or Bio::Annotation::TagTree instance =cut sub new { my ( $class, @args ) = @_; my $self = $class->SUPER::new(); my ( $node, $value, $tag, $format, $verbose ) = $self->_rearrange( [ qw( NODE VALUE TAGNAME TAGFORMAT VERBOSE) ], @args ); $self->throw("Cant use both node and value; mutually exclusive") if defined $node && defined $value; defined $tag && $self->tagname($tag); $format ||= 'itext'; $self->tagformat($format); defined $value && $self->value($value); defined $node && $self->node($node); defined $verbose && $self->verbose($verbose); return $self; } =head1 AnnotationI implementing functions =cut =head2 as_text Title : as_text Usage : my $text = $obj->as_text Function: return the string "Value: $v" where $v is the value Returns : string Args : none =cut sub as_text { my ($self) = @_; return "TagTree: " . $self->value; } =head2 display_text Title : display_text Usage : my $str = $ann->display_text(); Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for the specific implementation. One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned Example : Returns : a string Args : [optional] callback =cut { my $DEFAULT_CB = sub { $_[0]->value || '' }; sub display_text { my ( $self, $cb ) = @_; $cb ||= $DEFAULT_CB; $self->throw("Callback must be a code reference") if ref $cb ne 'CODE'; return $cb->($self); } } =head2 hash_tree Title : hash_tree Usage : my $hashtree = $value->hash_tree Function: For supporting the AnnotationI interface just returns the value as a hashref with the key 'value' pointing to the value Maybe reimplement using Data::Stag::hash()? Returns : hashrf Args : none =cut sub hash_tree { my ($self) = @_; my $h = {}; $h->{'value'} = $self->value; } =head2 tagname Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to AnnotationCollection when adding this object. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional) =cut sub tagname { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'tagname'} = $value; } return $self->{'tagname'}; } =head1 Specific accessors for TagTree =cut =head2 value Title : value Usage : $obj->value($newval) Function: Get/set the value for this annotation. Returns : value of value Args : newvalue (optional) =cut sub value { my ( $self, $value ) = @_; # set mode? This resets the entire tagged database my $format = $self->tagformat; if ($value) { if ( ref $value ) { if ( ref $value eq 'ARRAY' ) { # note the tagname() is not used here; it is only used for # storing this AnnotationI in the annotation collection eval { $self->{db} = Data::Stag->nodify($value) }; } else { # assuming this is blessed; passing on to node() and copy $self->node( $value, 'copy' ); } } else { # not trying to guess here for now; we go by the tagformat() setting my $h = Data::Stag->getformathandler($format); eval { $self->{db} = Data::Stag->from( $format . 'str', $value ) }; } $self->throw("Data::Stag error:\n$@") if $@; } # get mode? # How do we return a data structure? # for now, we use the output (if there is a Data::Stag node present) # may need to run an eval {} to catch Data::Stag output errors $self->node->$format; } =head2 tagformat Title : tagformat Usage : $obj->tagformat($newval) Function: Get/set the output tag format for this annotation. Returns : value of tagformat Args : newvalue (optional) - format for the data passed into value must be of values 'xml', 'indent', 'sxpr', 'itext', 'perl' =cut my %IS_VALID_FORMAT = map { $_ => 1 } qw(xml indent sxpr itext); sub tagformat { my ( $self, $value ) = @_; if ( defined $value ) { $self->throw( "$value is not a valid format; valid format types:\n" . join( ',', map { "'$_'" } keys %IS_VALID_FORMAT ) ) if !exists $IS_VALID_FORMAT{$value}; $self->{'tagformat'} = $value; } return $self->{'tagformat'}; } =head2 node Title : node Usage : $obj->node() Function: Get/set the topmost Data::Stag node used for this annotation. Returns : Data::Stag node implementation (default is Data::Stag::StagImpl) Args : (optional) Data::Stag node implementation (optional)'copy' => flag to create a copy of the node =cut sub node { my ( $self, $value, $copy ) = @_; if ( defined $value && ref $value ) { $self->{'db'} = $value->isa('Data::Stag::StagI') ? ( $copy && $copy eq 'copy' ? $value->duplicate : $value ) : $value->isa('Bio::Annotation::TagTree') ? ( $copy && $copy eq 'copy' ? $value->node->duplicate : $value->node ) : $self->throw( 'Object must be Data::Stag::StagI or Bio::Annotation::TagTree'); } # lazily create Data::Stag instance if not present if (!$self->{'db'}) { $self->{'db'} = Data::Stag->new(); } return $self->{'db'}; } =head2 Data::Stag convenience methods Because Data::Stag uses blessed arrays and the core Bioperl class uses blessed hashes, TagTree uses an internal instance of a Data::Stag node for data storage. Therefore the following methods actually delegate to the Data:::Stag internal instance. For consistency (since one could recursively check child nodes), methods retain the same names as Data::Stag. Also, no 'magic' (AUTOLOAD'ed) methods are employed, simply b/c full-fledged Data::Stag functionality can be attained by grabbing the Data::Stag instance using node(). =head2 element Title : element Usage : Function: Returns the element name (key name) for this node Example : Returns : scalar Args : none =cut sub element { my $self = shift; return $self->node->element; } =head2 data Title : data Usage : Function: Returns the data structure (array ref) for this node Example : Returns : array ref Args : none =cut sub data { my $self = shift; return $self->node->data; } =head2 children Title : children Usage : Function: Get the top-level array of Data::Stag nodes or (if the top level is a terminal node) a scalar value. This is similar to StructuredValue's get_values() method, with the key difference being instead of array refs and scalars you get either Data::Stag nodes or the value for this particular node. For consistency (since one could recursively check nodes), we use the same method name as Data::Stag children(). Example : Returns : an array Args : none =cut sub children { my $self = shift; return $self->node->children; } =head2 subnodes Title : subnodes Usage : Function: Get the top-level array of Data::Stag nodes. Unlike children(), this only returns an array of nodes (if this is a terminal node, no value is returned) Example : Returns : an array of nodes Args : none =cut sub subnodes { my $self = shift; return $self->node->subnodes; } =head2 get Title : get Usage : Function: Returns the nodes or value for the named element or path Example : Returns : returns array of nodes or a scalar (if node is terminal) dependent on wantarray Args : none =cut sub get { my ( $self, @vals ) = @_; return $self->node->get(@vals); } =head2 find Title : find Usage : Function: Recursively searches for and returns the nodes or values for the named element or path Example : Returns : returns array of nodes or scalars (for terminal nodes) Args : none =cut sub find { my ( $self, @vals ) = @_; return $self->node->find(@vals); } =head2 findnode Title : findnode Usage : Function: Recursively searches for and returns a list of nodes of the given element path Example : Returns : returns array of nodes Args : none =cut sub findnode { my ( $self, @vals ) = @_; return $self->node->findnode(@vals); } =head2 findval Title : findval Usage : Function: Example : Returns : returns array of nodes or values Args : none =cut sub findval { my ( $self, @vals ) = @_; return $self->node->findval(@vals); } =head2 addchild Title : addchild Usage : $struct->addchild(['name' => [['foo'=> 'bar1']]]); Function: add new child node to the current node. One can pass in a node, TagTree, or data structure; for instance, in the above, this would translate to (in XML): bar1 Returns : node Args : first arg = element name all other args are added as tag-value pairs =cut sub addchild { my ( $self, @vals ) = @_; # check for element tag first (if no element, must be empty Data::Stag node) if ( !$self->element ) { # try to do the right thing; if more than one element, wrap in array ref @vals > 1 ? $self->value( \@vals ) : $self->value( $vals[0] ); return $self->{db}; } elsif ( !$self->node->ntnodes ) { # if this is a terminal node, can't add to it (use set?) $self->throw("Can't add child to node; only terminal node is present!"); } else { return $self->node->addchild(@vals); } } =head2 add Title : add Usage : $struct->add('foo', 'bar1', 'bar2', 'bar3'); Function: add tag-value nodes to the current node. In the above, this would translate to (in XML): bar1 bar2 bar3 Returns : Args : first arg = element name all other args are added as tag-value pairs =cut sub add { my ( $self, @vals ) = @_; # check for empty object and die for now if ( !$self->node->element ) { $self->throw("Can't add to terminal element!"); } return $self->node->add(@vals); } =head2 set Title : set Usage : $struct->set('foo','bar'); Function: sets a single tag-value pair in the current node. Note this differs from add() in that this replaces any data already present Returns : node Args : first arg = element name all other args are added as tag-value pairs =cut sub set { my ( $self, @vals ) = @_; # check for empty object if ( !$self->node->element ) { $self->throw("Can't add to tree; empty tree!"); } return $self->node->set(@vals); } =head2 unset Title : unset Usage : $struct->unset('foo'); Function: unsets all key-value pairs of the passed element from the current node Returns : node Args : element name =cut sub unset { my ( $self, @vals ) = @_; return $self->node->unset(@vals); } =head2 free Title : free Usage : $struct->free Function: removes all data from the current node Returns : Args : =cut sub free { my ($self) = @_; return $self->node->free; } =head2 hash Title : hash Usage : $struct->hash; Function: turns the tag-value tree into a hash, all data values are array refs Returns : hash Args : first arg = element name all other args are added as tag-value pairs =cut sub hash { my ($self) = @_; return $self->node->hash; } =head2 pairs Title : pairs Usage : $struct->pairs; Function: turns the tag-value tree into a hash, all data values are scalar Returns : hash Args : first arg = element name all other args are added as tag-value pairs, note that duplicates will be lost =cut sub pairs { my ($self) = @_; return $self->node->pairs; } =head2 qmatch Title : qmatch Usage : @persons = $s->qmatch('person', ('name'=>'fred')); Function : returns all elements in the node tree which match the element name and the key-value pair Returns : Array of nodes Args : return-element str, match-element str, match-value str =cut sub qmatch { my ( $self, @vals ) = @_; return $self->node->qmatch(@vals); } =head2 tnodes Title : tnodes Usage : @termini = $s->tnodes; Function : returns all terminal nodes below this node Returns : Array of nodes Args : return-element str, match-element str, match-value str =cut sub tnodes { my ($self) = @_; return $self->node->tnodes; } =head2 ntnodes Title : ntnodes Usage : @termini = $s->ntnodes; Function : returns all nonterminal nodes below this node Returns : Array of nodes Args : return-element str, match-element str, match-value str =cut sub ntnodes { my ($self) = @_; return $self->node->ntnodes; } =head2 StructureValue-like methods =cut =head2 get_all_values Title : get_all_values Usage : @termini = $s->get_all_values; Function : returns all terminal node values Returns : Array of values Args : return-element str, match-element str, match-value str This is meant to emulate the values one would get from StructureValue's get_all_values() method. Note, however, using this method dissociates the tag-value relationship (i.e. you only get the value list, no elements) =cut sub get_all_values { my $self = shift; my @kids = $self->children; my @vals; while ( my $val = shift @kids ) { ( ref $val ) ? push @kids, $val->children : push @vals, $val; } return @vals; } 1; BioPerl-1.007002/Bio/Annotation/Target.pm000444000766000024 1061613155576320 20146 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Annotation::Target # # Please direct questions and support issues to # # Cared for by Scott Cain # # Copyright Scott Cain # # Based on the Bio::Annotation::DBLink by Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Annotation::Target - Provides an object which represents a target (ie, a similarity hit) from one object to something in another database =head1 SYNOPSIS $target1 = Bio::Annotation::Target->new(-target_id => 'F321966.1', -start => 1, -end => 200, -strand => 1, # or -1 ); # or $target2 = Bio::Annotation::Target->new(); $target2->target_id('Q75IM5'); $target2->start(7); # ... etc ... # Target is-a Bio::AnnotationI object, can be added to annotation # collections, e.g. the one on features or seqs $feat->annotation->add_Annotation('Target', $target2); =head1 DESCRIPTION Provides an object which represents a target (ie, a similarity hit) from one object to something in another database without prescribing what is in the other database =head1 AUTHOR - Scott Cain Scott Cain - cain@cshl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Annotation::Target; use strict; use base qw(Bio::Annotation::DBLink Bio::AnnotationI Bio::Range); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($target_id, $tstart, $tend, $tstrand) = $self->_rearrange([ qw( TARGET_ID START END STRAND ) ], @args); $target_id && $self->target_id($target_id); $tstart && $self->start($tstart); $tend && $self->end($tend); $tstrand && $self->strand($tstrand); return $self; } =head1 AnnotationI implementing functions =cut =head2 as_text Title : as_text Usage : Function: Example : Returns : Args : =cut sub as_text{ my ($self) = @_; my $target = $self->target_id || ''; my $start = $self->start || ''; my $end = $self->end || ''; my $strand = $self->strand || ''; return "Target=".$target." ".$start." ".$end." ".$strand; } =head2 display_text Title : display_text Usage : my $str = $ann->display_text(); Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for te specific implementation. One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned Example : Returns : a string Args : [optional] callback =cut { my $DEFAULT_CB = sub { $_[0]->as_text || ''}; sub display_text { my ($self, $cb) = @_; $cb ||= $DEFAULT_CB; $self->throw("Callback must be a code reference") if ref $cb ne 'CODE'; return $cb->($self); } } =head2 tagname Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to Bio::AnnotationCollectionI when adding this object. When obtaining an AnnotationI object from the collection, the collection will set the value to the tag under which it was stored unless the object has a tag stored already. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional) =cut sub tagname{ my ($self,$value) = @_; if( defined $value) { $self->{'tagname'} = $value; } return $self->{'tagname'}; } =head1 Specific accessors for Targets =cut =head2 target_id =over =item Usage $obj->target_id() #get existing value $obj->target_id($newval) #set new value =item Function =item Returns value of target_id (a scalar) =item Arguments new value of target_id (to set) =back =cut sub target_id { my $self = shift; return $self->{'target_id'} = shift if defined($_[0]); return $self->{'target_id'} || $self->primary_id(); } 1; BioPerl-1.007002/Bio/Annotation/Tree.pm000444000766000024 1277213155576320 17624 0ustar00cjfieldsstaff000000000000# BioPerl module for Bio::Annotation::Tree # # Please direct questions and support issues to # # Cared for by Weigang Qiu # # Based on the Bio::Annotation::DBLink by Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Annotation::Tree - Provide a tree as an annotation to a Bio::AnnotatableI object =head1 SYNOPSIS # Read a tree and an alignment $treeio=Bio::TreeIO->new(-file=>'foo.dnd', -format=>'newic'); $tree=$treeio->next_tree; $alnio=Bio::AlignIO->new(-file=>'foo.aln', -format=>'clustalw'); $aln=$alnio->next_aln; # Construct a tree annotation $ann_tree = Bio::Annotation::Tree->new (-tree_id => 'mytree', -tree_obj => $tree, ); # Add the tree annotation to AlignI $ac = Bio::Annotation::Collection->new(); $ac->add_Annotation('tree', $ann_tree); $aln->annotation($ac); # NOTE & TODO: # The above procedures are sensible only if # the tree is generated from the alignment. However, # currently no effort has been made to check the consistency # between the tree OTU names and the sequence names =head1 DESCRIPTION Provides a Bio::AnnotationI object which contains a Bio::Tree::TreeI, which can be added to a Bio::AnnotationCollectionI, which in turn be attached to a Bio::AnnotatableI (typically a Bio::AlignI object) =head1 AUTHOR Weigang Qiu - weigang at genectr.hunter.cuny.edu =head1 CONTRIBUTORS Aaron Mackey Jason Stajich =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a '_' =cut # Let the code begin... package Bio::Annotation::Tree; use strict; use base qw(Bio::Root::Root Bio::AnnotationI Bio::TreeIO); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($tree_id, $tree_obj, $tag) = $self->_rearrange([ qw( TREE_ID TREE_OBJ TAGNAME ) ], @args); defined $tag && $self->tagname($tag); defined $tree_id && $self->tree_id($tree_id); defined $tree_obj && $self->tree($tree_obj); return $self; # other possible variables to store # TREE_PROGRAM # TREE_METHOD # TREE_FREQUENCY # defined $program && $self->program($program); # defined $method && $self->method($method); # defined $freq && $self->freq($tree_freq); } =head1 AnnotationI implementing functions =cut =head2 as_text Title : as_text Usage : $ann_tree->as_text(); Function: output tree as a string Returns : a newic tree file Args : None =cut sub as_text{ my ($self) = @_; my $tree = $self->tree || $self->throw("Tree object absent"); my $treeio = Bio::TreeIO->new(); $treeio->write_tree($tree); } =head2 display_text Title : display_text Usage : my $str = $ann->display_text(); Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for te specific implementation. One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned Example : Returns : a string Args : [optional] callback =cut { my $DEFAULT_CB = sub { $_[0]->as_text || ''}; sub display_text { my ($self, $cb) = @_; $cb ||= $DEFAULT_CB; $self->throw("Callback must be a code reference") if ref $cb ne 'CODE'; return $cb->($self); } } =head2 hash_tree Title : hash_tree Usage : my $hashtree = $value->hash_tree Function: For supporting the AnnotationI interface just returns the value as a hashref with the key 'value' pointing to the value Returns : hashrf to tree Args : none =cut sub hash_tree{ my $self = shift; my $h = {}; $h->{'value'} = $self->tree(); return $h; } =head2 tagname Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to Bio::AnnotationCollectionI when adding this object. When obtaining an AnnotationI object from the collection, the collection will set the value to the tag under which it was stored unless the object has a tag stored already. Returns : value of tagname (a scalar) Args : new value (a scalar, optional) =cut sub tagname{ my ($self,$value) = @_; if( defined $value) { $self->{'tagname'} = $value; } return $self->{'tagname'}; } =head1 Specific accessors for Tree =head2 tree_id Title : tree_id Usage : $obj->tree_id($newval) Function: Get/set a name for the tree Returns : value of tagname (a scalar) Args : new value (a scalar, optional) =cut sub tree_id { my $self = shift; return $self->{'tree_id'} = shift if defined($_[0]); return $self->{'tree_id'}; } =head2 tree Title : tree Usage : $obj->tree($newval) Function: Get/set tree Returns : tree ref Args : new value (a tree ref, optional) =cut sub tree { my $self = shift; return $self->{'tree'} = shift if defined($_[0]); return $self->{'tree'}; } 1; BioPerl-1.007002/Bio/Annotation/TypeManager.pm000444000766000024 644113155576320 21115 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Annotation::TypeManager # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Annotation::TypeManager - Manages types for annotation collections =head1 SYNOPSIS # default type manager $tm = Bio::Annotation::TypeManager->new(); # $key is a string or a Bio::Ontology::TermI compliant object print "The type for $key is ",$tm->type_for_key($key),"\n"; if( !$tm->is_valid($key,$object) ) { $self->throw("Invalid object for key $key"); } =head1 DESCRIPTION Manages types for annotation collections. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Annotation::TypeManager; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root); # new() can be inherited from Bio::Root::Root =head2 new Title : new Usage : Function: Example : Returns : Args : =cut sub new{ my ($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_type'} = {}; $self->_add_type_map('reference',"Bio::Annotation::Reference"); $self->_add_type_map('comment',"Bio::Annotation::Comment"); $self->_add_type_map('dblink',"Bio::Annotation::DBLink"); return $self; } =head2 type_for_key Title : type_for_key Usage : Function: Example : Returns : Args : =cut sub type_for_key{ my ($self,$key) = @_; $key = $key->name() if ref($key) && $key->isa("Bio::Ontology::TermI"); return $self->{'_type'}->{$key}; } =head2 is_valid Title : is_valid Usage : Function: Example : Returns : Args : =cut sub is_valid{ my ($self,$key,$object) = @_; if( !defined $object || !ref $object ) { $self->throw("Cannot type an object [$object]!"); } if( !$object->isa($self->type_for_key($key)) ) { return 0; } else { return 1; } } =head2 _add_type_map Title : _add_type_map Usage : Function: Example : Returns : Args : =cut sub _add_type_map{ my ($self,$key,$type) = @_; $key = $key->name() if ref($key) && $key->isa("Bio::Ontology::TermI"); $self->{'_type'}->{$key} = $type; } 1; BioPerl-1.007002/Bio/Assembly000755000766000024 013155576320 15646 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Assembly/Contig.pm000444000766000024 20127513155576320 17633 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Assembly::Contig # Mostly based on Bio::SimpleAlign by Ewan Birney # # Please direct questions and support issues to # # Cared for by Robson Francisco de Souza # # Copyright Robson Francisco de Souza # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Assembly::Contig - Perl module to hold and manipulate sequence assembly contigs. =head1 SYNOPSIS # Module loading use Bio::Assembly::IO; # Assembly loading methods $aio = Bio::Assembly::IO->new(-file=>"test.ace.1", -format=>'phrap'); $assembly = $aio->next_assembly; foreach $contig ($assembly->all_contigs) { # do something } # OR, if you want to build the contig yourself, use Bio::Assembly::Contig; $c = Bio::Assembly::Contig->new(-id=>"1"); $ls = Bio::LocatableSeq->new(-seq=>"ACCG-T", -id=>"r1", -alphabet=>'dna'); $ls2 = Bio::LocatableSeq->new(-seq=>"ACA-CG-T", -id=>"r2", -alphabet=>'dna'); $ls_coord = Bio::SeqFeature::Generic->new(-start=>3, -end=>8, -strand=>1); $ls2_coord = Bio::SeqFeature::Generic->new(-start=>1, -end=>8, -strand=>1); $c->add_seq($ls); $c->add_seq($ls2); $c->set_seq_coord($ls_coord,$ls); $c->set_seq_coord($ls2_coord,$ls2); $con = Bio::LocatableSeq->new(-seq=>"ACACCG-T", -alphabet=>'dna'); $c->set_consensus_sequence($con); $l = $c->change_coord('unaligned r2','ungapped consensus',6); print "6 in unaligned r2 => $l in ungapped consensus\n"; =head1 DESCRIPTION A contig is as a set of sequences, locally aligned to each other, so that every sequence has overlapping regions with at least one sequence in the contig, such that a continuous of overlapping sequences is formed, allowing the deduction of a consensus sequence which may be longer than any of the sequences from which it was deduced. In this documentation we refer to the overlapping sequences used to build the contig as "aligned sequences" and to the sequence deduced from the overlap of aligned sequences as the "consensus". Methods to deduce the consensus sequence from aligned sequences were not yet implemented in this module, but its posssible to add a consensus sequence deduced by other means, e.g, by the assembly program used to build the alignment. All aligned sequences in a Bio::Assembly::Contig must be Bio::Assembly::Locatable objects and have a unique ID. The unique ID restriction is due to the nature of the module's internal data structures and is also a request of some assembly programs. If two sequences with the same ID are added to a contig, the first sequence added is replaced by the second one. =head2 Coordinate_systems There are four base coordinate systems in Bio::Assembly::Contig. When you need to access contig elements or data that exists on a certain range or location, you may be specifying coordinates in relation to different sequences, which may be either the contig consensus or one of the aligned sequences that were used to do the assembly. ========================================================= Name | Referenced sequence --------------------------------------------------------- "gapped consensus" | Contig (with gaps) "ungapped consensus" | Contig (without gaps) "aligned $seqID" | sequence $seqID (with gaps) "unaligned $seqID" | sequence $seqID (without gaps) ========================================================= "gapped consensus" refers to positions in the aligned consensus sequence, which is the consensus sequence including the gaps inserted to align it against the aligned sequences that were used to assemble the contig. So, its limits are [ 1, (consensus length + number of gaps in consensus) ] "ungapped consensus" is a coordinate system based on the consensus sequence, but excluding consensus gaps. This is just the coordinate system that you have when considering the consensus sequence alone, instead of aligned to other sequences. "aligned $seqID" refers to locations in the sequence $seqID after alignment of $seqID against the consensus sequence (reverse complementing the original sequence, if needed). Coordinate 1 in "aligned $seqID" is equivalent to the start location (first base) of $seqID in the consensus sequence, just like if the aligned sequence $seqID was a feature of the consensus sequence. "unaligned $seqID" is equivalent to a location in the isolated sequence, just like you would have when considering the sequence alone, out of an alignment. When changing coordinates from "aligned $seq2" to "unaligned $seq2", if $seq2 was reverse complemented when included in the alignment, the output coordinates will be reversed to fit that fact, i.e. 1 will be changed to length($seq2), 2 will be length($seq)-1 and so on. An important note: when you change gap coordinates from a gapped system ("gapped consensus" or "aligned $seqID") to a system that does not include gaps ("ungapped consensus" or "unaligned $seqID"), the position returned will be the first location before all gaps neighboring the input location. =head2 Feature_collection Bio::Assembly::Contig stores much information about a contig in a Bio::Assembly::SeqFeature::Collection object. Relevant information on the alignment is accessed by selecting features based on their primary tags (e.g. all features which have a primary tag of the form '_aligned_coord:$seqID', where $seqID is an aligned sequence ID, are coordinates for sequences in the contig alignment) and, by using methods from Bio::Assembly::SeqFeature::Collection, it's possible to select features by overlap with other features. We suggest that you use the primary tags of features as identifiers for feature classes. By convention, features with primary tags starting with a '_' are generated by modules that populate the contig data structure and return the contig object, maybe as part of an assembly object, e.g. drivers from the Bio::Assembly::IO set. Features in the features collection may be associated with particular aligned sequences. To obtain this, you must attach the sequence to the feature, using attach() seq from Bio::Assembly::SeqFeatureI, before you add the feature to the feature collection. We also suggest to add the sequence id to the primary tag, so that is easy to select feature for a particular sequence. There is only one feature class that some methods in Bio::Assembly::Contig expect to find in the feature collection: features with primary tags of the form '_aligned_coord:$seqID', where $seqID is the aligned sequence id (like returned by $seq-Eid()). These features describe the position (in "gapped consensus" coordinates) of aligned sequences, and the method set_seq_coord() automatically changes a feature's primary tag to this form whenever the feature is added to the collection by this method. Only two methods in Bio::Assembly::Contig will not work unless there are features from this class: change_coord() and get_seq_coord(). Other feature classes will be automatically available only when Bio::Assembly::Contig objects are created by a specific module. Such feature classes are (or should be) documented in the documentation of the module which create them, to which the user should refer. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Robson Francisco de Souza rfsouza@citri.iq.usp.br =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' package Bio::Assembly::Contig; use strict; use Bio::DB::SeqFeature::Store; # isa Bio::SeqFeature::CollectionI use Bio::Seq::PrimaryQual; # isa Bio::Seq::QualI use Scalar::Util qw(weaken); use base qw(Bio::Root::Root Bio::Align::AlignI); =head1 Object creator =head2 new Title : new Usage : my $contig = Bio::Assembly::Contig->new(); Function : Creates a new contig object Returns : Bio::Assembly::Contig Args : -id => unique contig ID -source => string for the sequence assembly program used -collection => Bio::SeqFeature::CollectionI instance =cut #----------- sub new { #----------- my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($src, $id, $collection) = $self->_rearrange([qw(SOURCE ID COLLECTION)], @args); $src && $self->source($src); ($id && $self->id($id)) || ($self->{'_id'} = 'NoName'); # Alignment (contig) name ($id && $self->id($id)) || ($self->{'_source'} = 'Unknown'); # Program used to build the contig # we need to set up internal hashes first! # Bio::SimpleAlign derived fields (check which ones are needed for AlignI compatibility) $self->{'_elem'} = {}; # contig elements: aligned sequence objects (keyed by ID) $self->{'_order'} = {}; # store sequence order # $self->{'start_end_lists'} = {}; # References to entries in {'_seq'}. Keyed by seq ids. # $self->{'_dis_name'} = {}; # Display names for each sequence $self->{'_symbols'} = {}; # List of symbols #Contig specific slots $self->{'_consensus_sequence'} = undef; $self->{'_consensus_quality'} = undef; $self->{'_nof_residues'} = 0; $self->{'_nof_seqs'} = 0; # $self->{'_nof_segments'} = 0; # Let's not make it heavier than needed by now... # for cases where SF::Collection is shared between Bio::Assembly::Contig if ($collection) { $self->throw("Collection must implement Bio::SeqFeature::CollectionI") unless $collection->isa('Bio::SeqFeature::CollectionI'); $self->{'_sfc'} = $collection; } else { $self->{'_sfc'} = Bio::DB::SeqFeature::Store->new( -adaptor => 'memory', -index_subfeatures => 1, ); } # Assembly specifics $self->{'_assembly'} = undef; # Bio::Assembly::Scaffold the contig belongs to $self->{'_strand'} = 0; # Reverse (-1) or forward (1), if contig is in a scaffold. 0 otherwise $self->{'_neighbor_start'} = undef; # Neighbor Bio::Assembly::Contig $self->{'_neighbor_end'} = undef; # Neighbor Bio::Assembly::Contig return $self; # success - we hope! } =head1 Assembly related methods These methods exist to enable adding information about possible relations among contigs, e.g. when you already have a scaffold for your assembly, describing the ordering of contigs in the final assembly, but no sequences covering the gaps between neighboring contigs. =head2 source Title : source Usage : $contig->source($program); Function : Get/Set program used to build this contig Returns : string Argument : [optional] string =cut sub source { my $self = shift; my $source = shift; $self->{'_source'} = $source if (defined $source); return $self->{'_source'}; } =head2 assembly Title : assembly Usage : $contig->assembly($assembly); Function : Get/Set assembly object for this contig Returns : a Bio::Assembly::Scaffold object Argument : a Bio::Assembly::Scaffold object =cut sub assembly { my $self = shift; my $assembly = shift; $self->throw("Using non Bio::Assembly::Scaffold object when assign contig to assembly") if (defined $assembly && ! $assembly->isa("Bio::Assembly::Scaffold")); # We create a circular reference to a Scaffold object. It is made weak # to prevent memory leaks. $self->{'_assembly'} = $assembly if (defined $assembly); weaken($self->{'_assembly'}); return $self->{'_assembly'}; } =head2 strand Title : strand Usage : $contig->strand($num); Function : Get/Set contig orientation in a scaffold/assembly. Its equivalent to the strand property of sequence objects and sets whether the contig consensus should be reversed and complemented before being added to a scaffold or assembly. Returns : integer Argument : 1 if orientaion is forward, -1 if reverse and 0 if none =cut sub strand { my $self = shift; my $ori = shift; if (defined $ori) { $self->throw("Contig strand must be either 1, -1 or 0") unless $ori == 1 || $ori == 0 || $ori == -1; $self->{'_strand'} = $ori; } return $self->{'_strand'}; } =head2 upstream_neighbor Title : upstream_neighbor Usage : $contig->upstream_neighbor($contig); Function : Get/Set a contig neighbor for the current contig when building a scaffold. The upstream neighbor is located before $contig first base Returns : nothing Argument : Bio::Assembly::Contig =cut sub upstream_neighbor { my $self = shift; my $ref = shift; $self->throw("Trying to assign a non Bio::Assembly::Contig object to upstream contig") if (defined $ref && ! $ref->isa("Bio::Assembly::Contig")); $self->{'_neighbor_start'} = $ref if (defined $ref); return $self->{'_neighbor_start'}; } =head2 downstream_neighbor Title : downstream_neighbor Usage : $contig->downstream_neighbor($num); Function : Get/Set a contig neighbor for the current contig when building a scaffold. The downstream neighbor is located after $contig last base Returns : nothing Argument : Bio::Assembly::Contig =cut sub downstream_neighbor { my $self = shift; my $ref = shift; $self->throw("Trying to assign a non Bio::Assembly::Contig object to downstream contig") if (defined $ref && ! $ref->isa("Bio::Assembly::Contig")); $self->{'_neighbor_end'} = $ref if (defined $ref); return $self->{'_neighbor_end'}; } =head1 Contig feature collection methods =head2 add_features Title : add_features Usage : $contig->add_features($feat,$flag) Function : Add an array of features to the contig feature collection. The consensus sequence may be attached to the added feature, if $flag is set to 1. If $flag is 0 and the feature attached to one of the contig aligned sequences, the feature is registered as an aligned sequence feature. If $flag is 0 and the feature is not attached to any sequence in the contig, the feature is simply added to the feature collection and no attachment or registration is made. Note: You must attach aligned sequences to their features prior to calling add_features, otherwise you won't be able to access the feature through get_seq_feat_by_tag() method. Returns : number of features added. Argument : $feat : A reference to an array of Bio::SeqFeatureI $flag : boolean - true if consensus sequence object should be attached to this feature, false if no consensus attachment should be made. Default: false. =cut sub add_features { my ($self, $args, $flag) = @_; # Adding shortcuts for aligned sequence features $flag = 0 unless (defined $flag); if ($flag && defined $self->{'_consensus_sequence'}) { foreach my $feat (@$args) { next if (defined $feat->seq); $feat->attach_seq($self->{'_consensus_sequence'}); } } elsif (!$flag) { # Register aligned sequence features foreach my $feat (@$args) { if (my $seq = $feat->entire_seq()) { my $seqID = $seq->id() || $seq->display_id || $seq->primary_id; $self->warn("Adding contig feature attached to unknown sequence $seqID!") unless (exists $self->{'_elem'}{$seqID}); my $tag = $feat->primary_tag; $self->{'_elem'}{$seqID}{'_feat'}{$tag} = $feat; } } } # Add feature to feature collection my $nof_added = $self->get_features_collection->add_features($args); return $nof_added; } =head2 remove_features Title : remove_features Usage : $contig->remove_features(@feat) Function : Remove an array of contig features Returns : true if successful Argument : An array of Bio::SeqFeature::Generic (Bio::SeqFeatureI) =cut sub remove_features { my ($self, @args) = @_; # Removing shortcuts for aligned sequence features for my $feat (@args) { if (my $seq = $feat->entire_seq()) { my $seqID = $seq->id || $seq->display_id || $seq->primary_id; my $tag = $feat->primary_tag; $tag =~ s/:$seqID$/$1/g; delete( $self->{'_elem'}{$seqID}{'_feat'}{$tag} ) if (exists $self->{'_elem'}{$seqID}{'_feat'}{$tag} && $self->{'_elem'}{$seqID}{'_feat'}{$tag} eq $feat); } } # Removing Bio::SeqFeature objects return $self->get_features_collection->delete(@args); } =head2 get_features_collection Title : get_features_collection Usage : $contig->get_features_collection() Function : Get the collection of all contig features and seqfeatures Returns : Bio::DB::SeqFeature::Store (Bio::SeqFeature::CollectionI) Argument : none =cut sub get_features_collection { my $self = shift; return $self->{'_sfc'}; } =head2 remove_features_collection Title : remove_features_collection Usage : $contig->remove_features_collection() Function : Remove the collection of all contig features. It is useful to save some memory (when contig features are not needed). Returns : none Argument : none =cut sub remove_features_collection { my $self = shift; # Removing shortcuts for aligned sequence features for my $seqID (keys %{$self->{'_elem'}}) { delete $self->{'_elem'}{$seqID}; } # Removing Bio::SeqFeature::Collection features $self->{'_sfc'} = {}; return; } =head1 Coordinate system's related methods See L above. =head2 change_coord Title : change_coord Usage : $contig->change_coord($in,$out,$query) Function : Change coordinate system for $query. This method transforms locations between coordinate systems described in section "Coordinate Systems" of this document. Note: this method will throw an exception when changing coordinates between "ungapped consensus" and other systems if consensus sequence was not set. It will also throw exceptions when changing coordinates among aligned sequence, either with or without gaps, and other systems if sequence locations were not set with set_seq_coord(). Returns : integer Argument : $in : [string] input coordinate system $out : [string] output coordinate system $query : [integer] a position in a sequence =cut sub change_coord { my $self = shift; my $type_in = shift; my $type_out = shift; my $query = shift; # Parsing arguments # Loading read objects (these calls will throw exceptions whether $read_in or # $read_out is not found my ($read_in,$read_out) = (undef,undef); my $in_ID = ( split(' ',$type_in) )[1]; my $out_ID = ( split(' ',$type_out) )[1]; if ($in_ID ne 'consensus') { $read_in = $self->get_seq_coord( $self->get_seq_by_name($in_ID) ); $self->throw("Can't change coordinates without sequence location for $in_ID") unless (defined $read_in); } if ($out_ID ne 'consensus') { $read_out = $self->get_seq_coord( $self->get_seq_by_name($out_ID) ); $self->throw("Can't change coordinates without sequence location for $out_ID") unless (defined $read_out); } # Performing transformation between coordinates SWITCH1: { # Transformations between contig padded and contig unpadded (($type_in eq 'gapped consensus') && ($type_out eq 'ungapped consensus')) && do { $self->throw("Can't use ungapped consensus coordinates without a consensus sequence") unless (defined $self->{'_consensus_sequence'}); $query = &_padded_unpadded($self->{'_consensus_gaps'}, $query); last SWITCH1; }; (($type_in eq 'ungapped consensus') && ($type_out eq 'gapped consensus')) && do { $self->throw("Can't use ungapped consensus coordinates without a consensus sequence") unless (defined $self->{'_consensus_sequence'}); $query = &_unpadded_padded($self->{'_consensus_gaps'},$query); last SWITCH1; }; # Transformations between contig (padded) and read (padded) (($type_in eq 'gapped consensus') && ($type_out =~ /^aligned /) && defined($read_out)) && do { $query = $query - $read_out->start() + 1; last SWITCH1; }; (($type_in =~ /^aligned /) && defined($read_in) && ($type_out eq 'gapped consensus')) && do { $query = $query + $read_in->start() - 1; last SWITCH1; }; # Transformations between contig (unpadded) and read (padded) (($type_in eq 'ungapped consensus') && ($type_out =~ /^aligned /) && defined($read_out)) && do { $query = $self->change_coord('ungapped consensus','gapped consensus',$query); $query = $self->change_coord('gapped consensus',"aligned $out_ID",$query); last SWITCH1; }; (($type_in =~ /^aligned /) && defined($read_in) && ($type_out eq 'ungapped consensus')) && do { $query = $self->change_coord("aligned $in_ID",'gapped consensus',$query); $query = $self->change_coord('gapped consensus','ungapped consensus',$query); last SWITCH1; }; # Transformations between seq $read_in padded and seq $read_out padded (defined($read_in) && ($type_in =~ /^aligned /) && defined($read_out) && ($type_out =~ /^aligned /)) && do { $query = $self->change_coord("aligned $in_ID",'gapped consensus',$query); $query = $self->change_coord('gapped consensus',"aligned $out_ID",$query); last SWITCH1; }; # Transformations between seq $read_in padded and seq $read_out unpadded (defined($read_in) && ($type_in =~ /^aligned /) && defined($read_out) && ($type_out =~ /^unaligned /)) && do { if ($read_in ne $read_out) { $query = $self->change_coord("aligned $in_ID",'gapped consensus',$query); $query = $self->change_coord('gapped consensus',"aligned $out_ID",$query); } my $list_out = $self->{'_elem'}{$out_ID}{'_gaps'}; $query = &_padded_unpadded($list_out,$query); # Changing read orientation if read was reverse complemented when aligned if ($read_out->strand == -1) { my ($length) = $read_out->length(); $length = $length - &_nof_gaps($list_out,$length); $query = $length - $query + 1; } last SWITCH1; }; (defined($read_in) && ($type_in =~ /^unaligned /) && defined($read_out) && ($type_out =~ /^aligned /)) && do { my $list_in = $self->{'_elem'}{$in_ID}{'_gaps'}; # Changing read orientation if read was reverse complemented when aligned if ($read_in->strand == -1) { my ($length) = $read_in->length(); $length = $length - &_nof_gaps($list_in,$length); $query = $length - $query + 1; } $query = &_unpadded_padded($list_in,$query); if ($read_in ne $read_out) { $query = $self->change_coord("aligned $in_ID",'gapped consensus',$query); $query = $self->change_coord('gapped consensus',"aligned $out_ID",$query); } last SWITCH1; }; # Transformations between seq $read_in unpadded and seq $read_out unpadded (defined($read_in) && ($type_in =~ /^unaligned /) && defined($read_out) && ($type_out =~ /^unaligned /)) && do { $query = $self->change_coord("unaligned $in_ID","aligned $out_ID",$query); $query = $self->change_coord("aligned $out_ID","unaligned $out_ID",$query); last SWITCH1; }; # Transformations between contig (padded) and read (unpadded) (($type_in eq 'gapped consensus') && ($type_out =~ /^unaligned /) && defined($read_out)) && do { $query = $self->change_coord('gapped consensus',"aligned $out_ID",$query); $query = $self->change_coord("aligned $out_ID","unaligned $out_ID",$query); last SWITCH1; }; (($type_in =~ /^unaligned /) && defined($read_in) && ($type_out eq 'gapped consensus')) && do { $query = $self->change_coord("unaligned $in_ID","aligned $in_ID",$query); $query = $self->change_coord("aligned $in_ID",'gapped consensus',$query); last SWITCH1; }; # Transformations between contig (unpadded) and read (unpadded) (($type_in eq 'ungapped consensus') && ($type_out =~ /^unaligned /) && defined($read_out)) && do { $query = $self->change_coord('ungapped consensus','gapped consensus',$query); $query = $self->change_coord('gapped consensus',"unaligned $out_ID",$query); last SWITCH1; }; (($type_in =~ /^unaligned /) && defined($read_in) && ($type_out eq 'ungapped consensus')) && do { $query = $self->change_coord("unaligned $in_ID",'gapped consensus',$query); $query = $self->change_coord('gapped consensus','ungapped consensus',$query); last SWITCH1; }; $self->throw("Unknow coordinate system. Args: $type_in, $type_out."); $query = undef; # If a coordinate systems just requested is unknown } return $query; } =head2 get_seq_coord Title : get_seq_coord Usage : $contig->get_seq_coord($seq); Function : Get "gapped consensus" location for aligned sequence Returns : Bio::SeqFeature::Generic for coordinates or undef. A warning is printed if sequence coordinates were not set. Argument : Bio::LocatableSeq object =cut sub get_seq_coord { my ($self,$seq) = @_; if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) { $self->throw("$seq is not a Bio::LocatableSeq"); } my $seqID = $seq->id() || $seq->display_id || $seq->primary_id; unless (exists( $self->{'_elem'}{$seqID} )) { $self->warn("No such sequence ($seqID) in contig ".$self->id); return; } unless (exists( $self->{'_elem'}{$seqID}{'_feat'}{"_aligned_coord:$seqID"} )) { # $self->warn("Chad. Location not set for sequence ($seqID) in contig ".$self->id); return; } return $self->{'_elem'}{$seqID}{'_feat'}{"_aligned_coord:$seqID"}; } =head2 set_seq_coord Title : set_seq_coord Usage : $contig->set_seq_coord($feat,$seq); Function : Set "gapped consensus" location for an aligned sequence. If the sequence was previously added using add_seq, its coordinates are changed/set. Otherwise, add_seq is called and the sequence is added to the contig. Returns : Bio::SeqFeature::Generic for old coordinates or undef. Argument : $feat : a Bio::SeqFeature::Generic object representing a location for the aligned sequence, in "gapped consensus" coordinates. Note: the original feature primary tag will be lost. $seq : a Bio::LocatableSeq object =cut sub set_seq_coord { my ($self,$feat,$seq) = @_; if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) { $self->throw("Unable to process non locatable sequences [".ref($seq)."]"); } # Complaining about inadequate feature object $self->throw("Coordinates must be a Bio::SeqFeature::Generic object!") unless ( $feat->isa("Bio::SeqFeature::Generic") ); $self->throw("Sequence coordinates must have an end!") unless (defined $feat->end); $self->throw("Sequence coordinates must have a start!") unless (defined $feat->start); my $seqID = $seq->id() || $seq->display_id || $seq->primary_id; if ( exists( $self->{'_elem'}{$seqID} ) && exists( $self->{'_elem'}{$seqID}{'_seq'} ) && defined( $self->{'_elem'}{$seqID}{'_seq'} ) && ($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { $self->warn("Replacing sequence $seqID\n"); $self->remove_seq($self->{'_elem'}{$seqID}{'_seq'}); $self->remove_features($feat); } # Add new sequence and Bio::Generic::SeqFeature $self->add_seq($seq); $feat->add_tag_value('contig',$self->id) unless ( $feat->has_tag('contig') ); $feat->primary_tag("_aligned_coord"); $feat->source_tag($seqID); $feat->attach_seq($seq); $self->{'_elem'}{$seqID}{'_feat'}{"_aligned_coord:$seqID"} = $feat; $self->add_features([ $feat ]); } =head1 Bio::Assembly::Contig consensus methods =head2 set_consensus_sequence Title : set_consensus_sequence Usage : $contig->set_consensus_sequence($seq) Function : Set the consensus sequence object for this contig Returns : consensus length Argument : Bio::LocatableSeq =cut sub set_consensus_sequence { my $self = shift; my $seq = shift; $self->throw("Consensus sequence must be a Bio::LocatableSeq!") unless ($seq->isa("Bio::LocatableSeq")); $self->{'_consensus_gaps'} = []; # Consensus Gap registry $self->_register_gaps( $seq->seq, $self->{'_consensus_gaps'} ); $self->{'_consensus_sequence'} = $seq; $seq->start(1); $seq->end($seq->_ungapped_len); my $con_len = $seq->length; return $con_len; } =head2 set_consensus_quality Title : set_consensus_quality Usage : $contig->set_consensus_quality($qual) Function : Set the quality object for consensus sequence Returns : nothing Argument : Bio::Seq::QualI object =cut sub set_consensus_quality { my ($self, $qual) = @_; $self->throw("Consensus quality must be a Bio::Seq::QualI object!") unless ( $qual->isa("Bio::Seq::QualI") ); $self->throw("Consensus quality can't be added before you set the consensus sequence!") unless (defined $self->{'_consensus_sequence'}); $self->{'_consensus_quality'} = $qual; } =head2 get_consensus_length Title : get_consensus_length Usage : $contig->get_consensus_length() Function : Get consensus sequence length Returns : integer Argument : none =cut sub get_consensus_length { my $self = shift; return $self->{'_consensus_sequence'}->length(); } =head2 get_consensus_sequence Title : get_consensus_sequence Usage : $contig->get_consensus_sequence() Function : Get a reference to the consensus sequence object for this contig Returns : Bio::SeqI object Argument : none =cut sub get_consensus_sequence { my ($self, @args) = @_; return $self->{'_consensus_sequence'}; } =head2 get_consensus_quality Title : get_consensus_quality Usage : $contig->get_consensus_quality() Function : Get a reference to the consensus quality object for this contig. Returns : A Bio::Seq::QualI object Argument : none =cut sub get_consensus_quality { my ($self, @args) = @_; return $self->{'_consensus_quality'}; } =head1 Bio::Assembly::Contig aligned sequences methods =head2 set_seq_qual Title : set_seq_qual Usage : $contig->set_seq_qual($seq,$qual); Function : Adds quality to an aligned sequence. Returns : nothing Argument : a Bio::LocatableSeq object and a Bio::Seq::QualI object See L for more information. =cut sub set_seq_qual { my ($self,$seq,$qual) = @_; if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) { $self->throw("Unable to process non locatable sequences [".ref($seq)."]"); } my $seqID = $seq->id() || $seq->display_id || $seq->primary_id; $self->throw("Consensus quality must be a Bio::Seq::QualI object!") unless ( $qual->isa("Bio::Seq::QualI") ); $self->throw("Use add_seq first: aligned sequence qualities can't be added before you load the sequence!") unless (exists $self->{'_elem'}{$seqID}{'_seq'}); $self->throw("Use set_seq_coord first: aligned sequence qualities can't be added before you add coordinates for the sequence!") unless (defined( $self->get_seq_coord($seq) )); # Adding gaps to quality object my $sequence = $self->{'_elem'}{$seqID}{'_seq'}->seq(); my $tmp = $qual->qual(); @{$tmp} = reverse(@{$tmp}) if ($self->get_seq_coord($seq)->strand() == -1); my @quality = (); my $previous = 0; my $next = 0; my $i = 0; my $j = 0; while ($i <= $#{$tmp}) { # IF base is a gap, quality is the average for neighbouring sites if ($j > $i && substr($sequence,$j,1) eq '-') { $previous = $tmp->[$i-1] unless ($i == 0); if ($i < $#{$tmp}) { $next = $tmp->[$i+1]; } else { $next = 0; } push(@quality,int( ($previous+$next)/2 )); } else { push(@quality,$tmp->[$i]); $i++; } $j++; } $self->{'_elem'}{$seqID}{'_qual'} = Bio::Seq::PrimaryQual->new( -qual=>join(" ",@quality), -id=>$seqID ); } =head2 get_seq_ids Title : get_seq_ids Usage : $contig->get_seq_ids( -start => $start, -end => $end, -type => "gapped A0QR67B08.b" ); Function : Get list of sequence IDs overlapping interval [$start, $end] The default interval is [1,$contig->length] Default coordinate system is "gapped contig" Returns : An array Argument : A hash with optional elements: -start : consensus subsequence start -end : consensus subsequence end -type : the coordinate system type for $start and $end arguments Coordinate system available are: "gapped consensus" : consensus coordinates with gaps "ungapped consensus" : consensus coordinates without gaps "aligned $ReadID" : read $ReadID coordinates with gaps "unaligned $ReadID" : read $ReadID coordinates without gaps =cut sub get_seq_ids { my ($self, @args) = @_; my ($type, $start, $end) = $self->_rearrange([qw(TYPE START END)], @args); my @list; if (defined($start) && defined($end)) { if (defined($type) && ($type ne 'gapped consensus')) { $start = $self->change_coord($type,'gapped consensus',$start); $end = $self->change_coord($type,'gapped consensus',$end); } @list = $self->get_features_collection->features( -type => '_aligned_coord', # primary tag -start => $start, -end => $end, #-contain => 0, #-strandmatch => 'ignore', ); @list = map { $_->entire_seq->id } @list; } else { # Entire aligned sequences list @list = map { $self->{'_order'}{$_} } sort { $a cmp $b } keys %{ $self->{'_order'} }; } return @list; } =head2 get_seq_feat_by_tag Title : get_seq_feat_by_tag Usage : $seq = $contig->get_seq_feat_by_tag($seq,"_aligned_coord:$seqID") Function : Get a sequence feature based on its primary_tag. Returns : a Bio::SeqFeature object Argument : a Bio::LocatableSeq and a string (feature primary tag) =cut sub get_seq_feat_by_tag { my ($self,$seq,$tag) = @_; if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) { $self->throw("Unable to process non locatable sequences [".ref($seq)."]"); } my $seqID = $seq->id || $seq->display_id || $seq->primary_id; return $self->{'_elem'}{$seqID}{'_feat'}{$tag}; } =head2 get_seq_by_name Title : get_seq_by_name Usage : $seq = $contig->get_seq_by_name('Seq1') Function : Gets a sequence based on its id. Returns : a Bio::LocatableSeq object undef if name is not found Argument : string =cut sub get_seq_by_name { my $self = shift; my ($seqID) = @_; unless (exists $self->{'_elem'}{$seqID}{'_seq'}) { $self->throw("Could not find sequence $seqID in contig ".$self->id); return; } return $self->{'_elem'}{$seqID}{'_seq'}; } =head2 get_qual_by_name Title : get_qual_by_name Usage : $seq = $contig->get_qual_by_name('Seq1') Function : Gets Bio::Seq::QualI object for a sequence through its id ( as given by $qual->id() ). Returns : a Bio::Seq::QualI object. undef if name is not found Argument : string =cut sub get_qual_by_name { my $self = shift; my ($seqID) = @_; unless (exists $self->{'_elem'}{$seqID}{'_qual'}) { $self->warn("Could not find quality for $seqID in contig!"); return; } return $self->{'_elem'}{$seqID}{'_qual'}; } =head1 Bio::Align::AlignI compatible methods =head2 Modifier methods These methods modify the MSE by adding, removing or shuffling complete sequences. =head2 add_seq Title : add_seq Usage : $contig->add_seq($newseq); Function : Adds a sequence to the contig. *Does* *not* align it - just adds it to the hashes. Returns : nothing Argument : a Bio::LocatableSeq object See L for more information. =cut sub add_seq { my $self = shift; my $seq = shift; if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) { $self->throw("Unable to process non locatable sequences [".ref($seq)."]"); } my $seqID = $seq->id() || $seq->display_id || $seq->primary_id; $self->{'_elem'}{$seqID} = {} unless (exists $self->{'_elem'}{$seqID}); if (exists( $self->{'_elem'}{$seqID}{'_seq'} ) && ($seq eq $self->{'_elem'}{$seqID}{'_seq'}) ) { $self->warn("Adding sequence $seqID, which has already been added"); } # Our locatable sequences are always considered to be complete sequences $seq->start(1); $seq->end($seq->_ungapped_len); my $alphabet = $seq->alphabet; $alphabet = lc($alphabet) if defined $alphabet; $self->warn("Adding non-nucleotidic sequence ".$seqID) if (!$alphabet || ($alphabet ne 'dna' && $alphabet ne 'rna')); # build the symbol list for this sequence, # will prune out the gap and missing/match chars # when actually asked for the symbol list in the # symbol_chars if (defined $seq->seq) { map { $self->{'_symbols'}->{$_} = 1; } split(//,$seq->seq); } else { $self->{'_symbols'} = {}; } my $seq_no = ++$self->{'_nof_seqs'}; if (ref( $self->{'_elem'}{$seqID}{'_seq'} )) { $self->warn("Replacing one sequence [$seqID]\n"); } else { #print STDERR "Assigning $seqID to $order\n"; $self->{'_order'}->{$seq_no} = $seqID; # $self->{'_start_end_lists'}->{$id} = [] # unless(exists $self->{'_start_end_lists'}->{$id}); # push @{$self->{'_start_end_lists'}->{$id}}, $seq; } $self->{'_elem'}{$seqID}{'_seq'} = $seq; $self->{'_elem'}{$seqID}{'_feat'} = {}; $self->{'_elem'}{$seqID}{'_gaps'} = []; my $dbref = $self->{'_elem'}{$seqID}{'_gaps'}; my $nofgaps = $self->_register_gaps($seq->seq,$dbref); # Updating residue count $self->{'_nof_residues'} += $seq->length - $nofgaps; return 1; } =head2 remove_seq Title : remove_seq Usage : $contig->remove_seq($seq); Function : Removes a single sequence from a contig Returns : 1 on success, 0 otherwise Argument : a Bio::LocatableSeq object =cut sub remove_seq { my ($self,$seq) = @_; if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) { $self->throw("Unable to process non locatable sequences [".ref($seq)."]"); } my $seqID = $seq->id() || $seq->display_id || $seq->primary_id; unless (exists $self->{'_elem'}{$seqID} ) { $self->warn("No sequence named $seqID [$seq]"); return 0; } # Updating residue count $self->{'_nof_residues'} -= $seq->length() + &_nof_gaps( $self->{'_elem'}{$seqID}{'_gaps'}, $seq->length ); # Update number of sequences $self->{'_nof_seqs'}--; # Update order of sequences (order starts at 1) my $max_order = $self->{'_nof_seqs'} + 1; my $target_order = $max_order + 1; for (my $order = 1 ; $order <= $max_order ; $order++) { if ($self->{'_order'}->{$order} eq $seqID) { # Found the wanted sequence order $target_order = $order; } if ($order > $target_order) { # Decrement this sequence order by one order $self->{'_order'}->{$order-1} = $self->{'_order'}->{$order}; } if ($order == $max_order) { # Remove last order delete $self->{'_order'}->{$order}; } } # Remove all references to features of this sequence my @feats = (); for my $tag (keys %{ $self->{'_elem'}{$seqID}{'_feat'} }) { push(@feats, $self->{'_elem'}{$seqID}{'_feat'}{$tag}); } $self->{'_sfc'}->remove_features(\@feats); delete $self->{'_elem'}{$seqID}; return 1; } =head2 purge Title : purge Usage : $contig->purge(0.7); Function: Removes sequences above whatever %id. This function will grind on large alignments. Beware! (perhaps not ideally implemented) Example : Returns : An array of the removed sequences Argument: =cut sub purge { my ($self) = @_; $self->throw_not_implemented(); } =head2 sort_alphabetically Title : sort_alphabetically Usage : $contig->sort_alphabetically Function : Changes the order of the alignment to alphabetical on name followed by numerical by number. Returns : Argument : =cut sub sort_alphabetically { my ($self) = @_; $self->throw_not_implemented(); } =head2 Sequence selection methods Methods returning one or more sequences objects. =head2 each_seq Title : each_seq Usage : foreach $seq ( $contig->each_seq() ) Function : Gets an array of Seq objects from the alignment Returns : an array Argument : =cut sub each_seq { my ($self) = @_; my (@arr,$seqID); foreach $seqID ( map { $self->{'_order'}{$_} } sort { $a <=> $b } keys %{$self->{'_order'}} ) { push(@arr,$self->{'_elem'}{$seqID}{'_seq'}); } return @arr; } =head2 each_alphabetically Title : each_alphabetically Usage : foreach $seq ( $contig->each_alphabetically() ) Function : Returns an array of sequence object sorted alphabetically by name and then by start point. Does not change the order of the alignment Returns : Argument : =cut sub each_alphabetically { my($self) = @_; $self->throw_not_implemented(); } =head2 each_seq_with_id Title : each_seq_with_id Usage : foreach $seq ( $contig->each_seq_with_id() ) Function : Gets an array of Seq objects from the alignment, the contents being those sequences with the given name (there may be more than one) Returns : an array Argument : a seq name =cut sub each_seq_with_id { my ($self) = @_; $self->throw_not_implemented(); } =head2 get_seq_by_pos Title : get_seq_by_pos Usage : $seq = $contig->get_seq_by_pos(3) Function : Gets a sequence based on its position in the alignment. Numbering starts from 1. Sequence positions larger than num_sequences() will thow an error. Returns : a Bio::LocatableSeq object Argument : positive integer for the sequence osition =cut sub get_seq_by_pos { my $self = shift; my ($pos) = @_; $self->throw("Sequence position has to be a positive integer, not [$pos]") unless $pos =~ /^\d+$/ and $pos > 0; $self->throw("No sequence at position [$pos]") unless $pos <= $self->num_sequences ; my $seqID = $self->{'_order'}->{--$pos}; return $self->{'_elem'}{$seqID}{'_seq'}; } =head2 Create new alignments The result of these methods are horizontal or vertical subsets of the current MSE. =head2 select Title : select Usage : $contig2 = $contig->select(1, 3) # three first sequences Function : Creates a new alignment from a continuous subset of sequences. Numbering starts from 1. Sequence positions larger than num_sequences() will thow an error. Returns : a Bio::Assembly::Contig object Argument : positive integer for the first sequence positive integer for the last sequence to include (optional) =cut sub select { my ($self) = @_; $self->throw_not_implemented(); } =head2 select_noncont Title : select_noncont Usage : $contig2 = $contig->select_noncont(1, 3) # first and 3rd sequences Function : Creates a new alignment from a subset of sequences. Numbering starts from 1. Sequence positions larger than num_sequences() will throw an error. Returns : a Bio::Assembly::Contig object Args : array of integers for the sequences =cut sub select_noncont { my ($self) = @_; $self->throw_not_implemented(); } =head2 slice Title : slice Usage : $contig2 = $contig->slice(20, 30) Function : Creates a slice from the alignment inclusive of start and end columns. Sequences with no residues in the slice are excluded from the new alignment and a warning is printed. Slice beyond the length of the sequence does not do padding. Returns : a Bio::Assembly::Contig object Argument : positive integer for start column positive integer for end column =cut sub slice { my ($self) = @_; $self->throw_not_implemented(); } =head2 Change sequences within the MSE These methods affect characters in all sequences without changeing the alignment. =head2 map_chars Title : map_chars Usage : $contig->map_chars('\.','-') Function : Does a s/$arg1/$arg2/ on the sequences. Useful for gap characters Notice that the from (arg1) is interpretted as a regex, so be careful about quoting meta characters (eg $contig->map_chars('.','-') won't do what you want) Returns : Argument : 'from' rexexp 'to' string =cut sub map_chars { my ($self) = @_; $self->throw_not_implemented(); } =head2 uppercase Title : uppercase() Usage : $contig->uppercase() Function : Sets all the sequences to uppercase Returns : Argument : =cut sub uppercase { my ($self) = @_; $self->throw_not_implemented(); } =head2 match_line Title : match_line() Usage : $contig->match_line() Function : Generates a match line - much like consensus string except that a line indicating the '*' for a match. Argument : (optional) Match line characters ('*' by default) (optional) Strong match char (':' by default) (optional) Weak match char ('.' by default) =cut sub match_line { my ($self) = @_; $self->throw_not_implemented(); } =head2 match Title : match() Usage : $contig->match() Function : Goes through all columns and changes residues that are identical to residue in first sequence to match '.' character. Sets match_char. USE WITH CARE: Most MSE formats do not support match characters in sequences, so this is mostly for output only. NEXUS format (Bio::AlignIO::nexus) can handle it. Returns : 1 Argument : a match character, optional, defaults to '.' =cut sub match { my ($self) = @_; $self->throw_not_implemented(); } =head2 unmatch Title : unmatch() Usage : $contig->unmatch() Function : Undoes the effect of method match. Unsets match_char. Returns : 1 Argument : a match character, optional, defaults to '.' =cut sub unmatch { my ($self) = @_; $self->throw_not_implemented(); } =head2 MSE attibutes Methods for setting and reading the MSE attributes. Note that the methods defining character semantics depend on the user to set them sensibly. They are needed only by certain input/output methods. Unset them by setting to an empty string (''). =head2 id Title : id Usage : $contig->id("Ig") Function : Gets/sets the id field of the alignment Returns : An id string Argument : An id string (optional) =cut sub id { my ($self, $contig_name) = @_; if (defined( $contig_name )) { $self->{'_id'} = $contig_name; } return $self->{'_id'}; } =head2 missing_char Title : missing_char Usage : $contig->missing_char("?") Function : Gets/sets the missing_char attribute of the alignment It is generally recommended to set it to 'n' or 'N' for nucleotides and to 'X' for protein. Returns : An missing_char string, Argument : An missing_char string (optional) =cut sub missing_char { my ($self) = @_; $self->throw_not_implemented(); } =head2 match_char Title : match_char Usage : $contig->match_char('.') Function : Gets/sets the match_char attribute of the alignment Returns : An match_char string, Argument : An match_char string (optional) =cut sub match_char { my ($self) = @_; $self->throw_not_implemented(); } =head2 gap_char Title : gap_char Usage : $contig->gap_char('-') Function : Gets/sets the gap_char attribute of the alignment Returns : An gap_char string, defaults to '-' Argument : An gap_char string (optional) =cut sub gap_char { my ($self) = @_; $self->throw_not_implemented(); } =head2 symbol_chars Title : symbol_chars Usage : my @symbolchars = $contig->symbol_chars; Function: Returns all the seen symbols (other than gaps) Returns : array of characters that are the seen symbols Argument: boolean to include the gap/missing/match characters =cut sub symbol_chars{ my ($self) = @_; $self->throw_not_implemented(); } =head2 Alignment descriptors These read only methods describe the MSE in various ways. =head2 consensus_string Title : consensus_string Usage : $str = $contig->consensus_string($threshold_percent) Function : Makes a strict consensus Returns : Argument : Optional threshold ranging from 0 to 100. The consensus residue has to appear at least threshold % of the sequences at a given location, otherwise a '?' character will be placed at that location. (Default value = 0%) =cut sub consensus_string { my ($self) = @_; $self->throw_not_implemented(); } =head2 consensus_iupac Title : consensus_iupac Usage : $str = $contig->consensus_iupac() Function : Makes a consensus using IUPAC ambiguity codes from DNA and RNA. The output is in upper case except when gaps in a column force output to be in lower case. Note that if your alignment sequences contain a lot of IUPAC ambiquity codes you often have to manually set alphabet. Bio::PrimarySeq::_guess_type thinks they indicate a protein sequence. Returns : consensus string Argument : none Throws : on protein sequences =cut sub consensus_iupac { my ($self) = @_; $self->throw_not_implemented(); } =head2 is_flush Title : is_flush Usage : if( $contig->is_flush() ) : : Function : Tells you whether the alignment : is flush, ie all of the same length : : Returns : 1 or 0 Argument : =cut sub is_flush { my ($self) = @_; $self->throw_not_implemented(); } =head2 length Title : length() Usage : $len = $contig->length() Function : Returns the maximum length of the alignment. To be sure the alignment is a block, use is_flush Returns : Argument : =cut sub length { my ($self) = @_; $self->throw_not_implemented(); } =head2 maxname_length Title : maxname_length Usage : $contig->maxname_length() Function : Gets the maximum length of the displayname in the alignment. Used in writing out various MSE formats. Returns : integer Argument : =cut sub maxname_length { my ($self) = @_; $self->throw_not_implemented(); } =head2 num_residues Title : num_residues Usage : $no = $contig->num_residues Function : number of residues in total in the alignment Returns : integer Argument : Note : replaces no_residues =cut sub num_residues { my ($self) = @_; return $self->{'_nof_residues'}; } =head2 num_sequences Title : num_sequences Usage : $depth = $contig->num_sequences Function : number of sequence in the sequence alignment Returns : integer Argument : None Note : replaces no_sequences =cut sub num_sequences { my ($self) = @_; return scalar( keys %{ $self->{'_elem'} } ); } =head2 percentage_identity Title : percentage_identity Usage : $id = $contig->percentage_identity Function: The function calculates the percentage identity of the alignment Returns : The percentage identity of the alignment (as defined by the implementation) Argument: None =cut sub percentage_identity{ my ($self) = @_; $self->throw_not_implemented(); } =head2 overall_percentage_identity Title : percentage_identity Usage : $id = $contig->percentage_identity Function: The function calculates the percentage identity of the conserved columns Returns : The percentage identity of the conserved columns Args : None =cut sub overall_percentage_identity{ my ($self) = @_; $self->throw_not_implemented(); } =head2 average_percentage_identity Title : average_percentage_identity Usage : $id = $contig->average_percentage_identity Function: The function uses a fast method to calculate the average percentage identity of the alignment Returns : The average percentage identity of the alignment Args : None =cut sub average_percentage_identity { my ($self) = @_; $self->throw_not_implemented(); } =head2 Alignment positions Methods to map a sequence position into an alignment column and back. column_from_residue_number() does the former. The latter is really a property of the sequence object and can done using L: # select somehow a sequence from the alignment, e.g. my $seq = $contig->get_seq_by_pos(1); #$loc is undef or Bio::LocationI object my $loc = $seq->location_from_column(5); =head2 column_from_residue_number Title : column_from_residue_number Usage : $col = $contig->column_from_residue_number( $seqname, $resnumber) Function: This function gives the position in the alignment (i.e. column number) of the given residue number in the sequence with the given name. For example, for the alignment Seq1/91-97 AC..DEF.GH Seq2/24-30 ACGG.RTY.. Seq3/43-51 AC.DDEFGHI column_from_residue_number( "Seq1", 94 ) returns 5. column_from_residue_number( "Seq2", 25 ) returns 2. column_from_residue_number( "Seq3", 50 ) returns 9. An exception is thrown if the residue number would lie outside the length of the aligment (e.g. column_from_residue_number( "Seq2", 22 ) Note: If the the parent sequence is represented by more than one alignment sequence and the residue number is present in them, this method finds only the first one. Returns : A column number for the position in the alignment of the given residue in the given sequence (1 = first column) Args : A sequence id/name (not a name/start-end) A residue number in the whole sequence (not just that segment of it in the alignment) =cut sub column_from_residue_number { my ($self) = @_; $self->throw_not_implemented(); } =head2 Sequence names Methods to manipulate the display name. The default name based on the sequence id and subsequence positions can be overridden in various ways. =head2 displayname Title : displayname Usage : $contig->displayname("Ig", "IgA") Function : Gets/sets the display name of a sequence in the alignment : Returns : A display name string Argument : name of the sequence displayname of the sequence (optional) =cut sub displayname { # Do nothing } =head2 set_displayname_count Title : set_displayname_count Usage : $contig->set_displayname_count Function : Sets the names to be name_# where # is the number of times this name has been used. Returns : None Argument : None =cut sub set_displayname_count { my ($self) = @_; $self->throw_not_implemented(); } =head2 set_displayname_flat Title : set_displayname_flat Usage : $contig->set_displayname_flat() Function : Makes all the sequences be displayed as just their name, not name/start-end Returns : 1 Argument : None =cut sub set_displayname_flat { # Do nothing! } =head2 set_displayname_normal Title : set_displayname_normal Usage : $contig->set_displayname_normal() Function : Makes all the sequences be displayed as name/start-end Returns : None Argument : None =cut sub set_displayname_normal { # Do nothing! } =head1 Internal Methods =head2 _binary_search Title : _binary_search Usage : _binary_search($list,$query) Function : Find a number in a sorted list of numbers. Return values may be on or two integers. One positive integer or zero (>=0) is the index of the element that stores the queried value. Two positive integers (or zero and another number) are the indexes of elements among which the queried value should be placed. Negative single values mean: -1: $query is smaller than smallest element in list -2: $query is greater than greatest element in list Returns : array of integers Argument : $list : array reference $query : integer =cut sub _binary_search { my $list = shift; my $query = shift; # # If there is only one element in list if (!$#{$list} && ($query == $list->[0])) { return (0) } # If there are others... my $start = 0; my $end = $#{$list}; (&_compare($query,$list->[$start]) == 0) && do { return ($start) }; (&_compare($query,$list->[$end]) == 0) && do { return ($end) }; (&_compare($query,$list->[$start]) < 0) && do { return (-1) }; (&_compare($query,$list->[$end]) > 0) && do { return (-2) }; my $middle = 0; while ($end - $start > 1) { $middle = int(($end+$middle)/2); (&_compare($query,$list->[$middle]) == 0) && return ($middle); (&_compare($query,$list->[$middle]) < 0) && do { $end = $middle ; $middle = 0; next }; $start = $middle; # If &_compare() > 0, move region beggining } return ($start,$end); } =head2 _compare Title : _compare Usage : _compare($arg1,$arg2) Function: Perform numeric or string comparisons Returns : integer (0, 1 or -1) Args : values to be compared =cut sub _compare { my $arg1 = shift; my $arg2 = shift; # if (($arg1 =~ /^\d+$/) && ($arg2 =~ /^\d+$/)) { return $arg1 <=> $arg2 } else { return $arg1 cmp $arg2 } } =head2 _nof_gaps Title : _nof_gaps Usage : _nof_gaps($array_ref, $query) Function: number of gaps found before position $query Returns : integer Args : $array_ref : gap registry reference $query : [integer] a position in a sequence =cut #' emacs... sub _nof_gaps { my $list = shift; my $query = shift; # If there are no gaps in this contig return 0 unless (defined($list) && scalar(@{$list})); # Locate query index in gap list (if any) my @index = &_binary_search($list,$query); # If after all alignments, correct using total number of align if ($index[0] == -2) { $query = scalar(@{$list}) } # If before any alignment, return 0 elsif ($index[0] == -1) { $query = 0 } elsif ($index[0] >= 0) { # If query is between alignments, translate coordinates if ($#index > 0) { $query = $index[0] + 1 } # If query sits upon an alignment, do another correction elsif ($#index == 0) { $query = $index[0] } } # return $query; } =head2 _padded_unpadded Title : _padded_unpadded Usage : _padded_unpadded($array_ref, $query) Function: Returns a coordinate corresponding to position $query after gaps were removed from a sequence. Returns : integer Args : $array_ref : reference to this gap registry $query : [integer] coordionate to change =cut sub _padded_unpadded { my $list = shift; my $query = shift; my $align = &_nof_gaps($list,$query); $query-- if (defined($list->[$align]) && ($list->[$align] == $query)); $query = $query - $align; # return $query; } =head2 _unpadded_padded Title : _unpadded_padded Usage : _unpadded_padded($array_ref, $query) Function: Returns the value corresponding to ungapped position $query when gaps are counted as valid sites in a sequence Returns : Args : $array_ref = a reference to this sequence's gap registry $query = [integer] location to change =cut #' sub _unpadded_padded { my $list = shift; my $query = shift; my $align = &_nof_gaps($list,$query); $query = $query + $align; my $new_align = &_nof_gaps($list,$query); while ($new_align - $align > 0) { $query = $query + $new_align - $align; $align = $new_align; $new_align = &_nof_gaps($list,$query); } # If current position is also a align, look for the first upstream base while (defined($list->[$align]) && ($list->[$align] == $query)) { $query++; $align++; } # return $query; } =head2 _register_gaps Title : _register_gaps Usage : $self->_register_gaps($seq, $array_ref) Function: stores gap locations for a sequence Returns : number of gaps found Args : $seq : sequence string $array_ref : a reference to an array, where gap locations will be stored =cut sub _register_gaps { my $self = shift; my $sequence = shift; my $dbref = shift; $self->throw("Not an aligned sequence string to register gaps") if (ref($sequence)); $self->throw("Not an array reference for gap registry") unless (ref($dbref) eq 'ARRAY'); # Registering alignments @{$dbref} = (); # Cleaning registry if (defined $sequence) { my $i = -1; while(1) { $i = index($sequence,"-",$i+1); last if ($i == -1); push(@{$dbref},$i+1); } } else { # $self->warn("Found undefined sequence while registering gaps"); return 0; } return scalar(@{$dbref}); } =head1 Deprecated methods =cut =head2 no_residues Title : no_residues Usage : $no = $ali->no_residues Function : number of residues in total in the alignment Returns : integer Argument : Note : deprecated in favor of num_residues() =cut sub no_residues { my $self = shift; $self->deprecated(-warn_version => 1.0069, -throw_version => 1.0075); $self->num_residues(@_); } =head2 no_sequences Title : no_sequences Usage : $depth = $ali->no_sequences Function : number of sequence in the sequence alignment Returns : integer Argument : Note : deprecated in favor of num_sequences() =cut sub no_sequences { my $self = shift; $self->deprecated(-warn_version => 1.0069, -throw_version => 1.0075); $self->num_sequences(@_); } 1; BioPerl-1.007002/Bio/Assembly/ContigAnalysis.pm000444000766000024 4412713155576320 21320 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Assembly::ContigAnalysis # # Please direct questions and support issues to # # Cared for by Robson francisco de Souza # # Copyright Robson Francisco de Souza # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Assembly::ContigAnalysis - Perform analysis on sequence assembly contigs. =head1 SYNOPSIS # Module loading use Bio::Assembly::ContigAnalysis; # Assembly loading methods my $ca = Bio::Assembly::ContigAnalysis->new( -contig=>$contigOBJ ); my @lcq = $ca->low_consensus_quality; my @hqd = $ca->high_quality_discrepancies; my @ss = $ca->single_strand_regions; =head1 DESCRIPTION A contig is as a set of sequences, locally aligned to each other, when the sequences in a pair may be aligned. It may also include a consensus sequence. Bio::Assembly::ContigAnalysis is a module holding a collection of methods to analyze contig objects. It was developed around the Bio::Assembly::Contig implementation of contigs and can not work with another contig interface. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Robson Francisco de Souza Email: rfsouza@citri.iq.usp.br =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Assembly::ContigAnalysis; use strict; use base qw(Bio::Root::Root); =head1 Object creator =head2 new Title : new Usage : my $contig = Bio::Assembly::ContigAnalysis->new(-contig=>$contigOBJ); Function : Creates a new contig analysis object Returns : Bio::Assembly::ContigAnalysis Args : -contig : a Bio::Assembly::Contig object =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($contigOBJ) = $self->_rearrange([qw(CONTIG)],@args); unless ($contigOBJ->isa("Bio::Assembly::Contig")) { $self->throw("ContigAnal works only on Bio::Assembly::Contig objects\n"); } $self->{'_objref'} = $contigOBJ; return $self; } =head1 Analysis methods =head2 high_quality_discrepancies Title : high_quality_discrepancies Usage : my $sfc = $ContigAnal->high_quality_discrepancies(); Function : Locates all high quality discrepancies among aligned sequences and the consensus sequence. Note: see Bio::Assembly::Contig POD documentation, section "Coordinate System", for a definition of available types. Default coordinate system type is "gapped consensus", i.e. consensus sequence (with gaps) coordinates. If limits are not specified, the entire alignment is analyzed. Returns : Bio::SeqFeature::Collection Args : optional arguments are -threshold : cutoff value for low quality (minimum high quality) Default: 40 -ignore : number of bases that will not be analysed at both ends of contig aligned elements Default: 5 -start : start of interval that will be analyzed -end : start of interval that will be analyzed -type : coordinate system type for interval =cut sub high_quality_discrepancies { my ($self,@args) = shift; # Package reference my ($threshold,$ignore,$start,$end,$type) = $self->_rearrange([qw(THRESHOLD IGNORE START END TYPE)],@args); # Defining default threhold and HQD_ignore $threshold = 40 unless (defined($threshold)); $ignore = 5 unless (defined($ignore)); $type = 'gapped consensus' unless (defined($type)); # Changing input coordinates system (if needed) if (defined $start && $type ne 'gapped consensus') { $start = $self->{'_objref'}->change_coord($type,'gapped consensus',$start); } elsif (!defined $start) { $start = 1; } if (defined $end && $type ne 'gapped consensus') { $end = $self->{'_objref'}->change_coord($type,'gapped consensus',$end); } elsif (!defined $end) { $end = $self->{'_objref'}->get_consensus_length(); } # Scanning each read sequence and the contig sequence and # adding discrepancies to Bio::SeqFeature::Collection my @seqIDs = $self->{'_objref'}->get_seq_ids(-start=>$start, -end=>$end, -type=>$type); my $consensus = $self->{'_objref'}->get_consensus_sequence()->seq; my @HQD = (); foreach my $seqID (@seqIDs) { # Setting aligned read sub-sequence limits and loading data my $seq = $self->{'_objref'}->get_seq_by_name($seqID); my $qual = $self->{'_objref'}->get_qual_by_name($seqID); unless (defined $qual) { $self->warn("Can't correctly evaluate HQD without aligned sequence qualities for $seqID"); next; } my $sequence = $seq->seq; my @quality = @{ $qual->qual }; # Scanning the aligned region of each read my $seq_ix = 0; my $coord = $self->{'_objref'}->get_seq_feat_by_tag($seq,"_align_clipping:$seqID"); if (!$coord) { $self->warn("Read $seqID has no alignment coordinates; considered low quality.\nSkipping..."); next; } my ($astart,$aend) = ($coord->start,$coord->end); $astart = $astart + $ignore; # Redefining limits to evaluate HQDs (jump $ignore at start) $aend = $aend - $ignore; # Redefining limits to evaluate HQDs (stop $ignore before end) my ($d_start,$d_end,$i); for ($i=$astart-1; $i<=$aend-1; $i++) { # Changing coordinate $i+1 from 'gapped consensus' mode to "aligned $seqID" (coordinate $seq_ix) $seq_ix = $self->{'_objref'}->change_coord('gapped consensus',"aligned $seqID",$i+1); next unless (($i >= $start) && ($i <= $end)); my $r_base = uc(substr($sequence,$seq_ix-1,1)); my $c_base = uc(substr($consensus,$i,1)); # Discrepant region start: store $d_start and $type (!defined($d_start) && ($r_base ne $c_base) && ($quality[$seq_ix-1] >= $threshold)) && do { $d_start = $self->{'_objref'}->change_coord('gapped consensus','ungapped consensus',$i+1); #print $seqID," ",$r_base," ",$i+1," ",$c_base," ",$contig_ix-1," ",$quality[$i]," $type\n"; next; }; # Quality change or end of discrepant region: store limits and undef $d_start if (defined($d_start) && (($quality[$seq_ix-1] < $threshold) || (uc($r_base) eq uc($c_base)))) { $d_end = $self->{'_objref'}->change_coord('gapped consensus','ungapped consensus',$i); #print $seqID," ",$r_base," ",$i+1," ",$c_base," ",$contig_ix-1," ",$quality[$i]," $type\n"; push(@HQD, Bio::SeqFeature::Generic->new(-primary=>"high_quality_discrepancy:$seqID", -start=>$d_start, -end=>$d_end, -strand=>$seq->strand()) ); $d_start = undef; next; } } # for ($i=$astart-1; $i<=$aend-1; $i++) # Loading discrepancies located at sub-sequence end, if any. if (defined($d_start)) { $d_end = $self->{'_objref'}->change_coord('gapped consensus','ungapped consensus',$i); push(@HQD, Bio::SeqFeature::Generic->new(-primary=>"high_quality_discrepancy:$seqID", -start=>$d_start, -end=>$d_end, -strand=>$seq->strand()) ); } } # foreach my $seqID (@seqIDs) return @HQD; } =head2 low_consensus_quality Title : low_consensus_quality Usage : my $sfc = $ContigAnal->low_consensus_quality(); Function : Locates all low quality regions in the consensus Returns : an array of Bio::SeqFeature::Generic objects Args : optional arguments are -threshold : cutoff value for low quality (minimum high quality) Default: 25 -start : start of interval that will be analyzed -end : start of interval that will be analyzed -type : coordinate system type for interval =cut sub low_consensus_quality { my ($self,@args) = shift; # Packege reference my ($threshold,$start,$end,$type) = $self->_rearrange([qw(THRESHOLD START END TYPE)],@args); # Setting default value for threshold $threshold = 25 unless (defined($threshold)); # Loading qualities my @quality = @{ $self->{'_objref'}->get_consensus_quality()->qual }; # Changing coordinates to gap mode noaln (consed: consensus without alignments) $start = 1 unless (defined($start)); if (defined $start && defined $type && ($type ne 'gapped consensus')) { $start = $self->{'objref'}->change_coord($type,'gapped consensus',$start); $end = $self->{'objref'}->change_coord($type,'gapped consensus',$end) if (defined($end)); } $end = $self->{'_objref'}->get_consensus_length unless (defined $end); # Scanning @quality vector and storing intervals limits with base qualities less then # the threshold value my ($lcq_start); my ($i,@LCQ); for ($i=$start-1; $i<=$end-1; $i++) { # print $quality[$i],"\t",$i,"\n"; if (!defined($lcq_start) && (($quality[$i] <= $threshold) || ($quality[$i] == 98))) { $lcq_start = $i+1; } elsif (defined($lcq_start) && ($quality[$i] > $threshold)) { $lcq_start = $self->{'_objref'}->change_coord('gapped consensus','ungapped consensus',$lcq_start); my $lcq_end = $self->{'_objref'}->change_coord('gapped consensus','ungapped consensus',$i); push(@LCQ, Bio::SeqFeature::Generic->new(-start=>$lcq_start, -end=>$lcq_end, -primary=>'low_consensus_quality') ); $lcq_start = undef; } } if (defined $lcq_start) { $lcq_start = $self->{'_objref'}->change_coord('gapped consensus','ungapped consensus',$lcq_start); my $lcq_end = $self->{'_objref'}->change_coord('gapped consensus','ungapped consensus',$i); push(@LCQ, Bio::SeqFeature::Generic->new(-start=>$lcq_start, -end=>$lcq_end, -primary=>'low_consensus_quality') ); } return @LCQ; } =head2 not_confirmed_on_both_strands Title : low_quality_consensus Usage : my $sfc = $ContigAnal->low_quality_consensus(); Function : Locates all regions whose consensus bases were not confirmed by bases from sequences aligned in both orientations, i.e., in such regions, no bases in aligned sequences of either +1 or -1 strand agree with the consensus bases. Returns : an array of Bio::SeqFeature::Generic objects Args : optional arguments are -start : start of interval that will be analyzed -end : start of interval that will be analyzed -type : coordinate system type for interval =cut sub not_confirmed_on_both_strands { my ($self,@args) = shift; # Package reference my ($start,$end,$type) = $self->_rearrange([qw(START END TYPE)],@args); # Changing coordinates to default system 'align' (contig sequence with alignments) $start = 1 unless (defined($start)); if (defined($type) && ($type ne 'gapped consensus')) { $start = $self->{'_objref'}->change_coord($type,'gapped consensus',$start); $end = $self->{'_objref'}->change_coord($type,'gapped consensus',$end) if (defined($end)); } $end = $self->{'_objref'}->get_consensus_length unless (defined($end)); # Scanning alignment my %confirmed = (); # If ($confirmed{$orientation}[$i] > 0) then $i is confirmed in $orientation strand my ($i); my $consensus = $self->{'_objref'}->get_consensus_sequence()->seq; foreach my $seqID ($self->{'_objref'}->get_seq_ids) { # Setting aligned read sub-sequence limits and loading data my $seq = $self->{'_objref'}->get_seq_by_name($seqID); my $sequence = $seq->seq; # Scanning the aligned regions of each read and registering confirmed sites my $contig_ix = 0; my $coord = $self->{'_objref'}->get_seq_feat_by_tag($seq,"_align_clipping:$seqID"); my ($astart,$aend,$orientation) = ($coord->start,$coord->end,$coord->strand); $astart = $self->{'_objref'}->change_coord('gapped consensus',"aligned $seqID",$astart); $aend = $self->{'_objref'}->change_coord('gapped consensus',"aligned $seqID",$aend); for ($i=$astart-1; $i<=$aend-1; $i++) { # $i+1 in 'align' mode is $contig_ix $contig_ix = $self->{'_objref'}->change_coord("aligned $seqID",'gapped consensus',$i+1); next unless (($contig_ix >= $start) && ($contig_ix <= $end)); my $r_base = uc(substr($sequence,$i,1)); my $c_base = uc(substr($consensus,$contig_ix-1,1)); if ($c_base eq '-') { $confirmed{$orientation}[$contig_ix] = -1; } elsif (uc($r_base) eq uc($c_base)) { # Non discrepant region found $confirmed{$orientation}[$contig_ix]++; } } # for ($i=$astart-1; $i<=$aend-1; $i++) } # foreach $seqID (@reads) # Locating non-confirmed aligned regions for each orientation in $confirmed registry my ($orientation); my @NCBS = (); foreach $orientation (keys %confirmed) { my ($ncbs_start,$ncbs_end); for ($i=$start; $i<=$end; $i++) { if (!defined($ncbs_start) && (!defined($confirmed{$orientation}[$i]) || ($confirmed{$orientation}[$i] == 0))) { $ncbs_start = $self->{'_objref'}->change_coord('gapped consensus','ungapped consensus',$i); } elsif (defined($ncbs_start) && defined($confirmed{$orientation}[$i]) && ($confirmed{$orientation}[$i] > 0)) { $ncbs_end = $self->{'_objref'}->change_coord('gapped consensus','ungapped consensus',$i-1); push(@NCBS, Bio::SeqFeature::Generic->new(-start=>$ncbs_start, -end=>$ncbs_end, -strand=>$orientation, -primary=>"not_confirmed_on_both_strands") ); $ncbs_start = undef; } } if (defined($ncbs_start)) { # NCBS at the end of contig $ncbs_end = $self->{'_objref'}->change_coord('gapped consensus','ungapped consensus',$end); push(@NCBS, Bio::SeqFeature::Generic->new(-start=>$ncbs_start, -end=>$ncbs_end, -strand=>$orientation, -primary=>'not_confirmed_on_both_strands') ); } } return @NCBS; } =head2 single_strand Title : single_strand Usage : my $sfc = $ContigAnal->single_strand(); Function : Locates all regions covered by aligned sequences only in one of the two strands, i.e., regions for which aligned sequence's strand() method returns +1 or -1 for all sequences. Returns : an array of Bio::SeqFeature::Generic objects Args : optional arguments are -start : start of interval that will be analyzed -end : start of interval that will be analyzed -type : coordinate system type for interval =cut #' sub single_strand { my ($self,@args) = shift; # Package reference my ($start,$end,$type) = $self->_rearrange([qw(START END TYPE)],@args); # Changing coordinates to gap mode align (consed: consensus sequence with alignments) $type = 'gapped consensus' unless(defined($type)); $start = 1 unless (defined($start)); if (defined($type) && $type ne 'gapped consensus') { $start = $self->{'objref'}->change_coord($type,'gapped consensus',$start); $end = $self->{'objref'}->change_coord($type,'gapped consensus',$end) if (defined($end)); } ($end) = $self->{'_objref'}->get_consensus_length unless (defined($end)); # Loading complete list of coordinates for aligned sequences my $sfc = $self->{'_objref'}->get_features_collection(); my @forward = grep { $_->primary_tag =~ /^_aligned_coord:/ } $sfc->features_in_range(-start=>$start, -end=>$end, -contain=>0, -strand=>1, -strandmatch=>'strong'); my @reverse = grep { $_->primary_tag =~ /^_aligned_coord:/ } $sfc->features_in_range(-start=>$start, -end=>$end, -contain=>0, -strand=>-1, -strandmatch=>'strong'); # Merging overlapping features @forward = $self->_merge_overlapping_features(@forward); @reverse = $self->_merge_overlapping_features(@reverse); # Finding single stranded regions my ($length) = $self->{'_objref'}->get_consensus_length; $length = $self->{'_objref'}->change_coord('gapped consensus','ungapped consensus',$length); @forward = $self->_complementary_features_list(1,$length,@forward); @reverse = $self->_complementary_features_list(1,$length,@reverse); my @SS = (); foreach my $feat (@forward, @reverse) { $feat->primary_tag('single_strand_region'); push(@SS,$feat); } return @SS; } =head1 Internal Methods =head2 _merge_overlapping_features Title : _merge_overlapping_features Usage : my @feat = $ContigAnal->_merge_overlapping_features(@features); Function : Merge all overlapping features into features that hold original features as sub-features Returns : array of Bio::SeqFeature::Generic objects Args : array of Bio::SeqFeature::Generic objects =cut sub _merge_overlapping_features { my ($self,@feat) = @_; $self->throw_not_implemented(); } =head2 _complementary_features_list Title : _complementary_features_list Usage : @feat = $ContigAnal->_complementary_features_list($start,$end,@features); Function : Build a list of features for regions not covered by features in @features array Returns : array of Bio::SeqFeature::Generic objects Args : $start : [integer] start of first output feature $end : [integer] end of last output feature @features : array of Bio::SeqFeature::Generic objects =cut sub _complementary_features_list { my ($self,$start,$end,@feat) = @_; $self->throw_not_implemented(); } 1; __END__ BioPerl-1.007002/Bio/Assembly/IO.pm000444000766000024 2273613155576320 16702 0ustar00cjfieldsstaff000000000000# $Id: IO.pm 16690 2010-01-14 07:27:29Z kortsch $ # # BioPerl module for Bio::Assembly::IO # # based on the Bio::SeqIO module # by Ewan Birney # and Lincoln Stein # # Copyright Robson Francisco de Souza # # You may distribute this module under the same terms as perl itself # # _history # POD documentation - main docs before the code =head1 NAME Bio::Assembly::IO - Handler for Assembly::IO Formats =head1 SYNOPSIS use Bio::Assembly::IO; $in = Bio::Assembly::IO->new(-file=>"'phrap'); $out = Bio::Assembly::IO->new(-file=>">outputfilename", -format=>'phrap'); while ( my $scaffold = $in->next_assembly() ) { # do something with Bio::Assembly::Scaffold instance # ... $out->write_assembly(-scaffold => $scaffold); } $in->close; $out->close; =head1 DESCRIPTION Bio::Assembly::IO is a handler module for formats in the Assembly::IO set (e.g. Bio::Assembly::IO::phrap). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Robson Francisco de Souza E-mail: rfsouza@citri.iq.usp.br =head1 CONTRIBUTORS # =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Assembly::IO; use strict; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : $stream = Bio::Assembly::IO->new( -file => $filename, -format =>'format' ) Function: Returns a new assembly stream Returns : A Bio::Assembly::IO::Handler initialised with the appropriate format Args : -file => $filename -format => format =cut sub new { my ($caller,@args) = @_; my $class = ref($caller) || $caller; # or do we want to call SUPER on an object if $caller is an # object? if( $class =~ /Bio::Assembly::IO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys $class->throw("Need at least a file name to proceed!") unless (defined $param{'-file'} || defined $ARGV[0]); my $format = $param{'-format'} || $class->_guess_format( $param{-file} || $ARGV[0] ); $format = "\L$format"; # normalize capitalization to lower case if ($format =~ /-/) { ($format, my $variant) = split('-', $format, 2); push @args, (-variant => $variant); } return unless( $class->_load_format_module($format) ); return "Bio::Assembly::IO::$format"->new(@args); } } =head2 format Title : format Usage : $format = $stream->format() Function: Get the assembly format Returns : assembly format Args : none =cut # format() method inherited from Bio::Root::IO # _initialize is chained for all SeqIO classes sub _initialize { my($self, @args) = @_; # initialize the IO part $self->_initialize_io(@args); } =head2 next_assembly Title : next_assembly Usage : $scaffold = $stream->next_assembly() Function: Reads the next assembly object from the stream and returns it. Returns : a Bio::Assembly::ScaffoldI compliant object Args : none =cut sub next_assembly { my ($self) = @_; $self->throw("Cannot read from a generic Bio::Assembly::IO object."); } =head2 next_contig Title : next_contig Usage : $contig = $stream->next_contig() Function: Reads the next contig or singlet from the stream and returns it. Returns : a Bio::Assembly::Contig or Bio::Contig::Assembly::Singlet Args : none =cut sub next_contig { my ($self) = @_; $self->throw("Cannot read from a generic Bio::Assembly::IO object."); } =head2 write_assembly Title : write_assembly Usage : $stream->write_assembly($assembly) Function: Write the assembly object in desired format. This method calls write_header(), write_contigs() and write_footer() internally. Returns : 1 on success, 0 for error Args : A Bio::Assembly::Scaffold object =cut sub write_assembly { my ($self, @args) = @_; my ($scaf, $write_singlets) = $self->_rearrange([qw(SCAFFOLD SINGLETS)], @args); # Sanity check if ( !$scaf || !$scaf->isa('Bio::Assembly::ScaffoldI') ) { $self->throw("Must provide a Bio::Assembly::Scaffold object when calling write_assembly"); } # Write header $self->write_header($scaf); # ID-sorted contig and read entries my @contig_ids = $scaf->get_contig_ids; if ($write_singlets) { push @contig_ids, $scaf->get_singlet_ids; } @contig_ids = _sort(@contig_ids); # Write contigs for my $contig_id ( @contig_ids ) { my $contig = $scaf->get_contig_by_id($contig_id) || $scaf->get_singlet_by_id($contig_id); $self->write_contig($contig); } # Write footer $self->write_footer($scaf); return 1; } =head2 write_header Title : write_header Usage : $stream->write_header($assembly) Function: Write the start of the assembly file. It can be called at any time, not when starting to write the assembly file. Returns : 1 on success, 0 for error Args : A Bio::Assembly::Scaffold object or ... (check the specific format driver for more details) =cut sub write_header { my ($self) = @_; $self->throw("Cannot write from a generic Bio::Assembly::IO object."); } =head2 write_contig Title : write_contig Usage : $stream->write_contig($contig) Function: Write a contig object in the desired format. Returns : 1 on success, 0 for error Args : A Bio::Assembly::Contig object =cut sub write_contig { my ($self) = @_; $self->throw("Cannot write from a generic Bio::Assembly::IO object."); } =head2 write_footer Title : write_footer Usage : $stream->write_footer($assembly) Function: Write the start of the assembly file. Returns : 1 on success, 0 for error Args : A Bio::Assembly::Scaffold object or ... (check the specific format driver for more details) =cut sub write_footer { my ($self) = @_; $self->throw("Cannot write from a generic Bio::Assembly::IO object."); } =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL Assembly::IO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($self,$format) = @_; my $module = "Bio::Assembly::IO::" . $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <_guess_format($filename) Function: guess format based on file suffix Example : Returns : guessed format of filename (lower case) Args : Notes : formats that _filehandle() will guess includes ace, phrap and tigr at the moment =cut sub _guess_format { my $class = shift; my $arg = shift; return unless defined($arg); return 'ace' if ($arg =~ /\.ace/i); return 'phrap' if ($arg =~ /\.phrap/i); return 'tigr' if ($arg =~ /\.tigr/i); return 'maq' if ($arg =~ /\.maq/i); return 'sam' if ($arg =~ /\.[bs]am/i); return 'bowtie' if ($arg =~ /\.bowtie/i); } =head2 _sort Title : _sort Usage : @sorted_values = $ass_io->_sort(@values) Function: Sort a list of values naturally if Sort::Naturally is installed (nicer), lexically otherwise (not as nice, but safe) Returns : array of sorted values Args : array of values to sort =cut sub _sort { my @arr = @_; my @sorted_arr; if (eval { require Sort::Naturally }) { @sorted_arr = Sort::Naturally::nsort( @arr ); # natural sort (better) } else { @sorted_arr = sort @arr; # lexical sort (safe) } return @sorted_arr; } sub DESTROY { my $self = shift; $self->close(); } # I need some direction on these!! The module works so I haven't fiddled with them! # Me neither! (rfsouza) sub TIEHANDLE { my ($class,$val) = @_; return bless {'seqio' => $val}, $class; } sub READLINE { my $self = shift; return $self->{'seqio'}->next_seq() || undef unless wantarray; my (@list, $obj); push @list, $obj while $obj = $self->{'seqio'}->next_seq(); return @list; } sub PRINT { my $self = shift; $self->{'seqio'}->write_seq(@_); } 1; BioPerl-1.007002/Bio/Assembly/Scaffold.pm000444000766000024 4452113155576320 20110 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Assembly::Scaffold # # Copyright by Robson F. de Souza # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Assembly::Scaffold - Perl module to hold and manipulate sequence assembly data. =head1 SYNOPSIS # # Module loading use Bio::Assembly::IO; # Assembly loading methods my $aio = Bio::Assembly::IO->new(-file=>"test.ace.1", -format=>'phrap'); my $assembly = $aio->next_assembly; foreach my $contig ($assembly->all_contigs) { # do something... (see Bio::Assembly::Contig) } =head1 DESCRIPTION Bio::Assembly::Scaffold was developed to store and manipulate data from sequence assembly programs like Phrap. It implements the ScaffoldI interface and intends to be generic enough to be used by Bio::Assembly::IO drivers written to programs other than Phrap. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Robson Francisco de Souza rfsouza@citri.iq.usp.br =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Assembly::Scaffold; use strict; use Bio::Annotation::Collection; use base qw(Bio::Root::Root Bio::Assembly::ScaffoldI); =head2 new () Title : new Usage : $scaffold = new ( -id => "assembly 1", -source => 'program_name', -contigs => \@contigs, -singlets => \@singlets ); Function: creates a new scaffold object Returns : Bio::Assembly::Scaffold Args : -id : [string] scaffold name -source : [string] sequence assembly program -contigs : reference to array of Bio::Assembly::Contig objects -singlets : reference to array of Bio::Assembly::Singlet objects =cut sub new { my($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($id, $src, $contigs, $singlets) = $self->_rearrange( [qw(ID SOURCE CONTIGS SINGLETS)], @args); # Scaffold defaults $self->{'_id'} = 'NoName'; $self->{'_source'} = 'Unknown'; $self->{'_contigs'} = {}; $self->{'_singlets'} = {}; $self->{'_seqs'} = {}; $self->{'_annotation'} = Bio::Annotation::Collection->new(); # Import manual info $self->{'_id'} = $id if (defined $id); $self->{'_source'} = $src if (defined $src); # Add contigs and singlets to scaffold if (defined $contigs && ref($contigs = 'ARRAY')) { for my $contig (@{$contigs}) { if( ! ref $contig || ! $contig->isa('Bio::Assembly::Contig') ) { $self->throw("Bio::Assembly::Scaffold::new is unable to process non". "Bio::Assembly::Contig object [", ref($contig), "]"); } $self->add_contig($contig); } } if (defined $singlets && ref($singlets = 'ARRAY')) { for my $singlet (@{$singlets}) { if( ! ref $singlet || ! $singlet->isa('Bio::Assembly::Singlet') ) { $self->throw("Bio::Assembly::Scaffold::new is unable to process non". "Bio::Assembly::Singlet object [", ref($singlet), "]"); } $self->add_singlet($singlet); } } return $self; } =head1 Accessing general assembly data =cut =head2 id Title : id Usage : $assembly->id() Function: Get/Set assembly ID Returns : string or undef Args : string =cut sub id { my ($self, $id) = @_; return $self->{'_id'} = $id if (defined $id); return $self->{'_id'}; } =head2 annotation Title : annotation Usage : $assembly->annotation() Function: Get/Set assembly annotation object Returns : Bio::Annotation::Collection Args : none =cut sub annotation { my ($self, $ref) = shift; $self->{'_annotation'} = $ref if (defined $ref); return $self->{'_annotation'}; } =head2 get_nof_contigs Title : get_nof_contigs Usage : $assembly->get_nof_contigs() Function: Get the number of contigs included in the scaffold Returns : integer Args : none =cut sub get_nof_contigs { my $self = shift; return scalar( $self->get_contig_ids() ); } =head2 get_nof_contig_seqs Title : get_nof_contig_seqs Usage : $assembly->get_nof_contig_seqs() Function: Get the number of sequences included in contigs of the scaffold (no consensus sequences or singlets) Returns : integer Args : none =cut sub get_nof_contig_seqs { my $self = shift; my $nof_seqs = 0; foreach my $contig ($self->all_contigs) { $nof_seqs += scalar( $contig->get_seq_ids() ); } return $nof_seqs; } # function alias for backward compatibility *get_nof_sequences_in_contigs = \&get_nof_contig_seqs; =head2 get_nof_singlets (get_nof_singlet_seqs) Title : nof_singlets Usage : $assembly->nof_singlets() Function: Get the number of singlets included in the assembly Returns : integer Args : none =cut sub get_nof_singlets { my $self = shift; return scalar( $self->get_singlet_ids() ); } *get_nof_singlet_seqs = \&get_nof_singlets; =head2 get_all_seq_ids Title : get_all_seq_ids Usage : $assembly->get_all_seq_ids() Function: Get the ID of all sequences making up the scaffold (sequences from contigs and singlets, not consensus). Returns : array of strings Args : none =cut sub get_all_seq_ids { my $self = shift; return keys %{ $self->{'_seqs'} }; } =head2 get_nof_seqs Title : get_nof_seqs Usage : $assembly->get_nof_seqs() Function: Get total number of sequences making up the scaffold (sequences from contigs and singlets, not consensus). Returns : integer Args : none =cut sub get_nof_seqs { my $self = shift; return scalar $self->get_all_seq_ids; } =head2 get_contig_seq_ids Title : get_contig_seq_ids Usage : $assembly->get_contig_seq_ids() Function: Get the ID of all sequences in contigs Returns : array of strings Args : none =cut sub get_contig_seq_ids { my $self = shift; my @ids; for my $contig ( $self->all_contigs ) { push @ids, $contig->get_seq_ids; } return @ids; } # function alias for backward compatibility *get_seq_ids = \&get_contig_seq_ids; =head2 get_contig_ids Title : get_contig_ids Usage : $assembly->get_contig_ids() Function: Access list of contig IDs from assembly Returns : an array, if there are any contigs in the assembly. An empty array otherwise Args : none =cut sub get_contig_ids { my $self = shift; return wantarray ? sort keys %{$self->{'_contigs'}} : scalar keys %{$self->{'_contigs'}}; } =head2 get_singlet_ids (get_singlet_seq_ids) Title : get_singlet_ids Usage : $assembly->get_singlet_ids() Function: Access list of singlet IDs from assembly Returns : array of strings if there are any singlets otherwise an empty array Args : none =cut sub get_singlet_ids { my $self = shift; return wantarray ? sort keys %{$self->{'_singlets'}} : scalar keys %{$self->{'_singlets'}}; } *get_singlet_seq_ids = \&get_singlet_ids; =head2 get_seq_by_id Title : get_seq_by_id Usage : $assembly->get_seq_by_id($id) Function: Get a reference for an sequence making up the scaffold (from a contig or singlet, not consensus) Returns : a Bio::LocatableSeq object undef if sequence $id is not found in the scaffold Args : [string] sequence identifier (id) =cut sub get_seq_by_id { my $self = shift; my $seqID = shift; return unless (exists $self->{'_seqs'}{$seqID}); return $self->{'_seqs'}{$seqID}->get_seq_by_name($seqID); } =head2 get_contig_by_id Title : get_contig_by_id Usage : $assembly->get_contig_by_id($id) Function: Get a reference for a contig Returns : a Bio::Assembly::Contig object or undef Args : [string] contig unique identifier (ID) =cut sub get_contig_by_id { my $self = shift; my $contigID = shift; return unless (exists $self->{'_contigs'}{$contigID}); return $self->{'_contigs'}{$contigID}; } =head2 get_singlet_by_id Title : get_singlet_by_id Usage : $assembly->get_singlet_by_id() Function: Get a reference for a singlet Returns : Bio::Assembly::Singlet object or undef Args : [string] a singlet ID =cut sub get_singlet_by_id { my $self = shift; my $singletID = shift; return unless (exists $self->{'_singlets'}{$singletID}); return $self->{'_singlets'}{$singletID}; } =head1 Modifier methods =cut =head2 add_contig Title : add_contig Usage : $assembly->add_contig($contig) Function: Add a contig to the assembly Returns : 1 on success Args : a Bio::Assembly::Contig object order (optional) =cut sub add_contig { my ($self, $contig) = @_; # Input check if( !ref $contig || ! $contig->isa('Bio::Assembly::Contig') ) { $self->throw("Bio::Assembly::Scaffold::add_contig is unable to process". " non Bio::Assembly::Contig object [", ref($contig), "]"); } # Create and attribute contig ID my $contigID = $contig->id(); if( !defined $contigID ) { $contigID = 'Unknown_' . ($self->get_nof_contigs() + 1); $contig->id($contigID); $self->warn("Attributing ID $contigID to unnamed Bio::Assembly::Contig". " object."); } # Adding contig to scaffold $self->warn("Replacing contig $contigID with a new contig object") if (exists $self->{'_contigs'}{$contigID}); $self->{'_contigs'}{$contigID} = $contig; $contig->assembly($self); # weak circular reference # Put contig sequences in the list of sequences belonging to the scaffold foreach my $seqID ($contig->get_seq_ids()) { if (exists $self->{'_seqs'}{$seqID} && not($self->{'_seqs'}{$seqID} eq $contig) ) { $self->warn( "Sequence $seqID already assigned to object ". $self->{'_seqs'}{$seqID}->id().". Moving to contig $contigID"); } $self->{'_seqs'}{$seqID} = $contig; } return 1; } =head2 add_singlet Title : add_singlet Usage : $assembly->add_singlet($seq) Function: Add a singlet to the assembly Returns : 1 on success Args : a Bio::Assembly::Singlet object order (optional) =cut sub add_singlet { my ($self, $singlet) = @_; # Input check if ( !ref $singlet || ! $singlet->isa('Bio::Assembly::Singlet') ) { $self->throw("Bio::Assembly::Scaffold::add_singlet is unable to process". " non Bio::Assembly::Singlet object [", ref($singlet), "]"); } # Create and attribute singlet ID my $singletID = $singlet->id(); if( !defined $singletID ) { $singletID = 'Unknown_' . ($self->get_nof_singlets() + 1); $singlet->id($singletID); $self->warn("Attributing ID $singletID to unnamed Bio::Assembly::". "Singlet object."); } # Adding singlet to scaffold $self->warn("Replacing singlet $singletID with a new singlet object") if (exists $self->{'_singlets'}{$singletID}); $self->{'_singlets'}{$singletID} = $singlet; $singlet->assembly($self); # weak circular reference # Put singlet sequence in the list of sequences belonging to the scaffold my $seqID = $singlet->seqref->id(); if (exists $self->{'_seqs'}{$seqID} && not($self->{'_seqs'}{$seqID} eq $singlet) ) { $self->warn( "Sequence $seqID already assigned to object ". $self->{'_seqs'}{$seqID}->id().". Moving to singlet $singletID"); } $self->{'_seqs'}{$seqID} = $singlet; return 1; } =head2 update_seq_list Title : update_seq_list Usage : $assembly->update_seq_list() Function: Synchronizes the assembly registry for sequences in contigs and contig actual aligned sequences content. You probably want to run this after you remove/add a sequence from/to a contig in the assembly. Returns : 1 for success Args : none =cut sub update_seq_list { my $self = shift; $self->{'_seqs'} = {}; # Put sequences in contigs in list of sequences belonging to the scaffold foreach my $contig ($self->all_contigs) { my $contigID = $contig->id(); foreach my $seqID ($contig->get_seq_ids) { if (exists $self->{'_seqs'}{$seqID} && not($self->{'_seqs'}{$seqID} eq $contig) ) { $self->warn( "Sequence $seqID already assigned to object ". $self->{'_seqs'}{$seqID}->id().". Moving to contig $contigID"); } $self->{'_seqs'}{$seqID} = $contig; } } # Put singlet sequences in the list of sequences belonging to the scaffold foreach my $singlet ($self->all_singlets) { my $singletID = $singlet->id(); my $seqID = $singlet->seqref->id(); if (exists $self->{'_seqs'}{$seqID} && not($self->{'_seqs'}{$seqID} eq $singlet) ) { $self->warn( "Sequence $seqID already assigned to object ". $self->{'_seqs'}{$seqID}->id().". Moving to singlet $singletID"); } $self->{'_seqs'}{$seqID} = $singlet; } return 1; } =head2 remove_contigs Title : remove_contigs Usage : $assembly->remove_contigs(1..4) Function: Remove contig from assembly object Returns : an array of removed Bio::Assembly::Contig objects Args : an array of contig IDs See function get_contig_ids() above =cut sub remove_contigs { my ($self, @args) = @_; my @ret = (); foreach my $contigID (@args) { foreach my $seqID ($self->get_contig_by_id($contigID)->get_seq_ids()) { delete $self->{'_seqs'}{$seqID}; } push(@ret, $self->{'_contigs'}{$contigID}); delete $self->{'_contigs'}{$contigID}; } return @ret; } =head2 remove_singlets Title : remove_singlets Usage : $assembly->remove_singlets(@singlet_ids) Function: Remove singlet from assembly object Returns : the Bio::Assembly::Singlet objects removed Args : a list of singlet IDs See function get_singlet_ids() above =cut sub remove_singlets { my ($self,@args) = @_; my @ret = (); foreach my $singletID (@args) { push(@ret,$self->{'_singlets'}{$singletID}); delete $self->{'_singlets'}{$singletID}; } return @ret; } =head2 remove_features_collection Title : remove_features_collection Usage : $assembly->remove_features_collection() Function: Removes the collection of features associated to every contig and singlet of the scaffold. This can be useful to save some memory (when contig and singlet features are not needed). Returns : none Argument : none =cut sub remove_features_collection { my ($self) = @_; for my $obj ( $self->all_contigs, $self->all_singlets ) { $obj->remove_features_collection; } return; } =head1 Contig and singlet selection methods =cut =head2 select_contigs Title : select_contigs Usage : $assembly->select_contigs(@list) Function: Select an array of contigs from the assembly Returns : an array of Bio::Assembly::Contig objects Args : an array of contig ids See function get_contig_ids() above =cut sub select_contigs { my ($self,@args) = @_; my @contigs = (); foreach my $contig (@args) { unless (exists $self->{'_contigs'}{$contig}) { $self->warn("$contig contig not found. Ignoring..."); next; } push(@contigs, $self->{'_contigs'}{$contig}); } return @contigs; } =head2 select_singlets Title : select_singlets Usage : $assembly->select_singlets(@list) Function: Selects an array of singlets from the assembly Returns : an array of Bio::Assembly::Singlet objects Args : an array of singlet ids See function get_singlet_ids() above =cut sub select_singlets { my ($self,@args) = @_; my @singlets = (); foreach my $singlet (@args) { unless (exists $self->{'_singlets'}{$singlet}) { $self->warn("$singlet singlet not found. Ignoring..."); next; } push(@singlets, $self->{'_singlets'}{$singlet}); } return @singlets; } =head2 all_contigs Title : all_contigs Usage : my @contigs = $assembly->all_contigs Function: Returns a list of all contigs in this assembly. Contigs are both clusters and alignments of one or more reads, with an associated consensus sequence. Returns : array of Bio::Assembly::Contig (in lexical id order) Args : none =cut sub all_contigs { my ($self) = @_; my @contigs = (); foreach my $contig (sort { $a cmp $b } keys %{ $self->{'_contigs'} }) { push(@contigs, $self->{'_contigs'}{$contig}); } return @contigs; } =head2 all_singlets Title : all_singlets Usage : my @singlets = $assembly->all_singlets Function: Returns a list of all singlets in this assembly. Singlets are isolated reads, without non-vector matches to any other read in the assembly. Returns : array of Bio::Assembly::Singlet objects (in lexical order by id) Args : none =cut sub all_singlets { my ($self) = @_; my @singlets = (); foreach my $singlet (sort { $a cmp $b } keys %{ $self->{'_singlets'} }) { push(@singlets, $self->{'_singlets'}{$singlet}); } return @singlets; } 1; BioPerl-1.007002/Bio/Assembly/ScaffoldI.pm000444000766000024 1647413155576320 20227 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Assembly::ScaffoldI # # Copyright by Robson F. de Souza # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Assembly::ScaffoldI - Abstract Interface of Sequence Assemblies =head1 SYNOPSIS # get a Bio::Assembly::ScaffoldI object somehow foreach my $contig ($assembly->all_contigs) { # do something (see Bio::Assembly::Contig) } =head1 DESCRIPTION This interface defines the basic set of methods an object should have to manipulate assembly data. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Robson Francisco de Souza Email: rfsouza@citri.iq.usp.br =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # # Now, let's code! package Bio::Assembly::ScaffoldI; use strict; use Carp; # Inheritance use base qw(Bio::Root::RootI); # # Methods =head1 Accessing general assembly data =cut =head2 get_nof_contigs Title : get_nof_contigs Usage : $assembly->get_nof_contigs() Function: Get the number of contigs included in the assembly Returns : integer Args : none =cut sub get_nof_contigs { my $self = shift; $self->throw_not_implemented(); } =head2 get_nof_singlets Title : get_nof_singlets Usage : $assembly->get_nof_singlets() Function: Get the number of singlets included in the assembly Returns : integer Args : none =cut sub get_nof_singlets { my $self = shift; $self->throw_not_implemented(); } =head2 get_contig_ids Title : get_contig_ids Usage : $assembly->get_contig_ids() Function: Access list of contig IDs from assembly Returns : an array if there are any contigs in the assembly. undef otherwise Args : an array of contig IDs =cut sub get_contig_ids { my $self = shift; $self->throw_not_implemented(); } =head2 get_singlet_ids Title : get_singlet_ids Usage : $assembly->get_singlet_ids() Function: Access list of singlet IDs from assembly Returns : an array if there are any singlets in the assembly. undef otherwise Args : an array of singlet IDs =cut sub get_singlet_ids { my $self = shift; $self->throw_not_implemented(); } =head2 get_contig_by_id Title : get_contig_by_id Usage : $assembly->get_contig_by_id($id) Function: Get a reference for a contig from the assembly Returns : a Bio::Assembly::Contig object or undef Args : [string] contig unique identifier (ID) =cut sub get_contig_by_id { my $self = shift; $self->throw_not_implemented(); } =head2 get_singlet_by_id Title : get_singlet_by_id Usage : $assembly->get_singlet_by_id() Function: Get a reference for a singlet from the assembly Returns : Bio::Assembly::Singlet object or undef Args : [string] a singlet ID =cut sub get_singlet_by_id { my $self = shift; $self->throw_not_implemented(); } =head1 Modifier methods Implementation of these methods is optional in the sense that read-only implementations may not have these. If an object implements one of them, it should however implement all. =cut =head2 add_contig Title : add_contig Usage : $assembly->add_contig($contig) Function: Add another contig to the Bio::Assembly::ScaffoldI object Returns : 1 on success, 0 otherwise Args : a Bio::Assembly:Contig object See Bio::Assembly::Contig for more information =cut #--------------------- sub add_contig { #--------------------- my ($self) = @_; $self->throw_not_implemented(); } =head2 add_singlet Title : add_singlet Usage : $assembly->add_singlet($seq) Function: Add another singlet to the Bio::Assembly::ScaffoldI object Returns : 1 on success, 0 otherwise Args : a Bio::Assembly::Singlet object =cut #--------------------- sub add_singlet { #--------------------- my ($self) = @_; $self->throw_not_implemented(); } =head2 remove_contigs Title : remove_contigs Usage : $assembly->remove_contigs(1..4) Function: Remove contig from assembly object Returns : a Bio::Assembly::Contig object Args : a list of contig IDs See function get_contig_ids() above =cut #--------------------- sub remove_contigs { #--------------------- my ($self) = @_; $self->throw_not_implemented(); } =head2 remove_singlets Title : remove_singlets Usage : $assembly->remove_singlets(1..4) Function: Remove singlets from assembly object Returns : an array of Bio::Assembly::Singlet objects Args : an array of singlet IDs See function get_singlet_ids() above =cut #--------------------- sub remove_singlets { #--------------------- my ($self) = @_; $self->throw_not_implemented(); } =head1 Contig and singlet selection methos =cut =head2 select_contigs Title : select_contig Usage : $assembly->select_contig Function: Selects an array of contigs from the assembly Returns : an array of Bio::Assembly::Contig objects Args : an array of contig ids See function get_contig_ids() above =cut #--------------------- sub select_contigs { #--------------------- my ($self) = @_; $self->throw_not_implemented(); } =head2 select_singlets Title : select_singlets Usage : $assembly->select_singlets(@list) Function: Selects an array of singlets from the assembly Returns : an array of Bio::Assembly::Singlet objects Args : an array of singlet ids See function get_singlet_ids() above =cut #--------------------- sub select_singlets { #--------------------- my ($self) = @_; $self->throw_not_implemented(); } =head2 all_contigs Title : all_contigs Usage : my @contigs = $assembly->all_contigs Function: Returns a list of all contigs in this assembly. Contigs are both clusters and alignments of one or more reads, with an associated consensus sequence. Returns : array of Bio::Assembly::Contig Args : none =cut #--------------------- sub all_contigs { #--------------------- my ($self) = @_; $self->throw_not_implemented(); } =head2 all_singlets Title : all_singlets Usage : my @singlets = $assembly->all_singlets Function: Returns a list of all singlets in this assembly. Singlets are isolated reads, without non-vector matches to any other read in the assembly. Returns : array of Bio::Assembly::Singlet objects Args : none =cut #--------------------- sub all_singlets { #--------------------- my ($self) = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Assembly/Singlet.pm000444000766000024 1166413155576320 17776 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Assembly::Singlet # # Please direct questions and support issues to # # Cared for by Chad Matsalla # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Assembly::Singlet - Perl module to hold and manipulate singlets from sequence assembly contigs. =head1 SYNOPSIS # Module loading use Bio::Assembly::IO; # Assembly loading methods $aio = Bio::Assembly::IO->new( -file => 'test.ace.1', -format => 'phrap' ); $assembly = $aio->next_assembly; foreach $singlet ($assembly->all_singlets) { # do something } # OR, if you want to build the singlet yourself, use Bio::Assembly::Singlet; $singlet = Bio::Assembly::Singlet->new( -id => 'Singlet1', -seqref => $seq ); =head1 DESCRIPTION A singlet is a sequence that phrap was unable to align to any other sequences. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad S. Matsalla bioinformatics1 at dieselwurks.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' package Bio::Assembly::Singlet; use strict; use Bio::SeqFeature::Collection; use Bio::LocatableSeq; use Bio::Seq::PrimaryQual; use base qw(Bio::Assembly::Contig Bio::Root::Root Bio::Align::AlignI); =head2 new Title : new Usage : $singlet = $io->new( -seqref => $seq ) Function: Create a new singlet object Returns : A Bio::Assembly::Singlet object Args : -seqref => Bio::Seq-compliant sequence object for the singlet =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($seqref) = $self->_rearrange([qw(SEQREF)], @args); $self->{'_seqref'} = undef; if (defined $seqref) { $self->seqref($seqref); } return $self; } =head2 seqref Title : seqref Usage : $seqref = $singlet->seqref($seq); Function: Get/set the sequence to which this singlet refers Returns : A Bio::Seq-compliant object Args : A Bio::Seq-compliant or Bio::Seq::Quality object =cut sub seqref { my ($self,$seq) = @_; if (defined $seq) { $self->_seq_to_singlet($seq) }; return $self->{'_seqref'}; } =head2 _seq_to_singlet Title : _seq_to_singlet Usage : $singlet->seqref($seq) Function: Transform a sequence into a singlet Returns : 1 for success Args : A Bio::Seq-compliant object =cut sub _seq_to_singlet { my ($self, $seq) = @_; # Object type checking $self->throw("Unable to process non Bio::Seq-compliant object [".ref($seq)."]") unless ( defined $seq && ($seq->isa('Bio::PrimarySeqI') || $seq->isa('Bio::Seq::Quality')) ); # Sanity check $self->throw("Unable to have more than one sequence reference in a singlet") if (defined $self->{'_seqref'}); # From sequence to locatable sequence my $lseq = Bio::LocatableSeq->new( -id => $seq->id, -seq => $seq->seq, -strand => $seq->isa('Bio::LocatableSeq') ? $seq->strand : 1, -start => 1, #-end => we let Bio::LocatableSeq calculate it (Seq and LocatableSeq) ); # Get End from $seq if $lseq can't figure it out (e.g. phrap output) if (not defined $lseq->end) { $lseq->end($seq->end); } # Add new sequence and its coordinates to the contig my $lcoord = Bio::SeqFeature::Generic->new( -start => $lseq->start, -end => $lseq->end ); $self->set_seq_coord( $lcoord, $lseq ); $self->{'_seqref'} = $lseq; # Creating consensus $self->set_consensus_sequence($lseq); if ($seq->isa("Bio::Seq::Quality")) { my $qual = Bio::Seq::PrimaryQual->new( -id => $seq->id, -qual => $seq->qual ); $self->set_consensus_quality($qual); } return 1; } 1; BioPerl-1.007002/Bio/Assembly/IO000755000766000024 013155576320 16155 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Assembly/IO/ace.pm000444000766000024 11176213155576320 17450 0ustar00cjfieldsstaff000000000000# $Id: ace.pm 16969 2010-05-09 15:26:53Z fangly $ # ## BioPerl module for Bio::Assembly::IO::ace # # Copyright by Robson F. de Souza (the reading part) and Florent Angly (the # writing and ACE variants part) # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Assembly::IO::ace - module to load ACE files from various assembly programs =head1 SYNOPSIS # Building an input stream use Bio::Assembly::IO; # Load a reference ACE assembly my $in_io = Bio::Assembly::IO->new( -file => 'results.ace', -format => 'ace' ); # Read the entire scaffold my $scaffold = $in_io->next_assembly; # Or read one contig at a time to save resources while ( my $contig = $in_io->next_contig ) { # Do something ... } # Assembly writing methods my $out_io = Bio::Assembly::IO->new( -file => ">output.ace", -format => 'ace' ); $out_io->write_assembly( -scaffold => $scaffold, -singlets => 1 ); # Read the '454' Newbler variant of ACE instead of the default 'consed' # reference ACE variant my $in_io = Bio::Assembly::IO->new( -file => 'results.ace', -format => 'ace-454' ); # or ... my $in_io = Bio::Assembly::IO->new( -file => 'results.ace', -format => 'ace', -variant => '454' ); =head1 DESCRIPTION This package loads the standard ACE files generated by various assembly programs (Phrap, CAP3, Newbler, Arachne, ...). It was written to be used as a driver module for Bio::Assembly::IO input/output. =head2 Implemention Assemblies are loaded into Bio::Assembly::Scaffold objects composed by Bio::Assembly::Contig and Bio::Assembly::Singlet objects. Only the ACE file is used, so if you need singlets, make sure that they are present in the ACE file. A brief description of the ACE format is available at http://www.cbcb.umd.edu/research/contig_representation.shtml#ACE Read the full format description from http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt In addition to default "_aligned_coord:$seqID" feature class from Bio::Assembly::Contig, contig objects loaded by this module will have the following special feature classes in their feature collection: "_align_clipping:$seqID" (AF) Location of subsequence in read $seqID which is aligned to the contig. The coordinates are relative to the contig. If no feature containing this tag is present the read is considered low quality by Consed. "_quality_clipping:$seqID" (AF) The location of high quality subsequence in read $seqID (relative to contig) "_base_segments" (BS) Location of read subsequences used to build the consensus "_read_tags:$readID" (RT) Sequence features stored as sub_SeqFeatures of the sequence's coordinate feature (the corresponding "_aligned_coord:$seqID" feature, easily accessed through get_seq_coord() method). "_read_desc:$readID" (DS) Sequence features stored as sub_SeqFeatures of the read's coordinate feature "consensus tags" (CT) Equivalent to a bioperl sequence feature and, therefore, are added to the feature collection using their type field (see Consed's README.txt file) as primary tag. "whole assembly tags" (WA) They have no start and end, as they are not associated to any particular sequence in the assembly, and are added to the assembly's annotation collection using "whole assembly" as tag. =head2 Variants The default ACE variant is called 'consed' and corresponds to the reference ACE format. The ACE files produced by the 454 GS Assembler (Newbler) do not conform to the reference ACE format. In 454 ACE, the consensus sequence reported covers only its clear range and the start of the clear range consensus is defined as position 1. Consequently, aligned reads in the contig can have negative positions. Be sure to use the '454' variant to have positive alignment positions. No attempt is made to construct the missing part of the consensus sequence (beyond the clear range) based on the underlying reads in the contig. Instead the ends of the consensus are simply padded with the gap character '-'. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Robson Francisco de Souza Email rfsouza@citri.iq.usp.br =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Assembly::IO::ace; use strict; use Bio::Assembly::Scaffold; use Bio::Assembly::Contig; use Bio::Assembly::Singlet; use Bio::LocatableSeq; use Bio::Seq::PrimaryQual; use Bio::Annotation::SimpleValue; use Bio::SeqIO; use Bio::SeqFeature::Generic; use base qw(Bio::Assembly::IO); our $line_width = 50; our $qual_value = 20; our %variant = ( 'consed' => undef, # default '454' => undef ); =head1 Parser methods =head2 next_assembly Title : next_assembly Usage : $scaffold = $stream->next_assembly() Function: returns the next assembly in the stream Returns : a Bio::Assembly::Scaffold object Args : none =cut sub next_assembly { my $self = shift; my $assembly = Bio::Assembly::Scaffold->new(); # Load contigs and singlets in the scaffold while ( my $obj = $self->next_contig() ) { # Add contig /singlet to assembly if ($obj->isa('Bio::Assembly::Singlet')) { # a singlet $assembly->add_singlet($obj); } else { # a contig $assembly->add_contig($obj); } } # Load annotations of assembly and contigs $self->scaffold_annotations($assembly); return $assembly; } =head2 next_contig Title : next_contig Usage : $scaffold = $stream->next_contig() Function: Returns the next contig or singlet in the ACE stream. Returns : a Bio::Assembly::Contig or Bio::Assembly::Single object Args : none =cut sub next_contig { my ($self) = shift; local $/ = "\n"; my $contigOBJ; my $read_name; my $min_start; my $read_data = {}; # Temporary holder for read data # Keep reading the ACE stream starting at where we stopped while ( $_ = $self->_readline) { chomp; # Loading contig sequence (COntig sequence field) if (/^CO\s(\S+)\s(\d+)\s(\d+)\s(\d+)\s(\w+)/xms) { # New contig starts! if (not $contigOBJ) { # Start a new contig object my $contigID = $1; # Contig ID #my $nof_bases = $2; # Contig length in base pairs my $nof_reads = $3; # Number of reads in this contig #my $nof_segments = $4; # Number of read segments selected for consensus assembly my $ori = $5; # 'C' if contig was complemented or U if not (default) $ori = $ori eq 'U' ? 1 : -1; # Create a singlet or contig if ($nof_reads == 1) { # This is a singlet $contigOBJ = Bio::Assembly::Singlet->new( ); } elsif ( $nof_reads > 1 ) { # This is a contig $contigOBJ = Bio::Assembly::Contig->new( ); } $contigOBJ->id($contigID); $contigOBJ->strand($ori); my $consensus_sequence; while ($_ = $self->_readline) { # Looping over contig lines chomp; # Drop (\n) on current line last if (/^$/); # Stop if empty line (contig end) is found s/\*/-/g; # Forcing '-' as gap symbol $consensus_sequence .= $_; } $consensus_sequence = Bio::LocatableSeq->new( -seq => $consensus_sequence, -start => 1, -strand => $ori, ); $consensus_sequence->id($contigID); $contigOBJ->set_consensus_sequence($consensus_sequence); } else { # A second contig is about to start. Backtrack one line and go # to the return statement $self->_pushback($_); last; } } # Loading contig qualities... (Base Quality field) elsif (/^BQ/) { my $qual_string = ''; while ($_ = $self->_readline) { chomp; last if (/^$/); $qual_string .= "$_ "; } my @qual_arr = $self->_input_qual($qual_string, $contigOBJ->get_consensus_sequence->seq); my $qual = Bio::Seq::PrimaryQual->new(-qual => join(" ", @qual_arr), -id => $contigOBJ->id() ); $contigOBJ->set_consensus_quality($qual); } # Loading read info... (Assembled From field) elsif (/^AF (\S+) (C|U) (-*\d+)/) { $read_name = $1; # read ID my $ori = $2; # strand my $start = $3; # aligned start $ori = $ori eq 'U' ? 1 : -1; $read_data->{$read_name}{'strand'} = $ori; $read_data->{$read_name}{'padded_start'} = $start; if ( $self->variant eq '454' ) { if ( (not defined $min_start) || ($start < $min_start) ) { $min_start = $start; } } } # Base segments definitions (Base Segment field) # They indicate which read segments were used to calculate the consensus # Coordinates are relative to the contig elsif (/^BS (\d+) (\d+) (\S+)/) { my ($start, $end, $contig_id) = ($1, $2, $3); if ($self->variant eq '454') { $start += abs($min_start) + 1; $end += abs($min_start) + 1; } my $bs_feat = Bio::SeqFeature::Generic->new( -start => $start, -end => $end, -source => 'ace', -strand => 1, -primary => '_base_segments', -tag => { 'contig_id' => $contig_id} ); $contigOBJ->add_features([ $bs_feat ], 0); } # Loading reads... (ReaD sequence field) # They define the reads in each contig elsif (/^RD (\S+) (-*\d+) (\d+) (\d+)/) { $read_name = $1; $read_data->{$read_name}{'length'} = $2; # number_of_padded_bases $read_data->{$read_name}{'contig'} = $contigOBJ; # $read_data->{$read_name}{'number_of_read_info_items'} = $3; # $read_data->{$read_name}{'number_of_tags'} = $4; # Add a read to a contig my $read_sequence; while ($_ = $self->_readline) { chomp; last if (/^$/); s/\*/-/g; # Forcing '-' as gap symbol $read_sequence .= $_; # aligned read sequence } my $read = Bio::LocatableSeq->new( -seq => $read_sequence, -start => 1, -strand => $read_data->{$read_name}{'strand'}, -id => $read_name, -primary_id => $read_name, -alphabet => 'dna' ); # Adding read location and sequence to contig ("gapped consensus" coordinates) my $padded_start = $read_data->{$read_name}{'padded_start'}; if ($self->variant eq '454') { $padded_start += abs($min_start) + 1; } my $padded_end = $padded_start + $read_data->{$read_name}{'length'} - 1; my $coord = Bio::SeqFeature::Generic->new( -start => $padded_start, -end => $padded_end, -source => 'ace', -strand => $read_data->{$read_name}{'strand'}, -tag => { 'contig' => $contigOBJ->id } ); if ($contigOBJ->isa('Bio::Assembly::Singlet')) { # Set the the sequence in the singlet $contigOBJ->seqref($read); } else { # a contig # this sets the "_aligned_coord:$seqID" feature $contigOBJ->set_seq_coord($coord,$read); } } # Loading read trimming and alignment ranges... elsif (/^QA (-?\d+) (-?\d+) (-?\d+) (-?\d+)/) { my ($qual_start, $qual_end, $aln_start, $aln_end) = ($1, $2, $3, $4); # Regions of the read that were aligned to the consensus (see BS) unless ($aln_start == -1 && $aln_end == -1) { $aln_start = $contigOBJ->change_coord("aligned $read_name",'gapped consensus',$aln_start); $aln_end = $contigOBJ->change_coord("aligned $read_name",'gapped consensus',$aln_end); my $aln_feat = Bio::SeqFeature::Generic->new( -start => $aln_start, -end => $aln_end, -strand => $read_data->{$read_name}{'strand'}, -primary => '_align_clipping', -source => $read_name, ); $aln_feat->attach_seq( $contigOBJ->get_seq_by_name($read_name) ); $contigOBJ->add_features([ $aln_feat ], 0); } # Regions of the read with high quality score unless ($qual_start == -1 && $qual_end == -1) { $qual_start = $contigOBJ->change_coord("aligned $read_name",'gapped consensus',$qual_start); $qual_end = $contigOBJ->change_coord("aligned $read_name",'gapped consensus',$qual_end); my $qual_feat = Bio::SeqFeature::Generic->new( -start => $qual_start, -end => $qual_end, -strand => $read_data->{$read_name}{'strand'}, -primary => '_quality_clipping', -source => $read_name || '', ); $qual_feat->attach_seq( $contigOBJ->get_seq_by_name($read_name) ); $contigOBJ->add_features([ $qual_feat ], 0); } } # Loading read DeScription (DS) elsif (/^DS\s+(.*)/) { my $desc = $1; # Expected tags are CHROMAT_FILE, PHD_FILE, TIME and to a lesser # extent DYE, TEMPLATE, CHEM and DIRECTION, but any other tag is # allowed my (undef, %tags) = split /\s?(\S+):\s+/, $desc; my $coord = $contigOBJ->get_seq_coord( $contigOBJ->get_seq_by_name($read_name) ); my $start = $coord->start; my $end = $coord->end; my $read_desc = Bio::SeqFeature::Generic->new( -start => $start, -end => $end, -primary => '_read_desc', # primary_tag -source => $read_name || '', -tag => \%tags ); $contigOBJ->get_features_collection->add_features([$read_desc]); $contigOBJ->get_features_collection->add_SeqFeature($coord, $read_desc); } # Loading Read Tags elsif (/^RT\s*\{/) { my ($readID,$type,$source,$start,$end,$date) = split(' ',$self->_readline); my $extra_info = undef; while ($_ = $self->_readline) { last if (/\}/); $extra_info .= $_; } $start = $contigOBJ->change_coord("aligned $readID",'gapped consensus',$start); $end = $contigOBJ->change_coord("aligned $readID",'gapped consensus',$end); my $read_tag = Bio::SeqFeature::Generic->new( -start => $start, -end => $end, -primary => '_read_tags', -source => $readID || '', -tag => { 'type' => $type, 'source' => $source, 'creation_date' => $date} ); $read_tag->add_tag_value('extra_info', $extra_info) if defined $extra_info; my $contig = $read_data->{$readID}{'contig'}; my $coord = $contig->get_seq_coord( $contig->get_seq_by_name($readID) ); $contig->get_features_collection->add_features([$read_tag]); $contig->get_features_collection->add_SeqFeature($coord, $read_tag); } } # Adjust consensus sequence of 454 variant by padding its start and end if (($self->variant eq '454') && (defined $contigOBJ)) { my $pad_char = '-'; my $pad_score = 0; # Find maximum coordinate my $max_end; for my $readid ($contigOBJ->get_seq_ids) { my ($alncoord) = $contigOBJ->get_features_collection->get_features_by_type("_aligned_coord:$readid"); my $end = $alncoord->location->end; if ( (not defined $max_end) || ($end > $max_end) ) { $max_end = $end; } } # Pad consensus sequence my $cons_seq = $contigOBJ->get_consensus_sequence; my $cons_string = $cons_seq->seq; my $l_pad_len = abs($min_start) + 1; my $r_pad_len = $max_end - length($cons_string) - $l_pad_len; $cons_string = $pad_char x $l_pad_len . $cons_string . $pad_char x $r_pad_len; $cons_seq = Bio::LocatableSeq->new( -seq => $cons_string, -id => $cons_seq->id, -start => $cons_seq->start, -strand => $cons_seq->strand, ); $contigOBJ->set_consensus_sequence($cons_seq); # Pad consensus quality my $cons_qual = $contigOBJ->get_consensus_quality; if (defined $cons_qual) { my $cons_score = [ ($pad_score) x $l_pad_len, @{$cons_qual->qual}, ($pad_score) x $r_pad_len ]; $cons_qual = Bio::Seq::PrimaryQual->new( -qual => join(' ', @$cons_score), -id => $cons_qual->id ); $contigOBJ->set_consensus_quality($cons_qual); } } return $contigOBJ; } =head2 scaffold_annotations Title : scaffold_annotations Usage : $stream->scaffold_annotations($scaffold) Function: Add assembly and contig annotations to a scaffold. In the ACE format, annotations are the WA and CT tags. Returns : 1 for success Args : a Bio::Assembly::Scaffold object to attach the annotations to =cut sub scaffold_annotations { my ($self, $assembly) = @_; local $/ = "\n";; # Read the ACE stream from the beginning again seek($self->_fh, 0, 0); while ($_ = $self->_readline) { chomp; # Assembly information (ASsembly field) # Ignore it #(/^AS\s+(\d+)\s+(\d+)/) && do { # my $nof_contigs = $1; # my $nof_seq_in_contigs = $2; #}; # Loading Whole Assembly tags /^WA\s*\{/ && do { my ($type,$source,$date) = split(' ',$self->_readline); my $extra_info = undef; while ($_ = $self->_readline) { last if (/\}/); $extra_info .= $_; } my $assembly_tags = join(" ","TYPE:",$type,"PROGRAM:",$source, "DATE:",$date,"DATA:",$extra_info); $assembly_tags = Bio::Annotation::SimpleValue->new(-value=>$assembly_tags); $assembly->annotation->add_Annotation('whole assembly',$assembly_tags); }; # Loading Contig Tags (a.k.a. Bioperl features) /^CT\s*\{/ && do { my ($contigID,$type,$source,$start,$end,$date) = split(' ',$self->_readline); my %tags = ('source' => $source, 'creation_date' => $date); my $tag_type = 'extra_info'; while ($_ = $self->_readline) { if (/COMMENT\s*\{/) { $tag_type = 'comment'; } elsif (/C\}/) { $tag_type = 'extra_info'; } elsif (/\}/) { last; } else { $tags{$tag_type} .= "$_"; } } my $contig_tag = Bio::SeqFeature::Generic->new( -start => $start, -end => $end, -primary => $type, -source => 'ace', -tag => \%tags ); my $contig = $assembly->get_contig_by_id($contigID) || $assembly->get_singlet_by_id($contigID); $self->throw("Cannot add feature to unknown contig '$contigID'") unless defined $contig; $contig->add_features([ $contig_tag ],1); }; } return 1; } =head2 write_assembly Title : write_assembly Usage : $ass_io->write_assembly($assembly) Function: Write the assembly object in ACE compatible format. The contig IDs are sorted naturally if the Sort::Naturally module is present, or lexically otherwise. Internally, write_assembly use the write_contig, write_footer and write_header methods. Use these methods if you want more control on the writing process. Returns : 1 on success, 0 for error Args : A Bio::Assembly::Scaffold object =cut =head2 write_contig Title : write_contig Usage : $ass_io->write_contig($contig) Function: Write a contig or singlet object in ACE compatible format. Quality scores are automatically generated if the contig does not contain any Returns : 1 on success, 0 for error Args : A Bio::Assembly::Contig or Singlet object =cut sub write_contig { my ($self, @args) = @_; my ($contig) = $self->_rearrange([qw(CONTIG)], @args); # Sanity check if ( !$contig || !$contig->isa('Bio::Assembly::Contig') ) { $self->throw("Must provide a Bio::Assembly::Contig or Singlet object when calling write_contig"); } # Contig consensus sequence my $contig_id = $contig->id; my $cons = $contig->get_consensus_sequence; my $cons_seq = $cons->seq; my $cons_len = $cons->length; my $contig_num_reads = $contig->num_sequences; my $cons_strand = ($contig->strand == -1) ? 'C' : 'U'; my @bs_feats = $contig->get_features_collection->get_features_by_type('_base_segments'); my $nof_segments = scalar @bs_feats; $self->_print( "CO $contig_id $cons_len $contig_num_reads $nof_segments $cons_strand\n". _formatted_seq($cons_seq, $line_width). "\n" ); # Consensus quality scores $cons = $contig->get_consensus_quality; my $cons_qual = $cons->qual if defined $cons; $self->_print( "BQ\n". _formatted_qual($cons_qual, $cons_seq, $line_width, $qual_value). "\n" ); # Read entries my @reads = $contig->each_seq; for my $read (@reads) { my $read_id = $read->id; my $read_strand = ($read->strand == -1) ? 'C' : 'U'; my $read_start = $contig->change_coord("aligned $read_id",'gapped consensus',1); $self->_print( "AF $read_id $read_strand $read_start\n" ); } $self->_print( "\n" ); # Deal with base segments (BS) if ( @bs_feats ) { # sort segments by increasing start position @bs_feats = sort { $a->start <=> $b->start } @bs_feats; # write segments for my $bs_feat ( @bs_feats ) { my $start = $bs_feat->start; my $end = $bs_feat->end; my $id = ($bs_feat->get_tag_values('contig_id'))[0]; $self->_print( "BS $start $end $id\n" ); } $self->_print( "\n" ); } for my $read (@reads) { $self->_write_read($read, $contig); } return 1; } =head2 write_header Title : write_header Usage : $ass_io->write_header($scaffold) or $ass_io->write_header(\@contigs); or $ass_io->write_header(); Function: Write ACE header (AS tags). You can call this function at any time, i.e. not necessarily at the start of the stream - this is useful if you have an undetermined number of contigs to write to ACE, e.g: for my $contig (@list_of_contigs) { $ass_io->_write_contig($contig); } $ass_io->_write_header(); Returns : 1 on success, 0 for error Args : A Bio::Assembly::Scaffold or an arrayref of Bio::Assembly::Contig or nothing (the header is dynamically written based on the ACE file content) =cut sub write_header { my ($self, $input) = @_; # Input validation my @contigs; my $err_msg = "If an input is given to write_header, it must be a single ". "Bio::Assembly::Scaffold object or an arrayref of Bio::Assembly::Contig". " or Singlet objects"; my $ref = ref $input; if ( $ref eq 'ARRAY' ) { for my $obj ( @$input ) { $self->throw($err_msg) if not $obj->isa('Bio::Assembly::Contig'); push @contigs, $obj; } } elsif ( $ref =~ m/Bio::Assembly::Scaffold/ ) { @contigs = ($input->all_contigs, $input->all_singlets); } # Count number of contigs and reads my $num_contigs = 0; my $num_reads = 0; if ( scalar @contigs > 0 ) { # the contigs were provided $num_contigs = scalar @contigs; for my $contig ( @contigs ) { $num_reads += $contig->num_sequences; } } else { # need to read the contigs from file $self->flush; my $file = $self->file(); # e.g. '+>output.ace' $file =~ s/^\+?[><]?//; # e.g. 'output.ace' my $read_io = Bio::Assembly::IO->new( -file => $file, -format => 'ace' ); while ( my $contig = $read_io->next_contig ) { $num_contigs++; $num_reads += $contig->num_sequences; } $read_io->close; } # Write ASsembly tag at the start of the file my $header = "AS $num_contigs $num_reads\n\n"; $self->_insert($header, 1); return 1; } =head2 write_footer Title : write_footer Usage : $ass_io->write_footer($scaffold) Function: Write ACE footer (WA and CT tags). Returns : 1 on success, 0 for error Args : A Bio::Assembly::Scaffold object (optional) =cut sub write_footer { my ($self, $scaf) = @_; # Nothing to write if scaffold was not provided return 1 if not defined $scaf; # Verify that provided object is a scaffold if ($scaf->isa('Bio::Assembly:ScaffoldI')) { $self->throw("Must provide a Bio::Assembly::Scaffold object when calling write_footer"); } # Whole Assembly tags (WA) my $asm_anno = ($scaf->annotation->get_Annotations('whole assembly'))[0]; if ($asm_anno) { my $asm_tags = $asm_anno->value; if ($asm_tags =~ m/^TYPE: (\S+) PROGRAM: (\S+) DATE: (\S+) DATA: (.*)$/ms) { my ($type, $program, $date, $data) = ($1, $2, $3, $4); $data ||= ''; $self->_print( "WA{\n". "$type $program $date\n". $data. "}\n". "\n" ); } } # Contig Tags (CT) for my $contig_id ( Bio::Assembly::IO::_sort( $scaf->get_contig_ids ) ) { my $contig = $scaf->get_contig_by_id($contig_id) || $scaf->get_singlet_by_id($contig_id); # Is there a better way of doing this? Grepping is not very efficient... my @feats = (grep { not $_->primary_tag =~ m/^_/ } $contig->get_features_collection->features ); for my $feat (@feats) { my $type = $feat->primary_tag; my $start = $feat->start; my $end = $feat->end; my $source = ($feat->get_tag_values('source') )[0]; my $date = ($feat->get_tag_values('creation_date'))[0]; my $extra = ''; if ($feat->has_tag('extra_info')) { $extra = ($feat->get_tag_values('extra_info') )[0]; } $self->_print( "CT{\n". "$contig_id $type $source $start $end $date\n". $extra. "}\n". "\n" ); } } return 1; } =head2 variant Title : variant Usage : $variant = $ass_io->variant(); Function: Get and set method for the assembly variant. This is important since not all assemblers respect the reference ACE format. Returns : string Args : string: 'consed' (default) or '454' =cut # variant() method inherited from Bio::Root::IO =head2 _write_read Title : _write_read Usage : $ass_io->_write_read($read, $contig) Function: Write a read object in ACE compatible format Returns : 1 on success, 0 for error Args : a Bio::LocatableSeq read the Contig or Singlet object that this read belongs to =cut sub _write_read { my ($self, @args) = @_; my ($read, $contig) = $self->_rearrange([qw(READ CONTIG)], @args); # Sanity check if ( !$read || !$read->isa('Bio::LocatableSeq') ) { $self->throw("Must provide a Bio::LocatableSeq when calling write_read"); } if ( !$contig || !$contig->isa('Bio::Assembly::Contig') ) { $self->throw("Must provide a Bio::Assembly::Contig or Singlet object when calling write_read"); } # Read info my $read_id = $read->id; my $read_len = $read->length; # aligned length my $read_seq = $read->seq; my $nof_info = 0; # fea: could not find exactly the meaning of this? my @read_tags = $contig->get_features_collection->get_SeqFeatures( $contig->get_seq_coord($read), "_read_tags:$read_id"); my $nof_tags = scalar @read_tags; $self->_print( "RD $read_id $read_len $nof_info $nof_tags\n". _formatted_seq($read_seq, $line_width). "\n" ); # Aligned "align clipping" and quality coordinates if read object has them my $qual_clip_start = 1; my $qual_clip_end = length($read->seq); my ($qual_clip) = $contig->get_features_collection->get_features_by_type("_quality_clipping:$read_id"); if ( defined $qual_clip ) { $qual_clip_start = $qual_clip->location->start; $qual_clip_end = $qual_clip->location->end; $qual_clip_start = $contig->change_coord('gapped consensus',"aligned $read_id",$qual_clip_start); $qual_clip_end = $contig->change_coord('gapped consensus',"aligned $read_id",$qual_clip_end ); } my $aln_clip_start = 1; my $aln_clip_end = length($read->seq); my ($aln_clip) = $contig->get_features_collection->get_features_by_type("_align_clipping:$read_id"); if ( defined $aln_clip ) { $aln_clip_start = $aln_clip->location->start; $aln_clip_end = $aln_clip->location->end; $aln_clip_start = $contig->change_coord('gapped consensus',"aligned $read_id",$aln_clip_start ); $aln_clip_end = $contig->change_coord('gapped consensus',"aligned $read_id",$aln_clip_end ); } $self->_print( "QA $qual_clip_start $qual_clip_end $aln_clip_start $aln_clip_end\n". "\n" ); # Read description, if read object has them my $read_desc = ( $contig->get_features_collection->get_SeqFeatures( $contig->get_seq_coord($read), "_read_desc:$read_id") )[0]; if ($read_desc) { $self->_print("DS"); for my $tag_name ( $read_desc->get_all_tags ) { my $tag_value = ($read_desc->get_tag_values($tag_name))[0]; $self->_print(" $tag_name: $tag_value"); } $self->_print("\n\n"); } # Read tags, if read object has them for my $read_tag (@read_tags) { #my $type = $read_tag->primary_tag; my $start = $read_tag->start; my $end = $read_tag->end; my $type = ($read_tag->get_tag_values('type') )[0]; my $source = ($read_tag->get_tag_values('source') )[0]; my $date = ($read_tag->get_tag_values('creation_date'))[0]; my $extra = $read_tag->has_tag('extra_info') ? ($read_tag->get_tag_values('extra_info') )[0] : ''; $self->_print( "RT{\n". "$read_id $type $source $start $end $date\n". $extra. "}\n". "\n" ); } return 1; } =head2 _formatted_seq Title : _formatted_seq Usage : Bio::Assembly::IO::ace::_formatted_seq($sequence, $line_width) Function: Format a sequence for ACE output: i ) replace gaps in the sequence by the '*' char ii) split the sequence on multiple lines as needed Returns : new sequence string Args : sequence string on one line maximum line width =cut sub _formatted_seq { my ($seq_str, $line_width) = @_; my $new_str = ''; # In the ACE format, gaps are '*' $seq_str =~ s/-/*/g; # Split sequences on several lines while ( my $chunk = substr $seq_str, 0, $line_width, '' ) { $new_str .= "$chunk\n"; } return $new_str; } =head2 _formatted_qual Title : _formatted_qual Usage : Bio::Assembly::IO::ace::_formatted_qual($qual_arr, $sequence, $line_width, $qual_default) Function: Format quality scores for ACE output: i ) use the default quality values when they are missing ii ) remove gaps (they get no score in ACE) iii) split the quality scores on several lines as needed Returns : new quality score string Args : quality score array reference corresponding sequence string maximum line width default quality score =cut sub _formatted_qual { my ($qual_arr, $seq, $line_width, $qual_default) = @_; my $qual_str = ''; my @qual_arr; if (defined $qual_arr) { # Copy array @qual_arr = @$qual_arr; } else { # Default quality @qual_arr = map( $qual_default, (1 .. length $seq) ); } # Gaps get no quality score in ACE format my $gap_pos = -1; while ( 1 ) { $gap_pos = index($seq, '-', $gap_pos + 1); last if $gap_pos == -1; substr $seq, $gap_pos, 1, ''; splice @qual_arr, $gap_pos, 1; $gap_pos--; } # Split quality scores on several lines while ( my @chunks = splice @qual_arr, 0, $line_width ) { $qual_str .= "@chunks\n"; } return $qual_str; } =head2 _input_qual Title : _input_qual Usage : Bio::Assembly::IO::ace::_input_qual($qual_string, $sequence) Function: Reads input quality string and converts it to an array of quality scores. Gaps get a quality score equals to the average of the quality score of its neighbours. Returns : new quality score array Args : quality score string corresponding sequence string =cut sub _input_qual { my ($self, $qual_string, $sequence) = @_; my @qual_arr = (); # Remove whitespaces in front of qual string and split quality values $qual_string =~ s/^\s+//; my @tmp = split(/\s+/, $qual_string); # Remove gaps my $i = 0; # position in quality my $j = 0; # position in sequence my $prev = 0; my $next = 0; for $j (0 .. length($sequence)-1) { my $nt = substr($sequence, $j, 1); if ($nt eq '-') { if ($i > 0) { $prev = $tmp[$i-1]; } else { $prev = 0; } if ($i < $#tmp) { $next = $tmp[$i]; } else { $next = 0; } push @qual_arr, int(($prev+$next)/2); } else { push @qual_arr, $tmp[$i]; $i++; } } return @qual_arr; } =head2 _initialize Title : _initialize Usage : $ass_io->_initialize(@args) Function: Initialize the Bio::Assembly::IO object with the proper ACE variant Returns : Args : =cut sub _initialize { my($self, @args) = @_; $self->SUPER::_initialize(@args); my ($variant) = $self->_rearrange([qw(VARIANT)], @args); $variant ||= 'consed'; $self->variant($variant); } 1; __END__ BioPerl-1.007002/Bio/Assembly/IO/bowtie.pm000555000766000024 2407513155576320 20174 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Assembly::IO::sam # # Please direct questions and support issues to # # Cared for by Dan Kortschak # # Copyright Dan Kortschak # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Assembly::IO::bowtie - An IO module for assemblies in Bowtie format *BETA* =head1 SYNOPSIS $aio = Bio::Assembly::IO( -file => "mybowtie.bowtie", -index => "myindex", -format => "bowtie"); $assy = $aio->next_assembly; =head1 DESCRIPTION This is a read-only IO module designed to convert Bowtie (L) formatted alignments to L representations, containing L and L objects. It is a wrapper that converts the Bowtie format to BAM format taken by the Bio::Assembly::IO::sam module which in turn uses lstein's L to parse binary formatted SAM (.bam) files guided by a reference sequence fasta database. Some information is lost in conversion from bowtie format to SAM/BAM format that is provided by Bowtie using the SAM output option and the conversion to SAM format from bowtie format is slower than using bowtie's SAM option. If you plan to use SAM/BAM format it is preferable to use this Bowtie option rather than convert the format after the fact. See the Bio::Assembly::IO::sam documentation for relevant details. =head1 DETAILS =over =item * Required files A bowtie (C<.bowtie>) alignment and the bowtie index or fasta file used to generate the alignment are required. =item * Compressed files ...can be specified directly , if L is installed. Get it from your local CPAN mirror. =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: L rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Dan Kortschak Email dan.kortschak adelaide.edu.au =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Assembly::IO::bowtie; use strict; use warnings; # Object preamble - inherits from Bio::Root::Root use Bio::SeqIO; use Bio::Tools::Run::Samtools; use Bio::Assembly::IO; use base qw( Bio::Assembly::IO ); our $HD = "\@HD\tVN:1.0\tSO:unsorted\n"; our $PG = "\@PG\tID=Bowtie\n"; our $HAVE_IO_UNCOMPRESS; our $HAVE_BOWTIE; BEGIN { # check requirements eval "require Bio::Tools::Run::Bowtie; \$HAVE_BOWTIE = 1"; unless ( eval "require IO::Uncompress::Gunzip; \$HAVE_IO_UNCOMPRESS = 1") { Bio::Root::Root->warn("IO::Uncompress::Gunzip is not available; you'll have to do your decompression by hand."); } } =head2 new() Title : new Usage : my $obj = new Bio::Assembly::IO::bowtie(); Function: Builds a new Bio::Assembly::IO object Returns : an instance of Bio::Assembly::IO Args : hash of options: -file => bowtie_output_file -index => bowtie_index or fasta_file used to create index -no_head => boolean skip SAM header -no_sq => boolean skip SQ lines of SAM header Note : bowtie_output and fasta files may be gzipped =cut sub new { my $class = shift; my @args = @_; my $self = $class->SUPER::new(@args); $self->_initialize(@args); $self->{'_tempdir'} = $self->tempdir(CLEANUP=>1); my ($file, $index, $no_head, $no_sq) = $self->_rearrange([qw(FILE INDEX NO_HEAD NO_SQ)], @args); $file =~ s/^{'_no_head'} = $no_head; $self->{'_no_sq'} = $no_sq; # get the sequence so Bio::DB::Sam can work with it my $refdb; my $inspector; if (-e $index && -r _ ) { $refdb = ($index =~ m/\.gz[^.]*$/) ? $self->_uncompress($index) : $index; my $guesser = Bio::Tools::GuessSeqFormat->new(-file=>$refdb); $self->throw("'$index' is not a fasta file.") unless $guesser->guess =~ m/^fasta$/; } elsif ($HAVE_BOWTIE) { $inspector = Bio::Tools::Run::Bowtie->new( -command => 'inspect' ); $refdb = $inspector->run($index); } else { $self->throw("Bio::Tools::Run::Bowtie is not available - cannot extract refdb from index."); } my $bam_file = $self->_make_bam($self->_bowtie_to_sam($file, $refdb)); my $sam = Bio::Assembly::IO->new( -file => "<$bam_file", -refdb => $refdb , -format => 'sam' ); return $sam; } sub _bowtie_to_sam { my ($self, $file, $refdb) = @_; $self->throw("'$file' does not exist or is not readable.") unless ( -e $file && -r _ ); if ($file =~ m/\.gz[^.]*$/) { $file = $self->_uncompress($file); $self->close; open my $fh, '<', $file or $self->throw("Could not read file '$file': $!"); $self->file($file); $self->_fh($fh); } my $guesser = Bio::Tools::GuessSeqFormat->new(-file=>$file); $self->throw("'$file' is not a bowtie formatted file.") unless $guesser->guess =~ m/^bowtie$/; my %SQ; my $mapq = 255; my $in_pair; my @mate_line; my $mlen; # create temp file for working my ($sam_tmp_h, $sam_tmp_f) = $self->tempfile( -dir => $self->{'_tempdir'}, -suffix => '.sam' ); while (my $line = $self->_readline) { chomp($line); my ($qname,$strand,$rname,$pos,$seq,$qual,$m,$details)=split("\cI",$line); $SQ{$rname} = 1; my $paired_f = ($qname =~ m#/[12]#) ? 0x03 : 0; my $strand_f = ($strand eq '-') ? 0x10 : 0; my $op_strand_f = ($strand eq '+' && $paired_f) ? 0x20 : 0; my $first_f = ($qname =~ m#/1#) ? 0x40 : 0; my $second_f = ($qname =~ m#/2#) ? 0x80 : 0; my $flag = $paired_f | $strand_f | $op_strand_f | $first_f | $second_f; $pos++; my $len = length $seq; die unless $len == length $qual; my $cigar = $len.'M'; my @detail = split(',',$details); my $dist = 'NM:i:'.scalar @detail; my @mismatch; my $last_pos = 0; for (@detail) { m/(\d+):(\w)>\w/; my $err = ($1-$last_pos); $last_pos = $1+1; push @mismatch,($err,$2); } push @mismatch, $len-$last_pos; @mismatch = reverse @mismatch if $strand eq '-'; my $mismatch = join('',('MD:Z:',@mismatch)); if ($paired_f) { my $mrnm = '='; if ($in_pair) { my $mpos = $mate_line[3]; $mate_line[7] = $pos; my $isize = $mpos-$pos-$len; $mate_line[8] = -$isize; print $sam_tmp_h join("\t",@mate_line),"\n"; print $sam_tmp_h join("\t",$qname, $flag, $rname, $pos, $mapq, $cigar, $mrnm, $mpos, $isize, $seq, $qual, $mismatch, $dist),"\n"; $in_pair = 0; } else { $mlen = $len; @mate_line = ($qname, $flag, $rname, $pos, $mapq, $cigar, $mrnm, undef, undef, $seq, $qual, $mismatch, $dist); $in_pair = 1; } } else { my $mrnm = '*'; my $mpos = 0; my $isize = 0; print $sam_tmp_h join("\t",$qname, $flag, $rname, $pos, $mapq, $cigar, $mrnm, $mpos, $isize, $seq, $qual, $mismatch, $dist),"\n"; } } $sam_tmp_h->close; return $sam_tmp_f if $self->{'_no_head'}; my ($samh, $samf) = $self->tempfile( -dir => $self->{'_tempdir'}, -suffix => '.sam' ); # print header print $samh $HD; # print sequence dictionary unless ($self->{'_no_sq'}) { my $db = Bio::SeqIO->new( -file => $refdb, -format => 'fasta' ); while ( my $seq = $db->next_seq() ) { $SQ{$seq->id} = $seq->length if $SQ{$seq->id}; } map { print $samh join("\t", ('@SQ', "SN:$_", "LN:$SQ{$_}")), "\n" } keys %SQ; } # print program print $samh $PG; # print alignments open $sam_tmp_h, '<', $sam_tmp_f or $self->throw("Could not read file '$sam_tmp_f': $!"); print $samh $_ while (<$sam_tmp_h>); close($sam_tmp_h); $samh->close; return $samf; } sub _uncompress { my ($self, $file) = @_; unless ($HAVE_IO_UNCOMPRESS) { croak( "IO::Uncompress::Gunzip not available, can't expand '$file'" ); } my ($tfh, $tf) = $self->tempfile( -dir => $self->{'_tempdir'} ); my $z = IO::Uncompress::Gunzip->new($file); while (my $block = $z->getline) { print $tfh $block } close $tfh; $file = $tf; return $file } sub _make_bam { my ($self, $file) = @_; $self->throw("'$file' does not exist or is not readable") unless ( -e $file && -r _ ); # make a sorted bam file from a sam file input my ($bamh, $bamf) = $self->tempfile( -dir => $self->{'_tempdir'}, -suffix => '.bam' ); my ($srth, $srtf) = $self->tempfile( -dir => $self->{'_tempdir'}, -suffix => '.srt' ); $_->close for ($bamh, $srth); my $samt = Bio::Tools::Run::Samtools->new( -command => 'view', -sam_input => 1, -bam_output => 1 ); $samt->run( -bam => $file, -out => $bamf ); $samt = Bio::Tools::Run::Samtools->new( -command => 'sort' ); $samt->run( -bam => $bamf, -pfx => $srtf); return $srtf.'.bam' } 1; BioPerl-1.007002/Bio/Assembly/IO/maq.pm000555000766000024 4321513155576320 17456 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Assembly::IO::maq # # Copyright by Mark A. Jensen # # You may distribute this module under the same terms as Perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Assembly::IO::maq - Driver to read assembly files in maq format *BETA* =head1 SYNOPSIS # convert the native maq map format to plain text $ maq mapview all.map > all.maq # Building an input stream use Bio::Assembly::IO; # Assembly loading methods my $asmio = Bio::Assembly::IO->new( -file => 'all.maq', -format => 'maq' ); my $scaffold = $asmio->next_assembly; =head1 DESCRIPTION This package loads and writes map information in/from C map files converted by the C utility. This module is a driver module for Bio::Assembly::IO input/output. Parsing is based on Heng Li's description of C output, found at the C manpage: L. The basic C workflow is: map reads to a reference sequence (with C), then create a consensus from the map (with C). To read a complete assembly with this module, the following files need to be available: [basename].maq : created by maq mapview [basename].map > [basename].maq [basename].cns.fastq : created as follows $ maq assemble [basename].cns [refseq].bfa [basename].map $ maq cns2fq [basename].cns > [basename].cns.fastq C produces only one "contig"; all reads map to the reference sequence, which covers everything. This module breaks the reads into contigs by dividing the C consensus into pieces for which there are contiguous non-zero quality values. The module C will help in this process (eventually). This module has no write capability. =head2 Implementation Assemblies are loaded into Bio::Assembly::Scaffold objects composed of Bio::Assembly::Contig and Bio::Assembly::Singlet objects. Contigs are not explicitly specified in C files; the division of the map into contigs is calculated in this module. Additional assembly information is stored as features. Contig objects have SeqFeature information associated with the primary_tag: _main_contig_feature:$contig_id -> misc contig information Read objects have sub_seqFeature information associated with the primary_tag: _main_read_feature:$read_id -> misc read information Singlets are contigs of a single sequence, as calculated within this module. They are cataloged separately, as specified in L. =head1 TODO =over =item * Add pod descriptions of maq descriptive data (currently SeqFeatures added to each contig component) =item * Add features describing the aggregate status of reads and contigs based on the maq "paired flag" =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the BioPerl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Mark A. Jensen Email maj -at- fortinbras -dot- us =head1 CONTRIBUTORS Further improvements by Florent Angly (florent dot angly at gmail dot com) =head1 ACKNOWLEDGEMENT Code and some POD text ripped liberally from Florent Angly's L. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_". =cut package Bio::Assembly::IO::maq; use strict; use Bio::Seq::Quality; use Bio::Seq::PrimaryQual; use Bio::LocatableSeq; use Bio::Assembly::IO; use Bio::Assembly::Scaffold; use Bio::Assembly::Contig; use Bio::Assembly::Singlet; use Bio::SeqIO; use File::Spec; use File::Basename; use base qw(Bio::Assembly::IO); # paired flag constants use constant { FF => 1, FR => 2, RF => 4, RR => 8, PE => 16, XC => 32, UN => 64, CP => 18 }; my $progname = 'maq'; =head2 next_assembly Title : next_assembly Usage : $scaffold = $stream->next_assembly() Function: return the assembly defined by the map and cns files Returns : Bio::Assembly::Scaffold object Args : none =cut sub next_assembly { my $self = shift; my $assembly = Bio::Assembly::Scaffold->new( -progname => $progname ); # Load contigs and singlets in the scaffold while ( my $obj = $self->next_contig()) { # Add contig /singlet to assembly if ($obj->isa('Bio::Assembly::Singlet')) { # a singlet $assembly->add_singlet($obj); } else { # a contig $assembly->add_contig($obj); } } return $assembly; } =head2 next_contig Title : next_contig Usage : $scaffold = $stream->next_contig() Function: Returns the next contig or singlet in the ACE stream. Returns : a Bio::Assembly::Contig or Bio::Assembly::Single object Args : none =cut sub next_contig { my $self = shift; # object reference # Read the file of consensus sequences if it has not already been done for # this Bio:::Assembly::IO stream already if (not defined $self->_cons) { $self->_parse_cns_file or $self->throw("Associated maq consensus file is not available"); } # Contig and read related my $contigobj; my %contiginfo; # Loop over all assembly file lines while ($_ = $self->_readline) { chomp; next if /^$/; # mapview format parsing ; every line is a read... my %readinfo; @readinfo{ qw(read_name chr posn strand insert_size paired_flag map_qual se_map_qual alt_map_qual num_mm_best_hit sum_qual_mm_best_hit zero_mm_hits one_mm_hits read_len seqstr qualstr) } = split(/\s+/); # sanger conversion my @qual = map { ord($_)-33 } split('', $readinfo{qualstr}); $readinfo{seq} = Bio::Seq::Quality->new( -id => $readinfo{read_name}, -seq => $readinfo{seqstr}, -qual => \@qual ); if ( not defined $contiginfo{start} ) { # First read of new contig or singlet $contiginfo{'seqnum'} = 1; $contiginfo{'qualobj'} = $self->_next_cons; $contiginfo{'start'} = $contiginfo{'qualobj'}->start; $contiginfo{'end'} = $contiginfo{'qualobj'}->end; $contiginfo{'asmbl_id'} = 'maq_assy['.$self->_basename.']/'.$contiginfo{start}.'-'.$contiginfo{end}; # It may be a singlet, but assume it's a contig for now $contigobj = $self->_init_contig(\%contiginfo); $self->_store_read(\%readinfo, $contigobj); } else { if ( $readinfo{'posn'} <= $contiginfo{end} ) { # Add read to existing contig $contiginfo{'seqnum'}++; $self->_store_read(\%readinfo, $contigobj); } else { # Read belongs in a new contig if ($contiginfo{'seqnum'} > 1) { $self->_store_contig(\%contiginfo, $contigobj); } else { # singlet # Create a new singlet object from the read info $contigobj = $self->_store_singlet(\%contiginfo, $contigobj); } # do a pushback $self->_pushback($_); last; } } } return $contigobj; } =head2 _init_contig() Title : _init_contig Usage : my $contigobj; $contigobj = $self->_init_contig( \%contiginfo, $scaffoldobj); Function: store information of a contig belonging to a scaffold in the appropriate object Returns : Bio::Assembly::Contig object Args : hash, Bio::Assembly::Scaffold =cut sub _init_contig { my ($self, $contiginfo) = @_; # Create a contig and attach it to scaffold my $contigobj = Bio::Assembly::Contig->new( -id => $$contiginfo{'asmbl_id'}, -source => $progname, -strand => 1 ); return $contigobj; } =head2 _store_contig() Title : _store_contig Usage : my $contigobj; $contigobj = $self->_store_contig( \%contiginfo, $contigobj); Function: store information of a contig belonging to a scaffold in the appropriate object Returns : Bio::Assembly::Contig object Args : hash, Bio::Assembly::Contig =cut sub _store_contig { my ($self, $contiginfo, $contigobj) = @_; $self->throw("Contig object must be defined") unless $contigobj; my $consensus_seq = Bio::LocatableSeq->new( -id => $$contiginfo{'asmbl_id'}, -seq => $$contiginfo{'qualobj'}->seq, -start => 1, ); $contigobj->set_consensus_sequence($consensus_seq); my $consensus_qual = Bio::Seq::PrimaryQual->new( -id => $$contiginfo{'asmbl_id'}, -qual => $$contiginfo{'qualobj'}->qual, -start => 1, ); $contigobj->set_consensus_quality($consensus_qual); # Add other misc contig information as features of the contig # Add other misc read information as subsequence feature my @other = grep !/asmbl_id|end|qualobj|start/, keys %$contiginfo; my %other; @other{@other} = @$contiginfo{@other}; my $contigtags = Bio::SeqFeature::Generic->new( -primary => '_main_contig_feature', -source => $$contiginfo{'asmbl_id'}, -start => 1, -end => $contigobj->get_consensus_length(), -strand => 1, # dumping ground: -tag => \%other ); $contigobj->add_features([ $contigtags ], 1); return $contigobj; } =head2 _parse_cns_file() Title : _parse_cns_file Usage : $self->_parse_cns_file Function: parse the .cns.fastq (consensus) file associated with the present map; set the objects cns attribute Returns : true on success; nil if file dne Args : none =cut sub _parse_cns_file { my ($self) = @_; my @cons; $self->{'_cns_parsed'} = 1; my $file = $self->file; $file =~ s/^[<>+]*//; # byebye parasitic mode chars my ($fname, $dir, $suf) = fileparse($file, ".maq"); my $cnsf = File::Spec->catdir($dir, "$fname.cns.fastq"); return unless (-e $cnsf ); my $fqio = Bio::SeqIO->new( -file => $cnsf ); my $cns = $fqio->next_seq; # now, infer the contigs on the basis of quality values # - assuming quality of zero => no coverage my $qual = $cns->qual; # covered sites my @sites = grep { $$qual[$_] > 0 } (0..$#$qual); my @ranges = ($sites[0]+1); for my $i (1..$#sites) { if ($sites[$i]-$sites[$i-1]>1) { push @ranges, $sites[$i-1]+1, $sites[$i]+1; } } push @ranges, $sites[-1]; for (my $i = 0; $i<$#ranges; $i+=2) { push @cons, Bio::Seq::Quality->new( -display_id => "${fname}/".$ranges[$i]."-".$ranges[$i+1], -start => $ranges[$i], -end => $ranges[$i+1], -seq => $cns->subseq($ranges[$i], $ranges[$i+1]), -qual => [@{$cns->qual}[$ranges[$i]-1..$ranges[$i+1]-1]] ); } $self->{'_cons'} = \@cons; return 1; } =head2 _cons() Title : _cons Usage : @cons = $self->_cons Function: get the array of consensus fastq Bio::Seq::Quality objects Returns : array of Bio::Seq::Quality objects Args : none =cut sub _cons { my $self = shift; my $cons = undef; if (defined $self->{'_cons'}) { $cons = $self->{'_cons'}; } return $cons; } =head2 _next_cons() =cut sub _next_cons { shift(@{shift->{'_cons'}}) } =head2 _store_read() Title : _store_read Usage : my $readobj = $self->_store_read(\%readinfo, $contigobj); Function: store information of a read belonging to a contig in the appropriate object Returns : a Bio::LocatableSeq object Args : hash, Bio::Assembly::Contig =cut # @readinfo{ qw(read_name chr posn strand insert_size, # paired_flag map_qual se_map_qual alt_map_qual, # num_mm_best_hit sum_qual_mm_best_hit zero_mm_hits, # one_mm_hits seqstr qualstr) } = split(/\s+/); sub _store_read { my ($self, $readinfo, $contigobj) = @_; # Create an aligned read object $$readinfo{'strand'} = ($$readinfo{strand} eq '+' ? 1 : -1); my $readobj = Bio::LocatableSeq->new( -display_id => $$readinfo{'read_name'}, -primary_id => $$readinfo{'read_name'}, -seq => $$readinfo{'seqstr'}, -start => 1, -strand => $$readinfo{'strand'}, -alphabet => 'dna' ); # Add read location and sequence to contig (in 'gapped consensus' coordinates) $$readinfo{'aln_start'} = $$readinfo{'posn'}; $$readinfo{'aln_end'} = $$readinfo{'posn'} + length($$readinfo{'seqstr'})-1; my $alncoord = Bio::SeqFeature::Generic->new( -primary => $readobj->id, -start => $$readinfo{'aln_start'}, -end => $$readinfo{'aln_end'}, -strand => $$readinfo{'strand'}, -qual => join(' ', $$readinfo{seq}->qual), # check here, need to create contigs "by hand"... -tag => { 'contig' => $contigobj->id() } ); $contigobj->set_seq_coord($alncoord, $readobj); # Add other misc read information as subsequence feature my @other = grep !/aln_(?:end|start)|seq(?:str)?|strand/, keys %$readinfo; my %other; @other{@other} = @$readinfo{@other}; my $readtags = Bio::SeqFeature::Generic->new( -primary => '_main_read_feature', -source => $readobj->id, -start => $$readinfo{'aln_start'}, -end => $$readinfo{'aln_end'}, -strand => $$readinfo{'strand'}, # dumping ground: -tag => \%other ); $contigobj->get_features_collection->add_features([$readtags]); $contigobj->get_features_collection->add_SeqFeature($alncoord, $readtags); return $readobj; } #### revamp for maq =head2 _store_singlet() Title : _store_singlet Usage : my $singletobj = $self->_store_read(\%readinfo, \%contiginfo); Function: store information of a singlet belonging to a scaffold in a singlet object Returns : Bio::Assembly::Singlet Args : hash, hash =cut sub _store_singlet { my ($self, $contiginfo, $contigobj) = @_; my $contigid = $$contiginfo{'asmbl_id'}; my $seqref = ($contigobj->each_seq())[0]; my $singletobj = Bio::Assembly::Singlet->new( -id => $contigid, -seqref => $seqref ); # Add other misc contig information as features of the contig # Add other misc read information as subsequence feature #my @other = grep !/_sfc|_assembly|_elem/, keys %$contiginfo; # remove the objects; _elem contains a code ref and can't be frozen. Just shooting blind here. #my %other; #@other{@other} = @$contiginfo{@other}; #my $contigtags = Bio::SeqFeature::Generic->new( # -primary => '_main_contig_feature', # -source => $$contiginfo{asmbl_id}, # -start => 1, # -end => $singletobj->get_consensus_length(), # -strand => 1, # # dumping ground: # -tag => \%other #); #$singletobj->add_features([ $contigtags ], 1); #$$readinfo{'aln_start'} = $$readinfo{'start'}; #$$readinfo{'aln_end'} = $$readinfo{'end'}; #$$readinfo{'strand'} = ($$readinfo{strand} eq '+' ? 1 : -1); #my $alncoord = Bio::SeqFeature::Generic->new( # -primary => '_aligned_coord', # -source => $$readinfo{read_name}, # -start => $$readinfo{'start'}, # -end => $$readinfo{'end'}, # -strand => $$readinfo{'strand'}, # -tag => { 'contig' => $$contiginfo{asmbl_id} } # ); #$alncoord->attach_seq($singletobj->seqref); #$singletobj->add_features([ $alncoord ], 0); # Add other misc read information as subsequence feature #my @other = grep !/seqstr|strand/, keys %$readinfo; #my %other; #@other{@other} = @$readinfo{@other}; #my $readtags = Bio::SeqFeature::Generic->new( # -primary => '_main_read_feature', # -source => $$readinfo{read_name}, # -start => $$readinfo{'aln_start'}, # -end => $$readinfo{'aln_end'}, # -strand => $$readinfo{'strand'}, # # dumping ground: # -tag => \%other # ); #$singletobj->get_features_collection->add_features([$readtags]); #$singletobj->get_features_collection->add_SeqFeature($alncoord, $readtags); return $singletobj; } ###### writes -- need them?? =head2 write_assembly() Title : write_assembly Usage : Function: not currently available for maq assemblies Returns : throw Args : =cut sub write_assembly { my ($self,@args) = @_; $self->throw("Writes not currently available for maq assemblies. Complain to author.") } =head2 _basename() Title : _basename Usage : $self->_basename Function: return the basename of the associate IO file Returns : scalar string Args : none =cut sub _basename { my $self = shift; return (fileparse($self->file, ".maq"))[0]; } 1; __END__ BioPerl-1.007002/Bio/Assembly/IO/phrap.pm000444000766000024 3474213155576320 20014 0ustar00cjfieldsstaff000000000000# # BioPerl driver for phrap.out file # # Copyright by Robson F. de Souza # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Assembly::IO::phrap - driver to load phrap.out files. =head1 SYNOPSIS # Building an input stream use Bio::Assembly::IO; # Assembly loading methods my $io = Bio::Assembly::IO->new( -file => 'results.phrap', -format => 'phrap'); # Read the entire scaffold my $scaffold = $io->next_assembly; # Or read one contig at a time to save resources while ( my $contig = $io->next_contig ) { # Do something ... } =head1 DESCRIPTION This package was developed to load the phrap.out files from the (phred/phrap/consed) package by Phill Green. This files contain just the messages printed to standard out by phrap when building an assembly. This output is redirected by phredPhrap perl-script to a file in the project's directory and hold some bit of information regarding assembly quality, connections between contigs and clone's position inside contigs. It should be noted that such files have no data about the sequence. neither for contig consensus nor for any aligned sequence. Anyway, such information may be loaded from Fasta files in the projects directory and added to the assembly object later. Note that, because no sequence is loaded for the contig consensus and locations for aligned sequences are only given in "ungapped consensus" coordinates in a phrap.out file, you can't make coordinate changes in assemblies loaded by pharp.pm, unless you add an aligned coordinates for each sequence to each contig's features collection yourself. See L and L.. This driver also loads singlets into the assembly contigs as Bio::Assembly::Singlet objects, although without their sequence strings. It also adds a feature for the entire sequence, thus storing the singlet length in its end position, and adds a tag '_nof_trimmed_nonX' to the feature, which stores the number of non-vector bases in the singlet. =head2 Implementation Assemblies are loaded into Bio::Assembly::Scaffold objects composed by Bio::Assembly::Contig objects. No features are added to Bio::Assembly::Contig "_aligned_coord:$seqID" feature class, therefore you can't make coordinate changes in contigs loaded by this module. Contig objects created by this module will have the following special feature classes, identified by their primary tags, in their features collection: "_main_contig_feature:$ID" : main feature for contig $ID. This feature is used to store information about the entire consensus sequence. This feature always start at base 1 and its end position is the consensus sequence length. A tag, 'trimmed_length' holds the length of the trimmed good quality region inside the consensus sequence. "_covered_region:$index" : coordinates for valid clones inside the contig. $index is the covered region number, starting at 1 for the covered region closest to the consensus sequence first base. "_unalign_coord:$seqID" : location of a sequence in "ungapped consensus" coordinates (consensus sequence without gaps). Primary and secondary scores, indel and substitutions statistics are stored as feature tags. "_internal_clones:$cloneID" : clones inside contigs $cloneID should be used as the unique id for each clone. These features have six tags: '_1st_name', which is the id of the upstream (5') aligned sequence delimiting the clone; '_1st_strand', the upstream sequence strand in the alignment; '_2nd_name', downstream (3') sequence id; '_2nd_strand', the downstream sequence strand in the alignment; '_length', unaligned clone length; '_rejected', a boolean flag, which is false if the clone is valid and true if it was rejected. All coordinates for the features above are expressed as "ungapped consensus" coordinates (See L.. =head2 Feature collection # =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Robson Francisco de Souza Email rfsouza@citri.iq.usp.br head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Assembly::IO::phrap; use strict; use Bio::Assembly::Scaffold; use Bio::Assembly::Singlet; use Bio::Assembly::Contig; use Bio::LocatableSeq; use Bio::Seq; use Bio::SeqFeature::Generic; use base qw(Bio::Assembly::IO); our $progname = 'phrap'; =head1 Parser methods =head2 next_assembly Title : next_assembly Usage : $scaffold = $stream->next_assembly() Function: returns the next assembly in the stream Returns : a Bio::Assembly::Scaffold object Args : none =cut sub next_assembly { my $self = shift; my $assembly = Bio::Assembly::Scaffold->new( -source => $progname ); # Load contigs and singlets in the scaffold while ( my $obj = $self->next_contig()) { # Add contig /singlet to assembly if ($obj->isa('Bio::Assembly::Singlet')) { # a singlet $assembly->add_singlet($obj); } else { # a contig $assembly->add_contig($obj); } } # Load annotations of assembly and contigs $self->scaffold_annotations($assembly); return $assembly; } =head2 next_contig Title : next_contig Usage : $scaffold = $stream->next_contig() Function: Returns the next contig or singlet in the PHRAP stream. Returns : a Bio::Assembly::Contig or Bio::Assembly::Single object Args : none =cut sub next_contig { my $self = shift; # Package reference # Looping over all phrap out file lines my $contigOBJ; while ($_ = $self->_readline) { chomp; # Loading singlets reads data #/^(\d+) isolated singlet/ && do { # should it match 'singlets' and 'singletons'? # while ($_ = $self->_readline) { # chomp; # last if (/^$/); /^\s+(\S+)\s+(\d+)\s+\((\d+)\)/ && do { my ($singletID, $length, $nof_trimmed_nonX) = ($1, $2, $3); # Create singlet object, and add it to scaffold my $seq = Bio::LocatableSeq->new( -id => $singletID, -primary_id => $singletID, -start => 1, -end => $length, -strand => 1, -nowarnonempty => 1, -alphabet => 'dna' ); $contigOBJ = Bio::Assembly::Singlet->new( -id => $singletID, -seqref => $seq, -verbose => $self->verbose ); my $feat = Bio::SeqFeature::Generic->new( -start => 1, -end => $length, -primary => "_main_contig_feature", -source => $contigOBJ->id, -tag => { '_nof_trimmed_nonX' => $nof_trimmed_nonX } ); $contigOBJ->add_features([ $feat ],1); # Go to return statement last; }; # } #}; # Loading contig information /^Contig (\d+)\.\s+(\d+) reads?; (\d+) bp \(untrimmed\), (\d+) \(trimmed\)\./ && do { my ($contigID, $nof_reads, $length, $trimmed_length) = ($1, $2, $3, $4); $contigOBJ = Bio::Assembly::Contig->new( -id => $contigID, -verbose => $self->verbose, -source => 'phrap' ); my $feat = Bio::SeqFeature::Generic->new( -start => 1, -end => $length, -primary => "_main_contig_feature", -source => $contigOBJ->id, -tag => { '_trimmed_length' => $trimmed_length } ); $contigOBJ->add_features([ $feat ],1); }; # Loading read information /^(C?)\s+(-?\d+)\s+(\d+)\s+(\S+)\s+(\d+)\s+\(\s*(\d+)\)\s+(\d+\.\d*)\s+(\d+\.\d*)\s+(\d+\.\d*)/ && do { my ($strand, $start, $end, $readID, $primary_score, $secondary_score, $substitutions, $deletions, $insertions) = ($1, $2, $3, $4, $5, $6, $7, $8, $9); $strand = ($strand eq 'C' ? -1 : 1); my $seq = Bio::LocatableSeq->new( -start => $start, -end => $end, -nowarnonempty => 1, -strand => $strand, -id => $readID, -primary_id => $readID, -alphabet => 'dna'); my $unalign_coord = Bio::SeqFeature::Generic->new( -start => $start, -end => $end, -primary => "_unalign_coord", -source => $readID, -tag => {'_primary_score'=>$primary_score, '_secondary_score'=>$secondary_score, '_substitutions'=>$substitutions, '_insertions'=>,$insertions, '_deletions'=>$deletions } ); $unalign_coord->attach_seq($seq); $contigOBJ->add_seq($seq); $contigOBJ->add_features([ $unalign_coord ]); }; /^$/ && do { # blank line, could be the end of a contig if ($contigOBJ) { # Go to the return statement last; } }; } # while ($_ = $self->_readline) return $contigOBJ; } =head2 scaffold_annotations Title : scaffold_annotations Usage : $stream->scaffold_annotations($scaffold) Function: Adds ssembly and contig annotations to a scaffold. In the PHRAP format, this is the section starting with "INTERNAL" Returns : 1 for success Args : a Bio::Assembly::Scaffold object to attach the annotations to =cut sub scaffold_annotations { my ($self, $assembly) = @_; # Read the PHRAP stream from the beginning again seek($self->_fh, 0, 0); while ($_ = $self->_readline) { chomp; # Loading exact dupicated reads list # /Exact duplicate reads:/ && do { # my @exact_dupl; # while () { # last if (/^\s*$/); # /(\S+)\s+(\S+)/ && do { # push(@exact_dupl,[$1,$2]); # }; # $self->{'assembly'}{'exact_dupl_reads'} = # new Data::Table(\@exact_dupl,['included','excluded'],0); # } # }; # Loading INTERNAL clones description /INTERNAL\s+Contig\s+(\d+)\s+opp\s+sense/ && do { my $contigID = $1; my $contig = $assembly->get_contig_by_id($contigID) || $assembly->get_singlet_by_id($contigID); while ($_ = $self->_readline) { my (@data,$rejected,$c1_strand,$c2_strand); (@data = /\s+(\*?)\s+(C?)\s+(\S+)\s+(C?)\s+(\S+)\s+(-?\d+)\s+(-?\d+)\s+(-?\d+)/) && do { if ($data[0] eq '*') { $rejected = 1 } else { $rejected = 0 } $c1_strand = ($data[1] eq 'C' ? -1 : 1); $c2_strand = ($data[3] eq 'C' ? -1 : 1); (my $clone_name = $data[2]) =~ s/^(\S+)\.\w.*/$1/; my $clone = Bio::SeqFeature::Generic->new( -start => $data[6], -end => $data[7], -strand => 0, -primary => "_internal_clone", -source => $clone_name, -tag => {'_1st_strand'=>,$c1_strand, '_2nd_strand'=>,$c2_strand, '_1st_name'=>$data[2], '_2nd_name'=>$data[4], '_length'=>$data[5], '_rejected'=>$rejected} ); $contig->add_features([ $clone ]); }; /Covered regions:/ && do { my %coord = /(\d+)/g; my $i = 0; foreach my $start (sort { $a <=> $b } keys %coord) { my $cov = Bio::SeqFeature::Generic->new( -start => $start, -end => $coord{$start}, -primary => '_covered_region', -source => ++$i, ); # 1: attach feature to contig consensus, if any $contig->add_features([ $cov ],1); } last; # exit while loop }; # /Covered regions:/ } # while ($_ = $self->_readline) }; # /INTERNAL\s+Contig\s+(\d+)\s+opp\s+sense/ } # while ($_ = $self->_readline) return 1; } =head2 write_assembly (NOT IMPLEMENTED) Title : write_assembly Usage : $ass_io->write_assembly($assembly) Function: Write the assembly object in Phrap compatible ACE format Returns : 1 on success, 0 for error Args : A Bio::Assembly::Scaffold object =cut sub write_assembly { my $self = shift; $self->throw_not_implemented(); } 1; __END__ BioPerl-1.007002/Bio/Assembly/IO/sam.pm000555000766000024 5525313155576320 17465 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Assembly::IO::sam # # Please direct questions and support issues to # # Cared for by Mark A. Jensen # # Copyright Mark A. Jensen # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Assembly::IO::sam - An IO module for assemblies in Sam format *BETA* =head1 SYNOPSIS $aio = Bio::Assembly::IO( -file => "mysam.bam", -refdb => "myrefseqs.fas"); $assy = $aio->next_assembly; =head1 DESCRIPTION This is a (currently) read-only IO module designed to convert Sequence/Alignment Map (SAM; L) formatted alignments to L representations, containing .L and L objects. It uses lstein's L to parse binary formatted SAM (.bam) files guided by a reference sequence fasta database. B: C is not a BioPerl module; it can be obtained via CPAN. It in turn requires the C library; source can be downloaded at L. =head1 DETAILS =over =item * Required files A binary SAM (C<.bam>) alignment and a reference sequence database in FASTA format are required. Various required indexes (C<.fai>, C<.bai>) will be created as necessary (via L). =item * Compressed files ...can be specified directly , if L is installed. Get it from your local CPAN mirror. =item * BAM vs. SAM The input alignment should be in (possibly gzipped) binary SAM (C<.bam>) format. If it isn't, you will get a message explaining how to convert it, viz.: $ samtools view -Sb mysam.sam > mysam.bam The bam file must also be sorted on coordinates: do $ samtools sort mysam.unsorted.bam > mysam.bam =item * Contigs Contigs are calculated by this module, using the 'coverage' feature of the L object. A contig represents a contiguous portion of a reference sequence having non-zero coverage at each base. The bwa assembler (L) can assign read sequences to multiple reference sequence locations. The present implementation currently assigns such reads only to the first contig in which they appear. =item * Consensus sequences Consensus sequence and quality objects are calculated by this module, using the C callback feature of C. The consensus is (currently) simply the residue at a position that has the maximum sum of quality values. The consensus quality is the integer portion of the simple average of quality values for the consensus residue. =item * SeqFeatures Read sequences stored in contigs are accompanied by the following features: contig : name of associated contig cigar : CIGAR string for this read If the read is paired with a successfully mapped mate, these features will also be available: mate_start : coordinate of to which the mate was aligned mate_len : length of mate read mate_strand : strand of mate (-1 or 1) insert_size : size of insert spanned by the mate pair These features are obtained as follows: @ids = $contig->get_seq_ids; $an_id = $id[0]; # or whatever $seq = $contig->get_seq_by_name($an_id); # Bio::LocatableSeq's aren't SeqFeature containers, so... $feat = $contig->get_seq_feat_by_tag( $seq, "_aligned_coord:".$s->id ); ($cigar) = $feat->get_tag_values('cigar'); # etc. =back =head1 TODO =over =item * Supporting both text SAM (TAM) and binary SAM (BAM) =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: L rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Mark A. Jensen Email maj -at- fortinbras -dot- us =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Assembly::IO::sam; use strict; use warnings; # Object preamble - inherits from Bio::Root::Root use Bio::Seq::Quality; use Bio::Seq::PrimaryQual; use Bio::LocatableSeq; use Bio::Assembly::IO; use Bio::Assembly::Scaffold; use Bio::Assembly::Contig; use Bio::Assembly::Singlet; use Bio::SeqIO; use File::Spec; use File::Basename; use File::Temp qw(tempfile); use Carp; use Bio::Root::Root; use base qw(Bio::Root::Root Bio::Assembly::IO Bio::Root::IO); our $HAVE_IO_UNCOMPRESS; BEGIN { # check requirements unless ( eval "require Bio::DB::Sam; 1" ) { Bio::Root::Root->throw(__PACKAGE__.' requires installation of samtools (libbam) and Bio::DB::Sam (available on CPAN; not part of BioPerl)'); } unless ( eval "require IO::Uncompress::Gunzip; \$HAVE_IO_UNCOMPRESS = 1") { Bio::Root::Root->warn("IO::Uncompress::Gunzip is not available; you'll have to do your decompression by hand."); } } my $progname = 'sam'; sub new { my $class = shift; my @args = @_; my $self = $class->SUPER::new(@args); my ($file, $refdb, $format) = $self->_rearrange([qw(FILE REFDB FORMAT)], @args); $self->file($file); $refdb && $self->refdb($refdb); $self->_init_sam() or croak( "Sam initialization failed" ); $self->{_assigned} = {}; return $self; } =head1 Bio::Assembly::IO compliance =head2 next_assembly() Title : next_assembly Usage : my $scaffold = $asmio->next_assembly(); Function: return the next assembly in the sam-formatted stream Returns : Bio::Assembly::Scaffold object Args : none =cut sub next_assembly { my $self = shift; my @contig_set; # get Bio::DB::Sam object # could add a refdb or fasfile attribute to contain the reference db name # iterate through seq_ids... my @refseq_ids = $self->sam->seq_ids; my $assembly = Bio::Assembly::Scaffold->new( -progname => $progname ); foreach my $id (@refseq_ids) { #### this is choice 1: all refseqs into one assy...### $self->_current_refseq_id( $id ); # Load contigs and singlets in the scaffold while ( my $obj = $self->next_contig()) { # Add contig /singlet to assembly if ($obj->isa('Bio::Assembly::Singlet')) { # a singlet $assembly->add_singlet($obj); } else { # a contig $assembly->add_contig($obj); } } } return $assembly; } =head2 next_contig() Title : next_contig Usage : my $contig = $asmio->next_contig(); Function: return the next contig or singlet from the sam stream Returns : Bio::Assembly::Contig or Bio::Assembly::Singlet Args : none =cut sub next_contig { my $self = shift; if (!defined $self->_current_contig_seg_idx) { $self->_current_contig_seg_idx(0); } else { $self->_current_contig_seg_idx( 1+$self->_current_contig_seg_idx ); } unless ($self->_current_refseq_id) { croak("No current refseq id set"); } my $contig_segs = $self->_segset($self->_current_refseq_id); unless ($contig_segs && @$contig_segs) { croak("No contig segset for current id '".$self->_current_refseq_id."'") } # each segment in @$contig_segs represents a contig within the # current refseq my $contig_seg = $$contig_segs[$self->_current_contig_seg_idx]; return if (!defined $contig_seg); # iterator finished # each 'feature' in $contig_seg represents a read; # $seqio lets us iterate efficiently over the reads: my $seqio = $contig_seg->features(-iterator => 1); # Contig and read related my $contigobj = $self->_store_contig($contig_seg); my $numseq = 0; while ( my $read = $seqio->next_seq ) { if ($self->{_assigned}->{$read->name}) { next; } $self->{_assigned}->{$read->name}=1; $self->_store_read($read, $contigobj); $numseq++; } if ($numseq == 1) { # ooh! a singlet! $contigobj = $self->_store_singlet($contigobj); } return $contigobj; } =head2 write_assembly() Title : write_assembly Usage : Function: not implemented (module currrently read-only) Returns : Args : =cut sub write_assembly { my $self = shift; $self->throw( "This module is currently read-only" ); } =head1 Internal =head2 _store_contig() Title : _store_contig Usage : my $contigobj = $self->_store_contig(\%contiginfo); Function: create and load a contig object Returns : Bio::Assembly::Contig object Args : Bio::DB::Sam::Segment object =cut sub _store_contig { my ($self, $contig_seg) = @_; # Create a contig my $contigobj = Bio::Assembly::Contig->new( -id => 'sam_assy['.$self->_basename.':'.$self->_current_refseq_id.']/'.$contig_seg->start.'-'.$contig_seg->end, -source => $progname, -strand => 1 ); my $consobj = $self->_calc_consensus($contig_seg); my $consensus_seq = Bio::LocatableSeq->new( -id => $contigobj->id, -seq => $consobj->seq, -start => 1, ); $contigobj->set_consensus_sequence($consensus_seq); my $consensus_qual = Bio::Seq::PrimaryQual->new( -id => $contigobj->id, -qual => $consobj->qual, -start => 1, ); $contigobj->set_consensus_quality($consensus_qual); # Add other misc contig information as subsequence feature #my @other = grep !/asmbl_id|end|qualobj|start/, keys %$contiginfo; #my %other; #@other{@other} = @$contiginfo{@other}; #my $contigtags = Bio::SeqFeature::Generic->new( # -primary => '_main_contig_feature', # -source => $$contiginfo{'asmbl_id'}, # -start => 1, # -end => $contig_seg->length, # -strand => 1, # # dumping ground: # -tag => \%other #); #$contigobj->add_features([ $contigtags ], 1); return $contigobj; } =head2 _store_read() Title : _store_read Usage : my $readobj = $self->_store_read($readobj, $contigobj); Function: store information of a read belonging to a contig in a contig object Returns : Bio::LocatableSeq Args : Bio::DB::Bam::AlignWrapper, Bio::Assembly::Contig =cut sub _store_read { my $self = shift; my ($read, $contigobj) = @_; my $readseq = Bio::LocatableSeq->new( -display_id => $read->name, -primary_id => $read->name, -seq => $read->dna, -start => 1, -strand => $read->strand, -alphabet => 'dna' ); my $qual = Bio::Seq::PrimaryQual->new( -id => $read->name."_qual", -qual => [$read->qscore] ); # add pair information my @pair_info; if ($read->proper_pair) { # mate also aligned @pair_info = ( mate_start => $read->mate_start, mate_len => $read->mate_len, mate_strand => $read->mstrand, insert_size => $read->isize ); } my $alncoord = Bio::SeqFeature::Generic->new( -primary => $read->name, -start => $read->start, -end => $read->end, -strand => $read->strand, -qual => join(' ',$read->qscore), -tag => { 'contig' => $contigobj->id, 'cigar' => $read->cigar_str, @pair_info } ); $contigobj->set_seq_coord($alncoord, $readseq); $contigobj->set_seq_qual( $readseq, $qual ); #add other misc read info as subsequence feature: #my @other = grep !/aln_(?:end|start)|seq(?:str)?|strand/, keys %$readinfo; #my %other; #@other{@other} = @$readinfo{@other}; #my $readtags = Bio::SeqFeature::Generic->new( # -primary => '_main_read_feature', # -source => $readobj->id, # -start => $$readinfo{'aln_start'}, # -end => $$readinfo{'aln_end'}, # -strand => $$readinfo{'strand'}, # # dumping ground: # -tag => \%other #); #$contigobj->get_features_collection->add_features([$readtags]); #$contigobj->get_features_collection->add_SeqFeature($alncoord, $readtags); return $readseq; } =head2 _store_singlet() Title : _store_singlet Usage : my $singletobj = $self->_store_singlet($contigobj); Function: convert a contig object containing a single read into a singlet object Returns : Bio::Assembly::Singlet Args : Bio::Assembly::Contig (previously loaded with only one seq) =cut sub _store_singlet { my $self = shift; my ($contigobj) = @_; my ($readseq) = $contigobj->each_seq; my $singletobj = Bio::Assembly::Singlet->new( -id => $contigobj->id, -seqref => $readseq ); # may want to attach this someday # my $qual = $contigobj->get_qual_by_name($readseq->id); return $singletobj; } =head1 REALLY Internal =head2 _init_sam() Title : _init_sam Usage : $self->_init_sam($fasfile) Function: obtain a Bio::DB::Sam parsing of the associated sam file Returns : true on success Args : [optional] name of the fasta reference db (scalar string) Note : The associated file can be plain text (.sam) or binary (.bam); If the fasta file is not specified, and no file is contained in the refdb() attribute, a .fas file with the same basename as the sam file will be searched for. =cut sub _init_sam { my $self = shift; my $fasfile = shift; my $file = $self->file; my $sam; $fasfile ||= $self->refdb; $file =~ s/^[<>+]*//; # byebye parasitic mode chars my ($fname, $dir, $suf) = fileparse($file, ".sam", ".bam"); $self->_set_from_args({ '_basename' => $fname }, -methods => [qw( _basename)], -create => 1); if (!defined $fasfile) { for (qw( fas fa fasta fas.gz fa.gz fasta.gz )) { $fasfile = File::Spec->catdir($dir, $self->_basename.$_); last if -e $fasfile; undef $fasfile; } } unless (-e $fasfile) { croak( "Can't find associated reference fasta db" ); } !$self->refdb && $self->refdb($fasfile); # compression if ($fasfile =~ /\.gz[^.]*$/) { unless ($HAVE_IO_UNCOMPRESS) { croak( "IO::Uncompress::Gunzip not available; can't decompress on the fly"); } my ($tfh, $tf) = tempfile( UNLINK => 1); my $z = IO::Uncompress::Gunzip->new($fasfile) or croak("Can't expand: $@"); while (<$z>) { print $tfh $_ } close $tfh; $fasfile = $tf; } if ($file =~ /\.gz[^.]*$/) { unless ($HAVE_IO_UNCOMPRESS) { croak( "IO::Uncompress::Gunzip not available; can't decompress on the fly"); } my ($tfh, $tf) = tempfile( UNLINK => 1); my $z = IO::Uncompress::Gunzip->new($file) or croak("Can't expand: $@"); while (<$z>) { print $tfh $_; } close $tfh; $file = $tf; } # sam conversion : just barf for now if (-T $file) { my $bam = $file; $bam =~ s/\.sam/\.bam/; croak( "'$file' looks like a text file.\n\tTo convert to the required .bam (binary SAM) format, run\n\t\$ samtools view -Sb $file > $bam\n"); } $sam = Bio::DB::Sam->new( -bam => $file, -fasta => $fasfile, -autoindex => 1, -expand_flags => 1); unless (defined $sam) { croak( "Couldn't create the Bio::DB::Sam object" ); } $self->{sam} = $sam; # now produce the contig segments for each seq_id... for ($sam->seq_ids) { my $seg = $sam->segment(-seq_id=>$_, -start=>1, -end=>$sam->length($_)); ${$self->{_segset}}{$_} = [$self->_get_contig_segs_from_coverage($seg)]; } return 1; } =head2 _get_contig_segs_from_coverage() Title : _get_contig_segs_from_coverage Usage : Function: calculates separate contigs using coverage info in the segment Returns : array of Bio::DB::Sam::Segment objects, representing each contig Args : Bio::DB::Sam::Segment object =cut sub _get_contig_segs_from_coverage { my $self = shift; my $segment = shift; unless ($self->sam) { croak("Sam object not yet initialized (call _init_sam)"); } unless ( ref($segment) =~ /Bio::DB::Sam::Segment/ ) { croak("Requires Bio::DB::Sam::Segment object at arg 1"); } my ($cov, @covdata, @rngs, @segs); ($cov) = $segment->features('coverage'); unless ($cov) { croak("No coverage data!"); } @covdata = $cov->coverage; # calculate contigs: my $in_contig; my ($lf_end,$rt_end); for (0..$#covdata) { if ($covdata[$_]) { if ($in_contig) { $rt_end = $_+1; next; } else { $in_contig = 1; # push previous range if (defined $lf_end && defined $rt_end) { push @rngs, [$lf_end, $rt_end]; } $lf_end = $_+1; } } else { $in_contig = 0; } } # last one push @rngs, [$lf_end, $rt_end] if (defined $lf_end and defined $rt_end and $lf_end <= $rt_end); unless (@rngs) { carp ("No coverage for this segment!"); return; } for (@rngs) { push @segs, $self->sam->segment(-seq_id=>$segment->seq_id, -start=>$$_[0], -end=>$$_[1]); } return @segs; } =head2 _calc_consensus_quality() Title : _calc_consensus_quality Usage : @qual = $aio->_calc_consensus_quality( $contig_seg ); Function: calculate an average or other data-reduced quality over all sites represented by the features contained in a Bio::DB::Sam::Segment Returns : Args : a Bio::DB::Sam::Segment object =cut sub _calc_consensus_quality { # just an average over sites for now... my $self = shift; my $seg = shift; my @quals; my $region = $seg->seq_id.':'.$seg->start.'..'.$seg->end; my $qual_averager = sub { my ($seqid, $pos, $p) = @_; return unless ($seg->start <= $pos and $pos <= $seg->end); my $acc = 0; my $n = 0; for my $pileup (@$p) { my $b = $pileup->alignment; $acc += $b->qscore->[$pileup->qpos]; $n++; } push @quals, int($acc/$n); }; $self->sam->pileup($region, $qual_averager); return @quals; } =head2 _calc_consensus() Title : _calc_consensus Usage : @qual = $aio->_calc_consensus( $contig_seg ); Function: calculate a simple quality-weighted consensus sequence for the segment Returns : a SeqWithQuality object Args : a Bio::DB::Sam::Segment object =cut sub _calc_consensus { # just an average over sites for now... my $self = shift; my $seg = shift; my @quals; my $conseq =''; my $region = $seg->seq_id.':'.$seg->start.'-'.$seg->end; my $weighted_consensus = sub { my ($seqid, $pos, $p) = @_; return unless ($seg->start <= $pos and $pos <= $seg->end); my %wt_tbl; my %n; for my $pileup (@$p) { my $b = $pileup->alignment; my $res = substr($b->qseq,$pileup->qpos,1); $wt_tbl{$res} += $b->qscore->[$pileup->qpos] || 0; $n{$res} ||= 0; $n{$res}++; } # really simple my $c = (sort { $wt_tbl{$b}<=>$wt_tbl{$a} } keys %wt_tbl)[0]; $conseq .= $c; push @quals, int($wt_tbl{$c}/$n{$c}); }; $self->sam->pileup($region, $weighted_consensus); return Bio::Seq::Quality->new( -qual => join(' ', @quals ), -seq => $conseq, -id => $region ); } =head2 refdb() Title : refdb Usage : $obj->refdb($newval) Function: the name of the reference db fasta file Example : Returns : value of refdb (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub refdb { my $self = shift; return $self->{'refdb'} = shift if @_; return $self->{'refdb'}; } =head2 _segset() Title : _segset Usage : $segset_hashref = $self->_segset() Function: hash container for the Bio::DB::Sam::Segment objects that represent each set of contigs for each seq_id { $seq_id => [@contig_segments], ... } Example : Returns : value of _segset (a hashref) if no arg, or the arrayref of contig segments, if arg == a seq id Args : [optional] seq id (scalar string) Note : readonly; hash elt set in _init_sam() =cut sub _segset { my $self = shift; return $self->{'_segset'} unless @_; return ${$self->{'_segset'}}{shift()}; } =head2 _current_refseq_id() Title : _current_refseq_id Usage : $obj->_current_refseq_id($newval) Function: the "current" reference sequence id Example : Returns : value of _current_refseq (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub _current_refseq_id { my $self = shift; return $self->{'_current_refseq_id'} = shift if @_; return $self->{'_current_refseq_id'}; } =head2 _current_contig_seg_idx() Title : current_contig_seg_idx Usage : $obj->current_contig_seg_idx($newval) Function: the "current" segment index in the "current" refseq Example : Returns : value of current_contig_seg_idx (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub _current_contig_seg_idx { my $self = shift; return $self->{'_current_contig_seg_idx'} = shift if @_; return $self->{'_current_contig_seg_idx'}; } =head2 sam() Title : sam Usage : $obj->sam($newval) Function: store the associated Bio::DB::Sam object Example : Returns : value of sam (a Bio::DB::Sam object) Args : on set, new value (a scalar or undef, optional) =cut sub sam { my $self = shift; return $self->{'sam'}; } sub DESTROY { my $self = shift; undef $self->{'sam'}; delete $self->{_segset}->{$_} foreach (keys %{$self->{_segset}}); } 1; BioPerl-1.007002/Bio/Assembly/IO/tigr.pm000444000766000024 14527213155576320 17670 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Assembly::IO::tigr # # Copyright by Florent Angly # # You may distribute this module under the same terms as Perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Assembly::IO::tigr - Driver to read and write assembly files in the TIGR Assembler v2 default format. =head1 SYNOPSIS # Building an input stream use Bio::Assembly::IO; # Assembly loading methods my $asmio = Bio::Assembly::IO->new( -file => 'SGC0-424.tasm', -format => 'tigr' ); my $scaffold = $asmio->next_assembly; # Do some things on contigs... # Assembly writing methods my $outasm = Bio::Assembly::IO->new( -file => ">SGC0-modified.tasm", -format => 'tigr' ); $outasm->write_assembly( -scaffold => $assembly, -singlets => 1 ); =head1 DESCRIPTION This package loads and writes assembly information in/from files in the default TIGR Assembler v2 format. The files are lassie-formatted and often have the .tasm extension. This module was written to be used as a driver module for Bio::Assembly::IO input/output. =head2 Implementation Assemblies are loaded into Bio::Assembly::Scaffold objects composed of Bio::Assembly::Contig and Bio::Assembly::Singlet objects. Since aligned reads and contig gapped consensus can be obtained in the tasm files, only aligned/gapped sequences are added to the different BioPerl objects. Additional assembly information is stored as features. Contig objects have SeqFeature information associated with the primary_tag: _main_contig_feature:$contig_id -> misc contig information _quality_clipping:$read_id -> quality clipping position Read objects have sub_seqFeature information associated with the primary_tag: _main_read_feature:$read_id -> misc read information Singlets are considered by TIGR Assembler as contigs of one sequence. Contigs are represented here with features having these primary_tag: _main_contig_feature:$contig_id _quality_clipping:$read_primary_id _main_read_feature:$read_primary_id _aligned_coord:$read_primary_id =head1 THE TIGR TASM LASSIE FORMAT =head2 Description In the TIGR tasm lassie format, contigs are separated by a line containing a single pipe character "|", whereas the reads in a contig are separated by a blank line. Singlets can be present in the file and are represented as a contig composed of a single sequence. Other than the two above-mentioned separators, each line has an attribute name, followed a tab and then an attribute value. The tasm format is used by more TIGR applications than just TIGR Assembler. Some of the attributes are not used by TIGR Assembler or have constant values. They are indicated by an asterisk * Contigs have the following attributes: asmbl_id -> contig ID sequence -> contig ungapped consensus sequence (ambiguities are lowercase) lsequence -> gapped consensus sequence (lowercase ambiguities) quality -> gapped consensus quality score (in hexadecimal) seq_id -> * com_name -> * type -> * method -> always 'asmg' * ed_status -> * redundancy -> fold coverage of the contig consensus perc_N -> percent of ambiguities in the contig consensus seq# -> number of sequences in the contig full_cds -> * cds_start -> start of coding sequence * cds_end -> end of coding sequence * ed_pn -> name of editor (always 'GRA') * ed_date -> date and time of edition comment -> some comments * frameshift -> * Each read has the following attributes: seq_name -> read name asm_lend -> position of first base on contig ungapped consensus sequence asm_rend -> position of last base on contig ungapped consensus sequence seq_lend -> start of quality-trimmed sequence (aligned read coordinates) seq_rend -> end of quality-trimmed sequence (aligned read coordinates) best -> always '0' * comment -> some comments * db -> database name associated with the sequence (e.g. >my_db|seq1234) offset -> offset of the sequence (gapped consensus coordinates) lsequence -> aligned read sequence (ambiguities are uppercase) When asm_rend E asm_lend, the sequence was on the complementary DNA strand but its reverse complement is shown in the aligned sequence of the assembly file, not the original read. Ambiguities are reflected in the contig consensus sequence as lowercase IUPAC characters: a c g t u m r w s y k x n . In the read sequences, however, ambiguities are uppercase: M R W S Y K X N =head2 Example Example of a contig containing three sequences: sequence CGATGCTGTACGGCTGTTGCGACAGATTGCGCTGGGTCGATACCGCGTTGGTGATCGGCTTGTTCAGCGGGCTCTGGTTCGGCGACAGCGCGGCGATCTTGGCGGCTGCGAAGGTTGCCGGCGCAATCATGCGCTGCTGACCGTTGACCTGGTCCTGCCAGTACACCCAGTCGCCCACCATGACCTTCAGCGCGTAGCTGTCACAGCCGGCTGTGGTCAGCGCAGTGGCGACGGTGGTGTAGGAGGCGCCAGCAACACCTTGGGTGATCATGTAGCAGCCTTCTGACAGGCCGTAGGTCAGCATGGTCGGCCACTGGGTACCAGTCAGTCGGGTCAACCGAGATTCGCAsCTGAGCGCCACTGCCGCGCAGAGCGTACATGCCCTTGCGGGTCGCGCCGGTAACACCATCCACGCCGATCAGAACTGCGTCGGTGATGGTGGTGTTACCCGAGGTGCCAGTGGTGAAGGCGACGGTCTGGGTGCTGGCCACAGGCGCCAGAGTGGTCGCGCCAACGGTGGCGATGACCAGTTGCGATGGGCCACGGATACCTGACTGCCCGTTGTTCACGGCGCTGACGATGTTCTGCCACAGCGCCAGGCCAGAGCCGGTGATGTTGTCGAACACTTCGGGCGCAACGCCAGGGAGCGAGACGGTCAGCTTCCAGCTCGAAGCAGCGGAGCCAGTAGCCAGGGCGGCGCTGAGCGAGTTGCCGAGCGTGCCGGTGTAGAACGCGGTCAGCGTGGCGCCGGTGGCGGCGGCAGTGTCCTTCAGCGCACTGGTCGCGGCGGTGTCGGTGCCGTCAGTGACGCGCACGGCGCGGATGTTCGAGGCGCCGCCCTGGATTGATACCGCCAGCGCGGTGCACAGGTCGTACTTGCGCACGGTCyGAGTGCCGAACTTCTGCGATGCGTCACCTGGCGAGCCGATAaGCGTGGCGCTGTTCACCGGCCCCCAGTCAGCAATGCCGACGATGCCGAGAATGTCAGTCGGGACGCCATTGATGTAGCGGGTCTTGGGCGCCACTATTTGTATGTACAAATCTGGCGCAGATAAAGCCGCCGTATTCAAATAACCAGCAGGATAGATAGGCATCACGCCTCCAGAATGAAAAAGGCCACCGATTAGGTGGCCTTTGTTGTGTTCGGCTGGCTGTTAGAGCAGCAGCCCGTTTTCCCGCGCAAACGCGAATGGGTCCTTGTCATGCTTCCTGCAATTGCAGGTAGGACAAAGAATTTGCAGGTTGGATTTGTCGTTCGATCCGCCCTTTGCAAGCGGGAACACGTGGTCAACGTGATACCCATCCCTTATGGATATAGTGCACATGGCGCATTTCCAGCGCTGAGCAGCCAGCAAAAATTTTATGTCGTCGCCGGTGTGTGAGCCGACAGCATTTTTCTTGCGAGCCTTGTATGTCCGCGAGAGTGAACGAACTTGCTCCTTGTTGGCTGTCTTCCAGAGCTTTTGAGTAAGCGCACAGAGATCCTTGTTTCTTGATCTCCACTCTCTGGTTGCGGAAAT lsequence CGATGCTGTACGGCTGTTGCGACAGATTGCGCTGGGTCGATACCGCGTTGGTGATCGGCTTGTTCAGCGGGCTCTGGTTCGGCGACAGCGCGGCGATCTTGGCGGCTGCGAAGGTTGCCGGCGCAATCATGCGCTGCTGACCGTTGACCTGGTCCTGCCAGTACACCCAGTCGCCCACCATGACCTTCAGCGCGTAGCTGTCACAGCCGGCTGTGGTCAGCGCAGTGGCGACGGTGGTGTAGGAGGCGCCAGCAACACCTTGGGTGATCATGTAGCAGCCTTCTGACAGGCCGTAGGTCAGCATGGTCGGCCACTGGGTACCAGTCAGTCGGGTCAACCGAGATTCG-CAsCTGAGCGCCACTGCCGCGCAGAGCGTACATGCCCTTGCGGGTCGCGCCGGTAACACCATCCACGCCGATCAGAACTGCGTCGGTGATGGTGGTGTTACCCGAGGTGCCAGTGGTGAAGGCGACGGTCTGGGTGCTGGCCACAGGCGCCAGAGTGGTCGCGCCAACGGTGGCGATGACCAGTTGCGATGGGCCACGGATACCTGACTGCCCGTTGTTCACGGCGCTGACGATGTTCTGCCACAGCGCCAGGCCAGAGCCGGTGATGTTGTCGAACACTTCGGGCGCAACGCCAGGGAGCGAGACGGTCAGCTTCCAGCTCGAAGCAGCGGAGCCAGTAGCCAGGGCGGCGCTGAGCGAGTTGCCGAGCGTGCCGGTGTAGAACGCGGTCAGCGTGGCGCCGGTGGCGGCGGCAGTGTCCTTCAGCGCACTGGTCGCGGCGGTGTCGGTGCCGTCAGTGACGCGCACGGCGCGGATGTTCGAGGCGCCGCCCTGGATTGATACCGCCAGCGCGGTGCACAGGTCGTACTTGCGCACGGTCyGAGTGCCGAACTTCTGCGATGCGTCACCTGGCGAGCCGATAaGCGTGGCGCTGTTCACCGGCCCCCAGTCAGCAATGCCGACGATGCCGAGAATGTCAGTCGGGACGCCATTGATGTAGCGGGTCTTGGGCGCCACTATTTGTATGTACAAATCTGGCGCAGATAAAGCCGCCGTATTCAAATAACCAGCAGGATAGATAGGCATCACGCCTCCAGAATGAAAAAGGCCACCGATTAGGTGGCCTTTGTTGTGTTCGGCTGGCTGTTAGAGCAGCAGCCCGTTTTCCCGCGCAAACGCGAATGGGTCCTTGTCATGCTTCCTGCAATTGCAGGTAGGACAAAGAATTTGCAGGTTGGATTTGTCGTTCGATCCGCCCTTTGCAAGCGGGAACACGTGGTCAACGTGATACCCATCCCTTATGGATATAGTGCACATGGCGCATTTCCAGCGCTGAGCAGCCAGCAAAAATTTTATGTCGTCGCCGGTGTGTGAGCCGACAGCATTTTTCTTGCGAGCCTTGTATGTCCGCGAGAGTGAACGAACTTGCTCCTTGTTGGCTGTCTTCCAGAGCTTTTGAGTAAGCGCACAGAGATCCTTGTTTCTTGATCTCCACTCTCTGGTTGCGGAAAT quality 0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0505050505050505050E0505160505050505050505050505050505050505050505050505050505050303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0404040404040404041604040404040404040404040404040404040404040404040404040404040404040404040404040404040E0404040404040404040B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B asmbl_id 93 seq_id com_name type method asmg ed_status redundancy 1.11 perc_N 0.20 seq# 3 full_cds cds_start cds_end ed_pn GRA ed_date 08/16/07 17:10:12 comment frameshift seq_name SDSU_RFPERU_010_C09.x01.phd.1 asm_lend 1 asm_rend 4423 seq_lend 1 seq_rend 442 best 0 comment db offset 0 lsequence CGATGCTGTACGGCTGTTGCGACAGATTGCGCTGGGTCGATACCGCGTTGGTGATCGGCTTGTTCAGCGGGCTCTGGTTCGGCGACAGCGCGGCGATCTTGGCGGCTGCGAAGGTTGCCGGCGCAATCATGCGCTGCTGACCGTTGACCTGGTCCTGCCAGTACACCCAGTCGCCCACCATGACCTTCAGCGCGTAGCTGTCACAGCCGGCTGTGGTCAGCGCAGTGGCGACGGTGGTGTAGGAGGCGCCAGCAACACCTTGGGTGATCATGTAGCAGCCTTCTGACAGGCCGTAGGTCAGCATGGTCGGCCACTGGGTACCAGTCAGTCGGGTCAACCGAGATTCG-CAGCTGAGCGCCACTGCCGCGCAGAGCGTACATGCCCTTGCGGGTCGCGCCGGTAACACCATCCACGCCGATCAGAACTGCGTCGGTGATGGTGG seq_name SDSU_RFPERU_002_H12.x01.phd.1 asm_lend 339 asm_rend 940 seq_lend 1 seq_rend 602 best 0 comment db offset 338 lsequence CGAGATTCGCCACCTGAGCGCCACTGCCGCGCAGAGCGTACATGCCCTTGCGGGTCGCGCCGGTAACACCATCCACGCCGATCAGAACTGCGTCGGTGATGGTGGTGTTACCCGAGGTGCCAGTGGTGAAGGCGACGGTCTGGGTGCTGGCCACAGGCGCCAGAGTGGTCGCGCCAACGGTGGCGATGACCAGTTGCGATGGGCCACGGATACCTGACTGCCCGTTGTTCACGGCGCTGACGATGTTCTGCCACAGCGCCAGGCCAGAGCCGGTGATGTTGTCGAACACTTCGGGCGCAACGCCAGGGAGCGAGACGGTCAGCTTCCAGCTCGAAGCAGCGGAGCCAGTAGCCAGGGCGGCGCTGAGCGAGTTGCCGAGCGTGCCGGTGTAGAACGCGGTCAGCGTGGCGCCGGTGGCGGCGGCAGTGTCCTTCAGCGCACTGGTCGCGGCGGTGTCGGTGCCGTCAGTGACGCGCACGGCGCGGATGTTCGAGGCGCCGCCCTGGATTGATACCGCCAGCGCGGTGCACAGGTCGTACTTGCGCACGGTCCGAGTGCCGAACTTCTGCGATGCGTCACCTGGCGAGCCGATA-GCGTGGCGC seq_name SDSU_RFPERU_009_E07.x01.phd.1 asm_lend 880 asm_rend 1520 seq_lend 641 seq_rend 1 best 0 comment db offset 8803 lsequence CGCACGGTCTGAGTGCCGAACTTCTGCGATGCGTCACCTGGCGAGCCGATAAGCGTGGCGCTGTTCACCGGCCCCCAGTCAGCAATGCCGACGATGCCGAGAATGTCAGTCGGGACGCCATTGATGTAGCGGGTCTTGGGCGCCACTATTTGTATGTACAAATCTGGCGCAGATAAAGCCGCCGTATTCAAATAACCAGCAGGATAGATAGGCATCACGCCTCCAGAATGAAAAAGGCCACCGATTAGGTGGCCTTTGTTGTGTTCGGCTGGCTGTTAGAGCAGCAGCCCGTTTTCCCGCGCAAACGCGAATGGGTCCTTGTCATGCTTCCTGCAATTGCAGGTAGGACAAAGAATTTGCAGGTTGGATTTGTCGTTCGATCCGCCCTTTGCAAGCGGGAACACGTGGTCAACGTGATACCCATCCCTTATGGATATAGTGCACATGGCGCATTTCCAGCGCTGAGCAGCCAGCAAAAATTTTATGTCGTCGCCGGTGTGTGAGCCGACAGCATTTTTCTTGCGAGCCTTGTATGTCCGCGAGAGTGAACGAACTTGCTCCTTGTTGGCTGTCTTCCAGAGCTTTTGAGTAAGCGCACAGAGATCCTTGTTTCTTGATCTCCACTCTCTGGTTGCGGAAAT | ... =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the BioPerl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Florent E Angly Email florent dot angly at gmail dot com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_". =cut package Bio::Assembly::IO::tigr; use strict; use Bio::Seq::PrimaryQual; use Bio::LocatableSeq; use Bio::Seq::Quality; use Bio::Assembly::IO; use Bio::Assembly::Scaffold; use Bio::Assembly::Contig; use Bio::Assembly::Singlet; use base qw(Bio::Assembly::IO); our $progname = 'TIGR_Assembler'; =head2 next_assembly Title : next_assembly Usage : my $scaffold = $asmio->next_assembly(); Function: return the next assembly in the tasm-formatted stream Returns : Bio::Assembly::Scaffold object Args : none =cut sub next_assembly { my $self = shift; my $assembly = Bio::Assembly::Scaffold->new( -source => $progname ); # Load contigs and singlets in the scaffold while ( my $obj = $self->next_contig()) { # Add contig /singlet to assembly if ($obj->isa('Bio::Assembly::Singlet')) { # a singlet $assembly->add_singlet($obj); } else { # a contig $assembly->add_contig($obj); } } return $assembly; } =head2 next_contig Title : next_contig Usage : my $contig = $asmio->next_contig(); Function: return the next contig or singlet TIGR-formatted stream Returns : Bio::Assembly::Contig or Bio::Assembly::Singlet Args : none =cut sub next_contig { my $self = shift; # Contig and read related my $contigobj; my $iscontig = 1; my %contiginfo; my %readinfo; # Loop over all assembly file lines while ($_ = $self->_readline) { chomp; if ( /^\|/ ) { # a line with a single pipe | # The end of a read from a contig/singlet, the start of a new one last; } elsif ( /^$/ ) { # a blank line if ($contiginfo{'seqnum'} > 1) { if ($iscontig) { # The end of a contig, the start of a read in that contig $contigobj = $self->_store_contig(\%contiginfo, $contigobj); } else { # The end of a read in a contig, the start of a new read in $self->_store_read(\%readinfo, $contigobj); undef %readinfo; } } # else it's a singlet and we'll store the singlet and its unique # sequence all at once later $iscontig = 0; } else { if ($iscontig) { # Parse contig if (/^sequence\t(.*)/) {$contiginfo{'sequence'} = $1; next} elsif (/^lsequence\t(.*)/) {$contiginfo{'lsequence'} = $1; next} elsif (/^quality\t(.*)/) {$contiginfo{'quality'} = $1; next} elsif (/^asmbl_id\t(.*)/) {$contiginfo{'asmbl_id'} = $1; next} elsif (/^seq_id\t(.*)/) {$contiginfo{'seq_id'} = $1; next} elsif (/^com_name\t(.*)/) {$contiginfo{'com_name'} = $1; next} elsif (/^type\t(.*)/) {$contiginfo{'type'} = $1; next} elsif (/^method\t(.*)/) {$contiginfo{'method'} = $1; next} elsif (/^ed_status\t(.*)/) {$contiginfo{'ed_status'} = $1; next} elsif (/^redundancy\t(.*)/) {$contiginfo{'redundancy'} = $1; next} elsif (/^perc_N\t(.*)/) {$contiginfo{'perc_N'} = $1; next} elsif (/^seq\#\t(.*)/) {$contiginfo{'seqnum'} = $1; next} elsif (/^full_cds\t(.*)/) {$contiginfo{'full_cds'} = $1; next} elsif (/^cds_start\t(.*)/) {$contiginfo{'cds_start'} = $1; next} elsif (/^cds_end\t(.*)/) {$contiginfo{'cds_end'} = $1; next} elsif (/^ed_pn\t(.*)/) {$contiginfo{'ed_pn'} = $1; next} elsif (/^ed_date\t(.*\s.*)/) {$contiginfo{'ed_date'} = $1; next} elsif (/^comment\t(.*)/) {$contiginfo{'comment'} = $1; next} elsif (/^frameshift\t(.*)/) {$contiginfo{'frameshift'} = $1; next} else { $self->throw("Format unknown at line $.:\n$_\nIs your file". " really a TIGR Assembler tasm-formatted file?"); } } else { # Parse read info if (/^seq_name\t(.*)/) {$readinfo{'seq_name'} = $1; next} elsif (/^asm_lend\t(.*)/) {$readinfo{'asm_lend'} = $1; next} elsif (/^asm_rend\t(.*)/) {$readinfo{'asm_rend'} = $1; next} elsif (/^seq_lend\t(.*)/) {$readinfo{'seq_lend'} = $1; next} elsif (/^seq_rend\t(.*)/) {$readinfo{'seq_rend'} = $1; next} elsif (/^best\t(.*)/) {$readinfo{'best'} = $1; next} elsif (/^comment\t(.*)/) {$readinfo{'comment'} = $1; next} elsif (/^db\t(.*)/) {$readinfo{'db'} = $1; next} elsif (/^offset\t(.*)/) {$readinfo{'offset'} = $1; next} elsif (/^lsequence\t(.*)/) {$readinfo{'lsequence'} = $1; next} else { $self->throw("Format unknown at line $.:\n$_\nIs your file". " really a TIGR Assembler tasm-formatted file?"); } } } } # Store read info into a singlet or contig if (defined $contiginfo{'seqnum'}) { if ($contiginfo{'seqnum'} > 1) { # This is a read to attach to an existing contig object. $self->_store_read(\%readinfo, $contigobj); } elsif ($contiginfo{'seqnum'} == 1) { # This is a read. Save singlet and read together in a singlet object. $contigobj = $self->_store_singlet(\%readinfo, \%contiginfo); } else { # That should not happen $self->throw("Unhandled exception"); } } return $contigobj; } =head2 _qual_hex2dec Title : _qual_hex2dec Usage : my dec_quality = $self->_qual_hex2dec($hex_quality); Function: convert an hexadecimal quality score into a decimal quality score Returns : string Args : string =cut sub _qual_hex2dec { my ($self, $qual) = @_; $qual =~ s/^0x(.*)$/$1/; $qual =~ s/(..)/hex($1).' '/eg; return $qual; } =head2 _qual_dec2hex Title : _qual_dec2hex Usage : my hex_quality = $self->_qual_dec2hex($dec_quality); Function: convert a decimal quality score into an hexadecimal quality score Returns : string Args : string =cut sub _qual_dec2hex { my ($self, $qual) = @_; $qual =~ s/(\d+)\s*/sprintf('%02X', $1)/eg; $qual = '0x'.$qual; return $qual; } =head2 _store_contig Title : _store_contig Usage : my $contigobj = $self->_store_contig(\%contiginfo, $contigobj); Function: store information of a contig belonging to a scaffold in the appropriate object Returns : Bio::Assembly::Contig object Args : hash, Bio::Assembly::Contig =cut sub _store_contig { my ($self, $contiginfo, $contigobj) = @_; # Create a contig $contigobj = Bio::Assembly::Contig->new( -id => $$contiginfo{'asmbl_id'}, -strand => 1 ); # Create a gapped consensus sequence and attach it to contig #$$contiginfo{'llength'} = length($$contiginfo{'lsequence'}); my $consensus = Bio::LocatableSeq->new( -id => $$contiginfo{'asmbl_id'}, -seq => $$contiginfo{'lsequence'}, -start => 1, ); $contigobj->set_consensus_sequence($consensus); # Create an gapped consensus quality score and attach it to contig $$contiginfo{'quality'} = $self->_qual_hex2dec($$contiginfo{'quality'}); my $qual = Bio::Seq::PrimaryQual->new( -qual => $$contiginfo{'quality'}, -id => $$contiginfo{'asmbl_id'} ); $contigobj->set_consensus_quality($qual); # Add other misc contig information as features of the contig my $contigtags = Bio::SeqFeature::Generic->new( -primary => '_main_contig_feature', -source => $$contiginfo{'asmbl_id'}, -start => 1, -end => $contigobj->get_consensus_length(), -strand => 1, -tag => { 'seq_id' => $$contiginfo{'seq_id'}, 'com_name' => $$contiginfo{'com_name'}, 'type' => $$contiginfo{'type'}, 'method' => $$contiginfo{'method'}, 'ed_status' => $$contiginfo{'ed_status'}, 'full_cds' => $$contiginfo{'full_cds'}, 'cds_start' => $$contiginfo{'cds_start'}, 'cds_end' => $$contiginfo{'cds_end'}, 'ed_pn' => $$contiginfo{'ed_pn'}, 'ed_date' => $$contiginfo{'ed_date'}, 'comment' => $$contiginfo{'comment'}, 'frameshift' => $$contiginfo{'frameshift'} } ); $contigobj->add_features([ $contigtags ], 1); return $contigobj; } =head2 _store_read Title : _store_read Usage : my $readobj = $self->_store_read(\%readinfo, $contigobj); Function: store information of a read belonging to a contig in a contig object Returns : Bio::LocatableSeq Args : hash, Bio::Assembly::Contig =cut sub _store_read { my ($self, $readinfo, $contigobj) = @_; # Create an aligned read object #$$readinfo{'llength'} = length($$readinfo{'lsequence'}); $$readinfo{'strand'} = ($$readinfo{'seq_rend'} > $$readinfo{'seq_lend'} ? 1 : -1); my $readobj = Bio::LocatableSeq->new( # the ids of sequence objects are supposed to include the db name in it, i.e. "big_db|seq1234" # that's how sequence ids coming from the fasta parser are at least -display_id => $self->_merge_seq_name_and_db($$readinfo{'seq_name'}, $$readinfo{'db'}), -primary_id => $self->_merge_seq_name_and_db($$readinfo{'seq_name'}, $$readinfo{'db'}), -seq => $$readinfo{'lsequence'}, -start => 1, -strand => $$readinfo{'strand'}, -alphabet => 'dna' ); # Add read location and sequence to contig (in 'gapped consensus' coordinates) $$readinfo{'aln_start'} = $$readinfo{'offset'} + 1; # seq offset is in gapped coordinates $$readinfo{'aln_end'} = $$readinfo{'aln_start'} + length($$readinfo{'lsequence'}) - 1; # lsequence is aligned seq my $alncoord = Bio::SeqFeature::Generic->new( -primary => $readobj->id, -start => $$readinfo{'aln_start'}, -end => $$readinfo{'aln_end'}, -strand => $$readinfo{'strand'}, -tag => { 'contig' => $contigobj->id() } ); $contigobj->set_seq_coord($alncoord, $readobj); # Add quality clipping read information in contig features # (from 'aligned read' to 'gapped consensus' coordinates) $$readinfo{'clip_start'} = $contigobj->change_coord('aligned '.$readobj->id, 'gapped consensus', $$readinfo{'seq_lend'}); $$readinfo{'clip_end'} = $contigobj->change_coord('aligned '.$readobj->id, 'gapped consensus', $$readinfo{'seq_rend'}); my $clipcoord = Bio::SeqFeature::Generic->new( -primary => '_quality_clipping', -source => $readobj->id, -start => $$readinfo{'clip_start'}, -end => $$readinfo{'clip_end'}, -strand => $$readinfo{'strand'} ); $clipcoord->attach_seq($readobj); $contigobj->add_features([ $clipcoord ], 0); # Add other misc read information as subsequence feature my $readtags = Bio::SeqFeature::Generic->new( -primary => '_main_read_feature', -source => $readobj->id, -start => $$readinfo{'aln_start'}, -end => $$readinfo{'aln_end'}, -strand => $$readinfo{'strand'}, -tag => { 'best' => $$readinfo{'best'}, 'comment' => $$readinfo{'comment'} } ); $contigobj->get_features_collection->add_features([$readtags]); $contigobj->get_features_collection->add_SeqFeature($alncoord, $readtags); return $readobj; } =head2 _store_singlet Title : _store_singlet Usage : my $singletobj = $self->_store_read(\%readinfo, \%contiginfo); Function: store information of a singlet belonging to a scaffold in a singlet object Returns : Bio::Assembly::Singlet Args : hash, hash =cut sub _store_singlet { my ($self, $readinfo, $contiginfo) = @_; # Singlets in TIGR_Assembler are represented as a contig of one sequence # We try to simulate this duality by playing around with the Singlet object my $contigid = $$contiginfo{'asmbl_id'}; my $readid = $self->_merge_seq_name_and_db($$readinfo{'seq_name'}, $$readinfo{'db'}); # Create a sequence object #$$contiginfo{'llength'} = length($$contiginfo{'lsequence'}); my $seqobj = Bio::Seq::Quality->new( -primary_id => $readid, -display_id => $readid, -seq => $$contiginfo{'lsequence'}, # do not use $$readinfo as ambiguities are uppercase -start => 1, -strand => $$readinfo{'strand'}, -alphabet => 'dna', -qual => $self->_qual_hex2dec($$contiginfo{'quality'}) ); # Create singlet from sequence and add it to scaffold my $singletobj = Bio::Assembly::Singlet->new( -id => $contigid, -seqref => $seqobj ); # Add other misc contig information as features of the singlet my $contigtags = Bio::SeqFeature::Generic->new( -primary => '_main_contig_feature', -source => $contigid, -start => 1, -end => $singletobj->get_consensus_length(), -strand => 1, -tag => { 'seq_id' => $$contiginfo{'seq_id'}, 'com_name' => $$contiginfo{'com_name'}, 'type' => $$contiginfo{'type'}, 'method' => $$contiginfo{'method'}, 'ed_status' => $$contiginfo{'ed_status'}, 'full_cds' => $$contiginfo{'full_cds'}, 'cds_start' => $$contiginfo{'cds_start'}, 'cds_end' => $$contiginfo{'cds_end'}, 'ed_pn' => $$contiginfo{'ed_pn'}, 'ed_date' => $$contiginfo{'ed_date'}, 'comment' => $$contiginfo{'comment'}, 'frameshift' => $$contiginfo{'frameshift'} } ); $singletobj->add_features([ $contigtags ], 1); # Add read location and sequence to singlet features (in 'gapped consensus' coordinates) $$readinfo{'aln_start'} = $$readinfo{'offset'} + 1; # seq offset is in gapped coordinates $$readinfo{'aln_end'} = $$readinfo{'aln_start'} + length($$readinfo{'lsequence'}) - 1; # lsequence is aligned seq my $alncoord = Bio::SeqFeature::Generic->new( -primary => '_aligned_coord', -source => $readid, -start => $$readinfo{'aln_start'}, -end => $$readinfo{'aln_end'}, -strand => $$readinfo{'strand'}, -tag => { 'contig' => $contigid } ); $alncoord->attach_seq($singletobj->seqref); $singletobj->add_features([ $alncoord ], 0); # Add quality clipping read information in singlet features # (from 'aligned read' to 'gapped consensus' coordinates) $$readinfo{'clip_start'} = $$readinfo{'seq_lend'}; $$readinfo{'clip_end'} = $$readinfo{'seq_rend'}; my $clipcoord = Bio::SeqFeature::Generic->new( -primary => '_quality_clipping', -source => $readid, -start => $$readinfo{'clip_start'}, -end => $$readinfo{'clip_end'}, -strand => $$readinfo{'strand'}, -tag => { 'contig' => $contigid } ); $clipcoord->attach_seq($singletobj->seqref); $singletobj->add_features([ $clipcoord ], 0); # Add other misc read information as subsequence feature my $readtags = Bio::SeqFeature::Generic->new( -primary => '_main_read_feature', -source => $readid, -start => $$readinfo{'aln_start'}, -end => $$readinfo{'aln_end'}, -strand => $$readinfo{'strand'}, -tag => { 'best' => $$readinfo{'best'}, 'comment' => $$readinfo{'comment'} } ); $singletobj->get_features_collection->add_features([$readtags]); $singletobj->get_features_collection->add_SeqFeature($alncoord, $readtags); return $singletobj; } =head2 write_assembly Title : write_assembly Usage : $asmio->write_assembly($assembly) Function: Write the assembly object in TIGR Assembler compatible format. The contig IDs are sorted naturally if the Sort::Naturally module is present, or lexically otherwise. Internally, write_assembly use the write_contig, write_footer and write_header methods. Use these methods if you want more control on the writing process. Returns : 1 on success, 0 for error Args : A Bio::Assembly::Scaffold object 1 to write singlets in the assembly file, 0 otherwise =cut =head2 write_contig Title : write_contig Usage : $asmio->write_contig($contig) Function: Write a contig or singlet object in TIGR compatible format. Quality scores are automatically generated if the contig does not contain any Returns : 1 on success, 0 for error Args : A Bio::Assembly::Contig or Singlet object =cut sub write_contig { my ($self, @args) = @_; my ($contigobj) = $self->_rearrange([qw(CONTIG)], @args); # Sanity check if ( !$contigobj || !$contigobj->isa('Bio::Assembly::Contig') ) { $self->throw("Must provide a Bio::Assembly::Contig or Singlet object when calling write_contig"); } my $decimal_format = '%.2f'; my $contigid = $contigobj->id; my $numseqs = $contigobj->num_sequences; if ( $contigobj->isa('Bio::Assembly::Singlet') ) { # This is a singlet my $readid = $contigobj->seqref->id; my $singletobj = $contigobj; # Get contig information my ($contanno) = $singletobj->get_features_collection->get_features_by_type("_main_contig_feature:$contigid"); my %contiginfo; $contiginfo{'sequence'} = $singletobj->seqref->seq; $contiginfo{'lsequence'} = $contiginfo{'sequence'}; $contiginfo{'quality'} = $self->_qual_dec2hex( join ' ', @{$singletobj->get_consensus_quality->qual} ); $contiginfo{'asmbl_id'} = $contigid; $contiginfo{'seq_id'} = ($contanno->get_tag_values('seq_id'))[0]; $contiginfo{'com_name'} = ($contanno->get_tag_values('com_name'))[0]; $contiginfo{'type'} = ($contanno->get_tag_values('type'))[0]; $contiginfo{'method'} = ($contanno->get_tag_values('method'))[0]; $contiginfo{'ed_status'} = ($contanno->get_tag_values('ed_status'))[0]; $contiginfo{'redundancy'} = sprintf($decimal_format, 1); $contiginfo{'perc_N'} = sprintf( $decimal_format, $self->_perc_N($contiginfo{'sequence'})); $contiginfo{'seqnum'} = 1; $contiginfo{'full_cds'} = ($contanno->get_tag_values('full_cds'))[0]; $contiginfo{'cds_start'} = ($contanno->get_tag_values('cds_start'))[0]; $contiginfo{'cds_end'} = ($contanno->get_tag_values('cds_end'))[0]; $contiginfo{'ed_pn'} = ($contanno->get_tag_values('ed_pn'))[0]; $contiginfo{'ed_date'} = $self->_date_time; $contiginfo{'comment'} = ($contanno->get_tag_values('comment'))[0]; $contiginfo{'frameshift'} = ($contanno->get_tag_values('frameshift'))[0]; # Check that no tag value is undef $contiginfo{'seq_id'} = '' unless defined $contiginfo{'seq_id'}; $contiginfo{'com_name'} = '' unless defined $contiginfo{'com_name'}; $contiginfo{'type'} = '' unless defined $contiginfo{'type'}; $contiginfo{'method'} = '' unless defined $contiginfo{'method'}; $contiginfo{'ed_status'} = '' unless defined $contiginfo{'ed_status'}; $contiginfo{'full_cds'} = '' unless defined $contiginfo{'full_cds'}; $contiginfo{'cds_start'} = '' unless defined $contiginfo{'cds_start'}; $contiginfo{'cds_end'} = '' unless defined $contiginfo{'cds_end'}; $contiginfo{'ed_pn'} = '' unless defined $contiginfo{'ed_pn'}; $contiginfo{'comment'} = '' unless defined $contiginfo{'comment'}; $contiginfo{'frameshift'} = '' unless defined $contiginfo{'frameshift'}; # Print singlet information $self->_print( "sequence\t$contiginfo{'sequence'}\n". "lsequence\t$contiginfo{'lsequence'}\n". "quality\t$contiginfo{'quality'}\n". "asmbl_id\t$contiginfo{'asmbl_id'}\n". "seq_id\t$contiginfo{'seq_id'}\n". "com_name\t$contiginfo{'com_name'}\n". "type\t$contiginfo{'type'}\n". "method\t$contiginfo{'method'}\n". "ed_status\t$contiginfo{'ed_status'}\n". "redundancy\t$contiginfo{'redundancy'}\n". "perc_N\t$contiginfo{'perc_N'}\n". "seq#\t$contiginfo{'seqnum'}\n". "full_cds\t$contiginfo{'full_cds'}\n". "cds_start\t$contiginfo{'cds_start'}\n". "cds_end\t$contiginfo{'cds_end'}\n". "ed_pn\t$contiginfo{'ed_pn'}\n". "ed_date\t$contiginfo{'ed_date'}\n". "comment\t$contiginfo{'comment'}\n". "frameshift\t$contiginfo{'frameshift'}\n". "\n" ); # Get read information my ($seq_name, $db) = $self->_split_seq_name_and_db($readid); my ($clipcoord) = $singletobj->get_features_collection->get_features_by_type("_quality_clipping:$readid"); my ($alncoord) = $singletobj->get_features_collection->get_features_by_type("_aligned_coord:$readid"); my ($readanno) = $singletobj->get_features_collection->get_features_by_type("_main_read_feature:$readid"); my %readinfo; $readinfo{'seq_name'} = $seq_name; $readinfo{'asm_lend'} = $alncoord->location->start; $readinfo{'asm_rend'} = $alncoord->location->end; $readinfo{'seq_lend'} = $clipcoord->location->start; $readinfo{'seq_rend'} = $clipcoord->location->end; $readinfo{'best'} = ($readanno->get_tag_values('best'))[0]; $readinfo{'comment'} = ($readanno->get_tag_values('comment'))[0]; $readinfo{'db'} = $db; $readinfo{'offset'} = 0; # ambiguities in read sequence are uppercase $readinfo{'lsequence'} = uc($contiginfo{'lsequence'}); # Check that no tag value is undef $readinfo{'best'} = '' unless defined $readinfo{'best'}; $readinfo{'comment'} = '' unless defined $readinfo{'comment'}; # Print read information $self->_print( "seq_name\t$readinfo{'seq_name'}\n". "asm_lend\t$readinfo{'asm_lend'}\n". "asm_rend\t$readinfo{'asm_rend'}\n". "seq_lend\t$readinfo{'seq_lend'}\n". "seq_rend\t$readinfo{'seq_rend'}\n". "best\t$readinfo{'best'}\n". "comment\t$readinfo{'comment'}\n". "db\t$readinfo{'db'}\n". "offset\t$readinfo{'offset'}\n". "lsequence\t$readinfo{'lsequence'}\n" ); $self->_print("|\n"); } else { # This is a contig # Get contig information my ($contanno) = $contigobj->get_features_collection->get_features_by_type("_main_contig_feature:$contigid"); my %contiginfo; $contiginfo{'sequence'} = $self->_ungap( $contigobj->get_consensus_sequence->seq); $contiginfo{'lsequence'} = $contigobj->get_consensus_sequence->seq; $contiginfo{'quality'} = $self->_qual_dec2hex( join ' ', @{$contigobj->get_consensus_quality->qual}); $contiginfo{'asmbl_id'} = $contigid; $contiginfo{'seq_id'} = ($contanno->get_tag_values('seq_id'))[0]; $contiginfo{'com_name'} = ($contanno->get_tag_values('com_name'))[0]; $contiginfo{'type'} = ($contanno->get_tag_values('type'))[0]; $contiginfo{'method'} = ($contanno->get_tag_values('method'))[0]; $contiginfo{'ed_status'} = ($contanno->get_tag_values('ed_status'))[0]; $contiginfo{'redundancy'} = sprintf( $decimal_format, $self->_redundancy($contigobj)); $contiginfo{'perc_N'} = sprintf( $decimal_format, $self->_perc_N($contiginfo{'sequence'})); $contiginfo{'seqnum'} = $contigobj->num_sequences; $contiginfo{'full_cds'} = ($contanno->get_tag_values('full_cds'))[0]; $contiginfo{'cds_start'} = ($contanno->get_tag_values('cds_start'))[0]; $contiginfo{'cds_end'} = ($contanno->get_tag_values('cds_end'))[0]; $contiginfo{'ed_pn'} = ($contanno->get_tag_values('ed_pn'))[0]; $contiginfo{'ed_date'} = $self->_date_time; $contiginfo{'comment'} = ($contanno->get_tag_values('comment'))[0]; $contiginfo{'frameshift'} = ($contanno->get_tag_values('frameshift'))[0]; # Check that no tag value is undef $contiginfo{'seq_id'} = '' unless defined $contiginfo{'seq_id'}; $contiginfo{'com_name'} = '' unless defined $contiginfo{'com_name'}; $contiginfo{'type'} = '' unless defined $contiginfo{'type'}; $contiginfo{'method'} = '' unless defined $contiginfo{'method'}; $contiginfo{'ed_status'} = '' unless defined $contiginfo{'ed_status'}; $contiginfo{'full_cds'} = '' unless defined $contiginfo{'full_cds'}; $contiginfo{'cds_start'} = '' unless defined $contiginfo{'cds_start'}; $contiginfo{'cds_end'} = '' unless defined $contiginfo{'cds_end'}; $contiginfo{'ed_pn'} = '' unless defined $contiginfo{'ed_pn'}; $contiginfo{'comment'} = '' unless defined $contiginfo{'comment'}; $contiginfo{'frameshift'} = '' unless defined $contiginfo{'frameshift'}; # Print contig information $self->_print( "sequence\t$contiginfo{'sequence'}\n". "lsequence\t$contiginfo{'lsequence'}\n". "quality\t$contiginfo{'quality'}\n". "asmbl_id\t$contiginfo{'asmbl_id'}\n". "seq_id\t$contiginfo{'seq_id'}\n". "com_name\t$contiginfo{'com_name'}\n". "type\t$contiginfo{'type'}\n". "method\t$contiginfo{'method'}\n". "ed_status\t$contiginfo{'ed_status'}\n". "redundancy\t$contiginfo{'redundancy'}\n". "perc_N\t$contiginfo{'perc_N'}\n". "seq#\t$contiginfo{'seqnum'}\n". "full_cds\t$contiginfo{'full_cds'}\n". "cds_start\t$contiginfo{'cds_start'}\n". "cds_end\t$contiginfo{'cds_end'}\n". "ed_pn\t$contiginfo{'ed_pn'}\n". "ed_date\t$contiginfo{'ed_date'}\n". "comment\t$contiginfo{'comment'}\n". "frameshift\t$contiginfo{'frameshift'}\n". "\n" ); my $seqno = 0; for my $readobj ( $contigobj->each_seq() ) { $seqno++; # Get read information my ($seq_name, $db) = $self->_split_seq_name_and_db($readobj->id); my ($asm_lend, $asm_rend, $seq_lend, $seq_rend, $offset) = $self->_coord($readobj, $contigobj); my $readanno = ($contigobj->get_features_collection->get_SeqFeatures( $contigobj->get_seq_coord($readobj) , '_main_read_feature:'.$readobj->primary_id) )[0]; my %readinfo; $readinfo{'seq_name'} = $seq_name; $readinfo{'asm_lend'} = $asm_lend; $readinfo{'asm_rend'} = $asm_rend; $readinfo{'seq_lend'} = $seq_lend; $readinfo{'seq_rend'} = $seq_rend; $readinfo{'best'} = ($readanno->get_tag_values('best'))[0]; $readinfo{'comment'} = ($readanno->get_tag_values('comment'))[0]; $readinfo{'db'} = $db; $readinfo{'offset'} = $offset; $readinfo{'lsequence'} = $readobj->seq(); # Check that no tag value is undef $readinfo{'best'} = '' unless defined $readinfo{'best'}; $readinfo{'comment'} = '' unless defined $readinfo{'comment'}; # Print read information $self->_print( "seq_name\t$readinfo{'seq_name'}\n". "asm_lend\t$readinfo{'asm_lend'}\n". "asm_rend\t$readinfo{'asm_rend'}\n". "seq_lend\t$readinfo{'seq_lend'}\n". "seq_rend\t$readinfo{'seq_rend'}\n". "best\t$readinfo{'best'}\n". "comment\t$readinfo{'comment'}\n". "db\t$readinfo{'db'}\n". "offset\t$readinfo{'offset'}\n". "lsequence\t$readinfo{'lsequence'}\n" ); if ($seqno < $contiginfo{'seqnum'}) { $self->_print("\n"); } else { $self->_print("|\n") }; } } return 1; } =head2 write_header Title : write_header Usage : $asmio->write_header($assembly) Function: In the TIGR Asseformat assembly driver, this does nothing. The method is present for compatibility with other assembly drivers that need to write a file header. Returns : 1 on success, 0 for error Args : A Bio::Assembly::Scaffold object =cut sub write_header { my ($self) = @_; return 1; } =head2 write_footer Title : write_footer Usage : $asmio->write_footer($assembly) Function: Write TIGR footer, i.e. do nothing except making sure that the file does not end with a '|'. Returns : 1 on success, 0 for error Args : A Bio::Assembly::Scaffold object =cut sub write_footer { my ($self) = @_; # In this implementation, the TIGR file always ends with '|\n'. Remove it. seek $self->_fh, -length("|\n"), 2; $self->_print("\n\n"); return 1; } =head2 _perc_N Title : _perc_N Usage : my $perc_N = $asmio->_perc_N($sequence_string) Function: Calculate the percent of ambiguities in a sequence. M R W S Y K X N are regarded as ambiguities in an aligned read sequence by TIGR Assembler. In the case of a gapped contig consensus sequence, all lowercase symbols are ambiguities, i.e.: a c g t u m r w s y k x n. Returns : decimal number Args : string =cut sub _perc_N { my ($self, $seq_string) = @_; $self->throw("Cannot accept an empty sequence") if length($seq_string) == 0; my $perc_N = 0; for my $base ( split //, $seq_string ) { # individual base matches an ambiguity? if (( $base =~ m/[x|n|m|r|w|s|y|k]/i ) || ( $base =~ m/[a|c|g|t|u]/ ) ) { $perc_N++; } } $perc_N = $perc_N * 100 / length $seq_string; return $perc_N; } =head2 _redundancy Title : _redundancy Usage : my $ref = $asmio->_redundancy($contigobj) Function: Calculate the fold coverage (redundancy) of a contig consensus (average number of read base pairs covering the consensus) Returns : decimal number Args : Bio::Assembly::Contig =cut sub _redundancy { # redundancy = (sum of all aligned read lengths - ( number of gaps in gapped # consensus + number of gaps in aligned reads that are also in the consensus ) ) # / length of ungapped consensus my ($self, $contigobj) = @_; my $redundancy = 0; # sum of all aligned read lengths my $read_tot = 0; for my $readobj ( $contigobj->each_seq ) { my $read_length = length($readobj->seq); $read_tot += $read_length; } $redundancy += $read_tot; # - respected gaps my $consensus_sequence = $contigobj->get_consensus_sequence->seq; my @consensus_gaps = (); $contigobj->_register_gaps($consensus_sequence, \@consensus_gaps); my $respected_gaps = scalar(@consensus_gaps); if ($respected_gaps > 0) { my @cons_arr = split //, $consensus_sequence; for my $gap_pos_cons ( @consensus_gaps ) { for my $readobj ( $contigobj->each_seq ) { my $readid = $readobj->id; my $read_start = $contigobj->change_coord( "aligned $readid", 'gapped consensus', $readobj->start); my $read_end = $contigobj->change_coord( "aligned $readid", 'gapped consensus', $readobj->end ); # skip this if consensus gap position not within in the read boundaries next if ( ($gap_pos_cons < $read_start) || ($gap_pos_cons > $read_end) ); # does the read position have read have a gap? my @read_arr = split //, $readobj->seq; my $gap_pos_read = $contigobj->change_coord( 'gapped consensus', "aligned $readid", $gap_pos_cons); if ($read_arr[$gap_pos_read-1] eq $cons_arr[$gap_pos_cons-1]) { $respected_gaps++; } } } } $redundancy -= $respected_gaps; # / length of ungapped consensus my $contig_length = length($self->_ungap($contigobj->get_consensus_sequence->seq)); $redundancy /= $contig_length; return $redundancy; } =head2 _ungap Title : _ungap Usage : my $ungapped = $asmio->_ungap($gapped) Function: Remove the gaps from a sequence. Gaps are - in TIGR Assembler Returns : string Args : string =cut sub _ungap { my ($self, $seq_string) = @_; $seq_string =~ s/-//g; return $seq_string; } =head2 _date_time Title : _date_time Usage : my $timepoint = $asmio->date_time Function: Get date and time (MM//DD/YY HH:MM:SS) Returns : string Args : none =cut sub _date_time { my ($self) = @_; my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time); my $formatted_date_time = sprintf('%02d', $mon+1).'/'. sprintf('%02d', $mday).'/'. sprintf('%02d', $year % 100). ' '. sprintf('%02d', $hour).':'. sprintf('%02d', $min).':'. sprintf('%02d',$sec) ; return $formatted_date_time; } =head2 _split_seq_name_and_db Title : _split_seq_name_and_db Usage : my ($seqname, $db) = $asmio->_split_seq_name_and_db($id) Function: Extract seq_name and db from sequence id Returns : seq_name, db Args : id =cut sub _split_seq_name_and_db { my ($self, $id) = @_; my $seq_name = ''; my $db = ''; if ($id =~ m/(\S+)\|(\S+)/) { $db = $1; $seq_name = $2; } else { $seq_name = $id; } return ($seq_name, $db); } =head2 _merge_seq_name_and_db Title : _merge_seq_name_and_db Usage : my $id = $asmio->_merge_seq_name_and_db($seq_name, $db) Function: Construct id from seq_name and db Returns : id Args : seq_name, db =cut sub _merge_seq_name_and_db { my ($self, $seq_name, $db) = @_; my $id = ''; if ($db) { $id = $db.'|'.$seq_name; } else { $id = $seq_name; } return $id; } =head2 _coord Title : _coord Usage : my $id = $asmio->__coord($readobj, $contigobj) Function: Get different coordinates for the read Returns : number, number, number, number, number Args : Bio::Assembly::Seq, Bio::Assembly::Contig =cut sub _coord { my ($self, $readobj, $contigobj) = @_; my ($asm_lend, $asm_rend, $seq_lend, $seq_rend, $offset) = (0, 0, 0, 0, 0); # Get read gapped consensus coordinates from contig and calculate # asm_lend and asm_rend in ungapped consensus my $aln_lend = $contigobj->get_seq_coord($readobj)->location->start; my $aln_rend = $contigobj->get_seq_coord($readobj)->location->end; $asm_lend = $contigobj->change_coord( 'gapped consensus', 'ungapped consensus', $aln_lend); $asm_rend = $contigobj->change_coord( 'gapped consensus', 'ungapped consensus', $aln_rend); # Get gapped consensus coordinates for quality-clipped reads from contig # annotation and determine seq_lend and seq_rend in unaligned sequence coord my ($readclip) = $contigobj->get_features_collection->get_features_by_type('_quality_clipping:'.$readobj->primary_id); my $clip_lend = $readclip->location->start; my $clip_rend = $readclip->location->end; $seq_lend = $contigobj->change_coord( 'gapped consensus', 'aligned '.$readobj->id, $clip_lend); $seq_rend = $contigobj->change_coord( 'gapped consensus', 'aligned '.$readobj->id, $clip_rend); # Offset $offset = $aln_lend - 1; return ($asm_lend, $asm_rend, $seq_lend, $seq_rend, $offset); } 1; __END__ BioPerl-1.007002/Bio/Assembly/Tools000755000766000024 013155576320 16746 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Assembly/Tools/ContigSpectrum.pm000444000766000024 17715513155576320 22467 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Assembly::Tools::ContigSpectrum # # Copyright by Florent Angly # # You may distribute this module under the same terms as Perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Assembly::Tools::ContigSpectrum - create and manipulate contig spectra =head1 SYNOPSIS # Simple contig spectrum creation my $csp1 = Bio::Assembly::Tools::ContigSpectrum->new( -id => 'csp1', -spectrum => { 1 => 10, 2 => 2, 3 => 1 } ); # ...or another way to create a simple contig spectrum my $csp2 = Bio::Assembly::Tools::ContigSpectrum->new; $csp2->id('csp2'); $csp2->spectrum({ 1 => 20, 2 => 1, 4 => 1 }); # Get some information print "This is contig spectrum ".$csp->id."\n"; print "It contains ".$csp->nof_seq." sequences\n"; print "The largest contig has ".$csp->max_size." sequences\n"; print "The spectrum is: ".$csp->to_string($csp->spectrum)."\n"; # Let's add the contig spectra my $summed_csp = Bio::Assembly::Tools::ContigSpectrum->new; $summed_csp->add($csp1); $summed_csp->add($csp2); print "The summed contig spectrum is ".$summed_csp->to_string."\n"; # Make an average my $avg_csp = Bio::Assembly::Tools::ContigSpectrum->new; $avg_csp = $avg_csp->average([$csp1, $csp2]); print "The average contig spectrum is ".$avg_csp->to_string."\n"; # Get a contig spectrum from an assembly my $from_assembly = Bio::Assembly::Tools::ContigSpectrum->new( -assembly => $assembly_object, -eff_asm_params => 1); print "The contig spectrum from assembly is ".$from_assembly->to_string."\n"; # Report advanced information (possible because eff_asm_params = 1) print "Average sequence length: ".$from_assembly->avg_seq_len." bp\n"; print "Minimum overlap length: ".$from_assembly->min_overlap." bp\n"; print "Average overlap length: ".$from_assembly->avg_overlap." bp\n"; print "Minimum overlap match: ".$from_assembly->min_identity." %\n"; print "Average overlap match: ".$from_assembly->avg_identity." %\n"; # Assuming the assembly object contains sequences from several different # metagenomes, we have a mixed contig spectrum from which a cross contig # spectrum and dissolved contig spectra can be obtained my $mixed_csp = $from_assembly; # Calculate a dissolved contig spectrum my $meta1_dissolved = Bio::Assembly::Tools::ContigSpectrum->new( -dissolve => [$mixed_csp, 'metagenome1'] ); my $meta2_dissolved = Bio::Assembly::Tools::ContigSpectrum->new( -dissolve => [$mixed_csp, 'metagenome2'] ); print "The dissolved contig spectra are:\n". $meta1_dissolved->to_string."\n". $meta2_dissolved->to_string."\n"; # Determine a cross contig spectrum my $cross_csp = Bio::Assembly::Tools::ContigSpectrum->new( -cross => $mixed_csp ); print "The cross contig spectrum is ".$cross_csp->to_string."\n"; # Score a contig spectrum (the more abundant the contigs and the larger their # size, the larger the score) my $csp_score = $csp->score( $csp->nof_seq ); =head1 DESCRIPTION The Bio::Assembly::Tools::ContigSpectrum Perl module enables to manually create contig spectra, import them from assemblies, manipulate them, transform between different types of contig spectra and output them. Bio::Assembly::Tools::ContigSpectrum is a module to create, manipulate and output contig spectra, assembly-derived data used in metagenomics (community genomics) for diversity estimation. =head2 Background A contig spectrum is the count of the number of contigs of different size in an assembly. For example, the contig spectrum [100 5 1 0 0 ...] means that there were 100 singlets (1-contigs), 5 contigs of 2 sequences (2-contigs), 1 contig of 3 sequences (3-contig) and no larger contigs. An assembly can be produced from a mixture of sequences from different metagenomes. The contig obtained from this assembly is a mixed contig spectrum. The contribution of each metagenome in this mixed contig spectrum can be obtained by determining a dissolved contig spectrum. Finally, based on a mixed contig spectrum, a cross contig spectrum can be determined. In a cross contig spectrum, only contigs containing sequences from different metagenomes are kept; "pure" contigs are excluded. Additionally, the total number of singletons (1-contigs) from each region that assembles with any fragments from other regions is the number of 1-contigs in the cross contig spectrum. =head2 Implementation The simplest representation of a contig spectrum is as a hash representation where the key is the contig size (number of sequences making up the contig) and the value the number of contigs of this size. In fact, it is useful to have more information associated with the contig spectrum, hence the Bio::Assembly::Tools::ContigSpectrum module implements an object containing a contig spectrum hash and additional information. The get/set methods to access them are: id contig spectrum ID nof_rep number of repetitions (assemblies) used max_size size of (number of sequences in) the largest contig spectrum hash representation of a contig spectrum nof_seq number of sequences avg_seq_len average sequence length eff_asm_params reports effective assembly parameters nof_overlaps number of overlaps (needs eff_asm_params) min_overlap minimum overlap length in a contig (needs eff_asm_params) min_identity minimum sequence identity percentage (needs eff_asm_params) avg_overlap average overlap length (needs eff_asm_params) avg_identity average overlap identity percentage (needs eff_asm_params) Operations on the contig spectra: to_string create a string representation of the spectrum spectrum import a hash contig spectrum assembly determine a contig spectrum from an assembly, contig or singlet dissolve calculate a dissolved contig spectrum (depends on assembly) cross produce a cross contig spectrum (depends on assembly) add add a contig spectrum to an existing one average make an average of several contig spectra score score a contig spectrum: the higher the number of contigs and the larger their size, the higher the score. When using operations that rely on knowing "where" (from what metagenomes) a sequence came from (i.e. when creating a dissolved or cross contig spectrum), make sure that the sequences used for the assembly have a name header, e.g. Emetagenome1|seq1, Emetagenome2|seq1, ... Note: The following operations require the C module: eff_asm_params, cross, dissolve =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the BioPerl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Florent E Angly Email florent_dot_angly_at_gmail_dot_com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_". =cut package Bio::Assembly::Tools::ContigSpectrum; use strict; use Bio::Root::Root; use Bio::Assembly::Scaffold; use Bio::SimpleAlign; use Bio::LocatableSeq; use base 'Bio::Root::Root'; =head2 new Title : new Usage : my $csp = Bio::Assembly::Tools::ContigSpectrum->new(); or my $csp = Bio::Assembly::Tools::ContigSpectrum->new( -id => 'some_name', -spectrum => { 1 => 90 , 2 => 3 , 4 => 1 }, ); or my $csp = Bio::Assembly::Tools::ContigSpectrum->new( -assembly => $assembly_obj ); Function: create a new contig spectrum object Returns : reference to a contig spectrum object Args : none =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ( $id, $nof_seq, $nof_rep, $max_size, $nof_overlaps, $min_overlap, $min_identity, $avg_overlap, $avg_identity, $avg_seq_len, $spectrum, $assembly, $eff_asm_params, $dissolve, $cross) = $self->_rearrange( [qw(ID NOF_SEQ NOF_REP MAX_SIZE NOF_OVERLAPS MIN_OVERLAP MIN_IDENTITY AVG_OVERLAP AVG_IDENTITY AVG_SEQ_LEN SPECTRUM ASSEMBLY EFF_ASM_PARAMS DISSOLVE CROSS)], @args ); # First set up some defauts $self->{'_id'} = 'NoName'; $self->{'_nof_seq'} = 0; $self->{'_nof_rep'} = 0; $self->{'_max_size'} = 0; $self->{'_nof_overlaps'} = 0; $self->{'_min_overlap'} = undef; $self->{'_min_identity'} = undef; $self->{'_avg_overlap'} = 0; $self->{'_avg_identity'} = 0; $self->{'_avg_seq_len'} = 0; $self->{'_eff_asm_params'} = 0; $self->{'_spectrum'} = {1 => 0}; # contig spectrum hash representation $self->{'_assembly'} = []; # list of assembly, contigs and singlet objects # Then, according to user desires, override defaults $self->{'_id'} = $id if (defined $id); $self->{'_nof_seq'} = $nof_seq if (defined $nof_seq); $self->{'_nof_rep'} = $nof_rep if (defined $nof_rep); $self->{'_max_size'} = $max_size if (defined $max_size); $self->{'_nof_overlaps'} = $nof_overlaps if (defined $nof_overlaps); $self->{'_min_overlap'} = $min_overlap if (defined $min_overlap); $self->{'_avg_overlap'} = $avg_overlap if (defined $avg_overlap); $self->{'_min_identity'} = $min_identity if (defined $min_identity); $self->{'_avg_identity'} = $avg_identity if (defined $avg_identity); $self->{'_avg_seq_len'} = $avg_seq_len if (defined $avg_seq_len); $self->{'_eff_asm_params'} = $eff_asm_params if (defined $eff_asm_params); # Finally get stuff that can be obtained in an automated way $self->_import_spectrum($spectrum) if defined($spectrum); $self->_import_assembly($assembly) if defined($assembly); $self->_import_cross_csp($cross) if defined($cross); if (defined($dissolve)) { my ($mixed_csp, $header) = (@$dissolve[0], @$dissolve[1]); $self->_import_dissolved_csp($mixed_csp, $header); } return $self; } =head2 id Title : id Usage : $csp->id Function: get/set contig spectrum id Returns : string Args : string [optional] =cut sub id { my ($self, $id) = @_; if (defined $id) { $self->{'_id'} = $id; } $id = $self->{'_id'}; return $id; } =head2 nof_seq Title : nof_seq Usage : $csp->nof_seq Function: get/set the number of sequences making up the contig spectrum Returns : integer Args : integer [optional] =cut sub nof_seq { my ($self, $nof_seq) = @_; if (defined $nof_seq) { $self->throw("The number of sequences must be strictly positive. Got ". "'$nof_seq'") if $nof_seq < 1; $self->{'_nof_seq'} = $nof_seq; } $nof_seq = $self->{'_nof_seq'}; return $nof_seq; } =head2 nof_rep Title : nof_rep Usage : $csp->nof_rep Function: Get/Set the number of repetitions (assemblies) used to create the contig spectrum Returns : integer Args : integer [optional] =cut sub nof_rep { my ($self, $nof_rep) = @_; if (defined $nof_rep) { $self->throw("The number of repetitions must be strictly positive. Got ". "'$nof_rep'") if $nof_rep < 1; $self->{'_nof_rep'} = $nof_rep; } $nof_rep = $self->{'_nof_rep'}; return $nof_rep; } =head2 max_size Title : max_size Usage : $csp->max_size Function: get/set the size of (number of sequences in) the largest contig Returns : integer Args : integer [optional] =cut sub max_size { my ($self, $max_size) = @_; if (defined $max_size) { $self->throw("The contig maximum size must be strictly positive. Got ". "'$max_size'") if $max_size < 1; $self->{'_max_size'} = $max_size; } $max_size = $self->{'_max_size'}; return $max_size; } =head2 nof_overlaps Title : nof_overlaps Usage : $csp->nof_overlaps Function: Get/Set the number of overlaps in the assembly. Returns : integer Args : integer [optional] =cut sub nof_overlaps { my ($self, $nof_overlaps) = @_; if (defined $nof_overlaps) { $self->throw("The number of overlaps must be strictly positive. Got ". "'$nof_overlaps'") if $nof_overlaps < 1; $self->{'_nof_overlaps'} = $nof_overlaps; } $nof_overlaps = $self->{'_nof_overlaps'}; return $nof_overlaps; } =head2 min_overlap Title : min_overlap Usage : $csp->min_overlap Function: get/set the assembly minimum overlap length Returns : integer Args : integer [optional] =cut sub min_overlap { my ($self, $min_overlap) = @_; if (defined $min_overlap) { $self->throw("The minimum of overlap length must be strictly positive. Got". " '$min_overlap'") if $min_overlap < 1; $self->{'_min_overlap'} = $min_overlap; } $min_overlap = $self->{'_min_overlap'}; return $min_overlap; } =head2 avg_overlap Title : avg_overlap Usage : $csp->avg_overlap Function: get/set the assembly average overlap length Returns : decimal Args : decimal [optional] =cut sub avg_overlap { my ($self, $avg_overlap) = @_; if (defined $avg_overlap) { $self->throw("The average overlap length must be strictly positive. Got ". "'$avg_overlap'") if $avg_overlap < 1; $self->{'_avg_overlap'} = $avg_overlap; } $avg_overlap = $self->{'_avg_overlap'}; return $avg_overlap; } =head2 min_identity Title : min_identity Usage : $csp->min_identity Function: get/set the assembly minimum overlap identity percent Returns : 0 < decimal < 100 Args : 0 < decimal < 100 [optional] =cut sub min_identity { my ($self, $min_identity) = @_; if (defined $min_identity) { $self->throw("The minimum overlap percent identity must be strictly ". "positive. Got '$min_identity'") if $min_identity < 1; $self->{'_min_identity'} = $min_identity; } $min_identity = $self->{'_min_identity'}; return $min_identity; } =head2 avg_identity Title : avg_identity Usage : $csp->avg_identity Function: get/set the assembly average overlap identity percent Returns : 0 < decimal < 100 Args : 0 < decimal < 100 [optional] =cut sub avg_identity { my ($self, $avg_identity) = @_; if (defined $avg_identity) { $self->throw("The average overlap percent identity must be strictly ". "positive. Got '$avg_identity'") if $avg_identity < 1; $self->{'_avg_identity'} = $avg_identity; } $avg_identity = $self->{'_avg_identity'}; return $avg_identity; } =head2 avg_seq_len Title : avg_seq_len Usage : $csp->avg_seq_len Function: get/set the assembly average sequence length Returns : avg_seq_len Args : real [optional] =cut sub avg_seq_len { my ($self, $avg_seq_len) = @_; if (defined $avg_seq_len) { $self->throw("The average sequence length must be strictly positive. Got ". "'$avg_seq_len'") if $avg_seq_len < 1; $self->{'_avg_seq_len'} = $avg_seq_len; } $avg_seq_len = $self->{'_avg_seq_len'}; return $avg_seq_len; } =head2 eff_asm_params Title : eff_asm_params Usage : $csp->eff_asm_params(1) Function: Get/set the effective assembly parameters option. It defines if the effective assembly parameters should be determined when a contig spectrum based or derived from an assembly is calculated. The effective assembly parameters include avg_seq_length, nof_overlaps, min_overlap, avg_overlap, min_identity and avg_identity. 1 = get them, 0 = don't. Returns : integer Args : integer [optional] =cut sub eff_asm_params { my ($self, $eff_asm_params) = @_; if (defined $eff_asm_params) { $self->throw("eff_asm_params can only take values 0 or 1. Input value was ". "'$eff_asm_params'") unless $eff_asm_params == 0 || $eff_asm_params == 1; $self->{'_eff_asm_params'} = $eff_asm_params; } $eff_asm_params = $self->{'_eff_asm_params'}; return $eff_asm_params; } =head2 spectrum Title : spectrum Usage : my $spectrum = $csp->spectrum({1=>10, 2=>2, 3=>1}); Function: Get the current contig spectrum represented as a hash / Update a contig spectrum object based on a contig spectrum represented as a hash The hash representation of a contig spectrum is as following: key -> contig size (in number of sequences) value -> number of contigs of this size Returns : contig spectrum as a hash reference Args : contig spectrum as a hash reference [optional] =cut sub spectrum { my ($self, $spectrum) = @_; if (defined $spectrum) { $self->_import_spectrum($spectrum); } $spectrum = $self->{'_spectrum'}; return $spectrum; } =head2 assembly Title : assembly Usage : my @obj_list = $csp->assembly(); Function: get/set the contig spectrum object by adding an assembly, contig or singlet object to it, or get the list of objects associated with it Returns : arrayref of assembly, contig and singlet objects used in the contig spectrum object (Bio::Assembly::Scaffold, Bio::Assembly::Contig and Bio::Assembly::Singlet objects) Args : Bio::Assembly::Scaffold, Contig or Singlet object =cut sub assembly { my ($self, $assembly) = @_; if (defined $assembly) { $self->_import_assembly($assembly); } my @obj_list = @{$self->{'_assembly'}} if defined $self->{'_assembly'}; return @obj_list; } =head2 drop_assembly Title : drop_assembly Usage : $csp->drop_assembly(); Function: Remove all assembly objects associated with a contig spectrum. Assembly objects can take a lot of memory, which can be freed by calling this method. Don't call this method if you need the assembly object later on, for example for creating a dissolved or cross contig spectrum. Returns : 1 for success Args : none =cut sub drop_assembly { my ($self) = @_; $self->{'_assembly'} = []; return 1; } =head2 dissolve Title : dissolve Usage : $dissolved_csp->dissolve($mixed_csp, $seq_header); Function: Dissolve a mixed contig spectrum for the set of sequences that contain the specified header, i.e. determine the contribution of these sequences to the mixed contig spectrum. The mixed contig spectrum object must have one or several assembly object(s). In addition, min_overlap, min_identity and eff_asm_params are taken from the mixed contig spectrum, unless they are specified manually for the dissolved contig spectrum. The dissolved contigs underlying the contig spectrum can be obtained by calling the assembly() method. Returns : 1 for success Args : Bio::Assembly::Tools::ContigSpectrum reference sequence header string =cut sub dissolve { my ($self, $mixed_csp, $seq_header) = @_; $self->_import_dissolved_csp($mixed_csp, $seq_header); return 1; } =head2 cross Title : cross Usage : $cross_csp->cross($mixed_csp); Function: Calculate a cross contig_spectrum based on a mixed contig_spectrum. The underlying cross-contigs themselves can be obtained by calling the assembly() method. Returns : 1 for success Args : Bio::Assembly::Tools::ContigSpectrum reference =cut sub cross { my ($self, $mixed_csp) = @_; $self->_import_cross_csp($mixed_csp); return 1; } =head2 to_string Title : to_string Usage : my $csp_string = $csp->to_string; Function: Convert the contig spectrum into a string (easy to print!!). Returns : string Args : element separator (integer) [optional] 1 -> space-separated 2 -> tab-separated 3 -> newline-separated =cut sub to_string { my ($self, $element_separator) = @_; return 0 if $self->{'_max_size'} == 0; $element_separator ||= 1; if ($element_separator == 1) { $element_separator = ' '; } elsif ($element_separator == 2) { $element_separator = "\t"; } elsif ($element_separator == 3) { $element_separator = "\n"; } else { $self->throw("Unknown separator type '$element_separator'\n"); } my $str = ''; for (my $q = 1 ; $q <= $self->{'_max_size'} ; $q++) { my $val = 0; if (exists $self->{'_spectrum'}{$q}) { $val = $self->{'_spectrum'}{$q}; } $str .= $val.$element_separator; } $str =~ s/\s$//; return $str; } =head2 add Title : add Usage : $csp->add($additional_csp); Function: Add a contig spectrum to an existing one: sums the spectra, update the number of sequences, number of repetitions, ... Returns : 1 for success Args : Bio::Assembly::Tools::ContigSpectrum object =cut sub add { my ($self, $csp) = @_; # Sanity check if( !ref $csp || ! $csp->isa('Bio::Assembly::Tools::ContigSpectrum') ) { $self->throw("Unable to process non Bio::Assembly::Tools::ContigSpectrum ". "object [".ref($csp)."]"); } # Update overlap statistics if ( $self->{'_eff_asm_params'} > 0 ) { # Warnings if ( $csp->{'_eff_asm_params'} == 0 ) { $self->warn("The parent contig spectrum needs effective assembly ". "parameters (eff_asm_params = ".$self->{'_eff_asm_params'}.") but the ". "child contig spectrum doesn't have them (eff_asm_params = ". $csp->{'_eff_asm_params'}."). Skipping them..."); } elsif ( $csp->{'_eff_asm_params'} != $self->{'_eff_asm_params'} ) { $self->warn("The parent contig spectrum needs a different method for ". "detecting the effective assembly parameters (eff_asm_params = ". $self->{'_eff_asm_params'}.") than the one specified for the child ". "contig spectrum (eff_asm_params = ".$csp->{'_eff_asm_params'}."). ". "Ignoring the differences..."); } # Update existing stats ( $self->{'_avg_overlap'} , $self->{'_avg_identity'}, $self->{'_min_overlap'}, $self->{'_min_identity'}, $self->{'_nof_overlaps'} ) = $self->_update_overlap_stats( $self->{'_avg_overlap'} , $self->{'_avg_identity'}, $self->{'_min_overlap'}, $self->{'_min_identity'}, $self->{'_nof_overlaps'}, $csp->{'_avg_overlap'} , $csp->{'_avg_identity'} , $csp->{'_min_overlap'}, $csp->{'_min_identity'} , $csp->{'_nof_overlaps'} ); } # Update sequence average length (not number of sequences) ( $self->{'_avg_seq_len'} ) = $self->_update_seq_stats( $self->{'_avg_seq_len'}, $self->{'_nof_seq'}, $csp->{'_avg_seq_len'}, $csp->{'_nof_seq'} ); # Update spectrum (and nof_seq, max_size, and increment nof_rep by 1) $self->_import_spectrum($csp->{'_spectrum'}); # Update nof_rep $self->{'_nof_rep'}--; $self->{'_nof_rep'} += $csp->{'_nof_rep'}; # Update list of assembly objects used push @{$self->{'_assembly'}}, @{$csp->{'_assembly'}} if defined $csp->{'_assembly'}; return 1; } =head2 average Title : average Usage : my $avg_csp = $csp->average([$csp1, $csp2, $csp3]); Function: Average one contig spectrum or the sum of several contig spectra by the number of repetitions Returns : Bio::Assembly::Tools::ContigSpectrum Args : Bio::Assembly::Tools::ContigSpectrum array reference eff_asm_params =cut sub average { my ($self, $list) = @_; # Sanity check if ( ! ref $list || ! ref $list eq 'ARRAY') { $self->throw("Average takes an array reference but got [".ref($list)."]"); } # New average contig spectrum object my $avg = Bio::Assembly::Tools::ContigSpectrum->new; $avg->{'_eff_asm_params'} = $self->{'_eff_asm_params'}; # Cycle through contig spectra my $tot_nof_rep = 0; for my $csp (@$list) { # Sanity check if (not $csp->isa('Bio::Assembly::Tools::ContigSpectrum')) { $csp->throw("Unable to process non Bio::Assembly::Tools::ContigSpectrum ". "object [".ref($csp)."]"); } # Import contig spectrum $avg->add($csp); } # Average sum of contig spectra by number of repetitions for (my $q = 1 ; $q <= $avg->{'_max_size'} ; $q++) { $avg->{'_spectrum'}{$q} /= $avg->{'_nof_rep'} if (defined $avg->{'_spectrum'}{$q}); } # Average number of sequences $avg->{'_nof_seq'} /= $avg->{'_nof_rep'}; # Average number of overlaps $avg->{'_nof_overlaps'} /= $avg->{'_nof_rep'}; return $avg; } =head2 score Title : score Usage : my $score = $csp->score(); Function: Score a contig spectrum (or cross-contig spectrum) such that the higher the number of contigs (or cross-contigs) and the larger their size, the higher the score. Let n : total number of sequences c_q : number of contigs of size q q : number of sequence in a contig We define: score = n/(n-1) * (X - 1/n) where X = sum ( c_q * q^2 ) / n**2 The score ranges from 0 (singlets only) to 1 (a single large contig) It is possible to specify a value for the number of sequences to assume in the contig spectrum. Returns : contig score, or undef if there were no sequences in the contig spectrum Args : number of total sequences to assume [optional] =cut sub score { my ($self, $nof_seqs) = @_; # Sanity check my $n = $self->nof_seq; return undef if ($n <= 0); # Calculate X my $score = 0; my $q_max = $self->max_size; my $spec = $self->spectrum; for my $q ( 1 .. $q_max ) { my $c_q = $spec->{$q}; if ( $q == 1 && $nof_seqs ) { $c_q += $nof_seqs - $n; $n = $nof_seqs; } next if not $c_q; $score += $c_q * $q ** 2; } $score /= $n ** 2; # Rescale X to obtain the score $score = $n/($n-1) * ($score - 1/$n); return $score; } =head2 _naive_assembler Title : _naive_assembler Usage : Function: Reassemble the specified sequences only based on their position in the contig. This naive assembly only verifies that the minimum overlap length and percentage identity are respected. No actual alignment is done Returns : arrayref of contigs and singlets Args : Bio::Assembly::Contig array reference of sequence IDs to use [optional] minimum overlap length (integer) [optional] minimum percentage identity (integer) [optional] =cut sub _naive_assembler { my ($self, $contig, $seqlist, $min_overlap, $min_identity) = @_; # Use all reads if none was specified: if (not defined $seqlist) { for my $seq ($contig->each_seq) { push @$seqlist, $seq->id; } } # Sanity checks if ( ! ref $seqlist || ! ref($seqlist) eq 'ARRAY') { $self->throw('Expecting an array reference. Got ['.ref($seqlist)."] \n"); } my $max = scalar @$seqlist; $self->throw("Expecting at least 2 sequences as input for _naive_assembler") if ($max < 2); # Build contig graph my %seq_hash = map { $_ => undef } (@$seqlist) if (scalar @$seqlist > 0); my ($g, $overlaps) = $self->_contig_graph($contig, \%seq_hash, $min_overlap, $min_identity); # Construct sub-contigs my @contig_objs; my $num = 1; if (defined $g) { for my $connected_reads ($g->connected_components) { # reads that belong in contigs my $sub_id = $contig->id.'_'.$num; my $sub_contig = $self->_create_subcontig($contig, $connected_reads, $sub_id); push @contig_objs, $sub_contig; $num++; for my $read_id ( @$connected_reads ) { delete $seq_hash{$read_id}; } } } # Construct sub-singlets my @singlet_objs; for my $read_id ( keys %seq_hash ) { my $read = $contig->get_seq_by_name($read_id); my $sub_singlet = Bio::Assembly::Singlet->new( -id => $contig->id.'_'.$num, -seqref => $self->_obj_copy($read) ); $num++; push @singlet_objs, $sub_singlet; } return [@contig_objs, @singlet_objs]; } =head2 _create_subcontig Title : _create_subcontig Usage : Function: Create a subcontig from another contig Returns : Bio::Assembly::Contig object Args : Bio::Assembly::Contig arrayref of the IDs of the reads to includes in the subcontig ID to give to the subcontig =cut sub _create_subcontig { my ($self, $contig, $read_ids, $sub_contig_id) = @_; my $sub_contig = Bio::Assembly::Contig->new( -id => $sub_contig_id ); # Get min and max read coordinates my ($min, $max) = (undef, undef); for my $read_id ( @$read_ids ) { my ($aln_coord) = $contig->get_features_collection->get_features_by_type("_aligned_coord:$read_id"); my $seq_start = $aln_coord->location->start; my $seq_end = $aln_coord->location->end; $min = $seq_start if (not defined $min) || ((defined $min) && ($seq_start < $min)); $max = $seq_end if (not defined $max) || ((defined $max) && ($seq_end > $max)); } # Add reads to subcontig for my $read_id (@$read_ids) { my $read = $self->_obj_copy($contig->get_seq_by_name($read_id)); my $coord = $self->_obj_copy($contig->get_seq_coord($read)); if ($min > 1) { # adjust read coordinates $coord->start( $coord->start - $min + 1 ); $coord->end( $coord->end - $min + 1 ); } $sub_contig->set_seq_coord($coord, $read); } # Truncate copy of original consensus to new boundaries my $cons_seq = $contig->get_consensus_sequence; $sub_contig->set_consensus_sequence( $self->_obj_copy($cons_seq, $min, $max) ); my $cons_qual = $contig->get_consensus_quality; if ($cons_qual) { $sub_contig->set_consensus_quality( $self->_obj_copy($cons_qual, $min, $max) ); } return $sub_contig; } =head2 _obj_copy Title : _obj_copy Usage : Function: Copy (most of) an object, and optionally truncate it Returns : another a Bio::LocatableSeq, Bio::Seq::PrimaryQual, or Bio::SeqFeature::Generic object Args : a Bio::LocatableSeq, Bio::Seq::PrimaryQual, or Bio::SeqFeature::Generic object a start position an end position =cut sub _obj_copy { my ($self, $obj, $start, $end) = @_; my $new; if ($obj->isa('Bio::Seq::PrimaryQual')) { my $qual = [@{$obj->qual}]; # copy of the quality scores if (defined $start && defined $end && $start !=1 && $end != scalar(@$qual)) { # Truncate the quality scores $qual = [ splice @$qual, $start - 1, $end - $start + 1 ]; } $new = Bio::Seq::PrimaryQual->new( -qual => $qual, -id => $obj->id, ); } elsif ($obj->isa('Bio::LocatableSeq')) { my $seq = $obj->seq; if (defined $start && defined $end && $start != 1 && $end != length($seq)) { # Truncate the aligned sequence $seq = substr $seq, $start - 1, $end - $start + 1; } $new = Bio::LocatableSeq->new( -seq => $seq, -id => $obj->id, -start => $obj->start, -strand => $obj->strand, -alphabet => $obj->alphabet, ); } elsif ($obj->isa('Bio::SeqFeature::Generic')) { $new = Bio::SeqFeature::Generic->new( -start => $obj->start, -end => $obj->end ); } return $new; } =head2 _new_from_assembly Title : _new_from_assembly Usage : Function: Creates a new contig spectrum object based solely on the result of an assembly, contig or singlet Returns : Bio::Assembly::Tools::ContigSpectrum object Args : Bio::Assembly::Scaffold, Contig or Singlet object =cut sub _new_from_assembly { # Create new contig spectrum object based purely on what we can get from the # assembly object my ($self, $assemblyobj) = @_; my $csp = Bio::Assembly::Tools::ContigSpectrum->new(); # 1: Set id $csp->{'_id'} = $assemblyobj->id; # 2: Set overlap statistics: nof_overlaps, min_overlap, avg_overlap, # min_identity and avg_identity $csp->{'_eff_asm_params'} = $self->{'_eff_asm_params'}; $csp->{'_min_overlap'} = $self->{'_min_overlap'}; $csp->{'_min_identity'} = $self->{'_min_identity'}; if ( $csp->{'_eff_asm_params'} > 0 ) { ( $csp->{'_avg_overlap'}, $csp->{'_avg_identity'}, $csp->{'_min_overlap'}, $csp->{'_min_identity'}, $csp->{'_nof_overlaps'} ) = $csp->_get_assembly_overlap_stats($assemblyobj); } # 3: Set sequence statistics: nof_seq and avg_seq_len ($csp->{'_avg_seq_len'}, $csp->{'_nof_seq'}) = $self->_get_assembly_seq_stats($assemblyobj); ### any use in using _naive_assembler here to re-assemble with specific minmum criteria? # 4: Set the spectrum: spectrum and max_size for my $contigobj ( $self->_get_contig_like($assemblyobj) ) { my $size = $contigobj->num_sequences; if (defined $csp->{'_spectrum'}{$size}) { $csp->{'_spectrum'}{$size}++; } else { $csp->{'_spectrum'}{$size} = 1; } $csp->{'_max_size'} = $size if $size > $csp->{'_max_size'}; } # 5: Set list of assembly objects used push @{$csp->{'_assembly'}}, $assemblyobj; # 6: Set number of repetitions $csp->{'_nof_rep'} = 1; return $csp; } =head2 _new_dissolved_csp Title : _new_dissolved_csp Usage : Function: create a dissolved contig spectrum object Returns : dissolved contig spectrum Args : mixed contig spectrum header of sequences to keep in this contig spectrum =cut sub _new_dissolved_csp { my ($self, $mixed_csp, $seq_header) = @_; # Sanity checks on the mixed contig spectrum # min_overlap and min_identity must be specified if there are some overlaps # in the mixed contig if ($mixed_csp->{'_nof_overlaps'} > 0) { unless ( defined $self->{'_min_overlap'} || defined $mixed_csp->{'_min_overlap'} ) { $self->throw("min_overlap must be defined in the dissolved contig spectrum". " or mixed contig spectrum to dissolve a contig"); } unless ( defined $self->{'_min_identity'} || defined $mixed_csp->{'_min_identity'} ) { $self->throw("min_identity must be defined in the dissolved contig spectrum". " or mixed contig spectrum"); } } # there must be at least one assembly in mixed contig spectrum if (!defined $mixed_csp->{'_assembly'} || scalar @{$mixed_csp->{'_assembly'}} < 1) { $self->throw("The mixed contig spectrum must be based on at least one assembly"); } # New dissolved contig spectrum object my $dissolved = Bio::Assembly::Tools::ContigSpectrum->new(); # Take attributes of the parent contig spectrum if they exist, or those of the # mixed contig spectrum otherwise my ($eff_asm_params, $min_overlap, $min_identity); if ($self->{'_eff_asm_params'}) { $eff_asm_params = $self->{'_eff_asm_params'}; } else { $eff_asm_params = $mixed_csp->{'_eff_asm_params'}; } if ($self->{'_min_overlap'}) { $min_overlap = $self->{'_min_overlap'}; } else { $min_overlap = $mixed_csp->{'_min_overlap'}; } if ($self->{'_min_identity'}) { $min_identity = $self->{'_min_identity'}; } else { $min_identity = $mixed_csp->{'_min_identity'}; } ($dissolved->{'_eff_asm_params'}, $dissolved->{'_min_overlap'}, $dissolved->{'_min_identity'}) = ($eff_asm_params, $min_overlap, $min_identity); # Dissolve each assembly for my $obj (@{$mixed_csp->{'_assembly'}}) { for my $contig ( $self->_get_contig_like($obj) ) { # Dissolve this assembly/contig/singlet for the given sequences my $dissolved_objs = $self->_dissolve_contig( $contig, $seq_header, $min_overlap, $min_identity ); # Add dissolved contigs to contig spectrum for my $dissolved_obj (@$dissolved_objs) { $dissolved->assembly($dissolved_obj); $dissolved->{'_nof_rep'}--; } } } # Update nof_rep $dissolved->{'_nof_rep'} += $mixed_csp->{'_nof_rep'}; return $dissolved; } =head2 _dissolve_contig Title : _dissolve_contig Usage : Function: dissolve a contig Returns : arrayref of contigs and singlets Args : mixed contig spectrum header of sequences to keep in this contig spectrum minimum overlap minimum identity =cut sub _dissolve_contig { my ($self, $contig, $wanted_origin, $min_overlap, $min_identity) = @_; # List of reads my @seqs; if ($contig->isa('Bio::Assembly::Singlet')) { @seqs = $contig->seqref; } elsif ($contig->isa('Bio::Assembly::Contig')) { @seqs = $contig->each_seq; } # Get sequences from the desired metagenome my @contig_seqs; for my $seq (@seqs) { my $seq_id = $seq->id; # get sequence origin next unless $self->_seq_origin($seq_id) eq $wanted_origin; # add it to hash push @contig_seqs, $seq_id; } # Update spectrum my $size = scalar @contig_seqs; my $objs; if ($size == 1) { # create a singlet and add it to list of objects my $id = $contig_seqs[0]; my $seq = $contig->get_seq_by_name($id); push @$objs, Bio::Assembly::Singlet->new(-id => $contig->id, -seqref => $self->_obj_copy($seq) ); } elsif ($size > 1) { # Reassemble good sequences my $contig_objs = $self->_naive_assembler( $contig, \@contig_seqs, $min_overlap, $min_identity ); push @$objs, @$contig_objs; } return $objs; } =head2 _new_cross_csp Title : _new_cross_csp Usage : Function: create a cross contig spectrum object Returns : cross-contig spectrum Args : mixed contig spectrum =cut sub _new_cross_csp { my ($self, $mixed_csp) = @_; # Sanity check on the mixed contig spectrum # There must be at least one assembly if (!defined $mixed_csp->{'_assembly'} || scalar @{$mixed_csp->{'_assembly'}} < 1) { $self->throw("The mixed contig spectrum must be based on at least one ". "assembly."); } # New dissolved contig spectrum object my $cross = Bio::Assembly::Tools::ContigSpectrum->new(); # Take attributes from parent or from mixed contig spectrums my ($eff_asm_params, $min_overlap, $min_identity); if ($self->{'_eff_asm_params'}) { $eff_asm_params = $self->{'_eff_asm_params'}; } else { $eff_asm_params = $mixed_csp->{'_eff_asm_params'}; } if ($self->{'_min_overlap'}) { $min_overlap = $self->{'_min_overlap'}; } else { $min_overlap = $mixed_csp->{'_min_overlap'}; } if ($self->{'_min_identity'}) { $min_identity = $self->{'_min_identity'}; } else { $min_identity = $mixed_csp->{'_min_identity'}; } ($cross->{'_eff_asm_params'},$cross->{'_min_overlap'},$cross->{'_min_identity'}) = ($eff_asm_params, $min_overlap, $min_identity); # Get cross contig spectrum for each assembly for my $obj ( @{$mixed_csp->{'_assembly'}} ) { for my $contig ( $self->_get_contig_like($obj) ) { # Go through contigs and skip the pure ones my ($cross_contigs, $nof_cross_singlets) = $self->_cross_contig($contig, $min_overlap, $min_identity); # Add cross-contig for my $cross_contig ( @$cross_contigs ) { $cross->assembly($cross_contig); $cross->{'_nof_rep'}--; } # Add cross-singlets $cross->{'_spectrum'}->{'1'} += $nof_cross_singlets; } } # Update nof_rep $cross->{'_nof_rep'} += $mixed_csp->{'_nof_rep'}; return $cross; } =head2 _cross_contig Title : _cross_contig Usage : Function: calculate cross contigs Returns : arrayref of cross-contigs number of cross-singlets Args : contig minimum overlap minimum identity =cut sub _cross_contig { my ($self, $contig, $min_overlap, $min_identity) = @_; my $nof_cross_singlets = 0; my @cross_contigs; # Weed out pure contigs my %all_origins; for my $seq ($contig->each_seq) { my $seq_id = $seq->id; my $seq_origin = $self->_seq_origin($seq_id); if (not defined $seq_origin) { $self->warn("Sequence $seq_id doesn't have any header. Skipping it..."); next; } if ( scalar keys %all_origins > 1 ) { # a cross-contig spectrum last; } $all_origins{$seq_origin} = undef; } if ( scalar keys %all_origins <= 1 ) { # a pure contig return \@cross_contigs, $nof_cross_singlets; } %all_origins = (); # Break the cross-contigs using the specified stringency my $test_contigs = $self->_naive_assembler($contig, undef, $min_overlap, $min_identity); # Find cross contigs and singlets for my $test_contig ( @$test_contigs ) { # Find cross-contigs my %origins; for my $seq ($test_contig->each_seq) { my $seq_id = $seq->id; my $seq_origin = $self->_seq_origin($seq_id); next if not defined $seq_origin; push @{$origins{$seq_origin}}, $seq_id; } if (scalar keys %origins > 1) { # Found a cross-contig push @cross_contigs, $test_contig; } else { next; } # Find cross-singlets for my $origin (keys %origins) { my @ori_ids = @{$origins{$origin}}; if (scalar @ori_ids == 1) { $nof_cross_singlets++; } elsif (scalar @ori_ids > 1) { # Dissolve contig for the given origin ### consider using the minimum overlap and identity here again? my $ori_contigs = $self->_naive_assembler($test_contig, \@ori_ids, undef, undef); for my $ori_contig (@$ori_contigs) { $nof_cross_singlets++ if $ori_contig->num_sequences == 1; } } } } return \@cross_contigs, $nof_cross_singlets; } =head2 _seq_origin Title : _seq_origin Usage : Function: determines where a sequence comes from using its header. For example the origin of the sequence 'metagenome1|gi|9626988|ref|NC_001508.1|' is 'metagenome1' Returns : origin Args : sequence ID =cut sub _seq_origin { # Current sequence origin. Example: sequence with ID # 'metagenome1|gi|9626988|ref|NC_001508.1|' has header 'metagenome1' my ($self, $seq_id) = @_; my $origin; if ( $seq_id =~ m/^(.+?)\|/ ) { $origin = $1; } return $origin; } =head2 _import_assembly Title : _import_assembly Usage : $csp->_import_assembly($assemblyobj); Function: Update a contig spectrum object based on an assembly, contig or singlet object Returns : 1 for success Args : Bio::Assembly::Scaffold, Contig or Singlet object =cut sub _import_assembly { my ($self, $assemblyobj) = @_; # Sanity check if ( ! ref $assemblyobj || ( ! $assemblyobj->isa('Bio::Assembly::ScaffoldI') && ! $assemblyobj->isa('Bio::Assembly::Contig') )) { $self->throw("Unable to process non Bio::Assembly::ScaffoldI, Contig or ". "Singlet object [".ref($assemblyobj)."]"); } # Create new object from assembly my $csp = $self->_new_from_assembly($assemblyobj); # Update current contig spectrum object with new one $self->add($csp); return 1; } =head2 _import_spectrum Title : _import_spectrum Usage : $csp->_import_spectrum({ 1 => 90 , 2 => 3 , 4 => 1 }) Function: update a contig spectrum object based on a contig spectrum represented as a hash (key: contig size, value: number of contigs of this size) Returns : 1 for success Args : contig spectrum as a hash reference =cut sub _import_spectrum { my ($self, $spectrum) = @_; # Sanity check if( ! ref $spectrum || ! ref $spectrum eq 'HASH') { $self->throw("Spectrum should be a hash reference, but it is [". ref($spectrum)."]"); } # Update the spectrum (+ nof_rep, max_size and nof_seq) for my $size (keys %$spectrum) { # Get the number of contigs of different size if (defined $self->{'_spectrum'}{$size}) { $self->{'_spectrum'}{$size} += $$spectrum{$size}; } else { $self->{'_spectrum'}{$size} = $$spectrum{$size}; } # Update nof_seq $self->{'_nof_seq'} += $size * $$spectrum{$size}; # Update max_size $self->{'_max_size'} = $size if $size > $self->{'_max_size'}; } # If the contig spectrum has only zero 1-contigs, max_size is zero $self->{'_max_size'} = 0 if scalar keys %{$self->{'_spectrum'}} == 1 && defined $self->{'_spectrum'}{'1'} && $self->{'_spectrum'}{'1'} == 0; # Update nof_rep $self->{'_nof_rep'}++; return 1; } =head2 _import_dissolved_csp Title : _import_dissolved_csp Usage : $csp->_import_dissolved_csp($mixed_csp, $seq_header); Function: Update a contig spectrum object by dissolving a mixed contig spectrum based on the header of the sequences Returns : 1 for success Args : Bio::Assembly::Tools::ContigSpectrum sequence header string =cut sub _import_dissolved_csp { my ($self, $mixed_csp, $seq_header) = @_; # Sanity check if (not defined $mixed_csp || not defined $seq_header) { $self->throw("Expecting a contig spectrum reference and sequence header as". " arguments"); } # Create new object from assembly my $dissolved_csp = $self->_new_dissolved_csp($mixed_csp, $seq_header); # Update current contig spectrum object with new one $self->add($dissolved_csp); return 1; } =head2 _import_cross_csp Title : _import_cross_csp Usage : $csp->_import_cross_csp($mixed_csp); Function: Update a contig spectrum object by calculating the cross contig spectrum based on a mixed contig spectrum Returns : 1 for success Args : Bio::Assembly::Tools::ContigSpectrum =cut sub _import_cross_csp { my ($self, $mixed_csp) = @_; # Sanity check if (not defined $mixed_csp) { $self->throw("Expecting a contig spectrum reference as argument"); } # Create new object from assembly my $cross_csp = $self->_new_cross_csp($mixed_csp); my $nof_1_cross_contigs = $cross_csp->spectrum->{1}; # Update current contig spectrum object with new one $self->add($cross_csp); # Remove 1-contigs $self->{'_nof_seq'} -= $nof_1_cross_contigs; return 1; } =head2 _get_contig_like Title : _get_contig_like Usage : my @contig_like_objs = $csp->_get_contig_like($assembly_obj); Function: Get contigs and singlets from an assembly, contig or singlet Returns : array of Bio::Assembly::Contig and Singlet objects Args : a Bio::Assembly::Scaffold, Contig or singlet object =cut sub _get_contig_like { my ($self, $assembly_obj) = @_; my @contig_objs; if ($assembly_obj->isa('Bio::Assembly::ScaffoldI')) { # all contigs and singlets in the scaffold push @contig_objs, ($assembly_obj->all_contigs, $assembly_obj->all_singlets); } else { # a contig or singlet @contig_objs = $assembly_obj; } return @contig_objs; } =head2 _get_assembly_seq_stats Title : _get_assembly_seq_stats Usage : my $seqlength = $csp->_get_assembly_seq_stats($assemblyobj); Function: Get sequence statistics from an assembly: average sequence length, number of sequences Returns : average sequence length (decimal) number of sequences (integer) Args : Bio::Assembly::Scaffold, Contig or singlet object hash reference with the IDs of the sequences to consider [optional] =cut sub _get_assembly_seq_stats { my ($self, $assemblyobj, $seq_hash) = @_; # Sanity checks if ( !defined $assemblyobj || ( !$assemblyobj->isa('Bio::Assembly::ScaffoldI') && !$assemblyobj->isa('Bio::Assembly::Contig') ) ) { $self->throw("Must provide a Bio::Assembly::Scaffold, Contig or Singlet object"); } $self->throw("Expecting a hash reference. Got [".ref($seq_hash)."]") if (defined $seq_hash && ! ref($seq_hash) eq 'HASH'); # Update sequence stats my @asm_stats = (0,0); # asm_stats = (avg_seq_len, nof_seq) for my $contigobj ( $self->_get_contig_like($assemblyobj) ) { @asm_stats = $self->_update_seq_stats( @asm_stats, $self->_get_contig_seq_stats($contigobj, $seq_hash) ); } return @asm_stats; } =head2 _get_contig_seq_stats Title : _get_contig_seq_stats Usage : my $seqlength = $csp->_get_contig_seq_stats($contigobj); Function: Get sequence statistics from a contig: average sequence length, number of sequences Returns : average sequence length (decimal) number of sequences (integer) Args : contig object reference hash reference with the IDs of the sequences to consider [optional] =cut sub _get_contig_seq_stats { my ($self, $contigobj, $seq_hash) = @_; my @contig_stats = (0, 0); # contig_stats = (avg_length, nof_seq) for my $seqobj ($contigobj->each_seq) { next if defined $seq_hash && !defined $$seq_hash{$seqobj->id}; my $seq_string; if ($contigobj->isa('Bio::Assembly::Singlet')) { # a singlet $seq_string = $contigobj->seqref->seq; } else { # a contig $seq_string = $seqobj->seq; } # Number of non-gap characters in the sequence my $seq_len = $seqobj->_ungapped_len; my @seq_stats = ($seq_len); @contig_stats = $self->_update_seq_stats(@contig_stats, @seq_stats); } return @contig_stats; } =head2 _update_seq_stats Title : _update_seq_stats Usage : Function: Update the number of sequences and their average length 1 average identity 1 minimum length 1 minimum identity 1 number of overlaps 1 average sequence length Returns : average sequence length number of sequences Args : average sequence length 1 number of sequences 1 average sequence length 2 number of sequences 2 =cut sub _update_seq_stats { my ($self, $p_avg_length, $p_nof_seq, $n_avg_length, $n_nof_seq) = @_; # Defaults if (not defined $n_nof_seq) { $n_nof_seq = 1; } # Update overlap statistics my $avg_length = 0; my $nof_seq = $p_nof_seq + $n_nof_seq; if ($nof_seq != 0) { $avg_length = ($p_avg_length * $p_nof_seq + $n_avg_length * $n_nof_seq) / $nof_seq; } return $avg_length, $nof_seq; } =head2 _get_assembly_overlap_stats Title : _get_assembly_overlap_stats Usage : my ($avglength, $avgidentity, $minlength, $min_identity, $nof_overlaps) = $csp->_get_assembly_overlap_stats($assemblyobj); Function: Get statistics about pairwise overlaps in contigs of an assembly Returns : average overlap length average identity percent minimum overlap length minimum identity percent number of overlaps Args : Bio::Assembly::Scaffold, Contig or Singlet object hash reference with the IDs of the sequences to consider [optional] =cut sub _get_assembly_overlap_stats { my ($self, $assembly_obj, $seq_hash) = @_; # Sanity check if ( !defined $assembly_obj || ( !$assembly_obj->isa('Bio::Assembly::ScaffoldI') && !$assembly_obj->isa('Bio::Assembly::Contig') ) ) { $self->throw("Must provide a Bio::Assembly::ScaffoldI, Contig or Singlet object"); } $self->throw("Expecting a hash reference. Got [".ref($seq_hash)."]") if (defined $seq_hash && ! ref($seq_hash) eq 'HASH'); # Look at all the contigs (no singlets!) my @asm_stats = (0, 0, undef, undef, 0); # asm_stats = (avg_length, avg_identity, min_length, min_identity, nof_overlaps) for my $contig_obj ( $self->_get_contig_like($assembly_obj) ) { @asm_stats = $self->_update_overlap_stats( @asm_stats, $self->_get_contig_overlap_stats($contig_obj, $seq_hash) ); } return @asm_stats; } =head2 _get_contig_overlap_stats Title : _get_contig_overlap_stats Usage : my ($avglength, $avgidentity, $minlength, $min_identity, $nof_overlaps) = $csp->_get_contig_overlap_stats($contigobj); Function: Get statistics about pairwise overlaps in a contig or singlet. The statistics are obtained using graph theory: each read is a node and the edges between 2 reads are weighted by minus the number of conserved residues in the alignment between the 2 reads. The minimum spanning tree of this graph represents the overlaps that form the contig. Overlaps that do not satisfy the minimum overlap length and similarity get a malus on their score. Note: This function requires the optional BioPerl dependency module called 'Graph' Returns : average overlap length average identity percent minimum overlap length minimum identity percent number of overlaps Args : Bio::Assembly::Contig or Singlet object hash reference with the IDs of the sequences to consider [optional] =cut sub _get_contig_overlap_stats { my ($self, $contig_obj, $seq_hash) = @_; # Sanity check $self->throw("Must provide a Bio::Assembly::Contig object") if (!defined $contig_obj || !$contig_obj->isa("Bio::Assembly::Contig")); $self->throw("Expecting a hash reference. Got [".ref($seq_hash)."]") if (defined $seq_hash && ! ref($seq_hash) eq 'HASH'); my @contig_stats = (0, 0, undef, undef, 0); # contig_stats = (avg_length, avg_identity, min_length, min_identity, nof_overlaps) # Build contig graph ### consider providing the minima to _contig_graph here too? my ($g, $overlaps) = $self->_contig_graph($contig_obj, $seq_hash); if ( defined $g ) { # Graph minimum spanning tree (tree that goes through strongest overlaps) $g = $g->MST_Kruskal(); # Calculate minimum overlap length and identity for this contig for my $edge ( $g->edges ) { # Retrieve overlap information my ($id1, $id2) = @$edge; if (not exists $$overlaps{$id1}{$id2}) { ($id2, $id1) = @$edge; } my ($score, $length, $identity) = @{$$overlaps{$id1}{$id2}}; # Update contig stats my @overlap_stats = ($length, $identity); @contig_stats = $self->_update_overlap_stats(@contig_stats, @overlap_stats); } } return @contig_stats; } =head2 _update_overlap_stats Title : _update_overlap_stats Usage : Function: update the number of overlaps and their minimum and average length and identity Returns : Args : average length 1 average identity 1 minimum length 1 minimum identity 1 number of overlaps 1 average length 2 average identity 2 minimum length 2 minimum identity 2 number of overlaps 2 =cut sub _update_overlap_stats { my ($self, $p_avg_length, $p_avg_identity, $p_min_length, $p_min_identity, $p_nof_overlaps, $n_avg_length, $n_avg_identity, $n_min_length, $n_min_identity, $n_nof_overlaps) = @_; # Defaults if (not defined $n_nof_overlaps) { $n_nof_overlaps = 1 }; if ((not defined $n_min_length) && ($n_avg_length != 0)) { $n_min_length = $n_avg_length }; if ((not defined $n_min_identity) && ($n_avg_identity != 0)) { $n_min_identity = $n_avg_identity }; # Update overlap statistics my ($avg_length, $avg_identity, $min_length, $min_identity, $nof_overlaps) = (0, 0, undef, undef, 0); $nof_overlaps = $p_nof_overlaps + $n_nof_overlaps; if ($nof_overlaps > 0) { $avg_length = ($p_avg_length * $p_nof_overlaps + $n_avg_length * $n_nof_overlaps) / $nof_overlaps; $avg_identity = ($p_avg_identity * $p_nof_overlaps + $n_avg_identity * $n_nof_overlaps) / $nof_overlaps; } if ( not defined $p_min_length ) { $min_length = $n_min_length; } elsif ( not defined $n_min_length ) { $min_length = $p_min_length; } else { # both values are defined if ($n_min_length < $p_min_length) { $min_length = $n_min_length; } else { $min_length = $p_min_length; } } if ( not defined $p_min_identity ) { $min_identity = $n_min_identity; } elsif ( not defined $n_min_identity ) { $min_identity = $p_min_identity; } else { # both values are defined if ($n_min_identity < $p_min_identity) { $min_identity = $n_min_identity; } else { $min_identity = $p_min_identity; } } return $avg_length, $avg_identity, $min_length, $min_identity, $nof_overlaps; } =head2 _overlap_alignment Title : _overlap_alignment Usage : Function: Produce an alignment of the overlapping section of two sequences of a contig. Minimum overlap length and percentage identity can be specified. Return undef if the sequences do not overlap or do not meet the minimum overlap criteria. Return : Bio::SimpleAlign object reference alignment overlap length alignment overlap identity Args : Bio::Assembly::Contig object reference Bio::LocatableSeq contig sequence 1 Bio::LocatableSeq contig sequence 2 minimum overlap length [optional] minimum overlap identity percentage[optional] =cut sub _overlap_alignment { my ($self, $contig, $qseq, $tseq, $min_overlap, $min_identity) = @_; # get query and target sequence position my $qpos = $contig->get_seq_coord($qseq); my $tpos = $contig->get_seq_coord($tseq); # check that there is an overlap my $qend = $qpos->end; my $tstart = $tpos->start; return if $qend < $tstart; my $qstart = $qpos->start; my $tend = $tpos->end; return if $qstart > $tend; # get overlap boundaries and check overlap length my $left; if ($qstart >= $tstart) { $left = $qstart } else { $left = $tstart; } my $right; if ($qend > $tend) { $right = $tend; } else { $right = $qend; } my $overlap = $right - $left + 1; return if defined $min_overlap && $overlap < $min_overlap; # slice query and target sequence to overlap boundaries my $qleft = $contig->change_coord('gapped consensus', "aligned ".$qseq->id, $left); my $qstring = substr($qseq->seq, $qleft - 1, $overlap); my $tleft = $contig->change_coord('gapped consensus', "aligned ".$tseq->id, $left); my $tstring = substr($tseq->seq, $tleft - 1, $overlap); # remove gaps present in both sequences at the same position for (my $pos = 0 ; $pos < $overlap ; $pos++) { my $qnt = substr($qstring, $pos, 1); if ($qnt eq '-') { my $tnt = substr($tstring, $pos, 1); if ($tnt eq '-') { substr($qstring, $pos, 1, ''); substr($tstring, $pos, 1, ''); $pos--; $overlap--; } } } return if defined $min_overlap && $overlap < $min_overlap; # count the number of gaps remaining in each sequence my $qgaps = ($qstring =~ tr/-//); my $tgaps = ($tstring =~ tr/-//); # make an alignment object with the query and target sequences my $aln = Bio::SimpleAlign->new; my $alseq = Bio::LocatableSeq->new( -id => 1, -seq => $qstring, -start => 1, -end => $overlap - $qgaps, -alphabet => 'dna', ); $aln->add_seq($alseq); $alseq = Bio::LocatableSeq->new( -id => 2, -seq => $tstring, -start => 1, -end => $overlap - $tgaps, -alphabet => 'dna', ); $aln->add_seq($alseq); # check overlap percentage identity my $identity = $aln->overall_percentage_identity; return if defined $min_identity && $identity < $min_identity; # all checks passed, return alignment return $aln, $overlap, $identity; } =head2 _contig_graph Title : _contig_graph Usage : Function: Creates a graph data structure of the contig.The graph is undirected. The vertices are the reads of the contig and edges are the overlap between the reads. The edges are weighted by the opposite of the overlap, so it is negative and the better the overlap, the lower the weight. Return : Graph object or undef hashref of overlaps (score, length, identity) for each read pair Args : Bio::Assembly::Contig object reference hash reference with the IDs of the sequences to consider [optional] minimum overlap length (integer) [optional] minimum percentage identity (integer) [optional] =cut sub _contig_graph { my ($self, $contig_obj, $seq_hash, $min_overlap, $min_identity) = @_; # Sanity checks if( !ref $contig_obj || ! $contig_obj->isa('Bio::Assembly::Contig') ) { $self->throw("Unable to process non Bio::Assembly::Contig ". "object [".ref($contig_obj)."]"); } if (not eval { require Graph::Undirected }) { $self->throw("Error: the module 'Graph' is needed by the method ". "_contig_graph but could not be found\n$@"); } # Skip contigs of 1 sequence (they have no overlap) my @seq_objs = $contig_obj->each_seq; my $nof_seqs = scalar @seq_objs; return if ($nof_seqs <= 1); # Calculate alignment between all pairs of reads my %overlaps; for my $i (0 .. $nof_seqs-1) { my $seq_obj = $seq_objs[$i]; my $seq_id = $seq_obj->id; # Skip this read if not in list of wanted sequences next if defined $seq_hash && !exists $$seq_hash{$seq_id}; # What is the best sequence to align to? my ($best_score, $best_length, $best_identity); for my $j ($i+1 .. $nof_seqs-1) { # Skip this sequence if not in list of wanted sequences my $target_obj = $seq_objs[$j]; my $target_id = $target_obj->id; next if defined $seq_hash && !exists $$seq_hash{$target_id}; # How much overlap with this sequence? my ($aln_obj, $length, $identity) = $self->_overlap_alignment($contig_obj, $seq_obj, $target_obj, $min_overlap, $min_identity); next if ! defined $aln_obj; # there was no sequence overlap or overlap not good enough # Score the overlap as the number of conserved residues. In practice, it # seems to work better than giving +1 for match and -3 for errors # (mismatch or indels) my $score = $length * $identity / 100; # Apply a malus (square root) for scores that do not satisfy the minimum # overlap length similarity. It is necessary for overlaps that get a high # score without satisfying both the minimum values. if ( ( $min_overlap && ($length < $min_overlap ) ) || ( $min_identity && ($identity < $min_identity) ) ) { $score = sqrt($score); } $overlaps{$seq_id}{$target_id} = [$score, $length, $identity]; } } # Process overlaps my $g; # the Graph object if (scalar keys %overlaps >= 1) { # At least 1 overlap. Create a weighted undirected graph $g = Graph::Undirected->new(); for my $seq_id (keys %overlaps) { for my $target_id (keys %{$overlaps{$seq_id}}) { my $score = @{$overlaps{$seq_id}{$target_id}}[0]; my $weight = -$score; $g->add_weighted_edge($seq_id, $target_id, $weight); } } } return $g, \%overlaps; } =head2 _draw_graph Title : _draw_graph Usage : Function: Generates a PNG picture of the contig graph. It is mostly for debugging purposes. Return : 1 for success Args : a Graph object hashref of overlaps (score, length, identity) for each read pair name of output file overlap info to display: 'score' (default), 'length' or 'identity' =cut sub _draw_graph { my ($self, $g, $overlaps, $outfile, $edge_type) = @_; $self->throw("Error: need to provide a graph as input\n") if not defined $g; if (not eval { require GraphViz }) { $self->throw("Error: the module 'GraphViz' is needed by the method ". "_draw_graph but could not be found\n$@"); } $edge_type ||= 'score'; my $viz = GraphViz->new( directed => 0 ); for my $edge ( $g->edges ) { # Retrieve overlap information my ($id1, $id2) = @$edge; if (not exists $$overlaps{$id1}{$id2}) { ($id2, $id1) = @$edge; } my ($score, $length, $identity) = @{$$overlaps{$id1}{$id2}}; my $edge_val; if ($edge_type eq 'score') { $edge_val = $score; } elsif ($edge_type eq 'length') { $edge_val = $length; } elsif ($edge_type eq 'identity') { $edge_val = $identity; } else { $self->throw("Error: invalid edge type to display, '$edge_val'"); } $viz->add_edge($id1 => $id2, label => $edge_val); } open my $fh, '>', $outfile or $self->throw("Error: Could not write file '$outfile': $!"); print $fh $viz->as_png; close $fh; return 1; } 1; __END__ BioPerl-1.007002/Bio/Cluster000755000766000024 013155576320 15510 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Cluster/ClusterFactory.pm000444000766000024 1224613155576320 21201 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Cluster::ClusterFactory # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Cluster::ClusterFactory - Instantiates a new Bio::ClusterI (or derived class) through a factory =head1 SYNOPSIS use Bio::Cluster::ClusterFactory; # if you don't provide a default type, the factory will try # some guesswork based on display_id and namespace my $factory = Bio::Cluster::ClusterFactory->new(-type => 'Bio::Cluster::UniGene'); my $clu = $factory->create_object(-description => 'NAT', -display_id => 'Hs.2'); =head1 DESCRIPTION This object will build L objects generically. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Cluster::ClusterFactory; use strict; use Bio::Root::Root; use base qw(Bio::Factory::ObjectFactory); =head2 new Title : new Usage : my $obj = Bio::Cluster::ClusterFactory->new(); Function: Builds a new Bio::Cluster::ClusterFactory object Returns : Bio::Cluster::ClusterFactory Args : -type => string, name of a ClusterI derived class. If not provided, the factory will have to guess from ID and namespace, which may or may not be successful. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->interface("Bio::ClusterI"); $self->type($self->type) if $self->type; return $self; } =head2 create_object Title : create_object Usage : my $seq = $factory->create_object(); Function: Instantiates new Bio::ClusterI (or one of its child classes) This object allows us to genericize the instantiation of cluster objects. Returns : L compliant object The return type is configurable using new(-type =>"..."). Args : initialization parameters specific to the type of cluster object we want. Typically -display_id => $name -description => description of the cluster -members => arrayref, members of the cluster =cut sub create_object { my ($self,@args) = @_; my $type = $self->type(); if(! $type) { # we need to guess this $type = $self->_guess_type(@args); $self->throw("No cluster type set and unable to guess.") unless $type; $self->type($type); } return $type->new(-verbose => $self->verbose, @args); } =head2 _guess_type Title : _guess_type Usage : Function: Guesses the right type of L implementation based on initialization parameters for the prospective object. Example : Returns : the type (a string, the module name) Args : initialization parameters to be passed to the prospective cluster object =cut sub _guess_type{ my ($self,@args) = @_; my $type; # we can only guess from a certain number of arguments my ($dispid, $ns, $members) = $self->_rearrange([qw(DISPLAY_ID NAMESPACE MEMBERS )], @args); # Unigene namespace or ID? if($ns && (lc($ns) eq "unigene")) { $type = 'Bio::Cluster::UniGene'; } elsif($dispid && ($dispid =~ /^Hs\.[0-9]/)) { $type = 'Bio::Cluster::UniGene'; } # what else could we look for? return $type; } 1; BioPerl-1.007002/Bio/Cluster/FamilyI.pm000444000766000024 1022313155576320 17553 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Cluster::FamilyI # # Please direct questions and support issues to # # Cared for by Shawn Hoon # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Cluster::FamilyI - Family Interface =head1 SYNOPSIS # see the implementations of this interface for details my $cluster= $cluster->new(-description=>"POLYUBIQUITIN", -members =>[$seq1,$seq2]); my @members = $cluster->get_members(); my @sub_members = $cluster->get_members(-species=>"homo sapiens"); =head1 DESCRIPTION This interface if for a Family object representing a family of biological objects. A generic implementation for this may be found a L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Cluster::FamilyI; use strict; use base qw(Bio::ClusterI); =head2 new We don't mandate but encourage implementors to support at least the following named parameters upon object initialization. Arguments Description --------- ----------- -family_id the name of the family -description the consensus description of the family -annotation_score the confidence by which the consensus description is representative of the family -members the members belonging to the family -alignment the multiple alignment of the members =cut =head2 family_id Title : family_id Usage : Bio::Cluster::FamilyI->family_id("znfp"); Function: get/set for the family id Returns : the family id Args : the family id =cut sub family_id{ shift->throw_not_implemented(); } =head2 family_score Title : family_score Usage : Bio::Cluster::FamilyI->family_score(95); Function: get/set for the score of algorithm used to generate the family if present Returns : the score Args : the score =cut sub family_score { shift->throw_not_implemented(); } =head1 Methods inherited from L =cut =head2 display_id Title : display_id Usage : Function: Get the display name or identifier for the cluster Returns : a string Args : =cut =head2 get_members Title : get_members Usage : Bio::Cluster::FamilyI->get_members(); Function: get the members of the family Returns : the array of members Args : the array of members =cut =head2 description Title : description Usage : Bio::Cluster::FamilyI->description("Zinc Finger Protein"); Function: get/set for the description of the family Returns : the description Args : the description =cut =head2 size Title : size Usage : Bio::Cluster::FamilyI->size(); Function: get/set for the description of the family Returns : size Args : =cut =head2 cluster_score Title : cluster_score Usage : $cluster ->cluster_score(100); Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster. Returns : a number =cut 1; BioPerl-1.007002/Bio/Cluster/SequenceFamily.pm000444000766000024 2514113155576320 21140 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Cluster::SequenceFamily # # Please direct questions and support issues to # # Cared for by Shawn Hoon # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Cluster::SequenceFamily - Sequence Family object =head1 SYNOPSIS use Bio::SeqIO; use Bio::Cluster::SequenceFamily; use File::Spec; my $file = File::Spec->catfile('t','data','swiss.dat'); my $seqio= Bio::SeqIO->new(-format => 'swiss', -file => $file); my @mem; while(my $seq = $seqio->next_seq){ push @mem, $seq; } #create the family my $family = Bio::Cluster::SequenceFamily->new( -family_id=>"Family_1", -description=>"Family Description Here", -annotation_score=>"100", -members=>\@mem); #access the family foreach my $mem ($family->get_members){ print $mem->display_id."\t".$mem->desc."\n"; } #select members if members have a Bio::Species Object my @mem = $family->get_members(-binomial=>"Homo sapiens"); @mem = $family->get_members(-ncbi_taxid => 9606); @mem = $family->get_members(-common_name=>"Human"); @mem = $family->get_members(-species=>"sapiens"); @mem = $family->get_members(-genus=>"Homo"); =head1 DESCRIPTION This is a simple Family object that may hold any group of object. For more specific families, one should derive from FamilyI. =head1 FEEDBACK Email bioperl-l@bioperl.org for support and feedback. =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_". =cut # Let the code begin... package Bio::Cluster::SequenceFamily; use strict; use warnings; use base qw(Bio::Root::Root Bio::Cluster::FamilyI); =head2 new Title : new Usage : my $family = Bio::Cluster::SequenceFamily->new( -family_id=>"Family_1", -description=>"Family Description Here", -annotation_score=>"100", -members=>\@mem); Function: Constructor for SequenceFamily object Returns : Bio::Cluster::SequenceFamily object See L. =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($id,$description,$version,$annot_score, $family_score,$members) = $self->_rearrange([qw(FAMILY_ID DESCRIPTION VERSION ANNOTATION_SCORE FAMILY_SCORE MEMBERS)],@args); $self->{'_members'} = []; $id && $self->family_id($id); $description && $self->description($description); $version && $self->version($version); $annot_score && $self->annotation_score($annot_score); $family_score && $self->family_score($family_score); $members && $self->add_members($members); return $self; } =head2 version Title : version Usage : $family->version("1.0"); Function: get/set for version Returns : a string version of the family generated. =cut sub version{ my ($self,$value) = @_; if($value){ $self->{'_version'} =$value; } return $self->{'_version'}; } =head2 annotation_score Title : annotation_score Usage : $family->annotation_score(100); Function: get/set for annotation_score which represent the confidence in which the consensus description has been assigned to the family. Returns : Bio::SimpleAlign See L =cut sub annotation_score{ my ($self,$score) = @_; if($score){ $self->{'_annotation_score'} = $score; } return $self->{'_annotation_score'}; } =head2 alignment Title : alignment Usage : $family->alignment($align); Function: get/set for an alignment object representing the multiple alignment of the members of the family. Returns : Bio::SimpleAlign See L =cut sub alignment { my ($self,$align) = @_; if($align){ $self->{'_alignment'} = $align; } return $self->{'_alignment'}; } =head2 tree Title : tree Usage : $family->tree($tree); Function: get/set for an tree object representing the phylogenetic tree of the family. Returns : Bio::Tree See L =cut sub tree { my ($self,$tree) = @_; if($tree) { $self->{'_tree'} = $tree; } return $self->{'_tree'}; } =head1 L methods =cut =head2 family_score Title : family_score Usage : Bio::Cluster::FamilyI->family_score(95); Function: get/set for the score of algorithm used to generate the family if present This is aliased to cluster_score(). Returns : the score Args : the score =cut sub family_score { return shift->cluster_score(@_); } =head2 family_id Title : family_id Usage : $family->family_id("Family_1"); Function: get/set for family id This is aliased to display_id(). Returns : a string specifying identifier of the family =cut sub family_id{ return shift->display_id(@_); } =head1 L methods =cut =head2 display_id Title : display_id Usage : Function: Get/set the display name or identifier for the cluster Returns : a string Args : optional, on set the display ID ( a string) =cut sub display_id{ my ($self,$id) = @_; if($id){ $self->{'_cluster_id'} = $id; } return $self->{'_cluster_id'}; } =head2 description Title : description Usage : $fam->description("POLYUBIQUITIN") Function: get/set for the consensus description of the cluster Returns : the description string Args : Optional the description string =cut sub description{ my ($self,$desc) = @_; if($desc){ $self->{'_description'} = $desc; } return $self->{'_description'}; } =head2 get_members Title : get_members Usage : Valid criteria: -common_name -binomial -ncbi_taxid -organelle -genus $family->get_members(-common_name =>"human"); $family->get_members(-species =>"homo sapiens"); $family->get_members(-ncbi_taxid => 9606); For now, multiple critieria are ORed. Will return all members if no criteria are provided. Function: get members using methods from L the phylogenetic tree of the family. Returns : an array of objects that are member of this family. =cut sub get_members { my $self = shift; return @{$self->{'_members'}} unless @_; ## since the logic behind the checks is OR, we keep the ids in an hash for ## performance (skip the test if it's already there) and to avoid repats my %match; my %filter = @_; foreach my $key (keys %filter) { (my $method = $key) =~ s/^-//; %match = (%match, map { $_ => $_ } grep { ! $match{$_} && $_->species && ($_->species->can($method) || $self->throw("$method is an invalid criteria")) && $_->species->$method() eq $filter{$key} } @{$self->{'_members'}}); } return map {$match{$_}} keys (%match); } =head2 size Title : size Usage : $fam->size(); Function: get/set for the size of the family, calculated from the number of members Returns : the size of the family Args : =cut sub size { my ($self) = @_; return scalar(@{$self->{'_members'}}); } =head2 cluster_score Title : cluster_score Usage : $fam->cluster_score(100); Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster. Returns : a number =cut sub cluster_score{ my ($self,$score) = @_; if($score){ $self->{'_cluster_score'} = $score; } return $self->{'_cluster_score'}; } =head1 Implementation specific methods These are mostly for adding/removing/changing. =cut =head2 add_members Title : add_members Usage : $fam->add_member([$seq1,$seq1]); Function: add members to a family Returns : Args : the member(s) to add, as an array or arrayref =cut sub add_members{ my ($self,@mems) = @_; if (@mems) { my $mem = shift(@mems); if(ref($mem) eq "ARRAY"){ push @{$self->{'_members'}},@{$mem}; } else { push @{$self->{'_members'}},$mem; } push @{$self->{'_members'}}, @mems; } return 1; } =head2 remove_members Title : remove_members Usage : $fam->remove_members(); Function: remove all members from a family Returns : the previous array of members Args : none =cut sub remove_members{ my ($self) = @_; my $mems = $self->{'_members'}; $self->{'_members'} = []; return @$mems; } ##################################################################### # aliases for naming consistency or other reasons # ##################################################################### *flush_members = \&remove_members; *add_member = \&add_members; =head2 members Title : members Usage : $members = $fam->members([$seq1,$seq1]); Function: Deprecated. Use add_members() or get_members() instead =cut sub members{ my $self = shift; if(@_) { # this is in set mode $self->warn("setting members() in ".ref($self)." is deprecated.\n". "Use add_members() instead."); return $self->add_members(@_); } else { # get mode $self->warn("members() in ".ref($self)." is deprecated.\n". "Use get_members() instead."); return $self->get_members(); } } 1; BioPerl-1.007002/Bio/Cluster/UniGene.pm000444000766000024 10434313155576320 17602 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Cluster::UniGene.pm # # Please direct questions and support issues to # # Cared for by Andrew Macgregor # # Copyright Andrew Macgregor, Jo-Ann Stanton, David Green # Molecular Embryology Group, Anatomy & Structural Biology, University of Otago # http://meg.otago.ac.nz/ # # You may distribute this module under the same terms as perl itself # # _history # April 17, 2002 - Initial implementation by Andrew Macgregor # POD documentation - main docs before the code =head1 NAME Bio::Cluster::UniGene - UniGene object =head1 SYNOPSIS use Bio::Cluster::UniGene; use Bio::ClusterIO; $stream = Bio::ClusterIO->new('-file' => "Hs.data", '-format' => "unigene"); # note: we quote -format to keep older perl's from complaining. while ( my $in = $stream->next_cluster() ) { print $in->unigene_id() . "\n"; while ( my $sequence = $in->next_seq() ) { print $sequence->accession_number() . "\n"; } } =head1 DESCRIPTION This UniGene object implements the L interface for the representation if UniGene clusters in Bioperl. It is returned by the L parser for unigene format and contains all the data associated with one UniGene record. This class implements several interfaces and hence can be used wherever instances of such interfaces are expected. In particular, the interfaces are L as the base interface for all cluster representations, and in addition L and L. The following lists the UniGene specific methods that are available (see below for details). Be aware next_XXX iterators take a snapshot of the array property when they are first called, and this snapshot is not reset until the iterator is exhausted. Hence, once called you need to exhaust the iterator to see any changes that have been made to the property in the meantime. You will usually want to use the non-iterator equivalents and loop over the elements yourself. new() - standard new call unigene_id() - set/get unigene_id title() - set/get title (description) gene() - set/get gene cytoband() - set/get cytoband mgi() - set/get mgi locuslink() - set/get locuslink homol() - set/get homologene gnm_terminus() - set/get gnm_terminus scount() - set/get scount express() - set/get express, currently takes/returns a reference to an array of expressed tissues next_express() - returns the next tissue expression from the expressed tissue array chromosome() - set/get chromosome, currently takes/returns a reference to an array of chromosome lines next_chromosome() - returns the next chromosome line from the array of chromosome lines sts() - set/get sts, currently takes/returns a reference to an array of sts lines next_sts() - returns the next sts line from the array of sts lines txmap() - set/get txmap, currently takes/returns a reference to an array of txmap lines next_txmap() - returns the next txmap line from the array of txmap lines protsim() - set/get protsim, currently takes/returns a reference to an array of protsim lines next_protsim() - returns the next protsim line from the array of protsim lines sequences() - set/get sequence, currently takes/returns a reference to an array of references to seq info next_seq() - returns a Seq object that currently only contains an accession number =head1 Implemented Interfaces This class implementes the following interfaces. =over 4 =item Bio::Cluster::UniGeneI This includes implementing Bio::ClusterI. =item Bio::IdentifiableI =item Bio::DescribableI =item Bio::AnnotatableI =item Bio::Factory::SequenceStreamI =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Andrew Macgregor Email andrew at cbbc.murdoch.edu.au =head1 CONTRIBUTORS Hilmar Lapp, hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_". =cut # Let the code begin... package Bio::Cluster::UniGene; use strict; use Bio::Annotation::Collection; use Bio::Annotation::DBLink; use Bio::Annotation::SimpleValue; use Bio::Species; use Bio::Seq::SeqFactory; use base qw(Bio::Root::Root Bio::Cluster::UniGeneI Bio::IdentifiableI Bio::DescribableI Bio::AnnotatableI Bio::Factory::SequenceStreamI); my %species_map = ( 'Aga' => "Anopheles gambiae", 'Ame' => "Apis mellifera", 'At' => "Arabidopsis thaliana", 'Bmo' => "Bombyx mori", 'Bt' => "Bos taurus", 'Cel' => "Caenorhabditis elegans", 'Cfa' => "Canine familiaris", 'Cin' => "Ciona intestinalis", 'Cre' => "Chlamydomonas reinhardtii", 'Csa' => "Ciona savignyi", 'Csi' => "Citrus sinensis", 'Ddi' => "Dictyostelium discoideum", 'Dr' => "Danio rerio", 'Dm' => "Drosophila melanogaster", 'Gga' => "Gallus gallus", 'Gma' => "Glycine max", 'Han' => "Helianthus annus", 'Hs' => "Homo sapiens", 'Hma' => "Hydra magnipapillata", 'Hv' => "Hordeum vulgare", 'Lco' => "Lotus corniculatus", 'Les' => "Lycopersicon esculentum", 'Lsa' => "Lactuca sativa", 'Mdo' => "Malus x domestica", 'Mgr' => "Magnaporthe grisea", 'Mm' => "Mus musculus", 'Mtr' => "Medicago truncatula", 'Ncr' => "Neurospora crassa", 'Oar' => "Ovis aries", 'Omy' => "Oncorhynchus mykiss", 'Os' => "Oryza sativa", 'Ola' => "Oryzias latipes", 'Ppa' => "Physcomitrella patens", 'Pta' => "Pinus taeda", 'Ptp' => "Populus tremula x Populus tremuloides", 'Rn' => "Rattus norvegicus", 'Sbi' => "Sorghum bicolor", 'Sma' => "Schistosoma mansoni", 'Sof' => "Saccharum officinarum", 'Spu' => "Strongylocentrotus purpuratus", 'Ssa' => "Salmo salar", 'Ssc' => "Sus scrofa", 'Str' => "Xenopus tropicalis", 'Stu' => "Solanum tuberosum", 'Ta' => "Triticum aestivum", 'Tgo' => "Toxoplasma gondii", 'Tru' => "Takifugu rubripes", 'Vvi' => "Vitis vinifera", 'Xl' => "Xenopus laevis", 'Zm' => "Zea mays", ); =head2 new Title : new Usage : used by ClusterIO Returns : a new Bio::Cluster::Unigene object =cut sub new { # standard new call.. my($caller,@args) = @_; my $self = $caller->SUPER::new(@args); my ($ugid,$desc,$mems,$size,$species,$dispid,$id,$ns,$auth,$v,$seqfact) = $self->_rearrange([qw(UNIGENE_ID DESCRIPTION MEMBERS SIZE SPECIES DISPLAY_ID OBJECT_ID NAMESPACE AUTHORITY VERSION SEQFACTORY )], @args); $self->{'_alphabet'} = 'dna'; $self->unigene_id($ugid) if $ugid; $self->description($desc) if $desc; $self->sequences($mems) if $mems; $self->size($size) if defined($size); $self->display_id($dispid) if $dispid; # overwrites ugid $self->object_id($id) if $id; # overwrites dispid $self->namespace($ns || 'UniGene'); $self->authority($auth || 'NCBI'); $self->version($v) if defined($v); if( ! defined $seqfact ) { $seqfact = Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq'); } $self->sequence_factory($seqfact); if( (! $species) && (defined $self->unigene_id() && $self->unigene_id() =~ /^([A-Za-z]+)\.[0-9]/)) { # try set a default one depending on the ID $species = $species_map{$1}; } $self->species($species); return $self; } =head1 L methods =cut =head2 unigene_id Title : unigene_id Usage : unigene_id(); Function: Returns the unigene_id associated with the object. Example : $id = $unigene->unigene_id or $unigene->unigene_id($id) Returns : A string Args : None or an id =cut sub unigene_id { my ($obj,$value) = @_; if( defined $value) { $obj->{'unigene_id'} = $value; } return $obj->{'unigene_id'}; } =head2 title Title : title Usage : title(); Function: Returns the title associated with the object. Example : $title = $unigene->title or $unigene->title($title) Returns : A string Args : None or a title =cut sub title { my ($obj,$value) = @_; if( defined $value) { $obj->{'title'} = $value; } return $obj->{'title'}; } =head2 gene Title : gene Usage : gene(); Function: Returns the gene associated with the object. Example : $gene = $unigene->gene or $unigene->gene($gene) Returns : A string Args : None or a gene =cut sub gene { my $self = shift; return $self->_annotation_value('gene_name', @_); } =head2 cytoband Title : cytoband Usage : cytoband(); Function: Returns the cytoband associated with the object. Example : $cytoband = $unigene->cytoband or $unigene->cytoband($cytoband) Returns : A string Args : None or a cytoband =cut sub cytoband { my $self = shift; return $self->_annotation_value('cyto_band', @_); } =head2 mgi Title : mgi Usage : mgi(); Function: Returns the mgi associated with the object. Example : $mgi = $unigene->mgi or $unigene->mgi($mgi) Returns : A string Args : None or a mgi =cut sub mgi { my $self = shift; my $acc; if(@_) { # purge first $self->_remove_dblink('dblink','MGI'); # then add if a valid value is present if($acc = shift) { $self->_annotation_dblink('dblink','MGI',$acc); } } else { ($acc) = $self->_annotation_dblink('dblink','MGI'); } return $acc; } =head2 locuslink Title : locuslink Usage : locuslink(); Function: Returns or stores a reference to an array containing locuslink data. Returns : An array reference Args : None or an array reference =cut sub locuslink { my ($self,$ll) = @_; if($ll) { # purge first $self->_remove_dblink('dblink','LocusLink'); # then add as many accessions as are present foreach my $acc (@$ll) { $self->_annotation_dblink('dblink','LocusLink',$acc); } } else { my @accs = $self->_annotation_dblink('dblink','LocusLink'); $ll = [@accs]; } return $ll; } =head2 homol Title : homol Usage : homol(); Function: Returns the homol entry associated with the object. Example : $homol = $unigene->homol or $unigene->homol($homol) Returns : A string Args : None or a homol entry =cut sub homol { my $self = shift; return $self->_annotation_value('homol', @_); } =head2 restr_expr Title : restr_expr Usage : restr_expr(); Function: Returns the restr_expr entry associated with the object. Example : $restr_expr = $unigene->restr_expr or $unigene->restr_expr($restr_expr) Returns : A string Args : None or a restr_expr entry =cut sub restr_expr { my $self = shift; return $self->_annotation_value('restr_expr', @_); } =head2 gnm_terminus Title : gnm_terminus Usage : gnm_terminus(); Function: Returns the gnm_terminus associated with the object. Example : $gnm_terminus = $unigene->gnm_terminus or $unigene->gnm_terminus($gnm_terminus) Returns : A string Args : None or a gnm_terminus =cut sub gnm_terminus { my $self = shift; return $self->_annotation_value('gnm_terminus', @_); } =head2 scount Title : scount Usage : scount(); Function: Returns the scount associated with the object. Example : $scount = $unigene->scount or $unigene->scount($scount) Returns : A string Args : None or a scount =cut sub scount { my ($obj,$value) = @_; if( defined $value) { $obj->{'scount'} = $value; } elsif((! defined($obj->{'scount'})) && defined($obj->sequences())) { $obj->{'scount'} = $obj->size(); } return $obj->{'scount'}; } =head2 express Title : express Usage : express(); Function: Returns or stores a reference to an array containing tissue expression data Returns : An array reference Args : None or an array reference =cut sub express { my $self = shift; return $self->_annotation_value_ary('expressed',@_); } =head2 chromosome Title : chromosome Usage : chromosome(); Function: Returns or stores a reference to an array containing chromosome lines Returns : An array reference Args : None or an array reference =cut sub chromosome { my $self = shift; return $self->_annotation_value_ary('chromosome',@_); } =head2 sts Title : sts Usage : sts(); Function: Returns or stores a reference to an array containing sts lines Returns : An array reference Args : None or an array reference =cut sub sts { my $self = shift; return $self->_annotation_value_ary('sts',@_); } =head2 txmap Title : txmap Usage : txmap(); Function: Returns or stores a reference to an array containing txmap lines Returns : An array reference Args : None or an array reference =cut sub txmap { my $self = shift; return $self->_annotation_value_ary('txmap',@_); } =head2 protsim Title : protsim Usage : protsim(); Function: Returns or stores a reference to an array containing protsim lines This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference =cut sub protsim { my $self = shift; return $self->_annotation_value_ary('protsim',@_); } =head2 sequences Title : sequences Usage : sequences(); Function: Returns or stores a reference to an array containing sequence data. This is mostly reserved for ClusterIO parsers. You should use get_members() for get and add_member()/remove_members() for set. Returns : An array reference, or undef Args : None or an array reference or undef =cut sub sequences { my $self = shift; return $self->{'members'} = shift if @_; return $self->{'members'}; } =head2 species Title : species Usage : $obj->species($newval) Function: Get/set the species object for this Unigene cluster. Example : Returns : value of species (a L object) Args : on set, new value (a L object or the binomial name, or undef, optional) =cut sub species{ my $self = shift; if(@_) { my $species = shift; if($species && (! ref($species))) { my @class = reverse(split(' ',$species)); $species = Bio::Species->new(-classification => \@class); } return $self->{'species'} = $species; } return $self->{'species'}; } =head1 L methods =cut =head2 display_id Title : display_id Usage : Function: Get/set the display name or identifier for the cluster This is aliased to unigene_id(). Returns : a string Args : optional, on set the display ID ( a string) =cut sub display_id{ return shift->unigene_id(@_); } =head2 description Title : description Usage : Bio::ClusterI->description("POLYUBIQUITIN") Function: get/set for the consensus description of the cluster This is aliased to title(). Returns : the description string Args : Optional the description string =cut sub description{ return shift->title(@_); } =head2 size Title : size Usage : Bio::ClusterI->size(); Function: get for the size of the family, calculated from the number of members This is aliased to scount(). Returns : the size of the cluster Args : =cut sub size { my $self = shift; # hard-wiring the size is allowed if there are no sequences return $self->scount(@_) unless defined($self->sequences()); # but we can't change the number of members through this method my $n = scalar(@{$self->sequences()}); if(@_ && ($n != $_[0])) { $self->throw("Cannot change cluster size using size() from $n to ". $_[0]); } return $n; } =head2 cluster_score Title : cluster_score Usage : $cluster ->cluster_score(100); Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster. For UniGene clusters, there really is no cluster score that would come with the data. However, we provide an implementation here so that you can score UniGene clusters if you want to. Returns : a number Args : optionally, on set a number =cut sub cluster_score{ my $self = shift; return $self->{'cluster_score'} = shift if @_; return $self->{'cluster_score'}; } =head2 get_members Title : get_members Usage : Bio::ClusterI->get_members(($seq1, $seq2)); Function: retrieve the members of the family by some criteria Will return all members if no criteria are provided. At this time this implementation does not support specifying criteria and will always return all members. Returns : the array of members Args : =cut sub get_members { my $self = shift; my $mems = $self->sequences() || []; # already objects? if(@$mems && (ref($mems->[0]) eq "HASH")) { # nope, we need to build the object list from scratch my @memlist = (); while(my $seq = $self->next_seq()) { push(@memlist, $seq); } # we cache this array of objects as the new member list $mems = \@memlist; $self->sequences($mems); } # done return @$mems; } =head1 Annotatable view at the object properties =cut =head2 annotation Title : annotation Usage : $obj->annotation($newval) Function: Get/set the L object for this UniGene cluster. Many attributes of this class are actually stored within the annotation collection object as L compliant objects, so you can conveniently access them through the same interface as you would e.g. access L annotation properties. If you call this method in set mode and replace the annotation collection with another one you should know exactly what you are doing. Example : Returns : a L compliant object Args : on set, new value (a L compliant object or undef, optional) =cut sub annotation{ my $self = shift; if(@_) { return $self->{'annotation'} = shift; } elsif(! exists($self->{'annotation'})) { $self->{'annotation'} = Bio::Annotation::Collection->new(); } return $self->{'annotation'}; } =head1 Implementation specific methods These are mostly for adding/removing to array properties, and for methods with special functionality. =cut =head2 add_member Title : add_member Usage : Function: Adds a member object to the list of members. Example : Returns : TRUE if the new member was successfully added, and FALSE otherwise. Args : The member to add. =cut sub add_member{ my ($self,@mems) = @_; my $memlist = $self->{'members'} || []; # this is an object interface; is the member list already objects? if(@$memlist && (ref($memlist->[0]) eq "HASH")) { # nope, convert to objects $memlist = [$self->get_members()]; } # add new member(s) push(@$memlist, @mems); # store if we created this array ref ourselves $self->sequences($memlist); # done return 1; } =head2 remove_members Title : remove_members Usage : Function: Remove the list of members for this cluster such that the member list is undefined afterwards (as opposed to zero members). Example : Returns : the previous list of members Args : none =cut sub remove_members{ my $self = shift; my @mems = $self->get_members(); $self->sequences(undef); return @mems; } =head2 next_locuslink Title : next_locuslink Usage : next_locuslink(); Function: Returns the next locuslink from an array referred to using $obj->{'locuslink'} If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $locuslink = $in->next_locuslink() ) { print "$locuslink\n"; } Returns : String Args : None =cut sub next_locuslink { my ($obj) = @_; return $obj->_next_element("ll","locuslink"); } =head2 next_express Title : next_express Usage : next_express(); Function: Returns the next tissue from an array referred to using $obj->{'express'} If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $express = $in->next_express() ) { print "$express\n"; } Returns : String Args : None =cut sub next_express { my ($obj) = @_; return $obj->_next_element("express","express"); } =head2 next_chromosome Title : next_chromosome Usage : next_chromosome(); Function: Returns the next chromosome line from an array referred to using $obj->{'chromosome'} If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $chromosome = $in->next_chromosome() ) { print "$chromosome\n"; } Returns : String Args : None =cut sub next_chromosome { my ($obj) = @_; return $obj->_next_element("chr","chromosome"); } =head2 next_protsim Title : next_protsim Usage : next_protsim(); Function: Returns the next protsim line from an array referred to using $obj->{'protsim'} If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $protsim = $in->next_protsim() ) { print "$protsim\n"; } Returns : String Args : None =cut sub next_protsim { my ($obj) = @_; return $obj->_next_element("protsim","protsim"); } =head2 next_sts Title : next_sts Usage : next_sts(); Function: Returns the next sts line from an array referred to using $obj->{'sts'} If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $sts = $in->next_sts() ) { print "$sts\n"; } Returns : String Args : None =cut sub next_sts { my ($obj) = @_; return $obj->_next_element("sts","sts"); } =head2 next_txmap Title : next_txmap Usage : next_txmap(); Function: Returns the next txmap line from an array referred to using $obj->{'txmap'} If you call this iterator again after it returned undef, it will re-cycle through the list of elements. Changes in the underlying array property while you loop over this iterator will not be reflected until you exhaust the iterator. Example : while ( my $tsmap = $in->next_txmap() ) { print "$txmap\n"; } Returns : String Args : None =cut sub next_txmap { my ($obj) = @_; return $obj->_next_element("txmap","txmap"); } ############################### # private method # # args: prefix name for the queue # name of the method from which to re-fill # returns: the next element from that queue, or undef if the queue is empty ############################### sub _next_element{ my ($self,$queuename,$meth) = @_; $queuename = "_".$queuename."_queue"; if(! exists($self->{$queuename})) { # re-initialize from array of sequence data $self->{$queuename} = [@{$self->$meth() }]; } my $queue = $self->{$queuename}; # is queue exhausted (equivalent to end of stream)? if(! @$queue) { # yes, remove queue and signal to the caller delete $self->{$queuename}; return; } return shift(@$queue); } =head1 L methods =cut =head2 object_id Title : object_id Usage : $string = $obj->object_id() Function: a string which represents the stable primary identifier in this namespace of this object. For DNA sequences this is its accession_number, similarly for protein sequences This is aliased to unigene_id(). Returns : A scalar =cut sub object_id { return shift->unigene_id(@_); } =head2 version Title : version Usage : $version = $obj->version() Function: a number which differentiates between versions of the same object. Higher numbers are considered to be later and more relevant, but a single object described the same identifier should represent the same concept Unigene clusters usually won't have a version, so this will be mostly undefined. Returns : A number Args : on set, new value (a scalar or undef, optional) =cut sub version { my $self = shift; return $self->{'version'} = shift if @_; return $self->{'version'}; } =head2 authority Title : authority Usage : $authority = $obj->authority() Function: a string which represents the organisation which granted the namespace, written as the DNS name for organisation (eg, wormbase.org) Returns : A scalar Args : on set, new value (a scalar or undef, optional) =cut sub authority { my $self = shift; return $self->{'authority'} = shift if @_; return $self->{'authority'}; } =head2 namespace Title : namespace Usage : $string = $obj->namespace() Function: A string representing the name space this identifier is valid in, often the database name or the name describing the collection Returns : A scalar Args : on set, new value (a scalar or undef, optional) =cut sub namespace { my $self = shift; return $self->{'namespace'} = shift if @_; return $self->{'namespace'}; } =head1 L methods =cut =head2 display_name Title : display_name Usage : $string = $obj->display_name() Function: A string which is what should be displayed to the user the string should have no spaces (ideally, though a cautious user of this interface would not assume this) and should be less than thirty characters (though again, double checking this is a good idea) This is aliased to unigene_id(). Returns : A scalar Status : Virtual =cut sub display_name { return shift->unigene_id(@_); } =head2 description() Title : description Usage : $string = $obj->description() Function: A text string suitable for displaying to the user a description. This string is likely to have spaces, but should not have any newlines or formatting - just plain text. The string should not be greater than 255 characters and clients can feel justified at truncating strings at 255 characters for the purposes of display This is already demanded by Bio::ClusterI and hence is present anyway. Returns : A scalar =cut =head1 L methods =cut =head2 next_seq Title : next_seq Usage : next_seq(); Function: Returns the next seq as a Seq object as defined by $seq->sequence_factory(), at present an empty Bio::Seq::RichSeq object with just the accession_number() and pid() set This iterator will not exhaust the array of member sequences. If you call next_seq() again after it returned undef, it will re-cycle through the list of member sequences. Example : while ( my $sequence = $in->next_seq() ) { print $sequence->accession_number() . "\n"; } Returns : Bio::PrimarySeqI object Args : None =cut sub next_seq { my ($obj) = @_; if(! exists($obj->{'_seq_queue'})) { # re-initialize from array of sequence data $obj->{'_seq_queue'} = [@{$obj->sequences()}]; } my $queue = $obj->{'_seq_queue'}; # is queue exhausted (equivalent to end of stream)? if(! @$queue) { # yes, remove queue and signal to the caller delete $obj->{'_seq_queue'}; return; } # no, still data in the queue: get the next one from the queue my $seq_h = shift(@$queue); # if this is not a simple hash ref, it's an object already, and we'll # return just that return $seq_h if(ref($seq_h) ne 'HASH'); # nope, we need to assemble this object from scratch # # assemble the annotation collection my $ac = Bio::Annotation::Collection->new(); foreach my $k (keys %$seq_h) { next if $k =~ /acc|pid|nid|version/; my $ann = Bio::Annotation::SimpleValue->new(-tagname => $k, -value => $seq_h->{$k}); $ac->add_Annotation($ann); } # assemble the initialization parameters and create object my $seqobj = $obj->sequence_factory->create( -accession_number => $seq_h->{acc}, -pid => $seq_h->{pid}, # why does NCBI prepend a 'g' to its own identifiers?? -primary_id => $seq_h->{nid} && $seq_h->{nid} =~ /^g\d+$/ ? substr($seq_h->{nid},1) : $seq_h->{nid}, -display_id => $seq_h->{acc}, -seq_version => $seq_h->{version}, -alphabet => $obj->{'_alphabet'}, -namespace => $seq_h->{acc} =~ /^NM_/ ? 'RefSeq' : 'GenBank', -authority => $obj->authority(), # default is NCBI -species => $obj->species(), -annotation => $ac ); return $seqobj; } =head2 sequence_factory Title : sequence_factory Usage : $seqio->sequence_factory($seqfactory) Function: Get/Set the Bio::Factory::SequenceFactoryI Returns : Bio::Factory::SequenceFactoryI Args : [optional] Bio::Factory::SequenceFactoryI =cut sub sequence_factory { my ($self,$obj) = @_; if( defined $obj ) { if( ! ref($obj) || ! $obj->isa('Bio::Factory::SequenceFactoryI') ) { $self->throw("Must provide a valid Bio::Factory::SequenceFactoryI object to ".ref($self)." sequence_factory()"); } $self->{'_seqfactory'} = $obj; } $self->{'_seqfactory'}; } =head1 Private methods =cut =head2 _annotation_value Title : _annotation_value Usage : Function: Private method. Example : Returns : the value (a string) Args : annotation key (a string) on set, annotation value (a string) =cut sub _annotation_value{ my $self = shift; my $key = shift; my ($ann, $val); if(@_) { $val = shift; if(! defined($val)) { ($ann) = $self->annotation->remove_Annotations($key); return $ann ? $ann->value() : undef; } } ($ann) = $self->annotation->get_Annotations($key); if(defined $ann && (! $val)) { # get mode and exists $val = $ann->value(); } elsif($val) { # set mode if(!defined $ann) { $ann = Bio::Annotation::SimpleValue->new(-tagname => $key); $self->annotation->add_Annotation($ann); } $ann->value($val); } return $val; } =head2 _annotation_value_ary Title : _annotation_value_ary Usage : Function: Private method. Example : Returns : reference to the array of values Args : annotation key (a string) on set, reference to an array holding the values =cut sub _annotation_value_ary{ my ($self,$key,$arr) = @_; my $ac = $self->annotation; if($arr) { # purge first $ac->remove_Annotations($key); # then add as many values as are present foreach my $val (@$arr) { my $ann = Bio::Annotation::SimpleValue->new(-value => $val, -tagname => $key ); $ac->add_Annotation($ann); } } else { my @vals = map { $_->value(); } $ac->get_Annotations($key); $arr = [@vals]; } return $arr; } =head2 _annotation_dblink Title : _annotation_dblink Usage : Function: Private method. Example : Returns : array of accessions for the given database (namespace) Args : annotation key (a string) dbname (a string) (optional on get, mandatory on set) on set, accession or ID (a string), and version =cut sub _annotation_dblink{ my ($self,$key,$dbname,$acc,$version) = @_; if($acc) { # set mode -- this is adding here my $ann = Bio::Annotation::DBLink->new(-tagname => $key, -primary_id => $acc, -database => $dbname, -version => $version); $self->annotation->add_Annotation($ann); return 1; } else { # get mode my @anns = $self->annotation->get_Annotations($key); # filter out those that don't match the requested database if($dbname) { @anns = grep { $_->database() eq $dbname; } @anns; } return map { $_->primary_id(); } @anns; } } =head2 _remove_dblink Title : _remove_dblink Usage : Function: Private method. Example : Returns : array of accessions for the given database (namespace) Args : annotation key (a string) dbname (a string) (optional) =cut sub _remove_dblink{ my ($self,$key,$dbname) = @_; my $ac = $self->annotation(); my @anns = (); if($dbname) { foreach my $ann ($ac->remove_Annotations($key)) { if($ann->database() eq $dbname) { push(@anns, $ann); } else { $ac->add_Annotation($ann); } } } else { @anns = $ac->remove_Annotations($key); } return map { $_->primary_id(); } @anns; } ##################################################################### # aliases for naming consistency or other reasons # ##################################################################### *sequence = \&sequences; 1; BioPerl-1.007002/Bio/Cluster/UniGeneI.pm000444000766000024 2216613155576320 17675 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Cluster::UniGeneI.pm # # Please direct questions and support issues to # # Cared for by Andrew Macgregor # # Copyright Andrew Macgregor, Jo-Ann Stanton, David Green # Molecular Embryology Group, Anatomy & Structural Biology, University of Otago # http://anatomy.otago.ac.nz/meg # # You may distribute this module under the same terms as perl itself # # _history # April 31, 2002 - Initial implementation by Andrew Macgregor # POD documentation - main docs before the code =head1 NAME Bio::Cluster::UniGeneI - abstract interface of UniGene object =head1 SYNOPSIS # =head1 DESCRIPTION This is the general interface for a UniGene cluster representation in Bioperl. You cannot use this module directly, use an implementation instead. You can create UniGene cluster objects yourself by instantiating L. If you read UniGene clusters from a ClusterIO parser, you will get objects implementing this interface, most likely instances of said UniGene class. L inherits from L, so you can use it wherever a cluster object is expected. =head1 FEEDBACK # =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Andrew Macgregor Email andrew at cbbc.murdoch.edu.au =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_". =cut # Let the code begin... package Bio::Cluster::UniGeneI; use strict; use base qw(Bio::ClusterI); =head2 unigene_id Title : unigene_id Usage : unigene_id(); Function: Returns the unigene_id associated with the object. Example : $id = $unigene->unigene_id or $unigene->unigene_id($id) Returns : A string Args : None or an id =cut sub unigene_id { my ($self) = @_; $self->throw_not_implemented; } =head2 title Title : title Usage : title(); Function: Returns the title associated with the object. Example : $title = $unigene->title or $unigene->title($title) Returns : A string Args : None or a title =cut sub title { my ($self) = @_; $self->throw_not_implemented; } =head2 gene Title : gene Usage : gene(); Function: Returns the gene associated with the object. Example : $gene = $unigene->gene or $unigene->gene($gene) Returns : A string Args : None or a gene =cut sub gene { my ($self) = @_; $self->throw_not_implemented; } =head2 cytoband Title : cytoband Usage : cytoband(); Function: Returns the cytoband associated with the object. Example : $cytoband = $unigene->cytoband or $unigene->cytoband($cytoband) Returns : A string Args : None or a cytoband =cut sub cytoband { my ($self) = @_; $self->throw_not_implemented; } =head2 mgi Title : mgi Usage : mgi(); Function: Returns the mgi associated with the object. Example : $mgi = $unigene->mgi or $unigene->mgi($mgi) Returns : A string Args : None or a mgi =cut sub mgi { my ($self) = @_; $self->throw_not_implemented; } =head2 locuslink Title : locuslink Usage : locuslink(); Function: Returns or stores a reference to an array containing locuslink data. This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference =cut sub locuslink { my ($self) = @_; $self->throw_not_implemented; } =head2 homol Title : homol Usage : homol(); Function: Returns the homol entry associated with the object. Example : $homol = $unigene->homol or $unigene->homol($homol) Returns : A string Args : None or a homol entry =cut sub homol { my ($self) = @_; $self->throw_not_implemented; } =head2 restr_expr Title : restr_expr Usage : restr_expr(); Function: Returns the restr_expr entry associated with the object. Example : $restr_expr = $unigene->restr_expr or $unigene->restr_expr($restr_expr) Returns : A string Args : None or a restr_expr entry =cut sub restr_expr { my ($self) = @_; $self->throw_not_implemented; } =head2 gnm_terminus Title : gnm_terminus Usage : gnm_terminus(); Function: Returns the gnm_terminus associated with the object. Example : $gnm_terminus = $unigene->gnm_terminus or $unigene->gnm_terminus($gnm_terminus) Returns : A string Args : None or a gnm_terminus =cut sub gnm_terminus { my ($self) = @_; $self->throw_not_implemented; } =head2 scount Title : scount Usage : scount(); Function: Returns the scount associated with the object. Example : $scount = $unigene->scount or $unigene->scount($scount) Returns : A string Args : None or a scount =cut sub scount { my ($self) = @_; $self->throw_not_implemented; } =head2 express Title : express Usage : express(); Function: Returns or stores a reference to an array containing tissue expression data. This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference =cut sub express { my ($self) = @_; $self->throw_not_implemented; } =head2 chromosome Title : chromosome Usage : chromosome(); Function: Returns or stores a reference to an array containing chromosome lines This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference =cut sub chromosome { my ($self) = @_; $self->throw_not_implemented; } =head2 sts Title : sts Usage : sts(); Function: Returns or stores a reference to an array containing sts lines This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference =cut sub sts { my ($self) = @_; $self->throw_not_implemented; } =head2 txmap Title : txmap Usage : txmap(); Function: Returns or stores a reference to an array containing txmap lines Returns : An array reference Args : None or an array reference =cut sub txmap { my ($self) = @_; $self->throw_not_implemented; } =head2 protsim Title : protsim Usage : protsim(); Function: Returns or stores a reference to an array containing protsim lines This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference =cut sub protsim { my ($self) = @_; $self->throw_not_implemented; } =head2 sequence Title : sequence Usage : sequence(); Function: Returns or stores a reference to an array containing sequence data This should really only be used by ClusterIO, not directly Returns : An array reference Args : None or an array reference =cut sub sequence { my ($self) = @_; $self->throw_not_implemented; } =head2 species Title : species Usage : $obj->species($newval) Function: Get the species object for this Unigene cluster. Example : Returns : value of species (a L object) Args : =cut sub species{ shift->throw_not_implemented(); } =head1 Methods inherited from L =cut =head2 display_id Title : display_id Usage : Function: Get/set the display name or identifier for the cluster Returns : a string Args : optional, on set the display ID ( a string) =cut =head2 description Title : description Usage : Bio::ClusterI->description("POLYUBIQUITIN") Function: get/set for the consensus description of the cluster Returns : the description string Args : Optional the description string =cut =head2 size Title : size Usage : Bio::ClusterI->size(); Function: get/set for the size of the family, calculated from the number of members Returns : the size of the family Args : =cut =head2 cluster_score Title : cluster_score Usage : $cluster ->cluster_score(100); Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster. Returns : a number =cut =head2 get_members Title : get_members Usage : Bio::ClusterI->get_members(($seq1, $seq2)); Function: retrieve the members of the family by some criteria, for example : $cluster->get_members(-species => 'homo sapiens'); Will return all members if no criteria are provided. Returns : the array of members Args : =cut 1; BioPerl-1.007002/Bio/ClusterIO000755000766000024 013155576320 15740 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/ClusterIO/dbsnp.pm000444000766000024 2450613155576320 17570 0ustar00cjfieldsstaff000000000000# BioPerl module for Bio::ClusterIO::dbsnp # # Copyright Allen Day , Stan Nelson # Human Genetics, UCLA Medical School, University of California, Los Angeles # POD documentation - main docs before the code =head1 NAME Bio::ClusterIO::dbsnp - dbSNP input stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::ClusterIO class. =head1 DESCRIPTION Parse dbSNP XML files, one refSNP entry at a time. Note this handles dbSNPp output generated by NBCI's eutils and does NOT parse output derived from SNP's XML format (found at ftp://ftp.ncbi.nih.gov/snp/). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Allen Day Eallenday@ucla.eduE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::ClusterIO::dbsnp; use strict; use Bio::Root::Root; use Bio::Variation::SNP; use XML::SAX; use Data::Dumper; use IO::File; use Time::HiRes qw(tv_interval gettimeofday); use base qw(Bio::ClusterIO); our $DEBUG = 0; our %MAPPING = ( #the ones commented out i haven't written methods for yet... -Allen 'Rs_rsId' => 'id', # 'Rs_taxId' => 'tax_id', # 'Rs_organism' => 'organism', 'Rs_snpType' => {'type' => 'value'}, 'Rs_sequence_observed' => 'observed', 'Rs_sequence_seq5' => 'seq_5', 'Rs_sequence_seq3' => 'seq_3', # 'Rs_sequence_exemplarSs' => 'exemplar_subsnp', 'Rs_create_build' => 'ncbi_build', #?? 'Rs_update_build' => 'ncbi_build', # 'NSE-rs_ncbi-num-chr-hits' => 'ncbi_chr_hits', # 'NSE-rs_ncbi-num-ctg-hits' => 'ncbi_ctg_hits', # 'NSE-rs_ncbi-num-seq-loc' => 'ncbi_seq_loc', # 'NSE-rs_ncbi-mapweight' => 'ncbi_mapweight', # 'NSE-rs_ucsc-build-id' => 'ucsc_build', # 'NSE-rs_ucsc-num-chr-hits' => 'ucsc_chr_hits', # 'NSE-rs_ucsc-num-seq-loc' => 'ucsc_ctg_hits', # 'NSE-rs_ucsc-mapweight' => 'ucsc_mapweight', 'Rs_het_value' => 'heterozygous', 'Rs_het-stdError' => 'heterozygous_SE', 'Rs_validation' => {'validated' => 'value'}, #?? # 'NSE-rs_genotype' => {'genotype' => 'value'}, 'Ss_handle' => 'handle', 'Ss_batchId' => 'batch_id', 'Ss_locSnpId' => 'id', # 'Ss_locSnpId' => 'loc_id', # 'Ss_orient' => {'orient' => 'value'}, # 'Ss_buildId' => 'build', 'Ss_methodClass' => {'method' => 'value'}, # 'NSE-ss_accession_E' => 'accession', # 'NSE-ss_comment_E' => 'comment', # 'NSE-ss_genename' => 'gene_name', # 'NSE-ss_assay-5_E' => 'seq_5', # 'NSE-ss_assay-3_E' => 'seq_3', # 'NSE-ss_observed' => 'observed', # 'NSE-ss-popinfo_type' => 'pop_type', # 'NSE-ss-popinfo_batch-id' => 'pop_batch_id', # 'NSE-ss-popinfo_pop-name' => 'pop_name', # 'NSE-ss-popinfo_samplesize' => 'pop_samplesize', # 'NSE-ss_popinfo_est-het' => 'pop_est_heterozygous', # 'NSE-ss_popinfo_est-het-se-sq' => 'pop_est_heterozygous_se_sq', # 'NSE-ss-alleleinfo_type' => 'allele_type', # 'NSE-ss-alleleinfo_batch-id' => 'allele_batch_id', # 'NSE-ss-alleleinfo_pop-id' => 'allele_pop_id', # 'NSE-ss-alleleinfo_snp-allele' => 'allele_snp', # 'NSE-ss-alleleinfo_other-allele' => 'allele_other', # 'NSE-ss-alleleinfo_freq' => 'allele_freq', # 'NSE-ss-alleleinfo_count' => 'allele_count', # 'NSE-rsContigHit_contig-id' => 'contig_hit', # 'NSE-rsContigHit_accession' => 'accession_hit', # 'NSE-rsContigHit_version' => 'version', # 'NSE-rsContigHit_chromosome' => 'chromosome_hit', # 'NSE-rsMaploc_asn-from' => 'asn_from', # 'NSE-rsMaploc_asn-to' => 'asn_to', # 'NSE-rsMaploc_loc-type' => {'loc_type' => 'value'}, # 'NSE-rsMaploc_hit-quality' => {'hit_quality' => 'value'}, # 'NSE-rsMaploc_orient' => {'orient' => 'value'}, # 'NSE-rsMaploc_physmap-str' => 'phys_from', # 'NSE-rsMaploc_physmap-int' => 'phys_to', 'FxnSet_geneId' => 'locus_id', # does the code realise that there can be multiple of these 'FxnSet_symbol' => 'symbol', 'FxnSet_mrnaAcc' => 'mrna', 'FxnSet_protAcc' => 'protein', 'FxnSet_fxnClass' => {'functional_class' => 'value'}, #... #... #there are lots more, but i don't need them at the moment... -Allen ); sub _initialize{ my ($self,@args) = @_; $self->SUPER::_initialize(@args); my ($usetempfile) = $self->_rearrange([qw(TEMPFILE)],@args); defined $usetempfile && $self->use_tempfile($usetempfile); # start up the parser factory my $parserfactory = XML::SAX::ParserFactory->parser( Handler => $self); $self->{'_xmlparser'} = $parserfactory; $DEBUG = 1 if( ! defined $DEBUG && $self->verbose > 0); } =head2 next_cluster Title : next_cluster Usage : $dbsnp = $stream->next_cluster() Function: returns the next refSNP in the stream Returns : Bio::Variation::SNP object representing composite refSNP and its component subSNP(s). Args : NONE =cut ### #Adapted from Jason's blastxml.pm ### # you shouldn't have to preparse this; the XML is well-formed and refers # accurately to a remote DTD/schema sub next_cluster { my $self = shift; my $data = ''; my($tfh); if( $self->use_tempfile ) { $tfh = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!"); $tfh->autoflush(1); } my $start = 1; while( defined( $_ = $self->_readline ) ){ #skip to beginning of refSNP entry if($_ !~ m{]*>} && $start){ next; } elsif($_ =~ m{]*>} && $start){ $start = 0; } #slurp up the data if( defined $tfh ) { print $tfh $_; } else { $data .= $_; } #and stop at the end of the refSNP entry last if $_ =~ m{}; } #if we didn't find a start tag return if $start; my %parser_args; if( defined $tfh ) { seek($tfh,0,0); %parser_args = ('Source' => { 'ByteStream' => $tfh }, 'Handler' => $self); } else { %parser_args = ('Source' => { 'String' => $data }, 'Handler' => $self); } my $starttime; my $result; if( $DEBUG ) { $starttime = [ Time::HiRes::gettimeofday() ]; } eval { $result = $self->{'_xmlparser'}->parse(%parser_args); }; if( $@ ) { $self->warn("error in parsing a report:\n $@"); $result = undef; } if( $DEBUG ) { $self->debug( sprintf("parsing took %f seconds\n", Time::HiRes::tv_interval($starttime))); } return $self->refsnp; } =head2 SAX methods =cut =head2 start_document Title : start_document Usage : $parser->start_document; Function: SAX method to indicate starting to parse a new document. Creates a Bio::Variation::SNP Returns : none Args : none =cut sub start_document{ my ($self) = @_; $self->{refsnp} = Bio::Variation::SNP->new; } sub refsnp { return shift->{refsnp}; } =head2 end_document Title : end_document Usage : $parser->end_document; Function: SAX method to indicate finishing parsing a new document Returns : none Args : none =cut sub end_document{ my ($self,@args) = @_; } =head2 start_element Title : start_element Usage : $parser->start_element($data) Function: SAX method to indicate starting a new element Returns : none Args : hash ref for data =cut sub start_element{ my ($self,$data) = @_; my $nm = $data->{'Name'}; my $at = $data->{'Attributes'}->{'{}value'}; #$self->debug(Dumper($at)) if $nm = ; if($nm eq 'Ss'){ $self->refsnp->add_subsnp; return; } if(my $type = $MAPPING{$nm}){ if(ref $type eq 'HASH'){ #okay, this is nasty. what can you do? $self->{will_handle} = (keys %$type)[0]; $self->{last_data} = $at->{Value}; } else { $self->{will_handle} = $type; $self->{last_data} = undef; } } else { undef $self->{will_handle}; } } =head2 end_element Title : end_element Usage : $parser->end_element($data) Function: Signals finishing an element Returns : none Args : hash ref for data =cut sub end_element { my ($self,$data) = @_; my $nm = $data->{'Name'}; my $at = $data->{'Attributes'}; my $method = $self->{will_handle}; if($method){ if($nm =~ /^Rs/ or $nm =~ /^NSE-SeqLoc/ or $nm =~ /^FxnSet/){ $self->refsnp->$method($self->{last_data}); } elsif ($nm =~ /^Ss/){ $self->refsnp->subsnp->$method($self->{last_data}); } } } =head2 characters Title : characters Usage : $parser->characters($data) Function: Signals new characters to be processed Returns : characters read Args : hash ref with the key 'Data' =cut sub characters{ my ($self,$data) = @_; $self->{last_data} = $data->{Data} if $data->{Data} =~ /\S/; #whitespace is meaningless -ad } =head2 use_tempfile Title : use_tempfile Usage : $obj->use_tempfile($newval) Function: Get/Set boolean flag on whether or not use a tempfile Example : Returns : value of use_tempfile Args : newvalue (optional) =cut sub use_tempfile{ my ($self,$value) = @_; if( defined $value) { $self->{'_use_tempfile'} = $value; } return $self->{'_use_tempfile'}; } 1; BioPerl-1.007002/Bio/ClusterIO/unigene.pm000444000766000024 1775013155576320 20117 0ustar00cjfieldsstaff000000000000# BioPerl module for Bio::ClusterIO::unigene # # Please direct questions and support issues to # # Cared for by Andrew Macgregor # # Copyright Andrew Macgregor, Jo-Ann Stanton, David Green # Molecular Embryology Group, Anatomy & Structural Biology, University of Otago # http://meg.otago.ac.nz # # You may distribute this module under the same terms as perl itself # # _history # April 17, 2002 - Initial implementation by Andrew Macgregor # POD documentation - main docs before the code =head1 NAME Bio::ClusterIO::unigene - UniGene input stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::ClusterIO class. =head1 DESCRIPTION This object reads from Unigene *.data files downloaded from ftp://ftp.ncbi.nih.gov/repository/UniGene/. It does not download and decompress the file, you have to do that yourself. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Andrew Macgregor Email: andrew at cbbc.murdoch.edu.au =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::ClusterIO::unigene; use strict; use Bio::Cluster::UniGene; use Bio::Cluster::ClusterFactory; use base qw(Bio::ClusterIO); my %line_is = ( ID => q/ID\s+(\w{2,3}\.\d+)/, TITLE => q/TITLE\s+(\S.*)/, GENE => q/GENE\s+(\S.*)/, CYTOBAND => q/CYTOBAND\s+(\S.*)/, MGI => q/MGI\s+(\S.*)/, LOCUSLINK => q/LOCUSLINK\s+(\S.*)/, HOMOL => q/HOMOL\s+(\S.*)/, EXPRESS => q/EXPRESS\s+(\S.*)/, RESTR_EXPR => q/RESTR_EXPR\s+(\S.*)/, GNM_TERMINUS => q/GNM_TERMINUS\s+(\S.*)/, CHROMOSOME => q/CHROMOSOME\s+(\S.*)/, STS => q/STS\s+(\S.*)/, TXMAP => q/TXMAP\s+(\S.*)/, PROTSIM => q/PROTSIM\s+(\S.*)/, SCOUNT => q/SCOUNT\s+(\S.*)/, SEQUENCE => q/SEQUENCE\s+(\S.*)/, ACC => q/ACC=(\w+)(\.\d+)?/, NID => q/NID=\s*(\S.*)/, PID => q/PID=\s*(\S.*)/, CLONE => q/CLONE=\s*(\S.*)/, END => q/END=\s*(\S.*)/, LID => q/LID=\s*(\S.*)/, MGC => q/MGC=\s*(\S.*)/, SEQTYPE => q/SEQTYPE=\s*(\S.*)/, TRACE => q/TRACE=\s*(\S.*)/, PERIPHERAL => q/PERIPHERAL=\s*(\S.*)/, DELIMITER => q{^//}, ); # we set the right factory here sub _initialize { my($self, @args) = @_; $self->SUPER::_initialize(@args); if(! $self->cluster_factory()) { $self->cluster_factory(Bio::Cluster::ClusterFactory->new( -type => 'Bio::Cluster::UniGene')); } } =head2 next_cluster Title : next_cluster Usage : $unigene = $stream->next_cluster() Function: returns the next unigene in the stream Returns : Bio::Cluster::UniGene object Args : NONE =cut sub next_cluster { my( $self) = @_; local $/ = "\n//"; return unless my $entry = $self->_readline; # set up the variables we'll need my (%unigene,@express,@locuslink,@chromosome, @sts,@txmap,@protsim,@sequence); my $UGobj; # set up the regexes # add whitespace parsing and precompile regexes #foreach (values %line_is) { # $_ =~ s/\s+/\\s+/g; # print STDERR "Regex is $_\n"; # #$_ = qr/$_/x; #} #$line_is{'TITLE'} = qq/TITLE\\s+(\\S.+)/; # run each line in an entry against the regexes foreach my $line (split /\n/, $entry) { #print STDERR "Wanting to match $line\n"; if ($line =~ /$line_is{ID}/gcx) { $unigene{ID} = $1; } elsif ($line =~ /$line_is{TITLE}/gcx ) { #print STDERR "MATCHED with [$1]\n"; $unigene{TITLE} = $1; } elsif ($line =~ /$line_is{GENE}/gcx) { $unigene{GENE} = $1; } elsif ($line =~ /$line_is{CYTOBAND}/gcx) { $unigene{CYTOBAND} = $1; } elsif ($line =~ /$line_is{MGI}/gcx) { $unigene{MGI} = $1; } elsif ($line =~ /$line_is{LOCUSLINK}/gcx) { @locuslink = split /;/, $1; } elsif ($line =~ /$line_is{HOMOL}/gcx) { $unigene{HOMOL} = $1; } elsif ($line =~ /$line_is{EXPRESS}/gcx) { my $express = $1; # remove initial semicolon if present $express =~ s/^;//; @express = split /\s*;/, $express; } elsif ($line =~ /$line_is{RESTR_EXPR}/gcx) { $unigene{RESTR_EXPR} = $1; } elsif ($line =~ /$line_is{GNM_TERMINUS}/gcx) { $unigene{GNM_TERMINUS} = $1; } elsif ($line =~ /$line_is{CHROMOSOME}/gcx) { push @chromosome, $1; } elsif ($line =~ /$line_is{TXMAP}/gcx) { push @txmap, $1; } elsif ($line =~ /$line_is{STS}/gcx) { push @sts, $1; } elsif ($line =~ /$line_is{PROTSIM}/gcx) { push @protsim, $1; } elsif ($line =~ /$line_is{SCOUNT}/gcx) { $unigene{SCOUNT} = $1; } elsif ($line =~ /$line_is{SEQUENCE}/gcx) { # parse into each sequence line my $seq = {}; # add unigene id to each seq #$seq->{unigene_id} = $unigene{ID}; my @items = split(/;/, $1); foreach (@items) { if (/$line_is{ACC}/gcx) { $seq->{acc} = $1; # remove leading dot if version pattern matched $seq->{version} = substr($2,1) if defined $2; } elsif (/$line_is{NID}/gcx) { $seq->{nid} = $1; } elsif (/$line_is{PID}/gcx) { $seq->{pid} = $1; } elsif (/$line_is{CLONE}/gcx) { $seq->{clone} = $1; } elsif (/$line_is{END}/gcx) { $seq->{end} = $1; } elsif (/$line_is{LID}/gcx) { $seq->{lid} = $1; } elsif (/$line_is{MGC}/gcx) { $seq->{mgc} = $1; } elsif (/$line_is{SEQTYPE}/gcx) { $seq->{seqtype} = $1; } elsif (/$line_is{TRACE}/gcx) { $seq->{trace} = $1; } elsif (/$line_is{PERIPHERAL}/gcx) { $seq->{peripheral} = $1; } } push @sequence, $seq; } elsif ($line =~ /$line_is{DELIMITER}/gcx) { # at the end of the record, add data to the object $UGobj = $self->cluster_factory->create_object( -display_id => $unigene{ID}, -description => $unigene{TITLE}, -size => $unigene{SCOUNT}, -members => \@sequence); $UGobj->gene($unigene{GENE}) if defined ($unigene{GENE}); $UGobj->cytoband($unigene{CYTOBAND}) if defined($unigene{CYTOBAND}); $UGobj->mgi($unigene{MGI}) if defined ($unigene{MGI}); $UGobj->locuslink(\@locuslink); $UGobj->homol($unigene{HOMOL}) if defined ($unigene{HOMOL}); $UGobj->express(\@express); $UGobj->restr_expr($unigene{RESTR_EXPR}) if defined ($unigene{RESTR_EXPR}); $UGobj->gnm_terminus($unigene{GNM_TERMINUS}) if defined ($unigene{GNM_TERMINUS}); $UGobj->chromosome(\@chromosome); $UGobj->sts(\@sts); $UGobj->txmap(\@txmap); $UGobj->protsim(\@protsim); } } return $UGobj; } 1; BioPerl-1.007002/Bio/CodonUsage000755000766000024 013155576320 16116 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/CodonUsage/IO.pm000555000766000024 1344513155576320 17152 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::CodonUsage::IO # # Please direct questions and support issues to # # Cared for by Richard Adams (richard.adams@ed.ac.uk) # # Copyright Richard Adams # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::CodonUsage::IO - for reading and writing codon usage tables to file =head1 SYNOPSIS use Bio::CodonUsage::IO; ## read in a codon usage file my $io = Bio::CodonUsage::IO->new(-file => "in"); my $cut = $io->next_data(); ## write it out again my $out = Bio::CodonUsage::IO->new(-file => ">out"); $out->write_data($cut); =head1 DESCRIPTION This class provides standard IO methods for reading and writing text files of codon usage tables. These tables can initially be retrieved using Bio::DB::CUTG. At present only this format is supported for read/write. Reading a CUTG will return a Bio::CodonUsage::Table object. =head1 SEE ALSO L, L, L, L =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Richard Adams, Richard.Adams@ed.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin package Bio::CodonUsage::IO; use Bio::CodonUsage::Table; use base qw(Bio::Root::IO); =head2 new Title : new Usage : my $io = Bio::CodonUsage::IO->new(-file => "CUTfile"); Purpose: To read/write a Bio:CodonUsage::Table object Returns: A Bio:CodonUsage::IO object Args : a file or file handle =cut sub new { my ($class , @args) = @_; my $self = $class->SUPER::new(@args); } =head2 next_data Title : next_data Usage : my $cut = $io->next_data(); Purpose: To obtain a Bio:CodonUsage::Table object Returns: A Bio:CodonUsage::Table object Args : none =cut sub next_data { my $self = shift; my $cut = $self->_parse; return $cut; } =head2 write_data Title : write_data Usage : $io->write_data($cut); Purpose: To write a CUT to file Returns: void Args : a Bio::CodonUsage::Table object reference =cut sub write_data { my ($self, $cut) = @_; if (!$cut || ! $cut->isa(Bio::CodonUsage::Table)) { $self->throw("must supply a Bio::CodonUsage::Table object for writing\n"); } my $outstring = "Codon usage table\n\n"; my $sp_string = $cut->species . "[" . $cut->_gb_db . "] " . $cut->cds_count . " CDS's\n\n"; $outstring .= $sp_string; my $colhead = sprintf("%-9s%-9s%15s%12s%12s\n\n", "AmAcid", "Codon", "Number", "/1000", "Fraction"); $outstring .= $colhead; ### now write bulk of codon data ## my $ctable = Bio::Tools::CodonTable->new; for my $f (qw(G A T C)) { for my $s (qw(G A T C)) { for my $t (qw(G A T C)) { $cod = $f . $s . $t; my $aa =$Bio::SeqUtils::THREECODE {$ctable->translate($cod)}; my $codstr = sprintf("%-9s%-9s%15.2f%12.2f%12.2f\n", $aa, $cod, my $tt = $cut->codon_count($cod)|| 0.00, my $ll =$cut->{'_table'}{$aa}{$cod}{'per1000'}|| 0.00, my $ss = $cut->codon_rel_frequency($cod) || 0.00); $outstring .= $codstr; } $outstring .= "\n"; } } $outstring .= "\n\n"; ## now append GC data $outstring .= "Coding GC ". $cut->get_coding_gc('all'). "%\n"; $outstring .= "1st letter GC ". $cut->get_coding_gc(1). "%\n"; $outstring .= "2nd letter GC ". $cut->get_coding_gc(2). "%\n"; $outstring .= "3rd letter GC ". $cut->get_coding_gc(3). "%\n"; $outstring .= "Genetic code " . $cut->genetic_code() ."\n\n\n"; $self->_print ($outstring); $self->flush(); } sub _parse { my $self = shift; my $cdtableobj = Bio::CodonUsage::Table->new(); while (my $line = $self->_readline() ) { next if $line =~ /^$/ ; $line =~ s/End/Ter/; ## now parse in species name, cds number if ($line =~ /^(.+?)\s*\[(\w+)\].+?(\d+)/) { $cdtableobj->species($1); $cdtableobj->{'_gb_db'} = $2; $cdtableobj->cds_count($3); } ## now parse in bulk of codon usage table elsif ( $line =~ /^(\w\w\w)\s+(\w+)\s+(\d+\.\d+) \s+(\d+\.\d+)\s+(\d+\.\d+)/x){ if (defined ($1)) { $cdtableobj->{'_table'}{$1}{$2} = { 'abs_count'=>$3, 'per1000'=> $4, 'rel_freq'=> $5, }; } } ## now parse in gc data #### if($line =~ /^Cod.+?(\d\d\.\d\d)/ ){ $cdtableobj->{'_coding_gc'}{'all'} = $1; } elsif ($line =~ /^1st.+?(\d\d\.\d\d)/){ $cdtableobj->{'_coding_gc'}{'1'} = $1; } elsif($line =~ /^2nd.+?(\d\d\.\d\d)/){ $cdtableobj->{'_coding_gc'}{'2'} = $1; } elsif ($line =~ /^3rd.+?(\d\d\.\d\d)/){ $cdtableobj->{'_coding_gc'}{'3'} = $1; } elsif ($line =~ /^Gen.+?(\d+)/){ $cdtableobj->{'_genetic_code'} = $1; } } ## check has been parsed ok ## if (scalar keys %{$cdtableobj->{'_table'}} != 21) { $cdtableobj->warn("probable parsing error - should be 21 entries for 20aa + stop codon"); } return $cdtableobj; } 1; __END__ BioPerl-1.007002/Bio/CodonUsage/Table.pm000555000766000024 4254213155576320 17672 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::CodonUsage::Table # # Please direct questions and support issues to # # Cared for by Richard Adams (richard.adams@ed.ac.uk) # # Copyright Richard Adams # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::CodonUsage::Table - for access to the Codon usage Database at http://www.kazusa.or.jp/codon. =head1 SYNOPSIS use Bio::CodonUsage::Table; use Bio::DB::CUTG; use Bio::CodonUsage::IO; use Bio::Tools::SeqStats; # Get a codon usage table from web database my $cdtable = Bio::DB::CUTG->new(-sp => 'Mus musculus', -gc => 1); # Or from local file my $io = Bio::CodonUsage::IO->new(-file => "file"); my $cdtable = $io->next_data(); # Or create your own from a Bio::PrimarySeq compliant object, # $codonstats is a ref to a hash of codon name /count key-value pairs my $codonstats = Bio::Tools::SeqStats->count_codons($Seq_objct); # '-data' must be specified, '-species' and 'genetic_code' are optional my $CUT = Bio::CodonUsage::Table->new(-data => $codonstats, -species => 'Hsapiens_kinase'); print "leu frequency is ", $cdtable->aa_frequency('LEU'), "\n"; print "freq of ATG is ", $cdtable->codon_rel_frequency('ttc'), "\n"; print "abs freq of ATG is ", $cdtable->codon_abs_frequency('ATG'), "\n"; print "number of ATG codons is ", $cdtable->codon_count('ATG'), "\n"; print "GC content at position 1 is ", $cdtable->get_coding_gc('1'), "\n"; print "total CDSs for Mus musculus is ", $cdtable->cds_count(), "\n"; =head1 DESCRIPTION This class provides methods for accessing codon usage table data. All of the methods at present are simple look-ups of the table or are derived from simple calculations from the table. Future methods could include measuring the codon usage of a sequence , for example, or provide methods for examining codon usage in alignments. =head1 SEE ALSO L, L, L, L =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Richard Adams, Richard.Adams@ed.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::CodonUsage::Table; use strict; use vars qw(%STRICTAA @AA); use Bio::SeqUtils; use Bio::Tools::CodonTable; use base qw(Bio::Root::Root); BEGIN{ @AA = qw(A C D E F G H I K L M N P Q R S T V W Y *); map {$STRICTAA{$_} = undef} @AA; } =head2 new Title : new Usage : my $cut = Bio::CodonUsage::Table->new(-data => $cut_hash_ref, -species => 'H.sapiens_kinase' -genetic_code =>1); Returns : a reference to a new Bio::CodonUsage::Table object Args : none or a reference to a hash of codon counts. This constructor is designed to be compatible with the output of Bio::Tools::SeqUtils::count_codons() Species and genetic code parameters can be entered here or via the species() and genetic_code() methods separately. =cut sub new { my ($class, @args) = @_; my $self= $class->SUPER::new(@args); if (@args) { $self->_rearrange([qw(DATA)], @args); shift @args; # get rid of key my $arg = shift @args; $self->throw("need a hash reference, not a [" . ref($arg). "] reference") if ref($arg) ne 'HASH'; ### flags to detect argument type, can be either to start with ## my $is_codon_hash = 1; my $is_Aa_hash = 1; for my $k (keys %$arg) { ## convert to UC $k =~ s/(\w+)/\U$1/; if (!exists($STRICTAA{$k}) ){ $is_Aa_hash = 0; } elsif ($k =~ /[^ATCGatcg]/) { $is_codon_hash = 0; } } if (!$is_codon_hash && !$is_Aa_hash) { $self->throw(" invalid key values in CUT hash - must be unique aa or nucleotide identifiers"); } elsif ($is_Aa_hash) { $self->_init_from_aa($arg); } elsif($is_codon_hash) { $self->_init_from_cod($arg); } while (@args) { my $key = shift @args; $key =~ s/\-(\w+)/\L$1/; $self->$key(shift @args); } } return $self; } =head2 all_aa_frequencies Title : all_aa_frequencies Usage : my $freq = $cdtable->all_aa_frequencies(); Returns : a reference to a hash where each key is an amino acid and each value is its frequency in all proteins in that species. Args : none =cut sub all_aa_frequencies { my $self = shift; my %aa_freqs =(); for my $aa (keys %STRICTAA) { my $freq = $self->aa_frequency($aa); $aa_freqs{$aa} = $freq; } return \%aa_freqs; } =head2 codon_abs_frequency Title : codon_abs_frequency Usage : my $freq = $cdtable->codon_abs_frequency('CTG'); Purpose : To return the frequency of that codon as a percentage of all codons in the organism. Returns : a percentage frequency Args : a non-ambiguous codon string =cut sub codon_abs_frequency { my ($self, $a) = @_; my $cod = uc $a; if ($self->_check_codon($cod)) { my $ctable = Bio::Tools::CodonTable->new; $ctable->id($self->genetic_code() ); my $aa =$Bio::SeqUtils::THREECODE {$ctable->translate($cod)}; return $self->{'_table'}{$aa}{$cod}{'per1000'}/10 ; } else {return 0;} } =head2 codon_rel_frequency Title : codon_rel_frequency Usage : my $freq = $cdtable->codon_rel_frequency('CTG'); Purpose : To return the frequency of that codon as a percentage of codons coding for the same amino acid. E.g., ATG and TGG would return 100 as those codons are unique. Returns : a percentage frequency Args : a non-ambiguous codon string =cut sub codon_rel_frequency { my ($self, $a) = @_; my $cod = uc $a; if ($self->_check_codon($cod)) { my $ctable = Bio::Tools::CodonTable->new; $ctable->id($self->genetic_code () ); my $aa =$Bio::SeqUtils::THREECODE {$ctable->translate($cod)}; return $self->{'_table'}{$aa}{$cod}{'rel_freq'}; } else { return 0; } } =head2 probable_codons Title : probable_codons Usage : my $prob_codons = $cd_table->probable_codons(10); Purpose : to obtain a list of codons for the amino acid above a given threshold % relative frequency Returns : A reference to a hash where keys are 1 letter amino acid codes and values are references to arrays of codons whose frequency is above the threshold. Arguments: a minimum threshold frequency =cut sub probable_codons { my ($self, $threshold) = @_; if (!$threshold || $threshold < 0 || $threshold > 100) { $self->throw(" I need a threshold percentage "); } my %return_hash; for my $a(keys %STRICTAA) { my @common_codons; my $aa =$Bio::SeqUtils::THREECODE{$a}; for my $codon (keys %{ $self->{'_table'}{$aa}}) { if ($self->{'_table'}{$aa}{$codon}{'rel_freq'} > $threshold/100){ push @common_codons, $codon; } } $return_hash{$a} = \@common_codons; } ## check to make sure that all codons are populated ## if (grep{scalar @{$return_hash{$_}} == 0} keys %return_hash) { $self->warn("Threshold is too high, some amino acids do not" . " have any codon above the threshold!"); } return \%return_hash; } =head2 most_common_codons Title : most_common_codons Usage : my $common_codons = $cd_table->most_common_codons(); Purpose : To obtain the most common codon for a given amino acid Returns : A reference to a hash where keys are 1 letter amino acid codes and the values are the single most common codons for those amino acids Arguments: None =cut sub most_common_codons { my $self = shift; my %return_hash; for my $a ( keys %STRICTAA ) { my $common_codon = ''; my $rel_freq = 0; my $aa = $Bio::SeqUtils::THREECODE{$a}; if ( ! defined $self->{'_table'}{$aa} ) { $self->warn("Amino acid $aa ($a) does not have any codons!"); next; } for my $codon ( keys %{ $self->{'_table'}{$aa}} ) { if ($self->{'_table'}{$aa}{$codon}{'rel_freq'} > $rel_freq ){ $common_codon = $codon; $rel_freq = $self->{'_table'}{$aa}{$codon}{'rel_freq'}; } } $return_hash{$a} = $common_codon; } return \%return_hash; } =head2 codon_count Title : codon_count Usage : my $count = $cdtable->codon_count('CTG'); Purpose : To obtain the absolute number of the codons in the organism. Returns : an integer Args : a non-ambiguous codon string =cut sub codon_count { my $self = shift; if (@_) { my $a = shift; my $cod = uc $a; if ($self->_check_codon($cod)) { my $ctable = Bio::Tools::CodonTable->new; $ctable->id($self->genetic_code()); my $aa =$Bio::SeqUtils::THREECODE {$ctable->translate($cod)}; return $self->{'_table'}{$aa}{$cod}{'abs_count'}; } else {return 0;} } else { $self->warn(" need to give a codon sequence as a parameter "); return 0; } } =head2 get_coding_gc Title : get_coding_gc Usage : my $count = $cdtable->get_coding_gc(1); Purpose : To return the percentage GC composition for the organism at codon positions 1,2 or 3, or an average for all coding sequence ('all'). Returns : a number (%-age GC content) or 0 if these fields are undefined Args : 1,2,3 or 'all'. =cut sub get_coding_gc { my $self = shift; if (! @_) { $self->warn(" no parameters supplied must be a codon position (1,2,3) or 'all'"); return 0; } else{ my $n = shift; ##return request if valid ## if ( exists($self->{'_coding_gc'}{$n} ) ) { return sprintf("%.2f", $self->{'_coding_gc'}{$n}); } ##else return 'all' value if exists elsif (exists($self->{'_coding_gc'}{'all'} )) { $self->warn("coding gc doesn't have value for [$n], returning gc content for all CDSs"); return sprintf("%.2f", $self->{'_coding_gc'}{'all'}); } ### else return 0, else { $self->warn("coding gc values aren't defined, returning 0"); return 0; } }#end of outer else } =head2 set_coding_gc Title : set_coding_gc Usage : my $count = $cdtable->set_coding_gc(-1=>55.78); Purpose : To set the percentage GC composition for the organism at codon positions 1,2 or 3, or an average for all coding sequence ('all'). Returns : void Args : a hash where the key must be 1,2,3 or 'all' and the value the %age GC at that codon position.. =cut sub set_coding_gc { my ($self, $key, $value) = @_; my @allowed = qw(1 2 3 all); $key =~ s/\-//; if (!grep {$key eq $_} @allowed ) { $self->warn ("invalid key! - must be one of [ ". (join " ", @allowed) . "]"); return; } $self->{'_coding_gc'}{$key} = $value; } =head2 species Title : species Usage : my $sp = $cut->species(); Purpose : Get/setter for species name of codon table Returns : Void or species name string Args : None or species name string =cut sub species { my $self = shift; if (@_ ){ $self->{'_species'} = shift; } return $self->{'_species'} || "unknown"; } =head2 genetic_code Title : genetic_code Usage : my $sp = $cut->genetic_code(); Purpose : Get/setter for genetic_code name of codon table Returns : Void or genetic_code id, 1 by default Args : None or genetic_code id, 1 by default if invalid argument. =cut sub genetic_code { my $self = shift; if (@_ ){ my $val = shift; if ($val < 0 || $val >16 || $val =~ /[^\d]/ || $val ==7 || $val ==8) { $self->warn ("invalid genetic code - must be 1-16 but not 7 or 8,setting to default [1]"); $self->{'_genetic_code'} = 1; } else { $self->{'_genetic_code'} = shift; } } return $self->{'_genetic_code'} || 1; } =head2 cds_count Title : cds_count Usage : my $count = $cdtable->cds_count(); Purpose : To retrieve the total number of CDSs used to generate the Codon Table for that organism. Returns : an integer Args : none (if retrieving the value) or an integer( if setting ). =cut sub cds_count { my $self= shift; if (@_) { my $val = shift; if ($val < 0) { $self->warn("can't have negative count initializing to 1"); $self->{'_cds_count'} = 0.00; } else{ $self->{'_cds_count'} = $val; } } $self->warn("cds_count value is undefined, returning 0") if !exists($self->{'_cds_count'}); return $self->{'_cds_count'} || 0.00; } =head2 aa_frequency Title : aa_frequency Usage : my $freq = $cdtable->aa_frequency('Leu'); Purpose : To retrieve the frequency of an amino acid in the organism Returns : a percentage Args : a 1 letter or 3 letter string representing the amino acid =cut sub aa_frequency { my ($self, $a) = @_; ## process args ## ## deal with cases ## my $aa = lc $a; $aa =~ s/^(\w)/\U$1/; if (!exists($STRICTAA{$aa}) && !exists($Bio::SeqUtils::ONECODE{$aa}) ) { $self->warn("Invalid amino acid! must be a unique 1 letter or 3 letter identifier"); return; } #translate to 3 letter code for Ctable # my $aa3 = $Bio::SeqUtils::THREECODE{$aa} || $aa; ## return % of all amino acids in organism ## my $freq = 0; map {$freq += $self->{'_table'}{$aa3}{$_}{'per1000'} } keys %{$self->{'_table'}{$aa3}}; return sprintf("%.2f", $freq/10); } =head2 common_codon Title : common_codon Usage : my $freq = $cdtable->common_codon('Leu'); Purpose : To retrieve the frequency of the most common codon of that aa Returns : a percentage Args : a 1 letter or 3 letter string representing the amino acid =cut sub common_codon{ my ($self, $a) = @_; my $aa = lc $a; $aa =~ s/^(\w)/\U$1/; if ($self->_check_aa($aa)) { my $aa3 = $Bio::SeqUtils::THREECODE{$aa} ; $aa3 ||= $aa; my $max = 0; for my $cod (keys %{$self->{'_table'}{$aa3}}) { $max = ($self->{'_table'}{$aa3}{$cod}{'rel_freq'} > $max) ? $self->{'_table'}{$aa3}{$cod}{'rel_freq'}:$max; } return $max; }else {return 0;} } =head2 rare_codon Title : rare_codon Usage : my $freq = $cdtable->rare_codon('Leu'); Purpose : To retrieve the frequency of the least common codon of that aa Returns : a percentage Args : a 1 letter or 3 letter string representing the amino acid =cut sub rare_codon { my ($self, $a) = @_; my $aa = lc $a; $aa =~ s/^(\w)/\U$1/; if ($self->_check_aa($aa)) { my $aa3 = $Bio::SeqUtils::THREECODE{$aa}; $aa3 ||= $aa; my $min = 1; for my $cod (keys %{$self->{'_table'}{$aa3}}) { $min = ($self->{'_table'}{$aa3}{$cod}{'rel_freq'} < $min) ? $self->{'_table'}{$aa3}{$cod}{'rel_freq'}:$min; } return $min; }else {return 0;} } ## internal sub that checks a codon is correct format sub _check_aa { my ($self, $aa ) = @_; if (!exists($STRICTAA{$aa}) && !exists($Bio::SeqUtils::ONECODE{$aa}) ) { $self->warn("Invalid amino acid! must be a unique 1 letter or 3 letter identifier"); return 0; }else {return 1;} } sub _check_codon { my ($self, $cod) = @_; if ($cod =~ /[^ATCG]/ || $cod !~ /\w\w\w/) { $self->warn(" impossible codon - must be 3 letters and just containing ATCG"); return 0; } else {return 1;} } sub _init_from_cod { ## make hash based on aa and then send to _init_from_aa my ($self, $ref) = @_; my $ct = Bio::Tools::CodonTable->new(); my %aa_hash; for my $codon(keys %$ref ) { my $aa = $ct->translate($codon); $aa_hash{$aa}{$codon} = $ref->{$codon}; } $self->_init_from_aa(\%aa_hash); } sub _init_from_aa { my ($self, $ref) = @_; ## abs counts and count codons my $total_codons = 0; my %threeletter; map{$threeletter{$Bio::SeqUtils::THREECODE{$_}} = $ref->{$_} } keys %$ref; $ref = \%threeletter; for my $aa (keys %$ref) { for my $cod(keys %{$ref->{$aa}} ) { $self->{'_table'}{$aa}{$cod}{'abs_count'} = $ref->{$aa}{$cod}; $total_codons += $ref->{$aa}{$cod}; } } ## now calculate abs codon frequencies for my $aa (keys %$ref) { for my $cod(keys %{$ref->{$aa}} ) { $self->{'_table'}{$aa}{$cod}{'per1000'} = sprintf("%.2f",$ref->{$aa}{$cod} /$total_codons * 1000) ; } } ## now calculate rel codon_frequencies for my $aa (keys %$ref) { my $aa_freq = 0; map{$aa_freq += $ref->{$aa}{$_} } keys %{$ref->{$aa}}; for my $cod(keys %{$ref->{$aa}} ) { $self->{'_table'}{$aa}{$cod}{'rel_freq'}= sprintf("%.2f",$ref->{$aa}{$cod}/ $aa_freq ); } } ## now calculate gc fields my %GC; for my $aa (keys %$ref) { for my $cod(keys %{$ref->{$aa}} ) { for my $index (qw(1 2 3) ) { if (substr ($cod, $index -1, 1) =~ /g|c/oi) { $GC{$index} += $ref->{$aa}{$cod}; } } } } my $tot = 0; map{$tot += $GC{$_}} qw(1 2 3); $self->set_coding_gc('all', $tot/(3 *$total_codons) * 100); map{$self->set_coding_gc($_,$GC{$_}/$total_codons * 100)} qw(1 2 3); ## return $self; } sub _gb_db { my $self = shift; return $self->{'_gd_db'} || "unknown"; } 1; BioPerl-1.007002/Bio/DB000755000766000024 013155576320 14354 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/Ace.pm000444000766000024 1127413155576320 15564 0ustar00cjfieldsstaff000000000000 # # BioPerl module for Bio::DB::Ace # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Ace - Database object interface to ACeDB servers =head1 SYNOPSIS $db = Bio::DB::Ace->new( -server => 'myace.server.com', port => '120000'); $seq = $db->get_Seq_by_id('J00522'); # Unique ID # or ... $seq = $db->get_Seq_by_acc('J00522'); # Accession Number =head1 DESCRIPTION This provides a standard BioPerl database access to Ace, using Lincoln Steins excellent AcePerl module. You need to download and install the aceperl module from http://stein.cshl.org/AcePerl/ before this interface will work. This interface is designed at the moment to work through a aceclient/aceserver type mechanism =head1 INSTALLING ACEPERL Download the latest aceperl tar file, gunzip/untar and cd into the directory. This is a standard CPAN-style directory, so if you go Perl Makefile.PL make make install Then you will have installed Aceperl. Use the PREFIX mechanism to install elsewhere. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Ace; use strict; # Object preamble - inherits from Bio::DB::RandomAccessI use Bio::Seq; BEGIN { eval "require Ace;"; if( $@) { print STDERR "You have not installed Ace.pm.\n Read the docs in Bio::DB::Ace for more information about how to do this.\n It is very easy\n\nError message $@"; } } use base qw(Bio::DB::RandomAccessI); # new() is inherited from Bio::DB::Abstract # _initialize is where the heavy stuff will happen when new is called sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($host,$port) = $self->_rearrange([qw( HOST PORT )], @args, ); if( !$host || !$port ) { $self->throw("Must have a host and port for an acedb server to work"); } my $aceobj = Ace->connect(-host => $host, -port => $port) || $self->throw("Could not make acedb object to $host:$port"); $self->_aceobj($aceobj); return $self; } =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id($uid); Function: Gets a Bio::Seq object by its unique identifier/name Returns : a Bio::Seq object Args : $id : the id (as a string) of the desired sequence entry =cut sub get_Seq_by_id { my $self = shift; my $id = shift or $self->throw("Must supply an identifier!\n"); my $ace = $self->_aceobj(); my ($seq,$dna,$out); $seq = $ace->fetch( 'Sequence' , $id); # get out the sequence somehow! $dna = $seq->asDNA(); $dna =~ s/^>.*\n//; $dna =~ s/\n//g; $out = Bio::Seq->new( -id => $id, -alphabet => 'Dna', -seq => $dna, -name => "Sequence from Bio::DB::Ace $id"); return $out; } =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc($acc); Function: Gets a Bio::Seq object by its accession number Returns : a Bio::Seq object Args : $acc : the accession number of the desired sequence entry =cut sub get_Seq_by_acc { my $self = shift; my $acc = shift or $self->throw("Must supply an accession number!\n"); return $self->get_Seq_by_id($acc); } =head2 _aceobj Title : _aceobj Usage : $ace = $db->_aceobj(); Function: Get/Set on the acedb object Returns : Ace object Args : New value of the ace object =cut sub _aceobj { my ($self,$arg) = @_; if( $arg ) { $self->{'_aceobj'} = $arg; } return $self->{'_aceobj'}; } 1; BioPerl-1.007002/Bio/DB/BioFetch.pm000444000766000024 3350613155576320 16561 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::BioFetch # # Please direct questions and support issues to # # Cared for by Lincoln Stein # # Copyright Lincoln Stein # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code # package Bio::DB::BioFetch; use strict; use HTTP::Request::Common 'POST'; =head1 NAME Bio::DB::BioFetch - Database object interface to BioFetch retrieval =head1 SYNOPSIS use Bio::DB::BioFetch; $bf = Bio::DB::BioFetch->new(); $seq = $bf->get_Seq_by_id('HSFOS'); # EMBL or SWALL ID # change formats, storage procedures $bf = Bio::DB::BioFetch->new(-format => 'fasta', -retrievaltype => 'tempfile', -db => 'EMBL'); $stream = $bf->get_Stream_by_id(['HSFOS','J00231']); while (my $s = $stream->next_seq) { print $s->seq,"\n"; } # get a RefSeq entry $bf->db('refseq'); eval { $seq = $bf->get_Seq_by_version('NM_006732.1'); # RefSeq VERSION }; print "accession is ", $seq->accession_number, "\n" unless $@; =head1 DESCRIPTION Bio::DB::BioFetch is a guaranteed best effort sequence entry fetching method. It goes to the Web-based dbfetch server located at the EBI (http://www.ebi.ac.uk/Tools/dbfetch/dbfetch) to retrieve sequences in the EMBL or GenBank sequence repositories. This module implements all the Bio::DB::RandomAccessI interface, plus the get_Stream_by_id() and get_Stream_by_acc() methods that are found in the Bio::DB::SwissProt interface. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Lincoln Stein Email Lincoln Stein Elstein@cshl.orgE Also thanks to Heikki Lehvaslaiho Eheikki-at-bioperl-dot-orgE for the BioFetch server and interface specification. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... use vars qw(%FORMATMAP); use base qw(Bio::DB::WebDBSeqI Bio::Root::Root); # warning: names used here must map into Bio::SeqIO::* space use constant DEFAULT_LOCATION => 'http://www.ebi.ac.uk/Tools/dbfetch/dbfetch'; BEGIN { %FORMATMAP = ( 'embl' => { default => 'embl', # default BioFetch format/SeqIOmodule pair embl => 'embl', # alternative BioFetch format/module pair fasta => 'fasta', # alternative BioFetch format/module pair namespace => 'embl', }, 'swissprot' => { default => 'swiss', swissprot => 'swiss', fasta => 'fasta', namespace => 'uniprot', }, 'refseq' => { default => 'genbank', genbank => 'genbank', fasta => 'fasta', namespace => 'RefSeq', }, 'swall' => { default => 'swiss', swissprot => 'swiss', fasta => 'fasta', namespace => 'uniprot', }, 'uniprot' => { default => 'swiss', swissprot => 'swiss', fasta => 'fasta', namespace => 'uniprot', }, 'genbank' => { default => 'genbank', genbank => 'genbank', namespace => 'genbank', }, 'genpep' => { default => 'genbank', genbank => 'genbank', namespace => 'genpep', }, 'unisave' => { default => 'swiss', swissprot => 'swiss', fasta => 'fasta', namespace => 'unisave', } ); } =head2 new Title : new Usage : $bf = Bio::DB::BioFetch->new(@args) Function: Construct a new Bio::DB::BioFetch object Returns : a Bio::DB::BioFetch object Args : see below Throws : @args are standard -name=Evalue options as listed in the following table. If you do not provide any options, the module assumes reasonable defaults. Option Value Default ------ ----- ------- -baseaddress location of dbfetch server http://www.ebi.ac.uk/Tools/dbfetch/dbfetch -retrievaltype "tempfile" or "io_string" io_string -format "embl", "fasta", "swissprot", embl or "genbank" -db "embl", "genbank" or "swissprot" embl =cut #' sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($db) = $self->_rearrange([qw(DB)],@args); $db ||= $self->default_db; $self->db($db); $self->url_base_address(DEFAULT_LOCATION) unless $self->url_base_address; $self; } =head2 new_from_registry Title : new_from_registry Usage : $biofetch = $db->new_from_registry(%config) Function: Creates a BioFetch object from the registry config hash Returns : itself Args : A configuration hash (see Registry.pm) Throws : =cut sub new_from_registry { my ($class,%config)=@_; my $self = $class->SUPER::new( -BASEADDRESS=>$config{'location'} ); $self->db($config{'dbname'}) if $config{dbname}; return $self; } # from Bio::DB::RandomAccessI =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception =cut =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception =cut =head2 get_Seq_by_gi Title : get_Seq_by_gi Usage : $seq = $db->get_Seq_by_gi('405830'); Function: Gets a Bio::Seq object by gi number Returns : A Bio::Seq object Args : gi number (as a string) Throws : "gi does not exist" exception =cut =head2 get_Seq_by_version Title : get_Seq_by_version Usage : $seq = $db->get_Seq_by_version('X77802.1'); Function: Gets a Bio::Seq object by sequence version Returns : A Bio::Seq object Args : accession.version (as a string) Throws : "acc.version does not exist" exception =cut sub get_Seq_by_version { my ($self,$seqid) = @_; return $self->get_Seq_by_acc($seqid); } =head2 get_Stream_by_id Title : get_Stream_by_id Usage : $stream = $db->get_Stream_by_id( [$uid1, $uid2] ); Function: Gets a series of Seq objects by unique identifiers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of unique identifiers for the desired sequence entries =cut =head2 get_Stream_by_gi Title : get_Stream_by_gi Usage : $seq = $db->get_Seq_by_gi([$gi1, $gi2]); Function: Gets a series of Seq objects by gi numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of gi numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id() =cut =head2 get_Stream_by_batch Title : get_Stream_by_batch Usage : $seq = $db->get_Stream_by_batch($ref); Function: Get a series of Seq objects by their IDs Example : Returns : a Bio::SeqIO stream object Args : $ref : an array reference containing a list of unique ids/accession numbers. In some of the Bio::DB::* moduels, get_Stream_by_id() is called get_Stream_by_batch(). Since there seems to be no consensus, this is provided as an alias. =cut *get_Stream_by_batch = \&Bio::DB::WebDBSeqI::get_Stream_by_id; =head1 The remainder of these methods are for internal use =head2 get_request Title : get_request Usage : my $url = $self->get_request Function: returns a HTTP::Request object Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) =cut sub get_request { my ($self, @qualifiers) = @_; my ($uids, $format) = $self->_rearrange([qw(UIDS FORMAT)], @qualifiers); my $db = $self->db; my $namespace = $self->_namespace; $self->throw("Must specify a value for UIDs to fetch") unless defined $uids; my $tmp; my $format_string = ''; $format ||= $self->default_format; ($format, $tmp) = $self->request_format($format); my $base = $self->url_base_address; my $uid = join('+',ref $uids ? @$uids : $uids); $self->debug("\n$base$format_string&id=$uid\n"); return POST($base, [ db => $namespace, id => join('+',ref $uids ? @$uids : $uids), format => $format, style => 'raw' ]); } =head2 default_format Title : default_format Usage : $format = $self->default_format Function: return the default format Returns : a string Args : =cut sub default_format { return 'default'; } =head2 default_db Title : default_db Usage : $db = $self->default_db Function: return the default database Returns : a string Args : =cut sub default_db { 'embl' } =head2 db Title : db Usage : $db = $self->db([$db]) Function: get/set the database Returns : a string Args : new database =cut sub db { my $self = shift; if (@_) { my $db = lc shift; my $base = $self->url_base_address; $FORMATMAP{$db} or $self->throw("invalid db [$db] at [$base], must be one of [". join(' ',keys %FORMATMAP). "]"); $self->{_db} = $db; } return $self->{_db} || $self->default_db ; } sub _namespace { my $self = shift; my $db = $self->db; return $FORMATMAP{$db}{namespace} or $db; } =head2 postprocess_data Title : postprocess_data Usage : $self->postprocess_data ( 'type' => 'string', 'location' => \$datastr); Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - 'location' either file location or string reference containing data =cut sub postprocess_data { my ($self,%args) = @_; # check for errors in the stream if ($args{'type'} eq 'string') { my $stringref = $args{'location'}; if ($$stringref =~ /^ERROR (\d+) (.+)/m) { $self->throw("BioFetch Error $1: $2"); } } elsif ($args{'type'} eq 'file') { open my $F, '<', $args{'location'} or $self->throw("Could not read file '$args{location}': $!"); # this is dumb, but the error may be anywhere on the first three lines because the # CGI headers are sometimes printed out by the server... my @data = grep {defined $_} (scalar <$F>, scalar <$F>, scalar <$F>); close $F; if (join('',@data) =~ /^ERROR (\d+) (.+)/m) { $self->throw("BioFetch Error $1: $2"); } } else { $self->throw("Don't know how to postprocess data of type $args{'type'}"); } } =head2 request_format Title : request_format Usage : my ($req_format, $ioformat) = $self->request_format; $self->request_format("genbank"); $self->request_format("fasta"); Function: Get/Set sequence format retrieval. The get-form will normally not be used outside of this and derived modules. Returns : Array of two strings, the first representing the format for retrieval, and the second specifying the corresponding SeqIO format. Args : $format = sequence format =cut sub request_format { my ($self, $value) = @_; if ( defined $value ) { my $db = $self->db; my $namespace = $self->_namespace; my $format = lc $value; print "format:", $format, " module:", $FORMATMAP{$db}->{$format}, " ($namespace)\n" if $self->verbose > 0; $self->throw("Invalid format [$format], must be one of [". join(' ',keys %{$FORMATMAP{$db}}). "]") unless $format eq 'default' || $FORMATMAP{$db}->{$format}; $self->{'_format'} = [ $format, $FORMATMAP{$db}->{$format}]; } return @{$self->{'_format'}}; } =head2 Bio::DB::WebDBSeqI methods Overriding WebDBSeqI method to help newbies to retrieve sequences. EMBL database is all too often passed RefSeq accessions. This redirects those calls. See L. =head2 get_Stream_by_acc Title : get_Stream_by_acc Usage : $seq = $db->get_Seq_by_acc([$acc1, $acc2]); Function: Gets a series of Seq objects by accession numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession numbers for the desired sequence entries =cut sub get_Stream_by_acc { my ($self, $ids ) = @_; $self->_check_id($ids); return $self->get_seq_stream('-uids' => $ids, '-mode' => 'single'); } =head2 _check_id Title : _check_id Usage : Function: Throw on whole chromosome NCBI sequences not in sequence databases and redirect RefSeq accession requests sent to EMBL. Returns : Args : $id(s), $string Throws : if accessionn number indicates whole chromosome NCBI sequence =cut sub _check_id { my ($self, $id) = @_; # NT contigs can not be retrieved $self->throw("NT_ contigs are whole chromosome files which are not part of regular ". "database distributions. Go to ftp://ftp.ncbi.nih.gov/genomes/.") if $id =~ /NT_/; # Asking for a RefSeq from EMBL/GenBank if ($id =~ /N._/ && $self->db ne 'refseq') { $self->warn("[$id] is not a normal sequence entry but a RefSeq entry.". " Redirecting the request.\n") if $self->verbose >= 0; $self->db('RefSeq'); } } 1; BioPerl-1.007002/Bio/DB/CUTG.pm000555000766000024 2041213155576320 15633 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::CUTG # # Please direct questions and support issues to # # Cared for by Richard Adams (richard.adams@ed.ac.uk) # # Copyright Richard Adams # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::CUTG - for access to the Codon usage Database at http://www.kazusa.or.jp/codon. =head1 SYNOPSIS use Bio::CodonUsage::Table; use Bio::DB::CUTG; my $db = Bio::DB::CUTG->new(-sp =>'Pan troglodytes'); my $CUT = $db->get_request(); =head1 DESCRIPTION This class retrieves and objectifies codon usage tables either from the CUTG web database . The idea is that you can initially retrieve a CUT from the web database, and write it to file in a way that can be read in later, using the Bio::CodonUsage::IO module. For a web query, two parameters need to be specified: species(sp) and genetic code id (gc). The database is searched using regular expressions, therefore the full latin name must be given to specify the organism. If the species name is ambiguous the first CUT in the list is retrieved. Defaults are Homo sapiens and 1(standard genetic code). If you are retrieving CUTs from organisms using other genetic codes this needs to be put in as a parameter. Parameters can be entered in the constructor or in the get_web_request ()method. Allowable parameters are listed in the $QUERY_KEYS hash reference variable. I intend at a later date to allow retrieval of multiple codon tables e.g., from a wildcard search. Examples URLs: L L =head1 SEE ALSO L, L, L, L =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Richard Adams, Richard.Adams@ed.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::CUTG; use Bio::CodonUsage::IO; use IO::String; use URI::Escape; use vars qw($URL $QUERY_KEYS); use base qw(Bio::WebAgent); $QUERY_KEYS = { sp => 'full Latin species name', gc => 'genetic code id' }; BEGIN { $URL = "http://www.kazusa.or.jp"; } =head2 new Title : new Usage : my $db = Bio::DB::CUTG->new() Returns : a reference to a new Bio::DB::CUTG Args : hash of optional values for db query =cut sub new { my ( $class, @args ) = @_; _check_args(@args); my $self = $class->SUPER::new(@args); return $self; } =head2 query_keys Title : query_keys Usage : $db->query_keys() Purpose : To determine valid keys for parameters for db query. Returns : a reference to a hash describing valid query keys Args : none =cut sub query_keys { return $QUERY_KEYS; } =head2 sp Title : sp Usage : my $sp = $db->sp(); Purpose: Get/set method for species name Returns: void or species name string Args : None or species name string =cut sub sp { my $self = shift; if (@_) { my $name = shift; $self->{'_sp'} = $name; } return $self->{'_sp'} || "Homo sapiens"; } =head2 gc Title : gc Usage : my $gc = $db->gc(); Purpose: Get/set method for genetic code id Returns: void or genetic code integer Args : None or genetic code integer =cut sub gc { #### genetic code id for translations #### my $self = shift; if (@_) { if ( $_[0] =~ /^\d+$/ && $_[0] >= 1 && $_[0] <= 15 && $_[0] != 7 && $_[0] != 8 ) { $self->{'_gc'} = shift; } else { $self->warn( "invalid genetic code index - setting to standard default (1)"); $self->{'_gc'} = 1; } } return $self->{'_gc'} || 1; #return 1 if not defined } =head2 get_request Title : get_request Usage : my $cut = $db->get_request(); Purpose: To query remote CUT with a species name Returns: a new codon usage table object Args : species name(mandatory), genetic code id(optional) =cut sub get_request { my ( $self, @args ) = @_; _check_args(@args); shift; ### can put in parameters here as well while (@_) { my $key = shift; $key =~ s/^-//; $self->$key(shift); } $self->url($URL); ###1st of all search DB to check species exists and is unique my $nameparts = join "+", $self->sp =~ /(\S+)/g; my $search_url = $self->url . "/codon/cgi-bin/spsearch.cgi?species=" . $nameparts . "&c=s"; my $rq = HTTP::Request->new( GET => $search_url ); my $reply = $self->request($rq); if ( $reply->is_error ) { $self->throw( $reply->as_string() . "\nError getting for url $search_url!\n" ); } my $content = $reply->content; return 0 unless $content; $self->debug(" reply from query is \n $content"); ##### if no matches, assign defaults - or can throw here? ###### if ( $content =~ /not found/i ) { $self->warn("organism not found -selecting human [9606] as default"); $self->sp("9606"); $self->_db("gbpri"); } else { my @names = $content =~ /species=([^"]+)/g; ### get 1st species data from report #### my @dbs = $content =~ /\[([^\]]+)\]:\s+\d+/g; ## warn if more than 1 matching species ## ## if multiple species retrieved, choose first one by default ## $self->throw("No names returned for $nameparts") unless @names; if ( @names > 1 ) { $self->warn( "too many species - not a unique species id\n" . "selecting $names[0] using database [$dbs[0]]" ); } ### now assign species and database value $self->sp( $names[0] ); $self->_db( $dbs[0] ); } ######## now get codon table , all defaults established now ##construct URL## $nameparts = $self->sp; my $CT_url = $self->url . "/codon/cgi-bin/showcodon.cgi?species=" . $nameparts . "&aa=" . $self->gc . "&style=GCG"; $self->debug("URL : $CT_url\n"); ## retrieve data in html## my $rq2 = HTTP::Request->new( GET => $CT_url ); $reply = $self->request($rq2); if ( $reply->is_error ) { $self->throw( $reply->as_string() . "\nError getting for url $CT_url!\n" ); } my $content2 = $reply->content; ## strip html tags, basic but works here $content2 =~ s/<[^>]+>//sg; $content2 =~ s/Format.*//sg; $self->debug("raw DDB table is :\n $content2"); ### and pass to Bio::CodonUsage::IO for parsing my $iostr = IO::String->new($content2); my $io = Bio::CodonUsage::IO->new( -fh => $iostr ); ##return object ## return $io->next_data; } sub _check_args { ###checks parameters for matching $QUERYKEYS my @args = @_; while ( my $key = shift @args ) { $key = lc($key); $key =~ s/\-//; if ( !exists( $QUERY_KEYS->{$key} ) ) { Bio::Root::Root->throw( "invalid parameter - must be one of [" . ( join "] [", keys %$QUERY_KEYS ) . "]" ); } shift @args; } } #### internal URL parameter not specifiable ###### sub _db { my $self = shift; if (@_) { $self->{'_db'} = shift; } return $self->{'_db'}; } 1; BioPerl-1.007002/Bio/DB/DBFetch.pm000444000766000024 2320713155576320 16332 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::DBFetch # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::DBFetch - Database object for retrieving using the dbfetch script =head1 SYNOPSIS #do not use this module directly =head1 DESCRIPTION Allows the dynamic retrieval of entries from databases using the dbfetch script at EBI: LEwww.ebi.ac.ukEcgi-binEdbfetch>. In order to make changes transparent we have host type (currently only ebi) and location (defaults to ebi) separated out. This allows later additions of more servers in different geographical locations. This is a superclass which is called by instantiable subclasses with correct parameters. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email Heikki Lehvaslaiho Eheikki-at-bioperl-dot-orgE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::DBFetch; use strict; use vars qw($MODVERSION $DEFAULTFORMAT $DEFAULTLOCATION $DEFAULTSERVERTYPE); $MODVERSION = '0.1'; use HTTP::Request::Common; use base qw(Bio::DB::WebDBSeqI); # the new way to make modules a little more lightweight BEGIN { # global vars $DEFAULTSERVERTYPE = 'dbfetch'; $DEFAULTLOCATION = 'ebi'; } =head1 Routines from Bio::DB::WebDBSeqI =head2 get_request Title : get_request Usage : my $url = $self->get_request Function: returns a HTTP::Request object Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) =cut sub get_request { my ($self, @qualifiers) = @_; my ($uids, $format) = $self->_rearrange([qw(UIDS FORMAT)], @qualifiers); $self->throw("Must specify a value for UIDs to fetch") unless defined $uids; my $tmp; my $format_string = ''; $format ||= $self->default_format; ($format, $tmp) = $self->request_format($format); $format_string = "&format=$format"; my $url = $self->location_url(); my $uid; if( ref($uids) =~ /ARRAY/i ) { $uid = join (',', @$uids); $self->warn ('The server will accept maximum of 50 entries in a request. The rest are ignored.') if scalar @$uids >50; } else { $uid = $uids; } return GET $url. $format_string. '&id='. $uid; } =head2 postprocess_data Title : postprocess_data Usage : $self->postprocess_data ( 'type' => 'string', 'location' => \$datastr); Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - 'location' either file location or string reference containing data =cut # remove occasional blank lines at top of web output sub postprocess_data { my ($self, %args) = @_; if ($args{type} eq 'string') { ${$args{location}} =~ s/^\s+//; # get rid of leading whitespace } elsif ($args{type} eq 'file') { my $F; open $F,"<", $args{location} or $self->throw("Cannot open $args{location}: $!"); my @data = <$F>; for (@data) { last unless /^\s+$/; shift @data; } open $F,">", $args{location} or $self->throw("Cannot write to $args{location}: $!"); print $F @data; close $F; } } =head2 default_format Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none =cut sub default_format { my ($self) = @_; return $self->{'_default_format'}; } =head1 Bio::DB::DBFetch specific routines =head2 get_Stream_by_id Title : get_Stream_by_id Usage : $seq = $db->get_Stream_by_id($ref); Function: Retrieves Seq objects from the server 'en masse', rather than one at a time. For large numbers of sequences, this is far superior than get_Stream_by_[id/acc](). Example : Returns : a Bio::SeqIO stream object Args : $ref : either an array reference, a filename, or a filehandle from which to get the list of unique ids/accession numbers. NOTE: for backward compatibility, this method is also called get_Stream_by_batch. =cut sub get_Stream_by_id { my ($self, $ids) = @_; return $self->get_seq_stream('-uids' => $ids, '-mode' => 'batch'); } =head2 get_Seq_by_version Title : get_Seq_by_version Usage : $seq = $db->get_Seq_by_version('X77802.1'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : version number (as a string) Throws : "version does not exist" exception =cut sub get_Seq_by_version { my ($self,$seqid) = @_; my $seqio = $self->get_Stream_by_acc([$seqid]); $self->throw("version does not exist") if( !defined $seqio ); return $seqio->next_seq(); } =head2 request_format Title : request_format Usage : my ($req_format, $ioformat) = $self->request_format; $self->request_format("genbank"); $self->request_format("fasta"); Function: Get/Set sequence format retrieval. The get-form will normally not be used outside of this and derived modules. Returns : Array of two strings, the first representing the format for retrieval, and the second specifying the corresponding SeqIO format. Args : $format = sequence format =cut sub request_format { my ($self, $value) = @_; if( defined $value ) { $value = lc $value; $self->{'_format'} = $value; return ($value, $value); } $value = $self->{'_format'}; if( $value and defined $self->formatmap->{$value} ) { return ($value, $self->formatmap->{$value}); } else { # Try to fall back to a default. return ($self->default_format, $self->default_format ); } } =head2 servertype Title : servertype Usage : my $servertype = $self->servertype $self->servertype($servertype); Function: Get/Set server type Returns : string Args : server type string [optional] =cut sub servertype { my ($self, $servertype) = @_; if( defined $servertype && $servertype ne '') { $self->throw("You gave an invalid server type ($servertype)". " - available types are ". keys %{$self->hosts}) unless( $self->hosts->{$servertype} ); $self->{'_servertype'} = $servertype; } $self->{'_servertype'} = $DEFAULTSERVERTYPE unless $self->{'_servertype'}; return $self->{'_servertype'}; } =head2 hostlocation Title : hostlocation Usage : my $location = $self->hostlocation() $self->hostlocation($location) Function: Set/Get Hostlocation Returns : string representing hostlocation Args : string specifying hostlocation [optional] =cut sub hostlocation { my ($self, $location ) = @_; my $servertype = $self->servertype; $self->throw("Must have a valid servertype defined not $servertype") unless defined $servertype; my %hosts = %{$self->hosts->{$servertype}->{'hosts'}}; if( defined $location && $location ne '' ) { $location = lc $location; if( ! $hosts{$location} ) { $self->throw("Must specify a known host, not $location,". " possible values (". join(",", sort keys %hosts ). ")"); } $self->{'_hostlocation'} = $location; } $self->{'_hostlocation'} = $DEFAULTLOCATION unless $self->{'_hostlocation'}; return $self->{'_hostlocation'}; } =head2 location_url Title : location Usage : my $url = $self->location_url() Function: Get host url Returns : string representing url Args : none =cut sub location_url { my ($self) = @_; my $servertype = $self->servertype(); my $location = $self->hostlocation(); if( ! defined $location || !defined $servertype ) { $self->throw("must have a valid hostlocation and servertype set before calling location_url"); } return sprintf($self->hosts->{$servertype}->{'baseurl'}, $self->hosts->{$servertype}->{'hosts'}->{$location}); } =head1 Bio::DB::DBFetch routines These methods allow subclasses to pass parameters. =head2 hosts Title : hosts Usage : Function: get/set for host hash Returns : Args : optional hash =cut sub hosts { my ($self, $value) = @_; if (defined $value) { $self->{'_hosts'} = $value; } unless (exists $self->{'_hosts'}) { return (''); } else { return $self->{'_hosts'}; } } =head2 formatmap Title : formatmap Usage : Function: get/set for format hash Returns : Args : optional hash =cut sub formatmap { my ($self, $value) = @_; if (defined $value) { $self->{'_formatmap'} = $value; } unless (exists $self->{'_formatmap'}) { return (''); } else { return $self->{'_formatmap'}; } } 1; __END__ BioPerl-1.007002/Bio/DB/EMBL.pm000444000766000024 1341313155576320 15610 0ustar00cjfieldsstaff000000000000# # # BioPerl module for Bio::DB::EMBL # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::EMBL - Database object interface for EMBL entry retrieval =head1 SYNOPSIS use Bio::DB::EMBL; $embl = Bio::DB::EMBL->new(); # remember that EMBL_ID does not equal GenBank_ID! $seq = $embl->get_Seq_by_id('HSFOS'); # EMBL ID print "cloneid is ", $seq->id, "\n"; # or changeing to accession number and Fasta format ... $embl->request_format('fasta'); $seq = $embl->get_Seq_by_acc('J02231'); # EMBL ACC print "cloneid is ", $seq->id, "\n"; # especially when using versions, you better be prepared # in not getting what what want eval { $seq = $embl->get_Seq_by_version('J02231.1'); # EMBL VERSION }; print "cloneid is ", $seq->id, "\n" unless $@; # or ... best when downloading very large files, prevents # keeping all of the file in memory # also don't want features, just sequence so let's save bandwidth # and request Fasta sequence $embl = Bio::DB::EMBL->new(-retrievaltype => 'tempfile' , -format => 'fasta'); my $seqio = $embl->get_Stream_by_id(['AC013798', 'AC021953'] ); while( my $clone = $seqio->next_seq ) { print "cloneid is ", $clone->id, "\n"; } =head1 DESCRIPTION Allows the dynamic retrieval of sequence objects L from the EMBL database using the dbfetch script at EBI: L. In order to make changes transparent we have host type (currently only ebi) and location (defaults to ebi) separated out. This allows later additions of more servers in different geographical locations. The functionality of this module is inherited from L which implements L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email Heikki Lehvaslaiho Eheikki-at-bioperl-dot-orgE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::EMBL; use strict; use vars qw($MODVERSION %HOSTS %FORMATMAP $DEFAULTFORMAT); $MODVERSION = '0.2'; use Bio::DB::RefSeq; use base qw(Bio::DB::DBFetch); BEGIN { # you can add your own here theoretically. %HOSTS = ( 'dbfetch' => { baseurl => 'http://%s/Tools/dbfetch/dbfetch?db=embl&style=raw', hosts => { 'ebi' => 'www.ebi.ac.uk' } } ); %FORMATMAP = ( 'embl' => 'embl', 'fasta' => 'fasta' ); $DEFAULTFORMAT = 'embl'; } =head2 new Title : new Usage : $gb = Bio::DB::GenBank->new(@options) Function: Creates a new genbank handle Returns : New genbank handle Args : -delay number of seconds to delay between fetches (3s) NOTE: There are other options that are used internally. =cut sub new { my ($class, @args ) = @_; my $self = $class->SUPER::new(@args); $self->{ '_hosts' } = {}; $self->{ '_formatmap' } = {}; $self->hosts(\%HOSTS); $self->formatmap(\%FORMATMAP); $self->{'_default_format'} = $DEFAULTFORMAT; return $self; } =head2 Bio::DB::WebDBSeqI methods Overriding WebDBSeqI method to help newbies to retrieve sequences. EMBL database is all too often passed RefSeq accessions. This redirects those calls. See L. =head2 get_Stream_by_acc Title : get_Stream_by_acc Usage : $seq = $db->get_Seq_by_acc([$acc1, $acc2]); Function: Gets a series of Seq objects by accession numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id() =cut sub get_Stream_by_acc { my ($self, $ids ) = @_; my $newdb = $self->_check_id($ids); if ($newdb && $newdb->isa('Bio::DB::RefSeq')) { return $newdb->get_seq_stream('-uids' => $ids, '-mode' => 'single'); } else { return $self->get_seq_stream('-uids' => $ids, '-mode' => 'single'); } } =head2 _check_id Title : _check_id Usage : Function: Returns : A Bio::DB::RefSeq reference or throws Args : $id(s), $string =cut sub _check_id { my ($self, $ids) = @_; # NT contigs can not be retrieved $self->throw("NT_ contigs are whole chromosome files which are not part of regular". "database distributions. Go to ftp://ftp.ncbi.nih.gov/genomes/.") if $ids =~ /NT_/; # Asking for a RefSeq from EMBL/GenBank if ($ids =~ /N._/) { $self->warn("[$ids] is not a normal sequence entry but a RefSeq entry.". " Redirecting the request.\n") if $self->verbose >= 0; return Bio::DB::RefSeq->new(-verbose => $self->verbose); } } 1; BioPerl-1.007002/Bio/DB/EntrezGene.pm000444000766000024 1264513155576320 17145 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::EntrezGene # # Please direct questions and support issues to # # Cared for by Brian Osborne bosborne at alum.mit.edu # # Copyright Brian Osborne # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::EntrezGene - Database object interface to Entrez Gene =head1 SYNOPSIS use Bio::DB::EntrezGene; my $db = Bio::DB::EntrezGene->new; my $seq = $db->get_Seq_by_id(2); # Gene id # or ... my $seqio = $db->get_Stream_by_id([2, 4693, 3064]); # Gene ids while ( my $seq = $seqio->next_seq ) { print "id is ", $seq->display_id, "\n"; } =head1 DESCRIPTION Allows the dynamic retrieval of Sequence objects from the Entrez Gene database at NCBI, via an Entrez query using Gene ids. This module requires the CPAN Bio::ASN1 module. WARNING: Please do NOT spam the Entrez web server with multiple requests. NCBI offers Batch Entrez for this purpose. =head1 NOTES The Entrez eutils API does not allow Entrez Gene queries by name as of this writing, therefore there are only get_Seq_by_id and get_Stream_by_id methods in this module, and these expect Gene ids. There are no get_Seq_by_acc or get_Stream_by_acc methods. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Brian Osborne Email bosborne at alum.mit.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::EntrezGene; use strict; use vars qw($DEFAULTFORMAT $DEFAULTMODE %PARAMSTRING); use base qw(Bio::DB::NCBIHelper); BEGIN { $DEFAULTMODE = 'single'; $DEFAULTFORMAT = 'asn.1'; %PARAMSTRING = ('batch' => {'db' => 'gene', 'usehistory' => 'y', 'tool' => 'bioperl', 'retmode' => 'asn.1'}, 'gi' => {'db' => 'gene', 'usehistory' => 'y', 'tool' => 'bioperl', 'retmode' => 'asn.1'}, 'version' => {'db' => 'gene', 'usehistory' => 'y', 'tool' => 'bioperl', 'retmode' => 'asn.1'}, 'single' => {'db' => 'gene', 'usehistory' => 'y', 'tool' => 'bioperl', 'retmode' => 'asn.1'} ); } # the new way to make modules a little more lightweight sub new { my($class, @args) = @_; my $self = $class->SUPER::new(@args); # Seems that Bio::SeqIO::entrezgene requires this: $self->{_retrieval_type} = "tempfile"; $self->request_format($self->default_format); return $self; } =head2 get_params Title : get_params Usage : my %params = $self->get_params($mode) Function: Returns key,value pairs to be passed to NCBI database for either 'batch' or 'single' sequence retrieval method Returns : A key,value pair hash Args : 'single' or 'batch' mode for retrieval =cut sub get_params { my ($self, $mode) = @_; return defined $PARAMSTRING{$mode} ? %{$PARAMSTRING{$mode}} : %{$PARAMSTRING{$DEFAULTMODE}}; } =head2 default_format Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none =cut sub default_format { return $DEFAULTFORMAT; } # from Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI =head1 Routines from Bio::DB::WebDBSeqI and Bio::DB::RandomAccessI =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id(2) Function: Gets a Bio::Seq object by its name Returns : A Bio::Seq object Args : Gene id Throws : "id does not exist" exception =head1 Routines implemented by Bio::DB::NCBIHelper =head2 get_request Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) =head2 get_Stream_by_id Title : get_Stream_by_id Usage : $stream = $db->get_Stream_by_id( [$gid1, $gid2] ); Function: Gets a series of Seq objects using Gene ids Returns : A Bio::SeqIO stream object Args : A reference to an array of Gene ids =head2 request_format Title : request_format Usage : my $format = $self->request_format; $self->request_format($format); Function: Get or set sequence format retrieval Returns : String representing format Args : $format = sequence format =cut # override to force format sub request_format { my ($self) = @_; return $self->SUPER::request_format($self->default_format()); } 1; __END__ BioPerl-1.007002/Bio/DB/Expression.pm000444000766000024 1045413155576320 17232 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::Expression # # Please direct questions and support issues to # # Cared for by Allen Day # # Copyright Allen Day # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Expression - DESCRIPTION of Object =head1 SYNOPSIS use Bio::DB::Expression; my $db = Bio::DB::Expression->new( -source => 'geo' ); my @platforms = $db->get_platforms(); foreach my $platform ( @platforms ) { my @datasets = $platform->get_datasets(); foreach my $dataset ( @datasets ) { my @samples = $dataset->get_samples(); foreach my $sample ( @samples ) { #... } } } =head1 DESCRIPTION Describe the object here =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Allen Day Email allenday@ucla.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Expression; use strict; use base qw(Bio::Root::HTTPget Bio::Root::Root); use Bio::Root::HTTPget; our $DefaultSource = 'geo'; =head2 new() Usage : my $obj = Bio::DB::Expression->new(); Function: Builds a new Bio::DB::Expression object Returns : an instance of Bio::DB::Expression Args : =cut sub new { my($class,@args) = @_; if( $class =~ /Bio::DB::Expression::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $source = $param{'-source'} || $DefaultSource; $source = "\L$source"; # normalize capitalization to lower case # normalize capitalization return unless( $class->_load_expression_module($source) ); return "Bio::DB::Expression::$source"->new(@args); } } =head2 get_platforms() Usage : Function: Example : Returns : a list of Bio::Expression::Platform objects Args : =cut sub get_platforms { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_samples() Usage : Function: Example : Returns : a list of Bio::Expression::Sample objects Args : =cut sub get_samples { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_contacts() Usage : Function: Example : Returns : a list of Bio::Expression::Contact objects Args : =cut sub get_contacts { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_datasets() Usage : Function: Example : Returns : a list of Bio::Expression::DataSet objects Args : =cut sub get_datasets { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 _load_expression_module Title : _load_expression_module Usage : *INTERNAL Bio::DB::Expression stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_expression_module { my ($self, $source) = @_; my $module = "Bio::DB::Expression::" . $source; my $ok; eval { $ok = $self->_load_module($module) }; if ( $@ ) { print STDERR $@; print STDERR <new(); $failover->add_database($db); # fail over Bio::DB::RandomAccessI.pm # this will check each database in priority, returning when # the first one succeeds $seq = $failover->get_Seq_by_id($id); =head1 DESCRIPTION This module provides fail over access to a set of Bio::DB::RandomAccessI objects. =head1 CONTACT Ewan Birney Ebirney@ebi.ac.ukE originally wrote this class. =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Failover; use strict; use base qw(Bio::Root::Root Bio::DB::RandomAccessI); sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_database'} = []; return $self; } =head2 add_database Title : add_database Usage : add_database(%db) Function: Adds a database to the Failover object Returns : Count of number of databases Args : Array of db resources Throws : Not a RandomAccessI exception =cut sub add_database { my ($self,@db) = @_; for my $db ( @db ) { if ( !ref $db || !$db->isa('Bio::DB::RandomAccessI') ) { $self->throw("Database object $db is a not a Bio::DB::RandomAccessI"); next; } push(@{$self->{'_database'}},$db); } scalar @{$self->{'_database'}}; } =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "no id" exception =cut sub get_Seq_by_id { my ($self,$id) = @_; if( !defined $id ) { $self->throw("no id is given!"); } foreach my $db ( @{$self->{'_database'}} ) { my $seq; eval { $seq = $db->get_Seq_by_id($id); }; $self->warn($@) if $@; if ( defined $seq ) { return $seq; } else { $self->warn("No sequence retrieved by database " . ref($db)); } } return; } =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "no id" exception =cut sub get_Seq_by_acc { my ($self,$id) = @_; if( !defined $id ) { $self->throw("no id is given!"); } foreach my $db ( @{$self->{'_database'}} ) { my $seq; eval { $seq = $db->get_Seq_by_acc($id); }; $self->warn($@) if $@; if ( defined $seq ) { return $seq; } else { $self->warn("No sequence retrieved by database " . ref($db)); } } return; } =head2 get_Seq_by_version Title : get_Seq_by_version Usage : $seq = $db->get_Seq_by_acc('X77802.2'); Function: Gets a Bio::Seq object by versioned accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception =cut sub get_Seq_by_version { my ($self,$id) = @_; if( !defined $id ) { $self->throw("no acc is given!"); } foreach my $db ( @{$self->{'_database'}} ) { my $seq; eval { $seq = $db->get_Seq_by_version($id); }; $self->warn($@) if $@; if ( defined $seq ) { return $seq; } else { $self->warn("No sequence retrieved by database " . ref($db)); } } return; } ## End of Package 1; __END__ BioPerl-1.007002/Bio/DB/Fasta.pm000444000766000024 3436713155576320 16142 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::Fasta # # You may distribute this module under the same terms as perl itself # =head1 NAME Bio::DB::Fasta - Fast indexed access to fasta files =head1 SYNOPSIS use Bio::DB::Fasta; # Create database from a directory of Fasta files my $db = Bio::DB::Fasta->new('/path/to/fasta/files/'); my @ids = $db->get_all_primary_ids; # Simple access my $seqstr = $db->seq('CHROMOSOME_I', 4_000_000 => 4_100_000); my $revseq = $db->seq('CHROMOSOME_I', 4_100_000 => 4_000_000); my $length = $db->length('CHROMOSOME_I'); my $header = $db->header('CHROMOSOME_I'); my $alphabet = $db->alphabet('CHROMOSOME_I'); # Access to sequence objects. See Bio::PrimarySeqI. my $seq = $db->get_Seq_by_id('CHROMOSOME_I'); my $seqstr = $seq->seq; my $subseq = $seq->subseq(4_000_000 => 4_100_000); my $trunc = $seq->trunc(4_000_000 => 4_100_000); my $length = $seq->length; # Loop through sequence objects my $stream = $db->get_PrimarySeq_stream; while (my $seq = $stream->next_seq) { # Bio::PrimarySeqI stuff } # Filehandle access my $fh = Bio::DB::Fasta->newFh('/path/to/fasta/files/'); while (my $seq = <$fh>) { # Bio::PrimarySeqI stuff } # Tied hash access tie %sequences,'Bio::DB::Fasta','/path/to/fasta/files/'; print $sequences{'CHROMOSOME_I:1,20000'}; =head1 DESCRIPTION Bio::DB::Fasta provides indexed access to a single Fasta file, several files, or a directory of files. It provides persistent random access to each sequence entry (either as a Bio::PrimarySeqI-compliant object or a string), and to subsequences within each entry, allowing you to retrieve portions of very large sequences without bringing the entire sequence into memory. Bio::DB::Fasta is based on Bio::DB::IndexedBase. See this module's documentation for details. The Fasta files may contain any combination of nucleotide and protein sequences; during indexing the module guesses the molecular type. Entries may have any line length up to 65,536 characters, and different line lengths are allowed in the same file. However, within a sequence entry, all lines must be the same length except for the last. An error will be thrown if this is not the case. The module uses /^E(\S+)/ to extract the primary ID of each sequence from the Fasta header. See -makeid in Bio::DB::IndexedBase to pass a callback routine to reversibly modify this primary ID, e.g. if you wish to extract a specific portion of the gi|gb|abc|xyz GenBank IDs. =head1 DATABASE CREATION AND INDEXING The object-oriented constructor is new(), the filehandle constructor is newFh() and the tied hash constructor is tie(). They all allow one to index a single Fasta file, several files, or a directory of files. See Bio::DB::IndexedBase. =head1 SEE ALSO L L L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ For BioPerl-style access, the following methods are provided: =head2 get_Seq_by_id Title : get_Seq_by_id, get_Seq_by_acc, get_Seq_by_primary_id Usage : my $seq = $db->get_Seq_by_id($id); Function: Given an ID, fetch the corresponding sequence from the database. Returns : A Bio::PrimarySeq::Fasta object (Bio::PrimarySeqI compliant) Note that to save resource, Bio::PrimarySeq::Fasta sequence objects only load the sequence string into memory when requested using seq(). See L for methods provided by the sequence objects returned from get_Seq_by_id() and get_PrimarySeq_stream(). Args : ID =head2 get_PrimarySeq_stream Title : get_PrimarySeq_stream Usage : my $stream = $db->get_PrimarySeq_stream(); Function: Get a stream of Bio::PrimarySeq::Fasta objects. The stream supports a single method, next_seq(). Each call to next_seq() returns a new Bio::PrimarySeq::Fasta sequence object, until no more sequences remain. Returns : A Bio::DB::Indexed::Stream object Args : None =head1 For simple access, the following methods are provided: =cut package Bio::DB::Fasta; use strict; use IO::File; use File::Spec; use Bio::PrimarySeqI; use base qw(Bio::DB::IndexedBase); our $obj_class = 'Bio::PrimarySeq::Fasta'; our $file_glob = '*.{fa,FA,fasta,FASTA,fast,FAST,dna,DNA,fna,FNA,faa,FAA,fsa,FSA}'; =head2 new Title : new Usage : my $db = Bio::DB::Fasta->new( $path, %options); Function: Initialize a new database object. When indexing a directory, files ending in .fa,fasta,fast,dna,fna,faa,fsa are indexed by default. Returns : A new Bio::DB::Fasta object. Args : A single file, or path to dir, or arrayref of files Optional arguments: see Bio::DB::IndexedBase =cut sub _calculate_offsets { # Bio::DB::IndexedBase calls this to calculate offsets my ($self, $fileno, $file, $offsets) = @_; my $fh = IO::File->new($file) or $self->throw( "Could not open $file: $!"); binmode $fh; warn "Indexing $file\n" if $self->{debug}; my ($offset, @ids, $linelen, $alphabet, $headerlen, $count, $seq_lines, $last_line, %offsets); my ($l3_len, $l2_len, $l_len, $blank_lines) = (0, 0, 0, 0); my $termination_length = $self->{termination_length}; while (my $line = <$fh>) { # Account for crlf-terminated Windows files if (index($line, '>') == 0) { if ($line =~ /^>(\S+)/) { print STDERR "Indexed $count sequences...\n" if $self->{debug} && (++$count%1000) == 0; # please, do not enforce arbitrary line length requirements. # It's good practice but not enforced. #$self->_check_linelength($linelen); my $pos = tell($fh); if (@ids) { my $strlen = $pos - $offset - length($line); $strlen -= $termination_length * $seq_lines; my $ppos = &{$self->{packmeth}}($offset, $strlen, $strlen, $linelen, $headerlen, $alphabet, $fileno); $alphabet = Bio::DB::IndexedBase::NA; for my $id (@ids) { $offsets->{$id} = $ppos; } } @ids = $self->_makeid($line); ($offset, $headerlen, $linelen, $seq_lines) = ($pos, length $line, 0, 0); ($l3_len, $l2_len, $l_len, $blank_lines) = (0, 0, 0, 0); } else { # Catch bad header lines, bug 3172 $self->throw("FASTA header doesn't match '>(\\S+)': $line"); } } elsif ($line !~ /\S/) { # Skip blank line $blank_lines++; next; } else { # Need to check every line :( $l3_len = $l2_len; $l2_len = $l_len; $l_len = length $line; if (Bio::DB::IndexedBase::DIE_ON_MISSMATCHED_LINES) { if ( ($l3_len > 0) && ($l2_len > 0) && ($l3_len != $l2_len) ) { my $fap = substr($line, 0, 20).".."; $self->throw("Each line of the fasta entry must be the same ". "length except the last. Line above #$. '$fap' is $l2_len". " != $l3_len chars."); } if ($blank_lines) { # Blank lines not allowed in entry $self->throw("Blank lines can only precede header lines, ". "found preceding line #$."); } } $linelen ||= length $line; $alphabet ||= $self->_guess_alphabet($line); $seq_lines++; } $last_line = $line; } # Process last entry $self->_check_linelength($linelen); my $pos = tell $fh; if (@ids) { my $strlen = $pos - $offset; if ($linelen == 0) { # yet another pesky empty chr_random.fa file $strlen = 0; } else { if ($last_line !~ /\s$/) { $seq_lines--; } $strlen -= $termination_length * $seq_lines; } my $ppos = &{$self->{packmeth}}($offset, $strlen, $strlen, $linelen, $headerlen, $alphabet, $fileno); for my $id (@ids) { $offsets->{$id} = $ppos; } } return \%offsets; } =head2 seq Title : seq, sequence, subseq Usage : # Entire sequence string my $seqstr = $db->seq($id); # Subsequence my $subseqstr = $db->seq($id, $start, $stop, $strand); # or... my $subseqstr = $db->seq($compound_id); Function: Get a subseq of a sequence from the database. For your convenience, the sequence to extract can be specified with any of the following compound IDs: $db->seq("$id:$start,$stop") $db->seq("$id:$start..$stop") $db->seq("$id:$start-$stop") $db->seq("$id:$start,$stop/$strand") $db->seq("$id:$start..$stop/$strand") $db->seq("$id:$start-$stop/$strand") $db->seq("$id/$strand") In the case of DNA or RNA sequence, if $stop is less than $start, then the reverse complement of the sequence is returned. Avoid using it if possible since this goes against Bio::Seq conventions. Returns : A string Args : ID of sequence to retrieve or Compound ID of subsequence to fetch or ID, optional start (defaults to 1), optional end (defaults to length of sequence) and optional strand (defaults to 1). =cut sub subseq { my ($self, $id, $start, $stop, $strand) = @_; $self->throw('Need to provide a sequence ID') if not defined $id; ($id, $start, $stop, $strand) = $self->_parse_compound_id($id, $start, $stop, $strand); my $data; my $fh = $self->_fh($id) or return; my $filestart = $self->_calc_offset($id, $start); my $filestop = $self->_calc_offset($id, $stop ); seek($fh, $filestart,0); read($fh, $data, $filestop-$filestart+1); $data = Bio::DB::IndexedBase::_strip_crnl($data); if ($strand == -1) { # Reverse-complement the sequence $data = Bio::PrimarySeqI::_revcom_from_string($self, $data, $self->alphabet($id)); } return $data; } *seq = *sequence = \&subseq; =head2 length Title : length Usage : my $length = $qualdb->length($id); Function: Get the number of residues in the indicated sequence. Returns : Number Args : ID of entry =head2 header Title : header Usage : my $header = $db->header($id); Function: Get the header line (ID and description fields) of the specified sequence. Returns : String Args : ID of sequence =cut sub header { my ($self, $id) = @_; $self->throw('Need to provide a sequence ID') if not defined $id; my ($offset, $headerlen) = (&{$self->{unpackmeth}}($self->{offsets}{$id}))[0,4]; $offset -= $headerlen; my $data; my $fh = $self->_fh($id) or return; seek($fh, $offset, 0); read($fh, $data, $headerlen); # On Windows chomp remove '\n' but leaves '\r' # when reading '\r\n' in binary mode $data = Bio::DB::IndexedBase::_strip_crnl($data); substr($data, 0, 1) = ''; return $data; } =head2 alphabet Title : alphabet Usage : my $alphabet = $db->alphabet($id); Function: Get the molecular type of the indicated sequence: dna, rna or protein Returns : String Args : ID of sequence =cut #------------------------------------------------------------- # Bio::PrimarySeqI compatibility # package Bio::PrimarySeq::Fasta; use overload '""' => 'display_id'; use base qw(Bio::Root::Root Bio::PrimarySeqI); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($db, $id, $start, $stop) = $self->_rearrange( [qw(DATABASE ID START STOP)], @args); $self->{db} = $db; $self->{id} = $id; $self->{stop} = $stop || $db->length($id); $self->{start} = $start || ($self->{stop} > 0 ? 1 : 0); # handle 0-length seqs return $self; } sub fetch_sequence { return shift->seq(@_); } sub seq { my $self = shift; return $self->{db}->seq($self->{id}, $self->{start}, $self->{stop}); } sub subseq { my $self = shift; return $self->trunc(@_)->seq(); } sub trunc { # Override Bio::PrimarySeqI trunc() method. This way, we create an object # that does not store the sequence in memory. my ($self, $start, $stop) = @_; $self->throw("Stop cannot be smaller than start") if $stop < $start; if ($self->{start} <= $self->{stop}) { $start = $self->{start}+$start-1; $stop = $self->{start}+$stop-1; } else { $start = $self->{start}-($start-1); $stop = $self->{start}-($stop-1); } return $self->new( $self->{db}, $self->{id}, $start, $stop ); } sub is_circular { my $self = shift; return $self->{is_circular}; } sub display_id { my $self = shift; return $self->{id}; } sub accession_number { my $self = shift; return 'unknown'; } sub primary_id { # Following Bio::PrimarySeqI, since this sequence has no accession number, # its primary_id should be a stringified memory location. my $self = shift; return overload::StrVal($self); } sub can_call_new { return 0; } sub alphabet { my $self = shift; return $self->{db}->alphabet($self->{id}); } sub revcom { # Override Bio::PrimarySeqI revcom() with optimized method. my $self = shift; return $self->new(@{$self}{'db', 'id', 'stop', 'start'}); } sub length { # Get length from sequence location, not the sequence string (too expensive) my $self = shift; return $self->{start} < $self->{stop} ? $self->{stop} - $self->{start} + 1 : $self->{start} - $self->{stop} + 1 ; } sub description { my $self = shift; my $header = $self->{'db'}->header($self->{id}); # Remove the ID from the header return (split(/\s+/, $header, 2))[1]; } *desc = \&description; 1; BioPerl-1.007002/Bio/DB/FileCache.pm000444000766000024 1606413155576320 16701 0ustar00cjfieldsstaff000000000000# # POD documentation - main docs before the code # # =head1 NAME Bio::DB::FileCache - In file cache for BioSeq objects =head1 SYNOPSIS $cachedb = Bio::DB::FileCache->new($real_db); # # $real_db is a Bio::DB::RandomAccessI database # $seq = $cachedb->get_Seq_by_id('ROA1_HUMAN'); # # $seq is a Bio::Seq object # # more control provided with named-parameter form $cachedb = Bio::DB::FileCache->new( -seqdb => $real_db, -file => $path, -keep => $flag, ); =head1 DESCRIPTION This is a disk cache system which saves the objects returned by Bio::DB::RandomAccessI on disk. The disk cache grows without limit, while the process is running, but is automatically unlinked at process termination unless the -keep flag is set. This module requires DB_File and Storable. =head1 CONTACT Lincoln Stein Elstein@cshl.orgE =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::FileCache; use DB_File; use Storable qw(freeze thaw); use Fcntl qw(O_CREAT O_RDWR O_RDONLY); use File::Temp 'tmpnam'; use strict; use base qw(Bio::Root::Root Bio::DB::SeqI); use Bio::Seq::RichSeq; use Bio::Location::Split; use Bio::Location::Fuzzy; use Bio::Seq; use Bio::SeqFeature::Generic; use Bio::Species; use Bio::Annotation::Collection; =head2 new Title : new Usage : $db = Bio::DB::FileCache->new( -seqdb => $db, # Bio::DB::RandomAccessI database -file => $path, # path to index file -keep => $flag, # don't unlink index file ) Function: creates a new on-disk cache Returns : a Bio::DB::RandomAccessI database Args : as above Throws : "Must be a randomaccess database" exception "Could not open primary index file" exception If no index file is specified, will create a temporary file in your system's temporary file directory. The name of this temporary file can be retrieved using file_name(). =cut #' sub new { my ($class,@args) = @_; my $self = Bio::Root::Root->new(); bless $self,$class; my ($seqdb,$file_name,$keep) = $self->_rearrange([qw(SEQDB FILE KEEP)],@args); if( !defined $seqdb || !ref $seqdb || ! $seqdb->isa('Bio::DB::RandomAccessI') ) { $self->throw("Must be a randomaccess database not a [$seqdb]"); } $self->seqdb($seqdb); $file_name ||= tmpnam(); $self->file_name($file_name); $self->keep($keep); $self->_open_database($file_name); return $self; } =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception =cut sub get_Seq_by_id{ my ($self,$id) = @_; # look in the cache first my $obj = $self->_get('id' => $id); return $obj if defined $obj; # get object from seqdb $obj = $self->seqdb->get_Seq_by_id($id); $self->_store('id' => $id, $obj); return $obj; } =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception =cut sub get_Seq_by_acc{ my ($self,$acc) = @_; # look in the cache first my $obj = $self->_get('acc' => $acc); return $obj if defined $obj; # get object from seqdb $obj = $self->seqdb->get_Seq_by_acc($acc); $self->_store('acc' => $acc, $obj); return $obj; } =head2 seqdb Title : seqdb Usage : $seqdb = $db->seqdb([$seqdb]) Function: gets/sets the Bio::DB::RandomAccessI database Returns : a Bio::DB::RandomAccessI database Args : new sequence database (optional) Throws : nothing =cut sub seqdb { my ($self, $seqdb) = @_; if ($seqdb) { $self->{'seqdb'} = $seqdb; } else { return $self->{'seqdb'}; } } =head2 file_name Title : file_name Usage : $path = $db->file_name([$file_name]) Function: gets/sets the name of the cache file Returns : a path Args : new cache file name (optional) Throws : nothing It probably isn't useful to set the cache file name after you've opened it. =cut #' sub file_name { my $self = shift; my $d = $self->{file_name}; $self->{file_name} = shift if @_; $d; } =head2 keep Title : keep Usage : $keep = $db->keep([$flag]) Function: gets/sets the value of the "keep" flag Returns : current value Args : new value (optional) Throws : nothing The keep flag will cause the index file to be unlinked when the process exits. Since on some operating systems (Unix, OS/2) the unlinking occurs during the new() call immediately after opening the file, it probably isn't safe to change this value. =cut #' sub keep { my $self = shift; my $d = $self->{keep}; $self->{keep} = shift if @_; $d; } =head2 db Title : db Usage : $db->db Function: returns tied hash to index database Returns : a Berkeley DB tied hashref Args : none Throws : nothing =cut sub db { shift->{db} } =head2 flush Title : flush Usage : $db->flush Function: flushes the cache Returns : nothing Args : none Throws : nothing =cut sub flush { my $db = shift->db or return; %{$db} = (); } sub _get { my $self = shift; my ($type,$id) = @_; my $serialized = $self->db->{"${type}_${id}"}; my $obj = thaw($serialized); $obj; } sub _store { my $self = shift; my ($type,$id,$obj) = @_; if( ! defined $obj ) { # bug #1628 $self->debug("tried to store an undefined value for $id, skipping"); return; } my $serialized = freeze($obj); $self->db->{"${type}_${id}"} = $serialized; } =head2 get_Seq_by_version Title : get_Seq_by_version Usage : $seq = $db->get_Seq_by_version('X77802.1'); Function: Gets a Bio::Seq object by sequence version Returns : A Bio::Seq object Args : accession.version (as a string) Throws : "acc.version does not exist" exception =cut sub get_Seq_by_version{ my ($self,@args) = @_; $self->throw("Not implemented it"); } sub DESTROY { my $self = shift; unlink $self->file_name unless $self->keep; } sub _open_database { my $self = shift; my $file = shift; my $flags = O_CREAT|O_RDWR; my %db; tie(%db,'DB_File',$file,$flags,0666,$DB_BTREE) or $self->throw("Could not open primary index file"); $self->{db} = \%db; unlink $file unless $self->keep; } ## End of Package 1; BioPerl-1.007002/Bio/DB/Flat.pm000444000766000024 4153213155576320 15762 0ustar00cjfieldsstaff000000000000# # # BioPerl module for Bio::DB::Flat # # Please direct questions and support issues to # # Cared for by Lincoln Stein # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Flat - Interface for indexed flat files =head1 SYNOPSIS $db = Bio::DB::Flat->new(-directory => '/usr/share/embl', -dbname => 'mydb', -format => 'embl', -index => 'bdb', -write_flag => 1); $db->build_index('/usr/share/embl/primate.embl', '/usr/share/embl/protists.embl'); $seq = $db->get_Seq_by_id('HSFOS'); @sequences = $db->get_Seq_by_acc('DIV' => 'primate'); $raw = $db->fetch_raw('HSFOS'); =head1 DESCRIPTION This object provides the basic mechanism to associate positions in files with primary and secondary name spaces. Unlike Bio::Index::Abstract (see L), this is specialized to work with the "flat index" and BerkeleyDB indexed flat file formats worked out at the 2002 BioHackathon. This object is a general front end to the underlying databases. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Lincoln Stein Email - lstein@cshl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with an "_" (underscore). =cut # Let the code begin... package Bio::DB::Flat; use File::Spec; use base qw(Bio::Root::Root Bio::DB::RandomAccessI); use constant CONFIG_FILE_NAME => 'config.dat'; =head2 new Title : new Usage : my $db = Bio::DB::Flat->new( -directory => $root_directory, -dbname => 'mydb', -write_flag => 1, -index => 'bdb', -verbose => 0, -out => 'outputfile', -format => 'genbank'); Function: create a new Bio::DB::Flat object Returns : new Bio::DB::Flat object Args : -directory Root directory containing "config.dat" -write_flag If true, allows creation/updating. -verbose Verbose messages -out File to write to when write_seq invoked -index 'bdb' or 'binarysearch' Status : Public The required -directory argument indicates where the flat file indexes will be stored. The build_index() and write_seq() methods will automatically create subdirectories of this root directory. Each subdirectory will contain a human-readable configuration file named "config.dat" that specifies where the individual indexes are stored. The required -dbname argument gives a name to the database index. The index files will actually be stored in a like-named subdirectory underneath the root directory. The -write_flag enables writing new entries into the database as well as the creation of the indexes. By default the indexes will be opened read only. -index is one of "bdb" or "binarysearch" and indicates the type of index to generate. "bdb" corresponds to Berkeley DB. You *must* be using BerkeleyDB version 2 or higher, and have the Perl BerkeleyDB extension installed (DB_File will *not* work). "binarysearch" corresponds to the OBDA "flat" indexed file. The -out argument specifies the output file for writing objects created with write_seq(). The -format argument specifies the format of the input file or files. If the file suffix is one that Bioperl can already associate with a format then this is optional. =cut sub new { my $class = shift; $class = ref($class) if ref($class); my $self = $class->SUPER::new(@_); # first we initialize ourselves my ($flat_directory,$dbname,$format) = $self->_rearrange([qw(DIRECTORY DBNAME FORMAT)],@_); defined $flat_directory or $self->throw('Please supply a -directory argument'); defined $dbname or $self->throw('Please supply a -dbname argument'); # set values from configuration file $self->directory($flat_directory); $self->dbname($dbname); $self->throw("Base directory $flat_directory doesn't exist") unless -e $flat_directory; $self->throw("$flat_directory isn't a directory") unless -d _; my $dbpath = File::Spec->catfile($flat_directory,$dbname); unless (-d $dbpath) { $self->debug("creating db directory $dbpath\n"); mkdir $dbpath,0777 or $self->throw("Can't create $dbpath: $!"); } $self->_read_config(); # but override with initialization values $self->_initialize(@_); $self->throw('you must specify an indexing scheme') unless $self->indexing_scheme; # now we figure out what subclass to instantiate my $index_type = $self->indexing_scheme eq 'BerkeleyDB/1' ? 'BDB' :$self->indexing_scheme eq 'flat/1' ? 'Binary' :$self->throw("unknown indexing scheme: " . $self->indexing_scheme); $format = $self->file_format; # because Michele and Lincoln did it differently # Michele's way is via a standalone concrete class if ($index_type eq 'Binary') { my $child_class = 'Bio::DB::Flat::BinarySearch'; eval "use $child_class"; $self->throw($@) if $@; push @_, ('-format', $format); return $child_class->new(@_); } # Lincoln uses Bio::SeqIO style delegation. my $child_class= "Bio\:\:DB\:\:Flat\:\:$index_type\:\:\L$format"; eval "use $child_class"; $self->throw($@) if $@; # rebless & reinitialize with the new class # (this prevents subclasses from forgetting to call our own initialization) bless $self,$child_class; $self->_initialize(@_); $self->_set_namespaces(@_); $self; } sub _initialize { my $self = shift; my ($flat_write_flag,$dbname,$flat_indexing,$flat_verbose,$flat_outfile,$flat_format) = $self->_rearrange([qw(WRITE_FLAG DBNAME INDEX VERBOSE OUT FORMAT)],@_); $self->write_flag($flat_write_flag) if defined $flat_write_flag; if (defined $flat_indexing) { # very permissive $flat_indexing = 'BerkeleyDB/1' if $flat_indexing =~ /bdb/; $flat_indexing = 'flat/1' if $flat_indexing =~ /^(flat|binary)/; $self->indexing_scheme($flat_indexing); } $self->verbose($flat_verbose) if defined $flat_verbose; $self->dbname($dbname) if defined $dbname; $self->out_file($flat_outfile) if defined $flat_outfile; $self->file_format($flat_format) if defined $flat_format; } sub _set_namespaces { my $self = shift; $self->primary_namespace($self->default_primary_namespace) unless defined $self->{flat_primary_namespace}; $self->secondary_namespaces($self->default_secondary_namespaces) unless defined $self->{flat_secondary_namespaces}; $self->file_format($self->default_file_format) unless defined $self->{flat_format}; } =head2 new_from_registry Title : new_from_registry Usage : $db = Bio::DB::Flat->new_from_registry(%config) Function: creates a new Bio::DB::Flat object in a Bio::DB::Registry- compatible fashion Returns : new Bio::DB::Flat Args : provided by the registry, see below Status : Public The following registry-configuration tags are recognized: location Root of the indexed flat file; corresponds to the new() method's -directory argument. =cut sub new_from_registry { my ($self,%config) = @_; my $location = $config{'location'} or $self->throw('location tag must be specified.'); my $dbname = $config{'dbname'} or $self->throw('dbname tag must be specified.'); my $db = $self->new(-directory => $location, -dbname => $dbname, ); $db; } # accessors sub directory { my $self = shift; my $d = $self->{flat_directory}; $self->{flat_directory} = shift if @_; $d; } sub write_flag { my $self = shift; my $d = $self->{flat_write_flag}; $self->{flat_write_flag} = shift if @_; $d; } sub verbose { my $self = shift; my $d = $self->{flat_verbose}; $self->{flat_verbose} = shift if @_; $d; } sub out_file { my $self = shift; my $d = $self->{flat_outfile}; $self->{flat_outfile} = shift if @_; $d; } sub dbname { my $self = shift; my $d = $self->{flat_dbname}; $self->{flat_dbname} = shift if @_; $d; } sub primary_namespace { my $self = shift; my $d = $self->{flat_primary_namespace}; $self->{flat_primary_namespace} = shift if @_; $d; } # get/set secondary namespace(s) # pass an array ref. # get an array ref in scalar context, list in list context. sub secondary_namespaces { my $self = shift; my $d = $self->{flat_secondary_namespaces}; $self->{flat_secondary_namespaces} = (ref($_[0]) eq 'ARRAY' ? shift : [@_]) if @_; return unless $d; $d = [$d] if $d && ref($d) ne 'ARRAY'; # just paranoia return wantarray ? @$d : $d; } # return the file format sub file_format { my $self = shift; my $d = $self->{flat_format}; $self->{flat_format} = shift if @_; $d; } # return the alphabet sub alphabet { my $self = shift; my $d = $self->{flat_alphabet}; $self->{flat_alphabet} = shift if @_; $d; } sub parse_one_record { my $self = shift; my $fh = shift; my $parser = $self->{cached_parsers}{fileno($fh)} ||= Bio::SeqIO->new(-fh=>$fh,-format=>$self->default_file_format); my $seq = $parser->next_seq or return; $self->{flat_alphabet} ||= $seq->alphabet; my $ids = $self->seq_to_ids($seq); return $ids; } # return the indexing scheme sub indexing_scheme { my $self = shift; my $d = $self->{flat_indexing}; $self->{flat_indexing} = shift if @_; $d; } sub add_flat_file { my $self = shift; my ($file_path,$file_length,$nf) = @_; # check that file_path is absolute unless (File::Spec->file_name_is_absolute($file_path)) { $file_path = File::Spec->rel2abs($file_path); } -r $file_path or $self->throw("flat file $file_path cannot be read: $!"); my $current_size = -s _; if (defined $file_length) { $current_size == $file_length or $self->throw("flat file $file_path has changed size. Was $file_length bytes; now $current_size"); } else { $file_length = $current_size; } unless (defined $nf) { $self->{flat_file_index} = 0 unless exists $self->{flat_file_index}; $nf = $self->{flat_file_index}++; } $self->{flat_flat_file_path}{$nf} = $file_path; $self->{flat_flat_file_no}{$file_path} = $nf; $nf; } sub write_config { my $self = shift; $self->write_flag or $self->throw("cannot write configuration file because write_flag is not set"); my $path = $self->_config_path; open my $F, '>', $path or $self->throw("Could not write file '$path': $!"); my $index_type = $self->indexing_scheme; print $F "index\t$index_type\n"; my $format = $self->file_format; my $alphabet = $self->alphabet; my $alpha = $alphabet ? "/$alphabet" : ''; print $F "format\tURN:LSID:open-bio.org:${format}${alpha}\n"; my @filenos = $self->_filenos or $self->throw("cannot write config file because no flat files defined"); for my $nf (@filenos) { my $path = $self->{flat_flat_file_path}{$nf}; my $size = -s $path; print $F join("\t","fileid_$nf",$path,$size),"\n"; } # write primary namespace my $primary_ns = $self->primary_namespace or $self->throw('cannot write config file because no primary namespace defined'); print $F join("\t",'primary_namespace',$primary_ns),"\n"; # write secondary namespaces my @secondary = $self->secondary_namespaces; print $F join("\t",'secondary_namespaces',@secondary),"\n"; close $F or $self->throw("close error on $path: $!"); } sub files { my $self = shift; return unless $self->{flat_flat_file_no}; return keys %{$self->{flat_flat_file_no}}; } sub write_seq { my $self = shift; my $seq = shift; $self->write_flag or $self->throw("cannot write sequences because write_flag is not set"); my $file = $self->out_file or $self->throw('no outfile defined; use the -out argument to new()'); my $seqio = $self->{flat_cached_parsers}{$file} ||= Bio::SeqIO->new(-Format => $self->file_format, -file => ">$file") or $self->throw("couldn't create Bio::SeqIO object"); my $fh = $seqio->_fh or $self->throw("couldn't get filehandle from Bio::SeqIO object"); my $offset = tell($fh); $seqio->write_seq($seq); my $length = tell($fh)-$offset; my $ids = $self->seq_to_ids($seq); $self->_store_index($ids,$file,$offset,$length); $self->{flat_outfile_dirty}++; } sub close { my $self = shift; return unless $self->{flat_outfile_dirty}; $self->write_config; delete $self->{flat_outfile_dirty}; delete $self->{flat_cached_parsers}{$self->out_file}; } sub _filenos { my $self = shift; return unless $self->{flat_flat_file_path}; return keys %{$self->{flat_flat_file_path}}; } # read the configuration file sub _read_config { my $self = shift; my $path = $self->_config_path; return unless -e $path; open my $F, '<', $path or $self->throw("Could not read file '$path': $!"); my %config; while (<$F>) { chomp; my ($tag,@values) = split "\t"; $config{$tag} = \@values; } CORE::close $F or $self->throw("close error on $path: $!"); $config{index}[0] =~ m~(flat/1|BerkeleyDB/1)~ or $self->throw("invalid configuration file $path: no index line"); $self->indexing_scheme($1); if ($config{format}) { # handle LSID format if ($config{format}[0] =~ /^URN:LSID:open-bio\.org:(\w+)(?:\/(\w+))/) { $self->file_format($1); $self->alphabet($2); } else { # compatibility with older versions $self->file_format($config{format}[0]); } } # set up primary namespace my $primary_namespace = $config{primary_namespace}[0] or $self->throw("invalid configuration file $path: no primary namespace defined"); $self->primary_namespace($primary_namespace); # set up secondary namespaces (may be empty) $self->secondary_namespaces($config{secondary_namespaces}); # get file paths and their normalization information my @normalized_files = grep {$_ ne ''} map {/^fileid_(\S+)/ && $1} keys %config; for my $nf (@normalized_files) { my ($file_path,$file_length) = @{$config{"fileid_${nf}"}}; $self->add_flat_file($file_path,$file_length,$nf); } 1; } sub _config_path { my $self = shift; $self->_catfile($self->_config_name); } sub _catfile { my $self = shift; my $component = shift; File::Spec->catfile($self->directory,$self->dbname,$component); } sub _config_name { CONFIG_FILE_NAME } sub _path2fileno { my $self = shift; my $path = shift; return $self->add_flat_file($path) unless exists $self->{flat_flat_file_no}{$path}; $self->{flat_flat_file_no}{$path}; } sub _fileno2path { my $self = shift; my $fileno = shift; $self->{flat_flat_file_path}{$fileno}; } sub _files { my $self = shift; my $paths = $self->{flat_flat_file_no}; return keys %$paths; } =head2 fetch Title : fetch Usage : $index->fetch( $id ) Function: Returns a Bio::Seq object from the index Example : $seq = $index->fetch( 'dJ67B12' ) Returns : Bio::Seq object Args : ID Deprecated. Use get_Seq_by_id instead. =cut sub fetch { shift->get_Seq_by_id(@_) } =head2 To Be Implemented in Subclasses The following methods MUST be implemented by subclasses. =cut # create real live Bio::Seq object sub get_Seq_by_id { my $self = shift; my $id = shift; $self->throw_not_implemented; } # fetch array of Bio::Seq objects sub get_Seq_by_acc { my $self = shift; return $self->get_Seq_by_id(shift) if @_ == 1; my ($ns,$key) = @_; $self->throw_not_implemented; } sub fetch_raw { my ($self,$id,$namespace) = @_; $self->throw_not_implemented; } sub default_file_format { my $self = shift; $self->throw_not_implemented; } sub _store_index { my $self = shift; my ($ids,$file,$offset,$length) = @_; $self->throw_not_implemented; } =head2 May Be Overridden in Subclasses The following methods MAY be overridden by subclasses. =cut sub default_primary_namespace { return "ACC"; } sub default_secondary_namespaces { return; } sub seq_to_ids { my $self = shift; my $seq = shift; my %ids; $ids{$self->primary_namespace} = $seq->accession_number; \%ids; } sub DESTROY { my $self = shift; $self->close; } 1; BioPerl-1.007002/Bio/DB/GFF.pm000444000766000024 34751213155576320 15525 0ustar00cjfieldsstaff000000000000 =head1 NAME Bio::DB::GFF -- Storage and retrieval of sequence annotation data =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysqlopt', -dsn => 'dbi:mysql:elegans'); # fetch a 1 megabase segment of sequence starting at landmark "ZK909" my $segment = $db->segment('ZK909', 1 => 1000000); # pull out all transcript features my @transcripts = $segment->features('transcript'); # for each transcript, total the length of the introns my %totals; for my $t (@transcripts) { my @introns = $t->Intron; $totals{$t->name} += $_->length foreach @introns; } # Sort the exons of the first transcript by position my @exons = sort {$a->start <=> $b->start} $transcripts[0]->Exon; # Get a region 1000 bp upstream of first exon my $upstream = $exons[0]->subseq(-1000,0); # get its DNA my $dna = $upstream->seq; # and get all curated polymorphisms inside it @polymorphisms = $upstream->contained_features('polymorphism:curated'); # get all feature types in the database my @types = $db->types; # count all feature types in the segment my %type_counts = $segment->types(-enumerate=>1); # get an iterator on all curated features of type 'exon' or 'intron' my $iterator = $db->get_seq_stream(-type => ['exon:curated','intron:curated']); while (my $s = $iterator->next_seq) { print $s,"\n"; } # find all transcripts annotated as having function 'kinase' my $iterator = $db->get_seq_stream(-type=>'transcript', -attributes=>{Function=>'kinase'}); while (my $s = $iterator->next_seq) { print $s,"\n"; } =head1 DESCRIPTION Bio::DB::GFF provides fast indexed access to a sequence annotation database. It supports multiple database types (ACeDB, relational), and multiple schemas through a system of adaptors and aggregators. The following operations are supported by this module: - retrieving a segment of sequence based on the ID of a landmark - retrieving the DNA from that segment - finding all annotations that overlap with the segment - finding all annotations that are completely contained within the segment - retrieving all annotations of a particular type, either within a segment, or globally - conversion from absolute to relative coordinates and back again, using any arbitrary landmark for the relative coordinates - using a sequence segment to create new segments based on relative offsets The data model used by Bio::DB::GFF is compatible with the GFF flat file format (L). The module can load a set of GFF files into the database, and serves objects that have methods corresponding to GFF fields. The objects returned by Bio::DB::GFF are compatible with the SeqFeatureI interface, allowing their use by the Bio::Graphics and Bio::DAS modules. =head2 Auxiliary Scripts The bioperl distribution includes several scripts that make it easier to work with Bio::DB::GFF databases. They are located in the scripts directory under a subdirectory named Bio::DB::GFF: =over 4 =item * bp_load_gff.pl This script will load a Bio::DB::GFF database from a flat GFF file of sequence annotations. Only the relational database version of Bio::DB::GFF is supported. It can be used to create the database from scratch, as well as to incrementally load new data. This script takes a --fasta argument to load raw DNA into the database as well. However, GFF databases do not require access to the raw DNA for most of their functionality. load_gff.pl also has a --upgrade option, which will perform a non-destructive upgrade of older schemas to newer ones. =item * bp_bulk_load_gff.pl This script will populate a Bio::DB::GFF database from a flat GFF file of sequence annotations. Only the MySQL database version of Bio::DB::GFF is supported. It uses the "LOAD DATA INFILE" query in order to accelerate loading considerably; however, it can only be used for the initial load, and not for updates. This script takes a --fasta argument to load raw DNA into the database as well. However, GFF databases do not require access to the raw DNA for most of their functionality. =item * bp_fast_load_gff.pl This script is as fast as bp_bulk_load_gff.pl but uses Unix pipe tricks to allow for incremental updates. It only supports the MySQL database version of Bio::DB::GFF and is guaranteed not to work on non-Unix platforms. Arguments are the same as bp_load_gff.pl =item * gadfly_to_gff.pl This script will convert the GFF-like format used by the Berkeley Drosophila Sequencing project into a format suitable for use with this module. =item * sgd_to_gff.pl This script will convert the tab-delimited feature files used by the Saccharomyces Genome Database into a format suitable for use with this module. =back =head2 GFF Fundamentals The GFF format is a flat tab-delimited file, each line of which corresponds to an annotation, or feature. Each line has nine columns and looks like this: Chr1 curated CDS 365647 365963 . + 1 Transcript "R119.7" The 9 columns are as follows: =over 4 =item 1. reference sequence This is the ID of the sequence that is used to establish the coordinate system of the annotation. In the example above, the reference sequence is "Chr1". =item 2. source The source of the annotation. This field describes how the annotation was derived. In the example above, the source is "curated" to indicate that the feature is the result of human curation. The names and versions of software programs are often used for the source field, as in "tRNAScan-SE/1.2". =item 3. method The annotation method. This field describes the type of the annotation, such as "CDS". Together the method and source describe the annotation type. =item 4. start position The start of the annotation relative to the reference sequence. =item 5. stop position The stop of the annotation relative to the reference sequence. Start is always less than or equal to stop. =item 6. score For annotations that are associated with a numeric score (for example, a sequence similarity), this field describes the score. The score units are completely unspecified, but for sequence similarities, it is typically percent identity. Annotations that don't have a score can use "." =item 7. strand For those annotations which are strand-specific, this field is the strand on which the annotation resides. It is "+" for the forward strand, "-" for the reverse strand, or "." for annotations that are not stranded. =item 8. phase For annotations that are linked to proteins, this field describes the phase of the annotation on the codons. It is a number from 0 to 2, or "." for features that have no phase. =item 9. group GFF provides a simple way of generating annotation hierarchies ("is composed of" relationships) by providing a group field. The group field contains the class and ID of an annotation which is the logical parent of the current one. In the example given above, the group is the Transcript named "R119.7". The group field is also used to store information about the target of sequence similarity hits, and miscellaneous notes. See the next section for a description of how to describe similarity targets. The format of the group fields is "Class ID" with a single space (not a tab) separating the class from the ID. It is VERY IMPORTANT to follow this format, or grouping will not work properly. =back The sequences used to establish the coordinate system for annotations can correspond to sequenced clones, clone fragments, contigs or super-contigs. Thus, this module can be used throughout the lifecycle of a sequencing project. In addition to a group ID, the GFF format allows annotations to have a group class. For example, in the ACeDB representation, RNA interference experiments have a class of "RNAi" and an ID that is unique among the RNAi experiments. Since not all databases support this notion, the class is optional in all calls to this module, and defaults to "Sequence" when not provided. Double-quotes are sometimes used in GFF files around components of the group field. Strictly, this is only necessary if the group name or class contains whitespace. =head2 Making GFF files work with this module Some annotations do not need to be individually named. For example, it is probably not useful to assign a unique name to each ALU repeat in a vertebrate genome. Others, such as predicted genes, correspond to named biological objects; you probably want to be able to fetch the positions of these objects by referring to them by name. To accommodate named annotations, the GFF format places the object class and name in the group field. The name identifies the object, and the class prevents similarly-named objects, for example clones and sequences, from collding. A named object is shown in the following excerpt from a GFF file: Chr1 curated transcript 939627 942410 . + . Transcript Y95B8A.2 This object is a predicted transcript named Y95BA.2. In this case, the group field is used to identify the class and name of the object, even though no other annotation belongs to that group. It now becomes possible to retrieve the region of the genome covered by transcript Y95B8A.2 using the segment() method: $segment = $db->segment(-class=>'Transcript',-name=>'Y95B8A.2'); It is not necessary for the annotation's method to correspond to the object class, although this is commonly the case. As explained above, each annotation in a GFF file refers to a reference sequence. It is important that each reference sequence also be identified by a line in the GFF file. This allows the Bio::DB::GFF module to determine the length and class of the reference sequence, and makes it possible to do relative arithmetic. For example, if "Chr1" is used as a reference sequence, then it should have an entry in the GFF file similar to this one: Chr1 assembly chromosome 1 14972282 . + . Sequence Chr1 This indicates that the reference sequence named "Chr1" has length 14972282 bp, method "chromosome" and source "assembly". In addition, as indicated by the group field, Chr1 has class "Sequence" and name "Chr1". The object class "Sequence" is used by default when the class is not specified in the segment() call. This allows you to use a shortcut form of the segment() method: $segment = $db->segment('Chr1'); # whole chromosome $segment = $db->segment('Chr1',1=>1000); # first 1000 bp For your convenience, if, during loading a GFF file, Bio::DB::GFF encounters a line like the following: ##sequence-region Chr1 1 14972282 It will automatically generate the following entry: Chr1 reference Component 1 14972282 . + . Sequence Chr1 This is sufficient to use Chr1 as a reference point. The ##sequence-region line is frequently found in the GFF files distributed by annotation groups. =head2 Specifying the group tag A frequent problem with GFF files is the problem distinguishing which of the several tag/value pairs in the 9th column is the grouping pair. Ordinarily the first tag will be used for grouping, but some GFF manipulating tools do not preserve the order of attributes. To eliminate this ambiguity, this module provides two ways of explicitly specifying which tag to group on: =over 4 =item * Using -preferred_groups When you create a Bio::DB::GFF object, pass it a -preferred_groups=E argument. This specifies a tag that will be used for grouping. You can pass an array reference to specify a list of such tags. =item * In the GFF header The GFF file itself can specify which tags are to be used for grouping. Insert a comment like the following: ##group-tags Accession Locus This says to use the Accession tag for grouping. If it is not available, use the Locus tag. If neither tag is available, use the first pair to appear. =back These options only apply when B a GFF file into the database, and have no effect on existing databases. The group-tags comment in the GFF file will *override* the preferred groups set when you create the Bio::DB::GFF object. For backward compatibility, the tags Sequence and Transcript are always treated as grouping tags unless preferred_tags are specified. The "Target" tag is always used for grouping regardless of the preferred_groups() setting, and the tags "tstart", "tend" and "Note" cannot be used for grouping. These are historical artefacts coming from various interpretations of GFF2, and cannot be changed. =head2 Sequence alignments There are two cases in which an annotation indicates the relationship between two sequences. The first case is a similarity hit, where the annotation indicates an alignment. The second case is a map assembly, in which the annotation indicates that a portion of a larger sequence is built up from one or more smaller ones. Both cases are indicated by using the B tag in the group field. For example, a typical similarity hit will look like this: Chr1 BLASTX similarity 76953 77108 132 + 0 Target Protein:SW:ABL_DROME 493 544 The group field contains the Target tag, followed by an identifier for the biological object referred to. The GFF format uses the notation I:I for the biological object, and even though this is stylistically inconsistent, that's the way it's done. The object identifier is followed by two integers indicating the start and stop of the alignment on the target sequence. Unlike the main start and stop columns, it is possible for the target start to be greater than the target end. The previous example indicates that the the section of Chr1 from 76,953 to 77,108 aligns to the protein SW:ABL_DROME starting at position 493 and extending to position 544. A similar notation is used for sequence assembly information as shown in this example: Chr1 assembly Link 10922906 11177731 . . . Target Sequence:LINK_H06O01 1 254826 LINK_H06O01 assembly Cosmid 32386 64122 . . . Target Sequence:F49B2 6 31742 This indicates that the region between bases 10922906 and 11177731 of Chr1 are composed of LINK_H06O01 from bp 1 to bp 254826. The region of LINK_H0601 between 32386 and 64122 is, in turn, composed of the bases 5 to 31742 of cosmid F49B2. =head2 Attributes While not intended to serve as a general-purpose sequence database (see bioperl-db for that), GFF allows you to tag features with arbitrary attributes. Attributes appear in the Group field following the initial class/name pair. For example: Chr1 cur trans 939 942 . + . Transcript Y95B8A.2 ; Gene sma-3 ; Alias sma3 This line tags the feature named Transcript Y95B8A.2 as being "Gene" named sma-3 and having the Alias "sma3". Features having these attributes can be looked up using the fetch_feature_by_attribute() method. Two attributes have special meaning: "Note" is for backward compatibility and is used for unstructured text remarks. "Alias" is considered as a synonym for the feature name and will be consulted when looking up a feature by its name. =head2 Adaptors and Aggregators This module uses a system of adaptors and aggregators in order to make it adaptable to use with a variety of databases. =over 4 =item * Adaptors The core of the module handles the user API, annotation coordinate arithmetic, and other common issues. The details of fetching information from databases is handled by an adaptor, which is specified during Bio::DB::GFF construction. The adaptor encapsulates database-specific information such as the schema, user authentication and access methods. There are currently five adaptors recommended for general use: Adaptor Name Description ------------ ----------- memory A simple in-memory database suitable for testing and small data sets. berkeleydb An indexed file database based on the DB_File module, suitable for medium-sized read-only data sets. dbi::mysql An interface to a schema implemented in the Mysql relational database management system. dbi::oracle An interface to a schema implemented in the Oracle relational database management system. dbi::pg An interface to a schema implemented in the PostgreSQL relational database management system. Check the Bio/DB/GFF/Adaptor directory and subdirectories for other, more specialized adaptors, as well as experimental ones. =item * Aggregators The GFF format uses a "group" field to indicate aggregation properties of individual features. For example, a set of exons and introns may share a common transcript group, and multiple transcripts may share the same gene group. Aggregators are small modules that use the group information to rebuild the hierarchy. When a Bio::DB::GFF object is created, you indicate that it use a set of one or more aggregators. Each aggregator provides a new composite annotation type. Before the database query is generated each aggregator is called to "disaggregate" its annotation type into list of component types contained in the database. After the query is generated, each aggregator is called again in order to build composite annotations from the returned components. For example, during disaggregation, the standard "processed_transcript" aggregator generates a list of component feature types including "UTR", "CDS", and "polyA_site". Later, it aggregates these features into a set of annotations of type "processed_transcript". During aggregation, the list of aggregators is called in reverse order. This allows aggregators to collaborate to create multi-level structures: the transcript aggregator assembles transcripts from introns and exons; the gene aggregator then assembles genes from sets of transcripts. Three default aggregators are provided: transcript assembles transcripts from features of type exon, CDS, 5'UTR, 3'UTR, TSS, and PolyA clone assembles clones from Clone_left_end, Clone_right_end and Sequence features. alignment assembles gapped alignments from features of type "similarity". In addition, this module provides the optional "wormbase_gene" aggregator, which accommodates the WormBase representation of genes. This aggregator aggregates features of method "exon", "CDS", "5'UTR", "3'UTR", "polyA" and "TSS" into a single object. It also expects to find a single feature of type "Sequence" that spans the entire gene. The existing aggregators are easily customized. Note that aggregation will not occur unless you specifically request the aggregation type. For example, this call: @features = $segment->features('alignment'); will generate an array of aggregated alignment features. However, this call: @features = $segment->features(); will return a list of unaggregated similarity segments. For more informnation, see the manual pages for Bio::DB::GFF::Aggregator::processed_transcript, Bio::DB::GFF::Aggregator::clone, etc. =back =head2 Loading GFF3 Files This module will accept GFF3 files, as described at http://song.sourceforge.net/gff3.shtml. However, the implementation has some limitations. =over 4 =item GFF version string is required The GFF file B contain the version comment: ##gff-version 3 Unless this version string is present at the top of the GFF file, the loader will attempt to parse the file in GFF2 format, with less-than-desirable results. =item Only one level of nesting allowed A major restriction is that Bio::DB::GFF only allows one level of nesting of features. For nesting, the Target tag will be used preferentially followed by the ID tag, followed by the Parent tag. This means that if genes are represented like this: XXXX XXXX gene XXXX XXXX XXXX ID=myGene XXXX XXXX mRNA XXXX XXXX XXXX ID=myTranscript;Parent=myGene XXXX XXXX exon XXXX XXXX XXXX Parent=myTranscript XXXX XXXX exon XXXX XXXX XXXX Parent=myTranscript Then there will be one group called myGene containing the "gene" feature and one group called myTranscript containing the mRNA, and two exons. You can work around this restriction to some extent by using the Alias attribute literally: XXXX XXXX gene XXXX XXXX XXXX ID=myGene XXXX XXXX mRNA XXXX XXXX XXXX ID=myTranscript;Parent=myGene;Alias=myGene XXXX XXXX exon XXXX XXXX XXXX Parent=myTranscript;Alias=myGene XXXX XXXX exon XXXX XXXX XXXX Parent=myTranscript;Alias=myGene This limitation will be corrected in the next version of Bio::DB::GFF. =back =head1 API The following is the API for Bio::DB::GFF. =cut package Bio::DB::GFF; use strict; use IO::File; use File::Glob ':glob'; use Bio::DB::GFF::Util::Rearrange; use Bio::DB::GFF::RelSegment; use Bio::DB::GFF::Feature; use Bio::DB::GFF::Aggregator; use base qw(Bio::Root::Root Bio::DasI); my %valid_range_types = (overlaps => 1, contains => 1, contained_in => 1); =head1 Querying GFF Databases =head2 new Title : new Usage : my $db = Bio::DB::GFF->new(@args); Function: create a new Bio::DB::GFF object Returns : new Bio::DB::GFF object Args : lists of adaptors and aggregators Status : Public These are the arguments: -adaptor Name of the adaptor module to use. If none provided, defaults to "dbi::mysqlopt". -aggregator Array reference to a list of aggregators to apply to the database. If none provided, defaults to ['processed_transcript','alignment']. -preferred_groups When interpreteting the 9th column of a GFF2 file, the indicated group names will have preference over other attributes, even if they do not come first in the list of attributes. This can be a scalar value or an array reference. Any other named argument pairs are passed to the adaptor for processing. The adaptor argument must correspond to a module contained within the Bio::DB::GFF::Adaptor namespace. For example, the Bio::DB::GFF::Adaptor::dbi::mysql adaptor is loaded by specifying 'dbi::mysql'. By Perl convention, the adaptors names are lower case because they are loaded at run time. The aggregator array may contain a list of aggregator names, a list of initialized aggregator objects, or a string in the form "aggregator_name{subpart1,subpart2,subpart3/main_method}" (the "/main_method" part is optional, but if present a feature with the main_method must be present in order for aggregation to occur). For example, if you wish to change the components aggregated by the transcript aggregator, you could pass it to the GFF constructor this way: my $transcript = Bio::DB::Aggregator::transcript->new(-sub_parts=>[qw(exon intron utr polyA spliced_leader)]); my $db = Bio::DB::GFF->new(-aggregator=>[$transcript,'clone','alignment], -adaptor => 'dbi::mysql', -dsn => 'dbi:mysql:elegans42'); Alternatively, you could create an entirely new transcript aggregator this way: my $new_agg = 'transcript{exon,intron,utr,polyA,spliced_leader}'; my $db = Bio::DB::GFF->new(-aggregator=>[$new_agg,'clone','alignment], -adaptor => 'dbi::mysql', -dsn => 'dbi:mysql:elegans42'); See L for more details. The B<-preferred_groups> argument is used to change the default processing of the 9th column of GFF version 2 files. By default, the first tag/value pair is used to establish the group class and name. If you pass -preferred_groups a scalar, the parser will look for a tag of the indicated type and use it as the group even if it is not first in the file. If you pass this argument a list of group classes as an array ref, then the list will establish the precedence for searching. The commonly used 'dbi::mysql' adaptor recognizes the following adaptor-specific arguments: Argument Description -------- ----------- -dsn the DBI data source, e.g. 'dbi:mysql:ens0040' If a partial name is given, such as "ens0040", the "dbi:mysql:" prefix will be added automatically. -user username for authentication -pass the password for authentication -refclass landmark Class; defaults to "Sequence" The commonly used 'dbi::mysqlopt' adaptor also recognizes the following arguments. Argument Description -------- ----------- -fasta path to a directory containing FASTA files for the DNA contained in this database (e.g. "/usr/local/share/fasta") -acedb an acedb URL to use when converting features into ACEDB objects (e.g. sace://localhost:2005) =cut #' sub new { my $package = shift; my ($adaptor,$aggregators,$args,$refclass,$preferred_groups); if (@_ == 1) { # special case, default to dbi::mysqlopt $adaptor = 'dbi::mysqlopt'; $args = {DSN => shift}; } else { ($adaptor,$aggregators,$refclass,$preferred_groups,$args) = rearrange([ [qw(ADAPTOR FACTORY)], [qw(AGGREGATOR AGGREGATORS)], 'REFCLASS', 'PREFERRED_GROUPS' ],@_); } $adaptor ||= 'dbi::mysqlopt'; my $class = "Bio::DB::GFF::Adaptor::\L${adaptor}\E"; unless ($class->can('new')) { eval "require $class;1;" or $package->throw("Unable to load $adaptor adaptor: $@"); } # this hack saves the memory adaptor, which loads the GFF file in new() $args->{PREFERRED_GROUPS} = $preferred_groups if defined $preferred_groups; my $self = $class->new($args); # handle preferred groups $self->preferred_groups($preferred_groups) if defined $preferred_groups; $self->default_class($refclass || 'Sequence'); # handle the aggregators. # aggregators are responsible for creating complex multi-part features # from the GFF "group" field. If none are provided, then we provide a # list of the two used in WormBase. # Each aggregator can be a scalar or a ref. In the former case # it is treated as a class name to call new() on. In the latter # the aggreator is treated as a ready made object. $aggregators = $self->default_aggregators unless defined $aggregators; my @a = ref($aggregators) eq 'ARRAY' ? @$aggregators : $aggregators; for my $a (@a) { $self->add_aggregator($a); } # default settings go here..... $self->automerge(1); # set automerge to true $self; } =head2 types Title : types Usage : $db->types(@args) Function: return list of feature types in range or database Returns : a list of Bio::DB::GFF::Typename objects Args : see below Status : public This routine returns a list of feature types known to the database. The list can be database-wide or restricted to a region. It is also possible to find out how many times each feature occurs. For range queries, it is usually more convenient to create a Bio::DB::GFF::Segment object, and then invoke it's types() method. Arguments are as follows: -ref ID of reference sequence -class class of reference sequence -start start of segment -stop stop of segment -enumerate if true, count the features The returned value will be a list of Bio::DB::GFF::Typename objects, which if evaluated in a string context will return the feature type in "method:source" format. This object class also has method() and source() methods for retrieving the like-named fields. If -enumerate is true, then the function returns a hash (not a hash reference) in which the keys are type names in "method:source" format and the values are the number of times each feature appears in the database or segment. The argument -end is a synonum for -stop, and -count is a synonym for -enumerate. =cut sub types { my $self = shift; my ($refseq,$start,$stop,$enumerate,$refclass,$types) = rearrange ([ [qw(REF REFSEQ)], qw(START), [qw(STOP END)], [qw(ENUMERATE COUNT)], [qw(CLASS SEQCLASS)], [qw(TYPE TYPES)], ],@_); $types = $self->parse_types($types) if defined $types; $self->get_types($refseq,$refclass,$start,$stop,$enumerate,$types); } =head2 classes Title : classes Usage : $db->classes Function: return list of landmark classes in database Returns : a list of classes Args : none Status : public This routine returns the list of reference classes known to the database, or empty if classes are not used by the database. Classes are distinct from types, being essentially qualifiers on the reference namespaces. =cut sub classes { my $self = shift; return (); } =head2 segment Title : segment Usage : $db->segment(@args); Function: create a segment object Returns : segment object(s) Args : numerous, see below Status : public This method generates a segment object, which is a Perl object subclassed from Bio::DB::GFF::Segment. The segment can be used to find overlapping features and the raw DNA. When making the segment() call, you specify the ID of a sequence landmark (e.g. an accession number, a clone or contig), and a positional range relative to the landmark. If no range is specified, then the entire extent of the landmark is used to generate the segment. You may also provide the ID of a "reference" sequence, which will set the coordinate system and orientation used for all features contained within the segment. The reference sequence can be changed later. If no reference sequence is provided, then the coordinate system is based on the landmark. Arguments: -name ID of the landmark sequence. -class Database object class for the landmark sequence. "Sequence" assumed if not specified. This is irrelevant for databases which do not recognize object classes. -start Start of the segment relative to landmark. Positions follow standard 1-based sequence rules. If not specified, defaults to the beginning of the landmark. -end Stop of the segment relative to the landmark. If not specified, defaults to the end of the landmark. -stop Same as -end. -offset For those who prefer 0-based indexing, the offset specifies the position of the new segment relative to the start of the landmark. -length For those who prefer 0-based indexing, the length specifies the length of the new segment. -refseq Specifies the ID of the reference landmark used to establish the coordinate system for the newly-created segment. -refclass Specifies the class of the reference landmark, for those databases that distinguish different object classes. Defaults to "Sequence". -absolute Return features in absolute coordinates rather than relative to the parent segment. -nocheck Don't check the database for the coordinates and length of this feature. Construct a segment using the indicated name as the reference, a start coordinate of 1, an undefined end coordinate, and a strand of +1. -force Same as -nocheck. -seq,-sequence,-sourceseq Aliases for -name. -begin,-end Aliases for -start and -stop -off,-len Aliases for -offset and -length -seqclass Alias for -class Here's an example to explain how this works: my $db = Bio::DB::GFF->new(-dsn => 'dbi:mysql:human',-adaptor=>'dbi::mysql'); If successful, $db will now hold the database accessor object. We now try to fetch the fragment of sequence whose ID is A0000182 and class is "Accession." my $segment = $db->segment(-name=>'A0000182',-class=>'Accession'); If successful, $segment now holds the entire segment corresponding to this accession number. By default, the sequence is used as its own reference sequence, so its first base will be 1 and its last base will be the length of the accession. Assuming that this sequence belongs to a longer stretch of DNA, say a contig, we can fetch this information like so: my $sourceseq = $segment->sourceseq; and find the start and stop on the source like this: my $start = $segment->abs_start; my $stop = $segment->abs_stop; If we had another segment, say $s2, which is on the same contiguous piece of DNA, we can pass that to the refseq() method in order to establish it as the coordinate reference point: $segment->refseq($s2); Now calling start() will return the start of the segment relative to the beginning of $s2, accounting for differences in strandedness: my $rel_start = $segment->start; IMPORTANT NOTE: This method can be used to return the segment spanned by an arbitrary named annotation. However, if the annotation appears at multiple locations on the genome, for example an EST that maps to multiple locations, then, provided that all locations reside on the same physical segment, the method will return a segment that spans the minimum and maximum positions. If the reference sequence occupies ranges on different physical segments, then it returns them all in an array context, and raises a "multiple segment exception" exception in a scalar context. =cut #' sub segment { my $self = shift; my @segments = Bio::DB::GFF::RelSegment->new(-factory => $self, $self->setup_segment_args(@_)); foreach (@segments) { $_->absolute(1) if $self->absolute; } $self->_multiple_return_args(@segments); } sub _multiple_return_args { my $self = shift; my @args = @_; if (@args == 0) { return; } elsif (@args == 1) { return $args[0]; } elsif (wantarray) { # more than one reference sequence return @args; } else { $self->error($args[0]->name, " has more than one reference sequence in database. Please call in a list context to retrieve them all."); $self->throw('multiple segment exception'); return; } } # backward compatibility -- don't use! # (deliberately undocumented too) sub abs_segment { my $self = shift; return $self->segment($self->setup_segment_args(@_),-absolute=>1); } sub setup_segment_args { my $self = shift; return @_ if defined $_[0] && $_[0] =~ /^-/; return (-name=>$_[0],-start=>$_[1],-stop=>$_[2]) if @_ == 3; return (-class=>$_[0],-name=>$_[1]) if @_ == 2; return (-name=>$_[0]) if @_ == 1; } =head2 features Title : features Usage : $db->features(@args) Function: get all features, possibly filtered by type Returns : a list of Bio::DB::GFF::Feature objects Args : see below Status : public This routine will retrieve features in the database regardless of position. It can be used to return all features, or a subset based on their method and source. Arguments are as follows: -types List of feature types to return. Argument is an array reference containing strings of the format "method:source" -merge Whether to apply aggregators to the generated features. -rare Turn on optimizations suitable for a relatively rare feature type, where it makes more sense to filter by feature type first, and then by position. -attributes A hash reference containing attributes to match. -iterator Whether to return an iterator across the features. -binsize A true value will create a set of artificial features whose start and stop positions indicate bins of the given size, and whose scores are the number of features in the bin. The class and method of the feature will be set to "bin", its source to "method:source", and its group to "bin:method:source". This is a handy way of generating histograms of feature density. If -iterator is true, then the method returns a single scalar value consisting of a Bio::SeqIO object. You can call next_seq() repeatedly on this object to fetch each of the features in turn. If iterator is false or absent, then all the features are returned as a list. Currently aggregation is disabled when iterating over a series of features. Types are indicated using the nomenclature "method:source". Either of these fields can be omitted, in which case a wildcard is used for the missing field. Type names without the colon (e.g. "exon") are interpreted as the method name and a source wild card. Regular expressions are allowed in either field, as in: "similarity:BLAST.*". The -attributes argument is a hashref containing one or more attributes to match against: -attributes => { Gene => 'abc-1', Note => 'confirmed' } Attribute matching is simple string matching, and multiple attributes are ANDed together. =cut sub features { my $self = shift; my ($types,$automerge,$sparse,$iterator,$refseq,$start,$end,$other); if (defined $_[0] && $_[0] =~ /^-/) { ($types,$automerge,$sparse,$iterator, $refseq,$start,$end, $other) = rearrange([ [qw(TYPE TYPES)], [qw(MERGE AUTOMERGE)], [qw(RARE SPARSE)], 'ITERATOR', [qw(REFSEQ SEQ_ID)], 'START', [qw(STOP END)], ],@_); } else { $types = \@_; } # for whole database retrievals, we probably don't want to automerge! $automerge = $self->automerge unless defined $automerge; $other ||= {}; $self->_features({ rangetype => $refseq ? 'overlaps' : 'contains', types => $types, refseq => $refseq, start => $start, stop => $end, }, { sparse => $sparse, automerge => $automerge, iterator =>$iterator, %$other, } ); } =head2 get_seq_stream Title : get_seq_stream Usage : my $seqio = $self->get_seq_sream(@args) Function: Performs a query and returns an iterator over it Returns : a Bio::SeqIO stream capable of producing sequence Args : As in features() Status : public This routine takes the same arguments as features(), but returns a Bio::SeqIO::Stream-compliant object. Use it like this: $stream = $db->get_seq_stream('exon'); while (my $exon = $stream->next_seq) { print $exon,"\n"; } NOTE: This is also called get_feature_stream(), since that's what it really does. =cut sub get_seq_stream { my $self = shift; my @args = !defined($_[0]) || $_[0] =~ /^-/ ? (@_,-iterator=>1) : (-types=>\@_,-iterator=>1); $self->features(@args); } *get_feature_stream = \&get_seq_stream; =head2 get_feature_by_name Title : get_feature_by_name Usage : $db->get_feature_by_name($class => $name) Function: fetch features by their name Returns : a list of Bio::DB::GFF::Feature objects Args : the class and name of the desired feature Status : public This method can be used to fetch a named feature from the database. GFF annotations are named using the group class and name fields, so for features that belong to a group of size one, this method can be used to retrieve that group (and is equivalent to the segment() method). Any Alias attributes are also searched for matching names. An alternative syntax allows you to search for features by name within a circumscribed region: @f = $db->get_feature_by_name(-class => $class,-name=>$name, -ref => $sequence_name, -start => $start, -end => $end); This method may return zero, one, or several Bio::DB::GFF::Feature objects. Aggregation is performed on features as usual. NOTE: At various times, this function was called fetch_group(), fetch_feature(), fetch_feature_by_name() and segments(). These names are preserved for backward compatibility. =cut sub get_feature_by_name { my $self = shift; my ($gclass,$gname,$automerge,$ref,$start,$end); if (@_ == 1) { $gclass = $self->default_class; $gname = shift; } else { ($gclass,$gname,$automerge,$ref,$start,$end) = rearrange(['CLASS','NAME','AUTOMERGE', ['REF','REFSEQ'], 'START',['STOP','END'] ],@_); $gclass ||= $self->default_class; } $automerge = $self->automerge unless defined $automerge; # we need to refactor this... It's repeated code (see below)... my @aggregators; if ($automerge) { for my $a ($self->aggregators) { push @aggregators,$a if $a->disaggregate([],$self); } } my %groups; # cache the groups we create to avoid consuming too much unecessary memory my $features = []; my $callback = sub { push @$features,$self->make_feature(undef,\%groups,@_) }; my $location = [$ref,$start,$end] if defined $ref; $self->_feature_by_name($gclass,$gname,$location,$callback); warn "aggregating...\n" if $self->debug; foreach my $a (@aggregators) { # last aggregator gets first shot $a->aggregate($features,$self) or next; } @$features; } # horrible indecision regarding proper names! *fetch_group = *fetch_feature = *fetch_feature_by_name = \&get_feature_by_name; *segments = \&segment; =head2 get_feature_by_target Title : get_feature_by_target Usage : $db->get_feature_by_target($class => $name) Function: fetch features by their similarity target Returns : a list of Bio::DB::GFF::Feature objects Args : the class and name of the desired feature Status : public This method can be used to fetch a named feature from the database based on its similarity hit. =cut sub get_feature_by_target { shift->get_feature_by_name(@_); } =head2 get_feature_by_attribute Title : get_feature_by_attribute Usage : $db->get_feature_by_attribute(attribute1=>value1,attribute2=>value2) Function: fetch segments by combinations of attribute values Returns : a list of Bio::DB::GFF::Feature objects Args : the class and name of the desired feature Status : public This method can be used to fetch a set of features from the database. Attributes are a list of name=Evalue pairs. They will be logically ANDED together. =cut sub get_feature_by_attribute { my $self = shift; my %attributes = ref($_[0]) ? %{$_[0]} : @_; # we need to refactor this... It's repeated code (see above)... my @aggregators; if ($self->automerge) { for my $a ($self->aggregators) { unshift @aggregators,$a if $a->disaggregate([],$self); } } my %groups; # cache the groups we create to avoid consuming too much unecessary memory my $features = []; my $callback = sub { push @$features,$self->make_feature(undef,\%groups,@_) }; $self->_feature_by_attribute(\%attributes,$callback); warn "aggregating...\n" if $self->debug; foreach my $a (@aggregators) { # last aggregator gets first shot $a->aggregate($features,$self) or next; } @$features; } # more indecision... *fetch_feature_by_attribute = \&get_feature_by_attribute; =head2 get_feature_by_id Title : get_feature_by_id Usage : $db->get_feature_by_id($id) Function: fetch segments by feature ID Returns : a Bio::DB::GFF::Feature object Args : the feature ID Status : public This method can be used to fetch a feature from the database using its ID. Not all GFF databases support IDs, so be careful with this. =cut sub get_feature_by_id { my $self = shift; my $id = ref($_[0]) eq 'ARRAY' ? $_[0] : \@_; my %groups; # cache the groups we create to avoid consuming too much unecessary memory my $features = []; my $callback = sub { push @$features,$self->make_feature(undef,\%groups,@_) }; $self->_feature_by_id($id,'feature',$callback); return wantarray ? @$features : $features->[0]; } *fetch_feature_by_id = \&get_feature_by_id; =head2 get_feature_by_gid Title : get_feature_by_gid Usage : $db->get_feature_by_gid($id) Function: fetch segments by feature ID Returns : a Bio::DB::GFF::Feature object Args : the feature ID Status : public This method can be used to fetch a feature from the database using its group ID. Not all GFF databases support IDs, so be careful with this. The group ID is often more interesting than the feature ID, since groups can be complex objects containing subobjects. =cut sub get_feature_by_gid { my $self = shift; my $id = ref($_[0]) eq 'ARRAY' ? $_[0] : \@_; my %groups; # cache the groups we create to avoid consuming too much unecessary memory my $features = []; my $callback = sub { push @$features,$self->make_feature(undef,\%groups,@_) }; $self->_feature_by_id($id,'group',$callback); return wantarray ? @$features : $features->[0]; } *fetch_feature_by_gid = \&get_feature_by_gid; =head2 delete_fattribute_to_features Title : delete_fattribute_to_features Usage : $db->delete_fattribute_to_features(@ids_or_features) Function: delete one or more fattribute_to_features Returns : count of fattribute_to_features deleted Args : list of features or feature ids Status : public Pass this method a list of numeric feature ids or a set of features. It will attempt to remove the fattribute_to_features rows of those features from the database and return a count of the rows removed. NOTE: This method is also called delete_fattribute_to_feature(). Also see delete_groups() and delete_features(). =cut *delete_fattribute_to_feature = \&delete_fattribute_to_features; sub delete_fattribute_to_features { my $self = shift; my @features_or_ids = @_; my @ids = map {UNIVERSAL::isa($_,'Bio::DB::GFF::Feature') ? $_->id : $_} @features_or_ids; return unless @ids; $self->_delete_fattribute_to_features(@ids); } =head2 delete_features Title : delete_features Usage : $db->delete_features(@ids_or_features) Function: delete one or more features Returns : count of features deleted Args : list of features or feature ids Status : public Pass this method a list of numeric feature ids or a set of features. It will attempt to remove the features from the database and return a count of the features removed. NOTE: This method is also called delete_feature(). Also see delete_groups(). =cut *delete_feature = \&delete_features; sub delete_features { my $self = shift; my @features_or_ids = @_; my @ids = map {UNIVERSAL::isa($_,'Bio::DB::GFF::Feature') ? $_->id : $_} @features_or_ids; return unless @ids; $self->_delete_features(@ids); } =head2 delete_groups Title : delete_groups Usage : $db->delete_groups(@ids_or_features) Function: delete one or more feature groups Returns : count of features deleted Args : list of features or feature group ids Status : public Pass this method a list of numeric group ids or a set of features. It will attempt to recursively remove the features and ALL members of their group from the database. It returns a count of the number of features (not groups) returned. NOTE: This method is also called delete_group(). Also see delete_features(). =cut *delete_group = \&delete_groupss; sub delete_groups { my $self = shift; my @features_or_ids = @_; my @ids = map {UNIVERSAL::isa($_,'Bio::DB::GFF::Feature') ? $_->group_id : $_} @features_or_ids; return unless @ids; $self->_delete_groups(@ids); } =head2 delete Title : delete Usage : $db->delete(@args) Function: delete features Returns : count of features deleted -- if available Args : numerous, see below Status : public This method deletes all features that overlap the specified region or are of a particular type. If no arguments are provided and the -force argument is true, then deletes ALL features. Arguments: -name ID of the landmark sequence. -ref ID of the landmark sequence (synonym for -name). -class Database object class for the landmark sequence. "Sequence" assumed if not specified. This is irrelevant for databases which do not recognize object classes. -start Start of the segment relative to landmark. Positions follow standard 1-based sequence rules. If not specified, defaults to the beginning of the landmark. -end Stop of the segment relative to the landmark. If not specified, defaults to the end of the landmark. -offset Zero-based addressing -length Length of region -type,-types Either a single scalar type to be deleted, or an reference to an array of types. -force Force operation to be performed even if it would delete entire feature table. -range_type Control the range type of the deletion. One of "overlaps" (default) "contains" or "contained_in" Examples: $db->delete(-type=>['intron','repeat:repeatMasker']); # remove all introns & repeats $db->delete(-name=>'chr3',-start=>1,-end=>1000); # remove annotations on chr3 from 1 to 1000 $db->delete(-name=>'chr3',-type=>'exon'); # remove all exons on chr3 The short form of this call, as described in segment() is also allowed: $db->delete("chr3",1=>1000); $db->delete("chr3"); IMPORTANT NOTE: This method only deletes features. It does *NOT* delete the names of groups that contain the deleted features. Group IDs will be reused if you later load a feature with the same group name as one that was previously deleted. NOTE ON FEATURE COUNTS: The DBI-based versions of this call return the result code from the SQL DELETE operation. Some dbd drivers return the count of rows deleted, while others return 0E0. Caveat emptor. =cut sub delete { my $self = shift; my @args = $self->setup_segment_args(@_); my ($name,$class,$start,$end,$offset,$length,$type,$force,$range_type) = rearrange([['NAME','REF'],'CLASS','START',[qw(END STOP)],'OFFSET', 'LENGTH',[qw(TYPE TYPES)],'FORCE','RANGE_TYPE'],@args); $offset = 0 unless defined $offset; $start = $offset+1 unless defined $start; $end = $start+$length-1 if !defined $end and $length; $class ||= $self->default_class; my $types = $self->parse_types($type); # parse out list of types $range_type ||= 'overlaps'; $self->throw("range type must be one of {". join(',',keys %valid_range_types). "}\n") unless $valid_range_types{lc $range_type}; my @segments; if (defined $name && $name ne '') { my @args = (-name=>$name,-class=>$class); push @args,(-start=>$start) if defined $start; push @args,(-end =>$end) if defined $end; @segments = $self->segment(@args); return unless @segments; } $self->_delete({segments => \@segments, types => $types, range_type => $range_type, force => $force} ); } =head2 absolute Title : absolute Usage : $abs = $db->absolute([$abs]); Function: gets/sets absolute mode Returns : current setting of absolute mode boolean Args : new setting for absolute mode boolean Status : public $db-Eabsolute(1) will turn on absolute mode for the entire database. All segments retrieved will use absolute coordinates by default, rather than relative coordinates. You can still set them to use relative coordinates by calling $segment-Eabsolute(0). Note that this is not the same as calling abs_segment(); it continues to allow you to look up groups that are not used directly as reference sequences. =cut sub absolute { my $self = shift; my $d = $self->{absolute}; $self->{absolute} = shift if @_; $d; } =head2 strict_bounds_checking Title : strict_bounds_checking Usage : $flag = $db->strict_bounds_checking([$flag]) Function: gets/sets strict bounds checking Returns : current setting of bounds checking flag Args : new setting for bounds checking flag Status : public This flag enables extra checks for segment requests that go beyond the ends of their reference sequences. If bounds checking is enabled, then retrieved segments will be truncated to their physical length, and their truncated() methods will return true. If the flag is off (the default), then the module will return segments that appear to extend beyond their physical boundaries. Requests for features beyond the end of the segment will, however, return empty. =cut sub strict_bounds_checking { my $self = shift; my $d = $self->{strict}; $self->{strict} = shift if @_; $d; } =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception NOTE: Bio::DB::RandomAccessI compliant method =cut sub get_Seq_by_id { my $self = shift; $self->get_feature_by_name(@_); } =head2 get_Seq_by_accession Title : get_Seq_by_accession Usage : $seq = $db->get_Seq_by_accession('AL12234') Function: Gets a Bio::Seq object by its accession Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception NOTE: Bio::DB::RandomAccessI compliant method =cut sub get_Seq_by_accession { my $self = shift; $self->get_feature_by_name(@_); } =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception NOTE: Bio::DB::RandomAccessI compliant method =cut sub get_Seq_by_acc { my $self = shift; $self->get_feature_by_name(@_); } =head2 get_Stream_by_name Title : get_Stream_by_name Usage : $seq = $db->get_Stream_by_name(@ids); Function: Retrieves a stream of Seq objects given their names Returns : a Bio::SeqIO stream object Args : an array of unique ids/accession numbers, or an array reference NOTE: This is also called get_Stream_by_batch() =cut sub get_Stream_by_name { my $self = shift; my @ids = @_; my $id = ref($ids[0]) ? $ids[0] : \@ids; Bio::DB::GFF::ID_Iterator->new($self,$id,'name'); } =head2 get_Stream_by_id Title : get_Stream_by_id Usage : $seq = $db->get_Stream_by_id(@ids); Function: Retrieves a stream of Seq objects given their ids Returns : a Bio::SeqIO stream object Args : an array of unique ids/accession numbers, or an array reference NOTE: This is also called get_Stream_by_batch() =cut sub get_Stream_by_id { my $self = shift; my @ids = @_; my $id = ref($ids[0]) ? $ids[0] : \@ids; Bio::DB::GFF::ID_Iterator->new($self,$id,'feature'); } =head2 get_Stream_by_batch () Title : get_Stream_by_batch Usage : $seq = $db->get_Stream_by_batch(@ids); Function: Retrieves a stream of Seq objects given their ids Returns : a Bio::SeqIO stream object Args : an array of unique ids/accession numbers, or an array reference NOTE: This is the same as get_Stream_by_id(). =cut *get_Stream_by_batch = \&get_Stream_by_id; =head2 get_Stream_by_group () Bioperl compatibility. =cut sub get_Stream_by_group { my $self = shift; my @ids = @_; my $id = ref($ids[0]) ? $ids[0] : \@ids; Bio::DB::GFF::ID_Iterator->new($self,$id,'group'); } =head2 all_seqfeatures Title : all_seqfeatures Usage : @features = $db->all_seqfeatures(@args) Function: fetch all the features in the database Returns : an array of features, or an iterator Args : See below Status : public This is equivalent to calling $db-Efeatures() without any types, and will return all the features in the database. The -merge and -iterator arguments are recognized, and behave the same as described for features(). =cut sub all_seqfeatures { my $self = shift; my ($automerge,$iterator)= rearrange([ [qw(MERGE AUTOMERGE)], 'ITERATOR' ],@_); my @args; push @args,(-merge=>$automerge) if defined $automerge; push @args,(-iterator=>$iterator) if defined $iterator; $self->features(@args); } =head1 Creating and Loading GFF Databases =head2 initialize Title : initialize Usage : $db->initialize(-erase=>$erase,-option1=>value1,-option2=>value2); Function: initialize a GFF database Returns : true if initialization successful Args : a set of named parameters Status : Public This method can be used to initialize an empty database. It takes the following named arguments: -erase A boolean value. If true the database will be wiped clean if it already contains data. Other named arguments may be recognized by subclasses. They become database meta values that control various settable options. As a shortcut (and for backward compatibility) a single true argument is the same as initialize(-erase=E1). =cut sub initialize { my $self = shift; my ($erase,$meta) = rearrange(['ERASE'],@_); $meta ||= {}; # initialize (possibly erasing) return unless $self->do_initialize($erase); my @default = $self->default_meta_values; # this is an awkward way of uppercasing the # even-numbered values (necessary for case-insensitive SQL databases) for (my $i=0; $i<@default; $i++) { $default[$i] = uc $default[$i] if !($i % 2); } my %values = (@default,%$meta); foreach (keys %values) { $self->meta($_ => $values{$_}); } 1; } =head2 load_gff Title : load_gff Usage : $db->load_gff($file|$directory|$filehandle [,$verbose]); Function: load GFF data into database Returns : count of records loaded Args : a directory, a file, a list of files, or a filehandle Status : Public This method takes a single overloaded argument, which can be any of: =over 4 =item * a scalar corresponding to a GFF file on the system A pathname to a local GFF file. Any files ending with the .gz, .Z, or .bz2 suffixes will be transparently decompressed with the appropriate command-line utility. =item * an array reference containing a list of GFF files on the system For example ['/home/gff/gff1.gz','/home/gff/gff2.gz'] =item * directory path The indicated directory will be searched for all files ending in the suffixes .gff, .gff.gz, .gff.Z or .gff.bz2. =item * filehandle An open filehandle from which to read the GFF data. Tied filehandles now work as well. =item * a pipe expression A pipe expression will also work. For example, a GFF file on a remote web server can be loaded with an expression like this: $db->load_gff("lynx -dump -source http://stein.cshl.org/gff_test |"); =back The optional second argument, if true, will turn on verbose status reports that indicate the progress. If successful, the method will return the number of GFF lines successfully loaded. NOTE:this method used to be called load(), but has been changed. The old method name is also recognized. =cut sub load_gff { my $self = shift; my $file_or_directory = shift || '.'; my $verbose = shift; local $self->{__verbose__} = $verbose; return $self->do_load_gff($file_or_directory) if ref($file_or_directory) && tied *$file_or_directory; my $tied_stdin = tied(*STDIN); open my $SAVEIN, "<&STDIN" unless $tied_stdin; local @ARGV = $self->setup_argv($file_or_directory,'gff','gff3') or return; # to play tricks with reader my $result = $self->do_load_gff('ARGV'); open STDIN, '<', $SAVEIN unless $tied_stdin; # restore STDIN return $result; } *load = \&load_gff; =head2 load_gff_file Title : load_gff_file Usage : $db->load_gff_file($file [,$verbose]); Function: load GFF data into database Returns : count of records loaded Args : a path to a file Status : Public This is provided as an alternative to load_gff_file. It doesn't munge STDIN or play tricks with ARGV. =cut sub load_gff_file { my $self = shift; my $file = shift; my $verbose = shift; my $fh = IO::File->new($file) or return; return $self->do_load_gff($fh); } =head2 load_fasta Title : load_fasta Usage : $db->load_fasta($file|$directory|$filehandle); Function: load FASTA data into database Returns : count of records loaded Args : a directory, a file, a list of files, or a filehandle Status : Public This method takes a single overloaded argument, which can be any of: =over 4 =item * scalar corresponding to a FASTA file on the system A pathname to a local FASTA file. Any files ending with the .gz, .Z, or .bz2 suffixes will be transparently decompressed with the appropriate command-line utility. =item * array reference containing a list of FASTA files on the system For example ['/home/fasta/genomic.fa.gz','/home/fasta/genomic.fa.gz'] =item * path to a directory The indicated directory will be searched for all files ending in the suffixes .fa, .fa.gz, .fa.Z or .fa.bz2. =item * filehandle An open filehandle from which to read the FASTA data. =item * pipe expression A pipe expression will also work. For example, a FASTA file on a remote web server can be loaded with an expression like this: $db->load_gff("lynx -dump -source http://stein.cshl.org/fasta_test.fa |"); =back =cut sub load_fasta { my $self = shift; my $file_or_directory = shift || '.'; my $verbose = shift; local $self->{__verbose__} = $verbose; return $self->load_sequence($file_or_directory) if ref($file_or_directory) && tied *$file_or_directory; my $tied = tied(*STDIN); open my $SAVEIN, "<&STDIN" unless $tied; local @ARGV = $self->setup_argv($file_or_directory,'fa','dna','fasta') or return; # to play tricks with reader my $result = $self->load_sequence('ARGV'); open STDIN, '<', $SAVEIN unless $tied; # restore STDIN return $result; } =head2 load_fasta_file Title : load_fasta_file Usage : $db->load_fasta_file($file [,$verbose]); Function: load FASTA data into database Returns : count of records loaded Args : a path to a file Status : Public This is provided as an alternative to load_fasta. It doesn't munge STDIN or play tricks with ARGV. =cut sub load_fasta_file { my $self = shift; my $file = shift; my $verbose = shift; my $fh = IO::File->new($file) or return; return $self->do_load_fasta($fh); } =head2 load_sequence_string Title : load_sequence_string Usage : $db->load_sequence_string($id,$dna) Function: load a single DNA entry Returns : true if successfully loaded Args : a raw sequence string (DNA, RNA, protein) Status : Public =cut sub load_sequence_string { my $self = shift; my ($acc,$seq) = @_; my $offset = 0; $self->insert_sequence_chunk($acc,\$offset,\$seq) or return; $self->insert_sequence($acc,$offset,$seq) or return; 1; } sub setup_argv { my $self = shift; my $file_or_directory = shift; my @suffixes = @_; no strict 'refs'; # so that we can call fileno() on the argument my @argv; if (-d $file_or_directory) { # Because glob() is broken with long file names that contain spaces $file_or_directory = Win32::GetShortPathName($file_or_directory) if $^O =~ /^MSWin/i && eval 'use Win32; 1'; @argv = map { glob("$file_or_directory/*.{$_,$_.gz,$_.Z,$_.bz2}")} @suffixes; }elsif (my $fd = fileno($file_or_directory)) { open STDIN,"<&=$fd" or $self->throw("Can't dup STDIN"); @argv = '-'; } elsif (ref $file_or_directory) { @argv = @$file_or_directory; } else { @argv = $file_or_directory; } foreach (@argv) { if (/\.gz$/) { $_ = "gunzip -c $_ |"; } elsif (/\.Z$/) { $_ = "uncompress -c $_ |"; } elsif (/\.bz2$/) { $_ = "bunzip2 -c $_ |"; } } @argv; } =head2 lock_on_load Title : lock_on_load Usage : $lock = $db->lock_on_load([$lock]) Function: set write locking during load Returns : current value of lock-on-load flag Args : new value of lock-on-load-flag Status : Public This method is honored by some of the adaptors. If the value is true, the tables used by the GFF modules will be locked for writing during loads and inaccessible to other processes. =cut sub lock_on_load { my $self = shift; my $d = $self->{lock}; $self->{lock} = shift if @_; $d; } =head2 meta Title : meta Usage : $value = $db->meta($name [,$newval]) Function: get or set a meta variable Returns : a string Args : meta variable name and optionally value Status : abstract Get or set a named metavalues for the database. Metavalues can be used for database-specific settings. By default, this method does nothing! =cut sub meta { my $self = shift; my ($name,$value) = @_; return; } =head2 default_meta_values Title : default_meta_values Usage : %values = $db->default_meta_values Function: empty the database Returns : a list of tag=>value pairs Args : none Status : protected This method returns a list of tag=Evalue pairs that contain default meta information about the database. It is invoked by initialize() to write out the default meta values. The base class version returns an empty list. For things to work properly, meta value names must be UPPERCASE. =cut sub default_meta_values { my $self = shift; return (); } =head2 error Title : error Usage : $db->error( [$new error] ); Function: read or set error message Returns : error message Args : an optional argument to set the error message Status : Public This method can be used to retrieve the last error message. Errors are not reset to empty by successful calls, so contents are only valid immediately after an error condition has been detected. =cut sub error { my $self = shift; my $g = $self->{error}; $self->{error} = join '',@_ if @_; $g; } =head2 debug Title : debug Usage : $db->debug( [$flag] ); Function: read or set debug flag Returns : current value of debug flag Args : new debug flag (optional) Status : Public This method can be used to turn on debug messages. The exact nature of those messages depends on the adaptor in use. =cut sub debug { my $self = shift; my $g = $self->{debug}; $self->{debug} = shift if @_; $g; } =head2 automerge Title : automerge Usage : $db->automerge( [$new automerge] ); Function: get or set automerge value Returns : current value (boolean) Args : an optional argument to set the automerge value Status : Public By default, this module will use the aggregators to merge groups into single composite objects. This default can be changed to false by calling automerge(0). =cut sub automerge { my $self = shift; my $g = $self->{automerge}; $self->{automerge} = shift if @_; $g; } =head2 attributes Title : attributes Usage : @attributes = $db->attributes($id,$name) Function: get the "attributes" on a particular feature Returns : an array of string Args : feature ID Status : public Some GFF version 2 files use the groups column to store a series of attribute/value pairs. In this interpretation of GFF, the first such pair is treated as the primary group for the feature; subsequent pairs are treated as attributes. Two attributes have special meaning: "Note" is for backward compatibility and is used for unstructured text remarks. "Alias" is considered as a synonym for the feature name. If no name is provided, then attributes() returns a flattened hash, of attribute=Evalue pairs. This lets you do: %attributes = $db->attributes($id); If no arguments are provided, attributes() will return the list of all attribute names: @attribute_names = $db->attributes(); Normally, however, attributes() will be called by the feature: @notes = $feature->attributes('Note'); In a scalar context, attributes() returns the first value of the attribute if a tag is present, otherwise a hash reference in which the keys are attribute names and the values are anonymous arrays containing the values. =cut sub attributes { my $self = shift; my ($id,$tag) = @_; my @result = $self->do_attributes(@_) or return; return @result if wantarray; # what to do in an array context return $result[0] if $tag; my %result; while (my($key,$value) = splice(@result,0,2)) { push @{$result{$key}},$value; } return \%result; } =head2 fast_queries Title : fast_queries Usage : $flag = $db->fast_queries([$flag]) Function: turn on and off the "fast queries" option Returns : a boolean Args : a boolean flag (optional) Status : public The mysql database driver (and possibly others) support a "fast" query mode that caches results on the server side. This makes queries come back faster, particularly when creating iterators. The downside is that while iterating, new queries will die with a "command synch" error. This method turns the feature on and off. For databases that do not support a fast query, this method has no effect. =cut # override this method in order to set the mysql_use_result attribute, which is an obscure # but extremely powerful optimization for both performance and memory. sub fast_queries { my $self = shift; my $d = $self->{fast_queries}; $self->{fast_queries} = shift if @_; $d; } =head2 add_aggregator Title : add_aggregator Usage : $db->add_aggregator($aggregator) Function: add an aggregator to the list Returns : nothing Args : an aggregator Status : public This method will append an aggregator to the end of the list of registered aggregators. Three different argument types are accepted: 1) a Bio::DB::GFF::Aggregator object -- will be added 2) a string in the form "aggregator_name{subpart1,subpart2,subpart3/main_method}" -- will be turned into a Bio::DB::GFF::Aggregator object (the /main_method part is optional). 3) a valid Perl token -- will be turned into a Bio::DB::GFF::Aggregator subclass, where the token corresponds to the subclass name. =cut sub add_aggregator { my $self = shift; my $aggregator = shift; my $list = $self->{aggregators} ||= []; if (ref $aggregator) { # an object @$list = grep {$_->get_method ne $aggregator->get_method} @$list; push @$list,$aggregator; } elsif ($aggregator =~ /^(\w+)\{([^\/\}]+)\/?(.*)\}$/) { my($agg_name,$subparts,$mainpart) = ($1,$2,$3); my @subparts = split /,\s*/,$subparts; my @args = (-method => $agg_name, -sub_parts => \@subparts); if ($mainpart) { push @args,(-main_method => $mainpart, -whole_object => 1); } warn "making an aggregator with (@args), subparts = @subparts" if $self->debug; push @$list,Bio::DB::GFF::Aggregator->new(@args); } else { my $class = "Bio::DB::GFF::Aggregator::\L${aggregator}\E"; eval "require $class; 1" or $self->throw("Unable to load $aggregator aggregator: $@"); push @$list,$class->new(); } } =head2 aggregators Title : aggregators Usage : $db->aggregators([@new_aggregators]); Function: retrieve list of aggregators Returns : list of aggregators Args : a list of aggregators to set (optional) Status : public This method will get or set the list of aggregators assigned to the database. If 1 or more arguments are passed, the existing set will be cleared. =cut sub aggregators { my $self = shift; my $d = $self->{aggregators}; if (@_) { $self->clear_aggregators; $self->add_aggregator($_) foreach @_; } return unless $d; return @$d; } =head2 clear_aggregators Title : clear_aggregators Usage : $db->clear_aggregators Function: clears list of aggregators Returns : nothing Args : none Status : public This method will clear the aggregators stored in the database object. Use aggregators() or add_aggregator() to add some back. =cut sub clear_aggregators { shift->{aggregators} = [] } =head2 preferred_groups Title : preferred_groups Usage : $db->preferred_groups([$group_name_or_arrayref]) Function: get/set list of groups for altering GFF2 parsing Returns : a list of classes Args : new list (scalar or array ref) Status : public =cut sub preferred_groups { my $self = shift; my $d = $self->{preferred_groups}; if (@_) { my @v = map {ref($_) eq 'ARRAY' ? @$_ : $_} @_; $self->{preferred_groups} = \@v; delete $self->{preferred_groups_hash}; } return unless $d; return @$d; } sub _preferred_groups_hash { my $self = shift; my $gff3 = shift; return $self->{preferred_groups_hash} if exists $self->{preferred_groups_hash}; my $count = 0; my @preferred = $self->preferred_groups; # defaults if (!@preferred) { @preferred = $gff3 || $self->{load_data}{gff3_flag} ? qw(Target Parent ID) : qw(Target Sequence Transcript); } my %preferred = map {lc($_) => @preferred-$count++} @preferred; return $self->{preferred_groups_hash} = \%preferred; } =head1 Methods for use by Subclasses The following methods are chiefly of interest to subclasses and are not intended for use by end programmers. =head2 abscoords Title : abscoords Usage : $db->abscoords($name,$class,$refseq) Function: finds position of a landmark in reference coordinates Returns : ($ref,$class,$start,$stop,$strand) Args : name and class of landmark Status : public This method is called by Bio::DB::GFF::RelSegment to obtain the absolute coordinates of a sequence landmark. The arguments are the name and class of the landmark. If successful, abscoords() returns the ID of the reference sequence, its class, its start and stop positions, and the orientation of the reference sequence's coordinate system ("+" for forward strand, "-" for reverse strand). If $refseq is present in the argument list, it forces the query to search for the landmark in a particular reference sequence. =cut sub abscoords { my $self = shift; my ($name,$class,$refseq) = @_; $class ||= $self->{default_class}; $self->get_abscoords($name,$class,$refseq); } =head1 Protected API The following methods are not intended for public consumption, but are intended to be overridden/implemented by adaptors. =head2 default_aggregators Title : default_aggregators Usage : $db->default_aggregators; Function: retrieve list of aggregators Returns : array reference containing list of aggregator names Args : none Status : protected This method (which is intended to be overridden by adaptors) returns a list of standard aggregators to be applied when no aggregators are specified in the constructor. =cut sub default_aggregators { my $self = shift; return ['processed_transcript','alignment']; } =head2 do_load_gff Title : do_load_gff Usage : $db->do_load_gff($handle) Function: load a GFF input stream Returns : number of features loaded Args : A filehandle. Status : protected This method is called to load a GFF data stream. The method will read GFF features from EE and load them into the database. On exit the method must return the number of features loaded. Note that the method is responsible for parsing the GFF lines. This is to allow for differences in the interpretation of the "group" field, which are legion. You probably want to use load_gff() instead. It is more flexible about the arguments it accepts. =cut sub do_load_gff { my $self = shift; my $io_handle = shift; local $self->{load_data} = { lineend => (-t STDERR && !$ENV{EMACS} ? "\r" : "\n"), count => 0 }; $self->setup_load(); my $mode = 'gff'; while (<$io_handle>) { chomp; if ($mode eq 'gff') { if (/^>/) { # Sequence coming $mode = 'fasta'; $self->_load_sequence_start; $self->_load_sequence_line($_); } else { $self->_load_gff_line($_); } } elsif ($mode eq 'fasta') { if (/^##|\t/) { # Back to GFF mode $self->_load_sequence_finish; $mode = 'gff'; $self->_load_gff_line($_); } else { $self->_load_sequence_line($_); } } } $self->finish_load(); $self->_load_sequence_finish; return $self->{load_data}{count}; } sub _load_gff_line { my $self = shift; my $line = shift; my $lineend = $self->{load_data}{lineend}; $self->{load_data}{gff3_flag}++ if $line =~ /^\#\#\s*gff-version\s+3/; if (defined $self->{load_data}{gff3_flag} and !defined $self->{load_data}{gff3_warning}) { $self->print_gff3_warning(); $self->{load_data}{gff3_warning}=1; } $self->preferred_groups(split(/\s+/,$1)) if $line =~ /^\#\#\s*group-tags?\s+(.+)/; if ($line =~ /^\#\#\s*sequence-region\s+(\S+)\s+(-?\d+)\s+(-?\d+)/i) { # header line $self->load_gff_line( { ref => $1, class => 'Sequence', source => 'reference', method => 'Component', start => $2, stop => $3, score => undef, strand => undef, phase => undef, gclass => 'Sequence', gname => $1, tstart => undef, tstop => undef, attributes => [], } ); return $self->{load_data}{count}++; } return if /^#/; my ($ref,$source,$method,$start,$stop,$score,$strand,$phase,$group) = split "\t",$line; return unless defined($ref) && defined($method) && defined($start) && defined($stop); foreach (\$score,\$strand,\$phase) { undef $$_ if $$_ eq '.'; } my ($gclass,$gname,$tstart,$tstop,$attributes) = $self->split_group($group,$self->{load_data}{gff3_flag}); # no standard way in the GFF file to denote the class of the reference sequence -- drat! # so we invoke the factory to do it my $class = $self->refclass($ref); # call subclass to do the dirty work if ($start > $stop) { ($start,$stop) = ($stop,$start); if ($strand eq '+') { $strand = '-'; } elsif ($strand eq '-') { $strand = '+'; } } # GFF2/3 transition stuff $gclass = [$gclass] unless ref $gclass; $gname = [$gname] unless ref $gname; for (my $i=0; $i<@$gname;$i++) { $self->load_gff_line({ref => $ref, class => $class, source => $source, method => $method, start => $start, stop => $stop, score => $score, strand => $strand, phase => $phase, gclass => $gclass->[$i], gname => $gname->[$i], tstart => $tstart, tstop => $tstop, attributes => $attributes} ); $self->{load_data}{count}++; } } sub _load_sequence_start { my $self = shift; my $ld = $self->{load_data}; undef $ld->{id}; $ld->{offset} = 0; $ld->{seq} = ''; } sub _load_sequence_finish { my $self = shift; my $ld = $self->{load_data}; $self->insert_sequence($ld->{id},$ld->{offset},$ld->{seq}) if defined $ld->{id}; } sub _load_sequence_line { my $self = shift; my $line = shift; my $ld = $self->{load_data}; my $lineend = $ld->{lineend}; if (/^>(\S+)/) { $self->insert_sequence($ld->{id},$ld->{offset},$ld->{seq}) if defined $ld->{id}; $ld->{id} = $1; $ld->{offset} = 0; $ld->{seq} = ''; $ld->{count}++; print STDERR $ld->{count}," sequences loaded$lineend" if $self->{__verbose__} && $ld->{count} % 1000 == 0; } else { $ld->{seq} .= $_; $self->insert_sequence_chunk($ld->{id},\$ld->{offset},\$ld->{seq}); } } =head2 load_sequence Title : load_sequence Usage : $db->load_sequence($handle) Function: load a FASTA data stream Returns : number of sequences Args : a filehandle to the FASTA file Status : protected You probably want to use load_fasta() instead. =cut # note - there is some repeated code here sub load_sequence { my $self = shift; my $io_handle = shift; local $self->{load_data} = { lineend => (-t STDERR && !$ENV{EMACS} ? "\r" : "\n"), count => 0 }; $self->_load_sequence_start; while (<$io_handle>) { chomp; $self->_load_sequence_line($_); } $self->_load_sequence_finish; return $self->{load_data}{count}; } sub insert_sequence_chunk { my $self = shift; my ($id,$offsetp,$seqp) = @_; if (my $cs = $self->dna_chunk_size) { while (length($$seqp) >= $cs) { my $chunk = substr($$seqp,0,$cs); $self->insert_sequence($id,$$offsetp,$chunk); $$offsetp += length($chunk); substr($$seqp,0,$cs) = ''; } } return 1; # the calling routine may expect success or failure } # used to store big pieces of DNA in itty bitty pieces sub dna_chunk_size { return 0; } sub insert_sequence { my $self = shift; my($id,$offset,$seq) = @_; $self->throw('insert_sequence(): must be defined in subclass'); } # This is the default class for reference points. Defaults to Sequence. sub default_class { my $self = shift; return 'Sequence' unless ref $self; my $d = $self->{default_class}; $self->{default_class} = shift if @_; $d; } # gets name of the reference sequence, and returns its class # currently just calls default_class sub refclass { my $self = shift; my $name = shift; return $self->default_class; } =head2 setup_load Title : setup_load Usage : $db->setup_load Function: called before load_gff_line() Returns : void Args : none Status : abstract This abstract method gives subclasses a chance to do any schema-specific initialization prior to loading a set of GFF records. It must be implemented by a subclass. =cut sub setup_load { # default, do nothing } =head2 finish_load Title : finish_load Usage : $db->finish_load Function: called after load_gff_line() Returns : number of records loaded Args : none Status :abstract This method gives subclasses a chance to do any schema-specific cleanup after loading a set of GFF records. =cut sub finish_load { # default, do nothing } =head2 load_gff_line Title : load_gff_line Usage : $db->load_gff_line(@args) Function: called to load one parsed line of GFF Returns : true if successfully inserted Args : see below Status : abstract This abstract method is called once per line of the GFF and passed a hashref containing parsed GFF fields. The fields are: {ref => $ref, class => $class, source => $source, method => $method, start => $start, stop => $stop, score => $score, strand => $strand, phase => $phase, gclass => $gclass, gname => $gname, tstart => $tstart, tstop => $tstop, attributes => $attributes} =cut sub load_gff_line { shift->throw("load_gff_line(): must be implemented by an adaptor"); } =head2 do_initialize Title : do_initialize Usage : $db->do_initialize([$erase]) Function: initialize and possibly erase database Returns : true if successful Args : optional erase flag Status : protected This method implements the initialize() method described above, and takes the same arguments. =cut sub do_initialize { shift->throw('do_initialize(): must be implemented by an adaptor'); } =head2 dna Title : dna Usage : $db->dna($id,$start,$stop,$class) Function: return the raw DNA string for a segment Returns : a raw DNA string Args : id of the sequence, its class, start and stop positions Status : public This method is invoked by Bio::DB::GFF::Segment to fetch the raw DNA sequence. Arguments: -name sequence name -start start position -stop stop position -class sequence class If start and stop are both undef, then the entire DNA is retrieved. So to fetch the whole dna, call like this: $db->dna($name_of_sequence); or like this: $db->dna(-name=>$name_of_sequence,-class=>$class_of_sequence); NOTE: you will probably prefer to create a Segment and then invoke its dna() method. =cut # call to return the DNA string for the indicated region # real work is done by get_dna() sub dna { my $self = shift; my ($id,$start,$stop,$class) = rearrange([ [qw(NAME ID REF REFSEQ)], qw(START), [qw(STOP END)], 'CLASS', ],@_); # return unless defined $start && defined $stop; $self->get_dna($id,$start,$stop,$class); } sub fetch_sequence { shift->dna(@_) } sub features_in_range { my $self = shift; my ($range_type,$refseq,$class,$start,$stop,$types,$parent,$sparse,$automerge,$iterator,$other) = rearrange([ [qw(RANGE_TYPE)], [qw(REF REFSEQ)], qw(CLASS), qw(START), [qw(STOP END)], [qw(TYPE TYPES)], qw(PARENT), [qw(RARE SPARSE)], [qw(MERGE AUTOMERGE)], 'ITERATOR' ],@_); $other ||= {}; # $automerge = $types && $self->automerge unless defined $automerge; $automerge = $self->automerge unless defined $automerge; $self->throw("range type must be one of {". join(',',keys %valid_range_types). "}\n") unless $valid_range_types{lc $range_type}; $self->_features({ rangetype => lc $range_type, refseq => $refseq, refclass => $class, start => $start, stop => $stop, types => $types }, { sparse => $sparse, automerge => $automerge, iterator => $iterator, %$other, }, $parent); } =head2 get_dna Title : get_dna Usage : $db->get_dna($id,$start,$stop,$class) Function: get DNA for indicated segment Returns : the dna string Args : sequence ID, start, stop and class Status : protected If start E stop and the sequence is nucleotide, then this method should return the reverse complement. The sequence class may be ignored by those databases that do not recognize different object types. =cut sub get_dna { my $self = shift; my ($id,$start,$stop,$class,) = @_; $self->throw("get_dna() must be implemented by an adaptor"); } =head2 get_features Title : get_features Usage : $db->get_features($search,$options,$callback) Function: get list of features for a region Returns : count of number of features retrieved Args : see below Status : protected The first argument is a hash reference containing search criteria for retrieving features. It contains the following keys: rangetype One of "overlaps", "contains" or "contained_in". Indicates the type of range query requested. refseq ID of the landmark that establishes the absolute coordinate system. refclass Class of this landmark. Can be ignored by implementations that don't recognize such distinctions. start Start of the range, inclusive. stop Stop of the range, inclusive. types Array reference containing the list of annotation types to fetch from the database. Each annotation type is an array reference consisting of [source,method]. The second argument is a hash reference containing certain options that affect the way information is retrieved: sort_by_group A flag. If true, means that the returned features should be sorted by the group that they're in. sparse A flag. If true, means that the expected density of the features is such that it will be more efficient to search by type rather than by range. If it is taking a long time to fetch features, give this a try. binsize A true value will create a set of artificial features whose start and stop positions indicate bins of the given size, and whose scores are the number of features in the bin. The class of the feature will be set to "bin", and its name to "method:source". This is a handy way of generating histograms of feature density. The third argument, the $callback, is a code reference to which retrieved features are passed. It is described in more detail below. This routine is responsible for getting arrays of GFF data out of the database and passing them to the callback subroutine. The callback does the work of constructing a Bio::DB::GFF::Feature object out of that data. The callback expects a list of 13 fields: $refseq The reference sequence $start feature start $stop feature stop $source feature source $method feature method $score feature score $strand feature strand $phase feature phase $groupclass group class (may be undef) $groupname group ID (may be undef) $tstart target start for similarity hits (may be undef) $tstop target stop for similarity hits (may be undef) $feature_id A unique feature ID (may be undef) These fields are in the same order as the raw GFF file, with the exception that the group column has been parsed into group class and group name fields. The feature ID, if provided, is a unique identifier of the feature line. The module does not depend on this ID in any way, but it is available via Bio::DB::GFF-Eid() if wanted. In the dbi::mysql and dbi::mysqlopt adaptor, the ID is a unique row ID. In the acedb adaptor it is not used. =cut =head2 feature_summary(), coverage_array() The DBI adaptors provide methods for rapidly fetching coverage statistics across a region of interest. Please see L for more information about these methods. =cut sub get_features{ my $self = shift; my ($search,$options,$callback) = @_; $self->throw("get_features() must be implemented by an adaptor"); } =head2 _feature_by_name Title : _feature_by_name Usage : $db->_feature_by_name($class,$name,$location,$callback) Function: get a list of features by name and class Returns : count of number of features retrieved Args : name of feature, class of feature, and a callback Status : abstract This method is used internally. The callback arguments are the same as those used by make_feature(). This method must be overridden by subclasses. =cut sub _feature_by_name { my $self = shift; my ($class,$name,$location,$callback) = @_; $self->throw("_feature_by_name() must be implemented by an adaptor"); } sub _feature_by_attribute { my $self = shift; my ($attributes,$callback) = @_; $self->throw("_feature_by_name() must be implemented by an adaptor"); } =head2 _feature_by_id Title : _feature_by_id Usage : $db->_feature_by_id($ids,$type,$callback) Function: get a feature based Returns : count of number of features retrieved Args : arrayref to feature IDs to fetch Status : abstract This method is used internally to fetch features either by their ID or their group ID. $ids is a arrayref containing a list of IDs, $type is one of "feature" or "group", and $callback is a callback. The callback arguments are the same as those used by make_feature(). This method must be overridden by subclasses. =cut sub _feature_by_id { my $self = shift; my ($ids,$type,$callback) = @_; $self->throw("_feature_by_id() must be implemented by an adaptor"); } =head2 overlapping_features Title : overlapping_features Usage : $db->overlapping_features(@args) Function: get features that overlap the indicated range Returns : a list of Bio::DB::GFF::Feature objects Args : see below Status : public This method is invoked by Bio::DB::GFF::Segment-Efeatures() to find the list of features that overlap a given range. It is generally preferable to create the Segment first, and then fetch the features. This method takes set of named arguments: -refseq ID of the reference sequence -class Class of the reference sequence -start Start of the desired range in refseq coordinates -stop Stop of the desired range in refseq coordinates -types List of feature types to return. Argument is an array reference containing strings of the format "method:source" -parent A parent Bio::DB::GFF::Segment object, used to create relative coordinates in the generated features. -rare Turn on an optimization suitable for a relatively rare feature type, where it will be faster to filter by feature type first and then by position, rather than vice versa. -merge Whether to apply aggregators to the generated features. -iterator Whether to return an iterator across the features. If -iterator is true, then the method returns a single scalar value consisting of a Bio::SeqIO object. You can call next_seq() repeatedly on this object to fetch each of the features in turn. If iterator is false or absent, then all the features are returned as a list. Currently aggregation is disabled when iterating over a series of features. Types are indicated using the nomenclature "method:source". Either of these fields can be omitted, in which case a wildcard is used for the missing field. Type names without the colon (e.g. "exon") are interpreted as the method name and a source wild card. Regular expressions are allowed in either field, as in: "similarity:BLAST.*". =cut # call to return the features that overlap the named region # real work is done by get_features sub overlapping_features { my $self = shift; $self->features_in_range(-range_type=>'overlaps',@_); } =head2 contained_features Title : contained_features Usage : $db->contained_features(@args) Function: get features that are contained within the indicated range Returns : a list of Bio::DB::GFF::Feature objects Args : see overlapping_features() Status : public This call is similar to overlapping_features(), except that it only retrieves features whose end points are completely contained within the specified range. Generally you will want to fetch a Bio::DB::GFF::Segment object and call its contained_features() method rather than call this directly. =cut # The same, except that it only returns features that are completely contained within the # range (much faster usually) sub contained_features { my $self = shift; $self->features_in_range(-range_type=>'contains',@_); } =head2 contained_in Title : contained_in Usage : @features = $s->contained_in(@args) Function: get features that contain this segment Returns : a list of Bio::DB::GFF::Feature objects Args : see features() Status : Public This is identical in behavior to features() except that it returns only those features that completely contain the segment. =cut sub contained_in { my $self = shift; $self->features_in_range(-range_type=>'contained_in',@_); } =head2 get_abscoords Title : get_abscoords Usage : $db->get_abscoords($name,$class,$refseq) Function: get the absolute coordinates of sequence with name & class Returns : ($absref,$absstart,$absstop,$absstrand) Args : name and class of the landmark Status : protected Given the name and class of a genomic landmark, this function returns a four-element array consisting of: $absref the ID of the reference sequence that contains this landmark $absstart the position at which the landmark starts $absstop the position at which the landmark stops $absstrand the strand of the landmark, relative to the reference sequence If $refseq is provided, the function searches only within the specified reference sequence. =cut sub get_abscoords { my $self = shift; my ($name,$class,$refseq) = @_; $self->throw("get_abscoords() must be implemented by an adaptor"); } =head2 get_types Title : get_types Usage : $db->get_types($absref,$class,$start,$stop,$count) Function: get list of all feature types on the indicated segment Returns : list or hash of Bio::DB::GFF::Typename objects Args : see below Status : protected Arguments are: $absref the ID of the reference sequence $class the class of the reference sequence $start the position to start counting $stop the position to end counting $count a boolean indicating whether to count the number of occurrences of each feature type If $count is true, then a hash is returned. The keys of the hash are feature type names in the format "method:source" and the values are the number of times a feature of this type overlaps the indicated segment. Otherwise, the call returns a set of Bio::DB::GFF::Typename objects. If $start or $stop are undef, then all features on the indicated segment are enumerated. If $absref is undef, then the call returns all feature types in the database. =cut sub get_types { my $self = shift; my ($refseq,$class,$start,$stop,$count,$types) = @_; $self->throw("get_types() must be implemented by an adaptor"); } =head2 make_feature Title : make_feature Usage : $db->make_feature(@args) Function: Create a Bio::DB::GFF::Feature object from string data Returns : a Bio::DB::GFF::Feature object Args : see below Status : internal This takes 14 arguments (really!): $parent A Bio::DB::GFF::RelSegment object $group_hash A hashref containing unique list of GFF groups $refname The name of the reference sequence for this feature $refclass The class of the reference sequence for this feature $start Start of feature $stop Stop of feature $source Feature source field $method Feature method field $score Feature score field $strand Feature strand $phase Feature phase $group_class Class of feature group $group_name Name of feature group $tstart For homologies, start of hit on target $tstop Stop of hit on target The $parent argument, if present, is used to establish relative coordinates in the resulting Bio::DB::Feature object. This allows one feature to generate a list of other features that are relative to its coordinate system (for example, finding the coordinates of the second exon relative to the coordinates of the first). The $group_hash allows the group_class/group_name strings to be turned into rich database objects via the make_obect() method (see above). Because these objects may be expensive to create, $group_hash is used to uniquefy them. The index of this hash is the composite key {$group_class,$group_name,$tstart,$tstop}. Values are whatever object is returned by the make_object() method. The remainder of the fields are taken from the GFF line, with the exception that "Target" features, which contain information about the target of a homology search, are parsed into their components. =cut # This call is responsible for turning a line of GFF into a # feature object. # The $parent argument is a Bio::DB::GFF::Segment object and is used # to establish the coordinate system for the new feature. # The $group_hash argument is an hash ref that holds previously- # generated group objects. # Other arguments are taken right out of the GFF table. sub make_feature { my $self = shift; my ($parent,$group_hash, # these arguments provided by generic mechanisms $srcseq, # the rest is provided by adaptor $start,$stop, $source,$method, $score,$strand,$phase, $group_class,$group_name, $tstart,$tstop, $db_id,$group_id) = @_; return unless $srcseq; # return undef if called with no arguments. This behavior is used for # on-the-fly aggregation. my $group; # undefined if (defined $group_class && defined $group_name) { $tstart ||= ''; $tstop ||= ''; if ($group_hash) { $group = $group_hash->{$group_class,$group_name,$tstart,$tstop} ||= $self->make_object($group_class,$group_name,$tstart,$tstop); } else { $group = $self->make_object($group_class,$group_name,$tstart,$tstop); } } # fix for some broken GFF files # unfortunately - has undesired side effects # if (defined $tstart && defined $tstop && !defined $strand) { # $strand = $tstart <= $tstop ? '+' : '-'; # } if (ref $parent) { # note that the src sequence is ignored return Bio::DB::GFF::Feature->new_from_parent($parent,$start,$stop, $method,$source, $score,$strand,$phase, $group,$db_id,$group_id, $tstart,$tstop); } else { return Bio::DB::GFF::Feature->new($self,$srcseq, $start,$stop, $method,$source, $score,$strand,$phase, $group,$db_id,$group_id, $tstart,$tstop); } } sub make_aggregated_feature { my $self = shift; my ($accumulated_features,$parent,$aggregators) = splice(@_,0,3); my $feature = $self->make_feature($parent,undef,@_); return [$feature] if $feature && !$feature->group; # if we have accumulated features and either: # (1) make_feature() returned undef, indicated very end or # (2) the current group is different from the previous one local $^W = 0; # irritating uninitialized value warning in next statement if (@$accumulated_features && (!defined($feature) || ($accumulated_features->[-1]->group ne $feature->group))) { foreach my $a (@$aggregators) { # last aggregator gets first shot $a->aggregate($accumulated_features,$self) or next; } my @result = @$accumulated_features; @$accumulated_features = $feature ? ($feature) : (); return unless @result; return \@result ; } push @$accumulated_features,$feature; return; } =head2 make_match_sub Title : make_match_sub Usage : $db->make_match_sub($types) Function: creates a subroutine used for filtering features Returns : a code reference Args : a list of parsed type names Status : protected This method is used internally to generate a code subroutine that will accept or reject a feature based on its method and source. It takes an array of parsed type names in the format returned by parse_types(), and generates an anonymous subroutine. The subroutine takes a single Bio::DB::GFF::Feature object and returns true if the feature matches one of the desired feature types, and false otherwise. =cut # a subroutine that matches features indicated by list of types sub make_match_sub { my $self = shift; my $types = shift; return sub { 1 } unless ref $types && @$types; my @expr; for my $type (@$types) { my ($method,$source) = @$type; $method = $method ? "\\Q$method\\E" : ".*"; $source = $source ? ":\\Q$source\\E" : "(?::.+)?"; push @expr,"${method}${source}"; } my $expr = join '|',@expr; return $self->{match_subs}{$expr} if $self->{match_subs}{$expr}; my $sub =<type =~ /^($expr)\$/i; } END warn "match sub: $sub\n" if $self->debug; undef $@; my $compiled_sub = eval $sub; $self->throw($@) if $@; return $self->{match_subs}{$expr} = $compiled_sub; } =head2 make_object Title : make_object Usage : $db->make_object($class,$name,$start,$stop) Function: creates a feature object Returns : a feature object Args : see below Status : protected This method is called to make an object from the GFF "group" field. By default, all Target groups are turned into Bio::DB::GFF::Homol objects, and everything else becomes a Bio::DB::GFF::Featname. However, adaptors are free to override this method to generate more interesting objects, such as true BioPerl objects, or Acedb objects. Arguments are: $name database ID for object $class class of object $start for similarities, start of match inside object $stop for similarities, stop of match inside object =cut # abstract call to turn a feature into an object, given its class and name sub make_object { my $self = shift; my ($class,$name,$start,$stop) = @_; return Bio::DB::GFF::Homol->new($self,$class,$name,$start,$stop) if defined $start and length $start; return Bio::DB::GFF::Featname->new($class,$name); } =head2 do_attributes Title : do_attributes Usage : $db->do_attributes($id [,$tag]); Function: internal method to retrieve attributes given an id and tag Returns : a list of Bio::DB::GFF::Feature objects Args : a feature id and a attribute tag (optional) Status : protected This method is overridden by subclasses in order to return a list of attributes. If called with a tag, returns the value of attributes of that tag type. If called without a tag, returns a flattened array of (tag=Evalue) pairs. A particular tag can be present multiple times. =cut sub do_attributes { my $self = shift; my ($id,$tag) = @_; return (); } =head2 clone The clone() method should be used when you want to pass the Bio::DB::GFF object to a child process across a fork(). The child must call clone() before making any queries. The default behavior is to do nothing, but adaptors that use the DBI interface may need to implement this in order to avoid database handle errors. See the dbi adaptor for an example. =cut sub clone { } =head1 Internal Methods The following methods are internal to Bio::DB::GFF and are not guaranteed to remain the same. =head2 _features Title : _features Usage : $db->_features($search,$options,$parent) Function: internal method Returns : a list of Bio::DB::GFF::Feature objects Args : see below Status : internal This is an internal method that is called by overlapping_features(), contained_features() and features() to create features based on a parent segment's coordinate system. It takes three arguments, a search options hashref, an options hashref, and a parent segment. The search hashref contains the following keys: rangetype One of "overlaps", "contains" or "contained_in". Indicates the type of range query requested. refseq reference sequence ID refclass reference sequence class start start of range stop stop of range types arrayref containing list of types in "method:source" form The options hashref contains zero or more of the following keys: sparse turn on optimizations for a rare feature automerge if true, invoke aggregators to merge features iterator if true, return an iterator The $parent argument is a scalar object containing a Bio::DB::GFF::RelSegment object or descendent. =cut #' sub _features { my $self = shift; my ($search,$options,$parent) = @_; (@{$search}{qw(start stop)}) = (@{$search}{qw(stop start)}) if defined($search->{start}) && $search->{start} > $search->{stop}; $search->{refseq} = $search->{seq_id} if exists $search->{seq_id}; my $types = $self->parse_types($search->{types}); # parse out list of types my @aggregated_types = @$types; # keep a copy # allow the aggregators to operate on the original my @aggregators; if ($options->{automerge}) { for my $a ($self->aggregators) { $a = $a->clone if $options->{iterator}; unshift @aggregators,$a if $a->disaggregate(\@aggregated_types,$self); } } if ($options->{iterator}) { my @accumulated_features; my $callback = $options->{automerge} ? sub { $self->make_aggregated_feature(\@accumulated_features,$parent,\@aggregators,@_) } : sub { [$self->make_feature($parent,undef,@_)] }; return $self->get_features_iterator({ %$search, types => \@aggregated_types }, { %$options, sort_by_group => $options->{automerge} }, $callback ); } my %groups; # cache the groups we create to avoid consuming too much unecessary memory my $features = []; my $callback = sub { push @$features,$self->make_feature($parent,\%groups,@_) }; $self->get_features({ %$search, types => \@aggregated_types }, $options, $callback); if ($options->{automerge}) { warn "aggregating...\n" if $self->debug; foreach my $a (@aggregators) { # last aggregator gets first shot warn "Aggregator $a:\n" if $self->debug; $a->aggregate($features,$self); } } @$features; } =head2 get_features_iterator Title : get_features_iterator Usage : $db->get_features_iterator($search,$options,$callback) Function: get an iterator on a features query Returns : a Bio::SeqIO object Args : as per get_features() Status : Public This method takes the same arguments as get_features(), but returns an iterator that can be used to fetch features sequentially, as per Bio::SeqIO. Internally, this method is simply a front end to range_query(). The latter method constructs and executes the query, returning a statement handle. This routine passes the statement handle to the constructor for the iterator, along with the callback. =cut sub get_features_iterator { my $self = shift; my ($search,$options,$callback) = @_; $self->throw('feature iteration is not implemented in this adaptor'); } =head2 split_group Title : split_group Usage : $db->split_group($group_field,$gff3_flag) Function: parse GFF group field Returns : ($gclass,$gname,$tstart,$tstop,$attributes) Args : the gff group column and a flag indicating gff3 compatibility Status : internal This is a method that is called by load_gff_line to parse out the contents of one or more group fields. It returns the class of the group, its name, the start and stop of the target, if any, and an array reference containing any attributes that were stuck into the group field, in [attribute_name,attribute_value] format. =cut sub split_group { my $self = shift; my ($group,$gff3) = @_; if ($gff3) { my @groups = split /[;&]/,$group; # so easy! return $self->_split_gff3_group(@groups); } else { # handle group parsing # protect embedded semicolons in the group; there must be faster/more elegant way # to do this. $group =~ s/\\;/$;/g; while ($group =~ s/( \"[^\"]*);([^\"]*\")/$1$;$2/) { 1 } my @groups = split(/\s*;\s*/,$group); foreach (@groups) { s/$;/;/g } return $self->_split_gff2_group(@groups); } } =head2 _split_gff2_group This is an internal method called by split_group(). =cut # this has gotten quite nasty due to transition from GFF2 to GFF2.5 # (artemis) to GFF3. sub _split_gff2_group { my $self = shift; my @groups = @_; my $target_found; my ($gclass,$gname,$tstart,$tstop,@attributes,@notes); for (@groups) { my ($tag,$value) = /^(\S+)(?:\s+(.+))?/; $value = '' unless defined $value; if ($value =~ /^\"(.+)\"$/) { #remove quotes $value = $1; } $value =~ s/\\t/\t/g; $value =~ s/\\r/\r/g; $value =~ s/\s+$//; # Any additional groups become part of the attributes hash # For historical reasons, the tag "Note" is treated as an # attribute, even if it is the only group. $tag ||= ''; if ($tag eq 'tstart' && $target_found) { $tstart = $value; } elsif ($tag eq 'tend' && $target_found) { $tstop = $value; } elsif (ucfirst $tag eq 'Note') { push @notes, [$tag => $value]; } elsif ($tag eq 'Target' && /([^:\"\s]+):([^\"\s]+)/) { # major disagreement in implementors of GFF2 here $target_found++; ($gclass,$gname) = ($1,$2); ($tstart,$tstop) = / (\d+) (\d+)/; } elsif (!defined($value)) { push @notes, [Note => $tag]; # e.g. "Confirmed_by_EST" } else { push @attributes, [$tag => $value]; } } # group assignment if (@attributes && !($gclass && $gname) ) { my $preferred = ref($self) ? $self->_preferred_groups_hash : {}; for my $pair (@attributes) { my ($c,$n) = @$pair; ($gclass,$gname) = ($c,$n) if !$gclass # pick up first one || ($preferred->{lc $gclass}||0) < ($preferred->{lc $c}||0); # pick up higher priority one } @attributes = grep {$gclass ne $_->[0]} @attributes; } push @attributes, @notes; return ($gclass,$gname,$tstart,$tstop,\@attributes); } =head2 gff3_name_munging Title : gff3_name_munging Usage : $db->gff3_name_munging($boolean) Function: get/set gff3_name_munging flag Returns : $current value of flag Args : new value of flag (optional) Status : utility If this is set to true (default false), then features identified in gff3 files with an ID in the format foo:bar will be parsed so that "foo" is the class and "bar" is the name. This is mostly for backward compatibility with GFF2. =cut sub gff3_name_munging { my $self = shift; my $d = $self->{gff3_name_munging}; $self->{gff3_name_munging} = shift if @_; $d; } =head2 _split_gff3_group This is called internally from split_group(). =cut sub _split_gff3_group { my $self = shift; my @groups = @_; my $dc = $self->default_class; my (%id,@attributes); for my $group (@groups) { my ($tag,$value) = split /=/,$group; $tag = unescape($tag); my @values = map {unescape($_)} split /,/,$value; # GFF2 traditionally did not distinguish between a feature's name # and the group it belonged to. This code is a transition between # gff2 and the new parent/ID dichotomy in gff3. if ($tag eq 'Parent') { my (@names,@classes); for (@values) { my ($name,$class) = $self->_gff3_name_munging($_,$dc); push @names,$name; push @classes,$class; } $id{$tag} = @names > 1 ? [\@names,\@classes] : [$names[0],$classes[0]]; } elsif ($tag eq 'ID' || $tag eq 'Name') { $id{$tag} = [$self->_gff3_name_munging(shift(@values),$dc)]; } elsif ($tag eq 'Target') { my ($gname,$tstart,$tstop) = split /\s+/,shift @values; $id{$tag} = [$self->_gff3_name_munging($gname,$dc),$tstart,$tstop]; } elsif ($tag =~ /synonym/i) { $tag = 'Alias'; } push @attributes,[$tag=>$_] foreach @values; } my $priorities = $self->_preferred_groups_hash(1); my ($gclass,$gname,$tstart,$tstop); for my $preferred (sort {$priorities->{lc $b}<=>$priorities->{lc $a}} keys %id) { unless (defined $gname) { ($gname,$gclass,$tstart,$tstop) = @{$id{$preferred}}; } } # set null gclass to empty string to preserve compatibility with # programs that expect a defined gclass if no gname $gclass ||= '' if defined $gname; return ($gclass,$gname,$tstart,$tstop,\@attributes); } # accomodation for wormbase style of class:name naming sub _gff3_name_munging { my $self = shift; my ($name,$default_class) = @_; return ($name,$default_class) unless $self->gff3_name_munging; if ($name =~ /^(\w+):(.+)/) { return ($2,$1); } else { return ($name,$default_class); } } =head2 _delete_features(), _delete_groups(),_delete(),_delete_fattribute_to_features() Title : _delete_features(), _delete_groups(),_delete(),_delete_fattribute_to_features() Usage : $count = $db->_delete_features(@feature_ids) $count = $db->_delete_groups(@group_ids) $count = $db->_delete(\%delete_spec) $count = $db->_delete_fattribute_to_features(@feature_ids) Function: low-level feature/group deleter Returns : count of groups removed Args : list of feature or group ids removed Status : for implementation by subclasses These methods need to be implemented in adaptors. For _delete_features, _delete_groups and _delete_fattribute_to_features, the arguments are a list of feature or group IDs to remove. For _delete(), the argument is a hashref with the three keys 'segments', 'types' and 'force'. The first contains an arrayref of Bio::DB::GFF::RelSegment objects to delete (all FEATURES within the segment are deleted). The second contains an arrayref of [method,source] feature types to delete. The two are ANDed together. If 'force' has a true value, this forces the operation to continue even if it would delete all features. =cut sub _delete_features { my $self = shift; my @feature_ids = @_; $self->throw('_delete_features is not implemented in this adaptor'); } sub _delete_groups { my $self = shift; my @group_ids = @_; $self->throw('_delete_groups is not implemented in this adaptor'); } sub _delete { my $self = shift; my $delete_options = shift; $self->throw('_delete is not implemented in this adaptor'); } sub _delete_fattribute_to_features { my $self = shift; my @feature_ids = @_; $self->throw('_delete_fattribute_to_features is not implemented in this adaptor'); } sub unescape { my $v = shift; $v =~ tr/+/ /; $v =~ s/%([0-9a-fA-F]{2})/chr hex($1)/ge; return $v; } sub print_gff3_warning { my $self = shift; print STDERR <$ids,db=>$db,type=>$type},$class; } sub next_seq { my $self = shift; my $next = shift @{$self->{ids}}; return unless $next; my $name = ref($next) eq 'ARRAY' ? Bio::DB::GFF::Featname->new(@$next) : $next; my $segment = $self->{type} eq 'name' ? $self->{db}->segment($name) : $self->{type} eq 'feature' ? $self->{db}->fetch_feature_by_id($name) : $self->{type} eq 'group' ? $self->{db}->fetch_feature_by_gid($name) : $self->throw("Bio::DB::GFF::ID_Iterator called to fetch an unknown type of identifier"); $self->throw("id does not exist") unless $segment; return $segment; } package Bio::DB::GFF::FeatureIterator; sub new { my $self = shift; my @features = @_; return bless \@features,ref $self || $self; } sub next_seq { my $self = shift; return unless @$self; return shift @$self; } 1; __END__ =head1 BUGS Features can only belong to a single group at a time. This must be addressed soon. Start coordinate can be greater than stop coordinate for relative addressing. This breaks strict BioPerl compatibility and must be fixed. =head1 SEE ALSO L, L, L, L, L, L L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GenBank.pm000444000766000024 2754213155576320 16406 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::GenBank # # Please direct questions and support issues to # # Cared for by Aaron Mackey # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code # # Added LWP support - Jason Stajich 2000-11-6 # completely reworked by Jason Stajich 2000-12-8 # to use WebDBSeqI # Added batch entrez back when determined that new entrez cgi will # essentially work (there is a limit to the number of characters in a # GET request so I am not sure how we can get around this). The NCBI # Batch Entrez form has changed some and it does not support retrieval # of text only data. Still should investigate POST-ing (tried and # failed) a message to the entrez cgi to get around the GET # limitations. =head1 NAME Bio::DB::GenBank - Database object interface to GenBank =head1 SYNOPSIS use Bio::DB::GenBank; $gb = Bio::DB::GenBank->new(); $seq = $gb->get_Seq_by_id('J00522'); # Unique ID, *not always the LOCUS ID* # or ... $seq = $gb->get_Seq_by_acc('J00522'); # Accession Number $seq = $gb->get_Seq_by_version('J00522.1'); # Accession.version $seq = $gb->get_Seq_by_gi('405830'); # GI Number # get a stream via a query string my $query = Bio::DB::Query::GenBank->new (-query =>'Oryza sativa[Organism] AND EST', -reldate => '30', -db => 'nucleotide'); my $seqio = $gb->get_Stream_by_query($query); while( my $seq = $seqio->next_seq ) { print "seq length is ", $seq->length,"\n"; } # or ... best when downloading very large files, prevents # keeping all of the file in memory # also don't want features, just sequence so let's save bandwidth # and request Fasta sequence $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile' , -format => 'Fasta'); my $seqio = $gb->get_Stream_by_acc(['AC013798', 'AC021953'] ); while( my $clone = $seqio->next_seq ) { print "cloneid is ", $clone->display_id, " ", $clone->accession_number, "\n"; } # note that get_Stream_by_version is not implemented # don't want the entire sequence or more options my $gb = Bio::DB::GenBank->new(-format => 'Fasta', -seq_start => 100, -seq_stop => 200, -strand => 1, -complexity => 4); my $seqi = $gb->get_Stream_by_query($query); =head1 DESCRIPTION Allows the dynamic retrieval of L sequence objects from the GenBank database at NCBI, via an Entrez query. WARNING: Please do B spam the Entrez web server with multiple requests. NCBI offers Batch Entrez for this purpose. Note that when querying for GenBank accessions starting with 'NT_' you will need to call $gb-Erequest_format('fasta') beforehand, because in GenBank format (the default) the sequence part will be left out (the reason is that NT contigs are rather annotation with references to clones). Some work has been done to automatically detect and retrieve whole NT_ clones when the data is in that format (NCBI RefSeq clones). The former behavior prior to bioperl 1.6 was to retrieve these from EBI, but now these are retrieved directly from NCBI. The older behavior can be regained by setting the 'redirect_refseq' flag to a value evaluating to TRUE. =head2 Running Alternate methods are described at L NOTE: strand should be 1 for plus or 2 for minus. Complexity: gi is often a part of a biological blob, containing other gis complexity regulates the display: 0 - get the whole blob 1 - get the bioseq for gi of interest (default in Entrez) 2 - get the minimal bioseq-set containing the gi of interest 3 - get the minimal nuc-prot containing the gi of interest 4 - get the minimal pub-set containing the gi of interest 'seq_start' and 'seq_stop' will not work when setting complexity to any value other than 1. 'strand' works for any setting other than a complexity of 0 (whole glob); when you try this with a GenBank return format nothing happens, whereas using FASTA works but causes display problems with the other sequences in the glob. As Tao Tao says from NCBI, "Better left it out or set it to 1." =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Aaron Mackey, Jason Stajich Email amackey@virginia.edu Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::GenBank; use strict; use vars qw(%PARAMSTRING $DEFAULTFORMAT $DEFAULTMODE); use base qw(Bio::DB::NCBIHelper); BEGIN { $DEFAULTMODE = 'single'; $DEFAULTFORMAT = 'gbwithparts'; %PARAMSTRING = ( 'batch' => { 'db' => 'nucleotide', 'usehistory' => 'n', 'tool' => 'bioperl'}, 'query' => { 'usehistory' => 'y', 'tool' => 'bioperl', 'retmode' => 'text'}, 'gi' => { 'db' => 'nucleotide', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, 'version' => { 'db' => 'nucleotide', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, 'single' => { 'db' => 'nucleotide', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, 'webenv' => { 'query_key' => 'querykey', 'WebEnv' => 'cookie', 'db' => 'nucleotide', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, ); } # new is in NCBIHelper # helper method to get db specific options =head2 new Title : new Usage : $gb = Bio::DB::GenBank->new(@options) Function: Creates a new genbank handle Returns : a new Bio::DB::Genbank object Args : -delay number of seconds to delay between fetches (3s) NOTE: There are other options that are used internally. By NCBI policy, this module introduces a 3s delay between fetches. If you are fetching multiple genbank ids, it is a good idea to use get =cut =head2 get_params Title : get_params Usage : my %params = $self->get_params($mode) Function: Returns key,value pairs to be passed to NCBI database for either 'batch' or 'single' sequence retrieval method Returns : a key,value pair hash Args : 'single' or 'batch' mode for retrieval =cut sub get_params { my ($self, $mode) = @_; return defined $PARAMSTRING{$mode} ? %{$PARAMSTRING{$mode}} : %{$PARAMSTRING{$DEFAULTMODE}}; } # from Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI =head1 Routines Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc($acc); Function: Gets a Seq object by accession numbers Returns : a Bio::Seq object Args : the accession number as a string Note : For GenBank, this just calls the same code for get_Seq_by_id(). Caveat: this normally works, but in rare cases simply passing the accession can lead to odd results, possibly due to unsynchronized NCBI ID servers. Using get_Seq_by_version() is slightly better, but using the unique identifier (GI) and get_Seq_by_id is the most consistent Throws : "id does not exist" exception =head2 get_Seq_by_gi Title : get_Seq_by_gi Usage : $seq = $db->get_Seq_by_gi('405830'); Function: Gets a Bio::Seq object by gi number Returns : A Bio::Seq object Args : gi number (as a string) Throws : "gi does not exist" exception =head2 get_Seq_by_version Title : get_Seq_by_version Usage : $seq = $db->get_Seq_by_version('X77802.1'); Function: Gets a Bio::Seq object by sequence version Returns : A Bio::Seq object Args : accession.version (as a string) Note : Caveat: this normally works, but using the unique identifier (GI) and get_Seq_by_id is the most consistent Throws : "acc.version does not exist" exception =head1 Routines implemented by Bio::DB::NCBIHelper =head2 get_Stream_by_query Title : get_Stream_by_query Usage : $seq = $db->get_Stream_by_query($query); Function: Retrieves Seq objects from Entrez 'en masse', rather than one at a time. For large numbers of sequences, this is far superior than get_Stream_by_[id/acc](). Example : Returns : a Bio::SeqIO stream object Args : $query : An Entrez query string or a Bio::DB::Query::GenBank object. It is suggested that you create a Bio::DB::Query::GenBank object and get the entry count before you fetch a potentially large stream. =cut =head2 get_Stream_by_id Title : get_Stream_by_id Usage : $stream = $db->get_Stream_by_id( [$uid1, $uid2] ); Function: Gets a series of Seq objects by unique identifiers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of unique identifiers for the desired sequence entries =head2 get_Stream_by_acc Title : get_Stream_by_acc Usage : $seq = $db->get_Stream_by_acc([$acc1, $acc2]); Function: Gets a series of Seq objects by accession numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id() =cut =head2 get_Stream_by_gi Title : get_Stream_by_gi Usage : $seq = $db->get_Seq_by_gi([$gi1, $gi2]); Function: Gets a series of Seq objects by gi numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of gi numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id() =head2 get_Stream_by_batch Title : get_Stream_by_batch Usage : $seq = $db->get_Stream_by_batch($ref); Function: Retrieves Seq objects from Entrez 'en masse', rather than one at a time. Example : Returns : a Bio::SeqIO stream object Args : $ref : either an array reference, a filename, or a filehandle from which to get the list of unique ids/accession numbers. NOTE: This method is redundant and deprecated. Use get_Stream_by_id() instead. =head2 get_request Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) =cut =head2 default_format Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none =cut sub default_format { return $DEFAULTFORMAT; } 1; __END__ BioPerl-1.007002/Bio/DB/GenPept.pm000444000766000024 1452613155576320 16441 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::GenPept # # Please direct questions and support issues to # # Cared for by Aaron Mackey # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code # completely reworked by Jason Stajich to use Bio::DB::WebDBSeqI 2000-12-12 =head1 NAME Bio::DB::GenPept - Database object interface to GenPept =head1 SYNOPSIS $gb = Bio::DB::GenPept->new(); $seq = $gb->get_Seq_by_id('195055'); # Unique ID # or ... $seq = $gb->get_Seq_by_acc('DEECTH'); # Accession Number my $seqio = $gb->get_Stream_by_id(['195055', 'DEECTH']); while( my $seq = $seqio->next_seq ) { print "seq is is ", $seq->display_id, "\n"; } =head1 DESCRIPTION Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the GenPept database at NCBI, via an Entrez query. WARNING: Please do NOT spam the Entrez web server with multiple requests. NCBI offers Batch Entrez for this purpose. Batch Entrez support will likely be supported in a future version of DB::GenPept. Currently the only return format supported by NCBI Entrez for GenPept database is GenPept format, so any format specification passed to GenPept will be ignored still be forced to GenPept format (which is just GenBank format). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Aaron Mackey, Jason Stajich Email amackey@virginia.edu Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::GenPept; use strict; use vars qw($DEFAULTFORMAT $DEFAULTMODE %PARAMSTRING); use base qw(Bio::DB::NCBIHelper); BEGIN { $DEFAULTMODE = 'single'; $DEFAULTFORMAT = 'gp'; %PARAMSTRING = ( 'batch' => { 'db' => 'protein', 'usehistory' => 'n', 'tool' => 'bioperl'}, # no query? 'gi' => { 'db' => 'protein', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, 'version' => { 'db' => 'protein', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, 'single' => { 'db' => 'protein', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, 'webenv' => { 'query_key' => 'querykey', 'WebEnv' => 'cookie', 'db' => 'protein', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, ); } # the new way to make modules a little more lightweight sub new { my($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->request_format($self->default_format); return $self; } =head2 get_params Title : get_params Usage : my %params = $self->get_params($mode) Function: Returns key,value pairs to be passed to NCBI database for either 'batch' or 'single' sequence retrieval method Returns : a key,value pair hash Args : 'single' or 'batch' mode for retrieval =cut sub get_params { my ($self, $mode) = @_; return defined $PARAMSTRING{$mode} ? %{$PARAMSTRING{$mode}} : %{$PARAMSTRING{$DEFAULTMODE}}; } =head2 default_format Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none =cut sub default_format { return $DEFAULTFORMAT; } # from Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI =head1 Routines from Bio::DB::WebDBSeqI and Bio::DB::RandomAccessI =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('AAC73346'); Function: Gets a Seq objects by accession number Returns : Bio::Seq object Args : accession number to retrieve by =head1 Routines implemented by Bio::DB::NCBIHelper =head2 get_request Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) =head2 get_Stream_by_id Title : get_Stream_by_id Usage : $stream = $db->get_Stream_by_id( [$uid1, $uid2] ); Function: Gets a series of Seq objects by unique identifiers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of unique identifiers for the desired sequence entries =head2 get_Stream_by_acc (2) Title : get_Stream_by_acc Usage : $seq = $db->get_Stream_by_acc($acc); Function: Gets a series of Seq objects by accession numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id() =head2 request_format Title : request_format Usage : my $format = $self->request_format; $self->request_format($format); Function: Get/Set sequence format retrieval Returns : string representing format Args : $format = sequence format =cut # override to force format to be GenPept regardless sub request_format { my ($self) = @_; return $self->SUPER::request_format($self->default_format()); } 1; __END__ BioPerl-1.007002/Bio/DB/GenericWebAgent.pm000444000766000024 2431413155576320 20064 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::GenericWebAgent # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code # # Interfaces with new GenericWebAgent interface =head1 NAME Bio::DB::GenericWebAgent - helper base class for parameter-based remote server access and response retrieval. =head1 SYNOPSIS # DO NOT USE DIRECTLY See Bio::DB::EUtilities for an example implementation =head1 DESCRIPTION WARNING: Please do B spam the web servers with multiple requests. Bio::DB::GenericWebAgent is a generic wrapper around a web agent (LWP::UserAgent), an object which can retain, format, and build parameters for the user agent (Bio::ParameterBaseI), and a BioPerl class parser that processes response content received by the user agent. The Bio::ParameterBaseI object should be state-aware, e.g. know when changes occur to parameters, so that identical requests are not repeatedly sent to the server (this base class takes this into consideration). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@lists.open-bio.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web. https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Email cjfields at bioperl dot org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::GenericWebAgent; use strict; use warnings; use base qw(Bio::Root::Root); use LWP::UserAgent; my $LAST_INVOCATION_TIME = 0; my $TIME_HIRES = 0; BEGIN { eval { use Time::HiRes; }; unless ($@) { $TIME_HIRES = 1; } } =head2 new Title : new Usage : Bio::DB::GenericWebAgent->new(@args); Function: Create new Bio::DB::GenericWebAgent instance. Returns : Args : None specific to this base class. Inheriting classes will likely set specific parameters in their constructor; Bio::DB::GenericWebAgent is primarily a test bed. =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->ua(LWP::UserAgent->new(env_proxy => 1, agent => ref($self))); $self->delay($self->delay_policy); return $self; } =head1 GenericWebAgent methods =head2 parameter_base Title : parameter_base Usage : $dbi->parameter_base($pobj); Function: Get/Set Bio::ParameterBaseI. Returns : Bio::ParameterBaseI object Args : Bio::ParameterBaseI object =cut # this will likely be overridden in subclasses sub parameter_base { my ($self, $pobj) = @_; if ($pobj) { $self->throw('Not a Bio::ParameterBaseI') if !$pobj->isa('Bio::ParameterBaseI'); $self->{'_parameter_base'} = $pobj; } return $self->{'_parameter_base'}; } =head2 ua Title : ua Usage : $dbi->ua; Function: Get/Set LWP::UserAgent. Returns : LWP::UserAgent Args : LWP::UserAgent =cut sub ua { my ($self, $ua) = @_; if( defined $ua && $ua->isa("LWP::UserAgent") ) { $self->{'_ua'} = $ua; } return $self->{'_ua'}; } =head2 get_Response Title : get_Response Usage : $agent->get_Response; Function: Get the HTTP::Response object by passing it an HTTP::Request (generated from Bio::ParameterBaseI implementation). Returns : HTTP::Response object or data if callback is used Args : (optional) -cache_response - flag to cache HTTP::Response object; Default is 1 (TRUE, caching ON) These are passed on to LWP::UserAgent::request() if stipulated -cb - use a LWP::UserAgent-compliant callback -file - dumps the response to a file (handy for large responses) Note: can't use file and callback at the same time -read_size_hint - bytes of content to read in at a time to pass to callback Note : Caching and parameter checking are set =cut # TODO deal with small state-related bug with file sub get_Response { my ($self, @args) = @_; my ($cache, $file, $cb, $size) = $self->_rearrange([qw(CACHE_RESPONSE FILE CB READ_SIZE_HINT)],@args); $self->throw("Can't have both callback and file") if $file && $cb; # make -file accept more perl-like write-append type data. $file =~ s{^>}{} if $file; my @opts = grep {defined $_} ($file || $cb, $size); $cache = (defined $cache && $cache == 0) ? 0 : 1; my $pobj = $self->parameter_base; if ($pobj->parameters_changed || !$cache || !$self->{_response_cache} || !$self->{_response_cache}->content) { my $ua = $self->ua; $self->_sleep; # institute delay policy $self->throw('No parameter object set; cannot form a suitable remote request') unless $pobj; my $request = $pobj->to_request; if ($self->authentication) { $request->proxy_authorization_basic($self->authentication) } $self->debug("Request is: \n",$request->as_string); # I'm relying on the useragent to throw the proper errors here my $response = $ua->request($request, @opts); if ($response->is_error) { $self->throw("Response Error\n".$response->message); } return $self->{_response_cache} = $response; } else { $self->debug("Returning cached HTTP::Response object\n"); if ($file) { $self->_dump_request_content($file); # size isn't passed here, as the content is completely retrieved above } elsif ($cb) { $cb && ref($cb) eq 'CODE' && $cb->($self->{_response_cache}->content); } return $self->{_response_cache}; } } =head2 get_Parser Title : get_Parser Usage : $agent->get_Parser; Function: Return HTTP::Response content (file, fh, object) attached to defined parser Returns : None Args : None Note : Abstract method; defined by implementation =cut sub get_Parser { shift->throw_not_implemented; } =head2 delay Title : delay Usage : $secs = $self->delay($secs) Function: get/set number of seconds to delay between fetches Returns : number of seconds to delay Args : new value NOTE: the default is to use the value specified by delay_policy(). This can be overridden by calling this method. =cut sub delay { my $self = shift; return $self->{'_delay'} = shift if @_; return $self->{'_delay'}; } =head2 delay_policy Title : delay_policy Usage : $secs = $self->delay_policy Function: return number of seconds to delay between calls to remote db Returns : number of seconds to delay Args : none NOTE: The default delay policy is 3s. Override in subclasses to implement delays. The timer has only second resolution, so the delay will actually be +/- 1s. =cut sub delay_policy { my $self = shift; return 3; } =head2 _sleep Title : _sleep Usage : $self->_sleep Function: sleep for a number of seconds indicated by the delay policy Returns : none Args : none NOTE: This method keeps track of the last time it was called and only imposes a sleep if it was called more recently than the delay_policy() allows. =cut sub _sleep { my $self = shift; my $last_invocation = $LAST_INVOCATION_TIME; if (time - $LAST_INVOCATION_TIME < $self->delay) { my $delay = $self->delay - (time - $LAST_INVOCATION_TIME); $self->debug("sleeping for $delay seconds\n"); if ($TIME_HIRES) { # allows precise sleep timeout (builtin only allows integer seconds) Time::HiRes::sleep($delay); } else { # allows precise sleep timeout (builtin only allows integer seconds) # I hate this hack , but needed if we support 5.6.1 and # don't want additional Time::HiRes prereq select undef, undef, undef, $delay; } } $LAST_INVOCATION_TIME = time; } =head1 LWP::UserAgent related methods =head2 proxy Title : proxy Usage : $httpproxy = $db->proxy('http') or $db->proxy(['http','ftp'], 'http://myproxy' ) Function: Get/Set a proxy for use of proxy Returns : a string indicating the proxy Args : $protocol : an array ref of the protocol(s) to set/get $proxyurl : url of the proxy to use for the specified protocol $username : username (if proxy requires authentication) $password : password (if proxy requires authentication) =cut sub proxy { my ($self,$protocol,$proxy,$username,$password) = @_; return if ( !defined $protocol || !defined $proxy ); $self->authentication($username, $password) if ($username && $password); return $self->ua->proxy($protocol,$proxy); } =head2 authentication Title : authentication Usage : $db->authentication($user,$pass) Function: Get/Set authentication credentials Returns : Array of user/pass Args : Array or user/pass =cut sub authentication{ my ($self,$u,$p) = @_; if( defined $u && defined $p ) { $self->{'_authentication'} = [ $u,$p]; } $self->{'_authentication'} && return @{$self->{'_authentication'}}; } # private method to dump any cached request data content into a passed filename sub _dump_request_content { my ($self, $file) = @_; return unless defined $self->{_response_cache}; $self->throw("Must pass file name") unless $file; require Bio::Root::IO; my $out = Bio::Root::IO->new(-file => ">$file"); $out->_print($self->{_response_cache}->content); $out->flush(); $out->close; } 1; BioPerl-1.007002/Bio/DB/HIV.pm000555000766000024 5165313155576320 15532 0ustar00cjfieldsstaff000000000000# $Id: HIV.pm 232 2008-12-11 14:51:51Z maj $ # # BioPerl module for Bio::DB::HIV # # Please direct questions and support issues to # # Cared for by Mark A. Jensen # # Copyright Mark A. Jensen # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::HIV - Database object interface to the Los Alamos HIV Sequence Database =head1 SYNOPSIS $db = new Bio::DB::HIV; $seq = $db->get_Seq_by_id('94284'); # LANL sequence id $seq = $db->get_Seq_by_acc('EF432710'); # GenBank accession $q = new Bio::DB::Query::HIVQuery( " (C D)[subtype] SI[phenotype] (symptomatic AIDS)[patient_health] " ); $seqio = $db->get_Stream_by_query($q); $seq = $seqio->next_seq(); ($seq->annotation->get_Annotations('Virus'))[0]->{subtype} # returns 'D' ($seq->annotation->get_Annotations('Patient'))[0]->{patient_health} # returns 'AIDS' ($seq->annotation->get_Annotations('accession'))[0]->{value} # returns 'K03454' =head1 DESCRIPTION Bio::DB::HIV, along with L, provides an interface for obtaining annotated HIV and SIV sequences from the Los Alamos National Laboratory (LANL) HIV Sequence Database ( L ). Unannotated sequences can be retrieved directly from the database object, using either LANL ids or GenBank accessions. Annotations are obtained via a query object, and are attached to the correct C objects when the query is handled by C or C. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Mark A. Jensen Email maj@fortinbras.us =head1 CONTRIBUTORS Mark A. Jensen =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::HIV; use strict; use warnings; use vars qw( $LANL_BASE $LANL_MAP_DB $LANL_MAKE_SEARCH_IF $LANL_SEARCH ); # Object preamble - inherits from Bio::DB::WebDBSeqI use Bio::Root::Root; use HTTP::Request::Common; use Bio::DB::HIV::HIVAnnotProcessor; use base qw(Bio::DB::WebDBSeqI); BEGIN { # base change of 01/14/09 $LANL_BASE = "http://www.hiv.lanl.gov/components/sequence/HIV/asearch"; $LANL_MAP_DB = "map_db.comp"; $LANL_MAKE_SEARCH_IF = "make_search_if.comp"; $LANL_SEARCH = "search.comp"; @Bio::ResponseProblem::Exception::ISA = qw( Bio::Root::Exception ); @Bio::HIVSorry::Exception::ISA = qw ( Bio::Root::Exception ); @Bio::WebError::Exception::ISA = qw( Bio::Root::Exception ); } =head1 Constructor =head2 new Title : new Usage : my $obj = new Bio::DB::HIV(); Function: Builds a new Bio::DB::HIV object Returns : an instance of Bio::DB::HIV Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($lanl_base, $lanl_map_db, $lanl_make_search_if, $lanl_search) = $self->_rearrange([qw( LANL_BASE LANL_MAP_DB LANL_MAKE_SEARCH_IF LANL_SEARCH )], @args); $lanl_base && $self->lanl_base($lanl_base); $lanl_map_db && $self->map_db($lanl_map_db); $lanl_make_search_if && $self->make_search_if($lanl_make_search_if); $lanl_search && $self->search_($lanl_search); # defaults $self->lanl_base || $self->lanl_base($LANL_BASE); $self->map_db || $self->map_db($LANL_MAP_DB); $self->make_search_if || $self->make_search_if($LANL_MAKE_SEARCH_IF); $self->search_ || $self->search_($LANL_SEARCH); $self->url_base_address || $self->url_base_address($self->lanl_base); $self->request_format("fasta"); return $self; } =head1 WebDBSeqI compliance =head2 get_request Title : get_request Usage : my $url = $self->get_request Function: returns a HTTP::Request object Returns : Args : %qualifiers = a hash of qualifiers with keys in (-ids, -format, -mode, -query) Note : Several layers of requests are performed to get to the sequence; see Bio::DB::Query::HIVQuery. =cut sub get_request { my $self = shift; my %quals = @_; my ($resp); my (@ids, $mode, @interface, @query_parms, $query); # html parsing regexps my $tags_re = qr{(?:\s*<[^>]+>\s*)}; my $session_id_re = qr{]*action=".*/search.comp"}; my $seqs_found_re = qr{Displaying$tags_re*(?:\s*[0-9-]*\s*)*$tags_re*of$tags_re*\s*([0-9]+)$tags_re*sequences found}; my $no_seqs_found_re = qr{Sorry.*no sequences found}; my $too_many_re = qr{too many records: $tags_re*([0-9]+)}; # find something like: # tables without join:
SequenceAccessions
my $tbl_no_join_re = qr{tables without join}i; # my $sorry_bud_re = qr{}; # handle "qualifiers" foreach (keys %quals) { m/mode/ && do { $mode = $quals{$_}; next; }; m/uids/ && do { $self->throw(-class=>"Bio::Root::BadParameter", -text=>"Arrayref required for qualifier \"$_\"", -value=>$quals{$_}) unless ref($quals{$_}) eq 'ARRAY'; @ids = @{$quals{$_}}; next; }; m/query/ && do { $self->throw(-class=>"Bio::Root::BadParameter", -text=>"Bio::DB::Query::HIVQuery required for qualifier \"$_\"", -value=>$quals{$_}) unless $quals{$_}->isa("Bio::DB::Query::HIVQuery"); $query = $quals{$_}; next; }; do { 1; #else stub }; } # what kind of request? for my $m ($mode) { ($m =~ m/single/) && do { @interface = ( 'sequenceentry' => 'se_sequence', 'sequenceentry' => 'se_id', 'action' => 'Search Interface' ); @query_parms = map { ('sequenceentry.se_id' => $_ ) } @ids; push @query_parms, ( 'sequenceentry.se_sequence'=>'Any', 'order' => 'sequenceentry.se_id', 'sort_dir' => 'ASC', 'action' => 'Search' ); }; ($mode =~ m/acc/) && do { @interface = ( 'sequenceentry' => 'se_sequence', 'sequenceentry' => 'se_id', 'sequenceaccessions' => 'sa_genbankaccession', 'sequenceaccessions' => 'sa_se_id', 'action' => 'Search Interface' ); @query_parms = map {('sequenceaccessions.sa_genbankaccession' => $_)} @ids; push @query_parms, ( 'sequenceentry.se_sequence' => 'Any', 'order' => 'sequenceaccessions.sa_genbankaccession', 'sort_dir' => 'ASC', 'action' => 'Search' ); }; ($mode =~ m/gi/) && do { $self->_sorry("-mode=>gi"); }; ($mode =~ m/version/) && do { $self->_sorry("-mode=>version"); }; ($mode =~ m/query/) && do { $self->throw(-class=>"Bio::Root::BadParameter", -text=>"Query ".($query->{'_RUN_LEVEL'} ? "has been run only at run level ".$query->{'_RUN_LEVEL'} : "has not been run").", run at level 2 with _do_query(2)", -value=>$query->{'_RUN_LEVEL'}) unless $query->{'_RUN_LEVEL'} == 2; @interface = ( 'sequenceentry' => 'se_sequence', 'sequenceentry' => 'se_id', 'action' => 'Search Interface' ); @query_parms = ("sequenceentry.se_id" =>sprintf("'%s'",join("\t", $query->ids))); # @query_parms = map { ( "sequenceentry.se_id" => $_ ) } $query->ids; push @query_parms, ( 'sequenceentry.se_sequence' => 'Any', 'order' => 'sequenceentry.se_id', 'sort_dir' => 'ASC', 'action' => 'Search' ); }; do { 1; # else stub }; } # web work eval { # capture web errors; throw below... # negotiate a session with lanl db if (!$self->_session_id) { $resp = $self->ua->get($self->_map_db_uri); $resp->is_success || die "Connect failed"; # get the session id if (!$self->_session_id) { ($self->{'_session_id'}) = ($resp->content =~ /$session_id_re/); $self->_session_id || die "Session not established"; } } # establish correct "interface" for this session id $resp = $self->ua->post($self->_make_search_if_uri, [@interface, id=>$self->_session_id]); $resp->is_success || die "Interface request failed (1)"; $self->_response($resp); $resp->content =~ /$search_form_re/ || die "Interface request failed (2)"; # interface successful, do the "pre-search" $resp = $self->ua()->post($self->_search_uri, [(@query_parms, 'id' => $self->_session_id)] ); unless ($resp->is_success) { die "Search post failed"; } $self->_response($resp); # check for error conditions for ($resp->content) { /$no_seqs_found_re/ && do { die "No sequences found"; last; }; /$too_many_re/ && do { die "Too many records ($1): must be <10000"; last; }; /$tbl_no_join_re/ && do { die "Some required tables went unjoined to query"; last; }; /$seqs_found_re/ && do { last; }; do { die "Unparsed failure"; last; }; } }; $self->throw(-class=>'Bio::WebError::Exception', -text=>$@, -value=>$resp->content) if $@; # "pre-search" successful, return request ### check this post update return POST $self->_search_uri, ['action Download.x' => 1, 'action Download.y'=>1, 'id'=>$self->_session_id ]; } =head2 postprocess_data Title : postprocess_data Usage : $self->postprocess_data ( 'type' => 'string', 'location' => \$datastr); Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - 'location' either file location or string reference containing data =cut sub postprocess_data { # parse tab-separated value content from LANL db my ( $self, %args) = @_; my ($type, $loc) = ($args{type}, $args{location}); my (@data, @cols, %rec, $idkey, @flines); $self->throw(-class=>'Bio::Root::BadParameter', -text=>"Argument hash requires values for keys \"type\" and \"location\"", -value=>\%args) unless ($type && $loc); for ($type) { m/string/ && do { @data = split(/\n|\r/, ${$loc}); last; }; m/file/ && do { local $/ = undef; open my $F, '<', $loc or $self->throw( -class => 'Bio::Root::FileOpenException', -text => "Error opening tempfile '$loc' for reading", -value => $! ); @data = split( /\n|\r/, <$F>); close $F; last; }; do { 1; # else stub }; } $self->throw(-class=>'Bio::Root::BadParameter', -text=>'No data found in repsonse', -value=>%args) unless (@data); my $l; do { $l = shift @data; } while ( defined $l && $l !~ /Number/ ); # number-returned line @cols = split( /\t/, shift @data); # if Accession column is present, get_Stream_by_acc was called # otherwise, return lanl ids ($idkey) = grep /SE.id/i, @cols unless ($idkey) = grep /Accession/i, @cols; $self->throw(-class=>"Bio::ResponseProblem::Exception", -text=>"Trouble with column headers in LANL response", -value=>join(' ',@cols)) unless $idkey; foreach (@data) { chop; @rec{@cols} = split /\t/; push @flines, ">$rec{$idkey}\n".$rec{'Sequence'}."\n"; } for ($type) { m/string/ && do { ${$loc} = join("", @flines); last; }; m/file/ && do { open my $F, '>', $loc or $self->throw(-class=>'Bio::Root::FileOpenException', -text=>"Error opening tempfile '$loc' for writing", -value=>$!); print $F join("", @flines); close $F; last; }; do { 1; #else stub }; } return; } =head1 WebDBSeqI overrides =head2 get_seq_stream Title : get_seq_stream Usage : my $seqio = $self->get_seq_stream(%qualifiers) Function: builds a url and queries a web db Returns : a Bio::SeqIO stream capable of producing sequence Args : %qualifiers = a hash qualifiers that the implementing class will process to make a url suitable for web querying Note : Some tightening up of the baseclass version =cut sub get_seq_stream { my ($self, %qualifiers) = @_; my ($rformat, $ioformat) = $self->request_format(); my ($key) = grep /format$/, keys %qualifiers; $qualifiers{'-format'} = ($key ? $qualifiers{$key} : $rformat); ($rformat, $ioformat) = $self->request_format($qualifiers{'format'}); # web work is here/maj my $request = $self->get_request(%qualifiers); # authorization is here/maj $request->proxy_authorization_basic($self->authentication) if ( $self->authentication); $self->debug("request is ". $request->as_string(). "\n"); # workaround for MSWin systems (no forking available/maj) $self->retrieval_type('io_string') if $self->retrieval_type =~ /pipeline/ && $^O =~ /^MSWin/; if ($self->retrieval_type =~ /pipeline/) { # Try to create a stream using POSIX fork-and-pipe facility. # this is a *big* win when fetching thousands of sequences from # a web database because we can return the first entry while # transmission is still in progress. # Also, no need to keep sequence in memory or in a temporary file. # If this fails (Windows, MacOS 9), we fall back to non-pipelined access. # fork and pipe: _stream_request()=> my ($result,$stream) = $self->_open_pipe(); if (defined $result) { $DB::fork_TTY = File::Spec->devnull; # prevents complaints from debugge if (!$result) { # in child process $self->_stream_request($request,$stream); POSIX::_exit(0); #prevent END blocks from executing in this forked child } else { return Bio::SeqIO->new('-verbose' => $self->verbose, '-format' => $ioformat, '-fh' => $stream); } } else { $self->retrieval_type('io_string'); } } if ($self->retrieval_type =~ /temp/i) { my $dir = $self->io->tempdir( CLEANUP => 1); my ( $fh, $tmpfile) = $self->io()->tempfile( DIR => $dir ); close $fh; my $resp = $self->_request($request, $tmpfile); if( ! -e $tmpfile || -z $tmpfile || ! $resp->is_success() ) { $self->throw("WebDBSeqI Error - check query sequences!\n"); } $self->postprocess_data('type' => 'file','location' => $tmpfile); # this may get reset when requesting batch mode ($rformat,$ioformat) = $self->request_format(); if( $self->verbose > 0 ) { open my $ERR, '<', $tmpfile or $self->throw("Could not read file '$tmpfile': $!"); while(<$ERR>) { $self->debug($_);} close $ERR; } return Bio::SeqIO->new('-verbose' => $self->verbose, '-format' => $ioformat, '-file' => $tmpfile); } if ($self->retrieval_type =~ /io_string/i ) { my $resp = $self->_request($request); my $content = $resp->content_ref; $self->debug( "content is $$content\n"); if (!$resp->is_success() || length($$content) == 0) { $self->throw("WebDBSeqI Error - check query sequences!\n"); } ($rformat,$ioformat) = $self->request_format(); $self->postprocess_data('type'=> 'string', 'location' => $content); $self->debug( "str is $$content\n"); return Bio::SeqIO->new('-verbose' => $self->verbose, '-format' => $ioformat, '-fh' => new IO::String($$content)); } # if we got here, we don't know how to handle the retrieval type $self->throw("retrieval type " . $self->retrieval_type . " unsupported\n"); } =head2 get_Stream_by_acc Title : get_Stream_by_acc Usage : $seq = $db->get_Stream_by_acc([$acc1, $acc2]); Function: Gets a series of Seq objects by GenBank accession numbers Returns : a Bio::SeqIO stream object Args : an arrayref of accession numbers for the desired sequence entries Note : For LANL DB, alternative to LANL seqids =cut sub get_Stream_by_acc { my ($self, $ids ) = @_; return $self->get_seq_stream('-uids' => [$ids], '-mode' => 'acc'); } =head2 get_Stream_by_query Title : get_Stream_by_query Usage : $stream = $db->get_Stream_by_query($query); Function: Gets a series of Seq objects by way of a query string or oject Returns : a Bio::SeqIO stream object Args : $query : Currently, only a Bio::DB::Query::HIVQuery object. It's a good idea to create the query object first and interrogate it for the entry count before you fetch a potentially large stream. =cut sub get_Stream_by_query { my ($self, $query ) = @_; my $stream = $self->get_seq_stream('-query' => $query, '-mode'=>'query'); return new Bio::DB::HIV::HIVAnnotProcessor( -hiv_query=>$query, -source_stream=>$stream ); } sub _request { my ($self, $request,$tmpfile) = @_; my ($resp); if( defined $tmpfile && $tmpfile ne '' ) { $resp = $self->ua->request($request, $tmpfile); } else { $resp = $self->ua->request($request); } if( $resp->is_error ) { $self->throw("WebDBSeqI Request Error:\n".$resp->as_string); } return $resp; } =head1 Internals =head2 lanl_base Title : lanl_base Usage : $obj->lanl_base($newval) Function: get/set the base url of the LANL HIV database Example : Returns : value of lanl_base (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub lanl_base{ my $self = shift; return $self->{'lanl_base'} = shift if @_; return $self->{'lanl_base'}; } =head2 map_db Title : map_db Usage : $obj->map_db($newval) Function: get/set the cgi filename for map_db ("Database Map") Example : Returns : value of map_db (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub map_db{ my $self = shift; return $self->{'map_db'} = shift if @_; return $self->{'map_db'}; } =head2 make_search_if Title : make_search_if Usage : $obj->make_search_if($newval) Function: get/set the cgi filename for make_search_if ("Make Search Interface") Example : Returns : value of make_search_if (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub make_search_if{ my $self = shift; return $self->{'make_search_if'} = shift if @_; return $self->{'make_search_if'}; } =head2 search_ Title : search_ Usage : $obj->search_($newval) Function: get/set the cgi filename for the search query page ("Search Database") Example : Returns : value of search_ (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub search_{ my $self = shift; return $self->{'search_'} = shift if @_; return $self->{'search_'}; } =head2 _map_db_uri Title : _map_db_uri Usage : Function: return the full map_db uri ("Database Map") Example : Returns : scalar string Args : none =cut sub _map_db_uri{ my $self = shift; return $self->url_base_address."/".$self->map_db; } =head2 _make_search_if_uri Title : _make_search_if_uri Usage : Function: return the full make_search_if uri ("Make Search Interface") Example : Returns : scalar string Args : none =cut sub _make_search_if_uri{ my $self = shift; return $self->url_base_address."/".$self->make_search_if; } =head2 _search_uri Title : _search_uri Usage : Function: return the full search cgi uri ("Search Database") Example : Returns : scalar string Args : none =cut sub _search_uri{ my $self = shift; return $self->url_base_address."/".$self->search_; } =head2 _session_id Title : _session_id Usage : $obj->_session_id($newval) Function: Contains HIV db session id (initialized in _do_lanl_request) Example : Returns : value of _session_id (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub _session_id{ my $self = shift; return $self->{'_session_id'} = shift if @_; return $self->{'_session_id'}; } =head2 _response Title : _response Usage : $obj->_response($newval) Function: hold the response to search post Example : Returns : value of _response (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub _response{ my $self = shift; return $self->{'_response'} = shift if @_; return $self->{'_response'}; } =head2 Dude, sorry Title : _sorry Usage : $hiv->_sorry Function: Throws an exception for unsupported option or parameter Example : Returns : Args : scalar string =cut sub _sorry{ my $self = shift; my $parm = shift; $self->throw(-class=>"Bio::HIVSorry::Exception", -text=>"Sorry, option/parameter \"$parm\" not (yet) supported. See manpage to complain.", -value=>$parm); return; } 1; BioPerl-1.007002/Bio/DB/InMemoryCache.pm000444000766000024 1435313155576320 17560 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::InMemoryCache # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::DB::InMemoryCache - Abstract interface for a sequence database =head1 SYNOPSIS $cachedb = Bio::DB::InMemoryCache->new( -seqdb => $real_db, -number => 1000); # # get a database object somehow using a concrete class # $seq = $cachedb->get_Seq_by_id('ROA1_HUMAN'); # # $seq is a Bio::Seq object # =head1 DESCRIPTION This is a memory cache system which saves the objects returned by Bio::DB::RandomAccessI in memory to a hard limit of sequences. =head1 CONTACT Ewan Birney Ebirney@ebi.ac.ukE =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::InMemoryCache; use strict; use Bio::Seq; use base qw(Bio::Root::Root Bio::DB::SeqI); sub new { my ($class,@args) = @_; my $self = Bio::Root::Root->new(); bless $self,$class; my ($seqdb,$number,$agr) = $self->_rearrange([qw(SEQDB NUMBER AGRESSION)],@args); if( !defined $seqdb || !ref $seqdb || !$seqdb->isa('Bio::DB::RandomAccessI') ) { $self->throw("Must be a RandomAccess database not a [$seqdb]"); } if( !defined $number ) { $number = 1000; } $self->seqdb($seqdb); $self->number($number); $self->agr($agr); # we consider acc as the primary id here $self->{'_cache_number_hash'} = {}; $self->{'_cache_id_hash'} = {}; $self->{'_cache_acc_hash'} = {}; $self->{'_cache_number'} = 1; return $self; } =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception =cut sub get_Seq_by_id{ my ($self,$id) = @_; if( defined $self->{'_cache_id_hash'}->{$id} ) { my $acc = $self->{'_cache_id_hash'}->{$id}; my $seq = $self->{'_cache_acc_hash'}->{$acc}; $self->{'_cache_number_hash'}->{$seq->accession} = $self->{'_cache_number'}++; return $seq; } else { return $self->_load_Seq('id',$id); } } =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception =cut sub get_Seq_by_acc{ my ($self,$acc) = @_; #print STDERR "In cache get for $acc\n"; if( defined $self->{'_cache_acc_hash'}->{$acc} ) { #print STDERR "Returning cached $acc\n"; my $seq = $self->{'_cache_acc_hash'}->{$acc}; $self->{'_cache_number_hash'}->{$seq->accession} = $self->{'_cache_number'}++; return $seq; } else { return $self->_load_Seq('acc',$acc); } } sub number { my ($self, $number) = @_; if ($number) { $self->{'number'} = $number; } else { return $self->{'number'}; } } sub seqdb { my ($self, $seqdb) = @_; if ($seqdb) { $self->{'seqdb'} = $seqdb; } else { return $self->{'seqdb'}; } } sub agr { my ($self, $agr) = @_; if ($agr) { $self->{'agr'} = $agr; } else { return $self->{'agr'}; } } sub _load_Seq { my ($self,$type,$id) = @_; my $seq; if( $type eq 'id') { $seq = $self->seqdb->get_Seq_by_id($id); }elsif ( $type eq 'acc' ) { $seq = $self->seqdb->get_Seq_by_acc($id); } else { $self->throw("Bad internal error. Don't understand $type"); } if( ! $seq ) { # warding off bug #1628 $self->debug("could not find seq $id in seqdb\n"); return; } if( $self->agr() ) { #print STDERR "Pulling out into memory\n"; my $newseq = Bio::Seq->new( -display_id => $seq->display_id, -accession_number => $seq->accession, -seq => $seq->seq, -desc => $seq->desc, ); if( $self->agr() == 1 ) { foreach my $sf ( $seq->top_SeqFeatures() ) { $newseq->add_SeqFeature($sf); } $newseq->annotation($seq->annotation); } $seq = $newseq; } if( $self->_number_free < 1 ) { # remove the latest thing from the hash my @accs = sort { $self->{'_cache_number_hash'}->{$a} <=> $self->{'_cache_number_hash'}->{$b} } keys %{$self->{'_cache_number_hash'}}; my $acc = shift @accs; # remove this guy my $seq = $self->{'_cache_acc_hash'}->{$acc}; delete $self->{'_cache_number_hash'}->{$acc}; delete $self->{'_cache_id_hash'}->{$seq->id}; delete $self->{'_cache_acc_hash'}->{$acc}; } # up the number, register this sequence into the hash. $self->{'_cache_id_hash'}->{$seq->id} = $seq->accession; $self->{'_cache_acc_hash'}->{$seq->accession} = $seq; $self->{'_cache_number_hash'}->{$seq->accession} = $self->{'_cache_number'}++; return $seq; } sub _number_free { my $self = shift; return $self->number - scalar(keys %{$self->{'_cache_number_hash'}}); } =head2 get_Seq_by_version Title : get_Seq_by_version Usage : $seq = $db->get_Seq_by_version('X77802.1'); Function: Gets a Bio::Seq object by sequence version Returns : A Bio::Seq object Args : accession.version (as a string) Throws : "acc.version does not exist" exception =cut sub get_Seq_by_version{ my ($self,@args) = @_; $self->throw("Not implemented it"); } ## End of Package 1; BioPerl-1.007002/Bio/DB/IndexedBase.pm000444000766000024 10170013155576320 17261 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::IndexedBase # # You may distribute this module under the same terms as perl itself # =head1 NAME Bio::DB::IndexedBase - Base class for modules using indexed sequence files =head1 SYNOPSIS use Bio::DB::XXX; # a made-up class that uses Bio::IndexedBase # 1/ Bio::SeqIO-style access # Index some sequence files my $db = Bio::DB::XXX->new('/path/to/file'); # from a single file my $db = Bio::DB::XXX->new(['file1', 'file2']); # from multiple files my $db = Bio::DB::XXX->new('/path/to/files/'); # from a directory # Get IDs of all the sequences in the database my @ids = $db->get_all_primary_ids; # Get a specific sequence my $seq = $db->get_Seq_by_id('CHROMOSOME_I'); # Loop through all sequences my $stream = $db->get_PrimarySeq_stream; while (my $seq = $stream->next_seq) { # Do something... } # 2/ Access via filehandle my $fh = Bio::DB::XXX->newFh('/path/to/file'); while (my $seq = <$fh>) { # Do something... } # 3/ Tied-hash access tie %sequences, 'Bio::DB::XXX', '/path/to/file'; print $sequences{'CHROMOSOME_I:1,20000'}; =head1 DESCRIPTION Bio::DB::IndexedBase provides a base class for modules that want to index and read sequence files and provides persistent, random access to each sequence entry, without bringing the entire file into memory. This module is compliant with the Bio::SeqI interface and both. Bio::DB::Fasta and Bio::DB::Qual both use Bio::DB::IndexedBase. When you initialize the module, you point it at a single file, several files, or a directory of files. The first time it is run, the module generates an index of the content of the files using the AnyDBM_File module (BerkeleyDB preferred, followed by GDBM_File, NDBM_File, and SDBM_File). Subsequently, it uses the index file to find the sequence file and offset for any requested sequence. If one of the source files is updated, the module reindexes just that one file. You can also force reindexing manually at any time. For improved performance, the module keeps a cache of open filehandles, closing less-recently used ones when the cache is full. Entries may have any line length up to 65,536 characters, and different line lengths are allowed in the same file. However, within a sequence entry, all lines must be the same length except for the last. An error will be thrown if this is not the case! This module was developed for use with the C. elegans and human genomes, and has been tested with sequence segments as large as 20 megabases. Indexing the C. elegans genome (100 megabases of genomic sequence plus 100,000 ESTs) takes ~5 minutes on my 300 MHz pentium laptop. On the same system, average access time for any 200-mer within the C. elegans genome was E0.02s. =head1 DATABASE CREATION AND INDEXING The two constructors for this class are new() and newFh(). The former creates a Bio::DB::IndexedBase object which is accessed via method calls. The latter creates a tied filehandle which can be used Bio::SeqIO style to fetch sequence objects in a stream fashion. There is also a tied hash interface. =over =item $db = Bio::DB::IndexedBase-Enew($path [,%options]) Create a new Bio::DB::IndexedBase object from the files designated by $path $path may be a single file, an arrayref of files, or a directory containing such files. After the database is created, you can use methods like get_all_primary_ids() and get_Seq_by_id() to retrieve sequence objects. =item $fh = Bio::DB::IndexedBase-EnewFh($path [,%options]) Create a tied filehandle opened on a Bio::DB::IndexedBase object. Reading from this filehandle with EE will return a stream of sequence objects, Bio::SeqIO style. The path and the options should be specified as for new(). =item $obj = tie %db,'Bio::DB::IndexedBase', '/path/to/file' [,@args] Create a tied-hash by tieing %db to Bio::DB::IndexedBase using the indicated path to the files. The optional @args list is the same set used by new(). If successful, tie() returns the tied object, undef otherwise. Once tied, you can use the hash to retrieve an individual sequence by its ID, like this: my $seq = $db{CHROMOSOME_I}; The keys() and values() functions will return the sequence IDs and their sequences, respectively. In addition, each() can be used to iterate over the entire data set: while (my ($id,$sequence) = each %db) { print "$id => $sequence\n"; } When dealing with very large sequences, you can avoid bringing them into memory by calling each() in a scalar context. This returns the key only. You can then use tied(%db) to recover the Bio::DB::IndexedBase object and call its methods. while (my $id = each %db) { print "$id: $db{$sequence:1,100}\n"; print "$id: ".tied(%db)->length($id)."\n"; } In addition, you may invoke the FIRSTKEY and NEXTKEY tied hash methods directly to retrieve the first and next ID in the database, respectively. This allows one to write the following iterative loop using just the object-oriented interface: my $db = Bio::DB::IndexedBase->new('/path/to/file'); for (my $id=$db->FIRSTKEY; $id; $id=$db->NEXTKEY($id)) { # do something with sequence } =back =head1 INDEX CONTENT Several attributes of each sequence are stored in the index file. Given a sequence ID, these attributes can be retrieved using the following methods: =over =item offset($id) Get the offset of the indicated sequence from the beginning of the file in which it is located. The offset points to the beginning of the sequence, not the beginning of the header line. =item strlen($id) Get the number of characters in the sequence string. =item length($id) Get the number of residues of the sequence. =item linelen($id) Get the length of the line for this sequence. If the sequence is wrapped, then linelen() is likely to be much shorter than strlen(). =item headerlen($id) Get the length of the header line for the indicated sequence. =item header_offset Get the offset of the header line for the indicated sequence from the beginning of the file in which it is located. This attribute is not stored. It is calculated from offset() and headerlen(). =item alphabet($id) Get the molecular type (alphabet) of the indicated sequence. This method handles residues according to the IUPAC convention. =item file($id) Get the the name of the file in which the indicated sequence can be found. =back =head1 INTERFACE COMPLIANCE NOTES Bio::DB::IndexedBase is compliant with the Bio::DB::SeqI and hence with the Bio::RandomAccessI interfaces. Database do not necessarily provide any meaningful internal primary ID for the sequences they store. However, Bio::DB::IndexedBase's internal primary IDs are the IDs of the sequences. This means that the same ID passed to get_Seq_by_id() and get_Seq_by_primary_id() will return the same sequence. Since this database index has no notion of sequence version or namespace, the get_Seq_by_id(), get_Seq_by_acc() and get_Seq_by_version() are identical. =head1 BUGS When a sequence is deleted from one of the files, this deletion is not detected by the module and removed from the index. As a result, a "ghost" entry will remain in the index and will return garbage results if accessed. Also, if you are indexing a directory, it is wise to not add or remove files from it. In case you have changed the files in a directory, or the sequences in a file, you can to rebuild the entire index, either by deleting it manually, or by passing -reindex=E1 to new() when initializing the module. =head1 SEE ALSO L L L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. Florent Angly (for the modularization) This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::DB::IndexedBase; BEGIN { @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File) if(!$INC{'AnyDBM_File.pm'}); } use strict; use warnings; use IO::File; use AnyDBM_File; use Fcntl; use File::Spec; use File::Basename qw(basename dirname); use Bio::PrimarySeq; use base qw(Bio::DB::SeqI); # Store offset, strlen, linelen, headerlen, type and fileno use constant STRUCT => 'NNNnnCa*'; # 32-bit file offset and seq length use constant STRUCTBIG => 'QQQnnCa*'; # 64-bit use constant NA => 0; use constant DNA => 1; use constant RNA => 2; use constant PROTEIN => 3; # You can avoid dying if you want but you may get incorrect results use constant DIE_ON_MISSMATCHED_LINES => 1; # Remove carriage returns (\r) and newlines (\n) from a string. When # called from subseq, this can take a signficiant portion of time, in # Variant Effect Prediction. Therefore we compile the match portion. sub _strip_crnl { eval 'require Inline::C'; if ( $INC{'Inline/C.pm'} ) { # C can do _strip_crnl much faster. But this requires the # Inline::C module which we don't require people to have. So we make # this optional by wrapping the C code in an eval. If the eval works, # the Perl strip_crnl() function is overwritten. Inline->bind( C => q( /* Strip all newlines (\n) and carriage returns (\r) from the string */ char* _strip_crnl(char* str) { char *s; char *s2 = str; for (s = str; *s; *s++) { if (*s != '\n' && *s != '\r') { *s2++ = *s; } } *s2 = '\0'; return str; } ) ); } else { # "tr" is much faster than the regex, with "s" *Bio::DB::IndexedBase::_strip_crnl = sub { my $str = shift; $str =~ tr/\n\r//d; return $str; }; } return _strip_crnl(@_); } =head2 new Title : new Usage : my $db = Bio::DB::IndexedBase->new($path, -reindex => 1); Function: Initialize a new database object Returns : A Bio::DB::IndexedBase object Args : A single file, or path to dir, or arrayref of files Optional arguments: Option Description Default ----------- ----------- ------- -glob Glob expression to search for files in directories * -makeid A code subroutine for transforming IDs None -maxopen Maximum size of filehandle cache 32 -debug Turn on status messages 0 -reindex Force the index to be rebuilt 0 -dbmargs Additional arguments to pass to the DBM routine None -index_name Name of the file that will hold the indices -clean Remove the index file when finished 0 The -dbmargs option can be used to control the format of the index. For example, you can pass $DB_BTREE to this argument so as to force the IDs to be sorted and retrieved alphabetically. Note that you must use the same arguments every time you open the index! The -makeid option gives you a chance to modify sequence IDs during indexing. For example, you may wish to extract a portion of the gi|gb|abc|xyz nonsense that GenBank Fasta files use. The original header line can be recovered later. The option value for -makeid should be a code reference that takes a scalar argument (the full header line) and returns a scalar or an array of scalars (the ID or IDs you want to assign). For example: $db = Bio::DB::IndexedBase->new('file.fa', -makeid => \&extract_gi); sub extract_gi { # Extract GI from GenBank my $header = shift; my ($id) = ($header =~ /gi\|(\d+)/m); return $id || ''; } extract_gi() will be called with the full header line, e.g. a Fasta line would include the "E", the ID and the description: >gi|352962132|ref|NG_030353.1| Homo sapiens sal-like 3 (Drosophila) (SALL3) In the database, this sequence can now be retrieved by its GI instead of its complete ID: my $seq = $db->get_Seq_by_id(352962132); The -makeid option is ignored after the index is constructed. =cut sub new { my ($class, $path, %opts) = @_; my $self = bless { debug => $opts{-debug} || 0, makeid => $opts{-makeid}, glob => $opts{-glob} || eval '$'.$class.'::file_glob' || '*', maxopen => $opts{-maxopen} || 32, clean => $opts{-clean} || 0, dbmargs => $opts{-dbmargs} || undef, fhcache => {}, cacheseq => {}, curopen => 0, openseq => 1, dirname => undef, offsets => undef, index_name => $opts{-index_name}, obj_class => eval '$'.$class.'::obj_class', offset_meth => \&{$class.'::_calculate_offsets'}, fileno2path => [], filepath2no => {}, }, $class; my ($offsets, $dirname); my $ref = ref $path || ''; if ( $ref eq 'ARRAY' ) { $offsets = $self->index_files($path, $opts{-reindex}); require Cwd; $dirname = Cwd::getcwd(); } else { $self->{index_name} ||= $self->_default_index_name($path); if (-d $path) { # because Win32 glob() is broken with respect to long file names # that contain whitespace. $path = Win32::GetShortPathName($path) if $^O =~ /^MSWin/i && eval 'use Win32; 1'; $offsets = $self->index_dir($path, $opts{-reindex}); $dirname = $path; } elsif (-f _) { $offsets = $self->index_file($path, $opts{-reindex}); $dirname = dirname($path); } else { $self->throw( "No file or directory called '$path'"); } } @{$self}{qw(dirname offsets)} = ($dirname, $offsets); return $self; } =head2 newFh Title : newFh Usage : my $fh = Bio::DB::IndexedBase->newFh('/path/to/files/', %options); Function: Index and get a new Fh for a single file, several files or a directory Returns : Filehandle object Args : Same as new() =cut sub newFh { my ($class, @args) = @_; my $self = $class->new(@args); require Symbol; my $fh = Symbol::gensym; tie $$fh, 'Bio::DB::Indexed::Stream', $self or $self->throw("Could not tie filehandle: $!"); return $fh; } =head2 dbmargs Title : dbmargs Usage : my @args = $db->dbmargs; Function: Get stored dbm arguments Returns : Array Args : None =cut sub dbmargs { my $self = shift; my $args = $self->{dbmargs} or return; return ref($args) eq 'ARRAY' ? @$args : $args; } =head2 glob Title : glob Usage : my $glob = $db->glob; Function: Get the expression used to match files in directories Returns : String Args : None =cut sub glob { my $self = shift; return $self->{glob}; } =head2 index_dir Title : index_dir Usage : $db->index_dir($dir); Function: Index the files that match -glob in the given directory Returns : Hashref of offsets Args : Dirname Boolean to force a reindexing the directory =cut sub index_dir { my ($self, $dir, $force_reindex) = @_; my @files = glob( File::Spec->catfile($dir, $self->{glob}) ); return if scalar @files == 0; $self->{index_name} ||= $self->_default_index_name($dir); my $offsets = $self->_index_files(\@files, $force_reindex); return $offsets; } =head2 get_all_primary_ids Title : get_all_primary_ids, get_all_ids, ids Usage : my @ids = $db->get_all_primary_ids; Function: Get the IDs stored in all indexes. This is a Bio::DB::SeqI method implementation. Note that in this implementation, the internal database primary IDs are also the sequence IDs. Returns : List of ids Args : None =cut sub get_all_primary_ids { return keys %{shift->{offsets}}; } { no warnings 'once'; *ids = *get_all_ids = \&get_all_primary_ids; } =head2 index_file Title : index_file Usage : $db->index_file($filename); Function: Index the given file Returns : Hashref of offsets Args : Filename Boolean to force reindexing the file =cut sub index_file { my ($self, $file, $force_reindex) = @_; $self->{index_name} ||= $self->_default_index_name($file); my $offsets = $self->_index_files([$file], $force_reindex); return $offsets; } sub _default_index_name { my ($self,$path) = @_; return File::Spec->catfile($path,'directory.index') if -d $path; return "$path.index"; } =head2 index_files Title : index_files Usage : $db->index_files(\@files); Function: Index the given files Returns : Hashref of offsets Args : Arrayref of filenames Boolean to force reindexing the files =cut sub index_files { my ($self, $files, $force_reindex) = @_; my @paths = map { File::Spec->rel2abs($_) } @$files; require Digest::MD5; my $digest = Digest::MD5::md5_hex( join('', sort @paths) ); $self->{index_name} ||= "fileset_$digest.index"; # unique name for the given files my $offsets = $self->_index_files($files, $force_reindex); return $offsets; } =head2 index_name Title : index_name Usage : my $indexname = $db->index_name($path); Function: Get the full name of the index file Returns : String Args : None =cut sub index_name { return shift->{index_name}; } =head2 path Title : path Usage : my $path = $db->path($path); Function: When a single file or a directory of files is indexed, this returns the file directory. When indexing an arbitrary list of files, the return value is the path of the current working directory. Returns : String Args : None =cut sub path { return shift->{dirname}; } =head2 get_PrimarySeq_stream Title : get_PrimarySeq_stream Usage : my $stream = $db->get_PrimarySeq_stream(); Function: Get a SeqIO-like stream of sequence objects. The stream supports a single method, next_seq(). Each call to next_seq() returns a new PrimarySeqI compliant sequence object, until no more sequences remain. This is a Bio::DB::SeqI method implementation. Returns : A Bio::DB::Indexed::Stream object Args : None =cut sub get_PrimarySeq_stream { my $self = shift; return Bio::DB::Indexed::Stream->new($self); } =head2 get_Seq_by_id Title : get_Seq_by_id, get_Seq_by_acc, get_Seq_by_version, get_Seq_by_primary_id Usage : my $seq = $db->get_Seq_by_id($id); Function: Given an ID, fetch the corresponding sequence from the database. This is a Bio::DB::SeqI and Bio::DB::RandomAccessI method implementation. Returns : A sequence object Args : ID =cut sub get_Seq_by_id { my ($self, $id) = @_; $self->throw('Need to provide a sequence ID') if not defined $id; return if not exists $self->{offsets}{$id}; return $self->{obj_class}->new($self, $id); } { no warnings 'once'; *get_Seq_by_version = *get_Seq_by_primary_id = *get_Seq_by_acc = \&get_Seq_by_id; } =head2 _calculate_offsets Title : _calculate_offsets Usage : $db->_calculate_offsets($filename, $offsets); Function: This method calculates the sequence offsets in a file based on ID and should be implemented by classes that use Bio::DB::IndexedBase. Returns : Hash of offsets Args : File to process Hashref of file offsets keyed by IDs. =cut sub _calculate_offsets { my $self = shift; $self->throw_not_implemented(); } sub _index_files { # Do the indexing of the given files using the index file on record my ($self, $files, $force_reindex) = @_; $self->_set_pack_method( @$files ); # Get name of index file my $index = $self->index_name; # If caller has requested reindexing, unlink the index file. if ($force_reindex) { # Tied-hash in Strawberry Perl creates "$file.index" unlink $index if -e $index; # Tied-hash in ActivePerl creates "$file.index.pag" and "$file.index.dir" unlink "$index.dir" if -e "$index.dir"; unlink "$index.pag" if -e "$index.pag"; } # Get the modification time of the index my $indextime = (stat $index)[9] || 0; # Register files and find if there has been any update my $modtime = 0; my @updated; for my $file (@$files) { # Register file $self->_path2fileno(basename($file)); # Any update? my $m = (stat $file)[9] || 0; if ($m > $modtime) { $modtime = $m; } if ($m > $indextime) { push @updated, $file; } } # Get termination length from first file $self->{termination_length} = $self->_calc_termination_length( $files->[0] ); # Reindex contents of changed files if needed my $reindex = $force_reindex || (scalar @updated > 0); $self->{offsets} = $self->_open_index($index, $reindex) or return; if ($reindex) { $self->{indexing} = $index; for my $file (@updated) { my $fileno = $self->_path2fileno(basename($file)); &{$self->{offset_meth}}($self, $fileno, $file, $self->{offsets}); } delete $self->{indexing}; } # Closing and reopening might help corrupted index file problem on Windows $self->_close_index($self->{offsets}); return $self->{offsets} = $self->_open_index($index); } sub _open_index { # Open index file in read-only or write mode my ($self, $index_file, $write) = @_; my %offsets; my $flags = $write ? O_CREAT|O_RDWR : O_RDONLY; my @dbmargs = $self->dbmargs; tie %offsets, 'AnyDBM_File', $index_file, $flags, 0644, @dbmargs or $self->throw( "Could not open index file $index_file: $!"); return \%offsets; } sub _close_index { # Close index file my ($self, $index) = @_; untie %$index; return 1; } # Compiling the below regular expression speeds up _parse_compound_id my $compound_id = qr/^ (.+?) (?:\:([\d_]+)(?:,|-|\.\.)([\d_]+))? (?:\/(.+))? $/x; sub _parse_compound_id { # Handle compound IDs: # $db->seq($id) # $db->seq($id, $start, $stop, $strand) # $db->seq("$id:$start,$stop") # $db->seq("$id:$start..$stop") # $db->seq("$id:$start-$stop") # $db->seq("$id:$start,$stop/$strand") # $db->seq("$id:$start..$stop/$strand") # $db->seq("$id:$start-$stop/$strand") # $db->seq("$id/$strand") my ($self, $id, $start, $stop, $strand) = @_; if ( (not defined $start ) && (not defined $stop ) && (not defined $strand) && ($id =~ m{$compound_id}) ) { # Start, stop and strand not provided and ID looks like a compound ID ($id, $start, $stop, $strand) = ($1, $2, $3, $4); } # Start, stop and strand defaults $stop ||= $self->length($id) || 0; # 0 if sequence not found in database $start ||= ($stop > 0) ? 1 : 0; $strand ||= 1; # Convert numbers such as 1_000_000 to 1000000 $start =~ s/_//g; $stop =~ s/_//g; if ($start > $stop) { # Change the strand ($start, $stop) = ($stop, $start); $strand *= -1; } return $id, $start, $stop, $strand; } sub _guess_alphabet { # Determine the molecular type of the given sequence string: # 'dna', 'rna', 'protein' or '' (unknown/empty) my ($self, $string) = @_; # Handle IUPAC residues like PrimarySeq does my $alphabet = Bio::PrimarySeq::_guess_alphabet_from_string($self, $string, 1); return $alphabet eq 'dna' ? DNA : $alphabet eq 'rna' ? RNA : $alphabet eq 'protein' ? PROTEIN : NA; } sub _makeid { # Process the header line by applying any transformation given in -makeid my ($self, $header_line) = @_; return ref($self->{makeid}) eq 'CODE' ? $self->{makeid}->($header_line) : $1; } sub _check_linelength { # Check that the line length is valid. Generate an error otherwise. my ($self, $linelength) = @_; return if not defined $linelength; $self->throw( "Each line of the file must be less than 65,536 characters. Line ". "$. is $linelength chars." ) if $linelength > 65535; } sub _calc_termination_length { # Try the beginning of the file to determine termination length # Account for crlf-terminated Windows and Mac files my ($self, $file) = @_; my $fh = IO::File->new($file) or $self->throw( "Could not open $file: $!"); # In Windows, text files have '\r\n' as line separator, but when reading in # text mode Perl will only show the '\n'. This means that for a line "ABC\r\n", # "length $_" will report 4 although the line is 5 bytes in length. # We assume that all lines have the same line separator and only read current line. my $init_pos = tell($fh); my $curr_line = <$fh>; my $pos_diff = tell($fh) - $init_pos; my $correction = $pos_diff - length $curr_line; close $fh; $self->{termination_length} = ($curr_line =~ /\r\n$/) ? 2 : 1+$correction; return $self->{termination_length}; } sub _calc_offset { # Get the offset of the n-th residue of the sequence with the given ID # and termination length (tl) my ($self, $id, $n) = @_; my $tl = $self->{termination_length}; $n--; my ($offset, $seqlen, $linelen) = (&{$self->{unpackmeth}}($self->{offsets}{$id}))[0,1,3]; $n = 0 if $n < 0; $n = $seqlen-1 if $n >= $seqlen; return $offset + $linelen * int($n/($linelen-$tl)) + $n % ($linelen-$tl); } sub _fh { # Given a sequence ID, return the filehandle on which to find this sequence my ($self, $id) = @_; $self->throw('Need to provide a sequence ID') if not defined $id; my $file = $self->file($id) or return; return eval { $self->_fhcache( File::Spec->catfile($self->{dirname}, $file)); } or $self->throw( "Can't open file $file" ); } sub _fhcache { my ($self, $path) = @_; if (!$self->{fhcache}{$path}) { if ($self->{curopen} >= $self->{maxopen}) { my @lru = sort {$self->{cacheseq}{$a} <=> $self->{cacheseq}{$b};} keys %{$self->{fhcache}}; splice(@lru, $self->{maxopen} / 3); $self->{curopen} -= @lru; for (@lru) { delete $self->{fhcache}{$_}; } } $self->{fhcache}{$path} = IO::File->new($path) || return; binmode $self->{fhcache}{$path}; $self->{curopen}++; } $self->{cacheseq}{$path}++; return $self->{fhcache}{$path}; } #------------------------------------------------------------- # Methods to store and retrieve data from indexed file # =head2 offset Title : offset Usage : my $offset = $db->offset($id); Function: Get the offset of the indicated sequence from the beginning of the file in which it is located. The offset points to the beginning of the sequence, not the beginning of the header line. Returns : String Args : ID of sequence =cut sub offset { my ($self, $id) = @_; $self->throw('Need to provide a sequence ID') if not defined $id; my $offset = $self->{offsets}{$id} or return; return (&{$self->{unpackmeth}}($offset))[0]; } =head2 strlen Title : strlen Usage : my $length = $db->strlen($id); Function: Get the number of characters in the sequence string. Returns : Integer Args : ID of sequence =cut sub strlen { my ($self, $id) = @_; $self->throw('Need to provide a sequence ID') if not defined $id; my $offset = $self->{offsets}{$id} or return; return (&{$self->{unpackmeth}}($offset))[1]; } =head2 length Title : length Usage : my $length = $db->length($id); Function: Get the number of residues of the sequence. Returns : Integer Args : ID of sequence =cut sub length { my ($self, $id) = @_; $self->throw('Need to provide a sequence ID') if not defined $id; my $offset = $self->{offsets}{$id} or return; return (&{$self->{unpackmeth}}($offset))[2]; } =head2 linelen Title : linelen Usage : my $linelen = $db->linelen($id); Function: Get the length of the line for this sequence. Returns : Integer Args : ID of sequence =cut sub linelen { my ($self, $id) = @_; $self->throw('Need to provide a sequence ID') if not defined $id; my $offset = $self->{offsets}{$id} or return; return (&{$self->{unpackmeth}}($offset))[3]; } =head2 headerlen Title : headerlen Usage : my $length = $db->headerlen($id); Function: Get the length of the header line for the indicated sequence. Returns : Integer Args : ID of sequence =cut sub headerlen { my ($self, $id) = @_; $self->throw('Need to provide a sequence ID') if not defined $id; my $offset = $self->{offsets}{$id} or return; return (&{$self->{unpackmeth}}($offset))[4]; } =head2 header_offset Title : header_offset Usage : my $offset = $db->header_offset($id); Function: Get the offset of the header line for the indicated sequence from the beginning of the file in which it is located. Returns : String Args : ID of sequence =cut sub header_offset { my ($self, $id) = @_; $self->throw('Need to provide a sequence ID') if not defined $id; return if not $self->{offsets}{$id}; return $self->offset($id) - $self->headerlen($id); } =head2 alphabet Title : alphabet Usage : my $alphabet = $db->alphabet($id); Function: Get the molecular type of the indicated sequence: dna, rna or protein Returns : String Args : ID of sequence =cut sub alphabet { my ($self, $id) = @_; $self->throw('Need to provide a sequence ID') if not defined $id; my $offset = $self->{offsets}{$id} or return; my $alphabet = (&{$self->{unpackmeth}}($offset))[5]; return : $alphabet == Bio::DB::IndexedBase::DNA ? 'dna' : $alphabet == Bio::DB::IndexedBase::RNA ? 'rna' : $alphabet == Bio::DB::IndexedBase::PROTEIN ? 'protein' : ''; } =head2 file Title : file Usage : my $file = $db->file($id); Function: Get the the name of the file in which the indicated sequence can be found. Returns : String Args : ID of sequence =cut sub file { my ($self, $id) = @_; $self->throw('Need to provide a sequence ID') if not defined $id; my $offset = $self->{offsets}{$id} or return; return $self->_fileno2path((&{$self->{unpackmeth}}($offset))[6]); } sub _fileno2path { my ($self, $fileno) = @_; return $self->{fileno2path}->[$fileno]; } sub _path2fileno { my ($self, $path) = @_; if ( not exists $self->{filepath2no}->{$path} ) { my $fileno = ($self->{filepath2no}->{$path} = 0+ $self->{fileno}++); $self->{fileno2path}->[$fileno] = $path; # Save path } return $self->{filepath2no}->{$path}; } sub _packSmall { return pack STRUCT, @_; } sub _packBig { return pack STRUCTBIG, @_; } sub _unpackSmall { return unpack STRUCT, shift; } sub _unpackBig { return unpack STRUCTBIG, shift; } sub _set_pack_method { # Determine whether to use 32 or 64 bit integers for the given files. my $self = shift; # Find the maximum file size: my ($maxsize) = sort { $b <=> $a } map { -s $_ } @_; my $fourGB = (2 ** 32) - 1; if ($maxsize > $fourGB) { # At least one file exceeds 4Gb - we will need to use 64 bit ints $self->{packmeth} = \&_packBig; $self->{unpackmeth} = \&_unpackBig; } else { $self->{packmeth} = \&_packSmall; $self->{unpackmeth} = \&_unpackSmall; } return 1; } #------------------------------------------------------------- # Tied hash logic # sub TIEHASH { return shift->new(@_); } sub FETCH { return shift->subseq(@_); } sub STORE { shift->throw("Read-only database"); } sub DELETE { shift->throw("Read-only database"); } sub CLEAR { shift->throw("Read-only database"); } sub EXISTS { return defined shift->offset(@_); } sub FIRSTKEY { return tied(%{shift->{offsets}})->FIRSTKEY(@_); } sub NEXTKEY { return tied(%{shift->{offsets}})->NEXTKEY(@_); } sub DESTROY { my $self = shift; # Close filehandles while (my ($file, $fh) = each %{ $self->{fhcache} }) { if (defined $fh) { $fh->close; } } $self->_close_index($self->{offsets}); if ( $self->{clean} || $self->{indexing} ) { # Indexing aborted or cleaning requested. Delete the index file. my $index = $self->{index_name}; # Tied-hash in Strawberry Perl creates "$file.index" unlink $index if -e $index; # Tied-hash in ActivePerl creates "$file.index.pag" and "$file.index.dir" unlink "$index.dir" if -e "$index.dir"; unlink "$index.pag" if -e "$index.pag"; } return 1; } #------------------------------------------------------------- # stream-based access to the database # package Bio::DB::Indexed::Stream; use base qw(Tie::Handle Bio::DB::SeqI); sub new { my ($class, $db) = @_; my $key = $db->FIRSTKEY; return bless { db => $db, key => $key }, $class; } sub next_seq { my $self = shift; my ($key, $db) = @{$self}{'key', 'db'}; return if not defined $key; my $value = $db->get_Seq_by_id($key); $self->{key} = $db->NEXTKEY($key); return $value; } sub TIEHANDLE { my ($class, $db) = @_; return $class->new($db); } sub READLINE { my $self = shift; return $self->next_seq || undef; } 1; BioPerl-1.007002/Bio/DB/LocationI.pm000444000766000024 747113155576320 16741 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::LocationI # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::DB::LocationI - A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects =head1 SYNOPSIS # # get a database object somehow using a concrete class # $loc = $db->get_Location_by_id('123456'); # # $loc is a Bio::LocationI object # =head1 DESCRIPTION This is a pure interface class - in other words, all this does is define methods which other (concrete) classes will actually implement. The Bio::DB::LocationI class defines methods used to retrieve location data from a sequence. This is returned in the form of Bio::LocationI objects, which can include: Bio::Location::Simple Bio::Location::Fuzzy Bio::Location::Split At the moment it is just the ability to make Bio::LocationI objects from a name or unique id (id), an accession number (acc), and so on. =head1 CONTACT Ewan Birney originally wrote Bio::DB::RandomAccessI, from which this class is based. =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@lists.open-bio.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web. https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Email cjfields at bioperl dot org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::LocationI; use strict; use Bio::Root::RootI; use base qw(Bio::Root::Root); =head2 get_Location_by_id Title : get_Location_by_id Usage : $loc = $db->get_Location_by_id('123456') Function: Gets a Bio::LocationI-implementing object by its name (id) Returns : a Bio::LocationI object or undef if not found Args : the id (as a string) of a sequence =cut sub get_Location_by_id{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_Location_by_acc Title : get_Location_by_acc Usage : $loc = $db->get_Location_by_acc('X77802'); Function: Gets a Bio::LocationI object by accession number Returns : A Bio::LocationI object or undef if not found Args : accession number (as a string) Throws : "more than one sequences correspond to this accession" if the accession maps to multiple primary ids and method is called in a scalar context =cut sub get_Location_by_acc{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_Location_by_version Title : get_Location_by_version Usage : $loc = $db->get_Location_by_version('X77802.1'); Function: Gets a Bio::LocationI object by sequence version Returns : A Bio::LocationI object Args : accession.version (as a string) Throws : "acc.version does not exist" exception =cut sub get_Location_by_version{ my ($self,@args) = @_; $self->throw_not_implemented(); } ## End of Package 1; BioPerl-1.007002/Bio/DB/MeSH.pm000444000766000024 2326313155576320 15671 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::MeSH # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho, heikki-at-bioperl-dot-org # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::MeSH - Term retrieval from a Web MeSH database =head1 SYNOPSIS my $mesh = Bio::DB::MeSH->new(); my $term = $mesh->get_exact_term('Butter'); print $term->description; =head1 DESCRIPTION This class retrieves a term from the Medical Subject Headings database by the National Library of Medicine of USA. See L. It uses the latest data available (updates happen on weekdays). If it fails, an archive cgi scripts accessing older data from previous year is used. This class implements L and wraps its methods under L. By default, web access uses L, but in its absence falls back to bioperl module L which is a subclass of L. =head1 SEE ALSO L =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::MeSH; use strict; use Bio::Phenotype::MeSH::Term; use Bio::Phenotype::MeSH::Twig; use base qw(Bio::Tools::Analysis::SimpleAnalysisBase); my $URL = 'http://www.nlm.nih.gov/mesh/MBrowser.html'; my $ANALYSIS_SPEC= {name => 'MeSH term retrival', type => 'Entry retrieval'}; my $INPUT_SPEC = [ {mandatory=>'true', type => 'scalar', 'name'=> 'value', }, ]; my $RESULT_SPEC = { '' => 'Bio::Phenotype::MeSH::Term', raw => 'raw output', }; sub _init { # Note: Base URL is now set in _webmodule(), depending on which is selected my $self = shift; $self->{'_ANALYSIS_SPEC'} = $ANALYSIS_SPEC; $self->{'_INPUT_SPEC'} = $INPUT_SPEC; $self->{'_RESULT_SPEC'} = $RESULT_SPEC; $self->{'_ANALYSIS_NAME'} = $ANALYSIS_SPEC->{'name'}; $self->_webmodule; return $self; } sub _webmodule { my ($self) = shift; $self->{'_webmodule'} = ''; # Prefer WWW::Mechanize if available and use $URL eval { require WWW::Mechanize; }; unless ($@) { $self->{'_webmodule'} = 'WWW::Mechanize'; $self->url($URL); return; } # Bio::WebAgent uses cgi alternative URL $self->_set_cgi_base_url; # Use Bio::WebAgent alternative eval { require LWP::UserAgent; }; unless ($@) { $self->{'_webmodule'} = 'Bio::WebAgent'; return; } $self->throw("Bio::DB::MeSH needs either WWW::Mechanize or Bio::WebAgent"); } sub _set_cgi_base_url { my ($self) = shift; # Try to get webpage corresponding to current year. # If it fails, try to get previous years until success or 2003 my $year = 1900 + (localtime)[5]; my $pass = 0; while ($pass == 0 and $year > 2003) { my $response; eval { $response = $self->get( "http://www.nlm.nih.gov/cgi/mesh/$year/MB_cgi" ) }; # Note: error 404 is acceptable because it can mean that webpage is not yet # implemented for current year. Absence of internet generates error 500. if ($@ or $response->{'_rc'} > 404) { $self->warn("Could not connect to the server\n") and return; } # Success closes the loop, fail makes it try with the another year if ($response->is_success) { $pass = 1; } else { $year -= 1; } } $self->url("http://www.nlm.nih.gov/cgi/mesh/$year/MB_cgi"); } =head2 get_exact_term Title : get_exact_term Usage : $s = $db->get_exact_term($value); Function: Retrieve a single MeSH term using a unique ID or exact name. Example : Returns : a Bio::Phenotype::MeSH::Term object Args : scalar, UID or name of a MeSH term The returned term object contains information about the immediate vincinity of the term in the terminology hierarchy. See L. =cut sub get_exact_term { my ($self, $value) = @_; $self->{'_term'} = undef; $self->run($value) if $value; $self->throw("Could not connect to the server") unless $self->status eq 'COMPLETED'; return $self->result; } sub run { my ($self, $value) = @_; # check input $self->throw("Need a MeSH name or ID as an input [$value]") if ref $value; # internal run() $self->_run($value); } sub _cgi_url { my($self, $field, $term) = @_; # we don't bother to URI::Escape $field and $term as this is an untainted private sub my $base_url = $self->url; return "$base_url?field=$field&term=$term"; } sub _run { my ($self, $value) = @_; $self->throw('Need a value [$value]') unless $value;; # delay repeated calls by default by 3 sec, set delay() to change # $self->sleep; $self->status('TERMINATED_BY_ERROR'); if ($self->{'_webmodule'} eq 'WWW::Mechanize') { $self->debug("using WWW::Mechanize...\n"); my $agent = WWW::Mechanize->new(); $agent->get($self->url); $agent->status == 200 or $self->warn("Could not connect to the server\n") and return; $agent->form_name('MB'); $agent->field("term", $value); if ($value =~ /\w\d{6}/) { $agent->field("field", 'uid'); } else { $agent->field("field", 'entry'); } $agent->click("exact"); $self->{'_content'} = $agent->content(); $self->status('COMPLETED'); return; } elsif ($self->{'_webmodule'} eq 'Bio::WebAgent') { $self->debug("using LWP::UserAgent...\n"); my $response; if ($value =~ /\w\d{6}/) { $self->{'_content'} = $response = eval { $self->get( $self->_cgi_url('uid', $value) ) }; $self->warn("Could not connect to the server\n") and return if $@; } else { $self->{'_content'} = eval { $response = $self->get( $self->_cgi_url('entry', $value) ) }; $self->warn("Could not connect to the server\n") and return if $@; } if ($response->is_success) { $self->{'_content'} = $response->content; $self->status('COMPLETED'); } return; } } sub result { my ($self,$value) = @_; $self->throw("Could not retrieve results") unless $self->status('COMPLETED'); # no processing return $self->{'_content'} if $value && $value eq 'raw'; # create a MeSH::Term object $_ = $self->{'_content'}; $self->debug( substr($_, 0, 100) . "\n"); my ($id) = m|Unique \s+ ID ]+ )? > (.*?) # id |ix; my ($name) = m|MeSH \s+ Heading ]+ )? > (.*?) # name |ix; my ($desc) = m|Scope \s+ Note ]+ )? > (.*?) # desc |isx; $self->throw("No description returned: $_") unless defined $desc; $desc =~ s/<.*?>//sg; $desc =~ s/(?:\r)?\n/ /g; $desc =~ s/\( +/\(/g; $desc =~ s/ {2,}/ /g; my $term = Bio::Phenotype::MeSH::Term->new(-id => $id, -name => $name, -description => $desc ); my ($trees) = $self->{'_content'} =~ /MeSH Tree Structures(.*)/s; while (m|Entry Term]+)?>(.*?)|ig) { $term->add_synonym($1); $self->debug("Synonym: |$1|\n"); } foreach (split /
/i, $trees ) { next unless /$name/; s// /sgi; s/<.*?>//sg; s/ / /sg; #print "|$_|"; my ($treeno) = /$name \[([^]]+)]/; my ($parent_treeno) = $treeno =~ /(.*)\.\d{3}/; my ($parent) = /\n +(\w.+) \[$parent_treeno\]/; my $twig = Bio::Phenotype::MeSH::Twig->new(-parent => $parent); $term->add_twig($twig); $self->debug("Parent: |$parent|\n"); while (/\n +(\w.+) \[$treeno\./g ) { $twig->add_child($1); $self->debug("Child: |$1|\n"); } while (/\n +(\w.+) \[$parent_treeno\./g ) { next if $name eq $1; $twig->add_sister($1); $self->debug("Sister: |$1|\n"); } } return $term; } 1; BioPerl-1.007002/Bio/DB/NCBIHelper.pm000444000766000024 4350713155576320 16753 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::NCBIHelper # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code # # Interfaces with new WebDBSeqI interface =head1 NAME Bio::DB::NCBIHelper - A collection of routines useful for queries to NCBI databases. =head1 SYNOPSIS # Do not use this module directly. # get a Bio::DB::NCBIHelper object somehow my $seqio = $db->get_Stream_by_acc(['J00522']); foreach my $seq ( $seqio->next_seq ) { # process seq } =head1 DESCRIPTION Provides a single place to setup some common methods for querying NCBI web databases. This module just centralizes the methods for constructing a URL for querying NCBI GenBank and NCBI GenPept and the common HTML stripping done in L(). The base NCBI query URL used is: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web. https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::NCBIHelper; use strict; use Bio::DB::Query::GenBank; use HTTP::Request::Common; use URI; use Bio::Root::IO; use Bio::DB::RefSeq; use URI::Escape qw(uri_unescape); use base qw(Bio::DB::WebDBSeqI Bio::Root::Root); our $HOSTBASE = 'https://eutils.ncbi.nlm.nih.gov'; our $MAX_ENTRIES = 19000; our $REQUEST_DELAY = 3; our %CGILOCATION = ( 'batch' => [ 'post' => '/entrez/eutils/epost.fcgi' ], 'query' => [ 'get' => '/entrez/eutils/efetch.fcgi' ], 'single' => [ 'get' => '/entrez/eutils/efetch.fcgi' ], 'version' => [ 'get' => '/entrez/eutils/efetch.fcgi' ], 'gi' => [ 'get' => '/entrez/eutils/efetch.fcgi' ], 'webenv' => [ 'get' => '/entrez/eutils/efetch.fcgi' ] ); our %FORMATMAP = ( 'gb' => 'genbank', 'gp' => 'genbank', 'fasta' => 'fasta', 'asn.1' => 'entrezgene', 'gbwithparts' => 'genbank', ); our $DEFAULTFORMAT = 'gb'; =head2 new Title : new Usage : Function: the new way to make modules a little more lightweight Returns : Args : =cut sub new { my ( $class, @args ) = @_; my $self = $class->SUPER::new(@args); my ($seq_start, $seq_stop, $no_redirect, $redirect, $complexity, $strand ) = $self->_rearrange( [ qw(SEQ_START SEQ_STOP NO_REDIRECT REDIRECT_REFSEQ COMPLEXITY STRAND) ], @args ); $seq_start && $self->seq_start($seq_start); $seq_stop && $self->seq_stop($seq_stop); $no_redirect && $self->no_redirect($no_redirect); $redirect && $self->redirect_refseq($redirect); $strand && $self->strand($strand); # adjust statement to accept zero value defined $complexity && ( $complexity >= 0 && $complexity <= 4 ) && $self->complexity($complexity); return $self; } =head2 get_params Title : get_params Usage : my %params = $self->get_params($mode) Function: returns key,value pairs to be passed to NCBI database for either 'batch' or 'single' sequence retrieval method Returns : a key,value pair hash Args : 'single' or 'batch' mode for retrieval =cut sub get_params { my ($self, $mode) = @_; $self->throw("subclass did not implement get_params"); } =head2 default_format Title : default_format Usage : my $format = $self->default_format Function: returns default sequence format for this module Returns : string Args : none =cut sub default_format { return $DEFAULTFORMAT; } =head2 get_request Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) =cut sub get_request { my ( $self, @qualifiers ) = @_; my ( $mode, $uids, $format, $query, $seq_start, $seq_stop, $strand, $complexity ) = $self->_rearrange( [qw(MODE UIDS FORMAT QUERY SEQ_START SEQ_STOP STRAND COMPLEXITY)], @qualifiers ); $mode = lc $mode; ($format) = $self->request_format() unless ( defined $format ); if ( !defined $mode || $mode eq '' ) { $mode = 'single'; } my %params = $self->get_params($mode); if ( !%params ) { $self->throw( "must specify a valid retrieval mode 'single' or 'batch' not '$mode'" ); } my $url = URI->new( $HOSTBASE . $CGILOCATION{$mode}[1] ); unless ( $mode eq 'webenv' || defined $uids || defined $query ) { $self->throw("Must specify a query or list of uids to fetch"); } if ( $query && $query->can('cookie') ) { @params{ 'WebEnv', 'query_key' } = $query->cookie; $params{'db'} = $query->db; } elsif ($query) { $params{'id'} = join ',', $query->ids; } # for batch retrieval, non-query style elsif ( $mode eq 'webenv' && $self->can('cookie') ) { @params{ 'WebEnv', 'query_key' } = $self->cookie; } elsif ($uids) { if ( ref($uids) =~ /array/i ) { $uids = join( ",", @$uids ); } $params{'id'} = $uids; } $seq_start && ( $params{'seq_start'} = $seq_start ); $seq_stop && ( $params{'seq_stop'} = $seq_stop ); $strand && ( $params{'strand'} = $strand ); if ( defined $complexity && ( $seq_start || $seq_stop || $strand ) ) { $self->warn( "Complexity set to $complexity; seq_start and seq_stop may not work!" ) if ( $complexity != 1 && ( $seq_start || $seq_stop ) ); $self->warn( "Complexity set to 0; expect strange results with strand set to 2" ) if ( $complexity == 0 && $strand == 2 && $format eq 'fasta' ); } defined $complexity && ( $params{'complexity'} = $complexity ); $params{'rettype'} = $format unless $mode eq 'batch'; # for now, 'post' is batch retrieval if ( $CGILOCATION{$mode}[0] eq 'post' ) { my $response = $self->ua->request( POST $url, [%params] ); $response->proxy_authorization_basic( $self->authentication ) if ( $self->authentication ); $self->_parse_response( $response->content ); my ( $cookie, $querykey ) = $self->cookie; my %qualifiers = ( '-mode' => 'webenv', '-seq_start' => $seq_start, '-seq_stop' => $seq_stop, '-strand' => $strand, '-complexity' => $complexity, '-format' => $format ); return $self->get_request(%qualifiers); } else { $url->query_form(%params); return GET $url; } } =head2 get_Stream_by_batch Title : get_Stream_by_batch Usage : $seq = $db->get_Stream_by_batch($ref); Function: Retrieves Seq objects from Entrez 'en masse', rather than one at a time. For large numbers of sequences, this is far superior than get_Stream_by_id or get_Stream_by_acc. Example : Returns : a Bio::SeqIO stream object Args : $ref : either an array reference, a filename, or a filehandle from which to get the list of unique ids/accession numbers. NOTE: deprecated API. Use get_Stream_by_id() instead. =cut *get_Stream_by_batch = sub { my $self = shift; $self->deprecated('get_Stream_by_batch() is deprecated; use get_Stream_by_id() instead'); $self->get_Stream_by_id(@_) }; =head2 get_Stream_by_query Title : get_Stream_by_query Usage : $seq = $db->get_Stream_by_query($query); Function: Retrieves Seq objects from Entrez 'en masse', rather than one at a time. For large numbers of sequences, this is far superior to get_Stream_by_id and get_Stream_by_acc. Example : Returns : a Bio::SeqIO stream object Args : An Entrez query string or a Bio::DB::Query::GenBank object. It is suggested that you create a Bio::DB::Query::GenBank object and get the entry count before you fetch a potentially large stream. =cut sub get_Stream_by_query { my ($self, $query) = @_; unless (ref $query && $query->can('query')) { $query = Bio::DB::Query::GenBank->new($query); } return $self->get_seq_stream('-query' => $query, '-mode'=>'query'); } =head2 postprocess_data Title : postprocess_data Usage : $self->postprocess_data ( 'type' => 'string', 'location' => \$datastr ); Function: Process downloaded data before loading into a Bio::SeqIO. This works for Genbank and Genpept, other classes should override it with their own method. Returns : void Args : hash with two keys: 'type' can be 'string' or 'file' 'location' either file location or string reference containing data =cut sub postprocess_data { # retain this in case postprocessing is needed at a future date } =head2 request_format Title : request_format Usage : my ($req_format, $ioformat) = $self->request_format; $self->request_format("genbank"); $self->request_format("fasta"); Function: Get/Set sequence format retrieval. The get-form will normally not be used outside of this and derived modules. Returns : Array of two strings, the first representing the format for retrieval, and the second specifying the corresponding SeqIO format. Args : $format = sequence format =cut sub request_format { my ( $self, $value ) = @_; if ( defined $value ) { $value = lc $value; if ( defined $FORMATMAP{$value} ) { $self->{'_format'} = [ $value, $FORMATMAP{$value} ]; } else { # Try to fall back to a default. Alternatively, we could throw # an exception $self->{'_format'} = [ $value, $value ]; } } return @{ $self->{'_format'} }; } =head2 redirect_refseq Title : redirect_refseq Usage : $db->redirect_refseq(1) Function: simple getter/setter which redirects RefSeqs to use Bio::DB::RefSeq Returns : Boolean value Args : Boolean value (optional) Throws : 'unparseable output exception' Note : This replaces 'no_redirect' as a more straightforward flag to redirect possible RefSeqs to use Bio::DB::RefSeq (EBI interface) instead of retrieving the NCBI records =cut sub redirect_refseq { my $self = shift; return $self->{'_redirect_refseq'} = shift if @_; return $self->{'_redirect_refseq'}; } =head2 complexity Title : complexity Usage : $db->complexity(3) Function: get/set complexity value Returns : value from 0-4 indicating level of complexity Args : value from 0-4 (optional); if unset server assumes 1 Throws : if arg is not an integer or falls outside of noted range above Note : From efetch docs, the complexity regulates the display: 0 - get the whole blob 1 - get the bioseq for gi of interest (default in Entrez) 2 - get the minimal bioseq-set containing the gi of interest 3 - get the minimal nuc-prot containing the gi of interest 4 - get the minimal pub-set containing the gi of interest =cut sub complexity { my ( $self, $comp ) = @_; if ( defined $comp ) { $self->throw("Complexity value must be integer between 0 and 4") if $comp !~ /^\d+$/ || $comp < 0 || $comp > 4; $self->{'_complexity'} = $comp; } return $self->{'_complexity'}; } =head2 strand Title : strand Usage : $db->strand(1) Function: get/set strand value Returns : strand value if set Args : value of 1 (plus) or 2 (minus); if unset server assumes 1 Throws : if arg is not an integer or is not 1 or 2 Note : This differs from BioPerl's use of strand: 1 = plus, -1 = minus 0 = not relevant. We should probably add in some functionality to convert over in the future. =cut sub strand { my ($self, $str) = @_; if ($str) { $self->throw("strand() must be integer value of 1 (plus strand) or 2 (minus strand) if set") if $str !~ /^\d+$/ || $str < 1 || $str > 2; $self->{'_strand'} = $str; } return $self->{'_strand'}; } =head2 seq_start Title : seq_start Usage : $db->seq_start(123) Function: get/set sequence start location Returns : sequence start value if set Args : integer; if unset server assumes 1 Throws : if arg is not an integer =cut sub seq_start { my ($self, $start) = @_; if ($start) { $self->throw("seq_start() must be integer value if set") if $start !~ /^\d+$/; $self->{'_seq_start'} = $start; } return $self->{'_seq_start'}; } =head2 seq_stop Title : seq_stop Usage : $db->seq_stop(456) Function: get/set sequence stop (end) location Returns : sequence stop (end) value if set Args : integer; if unset server assumes 1 Throws : if arg is not an integer =cut sub seq_stop { my ($self, $stop) = @_; if ($stop) { $self->throw("seq_stop() must be integer if set") if $stop !~ /^\d+$/; $self->{'_seq_stop'} = $stop; } return $self->{'_seq_stop'}; } =head2 Bio::DB::WebDBSeqI methods Overriding WebDBSeqI method to help newbies to retrieve sequences =head2 get_Stream_by_acc Title : get_Stream_by_acc Usage : $seq = $db->get_Stream_by_acc([$acc1, $acc2]); Function: gets a series of Seq objects by accession numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id() =cut sub get_Stream_by_acc { my ( $self, $ids ) = @_; my $newdb = $self->_check_id($ids); if ( defined $newdb && ref($newdb) && $newdb->isa('Bio::DB::RefSeq') ) { return $newdb->get_seq_stream( '-uids' => $ids, '-mode' => 'single' ); } else { return $self->get_seq_stream( '-uids' => $ids, '-mode' => 'single' ); } } =head2 _check_id Title : _check_id Usage : Function: Returns : a Bio::DB::RefSeq reference or throws Args : $id(s), $string =cut sub _check_id { my ( $self, $ids ) = @_; # NT contigs can not be retrieved $self->throw("NT_ contigs are whole chromosome files which are not part of regular" . "database distributions. Go to ftp://ftp.ncbi.nih.gov/genomes/.") if $ids =~ /NT_/; # Asking for a RefSeq from EMBL/GenBank if ( $self->redirect_refseq ) { if ( $ids =~ /N._/ ) { $self->warn( "[$ids] is not a normal sequence database but a RefSeq entry." . " Redirecting the request.\n" ) if $self->verbose >= 0; return Bio::DB::RefSeq->new(); } } } =head2 delay_policy Title : delay_policy Usage : $secs = $self->delay_policy Function: NCBI requests a delay of 3 seconds between requests. This method implements that policy. Returns : number of seconds to delay Args : none =cut sub delay_policy { my $self = shift; return $REQUEST_DELAY; } =head2 cookie Title : cookie Usage : ($cookie,$querynum) = $db->cookie Function: return the NCBI query cookie, this information is used by Bio::DB::GenBank in conjunction with efetch, ripped from Bio::DB::Query::GenBank Returns : list of (cookie,querynum) Args : none =cut sub cookie { my $self = shift; if (@_) { $self->{'_cookie'} = shift; $self->{'_querynum'} = shift; } else { return @{$self}{qw(_cookie _querynum)}; } } =head2 _parse_response Title : _parse_response Usage : $db->_parse_response($content) Function: parse out response for cookie, this is a trimmed-down version of _parse_response from Bio::DB::Query::GenBank Returns : empty Args : none Throws : 'unparseable output exception' =cut sub _parse_response { my $self = shift; my $content = shift; if ( my ($warning) = $content =~ m!(.+)!s ) { $self->warn("Warning(s) from GenBank: $warning\n"); } if ( my ($error) = $content =~ /([^<]+)/ ) { $self->throw("Error from Genbank: $error"); } my ($cookie) = $content =~ m!(\S+)!; my ($querykey) = $content =~ m!(\d+)!; $self->cookie( uri_unescape($cookie), $querykey ); } =head2 no_redirect Title : no_redirect Usage : $db->no_redirect($content) Function: DEPRECATED - Used to indicate that Bio::DB::GenBank instance retrieves possible RefSeqs from EBI instead; default behavior is now to retrieve directly from NCBI Returns : None Args : None Throws : Method is deprecated in favor of positive flag method 'redirect_refseq' =cut sub no_redirect { shift->throw( "Use of no_redirect() is deprecated. Bio::DB::GenBank default is to always\n". "retrieve from NCBI. In order to redirect possible RefSeqs to EBI, set\n". "redirect_refseq flag to 1"); } 1; __END__ BioPerl-1.007002/Bio/DB/Qual.pm000444000766000024 4013313155576320 15772 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::Qual # # You may distribute this module under the same terms as perl itself # =head1 NAME Bio::DB::Qual - Fast indexed access to quality files =head1 SYNOPSIS use Bio::DB::Qual; # create database from directory of qual files my $db = Bio::DB::Qual->new('/path/to/qual/files/'); my @ids = $db->get_all_primary_ids; # Simple access my @qualarr = @{$db->qual('CHROMOSOME_I',4_000_000 => 4_100_000)}; my @revqual = @{$db->qual('CHROMOSOME_I',4_100_000 => 4_000_000)}; my $length = $db->length('CHROMOSOME_I'); my $header = $db->header('CHROMOSOME_I'); # Access to sequence objects. See Bio::PrimarySeqI. my $obj = $db->get_Qual_by_id('CHROMOSOME_I'); my @qual = @{$obj->qual}; my @subqual = @{$obj->subqual(4_000_000 => 4_100_000)}; my $length = $obj->length; # Loop through sequence objects my $stream = $db->get_PrimarySeq_stream; while (my $qual = $stream->next_seq) { # Bio::Seq::PrimaryQual operations } # Filehandle access my $fh = Bio::DB::Qual->newFh('/path/to/qual/files/'); while (my $qual = <$fh>) { # Bio::Seq::PrimaryQual operations } # Tied hash access tie %qualities,'Bio::DB::Qual','/path/to/qual/files/'; print $qualities{'CHROMOSOME_I:1,20000'}; =head1 DESCRIPTION Bio::DB::Qual provides indexed access to a single Fasta file, several files, or a directory of files. It provides random access to each quality score entry without having to read the file from the beginning. Access to subqualities (portions of a quality score) is provided, although contrary to Bio::DB::Fasta, the full quality score has to be brought in memory. Bio::DB::Qual is based on Bio::DB::IndexedBase. See this module's documentation for details. The qual files should contain decimal quality scores. Entries may have any line length up to 65,536 characters, and different line lengths are allowed in the same file. However, within a quality score entry, all lines must be the same length except for the last. An error will be thrown if this is not the case. The module uses /^E(\S+)/ to extract the primary ID of each quality score from the qual header. See -makeid in Bio::DB::IndexedBase to pass a callback routine to reversibly modify this primary ID, e.g. if you wish to extract a specific portion of the gi|gb|abc|xyz GenBank IDs. =head1 DATABASE CREATION AND INDEXING The object-oriented constructor is new(), the filehandle constructor is newFh() and the tied hash constructor is tie(). They all allow one to index a single Fasta file, several files, or a directory of files. See Bio::DB::IndexedBase. =head1 SEE ALSO L L L =head1 LIMITATIONS When a quality score is deleted from one of the qual files, this deletion is not detected by the module and removed from the index. As a result, a "ghost" entry will remain in the index and will return garbage results if accessed. Currently, the only way to accommodate deletions is to rebuild the entire index, either by deleting it manually, or by passing -reindex=E1 to new() when initializing the module. All quality score lines for a given quality score must have the same length except for the last (not sure why there is this limitation). This is not problematic for sequences but could be annoying for quality scores. A workaround is to make sure that your quality scores fit on no more than 2 lines. Another solution could be to padd them with blank spaces so that each line has the same number of characters (maybe this padding should be implemented in Bio::SeqIO::qual?). =head1 AUTHOR Florent E Angly Eflorent . angly @ gmail-dot-comE. Module largely based on and adapted from Bio::DB::Fasta by Lincoln Stein. Copyright (c) 2007 Florent E Angly. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ For BioPerl-style access, the following methods are provided: =head2 get_Seq_by_id Title : get_Seq_by_id, get_Seq_by_acc, get_Seq_by_version, get_Seq_by_primary_id, get_Qual_by_id, get_qual_by_acc, get_qual_by_version, get_qual_by_primary_id, Usage : my $seq = $db->get_Seq_by_id($id); Function: Given an ID, fetch the corresponding sequence from the database. Returns : A Bio::PrimarySeq::Fasta object (Bio::PrimarySeqI compliant) Note that to save resource, Bio::PrimarySeq::Fasta sequence objects only load the sequence string into memory when requested using seq(). See L for methods provided by the sequence objects returned from get_Seq_by_id() and get_PrimarySeq_stream(). Args : ID =head2 get_PrimarySeq_stream Title : get_Seq_stream, get_PrimarySeq_stream Usage : my $stream = $db->get_Seq_stream(); Function: Get a stream of Bio::PrimarySeq::Fasta objects. The stream supports a single method, next_seq(). Each call to next_seq() returns a new Bio::PrimarySeq::Fasta sequence object, until no more sequences remain. Returns : A Bio::DB::Indexed::Stream object Args : None =head1 For simple access, the following methods are provided: =cut package Bio::DB::Qual; use strict; use IO::File; use File::Spec; use base qw(Bio::DB::IndexedBase); our $obj_class = 'Bio::Seq::PrimaryQual::Qual'; our $file_glob = '*.{qual,QUAL,qa,QA}'; =head2 new Title : new Usage : my $db = Bio::DB::Qual->new( $path, %options); Function: Initialize a new database object. When indexing a directory, files ending in .qual,qa are indexed by default. Returns : A new Bio::DB::Qual object Args : A single file, or path to dir, or arrayref of files Optional arguments: see Bio::DB::IndexedBase =cut sub _calculate_offsets { # Bio::DB::IndexedBase calls this to calculate offsets my ($self, $fileno, $file, $offsets) = @_; my $fh = IO::File->new($file) or $self->throw("Could not open $file: $!"); binmode $fh; warn "Indexing $file\n" if $self->{debug}; my ($offset, @ids, $linelen, $headerlen, $count, $qual_lines, $last_line, $numres, %offsets); my ($l3_len, $l2_len, $l_len, $blank_lines) = (0, 0, 0, 0); my $termination_length = $self->{termination_length}; while (my $line = <$fh>) { # Account for crlf-terminated Windows files if (index($line, '>') == 0) { if ($line =~ /^>(\S+)/) { print STDERR "Indexed $count quality scores...\n" if $self->{debug} && (++$count%1000) == 0; $self->_check_linelength($linelen); my $pos = tell($fh); if (@ids) { my $strlen = $pos - $offset - length($line); $strlen -= $termination_length * $qual_lines; my $ppos = &{$self->{packmeth}}($offset, $strlen, $numres, $linelen, $headerlen, Bio::DB::IndexedBase::NA, $fileno); for my $id (@ids) { $offsets->{$id} = $ppos; } $numres = 0; } @ids = $self->_makeid($line); ($offset, $headerlen, $linelen, $qual_lines) = ($pos, length $line, 0, 0); ($l3_len, $l2_len, $l_len, $blank_lines) = (0, 0, 0, 0); } else { # Catch bad header lines, bug 3172 $self->throw("FASTA header doesn't match '>(\\S+)': $line"); } } elsif ($line !~ /\S/) { # Skip blank line $blank_lines++; next; } else { # Need to check every line :( $l3_len = $l2_len; $l2_len = $l_len; $l_len = length $line; if (Bio::DB::IndexedBase::DIE_ON_MISSMATCHED_LINES) { if ( ($l3_len > 0) && ($l2_len > 0) && ($l3_len != $l2_len) ) { my $fap = substr($line, 0, 20).".."; $self->throw("Each line of the qual entry must be the same ". "length except the last. Line above #$. '$fap' is $l2_len". " != $l3_len chars."); } if ($blank_lines) { # Blank lines not allowed in entry $self->throw("Blank lines can only precede header lines, ". "found preceding line #$."); } } $linelen ||= length $line; $qual_lines++; $numres += scalar(split /\s+/, $line); } $last_line = $line; } # Process last entry $self->_check_linelength($linelen); my $pos = tell($fh); if (@ids) { my $strlen = $pos - $offset; if ($linelen == 0) { $strlen = 0; } else { if ($last_line !~ /\s$/) { $qual_lines--; } $strlen -= $termination_length * $qual_lines; } my $ppos = &{$self->{packmeth}}($offset, $strlen, $numres, $linelen, $headerlen, Bio::DB::IndexedBase::NA, $fileno); for my $id (@ids) { $offsets->{$id} = $ppos; } } return \%offsets; } # for backward compatibility sub get_PrimaryQual_stream { my $self = shift; return $self->get_PrimarySeq_stream; } # for backward compatibility sub get_Qual_by_id { my ($self, $id) = @_; return $self->get_Seq_by_id($id); } *get_qual_by_version = *get_qual_by_primary_id = *get_qual_by_acc = \&get_Qual_by_id; =head2 qual Title : qual, quality, subqual Usage : # All quality scores my @qualarr = @{$qualdb->subqual($id)}; # Subset of the quality scores my @subqualarr = @{$qualdb->subqual($id, $start, $stop, $strand)}; # or... my @subqualarr = @{$qualdb->subqual($compound_id)}; Function: Get a subqual of an entry in the database. For your convenience, the sequence to extract can be specified with any of the following compound IDs: $db->qual("$id:$start,$stop") $db->qual("$id:$start..$stop") $db->qual("$id:$start-$stop") $db->qual("$id:$start,$stop/$strand") $db->qual("$id:$start..$stop/$strand") $db->qual("$id:$start-$stop/$strand") $db->qual("$id/$strand") If $stop is less than $start, then the reverse complement of the sequence is returned. Avoid using it if possible since this goes against Bio::Seq conventions. Returns : Reference to an array of quality scores Args : Compound ID of entry to retrieve or ID, optional start (defaults to 1), optional end (defaults to the number of quality scores for this sequence), and strand (defaults to 1). =cut sub subqual { my ($self, $id, $start, $stop, $strand) = @_; # Quality values in a quality score can have 1 or 2 digits and are separated # by one (or several?) spaces. Thus contrary to Bio::DB::Fasta, here there # is no easy way match the position of a quality value to its position in # the quality string. # As a consequence, if a subqual of the quality is requested, we still need # to grab the full quality string first - performance penalty for big # quality scores :( # I think there is no way around starting at the begining of the quality # score but maybe there is a resource-efficient way of starting at the # begining of the quality score and stopping when the the position of the # last quality value requested is reached?? $self->throw('Need to provide a sequence ID') if not defined $id; ($id, $start, $stop, $strand) = $self->_parse_compound_id($id, $start, $stop, $strand); # Position in quality string my $string_start = 1; my $string_stop = $self->strlen($id); # Fetch full quality string my $fh = $self->_fh($id) or return; my $filestart = $self->_calc_offset($id, $string_start); my $filestop = $self->_calc_offset($id, $string_stop ); seek($fh, $filestart,0); my $data; read($fh, $data, $filestop-$filestart+1); # Process quality score Bio::DB::IndexedBase::_strip_crnl($data); my $subqual = 0; $subqual = 1 if ( $start || $stop ); my @data; if ( $subqual || ($strand == -1) ) { @data = split / /, $data, $stop+1; my $length = scalar(@data); $start = 1 if $start < 1; $stop = $length if $stop > $length; pop @data if ($stop != $length); splice @data, 0, $start-1; @data = reverse(@data) if $strand == -1; $data = join ' ', @data; } else { @data = split / /, $data; } return \@data; } *qual = *quality = \&subqual; =head2 header Title : header Usage : my $header = $db->header($id); Function: Get the header line (ID and description fields) of the specified entry. Returns : String Args : ID of entry =cut sub header { my ($self, $id) = @_; $self->throw('Need to provide a sequence ID') if not defined $id; my ($offset, $headerlen) = (&{$self->{unpackmeth}}($self->{offsets}{$id}))[0,4]; $offset -= $headerlen; my $data; my $fh = $self->_fh($id) or return; seek($fh, $offset, 0); read($fh, $data, $headerlen); # On Windows chomp remove '\n' but leaves '\r' # when reading '\r\n' in binary mode, # _strip_crnl removes both $data = Bio::DB::IndexedBase::_strip_crnl($data); substr($data, 0, 1) = ''; return $data; } #------------------------------------------------------------- # Tied hash overrides # sub FETCH { return shift->subqual(@_); } #------------------------------------------------------------- # Bio::Seq::PrimaryQual compatibility # # Usage is the same as in Bio::Seq::PrimaryQual package Bio::Seq::PrimaryQual::Qual; use overload '""' => 'display_id'; use base qw(Bio::Root::Root Bio::Seq::PrimaryQual); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($db, $id, $start, $stop) = $self->_rearrange( [qw(DATABASE ID START STOP)], @args); $self->{db} = $db; $self->{id} = $id; $self->{stop} = $stop || $db->length($id); $self->{start} = $start || ($self->{stop} > 0 ? 1 : 0); # handle 0-length seqs return $self; } sub qual { my $self = shift; my $qual = $self->{db}->qual($self->{id}, $self->{start}, $self->{stop}); return $qual; } sub subqual { my ($self, $start, $stop) = @_; return $self->trunc($start, $stop)->qual; } sub trunc { # Override Bio::Seq::QualI trunc() method. This way, we create an object # that does not store the quality array in memory. my ($self, $start, $stop) = @_; $self->throw( "$stop is smaller than $stop. If you want to truncate and reverse ". "complement, you must call trunc followed by revcom." ) if $start > $stop; if ($self->{start} <= $self->{stop}) { $start = $self->{start}+$start-1; $stop = $self->{start}+$stop-1; } else { $start = $self->{start}-($start-1); $stop = $self->{start}-($stop-1); } my $obj = $self->new( -database => $self->{db}, -id => $self->{id}, -start => $start, -stop => $stop ); return $obj; } sub display_id { my $self = shift; return $self->{id}; } sub primary_id { my $self = shift; return overload::StrVal($self); } sub revcom { # Override Bio::QualI revcom() with optimized method. my $self = shift; return $self->new(@{$self}{'db', 'id', 'stop', 'start'}); } sub length { # Get length from quality location, not the quality array (too expensive) my $self = shift; return $self->{start} < $self->{stop} ? $self->{stop} - $self->{start} + 1 : $self->{start} - $self->{stop} + 1 ; } sub description { my $self = shift; my $header = $self->{'db'}->header($self->{id}); # remove the id from the header $header = (split(/\s+/, $header, 2))[2]; return $header; } *desc = \&description; 1; BioPerl-1.007002/Bio/DB/QueryI.pm000444000766000024 753213155576320 16274 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::QueryI.pm # # Please direct questions and support issues to # # Cared for by Lincoln Stein # # Copyright Lincoln Stein # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code # =head1 NAME Bio::DB::QueryI - Object Interface to queryable sequence databases =head1 SYNOPSIS # using Bio::DB::Query::GenBank as an example my $query_string = 'Oryza[Organism] AND EST[Keyword]'; my $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide', -query=>$query_string); my $count = $query->count; my @ids = $query->ids; # get a genbank database handle $gb = Bio::DB::GenBank->new(); my $stream = $db->get_Stream_by_query($query); while (my $seq = $stream->next_seq) { ... } # initialize the list yourself my $query = Bio::DB::Query::GenBank->new(-ids=>['X1012','CA12345']); =head1 DESCRIPTION This interface provides facilities for managing sequence queries such as those offered by Entrez. A query object is created by calling new() with a database-specific argument list. From the query object you can either obtain the list of IDs returned by the query, or a count of entries that would be returned. You can pass the query object to a Bio::DB::RandomAccessI object to return the entries themselves as a list or a stream. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Lincoln Stein Email lstein@cshl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::QueryI; use strict; use base qw(Bio::Root::RootI); =head2 new Title : new Usage : $db = Bio::DB::QueryI->new(@args); Function: constructor Returns : QueryI object Args : -query a query string -ids a list of ids as an arrayref Create new QueryI object. You may initialize with either a query string or with a list of ids. If both ids and a query are provided, the former takes precedence. Subclasses may recognize additional arguments. =cut =head2 count Title : count Usage : $count = $db->count; Function: return count of number of entries retrieved by query Returns : integer Args : none Returns the number of entries that are matched by the query. =cut sub count { my $self = shift; my @ids = $self->ids; scalar @ids; } =head2 ids Title : ids Usage : @ids = $db->ids([@ids]) Function: get/set matching ids Returns : array of sequence ids Args : (optional) array ref with new set of ids =cut sub ids { my $self = shift; $self->throw_not_implemented; } =head2 query Title : query Usage : $query = $db->query([$query]) Function: get/set query string Returns : string Args : (optional) new query string =cut sub query { my $self = shift; $self->throw_not_implemented; } 1; BioPerl-1.007002/Bio/DB/RandomAccessI.pm000444000766000024 575513155576320 17536 0ustar00cjfieldsstaff000000000000# POD documentation - main docs before the code # # =head1 NAME Bio::DB::RandomAccessI - Abstract interface for a sequence database =head1 SYNOPSIS # # get a database object somehow using a concrete class # $seq = $db->get_Seq_by_id('ROA1_HUMAN'); # # $seq is a Bio::Seq object # =head1 DESCRIPTION This is a pure interface class - in other words, all this does is define methods which other (concrete) classes will actually implement. The Bio::DB::RandomAccessI class defines what methods a generic database class should have. At the moment it is just the ability to make Bio::Seq objects from a name (id) or an accession number. =head1 CONTACT Ewan Birney Ebirney@ebi.ac.ukE originally wrote this class. =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::RandomAccessI; use strict; use Bio::Root::RootI; use base qw(Bio::Root::Root); =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object or undef if not found Args : the id (as a string) of a sequence, =cut sub get_Seq_by_id{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); $seq = $db->get_Seq_by_acc(Locus => 'X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object or undef if not found Args : accession number (as a string), or a two element list consisting of namespace=>accession Throws : "more than one sequences correspond to this accession" if the accession maps to multiple primary ids and method is called in a scalar context NOTE: The two-element form allows you to choose the namespace for the accession number. =cut sub get_Seq_by_acc{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_Seq_by_version Title : get_Seq_by_version Usage : $seq = $db->get_Seq_by_version('X77802.1'); Function: Gets a Bio::Seq object by sequence version Returns : A Bio::Seq object Args : accession.version (as a string) Throws : "acc.version does not exist" exception =cut sub get_Seq_by_version{ my ($self,@args) = @_; $self->throw_not_implemented(); } ## End of Package 1; BioPerl-1.007002/Bio/DB/RefSeq.pm000444000766000024 1101413155576320 16251 0ustar00cjfieldsstaff000000000000# # # BioPerl module for Bio::DB::EMBL # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::RefSeq - Database object interface for RefSeq retrieval =head1 SYNOPSIS use Bio::DB::RefSeq; $db = Bio::DB::RefSeq->new(); # most of the time RefSeq_ID eq RefSeq acc $seq = $db->get_Seq_by_id('NM_006732'); # RefSeq ID print "accession is ", $seq->accession_number, "\n"; # or changeing to accession number and Fasta format ... $db->request_format('fasta'); $seq = $db->get_Seq_by_acc('NM_006732'); # RefSeq ACC print "seq is ", $seq->seq, "\n"; # especially when using versions, you better be prepared # in not getting what what want eval { $seq = $db->get_Seq_by_version('NM_006732.1'); # RefSeq VERSION }; print "accesion is ", $seq->accession_number, "\n" unless $@; # or ... best when downloading very large files, prevents # keeping all of the file in memory # also don't want features, just sequence so let's save bandwidth # and request Fasta sequence $db = Bio::DB::RefSeq->new(-retrievaltype => 'tempfile' , -format => 'fasta'); my $seqio = $db->get_Stream_by_id(['NM_006732', 'NM_005252'] ); while( my $seq = $seqio->next_seq ) { print "seqid is ", $seq->id, "\n"; } =head1 DESCRIPTION Allows the dynamic retrieval of sequence objects L from the RefSeq database using the dbfetch script at EBI: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch In order to make changes transparent we have host type (currently only ebi) and location (defaults to ebi) separated out. This allows later additions of more servers in different geographical locations. The functionality of this module is inherited from L which implements L. This module retrieves entries from EBI although it retrieves database entries produced at NCBI. When read into bioperl objects, the parser for GenBank format it used. RefSeq is a NONSTANDARD GenBank file so be ready for surprises. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email Heikki Lehvaslaiho Eheikki-at-bioperl-dot-orgE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::RefSeq; use strict; use vars qw($MODVERSION %HOSTS %FORMATMAP $DEFAULTFORMAT); $MODVERSION = '0.1'; use base qw(Bio::DB::DBFetch); BEGIN { # you can add your own here theoretically. %HOSTS = ( 'dbfetch' => { baseurl => 'http://%s/Tools/dbfetch/dbfetch?db=refseq&style=raw', hosts => { 'ebi' => 'www.ebi.ac.uk' } } ); %FORMATMAP = ( 'embl' => 'embl', 'genbank' => 'genbank', 'fasta' => 'fasta' ); $DEFAULTFORMAT = 'genbank'; } sub new { my ($class, @args ) = @_; my $self = $class->SUPER::new(@args); $self->{ '_hosts' } = {}; $self->{ '_formatmap' } = {}; $self->hosts(\%HOSTS); $self->formatmap(\%FORMATMAP); $self->{'_default_format'} = $DEFAULTFORMAT; return $self; } sub get_seq_stream { my ($self,%qualifiers) = @_; if( exists $qualifiers{'-uids'} ) { if( ref($qualifiers{'-uids'}) =~ /ARRAY/i ) { foreach my $u ( @{$qualifiers{'-uids'}} ) { $u =~ s/^(\S+)\|//; } } else { $qualifiers{'-uids'} =~ s/^(\S+)\|//; } } $self->SUPER::get_seq_stream(%qualifiers); } 1; BioPerl-1.007002/Bio/DB/ReferenceI.pm000444000766000024 747213155576320 17070 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::ReferenceI # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::DB::ReferenceI - A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects =head1 SYNOPSIS # # get a database object somehow using a concrete class # $ref = $db->get_Reference_by_id('123456'); # # $ref is a Bio::Annotation::Reference object # =head1 DESCRIPTION This is a pure interface class - in other words, all this does is define methods which other (concrete) classes will actually implement. The Bio::DB::ReferenceI class defines methods used to retrieve reference data from a sequence. This is returned in the form of Bio::Annotation::Reference objects. At the moment it is just the ability to make Bio::Annotation::Reference objects from a name or unique id (id), an accession number (acc), and so on. =head1 CONTACT Ewan Birney originally wrote Bio::DB::RandomAccessI, from which this class is based. =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@lists.open-bio.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web. https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Email cjfields at bioperl dot org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::ReferenceI; use strict; =head2 get_Reference_by_id Title : get_Reference_by_id Usage : $ref = $db->get_Reference_by_id('123456') Function: Gets a Bio::Annotation::Reference-implementing object by its name (id) Returns : a Bio::Annotation::Reference object or undef if not found Args : the id (as a string) of a sequence =cut sub get_Reference_by_id{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_Reference_by_acc Title : get_Reference_by_acc Usage : $ref = $db->get_Reference_by_acc('X77802'); Function: Gets a Bio::Annotation::Reference object by accession number Returns : A Bio::Annotation::Reference object or undef if not found Args : accession number (as a string) Throws : "more than one sequences correspond to this accession" if the accession maps to multiple primary ids and method is called in a scalar context =cut sub get_Reference_by_acc{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_Reference_by_version Title : get_Reference_by_version Usage : $ref = $db->get_Reference_by_version('X77802.1'); Function: Gets a Bio::Annotation::Reference object by sequence version Returns : A Bio::Annotation::Reference object Args : accession.version (as a string) Throws : "acc.version does not exist" exception =cut sub get_Reference_by_version{ my ($self,@args) = @_; $self->throw_not_implemented(); } ## End of Package 1; BioPerl-1.007002/Bio/DB/Registry.pm000444000766000024 1761713155576320 16713 0ustar00cjfieldsstaff000000000000# # POD documentation - main docs before the code =head1 NAME Bio::DB::Registry - Access to the Open Bio Database Access registry scheme =head1 SYNOPSIS use Bio::DB::Registry(); $registry = Bio::DB::Registry->new(); @available_services = $registry->services; $db = $registry->get_database('embl'); # $db is a Bio::DB::SeqI implementing class $seq = $db->get_Seq_by_acc("J02231"); =head1 DESCRIPTION This module provides access to the Open Bio Database Access (OBDA) scheme, which provides a single cross-language and cross-platform specification of how to get to databases. These databases may be accessible through the Web, they may be BioSQL databases, or they may be local, indexed flatfile databases. If the user or system administrator has not installed the default init file, seqdatabase.ini, in /etc/bioinformatics or ${HOME}/.bioinformatics then creating the first Registry object copies the default settings from the www.open-bio.org. The Registry object will attempt to store these settings in a new file, ${HOME}/.bioinformatics/seqdatabase.ini. Users can specify one or more custom locations for the init file by setting $OBDA_SEARCH_PATH to those directories, where multiple directories should be separated by ';'. Please see the OBDA Access HOWTO for more information (L). =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Registry; use vars qw($OBDA_SPEC_VERSION $OBDA_SEARCH_PATH $HOME $PRIVATE_DIR $PUBLIC_DIR $REGISTRY $FALLBACK_REGISTRY); use strict; use Bio::DB::Failover; use Bio::Root::HTTPget; use base qw(Bio::Root::Root); BEGIN { $OBDA_SPEC_VERSION = 1.0; $HOME = $ENV{HOME} if (defined $ENV{HOME}); if (defined $ENV{OBDA_SEARCH_PATH}) { $OBDA_SEARCH_PATH = $ENV{OBDA_SEARCH_PATH} || ''; } } my %implement = ('flat' => 'Bio::DB::Flat', 'biosql' => 'Bio::DB::BioSQL::OBDA', 'biofetch' => 'Bio::DB::BioFetch' # 'biocorba' => 'Bio::CorbaClient::SeqDB', ); $FALLBACK_REGISTRY = 'http://www.open-bio.org/registry/seqdatabase.ini'; $PRIVATE_DIR = '.bioinformatics'; $PUBLIC_DIR = '/etc/bioinformatics'; $REGISTRY = 'seqdatabase.ini'; sub new { my ($class,@args) = shift; my $self = $class->SUPER::new(@args); # open files in order $self->{'_dbs'} = {}; $self->_load_registry(); return $self; } =head2 _load_registry Title : _load_registry Usage : Function: Looks for seqdatabase.ini files in the expected locations and in the directories specified by $OBDA_SEARCH_PATH. If no files are found download a default file from www.open-bio.org Returns : nothing Args : none =cut sub _load_registry { my $self = shift; eval { $HOME = (getpwuid($>))[7]; } unless $HOME; if ($@) { # Windows can have Win32::LoginName to get the Username, so check if it works before giving up ( defined &Win32::LoginName ) ? ( $HOME = Win32::LoginName() ) : $self->warn("This Perl doesn't implement function getpwuid(), no \$HOME"); } my @ini_files = $self->_get_ini_files(); @ini_files = $self->_make_private_registry() unless (@ini_files); my ($db,$hash) = (); for my $file (@ini_files) { open my $FH, '<', $file or $self->throw("Could not read file '$file': $!"); while( <$FH> ) { if (/^VERSION=([\d\.]+)/) { if ($1 > $OBDA_SPEC_VERSION or !$1) { $self->throw("Do not know about this version [$1] > $OBDA_SPEC_VERSION"); last; } next; } next if( /^#/ ); next if( /^\s/ ); if ( /^\[(\S+)\]/ ) { $db = $1; next; } my ($tag,$value) = split('=',$_); $value =~ s/\s//g; $tag =~ s/\s//g; $hash->{$db}->{"\L$tag"} = $value; } } for my $db ( keys %{$hash} ) { if ( !exists $self->{'_dbs'}->{$db} ) { my $failover = Bio::DB::Failover->new(); $self->{'_dbs'}->{$db} = $failover; } my $class; if (defined $implement{$hash->{$db}->{'protocol'}}) { $class = $implement{$hash->{$db}->{'protocol'}}; } else { $self->warn("Registry does not support protocol " . $hash->{$db}->{'protocol'}); next; } eval "require $class"; if ($@) { $self->warn("Couldn't load $class"); next; } else { eval { my $randi = $class->new_from_registry( %{$hash->{$db}} ); $self->{'_dbs'}->{$db}->add_database($randi); }; if ($@) { $self->warn("Couldn't call new_from_registry() on [$class]\n$@"); } } } } =head2 get_database Title : get_database Usage : my $db = $registry->get_database($dbname); Function: Retrieve a Database object which implements Bio::DB::SeqI interface Returns : Bio::DB::SeqI object Args : string describing the name of the database =cut sub get_database { my ($self,$dbname) = @_; $dbname = lc $dbname; if( !defined $dbname ) { $self->warn("must get_database with a database name"); return; } if( !exists $self->{'_dbs'}->{$dbname} ) { $self->warn("No database with name $dbname in Registry"); return; } return $self->{'_dbs'}->{$dbname}; } =head2 services Title : services Usage : my @available = $registry->services(); Function: returns list of possible services Returns : list of strings Args : none =cut sub services { my ($self) = @_; return () unless ( defined $self->{'_dbs'} && ref( $self->{'_dbs'} ) =~ /HASH/i); return keys %{$self->{'_dbs'}}; } =head2 _get_ini_files Title : _get_ini_files Usage : my @files = $self->_get_ini_files Function: To find all the seqdatabase.ini files Returns : list of seqdatabase.ini paths Args : None =cut sub _get_ini_files { my $self = shift; my @ini_files = (); if ( $OBDA_SEARCH_PATH ) { foreach my $dir ( split /;/, $OBDA_SEARCH_PATH ) { my $file = $dir . "/" . $REGISTRY; next unless -e $file; push @ini_files,$file; } } push @ini_files,"$HOME/$PRIVATE_DIR/$REGISTRY" if ( $HOME && -e "$HOME/$PRIVATE_DIR/$REGISTRY" ); push @ini_files, "$PUBLIC_DIR/$REGISTRY" if ( -e "$PUBLIC_DIR/$REGISTRY" ); @ini_files; } =head2 _make_private_registry Title : _make_private_registry Usage : Function: Make private registry in file in $HOME Returns : Path to private registry file Args : None =cut sub _make_private_registry { my $self = shift; my @ini_file; my $nor_in = $OBDA_SEARCH_PATH ? "nor in directory specified by\n$OBDA_SEARCH_PATH" : "and environment variable OBDA_SEARCH_PATH wasn't set"; $self->warn("No $REGISTRY file found in $HOME/$PRIVATE_DIR/\n" . "nor in $PUBLIC_DIR $nor_in.\n" . "Using web to get registry from\n$FALLBACK_REGISTRY"); # Last gasp. Try to use HTTPget module to retrieve the registry from # the web... my $f = Bio::Root::HTTPget::getFH($FALLBACK_REGISTRY); # store the default registry file eval { mkdir "$HOME/$PRIVATE_DIR" unless -e "$HOME/$PRIVATE_DIR"; }; $self->throw("Could not make directory $HOME/$PRIVATE_DIR, " . "no $REGISTRY file available") if $@; open my $F, '>', "$HOME/$PRIVATE_DIR/$REGISTRY" or $self->throw("Could not write file '$HOME/$PRIVATE_DIR/$REGISTRY': $!"); print $F while (<$F>); close $F; $self->warn("Stored $REGISTRY file in $HOME/$PRIVATE_DIR"); push @ini_file,"$HOME/$PRIVATE_DIR/$REGISTRY"; @ini_file; } 1; __END__ BioPerl-1.007002/Bio/DB/SeqFeature.pm000444000766000024 3045313155576320 17140 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature; =head1 NAME Bio::DB::SeqFeature -- Normalized feature for use with Bio::DB::SeqFeature::Store =head1 SYNOPSIS use Bio::DB::SeqFeature::Store; # Open the sequence database my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:test'); my ($feature) = $db->get_features_by_name('ZK909'); my @subfeatures = $feature->get_SeqFeatures(); my @exons_only = $feature->get_SeqFeatures('exon'); # create a new object my $new = $db->new_feature(-primary_tag=>'gene', -seq_id => 'chr3', -start => 10000, -end => 11000); # add a new exon $feature->add_SeqFeature($db->new_feature(-primary_tag=>'exon', -seq_id => 'chr3', -start => 5000, -end => 5551)); =head1 DESCRIPTION The Bio::DB::SeqFeature object is the default SeqFeature class stored in Bio::DB::SeqFeature databases. It implements both the Bio::DB::SeqFeature::NormalizedFeatureI and Bio::DB::SeqFeature::NormalizedTableFeatureI interfaces, which means that its subfeatures, if any, are stored in the database in a normalized fashion, and that the parent/child hierarchy of features and subfeatures are also stored in the database as set of tuples. This provides efficiencies in both storage and retrieval speed. Typically you will not create Bio::DB::SeqFeature directly, but will ask the database to do so on your behalf, as described in L. =cut # just like Bio::DB::SeqFeature::NormalizedFeature except that the parent/child # relationships are stored in a table in the Bio::DB::SeqFeature::Store use strict; use Carp 'croak'; use Bio::DB::SeqFeature::Store; use base qw(Bio::DB::SeqFeature::NormalizedFeature Bio::DB::SeqFeature::NormalizedTableFeatureI); =head2 new Title : new Usage : $feature = Bio::DB::SeqFeature::NormalizedFeature->new(@args) Function: create a new feature Returns : the new seqfeature Args : see below Status : public This method creates and, if possible stores into a database, a new Bio::DB::SeqFeature::NormalizedFeature object using the specialized Bio::DB::SeqFeature class. The arguments are the same to Bio::SeqFeature::Generic-Enew() and Bio::Graphics::Feature-Enew(). The most important difference is the B<-store> option, which if present creates the object in a Bio::DB::SeqFeature::Store database, and the B<-index> option, which controls whether the feature will be indexed for retrieval (default is true). Ordinarily, you would only want to turn indexing on when creating top level features, and off only when storing subfeatures. The default is on. Arguments are as follows: -seq_id the reference sequence -start the start position of the feature -end the stop position of the feature -display_name the feature name (returned by seqname) -primary_tag the feature type (returned by primary_tag) -source the source tag -score the feature score (for GFF compatibility) -desc a description of the feature -segments a list of subfeatures (see Bio::Graphics::Feature) -subtype the type to use when creating subfeatures -strand the strand of the feature (one of -1, 0 or +1) -phase the phase of the feature (0..2) -url a URL to link to when rendered with Bio::Graphics -attributes a hashref of tag value attributes, in which the key is the tag and the value is an array reference of values -store a previously-opened Bio::DB::SeqFeature::Store object -index index this feature if true Aliases: -id an alias for -display_name -seqname an alias for -display_name -display_id an alias for -display_name -name an alias for -display_name -stop an alias for end -type an alias for primary_tag =cut sub add_segment { my $self = shift; $self->_add_segment(0,@_); } =head2 Bio::SeqFeatureI methods The following Bio::SeqFeatureI methods are supported: seq_id(), start(), end(), strand(), get_SeqFeatures(), display_name(), primary_tag(), source_tag(), seq(), location(), primary_id(), overlaps(), contains(), equals(), intersection(), union(), has_tag(), remove_tag(), add_tag_value(), get_tag_values(), get_all_tags() Some methods that do not make sense in the context of a genome annotation database system, such as attach_seq(), are not supported. Please see L for more details. =cut =head2 add_SeqFeature Title : add_SeqFeature Usage : $flag = $feature->add_SeqFeature(@features) Function: Add subfeatures to the feature Returns : true if successful Args : list of Bio::SeqFeatureI objects Status : public Add one or more subfeatures to the feature. For best results, subfeatures should be of the same class as the parent feature (i.e. do not try mixing Bio::DB::SeqFeature::NormalizedFeature with other feature types). An alias for this method is add_segment(). =cut =head2 update Title : update Usage : $flag = $feature->update() Function: Update feature in the database Returns : true if successful Args : none Status : public After changing any fields in the feature, call update() to write it to the database. This is not needed for add_SeqFeature() as update() is invoked automatically. =cut =head2 get_SeqFeatures Title : get_SeqFeature Usage : @subfeatures = $feature->get_SeqFeatures([@types]) Function: return subfeatures of this feature Returns : list of subfeatures Args : list of subfeature primary_tags (optional) Status : public This method extends the Bio::SeqFeatureI get_SeqFeatures() slightly by allowing you to pass a list of primary_tags, in which case only subfeatures whose primary_tag is contained on the list will be returned. Without any types passed all subfeatures are returned. =cut =head2 object_store Title : object_store Usage : $store = $feature->object_store([$new_store]) Function: get or set the database handle Returns : current database handle Args : new database handle (optional) Status : public This method will get or set the Bio::DB::SeqFeature::Store object that is associated with the feature. After changing the store, you should probably unset the primary_id() of the feature and call update() to ensure that the object is written into the database as a new feature. =cut =head2 overloaded_names Title : overloaded_names Usage : $overload = $feature->overloaded_names([$new_overload]) Function: get or set overloading of object strings Returns : current flag Args : new flag (optional) Status : public For convenience, when objects of this class are stringified, they are represented in the form "primary_tag(display_name)". To turn this feature off, call overloaded_names() with a false value. You can invoke this on an individual feature object or on the class: Bio::DB::SeqFeature::NormalizedFeature->overloaded_names(0); =cut =head2 segment Title : segment Usage : $segment = $feature->segment Function: return a Segment object corresponding to feature Returns : a Bio::DB::SeqFeature::Segment Args : none Status : public This turns the feature into a Bio::DB::SeqFeature::Segment object, which you can then use to query for overlapping features. See L. =cut =head2 AUTOLOADED methods @subfeatures = $feature->Exon; If you use an unknown method that begins with a capital letter, then the feature autogenerates a call to get_SeqFeatures() using the lower-cased method name as the primary_tag. In other words $feature-EExon is equivalent to: @subfeature s= $feature->get_SeqFeatures('exon') =cut =head2 load_id Title : load_id Usage : $id = $feature->load_id Function: get the GFF3 load ID Returns : the GFF3 load ID (string) Args : none Status : public For features that were originally loaded by the GFF3 loader, this method returns the GFF3 load ID. This method may not be supported in future versions of the module. =cut =head2 primary_id Title : primary_id Usage : $id = $feature->primary_id([$new_id]) Function: get/set the database ID of the feature Returns : the current primary ID Args : none Status : public This method gets or sets the primary ID of the feature in the underlying Bio::DB::SeqFeature::Store database. If you change this field and then call update(), it will have the effect of making a copy of the feature in the database under a new ID. =cut =head2 target Title : target Usage : $segment = $feature->target Function: return the segment correspondent to the "Target" attribute Returns : a Bio::DB::SeqFeature::Segment object Args : none Status : public For features that are aligned with others via the GFF3 Target attribute, this returns a segment corresponding to the aligned region. The CIGAR gap string is not yet supported. =cut =head2 Internal methods =over 4 =item $feature-Eas_string() Internal method used to implement overloaded stringification. =item $boolean = $feature-Etype_match(@list_of_types) Internal method that will return true if the primary_tag of the feature and source_tag match any of the list of types (in primary_tag:source_tag format) provided. =back =cut # This adds subfeatures. It has the property of converting the # provided features into an object like itself and storing them # into the database. If the feature already has a primary id and # an object_store() method, then it is not stored into the database, # but its primary id is reused. sub _add_segment { my $self = shift; my $normalized = shift; my $store = $self->object_store; my $store_parentage = eval{$store->can_store_parentage}; return $self->SUPER::_add_segment($normalized,@_) unless $normalized && $store_parentage; my @segments = $self->_create_subfeatures($normalized,@_); my $pos = "@{$self}{'start','stop','ref','strand'}"; # fix boundaries $self->_fix_boundaries(\@segments,1); # freakish fixing of our non-standard Target attribute $self->_fix_target(\@segments); # write our children out if ($normalized) { $store->add_SeqFeature($self,@segments); } else { push @{$self->{segments}},@segments; } # write us back to disk $self->update if $self->primary_id && $pos ne "@{$self}{'start','stop','ref','strand'}"; } # segments can be stored directly in the object (legacy behavior) # or stored in the database # an optional list of types can be used to specify which types to return sub get_SeqFeatures { my $self = shift; my @types = @_; my @inline_segs = exists $self->{segments} ? @{$self->{segments}} : (); @inline_segs = grep {$_->type_match(@types)} @inline_segs if @types; my $store = $self->object_store; my @db_segs; if ($store && $store->can_store_parentage) { if (!@types || $store->subfeature_types_are_indexed) { @db_segs = $store->fetch_SeqFeatures($self,@types); } else { @db_segs = grep {$_->type_match(@types)} $store->fetch_SeqFeatures($self); } } my @segs = (@inline_segs,@db_segs); foreach (@segs) { eval {$_->object_store($store)}; } return @segs; } sub denormalized_segments { my $self = shift; return exists $self->{segments} ? @{$self->{segments}} : (); } sub denormalized_segment_count { my $self = shift; return 0 unless exists $self->{segments}; return scalar @{$self->{segments}}; } # for Bio::LocationI compatibility sub is_remote { return } # for Bio::LocationI compatibility sub location_type { return 'EXACT' } # for Bio::DB::GFF compatibility sub feature_id {shift->primary_id} 1; __END__ =head1 BUGS This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs. =head1 SEE ALSO L, L, L, L, L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2006 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/SeqI.pm000444000766000024 1115513155576320 15733 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::SeqI.pm # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # =head1 NAME Bio::DB::SeqI - Abstract Interface for Sequence databases =head1 SYNOPSIS # get a Bio::DB::SeqI somehow $seq = $seqdb->get_Seq_by_id('some-id'); $seq = $seqdb->get_Seq_by_acc('some-accession-number'); @ids = $seqdb->get_all_ids(); $stream = $seqdb->get_PrimarySeq_stream(); while((my $seq = $stream->next_seq()) { # $seq is a PrimarySeqI compliant object } =head1 DESCRIPTION Abstract interface for a sequence database =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::DB::SeqI; use strict; use base qw(Bio::DB::RandomAccessI); =head1 Methods inherited from Bio::DB::RandomAccessI =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception =head2 get_Seq_by_version Title : get_Seq_by_version Usage : $seq = $db->get_Seq_by_version('X77802.1'); Function: Gets a Bio::Seq object by sequence version Returns : A Bio::Seq object Args : accession.version (as a string) Throws : "acc.version does not exist" exception =head1 Methods [that were] specific for Bio::DB::SeqI =head2 get_PrimarySeq_stream Title : get_PrimarySeq_stream Usage : $stream = get_PrimarySeq_stream Function: Makes a Bio::SeqIO compliant object which provides a single method, next_seq Returns : Bio::SeqIO Args : none =cut sub get_PrimarySeq_stream{ my ($self,@args) = @_; $self->throw("Object did not provide a PrimarySeq stream object"); } =head2 get_all_primary_ids Title : get_all_ids Usage : @ids = $seqdb->get_all_primary_ids() Function: gives an array of all the primary_ids of the sequence objects in the database. These may be ids (display style) or accession numbers or something else completely different - they *are not* meaningful outside of this database implementation. Example : Returns : an array of strings Args : none =cut sub get_all_primary_ids{ my ($self,@args) = @_; $self->throw("Object did not provide a get_all_ids method"); } =head2 get_Seq_by_primary_id Title : get_Seq_by_primary_id Usage : $seq = $db->get_Seq_by_primary_id($primary_id_string); Function: Gets a Bio::Seq object by the primary id. The primary id in these cases has to come from $db->get_all_primary_ids. There is no other way to get (or guess) the primary_ids in a database. The other possibility is to get Bio::PrimarySeqI objects via the get_PrimarySeq_stream and the primary_id field on these objects are specified as the ids to use here. Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception =cut sub get_Seq_by_primary_id { my ($self,@args) = @_; $self->throw("Abstract database call of get_Seq_by_primary_id. Your database". " has not implemented this method!"); } 1; BioPerl-1.007002/Bio/DB/SeqVersion.pm000444000766000024 1004613155576320 17166 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::SeqVersion # # Please direct questions and support issues to # # Cared for by Brian Osborne # # Copyright Brian Osborne 2006 # # You may distribute this module under the same terms as Perl itself # # POD documentation - main docs before the code =head1 NAME Bio::DB::SeqVersion - front end to querying databases for identifier versions =head1 SYNOPSIS use Bio::DB::SeqVersion; my $query = Bio::DB::SeqVersion->new(-type => 'gi'); my @all_gis = $query->get_all(2); my $live_gi = $query->get_recent(2); =head1 DESCRIPTION The default type is 'gi'. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Brian Osborne Email bosborne at alum.mit.edu =head1 CONTRIBUTORS Torsten Seemann - torsten.seemann AT infotech.monash.edu.au =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::SeqVersion; use strict; use base qw(Bio::WebAgent Bio::Root::Root); # Private class variable my $DEFAULTIDTYPE = 'gi'; # sub default_id_type() =head2 new() Usage : my $obj = Bio::DB::SeqVersion->new(); Function: Create a Bio::DB::SeqVersion object Returns : An instance of Bio::DB::SeqVersion Args : -type Identifier namespace, default is 'gi' =cut sub new { my($class,@args) = @_; if( $class =~ /Bio::DB::SeqVersion::\S+/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys # we delete '-type' so it doesn't get passed to the sub-class constructor # note: delete() returns the value of the item deleted (undef if non-existent) my $type = lc( delete($param{'-type'}) || $DEFAULTIDTYPE ); return unless( $class->_load_seqversion_module($type) ); # we pass %param here, not @args, as we have filtered out -type return "Bio::DB::SeqVersion::$type"->new(%param); } } =head2 get_recent() Usage : Function: Example : Returns : Args : =cut sub get_recent { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_all() Usage : Function: Example : Returns : Args : =cut sub get_all { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 _load_seqversion_module Title : _load_seqversion_module Usage : Used internally Function: Loads up a module at run time on demand Example : Returns : Args : Name of identifier type =cut sub _load_seqversion_module { my ($self,$db) = @_; my $module = "Bio::DB::SeqVersion::" . $db; my $ok; eval { $ok = $self->_load_module($module) }; if ( $@ ) { print STDERR $@; print STDERR <default_id_type Function: Returns default identifier type for this module Returns : string Args : none =cut sub default_id_type { return $DEFAULTIDTYPE; } 1; BioPerl-1.007002/Bio/DB/SwissProt.pm000444000766000024 3675013155576320 17057 0ustar00cjfieldsstaff000000000000# # # BioPerl module for Bio::DB::SwissProt # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code # Reworked to use Bio::DB::WebDBSeqI 2000-12-11 =head1 NAME Bio::DB::SwissProt - Database object interface to SwissProt retrieval =head1 SYNOPSIS use Bio::DB::SwissProt; $sp = Bio::DB::SwissProt->new(); $seq = $sp->get_Seq_by_id('KPY1_ECOLI'); # SwissProt ID # <4-letter-identifier>_ # or ... $seq = $sp->get_Seq_by_acc('P43780'); # SwissProt AC # [OPQ]xxxxx # In fact in this implementation # these methods call the same webscript so you can use # then interchangeably # choose a different server to query $sp = Bio::DB::SwissProt->new('-servertype' => 'expasy', '-hostlocation' => 'us'); $seq = $sp->get_Seq_by_id('BOLA_HAEIN'); # SwissProtID =head1 DESCRIPTION SwissProt is a curated database of proteins managed by the Swiss Bioinformatics Institute. Additional tools for parsing and manipulating swissprot files can be found at ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/. Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the SwissProt database via an Expasy retrieval. In order to make changes transparent we have host type (currently only expasy) and location (default to Switzerland) separated out. This allows the user to pick the closest Expasy mirror for running their queries. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email Jason Stajich Ejason@bioperl.org E Thanks go to Alexandre Gattiker Egattiker@isb-sib.chE of Swiss Institute of Bioinformatics for helping point us in the direction of the correct expasy scripts and for swissknife references. Also thanks to Heikki Lehvaslaiho Eheikki-at-bioperl-dot-orgE for help with adding EBI swall server. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::SwissProt; use strict; use HTTP::Request::Common; our $MODVERSION = '0.8.1'; use base qw(Bio::DB::WebDBSeqI); # global vars our $DEFAULTSERVERTYPE = 'ebi'; our $DEFAULTFORMAT = 'swissprot'; # our $DEFAULTIDTRACKER = 'http://www.expasy.ch'; # you can add your own here theoretically. our %HOSTS = ( 'expasy' => { 'default' => 'us', 'baseurl' => 'http://%s/cgi-bin/sprot-retrieve-list.pl', 'hosts' => { 'switzerland' => 'ch.expasy.org', 'canada' => 'ca.expasy.org', 'china' => 'cn.expasy.org', 'taiwan' => 'tw.expasy.org', 'australia' => 'au.expasy.org', 'korea' => 'kr.expasy.org', 'us' => 'us.expasy.org', }, # ick, CGI variables 'jointype' => ' ', 'idvar' => 'list', 'basevars' => [ ], }, 'ebi' => { 'default' => 'uk', 'baseurl' => 'http://%s/Tools/dbfetch/dbfetch', 'hosts' => { 'uk' => 'www.ebi.ac.uk', }, 'jointype' => ',', 'idvar' => 'id', 'basevars' => [ 'db' => 'UniProtKB', 'style' => 'raw' ], } ); our %ID_MAPPING_DATABASES = map {$_ => 1} qw( ACC+ID ACC ID UPARC NF50 NF90 NF100 EMBL_ID EMBL PIR UNIGENE_ID P_ENTREZGENEID P_GI P_IPI P_REFSEQ_AC PDB_ID DISPROT_ID HSSP_ID DIP_ID MEROPS_ID PEROXIBASE_ID PPTASEDB_ID REBASE_ID TCDB_ID 2DBASE_ECOLI_ID AARHUS_GHENT_2DPAGE_ID ANU_2DPAGE_ID DOSAC_COBS_2DPAGE_ID ECO2DBASE_ID WORLD_2DPAGE_ID ENSEMBL_ID ENSEMBL_PRO_ID ENSEMBL_TRS_ID P_ENTREZGENEID GENOMEREVIEWS_ID KEGG_ID TIGR_ID UCSC_ID VECTORBASE_ID AGD_ID ARACHNOSERVER_ID BURULIST_ID CGD CYGD_ID DICTYBASE_ID ECHOBASE_ID ECOGENE_ID EUHCVDB_ID FLYBASE_ID GENECARDS_ID GENEDB_SPOMBE_ID GENEFARM_ID H_INVDB_ID HGNC_ID HPA_ID LEGIOLIST_ID LEPROMA_ID LISTILIST_ID MAIZEGDB_ID MIM_ID MGI_ID MYPULIST_ID NMPDR ORPHANET_ID PHARMGKB_ID PHOTOLIST_ID PSEUDOCAP_ID RGD_ID SAGALIST_ID SGD_ID SUBTILIST_ID TAIR_ID TUBERCULIST_ID WORMBASE_ID WORMPEP_ID XENBASE_ID ZFIN_ID EGGNOG_ID OMA_ID ORTHODB_ID BIOCYC_ID REACTOME_ID CLEANEX_ID GERMONLINE_ID DRUGBANK_ID NEXTBIO_ID); # new modules should be a little more lightweight and # should use Bio::Root::Root sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($format, $hostlocation,$servertype) = $self->_rearrange([qw(FORMAT HOSTLOCATION SERVERTYPE)], @args); if( $format && $format !~ /(swiss)|(fasta)/i ) { $self->warn("Requested Format $format is ignored because only SwissProt and Fasta formats are currently supported"); $format = $self->default_format; } $servertype = $DEFAULTSERVERTYPE unless $servertype; $servertype = lc $servertype; $self->servertype($servertype); if ( $hostlocation ) { $self->hostlocation(lc $hostlocation); } $self->request_format($format); # let's always override the format, as it must be swiss or fasta return $self; } =head2 Routines from Bio::DB::RandomAccessI =cut =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception =cut =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception =cut =head2 get_Stream_by_id Title : get_Stream_by_id Usage : $stream = $db->get_Stream_by_id( [$uid1, $uid2] ); Function: Gets a series of Seq objects by unique identifiers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of unique identifiers for the desired sequence entries =cut =head2 get_Stream_by_acc Title : get_Stream_by_acc Usage : $seq = $db->get_Seq_by_acc([$acc1, $acc2]); Function: Gets a series of Seq objects by accession numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id() =cut =head2 get_Stream_by_batch Title : get_Stream_by_batch Usage : $seq = $db->get_Stream_by_batch($ref); Function: Retrieves Seq objects from SwissProt 'en masse', rather than one at a time. This is implemented the same way as get_Stream_by_id, but is provided here in keeping with access methods of NCBI modules. Example : Returns : a Bio::SeqIO stream object Args : $ref : either an array reference, a filename, or a filehandle from which to get the list of unique ids/accession numbers. NOTE: deprecated API. Use get_Stream_by_id() instead. =cut *get_Stream_by_batch = sub { my $self = shift; $self->deprecated('get_Stream_by_batch() is deprecated; use get_Stream_by_id() instead'); $self->get_Stream_by_id(@_) }; =head2 Implemented Routines from Bio::DB::WebDBSeqI interface =cut =head2 get_request Title : get_request Usage : my $url = $self->get_request Function: returns a HTTP::Request object Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) =cut sub get_request { my ($self, @qualifiers) = @_; my ($uids, $format) = $self->_rearrange([qw(UIDS FORMAT)], @qualifiers); if( !defined $uids ) { $self->throw("Must specify a value for uids to query"); } my ($f,undef) = $self->request_format($format); my %vars = ( @{$HOSTS{$self->servertype}->{'basevars'}}, ( 'format' => $f ) ); my $url = $self->location_url; my $uid; my $jointype = $HOSTS{$self->servertype}->{'jointype'} || ' '; my $idvar = $HOSTS{$self->servertype}->{'idvar'} || 'id'; if( ref($uids) =~ /ARRAY/i ) { # HTTP::Request automagically converts the ' ' to %20 $uid = join($jointype, @$uids); } else { $uid = $uids; } $vars{$idvar} = $uid; return POST $url, \%vars; } =head2 postprocess_data Title : postprocess_data Usage : $self->postprocess_data ( 'type' => 'string', 'location' => \$datastr); Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - 'location' either file location or string reference containing data =cut # don't need to do anything sub postprocess_data { my ($self, %args) = @_; return; } =head2 default_format Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none =cut sub default_format { return $DEFAULTFORMAT; } =head2 Bio::DB::SwissProt specific routines =cut =head2 servertype Title : servertype Usage : my $servertype = $self->servertype $self->servertype($servertype); Function: Get/Set server type Returns : string Args : server type string [optional] =cut sub servertype { my ($self, $servertype) = @_; if( defined $servertype && $servertype ne '') { $self->throw("You gave an invalid server type ($servertype)". " - available types are ". keys %HOSTS) unless( $HOSTS{$servertype} ); $self->{'_servertype'} = $servertype; $self->{'_hostlocation'} = $HOSTS{$servertype}->{'default'}; # make sure format is reset properly in that different # servers have different syntaxes my ($existingformat,$seqioformat) = $self->request_format; $self->request_format($existingformat); } return $self->{'_servertype'} || $DEFAULTSERVERTYPE; } =head2 hostlocation Title : hostlocation Usage : my $location = $self->hostlocation() $self->hostlocation($location) Function: Set/Get Hostlocation Returns : string representing hostlocation Args : string specifying hostlocation [optional] =cut sub hostlocation { my ($self, $location ) = @_; my $servertype = $self->servertype; $self->throw("Must have a valid servertype defined not $servertype") unless defined $servertype; my %hosts = %{$HOSTS{$servertype}->{'hosts'}}; if( defined $location && $location ne '' ) { $location = lc $location; if( ! $hosts{$location} ) { $self->throw("Must specify a known host, not $location,". " possible values (". join(",", sort keys %hosts ). ")"); } $self->{'_hostlocation'} = $location; } return $self->{'_hostlocation'}; } =head2 location_url Title : location Usage : my $url = $self->location_url() Function: Get host url Returns : string representing url Args : none =cut sub location_url { my ($self) = @_; my $servertype = $self->servertype(); my $location = $self->hostlocation(); if( ! defined $location || !defined $servertype ) { $self->throw("must have a valid hostlocation and servertype set before calling location_url"); } return sprintf($HOSTS{$servertype}->{'baseurl'}, $HOSTS{$servertype}->{'hosts'}->{$location}); } =head2 request_format Title : request_format Usage : my ($req_format, $ioformat) = $self->request_format; $self->request_format("genbank"); $self->request_format("fasta"); Function: Get/Set sequence format retrieval. The get-form will normally not be used outside of this and derived modules. Returns : Array of two strings, the first representing the format for retrieval, and the second specifying the corresponding SeqIO format. Args : $format = sequence format =cut sub request_format { my ($self, $value) = @_; if( defined $value ) { if( $self->servertype =~ /expasy/ ) { if( $value =~ /sprot/ || $value =~ /swiss/ ) { $self->{'_format'} = [ 'sprot', 'swiss']; } elsif( $value =~ /^fa/ ) { $self->{'_format'} = [ 'fasta', 'fasta']; } else { $self->warn("Unrecognized format $value requested"); $self->{'_format'} = [ 'fasta', 'fasta']; } } elsif( $self->servertype =~ /ebi/ ) { if( $value =~ /sprot/ || $value =~ /swiss/ ) { $self->{'_format'} = [ 'swissprot', 'swiss' ]; } elsif( $value =~ /^fa/ ) { $self->{'_format'} = [ 'fasta', 'fasta']; } else { $self->warn("Unrecognized format $value requested"); $self->{'_format'} = [ 'swissprot', 'swiss']; } } } return @{$self->{'_format'}}; } =head2 idtracker Title : idtracker Usage : my ($newid) = $self->idtracker($oldid); Function: Retrieve new ID using old ID. Returns : single ID if one is found Args : ID to look for =cut sub idtracker { my ($self, $id) = @_; $self->deprecated( -message => 'The SwissProt IDTracker service is no longer available, '. 'use id_mapper() instead', -warn_version => 1.006, # warn if $VERSION is >= this version -throw_version => 1.007 # throw if $VERSION is >= this version ); } =head2 id_mapper Title : id_tracker Usage : my $map = $self->id_mapper( -from => '', -to => '', -ids => \@ids); Function: Retrieve new ID using old ID. Returns : hash reference of successfully mapped IDs Args : -from : database mapping from -to : database mapped to -ids : a single ID or array ref of IDs to map Note : For a list of valid database IDs, see: http://www.uniprot.org/faq/28#id_mapping_examples =cut sub id_mapper { my $self = shift; my ($from, $to, $ids) = $self->_rearrange([qw(FROM TO IDS)], @_); for ($from, $to) { $self->throw("$_ is not a recognized database") if !exists $ID_MAPPING_DATABASES{$_}; } my @ids = ref $ids ? @$ids : $ids; my $params = { from => $from, to => $to, format => 'tab', query => join(' ',@ids) }; my $ua = $self->ua; push @{ $ua->requests_redirectable }, 'POST'; my $response = $ua->post("http://www.uniprot.org/mapping/", $params); while (my $wait = $response->header('Retry-After')) { $self->debug("Waiting...\n"); $self->_sleep; $response = $ua->get($response->base); } my %map; if ($response->is_success) { for my $line (split("\n", $response->content)) { my ($id_from, $id_to) = split(/\s+/, $line, 2); next if $id_from eq 'From'; push @{$map{$id_from}}, $id_to; } } else { $self->throw("Error: ".$response->status_line."\n"); } \%map; } 1; __END__ BioPerl-1.007002/Bio/DB/TFBS.pm000444000766000024 1027113155576320 15626 0ustar00cjfieldsstaff000000000000# $Id: TFBS.pm,v 1.11 2006/08/12 11:00:03 sendu Exp $ # # BioPerl module for Bio::DB::TFBS # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::TFBS - Access to a Transcription Factor Binding Site database =head1 SYNOPSIS use Bio::DB::TFBS; my $db = Bio::DB::TFBS->new(-source => 'transfac'); my ($factor_id) = $db->get_factor_ids('PPAR-gamma1'); my ($matrix_id) = $db->get_matrix_ids('PPAR-gamma1'); # get a Bio::Map::TranscriptionFactor with all the positions of a given factor my $factor = $db->get_factor(-factor_id => $factor_id); # get a Bio::Map::GeneMap containing all the factors that bind near a given gene my $gene_map = $db->get_gene_map(-gene_name => 'AQP 7'); # get a PSM (Bio::Matrix::PSM) of a given matrix my $psm = $db->get_matrix(-matrix_id => $matrix_id); # get the aligned sequences (Bio::SimpleAlign) that were used to build a given # matrix my $align = $db->get_alignment(-matrix_id => $matrix_id); # get a specific instance sequence (Bio::LocatableSeq) my $seq = $db->get_seq($id); =head1 DESCRIPTION This is a front end module for access to a Transcription Factor Binding Site database. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 CONTRIBUTORS Based on Bio::DB::Taxonomy by Jason Stajich =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::TFBS; use strict; use Bio::Root::Root; use base qw(Bio::Root::Root); our $DefaultSource = 'transfac'; =head2 new Title : new Usage : my $obj = Bio::DB::TFBS->new(-source => 'transfac'); Function: Builds a new Bio::DB::TFBS object. Returns : an instance of Bio::DB::TFBS Args : -source => which database source: currently only 'transfac_pro' =cut sub new { my ($class, @args) = @_; if ($class =~ /Bio::DB::TFBS::(\S+)/) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $source = $param{'-source'} || $DefaultSource; $source = "\L$source"; # normalize capitalization to lower case # normalize capitalization return unless( $class->_load_tax_module($source) ); return "Bio::DB::TFBS::$source"->new(@args); } } # empty for now sub _initialize { } =head2 _load_tax_module Title : _load_tax_module Usage : *INTERNAL Bio::DB::TFBS stuff* Function: Loads up (like use) a module at run time on demand =cut sub _load_tax_module { my ($self, $source) = @_; my $module = "Bio::DB::TFBS::" . $source; my $ok; eval { $ok = $self->_load_module($module) }; if ( $@ ) { print STDERR $@; print STDERR < # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Taxonomy - Access to a taxonomy database =head1 SYNOPSIS use Bio::DB::Taxonomy; my $db = Bio::DB::Taxonomy->new(-source => 'entrez'); # use NCBI Entrez over HTTP my $taxonid = $db->get_taxonid('Homo sapiens'); # get a taxon my $taxon = $db->get_taxon(-taxonid => $taxonid); =head1 DESCRIPTION This is a front end module for access to a taxonomy database. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Sendu Bala: bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Taxonomy; use vars qw($DefaultSource $TAXON_IIDS); use strict; use Bio::Tree::Tree; use base qw(Bio::Root::Root); $DefaultSource = 'entrez'; $TAXON_IIDS = {}; =head2 new Title : new Usage : my $obj = Bio::DB::Taxonomy->new(-source => 'entrez'); Function: Builds a new Bio::DB::Taxonomy object. Returns : an instance of Bio::DB::Taxonomy Args : -source => which database source 'entrez' (NCBI taxonomy online), 'flatfile' (local NCBI taxonomy), 'greengenes' (local GreenGenes taxonomy), 'silva' (local Silva taxonomy), or 'list' (Do-It-Yourself taxonomy) =cut sub new { my($class,@args) = @_; if( $class =~ /Bio::DB::Taxonomy::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $source = $param{'-source'} || $DefaultSource; $source = "\L$source"; # normalize capitalization to lower case # normalize capitalization return unless( $class->_load_tax_module($source) ); return "Bio::DB::Taxonomy::$source"->new(@args); } } # empty for now sub _initialize { } =head2 get_num_taxa Title : get_num_taxa Usage : my $num = $db->get_num_taxa(); Function: Get the number of taxa stored in the database. Returns : A number Args : None =cut sub get_num_taxa { shift->throw_not_implemented(); } =head2 get_taxon Title : get_taxon Usage : my $taxon = $db->get_taxon(-taxonid => $taxonid); Function: Get a Bio::Taxon object from the database. Returns : Bio::Taxon object Args : just a single value which is the database id, OR named args: -taxonid => taxonomy id (to query by taxonid) OR -name => string (to query by a taxonomy name: common name, scientific name, etc) =cut sub get_taxon { shift->throw_not_implemented(); } *get_Taxonomy_Node = \&get_taxon; =head2 get_taxonids Title : get_taxonids Usage : my @taxonids = $db->get_taxonids('Homo sapiens'); Function: Searches for a taxonid (typically ncbi_taxon_id) based on a query string. Note that multiple taxonids can match to the same supplied name. Returns : array of integer ids in list context, one of these in scalar context Args : string representing the taxon's name =cut sub get_taxonids { shift->throw_not_implemented(); } *get_taxonid = \&get_taxonids; *get_taxaid = \&get_taxonids; =head2 get_tree Title : get_tree Usage : my $tree = $db->get_tree(@species_names); Function: Generate a tree comprised of the full lineages of all the supplied species names. The nodes for the requested species are given name('supplied') values corresponding to the supplied name, such that they can be identified if the real species name in the database (stored under node_name()) is different. The nodes are also given an arbitrary branch length of 1. Returns : Bio::Tree::Tree Args : A list of species names (strings) to include in the tree. =cut sub get_tree { my ($self, @species_names) = @_; # the full lineages of the species are merged into a single tree my $tree; for my $name (@species_names) { my @ids = $self->get_taxonids($name); if (not scalar @ids) { $self->throw("Could not find species $name in the taxonomy"); } for my $id (@ids) { my $node = $self->get_taxon(-taxonid => $id); $node->name('supplied', $name); if ($tree) { $tree->merge_lineage($node); } else { $tree = Bio::Tree::Tree->new(-verbose => $self->verbose, -node => $node); } } } # add arbitrary branch length for my $node ($tree->get_nodes) { $node->branch_length(1); } return $tree; } =head2 ancestor Title : ancestor Usage : my $ancestor_taxon = $db->ancestor($taxon); Function: Retrieve the full ancestor taxon of a supplied Taxon from the database. Returns : Bio::Taxon Args : Bio::Taxon (that was retrieved from this database) =cut sub ancestor { shift->throw_not_implemented(); } =head2 each_Descendent Title : each_Descendent Usage : my @taxa = $db->each_Descendent($taxon); Function: Get all the descendents of the supplied Taxon (but not their descendents, ie. not a recursive fetchall). Returns : Array of Bio::Taxon objects Args : Bio::Taxon (that was retrieved from this database) =cut sub each_Descendent { shift->throw_not_implemented(); } =head2 get_all_Descendents Title : get_all_Descendents Usage : my @taxa = $db->get_all_Descendents($taxon); Function: Like each_Descendent(), but do a recursive fetchall Returns : Array of Bio::Taxon objects Args : Bio::Taxon (that was retrieved from this database) =cut sub get_all_Descendents { my ($self, $taxon) = @_; my @taxa; foreach my $desc_taxon ($self->each_Descendent($taxon)) { push @taxa, ($desc_taxon, $self->get_all_Descendents($desc_taxon)); } return @taxa; } =head2 _load_tax_module Title : _load_tax_module Usage : *INTERNAL Bio::DB::Taxonomy stuff* Function: Loads up (like use) a module at run time on demand =cut sub _load_tax_module { my ($self, $source) = @_; my $module = "Bio::DB::Taxonomy::" . $source; my $ok; eval { $ok = $self->_load_module($module) }; if ( $@ ) { print STDERR $@; print STDERR <throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon'); my $taxid = $taxon->id || return; my $name = $taxon->scientific_name || ''; my $rank = $taxon->rank || 'no rank'; my $dbh = $try_name ? $taxon->db_handle : 'any'; my $iid = $TAXON_IIDS->{taxids}->{$dbh}->{$taxid}; if ( (not defined $iid) && $try_name && $name && exists $TAXON_IIDS->{names}->{$name}) { # Search for a suitable IID based on species name and ranks my %test_ranks = map {$_ => undef} ($rank, 'no rank'); SEARCH: while (my ($test_rank, undef) = each %test_ranks) { # Search at the specified rank first, then with 'no rank' while ( my ($test_iid, $test_info) = each %{$TAXON_IIDS->{names}->{$name}->{$rank}} ) { while (my ($test_db, $test_taxid) = each %$test_info) { if ( ($test_db eq $dbh) && not($test_taxid eq $taxid) ) { # Taxa are different (same database, different taxid) next; } # IID is acceptable since taxa are from different databases, # or from the same database but have the same taxid $iid = $test_iid; $TAXON_IIDS->{taxids}->{$dbh}->{$taxid} = $iid; last SEARCH; } } } } if (defined $iid) { # Assign Bio::DB::Taxonomy IID with risky Bio::Tree::Node internal method $taxon->_creation_id($iid); } else { # Register new IID in Bio::DB::Taxonomy $iid = $taxon->internal_id; $TAXON_IIDS->{taxids}->{$dbh}->{$taxid} = $iid; if ($name) { $TAXON_IIDS->{names}->{$name}->{$rank}->{$iid}->{$taxon->db_handle} = $taxid } } return $iid; } 1; BioPerl-1.007002/Bio/DB/Universal.pm000444000766000024 1272113155576320 17042 0ustar00cjfieldsstaff000000000000 # # BioPerl module for Bio::DB::Universal # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Universal - Artificial database that delegates to specific databases =head1 SYNOPSIS $uni = Bio::DB::Universal->new(); # by default connects to web databases. We can also # substitute local databases $embl = Bio::Index::EMBL->new( -filename => '/some/index/filename/locally/stored'); $uni->use_database('embl',$embl); # treat it like a normal database. Recognises strings # like gb|XXXXXX and embl:YYYYYY $seq1 = $uni->get_Seq_by_id("embl:HSHNRNPA"); $seq2 = $uni->get_Seq_by_acc("gb|A000012"); # with no separator, tries to guess database. In this case the # _ is considered to be indicative of swissprot $seq3 = $uni->get_Seq_by_id('ROA1_HUMAN'); =head1 DESCRIPTION Artificial database that delegates to specific databases, with a "smart" (well, smartish) guessing routine for what the ids. No doubt the smart routine can be made smarter. The hope is that you can make this database and just throw ids at it - for most easy cases it will sort you out. Personally, I would be making sure I knew where each id came from and putting it into its own database first - but this is a quick and dirty solution. By default this connects to web orientated databases, with all the reliability and network bandwidth costs this implies. However you can subsistute your own local databases - they could be Bio::Index databases (DBM file and flat file) or bioperl-db based (MySQL based) or biocorba-based (whatever you like behind the corba interface). Internally the tags for the databases are genbank - ncbi dna database embl - ebi's dna database (these two share accession number space) swiss - swissprot + sptrembl (EBI's protein database) We should extend this for RefSeq and other sequence databases which are out there... ;) Inspired by Lincoln Stein, written by Ewan Birney. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bio.perl.org =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Universal; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::DB::GenBank; use Bio::DB::SwissProt; use Bio::DB::EMBL; use base qw(Bio::DB::RandomAccessI Bio::Root::Root); # new() can be inherited from Bio::Root::Root sub new { my ($class) = @_; my $self = {}; bless $self,$class; $self->{'db_hash'} = {}; # default databases $self->use_database('embl',Bio::DB::EMBL->new); $self->use_database('genbank',Bio::DB::GenBank->new); $self->use_database('swiss',Bio::DB::GenBank->new); return $self; } =head2 get_Seq_by_id Title : get_Seq_by_id Usage : Function: Example : Returns : Args : =cut sub get_Seq_by_id{ my ($self,$str) = @_; my ($tag,$id) = $self->guess_id($str); return $self->{'db_hash'}->{$tag}->get_Seq_by_id($id); } =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : Function: Example : Returns : Args : =cut sub get_Seq_by_acc { my ($self,$str) = @_; my ($tag,$id) = $self->guess_id($str); return $self->{'db_hash'}->{$tag}->get_Seq_by_acc($id); } =head2 guess_id Title : guess_id Usage : Function: Example : Returns : Args : =cut sub guess_id{ my ($self,$str) = @_; if( $str =~ /(\S+)[:|\/;](\w+)/ ) { my $tag; my $db = $1; my $id = $2; if( $db =~ /gb/i || $db =~ /genbank/i || $db =~ /ncbi/i ) { $tag = 'genbank'; } elsif ( $db =~ /embl/i || $db =~ /emblbank/ || $db =~ /^em/i ) { $tag = 'embl'; } elsif ( $db =~ /swiss/i || $db =~ /^sw/i || $db =~ /sptr/ ) { $tag = 'swiss'; } else { # throw for the moment $self->throw("Could not guess database type $db from $str"); } return ($tag,$id); } else { my $tag; # auto-guess from just the id if( $str =~ /_/ ) { $tag = 'swiss'; } elsif ( $str =~ /^[QPR]\w+\d$/ ) { $tag = 'swiss'; } elsif ( $str =~ /[A-Z]\d+/ ) { $tag = 'genbank'; } else { # default genbank... $tag = 'genbank'; } return ($tag,$str); } } =head2 use_database Title : use_database Usage : Function: Example : Returns : Args : =cut sub use_database{ my ($self,$name,$database) = @_; $self->{'db_hash'}->{$name} = $database; } 1; BioPerl-1.007002/Bio/DB/UpdateableSeqI.pm000444000766000024 1327313155576320 17725 0ustar00cjfieldsstaff000000000000# # # BioPerl module for Bio::DB::UpdateableSeqI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # # _history # June 18, 2000 - module begun # # POD Doc - main docs before code =head1 NAME Bio::DB::UpdateableSeqI - An interface for writing to a database of sequences. =head1 SYNOPSIS # get a Bio::DB::UpdateableSeqI somehow eval { my ( @updatedseqs, @newseqs, @deadseqs); my $seq = $db->get_Seq_by_id('ROA1_HUMAN'); $seq->desc('a new description'); push @updatedseqs, $seq; $db->write_seq(\@updatedseqs, \@newseqs, \@deadseqs); }; if( $@ ) { print STDERR "an error when trying to write seq : $@\n"; } =head1 DESCRIPTION This module seeks to provide a simple method for pushing sequence changes back to a Sequence Database - which can be an SQL compliant database, a file based database, AceDB, etc. =head1 AUTHOR Jason Stajich Ejason@bioperl.orgE =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #Lets start some code package Bio::DB::UpdateableSeqI; use strict; use base qw(Bio::DB::SeqI); =head2 write_seq Title : write_seq Usage : write_seq(\@updatedseqs, \@addedseqs, \@deadseqs) Function: updates sequences in first array, adds sequences in the second array, and removes sequences in the third array. Example : Returns : Args : arrays of sequence objects that must be obtained from Bio::DB::UpdateableSeqI. =cut sub write_seq { my ($self) = @_; $self->throw("Abstract database call of write_seq. Your database has not implemented this method!"); } =head2 _add_seq Title : _add_seq Usage : _add_seq($seq) Function: Adds a new sequence Example : Returns : will throw an exception if sequences accession number already exists Args : a new seq object - should have an accession number =cut sub _add_seq { my ($self ) = @_; $self->throw("Abstract database call of _add_seq. Your database has not implemented this method!"); } =head2 _remove_seq Title : _remove_seq Usage : _remove_seq($seq) Function: Removes an existing sequence Example : Returns : will throw an exception if sequence does not exists for the primary_id Args : a seq object that was retrieved from Bio::DB::UpdateableSeqI =cut sub _remove_seq { my ($self) = @_; $self->throw("Abstract database call of _remove_seq. Your database has not implemented this method!"); } =head2 _update_seq Title : _update_seq Usage : _update_seq($seq) Function: Updates a sequence Example : Returns : will throw an exception if sequence is out of sync from expected val. Args : a seq object that was retrieved from Bio::DB::UpdateableSeqI =cut sub _update_seq { my ($self) = @_; $self->throw("Abstract database call of _update_seq. Your database has not implemented this method!"); } =head1 Methods inherieted from Bio::DB::RandomAccessI =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception =cut =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception =cut =head1 Methods inheirited from Bio::DB::SeqI =head2 get_PrimarySeq_stream Title : get_PrimarySeq_stream Usage : $stream = get_PrimarySeq_stream Function: Makes a Bio::DB::SeqStreamI compliant object which provides a single method, next_primary_seq Returns : Bio::DB::SeqStreamI Args : none =cut =head2 get_all_primary_ids Title : get_all_ids Usage : @ids = $seqdb->get_all_primary_ids() Function: gives an array of all the primary_ids of the sequence objects in the database. These maybe ids (display style) or accession numbers or something else completely different - they *are not* meaningful outside of this database implementation. Example : Returns : an array of strings Args : none =cut =head2 get_Seq_by_primary_id Title : get_Seq_by_primary_id Usage : $seq = $db->get_Seq_by_primary_id($primary_id_string); Function: Gets a Bio::Seq object by the primary id. The primary id in these cases has to come from $db->get_all_primary_ids. There is no other way to get (or guess) the primary_ids in a database. The other possibility is to get Bio::PrimarySeqI objects via the get_PrimarySeq_stream and the primary_id field on these objects are specified as the ids to use here. Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception =cut 1; BioPerl-1.007002/Bio/DB/WebDBSeqI.pm000444000766000024 6172413155576320 16606 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::WebDBSeqI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code # =head1 NAME Bio::DB::WebDBSeqI - Object Interface to generalize Web Databases for retrieving sequences =head1 SYNOPSIS # get a WebDBSeqI object somehow # assuming it is a nucleotide db my $seq = $db->get_Seq_by_id('ROA1_HUMAN') =head1 DESCRIPTION Provides core set of functionality for connecting to a web based database for retrieving sequences. Users wishing to add another Web Based Sequence Dabatase will need to extend this class (see L or L for examples) and implement the get_request method which returns a HTTP::Request for the specified uids (accessions, ids, etc depending on what query types the database accepts). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web. https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email E jason@bioperl.org E =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::WebDBSeqI; use strict; use vars qw($MODVERSION %RETRIEVAL_TYPES $DEFAULT_RETRIEVAL_TYPE $DEFAULTFORMAT $LAST_INVOCATION_TIME @ATTRIBUTES); use Bio::SeqIO; use Bio::Root::IO; use LWP::UserAgent; use POSIX 'setsid'; use HTTP::Request::Common; use HTTP::Response; use File::Spec; use IO::Pipe; use IO::String; use Bio::Root::Root; use base qw(Bio::DB::RandomAccessI); BEGIN { $MODVERSION = '0.8'; %RETRIEVAL_TYPES = ('io_string' => 1, 'tempfile' => 1, 'pipeline' => 1, ); $DEFAULT_RETRIEVAL_TYPE = 'pipeline'; $DEFAULTFORMAT = 'fasta'; $LAST_INVOCATION_TIME = 0; } sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($baseaddress, $params, $ret_type, $format,$delay,$db) = $self->_rearrange([qw(BASEADDRESS PARAMS RETRIEVALTYPE FORMAT DELAY DB)], @args); $ret_type = $DEFAULT_RETRIEVAL_TYPE unless ( $ret_type); $baseaddress && $self->url_base_address($baseaddress); $params && $self->url_params($params); $db && $self->db($db); $ret_type && $self->retrieval_type($ret_type); $delay = $self->delay_policy unless defined $delay; $self->delay($delay); # insure we always have a default format set for retrieval # even though this will be immedietly overwritten by most sub classes $format = $self->default_format unless ( defined $format && $format ne '' ); $self->request_format($format); my $ua = LWP::UserAgent->new(env_proxy => 1); $ua->agent(ref($self) ."/$MODVERSION"); $self->ua($ua); $self->{'_authentication'} = []; return $self; } # from Bio::DB::RandomAccessI =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception =cut sub get_Seq_by_id { my ($self,$seqid) = @_; $self->_sleep; my $seqio = $self->get_Stream_by_id([$seqid]); $self->throw("id does not exist") if( !defined $seqio ) ; if ($self->can('complexity') && defined $self->complexity && $self->complexity==0) { $self->warn("When complexity is set to 0, use get_Stream_by_id\n". "Returning Bio::SeqIO object"); return $seqio; } my @seqs; while( my $seq = $seqio->next_seq() ) { push @seqs, $seq; } # Since $seqio will not be used anymore, explicitly close its filehandle # or it will cause trouble later on cleanup $seqio->close; $self->throw("id '$seqid' does not exist") unless @seqs; if( wantarray ) { return @seqs } else { return shift @seqs } } =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception =cut sub get_Seq_by_acc { my ($self,$seqid) = @_; $self->_sleep; my $seqio = $self->get_Stream_by_acc($seqid); $self->throw("acc '$seqid' does not exist") if( ! defined $seqio ); if ($self->can('complexity') && defined $self->complexity && $self->complexity==0) { $self->warn("When complexity is set to 0, use get_Stream_by_acc\n". "Returning Bio::SeqIO object"); return $seqio; } my @seqs; while( my $seq = $seqio->next_seq() ) { push @seqs, $seq; } $self->throw("acc $seqid does not exist") unless @seqs; if( wantarray ) { return @seqs } else { return shift @seqs } } =head2 get_Seq_by_gi Title : get_Seq_by_gi Usage : $seq = $db->get_Seq_by_gi('405830'); Function: Gets a Bio::Seq object by gi number Returns : A Bio::Seq object Args : gi number (as a string) Throws : "gi does not exist" exception =cut sub get_Seq_by_gi { my ($self,$seqid) = @_; $self->_sleep; my $seqio = $self->get_Stream_by_gi($seqid); $self->throw("gi does not exist") if( !defined $seqio ); if ($self->can('complexity') && defined $self->complexity && $self->complexity==0) { $self->warn("When complexity is set to 0, use get_Stream_by_gi\n". "Returning Bio::SeqIO object"); return $seqio; } my @seqs; while( my $seq = $seqio->next_seq() ) { push @seqs, $seq; } $self->throw("gi does not exist") unless @seqs; if( wantarray ) { return @seqs } else { return shift @seqs } } =head2 get_Seq_by_version Title : get_Seq_by_version Usage : $seq = $db->get_Seq_by_version('X77802.1'); Function: Gets a Bio::Seq object by sequence version Returns : A Bio::Seq object Args : accession.version (as a string) Throws : "acc.version does not exist" exception =cut sub get_Seq_by_version { my ($self,$seqid) = @_; $self->_sleep; my $seqio = $self->get_Stream_by_version($seqid); $self->throw("accession.version does not exist") if( !defined $seqio ); if ($self->can('complexity') && defined $self->complexity && $self->complexity==0) { $self->warn("When complexity is set to 0, use get_Stream_by_version\n". "Returning Bio::SeqIO object"); return $seqio; } my @seqs; while( my $seq = $seqio->next_seq() ) { push @seqs, $seq; } $self->throw("accession.version does not exist") unless @seqs; if( wantarray ) { return @seqs } else { return shift @seqs } } # implementing class must define these =head2 get_request Title : get_request Usage : my $url = $self->get_request Function: returns a HTTP::Request object Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) =cut sub get_request { my ($self) = @_; my $msg = "Implementing class must define method get_request in class WebDBSeqI"; $self->throw($msg); } # class methods =head2 get_Stream_by_id Title : get_Stream_by_id Usage : $stream = $db->get_Stream_by_id( [$uid1, $uid2] ); Function: Gets a series of Seq objects by unique identifiers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of unique identifiers for the desired sequence entries =cut sub get_Stream_by_id { my ($self, $ids) = @_; my ($webfmt,$localfmt) = $self->request_format; return $self->get_seq_stream('-uids' => $ids, '-mode' => 'single', '-format' => $webfmt); } *get_Stream_by_batch = sub { my $self = shift; $self->deprecated('get_Stream_by_batch() is deprecated; use get_Stream_by_id() instead'); $self->get_Stream_by_id(@_) }; =head2 get_Stream_by_acc Title : get_Stream_by_acc Usage : $seq = $db->get_Stream_by_acc([$acc1, $acc2]); Function: Gets a series of Seq objects by accession numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id() =cut sub get_Stream_by_acc { my ($self, $ids ) = @_; return $self->get_seq_stream('-uids' => $ids, '-mode' => 'single'); } =head2 get_Stream_by_gi Title : get_Stream_by_gi Usage : $seq = $db->get_Stream_by_gi([$gi1, $gi2]); Function: Gets a series of Seq objects by gi numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of gi numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id() =cut sub get_Stream_by_gi { my ($self, $ids ) = @_; return $self->get_seq_stream('-uids' => $ids, '-mode' => 'gi'); } =head2 get_Stream_by_version Title : get_Stream_by_version Usage : $seq = $db->get_Stream_by_version([$version1, $version2]); Function: Gets a series of Seq objects by accession.versions Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession.version strings for the desired sequence entries Note : For GenBank, this is implemented in NCBIHelper =cut sub get_Stream_by_version { my ($self, $ids ) = @_; # $self->throw("Implementing class should define this method!"); return $self->get_seq_stream('-uids' => $ids, '-mode' => 'version'); # how it should work } =head2 get_Stream_by_query Title : get_Stream_by_query Usage : $stream = $db->get_Stream_by_query($query); Function: Gets a series of Seq objects by way of a query string or oject Returns : a Bio::SeqIO stream object Args : $query : A string that uses the appropriate query language for the database or a Bio::DB::QueryI object. It is suggested that you create the Bio::DB::Query object first and interrogate it for the entry count before you fetch a potentially large stream. =cut sub get_Stream_by_query { my ($self, $query ) = @_; return $self->get_seq_stream('-query' => $query, '-mode'=>'query'); } =head2 default_format Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none =cut sub default_format { return $DEFAULTFORMAT; } # sorry, but this is hacked in because of BioFetch problems... sub db { my $self = shift; my $d = $self->{_db}; $self->{_db} = shift if @_; $d; } =head2 request_format Title : request_format Usage : my ($req_format, $ioformat) = $self->request_format; $self->request_format("genbank"); $self->request_format("fasta"); Function: Get/Set sequence format retrieval. The get-form will normally not be used outside of this and derived modules. Returns : Array of two strings, the first representing the format for retrieval, and the second specifying the corresponding SeqIO format. Args : $format = sequence format =cut sub request_format { my ($self, $value) = @_; if( defined $value ) { $self->{'_format'} = [ $value, $value]; } return @{$self->{'_format'}}; } =head2 get_seq_stream Title : get_seq_stream Usage : my $seqio = $self->get_seq_stream(%qualifiers) Function: builds a url and queries a web db Returns : a Bio::SeqIO stream capable of producing sequence Args : %qualifiers = a hash qualifiers that the implementing class will process to make a url suitable for web querying =cut sub get_seq_stream { my ($self, %qualifiers) = @_; my ($rformat, $ioformat) = $self->request_format(); my $seen = 0; foreach my $key ( keys %qualifiers ) { if( $key =~ /format/i ) { $rformat = $qualifiers{$key}; $seen = 1; } } $qualifiers{'-format'} = $rformat if( !$seen); ($rformat, $ioformat) = $self->request_format($rformat); # These parameters are implemented for Bio::DB::GenBank objects only if($self->isa('Bio::DB::GenBank')) { $self->seq_start() && ($qualifiers{'-seq_start'} = $self->seq_start()); $self->seq_stop() && ($qualifiers{'-seq_stop'} = $self->seq_stop()); $self->strand() && ($qualifiers{'-strand'} = $self->strand()); defined $self->complexity() && ($qualifiers{'-complexity'} = $self->complexity()); } my $request = $self->get_request(%qualifiers); $request->proxy_authorization_basic($self->authentication) if ( $self->authentication); $self->debug("request is ". $request->as_string(). "\n"); # workaround for MSWin systems $self->retrieval_type('io_string') if $self->retrieval_type =~ /pipeline/ && $^O =~ /^MSWin/; if ($self->retrieval_type =~ /pipeline/) { # Try to create a stream using POSIX fork-and-pipe facility. # this is a *big* win when fetching thousands of sequences from # a web database because we can return the first entry while # transmission is still in progress. # Also, no need to keep sequence in memory or in a temporary file. # If this fails (Windows, MacOS 9), we fall back to non-pipelined access. # fork and pipe: _stream_request()=> my ($result,$stream) = $self->_open_pipe(); if (defined $result) { $DB::fork_TTY = File::Spec->devnull; # prevents complaints from debugger if (!$result) { # in child process $self->_stream_request($request,$stream); POSIX::_exit(0); #prevent END blocks from executing in this forked child } else { return Bio::SeqIO->new('-verbose' => $self->verbose, '-format' => $ioformat, '-fh' => $stream); } } else { $self->retrieval_type('io_string'); } } if ($self->retrieval_type =~ /temp/i) { my $dir = $self->io->tempdir( CLEANUP => 1); my ( $fh, $tmpfile) = $self->io()->tempfile( DIR => $dir ); close $fh; my $resp = $self->_request($request, $tmpfile); if( ! -e $tmpfile || -z $tmpfile || ! $resp->is_success() ) { $self->throw("WebDBSeqI Error - check query sequences!\n"); } $self->postprocess_data('type' => 'file', 'location' => $tmpfile); # this may get reset when requesting batch mode ($rformat,$ioformat) = $self->request_format(); if( $self->verbose > 0 ) { open my $ERR, '<', $tmpfile or $self->throw("Could not read file '$tmpfile': $!"); while(<$ERR>) { $self->debug($_);} close $ERR; } return Bio::SeqIO->new('-verbose' => $self->verbose, '-format' => $ioformat, '-file' => $tmpfile); } if ($self->retrieval_type =~ /io_string/i ) { my $resp = $self->_request($request); my $content = $resp->content_ref; $self->debug( "content is $$content\n"); if (!$resp->is_success() || length($$content) == 0) { $self->throw("WebDBSeqI Error - check query sequences!\n"); } ($rformat,$ioformat) = $self->request_format(); $self->postprocess_data('type'=> 'string', 'location' => $content); $self->debug( "str is $$content\n"); return Bio::SeqIO->new('-verbose' => $self->verbose, '-format' => $ioformat, '-fh' => new IO::String($$content)); } # if we got here, we don't know how to handle the retrieval type $self->throw("retrieval type " . $self->retrieval_type . " unsupported\n"); } =head2 url_base_address Title : url_base_address Usage : my $address = $self->url_base_address or $self->url_base_address($address) Function: Get/Set the base URL for the Web Database Returns : Base URL for the Web Database Args : $address - URL for the WebDatabase =cut sub url_base_address { my $self = shift; my $d = $self->{'_baseaddress'}; $self->{'_baseaddress'} = shift if @_; $d; } =head2 proxy Title : proxy Usage : $httpproxy = $db->proxy('http') or $db->proxy(['http','ftp'], 'http://myproxy' ) Function: Get/Set a proxy for use of proxy Returns : a string indicating the proxy Args : $protocol : an array ref of the protocol(s) to set/get $proxyurl : url of the proxy to use for the specified protocol $username : username (if proxy requires authentication) $password : password (if proxy requires authentication) =cut sub proxy { my ($self,$protocol,$proxy,$username,$password) = @_; return if ( !defined $self->ua || !defined $protocol || !defined $proxy ); $self->authentication($username, $password) if ($username && $password); return $self->ua->proxy($protocol,$proxy); } =head2 authentication Title : authentication Usage : $db->authentication($user,$pass) Function: Get/Set authentication credentials Returns : Array of user/pass Args : Array or user/pass =cut sub authentication{ my ($self,$u,$p) = @_; if( defined $u && defined $p ) { $self->{'_authentication'} = [ $u,$p]; } return @{$self->{'_authentication'}}; } =head2 retrieval_type Title : retrieval_type Usage : $self->retrieval_type($type); my $type = $self->retrieval_type Function: Get/Set a proxy for retrieval_type (pipeline, io_string or tempfile) Returns : string representing retrieval type Args : $value - the value to store This setting affects how the data stream from the remote web server is processed and passed to the Bio::SeqIO layer. Three types of retrieval types are currently allowed: pipeline Perform a fork in an attempt to begin streaming while the data is still downloading from the remote server. Disk, memory and speed efficient, but will not work on Windows or MacOS 9 platforms. io_string Store downloaded database entry(s) in memory. Can be problematic for batch downloads because entire set of entries must fit in memory. Alll entries must be downloaded before processing can begin. tempfile Store downloaded database entry(s) in a temporary file. All entries must be downloaded before processing can begin. The default is pipeline, with automatic fallback to io_string if pipelining is not available. =cut sub retrieval_type { my ($self, $value) = @_; if( defined $value ) { $value = lc $value; if( ! $RETRIEVAL_TYPES{$value} ) { $self->warn("invalid retrieval type $value must be one of (" . join(",", keys %RETRIEVAL_TYPES), ")"); $value = $DEFAULT_RETRIEVAL_TYPE; } $self->{'_retrieval_type'} = $value; } return $self->{'_retrieval_type'}; } =head2 url_params Title : url_params Usage : my $params = $self->url_params or $self->url_params($params) Function: Get/Set the URL parameters for the Web Database Returns : url parameters for Web Database Args : $params - parameters to be appended to the URL for the WebDatabase =cut sub url_params { my ($self, $value) = @_; if( defined $value ) { $self->{'_urlparams'} = $value; } } =head2 ua Title : ua Usage : my $ua = $self->ua or $self->ua($ua) Function: Get/Set a LWP::UserAgent for use Returns : reference to LWP::UserAgent Object Args : $ua - must be a LWP::UserAgent =cut sub ua { my ($self, $ua) = @_; if( defined $ua && $ua->isa("LWP::UserAgent") ) { $self->{'_ua'} = $ua; } return $self->{'_ua'}; } =head2 postprocess_data Title : postprocess_data Usage : $self->postprocess_data ( 'type' => 'string', 'location' => \$datastr); Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - 'location' either file location or string reference containing data =cut sub postprocess_data { my ( $self, %args) = @_; return; } # private methods sub _request { my ($self, $url,$tmpfile) = @_; my ($resp); if( defined $tmpfile && $tmpfile ne '' ) { $resp = $self->ua->request($url, $tmpfile); } else { $resp = $self->ua->request($url); } if( $resp->is_error ) { $self->throw("WebDBSeqI Request Error:\n".$resp->as_string); } return $resp; } #mod_perl-safe replacement for the open(BLEH,'-|') call. if running #under mod_perl, detects it and closes the child's STDIN and STDOUT #handles sub _open_pipe { my ($self) = @_; # is mod_perl running? Which API? my $mp = $self->mod_perl_api; if($mp and ! our $loaded_apache_sp) { my $load_api = ($mp == 1) ? 'use Apache::SubProcess': 'use Apache2::SubProcess'; eval $load_api; $@ and $self->throw("$@\n$load_api module required for running under mod_perl"); $loaded_apache_sp = 1; } my $pipe = IO::Pipe->new(); local $SIG{CHLD} = 'IGNORE'; defined(my $pid = fork) or $self->throw("Couldn't fork: $!"); unless($pid) { #CHILD $pipe->writer(); #if we're running under mod_perl, clean up some things after this fork if ($ENV{MOD_PERL} and my $r = eval{Apache->request} ) { $r->cleanup_for_exec; #don't read or write the mod_perl parent's tied filehandles close STDIN; close STDOUT; setsid() or $self->throw('Could not detach from parent'); } } else { #PARENT $pipe->reader(); } return ( $pid, $pipe ); } # send web request to specified filehandle, or stdout, for streaming purposes sub _stream_request { my $self = shift; my $request = shift; my $dest_fh = shift || \*STDOUT; # fork so as to pipe output of fetch process through to # postprocess_data method call. my ($child,$fetch) = $self->_open_pipe(); if ($child) { #PARENT local ($/) = "//\n"; # assume genbank/swiss format $| = 1; my $records = 0; while (my $record = <$fetch>) { $records++; $self->postprocess_data('type' => 'string', 'location' => \$record); print $dest_fh $record; } $/ = "\n"; # reset to be safe; close $dest_fh; #must explicitly close here, because the hard #exits don't cloes them for us } else { #CHILD $| = 1; my $resp = $self->ua->request($request, sub { print $fetch $_[0] } ); if( $resp->is_error ) { $self->throw("WebDBSeqI Request Error:\n".$resp->as_string); } close $fetch; #must explicitly close here, because the hard exists #don't close them for us POSIX::_exit(0); } } sub io { my ($self,$io) = @_; if(defined($io) || (! exists($self->{'_io'}))) { $io = Bio::Root::IO->new() unless $io; $self->{'_io'} = $io; } return $self->{'_io'}; } =head2 delay Title : delay Usage : $secs = $self->delay([$secs]) Function: get/set number of seconds to delay between fetches Returns : number of seconds to delay Args : new value NOTE: the default is to use the value specified by delay_policy(). This can be overridden by calling this method, or by passing the -delay argument to new(). =cut sub delay { my $self = shift; my $d = $self->{'_delay'}; $self->{'_delay'} = shift if @_; $d; } =head2 delay_policy Title : delay_policy Usage : $secs = $self->delay_policy Function: return number of seconds to delay between calls to remote db Returns : number of seconds to delay Args : none NOTE: The default delay policy is 0s. Override in subclasses to implement delays. The timer has only second resolution, so the delay will actually be +/- 1s. =cut sub delay_policy { my $self = shift; return 0; } =head2 _sleep Title : _sleep Usage : $self->_sleep Function: sleep for a number of seconds indicated by the delay policy Returns : none Args : none NOTE: This method keeps track of the last time it was called and only imposes a sleep if it was called more recently than the delay_policy() allows. =cut sub _sleep { my $self = shift; my $last_invocation = $LAST_INVOCATION_TIME; if (time - $LAST_INVOCATION_TIME < $self->delay) { my $delay = $self->delay - (time - $LAST_INVOCATION_TIME); warn "sleeping for $delay seconds\n" if $self->verbose > 0; sleep $delay; } $LAST_INVOCATION_TIME = time; } =head2 mod_perl_api Title : mod_perl_api Usage : $version = self->mod_perl_api Function: Returns API version of mod_perl being used based on set env. variables Returns : mod_perl API version; if mod_perl isn't loaded, returns 0 Args : none =cut sub mod_perl_api { my $self = shift; my $v = $ENV{MOD_PERL} ? ( exists $ENV{MOD_PERL_API_VERSION} && $ENV{MOD_PERL_API_VERSION} >= 2 ) ? 2 : 1 : 0; return $v; } 1; BioPerl-1.007002/Bio/DB/Expression000755000766000024 013155576320 16513 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/Expression/geo.pm000444000766000024 1744413155576320 20012 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::Expression::geo - *** DESCRIPTION of Class =head1 SYNOPSIS *** Give standard usage here =head1 DESCRIPTION *** Describe the object here =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Allen Day Eallenday@ucla.eduE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a '_'. Methods are in alphabetical order for the most part. =cut # Let the code begin... package Bio::DB::Expression::geo; use strict; use base qw(Bio::DB::Expression); use Bio::Expression::Contact; use Bio::Expression::DataSet; use Bio::Expression::Platform; use Bio::Expression::Sample; use constant URL_PLATFORMS => 'https://www.ncbi.nlm.nih.gov/geo/browse/?view=platforms'; use constant URL_PLATFORM => 'https://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?form=text&view=full&acc='; use constant URL_DATASET => 'https://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?form=text&view=full&acc='; use constant URL_SAMPLE => 'https://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?form=text&view=full&acc='; =head2 _initialize() Usage : $obj->_initialize(%arg); Function: Internal method to initialize a new Bio::DB::Expression::geo object Returns : true on success Args : Arguments passed to new() =cut sub _initialize { my($self,%arg) = @_; foreach my $arg (keys %arg){ my $marg = $arg; $marg =~ s/^-//; $self->$marg($arg{$arg}) if $self->can($marg); } return 1; } =head2 get_platforms() Usage : Function: Example : Returns : a list of Bio::Expression::Platform objects Args : =cut sub get_platforms { my ($self,@args) = @_; my $doc = $self->_get_url( URL_PLATFORMS ); $doc =~ s!^.+?>Release date<.+?(.+)!$1!gs; my @platforms = (); my @records = split m!\s+!, $doc; foreach my $record ( @records ) { my ($platform_acc,$name,$tax_acc,$contact_acc,$contact_name) = $record =~ m!acc\.cgi\?acc=(.+?)".+?(.+?)<.+?.+?<.+?.+?href=".+?id=(.+?)".+?(.+?)new( -accession => $platform_acc, -name => $name, -_taxon_id => $tax_acc, -contact => Bio::Expression::Contact->new( -source => 'geo', -accession => $contact_acc, -name => $contact_name, -db => $self ), -db => $self, ); push @platforms, $platform; } return @platforms; } =head2 get_samples() Usage : Function: Example : Returns : a list of Bio::Expression::Sample objects Args : =cut sub get_samples { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_contacts() Usage : Function: Example : Returns : a list of Bio::Expression::Contact objects Args : =cut sub get_contacts { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_datasets() Usage : $db->get_datasets('accession'); Function: Example : Returns : a list of Bio::Expression::DataSet objects Args : =cut sub get_datasets { my ($self,$platform) = @_; my @lines = split /\n/, $self->_get_url( URL_PLATFORM . $platform->accession ); my @datasets = (); foreach my $line ( @lines ) { my ($dataset_acc) = $line =~ /^\!Platform_series_id = (\S+?)\s*$/; next unless $dataset_acc; my $dataset = Bio::Expression::DataSet->new( -accession => $dataset_acc, -platform => $platform, -db => $self, ); push @datasets, $dataset; } return @datasets; } sub fill_sample { my ( $self, $sample ) = @_; my @lines = split /\n/, $self->_get_url( URL_SAMPLE. $sample->accession ); foreach my $line ( @lines ) { if ( my ($name) = $line =~ /^\!Sample_title = (.+?)\s*$/ ) { $sample->name( $name ); } elsif ( my ($desc) = $line =~ /^\!Sample_characteristics.*? = (.+?)\s*$/ ) { $sample->description( $desc ); } elsif ( my ($source_name) = $line =~ /^\!Sample_source_name.*? = (.+?)\s*$/ ) { $sample->source_name( $source_name ); } elsif ( my ($treatment_desc) = $line =~ /^\!Sample_treatment_protocol.*? = (.+?)\s*$/ ) { $sample->treatment_description( $treatment_desc ); } } return 1; } sub fill_dataset { my ( $self, $dataset ) = @_; my @lines = split /\n/, $self->_get_url( URL_DATASET . $dataset->accession ); my @samples = (); foreach my $line ( @lines ) { if ( my ($sample_acc) = $line =~ /^\!Series_sample_id = (\S+?)\s*$/ ) { my $sample = Bio::Expression::Sample->new( -accession => $sample_acc, -dataset => $dataset, -db => $self, ); push @samples, $sample; } elsif ( my ($pubmed_acc) = $line =~ /^\!Series_pubmed_id = (.+?)\s*$/ ) { $dataset->pubmed_id( $pubmed_acc ); } elsif ( my ($web_link) = $line =~ /^\!Series_web_link = (.+?)\s*$/ ) { $dataset->web_link( $web_link ); } elsif ( my ($contact) = $line =~ /^\!Series_contact_name = (.+?)\s*$/ ) { $dataset->contact( $contact ); } elsif ( my ($name) = $line =~ /^\!Series_title = (.+?)\s*$/ ) { $dataset->name( $name ); } elsif ( my ($desc) = $line =~ /^\!Series_summary = (.+?)\s*$/ ) { $dataset->description( $desc ); } elsif ( my ($design) = $line =~ /^\!Series_type = (.+?)\s*$/ ) { $dataset->design( $design ); } elsif ( my ($design_desc) = $line =~ /^\!Series_overall_design = (.+?)\s*$/ ) { $dataset->design_description( $design_desc ); } } $dataset->samples(\@samples); } ################################################# =head2 _platforms_doc() Usage : Function: Example : Returns : an HTML document containing a table of all platforms Args : =cut sub _get_url { my ($self,$url) = @_; my $response; eval { $response = $self->get( $url ); }; if( $@ ) { $self->warn("Can't query website: $@"); return; } $self->debug( "resp is $response\n"); return $response; } 1; BioPerl-1.007002/Bio/DB/Flat000755000766000024 013155576320 15242 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/Flat/BDB.pm000444000766000024 3225313155576320 16351 0ustar00cjfieldsstaff000000000000# # # BioPerl module for Bio::DB::Flat::BDB # # Please direct questions and support issues to # # Cared for by Lincoln Stein # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Flat::BDB - Interface for BioHackathon standard BDB-indexed flat file =head1 SYNOPSIS #You should not be using this module directly. See L. =head1 DESCRIPTION This object provides the basic mechanism to associate positions in files with primary and secondary name spaces. Unlike Bio::Index::Abstract (see L), this is specialized to work with the BerkeleyDB-indexed "common" flat file format worked out at the 2002 BioHackathon. This object is the guts to the mechanism, which will be used by the specific objects inheriting from it. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Lincoln Stein Email - lstein@cshl.org =head1 SEE ALSO L, =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with an "_" (underscore). =cut # Let the code begin... package Bio::DB::Flat::BDB; use strict; use DB_File; use IO::File; use Fcntl qw(O_CREAT O_RDWR O_RDONLY); use File::Spec; use Bio::SeqIO; use Bio::DB::RandomAccessI; use Bio::Root::Root; use Bio::Root::IO; use base qw(Bio::DB::Flat); sub _initialize { my $self = shift; my ($max_open) = $self->_rearrange(['MAXOPEN'],@_); $self->{bdb_maxopen} = $max_open || 32; } # return a filehandle seeked to the appropriate place # this only works with the primary namespace sub _get_stream { my ($self,$id) = @_; my ($filepath,$offset,$length) = $self->_lookup_primary($id) or $self->throw("Unable to find a record for $id in the flat file index"); my $fh = $self->_fhcache($filepath) or $self->throw("couldn't open $filepath: $!"); seek($fh,$offset,0) or $self->throw("can't seek on $filepath: $!"); $fh; } # return records corresponding to the indicated index # if there are multiple hits will return a list in list context, # otherwise will throw an exception sub fetch_raw { my ($self,$id,$namespace) = @_; # secondary lookup if (defined $namespace && $namespace ne $self->primary_namespace) { my @hits = $self->_lookup_secondary($namespace,$id); $self->throw("Multiple records correspond to $namespace=>$id but function called in a scalar context") unless wantarray; return map {$self->_read_record(@$_)} @hits; } # primary lookup my @args = $self->_lookup_primary($id) or $self->throw("Unable to find a record for $id in the flat file index"); return $self->_read_record(@args); } # create real live Bio::Seq object sub get_Seq_by_id { my $self = shift; my $id = shift; my $fh = eval {$self->_get_stream($id)} or return; my $seqio = $self->{bdb_cached_parsers}{fileno $fh} ||= Bio::SeqIO->new( -Format => $self->file_format, -fh => $fh); return $seqio->next_seq; } # fetch array of Bio::Seq objects sub get_Seq_by_acc { my $self = shift; unshift @_,'ACC' if @_==1; my ($ns,$key) = @_; my @primary_ids = $self->expand_ids($ns => $key); $self->throw("more than one sequences correspond to this accession") if @primary_ids > 1 && ! wantarray; my @rc = map {$self->get_Seq_by_id($_)} @primary_ids; return wantarray ? @rc : $rc[0]; } # fetch array of Bio::Seq objects sub get_Seq_by_version { my $self = shift; unshift @_,'VERSION' if @_==1; my ($ns,$key) = @_; my @primary_ids = $self->expand_ids($ns => $key); $self->throw("more than one sequences correspond to this accession") if @primary_ids > 1 && !wantarray; my @rc = map {$self->get_Seq_by_id($_)} @primary_ids; return wantarray ? @rc : $rc[0]; } =head2 get_PrimarySeq_stream Title : get_PrimarySeq_stream Usage : $stream = get_PrimarySeq_stream Function: Makes a Bio::DB::SeqStreamI compliant object which provides a single method, next_primary_seq Returns : Bio::DB::SeqStreamI Args : none =cut sub get_PrimarySeq_stream { my $self = shift; my @files = $self->files || 0; my $out = Bio::SeqIO::MultiFile->new( -format => $self->file_format , -files => \@files); return $out; } sub get_all_primary_ids { my $self = shift; my $db = $self->primary_db; return keys %$db; } =head2 get_all_primary_ids Title : get_all_primary_ids Usage : @ids = $seqdb->get_all_primary_ids() Function: gives an array of all the primary_ids of the sequence objects in the database. Example : Returns : an array of strings Args : none =cut # this will perform an ID lookup on a (possibly secondary) # id, returning all the corresponding ids sub expand_ids { my $self = shift; my ($ns,$key) = @_; return $key unless defined $ns; return $key if $ns eq $self->primary_namespace; my $db = $self->secondary_db($ns) or $self->throw("invalid secondary namespace $ns"); my $record = $db->{$key} or return; # nothing there return $self->unpack_secondary($record); } # build index from files listed sub build_index { my $self = shift; my @files = @_; my $count = 0; for my $file (@files) { $file = File::Spec->rel2abs($file) unless File::Spec->file_name_is_absolute($file); $count += $self->_index_file($file); } $self->write_config; $count; } sub _index_file { my $self = shift; my $file = shift; my $fileno = $self->_path2fileno($file); defined $fileno or $self->throw("could not create a file number for $file"); my $fh = $self->_fhcache($file) or $self->throw("could not open $file for indexing: $!"); my $offset = 0; my $count = 0; while (!eof($fh)) { my ($ids,$adjustment) = $self->parse_one_record($fh) or next; $adjustment ||= 0; # prevent uninit variable warning my $pos = tell($fh) + $adjustment; $self->_store_index($ids,$file,$offset,$pos-$offset); $offset = $pos; $count++; } $count; } =head2 To Be Implemented in Subclasses The following methods MUST be implemented by subclasses. =cut =head2 May Be Overridden in Subclasses The following methods MAY be overridden by subclasses. =cut sub default_primary_namespace { return "ACC"; } sub default_secondary_namespaces { return; } sub _read_record { my $self = shift; my ($filepath,$offset,$length) = @_; my $fh = $self->_fhcache($filepath) or $self->throw("couldn't open $filepath: $!"); seek($fh,$offset,0) or $self->throw("can't seek on $filepath: $!"); my $record; read($fh,$record,$length) or $self->throw("can't read $filepath: $!"); $record } # return a list in the form ($filepath,$offset,$length) sub _lookup_primary { my $self = shift; my $primary = shift; my $db = $self->primary_db or $self->throw("no primary namespace database is open"); my $record = $db->{$primary} or return; # nothing here my($fileid,$offset,$length) = $self->unpack_primary($record); my $filepath = $self->_fileno2path($fileid) or $self->throw("no file path entry for fileid $fileid"); return ($filepath,$offset,$length); } # return a list of array refs in the form [$filepath,$offset,$length] sub _lookup_secondary { my $self = shift; my ($namespace,$secondary) = @_; my @primary = $self->expand_ids($namespace=>$secondary); return map {[$self->_lookup_primary($_)]} @primary; } # store indexing information into a primary & secondary record # $namespaces is one of: # 1. a scalar corresponding to the primary name # 2. a hashref corresponding to namespace=>id identifiers # it is valid for secondary id to be an arrayref sub _store_index { my $self = shift; my ($keys,$filepath,$offset,$length) = @_; my ($primary,%secondary); if (ref $keys eq 'HASH') { my %valid_secondary = map {$_=>1} $self->secondary_namespaces; while (my($ns,$value) = each %$keys) { if ($ns eq $self->primary_namespace) { $primary = $value; } else { $valid_secondary{$ns} or $self->throw("invalid secondary namespace $ns"); push @{$secondary{$ns}},$value; } } $primary or $self->throw("no primary namespace ID provided"); } else { $primary = $keys; } $self->throw("invalid primary ID; must be a scalar") if ref($primary) =~ /^(ARRAY|HASH)$/; # but allow stringified objects $self->_store_primary($primary,$filepath,$offset,$length); for my $ns (keys %secondary) { my @ids = ref $secondary{$ns} ? @{$secondary{$ns}} : $secondary{$ns}; $self->_store_secondary($ns,$_,$primary) foreach @ids; } 1; } # store primary index sub _store_primary { my $self = shift; my ($id,$filepath,$offset,$length) = @_; my $db = $self->primary_db or $self->throw("no primary namespace database is open"); my $fileno = $self->_path2fileno($filepath); defined $fileno or $self->throw("could not create a file number for $filepath"); my $record = $self->pack_primary($fileno,$offset,$length); $db->{$id} = $record or return; # nothing here 1; } # store a primary index name under a secondary index sub _store_secondary { my $self = shift; my ($secondary_ns,$secondary_id,$primary_id) = @_; my $db = $self->secondary_db($secondary_ns) or $self->throw("invalid secondary namespace $secondary_ns"); # first get whatever secondary ids are already stored there my @primary = $self->unpack_secondary($db->{$secondary_id}); # uniqueify my %unique = map {$_=>undef} @primary,$primary_id; my $record = $self->pack_secondary(keys %unique); $db->{$secondary_id} = $record; } # get output file handle sub _outfh { my $self = shift; #### XXXXX FINISH ##### # my $ } # unpack a primary record into fileid,offset,length sub unpack_primary { my $self = shift; my $index_record = shift; return split "\t",$index_record; } # unpack a secondary record into a list of primary ids sub unpack_secondary { my $self = shift; my $index_record = shift or return; return split "\t",$index_record; } # pack a list of fileid,offset,length into a primary id record sub pack_primary { my $self = shift; my ($fileid,$offset,$length) = @_; return join "\t",($fileid,$offset,$length); } # pack a list of primary ids into a secondary id record sub pack_secondary { my $self = shift; my @secondaries = @_; return join "\t",@secondaries; } sub primary_db { my $self = shift; # lazy opening $self->_open_bdb unless exists $self->{bdb_primary_db}; return $self->{bdb_primary_db}; } sub secondary_db { my $self = shift; my $secondary_namespace = shift or $self->throw("usage: secondary_db(\$secondary_namespace)"); $self->_open_bdb unless exists $self->{bdb_primary_db}; return $self->{bdb_secondary_db}{$secondary_namespace}; } sub _open_bdb { my $self = shift; my $flags = $self->write_flag ? O_CREAT|O_RDWR : O_RDONLY; my $primary_db = {}; tie(%$primary_db,'DB_File',$self->_catfile($self->_primary_db_name),$flags,0666,$DB_BTREE) or $self->throw("Could not open primary index file: $! (did you remember to use -write_flag=>1?)"); $self->{bdb_primary_db} = $primary_db; for my $secondary ($self->secondary_namespaces) { my $secondary_db = {}; tie(%$secondary_db,'DB_File',$self->_catfile($self->_secondary_db_name($secondary)),$flags,0666,$DB_BTREE) or $self->throw("Could not open primary index file"); $self->{bdb_secondary_db}{$secondary} = $secondary_db; } 1; } sub _primary_db_name { my $self = shift; my $pns = $self->primary_namespace or $self->throw('no primary namespace defined'); return "key_$pns"; } sub _secondary_db_name { my $self = shift; my $sns = shift; return "id_$sns"; } sub _fhcache { my $self = shift; my $path = shift; my $write = shift; if (!$self->{bdb_fhcache}{$path}) { $self->{bdb_curopen} ||= 0; if ($self->{bdb_curopen} >= $self->{bdb_maxopen}) { my @lru = sort {$self->{bdb_cacheseq}{$a} <=> $self->{bdb_cacheseq}{$b};} keys %{$self->{bdb_fhcache}}; splice(@lru, $self->{bdb_maxopen} / 3); $self->{bdb_curopen} -= @lru; for (@lru) { delete $self->{bdb_fhcache}{$_} } } if ($write) { my $modifier = $self->{bdb_fhcache_seenit}{$path}++ ? '>' : '>>'; $self->{bdb_fhcache}{$path} = IO::File->new("${modifier}${path}") or return; } else { $self->{bdb_fhcache}{$path} = IO::File->new($path) or return; } $self->{bdb_curopen}++; } $self->{bdb_cacheseq}{$path}++; $self->{bdb_fhcache}{$path} } 1; BioPerl-1.007002/Bio/DB/Flat/BinarySearch.pm000444000766000024 13003313155576320 20347 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::Flat::BinarySearch # # Please direct questions and support issues to # # Cared for by Michele Clamp > # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Flat::BinarySearch - BinarySearch search indexing system for sequence files =head1 SYNOPSIS TODO: SYNOPSIS NEEDED! =head1 DESCRIPTION This module can be used both to index sequence files and also to retrieve sequences from existing sequence files. This object allows indexing of sequence files both by a primary key (say accession) and multiple secondary keys (say ids). This is different from the Bio::Index::Abstract (see L) which uses DBM files as storage. This module uses a binary search to retrieve sequences which is more efficient for large datasets. =head2 Index creation my $sequencefile; # Some fasta sequence file Patterns have to be entered to define where the keys are to be indexed and also where the start of each record. E.g. for fasta my $start_pattern = '^>'; my $primary_pattern = '^>(\S+)'; So the start of a record is a line starting with a E and the primary key is all characters up to the first space after the E A string also has to be entered to defined what the primary key (primary_namespace) is called. The index can now be created using my $index = Bio::DB::Flat::BinarySearch->new( -directory => "/home/max/", -dbname => "mydb", -start_pattern => $start_pattern, -primary_pattern => $primary_pattern, -primary_namespace => "ID", -format => "fasta" ); my @files = ("file1","file2","file3"); $index->build_index(@files); The index is now ready to use. For large sequence files the perl way of indexing takes a *long* time and a *huge* amount of memory. For indexing things like dbEST I recommend using the DB_File indexer, BDB. The formats currently supported by this module are fasta, Swissprot, and EMBL. =head2 Creating indices with secondary keys Sometimes just indexing files with one id per entry is not enough. For instance you may want to retrieve sequences from swissprot using their accessions as well as their ids. To be able to do this when creating your index you need to pass in a hash of secondary_patterns which have their namespaces as the keys to the hash. e.g. For Indexing something like ID 1433_CAEEL STANDARD; PRT; 248 AA. AC P41932; DT 01-NOV-1995 (Rel. 32, Created) DT 01-NOV-1995 (Rel. 32, Last sequence update) DT 15-DEC-1998 (Rel. 37, Last annotation update) DE 14-3-3-LIKE PROTEIN 1. GN FTT-1 OR M117.2. OS Caenorhabditis elegans. OC Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; OC Rhabditidae; Peloderinae; Caenorhabditis. OX NCBI_TaxID=6239; RN [1] where we want to index the accession (P41932) as the primary key and the id (1433_CAEEL) as the secondary id. The index is created as follows my %secondary_patterns; my $start_pattern = '^ID (\S+)'; my $primary_pattern = '^AC (\S+)\;'; $secondary_patterns{"ID"} = '^ID (\S+)'; my $index = Bio::DB::Flat::BinarySearch->new( -directory => $index_directory, -dbname => "ppp", -write_flag => 1, -verbose => 1, -start_pattern => $start_pattern, -primary_pattern => $primary_pattern, -primary_namespace => 'AC', -secondary_patterns => \%secondary_patterns); $index->build_index($seqfile); Of course having secondary indices makes indexing slower and use more memory. =head2 Index reading To fetch sequences using an existing index first of all create your sequence object my $index = Bio::DB::Flat::BinarySearch->new( -directory => $index_directory); Now you can happily fetch sequences either by the primary key or by the secondary keys. my $entry = $index->get_entry_by_id('HBA_HUMAN'); This returns just a string containing the whole entry. This is useful is you just want to print the sequence to screen or write it to a file. Other ways of getting sequences are my $fh = $index->get_stream_by_id('HBA_HUMAN'); This can then be passed to a seqio object for output or converting into objects. my $seq = Bio::SeqIO->new(-fh => $fh, -format => 'fasta'); The last way is to retrieve a sequence directly. This is the slowest way of extracting as the sequence objects need to be made. my $seq = $index->get_Seq_by_id('HBA_HUMAN'); To access the secondary indices the secondary namespace needs to be known $index->secondary_namespaces("ID"); Then the following call can be used my $seq = $index->get_Seq_by_secondary('ID','1433_CAEEL'); These calls are not yet implemented my $fh = $index->get_stream_by_secondary('ID','1433_CAEEL'); my $entry = $index->get_entry_by_secondary('ID','1433_CAEEL'); =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Michele Clamp Email - michele@sanger.ac.uk =head1 CONTRIBUTORS Jason Stajich, jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with an "_" (underscore). =cut package Bio::DB::Flat::BinarySearch; use strict; use Fcntl qw(SEEK_END SEEK_CUR); # rather than using tell which might be buffered sub systell { sysseek( $_[0], 0, SEEK_CUR ) } sub syseof { sysseek( $_[0], 0, SEEK_END ) } use File::Spec; use Bio::Root::RootI; use Bio::SeqIO; use Bio::Seq; use base qw(Bio::DB::RandomAccessI); use constant CONFIG_FILE_NAME => 'config.dat'; use constant HEADER_SIZE => 4; use constant DEFAULT_FORMAT => 'fasta'; my @formats = [ 'FASTA', 'SWISSPROT', 'EMBL' ]; =head2 new Title : new Usage : For reading my $index = Bio::DB::Flat::BinarySearch->new( -directory => '/Users/michele/indices/dbest', -dbname => 'mydb', -format => 'fasta'); For writing my %secondary_patterns = {"ACC" => "^>\\S+ +(\\S+)"} my $index = Bio::DB::Flat::BinarySearch->new( -directory => '/Users/michele/indices', -dbname => 'mydb', -primary_pattern => "^>(\\S+)", -secondary_patterns => \%secondary_patterns, -primary_namespace => "ID"); my @files = ('file1','file2','file3'); $index->build_index(@files); Function: create a new Bio::DB::Flat::BinarySearch object Returns : new Bio::DB::Flat::BinarySearch Args : -directory Root directory for index files -dbname Name of subdirectory containing indices for named database -write_flag Allow building index -primary_pattern Regexp defining the primary id -secondary_patterns A hash ref containing the secondary patterns with the namespaces as keys -primary_namespace A string defining what the primary key is Status : Public =cut sub new { my ( $class, @args ) = @_; my $self = $class->SUPER::new(@args); bless $self, $class; my ( $index_dir, $dbname, $format, $write_flag, $primary_pattern, $primary_namespace, $start_pattern, $secondary_patterns ) = $self->_rearrange( [ qw(DIRECTORY DBNAME FORMAT WRITE_FLAG PRIMARY_PATTERN PRIMARY_NAMESPACE START_PATTERN SECONDARY_PATTERNS) ], @args ); $self->index_directory($index_dir); $self->dbname($dbname); if ( $self->index_directory && $self->read_config_file ) { my $fh = $self->primary_index_filehandle; my $record_width = $self->read_header($fh); $self->record_size($record_width); } $format ||= DEFAULT_FORMAT; $self->format($format); $self->write_flag($write_flag); if ( $self->write_flag && !$primary_namespace ) { ( $primary_namespace, $primary_pattern, $start_pattern, $secondary_patterns ) = $self->_guess_patterns( $self->format ); } $self->primary_pattern($primary_pattern); $self->primary_namespace($primary_namespace); $self->start_pattern($start_pattern); $self->secondary_patterns($secondary_patterns); return $self; } sub new_from_registry { my ( $self, %config ) = @_; my $dbname = $config{'dbname'}; my $location = $config{'location'}; my $index = Bio::DB::Flat::BinarySearch->new( -dbname => $dbname, -index_dir => $location, ); } =head2 get_Seq_by_id Title : get_Seq_by_id Usage : $obj->get_Seq_by_id($newval) Function: Example : Returns : value of get_Seq_by_id Args : newvalue (optional) =cut sub get_Seq_by_id { my ( $self, $id ) = @_; # too many uninit variables... local $^W = 0; my ( $fh, $length ) = $self->get_stream_by_id($id); unless ( defined( $self->format ) ) { $self->throw("Can't create sequence - format is not defined"); } return unless $fh; unless ( defined( $self->{_seqio} ) ) { $self->{_seqio} = Bio::SeqIO->new( -fh => $fh, -format => $self->format ); } else { $self->{_seqio}->_fh($fh); } return $self->{_seqio}->next_seq; } =head2 get_entry_by_id Title : get_entry_by_id Usage : $obj->get_entry_by_id($newval) Function: Get a Bio::SeqI object for a unique ID Returns : Bio::SeqI Args : string =cut sub get_entry_by_id { my ( $self, $id ) = @_; my ( $fh, $length ) = $self->get_stream_by_id($id); my $entry; sysread( $fh, $entry, $length ); return $entry; } =head2 get_stream_by_id Title : get_stream_by_id Usage : $obj->get_stream_by_id($id) Function: Gets a Sequence stream for an id Returns : Bio::SeqIO stream Args : Id to lookup by =cut sub get_stream_by_id { my ( $self, $id ) = @_; unless ( $self->record_size ) { if ( $self->index_directory && $self->read_config_file ) { my $fh = $self->primary_index_filehandle; my $record_width = $self->read_header($fh); $self->record_size($record_width); } } my $indexfh = $self->primary_index_filehandle; syseof($indexfh); my $filesize = systell($indexfh); $self->throw("file was not parsed properly, record size is empty") unless $self->record_size; my $end = ( $filesize - $self->{'_start_pos'} ) / $self->record_size; my ( $newid, $rest, $fhpos ) = $self->find_entry( $indexfh, 0, $end, $id, $self->record_size ); my ( $fileid, $pos, $length ) = split( /\t/, $rest ); #print STDERR "BinarySearch Found id entry $newid $fileid $pos $length:$rest\n"; if ( !$newid ) { return; } my $file = $self->{_file}{$fileid}; open my $IN, '<', $file or $self->throw("Could not read file '$file': $!"); my $entry; sysseek( $IN, $pos, 0 ); return ( $IN, $length ); } =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : $obj->get_Seq_by_acc($acc) Function: Gets a Bio::SeqI object by accession number Returns : Bio::SeqI object Args : string representing accession number =cut sub get_Seq_by_acc { my ( $self, $acc ) = @_; # too many uninit variables... local $^W = 0; if ( $self->primary_namespace eq "ACC" ) { return $self->get_Seq_by_id($acc); } else { return $self->get_Seq_by_secondary( "ACC", $acc ); } } =head2 get_Seq_by_version Title : get_Seq_by_version Usage : $obj->get_Seq_by_version($version) Function: Gets a Bio::SeqI object by accession.version number Returns : Bio::SeqI object Args : string representing accession.version number =cut sub get_Seq_by_version { my ( $self, $acc ) = @_; # too many uninit variables... local $^W = 0; if ( $self->primary_namespace eq "VERSION" ) { return $self->get_Seq_by_id($acc); } else { return $self->get_Seq_by_secondary( "VERSION", $acc ); } } =head2 get_Seq_by_secondary Title : get_Seq_by_secondary Usage : $obj->get_Seq_by_secondary($namespace,$acc) Function: Gets a Bio::SeqI object looking up secondary accessions Returns : Bio::SeqI object Args : namespace name to check secondary namespace and an id =cut sub get_Seq_by_secondary { my ( $self, $name, $id ) = @_; my @names = $self->secondary_namespaces; my $found = 0; foreach my $tmpname (@names) { if ( $name eq $tmpname ) { $found = 1; } } if ( $found == 0 ) { $self->throw("Secondary index for $name doesn't exist\n"); } my $fh = $self->open_secondary_index($name); syseof($fh); my $filesize = systell($fh); my $recsize = $self->{'_secondary_record_size'}{$name}; # print "Name " . $recsize . "\n"; my $end = ( $filesize - $self->{'_start_pos'} ) / $recsize; # print "End $end $filesize\n"; my ( $newid, $primary_id, $pos ) = $self->find_entry( $fh, 0, $end, $id, $recsize ); sysseek( $fh, $pos, 0 ); # print "Found new id $newid $primary_id\n"; # We now need to shuffle up the index file to find the top secondary entry my $record = $newid; while ( $record =~ /^$newid/ && $pos >= 0 ) { $record = $self->read_record( $fh, $pos, $recsize ); $pos = $pos - $recsize; # print "Up record = $record:$newid\n"; } $pos += $recsize; # print "Top position is $pos\n"; # Now we have to shuffle back down again to read all the secondary entries my $current_id = $newid; my %primary_id; $primary_id{$primary_id} = 1; while ( $current_id eq $newid ) { $record = $self->read_record( $fh, $pos, $recsize ); # print "Record is :$record:\n"; my ( $secid, $primary_id ) = split( /\t/, $record, 2 ); $current_id = $secid; if ( $current_id eq $newid ) { $primary_id =~ s/ //g; # print "Primary $primary_id\n"; $primary_id{$primary_id} = 1; $pos = $pos + $recsize; # print "Down record = $record\n"; } } if ( !defined($newid) ) { return; } my @entry; foreach my $id ( keys %primary_id ) { push @entry, $self->get_Seq_by_id($id); } return wantarray ? @entry : $entry[0]; } =head2 read_header Title : read_header Usage : $obj->read_header($fhl) Function: Reads the header from the db file Returns : width of a record Args : filehandle =cut sub read_header { my ( $self, $fh ) = @_; my $record_width; sysread( $fh, $record_width, HEADER_SIZE ); $self->{'_start_pos'} = HEADER_SIZE; $record_width =~ s/ //g; $record_width = $record_width * 1; return $record_width; } =head2 read_record Title : read_record Usage : $obj->read_record($fh,$pos,$len) Function: Reads a record from a filehandle Returns : String Args : filehandle, offset, and length =cut sub read_record { my ( $self, $fh, $pos, $len ) = @_; sysseek( $fh, $pos, 0 ); my $record; sysread( $fh, $record, $len ); return $record; } =head2 get_all_primary_ids Title : get_all_primary_ids Usage : @ids = $seqdb->get_all_primary_ids() Function: gives an array of all the primary_ids of the sequence objects in the database. Returns : an array of strings Args : none =cut sub get_all_primary_ids { my $self = shift; my $fh = $self->primary_index_filehandle; syseof($fh); my $filesize = systell($fh); my $recsize = $self->record_size; my $end = $filesize; my @ids; for ( my $pos = $self->{'_start_pos'} ; $pos < $end ; $pos += $recsize ) { my $record = $self->read_record( $fh, $pos, $recsize ); my ($entryid) = split( /\t/, $record ); push @ids, $entryid; } @ids; } =head2 find_entry Title : find_entry Usage : $obj->find_entry($fh,$start,$end,$id,$recsize) Function: Extract an entry based on the start,end,id and record size Returns : string Args : filehandle, start, end, id, recordsize =cut sub find_entry { my ( $self, $fh, $start, $end, $id, $recsize ) = @_; my $mid = int( ( $end + 1 + $start ) / 2 ); my $pos = ( $mid - 1 ) * $recsize + $self->{'_start_pos'}; my ($record) = $self->read_record( $fh, $pos, $recsize ); my ( $entryid, $rest ) = split( /\t/, $record, 2 ); $rest =~ s/\s+$//; # print "Mid $recsize $mid $pos:$entryid:$rest:$record\n"; # print "Entry :$id:$entryid:$rest\n"; my ( $first, $second ) = $id le $entryid ? ( $id, $entryid ) : ( $entryid, $id ); if ( $id eq $entryid ) { return ( $id, $rest, $pos - $recsize ); } elsif ( $first eq $id ) { if ( $end - $start <= 1 ) { return; } my $end = $mid; # print "Moving up $entryid $id\n"; $self->find_entry( $fh, $start, $end, $id, $recsize ); } elsif ( $second eq $id ) { # print "Moving down $entryid $id\n"; if ( $end - $start <= 1 ) { return; } $start = $mid; $self->find_entry( $fh, $start, $end, $id, $recsize ); } } =head2 build_index Title : build_index Usage : $obj->build_index(@files) Function: Build the index based on a set of files Returns : count of the number of entries Args : List of filenames =cut sub build_index { my ( $self, @files ) = @_; $self->write_flag or $self->throw('Cannot build index unless -write_flag is true'); my $rootdir = $self->index_directory; if ( !defined($rootdir) ) { $self->throw("No index directory set - can't build indices"); } if ( !-d $rootdir ) { $self->throw( "Index directory [$rootdir] is not a directory. Cant' build indices" ); } my $dbpath = File::Spec->catfile( $rootdir, $self->dbname ); if ( !-d $dbpath ) { warn "Creating directory $dbpath\n"; mkdir $dbpath, 0777 or $self->throw("Couldn't create $dbpath: $!"); } unless (@files) { $self->throw("Must enter an array of filenames to index"); } foreach my $file (@files) { $file = File::Spec->rel2abs($file) unless File::Spec->file_name_is_absolute($file); unless ( -e $file ) { $self->throw("Can't index file [$file] as it doesn't exist"); } } if ( my $filehash = $self->{_dbfile} ) { push @files, keys %$filehash; } my %seen; @files = grep { !$seen{$_}++ } @files; # Lets index $self->make_config_file( \@files ); my $entries = 0; foreach my $file (@files) { $entries += $self->_index_file($file); } # update alphabet if necessary $self->make_config_file( \@files ); # And finally write out the indices $self->write_primary_index; $self->write_secondary_indices; $entries; } =head2 _index_file Title : _index_file Usage : $obj->_index_file($newval) Function: Example : Returns : value of _index_file Args : newvalue (optional) =cut sub _index_file { my ( $self, $file ) = @_; my $v = $self->verbose; open my $FILE, '<', $file or $self->throw("Could not read file '$file': $!"); my $recstart = 0; my $fileid = $self->get_fileid_by_filename($file); my $found = 0; my $id; my $count = 0; my $primary = $self->primary_pattern; my $start_pattern = $self->start_pattern; my $pos = 0; my $new_primary_entry; my $length; my $fh = $FILE; my $done = -1; my @secondary_names = $self->secondary_namespaces; my %secondary_id; my $last_one; # In Windows, text files have '\r\n' as line separator, but when reading in # text mode Perl will only show the '\n'. This means that for a line "ABC\r\n", # "length $_" will report 4 although the line is 5 bytes in length. # We assume that all lines have the same line separator and only read current line. my $init_pos = tell($fh); my $curr_line = <$fh>; my $pos_diff = tell($fh) - $init_pos; my $correction = $pos_diff - length $curr_line; seek $fh, $init_pos, 0; # Rewind position to proceed to read the file while (<$fh>) { $last_one = $_; $self->{alphabet} ||= $self->guess_alphabet($_); if ( $_ =~ /$start_pattern/ ) { if ( $done == 0 ) { $id = $new_primary_entry; $self->{alphabet} ||= $self->guess_alphabet($_); my $tmplen = ( tell $fh ) - length($_) - $correction; $length = $tmplen - $pos; unless ( defined($id) ) { $self->throw("No id defined for sequence"); } unless ( defined($fileid) ) { $self->throw("No fileid defined for file $file"); } unless ( defined($pos) ) { $self->throw( "No position defined for " . $id . "\n" ); } unless ( defined($length) ) { $self->throw( "No length defined for " . $id . "\n" ); } $self->_add_id_position( $id, $pos, $fileid, $length, \%secondary_id ); $pos = $tmplen; if ( $count > 0 && $count % 1000 == 0 ) { $self->debug("Indexed $count ids\n") if $v > 0; } $count++; } else { $done = 0; } } if ( $_ =~ /$primary/ ) { $new_primary_entry = $1; } my $secondary_patterns = $self->secondary_patterns; foreach my $sec (@secondary_names) { my $pattern = $secondary_patterns->{$sec}; if ( $_ =~ /$pattern/ ) { $secondary_id{$sec} = $1; } } } # Remember to add in the last one $id = $new_primary_entry; # my $tmplen = (tell $fh) - length($last_one); my $tmplen = ( tell $fh ); $length = $tmplen - $pos; if ( !defined($id) ) { $self->throw("No id defined for sequence"); } if ( !defined($fileid) ) { $self->throw("No fileid defined for file $file"); } if ( !defined($pos) ) { $self->throw( "No position defined for " . $id . "\n" ); } if ( !defined($length) ) { $self->throw( "No length defined for " . $id . "\n" ); } $self->_add_id_position( $id, $pos, $fileid, $length, \%secondary_id ); $count++; close $FILE; $count; } =head2 write_primary_index Title : write_primary_index Usage : $obj->write_primary_index($newval) Function: Example : Returns : value of write_primary_index Args : newvalue (optional) =cut sub write_primary_index { my ($self) = @_; my @ids = keys %{ $self->{_id} }; @ids = sort { $a cmp $b } @ids; open my $INDEX, '>', $self->primary_index_file or $self->throw( "Could not write primary index file '" . $self->primary_index_file . "': $!" ); my $recordlength = $self->{_maxidlength} + $self->{_maxfileidlength} + $self->{_maxposlength} + $self->{_maxlengthlength} + 3; print $INDEX sprintf( "%04d", $recordlength ); foreach my $id (@ids) { if ( !defined( $self->{_id}{$id}{_fileid} ) ) { $self->throw("No fileid for $id\n"); } if ( !defined( $self->{_id}{$id}{_pos} ) ) { $self->throw("No position for $id\n"); } if ( !defined( $self->{_id}{$id}{_length} ) ) { $self->throw("No length for $id"); } my $record = $id . "\t" . $self->{_id}{$id}{_fileid} . "\t" . $self->{_id}{$id}{_pos} . "\t" . $self->{_id}{$id}{_length}; print $INDEX sprintf( "%-${recordlength}s", $record ); } } =head2 write_secondary_indices Title : write_secondary_indices Usage : $obj->write_secondary_indices($newval) Function: Example : Returns : value of write_secondary_indices Args : newvalue (optional) =cut sub write_secondary_indices { my ($self) = @_; # These are the different my @names = keys( %{ $self->{_secondary_id} } ); foreach my $name (@names) { my @seconds = keys %{ $self->{_secondary_id}{$name} }; # First we need to loop over to get the longest record. my $length = 0; foreach my $second (@seconds) { my $tmplen = length($second) + 1; my @prims = keys %{ $self->{_secondary_id}{$name}{$second} }; foreach my $prim (@prims) { my $recordlen = $tmplen + length($prim); if ( $recordlen > $length ) { $length = $recordlen; } } } # Now we can print the index my $fh = $self->new_secondary_filehandle($name); print $fh sprintf( "%04d", $length ); @seconds = sort @seconds; foreach my $second (@seconds) { my @prims = keys %{ $self->{_secondary_id}{$name}{$second} }; my $tmp = $second; foreach my $prim (@prims) { my $record = $tmp . "\t" . $prim; if ( length($record) > $length ) { $self->throw( "Something has gone horribly wrong - length of record is more than we thought [$length]\n" ); } else { print $fh sprintf( "%-${length}s", $record ); } } } close($fh); } } =head2 new_secondary_filehandle Title : new_secondary_filehandle Usage : $obj->new_secondary_filehandle($newval) Function: Example : Returns : value of new_secondary_filehandle Args : newvalue (optional) =cut sub new_secondary_filehandle { my ( $self, $name ) = @_; my $indexdir = $self->_config_path; my $secindex = File::Spec->catfile( $indexdir, "id_$name.index" ); open my $fh, '>', $secindex or $self->throw("Could not write file '$secindex': $!"); return $fh; } =head2 open_secondary_index Title : open_secondary_index Usage : $obj->open_secondary_index($newval) Function: Example : Returns : value of open_secondary_index Args : newvalue (optional) =cut sub open_secondary_index { my ( $self, $name ) = @_; if ( !defined( $self->{_secondary_filehandle}{$name} ) ) { my $indexdir = $self->_config_path; my $secindex = $indexdir . "/id_$name.index"; if ( !-e $secindex ) { $self->throw("Index is not present for namespace [$name]\n"); } open my $newfh, '<', $secindex or $self->throw("Could not read file '$secindex': $!"); my $reclen = $self->read_header($newfh); $self->{_secondary_filehandle}{$name} = $newfh; $self->{_secondary_record_size}{$name} = $reclen; } return $self->{_secondary_filehandle}{$name}; } =head2 _add_id_position Title : _add_id_position Usage : $obj->_add_id_position($newval) Function: Example : Returns : value of _add_id_position Args : newvalue (optional) =cut sub _add_id_position { my ( $self, $id, $pos, $fileid, $length, $secondary_id ) = @_; if ( !defined($id) ) { $self->throw("No id defined. Can't add id position"); } if ( !defined($pos) ) { $self->throw("No position defined. Can't add id position"); } if ( !defined($fileid) ) { $self->throw("No fileid defined. Can't add id position"); } if ( !defined($length) || $length <= 0 ) { $self->throw( "No length defined or <= 0 [$length]. Can't add id position"); } $self->{_id}{$id}{_pos} = $pos; $self->{_id}{$id}{_length} = $length; $self->{_id}{$id}{_fileid} = $fileid; # Now the secondary ids foreach my $sec ( keys(%$secondary_id) ) { my $value = $secondary_id->{$sec}; $self->{_secondary_id}{$sec}{$value}{$id} = 1; } $self->{_maxidlength} = length($id) if !exists $self->{_maxidlength} or length($id) >= $self->{_maxidlength}; $self->{_maxfileidlength} = length($fileid) if !exists $self->{_maxfileidlength} or length($fileid) >= $self->{_maxfileidlength}; $self->{_maxposlength} = length($pos) if !exists $self->{_maxposlength} or length($pos) >= $self->{_maxposlength}; $self->{_maxlengthlength} = length($length) if !exists $self->{_maxlengthlength} or length($length) >= $self->{_maxlengthlength}; } =head2 make_config_file Title : make_config_file Usage : $obj->make_config_file($newval) Function: Example : Returns : value of make_config_file Args : newvalue (optional) =cut sub make_config_file { my ( $self, $files ) = @_; my @files = @$files; my $configfile = $self->_config_file; open my $CON, '>', $configfile or $self->throw("Could not write config file '$configfile': $!"); # First line must be the type of index - in this case flat print $CON "index\tflat/1\n"; # Now the fileids my $count = 0; foreach my $file (@files) { my $size = -s $file; print $CON "fileid_$count\t$file\t$size\n"; $self->{_file}{$count} = $file; $self->{_dbfile}{$file} = $count; $self->{_size}{$count} = $size; $count++; } # Now the namespaces print $CON "primary_namespace\t" . $self->primary_namespace . "\n"; # Needs fixing for the secondary stuff my $second_patterns = $self->secondary_patterns; my @second = keys %$second_patterns; if ( (@second) ) { print $CON "secondary_namespaces"; foreach my $second (@second) { print $CON "\t$second"; } print $CON "\n"; } # Now the config format unless ( defined( $self->format ) ) { $self->throw( "Format does not exist in module - can't write config file"); } else { my $format = $self->format; my $alphabet = $self->alphabet; my $alpha = $alphabet ? "/$alphabet" : ''; print $CON "format\t" . "$format\n"; } close $CON; } =head2 read_config_file Title : read_config_file Usage : $obj->read_config_file($newval) Function: Example : Returns : value of read_config_file Args : newvalue (optional) =cut sub read_config_file { my ($self) = @_; my $configfile = $self->_config_file; return unless -e $configfile; open my $CON, '<', $configfile or $self->throw("Could not read config file '$configfile': $!"); # First line must be type my $line = <$CON>; chomp($line); my $version; # This is hard coded as we only index flatfiles here if ( $line =~ m{index\tflat/(\d+)} ) { $version = $1; } else { $self->throw( "First line not compatible with flat file index. Should be something like\n\nindex\tflat/1" ); } $self->index_type("flat"); $self->index_version($version); while (<$CON>) { chomp; # Look for fileid lines if ( $_ =~ /^fileid_(\d+)\t(.+)\t(\d+)/ ) { my $fileid = $1; my $filename = $2; my $filesize = $3; if ( !-e $filename ) { $self->throw("File [$filename] does not exist!"); } if ( -s $filename != $filesize ) { $self->throw( "Flatfile size for $filename differs from what the index thinks it is. Real size [" . ( -s $filename ) . "] Index thinks it is [" . $filesize . "]" ); } $self->{_file}{$fileid} = $filename; $self->{_dbfile}{$filename} = $fileid; $self->{_size}{$fileid} = $filesize; } # Look for namespace lines if (/(.*)_namespaces?\t(.+)/) { if ( $1 eq "primary" ) { $self->primary_namespace($2); } elsif ( $1 eq "secondary" ) { $self->secondary_namespaces( split "\t", $2 ); } else { $self->throw("Unknown namespace name in config file [$1"); } } # Look for format lines if ( $_ =~ /format\t(\S+)/ ) { # Check the format here? my $format = $1; # handle LSID format if ( $format =~ /^URN:LSID:open-bio\.org:(\w+)(?:\/(\w+))?/ ) { $self->format($1); $self->alphabet($2); } else { # compatibility with older versions $self->format($1); } } } close($CON); # Now check we have all that we need my @fileid_keys = keys( %{ $self->{_file} } ); if ( !(@fileid_keys) ) { $self->throw( "No flatfile fileid files in config - check the index has been made correctly" ); } if ( !defined( $self->primary_namespace ) ) { $self->throw("No primary namespace exists"); } if ( !-e $self->primary_index_file ) { $self->throw( "Primary index file [" . $self->primary_index_file . "] doesn't exist" ); } 1; } =head2 get_fileid_by_filename Title : get_fileid_by_filename Usage : $obj->get_fileid_by_filename($newval) Function: Example : Returns : value of get_fileid_by_filename Args : newvalue (optional) =cut sub get_fileid_by_filename { my ( $self, $file ) = @_; if ( !defined( $self->{_dbfile} ) ) { $self->throw( "No file to fileid mapping present. Has the fileid file been read?" ); } return $self->{_dbfile}{$file}; } =head2 get_filehandle_by_fileid Title : get_filehandle_by_fileid Usage : $obj->get_filehandle_by_fileid($newval) Function: Example : Returns : value of get_filehandle_by_fileid Args : newvalue (optional) =cut sub get_filehandle_by_fileid { my ( $self, $fileid ) = @_; if ( !defined( $self->{_file}{$fileid} ) ) { $self->throw("ERROR: undefined fileid in index [$fileid]"); } open my $fh, '<', $self->{_file}{$fileid} or $self->throw("Could not read file '$self->{_file}{$fileid}': $!"); return $fh; } =head2 primary_index_file Title : primary_index_file Usage : $obj->primary_index_file($newval) Function: Example : Returns : value of primary_index_file Args : newvalue (optional) =cut sub primary_index_file { my ($self) = @_; return File::Spec->catfile( $self->_config_path, "key_" . $self->primary_namespace . ".key" ); } =head2 primary_index_filehandle Title : primary_index_filehandle Usage : $obj->primary_index_filehandle($newval) Function: Example : Returns : value of primary_index_filehandle Args : newvalue (optional) =cut sub primary_index_filehandle { my ($self) = @_; unless ( defined( $self->{'_primary_index_handle'} ) ) { my $primary_file = $self->primary_index_file; open $self->{'_primary_index_handle'}, '<', $primary_file or self->throw("Could not read file '$primary_file': $!\n"); } return $self->{'_primary_index_handle'}; } =head2 format Title : format Usage : $obj->format($newval) Function: Example : Returns : value of format Args : newvalue (optional) =cut sub format { my ( $obj, $value ) = @_; if ( defined $value ) { $obj->{'format'} = $value; } return $obj->{'format'}; } sub alphabet { my ( $obj, $value ) = @_; if ( defined $value ) { $obj->{alphabet} = $value; } return $obj->{alphabet}; } =head2 write_flag Title : write_flag Usage : $obj->write_flag($newval) Function: Example : Returns : value of write_flag Args : newvalue (optional) =cut sub write_flag { my ( $obj, $value ) = @_; if ( defined $value ) { $obj->{'write_flag'} = $value; } return $obj->{'write_flag'}; } =head2 dbname Title : dbname Usage : $obj->dbname($newval) Function: get/set database name Example : Returns : value of dbname Args : newvalue (optional) =cut sub dbname { my $self = shift; my $d = $self->{flat_dbname}; $self->{flat_dbname} = shift if @_; $d; } =head2 index_directory Title : index_directory Usage : $obj->index_directory($newval) Function: Example : Returns : value of index_directory Args : newvalue (optional) =cut sub index_directory { my ( $self, $arg ) = @_; if ( defined($arg) ) { if ( $arg !~ m{/$} ) { $arg .= "/"; } $self->{_index_directory} = $arg; } return $self->{_index_directory}; } sub _config_path { my $self = shift; my $root = $self->index_directory; my $dbname = $self->dbname; File::Spec->catfile( $root, $dbname ); } sub _config_file { my $self = shift; my $path = $self->_config_path; File::Spec->catfile( $path, CONFIG_FILE_NAME ); } =head2 record_size Title : record_size Usage : $obj->record_size($newval) Function: Example : Returns : value of record_size Args : newvalue (optional) =cut sub record_size { my $self = shift; $self->{_record_size} = shift if @_; return $self->{_record_size}; } =head2 primary_namespace Title : primary_namespace Usage : $obj->primary_namespace($newval) Function: Example : Returns : value of primary_namespace Args : newvalue (optional) =cut sub primary_namespace { my $self = shift; $self->{_primary_namespace} = shift if @_; return $self->{_primary_namespace}; } =head2 index_type Title : index_type Usage : $obj->index_type($newval) Function: Example : Returns : value of index_type Args : newvalue (optional) =cut sub index_type { my $self = shift; $self->{_index_type} = shift if @_; return $self->{_index_type}; } =head2 index_version Title : index_version Usage : $obj->index_version($newval) Function: Example : Returns : value of index_version Args : newvalue (optional) =cut sub index_version { my $self = shift; $self->{_index_version} = shift if @_; return $self->{_index_version}; } =head2 primary_pattern Title : primary_pattern Usage : $obj->primary_pattern($newval) Function: Example : Returns : value of primary_pattern Args : newvalue (optional) =cut sub primary_pattern { my $obj = shift; $obj->{'primary_pattern'} = shift if @_; return $obj->{'primary_pattern'}; } =head2 start_pattern Title : start_pattern Usage : $obj->start_pattern($newval) Function: Example : Returns : value of start_pattern Args : newvalue (optional) =cut sub start_pattern { my $obj = shift; $obj->{'start_pattern'} = shift if @_; return $obj->{'start_pattern'}; } =head2 secondary_patterns Title : secondary_patterns Usage : $obj->secondary_patterns($newval) Function: Example : Returns : value of secondary_patterns Args : newvalue (optional) =cut sub secondary_patterns { my ( $obj, $value ) = @_; if ( defined $value ) { $obj->{'secondary_patterns'} = $value; my @names = keys %$value; foreach my $name (@names) { $obj->secondary_namespaces($name); } } return $obj->{'secondary_patterns'}; } =head2 secondary_namespaces Title : secondary_namespaces Usage : $obj->secondary_namespaces($newval) Function: Example : Returns : value of secondary_namespaces Args : newvalue (optional) =cut sub secondary_namespaces { my ( $obj, @values ) = @_; if (@values) { push( @{ $obj->{'secondary_namespaces'} }, @values ); } return @{ $obj->{'secondary_namespaces'} || [] }; } ## These are indexing routines to index commonly used format - fasta ## swissprot and embl sub new_SWISSPROT_index { my ( $self, $index_dir, @files ) = @_; my %secondary_patterns; my $start_pattern = "^ID (\\S+)"; my $primary_pattern = "^AC (\\S+)\\;"; $secondary_patterns{"ID"} = $start_pattern; my $index = Bio::DB::Flat::BinarySearch->new( -index_dir => $index_dir, -format => 'swissprot', -primary_pattern => $primary_pattern, -primary_namespace => "ACC", -start_pattern => $start_pattern, -secondary_patterns => \%secondary_patterns ); $index->build_index(@files); } sub new_EMBL_index { my ( $self, $index_dir, @files ) = @_; my %secondary_patterns; my $start_pattern = "^ID (\\S+)"; my $primary_pattern = "^AC (\\S+)\\;"; my $primary_namespace = "ACC"; $secondary_patterns{"ID"} = $start_pattern; my $index = Bio::DB::Flat::BinarySearch->new( -index_dir => $index_dir, -format => 'embl', -primary_pattern => $primary_pattern, -primary_namespace => "ACC", -start_pattern => $start_pattern, -secondary_patterns => \%secondary_patterns ); $index->build_index(@files); return $index; } sub new_FASTA_index { my ( $self, $index_dir, @files ) = @_; my %secondary_patterns; my $start_pattern = "^>"; my $primary_pattern = "^>(\\S+)"; my $primary_namespace = "ACC"; $secondary_patterns{"ID"} = "^>\\S+ +(\\S+)"; my $index = Bio::DB::Flat::BinarySearch->new( -index_dir => $index_dir, -format => 'fasta', -primary_pattern => $primary_pattern, -primary_namespace => "ACC", -start_pattern => $start_pattern, -secondary_patterns => \%secondary_patterns ); $index->build_index(@files); return $index; } # EVERYTHING THAT FOLLOWS THIS # is an awful hack - in reality Michele's code needs to be rewritten # to use Bio::SeqIO, but I have too little time to do this -- LS sub guess_alphabet { my $self = shift; my $line = shift; my $format = $self->format; return 'protein' if $format eq 'swissprot'; if ( $format eq 'genbank' ) { return unless $line =~ /^LOCUS/; return 'dna' if $line =~ /\s+\d+\s+bp/i; return 'protein'; } if ( $format eq 'embl' ) { return unless $line =~ /^ID/; return 'dna' if $line =~ / DNA;/i; return 'rna' if $line =~ / RNA;/i; return 'protein'; } return; } # return (namespace,primary_pattern,start_pattern,secondary_pattern) sub _guess_patterns { my $self = shift; my $format = shift; if ( $format =~ /swiss(prot)?/i ) { return ( 'ID', "^ID (\\S+)", "^ID (\\S+)", { ACC => "^AC (\\S+);" } ); } if ($format =~ /embl/i) { return ('ID', "^ID (\\S+[^; ])", "^ID (\\S+[^; ])", { ACC => q/^AC (\S+);/, VERSION => q/^SV\s+(\S+)/ }); } if ( $format =~ /genbank/i ) { return ( 'ID', q/^LOCUS\s+(\S+)/, q/^LOCUS/, { ACC => q/^ACCESSION\s+(\S+)/, VERSION => q/^VERSION\s+(\S+)/ } ); } if ( $format =~ /fasta/i ) { return ( 'ACC', '^>(\S+)', '^>(\S+)', ); } $self->throw("I can't handle format $format"); } 1; BioPerl-1.007002/Bio/DB/Flat/BDB000755000766000024 013155576320 15631 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/Flat/BDB/embl.pm000444000766000024 443313155576320 17247 0ustar00cjfieldsstaff000000000000# # # BioPerl module for Bio::DB::Flat::BDB # # Please direct questions and support issues to # # Cared for by Lincoln Stein # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Flat::BDB::embl - embl adaptor for Open-bio standard BDB-indexed flat file =head1 SYNOPSIS See Bio::DB::Flat. =head1 DESCRIPTION This module allows embl files to be stored in Berkeley DB flat files using the Open-Bio standard BDB-indexed flat file scheme. You should not be using this directly, but instead use it via Bio::DB::Flat. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Lincoln Stein Email - lstein@cshl.org =head1 SEE ALSO L, =cut package Bio::DB::Flat::BDB::embl; use strict; use base qw(Bio::DB::Flat::BDB); sub seq_to_ids { my $self = shift; my $seq = shift; my $display_id = $seq->display_id; my $accession = $seq->accession_number; my $version = $seq->seq_version; my %ids; $ids{ID} = $display_id; $ids{ACC} = $accession if defined $accession; $ids{VERSION} = "$accession.$version" if defined $accession && defined $version; return \%ids; } sub default_primary_namespace { return "ID"; } sub default_secondary_namespaces { return qw(ACC VERSION); } sub default_file_format { "embl" } 1; BioPerl-1.007002/Bio/DB/Flat/BDB/fasta.pm000444000766000024 456413155576320 17433 0ustar00cjfieldsstaff000000000000# # # BioPerl module for Bio::DB::Flat::BDB # # Please direct questions and support issues to # # Cared for by Lincoln Stein # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Flat::BDB::fasta - fasta adaptor for Open-bio standard BDB-indexed flat file =head1 SYNOPSIS See Bio::DB::Flat. =head1 DESCRIPTION This module allows fasta files to be stored in Berkeley DB flat files using the Open-Bio standard BDB-indexed flat file scheme. You should not be using this directly, but instead use it via Bio::DB::Flat. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 SEE ALSO L, =head1 AUTHOR - Lincoln Stein Email - lstein@cshl.org =cut package Bio::DB::Flat::BDB::fasta; use strict; use base qw(Bio::DB::Flat::BDB); sub default_file_format { "fasta" } sub seq_to_ids { my $self = shift; my $seq = shift; my %ids; $ids{$self->primary_namespace} = $seq->primary_id; \%ids; } sub parse_one_record { my $self = shift; my $fh = shift; # fasta parses by changing $/ to '\n>', need to adjust accordingly my $adj = -1; my $parser = $self->{cached_parsers}{fileno($fh)} ||= Bio::SeqIO->new(-fh=>$fh,-format=>$self->default_file_format); my $seq = $parser->next_seq or return; $self->{flat_alphabet} ||= $seq->alphabet; my $ids = $self->seq_to_ids($seq); return ($ids, $adj); } 1; BioPerl-1.007002/Bio/DB/Flat/BDB/genbank.pm000444000766000024 463213155576320 17736 0ustar00cjfieldsstaff000000000000# # # BioPerl module for Bio::DB::Flat::BDB # # Please direct questions and support issues to # # Cared for by Lincoln Stein # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Flat::BDB::genbank - genbank adaptor for Open-bio standard BDB-indexed flat file =head1 SYNOPSIS See Bio::DB::Flat. =head1 DESCRIPTION This module allows genbank files to be stored in Berkeley DB flat files using the Open-Bio standard BDB-indexed flat file scheme. You should not be using this directly, but instead use it via Bio::DB::Flat. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Lincoln Stein Email - lstein@cshl.org =head1 SEE ALSO L, =cut package Bio::DB::Flat::BDB::genbank; use strict; use base qw(Bio::DB::Flat::BDB); sub seq_to_ids { my $self = shift; my $seq = shift; my $display_id = $seq->display_id; my $accession = $seq->accession_number; my $version = $seq->seq_version; my $gi = $seq->primary_id; my %ids; $ids{ID} = $display_id; $ids{ACC} = $accession if defined $accession; $ids{VERSION} = "$accession.$version" if defined $accession && defined $version; $ids{GI} = $gi if defined $gi && $gi =~ /^\d+$/; return \%ids; } sub default_primary_namespace { return "ID"; } sub default_secondary_namespaces { return qw(ACC GI VERSION); } sub default_file_format { "genbank" } 1; BioPerl-1.007002/Bio/DB/Flat/BDB/swiss.pm000444000766000024 452513155576320 17502 0ustar00cjfieldsstaff000000000000# # # BioPerl module for Bio::DB::Flat::BDB::swiss # # Please direct questions and support issues to # # Cared for by Lincoln Stein # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Flat::BDB::swiss - swissprot adaptor for Open-bio standard BDB-indexed flat file =head1 SYNOPSIS See Bio::DB::Flat. =head1 DESCRIPTION This module allows swissprot files to be stored in Berkeley DB flat files using the Open-Bio standard BDB-indexed flat file scheme. You should not be using this directly, but instead use it via Bio::DB::Flat. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 SEE ALSO L, =head1 AUTHOR - Lincoln Stein Email - lstein@cshl.org =cut package Bio::DB::Flat::BDB::swiss; use strict; use base qw(Bio::DB::Flat::BDB); sub default_file_format { "swiss" } sub default_primary_namespace { return "ID"; } sub default_secondary_namespaces { return qw(ACC VERSION); } sub seq_to_ids { my $self = shift; my $seq = shift; my $display_id = $seq->display_id; my $accession = $seq->accession_number; my $version = $seq->seq_version; my $gi = $seq->primary_id; my %ids; $ids{ID} = $display_id; $ids{ACC} = $accession if defined $accession; $ids{VERSION} = "$accession.$version" if defined $accession && defined $version; return \%ids; } 1; BioPerl-1.007002/Bio/DB/GFF000755000766000024 013155576320 14756 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/GFF/Aggregator.pm000444000766000024 4143613155576320 17563 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator -- Aggregate GFF groups into composite features =head1 SYNOPSIS use Bio::DB::GFF; my $agg1 = Bio::DB::GFF::Aggregator->new(-method => 'cistron', -main_method => 'locus', -sub_parts => ['allele','variant'] ); my $agg2 = Bio::DB::GFF::Aggregator->new(-method => 'splice_group', -sub_parts => 'transcript'); my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -aggregator => [$agg1,$agg2], -dsn => 'dbi:mysql:elegans42', ); =head1 DESCRIPTION Bio::DB::GFF::Aggregator is used to aggregate GFF groups into composite features. Each composite feature has a "main part", the top-level feature, and a series of zero or more subparts, retrieved with the sub_SeqFeature() method. The aggregator class is designed to be subclassable, allowing a variety of GFF feature types to be supported. The base Bio::DB::GFF::Aggregator class is generic, and can be used to create specific instances to be passed to the -aggregator argument of Bio::DB::GFF-Enew() call. The various subclasses of Bio::DB::GFF::Aggregator are tuned for specific common feature types such as clones, gapped alignments and transcripts. Instances of Bio::DB::GFF::Aggregator have three attributes: =over 3 =item * method This is the GFF method field of the composite feature as a whole. For example, "transcript" may be used for a composite feature created by aggregating individual intron, exon and UTR features. =item * main method Sometimes GFF groups are organized hierarchically, with one feature logically containing another. For example, in the C. elegans schema, methods of type "Sequence:curated" correspond to regions covered by curated genes. There can be zero or one main methods. =item * subparts This is a list of one or more methods that correspond to the component features of the aggregates. For example, in the C. elegans database, the subparts of transcript are "intron", "exon" and "CDS". =back Aggregators have two main methods that can be overridden in subclasses: =over 4 =item * disaggregate() This method is called by the Adaptor object prior to fetching a list of features. The method is passed an associative array containing the [method,source] pairs that the user has requested, and it returns a list of raw features that it would like the adaptor to fetch. =item * aggregate() This method is called by the Adaptor object after it has fetched features. The method is passed a list of raw features and is expected to add its composite features to the list. =back The disaggregate() and aggregate() methods provided by the base Aggregator class should be sufficient for many applications. In this case, it suffices for subclasses to override the following methods: =over 4 =item * method() Return the default method for the composite feature as a whole. =item * main_name() Return the default main method name. =item * part_names() Return a list of subpart method names. =back Provided that method() and part_names() are overridden (and optionally main_name() as well), then the bare name of the aggregator subclass can be passed to the -aggregator of Bio::DB::GFF-Enew(). For example, this is a small subclass that will aggregate features of type "allele" and "polymorphism" into an aggregate named "mutant": package Bio::DB::GFF::Aggregator::mutant; use strict; use Bio::DB::GFF::Aggregator; use base qw(Bio::DB::GFF::Aggregator); sub method { 'mutant' } sub part_names { return qw(allele polymorphism); } 1; Once installed, this aggregator can be passed to Bio::DB::GFF-Enew() by name like so: my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -aggregator => 'mutant', -dsn => 'dbi:mysql:elegans42', ); =head1 API The remainder of this document describes the public and private methods implemented by this module. =cut package Bio::DB::GFF::Aggregator; use strict; use Bio::DB::GFF::Util::Rearrange; # for rearrange() use Bio::DB::GFF::Feature; use base qw(Bio::Root::Root); my $ALWAYS_TRUE = sub { 1 }; =head2 new Title : new Usage : $a = Bio::DB::GFF::Aggregator->new(@args) Function: create a new aggregator Returns : a Bio::DB::GFF::Aggregator object Args : see below Status : Public This is the constructor for Bio::DB::GFF::Aggregator. Named arguments are as follows: -method the method for the composite feature -main_method the top-level raw feature, if any -sub_parts the list of raw features that will form the subparts of the composite feature (array reference or scalar) =cut sub new { my $class = shift; my ($method,$main,$sub_parts,$whole_object) = rearrange(['METHOD', ['MAIN_PART','MAIN_METHOD'], ['SUB_METHODS','SUB_PARTS'], 'WHOLE_OBJECT' ],@_); return bless { method => $method, main_method => $main, sub_parts => $sub_parts, require_whole_object => $whole_object, },$class; } =head2 disaggregate Title : disaggregate Usage : $a->disaggregate($types,$factory) Function: disaggregate type list into components Returns : a true value if this aggregator should be called to reaggregate Args : see below Status : Public This method is called to disaggregate a list of types into the set of low-level features to be retrieved from the GFF database. The list of types is passed as an array reference containing a series of [method,source] pairs. This method synthesizes a new set of [method,source] pairs, and appends them to the list of requested types, changing the list in situ. Arguments: $types reference to an array of [method,source] pairs $factory reference to the Adaptor object that is calling this method Note that the API allows disaggregate() to remove types from the type list. This feature is probably not desirable and may be deprecated in the future. =cut # this is called at the beginning to turn the pseudo-type # into its component feature types sub disaggregate { my $self = shift; my $types = shift; my $factory = shift; my $sub_features = $factory->parse_types($self->get_part_names); my $main_feature = $factory->parse_types($self->get_main_name); if (@$types) { my (@synthetic_types,@unchanged); foreach (@$types) { my ($method,$source) = @$_; if (lc $method eq lc $self->get_method) { # e.g. "transcript" push @synthetic_types,map { [$_->[0],$_->[1] || $source] } @$sub_features,@$main_feature; } else { push @unchanged,$_; } } # remember what we're searching for $self->components(\@synthetic_types); $self->passthru(\@unchanged); @$types = (@unchanged,@synthetic_types); } # we get here when no search types are listed else { my @stypes = map { [$_->[0],$_->[1]] } @$sub_features,@$main_feature; $self->components(\@stypes); $self->passthru(undef); } return $self->component_count > 0; } =head2 aggregate Title : aggregate Usage : $features = $a->aggregate($features,$factory) Function: aggregate a feature list into composite features Returns : an array reference containing modified features Args : see below Status : Public This method is called to aggregate a list of raw GFF features into the set of composite features. The method is called an array reference to a set of Bio::DB::GFF::Feature objects. It runs through the list, creating new composite features when appropriate. The method result is an array reference containing the composite features. Arguments: $features reference to an array of Bio::DB::GFF::Feature objects $factory reference to the Adaptor object that is calling this method NOTE: The reason that the function result contains the raw features as well as the aggregated ones is to allow queries like this one: @features = $segment->features('exon','transcript:curated'); Assuming that "transcript" is the name of an aggregated feature and that "exon" is one of its components, we do not want the transcript aggregator to remove features of type "exon" because the user asked for them explicitly. =cut sub aggregate { my $self = shift; my $features = shift; my $factory = shift; my $main_method = $self->get_main_name; my $matchsub = $self->match_sub($factory) or return; my $strictmatch = $self->strict_match(); my $passthru = $self->passthru_sub($factory); my (%aggregates,@result); for my $feature (@$features) { if ($feature->group && $matchsub->($feature)) { my $key = $strictmatch->{lc $feature->method,lc $feature->source} ? join ($;,$feature->group,$feature->refseq,$feature->source) : join ($;,$feature->group,$feature->refseq); if ($main_method && lc $feature->method eq lc $main_method) { $aggregates{$key}{base} ||= $feature->clone; } else { push @{$aggregates{$key}{subparts}},$feature; } push @result,$feature if $passthru && $passthru->($feature); } else { push @result,$feature; } } # aggregate components my $pseudo_method = $self->get_method; my $require_whole_object = $self->require_whole_object; foreach (keys %aggregates) { if ($require_whole_object && $self->components) { next unless $aggregates{$_}{base}; # && $aggregates{$_}{subparts}; } my $base = $aggregates{$_}{base}; unless ($base) { # no base, so create one my $first = $aggregates{$_}{subparts}[0]; $base = $first->clone; # to inherit parent coordinate system, etc $base->score(undef); $base->phase(undef); } $base->method($pseudo_method); $base->add_subfeature($_) foreach @{$aggregates{$_}{subparts}}; $base->adjust_bounds; $base->compound(1); # set the compound flag push @result,$base; } @$features = @result; } =head2 method Title : method Usage : $string = $a->method Function: get the method type for the composite feature Returns : a string Args : none Status : Protected This method is called to get the method to be assigned to the composite feature once it is aggregated. It is called if the user did not explicitly supply a -method argument when the aggregator was created. This is the method that should be overridden in aggregator subclasses. =cut # default method - override in subclasses sub method { my $self = shift; $self->{method}; } =head2 main_name Title : main_name Usage : $string = $a->main_name Function: get the method type for the "main" component of the feature Returns : a string Args : none Status : Protected This method is called to get the method of the "main component" of the composite feature. It is called if the user did not explicitly supply a -main-method argument when the aggregator was created. This is the method that should be overridden in aggregator subclasses. =cut # no default main method sub main_name { my $self = shift; return; } =head2 part_names Title : part_names Usage : @methods = $a->part_names Function: get the methods for the non-main various components of the feature Returns : a list of strings Args : none Status : Protected This method is called to get the list of methods of the "main component" of the composite feature. It is called if the user did not explicitly supply a -main-method argument when the aggregator was created. This is the method that should be overridden in aggregator subclasses. =cut # no default part names sub part_names { my $self = shift; return; } =head2 require_whole_object Title : require_whole_object Usage : $bool = $a->require_whole_object Function: see below Returns : a boolean flag Args : none Status : Internal This method returns true if the aggregator should refuse to aggregate an object unless both its main part and its subparts are present. =cut sub require_whole_object { my $self = shift; my $d = $self->{require_whole_object}; $self->{require_whole_object} = shift if @_; $d; } =head2 match_sub Title : match_sub Usage : $coderef = $a->match_sub($factory) Function: generate a code reference that will match desired features Returns : a code reference Args : see below Status : Internal This method is used internally to generate a code sub that will quickly filter out the raw features that we're interested in aggregating. The returned sub accepts a Feature and returns true if we should aggregate it, false otherwise. =cut #' make emacs happy sub match_sub { my $self = shift; my $factory = shift; my $types_to_aggregate = $self->components() or return; # saved from disaggregate call return unless @$types_to_aggregate; return $factory->make_match_sub($types_to_aggregate); } =head2 strict_match Title : strict_match Usage : $strict = $a->strict_match Function: generate a hashref that indicates which subfeatures need to be tested strictly for matching sources before aggregating Returns : a hash ref Status : Internal =cut sub strict_match { my $self = shift; my $types_to_aggregate = $self->components(); my %strict; for my $t (@$types_to_aggregate) { $strict{lc $t->[0],lc $t->[1]}++ if defined $t->[1]; } \%strict; } sub passthru_sub { my $self = shift; my $factory = shift; my $passthru = $self->passthru() or return; return unless @$passthru; return $factory->make_match_sub($passthru); } =head2 components Title : components Usage : @array= $a->components([$components]) Function: get/set stored list of parsed raw feature types Returns : an array in list context, an array ref in scalar context Args : new arrayref of feature types Status : Internal This method is used internally to remember the parsed list of raw features that we will aggregate. The need for this subroutine is seen when a user requests a composite feature of type "clone:cosmid". This generates a list of components in which the source is appended to the method, like "clone_left_end:cosmid" and "clone_right_end:cosmid". components() stores this information for later use. =cut sub components { my $self = shift; my $d = $self->{components}; $self->{components} = shift if @_; return unless ref $d; return wantarray ? @$d : $d; } sub component_count { my @c = shift->components; scalar @c; } sub passthru { my $self = shift; my $d = $self->{passthru}; $self->{passthru} = shift if @_; return unless ref $d; return wantarray ? @$d : $d; } sub clone { my $self = shift; my %new = %{$self}; return bless \%new,ref($self); } =head2 get_part_names Title : get_part_names Usage : @array = $a->get_part_names Function: get list of sub-parts for this type of feature Returns : an array Args : none Status : Internal This method is used internally to fetch the list of feature types that form the components of the composite feature. Type names in the format "method:source" are recognized, as are "method" and Bio::DB::GFF::Typename objects as well. It checks instance variables first, and if not defined calls the part_names() method. =cut sub get_part_names { my $self = shift; if ($self->{sub_parts}) { return ref $self->{sub_parts} ? @{$self->{sub_parts}} : $self->{sub_parts}; } else { return $self->part_names; } } =head2 get_main_name Title : get_main_name Usage : $string = $a->get_main_name Function: get the "main" method type for this feature Returns : a string Args : none Status : Internal This method is used internally to fetch the type of the "main part" of the feature. It checks instance variables first, and if not defined calls the main_name() method. =cut sub get_main_name { my $self = shift; return $self->{main_method} if defined $self->{main_method}; return $self->main_name; } =head2 get_method Title : get_method Usage : $string = $a->get_method Function: get the method type for the composite feature Returns : a string Args : none Status : Internal This method is used internally to fetch the type of the method that will be assigned to the composite feature once it is synthesized. =cut sub get_method { my $self = shift; return $self->{method} if defined $self->{method}; return $self->method; } 1; =head1 BUGS None known yet. =head1 SEE ALSO L, L, L, L, L, L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Featname.pm000444000766000024 551113155576320 17173 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Featname -- The name of a feature =head1 SYNOPSIS use Bio::DB::GFF; my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42'); my $feature = Bio::DB::GFF::Featname->new(Locus => 'unc-19'); my $segment = $db->segment($feature); =head1 DESCRIPTION Bio::DB::GFF::Featname is the name of a feature. It contains two fields: name and class. It is typically used by the Bio::DB::GFF module to denote a group, and is accepted by Bio::DB::Relsegment-Enew() and Bio::DB::GFF-Esegment() as a replacement for the -name and -class arguments. =head1 METHODS =cut package Bio::DB::GFF::Featname; use strict; use base qw(Bio::Root::RootI); use overload '""' => 'asString', fallback => 1; =head2 new Title : new Usage : $name = Bio::DB::GFF::Featname->new($class,$name) Function: create a new Bio::DB::GFF::Featname object Returns : a new Bio::DB::GFF::Featname object Args : class and ID Status : Public =cut sub new { # use a blessed array for speed my $pack = shift; bless [@_],$pack; # class,name } sub _cleanup_methods { return; } =head2 id Title : id Usage : $id = $name->id Function: return a unique ID for the combination of class and name Returns : a string Args : none Status : Public This method returns a unique combination of the name and class in the form "class:name". Coincidentally, this is the same format used by AceDB. =cut sub id { my $self = shift; return join ':',@$self; } =head2 name Title : name Usage : $name = $name->name Function: return the name of the Featname Returns : a string Args : none Status : Public =cut sub name { shift->[1] } =head2 class Title : class Usage : $class = $name->class Function: return the name of the Featname Returns : a string Args : none Status : Public =cut sub class { shift->[0] } =head2 asString Title : asString Usage : $string = $name->asString Function: same as name() Returns : a string Args : none Status : Public This method is used to overload the "" operator. It is equivalent to calling name(). =cut sub asString { shift->name } =head2 clone Title : clone Usage : $new_clone = $type->clone; Function: clone this object Returns : a new Bio::DB::GFF::Featname object Args : none Status : Public This method creates an exact copy of the object. =cut sub clone { my $self = shift; return bless [@$self],ref $self; } =head1 BUGS This module is still under development. =head1 SEE ALSO L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut 1; BioPerl-1.007002/Bio/DB/GFF/Feature.pm000444000766000024 10656513155576320 17121 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Feature -- A relative segment identified by a feature type =head1 SYNOPSIS See L. =head1 DESCRIPTION Bio::DB::GFF::Feature is a stretch of sequence that corresponding to a single annotation in a GFF database. It inherits from Bio::DB::GFF::RelSegment, and so has all the support for relative addressing of this class and its ancestors. It also inherits from Bio::SeqFeatureI and so has the familiar start(), stop(), primary_tag() and location() methods (it implements Bio::LocationI too, if needed). Bio::DB::GFF::Feature adds new methods to retrieve the annotation type, group, and other GFF attributes. Annotation types are represented by Bio::DB::GFF::Typename objects, a simple class that has two methods called method() and source(). These correspond to the method and source fields of a GFF file. Annotation groups serve the dual purpose of giving the annotation a human-readable name, and providing higher-order groupings of subfeatures into features. The groups returned by this module are objects of the Bio::DB::GFF::Featname class. Bio::DB::GFF::Feature inherits from and implements the abstract methods of Bio::SeqFeatureI, allowing it to interoperate with other Bioperl modules. Generally, you will not create or manipulate Bio::DB::GFF::Feature objects directly, but use those that are returned by the Bio::DB::GFF::RelSegment-Efeatures() method. =head2 Important note about start() vs end() If features are derived from segments that use relative addressing (which is the default), then start() will be less than end() if the feature is on the opposite strand from the reference sequence. This breaks Bio::SeqI compliance, but is necessary to avoid having the real genomic locations designated by start() and end() swap places when changing reference points. To avoid this behavior, call $segment-Eabsolute(1) before fetching features from it. This will force everything into absolute coordinates. For example: my $segment = $db->segment('CHROMOSOME_I'); $segment->absolute(1); my @features = $segment->features('transcript'); =head1 API The remainder of this document describes the public and private methods implemented by this module. =cut package Bio::DB::GFF::Feature; use strict; use Bio::DB::GFF::Util::Rearrange; use Bio::DB::GFF::Featname; use Bio::DB::GFF::Typename; use Bio::DB::GFF::Homol; use Bio::LocationI; use Data::Dumper; use vars qw($AUTOLOAD); use base qw(Bio::DB::GFF::RelSegment Bio::SeqFeatureI Bio::Root::Root); #' *segments = *get_SeqFeatures = \&sub_SeqFeature; my %CONSTANT_TAGS = (method=>1, source=>1, score=>1, phase=>1, notes=>1, id=>1, group=>1); =head2 new_from_parent Title : new_from_parent Usage : $f = Bio::DB::GFF::Feature->new_from_parent(@args); Function: create a new feature object Returns : new Bio::DB::GFF::Feature object Args : see below Status : Internal This method is called by Bio::DB::GFF to create a new feature using information obtained from the GFF database. It is one of two similar constructors. This one is called when the feature is generated from a RelSegment object, and should inherit the coordinate system of that object. The 13 arguments are positional (sorry): $parent a Bio::DB::GFF::RelSegment object (or descendent) $start start of this feature $stop stop of this feature $method this feature's GFF method $source this feature's GFF source $score this feature's score $fstrand this feature's strand (relative to the source sequence, which has its own strandedness!) $phase this feature's phase $group this feature's group (a Bio::DB::GFF::Featname object) $db_id this feature's internal database ID $group_id this feature's internal group database ID $tstart this feature's target start $tstop this feature's target stop tstart and tstop are not used for anything at the moment, since the information is embedded in the group object. =cut # this is called for a feature that is attached to a parent sequence, # in which case it inherits its coordinate reference system and strandedness sub new_from_parent { my $package = shift; my ($parent, $start,$stop, $method,$source,$score, $fstrand,$phase, $group,$db_id,$group_id, $tstart,$tstop) = @_; ($start,$stop) = ($stop,$start) if defined($fstrand) and $fstrand eq '-'; my $class = $group ? $group->class : $parent->class; my $self = bless { factory => $parent->{factory}, sourceseq => $parent->{sourceseq}, strand => $parent->{strand}, ref => $parent->{ref}, refstart => $parent->{refstart}, refstrand => $parent->{refstrand}, absolute => $parent->{absolute}, start => $start, stop => $stop, type => Bio::DB::GFF::Typename->new($method,$source), fstrand => $fstrand, score => $score, phase => $phase, group => $group, db_id => $db_id, group_id => $group_id, class => $class, },$package; $self; } =head2 new Title : new Usage : $f = Bio::DB::GFF::Feature->new(@args); Function: create a new feature object Returns : new Bio::DB::GFF::Feature object Args : see below Status : Internal This method is called by Bio::DB::GFF to create a new feature using information obtained from the GFF database. It is one of two similar constructors. This one is called when the feature is generated without reference to a RelSegment object, and should therefore use its default coordinate system (relative to itself). The 11 arguments are positional: $factory a Bio::DB::GFF adaptor object (or descendent) $srcseq the source sequence $start start of this feature $stop stop of this feature $method this feature's GFF method $source this feature's GFF source $score this feature's score $fstrand this feature's strand (relative to the source sequence, which has its own strandedness!) $phase this feature's phase $group this feature's group $db_id this feature's internal database ID =cut # 'This is called when creating a feature from scratch. It does not have # an inherited coordinate system. sub new { my $package = shift; my ($factory, $srcseq, $start,$stop, $method,$source, $score,$fstrand,$phase, $group,$db_id,$group_id, $tstart,$tstop) = @_; my $self = bless { },$package; ($start,$stop) = ($stop,$start) if defined($fstrand) and $fstrand eq '-'; my $class = $group ? $group->class : 'Sequence'; @{$self}{qw(factory sourceseq start stop strand class)} = ($factory,$srcseq,$start,$stop,$fstrand,$class); # if the target start and stop are defined, then we use this information to create # the reference sequence # THIS SHOULD BE BUILT INTO RELSEGMENT if (0 && $tstart ne '' && $tstop ne '') { if ($tstart < $tstop) { @{$self}{qw(ref refstart refstrand)} = ($group,$start - $tstart + 1,'+'); } else { @{$self}{'start','stop'} = @{$self}{'stop','start'}; @{$self}{qw(ref refstart refstrand)} = ($group,$tstop + $stop - 1,'-'); } } else { @{$self}{qw(ref refstart refstrand)} = ($srcseq,1,'+'); } @{$self}{qw(type fstrand score phase group db_id group_id absolute)} = (Bio::DB::GFF::Typename->new($method,$source),$fstrand,$score,$phase, $group,$db_id,$group_id,$factory->{absolute}); $self; } =head2 type Title : type Usage : $type = $f->type([$newtype]) Function: get or set the feature type Returns : a Bio::DB::GFF::Typename object Args : a new Typename object (optional) Status : Public This method gets or sets the type of the feature. The type is a Bio::DB::GFF::Typename object, which encapsulates the feature method and source. The method() and source() methods described next provide shortcuts to the individual fields of the type. =cut sub type { my $self = shift; my $d = $self->{type}; $self->{type} = shift if @_; $d; } =head2 method Title : method Usage : $method = $f->method([$newmethod]) Function: get or set the feature method Returns : a string Args : a new method (optional) Status : Public This method gets or sets the feature method. It is a convenience feature that delegates the task to the feature's type object. =cut sub method { my $self = shift; my $d = $self->{type}->method; $self->{type}->method(shift) if @_; $d; } =head2 source Title : source Usage : $source = $f->source([$newsource]) Function: get or set the feature source Returns : a string Args : a new source (optional) Status : Public This method gets or sets the feature source. It is a convenience feature that delegates the task to the feature's type object. =cut sub source { my $self = shift; my $d = $self->{type}->source; $self->{type}->source(shift) if @_; $d; } =head2 score Title : score Usage : $score = $f->score([$newscore]) Function: get or set the feature score Returns : a string Args : a new score (optional) Status : Public This method gets or sets the feature score. =cut sub score { my $self = shift; my $d = $self->{score}; $self->{score} = shift if @_; $d; } =head2 phase Title : phase Usage : $phase = $f->phase([$phase]) Function: get or set the feature phase Returns : a string Args : a new phase (optional) Status : Public This method gets or sets the feature phase. =cut sub phase { my $self = shift; my $d = $self->{phase}; $self->{phase} = shift if @_; $d; } =head2 strand Title : strand Usage : $strand = $f->strand Function: get the feature strand Returns : +1, 0 -1 Args : none Status : Public Returns the strand of the feature. Unlike the other methods, the strand cannot be changed once the object is created (due to coordinate considerations). =cut sub strand { my $self = shift; return 0 unless $self->{fstrand}; if ($self->absolute) { return Bio::DB::GFF::RelSegment::_to_strand($self->{fstrand}); } return $self->SUPER::strand || Bio::DB::GFF::RelSegment::_to_strand($self->{fstrand}); } =head2 group Title : group Usage : $group = $f->group([$new_group]) Function: get or set the feature group Returns : a Bio::DB::GFF::Featname object Args : a new group (optional) Status : Public This method gets or sets the feature group. The group is a Bio::DB::GFF::Featname object, which has an ID and a class. =cut sub group { my $self = shift; my $d = $self->{group}; $self->{group} = shift if @_; $d; } =head2 display_id Title : display_id Usage : $display_id = $f->display_id([$display_id]) Function: get or set the feature display id Returns : a Bio::DB::GFF::Featname object Args : a new display_id (optional) Status : Public This method is an alias for group(). It is provided for Bio::SeqFeatureI compatibility. =cut =head2 info Title : info Usage : $info = $f->info([$new_info]) Function: get or set the feature group Returns : a Bio::DB::GFF::Featname object Args : a new group (optional) Status : Public This method is an alias for group(). It is provided for AcePerl compatibility. =cut *info = \&group; *display_id = \&group; *display_name = \&group; =head2 target Title : target Usage : $target = $f->target([$new_target]) Function: get or set the feature target Returns : a Bio::DB::GFF::Homol object Args : a new group (optional) Status : Public This method works like group(), but only returns the group if it implements the start() method. This is typical for similarity/assembly features, where the target encodes the start and stop location of the alignment. The returned object is of type Bio::DB::GFF::Homol, which is a subclass of Bio::DB::GFF::Segment. =cut sub target { my $self = shift; my $group = $self->group or return; return unless $group->can('start'); $group; } =head2 flatten_target Title : flatten_target Usage : $target = $f->flatten_target($f->target) Function: flatten a target object Returns : a string (GFF2), an array [GFF2.5] or an array ref [GFF3] Args : a target object (required), GFF version (optional) Status : Public This method flattens a target object into text for GFF dumping. If a second argument is provided, version-specific vocabulary is used for the flattened target. =cut sub flatten_target { my $self = shift; my $t = shift || return; my $v = shift; return 0 unless $t->can('start'); my $class = $t->class; my $name = $t->name; my $start = $t->start; my $stop = $t->stop; $v ||=2; if ( $v == 2.5 ) { print STDERR qq(Target "$class:$name"), "tstart $start", "tstop $stop\n"; return (qq(Target "$class:$name"), "tstart $start", "tstop $stop"); } elsif ( $v == 3 ) { return [Target=>"$name $start $stop"]; } else { return qq(Target "$class:$name" $start $stop); } } # override parent a smidgeon so that setting the ref for top-level feature # sets ref for all subfeatures sub refseq { my $self = shift; my $result = $self->SUPER::refseq(@_); if (@_) { my $newref = $self->SUPER::refseq; for my $sub ($self->get_SeqFeatures) { $sub->refseq(@_); } } $result; } =head2 hit Title : hit Usage : $hit = $f->hit([$new_hit]) Function: get or set the feature hit Returns : a Bio::DB::GFF::Featname object Args : a new group (optional) Status : Public This is the same as target(), for compatibility with Bio::SeqFeature::SimilarityPair. =cut *hit = \⌖ =head2 id Title : id Usage : $id = $f->id Function: get the feature ID Returns : a database identifier Args : none Status : Public This method retrieves the database identifier for the feature. It cannot be changed. =cut sub id { shift->{db_id} } sub primary_id { shift->{db_id} } =head2 group_id Title : group_id Usage : $id = $f->group_id Function: get the feature ID Returns : a database identifier Args : none Status : Public This method retrieves the database group identifier for the feature. It cannot be changed. Often the group identifier is more useful than the feature identifier, since it is used to refer to a complex object containing subparts. =cut sub group_id { shift->{group_id} } =head2 clone Title : clone Usage : $feature = $f->clone Function: make a copy of the feature Returns : a new Bio::DB::GFF::Feature object Args : none Status : Public This method returns a copy of the feature. =cut sub clone { my $self = shift; my $clone = $self->SUPER::clone; if (ref(my $t = $clone->type)) { my $type = $t->can('clone') ? $t->clone : bless {%$t},ref $t; $clone->type($type); } if (ref(my $g = $clone->group)) { my $group = $g->can('clone') ? $g->clone : bless {%$g},ref $g; $clone->group($group); } if (my $merged = $self->{merged_segs}) { $clone->{merged_segs} = { %$merged }; } $clone; } =head2 compound Title : compound Usage : $flag = $f->compound([$newflag]) Function: get or set the compound flag Returns : a boolean Args : a new flag (optional) Status : Public This method gets or sets a flag indicated that the feature is not a primary one from the database, but the result of aggregation. =cut sub compound { my $self = shift; my $d = $self->{compound}; $self->{compound} = shift if @_; $d; } =head2 sub_SeqFeature Title : sub_SeqFeature Usage : @feat = $feature->sub_SeqFeature([$method]) Function: get subfeatures Returns : a list of Bio::DB::GFF::Feature objects Args : a feature method (optional) Status : Public This method returns a list of any subfeatures that belong to the main feature. For those features that contain heterogeneous subfeatures, you can retrieve a subset of the subfeatures by providing a method name to filter on. This method may also be called as segments() or get_SeqFeatures(). =cut sub sub_SeqFeature { my $self = shift; my $type = shift; my $subfeat = $self->{subfeatures} or return; $self->sort_features; my @a; if ($type) { my $features = $subfeat->{lc $type} or return; @a = @{$features}; } else { @a = map {@{$_}} values %{$subfeat}; } return @a; } =head2 add_subfeature Title : add_subfeature Usage : $feature->add_subfeature($feature) Function: add a subfeature to the feature Returns : nothing Args : a Bio::DB::GFF::Feature object Status : Public This method adds a new subfeature to the object. It is used internally by aggregators, but is available for public use as well. =cut sub add_subfeature { my $self = shift; my $feature = shift; my $type = $feature->method; my $subfeat = $self->{subfeatures}{lc $type} ||= []; push @{$subfeat},$feature; } =head2 attach_seq Title : attach_seq Usage : $sf->attach_seq($seq) Function: Attaches a Bio::Seq object to this feature. This Bio::Seq object is for the *entire* sequence: ie from 1 to 10000 Example : Returns : TRUE on success Args : a Bio::PrimarySeqI compliant object =cut sub attach_seq { } =head2 location Title : location Usage : my $location = $seqfeature->location() Function: returns a location object suitable for identifying location of feature on sequence or parent feature Returns : Bio::LocationI object Args : none =cut sub location { my $self = shift; require Bio::Location::Split unless Bio::Location::Split->can('new'); require Bio::Location::Simple unless Bio::Location::Simple->can('new'); my $location; if (my @segments = $self->segments) { $location = Bio::Location::Split->new(-seq_id => $self->seq_id); foreach (@segments) { $location->add_sub_Location($_->location); } } else { $location = Bio::Location::Simple->new(-start => $self->start, -end => $self->stop, -strand => $self->strand, -seq_id => $self->seq_id); } $location; } =head2 entire_seq Title : entire_seq Usage : $whole_seq = $sf->entire_seq() Function: gives the entire sequence that this seqfeature is attached to Example : Returns : a Bio::PrimarySeqI compliant object, or undef if there is no sequence attached Args : none =cut sub entire_seq { my $self = shift; $self->factory->segment($self->sourceseq); } =head2 merged_segments Title : merged_segments Usage : @segs = $feature->merged_segments([$method]) Function: get merged subfeatures Returns : a list of Bio::DB::GFF::Feature objects Args : a feature method (optional) Status : Public This method acts like sub_SeqFeature, except that it merges overlapping segments of the same time into contiguous features. For those features that contain heterogeneous subfeatures, you can retrieve a subset of the subfeatures by providing a method name to filter on. A side-effect of this method is that the features are returned in sorted order by their start tposition. =cut #' sub merged_segments { my $self = shift; my $type = shift; $type ||= ''; # prevent uninitialized variable warnings my $truename = overload::StrVal($self); return @{$self->{merged_segs}{$type}} if exists $self->{merged_segs}{$type}; my @segs = map { $_->[0] } sort { $a->[1] <=> $b->[1] || $a->[2] cmp $b->[2] } map { [$_, $_->start, $_->type] } $self->sub_SeqFeature($type); # attempt to merge overlapping segments my @merged = (); for my $s (@segs) { my $previous = $merged[-1] if @merged; my ($pscore,$score) = (eval{$previous->score}||0,eval{$s->score}||0); if (defined($previous) && $previous->stop+1 >= $s->start && $pscore == $score && $previous->method eq $s->method ) { if ($self->absolute && $self->strand < 0) { $previous->{start} = $s->{start}; } else { $previous->{stop} = $s->{stop}; } # fix up the target too my $g = $previous->{group}; if ( ref($g) && $g->isa('Bio::DB::GFF::Homol')) { my $cg = $s->{group}; $g->{stop} = $cg->{stop}; } } elsif (defined($previous) && $previous->start == $s->start && $previous->stop == $s->stop && $previous->method eq $s->method ) { next; } else { my $copy = $s->clone; push @merged,$copy; } } $self->{merged_segs}{$type} = \@merged; @merged; } =head2 sub_types Title : sub_types Usage : @methods = $feature->sub_types Function: get methods of all sub-seqfeatures Returns : a list of method names Args : none Status : Public For those features that contain subfeatures, this method will return a unique list of method names of those subfeatures, suitable for use with sub_SeqFeature(). =cut sub sub_types { my $self = shift; my $subfeat = $self->{subfeatures} or return; return keys %$subfeat; } =head2 attributes Title : attributes Usage : @attributes = $feature->attributes($name) Function: get the "attributes" on a particular feature Returns : an array of string Args : feature ID Status : public Some GFF version 2 files use the groups column to store a series of attribute/value pairs. In this interpretation of GFF, the first such pair is treated as the primary group for the feature; subsequent pairs are treated as attributes. Two attributes have special meaning: "Note" is for backward compatibility and is used for unstructured text remarks. "Alias" is considered as a synonym for the feature name. @gene_names = $feature->attributes('Gene'); @aliases = $feature->attributes('Alias'); If no name is provided, then attributes() returns a flattened hash, of attribute=Evalue pairs. This lets you do: %attributes = $db->attributes; =cut sub attributes { my $self = shift; my $factory = $self->factory; defined(my $id = $self->id) or return; $factory->attributes($id,@_) } =head2 notes Title : notes Usage : @notes = $feature->notes Function: get the "notes" on a particular feature Returns : an array of string Args : feature ID Status : public Some GFF version 2 files use the groups column to store various notes and remarks. Adaptors can elect to store the notes in the database, or just ignore them. For those adaptors that store the notes, the notes() method will return them as a list. =cut sub notes { my $self = shift; $self->attributes('Note'); } =head2 aliases Title : aliases Usage : @aliases = $feature->aliases Function: get the "aliases" on a particular feature Returns : an array of string Args : feature ID Status : public This method will return a list of attributes of type 'Alias'. =cut sub aliases { my $self = shift; $self->attributes('Alias'); } =head2 Autogenerated Methods Title : AUTOLOAD Usage : @subfeat = $feature->Method Function: Return subfeatures using autogenerated methods Returns : a list of Bio::DB::GFF::Feature objects Args : none Status : Public Any method that begins with an initial capital letter will be passed to AUTOLOAD and treated as a call to sub_SeqFeature with the method name used as the method argument. For instance, this call: @exons = $feature->Exon; is equivalent to this call: @exons = $feature->sub_SeqFeature('exon'); =cut =head2 SeqFeatureI methods The following Bio::SeqFeatureI methods are implemented: primary_tag(), source_tag(), all_tags(), has_tag(), each_tag_value() [renamed get_tag_values()]. =cut *primary_tag = \&method; *source_tag = \&source; sub all_tags { my $self = shift; my %atts = $self->attributes; my @tags = keys %atts; # autogenerated methods #if (my $subfeat = $self->{subfeatures}) { # push @tags,keys %$subfeat; #} @tags; } *get_all_tags = \&all_tags; sub has_tag { my $self = shift; my $tag = shift; my %att = $self->attributes; my %tags = map {$_=>1} ( $self->all_tags ); return $tags{$tag}; } *each_tag_value = \&get_tag_values; sub get_tag_values { my $self = shift; my $tag = shift; return $self->$tag() if $CONSTANT_TAGS{$tag}; my $atts = $self->attributes; return @{$atts->{$tag}} if $atts && $atts->{$tag}; $tag = ucfirst $tag; return $self->$tag(); # try autogenerated tag } sub AUTOLOAD { my($pack,$func_name) = $AUTOLOAD=~/(.+)::([^:]+)$/; my $sub = $AUTOLOAD; my $self = $_[0]; # ignore DESTROY calls return if $func_name eq 'DESTROY'; # fetch subfeatures if func_name has an initial cap # return sort {$a->start <=> $b->start} $self->sub_SeqFeature($func_name) if $func_name =~ /^[A-Z]/; return $self->sub_SeqFeature($func_name) if $func_name =~ /^[A-Z]/; # error message of last resort $self->throw(qq(Can't locate object method "$func_name" via package "$pack")); }#' =head2 adjust_bounds Title : adjust_bounds Usage : $feature->adjust_bounds Function: adjust the bounds of a feature Returns : ($start,$stop,$strand) Args : none Status : Public This method adjusts the boundaries of the feature to enclose all its subfeatures. It returns the new start, stop and strand of the enclosing feature. =cut # adjust a feature so that its boundaries are synched with its subparts' boundaries. # this works recursively, so subfeatures can contain other features sub adjust_bounds { my $self = shift; my $shrink = shift; my $g = $self->{group}; my $first = 0; my $tfirst = 0; if (my $subfeat = $self->{subfeatures}) { for my $list (values %$subfeat) { for my $feat (@$list) { # fix up our bounds to hold largest subfeature my($start,$stop,$strand) = $feat->adjust_bounds($shrink); if (defined($self->{fstrand})) { $self->debug("Subfeature's strand ($strand) doesn't match parent strand ($self->{fstrand})\n") if $self->{fstrand} ne $strand; } else { $self->{fstrand} = $strand; } my ($low,$high) = $start < $stop ? ($start,$stop) : ($stop,$start); if ($shrink && !$first++) { # first subfeature resets start & stop: $self->{start} = $self->{fstrand} ne '-' ? $low : $high; $self->{stop} = $self->{fstrand} ne '-' ? $high : $low; } else { if ($self->{fstrand} ne '-') { $self->{start} = $low if (!defined($self->{start})) || $low < $self->{start}; $self->{stop} = $high if (!defined($self->{stop})) || $high > $self->{stop}; } else { $self->{start} = $high if (!defined($self->{start})) || $high > $self->{start}; $self->{stop} = $low if (!defined($self->{stop})) || $low < $self->{stop}; } } # fix up endpoints of targets too (for homologies only) my $h = $feat->group; next unless $h && $h->isa('Bio::DB::GFF::Homol'); next unless $g && $g->isa('Bio::DB::GFF::Homol'); ($start,$stop) = ($h->{start},$h->{stop}); if ($shrink && !$tfirst++) { $g->{start} = $start; $g->{stop} = $stop; } else { if ($start <= $stop) { $g->{start} = $start if (!defined($g->{start})) || $start < $g->{start}; $g->{stop} = $stop if (!defined($g->{stop})) || $stop > $g->{stop}; } else { $g->{start} = $start if (!defined($g->{start})) || $start > $g->{start}; $g->{stop} = $stop if (!defined($g->{stop})) || $stop < $g->{stop}; } } } } } ($self->{start},$self->{stop},$self->strand); } =head2 sort_features Title : sort_features Usage : $feature->sort_features Function: sort features Returns : nothing Args : none Status : Public This method sorts subfeatures in ascending order by their start position. For reverse strand features, it sorts subfeatures in descending order. After this is called sub_SeqFeature will return the features in order. This method is called internally by merged_segments(). =cut # sort features sub sort_features { my $self = shift; return if $self->{sorted}++; my $strand = $self->strand or return; my $subfeat = $self->{subfeatures} or return; for my $type (keys %$subfeat) { $subfeat->{$type} = [map { $_->[0] } sort {$a->[1] <=> $b->[1] } map { [$_,$_->start] } @{$subfeat->{$type}}] if $strand > 0; $subfeat->{$type} = [map { $_->[0] } sort {$b->[1] <=> $a->[1]} map { [$_,$_->start] } @{$subfeat->{$type}}] if $strand < 0; } } =head2 asString Title : asString Usage : $string = $feature->asString Function: return human-readabled representation of feature Returns : a string Args : none Status : Public This method returns a human-readable representation of the feature and is called by the overloaded "" operator. =cut sub asString { my $self = shift; my $type = $self->type; my $name = $self->group; return "$type($name)" if $name; return $type; # my $type = $self->method; # my $id = $self->group || 'unidentified'; # return join '/',$id,$type,$self->SUPER::asString; } sub name { my $self =shift; return $self->group || $self->SUPER::name; } =head2 gff_string Title : gff_string Usage : $string = $feature->gff_string Function: return GFF2 of GFF2.5 representation of feature Returns : a string Args : none Status : Public =cut sub gff_string { my $self = shift; my $version = $self->version; # gff3_string and gff_string are synonymous if the version is set to 3 return $self->gff3_string(@_) if $version == 3; my ($start,$stop) = ($self->start,$self->stop); # the defined() tests prevent uninitialized variable warnings, when dealing with clone objects # whose endpoints may be undefined ($start,$stop) = ($stop,$start) if defined($start) && defined($stop) && $start > $stop; my ($class,$name) = ('',''); my $strand = ('-','.','+')[$self->strand+1]; my @group; if (my $t = $self->target) { push @group, $version == 2.5 ? $self->flatten_target($t,2.5) : $self->flatten_target($t); } elsif (my $g = $self->group) { $class = $g->class || ''; $name = $g->name || ''; ($name =~ /\S\s\S/)?(push @group, "$class '$name'"):(push @group,"$class $name"); } # add exhaustive list of attributes my $att = $self->attributes; for ( keys %$att ) { for my $v ( @{$att->{$_}} ) { $v = qq("$v") if $v=~ /\S\s+\S/; push @group, qq($_ $v); } } my $group_field = join ' ; ',@group; my $ref = $self->refseq; my $n = ref($ref) ? $ref->name : $ref; my $phase = $self->phase; $phase = '.' unless defined $phase; return join("\t", $n, $self->source,$self->method, (defined $start ? $start : '.'), (defined $stop ? $stop : '.'), (defined $self->score ? $self->score : '.'), (defined $strand ? $strand : '.'), $phase, $group_field); } =head2 gff3_string Title : gff3_string Usage : $string = $feature->gff3_string([$recurse]) Function: return GFF3 representation of feature Returns : a string Args : An optional flag, which if true, will cause the feature to recurse over subfeatures. Status : Public =cut sub gff3_string { my $self = shift; my ($recurse,$parent) = @_; my ($start,$stop) = ($self->start,$self->stop); # the defined() tests prevent uninitialized variable warnings, when dealing with clone objects # whose endpoints may be undefined ($start,$stop) = ($stop,$start) if defined($start) && defined($stop) && $start > $stop; my $strand = ('-','.','+')[$self->strand+1]; my $ref = $self->refseq; my $n = ref($ref) ? $ref->name : $ref; my $phase = $self->phase; $phase = '.' unless defined $phase; my ($class,$name) = ('',''); my @group; if (my $g = $self->group) { $class = $g->class || ''; $name = $g->name || ''; $name = "$class:$name" if defined $class; push @group,[ID => $name] if !defined($parent) || $name ne $parent; } push @group,[Parent => $parent] if defined $parent && $parent ne ''; if (my $t = $self->target) { $strand = '-' if $t->stop < $t->start; push @group, $self->flatten_target($t,3); } my @attributes = $self->attributes; while (@attributes) { push @group,[shift(@attributes),shift(@attributes)] } my $group_field = join ';',map {join '=',_escape($_->[0]),_escape($_->[1])} @group; my $string = join("\t",$n,$self->source,$self->method,$start||'.',$stop||'.', $self->score||'.',$strand||'.',$phase,$group_field); $string .= "\n"; if ($recurse) { foreach ($self->sub_SeqFeature) { $string .= $_->gff3_string(1,$name); } } $string; } =head2 version Title : version Usage : $feature->version() Function: get/set the GFF version to be returned by gff_string Returns : the GFF version (default is 2) Args : the GFF version (2, 2.5 of 3) Status : Public =cut sub version { my ($self, $version) = @_; $self->{version} = $version if $version; return $self->{version} || 2; } sub _escape { my $toencode = shift; $toencode =~ s/([^a-zA-Z0-9_. :?^*\(\)\[\]@!-])/uc sprintf("%%%02x",ord($1))/eg; $toencode =~ tr/ /+/; $toencode; } =head2 cmap_link() Title : cmap_link Usage : $link = $feature->cmap_link Function: returns a URL link to the corresponding feature in cmap Returns : a string Args : none Status : Public If integrated cmap/gbrowse installation, it returns a link to the map otherwise it returns a link to a feature search on the feature name. See the cmap documentation for more information. This function is intended primarily to be used in gbrowse conf files. For example: link = sub {my $self = shift; return $self->cmap_viewer_link(data_source);} =cut sub cmap_viewer_link { # Use ONLY if CMap is installed my $self = shift; my $data_source = shift; my $group_id = $self->group_id; my $factory = $self->factory; # aka adaptor my $link_str; if ($factory->can("create_cmap_viewer_link")){ $link_str = $factory->create_cmap_viewer_link( data_source => $data_source, group_id => $group_id, ); } my $name = $self->name(); $link_str = '/cgi-bin/cmap/feature_search?features=' . $name . '&search_field=feature_name&order_by=&data_source=' . $data_source . '&submit=Submit' unless $link_str; return $link_str; } =head1 A Note About Similarities The current default aggregator for GFF "similarity" features creates a composite Bio::DB::GFF::Feature object of type "gapped_alignment". The target() method for the feature as a whole will return a RelSegment object that is as long as the extremes of the similarity hit target, but will not necessarily be the same length as the query sequence. The length of each "similarity" subfeature will be exactly the same length as its target(). These subfeatures are essentially the HSPs of the match. The following illustrates this: @similarities = $segment->feature('similarity:BLASTN'); $sim = $similarities[0]; print $sim->type; # yields "gapped_similarity:BLASTN" $query_length = $sim->length; $target_length = $sim->target->length; # $query_length != $target_length @matches = $sim->Similarity; # use autogenerated method $query1_length = $matches[0]->length; $target1_length = $matches[0]->target->length; # $query1_length == $target1_length If you merge segments by calling merged_segments(), then the length of the query sequence segments will no longer necessarily equal the length of the targets, because the alignment information will have been lost. Nevertheless, the targets are adjusted so that the first and last base pairs of the query match the first and last base pairs of the target. =cut 1; =head1 BUGS This module is still under development. =head1 SEE ALSO L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Homol.pm000444000766000024 357413155576320 16540 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Homol -- A segment of DNA that is homologous to another =head1 SYNOPSIS See L. =head1 DESCRIPTION Bio::DB::GFF::Homol is a named subtype of Bio::DB::GFF::Segment. It inherits all the methods of its parent, and was created primarily to allow for isa() queries and for compatibility with Ace::Sequence::Homol. A Homol object is typically returned as the method result of the Bio::DB::GFF::Feature-Etarget() method. =head1 METHODS =cut package Bio::DB::GFF::Homol; use strict; use base qw(Bio::DB::GFF::Segment); =head2 name Title : name Usage : $name = $homol->name Function: get the ID of the homology object Returns : a string Args : none Status : Public =cut sub name { shift->refseq } =head2 asString Title : asString Usage : $name = $homol->asString Function: same as name(), for operator overloading Returns : a string Args : none Status : Public =cut sub asString { shift->name } =head2 id Title : id Usage : $id = $homol->id Function: get database ID in class:id format Returns : a string Args : none Status : Public =cut sub id { my $self = shift; return "$self->{class}:$self->{name}"; } sub new_from_segment { my $package = shift; $package = ref $package if ref $package; my $segment = shift; my $new = {}; @{$new}{qw(factory sourceseq start stop strand class ref refstart refstrand)} = @{$segment}{qw(factory sourceseq start stop strand class ref refstart refstrand)}; return bless $new,__PACKAGE__; } =head1 BUGS This module is still under development. =head1 SEE ALSO L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut 1; BioPerl-1.007002/Bio/DB/GFF/RelSegment.pm000444000766000024 10344513155576320 17565 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::RelSegment -- Sequence segment with relative coordinate support =head1 SYNOPSIS See L. =head1 DESCRIPTION Bio::DB::GFF::RelSegment is a stretch of sequence that can handle relative coordinate addressing. It inherits from Bio::DB::GFF::Segment, and is the base class for Bio::DB::GFF::Feature. In addition to the source sequence, a relative segment has a "reference sequence", which is used as the basis for its coordinate system. The reference sequence can be changed at will, allowing you freedom to change the "frame of reference" for features contained within the segment. For example, by setting a segment's reference sequence to the beginning of a gene, you can view all other features in gene-relative coordinates. The reference sequence and the source sequence must be on the same physical stretch of DNA, naturally. However, they do not have to be on the same strand. The strandedness of the reference sequence determines whether coordinates increase to the right or the left. Generally, you will not create or manipulate Bio::DB::GFF::RelSeg0ment objects directly, but use those that are returned by the Bio::DB::GFF module. =head2 An Example To understand how relative coordinates work, consider the following example from the C. elegans database. First we create the appropriate GFF accessor object (the factory): my $db = Bio::DB::GFF->new(-dsn => 'dbi:mysql:elegans', -adaptor=>'dbi:mysqlopt'); Now we fetch out a segment based on cosmid clone ZK909: my $seg = $db->segment('ZK909'); If we call the segment's refseq() method, we see that the base of the coordinate system is the sequence "ZK154", and that its start and stop positions are 1 and the length of the cosmid: print $seg->refseq; => ZK909 print $seg->start,' - ',$seg->stop; => 1 - 33782 As a convenience, the "" operator is overloaded in this class, to give the reference sequence, and start and stop positions: print $seg; => ZK909:1,33782 Internally, Bio::DB::GFF::RelSegment has looked up the absolute coordinates of this segment and maintains the source sequence and the absolute coordinates relative to the source sequence. We can see this information using sourceseq() (inherited from Bio::DB::GFF::Segment) and the abs_start() and abs_end() methods: print $seg->sourceseq; => CHROMOSOME_I print $seg->abs_start,' - ',$seg->abs_end; => 14839545 - 14873326 We can also put the segment into absolute mode, so that it behaves like Bio::DB::Segment, and always represents coordinates on the source sequence. This is done by passing a true value to the absolute() method: $seq->absolute(1); print $seg; => CHROMOSOME_I:14839545,14873326 We can change the reference sequence at any time. One way is to call the segment's ref() method, giving it the ID (and optionally the class) of another landmark on the genome. For example, if we know that cosmid ZK337 is adjacent to ZK909, then we can view ZK909 in ZK337-relative coordinates: $seg->refseq('ZK337'); print $seg; => ZK337:-33670,111 We can call the segment's features() method in order to get the list of contigs that overlap this segment (in the C. elegans database, contigs have feature type "Sequence:Link"): @links = $seg->features('Sequence:Link'); We can now set the reference sequence to the first of these contigs like so: $seg->refseq($links[0]); print $seg; => Sequence:Link(LINK_Y95D11A):3997326,4031107 =cut package Bio::DB::GFF::RelSegment; use strict; use Bio::DB::GFF::Feature; use Bio::DB::GFF::Util::Rearrange; use Bio::RangeI; use base qw(Bio::DB::GFF::Segment); use overload '""' => 'asString', 'bool' => sub { overload::StrVal(shift) }, fallback=>1; =head1 API The remainder of this document describes the API for Bio::DB::GFF::Segment. =cut =head2 new Title : new Usage : $s = Bio::DB::GFF::RelSegment->new(@args) Function: create a new relative segment Returns : a new Bio::DB::GFF::RelSegment object Args : see below Status : Public This method creates a new Bio::DB::GFF::RelSegment object. Generally this is called automatically by the Bio::DB::GFF module and derivatives. This function uses a named-argument style: -factory a Bio::DB::GFF::Adaptor to use for database access -seq ID of the source sequence -class class of the source sequence -start start of the desired segment relative to source sequence -stop stop of the desired segment relative to source sequence -ref ID of the reference sequence -refclass class of the reference sequence -offset 0-based offset from source sequence to start of segment -length length of desired segment -absolute, -force_absolute use absolute coordinates, rather than coordinates relative to the start of self or the reference sequence The -seq argument accepts the ID of any landmark in the database. The stored source sequence becomes whatever the GFF file indicates is the proper sequence for this landmark. A class of "Sequence" is assumed unless otherwise specified in the -class argument. If the argument to -seq is a Bio::GFF::Featname object (such as returned by the group() method), then the class is taken from that. The optional -start and -stop arguments specify the end points for the retrieved segment. For those who do not like 1-based indexing, -offset and -length are provided. If both -start/-stop and -offset/-length are provided, the latter overrides the former. Generally it is not a good idea to mix metaphors. -ref and -refclass together indicate a sequence to be used for relative coordinates. If not provided, the source sequence indicated by -seq is used as the reference sequence. If the argument to -ref is a Bio::GFF::Featname object (such as returned by the group() method), then the class is taken from that. -force_absolute should be used if you wish to skip the lookup of the absolute position of the source sequence that ordinarily occurs when you create a relative segment. In this case, the source sequence must be a sequence that has been specified as the "source" in the GFF file. =cut # Create a new Bio::DB::GFF::RelSegment Object # arguments are: # -factory => factory and DBI interface # -seq => $sequence_name # -start => $start_relative_to_sequence # -stop => $stop_relative_to_sequence # -ref => $sequence which establishes coordinate system # -offset => 0-based offset relative to sequence # -length => length of segment # -nocheck => turn off checking, force segment to be constructed # -absolute => use absolute coordinate addressing sub new { my $package = shift; my ($factory,$name,$start,$stop,$refseq,$class,$refclass,$offset,$length,$force_absolute,$nocheck) = rearrange([ 'FACTORY', [qw(NAME SEQ SEQUENCE SOURCESEQ)], [qw(START BEGIN)], [qw(STOP END)], [qw(REFSEQ REF REFNAME)], [qw(CLASS SEQCLASS)], qw(REFCLASS), [qw(OFFSET OFF)], [qw(LENGTH LEN)], [qw(ABSOLUTE)], [qw(NOCHECK FORCE)], ],@_); $package = ref $package if ref $package; $factory or $package->throw("new(): provide a -factory argument"); # to allow people to use segments as sources if (ref($name) && $name->isa('Bio::DB::GFF::Segment')) { $start = 1 unless defined $start; $stop = $name->length unless defined $stop; return $name->subseq($start,$stop); } my @object_results; # support for Featname objects if (ref($name) && $name->can('class')) { $class = $name->class; $name = $name->name; } # if the class of the landmark is not specified then default to 'Sequence' $class ||= eval{$factory->default_class} || 'Sequence'; # confirm that indicated sequence is actually in the database! my @abscoords; # abscoords() will now return an array ref, each element of which is # ($absref,$absclass,$absstart,$absstop,$absstrand) if ($nocheck) { $force_absolute++; $start = 1; } # if ($force_absolute && defined($start)) { # absolute position is given to us # @abscoords = ([$name,$class,$start,$stop,'+']); # } else { my $result = $factory->abscoords($name,$class,$force_absolute ? $name : ()) or return; @abscoords = @$result; # } foreach (@abscoords) { my ($absref,$absclass,$absstart,$absstop,$absstrand,$sname) = @$_; $sname = $name unless defined $sname; my ($this_start,$this_stop,$this_length) = ($start,$stop,$length); # partially fill in object my $self = bless { factory => $factory },$package; $absstrand ||= '+'; if ($absstart > $absstop) { # AAARGH! DATA FORMAT ERROR! FIX. ($absstart,$absstop) = ($absstop,$absstart); $absstrand = $absstrand eq '+' ? '-' : '+'; } # an explicit length overrides start and stop if (defined $offset) { warn "new(): bad idea to call new() with both a start and an offset" if defined $this_start; $this_start = $offset+1; } if (defined $this_length) { warn "new(): bad idea to call new() with both a stop and a length" if defined $this_stop; $this_stop = $this_start + $length - 1; } # this allows a SQL optimization way down deep $self->{whole}++ if $absref eq $sname and !defined($this_start) and !defined($this_stop); $this_start = 1 if !defined $this_start; $this_stop = $absstop-$absstart+1 if !defined $this_stop; $this_length = $this_stop - $this_start + 1; # now offset to correct subsegment based on desired start and stop if ($force_absolute) { # ($this_start,$this_stop) = ($absstart,$absstop); $self->absolute(1); } elsif ($absstrand eq '+') { $this_start = $absstart + $this_start - 1; $this_stop = $this_start + $this_length - 1; } else { $this_start = $absstop - ($this_start - 1); $this_stop = $absstop - ($this_stop - 1); } # handle truncation in either direction # This only happens if the segment runs off the end of # the reference sequence if ($factory->strict_bounds_checking && (($this_start < $absstart) || ($this_stop > $absstop))) { # return empty if we are completely off the end of the ref se next unless $this_start<=$absstop && $this_stop>=$absstart; if (my $a = $factory->abscoords($absref,'Sequence')) { my $refstart = $a->[0][2]; my $refstop = $a->[0][3]; if ($this_start < $refstart) { $this_start = $refstart; $self->{truncated}{start}++; } if ($this_stop > $refstop) { $this_stop = $absstop; $self->{truncated}{stop}++; } } } @{$self}{qw(sourceseq start stop strand class)} = ($absref,$this_start,$this_stop,$absstrand,$absclass); # handle reference sequence if (defined $refseq) { $refclass = $refseq->class if $refseq->can('class'); $refclass ||= 'Sequence'; my ($refref,$refstart,$refstop,$refstrand) = $factory->abscoords($refseq,$refclass); unless ($refref eq $absref) { $self->error("reference sequence is on $refref but source sequence is on $absref"); return; } $refstart = $refstop if $refstrand eq '-'; @{$self}{qw(ref refstart refstrand)} = ($refseq,$refstart,$refstrand); } else { $absstart = $absstop if $absstrand eq '-'; @{$self}{qw(ref refstart refstrand)} = ($sname,$absstart,$absstrand); } push @object_results,$self; } return wantarray ? @object_results : $object_results[0]; } # overridden methods # start, stop, length sub start { my $self = shift; return $self->strand < 0 ? $self->{stop} : $self->{start} if $self->absolute; $self->_abs2rel($self->{start}); } sub end { my $self = shift; return $self->strand < 0 ? $self->{start} : $self->{stop} if $self->absolute; $self->_abs2rel($self->{stop}); } *stop = \&end; sub length { my $self = shift; return unless defined $self->abs_end; abs($self->abs_end - $self->abs_start) + 1; } sub abs_start { my $self = shift; if ($self->absolute) { my ($a,$b) = ($self->SUPER::abs_start,$self->SUPER::abs_end); return ($a<$b) ? $a : $b; } else { return $self->SUPER::abs_start(@_); } } sub abs_end { my $self = shift; if ($self->absolute) { my ($a,$b) = ($self->SUPER::abs_start,$self->SUPER::abs_end); return ($a>$b) ? $a : $b; } else { return $self->SUPER::abs_end(@_); } } *abs_stop = \&abs_end; =head2 refseq Title : refseq Usage : $ref = $s->refseq([$newseq] [,$newseqclass]) Function: get/set reference sequence Returns : current reference sequence Args : new reference sequence and class (optional) Status : Public This method will get or set the reference sequence. Called with no arguments, it returns the current reference sequence. Called with either a sequence ID and class, a Bio::DB::GFF::Segment object (or subclass) or a Bio::DB::GFF::Featname object, it will set the current reference sequence and return the previous one. The method will generate an exception if you attempt to set the reference sequence to a sequence that isn't contained in the database, or one that has a different source sequence from the segment. =cut #' sub refseq { my $self = shift; my $g = $self->{ref}; if (@_) { my ($newref,$newclass); if (@_ == 2) { $newclass = shift; $newref = shift; } else { $newref = shift; $newclass = 'Sequence'; } defined $newref or $self->throw('refseq() called with an undef reference sequence'); # support for Featname objects $newclass = $newref->class if ref($newref) && $newref->can('class'); # $self->throw("Cannot define a segment's reference sequence in terms of itself!") # if ref($newref) and overload::StrVal($newref) eq overload::StrVal($self); my ($refsource,undef,$refstart,$refstop,$refstrand); if ($newref->isa('Bio::DB::GFF::RelSegment')) { ($refsource,undef,$refstart,$refstop,$refstrand) = ($newref->sourceseq,undef,$newref->abs_start,$newref->abs_end,$newref->abs_strand >= 0 ? '+' : '-'); } else { my $coords = $self->factory->abscoords($newref,$newclass); foreach (@$coords) { # find the appropriate one ($refsource,undef,$refstart,$refstop,$refstrand) = @$_; last if $refsource eq $self->{sourceseq}; } } $self->throw("can't set reference sequence: $newref and $self are on different sequence segments") unless $refsource eq $self->{sourceseq}; @{$self}{qw(ref refstart refstrand)} = ($newref,$refstart,$refstrand); $self->absolute(0); } return $self->absolute ? $self->sourceseq : $g; } =head2 abs_low Title : abs_low Usage : $s->abs_low Function: the absolute lowest coordinate of the segment Returns : an integer Args : none Status : Public This is for GadFly compatibility, and returns the low coordinate in absolute coordinates; =cut sub abs_low { my $self = shift; my ($a,$b) = ($self->abs_start,$self->abs_end); return ($a<$b) ? $a : $b; } =head2 abs_high Title : abs_high Usage : $s->abs_high Function: the absolute highest coordinate of the segment Returns : an integer Args : none Status : Public This is for GadFly compatibility, and returns the high coordinate in absolute coordinates; =cut sub abs_high { my $self = shift; my ($a,$b) = ($self->abs_start,$self->abs_end); return ($a>$b) ? $a : $b; } =head2 asString Title : asString Usage : $s->asString Function: human-readable representation of the segment Returns : a string Args : none Status : Public This method will return a human-readable representation of the segment. It is the overloaded method call for the "" operator. Currently the format is: refseq:start,stop =cut sub asString { my $self = shift; return $self->SUPER::asString if $self->absolute; my $label = $self->{ref}; my $start = $self->start || ''; my $stop = $self->stop || ''; if (ref($label) && overload::StrVal($self) eq overload::StrVal($label->ref)) { $label = $self->abs_ref; $start = $self->abs_start; $stop = $self->abs_end; } return "$label:$start,$stop"; } =head2 name Title : name Usage : Alias for asString() =cut sub name { shift->asString } =head2 absolute Title : absolute Usage : $abs = $s->absolute([$abs]) Function: get/set absolute coordinates Returns : a boolean flag Args : new setting for flag (optional) Status : Public Called with a boolean flag, this method controls whether to display relative coordinates (relative to the reference sequence) or absolute coordinates (relative to the source sequence). It will return the previous value of the setting. =cut sub absolute { my $self = shift; my $g = $self->{absolute}; $self->{absolute} = shift if @_; $g; } =head2 features Title : features Usage : @features = $s->features(@args) Function: get features that overlap this segment Returns : a list of Bio::DB::GFF::Feature objects Args : see below Status : Public This method will find all features that overlap the segment and return a list of Bio::DB::GFF::Feature objects. The features will use coordinates relative to the reference sequence in effect at the time that features() was called. The returned list can be limited to certain types of feature by filtering on their method and/or source. In addition, it is possible to obtain an iterator that will step through a large number of features sequentially. Arguments can be provided positionally or using the named arguments format. In the former case, the arguments are a list of feature types in the format "method:source". Either method or source can be omitted, in which case the missing component is treated as a wildcard. If no colon is present, then the type is treated as a method name. Multiple arguments are ORed together. Examples: @f = $s->features('exon:curated'); # all curated exons @f = $s->features('exon:curated','intron'); # curated exons and all introns @f = $s->features('similarity:.*EST.*'); # all similarities # having something to do # with ESTs The named parameter form gives you control over a few options: -types an array reference to type names in the format "method:source" -merge Whether to apply aggregators to the generated features (default yes) -rare Turn on an optimization suitable for a relatively rare feature type, where it will be faster to filter by feature type first and then by position, rather than vice versa. -attributes a hashref containing a set of attributes to match -range_type One of 'overlapping', 'contains', or 'contained_in' -iterator Whether to return an iterator across the features. -binsize A true value will create a set of artificial features whose start and stop positions indicate bins of the given size, and whose scores are the number of features in the bin. The class and method of the feature will be set to "bin", its source to "method:source", and its group to "bin:method:source". This is a handy way of generating histograms of feature density. -merge is a boolean flag that controls whether the adaptor's aggregators wll be applied to the features returned by this method. If -iterator is true, then the method returns a single scalar value consisting of a Bio::SeqIO object. You can call next_seq() repeatedly on this object to fetch each of the features in turn. If iterator is false or absent, then all the features are returned as a list. The -attributes argument is a hashref containing one or more attributes to match against: -attributes => { Gene => 'abc-1', Note => 'confirmed' } Attribute matching is simple string matching, and multiple attributes are ANDed together. =cut #' # return all features that overlap with this segment; # optionally modified by a list of types to filter on sub features { my $self = shift; my @args = $self->_process_feature_args(@_); return $self->factory->overlapping_features(@args); } =head2 get_SeqFeatures Title : get_SeqFeatures Usage : Function: returns the top level sequence features Returns : L objects Args : none Segments do not ordinarily return any subfeatures. =cut # A SEGMENT DOES NOT HAVE SUBFEATURES! sub get_SeqFeatures { return } =head2 feature_count Title : feature_count Usage : $seq->feature_count() Function: Return the number of SeqFeatures attached to a sequence Returns : integer representing the number of SeqFeatures Args : none This method comes through extension of Bio::FeatureHolderI. See L for more information. =cut sub feature_count { my $self = shift; my $ct = 0; my %type_counts = $self->types(-enumerate=>1); map { $ct += $_ } values %type_counts; $ct; } =head2 get_feature_stream Title : features Usage : $stream = $s->get_feature_stream(@args) Function: get a stream of features that overlap this segment Returns : a Bio::SeqIO::Stream-compliant stream Args : see below Status : Public This is the same as features(), but returns a stream. Use like this: $stream = $s->get_feature_stream('exon'); while (my $exon = $stream->next_seq) { print $exon->start,"\n"; } =cut sub get_feature_stream { my $self = shift; my @args = defined($_[0]) && $_[0] =~ /^-/ ? (@_,-iterator=>1) : (-types=>\@_,-iterator=>1); $self->features(@args); } =head2 get_seq_stream Title : get_seq_stream Usage : $stream = $s->get_seq_stream(@args) Function: get a stream of features that overlap this segment Returns : a Bio::SeqIO::Stream-compliant stream Args : see below Status : Public This is the same as feature_stream(), and is provided for Bioperl compatibility. Use like this: $stream = $s->get_seq_stream('exon'); while (my $exon = $stream->next_seq) { print $exon->start,"\n"; } =cut *get_seq_stream = \&get_feature_stream; =head2 overlapping_features Title : overlapping_features Usage : @features = $s->overlapping_features(@args) Function: get features that overlap this segment Returns : a list of Bio::DB::GFF::Feature objects Args : see features() Status : Public This is an alias for the features() method, and takes the same arguments. =cut *overlapping_features = \&features; =head2 contained_features Title : contained_features Usage : @features = $s->contained_features(@args) Function: get features that are contained by this segment Returns : a list of Bio::DB::GFF::Feature objects Args : see features() Status : Public This is identical in behavior to features() except that it returns only those features that are completely contained within the segment, rather than any that overlap. =cut # return all features completely contained within this segment sub contained_features { my $self = shift; local $self->{whole} = 0; my @args = $self->_process_feature_args(@_); return $self->factory->contained_features(@args); } # *contains = \&contained_features; =head2 contained_in Title : contained_in Usage : @features = $s->contained_in(@args) Function: get features that contain this segment Returns : a list of Bio::DB::GFF::Feature objects Args : see features() Status : Public This is identical in behavior to features() except that it returns only those features that completely contain the segment. =cut # return all features completely contained within this segment sub contained_in { my $self = shift; local $self->{whole} = 0; my @args = $self->_process_feature_args(@_); return $self->factory->contained_in(@args); } =head2 delete Title : delete Usage : $db->delete(@args) Function: delete features Returns : count of features deleted -- if available Args : numerous, see below Status : public This method deletes all features that overlap the specified region or are of a particular type. If no arguments are provided and the -force argument is true, then deletes ALL features. Arguments: -type,-types Either a single scalar type to be deleted, or an reference to an array of types. -range_type Control the range type of the deletion. One of "overlaps" (default) "contains" or "contained_in" Examples: $segment->delete(-type=>['intron','repeat:repeatMasker']); # remove all introns & repeats $segment->delete(-type=>['intron','repeat:repeatMasker'] -range_type => 'contains'); # remove all introns & repeats # strictly contained in segment IMPORTANT NOTE: This method only deletes features. It does *NOT* delete the names of groups that contain the deleted features. Group IDs will be reused if you later load a feature with the same group name as one that was previously deleted. NOTE ON FEATURE COUNTS: The DBI-based versions of this call return the result code from the SQL DELETE operation. Some dbd drivers return the count of rows deleted, while others return 0E0. Caveat emptor. =cut # return all features completely contained within this segment sub delete { my $self = shift; my ($type,$range_type) = rearrange([[qw(TYPE TYPES)],'RANGE_TYPE'],@_); my $types = $self->factory->parse_types($type); # parse out list of types $range_type ||= 'overlaps'; return $self->factory->_delete({ segments => [$self], types => $types, range_type => $range_type }); } =head2 _process_feature_args Title : _process_feature_args Usage : @args = $s->_process_feature_args(@args) Function: preprocess arguments passed to features, contained_features, and overlapping_features Returns : a list of parsed arguents Args : see feature() Status : Internal This is an internal method that is used to check and format the arguments to features() before passing them on to the adaptor. =cut sub _process_feature_args { my $self = shift; my ($ref,$class,$start,$stop,$strand,$whole) = @{$self}{qw(sourceseq class start stop strand whole)}; ($start,$stop) = ($stop,$start) if defined $strand && $strand eq '-'; my @args = (-ref=>$ref,-class=>$class); # indicating that we are fetching the whole segment allows certain # SQL optimizations. push @args,(-start=>$start,-stop=>$stop) unless $whole; if (@_) { if ($_[0] =~ /^-/) { push @args,@_; } else { my @types = @_; push @args,-types=>\@types; } } push @args,-parent=>$self; @args; } =head2 types Title : types Usage : @types = $s->types([-enumerate=>1]) Function: list feature types that overlap this segment Returns : a list of Bio::DB::GFF::Typename objects or a hash Args : see below Status : Public The types() method will return a list of Bio::DB::GFF::Typename objects, each corresponding to a feature that overlaps the segment. If the optional -enumerate parameter is set to a true value, then the method will return a hash in which the keys are the type names and the values are the number of times a feature of that type is present on the segment. For example: %count = $s->types(-enumerate=>1); =cut # wrapper for lower-level types() call. sub types { my $self = shift; my ($ref,$class,$start,$stop,$strand) = @{$self}{qw(sourceseq class start stop strand)}; ($start,$stop) = ($stop,$start) if $strand eq '-'; my @args; if (@_ && $_[0] !~ /^-/) { @args = (-type => \@_) } else { @args = @_; } $self->factory->types(-ref => $ref, -start=> $start, -stop => $stop, @args); } =head1 Internal Methods The following are internal methods and should not be called directly. =head2 new_from_segment Title : new_from_segment Usage : $s = $segment->new_from_segment(@args) Function: create a new relative segment Returns : a new Bio::DB::GFF::RelSegment object Args : see below Status : Internal This constructor is used internally by the subseq() method. It forces the new segment into the Bio::DB::GFF::RelSegment package, regardless of the package that it is called from. This causes subclass-specfic information, such as feature types, to be dropped when a subsequence is created. =cut sub new_from_segment { my $package = shift; $package = ref $package if ref $package; my $segment = shift; my $new = {}; @{$new}{qw(factory sourceseq start stop strand class ref refstart refstrand)} = @{$segment}{qw(factory sourceseq start stop strand class ref refstart refstrand)}; return bless $new,__PACKAGE__; } =head2 _abs2rel Title : _abs2rel Usage : @coords = $s->_abs2rel(@coords) Function: convert absolute coordinates into relative coordinates Returns : a list of relative coordinates Args : a list of absolute coordinates Status : Internal This is used internally to map from absolute to relative coordinates. It does not take the offset of the reference sequence into account, so please use abs2rel() instead. =cut sub _abs2rel { my $self = shift; my @result; return unless defined $_[0]; if ($self->absolute) { @result = @_; } else { my ($refstart,$refstrand) = @{$self}{qw(refstart refstrand)}; @result = defined($refstrand) && $refstrand eq '-' ? map { $refstart - $_ + 1 } @_ : map { $_ - $refstart + 1 } @_; } # if called with a single argument, caller will expect a single scalar reply # not the size of the returned array! return $result[0] if @result == 1 and !wantarray; @result; } =head2 rel2abs Title : rel2abs Usage : @coords = $s->rel2abs(@coords) Function: convert relative coordinates into absolute coordinates Returns : a list of absolute coordinates Args : a list of relative coordinates Status : Public This function takes a list of positions in relative coordinates to the segment, and converts them into absolute coordinates. =cut sub rel2abs { my $self = shift; my @result; if ($self->absolute) { @result = @_; } else { my ($abs_start,$abs_strand) = ($self->abs_start,$self->abs_strand); @result = $abs_strand < 0 ? map { $abs_start - $_ + 1 } @_ : map { $_ + $abs_start - 1 } @_; } # if called with a single argument, caller will expect a single scalar reply # not the size of the returned array! return $result[0] if @result == 1 and !wantarray; @result; } =head2 abs2rel Title : abs2rel Usage : @rel_coords = $s->abs2rel(@abs_coords) Function: convert absolute coordinates into relative coordinates Returns : a list of relative coordinates Args : a list of absolute coordinates Status : Public This function takes a list of positions in absolute coordinates and returns a list expressed in relative coordinates. =cut sub abs2rel { my $self = shift; my @result; if ($self->absolute) { @result = @_; } else { my ($abs_start,$abs_strand) = ($self->abs_start,$self->abs_strand); @result = $abs_strand < 0 ? map { $abs_start - $_ + 1 } @_ : map { $_ - $abs_start + 1 } @_; } # if called with a single argument, caller will expect a single scalar reply # not the size of the returned array! return $result[0] if @result == 1 and !wantarray; @result; } sub subseq { my $self = shift; my $obj = $self->SUPER::subseq(@_); bless $obj,__PACKAGE__; # always bless into the generic RelSegment package } sub strand { my $self = shift; if ($self->absolute) { return _to_strand($self->{strand}); } my $start = $self->start; my $stop = $self->stop; return 0 unless defined $start and defined $stop; return $stop <=> $start; } sub _to_strand { my $s = shift; return -1 if $s eq '-'; return +1 if $s eq '+'; return 0; } =head2 Bio::RangeI Methods The following Bio::RangeI methods are supported: overlaps(), contains(), equals(),intersection(),union(),overlap_extent() =cut sub intersection { my $self = shift; my (@ranges) = @_; unshift @ranges,$self if ref $self; $ranges[0]->isa('Bio::DB::GFF::RelSegment') or return $self->SUPER::intersection(@_); my $ref = $ranges[0]->abs_ref; my ($low,$high); foreach (@ranges) { return unless $_->can('abs_ref'); $ref eq $_->abs_ref or return; $low = $_->abs_low if !defined($low) or $low < $_->abs_low; $high = $_->abs_high if !defined($high) or $high > $_->abs_high; } return unless $low < $high; return Bio::DB::GFF::RelSegment->new(-factory => $self->factory, -seq => $ref, -start => $low, -stop => $high, ); } sub overlaps { my $self = shift; my($other,$so) = @_; return $self->SUPER::overlaps(@_) unless $other->isa('Bio::DB::GFF::RelSegment'); return if $self->abs_ref ne $other->abs_ref; return if $self->abs_low > $other->abs_high; return if $self->abs_high < $other->abs_low; 1; } sub contains { my $self = shift; my($other,$so) = @_; return $self->SUPER::overlaps(@_) unless $other->isa('Bio::DB::GFF::RelSegment'); return if $self->abs_ref ne $other->abs_ref; return unless $self->abs_low <= $other->abs_low; return unless $self->abs_high >= $other->abs_high; 1; } sub union { my $self = shift; my (@ranges) = @_; unshift @ranges,$self if ref $self; $ranges[0]->isa('Bio::DB::GFF::RelSegment') or return $self->SUPER::union(@_); my $ref = $ranges[0]->abs_ref; my ($low,$high); foreach (@ranges) { return unless $_->can('abs_ref'); $ref eq $_->abs_ref or return; $low = $_->abs_low if !defined($low) or $low > $_->abs_low; $high = $_->abs_high if !defined($high) or $high < $_->abs_high; } $self->new(-factory=> $self->factory, -seq => $ref, -start => $low, -stop => $high); } sub version { 0 } 1; __END__ =head1 BUGS Schemas need some work. =head1 SEE ALSO L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Segment.pm000444000766000024 4503613155576320 17103 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Segment -- Simple DNA segment object =head1 SYNOPSIS See L. =head1 DESCRIPTION Bio::DB::GFF::Segment provides the basic representation of a range of DNA contained in a GFF database. It is the base class from which the Bio::DB::GFF::RelSegment and Bio::DB::GFF::Feature classes are derived. Generally, you will not create or manipulate Bio::DB::GFF::Segment objects directly, but use those that are returned by the Bio::DB::GFF module. =cut package Bio::DB::GFF::Segment; use strict; use Bio::Annotation::Collection; use base qw(Bio::Root::Root Bio::RangeI Bio::SeqI Bio::Das::SegmentI); use overload '""' => 'asString', eq => 'equals', fallback => 1; =head1 API The remainder of this document describes the API for Bio::DB::GFF::Segment. =cut =head2 new Title : new Usage : $s = Bio::DB::GFF::Segment->new(@args) Function: create a new segment Returns : a new Bio::DB::GFF::Segment object Args : see below Status : Public This method creates a new Bio::DB::GFF::Segment object. Generally this is called automatically by the Bio::DB::GFF module and derivatives. There are five positional arguments: $factory a Bio::DB::GFF::Adaptor to use for database access $sourceseq ID of the source sequence $sourceclass class of the source sequence $start start of the desired segment relative to source sequence $stop stop of the desired segment relative to source sequence =cut sub new { my $class = shift; my ($factory,$segclass,$segname,$start,$stop) = @_; $segclass = $segname->class if ref($segname) && $segname->can('class'); $segclass ||= 'Sequence'; $factory or $class->throw("->new(): provide a factory argument"); $class = ref $class if ref $class; return bless { factory => $factory, sourceseq => $segname, class => $segclass, start => $start, stop => $stop, strand => 0, },$class; } # read-only accessors =head2 factory Title : factory Usage : $s->factory Function: get the factory object Returns : a Bio::DB::GFF::Adaptor Args : none Status : Public This is a read-only accessor for the Bio::DB::GFF::Adaptor object used to create the segment. =cut sub factory { shift->{factory} } # start, stop, length =head2 start Title : start Usage : $s->start Function: start of segment Returns : integer Args : none Status : Public This is a read-only accessor for the start of the segment. =cut sub start { shift->{start} } =head2 end Title : end Usage : $s->end Function: end of segment Returns : integer Args : none Status : Public This is a read-only accessor for the end of the segment. =cut sub end { shift->{stop} } =head2 stop Title : stop Usage : $s->stop Function: stop of segment Returns : integer Args : none Status : Public This is an alias for end(), provided for AcePerl compatibility. =cut *stop = \&end; =head2 length Title : length Usage : $s->length Function: length of segment Returns : integer Args : none Status : Public Returns the length of the segment. Always a positive number. =cut sub length { abs($_[0]->{start} - $_[0]->{stop})+1 } =head2 strand Title : strand Usage : $s->strand Function: strand of segment Returns : +1,0,-1 Args : none Status : Public Returns the strand on which the segment resides, either +1, 0 or -1. =cut sub strand { my $self = shift; 0; } =head2 low Title : low Usage : $s->low Function: return lower coordinate Returns : lower coordinate Args : none Status : Public Returns the lower coordinate, either start or end. =cut sub low { my $self = shift; my ($start,$stop) = ($self->start,$self->stop); return $start < $stop ? $start : $stop; } *abs_low = \&low; =head2 high Title : high Usage : $s->high Function: return higher coordinate Returns : higher coordinate Args : none Status : Public Returns the higher coordinate, either start or end. =cut sub high { my $self = shift; my ($start,$stop) = ($self->start,$self->stop); return $start > $stop ? $start : $stop; } *abs_high = \&high; =head2 sourceseq Title : sourceseq Usage : $s->sourceseq Function: get the segment source Returns : a string Args : none Status : Public Returns the name of the source sequence for this segment. =cut sub sourceseq { shift->{sourceseq} } =head2 class Title : class Usage : $s->class([$newclass]) Function: get the source sequence class Returns : a string Args : new class (optional) Status : Public Gets or sets the class for the source sequence for this segment. =cut sub class { my $self = shift; my $d = $self->{class}; $self->{class} = shift if @_; $d; } =head2 subseq Title : subseq Usage : $s->subseq($start,$stop) Function: generate a subsequence Returns : a Bio::DB::GFF::Segment object Args : start and end of subsequence Status : Public This method generates a new segment from the start and end positions given in the arguments. If stop E start, then the strand is reversed. =cut sub subseq { my $self = shift; my ($newstart,$newstop) = @_; my ($refseq,$start,$stop,$class) = ($self->{sourceseq}, $self->{start},$self->{stop}, $self->class); # We deliberately force subseq to return objects of type RelSegment # Otherwise, when we get a subsequence from a Feature object, # its method and source go along for the ride, which is incorrect. my $new = $self->new_from_segment($self); if ($start <= $stop) { @{$new}{qw(start stop)} = ($start + $newstart - 1, $start + $newstop - 1); } else { @{$new}{qw(start stop)} = ($start - ($newstart - 1), $start - ($newstop - 1)), } $new; } =head2 seq Title : seq Usage : $s->seq Function: get the sequence string for this segment Returns : a Bio::PrimarySeq Args : none Status : Public Returns the sequence for this segment as a Bio::PrimarySeq. (-) strand segments are automatically reverse complemented The method is called dna() return the data as a simple sequence string. =cut sub seq { my $self = shift; my $dna = $self->dna; require Bio::PrimarySeq unless Bio::PrimarySeq->can('new'); return Bio::PrimarySeq->new(-id => $self->display_name) unless $dna; return Bio::PrimarySeq->new(-seq => $dna, -id => $self->display_name); } =head2 dna Title : dna Usage : $s->dna Function: get the DNA string for this segment Returns : a string Args : none Status : Public Returns the sequence for this segment as a simple string. (-) strand segments are automatically reverse complemented The method is also called protein(). =cut sub dna { my $self = shift; my ($ref,$class,$start,$stop,$strand) = @{$self}{qw(sourceseq class start stop strand)}; return $self->factory->dna($ref,$start,$stop,$class); } *protein = \&dna; =head2 primary_seq Title : primary_seq Usage : $s->primary_seq Function: returns a Bio::PrimarySeqI compatible object Returns : a Bio::PrimarySeqI object Args : none Status : Public This is for compatibility with BioPerl's separation of SeqI from PrimarySeqI. It just returns itself. =cut #' sub primary_seq { shift } =head2 type Title : type Usage : $s->type Function: return the string "feature" Returns : the string "feature" Args : none Status : Public This is for future sequence ontology-compatibility and represents the default type of a feature on the genome =cut sub type { "feature" } =head2 equals Title : equals Usage : $s->equals($d) Function: segment equality Returns : true, if two segments are equal Args : another segment Status : Public Returns true if the two segments have the same source sequence, start and stop. =cut sub equals { my $self = shift; my $peer = shift; return unless defined $peer; return $self->asString eq $peer unless ref($peer) && $peer->isa('Bio::DB::GFF::Segment'); return $self->{start} eq $peer->{start} && $self->{stop} eq $peer->{stop} && $self->{sourceseq} eq $peer->{sourceseq}; } =head2 asString Title : asString Usage : $s->asString Function: human-readable string for segment Returns : a string Args : none Status : Public Returns a human-readable string representing this sequence. Format is: sourceseq/start,stop =cut sub asString { my $self = shift; my $label = $self->refseq; my $start = $self->start; my $stop = $self->stop; return "$label:$start,$stop"; } =head2 clone Title : clone Usage : $copy = $s->clone Function: make a copy of this segment Returns : a Bio::DB::GFF::Segment object Args : none Status : Public This method creates a copy of the segment and returns it. =cut # deep copy of the thing sub clone { my $self = shift; my %h = %$self; return bless \%h,ref($self); } =head2 error Title : error Usage : $error = $s->error([$new_error]) Function: get or set the last error Returns : a string Args : an error message (optional) Status : Public In case of a fault, this method can be used to obtain the last error message. Internally it is called to set the error message. =cut sub error { my $self = shift; my $g = $self->{error}; $self->{error} = shift if @_; $g; } =head1 Relative Addressing Methods The following methods are provided for compatibility with Bio::DB::GFF::RelSegment, which provides relative addressing functions. =head2 abs_start Title : abs_start Usage : $s->abs_start Function: the absolute start of the segment Returns : an integer Args : none Status : Public This is an alias to start(), and provided for API compatibility with Bio::DB::GFF::RelSegment. =cut *abs_start = \&start; =head2 abs_end Title : abs_end Usage : $s->abs_end Function: the absolute stop of the segment Returns : an integer Args : none Status : Public This is an alias to stop(), and provided for API compatibility with Bio::DB::GFF::RelSegment. =cut *abs_stop = \&stop; *abs_end = \&stop; =head2 abs_strand Title : abs_strand Usage : $s->abs_strand Function: the absolute strand of the segment Returns : +1,0,-1 Args : none Status : Public This is an alias to strand(), and provided for API compatibility with Bio::DB::GFF::RelSegment. =cut sub abs_strand { my $self = shift; return $self->abs_end <=> $self->abs_start; } =head2 abs_ref Title : abs_ref Usage : $s->abs_ref Function: the reference sequence for this segment Returns : a string Args : none Status : Public This is an alias to sourceseq(), and is here to provide API compatibility with Bio::DB::GFF::RelSegment. =cut *abs_ref = \&sourceseq; =head2 refseq Title : refseq Usage : $s->refseq Function: get or set the reference sequence Returns : a string Args : none Status : Public Examine or change the reference sequence. This is an alias to sourceseq(), provided here for API compatibility with Bio::DB::GFF::RelSegment. =cut *refseq = \&sourceseq; =head2 ref Title : ref Usage : $s->refseq Function: get or set the reference sequence Returns : a string Args : none Status : Public An alias for refseq() =cut sub ref { shift->refseq(@_) } =head2 seq_id Title : seq_id Usage : $ref = $s->seq_id Function: get the reference sequence in a LocationI-compatible way Returns : a string Args : none Status : Public An alias for refseq() but only allows reading. =cut sub seq_id { shift->refseq } *seqname = \&seq_id; =head2 truncated Title : truncated Usage : $truncated = $s->truncated Function: Flag indicating that the segment was truncated during creation Returns : A boolean flag Args : none Status : Public This indicates that the sequence was truncated during creation. The returned flag is undef if no truncation occurred. If truncation did occur, the flag is actually an array ref in which the first element is true if truncation occurred on the left, and the second element occurred if truncation occurred on the right. =cut sub truncated { my $self = shift; my $hash = $self->{truncated} or return; CORE::ref($hash) eq 'HASH' or return [1,1]; # paranoia -- not that this would ever happen ;-) return [$hash->{start},$hash->{stop}]; } =head2 Bio::RangeI Methods The following Bio::RangeI methods are supported: overlaps(), contains(), equals(),intersection(),union(),overlap_extent() =cut sub overlaps { my $self = shift; my($other,$so) = @_; if ($other->isa('Bio::DB::GFF::RelSegment')) { return if $self->abs_ref ne $other->abs_ref; } $self->SUPER::overlaps(@_); } sub contains { my $self = shift; my($other,$so) = @_; if ($other->isa('Bio::DB::GFF::RelSegment')) { return if $self->abs_ref ne $other->abs_ref; } $self->SUPER::contains(@_); } #sub equals { # my $self = shift; # my($other,$so) = @_; # if ($other->isa('Bio::DB::GFF::RelSegment')) { # return if $self->abs_ref ne $other->abs_ref; # } # $self->SUPER::equals(@_); #} sub intersection { my $self = shift; my($other,$so) = @_; if ($other->isa('Bio::DB::GFF::RelSegment')) { return if $self->abs_ref ne $other->abs_ref; } $self->SUPER::intersection(@_); } sub union { my $self = shift; my($other) = @_; if ($other->isa('Bio::DB::GFF::RelSegment')) { return if $self->abs_ref ne $other->abs_ref; } $self->SUPER::union(@_); } sub overlap_extent { my $self = shift; my($other) = @_; if ($other->isa('Bio::DB::GFF::RelSegment')) { return if $self->abs_ref ne $other->abs_ref; } $self->SUPER::overlap_extent(@_); } =head2 Bio::SeqI implementation =cut =head2 primary_id Title : primary_id Usage : $unique_implementation_key = $obj->primary_id; Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a way the implementation can control clients can expect one id to map to one object. For sequences with no accession number, this method should return a stringified memory location. Returns : A string Args : None Status : Virtual =cut sub primary_id { my ($obj,$value) = @_; if( defined $value) { $obj->{'primary_id'} = $value; } if( ! exists $obj->{'primary_id'} ) { return "$obj"; } return $obj->{'primary_id'}; } =head2 display_name Title : display_name Usage : $id = $obj->display_name or $obj->display_name($newid); Function: Gets or sets the display id, also known as the common name of the Seq object. The semantics of this is that it is the most likely string to be used as an identifier of the sequence, and likely to have "human" readability. The id is equivalent to the LOCUS field of the GenBank/EMBL databanks and the ID field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. Notice that $seq->id() maps to this function, mainly for legacy/convenience issues. Returns : A string Args : None or a new id Note, this used to be called display_id(), and this name is preserved for backward compatibility. The default is to return the seq_id(). =cut sub display_name { shift->seq_id } *display_id = \&display_name; =head2 accession_number Title : accession_number Usage : $unique_biological_key = $obj->accession_number; Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". Returns : A string Args : None =cut sub accession_number { return 'unknown'; } =head2 alphabet Title : alphabet Usage : if( $obj->alphabet eq 'dna' ) { /Do Something/ } Function: Returns the type of sequence being one of 'dna', 'rna' or 'protein'. This is case sensitive. This is not called because this would cause upgrade problems from the 0.5 and earlier Seq objects. Returns : a string either 'dna','rna','protein'. NB - the object must make a call of the type - if there is no type specified it has to guess. Args : none Status : Virtual =cut sub alphabet{ return 'dna'; # no way this will be anything other than dna! } =head2 desc Title : desc Usage : $seqobj->desc($string) or $seqobj->desc() Function: Sets or gets the description of the sequence Example : Returns : The description Args : The description or none =cut sub desc { shift->asString } *description = \&desc; =head2 species Title : species Usage : $species = $seq->species() or $seq->species($species) Function: Gets or sets the species Example : Returns : Bio::Species object Args : None or Bio::Species object See L for more information =cut sub species { my ($self, $species) = @_; if ($species) { $self->{'species'} = $species; } else { return $self->{'species'}; } } =head2 annotation Title : annotation Usage : $ann = $seq->annotation or $seq->annotation($annotation) Function: Gets or sets the annotation Example : Returns : Bio::Annotation object Args : None or Bio::Annotation object See L for more information =cut sub annotation { my ($obj,$value) = @_; if( defined $value || ! defined $obj->{'annotation'} ) { $value = Bio::Annotation::Collection->new() unless defined $value; $obj->{'annotation'} = $value; } return $obj->{'annotation'}; } =head2 is_circular Title : is_circular Usage : if( $obj->is_circular) { /Do Something/ } Function: Returns true if the molecule is circular Returns : Boolean value Args : none =cut sub is_circular{ return 0; } 1; __END__ =head1 BUGS Report them please. =head1 SEE ALSO L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 CONTRIBUTORS Jason Stajich Ejason@bioperl.orgE. =cut BioPerl-1.007002/Bio/DB/GFF/Typename.pm000444000766000024 752113155576320 17240 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Typename -- The name of a feature type =head1 SYNOPSIS use Bio::DB::GFF; my $type = Bio::DB::GFF::Typename->new(similarity => 'BLAT_EST_GENOME'); my $segment = $segment->features($type); =head1 DESCRIPTION Bio::DB::GFF::Typename objects encapsulate the combination of feature method and source used by the GFF flat file format. They can be used in the Bio::DB::GFF modules wherever a feature type is called for. Since there are relatively few types and many features, this module maintains a memory cache of unique types so that two features of the same type will share the same Bio::DB::GFF::Typename object. =head1 METHODS =cut package Bio::DB::GFF::Typename; use strict; use overload '""' => 'asString', fallback => 1; use base qw(Bio::Root::Root Bio::Das::FeatureTypeI); # cut down on the number of equivalent objects we have to create my %OBJECT_CACHE; =head2 new Title : new Usage : $type = Bio::DB::GFF::Typename->new($method,$source) Function: create a new Bio::DB::GFF::Typename object Returns : a new Bio::DB::GFF::Typename object Args : method and source Status : Public =cut sub new { my $package = shift; my ($method,$source) = @_; $method ||= ''; $source ||= ''; if ($source eq '' && $method =~ /^([\w-\.]+):([\w-\.]*)$/) { $method = $1; $source = $2; } return $OBJECT_CACHE{"$method:$source"} ||= bless [$method,$source],$package; } =head2 method Title : method Usage : $method = $type->method([$newmethod]) Function: get or set the method Returns : a method name Args : new method name (optional) Status : Public =cut sub method { my $self = shift; my $d = $self->[0]; $self->[0] = shift if @_; $d; } =head2 source Title : source Usage : $source = $type->source([$newsource]) Function: get or set the source Returns : a source name Args : new source name (optional) Status : Public =cut sub source { my $self = shift; my $d = $self->[1]; $self->[1] = shift if @_; $d; } =head2 asString Title : asString Usage : $string = $type->asString Function: get the method and source as a string Returns : a string in "method:source" format Args : none Status : Public This method is used by operator overloading to overload the '""' operator. =cut sub asString { $_[0]->[1] ? join ':',@{$_[0]} : $_[0]->[0]; } =head2 clone Title : clone Usage : $new_clone = $type->clone; Function: clone this object Returns : a new Bio::DB::GFF::Typename object Args : none Status : Public This method creates an exact copy of the object. =cut sub clone { my $self = shift; return bless [@$self],ref $self; } =head2 match Title : match Usage : $boolean = $type->match($type_or_string) Function: fuzzy match on types Returns : a flag indicating that the argument matches the object Args : a Bio::DB::GFF::typename object, or a string in method:source format Status : Public This match allows Sequence:Link and Sequence: to match, but not Sequence:Link and Sequence:Genomic_canonical. =cut sub match { my $self = shift; my $target = shift; my ($method,$source); if (UNIVERSAL::isa($target,'Bio::DB::GFF::Typename')) { ($method,$source) = ($target->method,$target->source); } else { ($method,$source) = split /:/,$target; } $source ||= ''; # quash uninit variable warnings return if $method ne '' && $self->method ne '' && $method ne $self->method; return if $source ne '' && $self->source ne '' && $source ne $self->source; 1; } 1; =head1 BUGS This module is still under development. =head1 SEE ALSO L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor000755000766000024 013155576320 16350 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/GFF/Adaptor/ace.pm000444000766000024 242513155576320 17576 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::ace; =head1 NAME Bio::DB::GFF::Adaptor::ace -- ace interface (for multiple inheritance) =head1 SYNOPSIS Pending See L and L =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2002 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use strict; use Ace; use Bio::DB::GFF::Util::Rearrange; # for rearrange() sub dna_db { my $self = shift; my $d = $self->{dna_db}; $self->{dna_db} = shift if @_; $d; } sub acedb { my $self = shift; my $d = $self->{acedb}; $self->{acedb} = shift if @_; $d; } =head2 freshen_ace Title : freshen Usage : $flag = Bio::DB::GFF->freshen_ace; Function: Refresh internal acedb handle Returns : flag if correctly freshened Args : none Status : Public ACeDB has an annoying way of timing out, leaving dangling database handles. This method will invoke the ACeDB reopen() method, which causes dangling handles to be refreshed. It has no effect if you are not using ACeDB to create ACeDB objects. =cut sub freshen_ace { my $acedb = shift->acedb or return; $acedb->reopen(); } 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor/berkeleydb.pm000444000766000024 7451213155576320 21204 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::berkeleydb; =head1 NAME Bio::DB::GFF::Adaptor::berkeleydb -- Bio::DB::GFF database adaptor for in-memory databases =head1 SYNOPSIS use Bio::DB::GFF; my $db = Bio::DB::GFF->new(-adaptor=> 'berkeleydb', -create => 1, # on initial build you need this -dsn => '/usr/local/share/gff/dmel'); # initialize an empty database, then load GFF and FASTA files $db->initialize(1); $db->load_gff('/home/drosophila_R3.2.gff'); $db->load_fasta('/home/drosophila_R3.2.fa'); # do queries my $segment = $db->segment(Chromosome => '1R'); my $subseg = $segment->subseq(5000,6000); my @features = $subseg->features('gene'); See L for other methods. =head1 DESCRIPTION This adaptor implements a berkeleydb-indexed version of Bio::DB::GFF. It requires the DB_File and Storable modules. It can be used to store and retrieve short to medium-length GFF files of several million features in length. =head1 CONSTRUCTOR Use Bio::DB::GFF-Enew() to construct new instances of this class. Three named arguments are recommended: Argument Description -------- ----------- -adaptor Set to "berkeleydb" to create an instance of this class. -dsn Path to directory where the database index files will be stored (alias -db) -autoindex Monitor the indicated directory path for FASTA and GFF files, and update the indexes automatically if they change (alias -dir) -write Set to a true value in order to update the database. -create Set to a true value to create the database the first time (implies -write) -tmp Location of temporary directory for storing intermediate files during certain queries. -preferred_groups Specify the grouping tag. See L The -dsn argument selects the directory in which to store the database index files. If the directory does not exist it will be created automatically, provided that the current process has sufficient privileges. If no -dsn argument is specified, a database named "test" will be created in your system's temporary files directory. The -tmp argument specifies the temporary directory to use for storing intermediate search results. If not specified, your system's temporary files directory will be used. On Unix systems, the TMPDIR environment variable is honored. Note that some queries can require a lot of space. The -autoindex argument, if present, selects a directory to be monitored for GFF and FASTA files (which can be compressed with the gzip program if desired). Whenever any file in this directory is changed, the index files will be updated. Note that the indexing can take a long time to run: anywhere from 5 to 10 minutes for a million features. An alias for this argument is -dir, which gives this adaptor a similar flavor to the "memory" adaptor. -dsn and -dir can point to the same directory. If -dir is given but -dsn is absent the index files will be stored into the directory containing the source files. For autoindexing to work, you must specify the same -dir path each time you open the database. If you do not choose autoindexing, then you will want to load the database using the bp_load_gff.pl command-line tool. For example: bp_load_gff.pl -a berkeleydb -c -d /usr/local/share/gff/dmel dna1.fa dna2.fa features.gff =head1 METHODS See L for inherited methods =head1 BUGS The various get_Stream_* methods and the features() method with the -iterator argument only return an iterator after the query runs completely and the module has been able to generate a temporary results file on disk. This means that iteration is not as big a win as it is for the relational-database adaptors. Like the dbi::mysqlopt adaptor, this module uses a binning scheme to speed up range-based searches. The binning scheme used here imposes a hard-coded 1 gigabase (1000 Mbase) limit on the size of the largest chromosome or other reference sequence. =head1 SEE ALSO L, L =head1 AUTHORS Vsevolod (Simon) Ilyushchenko Esimonf@cshl.eduE Lincoln Stein Elstein@cshl.eduE Copyright (c) 2005 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use strict; use DB_File; use File::Path 'mkpath'; use File::Spec; use File::Temp 'tempfile'; use Bio::DB::GFF::Util::Rearrange; # for rearrange() use Bio::DB::GFF::Util::Binning; use Bio::DB::Fasta; use Bio::DB::GFF::Adaptor::berkeleydb::iterator; use Bio::DB::GFF::Adaptor::memory::feature_serializer; # qw(feature2string string2feature @hash2array_map); # this is the smallest bin (1 K) use constant MIN_BIN => 1000; # this is the largest that any reference sequence can be (1000 megabases) use constant MAX_BIN => 1_000_000_000; use constant MAX_SEGMENT => 1_000_000_000; # the largest a segment can get #We have to define a limit because Berkeleydb sorts in lexicografic order, #so all the numbers have to have the same length. use constant MAX_NUM_LENGTH => length(MAX_BIN); use base 'Bio::DB::GFF::Adaptor::memory'; sub new { my $class = shift ; my ($dbdir,$preferred_groups,$autoindex,$write,$create,$tmpdir) = rearrange([ [qw(DSN DB)], 'PREFERRED_GROUPS', [qw(DIR AUTOINDEX)], [qw(WRITE WRITABLE)], 'CREATE', 'TMP', ],@_); $tmpdir ||= File::Spec->tmpdir; $dbdir ||= $autoindex; $dbdir ||= "$tmpdir/test"; $write ||= $create; my $self = bless {},$class; $self->dsn($dbdir); $self->tmpdir($tmpdir); $self->preferred_groups($preferred_groups) if defined $preferred_groups; $self->_autoindex($autoindex) if $autoindex; $self->_open_databases($write,$create); return $self; } sub _autoindex { my $self = shift; my $autodir = shift; my $dir = $self->dsn; my %ignore = map {$_=>1} ($self->_index_file,$self->_data_file, $self->_fasta_file,$self->_temp_file, $self->_notes_file, $self->_timestamp_file); my $maxtime = 0; my $maxfatime = 0; opendir (my $D,$autodir) or $self->throw("Couldn't open directory $autodir for reading: $!"); while (defined (my $node = readdir($D))) { next if $node =~ /^\./; my $path = "$dir/$node"; next if $ignore{$path}; next unless -f $path; my $mtime = _mtime(\*_); # not a typo $maxtime = $mtime if $mtime > $maxtime; $maxfatime = $mtime if $mtime > $maxfatime && $node =~ /\.(?:fa|fasta|dna)(?:\.gz)?$/; } close $D; my $timestamp_time = _mtime($self->_timestamp_file) || 0; my $all_files_exist = -e $self->_index_file && -e $self->_data_file && (-e $self->_fasta_file || !$maxfatime); # to avoid rebuilding FASTA files if not changed my $spare_fasta = $maxfatime > 0 && $maxfatime < $timestamp_time && -e $self->_fasta_file; if ($maxtime > $timestamp_time || !$all_files_exist) { print STDERR __PACKAGE__,": Reindexing files in $dir. This may take a while....\n"; $self->do_initialize(1,$spare_fasta); $self->load_gff($autodir,1); $self->load_fasta($autodir,1) unless $spare_fasta; print STDERR __PACKAGE__,": Reindexing done\n"; } else { $self->_open_databases(); } } sub _open_databases { my $self = shift; my ($write,$create) = @_; my $dsn = $self->dsn; unless (-d $dsn) { # directory does not exist $create or $self->throw("Directory $dsn does not exist and you did not specify the -create flag"); mkpath($dsn) or $self->throw("Couldn't create database directory $dsn: $!"); } my %db; local $DB_BTREE->{flags} = R_DUP; $DB_BTREE->{compare} = sub { lc($_[0]) cmp lc($_[1]) }; my $flags = O_RDONLY; $flags |= O_RDWR if $write; $flags |= O_CREAT if $create; tie(%db,'DB_File',$self->_index_file,$flags,0666,$DB_BTREE) or $self->throw("Couldn't tie ".$self->_index_file.": $!"); $self->{db} = \%db; $self->{data} = FeatureStore->new($self->_data_file,$write,$create); if (-e $self->_fasta_file) { my $dna_db = Bio::DB::Fasta->new($self->_fasta_file) or $self->throw("Can't reindex sequence file: $@"); $self->dna_db($dna_db); } my $mode = $write ? "+>>" : $create ? "+>" : "<"; my $notes_file = $self->_notes_file; open my $F, $mode, $notes_file or $self->throw("Could not open file '$notes_file': $!"); $self->{notes} = $F; } sub _close_databases { my $self = shift; delete $self->{db}; delete $self->{data}; delete $self->{notes}; } sub _delete_features { my $self = shift; my @feature_ids = @_; my $removed = 0; my $last_id = $self->{data}->last_id; for my $id (@feature_ids) { next unless $id >= 0 && $id < $last_id; my $feat = $self->{data}->get($id) or next; $self->{data}->remove($id); $self->_bump_class_count($feat->{gclass},-1); my @keys = $self->_secondary_keys($feat); $self->db->del_dup($_,$id) foreach @keys; $removed++; } $removed; } sub _secondary_keys { my $self = shift; my $feat = shift; return ( "__name__".lc(join ":",$feat->{gclass},$feat->{gname}), "__bin__".lc("$feat->{ref}$;$feat->{bin}"), "__type__".join(':',$feat->{method},$feat->{source}), map {"__attr__".lc(join(':',$_->[0],$_->[1]))} @{$feat->{attributes}} ); } sub _delete { my $self = shift; my $delete_spec = shift; return $self->SUPER::_delete($delete_spec) if @{$delete_spec->{segments}} or @{$delete_spec->{types}}; $self->throw("This operation would delete all feature data and -force not specified") unless $delete_spec->{force}; my $deleted = $self->{db}{__count__}; $self->{data} = FeatureStore->new($self->_data_file,1,1); %{$self->{db}} = (); $deleted; } # with duplicates enabled, we cannot simply do $db->{__index__}++; sub _bump_feature_count { my $self = shift; my $db = $self->{db}; if (@_) { delete $db->{__count__}; return $db->{__count__} = shift; } else { my $index = ${db}->{__count__}; delete $db->{__count__}; $db->{__count__} = ($index || 0) + 1; return $index; } } sub _bump_class_count { my $self = shift; my ($class,$count) = @_; $count ||= 1; my $db = $self->{db}; my $key = "__class__$class"; my $newcount = ($db->{$key} || 0) + $count; delete $db->{$key}; $db->{$key} = $newcount; } sub classes { my $self = shift; my $db = $self->db; my ($key,$value) = ('__class__',undef); my %classes; for (my $status = $db->seq($key,$value,R_CURSOR); $status == 0; $status = $db->seq($key,$value,R_NEXT)) { my ($class) = $key =~ /^__class__(.+)/ or last; $classes{$class}++ if $value > 0; } my @classes = sort keys %classes; return @classes; } sub do_initialize { my $self = shift; my $erase = shift; my $spare_fasta = shift; # used internally only! if ($erase) { $self->_close_databases; unlink $self->_index_file; unlink $self->_data_file; unlink $self->_notes_file; unless ($spare_fasta) { unlink $self->_fasta_file; unlink $self->_fasta_file.'.index'; } unlink $self->_timestamp_file; $self->_open_databases(1,1); } 1; } # load_sequence($fasta_filehandle,$first_sequence_id) sub load_sequence { my $self = shift; my ($io_handle,$id) = @_; my $file = $self->_fasta_file; my $loaded = 0; open my $F, '>>', $file or $self->throw("Could not append file '$file': $!"); if (defined $id) { print $F ">$id\n"; $loaded++; } while (<$io_handle>) { $loaded++ if /^>/; print $F $_; } close $F; my $dna_db = Bio::DB::Fasta->new($file) or $self->throw("Can't reindex sequence file: $@"); $self->dna_db($dna_db); $self->_touch_timestamp; return $loaded; } sub _mtime { my $file = shift; my @stat = stat($file); return $stat[9]; } sub _index_file { my $self = shift; return $self->dsn . "/bdb_features.btree"; } sub _data_file { my $self = shift; return $self->dsn . "/bdb_features.data"; } sub _fasta_file { my $self = shift; return $self->dsn . "/bdb_sequence.fa"; } sub _notes_file { my $self = shift; return $self->dsn . "/bdb_notes.idx"; } sub _temp_file { my $self = shift; local $^W=0; my (undef,$filename) = tempfile("bdb_temp_XXXXXX",DIR=>$self->tmpdir,OPEN=>0); return $filename; } sub _timestamp_file { my $self = shift; return $self->dsn ."/bdb_timestamp"; } sub db { my $db = shift()->{db} or return; return tied(%$db); } sub dsn { my $self = shift; my $d = $self->{dsn}; $self->{dsn} = shift if @_; $d; } sub tmpdir { my $self = shift; my $d = $self->{tmpdir}; $self->{tmpdir} = shift if @_; $d; } sub load_gff_line { my ($self, $feat) = @_; $feat->{strand} = '' if $feat->{strand} && $feat->{strand} eq '.'; $feat->{phase} = '' if $feat->{phase} && $feat->{phase} eq '.'; my $start = $feat->{start}; my $stop = $feat->{stop}; my $type = join(':',$feat->{method},$feat->{source}); my $bin = bin($feat->{start},$feat->{stop},MIN_BIN); $feat->{bin} = $bin; my $id = $self->{data}->put($feat); $bin = $self->normalizeNumber($bin); my $db = $self->{db}; for my $skey ($self->_secondary_keys($feat)) { $db->{$skey} = $id; } # save searchable notes to separate index my $fh = $self->{notes}; my @notes = map {$_->[1]} grep {lc $_->[0] eq 'note'} @{$feat->{attributes}}; print $fh $_,"\t",pack("u*",$id) or $self->throw("An error occurred while updating indexes: $!") foreach @notes; $self->{records_loaded}++; $self->_bump_feature_count(); $self->_bump_class_count($feat->{gclass}); } # do nothing! sub setup_load { my $self = shift; $self->{records_loaded} = 0; 1; } sub finish_load { my $self = shift; $self->db->sync && $self->throw("An error occurred while updating indexes: $!"); $self->_touch_timestamp; $self->{records_loaded}; } sub _touch_timestamp { my $self = shift; my $tsf = $self->_timestamp_file; open my $F, '>', $tsf or $self->throw("Could not write file '$tsf': $!"); print $F scalar(localtime); close $F; } # given sequence name, return (reference,start,stop,strand) sub get_abscoords { my $self = shift; my ($name,$class,$refseq) = @_; my %refs; my $regexp; if ($name =~ /[*?]/) { # uh oh regexp time $name = quotemeta($name); $name =~ s/\\\*/.*/g; $name =~ s/\\\?/.?/g; $regexp++; } # Find all features that have the requested name and class. # Sort them by reference point. my @features = @{$self->retrieve_features(-table => 'name', -key=>"$class:$name")}; if (!@features) { # nothing matched exactly, so try aliases @features = @{$self->retrieve_features(-table=>'attr',-key=>"Alias:$name")}; } foreach my $feature (@features){ push @{$refs{$feature->{ref}}},$feature; } # find out how many reference points we recovered if (! %refs) { $self->error("$name not found in database"); return; } # compute min and max my ($ref) = keys %refs; my @found = @{$refs{$ref}}; my ($strand,$start,$stop); my @found_segments; foreach my $ref (keys %refs) { next if defined($refseq) and $ref ne $refseq; my @found = @{$refs{$ref}}; my ($strand,$start,$stop,$name); foreach (@found) { $strand ||= $_->{strand}; $strand = '+' if $strand && $strand eq '.'; $start = $_->{start} if !defined($start) || $start > $_->{start}; $stop = $_->{stop} if !defined($stop) || $stop < $_->{stop}; $name ||= $_->{gname}; } push @found_segments,[$ref,$class,$start,$stop,$strand,$name]; } return \@found_segments; } sub get_types { my $self = shift; my ($srcseq,$class,$start,$stop,$want_count,$typelist) = @_; my (%obj,%result,$key,$value); $key = "__type__"; if (!$srcseq) { # optimized full type list my $db = $self->db; my $status = $db->seq($key,$value,R_CURSOR); while ($status == 0 && $key =~ /^__type__(.+)/) { my $type = $1; my ($method,$source) = split ':',$type; $obj{$type} = Bio::DB::GFF::Typename->new($method,$source); $result{$type}++; if ($want_count) { $status = $db->seq($key,$value,R_NEXT); } else { # skip to next key set $key .= "\0"; $status = $db->seq($key,$value,R_CURSOR) } } } else { # range search for my $feature (@{$self->_get_features_by_search_options( {rangetype => 'overlaps', refseq => $srcseq, refclass => ($class || undef), start => ($start || undef), stop => ($stop || undef), }, {} )} ) { my $type = Bio::DB::GFF::Typename->new($feature->{method},$feature->{source}); $obj{$type} = $type; $result{$type}++; } } return $want_count ? %result : values %obj; } # Low level implementation of fetching a named feature. # GFF annotations are named using the group class and name fields. # May return zero, one, or several Bio::DB::GFF::Feature objects. =head2 _feature_by_name Title : _feature_by_name Usage : $db->get_features_by_name($class,$name,$callback) Function: get a list of features by name and class Returns : count of number of features retrieved Args : name of feature, class of feature, and a callback Status : protected This method is used internally. The callback arguments are those used by make_feature(). =cut sub _feature_by_name { my $self = shift; my ($class,$name,$location,$callback) = @_; $callback || $self->throw('must provide a callback argument'); #use Devel::StackTrace; #warn Devel::StackTrace->new->as_string; my $count = 0; my $id = -1; my ($use_regexp, $use_glob,$using_alias_search); if ($name =~ /[*?]/) { # uh oh regexp time #If there is only one trailing *, do a range search if ($name =~ /^([^\*]+)\*$/) { $name = $1; $use_glob++; } else { $name = quotemeta($name); $name =~ s/\\\*/.*/g; $name =~ s/\\\?/.?/g; $use_regexp++; } } my @features; if ($use_glob) { my $callback = sub {my $feat = shift; $feat->{gname} =~ /^$name/i}; @features = @{$self->retrieve_features_range (-table => 'name', -start => "$class:$name", -do_while => $callback) }; } elsif ($use_regexp) { my $filter = sub {my $feat = shift; $feat->{gname} =~ /$name/i}; @features = @{$self->filter_features(-table =>'name', -filter => $filter)}; } else { @features = @{$self->retrieve_features(-table=>'name', -key => "$class:$name")}; } unless (@features) { $using_alias_search++; @features = @{$self->retrieve_features(-table=>'attr', -key=>"Alias:$name")}; } foreach my $feature (@features){ $id++; next unless $using_alias_search || $feature->{gclass} eq $class; if ($location) { next if $location->[0] ne $feature->{ref}; next if $location->[1] && $location->[1] > $feature->{stop}; next if $location->[2] && $location->[2] < $feature->{start}; } $count++; $callback->(@{$feature}{@hash2array_map},0); } return $count; } #sub get_feature_by_attribute{ sub _feature_by_attribute{ my $self = shift; my ($attributes,$callback) = @_; $callback || $self->throw('must provide a callback argument'); my $count = 0; my $feature_group_id = undef; #there could be more than one set of attributes...... while (my ($key, $value) = each %$attributes) { my @features = @{$self->retrieve_features (-table => "attr", -key => "$key:$value")}; for my $feature (@features) { $callback->(@{$feature}{@hash2array_map},$feature_group_id); $count++; } } } sub search_notes { my $self = shift; my ($search_string,$limit) = @_; $search_string =~ tr/*?//d; my @results; my @words = map {quotemeta($_)} $search_string =~ /(\w+)/g; my $search = join '|',@words; my (%found,$found); my $note_index = $self->{notes}; seek($note_index,0,0); # back to start while (<$note_index>) { next unless /$search/; chomp; my ($note,$uu) = split "\t"; $found{unpack("u*",$uu)}++; last if $limit && ++$found >= $limit; } my (@features, @matches); for my $idx (keys %found) { my $feature = $self->{data}->get($idx) or next; my @attributes = @{$feature->{attributes}}; my @values = map {lc $_->[0] eq 'note' ? $_->[1] : ()} @attributes; my $value = "@values"; my $hits; $hits++ while $value =~ /($search)/ig; # count the number of times we were hit push @matches,$hits; push @features,$feature; } for (my $i=0; $i<@matches; $i++) { my $feature = $features[$i]; my $matches = $matches[$i]; my $relevance = 10 * $matches; my $featname = Bio::DB::GFF::Featname->new($feature->{gclass}=>$feature->{gname}); my $type = Bio::DB::GFF::Typename->new($feature->{method}=>$feature->{source}); my $note; $note = join ' ',map {$_->[1]} grep {$_->[0] eq 'Note'} @{$feature->{attributes}}; push @results,[$featname,$note,$relevance,$type]; } return @results; } sub _get_features_by_search_options { #The $data argument is not used and is preserved for superclass compatibility my ($self, $search,$options) = @_; my $count = 0; my ($rangetype,$refseq,$class,$start,$stop,$types,$sparse,$order_by_group,$attributes,$temp_file) = (@{$search}{qw(rangetype refseq refclass start stop types)}, @{$options}{qw(sparse sort_by_group ATTRIBUTES temp_file)}) ; $start = 0 unless defined($start); $stop = MAX_BIN unless defined($stop); my $bin = bin($start,$stop,MIN_BIN); $bin = $self->normalizeNumber($bin); my ($results,@features,%found,%results_table); if ($temp_file) { local $DB_BTREE->{flags} = R_DUP; # note: there is a race condition possible here, if someone reuses the # same name between the time we get the tmpfile name and the time we # ask DB_File to open it. tie(%results_table,'DB_File',$temp_file,O_RDWR|O_CREAT,0666,$DB_BTREE) or $self->throw("Couldn't tie temporary file ".$temp_file." for writing: $!"); $results = \%results_table; } else { $results = \@features; } my $filter = sub { my $feature = shift; my $ref = $feature->{ref}; my $feature_start = $feature->{start}; my $feature_stop = $feature->{stop}; my $feature_id = $feature->{feature_id}; return 0 if $found{$feature_id}++; if (defined $refseq) { return 0 unless lc $refseq eq lc $ref; $start = 0 unless defined($start); $stop = MAX_SEGMENT unless defined($stop); if ($rangetype eq 'overlaps') { return 0 unless $feature_stop >= $start && $feature_start <= $stop; } elsif ($rangetype eq 'contains') { return 0 unless $feature_start >= $start && $feature_stop <= $stop; } elsif ($rangetype eq 'contained_in') { return 0 unless $feature_start <= $start && $feature_stop >= $stop; } else { return 0 unless $feature_start == $start && $feature_stop == $stop; } } my $feature_source = $feature->{source}; my $feature_method = $feature->{method}; if (defined $types && @$types){ return 0 unless $self->_matching_typelist($feature_method,$feature_source,$types); } my $feature_attributes = $feature->{attributes}; if (defined $attributes){ return 0 unless $self->_matching_attributes($feature_attributes,$attributes); } return 1; }; if (defined $refseq && !$sparse) { my $tier = MAX_BIN; while ($tier >= MIN_BIN) { my ($tier_start,$tier_stop) = (bin_bot($tier,$start),bin_top($tier,$stop)); # warn "Using $tier_start $tier_stop\n"; if ($tier_start == $tier_stop) { $self->retrieve_features(-table => "bin", -key => "$refseq$;$tier_start", -filter => $filter, -result => $results); } else { my $callback = sub {my $feat = shift; $feat->{bin} <= $tier_stop}; $self->retrieve_features_range(-table => "bin", -start => "$refseq$;$tier_start", -do_while => $callback, -filter => $filter, -result => $results); } $tier /= 10; } } elsif (@$types) { foreach (@$types) { my $type = join ':',@$_; $self->retrieve_features_range(-table => 'type', -start => $type, -filter => $filter, -do_while => sub { my $f = shift; lc($f->{method}) eq lc($_->[0]) && lc($f->{source}||$_->[1]||'') eq lc($_->[1]||'') }, -result => $results); } } elsif (defined $attributes) { my ($attribute_name,$attribute_value) = each %$attributes; # pick first one $self->retrieve_features(-table => 'attr', -key => "${attribute_name}:${attribute_value}", -filter => $filter, -result => $results); } else { $self->filter_features(-filter => $filter,-result=>$results); } return $results; } sub retrieve_features { my $self = shift; my ($table, $key, $filter, $result) = rearrange(['TABLE','KEY','FILTER', 'RESULT'],@_); my @result; $result ||= \@result; my $frozen; my @ids = $self->db->get_dup("__".lc($table)."__".lc($key)); my $data = $self->{data}; local $^W = 0; # because _hash_to_array() will generate lots of uninit values foreach my $id (@ids) { my $feat = $data->get($id); my $filter_result = $filter ? $filter->($feat) : 1; next unless $filter_result; if (ref $result eq 'HASH') { $result->{"$feat->{gclass}:$feat->{gname}"} = join ($;,$self->_hash_to_array($feat)); } else { push @$result, $feat; } last if $filter_result == -1; } return $result; } sub retrieve_features_range { my ($self) = shift; my ($table, $start, $do_while, $filter, $result) = rearrange(['TABLE','START','DO_WHILE', 'FILTER', 'RESULT'],@_); local $^W = 0; # because _hash_to_array will generate lots of uninit warnings my @result; $result ||= \@result; my ($id, $key, $value); $key = "__".$table."__".$start; my $db = $self->db; for (my $status = $db->seq($key,$value,R_CURSOR); $status == 0; $status = $db->seq($key,$value,R_NEXT)) { my $feat = $self->{data}->get($value); last unless $do_while->($feat,$key); my $filter_result = $filter ? $filter->($feat) : 1; next unless $filter_result; if (ref $result eq 'HASH') { $result->{"$feat->{gclass}:$feat->{gname}"} = join($;,$self->_hash_to_array($feat)); } else { push @$result,$feat; } last if $filter_result == -1; } return $result; } sub filter_features { my ($self) = shift; my ($filter,$result) = rearrange(['FILTER','RESULT'],@_); my @result; $result ||= \@result; my ($key, $frozen); my $data = $self->{data}; $data->reset; while (my $feat = $data->next) { my $filter_result = $filter ? $filter->($feat) : 1; next unless $filter_result; if (ref($result) eq 'HASH') { $result->{"$feat->{gclass}:$feat->{gname}"} = join($;,$self->_hash_to_array($feat)); } else { push @$result,$feat; } last if $filter_result == -1; } return $result; } sub _basic_features_by_id{ my $self = shift; my ($ids) = @_; $ids = [$ids] unless ref $ids =~ /ARRAY/; my @result; my $data = $self->{data}; for my $feature_id (@$ids){ push @result, $data->get($feature_id); } return wantarray() ? @result : $result[0]; } sub normalizeNumber { my ($self, $num) = @_; while ((length $num) < MAX_NUM_LENGTH) { $num = "0".$num; } return $num; } sub get_features_iterator { my $self = shift; my ($search,$options,$callback) = @_; $callback || $self->throw('must provide a callback argument'); $options->{temp_file} = $self->_temp_file; my $results = $self->_get_features_by_search_options($search,$options); return Bio::DB::GFF::Adaptor::berkeleydb::iterator->new($results,$callback,$options->{temp_file}); } #--------------------------------------------------------------------------# package FeatureStore; # This is a very specialized package that stores serialized features onto a file-based # array. The array is indexed by the physical offset to the beginning of each serialized # feature. use strict; use Fcntl qw(SEEK_SET SEEK_END); use base 'Bio::Root::Root'; use Bio::DB::GFF::Adaptor::memory::feature_serializer; # qw(feature2string string2feature @hash2array_map); sub new { my $class = shift; my $dbname = shift or $class->throw("must provide a filepath argument"); my ($write,$create) = @_; my $mode = $create ? "+>" : $write ? "+>>" : "<"; open my $F, $mode, $dbname or $class->throw("Could not open file '$dbname': $!"); my $self = bless { fh => $F, next_idx => 0, last_id => 0, },$class; return $self; } sub put { my $self = shift; my $feature = shift; my $fh = $self->{fh}; seek($fh,0,SEEK_END); my $offset = tell($fh) || 0; $self->{last_id} = $offset; my $id = pack("L",$offset); $feature->{feature_id} = $id; my $value = feature2string($feature); print $fh pack("n/a*",$value) or $self->throw("An error occurred while updating the data file: $!"); return $id; } sub last_id { shift->{last_id}; } sub get { my $self = shift; my $idx = shift; my $offset = unpack("L",$idx); my $fh = $self->{fh}; my ($value,$length); $offset ||= 0; seek($fh,$offset,SEEK_SET); return unless read($fh,$length,2); return unless read($fh,$value,unpack("n",$length)); $self->{next_idx} = tell($fh); return if substr($value,0,1) eq "\0"; return string2feature($value); } sub next { my $self = shift; my $fh = $self->{fh}; my $result; do { $result = $self->get(pack("L",$self->{next_idx})); } until $result || eof($fh); $self->{next_idx} = 0 unless $result; $result; } sub remove { my $self = shift; my $id = shift; my $offset = unpack("L",$id); my $fh = $self->{fh}; my ($value,$length); seek($fh,$offset,SEEK_SET); return unless read($fh,$length,2); print $fh "\0"x$length; # null it out 1; } sub _seek { my $self = shift; my $idx = shift; my $offset = unpack("L",$idx); seek($self->{fh},$offset,SEEK_SET); $self->{next_idx} = tell($self->{fh}); } sub reset { my $self = shift; $self->_seek(pack("L",0)); } sub _feature2string { my $feature = shift; my @a = @{$feature}{@hash2array_map}; push @a,map {@$_} @{$feature->{attributes}} if $feature->{attributes}; return join $;,@a; } sub _string2feature { my $string = shift; my (%feature,@attributes); (@feature{@hash2array_map},@attributes) = split $;,$string; while (@attributes) { my ($key,$value) = splice(@attributes,0,2); push @{$feature{attributes}},[$key,$value]; } $feature{group_id} = undef; \%feature; } 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor/biofetch.pm000444000766000024 2343213155576320 20652 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::biofetch; #$Id$ =head1 NAME Bio::DB::GFF::Adaptor::biofetch -- Cache BioFetch objects in a Bio::DB::GFF database =head1 SYNOPSIS Proof of principle. Not for production use. =head1 DESCRIPTION This adaptor is a proof-of-principle. It is used to fetch BioFetch sequences into a Bio::DB::GFF database (currently uses a hard-coded EMBL database) as needed. This allows the Generic Genome Browser to be used as a Genbank/EMBL browser. =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright 2002 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use strict; use Bio::DB::GFF::Util::Rearrange; # for rearrange() use Bio::DB::BioFetch; use Bio::SeqIO; use vars qw(%preferred_tags); # THIS IS WRONG: biofetch should delegate to an underlying # database adaptor, and not inherit from one. use base qw(Bio::DB::GFF::Adaptor::dbi::mysql); # priority for choosing names of CDS tags, higher is higher priority %preferred_tags = ( strain => 10, organism => 20, protein_id => 40, locus_tag => 50, locus => 60, gene => 70, standard_name => 80, ); =head2 new Title : new Usage : $db = Bio::DB::GFF->new(-adaptor=>'biofetch',@args) Function: create a new adaptor Returns : a Bio::DB::GFF object Args : -adaptor : required. Which adaptor to use; biofetch for mysql, biofetch_oracle for Oracle -preferred_tags : optional. A hash of {classname => weight,...} used to determine the class and name of the feature when a choice of possible feature classes is available (e.g. a feature has both a 'gene' and a 'locus' tag). Common defaults are provided that work well for eukaryotic features (but not well for viral/prokaryotic) see below for additional arguments. Status : Public This is the constructor for the adaptor. It is called automatically by Bio::DB::GFF-Enew. In addition to arguments that are common among all adaptors, the following class-specific arguments are recgonized: Argument Description -------- ----------- -dsn the DBI data source, e.g. 'dbi:mysql:ens0040' -user username for authentication -pass the password for authentication -proxy [['http','ftp'],'http://proxy:8080'] -source source to use for loaded features ('EMBL') -dsn,-user and -pass indicate the local database to cache results in, and as are per Bio::DB::GFF::Adaptor::dbi. The -proxy argument allows you to set the biofetch web proxy, and uses the same syntax described for the proxy() method of L, except that the argument must be passed as an array reference. =cut sub new { my $class = shift; my $self = $class->SUPER::new(@_); my ($preferred,$proxy,$source) = rearrange(['PREFERRED_TAGS','PROXY','SOURCE'],@_); # if the caller sent their own preferences, then use these, otherwise use defaults. $self->_preferred_tags($preferred ? $preferred : \%preferred_tags); $self->_source($source || 'EMBL'); if ($proxy) { my @args = ref($proxy) ? @$proxy : eval $proxy; $self->{_proxy} = \@args if @args; } $self; } sub segment { my $self = shift; my @segments = $self->SUPER::segment(@_); if (!@segments) { my $refclass = $self->refclass; my %args = $self->setup_segment_args(@_); if ($args{-class} && $args{-class} =~ /$refclass/oi) { return unless $self->load_from_embl('embl'=>$args{-name}); @segments = $self->SUPER::segment(@_); } elsif ($args{-class} && $args{-class} =~ /refseq|swall|embl/i) { #hack to get refseq names return unless $self->load_from_embl(lc($args{-class})=>$args{-name}); $args{-class} = $self->refclass; @segments = $self->SUPER::segment(%args); } } $self->_multiple_return_args(@segments); } # default is to return 'Sequence' as the class of all references sub refclass { my $self = shift; my $refname = shift; 'Sequence'; } sub load_from_embl { my $self = shift; my $db = shift; my $acc = shift or $self->throw('Must provide an accession ID'); my $biofetch; if ($self->{_biofetch}{$db}) { $biofetch = $self->{_biofetch}{$db}; } else { $biofetch = $self->{_biofetch}{$db} = Bio::DB::BioFetch->new(-db=>$db); $biofetch->retrieval_type('tempfile'); $biofetch->proxy(@{$self->{_proxy}}) if $self->{_proxy}; } my $seq = eval {$biofetch->get_Seq_by_id($acc)} or return; $self->_load_embl($acc,$seq); 1; } sub load_from_file { my $self = shift; my $file = shift; my $format = $file =~ /\.(gb|genbank|gbk)$/i ? 'genbank' : 'embl'; my $seqio = Bio::SeqIO->new( '-format' => $format, -file => $file); my $seq = $seqio->next_seq; $self->_load_embl($seq->accession,$seq); 1; } sub _load_embl { my $self = shift; my $acc = shift; my $seq = shift; my $refclass = $self->refclass; my $locus = $seq->id; my $source = $self->_source; # begin loading $self->setup_load(); # first synthesize the entry for the top-level feature my @aliases; foreach ($seq->accession,$seq->get_secondary_accessions) { next if lc($_) eq lc($acc); push @aliases,[Alias => $_]; } $self->load_gff_line( { ref => $acc, class => $refclass, source => $source, # method => 'origin', method => 'region', start => 1, stop => $seq->length, score => undef, strand => '.', phase => '.', gclass => $self->refclass, gname => $acc, tstart => undef, tstop => undef, attributes => [[Note => $seq->desc],@aliases], } ); # now load each feature in turn my ($transcript_version,$mRNA_version) = (0,0); for my $feat ($seq->all_SeqFeatures) { my $attributes = $self->get_attributes($feat); my $name = $self->guess_name($attributes); my $location = $feat->location; my @segments = map {[$_->start,$_->end,$_->seq_id]} $location->can('sub_Location') ? $location->sub_Location : $location; # this changed CDS to coding, but that is the wrong thing to do, since # CDS is in SOFA and coding is not # my $type = $feat->primary_tag eq 'CDS' ? 'coding' # : $feat->primary_tag; my $type= $feat->primary_tag; next if (lc($type) eq 'contig'); # next if (lc($type) eq 'variation'); if (lc($type) eq 'variation' and $feat->length == 1) { $type = 'SNP'; } elsif (lc($type) eq 'variation' ) { $type = 'chromosome_variation'; } if ($type eq 'source') { $type = 'region'; } if ($type =~ /misc.*RNA/i) { $type = 'RNA'; } if ($type eq 'misc_feature' and $name->[1] =~ /similar/i) { $type = 'computed_feature_by_similarity'; } elsif ($type eq 'misc_feature') { warn "skipping a misc_feature\n"; next; } my $parttype = $feat->primary_tag eq 'mRNA' ? 'exon' : $feat->primary_tag; if ($type eq 'gene') { $transcript_version = 0; $mRNA_version = 0; } elsif ($type eq 'mRNA') { $name->[1] = sprintf("%s.t%02d",$name->[1],++$transcript_version); } elsif ($type eq 'CDS') { $name->[0] = 'mRNA'; $name->[1] = sprintf("%s.t%02d",$name->[1],$transcript_version); } my $strand = $feat->strand; my $str = defined $strand ? ($strand > 0 ? '+' : '-') : '.'; $self->load_gff_line( { ref => $acc, class => $refclass, source => $source, method => $type, start => $location->start, stop => $location->end, score => $feat->score || undef, strand => $str, phase => $feat->frame || '.', gclass => $name->[0], gname => $name->[1], tstart => undef, tstop => undef, attributes => $attributes, } ) if ($type && ($type ne 'CDS'||($type eq 'CDS'&&@segments==1) ) ); @$attributes = (); next if @segments == 1; for my $segment (@segments) { my $strand = $feat->strand; my $str = defined $strand ? ($strand > 0 ? '+' : '-') : '.'; $self->load_gff_line( { ref => $segment->[2] eq $locus ? $acc : $segment->[2], class => $refclass, source => $source, method => $parttype, start => $segment->[0], stop => $segment->[1], score => $feat->score || undef, strand => $str, phase => $feat->frame || '.', gclass => $name->[0], gname => $name->[1], tstart => undef, tstop => undef, attributes => $attributes, } ); } } # finish loading $self->finish_load(); # now load the DNA $self->load_sequence_string($acc,$seq->seq); 1; } sub get_attributes { my $self = shift; my $seq = shift; my @tags = $seq->all_tags or return; my @result; foreach my $tag (@tags) { foreach my $value ($seq->each_tag_value($tag)) { push @result,[$tag=>$value]; } } \@result; } sub guess_name { my $self = shift; my $attributes = shift; # remove this fix when Lincoln fixes it properly return ["Misc" => "Misc"] unless ($attributes); # these are arbitrary, and possibly destructive defaults my @ordered_attributes = sort {($self->_preferred_tags->{$a->[0]} || 0) <=> ($self->_preferred_tags->{$b->[0]} || 0)} @$attributes; my $best = pop @ordered_attributes; @$attributes = @ordered_attributes; return $best; } sub _preferred_tags { my $self = shift; $self->{preferred_tags} = shift if @_; return $self->{preferred_tags}; } sub _source { my $self = shift; $self->{source} = shift if @_; $self->{source}; } 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor/biofetch_oracle.pm000444000766000024 2055613155576320 22203 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::biofetch_oracle; #$Id$ =head1 NAME Bio::DB::GFF::Adaptor::biofetch_oracle -- Cache BioFetch objects in a Bio::DB::GFF database =head1 SYNOPSIS Proof of principle. Not for production use. =head1 DESCRIPTION This adaptor is a proof-of-principle. It is used to fetch BioFetch sequences into a Bio::DB::GFF database (currently uses a hard-coded EMBL database) as needed. This allows the Generic Genome Browser to be used as a Genbank/EMBL browser. =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright 2002 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use strict; use Bio::DB::GFF::Util::Rearrange; # for rearrange() use Bio::DB::BioFetch; use Bio::SeqIO; use vars qw(%default_preferred_tags); use base qw(Bio::DB::GFF::Adaptor::dbi::oracle); # priority for choosing names of CDS tags, higher is higher priority %default_preferred_tags = ( strain => 10, organism => 20, protein_id => 40, locus_tag => 50, locus => 60, gene => 70, standard_name => 80, ); sub _preferred_tags { my ($self, $tags) = @_; if ($tags && (ref($tags) =~ /HASH/)){ $self->{preferred_tags} = $tags; } return $self->{preferred_tags}; } =head2 new Title : new Usage : $db = Bio::DB::GFF->new(-adaptor=>'biofetch_oracle', -preferred_tags => \%preferred, @args) Function: create a new adaptor Returns : a Bio::DB::GFF object Args : -adaptor : required. Which adaptor to use; biofetch for mysql, biofetch_oracle for Oracle -preferred_tags : optional. A hash of {classname => weight,...} used to determine the class and name of the feature when a choice of possible feature classes is available (e.g. a feature has both a 'gene' and a 'locus' tag). Common defaults are provided that work well for eukaryotic features (but not well for viral/prokaryotic) see below for additional arguments. Status : Public This is the constructor for the adaptor. It is called automatically by Bio::DB::GFF-Enew. In addition to arguments that are common among all adaptors, the following class-specific arguments are recgonized: Argument Description -------- ----------- -dsn the DBI data source, e.g. 'dbi:mysql:ens0040' -user username for authentication -pass the password for authentication -proxy [['http','ftp'],'http://proxy:8080'] -create initialize the database -dsn,-user and -pass indicate the local database to cache results in, and as are per Bio::DB::GFF::Adaptor::dbi. The -proxy argument allows you to set the biofetch web proxy, and uses the same syntax described for the proxy() method of L, except that the argument must be passed as an array reference. =cut sub new { my $class = shift; my $args = shift; my $self = $class->SUPER::new($args); my ($preferred) = rearrange(['PREFERRED_TAGS'],$args); $self->_preferred_tags($preferred?$preferred:\%default_preferred_tags); # if the caller sent their own preferences, then use these, otherwise use defaults. my ($proxy) = rearrange(['PROXY'],$args); if ($proxy) { my @args = ref($proxy) ? @$proxy : eval $proxy; $self->{_proxy} = \@args if @args; } $self; } sub segment { my $self = shift; my @segments = $self->SUPER::segment(@_); if (!@segments) { my $refclass = $self->refclass; my %args = $self->setup_segment_args(@_); if ($args{-class} && $args{-class} =~ /$refclass/oi) { return unless $self->load_from_embl('embl'=>$args{-name}); @segments = $self->SUPER::segment(@_); } elsif ($args{-class} && $args{-class} =~ /refseq|swall|embl/i) { #hack to get refseq names return unless $self->load_from_embl(lc($args{-class})=>$args{-name}); $args{-class} = $self->refclass; @segments = $self->SUPER::segment(%args); } } $self->_multiple_return_args(@segments); } # default is to return 'Sequence' as the class of all references sub refclass { my $self = shift; my $refname = shift; 'Accession'; } sub load_from_embl { my $self = shift; my $db = shift; my $acc = shift or $self->throw('Must provide an accession ID'); my $biofetch; if ($self->{_biofetch}{$db}) { $biofetch = $self->{_biofetch}{$db}; } else { $biofetch = $self->{_biofetch}{$db} = Bio::DB::BioFetch->new(-db=>$db); $biofetch->retrieval_type('tempfile'); $biofetch->proxy(@{$self->{_proxy}}) if $self->{_proxy}; } my $seq = eval {$biofetch->get_Seq_by_id($acc)} or return; $self->_load_embl($acc,$seq); 1; } sub load_from_file { my $self = shift; my $file = shift; my $format = $file =~ /\.(gb|genbank|gbk)$/i ? 'genbank' : 'embl'; my $seqio = Bio::SeqIO->new( '-format' => $format, -file => $file); my $seq = $seqio->next_seq; $self->_load_embl($seq->accession,$seq); 1; } sub _load_embl { my $self = shift; my $acc = shift; my $seq = shift; my $refclass = $self->refclass; my $locus = $seq->id; # begin loading $self->setup_load(); # first synthesize the entry for the top-level feature my @aliases; foreach ($seq->accession,$seq->get_secondary_accessions) { next if lc($_) eq lc($acc); push @aliases,[Alias => $_]; } $self->load_gff_line( { ref => $acc, class => $refclass, source => 'EMBL', method => 'origin', start => 1, stop => $seq->length, score => undef, strand => '.', phase => '.', gclass => $self->refclass, gname => $acc, tstart => undef, tstop => undef, attributes => [[Note => $seq->desc],@aliases], } ); # now load each feature in turn for my $feat ($seq->all_SeqFeatures) { my $attributes = $self->get_attributes($feat); my $name = $self->guess_name($attributes); my $location = $feat->location; my @segments = map {[$_->start,$_->end,$_->seq_id]} $location->can('sub_Location') ? $location->sub_Location : $location; my $type = $feat->primary_tag eq 'CDS' ? 'mRNA' : $feat->primary_tag; my $parttype = $feat->primary_tag eq 'gene' ? 'exon' : $feat->primary_tag; if ($feat->primary_tag =~ /^(gene|CDS)$/) { $self->load_gff_line( { ref => $acc, class => $refclass, source => 'EMBL', method => $type, start => $location->start, stop => $location->end, score => $feat->score || undef, strand => $feat->strand > 0 ? '+' : ($feat->strand < 0 ? '-' : '.'), phase => $feat->frame || '.', gclass => $name->[0], gname => $name->[1], tstart => undef, tstop => undef, attributes => $attributes, } ); @$attributes = (); } for my $segment (@segments) { $self->load_gff_line( { ref => $segment->[2] eq $locus ? $acc : $segment->[2], class => $refclass, source => 'EMBL', method => $parttype, start => $segment->[0], stop => $segment->[1], score => $feat->score || undef, strand => $feat->strand > 0 ? '+' : ($feat->strand < 0 ? '-' : '.'), phase => $feat->frame || '.', gclass => $name->[0], gname => $name->[1], tstart => undef, tstop => undef, attributes => $attributes, } ); } } # finish loading $self->finish_load(); # now load the DNA $self->load_sequence_string($acc,$seq->seq); 1; } sub get_attributes { my $self = shift; my $seq = shift; my @tags = $seq->all_tags or return; my @result; foreach my $tag (@tags) { foreach my $value ($seq->each_tag_value($tag)) { push @result,[$tag=>$value]; } } \@result; } sub guess_name { my $self = shift; my $attributes = shift; # remove this fix when Lincoln fixes it properly return ["Misc" => "Misc"] unless ($attributes); # these are arbitrary, and possibly destructive defaults my @ordered_attributes = sort {($self->_preferred_tags->{$a->[0]} || 0) <=> ($self->_preferred_tags->{$b->[0]} || 0)} @$attributes; my $best = pop @ordered_attributes; @$attributes = @ordered_attributes; return $best; } 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor/dbi.pm000444000766000024 22002113155576320 17636 0ustar00cjfieldsstaff000000000000 =head1 NAME Bio::DB::GFF::Adaptor::dbi -- Database adaptor for DBI (SQL) databases =head1 SYNOPSIS See L =head1 DESCRIPTION This is the base class for DBI-based adaptors. It does everything except generating the text of the queries to be used. See the section QUERIES TO IMPLEMENT for the list of methods that must be implemented. =cut package Bio::DB::GFF::Adaptor::dbi; # base class for dbi-based implementations use strict; use DBI; use Bio::DB::GFF::Util::Rearrange; # for rearrange() use Bio::DB::GFF::Util::Binning; use Bio::DB::GFF::Adaptor::dbi::iterator; use Bio::DB::GFF::Adaptor::dbi::caching_handle; use base qw(Bio::DB::GFF); # constants for choosing use constant MAX_SEGMENT => 1_000_000_000; # the largest a segment can get # this is the largest that any reference sequence can be (100 megabases) use constant MAX_BIN => 1_000_000_000; # this is the smallest bin (1 K) use constant MIN_BIN => 1000; # size of range over which it is faster to force the database to use the range for indexing use constant STRAIGHT_JOIN_LIMIT => 200_000; # this is the size to which DNA should be shredded use constant DNA_CHUNK_SIZE => 2000; # size of summary bins for interval coverage statistics use constant SUMMARY_BIN_SIZE => 1000; # for debugging fbin optimization use constant EPSILON => 1e-7; # set to zero if you trust mysql's floating point comparisons use constant OPTIMIZE => 1; # set to zero to turn off optimization completely ############################################################################## =head2 new Title : new Usage : $db = Bio::DB::GFF->new(@args) Function: create a new adaptor Returns : a Bio::DB::GFF object Args : see below Status : Public This is the constructor for the adaptor. It is called automatically by Bio::DB::GFF-Enew. In addition to arguments that are common among all adaptors, the following class-specific arguments are recgonized: Argument Description -------- ----------- -dsn the DBI data source, e.g. 'dbi:mysql:ens0040' -user username for authentication -pass the password for authentication =cut # Create a new Bio::DB::GFF::Adaptor::dbi object sub new { my $class = shift; my ($features_db,$username,$auth,$other) = rearrange([ [qw(FEATUREDB DB DSN)], [qw(USERNAME USER)], [qw(PASSWORD PASSWD PASS)], ],@_); $features_db || $class->throw("new(): Provide a data source or DBI database"); if (!ref($features_db)) { my $dsn = $features_db; my @args; push @args,$username if defined $username; push @args,$auth if defined $auth; $features_db = Bio::DB::GFF::Adaptor::dbi::caching_handle->new($dsn,@args) || $class->throw("new(): Failed to connect to $dsn: " . Bio::DB::GFF::Adaptor::dbi::caching_handle->errstr); } else { $features_db->isa('DBI::db') || $class->throw("new(): $features_db is not a DBI handle"); } # fill in object return bless { features_db => $features_db },$class; } sub debug { my $self = shift; $self->features_db->debug(@_); $self->SUPER::debug(@_); } =head2 features_db Title : features_db Usage : $dbh = $db->features_db Function: get database handle Returns : a DBI handle Args : none Status : Public Note: what is returned is not really a DBI::db handle, but a subclass of one. This means that you cannot manipulate the handle's attributes directly. Instead call the attribute method: my $dbh = $db->features_db; $dbh->attribute(AutoCommit=>0); =cut sub features_db { shift->{features_db} } sub dbh { shift->{features_db} } =head2 get_dna Title : get_dna Usage : $string = $db->get_dna($name,$start,$stop,$class) Function: get DNA string Returns : a string Args : name, class, start and stop of desired segment Status : Public This method performs the low-level fetch of a DNA substring given its name, class and the desired range. It is actually a front end to the abstract method make_dna_query(), which it calls after some argument consistency checking. =cut sub get_dna { my $self = shift; my ($ref,$start,$stop,$class) = @_; my ($offset_start,$offset_stop); my $has_start = defined $start; my $has_stop = defined $stop; my $reversed; if ($has_start && $has_stop && $start > $stop) { $reversed++; ($start,$stop) = ($stop,$start); } # turn start and stop into 0-based offsets my $cs = $self->dna_chunk_size; $start -= 1; $stop -= 1; $offset_start = int($start/$cs)*$cs; $offset_stop = int($stop/$cs)*$cs; my $sth; # special case, get it all if (!($has_start || $has_stop)) { $sth = $self->dbh->do_query('select fdna,foffset from fdna where fref=? order by foffset',$ref); } elsif (!$has_stop) { $sth = $self->dbh->do_query('select fdna,foffset from fdna where fref=? and foffset>=? order by foffset', $ref,$offset_start); } else { # both start and stop defined $sth = $self->dbh->do_query('select fdna,foffset from fdna where fref=? and foffset>=? and foffset<=? order by foffset', $ref,$offset_start,$offset_stop); } my $dna = ''; while (my($frag,$offset) = $sth->fetchrow_array) { substr($frag,0,$start-$offset) = '' if $has_start && $start > $offset; $dna .= $frag; } substr($dna,$stop-$start+1) = '' if $has_stop && $stop-$start+1 < length($dna); if ($reversed) { $dna = reverse $dna; $dna =~ tr/gatcGATC/ctagCTAG/; } $sth->finish; $dna; } =head2 get_abscoords Title : get_abscoords Usage : ($refseq,$refclass,$start,$stop,$strand) = $db->get_abscoords($name,$class) Function: get absolute coordinates for landmark Returns : an array ref -- see below Args : name and class of desired landmark Status : Public This method performs the low-level resolution of a landmark into a reference sequence and position. The result is an array ref, each element of which is a five-element list containing reference sequence name, class, start, stop and strand. =cut sub get_abscoords { my $self = shift; my ($name,$class,$refseq) = @_; my $sth = $self->make_abscoord_query($name,$class,$refseq); my @result; while (my @row = $sth->fetchrow_array) { push @result,\@row } $sth->finish; if (@result == 0) { #$self->error("$name not found in database"); my $sth2 = $self->make_aliasabscoord_query($name,$class); while (my @row2 = $sth2->fetchrow_array) { push @result,\@row2 } $sth->finish; if (@result == 0){ $self->error("$name not found in database"); return; } } return \@result; } =head2 get_features Title : get_features Usage : $db->get_features($search,$options,$callback) Function: retrieve features from the database Returns : number of features retrieved Args : see below Status : Public This is the low-level method that is called to retrieve GFF lines from the database. It is responsible for retrieving features that satisfy range and feature type criteria, and passing the GFF fields to a callback subroutine. See the manual page for Bio::DB::GFF for the interpretation of the arguments and how the information retrieved by get_features is passed to the callback for processing. Internally, get_features() is a front end for range_query(). The latter method constructs the query and executes it. get_features() calls fetchrow_array() to recover the fields and passes them to the callback. =cut # Given sequence name, range, and optional filter, retrieve list of # all features. Passes features through callback. sub get_features { my $self = shift; my ($search,$options,$callback) = @_; $callback || $self->throw('must provide a callback argument'); my $sth = $self->range_query(@{$search}{qw(rangetype refseq refclass start stop types) }, @{$options}{qw( sparse sort_by_group ATTRIBUTES BINSIZE)}) or return; my $count = 0; while (my @row = $sth->fetchrow_array) { $callback->(@row); $count++; } $sth->finish; return $count; } =head2 classes Title : classes Usage : $db->classes Function: return list of landmark classes in database Returns : a list of classes Args : none Status : public This routine returns the list of reference classes known to the database, or empty if classes are not used by the database. Classes are distinct from types, being essentially qualifiers on the reference namespaces. NOTE: In the current mysql-based schema, this query takes a while to run due to the classes not being normalized. =cut sub classes { my $self = shift; my ($query,@args) = $self->make_classes_query or return; my $sth = $self->dbh->do_query($query,@args); my @classes; while (my ($c) = $sth->fetchrow_array) { push @classes,$c; } @classes; } =head2 make_classes_query Title : make_classes_query Usage : ($query,@args) = $db->make_classes_query Function: return query fragment for generating list of reference classes Returns : a query and args Args : none Status : public =cut sub make_classes_query { my $self = shift; return; } =head2 _feature_by_name Title : _feature_by_name Usage : $db->get_features_by_name($name,$class,$callback) Function: get a list of features by name and class Returns : count of number of features retrieved Args : name of feature, class of feature, and a callback Status : protected This method is used internally. The callback arguments are those used by make_feature(). Internally, it invokes the following abstract procedures: make_features_select_part make_features_from_part make_features_by_name_where_part make_features_by_alias_where_part (for aliases) make_features_join_part =cut sub _feature_by_name { my $self = shift; my ($class,$name,$location,$callback) = @_; $callback || $self->throw('must provide a callback argument'); my $select = $self->make_features_select_part; my $from = $self->make_features_from_part(undef,{sparse_groups=>1}); my ($where,@args) = $self->make_features_by_name_where_part($class,$name); my $join = $self->make_features_join_part; my $range = $self->make_features_by_range_where_part('overlaps', {refseq=>$location->[0], class =>'', start=>$location->[1], stop =>$location->[2]}) if $location; # group query my $query1 = "SELECT $select FROM $from WHERE $where AND $join"; $query1 .= " AND $range" if $range; # alias query $from = $self->make_features_from_part(undef,{attributes=>1}); ($where,@args) = $self->make_features_by_alias_where_part($class,$name); # potential bug - @args1==@args2? my $query2 = "SELECT $select FROM $from WHERE $where AND $join"; $query2 .= " AND $range" if $range; my $count = 0; for my $query ($query1,$query2) { my $sth = $self->dbh->do_query($query,@args); while (my @row = $sth->fetchrow_array) { $callback->(@row); $count++; } $sth->finish; } return $count; } =head2 _feature_by_id Title : _feature_by_id Usage : $db->_feature_by_id($ids,$type,$callback) Function: get a list of features by ID Returns : count of number of features retrieved Args : arrayref containing list of IDs to fetch and a callback Status : protected This method is used internally. The $type selector is one of "feature" or "group". The callback arguments are those used by make_feature(). Internally, it invokes the following abstract procedures: make_features_select_part make_features_from_part make_features_by_id_where_part make_features_join_part =cut sub _feature_by_id { my $self = shift; my ($ids,$type,$callback) = @_; $callback || $self->throw('must provide a callback argument'); my $select = $self->make_features_select_part; my $from = $self->make_features_from_part; my ($where,@args) = $type eq 'feature' ? $self->make_features_by_id_where_part($ids) : $self->make_features_by_gid_where_part($ids); my $join = $self->make_features_join_part; my $query = "SELECT $select FROM $from WHERE $where AND $join"; my $sth = $self->dbh->do_query($query,@args); my $count = 0; while (my @row = $sth->fetchrow_array) { $callback->(@row); $count++; } $sth->finish; return $count; } sub _feature_by_attribute { my $self = shift; my ($attributes,$callback) = @_; $callback || $self->throw('must provide a callback argument'); my $select = $self->make_features_select_part; my $from = $self->make_features_from_part(undef,{attributes=>$attributes}); my ($where,@args) = $self->make_features_by_range_where_part('',{attributes=>$attributes}); my $join = $self->make_features_join_part({attributes=>$attributes}); my $query = "SELECT $select FROM $from WHERE $where AND $join"; my $sth = $self->dbh->do_query($query,@args); my $count = 0; while (my @row = $sth->fetchrow_array) { $callback->(@row); $count++; } $sth->finish; return $count; } =head2 get_types Title : get_types Usage : $db->get_types($refseq,$refclass,$start,$stop,$count) Function: get list of types Returns : a list of Bio::DB::GFF::Typename objects Args : see below Status : Public This method is responsible for fetching the list of feature type names from the database. The query may be limited to a particular range, in which case the range is indicated by a landmark sequence name and class and its subrange, if any. These arguments may be undef if it is desired to retrieve all feature types in the database (which may be a slow operation in some implementations). If the $count flag is false, the method returns a simple list of vBio::DB::GFF::Typename objects. If $count is true, the method returns a list of $name=E$count pairs, where $count indicates the number of times this feature occurs in the range. Internally, this method calls upon the following functions to generate the SQL and its bind variables: ($q1,@args) = make_types_select_part(@args); ($q2,@args) = make_types_from_part(@args); ($q3,@args) = make_types_where_part(@args); ($q4,@args) = make_types_join_part(@args); ($q5,@args) = make_types_group_part(@args); The components are then combined as follows: $query = "SELECT $q1 FROM $q2 WHERE $q3 AND $q4 GROUP BY $q5"; If any of the query fragments contain the ? bind variable, then the same number of bind arguments must be provided in @args. The fragment-generating functions are described below. =cut sub get_types { my $self = shift; my ($srcseq,$class,$start,$stop,$want_count,$typelist) = @_; my $straight = $self->do_straight_join($srcseq,$start,$stop,[]) ? 'straight_join' : ''; my ($select,@args1) = $self->make_types_select_part($srcseq,$start,$stop,$want_count,$typelist); my ($from,@args2) = $self->make_types_from_part($srcseq,$start,$stop,$want_count,$typelist); my ($join,@args3) = $self->make_types_join_part($srcseq,$start,$stop,$want_count,$typelist); my ($where,@args4) = $self->make_types_where_part($srcseq,$start,$stop,$want_count,$typelist); my ($group,@args5) = $self->make_types_group_part($srcseq,$start,$stop,$want_count,$typelist); my $query = "SELECT $straight $select FROM $from WHERE $join AND $where"; $query .= " GROUP BY $group" if $group; my @args = (@args1,@args2,@args3,@args4,@args5); my $sth = $self->dbh->do_query($query,@args) or return; my (%result,%obj); while (my ($method,$source,$count) = $sth->fetchrow_array) { my $type = Bio::DB::GFF::Typename->new($method,$source); $result{$type} = $count; $obj{$type} = $type; } return $want_count ? %result : values %obj; } =head2 range_query Title : range_query Usage : $db->range_query($range_type,$refseq,$refclass,$start,$stop,$types,$order_by_group,$attributes,$binsize) Function: create statement handle for range/overlap queries Returns : a DBI statement handle Args : see below Status : Protected This method constructs the statement handle for this module's central query: given a range and/or a list of feature types, fetch their GFF records. The positional arguments are as follows: Argument Description $isrange A flag indicating that this is a range. query. Otherwise an overlap query is assumed. $refseq The reference sequence name (undef if no range). $refclass The reference sequence class (undef if no range). $start The start of the range (undef if none). $stop The stop of the range (undef if none). $types Array ref containing zero or feature types in the format [method,source]. $order_by_group A flag indicating that statement handler should group the features by group id (handy for iterative fetches) $attributes A hash containing select attributes. $binsize A bin size for generating tables of feature density. If successful, this method returns a statement handle. The handle is expected to return the fields described for get_features(). Internally, range_query() makes calls to the following methods, each of which is expected to be overridden in subclasses: $select = $self->make_features_select_part; $from = $self->make_features_from_part; $join = $self->make_features_join_part; ($where,@args) = $self->make_features_by_range_where_part($isrange,$srcseq,$class, $start,$stop,$types,$class); The query that is constructed looks like this: SELECT $select FROM $from WHERE $join AND $where The arguments that are returned from make_features_by_range_where_part() are passed to the statement handler's execute() method. range_query() also calls a do_straight_join() method, described below. If this method returns true, then the keyword "straight_join" is inserted right after SELECT. =cut sub range_query { my $self = shift; my($rangetype,$refseq,$class,$start,$stop,$types,$sparse,$order_by_group,$attributes,$bin) = @_; my $dbh = $self->features_db; # NOTE: straight_join is necessary in some database to force the right index to be used. my %a = (refseq=>$refseq,class=>$class,start=>$start,stop=>$stop,types=>$types,attributes=>$attributes,bin_width=>$bin); my $straight = $self->do_straight_join(\%a) ? 'straight_join' : ''; my $select = $self->make_features_select_part(\%a); my $from = $self->make_features_from_part($sparse,\%a); my $join = $self->make_features_join_part(\%a); my ($where,@args) = $self->make_features_by_range_where_part($rangetype,\%a); my ($group_by,@more_args) = $self->make_features_group_by_part(\%a); my $order_by = $self->make_features_order_by_part(\%a) if $order_by_group; my $query = "SELECT $straight $select FROM $from WHERE $join"; $query .= " AND $where" if $where; if ($group_by) { $query .= " GROUP BY $group_by"; push @args,@more_args; } $query .= " ORDER BY $order_by" if $order_by; my $sth = $self->dbh->do_query($query,@args); $sth; } =head2 make_features_by_range_where_part Title : make_features_by_range_where_part Usage : ($string,@args) = $db->make_features_select_part($isrange,$refseq,$class,$start,$stop,$types) Function: make where part of the features query Returns : the list ($query,@bind_args) Args : see below Status : Protected This method creates the part of the features query that immediately follows the WHERE keyword and is ANDed with the string returned by make_features_join_part(). The six positional arguments are a flag indicating whether to perform a range search or an overlap search, the reference sequence, class, start and stop, all of which define an optional range to search in, and an array reference containing a list [$method,$souce] pairs. The method result is a multi-element list containing the query string and the list of runtime arguments to bind to it with the execute() method. This method's job is to clean up arguments and perform consistency checking. The real work is done by the following abstract methods: Method Description refseq_query() Return the query string needed to match the reference sequence. range_query() Return the query string needed to find all features contained within a range. overlap_query() Return the query string needed to find all features that overlap a range. See Bio::DB::Adaptor::dbi::mysql for an example of how this works. =cut #' sub make_features_by_range_where_part { my $self = shift; my ($rangetype,$options) = @_; $options ||= {}; my ($refseq,$class,$start,$stop,$types,$attributes) = @{$options}{qw(refseq class start stop types attributes)}; my (@query,@args); if ($refseq) { my ($q,@a) = $self->refseq_query($refseq,$class); push @query,$q; push @args,@a; } if (defined $start or defined $stop) { $start = 0 unless defined($start); $stop = MAX_SEGMENT unless defined($stop); my ($range_query,@range_args) = $rangetype eq 'overlaps' ? $self->overlap_query($start,$stop) : $rangetype eq 'contains' ? $self->contains_query($start,$stop) : $rangetype eq 'contained_in' ? $self->contained_in_query($start,$stop) : (); push @query,$range_query; push @args,@range_args; } if (defined $types && @$types) { my ($type_query,@type_args) = $self->types_query($types); push @query,$type_query; push @args,@type_args; } if ($attributes) { my ($attribute_query,@attribute_args) = $self->make_features_by_attribute_where_part($attributes); push @query,"($attribute_query)"; push @args,@attribute_args; } my $query = join "\n\tAND ",@query; return wantarray ? ($query,@args) : $self->dbh->dbi_quote($query,@args); } =head2 do_straight_join Title : do_straight_join Usage : $boolean = $db->do_straight_join($refseq,$class,$start,$stop,$types) Function: optimization flag Returns : a flag Args : see range_query() Status : Protected This subroutine, called by range_query() returns a boolean flag. If true, range_query() will perform a straight join, which can be used to optimize certain SQL queries. The four arguments correspond to similarly-named arguments passed to range_query(). =cut sub do_straight_join { 0 } # false by default =head2 string_match Title : string_match Usage : $string = $db->string_match($field,$value) Function: create a SQL fragment for performing exact or regexp string matching Returns : query string Args : the table field and match value Status : public This method examines the passed value for meta characters. If so it produces a SQL fragment that performs a regular expression match. Otherwise, it produces a fragment that performs an exact string match. This method is not used in the module, but is available for use by subclasses. =cut sub string_match { my $self = shift; my ($field,$value) = @_; return qq($field = ?) if $value =~ /^[!@%&a-zA-Z0-9_\'\" ~-]+$/; return qq($field REGEXP ?); } =head2 exact_match Title : exact_match Usage : $string = $db->exact_match($field,$value) Function: create a SQL fragment for performing exact string matching Returns : query string Args : the table field and match value Status : public This method produces the SQL fragment for matching a field name to a constant string value. =cut sub exact_match { my $self = shift; my ($field,$value) = @_; return qq($field = ?); } =head2 search_notes Title : search_notes Usage : @search_results = $db->search_notes("full text search string",$limit) Function: Search the notes for a text string, using mysql full-text search Returns : array of results Args : full text search string, and an optional row limit Status : public This is a mysql-specific method. Given a search string, it performs a full-text search of the notes table and returns an array of results. Each row of the returned array is a arrayref containing the following fields: column 1 A Bio::DB::GFF::Featname object, suitable for passing to segment() column 2 The text of the note column 3 A relevance score. column 4 A Bio::DB::GFF::Typename object =cut sub search_notes { my $self = shift; my ($search_string,$limit) = @_; $search_string =~ tr/*?//d; my @words = $search_string =~ /(\w+)/g; my $regex = join '|',@words; my @searches = map {"fattribute_value LIKE '%${_}%'"} @words; my $search = join(' OR ',@searches); my $query = <dbh->do_query($query); my @results; while (my ($class,$name,$note,$method,$source) = $sth->fetchrow_array) { next unless $class && $name; # sorry, ignore NULL objects my @matches = $note =~ /($regex)/g; my $relevance = 10*@matches; my $featname = Bio::DB::GFF::Featname->new($class=>$name); my $type = Bio::DB::GFF::Typename->new($method,$source); push @results,[$featname,$note,$relevance,$type]; last if $limit && @results >= $limit; } @results; } =head2 meta Title : meta Usage : $value = $db->meta($name [,$newval]) Function: get or set a meta variable Returns : a string Args : meta variable name and optionally value Status : public Get or set a named metavariable for the database. Metavariables can be used for database-specific settings. This method calls two class-specific methods which must be implemented: make_meta_get_query() Returns a sql fragment which given a meta parameter name, returns its value. One bind variable. make_meta_set_query() Returns a sql fragment which takes two bind arguments, the parameter name and its value Don't make changes unless you know what you're doing! It will affect the persistent database. =cut sub meta { my $self = shift; my $param_name = uc shift; # getting if (@_) { my $value = shift; my $sql = $self->make_meta_set_query() or return; my $sth = $self->dbh->prepare_delayed($sql) or $self->error("Can't prepare $sql: ",$self->dbh->errstr), return; $sth->execute($param_name,$value) or $self->error("Can't execute $sql: ",$self->dbh->errstr), return; $sth->finish; return $self->{meta}{$param_name} = $value; } elsif (exists $self->{meta}{$param_name}) { return $self->{meta}{$param_name}; } else { undef $self->{meta}{$param_name}; # so that we don't check again my $sql = $self->make_meta_get_query() or return; my $sth = $self->dbh->prepare_delayed($sql) or $self->error("Can't prepare $sql: ",$self->dbh->errstr), return; $sth->execute($param_name) or $self->error("Can't execute $sql: ",$sth->errstr),return; my ($value) = $sth->fetchrow_array; $sth->finish; return $self->{meta}{$param_name} = $value; } } =head2 make_meta_get_query Title : make_meta_get_query Usage : $sql = $db->make_meta_get_query Function: return SQL fragment for getting a meta parameter Returns : SQL fragment Args : none Status : public By default this does nothing; meta parameters are not stored or retrieved. =cut sub make_meta_get_query { return 'SELECT fvalue FROM fmeta WHERE fname=?'; } sub dna_chunk_size { my $self = shift; $self->meta('chunk_size') || DNA_CHUNK_SIZE; } =head2 make_meta_set_query Title : make_meta_set_query Usage : $sql = $db->make_meta_set_query Function: return SQL fragment for setting a meta parameter Returns : SQL fragment Args : none Status : public By default this does nothing; meta parameters are not stored or retrieved. =cut sub make_meta_set_query { return; } =head2 default_meta_values Title : default_meta_values Usage : %values = $db->default_meta_values Function: empty the database Returns : a list of tag=>value pairs Args : none Status : protected This method returns a list of tag=Evalue pairs that contain default meta information about the database. It is invoked by initialize() to write out the default meta values. The base class version returns an empty list. For things to work properly, meta value names must be UPPERCASE. =cut sub default_meta_values { my $self = shift; my @values = $self->SUPER::default_meta_values; return ( @values, max_bin => MAX_BIN, min_bin => MIN_BIN, straight_join_limit => STRAIGHT_JOIN_LIMIT, chunk_size => DNA_CHUNK_SIZE, ); } sub min_bin { my $self = shift; return $self->meta('min_bin') || MIN_BIN; } sub max_bin { my $self = shift; return $self->meta('max_bin') || MAX_BIN; } sub straight_join_limit { my $self = shift; return $self->meta('straight_join_limit') || STRAIGHT_JOIN_LIMIT; } =head2 get_features_iterator Title : get_features_iterator Usage : $iterator = $db->get_features_iterator($search,$options,$callback) Function: create an iterator on a features() query Returns : A Bio::DB::GFF::Adaptor::dbi::iterator object Args : see get_features() Status : public This method is similar to get_features(), except that it returns an iterator across the query. See L. =cut sub get_features_iterator { my $self = shift; my ($search,$options,$callback) = @_; $callback || $self->throw('must provide a callback argument'); my $sth = $self->range_query(@{$search}{qw(rangetype refseq refclass start stop types)}, @{$options}{qw( sparse sort_by_group ATTRIBUTES BINSIZE)}) or return; return Bio::DB::GFF::Adaptor::dbi::iterator->new($sth,$callback); } ########################## loading and initialization ##################### =head2 do_initialize Title : do_initialize Usage : $success = $db->do_initialize($drop_all) Function: initialize the database Returns : a boolean indicating the success of the operation Args : a boolean indicating whether to delete existing data Status : protected This method will load the schema into the database. If $drop_all is true, then any existing data in the tables known to the schema will be deleted. Internally, this method calls schema() to get the schema data. =cut # Create the schema from scratch. # You will need create privileges for this. sub do_initialize { #shift->throw("do_initialize(): must be implemented by subclass"); my $self = shift; my $erase = shift; $self->drop_all if $erase; my $dbh = $self->features_db; my $schema = $self->schema; foreach my $table_name ($self->tables) { my $create_table_stmt = $schema->{$table_name}{table} ; $dbh->do($create_table_stmt) || warn $dbh->errstr; $self->create_other_schema_objects(\%{$schema->{$table_name}}); } 1; } =head2 finish_load Title : finish_load Usage : $db->finish_load Function: called after load_gff_line() Returns : number of records loaded Args : none Status : protected This method performs schema-specific cleanup after loading a set of GFF records. It finishes each of the statement handlers prepared by setup_load(). =cut sub finish_load { my $self = shift; my $dbh = $self->features_db or return; $dbh->do('UNLOCK TABLES') if $self->lock_on_load; foreach (keys %{$self->{load_stuff}{sth}}) { $self->{load_stuff}{sth}{$_}->finish; } my $counter = $self->{load_stuff}{counter}; delete $self->{load_stuff}; return $counter; } =head2 create_other_schema_objects Title : create_other_schema_objects Usage : $self->create_other_schema_objects($table_name) Function: create other schema objects like : indexes, sequences, triggers Returns : Args : Status : Abstract =cut sub create_other_schema_objects{ #shift->throw("create_other_schema_objects(): must be implemented by subclass"); my $self = shift ; my $table_schema = shift ; my $dbh = $self->features_db; foreach my $object_type(keys %$table_schema){ if ($object_type !~ /table/) { foreach my $object_name(keys %{$table_schema->{$object_type}}){ my $create_object_stmt = $table_schema->{$object_type}{$object_name}; $dbh->do($create_object_stmt) || warn $dbh->errstr; } } } 1; } =head2 drop_all Title : drop_all Usage : $db->drop_all Function: empty the database Returns : void Args : none Status : protected This method drops the tables known to this module. Internally it calls the abstract tables() method. =cut # Drop all the GFF tables -- dangerous! sub drop_all { #shift->throw("drop_all(): must be implemented by subclass"); my $self = shift; my $dbh = $self->features_db; my $schema = $self->schema; local $dbh->{PrintError} = 0; foreach ($self->tables) { $dbh->do("drop table $_") || warn $dbh->errstr; #when dropping a table - the indexes and triggers are being dropped automatically # sequences needs to be dropped - if there are any (Oracle, PostgreSQL) if ($schema->{$_}{sequence}){ foreach my $sequence_name(keys %{$schema->{$_}{sequence}}) { $dbh->do("drop sequence $sequence_name"); } } #$self->drop_other_schema_objects($_); } } =head2 clone The clone() method should be used when you want to pass the Bio::DB::GFF object to a child process across a fork(). The child must call clone() before making any queries. This method does two things: (1) it sets the underlying database handle's InactiveDestroy parameter to 1, thereby preventing the database connection from being destroyed in the parent when the dbh's destructor is called; (2) it replaces the dbh with the result of dbh-Eclone(), so that we now have an independent handle. =cut sub clone { my $self = shift; $self->features_db->clone; } =head1 QUERIES TO IMPLEMENT The following astract methods either return DBI statement handles or fragments of SQL. They must be implemented by subclasses of this module. See Bio::DB::GFF::Adaptor::dbi::mysql for examples. =head2 drop_other_schema_objects Title : drop_other_schema_objects Usage : $self->create_other_schema_objects($table_name) Function: create other schema objects like : indexes, sequences, triggers Returns : Args : Status : Abstract =cut sub drop_other_schema_objects{ #shift->throw("drop_other_schema_objects(): must be implemented by subclass"); } =head2 make_features_select_part Title : make_features_select_part Usage : $string = $db->make_features_select_part() Function: make select part of the features query Returns : a string Args : none Status : Abstract This abstract method creates the part of the features query that immediately follows the SELECT keyword. =cut sub make_features_select_part { shift->throw("make_features_select_part(): must be implemented by subclass"); } =head2 tables Title : tables Usage : @tables = $db->tables Function: return list of tables that belong to this module Returns : list of tables Args : none Status : protected This method lists the tables known to the module. =cut # return list of tables that "belong" to us. sub tables { my $schema = shift->schema; return keys %$schema; } =head2 schema Title : schema Usage : $schema = $db->schema Function: return the CREATE script for the schema Returns : a hashref Args : none Status : abstract This method returns an array ref containing the various CREATE statements needed to initialize the database tables. The keys are the table names, and the values are strings containing the appropriate CREATE statement. =cut sub schema { shift->throw("The schema() method must be implemented by subclass"); } =head2 DESTROY Title : DESTROY Usage : $db->DESTROY Function: disconnect database at destruct time Returns : void Args : none Status : protected This is the destructor for the class. =cut sub DESTROY { my $self = shift; $self->features_db->disconnect if defined $self->features_db; } ################## query cache ################## ######################################### ## Moved from mysql.pm and mysqlopt.pm ## ######################################### =head2 make_features_by_name_where_part Title : make_features_by_name_where_part Usage : $db->make_features_by_name_where_part Function: create the SQL fragment needed to select a feature by its group name & class Returns : a SQL fragment and bind arguments Args : see below Status : Protected =cut sub make_features_by_name_where_part { my $self = shift; my ($class,$name) = @_; if ($name =~ /\*/) { $name =~ s/%/\\%/g; $name =~ s/_/\\_/g; $name =~ tr/*/%/; return ("fgroup.gclass=? AND fgroup.gname LIKE ?",$class,$name); } else { return ("fgroup.gclass=? AND fgroup.gname=?",$class,$name); } } sub make_features_by_alias_where_part { my $self = shift; my ($class,$name) = @_; if ($name =~ /\*/) { $name =~ tr/*/%/; $name =~ s/_/\\_/g; return ("fgroup.gclass=? AND fattribute_to_feature.fattribute_value LIKE ? AND fgroup.gid=fdata.gid AND fattribute.fattribute_name in ('Alias','Name') AND fattribute_to_feature.fattribute_id=fattribute.fattribute_id AND fattribute_to_feature.fid=fdata.fid AND ftype.ftypeid=fdata.ftypeid",$class,$name) } else { return ("fgroup.gclass=? AND fattribute_to_feature.fattribute_value=? AND fgroup.gid=fdata.gid AND fattribute.fattribute_name in ('Alias','Name') AND fattribute_to_feature.fattribute_id=fattribute.fattribute_id AND fattribute_to_feature.fid=fdata.fid AND ftype.ftypeid=fdata.ftypeid",$class,$name); } } sub make_features_by_attribute_where_part { my $self = shift; my $attributes = shift; my @args; my @sql; foreach (keys %$attributes) { push @sql,"(fattribute.fattribute_name=? AND fattribute_to_feature.fattribute_value=?)"; push @args,($_,$attributes->{$_}); } return (join(' OR ',@sql),@args); } =head2 make_features_by_id_where_part Title : make_features_by_id_where_part Usage : $db->make_features_by_id_where_part($ids) Function: create the SQL fragment needed to select a set of features by their ids Returns : a SQL fragment and bind arguments Args : arrayref of IDs Status : Protected =cut sub make_features_by_id_where_part { my $self = shift; my $ids = shift; my $set = join ",",@$ids; return ("fdata.fid IN ($set)"); } =head2 make_features_by_gid_where_part Title : make_features_by_id_where_part Usage : $db->make_features_by_gid_where_part($ids) Function: create the SQL fragment needed to select a set of features by their ids Returns : a SQL fragment and bind arguments Args : arrayref of IDs Status : Protected =cut sub make_features_by_gid_where_part { my $self = shift; my $ids = shift; my $set = join ",",@$ids; return ("fgroup.gid IN ($set)"); } =head2 make_features_from_part Title : make_features_from_part Usage : $string = $db->make_features_from_part() Function: make from part of the features query Returns : a string Args : none Status : protected This method creates the part of the features query that immediately follows the FROM keyword. =cut sub make_features_from_part { my $self = shift; my $sparse = shift; my $options = shift || {}; return $options->{attributes} ? "fdata,ftype,fgroup,fattribute,fattribute_to_feature\n" : "fdata,ftype,fgroup\n"; } =head2 make_features_join_part Title : make_features_join_part Usage : $string = $db->make_features_join_part() Function: make join part of the features query Returns : a string Args : none Status : protected This method creates the part of the features query that immediately follows the WHERE keyword. =cut sub make_features_join_part { my $self = shift; my $options = shift || {}; return !$options->{attributes} ? <make_features_order_by_part() Function: make the ORDER BY part of the features() query Returns : a SQL fragment and bind arguments, if any Args : none Status : protected This method creates the part of the features query that immediately follows the ORDER BY part of the query issued by features() and related methods. =cut sub make_features_order_by_part { my $self = shift; my $options = shift || {}; return "fgroup.gname"; } =head2 make_features_group_by_part Title : make_features_group_by_part Usage : ($query,@args) = $db->make_features_group_by_part() Function: make the GROUP BY part of the features() query Returns : a SQL fragment and bind arguments, if any Args : none Status : protected This method creates the part of the features query that immediately follows the GROUP BY part of the query issued by features() and related methods. =cut sub make_features_group_by_part { my $self = shift; my $options = shift || {}; if (my $att = $options->{attributes}) { my $key_count = keys %$att; return unless $key_count > 1; return ("fdata.fid,fref,fstart,fstop,fsource, fmethod,fscore,fstrand,fphase,gclass,gname,ftarget_start, ftarget_stop,fdata.gid HAVING count(fdata.fid) > ?",$key_count-1); } elsif (my $b = $options->{bin_width}) { return "fref,fstart,fdata.ftypeid"; } } =head2 refseq_query Title : refseq_query Usage : ($query,@args) = $db->refseq_query($name,$class) Function: create SQL fragment that selects the desired reference sequence Returns : a list containing the query and bind arguments Args : reference sequence name and class Status : protected This method is called by make_features_by_range_where_part() to construct the part of the select WHERE section that selects a particular reference sequence. It returns a mult-element list in which the first element is the SQL fragment and subsequent elements are bind values. For example: sub refseq_query { my ($name,$class) = @_; return ('gff.refseq=? AND gff.refclass=?', $name,$class); } The current schema does not distinguish among different classes of reference sequence. =cut # IMPORTANT NOTE: THE MYSQL SCHEMA IGNORES THE SEQUENCE CLASS # THIS SHOULD BE FIXED sub refseq_query { my $self = shift; my ($refseq,$refclass) = @_; my $query = "fdata.fref=?"; return wantarray ? ($query,$refseq) : $self->dbh->dbi_quote($query,$refseq); } =head2 attributes Title : attributes Usage : @attributes = $db->attributes($id,$name) Function: get the attributes on a particular feature Returns : an array of string Args : feature ID Status : public Some GFF version 2 files use the groups column to store a series of attribute/value pairs. In this interpretation of GFF, the first such pair is treated as the primary group for the feature; subsequent pairs are treated as attributes. Two attributes have special meaning: "Note" is for backward compatibility and is used for unstructured text remarks. "Alias" is considered as a synonym for the feature name. If no name is provided, then attributes() returns a flattened hash, of attribute=Evalue pairs. This lets you do: %attributes = $db->attributes($id); Normally, attributes() will be called by the feature: @notes = $feature->attributes('Note'); =cut sub do_attributes { my $self = shift; my ($id,$tag) = @_; my $sth; if ($id) { my $from = 'fattribute_to_feature,fattribute'; my $join = 'fattribute.fattribute_id=fattribute_to_feature.fattribute_id'; my $where1 = 'fid=? AND fattribute_name=?'; my $where2 = 'fid=?'; $sth = defined($tag) ? $self->dbh->do_query("SELECT fattribute_value FROM $from WHERE $where1 AND $join",$id,$tag) : $self->dbh->do_query("SELECT fattribute_name,fattribute_value FROM $from WHERE $where2 AND $join",$id); } else { $sth = $self->dbh->do_query("SELECT fattribute_name FROM fattribute"); } my @result; while (my @stuff = $sth->fetchrow_array) { push @result,@stuff; } $sth->finish; return @result; } =head2 overlap_query_nobin Title : overlap_query Usage : ($query,@args) = $db->overlap_query($start,$stop) Function: create SQL fragment that selects the desired features by range Returns : a list containing the query and bind arguments Args : the start and stop of a range, inclusive Status : protected This method is called by make_features_byrange_where_part() to construct the part of the select WHERE section that selects a set of features that overlap a range. It returns a multi-element list in which the first element is the SQL fragment and subsequent elements are bind values. sub overlap_query_nobin { my ($start,$stop) = @_; return ('gff.stopE=? AND gff.startE=?', $start,$stop); =cut # find features that overlap a given range sub overlap_query_nobin { my $self = shift; my ($start,$stop) = @_; my $query = qq(fdata.fstop>=? AND fdata.fstart<=?); return wantarray ? ($query,$start,$stop) : $self->dbh->dbi_quote($query,$start,$stop); } =head2 contains_query_nobin Title : contains_query Usage : ($query,@args) = $db->contains_query_nobin($start,$stop) Function: create SQL fragment that selects the desired features by range Returns : a list containing the query and bind arguments Args : the start and stop of a range, inclusive Status : protected This method is called by make_features_byrange_where_part() to construct the part of the select WHERE section that selects a set of features entirely enclosed by a range. It returns a multi-element list in which the first element is the SQL fragment and subsequent elements are bind values. For example: sub contains_query_nobin { my ($start,$stop) = @_; return ('gff.start>=? AND gff.stop<=?', $start,$stop); =cut # find features that are completely contained within a range sub contains_query_nobin { my $self = shift; my ($start,$stop) = @_; my $query = qq(fdata.fstart>=? AND fdata.fstop<=?); return wantarray ? ($query,$start,$stop) : $self->dbh->dbi_quote($query,$start,$stop); } =head2 contained_in_query_nobin Title : contained_in_query_nobin Usage : ($query,@args) = $db->contained_in_query($start,$stop) Function: create SQL fragment that selects the desired features by range Returns : a list containing the query and bind arguments Args : the start and stop of a range, inclusive Status : protected This method is called by make_features_byrange_where_part() to construct the part of the select WHERE section that selects a set of features entirely enclosed by a range. It returns a multi-element list in which the first element is the SQL fragment and subsequent elements are bind values.For example: sub contained_in_query_nobin { my ($start,$stop) = @_; return ('gff.start<=? AND gff.stop>=?', $start,$stop); } =cut # find features that are completely contained within a range sub contained_in_query_nobin { my $self = shift; my ($start,$stop) = @_; my $query = qq(fdata.fstart<=? AND fdata.fstop>=?); return wantarray ? ($query,$start,$stop) : $self->dbh->dbi_quote($query,$start,$stop); } =head2 types_query Title : types_query Usage : ($query,@args) = $db->types_query($types) Function: create SQL fragment that selects the desired features by type Returns : a list containing the query and bind arguments Args : an array reference containing the types Status : protected This method is called by make_features_byrange_where_part() to construct the part of the select WHERE section that selects a set of features based on their type. It returns a multi-element list in which the first element is the SQL fragment and subsequent elements are bind values. The argument is an array reference containing zero or more [$method,$source] pairs. =cut # generate the fragment of SQL responsible for searching for # features with particular types and methods sub types_query { my $self = shift; my $types = shift; my @method_queries; my @args; for my $type (@$types) { my ($method,$source) = @$type; my ($mlike, $slike) = (0, 0); if ($method && $method =~ m/\.\*/) { $method =~ s/%/\\%/g; $method =~ s/_/\\_/g; $method =~ s/\.\*\??/%/g; $mlike++; } if ($source && $source =~ m/\.\*/) { $source =~ s/%/\\%/g; $source =~ s/_/\\_/g; $source =~ s/\.\*\??/%/g; $slike++; } my @pair; if (defined $method && length $method) { push @pair, $mlike ? qq(fmethod LIKE ?) : qq(fmethod = ?); push @args, $method; } if (defined $source && length $source) { push @pair, $slike ? qq(fsource LIKE ?) : qq(fsource = ?); push @args, $source; } push @method_queries,"(" . join(' AND ',@pair) .")" if @pair; } my $query = " (".join(' OR ',@method_queries).")\n" if @method_queries; return wantarray ? ($query,@args) : $self->dbh->dbi_quote($query,@args); } =head2 make_types_select_part Title : make_types_select_part Usage : ($string,@args) = $db->make_types_select_part(@args) Function: create the select portion of the SQL for fetching features type list Returns : query string and bind arguments Args : see below Status : protected This method is called by get_types() to generate the query fragment and bind arguments for the SELECT part of the query that retrieves lists of feature types. The four positional arguments are as follows: $refseq reference sequence name $start start of region $stop end of region $want_count true to return the count of this feature type If $want_count is false, the SQL fragment returned must produce a list of feature types in the format (method, source). If $want_count is true, the returned fragment must produce a list of feature types in the format (method, source, count). =cut #------------------------- support for the types() query ------------------------ sub make_types_select_part { my $self = shift; my ($srcseq,$start,$stop,$want_count) = @_; my $query = $want_count ? 'ftype.fmethod,ftype.fsource,count(fdata.ftypeid)' : 'fmethod,fsource'; return $query; } =head2 make_types_from_part Title : make_types_from_part Usage : ($string,@args) = $db->make_types_from_part(@args) Function: create the FROM portion of the SQL for fetching features type lists Returns : query string and bind arguments Args : see below Status : protected This method is called by get_types() to generate the query fragment and bind arguments for the FROM part of the query that retrieves lists of feature types. The four positional arguments are as follows: $refseq reference sequence name $start start of region $stop end of region $want_count true to return the count of this feature type If $want_count is false, the SQL fragment returned must produce a list of feature types in the format (method, source). If $want_count is true, the returned fragment must produce a list of feature types in the format (method, source, count). =cut sub make_types_from_part { my $self = shift; my ($srcseq,$start,$stop,$want_count) = @_; my $query = defined($srcseq) || $want_count ? 'fdata,ftype' : 'ftype'; return $query; } =head2 make_types_join_part Title : make_types_join_part Usage : ($string,@args) = $db->make_types_join_part(@args) Function: create the JOIN portion of the SQL for fetching features type lists Returns : query string and bind arguments Args : see below Status : protected This method is called by get_types() to generate the query fragment and bind arguments for the JOIN part of the query that retrieves lists of feature types. The four positional arguments are as follows: $refseq reference sequence name $start start of region $stop end of region $want_count true to return the count of this feature type =cut sub make_types_join_part { my $self = shift; my ($srcseq,$start,$stop,$want_count) = @_; my $query = defined($srcseq) || $want_count ? 'fdata.ftypeid=ftype.ftypeid' : ''; return $query || '1=1'; } =head2 make_types_where_part Title : make_types_where_part Usage : ($string,@args) = $db->make_types_where_part(@args) Function: create the WHERE portion of the SQL for fetching features type lists Returns : query string and bind arguments Args : see below Status : protected This method is called by get_types() to generate the query fragment and bind arguments for the WHERE part of the query that retrieves lists of feature types. The four positional arguments are as follows: $refseq reference sequence name $start start of region $stop end of region $want_count true to return the count of this feature type =cut sub make_types_where_part { my $self = shift; my ($srcseq,$start,$stop,$want_count,$typelist) = @_; my (@query,@args); if (defined($srcseq)) { push @query,'fdata.fref=?'; push @args,$srcseq; if (defined $start or defined $stop) { $start = 1 unless defined $start; $stop = MAX_SEGMENT unless defined $stop; my ($q,@a) = $self->overlap_query($start,$stop); push @query,"($q)"; push @args,@a; } } if (defined $typelist && @$typelist) { my ($q,@a) = $self->types_query($typelist); push @query,($q); push @args,@a; } my $query = @query ? join(' AND ',@query) : '1=1'; return wantarray ? ($query,@args) : $self->dbh->dbi_quote($query,@args); } =head2 make_types_group_part Title : make_types_group_part Usage : ($string,@args) = $db->make_types_group_part(@args) Function: create the GROUP BY portion of the SQL for fetching features type lists Returns : query string and bind arguments Args : see below Status : protected This method is called by get_types() to generate the query fragment and bind arguments for the GROUP BY part of the query that retrieves lists of feature types. The four positional arguments are as follows: $refseq reference sequence name $start start of region $stop end of region $want_count true to return the count of this feature type =cut sub make_types_group_part { my $self = shift; my ($srcseq,$start,$stop,$want_count) = @_; return unless $srcseq or $want_count; return 'ftype.ftypeid,ftype.fmethod,ftype.fsource'; } =head2 get_feature_id Title : get_feature_id Usage : $integer = $db->get_feature_id($ref,$start,$stop,$typeid,$groupid) Function: get the ID of a feature Returns : an integer ID or undef Args : none Status : private This internal method is called by load_gff_line to look up the integer ID of an existing feature. It is ony needed when replacing a feature with new information. =cut # this method is called when needed to look up a feature's ID sub get_feature_id { my $self = shift; my ($ref,$start,$stop,$typeid,$groupid) = @_; my $s = $self->{load_stuff}; unless ($s->{get_feature_id}) { my $dbh = $self->features_db; $s->{get_feature_id} = $dbh->prepare_delayed('SELECT fid FROM fdata WHERE fref=? AND fstart=? AND fstop=? AND ftypeid=? AND gid=?'); } my $sth = $s->{get_feature_id} or return; $sth->execute($ref,$start,$stop,$typeid,$groupid) or return; my ($fid) = $sth->fetchrow_array; return $fid; } =head2 make_abscoord_query Title : make_abscoord_query Usage : $sth = $db->make_abscoord_query($name,$class); Function: create query that finds the reference sequence coordinates given a landmark & classa Returns : a DBI statement handle Args : name and class of landmark Status : protected The statement handler should return rows containing five fields: 1. reference sequence name 2. reference sequence class 3. start position 4. stop position 5. strand ("+" or "-") This query always returns "Sequence" as the class of the reference sequence. =cut # given sequence name, return (reference,start,stop,strand) sub make_abscoord_query { my $self = shift; my ($name,$class,$refseq) = @_; #my $query = GETSEQCOORDS; my $query = $self->getseqcoords_query(); my $getforcedseqcoords = $self->getforcedseqcoords_query() ; if ($name =~ /\*/) { $name =~ s/%/\\%/g; $name =~ s/_/\\_/g; $name =~ tr/*/%/; $query =~ s/gname=\?/gname LIKE ?/; } defined $refseq ? $self->dbh->do_query($getforcedseqcoords,$name,$class,$refseq) : $self->dbh->do_query($query,$name,$class); } sub make_aliasabscoord_query { my $self = shift; my ($name,$class) = @_; #my $query = GETALIASCOORDS; my $query = $self->getaliascoords_query(); if ($name =~ /\*/) { $name =~ s/%/\\%/g; $name =~ s/_/\\_/g; $name =~ tr/*/%/; $query =~ s/gname=\?/gname LIKE ?/; } $self->dbh->do_query($query,$name,$class); } sub getseqcoords_query { shift->throw("getseqcoords_query(): must be implemented by a subclass"); } sub getaliascoords_query { shift->throw("getaliascoords_query(): must be implemented by a subclass"); } sub bin_query { my $self = shift; my ($start,$stop,$minbin,$maxbin) = @_; if ($start && $start < 0 && $stop > 0) { # split the queries my ($lower_query,@lower_args) = $self->_bin_query($start,0,$minbin,$maxbin); my ($upper_query,@upper_args) = $self->_bin_query(0,$stop,$minbin,$maxbin); my $query = "$lower_query\n\t OR $upper_query"; my @args = (@lower_args,@upper_args); return wantarray ? ($query,@args) : $self->dbh->dbi_quote($query,@args); } else { return $self->_bin_query($start,$stop,$minbin,$maxbin); } } sub _bin_query { my $self = shift; my ($start,$stop,$minbin,$maxbin) = @_; my ($query,@args); $start = 0 unless defined($start); $stop = $self->meta('max_bin') unless defined($stop); my @bins; $minbin = defined $minbin ? $minbin : $self->min_bin; $maxbin = defined $maxbin ? $maxbin : $self->max_bin; my $tier = $maxbin; while ($tier >= $minbin) { my ($tier_start,$tier_stop) = (bin_bot($tier,$start)-EPSILON(),bin_top($tier,$stop)+EPSILON()); ($tier_start,$tier_stop) = ($tier_stop,$tier_start) if $tier_start > $tier_stop; # can happen when working with negative coordinates if ($tier_start == $tier_stop) { push @bins,'fbin=?'; push @args,$tier_start; } else { push @bins,'fbin between ? and ?'; push @args,($tier_start,$tier_stop); } $tier /= 10; } $query = join("\n\t OR ",@bins); return wantarray ? ($query,@args) : $self->dbh->dbi_quote($query,@args); } # find features that overlap a given range sub overlap_query { my $self = shift; my ($start,$stop) = @_; my ($query,@args); my ($iq,@iargs) = $self->overlap_query_nobin($start,$stop); if (OPTIMIZE) { my ($bq,@bargs) = $self->bin_query($start,$stop); $query = "($bq)\n\tAND $iq"; @args = (@bargs,@iargs); } else { $query = $iq; @args = @iargs; } return wantarray ? ($query,@args) : $self->dbh->dbi_quote($query,@args); } # find features that are completely contained within a ranged sub contains_query { my $self = shift; my ($start,$stop) = @_; my ($bq,@bargs) = $self->bin_query($start,$stop,undef,bin($start,$stop,$self->min_bin)); my ($iq,@iargs) = $self->contains_query_nobin($start,$stop); my $query = "($bq)\n\tAND $iq"; my @args = (@bargs,@iargs); return wantarray ? ($query,@args) : $self->dbh->dbi_quote($query,@args); } # find features that are completely contained within a range sub contained_in_query { my $self = shift; my ($start,$stop) = @_; my ($bq,@bargs) = $self->bin_query($start,$stop,abs($stop-$start)+1,undef); my ($iq,@iargs) = $self->contained_in_query_nobin($start,$stop); my $query = "($bq)\n\tAND $iq"; my @args = (@bargs,@iargs); return wantarray ? ($query,@args) : $self->dbh->dbi_quote($query,@args); } # implement the _delete_fattribute_to_feature() method sub _delete_fattribute_to_feature { my $self = shift; my @feature_ids = @_; my $dbh = $self->features_db; my $fields = join ',',map{$dbh->quote($_)} @feature_ids; my $query = "delete from fattribute_to_feature where fid in ($fields)"; warn "$query\n" if $self->debug; my $result = $dbh->do($query); defined $result or $self->throw($dbh->errstr); $result; } # implement the _delete_features() method sub _delete_features { my $self = shift; my @feature_ids = @_; my $dbh = $self->features_db; my $fields = join ',',map{$dbh->quote($_)} @feature_ids; # delete from fattribute_to_feature $self->_delete_fattribute_to_feature(@feature_ids); my $query = "delete from fdata where fid in ($fields)"; warn "$query\n" if $self->debug; my $result = $dbh->do($query); defined $result or $self->throw($dbh->errstr); $result; } # implement the _delete_groups() method sub _delete_groups { my $self = shift; my @group_ids = @_; my $dbh = $self->features_db; my $fields = join ',',map{$dbh->quote($_)} @group_ids; foreach my $gid (@group_ids){ my @features = $self->get_feature_by_gid($gid); $self->delete_features(@features); } my $query = "delete from fgroup where gid in ($fields)"; warn "$query\n" if $self->debug; my $result = $dbh->do($query); defined $result or $self->throw($dbh->errstr); $result; } # implement the _delete() method sub _delete { my $self = shift; my $delete_spec = shift; my $ranges = $delete_spec->{segments} || []; my $types = $delete_spec->{types} || []; my $force = $delete_spec->{force}; my $range_type = $delete_spec->{range_type}; my $dbh = $self->features_db; my $query = 'delete from fdata'; my @where; my @range_part; for my $segment (@$ranges) { my $ref = $dbh->quote($segment->abs_ref); my $start = $segment->abs_start; my $stop = $segment->abs_stop; my $range = $range_type eq 'overlaps' ? $self->overlap_query($start,$stop) : $range_type eq 'contains' ? $self->contains_query($start,$stop) : $range_type eq 'contained_in' ? $self->contained_in_query($start,$stop) : $self->throw("Invalid range type '$range_type'"); push @range_part,"(fref=$ref AND $range)"; } push @where,'('. join(' OR ',@range_part).')' if @range_part; # get all the types if (@$types) { my $types_where = $self->types_query($types); my $types_query = "select ftypeid from ftype where $types_where"; my $result = $dbh->selectall_arrayref($types_query); my @typeids = map {$_->[0]} @$result; my $typelist = join ',',map{$dbh->quote($_)} @typeids; $typelist ||= "0"; # don't cause DBI to die with invalid SQL when # unknown feature types were requested. push @where,"(ftypeid in ($typelist))"; } $self->throw("This operation would delete all feature data and -force not specified") unless @where || $force; $query .= " where ".join(' and ',@where) if @where; warn "$query\n" if $self->debug; my $result = $dbh->do($query); defined $result or $self->throw($dbh->errstr); $result; } =head2 feature_summary Title : feature_summary Usage : $summary = $db->feature_summary(@args) Function: returns a coverage summary across indicated region/type Returns : a Bio::SeqFeatureI object containing the "coverage" tag Args : see below Status : public This method is used to get coverage density information across a region of interest. You provide it with a region of interest, optional a list of feature types, and a count of the number of bins over which you want to calculate the coverage density. An object is returned corresponding to the requested region. It contains a tag called "coverage" that will return an array ref of "bins" length. Each element of the array describes the number of features that overlap the bin at this position. Arguments: Argument Description -------- ----------- -seq_id Sequence ID for the region -start Start of region -end End of region -type/-types Feature type of interest or array ref of types -bins Number of bins across region. Defaults to 1000. -iterator Return an iterator across the region Note that this method uses an approximate algorithm that is only accurate to 500 bp, so when dealing with bins that are smaller than 1000 bp, you may see some shifting of counts between adjacent bins. Although an -iterator option is provided, the method only ever returns a single feature, so this is fairly useless. =cut sub feature_summary { my $self = shift; my ($seq_name,$start,$end,$types,$bins,$iterator) = rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'], ['TYPES','TYPE','PRIMARY_TAG'], 'BINS', 'ITERATOR', ],@_); my ($coverage,$tag) = $self->coverage_array(-seqid=> $seq_name, -start=> $start, -end => $end, -type => $types, -bins => $bins) or return; my $score = 0; for (@$coverage) { $score += $_ } $score /= @$coverage; my $feature = Bio::SeqFeature::Lite->new(-seq_id => $seq_name, -start => $start, -end => $end, -type => $tag, -score => $score, -attributes => { coverage => [$coverage] }); return $iterator ? Bio::DB::GFF::FeatureIterator->new($feature) : $feature; } =head2 coverage_array Title : coverage_array Usage : $arrayref = $db->coverage_array(@args) Function: returns a coverage summary across indicated region/type Returns : an array reference Args : see below Status : public This method is used to get coverage density information across a region of interest. The arguments are identical to feature_summary, except that instead of returning a Bio::SeqFeatureI object, it returns an array reference of the desired number of bins. The value of each element corresponds to the number of features in the bin. Arguments: Argument Description -------- ----------- -seq_id Sequence ID for the region -start Start of region -end End of region -type/-types Feature type of interest or array ref of types -bins Number of bins across region. Defaults to 1000. Note that this method uses an approximate algorithm that is only accurate to 500 bp, so when dealing with bins that are smaller than 1000 bp, you may see some shifting of counts between adjacent bins. =cut sub coverage_array { my $self = shift; my ($seq_name,$start,$end,$types,$bins) = rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'], ['TYPES','TYPE','PRIMARY_TAG'],'BINS'],@_); $types = $self->parse_types($types); my $dbh = $self->features_db; $bins ||= 1000; $start ||= 1; unless ($end) { my $segment = $self->segment($seq_name) or $self->throw("unknown seq_id $seq_name"); $end = $segment->end; } my $binsize = ($end-$start+1)/$bins; my $seqid = $seq_name; return [] unless $seqid; # where each bin starts my @his_bin_array = map {$start + $binsize * $_} (0..$bins); my @sum_bin_array = map {int(($_-1)/SUMMARY_BIN_SIZE)} @his_bin_array; my $interval_stats_table = 'finterval_stats'; # pick up the type ids my ($type_from,@a) = $self->types_query($types); my $query = "select ftypeid,fmethod,fsource from ftype where $type_from"; my $sth = $dbh->prepare_delayed($query); my (@t,$report_tag); $sth->execute(@a); while (my ($t,$method,$source) = $sth->fetchrow_array) { $report_tag ||= "$method:$source"; push @t,$t; } my %bins; my $sql = <= ? LIMIT 1 END ; $sth = $dbh->prepare_delayed($sql) or warn $dbh->errstr; eval { for my $typeid (@t) { for (my $i=0;$i<@sum_bin_array;$i++) { my @args = ($typeid,$seqid,$sum_bin_array[$i]); $self->_print_query($sql,@args) if $self->debug; $sth->execute(@args) or $self->throw($sth->errstr); my ($bin,$cum_count) = $sth->fetchrow_array; push @{$bins{$typeid}},[$bin,$cum_count]; } } }; return unless %bins; my @merged_bins; my $firstbin = int(($start-1)/$binsize); for my $type (keys %bins) { my $arry = $bins{$type}; my $last_count = $arry->[0][1]; my $last_bin = -1; my $i = 0; my $delta; for my $b (@$arry) { my ($bin,$count) = @$b; $delta = $count - $last_count if $bin > $last_bin; $merged_bins[$i++] = $delta; $last_count = $count; $last_bin = $bin; } } return wantarray ? (\@merged_bins,$report_tag) : \@merged_bins; } =head2 build_summary_statistics Title : build_summary_statistics Usage : $db->build_summary_statistics Function: prepares the table needed to call feature_summary() Returns : nothing Args : none Status : public This method is used to build the summary statistics table that is used by the feature_summary() and coverage_array() methods. It needs to be called whenever the database is updated. =cut sub build_summary_statistics { my $self = shift; my $interval_stats_table = 'finterval_stats'; my $dbh = $self->dbh; $dbh->begin_work; my $sbs = SUMMARY_BIN_SIZE; my $result = eval { $self->_add_interval_stats_table; $self->disable_keys($interval_stats_table); $dbh->do("DELETE FROM $interval_stats_table"); my $insert = $dbh->prepare(<throw($dbh->errstr); INSERT INTO $interval_stats_table (ftypeid,fref,fbin,fcum_count) VALUES (?,?,?,?) END ; my $sql = 'select ftypeid,fref,fstart,fstop from fdata order by ftypeid,fref,fstart'; my $select = $dbh->prepare($sql) or $self->throw($dbh->errstr); my $current_bin = -1; my ($current_type,$current_seqid,$count); my $cum_count = 0; my (%residuals,$last_bin); my $le = -t \*STDERR ? "\r" : "\n"; $select->execute; while (my($typeid,$seqid,$start,$end) = $select->fetchrow_array) { print STDERR $count," features processed$le" if ++$count % 1000 == 0; my $bin = int($start/$sbs); $current_type ||= $typeid; $current_seqid ||= $seqid; # because the input is sorted by start, no more features will contribute to the # current bin so we can dispose of it if ($bin != $current_bin) { if ($seqid != $current_seqid or $typeid != $current_type) { # load all bins left over $self->_load_bins($insert,\%residuals,\$cum_count,$current_type,$current_seqid); %residuals = () ; $cum_count = 0; } else { # load all up to current one $self->_load_bins($insert,\%residuals,\$cum_count,$current_type,$current_seqid,$current_bin); } } $last_bin = $current_bin; ($current_seqid,$current_type,$current_bin) = ($seqid,$typeid,$bin); # summarize across entire spanned region my $last_bin = int(($end-1)/$sbs); for (my $b=$bin;$b<=$last_bin;$b++) { $residuals{$b}++; } } # handle tail case # load all bins left over $self->_load_bins($insert,\%residuals,\$cum_count,$current_type,$current_seqid); $self->enable_keys($interval_stats_table); 1; }; if ($result) { $dbh->commit } else { warn "Can't build summary statistics: $@"; $dbh->rollback }; print STDERR "\n"; } sub _load_bins { my $self = shift; my ($insert,$residuals,$cum_count,$type,$seqid,$stop_after) = @_; for my $b (sort {$a<=>$b} keys %$residuals) { last if defined $stop_after and $b > $stop_after; $$cum_count += $residuals->{$b}; my @args = ($type,$seqid,$b,$$cum_count); $insert->execute(@args) or warn $insert->errstr; delete $residuals->{$b}; # no longer needed } } sub _add_interval_stats_table { my $self = shift; my $schema = $self->schema; my $create_table_stmt = $schema->{'finterval_stats'}{'table'}; my $dbh = $self->features_db; $dbh->do("drop table finterval_stats"); $dbh->do($create_table_stmt) || warn $dbh->errstr; } sub disable_keys { } # noop sub enable_keys { } # noop 1; __END__ =head1 BUGS Schemas need work to support multiple hierarchical groups. =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Adaptor/memory.pm000444000766000024 5103113155576320 20373 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::memory; =head1 NAME Bio::DB::GFF::Adaptor::memory -- Bio::DB::GFF database adaptor for in-memory databases =head1 SYNOPSIS use Bio::DB::GFF; my $db = Bio::DB::GFF->new(-adaptor=> 'memory', -gff => 'my_features.gff', -fasta => 'my_dna.fa' ); or my $db = Bio::DB::GFF->new(-adaptor=>'memory'); $db->load_gff_file('my_features.gff'); $db->load_fasta_file('my_dna.fa'); See L for other methods. =head1 DESCRIPTION This adaptor implements an in-memory version of Bio::DB::GFF. It can be used to store and retrieve SHORT GFF files. It inherits from Bio::DB::GFF. =head1 CONSTRUCTOR Use Bio::DB::GFF-Enew() to construct new instances of this class. Three named arguments are recommended: Argument Description -adaptor Set to "memory" to create an instance of this class. -gff Read the indicated file or directory of .gff file. -fasta Read the indicated file or directory of fasta files. -dir Indicates a directory containing .gff and .fa files If you use the -dir option and the indicated directory is writable by the current process, then this library will create a FASTA file index that greatly diminishes the memory usage of this module. Alternatively you may create an empty in-memory object using just the -adaptor=E'memory' argument and then call the load_gff_file() and load_fasta_file() methods to load GFF and/or sequence information. This is recommended in CGI/mod_perl/fastCGI environments because these methods do not modify STDIN, unlike the constructor. =head1 METHODS See L for inherited methods. =head1 BUGS none ;-) =head1 SEE ALSO L, L =head1 AUTHOR Shuly Avraham Eavraham@cshl.orgE. Copyright (c) 2002 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use strict; # AUTHOR: Shulamit Avraham # This module needs to be cleaned up and documented # Bio::DB::GFF::Adaptor::memory -- in-memory db adaptor # implements the low level handling of data which stored in memory. # This adaptor implements a specific in memory schema that is compatible with Bio::DB::GFF. # Inherits from Bio::DB::GFF. use Bio::DB::GFF::Util::Rearrange; # for rearrange() use Bio::DB::GFF::Adaptor::memory::iterator; use File::Basename 'dirname'; use Bio::DB::GFF::Adaptor::memory::feature_serializer qw(@hash2array_map); use constant MAX_SEGMENT => 1_000_000_000; # the largest a segment can get use base qw(Bio::DB::GFF); sub new { my $class = shift ; my ($file,$fasta,$dbdir,$preferred_groups) = rearrange([ [qw(GFF FILE)], 'FASTA', [qw(DSN DB DIR DIRECTORY)], 'PREFERRED_GROUPS', ],@_); # fill in object my $self = bless{ data => [] },$class; $self->preferred_groups($preferred_groups) if defined $preferred_groups; $file ||= $dbdir; $fasta ||= $dbdir; $self->load_gff($file) if $file; $self->load_or_store_fasta($fasta) if $fasta; return $self; } sub load_or_store_fasta { my $self = shift; my $fasta = shift; if ((-f $fasta && -w dirname($fasta)) or (-d $fasta && -w $fasta)) { require Bio::DB::Fasta; my $dna_db = eval {Bio::DB::Fasta->new($fasta);} or warn "$@\nCan't open sequence file(s). Use -gff instead of -dir if you wish to load features without sequence.\n"; $dna_db && $self->dna_db($dna_db); } else { $self->load_fasta($fasta); } } sub dna_db { my $self = shift; my $d = $self->{dna_db}; $self->{dna_db} = shift if @_; $d; } sub insert_sequence { my $self = shift; my($id,$offset,$seq) = @_; $self->{dna}{$id} .= $seq; } # low-level fetch of a DNA substring given its # name, class and the desired range. sub get_dna { my $self = shift; my ($id,$start,$stop,$class) = @_; if (my $dna_db = $self->dna_db) { return $dna_db->seq($id,$start=>$stop); } return '' unless $self->{dna}; return $self->{dna}{$id} unless defined $start || defined $stop; $start = 1 if !defined $start; my $reversed = 0; if ($start > $stop) { $reversed++; ($start,$stop) = ($stop,$start); } my $dna = substr($self->{dna}{$id},$start-1,$stop-$start+1); if ($reversed) { $dna =~ tr/gatcGATC/ctagCTAG/; $dna = reverse $dna; } $dna; } sub setup_load { my $self = shift; $self->{tmp} = {}; $self->{data} = []; 1; } sub finish_load { my $self = shift; my $idx = 0; foreach my $arrayref (values %{$self->{tmp}}) { foreach (@$arrayref) {$_->{feature_id} = $idx++; } push @{$self->{data}},@$arrayref; } 1; } # this method loads the feature as a hash into memory - # keeps an array of features-hashes as an in-memory db sub load_gff_line { my $self = shift; my $feature_hash = shift; $feature_hash->{strand} = '' if $feature_hash->{strand} && $feature_hash->{strand} eq '.'; $feature_hash->{phase} = '' if $feature_hash->{phase} && $feature_hash->{phase} eq '.'; $feature_hash->{gclass} = 'Sequence' unless length $feature_hash->{gclass} > 0; # sort by group please push @{$self->{tmp}{$feature_hash->{gclass},$feature_hash->{gname}}},$feature_hash; } # given sequence name, return (reference,start,stop,strand) sub get_abscoords { my $self = shift; my ($name,$class,$refseq) = @_; my %refs; my $regexp; if ($name =~ /[*?]/) { # uh oh regexp time $name = quotemeta($name); $name =~ s/\\\*/.*/g; $name =~ s/\\\?/.?/g; $regexp++; } # Find all features that have the requested name and class. # Sort them by reference point. for my $feature (@{$self->{data}}) { my $no_match_class_name; my $empty_class_name; my $class_matches = !defined($feature->{gclass}) || length($feature->{gclass}) == 0 || $feature->{gclass} eq $class; if (defined $feature->{gname}) { my $matches = $class_matches && ($regexp ? $feature->{gname} =~ /$name/i : lc($feature->{gname}) eq lc($name)); $no_match_class_name = !$matches; # to accomodate Shuly's interesting logic } else{ $empty_class_name = 1; } if ($no_match_class_name){ my $feature_attributes = $feature->{attributes}; my $attributes = {Alias => $name}; if (!$self->_matching_attributes($feature_attributes,$attributes)){ next; } } push @{$refs{$feature->{ref}}},$feature; } # find out how many reference points we recovered if (! %refs) { $self->error("$name not found in database"); return; } # compute min and max my ($ref) = keys %refs; my @found = @{$refs{$ref}}; my ($strand,$start,$stop); my @found_segments; foreach my $ref (keys %refs) { next if defined($refseq) and lc($ref) ne lc($refseq); my @found = @{$refs{$ref}}; my ($strand,$start,$stop,$name); foreach (@found) { $strand ||= $_->{strand}; $strand = '+' if $strand && $strand eq '.'; $start = $_->{start} if !defined($start) || $start > $_->{start}; $stop = $_->{stop} if !defined($stop) || $stop < $_->{stop}; $name ||= $_->{gname}; } push @found_segments,[$ref,$class,$start,$stop,$strand,$name]; } return \@found_segments; } sub search_notes { my $self = shift; my ($search_string,$limit) = @_; $search_string =~ tr/*?//d; my @results; my @words = map {quotemeta($_)} $search_string =~ /(\w+)/g; my $search = join '|',@words; for my $feature (@{$self->{data}}) { next unless defined $feature->{gclass} && defined $feature->{gname}; # ignore NULL objects next unless $feature->{attributes}; my @attributes = @{$feature->{attributes}}; my @values = map {$_->[1]} @attributes; my $value = "@values"; my $matches = 0; for my $w (@words) { my @hits = $value =~ /($w)/ig; $matches += @hits; } next unless $matches; my $relevance = 10 * $matches; my $featname = Bio::DB::GFF::Featname->new($feature->{gclass}=>$feature->{gname}); my $note; $note = join ' ',map {$_->[1]} grep {$_->[0] eq 'Note'} @{$feature->{attributes}}; $note .= join ' ',grep /$search/,map {$_->[1]} grep {$_->[0] ne 'Note'} @{$feature->{attributes}}; my $type = Bio::DB::GFF::Typename->new($feature->{method},$feature->{source}); push @results,[$featname,$note,$relevance,$type]; last if defined $limit && @results >= $limit; } #added result filtering so that this method returns the expected results #this section of code used to be in GBrowse's do_keyword_search method my $match_sub = 'sub {'; foreach (split /\s+/,$search_string) { $match_sub .= "return unless \$_[0] =~ /\Q$_\E/i; "; } $match_sub .= "};"; my $match = eval $match_sub; my @matches = grep { $match->($_->[1]) } @results; return @matches; } sub _delete_features { my $self = shift; my @feature_ids = sort {$b<=>$a} @_; my $removed = 0; foreach (@feature_ids) { next unless $_ >= 0 && $_ < @{$self->{data}}; $removed += defined splice(@{$self->{data}},$_,1); } $removed; } sub _delete { my $self = shift; my $delete_spec = shift; my $ranges = $delete_spec->{segments} || []; my $types = $delete_spec->{types} || []; my $force = $delete_spec->{force}; my $range_type = $delete_spec->{range_type}; my $deleted = 0; if (@$ranges) { my @args = @$types ? (-type=>$types) : (); push @args,(-range_type => $range_type); my %ids_to_remove = map {$_->id => 1} map {$_->features(@args)} @$ranges; $deleted = $self->delete_features(keys %ids_to_remove); } elsif (@$types) { my %ids_to_remove = map {$_->id => 1} $self->features(-type=>$types); $deleted = $self->delete_features(keys %ids_to_remove); } else { $self->throw("This operation would delete all feature data and -force not specified") unless $force; $deleted = @{$self->{data}}; @{$self->{data}} = (); } $deleted; } # attributes - # Some GFF version 2 files use the groups column to store a series of # attribute/value pairs. In this interpretation of GFF, the first such # pair is treated as the primary group for the feature; subsequent pairs # are treated as attributes. Two attributes have special meaning: # "Note" is for backward compatibility and is used for unstructured text # remarks. "Alias" is considered as a synonym for the feature name. # If no name is provided, then attributes() returns a flattened hash, of # attribute=>value pairs. sub do_attributes{ my $self = shift; my ($feature_id,$tag) = @_; my $attr ; #my $feature = ${$self->{data}}[$feature_id]; my $feature = $self->_basic_features_by_id($feature_id); my @result; for my $attr (@{$feature->{attributes}}) { my ($attr_name,$attr_value) = @$attr ; if (defined($tag) && lc($attr_name) eq lc($tag)){push @result,$attr_value;} elsif (!defined($tag)) {push @result,($attr_name,$attr_value);} } return @result; } #sub get_feature_by_attribute{ sub _feature_by_attribute{ my $self = shift; my ($attributes,$callback) = @_; $callback || $self->throw('must provide a callback argument'); my $count = 0; my $feature_id = -1; my $feature_group_id = undef; for my $feature (@{$self->{data}}) { $feature_id++; for my $attr (@{$feature->{attributes}}) { my ($attr_name,$attr_value) = @$attr ; #there could be more than one set of attributes...... foreach (keys %$attributes) { if (lc($_) eq lc($attr_name) && lc($attributes->{$_}) eq lc($attr_value)) { $callback->($self->_hash_to_array($feature)); $count++; } } } } } # This is the low-level method that is called to retrieve GFF lines from # the database. It is responsible for retrieving features that satisfy # range and feature type criteria, and passing the GFF fields to a # callback subroutine. sub get_features{ my $self = shift; my $count = 0; my ($search,$options,$callback) = @_; my $found_features; $found_features = $self->_get_features_by_search_options($search,$options); # only true if the sort by group option was specified @{$found_features} = sort {lc("$a->{gclass}:$a->{gname}") cmp lc("$b->{gclass}:$b->{gname}")} @{$found_features} if $options->{sort_by_group} ; for my $feature (@{$found_features}) { # only true if the sort by group option was specified $count++; $callback->( $self->_hash_to_array($feature) ); } return $count; } # Low level implementation of fetching a named feature. # GFF annotations are named using the group class and name fields. # May return zero, one, or several Bio::DB::GFF::Feature objects. =head2 _feature_by_name Title : _feature_by_name Usage : $db->get_features_by_name($name,$class,$callback) Function: get a list of features by name and class Returns : count of number of features retrieved Args : name of feature, class of feature, and a callback Status : protected This method is used internally. The callback arguments are those used by make_feature(). =cut sub _feature_by_name { my $self = shift; my ($class,$name,$location,$callback) = @_; $callback || $self->throw('must provide a callback argument'); my $count = 0; my $regexp; if ($name =~ /[*?]/) { # uh oh regexp time $name = quotemeta($name); $name =~ s/\\\*/.*/g; $name =~ s/\\\?/.?/g; $regexp++; } for my $feature (@{$self->{data}}) { next unless ($regexp && $feature->{gname} =~ /$name/i) || lc($feature->{gname}) eq lc($name); next if defined($feature->{gclass}) && length($feature->{gclass}) > 0 && $feature->{gclass} ne $class; if ($location) { next if $location->[0] ne $feature->{ref}; next if $location->[1] && $location->[1] > $feature->{stop}; next if $location->[2] && $location->[2] < $feature->{start}; } $count++; $callback->($self->_hash_to_array($feature),0); } return $count; } # Low level implementation of fetching a feature by it's id. # The id of the feature as implemented in the in-memory db, is the location of the # feature in the features hash array. sub _feature_by_id{ my $self = shift; my ($ids,$type,$callback) = @_; $callback || $self->throw('must provide a callback argument'); my $feature_group_id = undef; my $count = 0; if ($type eq 'feature'){ for my $feature_id (@$ids){ my $feature = $self->_basic_features_by_id($feature_id); $callback->($self->_hash_to_array($feature)) if $callback; $count++; } } } sub _basic_features_by_id{ my $self = shift; my ($ids) = @_; $ids = [$ids] unless ref $ids =~ /ARRAY/; my @result; for my $feature_id (@$ids){ push @result, ${$self->{data}}[$feature_id]; } return wantarray() ? @result : $result[0]; } # This method is similar to get_features(), except that it returns an # iterator across the query. # See Bio::DB::GFF::Adaptor::memory::iterator. sub get_features_iterator { my $self = shift; my ($search,$options,$callback) = @_; $callback || $self->throw('must provide a callback argument'); my $results = $self->_get_features_by_search_options($search,$options); my $results_array = $self->_convert_feature_hash_to_array($results); return Bio::DB::GFF::Adaptor::memory::iterator->new($results_array,$callback); } # This method is responsible for fetching the list of feature type names. # The query may be limited to a particular range, in # which case the range is indicated by a landmark sequence name and # class and its subrange, if any. These arguments may be undef if it is # desired to retrieve all feature types. # If the count flag is false, the method returns a simple list of # Bio::DB::GFF::Typename objects. If $count is true, the method returns # a list of $name=>$count pairs, where $count indicates the number of # times this feature occurs in the range. sub get_types { my $self = shift; my ($srcseq,$class,$start,$stop,$want_count,$typelist) = @_; my(%result,%obj); for my $feature (@{$self->{data}}) { my $feature_start = $feature->{start}; my $feature_stop = $feature->{stop}; my $feature_ref = $feature->{ref}; my $feature_class = $feature->{class}; my $feature_method = $feature->{method}; my $feature_source = $feature->{source}; if (defined $srcseq){ next unless lc($feature_ref) eq lc($srcseq); } if (defined $class){ next unless defined $feature_class && $feature_class eq $class ; } # the requested range should OVERLAP the retrieved features if (defined $start or defined $stop) { $start = 1 unless defined $start; $stop = MAX_SEGMENT unless defined $stop; next unless $feature_stop >= $start && $feature_start <= $stop; } if (defined $typelist && @$typelist){ next unless $self->_matching_typelist($feature_method,$feature_source,$typelist); } my $type = Bio::DB::GFF::Typename->new($feature_method,$feature_source); $result{$type}++; $obj{$type} = $type; } #end features loop return $want_count ? %result : values %obj; } sub classes { my $self = shift; my %classes; for my $feature (@{$self->{data}}) { $classes{$feature->{gclass}}++; } my @classes = sort keys %classes; return @classes; } # Internal method that performs a search on the features array, # sequentialy retrieves the features, and performs a check on each feature # according to the search options. sub _get_features_by_search_options{ my $count = 0; my ($self, $search,$options) = @_; my ($rangetype,$refseq,$class,$start,$stop,$types,$sparse,$order_by_group,$attributes) = (@{$search}{qw(rangetype refseq refclass start stop types)}, @{$options}{qw(sparse sort_by_group ATTRIBUTES)}) ; my @found_features; my $data = $self->{data}; my $feature_id = -1 ; my $feature_group_id = undef; for my $feature (@{$data}) { $feature_id++; my $feature_start = $feature->{start}; my $feature_stop = $feature->{stop}; my $feature_ref = $feature->{ref}; if (defined $refseq){ next unless lc($feature_ref) eq lc($refseq); } if (defined $start or defined $stop) { $start = 0 unless defined($start); $stop = MAX_SEGMENT unless defined($stop); if ($rangetype eq 'overlaps') { next unless $feature_stop >= $start && $feature_start <= $stop; } elsif ($rangetype eq 'contains') { next unless $feature_start >= $start && $feature_stop <= $stop; } elsif ($rangetype eq 'contained_in') { next unless $feature_start <= $start && $feature_stop >= $stop; } else { next unless $feature_start == $start && $feature_stop == $stop; } } my $feature_source = $feature->{source}; my $feature_method = $feature->{method}; if (defined $types && @$types){ next unless $self->_matching_typelist($feature_method,$feature_source,$types); } my $feature_attributes = $feature->{attributes}; if (defined $attributes){ next unless $self->_matching_attributes($feature_attributes,$attributes); } # if we get here, then we have a feature that meets the criteria. # Then we just push onto an array # of found features and continue. my $found_feature = $feature ; $found_feature->{feature_id} = $feature_id; $found_feature->{group_id} = $feature_group_id; push @found_features,$found_feature; } return \@found_features; } sub _hash_to_array { my ($self,$feature_hash) = @_; my @array = @{$feature_hash}{@hash2array_map}; return wantarray ? @array : \@array; } # this subroutine is needed for convertion of the feature from hash to array in order to # pass it to the callback subroutine sub _convert_feature_hash_to_array{ my ($self, $feature_hash_array) = @_; my @features_array_array = map {scalar $self->_hash_to_array($_)} @$feature_hash_array; return \@features_array_array; } sub _matching_typelist{ my ($self, $feature_method,$feature_source,$typelist) = @_; foreach (@$typelist) { my ($search_method,$search_source) = @$_; next if lc($search_method) ne lc($feature_method); next if defined($search_source) && lc($search_source) ne lc($feature_source); return 1; } return 0; } sub _matching_attributes { my ($self, $feature_attributes,$attributes) = @_ ; foreach (keys %$attributes) { return 0 if !_match_all_attr_in_feature($_,$attributes->{$_},$feature_attributes) } return 1; } sub _match_all_attr_in_feature{ my ($attr_name,$attr_value,$feature_attributes) = @_; for my $attr (@$feature_attributes) { my ($feature_attr_name,$feature_attr_value) = @$attr ; next if ($attr_name ne $feature_attr_name || $attr_value ne $feature_attr_value); return 1; } return 0; } sub do_initialize { 1; } sub get_feature_by_group_id{ 1; } 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor/berkeleydb000755000766000024 013155576320 20460 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm000444000766000024 346713155576320 23016 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Adaptor::berkeleydb::iterator - iterator for Bio::DB::GFF::Adaptor::berkeleydb =head1 SYNOPSIS For internal use only =head1 DESCRIPTION This is an internal module that is used by the Bio::DB::GFF in-memory adaptor to return an iterator across a sequence feature query. The object has a single method, next_feature(), that returns the next feature from the query. The method next_seq() is an alias for next_feature(). =head1 BUGS None known yet. =head1 SEE ALSO L, =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut package Bio::DB::GFF::Adaptor::berkeleydb::iterator; use strict; use DB_File qw(R_FIRST R_NEXT); # this module needs to be cleaned up and documented use Bio::Root::Version; *next_seq = \&next_feature; sub new { my $class = shift; my ($data,$callback,$tmpfile) = @_; return bless {data => $data, callback => $callback, tmpfile => $tmpfile, cache => []},$class; } sub next_feature { my $self = shift; return shift @{$self->{cache}} if @{$self->{cache}}; my $data = $self->{data} or return; my $callback = $self->{callback}; my $features; my $db = tied(%$data); my ($key,$value); for (my $status = $db->seq($key,$value,$self->{iter}++ ? R_NEXT : R_FIRST); $status == 0; $status = $db->seq($key,$value,R_NEXT)) { my @feature = split ($;,$value); $features = $callback->(@feature); last if $features; } unless ($features) { $features = $callback->(); undef $self->{data}; undef $self->{cache}; unlink $self->{tmpfile}; } $self->{cache} = $features or return; shift @{$self->{cache}}; } 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor/dbi000755000766000024 013155576320 17106 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm000444000766000024 1552513155576320 22540 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::dbi::caching_handle; use strict; use DBI; use vars '$AUTOLOAD'; use base qw(Bio::Root::Root); =head1 NAME Bio::DB::GFF::Adaptor::dbi::caching_handle -- Cache for database handles =head1 SYNOPSIS use Bio::DB::GFF::Adaptor::dbi::caching_handle; $db = Bio::DB::GFF::Adaptor::dbi::caching_handle->new('dbi:mysql:test'); $sth = $db->prepare('select * from foo'); @h = $sth->fetch_rowarray; $sth->finish =head1 DESCRIPTION This module handles a pool of database handles. It was motivated by the MYSQL driver's {mysql_use_result} attribute, which dramatically improves query speed and memory usage, but forbids additional query statements from being evaluated while an existing one is in use. This module is a plug-in replacement for vanilla DBI. It automatically activates the {mysql_use_result} attribute for the mysql driver, but avoids problems with multiple active statement handlers by creating new database handles as needed. =head1 USAGE The object constructor is Bio::DB::GFF::Adaptor::dbi::caching_handle-Enew(). This is called like DBI-Econnect() and takes the same arguments. The returned object looks and acts like a conventional database handle. In addition to all the standard DBI handle methods, this package adds the following: =head2 dbi_quote Title : dbi_quote Usage : $string = $db->dbi_quote($sql,@args) Function: perform bind variable substitution Returns : query string Args : the query string and bind arguments Status : public This method replaces the bind variable "?" in a SQL statement with appropriately quoted bind arguments. It is used internally to handle drivers that don't support argument binding. =head2 do_query Title : do_query Usage : $sth = $db->do_query($query,@args) Function: perform a DBI query Returns : a statement handler Args : query string and list of bind arguments Status : Public This method performs a DBI prepare() and execute(), returning a statement handle. You will typically call fetch() of fetchrow_array() on the statement handle. The parsed statement handle is cached for later use. =head2 debug Title : debug Usage : $debug = $db->debug([$debug]) Function: activate debugging messages Returns : current state of flag Args : optional new setting of flag Status : public =cut sub new { my $class = shift; my @dbi_args = @_; my $self = bless { dbh => [], args => \@dbi_args, debug => 0, },$class; $self->dbh || $self->throw("Can't connect to database: " . DBI->errstr); $self; } sub AUTOLOAD { my($pack,$func_name) = $AUTOLOAD=~/(.+)::([^:]+)$/; return if $func_name eq 'DESTROY'; my $self = shift or return DBI->$func_name(@_); $self->dbh->$func_name(@_); } sub debug { my $self = shift; my $d = $self->{debug}; $self->{debug} = shift if @_; $d; } sub prepare { my $self = shift; my $query = shift; # find a non-busy dbh my $dbh = $self->dbh || $self->throw("Can't connect to database: " . DBI->errstr); warn "Using prepare_cache\n" if $self->debug; my $sth = $dbh->prepare_cached($query, {}, 3) || $self->throw("Couldn't prepare query $query:\n ".DBI->errstr."\n"); return $sth; } sub do_query { my $self = shift; my ($query,@args) = @_; warn $self->dbi_quote($query,@args),"\n" if $self->debug; my $sth = $self->prepare($query); $sth->execute(@args) || $self->throw("Couldn't execute query $query:\n ".DBI->errstr."\n"); $sth; } sub dbh { my $self = shift; foreach (@{$self->{dbh}}) { return $_ if $_->inuse == 0; } # if we get here, we must create a new one warn "(Re)connecting to database\n" if $self->debug; my $dbh = DBI->connect(@{$self->{args}}) or return; $dbh->{PrintError} = 0; # for Oracle - to retrieve LOBs, need to define the length (Jul 15, 2002) $dbh->{LongReadLen} = 100*65535; $dbh->{LongTruncOk} = 0; $dbh->{mysql_auto_reconnect} = 1; my $wrapper = Bio::DB::GFF::Adaptor::dbi::faux_dbh->new($dbh); push @{$self->{dbh}},$wrapper; $wrapper; } # The clone method should only be called in child processes after a fork(). # It does two things: (1) it sets the "real" dbh's InactiveDestroy to 1, # thereby preventing the database connection from being destroyed in # the parent when the dbh's destructor is called; (2) it replaces the # "real" dbh with the result of dbh->clone(), so that we now have an # independent handle. sub clone { my $self = shift; foreach (@{$self->{dbh}}) { $_->clone }; } =head2 attribute Title : attribute Usage : $value = $db->attribute(AttributeName , [$newvalue]) Function: get/set DBI::db handle attribute Returns : current state of the attribute Args : name of the attribute and optional new setting of attribute Status : public Under Bio::DB::GFF::Adaptor::dbi::caching_handle the DBI::db attributes that are usually set using hashref calls are unavailable. Use attribute() instead. For example, instead of: $dbh->{AutoCommit} = 0; use $dbh->attribute(AutoCommit=>0); =cut sub attribute { my $self = shift; my $dbh = $self->dbh->{dbh}; return $dbh->{$_[0]} = $_[1] if @_ == 2; return $dbh->{$_[0]} if @_ == 1; return; } sub disconnect { my $self = shift; $_ && $_->disconnect foreach @{$self->{dbh}}; $self->{dbh} = []; } sub dbi_quote { my $self = shift; my ($query,@args) = @_; my $dbh = $self->dbh; $query =~ s/\?/$dbh->quote(shift @args)/eg; $query; } package Bio::DB::GFF::Adaptor::dbi::faux_dbh; use vars '$AUTOLOAD'; sub new { my $class = shift; my $dbh = shift; bless {dbh=>$dbh},$class; } sub prepare { my $self = shift; my $sth = $self->{dbh}->prepare(@_) or return; $sth->{mysql_use_result} = 1 if $self->{dbh}->{Driver}{Name} eq 'mysql'; $sth; } sub prepare_delayed { my $self = shift; my $sth = $self->{dbh}->prepare(@_) or return; $sth; } sub inuse { shift->{dbh}->{ActiveKids}; } # The clone method should only be called in child processes after a fork(). # It does two things: (1) it sets the "real" dbh's InactiveDestroy to 1, # thereby preventing the database connection from being destroyed in # the parent when the dbh's destructor is called; (2) it replaces the # "real" dbh with the result of dbh->clone(), so that we now have an # independent handle. sub clone { my $self = shift; $self->{dbh}{InactiveDestroy} = 1; $self->{dbh} = $self->{dbh}->clone; } sub DESTROY { } sub AUTOLOAD { my($pack,$func_name) = $AUTOLOAD=~/(.+)::([^:]+)$/; return if $func_name eq 'DESTROY'; my $self = shift; if( defined $self->{dbh} ) { $self->{dbh}->$func_name(@_); } } 1; __END__ =head1 BUGS Report to the author. =head1 SEE ALSO L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Adaptor/dbi/iterator.pm000444000766000024 275713155576320 21445 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Adaptor::dbi::iterator - iterator for Bio::DB::GFF::Adaptor::dbi =head1 SYNOPSIS For internal use only =head1 DESCRIPTION This is an internal module that is used by the Bio::DB::GFF DBI adaptor to return an iterator across a sequence feature query. The object has a single method, next_feature(), that returns the next feature from the query. The method next_seq() is an alias for next_feature(). =head1 BUGS None known yet. =head1 SEE ALSO L, =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut package Bio::DB::GFF::Adaptor::dbi::iterator; use strict; use Bio::Root::Version; use constant STH => 0; use constant CALLBACK => 1; use constant CACHE => 2; *next_seq = \&next_feature; sub new { my $class = shift; my ($sth,$callback) = @_; return bless [$sth,$callback,[]],$class; } sub next_feature { my $self = shift; return shift @{$self->[CACHE]} if @{$self->[CACHE]}; my $sth = $self->[STH] or return; my $callback = $self->[CALLBACK]; my $features; while (1) { if (my @row = $sth->fetchrow_array) { $features = $callback->(@row); last if $features; } else { $sth->finish; undef $self->[STH]; $features = $callback->(); last; } } $self->[CACHE] = $features or return; shift @{$self->[CACHE]}; } 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor/dbi/mysql.pm000444000766000024 6245513155576320 21002 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::dbi::mysql; =head1 NAME Bio::DB::GFF::Adaptor::dbi::mysql -- Database adaptor for a specific mysql schema =head1 SYNOPSIS See L =cut # a simple mysql adaptor use strict; use Bio::DB::GFF::Util::Rearrange; # for rearrange() use Bio::DB::GFF::Util::Binning; use base qw(Bio::DB::GFF::Adaptor::dbi); use constant MAX_SEGMENT => 100_000_000; # the largest a segment can get use constant GETSEQCOORDS =><<<< < select * from fgroup where gname='sjj_2L52.1'; +-------+-------------+------------+ | gid | gclass | gname | +-------+-------------+------------+ | 69736 | PCR_product | sjj_2L52.1 | +-------+-------------+------------+ 1 row in set (0.70 sec) mysql> select fref,fstart,fstop from fdata,fgroup where gclass='PCR_product' and gname = 'sjj_2L52.1' and fdata.gid=fgroup.gid; +---------------+--------+-------+ | fref | fstart | fstop | +---------------+--------+-------+ | CHROMOSOME_II | 1586 | 2355 | +---------------+--------+-------+ 1 row in set (0.03 sec) =item ftype This table contains the feature types, one per row. Columns are: ftypeid the feature type ID (integer) fmethod the feature type method name (string) fsource the feature type source name (string) The ftype.ftypeid field joins with the fdata.ftypeid field. Example: mysql> select fref,fstart,fstop,fmethod,fsource from fdata,fgroup,ftype where gclass='PCR_product' and gname = 'sjj_2L52.1' and fdata.gid=fgroup.gid and fdata.ftypeid=ftype.ftypeid; +---------------+--------+-------+-------------+-----------+ | fref | fstart | fstop | fmethod | fsource | +---------------+--------+-------+-------------+-----------+ | CHROMOSOME_II | 1586 | 2355 | PCR_product | GenePairs | +---------------+--------+-------+-------------+-----------+ 1 row in set (0.08 sec) =item fdna This table holds the raw DNA of the reference sequences. It has three columns: fref reference sequence name (string) foffset offset of this sequence fdna the DNA sequence (longblob) To overcome problems loading large blobs, DNA is automatically fragmented into multiple segments when loading, and the position of each segment is stored in foffset. The fragment size is controlled by the -clump_size argument during initialization. =item fattribute_to_feature This table holds "attributes", which are tag/value pairs stuffed into the GFF line. The first tag/value pair is treated as the group, and anything else is treated as an attribute (weird, huh?). CHR_I assembly_tag Finished 2032 2036 . + . Note "Right: cTel33B" CHR_I assembly_tag Polymorphism 668 668 . + . Note "A->C in cTel33B" The columns of this table are: fid feature ID (integer) fattribute_id ID of the attribute (integer) fattribute_value text of the attribute (text) The fdata.fid column joins with fattribute_to_feature.fid. =item fattribute This table holds the normalized names of the attributes. Fields are: fattribute_id ID of the attribute (integer) fattribute_name Name of the attribute (varchar) =back =head2 Data Loading Methods In addition to implementing the abstract SQL-generating methods of Bio::DB::GFF::Adaptor::dbi, this module also implements the data loading functionality of Bio::DB::GFF. =cut =head2 new Title : new Usage : $db = Bio::DB::GFF->new(@args) Function: create a new adaptor Returns : a Bio::DB::GFF object Args : see below Status : Public The new constructor is identical to the "dbi" adaptor's new() method, except that the prefix "dbi:mysql" is added to the database DSN identifier automatically if it is not there already. Argument Description -------- ----------- -dsn the DBI data source, e.g. 'dbi:mysql:ens0040' or "ens0040" -user username for authentication -pass the password for authentication =cut #' sub new { my $class = shift; my ($dsn,$other) = rearrange([ [qw(FEATUREDB DB DSN)], ],@_); $dsn = "dbi:mysql:$dsn" if !ref($dsn) && $dsn !~ /^(?:dbi|DBI):/; my $self = $class->SUPER::new(-dsn=>$dsn,%$other); $self; } =head2 get_dna Title : get_dna Usage : $string = $db->get_dna($name,$start,$stop,$class) Function: get DNA string Returns : a string Args : name, class, start and stop of desired segment Status : Public This method performs the low-level fetch of a DNA substring given its name, class and the desired range. This should probably be moved to the parent class. =cut sub getseqcoords_query { my $self = shift; return GETSEQCOORDS ; } sub getaliascoords_query{ my $self = shift; return GETALIASCOORDS ; } sub getforcedseqcoords_query{ my $self = shift; return GETFORCEDSEQCOORDS ; } sub getaliaslike_query{ my $self = shift; return GETALIASLIKE ; } # override parent sub get_abscoords_bkup { my $self = shift; my ($name,$class,$refseq) = @_; my $result = $self->SUPER::get_abscoords(@_); return $result if $result; my $sth; if ($name =~ s/\*/%/g) { $sth = $self->dbh->do_query(GETALIASLIKE,$name,$class); } else { $sth = $self->dbh->do_query(GETALIASCOORDS,$name,$class); } my @result; while (my @row = $sth->fetchrow_array) { push @result,\@row } $sth->finish; if (@result == 0) { $self->error("$name not found in database"); return; } else { return \@result; } } sub make_features_select_part { my $self = shift; my $options = shift || {}; my $s; if (my $b = $options->{bin_width}) { $s = <{attributes} && keys %{$options->{attributes}}>1; $s; } # IMPORTANT NOTE: # WHETHER OR NOT THIS WORKS IS CRITICALLY DEPENDENT ON THE RELATIVE MAGNITUDE OF THE sub make_features_from_part { my $self = shift; my $sparse_types = shift; my $options = shift || {}; my $sparse_groups = $options->{sparse_groups}; my $index = $sparse_groups ? ' USE INDEX(gid)' : $sparse_types ? ' USE INDEX(ftypeid)' : ''; return $options->{attributes} ? "fdata${index},ftype,fgroup,fattribute,fattribute_to_feature\n" : "fdata${index},ftype,fgroup\n"; } =head2 search_notes Title : search_notes Usage : @search_results = $db->search_notes("full text search string",$limit) Function: Search the notes for a text string, using mysql full-text search Returns : array of results Args : full text search string, and an optional row limit Status : public This is a mysql-specific method. Given a search string, it performs a full-text search of the notes table and returns an array of results. Each row of the returned array is a arrayref containing the following fields: column 1 A Bio::DB::GFF::Featname object, suitable for passing to segment() column 2 The text of the note column 3 A relevance score. =cut sub search_notes { my $self = shift; my ($search_string,$limit) = @_; $search_string =~ tr/*?//d; my $query = FULLTEXTSEARCH; $query .= " limit $limit" if defined $limit; my $sth = $self->dbh->do_query($query,$search_string,$search_string); my @results; while (my ($class,$name,$note,$relevance,$method,$source) = $sth->fetchrow_array) { next unless $class && $name; # sorry, ignore NULL objects $relevance = sprintf("%.2f",$relevance); # trim long floats my $featname = Bio::DB::GFF::Featname->new($class=>$name); my $type = Bio::DB::GFF::Typename->new($method,$source); push @results,[$featname,$note,$relevance,$type]; } #added result filtering so that this method returns the expected results #this section of code used to be in GBrowse's do_keyword_search method my $match_sub = 'sub {'; foreach (split /\s+/,$search_string) { $match_sub .= "return unless \$_[0] =~ /\Q$_\E/i; "; } $match_sub .= "};"; my $match = eval $match_sub; my @matches = grep { $match->($_->[1]) } @results; return @matches; } ################################ loading and initialization ################################## =head2 schema Title : schema Usage : $schema = $db->schema Function: return the CREATE script for the schema Returns : a list of CREATE statemetns Args : none Status : protected This method returns a list containing the various CREATE statements needed to initialize the database tables. =cut sub schema { my $self = shift; my $dbh = $self->dbh; my ($version) = $dbh->selectrow_array('select version()'); my ($major, $minor) = split /\./, $version; $version = "$major.$minor"; my $engine = $version >= 4.1 ? 'ENGINE' : 'TYPE'; my %schema = ( fdata =>{ table=> qq{ create table fdata ( fid int not null auto_increment, fref varchar(100) not null, fstart int not null, fstop int not null, fbin double precision, ftypeid int not null, fscore float, fstrand enum('+','-'), fphase enum('0','1','2'), gid int not null, ftarget_start int, ftarget_stop int, primary key(fid), unique index(fref,fbin,fstart,fstop,ftypeid,gid), index(ftypeid), index(gid) ) $engine=MyISAM } # fdata table }, # fdata fgroup =>{ table=> qq{ create table fgroup ( gid int not null auto_increment, gclass varchar(100), gname varchar(100), primary key(gid), unique(gclass,gname) ) $engine=MyISAM } }, ftype => { table=> qq{ create table ftype ( ftypeid int not null auto_increment, fmethod varchar(100) not null, fsource varchar(100), primary key(ftypeid), index(fmethod), index(fsource), unique ftype (fmethod,fsource) ) $engine=MyISAM } #ftype table }, #ftype fdna => { table=> qq{ create table fdna ( fref varchar(100) not null, foffset int(10) unsigned not null, fdna longblob, primary key(fref,foffset) ) $engine=MyISAM } # fdna table },#fdna fmeta => { table=> qq{ create table fmeta ( fname varchar(255) not null, fvalue varchar(255) not null, primary key(fname) ) $engine=MyISAM } # fmeta table },#fmeta fattribute => { table=> qq{ create table fattribute ( fattribute_id int(10) unsigned not null auto_increment, fattribute_name varchar(255) not null, primary key(fattribute_id) ) $engine=MyISAM } #fattribute table },#fattribute fattribute_to_feature => { table=> qq{ create table fattribute_to_feature ( fid int(10) not null, fattribute_id int(10) not null, fattribute_value text, key(fid,fattribute_id), key(fattribute_value(48)), fulltext(fattribute_value) ) $engine=MyISAM } # fattribute_to_feature table },# fattribute_to_feature finterval_stats => { table=> qq{ create table finterval_stats ( ftypeid integer not null, fref varchar(100) not null, fbin integer not null, fcum_count integer not null, primary key(ftypeid,fref,fbin) ) $engine=MyISAM } # finterval_stats table },# finterval_stats ); return \%schema; } =head2 make_classes_query Title : make_classes_query Usage : ($query,@args) = $db->make_classes_query Function: return query fragment for generating list of reference classes Returns : a query and args Args : none Status : public =cut sub make_classes_query { my $self = shift; return 'SELECT DISTINCT gclass FROM fgroup WHERE NOT ISNULL(gclass)'; } =head2 make_meta_set_query Title : make_meta_set_query Usage : $sql = $db->make_meta_set_query Function: return SQL fragment for setting a meta parameter Returns : SQL fragment Args : none Status : public By default this does nothing; meta parameters are not stored or retrieved. =cut sub make_meta_set_query { return 'REPLACE INTO fmeta VALUES (?,?)'; } =head2 setup_load Title : setup_load Usage : $db->setup_load Function: called before load_gff_line() Returns : void Args : none Status : protected This method performs schema-specific initialization prior to loading a set of GFF records. It prepares a set of DBI statement handlers to be used in loading the data. =cut sub setup_load { my $self = shift; my $dbh = $self->features_db; if ($self->lock_on_load) { my @tables = map { "$_ WRITE"} $self->tables; my $tables = join ', ',@tables; $dbh->do("LOCK TABLES $tables"); } # for my $table (qw(fdata)) { # $dbh->do("alter table $table disable keys"); # } my $lookup_type = $dbh->prepare_delayed('SELECT ftypeid FROM ftype WHERE fmethod=? AND fsource=?'); my $insert_type = $dbh->prepare_delayed('INSERT INTO ftype (fmethod,fsource) VALUES (?,?)'); my $lookup_group = $dbh->prepare_delayed('SELECT gid FROM fgroup WHERE gname=? AND gclass=?'); my $insert_group = $dbh->prepare_delayed('INSERT INTO fgroup (gname,gclass) VALUES (?,?)'); my $lookup_attribute = $dbh->prepare_delayed('SELECT fattribute_id FROM fattribute WHERE fattribute_name=?'); my $insert_attribute = $dbh->prepare_delayed('INSERT INTO fattribute (fattribute_name) VALUES (?)'); my $insert_attribute_value = $dbh->prepare_delayed('INSERT INTO fattribute_to_feature (fid,fattribute_id,fattribute_value) VALUES (?,?,?)'); my $insert_data = $dbh->prepare_delayed(<{load_stuff}{sth}{lookup_ftype} = $lookup_type; $self->{load_stuff}{sth}{insert_ftype} = $insert_type; $self->{load_stuff}{sth}{lookup_fgroup} = $lookup_group; $self->{load_stuff}{sth}{insert_fgroup} = $insert_group; $self->{load_stuff}{sth}{insert_fdata} = $insert_data; $self->{load_stuff}{sth}{lookup_fattribute} = $lookup_attribute; $self->{load_stuff}{sth}{insert_fattribute} = $insert_attribute; $self->{load_stuff}{sth}{insert_fattribute_value} = $insert_attribute_value; $self->{load_stuff}{types} = {}; $self->{load_stuff}{groups} = {}; $self->{load_stuff}{counter} = 0; } =head2 load_gff_line Title : load_gff_line Usage : $db->load_gff_line($fields) Function: called to load one parsed line of GFF Returns : true if successfully inserted Args : hashref containing GFF fields Status : protected This method is called once per line of the GFF and passed a series of parsed data items that are stored into the hashref $fields. The keys are: ref reference sequence source annotation source method annotation method start annotation start stop annotation stop score annotation score (may be undef) strand annotation strand (may be undef) phase annotation phase (may be undef) group_class class of annotation's group (may be undef) group_name ID of annotation's group (may be undef) target_start start of target of a similarity hit target_stop stop of target of a similarity hit attributes array reference of attributes, each of which is a [tag=>value] array ref =cut sub load_gff_line { my $self = shift; my $gff = shift; my $s = $self->{load_stuff}; my $dbh = $self->features_db; local $dbh->{PrintError} = 0; defined(my $typeid = $self->get_table_id('ftype', $gff->{method} => $gff->{source})) or return; defined(my $groupid = $self->get_table_id('fgroup',$gff->{gname} => $gff->{gclass})) or return; if ($gff->{stop}-$gff->{start}+1 > $self->max_bin) { warn "$gff->{gclass}:$gff->{gname} is ",$gff->{stop}-$gff->{start}+1, " bp long, but the maximum indexable feature is set to ",$self->max_bin," bp.\n"; warn "Please set the maxbin value to a length at least as large as the largest feature you wish to store.\n"; warn "\n* You will need to reinitialize the database from scratch.\n"; warn "* With the Perl API you do this using the -max_bin argument to \$db->initialize().\n"; warn "* With the command-line tools you do with this with --maxfeature option.\n"; } my $bin = bin($gff->{start},$gff->{stop},$self->min_bin); my $result = $s->{sth}{insert_fdata}->execute($gff->{ref}, $gff->{start},$gff->{stop},$bin, $typeid, $gff->{score},$gff->{strand},$gff->{phase}, $groupid, $gff->{tstart},$gff->{tstop}); warn $dbh->errstr,"\n" && return unless $result; my $fid = $dbh->{mysql_insertid} || $self->get_feature_id($gff->{ref},$gff->{start},$gff->{stop},$typeid,$groupid); # insert attributes foreach (@{$gff->{attributes}}) { defined(my $attribute_id = $self->get_table_id('fattribute',$_->[0])) or return; $s->{sth}{insert_fattribute_value}->execute($fid,$attribute_id,$_->[1]); } if ( (++$s->{counter} % 1000) == 0) { print STDERR "$s->{counter} records loaded..."; print STDERR -t STDOUT && !$ENV{EMACS} ? "\r" : "\n"; } $fid; } sub finish_load { my $self = shift; my $dbh = $self->features_db; local $dbh->{PrintError} = 0; # for my $table (qw(fdata)) { # $dbh->do("alter table $table enable keys"); # } $self->SUPER::finish_load; } sub insert_sequence { my $self = shift; my($id,$offset,$seq) = @_; my $sth = $self->{_insert_sequence} ||= $self->dbh->prepare_delayed('replace into fdna values (?,?,?)'); $sth->execute($id,$offset,$seq) or $self->throw($sth->errstr); } =head2 get_table_id Title : get_table_id Usage : $integer = $db->get_table_id($table,@ids) Function: get the ID of a group or type Returns : an integer ID or undef Args : none Status : private This internal method is called by load_gff_line to look up the integer ID of an existing feature type or group. The arguments are the name of the table, and two string identifiers. For feature types, the identifiers are the method and source. For groups, the identifiers are group name and class. This method requires that a statement handler named I, have been created previously by setup_load(). It is here to overcome deficiencies in mysql's INSERT syntax. =cut #' # get the object ID from a named table sub get_table_id { my $self = shift; my $table = shift; my @ids = @_; # irritating warning for null id my $id_key; { local $^W=0; $id_key = join ':',@ids; } my $s = $self->{load_stuff}; my $sth = $s->{sth}; my $dbh = $self->features_db; unless (defined($s->{$table}{$id_key})) { ######################################### # retrieval of the last inserted id is now located at the adaptor and not in caching_handle ####################################### if ( (my $result = $sth->{"lookup_$table"}->execute(@ids)) > 0) { $s->{$table}{$id_key} = ($sth->{"lookup_$table"}->fetchrow_array)[0]; } else { $sth->{"insert_$table"}->execute(@ids) && ($s->{$table}{$id_key} = $self->insertid($sth->{"insert_$table"})); #&& ($s->{$table}{$id_key} = $sth->{"insert_$table"}{sth}{mysql_insertid}); #&& ($s->{$table}{$id_key} = $sth->{"insert_$table"}->insertid); } } my $id = $s->{$table}{$id_key}; unless (defined $id) { warn "No $table id for $id_key ",$dbh->errstr," Record skipped.\n"; return; } $id; } sub insertid { my $self = shift; my $s = shift ; $s->{mysql_insertid}; } =head2 get_feature_id Title : get_feature_id Usage : $integer = $db->get_feature_id($ref,$start,$stop,$typeid,$groupid) Function: get the ID of a feature Returns : an integer ID or undef Args : none Status : private This internal method is called by load_gff_line to look up the integer ID of an existing feature. It is ony needed when replacing a feature with new information. =cut # this method is called when needed to look up a feature's ID sub get_feature_id { my $self = shift; my ($ref,$start,$stop,$typeid,$groupid) = @_; my $s = $self->{load_stuff}; unless ($s->{get_feature_id}) { my $dbh = $self->features_db; $s->{get_feature_id} = $dbh->prepare_delayed('SELECT fid FROM fdata WHERE fref=? AND fstart=? AND fstop=? AND ftypeid=? AND gid=?'); } my $sth = $s->{get_feature_id} or return; $sth->execute($ref,$start,$stop,$typeid,$groupid) or return; my ($fid) = $sth->fetchrow_array; return $fid; } sub _add_interval_stats_table { my $self = shift; my $schema = $self->schema; my $create_table_stmt = $schema->{'finterval_stats'}{'table'}; $create_table_stmt =~ s/create table/create table if not exists/i; my $dbh = $self->features_db; $dbh->do($create_table_stmt) || warn $dbh->errstr; } sub disable_keys { my $self = shift; my $table = shift; my $dbh = $self->dbh; $dbh->do("alter table $table disable keys"); } sub enable_keys { my $self = shift; my $table = shift; my $dbh = $self->dbh; $dbh->do("alter table $table enable keys"); } 1; __END__ =head1 BUGS none ;-) =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2002 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm000444000766000024 553013155576320 21422 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::dbi::mysqlace; =head1 NAME Bio::DB::GFF::Adaptor::dbi::mysqlace -- Unholy union between mysql GFF database and acedb database =head1 SYNOPSIS Pending See L and L =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2002 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use strict; use Bio::DB::GFF::Util::Rearrange; # for rearrange() use base qw(Bio::DB::GFF::Adaptor::dbi::mysql Bio::DB::GFF::Adaptor::ace); # Create a new Bio::DB::GFF::Adaptor::dbi object sub new { my $class = shift; my $self = $class->SUPER::new(@_); my ($dna_db,$acedb) = rearrange([[qw(DNADB DNA FASTA FASTA_DIR)],'ACEDB'],@_); if ($dna_db) { if (!ref($dna_db)) { require Bio::DB::Fasta; my $fasta_dir = $dna_db; $dna_db = Bio::DB::Fasta->new($fasta_dir); $dna_db or $class->throw("new(): Failed to create new Bio::DB::Fasta from files in $fasta_dir"); } else { $dna_db->isa('Bio::DB::Fasta') or $class->throw("new(): $dna_db is not a Bio::DB::Fasta object"); } $self->dna_db($dna_db); } if ($acedb) { $acedb->isa('Ace') or $class->throw("$acedb is not an acedb accessor object"); $self->acedb($acedb); } $self; } =head2 freshen_ace Title : freshen Usage : $flag = Bio::DB::GFF->freshen_ace; Function: Refresh internal acedb handle Returns : flag if correctly freshened Args : none Status : Public ACeDB has an annoying way of timing out, leaving dangling database handles. This method will invoke the ACeDB reopen() method, which causes dangling handles to be refreshed. It has no effect if you are not using ACeDB to create ACeDB objects. =cut ######################### # Moved from mysqlopt.pm ######################### sub make_object { my $self = shift; my ($class,$name,$start,$stop) = @_; if (my $db = $self->acedb) { # for Notes we just return a text, no database associated return $class->new(Text=>$name) if $class eq 'Note'; # for homols, we create the indicated Protein or Sequence object # then generate a bogus Homology object (for future compatability??) if ($start ne '') { require Ace::Sequence::Homol; return Ace::Sequence::Homol->new_homol($class,$name,$db,$start,$stop); } # General case: my $obj = $db->class->new($class=>$name,$self->acedb); return $obj if defined $obj; # Last resort, return a Text return $class->new(Text=>$name); } return $self->SUPER::make_object($class,$name,$start,$stop); } sub get_dna { my $self = shift; my ($ref,$start,$stop,$class) = @_; my $dna_db = $self->dna_db or return $self->SUPER::get_dna(@_); return $dna_db->seq($ref,$start,$stop,$class); } 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm000444000766000024 10516413155576320 21656 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::dbi::mysqlcmap; =head1 NAME Bio::DB::GFF::Adaptor::dbi::mysqlcmap -- Database adaptor for an integraded CMap/GBrowse mysql schema =head1 SYNOPSIS See L =cut # a simple mysql adaptor use strict; use Data::Dumper; use Bio::DB::GFF::Adaptor::dbi; use Bio::DB::GFF::Util::Rearrange; # for rearrange() use Bio::DB::GFF::Util::Binning; use base qw(Bio::DB::GFF::Adaptor::dbi::mysql); require Bio::DB::GFF::Adaptor::dbi::mysql; use constant GETSEQCOORDS =><<<< < select * from cmap_feature where feature_name='sjj_2L52.1'; +--------------+-------------+--------------+ | feature_id | gclass | feature_name | +--------------+-------------+--------------+ | 69736 | PCR_product | sjj_2L52.1 | +--------------+-------------+--------------+ 1 row in set (0.70 sec) mysql> select fref,fstart,fstop from fdata,cmap_feature where gclass='PCR_product' and feature_name = 'sjj_2L52.1' and fdata.feature_id=cmap_feature.feature_id; +---------------+--------+-------+ | fref | fstart | fstop | +---------------+--------+-------+ | CHROMOSOME_II | 1586 | 2355 | +---------------+--------+-------+ 1 row in set (0.03 sec) =item ftype This table contains the feature types, one per row. Columns are: ftypeid the feature type ID (integer) fmethod the feature type method name (string) fsource the feature type source name (string) The ftype.ftypeid field joins with the fdata.ftypeid field. Example: mysql> select fref,fstart,fstop,fmethod,fsource from fdata,cmap_feature,ftype where gclass='PCR_product' and feature_name = 'sjj_2L52.1' and fdata.feature_id=cmap_feature.feature_id and fdata.ftypeid=ftype.ftypeid; +---------------+--------+-------+-------------+-----------+ | fref | fstart | fstop | fmethod | fsource | +---------------+--------+-------+-------------+-----------+ | CHROMOSOME_II | 1586 | 2355 | PCR_product | GenePairs | +---------------+--------+-------+-------------+-----------+ 1 row in set (0.08 sec) =item fdna This table holds the raw DNA of the reference sequences. It has three columns: fref reference sequence name (string) foffset offset of this sequence fdna the DNA sequence (longblob) To overcome problems loading large blobs, DNA is automatically fragmented into multiple segments when loading, and the position of each segment is stored in foffset. The fragment size is controlled by the -clump_size argument during initialization. =item fattribute_to_feature This table holds "attributes", which are tag/value pairs stuffed into the GFF line. The first tag/value pair is treated as the group, and anything else is treated as an attribute (weird, huh?). CHR_I assembly_tag Finished 2032 2036 . + . Note "Right: cTel33B" CHR_I assembly_tag Polymorphism 668 668 . + . Note "A->C in cTel33B" The columns of this table are: fid feature ID (integer) fattribute_id ID of the attribute (integer) fattribute_value text of the attribute (text) The fdata.fid column joins with fattribute_to_feature.fid. =item fattribute This table holds the normalized names of the attributes. Fields are: fattribute_id ID of the attribute (integer) fattribute_name Name of the attribute (varchar) =back =head2 Data Loading Methods In addition to implementing the abstract SQL-generating methods of Bio::DB::GFF::Adaptor::dbi, this module also implements the data loading functionality of Bio::DB::GFF. =cut =head2 new Title : new Usage : $db = Bio::DB::GFF->new(@args) Function: create a new adaptor Returns : a Bio::DB::GFF object Args : see below Status : Public The new constructor is identical to the "dbi" adaptor's new() method, except that the prefix "dbi:mysql" is added to the database DSN identifier automatically if it is not there already. Argument Description -------- ----------- -dsn the DBI data source, e.g. 'dbi:mysql:ens0040' or "ens0040" -user username for authentication -pass the password for authentication =cut #' #Defined in mysql.pm =head2 get_dna Title : get_dna Usage : $string = $db->get_dna($name,$start,$stop,$class) Function: get DNA string Returns : a string Args : name, class, start and stop of desired segment Status : Public This method performs the low-level fetch of a DNA substring given its name, class and the desired range. This should probably be moved to the parent class. =cut sub make_features_select_part { my $self = shift; my $options = shift || {}; my $s; if (my $b = $options->{bin_width}) { $s = <{attributes} && keys %{$options->{attributes}}>1; $s; } # IMPORTANT NOTE: # WHETHER OR NOT THIS WORKS IS CRITICALLY DEPENDENT ON THE RELATIVE MAGNITUDE OF THE sub make_features_from_part { my $self = shift; my $sparse_types = shift; my $options = shift || {}; my $sparse_groups = $options->{sparse_groups}; my $index = $sparse_groups ? ' USE INDEX(feature_id)' : $sparse_types ? ' USE INDEX(ftypeid)' : ''; return $options->{attributes} ? "fdata${index},ftype,cmap_feature,fattribute,fattribute_to_feature\n" : "fdata${index},ftype,cmap_feature\n"; } ################################ loading and initialization ################################## =head2 schema Title : schema Usage : $schema = $db->schema Function: return the CREATE script for the schema Returns : a list of CREATE statemetns Args : none Status : protected This method returns a list containing the various CREATE statements needed to initialize the database tables. =cut sub schema { my %schema = ( fdata =>{ table=> q{ #create table fdata ( # fid int not null auto_increment, # fref varchar(100) not null, # fstart int unsigned not null, # fstop int unsigned not null, # ftypeid int not null, # fscore float, # fstrand enum('+','-'), # fphase enum('0','1','2'), # feature_id int not null, # ftarget_start int unsigned, # ftarget_stop int unsigned, # primary key(fid), # unique index(fref,fstart,fstop,ftypeid,feature_id), # index(ftypeid), # index(feature_id) #) type=MyISAM create table fdata ( fid int not null auto_increment, fref varchar(100) not null, fstart int unsigned not null, fstop int unsigned not null, fbin double(20,6) not null, ftypeid int not null, fscore float, fstrand enum('+','-'), fphase enum('0','1','2'), feature_id int not null, ftarget_start int unsigned, ftarget_stop int unsigned, primary key(fid), unique index(fref,fbin,fstart,fstop,ftypeid,feature_id), index(ftypeid), index(feature_id) ) type=MyISAM } # fdata table }, # fdata ftype => { table=> q{ create table ftype ( ftypeid int not null auto_increment, fmethod varchar(100) not null, fsource varchar(100), primary key(ftypeid), index(fmethod), index(fsource), unique ftype (fmethod,fsource) )type=MyISAM } #ftype table }, #ftype fdna => { table=> q{ create table fdna ( fref varchar(100) not null, foffset int(10) unsigned not null, fdna longblob, primary key(fref,foffset) )type=MyISAM } # fdna table },#fdna fmeta => { table=> q{ create table fmeta ( fname varchar(255) not null, fvalue varchar(255) not null, primary key(fname) )type=MyISAM } # fmeta table },#fmeta fattribute => { table=> q{ create table fattribute ( fattribute_id int(10) unsigned not null auto_increment, fattribute_name varchar(255) not null, primary key(fattribute_id) )type=MyISAM } #fattribute table },#fattribute fattribute_to_feature => { table=> q{ create table fattribute_to_feature ( fid int(10) not null, fattribute_id int(10) not null, fattribute_value text, key(fid,fattribute_id), key(fattribute_value(48)), fulltext(fattribute_value) )type=MyISAM } # fattribute_to_feature table }, # fattribute_to_feature cmap_attribute => { table=>q{ create table cmap_attribute ( attribute_id int(11) NOT NULL default '0', table_name varchar(30) NOT NULL default '', object_id int(11) NOT NULL default '0', display_order int(11) NOT NULL default '1', is_public tinyint(4) NOT NULL default '1', attribute_name varchar(200) NOT NULL default '', attribute_value text NOT NULL, PRIMARY KEY (attribute_id), KEY table_name (table_name,object_id,display_order,attribute_name) ) TYPE=MyISAM; } # table }, cmap_correspondence_evidence => { table=>q{ create table cmap_correspondence_evidence ( correspondence_evidence_id int(11) NOT NULL default '0', accession_id varchar(20) NOT NULL default '', feature_correspondence_id int(11) NOT NULL default '0', evidence_type_accession varchar(20) NOT NULL default '0', score double(8,2) default NULL, rank int(11) NOT NULL default '0', PRIMARY KEY (correspondence_evidence_id), UNIQUE KEY accession_id (accession_id), KEY feature_correspondence_id (feature_correspondence_id) ) TYPE=MyISAM; } # table }, cmap_correspondence_lookup => { table=>q{ create table cmap_correspondence_lookup ( feature_id1 int(11) default NULL, feature_id2 int(11) default NULL, feature_correspondence_id int(11) default NULL, start_position1 double(11,2) default NULL, start_position2 double(11,2) default NULL, stop_position1 double(11,2) default NULL, stop_position2 double(11,2) default NULL, map_id1 int(11) default NULL, map_id2 int(11) default NULL, feature_type_accession1 varchar(20) default NULL, feature_type_accession2 varchar(20) default NULL, KEY feature_id1 (feature_id1), KEY corr_id (feature_correspondence_id), KEY cl_map_id1 (map_id1), KEY cl_map_id2 (map_id2), KEY cl_map_id1_map_id2 (map_id1,map_id2), KEY cl_map_id2_map_id1 (map_id2,map_id1) ) TYPE=MyISAM; } # table }, cmap_correspondence_matrix => { table=>q{ create table cmap_correspondence_matrix ( reference_map_aid varchar(20) NOT NULL default '0', reference_map_name varchar(32) NOT NULL default '', reference_map_set_aid varchar(20) NOT NULL default '0', reference_species_aid varchar(20) NOT NULL default '0', link_map_aid varchar(20) default NULL, link_map_name varchar(32) default NULL, link_map_set_aid varchar(20) NOT NULL default '0', link_species_aid varchar(20) NOT NULL default '0', no_correspondences int(11) NOT NULL default '0' ) TYPE=MyISAM; } # table }, cmap_feature => { table=>q{ create table cmap_feature ( feature_id int(11) NOT NULL default '0', accession_id varchar(20) NOT NULL default '', map_id int(11) default NULL, feature_type_accession varchar(20) NOT NULL default '0', feature_name varchar(32) NOT NULL default '', is_landmark tinyint(4) NOT NULL default '0', start_position double(11,2) NOT NULL default '0.00', stop_position double(11,2) default NULL, default_rank int(11) NOT NULL default '1', direction tinyint(4) NOT NULL default '1', gclass varchar(100) default NULL, PRIMARY KEY (feature_id), UNIQUE KEY gclass (gclass,feature_name), UNIQUE KEY accession_id (accession_id), KEY feature_name (feature_name), KEY feature_id_map_id (feature_id,map_id), KEY feature_id_map_id_start (feature_id,map_id,start_position), KEY map_id (map_id), KEY map_id_feature_id (map_id,feature_id) ) TYPE=MyISAM; } # table }, cmap_feature_alias => { table=>q{ create table cmap_feature_alias ( feature_alias_id int(11) NOT NULL default '0', feature_id int(11) NOT NULL default '0', alias varchar(255) default NULL, PRIMARY KEY (feature_alias_id), UNIQUE KEY feature_id_2 (feature_id,alias), KEY feature_id (feature_id), KEY alias (alias) ) TYPE=MyISAM; } # table }, cmap_feature_correspondence => { table=>q{ create table cmap_feature_correspondence ( feature_correspondence_id int(11) NOT NULL default '0', accession_id varchar(20) NOT NULL default '', feature_id1 int(11) NOT NULL default '0', feature_id2 int(11) NOT NULL default '0', is_enabled tinyint(4) NOT NULL default '1', PRIMARY KEY (feature_correspondence_id), UNIQUE KEY accession_id (accession_id), KEY feature_id1 (feature_id1), KEY cmap_feature_corresp_idx (is_enabled,feature_correspondence_id) ) TYPE=MyISAM; } # table }, cmap_map => { table=>q{ create table cmap_map ( map_id int(11) NOT NULL default '0', accession_id varchar(20) NOT NULL default '', map_set_id int(11) NOT NULL default '0', map_name varchar(32) NOT NULL default '', display_order int(11) NOT NULL default '1', start_position double(11,2) default NULL, stop_position double(11,2) default NULL, PRIMARY KEY (map_id), UNIQUE KEY accession_id (accession_id), UNIQUE KEY map_id (map_id,map_set_id,map_name,accession_id), KEY map_set_id_index (map_set_id) ) TYPE=MyISAM; } # table }, cmap_map_set => { table=>q{ create table cmap_map_set ( map_set_id int(11) NOT NULL default '0', accession_id varchar(20) NOT NULL default '', map_set_name varchar(64) NOT NULL default '', short_name varchar(30) NOT NULL default '', map_type_accession varchar(20) NOT NULL default '0', species_id int(11) NOT NULL default '0', published_on date default NULL, can_be_reference_map tinyint(4) NOT NULL default '1', display_order int(11) NOT NULL default '1', is_enabled tinyint(4) NOT NULL default '1', shape varchar(12) default NULL, color varchar(20) default NULL, width int(11) default NULL, map_units varchar(12) NOT NULL default '', is_relational_map tinyint(11) NOT NULL default '0', PRIMARY KEY (map_set_id), UNIQUE KEY accession_id (accession_id), UNIQUE KEY map_set_id (map_set_id,species_id,short_name,accession_id), KEY cmap_map_set_idx (can_be_reference_map,is_enabled,species_id,display_order,published_on,short_name) ) TYPE=MyISAM; } # table }, cmap_next_number => { table=>q{ create table cmap_next_number ( table_name varchar(40) NOT NULL default '', next_number int(11) NOT NULL default '0', PRIMARY KEY (table_name) ) TYPE=MyISAM; }, # table insert=>{next_num=>q[ insert into cmap_next_number (table_name,next_number) VALUES ('cmap_feature',82);]} }, cmap_species => { table=>q{ create table cmap_species ( species_id int(11) NOT NULL default '0', accession_id varchar(20) NOT NULL default '', common_name varchar(64) NOT NULL default '', full_name varchar(64) NOT NULL default '', display_order int(11) NOT NULL default '1', PRIMARY KEY (species_id), KEY acc_id_species_id (accession_id,species_id) ) TYPE=MyISAM; } # table }, cmap_xref => { table=>q{ create table cmap_xref ( xref_id int(11) NOT NULL default '0', table_name varchar(30) NOT NULL default '', object_id int(11) default NULL, display_order int(11) NOT NULL default '1', xref_name varchar(200) NOT NULL default '', xref_url text NOT NULL, PRIMARY KEY (xref_id), KEY table_name (table_name,object_id,display_order) ) TYPE=MyISAM; } # table }, ); return \%schema; } =head2 make_classes_query Title : make_classes_query Usage : ($query,@args) = $db->make_classes_query Function: return query fragment for generating list of reference classes Returns : a query and args Args : none Status : public =cut sub make_classes_query { my $self = shift; return 'SELECT DISTINCT gclass FROM cmap_feature WHERE NOT ISNULL(gclass)'; } =head2 setup_load Title : setup_load Usage : $db->setup_load Function: called before load_gff_line() Returns : void Args : none Status : protected This method performs schema-specific initialization prior to loading a set of GFF records. It prepares a set of DBI statement handlers to be used in loading the data. =cut sub setup_load { my $self = shift; my $dbh = $self->features_db; if ($self->lock_on_load) { my @tables = map { "$_ WRITE"} $self->tables; my $tables = join ', ',@tables; $dbh->do("LOCK TABLES $tables"); } #xx1 my $lookup_type = $dbh->prepare_delayed('SELECT ftypeid FROM ftype WHERE fmethod=? AND fsource=?'); my $insert_type = $dbh->prepare_delayed('INSERT INTO ftype (fmethod,fsource) VALUES (?,?)'); my $lookup_group = $dbh->prepare_delayed('SELECT feature_id FROM cmap_feature WHERE feature_name=? AND gclass=?'); my $insert_group = $dbh->prepare_delayed(' INSERT into cmap_feature (feature_id, accession_id,feature_name, gclass ) VALUES (?,feature_id,?,?)'); my $aux_insert_group = $dbh->prepare_delayed(' update cmap_next_number set next_number = next_number +1 where table_name=\'cmap_feature\''); my $next_id_group = $dbh->prepare_delayed('select next_number from cmap_next_number where table_name=\'cmap_feature\''); my $lookup_attribute = $dbh->prepare_delayed('SELECT fattribute_id FROM fattribute WHERE fattribute_name=?'); my $insert_attribute = $dbh->prepare_delayed('INSERT INTO fattribute (fattribute_name) VALUES (?)'); my $insert_attribute_value = $dbh->prepare_delayed('INSERT INTO fattribute_to_feature (fid,fattribute_id,fattribute_value) VALUES (?,?,?)'); my $insert_data = $dbh->prepare_delayed(<{load_stuff}{sth}{lookup_ftype} = $lookup_type; $self->{load_stuff}{sth}{insert_ftype} = $insert_type; #$self->{load_stuff}{sth}{lookup_fgroup} = $lookup_group; #$self->{load_stuff}{sth}{insert_fgroup} = $insert_group; $self->{load_stuff}{sth}{lookup_cmap_feature} = $lookup_group; $self->{load_stuff}{sth}{insert_cmap_feature} = $insert_group; $self->{load_stuff}{sth}{aux_insert_cmap_feature} = $aux_insert_group; $self->{load_stuff}{sth}{next_id_cmap_feature} = $next_id_group; $self->{load_stuff}{sth}{insert_fdata} = $insert_data; $self->{load_stuff}{sth}{lookup_fattribute} = $lookup_attribute; $self->{load_stuff}{sth}{insert_fattribute} = $insert_attribute; $self->{load_stuff}{sth}{insert_fattribute_value} = $insert_attribute_value; $self->{load_stuff}{types} = {}; $self->{load_stuff}{groups} = {}; $self->{load_stuff}{counter} = 0; } =head2 load_gff_line Title : load_gff_line Usage : $db->load_gff_line($fields) Function: called to load one parsed line of GFF Returns : true if successfully inserted Args : hashref containing GFF fields Status : protected This method is called once per line of the GFF and passed a series of parsed data items that are stored into the hashref $fields. The keys are: ref reference sequence source annotation source method annotation method start annotation start stop annotation stop score annotation score (may be undef) strand annotation strand (may be undef) phase annotation phase (may be undef) group_class class of annotation's group (may be undef) group_name ID of annotation's group (may be undef) target_start start of target of a similarity hit target_stop stop of target of a similarity hit attributes array reference of attributes, each of which is a [tag=>value] array ref =cut sub load_gff_line { my $self = shift; my $gff = shift; my $s = $self->{load_stuff}; my $dbh = $self->features_db; local $dbh->{PrintError} = 0; defined(my $typeid = $self->get_table_id('ftype', $gff->{method} => $gff->{source})) or return; defined(my $groupid = $self->get_table_id('cmap_feature',$gff->{gname} => $gff->{gclass})) or return; if ($gff->{stop}-$gff->{start}+1 > $self->max_bin) { warn "$gff->{gclass}:$gff->{gname} is longer than ",$self->maxbin,".\n"; warn "Please set the maxbin value to a larger length than the largest feature you wish to store.\n"; warn "With the command-line tools you do with this with --maxfeature option.\n"; } my $bin = bin($gff->{start},$gff->{stop},$self->min_bin); my $result = $s->{sth}{insert_fdata}->execute($gff->{ref}, $gff->{start},$gff->{stop},$bin, $typeid, $gff->{score},$gff->{strand},$gff->{phase}, $groupid, $gff->{tstart},$gff->{tstop}); warn $dbh->errstr,"\n" && return unless $result; my $fid = $dbh->{mysql_insertid} || $self->get_feature_id($gff->{ref},$gff->{start},$gff->{stop},$typeid,$groupid); # insert attributes foreach (@{$gff->{attributes}}) { defined(my $attribute_id = $self->get_table_id('fattribute',$_->[0])) or return; $s->{sth}{insert_fattribute_value}->execute($fid,$attribute_id,$_->[1]); } if ( (++$s->{counter} % 1000) == 0) { print STDERR "$s->{counter} records loaded..."; print STDERR -t STDOUT && !$ENV{EMACS} ? "\r" : "\n"; } $fid; } =head2 get_feature_id Title : get_feature_id Usage : $integer = $db->get_feature_id($ref,$start,$stop,$typeid,$groupid) Function: get the ID of a feature Returns : an integer ID or undef Args : none Status : private This internal method is called by load_gff_line to look up the integer ID of an existing feature. It is ony needed when replacing a feature with new information. =cut # this method is called when needed to look up a feature's ID sub get_feature_id { my $self = shift; my ($ref,$start,$stop,$typeid,$groupid) = @_; my $s = $self->{load_stuff}; unless ($s->{get_feature_id}) { my $dbh = $self->features_db; $s->{get_feature_id} = $dbh->prepare_delayed('SELECT fid FROM fdata WHERE fref=? AND fstart=? AND fstop=? AND ftypeid=? AND feature_id=?'); } my $sth = $s->{get_feature_id} or return; $sth->execute($ref,$start,$stop,$typeid,$groupid) or return; my ($fid) = $sth->fetchrow_array; return $fid; } =head2 get_table_id Title : get_table_id Usage : $integer = $db->get_table_id($table,@ids) Function: get the ID of a group or type Returns : an integer ID or undef Args : none Status : private This internal method is called by load_gff_line to look up the integer ID of an existing feature type or group. The arguments are the name of the table, and two string identifiers. For feature types, the identifiers are the method and source. For groups, the identifiers are group name and class. This method requires that a statement handler named I, have been created previously by setup_load(). It is here to overcome deficiencies in mysql's INSERT syntax. =cut #' # get the object ID from a named table sub get_table_id { my $self = shift; my $table = shift; my @ids = @_; # irritating warning for null id my $id_key; { local $^W=0; $id_key = join ':',@ids; } my $s = $self->{load_stuff}; my $sth = $s->{sth}; my $dbh = $self->features_db; unless (defined($s->{$table}{$id_key})) { ######################################### # retrieval of the last inserted id is now located at the adaptor and not in caching_handle ####################################### if ( (my $result = $sth->{"lookup_$table"}->execute(@ids)) > 0) { $s->{$table}{$id_key} = ($sth->{"lookup_$table"}->fetchrow_array)[0]; } else { if (defined($sth->{"next_id_$table"})){ $sth->{"insert_$table"}->execute(3,'string1','string2'); # Can't use auto incrementing $sth->{"next_id_$table"}->execute(); $s->{$table}{$id_key} = ($sth->{"next_id_$table"}->fetchrow_array)[0]; if ($s->{$table}{$id_key}){ $sth->{"insert_$table"}->execute($s->{$table}{$id_key},@ids); $sth->{"aux_insert_$table"}->execute() if $sth->{"aux_insert_$table"}; } } else{ $sth->{"insert_$table"}->execute(@ids); $s->{$table}{$id_key} = $self->insertid($sth->{"insert_$table"}) unless $s->{$table}{$id_key}; $sth->{"aux_insert_$table"}->execute() if $sth->{"aux_insert_$table"}; } } } my $id = $s->{$table}{$id_key}; unless (defined $id) { warn "No $table id for $id_key ",$dbh->errstr," Record skipped.\n"; return; } $id; } #----------------------------------- =head2 make_features_by_name_where_part Title : make_features_by_name_where_part Usage : $db->make_features_by_name_where_part Function: create the SQL fragment needed to select a feature by its group name & class Returns : a SQL fragment and bind arguments Args : see below Status : Protected =cut sub make_features_by_name_where_part { my $self = shift; my ($class,$name) = @_; if ($name =~ /\*/) { $name =~ tr/*/%/; return ("cmap_feature.gclass=? AND cmap_feature.feature_name LIKE ?",$class,$name); } else { return ("cmap_feature.gclass=? AND cmap_feature.feature_name=?",$class,$name); } } =head2 make_features_join_part Title : make_features_join_part Usage : $string = $db->make_features_join_part() Function: make join part of the features query Returns : a string Args : none Status : protected This method creates the part of the features query that immediately follows the WHERE keyword. =cut sub make_features_join_part { my $self = shift; my $options = shift || {}; return !$options->{attributes} ? <search_notes("full text search string",$limit) Function: Search the notes for a text string, using mysql full-text search Returns : array of results Args : full text search string, and an optional row limit Status : public This is a mysql-specific method. Given a search string, it performs a full-text search of the notes table and returns an array of results. Each row of the returned array is a arrayref containing the following fields: column 1 A Bio::DB::GFF::Featname object, suitable for passing to segment() column 2 The text of the note column 3 A relevance score. =cut sub search_notes { my $self = shift; my ($search_string,$limit) = @_; $search_string =~ tr/*?//d; my @words = $search_string =~ /(\w+)/g; my $regex = join '|',@words; my @searches = map {"fattribute_value LIKE '%${_}%'"} @words; my $search = join(' OR ',@searches); my $query = <dbh->do_query($query); my @results; while (my ($class,$name,$note) = $sth->fetchrow_array) { next unless $class && $name; # sorry, ignore NULL objects my @matches = $note =~ /($regex)/g; my $relevance = 10*@matches; my $featname = Bio::DB::GFF::Featname->new($class=>$name); push @results,[$featname,$note,$relevance]; last if $limit && @results >= $limit; } @results; } # sub search_notes { # my $self = shift; # my ($search_string,$limit) = @_; # my $query = FULLTEXTSEARCH; # $query .= " limit $limit" if defined $limit; # my $sth = $self->dbh->do_query($query,$search_string,$search_string); # my @results; # while (my ($class,$name,$note,$relevance) = $sth->fetchrow_array) { # next unless $class && $name; # sorry, ignore NULL objects # $relevance = sprintf("%.2f",$relevance); # trim long floats # my $featname = Bio::DB::GFF::Featname->new($class=>$name); # push @results,[$featname,$note,$relevance]; # } # @results; # } =head2 make_features_order_by_part Title : make_features_order_by_part Usage : ($query,@args) = $db->make_features_order_by_part() Function: make the ORDER BY part of the features() query Returns : a SQL fragment and bind arguments, if any Args : none Status : protected This method creates the part of the features query that immediately follows the ORDER BY part of the query issued by features() and related methods. =cut sub make_features_order_by_part { my $self = shift; my $options = shift || {}; return "cmap_feature.feature_name"; } =head2 create_cmap_viewer_link Title : create_cmap_viewer_link Usage : $link_str = $db->create_cmap_viewer_link(data_source=>$ds,group_id=>$gid) Function: Returns : Args : Status : =cut sub create_cmap_viewer_link { my $self = shift; my %args = @_; my $data_source = $args{'data_source'}; my $gid = $args{'group_id'}; my $link_str = undef; my $db = $self->features_db; my $sql_str = qq[ select f.feature_name, f.feature_type_accession feature_type_aid, m.accession_id as map_aid, ms.accession_id as map_set_aid from cmap_feature f, cmap_map m, cmap_map_set ms where f.map_id=m.map_id and ms.map_set_id=m.map_set_id and f.feature_id=$gid ]; my $result_ref = $db->selectrow_hashref($sql_str,{ Columns => {} }); if ( $result_ref ) { $link_str='/cgi-bin/cmap/viewer?ref_map_set_aid=' . $result_ref->{'map_set_aid'} . '&ref_map_aids=' . $result_ref->{'map_aid'} . '&data_source=' . $data_source . '&highlight=' .$result_ref->{'feature_name'} . '&feature_type_' .$result_ref->{'feature_type_aid'} . '=2'; } return $link_str; } 1; __END__ =head1 BUGS none ;-) =head1 SEE ALSO L, L =head1 AUTHOR Ben Faga Efaga@cshl.orgE. Modified from mysql.pm by: Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2002 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm000444000766000024 114613155576320 21473 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::dbi::mysqlopt; =head1 NAME Bio::DB::GFF::Adaptor::dbi::mysqlopt -- Deprecated database adaptor =head1 SYNOPSIS This adaptor has been superseded by Bio::DB::GFF::Adaptor::dbi::mysql. See L and L =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2002 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use strict; use base qw(Bio::DB::GFF::Adaptor::dbi::mysql); 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor/dbi/oracle.pm000444000766000024 6773413155576320 21107 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::dbi::oracle; =head1 NAME Bio::DB::GFF::Adaptor::dbi::oracle -- Database adaptor for a specific oracle schema =head1 SYNOPSIS See L =cut # a simple oracle adaptor use strict; #use Bio::DB::GFF::Adaptor::dbi::mysql; #use Bio::DB::GFF::Adaptor::dbi::mysqlopt; use Bio::DB::GFF::Util::Binning; use Bio::DB::GFF::Util::Rearrange; # for rearrange() use base qw(Bio::DB::GFF::Adaptor::dbi); use constant MAX_SEGMENT => 100_000_000; # the largest a segment can get use constant DEFAULT_CHUNK => 2000; use constant GETSEQCOORDS =><<<< 100_000_000; # this is the smallest bin (1 K) use constant MIN_BIN => 1000; # size of range over which it is faster to force mysql to use the range for indexing use constant STRAIGHT_JOIN_LIMIT => 200_000; ############################################################################## =head1 DESCRIPTION This adaptor implements a specific oracle database schema that is compatible with Bio::DB::GFF. It inherits from Bio::DB::GFF::Adaptor::dbi, which itself inherits from Bio::DB::GFF. The schema uses several tables: =over 4 =item fdata This is the feature data table. Its columns are: fid feature ID (integer) fref reference sequence name (string) fstart start position relative to reference (integer) fstop stop position relative to reference (integer) ftypeid feature type ID (integer) fscore feature score (float); may be null fstrand strand; one of "+" or "-"; may be null fphase phase; one of 0, 1 or 2; may be null gid group ID (integer) ftarget_start for similarity features, the target start position (integer) ftarget_stop for similarity features, the target stop position (integer) Note that it would be desirable to normalize the reference sequence name, since there are usually many features that share the same reference feature. However, in the current schema, query performance suffers dramatically when this additional join is added. =item fgroup This is the group table. There is one row for each group. Columns: gid the group ID (integer) gclass the class of the group (string) gname the name of the group (string) The group table serves multiple purposes. As you might expect, it is used to cluster features that logically belong together, such as the multiple exons of the same transcript. It is also used to assign a name and class to a singleton feature. Finally, the group table is used to identify the target of a similarity hit. This is consistent with the way in which the group field is used in the GFF version 2 format. The fgroup.gid field joins with the fdata.gid field. Examples: sql> select * from fgroup where gname='sjj_2L52.1'; +-------+-------------+------------+ | gid | gclass | gname | +-------+-------------+------------+ | 69736 | PCR_product | sjj_2L52.1 | +-------+-------------+------------+ 1 row in set (0.70 sec) sql> select fref,fstart,fstop from fdata,fgroup where gclass='PCR_product' and gname = 'sjj_2L52.1' and fdata.gid=fgroup.gid; +---------------+--------+-------+ | fref | fstart | fstop | +---------------+--------+-------+ | CHROMOSOME_II | 1586 | 2355 | +---------------+--------+-------+ 1 row in set (0.03 sec) =item ftype This table contains the feature types, one per row. Columns are: ftypeid the feature type ID (integer) fmethod the feature type method name (string) fsource the feature type source name (string) The ftype.ftypeid field joins with the fdata.ftypeid field. Example: sql> select fref,fstart,fstop,fmethod,fsource from fdata,fgroup,ftype where gclass='PCR_product' and gname = 'sjj_2L52.1' and fdata.gid=fgroup.gid and fdata.ftypeid=ftype.ftypeid; +---------------+--------+-------+-------------+-----------+ | fref | fstart | fstop | fmethod | fsource | +---------------+--------+-------+-------------+-----------+ | CHROMOSOME_II | 1586 | 2355 | PCR_product | GenePairs | +---------------+--------+-------+-------------+-----------+ 1 row in set (0.08 sec) =item fdna This table holds the raw DNA of the reference sequences. It has three columns: fref reference sequence name (string) foffset offset of this sequence fdna the DNA sequence (longblob) To overcome problems loading large blobs, DNA is automatically fragmented into multiple segments when loading, and the position of each segment is stored in foffset. The fragment size is controlled by the -clump_size argument during initialization. =item fattribute_to_feature This table holds "attributes", which are tag/value pairs stuffed into the GFF line. The first tag/value pair is treated as the group, and anything else is treated as an attribute (weird, huh?). CHR_I assembly_tag Finished 2032 2036 . + . Note "Right: cTel33B" CHR_I assembly_tag Polymorphism 668 668 . + . Note "A->C in cTel33B" The columns of this table are: fid feature ID (integer) fattribute_id ID of the attribute (integer) fattribute_value text of the attribute (text) The fdata.fid column joins with fattribute_to_feature.fid. =item fattribute This table holds the normalized names of the attributes. Fields are: fattribute_id ID of the attribute (integer) fattribute_name Name of the attribute (varchar) =back =head2 Data Loading Methods In addition to implementing the abstract SQL-generating methods of Bio::DB::GFF::Adaptor::dbi, this module also implements the data loading functionality of Bio::DB::GFF. =cut =head2 new Title : new Usage : $db = Bio::DB::GFF->new(@args) Function: create a new adaptor Returns : a Bio::DB::GFF object Args : see below Status : Public The new constructor is identical to the "dbi" adaptor's new() method, except that the prefix "dbi:oracle" is added to the database DSN identifier automatically if it is not there already. Argument Description -------- ----------- -dsn the DBI data source, e.g. 'dbi:mysql:ens0040' or "ens0040" -user username for authentication -pass the password for authentication =cut #' sub new { my $class = shift; my ($dsn,$other) = rearrange([ [qw(FEATUREDB DB DSN)], ],@_); $dsn = "dbi:Oracle:$dsn" if !ref($dsn) && $dsn !~ /^(dbi|DBI):/; my $self = $class->SUPER::new(-dsn=>$dsn,%$other); $self; } =head2 schema Title : schema Usage : $schema = $db->schema Function: return the CREATE script for the schema Returns : a list of CREATE statemetns Args : none Status : protected This method returns a list containing the various CREATE statements needed to initialize the database tables. =cut sub schema { my %schema = ( fdata =>{ table=> q{ create table fdata ( fid INTEGER NOT NULL, fref VARCHAR(100) DEFAULT '' NOT NULL, fstart INTEGER DEFAULT '0' NOT NULL, fstop INTEGER DEFAULT '0' NOT NULL, fbin NUMBER DEFAULT '0.000000' NOT NULL, ftypeid INTEGER DEFAULT '0' NOT NULL, fscore NUMBER , fstrand VARCHAR2(3) CHECK (fstrand IN ('+','-')), fphase VARCHAR2(3) CHECK (fphase IN ('0','1','2')), gid INTEGER DEFAULT '0' NOT NULL, ftarget_start INTEGER , ftarget_stop INTEGER , CONSTRAINT fdata_pk PRIMARY KEY (fid) ) }, # fdata table index=>{ fdata_fref_idx => q{ CREATE UNIQUE INDEX fdata_fref_idx ON fdata (fref,fbin,fstart,fstop,ftypeid,gid) }, fdata_ftypeid_idx => q{ CREATE INDEX fdata_ftypeid_idx ON fdata (ftypeid) }, fdata_gid_idx => q{ CREATE INDEX fdata_gid_idx ON fdata (gid) } }, # fdata indexes sequence=> { fdata_fid_sq => q{ CREATE SEQUENCE fdata_fid_sq START WITH 1 } }, # fdata sequences trigger=> { fdata_fid_ai => q{ CREATE OR REPLACE TRIGGER fdata_fid_ai BEFORE INSERT ON fdata FOR EACH ROW WHEN (new.fid IS NULL OR new.fid = 0) BEGIN SELECT fdata_fid_sq.nextval INTO :new.fid FROM dual; END; } }# fdata triggers }, # fdata fgroup => { table => q{ CREATE TABLE fgroup ( gid INTEGER NOT NULL, gclass VARCHAR(100) , gname VARCHAR(100) , CONSTRAINT fgroup_pk PRIMARY KEY (gid) ) }, # fgroup table index => { fgroup_gclass_idx => q{ CREATE UNIQUE INDEX fgroup_gclass_idx ON fgroup (gclass,gname) } }, # fgroup indexes sequence => { fgroup_gid_sq => q{ CREATE SEQUENCE fgroup_gid_sq START WITH 1 } }, # fgroup sequences trigger => { fgroup_gid_ai => q{ CREATE OR REPLACE TRIGGER fgroup_gid_ai BEFORE INSERT ON fgroup FOR EACH ROW WHEN (new.gid IS NULL OR new.gid = 0) BEGIN SELECT fgroup_gid_sq.nextval INTO :new.gid FROM dual; END; } } # fgroup triggers }, # fgroup ftype => { table => q{ CREATE TABLE ftype ( ftypeid INTEGER NOT NULL, fmethod VARCHAR(100) DEFAULT '' NOT NULL, fsource VARCHAR(100), CONSTRAINT ftype_pk PRIMARY KEY (ftypeid) ) }, # ftype table index => { ftype_fmethod_idx => q{ CREATE INDEX ftype_fmethod_idx ON ftype (fmethod) }, ftype_fsource_idx => q{ CREATE INDEX ftype_fsource_idx ON ftype (fsource) }, ftype_ftype_idx => q{ CREATE UNIQUE INDEX ftype_ftype_idx ON ftype (fmethod,fsource) } }, # ftype indexes sequence => { ftype_ftypeid_sq => q{ CREATE SEQUENCE ftype_ftypeid_sq START WITH 1 } }, #ftype sequences trigger => { ftype_ftypeid_ai => q{ CREATE OR REPLACE TRIGGER ftype_ftypeid_ai BEFORE INSERT ON ftype FOR EACH ROW WHEN (new.ftypeid IS NULL OR new.ftypeid = 0) BEGIN SELECT ftype_ftypeid_sq.nextval INTO :new.ftypeid FROM dual; END; } } #ftype triggers }, # ftype fdna => { table => q{ CREATE TABLE fdna ( fref VARCHAR(100) DEFAULT '' NOT NULL, foffset INTEGER DEFAULT '0' NOT NULL, fdna LONG /* LONGBLOB */ , CONSTRAINT fdna_pk PRIMARY KEY (fref,foffset) ) } #fdna table }, #fdna fmeta => { table => q{ CREATE TABLE fmeta ( fname VARCHAR(255) DEFAULT '' NOT NULL, fvalue VARCHAR(255) DEFAULT '' NOT NULL, CONSTRAINT fmeta_pk PRIMARY KEY (fname) ) } # fmeta table }, # fmeta fattribute => { table => q{ CREATE TABLE fattribute ( fattribute_id INTEGER NOT NULL, fattribute_name VARCHAR(255) DEFAULT '' NOT NULL, CONSTRAINT fattribute_pk PRIMARY KEY (fattribute_id) ) }, # fattribute table sequence=> { fattribute_fattribute_id_sq => q{ CREATE SEQUENCE fattribute_fattribute_id_sq START WITH 1 } }, # fattribute sequences trigger => { fattribute_fattribute_id_ai => q{ CREATE OR REPLACE TRIGGER fattribute_fattribute_id_ai BEFORE INSERT ON fattribute FOR EACH ROW WHEN (new.fattribute_id IS NULL OR new.fattribute_id = 0) BEGIN SELECT fattribute_fattribute_id_sq.nextval INTO :new.fattribute_id FROM dual; END; } } # fattribute triggers }, # fattribute fattribute_to_feature => { table => q{ CREATE TABLE fattribute_to_feature ( fid INTEGER DEFAULT '0' NOT NULL, fattribute_id INTEGER DEFAULT '0' NOT NULL, fattribute_value VARCHAR2(255) /* TEXT */ ) }, # fattribute_to_feature table index => { fattribute_to_feature_fid => q{ CREATE INDEX fattribute_to_feature_fid ON fattribute_to_feature (fid,fattribute_id) } } # fattribute_to_feature indexes }, # fattribute_to_feature finterval_stats => { table=> q{ CREATE TABLE "finterval_stats" ( "ftypeid" integer DEFAULT '0' NOT NULL, "fref" VARCHAR(100) DEFAULT '' NOT NULL, "fbin" integer DEFAULT '0' NOT NULL, "fcum_count" integer DEFAULT '0' NOT NULL, CONSTRAINT finterval_stats_pk PRIMARY KEY (ftypeid,fref,fbin) ) } # finterval_stats table },# finterval_stats ); return \%schema; } =head2 do_initialize Title : do_initialize Usage : $success = $db->do_initialize($drop_all) Function: initialize the database Returns : a boolean indicating the success of the operation Args : a boolean indicating whether to delete existing data Status : protected This method will load the schema into the database. If $drop_all is true, then any existing data in the tables known to the schema will be deleted. Internally, this method calls schema() to get the schema data. =cut # Create the schema from scratch. # You will need create privileges for this. #sub do_initialize { # my $self = shift; # my $erase = shift; # $self->drop_all if $erase; # my $dbh = $self->features_db; # my $schema = $self->schema; # foreach my $table_name(keys %$schema) { # my $create_table_stmt = $$schema{$table_name}{table} ; # $dbh->do($create_table_stmt) || warn $dbh->errstr; # } # 1; #} =head2 drop_all Title : drop_all Usage : $db->drop_all Function: empty the database Returns : void Args : none Status : protected This method drops the tables known to this module. Internally it calls the abstract tables() method. =cut # Drop all the GFF tables -- dangerous! #sub drop_all { # my $self = shift; # my $dbh = $self->features_db; # local $dbh->{PrintError} = 0; # foreach ($self->tables) { # $dbh->do("drop table $_"); # } #} =head2 setup_load Title : setup_load Usage : $db->setup_load Function: called before load_gff_line() Returns : void Args : none Status : protected This method performs schema-specific initialization prior to loading a set of GFF records. It prepares a set of DBI statement handlers to be used in loading the data. =cut sub setup_load { my $self = shift; my $schema = $self->schema; my $dbh = $self->features_db; if ($self->lock_on_load) { my @tables = map { "$_ WRITE"} $self->tables; my $tables = join ', ',@tables; $dbh->do("LOCK TABLES $tables"); } my $lookup_type = $dbh->prepare_delayed('SELECT ftypeid FROM ftype WHERE fmethod=? AND fsource=?'); my $insert_type = $dbh->prepare_delayed('INSERT INTO ftype (fmethod,fsource) VALUES (?,?)'); my $sequence_type = (keys %{$schema->{ftype}{sequence}})[0]; my $insertid_type = $dbh->prepare_delayed("SELECT $sequence_type.CURRVAL FROM dual"); my $lookup_group = $dbh->prepare_delayed('SELECT gid FROM fgroup WHERE gname=? AND gclass=?'); my $insert_group = $dbh->prepare_delayed('INSERT INTO fgroup (gname,gclass) VALUES (?,?)'); my $sequence_group = (keys %{$schema->{fgroup}{sequence}})[0]; my $insertid_group = $dbh->prepare_delayed("SELECT $sequence_group.CURRVAL FROM dual"); my $lookup_attribute = $dbh->prepare_delayed('SELECT fattribute_id FROM fattribute WHERE fattribute_name=?'); my $insert_attribute = $dbh->prepare_delayed('INSERT INTO fattribute (fattribute_name) VALUES (?)'); my $sequence_attribute = (keys %{$schema->{fattribute}{sequence}})[0]; my $insertid_attribute = $dbh->prepare_delayed("SELECT $sequence_attribute.CURRVAL FROM dual"); my $insert_attribute_value = $dbh->prepare_delayed('INSERT INTO fattribute_to_feature (fid,fattribute_id,fattribute_value) VALUES (?,?,?)'); my $insert_data = $dbh->prepare_delayed(<prepare_delayed('DELETE FROM fdata WHERE fref=? AND fstart=? AND fstop=? AND fbin=? AND ftypeid=? AND GID=?'); my $sequence_data = (keys %{$schema->{fdata}{sequence}})[0]; my $insertid_data = $dbh->prepare_delayed("SELECT $sequence_data.CURRVAL FROM dual"); $self->{load_stuff}{sth}{lookup_ftype} = $lookup_type; $self->{load_stuff}{sth}{insert_ftype} = $insert_type; $self->{load_stuff}{sth}{insertid_ftype} = $insertid_type; $self->{load_stuff}{sth}{lookup_fgroup} = $lookup_group; $self->{load_stuff}{sth}{insert_fgroup} = $insert_group; $self->{load_stuff}{sth}{insertid_fgroup} = $insertid_group; $self->{load_stuff}{sth}{insert_fdata} = $insert_data; $self->{load_stuff}{sth}{insertid_fdata} = $insertid_data; $self->{load_stuff}{sth}{delete_existing_fdata} = $delete_existing_data; $self->{load_stuff}{sth}{lookup_fattribute} = $lookup_attribute; $self->{load_stuff}{sth}{insert_fattribute} = $insert_attribute; $self->{load_stuff}{sth}{insertid_fattribute} = $insertid_attribute; $self->{load_stuff}{sth}{insert_fattribute_value} = $insert_attribute_value; $self->{load_stuff}{types} = {}; $self->{load_stuff}{groups} = {}; $self->{load_stuff}{counter} = 0; } =head2 load_gff_line Title : load_gff_line Usage : $db->load_gff_line($fields) Function: called to load one parsed line of GFF Returns : true if successfully inserted Args : hashref containing GFF fields Status : protected This method is called once per line of the GFF and passed a series of parsed data items that are stored into the hashref $fields. The keys are: ref reference sequence source annotation source method annotation method start annotation start stop annotation stop score annotation score (may be undef) strand annotation strand (may be undef) phase annotation phase (may be undef) group_class class of annotation's group (may be undef) group_name ID of annotation's group (may be undef) target_start start of target of a similarity hit target_stop stop of target of a similarity hit attributes array reference of attributes, each of which is a [tag=>value] array ref =cut sub load_gff_line { my $self = shift; my $gff = shift; if (defined $gff->{phase}){ chomp($gff->{phase}); undef($gff->{phase}) if $gff->{phase} eq '.'; } if (defined $gff->{strand} && $gff->{strand} eq '.'){undef($gff->{strand})}; if (defined $gff->{score} && $gff->{score} eq '.'){undef($gff->{score})}; my $s = $self->{load_stuff}; my $dbh = $self->features_db; local $dbh->{PrintError} = 0; defined(my $typeid = $self->get_table_id('ftype', $gff->{method} => $gff->{source})) or return; defined(my $groupid = $self->get_table_id('fgroup',$gff->{gname} => $gff->{gclass})) or return; my $bin = bin($gff->{start},$gff->{stop},$self->min_bin); my $result = $s->{sth}{insert_fdata}->execute($gff->{ref}, $gff->{start},$gff->{stop},$bin, $typeid, $gff->{score},$gff->{strand},$gff->{phase}, $groupid, $gff->{tstart},$gff->{tstop}); if (defined ($dbh->errstr)){ print $dbh->errstr,"\n" ,%$gff,"\n"; if ($dbh->errstr =~ /ORA-02290: check constraint/){ print "PHASE=$gff->{phase}"."===","\n"; } if ($dbh->errstr =~ /ORA-00001: unique constraint/){ $result = $s->{sth}{delete_existing_fdata}->execute($gff->{ref}, $gff->{start},$gff->{stop},$bin, $typeid, $groupid); print "delete row result=$result\n"; $result = $s->{sth}{insert_fdata}->execute($gff->{ref}, $gff->{start},$gff->{stop},$bin, $typeid, $gff->{score},$gff->{strand},$gff->{phase}, $groupid, $gff->{tstart},$gff->{tstop}); print "insert row result=$result\n"; } } warn $dbh->errstr,"\n" and print "ref=",$gff->{ref}," start=",$gff->{start}," stop=",$gff->{stop}," bin=",$bin," typeid=",$typeid," groupid=",$groupid,"\n" and return unless $result; my $fid = $self->insertid($s->{sth},'fdata') || $self->get_feature_id($gff->{ref},$gff->{start},$gff->{stop},$typeid,$groupid); # insert attributes # print STDERR map {"$fid attribute:". $_->[0]."=".$_->[1]."\n"} @{$gff->{attributes}}; foreach (@{$gff->{attributes}}) { defined(my $attribute_id = $self->get_table_id('fattribute',$_->[0])) or return; $s->{sth}{insert_fattribute_value}->execute($fid,$attribute_id,$_->[1]); } if ( (++$s->{counter} % 1000) == 0) { print STDERR "$s->{counter} records loaded..."; print STDERR -t STDOUT && !$ENV{EMACS} ? "\r" : "\n"; } $fid; } =head2 get_table_id Title : get_table_id Usage : $integer = $db->get_table_id($table,@ids) Function: get the ID of a group or type Returns : an integer ID or undef Args : none Status : private This internal method is called by load_gff_line to look up the integer ID of an existing feature type or group. The arguments are the name of the table, and two string identifiers. For feature types, the identifiers are the method and source. For groups, the identifiers are group name and class. This method requires that a statement handler named I, have been created previously by setup_load(). It is here to overcome deficiencies in mysql's INSERT syntax. =cut #' # get the object ID from a named table sub get_table_id { my $self = shift; my $table = shift; my @ids = @_; # irritating warning for null id my $id_key; { local $^W=0; $id_key = join ':',@ids; } my $s = $self->{load_stuff}; my $sth = $s->{sth}; my $dbh = $self->features_db; unless (defined($s->{$table}{$id_key})) { $sth->{"lookup_$table"}->execute(@ids); my @result = $sth->{"lookup_$table"}->fetchrow_array; if (@result > 0) { $s->{$table}{$id_key} = $result[0]; } else { $sth->{"insert_$table"}->execute(@ids) && ($s->{$table}{$id_key} = $self->insertid($sth,$table)); #&& ($s->{$table}{$id_key} = $self->insertid($sth->{"insertid_$table"})); #&& ($s->{$table}{$id_key} = $sth->{"insert_$table"}->insertid); } } my $id = $s->{$table}{$id_key}; unless (defined $id) { warn "No $table id for $id_key ",$dbh->errstr," Record skipped.\n"; return; } $id; } sub insertid { my $self = shift; my $sth = shift ; my $table = shift; my $insert_id; if ($sth->{"insertid_$table"}->execute()){ $insert_id = ($sth->{"insertid_$table"}->fetchrow_array)[0]; } else{ warn "No CURRVAL for SEQUENCE of table $table ",$sth->errstr,"\n"; return; } return $insert_id; } #sub insertid { # my $self = shift; # my $insertid_sth = shift ; # my $insert_id; # if ($insertid_sth->execute){ # $insert_id = ($insertid_sth->fetchrow_array)[0]; # } # else{ # warn "No CURRVAL for SEQUENCE ",$insertid_sth->errstr,"\n"; # return; # } # return $insert_id; #} sub insert_sequence { my $self = shift; my($id,$offset,$seq) = @_; my $sth = $self->{_insert_sequence} ||= $self->dbh->prepare_delayed('insert into fdna values (?,?,?)'); $sth->execute($id,$offset,$seq) or $self->throw($sth->errstr); } =head2 search_notes Title : search_notes Usage : @search_results = $db->search_notes("full text search string",$limit) Function: Search the notes for a text string, using mysql full-text search Returns : array of results Args : full text search string, and an optional row limit Status : public This is a mysql-specific method. Given a search string, it performs a full-text search of the notes table and returns an array of results. Each row of the returned array is a arrayref containing the following fields: column 1 A Bio::DB::GFF::Featname object, suitable for passing to segment() column 2 The text of the note column 3 A relevance score. column 4 A Bio::DB::GFF::Typename object =cut sub search_notes { my $self = shift; my ($search_string,$limit) = @_; $search_string =~ tr/*?//d; my @words = $search_string =~ /(\w+)/g; my $regex = join '|',@words; my @searches = map {"fattribute_value LIKE '%${_}%'"} @words; my $search = join(' OR ',@searches); my $query = <dbh->do_query($query); my @results; while (my ($class,$name,$note,$method,$source) = $sth->fetchrow_array) { next unless $class && $name; # sorry, ignore NULL objects my @matches = $note =~ /($regex)/g; my $relevance = 10*@matches; my $featname = Bio::DB::GFF::Featname->new($class=>$name); my $type = Bio::DB::GFF::Typename->new($method,$source); push @results,[$featname,$note,$relevance,$type]; last if $limit && @results >= $limit; } @results; } =head2 make_meta_set_query Title : make_meta_set_query Usage : $sql = $db->make_meta_set_query Function: return SQL fragment for setting a meta parameter Returns : SQL fragment Args : none Status : public By default this does nothing; meta parameters are not stored or retrieved. =cut sub make_meta_set_query { return 'INSERT INTO fmeta VALUES (?,?)'; } sub make_classes_query { my $self = shift; return 'SELECT DISTINCT gclass FROM fgroup WHERE NOT gclass IS NULL'; } sub chunk_size { my $self = shift; $self->meta('chunk_size') || DEFAULT_CHUNK; } sub getseqcoords_query { my $self = shift; return GETSEQCOORDS ; } sub getaliascoords_query{ my $self = shift; return GETALIASCOORDS ; } sub getforcedseqcoords_query{ my $self = shift; return GETFORCEDSEQCOORDS ; } sub getaliaslike_query{ my $self = shift; return GETALIASLIKE ; } sub make_features_select_part { my $self = shift; my $options = shift || {}; my $s; if (my $b = $options->{bin_width}) { $s = <{attributes} && keys %{$options->{attributes}}>1; $s; } sub make_features_from_part_bkup { my $self = shift; my $sparse = shift; my $options = shift || {}; #my $index = $sparse ? ' USE INDEX(ftypeid)': ''; my $index = ''; return $options->{attributes} ? "fdata${index},ftype,fgroup,fattribute,fattribute_to_feature\n" : "fdata${index},ftype,fgroup\n"; } #################################### # moved from mysqlopt.pm ################################### # meta values sub default_meta_values { my $self = shift; my @values = $self->SUPER::default_meta_values; return ( @values, max_bin => MAX_BIN, min_bin => MIN_BIN, straight_join_limit => STRAIGHT_JOIN_LIMIT, ); } sub min_bin { my $self = shift; return $self->meta('min_bin') || MIN_BIN; } sub max_bin { my $self = shift; return $self->meta('max_bin') || MAX_BIN; } sub straight_join_limit { my $self = shift; return $self->meta('straight_join_limit') || STRAIGHT_JOIN_LIMIT; } 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor/dbi/oracleace.pm000444000766000024 542013155576320 21520 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::dbi::oracleace; =head1 NAME Bio::DB::GFF::Adaptor::dbi::oracleace -- Unholy union between oracle GFF database and acedb database =head1 SYNOPSIS Pending See L and L =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2002 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use strict; use Bio::DB::GFF::Util::Rearrange; # for rearrange() use base qw(Bio::DB::GFF::Adaptor::ace Bio::DB::GFF::Adaptor::dbi::oracle); # Create a new Bio::DB::GFF::Adaptor::dbi object sub new { my $class = shift; my $self = $class->SUPER::new(@_); my ($dna_db,$acedb) = rearrange([[qw(DNADB DNA FASTA FASTA_DIR)],'ACEDB'],@_); if ($dna_db) { if (!ref($dna_db)) { require Bio::DB::Fasta; my $fasta_dir = $dna_db; $dna_db = Bio::DB::Fasta->new($fasta_dir); $dna_db or $class->throw("new(): Failed to create new Bio::DB::Fasta from files in $fasta_dir"); } else { $dna_db->isa('Bio::DB::Fasta') or $class->throw("new(): $dna_db is not a Bio::DB::Fasta object"); } $self->dna_db($dna_db); } if ($acedb) { $acedb->isa('Ace') or $class->throw("$acedb is not an acedb accessor object"); $self->acedb($acedb); } $self; } sub make_object { my $self = shift; my ($class,$name,$start,$stop) = @_; if (my $db = $self->acedb) { # for Notes we just return a text, no database associated return $class->new(Text=>$name) if $class eq 'Note'; # for homols, we create the indicated Protein or Sequence object # then generate a bogus Homology object (for future compatability??) if ($start ne '') { require Ace::Sequence::Homol; return Ace::Sequence::Homol->new_homol($class,$name,$db,$start,$stop); } # General case: my $obj = $db->class->new($class=>$name,$self->acedb); return $obj if defined $obj; # Last resort, return a Text return $class->new(Text=>$name); } return $self->SUPER::make_object($class,$name,$start,$stop); } sub get_dna { my $self = shift; my ($ref,$start,$stop,$class) = @_; my $dna_db = $self->dna_db or return $self->SUPER::get_dna(@_); return $dna_db->seq($ref,$start,$stop,$class); } =head2 freshen_ace Title : freshen Usage : $flag = Bio::DB::GFF->freshen_ace; Function: Refresh internal acedb handle Returns : flag if correctly freshened Args : none Status : Public ACeDB has an annoying way of timing out, leaving dangling database handles. This method will invoke the ACeDB reopen() method, which causes dangling handles to be refreshed. It has no effect if you are not using ACeDB to create ACeDB objects. =cut 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor/dbi/pg.pm000444000766000024 12264313155576320 20257 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::dbi::pg; =head1 NAME Bio::DB::GFF::Adaptor::dbi::pg -- Database adaptor for a specific postgres schema =head1 NOTES SQL commands that need to be executed before this adaptor will work: CREATE DATABASE ; Also, select permission needs to be granted for each table in the database to the owner of the httpd process (usually 'nobody', but for some RedHat systems it is 'apache') if this adaptor is to be used with the Generic Genome Browser (gbrowse): CREATE USER nobody; GRANT SELECT ON TABLE fmeta TO nobody; GRANT SELECT ON TABLE fgroup TO nobody; GRANT SELECT ON TABLE fdata TO nobody; GRANT SELECT ON TABLE fattribute_to_feature TO nobody; GRANT SELECT ON TABLE fdna TO nobody; GRANT SELECT ON TABLE fattribute TO nobody; GRANT SELECT ON TABLE ftype TO nobody; =head2 Optimizing the database PostgreSQL generally requires some tuning before you get very good performance for large databases. For general information on tuning a PostgreSQL server, see http://www.varlena.com/GeneralBits/Tidbits/perf.html Of particular importance is executing VACUUM FULL ANALYZE whenever you change the database. Additionally, for a GFF database, there are a few items you can tune. For each automatic class in your GBrowse conf file, there will be one or two searches done when searching for a feature. If there are lots of features, these search can take several seconds. To speed these searches, do two things: =over =item 1 Set 'enable_seqscan = false' in your postgresql.conf file (and restart your server). =item 2 Create 'partial' indexes for each automatic class, doing this for the example class 'Allele': CREATE INDEX partial_allele_gclass ON fgroup (lower('gname')) WHERE gclass='Allele'; And be sure to run VACUUM FULL ANALYZE after creating the indexes. =back =cut # a simple postgres adaptor use strict; use Bio::DB::GFF::Util::Binning; use Bio::DB::GFF::Util::Rearrange; # for rearrange() use base qw(Bio::DB::GFF::Adaptor::dbi); use constant MAX_SEGMENT => 100_000_000; # the largest a segment can get use constant DEFAULT_CHUNK => 2000; use constant GETSEQCOORDS =><<<< < 100_000_000; # this is the smallest bin (1 K) use constant MIN_BIN => 1000; # size of range over which it is faster to force mysql to use the range for indexing use constant STRAIGHT_JOIN_LIMIT => 200_000; ############################################################################## =head1 DESCRIPTION This adaptor implements a specific postgres database schema that is compatible with Bio::DB::GFF. It inherits from Bio::DB::GFF::Adaptor::dbi, which itself inherits from Bio::DB::GFF. The schema uses several tables: =over 4 =item fdata This is the feature data table. Its columns are: fid feature ID (integer) fref reference sequence name (string) fstart start position relative to reference (integer) fstop stop position relative to reference (integer) ftypeid feature type ID (integer) fscore feature score (float); may be null fstrand strand; one of "+" or "-"; may be null fphase phase; one of 0, 1 or 2; may be null gid group ID (integer) ftarget_start for similarity features, the target start position (integer) ftarget_stop for similarity features, the target stop position (integer) Note that it would be desirable to normalize the reference sequence name, since there are usually many features that share the same reference feature. However, in the current schema, query performance suffers dramatically when this additional join is added. =item fgroup This is the group table. There is one row for each group. Columns: gid the group ID (integer) gclass the class of the group (string) gname the name of the group (string) The group table serves multiple purposes. As you might expect, it is used to cluster features that logically belong together, such as the multiple exons of the same transcript. It is also used to assign a name and class to a singleton feature. Finally, the group table is used to identify the target of a similarity hit. This is consistent with the way in which the group field is used in the GFF version 2 format. The fgroup.gid field joins with the fdata.gid field. Examples: sql> select * from fgroup where gname='sjj_2L52.1'; +-------+-------------+------------+ | gid | gclass | gname | +-------+-------------+------------+ | 69736 | PCR_product | sjj_2L52.1 | +-------+-------------+------------+ 1 row in set (0.70 sec) sql> select fref,fstart,fstop from fdata,fgroup where gclass='PCR_product' and gname = 'sjj_2L52.1' and fdata.gid=fgroup.gid; +---------------+--------+-------+ | fref | fstart | fstop | +---------------+--------+-------+ | CHROMOSOME_II | 1586 | 2355 | +---------------+--------+-------+ 1 row in set (0.03 sec) =item ftype This table contains the feature types, one per row. Columns are: ftypeid the feature type ID (integer) fmethod the feature type method name (string) fsource the feature type source name (string) The ftype.ftypeid field joins with the fdata.ftypeid field. Example: sql> select fref,fstart,fstop,fmethod,fsource from fdata,fgroup,ftype where gclass='PCR_product' and gname = 'sjj_2L52.1' and fdata.gid=fgroup.gid and fdata.ftypeid=ftype.ftypeid; +---------------+--------+-------+-------------+-----------+ | fref | fstart | fstop | fmethod | fsource | +---------------+--------+-------+-------------+-----------+ | CHROMOSOME_II | 1586 | 2355 | PCR_product | GenePairs | +---------------+--------+-------+-------------+-----------+ 1 row in set (0.08 sec) =item fdna This table holds the raw DNA of the reference sequences. It has three columns: fref reference sequence name (string) foffset offset of this sequence fdna the DNA sequence (longblob) To overcome problems loading large blobs, DNA is automatically fragmented into multiple segments when loading, and the position of each segment is stored in foffset. The fragment size is controlled by the -clump_size argument during initialization. =item fattribute_to_feature This table holds "attributes", which are tag/value pairs stuffed into the GFF line. The first tag/value pair is treated as the group, and anything else is treated as an attribute (weird, huh?). CHR_I assembly_tag Finished 2032 2036 . + . Note "Right: cTel33B" CHR_I assembly_tag Polymorphism 668 668 . + . Note "A->C in cTel33B" The columns of this table are: fid feature ID (integer) fattribute_id ID of the attribute (integer) fattribute_value text of the attribute (text) The fdata.fid column joins with fattribute_to_feature.fid. =item fattribute This table holds the normalized names of the attributes. Fields are: fattribute_id ID of the attribute (integer) fattribute_name Name of the attribute (varchar) =back =head2 Data Loading Methods In addition to implementing the abstract SQL-generating methods of Bio::DB::GFF::Adaptor::dbi, this module also implements the data loading functionality of Bio::DB::GFF. =cut =head2 new Title : new Usage : $db = Bio::DB::GFF->new(@args) Function: create a new adaptor Returns : a Bio::DB::GFF object Args : see below Status : Public The new constructor is identical to the "dbi" adaptor's new() method, except that the prefix "dbi:pg" is added to the database DSN identifier automatically if it is not there already. Argument Description -------- ----------- -dsn the DBI data source, e.g. 'dbi:Pg:dbname=:ens0040' or "ens0040" -user username for authentication -pass the password for authentication =cut #' sub new { my $class = shift; my ($dsn,$other) = rearrange([ [qw(FEATUREDB DB DSN)], ],@_); $dsn = "dbi:Pg:dbname=$dsn" if !ref($dsn) && $dsn !~ /^(dbi|DBI):/; my $self = $class->SUPER::new(-dsn=>$dsn,%$other); $self; } =head2 schema Title : schema Usage : $schema = $db->schema Function: return the CREATE script for the schema Returns : a list of CREATE statemetns Args : none Status : protected This method returns a list containing the various CREATE statements needed to initialize the database tables. =cut sub schema { my %schema = ( fdata =>{ table=> q{ CREATE TABLE "fdata" ( "fid" serial NOT NULL, "fref" character varying(100) DEFAULT '' NOT NULL, "fstart" integer DEFAULT '0' NOT NULL, "fstop" integer DEFAULT '0' NOT NULL, "fbin" double precision DEFAULT '0.000000' NOT NULL, "ftypeid" integer DEFAULT '0' NOT NULL, "fscore" double precision DEFAULT NULL, "fstrand" character varying(3) DEFAULT NULL, "fphase" character varying(3) DEFAULT NULL, "gid" integer DEFAULT '0' NOT NULL, "ftarget_start" integer DEFAULT NULL, "ftarget_stop" integer DEFAULT NULL, CONSTRAINT chk_fdata_fstrand CHECK (fstrand IN ('+','-')), CONSTRAINT chk_fdata_fphase CHECK (fphase IN ('0','1','2')), CONSTRAINT pk_fdata PRIMARY KEY (fid) ) }, # fdata table #CONSTRAINT fref_fdata UNIQUE (fref, fbin, fstart, fstop, ftypeid, gid) # fdata_fref_idx => q{ CREATE UNIQUE INDEX fdata_fref_idx ON fdata (fref,fbin,fstart,fstop,ftypeid,gid)}, index=>{ fdata_fref_idx => q{ CREATE INDEX fdata_fref_idx ON fdata (fref,fbin,fstart,fstop,ftypeid,gid) }, fdata_ftypeid_idx => q{ CREATE INDEX fdata_ftypeid_idx ON fdata (ftypeid) }, fdata_gid_idx => q{ CREATE INDEX fdata_gid_idx ON fdata (gid) } }, # fdata indexes }, # fdata fgroup => { table => q{ CREATE TABLE "fgroup" ( "gid" serial NOT NULL, "gclass" character varying(100) DEFAULT NULL, "gname" character varying(100) DEFAULT NULL, CONSTRAINT pk_fgroup PRIMARY KEY (gid) ) }, # fgroup table index => { fgroup_gclass_idx => q{ CREATE UNIQUE INDEX fgroup_gclass_idx ON fgroup (gclass,gname) }, fgroup_gname_idx => q{ CREATE INDEX fgroup_gname_idx ON fgroup(gname) }, fgroup_lower_gname_idx => q{ CREATE INDEX fgroup_lower_gname_idx ON fgroup (lower(gname)) }, }, # fgroup indexes }, # fgroup ftype => { table => q{ CREATE TABLE "ftype" ( "ftypeid" serial NOT NULL, "fmethod" character varying(100) DEFAULT '' NOT NULL, "fsource" character varying(100) DEFAULT NULL, CONSTRAINT pk_ftype PRIMARY KEY (ftypeid), CONSTRAINT ftype_ftype UNIQUE (fmethod, fsource) ) }, # ftype table index => { ftype_fmethod_idx => q{ CREATE INDEX ftype_fmethod_idx ON ftype (fmethod) }, ftype_fsource_idx => q{ CREATE INDEX ftype_fsource_idx ON ftype (fsource) }, ftype_ftype_idx => q{ CREATE UNIQUE INDEX ftype_ftype_idx ON ftype (fmethod,fsource) } }, # ftype indexes }, # ftype fdna => { table => q{ CREATE TABLE "fdna" ( "fref" character varying(100) DEFAULT '' NOT NULL, "foffset" integer DEFAULT '0' NOT NULL, "fdna" bytea, CONSTRAINT pk_fdna PRIMARY KEY (fref, foffset) ) } #fdna table }, #fdna fmeta => { table => q{ CREATE TABLE "fmeta" ( "fname" character varying(255) DEFAULT '' NOT NULL, "fvalue" character varying(255) DEFAULT '' NOT NULL, CONSTRAINT pk_fmeta PRIMARY KEY (fname) ) } # fmeta table }, # fmeta fattribute => { table => q{ CREATE TABLE "fattribute" ( "fattribute_id" serial NOT NULL, "fattribute_name" character varying(255) DEFAULT '' NOT NULL, CONSTRAINT pk_fattribute PRIMARY KEY (fattribute_id) ) }, # fattribute table }, # fattribute fattribute_to_feature => { table => q{ CREATE TABLE "fattribute_to_feature" ( "fid" integer DEFAULT '0' NOT NULL, "fattribute_id" integer DEFAULT '0' NOT NULL, "fattribute_value" text ) }, # fattribute_to_feature table index => { fattribute_to_feature_fid => q{ CREATE INDEX fattribute_to_feature_fid ON fattribute_to_feature (fid,fattribute_id) }, fattribute_txt_idx => q{ CREATE INDEX fattribute_txt_idx ON fattribute_to_feature (fattribute_value) }, fattribute_lower_idx => q{ CREATE INDEX fattribute_lower_idx ON fattribute_to_feature (lower(fattribute_value)) }, } # fattribute_to_feature indexes }, # fattribute_to_feature finterval_stats => { table=> q{ CREATE TABLE "finterval_stats" ( "ftypeid" integer DEFAULT '0' NOT NULL, "fref" character varying(100) DEFAULT '' NOT NULL, "fbin" integer DEFAULT '0' NOT NULL, "fcum_count" integer DEFAULT '0' NOT NULL, CONSTRAINT pk_finterval_stats PRIMARY KEY (ftypeid,fref,fbin) ) } # finterval_stats table },# finterval_stats ); return \%schema; } =head2 setup_load Title : setup_load Usage : $db->setup_load Function: called before load_gff_line() Returns : void Args : none Status : protected This method performs schema-specific initialization prior to loading a set of GFF records. It prepares a set of DBI statement handlers to be used in loading the data. =cut sub setup_load { my $self = shift; my $schema = $self->schema; my $dbh = $self->features_db; if ($self->lock_on_load) { my @tables = map { "$_ WRITE"} $self->tables; my $tables = join ', ',@tables; $dbh->do("LOCK TABLES $tables"); } my $lookup_type = $dbh->prepare_delayed('SELECT ftypeid FROM ftype WHERE fmethod=? AND fsource=?'); my $insert_type = $dbh->prepare_delayed('INSERT INTO ftype (fmethod,fsource) VALUES (?,?)'); my $insertid_type = $dbh->prepare_delayed("SELECT currval('ftype_ftypeid_seq')"); my $lookup_group = $dbh->prepare_delayed('SELECT gid FROM fgroup WHERE lower(gname)=lower(?) AND gclass=?'); my $insert_group = $dbh->prepare_delayed('INSERT INTO fgroup (gname,gclass) VALUES (?,?)'); my $insertid_group = $dbh->prepare_delayed("SELECT currval('fgroup_gid_seq')"); my $lookup_attribute = $dbh->prepare_delayed('SELECT fattribute_id FROM fattribute WHERE fattribute_name=?'); my $insert_attribute = $dbh->prepare_delayed('INSERT INTO fattribute (fattribute_name) VALUES (?)'); my $insertid_attribute = $dbh->prepare_delayed("SELECT currval('fattribute_fattribute_id_seq')"); my $insert_attribute_value = $dbh->prepare_delayed('INSERT INTO fattribute_to_feature (fid,fattribute_id,fattribute_value) VALUES (?,?,?)'); my $insert_data = $dbh->prepare_delayed(<prepare_delayed('DELETE FROM fdata WHERE fref=? AND fstart=? AND fstop=? AND fbin=? AND ftypeid=? AND GID=?'); my $insertid_data = $dbh->prepare_delayed("SELECT currval('fdata_fid_seq')"); $self->{load_stuff}{sth}{lookup_ftype} = $lookup_type; $self->{load_stuff}{sth}{insert_ftype} = $insert_type; $self->{load_stuff}{sth}{insertid_ftype} = $insertid_type; $self->{load_stuff}{sth}{lookup_fgroup} = $lookup_group; $self->{load_stuff}{sth}{insert_fgroup} = $insert_group; $self->{load_stuff}{sth}{insertid_fgroup} = $insertid_group; $self->{load_stuff}{sth}{insertid_fdata} = $insertid_data; $self->{load_stuff}{sth}{insert_fdata} = $insert_data; $self->{load_stuff}{sth}{delete_existing_fdata} = $delete_existing_data; $self->{load_stuff}{sth}{lookup_fattribute} = $lookup_attribute; $self->{load_stuff}{sth}{insert_fattribute} = $insert_attribute; $self->{load_stuff}{sth}{insertid_fattribute} = $insertid_attribute; $self->{load_stuff}{sth}{insert_fattribute_value} = $insert_attribute_value; $self->{load_stuff}{types} = {}; $self->{load_stuff}{groups} = {}; $self->{load_stuff}{counter} = 0; } =head2 load_gff_line Title : load_gff_line Usage : $db->load_gff_line($fields) Function: called to load one parsed line of GFF Returns : true if successfully inserted Args : hashref containing GFF fields Status : protected This method is called once per line of the GFF and passed a series of parsed data items that are stored into the hashref $fields. The keys are: ref reference sequence source annotation source method annotation method start annotation start stop annotation stop score annotation score (may be undef) strand annotation strand (may be undef) phase annotation phase (may be undef) group_class class of annotation's group (may be undef) group_name ID of annotation's group (may be undef) target_start start of target of a similarity hit target_stop stop of target of a similarity hit attributes array reference of attributes, each of which is a [tag=>value] array ref =cut sub load_gff_line { my $self = shift; my $gff = shift; if (defined $gff->{phase}){ chomp($gff->{phase}); undef($gff->{phase}) if $gff->{phase} eq '.'; } if (defined $gff->{strand} && $gff->{strand} eq '.'){undef($gff->{strand})}; if (defined $gff->{score} && $gff->{score} eq '.'){undef($gff->{score})}; my $s = $self->{load_stuff}; my $dbh = $self->features_db; local $dbh->{PrintError} = 0; defined(my $typeid = $self->get_table_id('ftype', $gff->{method} => $gff->{source})) or return; defined(my $groupid = $self->get_table_id('fgroup',$gff->{gname} => $gff->{gclass})) or return; my $bin = bin($gff->{start},$gff->{stop},$self->min_bin); my $result = $s->{sth}{insert_fdata}->execute($gff->{ref}, $gff->{start},$gff->{stop},$bin, $typeid, $gff->{score},$gff->{strand},$gff->{phase}, $groupid, $gff->{tstart},$gff->{tstop}); warn $dbh->errstr,"\n" and print "ref=",$gff->{ref}," start=",$gff->{start}," stop=",$gff->{stop}," bin=",$bin," typeid=",$typeid," groupid=",$groupid,"\n" and return unless $result; my $fid = $self->insertid($s->{sth},'fdata') || $self->get_feature_id($gff->{ref},$gff->{start},$gff->{stop},$typeid,$groupid); # insert attributes foreach (@{$gff->{attributes}}) { defined(my $attribute_id = $self->get_table_id('fattribute',$_->[0])) or return; $s->{sth}{insert_fattribute_value}->execute($fid,$attribute_id,$_->[1]); } if ( (++$s->{counter} % 1000) == 0) { print STDERR "$s->{counter} records loaded..."; print STDERR -t STDOUT && !$ENV{EMACS} ? "\r" : "\n"; } $fid; } sub insertid { my $self = shift; my $sth = shift ; my $table = shift; my $insert_id; if ($sth->{"insertid_$table"}->execute()){ $insert_id = ($sth->{"insertid_$table"}->fetchrow_array)[0]; } else{ warn "No CURRVAL for SEQUENCE of table $table ",$sth->errstr,"\n"; return; } return $insert_id; } =head2 get_table_id Title : get_table_id Usage : $integer = $db->get_table_id($table,@ids) Function: get the ID of a group or type Returns : an integer ID or undef Args : none Status : private This internal method is called by load_gff_line to look up the integer ID of an existing feature type or group. The arguments are the name of the table, and two string identifiers. For feature types, the identifiers are the method and source. For groups, the identifiers are group name and class. This method requires that a statement handler named I, have been created previously by setup_load(). It is here to overcome deficiencies in mysql's INSERT syntax. =cut #' # get the object ID from a named table sub get_table_id { my $self = shift; my $table = shift; my @ids = @_; # irritating warning for null id my $id_key; { local $^W=0; $id_key = join ':',@ids; } my $s = $self->{load_stuff}; my $sth = $s->{sth}; my $dbh = $self->features_db; unless (defined($s->{$table}{$id_key})) { $sth->{"lookup_$table"}->execute(@ids); my @result = $sth->{"lookup_$table"}->fetchrow_array; if (@result > 0) { $s->{$table}{$id_key} = $result[0]; } else { $sth->{"insert_$table"}->execute(@ids) && ($s->{$table}{$id_key} = $self->insertid($sth,$table)); #&& ($s->{$table}{$id_key} = $self->insertid($sth->{"insertid_$table"})); #&& ($s->{$table}{$id_key} = $sth->{"insert_$table"}->insertid); } } my $id = $s->{$table}{$id_key}; unless (defined $id) { warn "No $table id for $id_key ",$dbh->errstr," Record skipped.\n"; return; } $id; } #sub insertid { # my $self = shift; # my $insertid_sth = shift ; # my $insert_id; # if ($insertid_sth->execute){ # $insert_id = ($insertid_sth->fetchrow_array)[0]; # } # else{ # warn "No CURRVAL for SEQUENCE ",$insertid_sth->errstr,"\n"; # return; # } # return $insert_id; #} sub insert_sequence { my $self = shift; my($id,$offset,$seq) = @_; my $sth = $self->{_insert_sequence} ||= $self->dbh->prepare_delayed('insert into fdna values (?,?,?)'); $sth->execute($id,$offset,$seq) or $self->throw($sth->errstr); } =head2 range_query Title : range_query Usage : $db->range_query($range_type,$refseq,$refclass,$start,$stop,$types,$order_by_group,$attributes,$binsize) Function: create statement handle for range/overlap queries Returns : a DBI statement handle Args : see below Status : Protected This method constructs the statement handle for this module's central query: given a range and/or a list of feature types, fetch their GFF records. It overrides a method in dbi.pm so that the overlaps query can write SQL optimized for Postgres. Specifically, instead of writing the bin related section as a set of ORs, each bin piece is place in a separate select and then they are UNIONed together. This subroutine requires several replacements for other subroutines in dbi.pm. In this module, they are named the same as those in dbi.pm but prefixed with "pg_". The positional arguments are as follows: Argument Description $isrange A flag indicating that this is a range. query. Otherwise an overlap query is assumed. $refseq The reference sequence name (undef if no range). $refclass The reference sequence class (undef if no range). $start The start of the range (undef if none). $stop The stop of the range (undef if none). $types Array ref containing zero or feature types in the format [method,source]. $order_by_group A flag indicating that statement handler should group the features by group id (handy for iterative fetches) $attributes A hash containing select attributes. $binsize A bin size for generating tables of feature density. =cut sub range_query { my $self = shift; my($rangetype,$refseq,$class,$start,$stop,$types,$sparse,$order_by_group,$attributes,$bin) = @_; my $dbh = $self->features_db; # my @bin_parts = split /\n\s+OR/, $self->bin_query($start,$stop); # warn "bin_part: @bin_parts\n"; my %a = (refseq=>$refseq,class=>$class,start=>$start,stop=>$stop,types=>$types,attributes=>$attributes,bin_width=>$bin); my ($query, @args, $order_by); if ($rangetype ne 'overlaps') { my $select = $self->make_features_select_part(\%a); my $from = $self->make_features_from_part($sparse,\%a); my $join = $self->make_features_join_part(\%a); my $where; ($where,@args) = $self->make_features_by_range_where_part($rangetype,\%a); my ($group_by,@more_args) = $self->make_features_group_by_part(\%a); $order_by = $self->make_features_order_by_part(\%a) if $order_by_group; $query = "SELECT $select FROM $from WHERE $join"; $query .= " AND $where" if $where; if ($group_by) { $query .= " GROUP BY $group_by"; push @args,@more_args; } } else { # most common case: overlaps query my @bin_parts = split /\s*OR/, $self->bin_query($start,$stop); my $select = $self->make_features_select_part(\%a); my $from = $self->make_features_from_part($sparse,\%a); my $join = $self->make_features_join_part(\%a); my $where; ($where,@args) = $self->pg_make_features_by_range_where_part($rangetype,\%a); my ($group_by,@more_args)= $self->make_features_group_by_part(\%a); $order_by = $self->pg_make_features_order_by_part(\%a) if $order_by_group; my @temp_args; my @query_pieces; foreach my $bin (@bin_parts) { my $temp_query = "SELECT $select FROM $from WHERE $join AND $where AND $bin\n"; push @temp_args, @args; if ($group_by) { $temp_query .= " GROUP BY $group_by"; push @temp_args,@more_args; } push @query_pieces, $temp_query; } @args = @temp_args; $query = join("UNION\n", @query_pieces); } $query .= " ORDER BY $order_by" if $order_by; $self->dbh->do('set enable_seqscan=off'); my $sth = $self->dbh->do_query($query,@args); $sth; } sub pg_make_features_by_range_where_part { my $self = shift; my ($rangetype,$options) = @_; return unless $rangetype eq 'overlaps'; $options ||= {}; my ($refseq,$class,$start,$stop,$types,$attributes) = @{$options}{qw(refseq class start stop types attributes)}; my (@query,@args); if ($refseq) { my ($q,@a) = $self->refseq_query($refseq,$class); push @query,$q; push @args,@a; } if (defined $start or defined $stop) { $start = 0 unless defined($start); $stop = MAX_SEGMENT unless defined($stop); my ($range_query,@range_args) = $self->pg_overlap_query($start,$stop); push @query,$range_query; push @args,@range_args; } if (defined $types && @$types) { my ($type_query,@type_args) = $self->types_query($types); push @query,$type_query; push @args,@type_args; } if ($attributes) { my ($attribute_query,@attribute_args) = $self->make_features_by_attribute_where_part($attributes); push @query,"($attribute_query)"; push @args,@attribute_args; } my $query = join "AND",@query; return wantarray ? ($query,@args) : $self->dbh->dbi_quote($query,@args); } sub pg_overlap_query { my $self = shift; my ($start,$stop) = @_; my ($iq,@iargs) = $self->overlap_query_nobin($start,$stop); my $query = "\n$iq\n"; my @args = @iargs; return wantarray ? ($query,@args) : $self->dbh->dbi_quote($query,@args); } sub pg_make_features_order_by_part { my $self = shift; my $options = shift || {}; return "gname"; } =head2 search_notes This PostgreSQL adaptor does not implement the search notes method because it can be very slow (although the code for the method is contained in this method but commented out). There is, however, a PostgreSQL adaptor that does implement it in a more efficient way: L, which inherits from this adaptor and uses the optional PostgreSQL module TSearch2 for full text indexing. See that adaptor's documentation for more information. See also L Title : search_notes Usage : @search_results = $db->search_notes("full text search string",$limit) Function: Search the notes for a text string, using mysql full-text search Returns : array of results Args : full text search string, and an optional row limit Status : public This is a replacement for the mysql-specific method. Given a search string, it performs a ILIKE search of the notes table and returns an array of results. Each row of the returned array is a arrayref containing the following fields: column 1 A Bio::DB::GFF::Featname object, suitable for passing to segment() column 2 The text of the note column 3 A relevance score. Note that for large databases this can be very slow and may result in time out or 500-cgi errors. If this is happening on a regular basis, you should look into using L which implements the TSearch2 full text indexing scheme. =cut sub search_notes{ # my $self = shift; # my ($search_string,$limit) = @_; # # $search_string =~ tr/*/%/s; # $search_string = '%'.$search_string unless $search_string =~ /^\%/; # $search_string = $search_string.'%' unless $search_string =~ /\%$/; # warn "search_string:$search_string"; # my $query = FULLTEXTWILDCARD; # $query .= " limit $limit" if defined $limit; # my $sth = $self->dbh->do_query($query,$search_string); # # my @results; # while (my ($class,$name,$note) = $sth->fetchrow_array) { # # next unless $class && $name; # sorry, ignore NULL objects # my $featname = Bio::DB::GFF::Featname->new($class=>$name); # # push @results,[$featname,$note,0]; #gbrowse expects a score, but # #pg doesn't give one, thus the 0 # } # warn @results; # # return @results; } =head2 make_meta_set_query Title : make_meta_set_query Usage : $sql = $db->make_meta_set_query Function: return SQL fragment for setting a meta parameter Returns : SQL fragment Args : none Status : public By default this does nothing; meta parameters are not stored or retrieved. =cut sub make_meta_set_query { return 'INSERT INTO fmeta VALUES (?,?)'; } sub make_classes_query { my $self = shift; return 'SELECT DISTINCT gclass FROM fgroup WHERE NOT gclass IS NULL'; } sub chunk_size { my $self = shift; $self->meta('chunk_size') || DEFAULT_CHUNK; } sub getseqcoords_query { my $self = shift; return GETSEQCOORDS ; } sub getaliascoords_query{ my $self = shift; return GETALIASCOORDS ; } sub getforcedseqcoords_query{ my $self = shift; return GETFORCEDSEQCOORDS ; } sub getaliaslike_query{ my $self = shift; return GETALIASLIKE ; } sub make_features_select_part { my $self = shift; my $options = shift || {}; my $s; if (my $b = $options->{bin_width}) { $s = <{attributes} && keys %{$options->{attributes}}>1; $s; } sub make_features_from_part_bkup { my $self = shift; my $sparse = shift; my $options = shift || {}; #my $index = $sparse ? ' USE INDEX(ftypeid)': ''; my $index = ''; return $options->{attributes} ? "fdata${index},ftype,fgroup,fattribute,fattribute_to_feature\n" : "fdata${index},ftype,fgroup\n"; } #################################### # moved from mysqlopt.pm ################################### # meta values sub default_meta_values { my $self = shift; my @values = $self->SUPER::default_meta_values; return ( @values, max_bin => MAX_BIN, min_bin => MIN_BIN, straight_join_limit => STRAIGHT_JOIN_LIMIT, ); } sub min_bin { my $self = shift; return $self->meta('min_bin') || MIN_BIN; } sub max_bin { my $self = shift; return $self->meta('max_bin') || MAX_BIN; } sub straight_join_limit { my $self = shift; return $self->meta('straight_join_limit') || STRAIGHT_JOIN_LIMIT; } sub _feature_by_name { my $self = shift; my ($class,$name,$location,$callback) = @_; $callback || $self->throw('must provide a callback argument'); my @bin_parts = split /\s*OR/, $self->bin_query($location->[1],$location->[2]) if $location; my $select = $self->make_features_select_part; my $from = $self->make_features_from_part(undef,{sparse_groups=>1}); my ($where,@args) = $self->make_features_by_name_where_part($class,$name); my $join = $self->make_features_join_part; my $range = $self->pg_make_features_by_range_where_part('overlaps', {refseq=>$location->[0], class =>'', start=>$location->[1], stop =>$location->[2]}) if $location; my @temp_args; my @query_pieces; my $query; if (@bin_parts) { foreach my $bin (@bin_parts) { my $temp_query = "SELECT $select FROM $from WHERE $join AND $where AND $range AND $bin\n"; push @temp_args, @args; push @query_pieces, $temp_query; } @args = @temp_args; $query = join("UNION\n", @query_pieces); } else { $query = "SELECT $select FROM $from WHERE $where AND $join"; } my $sth = $self->dbh->do_query($query,@args); my $count = 0; while (my @row = $sth->fetchrow_array) { $callback->(@row); $count++; } $sth->finish; return $count; } sub update_sequences { my $self = shift; my $dbh = $self->features_db; $dbh->do("SELECT setval('public.fdata_fid_seq', max(fid)+1) FROM fdata"); $dbh->do("SELECT setval('public.fattribute_fattribute_id_seq', max(fattribute_id)+1) FROM fattribute"); $dbh->do("SELECT setval('public.fgroup_gid_seq', max(gid)+1) FROM fgroup"); $dbh->do("SELECT setval('public.ftype_ftypeid_seq', max(ftypeid)+1) FROM ftype"); 1; } =head2 make_features_by_name_where_part Title : make_features_by_name_where_part Usage : $db->make_features_by_name_where_part Function: Overrides a function in Bio::DB::GFF::Adaptor::dbi to insure that searches will be case insensitive. It creates the SQL fragment needed to select a feature by its group name & class Returns : a SQL fragment and bind arguments Args : see below Status : Protected =cut sub make_features_by_name_where_part { my $self = shift; my ($class,$name) = @_; if ($name !~ /\*/) { #allows utilization of an index on lower(gname) return ("fgroup.gclass=? AND lower(fgroup.gname) = lower(?)",$class,$name); } else { $name =~ tr/*/%/; return ("fgroup.gclass=? AND lower(fgroup.gname) LIKE lower(?)",$class,$name); } } # # Methods from dbi.pm that need to be overridden to make # searching for fref case insensitive # # sub get_dna { my $self = shift; my ($ref,$start,$stop,$class) = @_; my ($offset_start,$offset_stop); my $has_start = defined $start; my $has_stop = defined $stop; my $reversed; if ($has_start && $has_stop && $start > $stop) { $reversed++; ($start,$stop) = ($stop,$start); } # turn start and stop into 0-based offsets my $cs = $self->dna_chunk_size; $start -= 1; $stop -= 1; $offset_start = int($start/$cs)*$cs; $offset_stop = int($stop/$cs)*$cs; my $sth; # special case, get it all if (!($has_start || $has_stop)) { $sth = $self->dbh->do_query('select fdna,foffset from fdna where lower(fref)=lower(?) order by foffset',$ref); } elsif (!$has_stop) { $sth = $self->dbh->do_query('select fdna,foffset from fdna where lower(fref)=lower(?) and foffset>=? order by foffset', $ref,$offset_start); } else { # both start and stop defined $sth = $self->dbh->do_query('select fdna,foffset from fdna where lower(fref)=lower(?) and foffset>=? and foffset<=? order by foffset', $ref,$offset_start,$offset_stop); } my $dna = ''; while (my($frag,$offset) = $sth->fetchrow_array) { substr($frag,0,$start-$offset) = '' if $has_start && $start > $offset; $dna .= $frag; } substr($dna,$stop-$start+1) = '' if $has_stop && $stop-$start+1 < length($dna); if ($reversed) { $dna = reverse $dna; $dna =~ tr/gatcGATC/ctagCTAG/; } $sth->finish; $dna; } sub refseq_query { my $self = shift; my ($refseq,$refclass) = @_; my $query = "lower(fdata.fref)=lower(?)"; return wantarray ? ($query,$refseq) : $self->dbh->dbi_quote($query,$refseq); } sub make_types_where_part { my $self = shift; my ($srcseq,$start,$stop,$want_count,$typelist) = @_; my (@query,@args); if (defined($srcseq)) { push @query,'lower(fdata.fref)=lower(?)'; push @args,$srcseq; if (defined $start or defined $stop) { $start = 1 unless defined $start; $stop = MAX_SEGMENT unless defined $stop; my ($q,@a) = $self->overlap_query($start,$stop); push @query,"($q)"; push @args,@a; } } if (defined $typelist && @$typelist) { my ($q,@a) = $self->types_query($typelist); push @query,($q); push @args,@a; } my $query = @query ? join(' AND ',@query) : '1=1'; return wantarray ? ($query,@args) : $self->dbh->dbi_quote($query,@args); } sub get_feature_id { my $self = shift; my ($ref,$start,$stop,$typeid,$groupid) = @_; my $s = $self->{load_stuff}; unless ($s->{get_feature_id}) { my $dbh = $self->features_db; $s->{get_feature_id} = $dbh->prepare_delayed('SELECT fid FROM fdata WHERE lower(fref)=lower(?) AND fstart=? AND fstop=? AND ftypeid=? AND gid=?'); } my $sth = $s->{get_feature_id} or return; $sth->execute($ref,$start,$stop,$typeid,$groupid) or return; my ($fid) = $sth->fetchrow_array; return $fid; } sub _delete { my $self = shift; my $delete_spec = shift; my $ranges = $delete_spec->{segments} || []; my $types = $delete_spec->{types} || []; my $force = $delete_spec->{force}; my $range_type = $delete_spec->{range_type}; my $dbh = $self->features_db; my $query = 'delete from fdata'; my @where; my @range_part; for my $segment (@$ranges) { my $ref = $dbh->quote($segment->abs_ref); my $start = $segment->abs_start; my $stop = $segment->abs_stop; my $range = $range_type eq 'overlaps' ? $self->overlap_query($start,$stop) : $range_type eq 'contains' ? $self->contains_query($start,$stop) : $range_type eq 'contained_in' ? $self->contained_in_query($start,$stop) : $self->throw("Invalid range type '$range_type'"); push @range_part,"(lower(fref)=lower($ref) AND $range)"; } push @where,'('. join(' OR ',@range_part).')' if @range_part; # get all the types if (@$types) { my $types_where = $self->types_query($types); my $types_query = "select ftypeid from ftype where $types_where"; my $result = $dbh->selectall_arrayref($types_query); my @typeids = map {$_->[0]} @$result; my $typelist = join ',',map{$dbh->quote($_)} @typeids; $typelist ||= "0"; # don't cause DBI to die with invalid SQL when # unknown feature types were requested. push @where,"(ftypeid in ($typelist))"; } $self->throw("This operation would delete all feature data and -force not specified") unless @where || $force; $query .= " where ".join(' and ',@where) if @where; warn "$query\n" if $self->debug; my $result = $dbh->do($query); defined $result or $self->throw($dbh->errstr); $result; } sub make_abscoord_query { my $self = shift; my ($name,$class,$refseq) = @_; #my $query = GETSEQCOORDS; my $query = $self->getseqcoords_query(); my $getforcedseqcoords = $self->getforcedseqcoords_query() ; if ($name =~ /\*/) { $name =~ s/%/\\%/g; $name =~ s/_/\\_/g; $name =~ tr/*/%/; $query =~ s/gname\) = lower/gname) LIKE lower/; } defined $refseq ? $self->dbh->do_query($getforcedseqcoords,$name,$class,$refseq) : $self->dbh->do_query($query,$name,$class); } sub make_aliasabscoord_query { my $self = shift; my ($name,$class) = @_; #my $query = GETALIASCOORDS; my $query = $self->getaliascoords_query(); if ($name =~ /\*/) { $name =~ s/%/\\%/g; $name =~ s/_/\\_/g; $name =~ tr/*/%/; $query =~ s/gname\) = lower/gname) LIKE lower/; } $self->dbh->do_query($query,$name,$class); } 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm000444000766000024 2417413155576320 21113 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::dbi::pg_fts; =head1 NAME Bio::DB::GFF::Adaptor::dbi::pg_fts -- Database adaptor for a specific postgres schema with a TSearch2 implementation =head1 SYNOPSIS #create new GFF database connection my $db = Bio::DB::GFF->new( -adaptor => 'dbi::pg_fts', -dsn => 'dbi:Pg:dbname=worm'); #add full text indexing 'stuff' #assumes that TSearch2 is available to PostgreSQL #this will take a VERY long time for a reasonably large database $db->install_TSearch2(); ...some time later... #we don't like full text searching... $db->remove_TSearch2(); =head1 DESCRIPTION This adaptor is based on Bio::DB::GFF::Adaptor::dbi::pg but it implements the TSearch2 PostgreSQL contrib module for fast full text searching. To use this module with your PostgreSQL GFF database, you need to make TSearch2 available in the database. To use this adaptor, follow these steps: =over =item Install TSearch2 contrib module for Pg Can be as easy as `sudo yum install postgresql-contrib`, or you may need to recompile PostgreSQL to include it. See L for more details =item Load the TSearch2 functions to you database % cat tsearch2.sql | psql =item Load your data using the pg adaptor: % bp_pg_bulk_load_gff.pl -c -d yeast saccharomyces_cerevisiae.gff or % bp_load_gff.pl -c -d yeast -a dbi::pg saccharomyces_cerevisiae.gff =item Add GFF/TSearch2 specific modifications Execute a perl script like this one: #!/usr/bin/perl -w use strict; use Bio::DB::GFF; my $db = Bio::DB::GFF->new( -adaptor => 'dbi::pg_fts', -dsn => 'dbi:Pg:dbname=yeast', -user => 'scott', ); print "Installing TSearch2 columns...\n"; $db->install_TSearch2(); print "Done\n"; =back Note that this last step will take a long time. For a S. cerevisiae database with 15K rows, it took over an hour on my laptop, and with a C. elegans database (~10 million rows) it took well over a day. If at some point you add more data you your database, you need to run a similar script to the one above, only executing the update_TSearch2() method. Finally, if you want to remove the TSearch2 columns from your database and go back to using the pg adaptor, you can execute a script like the one above, only executing the remove_TSearch2() method. =head1 NOTES ABOUT TSearch2 SEARCHING You should know a few things about how searching with TSearch2 works in the GBrowse environment: =over =item 1 TSearch2 does not do wild cards, so you should encourage your users not to use them. If wild cards are used, the adaptor will fall back on an ILIKE search, which will be much slower. =item 2 However, TSearch2 does do 'word stemming'. That is, if you search for 'copy', it will find 'copy', 'copies', and 'copied'. =item 3 TSearch2 does not do phrase searching; all of the terms in the search string are ANDed together. =back =head1 ACKNOWLEDGEMENTS Special thanks to Russell Smithies and Paul Smale at AgResearch in New Zealand for giving me their recipe for doing full text indexing in a GFF database. =head1 BUGS Please report bugs to the BioPerl and/or GBrowse mailing lists (L and L respectively). =head1 SEE ALSO Please see L for more information about tuning your PostgreSQL server for GFF data, and for general information about GFF database access, see L. =head1 AUTHOR Scott Cain, cain@cshl.edu =head1 APPENDIX =cut # a simple postgres adaptor use strict; use Bio::DB::GFF::Adaptor::dbi; use base qw(Bio::DB::GFF::Adaptor::dbi::pg); use constant FULLTEXTSEARCH => < <SUPER::new(@_); return $self; } =head2 search_notes Title : search_notes Usage : @search_results = $db->search_notes("full text string",$limit) Function: Search the notes for a text string, using PostgreSQL TSearch2 Returns : array of results Args : full text search string, and an optional row limit Status : public This is based on the mysql-specific method that makes use of the TSearch2 functionality in PosgreSQL's contrib directory. Given a search string, it performs a full-text search of the notes table and returns an array of results. Each row of the returned array is a arrayref containing the following fields: column 1 A Bio::DB::GFF::Featname object, for passing to segment() column 2 The text of the note column 3 A relevance score. =cut sub search_notes { my $self = shift; my ($search_string,$limit) = @_; my @terms = split /\s+/, $search_string; my $sth; if ($search_string =~ /\*/) { $search_string =~ tr/*/%/s; my $query = FULLTEXTWILDCARD; $query .= " limit $limit" if defined $limit; $sth = $self->dbh->do_query($query,$search_string); } elsif (@terms == 1) { my $query = FULLTEXTSEARCH; $query .= " limit $limit" if defined $limit; $sth = $self->dbh->do_query($query,$search_string); } else { my $query = FULLTEXTSEARCH; my $andstring = join (' & ', @terms); # $query .= qq{ AND (fattribute_to_feature.fattribute_value ILIKE '\%$search_string%')}; $query .= " LIMIT $limit" if defined $limit; $sth = $self->dbh->do_query($query,$andstring); } my @results; while (my ($class,$name,$note,$method,$source) = $sth->fetchrow_array) { next unless $class && $name; # sorry, ignore NULL objects my $featname = Bio::DB::GFF::Featname->new($class=>$name); my $type = Bio::DB::GFF::Typename->new($method,$source); push @results,[$featname,$note,0,$type]; #gbrowse expects a score, but #pg doesn't give one, thus the 0 } return @results; } =head2 make_features_by_name_where_part Title : make_features_by_name_where_part Function: constructs a TSearch2-compliant WHERE clause for a name search Status : protected =cut #need a make_features_by_name_where_part method to override pg sub make_features_by_name_where_part { my $self = shift; my ($class,$name) = @_; my @terms = split /\s+/, $name; if ($name =~ /\*/) { $name =~ tr/*/%/s; return ("fgroup.gclass=? AND lower(fgroup.gname) LIKE lower(?)",$class,$name); } else { my $where_str = "fgroup.gclass=? AND (fgroup.idxfti @@ to_tsquery('default', ?)) "; if (@terms == 1) { return ($where_str,$class,$name); } else { my $andstring = join (' & ', @terms); # $where_str .= qq{ AND (fgroup.gname ILIKE '\%$name%')}; return ($where_str,$class,$andstring); } } } =head2 install_TSearch2 Title : install_TSearch2 Function: installs schema modifications for use with TSearch2 Usage : $db->install_TSearch2 Status : public =cut #needs method for installing TSearch2 (does that mean that the SQL for #creating the tables and functions should go in here? That would be #the safest and easiest thing to do sub install_TSearch2 { my $self = shift; my $dbh = $self->features_db; $dbh->do('ALTER TABLE fattribute_to_feature ADD COLUMN idxFTI tsvector') or $self->throw('adding FTI column to f_to_f failed'); $dbh->do('ALTER TABLE fgroup ADD COLUMN idxFTI tsvector') or $self->throw('adding FTI column to fgroup failed'); $self->update_TSearch2(); return; } =head2 update_TSearch2 Title : update_TSearch2 Function: Updates TSearch2 columns Usage : $db->update_TSearch2 Status : public =cut sub update_TSearch2 { my $self = shift; my $dbh = $self->features_db; $self->warn('updating full text column; this may take a very long time...'); $dbh->do("UPDATE fattribute_to_feature " ."SET idxFTI= to_tsvector('default', fattribute_value) " ."WHERE idxFTI IS NULL") or $self->throw('updating fti column failed'); $dbh->do("UPDATE fgroup " ."SET idxFTI= to_tsvector('default', gname) " ."WHERE idxFTI IS NULL") or $self->throw('updating fgroup fti column failed'); $self->warn('Preliminary optimization of database; this may also take a long time...'); $dbh->do('VACUUM FULL ANALYZE') or $self->throw('vacuum failed'); $self->warn('Updating full text index; again, this may take a long time'); $dbh->do('CREATE INDEX idxFTI_idx ON fattribute_to_feature ' .'USING gist(idxFTI)') or $self->warn('creating full text index failed'); $dbh->do('CREATE INDEX fgroup_idxFTI_idx ON fgroup ' .'USING gist(idxFTI)') or $self->warn('creating fgroup full text index failed'); $self->warn('Optimizing database; hopefully, this will not take as long as other steps'); $dbh->do('VACUUM FULL ANALYZE'); $dbh->do("SELECT set_curcfg('default')"); return; } =head2 remove_TSearch2 Title : remove_TSearch2 Function: Removes TSearch2 columns Usage : $db->remove_TSearch2 Status : public =cut sub remove_TSearch2 { my $self = shift; my $dbh = $self->features_db; $self->warn('Removing full text search capabilities'); $dbh->do('DROP INDEX idxFTI_idx') or $self->throw('dropping full text index failed'); $dbh->do('DROP INDEX fgroup_idxFTI_idx') or $self->throw('dropping full text index failed'); $dbh->do('ALTER TABLE fattribute_to_feature DROP COLUMN idxFTI') or $self->throw('dropping full text column failed'); $dbh->do('ALTER TABLE fgroup DROP COLUMN idxFTI') or $self->throw('dropping full text column failed'); return; } 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor/memory000755000766000024 013155576320 17660 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm000444000766000024 170013155576320 24235 0ustar00cjfieldsstaff000000000000package Bio::DB::GFF::Adaptor::memory::feature_serializer; =head1 NAME Bio::DB::GFF::Adaptor::memory::feature_serializer - utility methods for serializing and deserializing GFF features =cut use strict; require Exporter; use vars qw(@EXPORT @EXPORT_OK @hash2array_map); use base qw(Exporter); @EXPORT_OK = qw(feature2string string2feature @hash2array_map); @EXPORT = @EXPORT_OK; @hash2array_map = qw(ref start stop source method score strand phase gclass gname tstart tstop feature_id group_id bin); sub feature2string { my $feature = shift; local $^W = 0; my @a = @{$feature}{@hash2array_map}; push @a,map {join "\0",@$_} @{$feature->{attributes}} if $feature->{attributes}; return join $;,@a; } sub string2feature { my $string = shift; my (@attributes,%feature); (@feature{@hash2array_map},@attributes) = split $;,$string; $feature{attributes} = [map {[split "\0",$_]} @attributes]; undef $feature{group_id}; \%feature; } 1; BioPerl-1.007002/Bio/DB/GFF/Adaptor/memory/iterator.pm000444000766000024 324513155576320 22210 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Adaptor::memory::iterator - iterator for Bio::DB::GFF::Adaptor::memory =head1 SYNOPSIS For internal use only =head1 DESCRIPTION This is an internal module that is used by the Bio::DB::GFF in-memory adaptor to return an iterator across a sequence feature query. The object has a single method, next_feature(), that returns the next feature from the query. The method next_seq() is an alias for next_feature(). =head1 BUGS None known yet. =head1 SEE ALSO L, =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut package Bio::DB::GFF::Adaptor::memory::iterator; use strict; # this module needs to be cleaned up and documented use Bio::Root::Version; *next_seq = \&next_feature; sub new { my $class = shift; my ($data,$callback) = @_; my $pos = 0; return bless {data => $data, pos => $pos, callback => $callback, cache => []},$class; #return bless [$sth,$callback,[]],$class; } sub next_feature { my $self = shift; return shift @{$self->{cache}} if @{$self->{cache}}; my $data = $self->{data} or return; my $callback = $self->{callback}; my $features; while (1) { my $feature = $data->[$self->{pos}++]; if ($feature) { $features = $callback->(@{$feature}); last if $features; } else { $features = $callback->(); undef $self->{pos}; undef $self->{data}; undef $self->{cache}; last; } } $self->{cache} = $features or return; shift @{$self->{cache}}; } 1; BioPerl-1.007002/Bio/DB/GFF/Aggregator000755000766000024 013155576320 17040 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/GFF/Aggregator/alignment.pm000444000766000024 704513155576320 21517 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::alignment -- Alignment aggregator =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['alignment'], ); ----------------------------- Aggregator method: alignment Main method: (none) Sub methods: nucleotide_match,EST_match,cDNA_match,expressed_sequence_match, translated_nucleotide_match,protein_match,HSP ----------------------------- =head1 DESCRIPTION Bio::DB::GFF::Aggregator::alignment is one of the default aggregators, and was written to be compatible with the C elegans GFF files. It aggregates raw "similarity" features into composite features of type "alignment". A better name for this class might be "gapped_alignment." This aggregator does not insist that there be a single top-level feature that spans one end of the alignment to the other. As a result, it can produce truncated alignments if the entire alignment is not contained within the segment of interest. =cut package Bio::DB::GFF::Aggregator::alignment; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 aggregate Title : aggregate Usage : $features = $a->aggregate($features,$factory) Function: aggregate a feature list into composite features Returns : an array reference containing modified features Args : see L Status : Public Because of the large number of similarity features, the aggregate() method is overridden in order to perform some optimizations. =cut # we look for features of type Sequence and add them to a pseudotype transcript sub aggregate { my $self = shift; my $features = shift; my $factory = shift; my $matchsub = $self->match_sub($factory) or return; my $passthru = $self->passthru_sub($factory); my $method = $self->get_method; my (%alignments,%targets,@result); warn "running alignment aggregator" if $factory->debug; for my $feature (@$features) { if ($matchsub->($feature)) { my $group = $feature->{group}; my $source = $feature->source; unless (exists $alignments{$group,$source}) { my $type = Bio::DB::GFF::Typename->new($method,$source); my $f = $feature->clone; # this is a violation of OO encapsulation, but need to do it this way # to achieve desired performance @{$f}{qw(type score phase)} = ($type,undef,undef); $alignments{$group,$source} = $f or next; } my $main = $alignments{$group,$source}; $main->add_subfeature($feature); push @result,$feature if $passthru && $passthru->($feature); } else { push @result,$feature; } } warn "running aligner adjuster" if $factory->debug; for my $alignment (values %alignments) { $alignment->adjust_bounds; $alignment->compound(1); push @result,$alignment; } warn "aligner done" if $factory->debug; @$features = @result; } =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "alignment" Args : none Status : Public =cut sub method { 'alignment' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : the full list of aggregated methods Args : none Status : Public =cut sub part_names { my $self = shift; return qw(nucleotide_match EST_match cDNA_match expressed_sequence_match translated_nucleotide_match protein_match HSP); } 1; BioPerl-1.007002/Bio/DB/GFF/Aggregator/clone.pm000444000766000024 1040013155576320 20646 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::clone -- Clone aggregator =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['transcript','clone'], ); ---------------------------------------------------------------------------- Aggregator method: clone Main method: -none- Sub methods: Clone_left_end Clone_right_end region:Genomic_canonical ---------------------------------------------------------------------------- =head1 DESCRIPTION Bio::DB::GFF::Aggregator::clone is one of the default aggregators, and was written to be compatible with the C elegans GFF files. It aggregates raw "Clone_left_end", "Clone_right_end", and "region:Genomic_canonical" features into composite features of type "clone". =cut package Bio::DB::GFF::Aggregator::clone; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 aggregate Title : aggregate Usage : $features = $a->aggregate($features,$factory) Function: aggregate a feature list into composite features Returns : an array reference containing modified features Args : see L Status : Public The WormBase GFF model is unusual in that clones aren't identified as a single feature with start and stop positions, but as two features, a "left end" and a "right end". One or both of these features may be absent. In order to accommodate this, the aggregator will return undef for the start and/or stop if one or both of the ends are missing. =cut #' # we look for features of type Sequence and add them to a pseudotype transcript sub aggregate { my $self = shift; my $features = shift; my $factory = shift; my $matchsub = $self->match_sub($factory) or return; my $passthru = $self->passthru_sub($factory); my $method = $self->get_method; my (%clones,%types,@result); for my $feature (@$features) { if ($feature->group && $matchsub->($feature)) { if ($feature->method =~ /^region|Sequence$/ && $feature->source eq 'Genomic_canonical') { $clones{$feature->group}{canonical} = $feature; } elsif ($feature->method eq 'Clone_left_end') { $clones{$feature->group}{left} = $feature; } elsif ($feature->method eq 'Clone_right_end') { $clones{$feature->group}{right} = $feature; } push @result,$feature if $passthru && $passthru->($feature); } else { push @result,$feature; } } for my $clone (keys %clones) { my $canonical = $clones{$clone}{canonical} or next; # the genomic_canonical doesn't tell us where the clone starts and stops # so don't assume it my $duplicate = $canonical->clone; # make a duplicate of the feature # munge the method and source fields my $source = $duplicate->source; my $type = $types{$method,$source} ||= Bio::DB::GFF::Typename->new($method,$source); $duplicate->type($type); my ($start,$stop) = $duplicate->strand > 0 ? ('start','stop') : ('stop','start'); @{$duplicate}{$start,$stop} =(undef,undef); $duplicate->{$start} = $clones{$clone}{left}{$start} if exists $clones{$clone}{left}; $duplicate->{$stop} = $clones{$clone}{right}{$stop} if exists $clones{$clone}{right}; $duplicate->method($self->method); push @result,$duplicate; } @$features = @result; } =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "clone" Args : none Status : Public =cut sub method { 'clone' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : the list ("Clone_left_end", "Clone_right_end", "region:Genomic_canonical") Args : none Status : Public =cut sub part_names { my $self = shift; return qw(Clone_left_end Clone_right_end region:Genomic_canonical Sequence:Genomic_canonical); } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/coding.pm000444000766000024 366613155576320 21011 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::coding -- The Coding Region Aggregator =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['coding'], ); ------------------------------------------------------------------------ Aggregator method: coding Main method: mRNA Sub methods: CDS ------------------------------------------------------------------------ =head1 DESCRIPTION Bio::DB::GFF::Aggregator::coding aggregates "CDS" features into a feature called "coding" and was written to be compatible with the Sequence Ontology canonical gene. The CDS features are expected to belong to a parent of type "mRNA," but the aggregator will work even if this isn't the case. =cut package Bio::DB::GFF::Aggregator::coding; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "coding" Args : none Status : Public =cut sub method { 'coding' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : the list (CDS cds) Args : none Status : Public =cut sub part_names { return qw(CDS cds); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "mRNA" Args : none Status : Public =cut sub main_name { return 'mRNA'; } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/gene.pm000444000766000024 456313155576320 20461 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::gene -- Sequence Ontology Geene =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['gene'], ); ------------------------------------------------------------------------ Aggregator method: gene Main method: mRNA Sub methods: CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site ------------------------------------------------------------------------ =head1 DESCRIPTION Bio::DB::GFF::Aggregator::gene is identical to so_transcript, but is used in those cases where you would like the name of the aggregated feature to be "gene" rather than "processed_transcript". It aggregates raw "exon," "CDS", "five_prime_UTR", "three_prime_UTR", "transcription_start_site" and "polyA_site" features into "mRNA" features. The UTRs may also be named "untranslated_region," "five_prime_untranslated_region," "three_prime_untranslated_region,", "5'-UTR," and other synonyms. =cut package Bio::DB::GFF::Aggregator::gene; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "gene" Args : none Status : Public =cut sub method { 'gene' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : the list CDS 5'-UTR 3'-UTR transcription_start_site polyA_site Args : none Status : Public =cut sub part_names { return qw(CDS transcription_start_site polyA_site UTR five_prime_untranslated_region three_prime_untranslated_region five_prime_UTR three_prime_UTR exon); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "mRNA" Args : none Status : Public =cut sub main_name { return 'mRNA'; } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2008 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/match.pm000444000766000024 360113155576320 20627 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::match -- Match aggregator =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['match'], ); ------------------------------------------------- Aggregator method: match Main method: match Sub methods: similarity HSP ------------------------------------------------- =head1 DESCRIPTION This aggregator is used for Sequence Ontology-compatible gapped alignments, in which there is a single top-level alignment called "match" and a series of subalignments called either "similarity" or "HSP". Also see the "alignment" aggregator. =cut package Bio::DB::GFF::Aggregator::match; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "match" Args : none Status : Public =cut sub method { 'match' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : the list "similarity", "HSP" Args : none Status : Public =cut sub part_names { return qw(similarity HSP); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "match" Args : none Status : Public =cut sub main_name { return 'match'; } sub require_whole_object {1} 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/none.pm000444000766000024 150713155576320 20475 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::none -- No aggregation =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => 'none' ); =head1 DESCRIPTION Bio::DB::GFF::Aggregator::none can be used to indicate that you do not want any aggregation performed. It is equivalent to providing undef to the B<-aggregator> argument. It overrides disaggregate() and aggregate() so that they do exactly nothing. =cut package Bio::DB::GFF::Aggregator::none; use strict; use base qw(Bio::DB::GFF::Aggregator); sub disaggregate { my $self = shift; my $types = shift; # no change } sub aggregate { my $self = shift; my $features = shift; return; # no change } 1; BioPerl-1.007002/Bio/DB/GFF/Aggregator/orf.pm000444000766000024 330413155576320 20321 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::orf -- An aggregator for orf regions =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['orf','clone'], ); --------------------------- Aggregator method: orf Main method: -none- Sub methods: ORF --------------------------- =head1 DESCRIPTION Bio::DB::GFF::Aggregator::orf was written to work with the "cds" glyph. GFF files. It aggregates raw "ORF" features into "coding" features. This is basically identical to the "coding" aggregator, except that it looks for features of type "ORF" rather than "cds". =cut package Bio::DB::GFF::Aggregator::orf; use strict; use Bio::DB::GFF::Aggregator; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "orf" Args : none Status : Public =cut sub method { 'orf' } # sub require_whole_object { 1; } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : the list "CDS" Args : none Status : Public =cut sub part_names { return qw(ORF); } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/processed_transcript.pm000444000766000024 472113155576320 23777 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::processed_transcript -- Sequence Ontology Transcript =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['processed_transcript'], ); ------------------------------------------------------------------------ Aggregator method: processed_transcript Main method: mRNA Sub methods: CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site 5'-UTR 3'-UTR ------------------------------------------------------------------------ =head1 DESCRIPTION Bio::DB::GFF::Aggregator::processed_transcript is one of the default aggregators, and was written to be compatible with the Sequence Ontology canonical gene. It aggregates raw "exon," "CDS", "five_prime_UTR", "three_prime_UTR", "transcription_start_site" and "polyA_site" features into "mRNA" features. The UTRs may also be named "untranslated_region," "five_prime_untranslated_region," "three_prime_untranslated_region,", "5'-UTR," and other synonyms. =cut package Bio::DB::GFF::Aggregator::processed_transcript; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "processed_transcript" Args : none Status : Public =cut sub method { 'processed_transcript' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : the list CDS 5'-UTR 3'-UTR transcription_start_site polyA_site Args : none Status : Public =cut sub part_names { return qw(CDS 5'-UTR 3'-UTR transcription_start_site polyA_site UTR five_prime_untranslated_region three_prime_untranslated_region five_prime_UTR three_prime_UTR exon); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "mRNA" Args : none Status : Public =cut sub main_name { return 'mRNA'; } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/so_transcript.pm000444000766000024 506113155576320 22427 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::so_transcript -- Sequence Ontology Transcript =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['so_transcript'], ); ------------------------------------------------------------------------ Aggregator method: processed_transcript Main method: mRNA Sub methods: CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site 5'-UTR 3'-UTR ------------------------------------------------------------------------ =head1 DESCRIPTION Bio::DB::GFF::Aggregator::so_transcript is identical to the processed_transcript aggregator, which was designed to be compatible with the Sequence Ontology canonical gene. It aggregates raw "exon," "CDS", "five_prime_UTR", "three_prime_UTR", "transcription_start_site" and "polyA_site" features into "mRNA" features. The UTRs may also be named "untranslated_region," "five_prime_untranslated_region," "three_prime_untranslated_region,", "5'-UTR," and other synonyms. The processed_transcript aggregator is loaded by default, so this is only needed for backward compatibility. =cut package Bio::DB::GFF::Aggregator::so_transcript; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "processed_transcript" Args : none Status : Public =cut sub method { 'so_transcript' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : the list CDS 5'-UTR 3'-UTR transcription_start_site polyA_site Args : none Status : Public =cut sub part_names { return qw(CDS 5'-UTR 3'-UTR transcription_start_site polyA_site UTR five_prime_untranslated_region three_prime_untranslated_region five_prime_UTR three_prime_UTR exon); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "mRNA" Args : none Status : Public =cut sub main_name { return 'mRNA'; } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/transcript.pm000444000766000024 477113155576320 21735 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::transcript -- Transcript aggregator =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['transcript','clone'], ); ------------------------------------------------- Aggregator method: transcript Main method: transcript Sub methods: exon CDS 5'UTR 3'UTR TSS PolyA ------------------------------------------------- =head1 DESCRIPTION Bio::DB::GFF::Aggregator::transcript is one of the default aggregators, and was written to be compatible with the C elegans GFF files. It aggregates raw ""exon", "CDS", "5'UTR", "3'UTR", "polyA" and "TSS" features into "transcript" features. For compatibility with the idiosyncrasies of the Sanger GFF format, it expects that the full range of the transcript is contained in a main feature of type "Transcript" (notice the capital "T"). Internally this module is very simple. To override it with one that recognizes a main feature named "gene", simply follow this template: my $db = Bio::DB::GFF->new(...etc...) my $aggregator = Bio::DB::GFF::Aggregator->new(-method => 'transcript', -main_method => 'gene', -sub_parts => ['exon','CDS']); $db->add_aggregator($aggregator); =cut package Bio::DB::GFF::Aggregator::transcript; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "transcript" Args : none Status : Public =cut sub method { 'transcript' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : the list "intron", "exon" and "CDS" Args : none Status : Public =cut sub part_names { return qw(exon CDS 5'UTR 3'UTR TSS PolyA); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "transcript" Args : none Status : Public =cut sub main_name { return 'transcript'; } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/ucsc_acembly.pm000444000766000024 334213155576320 22166 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::ucsc_acembly -- UCSC acembly aggregator =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['transcript','clone'], ); ------------------------------------------------- Aggregator method: transcript Main method: transcript Sub methods: exon CDS 5'UTR 3'UTR TSS PolyA ------------------------------------------------- =head1 DESCRIPTION L =cut package Bio::DB::GFF::Aggregator::ucsc_acembly; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "acembly" Args : none Status : Public =cut sub method { 'acembly' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : empty list Args : none Status : Public =cut sub part_names { return (); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "transcript:acembly" Args : none Status : Public =cut sub main_name { return 'transcript:acembly'; } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Allen Day Eallenday@ucla.eduE. Copyright (c) 2002 Allen Day, University of California, Los Angeles. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm000444000766000024 331013155576320 22171 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::ucsc_ensgene -- UCSC ensGene aggregator =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['transcript','clone'], ); ------------------------------------------------- Aggregator method: ensgene Main method: transcript Sub methods: ensGene ------------------------------------------------- =head1 DESCRIPTION L =cut package Bio::DB::GFF::Aggregator::ucsc_ensgene; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "ensgene" Args : none Status : Public =cut sub method { 'ensgene' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : empty list Args : none Status : Public =cut sub part_names { return (); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "transcript:ensGene" Args : none Status : Public =cut sub main_name { return 'transcript:ensGene'; } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Allen Day Eallenday@ucla.eduE. Copyright (c) 2002 Allen Day, University of California, Los Angeles. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/ucsc_genscan.pm000444000766000024 330713155576320 22171 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::ucsc_genscan -- UCSC genscan aggregator =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['transcript','clone'], ); ------------------------------------------------- Aggregator method: genscan Main method: transcript Sub methods: genscan ------------------------------------------------- =head1 DESCRIPTION L =cut package Bio::DB::GFF::Aggregator::ucsc_genscan; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "genscan" Args : none Status : Public =cut sub method { 'genscan' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : empty list Args : none Status : Public =cut sub part_names { return (); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "transcript:genscan" Args : none Status : Public =cut sub main_name { return 'transcript:genscan'; } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Allen Day Eallenday@ucla.eduE. Copyright (c) 2002 Allen Day, University of California, Los Angeles. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/ucsc_refgene.pm000444000766000024 330713155576320 22166 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::ucsc_refgene -- UCSC refGene aggregator =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['transcript','clone'], ); ------------------------------------------------- Aggregator method: refgene Main method: transcript Sub methods: refGene ------------------------------------------------- =head1 DESCRIPTION L =cut package Bio::DB::GFF::Aggregator::ucsc_refgene; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "refgene" Args : none Status : Public =cut sub method { 'refgene' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : empty list Args : none Status : Public =cut sub part_names { return (); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "transcript:refGene" Args : none Status : Public =cut sub main_name { return 'transcript:refGene'; } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Allen Day Eallenday@ucla.eduE. Copyright (c) 2002 Allen Day, University of California, Los Angeles. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm000444000766000024 332113155576320 22172 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::ucsc_sanger22 -- UCSC sanger22 aggregator =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['transcript','clone'], ); ------------------------------------------------- Aggregator method: sanger22 Main method: transcript Sub methods: sanger22 ------------------------------------------------- =head1 DESCRIPTION L =cut package Bio::DB::GFF::Aggregator::ucsc_sanger22; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "sanger22" Args : none Status : Public =cut sub method { 'sanger22' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : empty list Args : none Status : Public =cut sub part_names { return (); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "transcript:sanger22" Args : none Status : Public =cut sub main_name { return 'transcript:sanger22'; } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Allen Day Eallenday@ucla.eduE. Copyright (c) 2002 Allen Day, University of California, Los Angeles. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm000444000766000024 340713155576320 23417 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo -- UCSC sanger22pseudo aggregator =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['transcript','clone'], ); ------------------------------------------------- Aggregator method: sanger22pseudo Main method: transcript Sub methods: sanger22pseudo ------------------------------------------------- =head1 DESCRIPTION L =cut package Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "sanger22pseudo" Args : none Status : Public =cut sub method { 'sanger22pseudo' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : empty list Args : none Status : Public =cut sub part_names { return (); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "transcript:sanger22pseudo" Args : none Status : Public =cut sub main_name { return 'transcript:sanger22pseudo'; } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Allen Day Eallenday@ucla.eduE. Copyright (c) 2002 Allen Day, University of California, Los Angeles. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/ucsc_softberry.pm000444000766000024 334513155576320 22574 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::ucsc_softberry -- UCSC softberry aggregator =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['transcript','clone'], ); ------------------------------------------------- Aggregator method: softberry Main method: transcript Sub methods: softberryGene ------------------------------------------------- =head1 DESCRIPTION L =cut package Bio::DB::GFF::Aggregator::ucsc_softberry; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "softberry" Args : none Status : Public =cut sub method { 'softberry' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : empty list Args : none Status : Public =cut sub part_names { return (); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "transcript:softberryGene" Args : none Status : Public =cut sub main_name { return 'transcript:softberryGene'; } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Allen Day Eallenday@ucla.eduE. Copyright (c) 2002 Allen Day, University of California, Los Angeles. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm000444000766000024 332013155576320 22374 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::ucsc_twinscan -- UCSC twinscan aggregator =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['transcript','clone'], ); ------------------------------------------------- Aggregator method: twinscan Main method: transcript Sub methods: twinscan ------------------------------------------------- =head1 DESCRIPTION L =cut package Bio::DB::GFF::Aggregator::ucsc_twinscan; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "twinscan" Args : none Status : Public =cut sub method { 'twinscan' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : empty list Args : none Status : Public =cut sub part_names { return (); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "transcript:twinscan" Args : none Status : Public =cut sub main_name { return 'transcript:twinscan'; } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Allen Day Eallenday@ucla.eduE. Copyright (c) 2002 Allen Day, University of California, Los Angeles. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Aggregator/ucsc_unigene.pm000444000766000024 332013155576320 22200 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Aggregator::ucsc_unigene -- UCSC UniGene aggregator =head1 SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['transcript','clone'], ); ------------------------------------------------- Aggregator method: unigene Main method: transcript Sub methods: unigene_2 ------------------------------------------------- =head1 DESCRIPTION L =cut package Bio::DB::GFF::Aggregator::ucsc_unigene; use strict; use base qw(Bio::DB::GFF::Aggregator); =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "unigene" Args : none Status : Public =cut sub method { 'unigene' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : empty list Args : none Status : Public =cut sub part_names { return (); } =head2 main_name Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "transcript" Args : none Status : Public =cut sub main_name { #transcript return 'transcript:uniGene_2'; } 1; __END__ =head1 BUGS None reported. =head1 SEE ALSO L, L =head1 AUTHOR Allen Day Eallenday@ucla.eduE. Copyright (c) 2002 Allen Day, University of California, Los Angeles. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Util000755000766000024 013155576320 15673 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/GFF/Util/Binning.pm000444000766000024 461413155576320 17757 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Util::Binning - binning utility for Bio::DB::GFF index =head1 SYNOPSIS use Bio::DB::GFF::Util::Binning qw(bin bin_bot bin_top); my $tier = bin($start,$stop,$min); =head1 DESCRIPTION This is a utility module that exports the functions bin(), bin_bot() and bin_top(). These functions translate a range on the genome into a named bin that is used as an index in the Bio::DB::GFF schema. The index makes certain range retrieval queries much faster. =head1 API The remainder of the document describes the function calls. No calls are exported by default, but must be imported explicitly. =over 4 =cut package Bio::DB::GFF::Util::Binning; use strict; require Exporter; use vars qw(@EXPORT @EXPORT_OK); use base qw(Exporter); @EXPORT_OK = qw(bin bin_bot bin_top); @EXPORT = @EXPORT_OK; use Bio::Root::Version; =item $bin_name = bin($start,$stop,$bin_size) Given a start, stop and bin size on the genome, translate this location into a bin name. In a list context, returns the bin tier name and the position that the bin begins. =cut sub bin { my ($start,$stop,$min) = @_; $start = abs($start); # to allow negative coordinates $stop = abs($stop); my $tier = $min; my ($bin_start,$bin_end); while (1) { $bin_start = int $start/$tier; $bin_end = int $stop/$tier; last if $bin_start == $bin_end; $tier *= 10; } return wantarray ? ($tier,$bin_start) : bin_name($tier,$bin_start); } =item $bottom = bin_bot($tier,$start) Given a tier name and a range start position, returns the lower end of the bin range. =cut sub bin_bot { my $tier = shift; my $pos = shift; bin_name($tier,int(abs($pos)/$tier)); } =item $top = bin_top($tier,$end) Given a tier name and the end of a range, returns the upper end of the bin range. =cut sub bin_top { my $tier = shift; my $pos = shift; bin_name($tier,int(abs($pos)/$tier)); # bin_name($tier,int($pos/$tier),+1); } sub bin_name { my ($tier, $int, $fudge) = @_; my $pos = abs($int) + ($fudge || 0); $pos = 0 if $pos < 0; sprintf("%d.%06d",$tier, $pos); } sub log10 { my $i = shift; log($i)/log(10); } 1; =back =head1 BUGS None known yet. =head1 SEE ALSO L, =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/GFF/Util/Rearrange.pm000444000766000024 507613155576320 20304 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::DB::GFF::Util::Rearrange - rearrange utility =head1 SYNOPSIS use Bio::DB::GFF::Util::Rearrange 'rearrange'; my ($arg1,$arg2,$arg3,$others) = rearrange(['ARG1','ARG2','ARG3'],@args); =head1 DESCRIPTION This is a different version of the _rearrange() method from Bio::Root::Root. It runs as a function call, rather than as a method call, and it handles unidentified parameters slightly differently. It exports a single function call: =over 4 =item @rearranged_args = rearrange(\@parameter_names,@parameters); The first argument is an array reference containing list of parameter names in the desired order. The second and subsequent arguments are a list of parameters in the format: (-arg1=>$arg1,-arg2=>$arg2,-arg3=>$arg3...) The function calls returns the parameter values in the order in which they were specified in @parameter_names. Any parameters that were not found in @parameter_names are returned in the form of a hash reference in which the keys are the uppercased forms of the parameter names, and the values are the parameter values. =back =head1 BUGS None known yet. =head1 SEE ALSO L, =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut package Bio::DB::GFF::Util::Rearrange; use strict; require Exporter; use vars qw(@EXPORT @EXPORT_OK); use base qw(Exporter); @EXPORT_OK = qw(rearrange); @EXPORT = qw(rearrange); use Bio::Root::Version; # default export sub rearrange { my($order,@param) = @_; return unless @param; my %param; if (ref $param[0] eq 'HASH') { %param = %{$param[0]}; } else { return @param unless (defined($param[0]) && substr($param[0],0,1) eq '-'); my $i; for ($i=0;$i<@param;$i+=2) { $param[$i]=~s/^\-//; # get rid of initial - if present $param[$i]=~tr/a-z/A-Z/; # parameters are upper case } %param = @param; # convert into associative array } my(@return_array); local($^W) = 0; my($key)=''; foreach $key (@$order) { my($value); if (ref($key) eq 'ARRAY') { foreach (@$key) { last if defined($value); $value = $param{$_}; delete $param{$_}; } } else { $value = $param{$key}; delete $param{$key}; } push(@return_array,$value); } push (@return_array,\%param) if %param; return @return_array; } 1; BioPerl-1.007002/Bio/DB/HIV000755000766000024 013155576320 15002 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/HIV/HIVAnnotProcessor.pm000555000766000024 1224113155576320 21046 0ustar00cjfieldsstaff000000000000# $Id: HIVAnnotProcessor.pm 221 2008-12-11 13:05:24Z maj $ # # BioPerl module for HIVAnnotProcessor # # Please direct questions and support issues to # # Cared for by Mark A. Jensen # # Copyright Mark A. Jensen # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME HIVAnnotProcessor - Adds HIV-specific annotations to Bio::SeqIO streams =head1 SYNOPSIS sub get_Stream_by_query { my ($self, $query ) = @_; my $stream = $self->get_seq_stream('-query' => $query, '-mode'=>'query'); return new Bio::DB::HIV::HIVAnnotProcessor( -hiv_query=>$query, -source_stream=>$stream ); } =head1 DESCRIPTION Bio::DB::HIV::HIVAnnotProcessor is chained to the C of a sequence stream returned from a query to the Los Alamos HIV sequence database made using L and L. It adds the annotations obtained in the C to the Bio::Seq objects themselves via the C<$seq-Eannotation> method. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Mark A. Jensen Email maj@fortinbras.us =head1 CONTRIBUTORS Mark A. Jensen =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::HIV::HIVAnnotProcessor; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Root::Root; use base qw( Bio::Root::Root); =head1 Constructor =head2 new Title : new Usage : my $obj = new HIVAnnotProcessor(); Function: Builds a new HIVAnnotProcessor object Returns : an instance of HIVAnnotProcessor Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($hiv_query, $source_stream) = $self->_rearrange([qw(HIV_QUERY SOURCE_STREAM)], @args); $hiv_query && $self->hiv_query($hiv_query); $source_stream && $self->source_stream($source_stream); return $self; } =head1 Bio::Factory::SequenceProcessorI compliance =head2 source_stream Title : source_stream Usage : $hap->source_stream($newval) Function: Example : Returns : value of source_stream (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub source_stream{ my $self = shift; if (@_) { $self->throw(-class=>'Bio::Root::BadParameter', -text=>'Requires a Bio::SeqIO as argument', -value=>$_[0]) unless $_[0]->isa('Bio::SeqIO'); } return $self->{'source_stream'} = shift if @_; return $self->{'source_stream'}; } =head2 next_seq Title : next_seq Usage : $seqobj = stream->next_seq Function: Reads the next sequence object from the stream, : adds annotations from the HIVQuery object according : to the sequence id, and returns sequence object Returns : a Bio::Seq sequence object Args : none =cut sub next_seq { my $self = shift; my $q = $self->hiv_query; my $seqo = $self->source_stream->next_seq; return $seqo unless ($q && $seqo); my $ac = $q->get_annotations_by_id($seqo->primary_id); $seqo->annotation($ac) if $ac; my $acc = $q->get_accessions_by_id($seqo->primary_id); $seqo->accession_number($acc) if $acc; return $seqo; } =head2 write_seq Title : write_seq Usage : $seqobj->write_seq Function: for HIVAnnotProcessor, throw an exception Example : Returns : Bio::Root::IOException Args : =cut sub write_seq{ my ($self,@args) = @_; $self->throw(-class=>'Bio::Root::IOException', -text=>'This stream is read-only', -value=>""); } =head1 HIVAnnotProcessor-specific methods =head2 hiv_query Title : hiv_query Usage : $obj->hiv_query($newval) Function: Example : Returns : value of hiv_query (a Bio::DB::Query::HIVQuery object) Args : on set, new value (an HIVQuery object, optional) =cut sub hiv_query{ my $self = shift; if (@_) { $self->throw(-class=>'Bio::Root::BadParameter', -text=>'Requires a Bio::DB::Query::HIVQuery as argument', -value=>$_[0]) unless ref $_[0] && $_[0]->isa('Bio::DB::Query::HIVQuery'); } return $self->{'hiv_query'} = shift if @_; return $self->{'hiv_query'}; } 1; BioPerl-1.007002/Bio/DB/HIV/HIVQueryHelper.pm000555000766000024 15361513155576320 20367 0ustar00cjfieldsstaff000000000000# $Id: HIVQueryHelper.pm 231 2008-12-11 14:32:00Z maj $ # # BioPerl module for Bio::DB::HIV::HIVQueryHelper # # Please direct questions and support issues to # # Cared for by Mark A. Jensen # # Copyright Mark A. Jensen # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::HIV::HIVQueryHelper - Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery =head1 SYNOPSIS Used in Bio::DB::Query::HIVQuery. No need to use directly. =head1 DESCRIPTION C contains a number of packages for use by L. Package C parses the C file, and allows access to it in the context of the relational database it represents (see APPENDIX for excruciating detail). Packages C, C, and C together create the query string parser that enables NCBI-like queries to be understood by C. They provide objects and operators to perform and simplify logical expressions involving C, C, and C<()> and return hash structures that can be handled by C routines. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Mark A. Jensen Email maj@fortinbras.us =head1 CONTRIBUTORS Mark A. Jensen =head1 APPENDIX The rest of the documentation details each of the contained packages. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::HIV::HIVQueryHelper; use strict; use Bio::Root::Root; # globals BEGIN { #exceptions @Bio::QueryStringSyntax::Exception::ISA = qw( Bio::Root::Exception); } 1; =head2 HIVSchema - objects/methods to manipulate a version of the LANL HIV DB schema =head3 HIVSchema SYNOPSIS $schema = new HIVSchema( 'lanl-schema.xml' ); @tables = $schema->tables; @validFields = $schema->fields; @validAliases = $schema->aliases; @query_aliases_for_coreceptor = $schema->aliases( 'SEQ_SAMple.SSAM_second_receptor' ); $pk_for_SequenceEntry = $schema->primarykey('SequenceEntry'); # returns 'SequenceEntry.SE_id' $fk_for_SEQ_SAMple_to_SequenceEntry = $schema->foreignkey('SEQ_SAMple', 'SequenceEntry'); # returns 'SEQ_SAMple.SSAM_SE_id' $table = $schema->tablepart('SEQ_SAMple.SSAM_badseq'); # returns 'SEQ_SAMple' $column = $schema->columnpart('SEQ_SAMple.SSAM_badseq'); # returns 'SSAM_badseq' =head3 HIVSchema DESCRIPTION HIVSchema methods are used in L for table, column, primary/foreign key manipulations based on the observed Los Alamos HIV Sequence Database (LANL DB) naming conventions for their CGI parameters. The schema is contained in an XML file (C) which is read into an HIVSchema object, in turn a property of the HIVQuery object. HIVSchema methods are used to build correct cgi queries in a way that attempts to preserve the context of the relational database the query parameters represent. =cut package # hide from PAUSE HIVSchema; # objects/methods to manipulate a version of the LANL HIV DB schema # stored in XML use XML::Simple; use Bio::Root::Root; use strict; ### constructor =head3 HIVSchema CONSTRUCTOR =head4 HIVSchema::new Title : new Usage : $schema = new HIVSchema( "lanl-schema.xml "); Function: Example : Returns : an HIVSchema object Args : XML filename =cut sub new { my $class = shift; my @args = @_; my $self = {}; if ($args[0]) { $self->{schema_ref} = loadHIVSchema($args[0]); } bless($self, $class); return $self; } ### object methods =head3 HIVSchema INSTANCE METHODS =head4 HIVSchema tables Title : tables Usage : $schema->tables() Function: get all table names in schema Example : Returns : array of table names Args : none =cut sub tables { # return array of all tables in schema local $_; my $self = shift; my $sref = $self->{schema_ref}; Bio::Root::Root->throw("schema not initialized") unless $sref; my @k = grep(/\./, keys %$sref); my %ret; foreach (@k) { s/\..*$//; $ret{$_}++; } @k = sort keys %ret; return @k; } =head4 HIVSchema columns Title : columns Usage : $schema->columns( [$tablename] ); Function: return array of columns for specified table, or all columns in schema, if called w/o args Example : Returns : Args : tablename or fieldname string =cut sub columns { # return array of columns for specified table # all columns in schema, if called w/o args local $_; my $self = shift; my ($tbl) = @_; my $sref = $self->{schema_ref}; Bio::Root::Root->throw("schema not initialized") unless $sref; # trim column name $tbl =~ s/\..*$//; # check if table exists return () unless grep(/^$tbl$/i, $self->tables); my @k = sort keys %$sref; @k = grep (/^$tbl\./i, @k); foreach (@k) { s/^$tbl\.//; } return @k; } =head4 HIVSchema fields Title : fields Usage : $schema->fields(); Function: return array of all fields in schema, in format "table.column" Example : Returns : array of all fields Args : none =cut sub fields { # return array of all fields (Table.Column format) in schema my $self = shift; my $sref = $self->{schema_ref}; Bio::Root::Root->throw("schema not initialized") unless $sref; my @k = sort keys %{$sref}; return @k; } =head4 HIVSchema options Title : options Usage : $schema->options(@fieldnames) Function: get array of options (i.e., valid match data strings) available to specified field Example : Returns : array of match data strings Args : [array of] fieldname string[s] in "table.column" format =cut sub options { # return array of options available to specified field my $self = shift; my ($sfield) = @_; my $sref = $self->{schema_ref}; Bio::Root::Root->throw("schema not initialized") unless $sref; return $$sref{$sfield}{option} ? @{$$sref{$sfield}{option}} : (); } =head4 HIVSchema aliases Title : aliases Usage : $schema->aliases(@fieldnames) Function: get array of aliases to specified field[s] Example : Returns : array of valid query aliases for fields as spec'd in XML file Args : [an array of] fieldname[s] in "table.column" format =cut sub aliases { # return array of aliases to specified field my $self = shift; my ($sfield) = @_; my $sref = $self->{schema_ref}; my @ret; Bio::Root::Root->throw("schema not initialized") unless $sref; if ($sfield) { return $$sref{$sfield}{alias} ? @{$$sref{$sfield}{alias}} : (); } else { # all valid aliases map {push @ret, @{$$sref{$_}{alias}} if $$sref{$_}{alias}} $self->fields; return @ret; } } =head4 HIVSchema ankh Title : ankh (annotation key hash) Usage : $schema->ankh(@fieldnames) Function: return a hash translating fields to annotation keys for the spec'd fields. (Annotation keys are used for parsing the tab-delimited response to Bio::DB::Query::HIVQuery::_do_lanl_request.) Example : Returns : hash ref Args : [an array of] fieldname[s] in "table.column" format =cut sub ankh { # return hash translating sfields to annotation keys for specified sfield(s) my $self = shift; my %ret = (); my @sfields = @_; my $sref = $self->{schema_ref}; Bio::Root::Root->throw("schema not initialized") unless $sref; foreach (@sfields) { next unless $$sref{$_}{ankey}; $ret{$_} = {'ankey'=>$$sref{$_}{ankey},'antype'=>$$sref{$_}{antype}}; } return %ret; } =head4 HIVSchema tablepart Title : tablepart (alias: tbl) Usage : $schema->tbl(@fieldnames) Function: return the portion of the fieldname[s] that refer to the db table Example : $schema->tbl('SequenceEntry.SE_id'); # returns 'SequenceEntry' Returns : table name as string Args : [an array of] fieldname[s] in "table.column" format =cut sub tablepart { # return the 'Table' part of the specified field(s) my $self = shift; my @sfields = @_; Bio::Root::Root->throw("schema not initialized") unless $self->{schema_ref}; my ($squish,@ret, %ret); if ($sfields[0] eq '-s') { # squish : remove duplicates from the returned array $squish=1; shift @sfields; } foreach (@sfields) { push @ret, /^(.*)\./; } if ($squish) { # arg order is clobbered @ret{@ret} = undef; @ret = keys %ret; } return (wantarray ? @ret : $ret[0]); } sub tbl { # tablepart alias shift->tablepart(@_); } =head4 HIVSchema columnpart Title : columnpart (alias: col) Usage : $schema->col(@fieldnames) Function: return the portion of the fieldname[s] that refer to the db column Example : $schema->col('SequenceEntry.SE_id'); # returns 'SE_id' Returns : column name as string Args : [an array of] fieldname[s] in "table.column" format =cut sub columnpart { # return the 'Column' part of the specified field(s) my $self = shift; my @sfields = @_; Bio::Root::Root->throw("schema not initialized") unless $self->{schema_ref}; my @ret; foreach (@sfields) { push @ret, /\.(.*)$/; } return (wantarray ? @ret : $ret[0]); } sub col { # columnpart alias shift->columnpart(@_); } =head4 HIVSchema primarykey Title : primarykey [alias: pk] Usage : $schema->pk(@tablenames); Function: return the primary key of the specified table[s], as judged by the syntax of the table's[s'] fieldnames Example : $schema->pk('SequenceEntry') # returns 'SequenceEntry.SE_id' Returns : primary key fieldname[s] in "table.column" format, or null if no pk exists Args : [an array of] table name[s] (fieldnames are ok, table part used) =cut sub primarykey { # return the primary key (in Table.Column format) of specified table(s) my $self = shift; my @tbl = @_; my @ret; Bio::Root::Root->throw("schema not initialized") unless $self->{schema_ref}; foreach my $tbl (@tbl) { # trim column name $tbl =~ s/\..*$//; grep(/^$tbl$/i, $self->tables) ? push(@ret, grep(/\.[0-9a-zA-Z]+_id/, grep(/$tbl/i,$self->fields))) : push(@ret, ""); } return (wantarray ? @ret : $ret[0]); } sub pk { # primarykey alias shift->primarykey(@_); } =head4 HIVSchema foreignkey Title : foreignkey [alias: fk] Usage : $schema->fk($intable [, $totable]) Function: return foreign key fieldname in table $intable referring to table $totable, or all foreign keys in $intable if $totable unspec'd Example : $schema->fk('AUthor', 'SequenceEntry'); # returns 'AUthor_AU_SE_id' Returns : foreign key fieldname[s] in "table.column" format Args : tablename [, optional foreign table name] (fieldnames are ok, table part used) =cut sub foreignkey { # return foreign key in in-table ($intbl) to to-table ($totbl) # or all foreign keys in in-table if to-table not specified # keys returned in Table.Column format my $self = shift; my ($intbl, $totbl) = @_; Bio::Root::Root->throw("schema not initialized") unless $self->{schema_ref}; # trim col names $intbl =~ s/\..*$//; $totbl =~ s/\..*$// if $totbl; # check if in-table exists return () unless grep( /^$intbl/i, $self->tables); my @ret = grep( /$intbl\.(?:[0-9a-zA-Z]+_){2,}id/i, $self->fields); if ($totbl) { my $tpk = $self->primarykey($totbl); return (wantarray ? () : "") unless grep( /^$totbl/i, $self->tables) && $tpk; ($tpk) = ($tpk =~ /\.(.*)$/); @ret = grep( /$tpk$/, @ret); return (wantarray ? @ret : $ret[0]); } else { # return all foreign keys in in-table return @ret; } } sub fk { # foreignkey alias shift->foreignkey(@_); } =head4 HIVSchema foreigntable Title : foreigntable [alias ftbl] Usage : $schema->ftbl( @foreign_key_fieldnames ); Function: return tablename of table that foreign keys points to Example : $schema->ftbl( 'AUthor.AU_SE_id' ); # returns 'SequenceEntry' Returns : tablename Args : [an array of] fieldname[s] in "table.column" format =cut sub foreigntable { # return table name that foreign key(s) point(s) to my $self = shift; my @fk = @_; my @ret; Bio::Root::Root->throw("schema not initialized") unless $self->{schema_ref}; foreach (@fk) { my ($mnem, $fmnem) = /\.([0-9a-zA-Z]+)_([0-9a-zA-Z]+)_.*$/; next unless $mnem && $fmnem; # lookup based on Table.Column format of fields my $sf = [grep( /^[0-9a-zA-Z]+\.$fmnem\_/, $self->fields )]->[0]; next unless $sf; ($sf) = ($sf =~ /^([0-9a-zA-Z]+)\./); push @ret, $sf; } return (wantarray ? @ret : $ret[0]); } sub ftbl { # foreigntable alias shift->foreigntable(@_); } =head4 HIVSchema find_join Title : find_join Usage : $sch->find_join('Table1', 'Table2') Function: Retrieves a set of foreign and primary keys (in table.column format) that represents a join path from Table1 to Table2 Example : Returns : an array of keys (as table.column strings) -or- an empty array if Table1 == Table2 -or- undef if no path exists Args : two table names as strings =cut sub find_join { my $self = shift; my ($tgt, $tbl) = @_; my ($stack, $revstack, $found, $revcut) = ([],[], 0, 4); $self->_find_join_guts($tgt, $tbl, $stack, \$found); if ($found) { if (@$stack > $revcut) { # reverse order of tables, see if a shorter path emerges $found = 0; $self->_find_join_guts($tgt, $tbl, $revstack, \$found, 1); return (@$stack <= @$revstack ? @$stack : @$revstack); } return @$stack; } else { return undef; } } =head4 HIVSchema _find_join_guts Title : _find_join_guts Usage : $sch->_find_join_guts($table1, $table2, $stackref, \$found, $reverse) (call with $stackref = [], $found=0) Function: recursive guts of find_join Example : Returns : if a path is found, $found==1 and @$stackref contains the keys in table.column format representing the path; if a path is not found, $found == 0 and @$stackref contains garbage Args : $table1, $table2 : table names as strings $stackref : an arrayref to an empty array \$found : a scalar ref to the value 0 $rev : if $rev==1, the arrays of table names will be reversed; this can give a shorter path if cycles exist in the schema graph =cut sub _find_join_guts { my $self = shift; my ($tbl, $tgt, $stack, $found, $rev) = @_; return () if $tbl eq $tgt; my $k = $self->pk($tbl); if ($k) { # all fks pointing to pk my @fk2pk = map { $self->fk($_, $k) || () } ($rev ? reverse $self->tables : $self->tables); # skip keys already on stack if (@$stack) { (@$stack == 1) && do { @fk2pk = grep (!/$$stack[0]/, @fk2pk); }; (@$stack > 1 ) && do { @fk2pk = map { my $f=$_; grep(/$f/, @$stack) ? () : $f } @fk2pk; }; } foreach my $f2p (@fk2pk) { # tables with fks pointing to pk push @$stack, $f2p; if ($self->tbl($f2p) eq $tgt) { # this fk's table is the target # found it $$found = 1; return; } else { #keep looking $self->_find_join_guts($self->tbl($f2p), $tgt, $stack, $found, $rev); return if $$found; } } } # all fks in $tbl my @fks = ($rev ? reverse $self->fk($tbl) : $self->fk($tbl)); #skip keys already on stack if (@$stack) { (@$stack == 1) && do { @fks = grep(!/$$stack[0]/, @fks); }; (@$stack > 1) && do { @fks = map { my $f=$_; grep(/$f/, @$stack) ? () : $f } @fks; }; } # all fks in table if (@fks) { for my $f (@fks) { push @$stack, $f; if ($self->ftbl($f) eq $tgt) { #found it $$found = 1; return; } else { $self->_find_join_guts($self->ftbl($f), $tgt, $stack, $found, $rev); $$found ? return : pop @$stack; } } } else { pop @$stack; return; } } =head4 HIVSchema loadSchema Title : loadHIVSchema [alias: loadSchema] Usage : $schema->loadSchema( $XMLfilename ) Function: read (LANL DB) schema spec from XML Example : $schema->loadSchema('lanl-schema.xml'); Returns : hashref to schema data Keys are fieldnames in "table.column" format. Each value is a hashref with the following properties: {name} : HIVWEB 'table.column' format fieldname, can be used directly in the cgi query {aliases} : ref to array containing valid aliases/shortcuts for {name}; can be used in routines creating the HTML query {options} : ref to array containing valid matchdata for this field can be used directly in the HTML query {ankey} : contains the annotation key for this field used with Bioperl annotation objects {..attr..}: ..value_of_attr.. for this field (app-specific metadata) Args : =cut sub loadHIVSchema { my $fn = shift; Bio::Root::Root->throw("loadHIVSchema: schema file not found") unless -e $fn; my $q = XML::Simple->new(ContentKey=>'name',NormalizeSpace=>2,ForceArray=>1); my %ret; my $ref = $q->XMLin($fn); my @sf = keys %{$$ref{sfield}}; foreach (@sf) { my $h = $$ref{sfield}{$_}; $ret{$_} = $h; foreach my $ptr ($$h{option}, $$h{alias}) { if ($ptr) { # kludge for XMLin: appears to convert to arrays, if there # exists a tag without content, but to convert to hashes # with content as key, if all tags possess content if (ref($ptr) eq 'HASH') { my @k = keys %{$ptr}; if (grep /desc/, keys %{$ptr->{$k[0]}}) { # slurp the desc's $$h{desc} = [ map { $$ptr{$_}->{desc} } @k ]; } # now overwrite with keys (descs in same order...) $ptr = [@k]; } elsif (ref($ptr) eq 'ARRAY') { $ptr = [map { ref eq 'HASH' ? $_->{name} : $_ } @{$ptr}] } else { 1; # stub : doh! } } } for my $ptr ($$h{ankey}) { # flatten my $ank = [keys %{$ptr}]->[0]; if (!defined $ank) { delete $$h{ankey}; } else { $h->{antype} = $ptr->{$ank}{antype}; $ptr = $ank; } } } return \%ret; } sub loadSchema { my $self = shift; $self->{schema_ref} = loadHIVSchema(shift); } # below, dangerous =head4 HIVSchema _sfieldh Title : _sfieldh Usage : $schema->_sfieldh($fieldname) Function: get hashref to the specified field hash Example : Returns : hashref Args : fieldname in "table.column" format =cut sub _sfieldh { # return reference to the specified field hash my $self = shift; my ($sfield) = @_; return ${$self->{schema_ref}}{$sfield}; } 1; =head2 Class QRY - a query algebra for HIVQuery =head3 QRY SYNOPSIS $Q = new QRY( new R( new Q('coreceptor', 'CXCR4'), new Q('country', 'ZA') ) ); QRY::Eq(QRY::And($Q, $Q), $Q); # returns 1 QRY::Eq(QRY::Or($Q, $Q), $Q); # returns 1 $Q2 = $Q1->clone; $Q2 = new QRY( new R( new Q( 'coreceptor', 'CCR5' ), new Q( 'country', 'ZA') ) ); (QRY::And($Q, $Q2))->isnull; # returns 1 $Q3 = QRY::Or($Q, $Q2); print $Q3->A; # prints '(CCR5 CXCR4)[coreceptor] (ZA)[country]' =head3 QRY DESCRIPTION The QRY package provides a query parser for L. Currently, the parser supports AND, OR, and () operations. The structure of the LANL cgi makes it tricky to perform NOTs, though this could be implemented if the desire were great. Two class methods do the work. C does a first-pass parse of the query string. C interprets the parse tree as returned by C and produces an array of hash structures that can be used directly by C query execution methods. Validation of query fields and options is performed at the C level, not here. C objects are collections of C (or request) objects, which are in turn collections of C (or atomic query) objects. C objects represent a query on a single field, with match data options Ced together, e.g. C<(A B)[subtype]>. C objects collect C objects that could be processed in a single HTTP request; i.e., a set of atomic queries each having different fields Ced together, such as (A B)[subtype] AND ('CCR5')[coreceptor] AND (US CA)[country] The C object collects Cs that cannot be reduced (through logical operations) to a single HTTP request, e.g. ((C)[subtype] AND (SI)[phenotype]) OR ( (D)[subtype] AND (NSI)[phenotype] ), which cannot be got in one go through the current LANL cgi implementation (as far as I can tell). The parser will simplify something like ((C)[subtype] AND (SI)[phenotype]) OR ((C)[subtype] AND (NSI)[phenotype]) to the single request (C)[subtype] AND (NSI SI)[phenotype] however. The operators C<&> and C<|> are overloaded to C and C, to get Perl precedence and grouping for free. C is overloaded to get symbolic tests such as C. C<==> is overloaded with C for convenience. No overloading is done for C or C. =cut # a query algebra for HIVQuery # # Each Q object is an 'atomic' query, written as (data)[field] # (a b ...)[X] equals (a)[X] | (b)[X] | ... # Each R object represents a single HTTP request to the db # contains an array of Q (atomic) objects (q1, q2, ...) # the R object is interpreted as q1 & q2 & ... # Each QRY object represents a series of HTTP requests to the db # contains an array of R (request) objects (R1, R2, ...) # the QRY object is interpreted as R1 | R2 | ... # # & and | operations are specified for each type package # hide from PAUSE QRY; use strict; $QRY::NULL = new QRY(); use overload "|" => \&Or, "&" => \&And, "bool" => \&Bool, "==" => \&Eq; # query language emulator # supports only AND and OR, any groupings # # syntax rules: # query atom: bareword [field] OR (bareword ...) [field] # only single bareword allowed between [] # annotation fields in {} (only bareword lists allowed between {}) # () can group query atoms joined by operators (AND or OR) # () containing only barewords MUST be followed by a field descriptor [field] # empty [] not allowed # query atoms joined with AND by default # barewords are associated (ORed within) the next field descriptor in the line # follow the parse tree, creating new QRY objects as needed in @q, and # construct a logical expression using & and | symbols. # These are overloaded for doing ands and ors on QRY objects; # to get the final QRY object, eval the resulting expression $q_expr. # QRY object will be translated into (possibly multiple) hashes # conforming to HIVQuery parameter requirements. =head4 QRY _make_q Title : _make_q Usage : QRY::_make_q($parsetree) Function: creates hash structures suitable for HIVQuery from parse tree returned by QRY::_parse_q Example : Returns : array of hashrefs of query specs Args : a hashref =cut sub _make_q { my $ptree = shift; my ($q_expr, @q, @an, $query, @dbq); _make_q_guts($ptree, \$q_expr, \@q, \@an); $query = eval $q_expr; throw Bio::Root::Root(-class=>'Bio::Root::Exception', -text=>$@, -value=>$q_expr) if $@; return {} if $query->isnull; foreach my $rq ($query->requests) { my $h = {'query'=>{}}; foreach ($rq->atoms) { my @d = split(/\s+/, $_->dta); foreach my $d (@d) { $d =~ s/[+]/ /g; ###! _ to [+] $d =~ s/'//g; } $h->{'query'}{$_->fld} = (@d == 1) ? $d[0] : [@d]; } $h->{'annot'} = [@an] if @an; push @dbq, $h; } return @dbq; } =head4 QRY _make_q_guts Title : _make_q_guts (Internal class method) Usage : _make_q_guts($ptree, $q_expr, $qarry, $anarry) Function: traverses the parse tree returned from QRY::_parse_q, checking syntax and creating HIVQuery-compliant query structures Example : Returns : Args : $parse_tree (hashref), $query_expression (scalar string ref), $query_array (array ref : stack for returning query structures), $annotation_array (array ref : stack for returning annotation fields) =cut sub _make_q_guts { my ($ptree, $q_expr, $qarry, $anarry) = @_; my (@words, $o); eval { # catch foreach (@{$ptree->{cont}}) { m{^AND$} && do { $$q_expr .= "&"; next; }; m{^OR$} && do { $$q_expr .= "|"; next; }; m{^HASH} && do { for my $dl ($_->{delim}) { ($dl =~ m{\(}) && do { if (grep /^HASH/, @{$_->{cont}}) { $$q_expr .= "&" unless !$$q_expr || !length($$q_expr) || (substr($$q_expr, -1, 1) =~ /[&|(]/); $$q_expr .= "("; _make_q_guts($_,$q_expr,$qarry,$anarry); $$q_expr .= ")"; } else { my @c; my $c = join(' ',@{$_->{cont}}); $c =~ s/,/ /g; Bio::Root::Root->throw("query syntax error: unmatched ['\"]") if (@c = ($c =~ /(['"])/g)) % 2; @c = split(/\s*(['"])\s*/, $c); do { $c = shift @c; if ($c =~ m{['"]}) { $c = join('', ($c, shift @c, shift @c)); $c =~ s/\s+/+/g; ###! _ to + push @words, $c; } else { push @words, split(/\s+/,$c); } } while @c; } last; }; ($dl =~ m{\[}) && do { Bio::Root::Root->throw("syntax error: empty field descriptor") unless @{$_->{cont}}; Bio::Root::Root->throw("syntax error: more than one field descriptor in square brackets") unless @{$_->{cont}} == 1; push @{$qarry}, new QRY( new R( new Q( $_->{cont}->[0], @words))); # add default operation if nec $$q_expr .= "&" unless !$$q_expr || !length($$q_expr) || (substr($$q_expr, -1, 1) =~ /[&|(]/); $$q_expr .= "\$q[".$#$qarry."]"; @words = (); last; }; ($dl =~ m{\{}) && do { foreach my $an (@{$_->{cont}}) { ($an =~ /^HASH/) && do { if ($an->{delim} eq '[') { push @$anarry, @{$an->{cont}}; } else { Bio::Root::Root->throw("query syntax error: only field descriptors (with or without square brackets) allowed in annotation spec"); } next; }; do { #else push @$anarry, $an; next; }; } last; }; do { 1; #else stub }; } next; }; do { # else, bareword if ($o) { $words[-1] .= "+$_"; ####! _ to + } else { push @words, $_; } m/['"]/ && ($o = !$o); }; } # @{ptree->{cont}} Bio::Root::Root->throw("query syntax error: no search fields specified") unless $$q_expr =~ /q\[[0-9]+\]/; }; $@ ? throw Bio::Root::Root(-class=>'Bio::QueryStringSyntax::Exception', -text=>$@, -value=>$$q_expr) : return 1; } =head4 QRY _parse_q Title : _parse_q Usage : QRY::_parse_q($query_string) Function: perform first pass parse of a query string with some syntax checking, return a parse tree suitable for QRY::_make_q Example : QRY::_parse_q(" to[be] OR (not to)[be] "); Returns : hashref Args : query string =cut # parse qry string into a branching tree structure # each branch tagged by the opening delimiter ( key 'delim' ) # content (tokens and subbranch hashes) placed in l2r order in # @{p->{cont}} sub _parse_q { local $_; my $qstr = shift; my $illegal = qr/[^a-zA-Z0-9-_<>=,\.\(\[\{\}\]\)\s'"]/; my $pdlm = qr/[\{\[\(\)\]\}]/; my %md = ('('=>')', '['=>']','{'=>'}'); my @tok = grep !/^\s*$/, split /($pdlm)/, $qstr; return {} unless @tok; my @pstack = (); my @dstack = (); my ($ptree, $p); eval { #catch Bio::Root::Root->throw("query syntax error: illegal character") if $qstr =~ /$illegal/; $ptree = $p = {'delim'=>'*'}; foreach (@tok) { #trim whsp s/^\s+//; s/\s+$//; m{[\(\[\{]} && do { my $new = {'delim'=>$_}; $p->{cont} = [] unless $p->{cont}; push @{$p->{cont}}, $new; push @pstack, $p; push @dstack, $_; $p = $new; next; }; m{[\)\]\}]} && do { my $d = pop @dstack; if ($md{$d} eq $_) { $p = pop @pstack; Bio::Root::Root->throw("query syntax error: unmatched \"$_\"") unless $p; } else { Bio::Root::Root->throw("query syntax error: saw \"$_\" before matching \"$md{$d}\""); } next; }; do { # else $p->{cont} = [] unless $p->{cont}; push @{$p->{cont}}, split(/\s+/); }; } }; $@ ? throw Bio::Root::Root(-class=>'Bio::QueryStringSyntax::Exception', -text=>$@, -value=>"") : return $ptree; } ## QRY constructor =head3 QRY CONSTRUCTOR =head4 QRY Constructor Title : QRY constructor Usage : $QRY = new QRY() Function: Example : Returns : Args : array of R objects, optional =cut sub new { my $class = shift; my @args = @_; my $self = {}; $self->{requests} = []; bless($self, $class); $self->put_requests(@args) if @args; return $self; } ## QRY instance methods =head3 QRY INSTANCE METHODS =head4 QRY requests Title : requests Usage : $QRY->requests Function: get/set array of requests comprising this QRY object Example : Returns : Args : array of class R objects =cut sub requests { my $self = shift; $self->put_requests(@_) if @_; return @{$self->{'requests'}}; } =head4 QRY put_requests Title : put_requests Usage : $QRY->put_request(@R) Function: add object of class R to $QRY Example : Returns : Args : [an array of] of class R object[s] =cut sub put_requests { my $self = shift; my @args = @_; foreach (@args) { Bio::Root::Root->throw('requires type R (request)') unless ref && $_->isa('R'); push @{$self->{requests}}, $_; } return @args; } =head4 QRY isnull Title : isnull Usage : $QRY->isnull Function: test if QRY object is null Example : Returns : 1 if null, 0 otherwise Args : =cut sub isnull { my $self = shift; return ($self->requests) ? 0 : 1; } =head4 QRY A Title : A Usage : print $QRY->A Function: get a string representation of QRY object Example : Returns : string scalar Args : =cut sub A { my $self = shift; return join( "\n", map {$_->A} $self->requests ); } =head4 QRY len Title : len Usage : $QRY->len Function: get number of class R objects contained by QRY object Example : Returns : scalar Args : =cut sub len { my $self = shift; return scalar @{$self->{'requests'}}; } =head4 QRY clone Title : clone Usage : $QRY2 = $QRY1->clone; Function: create and return a clone of the object Example : Returns : object of class QRY Args : =cut sub clone { local $_; my $self = shift; my $ret = QRY->new(); foreach ($self->requests) { $ret->put_requests($_->clone); } return $ret; } ## QRY class methods =head3 QRY CLASS METHODS =head4 QRY Or Title : Or Usage : $QRY3 = QRY::Or($QRY1, $QRY2) Function: logical OR for QRY objects Example : Returns : a QRY object Args : two class QRY objects =cut sub Or { local $_; my ($q, $r, $rev_f) = @_; Bio::Root::Root->throw('requires type QRY') unless ref($q) && $q->isa('QRY'); Bio::Root::Root->throw('requires type QRY') unless ref($r) && $r->isa('QRY'); if ($q->isnull) { return $r->clone; } elsif ($r->isnull) { return $q->clone; } do {my $qq = $q; $q=$r; $r=$qq} if ($q->len > $r->len); my @rq_r = $r->requests; my @rq_q = $q->requests; my (@cand_rq, @ret_rq); # search for simplifications my @now = @rq_q; my @nxt =(); foreach (@rq_r) { my $found = 0; while (my $rq = pop @now) { my @result = R::Or($rq, $_); if (@result==1) { push @cand_rq, $result[0]->clone; $found = 1; last; } else { push @nxt, $rq; } } push @cand_rq, $_->clone unless ($found); # @now becomes unexamined @rq_q's plus failed @rq_q's @now = (@now, @nxt); } push @cand_rq, map {$_->clone} @now; # add all failed @rq_q's # squeeze out redundant requests while (my $rq = pop @cand_rq) { push @ret_rq, $rq unless @cand_rq && grep {R::Eq($rq, $_)} @cand_rq; } return new QRY( @ret_rq ); } =head4 QRY And Title : And Usage : $QRY3 = QRY::And($QRY1, $QRY2) Function: logical AND for QRY objects Example : Returns : a QRY object Args : two class QRY objects =cut sub And { my ($q, $r, $rev_f) = @_; Bio::Root::Root->throw('requires type QRY') unless ref($q) && $q->isa('QRY'); Bio::Root::Root->throw('requires type QRY') unless ref($r) && $r->isa('QRY'); return ($QRY::NULL) if ($q->isnull || $r->isnull); my (@cand_rq, @ret_rq); foreach my $rq_r ($r->requests) { foreach my $rq_q ($q->requests) { my ($rq) = R::And($rq_r, $rq_q); push @cand_rq, $rq unless $rq->isnull; } } return $QRY::NULL unless @cand_rq; # squeeze out redundant requests while (my $rq = pop @cand_rq) { push @ret_rq, $rq unless @cand_rq && grep {R::Eq($rq, $_)} @cand_rq; } return new QRY( @ret_rq ); } =head4 QRY Bool Title : Bool Usage : QRY::Bool($QRY1) Function: allows symbolic testing of QRY object when bool overloaded Example : do {stuff} if $QRY1 *same as* do {stuff} if !$QRY1->isnull Returns : Args : a class QRY object =cut sub Bool { my $q = shift; Bio::Root::Root->throw('requires type QRY') unless ref($q) && $q->isa('QRY'); return $q->isnull ? 0 : 1; } =head4 QRY Eq Title : Eq Usage : QRY::Eq($QRY1, $QRY2) Function: test if R objects in two QRY objects are the same (irrespective of order) Example : Returns : 1 if equal, 0 otherwise Args : two class QRY objects =cut sub Eq { my ($q, $r, $rev_f) = @_; Bio::Root::Root->throw('requires type QRY') unless ref($q) && $q->isa('QRY'); Bio::Root::Root->throw('requires type QRY') unless ref($r) && $r->isa('QRY'); return 0 unless $q->len == $r->len; foreach my $rq_q ($q->requests) { my $found = 0; foreach my $rq_r ($r->requests) { if (R::Eq($rq_q,$rq_r)) { $found = 1; last; } } return 0 unless $found; } return 1; } 1; =head2 Class R - request objects for QRY algebra =head3 R SYNOPSIS $R = new R( $q1, $q2 ); $R->put_atoms($q3); $R->del_atoms('coreceptor', 'phenotype'); return $R->clone; $R1 = new R( new Q('subtype', 'B') ); $R2 = new R( new Q('subtype', 'B C'), new Q('country', 'US') ); R::Eq( (R::And($R1, $R2))[0], new R( new Q('subtype', 'B' ), new Q('country', 'US') )); # returns 1 QRY::Eq( new QRY(R::Or($R1, $R2)), new QRY($R1, $R2) ); # returns 1 R::In( (R::And($R1, $R2))[0], $R1 ); # returns 1 =head3 R DESCRIPTION Class R objects contain a list of atomic queries (class Q objects). Each class R object represents a single HTTP request to the LANL DB. When converted to a DB query, the class Q objects contained by an R object are effectively Ced. =cut package # hide from PAUSE R; use strict; $R::NULL = R->new(); ## R constructor =head3 R CONSTRUCTOR =head4 R constructor Title : R constructor Usage : $R = new R() Function: create a new R (request) object Example : Returns : class R (request) object Args : optional, array of class Q objects =cut sub new { my $class = shift; my @args = @_; my $self = {}; $self->{atoms} = {}; bless($self, $class); $self->put_atoms(@args) if @args; return $self; } ## R instance methods =head3 R INSTANCE METHODS =head4 R len Title : len Usage : $R->len Function: get number of class Q objects contained in R object Example : Returns : scalar Args : =cut sub len { my $self = shift; return scalar @{[keys %{$self->{'atoms'}}]}; } =head4 R atoms Title : atoms Usage : $R->atoms( [optional $field]) Function: get array of class Q (atomic query) objects in class R object Example : $R->atoms(); $R->atoms('coreceptor') Returns : array of class Q objects (all Qs or those corresponding to $field if present) Args : optional, scalar string =cut sub atoms { local $_; # returns an array of atoms # no arg: all atoms; # args: atoms with specified fields my $self = shift; my @flds = (@_ ? @_ : keys %{$self->{'atoms'}}); return wantarray ? map { $self->{'atoms'}->{$_} } @flds : $self->{'atoms'}->{$flds[0]}; } =head4 R fields Title : fields Usage : $R->fields Function: get array of fields of all Q objects contained in $R Example : Returns : array of scalars Args : =cut sub fields { my $self = shift; return keys %{$self->{'atoms'}}; } =head4 R put_atoms Title : put_atoms Usage : $R->put_atoms( @q ) Function: AND an atomic query (class Q object) to the class R object's list Example : Returns : void Args : an [array of] class Q object[s] =cut sub put_atoms { # AND this atom to the request local $_; my $self = shift; my @args = @_; foreach (@args) { Bio::Root::Root->throw('requires type Q (atom)') unless ref && $_->isa('Q'); if ($self->atoms($_->fld)) { my $a = Q::qand( $self->atoms($_->fld), $_ ); if ($a->isnull) { delete $self->{'atoms'}->{$_->fld}; } else { $self->{atoms}->{$_->fld} = $a->clone; } } else { $self->{atoms}->{$_->fld} = $_->clone; } } return; } =head4 R del_atoms Title : del_atoms Usage : $R->del_atoms( @qfields ) Function: removes class Q objects from R object's list according to the field names given in arguments Example : Returns : the class Q objects deleted Args : scalar array of field names =cut sub del_atoms { # remove atoms by field from request local $_; my $self = shift; my @args = @_; return () unless @args; my @ret; foreach (@args) { push @ret, delete $self->{'atoms'}->{$_}; } return @ret; } =head4 R isnull Title : isnull Usage : $R->isnull Function: test if class R object is null Example : Returns : 1 if null, 0 otherwise Args : =cut sub isnull { my $self = shift; return ($self->len) ? 0 : 1; } =head4 R A Title : A Usage : print $R->A Function: get a string representation of class R object Example : Returns : string scalar Args : =cut sub A { my $self = shift; my @a = sort {$a->fld cmp $b->fld} $self->atoms; return join(" ", map {$_->A} @a); } =head4 R clone Title : clone Usage : $R2 = $R1->clone; Function: create and return a clone of the object Example : Returns : object of class R Args : =cut sub clone { local $_; my $self = shift; my $ret = R->new(); foreach ($self->atoms) { $ret->put_atoms($_->clone); } return $ret; } ## R class methods =head3 R CLASS METHODS =head4 R In Title : In Usage : R::In($R1, $R2) Function: tests whether the query represented by $R1 would return a subset of items returned by the query represented by $R2 Example : print "R2 gets those and more" if R::In($R1, $R2); Returns : 1 if R1 is subset of R2, 0 otherwise Args : two class R objects =cut sub In { local $_; my ($s, $t) = @_; Bio::Root::Root->throw('requires type R (request)') unless ref($s) && $s->isa('R'); Bio::Root::Root->throw('requires type R (request)') unless ref($t) && $t->isa('R'); return 1 if ($s->isnull); # common fields my @cf = grep {defined} map {my $f=$_; grep /^$f$/,$s->fields} $t->fields; return 0 unless @cf==$t->len; foreach (@cf) { my @sd = split(/\s+/, $s->atoms($_)->dta); my @td = split(/\s+/, $t->atoms($_)->dta); my @cd = grep {defined} map {my $d=$_; grep /^$d$/, @td} @sd; return 0 unless @cd==@sd; } return 1; } =head4 R And Title : And Usage : @Rresult = R::And($R1, $R2) Function: logical AND for R objects Example : Returns : an array containing class R objects Args : two class R objects =cut sub And { local $_; my ($s, $t) = @_; Bio::Root::Root->throw('requires type R (request)') unless ref($s) && $s->isa('R'); Bio::Root::Root->throw('requires type R (request)') unless ref($t) && $t->isa('R'); return ($R::NULL) if ($s->isnull || $t->isnull); do { my $ss = $s; $s = $t; $t = $ss } if ( $s->len > $t->len ); # $t has at least as many fields defined than $s ($t is more restrictive) # common fields my @cf = grep {defined} map {my $sf = $_; grep /$sf/, $t->fields } $s->fields; my $ret = R->new(); my $v = $t->clone; $v->del_atoms(@cf); my $u = $s->clone; $u->del_atoms(@cf); # And the atoms with identical fields foreach (@cf) { my ($a) = Q::qand($s->atoms($_), $t->atoms($_)); if ($a->isnull) { return $R::NULL; } else { $ret->put_atoms($a); } } # put the private atoms $ret->put_atoms($u->atoms, $v->atoms); return ($ret); } =head4 R Or Title : Or Usage : @Rresult = R::Or($R1, $R2) Function: logical OR for R objects Example : Returns : an array containing class R objects Args : two class R objects =cut sub Or { local $_; my ($s, $t) = @_; Bio::Root::Root->throw('requires type R (request)') unless ref($s) && $s->isa('R'); Bio::Root::Root->throw('requires type R (request)') unless ref($t) && $t->isa('R'); if ($s->isnull) { return $t->clone; } elsif ($t->isnull) { return $s->clone; } return $s->clone if (R::In($t, $s)); return $t->clone if (R::In($s, $t)); # try simplifying do { my $ss = $s; $s = $t; $t = $ss } if ( $s->len > $t->len ); # common fields my @cf = grep {defined} map {my $sf = $_; grep /$sf/, $t->fields } $s->fields; # if ($t->len == @cf) { # all atoms equal within fields but one? If yes, simplify... my @df = grep {!Q::qeq($s->atoms($_), $t->atoms($_))} @cf; if (@df == 1) { my ($a) = Q::qor($s->atoms($df[0]), $t->atoms($df[0])); my $ret = $s->clone; $ret->del_atoms($df[0]); $ret->put_atoms($a); return ($ret); } } # neither request contains the other, and the requests cannot be # simplified; reflect back (clones of) the input... return ($s->clone, $t->clone); } =head4 R Eq Title : Eq Usage : R::Eq($R1, $R2) Function: test if class Q objects in two R objects are the same (irrespective of order) Example : Returns : 1 if equal, 0 otherwise Args : two class R objects =cut sub Eq { local $_; my ($s, $t) = @_; Bio::Root::Root->throw('requires type R (request)') unless ref($s) && $s->isa('R'); Bio::Root::Root->throw('requires type R (request)') unless ref($t) && $t->isa('R'); my @sf = $s->fields; my @tf = $t->fields; return 0 unless @sf==@tf; my @cf = grep {defined} map {my $f=$_; grep /^$f$/,@sf} @tf; return 0 unless @cf==@tf; foreach (@cf) { return 0 unless Q::qeq($s->atoms($_), $t->atoms($_)); } return 1; } 1; =head2 Class Q - atomic query objects for QRY algebra =head3 Q SYNOPSIS $q = new Q('coreceptor', 'CXCR4 CCR5'); $u = new Q('coreceptor', 'CXCR4'); $q->fld; # returns 'coreceptor' $q->dta; # returns 'CXCR4 CCR5' print $q->A; # prints '(CXCR4 CCR5)[coreceptor] Q::qeq($q, $u); # returns 0 Q::qeq( Q::qor($q, $q), $q ); # returns 1 Q::qin($u, $q) # returns 1 Q::qeq(Q::qand($u, $q), $u ); # returns 1 =head3 Q DESCRIPTION Class Q objects represent atomic queries, that can be described by a single LANL cgi parameter=value pair. Class R objects (requests) are built from class Qs. The logical operations at the higher levels (C) ultimately depend on the lower level operations on Qs: C. =cut package # hide from PAUSE Q; use strict; $Q::NULL = Q->new(); ## Q constructor =head3 Q CONSTRUCTOR =head4 Q constructor Title : Q constructor Usage : $q = new Q($field, $data) Function: create a new Q (atomic query) object Example : Returns : class Q object Args : optional $field, $data strings =cut sub new { local $_; my ($class,@args) = @_; my $self={}; foreach (@args) { s/^\s+//; s/\s+$//; } my ($fld, @dta) = @args; $self->{fld}=$fld; $self->{dta}=join(" ", @dta); bless($self, $class); return $self; } ## Q instance methods =head3 Q INSTANCE METHODS =head4 Q isnull Title : isnull Usage : $q->isnull Function: test if class Q object is null Example : Returns : 1 if null, 0 otherwise Args : =cut sub isnull { my $self = shift; Bio::Root::Root->throw("requires type Q (atom)") unless ref($self) && $self->isa('Q'); return 1 unless (($self->fld && length($self->fld)) || ($self->dta && length($self->dta))); return 0; } =head4 Q fld Title : fld Usage : $q->fld($field) Function: get/set fld (field name) property Example : Returns : scalar Args : scalar =cut sub fld { my $self = shift; Bio::Root::Root->throw("requires type Q (atom)") unless ref($self) && $self->isa('Q'); my $f = shift; if ($f) { $f =~ s/^\s+//; $f =~ s/\s+$//; return $self->{fld}=$f; } return $self->{fld}; } =head4 Q dta Title : dta Usage : $q->dta($data) Function: get/set dta (whsp-separated data string) property Example : Returns : scalar Args : scalar =cut sub dta { my $self = shift; Bio::Root::Root->throw("requires type Q (atom)") unless ref($self) && $self->isa('Q'); my $d = join(" ", @_); if ($d) { $d =~ s/^\s+//; $d =~ s/\s+$//; return $self->{dta} = $d; } return $self->{dta}; } =head4 Q A Title : A Usage : print $q->A Function: get a string representation of class Q object Example : Returns : string scalar Args : =cut sub A { my $self = shift; Bio::Root::Root->throw("requires type Q (atom)") unless ref($self) && $self->isa('Q'); my @a = split(/\s+/, $self->dta); return "(".join(' ', sort {$a cmp $b} @a).")[".$self->fld."]"; } =head4 Q clone Title : clone Usage : $q2 = $q1->clone; Function: create and return a clone of the object Example : Returns : object of class Q Args : =cut sub clone { my $self = shift; Bio::Root::Root->throw("requires type Q (atom)") unless ref($self) && $self->isa('Q'); my $ret = Q->new($self->fld, $self->dta); return $ret; } ### Q class methods =head3 Q CLASS METHODS =head4 Q qin Title : qin Usage : Q::qin($q1, $q2) Function: tests whether the query represented by $q1 would return a subset of items returned by the query represented by $q2 Example : print "q2 gets those and more" if Q::qin($q1, $q2); Returns : 1 if q1 is subset of q2, 0 otherwise Args : two class Q objects =cut sub qin { my ($a, $b) = @_; Bio::Root::Root->throw('requires type Q (atom)') unless (ref $a) && $a->isa('Q') && (ref $b) && $b->isa('Q'); return 0 unless $a->fld eq $b->fld; return Q::qeq( $b, Q::qor($a, $b) ); } =head4 Q qeq Title : qeq Usage : Q::qeq($q1, $q2) Function: test if fld and dta properties in two class Q objects are the same (irrespective of order) Example : Returns : 1 if equal, 0 otherwise Args : two class Q objects =cut sub qeq { local $_; my ($a, $b) = @_; Bio::Root::Root->throw('requires type Q (atom)') unless (ref $a) && $a->isa('Q') && (ref $b) && $b->isa('Q'); return 0 unless $a->fld eq $b->fld; my @ad = unique(split(/\s+/,$a->dta)); my @bd = unique(split(/\s+/,$b->dta)); return 0 unless @ad==@bd; my @cd = grep {defined} map {my $f = $_; grep /^$f$/, @ad} @bd; return @cd == @bd; } =head4 Q qor Title : qor Usage : @qresult = Q::qor($q1, $q2) Function: logical OR for Q objects Example : Returns : an array of class Q objects Args : two class Q objects =cut sub qor { local $_; my @a = @_; foreach (@a) { Bio::Root::Root->throw("requires type Q (atom)") unless ref && $_->isa('Q'); } my @ret; my (%f, @f); @a = grep {!$_->isnull} @a; return ($Q::NULL) unless @a > 0; # list of unique flds @f = unique(map {$_->fld} @a); foreach my $f (@f) { my @fobjs = grep {$_->fld eq $f} @a; my @d = unique(map {split(/\s/, $_->dta)} @fobjs ); my $r = Q->new($f, @d); push @ret, $r; } return @ret; } =head4 Q qand Title : qand Usage : @qresult = Q::And($q1, $q2) Function: logical AND for R objects Example : Returns : an array of class Q objects Args : two class Q objects =cut sub qand { local $_; my ($a, $b) = @_; Bio::Root::Root->throw('requires type Q (atom)') unless (ref $a) && $a->isa('Q') && (ref $b) && $b->isa('Q'); my @ret; if (ref $a eq 'ARRAY') { foreach my $ea (@$a) { push @ret, qand( $ea, $b ); } return qor(@ret); # simplify } elsif (ref $b eq 'ARRAY') { foreach my $eb (@$b) { push @ret, qand( $a, $eb); 1; } return qor(@ret); # simplify } else { return ($Q::NULL) if ($a->isnull || $b->isnull); if ($a->fld eq $b->fld) { # find intersection of data my (%ad, @ad, @bd); @ad = split(/\s+/, $a->dta); @ad{@ad} = (1) x @ad; @bd = split(/\s+/, $b->dta); foreach (@bd) { $ad{$_}++; } my $r = Q->new($a->fld, grep {$_} map {$ad{$_} == 2 ? $_ : undef} keys %ad); return (length($r->dta) > 0) ? ($r) : ($Q::NULL); } else { return ($a, $b); } } } =head3 Q INTERNALS =head4 Q unique Title : unique Usage : @ua = unique(@a) Function: return contents of @a with duplicates removed Example : Returns : Args : an array =cut sub unique { my @a = @_; my %a; @a{@a} = undef; return keys %a; } 1; =head2 Additional tools for Bio::AnnotationCollectionI =head3 Bio::AnnotationCollectionI SYNOPSIS (additional methods) $seq->annotation->put_value('patient_id', 1401) $seq->annotation->get_value('patient_ids') # returns 1401 $seq->annotation->put_value('patient_group', 'MassGenH') $seq->annotation->put_value(['clinical', 'cd4count'], 503); $seq->annotation->put_value(['clinical', 'virus_load'], 150805); foreach ( qw( cd4count virus_load ) ) { $blood_readings{$_} = $seq->annonation->get_value(['clinical', $_]); } =head3 Bio::AnnotationCollectionI DESCRIPTION (additional methods) C and C allow easy creation of and access to an annotation collection tree with nodes of L. These methods obiviate direct accession of the SimpleValue objects. =cut package Bio::AnnotationCollectionI; use strict; use Bio::Annotation::SimpleValue; =head2 get_value Title : get_value Usage : $ac->get_value($tagname) -or- $ac->get_value( $tag_level1, $tag_level2,... ) Function: access the annotation value associated with the given tags Example : Returns : a scalar Args : an array of tagnames that descend into the annotation tree =cut sub get_value { local $_; my $self = shift; my @args = @_; my @h; return "" unless @_; while ($_ = shift @args) { @h = $self->get_Annotations($_); if (ref($h[0]->{value})) { $self = $h[0]->{value}; # must be another Bio::AnnotationCollectionI } else { last; } } return $h[0] && $h[0]->{value} ; # now the last value. } =head2 put_value Title : put_value Usage : $ac->put_value($tagname, $value) -or- $ac->put_value([$tag_level1, $tag_level2, ...], $value) -or- $ac->put_value( [$tag_level1, $tag_level2, ...] ) Function: create a node in an annotation tree, and assign a scalar value to it if a value is specified Example : Returns : scalar or a Bio::AnnotationCollection object Args : $tagname, $value scalars (can be specified as -KEYS=>$tagname, -VALUE=>$value) -or- \@tagnames, $value (or as -KEYS=>\@tagnames, -VALUE=>$value ) Note : If intervening nodes do not exist, put_value creates them, replacing existing nodes. So if $ac->put_value('x', 10) was done, then later, $ac->put_value(['x', 'y'], 20), the original value of 'x' is trashed, and $ac->get_value('x') will now return the annotation collection with tagname 'y'. =cut sub put_value { local $_; my $self = shift; my @args = @_; my ($keys, $value) = $self->_rearrange([qw( KEYS VALUE )], @args); my (@keys, $lastkey); # $value ||= new Bio::Annotation::Collection; @keys = (ref($keys) eq 'ARRAY') ? @$keys : ($keys); $lastkey = pop @keys; foreach (@keys) { my $a = $self->get_value($_); if (ref($a) && $a->isa('Bio::Annotation::Collection')) { $self = $a; } else { # replace an old value $self->remove_Annotations($_) if $a; my $ac = Bio::Annotation::Collection->new(); $self->add_Annotation(Bio::Annotation::SimpleValue->new( -tagname => $_, -value => $ac ) ); $self = $ac; } } if ($self->get_value($lastkey)) { # replace existing value ($self->get_Annotations($lastkey))[0]->{value} = $value; } else { $self->add_Annotation(Bio::Annotation::SimpleValue->new( -tagname=>$lastkey, -value=>$value )); } return $value; } =head2 get_keys Title : get_keys Usage : $ac->get_keys($tagname_level_1, $tagname_level_2,...) Function: Get an array of tagnames underneath the named tag nodes Example : # prints the values of the members of Category 1... print map { $ac->get_value($_) } $ac->get_keys('Category 1') ; Returns : array of tagnames or empty list if the arguments represent a leaf Args : [array of] tagname[s] =cut sub get_keys { my $self = shift; my @keys = @_; foreach (@keys) { my $a = $self->get_value($_); if (ref($a) && $a->isa('Bio::Annotation::Collection')) { $self = $a; } else { return (); } } return $self->get_all_annotation_keys(); } 1; BioPerl-1.007002/Bio/DB/HIV/lanl-schema.xml000555000766000024 21643213155576320 20120 0ustar00cjfieldsstaff000000000000 author.au_authornumberau_authornumber author_number authornumber author.au_per_idau_per_id per_id(au) per_id author.au_pub_idau_pub_id pub_id(au) location2.loc_descriptionloc_description description(loc) description location2.loc_entryfeaturetypeloc_entryfeaturetype feature_type(loc) entryfeaturetype location2.loc_idloc_id loc_id id location2.loc_se_idloc_se_id se_id(loc) mapimage.mi_se_idmi_se_id map_image(se_id) mapimage.mi_startmi_start mi_start mapimage.mi_stopmi_stop mi_stop max_rec order patient.pat_codepat_code patient_code code patient.pat_commentpat_comment patient_comment patient.pat_ethnicitypat_ethnicity patient_ethnicity ethnicity patient.pat_hla_typepat_hla_type hla_type hla_type patient.pat_id pat_id patient.pat_infection_citypat_infection_city infection_city infection_city patient.pat_infection_countrypat_infection_country infection_country infection_country patient.pat_infection_yearpat_infection_year infection_year infection_year patient.pat_num_seqpat_num_seq #_of_patient_seqs num_seq patient.pat_num_timepointspat_num_timepoints #_of_patient_timepoints num_timepoints patient.pat_progressionpat_progression progression progression patient.pat_projectpat_project project project patient.pat_risk_factorpat_risk_factor risk_factor risk_factor patient.pat_sexpat_sex patient_sex sex patient.pat_speciespat_species host_species species person.per_id per_id person.per_lnameper_lname last_name lname publication.pub_articletitlepub_articletitle title articletitle publication.pub_consortiumpub_consortium consortium consortium publication.pub_id pub_id publication.pub_pubmedentrypub_pubmedentry pubmed_id pubmedentry publication.pub_sourcetitlepub_sourcetitle journal sourcetitle se_pub_link.spl_pub_idspl_pub_id pub_id(spl) pub_id se_pub_link.spl_pubnumberspl_pubnumber publication_number pubnumber se_pub_link.spl_se_idspl_se_id se_id(spl) se_id select_all seq_sample.ssam_amplification_strategyssam_amplification_strategy amplification_strategy amplification_strategy seq_sample.ssam_annotatedssam_annotated annotated annotated seq_sample.ssam_badseqssam_badseq problematic badseq seq_sample.ssam_cd4countssam_cd4count cd4_count cd4count seq_sample.ssam_cd8countssam_cd8count cd8_count cd8count seq_sample.ssam_clone_name_numberssam_clone_name_number clone_name clone_name_number seq_sample.ssam_common_namessam_common_name name common_name seq_sample.ssam_culture_methodssam_culture_method culture_method culture_method seq_sample.ssam_drug_naivessam_drug_naive drug_naive drug_naive seq_sample.ssam_fiebigssam_fiebig fiebig_stage fiebig seq_sample.ssam_health_statusssam_health_status patient_health health_status seq_sample.ssam_isolate_name_numberssam_isolate_name_number isolate_name isolate_name_number seq_sample.ssam_locus_namessam_locus_name locus_name locus_name seq_sample.ssam_molecule_typessam_molecule_type molecule_type molecule_type seq_sample.ssam_organismssam_organism organism organism seq_sample.ssam_pat_idssam_pat_id pat_id(ssam) pat_id seq_sample.ssam_patient_agessam_patient_age patient_age patient_age seq_sample.ssam_phenotypessam_phenotype phenotype phenotype seq_sample.ssam_postendtreatment_daysssam_postendtreatment_days days_from_treatment_end postendtreatment_days seq_sample.ssam_postfirstsample_daysssam_postfirstsample_days days_from_first_sample postfirstsample_days seq_sample.ssam_postinfect_daysssam_postinfect_days days_from_infection postinfect_days seq_sample.ssam_postseroconv_daysssam_postseroconv_days days_from_seroconversion postseroconv_days seq_sample.ssam_poststarttreatment_daysssam_poststarttreatment_days days_from_treatment_start poststarttreatment_days seq_sample.ssam_sample_cityssam_sample_city sampling_city sample_city seq_sample.ssam_sample_countryssam_sample_country country sample_country country seq_sample.ssam_sample_georegionssam_sample_georegion georegion sample_georegion seq_sample.ssam_sample_tissuessam_sample_tissue sample_tissue sample_tissue seq_sample.ssam_sample_yearssam_sample_year sampling_year sample_year year seq_sample.ssam_sample_year_upperssam_sample_year_upper sampling_year_upper sample_year_upper seq_sample.ssam_se_idssam_se_id se_id(ssam) seq_sample.ssam_second_receptorcoreceptor coreceptor ssam_second_receptor second_receptor seq_sample.ssam_sequencing_methodssam_sequencing_method sequencing_method sequencing_method seq_sample.ssam_subtypessam_subtype subtype subtype seq_sample.ssam_viralloadssam_viralload viral_load viralload seqentryfeature.sef_descriptionsef_description description(sef) seqentryfeature.sef_entryfeaturetypesef_entryfeaturetype feature_type(sef) seqentryfeature.sef_pub_idsef_pub_id pub_id(sef) seqentryfeature.sef_se_idsef_se_id se_id(sef) sequenceaccessions.sa_genbankaccessionsa_genbankaccession accession genbankaccession accession sequenceaccessions.sa_gisa_gi gi_number gi sequenceaccessions.sa_se_idsa_se_id se_id(sa) sequenceaccessions.sa_versionsa_version version version sequenceentry.se_db_commentse_db_comment db_comment db_comment comment sequenceentry.se_gb_commentse_gb_comment gb_comment gb_comment sequenceentry.se_gb_createse_gb_create gb_create_date gb_create sequenceentry.se_gb_updatese_gb_update gb_update_date gb_update sequenceentry.se_id se_id sequenceentry.se_sequencese_sequence sequence sequence sequenceentry.se_sequencelengthse_sequencelength sequence_length sequencelength sequencefeature2.sf_featuretypesf_featuretype feature_type(sf) featuretype sequencefeature2.sf_featurevaluesf_featurevalue feature_value(sf) featurevalue sequencefeature2.sf_loc_idsf_loc_id loc_id(sf) sequencemap.sm_se_idsm_se_id se_id(sm) sequencemap.sm_startsm_start start hxb2_start sequencemap.sm_stopsm_stop stop hxb2_stop show_sql sort_dir COMMAND.CLIP COMMAND.genomic_regiongenegenomic_region BioPerl-1.007002/Bio/DB/Query000755000766000024 013155576320 15461 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/Query/GenBank.pm000444000766000024 2363613155576320 17513 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::Query::GenBank.pm # # Please direct questions and support issues to # # Cared for by Lincoln Stein # # Copyright Lincoln Stein # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code # =head1 NAME Bio::DB::Query::GenBank - Build a GenBank Entrez Query =head1 SYNOPSIS use Bio::DB::Query::GenBank; use Bio::DB::GenBank; my $query_string = 'Oryza[Organism] AND EST[Keyword]'; my $query = Bio::DB::Query::GenBank->new(-db => 'nucleotide', -query => $query_string, -mindate => '2001', -maxdate => '2002'); print $query->count,"\n"; # get a Genbank database handle my $gb = Bio::DB::GenBank->new(); my $stream = $gb->get_Stream_by_query($query); while (my $seq = $stream->next_seq) { # do something with the sequence object } # initialize the list yourself my $query = Bio::DB::Query::GenBank->new(-ids=>[195052,2981014,11127914]); =head1 DESCRIPTION This class encapsulates NCBI Entrez queries. It can be used to store a list of GI numbers, to translate an Entrez query expression into a list of GI numbers, or to count the number of terms that would be returned by a query. Once created, the query object can be passed to a Bio::DB::GenBank object in order to retrieve the entries corresponding to the query. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Lincoln Stein Email lstein@cshl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Query::GenBank; use strict; use URI::Escape 'uri_unescape'; use Bio::DB::NCBIHelper; #use constant EPOST => $Bio::DB::NCBIHelper::HOSTBASE . '/entrez/eutils/epost.fcgi'; #use constant ESEARCH => $Bio::DB::NCBIHelper::HOSTBASE . '/entrez/eutils/esearch.fcgi'; # the reference to the our variable of the $Bio::DB::NCBIHelper::HOSTBASE doesn't seem to work in # the constant definition in perl 5.10.1 or 5.16.3 use constant EPOST => '/entrez/eutils/epost.fcgi'; use constant ESEARCH => '/entrez/eutils/esearch.fcgi'; use constant DEFAULT_DB => 'protein'; use constant MAXENTRY => 100; use vars qw(@ATTRIBUTES); use base qw(Bio::DB::Query::WebQuery); BEGIN { @ATTRIBUTES = qw(db reldate mindate maxdate datetype maxids); for my $method (@ATTRIBUTES) { eval <{'_$method'}; \$self->{'_$method'} = shift if \@_; \$d; } END } } =head2 new Title : new Usage : $db = Bio::DB::Query::GenBank->new(@args) Function: create new query object Returns : new query object Args : -db database (see below for allowable values) -query query string -mindate minimum date to retrieve from (YYYY/MM/DD) -maxdate maximum date to retrieve from (YYYY/MM/DD) -reldate relative date to retrieve from (days) -datetype date field to use ('edat' or 'mdat') -ids array ref of gids (overrides query) -maxids the maximum number of IDs you wish to collect (defaults to 100) This method creates a new query object. Typically you will specify a -db and a -query argument, possibly modified by -mindate, -maxdate, or -reldate. -mindate and -maxdate specify minimum and maximum dates for entries you are interested in retrieving, expressed in the form YYYY/MM/DD. -reldate is used to fetch entries that are more recent than the indicated number of days. If you provide an array reference of IDs in -ids, the query will be ignored and the list of IDs will be used when the query is passed to a Bio::DB::GenBank object's get_Stream_by_query() method. A variety of IDs are automatically recognized, including GI numbers, Accession numbers, Accession.version numbers and locus names. By default, the query will collect only the first 100 IDs and will generate an exception if you call the ids() method and the query returned more than that number. To increase this maximum, set -maxids to a number larger than the number of IDs you expect to obtain. This only affects the list of IDs you obtain when you call the ids() method, and does not affect in any way the number of entries you receive when you generate a SeqIO stream from the query. -db option values: The most commonly used databases are: protein nucleotide nuccore nucgss nucest unigene An up to date list of database names supported by NCBI eUtils is always available at: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? However, note that not all of these databases return datatypes that are parsable by Bio::DB::GenBank =cut sub new { my $class = shift; my $self = $class->SUPER::new(@_); my ($query,$db,$reldate,$mindate,$maxdate,$datetype,$ids,$maxids) = $self->_rearrange([qw(QUERY DB RELDATE MINDATE MAXDATE DATETYPE IDS MAXIDS)],@_); $self->db($db || DEFAULT_DB); $reldate && $self->reldate($reldate); $mindate && $self->mindate($mindate); $maxdate && $self->maxdate($maxdate); $maxids && $self->maxids($maxids); $datetype ||= 'mdat'; $datetype && $self->datetype($datetype); $self; } =head2 cookie Title : cookie Usage : ($cookie,$querynum) = $db->cookie Function: return the NCBI query cookie Returns : list of (cookie,querynum) Args : none NOTE: this information is used by Bio::DB::GenBank in conjunction with efetch. =cut sub cookie { my $self = shift; if (@_) { $self->{'_cookie'} = shift; $self->{'_querynum'} = shift; } else { $self->_run_query; @{$self}{qw(_cookie _querynum)}; } } =head2 _request_parameters Title : _request_parameters Usage : ($method,$base,@params = $db->_request_parameters Function: return information needed to construct the request Returns : list of method, url base and key=>value pairs Args : none =cut sub _request_parameters { my $self = shift; my ($method,$base); my @params = map {eval("\$self->$_") ? ($_ => eval("\$self->$_")) : () } @ATTRIBUTES; push @params,('usehistory'=>'y','tool'=>'bioperl'); $method = 'get'; $base = $Bio::DB::NCBIHelper::HOSTBASE.ESEARCH; # this seems to need to be dynamic push @params,('term' => $self->query); # Providing 'retmax' limits queries to 500 sequences ?? I don't think so LS push @params,('retmax' => $self->maxids || MAXENTRY); # And actually, it seems that we need 'retstart' equal to 0 ?? I don't think so LS # push @params, ('retstart' => 0); ($method,$base,@params); } =head2 count Title : count Usage : $count = $db->count; Function: return count of number of entries retrieved by query Returns : integer Args : none Returns the number of entries that are matched by the query. =cut sub count { my $self = shift; if (@_) { my $d = $self->{'_count'}; $self->{'_count'} = shift; return $d; } else { $self->_run_query; return $self->{'_count'}; } } =head2 ids Title : ids Usage : @ids = $db->ids([@ids]) Function: get/set matching ids Returns : array of sequence ids Args : (optional) array ref with new set of ids =cut =head2 query Title : query Usage : $query = $db->query([$query]) Function: get/set query string Returns : string Args : (optional) new query string =cut =head2 _parse_response Title : _parse_response Usage : $db->_parse_response($content) Function: parse out response Returns : empty Args : none Throws : 'unparseable output exception' =cut sub _parse_response { my $self = shift; my $content = shift; if (my ($warning) = $content =~ m!(.+)!s) { $self->warn("Warning(s) from GenBank: $warning\n"); } if (my ($error) = $content =~ /([^<]+)/) { $self->throw("Error from Genbank: $error"); } my ($count) = $content =~ /(\d+)/; my ($max) = $content =~ /(\d+)/; my $truncated = $count > $max; $self->count($count); if (!$truncated) { my @ids = $content =~ /(\d+)/g; $self->ids(\@ids); } else { $self->debug("ids truncated at $max\n"); } $self->_truncated($truncated); my ($cookie) = $content =~ m!(\S+)!; my ($querykey) = $content =~ m!(\d+)!; $self->cookie(uri_unescape($cookie),$querykey); } =head2 _generate_id_string Title : _generate_id_string Usage : $string = $db->_generate_id_string Function: joins IDs together in string (possibly implementation-dependent) Returns : string of concatenated IDs Args : array ref of ids (normally passed into the constructor) =cut sub _generate_id_string { my ($self, $ids) = @_; # this attempts to separate out accs (alphanumeric) from UIDs (numeric only) # recent changes to esearch has wrought this upon us.. cjf 4/19/07 return sprintf('%s',join('|',map { ($_ =~ m{^\d+$}) ? $_.'[UID]' : $_.'[PACC]' } @$ids)); } 1; BioPerl-1.007002/Bio/DB/Query/HIVQuery.pm000555000766000024 12536713155576320 17711 0ustar00cjfieldsstaff000000000000# to do: support for comment, reference annotations # $Id: HIVQuery.pm 232 2008-12-11 14:51:51Z maj $ # # BioPerl module for Bio::DB::Query::LANLQuery # # Please direct questions and support issues to # # Cared for by Mark A. Jensen # # Copyright Mark A. Jensen # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Query::HIVQuery - Query interface to the Los Alamos HIV Sequence Database =head1 SYNOPSIS $q = new Bio::DB::Query::HIVQuery(" C[subtype] ZA[country] CXCR4[coreceptor] "); $q = new Bio::DB::Query::HIVQuery( -query=>{'subtype'=>'C', 'country'=>'ZA', 'coreceptor'=>'CXCR4'}); $ac = $q->get_annotations_by_id(($q->ids)[0]); $ac->get_value('Geo', 'country') # returns 'SOUTH AFRICA' $db = new Bio::DB::HIV(); $seqio = $db->get_Stream_by_query($q); # returns annotated Bio::Seqs # get subtype C sequences from South Africa and Brazil, # with associated info on patient health, coreceptor use, and # infection period: $q = new Bio::DB::Query::HIVQuery( -query => { 'query' => {'subtype'=>'C', 'country'=>['ZA', 'BR']}, 'annot' => ['patient_health', 'coreceptor', 'days_post_infection'] }); =head1 DESCRIPTION Bio::DB::Query::HIVQuery provides a query-like interface to the cgi-based Los Alamos National Laboratory (LANL) HIV Sequence Database. It uses Bioperl facilities to capture both sequences and annotations in batch in an automated and computable way. Use with L to create C objects and annotated C streams. =head2 Query format The interface implements a simple query language emulation that understands AND, OR, and parenthetical nesting. The basic query unit is (match1 match2 ...)[fieldname] Sequences are returned for which C equals C. These units can be combined with AND, OR and parentheses. For example: (B, C)[subtype] AND (2000, 2001, 2002, 2003)[year] AND ((CN)[country] OR (ZA)[country]) which can be shortened to (B C)[subtype] (2000 2001 2002 2003)[year] (CN ZA)[country] The user can specify annotation fields, that do not restrict the query, but arrange for the return of the associated field data for each sequence returned. Specify annotation fields between curly braces, as in: (B C)[subtype] 2000[year] {country cd4_count cd8_count} Annotations can be accessed off the query using methods described in APPENDIX. =head2 Hash specifications for query construction Single query specifications can be made as hash references provided to the C<-query> argument of the constructor. There are two forms: -query => { 'country'=>'BR', 'phenotype'=>'NSI', 'cd4_count'=>'Any' } equivalent to -query => [ 'country'=>'BR', 'phenotype'=>'NSI', 'cd4_count'=>'Any' ] or -query => { 'query' => {'country'=>'BR', 'phenotype'=>'NSI'}, 'annot' => ['cd4_count'] } In both cases, the CD4 count is included in the annotations returned, but does not restrict the rest of the query. To 'OR' multiple values of a field, use an anonymous array ref: -query => { 'country'=>['ZA','BR','NL'], 'subtype'=>['A', 'C', 'D'] } =head2 Valid query field names An attempt was made to make the query field names natural and easy to remember. Aliases are specified in an XML file (C) that is part of the distribution. Custom field aliases can be set up by modifying this file. An HTML cheatsheet with valid field names, aliases, and match data can be generated from the XML by using Chelp('help.html')>. A query can also be validated locally before it is unleashed on the server; see below. =head2 Annotations LANL DB annotations have been organized into a number of natural groupings, tagged C, C, C, and C. After a successful query, each id is associated with a tree of L objects. These can be accessed with methods C and C described in APPENDIX. =head2 Delayed/partial query runs Accessing the LANL DB involves multiple HTTP requests. The query can be instructed to proceed through all (the default) or only some of them, using the named parameter C. To validate a query locally, use $q = new Bio::DB::Query::HIVQuery( -query => {...}, -RUN_OPTION=>0 ) which will throw an exception if a field name or option is invalid. To get a query count only, you can save a server hit by using $q = new Bio::DB::Query::HIVQuery( -query => {...}, -RUN_OPTION=>1 ) and asking for C<$q-Ecount>. To finish the query, do $q->_do_query(2) which picks up where you left off. C<-RUN_OPTION=E2>, the default, runs the full query, returning ids and annotations. =head2 Query re-use You can clear the query results, retaining the same LANL session and query spec, by doing C<$q-E_reset>. Change the query, and rerun with C<$q-E_do_query($YOUR_RUN_OPTION)>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Mark A. Jensen Email maj@fortinbras.us =head1 CONTRIBUTORS Mark A. Jensen =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Query::HIVQuery; use strict; use vars qw( $LANL_BASE $LANL_MAP_DB $LANL_MAKE_SEARCH_IF $LANL_SEARCH $SCHEMA_FILE $RUN_OPTION ); # Object preamble - inherits from Bio::DB::QueryI use Bio::Root::Root; use Bio::Annotation::Collection; use Bio::Annotation::Comment; use Bio::Annotation::Reference; use Bio::WebAgent; use XML::Simple; use CGI; use Bio::DB::HIV::HIVQueryHelper; use base qw(Bio::Root::Root Bio::DB::QueryI); # globals BEGIN { # change base to new search page 01/14/09 /maj $LANL_BASE = "http://www.hiv.lanl.gov/components/sequence/HIV/asearch"; $LANL_MAP_DB = "map_db.comp"; $LANL_MAKE_SEARCH_IF = "make_search_if.comp"; $LANL_SEARCH = "search.comp"; $SCHEMA_FILE = Bio::Root::IO->catfile(qw(Bio DB HIV lanl-schema.xml)); $RUN_OPTION = 2; # execute query # exceptions @Bio::SchemaNotInit::Exception::ISA = qw( Bio::Root::Exception ); @Bio::WebError::Exception::ISA = qw( Bio::Root::Exception ); @Bio::QueryNotMade::Exception::ISA = qw( Bio::Root::Exception ); @Bio::QueryStringException::Exception::ISA = qw( Bio::Root::Exception ); @Bio::HIVSorry::Exception::ISA = qw ( Bio::Root::Exception ); } =head1 Constructor =head2 new Title : new Usage : my $hiv_query = new Bio::DB::Query::HIVQuery(); Function: Builds a new Bio::DB::Query::HIVQuery object, running a sequence query against the Los Alamos HIV sequence database Returns : an instance of Bio::DB::Query::HIVQuery Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); # constructor option for web agent parameter spec: added 01/14/09 /maj my ($query, $ids, $lanl_base, $lanl_map_db, $lanl_make_search_if, $lanl_search, $schema_file,$run_option, $uahash) = $self->_rearrange([ qw(QUERY IDS LANL_BASE LANL_MAP_DB LANL_MAKE_SEARCH_IF LANL_SEARCH SCHEMA_FILE RUN_OPTION USER_AGENT_HASH )], @args); # default globals $lanl_base||= $LANL_BASE; $lanl_map_db||=$LANL_MAP_DB; $lanl_make_search_if||=$LANL_MAKE_SEARCH_IF; $lanl_search||=$LANL_SEARCH; $schema_file||=$SCHEMA_FILE; $uahash ||= {timeout => 90}; defined $run_option || ($run_option = $RUN_OPTION); $self->lanl_base($lanl_base); $self->map_db($lanl_map_db); $self->make_search_if($lanl_make_search_if); $self->search_($lanl_search); $self->_run_option($run_option); $self->_ua_hash($uahash); # catch this at the top if (-e $schema_file) { $self->_schema_file($schema_file); } else { # look around my ($p) = $self->_schema_file( [grep {$_} map { my $p = Bio::Root::IO->catfile($_, $schema_file); $p if -e $p } (@INC,"")]->[0]); $self->throw(-class=>"Bio::Root::NoSuchThing", -text=>"Schema file \"".$self->_schema_file."\" cannot be found", -value=>$self->_schema_file) unless -e $self->_schema_file; } $self->count(0); $self->{_schema} = HIVSchema->new($self->_schema_file); # internal storage and flags $self->{'_lanl_query'} = []; $self->{'_lanl_response'} = []; $self->{'_annotations'} = {}; # container for annotation collections assoc. with ids $self->{'_RUN_LEVEL'} = undef; # set in _do_query() # work defined $query && $self->query($query); defined $ids && $self->ids($ids); # exec query $self->_do_query($self->_run_option) if $self->query; return $self; } =head1 QueryI compliance =head2 count Title : count Usage : $hiv_query->count($newval) Function: return number of sequences found Example : Returns : value of count (a scalar) Args : on set, new value (a scalar or undef, optional) Note : count warns if it is accessed for reading before query has been executed to at least level 1 =cut sub count{ my $self = shift; return $self->{'count'} = shift if @_; if (!$self->{'_RUN_LEVEL'} || ($self->{'_RUN_LEVEL'} < 1)) { $self->warn('Query not yet run at > level 1'); } return $self->{'count'}; } =head2 ids Title : ids Usage : $hiv_query->ids($newval) Function: LANL ids of returned sequences Example : Returns : value of ids (an arrayref of sequence accessions/ids) Args : on set, new value (an arrayref or undef, optional) =cut sub ids{ my $self = shift; if (@_) { my $a = shift; $self->throw(-class=>'Bio::Root::BadParameter', -text=>'Arrayref required', -value=> ref $a) unless ref($a) eq 'ARRAY'; if (@$a) { @{$self->{'ids'}}{@$a} = (1) x @$a; return $a; } else { #with empty arrayref, clear the hash $self->{'ids'} = {}; } } return keys %{$self->{'ids'}} if $self->{'ids'}; } =head2 query Title : query Usage : $hiv_query->query Function: Get/set the submitted query hash or string Example : Returns : hashref or string Args : query in hash or string form (see DESCRIPTION) =cut sub query { my $self = shift; return $self->{'query'} = shift if @_; return $self->{'query'}; } =head1 Bio::DB::Query::HIVQuery specific methods =head2 help Title : help Usage : $hiv_query->help("help.html") Function: get html-formatted listing of valid fields/aliases/options based on current schema xml Example : perl -MBio::DB::Query::HIVQuery -e "new Bio::DB::Query::HIVQuery()->help" | lynx -stdin Returns : HTML Args : optional filename; otherwise prints to stdout =cut sub help{ my ($self, $fname) = @_; my (@ret, @tok); my $schema = $self->_schema; my $h = CGI->new(); my (@tbls, @flds, @als, @opts, $fh); if ($fname) { open $fh, '>', $fname or $self->throw(-class => 'Bio::Root::IOException', -text => "Error opening help html file $fname for writing", -value => $!); } else { open $fh, ">&1"; } @tbls = $schema->tables; @tbls = ('COMMAND', grep !/COMMAND/,@tbls); print $fh ( $h->start_html(-title=>"HIVQuery Help") ); print $fh $h->a({-id=>'TOP'}, $h->h2("Valid HIVQuery query fields and match data")); print $fh "Fields are organized below according to their Los Alamos HIV database tables. Use aliases in place of full field names in queries; for example:
"; print $fh "
(CCR5 CXCR4)[coreceptor]
"; print $fh "rather than"; print $fh "
(CCR5 CXCR4)[seq_sample.ssam_second_receptor]
"; print $fh "(which does work, however). Click hyperlinks to see valid search options within the field. The token Any is the wildcard for all fields.

"; print $fh $h->start_table({-style=>"font-family:sans-serif;"}) ; foreach my $tbl (@tbls) { @flds = grep /^$tbl/, $schema->fields; @flds = grep !/_id/, @flds; print $fh ( $h->start_Tr({-style=>"background-color: lightblue;"}), $h->td([$h->a({-id=>$tbl},$tbl), $h->span({-style=>"font-style:italic"},"fields"), $h->span({-style=>"font-style:italic"}, "aliases")]), $h->end_Tr ); foreach my $fld (@flds) { @als = reverse $schema->aliases($fld); print $fh ( # note that aliases can sometimes be empty $h->Tr( $h->td( ["", $h->a({-href=>"#opt$fld"}, shift @als || '???'), $h->code(join(',',@als))] )) ); my @tmp = grep {$_} $schema->options($fld); @tmp = sort {(($a =~ /^[0-9]+$/) && $b =~ /^[0-9]+$/) ? $a<=>$b : $a cmp $b} @tmp; if (grep /Any/,@tmp) { @tmp = grep !/Any/, @tmp; unshift @tmp, 'Any'; } #print STDERR join(', ',@tmp)."\n"; push @opts, $h->div( {-style=>"font-family:sans-serif;font-size:small"}, $h->hr, $h->a( {-id=>"opt$fld"}, "Valid options for $fld: " ), $h->blockquote( @tmp ? $h->code(join(", ", @tmp)) : $h->i("free text") ), $h->span( "Other aliases: " ), $h->blockquote( @als ? $h->code(join(",",@als)) : "none" ), " ", $h->table( $h->Tr( $h->td([ $h->a({-href=>"#$tbl"}, $h->small('BACK')), $h->a({-href=>"#TOP"}, $h->small('TOP')) ]) ) ) ); } } print $fh $h->end_table; print $fh @opts; print $fh $h->end_html; close($fh); return 1; } =head1 Annotation manipulation methods =head2 get_annotations_by_ids Title : get_annotations_by_ids (or ..._by_id) Usage : $ac = $hiv_query->get_annotations_by_ids(@ids) Function: Get the Bio::Annotation::Collection for these sequence ids Example : Returns : A Bio::Annotation::Collection object Args : an array of sequence ids =cut sub get_annotations_by_ids{ my $self = shift; my @ids = @_; my @ret; if (!$self->{'_RUN_LEVEL'} || ($self->{'_RUN_LEVEL'} < 2)) { $self->warn('Requires query run at level 2'); return (); } @ret = map {$self->{'_annotations'}->{$_}} @ids if exists($self->{'_annotations'}); return (wantarray ? @ret : $ret[0]) if @ret; return {}; } # singular alias sub get_annotations_by_id { shift->get_annotations_by_ids(@_); } =head2 add_annotations_for_id Title : add_annotations_for_id Usage : $hiv_query->add_annotations_for_id( $id ) to create a new empty collection for $id $hiv_query->add_annotations_for_id( $id, $ac ) to associate $ac with $id Function: Associate a Bio::Annotation::Collection with this sequence id Example : Returns : a Bio::Annotation::Collection object Args : sequence id [, Bio::Annotation::Collection object] =cut sub add_annotations_for_id{ my $self = shift; my ($id, $ac) = @_; $id = "" unless defined $id; # avoid warnings $ac = Bio::Annotation::Collection->new() unless defined $ac; $self->throw(-class=>'Bio::Root::BadParameter' -text=>'Bio::Annotation::Collection required at arg 2', -value=>"") unless ref($ac) eq 'Bio::Annotation::Collection'; $self->{'_annotations'}->{$id} = $ac unless exists($self->{'_annotations'}->{$id}); return $ac; } =head2 remove_annotations_for_ids Title : remove_annotations_for_ids (or ..._for_id) Usage : $hiv_query->remove_annotations_for_ids( @ids) Function: Remove annotation collection for this sequence id Example : Returns : An array of the previous annotation collections for these ids Args : an array of sequence ids =cut sub remove_annotations_for_ids { my $self = shift; my @ids = @_; my @ac; foreach (@ids) { push @ac, delete $self->{'_annotations'}->{$_}; } return @ac; } # singular alias sub remove_annotations_for_id { shift->remove_annotations_for_ids(@_); } =head2 remove_annotations Title : remove_annotations Usage : $hiv_query->remove_annotations() Function: Remove all annotation collections for this object Example : Returns : The previous annotation collection hash for this object Args : none =cut sub remove_annotations { my $self = shift; my $ach = $self->{'_annotations'}; $self->{'_annotations'} = {}; return $ach; } =head2 get_value Title : get_value Usage : $ac->get_value($tagname) -or- $ac->get_value( $tag_level1, $tag_level2,... ) Function: access the annotation value associated with the given tags Example : Returns : a scalar Args : an array of tagnames that descend into the annotation tree Note : this is a L method added in L =cut =head2 put_value Title : put_value Usage : $ac->put_value($tagname, $value) -or- $ac->put_value([$tag_level1, $tag_level2, ...], $value) -or- $ac->put_value( [$tag_level1, $tag_level2, ...] ) Function: create a node in an annotation tree, and assign a scalar value to it if a value is specified Example : Returns : scalar or a Bio::AnnotationCollection object Args : $tagname, $value scalars (can be specified as -KEYS=>$tagname, -VALUE=>$value) -or- \@tagnames, $value (or as -KEYS=>\@tagnames, -VALUE=>$value ) Notes : This is a L method added in L. If intervening nodes do not exist, put_value creates them, replacing existing nodes. So if $ac->put_value('x', 10) was done, then later, $ac->put_value(['x', 'y'], 20), the original value of 'x' is trashed, and $ac->get_value('x') will now return the annotation collection with tagname 'y'. =cut =head2 get_keys Title : get_keys Usage : $ac->get_keys($tagname_level_1, $tagname_level_2,...) Function: Get an array of tagnames underneath the named tag nodes Example : # prints the values of the members of Category 1... print map { $ac->get_value($_) } $ac->get_keys('Category 1') ; Returns : array of tagnames or empty list if the arguments represent a leaf Args : [array of] tagname[s] =cut =head1 GenBank accession manipulation methods =head2 get_accessions Title : get_accessions Usage : $hiv_query->get_accessions() Function: Return an array of GenBank accessions associated with these sequences (available only after a query is subjected to a full run (i.e., when $RUN_OPTION == 2) Example : Returns : array of gb accession numbers, or () if none found for this query Args : none =cut sub get_accessions{ my $self = shift; my @ret; if (!$self->{'_RUN_LEVEL'} || ($self->{'_RUN_LEVEL'} < 2)) { $self->warn('Requires query run at level 2'); return (); } my @ac = $self->get_annotations_by_ids($self->ids); foreach (@ac) { push @ret, $_->get_value('Special','accession'); }; return @ret; } =head2 get_accessions_by_ids Title : get_accessions_by_ids (or ..._by_id) Usage : $hiv_query->get_accessions_by_ids(@ids) Function: Return an array of GenBank accessions associated with these LANL ids (available only after a query is subjected to a full run (i.e., when $RUN_OPTION == 2) Example : Returns : array of gb accession numbers, or () if none found for this query Args : none =cut sub get_accessions_by_ids { my $self = shift; my @ids = @_; my @ret; if (!$self->{'_RUN_LEVEL'} || ($self->{'_RUN_LEVEL'} < 2)) { $self->warn('Requires query run at level 2'); return (); } my @ac = $self->get_annotations_by_ids(@ids); foreach (@ac) { push @ret, $_->get_value('Special', 'accession'); }; return wantarray ? @ret : $ret[0]; } # singular alias sub get_accessions_by_id { shift->get_accessions_by_ids(@_); } ########## =head1 Query control methods =head2 _do_query Title : _do_query Usage : $hiv_query->_do_query or $hiv_query->_do_query($run_level) Function: Execute the query according to argument or $RUN_OPTION and set _RUN_LEVEL extent of query reflects the value of argument 0 : validate only (no HTTP action) 1 : return sequence count only 2 : return sequence ids (full query, returns with annotations) noop if current _RUN_LEVEL of query is >= argument or $RUN_OPTION, Example : Returns : actual _RUN_LEVEL (0, 1, or 2) achieved Args : desired run level (optional, global $RUN_OPTION is default) =cut sub _do_query{ my ($self,$rl) = @_; $rl = $RUN_OPTION unless defined $rl; $self->throw(-class=>"Bio::Root::BadParameter", -text=>"Invalid run option \"$RUN_OPTION\"", -value=>$RUN_OPTION) unless grep /^$RUN_OPTION$/, (0, 1, 2); (!defined($self->{'_RUN_LEVEL'})) && do { $self->_create_lanl_query(); $self->{'_RUN_LEVEL'} = 0; }; ($rl > 0) && (!defined($self->{'_RUN_LEVEL'}) || ($self->{'_RUN_LEVEL'} <= 0)) && do { $self->_do_lanl_request(); $self->{'_RUN_LEVEL'} = 1; }; ($rl > 1) && (!defined($self->{'_RUN_LEVEL'}) || ($self->{'_RUN_LEVEL'} <= 1)) && do { $self->_parse_lanl_response(); $self->{'_RUN_LEVEL'} = 2; }; return $self->{'_RUN_LEVEL'}; } =head2 _reset Title : _reset Usage : $hiv_query->_reset Function: Resets query storage, count, and ids, while retaining session id, original query string, and db schema Example : Returns : void Args : none =cut sub _reset{ my $self = shift; $self->ids([]); $self->count(0); $self->{'_annotations'} = {}; $self->{'_lanl_response'} = []; $self->{'_lanl_query'} = []; $self->{'_RUN_LEVEL'} = undef; return; } =head2 _session_id Title : _session_id Usage : $hiv_query->_session_id($newval) Function: Get/set HIV db session id (initialized in _do_lanl_request) Example : Returns : value of _session_id (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub _session_id{ my $self = shift; return $self->{'_session_id'} = shift if @_; return $self->{'_session_id'}; } =head2 _run_level Title : _run_level Usage : $obj->_run_level($newval) Function: returns the level at which the query has so far been run Example : Returns : value of _run_level (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub _run_level{ my $self = shift; return $self->{'_RUN_LEVEL'} = shift if @_; return $self->{'_RUN_LEVEL'}; } =head2 _run_option Title : _run_option Usage : $hiv_query->_run_option($newval) Function: Get/set HIV db query run option (see _do_query for values) Example : Returns : value of _run_option (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub _run_option{ my $self = shift; return $self->{'_run_option'} = shift if @_; return $self->{'_run_option'}; } =head2 _ua_hash Title : _ua_hash Usage : $obj->_ua_hash($newval) Function: Example : Returns : value of _ua_hash (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub _ua_hash{ my $self = shift; if (@_) { for (ref $_[0]) { $_ eq 'HASH' && do { $self->{'_ua_hash'} = $_[0]; last; }; !$_ && do { $self->{'_ua_hash'} = {@_}; last; }; do { $self->throw("Type ".ref($_)." unsupported as arg in _ua_hash"); }; } } return %{$self->{'_ua_hash'}}; } ####### =head1 Internals =head2 add_id Title : add_id Usage : $hiv_query->add_id($id) Function: Add new id to ids Example : Returns : the new id Args : a sequence id =cut sub add_id { my $self = shift; my $id = shift; $id = "" unless defined $id; # avoid warnings ${$self->{'ids'}}{$id}++; return $id; } sub lanl_base{ my $self = shift; return $self->{'lanl_base'} = shift if @_; return $self->{'lanl_base'}; } =head2 map_db Title : map_db Usage : $obj->map_db($newval) Function: Example : Returns : value of map_db (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub map_db{ my $self = shift; return $self->{'map_db'} = shift if @_; return $self->{'map_db'}; } =head2 make_search_if Title : make_search_if Usage : $obj->make_search_if($newval) Function: Example : Returns : value of make_search_if (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub make_search_if{ my $self = shift; return $self->{'make_search_if'} = shift if @_; return $self->{'make_search_if'}; } =head2 search_ Title : search_ Usage : $obj->search_($newval) Function: Example : Returns : value of search_ (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub search_{ my $self = shift; return $self->{'search_'} = shift if @_; return $self->{'search_'}; } =head2 _map_db_uri Title : _map_db_uri Usage : Function: return the full map_db uri ("Database Map") Example : Returns : scalar string Args : none =cut sub _map_db_uri{ my $self = shift; return $self->lanl_base."/".$self->map_db; } =head2 _make_search_if_uri Title : _make_search_if_uri Usage : Function: return the full make_search_if uri ("Make Search Interface") Example : Returns : scalar string Args : none =cut sub _make_search_if_uri{ my $self = shift; return $self->lanl_base."/".$self->make_search_if; } =head2 _search_uri Title : _search_uri Usage : Function: return the full search cgi uri ("Search Database") Example : Returns : scalar string Args : none =cut sub _search_uri{ my $self = shift; return $self->lanl_base."/".$self->search_; } =head2 _schema_file Title : _schema_file Usage : $hiv_query->_schema_file($newval) Function: Example : Returns : value of _schema_file (an XML string or filename) Args : on set, new value (an XML string or filename, or undef, optional) =cut sub _schema_file { my $self = shift; return $self->{'_schema_file'} = shift if @_; return $self->{'_schema_file'}; } =head2 _schema Title : _schema Usage : $hiv_query->_schema($newVal) Function: Example : Returns : value of _schema (an HIVSchema object in package L) Args : none (field set directly in new()) =cut sub _schema{ my $self = shift; $self->{'_schema'} ? return $self->{'_schema'} : $self->throw(-class=>'Bio::SchemaNotInit::Exception', -text=>"DB schema not initialized", -value=>""); } =head2 _lanl_query Title : _lanl_query Usage : $hiv_query->_lanl_query(\@query_parms) Function: pushes \@query_parms onto @{$self->{'_lanl_query'} Example : Returns : value of _lanl_query (an arrayref) Args : on set, new value (an arrayref or undef, optional) =cut sub _lanl_query{ my $self = shift; my $a = shift; return $self->{'_lanl_query'} unless $a; if (ref $a eq 'ARRAY') { push @{$self->{'_lanl_query'}}, $a; return $a; } else { $self->throw(-class=>'Bio::Root::BadParameter', -text=>'Array ref required for argument.', -value=>$a); } } =head2 _lanl_response Title : _lanl_response Usage : $hiv_query->_lanl_response($response) Function: pushes $response onto @{$hiv_query->{'_lanl_response'}} Example : Returns : value of _lanl_response (an arrayref of HTTP::Response objects) Args : on set, new value (an HTTP::Response object or undef, optional) =cut sub _lanl_response{ my $self = shift; if (@_) { my $r = shift; $self->throw(-class=>'Bio::Root::BadParameter', -text=>'Requires an HTTP::Response object', -value=> ref $r) unless ref($r) eq 'HTTP::Response'; push @{$self->{'_lanl_response'}}, $r; return $r; } return $self->{'_lanl_response'}; } =head2 _create_lanl_query Title : _create_lanl_query Usage : $hiv_query->_create_lanl_query() Function: validate query hash or string, prepare for _do_lanl_request Example : Returns : 1 if successful; throws exception on invalid query Args : =cut sub _create_lanl_query { my $self = shift; my (%inhash, @query, @qhashes); my ($schema, @validFields, @validAliases); for ($self->query) { !defined && do { $self->throw(-class=>'Bio::Root::NoSuchThing', -text=>'Query not specified', -value=>''); last; }; ref eq 'HASH' && do { %inhash = %$_; if ( grep /HASH/, map {ref} values %inhash ) { # check for {query=>{},annot=>[]} style $self->throw(-class=>'Bio::Root::BadParameter', -text=>'Query style unrecognized', -value=>"") unless defined $inhash{query}; push @qhashes, $_; } last; }; ref eq 'ARRAY' && do { $inhash{'query'} = {@$_}; push @qhashes, \%inhash; last; }; #else do { @qhashes = $self->_parse_query_string($_); }; } $schema = $self->_schema; @validFields = $schema->fields; @validAliases = $schema->aliases; # validate args based on the xml specification file # only checks blanks and fields with explicitly specified options # text fields can put anything, and the query will be run before # an error is caught in these foreach my $qh (@qhashes) { @query=(); foreach my $k (keys %{$$qh{'query'}}) { my $fld; # validate field if (grep /^$k$/, @validFields) { $fld = $k; } elsif (grep /^$k$/, @validAliases) { foreach (@validFields) { if (grep (/^$k$/, $schema->aliases($_))) { $fld = $_; last; } # $fld contains the field corresp. to the alias } } else { $self->throw(-class=>'Bio::Root::BadParameter', -text=>"Invalid field or alias \"$k\"", -value=>$qh); } # validate matchdata my $vf = $schema->_sfieldh($fld); my @md = (ref($qh->{'query'}{$k}) eq 'ARRAY') ? @{$qh->{'query'}{$k}} : $qh->{'query'}{$k}; if ($$vf{type} eq 'text') { foreach (@md) { $self->throw(-class=>'Bio::Root::BadParameter', -text=>'Value for field \"$k\" cannot be empty', -value=>$qh) if ($_ eq "") && ($$vf{blank_ok} eq 'false'); } } elsif ($$vf{type} eq 'option') { foreach my $md (@md) { $self->throw(-class=>'Bio::Root::BadParameter', -text=>"Invalid value \"".$md."\" for field \"$fld\"", -value=>$md) unless $$vf{option} && grep {defined $_ && /^$md$/} @{$$vf{option}}; } } # validated; add to query foreach (@md) { push @query, ($fld => $_); } } if ($qh->{'annot'}) { # validate the column names to be included in the query # to obtain annotations my @annot_cols = @{$qh->{'annot'}}; foreach my $k (@annot_cols) { my $fld; # validate field if (grep /^$k$/, @validFields) { $fld = $k; } elsif (grep /^$k$/, @validAliases) { foreach (@validFields) { if (grep (/^$k$/, $schema->aliases($_))) { $fld = $_; last; } # $fld should contain the field corresp. to the alias } } else { $self->throw(-class=>'Bio::Root::NoSuchThing', -text=>"Invalid field or alias \"$k\"", -value=>$k); } # lazy: 'Any' may not be the right default (but appears to # be, based on the lanl html) push @query, ($fld => 'Any'); } } # insure that LANL and GenBank ids are retrieved push @query, ('sequenceentry.se_id' => 'Any') unless grep /SequenceEntry\.SE_id/, @query; push @query, ('sequenceaccessions.sa_genbankaccession' => 'Any') unless grep /SequenceAccessions\.SA_GenBankAccession/, @query; # an "order" field is required by the LANL CGI # if not specified, default to SE_id push @query, ('order'=>'sequenceentry.se_id') unless grep /order/, @query; # @query now contains sfield=>matchdata pairs, as specified by user # include appropriate indexes to create correct automatic joins # established by the LANL CGI my (@qtbl, @qpk, @qfk); # the tables represented in query: my %q = @query; # squish the tables in the current query into hash keys @qtbl = $schema->tbl('-s', keys %q); if (@qtbl > 1) { # more than one table, see if they can be connected # get primary keys of query tables @qpk = $schema->pk(@qtbl); # we need to get each query table to join to # SequenceEntry. # # The schema is a graph with tables as nodes and # foreign keys<->primary keys as branches. To get a # join that works, need to include in the query # all branches along a path from SequenceEntry # to each query table. # # find_join does it... my @joink = map { my @k = $schema->find_join($_,'sequenceentry'); map {$_ || ()} @k } @qtbl; # squish the keys in @joink my %j; @j{@joink} = (1) x @joink; @joink = keys %j; # add the fields not currently in the query foreach (@qpk, @joink) { my $fld = $_; if (!grep(/^$fld$/,keys %q)) { # lazy: 'Any' may not be the right default (but appears to # be, based on the lanl html) push @query, ($_ => 'Any'); } } } # set object property $self->_lanl_query([@query]); } return 1; } # _do_lanl_request : post the queries created by _create_lanl_query # # @args (or {@args}) should be unaliased Table.Column=>Matchdata # pairs (these will be used directly in the POSTs) =head2 _do_lanl_request Title : _do_lanl_request Usage : $hiv_query->_do_lanl_request() Function: Perform search request on _create_lanl_query-validated query Example : Returns : 1 if successful Args : =cut sub _do_lanl_request { my $self = shift; my (@queries, @query, @interface,$interfGet,$searchGet,$response); my ($numseqs, $count); # handle args if (!$self->_lanl_query) { $self->throw(-class=>"Bio::Root::BadParameter", -text=>"_lanl_query empty, run _create_lanl_request first", -value=>""); } else { @queries = @{$self->_lanl_query}; } ## utility vars ## search site specific CGI parms my @search_pms = ('action'=>'Search'); my @searchif_pms = ('action'=>'Search Interface'); # don't get the actual sequence data here (i.e., the cgi parm # 'incl_seq' remains undefined... my @download_pms = ('action Download.x'=>1, 'action Download.y'=>1); ## HTML-testing regexps my $tags_re = qr{(?:\s*<[^>]+>\s*)}; my $session_id_re = qr{]*action=".*/search.comp"}; my $seqs_found_re = qr{Displaying$tags_re*(?:\s*[0-9-]*\s*)*$tags_re*of$tags_re*\s*([0-9]+)$tags_re*sequences found}; my $no_seqs_found_re = qr{Sorry.*no sequences found}; my $too_many_re = qr{too many records: $tags_re*([0-9]+)}; my $sys_error_re = qr{[Ss]ystem error}; my $sys_error_extract_re = qr{${tags_re}error:.*?]+>${tags_re}(.*?)
}; # find something like: # tables without join:
SequenceAccessions
my $tbl_no_join_re = qr{tables without join}i; # my $sorry_bud_re = qr{}; foreach my $q (@queries) { @query = @$q; # default query control parameters my %qctrl = ( max_rec=>100, sort_dir=>'ASC', translate=>'FALSE' # nucleotides ); # do work... # pull out commands, designated by the COMMAND pseudo-table... my @commands = map { $query[$_] =~ s/^COMMAND\.// ? @query[$_..$_+1] : () } (0..$#query-1); @query = map { $query[$_] =~ /^COMMAND/ ? () : @query[2*$_..2*$_+1] } (0..($#query-1)/2); # set control parameters explicitly made in query foreach my $cp (keys %qctrl) { if (!grep( /^$cp$/, @query)) { push @query, ($cp, $qctrl{$cp}); } } # note that @interface must be an array, since a single 'key' (the table) # can be associated with multiple 'values' (the columns) in the POST # squish fieldnames into hash keys my %q = @query; @interface = grep {defined} map {my ($tbl,$col) = /^(.*)\.(.*)$/} keys %q; my $err_val = ""; # to contain informative (ha!) value if error is parsed eval { # encapsulate communication errors here, defer biothrows... #mark the useragent should be setable from outside (so we can modify timeouts, etc) my $ua = Bio::WebAgent->new($self->_ua_hash); my $idPing = $ua->get($self->_map_db_uri); $idPing->is_success || do { $response=$idPing; die "Connect failed"; }; # get the session id if (!$self->_session_id) { ($self->{'_session_id'}) = ($idPing->content =~ /$session_id_re/); $self->_session_id || do { $response=$idPing; die "Session not established"; }; } # 10/07/08: # strange bug: if action=>'Search+Interface' below (note "+"), # the response to the search (in $searchGet) shows the correct # >number< of sequences found, but also an error "No sequences # match" and an SQL barf. Changing the "+" to a " " sets up the # interface to lead to the actual sequences being delivered as # expected. maj $interfGet = $ua->post($self->_make_search_if_uri, [@interface, @searchif_pms, id=>$self->_session_id]); $interfGet->is_success || do { $response=$interfGet; die "Interface request failed"; }; # see if a search form was returned... $interfGet->content =~ /$search_form_re/ || do { $response=$interfGet; die "Interface request failed"; }; $searchGet = $ua->post($self->_search_uri, [@query, @commands, @search_pms, id=>$self->_session_id]); $searchGet->is_success || do { $response = $searchGet; die "Search failed"; }; $response = $searchGet; for ($searchGet->content) { /$no_seqs_found_re/ && do { $err_val = 0; die "No sequences found"; last; }; /$too_many_re/ && do { $err_val = $1; die "Too many records ($1): must be <10000"; last; }; /$tbl_no_join_re/ && do { die "Some required tables went unjoined to query"; last; }; /$sys_error_re/ && do { /$sys_error_extract_re/; $err_val = $1; die "LANL system error"; }; /$seqs_found_re/ && do { $numseqs = $1; $count += $numseqs; last; }; # else... do { die "Search failed (response not parsed)"; }; } $response = $ua->post($self->_search_uri, [@download_pms, id=>$self->_session_id]); $response->is_success || die "Query failed"; # $response->content is a tab-separated value table of sequences # and metadata, first line starts with \# and contains fieldnames }; $self->_lanl_response($response); # throw, if necessary if ($@) { ($@ !~ "No sequences found") && do { $self->throw(-class=>'Bio::WebError::Exception', -text=>$@, -value=>$err_val); }; } } $self->warn("No sequences found for this query") unless $count; $self->count($count); return 1; # made it. } =head2 _parse_lanl_response Title : _parse_lanl_response Usage : $hiv_query->_parse_lanl_response() Function: Parse the tab-separated-value response obtained by _do_lanl_request for sequence ids, accessions, and annotations Example : Returns : 1 if successful Args : =cut sub _parse_lanl_response { ### handle parsing and merging multiple responses into the query object ### (ids and annotations) my $self = shift; my ($seqGet) = (@_); my (@data, @cols, %antbl, %antype); my $numseq = 0; my ($schema, @retseqs, %rec, $ac); $schema = $self->_schema; $self->_lanl_response || $self->throw(-class=>"Bio::QueryNotMade::Exception", -text=>"Query not yet performed; call _do_lanl_request()", -value=>""); foreach my $rsp (@{$self->_lanl_response}) { @data = split(/\r|\n/, $rsp->content); my $l; do { $l = shift @data; } while ($l !~ /Number/); $numseq += ( $l =~ /Number.*:\s([0-9]+)/ )[0]; @cols = split(/\t/, shift(@data)); # mappings from column headings to annotation keys # squish into hash keys my %q = @{ shift @{$self->_lanl_query} }; %antbl = $schema->ankh(keys %q); # get the category for each annotation map { $antype{ $_->{ankey} } = $_->{antype} } values %antbl; # normalize column headers map { tr/ /_/; $_ = lc; } @cols; foreach (@data) { @rec{@cols} = split /\t/; my $id = $rec{'se_id'}; $self->add_id($id); $ac = Bio::Annotation::Collection->new(); #create annotations foreach (@cols) { next if $_ eq '#'; my $t = $antype{$_} || "Unclassified"; my $d = $rec{$_}; # the data $ac->put_value(-KEYS=>[$t, $_], -VALUE=>$d); } $self->add_annotations_for_id($id, $ac); } 1; } return 1; # made it. } =head2 _parse_query_string Title : _parse_query_string Usage : $hiv_query->_parse_query_string($str) Function: Parses a query string using query language emulator QRY : in L Example : Returns : arrayref of hash structures suitable for passing to _create_lanl_query Args : a string scalar =cut sub _parse_query_string { my $self = shift; my $qstring = shift; my ($ptree, @ret); #syntax errors thrown in QRY (in HIVQueryHelper module) $ptree = QRY::_parse_q( $qstring ); @ret = QRY::_make_q($ptree); return @ret; } =head1 Dude, sorry- =head2 _sorry Title : _sorry Usage : $hiv_query->_sorry("-president=>Powell") Function: Throws an exception for unsupported option or parameter Example : Returns : Args : scalar string =cut sub _sorry{ my $self = shift; my $parm = shift; $self->throw(-class=>"Bio::HIVSorry::Exception", -text=>"Sorry, option/parameter \"$parm\" not (yet) supported. See manpage to complain.", -value=>$parm); return; } 1; BioPerl-1.007002/Bio/DB/Query/WebQuery.pm000444000766000024 2145213155576320 17743 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::WebQuery.pm # # Please direct questions and support issues to # # Cared for by Lincoln Stein # # Copyright Lincoln Stein # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code # =head1 NAME Bio::DB::Query::WebQuery - Helper class for web-based sequence queryies =head1 SYNOPSIS # Do not use this class directly. See Bio::DB::QueryI and one of # the implementor classes (such as Bio::DB::GenBankQuery) for # information. See L, L =head1 DESCRIPTION Do not use this class directly. See Bio::DB::QueryI and one of the implementor classes (such as Bio::DB::Query::GenBank) for information. Those writing subclasses must define _get_params() and _parse_response(), and possibly override _request_method(). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Lincoln Stein Email lstein@cshl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Query::WebQuery; use strict; use URI; use LWP::UserAgent; use HTTP::Request::Common; use base qw(Bio::Root::Root Bio::DB::QueryI); =head2 new Title : new Usage : $db = Bio::DB::WebQuery->new(@args) Function: create new query object Returns : new query object Args : -db database (e.g. 'protein') -ids array ref of ids (overrides query) -verbose turn on verbose debugging This method creates a new query object. Typically you will specify a -db and a -query argument. The value of -query is a database-specific string. If you provide an array reference of IDs in -ids, the query will be ignored and the list of IDs will be used when the query is passed to the database. =cut # Borrowed shamelessly from WebDBSeqI. Some of this code should be # refactored. sub new { my $class = shift; my $self = $class->SUPER::new(@_); my ($query,$ids,$verbose) = $self->_rearrange(['QUERY','IDS','VERBOSE'],@_); $self->throw('must provide one of the the -query or -ids arguments') unless defined($query) || defined($ids); if ($ids) { $query = $self->_generate_id_string($ids); } $self->query($query); $verbose && $self->verbose($verbose); my $ua = LWP::UserAgent->new(env_proxy => 1); $ua->agent(ref($self) ."/".($Bio::DB::Query::WebQuery::VERSION || '0.1')); $self->ua($ua); $self->{'_authentication'} = []; $self; } =head2 ua Title : ua Usage : my $ua = $self->ua or $self->ua($ua) Function: Get/Set a LWP::UserAgent for use Returns : reference to LWP::UserAgent Object Args : $ua - must be a LWP::UserAgent =cut sub ua { my ($self, $ua) = @_; my $d = $self->{'_ua'}; if( defined $ua && $ua->isa("LWP::UserAgent") ) { $self->{'_ua'} = $ua; } $d; } =head2 proxy Title : proxy Usage : $httpproxy = $db->proxy('http') or $db->proxy(['http','ftp'], 'http://myproxy' ) Function: Get/Set a proxy for use of proxy Returns : a string indicating the proxy Args : $protocol : an array ref of the protocol(s) to set/get $proxyurl : url of the proxy to use for the specified protocol $username : username (if proxy requires authentication) $password : password (if proxy requires authentication) =cut sub proxy { my ($self,$protocol,$proxy,$username,$password) = @_; return undef if ( !defined $self->ua || !defined $protocol || !defined $proxy ); $self->authentication($username, $password) if ($username && $password); return $self->ua->proxy($protocol,$proxy); } =head2 authentication Title : authentication Usage : $db->authentication($user,$pass) Function: Get/Set authentication credentials Returns : Array of user/pass Args : Array or user/pass =cut sub authentication{ my ($self,$u,$p) = @_; if( defined $u && defined $p ) { $self->{'_authentication'} = [ $u,$p]; } return @{$self->{'_authentication'}}; } =head2 ids Title : ids Usage : @ids = $db->ids([@ids]) Function: get/set matching ids Returns : array of sequence ids Args : (optional) array ref with new set of ids =cut sub ids { my $self = shift; if (@_) { my $d = $self->{'_ids'}; my $arg = shift; $self->{'_ids'} = ref $arg ? $arg : [$arg]; return $d ? @$d : (); } else { $self->_fetch_ids; return @{$self->{'_ids'} || []}; } } =head2 query Title : query Usage : $query = $db->query([$query]) Function: get/set query string Returns : string Args : (optional) new query string =cut sub query { my $self = shift; my $d = $self->{'_query'}; $self->{'_query'} = shift if @_; $d; } =head2 _fetch_ids Title : _fetch_ids Usage : @ids = $db->_fetch_ids Function: run query, get ids Returns : array of sequence ids Args : none =cut sub _fetch_ids { my $self = shift; $self->_run_query; $self->_run_query(1) if $self->_truncated; $self->throw('Id list has been truncated even after maxids requested') if $self->_truncated; return @{$self->{'_ids'}} if $self->{'_ids'}; } =head2 _run_query Title : _run_query Usage : $success = $db->_run_query Function: run query, parse results Returns : true if successful Args : none =cut sub _run_query { my $self = shift; my $force = shift; # allow the query to be run one extra time if truncated return $self->{'_ran_query'} if $self->{'_ran_query'}++ && !$force; my $request = $self->_get_request; $self->debug("request is ".$request->url."\n"); my $response = $self->ua->request($request); return unless $response->is_success; $self->debug("response is ".$response->content."\n"); $self->_parse_response($response->content); 1; } =head2 _truncated Title : _truncated Usage : $flag = $db->_truncated([$newflag]) Function: get/set truncation flag Returns : boolean Args : new flag Some databases will truncate output unless explicitly asked not to. This flag allows a "two probe" attempt. =cut sub _truncated { my $self = shift; my $d = $self->{'_truncated'}; $self->{'_truncated'} = shift if @_; $d; } =head2 _get_request Title : _get_request Usage : $http_request = $db->_get_request(@params) Function: create an HTTP::Request with indicated parameters Returns : HTTP::Request object Args : CGI parameter list =cut sub _get_request { my $self = shift; my ($method,$base,@params) = $self->_request_parameters; my $uri = URI->new($base); my $request; if ($method eq 'get') { $uri->query_form(@params); $request = GET $uri; } else { $request = POST $uri,\@params; } $request->proxy_authorization_basic($self->authentication) if $self->authentication; $request; } =head2 _parse_response Title : _parse_response Usage : $db->_parse_response($content) Function: parse out response Returns : empty Args : none Throws : 'unparseable output exception' NOTE: This method must be implemented by subclass. =cut sub _parse_response { my $self = shift; my $content = shift; $self->throw_not_implemented; } =head2 _request_parameters Title : _request_parameters Usage : ($method,$base,@params = $db->_request_parameters Function: return information needed to construct the request Returns : list of method, url base and key=>value pairs Args : none NOTE: This method must be implemented by subclass. =cut sub _request_parameters { my $self = shift; $self->throw_not_implemented; } =head2 _generate_id_string Title : _generate_id_string Usage : $string = $db->_generate_id_string Function: joins IDs together in string (implementation-dependent) Returns : string of concatenated IDs Args : array ref of ids (normally passed into the constructor) NOTE: This method must be implemented by subclass. =cut sub _generate_id_string { my $self = shift; $self->throw_not_implemented; } 1; BioPerl-1.007002/Bio/DB/SeqFeature000755000766000024 013155576320 16420 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/SeqFeature/NormalizedFeature.pm000444000766000024 5351413155576320 22563 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::NormalizedFeature; =head1 NAME Bio::DB::SeqFeature::NormalizedFeature -- Normalized feature for use with Bio::DB::SeqFeature::Store =head1 SYNOPSIS use Bio::DB::SeqFeature::Store; # Open the sequence database my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:test'); my ($feature) = $db->get_features_by_name('ZK909'); my @subfeatures = $feature->get_SeqFeatures(); my @exons_only = $feature->get_SeqFeatures('exon'); # create a new object $db->seqfeature_class('Bio::DB::SeqFeature::NormalizedFeature'); my $new = $db->new_feature(-primary_tag=>'gene', -seq_id => 'chr3', -start => 10000, -end => 11000); # add a new exon $feature->add_SeqFeature($db->new_feature(-primary_tag=>'exon', -seq_id => 'chr3', -start => 5000, -end => 5551)); =head1 DESCRIPTION The Bio::DB::SeqFeature::NormalizedFeature object is an alternative representation of SeqFeatures for use with Bio::DB::SeqFeature::Store database system. It is identical to Bio::DB::SeqFeature, except that instead of storing feature/subfeature relationships in a database table, the information is stored in the object itself. This actually makes the objects somewhat inconvenient to work with from SQL, but does speed up access somewhat. To use this class, pass the name of the class to the Bio::DB::SeqFeature::Store object's seqfeature_class() method. After this, $db-Enew_feature() will create objects of type Bio::DB::SeqFeature::NormalizedFeature. If you are using the GFF3 loader, pass Bio::DB::SeqFeature::Store::GFF3Loader-Enew() the -seqfeature_class argument: use Bio::DB::SeqFeature::Store::GFF3Loader; my $store = connect_to_db_somehow(); my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new( -store=>$db, -seqfeature_class => 'Bio::DB::SeqFeature::NormalizedFeature' ); =cut use strict; use Carp 'croak'; use base 'Bio::SeqFeature::Lite'; use base 'Bio::DB::SeqFeature::NormalizedFeatureI'; use overload '""' => \&as_string, eq => \&eq, ne => \&ne, fallback => 1; use vars '$AUTOLOAD'; my $USE_OVERLOADED_NAMES = 1; # some of this is my fault and some of it is changing bioperl API *get_all_SeqFeatures = *sub_SeqFeature = *merged_segments = \&segments; ##### CLASS METHODS #### =head2 new Title : new Usage : $feature = Bio::DB::SeqFeature::NormalizedFeature->new(@args) Function: create a new feature Returns : the new seqfeature Args : see below Status : public This method creates and, if possible stores into a database, a new Bio::DB::SeqFeature::NormalizedFeature object using the specialized Bio::DB::SeqFeature class. The arguments are the same to Bio::SeqFeature::Generic-Enew() and Bio::Graphics::Feature-Enew(). The most important difference is the B<-store> option, which if present creates the object in a Bio::DB::SeqFeature::Store database, and he B<-index> option, which controls whether the feature will be indexed for retrieval (default is true). Ordinarily, you would only want to turn indexing on when creating top level features, and off only when storing subfeatures. The default is on. Arguments are as follows: -seq_id the reference sequence -start the start position of the feature -end the stop position of the feature -display_name the feature name (returned by seqname) -primary_tag the feature type (returned by primary_tag) -source the source tag -score the feature score (for GFF compatibility) -desc a description of the feature -segments a list of subfeatures (see Bio::Graphics::Feature) -subtype the type to use when creating subfeatures -strand the strand of the feature (one of -1, 0 or +1) -phase the phase of the feature (0..2) -url a URL to link to when rendered with Bio::Graphics -attributes a hashref of tag value attributes, in which the key is the tag and the value is an array reference of values -store a previously-opened Bio::DB::SeqFeature::Store object -index index this feature if true Aliases: -id an alias for -display_name -seqname an alias for -display_name -display_id an alias for -display_name -name an alias for -display_name -stop an alias for end -type an alias for primary_tag =cut sub new { my $class = shift; my %args = @_; my $db = $args{-store} || $args{-factory}; my $index = exists $args{-index} ? $args{-index} : 1; my $self = $class->SUPER::new(@_); if ($db) { if ($index) { $db->store($self); # this will set the primary_id } else { $db->store_noindex($self); # this will set the primary_id } $self->object_store($db); } $self; } =head2 Bio::SeqFeatureI methods The following Bio::SeqFeatureI methods are supported: seq_id(), start(), end(), strand(), get_SeqFeatures(), display_name(), primary_tag(), source_tag(), seq(), location(), primary_id(), overlaps(), contains(), equals(), intersection(), union(), has_tag(), remove_tag(), add_tag_value(), get_tag_values(), get_all_tags() Some methods that do not make sense in the context of a genome annotation database system, such as attach_seq(), are not supported. Please see L for more details. =cut sub seq { my $self = shift; require Bio::PrimarySeq unless Bio::PrimarySeq->can('new'); my ($start,$end) = ($self->start,$self->end); if ($self->strand < 0) { ($start,$end) = ($end,$start); } if (my $store = $self->object_store) { return Bio::PrimarySeq->new(-seq => $store->fetch_sequence($self->seq_id,$start,$end) || '', -id => $self->display_name); } else { return $self->SUPER::seq($self->seq_id,$start,$end); } } sub subseq { my $self = shift; my ($newstart,$newstop) = @_; my $store = $self->object_store or return; my ($start,$stop) = ($self->start+$newstart-1,$self->end+$newstop-1); if ($self->strand < 0) { ($start,$stop) = ($stop,$start); } my $seq = $store->fetch_sequence($self->seq_id,$start,$stop); return Bio::PrimarySeq->new($seq); } =head2 add_SeqFeature Title : add_SeqFeature Usage : $flag = $feature->add_SeqFeature(@features) Function: Add subfeatures to the feature Returns : true if successful Args : list of Bio::SeqFeatureI objects Status : public Add one or more subfeatures to the feature. For best results, subfeatures should be of the same class as the parent feature (i.e. don't try mixing Bio::DB::SeqFeature::NormalizedFeature with other feature types). An alias for this method is add_segment(). =cut sub add_SeqFeature { my $self = shift; $self->_add_segment(1,@_); } =head2 update Title : update Usage : $flag = $feature->update() Function: Update feature in the database Returns : true if successful Args : none Status : public After changing any fields in the feature, call update() to write it to the database. This is not needed for add_SeqFeature() as update() is invoked automatically. =cut sub update { my $self = shift; my $store = $self->object_store or return; $store->store($self); } =head2 get_SeqFeatures Title : get_SeqFeature Usage : @subfeatures = $feature->get_SeqFeatures([@types]) Function: return subfeatures of this feature Returns : list of subfeatures Args : list of subfeature primary_tags (optional) Status : public This method extends the Bio::SeqFeatureI get_SeqFeatures() slightly by allowing you to pass a list of primary_tags, in which case only subfeatures whose primary_tag is contained on the list will be returned. Without any types passed all subfeatures are returned. =cut # segments can be either normalized IDs or ordinary feature objects sub get_SeqFeatures { my $self = shift; my @types = @_; my $s = $self->{segments} or return; my $store = $self->object_store; my (@ordinary,@ids); for (@$s) { if (ref ($_)) { push @ordinary,$_; } else { push @ids,$_; } } my @r = grep {$_->type_match(@types)} (@ordinary,$store->fetch_many(\@ids)); for my $r (@r) { eval {$r->object_store($store) }; } return @r; } =head2 object_store Title : object_store Usage : $store = $feature->object_store([$new_store]) Function: get or set the database handle Returns : current database handle Args : new database handle (optional) Status : public This method will get or set the Bio::DB::SeqFeature::Store object that is associated with the feature. After changing the store, you should probably unset the feature's primary_id() and call update() to ensure that the object is written into the database as a new feature. =cut sub object_store { my $self = shift; my $d = $self->{store}; $self->{store} = shift if @_; $d; } =head2 overloaded_names Title : overloaded_names Usage : $overload = $feature->overloaded_names([$new_overload]) Function: get or set overloading of object strings Returns : current flag Args : new flag (optional) Status : public For convenience, when objects of this class are stringified, they are represented in the form "primary_tag(display_name)". To turn this feature off, call overloaded_names() with a false value. You can invoke this on an individual feature object or on the class: Bio::DB::SeqFeature::NormalizedFeature->overloaded_names(0); =cut sub overloaded_names { my $class = shift; my $d = $USE_OVERLOADED_NAMES; $USE_OVERLOADED_NAMES = shift if @_; $d; } =head2 segment Title : segment Usage : $segment = $feature->segment Function: return a Segment object corresponding to feature Returns : a Bio::DB::SeqFeature::Segment Args : none Status : public This turns the feature into a Bio::DB::SeqFeature::Segment object, which you can then use to query for overlapping features. See L. =cut sub segment { my $self = shift; return Bio::DB::SeqFeature::Segment->new($self); } ### instance methods =head2 AUTOLOADED methods @subfeatures = $feature->Exon; If you use an unknown method that begins with a capital letter, then the feature autogenerates a call to get_SeqFeatures() using the lower-cased method name as the primary_tag. In other words $feature-EExon is equivalent to: @subfeature s= $feature->get_SeqFeatures('exon') If you use an unknown method that begins with Tag_(tagname), Att_(tagname) Is_(tagname), then it will be the same as calling the each_tag_value() method with the tagname. In a list context, these autogenerated procedures return the list of results. In scalar context, they return the first item in the list!! =cut sub AUTOLOAD { my($pack,$func_name) = $AUTOLOAD=~/(.+)::([^:]+)$/; my $sub = $AUTOLOAD; my $self = $_[0]; # ignore DESTROY calls return if $func_name eq 'DESTROY'; # call attributes if func_name begins with "Tag_" or "Att_": if ($func_name =~ /^(Tag|Att|Is)_(\w+)/) { my @result = $self->each_tag_value($2); return wantarray ? @result : $result[0]; } # fetch subfeatures if func_name has an initial cap if ($func_name =~ /^[A-Z]/) { return $self->get_SeqFeatures(lc $func_name); } # error message of last resort $self->throw(qq(Can't locate object method "$func_name" via package "$pack")); }#' sub add_segment { my $self = shift; $self->_add_segment(0,@_); } # This adds subfeatures. It has the property of converting the # provided features into an object like itself and storing them # into the database. If the feature already has a primary id and # an object_store() method, then it is not stored into the database, # but its primary id is reused. sub _add_segment { my $self = shift; my $normalized = shift; my $store = $self->object_store; my @segments = $self->_create_subfeatures($normalized,@_); # fix boundaries $self->_fix_boundaries(\@segments); # freakish fixing of our non-standard Target attribute $self->_fix_target(\@segments); for my $seg (@segments) { my $id = $normalized ? $seg->primary_id : $seg; defined $id or $self->throw("No primary ID when there should be"); push @{$self->{segments}},$id; }; $self->update if $self->primary_id; # write us back to disk } sub _fix_boundaries { my $self = shift; my $segments = shift; my $normalized = shift; my $min_start = $self->start || 999_999_999_999; my $max_stop = $self->end || -999_999_999_999; for my $seg (@$segments) { $min_start = $seg->start if $seg->start < $min_start; $max_stop = $seg->end if $seg->end > $max_stop; } # adjust our boundaries, etc. $self->start($min_start) if $min_start < $self->start; $self->end($max_stop) if $max_stop > $self->end; $self->{ref} ||= $segments->[0]->seq_id; $self->{strand} ||= $segments->[0]->strand; } sub _fix_target { my $self = shift; my $segs = shift; my $normalized = shift; # ignored for now # freakish fixing of our non-standard Target attribute if (my $t = ($self->attributes('Target'))[0]) { my ($seqid,$tstart,$tend,$strand) = split /\s+/,$t; if (defined $tstart && defined $tend) { my $min_tstart = $tstart; my $max_tend = $tend; for my $seg (@$segs) { my $st = ($seg->attributes('Target'))[0] or next; (undef,$tstart,$tend) = split /\s+/,$st; next unless defined $tstart && defined $tend; $min_tstart = $tstart if $tstart < $min_tstart; $max_tend = $tend if $tend > $max_tend; } if ($min_tstart < $tstart or $max_tend > $tend) { $self->{attributes}{Target}[0] = join ' ',($seqid,$min_tstart,$max_tend,$strand||''); } } } } # undo the load_id and Target hacks on the way out sub format_attributes { my $self = shift; my $parent = shift; my $fallback_id = shift; my $load_id = $self->load_id || ''; my $targobj = ($self->attributes('Target'))[0]; # was getting an 'Use of uninitialized value with split' here, changed to cooperate -cjf 7/10/07 my ($target) = $targobj ? split /\s+/,($self->attributes('Target'))[0] : (''); my @tags = $self->all_tags; my @result; for my $t (@tags) { my @values = $self->each_tag_value($t); # This line prevents Alias from showing up if it matches the load id, but this is not good # @values = grep {$_ ne $load_id && $_ ne $target} @values if $t eq 'Alias'; # these are hacks, which we don't want to appear in the file next if $t eq 'load_id'; next if $t eq 'parent_id'; foreach (@values) { s/\s+$// } # get rid of trailing whitespace push @result,join '=',$self->escape($t),join(',', map {$self->escape($_)} @values) if @values; } my $id = $self->primary_id || $fallback_id; my $parent_id; if (@$parent) { $parent_id = join (',',map {$self->escape($_)} @$parent); } my $name = $self->display_name; unshift @result,"ID=".$self->escape($id) if defined $id; unshift @result,"Parent=".$parent_id if defined $parent_id; unshift @result,"Name=".$self->escape($name) if defined $name; return join ';',@result; } sub _create_subfeatures { my $self = shift; my $normalized = shift; my $type = $self->{subtype} || $self->{type}; my $ref = $self->seq_id; my $name = $self->name; my $class = $self->class; my $store = $self->object_store; my $source = $self->source; if ($normalized) { $store or $self->throw("Feature must be associated with a Bio::DB::SeqFeature::Store database before attempting to add subfeatures to a normalized object"); } my $index_subfeatures_policy = eval{$store->index_subfeatures}; my @segments; for my $seg (@_) { if (UNIVERSAL::isa($seg,ref $self)) { if (!$normalized) { # make sure the object has no lazy behavior $seg->primary_id(undef); $seg->object_store(undef); } push @segments,$seg; } elsif (ref($seg) eq 'ARRAY') { my ($start,$stop) = @{$seg}; next unless defined $start && defined $stop; # fixes an obscure bug somewhere above us my $strand = $self->{strand}; if ($start > $stop) { ($start,$stop) = ($stop,$start); $strand = -1; } push @segments,$self->new(-start => $start, -stop => $stop, -strand => $strand, -ref => $ref, -type => $type, -name => $name, -class => $class, -source => $source, ); } elsif (UNIVERSAL::isa($seg,'Bio::SeqFeatureI')) { my $score = $seg->score if $seg->can('score'); my $f = $self->new(-start => $seg->start, -end => $seg->end, -strand => $seg->strand, -seq_id => $seg->seq_id, -name => $seg->display_name, -primary_tag => $seg->primary_tag, -source_tag => $seg->source, -score => $score, -source => $source, ); for my $tag ($seg->get_all_tags) { my @values = $seg->get_tag_values($tag); $f->{attributes}{$tag} = \@values; } push @segments,$f; } else { croak "$seg is neither a Bio::SeqFeatureI object nor an arrayref"; } } return unless @segments; if ($normalized && $store) { # parent/child data is going to be stored in the database my @need_loading = grep {!defined $_->primary_id || $_->object_store ne $store} @segments; if (@need_loading) { my $result; if ($index_subfeatures_policy) { $result = $store->store(@need_loading); } else { $result = $store->store_noindex(@need_loading); } $result or croak "Couldn't store one or more subseqfeatures"; } } return @segments; } =head2 load_id Title : load_id Usage : $id = $feature->load_id Function: get the GFF3 load ID Returns : the GFF3 load ID (string) Args : none Status : public For features that were originally loaded by the GFF3 loader, this method returns the GFF3 load ID. This method may not be supported in future versions of the module. =cut sub load_id { return (shift->attributes('load_id'))[0]; } =head2 notes Title : notes Usage : @notes = $feature->notes Function: get contents of the GFF3 Note tag Returns : List of GFF3 Note tags Args : none Status : public For features that were originally loaded by the GFF3 loader, this method returns the contents of the Note tag as a list. This is a convenience for Bio::Graphics, which looks for notes() when it constructs a default description line. =cut sub notes { return shift->attributes('Note'); } =head2 primary_id Title : primary_id Usage : $id = $feature->primary_id([$new_id]) Function: get/set the feature's database ID Returns : the current primary ID Args : none Status : public This method gets or sets the primary ID of the feature in the underlying Bio::DB::SeqFeature::Store database. If you change this field and then call update(), it will have the effect of making a copy of the feature in the database under a new ID. =cut sub primary_id { my $self = shift; my $d = $self->{primary_id}; $self->{primary_id} = shift if @_; $d; } =head2 target Title : target Usage : $segment = $feature->target Function: return the segment correspondent to the "Target" attribute Returns : a Bio::DB::SeqFeature::Segment object Args : none Status : public For features that are aligned with others via the GFF3 Target attribute, this returns a segment corresponding to the aligned region. The CIGAR gap string is not yet supported. =cut sub target { my $self = shift; my @targets = $self->attributes('Target'); my @result; for my $t (@targets) { my ($seqid,$start,$end,$strand) = split /\s+/,$t; $strand ||= ''; $strand = $strand eq '+' ? 1 : $strand eq '-' ? -1 : 0; push @result,Bio::DB::SeqFeature::Segment->new($self->object_store, $seqid, $start, $end, $strand); } return wantarray ? @result : $result[0]; } =head2 Internal methods =over 4 =item $feature-Eas_string() Internal method used to implement overloaded stringification. =item $boolean = $feature-Etype_match(@list_of_types) Internal method that will return true if the feature's primary_tag and source_tag match any of the list of types (in primary_tag:source_tag format) provided. =back =cut sub as_string { my $self = shift; return overload::StrVal($self) unless $self->overloaded_names; my $name = $self->display_name || $self->load_id; $name ||= "id=".$self->primary_id if $self->primary_id; $name ||= ""; my $method = $self->primary_tag; my $source= $self->source_tag; my $type = $source ? "$method:$source" : $method; return "$type($name)"; } sub eq { my $self = shift; my $b = shift; my $store1 = $self->object_store; my $store2 = eval {$b->object_store} || ''; return $store1 eq $store2 && $self->primary_id eq $b->primary_id; } sub ne { my $self = shift; return !$self->eq(shift); } # completely case insensitive sub type_match { my $self = shift; my @types = @_; my $method = lc $self->primary_tag; my $source = lc $self->source_tag; for my $t (@types) { my ($m,$s) = map {lc $_} split /:/,$t; return 1 if $method eq $m && (!defined $s || $source eq $s); } return; } sub segments { shift->get_SeqFeatures(@_) } 1; __END__ =head1 BUGS This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs. =head1 SEE ALSO L, L, L, L, L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2006 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/SeqFeature/NormalizedFeatureI.pm000444000766000024 223113155576320 22642 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::NormalizedFeatureI; =head1 NAME Bio::DB::SeqFeature::NormalizedFeatureI -- Interface for normalized features =head1 SYNOPSIS none =head1 DESCRIPTION This is an extremely simple interface that contains a single method, subfeatures_are_normalized(). This method returns a true value. Bio::DB::SeqFeature::Store feature classes will inherit this interface to flag that they are able to store subfeatures in a normalized way such that the subfeature is actually contained in the Bio::DB::SeqFeature::Store database and the parent feature contains only the subfeatures primary ID. =head1 BUGS None, but the whole class design might be flawed. =head1 SEE ALSO L, L, L, L, L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2006 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut sub subfeatures_are_normalized { 1 } 1; BioPerl-1.007002/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm000444000766000024 254213155576320 23617 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::NormalizedTableFeatureI; =head1 NAME Bio::DB::SeqFeature::NormalizedTableFeatureI -- Interface for normalized features whose hierarchy is stored in a table =head1 SYNOPSIS none =head1 DESCRIPTION This is an extremely simple interface that contains a single method, subfeatures_are_stored_in_a_table(). This method returns a true value. Bio::DB::SeqFeature::Store feature classes will inherit this interface to flag that in addition to being able to store features in a normalized way, they will use the Bio::DB::SeqFeature::Store database to record their parent/child relationships. A class that inherits from NormalizedTableFeatureI will also inherit from NormalizedFeatureI, as the first is a subclass of the second. =head1 BUGS None, but the whole class design might be flawed. =head1 SEE ALSO L, L, L, L, L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2006 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use base 'Bio::DB::SeqFeature::NormalizedFeatureI'; sub subfeatures_are_stored_in_a_table { 1 } 1; BioPerl-1.007002/Bio/DB/SeqFeature/Segment.pm000444000766000024 3376013155576320 20546 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::Segment; =head1 NAME Bio::DB::SeqFeature::Segment -- Location-based access to genome annotation data =head1 SYNOPSIS use Bio::DB::SeqFeature::Store; # Open the sequence database my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:test'); my $segment = $db->segment('Chr1',5000=>6000); my @features = $segment->features('mRNA','match'); =head1 DESCRIPTION The segment object simplifies access to Bio::DB::SeqFeature store by acting as a placeholder for a region of the genome. You can replace this statement: @features = $db->features(-seq_id=>'Chr1', -start=>5000, -end=>6000, -types=>['mRNA','match','repeat_region']); with these statements: $segment = $db->segment('Chr1',5000=>6000); @features = $segment->features('mRNA','match','repeat_region'); You can also initialize a segment from an existing SeqFeature object. The range will be picked up from the SeqFeature boundaries: $segment = Bio::DB::SeqFeature::Segment->new($feature); # for Bio::DB::SeqFeature $segment = Bio::DB::SeqFeature::Segment->new($feature,$store); # for other Bio::SeqFeatureI objects The segment object implements the full Bio::SeqFeature::CollectionI interface, thereby allowing you to iterate over all features in the range. =cut use strict; use base 'Bio::SeqFeature::CollectionI','Bio::RangeI'; use Bio::DB::GFF::Util::Rearrange; use overload '""' => \&as_string, fallback => 1; =head1 PUBLIC METHODS The following are public methods intended for external use. =head2 new Title : new Usage : $segment = Bio::DB::SeqFeature::Segment->new(@options) Function: create a new Segment object Returns : A Bio::DB::SeqFeature::Segment object Args : several - see below Status : public This class method creates a Bio::DB::SeqFeature::Segment object. You must provide a Bio::DB::SeqFeature::Store as well as the coordinates of the segment. These arguments can be provided explicitly or indirectly. First form: $segment = Bio::DB::SeqFeature::Segment->new($store,$seqid,$start,$end,$strand) In this form a segment is defined by a Bio::DB::SeqFeature::Store, the sequence ID, the start, end and strand. This is the form that is invoked internally by Bio::DB::SeqFeature::Store when you call its segment() method. Second form: $segment = Bio::DB::SeqFeature::Segment->new($seqfeature [,$store]); In this form, you pass new() a Bio::SeqFeatureI object. The segment is constructed from the seq_id and coordinates are taken from the object. If you pass a store-aware seqfeature object (e.g. Bio::DB::SeqFeature) then the store database is also derived from the feature. Otherwise you will have to pass the store as a second argument. =cut ### # new() # # Call as Bio::DB::SeqFeature::Segment->new($seqfeature,$store) # # or # Bio::DB::SeqFeature::Segment->new(-seqid=>$seqid,-start=>$start,-end=>$end,-strand=>$strand,-store=>$store) # sub new { my $class = shift; my ($store,$seqid,$start,$end,$strand,$id); if (ref $_[0] && UNIVERSAL::isa($_[0],'Bio::SeqFeatureI')) { my $seqfeature = shift; $store = shift; $store ||= eval {$seqfeature->object_store}; $class->throw("I could not derive the Bio::DB::SeqFeature::Store object from the arguments passed to Bio::DB::SeqFeature::Segment->new(). Please pass the Store object as the second argument") unless $store; $seqid = $seqfeature->seq_id; $start = $seqfeature->start; $end = $seqfeature->end; $strand= $seqfeature->strand; $id = eval{$seqfeature->primary_id}; } else { ($store,$seqid,$start,$end,$strand,$id) = @_; } return bless { store => $store, seqid => $seqid, start => $start, end => $end, strand => $strand, primary_id => $id, },ref($class) || $class; } =head2 features Title : features Usage : @features = $segment->features(@args) Function: fetch seqfeatures that overlap the segment Returns : list of features Args : see below Status : Public This is the workhorse for feature query and retrieval. It takes a series of -name=E$value arguments filter arguments. Features that match all the filters are returned. Argument Value -------- ----- Location filters: -strand Strand -range_type Type of range match ('overlaps','contains','contained_in') Name filters: -name Name of feature (may be a glob expression) -aliases If true, match aliases as well as display names -class Archaic argument for backward compatibility. (-class=>'Clone',-name=>'ABC123') is equivalent to (-name=>'Clone:ABC123') Type filters: -types List of feature types (array reference) or one type (scalar) -type Synonym for the above -primary_tag Synonym for the above -attributes Hashref of attribute=>value pairs as per get_features_by_attribute(). Multiple alternative values can be matched by providing an array reference. -attribute synonym for -attributes This is identical to the Bio::DB::SeqFeature::Store-Efeatures() method, except that the -seq_id, -start, and -end arguments are provided by the segment object. If a simple list of arguments is provided, then the list is taken to be the set of feature types (primary tags) to filter on. Examples: All features that overlap the current segment: @features = $segment->features; All features of type mRNA that overlap the current segment: @features = $segment->features('mRNA'); All features that are completely contained within the current segment: @features = $segment->features(-range_type=>'contains'); All "confirmed" mRNAs that overlap the current segment: @features = $segment->features(-attributes=>{confirmed=>1},-type=>'mRNA'); =cut sub features { my $self = shift; my @args; if (@_ == 0) { @args = (); } elsif ($_[0] !~/^-/) { my @types = @_; @args = (-type=>\@types); } else { @args = @_; } $self->{store}->features(@args,-seqid=>$self->{seqid},-start=>$self->{start},-end=>$self->{end}); } sub types { my $self = shift; my %types; my $iterator = $self->get_seq_stream(@_); while (my $f = $iterator->next_seq) { $types{$f->type}++; } return %types; } =head2 get_seq_stream Title : get_seq_stream Usage : $iterator = $segment->get_seq_stream(@args) Function: return an iterator across all features in the database Returns : a Bio::DB::SeqFeature::Store::Iterator object Args : (optional) the feature() method Status : public This is identical to Bio::DB::SeqFeature::Store-Eget_seq_stream() except that the location filter is always automatically applied so that the iterator you receive returns features that overlap the segment's region. When called without any arguments this method will return an iterator object that will traverse all indexed features in the database that overlap the segment's region. Call the iterator's next_seq() method to step through them (in no particular order): my $iterator = $db->get_seq_stream; while (my $feature = $iterator->next_seq) { print $feature->primary_tag,' ',$feature->display_name,"\n"; } You can select a subset of features by passing a series of filter arguments. The arguments are identical to those accepted by $segment-Efeatures(). get_feature_stream() ican be used as a synonym for this method. =cut #' sub get_seq_stream { my $self = shift; $self->{store}->get_seq_stream(@_,-seqid=>$self->{seqid},-start=>$self->{start},-end=>$self->{end}); } sub get_feature_stream { shift->get_seq_stream(@_) } =head2 store Title : store Usage : $store = $segment->store Function: return the Bio::DB::SeqFeature::Store object associated with the segment Returns : a Bio::DB::SeqFeature::Store: object Args : none Status : public =cut sub factory { shift->{store} } sub store { shift->{store} } =head2 primary_tag, type, Title : primary_tag,type Usage : $primary_tag = $segment->primary_tag Function: returns the string "region" Returns : "region" Args : none Status : public The primary_tag method returns the constant tag "region". type() is a synonym for this method. =cut sub type { shift->primary_tag } =head2 as_string Title : as_string Usage : $name = $segment->as_string Function: expands the object into a human-readable string Returns : "seq_id:start..end" Args : none Status : public The as_string() method is overloaded into the "" operator so that the object is represented as a human readable string in the form "seq_id:start..end" when used in a string context. =cut sub as_string { my $self = shift; my $label = $self->seq_id; my $start = $self->start || ''; my $end = $self->end || ''; return "$label:$start..$end"; } =head2 rel2abs Title : rel2abs Usage : @coords = $s->rel2abs(@coords) Function: convert relative coordinates into absolute coordinates Returns : a list of absolute coordinates Args : a list of relative coordinates Status : Public This function takes a list of positions in relative coordinates to the segment, and converts them into absolute coordinates. =cut sub rel2abs { my $self = shift; my @result; my ($start,$strand) = ($self->start,$self->strand); @result = $strand < 0 ? map { $start - $_ + 1 } @_ : map { $_ + $start - 1 } @_; # if called with a single argument, caller will expect a single scalar reply # not the size of the returned array! return $result[0] if @result == 1 and !wantarray; @result; } =head2 abs2rel Title : abs2rel Usage : @rel_coords = $s->abs2rel(@abs_coords) Function: convert absolute coordinates into relative coordinates Returns : a list of relative coordinates Args : a list of absolute coordinates Status : Public This function takes a list of positions in absolute coordinates and returns a list expressed in relative coordinates. =cut sub abs2rel { my $self = shift; my @result; my ($start,$strand) = ($self->start,$self->abs_strand); @result = $strand < 0 ? map { $start - $_ + 1 } @_ : map { $_ - $start + 1 } @_; # if called with a single argument, caller will expect a single scalar reply # not the size of the returned array! return $result[0] if @result == 1 and !wantarray; @result; } =head2 Bio::SeqFeatureI compatibility methods For convenience, segments are interchangeable with Bio::SeqFeature objects in many cases. This means that segments can be passed to BioPerl modules that expect Bio::SeqFeature objects and they should work as expected. The primary tag of segment objects is "region" (SO:0000001 "Continous sequence E=1 base pair"). All these methods are read-only except for the primary_id, which can be get or set. The following Bio::SeqFeatureI methods are supported: =over 4 =item start =item end =item seq_id =item strand =item length =item display_name =item primary_id =item primary_tag (always returns "region") =item source_tag (always returns "Bio::DB::SeqFeature::Segment") =item get_SeqFeatures (always returns an empty list) =item seq =item entire_seq =item location =item All Bio::RangeI methods =back =cut sub start { shift->{start} } sub end { shift->{end} } sub seq_id { shift->{seqid} } sub strand { shift->{strand} } sub ref { shift->seq_id } *refseq = \&ref; sub length { my $self = shift; return abs($self->end - $self->start) +1; } sub primary_tag { 'region' } sub source_tag { __PACKAGE__ } sub display_name { shift->as_string } sub name { shift->display_name } sub class { 'region' } sub abs_ref { shift->ref} sub abs_start { shift->start} sub abs_end { shift->end} sub abs_strand { shift->strand} sub get_SeqFeatures { } sub get_all_tags { } sub get_tag_values { } sub add_tag_value { } sub remove_tag { } sub has_tag { } sub seq { my $self = shift; require Bio::PrimarySeq unless Bio::PrimarySeq->can('new'); my ($start,$end) = ($self->start,$self->end); if ($self->strand < 0) { ($start,$end) = ($end,$start); } return Bio::PrimarySeq->new( -seq => $self->store->fetch_sequence($self->seq_id,$start,$end), -id => $self->display_name); } sub subseq { my $self = shift; my ($newstart,$newstop) = @_; my $store = $self->store or return; my $seq = $store->fetch_sequence($self->seq_id,$self->start+$newstart-1,$self->end+$newstop-1); return Bio::PrimarySeq->new(-seq=>$seq); } sub dna { my $seq = shift->seq; $seq = $seq->seq if CORE::ref($seq); return $seq; } sub entire_seq { my $self = shift; require Bio::PrimarySeq unless Bio::PrimarySeq->can('new'); return Bio::PrimarySeq->new( -seq => $self->store->fetch_sequence($self->seq_id), -id => $self->seq_id); } sub location { my $self = shift; require Bio::Location::Simple unless Bio::Location::Simple->can('new'); my $loc = Bio::Location::Simple->new(-start => $self->start, -end => $self->end, -strand => $self->strand); $loc->strand($self->strand); return $loc; } sub primary_id { my $self = shift; my $d = $self->{primary_id}; $self->{primary_id} = shift if @_; $d; } sub target { return } sub score { return } sub stop { shift->end } sub absolute { return 1 } sub desc { shift->as_string } sub display_id { shift->display_name } sub primary_seq { shift->seq } sub accession_number { return undef } # intended return undef sub alphabet { return undef } # intended return undef 1; __END__ =head1 BUGS This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs. =head1 SEE ALSO L, L, L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2006 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/SeqFeature/Store.pm000444000766000024 23717713155576320 20270 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::Store; =head1 NAME Bio::DB::SeqFeature::Store -- Storage and retrieval of sequence annotation data =head1 SYNOPSIS use Bio::DB::SeqFeature::Store; # Open the feature database my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:test', -create => 1 ); # Get a feature from somewhere my $feature = Bio::SeqFeature::Generic->new(...); # Store it $db->store($feature) or die "Couldn't store!"; # If absent, a primary ID is added to the feature when it is stored in the # database. Retrieve the primary ID my $id = $feature->primary_id; # Get the feature back out my $feature = $db->fetch($id); # .... which is identical to my $feature = $db->get_feature_by_primary_id($id); # Change the feature and update it $f->start(100); $db->store($f) or die "Couldn't update!"; # Get all features at once my @features = $db->features( ); # Retrieve multiple features by primary id my @features = $db->fetch_many(@list_of_ids); # ...by name @features = $db->get_features_by_name('ZK909'); # ...by alias @features = $db->get_features_by_alias('sma-3'); # ...by type @features = $db->get_features_by_type('gene'); # ...by location @features = $db->get_features_by_location(-seq_id=>'Chr1',-start=>4000,-end=>600000); # ...by attribute @features = $db->get_features_by_attribute({description => 'protein kinase'}) # ...by the GFF "Note" field @result_list = $db->search_notes('kinase'); # ...by arbitrary combinations of selectors @features = $db->features(-name => $name, -type => $types, -seq_id => $seqid, -start => $start, -end => $end, -attributes => $attributes); # Loop through the features using an iterator my $iterator = $db->get_seq_stream(-name => $name, -type => $types, -seq_id => $seqid, -start => $start, -end => $end, -attributes => $attributes); while (my $feature = $iterator->next_seq) { # do something with the feature } # ...limiting the search to a particular region my $segment = $db->segment('Chr1',5000=>6000); my @features = $segment->features(-type=>['mRNA','match']); # Getting coverage statistics across a region my $summary = $db->feature_summary('Chr1',10_000=>1_110_000); my ($bins) = $summary->get_tag_values('coverage'); my $first_bin = $bins->[0]; # Getting & storing sequence information # Warning: this returns a string, and not a PrimarySeq object $db->insert_sequence('Chr1','GATCCCCCGGGATTCCAAAA...'); my $sequence = $db->fetch_sequence('Chr1',5000=>6000); # What feature types are defined in the database? my @types = $db->types; # Create a new feature in the database my $feature = $db->new_feature(-primary_tag => 'mRNA', -seq_id => 'chr3', -start => 10000, -end => 11000); # Load an entire GFF3 file, using the GFF3 loader... my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store => $db, -verbose => 1, -fast => 1); $loader->load('./my_genome.gff3'); =head1 DESCRIPTION Bio::DB::SeqFeature::Store implements the Bio::SeqFeature::CollectionI interface to allow you to persistently store Bio::SeqFeatureI objects in a database and to later to retrieve them by a variety of searches. This module is similar to the older Bio::DB::GFF module, with the following differences: =over 4 =item 1. No limitation on Bio::SeqFeatureI implementations Unlike Bio::DB::GFF, Bio::DB::SeqFeature::Store works with any Bio::SeqFeatureI object. =item 2. No limitation on nesting of features & subfeatures Bio::DB::GFF is limited to features that have at most one level of subfeature. Bio::DB::SeqFeature::Store can work with features that have unlimited levels of nesting. =item 3. No aggregators The aggregator architecture, which was necessary to impose order on the GFF2 files that Bio::DB::GFF works with, does not apply to Bio::DB::SeqFeature::Store. It is intended to store features that obey well-defined ontologies, such as the Sequence Ontology (http://song.sourceforge.net). =item 4. No relative locations All locations defined by this module are relative to an absolute sequence ID, unlike Bio::DB::GFF which allows you to define the location of one feature relative to another. =back We'll discuss major concepts in Bio::DB::SeqFeature::Store and then describe how to use the module. =head2 Adaptors Bio::DB::SeqFeature::Store is designed to work with a variety of storage back ends called "adaptors." Adaptors are subclasses of Bio::DB::SeqFeature::Store and provide the interface between the store() and fetch() methods and the physical database. Currently the number of adaptors is quite limited, but the number will grow soon. =over 4 =item memory An implementation that stores all data in memory. This is useful for small data sets of no more than 10,000 features (more or less, depending on system memory). =item DBI::mysql A full-featured implementation on top of the MySQL relational database system. =item berkeleydb A full-feature implementation that runs on top of the BerkeleyDB database. See L. =back If you do not explicitly specify the adaptor, then DBI::mysql will be used by default. =head2 Serializers When Bio::DB::SeqFeature::Store stores a Bio::SeqFeatureI object into the database, it serializes it into binary or text form. When it later fetches the feature from the database, it unserializes it. Two serializers are available: Recent versions of =over 4 =item Storable This is a fast binary serializer. It is available in Perl versions 5.8.7 and higher and is used when available. =item Data::Dumper This is a slow text serializer that is available in Perl 5.8.0 and higher. It is used when Storable is unavailable. =back If you do not specify the serializer, then Storable will be used if available; otherwise Data::Dumper. =head2 Loaders and Normalized Features The Bio::DB::SeqFeature::Store::GFF3Loader parses a GFF3-format file and loads the annotations and sequence data into the database of your choice. The script bp_seqfeature_load.pl (found in the scripts/Bio-SeqFeature-Store/ subdirectory) is a thin front end to the GFF3Loader. Other loaders may be written later. Although Bio::DB::SeqFeature::Store should work with any Bio::SeqFeatureI object, there are some disadvantages to using Bio::SeqFeature::Generic and other vanilla implementations. The major issue is that if two vanilla features share the same subfeature (e.g. two transcripts sharing an exon), the shared subfeature will be cloned when stored into the database. The special-purpose L class is able to normalize its subfeatures in the database, so that shared subfeatures are stored only once. This minimizes wasted storage space. In addition, when in-memory caching is turned on, each shared subfeature will usually occupy only a single memory location upon restoration. =cut use strict; use warnings; use base 'Bio::SeqFeature::CollectionI'; use Carp 'croak'; use Bio::DB::GFF::Util::Rearrange; use Bio::DB::SeqFeature::Segment; use Scalar::Util 'blessed'; # this probably shouldn't be here use Bio::DB::SeqFeature; *dna = *get_dna = *get_sequence = \&fetch_sequence; *get_SeqFeatures = \&fetch_SeqFeatures; # local version sub api_version { 1.2 } =head1 Methods for Connecting and Initializating a Database ## TODO: http://iowg.brcdevel.org/gff3.html#a_fasta is a dead link =head2 new Title : new Usage : $db = Bio::DB::SeqFeature::Store->new(@options) Function: connect to a database Returns : A descendent of Bio::DB::Seqfeature::Store Args : several - see below Status : public This class method creates a new database connection. The following -name=E$value arguments are accepted: Name Value ---- ----- -adaptor The name of the Adaptor class (default DBI::mysql) -serializer The name of the serializer class (default Storable) -index_subfeatures Whether or not to make subfeatures searchable (default false) -cache Activate LRU caching feature -- size of cache -compress Compresses features before storing them in database using Compress::Zlib -create (Re)initialize the database. The B<-index_subfeatures> argument, if true, tells the module to create indexes for a feature and all its subfeatures (and its subfeatures' subfeatures). Indexing subfeatures means that you will be able to search for the gene, its mRNA subfeatures and the exons inside each mRNA. It also means when you search the database for all features contained within a particular location, you will get the gene, the mRNAs and all the exons as individual objects as well as subfeatures of each other. NOTE: this option is only honored when working with a normalized feature class such as Bio::DB::SeqFeature. The B<-cache> argument, if true, tells the module to try to create a LRU (least-recently-used) object cache using the Tie::Cacher module. Caching will cause two objects that share the same primary_id to (often, but not always) share the same memory location, and may improve performance modestly. The argument is taken as the desired size for the cache. If you pass "1" as the cache value, a reasonable default cache size will be chosen. Caching requires the Tie::Cacher module to be installed. If the module is not installed, then caching will silently be disabled. The B<-compress> argument, if true, will cause the feature data to be compressed before storing it. This will make the database somewhat smaller at the cost of decreasing performance. The B<-create> argument, if true, will either initialize or reinitialize the database. It is needed the first time a database is used. The new() method of individual adaptors recognize additional arguments. The default DBI::mysql adaptor recognizes the following ones: Name Value ---- ----- -dsn DBI data source (default dbi:mysql:test) -autoindex A flag that controls whether or not to update all search indexes whenever a feature is stored or updated (default true). -namespace A string that will be used to qualify each table, thereby allowing you to store several independent sequence feature databases in a single Mysql database. -dumpdir The path to a temporary directory that will be used during "fast" loading. See L for a description of this. Default is the current directory. -write Make the database writable (implied by -create) -fasta Provide an alternative DNA accessor object or path. By default the database will store DNA sequences internally. However, you may override this behavior by passing either a path to a FASTA file, or any Perl object that recognizes the seq($seqid,$start,$end) method. In the former case, the FASTA path will be passed to Bio::DB::Fasta, possibly causing an index to be constructed. Suitable examples of the latter type of object include the Bio::DB::Sam and Bio::DB::Sam::Fai classes. =cut ### # object constructor # sub new { my $self = shift; my ($adaptor,$serializer,$index_subfeatures,$cache,$compress,$debug,$create,$fasta,$args); if (@_ == 1) { $args = {DSN => shift} } else { ($adaptor,$serializer,$index_subfeatures,$cache,$compress,$debug,$create,$fasta,$args) = rearrange(['ADAPTOR', 'SERIALIZER', 'INDEX_SUBFEATURES', 'CACHE', 'COMPRESS', 'DEBUG', 'CREATE', 'FASTA', ],@_); } $adaptor ||= 'DBI::mysql'; $args->{WRITE}++ if $create; $args->{CREATE}++ if $create; my $class = "Bio::DB::SeqFeature::Store::$adaptor"; eval "require $class " or croak $@; $cache &&= eval "require Tie::Cacher; 1"; my $obj = $class->new_instance(); $obj->debug($debug) if defined $debug; $obj->init($args); $obj->init_cache($cache) if $cache; $obj->do_compress($compress); $obj->serializer($serializer) if defined $serializer; $obj->index_subfeatures($index_subfeatures) if defined $index_subfeatures; $obj->seqfeature_class('Bio::DB::SeqFeature'); $obj->set_dna_accessor($fasta) if defined $fasta; $obj->post_init($args); $obj; } =head2 init_database Title : init_database Usage : $db->init_database([$erase_flag]) Function: initialize a database Returns : true Args : (optional) flag to erase current data Status : public Call this after Bio::DB::SeqFeature::Store-Enew() to initialize a new database. In the case of a DBI database, this method installs the schema but does B create the database. You have to do this offline using the appropriate command-line tool. In the case of the "berkeleydb" adaptor, this creates an empty BTREE database. If there is any data already in the database, init_database() called with no arguments will have no effect. To permanently erase the data already there and prepare to receive a fresh set of data, pass a true argument. =cut ### # wipe database clean and reinstall schema # sub init_database { my $self = shift; $self->_init_database(@_); } =head2 post_init This method is invoked after init_database for use by certain adaptors (currently only the memory adaptor) to do automatic data loading after initialization. It is passed a copy of the init_database() args. =cut sub post_init { } =head2 add_features Title : add_features Usage : $success = $db->add_features(\@features) Function: store one or more features into the database Returns : true if successful Args : array reference of Bio::SeqFeatureI objects Status : public =cut sub add_features { my ($self, $feats) = @_; my $result = $self->store_and_cache(1, @$feats); } =head2 store Title : store Usage : $success = $db->store(@features) Function: store one or more features into the database Returns : true if successful Args : list of Bio::SeqFeatureI objects Status : public This method stores a list of features into the database. Each feature is updated so that its primary_id becomes the primary ID of the serialized feature stored in the database. If all features were successfully stored, the method returns true. In the DBI implementation, the store is performed as a single transaction and the transaction is rolled back if one or more store operations failed. In most cases, you should let the database assign the primary id. If the object you store already has a primary_id, then the ID must adhere to the datatype expected by the adaptor: an integer in the case of the various DB adaptors, and a string in the case of the memory and berkeley adaptors. You can find out what the primary ID of the feature has become by calling the feature's primary_id() method: $db->store($my_feature) or die "Oh darn"; my $id = $my_feature->primary_id; If the feature contains subfeatures, they will all be stored recursively. In the case of Bio::DB::SeqFeature and Bio::DB::SeqFeature::Store::NormalizedFeature, the subfeatures will be stored in a normalized way so that each subfeature appears just once in the database. Subfeatures will be indexed for separate retrieval based on the current value of index_subfeatures(). If you call store() with one or more features that already have valid primary_ids, then any existing objects will be B. Note that when using normalized features such as Bio::DB::SeqFeature, the subfeatures are not recursively updated when you update the parent feature. You must manually update each subfeatures that has changed. =cut ### # store one or more Bio::SeqFeatureI objects # if they already have a primary_id will replace into the database # otherwise will insert and primary_id will be added # # this version stores the object and flags it to be indexed # for search via attributes, name, type or location sub store { my ($self, @feats) = @_; for my $feat (@feats) { if ( (not ref $feat) || (not $feat->isa('Bio::SeqFeatureI')) ) { die "Cannot store non-Bio::SeqFeatureI object '$feat'\n"; } } my $result = $self->store_and_cache(1,@feats); } =head2 store_noindex Title : store_noindex Usage : $success = $db->store_noindex(@features) Function: store one or more features into the database without indexing Returns : true if successful Args : list of Bio::SeqFeatureI objects Status : public This method stores a list of features into the database but does not make them searchable. The only way to access the features is via their primary IDs. This method is ordinarily only used internally to store subfeatures that are not indexed. =cut # this version stores the object and flags it so that it is # not searchable via attributes, name, type or location # (typically used only for subfeatures) sub store_noindex { my $self = shift; $self->store_and_cache(0,@_); } =head2 no_blobs Title : no_blobs Usage : $db->no_blobs(1); Function: decide if objects should be stored in the database as blobs. Returns : boolean (default false) Args : boolean (true to no longer store objects; when the corresponding feature is retrieved it will instead be a minimal representation of the object that was stored, as some simple Bio::SeqFeatureI object) Status : dubious (new) This method saves lots of space in the database, which may in turn lead to large performance increases in extreme cases (over 7 million features in the db). =cut sub no_blobs { my $self = shift; if (@_) { $self->{no_blobs} = shift } return $self->{no_blobs} || 0; } =head2 new_feature Title : new_feature Usage : $feature = $db->new_feature(@args) Function: create a new Bio::DB::SeqFeature object in the database Returns : the new seqfeature Args : see below Status : public This method creates and stores a new Bio::SeqFeatureI object using the specialized Bio::DB::SeqFeature class. This class is able to store its subfeatures in a normalized fashion, allowing subfeatures to be shared among multiple parents (e.g. multiple exons shared among several mRNAs). The arguments are the same as for Bio::DB::SeqFeature-Enew(), which in turn are similar to Bio::SeqFeature::Generic-Enew() and Bio::Graphics::Feature-Enew(). The most important difference is the B<-index> option, which controls whether the feature will be indexed for retrieval (default is true). Ordinarily, you would only want to turn indexing off when creating subfeatures, because features stored without indexes will only be reachable via their primary IDs or their parents. Arguments are as follows: -seq_id the reference sequence -start the start position of the feature -end the stop position of the feature -display_name the feature name (returned by seqname) -primary_tag the feature type (returned by primary_tag) -source the source tag -score the feature score (for GFF compatibility) -desc a description of the feature -segments a list of subfeatures (see Bio::Graphics::Feature) -subtype the type to use when creating subfeatures -strand the strand of the feature (one of -1, 0 or +1) -phase the phase of the feature (0..2) -url a URL to link to when rendered with Bio::Graphics -attributes a hashref of tag value attributes, in which the key is the tag and the value is an array reference of values -index index this feature if true Aliases: -id an alias for -display_name -seqname an alias for -display_name -display_id an alias for -display_name -name an alias for -display_name -stop an alias for end -type an alias for primary_tag You can change the seqfeature implementation generated by new() by passing the name of the desired seqfeature class to $db-Eseqfeature_class(). =cut sub new_feature { my $self = shift; return $self->seqfeature_class->new(-store=>$self,@_); } =head2 delete Title : delete Usage : $success = $db->delete(@features) Function: delete a list of feature from the database Returns : true if successful Args : list of features Status : public This method looks up the primary IDs from a list of features and deletes them from the database, returning true if all deletions are successful. WARNING: The current DBI::mysql implementation has some issues that need to be resolved, namely (1) normalized subfeatures are NOT recursively deleted; and (2) the deletions are not performed in a transaction. =cut sub delete { my $self = shift; my $success = 1; for my $object (@_) { my $id = $object->primary_id; if ( not defined $id ) { warn "Could not delete feature without primary_id: $object"; $success = 0; next; } my $result = $self->_deleteid($id); warn "Could not delete feature with id=$id" unless $result; $success &&= $result; } $success; } =head2 fetch / get_feature_by_id / get_feature_by_primary_id Title : fetch get_feature_by_id get_feature_by_primary_id Usage : $feature = $db->fetch($primary_id) Function: fetch a feature from the database using its primary ID Returns : a feature Args : primary ID of desired feature Status : public This method returns a previously-stored feature from the database using its primary ID. If the primary ID is invalid, it returns undef. Use fetch_many() to rapidly retrieve multiple features. =cut ### # Fetch a Bio::SeqFeatureI from database using its primary_id # sub fetch { my $self = shift; @_ or croak "usage: fetch(\$primary_id)"; my $primary_id = shift; if (my $cache = $self->cache()) { return $cache->fetch($primary_id) if $cache->exists($primary_id); my $object = $self->_fetch($primary_id); $cache->store($primary_id,$object); return $object; } else { return $self->_fetch($primary_id); } } *get_feature_by_id = *get_feature_by_primary_id = \&fetch; =head2 fetch_many Title : fetch_many Usage : @features = $db->fetch_many($primary_id,$primary_id,$primary_id...) Function: fetch many features from the database using their primary ID Returns : list of features Args : a list of primary IDs or an array ref of primary IDs Status : public Same as fetch() except that you can pass a list of primary IDs or a ref to an array of IDs. =cut ### # Efficiently fetch a series of IDs from the database # Can pass an array or an array ref # sub fetch_many { my $self = shift; @_ or croak 'usage: fetch_many($id1,$id2,$id3...)'; my @ids = map {ref($_) ? @$_ : $_} @_ or return; $self->_fetch_many(@ids); } =head2 get_seq_stream Title : get_seq_stream Usage : $iterator = $db->get_seq_stream(@args) Function: return an iterator across all features in the database Returns : a Bio::DB::SeqFeature::Store::Iterator object Args : feature filters (optional) Status : public When called without any arguments this method will return an iterator object that will traverse all indexed features in the database. Call the iterator's next_seq() method to step through them (in no particular order): my $iterator = $db->get_seq_stream; while (my $feature = $iterator->next_seq) { print $feature->primary_tag,' ',$feature->display_name,"\n"; } You can select a subset of features by passing a series of filter arguments. The arguments are identical to those accepted by $db-Efeatures(). =cut ### # Return an iterator across all features that are indexable # sub get_seq_stream { my $self = shift; $self->_features(-iterator=>1,@_); } =head2 get_features_by_name Title : get_features_by_name Usage : @features = $db->get_features_by_name($name) Function: looks up features by their display_name Returns : a list of matching features Args : the desired name Status : public This method searches the display_name of all features for matches against the provided name. GLOB style wildcares ("*", "?") are accepted, but may be slow. The method returns the list of matches, which may be zero, 1 or more than one features. Be prepared to receive more than one result, as display names are not guaranteed to be unique. For backward compatibility with gbrowse, this method is also known as get_feature_by_name(). =cut ### # get_feature_by_name() return 0 or more features using a name lookup # uses the Bio::DB::GFF API # sub get_features_by_name { my $self = shift; my ($class,$name,$types,$allow_alias); if (@_ == 1) { # get_features_by_name('name'); $name = shift; } else { # get_features_by_name('class'=>'name'), get_feature_by_name(-name=>'name') ($class,$name,$allow_alias,$types) = rearrange([qw(CLASS NAME ALIASES),[qw(TYPE TYPES)]],@_); } # hacky workaround for assumption in Bio::DB::GFF that unclassed reference points were of type "Sequence" undef $class if $class && $class eq 'Sequence'; $self->_features(-name=>$name,-class=>$class,-aliases=>$allow_alias,-type=>$types); } =head2 get_feature_by_name Title : get_feature_by_name Usage : @features = $db->get_feature_by_name($name) Function: looks up features by their display_name Returns : a list of matching features Args : the desired name Status : Use get_features_by_name instead. This method is provided for backward compatibility with gbrowse. =cut sub get_feature_by_name { shift->get_features_by_name(@_) } =head2 get_features_by_alias Title : get_features_by_alias Usage : @features = $db->get_features_by_alias($name) Function: looks up features by their display_name or alias Returns : a list of matching features Args : the desired name Status : public This method is similar to get_features_by_name() except that it will also search through the feature aliases. Aliases can be created by storing features that contain one or more Alias tags. Wildards are accepted. =cut sub get_features_by_alias { my $self = shift; my @args = @_; if (@_ == 1) { @args = (-name=>shift); } push @args,(-aliases=>1); $self->get_features_by_name(@args); } =head2 get_features_by_type Title : get_features_by_type Usage : @features = $db->get_features_by_type(@types) Function: looks up features by their primary_tag Returns : a list of matching features Args : list of primary tags Status : public This method will return a list of features that have any of the primary tags given in the argument list. For compatibility with gbrowse and Bio::DB::GFF, types can be qualified using a colon: primary_tag:source_tag in which case only features that match both the primary_tag B the indicated source_tag will be returned. If the database was loaded from a GFF3 file, this corresponds to the third and second columns of the row, in that order. For example, given the GFF3 lines: ctg123 geneFinder exon 1300 1500 . + . ID=exon001 ctg123 fgenesH exon 1300 1520 . + . ID=exon002 exon001 and exon002 will be returned by searching for type "exon", but only exon001 will be returned by searching for type "exon:fgenesH". =cut sub get_features_by_type { my $self = shift; my @types = @_; $self->_features(-type=>\@types); } =head2 get_features_by_location Title : get_features_by_location Usage : @features = $db->get_features_by_location(@args) Function: looks up features by their location Returns : a list of matching features Args : see below Status : public This method fetches features based on a location range lookup. You call it using a positional list of arguments, or a list of (-argument=E$value) pairs. The positional form is as follows: $db->get_features_by_location($seqid [[,$start,]$end]) The $seqid is the name of the sequence on which the feature resides, and start and end are optional endpoints for the match. If the endpoints are missing then any feature on the indicated seqid is returned. Examples: get_features_by_location('chr1'); # all features on chromosome 1 get_features_by_location('chr1',5000); # features between 5000 and the end get_features_by_location('chr1',5000,8000); # features between 5000 and 8000 Location lookups are overlapping. A feature will be returned if it partially or completely overlaps the indicated range. The named argument form gives you more control: Argument Value -------- ----- -seq_id The name of the sequence on which the feature resides -start Start of the range -end End of the range -strand Strand of the feature -range_type Type of range to search over The B<-strand> argument, if present, can be one of "0" to find features that are on both strands, "+1" to find only plus strand features, and "-1" to find only minus strand features. Specifying a strand of undef is the same as not specifying this argument at all, and retrieves all features regardless of their strandedness. The B<-range_type> argument, if present, can be one of "overlaps" (the default), to find features whose positions overlap the indicated range, "contains," to find features whose endpoints are completely contained within the indicated range, and "contained_in" to find features whose endpoints are both outside the indicated range. =cut sub get_features_by_location { my $self = shift; my ($seqid,$start,$end,$strand,$rangetype) = rearrange([['SEQ_ID','SEQID','REF'],'START',['STOP','END'],'STRAND','RANGE_TYPE'],@_); $self->_features(-seqid=>$seqid, -start=>$start||undef, -end=>$end||undef, -strand=>$strand||undef, -range_type=>$rangetype); } =head2 get_features_by_attribute Title : get_features_by_attribute Usage : @features = $db->get_features_by_attribute(@args) Function: looks up features by their attributes/tags Returns : a list of matching features Args : see below Status : public This implements a simple tag filter. Pass a list of tag names and their values. The module will return a list of features whose tag names and values match. Tag names are case insensitive. If multiple tag name/value pairs are present, they will be ANDed together. To match any of a list of values, use an array reference for the value. Examples: # return all features whose "function" tag is "GO:0000123" @features = $db->get_features_by_attribute(function => 'GO:0000123'); # return all features whose "function" tag is "GO:0000123" or "GO:0000555" @features = $db->get_features_by_attribute(function => ['GO:0000123','GO:0000555']); # return all features whose "function" tag is "GO:0000123" or "GO:0000555" # and whose "confirmed" tag is 1 @features = $db->get_features_by_attribute(function => ['GO:0000123','GO:0000555'], confirmed => 1); =cut sub get_features_by_attribute { my $self = shift; my %attributes = ref($_[0]) ? %{$_[0]} : @_; %attributes or $self->throw("Usage: get_feature_by_attribute(attribute_name=>\$attribute_value...)"); $self->_features(-attributes=>\%attributes); } ### # features() call -- main query interface # =head2 features Title : features Usage : @features = $db->features(@args) Function: generalized query & retrieval interface Returns : list of features Args : see below Status : Public This is the workhorse for feature query and retrieval. It takes a series of -name=E$value arguments filter arguments. Features that match all the filters are returned. Argument Value -------- ----- Location filters: -seq_id Chromosome, contig or other DNA segment -seqid Synonym for -seq_id -ref Synonym for -seqid -start Start of range -end End of range -stop Synonym for -end -strand Strand -range_type Type of range match ('overlaps','contains','contained_in') Name filters: -name Name of feature (may be a glob expression) -aliases If true, match aliases as well as display names -class Archaic argument for backward compatibility. (-class=>'Clone',-name=>'ABC123') is equivalent to (-name=>'Clone:ABC123') Type filters: -types List of feature types (array reference) or one type (scalar) -type Synonym for the above -primary_tag Synonym for the above -attributes Hashref of attribute=>value pairs as per get_features_by_attribute(). Multiple alternative values can be matched by providing an array reference. -attribute synonym for -attributes You may also provide features() with a list of scalar values (the first element of which must B begin with a dash), in which case it will treat the list as a feature type filter. Examples: All features: @features = $db->features( ); All features on chromosome 1: @features = $db->features(-seqid=>'Chr1'); All features on chromosome 1 between 5000 and 6000: @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000); All mRNAs on chromosome 1 between 5000 and 6000: @features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA'); All confirmed mRNAs and repeats on chromosome 1 that overlap the range 5000..6000: @features = $db->features(-seqid => 'Chr1',-start=>5000,-end=>6000, -types => ['mRNA','repeat'], -attributes=> {confirmed=>1} ); All confirmed mRNAs and repeats on chromosome 1 strictly contained within the range 5000..6000: @features = $db->features(-seqid => 'Chr1',-start=>5000,-end=>6000, -types => ['mRNA','repeat'], -attributes=> {confirmed=>1} -range_type => 'contained_in', ); All genes and repeats: @features = $db->features('gene','repeat_region'); =cut # documentation of args # my ($seq_id,$start,$end,$strand, # $name,$class,$allow_aliases, # $types, # $attributes, # $range_type, # $iterator, # ) = rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'],'STRAND', # 'NAME','CLASS','ALIASES', # ['TYPES','TYPE','PRIMARY_TAG'], # ['ATTRIBUTES','ATTRIBUTE'], # 'RANGE_TYPE', # ],@_); # $range_type ||= 'overlaps'; sub features { my $self = shift; my @args; if (@_ == 0) { @args = (); } elsif ($_[0] !~/^-/) { my @types = @_; @args = (-type=>\@types); } else { @args = @_; } $self->_features(@args); } =head2 get_all_features Title : get_all_features Usage : @features = $db->get_all_features() Function: get all feature in the database Returns : list of features Args : none Status : Public =cut # for compatibility with Bio::SeqFeature::Collection sub get_all_features { shift->features(); } =head2 seq_ids Title : seq_ids Usage : @ids = $db->seq_ids() Function: Return all sequence IDs contained in database Returns : list of sequence Ids Args : none Status : public =cut sub seq_ids { my $self = shift; return $self->_seq_ids(); } =head2 search_attributes Title : search_attributes Usage : @result_list = $db->search_attributes("text search string",[$tag1,$tag2...],$limit) Function: Search attributes for keywords occurring in a text string Returns : array of results Args : full text search string, array ref of attribute names, and an optional feature limit Status : public Given a search string, this method performs a full-text search of the specified attributes and returns an array of results. You may pass a scalar attribute name to search the values of one attribute (e.g. "Note") or you may pass an array reference to search inside multiple attributes (['Note','Alias','Parent']).Each row of the returned array is a arrayref containing the following fields: column 1 The display name of the feature column 2 The text of the note column 3 A relevance score. column 4 The feature type column 5 The unique ID of the feature NOTE: This search will fail to find features that do not have a display name! You can use fetch() or fetch_many() with the returned IDs to get to the features themselves. =cut sub search_attributes { my $self = shift; my ($search_string,$attribute_names,$limit) = @_; my $attribute_array = ref $attribute_names && ref $attribute_names eq 'ARRAY' ? $attribute_names : [$attribute_names]; return $self->_search_attributes($search_string,$attribute_array,$limit); } =head2 search_notes Title : search_notes Usage : @result_list = $db->search_notes("full text search string",$limit) Function: Search the notes for a text string Returns : array of results Args : full text search string, and an optional feature limit Status : public Given a search string, this method performs a full-text search of the "Notes" attribute and returns an array of results. Each row of the returned array is a arrayref containing the following fields: column 1 The display_name of the feature, suitable for passing to get_feature_by_name() column 2 The text of the note column 3 A relevance score. column 4 The type NOTE: This is equivalent to $db-Esearch_attributes('full text search string','Note',$limit). This search will fail to find features that do not have a display name! =cut ### # search_notes() # sub search_notes { my $self = shift; my ($search_string,$limit) = @_; return $self->_search_attributes($search_string,['Note'],$limit); } =head2 types Title : types Usage : @type_list = $db->types Function: Get all the types in the database Returns : array of Bio::DB::GFF::Typename objects Args : none Status : public =cut sub types { shift->throw_not_implemented; } =head2 insert_sequence Title : insert_sequence Usage : $success = $db->insert_sequence($seqid,$sequence_string,$offset) Function: Inserts sequence data into the database at the indicated offset Returns : true if successful Args : see below Status : public This method inserts the DNA or protein sequence fragment $sequence_string, identified by the ID $seq_id, into the database at the indicated offset $offset. It is used internally by the GFF3Loader to load sequence data from the files. =cut ### # insert_sequence() # # insert a bit of primary sequence into the database # sub insert_sequence { my $self = shift; my ($seqid,$seq,$offset) = @_; $offset ||= 0; $self->_insert_sequence($seqid,$seq,$offset); } =head2 fetch_sequence Title : fetch_sequence Usage : $sequence = $db->fetch_sequence(-seq_id=>$seqid,-start=>$start,-end=>$end) Function: Fetch the indicated subsequene from the database Returns : The sequence string (not a Bio::PrimarySeq object!) Args : see below Status : public This method retrieves a portion of the indicated sequence. The arguments are: Argument Value -------- ----- -seq_id Chromosome, contig or other DNA segment -seqid Synonym for -seq_id -name Synonym for -seq_id -start Start of range -end End of range -class Obsolete argument used for Bio::DB::GFF compatibility. If specified will qualify the seq_id as "$class:$seq_id". -bioseq Boolean flag; if true, returns a Bio::PrimarySeq object instead of a sequence string. You can call fetch_sequence using the following shortcuts: $seq = $db->fetch_sequence('chr3'); # entire chromosome $seq = $db->fetch_sequence('chr3',1000); # position 1000 to end of chromosome $seq = $db->fetch_sequence('chr3',undef,5000); # position 1 to 5000 $seq = $db->fetch_sequence('chr3',1000,5000); # positions 1000 to 5000 =cut ### # fetch_sequence() # # equivalent to old Bio::DB::GFF->dna() method # sub fetch_sequence { my $self = shift; my ($seqid,$start,$end,$class,$bioseq) = rearrange([['NAME','SEQID','SEQ_ID'], 'START',['END','STOP'],'CLASS','BIOSEQ'],@_); $seqid = "$seqid:$class" if defined $class; my $seq = $self->seq($seqid,$start,$end); return $seq unless $bioseq; require Bio::Seq unless Bio::Seq->can('new'); my $display_id = defined $start ? "$seqid:$start..$end" : $seqid; return Bio::Seq->new(-display_id=>$display_id,-seq=>$seq); } =head2 segment Title : segment Usage : $segment = $db->segment($seq_id [,$start] [,$end] [,$absolute]) Function: restrict the database to a sequence range Returns : a Bio::DB::SeqFeature::Segment object Args : sequence id, start and end ranges (optional) Status : public This is a convenience method that can be used when you are interested in the contents of a particular sequence landmark, such as a contig. Specify the ID of a sequence or other landmark in the database and optionally a start and endpoint relative to that landmark. The method will look up the region and return a Bio::DB::SeqFeature::Segment object that spans it. You can then use this segment object to make location-restricted queries on the database. Example: $segment = $db->segment('contig23',1,1000); # first 1000 bp of contig23 my @mRNAs = $segment->features('mRNA'); # all mRNAs that overlap segment Although you will usually want to fetch segments that correspond to physical sequences in the database, you can actually use any feature in the database as the sequence ID. The segment() method will perform a get_features_by_name() internally and then transform the feature into the appropriate coordinates. The named feature should exist once and only once in the database. If it exists multiple times in the database and you attempt to call segment() in a scalar context, you will get an exception. A workaround is to call the method in a list context, as in: my ($segment) = $db->segment('contig23',1,1000); or my @segments = $db->segment('contig23',1,1000); However, having multiple same-named features in the database is often an indication of underlying data problems. If the optional $absolute argument is a true value, then the specified coordinates are relative to the reference (absolute) coordinates. =cut ### # Replacement for Bio::DB::GFF->segment() method # sub segment { my $self = shift; my (@features,@args); if (@_ == 1 && blessed($_[0])) { @features = @_; @args = (); } else { @args = $self->setup_segment_args(@_); @features = $self->get_features_by_name(@args); } if (!wantarray && @features > 1) { $self->throw(<seq_id; my $strand = $f->strand; my ($start,$end); if ($abs) { $start = $rel_start; $end = defined $rel_end ? $rel_end : $start + $f->length - 1; } else { my $re = defined $rel_end ? $rel_end : $f->end - $f->start + 1; if ($strand >= 0) { $start = $f->start + $rel_start - 1; $end = $f->start + $re - 1; } else { $start = $f->end - $re + 1; $end = $f->end - $rel_start + 1; } } my $id = eval{$f->primary_id}; push @segments,Bio::DB::SeqFeature::Segment->new($self,$seqid,$start,$end,$strand,$id); } return wantarray ? @segments : $segments[0]; } =head2 seqfeature_class Title : seqfeature_class Usage : $classname = $db->seqfeature_class([$new_classname]) Function: get or set the name of the Bio::SeqFeatureI class generated by new_feature() Returns : name of class Args : new classname (optional) Status : public =cut sub seqfeature_class { my $self = shift; my $d = $self->{seqfeatureclass}; if (@_) { my $class = shift; eval "require $class"; $self->throw("$class does not implement the Bio::SeqFeatureI interface") unless $class->isa('Bio::SeqFeatureI'); $self->{seqfeatureclass} = $class; } $d; } =head2 reindex Title : reindex Usage : $db->reindex Function: reindex the database Returns : nothing Args : nothing Status : public This method will force the secondary indexes (name, location, attributes, feature types) to be recalculated. It may be useful to rebuild a corrupted database. =cut ### # force reindexing # sub reindex { my $self = shift; my $count = 0; my $now; my $last_time = time(); $self->_start_reindexing; my $iterator = $self->get_seq_stream; while (my $f = $iterator->next_seq) { if (++$count %1000 == 0) { $now = time(); my $elapsed = sprintf(" in %5.2fs",$now - $last_time); $last_time = $now; print STDERR "$count features indexed$elapsed...",' 'x60; print STDERR -t STDOUT && !$ENV{EMACS} ? "\r" : "\n"; } $self->_update_indexes($f); } $self->_end_reindexing; } =head2 attributes Title : attributes Usage : @a = $db->attributes Function: Returns list of all known attributes Returns : Returns list of all known attributes Args : nothing Status : public =cut sub attributes { my $self = shift; shift->throw_not_implemented; } =head2 start_bulk_update,finish_bulk_update Title : start_bulk_update,finish_bulk_update Usage : $db->start_bulk_update $db->finish_bulk_update Function: Activate optimizations for large number of insertions/updates Returns : nothing Args : nothing Status : public With some adaptors (currently only the DBI::mysql adaptor), these methods signal the adaptor that a large number of insertions or updates are to be performed, and activate certain optimizations. These methods are called automatically by the Bio::DB::SeqFeature::Store::GFF3Loader module. Example: $db->start_bulk_update; for my $f (@features) { $db->store($f); } $db->finish_bulk_update; =cut sub start_bulk_update { shift->_start_bulk_update(@_) } sub finish_bulk_update { shift->_finish_bulk_update(@_) } =head2 add_SeqFeature Title : add_SeqFeature Usage : $count = $db->add_SeqFeature($parent,@children) Function: store a parent/child relationship between a $parent and @children features that are already stored in the database Returns : number of children successfully stored Args : parent feature or primary ID and children features or primary IDs Status : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS If can_store_parentage() returns true, then some store-aware features (e.g. Bio::DB::SeqFeature) will invoke this method to store feature/subfeature relationships in a normalized table. =cut # these two are called only if _can_store_subFeatures() returns true # _add_SeqFeature ($parent,@children) sub add_SeqFeature { shift->_add_SeqFeature(@_) } =head2 fetch_SeqFeatures Title : fetch_SeqFeatures Usage : @children = $db->fetch_SeqFeatures($parent_feature) Function: return the immediate subfeatures of the indicated feature Returns : list of subfeatures Args : the parent feature and an optional list of children types Status : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS If can_store_parentage() returns true, then some store-aware features (e.g. Bio::DB::SeqFeature) will invoke this method to retrieve feature/subfeature relationships from the database. =cut # _get_SeqFeatures($parent,@child_types) sub fetch_SeqFeatures { my ($self, $parent, @child_types) = @_; return unless defined $parent->primary_id; $self->_fetch_SeqFeatures($parent,@child_types); } =head1 Changing the Behavior of the Database These methods allow you to modify the behavior of the database. =head2 debug Title : debug Usage : $debug_flag = $db->debug([$new_flag]) Function: set the debug flag Returns : current debug flag Args : new debug flag Status : public This method gets/sets a flag that turns on verbose progress messages. Currently this will not do very much. =cut sub debug { my $self = shift; my $d = $self->{debug}; $self->{debug} = shift if @_; $d; } =head2 serializer Title : serializer Usage : $serializer = $db->serializer([$new_serializer]) Function: get/set the name of the serializer Returns : the name of the current serializer class Args : (optional) the name of a new serializer Status : public You can use this method to set the serializer, but do not attempt to change the serializer once the database is initialized and populated. =cut ### # serializer # sub serializer { my $self = shift; my $d = $self->setting('serializer'); if (@_) { my $serializer = shift; eval "require $serializer; 1" or croak $@; $self->setting(serializer=>$serializer); } $d; } =head2 dna_accessor Title : dna_accessor Usage : $dna_accessor = $db->dna_accessor([$new_dna_accessor]) Function: get/set the name of the dna_accessor Returns : the current dna_accessor object, if any Args : (optional) the dna_accessor object Status : public You can use this method to request or set the DNA accessor. =cut ### # dna_accessor # sub dna_accessor { my $self = shift; my $d = $self->{dna_accessor}; $self->{dna_accessor} = shift if @_; $d; } sub can_do_seq { my $self = shift; my $obj = shift; return UNIVERSAL::can($obj,'seq') || UNIVERSAL::can($obj,'fetch_sequence'); } sub set_dna_accessor { my $self = shift; my $accessor = shift; if (-e $accessor) { # a file, assume it is a fasta file eval "require Bio::DB::Fasta" unless Bio::DB::Fasta->can('new'); my $a = Bio::DB::Fasta->new($accessor) or croak "Can't open FASTA file $accessor: $!"; $self->dna_accessor($a); } if (ref $accessor && $self->can_do_seq($accessor)) { $self->dna_accessor($accessor); # already built } return; } sub do_compress { my $self = shift; if (@_) { my $do_compress = shift; $self->setting(compress => $do_compress); } my $d = $self->setting('compress'); if ($d) { eval "use Compress::Zlib; 1" or croak $@ unless Compress::Zlib->can('compress'); } $d; } =head2 index_subfeatures Title : index_subfeatures Usage : $flag = $db->index_subfeatures([$new_value]) Function: flag whether to index subfeatures Returns : current value of the flag Args : (optional) new value of the flag Status : public If true, the store() method will add a searchable index to both the top-level feature and all its subfeatures, allowing the search functions to return features at any level of the containment hierarchy. If false, only the top level feature will be indexed, meaning that you will only be able to get at subfeatures by fetching the top-level feature and then traversing downward using get_SeqFeatures(). You are free to change this setting at any point during the creation and population of a database. One database can contain both indexed and unindexed subfeatures. =cut ### # whether to index subfeatures by default # sub index_subfeatures { my $self = shift; my $d = $self->setting('index_subfeatures'); $self->setting('index_subfeatures'=>shift) if @_; $d; } =head2 clone The clone() method should be used when you want to pass the Bio::DB::SeqFeature::Store object to a child process across a fork(). The child must call clone() before making any queries. The default behavior is to do nothing, but adaptors that use the DBI interface may need to implement this in order to avoid database handle errors. See the dbi adaptor for an example. =cut sub clone { } ################################# TIE interface #################### =head1 TIE Interface This module implements a full TIEHASH interface. The keys are the primary IDs of the features in the database. Example: tie %h,'Bio::DB::SeqFeature::Store',-adaptor=>'DBI::mysql',-dsn=>'dbi:mysql:elegans'; $h{123} = $feature1; $h{124} = $feature2; print $h{123}->display_name; =cut sub TIEHASH { my $class = shift; return $class->new(@_); } sub STORE { my $self = shift; my ($key,$feature) = @_; $key =~ /^\d+$/ && $key > 0 or croak "keys must be positive integers"; $self->load_class($feature); $feature->primary_id($key); $self->store($feature); } sub FETCH { my $self = shift; $self->fetch(@_); } sub FIRSTKEY { my $self = shift; $self->_firstid; } sub NEXTKEY { my $self = shift; my $lastkey = shift; $self->_nextid($lastkey); } sub EXISTS { my $self = shift; my $key = shift; $self->existsid($key); } sub DELETE { my $self = shift; my $key = shift; $self->_deleteid($key); } sub CLEAR { my $self = shift; $self->_clearall; } sub SCALAR { my $self = shift; $self->_featurecount; } ###################### TO BE IMPLEMENTED BY ADAPTOR ########## =head2 _init_database Title : _init_database Usage : $success = $db->_init_database([$erase]) Function: initialize an empty database Returns : true on success Args : optional boolean flag to erase contents of an existing database Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR This method is the back end for init_database(). It must be implemented by an adaptor that inherits from Bio::DB::SeqFeature::Store. It returns true on success. @features = $db->features(-seqid=>'Chr1'); =cut sub _init_database { shift->throw_not_implemented } =head2 _store Title : _store Usage : $success = $db->_store($indexed,@objects) Function: store seqfeature objects into database Returns : true on success Args : a boolean flag indicating whether objects are to be indexed, and one or more objects Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR This method is the back end for store() and store_noindex(). It should write the seqfeature objects into the database. If indexing is requested, the features should be indexed for query and retrieval. Otherwise the features should be stored without indexing (it is not required that adaptors respect this). If the object has no primary_id (undef), then the object is written into the database and assigned a new primary_id. If the object already has a primary_id, then the system will perform an update, replacing whatever was there before. In practice, the implementation will serialize each object using the freeze() method and then store it in the database under the corresponding primary_id. The object is then updated with the primary_id. =cut # _store($indexed,@objs) sub _store { my $self = shift; my $indexed = shift; my @objs = @_; $self->throw_not_implemented; } =head2 _fetch Title : _fetch Usage : $feature = $db->_fetch($primary_id) Function: fetch feature from database Returns : feature Args : primary id Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR This method is the back end for fetch(). It accepts a primary_id and returns a feature object. It must be implemented by the adaptor. In practice, the implementation will retrieve the serialized Bio::SeqfeatureI object from the database and pass it to the thaw() method to unserialize it and synchronize the primary_id. =cut # _fetch($id) sub _fetch { shift->throw_not_implemented } =head2 _fetch_many Title : _fetch_many Usage : $feature = $db->_fetch_many(@primary_ids) Function: fetch many features from database Returns : feature Args : primary id Status : private -- does not need to be implemented This method fetches many features specified by a list of IDs. The default implementation simply calls _fetch() once for each primary_id. Implementors can override it if needed for efficiency. =cut # _fetch_many(@ids) # this one will fall back to many calls on fetch() if you don't # override it sub _fetch_many { my $self = shift; return map {$self->_fetch($_)} @_; } =head2 _update_indexes Title : _update_indexes Usage : $success = $db->_update_indexes($feature) Function: update the indexes for a feature Returns : true on success Args : A seqfeature object Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR This method is called by reindex() to update the searchable indexes for a feature object that has changed. =cut # this is called to index a feature sub _update_indexes { shift->throw_not_implemented } =head2 _start_reindexing, _end_reindexing Title : _start_reindexing, _end_reindexing Usage : $db->_start_reindexing() $db->_end_reindexing Function: flag that a series of reindexing operations is beginning/ending Returns : true on success Args : none Status : MAY BE IMPLEMENTED BY AN ADAPTOR (optional) These methods are called by reindex() before and immediately after a series of reindexing operations. The default behavior is to do nothing, but these methods can be overridden by an adaptor in order to perform optimizations, turn off autocommits, etc. =cut # these do not necessary have to be overridden # they are called at beginning and end of reindexing process sub _start_reindexing {} sub _end_reindexing {} =head2 _features Title : _features Usage : @features = $db->_features(@args) Function: back end for all get_feature_by_*() queries Returns : list of features Args : see below Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR This is the backend for features(), get_features_by_name(), get_features_by_location(), etc. Arguments are as described for the features() method, except that only the named-argument form is recognized. =cut # bottleneck query generator sub _features { shift->throw_not_implemented } =head2 _search_attributes Title : _search_attributes Usage : @result_list = $db->_search_attributes("text search string",[$tag1,$tag2...],$limit) Function: back end for the search_attributes() method Returns : results list Args : as per search_attributes() Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR See search_attributes() for the format of the results list. The only difference between this and the public method is that the tag list is guaranteed to be an array reference. =cut sub _search_attributes { shift->throw_not_implemented } =head2 can_store_parentage Title : can_store_parentage Usage : $flag = $db->can_store_parentage Function: return true if this adaptor can store parent/child relationships Returns : boolean Args : none Status : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS Override this method and return true if this adaptor supports the _add_SeqFeature() and _get_SeqFeatures() methods, which are used for storing feature parent/child relationships in a normalized fashion. Default is false (parent/child relationships are stored in denormalized form in each feature). =cut # return true here if the storage engine is prepared to store parent/child # relationships using _add_SeqFeature and return them using _fetch_SeqFeatures sub can_store_parentage { return; } =head2 _add_SeqFeature Title : _add_SeqFeature Usage : $count = $db->_add_SeqFeature($parent,@children) Function: store a parent/child relationship between $parent and @children Returns : number of children successfully stored Args : parent feature and one or more children Status : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS If can_store_parentage() returns true, then some store-aware features (e.g. Bio::DB::SeqFeature) will invoke this method to store feature/subfeature relationships in a normalized table. =cut sub _add_SeqFeature { shift->throw_not_implemented } =head2 _fetch_SeqFeatures Title : _fetch_SeqFeatures Usage : @children = $db->_fetch_SeqFeatures($parent_feature) Function: return the immediate subfeatures of the indicated feature Returns : list of subfeatures Args : the parent feature Status : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS If can_store_parentage() returns true, then some store-aware features (e.g. Bio::DB::SeqFeature) will invoke this method to retrieve feature/subfeature relationships from the database. =cut # _get_SeqFeatures($parent,@list_of_child_types) sub _fetch_SeqFeatures {shift->throw_not_implemented } =head2 _insert_sequence Title : _insert_sequence Usage : $success = $db->_insert_sequence($seqid,$sequence_string,$offset) Function: Inserts sequence data into the database at the indicated offset Returns : true if successful Args : see below Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR This is the back end for insert_sequence(). Adaptors must implement this method in order to store and retrieve nucleotide or protein sequence. =cut sub _insert_sequence { shift->throw_not_implemented } # _fetch_sequence() is similar to old dna() method =head2 _fetch_sequence Title : _fetch_sequence Usage : $sequence = $db->_fetch_sequence(-seq_id=>$seqid,-start=>$start,-end=>$end) Function: Fetch the indicated subsequence from the database Returns : The sequence string (not a Bio::PrimarySeq object!) Args : see below Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR This is the back end for fetch_sequence(). Adaptors must implement this method in order to store and retrieve nucleotide or protein sequence. =cut sub _fetch_sequence { shift->throw_not_implemented } sub seq { my $self = shift; my ($seq_id,$start,$end) = @_; if (my $a = $self->dna_accessor) { return $a->can('seq') ? $a->seq($seq_id,$start,$end) :$a->can('fetch_sequence')? $a->fetch_sequence($seq_id,$start,$end) : undef; } else { return $self->_fetch_sequence($seq_id,$start,$end); } } =head2 _seq_ids Title : _seq_ids Usage : @ids = $db->_seq_ids() Function: Return all sequence IDs contained in database Returns : list of sequence Ids Args : none Status : TO BE IMPLEMENTED BY ADAPTOR This method is invoked by seq_ids() to return all sequence IDs (coordinate systems) known to the database. =cut sub _seq_ids { shift->throw_not_implemented } =head2 _start_bulk_update,_finish_bulk_update Title : _start_bulk_update, _finish_bulk_update Usage : $db->_start_bulk_update $db->_finish_bulk_update Function: Activate optimizations for large number of insertions/updates Returns : nothing Args : nothing Status : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTOR These are the backends for start_bulk_update() and finish_bulk_update(). The default behavior of both methods is to do nothing. =cut # Optional flags to change behavior to optimize bulk updating. sub _start_bulk_update { } sub _finish_bulk_update { } # for full TIE() interface - not necessary to implement in most cases =head2 Optional methods needed to implement full TIEHASH interface The core TIEHASH interface will work if just the _store() and _fetch() methods are implemented. To support the full TIEHASH interface, including support for keys(), each(), and exists(), the following methods should be implemented: =over 4 =item $id = $db-E_firstid() Return the first primary ID in the database. Needed for the each() function. =item $next_id = $db-E_nextid($id) Given a primary ID, return the next primary ID in the series. Needed for the each() function. =item $boolean = $db-E_existsid($id) Returns true if the indicated primary ID is in the database. Needed for the exists() function. =item $db-E_deleteid($id) Delete the feature corresponding to the given primary ID. Needed for delete(). =item $db-E_clearall() Empty the database. Needed for %tied_hash = (). =item $count = $db-E_featurecount() Return the number of features in the database. Needed for scalar %tied_hash. =back =cut sub _firstid { shift->throw_not_implemented } sub _nextid { shift->throw_not_implemented } sub _existsid { shift->throw_not_implemented } sub _deleteid { shift->throw_not_implemented } sub _clearall { shift->throw_not_implemented } sub _featurecount { shift->throw_not_implemented } =head1 Internal Methods These methods are internal to Bio::DB::SeqFeature::Store and adaptors. =head2 new_instance Title : new_instance Usage : $db = $db->new_instance() Function: class constructor Returns : A descendent of Bio::DB::SeqFeature::Store Args : none Status : internal This method is called internally by new() to create a new uninitialized instance of Bio::DB::SeqFeature::Store. It is used internally and should not be called by application software. =cut sub new_instance { my $class = shift; return bless {},ref($class) || $class; } =head2 init Title : init Usage : $db->init(@args) Function: initialize object Returns : none Args : Arguments passed to new() Status : private This method is called internally by new() to initialize a newly-created object using the arguments passed to new(). It is to be overridden by Bio::DB::SeqFeature::Store adaptors. =cut sub init { my $self = shift; $self->default_settings(); } =head2 default_settings Title : default_settings Usage : $db->default_settings() Function: set up default settings for the adaptor Returns : none Args : none Status : private This method is may be overridden by adaptors. It is responsible for setting up object default settings. =cut ### # default settings -- set up whatever are the proper default settings # sub default_settings { my $self = shift; $self->serializer($self->default_serializer); $self->index_subfeatures(1); } =head2 default_serializer Title : default_serializer Usage : $serializer = $db->default_serializer Function: finds an available serializer Returns : the name of an available serializer Args : none Status : private This method returns the name of an available serializer module. =cut ### # choose a serializer # sub default_serializer { my $self = shift; # try Storable eval "require Storable; 1" and return 'Storable'; eval "require Data::Dumper; 1" and return 'Data::Dumper'; croak "Unable to load either Storable or Data::Dumper. Please provide a serializer using -serializer"; } =head2 setting Title : setting Usage : $value = $db->setting('setting_name' [=> $new_value]) Function: get/set the value of a setting Returns : the value of the current setting Args : the name of the setting and optionally a new value for the setting Status : private This is a low-level procedure for persistently storing database settings. It can be overridden by adaptors. =cut # persistent settings # by default we store in the object sub setting { my $self = shift; my $variable_name = shift; my $d = $self->{setting}{$variable_name}; $self->{setting}{$variable_name} = shift if @_; $d; } =head2 subfeatures_are_indexed Title : subfeatures_are_indexed Usage : $flag = $db->subfeatures_are_indexed([$new_value]) Function: flag whether subfeatures are indexed Returns : a flag indicating that all subfeatures are indexed Args : (optional) new value of the flag Status : private This method is used internally by the Bio::DB::SeqFeature class to optimize some of its operations. It returns true if all of the subfeatures in the database are indexed; it returns false if at least one of the subfeatures is not indexed. Do not attempt to change the value of this setting unless you are writing an adaptor. =cut ### # whether subfeatures are all indexed # sub subfeatures_are_indexed { my $self = shift; my $d = $self->setting('subfeatures_are_indexed'); $self->setting(subfeatures_are_indexed => shift) if @_; $d; } =head2 subfeature_types_are_indexed Title : subfeature_types_are_indexed Usage : $flag = $db->subfeature_types_are_indexed Function: whether subfeatures are indexed by type Returns : a flag indicating that all subfeatures are indexed Args : none Status : private This method returns true if subfeature types are indexed. Default is to return the value of subfeatures_are_indexed(). =cut sub subfeature_types_are_indexed { my $self = shift; return $self->subfeatures_are_indexed; } =head2 subfeature_locations_are_indexed Title : subfeature_locations_are_indexed Usage : $flag = $db->subfeature_locations_are_indexed Function: whether subfeatures are indexed by type Returns : a flag indicating that all subfeatures are indexed Args : none Status : private This method returns true if subfeature locations are indexed. Default is to return the value of subfeatures_are_indexed(). =cut sub subfeature_locations_are_indexed { my $self = shift; return $self->subfeatures_are_indexed; } =head2 setup_segment_args Title : setup_segment_args Usage : @args = $db->setup_segment_args(@args) Function: munge the arguments to the segment() call Returns : munged arguments Args : see below Status : private This method is used internally by segment() to translate positional arguments into named argument=Evalue pairs. =cut sub setup_segment_args { my $self = shift; return @_ if defined $_[0] && $_[0] =~ /^-/; return (-name=>$_[0],-start=>$_[1],-end=>$_[2]) if @_ == 3; return (-class=>$_[0],-name=>$_[1]) if @_ == 2; return (-name=>$_[0]) if @_ == 1; return; } =head2 store_and_cache Title : store_and_cache Usage : $success = $db->store_and_cache(@features) Function: store features into database and update cache Returns : number of features stored Args : index the features? (0 or 1) and list of features Status : private This private method stores the list of Bio::SeqFeatureI objects into the database and caches them in memory for retrieval. =cut sub store_and_cache { my $self = shift; my $indexit = shift; my $result = $self->_store($indexit,@_); if (my $cache = $self->cache) { for my $obj (@_) { defined (my $id = eval {$obj->primary_id}) or next; $cache->store($id,$obj); } } $result; } =head2 init_cache Title : init_cache Usage : $db->init_cache($size) Function: initialize the in-memory feature cache Returns : the Tie::Cacher object Args : desired size of the cache Status : private This method is used internally by new() to create the Tie::Cacher instance used for the in-memory feature cache. =cut sub init_cache { my $self = shift; my $cache_size = shift; $cache_size = 5000 if $cache_size == 1; # in case somebody treats it as a flag $self->{cache} = Tie::Cacher->new($cache_size) or $self->throw("Couldn't tie cache: $!"); } =head2 cache Title : cache Usage : $cache = $db->cache Function: return the cache object Returns : the Tie::Cacher object Args : none Status : private This method returns the Tie::Cacher object used for the in-memory feature cache. =cut sub cache { shift->{cache} } =head2 load_class Title : load_class Usage : $db->load_class($blessed_object) Function: loads the module corresponding to a blessed object Returns : empty Args : a blessed object Status : private This method is used by thaw() to load the code for a blessed object. This ensures that all the object's methods are available. =cut sub load_class { my $self = shift; my $obj = shift; return unless defined $obj; return if $self->{class_loaded}{ref $obj}++; unless ($obj && $obj->can('primary_id')) { my $class = ref $obj; eval "require $class"; } } #################################### Internal methods #################### =head2 freeze Title : freeze Usage : $serialized_object = $db->freeze($feature) Function: serialize a feature object into a string Returns : serialized feature object Args : a seqfeature object Status : private This method converts a Bio::SeqFeatureI object into a serialized form suitable for storage into a database. The feature's primary ID is set to undef before it is serialized. This avoids any potential mismatch between the primary ID used as the database key and the primary ID stored in the serialized object. =cut sub freeze { my $self = shift; my $obj = shift; # Bio::SeqFeature::Generic contains cleanup methods, so we need to # localize the methods to undef temporarily so that we can serialize local $obj->{'_root_cleanup_methods'} if exists $obj->{'_root_cleanup_methods'}; my ($id,$store); $id = $obj->primary_id(); $obj->primary_id(undef); # don't want primary ID to be stored in object eval { $store = $obj->object_store; $obj->object_store(undef); # don't want a copy of the store in the object }; my $serializer = $self->serializer; my $data; if ($serializer eq 'Data::Dumper') { my $d = Data::Dumper->new([$obj]); $d->Terse(1); $d->Deepcopy(1); $d->Deparse(1); $data = $d->Dump; } elsif ($serializer eq 'Storable') { local $Storable::forgive_me = 1; local $Storable::Deparse = 1; $data = Storable::nfreeze($obj); } $obj->primary_id($id); # restore to original state eval { $obj->object_store($store); }; $data = compress($data) if $self->do_compress; return $data; } =head2 thaw Title : thaw Usage : $feature = $db->thaw($serialized_object,$primary_id) Function: unserialize a string into a feature object Returns : Bio::SeqFeatureI object Args : serialized form of object from freeze() and primary_id of object Status : private This method is the reverse of the freeze(). The supplied primary_id becomes the primary_id() of the returned Bio::SeqFeatureI object. This implementation checks for a deserialized object in the cache before it calls thaw_object() to do the actual deserialization. =cut sub thaw { my $self = shift; my ($obj,$primary_id) = @_; if (my $cache = $self->cache) { return $cache->fetch($primary_id) if $cache->exists($primary_id); my $object = $self->thaw_object($obj,$primary_id) or return; $cache->store($primary_id,$object); return $object; } else { return $self->thaw_object($obj,$primary_id); } } =head2 thaw_object Title : thaw_object Usage : $feature = $db->thaw_object($serialized_object,$primary_id) Function: unserialize a string into a feature object Returns : Bio::SeqFeatureI object Args : serialized form of object from freeze() and primary_id of object Status : private After thaw() checks the cache and comes up empty, this method is invoked to thaw the object. =cut sub thaw_object { my $self = shift; my ($obj,$primary_id) = @_; my $serializer = $self->serializer; my $object; $obj = uncompress($obj) if $self->do_compress; if ($serializer eq 'Data::Dumper') { $object = eval $obj; } elsif ($serializer eq 'Storable') { local $Storable::forgive_me = 1; local $Storable::Eval = 1; $object = Storable::thaw($obj); } # remember the primary ID of this object as well as the # identity of the store, so that we can do lazy loading; # both of these are wrapped in an eval because not all # bioseqfeatures support them (or want to) $self->load_class($object); eval { $object->primary_id($primary_id); $object->object_store($self); }; $object; } =head2 feature_names Title : feature_names Usage : ($names,$aliases) = $db->feature_names($feature) Function: get names and aliases for a feature Returns : an array of names and an array of aliases Args : a Bio::SeqFeatureI object Status : private This is an internal utility function which, given a Bio::SeqFeatureI object, returns two array refs. The first is a list of official names for the feature, and the second is a list of aliases. This is slightly skewed towards GFF3 usage, so the official names are the display_name(), plus all tag values named 'Name', plus all tag values named 'ID'. The aliases are all tag values named 'Alias'. =cut sub feature_names { my $self = shift; my $obj = shift; my $primary_id = $obj->primary_id; my @names; push @names,$obj->display_name if defined $obj->display_name; push @names,$obj->get_tag_values('Name') if $obj->has_tag('Name'); push @names,$obj->get_tag_values('ID') if $obj->has_tag('ID'); # don't think this is desired behavior # @names = grep {defined $_ && $_ ne $primary_id} @names; my @aliases = grep {defined} $obj->get_tag_values('Alias') if $obj->has_tag('Alias'); return (\@names,\@aliases); } =head2 feature_summary Title : feature_summary Usage : $summary = $db->feature_summary(@args) Function: returns a coverage summary across indicated region/type Returns : a Bio::SeqFeatureI object containing the "coverage" tag Args : see below Status : public This method is used to get coverage density information across a region of interest. You provide it with a region of interest, optional a list of feature types, and a count of the number of bins over which you want to calculate the coverage density. An object is returned corresponding to the requested region. It contains a tag called "coverage" that will return an array ref of "bins" length. Each element of the array describes the number of features that overlap the bin at this position. Arguments: Argument Description -------- ----------- -seq_id Sequence ID for the region -start Start of region -end End of region -type/-types Feature type of interest or array ref of types -bins Number of bins across region. Defaults to 1000. -iterator Return an iterator across the region Note that this method uses an approximate algorithm that is only accurate to 500 bp, so when dealing with bins that are smaller than 1000 bp, you may see some shifting of counts between adjacent bins. Although an -iterator option is provided, the method only ever returns a single feature, so this is fairly useless. =cut sub feature_summary { my $self = shift; my ($seq_name,$start,$end,$types,$bins,$iterator) = rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'], ['TYPES','TYPE','PRIMARY_TAG'], 'BINS', 'ITERATOR', ],@_); my ($coverage,$tag) = $self->coverage_array(-seqid=> $seq_name, -start=> $start, -end => $end, -type => $types, -bins => $bins) or return; my $score = 0; for (@$coverage) { $score += $_ } $score /= @$coverage; my $feature = Bio::SeqFeature::Lite->new(-seq_id => $seq_name, -start => $start, -end => $end, -type => $tag, -score => $score, -attributes => { coverage => [$coverage] }); return $iterator ? Bio::DB::SeqFeature::Store::FeatureIterator->new($feature) : $feature; } =head2 coverage_array Title : coverage_array Usage : $arrayref = $db->coverage_array(@args) Function: returns a coverage summary across indicated region/type Returns : an array reference Args : see below Status : public This method is used to get coverage density information across a region of interest. The arguments are identical to feature_summary, except that instead of returning a Bio::SeqFeatureI object, it returns an array reference of the desired number of bins. The value of each element corresponds to the number of features in the bin. Arguments: Argument Description -------- ----------- -seq_id Sequence ID for the region -start Start of region -end End of region -type/-types Feature type of interest or array ref of types -bins Number of bins across region. Defaults to 1000. Note that this method uses an approximate algorithm that is only accurate to 500 bp, so when dealing with bins that are smaller than 1000 bp, you may see some shifting of counts between adjacent bins. =cut sub coverage_array { shift->throw_not_implemented; } package Bio::DB::SeqFeature::Store::FeatureIterator; sub new { my $self = shift; my @features = @_; return bless \@features,ref $self || $self; } sub next_seq { my $self = shift; return unless @$self; return shift @$self; } sub begin_work { }# noop sub commit { }# noop sub rollback { }# noop 1; __END__ =head1 BUGS This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs. =head1 SEE ALSO L, L, L, L, L L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2006 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/SeqFeature/Store000755000766000024 013155576320 17514 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm000444000766000024 6162313155576320 23561 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::Store::FeatureFileLoader; =head1 NAME Bio::DB::SeqFeature::Store::FeatureFileLoader -- feature file loader for Bio::DB::SeqFeature::Store =head1 SYNOPSIS use Bio::DB::SeqFeature::Store; use Bio::DB::SeqFeature::Store::FeatureFileLoader; # Open the sequence database my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:test', -write => 1 ); my $loader = Bio::DB::SeqFeature::Store::FeatureFileLoader->new(-store => $db, -verbose => 1, -fast => 1); $loader->load('./my_genome.fff'); =head1 DESCRIPTION The Bio::DB::SeqFeature::Store::FeatureFileLoader object parsers FeatureFile-format sequence annotation files and loads Bio::DB::SeqFeature::Store databases. For certain combinations of SeqFeature classes and SeqFeature::Store databases it features a "fast load" mode which will greatly accelerate the loading of databases by a factor of 5-10. FeatureFile Format (.fff) is very simple: mRNA B0511.1 Chr1:1..100 Type=UTR;Note="putative primase" mRNA B0511.1 Chr1:101..200,300..400,500..800 Type=CDS mRNA B0511.1 Chr1:801..1000 Type=UTR reference = Chr3 Cosmid B0511 516..619 Cosmid B0511 3185..3294 Cosmid B0511 10946..11208 Cosmid B0511 13126..13511 Cosmid B0511 11394..11539 EST yk260e10.5 15569..15724 EST yk672a12.5 537..618,3187..3294 EST yk595e6.5 552..618 EST yk595e6.5 3187..3294 EST yk846e07.3 11015..11208 EST yk53c10 yk53c10.3 15000..15500,15700..15800 yk53c10.5 18892..19154 EST yk53c10.5 16032..16105 SwissProt PECANEX 13153-13656 Note="Swedish fish" FGENESH "Predicted gene 1" 1-205,518-616,661-735,3187-3365,3436-3846 "Pfam domain" # file ends There are up to four columns of WHITESPACE (not necessarily tab) delimited text. Embedded whitespace must be escaped using shell escaping rules (quoting the column or backslashing whitespace). Column 1: The feature type. You may use type:subtype as a convention for method:source. Column 2: The feature name/ID. Column 3: The position of this feature in base pair coordinates. Ranges can be given as either start-end or start..end. A chromosome position can be specified using the format "reference:start..end". A discontinuous feature can be specified by giving multiple ranges separated by commas. Minus-strand features are indicated by specifying a start > end. Column 4: Comment/attribute field. A single Note can be given, or a series of attribute=value pairs, separated by spaces or semicolons, as in "score=23;type=transmembrane" =head2 Specifying Positions and Ranges A feature position is specified using a sequence ID (a genbank accession number, a chromosome name, a contig, or any other meaningful reference system, followed by a colon and a position range. Ranges are two integers separated by double dots or the hyphen. Examples: "Chr1:516..11208", "ctgA:1-5000". Negative coordinates are allowed, as in "Chr1:-187..1000". A discontinuous range ("split location") uses commas to separate the ranges. For example: Gene B0511.1 Chr1:516..619,3185..3294,10946..11208 In the case of a split location, the sequence id only has to appear in front of the first range. Alternatively, a split location can be indicated by repeating the features type and name on multiple adjacent lines: Gene B0511.1 Chr1:516..619 Gene B0511.1 Chr1:3185..3294 Gene B0511.1 Chr1:10946..11208 If all the locations are on the same reference sequence, you can specify a default chromosome using a "reference=EseqidE": reference=Chr1 Gene B0511.1 516..619 Gene B0511.1 3185..3294 Gene B0511.1 10946..11208 The default seqid is in effect until the next "reference" line appears. =head2 Feature Tags Tags can be added to features by adding a fourth column consisting of "tag=value" pairs: Gene B0511.1 Chr1:516..619,3185..3294 Note="Putative primase" Tags and their values take any form you want, and multiple tags can be separated by semicolons. You can also repeat tags multiple times: Gene B0511.1 Chr1:516..619,3185..3294 GO_Term=GO:100;GO_Term=GO:2087 Several tags have special meanings: Tag Meaning --- ------- Type The primary tag for a subfeature. Score The score of a feature or subfeature. Phase The phase of a feature or subfeature. URL A URL to link to (via the Bio::Graphics library). Note A note to attach to the feature for display by the Bio::Graphics library. For example, in the common case of an mRNA, you can use the "Type" tag to distinguish the parts of the mRNA into UTR and CDS: mRNA B0511.1 Chr1:1..100 Type=UTR mRNA B0511.1 Chr1:101..200,300..400,500..800 Type=CDS mRNA B0511.1 Chr1:801..1000 Type=UTR The top level feature's primary tag will be "mRNA", and its subparts will have types UTR and CDS as indicated. Additional tags that are placed in the first line of the feature will be applied to the top level. In this example, the note "Putative primase" will be applied to the mRNA at the top level of the feature: mRNA B0511.1 Chr1:1..100 Type=UTR;Note="Putative primase" mRNA B0511.1 Chr1:101..200,300..400,500..800 Type=CDS mRNA B0511.1 Chr1:801..1000 Type=UTR =head2 Feature Groups Features can be grouped so that they are rendered by the "group" glyph. To start a group, create a two-column feature entry showing the group type and a name for the group. Follow this with a list of feature entries with a blank type. For example: EST yk53c10 yk53c10.3 15000-15500,15700-15800 yk53c10.5 18892-19154 This example is declaring that the ESTs named yk53c10.3 and yk53c10.5 belong to the same group named yk53c10. =head2 Comments and the #include Directive Lines that begin with the # sign are treated as comments and ignored. When a # sign appears within a line, everything to the right of the symbol is also ignored, unless it looks like an HTML fragment or an HTML color, e.g.: # this is ignored [Example] glyph = generic # this comment is ignored bgcolor = #FF0000 link = http://www.google.com/search?q=$name#results Be careful, because the processing of # signs uses a regexp heuristic. To be safe, always put a space after the # sign to make sure it is treated as a comment. The special comment "#include 'filename'" acts like the C preprocessor directive and will insert the comments of a named file into the position at which it occurs. Relative paths will be treated relative to the file in which the #include occurs. Nested #include directives are allowed: #include "/usr/local/share/my_directives.txt" #include 'my_directives.txt' #include chromosome3_features.gff3 You can enclose the file path in single or double quotes as shown above. If there are no spaces in the filename the quotes are optional. Include file processing is not very smart. Avoid creating circular #include references. You have been warned! =head2 Caveats Note that this loader always creates denormalized features such that subfeatures and their parents are stored as one big database object. The GFF3 format and its loader is usually preferred for both space and execution efficiency. =head1 METHODS =cut use strict; use Carp 'croak'; use File::Spec; use Text::ParseWords 'shellwords','quotewords'; use base 'Bio::DB::SeqFeature::Store::Loader'; =head2 new Title : new Usage : $loader = Bio::DB::SeqFeature::Store::FeatureFileLoader->new(@options) Function: create a new parser Returns : a Bio::DB::SeqFeature::Store::FeatureFileLoader parser and loader Args : several - see below Status : public This method creates a new FeatureFile loader and establishes its connection with a Bio::DB::SeqFeature::Store database. Arguments are -name=E$value pairs as described in this table: Name Value ---- ----- -store A writable Bio::DB::SeqFeature::Store database handle. -seqfeature_class The name of the type of Bio::SeqFeatureI object to create and store in the database (Bio::DB::SeqFeature by default) -sf_class A shorter alias for -seqfeature_class -verbose Send progress information to standard error. -fast If true, activate fast loading (see below) -chunk_size Set the storage chunk size for nucleotide/protein sequences (default 2000 bytes) -tmp Indicate a temporary directory to use when loading non-normalized features. When you call new(), a connection to a Bio::DB::SeqFeature::Store database should already have been established and the database initialized (if appropriate). Some combinations of Bio::SeqFeatures and Bio::DB::SeqFeature::Store databases support a fast loading mode. Currently the only reliable implementation of fast loading is the combination of DBI::mysql with Bio::DB::SeqFeature. The other important restriction on fast loading is the requirement that a feature that contains subfeatures must occur in the FeatureFile file before any of its subfeatures. Otherwise the subfeatures that occurred before the parent feature will not be attached to the parent correctly. This restriction does not apply to normal (slow) loading. If you use an unnormalized feature class, such as Bio::SeqFeature::Generic, then the loader needs to create a temporary database in which to cache features until all their parts and subparts have been seen. This temporary databases uses the "bdb" adaptor. The -tmp option specifies the directory in which that database will be created. If not present, it defaults to the system default tmp directory specified by File::Spec-Etmpdir(). The -chunk_size option allows you to tune the representation of DNA/Protein sequence in the Store database. By default, sequences are split into 2000 base/residue chunks and then reassembled as needed. This avoids the problem of pulling a whole chromosome into memory in order to fetch a short subsequence from somewhere in the middle. Depending on your usage patterns, you may wish to tune this parameter using a chunk size that is larger or smaller than the default. =cut # sub new {} inherited =head2 load Title : load Usage : $count = $loader->load(@ARGV) Function: load the indicated files or filehandles Returns : number of feature lines loaded Args : list of files or filehandles Status : public Once the loader is created, invoke its load() method with a list of FeatureFile or FASTA file paths or previously-opened filehandles in order to load them into the database. Compressed files ending with .gz, .Z and .bz2 are automatically recognized and uncompressed on the fly. Paths beginning with http: or ftp: are treated as URLs and opened using the LWP GET program (which must be on your path). FASTA files are recognized by their initial "E" character. Do not feed the loader a file that is neither FeatureFile nor FASTA; I don't know what will happen, but it will probably not be what you expect. =cut # sub load {} inherited =head2 accessors The following read-only accessors return values passed or created during new(): store() the long-term Bio::DB::SeqFeature::Store object tmp_store() the temporary Bio::DB::SeqFeature::Store object used during loading sfclass() the Bio::SeqFeatureI class fast() whether fast loading is active seq_chunk_size() the sequence chunk size verbose() verbose progress messages =cut # sub store {} inherited # sub tmp_store {} inherited # sub sfclass {} inherited # sub fast {} inherited # sub seq_chunk_size {} inherited # sub verbose {} inherited =head2 default_seqfeature_class $class = $loader->default_seqfeature_class Return the default SeqFeatureI class (Bio::Graphics::Feature). =cut sub default_seqfeature_class { #override my $self = shift; return 'Bio::Graphics::Feature'; } =head2 load_fh $count = $loader->load_fh($filehandle) Load the FeatureFile data at the other end of the filehandle and return true if successful. Internally, load_fh() invokes: start_load(); do_load($filehandle); finish_load(); =cut # sub load_fh { } inherited =head2 start_load, finish_load These methods are called at the start and end of a filehandle load. =cut sub create_load_data { my $self = shift; $self->SUPER::create_load_data(); $self->{load_data}{mode} = 'fff'; $self->{load_data}{CurrentGroup} = undef; } sub finish_load { my $self = shift; $self->_store_group; $self->SUPER::finish_load; } =head2 load_line $loader->load_line($data); Load a line of a FeatureFile file. You must bracket this with calls to start_load() and finish_load()! $loader->start_load(); $loader->load_line($_) while ; $loader->finish_load(); =cut sub load_line { my $self = shift; my $line = shift; chomp($line); return unless $line =~ /\S/; # blank line my $load_data = $self->{load_data}; $load_data->{mode} = 'fff' if /\s/; # if it has any whitespace in # it, then back to fff mode if ($line =~ /^\#\s?\#\s*([\#]+)/) { ## meta instruction $load_data->{mode} = 'fff'; $self->handle_meta($1); } elsif ($line =~ /^\#/) { $load_data->{mode} = 'fff'; # just to be safe return; # comment } elsif ($line =~ /^>\s*(\S+)/) { # FASTA lines are coming $load_data->{mode} = 'fasta'; $self->start_or_finish_sequence($1); } elsif ($load_data->{mode} eq 'fasta') { $self->load_sequence($line); } elsif ($load_data->{mode} eq 'fff') { $self->handle_feature($line); if (++$load_data->{count} % 1000 == 0) { my $now = $self->time(); my $nl = -t STDOUT && !$ENV{EMACS} ? "\r" : "\n"; $self->msg(sprintf("%d features loaded in %5.2fs...$nl", $load_data->{count},$now - $load_data->{start_time})); $load_data->{start_time} = $now; } } else { $self->throw("I don't know what to do with this line:\n$line"); } } =head2 handle_meta $loader->handle_meta($meta_directive) This method is called to handle meta-directives such as ##sequence-region. The method will receive the directive with the initial ## stripped off. =cut # sub handle_meta { } inherited =head2 handle_feature $loader->handle_feature($gff3_line) This method is called to process a single FeatureFile line. It manipulates information stored a data structure called $self-E{load_data}. =cut sub handle_feature { my $self = shift; local $_ = shift; my $ld = $self->{load_data}; # handle reference line if (/^reference\s*=\s*(.+)/) { $ld->{reference} = $1; return; } # parse data lines my @tokens = quotewords('\s+',1,$_); for (0..2) { # remove quotes from everything but last column next unless defined $tokens[$_]; $tokens[$_] =~ s/^"//; $tokens[$_] =~ s/"$//; } if (@tokens < 3) { # short line; assume a group identifier $self->store_current_feature(); my $type = shift @tokens; my $name = shift @tokens; $ld->{CurrentGroup} = $self->_make_indexed_feature($name,$type,'',{_ff_group=>1}); $self->_indexit($name => 1); return; } my($type,$name,$strand,$bounds,$attributes); if ($tokens[2] =~ /^([+-.]|[+-]?[01])$/) { # old version ($type,$name,$strand,$bounds,$attributes) = @tokens; } else { # new version ($type,$name,$bounds,$attributes) = @tokens; } # handle case of there only being one value in the last column, # in which case we treat it the same as Note="value" my $attr = $self->parse_attributes($attributes); # @parts is an array of ([ref,start,end],[ref,start,end],...) my @parts = map { [/(?:(\w+):)?(-?\d+)(?:-|\.\.)(-?\d+)/]} split /(?:,| )\s*/,$bounds; # deal with groups -- a group is ending if $type is defined # and CurrentGroup is set if ($type && $ld->{CurrentGroup}) { $self->_store_group(); } $type = '' unless defined $type; $name = '' unless defined $name; $type ||= $ld->{CurrentGroup}->primary_tag if $ld->{CurrentGroup}; my $reference = $ld->{reference} || 'ChrUN'; foreach (@parts) { if (defined $_ && ref($_) eq 'ARRAY' && defined $_->[1] && defined $_->[2]) { $strand ||= $_->[1] <= $_->[2] ? '+' : '-'; ($_->[1],$_->[2]) = ($_->[2],$_->[1]) if $_->[1] > $_->[2]; } $reference = $_->[0] if defined $_->[0]; $_ = [@{$_}[1,2]]; # strip off the reference. } # now @parts is an array of [start,end] and $reference contains the seqid # apply coordinate mapper if ($self->{coordinate_mapper} && $reference) { my @remapped = $self->{coordinate_mapper}->($reference,@parts); ($reference,@parts) = @remapped if @remapped; } # either create a new feature or add a segment to it my $feature = $ld->{CurrentFeature}; $ld->{OldPartType} = $ld->{PartType}; if (exists $attr->{Type} || exists $attr->{type}) { $ld->{PartType} = $attr->{Type}[0] || $attr->{type}[0]; } else { $ld->{PartType} = $type; } if ($feature) { local $^W = 0; # avoid uninit warning when display_name() is called # if this is a different feature from what we have now, then we # store the current one, and create a new one if ($feature->display_name ne $name || $feature->method ne $type) { $self->store_current_feature; # new feature, store old one undef $feature; } else { # create a new multipart feature $self->_multilevel_feature($feature,$ld->{OldPartType}) unless $feature->get_SeqFeatures; my $part = $self->_make_feature($name, $ld->{PartType}, $strand, $attr, $reference, @{$parts[0]}); $feature->add_SeqFeature($part); } } $feature ||= $self->_make_indexed_feature($name, $type, # side effect is to set CurrentFeature $strand, $attr, $reference, @{$parts[0]}); # add more segments to the current feature if (@parts > 1) { for my $part (@parts) { $type ||= $feature->primary_tag; my $sp = $self->_make_feature($name, $ld->{PartType}, $strand, $attr, $reference, @{$part}); $feature->add_SeqFeature($sp); } } } sub _multilevel_feature { # turn a single-level feature into a multilevel one my $self = shift; my $f = shift; my $type = shift; my %attributes = $f->attributes; $attributes{Score} = [$f->score] if defined $f->score; $attributes{Phase} = [$f->phase] if defined $f->phase; my @args = ($f->display_name, $type||$f->type, $f->strand, \%attributes, $f->seq_id, $f->start, $f->end); my $subpart = $self->_make_feature(@args); $f->add_SeqFeature($subpart); } sub _make_indexed_feature { my $self = shift; my $f = $self->_make_feature(@_); my $name = $f->display_name; $self->{load_data}{CurrentFeature} = $f; $self->{load_data}{CurrentID} = $name; $self->_indexit($name => 1); return $f; } sub _make_feature { my $self = shift; my ($name,$type,$strand,$attributes,$ref,$start,$end) = @_; # some basic error checking $self->throw("syntax error at line $.: '$_'") if ($ref && !defined $start) or ($ref && !defined $end) or ($start && $start !~ /^[-\d]+$/) or ($end && $end !~ /^[-\d]+$/) or !defined $type or !defined $name; $strand ||= ''; my @args = (-name => $name, -strand => $strand eq '+' ? 1 :$strand eq '-' ? -1 :$strand eq '' ? 0 :$strand eq '.' ? 0 :$strand == 1 ? 1 :$strand == -1 ? -1 :0, -attributes => $attributes, ); if (my ($method,$source) = $type =~ /(\S+):(\S+)/) { push @args,(-primary_tag => $method, -source => $source); } else { push @args,(-primary_tag => $type); } push @args,(-seq_id => $ref) if defined $ref; push @args,(-start => $start) if defined $start; push @args,(-end => $end) if defined $end; # pull out special attributes if (my $score = $attributes->{Score} || $attributes->{score}) { push @args,(-score => $score->[0]); delete $attributes->{$_} foreach qw(Score score); } if (my $note = $attributes->{Note} || $attributes->{note}) { push @args,(-desc => join '; ',@$note); delete $attributes->{$_} foreach qw(Note note); } if (my $url = $attributes->{url} || $attributes->{Url}) { push @args,(-url => $url->[0]); delete $attributes->{$_} foreach qw (Url url); } if (my $phase = $attributes->{phase} || $attributes->{Phase}) { push @args,(-phase => $phase->[0]); delete $attributes->{$_} foreach qw (Phase phase); } $self->_indexit($name=>1) if $self->index_subfeatures && $name; return $self->sfclass->new(@args); } =head2 store_current_feature $loader->store_current_feature() This method is called to store the currently active feature in the database. It uses a data structure stored in $self-E{load_data}. =cut sub store_current_feature { # overridden my $self = shift; # handle open groups # if there is an open group, then we simply add the current # feature to the group. my $ld = $self->{load_data}; if ($ld->{CurrentGroup} && $ld->{CurrentFeature}) { $ld->{CurrentGroup}->add_SeqFeature($ld->{CurrentFeature}) unless $ld->{CurrentGroup} eq $ld->{CurrentFeature}; # paranoia - shouldn't happen return; } else { $self->SUPER::store_current_feature(); } } sub _store_group { my $self = shift; my $ld = $self->{load_data}; my $group = $ld->{CurrentGroup} or return; # if there is an unattached feature, then add it $self->store_current_feature() if $ld->{CurrentFeature}; $ld->{CurrentFeature} = $group; $ld->{CurrentID} = $group->display_name; $self->_indexit($ld->{CurrentID} => 1); undef $ld->{CurrentGroup}; $self->store_current_feature(); } =head2 build_object_tree $loader->build_object_tree() This method gathers together features and subfeatures and builds the graph that connects them. =cut ### # put objects together # sub build_object_tree { croak "We shouldn't be building an object tree in the FeatureFileLoader"; } =head2 build_object_tree_in_tables $loader->build_object_tree_in_tables() This method gathers together features and subfeatures and builds the graph that connects them, assuming that parent/child relationships will be stored in a database table. =cut sub build_object_tree_in_tables { croak "We shouldn't be building an object tree in the FeatureFileLoader"; } =head2 build_object_tree_in_features $loader->build_object_tree_in_features() This method gathers together features and subfeatures and builds the graph that connects them, assuming that parent/child relationships are stored in the seqfeature objects themselves. =cut sub build_object_tree_in_features { croak "We shouldn't be building an object tree in the FeatureFileLoader"; } =head2 attach_children $loader->attach_children($store,$load_data,$load_id,$feature) This recursively adds children to features and their subfeatures. It is called when subfeatures are directly contained within other features, rather than stored in a relational table. =cut sub attach_children { croak "We shouldn't be attaching children in the FeatureFileLoader!"; } =head2 parse_attributes @attributes = $loader->parse_attributes($attribute_line) This method parses the information contained in the $attribute_line into a flattened hash (array). It may return one element, in which case it is an implicit =cut sub parse_attributes { my $self = shift; my $att = shift; $att ||= ''; # to prevent uninit variable warnings from quotewords() my @pairs = quotewords('[;\s]',1,$att); my %attributes; for my $pair (@pairs) { unless ($pair =~ /=/) { push @{$attributes{Note}},(quotewords('',0,$pair))[0] || $pair; } else { my ($tag,$value) = quotewords('\s*=\s*',0,$pair); $tag = 'Note' if $tag eq 'description'; push @{$attributes{$tag}},$value; } } return \%attributes; } =head2 start_or_finish_sequence $loader->start_or_finish_sequence('Chr9') This method is called at the beginning and end of a fasta section. =cut 1; __END__ =head1 BUGS This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs. =head1 SEE ALSO L, L, L, L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2006 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/SeqFeature/Store/GFF2Loader.pm000444000766000024 3277313155576320 22056 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::Store::GFF2Loader; # $Id: GFF2Loader.pm 11755 2007-11-08 02:19:29Z cjfields $ =head1 NAME Bio::DB::SeqFeature::Store::GFF2Loader -- GFF2 file loader for Bio::DB::SeqFeature::Store =head1 SYNOPSIS use Bio::DB::SeqFeature::Store; use Bio::DB::SeqFeature::Store::GFF2Loader; # Open the sequence database my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:test', -write => 1 ); my $loader = Bio::DB::SeqFeature::Store::GFF2Loader->new(-store => $db, -verbose => 1, -fast => 1); $loader->load('./my_genome.gff'); =head1 DESCRIPTION The Bio::DB::SeqFeature::Store::GFF2Loader object parsers GFF2-format sequence annotation files and loads Bio::DB::SeqFeature::Store databases. For certain combinations of SeqFeature classes and SeqFeature::Store databases it features a "fast load" mode which will greatly accelerate the loading of GFF2 databases by a factor of 5-10. The GFF2 file format has been extended very slightly to accommodate Bio::DB::SeqFeature::Store. First, the loader recognizes is a new directive: # #index-subfeatures [0|1] Note that you can place a space between the two #'s in order to prevent GFF2 validators from complaining. If this is true, then subfeatures are indexed (the default) so that they can be retrieved with a query. See L for an explanation of this. If false, then subfeatures can only be accessed through their parent feature. The default is to index all subfeatures. Second, the loader recognizes a new attribute tag called index, which if present, controls indexing of the current feature. Example: ctg123 . TF_binding_site 1000 1012 . + . ID=tfbs00001;index=1 You can use this to turn indexing on and off, overriding the default for a particular feature. =cut # load utility - incrementally load the store based on GFF2 file # # two modes: # slow mode -- features can occur in any order in the GFF2 file # fast mode -- all features with same ID must be contiguous in GFF2 file use strict; use Carp 'croak'; use Bio::DB::GFF::Util::Rearrange; use Text::ParseWords 'quotewords'; use base 'Bio::DB::SeqFeature::Store::GFF3Loader'; my %Special_attributes =( Gap => 1, Target => 1, Parent => 1, Name => 1, Alias => 1, ID => 1, index => 1, Index => 1, ); =head2 new Title : new Usage : $loader = Bio::DB::SeqFeature::Store::GFF2Loader->new(@options) Function: create a new parser Returns : a Bio::DB::SeqFeature::Store::GFF2Loader gff2 parser and loader Args : several - see below Status : public This method creates a new GFF2 loader and establishes its connection with a Bio::DB::SeqFeature::Store database. Arguments are -name=E$value pairs as described in this table: Name Value ---- ----- -store A writable Bio::DB::SeqFeature::Store database handle. -seqfeature_class The name of the type of Bio::SeqFeatureI object to create and store in the database (Bio::DB::SeqFeature by default) -sf_class A shorter alias for -seqfeature_class -verbose Send progress information to standard error. -fast If true, activate fast loading (see below) -chunk_size Set the storage chunk size for nucleotide/protein sequences (default 2000 bytes) -tmp Indicate a temporary directory to use when loading non-normalized features. When you call new(), a connection to a Bio::DB::SeqFeature::Store database should already have been established and the database initialized (if appropriate). Some combinations of Bio::SeqFeatures and Bio::DB::SeqFeature::Store databases support a fast loading mode. Currently the only reliable implementation of fast loading is the combination of DBI::mysql with Bio::DB::SeqFeature. The other important restriction on fast loading is the requirement that a feature that contains subfeatures must occur in the GFF2 file before any of its subfeatures. Otherwise the subfeatures that occurred before the parent feature will not be attached to the parent correctly. This restriction does not apply to normal (slow) loading. If you use an unnormalized feature class, such as Bio::SeqFeature::Generic, then the loader needs to create a temporary database in which to cache features until all their parts and subparts have been seen. This temporary databases uses the "berkeleydb" adaptor. The -tmp option specifies the directory in which that database will be created. If not present, it defaults to the system default tmp directory specified by File::Spec-Etmpdir(). The -chunk_size option allows you to tune the representation of DNA/Protein sequence in the Store database. By default, sequences are split into 2000 base/residue chunks and then reassembled as needed. This avoids the problem of pulling a whole chromosome into memory in order to fetch a short subsequence from somewhere in the middle. Depending on your usage patterns, you may wish to tune this parameter using a chunk size that is larger or smaller than the default. =cut # sub new { } inherited =head2 load Title : load Usage : $count = $loader->load(@ARGV) Function: load the indicated files or filehandles Returns : number of feature lines loaded Args : list of files or filehandles Status : public Once the loader is created, invoke its load() method with a list of GFF2 or FASTA file paths or previously-opened filehandles in order to load them into the database. Compressed files ending with .gz, .Z and .bz2 are automatically recognized and uncompressed on the fly. Paths beginning with http: or ftp: are treated as URLs and opened using the LWP GET program (which must be on your path). FASTA files are recognized by their initial "E" character. Do not feed the loader a file that is neither GFF2 nor FASTA; I don't know what will happen, but it will probably not be what you expect. =cut # sub load { } inherited =head2 accessors The following read-only accessors return values passed or created during new(): store() the long-term Bio::DB::SeqFeature::Store object tmp_store() the temporary Bio::DB::SeqFeature::Store object used during loading sfclass() the Bio::SeqFeatureI class fast() whether fast loading is active seq_chunk_size() the sequence chunk size verbose() verbose progress messages =cut # sub store inherited # sub tmp_store inherited # sub sfclass inherited # sub fast inherited # sub seq_chunk_size inherited # sub verbose inherited =head2 Internal Methods The following methods are used internally and may be overridden by subclasses. =over 4 =item default_seqfeature_class $class = $loader->default_seqfeature_class Return the default SeqFeatureI class (Bio::DB::SeqFeature). =cut # sub default_seqfeature_class { } inherited =item subfeatures_normalized $flag = $loader->subfeatures_normalized([$new_flag]) Get or set a flag that indicates that the subfeatures are normalized. This is deduced from the SeqFeature class information. =cut # sub subfeatures_normalized { } inherited =item subfeatures_in_table $flag = $loader->subfeatures_in_table([$new_flag]) Get or set a flag that indicates that feature/subfeature relationships are stored in a table. This is deduced from the SeqFeature class and Store information. =cut # sub subfeatures_in_table { } inherited =item load_fh $count = $loader->load_fh($filehandle) Load the GFF2 data at the other end of the filehandle and return true if successful. Internally, load_fh() invokes: start_load(); do_load($filehandle); finish_load(); =cut # sub load_fh { } inherited =item start_load, finish_load These methods are called at the start and end of a filehandle load. =cut # sub create_load_data { } #inherited # sub finish_load { } #inherite =item do_load $count = $loader->do_load($fh) This is called by load_fh() to load the GFF2 file's filehandle and return the number of lines loaded. =cut # sub do_load { } inherited =item load_line $loader->load_line($data); Load a line of a GFF2 file. You must bracket this with calls to start_load() and finish_load()! $loader->start_load(); $loader->load_line($_) while ; $loader->finish_load(); =cut # sub load_line { } # inherited =item handle_meta $loader->handle_meta($meta_directive) This method is called to handle meta-directives such as ##sequence-region. The method will receive the directive with the initial ## stripped off. =cut # sub handle_meta {} # inherited =item handle_feature $loader->handle_feature($gff2_line) This method is called to process a single GFF2 line. It manipulates information stored a data structure called $self-E{load_data}. =cut # sub handle_feature { } # inherited =item store_current_feature $loader->store_current_feature() This method is called to store the currently active feature in the database. It uses a data structure stored in $self-E{load_data}. =cut # sub store_current_feature { } inherited =item build_object_tree $loader->build_object_tree() This method gathers together features and subfeatures and builds the graph that connects them. =cut # sub build_object_tree { } # inherited =item build_object_tree_in_tables $loader->build_object_tree_in_tables() This method gathers together features and subfeatures and builds the graph that connects them, assuming that parent/child relationships will be stored in a database table. =cut # sub build_object_tree_in_tables { } # inherited =item build_object_tree_in_features $loader->build_object_tree_in_features() This method gathers together features and subfeatures and builds the graph that connects them, assuming that parent/child relationships are stored in the seqfeature objects themselves. =cut # sub build_object_tree_in_features { } # inherited =item attach_children $loader->attach_children($store,$load_data,$load_id,$feature) This recursively adds children to features and their subfeatures. It is called when subfeatures are directly contained within other features, rather than stored in a relational table. =cut # sub attach_children { } # inherited =item fetch my $feature = $loader->fetch($load_id) Given a load ID (from the ID= attribute) this method returns the feature from the temporary database or the permanent one, depending on where it is stored. =cut # sub fetch { } # inherited =item add_segment $loader->add_segment($parent,$child) This method is used to add a split location to the parent. =cut # sub add_segment { } # inherited =item parse_attributes ($reserved,$unreserved) = $loader->parse_attributes($attribute_line) This method parses the information contained in the $attribute_line into two hashrefs, one containing the values of reserved attribute tags (e.g. ID) and the other containing the values of unreserved ones. =cut sub parse_attributes { # overridden my $self = shift; my $att = shift; my @groups = quotewords('\s*;\s*',0,$att); my (%reserved,%unreserved); my $found_name; for (@groups) { my ($tag,$value); if (/^(\S+)\s+(.+)/) { # Tag value pair ($tag,$value) = ($1,$2); } else { $tag = 'Note'; $value = $_; } if ($tag eq 'Target') { my ($target,$start,$end) = split /\s+/,$value; push @{$reserved{ID}},$target; $found_name++; if ($start <= $end) { $value .= ' +' } else { $value .= ' -' } } if (!$found_name++) { push @{$reserved{Alias}},$value; $value = "$tag:$value"; push @{$reserved{ID}},$value; $tag = 'Name'; } if ($Special_attributes{$tag}) { # reserved attribute push @{$reserved{$tag}},$value; } else { push @{$unreserved{$tag}},$value; } } return (\%reserved,\%unreserved); } =item start_or_finish_sequence $loader->start_or_finish_sequence('Chr9') This method is called at the beginning and end of a fasta section. =cut # sub start_or_finish_sequence { } inherited =item load_sequence $loader->load_sequence('gatttcccaaa') This method is called to load some amount of sequence after start_or_finish_sequence() is first called. =cut # sub load_sequence { } inherited =item open_fh my $io_file = $loader->open_fh($filehandle_or_path) This method opens up the indicated file or pipe, using some intelligence to recognized compressed files and URLs and doing the right thing. =cut # sub open_fh { } inherited # sub msg { } inherited =item time my $time = $loader->time This method returns the current time in seconds, using Time::HiRes if available. =cut # sub time { } inherited =item unescape my $unescaped = GFF2Loader::unescape($escaped) This is an internal utility. It is the same as CGI::Util::unescape, but doesn't change pluses into spaces and ignores unicode escapes. =cut # sub unescape { } inherited 1; __END__ =back =head1 BUGS This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs. =head1 SEE ALSO L, L, L, L, L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2006 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/SeqFeature/Store/GFF3Loader.pm000444000766000024 7441513155576320 22056 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::Store::GFF3Loader; =head1 NAME Bio::DB::SeqFeature::Store::GFF3Loader -- GFF3 file loader for Bio::DB::SeqFeature::Store =head1 SYNOPSIS use Bio::DB::SeqFeature::Store; use Bio::DB::SeqFeature::Store::GFF3Loader; # Open the sequence database my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:test', -write => 1 ); my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store => $db, -verbose => 1, -fast => 1); $loader->load('./my_genome.gff3'); =head1 DESCRIPTION The Bio::DB::SeqFeature::Store::GFF3Loader object parsers GFF3-format sequence annotation files and loads Bio::DB::SeqFeature::Store databases. For certain combinations of SeqFeature classes and SeqFeature::Store databases it features a "fast load" mode which will greatly accelerate the loading of GFF3 databases by a factor of 5-10. The GFF3 file format has been extended very slightly to accommodate Bio::DB::SeqFeature::Store. First, the loader recognizes is a new directive: # #index-subfeatures [0|1] Note that you can place a space between the two #'s in order to prevent GFF3 validators from complaining. If this is true, then subfeatures are indexed (the default) so that they can be retrieved with a query. See L for an explanation of this. If false, then subfeatures can only be accessed through their parent feature. Second, the loader recognizes a new attribute tag called index, which if present, controls indexing of the current feature. Example: ctg123 . TF_binding_site 1000 1012 . + . ID=tfbs00001;index=1 You can use this to turn indexing on and off, overriding the default for a particular feature. Note that the loader keeps a record -- in memory -- of each feature that it has processed. If you find the loader running out of memory on particularly large GFF3 files, please split the input file into smaller pieces and do the load in steps. =cut # load utility - incrementally load the store based on GFF3 file # # two modes: # slow mode -- features can occur in any order in the GFF3 file # fast mode -- all features with same ID must be contiguous in GFF3 file use strict; use Carp 'croak'; use Bio::DB::GFF::Util::Rearrange; use Bio::DB::SeqFeature::Store::LoadHelper; use constant DEBUG => 0; use base 'Bio::DB::SeqFeature::Store::Loader'; my %Special_attributes =( Gap => 1, Target => 1, Parent => 1, Name => 1, Alias => 1, ID => 1, index => 1, Index => 1, ); my %Strandedness = ( '+' => 1, '-' => -1, '.' => 0, '' => 0, 0 => 0, 1 => 1, -1 => -1, +1 => 1, undef => 0, ); =head2 new Title : new Usage : $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(@options) Function: create a new parser Returns : a Bio::DB::SeqFeature::Store::GFF3Loader gff3 parser and loader Args : several - see below Status : public This method creates a new GFF3 loader and establishes its connection with a Bio::DB::SeqFeature::Store database. Arguments are -name=E$value pairs as described in this table: Name Value ---- ----- -store A writable Bio::DB::SeqFeature::Store database handle. -seqfeature_class The name of the type of Bio::SeqFeatureI object to create and store in the database (Bio::DB::SeqFeature by default) -sf_class A shorter alias for -seqfeature_class -verbose Send progress information to standard error. -fast If true, activate fast loading (see below) -chunk_size Set the storage chunk size for nucleotide/protein sequences (default 2000 bytes) -tmp Indicate a temporary directory to use when loading non-normalized features. -ignore_seqregion Ignore ##sequence-region directives. The default is to create a feature corresponding to the directive. -noalias_target Don't create an Alias attribute for a target_id named in a Target attribute. The default is to create an Alias attribute containing the target_id found in a Target attribute. When you call new(), a connection to a Bio::DB::SeqFeature::Store database should already have been established and the database initialized (if appropriate). Some combinations of Bio::SeqFeatures and Bio::DB::SeqFeature::Store databases support a fast loading mode. Currently the only reliable implementation of fast loading is the combination of DBI::mysql with Bio::DB::SeqFeature. The other important restriction on fast loading is the requirement that a feature that contains subfeatures must occur in the GFF3 file before any of its subfeatures. Otherwise the subfeatures that occurred before the parent feature will not be attached to the parent correctly. This restriction does not apply to normal (slow) loading. If you use an unnormalized feature class, such as Bio::SeqFeature::Generic, then the loader needs to create a temporary database in which to cache features until all their parts and subparts have been seen. This temporary databases uses the "berkeleydb" adaptor. The -tmp option specifies the directory in which that database will be created. If not present, it defaults to the system default tmp directory specified by File::Spec-Etmpdir(). The -chunk_size option allows you to tune the representation of DNA/Protein sequence in the Store database. By default, sequences are split into 2000 base/residue chunks and then reassembled as needed. This avoids the problem of pulling a whole chromosome into memory in order to fetch a short subsequence from somewhere in the middle. Depending on your usage patterns, you may wish to tune this parameter using a chunk size that is larger or smaller than the default. =cut sub new { my $class = shift; my $self = $class->SUPER::new(@_); my ($ignore_seqregion) = rearrange(['IGNORE_SEQREGION'],@_); $self->ignore_seqregion($ignore_seqregion); my ($noalias_target) = rearrange(['NOALIAS_TARGET'],@_); $self->noalias_target($noalias_target); $self; } =head2 ignore_seqregion $ignore_it = $loader->ignore_seqregion([$new_flag]) Get or set the ignore_seqregion flag, which if true, will cause GFF3 ##sequence-region directives to be ignored. The default behavior is to create a feature corresponding to the region. =cut sub ignore_seqregion { my $self = shift; my $d = $self->{ignore_seqregion}; $self->{ignore_seqregion} = shift if @_; $d; } =head2 noalias_target $noalias_target = $loader->noalias_target([$new_flag]) Get or set the noalias_target flag, which if true, will disable the creation of an Alias attribute for a target_id named in a Target attribute. The default is to create an Alias attribute containing the target_id found in a Target attribute. =cut sub noalias_target { my $self = shift; my $d = $self->{noalias_target}; $self->{noalias_target} = shift if @_; $d; } =head2 load Title : load Usage : $count = $loader->load(@ARGV) Function: load the indicated files or filehandles Returns : number of feature lines loaded Args : list of files or filehandles Status : public Once the loader is created, invoke its load() method with a list of GFF3 or FASTA file paths or previously-opened filehandles in order to load them into the database. Compressed files ending with .gz, .Z and .bz2 are automatically recognized and uncompressed on the fly. Paths beginning with http: or ftp: are treated as URLs and opened using the LWP GET program (which must be on your path). FASTA files are recognized by their initial "E" character. Do not feed the loader a file that is neither GFF3 nor FASTA; I don't know what will happen, but it will probably not be what you expect. =cut # sub load { } inherited =head2 accessors The following read-only accessors return values passed or created during new(): store() the long-term Bio::DB::SeqFeature::Store object tmp_store() the temporary Bio::DB::SeqFeature::Store object used during loading sfclass() the Bio::SeqFeatureI class fast() whether fast loading is active seq_chunk_size() the sequence chunk size verbose() verbose progress messages =cut # sub store inherited # sub tmp_store inherited # sub sfclass inherited # sub fast inherited # sub seq_chunk_size inherited # sub verbose inherited =head2 Internal Methods The following methods are used internally and may be overridden by subclasses. =over 4 =item default_seqfeature_class $class = $loader->default_seqfeature_class Return the default SeqFeatureI class (Bio::DB::SeqFeature). =cut # sub default_seqfeature_class { } inherited =item subfeatures_normalized $flag = $loader->subfeatures_normalized([$new_flag]) Get or set a flag that indicates that the subfeatures are normalized. This is deduced from the SeqFeature class information. =cut # sub subfeatures_normalized { } inherited =item subfeatures_in_table $flag = $loader->subfeatures_in_table([$new_flag]) Get or set a flag that indicates that feature/subfeature relationships are stored in a table. This is deduced from the SeqFeature class and Store information. =cut # sub subfeatures_in_table { } inherited =item load_fh $count = $loader->load_fh($filehandle) Load the GFF3 data at the other end of the filehandle and return true if successful. Internally, load_fh() invokes: start_load(); do_load($filehandle); finish_load(); =cut # sub load_fh { } inherited =item start_load, finish_load These methods are called at the start and end of a filehandle load. =cut sub create_load_data { #overridden my $self = shift; $self->SUPER::create_load_data; $self->{load_data}{TemporaryID} = "GFFLoad0000000"; $self->{load_data}{IndexSubfeatures} = $self->index_subfeatures(); $self->{load_data}{mode} = 'gff'; $self->{load_data}{Helper} = Bio::DB::SeqFeature::Store::LoadHelper->new($self->{tmpdir}); } sub finish_load { #overridden my $self = shift; $self->store_current_feature(); # during fast loading, we will have a feature left at the very end $self->start_or_finish_sequence(); # finish any half-loaded sequences $self->msg("Building object tree..."); my $start = $self->time(); $self->build_object_tree; $self->msg(sprintf "%5.2fs\n",$self->time()-$start); if ($self->fast) { $self->msg("Loading bulk data into database..."); $start = $self->time(); $self->store->finish_bulk_update; $self->msg(sprintf "%5.2fs\n",$self->time()-$start); } eval {$self->store->commit}; # don't delete load data so that caller can ask for the loaded IDs # $self->delete_load_data; } =item do_load $count = $loader->do_load($fh) This is called by load_fh() to load the GFF3 file's filehandle and return the number of lines loaded. =cut # sub do_load { } inherited =item load_line $loader->load_line($data); Load a line of a GFF3 file. You must bracket this with calls to start_load() and finish_load()! $loader->start_load(); $loader->load_line($_) while ; $loader->finish_load(); =cut sub load_line { #overridden my $self = shift; my $line = shift; chomp($line); my $load_data = $self->{load_data}; $load_data->{line}++; return unless $line =~ /^\S/; # blank line # if it has a tab in it or looks like a chrom.sizes file, switch to gff mode $load_data->{mode} = 'gff' if $line =~ /\t/ or $line =~ /^\w+\s+\d+\s*$/; if ($line =~ /^\#\s?\#\s*(.+)/) { ## meta instruction $load_data->{mode} = 'gff'; $self->handle_meta($1); } elsif ($line =~ /^\#/) { $load_data->{mode} = 'gff'; # just to be safe return; # comment } elsif ($line =~ /^>\s*(\S+)/) { # FASTA lines are coming $load_data->{mode} = 'fasta'; $self->start_or_finish_sequence($1); } elsif ($load_data->{mode} eq 'fasta') { $self->load_sequence($line); } elsif ($load_data->{mode} eq 'gff') { $self->handle_feature($line); if (++$load_data->{count} % 1000 == 0) { my $now = $self->time(); my $nl = -t STDOUT && !$ENV{EMACS} ? "\r" : "\n"; local $^W = 0; # kill uninit variable warning $self->msg(sprintf("%d features loaded in %5.2fs (%5.2fs/1000 features)...%s$nl", $load_data->{count},$now - $load_data->{start_time}, $now - $load_data->{millenium_time}, ' ' x 80 )); $load_data->{millenium_time} = $now; } } else { $self->throw("I don't know what to do with this line:\n$line"); } } =item handle_meta $loader->handle_meta($meta_directive) This method is called to handle meta-directives such as ##sequence-region. The method will receive the directive with the initial ## stripped off. =cut sub handle_meta { my $self = shift; my $instruction = shift; if ( $instruction =~ /^#$/ ) { $self->store_current_feature() ; # during fast loading, we will have a feature left at the very end $self->start_or_finish_sequence(); # finish any half-loaded sequences if ( $self->store->can('handle_resolution_meta') ) { $self->store->handle_resolution_meta($instruction); } return; } if ($instruction =~ /sequence-region\s+(.+)\s+(-?\d+)\s+(-?\d+)/i && !$self->ignore_seqregion()) { my($ref,$start,$end,$strand) = $self->_remap($1,$2,$3,+1); my $feature = $self->sfclass->new(-name => $ref, -seq_id => $ref, -start => $start, -end => $end, -strand => $strand, -primary_tag => 'region'); $self->store->store($feature); return; } if ($instruction =~/index-subfeatures\s+(\S+)/i) { $self->{load_data}{IndexSubfeatures} = $1; $self->store->index_subfeatures($1); return; } if ( $self->store->can('handle_unrecognized_meta') ) { $self->store->handle_unrecognized_meta($instruction); return; } } =item handle_feature $loader->handle_feature($gff3_line) This method is called to process a single GFF3 line. It manipulates information stored a data structure called $self-E{load_data}. =cut sub handle_feature { #overridden my $self = shift; my $gff_line = shift; my $ld = $self->{load_data}; my $allow_whitespace = $self->allow_whitespace; # special case for a chrom.sizes-style line my @columns; if ($gff_line =~ /^(\w+)\s+(\d+)\s*$/) { @columns = ($1,undef,'chromosome',1,$2,undef,undef,undef,"Name=$1"); } else { $gff_line =~ s/\s+/\t/g if $allow_whitespace; @columns = map {$_ eq '.' ? undef : $_ } split /\t/,$gff_line; } $self->invalid_gff($gff_line) if @columns < 4; $self->invalid_gff($gff_line) if @columns > 9 && $allow_whitespace; { local $^W = 0; if (@columns > 9) { #oops, split too much due to whitespace $columns[8] = join(' ',@columns[8..$#columns]); } } my ($refname,$source,$method,$start,$end,$score,$strand,$phase,$attributes) = @columns; $self->invalid_gff($gff_line) unless defined $refname; $self->invalid_gff($gff_line) unless !defined $start || $start =~ /^[\d.-]+$/; $self->invalid_gff($gff_line) unless !defined $end || $end =~ /^[\d.-]+$/; $self->invalid_gff($gff_line) unless defined $method; $strand = $Strandedness{$strand||0}; my ($reserved,$unreserved) = $attributes ? $self->parse_attributes($attributes) : (); my $name = ($reserved->{Name} && $reserved->{Name}[0]); my $has_loadid = defined $reserved->{ID}[0]; my $feature_id = defined $reserved->{ID}[0] ? $reserved->{ID}[0] : $ld->{TemporaryID}++; my @parent_ids = @{$reserved->{Parent}} if defined $reserved->{Parent}; my $index_it = $ld->{IndexSubfeatures}; if (exists $reserved->{Index} || exists $reserved->{index}) { $index_it = $reserved->{Index}[0] || $reserved->{index}[0]; } # Everything in the unreserved hash becomes an attribute, so we copy # some attributes over $unreserved->{Note} = $reserved->{Note} if exists $reserved->{Note}; $unreserved->{Alias} = $reserved->{Alias} if exists $reserved->{Alias}; $unreserved->{Target} = $reserved->{Target} if exists $reserved->{Target}; $unreserved->{Gap} = $reserved->{Gap} if exists $reserved->{Gap}; $unreserved->{load_id}= $reserved->{ID} if exists $reserved->{ID}; # mec@stowers-institute.org, wondering why not all attributes are # carried forward, adds ID tag in particular service of # round-tripping ID, which, though present in database as load_id # attribute, was getting lost as itself # $unreserved->{ID}= $reserved->{ID} if exists $reserved->{ID}; # TEMPORARY HACKS TO SIMPLIFY DEBUGGING $feature_id = '' unless defined $feature_id; $name = '' unless defined $name; # prevent uninit variable warnings # push @{$unreserved->{Alias}},$feature_id if $has_loadid && $feature_id ne $name; # If DEBUG != 0, any Parent attribute is also copied over (as 'parent_id') $unreserved->{parent_id} = \@parent_ids if DEBUG && @parent_ids; # POSSIBLY A PERMANENT HACK -- TARGETS BECOME ALIASES # THIS IS TO ALLOW FOR TARGET-BASED LOOKUPS if (exists $reserved->{Target} && !$self->{noalias_target}) { my %aliases = map {$_=>1} @{$unreserved->{Alias}}; for my $t (@{$reserved->{Target}}) { (my $tc = $t) =~ s/\s+.*$//; # get rid of coordinates $name ||= $tc; push @{$unreserved->{Alias}},$tc unless $name eq $tc || $aliases{$tc}; } } ($refname,$start,$end,$strand) = $self->_remap($refname,$start,$end,$strand) or return; my @args = (-display_name => $name, -seq_id => $refname, -start => $start, -end => $end, -strand => $strand || 0, -score => $score, -phase => $phase, -primary_tag => $method || 'feature', -source => $source, -tag => $unreserved, -attributes => $unreserved, ); # Here's where we handle feature lines that have the same ID (multiple locations, not # parent/child relationships) my $old_feat; # Current feature is the same as the previous feature, which hasn't yet been loaded if (defined $ld->{CurrentID} && $ld->{CurrentID} eq $feature_id) { $old_feat = $ld->{CurrentFeature}; } # Current feature is the same as a feature that was loaded earlier elsif (defined(my $id = $self->{load_data}{Helper}->local2global($feature_id))) { $old_feat = $self->fetch($feature_id) or $self->warn(<{TemporaryID}++; # AND they have a Parent attribute, this causes an undesirable } # additional layer of aggregation. Changing the ID fixes this. elsif ( $old_feat->seq_id ne $refname || $old_feat->start != $start || $old_feat->end != $end # make sure endpoints are distinct ) { $self->add_segment($old_feat,$self->sfclass->new(@args)); return; } } # we get here if this is a new feature # first of all, store the current feature if it is there $self->store_current_feature() if defined $ld->{CurrentID}; # now create the new feature # (index top-level features only if policy asks us to) my $feature = $self->sfclass->new(@args); $feature->object_store($self->store) if $feature->can('object_store'); # for lazy table features $ld->{CurrentFeature} = $feature; $ld->{CurrentID} = $feature_id; my $top_level = !@parent_ids; my $has_id = defined $reserved->{ID}[0]; $index_it ||= $top_level; my $helper = $ld->{Helper}; $helper->indexit($feature_id=>1) if $index_it; $helper->toplevel($feature_id=>1) if !$self->{fast} && $top_level; # need to track top level features # remember parentage for my $parent (@parent_ids) { $helper->add_children($parent=>$feature_id); } } sub invalid_gff { my $self = shift; my $line = shift; $self->throw("invalid GFF line at line $self->{load_data}{line}.\n".$line); } =item allow_whitespace $allow_it = $loader->allow_whitespace([$newvalue]); Get or set the allow_whitespace flag. If true, then GFF3 files are allowed to be delimited with whitespace in addition to tabs. =cut sub allow_whitespace { my $self = shift; my $d = $self->{allow_whitespace}; $self->{allow_whitespace} = shift if @_; $d; } =item store_current_feature $loader->store_current_feature() This method is called to store the currently active feature in the database. It uses a data structure stored in $self-E{load_data}. =cut # sub store_current_feature { } inherited =item build_object_tree $loader->build_object_tree() This method gathers together features and subfeatures and builds the graph that connects them. =cut ### # put objects together # sub build_object_tree { my $self = shift; $self->subfeatures_in_table ? $self->build_object_tree_in_tables : $self->build_object_tree_in_features; } =item build_object_tree_in_tables $loader->build_object_tree_in_tables() This method gathers together features and subfeatures and builds the graph that connects them, assuming that parent/child relationships will be stored in a database table. =cut sub build_object_tree_in_tables { my $self = shift; my $store = $self->store; my $helper = $self->{load_data}{Helper}; while (my ($load_id,$children) = $helper->each_family()) { my $parent_id = $helper->local2global($load_id); die $self->throw("$load_id doesn't have a primary id") unless defined $parent_id; my @children = map {$helper->local2global($_)} @$children; # this updates the table that keeps track of parent/child relationships, # but does not update the parent object -- so (start,end) had better be right!!! $store->add_SeqFeature($parent_id,@children); } } =item build_object_tree_in_features $loader->build_object_tree_in_features() This method gathers together features and subfeatures and builds the graph that connects them, assuming that parent/child relationships are stored in the seqfeature objects themselves. =cut sub build_object_tree_in_features { my $self = shift; my $store = $self->store; my $tmp = $self->tmp_store; my $ld = $self->{load_data}; my $normalized = $self->subfeatures_normalized; my $helper = $ld->{Helper}; while (my $load_id = $helper->each_toplevel) { my $feature = $self->fetch($load_id) or $self->throw("$load_id (id=" .$helper->local2global($load_id) ." should have a database entry, but doesn't"); $self->attach_children($store,$ld,$load_id,$feature); # Indexed objects are updated, not created anew $feature->primary_id(undef) unless $helper->indexit($load_id); $store->store($feature); } } =item attach_children $loader->attach_children($store,$load_data,$load_id,$feature) This recursively adds children to features and their subfeatures. It is called when subfeatures are directly contained within other features, rather than stored in a relational table. =cut sub attach_children { my $self = shift; my ($store,$ld,$load_id,$feature) = @_; my $children = $ld->{Helper}->children() or return; for my $child_id (@$children) { my $child = $self->fetch($child_id) or $self->throw("$child_id should have a database entry, but doesn't"); $self->attach_children($store,$ld,$child_id,$child); # recursive call $feature->add_SeqFeature($child); } } =item fetch my $feature = $loader->fetch($load_id) Given a load ID (from the ID= attribute) this method returns the feature from the temporary database or the permanent one, depending on where it is stored. =cut sub fetch { my $self = shift; my $load_id = shift; my $helper = $self->{load_data}{Helper}; my $id = $helper->local2global($load_id); return ($self->subfeatures_normalized || $helper->indexit($load_id) ? $self->store->fetch($id) : $self->tmp_store->fetch($id) ); } =item add_segment $loader->add_segment($parent,$child) This method is used to add a split location to the parent. =cut sub add_segment { my $self = shift; my ($parent,$child) = @_; if ($parent->can('add_segment')) { # probably a lazy table feature my $segment_count = $parent->can('denormalized_segment_count') ? $parent->denormalized_segment_count : $parent->can('denormalized_segments ') ? $parent->denormalized_segments : $parent->can('segments') ? $parent->segments : 0; unless ($segment_count) { # convert into a segmented object my $segment; if ($parent->can('clone')) { $segment = $parent->clone; } else { my %clone = %$parent; $segment = bless \%clone,ref $parent; } delete $segment->{segments}; eval {$segment->object_store(undef) }; $segment->primary_id(undef); # this updates the object and expands its start and end positions without writing # the segments into the database as individual objects $parent->add_segment($segment); } $parent->add_segment($child); 1; # for debugging } # a conventional Bio::SeqFeature::Generic object - create a split location else { my $current_location = $parent->location; if ($current_location->can('add_sub_Location')) { $current_location->add_sub_Location($child->location); } else { eval "require Bio::Location::Split" unless Bio::Location::Split->can('add_sub_Location'); my $new_location = Bio::Location::Split->new(); $new_location->add_sub_Location($current_location); $new_location->add_sub_Location($child->location); $parent->location($new_location); } } } =item parse_attributes ($reserved,$unreserved) = $loader->parse_attributes($attribute_line) This method parses the information contained in the $attribute_line into two hashrefs, one containing the values of reserved attribute tags (e.g. ID) and the other containing the values of unreserved ones. =cut sub parse_attributes { my $self = shift; my $att = shift; unless ($att =~ /=/) { # ouch! must be a GFF line require Bio::DB::SeqFeature::Store::GFF2Loader unless Bio::DB::SeqFeature::Store::GFF2Loader->can('parse_attributes'); return $self->Bio::DB::SeqFeature::Store::GFF2Loader::parse_attributes($att); } my @pairs = map { my ($name,$value) = split '='; [$self->unescape($name) => $value]; } split ';',$att; my (%reserved,%unreserved); foreach (@pairs) { my $tag = $_->[0]; unless (defined $_->[1]) { warn "$tag does not have a value at GFF3 file line $.\n"; next; } my @values = split ',',$_->[1]; map {$_ = $self->unescape($_);} @values; if ($Special_attributes{$tag}) { # reserved attribute push @{$reserved{$tag}},@values; } else { push @{$unreserved{$tag}},@values } } return (\%reserved,\%unreserved); } =item start_or_finish_sequence $loader->start_or_finish_sequence('Chr9') This method is called at the beginning and end of a fasta section. =cut # sub start_or_finish_sequence { } inherited =item load_sequence $loader->load_sequence('gatttcccaaa') This method is called to load some amount of sequence after start_or_finish_sequence() is first called. =cut # sub load_sequence { } inherited =item open_fh my $io_file = $loader->open_fh($filehandle_or_path) This method opens up the indicated file or pipe, using some intelligence to recognized compressed files and URLs and doing the right thing. =cut # sub open_fh { } inherited # sub msg { } inherited =item time my $time = $loader->time This method returns the current time in seconds, using Time::HiRes if available. =cut # sub time { } inherited =item unescape my $unescaped = GFF3Loader::unescape($escaped) This is an internal utility. It is the same as CGI::Util::unescape, but doesn't change pluses into spaces and ignores unicode escapes. =cut # sub unescape { } inherited sub _remap { my $self = shift; my ($ref,$start,$end,$strand) = @_; my $mapper = $self->coordinate_mapper; return ($ref,$start,$end,$strand) unless $mapper; my ($newref,$coords) = $mapper->($ref,[$start,$end]); return unless defined $coords->[0]; if ($coords->[0] > $coords->[1]) { @{$coords} = reverse(@{$coords}); $strand *= -1; } return ($newref,@{$coords},$strand); } sub _indexit { # override my $self = shift; return $self->{load_data}{Helper}->indexit(@_); } sub _local2global { # override my $self = shift; return $self->{load_data}{Helper}->local2global(@_); } =item local_ids my $ids = $self->local_ids; my $id_cnt = @$ids; After performing a load, this returns an array ref containing all the load file IDs that were contained within the file just loaded. =cut sub local_ids { # override my $self = shift; return $self->{load_data}{Helper}->local_ids(@_); } =item loaded_ids my $ids = $loader->loaded_ids; my $id_cnt = @$ids; After performing a load, this returns an array ref containing all the feature primary ids that were created during the load. =cut sub loaded_ids { # override my $self = shift; return $self->{load_data}{Helper}->loaded_ids(@_); } 1; __END__ =back =head1 BUGS This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs. =head1 SEE ALSO L, L, L, L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2006 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/SeqFeature/Store/LoadHelper.pm000444000766000024 1131213155576320 22244 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::Store::LoadHelper; =head1 NAME Bio::DB::SeqFeature::Store::LoadHelper -- Internal utility for Bio::DB::SeqFeature::Store =head1 SYNOPSIS # For internal use only. =head1 DESCRIPTION For internal use only =head1 SEE ALSO L, L, L, L, L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2006 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use strict; use DB_File; use File::Path 'rmtree'; use File::Temp 'tempdir'; use File::Spec; use Fcntl qw(O_CREAT O_RDWR); our $VERSION = '1.12'; my %DBHandles; sub new { my $class = shift; my $tmpdir = shift; my $template = 'SeqFeatureLoadHelper_XXXXXX'; my @tmpargs = $tmpdir ? ($template,DIR=>$tmpdir) : ($template); my $tmppath = tempdir(@tmpargs,CLEANUP=>1); my $self = $class->create_dbs($tmppath); $self->{tmppath} = $tmppath; return bless $self,$class; } sub DESTROY { my $self = shift; # Destroy all filehandle references # before trying to delete files and folder %DBHandles = (); undef $self->{IndexIt}; undef $self->{TopLevel}; undef $self->{Local2Global}; undef $self->{Parent2Child}; rmtree $self->{tmppath}; # File::Temp::cleanup() unless $self->{keep}; } sub create_dbs { my $self = shift; my $tmp = shift; my %self; # experiment with caching these handles in memory my $hash_options = DB_File::HASHINFO->new(); # Each of these hashes allow only unique keys for my $dbname (qw(IndexIt TopLevel Local2Global)) { unless ($DBHandles{$dbname}) { my %h; tie(%h,'DB_File',File::Spec->catfile($tmp,$dbname), O_CREAT|O_RDWR,0666,$hash_options); $DBHandles{$dbname} = \%h; } $self{$dbname} = $DBHandles{$dbname}; %{$self{$dbname}} = (); } # The Parent2Child hash allows duplicate keys, so we # create it with the R_DUP flag. my $btree_options = DB_File::BTREEINFO->new(); $btree_options->{flags} = R_DUP; unless ($DBHandles{'Parent2Child'}) { my %h; tie(%h,'DB_File',File::Spec->catfile($tmp,'Parent2Child'), O_CREAT|O_RDWR,0666,$btree_options); $DBHandles{'Parent2Child'} = \%h; } $self{Parent2Child} = $DBHandles{'Parent2Child'}; %{$self{Parent2Child}} = (); return \%self; } sub indexit { my $self = shift; my $id = shift; $self->{IndexIt}{$id} = shift if @_; return $self->{IndexIt}{$id}; } sub toplevel { my $self = shift; my $id = shift; $self->{TopLevel}{$id} = shift if @_; return $self->{TopLevel}{$id}; } sub each_toplevel { my $self = shift; my ($id) = each %{$self->{TopLevel}}; $id; } sub local2global { my $self = shift; my $id = shift; $self->{Local2Global}{$id} = shift if @_; return $self->{Local2Global}{$id}; } sub add_children { my $self = shift; my $parent_id = shift; # (@children) = @_; $self->{Parent2Child}{$parent_id} = shift while @_; } sub children { my $self = shift; my $parent_id = shift; my @children; my $db = tied(%{$self->{Parent2Child}}); my $key = $parent_id; my $value = ''; for (my $status = $db->seq($key,$value,R_CURSOR); $status == 0 && $key eq $parent_id; $status = $db->seq($key,$value,R_NEXT) ) { push @children,$value; } return wantarray ? @children: \@children; } # this acts like each() and returns each parent id and an array ref of children sub each_family { my $self = shift; my $db = tied(%{$self->{Parent2Child}}); if ($self->{_cursordone}) { undef $self->{_cursordone}; undef $self->{_parent}; undef $self->{_child}; return; } # do a slightly tricky cursor search unless (defined $self->{_parent}) { return unless $db->seq($self->{_parent},$self->{_child},R_FIRST) == 0; } my $parent = $self->{_parent}; my @children = $self->{_child}; my $status; while (($status = $db->seq($self->{_parent},$self->{_child},R_NEXT)) == 0 && $self->{_parent} eq $parent ) { push @children,$self->{_child}; } $self->{_cursordone}++ if $status != 0; return ($parent,\@children); } sub local_ids { my $self = shift; my @ids = keys %{$self->{Local2Global}} if $self->{Local2Global}; return \@ids; } sub loaded_ids { my $self = shift; my @ids = values %{$self->{Local2Global}} if $self->{Local2Global}; return \@ids; } 1; BioPerl-1.007002/Bio/DB/SeqFeature/Store/Loader.pm000444000766000024 5071513155576320 21445 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::Store::Loader; =head1 NAME Bio::DB::SeqFeature::Store::Loader -- Loader =head1 SYNOPSIS # non-instantiable base class =head1 DESCRIPTION This is the base class for Bio::DB::SeqFeature::Loader::GFF3Loader, Bio::DB::SeqFeature::Loader::GFFLoader, and Bio::DB::SeqFeature::FeatureFileLoader. Please see the manual pages for these modules. =cut # load utility - incrementally load the store based on GFF3 file # # two modes: # slow mode -- features can occur in any order in the GFF3 file # fast mode -- all features with same ID must be contiguous in GFF3 file use strict; use Carp 'croak'; use IO::File; use Bio::DB::GFF::Util::Rearrange; use Bio::DB::SeqFeature::Store; use File::Spec; use File::Temp 'tempdir'; use base 'Bio::Root::Root'; use constant DEFAULT_SEQ_CHUNK_SIZE => 2000; =head2 new Title : new Usage : $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(@options) Function: create a new parser Returns : a Bio::DB::SeqFeature::Store::GFF3Loader gff3 parser and loader Args : several - see below Status : public This method creates a new GFF3 loader and establishes its connection with a Bio::DB::SeqFeature::Store database. Arguments are -name=E$value pairs as described in this table: Name Value ---- ----- -store A writable Bio::DB::SeqFeature::Store database handle. -seqfeature_class The name of the type of Bio::SeqFeatureI object to create and store in the database (Bio::DB::SeqFeature by default) -sf_class A shorter alias for -seqfeature_class -verbose Send progress information to standard error. -fast If true, activate fast loading (see below) -chunk_size Set the storage chunk size for nucleotide/protein sequences (default 2000 bytes) -tmp Indicate a temporary directory to use when loading non-normalized features. -map_coords A code ref that will transform a list of ($ref,[$start1,$end1]...) coordinates into a list of ($newref,[$newstart1,$newend1]...) -index_subfeatures Indicate true if subfeatures should be indexed. Default is true. -summary_stats Rebuild summary stats at the end of loading (not incremental, so takes a long time) When you call new(), a connection to a Bio::DB::SeqFeature::Store database should already have been established and the database initialized (if appropriate). Some combinations of Bio::SeqFeatures and Bio::DB::SeqFeature::Store databases support a fast loading mode. Currently the only reliable implementation of fast loading is the combination of DBI::mysql with Bio::DB::SeqFeature. The other important restriction on fast loading is the requirement that a feature that contains subfeatures must occur in the GFF3 file before any of its subfeatures. Otherwise the subfeatures that occurred before the parent feature will not be attached to the parent correctly. This restriction does not apply to normal (slow) loading. If you use an unnormalized feature class, such as Bio::SeqFeature::Generic, then the loader needs to create a temporary database in which to cache features until all their parts and subparts have been seen. This temporary databases uses the "berkeleydb" adaptor. The -tmp option specifies the directory in which that database will be created. If not present, it defaults to the system default tmp directory specified by File::Spec-Etmpdir(). The -chunk_size option allows you to tune the representation of DNA/Protein sequence in the Store database. By default, sequences are split into 2000 base/residue chunks and then reassembled as needed. This avoids the problem of pulling a whole chromosome into memory in order to fetch a short subsequence from somewhere in the middle. Depending on your usage patterns, you may wish to tune this parameter using a chunk size that is larger or smaller than the default. =cut sub new { my $self = shift; my ($store,$seqfeature_class,$tmpdir,$verbose,$fast, $seq_chunk_size,$coordinate_mapper,$index_subfeatures,$summary_stats,$no_close_fasta) = rearrange(['STORE', ['SF_CLASS','SEQFEATURE_CLASS'], ['TMP','TMPDIR'], 'VERBOSE', 'FAST', 'CHUNK_SIZE', 'MAP_COORDS', 'INDEX_SUBFEATURES', 'SUMMARY_STATS', 'NO_CLOSE_FASTA', ],@_); $seqfeature_class ||= $self->default_seqfeature_class; eval "require $seqfeature_class" unless $seqfeature_class->can('new'); $self->throw($@) if $@; my $normalized = $seqfeature_class->can('subfeatures_are_normalized') && $seqfeature_class->subfeatures_are_normalized; my $in_table = $seqfeature_class->can('subfeatures_are_stored_in_a_table') && $seqfeature_class->subfeatures_are_stored_in_a_table; if ($fast) { my $canfast = $normalized && $in_table; warn <tmpdir(); my ($tmp_store,$temp_load); unless ($normalized) { # remember the temporary directory in order to delete it on exit $temp_load = tempdir( 'BioDBSeqFeature_XXXXXXX', DIR=>$tmpdir, CLEANUP=>1 ); $tmp_store = Bio::DB::SeqFeature::Store->new(-adaptor => 'berkeleydb', -temporary=> 1, -dsn => $temp_load, -cache => 1, -write => 1) unless $normalized; } $index_subfeatures = 1 unless defined $index_subfeatures; return bless { store => $store, tmp_store => $tmp_store, seqfeature_class => $seqfeature_class, fast => $fast, seq_chunk_size => $seq_chunk_size || DEFAULT_SEQ_CHUNK_SIZE, verbose => $verbose, load_data => {}, tmpdir => $tmpdir, temp_load => $temp_load, subfeatures_normalized => $normalized, subfeatures_in_table => $in_table, coordinate_mapper => $coordinate_mapper, index_subfeatures => $index_subfeatures, summary_stats => $summary_stats, no_close_fasta => $no_close_fasta, },ref($self) || $self; } sub coordinate_mapper { my $self = shift; my $d = $self->{coordinate_mapper}; $self->{coordinate_mapper} = shift if @_; $d; } sub index_subfeatures { my $self = shift; my $d = $self->{index_subfeatures}; $self->{index_subfeatures} = shift if @_; $d; } sub summary_stats { my $self = shift; my $d = $self->{summary_stats}; $self->{summary_stats} = shift if @_; $d; } =head2 load Title : load Usage : $count = $loader->load(@ARGV) Function: load the indicated files or filehandles Returns : number of feature lines loaded Args : list of files or filehandles Status : public Once the loader is created, invoke its load() method with a list of GFF3 or FASTA file paths or previously-opened filehandles in order to load them into the database. Compressed files ending with .gz, .Z and .bz2 are automatically recognized and uncompressed on the fly. Paths beginning with http: or ftp: are treated as URLs and opened using the LWP GET program (which must be on your path). FASTA files are recognized by their initial "E" character. Do not feed the loader a file that is neither GFF3 nor FASTA; I don't know what will happen, but it will probably not be what you expect. =cut sub load { my $self = shift; my $start = $self->time(); my $count = 0; for my $file_or_fh (@_) { $self->msg("loading $file_or_fh...\n"); my $fh = $self->open_fh($file_or_fh) or $self->throw("Couldn't open $file_or_fh: $!"); $count += $self->load_fh($fh); $self->msg(sprintf "load time: %5.2fs\n",$self->time()-$start); } if ($self->summary_stats) { $self->msg("Building summary statistics for coverage graphs..."); my $start = $self->time(); $self->build_summary; $self->msg(sprintf "coverage graph build time: %5.2fs\n",$self->time()-$start); } $self->msg(sprintf "total load time: %5.2fs\n",$self->time()-$start); $count; } =head2 accessors The following read-only accessors return values passed or created during new(): store() the long-term Bio::DB::SeqFeature::Store object tmp_store() the temporary Bio::DB::SeqFeature::Store object used during loading sfclass() the Bio::SeqFeatureI class fast() whether fast loading is active seq_chunk_size() the sequence chunk size verbose() verbose progress messages =cut sub store { shift->{store} } sub tmp_store { shift->{tmp_store} } sub sfclass { shift->{seqfeature_class} } sub fast { shift->{fast} } sub seq_chunk_size { shift->{seq_chunk_size} } sub verbose { shift->{verbose} } =head2 Internal Methods The following methods are used internally and may be overridden by subclasses. =over 4 =item default_seqfeature_class $class = $loader->default_seqfeature_class Return the default SeqFeatureI class (Bio::DB::SeqFeature). =cut sub default_seqfeature_class { my $self = shift; return 'Bio::DB::SeqFeature'; } =item subfeatures_normalized $flag = $loader->subfeatures_normalized([$new_flag]) Get or set a flag that indicates that the subfeatures are normalized. This is deduced from the SeqFeature class information. =cut sub subfeatures_normalized { my $self = shift; my $d = $self->{subfeatures_normalized}; $self->{subfeatures_normalized} = shift if @_; $d; } =item subfeatures_in_table $flag = $loader->subfeatures_in_table([$new_flag]) Get or set a flag that indicates that feature/subfeature relationships are stored in a table. This is deduced from the SeqFeature class and Store information. =cut sub subfeatures_in_table { my $self = shift; my $d = $self->{subfeatures_in_table}; $self->{subfeatures_in_table} = shift if @_; $d; } =item load_fh $count = $loader->load_fh($filehandle) Load the GFF3 data at the other end of the filehandle and return true if successful. Internally, load_fh() invokes: start_load(); do_load($filehandle); finish_load(); =cut sub load_fh { my $self = shift; my $fh = shift; $self->start_load(); my $count = $self->do_load($fh); $self->finish_load(); $count; } =item start_load, finish_load These methods are called at the start and end of a filehandle load. =cut sub start_load { my $self = shift; $self->create_load_data; $self->store->start_bulk_update() if $self->fast; } sub create_load_data { my $self = shift; $self->{load_data}{CurrentFeature} = undef; $self->{load_data}{CurrentID} = undef; $self->{load_data}{IndexIt} = {}; $self->{load_data}{Local2GlobalID} = {}; $self->{load_data}{count} = 0; $self->{load_data}{mode} = undef; $self->{load_data}{start_time} = 0; } sub delete_load_data { my $self = shift; delete $self->{load_data}; } sub finish_load { my $self = shift; $self->store_current_feature(); # during fast loading, we will have a feature left at the very end $self->start_or_finish_sequence(); # finish any half-loaded sequences if ($self->fast) { $self->{load_data}{start_time} = $self->time(); $self->store->finish_bulk_update; } $self->msg(sprintf "%5.2fs\n",$self->time()-$self->{load_data}{start_time}); eval {$self->store->commit}; # don't delete load data so that caller can ask for the loaded IDs # $self->delete_load_data; } =item build_summary $loader->build_summary Call this to rebuild the summary coverage statistics. This is done automatically if new() was passed a true value for -summary_stats at create time. =cut sub build_summary { my $self = shift; $self->store->build_summary_statistics; } =item do_load $count = $loader->do_load($fh) This is called by load_fh() to load the GFF3 file's filehandle and return the number of lines loaded. =cut sub do_load { my $self = shift; my $fh = shift; $self->{load_data}{start_time} = $self->time(); $self->{load_data}->{millenium_time} = $self->{load_data}{start_time}; $self->load_line($_) while <$fh>; $self->msg(sprintf "%d features loaded in %5.2fs%s\r", $self->{load_data}->{count}, $self->time()-$self->{load_data}{start_time}, ' 'x80 ); $self->{load_data}{count}; } =item load_line $loader->load_line($data); Load a line of a GFF3 file. You must bracket this with calls to start_load() and finish_load()! $loader->start_load(); $loader->load_line($_) while ; $loader->finish_load(); =cut sub load_line { my $self = shift; my $line = shift; # don't do anything } =item handle_feature $loader->handle_feature($data_line) This method is called to process a single data line. It manipulates information stored a data structure called $self-E{load_data}. =cut sub handle_feature { my $self = shift; my $line = shift; # do nothing } =item handle_meta $loader->handle_meta($data_line) This method is called to process a single data line. It manipulates information stored a data structure called $self-E{load_data}. =cut sub handle_meta { my $self = shift; my $line = shift; # do nothing } sub _indexit { my $self = shift; my $id = shift; $id ||= ''; # avoid uninit warnings my $indexhash = $self->{load_data}{IndexIt}; $indexhash->{$id} = shift if @_; return $indexhash->{$id}; } sub _local2global { my $self = shift; my $id = shift; $id ||= ''; # avoid uninit warnings my $indexhash = $self->{load_data}{Local2GlobalID}; $indexhash->{$id} = shift if @_; return $indexhash->{$id}; } =item store_current_feature $loader->store_current_feature() This method is called to store the currently active feature in the database. It uses a data structure stored in $self-E{load_data}. =cut sub store_current_feature { my $self = shift; my $ld = $self->{load_data}; defined $ld->{CurrentFeature} or return; my $f = $ld->{CurrentFeature}; my $normalized = $self->subfeatures_normalized; my $indexed = $self->_indexit($ld->{CurrentID}); # logic is as follows: # 1. If the feature is an indexed feature, then we store it into the main database # so that it can be searched. It doesn't matter whether it is a top-level feature # or a subfeature. # 2. If the feature class is normalized, but not indexed, then we store it into the # main database using the "no_index" method. This will make it accessible to # queries on the top level parent, but it won't come up by itself in range or # attribute searches. # 3. Otherwise, this is an unindexed subfeature; we store it in the temporary database # until the object build step, at which point it gets integrated into its object tree # and copied into the main database. if ($indexed) { $self->store->store($f); } elsif ($normalized) { $self->store->store_noindex($f) } else { $self->tmp_store->store_noindex($f) } my $id = $f->primary_id; # assigned by store() $self->_local2global($ld->{CurrentID} => $id); $self->_indexit($ld->{CurrentID} => 0)if $normalized; # no need to remember this undef $ld->{CurrentID}; undef $ld->{CurrentFeature}; } =item parse_attributes ($reserved,$unreserved) = $loader->parse_attributes($attribute_line) This method parses the information contained in the $attribute_line into two hashrefs, one containing the values of reserved attribute tags (e.g. ID) and the other containing the values of unreserved ones. =cut sub parse_attributes { my $self = shift; my $att = shift; # do nothing } =item start_or_finish_sequence $loader->start_or_finish_sequence('Chr9') This method is called at the beginning and end of a fasta section. =cut # this gets called at the beginning and end of a fasta section sub start_or_finish_sequence { my $self = shift; my $seqid = shift; if (my $sl = $self->{fasta_load}) { if (defined $sl->{seqid}) { $self->store->insert_sequence($sl->{seqid},$sl->{sequence},$sl->{offset}); delete $self->{fasta_load}; } } if (defined $seqid) { $self->{fasta_load} = {seqid => $seqid, offset => 0, sequence => ''}; } } =item load_sequence $loader->load_sequence('gatttcccaaa') This method is called to load some amount of sequence after start_or_finish_sequence() is first called. =cut sub load_sequence { my $self = shift; my $seq = shift; my $sl = $self->{fasta_load} or return; my $cs = $self->seq_chunk_size; $sl->{sequence} .= $seq; while (length $sl->{sequence} >= $cs) { my $chunk = substr($sl->{sequence},0,$cs); $self->store->insert_sequence($sl->{seqid},$chunk,$sl->{offset}); $sl->{offset} += length $chunk; substr($sl->{sequence},0,$cs) = ''; } } =item open_fh my $io_file = $loader->open_fh($filehandle_or_path) This method opens up the indicated file or pipe, using some intelligence to recognized compressed files and URLs and doing the right thing. =cut sub open_fh { my $self = shift; my $thing = shift; no strict 'refs'; return $thing if defined fileno($thing); return IO::File->new("gunzip -c $thing |") if $thing =~ /\.gz$/; return IO::File->new("uncompress -c $thing |") if $thing =~ /\.Z$/; return IO::File->new("bunzip2 -c $thing |") if $thing =~ /\.bz2$/; return IO::File->new("GET $thing |") if $thing =~ /^(http|ftp):/; return $thing if ref $thing && $thing->isa('IO::String'); return IO::File->new($thing); } sub msg { my $self = shift; my @msg = @_; return unless $self->verbose; print STDERR @msg; } =item loaded_ids my $ids = $loader->loaded_ids; my $id_cnt = @$ids; After performing a load, this returns an array ref containing all the feature primary ids that were created during the load. =cut sub loaded_ids { my $self = shift; my @ids = values %{$self->{load_data}{Local2GlobalID}} if $self->{load_data}; return \@ids; } =item local_ids my $ids = $self->local_ids; my $id_cnt = @$ids; After performing a load, this returns an array ref containing all the load file IDs that were contained within the file just loaded. =cut sub local_ids { my $self = shift; my @ids = keys %{$self->{load_data}{Local2GlobalID}} if $self->{load_data}; return \@ids; } =item time my $time = $loader->time This method returns the current time in seconds, using Time::HiRes if available. =cut sub time { return Time::HiRes::time() if Time::HiRes->can('time'); return time(); } =item unescape my $unescaped = GFF3Loader::unescape($escaped) This is an internal utility. It is the same as CGI::Util::unescape, but doesn't change pluses into spaces and ignores unicode escapes. =cut sub unescape { my $self = shift; my $todecode = shift; $todecode =~ s/%([0-9a-fA-F]{2})/chr hex($1)/ge; return $todecode; } sub DESTROY { my $self = shift; # Close filehandles, so temporal files can be properly deleted my $store = $self->store; if ( $store->isa('Bio::DB::SeqFeature::Store::memory') or $store->isa('Bio::DB::SeqFeature::Store::berkeleydb3') ) { $store->private_fasta_file->close; if ($store->{fasta_db} && !$self->{no_close_fasta}) { while (my ($file, $fh) = each %{ $store->{fasta_db}->{fhcache} }) { $fh->close; } $store->{fasta_db}->_close_index($store->{fasta_db}->{offsets}); } } elsif ($store->isa('Bio::DB::SeqFeature::Store::DBI::SQLite')) { if (%DBI::installed_drh) { DBI->disconnect_all; %DBI::installed_drh = (); } undef $store->{dbh}; } if (my $ld = $self->{temp_load}) { unlink $ld; } } 1; __END__ =back =head1 BUGS This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs. =head1 SEE ALSO L, L, L, L, L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2006 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/SeqFeature/Store/bdb.pm000444000766000024 464313155576320 20745 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::Store::bdb; =head1 NAME Bio::DB::SeqFeature::Store::bdb - fetch and store objects from a BerkeleyDB =head1 DESCRIPTION This is a partial implementation -- just enough has been implemented so that we can fetch and store objects. It is used as a temporary failsafe store by the GFF3Loader module =cut use strict; use base 'Bio::DB::SeqFeature::Store'; use Bio::DB::GFF::Util::Rearrange 'rearrange'; use DB_File; use Fcntl qw(O_RDWR O_CREAT); use File::Temp 'tempdir'; use File::Path 'rmtree'; ### # object initialization # sub init { my $self = shift; my ($directory, $is_temporary) = rearrange([['DSN','DIR','DIRECTORY'], ['TMP','TEMP','TEMPORARY'] ],@_); $directory ||= $is_temporary ? File::Spec->tmpdir : '.'; $directory = tempdir(__PACKAGE__.'_XXXXXX',TMPDIR=>1,CLEANUP=>1,DIR=>$directory) if $is_temporary; -d $directory && -w _ or $self->throw("Can't write into the directory $directory"); $self->default_settings; $self->directory($directory); $self->temporary($is_temporary); my %h; tie (%h,'DB_File',$self->path,O_RDWR|O_CREAT,0666,$DB_HASH) or $self->throw("Couldn't tie: $!"); $self->db(\%h); $h{'.next_id'} ||= 1; } sub _store { my $self = shift; my $indexed = shift; my $db = $self->db; my $count = 0; for my $obj (@_) { my $primary_id = $obj->primary_id; $primary_id = $db->{'.next_id'}++ unless defined $primary_id; $db->{$primary_id} = $self->freeze($obj); $obj->primary_id($primary_id); $count++; } $count; } sub _update { my $self = shift; my ($object,$primary_id) = @_; my $db = $self->db; $self->throw("$object is not in database") unless exists $db->{$primary_id}; $db->{$primary_id} = $self->freeze($object); } sub _fetch { my $self = shift; my $id = shift; my $db = $self->db; my $obj = $self->thaw($db->{$id},$id); $obj; } sub db { my $self = shift; my $d = $self->setting('db'); $self->setting(db=>shift) if @_; $d; } sub directory { my $self = shift; my $d = $self->setting('directory'); $self->setting(directory=>shift) if @_; $d; } sub temporary { my $self = shift; my $d = $self->setting('temporary'); $self->setting(temporary=>shift) if @_; $d; } sub path { my $self = shift; return $self->directory .'/' . 'feature.bdb'; } sub DESTROY { my $self = shift; my $db = $self->db; untie %$db; rmtree($self->directory,0,1) if $self->temporary; } 1; BioPerl-1.007002/Bio/DB/SeqFeature/Store/berkeleydb.pm000444000766000024 12604313155576320 22365 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::Store::berkeleydb; use strict; use base 'Bio::DB::SeqFeature::Store'; use Bio::DB::GFF::Util::Rearrange 'rearrange'; use DB_File; use Fcntl qw(O_RDWR O_CREAT :flock); use IO::File; use File::Temp 'tempdir'; use File::Path 'rmtree','mkpath'; use File::Basename; use File::Spec; use Carp 'carp','croak'; use constant BINSIZE => 10_000; use constant MININT => -999_999_999_999; use constant MAXINT => 999_999_999_999; =head1 NAME Bio::DB::SeqFeature::Store::berkeleydb -- Storage and retrieval of sequence annotation data in Berkeleydb files =head1 SYNOPSIS use Bio::DB::SeqFeature::Store; # Create a database from the feature files located in /home/fly4.3 and store # the database index in the same directory: my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb', -dir => '/home/fly4.3'); # Create a database that will monitor the files in /home/fly4.3, but store # the indexes in /var/databases/fly4.3 $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb', -dir => '/home/fly4.3', -dsn => '/var/databases/fly4.3'); # Create a feature database from scratch $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb', -dsn => '/var/databases/fly4.3', -create => 1); # get a feature from somewhere my $feature = Bio::SeqFeature::Generic->new(...); # store it $db->store($feature) or die "Couldn't store!"; # primary ID of the feature is changed to indicate its primary ID # in the database... my $id = $feature->primary_id; # get the feature back out my $f = $db->fetch($id); # change the feature and update it $f->start(100); $db->update($f) or $self->throw("Couldn't update!"); # use the GFF3 loader to do a bulk write: my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store => $db, -verbose => 0, -fast => 1); $loader->load('/home/fly4.3/dmel-all.gff'); # searching... # ...by id my @features = $db->fetch_many(@list_of_ids); # ...by name @features = $db->get_features_by_name('ZK909'); # ...by alias @features = $db->get_features_by_alias('sma-3'); # ...by type @features = $db->get_features_by_type('gene'); # ...by location @features = $db->get_features_by_location(-seq_id=>'Chr1',-start=>4000,-end=>600000); # ...by attribute @features = $db->get_features_by_attribute({description => 'protein kinase'}) # ...by the GFF "Note" field @result_list = $db->search_notes('kinase'); # ...by arbitrary combinations of selectors @features = $db->features(-name => $name, -type => $types, -seq_id => $seqid, -start => $start, -end => $end, -attributes => $attributes); # ...using an iterator my $iterator = $db->get_seq_stream(-name => $name, -type => $types, -seq_id => $seqid, -start => $start, -end => $end, -attributes => $attributes); while (my $feature = $iterator->next_seq) { # do something with the feature } # ...limiting the search to a particular region my $segment = $db->segment('Chr1',5000=>6000); my @features = $segment->features(-type=>['mRNA','match']); # what feature types are defined in the database? my @types = $db->types; # getting & storing sequence information # Warning: this returns a string, and not a PrimarySeq object $db->insert_sequence('Chr1','GATCCCCCGGGATTCCAAAA...'); my $sequence = $db->fetch_sequence('Chr1',5000=>6000); # create a new feature in the database my $feature = $db->new_feature(-primary_tag => 'mRNA', -seq_id => 'chr3', -start => 10000, -end => 11000); =head1 DESCRIPTION Bio::DB::SeqFeature::Store::berkeleydb is the Berkeleydb adaptor for Bio::DB::SeqFeature::Store. You will not create it directly, but instead use Bio::DB::SeqFeature::Store-Enew() to do so. See L for complete usage instructions. =head2 Using the berkeleydb adaptor The Berkeley database consists of a series of Berkeleydb index files, and a couple of special purpose indexes. You can create the index files from scratch by creating a new database and calling new_feature() repeatedly, you can create the database and then bulk populate it using the GFF3 loader, or you can monitor a directory of preexisting GFF3 and FASTA files and rebuild the indexes whenever one or more of the fields changes. The last mode is probably the most convenient. Note that the indexer will only pay attention to files that end with .gff3, .wig and .fa. =over 4 =item The new() constructor The new() constructor method all the arguments recognized by Bio::DB::SeqFeature::Store, and a few additional ones. Standard arguments: Name Value ---- ----- -adaptor The name of the Adaptor class (default DBI::mysql) -serializer The name of the serializer class (default Storable) -index_subfeatures Whether or not to make subfeatures searchable (default true) -cache Activate LRU caching feature -- size of cache -compress Compresses features before storing them in database using Compress::Zlib Adaptor-specific arguments Name Value ---- ----- -dsn Where the index files are stored -dir Where the source (GFF3, FASTA) files are stored -autoindex An alias for -dir. -write Pass true to open the index files for writing. -create Pass true to create the index files if they don't exist (implies -write=>1) -locking Use advisory locking to avoid one process trying to read from the database while another is updating it (may not work properly over NFS). -temp Pass true to create temporary index files that will be deleted once the script exits. -verbose Pass true to report autoindexing operations on STDERR. (default is true). Examples: To create an empty database which will be populated using calls to store() or new_feature(), or which will be bulk-loaded using the GFF3 loader: $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb', -dsn => '/var/databases/fly4.3', -create => 1); To open a preexisting database in read-only mode: $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb', -dsn => '/var/databases/fly4.3'); To open a preexisting database in read/write (update) mode: $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb', -dsn => '/var/databases/fly4.3', -write => 1); To monitor a set of GFF3 and FASTA files located in a directory and create/update the database indexes as needed. The indexes will be stored in a new subdirectory named "indexes": $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb', -dir => '/var/databases/fly4.3'); As above, but store the source files and index files in separate directories: $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb', -dsn => '/var/databases/fly4.3', -dir => '/home/gff3_files/fly4.3'); To be indexed, files must end with one of .gff3 (GFF3 format), .fa (FASTA format) or .wig (WIG format). B<-autoindex> is an alias for B<-dir>. You should specify B<-locking> in a multiuser environment, including the case in which the database is being used by a web server at the same time another user might be updating it. =back See L for all the access methods supported by this adaptor. The various methods for storing and updating features and sequences into the database are supported, but there is no locking. If two processes try to update the same database simultaneously, the database will likely become corrupted. =cut ### # object initialization # sub init { my $self = shift; my ($directory, $autoindex, $is_temporary, $write, $create, $verbose, $locking, ) = rearrange([['DSN','DB'], [qw(DIR AUTOINDEX)], ['TMP','TEMP','TEMPORARY'], [qw(WRITE WRITABLE)], 'CREATE', 'VERBOSE', [qw(LOCK LOCKING)], ],@_); $verbose = 1 unless defined $verbose; if ($autoindex) { -d $autoindex or $self->throw("Invalid directory $autoindex"); $directory ||= "$autoindex/indexes"; } $directory ||= $is_temporary ? File::Spec->tmpdir : '.'; # my $pacname = __PACKAGE__; if ($^O =~ /mswin/i) { $pacname =~ s/:+/_/g; } $directory = tempdir($pacname.'_XXXXXX', TMPDIR => 1, CLEANUP => 1, DIR => $directory) if $is_temporary; mkpath($directory); -d $directory or $self->throw("Invalid directory $directory"); $create++ if $is_temporary; $write ||= $create; $self->throw("Can't write into the directory $directory") if $write && !-w $directory; $self->default_settings; $self->directory($directory); $self->temporary($is_temporary); $self->verbose($verbose); $self->locking($locking); $self->_delete_databases() if $create; if ($autoindex && -d $autoindex) { $self->auto_reindex($autoindex); } $self->lock('shared'); # this step may rebless $self into a subclass # to preserve backward compatibility with older # databases while providing better performance for # new databases. $self->possibly_rebless($create); $self->_open_databases($write,$create,$autoindex); $self->_permissions($write,$create); return $self; } sub version { return 2.0 }; sub possibly_rebless { my $self = shift; my $create = shift; my $do_rebless; if ($create) { $do_rebless++; } else { # probe database my %h; tie (%h,'DB_File',$self->_features_path,O_RDONLY,0666,$DB_HASH) or return; $do_rebless = $h{'.version'} >= 3.0; } if ($do_rebless) { eval "require Bio::DB::SeqFeature::Store::berkeleydb3"; bless $self,'Bio::DB::SeqFeature::Store::berkeleydb3'; } } sub can_store_parentage { 1 } sub auto_reindex { my $self = shift; my $autodir = shift; my $result = $self->needs_auto_reindexing($autodir); if ($result && %$result) { $self->flag_autoindexing(1); $self->lock('exclusive'); $self->reindex_wigfiles($result->{wig},$autodir) if $result->{wig}; $self->reindex_ffffiles($result->{fff},$autodir) if $result->{fff}; $self->reindex_gfffiles($result->{gff},$autodir) if $result->{gff}; $self->dna_db(Bio::DB::Fasta::Subdir->new($autodir)); $self->unlock; $self->flag_autoindexing(0); } else { $self->dna_db(Bio::DB::Fasta::Subdir->new($autodir)); } } sub autoindex_flagfile { return File::Spec->catfile(shift->directory,'autoindex.pid'); } sub auto_index_in_process { my $self = shift; my $flag_file = $self->autoindex_flagfile; return unless -e $flag_file; # if flagfile exists, then check that PID still exists open my $fh, '<', $flag_file or $self->throw("Could not read file '$flag_file': $!"); my $pid = <$fh>; close $fh; return 1 if kill 0=>$pid; warn "Autoindexing seems to be running in another process, but the process has gone away. Trying to override..."; if (unlink $flag_file) { warn "Successfully removed stale PID file." if $self->verbose; warn "Assuming partial reindexing process. Rebuilding indexes from scratch..." if $self->verbose; my $glob = File::Spec->catfile($self->directory,'*'); unlink glob($glob); return; } else { croak ("Cannot recover from apparent aborted autoindex process. Please remove files in ", $self->directory, " and allow the adaptor to reindex"); return 1; } } sub flag_autoindexing { my $self = shift; my $doit = shift; my $flag_file = $self->autoindex_flagfile; if ($doit) { open my $fh, '>', $flag_file or $self->throw("Could not write file '$flag_file': $!"); print $fh $$; close $fh; } else { unlink $flag_file; } } sub reindex_gfffiles { my $self = shift; my $files = shift; my $autodir = shift; warn "Reindexing GFF files...\n" if $self->verbose; my $exists = -e $self->_features_path; $self->_permissions(1,1); $self->_close_databases(); $self->_open_databases(1,!$exists); require Bio::DB::SeqFeature::Store::GFF3Loader unless Bio::DB::SeqFeature::Store::GFF3Loader->can('new'); my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store => $self, -sf_class => $self->seqfeature_class, -verbose => $self->verbose, ) or $self->throw("Couldn't create GFF3Loader"); my %seen; $loader->load(grep {!$seen{$_}++} @$files); $self->_touch_timestamp; } sub reindex_ffffiles { my $self = shift; my $files = shift; my $autodir = shift; warn "Reindexing FFF files...\n" if $self->verbose; $self->_permissions(1,1); $self->_close_databases(); $self->_open_databases(1,1); require Bio::DB::SeqFeature::Store::FeatureFileLoader unless Bio::DB::SeqFeature::Store::FeatureFileLoader->can('new'); my $loader = Bio::DB::SeqFeature::Store::FeatureFileLoader->new(-store => $self, -sf_class => $self->seqfeature_class, -verbose => $self->verbose, ) or $self->throw("Couldn't create FeatureFileLoader"); my %seen; $loader->load(grep {!$seen{$_}++} @$files); $self->_touch_timestamp; } sub reindex_wigfiles { my $self = shift; my $files = shift; my $autodir = shift; warn "Reindexing wig files...\n" if $self->verbose; unless (Bio::Graphics::Wiggle::Loader->can('new')) { eval "require Bio::Graphics::Wiggle::Loader; 1" or return; } for my $wig (@$files) { warn "Reindexing $wig...\n" if $self->verbose; my ($wib_name) = fileparse($wig,qr/\.[^.]*/); my $gff3_name = "$wib_name.gff3"; # unlink all wib files that share the basename my $wib_glob = File::Spec->catfile($self->directory,"$wib_name*.wib"); unlink glob($wib_glob); my $loader = Bio::Graphics::Wiggle::Loader->new($self->directory,$wib_name); my $fh = IO::File->new($wig) or die "Can't open $wig: $!"; $loader->load($fh); # will create one or more .wib files $fh->close; my $gff3_data = $loader->featurefile('gff3','microarray_oligo',$wib_name); my $gff3_path = File::Spec->catfile($autodir,$gff3_name); $fh = IO::File->new($gff3_path,'>') or die "Can't open $gff3_path for writing: $!"; $fh->print($gff3_data); $fh->close; my $conf_path = File::Spec->catfile($autodir,"$wib_name.conf"); $fh = IO::File->new($conf_path,'>'); $fh->print($loader->conf_stanzas('microarray_oligo',$wib_name)); $fh->close; } } # returns the following hashref # empty hash if nothing needs reindexing # {fasta => 1} if DNA database needs reindexing # {gff => [list,of,gff,paths]} if gff3 files need reindexing # {wig => [list,of,wig,paths]} if wig files need reindexing sub needs_auto_reindexing { my $self = shift; my $autodir = shift; my $result = {}; # don't allow two processes to reindex simultaneously $self->auto_index_in_process and croak "Autoindexing in process. Try again later"; # first interrogate the GFF3 files, using the timestamp file # as modification comparison my (@gff3,@fff,@wig,$fasta,$fasta_index_time); opendir (my $D,$autodir) or $self->throw("Couldn't open directory $autodir for reading: $!"); my $maxtime = 0; my $timestamp_time = _mtime($self->_mtime_path) || 0; while (defined (my $node = readdir($D))) { next if $node =~ /^\./; my $path = File::Spec->catfile($autodir,$node); next unless -f $path; if ($path =~ /\.gff\d?$/i) { my $mtime = _mtime(\*_); # not a typo $maxtime = $mtime if $mtime > $maxtime; push @gff3,$path; } elsif ($path =~ /\.fff?$/i) { my $mtime = _mtime(\*_); # not a typo $maxtime = $mtime if $mtime > $maxtime; push @fff,$path; } elsif ($path =~ /\.wig$/i) { my $wig = $path; (my $gff_file = $wig) =~ s/\.wig$/\.gff3/i; next if -e $gff_file && _mtime($gff_file) > _mtime($path); push @wig,$wig; push @gff3,$gff_file; $maxtime = time(); } elsif ($path =~ /\.(fa|fasta|dna)$/i) { $fasta_index_time = _mtime(File::Spec->catfile($self->directory,'fasta.index'))||0 unless defined $fasta_index_time; $fasta++ if _mtime($path) > $fasta_index_time; } } closedir $D; $result->{gff} = \@gff3 if $maxtime > $timestamp_time; $result->{wig} = \@wig if @wig; $result->{fff} = \@fff if @fff; $result->{fasta}++ if $fasta; return $result; } sub verbose { my $self = shift; my $d = $self->{verbose}; $self->{verbose} = shift if @_; return $d; } sub locking { my $self = shift; my $d = $self->{locking}; $self->{locking} = shift if @_; return $d; } sub lockfile { my $self = shift; return File::Spec->catfile($self->directory,'lock'); } sub lock { my $self = shift; my $mode = shift; return unless $self->locking; my $flag = $mode eq 'exclusive' ? LOCK_EX : LOCK_SH; my $lockfile = $self->lockfile; my $fh = $self->_flock_fh; unless ($fh) { my $open = -e $lockfile ? '<' : '>'; $fh = IO::File->new($lockfile,$open) or die "Cannot open $lockfile: $!"; } flock($fh,$flag); $self->_flock_fh($fh); } sub unlock { my $self = shift; return unless $self->locking; my $fh = $self->_flock_fh or return; flock($fh,LOCK_UN); undef $self->{flock_fh}; } sub _flock_fh { my $self = shift; my $d = $self->{flock_fh}; $self->{flock_fh} = shift if @_; $d; } sub _open_databases { my $self = shift; my ($write,$create,$ignore_errors) = @_; return if $self->db; # already open - don't reopen my $directory = $self->directory; unless (-d $directory) { # directory does not exist $create or $self->throw("Directory $directory does not exist and you did not specify the -create flag"); mkpath($directory) or $self->throw("Couldn't create database directory $directory: $!"); } my $flags = O_RDONLY; $flags |= O_RDWR if $write; $flags |= O_CREAT if $create; # Create the main database; this is a DB_HASH implementation my %h; my $result = tie (%h,'DB_File',$self->_features_path,$flags,0666,$DB_HASH); unless ($result) { return if $ignore_errors; # autoindex set, so defer this $self->throw("Couldn't tie: ".$self->_features_path . " $!"); } if ($create) { %h = (); $h{'.next_id'} = 1; $h{'.version'} = $self->version; } $self->db(\%h); $self->open_index_dbs($flags,$create); $self->open_parentage_db($flags,$create); $self->open_notes_db($write,$create); $self->open_seq_db($flags,$create) if -e $self->_fasta_path; } sub open_index_dbs { my $self = shift; my ($flags,$create) = @_; # Create the index databases; these are DB_BTREE implementations with duplicates allowed. $DB_BTREE->{flags} = R_DUP; $DB_BTREE->{compare} = sub { lc($_[0]) cmp lc($_[1]) }; for my $idx ($self->_index_files) { my $path = $self->_qualify("$idx.idx"); my %db; my $result = tie(%db,'DB_File',$path,$flags,0666,$DB_BTREE); # for backward compatibility, allow a failure when trying to open the is_indexed index. $self->throw("Couldn't tie $path: $!") unless $result || $idx eq 'is_indexed'; %db = () if $create; $self->index_db($idx=>\%db); } } sub open_parentage_db { my $self = shift; my ($flags,$create) = @_; # Create the parentage database my %p; tie (%p,'DB_File',$self->_parentage_path,$flags,0666,$DB_BTREE) or $self->throw("Couldn't tie: ".$self->_parentage_path . $!); %p = () if $create; $self->parentage_db(\%p); } sub open_notes_db { my $self = shift; my ($write,$create) = @_; my $mode = $write ? "+>>" : $create ? "+>" : "<"; my $notes_file = $self->_notes_path; open my $F, $mode, $notes_file or $self->throw("Could not open file '$notes_file': $!"); $self->notes_db($F); } sub open_seq_db { my $self = shift; if (-e $self->_fasta_path) { my $dna_db = Bio::DB::Fasta::Subdir->new($self->_fasta_path) or $self->throw("Can't reindex sequence file: $@"); $self->dna_db($dna_db); } } sub commit { # reindex fasta files my $self = shift; if (my $fh = $self->{fasta_fh}) { $fh->close; $self->dna_db(Bio::DB::Fasta::Subdir->new($self->{fasta_file})); } elsif (-d $self->directory) { $self->dna_db(Bio::DB::Fasta::Subdir->new($self->directory)); } } sub _close_databases { my $self = shift; $self->db(undef); $self->dna_db(undef); $self->notes_db(undef); $self->parentage_db(undef); $self->index_db($_=>undef) foreach $self->_index_files; } # do nothing -- new() with -create=>1 will do the trick sub _init_database { } sub _delete_databases { my $self = shift; for my $idx ($self->_index_files) { my $path = $self->_qualify("$idx.idx"); unlink $path; } unlink $self->_parentage_path; unlink $self->_fasta_path; unlink $self->_features_path; unlink $self->_mtime_path; } sub _touch_timestamp { my $self = shift; my $tsf = $self->_mtime_path; open my $F, '>', $tsf or $self->throw("Could not write file '$tsf': $!"); print $F scalar(localtime); close $F; } sub _store { my $self = shift; my $indexed = shift; my $db = $self->db; my $is_indexed = $self->index_db('is_indexed'); my $count = 0; for my $obj (@_) { my $primary_id = $obj->primary_id; $self->_delete_indexes($obj,$primary_id) if $indexed && $primary_id; $primary_id = $db->{'.next_id'}++ unless defined $primary_id; $db->{$primary_id} = $self->freeze($obj); $is_indexed->{$primary_id} = $indexed if $is_indexed; $obj->primary_id($primary_id); $self->_update_indexes($obj) if $indexed; $count++; } $count; } sub _delete_indexes { my $self = shift; my ($obj,$id) = @_; # the additional "1" causes the index to be deleted $self->_update_name_index($obj,$id,1); $self->_update_type_index($obj,$id,1); $self->_update_location_index($obj,$id,1); $self->_update_attribute_index($obj,$id,1); $self->_update_note_index($obj,$id,1); } sub _fetch { my $self = shift; my $id = shift; my $db = $self->db; my $obj = $self->thaw($db->{$id},$id); $obj; } sub _add_SeqFeature { my $self = shift; my $parent = shift; my @children = @_; my $parent_id = (ref $parent ? $parent->primary_id : $parent) or $self->throw("$parent should have a primary_id"); my $p = $self->parentage_db; for my $child (@children) { my $child_id = ref $child ? $child->primary_id : $child; defined $child_id or $self->throw("no primary ID known for $child"); $p->{$parent_id} = $child_id if tied(%$p)->find_dup($parent_id,$child_id); } return scalar @children; } sub _fetch_SeqFeatures { my $self = shift; my $parent = shift; my @types = @_; my $parent_id = $parent->primary_id or $self->throw("$parent should have a primary_id"); my $index = $self->parentage_db; my $db = tied %$index; my @children_ids = $db->get_dup($parent_id); my @children = map {$self->fetch($_)} @children_ids; if (@types) { foreach (@types) { my ($a,$b) = split ':',$_,2; $_ = quotemeta($a); if (length $b) { $_ .= ":".quotemeta($b).'$'; } else { $_ .= ':'; } } my $regexp = join '|', @types; return grep {($_->primary_tag.':'.$_->source_tag) =~ /^($regexp)/i} @children; } else { return @children; } } sub _update_indexes { my $self = shift; my $obj = shift; defined (my $id = $obj->primary_id) or return; $self->_update_name_index($obj,$id); $self->_update_type_index($obj,$id); $self->_update_location_index($obj,$id); $self->_update_attribute_index($obj,$id); $self->_update_note_index($obj,$id); } sub _update_name_index { my $self = shift; my ($obj,$id,$delete) = @_; my $db = $self->index_db('names') or $self->throw("Couldn't find 'names' index file"); my ($names,$aliases) = $self->feature_names($obj); # little stinky - needs minor refactoring foreach (@$names) { my $key = lc $_; $self->update_or_delete($delete,$db,$key,$id); } foreach (@$aliases) { my $key = lc($_)."_2"; # the _2 indicates a secondary (alias) ID $self->update_or_delete($delete,$db,$key,$id); } } sub _update_type_index { my $self = shift; my ($obj,$id,$delete) = @_; my $db = $self->index_db('types') or $self->throw("Couldn't find 'types' index file"); my $primary_tag = $obj->primary_tag; my $source_tag = $obj->source_tag || ''; return unless defined $primary_tag; $primary_tag .= ":$source_tag"; my $key = lc $primary_tag; $self->update_or_delete($delete,$db,$key,$id); } # Note: this indexing scheme is space-inefficient because it stores the # denormalized sequence ID followed by the bin in XXXXXX zero-leading # format. It should be replaced with a binary numeric encoding and the # BTREE {compare} attribute changed accordingly. sub _update_location_index { my $self = shift; my ($obj,$id,$delete) = @_; my $db = $self->index_db('locations') or $self->throw("Couldn't find 'locations' index file"); my $seq_id = $obj->seq_id || ''; my $start = $obj->start || ''; my $end = $obj->end || ''; my $strand = $obj->strand; my $bin_min = int $start/BINSIZE; my $bin_max = int $end/BINSIZE; for (my $bin = $bin_min; $bin <= $bin_max; $bin++ ) { my $key = sprintf("%s.%06d",lc($seq_id),$bin); $self->update_or_delete($delete,$db,$key,pack("i4",$id,$start,$end,$strand)); } } sub _update_attribute_index { my $self = shift; my ($obj,$id,$delete) = @_; my $db = $self->index_db('attributes') or $self->throw("Couldn't find 'attributes' index file"); for my $tag ($obj->get_all_tags) { for my $value ($obj->get_tag_values($tag)) { my $key = "${tag}:${value}"; $self->update_or_delete($delete,$db,$key,$id); } } } sub _update_note_index { my $self = shift; my ($obj,$id,$delete) = @_; return if $delete; # we don't know how to do this my $fh = $self->notes_db; my @notes = $obj->get_tag_values('Note') if $obj->has_tag('Note'); print $fh $_,"\t",pack("u*",$id) or $self->throw("An error occurred while updating note index: $!") foreach @notes; } sub update_or_delete { my $self = shift; my ($delete,$db,$key,$id) = @_; if ($delete) { tied(%$db)->del_dup($key,$id); } else { $db->{$key} = $id; } } # these methods return pointers to.... # the database that stores serialized objects sub db { my $self = shift; my $d = $self->setting('db'); $self->setting(db=>shift) if @_; $d; } sub parentage_db { my $self = shift; my $d = $self->setting('parentage_db'); $self->setting(parentage_db=>shift) if @_; $d; } # the Bio::DB::Fasta object sub dna_db { my $self = shift; my $d = $self->setting('dna_db'); $self->setting(dna_db=>shift) if @_; $d; } # the specialized notes database sub notes_db { my $self = shift; my $d = $self->setting('notes_db'); $self->setting(notes_db=>shift) if @_; $d; } # the is_indexed_db sub is_indexed_db { my $self = shift; my $d = $self->setting('is_indexed_db'); $self->setting(is_indexed_db=>shift) if @_; $d; } # The indicated index berkeley db sub index_db { my $self = shift; my $index_name = shift; my $d = $self->setting($index_name); $self->setting($index_name=>shift) if @_; $d; } sub _mtime { my $file = shift; my @stat = stat($file); return $stat[9]; } # return names of all the indexes sub _index_files { return qw(names types locations attributes is_indexed); } # the directory in which we store our indexes sub directory { my $self = shift; my $d = $self->setting('directory'); $self->setting(directory=>shift) if @_; $d; } # flag indicating that we are a temporary database sub temporary { my $self = shift; my $d = $self->setting('temporary'); $self->setting(temporary=>shift) if @_; $d; } sub _permissions { my $self = shift; my $d = $self->setting('permissions') or return; if (@_) { my ($write,$create) = @_; $self->setting(permissions=>[$write,$create]); } @$d; } # file name utilities... sub _qualify { my $self = shift; my $file = shift; return $self->directory .'/' . $file; } sub _features_path { shift->_qualify('features.bdb'); } sub _parentage_path { shift->_qualify('parentage.bdb'); } sub _type_path { shift->_qualify('types.idx'); } sub _location_path { shift->_qualify('locations.idx'); } sub _attribute_path { shift->_qualify('attributes.idx'); } sub _notes_path { shift->_qualify('notes.idx'); } sub _fasta_path { shift->_qualify('sequence.fa'); } sub _mtime_path { shift->_qualify('mtime.stamp'); } ########################################### # searching ########################################### sub _features { my $self = shift; my ($seq_id,$start,$end,$strand, $name,$class,$allow_aliases, $types, $attributes, $range_type, $iterator ) = rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'],'STRAND', 'NAME','CLASS','ALIASES', ['TYPES','TYPE','PRIMARY_TAG'], ['ATTRIBUTES','ATTRIBUTE'], 'RANGE_TYPE', 'ITERATOR', ],@_); my (@from,@where,@args,@group); $range_type ||= 'overlaps'; my @result; unless (defined $name or defined $seq_id or defined $types or defined $attributes) { my $is_indexed = $self->index_db('is_indexed'); @result = $is_indexed ? grep {$is_indexed->{$_}} keys %{$self->db} : grep { !/^\./ }keys %{$self->db}; } my %found = (); my $result = 1; if (defined($name)) { # hacky backward compatibility workaround undef $class if $class && $class eq 'Sequence'; $name = "$class:$name" if defined $class && length $class > 0; $result &&= $self->filter_by_name($name,$allow_aliases,\%found); } if (defined $seq_id) { $result &&= $self->filter_by_location($seq_id,$start,$end,$strand,$range_type,\%found); } if (defined $types) { $result &&= $self->filter_by_type($types,\%found); } if (defined $attributes) { $result &&= $self->filter_by_attribute($attributes,\%found); } push @result,keys %found if $result; return $iterator ? Bio::DB::SeqFeature::Store::berkeleydb::Iterator->new($self,\@result) : map {$self->fetch($_)} @result; } sub filter_by_name { my $self = shift; my ($name,$allow_aliases,$filter) = @_; my $index = $self->index_db('names'); my $db = tied(%$index); my ($stem,$regexp) = $self->glob_match($name); $stem ||= $name; $regexp ||= $name; $regexp .= "(?:_2)?" if $allow_aliases; my $key = $stem; my $value; my @results; for (my $status = $db->seq($key,$value,R_CURSOR); $status == 0 and $key =~ /^$regexp$/i; $status = $db->seq($key,$value,R_NEXT)) { next if %$filter && !$filter->{$value}; # don't bother push @results,$value; } $self->update_filter($filter,\@results); } sub filter_by_type { my $self = shift; my ($types,$filter) = @_; my @types = ref $types eq 'ARRAY' ? @$types : $types; my $index = $self->index_db('types'); my $db = tied(%$index); my @results; for my $type (@types) { my ($primary_tag,$source_tag); if (ref $type && $type->isa('Bio::DB::GFF::Typename')) { $primary_tag = $type->method; $source_tag = $type->source; } else { ($primary_tag,$source_tag) = split ':',$type,2; } my $match = defined $source_tag ? "^$primary_tag:$source_tag\$" : "^$primary_tag:"; $source_tag ||= ''; my $key = lc "$primary_tag:$source_tag"; my $value; # If filter is already provided, then it is usually faster to # fetch each object. if (%$filter) { for my $id (keys %$filter) { my $obj = $self->_fetch($id) or next; push @results,$id if $obj->type =~ /$match/i; } } else { for (my $status = $db->seq($key,$value,R_CURSOR); $status == 0 && $key =~ /$match/i; $status = $db->seq($key,$value,R_NEXT)) { next if %$filter && !$filter->{$value}; # don't even bother push @results,$value; } } } $self->update_filter($filter,\@results); } sub filter_by_location { my $self = shift; my ($seq_id,$start,$end,$strand,$range_type,$filter) = @_; $strand ||= 0; my $index = $self->index_db('locations'); my $db = tied(%$index); my $binstart = defined $start ? sprintf("%06d",int $start/BINSIZE) : ''; my $binend = defined $end ? sprintf("%06d",int $end/BINSIZE) : 'z'; # beyond a number my %seenit; my @results; $start = MININT if !defined $start; $end = MAXINT if !defined $end; my $version_2 = $self->db_version > 1; if ($range_type eq 'overlaps' or $range_type eq 'contains') { my $key = $version_2 ? "\L$seq_id\E.$binstart" : "\L$seq_id\E$binstart"; my $keystop = $version_2 ? "\L$seq_id\E.$binend" : "\L$seq_id\E$binend"; my $value; for (my $status = $db->seq($key,$value,R_CURSOR); $status == 0 && $key le $keystop; $status = $db->seq($key,$value,R_NEXT)) { my ($id,$fstart,$fend,$fstrand) = unpack("i4",$value); next if $seenit{$id}++; next if $strand && $fstrand != $strand; if ($range_type eq 'overlaps') { next unless $fend >= $start && $fstart <= $end; } elsif ($range_type eq 'contains') { next unless $fstart >= $start && $fend <= $end; } next if %$filter && !$filter->{$id}; # don't bother push @results,$id; } } # for contained in, we look for features originating and terminating outside the specified range # this is incredibly inefficient, but fortunately the query is rare (?) elsif ($range_type eq 'contained_in') { my $key = $version_2 ? "\L$seq_id." : "\L$seq_id"; my $keystop = $version_2 ? "\L$seq_id\E.$binstart" : "\L$seq_id\E$binstart"; my $value; # do the left part of the range for (my $status = $db->seq($key,$value,R_CURSOR); $status == 0 && $key le $keystop; $status = $db->seq($key,$value,R_NEXT)) { my ($id,$fstart,$fend,$fstrand) = unpack("i4",$value); next if $seenit{$id}++; next if $strand && $fstrand != $strand; next unless $fstart <= $start && $fend >= $end; next if %$filter && !$filter->{$id}; # don't bother push @results,$id; } # do the right part of the range $key = "\L$seq_id\E.$binend"; for (my $status = $db->seq($key,$value,R_CURSOR); $status == 0; $status = $db->seq($key,$value,R_NEXT)) { my ($id,$fstart,$fend,$fstrand) = unpack("i4",$value); next if $seenit{$id}++; next if $strand && $fstrand != $strand; next unless $fstart <= $start && $fend >= $end; next if %$filter && !$filter->{$id}; # don't bother push @results,$id; } } $self->update_filter($filter,\@results); } sub attributes { my $self = shift; my $index = $self->index_db('attributes'); my %a = map {s/:.+$//; $_=> 1} keys %$index; return keys %a; } sub filter_by_attribute { my $self = shift; my ($attributes,$filter) = @_; my $index = $self->index_db('attributes'); my $db = tied(%$index); my $result; for my $att_name (keys %$attributes) { my @result; my @search_terms = ref($attributes->{$att_name}) && ref($attributes->{$att_name}) eq 'ARRAY' ? @{$attributes->{$att_name}} : $attributes->{$att_name}; for my $v (@search_terms) { my ($stem,$regexp) = $self->glob_match($v); $stem ||= $v; $regexp ||= $v; my $key = "\L${att_name}:${stem}\E"; my $value; for (my $status = $db->seq($key,$value,R_CURSOR); $status == 0 && $key =~ /^$att_name:$regexp$/i; $status = $db->seq($key,$value,R_NEXT)) { next if %$filter && !$filter->{$value}; # don't bother push @result,$value; } } $result ||= $self->update_filter($filter,\@result); } $result; } sub _search_attributes { my $self = shift; my ($search_string,$attribute_array,$limit) = @_; $search_string =~ tr/*?//d; my @words = map {quotemeta($_)} $search_string =~ /(\w+)/g; my $search = join '|',@words; my $index = $self->index_db('attributes'); my $db = tied(%$index); my (%results,%notes); for my $tag (@$attribute_array) { my $id; my $key = "\L$tag:\E"; for (my $status = $db->seq($key,$id,R_CURSOR); $status == 0 and $key =~ /^$tag:(.*)/i; $status = $db->seq($key,$id,R_NEXT)) { my $text = $1; next unless $text =~ /$search/; for my $w (@words) { my @hits = $text =~ /($w)/ig or next; $results{$id} += @hits; } $notes{$id} .= "$text "; } } my @results; for my $id (keys %results) { my $hits = $results{$id}; my $note = $notes{$id}; $note =~ s/\s+$//; my $relevance = 10 * $hits; my $feature = $self->fetch($id) or next; my $name = $feature->display_name or next; my $type = $feature->type; push @results,[$name,$note,$relevance,$type,$id]; } return @results; } sub search_notes { my $self = shift; my ($search_string,$limit) = @_; $search_string =~ tr/*?//d; my @results; my @words = map {quotemeta($_)} $search_string =~ /(\w+)/g; my $search = join '|',@words; my (%found,$found); my $note_index = $self->notes_db; seek($note_index,0,0); # back to start while (<$note_index>) { next unless /$search/; chomp; my ($note,$uu) = split "\t"; $found{unpack("u*",$uu)}++; last if $limit && ++$found >= $limit; } my (@features, @matches); for my $idx (keys %found) { my $feature = $self->fetch($idx) or next; my @values = $feature->get_tag_values('Note') if $feature->has_tag('Note'); my $value = "@values"; my $hits; $hits++ while $value =~ /($search)/ig; # count the number of times we were hit push @matches,$hits; push @features,$feature; } for (my $i=0; $i<@matches; $i++) { my $feature = $features[$i]; my $matches = $matches[$i]; my $relevance = 10 * $matches; my $note; $note = join ' ',$feature->get_tag_values('Note') if $feature->has_tag('Note'); push @results,[$feature->display_name,$note,$relevance]; } return @results; } sub glob_match { my $self = shift; my $term = shift; return unless $term =~ /([^*?]*)(?:^|[^\\])?[*?]/; my $stem = $1; $term =~ s/(^|[^\\])([+\[\]^{}\$|\(\).])/$1\\$2/g; $term =~ s/(^|[^\\])\*/$1.*/g; $term =~ s/(^|[^\\])\?/$1./g; return ($stem,$term); } sub update_filter { my $self = shift; my ($filter,$results) = @_; return unless @$results; if (%$filter) { my @filtered = grep {$filter->{$_}} @$results; %$filter = map {$_=>1} @filtered; } else { %$filter = map {$_=>1} @$results; } } sub types { my $self = shift; eval "require Bio::DB::GFF::Typename" unless Bio::DB::GFF::Typename->can('new'); my $index = $self->index_db('types'); my $db = tied(%$index); return map {Bio::DB::GFF::Typename->new($_)} keys %$index; } # this is ugly sub _insert_sequence { my $self = shift; my ($seqid,$seq,$offset) = @_; my $dna_fh = $self->private_fasta_file or return; if ($offset == 0) { # start of the sequence print $dna_fh ">$seqid\n"; } print $dna_fh $seq,"\n"; } sub _fetch_sequence { my $self = shift; my ($seqid,$start,$end) = @_; my $db = $self->dna_db or return; return $db->seq($seqid,$start,$end); } sub private_fasta_file { my $self = shift; return $self->{fasta_fh} if exists $self->{fasta_fh}; $self->{fasta_file} = $self->_qualify("sequence.fa"); return $self->{fasta_fh} = IO::File->new($self->{fasta_file},">"); } sub finish_bulk_update { my $self = shift; if (my $fh = $self->{fasta_fh}) { $fh->close; $self->{fasta_db} = Bio::DB::Fasta::Subdir->new($self->{fasta_file}); } } sub db_version { my $self = shift; my $db = $self->db; return $db->{'.version'} || 1.00; } sub DESTROY { my $self = shift; $self->_close_databases(); $self->private_fasta_file->close; rmtree($self->directory,0,1) if $self->temporary && -e $self->directory; } # TIE interface -- a little annoying because we are storing magic ".variable" # meta-variables in the same data structure as the IDs, so these variables # must be skipped. sub _firstid { my $self = shift; my $db = $self->db; my ($key,$value); while ( ($key,$value) = each %{$db}) { last unless $key =~ /^\./; } $key; } sub _nextid { my $self = shift; my $id = shift; my $db = $self->db; my ($key,$value); while ( ($key,$value) = each %$db) { last unless $key =~ /^\./; } $key; } sub _existsid { my $self = shift; my $id = shift; return exists $self->db->{$id}; } sub _deleteid { my $self = shift; my $id = shift; my $obj = $self->fetch($id) or return; $self->_delete_indexes($obj,$id); delete $self->db->{$id}; 1; } sub _clearall { my $self = shift; $self->_close_databases(); $self->_delete_databases(); my ($write,$create) = $self->_permissions; $self->_open_databases($write,$create); } sub _featurecount { my $self = shift; return scalar %{$self->db}; } package Bio::DB::SeqFeature::Store::berkeleydb::Iterator; sub new { my $class = shift; my $store = shift; my $ids = shift; return bless {store => $store, ids => $ids},ref($class) || $class; } sub next_seq { my $self = shift; my $store = $self->{store} or return; my $id = shift @{$self->{ids}}; defined $id or return; return $store->fetch($id); } package Bio::DB::Fasta::Subdir; use base 'Bio::DB::Fasta'; # alter calling arguments so that the index file is placed in a subdirectory # named "indexes" sub new { my ($class, $path, %opts) = @_; if (-d $path) { $opts{-index_name} = File::Spec->catfile($path,'indexes','fasta.index'); } return Bio::DB::Fasta->new($path, %opts); } sub _calculate_offsets { my ($self, @args) = @_; return $self->SUPER::_calculate_offsets(@args); } 1; __END__ =head1 BUGS This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs. =head1 SEE ALSO L, L, L, L, L, L, L, =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2006 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/SeqFeature/Store/berkeleydb3.pm000444000766000024 5111313155576320 22423 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::Store::berkeleydb3; # $Id: berkeleydb3.pm 15987 2009-08-18 21:08:55Z lstein $ # faster implementation of berkeleydb =head1 NAME Bio::DB::SeqFeature::Store::berkeleydb3 -- Storage and retrieval of sequence annotation data in Berkeleydb files =head1 SYNOPSIS # Create a feature database from scratch $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb', -dsn => '/var/databases/fly4.3', -create => 1); # get a feature from somewhere my $feature = Bio::SeqFeature::Generic->new(...); # store it $db->store($feature) or die "Couldn't store!"; =head1 DESCRIPTION This is a faster version of the berkeleydb storage adaptor for Bio::DB::SeqFeature::Store. It is used automatically when you create a new database with the original berkeleydb adaptor. When opening a database created under the original adaptor, the old code is used for backward compatibility. Please see L for full usage instructions. =head1 BUGS This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs. =head1 SEE ALSO L, L, L, L, L, L, L, =head1 AUTHOR Lincoln Stein Elincoln.stein@gmail.comE. Copyright (c) 2009 Ontario Institute for Cancer Research This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut use strict; use base 'Bio::DB::SeqFeature::Store::berkeleydb'; use DB_File; use Fcntl qw(O_RDWR O_CREAT :flock); use Bio::DB::GFF::Util::Rearrange 'rearrange'; # can't have more sequence ids than this use constant MAX_SEQUENCES => 1_000_000_000; # used to construct the bin key use constant C1 => 500_000_000; # limits chromosome length to 500 megabases use constant C2 => 1000*C1; # at most 1000 chromosomes use constant BINSIZE => 10_000; use constant MININT => -999_999_999_999; use constant MAXINT => 999_999_999_999; use constant SUMMARY_BIN_SIZE => 1000; sub version { return 3.0 } sub open_index_dbs { my $self = shift; my ($flags,$create) = @_; # Create the main index databases; these are DB_BTREE implementations with duplicates allowed. $DB_BTREE->{flags} = R_DUP; my $string_cmp = DB_File::BTREEINFO->new; $string_cmp->{flags} = R_DUP; $string_cmp->{compare} = sub { lc $_[0] cmp lc $_[1] }; my $numeric_cmp = DB_File::BTREEINFO->new; $numeric_cmp->{flags} = R_DUP; $numeric_cmp->{compare} = sub { $_[0] <=> $_[1] }; for my $idx ($self->_index_files) { my $path = $self->_qualify("$idx.idx"); my %db; my $dbtype = $idx eq 'locations' ? $numeric_cmp :$idx eq 'summary' ? $numeric_cmp :$idx eq 'types' ? $numeric_cmp :$idx eq 'seqids' ? $DB_HASH :$idx eq 'typeids' ? $DB_HASH :$string_cmp; tie(%db,'DB_File',$path,$flags,0666,$dbtype) or $self->throw("Couldn't tie $path: $!"); %db = () if $create; $self->index_db($idx=>\%db); } } sub seqid_db { shift->index_db('seqids') } sub typeid_db { shift->index_db('typeids') } sub _delete_databases { my $self = shift; $self->SUPER::_delete_databases; } # given a seqid (name), return its denormalized numeric representation sub seqid_id { my $self = shift; my $seqid = shift; my $db = $self->seqid_db; return $db->{lc $seqid}; } sub add_seqid { my $self = shift; my $seqid = shift; my $db = $self->seqid_db; my $key = lc $seqid; $db->{$key} = ++$db->{'.nextid'} unless exists $db->{$key}; die "Maximum number of sequence ids exceeded. This module can handle up to ", MAX_SEQUENCES," unique ids" if $db->{$key} > MAX_SEQUENCES; return $db->{$key}; } # given a seqid (name), return its denormalized numeric representation sub type_id { my $self = shift; my $typeid = shift; my $db = $self->typeid_db; return $db->{$typeid}; } sub add_typeid { my $self = shift; my $typeid = shift; my $db = $self->typeid_db; my $key = lc $typeid; $db->{$key} = ++$db->{'.nextid'} unless exists $db->{$key}; return $db->{$key}; } sub _seq_ids { my $self = shift; if (my $fa = $self->{fasta_db}) { if (my @s = eval {$fa->ids}) { return @s; } } my $l = $self->seqid_db or return; return grep {!/^\./} keys %$l; } sub _index_files { return (shift->SUPER::_index_files,'seqids','typeids','summary'); } sub _update_indexes { my $self = shift; my $obj = shift; defined (my $id = $obj->primary_id) or return; $self->SUPER::_update_indexes($obj); $self->_update_seqid_index($obj,$id); } sub _update_seqid_index { my $self = shift; my ($obj,$id,$delete) = @_; my $seq_name = $obj->seq_id; $self->add_seqid(lc $seq_name); } sub _update_type_index { my $self = shift; my ($obj,$id,$delete) = @_; my $db = $self->index_db('types') or $self->throw("Couldn't find 'types' index file"); my $key = $self->_obj_to_type($obj); my $typeid = $self->add_typeid($key); $self->update_or_delete($delete,$db,$typeid,$id); } sub _obj_to_type { my $self = shift; my $obj = shift; my $tag = $obj->primary_tag; my $source_tag = $obj->source_tag || ''; return unless defined $tag; $tag .= ":$source_tag"; return lc $tag; } sub types { my $self = shift; eval "require Bio::DB::GFF::Typename" unless Bio::DB::GFF::Typename->can('new'); my $db = $self->typeid_db; return grep {!/^\./} map {Bio::DB::GFF::Typename->new($_)} keys %$db; } sub _id2type { my $self = shift; my $wanted_id = shift; my $db = $self->typeid_db; while (my($key,$id) = each %$db) { next if $key =~ /^\./; return $key if $id == $wanted_id; } return; } # return a hash of typeids that match a human-readable type sub _matching_types { my $self = shift; my $types = shift; my @types = ref $types eq 'ARRAY' ? @$types : $types; my $db = $self->typeid_db; my %result; my @all_types; for my $type (@types) { my ($primary_tag,$source_tag); if (ref $type && $type->isa('Bio::DB::GFF::Typename')) { $primary_tag = $type->method; $source_tag = $type->source; } else { ($primary_tag,$source_tag) = split ':',$type,2; } if (defined $source_tag) { my $id = $db->{lc "$primary_tag:$source_tag"}; $result{$id}++ if defined $id; } else { @all_types = $self->types unless @all_types; $result{$db->{$_}}++ foreach grep {/^$primary_tag:/} @all_types; } } return \%result; } sub _update_location_index { my $self = shift; my ($obj,$id,$delete) = @_; my $db = $self->index_db('locations') or $self->throw("Couldn't find 'locations' index file"); my $seq_id = $obj->seq_id || ''; my $start = $obj->start || ''; my $end = $obj->end || ''; my $strand = $obj->strand; my $bin_min = int $start/BINSIZE; my $bin_max = int $end/BINSIZE; my $typeid = $self->add_typeid($self->_obj_to_type($obj)); my $seq_no = $self->add_seqid($seq_id); for (my $bin = $bin_min; $bin <= $bin_max; $bin++ ) { my $key = $seq_no * MAX_SEQUENCES + $bin; $self->update_or_delete($delete,$db,$key,pack("i5",$id,$start,$end,$strand,$typeid)); } } sub _features { my $self = shift; my ($seq_id,$start,$end,$strand, $name,$class,$allow_aliases, $types, $attributes, $range_type, $iterator ) = rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'],'STRAND', 'NAME','CLASS','ALIASES', ['TYPES','TYPE','PRIMARY_TAG'], ['ATTRIBUTES','ATTRIBUTE'], 'RANGE_TYPE', 'ITERATOR', ],@_); my (@from,@where,@args,@group); $range_type ||= 'overlaps'; my @result; unless (defined $name or defined $seq_id or defined $types or defined $attributes) { my $is_indexed = $self->index_db('is_indexed'); @result = $is_indexed ? grep {$is_indexed->{$_}} keys %{$self->db} : grep { !/^\./ }keys %{$self->db}; } my %found = (); my $result = 1; if (defined($name)) { # hacky backward compatibility workaround undef $class if $class && $class eq 'Sequence'; $name = "$class:$name" if defined $class && length $class > 0; $result &&= $self->filter_by_name($name,$allow_aliases,\%found); } if (defined $seq_id) { # location with or without types my $typelist = defined $types ? $self->_matching_types($types) : undef; $result &&= $self->filter_by_type_and_location( $seq_id, $start, $end, $strand, $range_type, $typelist, \%found ); } elsif (defined $types) { # types without location $result &&= $self->filter_by_type($types,\%found); } if (defined $attributes) { $result &&= $self->filter_by_attribute($attributes,\%found); } push @result,keys %found if $result; return $iterator ? Bio::DB::SeqFeature::Store::berkeleydb::Iterator->new($self,\@result) : map {$self->fetch($_)} @result; } sub filter_by_type { my $self = shift; my ($types,$filter) = @_; my @types = ref $types eq 'ARRAY' ? @$types : $types; my $index = $self->index_db('types'); my $db = tied(%$index); my @results; for my $type (@types) { my ($primary_tag,$source_tag); if (ref $type && $type->isa('Bio::DB::GFF::Typename')) { $primary_tag = $type->method; $source_tag = $type->source; } else { ($primary_tag,$source_tag) = split ':',$type,2; } $source_tag ||= ''; $primary_tag = quotemeta($primary_tag); $source_tag = quotemeta($source_tag); my $match = length $source_tag ? "^$primary_tag:$source_tag\$" : "^$primary_tag:"; my $key = lc "$primary_tag:$source_tag"; my $value; # If filter is already provided, then it is usually faster to # fetch each object. if (%$filter) { for my $id (keys %$filter) { my $obj = $self->_fetch($id) or next; push @results,$id if $obj->type =~ /$match/i; } } else { my $types = $self->typeid_db; my @typeids = map {$types->{$_}} grep {/$match/} keys %$types; for my $t (@typeids) { my $k = $t; for (my $status = $db->seq($k,$value,R_CURSOR); $status == 0 && $k == $t; $status = $db->seq($k,$value,R_NEXT)) { next if %$filter && !$filter->{$value}; # don't even bother push @results,$value; } } } } $self->update_filter($filter,\@results); } sub filter_by_type_and_location { my $self = shift; my ($seq_id,$start,$end,$strand,$range_type,$typelist,$filter) = @_; $strand ||= 0; my $index = $self->index_db('locations'); my $db = tied(%$index); my $binstart = defined $start ? int $start/BINSIZE : 0; my $binend = defined $end ? int $end/BINSIZE : MAX_SEQUENCES-1; my %seenit; my @results; $start = MININT if !defined $start; $end = MAXINT if !defined $end; my $seq_no = $self->seqid_id($seq_id); return unless defined $seq_no; if ($range_type eq 'overlaps' or $range_type eq 'contains') { my $keystart = $seq_no * MAX_SEQUENCES + $binstart; my $keystop = $seq_no * MAX_SEQUENCES + $binend; my $value; for (my $status = $db->seq($keystart,$value,R_CURSOR); $status == 0 && $keystart <= $keystop; $status = $db->seq($keystart,$value,R_NEXT)) { my ($id,$fstart,$fend,$fstrand,$ftype) = unpack("i5",$value); next if $seenit{$id}++; next if $strand && $fstrand != $strand; next if $typelist && !$typelist->{$ftype}; if ($range_type eq 'overlaps') { next unless $fend >= $start && $fstart <= $end; } elsif ($range_type eq 'contains') { next unless $fstart >= $start && $fend <= $end; } next if %$filter && !$filter->{$id}; # don't bother push @results,$id; } } # for contained in, we look for features originating and terminating outside the specified range # this is incredibly inefficient, but fortunately the query is rare (?) elsif ($range_type eq 'contained_in') { my $keystart = $seq_no * MAX_SEQUENCES; my $keystop = $seq_no * MAX_SEQUENCES + $binstart; my $value; # do the left part of the range for (my $status = $db->seq($keystart,$value,R_CURSOR); $status == 0 && $keystart <= $keystop; $status = $db->seq($keystart,$value,R_NEXT)) { my ($id,$fstart,$fend,$fstrand,$ftype) = unpack("i5",$value); next if $seenit{$id}++; next if $strand && $fstrand != $strand; next if $typelist && !$typelist->{$ftype}; next unless $fstart <= $start && $fend >= $end; next if %$filter && !$filter->{$id}; # don't bother push @results,$id; } # do the right part of the range $keystart = $seq_no*MAX_SEQUENCES+$binend; for (my $status = $db->seq($keystart,$value,R_CURSOR); $status == 0; $status = $db->seq($keystart,$value,R_NEXT)) { my ($id,$fstart,$fend,$fstrand,$ftype) = unpack("i5",$value); next if $seenit{$id}++; next if $strand && $fstrand != $strand; next unless $fstart <= $start && $fend >= $end; next if $typelist && !$typelist->{$ftype}; next if %$filter && !$filter->{$id}; # don't bother push @results,$id; } } $self->update_filter($filter,\@results); } sub build_summary_statistics { my $self = shift; my $insert = $self->index_db('summary'); %$insert = (); my $current_bin = -1; my (%residuals,$last_bin); my $le = -t \*STDERR ? "\r" : "\n"; print STDERR "\n"; # iterate through all the indexed features my $sbs = SUMMARY_BIN_SIZE; # Sadly we have to do this in two steps. In the first step, we sort # features by typeid,seqid,start. In the second step, we read through # this sorted list. To avoid running out of memory, we use a db_file # temporary database my $fh = File::Temp->new() or $self->throw("Could not create temporary file '$name' for sorting: $!"); my $name = $fh->filename; my %sort; my $num_cmp_tre = DB_File::BTREEINFO->new; $num_cmp_tree->{compare} = sub { $_[0] <=> $_[1] }; $num_cmp_tree->{flags} = R_DUP; my $s = tie %sort, 'DB_File', $name, O_CREAT|O_RDWR, 0666, $num_cmp_tree or $self->throw("Could not create Berkeley DB in temporary file '$name': $!"); my $index = $self->index_db('locations'); my $db = tied(%$index); my $keystart = 0; my ($value,$count); my %seenit; for (my $status = $db->seq($keystart,$value,R_CURSOR); $status == 0; $status = $db->seq($keystart,$value,R_NEXT)) { my ($id,$start,$end,$strand,$typeid) = unpack('i5',$value); next if $seenit{$id}++; print STDERR $count," features sorted$le" if ++$count % 1000 == 0; my $seqid = int($keystart / MAX_SEQUENCES); my $key = $self->_encode_summary_key($typeid,$seqid,$start-1); $sort{$key}=$end; } print STDERR "COUNT = $count\n"; my ($current_type,$current_seqid,$end); my $cum_count = 0; $keystart = 0; $count = 0; # the second step allows us to iterate through this for (my $status = $s->seq($keystart,$end,R_CURSOR); $status == 0; $status = $s->seq($keystart,$end,R_NEXT)) { print STDERR $count," features processed$le" if ++$count % 1000 == 0; my ($typeid,$seqid,$start) = $self->_decode_summary_key($keystart); my $bin = int($start/$sbs); # because the input is sorted by start, no more features will contribute to the # current bin so we can dispose of it if ($bin != $current_bin) { if ($seqid != $current_seqid or $typeid != $current_type) { # load all bins left over $self->_load_bins($insert,\%residuals,\$cum_count,$current_type,$current_seqid); %residuals = () ; $cum_count = 0; } else { # load all up to current one $self->_load_bins($insert,\%residuals,\$cum_count,$current_type,$current_seqid,$current_bin); } } $last_bin = $current_bin; ($current_seqid,$current_type,$current_bin) = ($seqid,$typeid,$bin); # summarize across entire spanned region my $last_bin = int(($end-1)/$sbs); for (my $b=$bin;$b<=$last_bin;$b++) { $residuals{$b}++; } } # handle tail case # load all bins left over $self->_load_bins($insert,\%residuals,\$cum_count,$current_type,$current_seqid); undef %sort; undef $fh; } sub _load_bins { my $self = shift; my ($insert,$residuals,$cum_count,$typeid,$seqid,$stop_after) = @_; for my $b (sort {$a<=>$b} keys %$residuals) { last if defined $stop_after and $b > $stop_after; $$cum_count += $residuals->{$b}; my $key = $self->_encode_summary_key($typeid,$seqid,$b); $insert->{$key} = $$cum_count; delete $residuals->{$b}; # no longer needed } } sub coverage_array { my $self = shift; my ($seq_name,$start,$end,$types,$bins) = rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'], ['TYPES','TYPE','PRIMARY_TAG'],'BINS'],@_); $bins ||= 1000; $start ||= 1; unless ($end) { my $segment = $self->segment($seq_name) or $self->throw("unknown seq_id $seq_name"); $end = $segment->end; } my $binsize = ($end-$start+1)/$bins; my $seqid = $self->seqid_id($seq_name) || 0; return [] unless $seqid; # where each bin starts my @his_bin_array = map {$start + $binsize * $_} (0..$bins); my @sum_bin_array = map {int(($_-1)/SUMMARY_BIN_SIZE)} @his_bin_array; my $interval_stats_idx = $self->index_db('summary'); my $db = tied(%$interval_stats_idx); my $t = $self->_matching_types($types); my (%bins,$report_tag); for my $typeid (sort keys %$t) { $report_tag ||= $typeid; for (my $i=0;$i<@sum_bin_array;$i++) { my $cum_count; my $bin = $sum_bin_array[$i]; my $key = $self->_encode_summary_key($typeid,$seqid,$bin); my $status = $db->seq($key,$cum_count,R_CURSOR); next unless $status == 0; push @{$bins{$typeid}},[$bin,$cum_count]; } } my @merged_bins; my $firstbin = int(($start-1)/$binsize); for my $type (keys %bins) { my $arry = $bins{$type}; my $last_count = $arry->[0][1]-1; my $last_bin = -1; my $i = 0; my $delta; for my $b (@$arry) { my ($bin,$count) = @$b; $delta = $count - $last_count if $bin > $last_bin; $merged_bins[$i++] = $delta; $last_count = $count; $last_bin = $bin; } } my $returned_type = $self->_id2type($report_tag); return wantarray ? (\@merged_bins,$returned_type) : \@merged_bins; } sub _encode_summary_key { my $self = shift; my ($typeid,$seqid,$bin) = @_; $self->throw('Cannot index chromosomes larger than '.C1*SUMMARY_BIN_SIZE/1e6.' megabases') if $bin > C1; return ($typeid-1)*C2 + ($seqid-1)*C1 + $bin; } sub _decode_summary_key { my $self = shift; my $key = shift; my $typeid = int($key/C2); my $residual = $key%C2; my $seqid = int($residual/C1); my $bin = $residual%C1; return ($typeid+1,$seqid+1,$bin); } 1; BioPerl-1.007002/Bio/DB/SeqFeature/Store/memory.pm000444000766000024 5440613155576320 21550 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::Store::memory; =head1 NAME Bio::DB::SeqFeature::Store::memory -- In-memory implementation of Bio::DB::SeqFeature::Store =head1 SYNOPSIS use Bio::DB::SeqFeature::Store; # Open the sequence database my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'memory', -dsn => '/var/databases/test'); # search... by id my @features = $db->fetch_many(@list_of_ids); # ...by name @features = $db->get_features_by_name('ZK909'); # ...by alias @features = $db->get_features_by_alias('sma-3'); # ...by type @features = $db->get_features_by_type('gene'); # ...by location @features = $db->get_features_by_location(-seq_id=>'Chr1',-start=>4000,-end=>600000); # ...by attribute @features = $db->get_features_by_attribute({description => 'protein kinase'}) # ...by the GFF "Note" field @result_list = $db->search_notes('kinase'); # ...by arbitrary combinations of selectors @features = $db->features(-name => $name, -type => $types, -seq_id => $seqid, -start => $start, -end => $end, -attributes => $attributes); # ...using an iterator my $iterator = $db->get_seq_stream(-name => $name, -type => $types, -seq_id => $seqid, -start => $start, -end => $end, -attributes => $attributes); while (my $feature = $iterator->next_seq) { # do something with the feature } # ...limiting the search to a particular region my $segment = $db->segment('Chr1',5000=>6000); my @features = $segment->features(-type=>['mRNA','match']); # getting & storing sequence information # Warning: this returns a string, and not a PrimarySeq object $db->insert_sequence('Chr1','GATCCCCCGGGATTCCAAAA...'); my $sequence = $db->fetch_sequence('Chr1',5000=>6000); # what feature types are defined in the database? my @types = $db->types; # create a new feature in the database my $feature = $db->new_feature(-primary_tag => 'mRNA', -seq_id => 'chr3', -start => 10000, -end => 11000); =head1 DESCRIPTION Bio::DB::SeqFeature::Store::memory is the in-memory adaptor for Bio::DB::SeqFeature::Store. You will not create it directly, but instead use Bio::DB::SeqFeature::Store-Enew() to do so. See L for complete usage instructions. =head2 Using the memory adaptor Before using the memory adaptor, populate a readable-directory on the file system with annotation and/or sequence files. The annotation files must be in GFF3 format, and sholud end in the extension .gff or .gff3. They may be compressed with "compress", "gzip" or "bzip2" (in which case the appropriate compression extension must be present as well.) You may include sequence data inline in the GFF3 files, or put the sequence data in one or more separate FASTA-format files. These files must end with .fa or .fasta and may be compressed. Because of the way the adaptor works, you will get much better performance if you keep the sequence data in separate FASTA files. Initialize the database using the -dsn option. This should point to the directory creating the annotation and sequence files, or to a single GFF3 file. Examples: # load all GFF3 and FASTA files located in /var/databases/test directory $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'memory', -dsn => '/var/databases/test'); # load the data in a single compressed GFF3 file located at # /usr/annotations/worm.gf33.gz $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'memory', -dsn => '/usr/annotations/worm.gff3.gz'); For compatibility with the Bio::DB::GFF memory adaptor, -gff is recognized as an alias for -dsn. See L for all the access methods supported by this adaptor. The various methods for storing and updating features and sequences into the database are supported, including GFF3 loading support, but since this is an in-memory adaptor all changes you make will be lost when the script exits. =cut use strict; use base 'Bio::DB::SeqFeature::Store'; use Bio::DB::SeqFeature::Store::GFF3Loader; use Bio::DB::GFF::Util::Rearrange 'rearrange'; use File::Temp 'tempdir'; use IO::File; use Bio::DB::Fasta; use File::Glob ':glob'; use constant BINSIZE => 10_000; ### # object initialization # sub init { my ($self, $args) = @_; $self->SUPER::init($args); $self->{_data} = {}; $self->{_children} = {}; $self->{_index} = {}; $self; } sub post_init { my $self = shift; my ($file_or_dir) = rearrange([['DIR','DSN','FILE','GFF']],@_); return unless $file_or_dir; my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store => $self, -sf_class => $self->seqfeature_class, -no_close_fasta => 1 ) or $self->throw("Couldn't create GFF3Loader"); my @argv; if (-d $file_or_dir) { @argv = ( bsd_glob("$file_or_dir/*.size*"), bsd_glob("$file_or_dir/*.gff"), bsd_glob("$file_or_dir/*.gff3"), bsd_glob("$file_or_dir/*.gff.{gz,Z,bz2}"), bsd_glob("$file_or_dir/*.gff3.{gz,Z,bz2}") ); } else { @argv = $file_or_dir; } local $self->{file_or_dir} = $file_or_dir; $loader->load(@argv); warn $@ if $@; } sub commit { # reindex fasta files my $self = shift; my $db; if (my $fh = $self->{fasta_fh}) { $fh->close; $db = Bio::DB::Fasta->new($self->{fasta_file}); } elsif (exists $self->{file_or_dir} && -d $self->{file_or_dir}) { $db = Bio::DB::Fasta->new($self->{file_or_dir}); } $self->{fasta_db} = $db if $db; } sub can_store_parentage { 1 } # return a hash ref in which each key is primary id sub data { shift->{_data}; } sub _init_database { shift->init } sub _store { my $self = shift; my $indexed = shift; my @objs = @_; my $data = $self->data; my $count = 0; for my $obj (@objs) { # Add unique ID to feature if needed my $primary_id = $self->_autoid($obj); # Store feature (overwriting any existing feature with the same primary ID # as required by Bio::DB::SF::Store) $data->{$primary_id} = $obj; if ($indexed) { $self->{_index}{ids}{$primary_id} = undef; $self->_update_indexes($obj); } $count++; } return $count; } sub _autoid { # If a feature has no ID, assign it a unique ID my ($self, $obj) = @_; my $data = $self->data; my $primary_id = $obj->primary_id; if (not defined $primary_id) { # Create a unique ID $primary_id = 1 + scalar keys %{$data}; while (exists $data->{$primary_id}) { $primary_id++; } $obj->primary_id($primary_id); } return $primary_id; } sub _deleteid { my ($self, $id) = @_; if (exists $self->{_index}{ids}{$id}) { # $indexed was true $self->_update_indexes( $self->fetch($id), 1 ); delete $self->{_index}{ids}{$id}; } delete $self->data->{$id}; return 1; } sub _fetch { my ($self, $id) = @_; return $self->data->{$id}; } sub _add_SeqFeature { my ($self, $parent, @children) = @_; my $count = 0; my $parent_id = ref $parent ? $parent->primary_id : $parent; defined $parent_id or $self->throw("Parent $parent should have a primary ID"); for my $child (@children) { my $child_id = ref $child ? $child->primary_id : $child; defined $child_id or $self->throw("Child $child should have a primary ID"); $self->{_children}{$parent_id}{$child_id}++; $count++; } return $count; } sub _fetch_SeqFeatures { my ($self, $parent, @types) = @_; my $parent_id = $parent->primary_id; defined $parent_id or $self->throw("Parent $parent should have a primary ID"); my @children_ids = keys %{$self->{_children}{$parent_id}}; my @children = map {$self->fetch($_)} @children_ids; if (@types) { my $data; for my $c (@children) { push @{$$data{$c->primary_tag}{$c->source_tag||''}}, $c; } @children = (); for my $type (@types) { $type .= ':' if (not $type =~ m/:/); my ($primary_tag, undef, $source_tag) = ($type =~ m/^(.*?)(:(.*?))$/); $source_tag ||= ''; if ($source_tag eq '') { for my $source (keys %{$$data{$primary_tag}}) { if (exists $$data{$primary_tag}{$source_tag}) { push @children, @{$$data{$primary_tag}{$source_tag}}; } } } else { if (exists $$data{$primary_tag}{$source_tag}) { push @children, @{$$data{$primary_tag}{$source_tag}}; } } } } return @children; } sub _update_indexes { my ($self, $obj, $del) = @_; defined (my $id = $obj->primary_id) or return; $del ||= 0; $self->_update_name_index($obj,$id, $del); $self->_update_type_index($obj,$id, $del); $self->_update_location_index($obj, $id, $del); $self->_update_attribute_index($obj,$id, $del); } sub _update_name_index { my ($self, $obj, $id, $del) = @_; my ($names, $aliases) = $self->feature_names($obj); foreach (@$names) { if (not $del) { $self->{_index}{name}{lc $_}{$id} = 1; } else { delete $self->{_index}{name}{lc $_}{$id}; if (scalar keys %{ $self->{_index}{name}{lc $_} } == 0) { delete $self->{_index}{name}{lc $_}; } }; } foreach (@$aliases) { if (not $del) { $self->{_index}{name}{lc $_}{$id} ||= 2; } else { delete $self->{_index}{name}{lc $_}{$id}; if (scalar keys %{ $self->{_index}{name}{lc $_} } == 0) { delete $self->{_index}{name}{lc $_}; } } } } sub _update_type_index { my ($self, $obj, $id, $del) = @_; my $primary_tag = lc($obj->primary_tag) || return; my $source_tag = lc($obj->source_tag || ''); if (not $del) { $self->{_index}{type}{$primary_tag}{$source_tag}{$id} = undef; } else { delete $self->{_index}{type}{$primary_tag}{$source_tag}{$id}; if ( scalar keys %{$self->{_index}{type}{$primary_tag}{$source_tag}} == 0 ) { delete $self->{_index}{type}{$primary_tag}{$source_tag}; if (scalar keys %{$self->{_index}{type}{$primary_tag}} == 0 ) { delete $self->{_index}{type}{$primary_tag}; } } } } sub _update_location_index { my ($self, $obj, $id, $del) = @_; my $seq_id = $obj->seq_id || ''; my $start = $obj->start || 0; my $end = $obj->end || 0; my $strand = $obj->strand; my $bin_min = int $start/BINSIZE; my $bin_max = int $end/BINSIZE; for (my $bin = $bin_min; $bin <= $bin_max; $bin++ ) { if (not $del) { $self->{_index}{location}{lc $seq_id}{$bin}{$id} = undef; } else { delete $self->{_index}{location}{lc $seq_id}{$bin}{$id}; if (scalar keys %{$self->{_index}{location}{lc $seq_id}{$bin}{$id}} == 0) { delete $self->{_index}{location}{lc $seq_id}{$bin}{$id}; } if (scalar keys %{$self->{_index}{location}{lc $seq_id}{$bin}} == 0) { delete $self->{_index}{location}{lc $seq_id}{$bin}; } if (scalar keys %{$self->{_index}{location}{lc $seq_id}} == 0) { delete $self->{_index}{location}{lc $seq_id}; } } } } sub _update_attribute_index { my ($self, $obj, $id, $del) = @_; for my $tag ($obj->get_all_tags) { for my $value ($obj->get_tag_values($tag)) { if (not $del) { $self->{_index}{attribute}{lc $tag}{lc $value}{$id} = undef; } else { delete $self->{_index}{attribute}{lc $tag}{lc $value}{$id}; if ( scalar keys %{$self->{_index}{attribute}{lc $tag}{lc $value}} == 0) { delete $self->{_index}{attribute}{lc $tag}{lc $value}; } if ( scalar keys %{$self->{_index}{attribute}{lc $tag}} == 0) { delete $self->{_index}{attribute}{lc $tag}; } if ( scalar keys %{$self->{_index}{attribute}} == 0) { delete $self->{_index}{attribute}; } } } } } sub _features { my $self = shift; my ($seq_id,$start,$end,$strand, $name,$class,$allow_aliases, $types, $attributes, $range_type, $iterator ) = rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'],'STRAND', 'NAME','CLASS','ALIASES', ['TYPES','TYPE','PRIMARY_TAG'], ['ATTRIBUTES','ATTRIBUTE'], 'RANGE_TYPE', 'ITERATOR', ],@_); my (@from,@where,@args,@group); $range_type ||= 'overlaps'; my @result; unless (defined $name or defined $seq_id or defined $types or defined $attributes) { @result = keys %{$self->{_index}{ids}}; } my %found = (); my $result = 1; if (defined($name)) { # hacky backward compatibility workaround undef $class if $class && $class eq 'Sequence'; $name = "$class:$name" if defined $class && length $class > 0; $result &&= $self->filter_by_name($name,$allow_aliases,\%found); } if (defined $seq_id) { $result &&= $self->filter_by_location($seq_id,$start,$end,$strand,$range_type,\%found); } if (defined $types) { $result &&= $self->filter_by_type($types,\%found); } if (defined $attributes) { $result &&= $self->filter_by_attribute($attributes,\%found); } push @result,keys %found if $result; return $iterator ? Bio::DB::SeqFeature::Store::memory::Iterator->new($self,\@result) : map {$self->fetch($_)} @result; } sub filter_by_type { my ($self, $types_req, $filter) = @_; my @types_req = ref $types_req eq 'ARRAY' ? @$types_req : $types_req; my $types = $self->{_index}{type}; my @types_found = $self->find_types(\@types_req); my @results; for my $type_found (@types_found) { my ($primary_tag, undef, $source_tag) = ($type_found =~ m/^(.*?)(:(.*?))$/); next unless exists $types->{$primary_tag}{$source_tag}; push @results, keys %{$types->{$primary_tag}{$source_tag}}; } $self->update_filter($filter,\@results); } sub find_types { my ($self, $types_req) = @_; my @types_found; my $types = $self->{_index}{type}; for my $type_req (@$types_req) { # Type is the primary tag and an optional source tag my ($primary_tag, $source_tag); if (ref $type_req && $type_req->isa('Bio::DB::GFF::Typename')) { $primary_tag = $type_req->method; $source_tag = $type_req->source; } else { ($primary_tag, undef, $source_tag) = ($type_req =~ m/^(.*?)(:(.*))?$/); } ($primary_tag, $source_tag) = (lc $primary_tag, lc($source_tag || '')); next if not exists $$types{$primary_tag}; if ($source_tag eq '') { # Match all sources for this primary_tag push @types_found, map {"$primary_tag:$_"} (keys %{ $$types{$primary_tag} }); } else { # Match only the requested source push @types_found, "$primary_tag:$source_tag"; } } return @types_found; } sub attributes { my $self = shift; return keys %{$self->{_index}{attribute}}; } sub filter_by_attribute { my ($self, $attributes, $filter) = @_; my $index = $self->{_index}{attribute}; my $result; for my $att_name (keys %$attributes) { my @result; my @matching_values; my @search_terms = ref($attributes->{$att_name}) && ref($attributes->{$att_name}) eq 'ARRAY' ? @{$attributes->{$att_name}} : $attributes->{$att_name}; my @regexp_terms; my @terms; for my $v (@search_terms) { if (my $regexp = $self->glob_match($v)) { @regexp_terms = keys %{$index->{lc $att_name}} unless @regexp_terms; push @terms,grep {/^$v$/i} @regexp_terms; } else { push @terms,lc $v; } } for my $v (@terms) { push @result,keys %{$index->{lc $att_name}{$v}}; } $result ||= $self->update_filter($filter,\@result); } $result; } sub filter_by_location { my ($self, $seq_id, $start, $end, $strand, $range_type, $filter) = @_; $strand ||= 0; my $index = $self->{_index}{location}{lc $seq_id}; my @bins; if (!defined $start or !defined $end or $range_type eq 'contained_in') { @bins = sort {$a<=>$b} keys %{$index}; $start = $bins[0] * BINSIZE unless defined $start; $end = (($bins[-1] + 1) * BINSIZE) - 1 unless defined $end; } my %seenit; my $bin_min = int $start/BINSIZE; my $bin_max = int $end/BINSIZE; my @bins_in_range = $range_type eq 'contained_in' ? ($bins[0]..$bin_min,$bin_max..$bins[-1]) : ($bin_min..$bin_max); my @results; for my $bin (@bins_in_range) { next unless exists $index->{$bin}; my @found = keys %{$index->{$bin}}; for my $f (@found) { next if $seenit{$f}++; my $feature = $self->_fetch($f) or next; next if $strand && $feature->strand != $strand; if ($range_type eq 'overlaps') { next unless $feature->end >= $start && $feature->start <= $end; } elsif ($range_type eq 'contains') { next unless $feature->start >= $start && $feature->end <= $end; } elsif ($range_type eq 'contained_in') { next unless $feature->start <= $start && $feature->end >= $end; } push @results,$f; } } $self->update_filter($filter,\@results); } sub filter_by_name { my ($self, $name, $allow_aliases, $filter) = @_; my $index = $self->{_index}{name}; my @names_to_fetch; if (my $regexp = $self->glob_match($name)) { @names_to_fetch = grep {/^$regexp$/i} keys %{$index}; } else { @names_to_fetch = lc $name; } my @results; for my $n (@names_to_fetch) { if ($allow_aliases) { push @results,keys %{$index->{$n}}; } else { push @results,grep {$index->{$n}{$_} == 1} keys %{$index->{$n}}; } } $self->update_filter($filter,\@results); } sub glob_match { my ($self, $term) = @_; return unless $term =~ /(?:^|[^\\])[*?]/; $term =~ s/(^|[^\\])([+\[\]^{}\$|\(\).])/$1\\$2/g; $term =~ s/(^|[^\\])\*/$1.*/g; $term =~ s/(^|[^\\])\?/$1./g; return $term; } sub update_filter { my ($self, $filter, $results) = @_; return unless @$results; if (%$filter) { my @filtered = grep {$filter->{$_}} @$results; %$filter = map {$_=>1} @filtered; } else { %$filter = map {$_=>1} @$results; } } sub _search_attributes { my ($self, $search_string, $attribute_array, $limit) = @_; $search_string =~ tr/*?//d; my @words = map {quotemeta($_)} $search_string =~ /(\w+)/g; my $search = join '|',@words; my (%results,%notes); my $index = $self->{_index}{attribute}; for my $tag (@$attribute_array) { my $attributes = $index->{lc $tag}; for my $value (keys %{$attributes}) { next unless $value =~ /$search/i; my @ids = keys %{$attributes->{$value}}; for my $w (@words) { my @hits = $value =~ /($w)/ig or next; $results{$_} += @hits foreach @ids; } $notes{$_} .= "$value " foreach @ids; } } my @results; for my $id (keys %results) { my $hits = $results{$id}; my $note = $notes{$id}; $note =~ s/\s+$//; my $relevance = 10 * $hits; my $feature = $self->fetch($id); my $name = $feature->display_name or next; my $type = $feature->type; push @results,[$name,$note,$relevance,$type,$id]; } return @results; } =head2 types Title : types Usage : @type_list = $db->types Function: Get all the types in the database Returns : array of Bio::DB::GFF::Typename objects (arrayref in scalar context) Args : none Status : public =cut sub types { my $self = shift; eval "require Bio::DB::GFF::Typename" unless Bio::DB::GFF::Typename->can('new'); my @types; for my $primary_tag ( keys %{$$self{_index}{type}} ) { for my $source_tag ( keys %{$$self{_index}{type}{$primary_tag}} ) { push @types, Bio::DB::GFF::Typename->new($primary_tag,$source_tag); } } return @types; } # this is ugly sub _insert_sequence { my ($self, $seqid, $seq, $offset) = @_; my $dna_fh = $self->private_fasta_file or return; if ($offset == 0) { # start of the sequence print $dna_fh ">$seqid\n"; } print $dna_fh $seq,"\n"; } sub _fetch_sequence { my ($self, $seqid, $start, $end) = @_; my $db = $self->{fasta_db} or return; return $db->seq($seqid,$start,$end); } sub private_fasta_file { my $self = shift; return $self->{fasta_fh} if exists $self->{fasta_fh}; my $dir = tempdir (CLEANUP => 1); $self->{fasta_file} = "$dir/sequence.$$.fasta"; return $self->{fasta_fh} = IO::File->new($self->{fasta_file},">"); } # summary support sub coverage_array { my $self = shift; my ($seq_name,$start,$end,$types,$bins) = rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'], ['TYPES','TYPE','PRIMARY_TAG'],'BINS'],@_); my @features = $self->_features(-seq_id=> $seq_name, -start => $start, -end => $end, -types => $types); my $binsize = ($end-$start+1)/$bins; my $report_tag; my @coverage_array = (0) x $bins; for my $f (@features) { $report_tag ||= $f->primary_tag; my $fs = $f->start; my $fe = $f->end; my $start_bin = int(($fs-$start)/$binsize); my $end_bin = int(($fe-$start)/$binsize); $start_bin = 0 if $start_bin < 0; $end_bin = $bins-1 if $end_bin >= $bins; $coverage_array[$_]++ for ($start_bin..$end_bin); } return wantarray ? (\@coverage_array,$report_tag) : \@coverage_array; } sub _seq_ids { my $self = shift; if (my $fa = $self->{fasta_db}) { if (my @s = eval {$fa->ids}) { return @s; } } my $l = $self->{_index}{location} or return; return keys %$l; } package Bio::DB::SeqFeature::Store::memory::Iterator; sub new { my ($class, $store, $ids) = @_; return bless {store => $store, ids => $ids},ref($class) || $class; } sub next_seq { my $self = shift; my $store = $self->{store} or return; my $id = shift @{$self->{ids}}; defined $id or return; return $store->fetch($id); } 1; __END__ =head1 BUGS This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs. =head1 SEE ALSO L, L, L, L, L, L, L =head1 AUTHOR Lincoln Stein Elstein@cshl.orgE. Copyright (c) 2006 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut BioPerl-1.007002/Bio/DB/SeqFeature/Store/DBI000755000766000024 013155576320 20112 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/SeqFeature/Store/DBI/Iterator.pm000444000766000024 115213155576320 22375 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::Store::DBI::Iterator; =head1 NAME Bio::DB::SeqFeature::Store::DBI::Iterator - utility methods for creating and iterating over SeqFeature records =cut sub new { my $class = shift; my ($sth,$store) = @_; return bless {sth => $sth, store => $store },ref($class) || $class; } sub next_seq { my $self = shift; my $sth = $self->{sth} or return; my $store = $self->{store} or return; my $obj = $store->_sth2obj($sth); if (!$obj) { $self->{sth}->finish; undef $self->{sth}; undef $self->{store}; return; } return $obj; } 1; BioPerl-1.007002/Bio/DB/SeqFeature/Store/DBI/Pg.pm000444000766000024 7141613155576320 21204 0ustar00cjfieldsstaff000000000000 package Bio::DB::SeqFeature::Store::DBI::Pg; use DBD::Pg qw(:pg_types); use MIME::Base64; # $Id: Pg.pm 14656 2008-04-14 15:05:37Z lstein $ =head1 NAME Bio::DB::SeqFeature::Store::DBI::Pg -- PostgreSQL implementation of Bio::DB::SeqFeature::Store =head1 SYNOPSIS use Bio::DB::SeqFeature::Store; # Open the sequence database my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::Pg', -dsn => 'dbi:Pg:test'); # get a feature from somewhere my $feature = Bio::SeqFeature::Generic->new(...); # store it $db->store($feature) or die "Couldn't store!"; # primary ID of the feature is changed to indicate its primary ID # in the database... my $id = $feature->primary_id; # get the feature back out my $f = $db->fetch($id); # change the feature and update it $f->start(100); $db->update($f) or die "Couldn't update!"; # searching... # ...by id my @features = $db->fetch_many(@list_of_ids); # ...by name @features = $db->get_features_by_name('ZK909'); # ...by alias @features = $db->get_features_by_alias('sma-3'); # ...by type @features = $db->get_features_by_name('gene'); # ...by location @features = $db->get_features_by_location(-seq_id=>'Chr1',-start=>4000,-end=>600000); # ...by attribute @features = $db->get_features_by_attribute({description => 'protein kinase'}) # ...by the GFF "Note" field @result_list = $db->search_notes('kinase'); # ...by arbitrary combinations of selectors @features = $db->features(-name => $name, -type => $types, -seq_id => $seqid, -start => $start, -end => $end, -attributes => $attributes); # ...using an iterator my $iterator = $db->get_seq_stream(-name => $name, -type => $types, -seq_id => $seqid, -start => $start, -end => $end, -attributes => $attributes); while (my $feature = $iterator->next_seq) { # do something with the feature } # ...limiting the search to a particular region my $segment = $db->segment('Chr1',5000=>6000); my @features = $segment->features(-type=>['mRNA','match']); # getting & storing sequence information # Warning: this returns a string, and not a PrimarySeq object $db->insert_sequence('Chr1','GATCCCCCGGGATTCCAAAA...'); my $sequence = $db->fetch_sequence('Chr1',5000=>6000); # what feature types are defined in the database? my @types = $db->types; # create a new feature in the database my $feature = $db->new_feature(-primary_tag => 'mRNA', -seq_id => 'chr3', -start => 10000, -end => 11000); =head1 DESCRIPTION Bio::DB::SeqFeature::Store::Pg is the Pg adaptor for Bio::DB::SeqFeature::Store. You will not create it directly, but instead use Bio::DB::SeqFeature::Store-Enew() to do so. See L for complete usage instructions. =head2 Using the Pg adaptor Before you can use the adaptor, you must use the Pgadmin tool to create a database and establish a user account with write permission. In order to use "fast" loading, the user account must have "file" privileges. To establish a connection to the database, call Bio::DB::SeqFeature::Store-Enew(-adaptor=E'DBI::Pg',@more_args). The additional arguments are as follows: Argument name Description ------------- ----------- -dsn The database name. You can abbreviate "dbi:Pg:foo" as "foo" if you wish. -user Username for authentication. -pass Password for authentication. -namespace Creates a SCHEMA for the tables. This allows you to have several virtual databases in the same physical database. -temp Boolean flag. If true, a temporary database will be created and destroyed as soon as the Store object goes out of scope. (synonym -temporary) -autoindex Boolean flag. If true, features in the database will be reindexed every time they change. This is the default. -tmpdir Directory in which to place temporary files during "fast" loading. Defaults to File::Spec->tmpdir(). (synonyms -dump_dir, -dumpdir, -tmp) -dbi_options A hashref to pass to DBI->connect's 4th argument, the "attributes." (synonyms -options, -dbi_attr) -write Pass true to open database for writing or updating. If successful, a new instance of Bio::DB::SeqFeature::Store::DBI::Pg will be returned. In addition to the standard methods supported by all well-behaved Bio::DB::SeqFeature::Store databases, several following adaptor-specific methods are provided. These are described in the next sections. =cut use strict; use base 'Bio::DB::SeqFeature::Store::DBI::mysql'; use Bio::DB::SeqFeature::Store::DBI::Iterator; use DBI; use Memoize; use Cwd 'abs_path'; use Bio::DB::GFF::Util::Rearrange 'rearrange'; use File::Copy; use File::Spec; use constant DEBUG=>0; use constant MAX_INT => 2_147_483_647; use constant MIN_INT => -2_147_483_648; use constant MAX_BIN => 1_000_000_000; # size of largest feature = 1 Gb use constant MIN_BIN => 1000; # smallest bin we'll make - on a 100 Mb chromosome, there'll be 100,000 of these ### # object initialization # # NOTE: most of this code can be refactored and inherited from DBI or DBI::mysql adapter # sub init { my $self = shift; my ($dsn, $is_temporary, $autoindex, $namespace, $dump_dir, $user, $pass, $dbi_options, $writeable, $create, $schema, ) = rearrange(['DSN', ['TEMP','TEMPORARY'], 'AUTOINDEX', 'NAMESPACE', ['DUMP_DIR','DUMPDIR','TMP','TMPDIR'], 'USER', ['PASS','PASSWD','PASSWORD'], ['OPTIONS','DBI_OPTIONS','DBI_ATTR'], ['WRITE','WRITEABLE'], 'CREATE', 'SCHEMA' ],@_); $dbi_options ||= {pg_server_prepare => 0}; $writeable = 1 if $is_temporary or $dump_dir; $dsn or $self->throw("Usage: ".__PACKAGE__."->init(-dsn => \$dbh || \$dsn)"); my $dbh; if (ref $dsn) { $dbh = $dsn; } else { $dsn = "dbi:Pg:$dsn" unless $dsn =~ /^dbi:/; $dbh = DBI->connect($dsn,$user,$pass,$dbi_options) or $self->throw($DBI::errstr); } $dbh->do('set client_min_messages=warning') if $dbh; $self->{'original_arguments'} = { 'dsn' => $dsn, 'user' => $user, 'pass' => $pass, 'dbh_options' => $dbi_options, }; $self->{dbh} = $dbh; $self->{dbh}->{InactiveDestroy} = 1; $self->{is_temp} = $is_temporary; $self->{writeable} = $writeable; $self->{namespace} = $namespace || $schema || 'public'; $self->schema($self->{namespace}); $self->default_settings; $self->autoindex($autoindex) if defined $autoindex; $self->dumpdir($dump_dir) if $dump_dir; if ($self->is_temp) { # warn "creating a temp database isn't supported"; #$self->init_tmp_database(); $self->init_database('erase'); } elsif ($create) { $self->init_database('erase'); } } sub table_definitions { my $self = shift; return { feature => < < < < < < < < < <{'schema'} = $schema if defined($schema); if ($schema) { $self->_check_for_namespace(); $self->dbh->do("SET search_path TO " . $self->{'schema'} ); } else { $self->dbh->do("SET search_path TO public"); } return $self->{'schema'}; } ### # wipe database clean and reinstall schema # sub _init_database { my $self = shift; my $erase = shift; my $dbh = $self->dbh; my $namespace = $self->namespace; my $tables = $self->table_definitions; my $temporary = $self->is_temp ? 'TEMPORARY' : ''; foreach (keys %$tables) { next if $_ eq 'meta'; # don't get rid of meta data! my $table = $self->_qualify($_); $dbh->do("DROP TABLE IF EXISTS $table") if $erase; my @table_exists = $dbh->selectrow_array("SELECT * FROM pg_tables WHERE tablename = '$table' AND schemaname = '$self->namespace'"); if (!scalar(@table_exists)) { my $query = "CREATE $temporary TABLE $table $tables->{$_}"; $dbh->do($query) or $self->throw($dbh->errstr); } } $self->subfeatures_are_indexed(1) if $erase; 1; } sub maybe_create_meta { my $self = shift; return unless $self->writeable; my $namespace = $self->namespace; my $table = $self->_qualify('meta'); my $tables = $self->table_definitions; my $temporary = $self->is_temp ? 'TEMPORARY' : ''; my @table_exists = $self->dbh->selectrow_array("SELECT * FROM pg_tables WHERE tablename = 'meta' AND schemaname = '$namespace'"); $self->dbh->do("CREATE $temporary TABLE $table $tables->{meta}") unless @table_exists; } ### # check if the namespace/schema exists, if not create it # sub _check_for_namespace { my $self = shift; my $namespace = $self->namespace; return if $namespace eq 'public'; my $dbh = $self->dbh; my @schema_exists = $dbh->selectrow_array("SELECT * FROM pg_namespace WHERE nspname = '$namespace'"); if (!scalar(@schema_exists)) { my $query = "CREATE SCHEMA $namespace"; $dbh->do($query) or $self->throw($dbh->errstr); # if temp parameter is set and schema created for this process then enable removal in remove_namespace() if ($self->is_temp) { $self->{delete_schema} = 1; } } } ### # Overiding inherited mysql _qualify (We do not need to qualify for PostgreSQL as we have set the search_path above) # sub _qualify { my $self = shift; my $table_name = shift; return $table_name; } ### # when is_temp is set and the schema did not exist beforehand then we are able to remove it # sub remove_namespace { my $self = shift; if ($self->{delete_schema}) { my $namespace = $self->namespace; $self->dbh->do("DROP SCHEMA $namespace") or $self->throw($self->dbh->errstr); } } ####Overiding the inherited mysql function _prepare sub _prepare { my $self = shift; my $query = shift; my $dbh = $self->dbh; my $schema = $self->{namespace}; if ($schema) { $self->_check_for_namespace(); $dbh->do("SET search_path TO " . $self->{'schema'} ); } else { $dbh->do("SET search_path TO public"); } my $sth = $dbh->prepare_cached($query, {}, 3) or $self->throw($dbh->errstr); $sth; } sub _finish_bulk_update { my $self = shift; my $dbh = $self->dbh; my $dir = $self->{dumpdir} || '.'; for my $table ('feature',$self->index_tables) { my $fh = $self->dump_filehandle($table); my $path = $self->dump_path($table); $fh->close; my $qualified_table = $self->_qualify($table); copy($path, "$path.bak"); # Get stuff from file into STDIN so we don't have to be superuser open my $FH, '<', $path or $self->throw("Could not read file '$path': $!"); print STDERR "Loading file $path\n"; $dbh->do("COPY $qualified_table FROM STDIN CSV QUOTE '''' DELIMITER '\t'") or $self->throw($dbh->errstr); while (my $line = <$FH>) { $dbh->pg_putline($line); } $dbh->pg_endcopy() or $self->throw($dbh->errstr); close $FH; #unlink $path; } delete $self->{bulk_update_in_progress}; delete $self->{filehandles}; } ### # Add a subparts to a feature. Both feature and all subparts must already be in database. # sub _add_SeqFeature { my $self = shift; # special purpose method for case when we are doing a bulk update return $self->_dump_add_SeqFeature(@_) if $self->{bulk_update_in_progress}; my $parent = shift; my @children = @_; my $dbh = $self->dbh; local $dbh->{RaiseError} = 1; my $child_table = $self->_parent2child_table(); my $count = 0; my $querydel = "DELETE FROM $child_table WHERE id = ? AND child = ?"; my $query = "INSERT INTO $child_table (id,child) VALUES (?,?)"; my $sthdel = $self->_prepare($querydel); my $sth = $self->_prepare($query); my $parent_id = (ref $parent ? $parent->primary_id : $parent) or $self->throw("$parent should have a primary_id"); $self->begin_work or $self->throw($dbh->errstr); eval { for my $child (@children) { my $child_id = ref $child ? $child->primary_id : $child; defined $child_id or die "no primary ID known for $child"; $sthdel->execute($parent_id, $child_id); $sth->execute($parent_id,$child_id); $count++; } }; if ($@) { warn "Transaction aborted because $@"; $self->rollback; } else { $self->commit; } $sth->finish; $count; } # because this is a reserved word in postgresql ### # get primary sequence between start and end # sub _fetch_sequence { my $self = shift; my ($seqid,$start,$end) = @_; # backward compatibility to the old days when I liked reverse complementing # dna by specifying $start > $end my $reversed; if (defined $start && defined $end && $start > $end) { $reversed++; ($start,$end) = ($end,$start); } $start-- if defined $start; $end-- if defined $end; my $offset1 = $self->_offset_boundary($seqid,$start || 'left'); my $offset2 = $self->_offset_boundary($seqid,$end || 'right'); my $sequence_table = $self->_sequence_table; my $locationlist_table = $self->_locationlist_table; my $sth = $self->_prepare(<= ? AND "offset" <= ? ORDER BY "offset" END my $seq = ''; $sth->execute($seqid,$offset1,$offset2) or $self->throw($sth->errstr); while (my($frag,$offset) = $sth->fetchrow_array) { substr($frag,0,$start-$offset) = '' if defined $start && $start > $offset; $seq .= $frag; } substr($seq,$end-$start+1) = '' if defined $end && $end-$start+1 < length($seq); if ($reversed) { $seq = reverse $seq; $seq =~ tr/gatcGATC/ctagCTAG/; } $sth->finish; $seq; } sub _offset_boundary { my $self = shift; my ($seqid,$position) = @_; my $sequence_table = $self->_sequence_table; my $locationlist_table = $self->_locationlist_table; my $sql; $sql = $position eq 'left' ? "SELECT min(\"offset\") FROM $sequence_table as s,$locationlist_table as ll WHERE s.id=ll.id AND ll.seqname=?" :$position eq 'right' ? "SELECT max(\"offset\") FROM $sequence_table as s,$locationlist_table as ll WHERE s.id=ll.id AND ll.seqname=?" :"SELECT max(\"offset\") FROM $sequence_table as s,$locationlist_table as ll WHERE s.id=ll.id AND ll.seqname=? AND \"offset\"<=?"; my $sth = $self->_prepare($sql); my @args = $position =~ /^-?\d+$/ ? ($seqid,$position) : ($seqid); $sth->execute(@args) or $self->throw($sth->errstr); my $boundary = $sth->fetchall_arrayref->[0][0]; $sth->finish; return $boundary; } sub _name_sql { my $self = shift; my ($name,$allow_aliases,$join) = @_; my $name_table = $self->_name_table; my $from = "$name_table as n"; my ($match,$string) = $self->_match_sql($name); my $where = "n.id=$join AND lower(n.name) $match"; $where .= " AND n.display_name>0" unless $allow_aliases; return ($from,$where,'',$string); } sub _search_attributes { my $self = shift; my ($search_string,$attribute_names,$limit) = @_; my @words = map {quotemeta($_)} split /\s+/,$search_string; my $name_table = $self->_name_table; my $attribute_table = $self->_attribute_table; my $attributelist_table = $self->_attributelist_table; my $type_table = $self->_type_table; my $typelist_table = $self->_typelist_table; my @tags = @$attribute_names; my $tag_sql = join ' OR ',("al.tag=?") x @tags; my $perl_regexp = join '|',@words; my @wild_card_words = map { "%$_%" } @words; my $sql_regexp = join ' OR ',("a.attribute_value SIMILAR TO ?") x @words; my $sql = <_print_query($sql,@tags,@wild_card_words) if DEBUG || $self->debug; my $sth = $self->_prepare($sql); $sth->execute(@tags,@wild_card_words) or $self->throw($sth->errstr); my @results; while (my($name,$value,$type,$id) = $sth->fetchrow_array) { my (@hits) = $value =~ /$perl_regexp/ig; my @words_in_row = split /\b/,$value; my $score = int(@hits*100/@words/@words_in_row); push @results,[$name,$value,$score,$type,$id]; } $sth->finish; @results = sort {$b->[2]<=>$a->[2]} @results; return @results; } # overridden here because the mysql adapter uses # a non-standard query hint sub _attributes_sql { my $self = shift; my ($attributes,$join) = @_; my ($wf,@bind_args) = $self->_make_attribute_where('a','al',$attributes); my ($group_by,@group_args)= $self->_make_attribute_group('a',$attributes); my $attribute_table = $self->_attribute_table; my $attributelist_table = $self->_attributelist_table; my $from = "$attribute_table as a, $attributelist_table as al"; my $where = <_typelist_table; my $from = "$typelist AS tl"; my (@matches,@args); for my $type (@types) { if (ref $type && $type->isa('Bio::DB::GFF::Typename')) { $primary_tag = $type->method; $source_tag = $type->source; } else { ($primary_tag,$source_tag) = split ':',$type,2; } if ($source_tag) { push @matches,"lower(tl.tag)=lower(?)"; push @args,"$primary_tag:$source_tag"; } else { push @matches,"tl.tag ILIKE ?"; push @args,"$primary_tag:%"; } } my $matches = join ' OR ',@matches; my $where = <_meta_table; if (defined $value && $self->writeable) { my $querydel = "DELETE FROM $meta WHERE name = ?"; my $query = "INSERT INTO $meta (name,value) VALUES (?,?)"; my $sthdel = $self->_prepare($querydel); my $sth = $self->_prepare($query); $sthdel->execute($variable_name); $sth->execute($variable_name,$value) or $self->throw($sth->errstr); $sth->finish; $self->{settings_cache}{$variable_name} = $value; } else { return $self->{settings_cache}{$variable_name} if exists $self->{settings_cache}{$variable_name}; my $query = "SELECT value FROM $meta as m WHERE m.name=?"; my $sth = $self->_prepare($query); # $sth->execute($variable_name) or $self->throw($sth->errstr); unless ($sth->execute($variable_name)) { my $errstr = $sth->errstr; $sth = $self->_prepare("SHOW search_path"); $sth->execute(); $errstr .= "With search_path " . $sth->fetchrow_arrayref->[0] . "\n"; $self->throw($errstr); } my ($value) = $sth->fetchrow_array; $sth->finish; return $self->{settings_cache}{$variable_name} = $value; } } # overridden because of use of REPLACE in mysql adapter ### # Replace Bio::SeqFeatureI into database. # sub replace { my $self = shift; my $object = shift; my $index_flag = shift || undef; # ?? shouldn't need to do this # $self->_load_class($object); my $id = $object->primary_id; my $features = $self->_feature_table; my $query = "INSERT INTO $features (id,object,indexed,seqid,start,\"end\",strand,tier,bin,typeid) VALUES (?,?,?,?,?,?,?,?,?,?)"; my $query_noid = "INSERT INTO $features (object,indexed,seqid,start,\"end\",strand,tier,bin,typeid) VALUES (?,?,?,?,?,?,?,?,?)"; my $querydel = "DELETE FROM $features WHERE id = ?"; my $sthdel = $self->_prepare($querydel); my $sth = $self->_prepare($query); my $sth_noid = $self->_prepare($query_noid); my @location = $index_flag ? $self->_get_location_and_bin($object) : (undef)x6; my $primary_tag = $object->primary_tag; my $source_tag = $object->source_tag || ''; $primary_tag .= ":$source_tag"; my $typeid = $self->_typeid($primary_tag,1); if ($id) { $sthdel->execute($id); $sth->execute($id,encode_base64($self->freeze($object), ''),$index_flag||0,@location,$typeid) or $self->throw($sth->errstr); } else { $sth_noid->execute(encode_base64($self->freeze($object), ''),$index_flag||0,@location,$typeid) or $self->throw($sth->errstr); } my $dbh = $self->dbh; $object->primary_id($dbh->last_insert_id(undef, undef, undef, undef, {sequence=>$features."_id_seq"})) unless defined $id; $self->flag_for_indexing($dbh->last_insert_id(undef, undef, undef, undef, {sequence=>$features."_id_seq"})) if $self->{bulk_update_in_progress}; } =head2 types Title : types Usage : @type_list = $db->types Function: Get all the types in the database Returns : array of Bio::DB::GFF::Typename objects Args : none Status : public =cut # overridden because "offset" is reserved in postgres ### # Insert a bit of DNA or protein into the database # sub _insert_sequence { my $self = shift; my ($seqid,$seq,$offset) = @_; my $id = $self->_locationid($seqid); my $seqtable = $self->_sequence_table; my $sthdel = $self->_prepare("DELETE FROM $seqtable WHERE id = ? AND \"offset\" = ?"); my $sth = $self->_prepare(<execute($id,$offset); $sth->execute($id,$offset,$seq) or $self->throw($sth->errstr); } # overridden because of mysql adapter's use of REPLACE ### # This subroutine flags the given primary ID for later reindexing # sub flag_for_indexing { my $self = shift; my $id = shift; my $needs_updating = $self->_update_table; my $querydel = "DELETE FROM $needs_updating WHERE id = ?"; my $query = "INSERT INTO $needs_updating VALUES (?)"; my $sthdel = $self->_prepare($querydel); my $sth = $self->_prepare($query); $sthdel->execute($id); $sth->execute($id) or $self->throw($self->dbh->errstr); } # overridden because of the different ways that mysql and postgres # handle id sequences sub _genericid { my $self = shift; my ($table,$namefield,$name,$add_if_missing) = @_; my $qualified_table = $self->_qualify($table); my $sth = $self->_prepare(<execute($name) or die $sth->errstr; my ($id) = $sth->fetchrow_array; $sth->finish; return $id if defined $id; return unless $add_if_missing; $sth = $self->_prepare(<execute($name) or die $sth->errstr; my $dbh = $self->dbh; return $dbh->last_insert_id(undef, undef, undef, undef, {sequence=>$qualified_table."_id_seq"}); } # overridden because of differences in binding between mysql and postgres adapters # given a statement handler that is expected to return rows of (id,object) # unthaw each object and return a list of 'em sub _sth2objs { my $self = shift; my $sth = shift; my @result; my ($id, $o); $sth->bind_col(1, \$id); $sth->bind_col(2, \$o, { pg_type => PG_BYTEA}); #while (my ($id,$o) = $sth->fetchrow_array) { while ($sth->fetch) { my $obj = $self->thaw(decode_base64($o) ,$id); push @result,$obj; } $sth->finish; return @result; } # given a statement handler that is expected to return rows of (id,object) # unthaw each object and return a list of 'em sub _sth2obj { my $self = shift; my $sth = shift; my ($id,$o) = $sth->fetchrow_array; return unless $o; my $obj = $self->thaw(decode_base64($o) ,$id); $obj; } #################################################################################################### # SQL Fragment generators #################################################################################################### # overridden because of base64 encoding needed here ### # special-purpose store for bulk loading - write to a file rather than to the db # sub _dump_store { my $self = shift; my $indexed = shift; my $count = 0; my $store_fh = $self->dump_filehandle('feature'); my $dbh = $self->dbh; my $autoindex = $self->autoindex; for my $obj (@_) { my $id = $self->next_id; my ($seqid,$start,$end,$strand,$tier,$bin) = $indexed ? $self->_get_location_and_bin($obj) : (undef)x6; my $primary_tag = $obj->primary_tag; my $source_tag = $obj->source_tag || ''; $primary_tag .= ":$source_tag"; my $typeid = $self->_typeid($primary_tag,1); my $frozen_object = encode_base64($self->freeze($obj), ''); # TODO: Fix this, why does frozen object start with quote but not end with one print $store_fh join("\t",$id,$typeid,$seqid,$start,$end,$strand,$tier,$bin,$indexed,$frozen_object),"\n"; $obj->primary_id($id); $self->_update_indexes($obj) if $indexed && $autoindex; $count++; } # remember whether we are have ever stored a non-indexed feature unless ($indexed or $self->{indexed_flag}++) { $self->subfeatures_are_indexed(0); } $count; } sub _enable_keys { } # nullop sub _disable_keys { } # nullop sub _add_interval_stats_table { my $self = shift; my $tables = $self->table_definitions; my $interval_stats = $self->_interval_stats_table; ##check to see if it exists yet; if it does, just return because ##there is a drop from in the next step my $dbh = $self->dbh; my @table_exists = $dbh->selectrow_array("SELECT * FROM pg_tables WHERE tablename = '$interval_stats' AND schemaname = '".$self->namespace."'"); if (!scalar(@table_exists)) { my $query = "CREATE TABLE $interval_stats $tables->{interval_stats}"; $dbh->do($query) or $self->throw($dbh->errstr); } } sub _fetch_indexed_features_sql { my $self = shift; my $features = $self->_feature_table; return <new(-adaptor => 'DBI::SQLite', -dsn => '/path/to/database.db'); # get a feature from somewhere my $feature = Bio::SeqFeature::Generic->new(...); # store it $db->store($feature) or die "Couldn't store!"; # primary ID of the feature is changed to indicate its primary ID # in the database... my $id = $feature->primary_id; # get the feature back out my $f = $db->fetch($id); # change the feature and update it $f->start(100); $db->update($f) or die "Couldn't update!"; # searching... # ...by id my @features = $db->fetch_many(@list_of_ids); # ...by name @features = $db->get_features_by_name('ZK909'); # ...by alias @features = $db->get_features_by_alias('sma-3'); # ...by type @features = $db->get_features_by_name('gene'); # ...by location @features = $db->get_features_by_location(-seq_id=>'Chr1',-start=>4000,-end=>600000); # ...by attribute @features = $db->get_features_by_attribute({description => 'protein kinase'}) # ...by the GFF "Note" field @result_list = $db->search_notes('kinase'); # ...by arbitrary combinations of selectors @features = $db->features(-name => $name, -type => $types, -seq_id => $seqid, -start => $start, -end => $end, -attributes => $attributes); # ...using an iterator my $iterator = $db->get_seq_stream(-name => $name, -type => $types, -seq_id => $seqid, -start => $start, -end => $end, -attributes => $attributes); while (my $feature = $iterator->next_seq) { # do something with the feature } # ...limiting the search to a particular region my $segment = $db->segment('Chr1',5000=>6000); my @features = $segment->features(-type=>['mRNA','match']); # getting & storing sequence information # Warning: this returns a string, and not a PrimarySeq object $db->insert_sequence('Chr1','GATCCCCCGGGATTCCAAAA...'); my $sequence = $db->fetch_sequence('Chr1',5000=>6000); # what feature types are defined in the database? my @types = $db->types; # create a new feature in the database my $feature = $db->new_feature(-primary_tag => 'mRNA', -seq_id => 'chr3', -start => 10000, -end => 11000); =head1 DESCRIPTION Bio::DB::SeqFeature::Store::SQLite is the SQLite adaptor for Bio::DB::SeqFeature::Store. You will not create it directly, but instead use Bio::DB::SeqFeature::Store-Enew() to do so. See L for complete usage instructions. =head2 Using the SQLite adaptor To establish a connection to the database, call Bio::DB::SeqFeature::Store-Enew(-adaptor=E'DBI::SQLite',@more_args). The additional arguments are as follows: Argument name Description ------------- ----------- -dsn The path to the SQLite database file. -namespace A prefix to attach to each table. This allows you to have several virtual databases in the same physical database. -temp Boolean flag. If true, a temporary database will be created and destroyed as soon as the Store object goes out of scope. (synonym -temporary) -autoindex Boolean flag. If true, features in the database will be reindexed every time they change. This is the default. -fts Boolean flag. If true, when the -create flag is true, the attribute table will be created and indexed index for full-text search using the most recent FTS extension supported by DBD::SQLite. -tmpdir Directory in which to place temporary files during "fast" loading. Defaults to File::Spec->tmpdir(). (synonyms -dump_dir, -dumpdir, -tmp) -dbi_options A hashref to pass to DBI->connect's 4th argument, the "attributes." (synonyms -options, -dbi_attr) -write Pass true to open database for writing or updating. If successful, a new instance of Bio::DB::SeqFeature::Store::DBI::SQLite will be returned. In addition to the standard methods supported by all well-behaved Bio::DB::SeqFeature::Store databases, several following adaptor-specific methods are provided. These are described in the next sections. =cut use strict; use base 'Bio::DB::SeqFeature::Store::DBI::mysql'; use Bio::DB::SeqFeature::Store::DBI::Iterator; use DBD::SQLite; use DBI qw(:sql_types); use Memoize; use Cwd qw(abs_path getcwd); use Bio::DB::GFF::Util::Rearrange 'rearrange'; use Bio::SeqFeature::Lite; use File::Spec; use constant DEBUG=>0; use constant EXPERIMENTAL_COVERAGE=>1; # Using same limits as MySQL adaptor so I don't have to make something up. use constant MAX_INT => 2_147_483_647; use constant MIN_INT => -2_147_483_648; use constant SUMMARY_BIN_SIZE => 1000; # we checkpoint coverage this often, about 20 meg overhead per feature type on hg use constant USE_SPATIAL=>0; # The binning scheme places each feature into a bin. # Bins are variably sized as powers of two. For example, # there are 585 bins of size 2**17 (131072 bases) my (@BINS,%BINS); { @BINS = map {2**$_} (17, 20, 23, 26, 29); # TO DO: experiment with different bin sizes my $start=0; for my $b (sort {$b<=>$a} @BINS) { $BINS{$b} = $start; $start += $BINS[-1]/$b; } } # my %BINS = ( # 2**11 => 37449, # 2**14 => 4681, # 2**17 => 585, # 2**20 => 73, # 2**23 => 9, # 2**26 => 1, # 2**29 => 0 # ); # my @BINS = sort {$a<=>$b} keys %BINS; sub calculate_bin { my $self = shift; my ($start,$end) = @_; my $len = $end - $start; for my $bin (@BINS) { next if $len > $bin; # possibly fits here my $binstart = int $start/$bin; my $binend = int $end/$bin; return $binstart+$BINS{$bin} if $binstart == $binend; } die "unreasonable coordinates ",$start+1,"..$end"; } sub search_bins { my $self = shift; my ($start,$end) = @_; my @results; for my $bin (@BINS) { my $binstart = int $start/$bin; my $binend = int $end/$bin; push @results,$binstart+$BINS{$bin}..$binend+$BINS{$bin}; } return @results; } ### # object initialization # sub init { my $self = shift; my ($dsn, $is_temporary, $autoindex, $namespace, $dump_dir, $user, $pass, $dbi_options, $writeable, $fts, $create, ) = rearrange(['DSN', ['TEMP','TEMPORARY'], 'AUTOINDEX', 'NAMESPACE', ['DUMP_DIR','DUMPDIR','TMP','TMPDIR'], 'USER', ['PASS','PASSWD','PASSWORD'], ['OPTIONS','DBI_OPTIONS','DBI_ATTR'], ['WRITE','WRITEABLE'], 'FTS', 'CREATE', ],@_); $dbi_options ||= {}; $writeable = 1 if $is_temporary or $dump_dir; $dsn or $self->throw("Usage: ".__PACKAGE__."->init(-dsn => \$dbh || \$dsn)"); my $dbh; if (ref $dsn) { $dbh = $dsn; } else { $dsn = "dbi:SQLite:$dsn" unless $dsn =~ /^dbi:/; $dbh = DBI->connect($dsn,$user,$pass,$dbi_options) or $self->throw($DBI::errstr); $dbh->do("PRAGMA synchronous = OFF;"); # makes writes much faster $dbh->do("PRAGMA temp_store = MEMORY;"); # less disk I/O; some speedup $dbh->do("PRAGMA cache_size = 20000;"); # less disk I/O; some speedup # Keep track of database file location my $cwd = getcwd; my ($db_file) = ($dsn =~ m/(?:db(?:name)?|database)=(.+)$/); $self->{dbh_file} = "$cwd/$db_file"; } $self->{dbh} = $dbh; $self->{fts} = $fts; $self->{is_temp} = $is_temporary; $self->{namespace} = $namespace; $self->{writeable} = $writeable; $self->default_settings; $self->autoindex($autoindex) if defined $autoindex; $self->dumpdir($dump_dir) if $dump_dir; if ($self->is_temp) { $self->init_tmp_database(); } elsif ($create) { $self->init_database('erase'); } } sub table_definitions { my $self = shift; my $defs = { feature => < < < < < < < < <{'fts'}) { delete($defs->{attribute}); } unless ($self->_has_spatial_index) { $defs->{feature_location} = <{interval_stats} = <_create_spatial_index; $self->_create_attribute_fts; $self->SUPER::_init_database(@_); } # FIXME: ensure this works with _create_attribute_fts... sub init_tmp_database { my $self = shift; my $erase = shift; $self->_create_spatial_index; $self->_create_attribute_fts; $self->SUPER::init_tmp_database(@_); } sub _create_spatial_index{ my $self = shift; my $dbh = $self->dbh; local $dbh->{PrintError} = 0; $dbh->do("DROP TABLE IF EXISTS feature_index"); # spatial index if (USE_SPATIAL) { $dbh->do("CREATE VIRTUAL TABLE feature_index USING RTREE(id,seqid,bin,start,end)"); } } sub _create_attribute_fts{ my $self = shift; my $dbh = $self->dbh; if ($self->{'fts'}) { my @fts_versions; for (@fts_versions = grep(/^ENABLE_FTS[0-9]+$/, DBD::SQLite::compile_options)) { s/ENABLE_// } # use the latest supported FTS version. # DBD::SQLite::compile_options appears to be sorted # alphabetically, so this should work through version FTS9. die 'fts not supported by this version of DBD::SQLite' if (!@fts_versions); $dbh->do("DROP TABLE IF EXISTS attribute"); $dbh->do("CREATE VIRTUAL TABLE " . $self->_attribute_table . " USING " . $fts_versions[-1] . "(id, attribute_id, attribute_value)"); } } ### # return 1 if an existing attribute table in the connected database is an FTS # table, else 0 # sub _has_fts { my $self = shift; if (!defined($self->{'has_fts'})) { # If the attribute table is a virtual table, assume it is an FTS # table. Per http://www.sqlite.org/fileformat2.html: # For (sqlite_master) rows that define views, triggers, and virtual # tables, the rootpage column is 0 or NULL. ($self->{'has_fts'}) = $self->dbh->selectrow_array("select count(*) from sqlite_master where type = 'table' and name = '" . $self->_attribute_table . "' and (rootpage = 0 or rootpage is null);"); } return $self->{'has_fts'}; } sub _has_spatial_index { my $self = shift; return $self->{'_has_spatial_index'} if exists $self->{'_has_spatial_index'}; my $dbh = $self->dbh; my ($count) = $dbh->selectrow_array("select count(*) from sqlite_master where name='feature_index'"); return $self->{'_has_spatial_index'} = $count; } sub _finish_bulk_update { my $self = shift; my $dbh = $self->dbh; my $dir = $self->{dumpdir} || '.'; $self->begin_work; # making this a transaction greatly improves performance for my $table ('feature', $self->index_tables) { my $fh = $self->dump_filehandle($table); my $path = $self->dump_path($table); $fh->close; open $fh, '<', $path or $self->throw("Could not read file '$path': $!"); my $qualified_table = $self->_qualify($table); my $sth; if ($table =~ /feature$/) { $sth = $dbh->prepare("REPLACE INTO $qualified_table VALUES (?,?,?,?,?)"); while (<$fh>) { chomp(); my ($id,$typeid,$strand,$indexed,$obj) = split(/\t/); $sth->bind_param(1, $id); $sth->bind_param(2, $typeid); $sth->bind_param(3, $strand); $sth->bind_param(4, $indexed); $sth->bind_param(5, pack('H*',$obj), {TYPE => SQL_BLOB}); $sth->execute(); } } else { my $feature_index = $self->_feature_index_table; if ($table =~ /parent2child$/) { $sth = $dbh->prepare("REPLACE INTO $qualified_table VALUES (?,?)"); } elsif ($table =~ /$feature_index$/) { $sth = $dbh->prepare( $self->_has_spatial_index ?"REPLACE INTO $qualified_table VALUES (?,?,?,?,?)" :"REPLACE INTO $qualified_table (id,seqid,bin,start,end) VALUES (?,?,?,?,?)" ); } else { # attribute or name $sth = $dbh->prepare("REPLACE INTO $qualified_table VALUES (?,?,?)"); } while (<$fh>) { chomp(); $sth->execute(split(/\t/)); } } $fh->close(); unlink $path; } $self->commit; # commit the transaction delete $self->{bulk_update_in_progress}; delete $self->{filehandles}; } sub index_tables { my $self = shift; my @t = $self->SUPER::index_tables; return (@t,$self->_feature_index_table); } sub _enable_keys { } # nullop sub _disable_keys { } # nullop sub _fetch_indexed_features_sql { my $self = shift; my $location_table = $self->_qualify('feature_location'); my $feature_table = $self->_qualify('feature'); return < $end my $reversed; if (defined $start && defined $end && $start > $end) { $reversed++; ($start,$end) = ($end,$start); } $start-- if defined $start; $end-- if defined $end; my $offset1 = $self->_offset_boundary($seqid,$start || 'left'); my $offset2 = $self->_offset_boundary($seqid,$end || 'right'); my $sequence_table = $self->_sequence_table; my $locationlist_table = $self->_locationlist_table; # CROSS JOIN gives a hint to the SQLite query optimizer -- mucho speedup! my $sth = $self->_prepare(<= ? AND offset <= ? ORDER BY offset END my $seq = ''; $sth->execute($seqid,$offset1,$offset2) or $self->throw($sth->errstr); while (my($frag,$offset) = $sth->fetchrow_array) { substr($frag,0,$start-$offset) = '' if defined $start && $start > $offset; $seq .= $frag; } substr($seq,$end-$start+1) = '' if defined $end && $end-$start+1 < length($seq); if ($reversed) { $seq = reverse $seq; $seq =~ tr/gatcGATC/ctagCTAG/; } $sth->finish; $seq; } sub _offset_boundary { my $self = shift; my ($seqid,$position) = @_; my $sequence_table = $self->_sequence_table; my $locationlist_table = $self->_locationlist_table; my $sql; # use "CROSS JOIN" to give a hint to the SQLite query optimizer. $sql = $position eq 'left' ? "SELECT min(offset) FROM $locationlist_table as ll CROSS JOIN $sequence_table as s ON ll.id=s.id WHERE ll.seqname=?" :$position eq 'right' ? "SELECT max(offset) FROM $locationlist_table as ll CROSS JOIN $sequence_table as s ON ll.id=s.id WHERE ll.seqname=?" :"SELECT max(offset) FROM $locationlist_table as ll CROSS JOIN $sequence_table as s ON ll.id=s.id WHERE ll.seqname=? AND offset<=?"; my $sth = $self->_prepare($sql); my @args = $position =~ /^-?\d+$/ ? ($seqid,$position) : ($seqid); $sth->execute(@args) or $self->throw($sth->errstr); my $boundary = $sth->fetchall_arrayref->[0][0]; $sth->finish; return $boundary; } ### # Efficiently fetch a series of IDs from the database # Can pass an array or an array ref # sub _fetch_many { my $self = shift; @_ or $self->throw('usage: fetch_many($id1,$id2,$id3...)'); my $ids = join ',',map {ref($_) ? @$_ : $_} @_ or return; my $features = $self->_feature_table; my $sth = $self->_prepare(<execute() or $self->throw($sth->errstr); return $self->_sth2objs($sth); } sub _features { my $self = shift; my ($seq_id,$start,$end,$strand, $name,$class,$allow_aliases, $types, $attributes, $range_type, $fromtable, $iterator, $sources ) = rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'],'STRAND', 'NAME','CLASS','ALIASES', ['TYPES','TYPE','PRIMARY_TAG'], ['ATTRIBUTES','ATTRIBUTE'], 'RANGE_TYPE', 'FROM_TABLE', 'ITERATOR', ['SOURCE','SOURCES'] ],@_); my (@from,@where,@args,@group); $range_type ||= 'overlaps'; my $feature_table = $self->_feature_table; @from = "$feature_table as f"; if (defined $name) { # hacky backward compatibility workaround undef $class if $class && $class eq 'Sequence'; $name = "$class:$name" if defined $class && length $class > 0; # last argument is the join field my ($from,$where,$group,@a) = $self->_name_sql($name,$allow_aliases,'f.id'); push @from,$from if $from; push @where,$where if $where; push @group,$group if $group; push @args,@a; } if (defined $seq_id) { # last argument is the name of the features table my ($from,$where,$group,@a) = $self->_location_sql($seq_id,$start,$end,$range_type,$strand,'f'); push @from,$from if $from; push @where,$where if $where; push @group,$group if $group; push @args,@a; } if (defined($sources)) { my @sources = ref($sources) eq 'ARRAY' ? @{$sources} : ($sources); if (defined($types)) { my @types = ref($types) eq 'ARRAY' ? @{$types} : ($types); my @final_types; foreach my $type (@types) { # *** not sure what to do if user supplies both -source and -type # where the type includes a source! if ($type =~ /:/) { push(@final_types, $type); } else { foreach my $source (@sources) { push(@final_types, $type.':'.$source); } } } $types = \@final_types; } else { $types = [map { ':'.$_ } @sources]; } } if (defined($types)) { # last argument is the name of the features table my ($from,$where,$group,@a) = $self->_types_sql($types,'f'); push @from,$from if $from; push @where,$where if $where; push @group,$group if $group; push @args,@a; } if (defined $attributes) { # last argument is the join field my ($from,$where,$group,@a) = $self->_attributes_sql($attributes,'f.id'); push @from,$from if $from; push @where,$where if $where; push @group,$group if $group; push @args,@a; } if (defined $fromtable) { # last argument is the join field my ($from,$where,$group,@a) = $self->_from_table_sql($fromtable,'f.id'); push @from,$from if $from; push @where,$where if $where; push @group,$group if $group; push @args,@a; } # if no other criteria are specified, then # only fetch indexed (i.e. top level objects) @where = '"indexed"=1' unless @where; my $from = join ', ',@from; my $where = join ' AND ',map {"($_)"} @where; my $group = join ', ',@group; $group = "GROUP BY $group" if @group; my $query = <_print_query($query,@args) if DEBUG || $self->debug; my $sth = $self->_prepare($query); $sth->execute(@args) or $self->throw($sth->errstr); return $iterator ? Bio::DB::SeqFeature::Store::DBI::Iterator->new($sth,$self) : $self->_sth2objs($sth); } sub _make_attribute_group { my $self = shift; my ($table_name,$attributes) = @_; my $key_count = keys %$attributes or return; my $count = $key_count-1; return "f.id HAVING count(f.id)>$count"; } sub _location_sql { my $self = shift; my ($seq_id,$start,$end,$range_type,$strand,$location) = @_; # the additional join on the location_list table badly impacts performance # so we build a copy of the table in memory my $seqid = $self->_locationid_nocreate($seq_id) || 0; # zero is an invalid primary ID, so will return empty my $feature_index = $self->_feature_index_table; my $from = "$feature_index as fi"; my ($bin_where,@bin_args); if (defined $start && defined $end && !$self->_has_spatial_index) { my @bins = $self->search_bins($start,$end); $bin_where = ' AND bin in ('.join(',',@bins).')'; } $start = MIN_INT unless defined $start; $end = MAX_INT unless defined $end; my ($range,@range_args); if ($range_type eq 'overlaps') { $range = "fi.end>=? AND fi.start<=?".$bin_where; @range_args = ($start,$end,@bin_args); } elsif ($range_type eq 'contains') { $range = "fi.start>=? AND fi.end<=?".$bin_where; @range_args = ($start,$end,@bin_args); } elsif ($range_type eq 'contained_in') { $range = "fi.start<=? AND fi.end>=?"; @range_args = ($start,$end); } else { $self->throw("range_type must be one of 'overlaps', 'contains' or 'contained_in'"); } if (defined $strand) { $range .= " AND strand=?"; push @range_args,$strand; } my $where = <_has_spatial_index ? $self->_qualify('feature_index') : $self->_qualify('feature_location') } # Do a case-insensitive search a la the PostgreSQL adaptor sub _name_sql { my $self = shift; my ($name,$allow_aliases,$join) = @_; my $name_table = $self->_name_table; my $from = "$name_table as n"; my ($match,$string) = $self->_match_sql($name); my $where = "n.id=$join AND n.name $match COLLATE NOCASE"; $where .= " AND n.display_name>0" unless $allow_aliases; return ($from,$where,'',$string); } sub _search_attributes { my $self = shift; my ($search_string,$attribute_names,$limit) = @_; my @words = map {quotemeta($_)} split /\s+/,$search_string; my $name_table = $self->_name_table; my $attribute_table = $self->_attribute_table; my $attributelist_table = $self->_attributelist_table; my $type_table = $self->_type_table; my $typelist_table = $self->_typelist_table; my $has_fts = $self->_has_fts; my @tags = @$attribute_names; my $tag_sql = join ' OR ',("al.tag=?") x @tags; my $perl_regexp = join '|',@words; my $sql_regexp; my @wild_card_words; if ($has_fts) { $sql_regexp = "a.attribute_value MATCH ?"; @wild_card_words = join(' OR ', @words); } else { $sql_regexp = join ' OR ',("a.attribute_value LIKE ?") x @words; @wild_card_words = map { "%$_%" } @words; } # CROSS JOIN hinders performance with FTS attribute table for DBD::SQLite 1.42 my $sql = <_print_query($sql,@tags,@wild_card_words) if DEBUG || $self->debug; my $sth = $self->_prepare($sql); $sth->execute(@tags, @wild_card_words) or $self->throw($sth->errstr); my @results; while (my($name,$value,$type,$id) = $sth->fetchrow_array) { my (@hits) = $value =~ /$perl_regexp/ig; my @words_in_row = split /\b/,$value; my $score = int(@hits*100/@words/@words_in_row); push @results,[$name,$value,$score,$type,$id]; } $sth->finish; @results = sort {$b->[2]<=>$a->[2]} @results; return @results; } sub _match_sql { my $self = shift; my $name = shift; my ($match,$string); if ($name =~ /(?:^|[^\\])[*?]/) { $name =~ s/(^|[^\\])([%_])/$1\\$2/g; $name =~ s/(^|[^\\])\*/$1%/g; $name =~ s/(^|[^\\])\?/$1_/g; $match = "LIKE ?"; $string = $name; } else { $match = "= ? COLLATE NOCASE"; $string = $name; } return ($match,$string); } sub _attributes_sql { my $self = shift; my ($attributes,$join) = @_; my ($wf,@bind_args) = $self->_make_attribute_where('a','al',$attributes); my ($group_by,@group_args)= $self->_make_attribute_group('a',$attributes); my $attribute_table = $self->_attribute_table; my $attributelist_table = $self->_attributelist_table; my $from = "$attribute_table AS a" . ($self->_has_fts ? '' : " INDEXED BY index_attribute_id") . ", $attributelist_table AS al"; my $a_al_join = $self->_has_fts ? 'a.attribute_id MATCH al.id' : 'a.attribute_id=al.id'; my $where = <_typelist_table; my $from = "$typelist AS tl"; my (@matches,@args); for my $type (@types) { if (ref $type && $type->isa('Bio::DB::GFF::Typename')) { $primary_tag = $type->method; $source_tag = $type->source; } else { ($primary_tag,$source_tag) = split ':',$type,2; } if (length $source_tag) { push @matches,"tl.tag=? COLLATE NOCASE"; push @args,"$primary_tag:$source_tag"; } else { push @matches,"tl.tag LIKE ?"; push @args,"$primary_tag:%"; } } my $matches = join ' OR ',@matches; my $where = <dbh->do("ANALYZE $_") foreach $self->index_tables; } ### # Replace Bio::SeqFeatureI into database. # sub replace { my $self = shift; my $object = shift; my $index_flag = shift || undef; # ?? shouldn't need to do this # $self->_load_class($object); my $id = $object->primary_id; my $features = $self->_feature_table; my $sth = $self->_prepare(<_get_location_and_bin($object) : (undef)x6; my $primary_tag = $object->primary_tag; my $source_tag = $object->source_tag || ''; $primary_tag .= ":$source_tag"; my $typeid = $self->_typeid($primary_tag,1); my $frozen = $self->no_blobs() ? 0 : $self->freeze($object); $sth->bind_param(1, $id); $sth->bind_param(2, $frozen, {TYPE => SQL_BLOB}); $sth->bind_param(3, $index_flag||0); $sth->bind_param(4, $strand); $sth->bind_param(5, $typeid); $sth->execute() or $self->throw($sth->errstr); my $dbh = $self->dbh; $object->primary_id($dbh->func('last_insert_rowid')) unless defined $id; $self->flag_for_indexing($dbh->func('last_insert_rowid')) if $self->{bulk_update_in_progress}; } # doesn't work with this schema, since we have to update name and attribute # tables which need object ids, which we can only know by replacing feats in # the feature table one by one sub bulk_replace { my $self = shift; my $index_flag = shift || undef; my @objects = @_; my $features = $self->_feature_table; my @insert_values; foreach my $object (@objects) { my $id = $object->primary_id; my (undef,undef,undef,$strand) = $index_flag ? $self->_get_location_and_bin($object) : (undef)x4; my $primary_tag = $object->primary_tag; my $source_tag = $object->source_tag || ''; $primary_tag .= ":$source_tag"; my $typeid = $self->_typeid($primary_tag,1); push(@insert_values, ($id,0,$index_flag||0,$strand,$typeid)); } my @value_blocks; for (1..@objects) { push(@value_blocks, '(?,?,?,?,?)'); } my $value_blocks = join(',', @value_blocks); my $sql = qq{REPLACE INTO $features (id,object,"indexed",strand,typeid) VALUES $value_blocks}; my $sth = $self->_prepare($sql); $sth->execute(@insert_values) or $self->throw($sth->errstr); } sub _get_location_and_bin { my $self = shift; my $obj = shift; my $seqid = $self->_locationid($obj->seq_id||''); my $start = $obj->start; my $end = $obj->end; my $strand = $obj->strand; return ($seqid,$start,$end,$strand,$self->calculate_bin($start,$end)); } ### # Insert one Bio::SeqFeatureI into database. primary_id must be undef # sub insert { my $self = shift; my $object = shift; my $index_flag = shift || 0; $self->_load_class($object); defined $object->primary_id and $self->throw("$object already has a primary id"); my $features = $self->_feature_table; my $sth = $self->_prepare(<execute(undef,$self->freeze($object),$index_flag) or $self->throw($sth->errstr); my $dbh = $self->dbh; $object->primary_id($dbh->func('last_insert_rowid')); $self->flag_for_indexing($dbh->func('last_insert_rowid')) if $self->{bulk_update_in_progress}; } =head2 toplevel_types Title : toplevel_types Usage : @type_list = $db->toplevel_types Function: Get the toplevel types in the database Returns : array of Bio::DB::GFF::Typename objects Args : none Status : public This is similar to types() but only returns the types of INDEXED (toplevel) features. =cut sub toplevel_types { my $self = shift; eval "require Bio::DB::GFF::Typename" unless Bio::DB::GFF::Typename->can('new'); my $typelist_table = $self->_typelist_table; my $feature_table = $self->_feature_table; my $sql = <_print_query($sql) if DEBUG || $self->debug; my $sth = $self->_prepare($sql); $sth->execute() or $self->throw($sth->errstr); my @results; while (my($tag) = $sth->fetchrow_array) { push @results,Bio::DB::GFF::Typename->new($tag); } $sth->finish; return @results; } sub _genericid { my $self = shift; my ($table,$namefield,$name,$add_if_missing) = @_; my $qualified_table = $self->_qualify($table); my $sth = $self->_prepare(<execute($name) or die $sth->errstr; my ($id) = $sth->fetchrow_array; $sth->finish; return $id if defined $id; return unless $add_if_missing; $sth = $self->_prepare(<execute($name) or die $sth->errstr; my $dbh = $self->dbh; return $dbh->func('last_insert_rowid'); } ### # special-purpose store for bulk loading - write to a file rather than to the db # sub _dump_store { my $self = shift; my $indexed = shift; my $count = 0; my $store_fh = $self->dump_filehandle('feature'); my $dbh = $self->dbh; my $autoindex = $self->autoindex; for my $obj (@_) { my $id = $self->next_id; my ($seqid,$start,$end,$strand) = $indexed ? $self->_get_location_and_bin($obj) : (undef)x4; my $primary_tag = $obj->primary_tag; my $source_tag = $obj->source_tag || ''; $primary_tag .= ":$source_tag"; my $typeid = $self->_typeid($primary_tag,1); # Encode BLOB in hex so we can more easily import it into SQLite print $store_fh join("\t",$id,$typeid,$strand,$indexed, unpack('H*', $self->freeze($obj))),"\n"; $obj->primary_id($id); $self->_update_indexes($obj) if $indexed && $autoindex; $count++; } # remember whether we are have ever stored a non-indexed feature unless ($indexed or $self->{indexed_flag}++) { $self->subfeatures_are_indexed(0); } $count; } sub _dump_update_name_index { my $self = shift; my ($obj,$id) = @_; my $fh = $self->dump_filehandle('name'); my $dbh = $self->dbh; my ($names,$aliases) = $self->feature_names($obj); # unlike DBI::mysql, don't quote, as quotes will be quoted when loaded print $fh join("\t",$id,$_,1),"\n" foreach @$names; print $fh join("\t",$id,$_,0),"\n" foreach @$aliases; } sub _update_name_index { my $self = shift; my ($obj,$id) = @_; my $name = $self->_name_table; my $primary_id = $obj->primary_id; $self->_delete_index($name,$id); my ($names,$aliases) = $self->feature_names($obj); my $sth = $self->_prepare("INSERT INTO $name (id,name,display_name) VALUES (?,?,?)"); $sth->execute($id,$_,1) or $self->throw($sth->errstr) foreach @$names; $sth->execute($id,$_,0) or $self->throw($sth->errstr) foreach @$aliases; $sth->finish; } sub _dump_update_attribute_index { my $self = shift; my ($obj,$id) = @_; my $fh = $self->dump_filehandle('attribute'); my $dbh = $self->dbh; for my $tag ($obj->all_tags) { my $tagid = $self->_attributeid($tag); for my $value ($obj->each_tag_value($tag)) { # unlike DBI::mysql, don't quote, as quotes will be quoted when loaded print $fh join("\t",$id,$tagid,$value),"\n"; } } } sub _update_indexes { my $self = shift; my $obj = shift; defined (my $id = $obj->primary_id) or return; $self->SUPER::_update_indexes($obj); if ($self->{bulk_update_in_progress}) { $self->_dump_update_location_index($obj,$id); } else { $self->_update_location_index($obj,$id); } } sub _update_location_index { my $self = shift; my ($obj,$id) = @_; my ($seqid,$start,$end,$strand,$bin) = $self->_get_location_and_bin($obj); my $table = $self->_feature_index_table; $self->_delete_index($table,$id); my ($sql,@args); if ($self->_has_spatial_index) { $sql = "INSERT INTO $table (id,seqid,bin,start,end) values (?,?,?,?,?)"; @args = ($id,$seqid,$bin,$start,$end); } else { $sql = "INSERT INTO $table (id,seqid,bin,start,end) values (?,?,?,?,?)"; @args = ($id,$seqid,$bin,$start,$end); } my $sth = $self->_prepare($sql); $sth->execute(@args); $sth->finish; } sub _dump_update_location_index { my $self = shift; my ($obj,$id) = @_; my $table = $self->_feature_index_table; my $fh = $self->dump_filehandle($table); my $dbh = $self->dbh; my ($seqid,$start,$end,$strand,$bin) = $self->_get_location_and_bin($obj); my @args = $self->_has_spatial_index ? ($id,$seqid,$bin,$start,$end) : ($id,$seqid,$bin,$start,$end); print $fh join("\t",@args),"\n"; } sub DESTROY { my $self = shift; # Remove filehandles, so temporal files can be properly deleted if (%DBI::installed_drh) { DBI->disconnect_all; %DBI::installed_drh = (); } undef $self->{dbh}; } 1; =head1 AUTHOR Nathan Weeks - Nathan.Weeks@ars.usda.gov Copyright (c) 2009 Nathan Weeks Modified 2010 to support cumulative statistics by Lincoln Stein . This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See the Bioperl license for more details. =cut BioPerl-1.007002/Bio/DB/SeqFeature/Store/DBI/mysql.pm000444000766000024 16675613155576320 22037 0ustar00cjfieldsstaff000000000000package Bio::DB::SeqFeature::Store::DBI::mysql; =head1 NAME Bio::DB::SeqFeature::Store::DBI::mysql -- Mysql implementation of Bio::DB::SeqFeature::Store =head1 SYNOPSIS use Bio::DB::SeqFeature::Store; # Open the sequence database my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:test'); # get a feature from somewhere my $feature = Bio::SeqFeature::Generic->new(...); # store it $db->store($feature) or die "Couldn't store!"; # primary ID of the feature is changed to indicate its primary ID # in the database... my $id = $feature->primary_id; # get the feature back out my $f = $db->fetch($id); # change the feature and update it $f->start(100); $f->update($f) or die "Couldn't update!"; # searching... # ...by id my @features = $db->fetch_many(@list_of_ids); # ...by name @features = $db->get_features_by_name('ZK909'); # ...by alias @features = $db->get_features_by_alias('sma-3'); # ...by type @features = $db->get_features_by_name('gene'); # ...by location @features = $db->get_features_by_location(-seq_id=>'Chr1',-start=>4000,-end=>600000); # ...by attribute @features = $db->get_features_by_attribute({description => 'protein kinase'}) # ...by the GFF "Note" field @result_list = $db->search_notes('kinase'); # ...by arbitrary combinations of selectors @features = $db->features(-name => $name, -type => $types, -seq_id => $seqid, -start => $start, -end => $end, -attributes => $attributes); # ...using an iterator my $iterator = $db->get_seq_stream(-name => $name, -type => $types, -seq_id => $seqid, -start => $start, -end => $end, -attributes => $attributes); while (my $feature = $iterator->next_seq) { # do something with the feature } # ...limiting the search to a particular region my $segment = $db->segment('Chr1',5000=>6000); my @features = $segment->features(-type=>['mRNA','match']); # getting & storing sequence information # Warning: this returns a string, and not a PrimarySeq object $db->insert_sequence('Chr1','GATCCCCCGGGATTCCAAAA...'); my $sequence = $db->fetch_sequence('Chr1',5000=>6000); # what feature types are defined in the database? my @types = $db->types; # create a new feature in the database my $feature = $db->new_feature(-primary_tag => 'mRNA', -seq_id => 'chr3', -start => 10000, -end => 11000); =head1 DESCRIPTION Bio::DB::SeqFeature::Store::mysql is the Mysql adaptor for Bio::DB::SeqFeature::Store. You will not create it directly, but instead use Bio::DB::SeqFeature::Store-Enew() to do so. See L for complete usage instructions. =head2 Using the Mysql adaptor Before you can use the adaptor, you must use the mysqladmin tool to create a database and establish a user account with write permission. In order to use "fast" loading, the user account must have "file" privileges. To establish a connection to the database, call Bio::DB::SeqFeature::Store-Enew(-adaptor=E'DBI::mysql',@more_args). The additional arguments are as follows: Argument name Description ------------- ----------- -dsn The database name. You can abbreviate "dbi:mysql:foo" as "foo" if you wish. -user Username for authentication. -pass Password for authentication. -namespace A prefix to attach to each table. This allows you to have several virtual databases in the same physical database. -temp Boolean flag. If true, a temporary database will be created and destroyed as soon as the Store object goes out of scope. (synonym -temporary) -autoindex Boolean flag. If true, features in the database will be reindexed every time they change. This is the default. -tmpdir Directory in which to place temporary files during "fast" loading. Defaults to File::Spec->tmpdir(). (synonyms -dump_dir, -dumpdir, -tmp) -dbi_options A hashref to pass to DBI->connect's 4th argument, the "attributes." (synonyms -options, -dbi_attr) -write Pass true to open database for writing or updating. If successful, a new instance of Bio::DB::SeqFeature::Store::DBI::mysql will be returned. In addition to the standard methods supported by all well-behaved Bio::DB::SeqFeature::Store databases, several following adaptor-specific methods are provided. These are described in the next sections. =cut use strict; use base 'Bio::DB::SeqFeature::Store'; use Bio::DB::SeqFeature::Store::DBI::Iterator; use DBI; use Memoize; use Cwd 'abs_path'; use Bio::DB::GFF::Util::Rearrange 'rearrange'; use Bio::SeqFeature::Lite; use File::Spec; use Carp 'carp','cluck','croak'; use constant DEBUG=>0; # from the MySQL documentation... # WARNING: if your sequence uses coordinates greater than 2 GB, you are out of luck! use constant MAX_INT => 2_147_483_647; use constant MIN_INT => -2_147_483_648; use constant MAX_BIN => 1_000_000_000; # size of largest feature = 1 Gb use constant MIN_BIN => 1000; # smallest bin we'll make - on a 100 Mb chromosome, there'll be 100,000 of these use constant SUMMARY_BIN_SIZE => 1000; # tier 0 == 1000 bp bins # tier 1 == 10,000 bp bins # etc. memoize('_typeid'); memoize('_locationid'); memoize('_attributeid'); memoize('dump_path'); ### # object initialization # sub init { my $self = shift; my ($dsn, $is_temporary, $autoindex, $namespace, $dump_dir, $user, $pass, $dbi_options, $writeable, $create, ) = rearrange(['DSN', ['TEMP','TEMPORARY'], 'AUTOINDEX', 'NAMESPACE', ['DUMP_DIR','DUMPDIR','TMP','TMPDIR'], 'USER', ['PASS','PASSWD','PASSWORD'], ['OPTIONS','DBI_OPTIONS','DBI_ATTR'], ['WRITE','WRITEABLE'], 'CREATE', ],@_); $dbi_options ||= {}; $writeable = 1 if $is_temporary or $dump_dir; $dsn or $self->throw("Usage: ".__PACKAGE__."->init(-dsn => \$dbh || \$dsn)"); my $dbh; if (ref $dsn) { $dbh = $dsn; } else { $dsn = "dbi:mysql:$dsn" unless $dsn =~ /^dbi:/; $dbh = DBI->connect($dsn,$user,$pass,$dbi_options) or $self->throw($DBI::errstr); $dbh->{mysql_auto_reconnect} = 1; } $self->{dbh} = $dbh; $self->{is_temp} = $is_temporary; $self->{namespace} = $namespace; $self->{writeable} = $writeable; $self->default_settings; $self->autoindex($autoindex) if defined $autoindex; $self->dumpdir($dump_dir) if $dump_dir; if ($self->is_temp) { $self->init_tmp_database(); } elsif ($create) { $self->init_database('erase'); } } sub writeable { shift->{writeable} } sub can_store_parentage { 1 } sub table_definitions { my $self = shift; return { feature => < < < < < < < < < <maybe_create_meta(); $self->SUPER::default_settings; $self->autoindex(1); $self->dumpdir(File::Spec->tmpdir); } ### # retrieve database handle # sub dbh { my $self = shift; my $d = $self->{dbh}; $self->{dbh} = shift if @_; $d; } sub clone { my $self = shift; $self->{dbh}{InactiveDestroy} = 1; $self->{dbh} = $self->{dbh}->clone unless $self->is_temp; } ### # get/set directory for bulk load tables # sub dumpdir { my $self = shift; my $d = $self->{dumpdir}; $self->{dumpdir} = abs_path(shift) if @_; $d; } ### # table namespace (multiple dbs in one mysql db) # sub namespace { my $self = shift; my $d = $self->{namespace}; $self->{namespace} = shift if @_; $d; } ### # Required for Pg not mysql # sub remove_namespace { return; } ### # find a path that corresponds to a dump table # sub dump_path { my $self = shift; my $table = $self->_qualify(shift); return "$self->{dumpdir}/$table.$$"; } ### # make a filehandle (writeable) that corresponds to a dump table # sub dump_filehandle { my $self = shift; my $table = shift; eval "require IO::File" unless IO::File->can('new'); my $path = $self->dump_path($table); my $fh = $self->{filehandles}{$path} ||= IO::File->new(">$path"); $fh; } ### # find the next ID for a feature (used only during bulk loading) # sub next_id { my $self = shift; $self->{max_id} ||= $self->max_id; return ++$self->{max_id}; } ### # find the maximum ID for a feature (used only during bulk loading) # sub max_id { my $self = shift; my $features = $self->_feature_table; my $sth = $self->_prepare("SELECT max(id) from $features"); $sth->execute or $self->throw($sth->errstr); my ($id) = $sth->fetchrow_array; $id; } ### # wipe database clean and reinstall schema # sub _init_database { my $self = shift; my $erase = shift; my $dbh = $self->dbh; my $tables = $self->table_definitions; for my $t (keys %$tables) { next if $t eq 'meta'; # don't get rid of meta data! my $table = $self->_qualify($t); $dbh->do("DROP table IF EXISTS $table") if $erase; my $query = "CREATE TABLE IF NOT EXISTS $table $tables->{$t}"; $self->_create_table($dbh,$query); } $self->subfeatures_are_indexed(1) if $erase; 1; } sub init_tmp_database { my $self = shift; my $dbh = $self->dbh; my $tables = $self->table_definitions; for my $t (keys %$tables) { next if $t eq 'meta'; # done earlier my $table = $self->_qualify($t); my $query = "CREATE TEMPORARY TABLE $table $tables->{$t}"; $self->_create_table($dbh,$query); } 1; } sub _create_table { my $self = shift; my ($dbh,$query) = @_; for my $q (split ';',$query) { chomp($q); next unless $q =~ /\S/; $dbh->do("$q;\n") or $self->throw($dbh->errstr); } } sub maybe_create_meta { my $self = shift; return unless $self->writeable; my $meta = $self->_meta_table; my $tables = $self->table_definitions; my $temporary = $self->is_temp ? 'TEMPORARY' : ''; $self->dbh->do("CREATE $temporary TABLE IF NOT EXISTS $meta $tables->{meta}"); } ### # use temporary tables # sub is_temp { shift->{is_temp}; } sub attributes { my $self = shift; my $dbh = $self->dbh; my $attributelist_table = $self->_attributelist_table; my $a = $dbh->selectcol_arrayref("SELECT tag FROM $attributelist_table") or $self->throw($dbh->errstr); return @$a; } sub _store { my $self = shift; # special case for bulk updates return $self->_dump_store(@_) if $self->{bulk_update_in_progress}; my $indexed = shift; my $count = 0; my $autoindex = $self->autoindex; my $dbh = $self->dbh; local $dbh->{RaiseError} = 1; $self->begin_work; eval { for my $obj (@_) { $self->replace($obj,$indexed); $self->_update_indexes($obj) if $indexed && $autoindex; $count++; } }; if ($@) { warn "Transaction aborted because $@"; $self->rollback; } else { $self->commit; } # remember whether we are have ever stored a non-indexed feature unless ($indexed or $self->{indexed_flag}++) { $self->subfeatures_are_indexed(0); } $count; } # we memoize this in order to avoid making zillions of calls sub autoindex { my $self = shift; # special case for bulk update -- need to build the indexes # at the same time we build the main feature table return 1 if $self->{bulk_update_in_progress}; my $d = $self->setting('autoindex'); $self->setting(autoindex=>shift) if @_; $d; } sub _start_bulk_update { my $self = shift; my $dbh = $self->dbh; $self->begin_work; $self->{bulk_update_in_progress}++; } sub _finish_bulk_update { my $self = shift; my $dbh = $self->dbh; my $dir = $self->{dumpdir} || '.'; for my $table ($self->_feature_table,$self->index_tables) { my $fh = $self->dump_filehandle($table); my $path = $self->dump_path($table); $fh->close; #print STDERR "$path\n"; $dbh->do("LOAD DATA LOCAL INFILE '$path' REPLACE INTO TABLE $table FIELDS OPTIONALLY ENCLOSED BY '\\''") or $self->throw($dbh->errstr); unlink $path; } delete $self->{bulk_update_in_progress}; delete $self->{ filehandles}; $self->commit; } ### # Add a subparts to a feature. Both feature and all subparts must already be in database. # sub _add_SeqFeature { my $self = shift; # special purpose method for case when we are doing a bulk update return $self->_dump_add_SeqFeature(@_) if $self->{bulk_update_in_progress}; my $parent = shift; my @children = @_; my $dbh = $self->dbh; local $dbh->{RaiseError} = 1; my $parent2child = $self->_parent2child_table(); my $count = 0; my $sth = $self->_prepare(<primary_id : $parent) or $self->throw("$parent should have a primary_id"); $self->begin_work or $self->throw($dbh->errstr); eval { for my $child (@children) { my $child_id = ref $child ? $child->primary_id : $child; defined $child_id or die "no primary ID known for $child"; $sth->execute($parent_id,$child_id); $count++; } }; if ($@) { warn "Transaction aborted because $@"; $self->rollback; } else { $self->commit; } $sth->finish; $count; } sub _fetch_SeqFeatures { my $self = shift; my $parent = shift; my @types = @_; my $parent_id = $parent->primary_id or $self->throw("$parent should have a primary_id"); my $features = $self->_feature_table; my $parent2child = $self->_parent2child_table(); my @from = ("$features as f","$parent2child as c"); my @where = ('f.id=c.child','c.id=?'); my @args = $parent_id; if (@types) { my ($from,$where,undef,@a) = $self->_types_sql(\@types,'f'); push @from,$from if $from; push @where,$where if $where; push @args,@a; } my $from = join ', ',@from; my $where = join ' AND ',@where; my $query = <_print_query($query,@args) if DEBUG || $self->debug; my $sth = $self->_prepare($query) or $self->throw($self->dbh->errstr); $sth->execute(@args) or $self->throw($sth->errstr); return $self->_sth2objs($sth); } ### # get primary sequence between start and end # sub _fetch_sequence { my $self = shift; my ($seqid,$start,$end) = @_; # backward compatibility to the old days when I liked reverse complementing # dna by specifying $start > $end my $reversed; if (defined $start && defined $end && $start > $end) { $reversed++; ($start,$end) = ($end,$start); } $start-- if defined $start; $end-- if defined $end; my $id = $self->_locationid($seqid); my $offset1 = $self->_offset_boundary($id,$start || 'left'); my $offset2 = $self->_offset_boundary($id,$end || 'right'); my $sequence_table = $self->_sequence_table; my $sql = <= ? AND s.offset <= ? ORDER BY s.offset END my $sth = $self->_prepare($sql); my $seq = ''; $self->_print_query($sql,$id,$offset1,$offset2) if DEBUG || $self->debug; $sth->execute($id,$offset1,$offset2) or $self->throw($sth->errstr); while (my($frag,$offset) = $sth->fetchrow_array) { substr($frag,0,$start-$offset) = '' if defined $start && $start > $offset; $seq .= $frag; } substr($seq,$end-$start+1) = '' if defined $end && $end-$start+1 < length($seq); if ($reversed) { $seq = reverse $seq; $seq =~ tr/gatcGATC/ctagCTAG/; } $sth->finish; $seq; } sub _offset_boundary { my $self = shift; my ($seqid,$position) = @_; my $sequence_table = $self->_sequence_table; my $locationlist_table = $self->_locationlist_table; my $sql; $sql = $position eq 'left' ? "SELECT min(offset) FROM $sequence_table as s WHERE s.id=?" :$position eq 'right' ? "SELECT max(offset) FROM $sequence_table as s WHERE s.id=?" :"SELECT max(offset) FROM $sequence_table as s WHERE s.id=? AND offset<=?"; my $sth = $self->_prepare($sql); my @args = $position =~ /^-?\d+$/ ? ($seqid,$position) : ($seqid); $self->_print_query($sql,@args) if DEBUG || $self->debug; $sth->execute(@args) or $self->throw($sth->errstr); my $boundary = $sth->fetchall_arrayref->[0][0]; $sth->finish; return $boundary; } ### # add namespace to tablename # sub _qualify { my $self = shift; my $table_name = shift; my $namespace = $self->namespace; return $table_name if (!defined $namespace || # is namespace already present in table name? index($table_name, $namespace) == 0); return "${namespace}_${table_name}"; } ### # Fetch a Bio::SeqFeatureI from database using its primary_id # sub _fetch { my $self = shift; @_ or $self->throw("usage: fetch(\$primary_id)"); my $primary_id = shift; my $features = $self->_feature_table; my $sth = $self->_prepare(<execute($primary_id) or $self->throw($sth->errstr); my $obj = $self->_sth2obj($sth); $sth->finish; $obj; } ### # Efficiently fetch a series of IDs from the database # Can pass an array or an array ref # sub _fetch_many { my $self = shift; @_ or $self->throw('usage: fetch_many($id1,$id2,$id3...)'); my $ids = join ',',map {ref($_) ? @$_ : $_} @_ or return; my $features = $self->_feature_table; my $sth = $self->_prepare(<execute() or $self->throw($sth->errstr); return $self->_sth2objs($sth); } sub _features { my $self = shift; my ($seq_id,$start,$end,$strand, $name,$class,$allow_aliases, $types, $attributes, $range_type, $fromtable, $iterator, $sources, ) = rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'],'STRAND', 'NAME','CLASS','ALIASES', ['TYPES','TYPE','PRIMARY_TAG'], ['ATTRIBUTES','ATTRIBUTE'], 'RANGE_TYPE', 'FROM_TABLE', 'ITERATOR', ['SOURCE','SOURCES'], ],@_); my (@from,@where,@args,@group); $range_type ||= 'overlaps'; my $features = $self->_feature_table; @from = "$features as f"; if (defined $name) { # hacky backward compatibility workaround undef $class if $class && $class eq 'Sequence'; $name = "$class:$name" if defined $class && length $class > 0; # last argument is the join field my ($from,$where,$group,@a) = $self->_name_sql($name,$allow_aliases,'f.id'); push @from,$from if $from; push @where,$where if $where; push @group,$group if $group; push @args,@a; } if (defined $seq_id) { # last argument is the name of the features table my ($from,$where,$group,@a) = $self->_location_sql($seq_id,$start,$end,$range_type,$strand,'f'); push @from,$from if $from; push @where,$where if $where; push @group,$group if $group; push @args,@a; } if (defined($sources)) { my @sources = ref($sources) eq 'ARRAY' ? @{$sources} : ($sources); if (defined($types)) { my @types = ref($types) eq 'ARRAY' ? @{$types} : ($types); my @final_types; foreach my $type (@types) { # *** not sure what to do if user supplies both -source and -type # where the type includes a source! if ($type =~ /:/) { push(@final_types, $type); } else { foreach my $source (@sources) { push(@final_types, $type.':'.$source); } } } $types = \@final_types; } else { $types = [map { ':'.$_ } @sources]; } } if (defined($types)) { # last argument is the name of the features table my ($from,$where,$group,@a) = $self->_types_sql($types,'f'); push @from,$from if $from; push @where,$where if $where; push @group,$group if $group; push @args,@a; } if (defined $attributes) { # last argument is the join field my ($from,$where,$group,@a) = $self->_attributes_sql($attributes,'f.id'); push @from,$from if $from; push @where,$where if $where; push @group,$group if $group; push @args,@a; } if (defined $fromtable) { # last argument is the join field my ($from,$where,$group,@a) = $self->_from_table_sql($fromtable,'f.id'); push @from,$from if $from; push @where,$where if $where; push @group,$group if $group; push @args,@a; } # if no other criteria are specified, then # only fetch indexed (i.e. top level objects) @where = 'indexed=1' unless @where; my $from = join ', ',@from; my $where = join ' AND ',map {"($_)"} @where; my $group = join ', ',@group; $group = "GROUP BY $group" if @group; my $query = <_print_query($query,@args) if DEBUG || $self->debug; my $sth = $self->_prepare($query) or $self->throw($self->dbh->errstr); $sth->execute(@args) or $self->throw($sth->errstr); return $iterator ? Bio::DB::SeqFeature::Store::DBI::Iterator->new($sth,$self) : $self->_sth2objs($sth); } sub _aggregate_bins { my $self = shift; my $sth = shift; my (%types,$binsize,$binstart); while (my ($type,$seqname,$bin,$count,$bins,$start,$end) = $sth->fetchrow_array) { $binsize ||= ($end-$start+1)/$bins; $binstart ||= int($start/$binsize); $types{$type}{seqname} ||= $seqname; $types{$type}{min} ||= $start; $types{$type}{max} ||= $end; $types{$type}{bins} ||= [(0) x $bins]; $types{$type}{bins}[$bin-$binstart] = $count; $types{$type}{count} += $count; } my @results; for my $type (keys %types) { my $min = $types{$type}{min}; my $max = $types{$type}{max}; my $seqid= $types{$type}{seqname}; my $f = Bio::SeqFeature::Lite->new(-seq_id => $seqid, -start => $min, -end => $max, -type => "$type:bins", -score => $types{$type}{count}, -attributes => {coverage => join ',',@{$types{$type}{bins}}}); push @results,$f; } return @results; } sub _name_sql { my $self = shift; my ($name,$allow_aliases,$join) = @_; my $name_table = $self->_name_table; my $from = "$name_table as n"; my ($match,$string) = $self->_match_sql($name); my $where = "n.id=$join AND n.name $match"; $where .= " AND n.display_name>0" unless $allow_aliases; return ($from,$where,'',$string); } sub _search_attributes { my $self = shift; my ($search_string,$attribute_names,$limit) = @_; my @words = map {quotemeta($_)} split /\s+/,$search_string; my $name_table = $self->_name_table; my $attribute_table = $self->_attribute_table; my $attributelist_table = $self->_attributelist_table; my $type_table = $self->_type_table; my $typelist_table = $self->_typelist_table; my @tags = @$attribute_names; my $tag_sql = join ' OR ',("al.tag=?") x @tags; my $perl_regexp = join '|',@words; my $sql_regexp = join ' OR ',("a.attribute_value REGEXP ?") x @words; my $sql = <_print_query($sql,@tags,@words) if DEBUG || $self->debug; my $sth = $self->_prepare($sql); $sth->execute(@tags,@words) or $self->throw($sth->errstr); my @results; while (my($name,$value,$type,$id) = $sth->fetchrow_array) { my (@hits) = $value =~ /$perl_regexp/ig; my @words_in_row = split /\b/,$value; my $score = int(@hits * 10); push @results,[$name,$value,$score,$type,$id]; } $sth->finish; @results = sort {$b->[2]<=>$a->[2]} @results; return @results; } sub _match_sql { my $self = shift; my $name = shift; my ($match,$string); if ($name =~ /(?:^|[^\\])[*?]/) { $name =~ s/(^|[^\\])([%_])/$1\\$2/g; $name =~ s/(^|[^\\])\*/$1%/g; $name =~ s/(^|[^\\])\?/$1_/g; $match = "LIKE ?"; $string = $name; } else { $match = "= ?"; $string = $name; } return ($match,$string); } sub _from_table_sql { my $self = shift; my ($from_table,$join) = @_; my $from = "$from_table as ft"; my $where = "ft.id=$join"; return ($from,$where,''); } sub _attributes_sql { my $self = shift; my ($attributes,$join) = @_; my ($wf,@bind_args) = $self->_make_attribute_where('a','al',$attributes); my ($group_by,@group_args)= $self->_make_attribute_group('a',$attributes); my $attribute_table = $self->_attribute_table; my $attributelist_table = $self->_attributelist_table; my $from = "$attribute_table as a use index(attribute_id), $attributelist_table as al"; my $where = <_typelist_table; my $from = "$typelist AS tl"; my (@matches,@args); for my $type (@types) { if (ref $type && $type->isa('Bio::DB::GFF::Typename')) { $primary_tag = $type->method; $source_tag = $type->source; } else { ($primary_tag,$source_tag) = split ':',$type,2; } if (defined $source_tag && length $source_tag) { if (defined $primary_tag && length($primary_tag)) { push @matches,"tl.tag=?"; push @args,"$primary_tag:$source_tag"; } else { push @matches,"tl.tag LIKE ?"; push @args,"%:$source_tag"; } } else { push @matches,"tl.tag LIKE ?"; push @args,"$primary_tag:%"; } } my $matches = join ' OR ',@matches; my $where = <_locationid_nocreate($seq_id) || 0; # zero is an invalid primary ID, so will return empty $start = MIN_INT unless defined $start; $end = MAX_INT unless defined $end; my ($bin_where,@bin_args) = $self->bin_where($start,$end,$location); my ($range,@range_args); if ($range_type eq 'overlaps') { $range = "$location.end>=? AND $location.start<=? AND ($bin_where)"; @range_args = ($start,$end,@bin_args); } elsif ($range_type eq 'contains') { $range = "$location.start>=? AND $location.end<=? AND ($bin_where)"; @range_args = ($start,$end,@bin_args); } elsif ($range_type eq 'contained_in') { $range = "$location.start<=? AND $location.end>=?"; @range_args = ($start,$end); } else { $self->throw("range_type must be one of 'overlaps', 'contains' or 'contained_in'"); } if (defined $strand) { $range .= " AND strand=?"; push @range_args,$strand; } my $where = <dbh; my $count = 0; my $now; # try to bring in highres time() function eval "require Time::HiRes"; my $last_time = $self->time(); # tell _delete_index() not to bother removing the index rows corresponding # to each individual feature local $self->{reindexing} = 1; $self->begin_work; eval { my $update = $from_update_table; for my $table ($self->index_tables) { my $query = $from_update_table ? "DELETE $table FROM $table,$update WHERE $table.id=$update.id" : "DELETE FROM $table"; $dbh->do($query); $self->_disable_keys($dbh,$table); } my $iterator = $self->get_seq_stream(-from_table=>$from_update_table ? $update : undef); while (my $f = $iterator->next_seq) { if (++$count %1000 == 0) { $now = $self->time(); my $elapsed = sprintf(" in %5.2fs",$now - $last_time); $last_time = $now; print STDERR "$count features indexed$elapsed...",' 'x60; print STDERR -t STDOUT && !$ENV{EMACS} ? "\r" : "\n"; } $self->_update_indexes($f); } }; for my $table ($self->index_tables) { $self->_enable_keys($dbh,$table); } if (@_) { warn "Couldn't complete transaction: $@"; $self->rollback; return; } else { $self->commit; return 1; } } sub optimize { my $self = shift; $self->dbh->do("ANALYZE TABLE $_") foreach $self->index_tables; } sub all_tables { my $self = shift; my @index_tables = $self->index_tables; my $features = $self->_feature_table; return ($features,@index_tables); } sub index_tables { my $self = shift; return map {$self->_qualify($_)} qw(name attribute parent2child) } sub _firstid { my $self = shift; my $features = $self->_feature_table; my $query = <_prepare($query); $sth->execute(); my ($first) = $sth->fetchrow_array; $sth->finish; $first; } sub _nextid { my $self = shift; my $lastkey = shift; my $features = $self->_feature_table; my $query = <? END my $sth=$self->_prepare($query); $sth->execute($lastkey); my ($next) = $sth->fetchrow_array; $sth->finish; $next; } sub _existsid { my $self = shift; my $key = shift; my $features = $self->_feature_table; my $query = <_prepare($query); $sth->execute($key); my ($count) = $sth->fetchrow_array; $sth->finish; $count > 0; } sub _deleteid { my $self = shift; my $key = shift; my $dbh = $self->dbh; my $parent2child = $self->_parent2child_table; my $query = "SELECT child FROM $parent2child WHERE id=?"; my $sth=$self->_prepare($query); $sth->execute($key); my $success = 0; while (my ($cid) = $sth->fetchrow_array) { # Backcheck looking for multiple parents, delete only if one is present. I'm # sure there is a nice way to left join the parent2child table onto itself # to get this in one query above, just haven't worked it out yet... my $sth2 = $self->_prepare("SELECT count(id) FROM $parent2child WHERE child=?"); $sth2->execute($cid); my ($count) = $sth2->fetchrow_array; if ($count == 1) { $self->_deleteid($cid) || warn "An error occurred while removing subfeature id=$cid. Perhaps it was previously deleted?\n"; } } for my $table ($self->all_tables) { $success += $dbh->do("DELETE FROM $table WHERE id=$key") || 0; } return $success; } sub _clearall { my $self = shift; my $dbh = $self->dbh; for my $table ($self->all_tables) { $dbh->do("DELETE FROM $table"); } } sub _featurecount { my $self = shift; my $dbh = $self->dbh; my $features = $self->_feature_table; my $query = <_prepare($query); $sth->execute(); my ($count) = $sth->fetchrow_array; $sth->finish; $count; } sub _seq_ids { my $self = shift; my $dbh = $self->dbh; my $location = $self->_locationlist_table; my $sth = $self->_prepare("SELECT DISTINCT seqname FROM $location"); $sth->execute() or $self->throw($sth->errstr); my @result; while (my ($id) = $sth->fetchrow_array) { push @result,$id; } return @result; } sub setting { my $self = shift; my ($variable_name,$value) = @_; my $meta = $self->_meta_table; if (defined $value && $self->writeable) { my $query = <_prepare($query); $sth->execute($variable_name,$value) or $self->throw($sth->errstr); $sth->finish; $self->{settings_cache}{$variable_name} = $value; } else { return $self->{settings_cache}{$variable_name} if exists $self->{settings_cache}{$variable_name}; my $query = <_prepare($query); $sth->execute($variable_name) or $self->throw($sth->errstr); my ($value) = $sth->fetchrow_array; $sth->finish; return $self->{settings_cache}{$variable_name} = $value; } } ### # Replace Bio::SeqFeatureI into database. # sub replace { my $self = shift; my $object = shift; my $index_flag = shift || undef; # ?? shouldn't need to do this # $self->_load_class($object); my $id = $object->primary_id; my $features = $self->_feature_table; my $sth = $self->_prepare(<_get_location_and_bin($object) : (undef)x6; my $primary_tag = $object->primary_tag; my $source_tag = $object->source_tag || ''; $primary_tag .= ":$source_tag"; my $typeid = $self->_typeid($primary_tag,1); my $frozen = $self->no_blobs() ? 0 : $self->freeze($object); $sth->execute($id,$frozen,$index_flag||0,@location,$typeid) or $self->throw($sth->errstr); my $dbh = $self->dbh; $object->primary_id($dbh->{mysql_insertid}) unless defined $id; $self->flag_for_indexing($dbh->{mysql_insertid}) if $self->{bulk_update_in_progress}; } # doesn't work with this schema, since we have to update name and attribute # tables which need object ids, which we can only know by replacing feats in # the feature table one by one sub bulk_replace { my $self = shift; my $index_flag = shift || undef; my @objects = @_; my $features = $self->_feature_table; my @insert_values; foreach my $object (@objects) { my $id = $object->primary_id; my @location = $index_flag ? $self->_get_location_and_bin($object) : (undef)x6; my $primary_tag = $object->primary_tag; my $source_tag = $object->source_tag || ''; $primary_tag .= ":$source_tag"; my $typeid = $self->_typeid($primary_tag,1); push(@insert_values, ($id,0,$index_flag||0,@location,$typeid)); } my @value_blocks; for (1..@objects) { push(@value_blocks, '(?,?,?,?,?,?,?,?,?,?)'); } my $value_blocks = join(',', @value_blocks); my $sql = qq{REPLACE INTO $features (id,object,indexed,seqid,start,end,strand,tier,bin,typeid) VALUES $value_blocks}; my $sth = $self->_prepare($sql); $sth->execute(@insert_values) or $self->throw($sth->errstr); } ### # Insert one Bio::SeqFeatureI into database. primary_id must be undef # sub insert { my $self = shift; my $object = shift; my $index_flag = shift || 0; $self->_load_class($object); defined $object->primary_id and $self->throw("$object already has a primary id"); my $features = $self->_feature_table; my $sth = $self->_prepare(<execute(undef,$self->freeze($object),$index_flag) or $self->throw($sth->errstr); my $dbh = $self->dbh; $object->primary_id($dbh->{mysql_insertid}); $self->flag_for_indexing($dbh->{mysql_insertid}) if $self->{bulk_update_in_progress}; } =head2 types Title : types Usage : @type_list = $db->types Function: Get all the types in the database Returns : array of Bio::DB::GFF::Typename objects Args : none Status : public =cut sub types { my $self = shift; eval "require Bio::DB::GFF::Typename" unless Bio::DB::GFF::Typename->can('new'); my $typelist = $self->_typelist_table; my $sql = <_print_query($sql) if DEBUG || $self->debug; my $sth = $self->_prepare($sql); $sth->execute() or $self->throw($sth->errstr); my @results; while (my($tag) = $sth->fetchrow_array) { push @results,Bio::DB::GFF::Typename->new($tag); } $sth->finish; return @results; } =head2 toplevel_types Title : toplevel_types Usage : @type_list = $db->toplevel_types Function: Get the toplevel types in the database Returns : array of Bio::DB::GFF::Typename objects Args : none Status : public This is similar to types() but only returns the types of INDEXED (toplevel) features. =cut sub toplevel_types { my $self = shift; eval "require Bio::DB::GFF::Typename" unless Bio::DB::GFF::Typename->can('new'); my $typelist = $self->_typelist_table; my $features = $self->_feature_table; my $sql = <_print_query($sql) if DEBUG || $self->debug; my $sth = $self->_prepare($sql); $sth->execute() or $self->throw($sth->errstr); my @results; while (my($tag) = $sth->fetchrow_array) { push @results,Bio::DB::GFF::Typename->new($tag); } $sth->finish; return @results; } ### # Insert a bit of DNA or protein into the database # sub _insert_sequence { my $self = shift; my ($seqid,$seq,$offset) = @_; my $id = $self->_locationid($seqid); my $sequence = $self->_sequence_table; my $sth = $self->_prepare(<execute($id,$offset,$seq) or $self->throw($sth->errstr); } ### # This subroutine flags the given primary ID for later reindexing # sub flag_for_indexing { my $self = shift; my $id = shift; my $needs_updating = $self->_update_table; my $sth = $self->_prepare("REPLACE INTO $needs_updating VALUES (?)"); $sth->execute($id) or $self->throw($self->dbh->errstr); } ### # Update indexes for given object # sub _update_indexes { my $self = shift; my $obj = shift; defined (my $id = $obj->primary_id) or return; if ($self->{bulk_update_in_progress}) { $self->_dump_update_name_index($obj,$id); $self->_dump_update_attribute_index($obj,$id); } else { $self->_update_name_index($obj,$id); $self->_update_attribute_index($obj,$id); } } sub _update_name_index { my $self = shift; my ($obj,$id) = @_; my $name = $self->_name_table; my $primary_id = $obj->primary_id; $self->_delete_index($name,$id); my ($names,$aliases) = $self->feature_names($obj); my $sth = $self->_prepare("INSERT INTO $name (id,name,display_name) VALUES (?,?,?)"); $sth->execute($id,$_,1) or $self->throw($sth->errstr) foreach @$names; $sth->execute($id,$_,0) or $self->throw($sth->errstr) foreach @$aliases; $sth->finish; } sub _update_attribute_index { my $self = shift; my ($obj,$id) = @_; my $attribute = $self->_attribute_table; $self->_delete_index($attribute,$id); my $sth = $self->_prepare("INSERT INTO $attribute (id,attribute_id,attribute_value) VALUES (?,?,?)"); for my $tag ($obj->get_all_tags) { my $tagid = $self->_attributeid($tag); for my $value ($obj->get_tag_values($tag)) { $sth->execute($id,$tagid,$value) or $self->throw($sth->errstr); } } $sth->finish; } sub _genericid { my $self = shift; my ($table,$namefield,$name,$add_if_missing) = @_; my $qualified_table = $self->_qualify($table); my $sth = $self->_prepare(<execute($name) or die $sth->errstr; my ($id) = $sth->fetchrow_array; $sth->finish; return $id if defined $id; return unless $add_if_missing; $sth = $self->_prepare(<execute($name) or die $sth->errstr; my $dbh = $self->dbh; return $dbh->{mysql_insertid}; } sub _typeid { shift->_genericid('typelist','tag',shift,1); } sub _locationid { shift->_genericid('locationlist','seqname',shift,1); } sub _locationid_nocreate { shift->_genericid('locationlist','seqname',shift,0); } sub _attributeid { shift->_genericid('attributelist','tag',shift,1); } sub _get_location_and_bin { my $self = shift; my $feature = shift; my $seqid = $self->_locationid($feature->seq_id||''); my $start = $feature->start; my $end = $feature->end; my $strand = $feature->strand || 0; my ($tier,$bin) = $self->get_bin($start,$end); return ($seqid,$start,$end,$strand,$tier,$bin); } sub get_bin { my $self = shift; my ($start,$end) = @_; my $binsize = MIN_BIN; my ($bin_start,$bin_end,$tier); $tier = 0; while (1) { $bin_start = int $start/$binsize; $bin_end = int $end/$binsize; last if $bin_start == $bin_end; $binsize *= 10; $tier++; } return ($tier,$bin_start); } sub bin_where { my $self = shift; my ($start,$end,$f) = @_; my (@bins,@args); my $tier = 0; my $binsize = MIN_BIN; while ($binsize <= MAX_BIN) { my $bin_start = int($start/$binsize); my $bin_end = int($end/$binsize); push @bins,"($f.tier=? AND $f.bin between ? AND ?)"; push @args,($tier,$bin_start,$bin_end); $binsize *= 10; $tier++; } my $query = join ("\n\t OR ",@bins); return wantarray ? ($query,@args) : substitute($query,@args); } sub _delete_index { my $self = shift; my ($table_name,$id) = @_; return if $self->{reindexing}; my $sth = $self->_prepare("DELETE FROM $table_name WHERE id=?") or $self->throw($self->dbh->errstr); $sth->execute($id); } # given a statement handler that is expected to return rows of (id,object) # unthaw each object and return a list of 'em sub _sth2objs { my $self = shift; my $sth = shift; my @result; while (my ($id,$o,$typeid,$seqid,$start,$end,$strand) = $sth->fetchrow_array) { my $obj; if ($o eq '0') { # rebuild a new feat object from the data stored in the db $obj = $self->_rebuild_obj($id,$typeid,$seqid,$start,$end,$strand); } else { $obj = $self->thaw($o,$id); } push @result,$obj; } $sth->finish; return @result; } # given a statement handler that is expected to return rows of (id,object) # unthaw each object and return a list of 'em sub _sth2obj { my $self = shift; my $sth = shift; my ($id,$o,$typeid,$seqid,$start,$end,$strand) = $sth->fetchrow_array; return unless defined $o; my $obj; if ($o eq '0') { # I don't understand why an object ever needs to be rebuilt! # rebuild a new feat object from the data stored in the db $obj = $self->_rebuild_obj($id,$typeid,$seqid,$start,$end,$strand); } else { $obj = $self->thaw($o,$id); } $obj; } sub _rebuild_obj { my ($self, $id, $typeid, $db_seqid, $start, $end, $strand) = @_; my ($type, $source, $seqid); # convert typeid to type and source if (exists $self->{_type_cache}->{$typeid}) { ($type, $source) = @{$self->{_type_cache}->{$typeid}}; } else { my $sql = qq{ SELECT `tag` FROM typelist WHERE `id` = ? }; my $sth = $self->_prepare($sql) or $self->throw($self->dbh->errstr); $sth->execute($typeid); my $result; $sth->bind_columns(\$result); while ($sth->fetch()) { # there should be only one row returned, but we ensure to get all rows } ($type, $source) = split(':', $result); $self->{_type_cache}->{$typeid} = [$type, $source]; } # convert the db seqid to the sequence name if (exists $self->{_seqid_cache}->{$db_seqid}) { $seqid = $self->{_seqid_cache}->{$db_seqid}; } else { my $sql = qq{ SELECT `seqname` FROM locationlist WHERE `id` = ? }; my $sth = $self->_prepare($sql) or $self->throw($self->dbh->errstr); $sth->execute($db_seqid); $sth->bind_columns(\$seqid); while ($sth->fetch()) { # there should be only one row returned, but we ensure to get all rows } $self->{_seqid_cache}->{$db_seqid} = $seqid; } # get the names from name table? # get the attributes and store those in obj my $sql = qq{ SELECT attribute_id,attribute_value FROM attribute WHERE `id` = ? }; my $sth = $self->_prepare($sql) or $self->throw($self->dbh->errstr); $sth->execute($id); my ($attribute_id, $attribute_value); $sth->bind_columns(\($attribute_id, $attribute_value)); my %attribs; while ($sth->fetch()) { # convert the attribute_id to its real name my $attribute; if (exists $self->{_attribute_cache}->{$attribute_id}) { $attribute = $self->{_attribute_cache}->{$attribute_id}; } else { my $sql = qq{ SELECT `tag` FROM attributelist WHERE `id` = ? }; my $sth2 = $self->_prepare($sql) or $self->throw($self->dbh->errstr); $sth2->execute($attribute_id); $sth2->bind_columns(\$attribute); while ($sth2->fetch()) { # there should be only one row returned, but we ensure to get all rows } $self->{_attribute_cache}->{$attribute_id} = $attribute; } if ($source && $attribute eq 'source' && $attribute_value eq $source) { next; } $attribs{$attribute} = $attribute_value; } # if we weren't called with all the params, pull those out of the database too if ( not ( grep { defined($_) } ( $typeid, $db_seqid, $start, $end, $strand ))) { my $sql = qq{ SELECT start,end,tag,strand,seqname FROM feature,feature_location,typelist,locationlist WHERE feature.id=feature_location.id AND feature.typeid=typelist.id AND seqid=locationlist.id AND feature.id = ? }; my $sth = $self->_prepare($sql) or $self->throw($self->dbh->errstr); $sth->execute($id); my ($feature_start, $feature_end, $feature_type, $feature_strand,$feature_seqname); $sth->bind_columns(\($feature_start, $feature_end, $feature_type, $feature_strand, $feature_seqname)); while ($sth->fetch()) { # there should be only one row returned, but we call like this to # ensure we get all rows } $start ||= $feature_start; $end ||= $feature_end; $strand ||= $feature_strand; $seqid ||= $feature_seqname; my( $feature_typename , $feature_typesource ) = split /:/ , $feature_type; $type ||= $feature_typename; $source ||= $feature_typesource; } my $obj = Bio::SeqFeature::Lite->new(-primary_id => $id, $type ? (-type => $type) : (), $source ? (-source => $source) : (), $seqid ? (-seq_id => $seqid) : (), defined $start ? (-start => $start) : (), defined $end ? (-end => $end) : (), defined $strand ? (-strand => $strand) : (), keys %attribs ? (-attributes => \%attribs) : ()); return $obj; } sub _prepare { my $self = shift; my $query = shift; my $dbh = $self->dbh; my $sth = $dbh->prepare_cached($query, {}, 3) or $self->throw($dbh->errstr); $sth; } #################################################################################################### # SQL Fragment generators #################################################################################################### sub _attribute_table { shift->_qualify('attribute') } sub _attributelist_table { shift->_qualify('attributelist') } sub _feature_table { shift->_qualify('feature') } sub _interval_stats_table { shift->_qualify('interval_stats') } sub _location_table { shift->_qualify('location') } sub _locationlist_table { shift->_qualify('locationlist') } sub _meta_table { shift->_qualify('meta') } sub _name_table { shift->_qualify('name') } sub _parent2child_table { shift->_qualify('parent2child') } sub _sequence_table { shift->_qualify('sequence') } sub _type_table { shift->_qualify('feature') } sub _typelist_table { shift->_qualify('typelist') } sub _update_table { shift->_qualify('update_table') } sub _make_attribute_where { my $self = shift; my ($attributetable,$attributenametable,$attributes) = @_; my @args; my @sql; my $dbh = $self->dbh; foreach (keys %$attributes) { my @match_values; my @values = ref($attributes->{$_}) && ref($attributes->{$_}) eq 'ARRAY' ? @{$attributes->{$_}} : $attributes->{$_}; foreach (@values) { # convert * into % for wildcard matches s/\*/%/g; } my $match = join ' OR ',map { /%/ ? "$attributetable.attribute_value LIKE ?" : "$attributetable.attribute_value=?" } @values; push @sql,"($attributenametable.tag=? AND ($match))"; push @args,($_,@values); } return (join(' OR ',@sql),@args); } sub _make_attribute_group { my $self = shift; my ($table_name,$attributes) = @_; my $key_count = keys %$attributes or return; return "f.id,f.object,f.typeid,f.seqid,f.start,f.end,f.strand HAVING count(f.id)>?",$key_count-1; } sub _print_query { my $self = shift; my ($query,@args) = @_; while ($query =~ /\?/) { my $arg = $self->dbh->quote(shift @args); $query =~ s/\?/$arg/; } warn $query,"\n"; } ### # special-purpose store for bulk loading - write to a file rather than to the db # sub _dump_store { my $self = shift; my $indexed = shift; my $count = 0; my $store_fh = $self->dump_filehandle('feature'); my $dbh = $self->dbh; my $autoindex = $self->autoindex; for my $obj (@_) { my $id = $self->next_id; my ($seqid,$start,$end,$strand,$tier,$bin) = $indexed ? $self->_get_location_and_bin($obj) : (undef)x6; my $primary_tag = $obj->primary_tag; my $source_tag = $obj->source_tag || ''; $primary_tag .= ":$source_tag"; my $typeid = $self->_typeid($primary_tag,1); print $store_fh join("\t",$id,$typeid,$seqid,$start,$end,$strand,$tier,$bin,$indexed,$dbh->quote($self->freeze($obj))),"\n"; $obj->primary_id($id); $self->_update_indexes($obj) if $indexed && $autoindex; $count++; } # remember whether we are have ever stored a non-indexed feature unless ($indexed or $self->{indexed_flag}++) { $self->subfeatures_are_indexed(0); } $count; } sub _dump_add_SeqFeature { my $self = shift; my $parent = shift; my @children = @_; my $dbh = $self->dbh; my $fh = $self->dump_filehandle('parent2child'); my $parent_id = (ref $parent ? $parent->primary_id : $parent) or $self->throw("$parent should have a primary_id"); my $count = 0; for my $child_id (@children) { print $fh join("\t",$parent_id,$child_id),"\n"; $count++; } $count; } sub _dump_update_name_index { my $self = shift; my ($obj,$id) = @_; my $fh = $self->dump_filehandle('name'); my $dbh = $self->dbh; my ($names,$aliases) = $self->feature_names($obj); print $fh join("\t",$id,$dbh->quote($_),1),"\n" foreach @$names; print $fh join("\t",$id,$dbh->quote($_),0),"\n" foreach @$aliases; } sub _dump_update_attribute_index { my $self = shift; my ($obj,$id) = @_; my $fh = $self->dump_filehandle('attribute'); my $dbh = $self->dbh; for my $tag ($obj->all_tags) { my $tagid = $self->_attributeid($tag); for my $value ($obj->each_tag_value($tag)) { print $fh join("\t",$id,$tagid,$dbh->quote($value)),"\n"; } } } sub coverage_array { my $self = shift; my ($seq_name,$start,$end,$types,$bins) = rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'], ['TYPES','TYPE','PRIMARY_TAG'],'BINS'],@_); $bins ||= 1000; $start ||= 1; unless ($end) { my $segment = $self->segment($seq_name) or $self->throw("unknown seq_id $seq_name"); $end = $segment->end; } my $binsize = ($end-$start+1)/$bins; my $seqid = $self->_locationid_nocreate($seq_name) || 0; return [] unless $seqid; # where each bin starts my @his_bin_array = map {$start + $binsize * $_} (0..$bins-1); my @sum_bin_array = map {int(($_-1)/SUMMARY_BIN_SIZE)} @his_bin_array; my $interval_stats = $self->_interval_stats_table; my ($sth,@a); if ($types) { # pick up the type ids my ($from,$where,$group); ($from,$where,$group,@a) = $self->_types_sql($types,'b'); $where =~ s/.+AND//s; $sth = $self->_prepare(<_prepare(<execute(@a); while (my ($t,$tag) = $sth->fetchrow_array) { $report_tag ||= $tag; push @t,$t; } my %bins; my $sql = <= ? LIMIT 1 END ; $sth = $self->_prepare($sql); eval { for my $typeid (@t) { for (my $i=0;$i<@sum_bin_array;$i++) { my @args = ($typeid,$seqid,$sum_bin_array[$i]); $self->_print_query($sql,@args) if $self->debug; $sth->execute(@args) or $self->throw($sth->errstr); my ($bin,$cum_count) = $sth->fetchrow_array; push @{$bins{$typeid}},[$bin,$cum_count]; } } }; return unless %bins; my @merged_bins; my $firstbin = int(($start-1)/$binsize); for my $type (keys %bins) { my $arry = $bins{$type}; my $last_count = $arry->[0][1]; my $last_bin = -1; my $i = 0; my $delta; for my $b (@$arry) { my ($bin,$count) = @$b; $delta = $count - $last_count if $bin > $last_bin; $merged_bins[$i++] += $delta; $last_count = $count; $last_bin = $bin; } } return wantarray ? (\@merged_bins,$report_tag) : \@merged_bins; } sub build_summary_statistics { my $self = shift; my $interval_stats = $self->_interval_stats_table; my $dbh = $self->dbh; $self->begin_work; my $sbs = SUMMARY_BIN_SIZE; my $result = eval { $self->_add_interval_stats_table; $self->_disable_keys($dbh,$interval_stats); $dbh->do("DELETE FROM $interval_stats"); my $insert = $dbh->prepare(<throw($dbh->errstr); INSERT INTO $interval_stats (typeid,seqid,bin,cum_count) VALUES (?,?,?,?) END my $sql = $self->_fetch_indexed_features_sql; my $select = $dbh->prepare($sql) or $self->throw($dbh->errstr); my $current_bin = -1; my ($current_type,$current_seqid,$count); my $cum_count = 0; my (%residuals,$last_bin); my $le = -t \*STDERR ? "\r" : "\n"; print STDERR "\n"; $select->execute; while (my($typeid,$seqid,$start,$end) = $select->fetchrow_array) { print STDERR $count," features processed$le" if ++$count % 1000 == 0; my $bin = int($start/$sbs); $current_type ||= $typeid; $current_seqid ||= $seqid; # because the input is sorted by start, no more features will contribute to the # current bin so we can dispose of it if ($bin != $current_bin) { if ($seqid != $current_seqid or $typeid != $current_type) { # load all bins left over $self->_load_bins($insert,\%residuals,\$cum_count,$current_type,$current_seqid); %residuals = () ; $cum_count = 0; } else { # load all up to current one $self->_load_bins($insert,\%residuals,\$cum_count,$current_type,$current_seqid,$current_bin); } } $last_bin = $current_bin; ($current_seqid,$current_type,$current_bin) = ($seqid,$typeid,$bin); # summarize across entire spanned region my $last_bin = int(($end-1)/$sbs); for (my $b=$bin;$b<=$last_bin;$b++) { $residuals{$b}++; } } # handle tail case # load all bins left over $self->_load_bins($insert,\%residuals,\$cum_count,$current_type,$current_seqid); $self->_enable_keys($dbh,$interval_stats); 1; }; if ($result) { $self->commit } else { warn "Can't build summary statistics: $@"; $self->rollback }; print STDERR "\n"; } sub _load_bins { my $self = shift; my ($insert,$residuals,$cum_count,$type,$seqid,$stop_after) = @_; for my $b (sort {$a<=>$b} keys %$residuals) { last if defined $stop_after and $b > $stop_after; $$cum_count += $residuals->{$b}; my @args = ($type,$seqid,$b,$$cum_count); $insert->execute(@args); delete $residuals->{$b}; # no longer needed } } sub _add_interval_stats_table { my $self = shift; my $tables = $self->table_definitions; my $interval_stats = $self->_interval_stats_table; $self->dbh->do("CREATE TABLE IF NOT EXISTS $interval_stats $tables->{interval_stats}"); } sub _fetch_indexed_features_sql { my $self = shift; my $features = $self->_feature_table; return <do("ALTER TABLE $table DISABLE KEYS"); } sub _enable_keys { my $self = shift; my ($dbh,$table) = @_; $dbh->do("ALTER TABLE $table ENABLE KEYS"); } sub time { return Time::HiRes::time() if Time::HiRes->can('time'); return time(); } sub DESTROY { my $self = shift; if ($self->{bulk_update_in_progress}) { # be sure to remove temp files for my $table ($self->_feature_table,$self->index_tables) { my $path = $self->dump_path($table); unlink $path; } } } sub begin_work { my $self = shift; return if $self->{_in_transaction}++; my $dbh = $self->dbh; return unless $dbh->{AutoCommit}; $dbh->begin_work; } sub commit { my $self = shift; return unless $self->{_in_transaction}; delete $self->{_in_transaction}; $self->dbh->commit; } sub rollback { my $self = shift; return unless $self->{_in_transaction}; delete $self->{_in_transaction}; $self->dbh->rollback; } 1; BioPerl-1.007002/Bio/DB/SeqVersion000755000766000024 013155576320 16452 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/SeqVersion/gi.pm000444000766000024 1736313155576320 17576 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::SeqVersion::gi # # Please direct questions and support issues to # # Cared for by Brian Osborne # # Copyright Brian Osborne 2006 # # You may distribute this module under the same terms as Perl itself # # POD documentation - main docs before the code =head1 NAME Bio::DB::SeqVersion::gi - interface to NCBI Sequence Revision History page =head1 SYNOPSIS Do not use this module directly, use Bio::DB::SeqVersion. use Bio::DB::SeqVersion; my $query = Bio::DB::SeqVersion->new(-type => 'gi'); # all GIs, which will include the GI used to query my @all_gis = $query->get_all(2); # the most recent GI, which may or may not be the GI used to query my $live_gi = $query->get_recent(2); # get all the visible data on the Sequence Revision page my $array_ref = $query->get_history(11111111); These methods can also take accession numbers as arguments, just like the Sequence Revision page itself. =head1 DESCRIPTION All sequence entries at GenBank are identified by a pair of identifiers, an accession and a numeric identifier, and this number is frequently called a GI number (BenInfo Bdentifier). The accession is stable, but each new version of the sequence entry for the accession receives a new GI number (see L for more information on GenBank identifiers). One accession can have one or more GI numbers and the highest of these is the most recent, or "live", GI. Information on an accession and its associated GI numbers is available at the Sequence Revision History page at NCBI, L, this information is not available in file format. This module queries the Web page and retrieves GI numbers and related data given an accession (e.g. NP_111111, A11111, P12345) or a GI number (e.g. 2, 11111111) as query. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Brian Osborne Email E osborne at optonline dot net E =head1 CONTRIBUTORS Torsten Seemann - torsten.seemann AT infotech.monash.edu.au =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::SeqVersion::gi; use strict; use Encode; use HTML::TableExtract; use base qw(Bio::DB::SeqVersion); # Private class variables # TODO: this may be an unstable setting (text is actually minimal XHTML) my $URL = 'https://www.ncbi.nlm.nih.gov/nuccore/%s?report=girevhist&format=text'; =head2 new Title : new Usage : $gb = Bio::DB::SeqVersion::gi->new Function: Creates a new query object Returns : New query object =cut sub new { my ( $class, @args ) = @_; my $self = $class->SUPER::new(@args); $self->_initialize; return $self; } =head2 get_all Title : get_all Usage : my @gis = $q->get_all(2) Function: Get all GI numbers given a GI number Returns : An array of GI numbers, earliest GI number is the 0 element Args : A single GI number (string) =cut sub get_all { my ( $self, $id ) = @_; my ( @arr, $ref ); $id eq $self->{_last_id} ? $ref = $self->{_last_result} : $ref = $self->get_history($id); for my $row ( @{$ref} ) { push @arr, $$row[0]; } @arr; } =head2 get_recent Title : get_recent Usage : my $newest_gi = $q->get_recent(2) Function: Get most recent GI given a single GI Returns : String Args : A single GI number (string) =cut sub get_recent { my ( $self, $id ) = @_; my $ref; $id eq $self->{_last_id} ? $ref = $self->{_last_result} : $ref = $self->get_history($id); $ref->[0]->[0]; } =head2 get_status Title : get_status Usage : my $newest_gi = $q->get_status(2) Function: Get most recent GI given a single GI Returns : String Args : A single GI number (string) =cut sub get_status { my ( $self, $id ) = @_; $self->throw("Must pass an ID") if !defined $id; if ($id ne $self->{_last_id} ) { $self->get_history($id); } $self->{_last_status}; } =head2 get_history Title : get_history Usage : my $ref = $query_obj->get_history() Function: Queries the NCBI Revision page, gets the data from the HTML table Returns : Reference to an array of arrays where element 0 refers to the most recent version and the last element refers to the oldest version. In the second dimension the elements are: 0 GI number 1 Version 2 Update Date For example, to get the GI number of the first version: $ref->[$#{@$ref}]->[0] To get the Update Date of the latest version: $ref->[0]->[2] Args : One identifier (string) Note : Status of the GI was returned here previously as the last element in the row of elemnts above; however the status is currently only returned for the GI requested (e.g. a single value). One can get the status for this using the get_status() method above =cut sub get_history { my ( $self, $id ) = @_; my $html = $self->_get_request($id); my ( $ref, $status ) = $self->_process_data($html); # store the very last result in case some other methods # are called using the same identifier $self->{_last_result} = $ref; $self->{_last_id} = $id; $self->{_last_status} = $status; $ref; } =head2 _get_request Title : _get_request Usage : my $url = $self->_get_request Function: GET using NCBI Revision page URL, uses Root::HTTPget Returns : HTML Args : One identifier (string) =cut sub _get_request { my ( $self, $id ) = @_; $self->throw("Must specify a single id to query") if ( !defined($id) || ref($id) ); my $url = sprintf( $URL, $id ); my $response = $self->get($url); if ( not $response->is_success ) { $self->throw( "Can't query $url: " . $response->status_line . "\n" . "ID likely does not exist" ); } return $response->content; } =head2 _process_data Title : _process_data Usage : $self->_process_data($html) Function: extract data from HTML Args : HTML from Revision History page Returns : reference to an array of arrays =cut sub _process_data { my ( $self, $html ) = @_; # Only one status is returned (not one per revision). Setting once my $status; if ($html =~ /
Current status:\s+(\S+)<\/div>/) { $status = $1; } else { $self->warn("No current status found, setting to 'unknown'"); $status = 'unknown'; } my $te = HTML::TableExtract->new( headers => ['Gi', 'Version', 'Update Date'] , depth => 0); $te->parse(decode_utf8($html)); my $table = $te->first_table_found; $self->throw("No table found") unless defined $table; my $t = [$table->rows]; ($t, $status); } 1; __END__ BioPerl-1.007002/Bio/DB/TFBS000755000766000024 013155576320 15112 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/TFBS/transfac_pro.pm000444000766000024 24155513155576320 20342 0ustar00cjfieldsstaff000000000000# $Id: transfac_pro.pm,v 1.15 2006/08/12 11:00:03 sendu Exp $ # # BioPerl module for Bio::DB::TFBS::transfac_pro # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::TFBS::transfac_pro - An implementation of Bio::DB::TFBS which uses local flat files for transfac pro =head1 SYNOPSIS use Bio::DB::Taxonomy; my $db = new Bio::DB::Taxonomy(-source => 'transfac_pro' -dat_dir => $directory); # we're interested in the gene P5 my ($gene_id) = $db->get_gene_ids(-name => 'P5'); # G000001 # we want all the transcription factors that bind to our gene my @factor_ids = $db->get_factor_ids(-gene => $gene_id); # get info about those TFs foreach my $factor_id (@factor_ids) { my $factor = $db->get_factor($factor_id); my $name = $factor->universal_name; # etc. - see Bio::Map::TranscriptionFactor, eg. find out where it binds } # get a matrix my $matrix = $db->get_matrix('M00001'); # get a binding site sequence my $seq = $db->get_site('R00001'); =head1 DESCRIPTION This is an implementation which uses local flat files and the DB_File module RECNO data structures to manage a local copy of the Transfac Pro TFBS database. Required database files require a license which can be obtained via http://www.biobase-international.com/pages/index.php?id=170 Within the linux installation tarball you will find a cgibin tar ball, and inside that is a data directory containing the .dat files needed by this module. Point to that data directory with -dat_dir =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 CONTRIBUTORS Based on Bio::DB::Taxonomy::flatfile by Jason Stajich =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::TFBS::transfac_pro; use strict; use Bio::Annotation::Reference; use Bio::Annotation::SimpleValue; use Bio::LocatableSeq; use Bio::SimpleAlign; use Bio::Matrix::PSM::SiteMatrix; use Bio::AlignIO; use Bio::Map::GeneMap; use Bio::Map::TranscriptionFactor; use Bio::Map::Position; use Bio::Map::Relative; use DB_File; use constant SEPARATOR => ':!:'; use constant INTERNAL_SEPARATOR => '!:!'; $DB_BTREE->{'flags'} = R_DUP; # allow duplicate values in DB_File BTREEs use base qw(Bio::DB::TFBS); =head2 new Title : new Usage : my $obj = new Bio::DB::TFBS::transfac_pro(); Function: Builds a new Bio::DB::TFBS::transfac_pro object Returns : an instance of Bio::DB::TTFBS::transfac_pro Args : -dat_dir => name of directory where Transfac Pro .dat files (required to initially build indexes) -tax_db => Bio::DB::Taxonomy object, used when initially building indexes, gives better results for species information but not required. -index_dir => name of directory where index files should be created or already exist. (defaults to -dat_dir, required if -dat_dir not supplied) -force => 1 replace current indexes even if they exist =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($dat_dir, $index_dir, $tax_db, $force) = $self->_rearrange([qw(DAT_DIR INDEX_DIR TAX_DB FORCE)], @args); $self->throw("At least one of -dat_dir and -index_dir must be supplied") unless ($dat_dir || $index_dir); $self->index_directory($index_dir || $dat_dir); $self->{_tax_db} = $tax_db if $tax_db; if ($dat_dir) { $self->_build_index($dat_dir, $force); } $self->_db_connect; return $self; } =head2 Bio::DB::TFBS Interface implementation =cut sub _get_ids { my ($self, $dat, @args) = @_; @args % 2 == 0 || $self->throw("Must provide key => value pairs"); my $hash = $self->{$dat} || $self->throw("Unknown .dat type '$dat'"); if (@args) { # get a subset corresponding to args my @final; my %args = @args; my $multiple = 0; while (my ($type, $value) = each %args) { unless ($value) { $self->warn("Arguement '$type' has no value, ignored"); next; } $type =~ s/-//; $type = lc($type); my $converter = $hash->{$type}; unless ($converter) { $self->warn("Unknown search type '$type' for .dat type '$dat'"); next; } my @ids = $converter->get_dup($value); unless (@ids) { @ids = $converter->get_dup(lc($value)); } if ($multiple) { # we can have multiple types given at once, find the ids that # satisfy all criteria @final || return; my %final = map { $_ => 1 } @final; @final = grep { $final{$_} } @ids; } else { @final = @ids; $multiple++; } } return @final; } else { # get them all my $db_file_hash = $self->{$dat}->{id}; my ($key, $prev_key, $value) = ('_!_', '!_!'); my @ids; while (1) { $db_file_hash->seq($key, $value, R_NEXT); last if $prev_key eq $key; push(@ids, $value); # confusing? when creating objects we store # $value as accession and $key as id, but from # this method we return $value as id given $id! $prev_key = $key; } return @ids; } } =head2 get_reference Title : get_reference Usage : my $ref = $obj->get_reference($id); Function: Get a literature reference. Returns : Bio::Annotation::Reference Args : string - a reference id ('RE...') =cut sub get_reference { my ($self, $id) = @_; $id || return; my $data = $self->{reference}->{data}->{$id} || return; my @data = split(SEPARATOR, $data); return Bio::Annotation::Reference->new(-pubmed => $data[0], -authors => $data[1], -title => $data[2], -location => $data[3] ); } =head2 get_genemap Title : get_genemap Usage : my $map = $obj->get_genemap($id); Function: Get a GeneMap for a gene. Returns : Bio::Map::GeneMap Args : string - a gene id ('G...'), and optionally int (number of bp upstream) =cut sub get_genemap { my ($self, $id, $upstream) = @_; $id || return; return $self->{got_map}->{$id} if defined $self->{got_map}->{$id}; $upstream ||= 1000; my $data = $self->{gene}->{data}->{$id} || return; my @data = split(SEPARATOR, $data); # accession = id name description species_tax_id_or_raw_string my $taxon = $self->{_tax_db} ? $self->{_tax_db}->get_taxon($data[3]) || $data[3] : $data[3]; my $map = Bio::Map::GeneMap->get(-uid => $id, -gene => $data[1], -species => $taxon, -description => $data[2], -upstream => $upstream); $self->{got_map}->{$id} = $map; # prevents infinite recurse when we call get_factor below # spawn all the factors that belong on this gene map # get_factor_ids(-gene => ...) only works for genes that encode factors; # have to go via sites foreach my $sid ($self->get_site_ids(-gene => $id)) { foreach my $fid ($self->get_factor_ids(-site => $sid)) { # it is quite deliberate that we deeply recurse to arrive at the # correct answer, which involves pulling in most of the database no warnings "recursion"; $self->get_factor($fid); } } return $map; } =head2 get_seq Title : get_seq Usage : my $seq = $obj->get_seq($id); Function: Get the sequence of a site. The sequence will be annotated with the the tags 'relative_start', 'relative_end', 'relative_type' and 'relative_to'. Returns : Bio::Seq Args : string - a site id ('R...') =cut sub get_seq { my ($self, $id) = @_; $id || return; my $data = $self->{site}->{data}->{$id} || return; my @data = split(SEPARATOR, $data); my $seq = Bio::Seq->new(-seq => $data[2], -accession_number => $id, -description => $data[6] ? 'Genomic sequence' : 'Consensus or artificial sequence', -id => $data[0], -strand => 1, -alphabet => $data[7] || 'dna', -species => $data[6]); my $annot = $seq->annotation; my $sv = Bio::Annotation::SimpleValue->new(-tagname => 'relative_start', -value => $data[4] || 1); $annot->add_Annotation($sv); $sv = Bio::Annotation::SimpleValue->new(-tagname => 'relative_end', -value => $data[5] || ($data[4] || 1 + length($data[2]) - 1)); $annot->add_Annotation($sv); $sv = Bio::Annotation::SimpleValue->new(-tagname => 'relative_type', -value => $data[3] || 'artificial'); $annot->add_Annotation($sv); $sv = Bio::Annotation::SimpleValue->new(-tagname => 'relative_to', -value => $data[1]); $annot->add_Annotation($sv); return $seq; } =head2 get_fragment Title : get_fragment Usage : my $seq = $obj->get_fragment($id); Function: Get the sequence of a fragment. Returns : Bio::Seq Args : string - a site id ('FR...') =cut sub get_fragment { my ($self, $id) = @_; $id || return; my $data = $self->{fragment}->{data}->{$id} || return; my @data = split(SEPARATOR, $data); # accession = id gene_id1 gene_id2 species_tax_id_or_raw_string sequence source return new Bio::Seq( -seq => $data[4], -accession_number => $id, -description => 'Between genes '.$data[1].' and '.$data[2], -species => $data[3], -id => $data[0], -alphabet => 'dna' ); } =head2 get_matrix Title : get_matrix Usage : my $matrix = $obj->get_matrix($id); Function: Get a matrix that describes a binding site. Returns : Bio::Matrix::PSM::SiteMatrix Args : string - a matrix id ('M...'), optionally a sequence string from which base frequencies will be calculated for the matrix model (default 0.25 each) =cut sub get_matrix { my ($self, $id, $seq) = @_; $id || return; $seq ||= 'atgc'; $seq = lc($seq); my $data = $self->{matrix}->{data}->{$id} || return; my @data = split(SEPARATOR, $data); $data[4] || $self->throw("Matrix data missing for $id"); my ($a, $c, $g, $t); foreach my $position (split(INTERNAL_SEPARATOR, $data[4])) { my ($a_count, $c_count, $g_count, $t_count) = split("\t", $position); push(@{$a}, $a_count); push(@{$c}, $c_count); push(@{$g}, $g_count); push(@{$t}, $t_count); } # our psms include a simple background model so we can use # sequence_match_weight() if desired my $a_freq = ($seq =~ tr/a//) / length($seq); my $c_freq = ($seq =~ tr/c//) / length($seq); my $g_freq = ($seq =~ tr/g//) / length($seq); my $t_freq = ($seq =~ tr/t//) / length($seq); my $psm = Bio::Matrix::PSM::SiteMatrix->new(-pA => $a, -pC => $c, -pG => $g, -pT => $t, -id => $data[0], -accession_number => $id, -sites => $data[3], -width => scalar(@{$a}), -correction => 1, -model => { A => $a_freq, C => $c_freq, G => $g_freq, T => $t_freq } ); #*** used to make a Bio::Matrix::PSM::Psm and add references, but it # didn't seem worth it. You can get references from the database by: #foreach my $ref_id ($db->get_reference_ids(-matrix => $id)) { # my $ref = $db->get_reference($ref_id); #} return $psm; } =head2 get_aln Title : get_aln Usage : my $aln = $obj->get_aln($id); Function: Get the alignment that was used to generate a matrix. Each sequence in the alignment will have an accession_number corresponding to the Transfac site id, and id() based on that but unique within the alignment. Returns : Bio::SimpleAlign Args : string - a matrix id ('M...'), optionally true to, when a matrix lists no sequences, search for sequences via the matrix's factors, picking the sites that best match the matrix =cut my %VALID_STRAND = map {$_ => 1} qw(-1 0 1); sub get_aln { my ($self, $id, $via_factors) = @_; $id || return; my $data = $self->{matrix}->{data}->{$id} || $self->throw("matrix '$id' had no data in DB_File"); my @data = split(SEPARATOR, $data); if (! $data[5] && $via_factors) { # This is a matrix with no site sequences given in matrix.dat. # Find some matching site sequences via factors. # First, check its factors for sites my %site_seqs; my %factor_ids; foreach my $factor_id ($self->get_factor_ids(-matrix => $id)) { $factor_ids{$factor_id} = 1; foreach my $site_id ($self->get_site_ids(-factor => $factor_id)) { next if defined $site_seqs{$site_id}; my $seq = $self->get_seq($site_id); # skip sites that have no sequence, or have IUPAC symbols in # their sequence (most probably the 'consensus' sequence itself # that was used to make and exactly corresponds to the matrix) my $seq_str = $seq->seq || next; $seq_str =~ /[MRWSYKVHDB]/ and next; $site_seqs{$site_id} = $seq; } } my @seqs = values %site_seqs; if (@seqs > 1) { # pick the sub-seqs that match to the matrix with the best scores my $matrix = $self->get_matrix($id); my $desired_sequences = $matrix->sites; return if @seqs < $desired_sequences; my $desired_length = $matrix->width; my %best_seqs; foreach my $seq (@seqs) { my $for_str = $seq->seq; next if length($for_str) < $desired_length; my $rev_str = $seq->revcom->seq; my $best_score = 0; my $best_subseq = ''; my $best_i = 0; my $best_subseq_caps = 0; my $best_revcom; my $revcom = 0; foreach my $seq_str ($for_str, $rev_str) { for my $i (0..(length($seq_str) - $desired_length)) { my $subseq = substr($seq_str, $i, $desired_length); $subseq =~ s/[^ACGTacgt]//g; # can only score atcg next unless length($subseq) == $desired_length; # short or 0-length seqs could get the highest scores! my $score = $matrix->sequence_match_weight($subseq); # caps represent the author-chosen bit of a site # sequence so we would prefer to choose a subseq that # contains it my $caps = $subseq =~ tr/ACGT//; #*** (don't know why numeric == fails for comparing # scores, when the string eq works) if ($score > $best_score || ("$score" eq "$best_score" && $caps > $best_subseq_caps)) { $best_score = $score; $best_subseq_caps = $caps; $best_subseq = $subseq; $best_i = $i; $best_revcom = $revcom; } } $revcom++; } if ($best_score) { $best_seqs{$seq->accession_number} = [$best_subseq, $seq->accession_number, ($best_i + 1), $revcom ? -1 : 1, $best_score]; } } my @sorted = sort { $best_seqs{$b}->[-1] <=> $best_seqs{$a}->[-1] } keys %best_seqs; return if @sorted < $desired_sequences; splice(@sorted, $desired_sequences); my %wanted = map { $_ => 1 } @sorted; my @site_data; foreach my $seq (@seqs) { next unless exists $wanted{$seq->accession_number}; my @data = @{$best_seqs{$seq->accession_number}}; pop(@data); push(@site_data, join('_', @data)); } $data[5] = join(INTERNAL_SEPARATOR, @site_data); $self->{matrix}->{data}->{$id} = join(SEPARATOR, @data); } } $data[5] || return; my @blocks = split(INTERNAL_SEPARATOR, $data[5]); # append gap chars to all sequences to make them the same length # (applies to sequences found via factors, presumably, since we already # do this for matrix alignments in transfac_pro.pm) my $longest = 0; foreach (@blocks) { my ($seq) = split('_', $_); my $length = length($seq); if ($length > $longest) { $longest = $length; } } foreach my $i (0..$#blocks) { my $block = $blocks[$i]; my ($seq, $seq_id) = split('_', $block); my $length = length($seq); if ($length < $longest) { my $orig_seq = $seq; $seq .= '-'x($longest - $length); $block =~ s/^${orig_seq}_/${seq}_/; $blocks[$i] = $block; } } # build the alignment my $aln = Bio::SimpleAlign->new(-source => 'transfac_pro'); my %done_ids; foreach (@blocks) { my ($seq, $seq_acc, $start, $strand) = split('_', $_); $self->throw("Invalid strand $strand found in block $_") unless exists $VALID_STRAND{$strand}; # we can get back multiple different subparts of the same site (sequence), # so $seq_acc isn't unique across this loop. Can't use it as the seq id # of the alignment (ids must be unique in SimpleAlign), so we # uniquify the id and store the original id as the accession_number my $seq_id; $done_ids{$seq_acc}++; if ($done_ids{$seq_acc} > 1) { $seq_id = $seq_acc.'_'.$done_ids{$seq_acc}; } else { $seq_id = $seq_acc; } my $gaps = $seq =~ tr/-//; my $length = length($seq) - $gaps; $self->throw("seq '$seq_id' for matrix '$id' had seq '$seq'") unless $length; $aln->add_seq(Bio::LocatableSeq->new(-seq => $seq, -id => $seq_id, -accession_number => $seq_acc, -start => $start, -end => $start + $length - 1, -strand => $strand)); } $aln->id($id); # could also store score? of? return $aln; } =head2 get_factor Title : get_factor Usage : my $factor = $obj->get_factor($id); Function: Get the details of a transcription factor. Returns : Bio::Map::TranscriptionFactor Args : string - a factor id ('T...') =cut sub get_factor { my ($self, $id) = @_; $id || return; return $self->{got_factor}->{$id} if defined $self->{got_factor}->{$id}; my $data = $self->{factor}->{data}->{$id} || return; my @data = split(SEPARATOR, $data); # accession = id name species sequence my $tf = Bio::Map::TranscriptionFactor->get(-id => $id, -universal_name => $data[1]); #*** not sure what to do with species and sequence, since we don't want to # confuse the idea that a TF is a general thing that could bind to any # species... then again, you might want to model species-specific variants # of a TF with different binding abilities... #*** idea of having inclusion and exclusion species so you can prevent/ # ignore a tf that binds to the wrong species (a species that doesn't even # have the tf), and associating sequence with each species/tf combo so you # can see how diverged the tf is and make assumptions about site difference # allowance # place it on all its genemaps foreach my $sid ($self->get_site_ids(-factor => $id)) { my $s_data = $self->{site}->{data}->{$sid} || next; my @s_data = split(SEPARATOR, $s_data); # accession = id gene_id sequence relative_to first_position last_position species_tax_id_or_raw_string $s_data[1] || next; # site isn't relative to a gene, meaningless $s_data[4] || next; # don't know where its supposed to be, can't model it $s_data[5] ||= $s_data[4] + ($s_data[2] ? length($s_data[2]) - 1 : 0); # it is quite deliberate that we deeply recurse to arrive at the # correct answer, which involves pulling in most of the database no warnings "recursion"; my $gene_map = $self->get_genemap($s_data[1]) || next; return $self->{got_factor}->{$id} if defined $self->{got_factor}->{$id}; #*** not always relative to gene start... # we need Bio::Map::Gene s to have some default tss and atg positions # that we can be relative to my $rel = Bio::Map::Relative->new(-element => $gene_map->gene, -description => $s_data[3]); Bio::Map::Position->new(-map => $gene_map, -element => $tf, -start => $s_data[4], -end => $s_data[5], -relative => $rel); } $self->{got_factor}->{$id} = $tf; return $tf; } # since get_factor() is uncertain, just have direct access methods to factor # information sub get_factor_name { my ($self, $id) = @_; my $details = $self->_get_factor_details($id) || return; return $details->{name}; } sub get_factor_species { my ($self, $id) = @_; my $details = $self->_get_factor_details($id) || return; return $details->{species}; } sub get_factor_sequence { my ($self, $id) = @_; my $details = $self->_get_factor_details($id) || return; return $details->{sequence}; } sub _get_factor_details { my ($self, $id) = @_; $id || return; return $self->{factor_details}->{$id} if defined $self->{factor_details}->{$id}; my $data = $self->{factor}->{data}->{$id} || return; my @data = split(SEPARATOR, $data); # accession = id name species sequence my %details = (name => $data[1], species => $data[2], sequence => $data[3]); $self->{factor_details}->{$id} = \%details; return \%details; } =head2 get_reference_ids Title : get_reference_ids Usage : my @ids = $obj->get_reference_ids(-key => $value); Function: Get all the reference ids that are associated with the supplied args. Returns : list of strings (ids) Args : -key => value, where value is a string id, and key is one of: -pubmed -site -gene -matrix -factor =cut sub get_reference_ids { my $self = shift; return $self->_get_ids('reference', @_); } # -id -name -species -site -factor -reference sub get_gene_ids { my $self = shift; return $self->_get_ids('gene', @_); } =head2 get_site_ids Title : get_site_ids Usage : my @ids = $obj->get_site_ids(-key => $value); Function: Get all the site ids that are associated with the supplied args. Returns : list of strings (ids) Args : -key => value, where value is a string id, and key is one of: -id -species -gene -matrix -factor -reference =cut sub get_site_ids { my $self = shift; return $self->_get_ids('site', @_); } =head2 get_matrix_ids Title : get_matrix_ids Usage : my @ids = $obj->get_matrix_ids(-key => $value); Function: Get all the matrix ids that are associated with the supplied args. Returns : list of strings (ids) Args : -key => value, where value is a string id, and key is one of: -id -name -site -factor -reference =cut sub get_matrix_ids { my $self = shift; return $self->_get_ids('matrix', @_); } =head2 get_factor_ids Title : get_factor_ids Usage : my @ids = $obj->get_factor_ids(-key => $value); Function: Get all the factor ids that are associated with the supplied args. Returns : list of strings (ids) Args : -key => value, where value is a string id, and key is one of: -id -name -species -interactors -gene -matrix -site -reference NB: -gene only gets factor ids for genes that encode factors =cut sub get_factor_ids { my $self = shift; return $self->_get_ids('factor', @_); } =head2 get_fragment_ids Title : get_fragment_ids Usage : my @ids = $obj->get_fragment_ids(-key => $value); Function: Get all the fragment ids that are associated with the supplied args. Returns : list of strings (ids) Args : -key => value, where value is a string id, and key is one of: -id -species -gene -factor -reference =cut sub get_fragment_ids { my $self = shift; return $self->_get_ids('fragment', @_); } =head2 Helper methods =cut # internal method which does the indexing sub _build_index { my ($self, $dat_dir, $force) = @_; # MLDBM would give us transparent complex data structures with DB_File, # allowing just one index file, but its yet another requirement and we # don't strictly need it my $index_dir = $self->index_directory; my $gene_index = "$index_dir/gene.dat.index"; my $reference_index = "$index_dir/reference.dat.index"; my $matrix_index = "$index_dir/matrix.dat.index"; my $factor_index = "$index_dir/factor.dat.index"; my $fragment_index = "$index_dir/fragment.dat.index"; my $site_index = "$index_dir/site.dat.index"; my $reference_dat = "$dat_dir/reference.dat"; if (! -e $reference_index || $force) { open my $REF, '<', $reference_dat or $self->throw("Could not read reference file '$reference_dat': $!"); my %references; unlink $reference_index; my $ref = tie(%references, 'DB_File', $reference_index, O_RDWR|O_CREAT, 0644, $DB_HASH) or $self->throw("CCould not open file '$reference_index': $!"); my %pubmed; my $reference_pubmed = $reference_index.'.pubmed'; unlink $reference_pubmed; my $pub = tie(%pubmed, 'DB_File', $reference_pubmed, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$reference_pubmed': $!"); my %gene; my $reference_gene = $gene_index.'.reference'; unlink $reference_gene; my $gene = tie(%gene, 'DB_File', $reference_gene, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$reference_gene': $!"); my %site; my $reference_site = $site_index.'.reference'; unlink $reference_site; my $site = tie(%site, 'DB_File', $reference_site, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$reference_site': $!"); my %fragment; my $reference_fragment = $fragment_index.'.reference'; unlink $reference_fragment; my $fragment = tie(%fragment, 'DB_File', $reference_fragment, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$reference_fragment': $!"); my %factor; my $reference_factor = $factor_index.'.reference'; unlink $reference_factor; my $factor = tie(%factor, 'DB_File', $reference_factor, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$reference_factor': $!"); my %matrix; my $reference_matrix = $matrix_index.'.reference'; unlink $reference_matrix; my $matrix = tie(%matrix, 'DB_File', $reference_matrix, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$reference_matrix': $!"); # skip the first three header lines <$REF>; <$REF>; <$REF>; my @data; while (<$REF>) { if (/^AC (\S+)/) { $data[0] = $1; } elsif (/^RX PUBMED: (\d+)/) { $data[1] = $1; $pub->put("$1", $data[0]); } elsif (/^RA (.+)\n$/) { $data[2] = $1; } elsif (/^RT (.+?)\.?\n$/) { $data[3] = $1; } elsif (/^RL (.+?)\.?\n$/) { $data[4] = $1; } elsif (/^GE TRANSFAC: (\w\d+)/) { $gene->put($data[0], "$1"); } elsif (/^BS TRANSFAC: (\w\d+)/) { $site->put($data[0], "$1"); } elsif (/^FA TRANSFAC: (\w\d+)/) { $factor->put($data[0], "$1"); } elsif (/^FR TRANSFAC: (FR\d+)/) { $fragment->put($data[0], "$1"); } elsif (/^MX TRANSFAC: (\w\d+)/) { $matrix->put($data[0], "$1"); } elsif (/^\/\//) { # end of a record, store previous data and reset # accession = pubmed authors title location $references{$data[0]} = join(SEPARATOR, ($data[1] || '', $data[2] || '', $data[3] || '', $data[4] || '')); @data = (); } } close $REF; $ref = $pub = $gene = $site = $fragment = $factor = $matrix = undef; untie %references; untie %pubmed; untie %gene; untie %site; untie %fragment; untie %factor; untie %matrix; } my $gene_dat = "$dat_dir/gene.dat"; if (! -e $gene_index || $force) { open my $GEN, '<', $gene_dat or $self->throw("Could not read gene file '$gene_dat': $!"); my %genes; unlink $gene_index; my $gene = tie(%genes, 'DB_File', $gene_index, O_RDWR|O_CREAT, 0644, $DB_HASH) or $self->throw("Could not open file '$gene_index': $!"); my %id; my $gene_id = $gene_index.'.id'; unlink $gene_id; my $id = tie(%id, 'DB_File', $gene_id, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$gene_id': $!"); my %name; my $gene_name = $gene_index.'.name'; unlink $gene_name; my $name = tie(%name, 'DB_File', $gene_name, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$gene_name': $!"); my %species; my $gene_species = $gene_index.'.species'; unlink $gene_species; my $species = tie(%species, 'DB_File', $gene_species, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$gene_species': $!"); my %site; my $gene_site = $site_index.'.gene'; unlink $gene_site; my $site = tie(%site, 'DB_File', $gene_site, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$gene_site': $!"); my %factor; my $gene_factor = $factor_index.'.gene'; unlink $gene_factor; my $factor = tie(%factor, 'DB_File', $gene_factor, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$gene_factor': $!"); my %fragment; my $gene_fragment = $fragment_index.'.gene'; unlink $gene_fragment; my $fragment = tie(%fragment, 'DB_File', $gene_fragment, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$gene_fragment': $!"); my %reference; my $gene_reference = $reference_index.'.gene'; unlink $gene_reference; my $reference = tie(%reference, 'DB_File', $gene_reference, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$gene_reference': $!"); # skip the first three header lines <$GEN>; <$GEN>; <$GEN>; my @data; while (<$GEN>) { if (/^AC (\S+)/) { $data[0] = $1; } elsif (/^ID (\S+)/) { $data[1] = $1; $id->put("$1", $data[0]); } elsif (/^SD (.+)$/) { $data[2] = lc("$1"); $name->put(lc("$1"), $data[0]); } elsif (/^SY (.+)\.$/) { foreach (split('; ', lc("$1"))) { $name->put($_, $data[0]); } } elsif (/^DE (.+)$/) { $data[3] = $1; } elsif (/^OS (.+)$/) { my $raw_species = $1; my $taxid = $self->_species_to_taxid($raw_species); $data[4] = $taxid || $raw_species; $species->put($data[4], $data[0]); } elsif (/^RN .+?(RE\d+)/) { $reference->put($data[0], "$1"); } elsif (/^BS .+?(R\d+)/) { $site->put($data[0], "$1"); } elsif (/^FA (T\d+)/) { $factor->put($data[0], "$1"); } elsif (/^BR (FR\d+)/) { $fragment->put($data[0], "$1"); } elsif (/^\/\//) { # end of a record, store previous data and reset # accession = id name description species_tax_id_or_raw_string $genes{$data[0]} = join(SEPARATOR, ($data[1] || '', $data[2] || '', $data[3] || '', $data[4] || '')); @data = (); } } close $GEN; $gene = $id = $name = $species = $site = $factor = $reference = undef; untie %genes; untie %id; untie %name; untie %species; untie %site; untie %factor; untie %reference; } my $site_dat = "$dat_dir/site.dat"; if (! -e $site_index || $force) { open my $SIT, '<', $site_dat or $self->throw("Could not read site file '$site_dat': $!"); my %sites; unlink $site_index; my $site = tie(%sites, 'DB_File', $site_index, O_RDWR|O_CREAT, 0644, $DB_HASH) or $self->throw("Could not open file '$site_index': $!"); my %id; my $site_id = $site_index.'.id'; unlink $site_id; my $id = tie(%id, 'DB_File', $site_id, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$site_id': $!"); my %species; my $site_species = $site_index.'.species'; unlink $site_species; my $species = tie(%species, 'DB_File', $site_species, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$site_species': $!"); my %qualities; my $site_qualities = $site_index.'.qual'; unlink $site_qualities; my $quality = tie(%qualities, 'DB_File', $site_qualities, O_RDWR|O_CREAT, 0644, $DB_HASH) or $self->throw("Could not open file '$site_qualities': $!"); my %gene; my $site_gene = $gene_index.'.site'; unlink $site_gene; my $gene = tie(%gene, 'DB_File', $site_gene, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$site_gene': $!"); my %matrix; my $site_matrix = $matrix_index.'.site'; unlink $site_matrix; my $matrix = tie(%matrix, 'DB_File', $site_matrix, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$site_matrix': $!"); my %factor; my $site_factor = $factor_index.'.site'; unlink $site_factor; my $factor = tie(%factor, 'DB_File', $site_factor, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$site_factor': $!"); my %reference; my $site_reference = $reference_index.'.site'; unlink $site_reference; my $reference = tie(%reference, 'DB_File', $site_reference, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$site_reference': $!"); # skip the first three header lines <$SIT>; <$SIT>; <$SIT>; my @data; while (<$SIT>) { if (/^AC (\S+)/) { $data[0] = $1; } elsif (/^ID (\S+)/) { $data[1] = $1; $id->put("$1", $data[0]); } elsif (/^TY (.+)$/) { $data[8] = $1; } elsif (/^DE .*Gene: (G\d+)/) { $data[2] = $1; $gene->put($data[0], "$1"); # if it has no gene it is an artificial sequence, unless it # has a species (OS line), in which case it is unassigned # genomic; either way we won't be able to make a # Bio::Map::PositionI later on, so such sites won't be # on any MapI. } elsif (/^OS (.+)$/) { # Since not all sites in site.dat with a species have a gene, # (small handful are unassigned 'genomic') can't delegate to # gene.dat and must parse species here (effectively again) my $raw_species = $1; my $taxid = $self->_species_to_taxid($raw_species); $data[7] = $taxid || $raw_species; $species->put($data[7], $data[0]); } elsif (/^SQ (.+)\.$/) { $data[3] = $1; # there can actually be more than one SQ line, seemingly with # variations of the sequence (not a long sequence split over # two lines); not sure what to do with data; currently we end # up storing only the last variant. } elsif (/^S1 (.+)$/) { $data[4] = $1; # if S1 not present, means transcriptional start } elsif (/^SF (.+)$/) { $data[5] = $1; } elsif (/^ST (.+)$/) { $data[6] = $1; } elsif (/^RN .+?(RE\d+)/) { $reference->put($data[0], "$1"); } elsif (/^MX (M\d+)/) { $matrix->put($data[0], "$1"); } elsif (/^BF (T\d+); .+?; Quality: (\d)/) { $factor->put($data[0], "$1"); $qualities{$data[0].SEPARATOR.$1} = $2; } elsif (/^\/\//) { # end of a record, store previous data and reset # accession = id gene_id sequence relative_to first_position last_position species_tax_id_or_raw_string type $sites{$data[0]} = join(SEPARATOR, ($data[1] || '', $data[2] || '', $data[3] || '', $data[4] || 'TSS', $data[5] || '', $data[6] || '', $data[7] || '', $data[8] || '')); @data = (); } } close $SIT; $site = $id = $species = $quality = $gene = $matrix = $factor = $reference = undef; untie %sites; untie %id; untie %species; untie %qualities; untie %gene; untie %matrix; untie %factor; untie %reference; } my $matrix_dat = "$dat_dir/matrix.dat"; if (! -e $matrix_index || $force) { open my $MAT, '<', $matrix_dat or $self->throw("Could not read matrix file '$matrix_dat': $!"); my %matrices; unlink $matrix_index; my $matrix = tie(%matrices, 'DB_File', $matrix_index, O_RDWR|O_CREAT, 0644, $DB_HASH) or $self->throw("Could not open file '$matrix_index': $!"); my %id; my $matrix_id = $matrix_index.'.id'; unlink $matrix_id; my $id = tie(%id, 'DB_File', $matrix_id, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$matrix_id': $!"); my %name; my $matrix_name = $matrix_index.'.name'; unlink $matrix_name; my $name = tie(%name, 'DB_File', $matrix_name, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$matrix_name': $!"); my %site; my $matrix_site = $site_index.'.matrix'; unlink $matrix_site; my $site = tie(%site, 'DB_File', $matrix_site, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$matrix_site': $!"); my %factor; my $matrix_factor = $factor_index.'.matrix'; unlink $matrix_factor; my $factor = tie(%factor, 'DB_File', $matrix_factor, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$matrix_factor': $!"); my %reference; my $matrix_reference = $reference_index.'.matrix'; unlink $matrix_reference; my $reference = tie(%reference, 'DB_File', $matrix_reference, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$matrix_reference': $!"); # skip the first three header lines <$MAT>; <$MAT>; <$MAT>; my @data; my @matrix_data; my @site_data; while (<$MAT>) { if (/^AC (\S+)/) { $data[0] = $1; } elsif (/^ID (\S+)/) { $data[1] = $1; $id->put("$1", $data[0]); } elsif (/^NA (.+)$/) { $data[2] = $1; $name->put("$1", $data[0]); } elsif (/^DE (.+)$/) { $data[3] = $1; } elsif (/^\d\d \s*(\S+)\s+(\S+)\s+(\S+)\s+(\S+)/) { # a, c, g, t counts/weights push(@matrix_data, join("\t", ($1, $2, $3, $4))); # Work out the number of sites as the largest number of # sites amongst all positions in the sequences. (The BA # line isn't reliable for telling us the correct number of # sites all the time) my $num = $1 + $2 + $3 + $4; $data[4] ||= 0; if ($num > $data[4]) { $data[4] = $num; } } elsif (/^BS ([\sa-zA-Z]+); (.+?); (-?\d+); \d+;.*; ([np])/) { # sequence id start strand push(@site_data, join('_', ($1, $2, $3, $4 eq 'p' ? 1 : -1))); $site->put($data[0], $2); } elsif (/^BF (T\d+)/) { $factor->put($data[0], "$1"); } elsif (/^RN .+?(RE\d+)/) { $reference->put($data[0], "$1"); } elsif (/^\/\//) { # end of a record, store previous data and reset my $matrix_data = join(INTERNAL_SEPARATOR, @matrix_data) || ''; # sites of a matrix are pre-aligned but padded with spaces on # the left and no padding on the right; pad with -s both sides my $longest_seq = 0; # For all the work, does anything meaningful actually get passed # on here? Commenting out fixes the latest crashes on trunk. # 5-10-10 cjfields #foreach my $site_seq (map {my ($seq) = split("_", $_ ,2); $seq;} @site_data) { # $site_seq =~ s/ /-/g; # my $length = length($site_seq); # if ($length > $longest_seq) { # $longest_seq = $length; # } #} #foreach my $site (@site_data) { # my ($site_seq) = split("_", $site ,2); # my $length = length($site_seq); # if ($length < $longest_seq) { # $site_seq .= '-' x ($longest_seq - $length); # } #} my $site_data = join(INTERNAL_SEPARATOR, @site_data) || ''; # accession = id name description num_of_sites matrix_data site_data $matrices{$data[0]} = join(SEPARATOR, ($data[1] || '', $data[2] || '', $data[3] || '', $data[4], $matrix_data, $site_data)); @data = @matrix_data = @site_data = (); } } close $MAT; $matrix = $id = $name = $site = $factor = $reference = undef; untie %matrices; untie %id; untie %name; untie %site; untie %factor; untie %reference; } my $factor_dat = "$dat_dir/factor.dat"; if (! -e $factor_index || $force) { open my $FAC, '<', $factor_dat or $self->throw("Could not read factor file '$factor_dat': $!"); my %factors; unlink $factor_index; my $factor = tie(%factors, 'DB_File', $factor_index, O_RDWR|O_CREAT, 0644, $DB_HASH) or $self->throw("Could not open file '$factor_index': $!"); my %id; my $factor_id = $factor_index.'.id'; unlink $factor_id; my $id = tie(%id, 'DB_File', $factor_id, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$factor_id': $!"); my %name; my $factor_name = $factor_index.'.name'; unlink $factor_name; my $name = tie(%name, 'DB_File', $factor_name, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$factor_name': $!"); my %species; my $factor_species = $factor_index.'.species'; unlink $factor_species; my $species = tie(%species, 'DB_File', $factor_species, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$factor_species': $!"); my %interactors; my $factor_interactors = $factor_index.'.interactors'; unlink $factor_interactors; my $interact = tie(%interactors, 'DB_File', $factor_interactors, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$factor_interactors': $!"); my %gene; my $factor_gene = $gene_index.'.factor'; unlink $factor_gene; my $gene = tie(%gene, 'DB_File', $factor_gene, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$factor_gene': $!"); my %matrix; my $factor_matrix = $matrix_index.'.factor'; unlink $factor_matrix; my $matrix = tie(%matrix, 'DB_File', $factor_matrix, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$factor_matrix': $!"); my %site; my $factor_site = $site_index.'.factor'; unlink $factor_site; my $site = tie(%site, 'DB_File', $factor_site, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$factor_site': $!"); my %fragment; my $factor_fragment = $fragment_index.'.factor'; unlink $factor_fragment; my $fragment = tie(%fragment, 'DB_File', $factor_fragment, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$factor_fragment': $!"); my %reference; my $factor_reference = $reference_index.'.factor'; unlink $factor_reference; my $reference = tie(%reference, 'DB_File', $factor_reference, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$factor_reference': $!"); # skip the first three header lines <$FAC>; <$FAC>; <$FAC>; my @data; my $sequence = ''; while (<$FAC>) { if (/^AC (\S+)/) { $data[0] = $1; } elsif (/^ID (\S+)/) { # IDs are always the same as AC? Is this needed? $data[1] = $1; $id->put("$1", $data[0]); } elsif (/^FA (.+)$/) { $data[2] = $1; $name->put("$1", $data[0]); } elsif (/^OS (.+)$/) { # This is the species the actual factor came from, which may # differ from the species of any sequences it is described as # binding to. Not all factors that have a species have a gene, # so can't delegate species to a gene lookup. my $raw_species = $1; my $taxid = $self->_species_to_taxid($raw_species); $data[3] = $taxid || $raw_species; $species->put($data[3], $data[0]); } elsif (/^GE (G\d+)/) { $gene->put($data[0], "$1"); } elsif (/^SQ (.+)$/) { $sequence .= $1; } elsif (/^IN (T\d+)/) { $interact->put($data[0], "$1"); } elsif (/^MX (M\d+)/) { $matrix->put($data[0], "$1"); } elsif (/^BS (R\d+)/) { $site->put($data[0], "$1"); } elsif (/^BR (FR\d+)/) { $fragment->put($data[0], "$1"); } elsif (/^RN .+?(RE\d+)/) { $reference->put($data[0], "$1"); } elsif (/^\/\//) { # end of a record, store previous data and reset # accession = id name species sequence $factors{$data[0]} = join(SEPARATOR, ($data[1] || '', $data[2] || '', $data[3] || '', $sequence)); @data = (); $sequence = ''; } } close $FAC; $factor = $id = $name = $species = $interact = $gene = $matrix = $site = $fragment = $reference = undef; untie %factors; untie %id; untie %name; untie %species; untie %interactors; untie %gene; untie %matrix; untie %site; untie %fragment; untie %reference; } my $fragment_dat = "$dat_dir/fragment.dat"; if (! -e $fragment_index || $force) { if (open my $FRA, '<', $fragment_dat) { my %fragments; unlink $fragment_index; my $fragment = tie(%fragments, 'DB_File', $fragment_index, O_RDWR|O_CREAT, 0644, $DB_HASH) or $self->throw("Could not open file '$fragment_index': $!"); my %id; my $fragment_id = $fragment_index.'.id'; unlink $fragment_id; my $id = tie(%id, 'DB_File', $fragment_id, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$fragment_id': $!"); my %qualities; my $fragment_qualities = $fragment_index.'.qual'; unlink $fragment_qualities; my $quality = tie(%qualities, 'DB_File', $fragment_qualities, O_RDWR|O_CREAT, 0644, $DB_HASH) or $self->throw("Could not open file '$fragment_qualities': $!"); my %species; my $fragment_species = $fragment_index.'.species'; unlink $fragment_species; my $species = tie(%species, 'DB_File', $fragment_species, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$fragment_species': $!"); my %gene; my $fragment_gene = $gene_index.'.fragment'; unlink $fragment_gene; my $gene = tie(%gene, 'DB_File', $fragment_gene, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$fragment_gene': $!"); my %factor; my $fragment_factor = $factor_index.'.fragment'; unlink $fragment_factor; my $factor = tie(%factor, 'DB_File', $fragment_factor, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$fragment_factor': $!"); my %reference; my $fragment_reference = $reference_index.'.fragment'; unlink $fragment_reference; my $reference = tie(%reference, 'DB_File', $fragment_reference, O_RDWR|O_CREAT, 0644, $DB_BTREE) or $self->throw("Could not open file '$fragment_reference': $!"); # skip the first three header lines <$FRA>; <$FRA>; <$FRA>; my @data; while (<$FRA>) { if (/^AC (\S+)/) { $data[0] = $1; } elsif (/^ID (\S+)/) { # IDs are always the same as AC? Is this needed? $data[1] = $1; $id->put("$1", $data[0]); } elsif (/^DE Gene: (G\d+)(?:.+Gene: (G\d+))?/) { my ($gene1, $gene2) = ($1, $2); $data[2] = $gene1; $data[3] = $gene2; # could be undef $gene->put($data[0], $gene1); $gene->put($data[0], $gene2) if $gene2; } elsif (/^OS (.+)$/) { # As per the site.dat parsing my $raw_species = $1; my $taxid = $self->_species_to_taxid($raw_species); $data[4] = $taxid || $raw_species; $species->put($data[4], $data[0]); } elsif (/^SQ [atcgn]*([ATCGN]+)[atcgn]*/) { $data[5] .= $1; # there can be (usually are) multiple SQ lines with a single # long seq split over them. The 'real' sequence is in caps } elsif (/^SC Build (\S+):$/) { $data[6] = $1; # maybe parse it out a little more? We have build, # chromosomal coords and strand, eg. # SC Build HSA_May2004: Chr.2 43976692..43978487 (FORWARD). } elsif (/^RN .+?(RE\d+)/) { $reference->put($data[0], "$1"); } elsif (/^BF (T\d+); .+?; Quality: (\d)/) { $factor->put($data[0], "$1"); $qualities{$data[0].SEPARATOR.$1} = $2; } elsif (/^\/\//) { # end of a record, store previous data and reset # accession = id gene_id1 gene_id2 species_tax_id_or_raw_string sequence source $fragments{$data[0]} = join(SEPARATOR, ($data[1] || '', $data[2] || '', $data[3] || '', $data[4] || '', $data[5] || '', $data[6] || '')); @data = (); } } close $FRA; $fragment = $id = $species = $quality = $gene = $factor = $reference = undef; untie %fragments; untie %id; untie %species; untie %qualities; untie %gene; untie %factor; untie %reference; } else { $self->warn("Could not read fragment file '$fragment_dat', assuming you have an old version of Transfac Pro with no fragment.dat file"); } } } # connect the internal db handle sub _db_connect { my $self = shift; return if $self->{'_initialized'}; my $index_dir = $self->index_directory; my $gene_index = "$index_dir/gene.dat.index"; my $reference_index = "$index_dir/reference.dat.index"; my $matrix_index = "$index_dir/matrix.dat.index"; my $factor_index = "$index_dir/factor.dat.index"; my $site_index = "$index_dir/site.dat.index"; my $fragment_index = "$index_dir/fragment.dat.index"; foreach ($gene_index, $reference_index, $matrix_index, $factor_index, $site_index, $fragment_index) { if (! -e $_) { #$self->warn("Index files have not been created"); #return 0; } } # reference { $self->{reference}->{data} = {}; tie (%{$self->{reference}->{data}}, 'DB_File', $reference_index, O_RDWR, undef, $DB_HASH) || $self->throw("Cannot open file '$reference_index': $!"); my $reference_pubmed = $reference_index.'.pubmed'; $self->{reference}->{pubmed} = tie (%{$self->{reference}->{pubmed}}, 'DB_File', $reference_pubmed, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$reference_pubmed': $!"); my $reference_gene = $gene_index.'.reference'; $self->{gene}->{reference} = tie (%{$self->{gene}->{reference}}, 'DB_File', $reference_gene, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$reference_gene': $!"); my $reference_site = $site_index.'.reference'; $self->{site}->{reference} = tie (%{$self->{site}->{reference}}, 'DB_File', $reference_site, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$reference_site': $!"); my $reference_fragment = $fragment_index.'.reference'; $self->{fragment}->{reference} = tie (%{$self->{fragment}->{reference}}, 'DB_File', $reference_fragment, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$reference_fragment': $!"); my $reference_factor = $factor_index.'.reference'; $self->{factor}->{reference} = tie (%{$self->{factor}->{reference}}, 'DB_File', $reference_factor, undef, 0644, $DB_BTREE) || $self->throw("Cannot open file '$reference_factor': $!"); my $reference_matrix = $matrix_index.'.reference'; $self->{matrix}->{reference} = tie (%{$self->{matrix}->{reference}}, 'DB_File', $reference_matrix, undef, 0644, $DB_BTREE) || $self->throw("Cannot open file '$reference_matrix': $!"); } # gene { $self->{gene}->{data} = {}; tie (%{$self->{gene}->{data}}, 'DB_File', $gene_index, O_RDWR, undef, $DB_HASH) || $self->throw("Cannot open file '$gene_index': $!"); my $gene_id = $gene_index.'.id'; $self->{gene}->{id} = tie(%{$self->{gene}->{id}}, 'DB_File', $gene_id, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_id': $!"); my $gene_name = $gene_index.'.name'; $self->{gene}->{name} = tie(%{$self->{gene}->{name}}, 'DB_File', $gene_name, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_name': $!"); my $gene_species = $gene_index.'.species'; $self->{gene}->{species} = tie(%{$self->{gene}->{species}}, 'DB_File', $gene_species, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_species': $!"); my $gene_site = $site_index.'.gene'; $self->{site}->{gene} = tie(%{$self->{site}->{gene}}, 'DB_File', $gene_site, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_site': $!"); my $gene_fragment = $fragment_index.'.gene'; $self->{fragment}->{gene} = tie(%{$self->{fragment}->{gene}}, 'DB_File', $gene_fragment, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_fragment': $!"); my $gene_factor = $factor_index.'.gene'; $self->{factor}->{gene} = tie(%{$self->{factor}->{gene}}, 'DB_File', $gene_factor, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_factor': $!"); my $gene_reference = $reference_index.'.gene'; $self->{reference}->{gene} = tie(%{$self->{reference}->{gene}}, 'DB_File', $gene_reference, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_reference': $!"); } # site { $self->{site}->{data} = {}; tie (%{$self->{site}->{data}}, 'DB_File', $site_index, O_RDWR, undef, $DB_HASH) || $self->throw("Cannot open file '$site_index': $!"); my $site_id = $site_index.'.id'; $self->{site}->{id} = tie(%{$self->{site}->{id}}, 'DB_File', $site_id, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$site_id': $!"); my $site_species = $site_index.'.species'; $self->{site}->{species} = tie(%{$self->{site}->{species}}, 'DB_File', $site_species, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file $site_species': $!"); #*** quality not actually used by anything (yet) my $site_qualities = $site_index.'.qual'; $self->{quality} = {}; tie(%{$self->{quality}}, 'DB_File', $site_qualities, O_RDWR, undef, $DB_HASH) || $self->throw("Cannot open file '$site_qualities': $!"); my $site_gene = $gene_index.'.site'; $self->{gene}->{site} = tie(%{$self->{gene}->{site}}, 'DB_File', $site_gene, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$site_gene': $!"); my $site_matrix = $matrix_index.'.site'; $self->{matrix}->{site} = tie(%{$self->{matrix}->{site}}, 'DB_File', $site_matrix, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$site_matrix': $!"); my $site_factor = $factor_index.'.site'; $self->{factor}->{site} = tie(%{$self->{factor}->{site}}, 'DB_File', $site_factor, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$site_factor': $!"); my $site_reference = $reference_index.'.site'; $self->{reference}->{site} = tie(%{$self->{reference}->{site}}, 'DB_File', $site_reference, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$site_reference': $!"); } # fragment (may not be in older databases) if (-e $fragment_index) { $self->{fragment}->{data} = {}; tie (%{$self->{fragment}->{data}}, 'DB_File', $fragment_index, O_RDWR, undef, $DB_HASH) || $self->throw("Cannot open file '$fragment_index': $!"); my $fragment_id = $fragment_index.'.id'; $self->{fragment}->{id} = tie(%{$self->{fragment}->{id}}, 'DB_File', $fragment_id, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$fragment_id': $!"); my $fragment_species = $fragment_index.'.species'; $self->{fragment}->{species} = tie(%{$self->{fragment}->{species}}, 'DB_File', $fragment_species, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file $fragment_species': $!"); #*** quality not actually used by anything (yet) my $fragment_qualities = $fragment_index.'.qual'; $self->{fragment_quality} = {}; tie(%{$self->{fragment_quality}}, 'DB_File', $fragment_qualities, O_RDWR, undef, $DB_HASH) || $self->throw("Cannot open file '$fragment_qualities': $!"); my $fragment_gene = $gene_index.'.fragment'; $self->{gene}->{fragment} = tie(%{$self->{gene}->{fragment}}, 'DB_File', $fragment_gene, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$fragment_gene': $!"); my $fragment_factor = $factor_index.'.fragment'; $self->{factor}->{fragment} = tie(%{$self->{factor}->{fragment}}, 'DB_File', $fragment_factor, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$fragment_factor': $!"); my $fragment_reference = $reference_index.'.fragment'; $self->{reference}->{fragment} = tie(%{$self->{reference}->{fragment}}, 'DB_File', $fragment_reference, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$fragment_reference': $!"); } else { die "no fragment_index at '$fragment_index'\n"; } # matrix { $self->{matrix}->{data} = {}; tie (%{$self->{matrix}->{data}}, 'DB_File', $matrix_index, O_RDWR, undef, $DB_HASH) || $self->throw("Cannot open file '$matrix_index': $!"); my $matrix_id = $matrix_index.'.id'; $self->{matrix}->{id} = tie(%{$self->{matrix}->{id}}, 'DB_File', $matrix_id, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$matrix_id': $!"); my $matrix_name = $matrix_index.'.name'; $self->{matrix}->{name} = tie(%{$self->{matrix}->{name}}, 'DB_File', $matrix_name, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$matrix_name': $!"); my $matrix_site = $site_index.'.matrix'; $self->{site}->{matrix} = tie(%{$self->{site}->{matrix}}, 'DB_File', $matrix_site, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$matrix_site': $!"); my $matrix_factor = $factor_index.'.matrix'; $self->{factor}->{matrix} = tie(%{$self->{factor}->{matrix}}, 'DB_File', $matrix_factor, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$matrix_factor': $!"); my $matrix_reference = $reference_index.'.matrix'; $self->{reference}->{matrix} = tie(%{$self->{reference}->{matrix}}, 'DB_File', $matrix_reference, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$matrix_reference': $!"); } # factor { $self->{factor}->{data} = {}; tie (%{$self->{factor}->{data}}, 'DB_File', $factor_index, O_RDWR, undef, $DB_HASH) || $self->throw("Cannot open file '$factor_index': $!"); my $factor_id = $factor_index.'.id'; $self->{factor}->{id} = tie(%{$self->{factor}->{id}}, 'DB_File', $factor_id, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file 'factor_id': $!"); my $factor_name = $factor_index.'.name'; $self->{factor}->{name} = tie(%{$self->{factor}->{name}}, 'DB_File', $factor_name, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_name': $!"); my $factor_species = $factor_index.'.species'; $self->{factor}->{species} = tie(%{$self->{factor}->{species}}, 'DB_File', $factor_species, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_species': $!"); my $factor_interactors = $factor_index.'.interactors'; $self->{factor}->{interactors} = tie(%{$self->{factor}->{interactors}}, 'DB_File', $factor_interactors, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_interactors': $!"); my $factor_gene = $gene_index.'.factor'; $self->{gene}->{factor} = tie(%{$self->{gene}->{factor}}, 'DB_File', $factor_gene, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_gene': $!"); my $factor_matrix = $matrix_index.'.factor'; $self->{matrix}->{factor} = tie(%{$self->{matrix}->{factor}}, 'DB_File', $factor_matrix, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_matrix': $!"); my $factor_site = $site_index.'.factor'; $self->{site}->{factor} = tie(%{$self->{site}->{factor}}, 'DB_File', $factor_site, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_site': $!"); my $factor_fragment = $fragment_index.'.factor'; $self->{fragment}->{factor} = tie(%{$self->{fragment}->{factor}}, 'DB_File', $factor_fragment, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_fragment': $!"); my $factor_reference = $reference_index.'.factor'; $self->{reference}->{factor} = tie(%{$self->{reference}->{factor}}, 'DB_File', $factor_reference, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_reference': $!"); } $self->{'_initialized'} = 1; } =head2 index_directory Title : index_directory Function : Get/set the location that index files are stored. (this module will index the supplied database) Usage : $obj->index_directory($newval) Returns : value of index_directory (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub index_directory { my $self = shift; return $self->{'index_directory'} = shift if @_; return $self->{'index_directory'}; } # resolve a transfac species string into an ncbi taxid sub _species_to_taxid { my ($self, $raw_species) = @_; $raw_species or return; my $species_string; my @split = split(', ', $raw_species); (@split > 1) ? ($species_string = $split[1]) : ($species_string = $split[0]); my $ncbi_taxid; if ($species_string =~ /^[A-Z]\S+ \S+$/) { SWITCH: for ($species_string) { # some species don't classify so custom handling /^Darnel ryegrass/ && do { $ncbi_taxid = 34176; last; }; /^Coix lacryma/ && do { $ncbi_taxid = 4505; last; }; /^Rattus spec/ && do { $ncbi_taxid = 10116; last; }; /^Mus spec/ && do { $ncbi_taxid = 10090; last; }; /^Equus spec/ && do { $ncbi_taxid = 9796; last; }; /^Cavia sp/ && do { $ncbi_taxid = 10141; last; }; /^Marsh marigold/ && do { $ncbi_taxid = 3449; last; }; /^Phalaenopsis sp/ && do { $ncbi_taxid = 36900; last; }; /^Anthirrhinum majus/ && do { $ncbi_taxid = 4151; last; }; /^Equus spec/ && do { $ncbi_taxid = 9796; last; }; /^Lycopodium spec/ && do { $ncbi_taxid = 13840; last; }; /^Autographa californica/ && do { $ncbi_taxid = 307456; last; }; /^E26 AEV/ && do { $ncbi_taxid = 31920; last; }; /^Pseudocentrotus miliaris/ && do { $ncbi_taxid = 7677; last; }; # the genus is 7677 but this species isn't there /^SL3-3 (?:retro)?virus/ && do { $ncbi_taxid = 53454; last; }; # 53454 is unclassified MLV-related, SL3-3 a variant of that? /^Petunia sp/ && do { $ncbi_taxid = 4104; last; }; } if (! $ncbi_taxid && defined $self->{_tax_db}) { ($ncbi_taxid) = $self->{_tax_db}->get_taxonids($species_string); } } else { # some species lines are poorly formatted so custom handling SWITCH: for ($raw_species) { # for speed, go by common first letters my $first_letter = substr($raw_species, 0, 1); $first_letter eq 'A' && do { /^Adiantum raddianum/ && do { $ncbi_taxid = 32168; last; }; /^Avian sarcoma virus \(strain 17\)/ && do { $ncbi_taxid = 11877; last; }; /^AMV/ && do { $ncbi_taxid = 11866; last; }; /^AEV/ && do { $ncbi_taxid = 11861; last; }; /^AS42|^Avian musculoaponeurotic/ && do { $ncbi_taxid = 11873; last; }; /^Avian myelocytomatosis/ && do { $ncbi_taxid = 11869; last; }; /^ASV 31/ && do { $ncbi_taxid = 35270; last; }; /^A-MuLV/ && do { $ncbi_taxid = 188539; last; }; /^Asparagus officinalis/ && do { $ncbi_taxid = 4686; last; }; /^Agrobacterium tumefaciens/ && do { $ncbi_taxid = 358; last; }; /^ALV/ && do { $ncbi_taxid = 11864; last; }; /^AAV/ && do { $ncbi_taxid = 272636; last; }; /^AKV MLV/ && do { $ncbi_taxid = 11791; last; }; last; }; $first_letter eq 'B' && do { /^BPV-1/ && do { $ncbi_taxid = 10559; last; }; /^BKV/ && do { $ncbi_taxid = 10629; last; }; /^Bolivian squirrel monkey/ && do { $ncbi_taxid = 39432; last; }; last; }; $first_letter eq 'C' && do { /^Cauliflower/ && do { $ncbi_taxid = 3715; last; }; /^Chamek/ && do { $ncbi_taxid = 118643; last; }; /^Candida albicans/ && do { $ncbi_taxid = 5476; last; }; /^CaMV/ && do { $ncbi_taxid = 10641; last; }; last; }; $first_letter eq 'E' && do { /^Eucalyptus gunnii/ && do { $ncbi_taxid = 3933; last; }; /^EBV, Epstein-Barr virus/ && do { $ncbi_taxid = 10376; last; }; /^Eucalyptus globulus subsp. bicostata/ && do { $ncbi_taxid = 71272; last; }; /^Eucalyptus globulus subsp. globulus/ && do { $ncbi_taxid = 71271; last; }; last; }; $first_letter eq 'F' && do { /^FBR MuLV/ && do { $ncbi_taxid = 11806; last; }; /^FBJ MuLV/ && do { $ncbi_taxid = 11805; last; }; /^FeLV|Feline leukemia/ && do { $ncbi_taxid = 11923; last; }; /^Flaveria trinervia/ && do { $ncbi_taxid = 4227; last; }; /^FSV/ && do { $ncbi_taxid = 11885; last; }; /^F-MuLV/ && do { $ncbi_taxid = 11795; last; }; last; }; $first_letter eq 'H' && do { /^HSV-1/ && do { $ncbi_taxid = 10298; last; }; /^HTLV-I/ && do { $ncbi_taxid = 11908; last; }; /^HIV-1/ && do { $ncbi_taxid = 11676; last; }; /^HPV-16/ && do { $ncbi_taxid = 333760; last; }; /^HBV/ && do { $ncbi_taxid = 10407; last; }; /^HBI/ && do { $ncbi_taxid = 11867; last; }; /^HPV-8/ && do { $ncbi_taxid = 10579; last; }; /^HPV-11/ && do { $ncbi_taxid = 10580; last; }; /^HPV-18/ && do { $ncbi_taxid = 333761; last; }; /^HCMV/ && do { $ncbi_taxid = 10359; last; }; /^HSV/ && do { $ncbi_taxid = 126283; last; }; /^HSV-2/ && do { $ncbi_taxid = 10310; last; }; /^HCV/ && do { $ncbi_taxid = 11108; last; }; /^HIV-2/ && do { $ncbi_taxid = 11709; last; }; last; }; $first_letter eq 'M' && do { /^MMTV/ && do { $ncbi_taxid = 11757; last; }; /^Mo-MuLV/ && do { $ncbi_taxid = 11801; last; }; /^MuLV/ && do { $ncbi_taxid = 11786; last; }; /^MSV/ && do { $ncbi_taxid = 11802; last; }; /^MC29/ && do { $ncbi_taxid = 11868; last; }; /^MVM/ && do { $ncbi_taxid = 10794; last; }; /^MH2E21/ && do { $ncbi_taxid = 11955; last; }; # 11955 is a species, presumably MH2E21 is the strain last; }; $first_letter eq 'R' && do { /^Raphanus sativus/ && do { $ncbi_taxid = 3726; last; }; /^REV-T/ && do { $ncbi_taxid = 11636; last; }; /^RAV-0/ && do { $ncbi_taxid = 11867; last; }; # should be rous-associated virus 0 variant /^RSV/ && do { $ncbi_taxid = 11886; last; }; /^RadLV/ && do { $ncbi_taxid = 31689; last; }; /^RTBV/ && do { $ncbi_taxid = 10654; last; }; last; }; $first_letter eq 'S' && do { /^SV40/ && do { $ncbi_taxid = 10633; last; }; /^Sesbania rostrata/ && do { $ncbi_taxid = 3895; last; }; /^SIV/ && do { $ncbi_taxid = 11723; last; }; /^Spinacia oleracea/ && do { $ncbi_taxid = 3562; last; }; /^SCMV/ && do { $ncbi_taxid = 10364; last; }; # supposed to be AGM isolate last; }; # and lower case $first_letter eq 'a' && do { /^adenovirus type 5/ && do { $ncbi_taxid = 28285; last; }; /^adenovirus type 2/ && do { $ncbi_taxid = 10515; last; }; /^adenovirus/ && do { $ncbi_taxid = 189831; last; }; # 189831 ('unclassified Adenoviridae') is the closest I can get, but this has no genus and is not a species last; }; $first_letter eq 'b' && do { /^bell pepper/ && do { $ncbi_taxid = 4072; last; }; /^baculovirus, Autographa californica/ && do { $ncbi_taxid = 46015; last; }; /^broccoli/ && do { $ncbi_taxid = 36774; last; }; /^barley/ && do { $ncbi_taxid = 112509; last; }; last; }; $first_letter eq 'c' && do { /^clawed frog/ && do { $ncbi_taxid = 8355; last; }; /^chipmunk/ && do { $ncbi_taxid = 64680; last; }; /^common tree shrew/ && do { $ncbi_taxid = 37347; last; }; /^cat/ && do { $ncbi_taxid = 9685; last; }; last; }; # and misc /^NK24/ && do { $ncbi_taxid = 11955; last; }; /^OK10/ && do { $ncbi_taxid = 11871; last; }; /^Dendrobium grex/ && do { $ncbi_taxid = 84618; last; }; /^KSHV/ && do { $ncbi_taxid = 37296; last; }; /^Oncidium/ && do { $ncbi_taxid = 96474; last; }; /^Japanese quail/ && do { $ncbi_taxid = 93934; last; }; /^Nile tilapia/ && do { $ncbi_taxid = 8128; last; }; /^GALV/ && do { $ncbi_taxid = 11840; last; }; /^JCV/ && do { $ncbi_taxid = 10632; last; }; /^LPV/ && do { $ncbi_taxid = 10574; last; }; /^Py,/ && do { $ncbi_taxid = 36362; last; }; /^DHBV/ && do { $ncbi_taxid = 12639; last; }; /^VZV/ && do { $ncbi_taxid = 10335; last; }; /^Vicia faba/ && do { $ncbi_taxid = 3906; last; }; /^hamster/ && do { $ncbi_taxid = 10029; last; }; /^sea urchin/ && do { $ncbi_taxid = 7668; last; }; /^fruit fly/ && do { $ncbi_taxid = 7227; last; }; /^halibut/ && do { $ncbi_taxid = 8267; last; }; /^vaccinia virus/ && do { $ncbi_taxid = 10245; last; }; /^taxonomic class Mammalia/ && do { $ncbi_taxid = 40674; last; }; # not a species /^taxonomic class Vertebrata/ && do { $ncbi_taxid = 7742; last; }; # not a species /^dog/ && do { $ncbi_taxid = 9615; last; }; /^parsley/ && do { $ncbi_taxid = 4043; last; }; /^mouse, Mus domesticus Torino/ && do { $ncbi_taxid = 10092; last; }; # 10092 is domesticus subspecies, but not the Torino strain /^lemur, Eulemur fulvus collaris/ && do { $ncbi_taxid = 47178; last; }; /^red sea bream/ && do { $ncbi_taxid = 143350; last; }; /^zebra finch/ && do { $ncbi_taxid = 59729; last; }; /^mung bean/ && do { $ncbi_taxid = 3916; last; }; /^soybean/ && do { $ncbi_taxid = 3847; last; }; /^oat/ && do { $ncbi_taxid = 4498; last; }; /^pseudorabies virus/ && do { $ncbi_taxid = 10345; last; }; } } $self->warn("Didn't know what species '$raw_species' was, unable to classify") unless $ncbi_taxid; return $ncbi_taxid; } sub DESTROY { my $self = shift; # Destroy tied references to close filehandles # and allow proper temporary files deletion undef $self->{_tax_db}->{'_nodes'}; undef $self->{_tax_db}->{'_id2name'}; undef $self->{_tax_db}->{'_name2id'}; undef $self->{_tax_db}->{'_parent2children'}; undef $self->{_tax_db}->{'_parentbtree'}; } 1; BioPerl-1.007002/Bio/DB/Taxonomy000755000766000024 013155576320 16172 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/DB/Taxonomy/entrez.pm000444000766000024 5254413155576320 20226 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::Taxonomy::entrez # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Taxonomy::entrez - Taxonomy Entrez driver =head1 SYNOPSIS # Do not use this object directly, rather through the Bio::DB::Taxonomy # interface use Bio::DB::Taxonomy; my $db = Bio::DB::Taxonomy->new(-source => 'entrez'); my $taxonid = $db->get_taxonid('Homo sapiens'); my $node = $db->get_Taxonomy_Node(-taxonid => $taxonid); my $gi = 71836523; my $node = $db->get_Taxonomy_Node(-gi => $gi, -db => 'protein'); print $node->binomial, "\n"; my ($species,$genus,$family) = $node->classification; print "family is $family\n"; # Can also go up 4 levels my $p = $node; for ( 1..4 ) { $p = $db->get_Taxonomy_Node(-taxonid => $p->parent_id); } print $p->rank, " ", ($p->classification)[0], "\n"; # could then classify a set of BLAST hits based on their GI numbers # into taxonomic categories. It is not currently possibly to query a node for its children so we cannot completely replace the advantage of the flatfile Bio::DB::Taxonomy::flatfile module. =head1 DESCRIPTION A driver for querying NCBI Entrez Taxonomy database. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Sendu Bala: bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Taxonomy::entrez; use vars qw($EntrezLocation $UrlParamSeparatorValue %EntrezParams $EntrezGet $EntrezSummary $EntrezFetch %SequenceParams $XMLTWIG $DATA_CACHE $RELATIONS); use strict; use Bio::Taxon; use Bio::DB::NCBIHelper; eval { require XML::Twig; $XMLTWIG = 1; }; if( $@ ) { $XMLTWIG = 0; } use base qw(Bio::WebAgent Bio::DB::Taxonomy); $EntrezLocation = $Bio::DB::NCBIHelper::HOSTBASE . '/entrez/eutils/'; $EntrezGet = 'esearch.fcgi'; $EntrezFetch = 'efetch.fcgi'; $EntrezSummary = 'esummary.fcgi'; $DATA_CACHE = {}; $RELATIONS = {}; %EntrezParams = ( 'db' => 'taxonomy', 'report' => 'xml', 'retmode'=> 'xml', 'tool' => 'Bioperl'); %SequenceParams = ( 'db' => 'nucleotide', # or protein 'retmode' => 'xml', 'tool' => 'Bioperl'); $UrlParamSeparatorValue = '&'; =head2 new Title : new Usage : my $obj = Bio::DB::Taxonomy::entrez->new(); Function: Builds a new Bio::DB::Taxonomy::entrez object Returns : an instance of Bio::DB::Taxonomy::entrez Args : -location => URL to Entrez (if you want to override the default) -params => Hashref of URL params if you want to override the default =cut sub new { my ($class, @args) = @_; # need to initialise Bio::WebAgent... my ($self) = $class->SUPER::new(@args); # ... as well as our normal Bio::DB::Taxonomy selves: $self->_initialize(@args); return $self; } sub _initialize { my($self) = shift; $self->SUPER::_initialize(@_); my ($location,$params) = $self->_rearrange([qw(LOCATION PARAMS)],@_); if( $params ) { if( ref($params) !~ /HASH/i ) { $self->warn("Must have provided a valid HASHref for -params"); $params = \%EntrezParams; } } else { $params = \%EntrezParams; } $self->entrez_params($params); $self->entrez_url($location || $EntrezLocation ); } =head2 get_num_taxa Title : get_num_taxa Usage : my $num = $db->get_num_taxa(); Function: Get the number of taxa stored in the database. Returns : A number Args : None =cut sub get_num_taxa { my ($self) = @_; # Use this URL query to get the ID of all the taxa in the NCBI Taxonomy database: # https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=all[Filter] # Only the first 20 taxa IDs are returned (good because the list is long), # and the total number is reported as well (which is what we are interested # in). my %p = $self->entrez_params; $p{'term'} = 'all[Filter]'; my $twig = $self->_run_query($self->_build_url($EntrezGet, \%p)); my $count = $twig->root->first_child('Count')->first_child->text; return $count; } =head2 get_taxon Title : get_taxon Usage : my $taxon = $db->get_taxon(-taxonid => $taxonid) Function: Get a Bio::Taxon object from the database. Returns : Bio::Taxon object Args : just a single value which is the database id, OR named args: -taxonid => taxonomy id (to query by taxonid) OR -name => string (to query by a taxonomy name: common name, scientific name, etc) OR To retrieve a taxonomy node for a GI number provide the -gi option with the gi number and -db with either 'nucleotide' or 'protein' to define the db. AND optionally, -full => 1 (to force retrieval of full information - sometimes minimal information about your taxon may have been cached, which is normally used to save database accesses) =cut sub get_taxon { my $self = shift; if (! $XMLTWIG) { eval { require XML::Twig }; $self->throw("Could not load XML::Twig for get_taxon(): $@") if $@; } my %p = $self->entrez_params; # convert input request to one or more ids my (@taxonids, $taxonid, $want_full); if (@_ > 1) { my %params = @_; if ($params{'-taxonid'}) { $taxonid = $params{'-taxonid'}; } elsif ($params{'-gi'}) { my $db = $params{'-db'}; # we're going to do all the work here and then redirect # the call based on the TaxId my %p = %SequenceParams; my %items; if( ref($params{'-gi'}) =~ /ARRAY/i ) { $p{'id'} = join(',', @{$params{'-gi'}}); } else { $p{'id'} = $params{'-gi'}; } $p{'db'} = $db if defined $db; my $url = $self->_build_url($EntrezSummary, \%p); my @ids; if (exists $DATA_CACHE->{gi_to_ids}->{$url}) { @ids = @{$DATA_CACHE->{gi_to_ids}->{$url}}; } else { my $twig = $self->_run_query($url); my $root = $twig->root; for my $topnode ( $root->children('DocSum') ) { for my $child ( $topnode->children('Item') ) { if( uc($child->{att}->{'Name'}) eq 'TAXID' ) { push @ids, $child->text; } } } $DATA_CACHE->{gi_to_ids}->{$url} = \@ids; } return $self->get_taxon(-taxonid => \@ids); } elsif ($params{'-name'}) { @taxonids = $self->get_taxonid($params{'-name'}); } else { $self->warn("Need to have provided either a -taxonid or -name value to get_taxon"); } if ($params{'-full'}) { $want_full = 1; } } else { $taxonid = shift; } if (ref($taxonid) =~ /ARRAY/i ) { @taxonids = @{$taxonid}; } else { push(@taxonids, $taxonid) if $taxonid; } # return answer(s) from the cache if possible my @results; my @uncached; foreach my $taxonid (@taxonids) { $taxonid || $self->throw("In taxonids list one was undef! '@taxonids'\n"); if (defined $DATA_CACHE->{full_info}->{$taxonid}) { push(@results, $self->_make_taxon($DATA_CACHE->{full_info}->{$taxonid})); } elsif (! $want_full && defined $DATA_CACHE->{minimal_info}->{$taxonid}) { push(@results, $self->_make_taxon($DATA_CACHE->{minimal_info}->{$taxonid})); } else { push(@uncached, $taxonid); } } if (@uncached > 0) { $taxonid = join(',', @uncached); $p{'id'} = $taxonid; my $twig = $self->_run_query($self->_build_url($EntrezFetch, \%p)); my $root = $twig->root; for my $taxon ( $root->children('Taxon') ) { my $taxid = $taxon->first_child_text('TaxId'); $self->throw("Got a result with no TaxId!") unless $taxid; my $data = {}; if (exists $DATA_CACHE->{minimal_info}->{$taxid}) { $data = $DATA_CACHE->{minimal_info}->{$taxid}; } $data->{id} = $taxid; $data->{rank} = $taxon->first_child_text('Rank'); my $other_names = $taxon->first_child('OtherNames'); my @other_names = $other_names->children_text() if $other_names; my $sci_name = $taxon->first_child_text('ScientificName'); my $orig_sci_name = $sci_name; $sci_name =~ s/ \(class\)$//; push(@other_names, $orig_sci_name) if $orig_sci_name ne $sci_name; $data->{scientific_name} = $sci_name; $data->{common_names} = \@other_names; $data->{division} = $taxon->first_child_text('Division'); $data->{genetic_code} = $taxon->first_child('GeneticCode')->first_child_text('GCId'); $data->{mitochondrial_genetic_code} = $taxon->first_child('MitoGeneticCode')->first_child_text('MGCId'); $data->{create_date} = $taxon->first_child_text('CreateDate'); $data->{update_date} = $taxon->first_child_text('UpdateDate'); $data->{pub_date} = $taxon->first_child_text('PubDate'); # since we have some information about all the ancestors of our # requested node, we may as well cache data for the ancestors to # reduce the number of accesses to website in future my $lineage_ex = $taxon->first_child('LineageEx'); if (defined $lineage_ex) { my ($ancestor, $lineage_data, @taxa); foreach my $lineage_taxon ($lineage_ex->children) { my $lineage_taxid = $lineage_taxon->first_child_text('TaxId'); if (exists $DATA_CACHE->{minimal_info}->{$lineage_taxid} || exists $DATA_CACHE->{full_info}->{$lineage_taxid}) { $lineage_data = $DATA_CACHE->{minimal_info}->{$lineage_taxid} || $DATA_CACHE->{full_info}->{$lineage_taxid}; next; } else { $lineage_data = {}; } $lineage_data->{id} = $lineage_taxid; $lineage_data->{scientific_name} = $lineage_taxon->first_child_text('ScientificName'); $lineage_data->{rank} = $lineage_taxon->first_child_text('Rank'); $RELATIONS->{ancestors}->{$lineage_taxid} = $ancestor->{id} if $ancestor; $DATA_CACHE->{minimal_info}->{$lineage_taxid} = $lineage_data; } continue { $ancestor = $lineage_data; unshift(@taxa, $lineage_data); } $RELATIONS->{ancestors}->{$taxid} = $ancestor->{id} if $ancestor; # go through the lineage in reverse so we can remember the children my $child = $data; foreach my $lineage_data (@taxa) { $RELATIONS->{children}->{$lineage_data->{id}}->{$child->{id}} = 1; } continue { $child = $lineage_data; } } delete $DATA_CACHE->{minimal_info}->{$taxid}; $DATA_CACHE->{full_info}->{$taxid} = $data; push(@results, $self->_make_taxon($data)); } } wantarray() ? @results : shift @results; } *get_Taxonomy_Node = \&get_taxon; =head2 get_taxonids Title : get_taxonids Usage : my $taxonid = $db->get_taxonids('Homo sapiens'); Function: Searches for a taxonid (typically ncbi_taxon_id) based on a query string. Note that multiple taxonids can match to the same supplied name. Returns : array of integer ids in list context, one of these in scalar context Args : string representing taxon's name =cut sub get_taxonids { my ($self,$query) = @_; my %p = $self->entrez_params; # queries don't work correctly with special characters, so get rid of them. if ($query =~ /<.+>/) { # queries with will fail, so workaround by removing, doing # the query, getting multiple taxonids, then picking the one id that # has a parent node with a scientific_name() or common_names() # case-insensitive matching to the word(s) within <> $query =~ s/ <(.+?)>//; my $desired_parent_name = lc($1); ID: for my $start_id ($self->get_taxonids($query)) { my $node = $self->get_taxon($start_id) || next ID; # walk up the parents until we hit a node with a named rank while (1) { my $parent_node = $self->ancestor($node) || next ID; my $parent_sci_name = $parent_node->scientific_name || next ID; my @parent_common_names = $parent_node->common_names; unless (@parent_common_names) { # ensure we're not using a minimal-info cached version $parent_node = $self->get_taxon(-taxonid => $parent_node->id, -full => 1); @parent_common_names = $parent_node->common_names; } for my $name ($parent_sci_name, @parent_common_names) { if (lc($name) eq $desired_parent_name) { return wantarray() ? ($start_id) : $start_id; } } my $parent_rank = $parent_node->rank || 'no rank'; if ($parent_rank ne 'no rank') { last; } else { $node = $parent_node; } } } return; } $query =~ s/[\"\(\)]//g; # not an exhaustive list; these are just the ones we know cause problems $query =~ s/\s/+/g; my @data; if (defined $DATA_CACHE->{name_to_id}->{$query}) { @data = @{$DATA_CACHE->{name_to_id}->{$query}}; } else { $p{'term'} = $query; my $twig = $self->_run_query($self->_build_url($EntrezGet, \%p)); my $root = $twig->root; # Check that all words in the query are found, because we do not want to # match just 1 word if there are multiple words, e.g. if we query with # "Homo sapiens" both "homo" and "sapiens" must be found my $errorlist = $root->first_child('ErrorList'); if ( $errorlist ) { my @notfound = map { $_->text } $errorlist->children('PhraseNotFound'); if ( @notfound ) { for my $term ( @notfound ) { return "No hit" if $query =~ /$term/; } } } my $list = $root->first_child('IdList'); @data = map { $_->text } $list->children('Id'); $DATA_CACHE->{name_to_id}->{$query} = [@data]; } return wantarray() ? @data : shift @data; } *get_taxonid = \&get_taxonids; =head2 ancestor Title : ancestor Usage : my $ancestor_taxon = $db->ancestor($taxon) Function: Retrieve the ancestor taxon of a supplied Taxon from the database. Note that unless the ancestor has previously been directly requested with get_taxon(), the returned Taxon object will only have a minimal amount of information. Returns : Bio::Taxon Args : Bio::Taxon (that was retrieved from this database) =cut sub ancestor { my ($self, $taxon) = @_; $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon'); $self->throw("The supplied Taxon must belong to this database") unless $taxon->db_handle && $taxon->db_handle eq $self; my $id = $taxon->id || $self->throw("The supplied Taxon is missing its id!"); my $ancestor_id = $RELATIONS->{ancestors}->{$id} || return; return $self->_make_taxon($DATA_CACHE->{full_info}->{$ancestor_id} || $DATA_CACHE->{minimal_info}->{$ancestor_id}); } =head2 each_Descendent Title : each_Descendent Usage : my @taxa = $db->each_Descendent($taxon); Function: Get all the descendents of the supplied Taxon (but not their descendents, ie. not a recursive fetchall). Note that this implementation is unable to return a taxon that hasn't previously been directly fetched with get_taxon(), or wasn't an ancestor of such a fetch. Returns : Array of Bio::Taxon objects Args : Bio::Taxon (that was retrieved from this database) =cut sub each_Descendent { my ($self, $taxon) = @_; $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon'); $self->throw("The supplied Taxon must belong to this database") unless $taxon->db_handle && $taxon->db_handle eq $self; my $id = $taxon->id || $self->throw("The supplied Taxon is missing its id!"); my @children_ids = keys %{$RELATIONS->{children}->{$id} || {}}; my @children; foreach my $child_id (@children_ids) { push(@children, $self->_make_taxon($DATA_CACHE->{full_info}->{$child_id} || $DATA_CACHE->{minimal_info}->{$child_id})); } return @children; } =head2 Some Get/Setter methods =head2 entrez_url Title : entrez_url Usage : $obj->entrez_url($newval) Function: Get/set entrez URL Returns : value of entrez url (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub entrez_url{ my $self = shift; return $self->{'_entrez_url'} = shift if @_; return $self->{'_entrez_url'}; } =head2 entrez_params Title : entrez_params Usage : $obj->entrez_params($newval) Function: Get/set entrez params Returns : value of entrez_params (a hashref) Args : on set, new value Hashref =cut sub entrez_params{ my $self = shift; my $f; if( @_ ) { $f = $self->{'_entrez_params'} = shift; } else { $f = $self->{'_entrez_params'}; } return %$f; } =head2 Bio::DB::WebBase methods =head2 proxy_string Title : proxy_string Usage : my $proxy_string = $self->proxy_string($protocol) Function: Get the proxy string (plus user/pass ) Returns : string Args : protocol ('http' or 'ftp'), default 'http' =head2 proxy Title : proxy Usage : $httpproxy = $db->proxy('http') or $db->proxy(['http','ftp'], 'http://myproxy' ) Function: Get/Set a proxy for use of proxy Returns : a string indicating the proxy Args : $protocol : an array ref of the protocol(s) to set/get $proxyurl : url of the proxy to use for the specified protocol $username : username (if proxy requires authentication) $password : password (if proxy requires authentication) =head2 authentication Title : authentication Usage : $db->authentication($user,$pass) Function: Get/Set authentication credentials Returns : Array of user/pass Args : Array or user/pass =cut # make a Taxon object from data hash ref sub _make_taxon { my ($self, $data) = @_; my $taxon = Bio::Taxon->new(); my $taxid; while (my ($method, $value) = each %{$data}) { if ($method eq 'id') { $method = 'ncbi_taxid'; # since this is a real ncbi taxid, explicitly set it as one $taxid = $value; } $taxon->$method(ref($value) eq 'ARRAY' ? @{$value} : $value); } # we can't use -dbh or the db_handle() method ourselves or we'll go # infinite on the merge attempt $taxon->{'db_handle'} = $self; $self->_handle_internal_id($taxon); return $taxon; } sub _build_url { # Given a eutility (esearch.fcgi, efetch.fcgi or esummary.fcgi) and a # hashref or parameters, build a url suitable for eutil query my ($self, $eutility, $p) = @_; my $params = join($UrlParamSeparatorValue, map { $_.'='.$p->{$_} } keys %$p); my $url = $self->entrez_url.$eutility.'?'.$params; $self->debug("url is $url\n"); return $url; } sub _run_query { # Given an eutil url, run the eutil query and parse the response into an # XML Twig object my ($self, $url) = @_; my $response = $self->get($url); if ($response->is_success) { $response = $response->content; }else { $self->throw("Can't query website: ".$response->status_line); } $self->debug("response is $response\n"); my $twig = XML::Twig->new; $twig->parse($response); return $twig; } 1; BioPerl-1.007002/Bio/DB/Taxonomy/flatfile.pm000444000766000024 4276713155576320 20513 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::Taxonomy::flatfile # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Taxonomy::flatfile - Use the NCBI taxonomy from local indexed flat files =head1 SYNOPSIS use Bio::DB::Taxonomy; my $db = Bio::DB::Taxonomy->new(-source => 'flatfile' , -nodesfile => 'nodes.dmp', -namesfile => 'names.dmp'); =head1 DESCRIPTION This is an implementation of Bio::DB::Taxonomy which stores and accesses the NCBI taxonomy using flat files stored locally on disk and indexed using the DB_File module RECNO data structure for fast retrieval. The required database files, nodes.dmp and names.dmp can be obtained from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 CONTRIBUTORS Sendu Bala: bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Taxonomy::flatfile; use vars qw($DEFAULT_INDEX_DIR $DEFAULT_NODE_INDEX $DEFAULT_NAME2ID_INDEX $DEFAULT_ID2NAME_INDEX $DEFAULT_PARENT_INDEX @DIVISIONS); use strict; use DB_File; use Bio::Taxon; use File::Spec::Functions; use constant SEPARATOR => ':'; $DEFAULT_INDEX_DIR = $Bio::Root::IO::TEMPDIR; # /tmp $DEFAULT_NODE_INDEX = 'nodes'; $DEFAULT_NAME2ID_INDEX = 'names2id'; $DEFAULT_ID2NAME_INDEX = 'id2names'; $DEFAULT_PARENT_INDEX = 'parents'; $DB_BTREE->{'flags'} = R_DUP; # allow duplicate values in DB_File BTREEs # 8192 bytes; this seems to work to keep OS X from complaining $DB_HASH->{'bsize'} = 0x2000; @DIVISIONS = ([qw(BCT Bacteria)], [qw(INV Invertebrates)], [qw(MAM Mammals)], [qw(PHG Phages)], [qw(PLN Plants)], # (and fungi) [qw(PRI Primates)], [qw(ROD Rodents)], [qw(SYN Synthetic)], [qw(UNA Unassigned)], [qw(VRL Viruses)], [qw(VRT Vertebrates)], [qw(ENV 'Environmental samples')]); use base qw(Bio::DB::Taxonomy); =head2 new Title : new Usage : my $obj = Bio::DB::Taxonomy::flatfile->new(); Function: Builds a new Bio::DB::Taxonomy::flatfile object Returns : an instance of Bio::DB::Taxonomy::flatfile Args : -directory => name of directory where index files should be created -nodesfile => name of file containing nodes (nodes.dmp from NCBI) -namesfile => name of the file containing names(names.dmp from NCBI) -force => 1 to replace current indexes even if they exist =cut sub new { my($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($dir,$nodesfile,$namesfile,$force) = $self->_rearrange([qw(DIRECTORY NODESFILE NAMESFILE FORCE)], @args); $self->index_directory($dir || $DEFAULT_INDEX_DIR); if ( $nodesfile ) { $self->_build_index($nodesfile,$namesfile,$force); } $self->_db_connect; return $self; } =head2 Bio::DB::Taxonomy interface implementation =head2 get_num_taxa Title : get_num_taxa Usage : my $num = $db->get_num_taxa(); Function: Get the number of taxa stored in the database. Returns : A number Args : None =cut sub get_num_taxa { my ($self) = @_; if (not exists $self->{_num_taxa}) { my $num = 0; while ( my ($parent, undef) = each %{$self->{_parent2children}} ) { $num++; } $self->{_num_taxa} = $num; } return $self->{_num_taxa}; } =head2 get_taxon Title : get_taxon Usage : my $taxon = $db->get_taxon(-taxonid => $taxonid) Function: Get a Bio::Taxon object from the database. Returns : Bio::Taxon object Args : just a single value which is the database id, OR named args: -taxonid => taxonomy id (to query by taxonid) OR -name => string (to query by a taxonomy name: common name, scientific name, etc) =cut sub get_taxon { my ($self) = shift; my ($taxonid, $name); if (@_ > 1) { ($taxonid, $name) = $self->_rearrange([qw(TAXONID NAME)],@_); if ($name) { ($taxonid, my @others) = $self->get_taxonids($name); $self->warn("There were multiple ids ($taxonid @others) matching '$name', using '$taxonid'") if @others > 0; } } else { $taxonid = shift; } return unless $taxonid; $taxonid =~ /^\d+$/ || return; my $node = $self->{'_nodes'}->[$taxonid] || return; length($node) || return; my ($taxid, undef, $rank, $code, $divid, $gen_code, $mito) = split(SEPARATOR,$node); last unless defined $taxid; my ($taxon_names) = $self->{'_id2name'}->[$taxid]; my ($sci_name, @common_names) = split(SEPARATOR, $taxon_names); my $taxon = Bio::Taxon->new( -name => $sci_name, -common_names => [@common_names], -ncbi_taxid => $taxid, # since this is a real ncbi taxid, explicitly set it as one -rank => $rank, -division => $DIVISIONS[$divid]->[1], -genetic_code => $gen_code, -mito_genetic_code => $mito ); # we can't use -dbh or the db_handle() method ourselves or we'll go # infinite on the merge attempt $taxon->{'db_handle'} = $self; $self->_handle_internal_id($taxon); return $taxon; } *get_Taxonomy_Node = \&get_taxon; =head2 get_taxonids Title : get_taxonids Usage : my @taxonids = $db->get_taxonids('Homo sapiens'); Function: Searches for a taxonid (typically ncbi_taxon_id) based on a query string. Note that multiple taxonids can match to the same supplied name. Returns : array of integer ids in list context, one of these in scalar context Args : string representing taxon's name =cut sub get_taxonids { my ($self, $query) = @_; my $ids = $self->{'_name2id'}->{lc($query)}; unless ($ids) { if ($query =~ /_/) { # try again converting underscores to spaces $query =~ s/_/ /g; $ids = $self->{'_name2id'}->{lc($query)}; } $ids || return; } my @ids = split(SEPARATOR, $ids); return wantarray() ? @ids : shift @ids; } *get_taxonid = \&get_taxonids; =head2 get_Children_Taxids Title : get_Children_Taxids Usage : my @childrenids = $db->get_Children_Taxids Function: Get the ids of the children of a node in the taxonomy Returns : Array of Ids Args : Bio::Taxon or a taxon_id Status : deprecated (use each_Descendent()) =cut sub get_Children_Taxids { my ($self, $node) = @_; $self->warn("get_Children_Taxids is deprecated, use each_Descendent instead"); my $id; if( ref($node) ) { if( $node->can('object_id') ) { $id = $node->object_id; } elsif( $node->can('ncbi_taxid') ) { $id = $node->ncbi_taxid; } else { $self->warn("Don't know how to extract a taxon id from the object of type ".ref($node)."\n"); return; } } else { $id = $node } my @vals = $self->{'_parentbtree'}->get_dup($id); return @vals; } =head2 ancestor Title : ancestor Usage : my $ancestor_taxon = $db->ancestor($taxon) Function: Retrieve the full ancestor taxon of a supplied Taxon from the database. Returns : Bio::Taxon Args : Bio::Taxon (that was retrieved from this database) =cut sub ancestor { my ($self, $taxon) = @_; $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon'); $self->throw("The supplied Taxon must belong to this database") unless $taxon->db_handle && $taxon->db_handle eq $self; my $id = $taxon->id || $self->throw("The supplied Taxon is missing its id!"); my $node = $self->{'_nodes'}->[$id]; if (length($node)) { my (undef, $parent_id) = split(SEPARATOR,$node); $parent_id || return; $parent_id eq $id && return; # one of the roots return $self->get_taxon($parent_id); } return; } =head2 each_Descendent Title : each_Descendent Usage : my @taxa = $db->each_Descendent($taxon); Function: Get all the descendents of the supplied Taxon (but not their descendents, ie. not a recursive fetchall). Returns : Array of Bio::Taxon objects Args : Bio::Taxon (that was retrieved from this database) =cut sub each_Descendent { my ($self, $taxon) = @_; $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon'); $self->throw("The supplied Taxon must belong to this database") unless $taxon->db_handle && $taxon->db_handle eq $self; my $id = $taxon->id || $self->throw("The supplied Taxon is missing its id!"); my @desc_ids = $self->{'_parentbtree'}->get_dup($id); my @descs; foreach my $desc_id (@desc_ids) { push(@descs, $self->get_taxon($desc_id) || next); } return @descs; } =head2 Helper methods =cut # internal method which does the indexing sub _build_index { my ($self, $nodesfile, $namesfile, $force) = @_; my $dir = $self->index_directory; my $nodeindex = catfile($dir, $DEFAULT_NODE_INDEX); my $name2idindex = catfile($dir, $DEFAULT_NAME2ID_INDEX); my $id2nameindex = catfile($dir, $DEFAULT_ID2NAME_INDEX); my $parent2childindex = catfile($dir, $DEFAULT_PARENT_INDEX); $self->{'_nodes'} = []; $self->{'_id2name'} = []; $self->{'_name2id'} = {}; $self->{'_parent2children'} = {}; if (! -e $nodeindex || $force) { my (%parent2children,@nodes); open my $NODES, '<', $nodesfile or $self->throw("Could not read node file '$nodesfile': $!"); unlink $nodeindex; unlink $parent2childindex; my $nh = tie ( @nodes, 'DB_File', $nodeindex, O_RDWR|O_CREAT, 0644, $DB_RECNO) || $self->throw("Cannot open file '$nodeindex': $!"); my $btree = tie( %parent2children, 'DB_File', $parent2childindex, O_RDWR|O_CREAT, 0644, $DB_BTREE) || $self->throw("Cannot tie to file '$parent2childindex': $!"); while (<$NODES>) { next if /^$/; chomp; my ($taxid,$parent,$rank,$code,$divid,undef,$gen_code,undef,$mito) = split(/\t\|\t/,$_); # don't include the fake root node 'root' with id 1; we essentially have multiple roots here next if $taxid == 1; if ($parent == 1) { $parent = $taxid; } # keep this stringified $nodes[$taxid] = join(SEPARATOR, ($taxid,$parent,$rank,$code,$divid,$gen_code,$mito)); $btree->put($parent,$taxid); } close $NODES; $nh = $btree = undef; untie @nodes ; untie %parent2children; } if ((! -e $name2idindex || -z $name2idindex) || (! -e $id2nameindex || -z $id2nameindex) || $force) { open my $NAMES, '<', $namesfile or $self->throw("Could not read names file '$namesfile': $!"); unlink $name2idindex; unlink $id2nameindex; my (@id2name,%name2id); my $idh = tie (@id2name, 'DB_File', $id2nameindex, O_RDWR|O_CREAT, 0644, $DB_RECNO) || $self->throw("Cannot tie to file '$id2nameindex': $!"); my $nameh = tie ( %name2id, 'DB_File', $name2idindex, O_RDWR|O_CREAT, 0644, $DB_HASH) || $self->throw("Cannot tie to file '$name2idindex': $!"); while (<$NAMES>) { next if /^$/; chomp; my ($taxid, $name, $unique_name, $class) = split(/\t\|\t/,$_); # don't include the fake root node 'root' or 'all' with id 1 next if $taxid == 1; $class =~ s/\s+\|\s*$//; my $lc_name = lc($name); my $orig_name = $name; # unique names aren't always in the correct column, sometimes they # are uniqued by adding bracketed rank names to the normal name; # store the uniqued version then fix the name for normal use if ($lc_name =~ /\(class\)$/) { # it seems that only rank of class is ever used in this situation $name2id{$lc_name} = $taxid; $name =~ s/\s+\(class\)$//; $lc_name = lc($name); } # handle normal names which aren't necessarily unique my $taxids = $name2id{$lc_name} || ''; my %taxids = map { $_ => 1 } split(SEPARATOR, $taxids); unless (exists $taxids{$taxid}) { $taxids{$taxid} = 1; $name2id{$lc_name} = join(SEPARATOR, keys %taxids); } # store unique names in name2id if ($unique_name) { $name2id{lc($unique_name)} = $taxid; } # store all names in id2name array my $names = $id2name[$taxid] || ''; my @names = split(SEPARATOR, $names); if ($class && $class eq 'scientific name') { # the scientific name should be the first name stored unshift(@names, $name); push(@names, $orig_name) if ($orig_name ne $name); push(@names, $unique_name) if $unique_name; } else { # all other ('common' in this simplification) names get added after push(@names, $name); push(@names, $orig_name) if ($orig_name ne $name); push(@names, $unique_name) if $unique_name; } $id2name[$taxid] = join(SEPARATOR, @names); } close $NAMES; $idh = $nameh = undef; untie( %name2id); untie( @id2name); } } # connect the internal db handle sub _db_connect { my $self = shift; return if $self->{'_initialized'}; my $dir = $self->index_directory; my $nodeindex = catfile($dir, $DEFAULT_NODE_INDEX); my $name2idindex = catfile($dir, $DEFAULT_NAME2ID_INDEX); my $id2nameindex = catfile($dir, $DEFAULT_ID2NAME_INDEX); my $parent2childindex = catfile($dir, $DEFAULT_PARENT_INDEX); $self->{'_nodes'} = []; $self->{'_id2name'} = []; $self->{'_name2id'} = {}; $self->{'_parent2children'} = {}; if( ! -e $nodeindex || ! -e $name2idindex || ! -e $id2nameindex ) { $self->warn("Index files have not been created"); return 0; } tie ( @{$self->{'_nodes'}}, 'DB_File', $nodeindex, O_RDONLY,undef, $DB_RECNO) || $self->throw("$! $nodeindex"); tie (@{$self->{'_id2name'}}, 'DB_File', $id2nameindex,O_RDONLY, undef, $DB_RECNO) || $self->throw("$! $id2nameindex"); tie ( %{$self->{'_name2id'}}, 'DB_File', $name2idindex, O_RDONLY,undef, $DB_HASH) || $self->throw("$! $name2idindex"); $self->{'_parentbtree'} = tie( %{$self->{'_parent2children'}}, 'DB_File', $parent2childindex, O_RDONLY, 0644, $DB_BTREE); $self->{'_initialized'} = 1; } =head2 index_directory Title : index_directory Function : Get/set the location that index files are stored. (this module will index the supplied database) Usage : $obj->index_directory($newval) Returns : value of index_directory (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub index_directory { my $self = shift; return $self->{'index_directory'} = shift if @_; return $self->{'index_directory'}; } sub DESTROY { my $self = shift; # Destroy all filehandle references # to be able to remove temporary files undef $self->{_id2name}; undef $self->{_name2id}; undef $self->{_nodes}; undef $self->{_parent2children}; undef $self->{_parentbtree}; # Treat index files as temporary and delete them now if # 'index_directory' match $DEFAULT_INDEX_DIR (which means # that no "-directory" was specified or is an explicit # temporary file) my $default_temp = quotemeta $DEFAULT_INDEX_DIR; if ($self->{index_directory} =~ m/^$default_temp/) { unlink catfile($self->{index_directory},'id2names'); unlink catfile($self->{index_directory},'names2id'); unlink catfile($self->{index_directory},'nodes'); unlink catfile($self->{index_directory},'parents'); } } 1; BioPerl-1.007002/Bio/DB/Taxonomy/greengenes.pm000444000766000024 1121513155576320 21027 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::Taxonomy::greengenes # # Please direct questions and support issues to # # Cared for by Florent Angly # # Copyright Florent Angly # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Taxonomy::greengenes - Use the Greengenes taxonomy =head1 SYNOPSIS use Bio::DB::Taxonomy; my $db = Bio::DB::Taxonomy->new( -source => 'greengenes', -taxofile => 'taxonomy_16S_candiv_gg_2011_1.txt' ); =head1 DESCRIPTION I Bio::DB::Taxonomy::greengenes is an implementation of Bio::DB::Taxonomy which stores and accesses the Greengenes taxonomy of Bacteria and Archaea. Internally, it keeps the taxonomy into memory by using Bio::DB::Taxonomy::list. As a consequence, note that the IDs assigned to the taxonomy nodes, e.g. gg123, are arbitrary, contrary to the pre-defined IDs that NCBI assigns to taxons. The latest release of the Greengene taxonomy (2011) contains about 4,600 taxa and occupies about 4MB of memory once parsed into a Bio::DB::Taxonomy::greengenes object. The taxonomy files taxonomy_16S_all_gg_2011_1.txt and taxonomy_16S_candiv_gg_2011_1.txt that this module can use are available from L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Florent Angly florent.angly@gmail.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Taxonomy::greengenes; use strict; use base qw(Bio::DB::Taxonomy Bio::DB::Taxonomy::list); $Bio::DB::Taxonomy::list::prefix = 'gg'; =head2 new Title : new Usage : my $obj = Bio::DB::Taxonomy::greengenes->new(); Function: Builds a new Bio::DB::Taxonomy::greengenes object Returns : an instance of Bio::DB::Taxonomy::greengenes Args : -taxofile => name of the file containing the taxonomic information, typically 'taxonomy_16S_candiv_gg_2011_1.txt' (mandatory) =cut sub new { # Override Bio::DB::Taxonomy my($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($taxofile) = $self->_rearrange([qw(TAXOFILE)], @args); if ( $taxofile ) { $self = $self->_build_taxonomy($taxofile); } return $self; } sub _build_taxonomy { my ($self, $taxofile) = @_; my $all_ranks = ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']; my $taxonomy = Bio::DB::Taxonomy::list->new(); open my $fh, '<', $taxofile or $self->throw("Could not read file '$taxofile': $!"); # Will skip header line: prokMSA_id taxonomy my $prev_taxo_string = 'taxonomy'; my $line; # Parse taxonomy lines. Example: # 348902 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__Bacteroides plebeius while ($line = <$fh>) { chomp $line; my ($prokmsa_id, $taxo_string) = split "\t", $line; # Skip taxonomy string already seen on previous line (much faster!) next if $taxo_string eq $prev_taxo_string; $prev_taxo_string = $taxo_string; # Remove ambiguous taxons, i.e. go from: # k__Archaea; p__pMC2A384; c__; o__; f__; g__; s__ # to: # k__Archaea; p__pMC2A384 my $names = [split /;\s*/, $taxo_string]; while ( ($names->[-1] || '') =~ m/__$/) { pop @$names; } my $nof_ranks = scalar @$names; next if $nof_ranks < 1; $taxonomy->add_lineage( -ranks => [ @{$all_ranks}[0..$nof_ranks-1] ], -names => $names, ); } close $fh; return $taxonomy; } 1; BioPerl-1.007002/Bio/DB/Taxonomy/list.pm000444000766000024 3702113155576320 17663 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::Taxonomy::list # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Taxonomy::list - An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database =head1 SYNOPSIS use Bio::DB::Taxonomy; my $db = Bio::DB::Taxonomy->new( -source => 'list' ); my @ranks = ('superkingdom', 'class', 'genus', 'species'); my @names = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens'); $db->add_lineage(-names => \@names, -ranks => \@ranks); @names = ('Eukaryota', 'Mammalia', 'Mus', 'Mus musculus'); $db->add_lineage(-names => \@names, -ranks => \@ranks); =head1 DESCRIPTION This is an implementation which uses supplied lists of words to create a database from which you can extract Bio::Taxon objects. =head1 TODO It is possible this module could do something like store the data it builds up to disc. Would that be useful? At any rate, this is why the module is called 'list' and not 'in_memory' or similar. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Taxonomy::list; use strict; use Bio::Taxon; use base qw(Bio::DB::Taxonomy); our $prefix = 'list'; =head2 new Title : new Usage : my $obj = Bio::DB::Taxonomy::list->new(); Function: Builds a new Bio::DB::Taxonomy::list object Returns : an instance of Bio::DB::Taxonomy::list Args : optional, as per the add_lineage() method. =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my %args = @args; delete $args{'-source'}; $self->add_lineage(%args) if %args; return $self; } =head2 add_lineage Title : add_lineage Usage : my @names = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens'); my @ranks = ('superkingdom', 'class', 'genus', 'species'); $db->add_lineage( -names => \@names, -ranks => \@ranks ); Function: Add a lineage to the database, where the lineage is described by a list of scientific names in the order root->leaf. The rank of each name can optionally be described by supplying an additional list of rank names in the same order (eg. superkingdom->species). Returns : 1 for success Args : -names => [] : array ref of scientific names, REQUIRED -ranks => [] : array ref of rank names, same order as above, OPTIONAL =cut sub add_lineage { my ($self, @args) = @_; my ($names, $ranks) = $self->_rearrange([qw (NAMES RANKS)], @args); $self->throw("-names must be supplied and its value must be an array reference") unless $names && ref($names) eq 'ARRAY'; my $names_idx = scalar @$names - 1; if ($ranks) { $self->throw("-ranks must be an array reference") unless ref($ranks) eq 'ARRAY'; $self->throw("The -names and -ranks lists must be of equal length") unless $names_idx == scalar @$ranks - 1; } # This is non-trivial because names are not guaranteed unique in a taxonomy, # and neither are name&rank combinations. Furthermore, different name&rank # combinations can actually refer to the same taxon, eg. when one time # 'Homo'&'genus' is supplied, while another time 'Homo'&'no rank'. # # name&rank&ancestor could well be unique (or good enough 99.9999% of the # time), but we have the added complication that lineages could sometimes be # supplied with differing numbers of taxa. Ideally we want to realise that # the first of these two lineages shares all its nodes with the second: # ('Mammalia', 'Homo', 'Homo sapiens') # ('Mammalia', 'Hominidae', 'Homo', 'Homo sapiens') # # Clearly with limited information we can't do a perfect job, but we can try # and do a reasonable one. So, let's just do the trivial implementation now # and see how bad it is! (assumes ranks are unique except for 'no rank') my $ancestors = $self->{ancestors}; my $node_data = $self->{node_data}; my $name_to_id = $self->{name_to_id}; my $children = $self->{children}; my $my_ancestor_id = ''; my @node_ids; for my $i (0 .. $names_idx) { my $name = $names->[$i]; my $rank = $ranks->[$i]; # if undef, this node has 'no rank' # This is a new node with a new id if we haven't seen this name before. # It's also always a new node if this is the first lineage going into # the db. # # We need to handle, however, situations in the future where we try to # merge in a new lineage but we have non-unique names in the lineage # and possible missing classes in some lineages, e.g. # '... Anophelinae, Anopheles, Anopheles, Angusticorn, Anopheles...' # merged with # '... Anophelinae, Anopheles, Angusticorn, Anopheles...'), # but still need the 'tree' to be correct # Look for a node that is consistent with this lineage my $node_id; SAME_NAMED: for my $same_id (@{$name_to_id->{$name}}) { # Taxa are the same if it they have the same ancestor or none my $this_ancestor_id = $ancestors->{$same_id} || ''; if ($my_ancestor_id eq $this_ancestor_id) { $node_id = $same_id; last SAME_NAMED; } # Compare children next if $i >= $names_idx; # this taxon has no child my $my_child_name = $names->[$i + 1]; #while ( my ($this_child_id, undef) = each %{$children->{$same_id}} ) { for my $this_child_id (keys %{$children->{$same_id}}) { if ($my_child_name eq $node_data->{$this_child_id}->[0]) { # both children have same name if ($my_ancestor_id) { my @s_ancestors; while ($this_ancestor_id = $ancestors->{$this_ancestor_id}) { if ($my_ancestor_id eq $this_ancestor_id) { $my_ancestor_id = $ancestors->{$same_id}; push @node_ids, @s_ancestors, $my_ancestor_id; $node_id = $same_id; last SAME_NAMED; } unshift @s_ancestors, $this_ancestor_id; } } else { # This new lineage (@$names) doesn't start at the # same root as the existing lineages. Assuming # '$name' corresponds to node $same_id"); $node_id = $same_id; last SAME_NAMED; } } } } if (not defined $node_id) { # This is a new node. Add it to the database, using the prefix 'list' # for its ID to distinguish it from the IDs from other taxonomies. my $next_num = ++$self->{node_ids}; $node_id = $prefix.$next_num; push @{$self->{name_to_id}->{$name}}, $node_id; $self->{node_data}->{$node_id}->[0] = $name; } if ( (defined $rank) && (not defined $node_data->{$node_id}->[1]) ) { # Save rank if node in database has no rank but the current node has one $self->{node_data}->{$node_id}->[1] = $rank; } if ($my_ancestor_id) { if ($self->{ancestors}->{$node_id} && $self->{ancestors}->{$node_id} ne $my_ancestor_id) { $self->throw("The lineage '".join(', ', @$names)."' and a ". "previously stored lineage share a node name but have ". "different ancestries for that node. Can't cope!"); } $self->{ancestors}->{$node_id} = $my_ancestor_id; } $my_ancestor_id = $node_id; push @node_ids, $node_id; } # Go through the lineage in reverse so we can remember the children for (my $i = $names_idx - 1; $i >= 0; $i--) { $self->{children}->{$node_ids[$i]}->{$node_ids[$i+1]} = undef; } return 1; } =head2 Bio::DB::Taxonomy Interface implementation =head2 get_num_taxa Title : get_num_taxa Usage : my $num = $db->get_num_taxa(); Function: Get the number of taxa stored in the database. Returns : A number Args : None =cut sub get_num_taxa { my ($self) = @_; return $self->{node_ids} || 0; } =head2 get_taxon Title : get_taxon Usage : my $taxon = $db->get_taxon(-taxonid => $taxonid) Function: Get a Bio::Taxon object from the database. Returns : Bio::Taxon object Args : A single value which is the ID of the taxon to retrieve OR named args, as follows: -taxonid => Taxonomy ID (NB: these are not NCBI taxonomy ids but 'list' pre-fixed ids unique to the list database). OR -name => String (to query by a taxonomy name). A given taxon name can match different taxonomy objects. When that is the case, a warning is displayed and the first matching taxon is reported. See get_taxonids() to get all matching taxon IDs. OR -names => Array ref of lineage names, like in add_lineage(). To overcome the limitations of -name, you can use -names to provide the full lineage of the taxon you want and get a unique, unambiguous taxon object. =cut sub get_taxon { my ($self, @args) = @_; my $taxonid; if (scalar @args == 1) { # Argument is a taxon ID $taxonid = $args[0]; } else { # Got named arguments my ($name, $names); ($taxonid, $name, $names) = $self->_rearrange([qw(TAXONID NAME NAMES)], @args); if ($name) { $names = [$name]; } if ($names) { $name = $names->[-1]; my @taxonids = $self->get_taxonids($name); $taxonid = $taxonids[0]; # Use provided lineage to find correct ID amongst several matching IDs if ( (scalar @taxonids > 1) && (scalar @$names > 1) ) { for my $query_taxonid (@taxonids) { my $matched = 1; my $db_ancestor = $self->get_taxon($query_taxonid); for (my $i = $#$names-1; $i >= 0; $i--) { my $query_ancestor_name = $names->[$i]; $db_ancestor = $db_ancestor->ancestor; my $db_ancestor_name = ''; if ($db_ancestor) { $db_ancestor_name = $db_ancestor->node_name; } if (not ($query_ancestor_name eq $db_ancestor_name) ) { $matched = 0; last; # done testing this taxonid } } if ($matched == 1) { @taxonids = [$query_taxonid]; $taxonid = $query_taxonid; last; # done testing all taxonids } } } # Warn if several taxon IDs matched if (scalar @taxonids > 1) { $self->warn("There were multiple ids (@taxonids) matching '$name',". " using '$taxonid'") if scalar @taxonids > 1; } } } # Now that we have the taxon ID, retrieve the corresponding Taxon object my $taxon; my $node = $self->{node_data}->{$taxonid}; if ($node) { my ($sci_name, $rank) = @$node; $taxon = Bio::Taxon->new( -name => $sci_name, -object_id => $taxonid, # not an ncbi taxid, simply an object id ); if ($rank) { $taxon->rank($rank); } # we can't use -dbh or the db_handle() method ourselves or we'll go # infinite on the merge attempt $taxon->{'db_handle'} = $self; $self->_handle_internal_id($taxon, 1); } return $taxon; } *get_Taxonomy_Node = \&get_taxon; =head2 get_taxonids Title : get_taxonids Usage : my @taxonids = $db->get_taxonids('Homo sapiens'); Function: Searches for a taxonid (generated by the list module) based on a query string. Note that multiple taxonids can match to the same supplied name. Returns : array of integer ids in list context, one of these in scalar context Args : string representing taxon's name =cut sub get_taxonids { my ($self, $name) = @_; return wantarray() ? @{$self->{name_to_id}->{$name} || []} : $self->{name_to_id}->{$name}->[0]; } *get_taxonid = \&get_taxonids; =head2 ancestor Title : ancestor Usage : my $ancestor_taxon = $db->ancestor($taxon) Function: Retrieve the full ancestor taxon of a supplied Taxon from the database. Returns : Bio::Taxon Args : Bio::Taxon (that was retrieved from this database) =cut sub ancestor { my ($self, $taxon) = @_; $taxon || return; # for bug 2092, or something similar to it at least: shouldn't need this! $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon'); $self->throw("The supplied Taxon must belong to this database") unless $taxon->db_handle && $taxon->db_handle eq $self; my $id = $taxon->id || $self->throw("The supplied Taxon is missing its id!"); my $ancestor_id = $self->{ancestors}->{$id} || return; return $self->get_taxon($ancestor_id); } =head2 each_Descendent Title : each_Descendent Usage : my @taxa = $db->each_Descendent($taxon); Function: Get all the descendents of the supplied Taxon (but not their descendents, ie. not a recursive fetchall). Returns : Array of Bio::Taxon objects Args : Bio::Taxon (that was retrieved from this database) =cut sub each_Descendent { my ($self, $taxon) = @_; $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon'); $self->throw("The supplied Taxon must belong to this database") unless $taxon->db_handle && $taxon->db_handle eq $self; my $id = $taxon->id || $self->throw("The supplied Taxon is missing its id!"); my @children; while ( my ($child_id, undef) = each %{$self->{children}->{$id}} ) { push @children, ($self->get_taxon($child_id) || next); } return @children; } 1; BioPerl-1.007002/Bio/DB/Taxonomy/silva.pm000444000766000024 1110513155576320 20021 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::Taxonomy::silva # # Please direct questions and support issues to # # Copyright Florent Angly # # You may distribute this module under the same terms as perl itself =head1 NAME Bio::DB::Taxonomy::silva - Use the Silva taxonomy =head1 SYNOPSIS use Bio::DB::Taxonomy; my $db = Bio::DB::Taxonomy->new( -source => 'silva', -taxofile => 'SSURef_108_tax_silva_trunc.fasta', ); =head1 DESCRIPTION This is an implementation of Bio::DB::Taxonomy which stores and accesses the Silva taxonomy. Internally, Bio::DB::Taxonomy::silva keeps the taxonomy into memory by using Bio::DB::Taxonomy::list. As a consequence, note that the IDs assigned to the taxonomy nodes, e.g. sv72, are arbitrary, contrary to the pre-defined IDs that NCBI assigns to taxons. Note also that no rank names or common names are assigned to the taxa of Bio::DB::Taxonomy::silva. The latest Silva taxonomy (2011) contains about 126,000 taxa and occupies about 124 MB of memory once parsed into a Bio::DB::Taxonomy::silva object. Obviously, it can take a little while to load. The taxonomy file SSURef_108_tax_silva_trunc.fasta that this module uses is available from L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Florent Angly florent.angly@gmail.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::DB::Taxonomy::silva; use strict; use Bio::SeqIO; use base qw(Bio::DB::Taxonomy Bio::DB::Taxonomy::list); $Bio::DB::Taxonomy::list::prefix = 'sv'; =head2 new Title : new Usage : my $obj = Bio::DB::Taxonomy::silva->new(); Function: Builds a new Bio::DB::Taxonomy::silva object Returns : an instance of Bio::DB::Taxonomy::silva Args : -taxofile => name of the FASTA file containing the taxonomic information, typically 'SSURef_108_tax_silva_trunc.fasta' (mandatory) =cut sub new { # Override Bio::DB::Taxonomy my($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($taxofile) = $self->_rearrange([qw(TAXOFILE)], @args); if ( $taxofile ) { $self = $self->_build_taxonomy($taxofile); } return $self; } sub _build_taxonomy { my ($self, $taxofile) = @_; my $taxonomy = Bio::DB::Taxonomy::list->new(); my %taxas; my $desc_re = qr/^>\S+?(?:\s+(.+))?$/; # One could open the file using Bio::SeqIO::fasta, but it is slower and we # only need the sequence descriptions open my $in, '<', $taxofile or $self->throw("Could not read file '$taxofile': $!"); # Populate taxonomy with taxonomy obtained from sequence description while (my $line = <$in>) { next if $line !~ $desc_re; my $taxo_string = $1; next if not $taxo_string; # Example of taxonomy string: # 1/ Bacteria;Firmicutes;Bacilli;Lactobacillales;Enterococcaceae;Enterococcus;Enterococcus faecium DO # 2/ Eukaryota;Metazoa;Chordata;Craniata;Vertebrata;Euteleostomi;Mammalia;Eutheria;Euarchontoglires;Glires; # Rodentia;Sciurognathi;Muroidea;Muridae;Murinae;Rattus;;Rattus norvegicus (Norway rat) # Skip already seen taxas next if exists $taxas{$taxo_string}; $taxas{$taxo_string} = undef; # Strip the common name (could save it if Bio::DB::Taxonomy::list supported it) $taxo_string =~ s/ \(.*\)$//; # Save lineage # Unfortunately, we cannot easily add ranks since they vary from 2 to 23 for every entry my @names = split /;/, $taxo_string; $taxonomy->add_lineage( -names => \@names, ); } close $in; return $taxonomy; } 1; BioPerl-1.007002/Bio/DB/Taxonomy/sqlite.pm000444000766000024 5051213155576320 20211 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::DB::Taxonomy::flatfile # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::DB::Taxonomy::sqlite - SQLite-based implementation of Bio::DB::Taxonomy::flatfile =head1 SYNOPSIS use Bio::DB::Taxonomy; my $db = Bio::DB::Taxonomy->new(-source => 'sqlite', -db => 'mytax.db' # default 'taxonomy.sqlite' -nodesfile => 'nodes.dmp', -namesfile => 'names.dmp'); =head1 DESCRIPTION This is an implementation of Bio::DB::Taxonomy which stores and accesses the NCBI taxonomy using a simple SQLite3 database stored locally on disk. With this implementation, one can do the same basic searches as with the 'flatfile' database. A test lookup of 1000 NCBI TaxIDs with full lineage information took about 2 seconds on my older MacBook Pro laptop with an on-disk implementation. A few key differences: =over 4 =item * You can use typical SQL syntax to run a query search; for instance, if you want you can run: @ids = sort $db->get_taxonids('Chloroflexi%'); =item * In-memory database is allowed my $db = Bio::DB::Taxonomy->new(-source => 'sqlite', -db => ':memory:', -nodesfile => 'nodes.dmp', -namesfile => 'names.dmp'); =back The required database files, nodes.dmp and names.dmp can be obtained from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz =head1 TODO =over 4 =item * Small optimizations, such as optimizing name lookups =item * Possibly use L to do lineage lookups =item * Clean up SQL (still kind of a mess right now) =item * Check compat. with other NCBI-specific L implementations =item * Plan out feasibility of allowing other backends (Neo4J, other DBI, etc) =item * Optionally calculate left/right ID values for TaxID nodes =back Beyond completing the implementation and optimization, this will likely be rolled into a more flexible backend at some future point. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Fields Email cjfields-at-cpan-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Taxonomy::sqlite; use 5.010; use strict; use DB_File; use Bio::Taxon; use File::Spec::Functions; use Data::Dumper; use DBI; use constant SEPARATOR => ':'; our $DEFAULT_INDEX_DIR = $Bio::Root::IO::TEMPDIR; # /tmp our $DEFAULT_CACHE_SIZE = 0; # /tmp our $DEFAULT_DB_NAME = 'taxonomy.sqlite'; our @DIVISIONS = ( [qw(BCT Bacteria)], [qw(INV Invertebrates)], [qw(MAM Mammals)], [qw(PHG Phages)], [qw(PLN Plants)], # (and fungi) [qw(PRI Primates)], [qw(ROD Rodents)], [qw(SYN Synthetic)], [qw(UNA Unassigned)], [qw(VRL Viruses)], [qw(VRT Vertebrates)], [qw(ENV 'Environmental samples')] ); use base qw(Bio::DB::Taxonomy); =head2 new Title : new Usage : my $obj = Bio::DB::Taxonomy::flatfile->new(); Function: Builds a new Bio::DB::Taxonomy::flatfile object Returns : an instance of Bio::DB::Taxonomy::flatfile Args : -directory => name of directory where index files should be created -nodesfile => name of file containing nodes (nodes.dmp from NCBI) -namesfile => name of the file containing names(names.dmp from NCBI) -force => 1 to replace current indexes even if they exist =cut # TODO: get rid of globals! sub new { my ( $class, @args ) = @_; my $self = $class->SUPER::new(@args); my ( $dir, $nodesfile, $namesfile, $db, $force, $cs ) = $self->_rearrange( [qw(DIRECTORY NODESFILE NAMESFILE DB FORCE CACHE_SIZE)], @args ); $self->index_directory( $dir || $DEFAULT_INDEX_DIR ); $self->db_name( $db || $DEFAULT_DB_NAME ); $self->cache_size($cs // $DEFAULT_CACHE_SIZE); if ($nodesfile) { $self->_build_index( $nodesfile, $namesfile, $force ); } $self->_db_connect; return $self; } =head2 Bio::DB::Taxonomy interface implementation =head2 get_num_taxa Title : get_num_taxa Usage : my $num = $db->get_num_taxa(); Function: Get the number of taxa stored in the database. Returns : A number Args : None =cut sub get_num_taxa { my ($self) = @_; my $ct = $self->_dbh_fetch(<get_taxon(-taxonid => $taxonid) Function: Get a Bio::Taxon object from the database. Returns : Bio::Taxon object Args : just a single value which is the database id, OR named args: -taxonid => taxonomy id (to query by taxonid) OR -name => string (to query by a taxonomy name: common name, scientific name, etc) =cut sub get_taxon { my ($self) = shift; my ( $taxonid, $name ); if ( @_ > 1 ) { ( $taxonid, $name ) = $self->_rearrange( [qw(TAXONID NAME)], @_ ); if ($name) { ( $taxonid, my @others ) = $self->get_taxonids($name); $self->warn( "There were multiple ids ($taxonid @others) matching '$name', using '$taxonid'" ) if @others > 0; } } else { $taxonid = shift; } return unless $taxonid; $taxonid =~ /^\d+$/ || $self->throw("TaxID must be integer, got [$taxonid]"); my ( $parent_id, $rank, $code, $divid, $gen_code, $mito, $nm, $uniq, $class ); # single join or two calls? my $sth = $self->_prepare_cached(<bind_columns(\$parent_id, \$rank, \$code, \$divid, \$gen_code, \$mito, \$nm, \$uniq, \$class); $sth->execute($taxonid) or $self->throw($sth->errstr); my ($sci_name, @common_names); while ($sth->fetch) { if ($class eq 'scientific name') { $sci_name = $nm; } else { push @common_names, $nm; } } my $taxon = Bio::Taxon->new( -name => $sci_name, -common_names => [@common_names], -ncbi_taxid => $taxonid, -parent_id => $parent_id, -rank => $rank, -division => $DIVISIONS[$divid]->[1], -genetic_code => $gen_code, -mito_genetic_code => $mito ); # we can't use -dbh or the db_handle() method ourselves or we'll go # infinite on the merge attempt $taxon->{'db_handle'} = $self; $self->_handle_internal_id($taxon); return $taxon; } *get_Taxonomy_Node = \&get_taxon; =head2 get_taxonids Title : get_taxonids Usage : my @taxonids = $db->get_taxonids('Homo sapiens'); Function: Searches for a taxonid (typically ncbi_taxon_id) based on a query string. Note that multiple taxonids can match to the same supplied name. Returns : array of integer ids in list context, one of these in scalar context Args : string representing taxon's name =cut sub get_taxonids { my ( $self, $query ) = @_; # TODO: note we're not cleaning the query here, so you could technically # have a fuzzy match (or Bobby Tables someone) # TODO: OR'd match seems poor optimally my $taxids = $self->{dbh}->selectcol_arrayref(<get_Children_Taxids Function: Get the ids of the children of a node in the taxonomy Returns : Array of Ids Args : Bio::Taxon or a taxon_id Status : deprecated (use each_Descendent()) =cut sub get_Children_Taxids { my ( $self, $node ) = @_; $self->deprecated(); # ? #$self->warn( # "get_Children_Taxids is deprecated, use each_Descendent instead"); #my $id; #if ( ref($node) ) { # if ( $node->can('object_id') ) { # $id = $node->object_id; # } # elsif ( $node->can('ncbi_taxid') ) { # $id = $node->ncbi_taxid; # } # else { # $self->warn( # "Don't know how to extract a taxon id from the object of type " # . ref($node) # . "\n" ); # return; # } #} #else { $id = $node } #my @vals = $self->{'_parentbtree'}->get_dup($id); #return @vals; } =head2 ancestor Title : ancestor Usage : my $ancestor_taxon = $db->ancestor($taxon) Function: Retrieve the full ancestor taxon of a supplied Taxon from the database. Returns : Bio::Taxon Args : Bio::Taxon (that was retrieved from this database) =cut sub ancestor { my ( $self, $taxon ) = @_; $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon'); $self->throw("The supplied Taxon must belong to this database") unless $taxon->db_handle && $taxon->db_handle eq $self; my $id = $taxon->id || $self->throw("The supplied Taxon is missing its id!"); # TODO: # Note here we explicitly set the parent ID, but use a separate method to # check whether it is defined. Mixing back-end databases, even if from the # same source, should still work (since a different backend wouldn't # explicitly set the parent_id) if ($taxon->trusted_parent_id) { # this is the failsafe when we hit the root node if ($taxon->parent_id eq $id) { return; } return $self->get_taxon(-taxonid => $taxon->parent_id); } else { # TODO: would there be any other option? return; } } # TODO: this may act as a drop-in for a recursive CTE lookup #=head2 ancestors # # Title : ancestors # Usage : my @ancestor_taxa = $db->ancestors($taxon) # Function: Retrieve the full ancestor taxon of a supplied Taxon from the # database. # Returns : List of Bio::Taxon # Args : Bio::Taxon (that was retrieved from this database) # #=cut #sub ancestors { ... } =head2 each_Descendent Title : each_Descendent Usage : my @taxa = $db->each_Descendent($taxon); Function: Get all the descendents of the supplied Taxon (but not their descendents, ie. not a recursive fetchall). Returns : Array of Bio::Taxon objects Args : Bio::Taxon (that was retrieved from this database) =cut sub each_Descendent { my ( $self, $taxon ) = @_; $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon'); $self->throw("The supplied Taxon must belong to this database") unless $taxon->db_handle && $taxon->db_handle eq $self; # yikes my $id = $taxon->id || $self->throw("The supplied Taxon is missing its id!"); #my ( $parent_id, $rank, $code, $divid, $gen_code, $mito, $nm, $uniq, $class ); # single join or two calls? # probably not optimal, maybe set up as a cached statement with bindings? my $desc_ids = $self->{dbh}->selectcol_arrayref(<throw($self->{dbh}->errstr); SELECT tax.taxon_id FROM taxon as tax WHERE tax.parent_id = $id SQL return unless ref $desc_ids eq 'ARRAY'; my @descs; foreach my $desc_id (@$desc_ids) { push( @descs, $self->get_taxon($desc_id) || next ); } return @descs; } =head2 Helper methods =cut =head2 index_directory Title : index_directory Function : Get/set the location that index files are stored. (this module will index the supplied database) Usage : $obj->index_directory($newval) Returns : value of index_directory (a scalar) Args : on set, new value (a scalar or undef, optional) Note : kept for backwards compatibility with older DB_File implementation =cut sub index_directory { my $self = shift; return $self->{'index_directory'} = shift if @_; return $self->{'index_directory'}; } =head2 db_name Title : db_name Function : Get/set the name of the SQLite3 database where data is stored Usage : $obj->db_name($newval) Returns : value of db_name (a scalar) Args : on set, new value (a scalar or undef, optional) =cut # TODO: this may need some disambiguation w/ index_directory above; for now we # assume this doesn't have a full path name (though I see no reason why this # shouldn't allow that) sub db_name { my $self = shift; return $self->{'db_name'} = shift if @_; return $self->{'db_name'}; } =head2 cache_size Title : cache_size Function : Get/set the cachesize used for loading the SQLite3 database Usage : $obj->cache_size($newval) Returns : value of cache_size (a scalar) Args : on set, new value (a scalar or undef, optional) Note : we do no checking on whether this value is an integer (SQLite does this for use) =cut sub cache_size { my $self = shift; return $self->{'cache_size'} = shift if defined($_[0]); return $self->{'cache_size'}; } # internal method which does the indexing sub _build_index { my ( $self, $nodesfile, $namesfile, $force ) = @_; # TODO: need to disambiguate using index_directory here since we only have # one file. Mayeb ignore it in favor of having full path for db_name? my ($dir, $db_name) = ($self->index_directory, $self->db_name); if (! -e $db_name || $force) { # TODO: we're ignoring index_directory for now, may add support for this # down the way my $dbh = DBI->connect("dbi:SQLite:dbname=$db_name","","") or die $!; $self->debug("Running SQLite version:".$dbh->{sqlite_version}."\n"); #$dbh->do('PRAGMA synchronous = 0'); # Non transaction safe!!! if ($self->cache_size) { my $cs = $self->cache_size; $self->debug("Setting cache size $cs\n"); $dbh->do("PRAGMA cache_size = $cs") } $self->debug("Loading taxon table data\n"); $self->_init_db($dbh); open my $NODES, '<', $nodesfile or $self->throw("Could not read node file '$nodesfile': $!"); # TODO: this has the really unnecessary 'OR IGNORE' option added, # apparently b.c the test data expects to handle cases where the TaxID # is repeated in this table (which should never happen in this table). I # will likely change this to throw under those circumstances my $sth = $dbh->prepare_cached(<do("BEGIN"); while (<$NODES>) { next if /^\s*$/; chomp; my ($taxid,$parent,$rank,$code,$divid,undef,$gen_code,undef,$mito) = split(/\t\|\t/,$_); next if $taxid == 1; if ($parent == 1) { $parent = undef; } $sth->execute($taxid, $parent, $rank, $code, $divid, $gen_code, $mito) or die $sth->errstr.": TaxID $taxid"; } $dbh->do("COMMIT") or $self->throw($dbh->errstr); close $NODES; $self->debug("Loading name table data\n"); open my $NAMES, '<', $namesfile or $self->throw("Could not read names file '$namesfile': $!"); my $sth = $dbh->prepare_cached(<throw($dbh->errstr); INSERT INTO names (taxon_id, name, uniq_name, class) VALUES (?,?,?,?) SQL $dbh->do("BEGIN"); while (<$NAMES>) { next if /^$/; chomp; my ($taxid, $name, $unique_name, $class) = split(/\t\|\t/,$_); # don't include the fake root node 'root' or 'all' with id 1 next if $taxid == 1; $class =~ s/\s+\|\s*$//; #if ($name =~ /\(class\)$/) { # it seems that only rank of class is ever used in this situation # $name =~ s/\s+\(class\)$//; #} $sth->execute($taxid, $name, $unique_name, $class) or $self->throw($sth->errstr); } close $NAMES; $dbh->do("COMMIT"); $self->debug("Creating taxon index\n"); $dbh->do("CREATE INDEX parent_idx ON taxon (parent_id)") or $self->throw($dbh->errstr); $self->debug("Creating name index\n"); $dbh->do("CREATE INDEX name_idx ON names (name)") or $self->throw($dbh->errstr); $self->debug("Creating taxon name table index\n"); $dbh->do("CREATE INDEX taxon_name_idx ON names (taxon_id)") or $self->throw($dbh->errstr); $dbh->do("PRAGMA foreign_keys = ON"); #$dbh->do('PRAGMA synchronous = 1'); $self->{dbh} = $dbh; $self->{'_initialized'} = 1; } 1; } # connect the internal db handle sub _db_connect { my $self = shift; return if $self->{'_initialized'}; my ($dir, $db_name) = ($self->index_directory, $self->db_name); # TODO: we're ignoring index_directory for now, may add support for this # down the way my $dbh = DBI->connect("dbi:SQLite:dbname=$db_name","","") or die $!; $dbh->do("PRAGMA foreign_keys = ON"); if ($self->cache_size) { my $cs = $self->cache_size; $self->debug("Setting cache size $cs\n"); $dbh->do("PRAGMA cache_size = $cs") } $self->{dbh} = $dbh; $self->{'_initialized'} = 1; } sub _init_db { my ($self, $dbh) = @_; my $schema = $self->taxon_schema(); # TODO: set up handler parameters here for my $table (sort keys %$schema) { $dbh->do("DROP TABLE IF EXISTS $table") or $self->throw($dbh->errstr); $dbh->do("CREATE TABLE $table ".$schema->{$table}) or $self->throw($dbh->errstr); } 1; } sub _dbh_fetch { my ($self, $sql) = @_; # TODO: more sanity checks my $rows = $self->{dbh}->selectrow_arrayref($sql) or $self->throw( $self->{dbh}->errstr ); return $rows; } sub _prepare_cached { my ($self, $sql) = @_; # TODO: more sanity checks my $sth = $self->{dbh}->prepare_cached($sql) or $self->throw( $self->{dbh}->errstr ); $sth; } # TODO: check data size, this is a ballpark estimate (could be reduced) sub taxon_schema { my $self = shift; return { taxon => < <{dbh}; } 1; BioPerl-1.007002/Bio/Das000755000766000024 013155576320 14576 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Das/FeatureTypeI.pm000444000766000024 2452613155576320 17670 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Das::FeatureTypeI # # Please direct questions and support issues to # # Cared for by Lincoln Stein # # Copyright Lincoln Stein # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Das::FeatureTypeI - Simple interface to Sequence Ontology feature types =head1 SYNOPSIS # Get a Bio::Das::FeatureTypeI object from somewhere $term = $db->fetch.... # Get the name of the term $definition = $term->name; # Get the accession of the term $accession = $term->accession; # Get the definition of the term $definition = $term->definition; # Get the parents of the term, optionally filtered by relationship @parents = $term->parents($relationship); # Get the children of the term, optionally filtered by relationship @children = $term->children($relationship); # Given a parent and child, returns their relationship, or undef if # not directly related $relationship = $parent->relationship($child); # Return true if two terms are identical $match = $term1->equals($term2); # Return true if $term2 is a descendent of $term1, optionally # filtering by relationship ("isa" assumed) $match = $term1->is_descendent($term2,$relationship); # Return true if $term2 is a parent of $term1, optionally # filtering by relationship ("isa" assumed) $match = $term1->is_parent($term2,$relationship); # Return true if $term2 is equal to $term1 or if $term2 descends # from term 1 via the "isa" relationship $match = $term1->match($term2); # Create a new term de novo $term = Bio::Das::FeatureTypeI->new(-name => $name, -accession => $accession, -definition => $definition); # Add a child to a term $term1->add_child($term2,$relationship); # Delete a child from a term $term1->delete_child($term2); =head1 DESCRIPTION Bio::Das::FeatureTypeI is an interface to the Gene Ontology Consortium's Sequence Ontology (SO). The SO, like other ontologies, is a directed acyclic graph in which a child node may have multiple parents. The relationship between parent and child is one of a list of relationships. The SO currently recognizes two relationships "isa" and "partof". The intent of this interface is to interoperate with older software that uses bare strings to represent feature types. For this reason, the interface overloads the stringify ("") and string equals (eq) operations. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bio.perl.org =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Lincoln Stein Email lstein@cshl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::Das::FeatureTypeI; use strict; use overload '""' => 'name', eq => 'match', fallback => 1; # Object preamble - inherits from Bio::Root::RootI; =pod this is somehow FUBAR, implementation classes cannot successfully inherit from Bio::Das::FeatureTypeI =cut use base qw(Bio::Root::RootI); =head2 name Title : name Usage : $string = $term->name Function: return the term for the type Returns : a string Args : none Status : Public =cut sub name { shift->throw_not_implemented } =head2 accession Title : accession Usage : $string = $term->accession Function: return the accession number for the term Returns : a string Args : none Status : Public =cut sub accession { shift->throw_not_implemented } =head2 definition Title : definition Usage : $string = $term->definition Function: return the human-readable definition for the term Returns : a string Args : none Status : Public =cut sub definition { shift->throw_not_implemented } =head2 parents Title : parents Usage : @terms = $term->parents($relationship) Function: return parent terms Returns : list of Bio::Das::FeatureTypeI Args : none Status : Public Returns the parents for the current term, empty if there are none. An optional relationship argument will return those parents that are related via the specified relationship type. The relationship is one of "isa" or "partof". =cut sub parents { shift->throw_not_implemented; } =head2 children Title : children Usage : @terms = $term->children($relationship) Function: return children terms Returns : list of Bio::Das::FeatureTypeI Args : none Status : Public Returns the children for the current term, empty if there are none. An optional relationship argument will return those children that are related via the specified relationship type. The relationship is one of "isa" or "partof". =cut sub children { shift->throw_not_implemented; } =head2 relationship Title : relationship Usage : $relationship = $parent->relationship($child) Function: return the relationship between a parent and a child Returns : one of "isa" or "partof" Args : none Status : Public This method returns the relationship between a parent and one of its immediate descendents. It can return "isa", "partof", or undef if there is not a direct parent/child relationship (kissing cousins are *not* recognized). =cut sub relationship { shift->throw_not_implemented } =head2 equals Title : equals Usage : $boolean = $term1->equals($term2) Function: return true if $term1 and $term2 are the same Returns : boolean Args : second term Status : Public The two terms must be identical. In practice, this means that if term2 is a Bio::Das::FeatureI object, then its accession number must match the first term's accession number. Otherwise, if term2 is a bare string, then it must equal (in a case insensitive manner) the name of term1. NOTE TO IMPLEMENTORS: This method is defined in terms of other methods, so does not need to be implemented. =cut #' sub equals { my $self = shift; my $term2 = shift; if ($term2->isa('Bio::Das::FeatureTypeI')) { return $self->accession eq $term2->accession; } else { return lc $self->name eq lc $term2; } } =head2 is_descendent Title : is_descendent Usage : $boolean = $term1->is_descendent($term2 [,$relationship]) Function: return true of $term2 is a descendent of $term1 Returns : boolean Args : second term Status : Public This method returns true if $term2 descends from $term1. The operation traverses the tree. The traversal can be limited to the relationship type ("isa" or "partof") if desired. $term2 can be a bare string, in which case the term names will be used as the basis for term matching (see equals()). NOTE TO IMPLEMENTORS: this method is defined as the inverse of is_parent(). Do not implement it directly, but do implement is_parent(). =cut sub is_descendent { my $self = shift; my ($term,$relationship) = @_; $self->throw("$term is not a Bio::Das::FeatureTypeI") unless $term->isa('Bio::Das::FeatureTypeI'); $term->is_parent($self,$relationship); } =head2 is_parent Title : is_parent Usage : $boolean = $term1->is_parent($term2 [,$relationship]) Function: return true of $term2 is a parent of $term1 Returns : boolean Args : second term Status : Public This method returns true if $term2 is a parent of $term1. The operation traverses the tree. The traversal can be limited to the relationship type ("isa" or "partof") if desired. $term2 can be a bare string, in which case the term names will be used as the basis for term matching (see equals()). NOTE TO IMPLEMENTORS: Implementing this method will also implement is_descendent(). =cut sub is_parent { shift->throw_not_implemented } =head2 match Title : match Usage : $boolean = $term1->match($term2) Function: return true if $term1 equals $term2 or if $term2 is an "isa" descendent Returns : boolean Args : second term Status : Public This method combines equals() and is_descendent() in such a way that the two terms will match if they are the same or if the second term is an instance of the first one. This is also the basis of the operator overloading of eq. NOTE TO IMPLEMENTORS: This method is defined in terms of other methods and does not need to be implemented. =cut sub match { my $self = shift; my $term2 = shift; return 1 if $self->equals($term2); return $self->is_descendent($term2,'isa'); } =head2 new Title : new Usage : $term = Bio::Das::FeatureTypeI->new(@args) Function: create a new term Returns : new term Args : see below Status : Public This method creates a new Bio::Das::FeatureTypeI. Arguments: Argument Description -------- ------------ -name Name of this term -accession Accession number for the term -definition Definition of the term =cut sub new { shift->throw_not_implemented } =head2 add_child Title : add_child Usage : $boolean = $term->add_child($term2,$relationship) Function: add a child to a term Returns : a boolean indicating success Args : new child Throws : a "cycle detected" exception Status : Public This method adds a new child to the indicated node. It may detect a cycle in the DAG and throw a "cycle detected" exception. =cut sub add_child { shift->throw_not_implemented } =head2 delete_child Title : delete_child Usage : $boolean = $term->delete_child($term2); Function: delete a child of the term Returns : a boolean indicating success Args : child to be deleted Throws : a "not a child" exception Status : Public This method deletes a new child from the indicated node. It will throw an exception if the indicated child is not a direct descendent. =cut sub delete_child { shift->throw_not_implemented } 1; BioPerl-1.007002/Bio/Das/SegmentI.pm000444000766000024 3032713155576320 17031 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Das::SegmentI # # Please direct questions and support issues to # # Cared for by Lincoln Stein # # Copyright Lincoln Stein # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Das::SegmentI - DAS-style access to a feature database =head1 SYNOPSIS # Get a Bio::Das::SegmentI object from a Bio::DasI database... $segment = $das->segment(-name=>'Landmark', -start=>$start, -end => $end); @features = $segment->overlapping_features(-type=>['type1','type2']); # each feature is a Bio::SeqFeatureI-compliant object @features = $segment->contained_features(-type=>['type1','type2']); @features = $segment->contained_in(-type=>['type1','type2']); $stream = $segment->get_feature_stream(-type=>['type1','type2','type3']; while (my $feature = $stream->next_seq) { # do something with feature } $count = $segment->features_callback(-type=>['type1','type2','type3'], -callback => sub { ... { } ); =head1 DESCRIPTION Bio::Das::SegmentI is a simplified alternative interface to sequence annotation databases used by the distributed annotation system. In this scheme, the genome is represented as a series of landmarks. Each Bio::Das::SegmentI object ("segment") corresponds to a genomic region defined by a landmark and a start and end position relative to that landmark. A segment is created using the Bio::DasI segment() method. Features can be filtered by the following attributes: 1) their location relative to the segment (whether overlapping, contained within, or completely containing) 2) their type 3) other attributes using tag/value semantics Access to the feature list uses three distinct APIs: 1) fetching entire list of features at a time 2) fetching an iterator across features 3) a callback =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bio.perl.org =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Lincoln Stein Email lstein@cshl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::Das::SegmentI; use strict; # Object preamble - inherits from Bio::Root::RootI; use base qw(Bio::Root::RootI); =head2 seq_id Title : seq_id Usage : $ref = $s->seq_id Function: return the ID of the landmark Returns : a string Args : none Status : Public =cut sub seq_id { shift->throw_not_implemented } =head2 display_name Title : seq_name Usage : $ref = $s->seq_name Function: return the human-readable name for the landmark Returns : a string Args : none Status : Public This defaults to the same as seq_id. =cut sub display_name { shift->seq_id } =head2 start Title : start Usage : $s->start Function: start of segment Returns : integer Args : none Status : Public This is a read-only accessor for the start of the segment. Alias to low() for Gadfly compatibility. =cut sub start { shift->throw_not_implemented } sub low { shift->start } =head2 end Title : end Usage : $s->end Function: end of segment Returns : integer Args : none Status : Public This is a read-only accessor for the end of the segment. Alias to high() for Gadfly compatibility. =cut sub end { shift->throw_not_implemented } sub stop { shift->end } sub high { shift->end } =head2 length Title : length Usage : $s->length Function: length of segment Returns : integer Args : none Status : Public Returns the length of the segment. Always a positive number. =cut sub length { shift->throw_not_implemented; } =head2 seq Title : seq Usage : $s->seq Function: get the sequence string for this segment Returns : a string Args : none Status : Public Returns the sequence for this segment as a simple string. =cut sub seq {shift->throw_not_implemented} =head2 ref Title : ref Usage : $ref = $s->ref([$newlandmark]) Function: get/set the reference landmark for addressing Returns : a string Args : none Status : Public This method is used to examine/change the reference landmark used to establish the coordinate system. By default, the landmark cannot be changed and therefore this has the same effect as seq_id(). The new landmark might be an ID, or another Das::SegmentI object. =cut sub ref { shift->seq_id } *refseq = \&ref; =head2 absolute Title : absolute Usage : $s->absolute([$new_value]) Function: get/set absolute addressing mode Returns : flag Args : new flag (optional) Status : Public Turn on and off absolute-addressing mode. In absolute addressing mode, coordinates are relative to some underlying "top level" coordinate system (such as a chromosome). ref() returns the identity of the top level landmark, and start() and end() return locations relative to that landmark. In relative addressing mode, coordinates are relative to the landmark sequence specified at the time of segment creation or later modified by the ref() method. The default is to return false and to do nothing in response to attempts to set absolute addressing mode. =cut sub absolute { return } =head2 features Title : features Usage : @features = $s->features(@args) Function: get features that overlap this segment Returns : a list of Bio::SeqFeatureI objects Args : see below Status : Public This method will find all features that intersect the segment in a variety of ways and return a list of Bio::SeqFeatureI objects. The feature locations will use coordinates relative to the reference sequence in effect at the time that features() was called. The returned list can be limited to certain types, attributes or range intersection modes. Types of range intersection are one of: "overlaps" the default "contains" return features completely contained within the segment "contained_in" return features that completely contain the segment Two types of argument lists are accepted. In the positional argument form, the arguments are treated as a list of feature types. In the named parameter form, the arguments are a series of -name=Evalue pairs. Argument Description -------- ------------ -types An array reference to type names in the format "method:source" -attributes A hashref containing a set of attributes to match -rangetype One of "overlaps", "contains", or "contained_in". -iterator Return an iterator across the features. -callback A callback to invoke on each feature The -attributes argument is a hashref containing one or more attributes to match against: -attributes => { Gene => 'abc-1', Note => 'confirmed' } Attribute matching is simple string matching, and multiple attributes are ANDed together. More complex filtering can be performed using the -callback option (see below). If -iterator is true, then the method returns an object reference that implements the next_seq() method. Each call to next_seq() returns a new Bio::SeqFeatureI object. If -callback is passed a code reference, the code reference will be invoked on each feature returned. The code will be passed two arguments consisting of the current feature and the segment object itself, and must return a true value. If the code returns a false value, feature retrieval will be aborted. -callback and -iterator are mutually exclusive options. If -iterator is defined, then -callback is ignored. NOTE: the following methods all build on top of features(), and do not need to be explicitly implemented. overlapping_features() contained_features() contained_in() get_feature_stream() =cut sub features {shift->throw_not_implemented} =head2 overlapping_features Title : overlapping_features Usage : @features = $s->overlapping_features(@args) Function: get features that overlap this segment Returns : a list of Bio::SeqFeatureI objects Args : see below Status : Public This method is identical to features() except that it defaults to finding overlapping features. =cut sub overlapping_features { my $self = shift; my @args = $_[0] =~ /^-/ ? (@_, -rangetype=>'overlaps') : (-types=>\@_,-rangetype=>'overlaps'); $self->features(@args); } =head2 contained_features Title : contained_features Usage : @features = $s->contained_features(@args) Function: get features that are contained in this segment Returns : a list of Bio::SeqFeatureI objects Args : see below Status : Public This method is identical to features() except that it defaults to a range type of 'contained'. =cut sub contained_features { my $self = shift; my @args = $_[0] =~ /^-/ ? (@_, -rangetype=>'contained') : (-types=>\@_,-rangetype=>'contained'); $self->features(@args); } =head2 contained_in Title : contained_in Usage : @features = $s->contained_in(@args) Function: get features that contain this segment Returns : a list of Bio::SeqFeatureI objects Args : see below Status : Public This method is identical to features() except that it defaults to a range type of 'contained_in'. =cut sub contained_in { my $self = shift; my @args = $_[0] =~ /^-/ ? (@_, -rangetype=>'contained_in') : (-types=>\@_,-rangetype=>'contained_in'); $self->features(@args); } =head2 get_feature_stream Title : get_feature_stream Usage : $iterator = $s->get_feature_stream(@args) Function: get an iterator across the segment Returns : an object that implements next_seq() Args : see below Status : Public This method is identical to features() except that it always generates an iterator. NOTE: This is defined in the interface in terms of features(). You do not have to implement it. =cut sub get_feature_stream { my $self = shift; my @args = defined $_[0] && $_[0] =~ /^-/ ? (@_, -iterator=>1) : (-types=>\@_,-iterator=>1); $self->features(@args); } =head2 factory Title : factory Usage : $factory = $s->factory Function: return the segment factory Returns : a Bio::DasI object Args : see below Status : Public This method returns a Bio::DasI object that can be used to fetch more segments. This is typically the Bio::DasI object from which the segment was originally generated. =cut #' sub factory {shift->throw_not_implemented} =head2 primary_tag Title : primary_tag Usage : $tag = $s->primary_tag Function: identifies the segment as type "DasSegment" Returns : a string named "DasSegment" Args : none Status : Public, but see below This method provides Bio::Das::Segment objects with a primary_tag() field that identifies them as being of type "DasSegment". This allows the Bio::Graphics engine to render segments just like a feature in order nis way useful. This does not need to be implemented. It is defined by the interface. =cut #' sub primary_tag {"DasSegment"} =head2 strand Title : strand Usage : $strand = $s->strand Function: identifies the segment strand as 0 Returns : the number 0 Args : none Status : Public, but see below This method provides Bio::Das::Segment objects with a strand() field that identifies it as being strandless. This allows the Bio::Graphics engine to render segments just like a feature in order nis way useful. This does not need to be implemented. It is defined by the interface. =cut sub strand { 0 } 1; BioPerl-1.007002/Bio/Draw000755000766000024 013155576320 14764 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Draw/Pictogram.pm000444000766000024 3334413155576320 17433 0ustar00cjfieldsstaff000000000000# BioPerl module for Bio::Draw::Pictogram # # Please direct questions and support issues to # # Cared for by Shawn Hoon # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Draw::Pictogram - generate SVG output of Pictogram display for consensus motifs =head1 SYNOPSIS use Bio::Draw::Pictogram; use Bio::SeqIO; my $sio = Bio::SeqIO->new(-file=>$ARGV[0],-format=>'fasta'); my @seq; while(my $seq = $sio->next_seq){ push @seq, $seq; } my $picto = Bio::Draw::Pictogram->new(-width=>"800", -height=>"500", -fontsize=>"60", -plot_bits=>1, -background=>{ 'A'=>0.25, 'C'=>0.18, 'T'=>0.32, 'G'=>0.25}, -color=>{'A'=>'red', 'G'=>'blue', 'C'=>'green', 'T'=>'magenta'}); my $svg = $picto->make_svg(\@seq); print $svg->xmlify."\n"; #Support for Bio::Matrix::PSM::SiteMatrix now included use Bio::Matrix::PSM::IO; my $picto = Bio::Draw::Pictogram->new(-width=>"800", -height=>"500", -fontsize=>"60", -plot_bits=>1, -background=>{ 'A'=>0.25, 'C'=>0.18, 'T'=>0.32, 'G'=>0.25}, -color=>{'A'=>'red', 'G'=>'blue', 'C'=>'green', 'T'=>'magenta'}); my $psm = $psmIO->next_psm; my $svg = $picto->make_svg($psm); print $svg->xmlify; =head1 DESCRIPTION A module for generating SVG output of Pictogram display for consensus motifs. This method of representation was describe by Burge and colleagues: (Burge, C.B.,Tuschl, T., Sharp, P.A. in The RNA world II, 525-560, CSHL press, 1999) This is a simple module that takes in an array of sequences (assuming equal lengths) and calculates relative base frequencies where the height of each letter reflects the frequency of each nucleotide at a given position. It can also plot the information content at each position scaled by the background frequencies of each nucleotide. It requires the SVG-2.26 or later module by Ronan Oger available at http://www.cpan.org Recommended viewing of the SVG is the plugin available at Adobe: http://www.adobe.com/svg =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_". =cut package Bio::Draw::Pictogram; use strict; use SVG 2.26; use Bio::SeqIO; use base qw(Bio::Root::Root); use constant MAXBITS => 2; =head2 new Title : new Usage : my $picto = Bio::Draw::Pictogram->new(-width=>"800", -height=>"500", -fontsize=>"60", -plot_bits=>1, -background=>{ 'A'=>0.25, 'C'=>0.18, 'T'=>0.32, 'G'=>0.25}, -color=>{'A'=>'red', 'G'=>'blue', 'C'=>'green', 'T'=>'magenta'}); Function: Constructor for Pictogram Object Returns : L =cut sub new { my ($caller,@args) = @_; my $self = $caller->SUPER::new(@args); my ($width,$height,$fontsize,$color,$background,$bit,$normalize) = $self->_rearrange([qw(WIDTH HEIGHT FONTSIZE COLOR BACKGROUND PLOT_BITS NORMALIZE)],@args); $width||=800; $height||=600; my $svg = SVG->new(width=>$width,height=>$height); $self->svg_obj($svg); $fontsize ||= 80; $self->fontsize($fontsize) if $fontsize; $color = $color || {'T'=>'black','C'=>'blue','G'=>'green','A'=>'red'}; $self->color($color); $background = $background || {'T'=>0.25,'C'=>0.25,'G'=>0.25,'A'=>0.25}; $self->background($background); $self->plot_bits($bit) if $bit; $self->normalize($normalize) if $normalize; return $self; } =head2 make_svg Title : make_svg Usage : $picto->make_svg(); Function: make the SVG object Returns : L Arguments: A fasta file or array ref of L objects or a L =cut sub make_svg { my ($self,$input) = @_; my $fontsize = $self->fontsize; my $size = $fontsize * 0.75; my $width= $size; my $height= $size+40; my $color = $self->color; #starting x coordinate for pictogram my $x = 45+$size/2; my $pos_y = $size * 2; my $bit_y = $pos_y+40; my @pwm; my $bp = 1; #input can be file or array ref of sequences if(ref($input) eq 'ARRAY'){ @pwm = @{$self->_make_pwm($input)}; } elsif(ref($input) && $input->isa("Bio::Matrix::PSM::SiteMatrixI")){ @pwm = $self->_make_pwm_from_site_matrix($input); } else { my $sio = Bio::SeqIO->new(-file=>$input,-format=>"fasta"); my @seq; while (my $seq = $sio->next_seq){ push @seq, $seq; } @pwm = @{$self->_make_pwm(\@seq)}; } my $svg = $self->svg_obj; my $seq_length = scalar(@pwm + 1) * $width + $x + $x; my $seq_grp; #scale the svg if length greater than svg width if($seq_length > $svg->{-document}->{'width'}){ my $ratio = $svg->{-document}->{'width'}/($seq_length); $seq_grp = $svg->group(transform=>"scale($ratio,1)"); } else { $seq_grp= $svg->group(); } #do the drawing, each set is a base position foreach my $set(@pwm){ my ($A,$C,$G,$T,$bits) = @$set; my @array; push @array, ['a',($A)]; push @array, ['g',($G)]; push @array, ['c',($C)]; push @array, ['t',($T)]; @array = sort {$b->[1]<=>$a->[1]}@array; my $count = 1; my $pos_group = $seq_grp->group(id=>"bp $bp"); my $prev_size; my $y_trans; #draw each letter at each position foreach my $letter(@array){ my $scale; if($self->normalize){ $scale = $letter->[1]; } else { $scale = $letter->[1] * ($bits / MAXBITS); } if($count == 1){ if($self->normalize){ $y_trans = 0; } else { $y_trans = (1 - ($bits / MAXBITS)) * $size; } } else { $y_trans += $prev_size; } $pos_group->text('id'=> uc($letter->[0]).$bp,height=>$height, 'width'=>$width,x=>$x,y=>$size, 'transform'=>"translate(0,$y_trans),scale(1,$scale)", 'style'=>{"font-size"=>$fontsize, 'text-anchor'=>'middle', 'font-family'=>'Verdana', 'fill'=>$color->{uc $letter->[0]}})->cdata(uc $letter->[0]) if $scale > 0; $prev_size = $scale * $size; $count++; } #plot the bit if required if($self->plot_bits){ $seq_grp->text('x'=>$x, 'y'=>$bit_y, 'style'=>{"font-size"=>'10', 'text-anchor'=>'middle', 'font-family'=>'Verdana', 'fill'=>'black'})->cdata($bits); } $bp++; $x+=$width; } #plot the tags $seq_grp->text(x=>int($width/2),y=>$bit_y,style=>{"font-size"=>'10','text-anchor'=>'middle','font-family'=>'Verdana','fill'=>'black'})->cdata("Bits:") if $self->plot_bits; $seq_grp->text(x=>int($width/2),y=>$pos_y,style=>{"font-size"=>'10','text-anchor'=>'middle','font-family'=>'Verdana','fill'=>'black'})->cdata("Position:"); #plot the base positions $x = 45+$size/2-int($width/2); foreach my $nbr(1..($bp-1)){ $seq_grp->text(x=>$x+int($width/2),y=>$pos_y,style=>{"font-size"=>'10','text-anchor'=>'left','font-family'=>'Verdana','fill'=>'black'})->cdata($nbr); $x+=$width; } # $seq_grp->transform("scale(2,2)"); return $self->svg_obj($svg); } sub _make_pwm_from_site_matrix{ my ($self,$matrix) = @_; my $bgd = $self->background; my @pwm; my $consensus = $matrix->consensus; foreach my $i(1..length($consensus)){ my %base = $matrix->next_pos; my $bits; $bits+=($base{pA} * log2($base{pA}/$bgd->{'A'})); $bits+=($base{pC} * log2($base{pC}/$bgd->{'C'})); $bits+=($base{pG} * log2($base{pG}/$bgd->{'G'})); $bits+=($base{pT} * log2($base{pT}/$bgd->{'T'})); push @pwm, [$base{pA},$base{pC},$base{pG},$base{pT},abs(sprintf("%.3f",$bits))]; } return @pwm; } sub _make_pwm { my ($self,$input) = @_; my $count = 1; my %hash; my $bgd = $self->background; #sum up the frequencies at each base pair foreach my $seq(@$input){ my $string = $seq->seq; $string = uc $string; my @motif = split('',$string); my $pos = 1; foreach my $t(@motif){ $hash{$pos}{$t}++; $pos++; } $count++; } #calculate relative freq my @pwm; #decrement last count $count--; foreach my $pos(sort{$a<=>$b} keys %hash){ my @array; push @array,($hash{$pos}{'A'}||0)/$count; push @array,($hash{$pos}{'C'}||0)/$count; push @array,($hash{$pos}{'G'}||0)/$count; push @array,($hash{$pos}{'T'}||0)/$count; #calculate bits # relative entropy (RelEnt) or Kullback-Liebler distance # relent = sum fk * log2(fk/gk) where fk is frequency of nucleotide k and # gk the background frequency of nucleotide k my $bits; $bits+=(($hash{$pos}{'A'}||0) / $count) * log2((($hash{$pos}{'A'}||0)/$count) / ($bgd->{'A'})); $bits+=(($hash{$pos}{'C'}||0) / $count) * log2((($hash{$pos}{'C'}||0)/$count) / ($bgd->{'C'})); $bits+=(($hash{$pos}{'G'}||0) / $count) * log2((($hash{$pos}{'G'}||0)/$count) / ($bgd->{'G'})); $bits+=(($hash{$pos}{'T'}||0) / $count) * log2((($hash{$pos}{'T'}||0)/$count) / ($bgd->{'T'})); push @array, abs(sprintf("%.3f",$bits)); push @pwm,\@array; } return $self->pwm(\@pwm); } ###various get/sets =head2 fontsize Title : fontsize Usage : $picto->fontsize(); Function: get/set for fontsize Returns : int Arguments: int =cut sub fontsize { my ($self,$obj) = @_; if($obj){ $self->{'_fontsize'} = $obj; } return $self->{'_fontsize'}; } =head2 color Title : color Usage : $picto->color(); Function: get/set for color Returns : a hash reference Arguments: a hash reference =cut sub color { my ($self,$obj) = @_; if($obj){ $self->{'_color'} = $obj; } return $self->{'_color'}; } =head2 svg_obj Title : svg_obj Usage : $picto->svg_obj(); Function: get/set for svg_obj Returns : L Arguments: L =cut sub svg_obj { my ($self,$obj) = @_; if($obj){ $self->{'_svg_obj'} = $obj; } return $self->{'_svg_obj'}; } =head2 plot_bits Title : plot_bits Usage : $picto->plot_bits(); Function: get/set for plot_bits to indicate whether to plot information content at each base position Returns :1/0 Arguments: 1/0 =cut sub plot_bits { my ($self,$obj) = @_; if($obj){ $self->{'_plot_bits'} = $obj; } return $self->{'_plot_bits'}; } =head2 normalize Title : normalize Usage : $picto->normalize($newval) Function: get/set to make all columns the same height. default is to scale height with information content. Returns : value of normalize (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub normalize{ my $self = shift; return $self->{'normalize'} = shift if @_; return $self->{'normalize'}; } =head2 background Title : background Usage : $picto->background(); Function: get/set for hash reference of nucleodtide bgd frequencies Returns : hash reference Arguments: hash reference =cut sub background { my ($self,$obj) = @_; if($obj){ $self->{'_background'} = $obj; } return $self->{'_background'}; } =head2 pwm Title : pwm Usage : $picto->pwm(); Function: get/set for pwm Returns : int Arguments: int =cut sub pwm { my ($self,$pwm) = @_; if($pwm){ $self->{'_pwm'} = $pwm; } return $self->{'_pwm'}; } #utility method for returning log 2 sub log2 { my ($val) = @_; return 0 if $val==0; return log($val)/log(2); } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Event��������������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 15150� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Event/EventGeneratorI.pm�������������������������������������������������������000444��000766��000024�� 4330�13155576320� 20704� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Event::EventGeneratorI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Event::EventGeneratorI - This interface describes the basic event generator class. =head1 SYNOPSIS # Do not use this object directly # This object has the basic methods for describing an event generator =head1 DESCRIPTION This object describes the basic event generator system. It basically allows one to attach one or many event handlers. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Event::EventGeneratorI; use strict; use base qw(Bio::Root::RootI); =head2 attach_EventHandler Title : attach_EventHandler Usage : $parser->attatch_EventHandler($handler) Function: Adds an event handler to listen for events Returns : none Args : Bio::Event::EventHandlerI =cut sub attach_EventHandler{ my ($self) = @_; $self->throw_not_implemented(); } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Event/EventHandlerI.pm���������������������������������������������������������000444��000766��000024�� 21554�13155576320� 20362� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Event::EventHandlerI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Event::EventHandlerI - An Event Handler Interface =head1 SYNOPSIS # do not use this module directly # See Bio::SearchIO::SearchResultEventHandler for an example of # implementation. =head1 DESCRIPTION This interface describes the basic methods required for EventHandlers. These are essentially SAX methods. =head1 Developer Notes EventHandlerI implementations are used in the BioPerl IO systems to decouple the task of tokenizing the input stream into data elements and their attributes, which is format-specific, and the task of collecting those elements and attributes into whatever is the result of a parser, which is specific to the kind of result to be produced, such as BioPerl objects, a tabular or array data structure, etc. You can think of EventHandlerI-compliant parsers as faking a SAX XML parser, making their input (typically a non-XML document) behave as if it were XML. The overhead to do this can be quite substantial, at the gain of not having to duplicate the parsing code in order to change the parsing result, and not having to duplicate the logic of instantiating objects between parsers for different formats that all give rise to the same types of objects. This is perhaps best illustrated by the Bio::SearchIO system, where many different formats exist for sequence similarity and pairwise sequence alignment exist that essentially all result in Bio::Search objects. The method names and their invocation semantics follow their XML SAX equivalents, see http://www.saxproject.org/apidoc/, especially the org.xml.sax.ContentHandler interface. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Event::EventHandlerI; use strict; use Carp; use base qw(Bio::Root::RootI); =head2 will_handle Title : will_handle Usage : if( $handler->will_handle($event_type) ) { ... } Function: Tests if this event builder knows how to process a specific event Returns : boolean Args : event type name =cut sub will_handle{ my ($self,$type) = @_; $self->throw_not_implemented(); } =head2 SAX methods =cut =head2 start_document Title : start_document Usage : $resultObj = $parser->start_document(); Function: Receive notification of the beginning of a document (the input file of a parser). The parser will invoke this method only once, before any other event callbacks. Usually, a handler will reset any internal state structures when this method is called. Returns : none Args : none =cut sub start_document{ my ($self,@args) = @_; $self->throw_not_implemented; } =head2 end_document Title : end_document Usage : $parser->end_document(); Function: Receive notification of the end of a document (normally the input file of a parser). The parser will invoke this method only once, and it will be the last method invoked during the parse of the document. The parser shall not invoke this method until it has either abandoned parsing (because of an unrecoverable error) or reached the end of input. Unlike the XML SAX signature of this method, this method is expected to return the object representing the result of parsing the document. Returns : The object representing the result of parsing the input stream between the calls to start_document() and this method. Args : none =cut sub end_document{ my ($self,@args) = @_; $self->throw_not_implemented; } =head2 start_element Title : start_element Usage : $parser->start_element Function: Receive notification of the beginning of an element. The Parser will invoke this method at the beginning of every element in the input stream; there will be a corresponding end_element() event for every start_element() event (even when the element is empty). All of the element's content will be reported, in order, before the corresponding end_element() event. Returns : none Args : A hashref with at least 2 keys: 'Data' and 'Name'. The value for 'Name' is expected to be the type of element being encountered; the understood values will depend on the IO parser to which this interface is being applied. Likewise, the value for 'Data' will be specific to event handler implementions, and the specific data chunking needs of input formats to be handled efficiently. =cut sub start_element{ my ($self,@args) = @_; $self->throw_not_implemented; } =head2 end_element Title : end_element Usage : $parser->end_element Function: Receive notification of the end of an element. The parser will invoke this method at the end of every element in the input stream; there will be a corresponding start_element() event for every end_element() event (even when the element is empty). Returns : none Args : hashref with at least 2 keys, 'Data' and 'Name'. The semantics are the same as for start_element(). =cut sub end_element{ my ($self,@args) = @_; $self->throw_not_implemented; } =head2 in_element Title : in_element Usage : if( $handler->in_element($element) ) {} Function: Test if we are in a particular element. Normally, in_element() will test for particular attributes, or nested elements, within a containing element. Conversely, the containing element can be queries with within_element(). The names understood as argument should be the same as the ones understood for the 'Name' key in start_element() and end_element(). Typically, handler implementations will call this method from within the characters() method to determine the context of the data that were passed to characters(). Returns : boolean Args : A string, the name of the element (normally an attribute name or nested sub-element name). =cut sub in_element{ my ($self,@args) = @_; $self->throw_not_implemented; } =head2 within_element Title : within_element Usage : if( $handler->within_element($element) ) {} Function: Test if we are within a particular kind of element. Normally, the element type names understood as argument values will be for containing elements or data chunks. Conversely, in_element() can be used to test whether an attribute or nested element is the ccurrent context. Typically, a handler will call this method from within the characters() method to determine the context for the data that were passed to characters(). Returns : boolean Args : string element name =cut sub within_element{ my ($self,@args) = @_; $self->throw_not_implemented; } =head2 characters Title : characters Usage : $parser->characters($str) Function: Receive notification of character data. The parser will call this method to report values of attributes, or larger data chunks, depending on the IO subsystem and event handler implementation. Values may be whitespace-padded even if the whitespace is insignificant for the format. The context of the character data being passed can be determined by calling the in_element() and within_element() methods. Returns : none Args : string, the character data =cut sub characters{ my ($self,@args) = @_; $self->throw_not_implemented; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Factory������������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 15476� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Factory/AnalysisI.pm�����������������������������������������������������������000444��000766��000024�� 7740�13155576320� 20075� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Factory::AnalysisI # # Please direct questions and support issues to # # Cared for by Martin Senger # For copyright and disclaimer see below. # # POD documentation - main docs before the code =head1 NAME Bio::Factory::AnalysisI - An interface to analysis tool factory =head1 SYNOPSIS This is an interface module - you do not instantiate it. Use I module: use Bio::Tools::Run::AnalysisFactory; my $list = Bio::Tools::Run::AnalysisFactory->new->available_analyses; =head1 DESCRIPTION This interface contains all public methods for showing available analyses and for creating objects representing them. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Martin Senger (martin.senger@gmail.com) =head1 COPYRIGHT Copyright (c) 2003, Martin Senger and EMBL-EBI. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 SEE ALSO =over =item * http://www.ebi.ac.uk/Tools/webservices/soaplab/guide =back =head1 APPENDIX This is actually the main documentation... If you try to call any of these methods directly on this C object you will get a I error message. You need to call them on a C object instead. =cut # Let the code begin... package Bio::Factory::AnalysisI; use strict; use base qw(Bio::Root::RootI); # ----------------------------------------------------------------------------- =head2 available_categories Usage : $factory->available_categories; Returns : an array reference with the names of available categories Args : none The analysis tools may be grouped into categories by their functional similarity, or by the similar data types they deal with. This method shows all available such categories. =cut sub available_categories { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 available_analyses Usage : $factory->available_analyses; $factory->available_analyses ($category); Returns : an array reference with the names of all available analyses, or the analyses available in the given '$category' Args : none || category_name Show available analyses. Their names usually consist of category analysis names, separated by C<::>. =cut sub available_analyses { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 create_analysis Usage : $factory->create_analysis ($name); Returns : a Bio::Tools::Run::Analyis object Args : analysis name A real I method creating an analysis object. The created object gets all access and location information from the factory object. =cut sub create_analysis { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- 1; __END__ ��������������������������������BioPerl-1.007002/Bio/Factory/ApplicationFactoryI.pm�������������������������������������������������000444��000766��000024�� 4103�13155576320� 22073� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Factory::ApplicationFactoryI # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Factory::ApplicationFactoryI - Interface class for Application Factories =head1 SYNOPSIS You won't be using this as an object, but using a derived class. =head1 DESCRIPTION Holds common Application Factory attributes in place. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Factory::ApplicationFactoryI; use strict; use base qw(Bio::Root::RootI); =head2 version Title : version Usage : exit if $prog->version() < 1.8 Function: Determine the version number of the program Example : Returns : float or undef Args : none =cut sub version { shift->throw_not_implemented(); } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Factory/DriverFactory.pm�������������������������������������������������������000444��000766��000024�� 11121�13155576320� 20770� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Factory::DriverFactory # # Please direct questions and support issues to # # Cared for by Jason Stajich and # Hilmar Lapp # # Copyright Jason Stajich, Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Factory::DriverFactory - Base class for factory classes loading drivers =head1 SYNOPSIS #this class is not instantiable =head1 DESCRIPTION This a base class for factory classes that load drivers. Normally, you don't instantiate this class directly. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email Jason Stajich Ejason@bioperl.orgE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' package Bio::Factory::DriverFactory; use strict; use File::Spec; use vars qw(%DRIVERS); use base qw(Bio::Root::Root); BEGIN { %DRIVERS = (); } sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); return $self; } =head2 register_driver Title : register_driver Usage : $factory->register_driver("genscan", "Bio::Tools::Genscan"); Function: Registers a driver a factory class should be able to instantiate. This method can be called both as an instance and as a class method. Returns : Args : Key of the driver (string) and the module implementing the driver (string). =cut sub register_driver { my ($self, @args) = @_; my %drivers = @args; foreach my $drv (keys(%drivers)) { # note that this doesn't care whether $self is the class or the object $self->driver_table()->{$drv} = $drivers{$drv}; } } =head2 driver_table Title : driver_table Usage : $table = $factory->driver_table(); Function: Returns a reference to the hash table storing associations of methods with drivers. You use this table to look up registered methods (keys) and drivers (values). In this implementation the table is class-specific and therefore shared by all instances. You can override this in a derived class, but note that this method can be called both as an instance and a class method. This will be the table used by the object internally. You should definitely know what you're doing if you modify the table's contents. Modifications are shared by _all_ instances, those present and those yet to be created. Returns : A reference to a hash table. Args : =cut sub driver_table { my ($self, @args) = @_; return \%DRIVERS; } =head2 get_driver Title : get_driver Usage : $module = $factory->get_driver("genscan"); Function: Returns the module implementing a driver registered under the given key. Example : Returns : A string. Args : Key of the driver (string). =cut sub get_driver { my ($self, $key) = @_; if(exists($self->driver_table()->{$key})) { return $self->driver_table()->{$key}; } return; } =head2 _load_module Title : _load_module Usage : $self->_load_module("Bio::Tools::Genscan"); Function: Loads up (like use) a module at run time on demand. Example : Returns : TRUE on success Args : =cut sub _load_module { my ($self, $name) = @_; my ($module, $load, $m); $module = "_<$name.pm"; return 1 if $main::{$module}; $load = "$name.pm"; $load = File::Spec->catfile((split(/::/,$load))); eval { require $load; }; if ( $@ ) { $self->throw("$load: $name cannot be found: ".$@); } return 1; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Factory/FTLocationFactory.pm���������������������������������������������������000444��000766��000024�� 31374�13155576320� 21553� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Factory::FTLocationFactory # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gnf.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Factory::FTLocationFactory - A FeatureTable Location Parser =head1 SYNOPSIS # parse a string into a location object $loc = Bio::Factory::FTLocationFactory->from_string("join(100..200, 400..500"); =head1 DESCRIPTION Implementation of string-encoded location parsing for the Genbank feature table encoding of locations. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 CONTRIBUTORS Jason Stajich, jason-at-bioperl-dot-org Chris Fields, cjfields-at-uiuc-dot-edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Factory::FTLocationFactory; use vars qw($LOCREG); use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Location::Simple; use Bio::Location::Split; use Bio::Location::Fuzzy; use base qw(Bio::Root::Root Bio::Factory::LocationFactoryI); BEGIN { # the below is an optimized regex obj. from J. Freidl's Mastering Reg Exp. $LOCREG = qr{ (?> [^()]+ | \( (??{$LOCREG}) \) )* }x; } =head2 new Title : new Usage : my $obj = Bio::Factory::FTLocationFactory->new(); Function: Builds a new Bio::Factory::FTLocationFactory object Returns : an instance of Bio::Factory::FTLocationFactory Args : =cut =head2 from_string Title : from_string Usage : $loc = $locfactory->from_string("100..200"); Function: Parses the given string and returns a Bio::LocationI implementing object representing the location encoded by the string. This implementation parses the Genbank feature table encoding of locations. Example : Returns : A Bio::LocationI implementing object. Args : A string. =cut sub from_string { my ($self,$locstr,$op) = @_; my $loc; #$self->debug("$locstr\n"); # $op for operator (error handling) # run on first pass only # Note : These location types are now deprecated in GenBank (Oct. 2006) if (!defined($op)) { # convert all (X.Y) to [X.Y] $locstr =~ s{\((\d+\.\d+)\)}{\[$1\]}g; # convert ABC123:(X..Y) to ABC123:[X..Y] # we should never see the above $locstr =~ s{:\((\d+\.{2}\d+)\)}{:\[$1\]}g; } if ($locstr =~ m{(.*?)\(($LOCREG)\)(.*)}o) { # any matching parentheses? my ($beg, $mid, $end) = ($1, $2, $3); my (@sublocs) = (split(q(,),$beg), $mid, split(q(,),$end)); my @loc_objs; my $loc_obj; SUBLOCS: while (@sublocs) { my $subloc = shift @sublocs; next if !$subloc; my $oparg = ($subloc eq 'join' || $subloc eq 'bond' || $subloc eq 'order' || $subloc eq 'complement') ? $subloc : undef; # has operator, requires further work (recurse) if ($oparg) { my $sub = shift @sublocs; # simple split operators (no recursive calls needed) if (($oparg eq 'join' || $oparg eq 'order' || $oparg eq 'bond' ) && $sub !~ m{(?:join|order|bond)}) { my @splitlocs = split(q(,), $sub); $loc_obj = Bio::Location::Split->new(-verbose => 1, -splittype => $oparg); # Store strand values for later consistency check my @subloc_strands; my @s_objs; foreach my $splitloc (@splitlocs) { next unless $splitloc; my $sobj; if ($splitloc =~ m{\(($LOCREG)\)}) { my $comploc = $1; $sobj = $self->_parse_location($comploc); $sobj->strand(-1); push @subloc_strands, -1; } else { $sobj = $self->_parse_location($splitloc); push @subloc_strands, 1; } push @s_objs, $sobj; } # Sublocations strand values consistency check to set # Guide Strand and sublocations adding order if (scalar @s_objs > 0) { my $identical = 0; my $first_value = $subloc_strands[0]; foreach my $strand (@subloc_strands) { $identical++ if ($strand == $first_value); } if ($identical == scalar @subloc_strands) { # Set guide_strand if all sublocations have the same strand $loc_obj->guide_strand($first_value); # Reverse sublocation order for negative strand locations, e.g.: # Common (CAA24672.1): # join(complement(4918..5163),complement(2691..4571)) # Trans-splicing (NP_958375.1): # join(32737..32825,complement(174205..174384),complement(69520..71506)) if ($first_value == -1) { @s_objs = reverse @s_objs; } } else { # Mixed strand values $loc_obj->guide_strand(undef); } # Add sublocations foreach my $s_obj (@s_objs) { $loc_obj->add_sub_Location($s_obj); } } } else { $loc_obj = $self->from_string($sub, $oparg); # reinsure the operator is set correctly for this level # unless it is complement $loc_obj->splittype($oparg) unless $oparg eq 'complement'; } } # no operator, simple or fuzzy else { $loc_obj = $self->from_string($subloc,1); } if ($op && $op eq 'complement') { $loc_obj->strand(-1); } # For Split-type $loc_obj, if guide strand is set (meaning consistent strand for # all sublocs) and guide strand is the same than the last location from @loc_objs, # then recover the sublocations and add them to @loc_objs. This way, # "join(10..20,join(30..40,50..60))" becomes "join(10..20,30..40,50..60)" my $guide_strand = ($loc_obj->isa('Bio::Location::SplitLocationI')) ? ($loc_obj->guide_strand || 0) : 0; my $last_strand = (scalar @loc_objs > 0) ? $loc_objs[-1]->strand : 0; if ( $guide_strand != 0 and $guide_strand == $last_strand and $oparg eq $op # join(,join()) OK, order(join()) NOT OK ) { my @subloc_objs = $loc_obj->sub_Location(0); foreach my $subloc_obj (@subloc_objs) { push @loc_objs, $subloc_obj; } } else { push @loc_objs, $loc_obj; } } my $ct = @loc_objs; if ($op && !($op eq 'join' || $op eq 'order' || $op eq 'bond') && $ct > 1 ) { $self->throw("Bad operator $op: had multiple locations ". scalar(@loc_objs).", should be SplitLocationI"); } if ($ct > 1) { $loc = Bio::Location::Split->new(); $loc->add_sub_Location(shift @loc_objs) while (@loc_objs); return $loc; } else { $loc = shift @loc_objs; return $loc; } } else { # simple location(s) $loc = $self->_parse_location($locstr); $loc->strand(-1) if ($op && $op eq 'complement'); } return $loc; } =head2 _parse_location Title : _parse_location Usage : $loc = $locfactory->_parse_location( $loc_string) Function: Parses the given location string and returns a location object with start() and end() and strand() set appropriately. Note that this method is private. Returns : A Bio::LocationI implementing object or undef on failure Args : location string =cut sub _parse_location { my ($self, $locstr) = @_; my ($loc, $seqid); #$self->debug( "Location parse, processing $locstr\n"); # 'remote' location? if($locstr =~ m{^(\S+):(.*)$}o) { # yes; memorize remote ID and strip from location string $seqid = $1; $locstr = $2; } # split into start and end my ($start, $end) = split(/\.\./, $locstr); # remove enclosing parentheses if any; note that because of parentheses # possibly surrounding the entire location the parentheses around start # and/or may be asymmetrical # Note: these are from X.Y fuzzy locations, which are deprecated! $start =~ s/(?:^\[+|\]+$)//g if $start; $end =~ s/(?:^\[+|\]+$)//g if $end; # Is this a simple (exact) or a fuzzy location? Simples have exact start # and end, or is between two adjacent bases. Everything else is fuzzy. my $loctype = ".."; # exact with start and end as default $loctype = '?' if ( ($locstr =~ /\?/) && ($locstr !~ /\?\d+/) ); my $locclass = "Bio::Location::Simple"; if(! defined($end)) { if($locstr =~ /(\d+)([\.\^])(\d+)/) { $start = $1; $end = $3; $loctype = $2; $locclass = "Bio::Location::Fuzzy" unless (abs($end-$start) <= 1) && ($loctype eq "^"); } else { $end = $start; } } # start_num and end_num are for the numeric only versions of # start and end so they can be compared # in a few lines my ($start_num, $end_num) = ($start,$end); if ( ($start =~ /[\>\<\?\.\^]/) || ($end =~ /[\>\<\?\.\^]/) ) { $locclass = 'Bio::Location::Fuzzy'; if($start =~ /(\d+)/) { ($start_num) = $1; } else { $start_num = 0 } if ($end =~ /(\d+)/) { ($end_num) = $1; } else { $end_num = 0 } } my $strand = 1; if( $start_num > $end_num && $loctype ne '?') { ($start,$end,$strand) = ($end,$start,-1); } # instantiate location and initialize $loc = $locclass->new(-verbose => $self->verbose, -start => $start, -end => $end, -strand => $strand, -location_type => $loctype); # set remote ID if remote location if($seqid) { $loc->is_remote(1); $loc->seq_id($seqid); } # done (hopefully) return $loc; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Factory/LocationFactoryI.pm����������������������������������������������������000444��000766��000024�� 6410�13155576320� 21403� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Factory::LocationFactoryI # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gnf.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Factory::LocationFactoryI - A factory interface for generating locations from a string =head1 SYNOPSIS # Do not use directly, see Bio::Factory::LocationFactory for example use Bio::Factory::FTLocationFactory; my $locfact = Bio::Factory::FTLocationFactory->new(); my $location = $locfact->from_string("1..200"); print $location->start(), " ", $location->end(), " ", $location->strand,"\n"; =head1 DESCRIPTION An interface for Location Factories which generate Bio::LocationI objects from a string. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Factory::LocationFactoryI; use strict; use Carp; use base qw(Bio::Root::RootI); =head2 from_string Title : from_string Usage : $loc = $locfactory->from_string("100..200"); Function: Parses the given string and returns a Bio::LocationI implementing object representing the location encoded by the string. Different implementations may support different encodings. An example of a commonly used encoding is the Genbank feature table encoding of locations. Example : Returns : A Bio::LocationI implementing object. Args : A string. =cut sub from_string{ my ($self,@args) = @_; $self->throw_not_implemented(); } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Factory/MapFactoryI.pm���������������������������������������������������������000444��000766��000024�� 5010�13155576320� 20343� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Factory::MapFactoryI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Factory::MapFactoryI - A Factory for getting markers =head1 SYNOPSIS # get a Map Factory somehow likely from Bio::MapIO system while( my $map = $mapin->next_map ) { print "map name is ", $map->name, " length is ", $map->length, " ", $map->units, "\n"; $mapout->write_map($map); } =head1 DESCRIPTION This interface describes the necessary minimum methods for getting Maps from a data stream. It also supports writing Map data back to a stream. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Factory::MapFactoryI; use strict; use base qw(Bio::Root::RootI); =head2 next_map Title : next_map Usage : my $map = $factory->next_map; Function: Get a map from the factory Returns : L Args : none =cut sub next_map{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 write_map Title : write_map Usage : $factory->write_map($map); Function: Write a map out through the factory Returns : none Args : L =cut sub write_map{ my ($self,@args) = @_; $self->throw_not_implemented(); } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Factory/ObjectBuilderI.pm������������������������������������������������������000444��000766��000024�� 13100�13155576320� 21032� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Factory::ObjectBuilderI # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Factory::ObjectBuilderI - Interface for an object builder =head1 SYNOPSIS Give standard usage here =head1 DESCRIPTION An object builder is different from an object factory in that it accumulates information for the object and finally, or constantly, depending on the implementation, builds the object. It also allows for implementations that can tell the information feed in which kind of information the builder is interested in which not. In addition, the implementation may choose to filter, transform, or completely ignore certain content it is fed for certain slots. Implementations will hence be mostly used by stream-based parsers to parse only desired content, and/or skip over undesired entries. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Factory::ObjectBuilderI; use strict; use Carp; use base qw(Bio::Root::RootI); =head2 want_slot Title : want_slot Usage : Function: Whether or not the object builder wants to populate the specified slot of the object to be built. The slot can be specified either as the name of the respective method, or the initialization parameter that would be otherwise passed to new() of the object to be built. Example : Returns : TRUE if the object builder wants to populate the slot, and FALSE otherwise. Args : the name of the slot (a string) =cut sub want_slot{ shift->throw_not_implemented(); } =head2 add_slot_value Title : add_slot_value Usage : Function: Adds one or more values to the specified slot of the object to be built. Naming the slot is the same as for want_slot(). The object builder may further filter the content to be set, or even completely ignore the request. If this method reports failure, the caller should not add more values to the same slot. In addition, the caller may find it appropriate to abandon the object being built altogether. Example : Returns : TRUE on success, and FALSE otherwise Args : the name of the slot (a string) parameters determining the value to be set =cut sub add_slot_value{ shift->throw_not_implemented(); } =head2 want_object Title : want_object Usage : Function: Whether or not the object builder is still interested in continuing with the object being built. If this method returns FALSE, the caller should not add any more values to slots, or otherwise risks that the builder throws an exception. In addition, make_object() is likely to return undef after this method returned FALSE. Example : Returns : TRUE if the object builder wants to continue building the present object, and FALSE otherwise. Args : none =cut sub want_object{ shift->throw_not_implemented(); } =head2 make_object Title : make_object Usage : Function: Get the built object. This method is allowed to return undef if no value has ever been added since the last call to make_object(), or if want_object() returned FALSE (or would have returned FALSE) before calling this method. For an implementation that allows consecutive building of objects, a caller must call this method once, and only once, between subsequent objects to be built. I.e., a call to make_object implies 'end_object.' Example : Returns : the object that was built Args : none =cut sub make_object{ shift->throw_not_implemented(); } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Factory/ObjectFactory.pm�������������������������������������������������������000444��000766��000024�� 16142�13155576320� 20753� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Factory::ObjectFactory # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2003. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Factory::ObjectFactory - Instantiates a new Bio::Root::RootI (or derived class) through a factory =head1 SYNOPSIS use Bio::Factory::ObjectFactory; my $factory = Bio::Factory::ObjectFactory->new(-type => 'Bio::Ontology::GOterm'); my $term = $factory->create_object(-name => 'peroxisome', -ontology => 'Gene Factory', -identifier => 'GO:0005777'); =head1 DESCRIPTION This object will build L objects generically. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 CONTRIBUTORS This is mostly copy-and-paste with subsequent adaptation from Bio::Seq::SeqFactory by Jason Stajich. Most credits should in fact go to him. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Factory::ObjectFactory; use strict; use base qw(Bio::Root::Root Bio::Factory::ObjectFactoryI); =head2 new Title : new Usage : my $obj = Bio::Factory::ObjectFactory->new(); Function: Builds a new Bio::Factory::ObjectFactory object Returns : Bio::Factory::ObjectFactory Args : -type => string, name of a L derived class. There is no default. -interface => string, name of the interface or class any type specified needs to at least implement. The default is Bio::Root::RootI. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($type,$interface) = $self->_rearrange([qw(TYPE INTERFACE)], @args); $self->{'_loaded_types'} = {}; $self->interface($interface || "Bio::Root::RootI"); $self->type($type) if $type; return $self; } =head2 create_object Title : create_object Usage : my $seq = $factory->create_object(); Function: Instantiates a new object of the previously set type. This object allows us to genericize the instantiation of objects. You must have provided -type at instantiation, or have called type($mytype) before you can call this method. Returns : an object of the type returned by type() The return type is configurable using new(-type =>"..."), or by calling $self->type("My::Fancy::Class"). Args : Initialization parameters specific to the type of object we want. Check the POD of the class you set as type. =cut sub create_object { my ($self,@args) = @_; my $type = $self->type(); # type has already been loaded upon set return $type->new(-verbose => $self->verbose, @args); } =head2 type Title : type Usage : $obj->type($newval) Function: Get/set the type of object to be created. This may be changed at any time during the lifetime of this factory. Returns : value of type (a string) Args : newvalue (optional, a string) =cut sub type{ my $self = shift; if(@_) { my $type = shift; if($type && (! $self->{'_loaded_types'}->{$type})) { eval { $self->_load_module($type); }; if( $@ ) { $self->throw("module for '$type' failed to load: ". $@); } my $o = bless {},$type; if(!$self->_validate_type($o)) { # this may throw an exception $self->throw("'$type' is not valid for factory ".ref($self)); } $self->{'_loaded_types'}->{$type} = 1; } return $self->{'type'} = $type; } return $self->{'type'}; } =head2 interface Title : interface Usage : $obj->interface($newval) Function: Get/set the interface or base class that supplied types must at least implement (inherit from). Example : Returns : value of interface (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub interface{ my $self = shift; my $interface = shift; if($interface) { return $self->{'interface'} = $interface; } return $self->{'interface'}; } =head2 _validate_type Title : _validate_type Usage : $factory->_validate_type($object) Function: Called to let derived factories validate the type set via type(). The default implementation here checks whether the supplied object skeleton implements the interface set via -interface upon factory instantiation. Example : Returns : TRUE if the type is to be considered valid, and FALSE otherwise. Instead of returning FALSE this method may also just throw an informative exception. The default implementation here will throw an exception if the supplied object does not inherit from the interface provided by the interface() method. Args : A hash reference blessed into the specified type, allowing queries like isa(). =cut sub _validate_type{ my ($self,$obj) = @_; if(! $obj->isa($self->interface())) { $self->throw("invalid type: '".ref($obj). "' does not implement '".$self->interface()."'"); } return 1; } ##################################################################### # aliases for naming consistency or other reasons # ##################################################################### *create = \&create_object; 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Factory/ObjectFactoryI.pm������������������������������������������������������000444��000766��000024�� 5172�13155576320� 21045� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Factory::ObjectFactoryI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Factory::ObjectFactoryI - A General object creator factory =head1 SYNOPSIS # see the implementations of this interface for details but # basically my $obj = $factory->create(%args); =head1 DESCRIPTION This interface is the basic structure for a factory which creates new objects. In this case it is up to the implementer to check arguments and initialize whatever new object the implementing class is designed for. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Factory::ObjectFactoryI; use strict; use Carp; use base qw(Bio::Root::RootI); =head2 create Title : create Usage : $factory->create(%args) Function: Create a new object Returns : a new object Args : hash of initialization parameters =cut sub create{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 create_object Title : create_object Usage : $obj = $factory->create_object(%args) Function: Create a new object. This is supposed to supersede create(). Right now it only delegates to create(). Returns : a new object Args : hash of initialization parameters =cut sub create_object{ my ($self,@args) = @_; return $self->create(@args); } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Factory/SeqAnalysisParserFactory.pm��������������������������������������������000444��000766��000024�� 15502�13155576320� 23155� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Factory::SeqAnalysisParserFactory # # Please direct questions and support issues to # # Cared for by Jason Stajich , # and Hilmar Lapp # # Copyright Jason Stajich, Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Factory::SeqAnalysisParserFactory - class capable of creating SeqAnalysisParserI compliant parsers =head1 SYNOPSIS # initialize an object implementing this interface, e.g. $factory = Bio::Factory::SeqAnalysisParserFactory->new(); # find out the methods it knows about print "registered methods: ", join(', ', keys %{$factory->driver_table}), "\n"; # obtain a parser object $parser = $factory->get_parser(-input=>$inputobj, -params=>[@params], -method => $method); # $parser is an object implementing Bio::SeqAnalysisParserI # annotate sequence with features produced by parser while(my $feat = $parser->next_feature()) { $seq->add_SeqFeature($feat); } =head1 DESCRIPTION This is a factory class capable of instantiating SeqAnalysisParserI implementing parsers. The concept behind this class and the interface it implements (Bio::Factory::SeqAnalysisParserFactoryI) is a generic analysis result parsing in high-throughput automated sequence annotation pipelines. See Bio::SeqAnalysisParserI for more documentation of this concept. You can always find out the methods an instance of this class knows about by the way given in the SYNOPSIS section. By default, and assuming that the documentation is up-to-date, this will comprise of genscan, mzef, estscan, blast, hmmer, gff, and sim4 (all case-insensitive). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp, Jason Stajich Email Hilmar Lapp Ehlapp@gmx.netE, Jason Stajich Ejason@bioperl.orgE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Factory::SeqAnalysisParserFactory; use strict; use base qw(Bio::Factory::DriverFactory Bio::Factory::SeqAnalysisParserFactoryI); BEGIN { Bio::Factory::DriverFactory->register_driver ( "genscan" => "Bio::Tools::Genscan", "mzef" => "Bio::Tools::MZEF", "estscan" => "Bio::Tools::ESTScan", "hmmer" => "Bio::Tools::HMMER::Result", "gff" => "Bio::Tools::GFF", "sim4" => "Bio::Tools::Sim4::Results", "epcr" => "Bio::Tools::EPCR", "exonerate" => "Bio::Tools::Exonerate", ); } sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); # no per-object initialization right now - registration of default drivers # is only done once when the module is loaded return $self; } =head2 get_parser Title : get_parser Usage : $factory->get_parser(-input=>$inputobj, [ -params=>[@params] ], -method => $method) Function: Creates and returns a parser object for the given input and method. Both file names and streams (filehandles) are allowed. Parameters (-params argument) are passed on to the parser object and therefore are specific to the parser to be created. Example : Returns : A Bio::SeqAnalysisParserI implementing object. Exception if creation of the parser object fails. Args : B
\n"; my $afterdist = $self->mutation->prelabel - $firstexon->start; my $beforedist = $firstexon->end - $self->mutation->postlabel; my $exonvalue = $i + 1; $self->dnamut->region('exon'); $self->dnamut->region_value($exonvalue); if ($afterdist < $beforedist) { $afterdist++; $afterdist++; $self->dnamut->region_dist($afterdist); #print "splice site $afterdist nt upstream!
"; } else { $self->dnamut->region_dist($beforedist); #print "splice site $beforedist nt downstream!
"; } } else { #print "first exon : ", $firstexon->start, " - ", $firstexon->end, "
\n"; foreach $i (0..$#exons) { $after=$exons[$i]->start; #proximity test for intronic mutations if ( ($strand == 1 and $self->mutation->prelabel >= $before and $self->mutation->postlabel <= $after) or ($strand == -1 and $self->mutation->prelabel <= $before and $self->mutation->postlabel >= $after) ) { $self->dnamut->region('intron'); #$self->dnamut->region_value($i); my $afterdist = $self->mutation->prelabel - $before; my $beforedist = $after - $self->mutation->postlabel; my $intronvalue = $i + 1; if ($afterdist < $beforedist) { $afterdist++; $self->dnamut->region_value($intronvalue); $self->dnamut->region_dist($afterdist); #print "splice site $afterdist nt upstream!
"; } else { $self->dnamut->region_value($intronvalue); $self->dnamut->region_dist($beforedist * -1); #print "splice site $beforedist nt downstream!
"; } $self->rnachange(undef); last; } #proximity test for exon mutations #proximity test for exon mutations elsif ( ( $strand == 1 and $exons[$i]->start < $self->mutation->prelabel and $exons[$i]->end > $self->mutation->prelabel) or ( $strand == 1 and $exons[$i]->start < $self->mutation->postlabel and $exons[$i]->end > $self->mutation->postlabel) or ( $strand == -1 and $exons[$i]->start > $self->mutation->prelabel and $exons[$i]->end < $self->mutation->prelabel) or ( $strand == -1 and $exons[$i]->start > $self->mutation->postlabel and $exons[$i]->end < $self->mutation->postlabel) ) { $rnaAffected = 1; my $afterdist = $self->mutation->prelabel - $exons[$i]->start; my $beforedist = $exons[$i]->end - $self->mutation->postlabel; my $exonvalue = $i + 1; $self->dnamut->region('exon'); if ($afterdist < $beforedist) { $afterdist++; $self->dnamut->region_value($exonvalue+1); $self->dnamut->region_dist($afterdist); #print "splice site $afterdist nt upstream!
"; } else { #$beforedist; $self->dnamut->region_value($exonvalue+1); $self->dnamut->region_dist($beforedist * -1); #print "splice site $beforedist nt downstream!
"; } last; } $before=$exons[$i]->end; } } } } #$self->warn("RNA not affected because change occurs inside an intron"); #return(0); # if still not returned, then not affected, return 0 return $rnaAffected; } # # ### Creation of RNA and AA variation objects # =head2 _set_effects Title : _set_effects Usage : Function: Stores RNA and AA level mutation attributes before mutation into Bio::Variation::RNAChange and Bio::Variation::AAChange objects. Links them to SeqDiff object. Example : Returns : Args : Bio::Variation::SeqDiff object Bio::Variation::DNAMutation object See L, L, L, and L. =cut sub _set_effects { my ($self, $seqDiff, $dnamut) = @_; my ($rnapos_end, $upstreamseq, $dnstreamseq); my $flanklen = $self->{'flanklen'}; ($self->mutation->len == 0) ? ($rnapos_end = $self->mutation->transpos) : ($rnapos_end = $self->mutation->transpos + $self->mutation->len -1); my $rnachange = Bio::Variation::RNAChange->new(-start => $self->mutation->transpos, -end => $rnapos_end ); $rnachange->isMutation(1); # setting proof if ($seqDiff->numbering eq "coding") { $rnachange->proof('experimental'); } else { $rnachange->proof('computed'); } $seqDiff->add_Variant($rnachange); $self->rnachange($rnachange); $rnachange->DNAMutation($dnamut); $dnamut->RNAChange($rnachange); $rnachange->mut_number($self->mutation->issue); # setting the codon_position of the "start" nucleotide of the change $rnachange->codon_pos(($self->RNA->frame($self->mutation->label))+1); # codon_pos=frame+1 my @exons=$self->RNA->all_Exons; $self->exons(\@exons); #print `date`, " before flank, after exons. RNAObj query\n"; # if cannot retrieve from Transcript, Transcript::upstream_seq will be used # before "fac7 g 65" bug discovered # $uplabel=$self->RNA->label(1-$flanklen,$prelabel); my $RNAprelabel=$self->RNA->label(-1,$self->mutation->label); # to fix fac7g65 bug # for the fix, all prelabel used in the next block have been changed to RNAprelabel my $uplabel=$self->RNA->label(1-$flanklen,$RNAprelabel); if ($self->RNA->valid($uplabel)) { $upstreamseq = $self->RNA->labelsubseq($uplabel, undef, $RNAprelabel); } else { $upstreamseq = $self->RNA->labelsubseq($self->RNA->start, undef, $RNAprelabel) if $self->RNA->valid($RNAprelabel); my $lacking=$flanklen-length($upstreamseq); # how many missing my $upstream_atg=$exons[0]->subseq(-$lacking,-1); $upstreamseq=$upstream_atg . $upstreamseq; } $rnachange->upStreamSeq($upstreamseq); # won't work OK if postlabel NOT in Transcript # now added RNApostlabel but this has to be /fully tested/ # for the fix, all postlabel used in the next block have been changed to RNApostlabel my $RNApostlabel; # to fix fac7g64 bug if ($self->mutation->len == 0) { $RNApostlabel=$self->mutation->label; } else { my $mutlen = 1 + $self->mutation->len; $RNApostlabel=$self->RNA->label($mutlen,$self->mutation->label); } $dnstreamseq=$self->RNA->labelsubseq($RNApostlabel, $flanklen); if ($dnstreamseq eq '-1') { # if out of transcript was requested my $lastexon=$exons[-1]; my $lastexonlength=$lastexon->length; $dnstreamseq=$self->RNA->labelsubseq($RNApostlabel); # retrieves till RNAend my $lacking=$flanklen-length($dnstreamseq); # how many missing my $downstream_stop=$lastexon->subseq($lastexonlength+1,undef,$lacking); $dnstreamseq .= $downstream_stop; } else { $rnachange->dnStreamSeq($dnstreamseq); } # AAChange creation my $AAobj=$self->RNA->get_Translation; # storage of prelabel here, to be used in create_mut_objs_after my $aachange = Bio::Variation::AAChange->new(-start => $RNAprelabel ); $aachange->isMutation(1); $aachange->proof('computed'); $seqDiff->add_Variant($aachange); $self->aachange($aachange); $rnachange->AAChange($aachange); $aachange->RNAChange($rnachange); $aachange->mut_number($self->mutation->issue); # $before_mutation{aachange}=$aachange; my $ra_o = Bio::Variation::Allele->new; $ra_o->seq($dnamut->allele_ori->seq) if $dnamut->allele_ori->seq; $rnachange->allele_ori($ra_o); $rnachange->length(CORE::length $rnachange->allele_ori->seq); my $ra_m = Bio::Variation::Allele->new; $ra_m->seq($self->mutation->seq) if $self->mutation->seq; $rnachange->allele_mut($ra_m); $rnachange->add_Allele($ra_m); #$rnachange->allele_mut($seq); $rnachange->end($rnachange->start) if $rnachange->length == 0; # this holds the aminoacid sequence that will be affected by the mutation my $aa_allele_ori=$AAobj->labelsubseq($self->mutation->label,undef, $self->mutation->lastlabel); my $aa_o = Bio::Variation::Allele->new; $aa_o->seq($aa_allele_ori) if $aa_allele_ori; $aachange->allele_ori($aa_o); #$aachange->allele_ori($aa_allele_ori); my $aa_length_ori = length($aa_allele_ori); $aachange->length($aa_length_ori); #print "==========$aa_length_ori\n"; $aachange->end($aachange->start + $aa_length_ori - 1 ); } =head2 _untranslated Title : _untranslated Usage : Function: Stores RNA change attributes before mutation into Bio::Variation::RNAChange object. Links it to SeqDiff object. Example : Returns : Args : Bio::Variation::SeqDiff object Bio::Variation::DNAMutation object See L, L and L for details. =cut sub _untranslated { my ($self, $seqDiff, $dnamut) = @_; my $rnapos_end; ($self->mutation->len == 0) ? ($rnapos_end = $self->mutation->transpos) : ($rnapos_end = $self->mutation->transpos + $self->mutation->len -1); my $rnachange = Bio::Variation::RNAChange->new(-start => $self->mutation->transpos, -end => $rnapos_end ); #my $rnachange = Bio::Variation::RNAChange->new; $rnachange->isMutation(1); my $ra_o = Bio::Variation::Allele->new; $ra_o->seq($dnamut->allele_ori->seq) if $dnamut->allele_ori->seq; $rnachange->allele_ori($ra_o); my $ra_m = Bio::Variation::Allele->new; $ra_m->seq($dnamut->allele_mut->seq) if $dnamut->allele_mut->seq; $rnachange->allele_mut($ra_m); $rnachange->add_Allele($ra_m); $rnachange->upStreamSeq($dnamut->upStreamSeq); $rnachange->dnStreamSeq($dnamut->dnStreamSeq); $rnachange->length($dnamut->length); $rnachange->mut_number($dnamut->mut_number); # setting proof if ($seqDiff->numbering eq "coding") { $rnachange->proof('experimental'); } else { $rnachange->proof('computed'); } my $dist; if ($rnachange->end < 0) { $rnachange->region('5\'UTR'); $dnamut->region('5\'UTR'); my $dist = $dnamut->end ; $dnamut->region_dist($dist); $dist = $seqDiff->offset - $self->gene->maxtranscript->start + 1 + $dist; $rnachange->region_dist($dist); return if $dist < 1; # if mutation is not in mRNA } else { $rnachange->region('3\'UTR'); $dnamut->region('3\'UTR'); my $dist = $dnamut->start - $seqDiff->cds_end + $seqDiff->offset; $dnamut->region_dist($dist); $dist = $seqDiff->cds_end - $self->gene->maxtranscript->end -1 + $dist; $rnachange->region_dist($dist); return if $dist > 0; # if mutation is not in mRNA } $seqDiff->add_Variant($rnachange); $self->rnachange($rnachange); $rnachange->DNAMutation($dnamut); $dnamut->RNAChange($rnachange); } # args: reference to label changearray, reference to position changearray # Function: take care of the creation of mutation objects, with # information AFTER the change takes place sub _post_mutation { my ($self, $seqDiff) = @_; if ($self->rnachange and $self->rnachange->region eq 'coding') { #$seqDiff->add_Variant($self->rnachange); my $aachange=$self->aachange; my ($AAobj,$aa_start_prelabel,$aa_start,$mut_translation); $AAobj=$self->RNA->get_Translation; $aa_start_prelabel=$aachange->start; $aa_start=$AAobj->position($self->RNA->label(2,$aa_start_prelabel)); $aachange->start($aa_start); $mut_translation=$AAobj->seq; # this now takes in account possible preinsertions my $aa_m = Bio::Variation::Allele->new; $aa_m->seq(substr($mut_translation,$aa_start-1)) if substr($mut_translation,$aa_start-1); $aachange->allele_mut($aa_m); $aachange->add_Allele($aa_m); #$aachange->allele_mut(substr($mut_translation,$aa_start-1)); #$aachange->allele_mut($mut_translation); my ($rlenori, $rlenmut); $rlenori = CORE::length($aachange->RNAChange->allele_ori->seq); $rlenmut = CORE::length($aachange->RNAChange->allele_mut->seq); #point mutation if ($rlenori == 1 and $rlenmut == 1 and $aachange->allele_ori->seq ne '*') { my $alleleseq; if ($aachange->allele_mut->seq) { $alleleseq = substr($aachange->allele_mut->seq, 0, 1); $aachange->allele_mut->seq($alleleseq); } $aachange->end($aachange->start); $aachange->length(1); } elsif ( $rlenori == $rlenmut and $aachange->allele_ori->seq ne '*' ) { #complex inframe mutation $aachange->allele_mut->seq(substr $aachange->allele_mut->seq, 0, length($aachange->allele_ori->seq)); } #inframe mutation elsif ((int($rlenori-$rlenmut))%3 == 0) { if ($aachange->RNAChange->allele_mut->seq and $aachange->RNAChange->allele_ori->seq ) { # complex my $rna_len = length ($aachange->RNAChange->allele_mut->seq); my $len = $rna_len/3; $len++ unless $rna_len%3 == 0; $aachange->allele_mut->seq(substr $aachange->allele_mut->seq, 0, $len ); } elsif ($aachange->RNAChange->codon_pos == 1){ # deletion if ($aachange->RNAChange->allele_mut->seq eq '') { $aachange->allele_mut->seq(''); $aachange->end($aachange->start + $aachange->length - 1 ); } # insertion elsif ($aachange->RNAChange->allele_ori->seq eq '' ) { $aachange->allele_mut->seq(substr $aachange->allele_mut->seq, 0, length ($aachange->RNAChange->allele_mut->seq) / 3); $aachange->allele_ori->seq(''); $aachange->end($aachange->start + $aachange->length - 1 ); $aachange->length(0); } } else { #elsif ($aachange->RNAChange->codon_pos == 2){ # deletion if (not $aachange->RNAChange->allele_mut->seq ) { $aachange->allele_mut->seq(substr $aachange->allele_mut->seq, 0, 1); } # insertion elsif (not $aachange->RNAChange->allele_ori->seq) { $aachange->allele_mut->seq(substr $aachange->allele_mut->seq, 0, length ($aachange->RNAChange->allele_mut->seq) / 3 +1); } } } else { #frameshift #my $pos = index $aachange->allele_mut #$aachange->allele_mut(substr($aachange->allele_mut, 0, 1)); $aachange->length(CORE::length($aachange->allele_ori->seq)); my $aaend = $aachange->start + $aachange->length -1; $aachange->end($aachange->start); } # splicing site deletion check my @beforeexons=@{$self->exons}; my @afterexons=$self->RNA->all_Exons; my $i; if (scalar(@beforeexons) ne scalar(@afterexons)) { my $mut_number = $self->mutation->issue; $self->warn("Exons have been modified at mutation n.$mut_number!"); $self->rnachange->exons_modified(1); } else { EXONCHECK: foreach $i (0..$#beforeexons) { if ($beforeexons[$i] ne $afterexons[$i]) { my $mut_number = $self->mutation->issue; $self->warn("Exons have been modified at mutation n.$mut_number!"); $self->rnachange->exons_modified(1); last EXONCHECK; } } } } else { #$seqDiff->rnachange(undef); #print "getting here?"; } return 1; } 1; BioPerl-1.007002/Bio/LiveSeq/Prim_Transcript.pm000444000766000024 256113155576320 21256 0ustar00cjfieldsstaff000000000000# # bioperl module for Bio::LiveSeq::Prim_Transcript # # Please direct questions and support issues to # # Cared for by Joseph Insana # # Copyright Joseph Insana # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::LiveSeq::Prim_Transcript - Prim_Transcript class for LiveSeq =head1 SYNOPSIS # documentation needed =head1 DESCRIPTION Class for PRIM_TRANSCRIPT objects. They consist of a beginlabel, an endlabel (both referring to a LiveSeq DNA object) and a strand. The strand could be 1 (forward strand, default), -1 (reverse strand). =head1 AUTHOR - Joseph A.L. Insana Email: Insana@ebi.ac.uk, jinsana@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::LiveSeq::Prim_Transcript; use strict; use base qw(Bio::LiveSeq::Range); =head2 new Title : new Usage : $intron1=Bio::LiveSeq::Prim_Transcript->new(-seq => $objref, -start => $startlabel, -end => $endlabel, -strand => 1 ); Function: generates a new Bio::LiveSeq::Prim_Transcript Returns : reference to a new object of class Prim_Transcript Errorcode -1 Args : two labels and an integer =cut 1; BioPerl-1.007002/Bio/LiveSeq/Range.pm000444000766000024 600213155576320 17164 0ustar00cjfieldsstaff000000000000# # bioperl module for Bio::LiveSeq::Range # # Please direct questions and support issues to # # Cared for by Joseph Insana # # Copyright Joseph Insana # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::LiveSeq::Range - Range abstract class for LiveSeq =head1 SYNOPSIS # documentation needed =head1 DESCRIPTION This is used as parent for exon and intron classes. =head1 AUTHOR - Joseph A.L. Insana Email: Insana@ebi.ac.uk, jinsana@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::LiveSeq::Range; use strict; use base qw(Bio::LiveSeq::SeqI); =head2 new Title : new Usage : $range1 = Bio::LiveSeq::Range->new(-seq => $obj_ref, -start => $beginlabel, -end => $endlabel, -strand => 1); Function: generates a new Bio::LiveSeq::Range Returns : reference to a new object of class Range Errorcode -1 Args : two labels, an obj_ref and an integer strand 1=forward strand, strand -1=reverse strand if strand not specified, it defaults to 1 the -seq argument must point to the underlying DNA LiveSeq object =cut sub new { my ($thing, %args) = @_; my $class = ref($thing) || $thing; my ($obj,%range); my ($seq,$start,$end,$strand)=($args{-seq},$args{-start},$args{-end},$args{-strand}); $obj = \%range; $obj = bless $obj, $class; unless ($seq->valid($start)) { $obj->warn("$class not initialised because start label not valid"); return (-1); } unless ($seq->valid($end)) { $obj->warn("$class not initialised because end label not valid"); return (-1); } unless (defined $strand) { $strand = 1; } if (($strand != 1)&&($strand != -1)) { $obj->warn("$class not initialised because strand identifier not valid. Use 1 (forward strand) or -1 (reverse strand)."); return (-1); } if ($start eq $end) { $obj->warn("$class reports: start and end label are the same...."); } else { unless ($seq->follows($start,$end,$strand)==1) { $obj->warn("Fatal: end label $end doesn't follow start label $start for strand $strand!"); return (-1); } } #if ($strand == 1) { # unless ($seq->is_downstream($start,$end)==1) { # croak "Fatal: end label not downstream of start label for forward strand!"; # } #} else { # unless ($seq->is_upstream($start,$end)==1) { # croak "Fatal: end label not upstream of start label for reverse strand!"; # } #} $obj->{'seq'}=$seq; $obj->{'start'}=$start; $obj->{'end'}=$end; $obj->{'strand'}=$strand; return $obj; } =head2 valid Title : valid Usage : $boolean = $obj->valid($label) Function: tests if a label exists AND is part of the object Returns : boolean Args : label =cut 1; BioPerl-1.007002/Bio/LiveSeq/Repeat_Region.pm000444000766000024 253213155576320 20657 0ustar00cjfieldsstaff000000000000# # bioperl module for Bio::LiveSeq::Repeat_Region # # Please direct questions and support issues to # # Cared for by Joseph Insana # # Copyright Joseph Insana # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::LiveSeq::Repeat_Region - Repeat_Region class for LiveSeq =head1 SYNOPSIS # documentation needed =head1 DESCRIPTION Class for REPEAT_REGION objects. They consist of a beginlabel, an endlabel (both referring to a LiveSeq DNA object) and a strand. The strand could be 1 (forward strand, default), -1 (reverse strand). =head1 AUTHOR - Joseph A.L. Insana Email: Insana@ebi.ac.uk, jinsana@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::LiveSeq::Repeat_Region; use strict; use base qw(Bio::LiveSeq::Range); =head2 new Title : new Usage : $intron1=Bio::LiveSeq::Repeat_Region->new(-seq => $objref, -start => $startlabel, -end => $endlabel, -strand => 1); Function: generates a new Bio::LiveSeq::Repeat_Region Returns : reference to a new object of class Repeat_Region Errorcode -1 Args : two labels and an integer =cut 1; BioPerl-1.007002/Bio/LiveSeq/Repeat_Unit.pm000444000766000024 252113155576320 20351 0ustar00cjfieldsstaff000000000000# # bioperl module for Bio::LiveSeq::Repeat_Unit # # Please direct questions and support issues to # # Cared for by Joseph Insana # # Copyright Joseph Insana # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::LiveSeq::Repeat_Unit - Repeat_Unit class for LiveSeq =head1 SYNOPSIS # documentation needed =head1 DESCRIPTION Class for REPEAT_UNIT objects. They consist of a beginlabel, an endlabel (both referring to a LiveSeq DNA object) and a strand. The strand could be 1 (forward strand, default), -1 (reverse strand). =head1 AUTHOR - Joseph A.L. Insana Email: Insana@ebi.ac.uk, jinsana@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::LiveSeq::Repeat_Unit; use strict; use base qw(Bio::LiveSeq::Repeat_Region); =head2 new Title : new Usage : $intron1=Bio::LiveSeq::Repeat_Unit->new(-seq => $objref, -start => $startlabel, -end => $endlabel, -strand => 1); Function: generates a new Bio::LiveSeq::Repeat_Unit Returns : reference to a new object of class Repeat_Unit Errorcode -1 Args : two labels and an integer =cut 1; BioPerl-1.007002/Bio/LiveSeq/SeqI.pm000444000766000024 10460113155576320 17035 0ustar00cjfieldsstaff000000000000# # bioperl module for Bio::LiveSeq::SeqI # # Please direct questions and support issues to # # Cared for by Joseph Insana # # Copyright Joseph Insana # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::LiveSeq::SeqI - Abstract sequence interface class for LiveSeq =head1 SYNOPSIS # documentation needed =head1 DESCRIPTION This class implements BioPerl PrimarySeqI interface for Live Seq objects. One of the main difference in LiveSequence compared to traditional "string" sequences is that coordinate systems are flexible. Typically gene nucleotide numbering starts from 1 at the first character of the initiator codon (A in ATG). This means that negative positions are possible and common! Secondly, the sequence manipulation methods do not return a new sequence object but change the current object. The current status can be written out to BioPerl sequence objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Joseph A.L. Insana Email: Insana@ebi.ac.uk, jinsana@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ Some note on the terminology/notation of method names: label: a unique pointer to a single nucleotide position: the position of a nucleotide according to a particular coordinate system (e.g. counting downstream from a particular label taken as number 1) base: the one letter code for a nucleotide (i.e.: "a" "t" "c" "g") a base is the "value" that an "element" of a "chain" can assume (see documentation on the Chain datastructure if interested) =cut #' # Let the code begin... package Bio::LiveSeq::SeqI; use strict; use Bio::Tools::CodonTable; # for the translate() function use base qw(Bio::Root::Root Bio::LiveSeq::ChainI Bio::PrimarySeqI); =head2 seq Title : seq Usage : $string = $obj->seq() Function: Returns the complete sequence of an object as a string of letters. Suggested cases are upper case for proteins and lower case for DNA sequence (IUPAC standard), Returns : a string =cut sub seq { my $self = shift; my ($start,$end) = ($self->start(),$self->end()); if ($self->strand() == 1) { return $self->{'seq'}->down_chain2string($start,undef,$end); } else { # reverse strand my $str = $self->{'seq'}->up_chain2string($start,undef,$end); $str =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; return $str; } } =head2 all_labels Title : all_labels Usage : @labels = $obj->all_labels() Function: all the labels of every nucleotide an object is composed of Returns : an array of labels Args : none =cut sub all_labels { my $self = shift; my ($start,$end) = ($self->start(),$self->end()); my $labels; if ($self->strand() == 1) { $labels=$self->{'seq'}->down_labels($start,$end); } else { $labels=$self->{'seq'}->up_labels($start,$end); } return (@{$labels}); } =head2 labelsubseq Title : labelsubseq Usage : $dna->labelsubseq(); : $dna->labelsubseq($startlabel); : $dna->labelsubseq($startlabel,$length); : $dna->labelsubseq($startlabel,undef,$endlabel); e.g. : $dna->labelsubseq(4,undef,8); Function: prints the sequence as string. The difference between labelsubseq and normal subseq is that it uses /labels/ as arguments, instead than positions. This allows for faster and more efficient lookup, skipping the (usually) lengthy conversion of positions into labels. This is especially useful for manipulating with high power LiveSeq objects, knowing the labels and exploiting their usefulness. Returns : a string Errorcode -1 Args : without arguments it returns the entire sequence with a startlabel it returns the sequence downstream that label if a length is specified, it returns only that number of bases if an endlabel is specified, it overrides the length argument and prints instead up to that label (included) Defaults: $startlabel defaults to the beginning of the entire sequence $endlabel defaults to the end of the entire sequence =cut # NOTE: unsecuremode is to be used /ONLY/ if sure of the start and end labels, especially that they follow each other in the correct order!!!! sub labelsubseq { my ($self,$start,$length,$end,$unsecuremode) = @_; if (defined $unsecuremode && $unsecuremode eq "unsecuremoderequested") { # to skip security checks (faster) unless ($start) { $start=$self->start; } if ($end) { if ($end == $start) { $length=1; undef $end; } else { undef $length; } } else { unless ($length) { $end=$self->end; } } } else { if ($start) { unless ($self->{'seq'}->valid($start)) { $self->warn("Start label not valid"); return (-1); } } if ($end) { if ($end == $start) { $length=1; undef $end; } else { unless ($self->{'seq'}->valid($end)) { $self->warn("End label not valid"); return (-1); } unless ($self->follows($start,$end) == 1) { $self->warn("End label does not follow Start label!"); return (-1); } undef $length; } } } if ($self->strand() == 1) { return $self->{'seq'}->down_chain2string($start,$length,$end); } else { # reverse strand my $str = $self->{'seq'}->up_chain2string($start,$length,$end); $str =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; return $str; } } =head2 subseq Title : subseq Usage : $substring = $obj->subseq(10,40); : $substring = $obj->subseq(10,undef,4); Function: returns the subseq from start to end, where the first base is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence Start cannot be larger than end but can be equal. Allows for negative numbers $obj->subseq(-10,-1). By definition, there is no 0! -5 -1 1 5 gctagcgcccaac atggctcgctg This allows one to retrieve sequences upstream from given position. The precedence is from left to right: if END is given LENGTH is ignored. Examples: $obj->subseq(-10,undef,10) returns 10 elements before position 1 $obj->subseq(4,8) returns elements from the 4th to the 8th, inclusive Returns : a string Errorcode: -1 Args : start, integer, defaults to start of the sequence end, integer, '' or undef, defaults to end of the sequence length, integer, '' or undef an optional strand (1 or -1) 4th argument if strand argument is not given, it will default to the object argument. This argument is useful when a call is issued from a child of a parent object containing the subseq method =cut #' # check the fact about reverse strand! # is it feasible? Is it correct? Should we do it? How about exons? Does it # work when you ask subseq of an exon? # eliminated now (Mon night) sub subseq { ##my ($self,$pos1,$pos2,$length,$strand) = @_; my ($self,$pos1,$pos2,$length,$strand) = @_; ##unless (defined ($strand)) { # if optional [strand] argument not given ## $strand=$self->strand; ##} $strand=$self->strand; my ($str,$startlabel,$endlabel); if (defined ($length)) { if ($length < 1) { $self->warn("No sense asking for a subseq of length < 1"); return (-1); } } unless (defined ($pos1)) { #print "\n##### DEBUG pos1 not defined\n"; $startlabel=$self->start; } else { if ($pos1 == 0) { # if position = 0 complain $self->warn("Position cannot be 0!"); return (-1); } ##if ($strand == 1) { # CHECK THIS! if ((defined ($pos2))&&($pos1>$pos2)) { $self->warn("1st position($pos1) cannot be > 2nd position($pos2)!"); return (-1); } ##} else { # CHECK THIS! ## if ((defined ($pos2))&&($pos1<$pos2)) { ## $self->warn("1st position($pos1) cannot be < 2nd position($pos2) on reverse strand!)"; return (-1); ## } ##} $startlabel=$self->label($pos1); if ($startlabel < 1) { $self->warn("position $pos1 not valid as start of subseq!"); return (-1); } } unless (defined ($pos2)) { #print "\n##### pos2 not defined\n"; unless (defined ($length)) { $endlabel=$self->end; } } else { if ($pos2 == 0) { # if position = 0 complain $self->warn("Position cannot be 0!"); return (-1); } undef $length; ##if ($strand == 1) { # CHECK THIS! if ((defined ($pos1))&&($pos1>$pos2)) { $self->warn("1st position($pos1) cannot be > 2nd position($pos2)!"); return (-1); } ##} else { # CHECK THIS! ## if ((defined ($pos1))&&($pos1<$pos2)) { ## $self->warn("1st position($pos1) cannot be < 2nd position($pos2) on reverse strand!"); return (-1); ## } ##} $endlabel=$self->label($pos2); if ($endlabel < 1) { $self->warn("position $pos2 not valid as end of subseq!"); return (-1); } } #print "\n ####DEBUG: start $startlabel end $endlabel length $length strand $strand\n"; if ($strand == 1) { $str = $self->{'seq'}->down_chain2string($startlabel,$length,$endlabel); } else { # reverse strand $str = $self->{'seq'}->up_chain2string($startlabel,$length,$endlabel); $str =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; } return $str; } =head2 length Title : length Usage : $seq->length(); Function: returns the number of nucleotides (or the number of aminoacids) in the entire sequence Returns : an integer Errorcode -1 Args : none =cut sub length { my $self=shift; my ($start,$end,$strand)=($self->start(),$self->end(),$self->strand()); if ($strand == 1) { return $self->{'seq'}->down_subchain_length($start,$end); } else { return $self->{'seq'}->up_subchain_length($start,$end); } } =head2 display_id Title : display_id Usage : $id_string = $obj->display_id(); Function: returns the display id, alias the common name of the object The semantics of this is that it is the most likely string to be used as an identifier of the sequence, and likely to have "human" readability. The id is equivalent to the ID field of the GenBank/EMBL databanks and the id field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. See also: accession_number Returns : a string Args : none =cut sub display_id { my ($self,$value) = @_; if(defined $value) { $self->{'display_id'} = $value; } return $self->{'display_id'}; } =head2 accession_number Title : accession_number Usage : $unique_biological_key = $obj->accession_number; Function: Returns the unique biological id for a sequence, commonly called the accession_number. Notice that primary_id() provides the unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For objects with no accession_number this method returns "unknown". Returns : a string Args : none =cut sub accession_number { my ($self,$value) = @_; if (defined $value) { $self->{'accession_number'} = $value; } unless (exists $self->{'accession_number'}) { return "unknown"; } else { return $self->{'accession_number'}; } } =head2 primary_id Title : primary_id Usage : $unique_implementation_key = $obj->primary_id; Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a way the implementation can control. Clients can expect one id to map to one object. For sequences with no primary_id, this method returns a stringified memory location. Returns : A string Args : None =cut sub primary_id { my ($self,$value) = @_; if(defined $value) { $self->{'primary_id'} = $value; } unless (exists $self->{'primary_id'}) { return "$self"; } else { return $self->{'primary_id'}; } } =head2 change Title : change Usage : $substring = $obj->change('AA', 10); Function: changes, modifies, mutates the LiveSequence Examples: $obj->change('', 10); delete nucleotide #10 $obj->change('', 10, 2); delete two nucleotides starting from #10 $obj->change('G', 10); change nuc #10 to 'G' $obj->change('GA', 10, 4); replace #10 and 3 following with 'GA' $obj->change('GA', 10, 2)); is same as $obj->change('GA', 10); $obj->change('GA', 10, 0 ); insert 'GA' before nucleotide at #10 $obj->change('GA', 10, 1); GA inserted before #10, #10 deleted $obj->change('GATC', 10, 2); GATC inserted before #10, #10 deleted $obj->change('GATC', 10, 6); GATC inserted before #10, #10-#15 deleted Returns : a string of deleted bases (if any) or 1 (everything OK) Errorcode: -1 Args : seq, string, or '' ('' = undef = 0 = deletion) start, integer length, integer (optional) =cut sub change { &positionchange; } =head2 positionchange Title : positionchange Function: Exactly like change. I.e. change() defaults to positionchange() =cut sub positionchange { my ($self,$newseq,$position,$length)=@_; unless ($position) { $self->warn("Position not given or position 0"); return (-1); } my $label=$self->label($position); unless ($label > 0) { # label not found or error $self->warn("No valid label found at that position!"); return (-1); } return ($self->labelchange($newseq,$label,$length)); } =head2 labelchange Title : labelchange Function: Exactly like change but uses a /label/ instead than a position as second argument. This allows for multiple changes in a LiveSeq without the burden of recomputing positions. I.e. for a multiple change in two different points of the LiveSeq, the approach would be the following: fetch the correct labels out of the two different positions (method: label($position)) and then use the labelchange() method to modify the sequence using those labels instead than relying on the positions (that would have modified after the first change). =cut sub labelchange { my ($self,$newseq,$label,$length)=@_; unless ($self->valid($label)) { if ($self->{'seq'}->valid($label)) { #$self->warn("Label \'$label\' not valid for executing a LiveSeq change for the object asked but it's ok for DNAlevel change, reverting to that"); shift @_; return($self->{'seq'}->labelchange(@_)); } else { $self->warn("Label \'$label\' not valid for executing a LiveSeq change"); return (-1); } } unless ($newseq) { # it means this is a simple deletion if (defined($length)) { unless ($length >= 0) { $self->warn("No sense having length < 0 in a deletion"); return (-1); } } else { $self->warn("Length not defined for deletion!"); return (-1); } return $self->_delete($label,$length); } my $newseqlength=CORE::length($newseq); if (defined($length)) { unless ($length >= 0) { $self->warn("No sense having length < 0 in a change()"); return (-1); } } else { $length=$newseqlength; # defaults to pointmutation(s) } if ($length == 0) { # it means this is a simple insertion, length def&==0 my ($insertbegin,$insertend)=$self->_praeinsert($label,$newseq); if ($insertbegin == -1) { return (-1); } else { return (1); } } if ($newseqlength == $length) { # it means this is simple pointmutation(s) return $self->_mutate($label,$newseq,$length); } # if we arrived here then change is complex mixture my $strand=$self->strand(); my $afterendlabel=$self->label($length+1,$label,$strand); # get the label at $length+1 positions after $label unless ($afterendlabel > 0) { # label not found or error $self->warn("No valid afterendlabel found for executing the complex mutation!"); return (-1); } my $deleted=$self->_delete($label,$length); # first delete length nucs if ($deleted eq -1) { # if errors return (-1); } else { # then insert the newsequence my ($insertbegin,$insertend)=$self->_praeinsert($afterendlabel,$newseq); if ($insertbegin == -1) { return (-1); } else { return (1); } } } # internal methods for change() # arguments: label for beginning of deletion, new sequence to insert # returns: labels of beginning and end of the inserted sequence # errorcode: -1 sub _praeinsert { my ($self,$label,$newseq)=@_; my ($insertbegin,$insertend); my $strand=$self->strand(); if ($strand == 1) { ($insertbegin,$insertend)=($self->{'seq'}->praeinsert_string($newseq,$label)); } else { # since it's reverse strand and we insert in forward direction.... $newseq=reverse($newseq); $newseq =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; # since it's reverse strand we get the complementary bases ($insertend,$insertbegin)=($self->{'seq'}->postinsert_string($newseq,$label)); } if (($insertbegin==0)||($insertend==0)) { $self->warn("Some error occurred while inserting!"); return (-1); } else { return ($insertbegin,$insertend); } } # arguments: label for beginning of deletion, length of deletion # returns: string of deleted bases # errorcode: -1 sub _delete { my ($self,$label,$length)=@_; my $strand=$self->strand(); my $endlabel=$self->label($length,$label,$strand); # get the label at $length positions after $label unless ($endlabel > 0) { # label not found or error $self->warn("No valid endlabel found for executing the deletion!"); return (-1); } # this is important in Transcript to fix exon structure $self->_deletecheck($label,$endlabel); my $deletedseq; if ($strand == 1) { $deletedseq=$self->{'seq'}->splice_chain($label,undef,$endlabel); } else { $deletedseq=$self->{'seq'}->splice_chain($endlabel,undef,$label); $deletedseq=reverse($deletedseq); # because we are on reverse strand and we cut anyway # in forward direction $deletedseq =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; # since it's reverse strand we get the complementary bases } return ($deletedseq); } # empty function, overridden in Transcript, not useful here sub _deletecheck { } # arguments: label for beginning of mutation, newsequence, number of mutations # returns: 1 all OK # errorcode: -1 sub _mutate { my ($self,$label,$newseq,$length)=@_; # length is equal to length(newseq) my ($i,$base,$nextlabel); my @labels; # array of labels my $strand=$self->strand(); if ($length == 1) { # special cases first @labels=($label); } else { my $endlabel=$self->label($length,$label,$strand); # get the label at $length positions after $label unless ($endlabel > 0) { # label not found or error $self->warn("No valid endlabel found for executing the mutation!"); return (-1); } if ($length == 2) { # another special case @labels=($label,$endlabel); } else { # more than 3 bases changed # this wouldn't work for Transcript #my $labelsarrayref; #if ($strand == 1) { #$labelsarrayref=$self->{'seq'}->down_labels($label,$endlabel); #} else { #$labelsarrayref=$self->{'seq'}->up_labels($label,$endlabel); #} #@labels=@{$labelsarrayref}; #if ($length != scalar(@labels)) { # not enough labels returned #$self->warn("Not enough valid labels found for executing the mutation!"); #return (-1); #} # this should be more general @labels=($label); # put the first one while ($label != $endlabel) { $nextlabel=$self->label(2,$label,$strand); # retrieve the next label push (@labels,$nextlabel); $label=$nextlabel; # move on reference } } } if ($strand == -1) { # only for reverse strand $newseq =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; # since it's reverse strand we get the complementary bases } my $errorcheck; # if not equal to $length after summing for all changes, error did occurr $i = 0; foreach $base (split(//,$newseq)) { $errorcheck += $self->{'seq'}->set_value_at_label($base,$labels[$i]); $i++; } if ($errorcheck != $length) { $self->warn("Some error occurred while mutating!"); return (-1); } else { return (1); } } =head2 valid Title : valid Usage : $boolean = $obj->valid($label) Function: tests if a label exists inside the object Returns : boolean Args : label =cut # argument: label # returns: 1 YES 0 NO sub valid { my ($self,$label)=@_; my $checkme; my @labels=$self->all_labels; foreach $checkme (@labels) { if ($label == $checkme) { return (1); # found } } return (0); # not found } =head2 start Title : start Usage : $startlabel=$obj->start() Function: returns the label of the first nucleotide of the object (exon, CDS) Returns : label Args : none =cut sub start { my ($self) = @_; return $self->{'start'}; # common for all classes BUT DNA (which redefines it) and Transcript (that takes the information from the Exons) } =head2 end Title : end Usage : $endlabel=$obj->end() Function: returns the label of the last nucleotide of the object (exon, CDS) Returns : label Args : none =cut sub end { my ($self) = @_; return $self->{'end'}; } =head2 strand Title : strand Usage : $strand=$obj->strand() $obj->strand($strand) Function: gets or sets strand information, being 1 or -1 (forward or reverse) Returns : -1 or 1 Args : none OR -1 or 1 =cut sub strand { my ($self,$strand) = @_; if ($strand) { if (($strand != 1)&&($strand != -1)) { $self->warn("strand information not changed because strand identifier not valid"); } else { $self->{'strand'} = $strand; } } return $self->{'strand'}; } =head2 alphabet Title : alphabet Usage : if( $obj->alphabet eq 'dna' ) { /Do Something/ } Function: Returns the type of sequence being one of 'dna', 'rna' or 'protein'. This is case sensitive. Returns : a string either 'dna','rna','protein'. Args : none =cut sub alphabet { my %valid_type = map {$_, 1} qw( dna rna protein ); my ($self,$value) = @_; if (defined $value) { $value = 'dna' if $value =~ /dna/i; $value = 'rna' if $value =~ /rna/i; unless ( $valid_type{$value} ) { $self->warn("Molecular type '$value' is not a valid type"); } $self->{'alphabet'} = $value; } return $self->{'alphabet'}; } =head2 coordinate_start Title : coordinate_start Usage : $coordstartlabel=$obj->coordinate_start() : $coordstartlabel=$obj->coordinate_start($label) Function: returns and optionally sets the first label of the coordinate system used For some objects only labels inside the object or in frame (for Translation objects) will be allowed to get set as coordinate start Returns : label. It returns 0 if label not found. Errorcode -1 Args : an optional reference $label that is position 1 =cut sub coordinate_start { my ($self,$label) = @_; if ($label) { if ($self->valid($label)) { $self->{'coordinate_start'} = $label; } else { $self->warn("The label you are trying to set as coordinate_start is not valid for this object"); } } my $coord_start = $self->{'coordinate_start'}; if ($coord_start) { return $coord_start; } else { return $self->start(); } } =head2 label Title : label Usage : $seq->label($position) : $seq->label($position,$firstlabel) Examples: $nextlabel=$seq->label(2,$label) -> retrieves the following label : $prevlabel=$seq->label(-1,$label) -> retrieves the preceding label Function: returns the label of the nucleotide at $position from current coordinate start Returns : a label. It returns 0 if label not found. Errorcode -1 Args : a position, an optional reference $firstlabel that is to be used as position 1 an optional strand (1 or -1) argument if strand argument is not given, it will default to the object argument. This argument is useful when a call is issued from a child of a parent object containing the subseq method =cut sub label { my ($self,$position,$firstlabel,$strand)=@_; my $label; unless (defined ($firstlabel)) { $firstlabel=$self->coordinate_start; } unless ($position) { # if position = 0 complain ? $self->warn("Position not given or position 0"); return (-1); } unless (defined ($strand)) { # if optional [strand] argument not given $strand=$self->strand; } if ($strand == 1) { if ($position > 0) { $label=$self->{'seq'}->down_get_label_at_pos($position,$firstlabel) } else { # if < 0 $label=$self->{'seq'}->up_get_label_at_pos(1 - $position,$firstlabel) } } else { if ($position > 0) { $label=$self->{'seq'}->up_get_label_at_pos($position,$firstlabel) } else { # if < 0 $label=$self->{'seq'}->down_get_label_at_pos(1 - $position,$firstlabel) } } return $label; } =head2 position Title : position Usage : $seq->position($label) : $seq->position($label,$firstlabel) Function: returns the position of nucleotide at $label Returns : the position of the label from current coordinate start Errorcode 0 Args : a label pointing to a certain nucleotide (e.g. start of exon) an optional "firstlabel" as reference to count from an optional strand (1 or -1) argument if strand argument is not given, it will default to the object argument. This argument is useful when a call is issued from a child of a parent object containing the subseq method =cut sub position { my ($self,$label,$firstlabel,$strand)=@_; unless (defined ($strand)) { # if optional [strand] argument not given $strand=$self->strand; } unless (defined ($firstlabel)) { $firstlabel=$self->coordinate_start; } unless ($self->valid($label)) { $self->warn("label not valid"); return (0); } if ($firstlabel == $label) { return (1); } my ($coordpos,$position0,$position); $position0=$self->{'seq'}->down_get_pos_of_label($label); $coordpos=$self->{'seq'}->down_get_pos_of_label($firstlabel); $position=$position0-$coordpos+1; if ($position <= 0) { $position--; } if ($strand == -1) { #print "\n----------DEBUGSEQPOS label $label firstlabel $firstlabel strand $strand: position=",1-$position; return (1-$position); } else { #print "\n----------DEBUGSEQPOS label $label firstlabel $firstlabel strand $strand: position=",$position; return ($position); } } =head2 follows Title : follows Usage : $seq->follows($firstlabel,$secondlabel) : $seq->follows($firstlabel,$secondlabel,$strand) Function: checks if SECONDlabel follows FIRSTlabel, undependent of the strand i.e. it checks downstream for forward strand and upstream for reverse strand Returns : 1 or 0 Errorcode -1 Args : two labels an optional strand (1 or -1) argument if strand argument is not given, it will default to the object argument. This argument is useful when a call is issued from a child of a parent object containing the subseq method =cut #' # wraparound to is_downstream and is_upstream that chooses the correct one # depending on the strand sub follows { my ($self,$firstlabel,$secondlabel,$strand)=@_; unless (defined ($strand)) { # if optional [strand] argument not given $strand=$self->strand; } if ($strand == 1) { return ($self->{'seq'}->is_downstream($firstlabel,$secondlabel)); } else { return ($self->{'seq'}->is_upstream($firstlabel,$secondlabel)); } } # #=head2 translate # # Title : translate # Usage : $protein_seq = $obj->translate # Function: Provides the translation of the DNA sequence # using full IUPAC ambiguities in DNA/RNA and amino acid codes. # # The resulting translation is identical to EMBL/TREMBL database # translations. # # Returns : a string # Args : character for terminator (optional) defaults to '*' # character for unknown amino acid (optional) defaults to 'X' # frame (optional) valid values 0, 1, 3, defaults to 0 # codon table id (optional) defaults to 1 # #=cut # #sub translate { # my ($self) = shift; # return ($self->translate_string($self->seq,@_)); #} # #=head2 translate_string # # Title : translate_string # Usage : $protein_seq = $obj->translate_string("attcgtgttgatcgatta"); # Function: Like translate, but can be used to translate subsequences after # having retrieved them as string. # Args : 1st argument is a string. Optional following arguments: like in # the translate method # #=cut # # #sub translate_string { # my($self) = shift; # my($seq) = shift; # my($stop, $unknown, $frame, $tableid) = @_; # my($i, $len, $output) = (0,0,''); # my($codon) = ""; # my $aa; # # # ## User can pass in symbol for stop and unknown codons # unless(defined($stop) and $stop ne '') { $stop = "*"; } # unless(defined($unknown) and $unknown ne '') { $unknown = "X"; } # unless(defined($frame) and $frame ne '') { $frame = 0; } # # ## the codon table ID # if ($self->translation_table) { # $tableid = $self->translation_table; # } # unless(defined($tableid) and $tableid ne '') { $tableid = 1; } # # ##Error if monomer is "Amino" # $self->warn("Can't translate an amino acid sequence.") # if (defined $self->alphabet && $self->alphabet eq 'protein'); # # ##Error if frame is not 0, 1 or 2 # $self->warn("Valid values for frame are 0, 1, 2, not [$frame].") # unless ($frame == 0 or $frame == 1 or $frame == 2); # # #thows a warning if ID is invalid # my $codonTable = Bio::Tools::CodonTable->new( -id => $tableid); # # # deal with frame offset. # if( $frame ) { # $seq = substr ($seq,$frame); # } # # for $codon ( grep { CORE::length == 3 } split(/(.{3})/, $seq) ) { # my $aa = $codonTable->translate($codon); # if ($aa eq '*') { # $output .= $stop; # } # elsif ($aa eq 'X') { # $output .= $unknown; # } # else { # $output .= $aa ; # } # } # #if( substr($output,-1,1) eq $stop ) { # # chop $output; # #} # # return ($output); #} =head2 gene Title : gene Usage : my $gene=$obj->gene; Function: Gets or sets the reference to the LiveSeq::Gene object. Objects that are features of a LiveSeq Gene will have this attribute set automatically. Returns : reference to an object of class Gene Note : if Gene object is not set, this method will return 0; Args : none or reference to object of class Bio::LiveSeq::Gene =cut sub gene { my ($self,$value) = @_; if (defined $value) { $self->{'gene'} = $value; } unless (exists $self->{'gene'}) { return (0); } else { return $self->{'gene'}; } } =head2 obj_valid Title : obj_valid Usage : if ($obj->obj_valid) {do something;} Function: Checks if start and end labels are still valid for the ojbect, i.e. tests if the LiveSeq object is still valid Returns : boolean Args : none =cut sub obj_valid { my $self=shift; unless (($self->{'seq'}->valid($self->start()))&&($self->{'seq'}->valid($self->end()))) { return (0); } return (1); } =head2 name Title : name Usage : $name = $obj->name; : $name = $obj->name("ABCD"); Function: Returns or sets the name of the object. If there is no name, it will return "unknown"; Returns : A string Args : None =cut sub name { my ($self,$value) = @_; if (defined $value) { $self->{'name'} = $value; } unless (exists $self->{'name'}) { return "unknown"; } else { return $self->{'name'}; } } =head2 desc Title : desc Usage : $desc = $obj->desc; : $desc = $obj->desc("ABCD"); Function: Returns or sets the description of the object. If there is no description, it will return "unknown"; Returns : A string Args : None =cut sub desc { my ($self,$value) = @_; if (defined $value) { $self->{'desc'} = $value; } unless (exists $self->{'desc'}) { return "unknown"; } else { return $self->{'desc'}; } } =head2 source Title : source Usage : $name = $obj->source; : $name = $obj->source("Homo sapiens"); Function: Returns or sets the organism that is source of the object. If there is no source, it will return "unknown"; Returns : A string Args : None =cut sub source { my ($self,$value) = @_; if (defined $value) { $self->{'source'} = $value; } unless (exists $self->{'source'}) { return "unknown"; } else { return $self->{'source'}; } } sub delete_Obj { my $self = shift; my @values= values %{$self}; my @keys= keys %{$self}; foreach my $key ( @keys ) { delete $self->{$key}; } foreach my $value ( @values ) { if (index(ref($value),"LiveSeq") != -1) { # object case eval { # delete $self->{$value}; $value->delete_Obj; }; } elsif (index(ref($value),"ARRAY") != -1) { # array case my @array=@{$value}; my $element; foreach $element (@array) { eval { $element->delete_Obj; }; } } elsif (index(ref($value),"HASH") != -1) { # object case my %hash=%{$value}; my $element; foreach $element (%hash) { eval { $element->delete_Obj; }; } } } return(1); } 1; BioPerl-1.007002/Bio/LiveSeq/Transcript.pm000444000766000024 6057213155576320 20315 0ustar00cjfieldsstaff000000000000# # bioperl module for Bio::LiveSeq::Transcript # # Please direct questions and support issues to # # Cared for by Joseph Insana # # Copyright Joseph Insana # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::LiveSeq::Transcript - Transcript class for LiveSeq =head1 SYNOPSIS # documentation needed =head1 DESCRIPTION This stores information about coding sequences (CDS). The implementation is that a Transcript object accesses a collection of Exon objects, inferring from them the nucleotide structure and sequence. =head1 AUTHOR - Joseph A.L. Insana Email: Insana@ebi.ac.uk, jinsana@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::LiveSeq::Transcript; use strict; # use Carp qw(carp cluck); use Bio::LiveSeq::Exon; # uses Exon to create new exon in case of deletion use base qw(Bio::LiveSeq::SeqI); =head2 new Title : new Usage : $transcript = Bio::LiveSeq::Transcript->new(-exons => \@obj_refs); Function: generates a new Bio::LiveSeq::Transcript Returns : reference to a new object of class Transcript Errorcode -1 Args : reference to an array of Exon object references =cut sub new { my ($thing, %args) = @_; my $class = ref($thing) || $thing; my ($obj,%transcript); my @exons=@{$args{-exons}}; $obj = \%transcript; $obj = bless $obj, $class; unless (@exons) { $obj->warn("$class not initialised because exons array empty"); return(-1); } # now useless, after start and end methods have been overridden here my $firstexon = $exons[0]; #my $lastexon = $exons[-1]; #my $start = $firstexon->start; #my $end = $lastexon->end; my $strand = $firstexon->strand; my $seq = $firstexon->{'seq'}; $obj->alphabet('rna'); unless (_checkexons(\@exons)) { $obj->warn("$class not initialised because of problems in the exon structure"); return(-1); } $obj->{'strand'}=$strand; $obj->{'exons'}=\@exons; $obj->{'seq'}=$seq; # set Transcript into each Exon my $exon; foreach $exon (@exons) { $exon->{'transcript'}=$obj; } return $obj; } =head2 all_Exons Title : all_Exons Usage : $transcript_obj->all_Exons() Function: returns references to all Exon objects the Transcript is composed of Example : foreach $exon ($transcript->all_Exons()) { do_something } Returns : array of object references Args : none =cut sub all_Exons { my $self=shift; my $exonsref=$self->{'exons'}; my @exons=@{$exonsref}; my @newexons; my $exon; foreach $exon (@exons) { unless ($exon->obj_valid) { $self->warn("$exon no more valid, start or end label lost, skipping....",1); # ignorable } else { push(@newexons,$exon); } } if ($#exons != $#newexons) { # update exons field $self->{'exons'}=\@newexons; } return (@newexons); } =head2 downstream_seq Title : downstream_seq Usage : $transcript_obj->downstream_seq() : $transcript_obj->downstream_seq(64) Function: returns a string of nucleotides downstream of the end of the CDS. If there is some information of the real mRNA, from features in an attached Gene object, it will return up to those boundaries. Otherwise it will return 1000 nucleotides. If an argument is given it will override the default 1000 number and return instead /that/ requested number of nucleotides. But if a Gene object is attached, this argument will be ignored. Returns : string Args : an optional integer number of nucleotides to be returned instead of the default if no gene attached =cut sub downstream_seq { my ($self,$howmany)=@_; my $str; if (defined ($howmany)) { unless ($howmany > 0) { $self->throw("No sense in asking less than 1 downstream nucleotides!"); } } else { unless ($self->{'seq'}->alphabet eq 'rna') { # if rna retrieve until the end #$str=$DNAobj->labelsubseq($self->end,undef,undef,"unsecuremoderequested"); #return(substr($str,1)); # delete first nucleotide that is the last of Transcript if ($self->gene) { # if there is Gene object attached fetch relevant info $str=$self->{'seq'}->labelsubseq($self->end,undef,$self->gene->maxtranscript->end); # retrieve from end of this Transcript to end of the maxtranscript $str=substr($str,1); # delete first nucleotide that is the last of Transcript if (CORE::length($str) > 0) { return($str); } else { # if there was no downstream through the gene's maxtranscript, go the usual way $howmany = 1000; } } else { $howmany = 1000; } } } my @exons=$self->all_Exons; my $strand=$self->strand(); my $lastexon=$exons[-1]; my $lastexonlength=$lastexon->length; # $howmany nucs after end of last exon #my $downstream_seq=$lastexon->subseq($lastexonlength+1,undef,$howmany); my $downstream_seq; if ($howmany) { $downstream_seq=substr($lastexon->labelsubseq($self->end,$howmany,undef,"unsecuremoderequested"),1); } else { if ($strand == 1) { $downstream_seq=substr($lastexon->labelsubseq($self->end,undef,$self->{'seq'}->end,"unsecuremoderequested"),1); } else { $downstream_seq=substr($lastexon->labelsubseq($self->end,undef,$self->{'seq'}->start,"unsecuremoderequested"),1); } } return $downstream_seq; } =head2 upstream_seq Title : upstream_seq Usage : $transcript_obj->upstream_seq() : $transcript_obj->upstream_seq(64) Function: just like downstream_seq but returns nucleotides before the ATG Note : the default, if no Gene information present and no nucleotides number given, is to return up to 400 nucleotides. =cut sub upstream_seq { my ($self,$howmany)=@_; if (defined ($howmany)) { unless ($howmany > 0) { $self->throw("No sense in asking less than 1 upstream nucleotides!"); } } else { unless ($self->{'seq'}->alphabet eq 'rna') { # if rna retrieve from the start if ($self->gene) { # if there is Gene object attached fetch relevant info my $str=$self->{'seq'}->labelsubseq($self->gene->maxtranscript->start,undef,$self->start); # retrieve from start of maxtranscript to start of this Transcript chop $str; # delete last nucleotide that is the A of starting ATG if (length($str) > 0) { return($str); } else { # if there was no upstream through the gene's maxtranscript, go the usual way $howmany = 400; } } else { $howmany = 400; } } } my @exons=$self->all_Exons; my $firstexon=$exons[0]; my $upstream_seq; my $strand=$self->strand(); if ($howmany) {# $howmany nucs before begin of first exon my $labelbefore=$firstexon->label(-$howmany,$firstexon->start); if ($labelbefore < 1) { if ($strand == 1) { $labelbefore=$self->{'seq'}->start; } else { $labelbefore=$self->{'seq'}->end; } } $upstream_seq=$firstexon->labelsubseq($labelbefore,undef,$firstexon->start,"unsecuremoderequested"); chop $upstream_seq; } else { if ($strand == 1) { $upstream_seq=$firstexon->labelsubseq($self->{'seq'}->start,undef,$self->start,"unsecuremoderequested"); chop $upstream_seq; # delete last nucleotide that is the A of starting ATG } else { $upstream_seq=$firstexon->labelsubseq($self->{'seq'}->end,undef,$self->start,"unsecuremoderequested"); chop $upstream_seq; # delete last nucleotide that is the A of starting ATG } } return $upstream_seq; } # These get redefined here, overriding the SeqI one because they draw their # information from the Exons a Transcript is built of # optional argument: firstlabel. If not given, it checks coordinate_start # This is useful when called by Translation # also used by _delete sub label { my ($self,$position,$firstlabel)=@_; unless ($position) { # if position = 0 complain ? $self->warn("Position not given or position 0"); return (-1); } my ($start,$end,$strand)=($self->start(),$self->end(),$self->strand()); my ($label,@labels,$length,$arraypos); unless (defined ($firstlabel)) { $firstlabel=$self->coordinate_start; # this is inside Transcript obj } my $coord_pos=$self->_inside_position($firstlabel); $length=$self->length; #if ($strand == 1) { if ($position < 1) { $position++; # to account for missing of 0 position } $arraypos=$position+$coord_pos-2; #print "\n=-=-=-=-DEBUG: arraypos $arraypos, pos $position, coordpos: $coord_pos"; if ($arraypos < 0) { $label=$self->{'seq'}->label($arraypos,$start,$strand); #? } elsif ($arraypos >= $length) { $label=$self->{'seq'}->label($arraypos-$length+2,$end,$strand); #? } else { # inside the Transcript @labels=$self->all_labels; $label=$labels[$arraypos]; } #} } # argument: label # returns: position of label according to coord_start # errorcode: 0 label not found # optional argument: firstlabel. If not given, it checks coordinate_start # This is useful when called by Translation sub position { my ($self,$label,$firstlabel)=@_; unless ($self->{'seq'}->valid($label)) { $self->warn("label is not valid"); return (0); } unless (defined ($firstlabel)) { $firstlabel=$self->coordinate_start; # this is inside Transcript obj } if ($label == $firstlabel) { return (1); } my ($start,$end,$strand)=($self->start(),$self->end(),$self->strand()); my ($position,$in_pos,$out_pos,$coord_pos); my $length=$self->length; $coord_pos=$self->_inside_position($firstlabel); if ($self->valid($label)) { # if label is inside the Transcript $in_pos=$self->_inside_position($label); $position=$in_pos-$coord_pos+1; if ($position <= 0) { return ($position-1); # accounts for the missing of the 0 position } } else { if ($self->follows($end,$label)) { # label after end of transcript $out_pos=$self->{'seq'}->position($label,$end,$strand); #print "\n+++++++++DEBUG label $label FOLLOWS end $end outpos $out_pos coordpos $coord_pos"; $position=$out_pos+$length-$coord_pos; } elsif ($self->follows($label,$start)) { # label before begin of transcript #print "\n+++++++++DEBUG label $label BEFORE start $start outpos $out_pos coordpos $coord_pos"; $out_pos=$self->{'seq'}->position($label,$start,$strand); $position=$out_pos-$coord_pos+1; } else { # label is in intron (not valid, not after, not before)! $self->warn("Cannot give position of label pointing to intron according to CDS numbering!",1); return (0); } } return ($position); } sub seq { my $self=shift; my ($exon,$str); my @exons=$self->all_Exons(); foreach $exon (@exons) { $str .= $exon->seq(); } return $str; } sub length { my $self=shift; my ($exon,$length); my @exons=$self->all_Exons(); foreach $exon (@exons) { $length += $exon->length(); } return $length; } sub all_labels { my $self=shift; my ($exon,@labels); my @exons=$self->all_Exons(); foreach $exon (@exons) { push (@labels,$exon->all_labels()); } return @labels; } # redefined here so that it will retrieve effective subseq without introns # otherwise it would have retrieved an underlying DNA (possibly with introns) # subsequence # Drawback: this is really bulky, label->position and then a call to # subseq that will do the opposite position-> label # # one day this can be rewritten as the main one so that the normal subseq # will rely on this one and hence avoid this double (useless and lengthy) # conversion between labels and positions sub old_labelsubseq { my ($self,$start,$length,$end)=@_; my ($pos1,$pos2); if ($start) { unless ($self->valid($start)) { $self->warn("Start label not valid"); return (-1); } $pos1=$self->position($start); } if ($end) { if ($end == $start) { $length=1; } else { unless ($self->valid($end)) { $self->warn("End label not valid"); return (-1); } unless ($self->follows($start,$end) == 1) { $self->warn("End label does not follow Start label!"); return (-1); } $pos2=$self->position($end); undef $length; } } return ($self->subseq($pos1,$pos2,$length)); } # rewritten, eventually sub labelsubseq { my ($self,$start,$length,$end,$unsecuremode)=@_; unless (defined $unsecuremode && $unsecuremode eq "unsecuremoderequested") { # to skip security checks (faster) if ($start) { unless ($self->valid($start)) { $self->warn("Start label not valid"); return (-1); } } else { $start=$self->start; } if ($end) { if ($end == $start) { $length=1; undef $end; } else { undef $length; # end argument overrides length argument unless ($self->valid($end)) { $self->warn("End label not valid"); return (-1); } unless ($self->follows($start,$end) == 1) { $self->warn("End label does not follow Start label!"); return (-1); } } } else { $end=$self->end; } } my ($seq,$exon,$startexon,$endexon); my @exonlabels; my @exons=$self->all_Exons; EXONCHECK: foreach $exon (@exons) { if ((!(defined($startexon)))&&($exon->valid($start))) { # checks only if not yet found $startexon=$exon; } if ($exon->valid($end)) { $endexon=$exon; } if ((!(defined($seq)) && (defined($startexon)))) { # initializes only once if ((defined($endexon)) && ($endexon eq $startexon)) { # then perfect, we are finished if ($length) { $seq = $startexon->labelsubseq($start,$length,undef,"unsecuremoderequested"); last EXONCHECK; } else { $seq = $startexon->labelsubseq($start,undef,$end,"unsecuremoderequested"); } last EXONCHECK; } else { # get up to the end of the exon $seq = $startexon->labelsubseq($start,undef,undef,"unsecuremoderequested"); } } if (($startexon)&&($exon ne $startexon)) { if (defined($endexon)) { # we arrived to the last exon $seq .= $endexon->labelsubseq(undef,undef,$end,"unsecuremoderequested"); # get from the start of the exon last EXONCHECK; } elsif (defined($startexon)) { # we are in a whole-exon-in-the-middle case $seq .= $exon->seq; # we add it completely to the seq } # else, we still have to reach the start point, exon useless, we move on if ($length) { # if length argument specified if (($seq && (CORE::length($seq) >= $length))) { last EXONCHECK; } } } } if ($length) { return (substr($seq,0,$length)); } else { return ($seq); } } # argument: label # returns: the objref and progressive number of the Exon containing that label # errorcode: -1 sub in_which_Exon { my ($self,$label)=@_; my ($count,$exon); my @exons=$self->all_Exons; foreach $exon (@exons) { $count++; # 1st exon is numbered "1" if ($exon->valid($label)) { return ($exon,$count) } } return (-1); # if nothing found } # recoded to exploit the new fast labelsubseq() # valid only inside Transcript sub subseq { my ($self,$pos1,$pos2,$length) = @_; my ($str,$startlabel,$endlabel); if (defined ($pos1)) { if ($pos1 == 0) { # if position = 0 complain $self->warn("Position cannot be 0!"); return (-1); } if ((defined ($pos2))&&($pos1>$pos2)) { $self->warn("1st position($pos1) cannot be > 2nd position($pos2)!"); return (-1); } $startlabel=$self->label($pos1); unless ($self->valid($startlabel)) { $self->warn("Start label not valid"); return (-1); } if ($startlabel < 1) { $self->warn("position $pos1 not valid as start of subseq!"); return (-1); } } else { $startlabel=$self->start; } if (defined ($pos2)) { if ($pos2 == 0) { # if position = 0 complain $self->warn("Position cannot be 0!"); return (-1); } undef $length; if ((defined ($pos1))&&($pos1>$pos2)) { $self->warn("1st position($pos1) cannot be > 2nd position($pos2)!"); return (-1); } $endlabel=$self->label($pos2); unless ($self->valid($endlabel)) { $self->warn("End label not valid"); return (-1); } if ($endlabel < 1) { $self->warn("position $pos2 not valid as end of subseq!"); return (-1); } } else { unless (defined ($length)) { $endlabel=$self->end; } } return ($self->labelsubseq($startlabel,$length,$endlabel,"unsecuremoderequested")); } # works only inside the transcript, complains if asked outside sub old_subseq { my ($self,$pos1,$pos2,$length) = @_; my ($str,$startcount,$endcount,$seq,$seqlength); if (defined ($length)) { if ($length < 1) { $self->warn("No sense asking for a subseq of length < 1"); return (-1); } } my $firstlabel=$self->coordinate_start; # this is inside Transcript obj my $coord_pos=$self->_inside_position($firstlabel); # TESTME old $seq=$self->seq; $seqlength=CORE::length($seq); unless (defined ($pos1)) { $startcount=1+$coord_pos-1; # i.e. coord_pos } else { if ($pos1 == 0) { # if position = 0 complain $self->warn("Position cannot be 0!"); return (-1); } elsif ($pos1 < 0) { $pos1++; } if ((defined ($pos2))&&($pos1>$pos2)) { $self->warn("1st position ($pos1) cannot be > 2nd position ($pos2)!"); return (-1); } $startcount=$pos1+$coord_pos-1; } unless (defined ($pos2)) { ; } else { if ($pos2 == 0) { # if position = 0 complain $self->warn("Position cannot be 0!"); return (-1); } elsif ($pos2 < 0) { $pos2++; } if ((defined ($pos1))&&($pos1>$pos2)) { $self->warn("1st position ($pos1) cannot be > 2nd position ($pos2)!"); return (-1); } $endcount=$pos2+$coord_pos-1; if ($endcount > $seqlength) { #print "\n###DEBUG###: pos1 $pos1 pos2 $pos2 coordpos $coord_pos endcount $endcount seqln $seqlength\n"; $self->warn("Cannot access end position after the end of Transcript"); return (-1); } $length=$endcount-$startcount+1; } #print "\n###DEBUG pos1 $pos1 pos2 $pos2 start $startcount end $endcount length $length coordpos $coord_pos\n"; my $offset=$startcount-1; if ($offset < 0) { $self->warn("Cannot access startposition before the beginning of Transcript, returning from start",1); # ignorable return (substr($seq,0,$length)); } elsif ($offset >= $seqlength) { $self->warn("Cannot access startposition after the end of Transcript"); return (-1); } else { $str=substr($seq,$offset,$length); if (CORE::length($str) < $length) { $self->warn("Attention, cannot return the length requested ". "for subseq",1) if $self->verbose > 0; # ignorable } return $str; } } # redefined so that it doesn't require other methods (after deletions) to # reset it. sub start { my $self = shift; my $exonsref=$self->{'exons'}; my @exons=@{$exonsref}; return ($exons[0]->start); } sub end { my $self = shift; my $exonsref=$self->{'exons'}; my @exons=@{$exonsref}; return ($exons[-1]->end); } # internal methods begin here # returns: position of label in transcript's all_labels # with STARTlabel == 1 # errorcode 0 -> label not found # argument: label sub _inside_position { my ($self,$label)=@_; my ($start,$end,$strand)=($self->start(),$self->end(),$self->strand()); my ($position,$checkme); my @labels=$self->all_labels; foreach $checkme (@labels) { $position++; if ($label == $checkme) { return ($position); } } return (0); } # returns 1 OK or 0 ERROR # arguments: reference to array of Exon object references sub _checkexons { my ($exon,$thisstart); my $self=$exon; my $exonsref=$_[0]; my @exons=@{$exonsref}; my $firstexon = $exons[0]; unless (ref($firstexon) eq "Bio::LiveSeq::Exon") { $self->warn("Object not of class Exon"); return (0); } my $strand = $firstexon->strand; my $prevend = $firstexon->end; shift @exons; # skip first one foreach $exon (@exons) { unless (ref($exon) eq "Bio::LiveSeq::Exon") { # object class check $self->warn("Object not of class Exon"); return (0); } if ($exon->strand != $strand) { # strand consistency check $self->warn("Exons' strands not consistent when trying to create Transcript"); return (0); } $thisstart = $exon->start; unless ($exon->{'seq'}->follows($prevend,$thisstart,$strand)) { $self->warn("Exons not in correct order when trying to create Transcript"); return (0); } $prevend = $exon->end; } return (1); } =head2 get_Translation Title : valid Usage : $translation = $obj->get_Translation() Function: retrieves the reference to the object of class Translation (if any) attached to a LiveSeq object Returns : object reference Args : none =cut sub get_Translation { my $self=shift; return ($self->{'translation'}); # this is set when Translation->new is called } # this checks so that deletion spanning multiple exons is # handled accordingly and correctly # arguments: begin and end label of a deletion # this is called BEFORE any deletion in the chain sub _deletecheck { my ($self,$startlabel,$endlabel)=@_; my $exonsref=$self->{'exons'}; my @exons=@{$exonsref}; my ($startexon,$endexon,$exon); $startexon=$endexon=0; foreach $exon (@exons) { if (($startexon == 0)&&($exon->valid($startlabel))) { $startexon=$exon; # exon containing start of deletion } if (($endexon == 0)&&($exon->valid($endlabel))) { $endexon=$exon; # exon containing end of deletion } if (($startexon)&&($endexon)) { last; # don't check further } } my $nextend=$self->label(2,$endlabel); # retrieve the next label my $prevstart=$self->label(-1,$startlabel); # retrieve the prev label if ($startexon eq $endexon) { # intra-exon deletion if (($startexon->start eq $startlabel) && ($startexon->end eq $endlabel)) { # let's delete the entire exon my @newexons; foreach $exon (@exons) { unless ($exon eq $startexon) { push(@newexons,$exon); } } $self->{'exons'}=\@newexons; } elsif ($startexon->start eq $startlabel) { # special cases $startexon->{'start'}=$nextend; # set a new start of exon } elsif ($startexon->end eq $endlabel) { $startexon->{'end'}=$prevstart; # set a new end of exon } else { return; # no problem } } else { # two new exons to be created, inter-exons deletion my @newexons; my $exonobj; my $dna=$self->{'seq'}; my $strand=$self->strand; my $notmiddle=1; # flag for skipping exons in the middle of deletion foreach $exon (@exons) { if ($exon eq $startexon) { $exonobj=Bio::LiveSeq::Exon->new('-seq'=>$dna,'-start'=>$exon->start,'-end'=>$prevstart,'-strand'=>$strand); # new partial exon push(@newexons,$exonobj); $notmiddle=0; # now we enter totally deleted exons } elsif ($exon eq $endexon) { $exonobj=Bio::LiveSeq::Exon->new('-seq'=>$dna,'-start'=>$nextend,'-end'=>$exon->end,'-strand'=>$strand); # new partial exon push(@newexons,$exonobj); $notmiddle=1; # exiting totally deleted exons } else { if ($notmiddle) { # if before or after exons with deletion push(@newexons,$exon); }# else skip them } } $self->{'exons'}=\@newexons; } } =head2 translation_table Title : translation_table Usage : $name = $obj->translation_table; : $name = $obj->translation_table(11); Function: Returns or sets the translation_table used for translating the transcript. If it has never been set, it will return undef. Returns : an integer =cut sub translation_table { my ($self,$value) = @_; if (defined $value) { $self->{'translation_table'} = $value; } unless (exists $self->{'translation_table'}) { return; } else { return $self->{'translation_table'}; } } =head2 frame Title : frame Usage : $frame = $transcript->frame($label); Function: Returns the frame of a particular nucleotide. Frame can be 0 1 or 2 and means the position in the codon triplet of the particulat nucleotide. 0 is the first codon_position. Codon_position (1 2 3) is simply frame+1. If the label asked for is not inside the Transcript, -1 will be returned. Args : a label Returns : 0 1 or 2 Errorcode -1 =cut # args: label # returns: frame of nucleotide (0 1 2) # errorcode: -1 sub frame { my ($self,$inputlabel)=@_; my @labels=$self->all_labels; my ($label,$frame,$count); foreach $label (@labels) { if ($inputlabel == $label) { return ($count % 3); } $count++; # 0 1 2 3 4.... } return (-1); # label not found amid Transcript labels } 1; BioPerl-1.007002/Bio/LiveSeq/Translation.pm000444000766000024 2136313155576320 20455 0ustar00cjfieldsstaff000000000000# # bioperl module for Bio::LiveSeq::Translation # # Please direct questions and support issues to # # Cared for by Joseph Insana # # Copyright Joseph Insana # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::LiveSeq::Translation - Translation class for LiveSeq =head1 SYNOPSIS #documentation needed =head1 DESCRIPTION This stores information about aminoacids translations of transcripts. The implementation is that a Translation object is the translation of a Transcript object, with different possibilities of manipulation, different coordinate system and eventually its own ranges (protein domains). =head1 AUTHOR - Joseph A.L. Insana Email: Insana@ebi.ac.uk, jinsana@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::LiveSeq::Translation; use strict; #use Carp qw(croak carp cluck); use Bio::LiveSeq::SeqI; # uses SeqI, inherits from it use Bio::PrimarySeq; use base qw(Bio::LiveSeq::Transcript); =head2 new Title : new Usage : $protein = Bio::LiveSeq::Translation->new(-transcript => $transcr); Function: generates a new Bio::LiveSeq::Translation Returns : reference to a new object of class Translation Errorcode -1 Args : reference to an object of class Transcript =cut sub new { my ($thing, %args) = @_; my $class = ref($thing) || $thing; my ($obj,%translation); my $transcript=$args{-transcript}; $obj = \%translation; $obj = bless $obj, $class; unless ($transcript) { $obj->throw("$class not initialised because no -transcript given"); } unless (ref($transcript) eq "Bio::LiveSeq::Transcript") { $obj->throw("$class not initialised because no object of class Transcript given"); } #my $startbase = $transcript->start; #my $endbase = $transcript->end; my $strand = $transcript->strand; my $seq = $transcript->{'seq'}; $obj->{'strand'}=$strand; $obj->{'seq'}=$seq; $obj->{'transcript'}=$transcript; $obj->{'alphabet'}="protein"; $transcript->{'translation'}=$obj;# set the Translation ref into its Transcript return $obj; } =head2 get_Transcript Title : valid Usage : $transcript = $obj->get_Transcript() Function: retrieves the reference to the object of class Transcript (if any) attached to a LiveSeq object Returns : object reference Args : none =cut sub get_Transcript { my $self=shift; return ($self->{'transcript'}); } # These get redefined here, overriding the SeqI ones sub change { my ($self)=@_; $self->warn("Cannot change a Translation object!\nChanges have to be issued at the nucleotide level!"); return (-1); } sub positionchange { my ($self)=@_; $self->warn("Cannot change a Translation object!\nChanges have to be issued at the nucleotide level!"); return (-1); } sub labelchange { my ($self)=@_; $self->warn("Cannot change a Translation object!\nChanges have to be issued at the nucleotide level!"); return (-1); } # this just returns the translation of the transcript, without checking for # stop codons sub transl_seq { my $self=shift; my $transcript=$self->get_Transcript; my $translation=$transcript->translate(undef, undef, undef, $self->translation_table)->seq; return $translation; } # version 1.74 -> now the "*" is printed sub seq { my $self=shift; my $proteinseq; my $transcript=$self->get_Transcript; my $translation=$transcript->translate(undef, undef, undef, $self->translation_table)->seq; my $stop_pos=index($translation,"*"); if ($stop_pos == -1) { # no stop present, continue downstream my $downstreamseq=$transcript->downstream_seq(); #carp "the downstream is: $downstreamseq"; # debug my $cdnaseq=$transcript->seq(); my $extendedseq = Bio::PrimarySeq->new(-seq => "$cdnaseq$downstreamseq", -alphabet => 'dna' ); $translation=$extendedseq->translate(undef, undef, undef, $self->translation_table)->seq; #carp "the new translation is: $translation"; # debug $stop_pos=index($translation,"*"); if ($stop_pos == -1) { # still no stop present, return warning $self->warn("Warning: no stop codon found in the retrieved sequence downstream of Transcript ",1); undef $stop_pos; $proteinseq=$translation; } else { $proteinseq=substr($translation,0,$stop_pos+1); #carp "the new stopped translation is: $proteinseq, because the stop is at position $stop_pos"; # debug } } else { $proteinseq=substr($translation,0,$stop_pos+1); } return $proteinseq; } sub length { my $self=shift; my $seq=$self->seq; my $length=length($seq); return $length; } sub all_labels { my $self=shift; return $self->get_Transcript->all_labels; } # counts in triplet. Only a label matching the beginning of a triplet coding # for an aminoacid is considered valid when setting coordinate_start # (i.e. only in frame!) sub valid { my ($self,$label)=@_; my $i; my @labels=$self->get_Transcript->all_labels; my $length=$#labels; while ($i <= $length) { if ($label == $labels[$i]) { return (1); # found } $i=$i+3; } return (0); # not found } # returns the label to the first nucleotide of the triplet coding for $position aminoacid sub label { my ($self,$position)=@_; my $firstlabel=$self->coordinate_start; # this is in_frame checked if ($position > 0) { $position=$position*3-2; } else { # if position = 0 this will be caught by Transcript, error thrown $position=$position*3; } return $self->get_Transcript->label($position,$firstlabel); # check for coord_start different } # returns position (aminoacids numbering) of a particular label # used to return 0 for not in frame labels # now returns the position anyway (after version 1.66) sub position { my ($self,$label)=@_; my $firstlabel=$self->coordinate_start; # this is in_frame checked my $position=$self->get_Transcript->position($label,$firstlabel); use integer; my $modulus=$position % 3; if ($position == 0) { return (0); } elsif ($position > 0) { if ($modulus != 1) { $self->warn("Attention! Label $label is not in frame ". "(1st position of triplet) with protein",1) if $self->verbose > 0; # ignorable if ($modulus == 2) { return ($position / 3 + 1); } else { # i.e. modulus == 0 return ($position / 3); } } return ($position / 3 + 1); } else { # pos < 0 if ($modulus != 0) { $self->warn("Attention! Label $label is not in frame ". "(1st position of triplet) with protein",1) if $self->verbose > 0; # ignorable return ($position / 3 - 1); # ok for both other positions } return ($position / 3); } $self->throw( "WEIRD: execution shouldn't have reached here"); return (0); # this should never happen, but just in case } # note: it inherits subseq and labelsubseq from Transcript! sub start { my $self=shift; return ($self->{'transcript'}->start); } sub end { my $self=shift; return ($self->{'transcript'}->end); } =head2 aa_ranges Title : aa_ranges Usage : @proteinfeatures = $translation->aa_ranges() Function: to retrieve all the LiveSeq AARange objects attached to a Translation, usually created out of a SwissProt database entry crossreferenced from an EMBL CDS feature. Returns : an array Args : none =cut # returns an array of obj_ref of AARange objects attached to the Translation sub aa_ranges { my $self=shift; return ($self->{'aa_ranges'}); } sub translation_table { my $self=shift; $self->get_Transcript->translation_table(@_); } # returns all aminoacids "affected" i.e. all aminoacids coded by any codon # "touched" by the range selected between the labels, even if only partially. # it's not optimized for performance but it's useful sub labelsubseq { my ($self,$start,$length,$end)=@_; my ($pos1,$pos2); my $transcript=$self->get_Transcript; if ($start) { unless ($transcript->valid($start)) { $self->warn("Start label not valid"); return (-1); } $pos1=$self->position($start); } if ($end) { if ($end == $start) { $length=1; } else { unless ($transcript->valid($end)) { $self->warn("End label not valid"); return (-1); } unless ($transcript->follows($start,$end) == 1) { $self->warn("End label does not follow Start label!"); return (-1); } $pos2=$self->position($end); $length=$pos2-$pos1+1; } } my $sequence=$self->seq; return (substr($sequence,$pos1-1,$length)); } # return the offset in aminoacids from LiveSeq protein sequence and SwissProt # sequence (usually as a result of an INIT_MET or a gap) sub offset { my $self=shift; return ($self->{'offset'}); } 1; BioPerl-1.007002/Bio/LiveSeq/IO000755000766000024 013155576320 15746 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/LiveSeq/IO/BioPerl.pm000444000766000024 3335113155576320 20022 0ustar00cjfieldsstaff000000000000# # bioperl module for Bio::LiveSeq::IO::BioPerl # # Please direct questions and support issues to # # Cared for by Joseph Insana # # Copyright Joseph Insana # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::LiveSeq::IO::BioPerl - Loader for LiveSeq from EMBL entries with BioPerl =head1 SYNOPSIS my $db="EMBL"; my $file="../data/M20132"; my $id="HSANDREC"; my $loader=Bio::LiveSeq::IO::BioPerl->load(-db=>"$db", -file=>"$file"); # or my $loader=Bio::LiveSeq::IO::BioPerl->load(-db=>"$db", -id=>"$id"); my @translationobjects=$loader->entry2liveseq(); my $genename="AR"; my $gene=$loader->gene2liveseq(-gene_name => "$genename", -getswissprotinfo => 0); #NOTE1: The only -db now supported is EMBL. Hence it defaults to EMBL. #NOTE2: -file requires a filename (and path if necessary) containing an # EMBL entry # -id will use Bio::DB::EMBL.pm to fetch the sequence from the web, # (bioperl wraparound to [w]getz from SRS) #NOTE3: To retrieve the swissprot (if possible) attached to the embl entry # (to get protein domains at dna level), only Bio::DB::EMBL.pm # is supported under BioPerl. Refer to Bio::LiveSeq::IO::SRS # otherwise. #NOTE4: NOTE3 is not implemented yet for bioperl, working on it =head1 DESCRIPTION This package uses BioPerl (SeqIO) to fetch a sequence database entry, analyse it and create LiveSeq objects out of it. A filename (or an ID that will fetch entry through the web) has to be passed to this package which will return references to all translation objects created from the EMBL entry. References to Transcription, DNA and Exon objects can all be retrieved departing from these. Alternatively, a specific "gene" name can be specified, together with the embl-acc ID. This will create a LiveSeq::Gene object with all relevant gene features attached/created. ATTENTION: if web fetching is requested, the package HTTP::Request needs to be installed. =head1 AUTHOR - Joseph A.L. Insana Email: Insana@ebi.ac.uk, jinsana@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::LiveSeq::IO::BioPerl; # TODO->TOCHECK # each_secondary_access not working # why array from each_tag_value($qual) ? When will there be more than one # element in such array? # what is the annotation object? ($seqobj->annotation) # unsatisfied by both BioPerl binomial and SRS "org" to retrieve Organism info use strict; use Carp qw(cluck croak carp); use vars qw($DBEMBLLOADED); use Bio::SeqIO; # for -file entry loading # Note, the following requires HTTP::Request. If the modules are not installed # uncomment the following and use only -filename and don't request swissprotinfo eval { require Bio::DB::EMBL; # for -id entry loading $DBEMBLLOADED = 1; }; use base qw(Bio::LiveSeq::IO::Loader); # This package can in the future host other databases loading subroutines. # e.g. ensembl2hash =head2 load Title : load Usage : my $filename="../data/M20132"; $loader=Bio::LiveSeq::IO::BioPerl->load(-db=>"EMBL", -file=>"$filename"); or $loader=Bio::LiveSeq::IO::BioPerl->load(-db=>"EMBL", -id=>"HSANDREC"); Function: loads an entry with BioPerl from a database into a hash Returns : reference to a new object of class IO::BioPerl holding an entry Errorcode 0 Args : an filename containing an EMBL entry OR an ID or ACCESSION code =cut sub load { my ($thing, %args) = @_; my $class = ref($thing) || $thing; my ($obj,%loader); my ($db,$filename,$id)=($args{-db},$args{-file},$args{-id}); if (defined($db)) { unless ($db eq "EMBL") { carp "Note: only EMBL now supported!"; return(0); } } else { $db="EMBL"; } if (defined($id) && defined($filename)) { carp "You can either specify a -id or a -filename!"; return(0); } unless (defined($id) || defined($filename)) { carp "You must specify either a -id or a -filename!"; return(0); } my $hashref; if ($db eq "EMBL") { my $test_transl=0; # change to 0 to avoid comparison of translation # these can be changed for future needs my @embl_valid_feature_names=qw(CDS CDS_span exon prim_transcript intron repeat_unit repeat_region mRNA); my @embl_valid_qual_names=qw(gene codon_start db_xref product note number rpt_family transl_table); # dunno yet how to implement test_transl again.... # probably on a one-on-one basis with each translation? if ($test_transl) { push (@embl_valid_qual_names,"translation"); # needed for test_transl } my $seqobj; # bioperl sequence object, to be passed to embl2hash if (defined($filename)) { my $stream = Bio::SeqIO->new('-file' => $filename, '-format' => 'EMBL'); $seqobj = $stream->next_seq(); } else { # i.e. if -id if( $DBEMBLLOADED ) { my $embl = Bio::DB::EMBL->new(); $seqobj = $embl->get_Seq_by_id($id); # EMBL ID or ACC } else { my $root = Bio::Root::Root->new(); $root->warn("Must have HTTP::Request::Common installed, cannot run load without the -filename option specified, see docs for Bio::LiveSeq::IO::BioPerl"); return; } } $hashref=&embl2hash($seqobj,\@embl_valid_feature_names,\@embl_valid_qual_names); } unless ($hashref) { return (0); } %loader = (db => $db, filename => $filename, id => $id, hash => $hashref); $obj = \%loader; $obj = bless $obj, $class; return $obj; } =head2 embl2hash Title : embl2hash Function: retrieves with BioPerl an EMBL entry, parses it and creates a hash that contains all the information. Returns : a reference to a hash Errorcode: 0 Args : a BioPerl Sequence Object (from file or web fetching) two array references to skip features and qualifiers (for performance) Example: @valid_features=qw(CDS exon prim_transcript mRNA); @valid_qualifiers=qw(gene codon_start db_xref product rpt_family); $hashref=&embl2hash($seqobj,\@valid_features,\@valid_qualifiers); =cut # arguments: Bioperl $seqobj # to skip features and qualifiers (for performance), two array # references must be passed (this can change into string arguments to # be passed....) # returns: a reference to a hash containing the important features requested sub embl2hash { my $seqobj=$_[0]; my %valid_features; my %valid_names; if ($_[1]) { %valid_features = map {$_, 1} @{$_[1]}; # to skip features } if ($_[2]) { %valid_names = map {$_, 1} @{$_[2]}; # to skip qualifiers } my $annobj = $seqobj->annotation(); # what's this? my $entry_Sequence = lc($seqobj->seq()); # SRS returns lowercase my $entry_ID = $seqobj->display_id; my $entry_AccNumber = $seqobj->accession; # or maybe accession_number ? my $secondary_acc; # to fetch the other acc numbers foreach $secondary_acc ($seqobj->get_secondary_accessions) { # not working! $entry_AccNumber .= " $secondary_acc"; } my $entry_Molecule = $seqobj->molecule; # this alone returns molec+division my $entry_Division = $seqobj->division; # fixed: now Molecule works in BioPerl, no need for next lines #my @Molecule=split(" ",$entry_Molecule); #my $entry_Division = pop(@Molecule); # only division #$entry_Molecule = join(" ",@Molecule); # only molecule my $entry_Description = $seqobj->desc; my $speciesobj = $seqobj->species; my $entry_Organism = $speciesobj->binomial; my $entry_SeqLength = $seqobj->length; # put into the hash my %entryhash; $entryhash{ID}=$entry_ID; $entryhash{AccNumber}=$entry_AccNumber; $entryhash{Molecule}=$entry_Molecule; $entryhash{Division}=$entry_Division; $entryhash{Description}=$entry_Description; $entryhash{Organism}=$entry_Organism; $entryhash{Sequence}=$entry_Sequence; $entryhash{SeqLength}=$entry_SeqLength; my @topfeatures=$seqobj->top_SeqFeatures(); # create features array my $featuresnumber= scalar(@topfeatures); $entryhash{FeaturesNumber}=$featuresnumber; my $feature_name; my @feature_qual_names; my @feature_qual_value; my ($feature_qual_name,$feature_qual_number); my @features; my ($feat,$qual,$subfeat); my @subfeat; my $i=0; foreach $feat (@topfeatures) { my %feature; $feature_name = $feat->primary_tag; unless ($valid_features{$feature_name}) { #print "skipping $feature_name\n"; next; } # works ok with 0.6.2 # if ($feature_name eq "CDS_span") { # case of CDS with various exons 0.6.2 # $feature_name="CDS"; # 0.6.2 my $featlocation=$feat->location; # 0.7 if (($feature_name eq "CDS")&&($featlocation->isa('Bio::Location::SplitLocationI'))) { # case of CDS with various exons BioPerl 0.7 # @subfeat=$feat->sub_SeqFeature; # 0.6.2 @subfeat=$featlocation->sub_Location(); # 0.7 my @transcript; foreach $subfeat (@subfeat) { my @range; if ($subfeat->strand == -1) { @range=($subfeat->end,$subfeat->start,$subfeat->strand); } else { @range=($subfeat->start,$subfeat->end,$subfeat->strand); } push (@transcript,\@range); } $feature{range}=\@transcript; } else { my @range; ($feat->strand == -1) ? (@range = ($feat->end, $feat->start, $feat->strand) ) : (@range = ( $feat->start,$feat->end,$feat->strand) ); # works ok with 0.6.2 if ($feature_name eq "CDS") { # case of single exon CDS (CDS name but not split location) my @transcript=(\@range); $feature{range}=\@transcript; } else { # all other range features $feature{range}=\@range; } } $feature{location}="deprecated"; $feature{position}=$i; $feature{name}=$feature_name; @feature_qual_names= $feat->all_tags(); $feature_qual_number= scalar(@feature_qual_names); $feature{qual_number}=$feature_qual_number; my %feature_qualifiers; for $qual (@feature_qual_names) { $feature_qual_name=$qual; unless ($valid_names{$feature_qual_name}) { next; } @feature_qual_value=$feat->each_tag_value($qual); #print "$qual => @feature_qual_value \n"; $feature_qualifiers{$feature_qual_name}=$feature_qual_value[0]; # ? # maybe the whole array should be entered, not just the 1st element? # what could be the other elements? TOCHECK! } $feature{qualifiers}=\%feature_qualifiers; push (@features,\%feature); # array of features $i++; } $entryhash{Features}=\@features; # put this also into the hash my @cds; # array just of CDSs for $i (0..$#features) { if ($features[$i]->{'name'} eq "CDS") { push(@cds,$features[$i]); } } $entryhash{CDS}=\@cds; # put this also into the hash return (\%entryhash); } =head2 novelaasequence2gene Title : novelaasequence2gene Usage : $gene=Bio::LiveSeq::IO::BioPerl->novelaasequence2gene(-aasequence => "MGLAAPTRS*"); : $gene=Bio::LiveSeq::IO::BioPerl->novelaasequence2gene(-aasequence => "MGLAAPTRS*", -cusg_data => "58 44 7 29 3 3 480 267 105 143 122 39 144 162 14 59 53 25 233 292 19 113 88 246 28 68 161 231 27 102 128 151 67 60 138 131 48 61 153 19 233 73 150 31 129 38 147 71 138 43 181 81 44 15 255 118 312 392 236 82 20 10 14 141"); : $gene=Bio::LiveSeq::IO::BioPerl->novelaasequence2gene(-aasequence => "MGLAAPTRS*", -cusg_data => "58 44 7 29 3 3 480 267 105 143 122 39 144 162 14 59 53 25 233 292 19 113 88 246 28 68 161 231 27 102 128 151 67 60 138 131 48 61 153 19 233 73 150 31 129 38 147 71 138 43 181 81 44 15 255 118 312 392 236 82 20 10 14 141", -translation_table => "2", -gene_name => "tyr-kinase"); Function: creates LiveSeq objects from a novel amino acid sequence, using codon usage information (loaded from a file) to choose codons according to relative frequencies. If a codon_usage information is not specified, the default is to use Homo sapiens data (taxonomy ID 9606). If a translation_table ID is not specified, it will default to 1 (standard code). Returns : reference to a Gene object containing references to LiveSeq objects Errorcode 0 Args : string containing an amino acid sequence string (optional) with codon usage data (64 integer numbers) string (optional) specifying a gene_name integer (optional) specifying a translation_table ID =cut sub novelaasequence2gene { my ($self, %args) = @_; my ($gene_name,$cusg_data,$aasequence,$ttabid)=($args{-gene_name},$args{-cusg_data},$args{-aasequence},$args{-translation_table}); my @species_codon_usage; unless ($aasequence) { carp "aasequence not given"; return (0); } unless ($gene_name) { $gene_name="Novel Unknown"; } unless ($ttabid) { $ttabid=1; } unless ($cusg_data) { @species_codon_usage= qw(68664 118404 126679 51100 125600 123646 75667 210903 435317 139009 79303 135218 128429 192616 49456 161556 211962 131222 162837 213626 69346 140780 182506 219428 76684 189374 173010 310626 82647 202329 180955 250410 180001 118798 76398 160764 317359 119013 262630 359627 218376 186915 130857 377006 162826 113684 317703 441298 287040 245435 174805 133427 134523 108740 225633 185619 78463 240138 174021 244236 142435 8187 5913 14381); # updated 21Jul2000 } else { @species_codon_usage=split(/ /,$cusg_data); } my $gene=Bio::LiveSeq::IO::Loader::_common_novelaasequence2gene(\@species_codon_usage,$ttabid,$aasequence,$gene_name); return ($gene); } 1; BioPerl-1.007002/Bio/LiveSeq/IO/Loader.pm000444000766000024 10357013155576320 17715 0ustar00cjfieldsstaff000000000000# # bioperl module for Bio::LiveSeq::IO::Loader # # Please direct questions and support issues to # # Cared for by Joseph Insana # # Copyright Joseph Insana # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::LiveSeq::IO::Loader - Parent Loader for LiveSeq =head1 SYNOPSIS #documentation needed =head1 DESCRIPTION This package holds common methods used by BioPerl and file loaders. It contains methods to create LiveSeq objects out of entire entries or from a localized sequence region surrounding a particular gene. =head1 AUTHOR - Joseph A.L. Insana Email: Insana@ebi.ac.uk, jinsana@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::LiveSeq::IO::Loader; use strict; use Carp qw(cluck croak carp); use Bio::LiveSeq::DNA; use Bio::LiveSeq::Exon; use Bio::LiveSeq::Transcript ; use Bio::LiveSeq::Translation; use Bio::LiveSeq::Gene; use Bio::LiveSeq::Intron; use Bio::LiveSeq::Prim_Transcript; use Bio::LiveSeq::Repeat_Region; use Bio::LiveSeq::Repeat_Unit; use Bio::LiveSeq::AARange; use Bio::Tools::CodonTable; =head2 entry2liveseq Title : entry2liveseq Usage : @translationobjects=$loader->entry2liveseq(); : @translationobjects=$loader->entry2liveseq(-getswissprotinfo => 0); Function: creates LiveSeq objects from an entry previously loaded Returns : array of references to objects of class Translation Errorcode 0 Args : optional boolean flag to avoid the retrieval of SwissProt information for all Transcripts containing SwissProt x-reference default is 1 (to retrieve those information and create AARange LiveSeq objects) Note : this method can get really slow for big entries. The lightweight gene2liveseq method is recommended =cut sub entry2liveseq { my ($self, %args) = @_; my ($getswissprotinfo)=($args{-getswissprotinfo}); if (defined($getswissprotinfo)) { if (($getswissprotinfo ne 0)&&($getswissprotinfo ne 1)) { carp "-getswissprotinfo argument can take only boolean (1 or 0) values. Setting it to 0, i.e. not trying to retrieve SwissProt information...."; $getswissprotinfo=0; } } else { $getswissprotinfo=1; } my $hashref=$self->{'hash'}; unless ($hashref) { return (0); } my @translationobjects=$self->hash2liveseq($hashref,$getswissprotinfo); my $test_transl=0; if ($test_transl) { $self->test_transl($hashref,\@translationobjects);} return @translationobjects; } =head2 novelaasequence2gene Title : novelaasequence2gene Usage : $gene=$loader->novelaasequence2gene(-aasequence => "MGLAAPTRS*"); : $gene=$loader->novelaasequence2gene(-aasequence => "MGLAAPTRS*"); -taxon => 9606, -gene_name => "tyr-kinase"); Function: creates LiveSeq objects from a novel amino acid sequence, using codon usage database to choose codons according to relative frequencies. If a taxon ID is not specified, the default is to use the human one (taxonomy ID 9606). Returns : reference to a Gene object containing references to LiveSeq objects Errorcode 0 Args : string containing an amino acid sequence integer (optional) with a taxonomy ID string specifying a gene name =cut =head2 gene2liveseq Title : gene2liveseq Usage : $gene=$loader->gene2liveseq(-gene_name => "gene name"); : $gene=$loader->gene2liveseq(-gene_name => "gene name", -flanking => 64); : $gene=$loader->gene2liveseq(-gene_name => "gene name", -getswissprotinfo => 0); : $gene=$loader->gene2liveseq(-position => 4); Function: creates LiveSeq objects from an entry previously loaded It is a "light weight" creation because it creates a LiveSequence just for the interesting region in an entry (instead than for the total entry, like in entry2liveseq) and for the flanking regions up to 500 nucleotides (default) or up to the specified amount of nucleotides (given as argument) around the Gene. Returns : reference to a Gene object containing possibly alternative Transcripts. Errorcode 0 Args : string containing the gene name as in the EMBL feature qualifier integer (optional) "flanking": amount of flanking bases to be kept boolean (optional) "getswissprotinfo": if set to "0" it will avoid trying to fetch information from a crossreference to a SwissProt entry, avoiding the process of creation of AARange objects It is "1" (on) by default Alternative to a gene_name, a position can be given: an integer (1-) containing the position of the desired CDS in the loaded entry =cut sub gene2liveseq { my ($self, %args) = @_; my ($gene_name,$flanking,$getswissprotinfo,$cds_position)=($args{-gene_name},$args{-flanking},$args{-getswissprotinfo},$args{-position}); my $input; unless (($gene_name)||($cds_position)) { carp "Gene_Name or Position not specified for gene2liveseq loading function"; return (0); } if (($gene_name)&&($cds_position)) { carp "Gene_Name and Position cannot be given together"; return (0); } elsif ($gene_name) { $input=$gene_name; } else { $input="cds-position:".$cds_position; } if (defined($getswissprotinfo)) { if (($getswissprotinfo ne 0)&&($getswissprotinfo ne 1)) { carp "-getswissprotinfo argument can take only boolean (1 or 0) values. Setting it to 0, i.e. not trying to retrieve SwissProt information...."; $getswissprotinfo=0; } } else { $getswissprotinfo=1; } if (defined($flanking)) { unless ($flanking >= 0) { carp "No sense in specifying a number < 0 for flanking regions to be created for gene2liveseq loading function"; return (0); } } else { $flanking=500; # the default flanking length } my $hashref=$self->{'hash'}; unless ($hashref) { return (0); } my $gene=$self->hash2gene($hashref,$input,$flanking,$getswissprotinfo); unless ($gene) { # if $gene == 0 it means problems in hash2gene carp "gene2liveseq produced error"; return (0); } return $gene; } # TODO: update so that it will work even if CDS is not only accepted FEATURE!! # this method is for now deprecated and not supported sub test_transl { my ($self,$entry)=@_; my @features=@{$entry->{'Features'}}; my @translationobjects=@{$_[1]}; my ($i,$translation); my ($obj_transl,$hash_transl); my @cds=@{$entry->{'CDS'}}; foreach $translation (@translationobjects) { $obj_transl=$translation->seq; $hash_transl=$cds[$i]->{'qualifiers'}->{'translation'}; #before seq was changed in Translation 1.4# chop $obj_transl; # to remove trailing "*" unless ($obj_transl eq $hash_transl) { cluck "Serious error: Translation from the Entry does not match Translation from object's seq for CDS at position $i"; carp "\nEntry's transl: ",$hash_transl,"\n"; carp "\nObject's transl: ",$obj_transl,"\n"; exit; } $i++; } } # argument: hashref containing the EMBL entry datas, # getswissprotinfo boolean flag # creates the liveseq objects # returns: an array of Translation object references sub hash2liveseq { my ($self,$entry,$getswissprotinfo)=@_; my $i; my @transcripts; my $dna=Bio::LiveSeq::DNA->new(-seq => $entry->{'Sequence'} ); $dna->alphabet(lc($entry->{'Molecule'})); $dna->display_id($entry->{'ID'}); $dna->accession_number($entry->{'AccNumber'}); $dna->desc($entry->{'Description'}); my @cds=@{$entry->{'CDS'}}; my ($swissacc,$swisshash); my @swisshashes; for $i (0..$#cds) { #my @transcript=@{$cds[$i]->{'range'}}; #$transcript=\@transcript; #push (@transcripts,$transcript); push (@transcripts,$cds[$i]->{'range'}); if ($getswissprotinfo) { $swissacc=$cds[$i]->{'qualifiers'}->{'db_xref'}; $swisshash=$self->get_swisshash($swissacc); #$self->printswissprot($swisshash); # DEBUG push (@swisshashes,$swisshash); } } my @translations=($self->transexonscreation($dna,\@transcripts)); my $translation; my $j=0; foreach $translation (@translations) { if ($swisshashes[$j]) { # if not 0 $self->swisshash2liveseq($swisshashes[$j],$translation); } $j++; } return (@translations); } # only features pertaining to a specified gene are created # only the sequence of the gene and appropriate context flanking regions # are created as chain # arguments: hashref, gene_name (OR: cds_position), length_of_flanking_sequences, getswissprotinfo boolean flag # returns: reference to Gene object # # Note: if entry contains just one CDS, all the features get added # this is useful because often the features in these entries do not # carry the /gene qualifier # # errorcode: 0 sub hash2gene { my ($self,$entry,$input,$flanking,$getswissprotinfo)=@_; my $entryfeature; my $genefeatureshash; my @cds=@{$entry->{'CDS'}}; # checking if a position has been given instead than a gene_name if (index($input,"cds-position:") == 0 ) { my $cds_position=substr($input,13); # extracting the cds position if (($cds_position >= 1)&&($cds_position <= scalar(@cds))) { $genefeatureshash=$self->_findgenefeatures($entry,undef,$cds_position,$getswissprotinfo); } } else { $genefeatureshash=$self->_findgenefeatures($entry,$input,undef,$getswissprotinfo); } unless (($genefeatureshash)&&(scalar(@{$genefeatureshash->{'genefeatures'}}))) { # array empty, no gene features found my @genes=$self->genes($entry); my $cds_number=scalar(@cds); warn "Warning! Not even one genefeature found for /$input/.... The genes present in this entry are:\n\t@genes\n The number of CDS in this entry is:\n\t$cds_number\n"; return(0); } # get max and min, check flankings my ($min,$max)=$self->rangeofarray(@{$genefeatureshash->{'labels'}}); # gene "boundaries" my $seqlength=$entry->{'SeqLength'}; my ($mindna,$maxdna); # some flanking region next to the gene "boundaries" if ($min-$flanking < 1) { $mindna=1; } else { $mindna=$min-$flanking; } if ($max+$flanking > $seqlength) { $maxdna=$seqlength; } else { $maxdna=$max+$flanking; } my $subseq=substr($entry->{'Sequence'},$mindna-1,$maxdna-$mindna+1); # create LiveSeq objects # create DNA my $dna=Bio::LiveSeq::DNA->new(-seq => $subseq, -offset => $mindna); $dna->alphabet(lc($entry->{'Molecule'})); $dna->source($entry->{'Organism'}); $dna->display_id($entry->{'ID'}); $dna->accession_number($entry->{'AccNumber'}); $dna->desc($entry->{'Description'}); my @transcripts=@{$genefeatureshash->{'transcripts'}}; # create Translations, Transcripts, Exons out of the CDS unless (@transcripts) { cluck "no CDS feature found for /$input/...."; return(0); } my @translationobjs=$self->transexonscreation($dna,\@transcripts); my @transcriptobjs; # get the Transcript obj_refs my $translation; my $j=0; my @ttables=@{$genefeatureshash->{'ttables'}}; my @swisshashes=@{$genefeatureshash->{'swisshashes'}}; foreach $translation (@translationobjs) { push(@transcriptobjs,$translation->get_Transcript); if ($ttables[$j]) { # if not undef $translation->get_Transcript->translation_table($ttables[$j]); #} else { # DEBUG # print "\n\t\tno translation table information....\n"; } if ($swisshashes[$j]) { # if not 0 $self->swisshash2liveseq($swisshashes[$j],$translation); } $j++; } my %gene; # this is the hash to store created object references $gene{DNA}=$dna; $gene{Transcripts}=\@transcriptobjs; $gene{Translations}=\@translationobjs; my @exonobjs; my @intronobjs; my @repeatunitobjs; my @repeatregionobjs; my @primtranscriptobjs; my ($object,$range,$start,$end,$strand); my @exons=@{$genefeatureshash->{'exons'}}; my @exondescs=@{$genefeatureshash->{'exondescs'}}; if (@exons) { my $exoncount = 0; foreach $range (@exons) { ($start,$end,$strand)=@{$range}; $object = Bio::LiveSeq::Exon->new(-seq=>$dna,-start=>$start,-end=>$end,-strand=>$strand); if ($object != -1) { $object->desc($exondescs[$exoncount]) if defined $exondescs[$exoncount]; $exoncount++; push (@exonobjs,$object); } else { $exoncount++; } } $gene{Exons}=\@exonobjs; } my @introns=@{$genefeatureshash->{'introns'}}; my @introndescs=@{$genefeatureshash->{'introndescs'}}; if (@introns) { my $introncount = 0; foreach $range (@introns) { ($start,$end,$strand)=@{$range}; $object=Bio::LiveSeq::Intron->new(-seq=>$dna,-start=>$start,-end=>$end,-strand=>$strand); if ($object != -1) { $object->desc($introndescs[$introncount]); $introncount++; push (@intronobjs,$object); } else { $introncount++; } } $gene{Introns}=\@intronobjs; } my @prim_transcripts=@{$genefeatureshash->{'prim_transcripts'}}; if (@prim_transcripts) { foreach $range (@prim_transcripts) { ($start,$end,$strand)=@{$range}; $object=Bio::LiveSeq::Prim_Transcript->new(-seq=>$dna,-start=>$start,-end=>$end,-strand=>$strand); if ($object != -1) { push (@primtranscriptobjs,$object); } } $gene{Prim_Transcripts}=\@primtranscriptobjs; } my @repeat_regions=@{$genefeatureshash->{'repeat_regions'}}; my @repeat_regions_family=@{$genefeatureshash->{'repeat_regions_family'}}; if (@repeat_regions) { my $k=0; foreach $range (@repeat_regions) { ($start,$end,$strand)=@{$range}; $object=Bio::LiveSeq::Repeat_Region->new(-seq=>$dna,-start=>$start,-end=>$end,-strand=>$strand); if ($object != -1) { $object->desc($repeat_regions_family[$k]); $k++; push (@repeatregionobjs,$object); } else { $k++; } } $gene{Repeat_Regions}=\@repeatregionobjs; } my @repeat_units=@{$genefeatureshash->{'repeat_units'}}; my @repeat_units_family=@{$genefeatureshash->{'repeat_units_family'}}; if (@repeat_units) { my $k=0; foreach $range (@repeat_units) { ($start,$end,$strand)=@{$range}; $object=Bio::LiveSeq::Repeat_Unit->new(-seq=>$dna,-start=>$start,-end=>$end,-strand=>$strand); if ($object != -1) { $object->desc($repeat_units_family[$k]); $k++; push (@repeatunitobjs,$object); } else { $k++; } } $gene{Repeat_Units}=\@repeatunitobjs; } # create the Gene my $gene_name=$genefeatureshash->{'gene_name'}; # either a name or a cdspos return (Bio::LiveSeq::Gene->new(-name=>$gene_name,-features=>\%gene, -upbound=>$min,-downbound=>$max)); } # maybe this function will be moved to general utility package # argument: array of numbers # returns: (min,max) numbers in the array sub rangeofarray { my $self=shift; my @array=@_; #print "\n-=-=-=-=-=-=-=-=-=-=array: @array\n"; my ($max,$min,$element); $min=$max=shift(@array); foreach $element (@array) { $element = 0 unless defined $element; if ($element < $min) { $min=$element; } if ($element > $max) { $max=$element; } } #print "\n-=-=-=-=-=-=-=-=-=-=min: $min\tmax: $max\n"; return ($min,$max); } # argument: reference to DNA object, reference to array of transcripts # returns: an array of Translation object references sub transexonscreation { my $self=shift; my $dna=$_[0]; my @transcripts=@{$_[1]}; my (@transexons,$start,$end,$strand,$exonref,$exonobj,$transcript,$transcriptobj); my $translationobj; my @translationobjects; foreach $transcript (@transcripts) { foreach $exonref (@{$transcript}) { ($start,$end,$strand)=@{$exonref}; #print "Creating Exon: start $start end $end strand $strand\n"; $exonobj=Bio::LiveSeq::Exon->new(-seq=>$dna,-start=>$start,-end=>$end,-strand=>$strand); #push (@exonobjects,$exonobj); push (@transexons,$exonobj); } $transcriptobj=Bio::LiveSeq::Transcript->new(-exons => \@transexons ); if ($transcriptobj != -1) { $translationobj=Bio::LiveSeq::Translation->new(-transcript=>$transcriptobj); @transexons=(); # cleans it #push (@transcriptobjects,$transcriptobj); push (@translationobjects,$translationobj); } } return (@translationobjects); } #sub printgene { # deleted. Some functionality placed in Gene->printfeaturesnum =head2 printswissprot Title : printswissprot Usage : $loader->printswissprot($hashref); Function: prints out all information loaded from a database entry into the loader. Mainly used for testing purposes. Args : a hashref containing the SWISSPROT entry datas Note : the hashref can be obtained with a call to the method $loader->get_swisshash() (BioPerl via Bio::DB::EMBL.pm) that takes as argument a string like "SWISS-PROT:P10275" =cut # argument: hashref containing the SWISSPROT entry datas # prints out that hash, showing the information loaded sub printswissprot { my ($self,$entry)=@_; unless ($entry) { return; } printf "ID: %s\n", $entry->{'ID'}; printf "ACC: %s\n", $entry->{'AccNumber'}; printf "GENE: %s\n", $entry->{'Gene'}; printf "DES: %s\n", $entry->{'Description'}; printf "ORG: %s\n", $entry->{'Organism'}; printf "SEQLN: %s\n", $entry->{'SeqLength'}; printf "SEQ: %s\n", substr($entry->{'Sequence'},0,64); if ($entry->{'Features'}) { my @features=@{$entry->{'Features'}}; my $i; for $i (0..$#features) { print "|",$features[$i]->{'name'},"|"; print " at ",$features[$i]->{'location'},": "; print "",$features[$i]->{'desc'},"\n"; } } } =head2 printembl Title : printembl Usage : $loader->printembl(); Function: prints out all information loaded from a database entry into the loader. Mainly used for testing purposes. Args : none =cut # argument: hashref containing the EMBL entry datas # prints out that hash, showing the information loaded sub printembl { my ($self,$entry)=@_; unless ($entry) { $entry=$self->{'hash'}; } my ($i,$featurename); printf "ID: %s\n", $entry->{'ID'}; printf "ACC: %s\n", $entry->{'AccNumber'}; printf "MOL: %s\n", $entry->{'Molecule'}; printf "DIV: %s\n", $entry->{'Division'}; printf "DES: %s\n", $entry->{'Description'}; printf "ORG: %s\n", $entry->{'Organism'}; printf "SEQLN: %s\n", $entry->{'SeqLength'}; printf "SEQ: %s\n", substr($entry->{'Sequence'},0,64); my @features=@{$entry->{'Features'}}; my @cds=@{$entry->{'CDS'}}; print "\nFEATURES\nNumber of CDS: ",scalar(@cds)," (out of ",$entry->{'FeaturesNumber'}, " total features)\n"; my ($exonref,$transcript); my ($qualifiernumber,$qualifiers,$key); my ($start,$end,$strand); my $j=0; for $i (0..$#features) { $featurename=$features[$i]->{'name'}; if ($featurename eq "CDS") { print "|CDS| number $j at feature position: $i\n"; #print $features[$i]->{'location'},"\n"; $transcript=$features[$i]->{'range'}; foreach $exonref (@{$transcript}) { ($start,$end,$strand)=@{$exonref}; print "\tExon: start $start end $end strand $strand\n"; } $j++; } else { print "|$featurename| at feature position: $i\n"; print "\trange: "; print join("\t",@{$features[$i]->{'range'}}),"\n"; #print $features[$i]->{'location'},"\n"; } $qualifiernumber=$features[$i]->{'qual_number'}; $qualifiers=$features[$i]->{'qualifiers'}; # hash foreach $key (keys (%{$qualifiers})) { print "\t\t",$key,": "; print $qualifiers->{$key},"\n"; } } } =head2 genes Title : genes Usage : $loader->genes(); Function: Returns an array of gene_names (strings) contained in the loaded entry. Args : none =cut # argument: entryhashref # returns: array of genenames found in the entry sub genes { my ($self,$entry)=@_; unless ($entry) { $entry=$self->{'hash'}; } my @entryfeatures=@{$entry->{'Features'}}; my ($genename,$genenames,$entryfeature); for $entryfeature (@entryfeatures) { $genename=$entryfeature->{'qualifiers'}->{'gene'}; if ($genename) { if (index($genenames,$genename) == -1) { # if name is new $genenames .= $genename . " "; # add the name } } } return (split(/ /,$genenames)); # assumes no space inbetween each genename } # arguments: swisshash, translation objref # adds information to the Translation, creates AARange objects, sets the # aa_range attribute on the Translation, pointing to those objects sub swisshash2liveseq { my ($self,$entry,$translation)=@_; my $translength=$translation->length; $translation->desc($translation->desc . $entry->{'Description'}); $translation->display_id("SWISSPROT:" . $entry->{'ID'}); $translation->accession_number("SWISSPROT:" . $entry->{'AccNumber'}); $translation->name($entry->{'Gene'}); $translation->source($entry->{'Organism'}); my @aarangeobjects; my ($start,$end,$aarangeobj,$feature); my @features; my @newfeatures; if ($entry->{'Features'}) { @features=@{$entry->{'Features'}}; } my $cleavedmet=0; # check for cleaved Met foreach $feature (@features) { if (($feature->{'name'} eq "INIT_MET")&&($feature->{'location'} eq "0 0")) { $cleavedmet=1; $translation->{'offset'}="1"; # from swissprot to liveseq protein sequence } else { push(@newfeatures,$feature); } } my $swissseq=$entry->{'Sequence'}; my $liveseqtransl=$translation->seq; chop $liveseqtransl; # to take away the trailing STOP "*" my $translated=substr($liveseqtransl,$cleavedmet); my ($liveseq_aa,$swiss_aa,$codes_aa)=$self->_get_alignment($translated,$swissseq); # alignment after cleavage of possible initial met if ((index($liveseq_aa,"-") != -1)||(index($swiss_aa,"-") != -1)) { # there are gaps, how to proceed? print "LIVE-SEQ=\'$liveseq_aa\'\nIDENTITY=\'$codes_aa\'\nSWS-PROT=\'$swiss_aa\'\n"; carp "Nucleotides translation and SwissProt translation are different in size, cannot attach the SwissSequence to the EMBL one, cannot add any AminoAcidRange object/Domain information!"; return; } #my $i=0; # debug @features=@newfeatures; foreach $feature (@features) { #print "Processing SwissProtFeature: $i\n"; # debug ($start,$end)=split(/ /,$feature->{'location'}); # Note: cleavedmet is taken in account for updating numbering $aarangeobj=Bio::LiveSeq::AARange->new(-start => $start+$cleavedmet, -end => $end+$cleavedmet, -name => $feature->{'name'}, -description => $feature->{'description'}, -translation => $translation, -translength => $translength); if ($aarangeobj != -1) { push(@aarangeobjects,$aarangeobj); } # $i++; # debug } $translation->{'aa_ranges'}=\@aarangeobjects; } # if there is no SRS support, the default will be to return 0 # i.e. this function is overridden in SRS package sub get_swisshash { return (0); } # Args: $entry hashref, gene_name OR cds_position (undef is used to # choose between the two), getswissprotinfo boolean flag # Returns: an hash holding various arrayref used in the hash2gene method # Function: examines the nucleotide entry, identifying features belonging # to the gene (defined either by its name or by the position of its CDS in # the entry) sub _findgenefeatures { my ($self,$entry,$gene_name,$cds_position,$getswissprotinfo)=@_; my @entryfeatures=@{$entry->{'Features'}}; my @exons; my @introns; my @prim_transcripts; my @transcripts; my @repeat_units; my @repeat_regions; my @repeat_units_family; my @repeat_regions_family; my $rpt_family; my $entryfeature; my @genefeatures; my $desc; my @exondescs; my @introndescs; # for swissprot xreference my ($swissacc,$swisshash); my @swisshashes; # for translation_tables my @ttables; # to create labels my ($name,$exon); my @range; my @cdsexons; my @labels; # maybe here also could be added special case when there is no CDS feature # in the entry (e.g. tRNA entry -> TOCHECK). # let's deal with the special case in which there is just one gene per entry # usually without /gene qualifier my @cds=@{$entry->{'CDS'}}; my $skipgenematch=0; if (scalar(@cds) == 1) { #carp "Note: only one CDS in this entry. Treating all features found in entry as Gene features."; $skipgenematch=1; } my ($cds_begin,$cds_end,$proximity); if ($cds_position) { # if a position has been requested my @cds_exons=@{$cds[$cds_position-1]->{'range'}}; ($cds_begin,$cds_end)=($cds_exons[0]->[0],$cds_exons[-1]->[1]); # begin and end of CDS $gene_name=$cds[$cds_position-1]->{'qualifiers'}->{'gene'}; # DEBUG unless ($skipgenematch) { carp "--DEBUG-- cdsbegin $cds_begin cdsend $cds_end--------"; } $proximity=100; # proximity CONSTANT to decide whether a feature "belongs" to the CDS } for $entryfeature (@entryfeatures) { # get only features for the desired gene if (($skipgenematch)||(($cds_position)&&($self->_checkfeatureproximity($entryfeature->{'range'},$cds_begin,$cds_end,$proximity)))||(!($cds_position)&&($entryfeature->{'qualifiers'}->{'gene'} eq "$gene_name"))) { push(@genefeatures,$entryfeature); my @range=@{$entryfeature->{'range'}}; $name=$entryfeature->{'name'}; my %qualifierhash=%{$entryfeature->{'qualifiers'}}; if ($name eq "CDS") { # that has range containing array of exons # swissprot crossindexing (if without SRS support it will fill array # with zeros and do nothing if ($getswissprotinfo) { $swissacc=$entryfeature->{'qualifiers'}->{'db_xref'}; $swisshash=$self->get_swisshash($swissacc); #$self->printswissprot($swisshash); # DEBUG push (@swisshashes,$swisshash); } push (@ttables,$entryfeature->{'qualifiers'}->{'transl_table'}); # undef if not specified # create labels array for $exon (@range) { push(@labels,$exon->[0],$exon->[1]); # start and end of every exon of the CDS } push (@transcripts,$entryfeature->{'range'}); } else { # "simplifying" the joinedlocation features. I.e. changing them from # multijoined ones to simple plain start-end features, taking only # the start of the first "exon" and the end of the last "exon" as # start and end of the entire feature if ($entryfeature->{'locationtype'} && $entryfeature->{'locationtype'} eq "joined") { # joined location @range=($range[0]->[0],$range[-1]->[1]); } push(@labels,$range[0],$range[1]); # start and end of every feature if ($name eq "exon") { $desc=$entryfeature->{'qualifiers'}->{'number'}; if ($entryfeature->{'qualifiers'}->{'note'}) { if ($desc) { $desc .= "|" . $entryfeature->{'qualifiers'}->{'note'}; } else { $desc = $entryfeature->{'qualifiers'}->{'note'}; } } push (@exondescs,$desc || "unknown"); push(@exons,\@range); } if ($name eq "intron") { $desc=$entryfeature->{'qualifiers'}->{'number'}; if ($desc) { $desc .= "|" . $entryfeature->{'qualifiers'}->{'note'}; } else { $desc = $entryfeature->{'qualifiers'}->{'note'}; } push (@introndescs,$desc || "unknown"); push(@introns,\@range); } if (($name eq "prim_transcript")||($name eq "mRNA")) { push(@prim_transcripts,\@range); } if ($name eq "repeat_unit") { push(@repeat_units,\@range); $rpt_family=$entryfeature->{'qualifiers'}->{'rpt_family'}; push (@repeat_units_family,$rpt_family || "unknown"); } if ($name eq "repeat_region") { push(@repeat_regions,\@range); $rpt_family=$entryfeature->{'qualifiers'}->{'rpt_family'}; push (@repeat_regions_family,$rpt_family || "unknown"); } } } } unless ($gene_name) { $gene_name="cds-position:".$cds_position; } my %genefeatureshash; $genefeatureshash{gene_name}=$gene_name; $genefeatureshash{genefeatures}=\@genefeatures; $genefeatureshash{labels}=\@labels; $genefeatureshash{ttables}=\@ttables; $genefeatureshash{swisshashes}=\@swisshashes; $genefeatureshash{transcripts}=\@transcripts; $genefeatureshash{exons}=\@exons; $genefeatureshash{exondescs}=\@exondescs; $genefeatureshash{introns}=\@introns; $genefeatureshash{introndescs}=\@introndescs; $genefeatureshash{prim_transcripts}=\@prim_transcripts; $genefeatureshash{repeat_units}=\@repeat_units; $genefeatureshash{repeat_regions}=\@repeat_regions; $genefeatureshash{repeat_units_family}=\@repeat_units_family; $genefeatureshash{repeat_regions_family}=\@repeat_regions_family; return (\%genefeatureshash); } # used by _findgenefeatures, when a CDS at a certain position is requested, # to retrieve only features quite close to the wanted CDS. # Args: range hashref, begin and end positions of the CDS, $proximity # $proximity holds the maximum distance between the extremes of the CDS # and of the feature under exam. # Returns: boolean sub _checkfeatureproximity { my ($self,$range,$cds_begin,$cds_end,$proximity)=@_; my @range=@{$range}; my ($begin,$end,$strand); if (ref($range[0]) eq "ARRAY") { # like in CDS, whose range equivals to exons ($begin,$end,$strand)=($range[0]->[0],$range[-1]->[1],$range[0]->[2]); } else { ($begin,$end,$strand)=@range; } if ($cds_begin > $cds_end) { # i.e. reverse strand CDS ($cds_begin,$cds_end)=($cds_end,$cds_begin); # swap boundaries } if ($strand == -1) { # reverse strand ($begin,$end)=($end,$begin); # swap boundaries } if (($cds_begin-$end)>$proximity) { carp "--DEBUG-- feature rejected: begin $begin end $end -------"; return (0); } if (($begin-$cds_end)>$proximity) { carp "--DEBUG-- feature rejected: begin $begin end $end -------"; return (0); } carp "--DEBUG-- feature accepted: begin $begin end $end -------"; return (1); # otherwise ok, feature considered next to CDS } # function that calls the external program "align" (on the fasta2 package) # to create an alignment between two sequences, returning the aligned # strings and the codes for the identity (:: ::::) sub _get_alignment { my ($self,$seq1,$seq2)=@_; my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null'; my $fastafile1="/tmp/tmpfastafile1"; my $fastafile2="/tmp/tmpfastafile2"; my $grepcut='egrep -v "[[:digit:]]|^ *$|sequences" | cut -c8-'; # grep/cut my $alignprogram="/usr/local/etc/bioinfo/fasta2/align -s /usr/local/etc/bioinfo/fasta2/idnaa.mat $fastafile1 $fastafile2 2>$null | $grepcut"; # ALIGN open my $TMPFASTAFILE1, '>', $fastafile1 or croak "Could not write file '$fastafile1' for aa alignment: $!"; open my $TMPFASTAFILE2, '>', $fastafile2 or croak "Could not write file '$fastafile2' for aa alignment: $!"; print $TMPFASTAFILE1 ">firstseq\n$seq1\n"; print $TMPFASTAFILE2 ">secondseq\n$seq2\n"; close $TMPFASTAFILE1; close $TMPFASTAFILE2; my $alignment=`$alignprogram`; my @alignlines=split(/\n/,$alignment); my ($linecount,$seq1_aligned,$seq2_aligned,$codes); for ($linecount=0; $linecount < @alignlines; $linecount+=3) { $seq1_aligned .= $alignlines[$linecount]; $codes .= $alignlines[$linecount+1]; $seq2_aligned .= $alignlines[$linecount+2]; } return ($seq1_aligned,$seq2_aligned,$codes); } # common part of the function to create a novel liveseq gene structure # from an amino acid sequence, using codon usage frequencies # args: codon_usage_array transltableid aasequence gene_name sub _common_novelaasequence2gene { my ($species_codon_usage,$ttabid,$aasequence,$gene_name)=@_; my @species_codon_usage=@{$species_codon_usage}; my @codon_usage_label= qw (cga cgc cgg cgt aga agg cta ctc ctg ctt tta ttg tca tcc tcg tct agc agt aca acc acg act cca ccc ccg cct gca gcc gcg gct gga ggc ggg ggt gta gtc gtg gtt aaa aag aac aat caa cag cac cat gaa gag gac gat tac tat tgc tgt ttc ttt ata atc att atg tgg taa tag tga); my ($i,$j); my %codon_usage_value; my $aa_codon_total; for ($i=0;$i<64;$i++) { $codon_usage_value{$codon_usage_label[$i]}=$species_codon_usage[$i]; } my $CodonTable = Bio::Tools::CodonTable->new ( -id => $ttabid ); my @aminoacids = split(//,uc($aasequence)); my @alt_codons; my ($relativeusage,$dnasequence,$chosen_codon,$dice,$partial,$thiscodon); for $i (@aminoacids) { @alt_codons = $CodonTable->revtranslate($i); unless (@alt_codons) { carp "No reverse translation possible for aminoacid \'$i\'"; $dnasequence .= "???"; } else { $aa_codon_total=0; for $j (@alt_codons) { $aa_codon_total+=$codon_usage_value{$j}; } # print "aminoacid $i, codonchoice: "; # verbose #$partial=0; #for $j (@alt_codons) { #printf "%s %.2f ",$j,$partial+$codon_usage_value{$j}/$aa_codon_total; #$partial+=($codon_usage_value{$j}/$aa_codon_total); #} #print "\n"; $dice=rand(1); #print "roulette: $dice\n"; # verbose $partial=0; $chosen_codon=""; CODONCHOICE: for $j (0..@alt_codons) { # last one not accounted $thiscodon=$alt_codons[$j]; $relativeusage=($codon_usage_value{$thiscodon}/$aa_codon_total); if ($dice < $relativeusage+$partial) { $chosen_codon=$thiscodon; last CODONCHOICE; } else { $partial += $relativeusage; } } unless ($chosen_codon) { $chosen_codon = $alt_codons[-1]; # the last one } # print ".....adding $chosen_codon\n"; # verbose $dnasequence .= $chosen_codon; } } my $dna = Bio::LiveSeq::DNA->new(-seq => $dnasequence); my $min=1; my $max=length($dnasequence); my $exon = Bio::LiveSeq::Exon->new(-seq => $dna, -start => $min, -end => $max, -strand => 1); my @exons=($exon); my $transcript = Bio::LiveSeq::Transcript->new(-exons => \@exons); $transcript->translation_table($ttabid); my @transcripts=($transcript); my $translation = Bio::LiveSeq::Translation->new(-transcript => $transcript); my @translations=($translation); my %features=(DNA => $dna, Transcripts => \@transcripts, Translations => \@translations); my $gene = Bio::LiveSeq::Gene->new(-name => $gene_name, -features => \%features, -upbound => $min, -downbound => $max); # creation of gene unless ($gene) { # if $gene == 0 it means problems in hash2gene carp "Error in Gene creation phase"; return (0); } return $gene; } 1; BioPerl-1.007002/Bio/LiveSeq/IO/README000444000766000024 172513155576320 16770 0ustar00cjfieldsstaff000000000000# $Id$ README for Bio::LiveSeq::IO LiveSeq objects representing known gene structures and their sequences have to be created from nucleotide sequence files. The current IO files do it by reading in EMBL entries and parsing out sequences as well as CDS, exon and primary_transcript features from the feature table. Bio::LiveSeq::IO::Loader is a superclass holding methods common to other methods. Bio::LiveSeq::IO::BioPerl is the preferred method which uses Bio::DB::EMBL to retrieve sequences over the Web by accession number. Bio::LiveSeq::IO::SRS outdated, removed from distribution 13 Jan 2006 retrieves sequences from a local installation of SRS. It needs srsperl.pm which is part of SRS. SRS is short for Sequence Retrieval System, a comprehensive program suite for indexing and serving biological databases. SRS is a product of Lion BioSciences (http://www.lionbio.co.uk/). The license for academic users is free. BioPerl-1.007002/Bio/Location000755000766000024 013155576320 15637 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Location/Atomic.pm000444000766000024 3375413155576320 17602 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Location::Atomic # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Location::Atomic - Implementation of a Atomic Location on a Sequence =head1 SYNOPSIS use Bio::Location::Atomic; my $location = Bio::Location::Atomic->new(-start => 1, -end => 100, -strand => 1 ); if( $location->strand == -1 ) { printf "complement(%d..%d)\n", $location->start, $location->end; } else { printf "%d..%d\n", $location->start, $location->end; } =head1 DESCRIPTION This is an implementation of Bio::LocationI to manage simple location information on a Sequence. =head1 FEEDBACK User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Location::Atomic; use strict; use Bio::Location::WidestCoordPolicy; use base qw(Bio::Root::Root Bio::LocationI); our $coord_policy = Bio::Location::WidestCoordPolicy->new(); sub new { my ($class, @args) = @_; $class = ref $class || $class; my $self = {}; # This is for the case when we've done something like this # get a 2 features from somewhere (like Bio::Tools::GFF) # Do # my $location = $f1->location->union($f2->location); # We get an error without the following code which # explicitly loads the Bio::Location::Simple class unless( $class->can('start') ) { eval { Bio::Root::Root->_load_module($class) }; if ( $@ ) { Bio::Root::Root->throw("$class cannot be found\nException $@"); } } bless $self,$class; my ($v,$start,$end,$strand,$seqid) = $self->_rearrange([qw(VERBOSE START END STRAND SEQ_ID)],@args); defined $v && $self->verbose($v); defined $strand && $self->strand($strand); defined $start && $self->start($start); defined $end && $self->end($end); if( defined $self->start && defined $self->end && $self->start > $self->end && $self->strand != -1 ) { $self->warn("When building a location, start ($start) is expected to be less than end ($end), ". "however it was not. Switching start and end and setting strand to -1"); $self->strand(-1); my $e = $self->end; my $s = $self->start; $self->start($e); $self->end($s); } $seqid && $self->seq_id($seqid); return $self; } =head2 start Title : start Usage : $start = $loc->start(); Function: get/set the start of this range Returns : the start of this range Args : optionally allows the start to be set : using $loc->start($start) =cut sub start { my ($self, $value) = @_; $self->min_start($value) if( defined $value ); return $self->SUPER::start(); } =head2 end Title : end Usage : $end = $loc->end(); Function: get/set the end of this range Returns : the end of this range Args : optionally allows the end to be set : using $loc->end($start) =cut sub end { my ($self, $value) = @_; $self->min_end($value) if( defined $value ); return $self->SUPER::end(); } =head2 strand Title : strand Usage : $strand = $loc->strand(); Function: get/set the strand of this range Returns : the strandidness (-1, 0, +1) Args : optionally allows the strand to be set : using $loc->strand($strand) =cut sub strand { my $self = shift; if ( @_ ) { my $value = shift; if ( defined($value) ) { if ( $value eq '+' ) { $value = 1; } elsif ( $value eq '-' ) { $value = -1; } elsif ( $value eq '.' ) { $value = 0; } elsif ( $value != -1 && $value != 1 && $value != 0 ) { $self->throw("$value is not a valid strand info"); } $self->{'_strand'} = $value; } } # do not pretend the strand has been set if in fact it wasn't return $self->{'_strand'}; #return $self->{'_strand'} || 0; } =head2 flip_strand Title : flip_strand Usage : $location->flip_strand(); Function: Flip-flop a strand to the opposite Returns : None Args : None =cut sub flip_strand { my $self= shift; # Initialize strand if necessary to flip it if (not defined $self->strand) { $self->strand(1) } $self->strand($self->strand * -1); } =head2 seq_id Title : seq_id Usage : my $seqid = $location->seq_id(); Function: Get/Set seq_id that location refers to Returns : seq_id (a string) Args : [optional] seq_id value to set =cut sub seq_id { my ($self, $seqid) = @_; if( defined $seqid ) { $self->{'_seqid'} = $seqid; } return $self->{'_seqid'}; } =head2 length Title : length Usage : $len = $loc->length(); Function: get the length in the coordinate space this location spans Example : Returns : an integer Args : none =cut sub length { my ($self) = @_; return abs($self->end() - $self->start()) + 1; } =head2 min_start Title : min_start Usage : my $minstart = $location->min_start(); Function: Get minimum starting location of feature startpoint Returns : integer or undef if no minimum starting point. Args : none =cut sub min_start { my ($self,$value) = @_; if(defined($value)) { $self->{'_start'} = $value; } return $self->{'_start'}; } =head2 max_start Title : max_start Usage : my $maxstart = $location->max_start(); Function: Get maximum starting location of feature startpoint. In this implementation this is exactly the same as min_start(). Returns : integer or undef if no maximum starting point. Args : none =cut sub max_start { my ($self,@args) = @_; return $self->min_start(@args); } =head2 start_pos_type Title : start_pos_type Usage : my $start_pos_type = $location->start_pos_type(); Function: Get start position type (ie <,>, ^). In this implementation this will always be 'EXACT'. Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none =cut sub start_pos_type { my($self) = @_; return 'EXACT'; } =head2 min_end Title : min_end Usage : my $minend = $location->min_end(); Function: Get minimum ending location of feature endpoint Returns : integer or undef if no minimum ending point. Args : none =cut sub min_end { my($self,$value) = @_; if(defined($value)) { $self->{'_end'} = $value; } return $self->{'_end'}; } =head2 max_end Title : max_end Usage : my $maxend = $location->max_end(); Function: Get maximum ending location of feature endpoint In this implementation this is exactly the same as min_end(). Returns : integer or undef if no maximum ending point. Args : none =cut sub max_end { my($self,@args) = @_; return $self->min_end(@args); } =head2 end_pos_type Title : end_pos_type Usage : my $end_pos_type = $location->end_pos_type(); Function: Get end position type (ie <,>, ^) In this implementation this will always be 'EXACT'. Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none =cut sub end_pos_type { my($self) = @_; return 'EXACT'; } =head2 location_type Title : location_type Usage : my $location_type = $location->location_type(); Function: Get location type encoded as text Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN') Args : none =cut sub location_type { my ($self) = @_; return 'EXACT'; } =head2 is_remote Title : is_remote Usage : $is_remote_loc = $loc->is_remote() Function: Whether or not a location is a remote location. A location is said to be remote if it is on a different 'object' than the object which 'has' this location. Typically, features on a sequence will sometimes have a remote location, which means that the location of the feature is on a different sequence than the one that is attached to the feature. In such a case, $loc->seq_id will be different from $feat->seq_id (usually they will be the same). While this may sound weird, it reflects the location of the kind of AL445212.9:83662..166657 which can be found in GenBank/EMBL feature tables. Example : Returns : TRUE if the location is a remote location, and FALSE otherwise Args : Value to set to =cut sub is_remote { my $self = shift; if( @_ ) { my $value = shift; $self->{'is_remote'} = $value; } return $self->{'is_remote'}; } =head2 each_Location Title : each_Location Usage : @locations = $locObject->each_Location($order); Function: Conserved function call across Location:: modules - will return an array containing the component Location(s) in that object, regardless if the calling object is itself a single location or one containing sublocations. Returns : an array of Bio::LocationI implementing objects - for Simple locations, the return value is just itself. Args : =cut sub each_Location { my ($self) = @_; return ($self); } =head2 to_FTstring Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none =cut sub to_FTstring { my($self) = @_; if( $self->start == $self->end ) { return $self->start; } my $str = $self->start . ".." . $self->end; if( $self->strand == -1 ) { $str = sprintf("complement(%s)", $str); } return $str; } =head2 valid_Location Title : valid_Location Usage : if ($location->valid_location) {...}; Function: boolean method to determine whether location is considered valid (has minimum requirements for Simple implementation) Returns : Boolean value: true if location is valid, false otherwise Args : none =cut sub valid_Location { my ($self) = @_; return 1 if $self->{'_start'} && $self->{'_end'}; return 0; } =head2 coordinate_policy Title : coordinate_policy Usage : $policy = $location->coordinate_policy(); $location->coordinate_policy($mypolicy); # set may not be possible Function: Get the coordinate computing policy employed by this object. See L for documentation about the policy object and its use. The interface *does not* require implementing classes to accept setting of a different policy. The implementation provided here does, however, allow one to do so. Implementors of this interface are expected to initialize every new instance with a L object. The implementation provided here will return a default policy object if none has been set yet. To change this default policy object call this method as a class method with an appropriate argument. Note that in this case only subsequently created Location objects will be affected. Returns : A L implementing object. Args : On set, a L implementing object. See L for more information =cut sub coordinate_policy { my ($self, $policy) = @_; if(defined($policy)) { if(! $policy->isa('Bio::Location::CoordinatePolicyI')) { $self->throw("Object of class ".ref($policy)." does not implement". " Bio::Location::CoordinatePolicyI"); } if(ref($self)) { $self->{'_coordpolicy'} = $policy; } else { # called as class method $coord_policy = $policy; } } return (ref($self) && exists($self->{'_coordpolicy'}) ? $self->{'_coordpolicy'} : $coord_policy); } =head2 trunc Title : trunc Usage : $trunc_location = $location->trunc($start, $end, $relative_ori); Function: To truncate a location and keep annotations and features within the truncated segment intact. This might do things differently where the truncation splits the location in half. CAVEAT : As yet, this is an untested and unannounced method. Use with caution! Returns : A L object. Args : The start and end position for the trunction, and the relative orientation. =cut sub trunc { my ($self,$start,$end,$relative_ori) = @_; my $newstart = $self->start - $start+1; my $newend = $self->end - $start+1; my $newstrand = $relative_ori * $self->strand; my $out; if( $newstart < 1 || $newend > ($end-$start+1) ) { $out = Bio::Location::Atomic->new(); $out->start($self->start); $out->end($self->end); $out->strand($self->strand); $out->seq_id($self->seqid); $out->is_remote(1); } else { $out = Bio::Location::Atomic->new(); $out->start($newstart); $out->end($newend); $out->strand($newstrand); $out->seq_id(); } return $out; } 1; BioPerl-1.007002/Bio/Location/AvWithinCoordPolicy.pm000444000766000024 727613155576320 22246 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Location::AvWithinCoordPolicy # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # and Jason Stajich # # Copyright Hilmar Lapp, Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Location::AvWithinCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise =head1 SYNOPSIS See Bio::Location::CoordinatePolicyI =head1 DESCRIPTION CoordinatePolicyI implementing objects are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked for it. This class will compute the coordinates such that for fuzzy locations of type WITHIN and BETWEEN the average of the two limits will be returned, and for all other locations it will return the widest possible range, but by using some common sense. This means that e.g. locations like "E5..100" (start before position 5) will return 5 as start (returned values have to be positive integers). =head1 FEEDBACK User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp, Jason Stajich Email Ehlapp-at-gmx-dot-netE, Ejason-at-bioperl-dot-orgE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Location::AvWithinCoordPolicy; use strict; use base qw(Bio::Location::WidestCoordPolicy); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); return $self; } =head2 start Title : start Usage : $start = $policy->start($location); Function: Get the integer-valued start coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object. =cut sub start { my ($self,$loc) = @_; if(($loc->start_pos_type() eq 'WITHIN') || ($loc->start_pos_type() eq 'BETWEEN')) { my ($min, $max) = ($loc->min_start(), $loc->max_start()); return int(($min+$max)/2) if($min && $max); } return $self->SUPER::start($loc); } =head2 end Title : end Usage : $end = $policy->end($location); Function: Get the integer-valued end coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object. =cut sub end { my ($self,$loc) = @_; if(($loc->end_pos_type() eq 'WITHIN') || ($loc->end_pos_type() eq 'BETWEEN')) { my ($min, $max) = ($loc->min_end(), $loc->max_end()); return int(($min+$max)/2) if($min && $max); } return $self->SUPER::end($loc); } 1; BioPerl-1.007002/Bio/Location/CoordinatePolicyI.pm000444000766000024 706313155576320 21720 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Location::CoordinatePolicyI # Please direct questions and support issues to # # Cared for by Hilmar Lapp # and Jason Stajich # # Copyright Hilmar Lapp, Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location =head1 SYNOPSIS # get a location, e.g., from a SeqFeature $location = $feature->location(); # examine its coordinate computation policy print "Location of feature ", $feature->primary_tag(), " employs a ", ref($location->coordinate_policy()), " instance for coordinate computation\n"; # change the policy, e.g. because the user chose to do so $location->coordinate_policy(Bio::Location::NarrowestCoordPolicy->new()); =head1 DESCRIPTION Objects implementing this interface are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked for it. While this may seem trivial for simple locations, there are different ways to do it for fuzzy or compound (split) locations. Classes implementing this interface implement a certain policy, like 'always widest range', 'always smallest range', 'mean for BETWEEN locations', etc. By installing a different policy object in a Location object, the behaviour of coordinate computation can be changed on-the-fly, and with a single line of code client-side. =head1 FEEDBACK User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp, Jason Stajich Email hlapp@gmx.net, jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Location::CoordinatePolicyI; use strict; use base qw(Bio::Root::RootI); =head2 start Title : start Usage : $start = $policy->start($location); Function: Get the integer-valued start coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object. =cut sub start { my ($self) = @_; $self->throw_not_implemented(); } =head2 end Title : end Usage : $end = $policy->end($location); Function: Get the integer-valued end coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object. =cut sub end { my ($self) = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Location/Fuzzy.pm000444000766000024 4577613155576320 17524 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Location::Fuzzy # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Location::Fuzzy - Implementation of a Location on a Sequence which has unclear start and/or end locations =head1 SYNOPSIS use Bio::Location::Fuzzy; my $fuzzylocation = Bio::Location::Fuzzy->new( -start => '<30', -end => 90, -location_type => '..'); print "location string is ", $fuzzylocation->to_FTstring(), "\n"; print "location is of the type ", $fuzzylocation->location_type, "\n"; =head1 DESCRIPTION This module contains the necessary methods for representing a Fuzzy Location, one that does not have clear start and/or end points. This will initially serve to handle features from Genbank/EMBL feature tables that are written as 1^100 meaning between bases 1 and 100 or E100..300 meaning it starts somewhere before 100. Advanced implementations of this interface may be able to handle the necessary logic of overlaps/intersection/contains/union. It was constructed to handle fuzzy locations that can be represented in Genbank/EMBL and Swissprot. =head1 FEEDBACK User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Location::Fuzzy; use strict; use base qw(Bio::Location::Atomic Bio::Location::FuzzyLocationI); our @LOCATIONCODESBSANE = (undef, 'EXACT', 'WITHIN', 'BETWEEN', 'UNCERTAIN', 'BEFORE', 'AFTER'); our %FUZZYCODES = ( 'EXACT' => '..', # Position is 'exact # Exact position is unknown, but is within the range specified, ((1.2)..100) 'WITHIN' => '.', # 1^2 'BETWEEN' => '^', 'IN-BETWEEN' => '^', 'UNCERTAIN' => '?', # <100 'BEFORE' => '<', # >10 'AFTER' => '>'); # The following regular expressions map to fuzzy location types. Every # expression must match the complete encoded point string, and must # contain two groups identifying min and max. Empty matches are automatic. # converted to undef, except for 'EXACT', for which max is set to equal # min. our %FUZZYPOINTENCODE = ( '\>(\d+)(.{0})' => 'AFTER', '\<(.{0})(\d+)' => 'BEFORE', '(\d+)' => 'EXACT', '\?(\d*)' => 'UNCERTAIN', '(\d+)(.{0})\>' => 'AFTER', '(.{0})(\d+)\<' => 'BEFORE', '(\d+)\.(\d+)' => 'WITHIN', '(\d+)\^(\d+)' => 'BETWEEN', ); our %FUZZYRANGEENCODE = ( '\.' => 'WITHIN', '\.\.' => 'EXACT', '\^' => 'IN-BETWEEN' ); =head2 new Title : new Usage : my $fuzzyloc = Bio::Location::Fuzzy->new( @args); Function: Returns : Args : -start => value for start (initialize by superclass) -end => value for end (initialize by superclass) -strand => value for strand (initialize by superclass) -location_type => either ('EXACT','WITHIN','IN-BETWEEN', 'UNCERTAIN') OR ( 1,2,3,4) -start_ext=> extension for start - defaults to 0, -start_fuz= fuzzy code for start can be ('EXACT','WITHIN','BETWEEN','BEFORE','AFTER', 'UNCERTAIN' ) OR a value 1 - 5 corresponding to index+1 above -end_ext=> extension for end - defaults to 0, -end_fuz= fuzzy code for end can be ('EXACT','WITHIN','BETWEEN','BEFORE','AFTER', 'UNCERTAIN') OR a value 1 - 5 corresponding to index+1 above =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($location_type, $start_ext, $start_fuz, $end_ext, $end_fuz) = $self->_rearrange([ qw(LOCATION_TYPE START_EXT START_FUZ END_EXT END_FUZ ) ], @args); $location_type && $self->location_type($location_type); $start_ext && $self->max_start($self->min_start + $start_ext); $end_ext && $self->max_end($self->min_end + $end_ext); $start_fuz && $self->start_pos_type($start_fuz); $end_fuz && $self->end_pos_type($end_fuz); return $self; } =head2 location_type Title : location_type Usage : my $location_type = $location->location_type(); Function: Get location type encoded as text Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN', 'UNCERTAIN') Args : none =cut sub location_type { my ($self,$value) = @_; if( defined $value || ! defined $self->{'_location_type'} ) { $value = 'EXACT' unless defined $value; if(! defined $FUZZYCODES{$value} ) { $value = uc($value); if( $value =~ /\.\./ ) { $value = 'EXACT'; } elsif( $value =~ /^\.$/ ) { $value = 'WITHIN'; } elsif( $value =~ /\^/ ) { $value = 'IN-BETWEEN'; $self->throw("Use Bio::Location::Simple for IN-BETWEEN locations [". $self->start. "] and [". $self->end. "]") if defined $self->start && defined $self->end && ($self->end - 1 == $self->start); } elsif( $value =~ /\?/ ) { $value = 'UNCERTAIN'; } elsif( $value ne 'EXACT' && $value ne 'WITHIN' && $value ne 'IN-BETWEEN' ) { $self->throw("Did not specify a valid location type"); } } $self->{'_location_type'} = $value; } return $self->{'_location_type'}; } =head1 LocationI methods =head2 length Title : length Usage : $length = $fuzzy_loc->length(); Function: Get the length of this location. Note that the length of a fuzzy location will always depend on the currently active interpretation of start and end. The result will therefore vary for different CoordinatePolicy objects. Returns : an integer Args : none =cut #sub length { # my($self) = @_; # return $self->SUPER::length() if( !$self->start || !$self->end); # $self->warn('Length is not valid for a FuzzyLocation'); # return 0; #} =head2 start Title : start Usage : $start = $fuzzy->start(); Function: get/set start of this range, handling fuzzy_starts Returns : a positive integer representing the start of the location Args : start location on set (can be fuzzy point string) =cut sub start { my($self,$value) = @_; if( defined $value ) { my ($encode,$min,$max) = $self->_fuzzypointdecode($value); $self->start_pos_type($encode); $self->min_start($min); $self->max_start($max); } $self->throw("Use Bio::Location::Simple for IN-BETWEEN locations [" . $self->SUPER::start. "] and [". $self->SUPER::end. "]") if $self->location_type eq 'IN-BETWEEN' && defined $self->SUPER::end && ($self->SUPER::end - 1 == $self->SUPER::start); return $self->SUPER::start(); } =head2 end Title : end Usage : $end = $fuzzy->end(); Function: get/set end of this range, handling fuzzy_ends Returns : a positive integer representing the end of the range Args : end location on set (can be fuzzy string) =cut sub end { my($self,$value) = @_; if( defined $value ) { my ($encode,$min,$max) = $self->_fuzzypointdecode($value); $self->end_pos_type($encode); $self->min_end($min); $self->max_end($max); } $self->throw("Use Bio::Location::Simple for IN-BETWEEN locations [". $self->SUPER::start. "] and [". $self->SUPER::end. "]") if $self->location_type eq 'IN-BETWEEN' && defined $self->SUPER::start && ($self->SUPER::end - 1 == $self->SUPER::start); return $self->SUPER::end(); } =head2 min_start Title : min_start Usage : $min_start = $fuzzy->min_start(); Function: get/set the minimum starting point Returns : the minimum starting point from the contained sublocations Args : integer or undef on set =cut sub min_start { my ($self,@args) = @_; if(@args) { $self->{'_min_start'} = $args[0]; # the value may be undef! } return $self->{'_min_start'}; } =head2 max_start Title : max_start Usage : my $maxstart = $location->max_start(); Function: Get/set maximum starting location of feature startpoint Returns : integer or undef if no maximum starting point. Args : integer or undef on set =cut sub max_start { my ($self,@args) = @_; if(@args) { $self->{'_max_start'} = $args[0]; # the value may be undef! } return $self->{'_max_start'}; } =head2 start_pos_type Title : start_pos_type Usage : my $start_pos_type = $location->start_pos_type(); Function: Get/set start position type. Returns : type of position coded as text ('BEFORE','AFTER','EXACT','WITHIN','BETWEEN','UNCERTAIN') Args : a string on set =cut sub start_pos_type { my ($self,$value) = @_; if(defined $value && $value =~ /^\d+$/ ) { if( $value == 0 ) { $value = 'EXACT'; } else { my $v = $LOCATIONCODESBSANE[$value]; if( ! defined $v ) { $self->warn("Provided value $value which I don't understand,". " reverting to 'EXACT'"); $v = 'EXACT'; } $value = $v; } } if(defined($value)) { $self->{'_start_pos_type'} = $value; } return $self->{'_start_pos_type'}; } =head2 min_end Title : min_end Usage : my $minend = $location->min_end(); Function: Get/set minimum ending location of feature endpoint Returns : integer or undef if no minimum ending point. Args : integer or undef on set =cut sub min_end { my ($self,@args) = @_; if(@args) { $self->{'_min_end'} = $args[0]; # the value may be undef! } return $self->{'_min_end'}; } =head2 max_end Title : max_end Usage : my $maxend = $location->max_end(); Function: Get/set maximum ending location of feature endpoint Returns : integer or undef if no maximum ending point. Args : integer or undef on set =cut sub max_end { my ($self,@args) = @_; if(@args) { $self->{'_max_end'} = $args[0]; # the value may be undef! } return $self->{'_max_end'}; } =head2 end_pos_type Title : end_pos_type Usage : my $end_pos_type = $location->end_pos_type(); Function: Get/set end position type. Returns : type of position coded as text ('BEFORE','AFTER','EXACT','WITHIN','BETWEEN','UNCERTAIN') Args : a string on set =cut sub end_pos_type { my ($self,$value) = @_; if( defined $value && $value =~ /^\d+$/ ) { if( $value == 0 ) { $value = 'EXACT'; } else { my $v = $LOCATIONCODESBSANE[$value]; if( ! defined $v ) { $self->warn("Provided value $value which I don't understand,". " reverting to 'EXACT'"); $v = 'EXACT'; } $value = $v; } } if(defined($value)) { $self->{'_end_pos_type'} = $value; } return $self->{'_end_pos_type'}; } =head2 seq_id Title : seq_id Usage : my $seqid = $location->seq_id(); Function: Get/Set seq_id that location refers to Returns : seq_id Args : [optional] seq_id value to set =cut =head2 coordinate_policy Title : coordinate_policy Usage : $policy = $location->coordinate_policy(); $location->coordinate_policy($mypolicy); # set may not be possible Function: Get the coordinate computing policy employed by this object. See Bio::Location::CoordinatePolicyI for documentation about the policy object and its use. The interface *does not* require implementing classes to accept setting of a different policy. The implementation provided here does, however, allow one to do so. Implementors of this interface are expected to initialize every new instance with a CoordinatePolicyI object. The implementation provided here will return a default policy object if none has been set yet. To change this default policy object call this method as a class method with an appropriate argument. Note that in this case only subsequently created Location objects will be affected. Returns : A Bio::Location::CoordinatePolicyI implementing object. Args : On set, a Bio::Location::CoordinatePolicyI implementing object. See L =cut =head2 to_FTstring Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: Get/Set seq_id that location refers to Returns : seq_id Args : [optional] seq_id value to set =cut sub to_FTstring { my ($self) = @_; my (%vals) = ( 'start' => $self->start, 'min_start' => $self->min_start, 'max_start' => $self->max_start, 'start_code' => $self->start_pos_type, 'end' => $self->end, 'min_end' => $self->min_end, 'max_end' => $self->max_end, 'end_code' => $self->end_pos_type ); my (%strs) = ( 'start' => '', 'end' => ''); my ($delimiter) = $FUZZYCODES{$self->location_type}; $delimiter = $FUZZYCODES{'EXACT'} if ($self->location_type eq 'UNCERTAIN'); my $policy = ref($self->coordinate_policy); # I'm lazy, lets do this in a loop since behaviour will be the same for # start and end # The CoordinatePolicy now dictates start/end data here (bug 992) - cjf foreach my $point ( qw(start end) ) { if( ($vals{$point."_code"} ne 'EXACT') && ($vals{$point."_code"} ne 'UNCERTAIN') ) { # must have max and min defined to use 'WITHIN', 'BETWEEN' if ((!defined $vals{"min_$point"} || !defined $vals{"max_$point"}) && ( $vals{$point."_code"} eq 'WITHIN' || $vals{$point."_code"} eq 'BETWEEN')) { $vals{"min_$point"} = '' unless defined $vals{"min_$point"}; $vals{"max_$point"} = '' unless defined $vals{"max_$point"}; $self->warn("Fuzzy codes for start are in a strange state, (". join(",", ($vals{"min_$point"}, $vals{"max_$point"}, $vals{$point."_code"})). ")"); return ''; } if (defined $vals{$point."_code"} && ($vals{$point."_code"} eq 'BEFORE' || $vals{$point."_code"} eq 'AFTER')) { $strs{$point} .= $FUZZYCODES{$vals{$point."_code"}}; $strs{$point} .= $vals{"$point"}; } if( defined $vals{$point."_code"} && ($vals{$point."_code"} eq 'WITHIN' || $vals{$point."_code"} eq 'BETWEEN')) { # Expect odd results with anything but WidestCoordPolicy for now $strs{$point} .= ($point eq 'start') ? $vals{"$point"}. $FUZZYCODES{$vals{$point."_code"}}. $vals{'max_'.$point} : $vals{'min_'.$point}. $FUZZYCODES{$vals{$point."_code"}}. $vals{"$point"}; $strs{$point} = "(".$strs{$point}.")"; } } elsif ($vals{$point."_code"} eq 'UNCERTAIN') { $strs{$point} = $FUZZYCODES{$vals{$point."_code"}}; $strs{$point} .= $vals{$point} if defined $vals{$point}; } else { $strs{$point} = $vals{$point}; } } my $str = $strs{'start'} . $delimiter . $strs{'end'}; if($self->is_remote() && $self->seq_id()) { $str = $self->seq_id() . ":" . $str; } if( defined $self->strand && $self->strand == -1 && $self->location_type() ne "UNCERTAIN") { $str = "complement(" . $str . ")"; } elsif($self->location_type() eq "WITHIN") { $str = "(".$str.")"; } return $str; } =head2 valid_Location Title : valid_Location Usage : if ($location->valid_location) {...}; Function: boolean method to determine whether location is considered valid (has minimum requirements for Simple implementation) Returns : Boolean value: true if location is valid, false otherwise Args : none =cut =head2 _fuzzypointdecode Title : _fuzzypointdecode Usage : ($type,$min,$max) = $self->_fuzzypointdecode('<5'); Function: Decode a fuzzy string. Returns : A 3-element array consisting of the type of location, the minimum integer, and the maximum integer describing the range of coordinates this start or endpoint refers to. Minimum or maximum coordinate may be undefined. : Returns empty array on fail. Args : fuzzypoint string =cut sub _fuzzypointdecode { my ($self, $string) = @_; return () if( !defined $string); # strip off leading and trailing space $string =~ s/^\s*(\S+)\s*/$1/; foreach my $pattern ( keys %FUZZYPOINTENCODE ) { if( $string =~ /^$pattern$/ ) { my ($min,$max) = ($1,$2) unless (($1 eq '') && (!defined $2)); if( ($FUZZYPOINTENCODE{$pattern} eq 'EXACT') || ($FUZZYPOINTENCODE{$pattern} eq 'UNCERTAIN') ) { $max = $min; } else { $max = undef if((defined $max) && (length($max) == 0)); $min = undef if((defined $min) && (length($min) == 0)); } return ($FUZZYPOINTENCODE{$pattern},$min,$max); } } if( $self->verbose >= 1 ) { $self->warn("could not find a valid fuzzy encoding for $string"); } return (); } 1; BioPerl-1.007002/Bio/Location/FuzzyLocationI.pm000444000766000024 1351113155576320 21304 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Location::FuzzyLocationI # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence which has unclear start/end location =head1 SYNOPSIS # Get a FuzzyLocationI object somehow print "Fuzzy FT location string is ", $location->to_FTstring(); print "location is of the type ", $location->loc_type, "\n"; =head1 DESCRIPTION This interface encapsulates the necessary methods for representing a Fuzzy Location, one that does not have clear start and/or end points. This will initially serve to handle features from Genbank/EMBL feature tables that are written as 1^100 meaning between bases 1 and 100 or E100..300 meaning it starts somewhere before 100. Advanced implementations of this interface may be able to handle the necessary logic of overlaps/intersection/contains/union. It was constructed to handle fuzzy locations that can be represented in Genbank/EMBL. =head1 FEEDBACK User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Location::FuzzyLocationI; use strict; use base qw(Bio::LocationI); =head1 LocationI methods =head2 location_type Title : loc_type Usage : my $location_type = $location->location_type(); Function: Get location type encoded as text Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN') Args : none =cut sub location_type { my ($self) = @_; $self->throw_not_implemented(); } =head1 Bio::LocationI methods Bio::LocationI methods follow =head2 min_start Title : min_start Usage : my $minstart = $location->min_start(); Function: Get minimum starting location of feature startpoint Returns : integer or undef if no maximum starting point. Args : none =cut =head2 max_start Title : max_start Usage : my $maxstart = $location->max_start(); Function: Get maximum starting location of feature startpoint Returns : integer or undef if no maximum starting point. Args : none =cut =head2 start_pos_type Title : start_pos_type Usage : my $start_pos_type = $location->start_pos_type(); Function: Get start position type (ie <,>, ^) Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none =cut =head2 min_end Title : min_end Usage : my $minend = $location->min_end(); Function: Get minimum ending location of feature endpoint Returns : integer or undef if no minimum ending point. Args : none =cut =head2 max_end Title : max_end Usage : my $maxend = $location->max_end(); Function: Get maximum ending location of feature endpoint Returns : integer or undef if no maximum ending point. Args : none =cut =head2 end_pos_type Title : end_pos_type Usage : my $end_pos_type = $location->end_pos_type(); Function: Get end position type (ie <,>, ^) Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none =cut =head2 seq_id Title : seq_id Usage : my $seqid = $location->seq_id(); Function: Get/Set seq_id that location refers to Returns : seq_id Args : [optional] seq_id value to set =cut =head2 coordinate_policy Title : coordinate_policy Usage : $policy = $location->coordinate_policy(); $location->coordinate_policy($mypolicy); # set may not be possible Function: Get the coordinate computing policy employed by this object. See Bio::Location::CoordinatePolicyI for documentation about the policy object and its use. The interface *does not* require implementing classes to accept setting of a different policy. The implementation provided here does, however, allow one to do so. Implementors of this interface are expected to initialize every new instance with a CoordinatePolicyI object. The implementation provided here will return a default policy object if none has been set yet. To change this default policy object call this method as a class method with an appropriate argument. Note that in this case only subsequently created Location objects will be affected. Returns : A Bio::Location::CoordinatePolicyI implementing object. Args : On set, a Bio::Location::CoordinatePolicyI implementing object. =cut =head2 to_FTstring Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none =cut 1; BioPerl-1.007002/Bio/Location/NarrowestCoordPolicy.pm000444000766000024 724313155576320 22473 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Location::NarrowestCoordPolicy # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # and Jason Stajich # # Copyright Hilmar Lapp, Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Location::NarrowestCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range =head1 SYNOPSIS See Bio::Location::CoordinatePolicyI =head1 DESCRIPTION CoordinatePolicyI implementing objects are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked for it. This class will compute the coordinates such that always the narrowest possible range is returned, but by using some common sense. This means that e.g. locations like "E5..100" (start before position 5) will return 5 as start (returned values have to be positive integers). =head1 FEEDBACK User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp, Jason Stajich Email Ehlapp-at-gmx.netE, Ejason@bioperl.orgE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Location::NarrowestCoordPolicy; use strict; use base qw(Bio::Root::Root Bio::Location::CoordinatePolicyI); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); return $self; } =head2 start Title : start Usage : $start = $policy->start($location); Function: Get the integer-valued start coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object. =cut sub start { my ($self,$loc) = @_; # For performance reasons we don't check that it's indeed a Bio::LocationI # object. Hopefully, Location-object programmers are smart enough. my $pos = $loc->max_start(); # if max is not defined or equals 0 we resort to min $pos = $loc->min_start() if(! $pos); return $pos; } =head2 end Title : end Usage : $end = $policy->end($location); Function: Get the integer-valued end coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object. =cut sub end { my ($self,$loc) = @_; # For performance reasons we don't check that it's indeed a Bio::LocationI # object. Hopefully, Location-object programmers are smart enough. my $pos = $loc->min_end(); # if min is not defined or equals 0 we resort to max $pos = $loc->max_end() if(! $pos); return $pos; } 1; BioPerl-1.007002/Bio/Location/Simple.pm000444000766000024 2610713155576320 17611 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Location::Simple # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Location::Simple - Implementation of a Simple Location on a Sequence =head1 SYNOPSIS use Bio::Location::Simple; my $location = Bio::Location::Simple->new( -start => 1, -end => 100, -strand => 1, ); if( $location->strand == -1 ) { printf "complement(%d..%d)\n", $location->start, $location->end; } else { printf "%d..%d\n", $location->start, $location->end; } =head1 DESCRIPTION This is an implementation of Bio::LocationI to manage exact location information on a Sequence: '22' or '12..15' or '16^17'. You can test the type of the location using length() function () or directly location_type() which can one of two values: 'EXACT' or 'IN-BETWEEN'. =head1 FEEDBACK User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Location::Simple; use strict; use base qw(Bio::Location::Atomic); our %RANGEENCODE = ('\.\.' => 'EXACT', '\^' => 'IN-BETWEEN' ); our %RANGEDECODE = ('EXACT' => '..', 'IN-BETWEEN' => '^' ); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($locationtype) = $self->_rearrange([qw(LOCATION_TYPE)],@args); $locationtype && $self->location_type($locationtype); return $self; } =head2 start Title : start Usage : $start = $loc->start(); Function: get/set the start of this range Returns : the start of this range Args : optionally allows the start to be set using $loc->start($start) =cut sub start { my ($self, $value) = @_; $self->{'_start'} = $value if defined $value ; $self->throw("Only adjacent residues when location type ". "is IN-BETWEEN. Not [". $self->{'_start'}. "] and [". $self->{'_end'}. "]" ) if defined $self->{'_start'} && defined $self->{'_end'} && $self->location_type eq 'IN-BETWEEN' && ($self->{'_end'} - 1 != $self->{'_start'}); return $self->{'_start'}; } =head2 end Title : end Usage : $end = $loc->end(); Function: get/set the end of this range Returns : the end of this range Args : optionally allows the end to be set : using $loc->end($start) Note : If start is set but end is undefined, this now assumes that start is the same as end but throws a warning (i.e. it assumes this is a possible error). If start is undefined, this now throws an exception. =cut sub end { my ($self, $value) = @_; $self->{'_end'} = $value if defined $value ; # Assume end is the same as start if not defined if (!defined $self->{'_end'}) { if (!defined $self->{'_start'}) { $self->warn('Can not set Bio::Location::Simple::end() equal to start; start not set'); return; } $self->warn('Setting end to equal start['. $self->{'_start'}. ']'); $self->{'_end'} = $self->{'_start'}; } $self->throw("Only adjacent residues when location type ". "is IN-BETWEEN. Not [". $self->{'_start'}. "] and [". $self->{'_end'}. "]" ) if defined $self->{'_start'} && defined $self->{'_end'} && $self->location_type eq 'IN-BETWEEN' && ($self->{'_end'} - 1 != $self->{'_start'}); return $self->{'_end'}; } =head2 strand Title : strand Usage : $strand = $loc->strand(); Function: get/set the strand of this range Returns : the strandedness (-1, 0, +1) Args : optionally allows the strand to be set : using $loc->strand($strand) =cut =head2 length Title : length Usage : $len = $loc->length(); Function: get the length in the coordinate space this location spans Example : Returns : an integer Args : none =cut sub length { my ($self) = @_; if ($self->location_type eq 'IN-BETWEEN' ) { return 0; } else { return abs($self->end - $self->start) + 1; } } =head2 min_start Title : min_start Usage : my $minstart = $location->min_start(); Function: Get minimum starting location of feature startpoint Returns : integer or undef if no minimum starting point. Args : none =cut =head2 max_start Title : max_start Usage : my $maxstart = $location->max_start(); Function: Get maximum starting location of feature startpoint. In this implementation this is exactly the same as min_start(). Returns : integer or undef if no maximum starting point. Args : none =cut =head2 start_pos_type Title : start_pos_type Usage : my $start_pos_type = $location->start_pos_type(); Function: Get start position type (ie <,>, ^). Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none =cut =head2 min_end Title : min_end Usage : my $minend = $location->min_end(); Function: Get minimum ending location of feature endpoint Returns : integer or undef if no minimum ending point. Args : none =cut =head2 max_end Title : max_end Usage : my $maxend = $location->max_end(); Function: Get maximum ending location of feature endpoint In this implementation this is exactly the same as min_end(). Returns : integer or undef if no maximum ending point. Args : none =cut =head2 end_pos_type Title : end_pos_type Usage : my $end_pos_type = $location->end_pos_type(); Function: Get end position type (ie <,>, ^) Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none =cut =head2 location_type Title : location_type Usage : my $location_type = $location->location_type(); Function: Get location type encoded as text Returns : string ('EXACT' or 'IN-BETWEEN') Args : 'EXACT' or '..' or 'IN-BETWEEN' or '^' =cut sub location_type { my ($self, $value) = @_; if( defined $value || ! defined $self->{'_location_type'} ) { $value = 'EXACT' unless defined $value; $value = uc $value; if (! defined $RANGEDECODE{$value}) { $value = '\^' if $value eq '^'; $value = '\.\.' if $value eq '..'; $value = $RANGEENCODE{$value}; } $self->throw("Did not specify a valid location type. [$value] is no good") unless defined $value; $self->{'_location_type'} = $value; } $self->throw("Only adjacent residues when location type ". "is IN-BETWEEN. Not [". $self->{'_start'}. "] and [". $self->{'_end'}. "]" ) if $self->{'_location_type'} eq 'IN-BETWEEN' && defined $self->{'_start'} && defined $self->{'_end'} && ($self->{'_end'} - 1 != $self->{'_start'}); return $self->{'_location_type'}; } =head2 is_remote Title : is_remote Usage : $is_remote_loc = $loc->is_remote() Function: Whether or not a location is a remote location. A location is said to be remote if it is on a different 'object' than the object which 'has' this location. Typically, features on a sequence will sometimes have a remote location, which means that the location of the feature is on a different sequence than the one that is attached to the feature. In such a case, $loc->seq_id will be different from $feat->seq_id (usually they will be the same). While this may sound weird, it reflects the location of the kind of AL445212.9:83662..166657 which can be found in GenBank/EMBL feature tables. Example : Returns : TRUE if the location is a remote location, and FALSE otherwise Args : Value to set to =cut =head2 to_FTstring Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none =cut sub to_FTstring { my($self) = @_; my $str; if( $self->start == $self->end ) { $str = $self->start; } else { $str = $self->start . $RANGEDECODE{$self->location_type} . $self->end; } if($self->is_remote() && $self->seq_id()) { $str = $self->seq_id() . ":" . $str; } if( defined $self->strand && $self->strand == -1 ) { $str = "complement(".$str.")"; } return $str; } =head2 valid_Location Title : valid_Location Usage : if ($location->valid_location) {...}; Function: boolean method to determine whether location is considered valid (has minimum requirements for Simple implementation) Returns : Boolean value: true if location is valid, false otherwise Args : none =cut # comments, not function added by jason # # trunc is untested, and as of now unannounced method for truncating a # location. This is to eventually be part of the procedure to # truncate a sequence with annotation and properly remap the location # of all the features contained within the truncated segment. # presumably this might do things a little differently for the case # where the truncation splits the location in half # # in short- you probably don't want to use this method. sub trunc { my ($self,$start,$end,$relative_ori) = @_; my $newstart = $self->start - $start+1; my $newend = $self->end - $start+1; my $newstrand = $relative_ori * $self->strand; my $out; if( $newstart < 1 || $newend > ($end-$start+1) ) { $out = Bio::Location::Simple->new(); $out->start($self->start); $out->end($self->end); $out->strand($self->strand); $out->seq_id($self->seqid); $out->is_remote(1); } else { $out = Bio::Location::Simple->new(); $out->start($newstart); $out->end($newend); $out->strand($newstrand); $out->seq_id(); } return $out; } 1; BioPerl-1.007002/Bio/Location/Split.pm000444000766000024 6620113155576320 17452 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Location::Split # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Location::Split - Implementation of a Location on a Sequence which has multiple locations (start/end points) =head1 SYNOPSIS use Bio::Location::Split; my $splitlocation = Bio::Location::Split->new(); $splitlocation->add_sub_Location(Bio::Location::Simple->new(-start=>1, -end=>30, -strand=>1)); $splitlocation->add_sub_Location(Bio::Location::Simple->new(-start=>50, -end=>61, -strand=>1)); my @sublocs = $splitlocation->sub_Location(); my $count = 1; # print the start/end points of the sub locations foreach my $location ( sort { $a->start <=> $b->start } @sublocs ) { printf "sub feature %d [%d..%d]\n", $count, $location->start,$location->end, "\n"; $count++; } =head1 DESCRIPTION This implementation handles locations which span more than one start/end location, or and/or lie on different sequences, and can work with split locations that depend on the specific order of the sublocations ('join') or don't have a specific order but represent a feature spanning noncontiguous sublocations ('order', 'bond'). Note that the order in which sublocations are added may be very important, depending on the specific split location type. For instance, a 'join' must have the sublocations added in the order that one expects to join the sublocations, whereas all other types are sorted based on the sequence location. =head1 FEEDBACK User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-AT-bioperl_DOT_org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Location::Split; # as defined by BSANE 0.03 our @CORBALOCATIONOPERATOR = ('NONE','JOIN', undef, 'ORDER');; use Bio::Root::Root; use base qw(Bio::Location::Atomic Bio::Location::SplitLocationI); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); # initialize $self->{'_sublocations'} = []; my ( $type, $seqid, $locations ) = $self->_rearrange([qw(SPLITTYPE SEQ_ID LOCATIONS )], @args); if( defined $locations && ref($locations) =~ /array/i ) { $self->add_sub_Location(@$locations); } $seqid && $self->seq_id($seqid); $type ||= 'JOIN'; $type = lc ($type); $self->splittype($type); return $self; } =head2 each_Location Title : each_Location Usage : @locations = $locObject->each_Location($order); Function: Conserved function call across Location:: modules - will return an array containing the component Location(s) in that object, regardless if the calling object is itself a single location or one containing sublocations. Returns : an array of Bio::LocationI implementing objects Args : Optional sort order to be passed to sub_Location() =cut sub each_Location { my ($self, $order) = @_; my @locs = (); foreach my $subloc ($self->sub_Location($order)) { # Recursively check to get hierarchical split locations: push @locs, $subloc->each_Location($order); } return @locs; } =head2 sub_Location Title : sub_Location Usage : @sublocs = $splitloc->sub_Location(); Function: Returns the array of sublocations making up this compound (split) location. Those sublocations referring to the same sequence as the root split location will be sorted by start position (forward sort) or end position (reverse sort) and come first (before those on other sequences). The sort order can be optionally specified or suppressed by the value of the first argument. The default is no sort. Returns : an array of Bio::LocationI implementing objects Args : Optionally 1, 0, or -1 for specifying a forward, no, or reverse sort order =cut sub sub_Location { my ($self, $order) = @_; $order = 0 unless defined $order; if( defined($order) && ($order !~ /^-?\d+$/) ) { $self->throw("value $order passed in to sub_Location is $order, an invalid value"); } $order = 1 if($order > 1); $order = -1 if($order < -1); my @sublocs = defined $self->{'_sublocations'} ? @{$self->{'_sublocations'}} : (); # return the array if no ordering requested return @sublocs if( ($order == 0) || (! @sublocs) ); # sort those locations that are on the same sequence as the top (`master') # if the top seq is undefined, we take the first defined in a sublocation my $seqid = $self->seq_id(); my $i = 0; while((! defined($seqid)) && ($i <= $#sublocs)) { $seqid = $sublocs[$i++]->seq_id(); } if((! $self->seq_id()) && $seqid) { $self->warn("sorted sublocation array requested but ". "root location doesn't define seq_id ". "(at least one sublocation does!)"); } my @locs = ($seqid ? grep { $_->seq_id() eq $seqid; } @sublocs : @sublocs); if(@locs) { if($order == 1) { # Schwartzian transforms for performance boost @locs = map { $_->[0] } sort { (defined $a && defined $b) ? $a->[1] <=> $b->[1] : $a ? -1 : 1 } map { [$_, (defined $_->start ? $_->start : $_->end)] } @locs;; } else { # $order == -1 @locs = map { $_->[0]} sort { (defined $a && defined $b) ? $b->[1] <=> $a->[1] : $a ? -1 : 1 } map { [$_, (defined $_->end ? $_->end : $_->start)] } @locs; } } # push the rest unsorted if($seqid) { push(@locs, grep { $_->seq_id() ne $seqid; } @sublocs); } # done! return @locs; } =head2 add_sub_Location Title : add_sub_Location Usage : $splitloc->add_sub_Location(@locationIobjs); Function: add an additional sublocation Returns : number of current sub locations Args : list of Bio::LocationI implementing object(s) to add =cut sub add_sub_Location { my ($self,@args) = @_; my @locs; foreach my $loc ( @args ) { if( !ref($loc) || ! $loc->isa('Bio::LocationI') ) { $self->throw("Trying to add $loc as a sub Location but it doesn't implement Bio::LocationI!"); next; } push @{$self->{'_sublocations'}}, $loc; } return scalar @{$self->{'_sublocations'}}; } =head2 splittype Title : splittype Usage : $splittype = $location->splittype(); Function: get/set the split splittype Returns : the splittype of split feature (join, order) Args : splittype to set =cut sub splittype { my ($self, $value) = @_; if( defined $value || ! defined $self->{'_splittype'} ) { $value = 'JOIN' unless( defined $value ); $self->{'_splittype'} = uc ($value); } return $self->{'_splittype'}; } =head2 is_single_sequence Title : is_single_sequence Usage : if($splitloc->is_single_sequence()) { print "Location object $splitloc is split ". "but only across a single sequence\n"; } Function: Determine whether this location is split across a single or multiple sequences. This implementation ignores (sub-)locations that do not define seq_id(). The same holds true for the root location. Returns : TRUE if all sublocations lie on the same sequence as the root location (feature), and FALSE otherwise. Args : none =cut sub is_single_sequence { my ($self) = @_; my $seqid = $self->seq_id(); foreach my $loc ($self->sub_Location(0)) { $seqid = $loc->seq_id() if(! $seqid); if(defined($loc->seq_id()) && ($loc->seq_id() ne $seqid)) { return 0; } } return 1; } =head2 guide_strand Title : guide_strand Usage : $str = $loc->guide_strand(); Function: Get/Set the guide strand. Of use only if the split type is a 'join' (this helps determine the order of sublocation retrieval) Returns : value of guide strand (1, -1, or undef) Args : new value (-1 or 1, optional) =cut sub guide_strand { my $self = shift; return $self->{'strand'} = shift if @_; # Sublocations strand values consistency check to set Guide Strand my @subloc_strands; foreach my $loc ($self->sub_Location(0)) { push @subloc_strands, $loc->strand || 1; } if ($self->isa('Bio::Location::SplitLocationI')) { my $identical = 0; my $first_value = $subloc_strands[0]; foreach my $strand (@subloc_strands) { $identical++ if ($strand == $first_value); } if ($identical == scalar @subloc_strands) { $self->{'strand'} = $first_value; } else { $self->{'strand'} = undef; } } return $self->{'strand'}; } =head1 LocationI methods =head2 strand Title : strand Usage : $obj->strand($newval) Function: For SplitLocations, setting the strand of the container (this object) is a short-cut for setting the strand of all sublocations. In get-mode, checks if no sub-location is remote, and if all have the same strand. If so, it returns that shared strand value. Otherwise it returns undef. Example : Returns : on get, value of strand if identical between sublocations (-1, 1, or undef) Args : new value (-1 or 1, optional) =cut sub strand{ my ($self,$value) = @_; if( defined $value) { $self->{'strand'} = $value; # propagate to all sublocs foreach my $loc ($self->sub_Location(0)) { $loc->strand($value); } } else { my ($strand, $lstrand); foreach my $loc ($self->sub_Location(0)) { # we give up upon any location that doesn't have # the strand specified, or has a differing one set than # previously seen. # calling strand() is potentially expensive if the subloc # is also a split location, so we cache it $lstrand = $loc->strand(); if ( ! $lstrand or ($strand and ($strand != $lstrand)) ) { $strand = undef; last; } elsif (! $strand) { $strand = $lstrand; } } return $strand; } } =head2 flip_strand Title : flip_strand Usage : $location->flip_strand(); Function: Flip-flop a strand to the opposite. Also sets Split strand to be consistent with the sublocation strands (1, -1 or undef for mixed strand values) Returns : None Args : None =cut sub flip_strand { my $self = shift; my @sublocs; my @subloc_strands; for my $loc ( $self->sub_Location(0) ) { # Atomic "flip_strand" now initialize strand if necessary my $new_strand = $loc->flip_strand; # Store strand values for later consistency check push @sublocs, $loc; push @subloc_strands, $new_strand; } # Sublocations strand values consistency check to set Guide Strand if ($self->isa('Bio::Location::SplitLocationI')) { my $identical = 0; my $first_value = $subloc_strands[0]; foreach my $strand (@subloc_strands) { $identical++ if ($strand == $first_value); } if ($identical == scalar @subloc_strands) { $self->guide_strand($first_value); } else { # Mixed strand values, must reverse the sublocations order $self->guide_strand(undef); @{ $self->{_sublocations} } = reverse @sublocs; } } } =head2 start Title : start Usage : $start = $location->start(); Function: get the starting point of the first (sorted) sublocation Returns : integer Args : none =cut sub start { my ($self,$value) = @_; if( defined $value ) { $self->throw( "Trying to set the starting point of a split location, " . "that is not possible, try manipulating the sub Locations"); } return $self->SUPER::start(); } =head2 end Title : end Usage : $end = $location->end(); Function: get the ending point of the last (sorted) sublocation Returns : integer Args : none =cut sub end { my ($self,$value) = @_; if( defined $value ) { $self->throw( "Trying to set the ending point of a split location, " . "that is not possible, try manipulating the sub Locations"); } return $self->SUPER::end(); } =head2 min_start Title : min_start Usage : $min_start = $location->min_start(); Function: get the minimum starting point Returns : the minimum starting point from the contained sublocations Args : none =cut sub min_start { my ($self, $value) = @_; if( defined $value ) { $self->throw( "Trying to set the minimum starting point of a split " . "location, that is not possible, try manipulating the sub Locations"); } # No sort by default because it breaks circular cut by origin features # (like "join(2006035..2007700,1..257)"). Sorting is user responsability. # Assume Start to be 1st segment start and End to be last segment End. my @locs = $self->sub_Location(0); return ( @locs ) ? $locs[0]->min_start : undef; } =head2 max_start Title : max_start Usage : my $maxstart = $location->max_start(); Function: Get maximum starting location of feature startpoint Returns : integer or undef if no maximum starting point. Args : none =cut sub max_start { my ($self,$value) = @_; if( defined $value ) { $self->throw( "Trying to set the maximum starting point of a split " . "location, that is not possible, try manipulating the sub Locations"); } # No sort by default because it breaks circular cut by origin features # (like "join(2006035..2007700,1..257)"). Sorting is user responsability. # Assume Start to be 1st segment start and End to be last segment End. my @locs = $self->sub_Location(0); return ( @locs ) ? $locs[0]->max_start : undef; } =head2 start_pos_type Title : start_pos_type Usage : my $start_pos_type = $location->start_pos_type(); Function: Get start position type (ie <,>, ^) Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none =cut sub start_pos_type { my ($self,$value) = @_; if( defined $value ) { $self->throw( "Trying to set the start_pos_type of a split location, " . "that is not possible, try manipulating the sub Locations"); } # No sort by default because it breaks circular cut by origin features # (like "join(2006035..2007700,1..257)"). Sorting is user responsability. # Assume Start to be 1st segment start and End to be last segment End. my @locs = $self->sub_Location(0); return ( @locs ) ? $locs[0]->start_pos_type : undef; } =head2 min_end Title : min_end Usage : my $minend = $location->min_end(); Function: Get minimum ending location of feature endpoint Returns : integer or undef if no minimum ending point. Args : none =cut sub min_end { my ($self,$value) = @_; if( defined $value ) { $self->throw( "Trying to set the minimum end point of a split location, " . "that is not possible, try manipulating the sub Locations"); } # No sort by default because it breaks circular cut by origin features # (like "join(2006035..2007700,1..257)"). Sorting is user responsability. # Assume Start to be 1st segment start and End to be last segment End. my @locs = $self->sub_Location(0); # Return the End corresponding to the same sequence as the top ('master') # if the top seq is undefined, take the first defined in a sublocation. # Example: for "join(1..100,J00194.1:100..202)", End would be 100 my $seqid = $self->seq_id; my $i = 0; while (not defined $seqid and $i <= $#locs) { $seqid = $locs[$i++]->seq_id; } my @same_id_locs = ($seqid ? grep { $_->seq_id eq $seqid } @locs : @locs); # If there is a $seqid but no sublocations have the same id, # try with the first id found in the sublocations instead, # and if that fails return the last segment value if (@locs and not @same_id_locs) { my $first_id; while (not defined $first_id and $i <= $#locs) { $first_id = $locs[$i++]->seq_id; } @same_id_locs = ($first_id ? grep { $_->seq_id eq $first_id } @locs : @locs); } return ( @same_id_locs ) ? $same_id_locs[-1]->min_end : undef; } =head2 max_end Title : max_end Usage : my $maxend = $location->max_end(); Function: Get maximum ending location of feature endpoint Returns : integer or undef if no maximum ending point. Args : none =cut sub max_end { my ($self,$value) = @_; if( defined $value ) { $self->throw( "Trying to set the maximum end point of a split location, " ."that is not possible, try manipulating the sub Locations"); } # No sort by default because it breaks circular cut by origin features # (like "join(2006035..2007700,1..257)"). Sorting is user responsability. # Assume Start to be 1st segment start and End to be last segment End. my @locs = $self->sub_Location(0); # Return the End corresponding to the same sequence as the top ('master') # if the top seq is undefined, take the first defined in a sublocation. # Example: for "join(1..100,J00194.1:100..202)", End would be 100 my $seqid = $self->seq_id; my $i = 0; while (not defined $seqid and $i <= $#locs) { $seqid = $locs[$i++]->seq_id; } my @same_id_locs = ($seqid ? grep { $_->seq_id eq $seqid } @locs : @locs); # If there is a $seqid but no sublocations have the same id, # try with the first id found in the sublocations instead, # and if that fails return the last segment value if (@locs and not @same_id_locs) { my $first_id; while (not defined $first_id and $i <= $#locs) { $first_id = $locs[$i++]->seq_id; } @same_id_locs = ($first_id ? grep { $_->seq_id eq $first_id } @locs : @locs); } return ( @same_id_locs ) ? $same_id_locs[-1]->max_end : undef; } =head2 end_pos_type Title : end_pos_type Usage : my $end_pos_type = $location->end_pos_type(); Function: Get end position type (ie <,>, ^) Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none =cut sub end_pos_type { my ($self,$value) = @_; if( defined $value ) { $self->throw( "Trying to set end_pos_type of a split location, " . "that is not possible, try manipulating the sub Locations"); } # No sort by default because it breaks circular cut by origin features # (like "join(2006035..2007700,1..257)"). Sorting is user responsability. # Assume Start to be 1st segment start and End to be last segment End. my @locs = $self->sub_Location(0); # Return the End corresponding to the same sequence as the top ('master') # if the top seq is undefined, take the first defined in a sublocation. # Example: for "join(1..>100,J00194.1:100..202)", End pos type would be 'AFTER' my $seqid = $self->seq_id; my $i = 0; while (not defined $seqid and $i <= $#locs) { $seqid = $locs[$i++]->seq_id; } my @same_id_locs = ($seqid ? grep { $_->seq_id eq $seqid } @locs : @locs); # If there is a $seqid but no sublocations have the same id, # try with the first id found in the sublocations instead, # and if that fails return the last segment value if (@locs and not @same_id_locs) { my $first_id; while (not defined $first_id and $i <= $#locs) { $first_id = $locs[$i++]->seq_id; } @same_id_locs = ($first_id ? grep { $_->seq_id eq $first_id } @locs : @locs); } return ( @same_id_locs ) ? $same_id_locs[-1]->end_pos_type : undef; } =head2 length Title : length Usage : $len = $loc->length(); Function: get the length in the coordinate space this location spans Example : Returns : an integer Args : none =cut sub length { my ($self) = @_; my $length = 0; # Mixed strand values means transplicing (where exons can even # be in different chromosomes), so in that case only give the sum # of the lengths of the individual segments if (! defined $self->guide_strand) { for my $loc ( $self->sub_Location(0) ) { $length += abs($loc->end - $loc->start) + 1; } } else { my @sublocs = $self->sub_Location(0); my $start = $sublocs[0]->start; my $end = $sublocs[-1]->end; # If Start > ·End, its a possible case of cut by origin # location in circular sequences (e.g "join(16..20,1..2)") if ($start > $end) { # Figure out which segments are located before # and which are located after coordinate 1 # (END_SEQ - 1 - START_SEQ) my @end_seq_segments; my @start_seq_segments; my $switch = 0; foreach my $subloc (@sublocs) { if ($switch == 0) { if ($subloc->start == 1) { $switch = 1; push @start_seq_segments, $subloc; } else { push @end_seq_segments, $subloc; } } else { push @start_seq_segments, $subloc; } } # If its a cut by origin location, sum the whole length of each group if (scalar @end_seq_segments > 0 and @start_seq_segments > 0) { my $end_segments_length = abs( $end_seq_segments[0]->start - $end_seq_segments[-1]->end) + 1; my $start_segments_length = abs( $start_seq_segments[0]->start - $start_seq_segments[-1]->end) + 1; $length = $end_segments_length + $start_segments_length; } } else { $length = $end - $start + 1; } } # If for some reason nothing worked, fall back to previous behaviour if ($length == 0) { $length = abs($self->end - $self->start) + 1 } return $length; } =head2 seq_id Title : seq_id Usage : my $seqid = $location->seq_id(); Function: Get/Set seq_id that location refers to We override this here in order to propagate to all sublocations which are not remote (provided this root is not remote either) Returns : seq_id Args : [optional] seq_id value to set =cut sub seq_id { my $self = shift; if(@_ && !$self->is_remote()) { foreach my $subloc ($self->sub_Location(0)) { $subloc->seq_id(@_) if !$subloc->is_remote(); } } return $self->SUPER::seq_id(@_); } =head2 coordinate_policy Title : coordinate_policy Usage : $policy = $location->coordinate_policy(); $location->coordinate_policy($mypolicy); # set may not be possible Function: Get the coordinate computing policy employed by this object. See Bio::Location::CoordinatePolicyI for documentation about the policy object and its use. The interface *does not* require implementing classes to accept setting of a different policy. The implementation provided here does, however, allow one to do so. Implementors of this interface are expected to initialize every new instance with a CoordinatePolicyI object. The implementation provided here will return a default policy object if none has been set yet. To change this default policy object call this method as a class method with an appropriate argument. Note that in this case only subsequently created Location objects will be affected. Returns : A Bio::Location::CoordinatePolicyI implementing object. Args : On set, a Bio::Location::CoordinatePolicyI implementing object. =head2 to_FTstring Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none =cut sub to_FTstring { my ($self) = @_; my @strs; my $strand = $self->strand() || 0; my $stype = lc($self->splittype()); if( $strand < 0 ) { $self->flip_strand; # this will recursively set the strand # to +1 for all the sub locations } foreach my $loc ( $self->sub_Location(0) ) { $loc->verbose($self->verbose); my $str = $loc->to_FTstring(); # we only append the remote seq_id if it hasn't been done already # by the sub-location (which it should if it knows it's remote) # (and of course only if it's necessary) if( (! $loc->is_remote) && defined($self->seq_id) && defined($loc->seq_id) && ($loc->seq_id ne $self->seq_id) ) { $str = sprintf("%s:%s", $loc->seq_id, $str); } push @strs, $str; } $self->flip_strand if $strand < 0; my $str; if( @strs == 1 ) { ($str) = @strs; } elsif( @strs == 0 ) { $self->warn("no Sublocations for this splitloc, so not returning anything\n"); } else { $str = sprintf("%s(%s)",lc $self->splittype, join(",", @strs)); } if( $strand < 0 ) { # wrap this in a complement if it was unrolled $str = sprintf("%s(%s)",'complement',$str); } return $str; } =head2 valid_Location Title : valid_Location Usage : if ($location->valid_location) {...}; Function: boolean method to determine whether location is considered valid (has minimum requirements for Simple implementation) Returns : Boolean value: true if location is valid, false otherwise Args : none =cut # we'll probably need to override the RangeI methods since our locations will # not be contiguous. 1; BioPerl-1.007002/Bio/Location/SplitLocationI.pm000444000766000024 1510413155576320 21250 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Location::SplitLocationI # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Location::SplitLocationI - Abstract interface of a Location on a Sequence which has multiple locations (start/end points) =head1 SYNOPSIS # get a SplitLocationI somehow print $splitlocation->start, "..", $splitlocation->end, "\n"; my @sublocs = $splitlocation->sub_Location(); my $count = 1; # print the start/end points of the sub locations foreach my $location ( sort { $a->start <=> $b->start } @sublocs ) { printf "sub feature %d [%d..%d]\n", $location->start,$location->end; $count++; } =head1 DESCRIPTION This interface encapsulates the necessary methods for representing the location of a sequence feature that has more that just a single start/end pair. Some examples of this are the annotated exons in a gene or the annotated CDS in a sequence file. =head1 FEEDBACK User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Location::SplitLocationI; use strict; use Carp; use base qw(Bio::LocationI); =head2 sub_Location Title : sub_Location Usage : @locations = $feat->sub_Location(); Function: Returns an array of LocationI objects Returns : An array Args : none =cut sub sub_Location { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 splittype Title : splittype Usage : $splittype = $fuzzy->splittype(); Function: get/set the split splittype Returns : the splittype of split feature (join, order) Args : splittype to set =cut sub splittype { my($self) = @_; $self->throw_not_implemented(); } =head2 is_single_sequence Title : is_single_sequence Usage : if($splitloc->is_single_sequence()) { print "Location object $splitloc is split ". "but only across a single sequence\n"; } Function: Determine whether this location is split across a single or multiple sequences. Returns : TRUE if all sublocations lie on the same sequence as the root location (feature), and FALSE otherwise. Args : none =cut sub is_single_sequence { my ($self) = @_; $self->throw_not_implemented(); } =head1 Bio::LocationI methods Bio::LocationI inherited methods follow =head2 min_start Title : min_start Usage : my $minstart = $location->min_start(); Function: Get minimum starting location of feature startpoint Returns : integer or undef if no maximum starting point. Args : none =cut =head2 max_start Title : max_start Usage : my $maxstart = $location->max_start(); Function: Get maximum starting location of feature startpoint Returns : integer or undef if no maximum starting point. Args : none =cut =head2 start_pos_type Title : start_pos_type Usage : my $start_pos_type = $location->start_pos_type(); Function: Get start position type (ie <,>, ^) Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none =cut =head2 min_end Title : min_end Usage : my $minend = $location->min_end(); Function: Get minimum ending location of feature endpoint Returns : integer or undef if no minimum ending point. Args : none =cut =head2 max_end Title : max_end Usage : my $maxend = $location->max_end(); Function: Get maximum ending location of feature endpoint Returns : integer or undef if no maximum ending point. Args : none =cut =head2 end_pos_type Title : end_pos_type Usage : my $end_pos_type = $location->end_pos_type(); Function: Get end position type (ie <,>, ^) Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none =cut =head2 seq_id Title : seq_id Usage : my $seqid = $location->seq_id(); Function: Get/Set seq_id that location refers to Returns : seq_id Args : [optional] seq_id value to set =cut =head2 coordinate_policy Title : coordinate_policy Usage : $policy = $location->coordinate_policy(); $location->coordinate_policy($mypolicy); # set may not be possible Function: Get the coordinate computing policy employed by this object. See Bio::Location::CoordinatePolicyI for documentation about the policy object and its use. The interface *does not* require implementing classes to accept setting of a different policy. The implementation provided here does, however, allow one to do so. Implementors of this interface are expected to initialize every new instance with a CoordinatePolicyI object. The implementation provided here will return a default policy object if none has been set yet. To change this default policy object call this method as a class method with an appropriate argument. Note that in this case only subsequently created Location objects will be affected. Returns : A Bio::Location::CoordinatePolicyI implementing object. Args : On set, a Bio::Location::CoordinatePolicyI implementing object. =cut =head2 to_FTstring Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none =cut 1; BioPerl-1.007002/Bio/Location/WidestCoordPolicy.pm000444000766000024 724013155576320 21743 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Location::WidestCoordPolicy # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # and Jason Stajich # # Copyright Hilmar Lapp, Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Location::WidestCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range =head1 SYNOPSIS See Bio::Location::CoordinatePolicyI =head1 DESCRIPTION CoordinatePolicyI implementing objects are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked for it. This class will compute the coordinates such that always the widest possible range is returned, but by using some common sense. This means that e.g. locations like "E5..100" (start before position 5) will return 5 as start (returned values have to be positive integers). =head1 FEEDBACK User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp, Jason Stajich Email Ehlapp-at-gmx-dot-netE, Ejason-at-bioperl-dot-orgE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Location::WidestCoordPolicy; use strict; use base qw(Bio::Root::Root Bio::Location::CoordinatePolicyI); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); return $self; } =head2 start Title : start Usage : $start = $policy->start($location); Function: Get the integer-valued start coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object. =cut sub start { my ($self,$loc) = @_; # For performance reasons we don't check that it's indeed a Bio::LocationI # object. Hopefully, Location-object programmers are smart enough. my $pos = $loc->min_start(); # if min is not defined or equals 0 we resort to max $pos = $loc->max_start() if(! $pos); return $pos; } =head2 end Title : end Usage : $end = $policy->end($location); Function: Get the integer-valued end coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object. =cut sub end { my ($self,$loc) = @_; # For performance reasons we don't check that it's indeed a Bio::LocationI # object. Hopefully, Location-object programmers are smart enough. my $pos = $loc->max_end(); # if max is not defined or equals 0 we resort to min $pos = $loc->min_end() if(! $pos); return $pos; } 1; BioPerl-1.007002/Bio/Map000755000766000024 013155576320 14604 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Map/Clone.pm000444000766000024 2750413155576320 16367 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::clone # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Gaurav Gupta # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::Clone - An central map object representing a clone =head1 SYNOPSIS # get the clone object of $clone from the Bio::Map::Clone my $cloneobj = $physical->get_cloneobj($clone); # acquire all the markers that hit this clone foreach my $marker ($cloneobj->each_markerid()) { print " +++$marker\n"; } See L and L for more information. =head1 DESCRIPTION This object handles the notion of a clone. This clone will have a name and a position in a map. This object is intended to be used by a map parser like fpc.pm. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Gaurav Gupta Email gaurav@genome.arizona.edu =head1 CONTRIBUTORS Sendu Bala bix@sendu.me.uk =head1 PROJECT LEADERS Jamie Hatfield jamie@genome.arizona.edu Dr. Cari Soderlund cari@genome.arizona.edu =head1 PROJECT DESCRIPTION The project was done in Arizona Genomics Computational Laboratory (AGCoL) at University of Arizona. This work was funded by USDA-IFAFS grant #11180 titled "Web Resources for the Computation and Display of Physical Mapping Data". For more information on this project, please refer: http://www.genome.arizona.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::Clone; use strict; use Bio::Map::Position; use base qw(Bio::Root::Root Bio::Map::MappableI); =head2 new Title : new Usage : my $clone = Bio::Map::Clone->new ( -name => $clone, -markers => \@markers, -contig => $contig, -type => $type, -bands => $bands, -gel => $gel, -group => $group, -remark => $remark, -fpnumber=> $fp_number, -sequencetype => $seq_type, -sequencestatus=> $seq_status, -fpcremark => $fpc_remark, -matche => \@ematch, -matcha => \@amatch, -matchp => \@pmatch, -range => Bio::Range->new(-start => $startrange, -end => $endrange) ); Function: Initialize a new Bio::Map::Clone object Most people will not use this directly but get Clones through L Returns : L object Args : -name => marker name string, -markers => array ref of markers, -contig => contig name string, -type => type string, -bands => band string, -gel => gel string, -group => group name string, -remark => remark string, -fpnumber=> FP number string, -sequencetype => seq type string, -sequencestatus=> seq status string, -fpcremark => FPC remark, -matche => array ref, -matcha => array ref, -matchp => array ref, -range => L object, =cut sub new { my ($class,@args) = @_; my $self= $class->SUPER::new(@args); my ($name,$markers,$contig,$type,$bands,$gel,$group, $remark,$fpnumber,$seqtype,$seqstatus,$fpcremark, $matche,$matcha,$matchp, $range) = $self->_rearrange([qw(NAME MARKERS CONTIG TYPE BANDS GEL GROUP REMARK FPNUMBER SEQUENCETYPE SEQUENCESTATUS FPCREMARK MATCHE MATCHA MATCHP RANGE)],@args); $self->name($name) if defined $name; $self->markers($markers) if defined $markers; $self->contigid($contig) if defined $contig; $self->type($type) if defined $type; $self->bands($bands) if defined $bands; $self->gel($gel) if defined $gel; $self->group($group) if defined $group; $self->remark($remark) if defined $remark; $self->fp_number($fpnumber) if defined $fpnumber; $self->sequence_type($seqtype) if defined $seqtype; $self->sequence_status($seqstatus) if defined $seqstatus; $self->fpc_remark($fpcremark) if defined $fpcremark; $self->range($range) if defined $range; $self->set_match('approx', $matcha) if defined $matcha; $self->set_match('pseudo', $matchp) if defined $matchp; $self->set_match('exact', $matche) if defined $matche; return $self; } =head1 Access Methods These methods let you get and set the member variables =head2 name Title : name Usage : my $name = $cloneobj->name(); Function: Get/set the name for this Clone Returns : scalar representing the current name of this clone Args : none to get, OR string to set =cut sub name { my ($self) = shift; return $self->{'_name'} = shift if @_; return $self->{'_name'}; } =head2 type Title : type Usage : my $type = $cloneobj->type(); Function: Get/set the type for this clone Returns : scalar representing the current type of this clone Args : none to get, OR string to set =cut sub type { my ($self) = shift; return $self->{'_type'} = shift if @_; return $self->{'_type'}; } =head2 range Title : range Usage : my $range = $cloneobj->range(); Function: Get/set the range of the contig that this clone covers Returns : Bio::Range representing the current range of this contig, start and end of the contig can be thus found using: my $start = $contigobj->range()->start(); my $end = $contigobj->range()->end(); Args : none to get, OR Bio::Range to set =cut sub range { my ($self) = shift; return $self->{'_range'} = shift if @_; return $self->{'_range'}; } =head2 match Title : match Usage : @eclone = $cloneobj->match('exact'); @aclone = $cloneobj->match('approximate'); @pclone = $cloneobj->match('pseudo'); Function: get all matching clones Returns : list Args : scalar representing the type of clone to be queried. =cut sub match { my ($self,$type) = @_; $type = "_match" . lc(substr($type, 0, 1)); return @{$self->{$type} || []}; } =head2 each_match Title : each_match Function: Synonym of the match() method. =cut *each_match = \&match; =head2 set_match Title : set_match Usage : $clone->set_match($type,$values); Function: Set the Matches per type Returns : None Args : type (one of 'exact' 'approx' 'pseudo') array ref of match values =cut sub set_match{ my ($self,$type,$val) = @_; $type = "_match" . lc(substr($type, 0, 1)); $self->{$type} = $val; } =head2 gel Title : gel Usage : $clonegel = $cloneobj->gel(); Function: Get/set the gel number for this clone Returns : scalar representing the gel number of this clone Args : none to get, OR string to set =cut sub gel { my ($self) = shift; return $self->{'_gel'} = shift if @_; return $self->{'_gel'}; } =head2 remark Title : remark Usage : $cloneremark = $cloneobj->remark(); Function: Get/set the remark for this clone Returns : scalar representing the current remark of this clone Args : none to get, OR string to set =cut sub remark { my ($self) = shift; return $self->{'_remark'} = shift if @_; return $self->{'_remark'}; } =head2 fp_number Title : fp_number Usage : $clonefpnumber = $cloneobj->fp_number(); Function: Get/set the fp number for this clone Returns : scalar representing the fp number of this clone Args : none to get, OR string to set =cut sub fp_number { my ($self) = shift; return $self->{'_fpnumber'} = shift if @_; return $self->{'_fpnumber'}; } =head2 sequence_type Title : sequence_type Usage : $cloneseqtype = $cloneobj->sequence_type(); Function: Get/set the sequence type for this clone Returns : scalar representing the sequence type of this clone Args : none to get, OR string to set =cut sub sequence_type { my ($self) = shift; return $self->{'_sequencetype'} = shift if @_; return $self->{'_sequencetype'}; } =head2 sequence_status Title : sequence_status Usage : $cloneseqstatus = $cloneobj->sequence_status(); Function: Get/set the sequence status for this clone Returns : scalar representing the sequence status of this clone Args : none to get, OR string to set =cut sub sequence_status { my ($self) = shift; return $self->{'_sequencestatus'} = shift if @_; return $self->{'_sequencestatus'}; } =head2 fpc_remark Title : fpc_remark Usage : $clonefpcremark = $cloneobj->fpc_remark(); Function: Get/set the fpc remark for this clone Returns : scalar representing the fpc remark of this clone Args : none to get, OR string to set =cut sub fpc_remark { my ($self) = shift; return $self->{'_fpcremark'} = shift if @_; return $self->{'_fpcremark'}; } =head2 bands Title : bands Usage : @clonebands = $cloneobj->bands(); Function: Get/set the bands for this clone Returns : liat representing the band of this clone, if readcor = 1 while creating the MapIO object and the .cor exists Args : none to get, OR string to set =cut sub bands { my ($self) = shift; return $self->{'_bands'} = shift if @_; return $self->{'_bands'}; } =head2 group Title : group Usage : $cloneobj->group($chrno); Function: Get/set the group number for this clone. This is a generic term, used for Linkage-Groups as well as for Chromosomes. Returns : scalar representing the group number of this clone Args : none to get, OR string to set =cut sub group { my ($self) = shift; return $self->{'_group'} = shift if @_; return $self->{'_group'}; } =head2 contigid Title : contigid Usage : my $ctg = $cloneobj->contigid(); Function: Get/set the contig this clone belongs to Returns : scalar representing the contig Args : none to get, OR string to set =cut sub contigid { my ($self) = shift; $self->{'_contig'} = shift if @_; return $self->{'_contig'} || 0; } =head2 each_markerid Title : each_markerid Usage : @markers = $cloneobj->each_markerid(); Function: retrieves all the elements in a map unordered Returns : list of strings (ids) Args : none *** This only supplies the ids set with the set_markers method *** *** It has nothing to do with actual Bio::Map::MarkerI objects *** =cut sub each_markerid { my ($self,$value) = @_; return @{$self->{"_markers"}}; } =head2 set_markers Title : markers Usage : $obj->set_markers($newval) Function: Set list of Marker ids (arrayref) Returns : None Args : arrayref of strings (ids) *** This only sets a list of ids *** *** It has nothing to do with actual Bio::Map::MarkerI objects *** =cut sub set_markers { my ($self,$markers) = @_; if( defined $markers && ref($markers) =~ /ARRAY/ ) { $self->{'_markers'} = $markers; } } 1; BioPerl-1.007002/Bio/Map/Contig.pm000555000766000024 2543113155576320 16552 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::Contig # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Gaurav Gupta # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::Contig - A MapI implementation handling the contigs of a Physical Map (such as FPC) =head1 SYNOPSIS # get the contig object of $contig from the Bio::Map::Physical my $ctgobj = $physical->get_contigobj($contig); # acquire all the markers that lie in this contig foreach my $marker ($ctgobj->each_markerid()) { print " +++$marker\n"; } # find the group of this contig print "Group: ",$ctgobj->group(),"\n"; # find the range of this contig print "RANGE: start:",$ctgobj->range()->start(),"\tend: ", $ctgobj->range()->end(),"\n"; # find the position of this contig in $group (chromosome) print "Position in Group $group"," = ",$ctgobj->position($group),"\n"; =head1 DESCRIPTION This is an implementation of Bio::Map::MapI. It handles the essential storage of name, species, type, and units as well as in memory representation of the elements of a map. Bio::Map::Contig has been tailored to work for FPC physical maps, but could probably be used for others as well (with the appropriate MapIO module). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Gaurav Gupta Email gaurav@genome.arizona.edu =head1 CONTRIBUTORS Sendu Bala bix@sendu.me.uk =head1 PROJECT LEADERS Jamie Hatfield jamie@genome.arizona.edu Dr. Cari Soderlund cari@genome.arizona.edu =head1 PROJECT DESCRIPTION The project was done in Arizona Genomics Computational Laboratory (AGCoL) at University of Arizona. This work was funded by USDA-IFAFS grant #11180 titled "Web Resources for the Computation and Display of Physical Mapping Data". For more information on this project, please refer: http://www.genome.arizona.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::Contig; use vars qw($MAPCOUNT); use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Range; use base qw(Bio::Map::SimpleMap); BEGIN { $MAPCOUNT = 1; } =head2 new Title : new Usage : my $clone = Bio::Map::Contig->new ( -name => $name, -chr_remark => $cremark, -user_remark => $uremark, -trace_remark => $tremark, -group => $group, -subgroup=> $subgroup, -anchor => $anchor, -markers => \%markers, -clones => \%clones, -position => $pos -range => Bio::Range->new(-start =>$s,-end=>$e), ); Function: Initialize a new Bio::Map::Contig object Most people will not use this directly but get Markers through L Returns : L object Args : ( -name => name string, -chr_remark => chr remark string, -user_remark => userremark string, -trace_remark => tremark string, -group => group string, -subgroup=> subgroup string, -anchor => boolean if this is anchored or not, -markers => hashref of contained markers, -clones => hashref of contained clones, -position => position -range => L =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($name,$cremark,$uremark,$tremark, $group,$subgroup, $anchor,$markers, $clones, $position,$range) = $self->_rearrange([qw(NAME CHR_REMARK USER_REMARK TRACE_REMARK GROUP SUBGROUP ANCHOR MARKERS CLONES POSITION RANGE)],@args); $self->name($name) if defined $name; $self->chr_remark($cremark) if defined $cremark; $self->user_remark($uremark) if defined $uremark; $self->trace_remark($tremark) if defined $tremark; $self->group($group) if defined $group; $self->subgroup($group) if defined $subgroup; $self->anchor($anchor) if defined $anchor; $self->set_markers($markers) if defined $markers; $self->set_clones($clones) if defined $clones; $self->range($range) if defined $range; $self->position($position) if defined $position; return $self; } =head2 Modifier methods All methods present in L are implemented by this class. Most of the methods are inherited from SimpleMap. The following methods have been modified to reflect the needs of physical maps. =head2 chr_remark Title : chr_remark Usage : my $chrremark = $contigobj->chr_remark(); Function: Get/set the group remark for this contig Returns : scalar representing the current group_remark of this contig Args : none to get, OR string to set =cut sub chr_remark { my ($self) = shift; $self->{'_cremark'} = shift if @_; return defined $self->{'_cremark'} ? $self->{'_cremark'} : ''; } =head2 user_remark Title : user_remark Usage : my $userremark = $contigobj->user_remark(); Function: Get/set the user remark for this contig Returns : scalar representing the current user_remark of this contig Args : none to get, OR string to set =cut sub user_remark { my ($self) = shift; $self->{'_uremark'} = shift if @_; return defined $self->{'_uremark'} ? $self->{'_uremark'} : ''; } =head2 trace_remark Title : trace_remark Usage : my $traceremark = $contigobj->trace_remark(); Function: Get/set the trace remark for this contig Returns : scalar representing the current trace_remark of this contig Args : none to get, OR string to set =cut sub trace_remark { my ($self) = shift; $self->{'_tremark'} = shift if @_; return defined $self->{'_tremark'} ? $self->{'_tremark'} : ''; } =head2 range Title : range Usage : my $range = $contigobj->range(); Function: Get/set the range for this Contig Returns : Bio::Range representing the current range of this contig, start and end of the contig can be thus found using: my $start = $contigobj->range()->start(); my $end = $contigobj->range()->end(); Args : none to get, OR Bio::Range to set =cut sub range { my ($self) = shift; return $self->{'_range'} = shift if @_; return $self->{'_range'}; } =head2 position Title : position Usage : $ctgpos = $contigobj->position(); Function: Get/set the position of the contig in the group Returns : scalar representing the position of the contig in the group Args : none to get, OR string to set =cut sub position { my ($self) = shift; $self->{'_position'} = shift if @_; return $self->{'_position'} || 0; } =head2 anchor Title : anchor Usage : $ctganchor = $contig->anchor(); Function: Get/set the anchor value for this Contig (True | False) Returns : scalar representing the anchor (1 | 0) for this contig Args : none to get, OR string to set =cut sub anchor { my ($self) = shift; return $self->{'_anchor'} = shift if @_; return $self->{'_anchor'}; } =head2 group Title : group Usage : $groupno = $contigobj->group(); Function: Get/set the group number for this contig. This is a generic term, used for Linkage-Groups as well as for Chromosomes. Returns : scalar representing the group number of this contig Args : none =cut sub group { my ($self) = shift; $self->{'_group'} = shift if @_; return $self->{'_group'} || 0; } =head2 subgroup Title : subgroup Usage : $subgroup = $contig->subgroup(); Function: Get/set the subgroup for this contig. This is a generic term: subgroup here could represent subgroup of a Chromosome or of a Linkage Group. The user must take care of which subgroup he/she is querying for. Returns : A scalar representing the subgroup of this contig Args : none =cut sub subgroup { my ($self) = @_; return $self->{'_subgroup'} = shift if @_; return $self->{'_subgroup'} || 0; } =head2 each_cloneid Title : each_cloneid Usage : my @clones = $map->each_cloneid(); Function: retrieves all the clone ids in a map unordered Returns : list of strings (ids) Args : none *** This only supplies the ids set with the set_clones method *** *** It has nothing to do with actual Bio::Map::MappableI objects *** =cut sub each_cloneid { my ($self) = @_; return $self->_each_element('clones'); } =head2 each_markerid Title : each_markerid Usage : my @markers = $map->each_markerid(); Function: retrieves all the marker ids in a map unordered Returns : list of strings (ids) Args : none *** This only supplies the ids set with the set_markers method *** *** It has nothing to do with actual Bio::Map::MarkerI objects *** =cut sub each_markerid { my ($self) = @_; return $self->_each_element('markers'); } sub _each_element { my ($self, $type) = @_; $type = 'clones' if (!defined($type)); $type = lc("_$type"); return keys %{$self->{$type} || {}}; } =head2 set_clones Title : set_clones Usage : $marker->set_clones(\%clones) Function: Set the clones hashref Returns : None Args : Hashref of clone ids *** This only sets a hash of ids *** *** It has nothing to do with actual Bio::Map::MappableI objects *** =cut sub set_clones { my ($self,$clones) = @_; if( defined $clones && ref($clones) =~ /HASH/ ) { $self->{'_clones'} = $clones; } } =head2 set_markers Title : markers Usage : $obj->set_markers($newval) Function: Set list of Markers (hashref) Returns : None Args : Hashref of marker ids *** This only sets a hash of ids *** *** It has nothing to do with actual Bio::Map::MarkerI objects *** =cut sub set_markers { my ($self,$markers) = @_; if( defined $markers && ref($markers) =~ /HASH/ ) { $self->{'_markers'} = $markers; } } 1;BioPerl-1.007002/Bio/Map/CytoMap.pm000444000766000024 671213155576320 16661 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::CytoMap # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands =head1 SYNOPSIS use Bio::Map::CytoMap; my $map = Bio::Map::CytoMap->new(-name => 'human1', -species => $human); foreach my $marker ( @markers ) { # get a list of markers somewhere $map->add_element($marker); } =head1 DESCRIPTION This is the simple implementation of cytogenetic maps based on L. It handles the essential storage of name, species, type, and units as well as in memory representation of the elements of a map. For CytoMaps type is hard coded to be 'cytogeneticmap' and units are set to '' but can be set to something else. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email heikki-at-bioperl-dot-org =head1 CONTRIBUTORS Jason Stajich jason@bioperl.org Lincoln Stein lstein@cshl.org Sendu Bala bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Map::CytoMap; use vars qw($MAPCOUNT); use strict; use base qw(Bio::Map::SimpleMap); BEGIN { $MAPCOUNT = 1; } =head2 new Title : new Usage : my $obj = Bio::Map::CytoMap->new(); Function: Builds a new Bio::Map::CytoMap object Returns : Bio::Map::CytoMap Args : -name => name of map (string) -species => species for this map (Bio::Species) [optional] -elements=> elements to initialize with (arrayref of Bio::Map::MappableI objects) [optional] -uid => Unique Id =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->{'_uid'} = $MAPCOUNT++; my ($uid) = $self->_rearrange([qw(UID)], @args); defined $uid && $self->unique_id($uid); return $self; } =head2 type Title : type Usage : my $type = $map->type Function: Get hard-coded Map type Returns : String coding Map type (always 'cyto') Args : none =cut sub type { return 'cyto'; } =head2 length Title : length Usage : my $length = $map->length(); Function: Retrieves the length of the map, Returns : 0 since length is not calculatable for cytogenetic maps Args : none =cut sub length { return 0; } 1; BioPerl-1.007002/Bio/Map/CytoMarker.pm000444000766000024 722613155576320 17366 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::CytoMarker # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::CytoMarker - An object representing a marker. =head1 SYNOPSIS $o_usat = Bio::Map::CytoMarker->new(-name=>'Chad Super Marker 2', -position => $pos); =head1 DESCRIPTION This object handles markers with a position in a cytogenetic map known. This marker will have a name and a position. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email heikki-at-bioperl-dot-org =head1 CONTRIBUTORS Chad Matsalla bioinformatics1@dieselwurks.com Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org Sendu Bala bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::CytoMarker; use strict; use Bio::Map::CytoPosition; use base qw(Bio::Map::Marker); =head2 Bio::Map::MarkerI methods =cut =head2 get_position_object Title : get_position_class Usage : my $position = $marker->get_position_object(); Function: To get an object of the default Position class for this Marker. Subclasses should redefine this method. The Position returned needs to be a L with -element set to self. Returns : L Args : none for an 'empty' PositionI object, optionally Bio::Map::MapI and value string to set the Position's -map and -value attributes. =cut sub get_position_object { my ($self, $map, $value) = @_; $map ||= $self->default_map; if ($value) { $self->throw("Value better be scalar, not [$value]") unless ref($value) eq ''; } my $pos = Bio::Map::CytoPosition->new(); $pos->map($map) if $map; $pos->value($value) if $value; $pos->element($self); return $pos; } =head2 Comparison methods The numeric values for cutogeneic loctions go from the p tip of chromosome 1, down to the q tip and similarly throgh consecutive chromosomes, through X and end the the q tip of X. See L for more details. =cut =head2 New methods =cut =head2 get_chr Title : get_chr Usage : my $mychr = $marker->get_chr(); Function: Read only method for the chromosome string of the location. A shortcut to $marker->position->chr(). Returns : chromosome value Args : [optional] new chromosome value =cut sub get_chr { my ($self) = @_; return unless $self->position; return $self->position->chr; } 1; BioPerl-1.007002/Bio/Map/CytoPosition.pm000444000766000024 3651613155576320 17775 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::CytoPosition # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::CytoPosition - Marker class with cytogenetic band storing attributes =head1 SYNOPSIS $m1 = Bio::Map::CytoPosition->new ( '-id' => 'A1', '-value' => '2q1-3' ); $m2 = Bio::Map::CytoPosition->new ( '-id' => 'A2', '-value' => '2q2' ); if ($m1->cytorange->overlaps($m2->cytorange)) { print "Makers overlap\n"; } =head1 DESCRIPTION CytoPosition is marker (Bio::Map::MarkerI compliant) with a location in a cytogenetic map. See L for more information. Cytogenetic locations are names of bands visible in stained mitotic eucaryotic chromosomes. The naming follows strict rules which are consistent at least in higher vertebates, e.g. mammals. The chromosome name preceds the band names. The shorter arm of the chromosome is called 'p' ('petit') and usually drawn pointing up. The lower arm is called 'q' ('queue'). The bands are named from the region separating these, a centromere (cen), towards the tips or telomeric regions (ter) counting from 1 upwards. Depending of the resolution used the bands are identified with one or more digit. The first digit determines the major band and subsequent digits sub bands: p1 band can be divided into subbands p11, p12 and 13 and p11 can furter be divided into subbands p11.1 and p11.2. The dot after second digit makes it easier to read the values. A region between ands is given from the centromere outwards towards the telomere (e.g. 2p2-5 or 3p21-35) or from a band in the p arm to a band in the q arm. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 CONTRIBUTORS Sendu Bala bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::CytoPosition; use strict; use integer; use Bio::Range; use base qw(Bio::Map::Position); =head2 cytorange Title : cytorange Usage : my $range = $obj->cytorange(); Function: Converts cytogenetic location set by value method into an integer range. The chromosome number determines the "millions" in the values. Human X and Y chromosome symbols are represented by values 100 and 101. The localization within chromosomes are converted into values between the range of 0 and 200,000: pter cen qter |------------------------|-------------------------| 0 100,000 200,000 The values between -100,000 through 0 for centromere to 100,000 would have reflected the band numbering better but use of positive integers was chosen since the transformation is very easy. These values are not metric. Each band defines a range in a chromosome. A band string is converted into a range by padding it with lower and and higher end digits (for q arm: '0' and '9') to the length of five. The arm and chromosome values are added to these: e.g. 21000 & 21999 (band 21) + 100,000 (q arm) + 2,000,000 (chromosome 2) => 2q21 : 2,121,000 .. 2,121,999. Note that this notation breaks down if there is a band or a subband using digit 9 in its name! This is not the case in human karyotype. The full algorithm used for bands: if arm is 'q' then pad char for start is '0', for end '9' range is chromosome + 100,000 + padded range start or end elsif arm is 'p' then pad char for start is '9', for end '0' range is chromosome + 100,000 - padded range start or end Returns : Bio::Range object or undef Args : none =cut sub cytorange { my ($self) = @_; my ($chr, $r, $band, $band2, $arm, $arm2, $lc, $uc, $lcchar, $ucchar); return $r if not defined $self->{_value}; # returns undef $self->{_value} =~ # -----1----- --------2--------- -----3----- -------4------- ---6--- m/([XY]|[0-9]+)(cen|qcen|pcen|[pq])?(ter|[.0-9]+)?-?([pq]?(cen|ter)?)?([.0-9]+)?/; $self->warn("Not a valid value: ". $self->{_value}), return $r if not defined $1 ; # returns undef $chr = uc $1; $self->chr($chr); $chr = 100 if $chr eq 'X'; $chr = 101 if $chr eq 'Y'; $chr *= 1000000; $r = Bio::Range->new(); $band = ''; if (defined $3 ) { $2 || $self->throw("$& does not make sense: 'arm' or 'cen' missing"); $band = $3; $band =~ tr/\.//d; } if (defined $6 ) { $arm2 = $4; $arm2 = $2 if $4 eq ''; # it is not necessary to repeat the arm [p|q] $band2 = $6; $band2 =~ tr/\.//d; #find the correct order #print STDERR "-|$&|----2|$2|-----3|$band|---4|$4|--------arm2|$arm2|-------------\n"; if ($band ne '' and (defined $arm2 and $2 ne $arm2 and $arm2 eq 'q') ) { $lc = 'start'; $lcchar = '9'; $uc = 'end'; $ucchar = '9'; } elsif ($band ne 'ter' and $2 ne $arm2 and $arm2 eq 'p') { $lc = 'end'; $lcchar = '9'; $uc = 'start'; $ucchar = '9'; } elsif ($band eq 'ter' and $arm2 eq 'p') { $uc = 'start'; $ucchar = '9'; } # $2 eq $arm2 elsif ($arm2 eq 'q') { if (_pad($band, 5, '0') < _pad($band2, 5, '0')) { $lc = 'start'; $lcchar = '0'; $uc = 'end'; $ucchar = '9'; } else { $lc = 'end'; $lcchar = '9'; $uc = 'start'; $ucchar = '0'; } } elsif ($arm2 eq 'p') { if (_pad($band, 5, '0') < _pad($band2, 5, '0')) { $lc = 'end'; $lcchar = '0'; $uc = 'start'; $ucchar = '9'; } else { $lc = 'start'; $lcchar = '9'; $uc = 'end'; $ucchar = '0'; } } else { $self->throw("How did you end up here? $&"); } #print STDERR "-------$arm2--------$band2---------$ucchar--------------\n"; if ( (defined $arm2 and $arm2 eq 'p') or (defined $arm2 and $arm2 eq 'p') ) { $r->$uc(-(_pad($band2, 5, $ucchar)) + 100000 + $chr ); if (defined $3 and $3 eq 'ter') { $r->end(200000 + $chr); } elsif ($2 eq 'cen' or $2 eq 'qcen' or $2 eq 'pcen'){ $r->$lc(100000 + $chr); } elsif ($2 eq 'q') { $r->$lc(_pad($band, 5, $lcchar) + 100000 + $chr ); } else { $r->$lc(-(_pad($band, 5, $lcchar)) + 100000 + $chr ); } } else { #if:$arm2=q e.g. 9p22-q32 #print STDERR "-------$arm2--------$band2---------$ucchar--------------\n"; $r->$uc(_pad($band2, 5, $ucchar) + 100000 + $chr); if ($2 eq 'cen' or $2 eq 'pcen') { $r->$lc(100000 + $chr); } elsif ($2 eq 'p') { if ($3 eq 'ter') { $r->$lc(200000 + $chr); } else { $r->$lc(-(_pad($band, 5, $lcchar)) + 100000 + $chr); } } else { #$2.==q $r->$lc(_pad($band, 5, $lcchar) + 100000 + $chr); } } } # # e.g. 10p22.1-cen # elsif (defined $4 and $4 ne '') { #print STDERR "$4-----$&----\n"; if ($4 eq 'cen' || $4 eq 'qcen' || $4 eq 'pcen') { # e.g. 10p22.1-cen; # '10pcen-qter' does not really make sense but lets have it in anyway $r->end(100000 + $chr); if ($2 eq 'p') { if ($3 eq 'ter') { $r->start($chr); } else { $r->start(_pad($band, 5, '9') + $chr); } } elsif ($2 eq 'cen') { $self->throw("'cen-cen' does not make sense: $&"); } else { $self->throw("Only order p-cen is valid: $&"); } } elsif ($4 eq 'qter' || $4 eq 'ter') { # e.g. 10p22.1-qter, 1p21-qter, 10pcen-qter, 7q34-qter $r->end(200000 + $chr); if ($2 eq 'p'){ $r->start(-(_pad($band, 5, '9')) + 100000 + $chr); #??? OK? } elsif ($2 eq 'q') { $r->start(_pad($band, 5, '0') + 100000 + $chr); } elsif ($2 eq 'cen' || $2 eq 'qcen' || $2 eq 'pcen' ) { $r->start(100000 + $chr); } } elsif ($4 eq 'pter' ) { #print STDERR "$2,$3--$4-----$&----\n"; $r->start( $chr); if ($2 eq 'p'){ $r->end(-(_pad($band, 5, '0')) + 100000 + $chr); } elsif ($2 eq 'q') { $r->end(_pad($band, 5, '9') + 100000 + $chr); } elsif ($2 eq 'cen' || $2 eq 'qcen' || $2 eq 'pcen' ) { $r->end(100000 + $chr); } } else { # -p or -q at the end of the range $self->throw("lone '$4' in $& does not make sense"); } } # # e.g 10p22.1, 10pter # elsif (defined $3 ) { if ($2 eq 'p') { if ($3 eq 'ter') { # e.g. 10pter $r = Bio::Range->new('-start' => $chr, '-end' => $chr, ); } else { # e.g 10p22.1 $r = Bio::Range->new('-start' => -(_pad($band, 5, '9')) + 100000 + $chr, '-end' => -(_pad($band, 5, '0')) + 100000 + $chr, ); } } elsif ($2 eq 'q') { if ($3 eq 'ter') { # e.g. 10qter $r = Bio::Range->new('-start' => 200000 + $chr, '-end' => 200000 + $chr, ); } else { # e.g 10q22.1 $r = Bio::Range->new('-start' => _pad($band, 5, '0') + 100000 + $chr, '-end' => _pad($band, 5, '9') + 100000 + $chr, ); } } else { # e.g. 10qcen1.1 ! $self->throw("'cen' in $& does not make sense"); } } # # e.g. 10p # elsif (defined $2 ) { # e.g. 10p if ($2 eq 'p' ) { $r = Bio::Range->new('-start' => $chr, '-end' => 100000 + $chr ); } elsif ($2 eq 'q' ) { $r = Bio::Range->new('-start' => 100000 + $chr, '-end' => 200000 + $chr ); } else { # $2 eq 'cen' || 'qcen' $r = Bio::Range->new('-start' => 100000 + $chr, '-end' => 100000 + $chr ); } } # # chr only, e.g. X # else { $r = Bio::Range->new('-start' => $chr, '-end' => 200000 + $chr ); } if ($r) { $self->start($r->start); $self->end($r->end); } return $r; } sub _pad { my ($string, $len, $pad_char) = @_; __PACKAGE__->throw("function _pad needs a positive integer length, not [$len]") unless $len =~ /^\+?\d+$/; __PACKAGE__->throw("function _pad needs a single character pad_char, not [$pad_char]") unless length $pad_char == 1; $string ||= ''; return $string . $pad_char x ( $len - length( $string ) ); } =head2 range2value Title : range2value Usage : my $value = $obj->range2value($range); Function: Sets and returns the value string based on start and end values of the Bio::Range object passes as an argument. Returns : string or false Args : Bio::Range object =cut sub range2value { my ($self,$value) = @_; if( defined $value) { if( ! $value->isa('Bio::Range') ) { $self->throw("Is not a Bio::Range object but a [$value]"); return; } if( ! $value->start ) { $self->throw("Start is not defined in [$value]"); return; } if( ! $value->end ) { $self->throw("End is not defined in [$value]"); return; } if( $value->start < 100000 ) { $self->throw("Start value has to be in millions, not ". $value->start); return; } if( $value->end < 100000 ) { $self->throw("End value has to be in millions, not ". $value->end); return; } my ($chr, $arm, $band) = $value->start =~ /(\d+)(\d)(\d{5})/; my ($chr2, $arm2, $band2) = $value->end =~ /(\d+)(\d)(\d{5})/; my ($chrS, $armS, $bandS, $arm2S, $band2S, $sep) = ('', '', '', '', '', '' ); LOC: { # # chromosome # if ($chr == 100) { $chrS = 'X'; } elsif ($chr == 100) { $chrS = 'Y'; } else { $chrS = $chr; } last LOC if $arm == 0 and $arm2 == 2 and $band == 0 and $band2 == 0 ; # # arm # if ($arm == $arm2 ) { if ($arm == 0) { $armS = 'p'; #$armS = 'pter' if $band == 0 and $band2 == 0; $bandS = 'ter' if $band == 0; #$arm2S = 'p'; #? } elsif ($arm == 2) { $armS = 'q'; $bandS = 'ter' if $band == 0; } else { $armS = 'q'; #$arm2S = 'q'; #? $armS = 'cen', if $band == 0;# and $band2 == 0; } } else { if ($arm == 0) { $armS = 'p'; $arm2S = 'q'; $arm2S = '' if $band == 0 and $band2 == 0; } else { $armS = 'q'; $arm2S = 'p'; $arm2S = '' if $arm2 == 2 and $band == 0 and $band2 == 0; } } last LOC if $band == $band2 ; my $c; # # first band (ter is hadled with the arm) # if ($bandS ne 'ter') { if ($armS eq 'p') { $band = 100000 - $band; $c = '9'; } else { $c = '0'; } $band =~ s/$c+$//; $bandS = $band; $bandS = substr($band, 0, 2). '.'. substr($band, 2) if length $band > 2; } last LOC unless $band2; # # second band # if ($arm2 == 0) { $arm2S = 'p'; $band2 = 100000 - $band2; $c = '0'; } else { # 1 or 2 $arm2S = 'q'; $c = '9'; } if ($band2 == 0) { if ($arm2 == 1) { $arm2S = 'p'; $band2S = 'cen'; } else { $band2S = 'ter'; } last LOC; } last LOC if $band eq $band2 and $arm == $arm2; $band2 =~ s/$c+$//; $band2S = $band2; $band2S = substr($band2, 0, 2). '.'. substr($band2, 2) if length $band2 > 2; } # end of LOC: if ($armS eq 'p' and $arm2S eq 'p') { my $tmp = $band2S; $band2S = $bandS; $bandS = $tmp; } $band2S = '' if $bandS eq $band2S ; $armS = '' if $bandS eq 'cen'; $arm2S = '' if $armS eq $arm2S and $band2S ne 'ter'; $sep = '-' if $arm2S || $band2S; $self->value( $chrS. $armS. $bandS. $sep. $arm2S. $band2S); } return $self->value; } =head2 value Title : value Usage : my $pos = $position->value; Function: Get/Set the value for this position Returns : scalar, value Args : none to get, OR scalar to set =cut sub value { my ($self,$value) = @_; if( defined $value ) { $self->{'_value'} = $value; $self->cytorange; } return $self->{'_value'}; } =head2 numeric Title : numeric Usage : my $num = $position->numeric; Function: Read-only method that is guarantied to return a numeric representation of the start of this position. Returns : int (the start of the range) Args : optional Bio::RangeI object =cut sub numeric { my $self = shift; return $self->start(@_); } =head2 chr Title : chr Usage : my $mychr = $position->chr(); Function: Get/Set method for the chromosome string of the location. Returns : chromosome value Args : none to get, OR scalar to set =cut sub chr { my ($self,$chr) = @_; if( defined $chr ) { $self->{'_chr'} = $chr; } return $self->{'_chr'}; } 1; BioPerl-1.007002/Bio/Map/EntityI.pm000555000766000024 510013155576320 16663 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::EntityI # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::EntityI - An Entity Interface =head1 SYNOPSIS # do not use this module directly =head1 DESCRIPTION This interface describes the basic methods required for entities. An Entity is a kind of Bio::Map object that holds instance-specific data but relies on registering itself with a PositionHandler to handle its relationships with other entities. These relationships between objects are based around shared Positions, so Bio::Map::PositionI objects are a special kind of EntityI, along with Bio::Map::MappableI and Bio::Map::MapI objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::EntityI; use strict; use base qw(Bio::Root::RootI); =head2 get_position_handler Title : get_position_handler Usage : my $position_handler = $entity->get_position_handler(); Function: Gets a PositionHandlerI that $entity is registered with. Returns : Bio::Map::PositionHandlerI object Args : none =cut sub get_position_handler { my $self = shift; $self->throw_not_implemented(); } =head2 PositionHandlerI-based methods Any methods related to interation with other entities should be implemented as a call to the PositionHandler =cut 1; BioPerl-1.007002/Bio/Map/FPCMarker.pm000444000766000024 2600313155576320 17072 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::fpcmarker # # Please direct questions and support issues to # # Cared for by Gaurav Gupta # # Copyright Gaurav Gupta # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::FPCMarker - An central map object representing a marker =head1 SYNOPSIS # get the marker object of $marker from the Bio::Map::FPCMarker my $markerobj = $physical->get_markerobj($marker); # acquire all the clones that hit this marker foreach my $clone ($markerobj->each_cloneid()) { print " +++$clone\n"; } # find the position of this marker in $contig print "Position in contig $contig"," = ",$markerobj->position($contig), "\n"; # find the group of the marker print "Group : ",$markerobj->group(); See L and L for more information. =head1 DESCRIPTION This object handles the notion of a marker. This object is intended to be used by a map parser like fpc.pm. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Gaurav Gupta Email gaurav@genome.arizona.edu =head1 CONTRIBUTORS Sendu Bala bix@sendu.me.uk =head1 PROJECT LEADERS Jamie Hatfield jamie@genome.arizona.edu Dr. Cari Soderlund cari@genome.arizona.edu =head1 PROJECT DESCRIPTION The project was done in Arizona Genomics Computational Laboratory (AGCoL) at University of Arizona. This work was funded by USDA-IFAFS grant #11180 titled "Web Resources for the Computation and Display of Physical Mapping Data". For more information on this project, please refer: http://www.genome.arizona.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::FPCMarker; use strict; use Bio::Map::Position; use Time::Local; use base qw(Bio::Root::Root Bio::Map::MappableI); =head2 new Title : new Usage : my $clone = Bio::Map::FPCMarker->new ( -name => $marker, -type => $type, -global => $global, -frame => $frame, -group => $group, -subgroup=> $subgroup, -anchor => $anchor, -clones => \%clones, -contigs => \%contigs, -position => \%markerpos, -remark => $remark ); Function: Initialize a new Bio::Map::FPCMarker object Most people will not use this directly but get Markers through L Returns : L object Args : -name => marker name string, -type => type string, -global => global position for marker, -frame => boolean if marker is framework or placement, -group => group number for marker, -subgroup => subgroup number of marker, -anchor => boolean if marker is anchored, -clones => all the clone elements in map (hashref), -contigs => all the contig elements (hasref), -position => mapping of marker names to map position (hasref), -remark => remarks, separated by newlines =cut sub new { my ($class,@args) = @_; my $self= $class->SUPER::new(@args); my ($name,$type,$global,$frame,$group, $subgroup, $anchor, $clones,$contigs, $positions, $remark) = $self->_rearrange([qw(NAME TYPE GLOBAL FRAME GROUP SUBGROUP ANCHOR CLONES CONTIGS POSITIONS REMARK)],@args); $self->name($name) if defined $name; $self->type($type) if defined $type; $self->global($global) if defined $global; $self->group($group) if defined $group; $self->subgroup($group) if defined $subgroup; $self->anchor($anchor) if defined $anchor; $self->remark($remark) if defined $remark; $self->set_clones($clones) if defined $clones; $self->set_contigs($contigs) if defined $contigs; $self->set_positions($positions) if defined $positions; return $self; } =head1 Access Methods These methods let you get and set the member variables =head2 name Title : name Usage : my $name = $markerobj->name(); Function: Get/set the name for this marker Returns : scalar representing the current name of this marker Args : none to get, OR string to set =cut sub name { my ($self) = shift; return $self->{'_name'} = shift if @_; return $self->{'_name'}; } =head2 type Title : type Usage : my $type = $markerobj->type(); Function: Get/set the type for this marker Returns : scalar representing the current type of this marker Args : none to get, OR string to set =cut sub type { my ($self) = shift; return $self->{'_type'} = shift if @_; return $self->{'_type'}; } =head2 global Title : global Usage : my $type = $markerobj->global(); Function: Get/set the global position for this marker Returns : scalar representing the current global position of this marker Args : none to get, OR string to set =cut sub global { my ($self) = shift; return $self->{'_global'} = shift if @_; return $self->{'_global'}; } =head2 anchor Title : anchor Usage : my $anchor = $markerobj->anchor(); Function: indicate if the Marker is anchored or not (True | False) Returns : scalar representing the anchor (1 | 0) for this marker Args : none to get, OR 1|0 to set =cut sub anchor { my ($self) = shift; return $self->{'_anchor'} = shift if @_; return $self->{'_anchor'}; } =head2 framework Title : framework Usage : $frame = $markerobj->framework(); Function: indicate if the Marker is framework or placement (1 | 0) Returns : scalar representing if the marker is framework (1 if framework, 0 if placement) Args : none to get, OR 1|0 to set =cut sub framework { my ($self) = shift; return $self->{'_frame'} = shift if @_; return $self->{'_frame'}; } =head2 group Title : group Usage : $grpno = $markerobj->group(); Function: Get/set the group number for this marker. This is a generic term, used for Linkage-Groups as well as for Chromosomes. Returns : scalar representing the group number of this marker Args : none to get, OR string to set =cut sub group { my ($self) = shift; $self->{'_group'} = shift if @_; return $self->{'_group'} || 0; } =head2 subgroup Title : subgroup Usage : $subgroup = $marker->subgroup(); Function: Get/set the subgroup for this marker. This is a generic term: subgroup here could represent subgroup of a Chromosome or of a Linkage Group. The user must take care of which subgroup he/she is querying for. Returns : scalar representing the subgroup of this marker Args : none to get, OR string to set =cut sub subgroup { my ($self) = shift; $self->{'_subgroup'} = shift if @_; return $self->{'_subgroup'} || 0; } =head2 position Title : position Usage : $markerpos = $markerobj->position($ctg); Function: get the position of the marker in the contig Returns : scalar representing the position of the markernumber of the contig Args : $ctg is necessary to look for the position of the marker in that contig. *** This has nothing to do with an actual Bio::Map::PositionI object *** =cut sub position { my ($self,$ctg) = @_; return 0 unless defined $ctg; return 0 unless( defined $self->{'_position'} && defined $self->{'_position'}{$ctg}); return $self->{'_position'}{$ctg}; } =head2 remark Title : remark Usage : $markerremark = $markerobj->remark(); Function: get the remarks for this marker Returns : scalar of newline-separated markers Args : none =cut sub remark { my ($self) = shift; return $self->{'_remark'} = shift if @_; return $self->{'_remark'}; } =head2 each_cloneid Title : each_cloneid Usage : my @clones = $map->each_cloneid(); Function: retrieves all the clone ids in a map unordered Returns : list of strings (ids) Args : none *** This only supplies the ids set with the set_clones method *** *** It has nothing to do with actual Bio::Map::MappableI objects *** =cut sub each_cloneid { my ($self) = @_; return $self->_each_element('clones'); } =head2 each_contigid Title : each_contigid Usage : my @contigs = $map->each_contigid(); Function: retrieves all the contig ids in a map unordered Returns : list of strings (ids) Args : none *** This only supplies the ids set with the set_contigs method *** *** It has nothing to do with actual Bio::Map::MapI objects *** =cut sub each_contigid { my ($self) = @_; return $self->_each_element('contigs'); } sub _each_element{ my ($self, $type) = @_; $type = 'clones' unless defined $type; $type = lc("_$type"); return keys %{$self->{$type} || {}}; } =head2 set_clones Title : set_clones Usage : $marker->set_clones(\%clones) Function: Set the clone ids hashref Returns : None Args : Hashref of clone ids *** This only sets a hash of ids *** *** It has nothing to do with actual Bio::Map::MappableI objects *** =cut sub set_clones{ my ($self,$clones) = @_; if( defined $clones && ref($clones) =~ /HASH/ ) { $self->{'_clones'} = $clones; } } =head2 set_contigs Title : set_contigs Usage : $marker->set_contigs(\%contigs) Function: Set the contig ids hashref Returns : None Args : Hashref of contig ids *** This only sets a hash of ids *** *** It has nothing to do with actual Bio::Map::MapI objects *** =cut sub set_contigs{ my ($self,$contigs) = @_; if( defined $contigs && ref($contigs) =~ /HASH/ ) { $self->{'_contigs'} = $contigs; } } =head2 set_positions Title : set_positions Usage : $marker->set_positions(\%markerpos) Function: Set the positions hashref Returns : None Args : Hashref of marker positions *** This only sets a hash of numbers *** *** It has nothing to do with actual Bio::Map::PositionI objects *** =cut sub set_positions{ my ($self,$pos) = @_; if( defined $pos && ref($pos) =~ /HASH/ ) { $self->{'_positions'} = $pos; } } 1; BioPerl-1.007002/Bio/Map/Gene.pm000555000766000024 10476613155576320 16236 0ustar00cjfieldsstaff000000000000# $Id: Gene.pm,v 1.6 2006/07/17 14:16:53 sendu Exp $ # # BioPerl module for Bio::Map::Gene # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::Gene - An gene modelled as a mappable element. =head1 SYNOPSIS use Bio::Map::Gene; my $gene = Bio::Map::Gene->get(-universal_name => 'BRCA2', -description => 'breast cancer 2, early onset'); # Normally you get Gene objects from GeneMaps use Bio::Map::GeneMap; # Model a gene with its orthologous versions found in different species, # but at abstract locations within each genome my $map1 = Bio::Map::GeneMap->get(-universal_name => 'BRCA2', -species => $human); my $map2 = Bio::Map::GeneMap->get(-universal_name => 'BRCA2', -species => $mouse); $gene = $map1->gene; # Genes can have special kinds of positions (Bio::Map::GenePosition) that # define where various sub-regions of the gene are, relative to one of the # normal Positions the gene has placing it on a map. my $trans = Bio::Map::GenePosition->new(-start => 0, -length => 700, -map => $map1, -type => 'transcript'); $gene->add_transcript_position($trans); my $exon = Bio::Map::GenePosition->new(-start => 0, -length => 100, -map => $map1, -type => 'exon'); $gene->add_exon_position($exon, 1); # (so now the gene has 1 transcript 700bp long which starts at the beginning # of the gene, and we've defined the first of many exons which starts at the # start of the transcript and is 100bp long) =head1 DESCRIPTION Model a gene as an abstract mappable element. This is for when you don't care exactly where a gene is in a genome, but just want to model other things (like transcription factor binding sites) that are near it so you can answer questions like "what binds near this gene?", or "which genes does this bind near?". See t/Map/Map.t for more example usage. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::Gene; use strict; use Bio::Map::GenePosition; use base qw(Bio::Map::Mappable); our $USE_ENSEMBL; our $GENES = {}; our $SET_FROM_DB = 0; BEGIN { # Bio::Tools::Run::Ensembl is in bioperl-run package which may not be # installed, but its functionality is only optional here eval {require Bio::Tools::Run::Ensembl;}; $USE_ENSEMBL = ! $@; } =head2 new Title : new Usage : my $gene = Bio::Map::Gene->new(); Function: Builds a new Bio::Map::Gene object Returns : Bio::Map::Gene Args : -universal_name => string : name of the gene (in a form common to all species that have the gene, but unique amongst non-orthologous genes), REQUIRED -description => string : free text description of the gene =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($u_name, $desc) = $self->_rearrange([qw(UNIVERSAL_NAME DESCRIPTION)], @args); $u_name || $self->throw("You must supply a -universal_name"); $self->universal_name($u_name); defined $desc && $self->description($desc); return $self; } =head2 get Title : get Usage : my $gene = Bio::Map::Gene->get(); Function: Builds a new Bio::Map::Gene object (like new()), or gets a pre-existing one that shares the same universal_name. Returns : Bio::Map::Gene Args : -universal_name => string, name of the gene (in a form common to all species that have the gene, but unique amongst non-orthologous genes), REQUIRED -description => string, free text description of the gene =cut sub get { my ($class, @args) = @_; my ($u_name, $desc) = Bio::Root::Root->_rearrange([qw(UNIVERSAL_NAME DESCRIPTION)], @args); if ($u_name && defined $GENES->{$u_name}) { $GENES->{$u_name}->description($desc) if $desc; return $GENES->{$u_name}; } return $class->new(@args); } =head2 universal_name Title : universal_name Usage : my $name = $gene->universal_name Function: Get/Set Mappable name, corresponding to the name of the gene in a form shared by orthologous versions of the gene in different species, but otherwise unique. Returns : string Args : none to get, OR string to set =cut sub universal_name { my ($self, $value) = @_; if (defined $value) { delete $GENES->{$self->{'_uname'}} if $self->{'_uname'}; $self->{'_uname'} = $value; $GENES->{$value} = $self; } return $self->{'_uname'}; } =head2 description Title : description Usage : my $description = $gene->description(); $gene->description($description); Function: Get/set information relating to the gene, in this case the description (eg. 'full name of gene') Returns : string (empty string if not defined) Args : none to get general version, OR Bio::Map::GeneMap to get map-specific version. string to set general version, optionally AND Bio::Map::GeneMap to set map-specific version =cut sub description { my $self = shift; return $self->_gene_data('description', @_); } =head2 display_id Title : display_id Usage : my $display_id = $gene->display_id(); $gene->display_id($display_id); Function: Get/set information relating to the gene, in this case the display_id (eg. 'ENSG00000155287') Returns : string (empty string if not defined) Args : none to get general version, OR Bio::Map::GeneMap to get map-specific version. string to set general version, optionally AND Bio::Map::GeneMap to set map-specific version =cut sub display_id { my $self = shift; return $self->_gene_data('display_id', @_); } =head2 display_xref Title : display_xref Usage : my $display_xref = $gene->display_xref(); $gene->display_xref($display_xref); Function: Get/set information relating to the gene, in this case the display_xref (eg. 'HUGO:23472'). Returns : string (empty string if not defined) Args : none to get general version, OR Bio::Map::GeneMap to get map-specific version. string to set general version, optionally AND Bio::Map::GeneMap to set map-specific version =cut sub display_xref { my $self = shift; return $self->_gene_data('display_xref', @_); } =head2 external_db Title : external_db Usage : my $external_db = $gene->external_db(); $gene->external_db($external_db); Function: Get/set information relating to the gene, in this case the external_db (eg. 'HUGO'). Returns : string (empty string if not defined) Args : none to get general version, OR Bio::Map::GeneMap to get map-specific version. string to set general version, optionally AND Bio::Map::GeneMap to set map-specific version =cut sub external_db { my $self = shift; return $self->_gene_data('external_db', @_); } =head2 external_name Title : external_name Usage : my $external_name = $gene->external_name(); $gene->external_name($external_name); Function: Get/set information relating to the gene, in this case the (eg. 'gene_name', probably the same as or similar to what you set universal_name() to, but could be a species-specific alternative). Returns : string (empty string if not defined) Args : none to get general version, OR Bio::Map::GeneMap to get map-specific version. string to set general version, optionally AND Bio::Map::GeneMap to set map-specific version =cut sub external_name { my $self = shift; return $self->_gene_data('external_name', @_); } =head2 biotype Title : biotype Usage : my $biotype = $gene->biotype(); $gene->biotype($biotype); Function: Get/set information relating to the gene, in this case the biotype (eg. 'protein_coding'). Returns : string (empty string if not defined) Args : none to get general version, OR Bio::Map::GeneMap to get map-specific version. string to set general version, optionally AND Bio::Map::GeneMap to set map-specific version =cut sub biotype { my $self = shift; return $self->_gene_data('biotype', @_); } =head2 source Title : source Usage : my $source = $gene->source(); $gene->source($source); Function: Get/set information relating to the gene, in this case the source (eg. '??'). Returns : string (empty string if not defined) Args : none to get general version, OR Bio::Map::GeneMap to get map-specific version. string to set general version, optionally AND Bio::Map::GeneMap to set map-specific version =cut sub source { my $self = shift; return $self->_gene_data('source', @_); } =head2 position Title : position Usage : my $position = $mappable->position($map); Function: Get the main Position of this Mappable on a given map. (A gene may have many positions on a map, but all but one of them are Bio::Map::GenePosition objects that describe sub-regions of the gene which are relative to the 'main' Bio::Map::Position position, which is the only one that is directly relative to the map - this is the Position returned by this method.) Returns : Bio::Map::Position Args : L object. =cut sub position { my ($self, $map) = @_; ($map && $self->in_map($map)) || return; foreach my $pos ($self->get_positions($map, 1)) { next if $pos->isa('Bio::Map::GenePosition'); return $pos; #*** could do sanity checking; there should only be 1 non-GenePosition # object here, and it should have a relative of type 'map', and it # should sort before or equal to all other positions } } =head2 add_transcript_position Title : add_transcript_position Usage : $gene->add_transcript_position($position); Function: Set the bounds of a transcript on a map (that of the supplied position). All transcript positions added this way must have coordinates relative to the main position of the 'gene' mappable on this transcript's map. The first position added using this method must have a start of 0. The supplied Position will be given a type of 'transcript' and relative of (gene => 0). The active_transcript for the Position's map will be set to this one. Returns : n/a Args : Bio::Map::GenePosition (which must have its map() defined, and be for a map this gene is on) =cut sub add_transcript_position { my ($self, $pos) = @_; ($pos && $pos->isa('Bio::Map::GenePosition')) || return; my $map = $pos->map || $self->throw("Supplied GenePosition has no map"); $self->in_map($map) || $self->throw("Supplied GenePosition is not on a map that this gene belong to"); my @transcripts = $self->get_transcript_positions($map); if (@transcripts == 0) { # first transcript needs start of 0 if ($pos->start != 0) { $self->warn("The first transcript position added to a map needs a start of 0, not adding"); return; } } $pos->type('transcript'); $pos->relative->gene(0); $self->SUPER::add_position($pos); # need to remember the order these were added, but remember what we store # here could become invalid if positions are purged outside of this class push(@{$self->{t_order}->{$map}}, $pos); # adjust main position's length to hold this transcript my $main_pos = $self->position($map); my $increase = ($pos->length + $pos->start($pos->absolute_relative)) - ($main_pos->end + 1); if ($increase > 0) { $main_pos->end($main_pos->end + $increase); } # make this new transcript the active one $self->active_transcript($map, scalar(@transcripts) + 1); } =head2 active_transcript Title : active_transcript Usage : my $active = $gene->active_transcript($map); $gene->active_transcript($map, $int); Function: Get/set the active transcript number (an int of 1 would mean the 1st transcript position added to the object for the given map, ie. would correspond to the the 1st Position object in the list returned by get_transcript_positions($map)). The active transcript is the one considered by other methods and objects when dealing with positions relative to 'the' transcript. Returns : int, 0 means there were no transcript positions on the given map, undef is some other problem Args : Just Bio::Map::GeneMap to get Bio::Map::GeneMap AND int to set =cut sub active_transcript { my ($self, $map, $int) = @_; $map or return; my @transcripts = $self->get_transcript_positions($map); if (@transcripts > 0) { if (defined($int)) { if ($int > 0 && $int <= @transcripts) { $self->{active_transcript}->{$map} = $int; return $int; } else { $self->warn("Supplied int '$int' not a good number (higher than the number of transcripts on the map?)"); return; } } else { if (defined $self->{active_transcript}->{$map}) { return $self->{active_transcript}->{$map}; } else { # default to the total number of transcripts on the map, ie. the # most recently added $self->{active_transcript}->{$map} = @transcripts; return $self->{active_transcript}->{$map}; } } } return 0; } =head2 get_transcript_positions Title : get_transcript_positions Usage : my @transcript_positions = $gene->get_transcript_positions($map); Function: Get all the transcript positions of this gene on the given map, in the order they were added to the map. Returns : list of Bio::Map::GenePosition Args : Bio::Map::GeneMap =cut sub get_transcript_positions { my ($self, $map) = @_; $map or return; $map->isa('Bio::Map::GeneMap') or return; return $self->_get_typed_positions($map, 'transcript'); } =head2 get_transcript_position Title : get_transcript_position Usage : my $position = $gene->get_transcript_position($map, $int); Function: Get the $int'th transcript position added to the map. If no transcripts have been added to the map, and the default transcript was requested, $gene->position is returned, as that will have the same start and end as the first transcript. Returns : Bio::Map::GenePosition Args : Bio::Map::GeneMap AND int (if int not supplied, or 0, returns the currently active transcript position) =cut sub get_transcript_position { my ($self, $map, $value) = @_; $map or return; $value ||= $self->active_transcript($map); my @transcripts = $self->get_transcript_positions($map); if (@transcripts == 0 && $value == 0) { return $self->position($map); } return $self->_get_list_element($value, @transcripts); } =head2 coding_position Title : coding_position Usage : $gene->coding_position($position, $transcript_number); $gene->coding_position($map, $transcript_number); Function: Get/set the bounds of a coding region of a given transcript on a map (that of the supplied position). When setting, coordinates must be relative to the transcript start. The supplied position will be given a type 'coding' and a relative (-transcript => $transcript_number). There can be only one coding position per transcript (hence this is a get/set). When getting, if a coding region has not been defined for the requested transcript, $gene->get_transcript_position($map, $transcript_number) is returned, as if assuming the entirety of the transcript is coding. Returns : Bio::Map::GenePosition Args : Bio::Map::GeneMap AND int (the transcript number) to get, OR to set: Bio::Map::GenePosition (which must have its map() defined, and be for a map this gene is on) AND int (the transcript number) In both cases, if transcript number not supplied or 0 this will be resolved to the current active transcript number - there must be at least one transcript on the map =cut sub coding_position { my ($self, $thing, $transcript_num) = @_; ref($thing) || return; $transcript_num ||= 0; # deliberate test for PositionI so _add_type_position can do nothing if # its not a GenePosition if ($thing->isa('Bio::Map::PositionI')) { my $map = $thing->map || return; my ($existing_pos) = $self->_get_typed_positions($map, 'coding', $transcript_num); if ($existing_pos) { # purge it $self->purge_positions($existing_pos); } $self->_add_type_position('coding', $thing, $transcript_num); $thing = $map; } my ($pos) = $self->_get_typed_positions($thing, 'coding', $transcript_num); return $pos || $self->get_transcript_position($thing, $transcript_num); } =head2 add_exon_position Title : add_exon_position Usage : $gene->add_exon_position($position, $transcript_number); Function: Set the bounds of an exon of a given transcript on a map (that of the supplied position). Coordinates must be relative to the transcript start. The supplied position will be given a type 'exon' and a relative (-transcript => $transcript_number). Returns : n/a Args : Bio::Map::GenePosition (which must have its map() defined, and be for a map this gene is on) AND int (the transcript number; if not supplied or 0 this will be resolved to the current active transcript number - there must be at least one transcript on the map) =cut sub add_exon_position { my $self = shift; $self->_add_type_position('exon', @_); } =head2 get_exon_positions Title : get_exon_positions Usage : my @positions = $gene->get_exon_positions($map, $int); Function: Get all the exon positions that are relative to the $int'th transcript position added to the map. Exons are returned sorted by their start positions. Returns : array of Bio::Map::GenePosition Args : Bio::Map::GeneMap AND int (the transcript number; if second int not supplied, or 0, considers the currently active transcript) =cut sub get_exon_positions { my ($self, $map, $value) = @_; $map || return; $value ||= 0; return $self->_get_typed_positions($map, 'exon', $value); } =head2 get_exon_position Title : get_exon_position Usage : my $position = $gene->get_exon_position($map, $exon_num, $int); Function: Get the $exon_num'th exon position that is relative to the $int'th transcript position added to the map. Exons are numbered in Position order, not the order they were added to the map. If no exons have been added to the map, and the first exon was requested, $gene->get_transcript_position($map, $int) is returned, as that will have the same start as the first exon, and could have the same end for a single exon gene. Returns : Bio::Map::GenePosition Args : Bio::Map::GeneMap AND int (the exon you want) AND int (the transcript number; if second int not supplied, or 0, considers the currently active transcript) =cut sub get_exon_position { my ($self, $map, $exon_num, $value) = @_; my @exons = $self->get_exon_positions($map, $value); if (@exons == 0 && $exon_num == 1) { return $self->get_transcript_position($map, $value); } return $self->_get_list_element($exon_num, @exons); } =head2 add_intron_position Title : add_intron_position Usage : $gene->add_intron_position($position, $transcript_number); Function: Set the bounds of an intron of a given transcript on a map (that of the supplied position). Coordinates must be relative to the transcript start. The supplied position will be given a type 'intron' and a relative (-transcript => $transcript_number). Returns : n/a Args : Bio::Map::GenePosition (which must have its map() defined, and be for a map this gene is on) AND int (the transcript number; if not supplied or 0 this will be resolved to the current active transcript number - there must be at least one transcript on the map) =cut sub add_intron_position { my $self = shift; $self->_add_type_position('intron', @_); } =head2 get_intron_positions Title : get_intron_positions Usage : my @positions = $gene->get_intron_positions($map, $int); Function: Get all the intron positions that are relative to the $int'th transcript position added to the map. Introns are returned sorted by their start positions. Returns : array of Bio::Map::GenePosition Args : Bio::Map::GeneMap AND int (the transcript number; if second int not supplied, or 0, considers the currently active transcript) =cut sub get_intron_positions { my ($self, $map, $value) = @_; $map || return; $value ||= 0; return $self->_get_typed_positions($map, 'intron', $value); } =head2 get_intron_position Title : get_intron_position Usage : my $position = $gene->get_intron_position($map, $intron_num, $int); Function: Get the $intron_num'th intron position that is relative to the $int'th transcript position added to the map. Introns are numbered in Position order, not the order they were added to the map. Returns : Bio::Map::GenePosition Args : Bio::Map::GeneMap AND int (the intron you want) AND int (the transcript number; if second int not supplied, or 0, considers the currently active transcript) =cut sub get_intron_position { my ($self, $map, $intron_num, $value) = @_; my @introns = $self->get_intron_positions($map, $value); return $self->_get_list_element($intron_num, @introns); } =head2 set_from_db Title : set_from_db Usage : $gene->set_from_db(); # for an instance only Bio::Map::Gene->set_from_db(); # decide that all future genes added # to maps will be set from db Function: Creates all the various types of positions (transcripts, coding, exons, introns) for this gene on all its maps. The information comes from an Ensembl database via Bio::Tools::Run::Ensembl. NB: will purge any existing Bio::Map::GenePosition objects that were previously on the maps this gene is one. Returns : undef on failure, otherwise the number of maps that successfully had positions added to them Args : boolean (no argument/undef is treated as 1, ie. do set from db; supply 0 to turn off) NB: Bio::Tools::Run::Ensembl is available in the bioperl-run package; see it for details on setting up a database to use. Once set, any new maps (species) this gene is added to will automatically also have their positions set_from_db =cut sub set_from_db { my ($self, $bool) = @_; return unless $USE_ENSEMBL; return unless Bio::Tools::Run::Ensembl->registry_setup(); defined($bool) || ($bool = 1); unless (ref($self)) { $SET_FROM_DB = $bool; return 0; } $self->{_set_from_db} = $bool; my $success = 0; foreach my $map ($self->known_maps) { $success += $self->_set_from_db($map); } return $success; } # set from db for a particular map (species) sub _set_from_db { my ($self, $map) = @_; my $gene_name = $self->universal_name || return 0; $SET_FROM_DB || $self->{_set_from_db} || return; my $species = $map->species; my $slice_adaptor = Bio::Tools::Run::Ensembl->get_adaptor($species, 'Slice') || return 0; my $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => $species, -name => $gene_name, -use_orthologues => 'Homo sapiens', -use_swiss_lookup => 1, -use_entrez_lookup => 1) || return 0; # attach species(map)-specific gene info to self $self->description($gene->description, $map); $self->display_id($gene->display_id, $map); $self->display_xref($gene->display_xref->display_id, $map); $self->external_db($gene->external_db, $map); $self->external_name($gene->external_name, $map); $self->biotype($gene->biotype, $map); $self->source($gene->source, $map); # get the transcripts for this map my $trans_ref = $gene->get_all_Transcripts; unless ($trans_ref && @{$trans_ref} > 0) { return 0; } # purge all existing GenePositions from the map my $handler = $map->get_position_handler(); foreach my $pos ($map->get_positions) { if ($pos->isa('Bio::Map::GenePosition')) { $handler->purge_positions($pos); } } # assume all transcripts on the same strand, sort them my $strand = ${$trans_ref}[0]->strand; my @transcripts = sort { $strand == -1 ? ($b->end <=> $a->end) : ($a->start <=> $b->start) } @{$trans_ref}; # store slice of first transcript so we can use it to get seq data, and # add chromosome info to our map if not set my $primary_slice = $slice_adaptor->fetch_by_transcript_stable_id($transcripts[0]->stable_id, 0); my $uid = $map->unique_id; @{$self->{_ensembl}->{$uid}} = ($slice_adaptor, $primary_slice, $strand); #my $cyto = $map->location || Bio::Map::CytoPosition->new(); #unless ($cyto->chr) { # $cyto->chr($primary_slice->seq_region_name); #} #$map->location($cyto); # adjustment needed to make all transcript coords relative to the start of # the first transcript which must start at 0 my $adjust = $strand == -1 ? $transcripts[0]->end : $transcripts[0]->start; my $orig_adjust = $adjust; my $adjustment = sub { return $strand == -1 ? $adjust - shift() : shift() - $adjust; }; # go through all the transcripts, remembering the longest my $longest_trans = 0; my $longest = 1; my $count = 1; foreach my $transcript (@transcripts) { # length is the total number of bases the exons cover, not genomic span my $length = $transcript->length(); if ($length > $longest_trans) { $longest_trans = $length; $longest = $count; } # make positions for this transcript my $slice = $slice_adaptor->fetch_by_transcript_stable_id($transcript->stable_id, 0); my $start = &$adjustment($slice->start()); my $end = &$adjustment($slice->end()); ($start, $end) = ($end, $start) if $start > $end; my $trans_pos = Bio::Map::GenePosition->new(-map => $map, -start => $start, -end => $end, -type => 'transcript'); $self->add_transcript_position($trans_pos); # all subsequent coordinates need to be relative to the start of this # transcript $adjust = $strand == -1 ? $slice->end : $slice->start; # there may not be a coding region if (defined($transcript->coding_region_start)) { my $atg = &$adjustment($transcript->coding_region_start()); my $stop = &$adjustment($transcript->coding_region_end()); ($atg, $stop) = ($stop, $atg) if $atg > $stop; my $cod_pos = Bio::Map::GenePosition->new(-map => $map, -start => $atg, -end => $stop, -type => 'coding'); $self->coding_position($cod_pos); } # exons foreach my $exon (@{$transcript->get_all_Exons}) { my $start = &$adjustment($exon->start()); my $end = &$adjustment($exon->end()); ($start, $end) = ($end, $start) if $start > $end; my $throw_species = ref($species) ? $species->scientific_name : $species; defined($end) || $self->throw("gene $gene_name in species $throw_species (".$gene->display_id.") had exon $start with no end"); my $pos = Bio::Map::GenePosition->new(-map => $map, -start => $start, -end => $end, -type => 'exon'); $self->add_exon_position($pos); } # introns foreach my $intron (@{$transcript->get_all_Introns}) { my $start = &$adjustment($intron->start()); my $end = &$adjustment($intron->end()); ($start, $end) = ($end, $start) if $start > $end; my $pos = Bio::Map::GenePosition->new(-map => $map, -start => $start, -end => $end, -type => 'intron'); $self->add_intron_position($pos); } $adjust = $orig_adjust; } continue { $count++ }; $self->active_transcript($map, $longest); return 1; } # get safely sorted positions of a certain type sub _get_typed_positions { my ($self, $map, $type, $transcript_number) = @_; if (defined $transcript_number && $transcript_number == 0) { $transcript_number = $self->active_transcript($map); } my @positions; foreach my $pos ($self->get_positions($map, 1)) { $pos->isa('Bio::Map::GenePosition') || next; $pos->type eq $type || next; if (defined $transcript_number) { my $rel = $pos->relative || next; $rel->type eq 'transcript' || next; my $rel_transcript_num = $rel->transcript || $self->active_transcript($map); $rel_transcript_num == $transcript_number || next; } push(@positions, $pos); } # avoid sorting using $pos->sortable since we would go infinite from the # call to absolute_conversion - we don't need absolute_conversion here # since we know the raw starts are all relative to the same thing, or in # the case of transcripts, we want them sorted in the way they were added if (defined $transcript_number) { # ensure we get raw start; ask for starts relative to the things # the positions are relative to. Precompute answer for efficiency my @sort = map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [$_->start($_->relative), $_] } @positions; return @sort; } else { my @known_order = @{$self->{t_order}->{$map} || []}; @known_order || return; # transcripts might have been removed, so known_order could be invalid return @known_order if @known_order == @positions; #*** dangerous assumption? my %exists = map { $_ => $_ } @positions; my @new_order; foreach my $pos (@known_order) { exists $exists{$pos} || next; push(@new_order, $pos); } @{$self->{t_order}->{$map}} = @new_order; return @new_order; } } # get a certain element from an array, checking the array has that element sub _get_list_element { my ($self, $wanted, @list) = @_; ($wanted && $wanted > 0) || return; @list > 0 || return; my $index = $wanted - 1; if ($index >= 0 && $index <= $#list) { return $list[$index]; } return; } # add a certain type of posiiton sub _add_type_position { my ($self, $type, $pos, $transcript_num) = @_; ($pos && $pos->isa('Bio::Map::GenePosition')) || return; my $map = $pos->map || $self->throw("Supplied GenePosition has no map"); $self->in_map($map) || $self->throw("Supplied GenePosition is not on a map that this gene belong to"); $transcript_num ||= $self->active_transcript($map) || $self->throw("Asked to be relative to the active transcript, but there is no transcript"); # sanity check - must be within the transcript my $transcript_pos = $self->get_transcript_position($map, $transcript_num) || $self->throw("Asked to be relative to transcript $transcript_num, but there is no such transcript"); $transcript_pos->end || ($self->warn("no transcript pos end for pos for gene ".$self->universal_name." and species ".$pos->map->species."!") && exit); $pos->end || ($self->warn("no pos end for pos for gene ".$self->universal_name." and species ".$pos->map->species."!") && exit); unless ($transcript_pos->contains($pos)) { $self->warn("$type coordinates must lie within those of the transcript, not adding $type"); return; } $pos->type($type); $pos->relative->transcript($transcript_num); $self->SUPER::add_position($pos); } # get/setter for general/map-specific data sub _gene_data { my ($self, $type, $thing, $map) = @_; $thing or return ($self->{$type}->{general} || ''); if (ref($thing) && $thing->isa('Bio::Map::GeneMap')) { return $self->{$type}->{$thing} || ''; } if ($map && $map->isa('Bio::Map::GeneMap')) { $self->{$type}->{$map} = $thing; } else { $self->{$type}->{general} = $thing; } return $thing; } # for exclusive use by GeneMap so it can get sequence data sub _get_slice { my ($self, $map) = @_; $map || return; my $uid = $map->unique_id || return; if (defined $self->{_ensembl}->{$uid}) { return @{$self->{_ensembl}->{$uid}}; } return; } 1; BioPerl-1.007002/Bio/Map/GeneMap.pm000444000766000024 5111513155576320 16636 0ustar00cjfieldsstaff000000000000# $Id: GeneMap.pm,v 1.17 2006/07/17 14:16:53 sendu Exp $ # # BioPerl module for Bio::Map::GeneMap # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::GeneMap - A MapI implementation to represent the area around a gene =head1 SYNOPSIS use Bio::Map::GeneMap; use Bio::Map::Gene; use Bio::Map::TranscriptionFactor; use Bio::Map::GeneRelative; # make some maps that will represent an area around a particular gene in # particular species (by default, the map represents the area in the genome # 1000bp upstream of the gene) my $map1 = Bio::Map::GeneMap->get(-gene => 'BRCA2', -species => 'human', -description => 'breast cancer 2, early onset'); my $map2 = Bio::Map::GeneMap->get(-gene => 'BRCA2', -species => 'mouse'); # model a TF that binds 500bp upstream of the BRCA2 gene in humans and # 250bp upstream of BRCA2 in mice my $rel = Bio::Map::GeneRelative->new(-description => "gene start"); my $tf = Bio::Map::TranscriptionFactor->get(-universal_name => 'tf1'); Bio::Map::Position->new(-map => $map1, -element => $tf, -start => -500, -length => 10, -relative => $rel); Bio::Map::Position->new(-map => $map2, -element => $tf, -start => -250, -length => 10, -relative => $rel); # find out all the things that map near BRCA2 in all species foreach my $map ($gene->known_maps) { foreach my $thing ($map->get_elements) { next if $thing eq $gene; foreach my $pos ($thing->get_positions($map)) { print "In species ", $map->species, ", ", $thing->universal_name, " maps at ", $pos->value, " relative to ", $pos->relative->description, " of gene ", $gene->universal_name, "\n"; } } } # a GeneMap isa PrimarySeq and so can have sequence associated with it $map1->seq('ATGC'); my $subseq = $map1->subseq(2,3); # TG =head1 DESCRIPTION Model the abstract notion of the area around a gene - you don't care exactly where this area is in the genome, you just want to be able to say "something binds upstream of gene X" and "something else binds 20bp upstream of the first something" etc. It's useful for modelling transcription factor bindings sites, letting you find out which transcription factors bind near a gene of interest, or which genes are bound by a transcription factor of interest. See t/Map/Map.t for more example usage. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::GeneMap; use strict; use Bio::Map::Gene; use Bio::Map::Position; use base qw(Bio::Map::SimpleMap Bio::PrimarySeq); our $GENEMAPS = {}; =head2 new Title : new Usage : my $obj = Bio::Map::GeneMap->new(); Function: Builds a new Bio::Map::GeneMap object (that has placed on it a mappable element (Bio::Map::Gene) representing a gene). Returns : Bio::Map::GeneMap Args : -gene => string name of the gene this map will be for (in a form common to all species that have the gene, but unique amongst non-orthologous genes) or a Bio::Map::Gene object, REQUIRED -species => Bio::Taxon or string representing species, REQUIRED -uid => string, unique identifier for this map (must be unique amongst all gene/species combinations) -description => string, free text description of the gene -upstream => int, the number of bases the map extends before the start of the gene element (default 1000). -downstream => int, the number of bases the map extends beyond the end of the gene element (default 0). -seq => string, the sequence of the map, presumably the genomic sequence -upstream bases of the gene, including the gene, and -downstream bases of the gene =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($uid, $gene, $species, $desc, $up, $down, $seq) = $self->_rearrange([qw(UID GENE SPECIES DESCRIPTION UPSTREAM DOWNSTREAM SEQ)], @args); unless (defined $gene && defined $species) { $self->throw("You must supply both -species and -gene"); } $self->gene(-gene => $gene, -description => $desc, -upstream => $up, -downstream => $down); $self->seq($seq) if $seq; unless (defined($uid)) { # trigger the special behaviour in our unique_id method by supplying it # the unique_id we got from our parent class $self->unique_id($self->unique_id); } return $self; } =head2 get Title : get Usage : my $map = Bio::Map::GeneMap->get(); Function: Builds a new Bio::Map::GeneMap object (like new()), or gets a pre-existing one that corresponds to your arguments. Returns : Bio::Map::GeneMap Args : -gene => string name of the gene this map will be for (in a form common to all species that have the gene, but unique amongst non-orthologous genes) or a Bio::Map::Gene object, REQUIRED -species => Bio::Taxon or string representing species, REQUIRED -uid => string, unique identifier for this map (must be unique amongst all gene/species combinations) -description => string, free text description of the gene -upstream => int, the number of bases the map extends before the start of the gene element (default 1000). -downstream => int, the number of bases the map extends beyond the end of the gene element (default 0). -seq => string, the sequence of the map, presumably the genomic sequence -upstream bases of the gene, including the gene, and -downstream bases of the gene If you supply a -uid, and a map had previously been created and given that uid, that same map object will be returned. Otherwise, the combination of -gene and -species will be used to determine if the same map had previously been made. If a corresponding map hadn't previously been made, a new map object will be created and returned. =cut sub get { my ($class, @args) = @_; my ($uid, $gene, $species, $desc, $up, $down, $seq) = Bio::Root::Root->_rearrange([qw(UID GENE SPECIES DESCRIPTION UPSTREAM DOWNSTREAM SEQ)], @args); my $gene_map; if ($uid && defined $GENEMAPS->{by_uid}->{$uid}) { $gene_map = $GENEMAPS->{by_uid}->{$uid}; } elsif ($gene && $species) { my $name = ref($gene) ? $gene->universal_name : $gene; if (defined $GENEMAPS->{by_ns}->{$name}->{$species}) { $gene_map = $GENEMAPS->{by_ns}->{$name}->{$species}; } } if ($gene_map) { $gene_map->gene->description($desc) if $desc; $gene_map->upstream($up) if defined($up); $gene_map->downstream($down) if defined($down); $gene_map->seq($seq) if $seq; return $gene_map; } return $class->new(@args); } =head2 unique_id Title : unique_id Usage : my $id = $map->unique_id; Function: Get/set the unique ID for this map Returns : string Args : none to get, OR string to set =cut sub unique_id { my ($self, $id) = @_; if (defined $id) { delete $GENEMAPS->{by_uid}->{$self->{'_uid'}}; $self->{'_uid'} = $id; $GENEMAPS->{by_uid}->{$id} = $self; } return $self->{'_uid'}; } =head2 species Title : species Usage : my $species = $map->species; Function: Get/set Species for a map. It is not recommended to change this once set. Returns : Bio::Taxon object or string Args : none to get, OR Bio::Taxon or string to set =cut sub species { my ($self, $value) = @_; if ($value) { my $old_species = $self->{_species}; $self->{'_species'} = $value; my $name = $self->universal_name || return $value; if ($old_species) { delete $GENEMAPS->{by_ns}->{$name}->{$old_species}; } $GENEMAPS->{by_ns}->{$name}->{$value} = $self; } return $self->{'_species'}; } =head2 type Title : type Usage : my $type = $map->type Function: Get Map type Returns : string 'gene' Args : none =cut sub type { return 'gene'; } =head2 gene Title : gene Usage : my $gene = $map->gene; $map->gene(-gene => $gene); Function: Get/set the mappable element on this map that represents the gene this map is for. Once set, it is not recommended to re-set the gene to something else. Behaviour in that case is undefined. Returns : Bio::Map::Gene Args : none to get, OR to set: -gene => Bio::Map::Gene or string of the universal name (see Bio::Map::Gene docs), REQUIRED -description => string, applied to the Bio::Map::Gene -upstream => int, the number of bases the map extends before the start of the gene element (default 1000). -downstream => int, the number of bases the map extends beyond the end of the gene element (default 0). =cut sub gene { my ($self, @args) = @_; if (@args > 0) { my ($gene, $desc, $up, $down) = $self->_rearrange([qw(GENE DESCRIPTION UPSTREAM DOWNSTREAM)], @args); $self->throw("You must supply -gene") unless $gene; my $gene_obj = ref($gene) ? $gene : Bio::Map::Gene->get(-universal_name => $gene, -description => $desc); if (defined $self->{gene}) { if ($self->{gene} ne $gene_obj) { $self->warn("Changing the gene that this map is for, which could be bad"); $self->purge_positions($self->{gene}); delete $GENEMAPS->{by_ns}->{$self->universal_name}->{$self->species}; $self->{gene} = $gene_obj; } # change the gene's position on us if necessary $self->upstream($up) if defined $up; $self->downstream($down) if defined $down; } else { # give the gene object a position on us $up ||= 1000; $up >= 0 || $self->throw("-upstream must be a positive integer"); Bio::Map::Position->new(-map => $self, -start => ($up + 1), -element => $gene_obj); $self->{gene} = $gene_obj; $self->downstream($down || 0); # set other gene positions from db if already user-requested $gene_obj->_set_from_db($self); } $GENEMAPS->{by_ns}->{$self->universal_name}->{$self->species} = $self; } return $self->{gene}; } =head2 universal_name Title : universal_name Usage : my $name = $map->universal_name Function: Get/set the name of Bio::Map::Gene object associated with this map. It is not recommended to change this once set. Returns : string Args : none to get, OR string to set =cut sub universal_name { my ($self, $value) = @_; $self->gene || return; if ($value) { my $species = $self->species; delete $GENEMAPS->{by_ns}->{$self->gene->universal_name}->{$species}; $self->gene->universal_name($value); $GENEMAPS->{by_ns}->{$value}->{$species} = $self; } return $self->gene->universal_name; } =head2 upstream Title : upstream Usage : my $distance = $map->upstream; $map->upstream($distance); Function: Get/set how long the map is before the start of the Bio::Map::Gene object on this map. Returns : int Args : none to get, OR int to set (the number of bases the map extends before the start of the gene) =cut sub upstream { my ($self, $value) = @_; my $pos = $self->gene->position($self); if (defined($value)) { $value >= 0 || $self->throw("Supplied value must be a positive integer"); $pos->start($value + 1); } return $pos->start - 1; } =head2 downstream Title : downstream Usage : my $distance = $map->downstream; $map->downstream($distance); Function: Get/set the nominal end of the map relative to the end of the Bio::Map::Gene object on this map. Returns : int Args : none to get, OR int to set (the number of bases the map extends beyond the end of the gene) =cut sub downstream { my $self = shift; if (@_) { $self->{_downstream} = shift } return $self->{_downstream} || 0; } =head2 length Title : length Usage : my $length = $map->length(); Function: Retrieves the length of the map. This is normally the length of the upstream region + length of the gene + length of the downstream region, but may be longer if positions have been placed on the map beyond the end of the nominal downstream region. Returns : int Args : none =cut sub length { my $self = shift; my $expected_length = $self->gene->position($self)->length + $self->upstream + $self->downstream; my $actual_length = $self->SUPER::length; return $actual_length > $expected_length ? $actual_length : $expected_length; } =head2 seq Title : seq Usage : $string = $obj->seq() Function: Get/set the sequence as a string of letters. When getting, If the GeneMap object didn't have sequence attached directly to it for the region requested, the map's gene's database will be asked for the sequence, and failing that, the map's gene's positions will be asked for their sequences. Areas for which no sequence could be found will be filled with Ns, unless no sequence was found anywhere, in which case undef is returned. Returns : string Args : Optionally on set the new value (a string). An optional second argument presets the alphabet (otherwise it will be guessed). =cut sub seq { my ($self, @args) = @_; my $seq = $self->SUPER::seq(@args); my $expected_length = $self->length; if (! $seq || CORE::length($seq) < $expected_length) { my @have = split('', $seq || ''); my @result; for (0..($expected_length - 1)) { $result[$_] = shift(@have) || 'N'; } # build map sequence by asking gene or positions my @slice_stuff = $self->gene->_get_slice($self); if (@slice_stuff) { my ($slice_adaptor, $slice, $strand) = @slice_stuff; my ($start, $end, $gene_start) = (CORE::length($seq || '') + 1, $expected_length, $self->upstream + 1); # convert map coords to genomic coords my $adjust = $strand == -1 ? $slice->end : $slice->start; my $adjustment = sub { return $strand == -1 ? $adjust - shift() : shift() + $adjust; }; my $converted_start = &$adjustment($start - $gene_start); my $converted_end = &$adjustment($end - $gene_start); ($converted_start, $converted_end) = ($converted_end, $converted_start) if $converted_start > $converted_end; # get sequence from a new slice of desired region #*** what happens if desired region starts or ends off end of chromo?... my $new_slice = $slice_adaptor->fetch_by_region($slice->coord_system_name, $slice->seq_region_name, $converted_start, $converted_end); if ($new_slice && (my $seq_str = $new_slice->seq)) { if ($strand == -1) { $seq_str = $self->_revcom($seq_str); } splice(@result, CORE::length($seq || ''), CORE::length($seq_str), split('', $seq_str)); } } else { foreach my $pos ($self->get_positions) { next unless $pos->can('seq'); my @pos_seq = split('', $pos->seq(undef, undef, 1) || next); for my $i ($pos->start($pos->absolute_relative)..$pos->end($pos->absolute_relative)) { $i--; my $base = shift(@pos_seq); if ($result[$i] eq 'N') { $result[$i] = $base; } } } } $seq = join('', @result); } return $seq; } =head2 subseq Title : subseq Usage : $substring = $obj->subseq(10, 40); Function: Returns the subseq from start to end, where the first base is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. If the GeneMap object didn't have sequence attached directly to it for the region requested, the map's gene's database will be asked for the sequence, and failing that, the map's gene's positions will be asked for their sequences. Areas for which no sequence could be found will be filled with Ns, unless no sequence was found anywhere, in which case undef is returned. subseq requests that extend beyond the end of the map will throw. Returns : string Args : integer for start position AND integer for end position OR Bio::LocationI location for subseq (strand honored) OR Bio::RangeI (eg. a Bio::Map::PositionI) =cut sub subseq { my ($self, $start, $end) = @_; if ($start && ref($start) && $start->isa('Bio::RangeI')) { my $thing = $start; if ($start->isa('Bio::Map::Position')) { ($start, $end) = ($thing->start($thing->absolute_relative), $thing->end($thing->absolute_relative)); } else { ($start, $end) = ($thing->start, $thing->end); } } # *** this implementation potentially wastefull? Should duplicate code # from seq() to do this just for the desired region?? my $orig_seq = $self->{seq}; $self->{seq} = $self->seq(); my $subseq = $self->{seq} ? $self->SUPER::subseq($start, $end) : ''; $self->{seq} = $orig_seq; return $subseq; } # quick revcom for strings (silly to create a PrimarySeq just to revcom and then # return a string again) sub _revcom { my ($self, $seq) = @_; $seq or return; $seq = reverse($seq); $seq =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; return $seq; } 1; BioPerl-1.007002/Bio/Map/GenePosition.pm000555000766000024 2130213155576320 17723 0ustar00cjfieldsstaff000000000000# $Id: GenePosition.pm,v 1.19 2006/09/20 10:20:01 sendu Exp $ # # BioPerl module for Bio::Map::GenePosition # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::GenePosition - A typed position, suitable for modelling the various regions of a gene. =head1 SYNOPSIS use Bio::Map::GenePosition; use Bio::Map::GeneMap; # say that the first transcript of a particular gene on a particular map # (species) is 1000bp long my $map = Bio::Map:GeneMap->get(-universal_name => 'BRCA2', -species => 'human'); my $gene = $map->gene; Bio::Map::GenePosition->new(-map => $map, -element => $gene, -start => 0, -length => 1000, -type => 'transcript'); # say that the coding region of the gene starts 30bp into the first # transcript Bio::Map::GenePosition->new(-map => $map, -element => $gene, -start => 30, -length => 600, -type => 'coding'); # A GenePosition isa PositionWithSequence, so can have sequence associated # with it my $exon = Bio::Map::GenePosition->new(-map => $map, -element => $gene, -start => 0, -type => 'exon', -seq => 'ATGGGGTGGG'); my $length = $exon->length; # $length is 10 =head1 DESCRIPTION Define where various sub-regions (transcripts, exons, introns etc.) of a gene are. Do this so that you can then go onto to model other mappable elements as having positions 20bp upstream of transcript 2, or 10bp into intron 3 etc., all without having to know the absolute position of anything. See Bio::Map::GeneRelative and t/Map/Map.t for more example usage. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::GenePosition; use strict; use Bio::Map::GeneRelative; use base qw(Bio::Map::PositionWithSequence); =head2 new Title : new Usage : my $obj = Bio::Map::GenePosition->new(); Function: Builds a new Bio::Map::GenePosition object Returns : Bio::Map::GenePosition Args : -map => Bio::Map::GeneMap object -element => Bio::Map::Gene object -relative => Bio::Map::GeneRelative object -type => 'transcript|coding|exon|intron', REQUIRED -seq => string, length of this string will set the length of this position's range * If this position has no range, or if a single value can describe the range * -value => scalar : something that describes the single point position or range of this Position, most likely an int * Or if this position has a range, at least two of * -start => int : value of the start co-ordinate -end => int : value of the end co-ordinate -length => int : length of the range =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($type) = $self->_rearrange([qw( TYPE )], @args); $type || $self->throw("type must be supplied"); $self->type($type); $self->{_relative_not_implicit} = 1; return $self; } =head2 map Title : map Usage : my $map = $position->map(); $position->map($map); Function: Get/set the map the position is in. Returns : L Args : none to get new L to set =cut sub map { my ($self, $map) = @_; if ($map) { $map->isa('Bio::Map::GeneMap') || $self->throw("This is [$map], not a Bio::Map::GeneMap"); } return $self->SUPER::map($map); } =head2 element Title : element Usage : my $element = $position->element(); $position->element($element); Function: Get/set the element the position is for. Returns : L Args : none to get new L to set =cut sub element { my ($self, $element) = @_; if ($element) { $element->isa('Bio::Map::Gene') || $self->throw("This is [$element], not a Bio::Map::Gene"); } return $self->SUPER::element($element); } =head2 type Title : type Usage : my $type = $position->type(); $position->type($type); Function: Get/set the type of this position. Returns : string Args : none to get, OR string transcript|coding|exon|intron to set =cut sub type { my $self = shift; if (@_) { my $type = shift; if ($type !~ /transcript|coding|exon|intron/i) { $self->throw("type must be supplied and be one of 'transcript', 'coding', 'exon', 'intron'"); } $self->{type} = $type; } return $self->{type}; } =head2 relative Title : relative Usage : my $relative = $position->relative(); $position->relative($relative); Function: Get/set the thing this Position's coordinates (numerical(), start(), end()) are relative to, as described by a RelativeI object. Returns : Bio::Map::GeneRelative. The default GeneRelative returned has a meaning that depends on the type() of GenePosition this is: 'transcript' : "relative to the start of the gene on the Position's map" 'coding|exon|intron' : "relative to the start of the default transcript of the gene on the Position's map" Args : none to get, OR Bio::Map::GeneRelative to set =cut sub relative { my ($self, $relative) = @_; if ($relative) { $self->throw("Must supply an object") unless ref($relative); $self->throw("This is [$relative], not a Bio::Map::GeneRelative") unless $relative->isa('Bio::Map::GeneRelative'); $self->{_relative} = $relative; } return $self->{_relative} || $self->_default_relative; } =head2 seq Title : seq Usage : my $string = $position->seq(); Function: Get/set the sequence as a string of letters. If no sequence is manually set by you, the position's map will be asked for the sequence, and if available, that will be returned. Returns : scalar Args : Optionally on set the new value (a string). An optional second argument presets the alphabet (otherwise it will be guessed). =cut sub seq { # $shortcut is internal-use only by GeneMap my ($self, $str, $alpha, $shortcut) = @_; my $seq = $self->SUPER::seq($str, $alpha); if ($seq) { $self->length(CORE::length($seq)); return $seq; } elsif (! $shortcut && defined(my $map = $self->map) && ! defined $self->{_getting_seq}) { $self->{_getting_seq} = 1; $seq = $map->subseq($self); delete $self->{_getting_seq}; return $seq; } return; } # return a Relative that is suitable for the type sub _default_relative { my $self = shift; my $type = $self->type; if ($type eq 'transcript') { return Bio::Map::GeneRelative->new(-gene => 0, -description => 'start of gene'); } else { return Bio::Map::GeneRelative->new(-transcript => 0, -description => 'start of default transcript'); } } 1; BioPerl-1.007002/Bio/Map/GeneRelative.pm000555000766000024 2720313155576320 17700 0ustar00cjfieldsstaff000000000000# $Id: GeneRelative.pm,v 1.6 2006/09/20 11:53:29 sendu Exp $ # # BioPerl module for Bio::Map::GeneRelative # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::GeneRelative - Represents being relative to named sub-regions of a gene. =head1 SYNOPSIS use Bio::Map::GeneRelative; # say that a something will have a position relative to the start of the # gene on map my $rel = Bio::Map::GeneRelative->new(-gene => 0); # or that something will be relative to the third transcript of a gene # on a map $rel = Bio::Map::GeneRelative->new(-transcript => 3); # or to the 5th intron of the default transcript $rel = Bio::Map::GeneRelative->new(-intron => [0, 5]); # use the $rel as normal; see L =head1 DESCRIPTION Be able to say that a given position is relative to some standard part of a gene. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::GeneRelative; use strict; use Scalar::Util qw(looks_like_number); use base qw(Bio::Map::Relative); =head2 new Title : new Usage : my $relative = Bio::Map::Relative->new(); Function: Build a new Bio::Map::Relative object. Returns : Bio::Map::Relative object Args : -gene => int : coordinates are relative to the int'th base downstream of the Position's map's gene [default is gene => 0, ie. relative to the start of the gene], -transcript => int : or relative to the start of the int'th transcript of the Position's map's gene, -exon => [i, n] : or relative to the start of the n'th transcript's i'th exon, -intron => [i, n] : or intron, -coding => int : or the start of the int'th transcript's coding region. -description => string : Free text description of what this relative describes (To say a Position is relative to something and upstream of it, the Position's start() co-ordinate should be set negative) In all cases, a transcript number of 0 means the active transcript. =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($gene, $transcript, $exon, $intron, $coding) = $self->_rearrange([qw( GENE TRANSCRIPT EXON INTRON CODING )], @args); my $set = (defined $gene) + (defined $transcript) + (defined $exon) + (defined $intron) + (defined $coding); if ($set > 1) { $self->throw("-gene, -transcript, -exon, -intron and -coding are mutually exclusive"); } if ($exon && (! ref($exon) || ref($exon) ne 'ARRAY')) { $self->throw("-exon takes an array ref"); } if ($intron && (! ref($intron) || ref($intron) ne 'ARRAY')) { $self->throw("-intron takes an array ref"); } if ($set == 0) { # type could have been set already in the call to SUPER::new if ($self->type) { $self->warn("You set a type of relative not supported by GeneRelative; resetting to type 'gene'"); } $gene = 0; } $self->gene($gene) if defined $gene; $self->transcript($transcript) if defined $transcript; $self->exon(@{$exon}) if defined $exon; $self->intron(@{$intron}) if defined $intron; $self->coding($coding) if defined $coding; return $self; } =head2 absolute_conversion Title : absolute_conversion Usage : my $absolute_coord = $relative->absolute_conversion($pos); Function: Convert the start co-ordinate of the supplied position into a number relative to the start of its map. Returns : scalar number Args : Bio::Map::PositionI object =cut sub absolute_conversion { my ($self, $pos) = @_; $self->throw("Must supply an object") unless ref($pos); $self->throw("This is [$pos], not a Bio::Map::PositionI") unless $pos->isa('Bio::Map::PositionI'); # get the raw start position of our position my $raw = $pos->start($pos->relative); $self->throw("Can't convert co-ordinates when start isn't set") unless defined($raw); #*** needed? return undef? # what are we relative to? my $type = $self->type; my $value = $self->$type; $self->throw("Details not yet set for this Relative, cannot convert") unless defined($value); # get the absolute start of the thing we're relative to if ($type =~ /gene|transcript|exon|intron|coding/) { my $map = $pos->map; my $throw_desc = $type eq 'gene' ? 'gene' : "gene's transcript"; $self->throw("Relative to a map's $throw_desc, but the Position has no map") unless $map; $self->throw("Relative to a map's $throw_desc, but the Position's map isn't a Bio::Map::GeneMap") unless $map->isa('Bio::Map::GeneMap'); my $gene = $map->gene; if ($type eq 'gene') { my $gene_pos = $gene->position($map); my $rel = $gene_pos->relative; my $start = $rel->absolute_conversion($gene_pos); $value += $start; } else { my @values = ref($value) ? @{$value} : ($value); my $trans = ref($value) ? $values[1] : $value; my $throw_txt = $trans == 0 ? 'default/active transcript' : "transcript $trans"; my $throw_txt2 = ref($value) ? ", or no $type $values[0]" : ''; my $method = $type eq 'coding' ? 'coding_position' : "get_${type}_position"; $value = $gene->$method($map, @values) || $self->throw("Relative to $throw_txt of the map's gene, but there is no such transcript$throw_txt2"); } } else { return $self->SUPER::absolute_conversion($pos); } if (ref($value)) { # pseudo-recurse my $rel = $value->relative; $value = $rel->absolute_conversion($value); } if (defined($value)) { return $value + $raw; } return; } =head2 type Title : type Usage : my $type = $relative->type(); Function: Get the type of thing we are relative to. The types correspond to a method name, so the value of what we are relative to can subsequently be found by $value = $relative->$type; Note that type is set by the last method that was set, or during new(). Returns : 'gene', 'transcript', 'exon', 'intron' or 'coding' Args : none =cut =head2 gene Title : gene Usage : my $int = $relative->gene(); $relative->gene($int); Function: Get/set the distance from the start of the gene that the Position's co-ordiantes are relative to. Returns : int Args : none to get, OR int to set; a value of 0 means relative to the start of the gene. =cut sub gene { my ($self, $num) = @_; if (defined($num)) { $self->throw("This is [$num], not a number") unless looks_like_number($num); $self->{_use} = 'gene'; $self->{_gene} = $num; } return defined($self->{_gene}) ? $self->{_gene} : return; } =head2 transcript Title : transcript Usage : my $int = $relative->transcript(); $relative->transcript($int); Function: Get/set which transcript of the Position's map's gene the Position's co-ordinates are relative to. Returns : int Args : none to get, OR int to set; a value of 0 means the active (default) transcript. =cut sub transcript { my ($self, $num) = @_; if (defined($num)) { $self->throw("This is [$num], not a number") unless looks_like_number($num); $self->{_use} = 'transcript'; $self->{_transcript} = $num; } return defined($self->{_transcript}) ? $self->{_transcript} : return; } =head2 exon Title : exon Usage : my ($exon_number, $transcript_number) = @{$relative->exon()}; $relative->exon($exon_number, $transcript_number); Function: Get/set which exon of which transcript of the Position's map's gene the Position's co-ordinates are relative to. Returns : reference to list with two ints, exon number and transcript number Args : none to get, OR int (exon number) AND int (transcript number) to set. The second int is optional and defaults to 0 (meaning default/active transcript). =cut sub exon { my ($self, $num, $t_num) = @_; if (defined($num)) { if (defined($t_num)) { $self->throw("This is [$t_num], not a number") unless looks_like_number($t_num); } $t_num ||= 0; $self->throw("This is [$num], not a number") unless looks_like_number($num); $self->{_use} = 'exon'; $self->{_exon} = [$num, $t_num]; } return $self->{_exon} || return; } =head2 intron Title : intron Usage : my ($intron_number, $transcript_number) = @{$relative->intron()}; $relative->intron($intron_number, $transcript_number); Function: Get/set which intron of which transcript of the Position's map's gene the Position's co-ordinates are relative to. Returns : reference to list with two ints, intron number and transcript number Args : none to get, OR int (intron number) AND int (transcript number) to set. The second int is optional and defaults to 0 (meaning default/active transcript). =cut sub intron { my ($self, $num, $t_num) = @_; if (defined($num)) { if (defined($t_num)) { $self->throw("This is [$t_num], not a number") unless looks_like_number($t_num); } $t_num ||= 0; $self->throw("This is [$num], not a number") unless looks_like_number($num); $self->{_use} = 'intron'; $self->{_intron} = [$num, $t_num]; } return $self->{_intron} || return; } =head2 coding Title : coding Usage : my $transcript_number = $relative->coding; $relative->coding($transcript_number); Function: Get/set which transcript's coding region of the Position's map's gene the Position's co-ordinates are relative to. Returns : int Args : none to get, OR int to set (the transcript number, see transcript()) =cut sub coding { my ($self, $num) = @_; if (defined($num)) { $self->throw("This is [$num], not a number") unless looks_like_number($num); $self->{_use} = 'coding'; $self->{_coding} = $num; } return defined($self->{_coding}) ? $self->{_coding} : return; } 1; BioPerl-1.007002/Bio/Map/LinkageMap.pm000444000766000024 1317513155576320 17336 0ustar00cjfieldsstaff000000000000# BioPerl module for Bio::Map::LinkageMap # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::LinkageMap - A representation of a genetic linkage map. =head1 SYNOPSIS use Bio::Map::LinkageMap; # create a new map my $map = Bio::Map::LinkageMap->new(-name => 'Chads Superterriffic Map', -type => 'Linkage', -units=> 'cM'); # create the location of a marker for that map my $position = Bio::Map::LinkagePosition->new( -positions => 1, -distance => "22.3"); # create a marker and place it at that position my $marker = Bio::Map::Marker::Microsatellite->new( -name => 'SuuuperMarker', -position => $position); # place that marker on that map $map->add_element($marker); # done! =head1 DESCRIPTION This object describes the basic functionality of a genetic linkage map in Bioperl. Each 'position' can have one or more markers that map some number of units from the markers at the previous position. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics1@dieselwurks.com =head1 CONTRIBUTORS Lincoln Stein lstein@cshl.org Heikki Lehvaslaiho heikki-at-bioperl-dot-org Jason Stajich jason@bioperl.org Sendu Bala bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::LinkageMap; use strict; use base qw(Bio::Map::SimpleMap); =head2 new Title : new Usage : my $linkage_map = Bio::Map::LinkageMap->new(); Function: Builds a new Bio::Map::LinkageMap object Returns : Bio::Map::LinkageMap Args : -name => the name of the map (string) [optional] -type => the type of this map (string, defaults to Linkage) [optional] -species => species for this map (Bio::Species) [optional] -units => the map units (string, defaults to cM) [optional] -elements=> elements to initialize with (arrayref of Bio::Map::MappableI objects) [optional] -uid => Unique ID of this map =cut =head2 length Title : length Usage : my $length = $map->length(); Function: Retrieves the length of the map. In the case of a LinkageMap, the length is the sum of all marker distances. Returns : An integer representing the length of this LinkageMap. Will return 0 if length is not calculateable Args : None. =cut sub length { my ($self) = @_; $self->throw("Not yet implemented correctly"); my $total_distance; foreach my $element (@{$self->get_elements}) { #*** there is no such method ->each_position_value! $total_distance += ($element->position->each_position_value($self))[0]; } return $total_distance; } =head2 add_element($marker) Title : add_element($marker) Usage : $map->add_element($marker) Function: Add a Bio::Map::MappableI object to the Map Returns : none Args : Bio::Map::MappableI object Notes : It is strongly recommended that you use a Bio::Map::LinkagePosition as the position in any Bio::Map::Mappable that you create to place on this map. Using some other Bio::Map::Position might work but might be unpredictable. N.B. I've added Bio::Map::OrderedPosition which should achieve similar things from LinkagePosition and will work for RH markers too. =cut #*** what is this? what calls it? note that it seems to be private sub _add_element_will_be_deleted { my ($self,$marker) = @_; my $o_position = $marker->position(); $self->debug( "marker position is ". $marker->position()); # print("add_element: \$o_position is $o_position\n"); # print("add_element: \$marker is $marker\n"); my $position; unless ( $o_position->isa('Bio::Map::LinkagePosition') || $o_position->isa('Bio::Map::OrderedPosition') ) { $self->warn("You really should use a Linkage Position for this object. This insures that there is only one position. Trying anyway..."); my @p = ( $o_position->each_position_value($self)); $position = shift @p; if( ! defined $position ) { $self->throw("This marker ($marker) does not have a position in this map ($self)"); } } else { $position = $o_position->order; } if ($self->{'_elements'}[$position]) { $self->warn("Replacing the marker in position $position because in a linkage map the position is a key."); } $self->{'_elements'}[$position] = $marker; } 1; BioPerl-1.007002/Bio/Map/LinkagePosition.pm000444000766000024 562013155576320 20401 0ustar00cjfieldsstaff000000000000# BioPerl module for Bio::Map::LinkagePosition # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::LinkagePosition - Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap =head1 SYNOPSIS use Bio::Map::Position; my $position = Bio::Map::LinkagePosition->new(-positions => 1, -distance => 22.1 ); # can get listing of positions my @positions = $position->each_position; =head1 DESCRIPTION Position for a Bio::Map::MarkerI compliant object that will be placed on a Bio::Map::LinkageMap. See L and L for details =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics1@dieselwurks.com =head1 CONTRIBUTORS Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Jason Stajich jason@bioperl.org Sendu Bala bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::LinkagePosition; use strict; use base qw(Bio::Map::OrderedPosition); =head2 new Title : new Usage : my $obj = Bio::Map::LinkagePosition->new(-positions => $position, -distance => $distance); Function: Builds a new Bio::Map::LinkagePosition object Returns : Bio::Map::LinkagePosition Args : -order => the relative order of this marker on a linkage map -positions => positions on a map =cut =head2 Bio::Map::PositionI methods =cut =head2 order Title : order Usage : $o_position->order($order) my $order = $o_position->order() Function: get/set the order position of this position in a map Returns : int Args : none to get, int to set =cut 1; BioPerl-1.007002/Bio/Map/MapI.pm000444000766000024 2211513155576320 16146 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::MapI # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::MapI - Interface for describing Map objects in bioperl =head1 SYNOPSIS # get a MapI somehow my $name = $map->name(); # string my $length = $map->length(); # integer my $species= $map->species; # Bio::Species my $type = $map->type(); # genetic/sts/rh/ =head1 DESCRIPTION This object describes the basic functionality of a Map in bioperl. Maps are anything from Genetic Map to Sequence Map to Assembly Map to Restriction Enzyme to FPC. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 CONTRIBUTORS Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::MapI; use strict; use Bio::Map::PositionHandler; use base qw(Bio::Map::EntityI Bio::AnnotatableI); =head2 EntityI methods These are fundamental to coordination of Maps and other entities, so are implemented at the interface level =cut =head2 get_position_handler Title : get_position_handler Usage : my $position_handler = $entity->get_position_handler(); Function: Gets a PositionHandlerI that $entity is registered with. Returns : Bio::Map::PositionHandlerI object Args : none =cut sub get_position_handler { my $self = shift; unless (defined $self->{_eh}) { my $ph = Bio::Map::PositionHandler->new(-self => $self); $self->{_eh} = $ph; $ph->register; } return $self->{_eh}; } =head2 PositionHandlerI-related methods These are fundamental to coordination of Maps and other entities, so are implemented at the interface level =cut =head2 get_positions Title : get_positions Usage : my @positions = $mappable->get_positions(); Function: Get all the Positions on this Map (sorted). Returns : Array of L objects Args : none for all, OR L object for positions of the given Mappable =cut sub get_positions { my ($self, $mappable) = @_; my @positions = $self->get_position_handler->get_positions($mappable); # precompute sortable for effieciency and to avoid bugs @positions = map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [$_->sortable, $_] } @positions; return @positions; } =head2 each_position Title : each_position Function: Synonym of the get_positions() method. Status : deprecated, will be removed in next version =cut *each_position = \&get_positions; =head2 purge_positions Title : purge_positions Usage : $map->purge_position(); Function: Remove all positions from this map. Notifies the positions they are no longer on this map. Returns : n/a Args : none to remove all positions, OR L object to remove just that Position, OR L object to remove only those positions of the given mappable =cut sub purge_positions { my ($self, $thing) = @_; $self->get_position_handler->purge_positions($thing); } =head2 get_elements Title : get_elements Usage : my @elements = $map->get_elements; Function: Retrieves all the elements on a map (unordered) Returns : Array of Map elements (L) Args : none =cut sub get_elements { my $self = shift; return $self->get_position_handler->get_other_entities; } =head2 each_element Title : each_element Function: Synonym of the get_elements() method. Status : deprecated, will be removed in the next version =cut =head2 common_elements Title : common_elements Usage : my @common_elements = $map->common_elements(\@other_maps); my @common_elements = Bio::Map::SimpleMap->common_elements(\@maps); Function: Find the elements that are common to multiple maps. Returns : array of Bio::Map::MappableI Args : arg #1 = L to compare this one to, or an array ref of such objects (mandatory) arg #2 = optionally, one or more of the key => value pairs below -min_num => int : the minimum number of input maps an element must be found on before before returned [default is 1] -min_percent => number : as above, but the minimum percentage of input maps [default is 100 - note that this will effectively override all other options] -require_self => 1|0 : require that all output elements at least be on the calling map [default is 1, has no effect when the second usage form is used] -required => \@maps : require that all output elements be on at least all the maps supplied here =cut sub common_elements { my ($self, $maps_ref, @extra_args) = @_; $self->throw("Must supply a reference first argument") unless ref($maps_ref); my @maps; if (ref($maps_ref) eq 'ARRAY') { @maps = @{$maps_ref}; } elsif ($maps_ref->isa('Bio::Map::MapI')) { @maps = ($maps_ref); } if (ref($self)) { unshift(@maps, $self); } $self->throw("Need at least 2 maps") unless @maps >= 2; my %args = (-min_num => 1, -min_percent => 100, -require_self => 1, -required => undef, @extra_args); my $min_num = $args{-min_num}; if ($args{-min_percent}) { my $mn = @maps / 100 * $args{-min_percent}; if ($mn > $min_num) { $min_num = $mn; } } my %required = map { $_ => 1 } $args{-required} ? @{$args{-required}} : (); $required{$self} = 1 if ref($self) && $args{-require_self}; my @required = keys %required; my %map_elements; my %elements; my %count; foreach my $map (@maps) { $map_elements{$map} = {}; foreach my $element ($map->get_elements) { $map_elements{$map}->{$element} = 1; $elements{$element} = $element; $count{$element}++; } } my @elements; ELEMENT: while (my ($key, $value) = each %elements) { $count{$key} >= $min_num or next; foreach my $required (@required) { exists $map_elements{$required}->{$key} or next ELEMENT; } push(@elements, $value); } return @elements; } =head2 MapI-specific methods =cut =head2 species Title : species Usage : my $species = $map->species; Function: Get/Set Species for a map Returns : L object Args : (optional) Bio::Species =cut sub species{ my $self = shift; $self->throw_not_implemented(); } =head2 units Title : units Usage : $map->units('cM'); Function: Get/Set units for a map Returns : units for a map Args : units for a map (string) =cut sub units{ my $self = shift; $self->throw_not_implemented(); } =head2 type Title : type Usage : my $type = $map->type Function: Get/Set Map type Returns : String coding map type Args : (optional) string =cut sub type { my $self = shift; $self->throw_not_implemented(); } =head2 name Title : name Usage : my $name = $map->name Function: Get/Set Map name Returns : Map name Args : (optional) string =cut sub name { my $self = shift; $self->throw_not_implemented(); } =head2 length Title : length Usage : my $length = $map->length(); Function: Retrieves the length of the map. It is possible for the length to be unknown for maps such as Restriction Enzyme, will return 0 in that case Returns : integer representing length of map in current units will return undef if length is not calculateable Args : none =cut sub length { my $self = shift; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Map/Mappable.pm000555000766000024 6736313155576320 17062 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::Mappable # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::Mappable - An object representing a generic map element that can have multiple locations in several maps. =head1 SYNOPSIS # a map element in two different positions on the same map $map1 = Bio::Map::SimpleMap->new(); $position1 = Bio::Map::Position->new(-map => $map1, -value => 100); $position2 = Bio::Map::Position->new(-map => $map1, -value => 200); $mappable = Bio::Map::Mappable->new(-positions => [$position1, $position2] ); # add another position on a different map $map2 = Bio::Map::SimpleMap->new(); $position3 = Bio::Map::Position->new(-map => $map2, $value => 50); $mappable->add_position($position3); # get all the places our map element is found, on a particular map of interest foreach $pos ($mappable->get_positions($map1)) { print $pos->value, "\n"; } =head1 DESCRIPTION This object handles the notion of a generic map element. Mappables are entities with one or more positions on one or more maps. This object is a pure perl implementation of L. That interface implements some of its own methods so check the docs there for those. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::Mappable; use strict; use Bio::Map::Relative; use Bio::Map::Position; use base qw(Bio::Root::Root Bio::Map::MappableI); =head2 new Title : new Usage : my $mappable = Bio::Map::Mappable->new(); Function: Builds a new Bio::Map::Mappable object Returns : Bio::Map::Mappable Args : -name => string : name of the mappable element -id => string : id of the mappable element =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($name, $id) = $self->_rearrange([qw(NAME ID)], @args); $self->name($name) if $name; $self->id($id) if $id; return $self; } =head2 name Title : name Usage : $mappable->name($new_name); my $name = $mappable->name(); Function: Get/Set the name for this Mappable Returns : A scalar representing the current name of this Mappable Args : none to get string to set =cut sub name { my $self = shift; if (@_) { $self->{_name} = shift } return $self->{_name} || ''; } =head2 id Title : id Usage : my $id = $mappable->id(); $mappable->id($new_id); Function: Get/Set the id for this Mappable. Returns : A scalar representing the current id of this Mappable Args : none to get string to set =cut sub id { my $self = shift; if (@_) { $self->{_id} = shift } return $self->{_id} || return; } =head2 in_map Title : in_map Usage : if ($mappable->in_map($map)) {...} Function: Tests if this mappable is found on a specific map Returns : boolean Args : L =cut sub in_map { my ($self, $query_map) = @_; $self->throw("Must supply an argument") unless $query_map; $self->throw("This is [$query_map], not an object") unless ref($query_map); $self->throw("This is [$query_map], not a Bio::Map::MapI object") unless $query_map->isa('Bio::Map::MapI'); foreach my $map ($self->known_maps) { ($map eq $query_map) && return 1; } return 0; } =head2 Comparison methods =cut =head2 equals Title : equals Usage : if ($mappable->equals($other_mappable)) {...} my @equal_positions = $mappable->equals($other_mappable); Function: Finds the positions in this mappable that are equal to any comparison positions. Returns : array of L objects Args : arg #1 = L OR L to compare this one to (mandatory) arg #2 = optionally, one or more of the key => value pairs below -map => MapI : a Bio::Map::MapI to only consider positions on the given map -relative => RelativeI : a Bio::Map::RelativeI to calculate in terms of each Position's relative position to the thing described by that Relative =cut sub equals { my $self = shift; return $self->_compare('equals', @_); } =head2 less_than Title : less_than Usage : if ($mappable->less_than($other_mappable)) {...} my @lesser_positions = $mappable->less_than($other_mappable); Function: Finds the positions in this mappable that are less than all comparison positions. Returns : array of L objects Args : arg #1 = L OR L to compare this one to (mandatory) arg #2 = optionally, one or more of the key => value pairs below -map => MapI : a Bio::Map::MapI to only consider positions on the given map -relative => RelativeI : a Bio::Map::RelativeI to calculate in terms of each Position's relative position to the thing described by that Relative =cut sub less_than { my $self = shift; return $self->_compare('less_than', @_); } =head2 greater_than Title : greater_than Usage : if ($mappable->greater_than($other_mappable)) {...} my @greater_positions = $mappable->greater_than($other_mappable); Function: Finds the positions in this mappable that are greater than all comparison positions. Returns : array of L objects Args : arg #1 = L OR L to compare this one to (mandatory) arg #2 = optionally, one or more of the key => value pairs below -map => MapI : a Bio::Map::MapI to only consider positions on the given map -relative => RelativeI : a Bio::Map::RelativeI to calculate in terms of each Position's relative position to the thing described by that Relative =cut sub greater_than { my $self = shift; return $self->_compare('greater_than', @_); } =head2 overlaps Title : overlaps Usage : if ($mappable->overlaps($other_mappable)) {...} my @overlapping_positions = $mappable->overlaps($other_mappable); Function: Finds the positions in this mappable that overlap with any comparison positions. Returns : array of L objects Args : arg #1 = L OR L to compare this one to (mandatory) arg #2 = optionally, one or more of the key => value pairs below -map => MapI : a Bio::Map::MapI to only consider positions on the given map -relative => RelativeI : a Bio::Map::RelativeI to calculate in terms of each Position's relative position to the thing described by that Relative =cut sub overlaps { my $self = shift; return $self->_compare('overlaps', @_); } =head2 contains Title : contains Usage : if ($mappable->contains($other_mappable)) {...} my @container_positions = $mappable->contains($other_mappable); Function: Finds the positions in this mappable that contain any comparison positions. Returns : array of L objects Args : arg #1 = L OR L to compare this one to (mandatory) arg #2 = optionally, one or more of the key => value pairs below -map => MapI : a Bio::Map::MapI to only consider positions on the given map -relative => RelativeI : a Bio::Map::RelativeI to calculate in terms of each Position's relative position to the thing described by that Relative =cut sub contains { my $self = shift; return $self->_compare('contains', @_); } =head2 overlapping_groups Title : overlapping_groups Usage : my @groups = $mappable->overlapping_groups($other_mappable); my @groups = Bio::Map::Mappable->overlapping_groups(\@mappables); Function: Look at all the positions of all the supplied mappables and group them according to overlap. Returns : array of array refs, each ref containing the Bio::Map::PositionI objects that overlap with each other Args : arg #1 = L OR L to compare this one to, or an array ref of such objects (mandatory) arg #2 = optionally, one or more of the key => value pairs below -map => MapI : a Bio::Map::MapI to only consider positions on the given map -relative => RelativeI : a Bio::Map::RelativeI to calculate in terms of each Position's relative position to the thing described by that Relative -min_pos_num => int : the minimum number of positions that must be in a group before it will be returned [default is 1] -min_mappables_num => int : the minimum number of different mappables represented by the positions in a group before it will be returned [default is 1] -min_mappables_percent => number : as above, but the minimum percentage of input mappables [default is 0] -min_map_num => int : the minimum number of different maps represented by the positions in a group before it will be returned [default is 1] -min_map_percent => number : as above, but the minimum percentage of maps known by the input mappables [default is 0] -require_self => 1|0 : require that at least one of the calling object's positions be in each group [default is 1, has no effect when the second usage form is used] -required => \@mappables : require that at least one position for each mappable supplied in this array ref be in each group =cut sub overlapping_groups { my $self = shift; return $self->_compare('overlapping_groups', @_); } =head2 disconnected_intersections Title : disconnected_intersections Usage : @positions = $mappable->disconnected_intersections($other_mappable); @positions = Bio::Map::Mappable->disconnected_intersections(\@mappables); Function: Make the positions that are at the intersection of each group of overlapping positions, considering all the positions of the supplied mappables. Returns : new Bio::Map::Mappable who's positions on maps are the calculated disconnected unions Args : arg #1 = L OR L to compare this one to, or an array ref of such objects (mandatory) arg #2 = optionally, one or more of the key => value pairs below -map => MapI : a Bio::Map::MapI to only consider positions on the given map -relative => RelativeI : a Bio::Map::RelativeI to calculate in terms of each Position's relative position to the thing described by that Relative -min_pos_num => int : the minimum number of positions that must be in a group before the intersection will be calculated and returned [default is 1] -min_mappables_num => int : the minimum number of different mappables represented by the positions in a group before the intersection will be calculated and returned [default is 1] -min_mappables_percent => number : as above, but the minimum percentage of input mappables [default is 0] -min_map_num => int : the minimum number of different maps represented by the positions in a group before the intersection will be calculated and returned [default is 1] -min_map_percent => number : as above, but the minimum percentage of maps known by the input mappables [default is 0] -require_self => 1|0 : require that at least one of the calling object's positions be in each group [default is 1, has no effect when the second usage form is used] -required => \@mappables : require that at least one position for each mappable supplied in this array ref be in each group =cut sub disconnected_intersections { my $self = shift; return $self->_compare('intersection', @_); } =head2 disconnected_unions Title : disconnected_unions Usage : my @positions = $mappable->disconnected_unions($other_mappable); my @positions = Bio::Map::Mappable->disconnected_unions(\@mappables); Function: Make the positions that are the union of each group of overlapping positions, considering all the positions of the supplied mappables. Returns : new Bio::Map::Mappable who's positions on maps are the calculated disconnected unions Args : arg #1 = L OR L to compare this one to, or an array ref of such objects (mandatory) arg #2 = optionally, one or more of the key => value pairs below -map => MapI : a Bio::Map::MapI to only consider positions on the given map -relative => RelativeI : a Bio::Map::RelativeI to calculate in terms of each Position's relative position to the thing described by that Relative -min_pos_num => int : the minimum number of positions that must be in a group before the union will be calculated and returned [default is 1] -min_mappables_num => int : the minimum number of different mappables represented by the positions in a group before the union will be calculated and returned [default is 1] -min_mappables_percent => number : as above, but the minimum percentage of input mappables [default is 0] -min_map_num => int : the minimum number of different maps represented by the positions in a group before the union will be calculated and returned [default is 1] -min_map_percent => number : as above, but the minimum percentage of maps known by the input mappables [default is 0] -require_self => 1|0 : require that at least one of the calling object's positions be in each group [default is 1, has no effect when the second usage form is used] -required => \@mappables : require that at least one position for each mappable supplied in this array ref be in each group =cut sub disconnected_unions { my $self = shift; return $self->_compare('union', @_); } # do a RangeI-related comparison by calling the corresponding PositionI method # on all the requested Positions of our Mappables sub _compare { my ($self, $method, $input, @extra_args) = @_; $self->throw("Must supply an object or array ref of them") unless ref($input); $self->throw("Wrong number of extra args (should be key => value pairs)") unless @extra_args % 2 == 0; my @compares = ref($input) eq 'ARRAY' ? @{$input} : ($input); my %args = (-map => undef, -relative => undef, -min_pos_num => 1, -min_mappables_num => 1, -min_mappables_percent => 0, -min_map_num => 1, -min_map_percent => 0, -require_self => 0, -required => undef, -min_overlap_percent => 0, @extra_args); my $map = $args{-map}; my $rel = $args{-relative}; my $overlap = $args{-min_overlap_percent}; my $min_pos_num = $args{-min_pos_num}; my $min_pables_num = $args{-min_mappables_num}; if ($args{-min_mappables_percent}) { my $mn = (@compares + (ref($self) ? 1 : 0)) / 100 * $args{-min_mappables_percent}; if ($mn > $min_pables_num) { $min_pables_num = $mn; } } my $min_map_num = $args{-min_map_num}; if ($args{-min_map_percent}) { my %known_maps; foreach my $pable (@compares, ref($self) ? ($self) : ()) { foreach my $known ($pable->known_maps) { $known_maps{$known->unique_id} = 1; } } my $mn = scalar(keys %known_maps) / 100 * $args{-min_map_percent}; if ($mn > $min_map_num) { $min_map_num = $mn; } } my %required = map { $_ => 1 } $args{-required} ? @{$args{-required}} : (); my (@mine, @yours); if (ref($self)) { @mine = $self->get_positions($map); if ($args{-require_self}) { @mine > 0 or return; $required{$self} = 1; } } my @required = sort keys %required; foreach my $compare (@compares) { if ($compare->isa('Bio::Map::PositionI')) { push(@yours, $compare); } elsif ($compare->isa('Bio::Map::MappableI')) { push(@yours, $compare->get_positions($map)); } else { $self->throw("This is [$compare], not a Bio::Map::MappableI or Bio::Map::PositionI"); } } @yours > 0 or return; my @ok; SWITCH: for ($method) { /equals|overlaps|contains/ && do { @mine > 0 or return; foreach my $my_pos (@mine) { foreach my $your_pos (@yours) { if ($my_pos->$method($your_pos, undef, $rel)) { push(@ok, $my_pos); last; } } } last SWITCH; }; /less_than|greater_than/ && do { @mine > 0 or return; if ($method eq 'greater_than') { @mine = map { $_->[1] } sort { $b->[0] <=> $a->[0] } map { [$_->end($_->absolute_relative), $_] } @mine; @yours = map { $_->[1] } sort { $b->[0] <=> $a->[0] } map { [$_->end($_->absolute_relative), $_] } @yours; } my $test_pos = shift(@yours); foreach my $my_pos (@mine) { if ($my_pos->$method($test_pos, $rel)) { push(@ok, $my_pos); } else { last; } } if ($method eq 'greater_than') { @ok = map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [$_->sortable, $_] } @ok; } last SWITCH; }; /overlapping_groups|intersection|union/ && do { my @positions = (@mine, @yours); my $start_pos = shift(@positions); my $dr_able = $start_pos->disconnected_ranges(\@positions, $rel, $overlap) || return; my @disconnected_ranges = $dr_able->get_positions; #print "got ", scalar(@disconnected_ranges), " disconnected_ranges, first has range ", $disconnected_ranges[0]->toString, "\n"; #use Benchmark qw(:all); #my $t0 = new Benchmark; my %all_groups; my %done_ranges; for my $i (0..$#disconnected_ranges) { my $range = $disconnected_ranges[$i]; my $range_string = $range->toString; next if $done_ranges{$range_string}; $done_ranges{$range_string} = 1; foreach my $pos ($start_pos, @positions) { if ($pos->overlaps($range, undef, $rel)) { $all_groups{$range_string}->{$pos} = $pos; } } } #my $t1 = new Benchmark; #my $td = timediff($t1, $t0); #print "grouping took: ",timestr($td),"\n"; # purge the temporary working (not $dr_able->purge_positions since # that removes the element from each position, but leaves it on # the map. *** need complete purge that removes position from # memory... foreach my $pos (@disconnected_ranges) { my $map = $pos->map || next; $map->purge_positions($pos); } my @groups; GROUPS: foreach my $group_range (sort keys %all_groups) { my $group = $all_groups{$group_range}; my @group = sort values %{$group}; #print "* in group $group_range, there are ", scalar(@group), " members\n"; @group >= $min_pos_num or next; @group >= $min_pables_num or next; # shortcut before having to work it out properly @group >= $min_map_num or next; # shortcut before having to work it out properly my %mappables; foreach my $pos (@group) { my $mappable = $pos->element || next; $mappables{$mappable} = 1; } keys %mappables >= $min_pables_num || next; my %maps; foreach my $pos (@group) { my $map = $pos->map || next; $maps{$map->unique_id} = 1; } keys %maps >= $min_map_num || next; foreach my $required (@required) { exists $mappables{$required} or next GROUPS; } my @sorted = map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [$_->sortable, $_] } @group; push(@groups, \@sorted); } if ($method eq 'overlapping_groups') { return @groups; } else { foreach my $group (@groups) { my $start_pos = shift(@{$group}); unless (@{$group}) { # we'll consider the 'intersection' or 'union' of just # one position as the position itself push(@ok, Bio::Map::Position->new(-map => $start_pos->map, -start => $start_pos->start, -end => $start_pos->end)); } else { my @rel_arg = $method eq 'intersection' ? (undef, $rel) : ($rel); my $result = $start_pos->$method($group, @rel_arg) || next; push(@ok, $result->get_positions); } } # assign all the positions to a result mappable my $result = $self->new(); $result->add_position(@ok) if @ok; # add_position can actually take a list return $result; } last SWITCH; }; $self->throw("Unknown method '$method'"); } return @ok; } =head2 tuple Title : tuple Usage : Do Not Use! Function: tuple was supposed to be a private method; this method no longer does anything Returns : warning Args : none Status : deprecated, will be removed in next version =cut sub tuple { my $self = shift; $self->warn("The tuple method was supposed to be a private method, don't call it!"); } =head2 annotation Title : annotation Usage : $mappable->annotation($an_col); my $an_col = $mappable->annotation(); Function: Get the annotation collection (see Bio::AnnotationCollectionI) for this annotatable object. Returns : a Bio::AnnotationCollectionI implementing object, or undef Args : none to get, OR a Bio::AnnotationCollectionI implementing object to set =cut sub annotation { my $self = shift; if (@_) { $self->{_annotation} = shift } return $self->{_annotation} || return; } 1; BioPerl-1.007002/Bio/Map/MappableI.pm000444000766000024 2717713155576320 17167 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::MappableI # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::MappableI - An object that can be placed in a map =head1 SYNOPSIS # do not use this module directly # See Bio::Map::Mappable for an example of # implementation. =head1 DESCRIPTION This object handles the generic notion of an element placed on a (linear) Map. A Mappable can have multiple positions in multiple maps, such as is the case of Restriction enzyme cut sites on sequence maps. For exact information about a mappable's position in a map one must query the associate PositionI objects which are accessible through the get_positions() method. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 CONTRIBUTORS Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein lstein@cshl.org Sendu Bala bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::MappableI; use strict; use Bio::Map::PositionHandler; use base qw(Bio::Map::EntityI Bio::AnnotatableI); =head2 EntityI methods These are fundamental to coordination of Mappables and other entities, so are implemented at the interface level =cut =head2 get_position_handler Title : get_position_handler Usage : my $position_handler = $entity->get_position_handler(); Function: Gets a PositionHandlerI that $entity is registered with. Returns : Bio::Map::PositionHandlerI object Args : none =cut sub get_position_handler { my $self = shift; unless (defined $self->{_eh}) { my $ph = Bio::Map::PositionHandler->new(-self => $self); $self->{_eh} = $ph; $ph->register; } return $self->{_eh}; } =head2 PositionHandlerI-related methods These are fundamental to coordination of Mappables and other entities, so are implemented at the interface level =cut =head2 add_position Title : add_position Usage : $mappable->add_position($position); Function: Add a position to this mappable (defining where on which map it is). Returns : n/a Args : L object =cut sub add_position { my $self = shift; # actually, we allow multiple positions to be set at once $self->get_position_handler->add_positions(@_); } =head2 get_positions Title : get_positions Usage : my @positions = $mappable->get_positions(); Function: Get all the Positions of this Mappable (sorted). Returns : Array of L objects Args : none for all, OR L object for positions on the given map, AND/OR some other true value to avoid sorting =cut sub get_positions { my ($self, $thing, $no_sort) = @_; my $map; if (ref($thing) && $thing->isa('Bio::Map::MapI')) { $map = $thing; } else { $no_sort = $thing; } my @positions = $self->get_position_handler->get_positions($map); return @positions if @positions == 1; unless ($no_sort) { # don't do # @positions = sort { $a->sortable <=> $b->sortable } @positions; # directly since sortable() can result in the call of another sort # routine and cause problems; pre-compute sortable values instead # (which is also more efficient) @positions = map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [$_->sortable, $_] } @positions; } return @positions; } =head2 each_position Title : each_position Function: Synonym of the get_positions() method. Status : deprecated, will be removed in next version =cut *each_position = \&get_positions; =head2 purge_positions Title : purge_positions Usage : $mappable->purge_positions(); Function: Remove positions from this mappable. Returns : n/a Args : none to remove all positions, OR L object to remove just that Position, OR L object to remove only those positions on the given map =cut sub purge_positions { my ($self, $thing) = @_; $self->get_position_handler->purge_positions($thing); } =head2 known_maps Title : known_maps Usage : my @maps = $marker->known_maps() Function: Returns the maps that this mappable is found on Returns : Array of L objects Args : none =cut sub known_maps { my $self = shift; return $self->get_position_handler->get_other_entities; } =head2 MappableI-specific methods =cut =head2 name Title : name Usage : my $name = $marker->name(); $marker->name($new_name); Function: Get/Set the name for this Mappable. Returns : A scalar representing the current name of this Mappable Args : none to get string to set =cut sub name { my $self = shift; $self->throw_not_implemented(); } =head2 id Title : id Usage : my $id = $marker->id(); $marker->id($new_id); Function: Get/Set the id for this Mappable. Returns : A scalar representing the current id of this Mappable Args : none to get string to set =cut sub id { my $self = shift; $self->throw_not_implemented(); } =head2 in_map Title : in_map Usage : if ($marker->in_map($map)) {...} Function: Tests if this mappable is found on a specific map Returns : boolean Args : L =cut sub in_map { my $self = shift; $self->throw_not_implemented(); } =head1 RangeI-related Methods They throw an error if start and end are not defined in the Positions of the Mappables supplied. =cut =head2 equals Title : equals Usage : if ($mappable->equals($other_mappable)) {...} my @equal_positions = $mappable->equals($other_mappable); Function: Finds the positions in this mappable that are equal to any comparison positions. Returns : array of L objects Args : arg #1 = L OR L to compare this one to (mandatory) arg #2 = optionally, the key => value pairs below -map => Bio::Map::MapI : optionally a Map to only consider positions on the given map -relative => Bio::Map::RelativeI : optionally a Relative to ask if the Positions equal in terms of their relative position to the thing described by that Relative =cut sub equals { my $self = shift; $self->throw_not_implemented(); } =head2 overlaps Title : overlaps Usage : if ($mappable->overlaps($other_mappable)) {...} my @overlapping_positions = $mappable->overlaps($other_mappable); Function: Finds the positions in this mappable that overlap with any comparison positions. Returns : array of L objects Args : arg #1 = L OR L to compare this one to (mandatory) arg #2 = optionally, the key => value pairs below -map => Bio::Map::MapI : optionally a Map to only consider positions on the given map -relative => Bio::Map::RelativeI : optionally a Relative to ask if the Positions overlap in terms of their relative position to the thing described by that Relative =cut sub overlaps { my $self = shift; $self->throw_not_implemented(); } =head2 contains Title : contains Usage : if ($mappable->contains($other_mappable)) {...} my @container_positions = $mappable->contains($other_mappable); Function: Finds the positions in this mappable that contain any comparison positions. Returns : array of L objects Args : arg #1 = L OR L to compare this one to (mandatory) arg #2 = optionally, the key => value pairs below -map => Bio::Map::MapI : optionally a Map to only consider positions on the given map -relative => Bio::Map::RelativeI : optionally a Relative to ask if the Positions contains in terms of their relative position to the thing described by that Relative =cut sub contains { my $self = shift; $self->throw_not_implemented(); } =head2 intersection Title : intersection Usage : my $position = $mappable->intersection($other_mappable); my $position = Bio::Map::Mappable->intersection(\@mappables); Function: Make the position that is at the intersection of all positions of all supplied mappables. Returns : L object or undef (if not all positions overlap) Args : arg #1 = L OR L to compare this one to, or an array ref of such objects (mandatory) arg #2 = optionally, the key => value pairs below -map => Bio::Map::MapI : optionally a Map to only consider positions on the given map -relative => Bio::Map::RelativeI : optionally a Relative to to ask how the Positions intersect in terms of their relative position to the thing described by that Relative =cut sub intersection { my $self = shift; $self->throw_not_implemented(); } =head2 union Title : union Usage : my $position = $mappable->union($other_mappable); my $position = Bio::Map::Mappable->union(@mappables); Function: Make the minimal position that contains all of the positions of all supplied mappables. Returns : L object or undef (if not all positions overlap) Args : arg #1 = L OR L to compare this one to, or an array ref of such objects (mandatory) arg #2 = optionally, the key => value pairs below -map => Bio::Map::MapI : optionally a Map to only consider positions on the given map -relative => Bio::Map::RelativeI : optionally a Relative to to ask if the union of the Positions in terms of their relative position to the thing described by that Relative =cut sub union { my $self = shift; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Map/Marker.pm000444000766000024 2352013155576320 16542 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::Marker # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::Marker - An central map object representing a generic marker that can have multiple location in several maps. =head1 SYNOPSIS # get map objects somehow # a marker with complex localisation $o_usat = Bio::Map::Marker->new(-name=>'Chad Super Marker 2', -positions => [ [$map1, $position1], [$map1, $position2] ] ); # The markers deal with Bio::Map::Position objects which can also # be explicitly created and passed on to markers as an array ref: $o_usat2 = Bio::Map::Marker->new(-name=>'Chad Super Marker 3', -positions => [ $pos1, $pos2 ] ); # a marker with unique position in a map $marker1 = Bio::Map::Marker->new(-name=>'hypervariable1', -map => $map1, -position => 100 ); # another way of creating a marker with unique position in a map: $marker2 = Bio::Map::Marker->new(-name=>'hypervariable2'); $map1->add_element($marker2); $marker2->position(100); # position method is a short cut for get/setting unique positions # which overwrites previous values # to place a marker to other maps or to have multiple positions # for a map within the same map use add_position() $marker2->add_position(200); # new position in the same map $marker2->add_position($map2,200); # new map # setting a map() in a marker or adding a marker into a map are # identical mathods. Both set the bidirectional connection which is # used by the marker to remember its latest, default map. # Regardes of how marker positions are created, they are stored and # returned as Bio::Map::PositionI objects: # unique position print $marker1->position->value, "\n"; # several positions foreach $pos ($marker2->each_position($map1)) { print $pos->value, "\n"; } See L and L for more information. =head1 DESCRIPTION A Marker is a Bio::Map::Mappable with some properties particular to markers. It also offers a number of convienience methods to make dealing with map elements easier. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics1@dieselwurks.com =head1 CONTRIBUTORS Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org Sendu Bala bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::Marker; use strict; use Bio::Map::Position; use base qw(Bio::Map::Mappable Bio::Map::MarkerI); =head2 new Title : new Usage : my $marker = Bio::Map::Marker->new( -name => 'Whizzy marker', -position => $position); Function: Builds a new Bio::Map::Marker object Returns : Bio::Map::Marker Args : -name => name of this microsatellite [optional], string,default 'Unknown' -default_map => the default map for this marker, a Bio::Map::MapI -position => map position for this marker, a Bio::Map::PositionI -positions => array ref of Bio::Map::PositionI objects position and positions can also take as values anything the corresponding methods can take =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); bless($self, ref $class || $class); my ($name, $default_map, $map, $position, $positions) = $self->_rearrange([qw(NAME DEFAULT_MAP MAP POSITION POSITIONS )], @args); if ($name) { $self->name($name); } else {$self->name('Unnamed marker'); } $map && $self->default_map($map); $default_map && $self->default_map($default_map); $position && $self->position($position); $positions && $self->positions($positions); return $self; } =head2 default_map Title : default_map Usage : my $map = $marker->default_map(); Function: Get/Set the default map for the marker. Returns : L Args : [optional] new L =cut sub default_map { my ($self, $map) = @_; if (defined $map) { $self->thow("This is [$map], not Bio::Map::MapI object") unless $map->isa('Bio::Map::MapI'); $self->{'_default_map'} = $map; } return $self->{'_default_map'} || return; } =head2 map Title : map Function: This is a synonym of the default_map() method *** does not actually add this marker to the map! *** Status : deprecated, will be removed in next version =cut *map = \&default_map; =head2 get_position_object Title : get_position_class Usage : my $position = $marker->get_position_object(); Function: To get an object of the default Position class for this Marker. Subclasses should redefine this method. The Position returned needs to be a L with -element set to self. Returns : L Args : none for an 'empty' PositionI object, optionally Bio::Map::MapI and value string to set the Position's -map and -value attributes. =cut sub get_position_object { my ($self, $map, $value) = @_; $map ||= $self->default_map; if ($value) { $self->throw("Value better be scalar, not [$value]") unless ref($value) eq ''; } my $pos = Bio::Map::Position->new(); $pos->map($map) if $map; $pos->value($value) if defined($value); $pos->element($self); return $pos; } =head2 position Title : position Usage : my $position = $mappable->position(); $mappable->position($position); Function: Get/Set the Position of this Marker (where it is on which map), purging all other positions before setting. Returns : L Args : Bio::Map::PositionI OR Bio::Map::MapI AND scalar OR scalar, but only if the marker has a default map =cut sub position { my ($self, $pos, $pos_actual) = @_; if ($pos) { $self->purge_positions; $self->add_position($pos, $pos_actual); } my @positions = $self->each_position; $self->warn('This marker has more than one Position, returning the most recently added') if scalar @positions > 1; return pop(@positions); } =head2 add_position Title : add_position Usage : $marker->add_position($position); Function: Add a Position to this marker Returns : n/a Args : Bio::Map::PositionI OR Bio::Map::MapI AND scalar OR scalar, but only if the marker has a default map =cut sub add_position { my ($self, $pos, $pos_actual) = @_; $self->throw("Must give a Position") unless defined $pos; my $map = $self->default_map; my $pos_map; if (ref($pos)) { if (ref($pos) eq 'ARRAY') { ($pos, $pos_actual) = @{$pos}; unless ($pos && $pos_actual && ref($pos)) { $self->throw("Supplied an array ref but did not contain two values, the first an object"); } } if ($pos->isa('Bio::Map::PositionI')) { $pos_map = $pos->map; $self->default_map($pos_map) unless $map; $map = $pos_map if $pos_map; } elsif ($pos->isa('Bio::Map::MapI')) { $self->default_map($pos) unless $map; $map = $pos; $pos = $pos_actual; } else { $self->throw("This is [$pos], not a Bio::Map::PositionI or Bio::Map::MapI object"); } } $self->throw("You need to give a marker a default map before you can set positions without explicit map!" ) unless $map; if (ref($pos) && $pos->isa('Bio::Map::PositionI')) { $pos->map($map) unless $pos_map; $self->SUPER::add_position($pos); } else { $self->get_position_object($map, $pos); # adds position to us } } =head2 positions Title : positions Usage : $marker->positions([$pos1, $pos2, $pos3]); Function: Add multiple Bio::Map::PositionI to this marker Returns : n/a Args : array ref of $map/value tuples or array ref of Bio::Map::PositionI =cut sub positions { my ($self, $args_ref) = @_; foreach my $arg (@{$args_ref}) { if (ref($arg) eq 'ARRAY') { $self->add_position(@{$arg}); } else { $self->add_position($arg); } } } =head2 in_map Title : in_map Usage : if ( $marker->in_map($map) ) {} Function: Tests if this marker is found on a specific map Returns : boolean Args : a map unique id OR Bio::Map::MapI =cut sub in_map { my ($self, $query) = @_; $self->throw("Must supply an argument") unless defined($query); if (ref($query) eq '') { foreach my $map ($self->known_maps) { my $uid = $map->unique_id; if ($uid) { ($uid eq $query) && return 1; } } } else { return $self->SUPER::in_map($query); } return 0; } 1; BioPerl-1.007002/Bio/Map/MarkerI.pm000444000766000024 1007113155576320 16650 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::MarkerI # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::MarkerI - Interface for basic marker functionality =head1 SYNOPSIS # do not use this module directly # See Bio::Map::Marker for an example of # implementation. =head1 DESCRIPTION A Marker is a Bio::Map::Mappable with some properties particular to markers. It also offers a number of convienience methods to make dealing with map elements easier. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 CONTRIBUTORS Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org Chad Matsalla bioinformatics1@dieselwurks.com Sendu Bala bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Map::MarkerI; use strict; use base qw(Bio::Map::MappableI); =head2 get_position_object Title : get_position_class Usage : my $position = $marker->get_position_object(); Function: To get an object of the default Position class for this Marker. Subclasses should redefine this method. The Position returned needs to be a L with -element set to self. Returns : L Args : none for an 'empty' PositionI object, optionally Bio::Map::MapI and value string to set the Position's -map and -value attributes. =cut sub get_position_object { my $self = shift; $self->throw_not_implemented(); } =head2 position Title : position Usage : my $position = $mappable->position(); $mappable->position($position); Function: Get/Set the Position of this Marker (where it is on which map), purging all other positions before setting. Returns : L Args : Bio::Map::PositionI OR Bio::Map::MapI AND scalar OR scalar, but only if the marker has a default map =cut sub position { my $self = shift; $self->throw_not_implemented(); } =head2 positions Title : positions Usage : $marker->positions([$pos1, $pos2, $pos3]); Function: Add multiple Bio::Map::PositionI to this marker Returns : n/a Args : array ref of $map/value tuples or array ref of Bio::Map::PositionI =cut sub positions { my $self = shift; $self->throw_not_implemented(); } =head2 default_map Title : default_map Usage : my $map = $marker->default_map(); Function: Get/Set the default map for the marker. Returns : L Args : [optional] new L =cut sub default_map { my $self = shift; $self->throw_not_implemented(); } =head2 in_map Title : in_map Usage : if ( $marker->in_map($map) ) {} Function: Tests if this marker is found on a specific map Returns : boolean Args : a map unique id OR Bio::Map::MapI =cut 1; BioPerl-1.007002/Bio/Map/Microsatellite.pm000444000766000024 2317113155576320 20303 0ustar00cjfieldsstaff000000000000# BioPerl module for Bio::Map::Microsatellite # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::Microsatellite - An object representing a Microsatellite marker. =head1 SYNOPSIS $o_usat = Bio::Map::Microsatellite->new (-name=>'Chad Super Marker 2', -sequence => 'gctgactgatcatatatatatatatatatatatatatatatcgcgatcgtga', -motif => 'at', -repeats => 15, -repeat_start_position => 11 ); $sequence_before_usat = $o_usat->get_leading_flank(); $sequence_after_usat = $o_usat->get_trailing_flank(); =head1 DESCRIPTION This object handles the notion of an Microsatellite. This microsatellite can be placed on a (linear) Map or used on its own. If this Microsatellites will be used in a mapping context (it doesn't have to, you know) it can have multiple positions in a map. For information about a Microsatellite's position in a map one must query the associate PositionI object which is accessible through the position() method. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics1@dieselwurks.com =head1 CONTRIBUTORS Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org Sendu Bala bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::Microsatellite; use strict; use base qw(Bio::Map::Marker); =head2 new Title : new Usage : $o_usat = Function: Builds a new Bio::Map::Microsatellite object Returns : Bio::Map::Microsatellite Args : -name => name of this microsatellite (optional, string, default 'Unknown microsatellite') -positions => position(s) for this marker in maps[optional], An array reference of tuples (array refs themselves) Each tuple contains a Bio::Map::MapI-inherited object and a Bio::Map::PositionI-inherited obj, no default) -sequence => the sequence of this microsatellite (optional, scalar, no default) -motif => the repeat motif of this microsatellite (optional, scalar, no default) -repeats => the number of motif repeats for this microsatellite (optional, scalar, no default) -repeat_start_position => the starting position of the microsatellite in this sequence. The first base of the sequence is position "1". (optional, scalar, no default) Note : Creating a Bio::Map::Microsatellite object with no position might be useful for microsatellite people wanting to embrace and extend this module. Me! Me! Me! - using repeat_start_position will trigger a mechinism to calculate a value for repeat_end_position. =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($map, $position, $sequence, $motif, $repeats, $start) = $self->_rearrange([qw(MAP POSITION SEQUENCE MOTIF REPEATS REPEAT_START_POSITION )], @args); if( ! $self->name ) { $self->name('Unnamed microsatellite'); } $map && $self->map($map); $position && $self->position($position); $sequence && $self->sequence($sequence); $self->motif(defined $motif ? $motif : 'Unknown motif'); $repeats && $self->repeats($repeats); $start && $self->repeat_start_position($start); return $self; } =head2 motif Title : motif Usage : $o_usat->motif($new_motif); my $motif = $o_usat->motif(); Function: Get/Set the repeat motif for this Microsatellite. Returns : A scalar representing the current repeat motif of this Microsatellite. Args : none to get, OR string to set =cut sub motif { my ($self,$motif) = @_; if ($motif) { $self->{'_motif'} = $motif; } return $self->{'_motif'}; } =head2 sequence Title : sequence Usage : $o_usat->sequence($new_sequence); my $sequence = $o_usat->sequence(); Function: Get/Set the sequence for this Microsatellite. Returns : A scalar representing the current sequence of this Microsatellite. Args : none to get, OR string to set =cut sub sequence { my ($self,$sequence) = @_; if ($sequence) { $self->{'_sequence'} = $sequence; } return $self->{'_sequence'}; } =head2 repeats Title : repeats Usage : $o_usat->repeats($new_repeats); my $repeats = $o_usat->repeats() Function: Get/Set the repeat repeats for this Microsatellite. Returns : A scalar representing the current number of repeats of this Microsatellite. Args : none to get, OR int to set =cut sub repeats { my ($self,$repeats) = @_; if ($repeats) { $self->{'_repeats'} = $repeats; } return $self->{'_repeats'}; } =head2 repeat_start_position Title : repeat_start_position Usage : $o_usat->repeat_start_position($new_repeat_start_position); my $repeat_start_position = $o_usat->repeat_start_position(); Function: Get/Set the repeat repeat_start_position for this Microsatellite Returns : A scalar representing the repeat start position for this Microsatellite. Args : none to get, OR string to set This method will also try to set the repeat end position. This depends on having information for the motif and the number of repeats. If you want to use methods like get_trailing_flank or get_leading flank, be careful to include the right information. =cut sub repeat_start_position { my ($self,$repeat_start_position) = @_; if ($repeat_start_position) { $self->{'_repeat_start_position'} = $repeat_start_position; $self->repeat_end_position("set"); } return $self->{'_repeat_start_position'}; } =head2 repeat_end_position Title : repeat_end_position Usage : $o_usat->repeat_end_position("set"); $o_usat->repeat_end_position($value); $current_repeat_end_position = $o_usat->repeat_end_position(); Function: Get/set the end position of the repeat in this sequence. Returns : A scalar representing the base index of the end of the repeat in this Microsatellite. The first base in the sequence is base 1. Args : A scalar representing a value, the string "set", or no argument (see Notes). Notes : If you do not provide an argument to this method, the current end position of the repeat in this Microsatellite will be returned (a scalar). If you provide the string "set" to this method it will set the end position based on the start position, the length of the motif, and the number of repeats. If you specify a value the current end position of the repeat will be set to that value. This is a really bad idea. Don't do it. =cut sub repeat_end_position { my ($self,$caller) = @_; if( defined $caller ) { if ($caller eq "set") { $self->{'_repeat_end_position'} = $self->{'_repeat_start_position'} + (length($self->motif()) * $self->repeats()); } elsif ($caller) { $self->{'_repeat_end_position'} = $caller; } } return $self->{'_repeat_end_position'}; } =head2 equals Title : equals Usage : if ($mappable->equals($mapable2)) {...} Function: Test if a position is equal to another position Returns : boolean Args : Bio::Map::MappableI =cut sub equals { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 less_than Title : less_than Usage : if ($mappable->less_than($m2)) {...} Function: Tests if a position is less than another position Returns : boolean Args : Bio::Map::MappableI =cut sub less_than { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 greater_than Title : greater_than Usage : if ($mappable->greater_than($m2)) {...} Function: Tests if position is greater than another position Returns : boolean Args : Bio::Map::MappableI =cut sub greater_than { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_leading_flank Title : get_leading_flank Usage : $leading_sequence = $o_usat->get_leading_flank(); Returns : A scalar representing the sequence before the repeats in this Microsatellite. Args : none =cut sub get_leading_flank { my $self = shift; return substr $self->sequence(),0,$self->repeat_start_position-1; } =head2 get_trailing_flank Title : get_trailing_flank Usage : $trailing_flank = $o_usat->get_trailing_flank(); Returns : A scalar representing the sequence after the repeats in this Microsatellite. Args : none =cut sub get_trailing_flank { my $self = shift; return substr $self->sequence(),$self->repeat_end_position()-1; } 1; BioPerl-1.007002/Bio/Map/OrderedPosition.pm000444000766000024 1346213155576320 20436 0ustar00cjfieldsstaff000000000000# BioPerl module for Bio::Map::OrderedPosition # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::OrderedPosition - Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. =head1 SYNOPSIS use Bio::Map::OrderedPosition; # the first marker in the sequence my $position = Bio::Map::OrderedPosition->new(-order => 1, -positions => [ [ $map, 22.3] ] ); # the second marker in the sequence, 15.6 units from the fist one my $position2 = Bio::Map::OrderedPosition->new(-order => 2, -positions => [ [ $map, 37.9] ] ); # the third marker in the sequence, coincidental with the second # marker my $position3 = Bio::Map::OrderedPosition->new(-order => 3, -posititions => [ [ $map, 37.9]] ); =head1 DESCRIPTION This object is an implementation of the PositionI interface and the Position object handles the specific values of a position. OrderedPosition is intended to be slightly more specific then Position but only specific enough for a parser from the MarkerIO subsystem to create and then pass to a client application to bless into the proper type. For an example of how this is intended to work, see the Mapmaker.pm. No units are assumed here - units are handled by context of which Map a position is placed in. Se Bio::Map::Position for additional information. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics1@dieselwurks.com =head1 CONTRIBUTORS Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Jason Stajich, jason@bioperl.org Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::OrderedPosition; use strict; use base qw(Bio::Map::Position); =head2 new Title : new Usage : my $obj = Bio::Map::OrderedPosition->new(); Function: Builds a new Bio::Map::OrderedPosition object Returns : Bio::Map::OrderedPosition Args : -order : The order of this position =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($order) = $self->_rearrange([qw(ORDER)], @args); $order && $self->order($order); return $self; } =head2 order Title : order Usage : $o_position->order($new_order); my $order = $o_position->order(); Function: Get/set the order position of this position in a map. Returns : int, the order of this position Args : none to get, OR int to set =cut sub order { my ($self, $order) = @_; if ($order) { $self->{'_order'} = $order; } return $self->{'_order'} || return; } =head2 sortable Title : sortable Usage : my $num = $position->sortable(); Function: Read-only method that is guaranteed to return a value suitable for correctly sorting this kind of position amongst other positions of the same kind on the same map. Note that sorting different kinds of position together is unlikely to give sane results. Returns : numeric Args : none =cut sub sortable { my $self = shift; return $self->order; } =head2 equals Title : equals Usage : if ($mappable->equals($mapable2)) {...} Function: Test if a position is equal to another position. Returns : boolean Args : Bio::Map::PositionI =cut sub equals { my ($self,$compare) = @_; return 0 if (! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition')); return ($compare->order == $self->order); } # admittedly these aren't really the best comparisons in the world # but it is a first pass we'll need to refine the algorithm or not # provide general comparisons and require these to be implemented # by objects closer to the specific type of data =head2 less_than Title : less_than Usage : if ($mappable->less_than($m2)) {...} Function: Tests if a position is less than another position It is assumed that 2 positions are in the same map. Returns : boolean Args : Bio::Map::PositionI =cut sub less_than { my ($self,$compare) = @_; return 0 if (! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition')); return ($compare->order < $self->order); } =head2 greater_than Title : greater_than Usage : if ($mappable->greater_than($m2)) {...} Function: Tests if position is greater than another position. It is assumed that 2 positions are in the same map. Returns : boolean Args : Bio::Map::PositionI =cut sub greater_than { my ($self,$compare) = @_; return 0 if (! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition')); return ($compare->order > $self->order); } 1;BioPerl-1.007002/Bio/Map/OrderedPositionWithDistance.pm000444000766000024 1066213155576320 22744 0ustar00cjfieldsstaff000000000000### TO BE DELETED ### # BioPerl module for Bio::Map::OrderedPositionWithDistance # # Please direct questions and support issues to # # Cared for by Chad Matsalla # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::OrderedPositionWithDistance - Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. =head1 SYNOPSIS use Bio::Map::OrderedPositionWithDistance; # the first marker in the sequence my $position = Bio::Map::OrderedPositionWithDistance->new(-positions => 1, -distance => 22.3 ); # the second marker in the sequence, 15.6 units from the fist one my $position2 = Bio::Map::OrderedPositionWithDistance->new(-positions => 2, -distance => 15.6 ); # the third marker in the sequence, coincidental with the second # marker my $position3 = Bio::Map::OrderedPositionWithDistance->new(-positions => 3, -distance => 0 ); =head1 DESCRIPTION This object is an implementation of the PositionI interface and the Position object handles the specific values of a position. OrderedPositionWithDistance is intended to be slightly more specific then Position but only specific enough for a parser from the MarkerIO subsystem to create and then pass to a client application to bless into the proper type. For an example of how this is intended to work, see the Mapmaker.pm. No units are assumed here - units are handled by context of which Map a position is placed in. Se Bio::Map::Position for additional information. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics1@dieselwurks.com =head1 CONTRIBUTORS Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::OrderedPositionWithDistance; use strict; use base qw(Bio::Map::Position); =head2 new Title : new Usage : my $obj = Bio::Map::OrderedPositionWithDistance->new(); Function: Builds a new Bio::Map::OrderedPositionWithDistance object Returns : Bio::Map::OrderedPositionWithDistance Args : -positions - Should be a single value representing the order of this marker within the list of markers -distance - The distance this marker is from the marker before it. 0 reflects coincidentality. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_positions'} = []; my ($positions,$distance) = $self->_rearrange([qw(POSITIONS DISTANCE)], @args); if( ref($positions) =~ /array/i ) { foreach my $p ( @$positions ) { $self->add_position($p); } } else { $self->add_position($positions); } $distance && $self->distance($distance); return $self; } =head2 distance($new_distance) Title : distance($new_distance) Usage : $position->distance(new_distance) _or_ $position->distance() Function: get/set the distance of this position from the previous marker Returns : A scalar representing the current distance for this position. Args : If $new_distance is provided the distance of this Position will be set to $new_distance =cut sub distance { my ($self,$distance) = @_; if ($distance) { $self->{'_distance'} = $distance; } return $self->{'_distance'}; } 1; BioPerl-1.007002/Bio/Map/Physical.pm000555000766000024 10514113155576320 17120 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::Physical # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright AGCoL # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::Physical - A class for handling a Physical Map (such as FPC) =head1 SYNOPSIS use Bio::MapIO; # acquire a Bio::Map::Physical using Bio::MapIO::fpc my $mapio = Bio::MapIO->new(-format => "fpc",-file => "rice.fpc", -readcor => 0); my $physical = $mapio->next_map(); # get all the markers ids foreach my $marker ( $physical->each_markerid() ) { print "Marker $marker\n"; # acquire the marker object using Bio::Map::FPCMarker my $markerobj = $physical->get_markerobj($marker); # get all the clones hit by this marker foreach my $clone ($markerobj->each_cloneid() ) { print " +++$clone\n"; } } =head1 DESCRIPTION This class is basically a continer class for a collection of Contig maps and other physical map information. Bio::Map::Physical has been tailored to work for FPC physical maps, but could probably be used for others as well (with the appropriate MapIO module). This class also has some methods with specific functionalities: print_gffstyle() : Generates GFF; either Contigwise[Default] or Groupwise print_contiglist() : Prints the list of Contigs, markers that hit the contig, the global position and whether the marker is a placement (

) or a Framework () marker. print_markerlist() : Prints the markers list; contig and corresponding number of clones. matching_bands() : Given two clones [and tolerence], this method calculates how many matching bands do they have. coincidence_score() : Given two clones [,tolerence and gellen], this method calculates the Sulston Coincidence score. For faster access and better optimization, the data is stored internally in hashes. The corresponding objects are created on request. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Gaurav Gupta Email gaurav@genome.arizona.edu =head1 CONTRIBUTORS Sendu Bala bix@sendu.me.uk =head1 PROJECT LEADERS Jamie Hatfield jamie@genome.arizona.edu Dr. Cari Soderlund cari@genome.arizona.edu =head1 PROJECT DESCRIPTION The project was done in Arizona Genomics Computational Laboratory (AGCoL) at University of Arizona. This work was funded by USDA-IFAFS grant #11180 titled "Web Resources for the Computation and Display of Physical Mapping Data". For more information on this project, please refer: http://www.genome.arizona.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::Physical; use vars qw($MAPCOUNT); use strict; use POSIX; use Bio::Map::Clone; use Bio::Map::Contig; use Bio::Map::FPCMarker; use base qw(Bio::Map::SimpleMap); BEGIN { $MAPCOUNT = 1; } =head1 Access Methods These methods let you get and set the member variables =head2 version Title : version Usage : my $version = $map->version(); Function: Get/set the version of the program used to generate this map Returns : scalar representing the version Args : none to get, OR string to set =cut sub version { my ($self,$value) = @_; if (defined($value)) { $self->{'_version'} = $value; } return $self->{'_version'}; } =head2 modification_user Title : modification_user Usage : my $modification_user = $map->modification_user(); Function: Get/set the name of the user who last modified this map Returns : scalar representing the username Args : none to get, OR string to set =cut sub modification_user { my ($self,$value) = @_; if (defined($value)) { $self->{'_modification_user'} = $value; } return $self->{'_modification_user'}; } =head2 group_type Title : group_type Usage : $map->group_type($grptype); my $grptype = $map->group_type(); Function: Get/set the group type of this map Returns : scalar representing the group type Args : none to get, OR string to set =cut sub group_type { my ($self,$value) = @_; if (defined($value)) { $self->{'_grouptype'} = $value; } return $self->{'_grouptype'}; } =head2 group_abbr Title : group_abbr Usage : $map->group_abbr($grpabbr); my $grpabbr = $map->group_abbr(); Function: get/set the group abbrev of this map Returns : string representing the group abbrev Args : none to get, OR string to set =cut sub group_abbr { my ($self,$value) = @_; if (defined($value)) { $self->{'_groupabbr'} = $value; } return $self->{'_groupabbr'}; } =head2 core_exists Title : core_exists Usage : my $core_exists = $map->core_exists(); Function: Get/set if the FPC file is accompanied by COR file Returns : boolean Args : none to get, OR 1|0 to set =cut sub core_exists { my ($self,$value) = @_; if (defined($value)) { $self->{'_corexists'} = $value ? 1 : 0; } return $self->{'_corexists'}; } =head2 each_cloneid Title : each_cloneid Usage : my @clones = $map->each_cloneid(); Function: returns an array of clone names Returns : list of clone names Args : none =cut sub each_cloneid { my ($self) = @_; return keys %{$self->{'_clones'}}; } =head2 get_cloneobj Title : get_cloneobj Usage : my $cloneobj = $map->get_cloneobj('CLONEA'); Function: returns an object of the clone given in the argument Returns : object of the clone Args : scalar representing the clone name =cut sub get_cloneobj { my ($self,$clone) = @_; return 0 if(!defined($clone)); return if($clone eq ""); return if(!exists($self->{'_clones'}{$clone})); my ($type,$contig,$bands,$gel,$group,$remark,$fp_number); my ($sequence_type,$sequence_status,$fpc_remark,@amatch,@pmatch,@ematch, $startrange,$endrange); my %clones = %{$self->{'_clones'}{$clone}}; my @markers; if (ref($clones{'clone'}) eq 'Bio::Map::Clone') { return $clones{'clone'}; } $type = $clones{'type'} if (exists($clones{'type'})); @markers = (keys %{$clones{'markers'}}) if (exists($clones{'markers'})); $contig = $clones{'contig'} if (exists($clones{'contig'})); $bands = $clones{'bands'} if (exists($clones{'bands'})); $gel = $clones{'gel'} if (exists($clones{'gel'})); $group = $clones{'group'} if (exists($clones{'group'})); $remark = $clones{'remark'} if (exists($clones{'remark'})); $fp_number = $clones{'fp_number'} if (exists($clones{'fp_number'})); $fpc_remark = $clones{'fpc_remark'} if (exists($clones{'fpc_remark'})); $sequence_type = $clones{'sequence_type'} if (exists($clones{'sequence_type'})); $sequence_status = $clones{'sequence_status'} if (exists($clones{'sequence_status'} )); @amatch = (keys %{$clones{'matcha'}}) if (exists($clones{'matcha'})); @ematch = (keys %{$clones{'matche'}}) if (exists($clones{'matche'})); @pmatch = (keys %{$clones{'matchp'}}) if (exists($clones{'matchp'})); $startrange = $clones{'range'}{'start'} if (exists($clones{'range'}{'start'})); $endrange = $clones{'range'}{'end'} if (exists($clones{'range'}{'end'})); #*** why doesn't it call Bio::Map::Clone->new ? Seems dangerous... my $cloneobj = bless( { _name => $clone, _markers => \@markers, _contig => $contig, _type => $type, _bands => $bands, _gel => $gel, _group => $group, _remark => $remark, _fpnumber => $fp_number, _sequencetype => $sequence_type, _sequencestatus => $sequence_status, _fpcremark => $fpc_remark, _matche => \@ematch, _matcha => \@amatch, _matchp => \@pmatch, _range => Bio::Range->new(-start => $startrange, -end => $endrange), }, 'Bio::Map::Clone'); $self->{'_clones'}{$clone}{'clone'} = $cloneobj; return $cloneobj; } =head2 each_markerid Title : each_markerid Usage : my @markers = $map->each_markerid(); Function: returns list of marker names Returns : list of marker names Args : none =cut sub each_markerid { my ($self) = @_; return keys (%{$self->{'_markers'}}); } =head2 get_markerobj Title : get_markerobj Usage : my $markerobj = $map->get_markerobj('MARKERA'); Function: returns an object of the marker given in the argument Returns : object of the marker Args : scalar representing the marker name =cut sub get_markerobj { my ($self,$marker) = @_; return 0 if(!defined($marker)); return if($marker eq ""); return if(!exists($self->{'_markers'}{$marker})); my ($global,$framework,$group,$anchor,$remark,$type,$linkage,$subgroup); my %mkr = %{$self->{'_markers'}{$marker}}; return $mkr{'marker'} if (ref($mkr{'marker'}) eq 'Bio::Map::FPCMarker'); $type = $mkr{'type'} if(exists($mkr{'type'})); $global = $mkr{'global'} if(exists($mkr{'global'} )); $framework = $mkr{'framework'} if(exists($mkr{'framework'})); $anchor = $mkr{'anchor'} if(exists($mkr{'anchor'})); $group = $mkr{'group'} if(exists($mkr{'group'})); $subgroup = $mkr{'subgroup'} if(exists($mkr{'subgroup'})); $remark = $mkr{'remark'} if(exists($mkr{'remark'})); my %clones = %{$mkr{'clones'}}; my %contigs = %{$mkr{'contigs'}}; my %markerpos = %{$mkr{'posincontig'}} if(exists($mkr{'posincontig'})); #*** why doesn't it call Bio::Map::FPCMarker->new ? Seems dangerous... my $markerobj = bless( { _name => $marker, _type => $type, _global => $global, _frame => $framework, _group => $group, _subgroup => $subgroup, _anchor => $anchor, _remark => $remark, _clones => \%clones, _contigs => \%contigs, _position => \%markerpos, }, 'Bio::Map::FPCMarker'); $self->{'_markers'}{$marker}{'marker'} = $markerobj; return $markerobj; } =head2 each_contigid Title : each_contigid Usage : my @contigs = $map->each_contigid(); Function: returns a list of contigs (numbers) Returns : list of contigs Args : none =cut sub each_contigid { my ($self) = @_; return keys (%{$self->{'_contigs'}}); } =head2 get_contigobj Title : get_contigobj Usage : my $contigobj = $map->get_contigobj('CONTIG1'); Function: returns an object of the contig given in the argument Returns : object of the contig Args : scalar representing the contig number =cut sub get_contigobj { my ($self,$contig) = @_; return 0 if(!defined($contig)); return if($contig eq ""); return if(!exists($self->{'_contigs'}{$contig})); my ($group,$anchor,$uremark,$tremark,$cremark,$startrange,$endrange, $linkage,$subgroup); my %ctg = %{$self->{'_contigs'}{$contig}}; my (%position, %pos); return $ctg{'contig'} if (ref($ctg{'contig'}) eq 'Bio::Map::Contig'); $group = $ctg{'group'} if (exists($ctg{'group'})); $subgroup = $ctg{'subgroup'} if (exists($ctg{'subgroup'})); $anchor = $ctg{'anchor'} if (exists($ctg{'anchor'})); $cremark = $ctg{'chr_remark'} if (exists($ctg{'chr_remark'})); $uremark = $ctg{'usr_remark'} if (exists($ctg{'usr_remark'})); $tremark = $ctg{'trace_remark'} if (exists($ctg{'trace_remark'})); $startrange = $ctg{'range'}{'start'} if (exists($ctg{'range'}{'start'})); $endrange = $ctg{'range'}{'end'} if (exists($ctg{'range'}{'end'})); my %clones = %{$ctg{'clones'}} if (exists($ctg{'clones'})); my %markers = %{$ctg{'markers'}} if (exists($ctg{'markers'})); my $pos = $ctg{'position'}; #*** why doesn't it call Bio::Map::Contig->new ? Seems dangerous... my $contigobj = bless( { _group => $group, _subgroup => $subgroup, _anchor => $anchor, _markers => \%markers, _clones => \%clones, _name => $contig, _cremark => $cremark, _uremark => $uremark, _tremark => $tremark, _position => $pos, _range => Bio::Range->new(-start => $startrange, -end => $endrange), }, 'Bio::Map::Contig'); $self->{'_contigs'}{$contig}{'contig'} = $contigobj; return $contigobj; } =head2 matching_bands Title : matching_bands Usage : $self->matching_bands('cloneA','cloneB',[$tol]); Function: given two clones [and tolerence], this method calculates how many matching bands do they have. (this method is ported directly from FPC) Returns : scalar representing the number of matching bands Args : names of the clones ('cloneA', 'cloneB') [Default tolerence=7] =cut sub matching_bands { my($self,$cloneA,$cloneB,$tol) = @_; my($lstart,$kband,$match,$diff,$i,$j); return 0 if(!defined($cloneA) || !defined($cloneB) || !($self->core_exists())); $tol = 7 if (!defined($tol)); my %_clones = %{$self->{'_clones'}}; my @bandsA = @{$_clones{$cloneA}{'bands'}}; my @bandsB = @{$_clones{$cloneB}{'bands'}}; $match = 0; $lstart = 0; for ($i=0; $icoincidence_score('cloneA','cloneB'[,$tol,$gellen]); Function: given two clones [,tolerence and gellen], this method calculates the Sulston Coincidence score. (this method is ported directly from FPC) Returns : scalar representing the Sulston coincidence score. Args : names of the clones ('cloneA', 'cloneB') [Default tol=7 gellen=3300.0] =cut sub coincidence_score { my($self,$cloneA,$cloneB,$tol,$gellen) = @_; return 0 if(!defined($cloneA) || !defined($cloneB) || !($self->core_exists())); my %_clones = %{$self->{'_clones'}}; my $numbandsA = scalar(@{$_clones{$cloneA}{'bands'}}); my $numbandsB = scalar(@{$_clones{$cloneB}{'bands'}}); my ($nL,$nH,$m,$i,$psmn,$pp,$pa,$pb,$t,$c,$a,$n); my @logfact; my $score; $gellen = 3300.0 if (!defined($gellen)); $tol = 7 if (!defined($tol)); if ($numbandsA > $numbandsB) { $nH = $numbandsA; $nL = $numbandsB; } else { $nH = $numbandsB; $nL = $numbandsA; } $m = $self->matching_bands($cloneA, $cloneB,$tol); $logfact[0] = 0.0; $logfact[1] = 0.0; for ($i=2; $i<=$nL; $i++) { $logfact[$i] = $logfact[$i - 1] + log($i); } $psmn = 1.0 - ((2*$tol)/$gellen); $pp = $psmn ** $nH; $pa = log($pp); $pb = log(1 - $pp); $t = 1e-37; for ($n = $m; $n <= $nL; $n++) { $c = $logfact[$nL] - $logfact[$nL - $n] - $logfact[$n]; $a = exp($c + ($n * $pb) + (($nL - $n) * $pa)); $t += $a; } $score = sprintf("%.e",$t); return $score; } =head2 print_contiglist Title : print_contiglist Usage : $map->print_contiglist([showall]); #[Default 0] Function: prints the list of contigs, markers that hit the contig, the global position and whether the marker is a placement (P) or a Framework (F) marker. Returns : none Args : [showall] [Default 0], 1 includes all the discrepant markers =cut sub print_contiglist{ my ($self,$showall) = @_; my $pos; $showall = 0 if (!defined($showall)); my %_contigs = %{$self->{'_contigs'}}; my %_markers = %{$self->{'_markers'}}; my %_clones = %{$self->{'_clones'}}; my @contigs = $self->each_contigid(); my @sortedcontigs = sort {$a <=> $b } @contigs; print "\n\nContig List\n\n"; foreach my $contig (@sortedcontigs) { my %list; my %alist; my $ctgAnchor = $_contigs{$contig}{'anchor'}; my $ctgGroup = $_contigs{$contig}{'group'}; my @mkr = keys ( %{$_contigs{$contig}{'markers'}} ); foreach my $marker (@mkr) { my $mrkGroup = $_markers{$marker}{'group'}; my $mrkGlobal = $_markers{$marker}{'global'}; my $mrkFramework = $_markers{$marker}{'framework'}; my $mrkAnchor = $_markers{$marker}{'anchor'}; if($ctgGroup =~ /\d+|\w/ && $ctgGroup != 0) { if ($mrkGroup eq $ctgGroup) { if ($mrkFramework == 0) { $pos = $mrkGlobal."P"; } else { $pos = $mrkGlobal."F"; } $list{$marker} = $pos; } elsif ($showall == 1) { my $chr = $self->group_abbr().$mrkGroup; $alist{$marker} = $chr; } } elsif ($showall == 1 && $ctgGroup !~ /\d+/) { my $chr = $self->group_abbr().$mrkGroup; $alist{$marker} = $chr; } } my $chr = $ctgGroup; $chr = $self->group_abbr().$ctgGroup if ($ctgGroup =~ /\d+|\w/); if ($showall == 1 ) { print " ctg$contig ", $chr, " " if ($_contigs{$contig}{'group'} !~ /\d+|\w/); } elsif ($ctgGroup =~ /\d+|\w/ && $ctgGroup ne 0){ print " ctg",$contig, " ",$chr, " "; } while (my ($k,$v) = each %list) { print "$k/$v "; } print "\n" if ($showall == 0 && $ctgGroup =~ /\d+|\w/ && $ctgGroup ne 0 ); if ($showall == 1) { while (my ($k,$v) = each %alist) { print "$k/$v "; } print "\n"; } } } =head2 print_markerlist Title : print_markerlist Usage : $map->print_markerlist(); Function : prints the marker list; contig and corresponding number of clones for each marker. Returns : none Args : none =cut sub print_markerlist { my ($self) = @_; my %_contigs = %{$self->{'_contigs'}}; my %_markers = %{$self->{'_markers'}}; my %_clones = %{$self->{'_clones'}}; print "Marker List\n\n"; foreach my $marker ($self->each_markerid()) { print " ",$marker, " "; my %list; my %mclones = %{$_markers{$marker}{'clones'}}; foreach my $clone (%mclones) { if (exists($_clones{$clone}{'contig'}) ) { my $ctg = $_clones{$clone}{'contig'}; if (exists($list{$ctg})) { my $clonehits = $list{$ctg}; $clonehits++; $list{$ctg} = $clonehits; } else { $list{$ctg} = 1; } } } while (my ($k,$v) = each %list) { print "$k/$v "; } print "\n"; } } =head2 print_gffstyle Title : print_gffstyle Usage : $map->print_gffstyle([style]); Function : prints GFF; either Contigwise (default) or Groupwise Returns : none Args : [style] default = 0 contigwise, else 1 groupwise (chromosome-wise). =cut sub print_gffstyle { my ($self,$style) = @_; $style = 0 if(!defined($style)); my %_contigs = %{$self->{'_contigs'}}; my %_markers = %{$self->{'_markers'}}; my %_clones = %{$self->{'_clones'}}; my $i; my ($depth, $save_depth); my ($x, $y); my @stack; my ($k, $j, $s); my $pos; my $contig; # Calculate the position for the marker in the contig my @contigs = $self->each_contigid(); my @sortedcontigs = sort {$a <=> $b } @contigs; my $offset = 0; my %gffclones; my %gffcontigs; my %gffmarkers; my $basepair = 4096; foreach my $contig (@sortedcontigs) { if($_contigs{$contig}{'range'} ) { $offset = $_contigs{$contig}{'range'}{'start'}; if ($offset <= 0){ $offset = $offset * -1; $gffcontigs{$contig}{'start'} = 1; $gffcontigs{$contig}{'end'} = ($_contigs{$contig}{'range'}{'end'} + $offset ) * $basepair + 1; } else { $offset = 0; $gffcontigs{$contig}{'start'} = $_contigs{$contig}{'range'}{'start'} * $basepair; $gffcontigs{$contig}{'end'} = $_contigs{$contig}{'range'}{'end'} * $basepair; } } else { $gffcontigs{$contig}{'start'} = 1; $gffcontigs{$contig}{'end'} = 1; } my @clones = keys %{$_contigs{$contig}{'clones'}}; foreach my $clone (@clones) { if(exists ($_clones{$clone}{'range'}) ) { my $gffclone = $clone; $gffclone =~ s/sd1$//; $gffclones{$gffclone}{'start'} = (($_clones{$clone}{'range'}{'start'} + $offset) * $basepair + 1); $gffclones{$gffclone}{'end'} = (($_clones{$clone}{'range'}{'end'} + $offset) * $basepair + 1); } if(!$contig) { my %markers = %{$_clones{$clone}{'markers'}} if (exists($_clones{$clone}{'markers'})); while (my ($k,$v) = each %markers) { $gffmarkers{$contig}{$k} = ( ( $_clones{$clone}{'range'}{'start'} + $_clones{$clone}{'range'}{'end'} ) / 2 ) * $basepair + 1 ; } } } if($contig) { my %markers = %{$_contigs{$contig}{'markers'}} if (exists($_contigs{$contig}{'markers'})); while (my ($k,$v) = each %markers) { $gffmarkers{$contig}{$k} = ($v + $offset) * $basepair + 1; } } } if (!$style) { foreach my $contig (@sortedcontigs) { if(exists ($_contigs{$contig}{'range'} ) ) { print join("\t","ctg$contig","assembly","contig", $gffcontigs{$contig}{'start'}, $gffcontigs{$contig}{'end'},".",".",".", "Sequence \"ctg$contig\"; Name \"ctg$contig\"\n" ); } my @clones = (keys %{$_contigs{$contig}{'clones'}} ); foreach my $clone (@clones) { if(exists ($_clones{$clone}{'range'}) ) { print join("\t","ctg$contig","FPC"); my $type = $_clones{$clone}{'type'}; if($clone =~ /sd1$/) { $clone =~ s/sd1$//; $type = "sequenced"; } print join ("\t","\t$type",$gffclones{$clone}{'start'}, $gffclones{$clone}{'end'},".",".",".", "$type \"$clone\"; Name \"$clone\""); my @markers = keys %{$_clones{$clone}{'markers'}}; print "; Marker_hit" if (scalar(@markers)); foreach my $mkr(@markers) { if (exists($_markers{$mkr}{'framework'})) { print " \"$mkr ",$_markers{$mkr}{'group'}," ", $_markers{$mkr}{'global'},"\""; } else { print " \"$mkr 0 0\""; } } print "; Contig_hit \"",$_clones{$clone}{'contig'},"\" " if (defined($_clones{$clone}{'contig'})); } print "\n"; } if (exists ($_contigs{$contig}{'markers'}) ) { my %list = %{$_contigs{$contig}{'markers'}}; while (my ($k,$v) = each %list) { print "ctg", $contig, "\tFPC\t"; my $position = $gffmarkers{$contig}{$k}; my $type = "marker"; $type = "electronicmarker" if ($_markers{$k}{'type'} eq "eMRK"); if( exists($_markers{$k}{'framework'})) { $type = "frameworkmarker" if($_markers{$k}{'framework'} == 1); $type = "placementmarker" if($_markers{$k}{'framework'} == 0); } print join ("\t","$type",$position,$position,".",".", ".","$type \"$k\"; Name \"$k\""); my @clonelist; my @clones = keys %{$_markers{$k}{'clones'}}; foreach my $cl (@clones) { push (@clonelist, $cl) if($_clones{$cl}{'contig'} == $contig); } $" = " "; print("; Contig_hit \"ctg$contig - ",scalar(@clonelist), "\" (@clonelist)\n"); } } } } else { my %_groups; my $margin = 2 * $basepair; my $displacement = 0; my @grouplist; foreach my $contig (@sortedcontigs) { my $recordchr; my $chr = $_contigs{$contig}{'group'}; $chr = 0 if ($chr !~ /\d+|\w+/); $recordchr->{group} = $chr; $recordchr->{contig} = $contig; $recordchr->{position} = $_contigs{$contig}{'position'}; push @grouplist, $recordchr; } my @chr = keys (%{$_groups{'group'}}); my @sortedchr; if ($self->group_type eq 'Chromosome') { @sortedchr = sort { $a->{'group'} <=> $b->{'group'} || $a->{'contig'} <=> $b->{'contig'} } @grouplist; } else { @sortedchr = sort { $a->{'group'} cmp $b->{'group'} || $a->{'contig'} cmp $b->{'contig'} } @grouplist; } my $lastchr = -1; my $chrend = 0; foreach my $chr (@sortedchr) { my $chrname = $self->group_abbr().$chr->{'group'}; if ($lastchr eq -1 || $chr->{'group'} ne $lastchr ) { $lastchr = $chr->{'group'} if ($lastchr eq -1); $displacement = 0; # caluclate the end position of the contig my $ctgcount = 0; my $prevchr = 0; $chrend = 0; if ($chr->{contig} != 0) { foreach my $ch (@sortedchr) { if ($ch->{'group'} eq $chr->{'group'}) { if($ch->{'contig'} != 0) { my $ctg = $ch->{'contig'} if($ch->{'contig'} != 0); $chrend += $gffcontigs{$ctg}->{'end'}; ++$ctgcount; } } } $chrend += ($ctgcount-1) * $margin; } else { $chrend = $gffcontigs{'0'}->{'end'}; } $chrname = $self->group_abbr()."ctg0" if ($chr->{'contig'} == 0); print join ("\t", $chrname,"assembly","Chromosome",1, "$chrend",".",".",".", "Sequence \"$chrname\"; Name \"$chrname\"\n"); } print join ("\t", $chrname,"assembly","Chromosome",1, "$chrend",".",".",".", "Sequence \"$chrname\"; Name \"$chrname\"\n") if ($chr->{'group'} ne $lastchr && $chr->{'group'} eq 0 ); $lastchr = $chr->{'group'}; $lastchr = -1 if ($chr->{'contig'} == 0); my $contig = $chr->{'contig'}; if(exists ($_contigs{$contig}{'range'} ) ) { print join ("\t",$chrname, "FPC","contig", $gffcontigs{$contig}{'start'}+$displacement, $gffcontigs{$contig}{'end'}+$displacement, ".",".",".", "contig \"ctg$contig\"; Name \"ctg$contig\"\n"); } my @clones = (keys %{$_contigs{$contig}{'clones'}} ); foreach my $clone (@clones) { if(exists ($_clones{$clone}{'range'}) ) { print join ("\t",$chrname,"FPC"); my $type = $_clones{$clone}{'type'}; if ($clone =~ /sd1$/) { $clone =~ s/sd1$//; $type = "sequenced"; } print join ("\t","\t$type",$gffclones{$clone}{'start'} +$displacement,$gffclones{$clone}{'end'} +$displacement,".",".",".", "$type \"$clone\"; Name \"$clone\""); my @markers = keys %{$_clones{$clone}{'markers'}}; print "; Marker_hit" if (scalar(@markers)); foreach my $mkr(@markers) { if (exists($_markers{$mkr}{'framework'})) { print " \"$mkr ",$_markers{$mkr}{'group'}," ", $_markers{$mkr}{'global'},"\""; } else { print (" \"$mkr 0 0\""); } } print "; Contig_hit \"",$_clones{$clone}{'contig'},"\" " if (defined($_clones{$clone}{'contig'})); } print "\n"; } if (exists ($_contigs{$contig}{'markers'}) ) { my %list = %{$_contigs{$contig}{'markers'}}; while (my ($k,$v) = each %list) { print join ("\t",$chrname,"FPC"); my $type = "marker"; $type = "electronicmarker" if ($_markers{$k}{'type'} eq "eMRK"); if( exists($_markers{$k}{'framework'})) { $type = "frameworkmarker" if($_markers{$k}{'framework'} == 1); $type = "placementmarker" if($_markers{$k}{'framework'} == 0); } print join ("\t","\t$type",$gffmarkers{$contig}{$k} + $displacement,$gffmarkers{$contig}{$k} + $displacement,".",".",".", "$type \"$k\"; Name \"$k\""); my @clonelist; my @clones = keys %{$_markers{$k}{'clones'}}; foreach my $cl (@clones) { push (@clonelist, $cl) if($_clones{$cl}{'contig'} == $contig); } $" = " "; print("; Contig_hit \"ctg$contig - ", scalar(@clonelist),"\" (@clonelist)\n"); } } $displacement += $margin + $gffcontigs{$contig}{'end'}; } } } =head2 _calc_markerposition Title : _calc_markerposition Usage : $map->_calc_markerposition(); Function: Calculates the position of the marker in the contig Returns : none Args : none =cut sub _calc_markerposition { my ($self) = @_; my %_contigs = %{$self->{'_contigs'}}; my %_markers = %{$self->{'_markers'}}; my %_clones = %{$self->{'_clones'}}; my $i; my ($depth, $save_depth); my ($x, $y); my @stack; my ($k, $j, $s); my $pos; my $contig; # Calculate the position for the marker in the contig my @contigs = $self->each_contigid(); my @sortedcontigs = sort {$a <=> $b } @contigs; my $offset; my %gffclones; my %gffcontigs; foreach my $marker ($self->each_markerid()) { my (@ctgmarker, @sortedctgmarker); my @clones = (keys %{$_markers{$marker}{'clones'}}) if (exists ($_markers{$marker}{'clones'} )); foreach my $clone (@clones) { my $record; $record->{contig} = $_clones{$clone}{'contig'}; $record->{start} = $_clones{$clone}{'range'}{'start'}; $record->{end} = $_clones{$clone}{'range'}{'end'}; push @ctgmarker,$record; } # sorting by contig and left position @sortedctgmarker = sort { $a->{'contig'} <=> $b->{'contig'} || $b->{'start'} <=> $a->{'start'} || $b->{'end'} <=> $a->{'end'} } @ctgmarker; my $ctg = -1; for ($i=0; $i < scalar(@sortedctgmarker); $i++) { if ($ctg != $sortedctgmarker[$i]->{'contig'}) { if ($ctg == -1) { $ctg = $sortedctgmarker[$i]->{'contig'}; } else { if ($depth > $save_depth){ $pos = ($x + $y) >> 1; $_contigs{$ctg}{'markers'}{$marker} = $pos; $_markers{$marker}{'posincontig'}{$ctg} = $pos; } } $ctg = $sortedctgmarker[$i]->{'contig'}; $x = $sortedctgmarker[$i]->{'start'}; $y = $sortedctgmarker[$i]->{'end'}; $stack[0] = $y; $pos = ($x + $y) >> 1; $_contigs{$ctg}{'markers'}{$marker} = $pos; $_markers{$marker}{'posincontig'}{$ctg} = $pos; $depth = $save_depth = 1; } elsif ($sortedctgmarker[$i]->{'end'} <= $y) { $stack[$depth++] = $sortedctgmarker[$i]->{'end'}; # MAX if ($x < $sortedctgmarker[$i]->{'start'} ) { $x = $sortedctgmarker[$i]->{'start'}; } # MIN if ($y > $sortedctgmarker[$i]->{'end'}) { $y = $sortedctgmarker[$i]->{'end'}; } } else { if ($depth > $save_depth) { $save_depth = $depth; $pos = ($x + $y) >> 1; $_contigs{$ctg}{'markers'}{$marker} = $pos; $_markers{$marker}{'posincontig'}{$ctg} = $pos; } $x = $sortedctgmarker[$i]->{'start'}; $y = $sortedctgmarker[$i]->{'end'}; $stack[$depth++] = $y; for($j=-1, $k=0, $s=0; $s<$depth; $s++) { if ($stack[$s] <$x) { $stack[$s] = -1; $j = $s if ($j == -1); } else { $k++; # MIN $y = $stack[$s] if ($y > $stack[$s]); if ($stack[$j] == -1) { $stack[$j] = $stack[$s]; $stack[$s] = -1; while ($stack[$j] != -1) {$j++;} } else { $j = $s; } } $depth = $k; } } if ($depth > $save_depth) { $pos = ($x + $y) >> 1; $_contigs{$ctg}{'markers'}{$marker} = $pos; $_markers{$marker}{'posincontig'}{$ctg} = $pos; } } } } =head2 _calc_contigposition Title : _calc_contigposition Usage : $map->_calc_contigposition(); Function: calculates the position of the contig in the group Returns : none Args : none =cut sub _calc_contigposition{ my ($self) = @_; my %_contigs = %{$self->{'_contigs'}}; my %_markers = %{$self->{'_markers'}}; my %_clones = %{$self->{'_clones'}}; my @contigs = $self->each_contigid(); my @sortedcontigs = sort {$a <=> $b } @contigs; foreach my $contig (@sortedcontigs) { my $position = 0; my $group; if (exists($_contigs{$contig}{'group'}) ) { my %weightedmarkers; my @mkrs = keys (%{$_contigs{$contig}{'markers'}}) if (exists($_contigs{$contig}{'markers'})) ; my $chr = $_contigs{$contig}{'group'}; $chr = 0 if ($_contigs{$contig}{'group'} =~ /\?/); foreach my $mkr (@mkrs) { if (exists($_markers{$mkr}{'group'})) { if ( $_markers{$mkr}{'group'} == $chr ) { my @mkrclones = keys( %{$_markers{$mkr}{'clones'}}); my $clonescount = 0; foreach my $clone (@mkrclones) { ++$clonescount if ($_clones{$clone}{'contig'} == $contig); } $weightedmarkers{$_markers{$mkr}{'global'}} = $clonescount; } } } my $weightedctgsum = 0; my $totalhits = 0; while (my ($mpos,$hits) = each %weightedmarkers) { $weightedctgsum += ($mpos * $hits); $totalhits += $hits; } $position = sprintf("%.2f",$weightedctgsum / $totalhits) if ($totalhits != 0); $_contigs{$contig}{'position'} = $position; } } } =head2 _calc_contiggroup Title : _calc_contiggroup Usage : $map->_calc_contiggroup(); Function: calculates the group of the contig Returns : none Args : none =cut sub _calc_contiggroup { my ($self) = @_; my %_contig = %{$self->{'_contigs'}}; my @contigs = $self->each_contigid(); foreach my $ctg (@contigs) { my $chr = floor($ctg/1000); $_contig{$ctg}{'group'} = $chr; } } =head2 _setITypeE>Ref Title : _setRef Usage : These are used for initializing the reference of the hash in Bio::MapIO (fpc.pm) to the corresponding hash in Bio::Map (physical.pm). Should be used only from Bio::MapIO System. $map->setCloneRef(\%_clones); $map->setMarkerRef(\%_markers); $map->setContigRef(\%_contigs); Function: sets the hash references to the corresponding hashes Returns : none Args : reference of the hash. =cut sub _setCloneRef { my ($self, $ref) = @_; %{$self->{'_clones'}} = %{$ref}; } sub _setMarkerRef { my ($self, $ref) = @_; %{$self->{'_markers'}} = %{$ref}; } sub _setContigRef { my ($self, $ref) = @_; %{$self->{'_contigs'}} = %{$ref}; } 1; BioPerl-1.007002/Bio/Map/Position.pm000444000766000024 3431113155576320 17125 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::Position # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::Position - A single position of a Marker, or the range over which that marker lies, in a Map =head1 SYNOPSIS use Bio::Map::Position; my $position = Bio::Map::Position->new(-map => $map, -element => $marker, -value => 100 ); my $position_with_range = Bio::Map::Position->new(-map => $map, -element => $marker, -start => 100, -length => 10 ); =head1 DESCRIPTION This object is an implementation of the PositionI interface that handles the specific values of a position. This allows a map element (e.g. Marker) to have multiple positions within a map and still be treated as a single entity. This handles the concept of a relative map in which the order of elements and the distance between them is known, but does not directly handle the case when distances are unknown - in that case arbitrary values must be assigned for position values. No units are assumed here - units are handled by context of which Map a position is placed in or the subclass of this Position. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 CONTRIBUTORS Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Chad Matsalla, bioinformatics1@dieselwurks.com Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::Position; use strict; use Scalar::Util qw(looks_like_number); use Bio::Map::Relative; use base qw(Bio::Root::Root Bio::Map::PositionI); =head2 new Title : new Usage : my $obj = Bio::Map::Position->new(); Function: Builds a new Bio::Map::Position object Returns : Bio::Map::Position Args : -map => Bio::Map::MapI object -element => Bio::Map::MappableI object -relative => Bio::Map::RelativeI object * If this position has no range, or if a single value can describe the range * -value => scalar : something that describes the single point position or range of this Position, most likely an int * Or if this position has a range, at least two of * -start => int : value of the start co-ordinate -end => int : value of the end co-ordinate -length => int : length of the range =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($map, $marker, $element, $value, $start, $end, $length, $relative) = $self->_rearrange([qw( MAP MARKER ELEMENT VALUE START END LENGTH RELATIVE )], @args); my $do_range = defined($start) || defined($end); if ($value && $do_range) { $self->warn("-value and (-start|-end|-length) are mutually exclusive, ignoring value"); $value = undef; } $map && $self->map($map); $marker && $self->element($marker); # backwards compatibility $element && $self->element($element); $relative && $self->relative($relative); defined($value) && $self->value($value); if ($do_range) { defined($start) && $self->start($start); defined($end) && $self->end($end); if ($length) { if (defined($start) && ! defined($end)) { $self->end($start + $length - 1); } elsif (! defined($start)) { $self->start($end - $length + 1); } } defined($self->end) || $self->end($start); } return $self; } =head2 relative Title : relative Usage : my $relative = $position->relative(); $position->relative($relative); Function: Get/set the thing this Position's coordinates (numerical(), start(), end()) are relative to, as described by a Relative object. Returns : Bio::Map::RelativeI (default is one describing "relative to the start of the Position's map") Args : none to get, OR Bio::Map::RelativeI to set =cut sub relative { my ($self, $relative) = @_; if ($relative) { $self->throw("Must supply an object") unless ref($relative); $self->throw("This is [$relative], not a Bio::Map::RelativeI") unless $relative->isa('Bio::Map::RelativeI'); $self->{_relative_not_implicit} = 1; $self->{_relative} = $relative; } return $self->{_relative} || $self->absolute_relative; } =head2 absolute Title : absolute Usage : my $absolute = $position->absolute(); $position->absolute($absolute); Function: Get/set how this Position's co-ordinates (numerical(), start(), end()) are reported. When absolute is off, co-ordinates are relative to the thing described by relative(). Ie. the value returned by start() will be the same as the value you set start() to. When absolute is on, co-ordinates are converted to be relative to the start of the map. So if relative() currently points to a Relative object describing "relative to another position which is 100 bp from the start of the map", this Position's start() had been set to 50 and absolute() returns 1, $position->start() will return 150. If absolute() returns 0 in the same situation, $position->start() would return 50. Returns : boolean (default 0) Args : none to get, OR boolean to set =cut sub absolute { my $self = shift; if (@_) { $self->{_absolute} = shift } return $self->{_absolute} || 0; } =head2 value Title : value Usage : my $pos = $position->value; Function: Get/Set the value for this position Returns : scalar, value Args : [optional] new value to set =cut sub value { my ($self, $value) = @_; if (defined $value) { $self->{'_value'} = $value; $self->start($self->numeric) unless defined($self->start); $self->end($self->numeric) unless defined($self->end); } return $self->{'_value'}; } =head2 numeric Title : numeric Usage : my $num = $position->numeric; Function: Read-only method that is guaranteed to return a numeric representation of the start of this position. Returns : scalar numeric Args : none to get the co-ordinate normally (see absolute() method), OR Bio::Map::RelativeI to get the co-ordinate converted to be relative to what this Relative describes. =cut sub numeric { my ($self, $value) = @_; my $num = $self->{'_value'}; $self->throw("The value has not been set, can't convert to numeric") unless defined($num); $self->throw("This value [$num] is not numeric") unless looks_like_number($num); if (ref($value) && $value->isa('Bio::Map::RelativeI')) { # get the value after co-ordinate conversion my $raw = $num; my ($abs_start, $rel_start) = $self->_relative_handler($value); return $abs_start + $raw - $rel_start; } # get the value as per absolute if ($self->{_relative_not_implicit} && $self->absolute) { # this actually returns the start, but should be the same thing... return $self->relative->absolute_conversion($self); } return $num; } =head2 start Title : start Usage : my $start = $position->start(); $position->start($start); Function: Get/set the start co-ordinate of this position. Returns : the start of this position Args : scalar numeric to set, OR none to get the co-ordinate normally (see absolute() method), OR Bio::Map::RelativeI to get the co-ordinate converted to be relative to what this Relative describes. =cut sub start { my ($self, $value) = @_; if (defined $value) { if (ref($value) && $value->isa('Bio::Map::RelativeI')) { # get the value after co-ordinate conversion my $raw = $self->{start}; defined $raw || return; my ($abs_start, $rel_start) = $self->_relative_handler($value); return $abs_start + $raw - $rel_start; } else { # set the value $self->throw("This is [$value], not a number") unless looks_like_number($value); $self->{start} = $value; $self->value($value) unless defined($self->value); } } # get the value as per absolute if ($self->{_relative_not_implicit} && $self->absolute) { return $self->relative->absolute_conversion($self); } return defined($self->{start}) ? $self->{start} : return; } =head2 end Title : end Usage : my $end = $position->end(); $position->end($end); Function: Get/set the end co-ordinate of this position. Returns : the end of this position Args : scalar numeric to set, OR none to get the co-ordinate normally (see absolute() method), OR Bio::Map::RelativeI to get the co-ordinate converted to be relative to what this Relative describes. =cut sub end { my ($self, $value) = @_; if (defined $value) { if (ref($value) && $value->isa('Bio::Map::RelativeI')) { # get the value after co-ordinate conversion my $raw = $self->{end}; defined $raw || return; my ($abs_start, $rel_start) = $self->_relative_handler($value); return $abs_start + $raw - $rel_start; } else { # set the value $self->throw("This value [$value] is not numeric!") unless looks_like_number($value); $self->{end} = $value; } } # get the value as per absolute if ($self->{_relative_not_implicit} && $self->absolute) { my $raw = $self->{end} || return; my $abs_start = $self->relative->absolute_conversion($self) || return; return $abs_start + ($raw - $self->{start}); } return defined($self->{end}) ? $self->{end} : return; } =head2 length Title : length Usage : $length = $position->length(); Function: Get/set the length of this position's range, changing the end() if necessary. Getting and even setting the length will fail if both start() and end() are not already defined. Returns : the length of this range Args : none to get, OR scalar numeric (>0) to set. =cut sub length { my ($self, $length) = @_; if ($length) { $length > 0 || return; my $existing_length = $self->length || return; return $length if $existing_length == $length; $self->end($self->{start} + $length - 1); } if (defined($self->start) && defined($self->end)) { return $self->end - $self->start + 1; } return; } =head2 sortable Title : sortable Usage : my $num = $position->sortable(); Function: Read-only method that is guaranteed to return a value suitable for correctly sorting this kind of position amongst other positions of the same kind on the same map. Note that sorting different kinds of position together is unlikely to give sane results. Returns : numeric Args : none =cut sub sortable { my ($self, $given_map) = @_; my $answer = $self->numeric($self->absolute_relative); return $answer; } =head2 toString Title : toString Usage : print $position->toString(), "\n"; Function: stringifies this range Returns : a string representation of the range of this Position Args : optional Bio::Map::RelativeI to have the co-ordinates reported relative to the thing described by that Relative =cut sub toString { my ($self, $rel) = @_; if (defined($self->start) && defined($self->end)) { return $self->start($rel).'..'.$self->end($rel); } return ''; } =head2 absolute_relative Title : absolute_relative Usage : my $rel = $position->absolute_relative(); Function: Get a relative describing the start of the map. This is useful for supplying to the coordinate methods (start(), end() etc.) to get the temporary effect of having set absolute(1). Returns : Bio::Map::Relative Args : none =cut sub absolute_relative { return Bio::Map::Relative->new(-map => 0, -description => 'start of map'); } # get our own absolute start and that of the thing we want as a frame of # reference sub _relative_handler { my ($self, $value) = @_; my $own_relative = $self->relative; # if the requested relative position is the same as the actual # relative, the current co-ordinate values are correct so shortcut my ($own_type, $req_type) = ($own_relative->type, $value->type); if ($own_type && $req_type && $own_type eq $req_type && $own_relative->$own_type eq $value->$req_type) { return (0, 0); } my $abs_start = $own_relative->absolute_conversion($self); my $rel_start = $value->absolute_conversion($self); $self->throw("Unable to resolve co-ordinate because relative to something that ultimately isn't relative to the map start") unless defined($abs_start) && defined($rel_start); return ($abs_start, $rel_start); } 1; BioPerl-1.007002/Bio/Map/PositionHandler.pm000555000766000024 3040313155576320 20424 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::PositionHandler # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::PositionHandler - A Position Handler Implementation =head1 SYNOPSIS # This is used by modules when they want to implement being a # Position or being something that has Positions (when they are # a L) # Make a PositionHandler that knows about you my $ph = Bio::Map::PositionHandler->new($self); # Register with it so that it handles your Position-related needs $ph->register; # If you are a position, get/set the map you are on and the marker you are # for $ph->map($map); $ph->element($marker); my $map = $ph->map; my $marker = $ph->element; # If you are a marker, add a new position to yourself $ph->add_positions($pos); # And then get all your positions on a particular map foreach my $pos ($ph->get_positions($map)) { # do something with this Bio::Map::PositionI } # Or find out what maps you exist on my @maps = $ph->get_other_entities; # The same applies if you were a map =head1 DESCRIPTION A Position Handler copes with the coordination of different Bio::Map::EntityI objects, adding and removing them from each other and knowning who belongs to who. These relationships between objects are based around shared Positions, hence PositionHandler. This PositionHandler is able to cope with Bio::Map::PositionI objects, Bio::Map::MappableI objects and Bio::Map::MapI objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::PositionHandler; use strict; use base qw(Bio::Root::Root Bio::Map::PositionHandlerI); # globally accessible hash, via private instance methods my $RELATIONS = {}; =head2 General methods =cut =head2 new Title : new Usage : my $position_handler = Bio::Map::PositionHandler->new(-self => $self); Function: Get a Bio::Map::PositionHandler that knows who you are. Returns : Bio::Map::PositionHandler object Args : -self => Bio::Map::EntityI that is you =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($you) = $self->_rearrange([qw(SELF)], @args); $self->throw('Must supply -self') unless $you; $self->throw('-self must be a reference (object)') unless ref($you); $self->throw('This is [$you], not a Bio::Map::EntityI object') unless $you->isa('Bio::Map::EntityI'); $self->{_who} = $you; $self->{_rel} = $RELATIONS; return $self; } =head2 register Title : register Usage : $position_handler->register(); Function: Ask this Position Handler to look after your entity relationships. Returns : n/a Args : none =cut sub register { my $self = shift; my $you = $self->{_who}; $self->throw("Trying to re-register [$you], which could be bad") if $you->get_position_handler->index; $self->{_index} = ++$self->{_rel}->{assigned_indices}; $self->{_rel}->{registered}->{$self->{_index}} = $you; } =head2 index Title : index Usage : my $index = $position_handler->index(); Function: Get the unique registry index for yourself, generated during the resistration process. Returns : int Args : none =cut sub index { my $self = shift; return $self->{_index}; } =head2 get_entity Title : get_entity Usage : my $entity = $position_handler->get_entity($index); Function: Get the entity that corresponds to the supplied registry index. Returns : Bio::Map::EntityI object Args : int =cut sub get_entity { my ($self, $index) = @_; return $self->{_rel}->{registered}->{$index} || $self->throw("Requested registy index '$index' but that index isn't in the registry"); } =head2 Methods for Bio::Map::PositionI objects =cut =head2 map Title : map Usage : my $map = $position_handler->map(); $position_handler->map($map); Function: Get/Set the map you are on. You must be a Position. Returns : L Args : none to get, OR new L to set =cut sub map { my ($self, $entity) = @_; return $self->_pos_get_set($entity, 'position_maps', 'Bio::Map::MapI'); } =head2 element Title : element Usage : my $element = $position_handler->element(); $position_handler->element($element); Function: Get/Set the map element you are for. You must be a Position. Returns : L Args : none to get, OR new L to set =cut sub element { my ($self, $entity) = @_; return $self->_pos_get_set($entity, 'position_elements', 'Bio::Map::MappableI'); } =head2 Methods for all other Bio::Map::EntityI objects =cut =head2 add_positions Title : add_positions Usage : $position_handler->add_positions($pos1, $pos2, ...); Function: Add some positions to yourself. You can't be a position. Returns : n/a Args : Array of Bio::Map::PositionI objects =cut sub add_positions { my $self = shift; $self->throw('Must supply at least one Bio::Map::EntityI') unless @_ > 0; my $you_index = $self->_get_you_index(0); my $kind = $self->_get_kind; foreach my $pos (@_) { $self->_check_object($pos, 'Bio::Map::PositionI'); my $pos_index = $self->_get_other_index($pos); $self->_pos_set($pos_index, $you_index, $kind); } } =head2 get_positions Title : get_positions Usage : my @positions = $position_handler->get_positions(); Function: Get all your positions. You can't be a Position. Returns : Array of Bio::Map::PositionI objects Args : none for all, OR Bio::Map::EntityI object to limit the Positions to those that are shared by you and this other entity. =cut sub get_positions { my ($self, $entity) = @_; my $you_index = $self->_get_you_index(0); my @positions = keys %{$self->{_rel}->{has}->{$you_index}}; if ($entity) { my $entity_index = $self->_get_other_index($entity); my $pos_ref = $self->{_rel}->{has}->{$entity_index}; @positions = grep { $pos_ref->{$_} } @positions; } return map { $self->get_entity($_) } @positions; } =head2 purge_positions Title : purge_positions Usage : $position_handler->purge_positions(); Function: Remove all positions from yourself. You can't be a Position. Returns : n/a Args : none to remove all, OR Bio::Map::PositionI object to remove only that entity, OR Bio::Map::EntityI object to limit the removal to those Positions that are shared by you and this other entity. =cut sub purge_positions { my ($self, $thing) = @_; my $you_index = $self->_get_you_index(0); my $kind = $self->_get_kind; my @pos_indices; if ($thing) { $self->throw("Must supply an object") unless ref($thing); if ($thing->isa("Bio::Map::PositionI")) { @pos_indices = ($self->_get_other_index($thing)); } else { my $entity_index = $self->_get_other_index($thing); my $pos_ref = $self->{_rel}->{has}->{$entity_index}; @pos_indices = grep { $pos_ref->{$_} } keys %{$self->{_rel}->{has}->{$you_index}}; } } else { @pos_indices = keys %{$self->{_rel}->{has}->{$you_index}}; } foreach my $pos_index (@pos_indices) { $self->_purge_pos_entity($pos_index, $you_index, $kind); } } =head2 get_other_entities Title : get_other_entities Usage : my @entities = $position_handler->get_other_entities(); Function: Get all the entities that share your Positions. You can't be a Position. Returns : Array of Bio::Map::EntityI objects Args : none =cut sub get_other_entities { my $self = shift; my $you_index = $self->_get_you_index(0); my $kind = $self->_get_kind; my $want = $kind eq 'position_elements' ? 'position_maps' : 'position_elements'; my %entities; while (my ($pos_index) = each %{$self->{_rel}->{has}->{$you_index}}) { my $entity_index = $self->{_rel}->{$want}->{$pos_index}; $entities{$entity_index} = 1 if $entity_index; } return map { $self->get_entity($_) } keys %entities; } # do basic check on an object, make sure it is the right type sub _check_object { my ($self, $object, $interface) = @_; $self->throw("Must supply an arguement") unless $object; $self->throw("This is [$object], not an object") unless ref($object); $self->throw("This is [$object], not a $interface") unless $object->isa($interface); } # get the object we are the handler of, its index, and throw depending on if # we're a Position sub _get_you_index { my ($self, $should_be_pos) = @_; my $you = $self->{_who}; if ($should_be_pos) { $self->throw("This is not a Position, method invalid") unless $you->isa('Bio::Map::PositionI'); } else { $self->throw("This is a Position, method invalid") if $you->isa('Bio::Map::PositionI'); } return $self->index; } # check an entity is registered and get its index sub _get_other_index { my ($self, $entity) = @_; $self->throw("Must supply an object") unless ref($entity); my $index = $entity->get_position_handler->index; $self->throw("Entity doesn't seem like it's been registered") unless $index; $self->throw("Entity may have been registered with a different PositionHandler, can't deal with it") unless $entity eq $self->get_entity($index); return $index; } # which of the position hashes should we be recorded under? sub _get_kind { my $self = shift; my $you = $self->{_who}; return $you->isa('Bio::Map::MapI') ? 'position_maps' : $you->isa('Bio::Map::MappableI') ? 'position_elements' : $self->throw("This is [$you] which is an unsupported kind of entity"); } # get/set position entity sub _pos_get_set { my ($self, $entity, $kind, $interface) = @_; my $you_index = $self->_get_you_index(1); my $entity_index; if ($entity) { $self->_check_object($entity, $interface); my $new_entity_index = $self->_get_other_index($entity); $entity_index = $self->_pos_set($you_index, $new_entity_index, $kind); } $entity_index ||= $self->{_rel}->{$kind}->{$you_index} || 0; if ($entity_index) { return $self->get_entity($entity_index); } return; } # set position entity sub _pos_set { my ($self, $pos_index, $new_entity_index, $kind) = @_; my $current_entity_index = $self->{_rel}->{$kind}->{$pos_index} || 0; if ($current_entity_index) { if ($current_entity_index == $new_entity_index) { return $current_entity_index; } $self->_purge_pos_entity($pos_index, $current_entity_index, $kind); } $self->{_rel}->{has}->{$new_entity_index}->{$pos_index} = 1; $self->{_rel}->{$kind}->{$pos_index} = $new_entity_index; return $new_entity_index; } # disassociate position from one of its current entities sub _purge_pos_entity { my ($self, $pos_index, $entity_index, $kind) = @_; delete $self->{_rel}->{has}->{$entity_index}->{$pos_index}; delete $self->{_rel}->{$kind}->{$pos_index}; } 1; BioPerl-1.007002/Bio/Map/PositionHandlerI.pm000555000766000024 1272213155576320 20541 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::PositionHandlerI # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::PositionHandlerI - A Position Handler Interface =head1 SYNOPSIS # do not use this module directly # See Bio::Map::PositionHandler for an example of # implementation. =head1 DESCRIPTION This interface describes the basic methods required for Position Handlers. A Position Handler copes with the coordination of different Bio::Map::EntityI objects, adding and removing them from each other and knowning who belongs to who. These relationships between objects are based around shared Positions, hence PositionHandler. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::PositionHandlerI; use strict; use base qw(Bio::Root::RootI); =head2 General methods =cut =head2 register Title : register Usage : $position_handler->register(); Function: Ask this Position Handler to look after your entity relationships. Returns : n/a Args : none =cut sub register { my $self = shift; $self->throw_not_implemented(); } =head2 index Title : index Usage : my $index = $position_handler->index(); Function: Get the unique registry index for yourself, generated during the resistration process. Returns : int Args : none =cut sub index { my $self = shift; $self->throw_not_implemented(); } =head2 get_entity Title : get_entity Usage : my $entity = $position_handler->get_entity($index); Function: Get the entity that corresponds to the supplied registry index. Returns : Bio::Map::EntityI object Args : int =cut sub get_entity { my $self = shift; $self->throw_not_implemented(); } =head2 Methods for Bio::Map::PositionI objects =cut =head2 map Title : map Usage : my $map = $position_handler->map(); $position_handler->map($map); Function: Get/Set the map you are on. You must be a Position. Returns : L Args : none to get, OR new L to set =cut sub map { my $self = shift; $self->throw_not_implemented(); } =head2 element Title : element Usage : my $element = $position_handler->element(); $position_handler->element($element); Function: Get/Set the map element you are for. You must be a Position. Returns : L Args : none to get, OR new L to set =cut sub element { my $self = shift; $self->throw_not_implemented(); } =head2 Methods for all other Bio::Map::EntityI objects =cut =head2 add_positions Title : add_positions Usage : $position_handler->add_positions($pos1, $pos2, ...); Function: Add some positions to yourself. You can't be a position. Returns : n/a Args : Array of Bio::Map::PositionI objects =cut sub add_positions { my $self = shift; $self->throw_not_implemented(); } =head2 get_positions Title : get_positions Usage : my @positions = $position_handler->get_positions(); Function: Get all your positions. You can't be a Position. Returns : Array of Bio::Map::PositionI objects Args : none for all, OR Bio::Map::EntityI object to limit the Positions to those that are shared by you and this other entity. =cut sub get_positions { my $self = shift; $self->throw_not_implemented(); } =head2 purge_positions Title : purge_positions Usage : $position_handler->purge_positions(); Function: Remove all positions from yourself. You can't be a Position. Returns : n/a Args : none to remove all, OR Bio::Map::PositionI object to remove only that entity, OR Bio::Map::EntityI object to limit the removal to those Positions that are shared by you and this other entity. =cut sub purge_positions { my $self = shift; $self->throw_not_implemented(); } =head2 get_other_entities Title : get_other_entities Usage : my @entities = $position_handler->get_other_entities(); Function: Get all the entities that share your Positions. You can't be a Position. Returns : Array of Bio::Map::EntityI objects Args : none =cut sub get_other_entities { my $self = shift; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Map/PositionI.pm000444000766000024 7563313155576320 17252 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::PositionI # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::PositionI - Abstracts the notion of a position having a value in the context of a marker and a Map =head1 SYNOPSIS # do not use this module directly # See Bio::Map::Position for an example of # implementation. =head1 DESCRIPTION This object stores one of the positions that a mappable object (e.g. Marker) may have in a map. Positions can have non-numeric values or other methods to store the locations, so they have a method numeric() which does the conversion. numeric() returns the position in a form that can be compared between other positions of the same type. It is not necessarily a value suitable for sorting positions (it may be the distance from the previous position); for that purpose the result of sortable() should be used. A 'position', in addition to being a single point, can also be an area and so can be imagined as a range and compared with other positions on the basis of overlap, intersection etc. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Lincoln Stein, lstein-at-cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::PositionI; use strict; use Bio::Map::PositionHandler; use Bio::Map::Mappable; use Scalar::Util qw(looks_like_number); use base qw(Bio::Map::EntityI Bio::RangeI); =head2 EntityI methods These are fundamental to coordination of Positions and other entities, so are implemented at the interface level =cut =head2 get_position_handler Title : get_position_handler Usage : my $position_handler = $entity->get_position_handler(); Function: Gets a PositionHandlerI that $entity is registered with. Returns : Bio::Map::PositionHandlerI object Args : none =cut sub get_position_handler { my $self = shift; unless (defined $self->{_eh}) { my $ph = Bio::Map::PositionHandler->new(-self => $self); $self->{_eh} = $ph; $ph->register; } return $self->{_eh}; } =head2 PositionHandlerI-related methods These are fundamental to coordination of Positions and other entities, so are implemented at the interface level =cut =head2 map Title : map Usage : my $map = $position->map(); $position->map($map); Function: Get/Set the map the position is in. Returns : L Args : none to get new L to set =cut sub map { my ($self, $map) = @_; return $self->get_position_handler->map($map); } =head2 element Title : element Usage : my $element = $position->element(); $position->element($element); Function: Get/Set the element the position is for. Returns : L Args : none to get new L to set =cut sub element { my ($self, $element) = @_; return $self->get_position_handler->element($element); } =head2 marker Title : marker Function: This is a synonym of the element() method Status : deprecated, will be removed in the next version =cut *marker = \&element; =head2 PositionI-specific methods =cut =head2 value Title : value Usage : my $pos = $position->value(); Function: Get/Set the value for this position Returns : scalar, value Args : [optional] new value to set =cut sub value { my $self = shift; $self->throw_not_implemented(); } =head2 numeric Title : numeric Usage : my $num = $position->numeric; Function: Read-only method that is guaranteed to return a numeric representation of the start of this position. Returns : scalar numeric Args : none to get the co-ordinate normally (see absolute() method), OR Bio::Map::RelativeI to get the co-ordinate converted to be relative to what this Relative describes. =cut sub numeric { my $self = shift; $self->throw_not_implemented(); } =head2 sortable Title : sortable Usage : my $num = $position->sortable(); Function: Read-only method that is guaranteed to return a value suitable for correctly sorting this kind of position amongst other positions of the same kind on the same map. Note that sorting different kinds of position together is unlikely to give sane results. Returns : numeric Args : none =cut sub sortable { my $self = shift; $self->throw_not_implemented(); } =head2 relative Title : relative Usage : my $relative = $position->relative(); $position->relative($relative); Function: Get/set the thing this Position's coordinates (numerical(), start(), end()) are relative to, as described by a Relative object. Returns : Bio::Map::RelativeI (default is one describing "relative to the start of the Position's map") Args : none to get, OR Bio::Map::RelativeI to set =cut sub relative { my $self = shift; $self->throw_not_implemented(); } =head2 absolute Title : absolute Usage : my $absolute = $position->absolute(); $position->absolute($absolute); Function: Get/set how this Position's co-ordinates (numerical(), start(), end()) are reported. When absolute is off, co-ordinates are relative to the thing described by relative(). Ie. the value returned by start() will be the same as the value you set start() to. When absolute is on, co-ordinates are converted to be relative to the start of the map. So if relative() currently points to a Relative object describing "relative to another position which is 100 bp from the start of the map", this Position's start() had been set to 50 and absolute() returns 1, $position->start() will return 150. If absolute() returns 0 in the same situation, $position->start() would return 50. Returns : boolean (default 0) Args : none to get, OR boolean to set =cut sub absolute { my $self = shift; $self->throw_not_implemented(); } =head2 RangeI-based methods =cut =head2 start Title : start Usage : my $start = $position->start(); $position->start($start); Function: Get/set the start co-ordinate of this position. Returns : the start of this position Args : scalar numeric to set, OR none to get the co-ordinate normally (see absolute() method), OR Bio::Map::RelativeI to get the co-ordinate converted to be relative to what this Relative describes. =cut =head2 end Title : end Usage : my $end = $position->end(); $position->end($end); Function: Get/set the end co-ordinate of this position. Returns : the end of this position Args : scalar numeric to set, OR none to get the co-ordinate normally (see absolute() method), OR Bio::Map::RelativeI to get the co-ordinate converted to be relative to what this Relative describes. =cut =head2 length Title : length Usage : $length = $position->length(); Function: Get the length of this position. Returns : the length of this position Args : none =cut =head2 strand Title : strand Usage : $strand = $position->strand(); Function: Get the strand of this position; it is always 1 since maps to not have strands. Returns : 1 Args : none =cut sub strand { return 1; } =head2 toString Title : toString Usage : print $position->toString(), "\n"; Function: stringifies this range Returns : a string representation of the range of this Position Args : optional Bio::Map::RelativeI to have the co-ordinates reported relative to the thing described by that Relative =cut sub toString { my $self = shift; $self->throw_not_implemented(); } =head1 RangeI-related methods These methods work by considering only the values of start() and end(), as modified by considering every such co-ordinate relative to the start of the map (ie. absolute(1) is set temporarily during the calculation), or any supplied Relative. For the boolean methods, when the comparison Position is on the same map as the calling Position, there is no point supplying a Relative since the answer will be the same as without. Relative is most useful when comparing Positions on different maps and you have a Relative that describes some special place on each map like 'the start of the gene', where the actual start of the gene relative to the start of the map is different for each map. The methods do not consider maps during their calculations - things on different maps can overlap/contain/intersect/etc. each other. The geometrical methods (intersect, union etc.) do things to the geometry of ranges, and return Bio::Map::PositionI compliant objects or triplets (start, stop, strand) from which new positions could be built. When a PositionI is made it will have a map transferred to it if all the arguments shared the same map. If a Relative was supplied the result will have that same Relative. Note that the strand-testing args are there for compatibility with the RangeI interface. They have no meaning when only using PositionI objects since maps do not have strands. Typically you will just set the argument to undef if you want to supply the argument after it. =head2 equals Title : equals Usage : if ($p1->equals($p2)) {...} Function: Test whether $p1 has the same start, end, length as $p2. Returns : true if they are describing the same position (regardless of map) Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this one to (mandatory) arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore') arg #3 = optional Bio::Map::RelativeI to ask if the Positions equal in terms of their relative position to the thing described by that Relative =cut sub equals { # overriding the RangeI implementation so we can handle Relative my ($self, $other, $so, $rel) = @_; my ($own_start, $own_end) = $self->_pre_rangei($self, $rel); my ($other_start, $other_end) = $self->_pre_rangei($other, $rel); return ($self->_testStrand($other, $so) and $own_start == $other_start and $own_end == $other_end); } =head2 less_than Title : less_than Usage : if ($position->less_than($other_position)) {...} Function: Ask if this Position ends before another starts. Returns : boolean Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this one to (mandatory) arg #2 = optional Bio::Map::RelativeI to ask if the Position is less in terms of their relative position to the thing described by that Relative =cut sub less_than { my ($self, $other, $rel) = @_; my ($own_start, $own_end) = $self->_pre_rangei($self, $rel); my ($other_start, $other_end) = $self->_pre_rangei($other, $rel); return $own_end < $other_start; } =head2 greater_than Title : greater_than Usage : if ($position->greater_than($other_position)) {...} Function: Ask if this Position starts after another ends. Returns : boolean Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this one to (mandatory) arg #2 = optional Bio::Map::RelativeI to ask if the Position is greater in terms of their relative position to the thing described by that Relative =cut sub greater_than { my ($self, $other, $rel) = @_; my ($own_start, $own_end) = $self->_pre_rangei($self, $rel); my ($other_start, $other_end) = $self->_pre_rangei($other, $rel); return $own_start > $other_end; } =head2 overlaps Title : overlaps Usage : if ($p1->overlaps($p2)) {...} Function: Tests if $p1 overlaps $p2. Returns : True if the positions overlap (regardless of map), false otherwise Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this one to (mandatory) arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore') arg #3 = optional Bio::Map::RelativeI to ask if the Positions overlap in terms of their relative position to the thing described by that Relative arg #4 = optional minimum percentage length of the overlap before reporting an overlap exists (default 0) =cut sub overlaps { # overriding the RangeI implementation so we can handle Relative my ($self, $other, $so, $rel, $min_percent) = @_; $min_percent ||= 0; my ($own_min, $other_min) = (0, 0); if ($min_percent > 0) { $own_min = (($self->length / 100) * $min_percent) - 1; $other_min = (($other->length / 100) * $min_percent) - 1; } my ($own_start, $own_end) = $self->_pre_rangei($self, $rel); my ($other_start, $other_end) = $self->_pre_rangei($other, $rel); return ($self->_testStrand($other, $so) and not (($own_start + $own_min > $other_end or $own_end - $own_min < $other_start) || ($own_start > $other_end - $other_min or $own_end < $other_start + $other_min))); } =head2 contains Title : contains Usage : if ($p1->contains($p2)) {...} Function: Tests whether $p1 totally contains $p2. Returns : true if the argument is totally contained within this position (regardless of map), false otherwise Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this one to, or scalar number (mandatory) arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore') arg #3 = optional Bio::Map::RelativeI to ask if the Position is contained in terms of their relative position to the thing described by that Relative =cut sub contains { # overriding the RangeI implementation so we can handle Relative my ($self, $other, $so, $rel) = @_; my ($own_start, $own_end) = $self->_pre_rangei($self, $rel); my ($other_start, $other_end) = $self->_pre_rangei($other, $rel); return ($self->_testStrand($other, $so) and $other_start >= $own_start and $other_end <= $own_end); } =head2 intersection Title : intersection Usage : ($start, $stop, $strand) = $p1->intersection($p2) ($start, $stop, $strand) = Bio::Map::Position->intersection(\@positions); $mappable = $p1->intersection($p2, undef, $relative); $mappable = Bio::Map::Position->intersection(\@positions); Function: gives the range that is contained by all ranges Returns : undef if they do not overlap, OR Bio::Map::Mappable object who's positions are the cross-map-calculated intersection of the input positions on all the maps that the input positions belong to, OR, in list context, a three element array (start, end, strand) Args : arg #1 = [REQUIRED] a Bio::RangeI (eg. a Bio::Map::Position) to compare this one to, or an array ref of Bio::RangeI arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore') arg #3 = optional Bio::Map::RelativeI to ask how the Positions intersect in terms of their relative position to the thing described by that Relative =cut sub intersection { # overriding the RangeI implementation so we can transfer map and handle # Relative my ($self, $given, $so, $rel) = @_; $self->throw("missing arg: you need to pass in another argument") unless $given; my @positions; if ($self eq "Bio::Map::PositionI") { $self = "Bio::Map::Position"; $self->warn("calling static methods of an interface is deprecated; use $self instead"); } if (ref $self) { push(@positions, $self); } ref($given) eq 'ARRAY' ? push(@positions, @{$given}) : push(@positions, $given); $self->throw("Need at least 2 Positions") unless @positions >= 2; my ($intersect, $i_start, $i_end, $c_start, $c_end, %known_maps); while (@positions > 0) { unless ($intersect) { $intersect = shift(@positions); ($i_start, $i_end) = $self->_pre_rangei($intersect, $rel); my $map = $intersect->map; $known_maps{$map->unique_id} = $map; } my $compare = shift(@positions); ($c_start, $c_end) = $self->_pre_rangei($compare, $rel); return unless $compare->_testStrand($intersect, $so); if ($compare->isa('Bio::Map::PositionI')) { my $this_map = $compare->map; if ($this_map) { $known_maps{$this_map->unique_id} = $this_map; } } else { $self->throw("Only Bio::Map::PositionI objects are supported, not [$compare]"); } my @starts = sort {$a <=> $b} ($i_start, $c_start); my @ends = sort {$a <=> $b} ($i_end, $c_end); my $start = pop @starts; # larger of the 2 starts my $end = shift @ends; # smaller of the 2 ends my $intersect_strand; # strand for the intersection if (defined($intersect->strand) && defined($compare->strand) && $intersect->strand == $compare->strand) { $intersect_strand = $compare->strand; } else { $intersect_strand = 0; } if ($start > $end) { return; } else { $intersect = $self->new(-start => $start, -end => $end, -strand => $intersect_strand); } } $intersect || return; my ($start, $end, $strand) = ($intersect->start, $intersect->end, $intersect->strand); my @intersects; foreach my $known_map (values %known_maps) { my $new_intersect = $intersect->new(-start => $start, -end => $end, -strand => $strand, -map => $known_map); $new_intersect->relative($rel) if $rel; push(@intersects, $new_intersect); } unless (@intersects) { $intersect->relative($rel) if $rel; @intersects = ($intersect); } my $result = Bio::Map::Mappable->new(); $result->add_position(@intersects); # sneaky, add_position can take a list of positions return $result; } =head2 union Title : union Usage : ($start, $stop, $strand) = $p1->union($p2); ($start, $stop, $strand) = Bio::Map::Position->union(@positions); my $mappable = $p1->union($p2); my $mappable = Bio::Map::Position->union(@positions); Function: finds the minimal position/range that contains all of the positions Returns : Bio::Map::Mappable object who's positions are the cross-map-calculated union of the input positions on all the maps that the input positions belong to, OR, in list context, a three element array (start, end, strand) Args : a Bio::Map::PositionI to compare this one to, or a list of such OR a single Bio::Map::PositionI or array ref of such AND a Bio::Map::RelativeI to ask for the Position's union in terms of their relative position to the thing described by that Relative =cut sub union { # overriding the RangeI implementation so we can transfer map and handle # Relative my ($self, @args) = @_; $self->throw("Not enough arguments") unless @args >= 1; my @positions; my $rel; if ($self eq "Bio::Map::PositionI") { $self = "Bio::Map::Position"; $self->warn("calling static methods of an interface is deprecated; use $self instead"); } if (ref $self) { push(@positions, $self); } if (ref $args[0] eq 'ARRAY') { push(@positions, @{shift(@args)}); } else { push(@positions, shift(@args)); } if ($args[0] && $args[0]->isa('Bio::Map::RelativeI')) { $rel = shift(@args); } foreach my $arg (@args) { # avoid pushing undefined values into @positions push(@positions, $arg) if $arg; } $self->throw("Need at least 2 Positions") unless @positions >= 2; my (@starts, @ends, %known_maps, $union_strand); foreach my $compare (@positions) { # RangeI union allows start or end to be undefined; however _pre_rangei # will throw my ($start, $end) = $self->_pre_rangei($compare, $rel); if ($compare->isa('Bio::Map::PositionI')) { my $this_map = $compare->map; if ($this_map) { $known_maps{$this_map->unique_id} = $this_map; } } else { $self->throw("Only Bio::Map::PositionI objects are supported, not [$compare]"); } if (! defined $union_strand) { $union_strand = $compare->strand; } else { if (! defined $compare->strand or $union_strand ne $compare->strand) { $union_strand = 0; } } push(@starts, $start); push(@ends, $end); } @starts = sort { $a <=> $b } @starts; @ends = sort { $a <=> $b } @ends; my $start = shift @starts; my $end = pop @ends; my @unions; foreach my $known_map (values %known_maps) { my $new_union = $self->new(-start => $start, -end => $end, -strand => $union_strand, -map => $known_map); $new_union->relative($rel) if $rel; push(@unions, $new_union); } unless (@unions) { @unions = ($self->new(-start => $start, -end => $end, -strand => $union_strand)); $unions[0]->relative($rel) if $rel; } my $result = Bio::Map::Mappable->new(); $result->add_position(@unions); # sneaky, add_position can take a list of positions return $result; } =head2 overlap_extent Title : overlap_extent Usage : ($a_unique,$common,$b_unique) = $a->overlap_extent($b) Function: Provides actual amount of overlap between two different positions Example : Returns : array of values containing the length unique to the calling position, the length common to both, and the length unique to the argument position Args : a position =cut #*** should this be overridden from RangeI? =head2 disconnected_ranges Title : disconnected_ranges Usage : my @disc_ranges = Bio::Map::Position->disconnected_ranges(@ranges); Function: Creates the minimal set of positions such that each input position is fully contained by at least one output position, and none of the output positions overlap. Returns : Bio::Map::Mappable with the calculated disconnected ranges Args : a Bio::Map::PositionI to compare this one to, or a list of such, OR a single Bio::Map::PositionI or array ref of such AND a Bio::Map::RelativeI to consider all Position's co-ordinates in terms of their relative position to the thing described by that Relative, AND, optionally, an int for the minimum percentage of overlap that must be present before considering two ranges to be overlapping (default 0) =cut sub disconnected_ranges { # overriding the RangeI implementation so we can transfer map and handle # Relative my ($self, @args) = @_; $self->throw("Not enough arguments") unless @args >= 1; my @positions; my $rel; my $overlap = 0; if ($self eq "Bio::Map::PositionI") { $self = "Bio::Map::Position"; $self->warn("calling static methods of an interface is deprecated; use $self instead"); } if (ref $self) { push(@positions, $self); } if (ref $args[0] eq 'ARRAY') { push(@positions, @{shift(@args)}); } else { push(@positions, shift(@args)); } if ($args[0] && $args[0]->isa('Bio::Map::RelativeI')) { $rel = shift(@args); $overlap = shift(@args); } foreach my $arg (@args) { push(@positions, $arg) if $arg; } $self->throw("Need at least 2 Positions") unless @positions >= 2; my %known_maps; foreach my $pos (@positions) { $pos->isa('Bio::Map::PositionI') || $self->throw("Must supply only Bio::Map::PositionI objects, not [$pos]"); my $map = $pos->map || next; $known_maps{$map->unique_id} = $map; } my %prior_positions; foreach my $map (values %known_maps) { foreach my $pos ($map->get_positions) { $prior_positions{$pos} = 1; } } my @outranges = (); foreach my $inrange (@positions) { my @outranges_new = (); my %overlapping_ranges = (); for (my $i=0; $i<@outranges; $i++) { my $outrange = $outranges[$i]; if ($inrange->overlaps($outrange, undef, $rel, $overlap)) { my $union_able = $inrange->union($outrange, $rel); # using $inrange->union($outrange, $rel); gives >6x speedup, # but different answer, not necessarily incorrect... foreach my $pos ($union_able->get_positions) { $overlapping_ranges{$pos->toString} = $pos; # we flatten down to a result on a single map # to avoid creating 10s of thousands of positions during this process; # we then apply the final answer to all maps at the very end last; } } else { push(@outranges_new, $outrange); } } @outranges = @outranges_new; my @overlappers = values %overlapping_ranges; if (@overlappers) { if (@overlappers > 1) { my $merged_range_able = shift(@overlappers)->union(\@overlappers, $rel); push(@outranges, $merged_range_able->get_positions); } else { push(@outranges, @overlappers); } } else { push(@outranges, $self->new(-start => $inrange->start($rel), -end => $inrange->end($rel), -strand => $inrange->strand, -map => $inrange->map, -relative => $rel)); } } # purge positions that were created whilst calculating the answer, but # aren't the final answer and weren't there previously my %answers = map { $_ => 1 } @outranges; foreach my $map (values %known_maps) { foreach my $pos ($map->get_positions) { if (! exists $prior_positions{$pos} && ! exists $answers{$pos}) { $map->purge_positions($pos); } } } my %post_positions; foreach my $map (values %known_maps) { foreach my $pos ($map->get_positions) { $post_positions{$pos} = 1; } } @outranges || return; # make an outrange on all known maps my @final_positions; foreach my $map (values %known_maps) { foreach my $pos (@outranges) { if ($pos->map eq $map) { push(@final_positions, $pos); } else { push(@final_positions, $pos->new(-start => $pos->start, -end => $pos->end, -relative => $pos->relative, -map => $map)); } } } # assign the positions to a result mappable my $result = Bio::Map::Mappable->new(); $result->add_position(@final_positions); # sneaky, add_position can take a list of positions return $result; } # get start & end suitable for rangeI methods, taking relative into account sub _pre_rangei { my ($self, $other, $rel) = @_; $self->throw("Must supply an object") unless $other; if ($rel) { $self->throw("Must supply an object for the Relative argument") unless ref($rel); $self->throw("This is [$rel], not a Bio::Map::RelativeI") unless $rel->isa('Bio::Map::RelativeI'); } my ($other_start, $other_end); if (ref($other)) { if (ref($other) eq 'ARRAY') { $self->throw("_pre_rangei got an array"); } $self->throw("This is [$other], not a Bio::RangeI object") unless defined $other && $other->isa('Bio::RangeI'); if ($other->isa('Bio::Map::PositionI')) { # to get the desired start/end we need the position to be on a map; # if it isn't on one temporarily place it on self's map # - this lets us have 'generic' positions that aren't on any map # but have a relative defined and can thus be usefully compared to # positions that /are/ on maps my $other_map = $other->map; unless ($other_map) { my $self_map = $self->map || $self->throw("Trying to compare two positions but neither had been placed on a map"); $other->map($self_map); } # want start and end positions relative to the supplied rel or map start $rel ||= $other->absolute_relative; $other_start = $other->start($rel); $other_end = $other->end($rel); unless ($other_map) { $self->map->purge_positions($other); } } else { $other_start = $other->start; $other_end = $other->end; } } else { $self->throw("not a number") unless looks_like_number($other); $other_start = $other_end = $other; } $other->throw("start is undefined") unless defined $other_start; $other->throw("end is undefined") unless defined $other_end; return ($other_start, $other_end); } 1; BioPerl-1.007002/Bio/Map/PositionWithSequence.pm000444000766000024 1034513155576320 21453 0ustar00cjfieldsstaff000000000000# $Id: PositionWithSequence.pm,v 1.19 2006/09/20 10:20:01 sendu Exp $ # # BioPerl module for Bio::Map::PositionWithSequence # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::PositionWithSequence - A position with a sequence. =head1 SYNOPSIS use Bio::Map::PositionWithSequence; my $pos = Bio::Map::PositionWithSequence->new(-map => $map, -element => $element, -start => 0, -seq => 'ATGC'); =head1 DESCRIPTION Have a position with a sequence, eg. define what the binding site sequence of a certain transcription factor binding site is by modelling it as one of these objects with the -element assigned to a Bio::Map::TranscriptionFactor instance. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::PositionWithSequence; use strict; use base qw(Bio::Map::Position Bio::LocatableSeq); =head2 new Title : new Usage : my $obj = Bio::Map::PositionWithSequence->new(); Function: Builds a new Bio::Map::PositionWithSequence object Returns : Bio::Map::PositionWithSequence Args : -map => Bio::Map::GeneMap object -element => Bio::Map::Gene object -relative => Bio::Map::GeneRelative object -seq => string, length of this string will set the length of this position's range * If this position has no range, or if a single value can describe the range * -value => scalar : something that describes the single point position or range of this Position, most likely an int * Or if this position has a range, at least two of * -start => int : value of the start co-ordinate -end => int : value of the end co-ordinate -length => int : length of the range =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($seq) = $self->_rearrange([qw( SEQ )], @args); $self->seq($seq) if $seq; return $self; } =head2 seq Title : seq Usage : my $string = $obj->seq(); Function: Get/set the sequence as a string of letters. Returns : scalar Args : Optionally on set the new value (a string). An optional second argument presets the alphabet (otherwise it will be guessed). =cut sub seq { my ($self, $str, $alpha) = @_; # done like this because SUPER will set seq to undef if undef supplied, # but GeneMap wants to send undef, undef, 1 to decendants of this method my $seq; if ($str) { $alpha ? ($seq = $self->SUPER::seq($str, $alpha)) : ($seq = $self->SUPER::seq($str)); } else { $seq = $self->SUPER::seq; } if ($seq) { $self->length(length($seq)); return $seq; } return; } 1; BioPerl-1.007002/Bio/Map/Prediction.pm000444000766000024 1154113155576320 17421 0ustar00cjfieldsstaff000000000000# $Id: Prediction.pm,v 1.10 2006/09/28 14:09:40 sendu Exp $ # # BioPerl module for Bio::Map::Prediction # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::Prediction - An object representing the predictions of something that can have multiple locations in several maps. =head1 SYNOPSIS use Bio::Map::Prediction; use Bio::Map::Position; # normally you would get predictions from a run wrapper like # Bio::Tools::Run::Meme, but here we create some manually: my $pred1 = Bio::Map::Prediction->new(-source => 'meme'); Bio::Map::Position->new(-element => $prediction1, -map => Bio::Map::GeneMap->get(-gene => 'gene1', -species => 'species1'), -start => 950, -end => 960); Bio::Map::Position->new(-element => $prediction1, -map => Bio::Map::GeneMap->get(-gene => 'gene1', -species => 'species2'), -start => 1950, -end => 1960); Bio::Map::Position->new(-element => $prediction1, -map => Bio::Map::GeneMap->get(-gene => 'gene2', -species => 'species1'), -start => 955, -end => 965); Bio::Map::Position->new(-element => $prediction1, -map => Bio::Map::GeneMap->get(-gene => 'gene2', -species => 'species2'), -start => 1955, -end => 1965); my $pred2 = Bio::Map::Prediction->new(-source => 'gerp'); Bio::Map::Position->new(-element => $prediction2, -map => Bio::Map::GeneMap->get(-gene => 'gene1', -species => 'species1'), -start => 950, -end => 960); # etc. # find the places where predictions agree use Bio::Map::GeneRelative; my $rel = Bio::Map::GeneRelative->new(-gene => 0); my $di = Bio::Map::Mappable->disconnected_intersections([$pred1, $pred2], -min_mappables_percent => 100, -min_map_percent => 100, -relative => $rel); my @positions = $di->get_positions; =head1 DESCRIPTION For example, used to model transcription factor binding site predictions, which can have multiple locations in several maps. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::Prediction; use strict; use base qw(Bio::Map::Mappable); =head2 new Title : new Usage : my $prediction = Bio::Map::Prediction->new(); Function: Builds a new Bio::Map::Prediction object Returns : Bio::Map::Prediction Args : -name => string : name of the mappable element -id => string : id of the mappable element -source => string : name of the prediction program =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($source) = $self->_rearrange([qw(SOURCE)], @args); $self->source($source) if $source; return $self; } =head2 source Title : name Usage : $mappable->name($new_name); my $name = $mappable->name(); Function: Get/Set the name for this Mappable Returns : A scalar representing the current name of this Mappable Args : none to get string to set =cut sub source { my $self = shift; if (@_) { $self->{_source} = shift } return $self->{_source} || ''; } 1; BioPerl-1.007002/Bio/Map/Relative.pm000555000766000024 2334113155576320 17100 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::Relative # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::Relative - Represents what a Position's coordiantes are relative to. =head1 SYNOPSIS # Get a Bio::Map::PositionI somehow my $pos = Bio::Map::Position->new(-value => 100); # its co-ordinates are implicitly relative to the start of its map my $implicit_relative = $pos->relative; my $type = $implicit_relative->type; # $type eq 'map' my $value = $implicit_relative->$type(); # $value == 0 # make its co-ordinates relative to another Position my $pos_we_are_relative_to = Bio::Map::Position->new(-value => 200); my $relative = Bio::Map::Relative->new(-position => $pos_we_are_relative_to); $pos->relative($relative); # Get the start co-ordinate of $pos relative to $pos_we_are_relative_to my $start = $pos->start; # $start == 100 # Get the start co-ordinate of $pos relative to the start of the map my $abs_start = $relative->absolute_conversion($pos); # $abs_start == 300 # - or - $pos->absolute(1); my $abs_start = $pos->start; # $abs_start == 300 $pos->absolute(0); # Get the start co-ordinate of $pos relative to a third Position my $pos_frame_of_reference = Bio::Map::Position->new(-value => 10); my $relative2 = Bio::Map::Relative->new(-position => $pos_frame_of_reference); my $start = $pos->start($relative2); # $start == 290 =head1 DESCRIPTION A Relative object is used to describe what the co-ordinates (numerical(), start(), end()) of a Position are relative to. By default they are implicitly assumed to be relative to the start of the map the Position is on. But setting the relative() of a Position to one of these objects lets us define otherwise. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::Relative; use strict; use Scalar::Util qw(looks_like_number); use base qw(Bio::Root::Root Bio::Map::RelativeI); =head2 new Title : new Usage : my $relative = Bio::Map::Relative->new(); Function: Build a new Bio::Map::Relative object. Returns : Bio::Map::Relative object Args : -map => int : coordinates are relative to this point on the Position's map [default is map => 0, ie. relative to the start of the map], -element => Mappable : or relative to this element's (a Bio::Map::MappableI) position in the map (only works if the given element has only one position in the map the Position belongs to), -position => Position : or relative to this other Position (a Bio::Map::PositionI, fails if the other Position is on a different map to this map) -description => string: Free text description of what this relative describes (To say a Position is relative to something and upstream of it, the Position's start() co-ordinate should be set negative) =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($map, $element, $position, $desc) = $self->_rearrange([qw( MAP ELEMENT POSITION DESCRIPTION )], @args); if (defined($map) + defined($element) + defined($position) > 1) { $self->throw("-map, -element and -position are mutually exclusive"); } defined($map) && $self->map($map); $element && $self->element($element); $position && $self->position($position); $desc && $self->description($desc); return $self; } =head2 absolute_conversion Title : absolute_conversion Usage : my $absolute_coord = $relative->absolute_conversion($pos); Function: Convert the start co-ordinate of the supplied position into a number relative to the start of its map. Returns : scalar number Args : Bio::Map::PositionI object =cut sub absolute_conversion { my ($self, $pos) = @_; $self->throw("Must supply an object") unless ref($pos); $self->throw("This is [$pos], not a Bio::Map::PositionI") unless $pos->isa('Bio::Map::PositionI'); # get the raw start position of our position my $prior_abs = $pos->absolute; $pos->absolute(0) if $prior_abs; my $raw = $pos->start; $pos->absolute($prior_abs) if $prior_abs; $self->throw("Can't convert co-ordinates when start isn't set") unless defined($raw); #*** needed? return undef? # what are we relative to? my $type = $self->type; my $value = $self->$type; $self->throw("Details not yet set for this Relative, cannot convert") unless $type && defined($value); # get the absolute start of the thing we're relative to my $map = $pos->map; if ($type eq 'element') { $self->throw("Relative to a Mappable, but the Position has no map") unless $map; my @positions = $value->get_positions($map); $value = shift(@positions); $self->throw("Relative to a Mappable, but this Mappable has no positions on the supplied Position's map") unless $value; } if (ref($value)) { # pseudo-recurse my $rel = $value->relative; $value = $rel->absolute_conversion($value); } if (defined($value)) { return $value + $raw; } return; } =head2 type Title : type Usage : my $type = $relative->type(); Function: Get the type of thing we are relative to. The types correspond to a method name, so the value of what we are relative to can subsequently be found by $value = $relative->$type; Note that type is set by the last method that was set, or during new(). Returns : the string 'map', 'element' or 'position', or undef Args : none =cut sub type { my $self = shift; return $self->{_use} || return; } =head2 map Title : map Usage : my $int = $relative->map(); $relative->map($int); Function: Get/set the distance from the start of the map that the Position's co-ordiantes are relative to. Returns : int Args : none to get, OR int to set; a value of 0 means relative to the start of the map. =cut sub map { my ($self, $num) = @_; if (defined($num)) { $self->throw("This is [$num], not a number") unless looks_like_number($num); $self->{_use} = 'map'; $self->{_map} = $num; } return defined($self->{_map}) ? $self->{_map} : return; } =head2 element Title : element Usage : my $element = $relative->element(); $relative->element($element); Function: Get/set the map element (Mappable) the Position is relative to. If the Mappable has more than one Position on the Position's map, we will be relative to the Mappable's first Position on the map. Returns : Bio::Map::MappableI Args : none to get, OR Bio::Map::MappableI to set =cut sub element { my ($self, $element) = @_; if ($element) { $self->throw("Must supply an object") unless ref($element); $self->throw("This is [$element], not a Bio::Map::MappableI") unless $element->isa('Bio::Map::MappableI'); $self->{_use} = 'element'; $self->{_element} = $element; } return $self->{_element} || return; } =head2 position Title : position Usage : my $position = $relative->position(); $relative->position($position); Function: Get/set the Position your Position is relative to. Your Position will be made relative to the start of this supplied Position. It makes no difference what maps the Positions are on. Returns : Bio::Map::PositionI Args : none to get, OR Bio::Map::PositionI to set =cut sub position { my ($self, $pos) = @_; if ($pos) { $self->throw("Must supply an object") unless ref($pos); $self->throw("This is [$pos], not a Bio::Map::PositionI") unless $pos->isa('Bio::Map::PositionI'); $self->{_use} = 'position'; $self->{_position} = $pos; } return $self->{_position} || return; } =head2 description Title : description Usage : my $description = $relative->description(); $relative->description($description); Function: Get/set a textual description of what this relative describes. Returns : string Args : none to get, OR string to set =cut sub description { my $self = shift; if (@_) { $self->{desc} = shift } return $self->{desc} || ''; } 1; BioPerl-1.007002/Bio/Map/RelativeI.pm000555000766000024 1150013155576320 17203 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::RelativeI # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::RelativeI - Interface for describing what a Position's coordiantes are relative to. =head1 SYNOPSIS # do not use this module directly # See Bio::Map::Relative for an example of # implementation. =head1 DESCRIPTION A Relative object is used to describe what the co-ordinates (numerical(), start(), end()) of a Position are relative to. By default they are implicitly assumed to be relative to the start of the map the Position is on. But setting the relative() of a Position to one of these objects lets us define otherwise. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::RelativeI; use strict; use base qw(Bio::Root::RootI); =head2 absolute_conversion Title : absolute_conversion Usage : my $absolute_coord = $relative->absolute_conversion($pos); Function: Convert the start co-ordinate of the supplied position into a number relative to the start of its map. Returns : scalar number Args : Bio::Map::PositionI object =cut sub absolute_conversion { my $self = shift; $self->throw_not_implemented(); } =head2 type Title : type Usage : my $type = $relative->type(); Function: Get the type of thing we are relative to. The types correspond to a method name, so the value of what we are relative to can subsequently be found by $value = $relative->$type; Note that type is set by the last method that was set, or during new(). Returns : the string 'map', 'element' or 'position', or undef Args : none =cut sub type { my $self = shift; $self->throw_not_implemented(); } =head2 map Title : map Usage : my $int = $relative->map(); $relative->map($int); Function: Get/set the distance from the start of the map that the Position's co-ordiantes are relative to. Returns : int Args : none to get, OR int to set; a value of 0 means relative to the start of the map. =cut sub map { my $self = shift; $self->throw_not_implemented(); } =head2 element Title : element Usage : my $element = $relative->element(); $relative->element($element); Function: Get/set the map element (Mappable) the Position is relative to. If the Mappable has more than one Position on the Position's map, we will be relative to the Mappable's first Position on the map. Returns : Bio::Map::MappableI Args : none got get, OR Bio::Map::MappableI to set =cut sub element { my $self = shift; $self->throw_not_implemented(); } =head2 position Title : position Usage : my $position = $relative->position(); $relative->position($position); Function: Get/set the Position your Position is relative to. Your Position will be made relative to the start of this supplied Position. It makes no difference what maps the Positions are on. Returns : Bio::Map::PositionI Args : none got get, OR Bio::Map::PositionI to set =cut sub position { my $self = shift; $self->throw_not_implemented(); } =head2 description Title : description Usage : my $description = $relative->description(); $relative->description($description); Function: Get/set a textual description of what this relative describes. Returns : string Args : none to get, OR string to set =cut sub description { my $self = shift; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Map/SimpleMap.pm000444000766000024 2112713155576320 17211 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Map::SimpleMap # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::SimpleMap - A MapI implementation handling the basics of a Map =head1 SYNOPSIS use Bio::Map::SimpleMap; my $map = Bio::Map::SimpleMap->new(-name => 'genethon', -type => 'Genetic', -units=> 'cM', -species => $human); foreach my $marker ( @markers ) { # get a list of markers somewhere $map->add_element($marker); } foreach my $marker ($map->get_elements) { # do something with this Bio::Map::MappableI } =head1 DESCRIPTION This is the basic implementation of a Bio::Map::MapI. It handles the essential storage of name, species, type, and units. It knows which map elements (mappables) belong to it, and their position. Subclasses might need to redefine or hardcode type(), length() and units(). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 CONTRIBUTORS Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein lstein@cshl.org Sendu Bala bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::SimpleMap; use vars qw($MAPCOUNT); use strict; use base qw(Bio::Root::Root Bio::Map::MapI); BEGIN { $MAPCOUNT = 1; } =head2 new Title : new Usage : my $obj = Bio::Map::SimpleMap->new(); Function: Builds a new Bio::Map::SimpleMap object Returns : Bio::Map::SimpleMap Args : -name => name of map (string) -species => species for this map (Bio::Species) [optional] -units => map units (string) -uid => Unique Id [defaults to a unique integer] =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_name'} = ''; $self->{'_species'} = ''; $self->{'_units'} = ''; $self->{'_type'} = ''; $self->{'_uid'} = $MAPCOUNT++; my ($name, $type,$species, $units,$uid) = $self->_rearrange([qw(NAME TYPE SPECIES UNITS UID)], @args); defined $name && $self->name($name); defined $species && $self->species($species); defined $units && $self->units($units); defined $type && $self->type($type); defined $uid && $self->unique_id($uid); return $self; } =head2 species Title : species Usage : my $species = $map->species; Function: Get/Set Species for a map Returns : Bio::Taxon object or string Args : (optional) Bio::Taxon or string =cut sub species{ my ($self,$value) = @_; if( defined $value ) { $self->{'_species'} = $value; } return $self->{'_species'}; } =head2 units Title : units Usage : $map->units('cM'); Function: Get/Set units for a map Returns : units for a map Args : units for a map (string) =cut sub units{ my ($self,$value) = @_; if( defined $value ) { $self->{'_units'} = $value; } return $self->{'_units'}; } =head2 type Title : type Usage : my $type = $map->type Function: Get/Set Map type Returns : String coding map type Args : (optional) string =cut sub type { my ($self,$value) = @_; # this may be hardcoded/overriden by subclasses if( defined $value ) { $self->{'_type'} = $value; } return $self->{'_type'}; } =head2 name Title : name Usage : my $name = $map->name Function: Get/Set Map name Returns : Map name Args : (optional) string =cut sub name { my ($self,$value) = @_; if( defined $value ) { $self->{'_name'} = $value; } return $self->{'_name'}; } =head2 length Title : length Usage : my $length = $map->length(); Function: Retrieves the length of the map. It is possible for the length to be unknown for maps such as Restriction Enzyme, will return 0 in that case. Returns : integer representing length of map in current units will return 0 if length is not calculateable Args : none =cut sub length { my $self = shift; my $len = 0; foreach my $element ($self->get_elements) { foreach my $pos ($element->get_positions($self)) { if ($pos->value) { $len = $pos->end if $pos->end > $len; } } } return $len; } =head2 unique_id Title : unique_id Usage : my $id = $map->unique_id; Function: Get/Set the unique ID for this map Returns : a unique identifier Args : [optional] new identifier to set =cut sub unique_id { my ($self,$id) = @_; if( defined $id ) { $self->{'_uid'} = $id; } return $self->{'_uid'}; } =head2 add_element Title : add_element Usage : $map->add_element($element) Function: Tell a Bio::Map::MappableI object its default Map is this one; same as calling $element->default_map($map). *** does not actually add the element to this map! *** Returns : none Args : Bio::Map::MappableI object Status : Deprecated, will be removed in next version =cut sub add_element { my ($self, $element) = @_; return unless $element; $self->throw("This is not a Bio::Map::MappableI object but a [$element]") unless $element->isa('Bio::Map::MappableI'); $element->default_map($self); } =head2 get_elements Title : get_elements Usage : my @elements = $map->get_elements; Function: Retrieves all the elements on a map (unordered unless all elements have just 1 position on the map, in which case sorted) Returns : Array of Map elements (L) Args : none =cut sub get_elements { my $self = shift; my @elements = $self->SUPER::get_elements; # for backward compatability with MapIO tests, and for 'niceness', when # there is only 1 position per element we will return the elements in # order, as long as the positions have values set my $only_1 = 1; foreach my $element (@elements) { my @positions = $element->get_positions($self); if (@positions > 1 || (@positions == 1 && ! $positions[0]->value)) { $only_1 = 0; } } if ($only_1) { @elements = map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [${[$_->get_positions($self)]}[0]->sortable, $_] } @elements; } return @elements; } =head2 each_element Title : each_element Function: Synonym of the get_elements() method. Status : deprecated, will be removed in the next version =cut *each_element = \&get_elements; =head2 purge_element Title : purge_element Usage : $map->purge_element($element) Function: Purge an element from the map. Returns : none Args : Bio::Map::MappableI object =cut sub purge_element { my ($self, $element) = @_; $self->throw("Must supply an argument") unless $element; $self->throw("This is [$element], not an object") unless ref($element); $self->throw("This is [$element], not a Bio::Map::MappableI object") unless $element->isa('Bio::Map::MappableI'); $self->purge_positions($element); } =head2 annotation Title : annotation Usage : $map->annotation($an_col); my $an_col = $map->annotation(); Function: Get the annotation collection (see Bio::AnnotationCollectionI) for this annotatable object. Returns : a Bio::AnnotationCollectionI implementing object, or undef Args : none to get, OR a Bio::AnnotationCollectionI implementing object to set =cut sub annotation { my $self = shift; if (@_) { $self->{_annotation} = shift } return $self->{_annotation} || return; } 1; BioPerl-1.007002/Bio/Map/TranscriptionFactor.pm000444000766000024 1276213155576320 21325 0ustar00cjfieldsstaff000000000000# $Id: TranscriptionFactor.pm,v 1.6 2006/07/17 14:16:53 sendu Exp $ # # BioPerl module for Bio::Map::TranscriptionFactor # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::TranscriptionFactor - A transcription factor modelled as a mappable element =head1 SYNOPSIS use Bio::Map::TranscriptionFactor; use Bio::Map::GeneMap; use Bio::Map::Position; # model a TF that binds 500bp upstream of the BRCA2 gene in humans and # 250bp upstream of BRCA2 in mice my $tf = Bio::Map::TranscriptionFactor->get(-universal_name => 'tf1'); my $map1 = Bio::Map::GeneMap->get(-universal_name => "BRCA2", -species => "human"); my $map2 = Bio::Map::GeneMap->get(-universal_name => "BRCA2", -species => "mouse"); Bio::Map::Position->new(-map => $map1, -element => $tf, -start => -500, -length => 10); Bio::Map::Position->new(-map => $map2, -element => $tf, -start => -250, -length => 10); # Find out where the transcription factor binds foreach $pos ($tf->get_positions) { print $tf->universal_name, " binds at position " $pos->value, " relative to ", $pos->relative->description, " of gene ", $pos->map->universal_name, " in species ", $pos->map->species, "\n"; } =head1 DESCRIPTION A transcription factor modelled as a mappable element. It can have multiple binding sites (positions) near multiple genes (maps). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::TranscriptionFactor; use strict; use base qw(Bio::Map::Mappable); our $TFS = {}; =head2 new Title : new Usage : my $tf = Bio::Map::TranscriptionFactor->new(); Function: Builds a new Bio::Map::TranscriptionFactor object Returns : Bio::Map::TranscriptionFactor Args : -universal_name => string name of the TF (in a form common to all species that have the TF, but unique amongst non-orthologous TFs), REQUIRED -description => string, free text description of the TF =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($u_name, $desc) = $self->_rearrange([qw(UNIVERSAL_NAME DESCRIPTION)], @args); $u_name || $self->throw("You must supply a -universal_name"); $self->universal_name($u_name); defined $desc && $self->description($desc); return $self; } =head2 get Title : get Usage : my $obj = Bio::Map::TranscriptionFactor->get(); Function: Builds a new Bio::Map::TranscriptionFactor object (like new()), or gets a pre-existing one that shares the same universal_name. Returns : Bio::Map::TranscriptionFactor Args : -universal_name => string name of the TF (in a form common to all species that have the TF, but unique amongst non-orthologous TFs), REQUIRED -description => string, free text description of the TF =cut sub get { my ($class, @args) = @_; my ($u_name) = Bio::Root::Root->_rearrange([qw(UNIVERSAL_NAME)], @args); if ($u_name && defined $TFS->{$u_name}) { return $TFS->{$u_name}; } return $class->new(@args); } =head2 universal_name Title : universal_name Usage : my $name = $obj->universal_name Function: Get/Set TF name, corresponding to the name of the TF in a form shared by orthologous versions of the TF in different species, but otherwise unique. Returns : string Args : none to get, OR string to set =cut sub universal_name { my ($self, $value) = @_; if (defined $value) { delete $TFS->{$self->{'_uname'}} if $self->{'_uname'}; $self->{'_uname'} = $value; $TFS->{$value} = $self; } return $self->{'_uname'}; } =head2 description Title : description Usage : my $desc = $obj->description Function: Get/Set a description of the TF. Returns : string Args : none to get, OR string to set =cut sub description { my $self = shift; if (@_) { $self->{desc} = shift } return $self->{desc} || ''; } 1; BioPerl-1.007002/Bio/MapIO000755000766000024 013155576320 15034 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/MapIO/fpc.pm000444000766000024 3754413155576320 16334 0ustar00cjfieldsstaff000000000000# fpc.pm,v 1.2.2.1 2005/10/09 15:16:27 jason Exp # # BioPerl module for Bio::MapIO::fpc # # Please direct questions and support issues to # # Cared for by Gaurav Gupta # # Copyright AGCoL # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::MapIO::fpc - A FPC Map reader =head1 SYNOPSIS # do not use this object directly it is accessed through the Bio::MapIO system use Bio::MapIO; -format : specifies the format of the file format is "fpc", -file : specifies the name of the .fpc file -readcor : boolean argument, indicating if .cor is to be read or not. It looks for the .cor file in the same path as .fpc file. 0 : doesn't read .cor file 1 : reads the .cor file [default 0] -verbose : indicates the process of loading of fpc file my $mapio = Bio::MapIO->new(-format => "fpc", -file => "rice.fpc", -readcor => 0, -verbose => 0); my $map = $mapio->next_map(); foreach my $marker ( $map->each_markerid() ) { # loop through the markers associated with the map # likewise for contigs, clones, etc. } =head1 DESCRIPTION This object contains code for parsing and processing FPC files and creating L object from it. For faster access and better optimization, the data is stored internally in hashes. The corresponding objects are created on request. We handle reading of the FPC ourselves, since MapIO module of Bioperl adds too much overhead. =cut # Let the code begin... package Bio::MapIO::fpc; use strict; use POSIX; use Bio::Map::Physical; use Bio::Map::Clone; use Bio::Map::Contig; use Bio::Map::FPCMarker; use Bio::Range; use base qw(Bio::MapIO); my $_readcor; =head1 Initializer =head2 _initialize Title : _initialize Usage : called implicitly Function: calls the SUPER::_initialize Returns : nothing Args : species, readcor =cut sub _initialize{ my ($self,@args) = @_; my $species; $self->SUPER::_initialize(@args); ($species,$_readcor) = $self->_rearrange([qw(SPECIES READCOR)], @args); $_readcor = 0 unless (defined($_readcor)); } =head1 Access Methods These methods let you get and set the member variables =head2 next_map Title : next_map Usage : my $fpcmap = $mapio->next_map(); Function: gets the fpcmap from MapIO Returns : object of type L Args : none =cut sub next_map{ my ($self) = @_; my $line; my ($name,$fpcver,$moddate,$moduser,$contigcnt,$clonecnt,$markerscnt, $bandcnt,$marker,$seqclone); my ($corfile,$corindex,$BUFFER); my @cordata; my %fpcmarker; my ($contig, $contigNumber); my $curClone = 0; my $curMarker = 0; my $curContig = 0; my %_clones; my %_markers; my %_contigs; my $ctgzeropos = 1; my $map = Bio::Map::Physical->new('-units' => 'CB', '-type' => 'physical'); my $filename = $self->file(); my $fh = $self->{'_filehandle'}; if (defined($_readcor)) { $map->core_exists($_readcor); } else { $map->core_exists(0); } if ($map->core_exists()) { $corfile = substr($filename,0,length($filename)-3)."cor"; if (open my $CORE, '<', $corfile) { while( read($CORE, $BUFFER, 2) ) { push @cordata, unpack('n*', $BUFFER); } } else { $map->core_exists(0); } } ## Read in the header while (defined($line = <$fh>)) { chomp($line); if ($line =~ m{^//\s+fpc\s+project\s+(.+)}) { $map->name($1); } if ($line =~ m{^//\s+([\d.]+)}) { my $version = $1; $version =~ /((\d+)\.(\d+))(.*)/; $map->version($1); if ($line =~ /User:\s+(.+)/) { $map->modification_user($1); } } if ($line =~ m{^//\s+Framework\s+(\w+)\s+(\w+)\s+([-\w]+)\s+(\w+)\s+(\w+)\s+(.+)$}) { $map->group_type($3) if ($2 eq "Label"); $map->group_abbr($5) if ($4 eq "Abbrev"); } last unless ($line =~ m{^//}); } if (!defined($map->group_type()) || !defined($map->group_abbr()) ) { $map->group_type("Chromosome"); $map->group_abbr("Chr"); } $_contigs{0}{'range'}{'end'} = 0; $_contigs{0}{'range'}{'start'} = 0; ## Read in the clone data while (defined($line = <$fh>)) { $marker = 0; $contig = 0; $seqclone = 0; $contigNumber = 0; my ($type,$name); my (@amatch,@pmatch,@ematch); my $bandsread = 0; last if ($line =~ /^Markerdata/); $line =~ /^(\w+)\s+:\s+"(.+)"/; ## these will be set if we did find the clone line ($type, $name) = ($1, $2); if ($name =~ /sd1/) { $seqclone = 1; } $_clones{$name}{'type'} = $type; $_clones{$name}{'contig'} = 0; $_contigs{'0'}{'clones'}{$name} = 0; my $temp; ## Loop through the following lines, getting attributes for clone while (defined($line = <$fh>) && $line !~ /^\s*\n$/) { if ($line =~ /^Map "ctg(\d+)" Ends (Left|Right) ([-\d]+)/) { $_clones{$name}{'contig'} = $1; $_contigs{$1}{'clones'}{$name} = 0; delete($_contigs{'0'}{'clones'}{$name}); $temp = $3; $contigNumber = $1; $line = <$fh>; $line =~ /^Map "ctg(\d+)" Ends (Left|Right) ([\d]+)/; $_clones{$name}{'range'}{'start'} = $temp; $_contigs{$contigNumber}{'range'}{'start'} = $temp if (!exists($_contigs{$contigNumber}{'range'}{'start'}) || $_contigs{$contigNumber}{'range'}{'start'} > $temp ); $_clones{$name}{'range'}{'end'} = $3; $_contigs{$contigNumber}{'range'}{'end'} = $3 if (!exists($_contigs{$contigNumber}{'range'}{'end'}) || $_contigs{$contigNumber}{'range'}{'end'} < $3 ); } elsif ($line =~ /^([a-zA-Z]+)_match_to_\w+\s+"(.+)"/) { my $matchtype = "match" . lc(substr($1, 0, 1)); $_clones{$name}{$matchtype}{$2} = 0; } elsif ($line =~ /^Positive_(\w+)\s+"(.+)"/) { $_clones{$name}{'markers'}{$2} = 0; $_markers{$2}{'clones'}{$name} = 0; $_markers{$2}{'type'} = $1; $_markers{$2}{'contigs'}{$contigNumber} = 0; $_contigs{$contigNumber}{'markers'}{$2} = 0; } elsif ($line =~ /^Bands\s+(\d+)\s+(\d+)/ && !$bandsread) { my $i = 0; my @numbands; $bandsread = 1; if ($map->core_exists()) { while($i<$2){ push(@numbands,$cordata[($1-1)+$i]); $i++; } $_clones{$name}{'bands'} = \@numbands; } else { push(@numbands,$1,$2); $_clones{$name}{'bands'} = \@numbands; } if (exists($_contigs{0}{'clones'}{$name})) { $_clones{$name}{'range'}{'start'} = $ctgzeropos; $_clones{$name}{'range'}{'end'} = $ctgzeropos + $2; $_contigs{0}{'range'}{'end'} = $ctgzeropos + $2; $ctgzeropos += $2; } } elsif ($line =~ /^Gel_number\s+(.+)/) { $_clones{$name}{'gel'} = $1; } elsif ($line =~ /^Remark\s+"(.+)"/) { $_clones{$name}{'remark'} .= $1; $_clones{$name}{'remark'} .= "\n"; if($seqclone == 1 ) { if( $1 =~ /\,\s+Chr(\d+)\s+/){ $_clones{$name}{'group'} = $1; } } } elsif ($line =~ /^Fp_number\s+"(.+)"/) { $_clones{$name}{'fp_number'} = $1; } elsif ($line =~ /^Shotgun\s+(\w+)\s+(\w+)/) { $_clones{$name}{'sequence_type'} = $1; $_clones{$name}{'sequence_status'} = $2; } elsif ($line =~ /^Fpc_remark\s+"(.+)"/) { $_clones{$name}{'fpc_remark'} .= $1; $_clones{$name}{'fpc_remark'} .= "\n"; } } $curClone++; print "Adding clone $curClone...\n\r" if ($self->verbose() && $curClone % 1000 == 0); } $map->_setCloneRef(\%_clones); $line = <$fh>; while (defined($line = <$fh>) && $line !~ /Contigdata/) { my ($type,$name); last if ($line !~ /^Marker_(\w+)\s+:\s+"(.+)"/); ($type, $name) = ($1, $2); $_markers{$name}{'type'} = $type; $_markers{$name}{'group'} = 0; $_markers{$name}{'global'} = 0; $_markers{$name}{'anchor'} = 0; while (defined($line = <$fh>) && $line !~ /^\s*\n$/) { if ($line =~ /^Global_position\s+([\d.]+)\s*(Frame)?/) { my $position = $1 - floor($1/1000)*1000; $position = sprintf("%.2f",$position); $_markers{$name}{'global'} = $position; $_markers{$name}{'group'} = floor($1/1000); $_markers{$name}{'anchor'} = 1; if(defined($2)) { $_markers{$name}{'framework'} = 1; } else { $_markers{$name}{'framework'} = 0; } } elsif ($line =~ /^Anchor_bin\s+"([\w\d.]+)"/) { my $grpmatch = $1; my $grptype = $map->group_type(); $grpmatch =~ /(\d+|\w)(.*)/; my ($group,$subgroup); $group = $1; $subgroup = $2; $subgroup = substr($subgroup,1) if ($subgroup =~ /^\./); $_markers{$name}{'group'} = $group; $_markers{$name}{'subgroup'} = $subgroup; } elsif ($line =~ /^Anchor_pos\s+([\d.]+)\s+(F|P)?/){ $_markers{$name}{'global'} = $1; $_markers{$name}{'anchor'} = 1; if ($2 eq 'F') { $_markers{$name}{'framework'} = 1; } else { $_markers{$name}{'framework'} = 0; } } elsif ($line =~ /^anchor$/) { $_markers{$name}{'anchor'} = 1; } elsif ($line =~ /^Remark\s+"(.+)"/) { $_markers{$name}{'remark'} .= $1; $_markers{$name}{'remark'} .= "\n"; } } $curMarker++; print "Adding Marker $curMarker...\n" if ($self->verbose() && $curMarker % 1000 == 0); } $map->_setMarkerRef(\%_markers); my $ctgname; my $grpabbr = $map->group_abbr(); my $chr_remark; $_contigs{0}{'group'} = 0; while (defined($line = <$fh>)) { if ($line =~ /^Ctg(\d+)/) { $ctgname = $1; $_contigs{$ctgname}{'group'} = 0; $_contigs{$ctgname}{'anchor'} = 0; $_contigs{$ctgname}{'position'} = 0; if ($line =~ /#\w*(.*)\w*$/) { $_contigs{$ctgname}{'remark'} = $1; if ($line =~ /#\s+Chr(\d+)\s+/) { $_contigs{$ctgname}{'group'} = $1; $_contigs{$ctgname}{'anchor'} = 1; } } } elsif ($line =~ /^Chr_remark\s+"(-|\+|Chr(\d+))\s+(.+)"$/) { $_contigs{$ctgname}{'anchor'} = 1; $_contigs{$ctgname}{'chr_remark'} = $3 if(defined($3)); if (defined($2)) { $_contigs{$ctgname}{'group'} = $2; } else { $_contigs{$ctgname}{'group'} = "?"; } } elsif ($line =~ /^User_remark\s+"(.+)"/) { $_contigs{$ctgname}{'usr_remark'} = $1; } elsif ($line =~ /^Trace_remark\s+"(.+)"/) { $_contigs{$ctgname}{'trace_remark'} = $1; } elsif ($grpabbr && $line =~ /^Chr_remark\s+"(\W|$grpabbr((\d+)|(\w+)|([.\w\d]+)))\s*(\{(.*)\}|\[(.*)\])?"\s+(Pos\s+((\d.)+|NaN))(NOEDIT)?/) { my $grpmatch = $2; my $pos = $10; if ($pos eq "NaN") { $pos = 0; print "Warning: Nan encountered for Contig position \n"; } $_contigs{$ctgname}{'chr_remark'} = $6; $_contigs{$ctgname}{'position'} = $pos; $_contigs{$ctgname}{'subgroup'} = 0; if (defined($grpmatch)) { $_contigs{$ctgname}{'anchor'} = 1; if ($grpmatch =~ /((\d+)((\D\d.\d+)|(.\d+)))|((\w+)(\.\d+))/) { my ($group,$subgroup); $group = $2 if($grpabbr eq "Chr"); $subgroup = $3 if($grpabbr eq "Chr"); $group = $7 if($grpabbr eq "Lg"); $subgroup = $8 if($grpabbr eq "Lg"); $subgroup = substr($subgroup,1) if ($subgroup =~ /^\./); $_contigs{$ctgname}{'group'} = $group; $_contigs{$ctgname}{'subgroup'} = $subgroup; } else { $_contigs{$ctgname}{'group'} = $grpmatch; } } else { $_contigs{$ctgname}{'anchor'} = 1; $_contigs{$ctgname}{'group'} = "?"; } } $curContig++; print "Adding Contig $curContig...\n" if ($self->verbose() && $curContig % 100 == 0); } $map->_setContigRef(\%_contigs); $map->_calc_markerposition(); $map->_calc_contigposition() if ($map->version() < 7.0); $map->_calc_contiggroup() if ($map->version() == 4.6); return $map; } =head2 write_map Title : write_map Usage : $mapio->write_map($map); Function: Write a map out Returns : none Args : Bio::Map::MapI =cut sub write_map{ my ($self,@args) = @_; $self->throw_not_implemented(); } 1; =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Gaurav Gupta Email gaurav@genome.arizona.edu =head1 PROJECT LEADERS Jamie Hatfield jamie@genome.arizona.edu Dr. Cari Soderlund cari@genome.arizona.edu =head1 PROJECT DESCRIPTION The project was done in Arizona Genomics Computational Laboratory (AGCoL) at University of Arizona. This work was funded by USDA-IFAFS grant #11180 titled "Web Resources for the Computation and Display of Physical Mapping Data". For more information on this project, please refer: http://www.genome.arizona.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut BioPerl-1.007002/Bio/MapIO/mapmaker.pm000444000766000024 735113155576320 17332 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::MapIO::mapmaker # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::MapIO::mapmaker - A Mapmaker Map reader =head1 SYNOPSIS # do not use this object directly it is accessed through the Bio::MapIO system use Bio::MapIO; my $mapio = Bio::MapIO->new(-format => "mapmaker", -file => "mapfile.map"); while ( my $map = $mapio->next_map ) { # get each map foreach my $marker ( $map->each_element ) { # loop through the markers associated with the map } } =head1 DESCRIPTION This object contains code for parsing and processing Mapmaker output and creating L objects from it. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::MapIO::mapmaker; use strict; use Bio::Map::SimpleMap; use Bio::Map::LinkagePosition; use Bio::Map::Marker; use base qw(Bio::MapIO); =head2 next_map Title : next_map Usage : my $map = $factory->next_map; Function: Get one or more map objects from the Mapmaker input Returns : Bio::Map::MapI Args : none See L =cut sub next_map{ my ($self) = @_; my $map = Bio::Map::SimpleMap->new(-name => '', -units => 'cM', -type => 'Genetic'); # Mapmaker input can be free-form, like the result of a copy-paste # from a terminal, with no particular format before or after the # map data. The $in_map variable is a flag that's set to 1 when # we're reading map data lines and set back to 0 when we're finished. my ($in_map,$runningDistance); while ( defined ($_ = $self->_readline()) ) { if ( /^\s+Markers\s+Distance/ ) { $in_map = 1; next; } next unless $in_map; s/ +/\t/; my ($number,$name,$distance) = split; $runningDistance += $distance unless ($distance =~ /-+/); $runningDistance = '0.0' if ($runningDistance == 0 || $distance =~ /-+/); my $pos = Bio::Map::LinkagePosition->new(-order => $number, -map => $map, -value => $runningDistance ); my $marker = Bio::Map::Marker->new(-name => $name, -position => $pos ); if ($distance =~ /-+/) { # last marker $in_map = 0; return $map; } } } =head2 write_map Title : write_map Usage : $factory->write_map($map); Function: Write a map out through the factory Returns : none Args : Bio::Map::MapI =cut sub write_map{ my ($self,@args) = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Matrix000755000766000024 013155576320 15333 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Matrix/Generic.pm000444000766000024 5054713155576320 17435 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Matrix::Generic # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Matrix::Generic - A generic matrix implementation =head1 SYNOPSIS # A matrix has columns and rows my $matrix = Bio::Matrix::Generic->new; $matrix->add_column(1,$column1); $matrix->add_column(2,$column2); my $element = $matrix->entry_by_num(1,2); $matrix->entry_by_num(1,2,$newval); my $entry = $matrix->entry('human', 'mouse'); $matrix->entry('human','mouse', $newval); =head1 DESCRIPTION This is a general purpose matrix object for dealing with row+column data which is typical when enumerating all the pairwise combinations and desiring to get slices of the data. Data can be accessed by column and row names or indexes. Matrix indexes start at 0. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Matrix::Generic; use strict; use base qw(Bio::Root::Root Bio::Matrix::MatrixI); =head2 new Title : new Usage : my $obj = Bio::Matrix::Generic->new(); Function: Builds a new Bio::Matrix::Generic object Returns : an instance of Bio::Matrix::Generic Args : -values => arrayref of arrayrefs of data initialization -rownames => arrayref of row names -colnames => arrayref of col names -matrix_id => id of the matrix -matrix_name=> name of the matrix -matrix_init_value => default value to initialize empty cells =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($values, $rownames, $colnames, $id,$name,$init_val) = $self->_rearrange([qw(VALUES ROWNAMES COLNAMES MATRIX_ID MATRIX_NAME MATRIX_INIT_VALUE)],@args); $self->matrix_id($id) if defined $id; $self->matrix_name($name) if defined $name; if( defined $rownames && defined $colnames ) { if( ref($rownames) !~ /ARRAY/i ) { $self->throw("need an arrayref for the -rownames option"); } # insure we copy the values $self->{'_rownames'} = [ @$rownames ]; my $count = 0; %{$self->{'_rownamesmap'}} = map { $_ => $count++ } @$rownames; if( ref($colnames) !~ /ARRAY/i ) { $self->throw("need an arrayref for the -colnames option"); } # insure we copy the values $self->{'_colnames'} = [ @$colnames ]; $count = 0; %{$self->{'_colnamesmap'}} = map { $_ => $count++ } @$colnames; $self->{'_values'} = []; if( defined $values ) { if( ref($values) !~ /ARRAY/i ) { $self->throw("Need an arrayref of arrayrefs (matrix) for -values option"); } for my $v ( @$values ) { if( ref($v) !~ /ARRAY/i ) { $self->throw("Need and array of arrayrefs (matrix) for -values option"); } push @{$self->{'_values'}}, [@$v]; } } else { my @fill = ($init_val) x scalar @$colnames; # undef init_val will be default for ( @$rownames ) { push @{$self->{'_values'}}, [@fill]; } } } elsif( ! defined $rownames && ! defined $colnames && ! defined $values ) { $self->{'_values'} = []; $self->{'_rownames'} = []; $self->{'_colnames'} = []; } else { $self->throw("Must have either provided no values/colnames/rownames or provided all three"); } return $self; } =head2 matrix_id Title : matrix_id Usage : my $id = $matrix->matrix_id Function: Get/Set the matrix ID Returns : scalar value Args : [optional] new id value to store =cut sub matrix_id{ my $self = shift; return $self->{'_matid'} = shift if @_; return $self->{'_matid'}; } =head2 matrix_name Title : matrix_name Usage : my $name = $matrix->matrix_name(); Function: Get/Set the matrix name Returns : scalar value Args : [optional] new matrix name value =cut sub matrix_name{ my $self = shift; return $self->{'_matname'} = shift if @_; return $self->{'_matname'}; } =head2 entry Title : entry Usage : my $entry = $matrix->entry($row,$col,$value) Function: Get the value for a specific cell as specified by the row and column names Returns : scalar value or undef if row or col does not exist Args : $rowname - name of the row $colname - column name $value - [optional] New value for the entry =cut sub entry{ my ($self,$row,$column,$newvalue) = @_; if( ! defined $row || ! defined $column ) { $self->throw("Need at least 2 ids"); } my ($rownum) = $self->row_num_for_name($row); my ($colnum) = $self->column_num_for_name($column); return $self->entry_by_num($rownum,$colnum,$newvalue); } =head2 get_entry Title : get_entry Usage : my $entry = $matrix->get_entry($rowname,$columname,$value) Function: Get the entry for a given row,column pair Returns : scalar Args : $row name $column name $value =cut sub get_entry{ $_[0]->entry($_[1],$_[2]) } =head2 entry_by_num Title : entry_by_num Usage : my $entry = $matrix->entry_by_num($rownum,$colnum) Function: Get an entry by row and column numbers instead of by name (rows and columns start at 0) Returns : scalar value or undef if row or column name does not exist Args : $row - row number $col - column number [optional] $newvalue to store at this cell =cut sub entry_by_num { my ($self,$row,$col,$newvalue) = @_; if( ! defined $row || ! defined $col || $row !~ /^\d+$/ || $col !~ /^\d+$/ ) { $self->warn("expected to get 2 number for entry_by_num"); return; } if( defined $newvalue ) { return $self->_values->[$row][$col] = $newvalue; } else { return $self->_values->[$row][$col]; } } sub get_element { my $self = shift; $self->entry(@_); } =head2 column Title : column Usage : my @col = $matrix->column('ALPHA'); OR $matrix->column('ALPHA', \@col); Function: Get/Set a particular column Returns : Array (in array context) or arrayref (in scalar context) of values. For setting will warn if the new column is of a different length from the rest of the columns. Args : name of the column [optional] new column to store here =cut sub column{ my ($self,$column,$newcol) = @_; if( ! defined $column ) { $self->warn("Need at least a column id"); return; } my $colnum = $self->column_num_for_name($column); if( ! defined $colnum ) { $self->warn("could not find column number for $column"); return; } return $self->column_by_num($colnum,$newcol); } =head2 get_column Title : get_column Usage : my @row = $matrix->get_column('ALPHA'); Function: Get a particular column Returns : Array (in array context) or arrayref (in scalar context) of values Args : name of the column =cut sub get_column { $_[0]->column($_[1]) } =head2 column_by_num Title : column_by_num Usage : my @col = $matrix->column_by_num(1); OR $matrix->column_by_num(1,\@newcol); Function: Get/Set a column by its number instead of name (cols/rows start at 0) Returns : Array (in array context) or arrayref (in scalar context) of values Args : name of the column [optional] new value to store for a particular column =cut sub column_by_num{ my ($self,$colnum,$newcol) = @_; if( ! defined $colnum ) { $self->warn("need at least a column number"); return; } my $rowcount = $self->num_rows; my $colcount = $self->num_columns; my $ret; if( defined $newcol ) { if( ref($newcol) !~ /ARRAY/i) { $self->warn("expected a valid arrayref for resetting a column"); return; } if( scalar @$newcol != $rowcount ) { $self->warn("new column is not the correct length ($rowcount) - call add or remove row to shrink or grow the number of rows first"); return; } for(my $i=0; $i < $rowcount; $i++) { $self->entry_by_num($i,$colnum,$newcol->[$i]); } $ret = $newcol; } else { $ret = []; for(my $i=0; $i < $rowcount; $i++) { push @$ret,$self->entry_by_num($i,$colnum); } } if( wantarray ) { return @$ret } return $ret; } =head2 row Title : row Usage : my @row = $matrix->row($rowname); OR $matrix->row($rowname,\@rowvalues); Function: Get/Set the row of the matrix Returns : Array (in array context) or arrayref (in scalar context) Args : rowname [optional] new value of row to store =cut sub row { my ($self,$row,$newrow) = @_; if( ! defined $row) { $self->warn("Need at least a row id"); return; } my $rownum = $self->row_num_for_name($row); return $self->row_by_num($rownum,$newrow); } =head2 get_row Title : get_row Usage : my @row = $matrix->get_row('ALPHA'); Function: Get a particular row Returns : Array (in array context) or arrayref (in scalar context) of values Args : name of the row =cut sub get_row { $_[0]->row($_[1]) } =head2 row_by_num Title : row_by_num Usage : my @row = $matrix->row_by_num($rownum); OR $matrix->row($rownum,\@rowvalues); Function: Get/Set the row of the matrix Returns : Array (in array context) or arrayref (in scalar context) Args : rowname [optional] new value of row to store =cut sub row_by_num{ my ($self,$rownum,$newrow) = @_; if( ! defined $rownum ) { $self->warn("need at least a row number"); return; } my $colcount = $self->num_columns; my $ret; if( defined $newrow ) { if( ref($newrow) !~ /ARRAY/i) { $self->warn("expected a valid arrayref for resetting a row"); return; } if( scalar @$newrow != $colcount ) { $self->warn("new row is not the correct length ($colcount) - call add or remove column to shrink or grow the number of columns first"); return; } for(my $i=0; $i < $colcount; $i++) { $self->entry_by_num($rownum,$i, $newrow->[$i]); } $ret = $newrow; } else { $ret = []; for(my $i=0; $i < $colcount; $i++) { # we're doing this to explicitly # copy the entire row push @$ret, $self->entry_by_num($rownum,$i); } } if( wantarray ) { return @$ret } return $ret; } =head2 diagonal Title : diagonal Usage : my @diagonal = $matrix->get_diagonal() Function: Get the diagonal of a matrix Returns : Array (in array context) or arrayref (in scalar context) of values which lie along the diagonal Args : none =cut sub get_diagonal{ my ($self) = @_; my @diag; my $rowcount = $self->num_rows; my $colcount = $self->num_columns; for(my $i = 0; $i < $rowcount; $i++ ) { push @diag, $self->entry_by_num($i,$i); } return @diag; } =head2 add_row Title : add_row Usage : $matrix->add_row($index,\@newrow); Function: Adds a row at particular location in the matrix. If $index < the rowcount will shift all the rows down by the number of new rows. To add a single empty row, simply call $matrix->add_row($index,undef); Returns : the updated number of total rows in the matrix Args : index to store name of the row (header) newrow to add, if this is undef will add a single row with all values set to undef =cut sub add_row{ my ($self,$index,$name,$newrow) = @_; if( !defined $index || $index !~ /^\d+$/ ) { $self->warn("expected a valid row index in add_row"); return; } elsif( ! defined $name) { $self->warn("Need a row name or heading"); return; } elsif( defined $self->row_num_for_name($name) ) { $self->warn("Need a unqiue name for the column heading, $name is already used"); return; } my $colcount = $self->num_columns; my $rowcount = $self->num_rows; if( $index > $rowcount ) { $self->warn("cannot add a row beyond 1+last row at the end ($rowcount) not $index - adding at $rowcount instead"); $index = $rowcount; } if( ! defined $newrow ) { $newrow = []; $newrow->[$colcount] = undef; } elsif( ref($newrow) !~ /ARRAY/i ) { $self->throw("Expected either undef or a valid arrayref for add_row"); } # add this row to the matrix by carving out space for it with # splice splice(@{$self->{'_values'}}, $index,0,[]); for( my $i = 0; $i < $colcount; $i++ ) { $self->entry_by_num($index,$i,$newrow->[$i]); } splice(@{$self->{'_rownames'}}, $index,0,$name); # Sadly we have to remap these each time (except for the case # when we're adding a new column to the end, but I don't think # the speedup for that case warrants the extra code at this time. my $ct = 0; %{$self->{'_rownamesmap'}} = map { $_ => $ct++} @{$self->{'_rownames'}}; return $self->num_rows; } =head2 remove_row Title : remove_row Usage : $matrix->remove_row($colnum) Function: remove a row from the matrix shifting all the rows up by one Returns : Updated number of rows in the matrix Args : row index =cut sub remove_row{ my ($self,$rowindex) = @_; my $rowcount = $self->num_rows; if( $rowindex > $rowcount ) { $self->warn("rowindex $rowindex is greater than number of rows $rowcount, cannot process"); return 0; } else { splice(@{$self->_values},$rowindex,1); delete $self->{'_rownamesmap'}->{$self->{'_rownames'}->[$rowindex]}; splice(@{$self->{'_rownames'}},$rowindex,1); } my $ct = 0; %{$self->{'_rownamesmap'}} = map { $_ => $ct++} @{$self->{'_rownames'}}; return $self->num_rows; } =head2 add_column Title : add_column Usage : $matrix->add_column($index,$colname,\@newcol); Function: Adds a column at particular location in the matrix. If $index < the colcount will shift all the columns right by the number of new columns. To add a single empty column, simply call $matrix->add_column($index,undef); Returns : the updated number of total columns in the matrix Args : index to store name of the column (header) newcolumn to add, if this is undef will add a single column with all values set to undef =cut sub add_column{ my ($self,$index,$name,$newcol) = @_; if( !defined $index || $index !~ /^\d+$/ ) { $self->warn("expected a valid col index in add_column"); return; } elsif( ! defined $name) { $self->warn("Need a column name or heading"); return; } elsif( defined $self->column_num_for_name($name) ) { $self->warn("Need a unqiue name for the column heading, $name is already used"); return; } my $colcount = $self->num_columns; my $rowcount = $self->num_rows; if( $index > $colcount ) { $self->warn("cannot add a column beyond 1+last column at the end ($colcount) not $index - adding at $colcount instead"); $index = $colcount; } if( ! defined $newcol ) { $newcol = []; $newcol->[$rowcount] = undef; # make the array '$rowcount' long } elsif( ref($newcol) !~ /ARRAY/i ) { $self->throw("Expected either undef or a valid arrayref for add_row"); } for( my $i = 0; $i < $rowcount; $i++ ) { # add this column to each row splice(@{$self->_values->[$i]},$index,0,[]); $self->entry_by_num($i,$index,$newcol->[$i]); } splice(@{$self->{'_colnames'}}, $index,0,$name); # Sadly we have to remap these each time (except for the case # when we're adding a new column to the end, but I don't think # the speedup for that case warrants the extra code at this time. my $ct = 0; %{$self->{'_colnamesmap'}} = map {$_ => $ct++} @{$self->{'_colnames'}}; return $self->num_columns; } =head2 remove_column Title : remove_column Usage : $matrix->remove_column($colnum) Function: remove a column from the matrix shifting all the columns to the left by one Returns : Updated number of columns in the matrix Args : column index =cut sub remove_column{ my ($self,$colindex) = @_; my $colcount = $self->num_columns; my $rowcount = $self->num_rows; if( $colindex > $colcount ) { $self->warn("colindex $colindex is greater than number of columns ($colcount), cannot process"); return 0; } else { for(my $i = 0; $i < $rowcount; $i++ ) { splice(@{$self->_values->[$i]},$colindex,1); } delete $self->{'_colnamesmap'}->{$self->{'_colnames'}->[$colindex]}; splice(@{$self->{'_colnames'}},$colindex,1); } my $ct = 0; %{$self->{'_colnamesmap'}} = map {$_ => $ct++} @{$self->{'_colnames'}}; return $self->num_columns; } =head2 column_num_for_name Title : column_num_for_name Usage : my $num = $matrix->column_num_for_name($name) Function: Gets the column number for a particular column name Returns : integer Args : string =cut sub column_num_for_name{ my ($self,$name) = @_; return $self->{'_colnamesmap'}->{$name}; } =head2 row_num_for_name Title : row_num_for_name Usage : my $num = $matrix->row_num_for_name Function: Gets the row number for a particular row name Returns : integer Args : string =cut sub row_num_for_name{ my ($self,$name) = @_; return $self->{'_rownamesmap'}->{$name} } =head2 column_header Title : column_header Usage : my $name = $matrix->column_header(0) Function: Gets the column header for a particular column number Returns : string Args : integer =cut sub column_header{ my ($self,$num) = @_; return $self->{'_colnames'}->[$num]; } =head2 row_header Title : row_header Usage : my $name = $matrix->row_header(0) Function: Gets the row header for a particular row number Returns : string Args : integer =cut sub row_header{ my ($self,$num) = @_; return $self->{'_rownames'}->[$num]; } =head2 num_rows Title : num_rows Usage : my $rowcount = $matrix->num_rows; Function: Get the number of rows Returns : integer Args : none =cut sub num_rows{ my ($self) = @_; return scalar @{$self->_values}; } =head2 num_columns Title : num_columns Usage : my $colcount = $matrix->num_columns Function: Get the number of columns Returns : integer Args : none =cut sub num_columns{ my ($self) = @_; return scalar @{$self->_values->[0] || []}; } =head2 row_names Title : row_names Usage : my @rows = $matrix->row_names Function: The names of all the rows Returns : array in array context, arrayref in scalar context Args : none =cut sub row_names{ if( wantarray ) { return @{shift->{'_rownames'}}; } else { return shift->{'_rownames'}; } } =head2 column_names Title : column_names Usage : my @columns = $matrix->column_names Function: The names of all the columns Returns : array in array context, arrayref in scalar context Args : none =cut sub column_names{ if( wantarray ) { return @{shift->{'_colnames'}}; } else { return shift->{'_colnames'}; } } =head2 private methods Private methods for a Generic Matrix =head2 _values Title : _values Usage : $matrix->_values(); Function: get/set for array ref of the matrix containing distance values Returns : an array reference Args : an array reference =cut sub _values{ my ($self,$val) = @_; if( $val ){ $self->{'_values'} = $val; } return $self->{'_values'}; } 1; BioPerl-1.007002/Bio/Matrix/IO.pm000444000766000024 1430613155576320 16361 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Matrix::IO # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Matrix::IO - A factory for Matrix parsing =head1 SYNOPSIS use Bio::Matrix::IO; my $parser = Bio::Matrix::IO->new(-format => 'scoring', -file => 'BLOSUMN50'); my $matrix = $parser->next_matrix; =head1 DESCRIPTION This is a general factory framework for writing parsers for Matricies. This includes parsing output from distance output like PHYLIP's ProtDist. Additionally it should be possible to fit parsers for PWM and PSSMs once their Matrix objects are written. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Matrix::IO; use strict; use base qw(Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Matrix::IO->new(); Function: Builds a new Bio::Matrix::IO object Returns : an instance of Bio::Matrix::IO Args : =cut sub new { my($caller,@args) = @_; my $class = ref($caller) || $caller; # or do we want to call SUPER on an object if $caller is an # object? if( $class =~ /Bio::Matrix::IO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $format = $param{'-format'} || $class->_guess_format( $param{'-file'} || $ARGV[0] ) || 'scoring'; $format = "\L$format"; # normalize capitalization to lower case # normalize capitalization return unless( $class->_load_format_module($format) ); return "Bio::Matrix::IO::$format"->new(@args); } } =head2 newFh Title : newFh Usage : $fh = Bio::Matrix::IO->newFh(-file=>$filename,-format=>'Format') Function: does a new() followed by an fh() Example : $fh = Bio::Matrix::IO->newFh(-file=>$filename,-format=>'Format') $matrix = <$fh>; # read a matrix object print $fh $matrix; # write a matrix object Returns : filehandle tied to the Bio::SeqIO::Fh class Args : =cut sub newFh { my $class = shift; return unless my $self = $class->new(@_); return $self->fh; } =head2 fh Title : fh Usage : $obj->fh Function: Get a filehandle type access to the matrix parser Example : $fh = $obj->fh; # make a tied filehandle $matrix = <$fh>; # read a matrix object print $fh $matrix; # write a matrix object Returns : filehandle tied to Bio::Matrix::IO class Args : none =cut sub fh { my $self = shift; my $class = ref($self) || $self; my $s = Symbol::gensym; tie $$s,$class,$self; return $s; } =head2 format Title : format Usage : $format = $obj->format() Function: Get the matrix format Returns : matrix format Args : none =cut # format() method inherited from Bio::Root::IO =head2 next_matrix Title : next_matrix Usage : my $matrix = $matixio->next_matrix; Function: Parse the next matrix from the data stream Returns : L type object or undef when finished Args : none =cut sub next_matrix{ my ($self) = @_; $self->throw_not_implemented(); } =head2 write_matrix Title : write_matrix Usage : $io->write_matrix($matrix) Function: Writes a matrix out to the data stream Returns : none Args : Array of Bio::Matrix::MatrixI object - note that not all matricies can be converted to each format, beware with mixing matrix types and output formats =cut sub write_matrix{ my ($self) = @_; $self->throw_not_implemented(); } sub _initialize { my ($self,@args) = @_; $self->_initialize_io(@args); } =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL Matrix::IO stuff* Function: Loads up (like use) a module at run time on demand =cut sub _load_format_module { my ($self,$format) = @_; my $module = "Bio::Matrix::IO::" . $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <_guess_format($filename) Returns : guessed format of filename (lower case) Args : filename =cut sub _guess_format { my $class = shift; return unless $_ = shift; return 'scoring' if /BLOSUM|PAM$/i; return 'phylip' if /\.dist$/i; } sub DESTROY { my $self = shift; $self->close(); } sub TIEHANDLE { my $class = shift; return bless {'matrixio' => shift},$class; } sub READLINE { my $self = shift; return $self->{'matrixio'}->next_tree() || undef unless wantarray; my (@list,$obj); push @list,$obj while $obj = $self->{'treeio'}->next_tree(); return @list; } sub PRINT { my $self = shift; $self->{'matrixio'}->write_tree(@_); } 1; BioPerl-1.007002/Bio/Matrix/MatrixI.pm000444000766000024 1266413155576320 17434 0ustar00cjfieldsstaff000000000000# $Id $ # # BioPerl module for Bio::Matrix::MatrixI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Matrix::MatrixI - An interface for describing a Matrix =head1 SYNOPSIS # Get a Matrix object =head1 DESCRIPTION This is an interface describing how one should be able to interact with a matrix. One can have a lot of information I suppose and this outline won't really work for PWM or PSSMs. We will have to derive a particular interface for those. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Matrix::MatrixI; use strict; use base qw(Bio::Root::RootI); =head2 matrix_id Title : matrix_id Usage : my $id = $matrix->matrix_id Function: Get the matrix ID Returns : string value Args : =cut sub matrix_id{ my ($self) = @_; $self->throw_not_implemented(); } =head2 matrix_name Title : matrix_name Usage : my $name = $matrix->matrix_name(); Function: Get the matrix name Returns : string value Args : =cut sub matrix_name{ my ($self) = @_; $self->throw_not_implemented(); } =head2 get_entry Title : get_entry Usage : my $entry = $matrix->get_entry($rowname,$columname) Function: Get the entry for a given row,column pair Returns : scalar Args : $row name $column name =cut sub get_entry{ my ($self) = @_; $self->throw_not_implemented(); } =head2 get_column Title : get_column Usage : my @row = $matrix->get_column('ALPHA'); Function: Get a particular column Returns : Array (in array context) or arrayref (in scalar context) of values Args : name of the column =cut sub get_column{ my ($self) = @_; $self->throw_not_implemented(); } =head2 get_row Title : get_row Usage : my @row = $matrix->get_row('ALPHA'); Function: Get a particular row Returns : Array (in array context) or arrayref (in scalar context) of values Args : name of the row =cut sub get_row{ my ($self) = @_; $self->throw_not_implemented(); } =head2 get_diagonal Title : get_diagonal Usage : my @diagonal = $matrix->get_diagonal; Function: Get the diagonal of the matrix Returns : Array (in array context) or arrayref (in scalar context) Args : none =cut sub get_diagonal{ my ($self) = @_; $self->throw_not_implemented(); } =head2 column_num_for_name Title : column_num_for_name Usage : my $num = $matrix->column_num_for_name($name) Function: Gets the column number for a particular column name Returns : integer Args : string =cut sub column_num_for_name{ my ($self) = @_; $self->throw_not_implemented(); } =head2 row_num_for_name Title : row_num_for_name Usage : my $num = $matrix->row_num_for_name($name) Function: Gets the row number for a particular row name Returns : integer Args : string =cut sub row_num_for_name{ my ($self) = @_; $self->throw_not_implemented(); } =head2 num_rows Title : num_rows Usage : my $rowcount = $matrix->num_rows; Function: Get the number of rows Returns : integer Args : none =cut sub num_rows{ my ($self) = @_; $self->throw_not_implemented(); } =head2 num_columns Title : num_columns Usage : my $colcount = $matrix->num_columns Function: Get the number of columns Returns : integer Args : none =cut sub num_columns{ my ($self) = @_; $self->throw_not_implemented(); } # inverse? =head2 reverse Title : reverse Usage : my $matrix = $matrix->reverse Function: Get the reverse of a matrix Returns : Args : =cut sub reverse{ my ($self) = @_; $self->throw_not_implemented(); } =head2 row_names Title : row_names Usage : my @rows = $matrix->row_names Function: The names of all the rows Returns : array in array context, arrayref in scalar context Args : none =cut sub row_names{ my ($self) = @_; $self->throw_not_implemented(); } =head2 column_names Title : column_names Usage : my @columns = $matrix->column_names Function: The names of all the columns Returns : array in array context, arrayref in scalar context Args : none =cut sub column_names{ my ($self) = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Matrix/Mlagan.pm000444000766000024 1133613155576320 17251 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Matrix::Mlagan # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Matrix::Mlagan - A generic matrix with mlagan fields =head1 SYNOPSIS # See L for most methods. # These are relevant for mlagan IO: $matrix->gap_open(-400); $matrix->gap_continue(-25); =head1 DESCRIPTION This is based on Bio::Matrix::Generic, differing by storing gap_open and gap_continue data members to allow mlagan IO (see Bio::Matrix::IO::mlagan). (Those values are 'outside' the matrix.) It also limits the structure to a 6x6 matrix with row & column names 'A', 'C', 'G', 'T', '.' and 'N'. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Matrix::Mlagan; use strict; use base qw(Bio::Matrix::Generic); =head2 new Title : new Usage : my $obj = Bio::Matrix::Generic->new(); Function: Builds a new Bio::Matrix::Generic object Returns : an instance of Bio::Matrix::Generic Args : -values => arrayref of arrayrefs of data initialization -matrix_id => id of the matrix -matrix_name => name of the matrix -matrix_init_value => default value to initialize empty cells -gap_open => gap open penalty (int) -gap_continue => gap continue penalty (int) NB: -rownames and -colnames should not be given here, since they are always being set to 'A', 'C', 'G', 'T', '.' and 'N'. =cut sub new { my($class, @args) = @_; my %args = (@args, -rownames => [qw(A C G T . N)], -colnames => [qw(A C G T . N)]); my $self = $class->SUPER::new(%args); $self->_set_from_args(\@args, -methods => [qw(gap_open gap_continue)]); return $self; } =head2 gap_open Title : gap_open Usage : $obj->gap_open(-400); Function: Get/set the gap open amount. Returns : int Args : none to get, OR int to set =cut sub gap_open { my $self = shift; if (@_) { $self->{gap_open} = shift } return $self->{gap_open} || return; } =head2 gap_continue Title : gap_continue Usage : $obj->gap_continue(-25); Function: Get/set the gap continue amount. Returns : int Args : none to get, OR int to set =cut sub gap_continue { my $self = shift; if (@_) { $self->{gap_continue} = shift } return $self->{gap_continue} || return; } =head2 add_row Title : add_row Usage : Do not use Function: This generic method is not suitable for mlagan, where the number of rows is fixed. Returns : Warning Args : none =cut sub add_row { shift->warn("Mlagan matricies are fixed at 6x6"); } =head2 remove_row Title : remove_row Usage : Do not use Function: This generic method is not suitable for mlagan, where the number of rows is fixed. Returns : Warning Args : none =cut sub remove_row { shift->warn("Mlagan matricies are fixed at 6x6"); } =head2 add_column Title : add_column Usage : Do not use Function: This generic method is not suitable for mlagan, where the number of columns is fixed. Returns : Warning Args : none =cut sub add_column { shift->warn("Mlagan matricies are fixed at 6x6"); } =head2 remove_column Title : remove_column Usage : Do not use Function: This generic method is not suitable for mlagan, where the number of columns is fixed. Returns : Warning Args : none =cut sub remove_column { shift->warn("Mlagan matricies are fixed at 6x6"); } 1; BioPerl-1.007002/Bio/Matrix/PhylipDist.pm000444000766000024 2547613155576320 20155 0ustar00cjfieldsstaff000000000000# BioPerl module for Bio::Matrix::PhylipDist # # # Please direct questions and support issues to # # Cared for by Shawn Hoon # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Matrix::PhylipDist - A Phylip Distance Matrix object =head1 SYNOPSIS use Bio::Tools::Phylo::Phylip::ProtDist; my $dist = Bio::Tools::Phylo::Phylip::ProtDist->new( -file=>"protdist.out", -program=>"ProtDist"); #or my $dist = Bio::Tools::Phylo::Phylip::ProtDist->new( -fh=>"protdist.out", -program=>"ProtDist"); #get specific entries my $distance_value = $dist->get_entry('ALPHA','BETA'); my @columns = $dist->get_column('ALPHA'); my @rows = $dist->get_row('BETA'); my @diagonal = $dist->get_diagonal(); #print the matrix in phylip numerical format print $dist->print_matrix; =head1 DESCRIPTION Simple object for holding Distance Matrices generated by the following Phylip programs: 1) dnadist 2) protdist 3) restdist It currently handles parsing of the matrix without the data output option. 5 Alpha 0.00000 4.23419 3.63330 6.20865 3.45431 Beta 4.23419 0.00000 3.49289 3.36540 4.29179 Gamma 3.63330 3.49289 0.00000 3.68733 5.84929 Delta 6.20865 3.36540 3.68733 0.00000 4.43345 Epsilon 3.45431 4.29179 5.84929 4.43345 0.00000 =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org =head1 CONTRIBUTORS Jason Stajich, jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_". =cut # Let the code begin... package Bio::Matrix::PhylipDist; use strict; use base qw(Bio::Root::Root Bio::Matrix::MatrixI); =head2 new Title : new Usage : my $family = Bio::Matrix::PhylipDist->new(-file=>"protdist.out", -program=>"protdist"); Function: Constructor for PhylipDist Object Returns : L =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($matrix,$values, $names, $program,$matname, $matid) = $self->_rearrange([qw(MATRIX VALUES NAMES PROGRAM MATRIX_NAME MATRIX_ID )],@args); ($matrix && $values && $names) || $self->throw("Need matrix, values, and names fields all provided!"); $program && $self->matrix_name($program) if defined $program; $self->_matrix($matrix) if ref($matrix) =~ /HASH/i; $self->_values($values) if ref($values) =~ /ARRAY/i; $self->names($names) if ref($names) =~ /ARRAY/i; $self->matrix_name($matname) if defined $matname; $self->matrix_id ($matid) if defined $matid; return $self; } =head2 get_entry Title : get_entry Usage : $matrix->get_entry(); Function: returns a particular entry Returns : a float Arguments: string id1, string id2 =cut sub get_entry { my ($self,$row,$column) = @_; $row && $column || $self->throw("Need at least 2 ids"); my %matrix = %{$self->_matrix}; my @values = @{$self->_values}; if(ref $matrix{$row}{$column}){ my ($i,$j) = @{$matrix{$row}{$column}}; return $values[$i][$j]; } return; } =head2 get_row Title : get_row Usage : $matrix->get_row('ALPHA'); Function: returns a particular row Returns : an array of float Arguments: string id1 =cut sub get_row { my ($self,$row) = @_; $row || $self->throw("Need at least a row id"); my %matrix = %{$self->_matrix}; my @values = @{$self->_values}; my @names = @{$self->names}; $matrix{$row} || return; my ($val) = values %{$matrix{$row}}; my $row_pointer = $val->[0]; my $index = scalar(@names)-1; return @{$values[$row_pointer]}[0..$index]; } =head2 get_column Title : get_column Usage : $matrix->get_column('ALPHA'); Function: returns a particular column Returns : an array of floats Arguments: string id1 =cut sub get_column { my ($self,$column) = @_; $column || $self->throw("Need at least a column id"); my %matrix = %{$self->_matrix}; my @values = @{$self->_values}; my @names = @{$self->names}; $matrix{$column} || return (); my ($val) = values %{$matrix{$column}}; my $row_pointer = $val->[0]; my @ret; for(my $i=0; $i < scalar(@names); $i++) { push @ret, $values[$i][$row_pointer]; } return @ret; } =head2 get_diagonal Title : get_diagonal Usage : $matrix->get_diagonal(); Function: returns the diagonal of the matrix Returns : an array of float Arguments: string id1 =cut sub get_diagonal { my ($self) = @_; my %matrix = %{$self->_matrix}; my @values = @{$self->_values}; my @return; foreach my $name (@{$self->names}){ my ($i,$j) = @{$matrix{$name}{$name}}; push @return,$values[$i][$j]; } return @return; } =head2 print_matrix Title : print_matrix Usage : $matrix->print_matrix(); Function: returns a string of the matrix in phylip format Returns : a string Arguments: =cut sub print_matrix { my ($self) = @_; my @names = @{$self->names}; my @values = @{$self->_values}; my %matrix = %{$self->_matrix}; my $str; $str.= (" "x 4). scalar(@names)."\n"; foreach my $name (@names){ my $newname = $name. (" " x (15-length($name))); if( length($name) >= 15 ) { $newname .= " " } $str.=$newname; my $count = 0; foreach my $n (@names) { my ($i,$j) = @{$matrix{$name}{$n}}; if($count < $#names){ $str .= $values[$i][$j]. " "; } else { if( ! defined $values[$i][$j] ) { $self->debug("no value for $i,$j cell\n"); } else { $str .= $values[$i][$j]; } } $count++; } $str.="\n"; } return $str; } =head2 _matrix Title : _matrix Usage : $matrix->_matrix(); Function: get/set for hash reference of the pointers to the value matrix Returns : hash reference Arguments: hash reference =cut sub _matrix { my ($self,$val) = @_; if($val){ $self->{'_matrix'} = $val; } return $self->{'_matrix'}; } =head2 names Title : names Usage : $matrix->names(); Function: get/set for array ref of names of sequences Returns : an array reference Arguments: an array reference =cut sub names { my ($self,$val) = @_; if($val){ $self->{'_names'} = $val; } return $self->{'_names'}; } =head2 program Title : program Usage : $matrix->program(); Function: get/set for the program name generating this matrix Returns : string Arguments: string =cut sub program { my ($self) = shift; return $self->matrix_name(@_); } =head2 _values Title : _values Usage : $matrix->_values(); Function: get/set for array ref of the matrix containing distance values Returns : an array reference Arguments: an array reference =cut sub _values { my ($self,$val) = @_; if($val){ $self->{'_values'} = $val; } return $self->{'_values'}; } =head1 L implementation =head2 matrix_id Title : matrix_id Usage : my $id = $matrix->matrix_id Function: Get/Set the matrix ID Returns : scalar value Args : [optional] new id value to store =cut sub matrix_id{ my $self = shift; return $self->{'_matid'} = shift if @_; return $self->{'_matid'}; } =head2 matrix_name Title : matrix_name Usage : my $name = $matrix->matrix_name(); Function: Get/Set the matrix name Returns : scalar value Args : [optional] new matrix name value =cut sub matrix_name{ my $self = shift; return $self->{'_matname'} = shift if @_; return $self->{'_matname'}; } =head2 column_header Title : column_header Usage : my $name = $matrix->column_header(0) Function: Gets the column header for a particular column number Returns : string Args : integer =cut sub column_header{ my ($self,$num) = @_; my @coln = $self->column_names; return $coln[$num]; } =head2 row_header Title : row_header Usage : my $name = $matrix->row_header(0) Function: Gets the row header for a particular row number Returns : string Args : integer =cut sub row_header{ my ($self,$num) = @_; my @rown = $self->row_names; return $rown[$num]; } =head2 column_num_for_name Title : column_num_for_name Usage : my $num = $matrix->column_num_for_name($name) Function: Gets the column number for a particular column name Returns : integer Args : string =cut sub column_num_for_name{ my ($self,$name) = @_; my $ct = 0; foreach my $n ( $self->column_names ) { return $ct if $n eq $name; $ct++; } return; } =head2 row_num_for_name Title : row_num_for_name Usage : my $num = $matrix->row_num_for_name($name) Function: Gets the row number for a particular row name Returns : integer Args : string =cut sub row_num_for_name{ my ($self,$name) = @_; my $ct = 0; foreach my $n ( $self->row_names ) { return $ct if $n eq $name; $ct++; } } =head2 num_rows Title : num_rows Usage : my $rowcount = $matrix->num_rows; Function: Get the number of rows Returns : integer Args : none =cut sub num_rows{ return scalar @{shift->names} } =head2 num_columns Title : num_columns Usage : my $colcount = $matrix->num_columns Function: Get the number of columns Returns : integer Args : none =cut sub num_columns{ return scalar @{shift->names}; } =head2 row_names Title : row_names Usage : my @rows = $matrix->row_names Function: The names of all the rows Returns : array in array context, arrayref in scalar context Args : none =cut sub row_names{ return @{shift->names} } =head2 column_names Title : column_names Usage : my @columns = $matrix->column_names Function: The names of all the columns Returns : array in array context, arrayref in scalar context Args : none =cut sub column_names{ return @{shift->names} } 1; BioPerl-1.007002/Bio/Matrix/Scoring.pm000444000766000024 1346713155576320 17465 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Matrix::Scoring # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Matrix::Scoring - Object which can hold scoring matrix information =head1 SYNOPSIS use Bio::Matrix::Scoring; =head1 DESCRIPTION An object which can handle AA or NT scoring matrix information. Some transformation properties are available too. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Matrix::Scoring; use strict; use base qw(Bio::Matrix::Generic); =head2 new Title : new Usage : my $obj = Bio::Matrix::Scoring->new(); Function: Builds a new Bio::Matrix::Scoring object Returns : an instance of Bio::Matrix::Scoring Args : =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($entropy,$expected,$scale,$scaleval,$database, $lowestscore,$highestscore,$lambda,$H) = $self->_rearrange([qw( ENTROPY EXPECTED SCALE SCALE_VALUE DATABASE LOWEST_SCORE HIGHEST_SCORE LAMBDA H)], @args); $self->entropy ($entropy); $self->expected_score($expected); $self->scale ($scale); $self->scale_value($scaleval); $self->database ($database); $self->lowest_score($lowestscore); $self->highest_score($highestscore); $self->lambda($lambda); $self->H($H); return $self; } =head2 entropy Title : entropy Usage : $obj->entropy($newval) Function: Example : Returns : value of entropy (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub entropy{ my $self = shift; return $self->{'entropy'} = shift if @_; return $self->{'entropy'}; } =head2 expected_score Title : expected_score Usage : $obj->expected_score($newval) Function: Example : Returns : value of expected (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub expected_score{ my $self = shift; return $self->{'expected'} = shift if @_; return $self->{'expected'}; } =head2 scale Title : scale Usage : $obj->scale($newval) Function: Example : Returns : value of scale (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub scale{ my $self = shift; return $self->{'scale'} = shift if @_; return $self->{'scale'}; } =head2 scale_value Title : scale_value Usage : $obj->scale_value($newval) Function: Example : Returns : value of scale_value (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub scale_value{ my $self = shift; return $self->{'scale_value'} = shift if @_; return $self->{'scale_value'}; } =head2 description Title : description Usage : $obj->description($newval) Function: Example : Returns : value of description (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub description{ my $self = shift; return $self->{'description'} = shift if @_; return $self->{'description'}; } =head2 database Title : database Usage : $obj->database($newval) Function: Example : Returns : value of database (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub database{ my $self = shift; return $self->{'database'} = shift if @_; return $self->{'database'}; } =head2 lowest_score Title : lowest_score Usage : $obj->lowest_score($newval) Function: Example : Returns : value of lowest_score (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub lowest_score{ my $self = shift; return $self->{'lowest_score'} = shift if @_; return $self->{'lowest_score'}; } =head2 highest_score Title : highest_score Usage : $obj->highest_score($newval) Function: Example : Returns : value of highest_score (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub highest_score{ my $self = shift; return $self->{'highest_score'} = shift if @_; return $self->{'highest_score'}; } =head2 lambda Title : lambda Usage : $obj->lambda($newval) Function: Example : Returns : value of lambda (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub lambda{ my $self = shift; return $self->{'lambda'} = shift if @_; return $self->{'lambda'}; } =head2 H Title : H Usage : $obj->H($newval) Function: Example : Returns : value of H (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub H{ my $self = shift; return $self->{'H'} = shift if @_; return $self->{'H'}; } 1; BioPerl-1.007002/Bio/Matrix/IO000755000766000024 013155576320 15642 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Matrix/IO/mlagan.pm000444000766000024 772713155576320 17611 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Matrix::IO::mlagan # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Matrix::IO::mlagan - A parser for the mlagan substitution matrix =head1 SYNOPSIS use Bio::Matrix::IO; my $parser = Bio::Matrix::IO->new(-format => 'mlagan', -file => 'nucmatrix.txt'); my $matrix = $parser->next_matrix; my $gap_open = $parser->gap_open; my $gap_continue = $parser->gap_continue; =head1 DESCRIPTION Use to read in and write out substitution matrix files suitable for use by mlagan. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Matrix::IO::mlagan; use strict; use Bio::Matrix::Mlagan; use base qw(Bio::Matrix::IO); =head2 new Title : new Usage : my $obj = Bio::Matrix::IO::mlagan->new(); Function: Builds a new Bio::Matrix::IO::mlagan object Returns : an instance of Bio::Matrix::IO::mlagan Args : =cut =head2 next_matrix Title : next_matrix Usage : my $matrix = $obj->next_matrix(); Function: parses a matrix file Returns : L Args : none =cut sub next_matrix { my $self = shift; my (@matrix, $gap_open, $gap_cont); while (defined ($_ = $self->_readline)) { if (/^[ACGTN\.]/) { my (undef, @values) = split; push(@matrix, \@values); } elsif (/^[-\d]/) { ($gap_open, $gap_cont) = split; last; } } @matrix == 6 || $self->throw("Something wrong with file, was it the correct format?"); my $matrix = Bio::Matrix::Mlagan->new(-values => \@matrix, -gap_open => $gap_open, -gap_continue => $gap_cont); return $matrix; } =head2 write_matrix Title : write_matrix Usage : $obj->write_matrix($matrix) Function: Write out a matrix in mlagan format Returns : n/a Args : L =cut sub write_matrix { my ($self, $matrix) = @_; $matrix || $self->throw("Matrix required as input"); my $gap_open = $matrix->gap_open; my $gap_continue = $matrix->gap_continue; unless (defined $gap_open && defined $gap_continue) { $self->throw("gap_open() and gap_continue() in the supplied matrix object must both be set"); } $self->_print(" A C G T . N\n"); foreach my $char (qw(A C G T . N)) { my @row = $matrix->get_row($char); my $row = $char; foreach my $val (@row) { $row .= " " x (5 - length($val)) . $val; } $self->_print($row."\n"); } $self->_print("\n$gap_open $gap_continue"); return; } 1; BioPerl-1.007002/Bio/Matrix/IO/phylip.pm000444000766000024 1075713155576320 17674 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Matrix::IO::phylip # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Matrix::IO::phylip - A parser for PHYLIP distance matricies =head1 SYNOPSIS use Bio::Matrix::IO; my $parser = Bio::Matrix::IO->new(-format => 'phylip', -file => 't/data/phylipdist.out'); my $matrix = $parser->next_matrix; =head1 DESCRIPTION This is a parser for PHYLIP distance matrix output. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Matrix::IO::phylip; use vars qw($DEFAULTPROGRAM); use strict; $DEFAULTPROGRAM = 'phylipdist'; use Bio::Matrix::PhylipDist; use base qw(Bio::Matrix::IO); =head2 new Title : new Usage : my $obj = Bio::Matrix::IO::phylip->new(); Function: Builds a new Bio::Matrix::IO::phylip object Returns : an instance of Bio::Matrix::IO::phylip Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($prog) = $self->_rearrange([qw(PROGRAM)], @args); $self->{'_program'} = $prog || $DEFAULTPROGRAM; return $self; } =head2 next_matrix Title : next_matrix Usage : my $matrix = $parser->next_matrix Function: Get the next result set from parser data Returns : L Args : none =cut sub next_matrix { my ($self) = @_; my @names; my @values; my $entry; my $size = 0; while ($entry=$self->_readline) { if($#names >=0 && $entry =~/^\s+\d+\n$/){ $self->_pushback($entry); last; } elsif($entry=~/^\s+(\d+)\n$/){ $size = $1; next; } elsif( $entry =~ s/^\s+(\-?\d+\.\d+)/$1/ ) { my (@line) = split( /\s+/,$entry); push @{$values[-1]}, @line; next; } my ($n,@line) = split( /\s+/,$entry); push @names, $n; push @values, [@line]; } if( scalar @names != $size ) { $self->warn("The number of entries ".(scalar @names). " is not the same $size"); } $#names>=0 || return; my %dist; my $i=0; foreach my $name(@names){ my $j=0; foreach my $n(@names) { $dist{$name}{$n} = [$i,$j]; $j++; } $i++; } my $matrix = Bio::Matrix::PhylipDist->new (-matrix_name => $self->{'_program'}, -matrix => \%dist, -names => \@names, -values => \@values); return $matrix; } =head2 write_matrix Title : write_matrix Usage : $matio->write_matrix($matrix) Function: Write out a matrix in the phylip distance format Returns : none Args : L =cut sub write_matrix { my ($self,@matricies) = @_; foreach my $matrix ( @matricies ) { my @names = @{$matrix->names}; my @values = @{$matrix->_values}; my %matrix = %{$matrix->_matrix}; my $str; $str.= (" "x 4). scalar(@names)."\n"; foreach my $name (@names){ my $newname = $name. (" " x (15-length($name))); if( length($name) >= 15 ) { $newname .= " " } $str.=$newname; my $count = 0; foreach my $n (@names){ my ($i,$j) = @{$matrix{$name}{$n}}; if($count < $#names){ $str.= $values[$i][$j]. " "; } else { $str.= $values[$i][$j]; } $count++; } $str.="\n"; } $self->_print($str); } } 1; BioPerl-1.007002/Bio/Matrix/IO/scoring.pm000444000766000024 1062713155576320 20027 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Matrix::IO::scoring # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Matrix::IO::scoring - A parser for PAM/BLOSUM matricies =head1 SYNOPSIS use Bio::Matrix::IO; my $parser = Bio::Matrix::IO->new(-format => 'scoring', -file => 'BLOSUM50'); my $matrix = $parser->next_matrix; =head1 DESCRIPTION Describe the object here =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Matrix::IO::scoring; use strict; use Bio::Matrix::Scoring; use base qw(Bio::Matrix::IO); =head2 new Title : new Usage : my $obj = Bio::Matrix::IO::scoring->new(); Function: Builds a new Bio::Matrix::IO::scoring object Returns : an instance of Bio::Matrix::IO::scoring Args : =cut =head2 next_matrix Title : next_matrix Usage : my $matrux = $parser->next_matrix Function: parses a scoring matrix (BLOSUM,PAM styles) Returns : L Args : none =cut sub next_matrix{ my ($self) = @_; local ($_); my (@matrix,@cols,@rows,%extras,$inmatrix); while( defined ( $_ = $self->_readline ) ) { next if ( /^\s*$/); if( /^\#/ ) { if( $inmatrix ) { $self->_pushback($_); last; } if( m/Entropy\s+\=\s+(\S+)\,\s+ Expected\s+\=\s+(\S+)/ox ) { $extras{'-entropy'} = $1; $extras{'-expected'} = $2; } elsif ( m/Expected\s+score\s+\=\s+(\S+)\, \s+Entropy\s+\=\s+(\S+)/xo ){ $extras{'-entropy'} = $2; $extras{'-expected'} = $1; } elsif( m/(PAM\s+\d+)\s+substitution.+ scale\s+\=\s+(\S+)\s+\=\s+(\S+)/ox ) { $extras{'-matrix_name'} = $1; $extras{'-scale'} = $2; $extras{'-scale_value'} = $3; } elsif( /Blocks Database\s+\=\s+(\S+)/o ) { $extras{'-database'} = $1; } elsif( m/(\S+)\s+Bit\s+Units/ox ) { $extras{'-scale'} = $1; } elsif( m/Lowest score\s+\=\s+(\S+)\,\s+ Highest score\s+\=\s+(\S+)/ox ) { $extras{'-lowest_score'} = $1; $extras{'-highest_score'} = $2; } elsif( m/(Lambda)\s+\=\s+(\S+)\s+bits\, \s+(H)\s+\=\s+(\S+)/ox ) { # This is a DNA matrix $extras{$1} = $2; $extras{$3} = $4; } } elsif( s/^\s+(\S+)/$1/ ) { @cols = split; if( $cols[0] ne 'A' ) { $self->warn("Unrecognized first line of matrix, we might not have parsed it correctly"); } $inmatrix = 1; } elsif( $inmatrix ) { if( ! /^(\S+)/ ) { $inmatrix = 0; next } my ($rowname,@row) = split; push @rows, $rowname; push @matrix, [@row]; } else { print; } } my $matrix = Bio::Matrix::Scoring->new(-values => \@matrix, -rownames => \@rows, -colnames => \@cols, %extras); } =head2 write_matrix Title : write_matrix Usage : $matio->write_matrix($matrix) Function: Write out a matrix in the BLOSUM/PAM format Returns : none Args : L =cut sub write_matrix{ my ($self,@args) = @_; $self->warn("cannot actually use this function yet - it isn't finished"); return; } 1; BioPerl-1.007002/Bio/Matrix/PSM000755000766000024 013155576320 15772 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Matrix/PSM/IO.pm000444000766000024 1773213155576320 17026 0ustar00cjfieldsstaff000000000000#--------------------------------------------------------- =head1 NAME Bio::Matrix::PSM::IO - PSM parser =head1 SYNOPSIS use Bio::Matrix::PSM::IO; my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'transfac'); my $release=$psmIO->release; #Using Bio::Matrix::PSM::PsmHeader methods my $release=$psmIO->release; while (my $psm=$psmIO->next_psm) { my %psm_header=$psm->header; my $ic=$psm_header{IC}; my $sites=$psm_header{sites}; my $width=$psm_header{width}; my $score=$psm_header{e_val}; my $IUPAC=$psm->IUPAC; } my $instances=$psm->instances; foreach my $instance (@{$instances}) { my $id=$instance->primary_id; } =head1 DESCRIPTION This module allows you to read DNA position scoring matrices and/or their respective sequence matches from a file. There are two header methods, one belonging to Bio::Matrix::PSM::IO::driver and the other to Bio::Matrix::PSM::Psm. They provide general information about the file (driver) and for the current PSM result (Psm) respectively. Psm header method always returns the same thing, but some values in the hash might be empty, depending on the file you are parsing. You will get undef in this case (no exceptions are thrown). Please note that the file header data (commenatries, version, input data, configuration, etc.) might be obtained through Bio::Matrix::PSM::PsmHeader methods. Some methods are driver specific (meme, transfac, etc.): meme: weight mast: seq, instances If called when you parse a different file type you will get undef. For example: my $psmIO= Bio::Matrix::PSM::IO->new(file=>$file, format=>'transfac'); my %seq=$psmIO->seq; will return an empty hash. To see all methods and how to use them go to Bio::Matrix::PSM::PsmHeaderI. See also Bio::Matrix::PSM::PsmI for details on using and manipulating the parsed data. The only way to write PFM/PWM is through masta module (something like fasta for DNA matrices). You can see an example by reading Bio::Matrix::PSM::IO::masta documentation. =head1 See also Bio::Matrix::PSM::PsmI, Bio::Matrix::PSM::PsmHeaderI, Bio::Matrix::PSM::IO::masta =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::IO; use vars qw(@PSMFORMATS); use strict; use base qw(Bio::Root::IO); @PSMFORMATS = qw(meme transfac mast psiblast masta); =head2 new Title : new Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'meme', -file=>$file); Function: Associates a file with the appropriate parser Throws : Throws if the file passed is in HTML format or if some criteria for the file format are not met. See L and L for more details. Example : Returns : psm object, associated with a file with matrix file Args : hash =cut sub new { my($caller,@args) = @_; my $class = ref($caller) || $caller; my $self; # or do we want to call SUPER on an object if $caller is an # object? if( $class =~ /Bio::Matrix::PSM::IO(\S+)/ ) { $self = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $format = $param{'-format'} || $class->_guess_format( $param{'-file'} || $ARGV[0] ) || 'scoring'; $class->throw("$format format unrecognized or an argument error occurred\n.") if (!grep(/$format/,@Bio::Matrix::PSM::IO::PSMFORMATS)); $format = "\L$format"; # normalize capitalization to lower case # normalize capitalization return unless( $class->_load_format_module($format) ); return "Bio::Matrix::PSM::IO::$format"->new(@args); } } =head2 fh Title : fh Usage : $obj->fh Function: Get a filehandle type access to the matrix parser Example : $fh = $obj->fh; # make a tied filehandle $matrix = <$fh>; # read a matrix object Returns : filehandle tied to Bio::Matrix::PSM::IO class Args : none =cut sub fh { my $self = shift; my $class = ref($self) || $self; my $s = Symbol::gensym; tie $$s,$class,$self; return $s; } =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL Matrix::PSM::IO stuff* Function: Loads up (like use) a module at run time on demand =cut sub _load_format_module { my ($self,$format) = @_; my $module = "Bio::Matrix::PSM::IO::" . $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <_guess_format($filename) Returns : guessed format of filename (lower case) Args : filename =cut sub _guess_format { my $class = shift; return unless $_ = shift; return 'meme' if /.meme$|meme.html$/i; return 'transfac' if /\.dat$/i; return 'mast' if /^mast\.|\.mast.html$|.mast$/i; } =head2 next_psm Title : next_psm Usage : my $psm=$psmIO->next_psm(); Function: Reads the next PSM from the input file, associated with this object Throws : Throws if there ara format violations in the input file (checking is not very strict with all drivers). Example : Returns : Bio::Matrix::PSM::Psm object Args : none =cut sub next_psm { my $self = shift; $self->throw_not_implemented(); } =head2 _parseMatrix Title : _parseMatrix Usage : Function: Parses the next site matrix information in the meme file Throws : Example : Internal stuff Returns : hash as for constructing a SiteMatrix object (see SiteMatrixI) Args : string =cut sub _parseMatrix { my $self = shift; $self->throw_not_implemented(); } =head2 _parseInstance Title : _parseInstance Usage : Function: Parses the next sites instances from the meme file Throws : Example : Internal stuff Returns : Bio::Matrix::PSM::SiteMatrix object Args : array references =cut sub _parseInstance { my $self = shift; $self->throw_not_implemented(); } =head2 _parse_coordinates Title : _parse_coordinates Usage : Function: Throws : Example : Internal stuff Returns : Args : =cut sub _parse_coordinates { my $self = shift; $self->throw_not_implemented(); } =head2 header Title : header Usage : my %header=$psmIO->header; Function: Returns the header for the PSM file, format specific Throws : Example : Returns : Hash or a single string with driver specific information Args : none =cut sub header { my $self = shift; $self->throw_not_implemented(); } =head2 _make_matrix Title : _make_matrix Usage : Function: makes a matrix from 4 array references (A C G T) Throws : Example : Returns : SiteMatrix object Args : array of references(A C G T) =cut sub _make_matrix { my $self = shift; $self->throw_not_implemented(); } sub DESTROY { my $self = shift; $self->close(); } 1; BioPerl-1.007002/Bio/Matrix/PSM/InstanceSite.pm000444000766000024 1752213155576320 21105 0ustar00cjfieldsstaff000000000000 =head1 NAME Bio::Matrix::PSM::InstanceSite - A PSM site occurrence =head1 SYNOPSIS use Bio::Matrix::PSM::InstanceSite; #You can get an InstanceSite object either from a file: my ($instances,$matrix)=$SomePSMFile->parse_next; #or from memory my %params=(seq=>'TATAAT', id=>"TATAbox1", accession=>'ENSG00000122304', mid=>'TB1', desc=>'TATA box, experimentally verified in PRM1 gene', -relpos=>-35, -anchor=>'CHR7', -start=>35000921, -end=>35000926); #Last 2 arguments are passed to create a Bio::LocatableSeq object #Anchor shows the coordinates system for the Bio::LocatableSeq object =head1 DESCRIPTION Abstract interface to PSM site occurrence (PSM sequence match). InstanceSite objects may be used to describe a PSM (See L) sequence matches. The usual characteristic of such a match is sequence coordinates, score, sequence and sequence (gene) identifier- accession number or other id. This object inherits from Bio::LocatableSeq (which defines the real sequence) and might hold a SiteMatrix object, used to detect the CRE (cis-regulatory element), or created from this CRE. While the documentation states that the motif id and gene id (accession) combination should be unique, this is not entirely true- there might be more than one occurrence of the same cis-regulatory element in the upstream region of the same gene. Therefore relpos would be the third element to create a really unique combination. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head2 Description Bio::Matrix::PSM::InstanceSiteI implementation =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::InstanceSite; use strict; use base qw(Bio::LocatableSeq Bio::Matrix::PSM::InstanceSiteI); =head2 new Title : new Usage : my $isntance=Bio::Matrix::PSM::InstanceSite->new (-seq=>'TATAAT', -id=>"TATAbox1", -accession_number='ENSG00000122304', -mid=>'TB1', -desc=>'TATA box, experimentally verified in PRM1 gene', -relpos=>-35, -anchor=>'CHR7', -start=>35000921, -end=>35000926, strand=>1) Function: Creates an InstanceSite object from memory. Throws : Example : Returns : Bio::Matrix::PSM::InstanceSite object Args : hash =cut sub new { my ($class, @args) = @_; my %args = @args; #Too many things to rearrange, and I am creating >1K such objects routinely, so this is a performance issue $args{'-start'} ||= 1; my $end = $args{'-start'} + length($args{-seq}) -1; if (!defined($args{-strand})) { $args{-strand}=1; @args=%args; } my $self = $class->SUPER::new(@args,'-end',$end); while( @args ) { (my $key = shift @args) =~ s/-//gi; #deletes all dashes (only dashes)! $args{$key} = shift @args; } #should throw exception if seq is null, for now just warn if (($args{seq} eq '') || (!defined($args{seq}))) { $args{seq}="AGCT"; warn "No sequence?!\n"; } $self->{mid}=$args{mid}; $self->seq($args{seq}); $self->desc($args{desc}); $self->{score}=$args{score}; $self->{relpos}=$args{relpos}; $self->{frame}=$args{frame}; $self->{anchor}=$args{anchor}; return $self; } =head2 mid Title : mid Usage : my $mid=$instance->mid; Function: Get/Set the motif id Throws : Example : Returns : scalar Args : scalar =cut sub mid { my $self = shift; my $prev = $self->{mid}; if (@_) { $self->{mid} = shift; } return $prev; } =head2 score Title : score Usage : my $score=$instance->score; Function: Get/Set the score (mismatches) between the instance and the attached (or initial) PSM Throws : Example : Returns : real number Args : real number =cut sub score { my $self = shift; my $prev = $self->{score}; if (@_) { $self->{score} = shift; } return $prev; } =head2 anchor Title : anchor Usage : my $anchor=$instance->anchor; Function: Get/Set the anchor which shows what coordinate system start/end use Throws : Example : Returns : string Args : string =cut sub anchor { my $self = shift; my $prev = $self->{anchor}; if (@_) { $self->{anchor} = shift; } return $prev; } =head2 start Title : start Usage : my $start=$instance->start; Function: Get/Set the position of the instance on the sequence used Throws : Example : Returns : integer Args : integer =cut #Provided by LocatableSeq =head2 minstance Title : minstance Usage : my $minstance=$misntance->score; Function: Get/Set the unique identifier- sequence id/motif id, for example PRM1_TATAbox. Not necessarily human readable. Throws : Example : Returns : string Args : string =cut sub minstance { my $self = shift; my $prev = $self->{minstance}; if (@_) { $self->{minstance} = shift; } return $prev; } =head2 relpos Title : relpos Usage : my $seqpos=$instance->relpos; Function: Get/Set the relative position of the instance with respect to the transcription start site (if known). Can and usually is negative. Throws : Example : Returns : integer Args : integer =cut sub relpos { my $self = shift; my $prev = $self->{relpos}; if (@_) { $self->{relpos} = shift; } return $prev; } =head2 annotation Title : annotation Usage : $ann = $seq->annotation or $seq->annotation($annotation) Function: Gets or sets the annotation Returns : L object Args : None or L object See L and L for more information =cut sub annotation { my ($obj,$value) = @_; if( defined $value ) { $obj->throw("object of class ".ref($value)." does not implement ". "Bio::AnnotationCollectionI. Too bad.") unless $value->isa("Bio::AnnotationCollectionI"); $obj->{'_annotation'} = $value; } elsif( ! defined $obj->{'_annotation'}) { $obj->{'_annotation'} = Bio::Annotation::Collection->new(); } return $obj->{'_annotation'}; } =head2 species Title : species Usage : $species = $seq->species() or $seq->species($species) Function: Gets or sets the species Returns : L object Args : None or L object See L for more information =cut sub species { my ($self, $species) = @_; if ($species) { $self->{'species'} = $species; } else { return $self->{'species'}; } } =head2 frame Title : frame Usage : my $frane=$instance->frame; Function: Get/Set the frame of a DNA instance with respect to a protein motif used. Returns undef if the motif was not protein or the DB is protein. Throws : Example : Returns : integer Args : integer (0, 1, 2) =cut sub frame { my $self = shift; my $prev = $self->{frame}; if (@_) { $self->{frame} = shift; $self->throw("This is not a legitimate frame") unless (grep(/$self->{frame}/,qw[0 1 2])); } return $prev; } 1; BioPerl-1.007002/Bio/Matrix/PSM/InstanceSiteI.pm000444000766000024 1010613155576320 21205 0ustar00cjfieldsstaff000000000000 =head1 NAME Bio::Matrix::PSM::InstanceSiteI - InstanceSite interface, holds an instance of a PSM =head1 SYNOPSIS use Bio::Matrix::PSM::InstanceSite; #Y ou can get an InstanceSite object either from a file: my ($instances,$matrix)=$SomePSMFile->parse_next; #or from memory my %params=(seq => 'TATAAT', id => "TATAbox1", accession => 'ENSG00000122304', mid => 'TB1', desc => 'TATA box, experimentally verified in PRM1 gene', relpos => -35); =head1 DESCRIPTION Abstract interface to PSM site occurrence (PSM sequence match). InstanceSite objects may be used to describe a PSM (See Bio::Matrix::PSM::SiteMatrix) sequence matches. The usual characteristic of such a match is sequence coordinates, score, sequence and sequence (gene) identifier- accession number or other id. This object inherits from Bio::LocatableSeq (which defines the real sequence) and might hold a SiteMatrix object, used to detect the CRE (cis-regulatory element), or created from this CRE. While the documentation states that the motif id and gene id (accession) combination should be unique, this is not entirely true- there might be more than one occurrence of the same cis-regulatory element in the upstream region of the same gene. Therefore relpos would be the third element to create a really unique combination. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 SEE ALSO L, L, L =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::InstanceSiteI; use strict; use base qw(Bio::Root::RootI); =head2 mid Title : mid Usage : my $mid=$instance->mid; Function: Get/Set the motif id Throws : Returns : scalar Args : scalar =cut sub mid { my $self = shift; $self->throw_not_implemented(); } =head2 score Title : score Usage : my $score=$instance->score; Function: Get/Set the score (mismatches) between the instance and the attached (or initial) PSM Throws : Returns : real number Args : real number =cut sub score { my $self = shift; $self->throw_not_implemented(); } =head2 start Title : start Usage : my $start=$instance->start; Function: Get/Set the position of the instance on the sequence used Throws : Returns : integer Args : integer =cut sub start { my $self = shift; $self->throw_not_implemented(); } =head2 relpos Title : relpos Usage : my $seqpos=$instance->relpos; Function: Get/Set the relative position of the instance with respect to the transcription start site (if known). Can and usually is negative. Throws : Returns : integer Args : integer =cut sub relpos { my $self = shift; $self->throw_not_implemented(); } =head2 minstance Title : minstance Usage : my $minstance=$misntance->score; Function: Get/Set the unique identifier- sequence id/motif id, for example PRM1_TATAbox. Not necessarily human readable. Throws : Returns : string Args : string =cut sub minstance { my $self = shift; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Matrix/PSM/ProtMatrix.pm000444000766000024 6373713155576320 20636 0ustar00cjfieldsstaff000000000000#--------------------------------------------------------- =head1 NAME Bio::Matrix::PSM::ProtMatrix - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information. =head1 SYNOPSIS use Bio::Matrix::PSM::ProtMatrix; # Create from memory by supplying probability matrix hash both as strings or # arrays where the frequencies Hash entries of the form lN refer to an array # of position-specific log-odds scores for amino acid N. Hash entries of the # form pN represent the position-specific probability of finding amino acid N. my %param = ( 'id' => 'A. thaliana protein atp1', '-e_val' => $score, 'lS' => [ '-2', '3', '-3', '2', '-3', '1', '1', '3' ], 'lF' => [ '-1', '-4', '0', '-5', '0', '-5', '-4', '-4' ], 'lT' => [ '-1', '1', '0', '1', '-2', '-1', '0', '1' ], 'lN' => [ '-3', '-1', '-2', '3', '-5', '5', '-2', '0' ], 'lK' => [ '-2', '0', '-3', '2', '-3', '2', '-3', '-1' ], 'lY' => [ '-2', '-3', '-3', '-4', '-3', '-4', '-4', '-4' ], 'lE' => [ '-3', '4', '-3', '2', '-4', '-2', '-3', '2' ], 'lV' => [ '0', '-2', '1', '-4', '1', '-4', '-1', '-3' ], 'lQ' => [ '-1', '0', '-2', '3', '-4', '1', '-3', '0' ], 'lM' => [ '8', '-3', '8', '-3', '1', '-3', '-3', '-3' ], 'lC' => [ '-2', '-3', '-3', '-4', '-3', '-4', '-3', '-3' ], 'lL' => [ '1', '-3', '1', '-4', '3', '-4', '-2', '-4' ], 'lA' => [ '-2', '1', '-2', '0', '-2', '-2', '2', '2' ], 'lW' => [ '-2', '-4', '-3', '-5', '-4', '-5', '-5', '-5' ], 'lP' => [ '-3', '-2', '-4', '-3', '-1', '-3', '6', '-3' ], 'lH' => [ '-2', '-2', '-3', '-2', '-5', '-2', '-2', '-3' ], 'lD' => [ '-4', '-1', '-3', '1', '-3', '-1', '-3', '4' ], 'lR' => [ '-2', '-1', '-3', '0', '-4', '4', '-4', '-3' ], 'lI' => [ '0', '-3', '0', '-4', '6', '-4', '-2', '-2' ], 'lG' => [ '-4', '-2', '-4', '-2', '-5', '-3', '-1', '-2' ], 'pS' => [ '0', '33', '0', '16', '1', '12', '11', '25' ], 'pF' => [ '0', '0', '2', '0', '3', '0', '0', '0' ], 'pT' => [ '0', '8', '7', '10', '1', '2', '7', '8' ], 'pN' => [ '0', '0', '2', '13', '0', '36', '1', '4' ], 'pK' => [ '0', '5', '0', '13', '1', '15', '0', '2' ], 'pY' => [ '0', '0', '0', '0', '0', '0', '0', '0' ], 'pE' => [ '0', '41', '1', '12', '0', '0', '0', '15' ], 'pV' => [ '0', '3', '9', '0', '2', '0', '3', '1' ], 'pQ' => [ '0', '0', '0', '15', '0', '4', '0', '3' ], 'pM' => [ '100', '0', '66', '0', '2', '0', '0', '0' ], 'pC' => [ '0', '0', '0', '0', '0', '0', '0', '0' ], 'pL' => [ '0', '0', '8', '0', '25', '0', '4', '0' ], 'pA' => [ '0', '10', '1', '9', '2', '0', '22', '16' ], 'pW' => [ '0', '0', '0', '0', '0', '0', '0', '0' ], 'pP' => [ '0', '0', '0', '0', '3', '1', '45', '0' ], 'pH' => [ '0', '0', '0', '0', '0', '0', '1', '0' ], 'pD' => [ '0', '0', '1', '7', '2', '2', '0', '22' ], 'pR' => [ '0', '0', '0', '3', '0', '27', '0', '0' ], 'pI' => [ '0', '0', '3', '0', '59', '1', '2', '3' ], 'pG' => [ '0', '0', '0', '1', '0', '0', '4', '1' ], ); my $matrix = Bio::Matrix::PSM::ProtMatrix( %param ); my $site = Bio::Matrix::PSM::ProtMatrix->new(%param); # Or get it from a file: use Bio::Matrix::PSM::IO; my $psmIO = Bio::Matrix::PSM::IO->new(-file => $file, -format => 'psi-blast'); while (my $psm = $psmIO->next_psm) { #Now we have a Bio::Matrix::PSM::Psm object, # see Bio::Matrix::PSM::PsmI for details #This is a Bio::Matrix::PSM::ProtMatrix object now my $matrix = $psm->matrix; } # Get a simple consensus, where alphabet is: # {A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V,} # choosing the highest probability or N if prob is too low my $consensus = $site->consensus; # Retrieving and using regular expressions: my $regexp = $site->regexp; my $count = grep($regexp,$seq); my $count = ($seq=~ s/$regexp/$1/eg); print "Motif $mid is present $count times in this sequence\n"; =head1 DESCRIPTION ProtMatrix is designed to provide some basic methods when working with position scoring (weight) matrices related to protein sequences. A protein PSM consists of 20 vectors with 20 frequencies (one per amino acid per position). This is the minimum information you should provide to construct a PSM object. The vectors can be provided as strings with frequencies where the frequency is {0..a} and a=1. This is the way MEME compressed representation of a matrix and it is quite useful when working with relational DB. If arrays are provided as an input (references to arrays actually) they can be any number, real or integer (frequency or count). When creating the object the constructor will check for positions that equal 0. If such is found it will increase the count for all positions by one and recalculate the frequency. Potential bug - if you are using frequencies and one of the positions is 0 it will change significantly. However, you should never have frequency that equals 0. Throws an exception if: You mix as an input array and string (for example A matrix is given as array, C - as string). The position vector is (0,0,0,0). One of the probability vectors is shorter than the rest. Summary of the methods I use most frequently (details below): iupac - return IUPAC compliant consensus as a string score - Returns the score as a real number IC - information content. Returns a real number id - identifier. Returns a string accession - accession number. Returns a string next_pos - return the sequence probably for each letter, IUPAC symbol, IUPAC probability and simple sequence consenus letter for this position. Rewind at the end. Returns a hash. pos - current position get/set. Returns an integer. regexp - construct a regular expression based on IUPAC consensus. For example AGWV will be [Aa][Gg][AaTt][AaCcGg] width - site width get_string - gets the probability vector for a single base as a string. get_array - gets the probability vector for a single base as an array. get_logs_array - gets the log-odds vector for a single base as an array. New methods, which might be of interest to anyone who wants to store PSM in a relational database without creating an entry for each position is the ability to compress the PSM vector into a string with losing usually less than 1% of the data. this can be done with: my $str=$matrix->get_compressed_freq('A'); or my $str=$matrix->get_compressed_logs('A'); Loading from a database should be done with new, but is not yet implemented. However you can still uncompress such string with: my @arr=Bio::Matrix::PSM::_uncompress_string ($str,1,1); for PSM or my @arr=Bio::Matrix::PSM::_uncompress_string ($str,1000,2); for log odds =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - James Thompson Email tex@biosysadmin.com =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::ProtMatrix; use strict; use base qw(Bio::Root::Root Bio::Matrix::PSM::SiteMatrixI); =head2 new Title : new Usage : my $site = Bio::Matrix::PSM::ProtMatrix->new( %probs, %logs, -IC => $ic, -e_val => $score, -id => $mid -model => \%model ); Function : Creates a new Bio::Matrix::PSM::ProtMatrix object from memory Throws : If inconsistent data for all vectors (all 20 amino acids) is provided, if you mix input types (string vs array) or if a position freq is 0. Example : Returns : Bio::Matrix::PSM::ProtMatrix object Args : Hash references to log-odds scores and probabilities for position-specific scoring info, e-value (optional), information content (optional), id (optional), model for background distribution of proteins (optional). =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my $consensus; #Too many things to rearrange, and I am creating simultanuously >500 # such objects routinely, so this becomes performance issue my %input; while( @args ) { (my $key = shift @args) =~ s/-//gi; #deletes all dashes (only dashes)! $input{$key} = shift @args; } # get a protein alphabet for processing log-odds scores and probabilities # maybe change this later on to allow for non-standard aa lists? my @alphabet = qw/A R N D C Q E G H I L K M F P S T W Y V/; foreach my $aa (@alphabet) { $self->{"log$aa"} = defined($input{"l$aa"}) ? $input{"l$aa"} : $self->throw("Error: No log-odds information for $aa!"); $self->{"prob$aa"} = defined($input{"p$aa"}) ? $input{"p$aa"} : $self->throw("Error: No probability information for $aa!"); } $self->{_position} = 0; $self->{IC} = $input{IC}; $self->{e_val} = $input{e_val}; $self->{sites} = $input{sites}; $self->{width} = $input{width}; $self->{accession_number} = $input{accession_number}; $self->{_correction} = defined($input{correction}) ? $input{correction} : 1 ; # Correction might be unwanted- supply your own # No id provided, null for the sake of rel db $self->{id} = defined($input{id}) ? $input{id} : 'null'; $self->{_alphabet} = \@alphabet; #Make consensus, throw if any one of the vectors is shorter $self = _calculate_consensus($self,$input{model}); return $self; } =head2 alphabet Title : Returns an array (or array reference if desired) to the alphabet Usage : Function : Returns an array (or array reference) containing all of the allowable characters for this matrix. Throws : Example : Returns : Array or arrary reference. Args : =cut sub alphabet { my $self = shift; if ( wantarray ) { return $self->{_alphabet}; } else { return @{$self->{_alphabet}}; } } =head2 _calculate_consensus Title : _calculate_consensus Usage : Function : Calculates the consensus sequence for this matrix. Throws : Example : Returns : Args : =cut sub _calculate_consensus { my $self = shift; my $thresh = shift; # verify that all of the array lengths in %probs are the same my @lengths = map { scalar(@$_) } map {$self->{"prob$_"}} @{ $self->{_alphabet} }; my $len = shift @lengths; for ( @lengths ) { if ( $_ ne $len ) { $self->throw( "Probability matrix is damaged!\n" ) }; } # iterate over probs, generate the most likely sequence and put it into # $self->{seq}. Put the probability of this sequence into $self->{seqp}. for ( my $i = 0; $i < $len; $i++ ) { # get a list of all the probabilities at position $i, ordered by $self->{_alphabet} my @probs = map { ${$self->{"prob$_"}}[$i] } @{ $self->{_alphabet} }; # calculate the consensus of @probs, put sequence into seqp and probabilities into seqp (${$self->{seq}}[$i],${$self->{seqp}}[$i]) = $self->_to_cons( @probs, $thresh ); } return $self; } =head2 next_pos Title : next_pos Usage : Function : Retrieves the next position features: frequencies for all 20 amino acids, log-odds scores for all 20 amino acids at this position, the main (consensus) letter at this position, the probability for the consensus letter to occur at this position and the relative current position as an integer. Throws : Example : Returns : hash (or hash reference) (pA,pR,pN,pD,...,logA,logR,logN,logD,aa,prob,rel) - pN entries represent the probability for amino acid N to be at this position - logN entries represent the log-odds score for having amino acid N at this position - aa is the consensus amino acid - prob is the probability for the consensus amino acid to be at this position - rel is the relative index of the current position (integer) Args : none =cut sub next_pos { my $self = shift; $self->throw("instance method called on class") unless ref $self; my $len = @{$self->{seq}}; my $pos = $self->{_position}; # return a PSM if we're still within range if ($pos<$len) { my %probs = map { ("p$_", ${$self->{"prob$_"}}[$pos]) } @{$self->{_alphabet}}; my %logs = map { ("l$_", ${$self->{"log$_"}}[$pos]) } @{$self->{_alphabet}}; my $base = ${$self->{seq}}[$pos]; my $prob = ${$self->{seqp}}[$pos]; $self->{_position}++; my %hash = ( %probs, %logs, base => $base, rel => $pos, prob => $prob ); # decide whether to return the hash or a reference to it if ( wantarray ) { return %hash; } else { return \%hash; } } else { # otherwise, reset $self->{_position} and return nothing $self->{_position} = 0; return; } } =head2 curpos Title : curpos Usage : Function : Gets/sets the current position. Throws : Example : Returns : Current position (integer). Args : New position (integer). =cut sub curpos { my $self = shift; if (@_) { $self->{_position} = shift; } return $self->{_position}; } =head2 e_val Title : e_val Usage : Function : Gets/sets the e-value Throws : Example : Returns : Args : real number =cut sub e_val { my $self = shift; if (@_) { $self->{e_val} = shift; } return $self->{e_val}; } =head2 IC Title : IC Usage : Function : Position-specific information content. Throws : Example : Returns : Information content for current position. Args : Information content for current position. =cut sub IC { my $self = shift; if (@_) { $self->{IC} = shift; } return $self->{IC}; } =head2 accession_number Title : accession_number Usage : Function: accession number, this will be unique id for the ProtMatrix object as well for any other object, inheriting from ProtMatrix. Throws : Example : Returns : New accession number (string) Args : Accession number (string) =cut sub accession_number { my $self = shift; if (@_) { $self->{accession_number} = shift; } return $self->{accession_number}; } =head2 consensus Title : consensus Usage : Function : Returns the consensus sequence for this PSM. Throws : if supplied with thresold outisde 5..10 range Example : Returns : string Args : (optional) threshold value 5 to 10 (corresponds to 50-100% at each position =cut sub consensus { my $self = shift; my $thresh=shift; $self->_calculate_consensus($thresh) if ($thresh); #Change of threshold my $consensus=''; foreach my $letter (@{$self->{seq}}) { $consensus .= $letter; } return $consensus; } sub IUPAC { my $self = shift; return $self->consensus; } =head2 get_string Title : get_string Usage : Function: Returns given probability vector as a string. Useful if you want to store things in a rel database, where arrays are not first choice Throws : If the argument is outside {A,C,G,T} Example : Returns : string Args : character {A,C,G,T} =cut sub get_string { my $self = shift; my $base = shift; my $string = ''; my @prob = @{$self->{"prob$base"}}; if ( ! @prob ) { $self->throw( "No such base: $base\n"); } foreach my $prob (@prob) { my $corrected = $prob*10; my $next = sprintf("%.0f",$corrected); $next = 'a' if ($next eq '10'); $string .= $next; } return $string; } =head2 width Title : width Usage : Function : Returns the length of the site Throws : Example : Returns : number Args : =cut sub width { my $self = shift; my $width = @{$self->{probA}}; return $width; } =head2 get_array Title : get_array Usage : Function : Returns an array with frequencies for a specified amino acid. Throws : Example : Returns : Array representing frequencies for specified amino acid. Args : Single amino acid (character). =cut sub get_array { my $self = shift; my $letter = uc(shift); $self->throw ("No such base: $letter!\n") unless grep { /$letter/ } @{$self->{_alphabet}}; return @{$self->{"prob$letter"}}; } =head2 get_logs_array Title : get_logs_array Usage : Function : Returns an array with log_odds for a specified base Throws : Example : Returns : Array representing log-odds scores for specified amino acid. Args : Single amino acid (character). =cut sub get_logs_array { my $self = shift; my $letter = uc(shift); $self->throw ("No such base: $letter!\n") unless grep { /$letter/ } @{$self->{_alphabet}}; return @{$self->{"log$letter"}}; } =head2 id Title : id Usage : Function : Gets/sets the site id Throws : Example : Returns : string Args : string =cut sub id { my $self = shift; if (@_) { $self->{id} = shift; } return $self->{id}; } =head2 regexp Title : regexp Usage : Function : Returns a case-insensitive regular expression which matches the IUPAC convention. X's in consensus sequence will match anything. Throws : Example : Returns : string Args : Threshold for calculating consensus sequence (number in range 0-100 representing a percentage). Threshold defaults to 20. =cut sub regexp { my $self = shift; my $threshold = 20; if ( @_ ) { my $threshold = shift }; my @alphabet = @{$self->{_alphabet}}; my $width = $self->width; my (@regexp, $i); for ( $i = 0; $i < $width; $i++ ) { # get an array of the residues at this position with p > $threshold my @letters = map { uc($_).lc($_) } grep { $self->{"prob$_"}->[$i] >= $threshold } @alphabet; my $reg; if ( scalar(@letters) == 0 ) { $reg = '\.'; } else { $reg = '['.join('',@letters).']'; } push @regexp, $reg; } if ( wantarray ) { return @regexp; } else { return join '', @regexp; } } =head2 regexp_array Title : regexp_array Usage : Function : Returns an array of position-specific regular expressions. X's in consensus sequence will match anything. Throws : Example : Returns : Array of position-specific regular expressions. Args : Threshold for calculating consensus sequence (number in range 0-100 representing a percentage). Threshold defaults to 20. Notes : Simply calls regexp method in list context. =cut sub regexp_array { my $self = shift; return @{ $self->regexp }; } =head2 _compress_array Title : _compress_array Usage : Function : Will compress an array of real signed numbers to a string (ie vector of bytes) -127 to +127 for bi-directional(signed) and 0..255 for unsigned ; Throws : Example : Internal stuff Returns : String Args : array reference, followed by max value and direction (optional, defaults to 1), direction of 1 is unsigned, anything else is signed. =cut sub _compress_array { my ($array,$lm,$direct)=@_; my $str; return unless(($array) && ($lm)); $direct=1 unless ($direct); my $k1= ($direct==1) ? (255/$lm) : (127/$lm); foreach my $c (@{$array}) { $c=$lm if ($c>$lm); $c=-$lm if (($c<-$lm) && ($direct !=1)); $c=0 if (($c<0) && ($direct ==1)); my $byte=int($k1*$c); $byte=127+$byte if ($direct !=1);#Clumsy, should be really shift the bits my $char=chr($byte); $str.=$char; } return $str; } =head2 _uncompress_string Title : _uncompress_string Usage : Function : Will uncompress a string (vector of bytes) to create an array of real signed numbers (opposite to_compress_array) Throws : Example : Internal stuff Returns : string, followed by max value and direction (optional, defaults to 1), direction of 1 is unsigned, anything else is signed. Args : array =cut sub _uncompress_string { my ($str,$lm,$direct)=@_; my @array; return unless(($str) && ($lm)); $direct=1 unless ($direct); my $k1= ($direct==1) ? (255/$lm) : (127/$lm); while (my $c=chop($str)) { my $byte=ord($c); $byte=$byte-127 if ($direct !=1);#Clumsy, should be really shift the bits my $num=$byte/$k1; unshift @array,$num; } return @array; } =head2 get_compressed_freq Title : get_compressed_freq Usage : Function: A method to provide a compressed frequency vector. It uses one byte to code the frequence for one of the probability vectors for one position. Useful for relational database. Improvement of the previous 0..a coding. Throws : Example : my $strA=$self->get_compressed_freq('A'); Returns : String Args : char =cut sub get_compressed_freq { my $self=shift; my $base=shift; my $string=''; my @prob; BASE: { if ($base eq 'A') { @prob = @{$self->{probA}} unless (!defined($self->{probA})); last BASE; } if ($base eq 'G') { @prob = @{$self->{probG}} unless (!defined($self->{probG})); last BASE; } if ($base eq 'C') { @prob = @{$self->{probC}} unless (!defined($self->{probC})); last BASE; } if ($base eq 'T') { @prob = @{$self->{probT}} unless (!defined($self->{probT})); last BASE; } $self->throw ("No such base: $base!\n"); } my $str= _compress_array(\@prob,1,1); return $str; } =head2 sequence_match_weight Title : sequence_match_weight Usage : Function : This method will calculate the score of a match, based on the PSM if such is associated with the matrix object. Returns undef if no PSM data is available. Throws : if the length of the sequence is different from the matrix width Example : my $score=$matrix->sequence_match_weight('ACGGATAG'); Returns : Floating point Args : string =cut sub sequence_match_weight { my ($self,$seq)=@_; return unless ($self->{logA}); my $seqlen = length($seq); my $width = $self->width; $self->throw("Error: Input sequence size ($seqlen) not equal to PSM size ($width)!\n") unless (length($seq) == $self->width); my ($score,$i) = (0,0); foreach my $letter ( split //, $seq ) { # add up the score for this position $score += $self->{"log$letter"}->[$i]; $i++; } return $score; } =head2 _to_IUPAC Title : _to_IUPAC Usage : Function: Converts a single position to IUPAC compliant symbol and returns its probability. Currently returns the most likely amino acid/probability combination. Throws : Example : Returns : char, real number representing an amino acid and a probability. Args : real numbers for all 20 amino acids (ordered by alphabet contained in $self->{_alphabet}, minimum probability threshold. =cut sub _to_IUPAC { my ($self,@probs,$thresh) = @_; # provide a default threshold of 5, corresponds to 5% threshold for # inferring that the aa at any position is the true aa $thresh = 5 unless ( defined $thresh ); my ($IUPAC_aa,$max_prob) = ('X',$thresh); for my $aa ( @{$self->{_alphabet}} ) { my $prob = shift @probs; if ( $prob > $max_prob ) { $IUPAC_aa = $aa; $max_prob = $prob; } } return $IUPAC_aa, $max_prob; } =head2 _to_cons Title : _to_cons Usage : Function: Converts a single position to simple consensus character and returns its probability. Currently just calls the _to_IUPAC subroutine. Throws : Example : Returns : char, real number Args : real numbers for A,C,G,T (positional) =cut sub _to_cons { return _to_IUPAC( @_ ); } =head2 get_all_vectors Title : get_all_vectors Usage : Function : returns all possible sequence vectors to satisfy the PFM under a given threshold Throws : If threshold outside of 0..1 (no sense to do that) Example : my @vectors = $self->get_all_vectors(4); Returns : Array of strings Args : (optional) floating =cut #sub get_all_vectors { # my $self = shift; # my $thresh = shift; # # $self->throw("Out of range. Threshold should be >0 and 1<.\n") if (($thresh<0) || ($thresh>1)); # # my @seq = split(//,$self->consensus($thresh*10)); # my @perm; # for my $i (0..@{$self->{probA}}) { # push @{$perm[$i]},'A' if ($self->{probA}->[$i]>$thresh); # push @{$perm[$i]},'C' if ($self->{probC}->[$i]>$thresh); # push @{$perm[$i]},'G' if ($self->{probG}->[$i]>$thresh); # push @{$perm[$i]},'T' if ($self->{probT}->[$i]>$thresh); # push @{$perm[$i]},'N' if ($seq[$i] eq 'N'); # } # my $fpos=shift @perm; # my @strings=@$fpos; # foreach my $pos (@perm) { # my @newstr; # foreach my $let (@$pos) { # foreach my $string (@strings) { # my $newstring = $string . $let; # push @newstr,$newstring; # } # } # @strings=@newstr; # } # return @strings; #} 1; BioPerl-1.007002/Bio/Matrix/PSM/ProtPsm.pm000444000766000024 1756013155576320 20122 0ustar00cjfieldsstaff000000000000#--------------------------------------------------------- #ISA ProtMatrix, HAS InstanceSite =head1 NAME Bio::Matrix::PSM::ProtPsm - handle combination of site matricies =head1 SYNOPSIS use Bio::Matrix::PSM::IO; #To get a ProtPsm object from a file use the Psm parser: my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'psiblast', -file=>$file); # Now go through all entities in the file with next_psm, which # returns a Psm object see Bio::Matrix::PSM::IO for detailed # documentation (matrix predictions or matrix sequence matches or # both): while (my $psm=$psmIO->next_psm) { my %psm_header = $psm->header; my $ic = $psm_header{IC}; my $sites = $psm_header{sites}; my $width = $psm_header{width}; my $score = $psm_header{e_val}; my $IUPAC = $psm->IUPAC; my $instances = $psm->instances; foreach my $instance (@{$instances}) { my $id = $instance->primary_id; #Do something with the id } } =head1 DESCRIPTION To handle a combination of site matrices and/or their corresponding sequence matches (instances). This object inherits from Bio::Matrix::PSM::ProtMatrix, so you can methods from that class. It may hold also an array of Bio::Matrix::PSM::InstanceSite object, but you will have to retrieve these through Bio::Matrix::PSM::ProtPsm-Einstances method (see below). To some extent this is an expanded ProtMatrix object, holding data from analysis that also deal with sequence matches of a particular matrix. =head2 DESIGN ISSUES This does not make too much sense to me I am mixing PSM with PSM sequence matches Though they are very closely related, I am not satisfied by the way this is implemented here. Heikki suggested different objects when one has something like meme But does this mean we have to write a different objects for mast, meme, transfac, theiresias, etc.? To me the best way is to return SiteMatrix object + arrray of InstanceSite objects and then mast will return undef for SiteMatrix and transfac will return undef for InstanceSite. Probably I cannot see some other design issues that might arise from such approach, but it seems more straightforward. Hilmar does not like this because it is an exception from the general BioPerl rules. Should I leave this as an option? Also the header rightfully belongs the driver object, and could be retrieved as hashes. I do not think it can be done any other way, unless we want to create even one more object with very unclear content. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - James Thompson Email tex@biosysadmin.com =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 SEE ALSO ProtMatrix, meme, transfac, psiblast, InstanceSite =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::ProtPsm; use Bio::Matrix::PSM::InstanceSite; use strict; use base qw(Bio::Matrix::PSM::ProtMatrix Bio::Matrix::PSM::PsmI Bio::Annotation::Collection); @Bio::Matrix::PSM::Psm::HEADER = qw(e_val sites IC width); =head2 new Title : new Usage : my $psm = Bio::Matrix::PSM::ProtPsm->new( -pS => [ '0', '33', '0', '16', '1', '12', '11', '25' ], -pF => [ '0', '0', '2', '0', '3', '0', '0', '0' ], -pT => [ '0', '8', '7', '10', '1', '2', '7', '8' ], -pN => [ '0', '0', '2', '13', '0', '36', '1', '4' ], -pK => [ '0', '5', '0', '13', '1', '15', '0', '2' ], -pY => [ '0', '0', '0', '0', '0', '0', '0', '0' ], -pE => [ '0', '41', '1', '12', '0', '0', '0', '15' ], -pV => [ '0', '3', '9', '0', '2', '0', '3', '1' ], -pQ => [ '0', '0', '0', '15', '0', '4', '0', '3' ], -pM => [ '100', '0', '66', '0', '2', '0', '0', '0' ], -pC => [ '0', '0', '0', '0', '0', '0', '0', '0' ], -pL => [ '0', '0', '8', '0', '25', '0', '4', '0' ], -pA => [ '0', '10', '1', '9', '2', '0', '22', '16' ], -pW => [ '0', '0', '0', '0', '0', '0', '0', '0' ], -pP => [ '0', '0', '0', '0', '3', '1', '45', '0' ], -pH => [ '0', '0', '0', '0', '0', '0', '1', '0' ], -pD => [ '0', '0', '1', '7', '2', '2', '0', '22' ], -pR => [ '0', '0', '0', '3', '0', '27', '0', '0' ], -pI => [ '0', '0', '3', '0', '59', '1', '2', '3' ], -pG => [ '0', '0', '0', '1', '0', '0', '4', '1' ], -IC => $ic, -sites => $istes, -width => $width, -e_val => $e_val, -instances => $instances, } Function: Creates a new Bio::Matrix::PSM::ProtPsm object Throws : Example : Returns : Bio::Matrix::PSM::Psm object Args : hash =cut sub new { my ($caller,@args) = @_; my $class = ref($caller) || $caller; my $self = $class->SUPER::new(@args); $self->{'_annotation'} = {}; #Init from Annotation::Collection $self->_typemap(Bio::Annotation::TypeManager->new()); #same ($self->{instances})=$self->_rearrange(['INSTANCES'], @args); return $self; } =head2 instances Title : instances Usage : my @instances=@{$psm->instances}; Function: Gets/sets the instances (Bio::Matrix::PSM::InstanceSite objects) associated with the Psm object Throws : Example : Returns : array reference (Bio::Matrix::PSM::InstanceSite objects) Args : array reference (Bio::Matrix::PSM::InstanceSite objects) =cut sub instances { my $self = shift; my $prev = $self->{instances}; if (@_) { $self->{instances} = shift; } return $prev; } =head2 header Title : header Usage : my %header=$psm->header; my $ic=$psm->header('IC'); Function: Gets the general information, common for most files, dealing with PSM such as information content (IC), score (e-value, etc.), number of sites (sites) and width. This list may expand. The current list should be in @Bio::Matrix::PSM::Psm::HEADER. Returns an epty list if an argument is supplied that is not in @Bio::Matrix::PSM::meme::HEADER. Throws : Example : Returns : hash or string Args : string (IC, e_val...) =cut sub header { my $self = shift; return if ($self->{end}); my %header; if (@_) {my $key=shift; return $self->{$key}; } foreach my $key (@Bio::Matrix::PSM::ProtPsm::HEADER) { $header{$key}=$self->{$key}; } return %header; } =head2 matrix Title : matrix Usage : my $matrix = $psm->matrix; Function: Gets/sets the SiteMatrix related information Throws : Example : Returns : Bio::Matrix::PSM::SiteMatrix objects Args : Bio::Matrix::PSM::SiteMatrix objects =cut sub matrix { my $self = shift; if (@_) { my $matrix = shift; my @alphabet = $self->alphabet; foreach my $char (@alphabet) { $self->{"log$char"} = $matrix->{"log$char"}; $self->{"prob$char"} = $matrix->{"prob$char"}; } $self->{IC} = $matrix->IC; $self->{e_val} = $matrix->e_val; $self->{id} = $matrix->id; } return $self; } 1; BioPerl-1.007002/Bio/Matrix/PSM/Psm.pm000444000766000024 1641213155576320 17250 0ustar00cjfieldsstaff000000000000#--------------------------------------------------------- #ISA SiteMatrix, HAS InstanceSite =head1 NAME Bio::Matrix::PSM::Psm - handle combination of site matricies =head1 SYNOPSIS use Bio::Matrix::PSM::IO; #To get a Psm object from a file use the Psm parser: my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'meme', -file=>$file); # Now go through all entities in the file with next_psm, which # returns a Psm object see Bio::Matrix::PSM::IO for detailed # documentation (matrix predictions or matrix sequence matches or # both): while (my $psm=$psmIO->next_psm) { my %psm_header=$psm->header; my $ic=$psm_header{IC}; my $sites=$psm_header{sites}; my $width=$psm_header{width}; my $score=$psm_header{e_val}; my $IUPAC=$psm->IUPAC; my $instances=$psm->instances; foreach my $instance (@{$instances}) { my $id=$instance->primary_id; #Do something with the id } } #or create from memmory: my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT, -id=>$id, -instances=>$instances, -e_val=>$e_val, -IC=>$ic, -width=>$width, -sites=>$sites) # where pA through pG are the respective frequencies of the matrix (see also # Bio::Matrix::PSM::SiteMatrix), and everything else is self-explenatory, # except for -instances (reference to an array of # Bio::Matrix::PSM::InstanceSite objects) which is documented below. =head1 DESCRIPTION To handle a combination of site matrices and/or their corresponding sequence matches (instances). This object inherits from Bio::Matrix::PSM::SiteMatrix, so you can use the respective methods. It may hold also an array of Bio::Matrix::PSM::InstanceSite object, but you will have to retrieve these through Bio::Matrix::PSM::Psm-Einstances method (see below). To some extent this is an expanded SiteMatrix object, holding data from analysis that also deal with sequence matches of a particular matrix. =head2 DESIGN ISSUES This does not make too much sense to me I am mixing PSM with PSM sequence matches Though they are very closely related, I am not satisfied by the way this is implemented here. Heikki suggested different objects when one has something like meme But does this mean we have to write a different objects for mast, meme, transfac, theiresias, etc.? To me the best way is to return SiteMatrix object + arrray of InstanceSite objects and then mast will return undef for SiteMatrix and transfac will return undef for InstanceSite. Probably I cannot see some other design issues that might arise from such approach, but it seems more straightforward. Hilmar does not like this because it is an exception from the general BioPerl rules Should I leave this as an option? Also the header rightfully belongs the driver object, and could be retrieved as hashes. I do not think it can be done any other way, unless we want to create even one more object with very unclear content. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 SEE ALSO SiteMatrix, meme, transfac, InstanceSite =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::Psm; use Bio::Matrix::PSM::InstanceSite; use strict; use base qw(Bio::Matrix::PSM::SiteMatrix Bio::Matrix::PSM::PsmI Bio::Annotation::Collection); @Bio::Matrix::PSM::Psm::HEADER = qw(e_val sites IC width); =head2 new Title : new Usage : my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC, -pG=>\@pG,-pT=>\@pT,-id=>$id, -instances=>$instances, -e_val=>$e_val, -IC=>$ic, -width=>$width, -sites=>$sites) Function: Creates a new Bio::Matrix::PSM::Psm object Throws : Example : Returns : Bio::Matrix::PSM::Psm object Args : hash =cut sub new { my ($caller,@args) = @_; my $class = ref($caller) || $caller; my $self = $class->SUPER::new(@args); $self->{'_annotation'} = {}; #Init from Annotation::Collection $self->_typemap(Bio::Annotation::TypeManager->new()); #same ($self->{instances})=$self->_rearrange(['INSTANCES'], @args); return $self; } =head2 instances Title : instances Usage : my @instances=@{$psm->instances}; Function: Gets/sets the instances (Bio::Matrix::PSM::InstanceSite objects) associated with the Psm object Throws : Example : Returns : array reference (Bio::Matrix::PSM::InstanceSite objects) Args : array reference (Bio::Matrix::PSM::InstanceSite objects) =cut sub instances { my $self = shift; my $prev = $self->{instances}; if (@_) { $self->{instances} = shift; } return $prev; } =head2 header Title : header Usage : my %header=$psm->header; my $ic=$psm->header('IC'); Function: Gets the general information, common for most files, dealing with PSM such as information content (IC), score (e-value, etc.), number of sites (sites) and width. This list may expand. The current list should be in @Bio::Matrix::PSM::Psm::HEADER. Returns undef if an argument is supplied that is not in @Bio::Matrix::PSM::meme::HEADER. Throws : Example : Returns : hash or string Args : string (IC, e_val...) =cut sub header { my $self = shift; return if ($self->{end}); my %header; if (@_) {my $key=shift; return $self->{$key}; } foreach my $key (@Bio::Matrix::PSM::Psm::HEADER) { $header{$key}=$self->{$key}; } return %header; } =head2 matrix Title : matrix Usage : my $matrix=$psm->matrix; Function: Gets/sets the SiteMatrix related information Throws : Example : Returns : Bio::Matrix::PSM::SiteMatrix objects Args : Bio::Matrix::PSM::SiteMatrix objects =cut sub matrix { my $self = shift; my $prev = Bio::Matrix::PSM::SiteMatrix->new(-pA=>$self->{probA}, -pC=>$self->{probC}, -pG=>$self->{probG}, -pT=>$self->{probT}, -lA=>$self->{logA}, -lC=>$self->{logC}, -lG=>$self->{logG}, -lT=>$self->{logT}, -IC=>$self->{IC}, -e_val=>$self->{e_val}, -id=>$self->{id}); if (@_) { my $matrix=shift; $self->{IC} = $matrix->IC; $self->{probA}=$matrix->{probA}; $self->{probC}=$matrix->{probC}; $self->{probG}=$matrix->{probG}; $self->{probT}=$matrix->{probT}; $self->{e_val}=$matrix->e_val; $self->{id}=$matrix->id; } return $prev; } 1; BioPerl-1.007002/Bio/Matrix/PSM/PsmHeader.pm000444000766000024 1544013155576320 20361 0ustar00cjfieldsstaff000000000000 =head1 NAME Bio::Matrix::PSM::PsmHeader - PSM mast parser implementation =head1 SYNOPSIS # See Bio::Matrix::PSM::IO for detailed documentation on how to use # PSM parsers =head1 DESCRIPTION Parser for mast. This driver unlike meme or transfac for example is dedicated more to PSM sequence matches =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::PsmHeader; use Bio::Matrix::PSM::InstanceSite; use strict; use base qw(Bio::Root::Root Bio::Matrix::PSM::PsmHeaderI); #These define what structures within the @Bio::Matrix::PSM::PsmHeader::MASTHEADER=qw(html version release seq hid length instances unstructured); @Bio::Matrix::PSM::PsmHeader::MEMEHEADER=qw(html version release hid weight length unstructured); @Bio::Matrix::PSM::PsmHeader::TRANSFACHEADER=qw(unstructured version release); @Bio::Matrix::PSM::PsmHeader::PSIBLASTHEADER=qw(seq width ic); @Bio::Matrix::PSM::PsmHeader::ALLHEADER=qw(header release type version html release weight length id seq instances unstructured); =head2 new Title : new Usage : my $header= Bio::Matrix::PSM::PsmHeader->new(-seq=>\%seq, -mid=>\%mid, -width=>\%width, -instances=>\%instances, -header=>\@header, -type=>'mast'); Function: Creates a new Bio::Matrix::PSM::PsmHeader object Throws : Example : Returns : Bio::Matrix::PSM::PsmHeader object Args : hash =cut sub new { my ($class,@args)=@_; my $self = $class->SUPER::new(@args); return $self; } #parse version/release info here from the unstructured array sub _initialize { my $self = shift; my $type=ref($self); $type=~s/\w+:://g; $self->{_type} = $type; my $dat=join(" ",grep(/version|release/i,@{$self->{unstructured}})); if ($dat && ($dat=~/version\b/i)) { $self->{version}=substr($dat,$+[0]+1); $self->{version}=~s/\s.+[^\d\.\:\/]//g; $self->{version}=~s/^\D//; } if ($dat && ($dat=~/release\b/i)) { my $rel=substr($dat,$+[0]+1); $rel=~s/[^\d\.\:\/\-]//g; $rel=~s/^\D//; if ($rel=~/\d\d:\d\d:\d\d/) { #Reformat if time is available too my $time=substr($rel,$-[0]+1); my $dat= substr($rel,0,$-[0]); $self->{release}="$dat $time"; } else { $self->{release}=$rel; } } return $self; } =head2 seq Title : seq Usage : my %seq= $header->seq(); Function: Returns the sequence data as a hash, indexed by a sequence ID (motif id or accession number) In case the input data is a motif it would return the consenus seq for each of them (mast). Throws : Example : Returns : hash Args : =cut sub seq { my $self = shift; return () unless ($self->_check('seq')); return %{$self->{seq}}; } =head2 hid Title : hid Usage : my @hid= $header->hid(); Function: Returns array with the motif ids Throws : Example : Returns : array Args : =cut sub hid { my $self = shift; return unless ($self->_check('hid')); my @header=@{$self->{hid}}; return @header; } =head2 length Title : length Usage : my %length= $header->length(); Function: Returns the length of the input sequence or motifs as a hash, indexed by a sequence ID (motif id or accession number) Throws : Example : Returns : hash Args : =cut sub length { my $self = shift; return unless ($self->_check('length')); return $self->{length}; } =head2 instances Title : instances Usage : my %instances= $header->instances(); Function: Returns the info about the input data, contained in the header Throws : Example : Returns : hash Args : =cut sub instances { my $self = shift; return unless ($self->_check('instances')); return %{$self->{instances}}; } =head2 weight Title : weight Usage : my %weights= $header->weight(); Function: Returns the weights of the input sequence as a hash, indexed by a sequence ID Throws : Example : Returns : hash Args : =cut sub weight { my $self = shift; return () unless ($self->_check('weight')); return %{$self->{weight}}; } =head2 unstuctured Title : unstuctured Usage : my @unstructured= $header->unstuctured(); Function: Returns the unstructured data in the header as an array, one line per array element, all control symbols are removed with \W Throws : Example : Returns : array Args : =cut sub unstructured { my $self = shift; return @{$self->{unstructured}}; } =head2 version Title : version Usage : my $version= $header->version; Function: Returns the version of the file being parsed if such exists Throws : Example : Returns : string Args : =cut sub version { my $self = shift; return $self->{version}; } =head2 release Title : release Usage : my $release= $header->release; Function: Returns the release of the file being parsed if such exists Throws : Example : Returns : string Args : =cut sub release { my $self = shift; return $self->{release}; } =head2 _check Title : _check Usage : if ($self->_check('weights') { #do something} else {return 0;} Function: Checks if the method called is aplicable to the file format Throws : Example : Returns : boolean Args : string =cut sub _check { my ($self,$method) = @_; my $type= $self->{'_type'}; if ($type eq 'meme') { return 0 unless (grep(/$method/, @Bio::Matrix::PSM::PsmHeader::MEMEHEADER)); } elsif ($type eq 'mast') { return 0 unless (grep(/$method/, @Bio::Matrix::PSM::PsmHeader::MASTHEADER)); } elsif ($type eq 'transfac') { return 0 unless (grep(/$method/, @Bio::Matrix::PSM::PsmHeader::TRANSFACHEADER)); } elsif ($type eq 'psiblast') { return 0 unless (grep(/$method/, @Bio::Matrix::PSM::PsmHeader::PSIBLASTHEADER)); } return 1; } 1; BioPerl-1.007002/Bio/Matrix/PSM/PsmHeaderI.pm000444000766000024 1451313155576320 20472 0ustar00cjfieldsstaff000000000000#--------------------------------------------------------- =head1 NAME Bio::Matrix::PSM::PsmHeaderI - handles the header data from a PSM file =head1 SYNOPSIS use Bio::Matrix::PSM::IO; #Obtain an Bio::Matrix::PSM::IO object: my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'mast'); #Get some general data about the file you are parsing: my $release=$psmIO->release; my $version=$psmIO->version; print "This analysis was performed using MAST version $version, release $release\n"; #Now let's see what are the consensus sequences of the motifs fed as an input: my %seq=$psmIO->seq; #let's cycle through all consensus sequences now: foreach my $id ($psmIO->hid) { print "Motif $id is \t",$seq{$id},"\n"; } #Finally look at the stuff we do not parse: my @inputfile=grep(/datafile/i,$psmIO->unstructured); =head1 DESCRIPTION Generally you should not use this object directly, you can access the information through a PSM driver (See Bio::Matrix::PSM::IO). It is handling the header data from a PSM file which may be very different. This means that some of the methods will return undef naturally, because this information is not present in the file which is parsed. Some important data might be left over in the unstructured part, and you might have to parse it yourself. I will try to 'structure' this header more in the near future. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::PsmHeaderI; use Bio::Matrix::PSM::InstanceSite; use Bio::Matrix::PSM::Psm; use Bio::Matrix::PSM::IO; use strict; use base qw(Bio::Matrix::PSM::PsmI); #Accessor methods, based on the driver @Bio::Matrix::PSM::PsmHeader::MASTHEADER=qw(html version release seq hid length instances unstructured); @Bio::Matrix::PSM::PsmHeader::MEMEHEADER=qw(html version release hid weight length unstructured); @Bio::Matrix::PSM::PsmHeader::TRANSFACHEADER=qw(unstructured version release); @Bio::Matrix::PSM::PsmHeader::ALLHEADER=qw(header release type version html release weight length hid seq instances unstructured); =head2 new Title : new Usage : my $header= Bio::Matrix::PSM::PsmHeader->new ( -seq=>\%seq, -mid=>\%mid, -width=>\%width, -instances=>\%instances, -header=>\@header, -type=>'mast'); Function: Creates a new Bio::Matrix::PSM::PsmHeader object Throws : Example : Returns : Bio::Matrix::PSM::PsmHeaderI object Args : hash =cut =head2 seq Title : seq Usage : my %seq= $header->seq(); Function: Returns the sequence data as a hash, indexed by a sequence ID (motif id or accession number) In case the input data is a motif it would return the consenus seq for each of them (mast). Throws : Example : Returns : hash Args : =cut sub seq { my $self = shift; $self->throw_not_implemented(); } =head2 hid Title : hid Usage : my @ids= $header->hid(); Function: Returns array with the motif/instance ids Throws : Example : Returns : array Args : =cut sub hid { my $self = shift; $self->throw_not_implemented(); } =head2 length Title : length Usage : my %length= $header->length(); Function: Returns the length of the input sequence or motifs as a hash, indexed by a sequence ID (motif id or accession number) Throws : Example : Returns : hash Args : =cut sub length { my $self = shift; $self->throw_not_implemented(); } =head2 instances Title : instances Usage : my %instances= $header->length(); Function: Returns the instance, used as a hash, indexed by a sequence ID (motif id or accession number) Throws : Example : Returns : hash of Bio::Matrix::PSM::InstanceSite objects Args : =cut sub instances { my $self = shift; $self->throw_not_implemented(); } =head2 weights Title : weights Usage : my %weights= $header->weights(); Function: Returns the weights of the input sequence as a hash, indexed by a sequence ID Throws : Example : Returns : hash Args : =cut sub weights { my $self = shift; $self->throw_not_implemented(); } =head2 unstuctured Title : unstuctured Usage : my @unstructured= $header->unstuctured(); Function: Returns the unstructured data in the header as an array, one line per array element, all control symbols are removed with \W Throws : Example : Returns : array Args : =cut sub unstructured { my $self = shift; $self->throw_not_implemented(); } =head2 version Title : version Usage : my $version= $header->version; Function: Returns the version of the file being parsed if such exists Throws : Example : Returns : string Args : =cut sub version { my $self = shift; $self->throw_not_implemented(); } =head2 revision Title : revision Usage : my $revision= $header->revision; Function: Returns the revision of the file being parsed if such exists Throws : Example : Returns : string Args : =cut sub revision { my $self = shift; $self->throw_not_implemented(); } =head2 _check Title : _check Usage : if ($self->_check('weights') { #do something} else {return 0;} Function: Checks if the method called is aplicable to the file format Throws : Example : Returns : boolean Args : string =cut sub _check { my $self = shift; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Matrix/PSM/PsmI.pm000444000766000024 1454413155576320 17365 0ustar00cjfieldsstaff000000000000#--------------------------------------------------------- #ISA SiteMatrix, HAS InstanceSite =head1 NAME Bio::Matrix::PSM::PsmI - abstract interface to handler of site matricies =head1 SYNOPSIS use Bio::Matrix::PSM::IO; # To get a Psm object from a file use the Psm parser: my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'meme', -file=>$file); # Now go through all entities in the file with next_psm, which # returns a Psm object see Bio::Matrix::PSM::IO for detailed # documentation (matrix predictions or matrix sequence matches or # both): while (my $psm=$psmIO->next_psm) { my %psm_header=$psm->header; my $ic=$psm_header{IC}; my $sites=$psm_header{sites}; my $width=$psm_header{width}; my $score=$psm_header{e_val}; my $IUPAC=$psm->IUPAC; my $instances=$psm->instances; foreach my $instance (@{$instances}) { my $id=$instance->primary_id; #Do something with the id } } # or create from memmory: my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT, -id=>$id, -instances=>$instances, -e_val=>$e_val, -IC=>$ic, -width=>$width, -sites=>$sites) # where pA through pG are the respective frequencies of the matrix (see also # Bio::Matrix::PSM::SiteMatrix), and everything else is self-explenatory, # except for #-instances (reference to an array of Bio::Matrix::PSM::InstanceSite objects) # which is documented below. =head1 DESCRIPTION Supposed to handle a combination of site matrices and/or their corresponding sequence matches (instances). This object inherits from Bio::Matrix::PSM::SiteMatrix, so you can use the respective methods. It may hold also an array of Bio::Matrix::PSM::InstanceSite object, but you will have to retrieve these through Bio::Matrix::PSM::Psm-Einstances method (see below). To some extent this is an expanded SiteMatrix object, holding data from analysis that also deal with sequence matches of a particular matrix. =head2 DESIGN ISSUES This design is a bit of a compromise, so it might be a temporary solution I am mixing PSM with PSM sequence matches Though they are very closely related, I am not satisfied by the way this is implemented here. Heikki suggested different objects when one has something like meme But does this mean we have to write a different objects for mast, meme, transfac, theiresias, etc.? To me the best way is to return SiteMatrix object + arrray of InstanceSite objects and then mast will return undef for SiteMatrix and transfac will return undef for InstanceSite. Probably I cannot see some other design issues that might arise from such approach, but it seems more straightforward. Hilmar does not like this because it is an exception from the general BioPerl rules Should I leave this as an option? Also the header rightfully belongs the driver object, and could be retrieved as hashes. I do not think it can be done any other way, unless we want to create even one more object with very unclear content. =head1 SEE ALSO L, L, L, L =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::PsmI; use Bio::Matrix::PSM::SiteMatrix; use Bio::Matrix::PSM::InstanceSite; use strict; use base qw(Bio::Matrix::PSM::SiteMatrixI); =head2 new Title : new Usage : my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG, -pT=>\@pT,-id=>$id, -instances=>$instances, -e_val=>$e_val, -IC=>$ic, -width=>$width, -sites=>$sites) Function: Creates a new Bio::Matrix::PSM::Psm object Throws : Example : Returns : Bio::Matrix::PSM::Psm object Args : hash =cut sub new { my $self = shift; $self->throw_not_implemented(); } =head2 instances Title : instances Usage : my @instances=@{$psm->instances}; Function: Gets/sets the instances (Bio::Matrix::PSM::InstanceSite objects) associated with the Psm object Throws : Example : Returns : array reference (Bio::Matrix::PSM::InstanceSite objects) Args : array reference (Bio::Matrix::PSM::InstanceSite objects) =cut sub instances { my $self = shift; $self->throw_not_implemented(); } =head2 matrix Title : matrix Usage : my $matrix=$psm->matrix; Function: Gets/sets the SiteMatrix related information Throws : Example : Returns : Bio::Matrix::PSM::SiteMatrix objects Args : Bio::Matrix::PSM::SiteMatrix objects =cut sub matrix { my $self = shift; $self->throw_not_implemented(); } =head2 header Title : header Usage : my %header=$psm->header; my $ic=$psm->header('IC'); Function: Gets the general information, common for most files, dealing with PSM such as information content (IC), score (e-value, etc.), number of sites (sites) and width. This list may expand. The current list should be in @Bio::Matrix::PSM::Psm::HEADER. Returns undef if an argument is supplied that is not in @Bio::Matrix::PSM::meme::HEADER. Throws : Example : Returns : hash or string Args : string (IC, e_val...) =cut sub header { my $self = shift; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Matrix/PSM/SiteMatrix.pm000444000766000024 10001513155576320 20613 0ustar00cjfieldsstaff000000000000#--------------------------------------------------------- =head1 NAME Bio::Matrix::PSM::SiteMatrix - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds =head1 SYNOPSIS use Bio::Matrix::PSM::SiteMatrix; # Create from memory by supplying probability matrix hash # both as strings or arrays # where the frequencies $a,$c,$g and $t are supplied either as # arrayref or string. Accordingly, lA, lC, lG and lT are the log # odds (only as arrays, no checks done right now) my ($a,$c,$g,$t,$score,$ic, $mid)=@_; #or my ($a,$c,$g,$t,$score,$ic,$mid)=('05a011','110550','400001', '100104',0.001,19.2,'CRE1'); #Where a stands for all (this frequency=1), see explanation below my %param=(-pA=>$a,-pC=>$c,-pG=>$g,-pT=>$t, -lA=>$la, -lC=>$lc,-lG=>$lg,-lT=>$l, -IC=>$ic,-e_val=>$score, -id=>$mid); my $site=Bio::Matrix::PSM::SiteMatrix->new(%param); #Or get it from a file: use Bio::Matrix::PSM::IO; my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'transfac'); while (my $psm=$psmIO->next_psm) { #Now we have a Bio::Matrix::PSM::Psm object, # see Bio::Matrix::PSM::PsmI for details #This is a Bio::Matrix::PSM::SiteMatrix object now my $matrix=$psm->matrix; } # Get a simple consensus, where alphabet is {A,C,G,T,N}, # choosing the character that both satisfies a supplied or default threshold # frequency and is the most frequenct character at each position, or N. # So for the position with A, C, G, T frequencies of 0.5, 0.25, 0.10, 0.15, # the simple consensus character will be 'A', whilst for 0.5, 0.5, 0, 0 it # would be 'N'. my $consensus=$site->consensus; # Get the IUPAC ambiguity code representation of the data in the matrix. # Because the frequencies may have been pseudo-count corrected, insignificant # frequences (below 0.05 by default) are ignored. So a position with # A, C, G, T frequencies of 0.5, 0.5, 0.01, 0.01 will get the IUPAC code 'M', # while 0.97, 0.01, 0.01, 0.01 will get the code 'A' and # 0.25, 0.25, 0.25, 0.25 would get 'N'. my $iupac=$site->IUPAC; # Getting/using regular expression (a representation of the IUPAC string) my $regexp=$site->regexp; my $count=grep($regexp,$seq); my $count=($seq=~ s/$regexp/$1/eg); print "Motif $mid is present $count times in this sequence\n"; =head1 DESCRIPTION SiteMatrix is designed to provide some basic methods when working with position scoring (weight) matrices, such as transcription factor binding sites for example. A DNA PSM consists of four vectors with frequencies {A,C,G,T}. This is the minimum information you should provide to construct a PSM object. The vectors can be provided as strings with frequenciesx10 rounded to an int, going from {0..a} and 'a' represents the maximum (10). This is like MEME's compressed representation of a matrix and it is quite useful when working with relational DB. If arrays are provided as an input (references to arrays actually) they can be any number, real or integer (frequency or count). When creating the object you can ask the constructor to make a simple pseudo count correction by adding a number (typically 1) to all positions (with the -correction option). After adding the number the frequencies will be calculated. Only use correction when you supply counts, not frequencies. Throws an exception if: You mix as an input array and string (for example A matrix is given as array, C - as string). The position vector is (0,0,0,0). One of the probability vectors is shorter than the rest. Summary of the methods I use most frequently (details below): iupac - return IUPAC compliant consensus as a string score - Returns the score as a real number IC - information content. Returns a real number id - identifier. Returns a string accession - accession number. Returns a string next_pos - return the sequence probably for each letter, IUPAC symbol, IUPAC probability and simple sequence consenus letter for this position. Rewind at the end. Returns a hash. pos - current position get/set. Returns an integer. regexp - construct a regular expression based on IUPAC consensus. For example AGWV will be [Aa][Gg][AaTt][AaCcGg] width - site width get_string - gets the probability vector for a single base as a string. get_array - gets the probability vector for a single base as an array. get_logs_array - gets the log-odds vector for a single base as an array. New methods, which might be of interest to anyone who wants to store PSM in a relational database without creating an entry for each position is the ability to compress the PSM vector into a string with losing usually less than 1% of the data. this can be done with: my $str=$matrix->get_compressed_freq('A'); or my $str=$matrix->get_compressed_logs('A'); Loading from a database should be done with new, but is not yest implemented. However you can still uncompress such string with: my @arr=Bio::Matrix::PSM::_uncompress_string ($str,1,1); for PSM or my @arr=Bio::Matrix::PSM::_uncompress_string ($str,1000,2); for log odds =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 CONTRIBUTORS Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Matrix::PSM::SiteMatrix; use strict; use base qw(Bio::Root::Root Bio::Matrix::PSM::SiteMatrixI); =head2 new Title : new Usage : my $site=Bio::Matrix::PSM::SiteMatrix->new(-pA=>$a,-pC=>$c, -pG=>$g,-pT=>$t, -IC=>$ic, -e_val=>$score, -id=>$mid); Function: Creates a new Bio::Matrix::PSM::SiteMatrix object from memory Throws : If inconsistent data for all vectors (A,C,G and T) is provided, if you mix input types (string vs array) or if a position freq is 0. Returns : Bio::Matrix::PSM::SiteMatrix object Args : -pA => vector with the frequencies or counts of A -pC => vector for C -pG => vector for G -pt => vector for T -lA => vector for the log of A -lC => vector for the log of C -lG => vector for the log of G -lT => vector for the log of T -IC => real number, the information content of this matrix -e_val => real number, the expect value -id => string, an identifier -width => int, width of the matrix in nucleotides -sites => int, the number of sites that went into this matrix -model => hash ref, background frequencies for A, C, G and T -correction => number, the number to add to all positions to achieve pseudo count correction (default 0: no correction) NB: do not use correction when your input is frequences! -accession_number => string, an accession number Vectors can be strings of the frequencies where the frequencies are multiplied by 10 and rounded to the nearest whole number, and where 'a' is used to denote the maximal frequency 10. There should be no punctuation (spaces etc.) in the string. For example, 'a0501'. Alternatively frequencies or counts can be represented by an array ref containing the counts, frequencies or logs as any kind of number. =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my $consensus; # Too many things to rearrange, and I am creating simultanuously >500 # such objects routinely, so this becomes performance issue my %input; while (@args) { (my $key = shift @args) =~ s/-//g; #deletes all dashes (only dashes)! $input{$key} = shift @args; } $self->{_position} = 0; $self->{IC} = $input{IC}; $self->{e_val} = $input{e_val}; $self->{width} = $input{width}; $self->{logA} = $input{lA}; $self->{logC} = $input{lC}; $self->{logG} = $input{lG}; $self->{logT} = $input{lT}; $self->{sites} = $input{sites}; $self->{id} = $input{id} || 'null'; $self->{correction} = $input{correction} || 0; $self->{accession_number} = $input{accession_number}; return $self unless (defined($input{pA}) && defined($input{pC}) && defined($input{pG}) && defined($input{pT})); # This should go to _initialize? # Check for input type- no mixing alllowed, throw ex if (ref($input{pA}) =~ /ARRAY/i ) { $self->throw("Mixing matrix data types not allowed: C is not reference") unless(ref($input{pC})); $self->throw("Mixing matrix data types not allowed: G is not reference") unless (ref($input{pG})); $self->throw("Mixing matrix data types not allowed: T is not reference") unless (ref($input{pT})); $self->{probA} = $input{pA}; $self->{probC} = $input{pC}; $self->{probG} = $input{pG}; $self->{probT} = $input{pT}; } else { $self->throw("Mixing matrix data types not allowed: C is reference") if (ref($input{pC})); $self->throw("Mixing matrix data types not allowed: G is reference") if (ref($input{pG})); $self->throw("Mixing matrix data types not allowed: T is reference") if (ref($input{pT})); $self->{probA} = [split(//,$input{pA})]; $self->{probC} = [split(//,$input{pC})]; $self->{probG} = [split(//,$input{pG})]; $self->{probT} = [split(//,$input{pT})]; for (my $i=0; $i<= @{$self->{probA}}+1; $i++) { # we implictely assume these are MEME-style frequencies x 10, so # 'a' represents the 'maximum', 10. Other positions can actually # add up to over 10 due to rounding, but I don't think that is a # problem? if (${$self->{probA}}[$i] and ${$self->{probA}}[$i] eq 'a') { ${$self->{probA}}[$i]='10'; } if (${$self->{probC}}[$i] and ${$self->{probC}}[$i] eq 'a') { ${$self->{probC}}[$i]='10'; } if (${$self->{probG}}[$i] and ${$self->{probG}}[$i] eq 'a') { ${$self->{probG}}[$i]='10'; } if (${$self->{probT}}[$i] and ${$self->{probT}}[$i] eq 'a') { ${$self->{probT}}[$i]='10'; } } } # Check for position with 0 for all bases, throw exception if so for (my $i=0;$i <= $#{$self->{probA}}; $i++) { if ((${$self->{probA}}[$i] + ${$self->{probC}}[$i] + ${$self->{probG}}[$i] + ${$self->{probT}}[$i]) == 0) { $self->throw("Position meaningless-all frequencies are 0"); } # apply pseudo-count correction to all values - this will result in # very bad frequencies if the input is already frequences and a # correction value as large as 1 is used! if ($self->{correction}) { ${$self->{probA}}[$i] += $self->{correction}; ${$self->{probC}}[$i] += $self->{correction}; ${$self->{probG}}[$i] += $self->{correction}; ${$self->{probT}}[$i] += $self->{correction}; } # (re)calculate frequencies my $div= ${$self->{probA}}[$i] + ${$self->{probC}}[$i] + ${$self->{probG}}[$i] + ${$self->{probT}}[$i]; ${$self->{probA}}[$i]=${$self->{probA}}[$i]/$div; ${$self->{probC}}[$i]=${$self->{probC}}[$i]/$div; ${$self->{probG}}[$i]=${$self->{probG}}[$i]/$div; ${$self->{probT}}[$i]=${$self->{probT}}[$i]/$div; } # Calculate the logs if ((!defined($self->{logA})) && ($input{model})) { $self->calc_weight($input{model}); } # Make consensus, throw if any one of the vectors is shorter $self->_calculate_consensus; return $self; } =head2 _calculate_consensus Title : _calculate_consensus Function: Internal stuff =cut sub _calculate_consensus { my $self=shift; my ($lc,$lt,$lg)=($#{$self->{probC}},$#{$self->{probT}},$#{$self->{probG}}); my $len=$#{$self->{probA}}; $self->throw("Probability matrix is damaged for C: $len vs $lc") if ($len != $lc); $self->throw("Probability matrix is damaged for T: $len vs $lt") if ($len != $lt); $self->throw("Probability matrix is damaged for G: $len vs $lg") if ($len != $lg); for (my $i=0; $i<$len+1; $i++) { #*** IUPACp values not actually used (eg. by next_pos) (${$self->{IUPAC}}[$i],${$self->{IUPACp}}[$i])=_to_IUPAC(${$self->{probA}}[$i], ${$self->{probC}}[$i], ${$self->{probG}}[$i], ${$self->{probT}}[$i]); (${$self->{seq}}[$i], ${$self->{seqp}}[$i]) = _to_cons(${$self->{probA}}[$i], ${$self->{probC}}[$i], ${$self->{probG}}[$i], ${$self->{probT}}[$i]); } return $self; } =head2 calc_weight Title : calc_weight Usage : $obj->calc_weight({A=>0.2562, C=>0.2438, G=>0.2432, T=>0.2568}); Function: Recalculates the PSM (or weights) based on the PFM (the frequency matrix) and user supplied background model. Throws : if no model is supplied Returns : n/a Args : reference to a hash with background frequencies for A,C,G and T =cut sub calc_weight { my ($self, $model) = @_; my %model; $model{probA}=$model->{A}; $model{probC}=$model->{C}; $model{probG}=$model->{G}; $model{probT}=$model->{T}; foreach my $let (qw(probA probC probG probT)) { my @str; $self->throw('You did not provide valid model\n') unless (($model{$let}>0) && ($model{$let}<1)); foreach my $f (@{$self->{$let}}) { my $w=log($f)-log($model{$let}); push @str,$w; } my $llet=$let; $llet=~s/prob/log/; $self->{$llet}=\@str; } return $self; } =head2 next_pos Title : next_pos Usage : Function: Retrieves the next position features: frequencies for A,C,G,T, the main letter (as in consensus) and the probabilty for this letter to occur at this position and the current position Returns : hash (pA,pC,pG,pT,logA,logC,logG,logT,base,prob,rel) Args : none =cut sub next_pos { my $self = shift; $self->throw("instance method called on class") unless ref $self; my $len=@{$self->{seq}}; my $pos=$self->{_position}; # End reached? if ($pos<$len) { my $pA=${$self->{probA}}[$pos]; my $pC=${$self->{probC}}[$pos]; my $pG=${$self->{probG}}[$pos]; my $pT=${$self->{probT}}[$pos]; my $lA=${$self->{logA}}[$pos]; my $lC=${$self->{logC}}[$pos]; my $lG=${$self->{logG}}[$pos]; my $lT=${$self->{logT}}[$pos]; my $base=${$self->{seq}}[$pos]; my $prob=${$self->{seqp}}[$pos]; $self->{_position}++; my %seq=(pA=>$pA,pT=>$pT,pC=>$pC,pG=>$pG, lA=>$lA,lT=>$lT,lC=>$lC,lG=>$lG,base=>$base,rel=>$pos, prob=>$prob); return %seq; } else {$self->{_position}=0; return;} } =head2 curpos Title : curpos Usage : Function: Gets/sets the current position. Converts to 0 if argument is minus and to width if greater than width Returns : integer Args : integer =cut sub curpos { my $self = shift; my $prev = $self->{_position}; if (@_) { $self->{_position} = shift; } return $prev; } =head2 e_val Title : e_val Usage : Function: Gets/sets the e-value Returns : real number Args : none to get, real number to set =cut sub e_val { my $self = shift; my $prev = $self->{e_val}; if (@_) { $self->{e_val} = shift; } return $prev; } =head2 IC Title : IC Usage : Function: Get/set the Information Content Returns : real number Args : none to get, real number to set =cut sub IC { my $self = shift; my $prev = $self->{IC}; if (@_) { $self->{IC} = shift; } return $prev; } =head2 accession_number Title : accession_number Function: Get/set the accession number, this will be unique id for the SiteMatrix object as well for any other object, inheriting from SiteMatrix Returns : string Args : none to get, string to set =cut sub accession_number { my $self = shift; my $prev = $self->{accession_number}; if (@_) { $self->{accession_number} = shift; } return $prev; } =head2 consensus Title : consensus Usage : Function: Returns the consensus Returns : string Args : (optional) threshold value 1 to 10, default 5 '5' means the returned characters had a 50% or higher presence at their position =cut sub consensus { my ($self, $thresh) = @_; if ($thresh) { my $len=$#{$self->{probA}}; for (my $i=0; $i<$len+1; $i++) { (${$self->{seq}}[$i], ${$self->{seqp}}[$i]) = _to_cons(${$self->{probA}}[$i], ${$self->{probC}}[$i], ${$self->{probG}}[$i], ${$self->{probT}}[$i], $thresh); } } my $consensus=''; foreach my $letter (@{$self->{seq}}) { $consensus .= $letter; } return $consensus; } =head2 width Title : width Usage : Function: Returns the length of the sites in used to make this matrix Returns : int Args : none =cut sub width { my $self = shift; my $width=@{$self->{probA}}; return $width; } =head2 sites Title : sites Usage : Function: Get/set the number of sites that were used to make this matrix Returns : int Args : none to get, int to set =cut sub sites { my $self = shift; if (@_) { $self->{sites} = shift } return $self->{sites} || return; } =head2 IUPAC Title : IUPAC Usage : Function: Returns IUPAC compliant consensus Returns : string Args : optionally, also supply a whole number (int) of 1 or higher to set the significance level when considering the frequencies. 1 (the default) means a 0.05 significance level: frequencies lower than 0.05 will be ignored. 2 Means a 0.005 level, and so on. =cut sub IUPAC { my ($self, $thresh) = @_; if ($thresh) { my $len=$#{$self->{probA}}; for (my $i=0; $i<$len+1; $i++) { (${$self->{IUPAC}}[$i],${$self->{IUPACp}}[$i])=_to_IUPAC(${$self->{probA}}[$i], ${$self->{probC}}[$i], ${$self->{probG}}[$i], ${$self->{probT}}[$i], $thresh); } } my $iu=$self->{IUPAC}; my $iupac=''; foreach my $let (@{$iu}) { $iupac .= $let; } return $iupac; } =head2 _to_IUPAC Title : _to_IUPAC Usage : Function: Converts a single position to IUPAC compliant symbol. For rules see the implementation Returns : char, real number Args : real numbers for frequencies of A,C,G,T (positional) optionally, also supply a whole number (int) of 1 or higher to set the significance level when considering the frequencies. 1 (the default) means a 0.05 significance level: frequencies lower than 0.05 will be ignored. 2 Means a 0.005 level, and so on. =cut sub _to_IUPAC { my ($a, $c, $g, $t, $thresh) = @_; $thresh ||= 1; $thresh = int($thresh); $a = sprintf ("%.${thresh}f", $a); $c = sprintf ("%.${thresh}f", $c); $g = sprintf ("%.${thresh}f", $g); $t = sprintf ("%.${thresh}f", $t); my $total = $a + $c + $g + $t; return 'A' if ($a == $total); return 'G' if ($g == $total); return 'C' if ($c == $total); return 'T' if ($t == $total); my $r=$g+$a; return 'R' if ($r == $total); my $y=$t+$c; return 'Y' if ($y == $total); my $m=$a+$c; return 'M' if ($m == $total); my $k=$g+$t; return 'K' if ($k == $total); my $s=$g+$c; return 'S' if ($s == $total); my $w=$a+$t; return 'W' if ($w == $total); my $d=$r+$t; return 'D' if ($d == $total); my $v=$r+$c; return 'V' if ($v == $total); my $b=$y+$g; return 'B' if ($b == $total); my $h=$y+$a; return 'H' if ($h == $total); return 'N'; } =head2 _to_cons Title : _to_cons Usage : Function: Converts a single position to simple consensus character and returns its probability. For rules see the implementation Returns : char, real number Args : real numbers for A,C,G,T (positional), and optional 5th argument of threshold (as a number between 1 and 10, where 5 is default and means the returned character had a 50% or higher presence at this position) =cut sub _to_cons { my ($A, $C, $G, $T, $thresh) = @_; $thresh ||= 5; # this multiplication by 10 is just to satisfy the thresh range of 1-10 my $a = $A * 10; my $c = $C * 10; my $g = $G * 10; my $t = $T * 10; return 'N',10 if (($a<$thresh) && ($c<$thresh) && ($g<$thresh) && ($t<$thresh)); return 'N',10 if (($a==$t) && ($a==$c) && ($a==$g)); # threshold could be lower than 50%, so must check is not only over # threshold, but also the highest frequency return 'A',$a if (($a>=$thresh) && ($a>$t) && ($a>$c) && ($a>$g)); return 'C',$c if (($c>=$thresh) && ($c>$t) && ($c>$a) && ($c>$g)); return 'G',$g if (($g>=$thresh) && ($g>$t) && ($g>$c) && ($g>$a)); return 'T',$t if (($t>=$thresh) && ($t>$g) && ($t>$c) && ($t>$a)); return 'N',10; } =head2 get_string Title : get_string Usage : Function: Returns given probability vector as a string. Useful if you want to store things in a rel database, where arrays are not first choice Throws : If the argument is outside {A,C,G,T} Returns : string Args : character {A,C,G,T} =cut sub get_string { my $self=shift; my $base=shift; my $string=''; my @prob; BASE: { if ($base eq 'A') {@prob= @{$self->{probA}}; last BASE; } if ($base eq 'C') {@prob= @{$self->{probC}}; last BASE; } if ($base eq 'G') {@prob= @{$self->{probG}}; last BASE; } if ($base eq 'T') {@prob= @{$self->{probT}}; last BASE; } $self->throw ("No such base: $base!\n"); } foreach my $prob (@prob) { my $corrected = $prob*10; my $next=sprintf("%.0f",$corrected); $next='a' if ($next eq '10'); $string .= $next; } return $string; } =head2 get_array Title : get_array Usage : Function: Returns an array with frequencies for a specified base Returns : array Args : char =cut sub get_array { my $self=shift; my $base=uc(shift); return @{$self->{probA}} if ($base eq 'A'); return @{$self->{probC}} if ($base eq 'C'); return @{$self->{probG}} if ($base eq 'G'); return @{$self->{probT}} if ($base eq 'T'); $self->throw("No such base: $base!\n"); } =head2 get_logs_array Title : get_logs_array Usage : Function: Returns an array with log_odds for a specified base Returns : array Args : char =cut sub get_logs_array { my $self=shift; my $base=uc(shift); return @{$self->{logA}} if (($base eq 'A') && ($self->{logA})); return @{$self->{logC}} if (($base eq 'C') && ($self->{logC})); return @{$self->{logG}} if (($base eq 'G') && ($self->{logG})); return @{$self->{logT}} if (($base eq 'T') && ($self->{logT})); $self->throw ("No such base: $base!\n") if (!grep(/$base/,qw(A C G T))); return; } =head2 id Title : id Usage : Function: Gets/sets the site id Returns : string Args : string =cut sub id { my $self = shift; my $prev = $self->{id}; if (@_) { $self->{id} = shift; } return $prev; } =head2 regexp Title : regexp Usage : Function: Returns a regular expression which matches the IUPAC convention. N will match X, N, - and . Returns : string Args : none (works at the threshold last used for making the IUPAC string) =cut sub regexp { my $self=shift; my $regexp; foreach my $letter (@{$self->{IUPAC}}) { my $reg; LETTER: { if ($letter eq 'A') { $reg='[Aa]'; last LETTER; } if ($letter eq 'C') { $reg='[Cc]'; last LETTER; } if ($letter eq 'G') { $reg='[Gg]'; last LETTER; } if ($letter eq 'T') { $reg='[Tt]'; last LETTER; } if ($letter eq 'M') { $reg='[AaCcMm]'; last LETTER; } if ($letter eq 'R') { $reg='[AaGgRr]'; last LETTER; } if ($letter eq 'W') { $reg='[AaTtWw]'; last LETTER; } if ($letter eq 'S') { $reg='[CcGgSs]'; last LETTER; } if ($letter eq 'Y') { $reg='[CcTtYy]'; last LETTER; } if ($letter eq 'K') { $reg='[GgTtKk]'; last LETTER; } if ($letter eq 'V') { $reg='[AaCcGgVv]'; last LETTER; } if ($letter eq 'H') { $reg='[AaCcTtHh]'; last LETTER; } if ($letter eq 'D') { $reg='[AaGgTtDd]'; last LETTER; } if ($letter eq 'B') { $reg='[CcGgTtBb]'; last LETTER; } $reg='\S'; } $regexp .= $reg; } return $regexp; } =head2 regexp_array Title : regexp_array Usage : Function: Returns a regular expression which matches the IUPAC convention. N will match X, N, - and . Returns : array Args : none (works at the threshold last used for making the IUPAC string) To do : I have separated regexp and regexp_array, but maybe they can be rewritten as one - just check what should be returned =cut sub regexp_array { my $self=shift; my @regexp; foreach my $letter (@{$self->{IUPAC}}) { my $reg; LETTER: { if ($letter eq 'A') { $reg='[Aa]'; last LETTER; } if ($letter eq 'C') { $reg='[Cc]'; last LETTER; } if ($letter eq 'G') { $reg='[Gg]'; last LETTER; } if ($letter eq 'T') { $reg='[Tt]'; last LETTER; } if ($letter eq 'M') { $reg='[AaCcMm]'; last LETTER; } if ($letter eq 'R') { $reg='[AaGgRr]'; last LETTER; } if ($letter eq 'W') { $reg='[AaTtWw]'; last LETTER; } if ($letter eq 'S') { $reg='[CcGgSs]'; last LETTER; } if ($letter eq 'Y') { $reg='[CcTtYy]'; last LETTER; } if ($letter eq 'K') { $reg='[GgTtKk]'; last LETTER; } if ($letter eq 'V') { $reg='[AaCcGgVv]'; last LETTER; } if ($letter eq 'H') { $reg='[AaCcTtHh]'; last LETTER; } if ($letter eq 'D') { $reg='[AaGgTtDd]'; last LETTER; } if ($letter eq 'B') { $reg='[CcGgTtBb]'; last LETTER; } $reg='\S'; } push @regexp,$reg; } return @regexp; } =head2 _compress_array Title : _compress_array Usage : Function: Will compress an array of real signed numbers to a string (ie vector of bytes) -127 to +127 for bi-directional(signed) and 0..255 for unsigned Returns : String Args : array reference, followed by an max value and direction (optional, default 1-unsigned),1 unsigned, any other is signed. =cut sub _compress_array { my ($array,$lm,$direct)=@_; my $str; return unless(($array) && ($lm)); $direct=1 unless ($direct); my $k1= ($direct==1) ? (255/$lm) : (127/$lm); foreach my $c (@{$array}) { $c=$lm if ($c>$lm); $c=-$lm if (($c<-$lm) && ($direct !=1)); $c=0 if (($c<0) && ($direct ==1)); my $byte=int($k1*$c); $byte=127+$byte if ($direct !=1);#Clumsy, should be really shift the bits my $char=chr($byte); $str.=$char; } return $str; } =head2 _uncompress_string Title : _uncompress_string Usage : Function: Will uncompress a string (vector of bytes) to create an array of real signed numbers (opposite to_compress_array) Returns : string, followed by an max value and direction (optional, default 1-unsigned), 1 unsigned, any other is signed. Args : array =cut sub _uncompress_string { my ($str,$lm,$direct)=@_; my @array; return unless(($str) && ($lm)); $direct=1 unless ($direct); my $k1= ($direct==1) ? (255/$lm) : (127/$lm); foreach my $c (split(//,$str)) { my $byte=ord($c); $byte=$byte-127 if ($direct !=1);#Clumsy, should be really shift the bits my $num=$byte/$k1; push @array,$num; } return @array; } =head2 get_compressed_freq Title : get_compressed_freq Usage : Function: A method to provide a compressed frequency vector. It uses one byte to code the frequence for one of the probability vectors for one position. Useful for relational database. Improvement of the previous 0..a coding. Example : my $strA=$self->get_compressed_freq('A'); Returns : String Args : char =cut sub get_compressed_freq { my $self=shift; my $base=shift; my $string=''; my @prob; BASE: { if ($base eq 'A') { @prob= @{$self->{probA}} unless (!defined($self->{probA})); last BASE; } if ($base eq 'G') { @prob= @{$self->{probG}} unless (!defined($self->{probG})); last BASE; } if ($base eq 'C') { @prob= @{$self->{probC}} unless (!defined($self->{probC})); last BASE; } if ($base eq 'T') { @prob= @{$self->{probT}} unless (!defined($self->{probT})); last BASE; } $self->throw ("No such base: $base!\n"); } my $str= _compress_array(\@prob,1,1); return $str; } =head2 get_compressed_logs Title : get_compressed_logs Usage : Function: A method to provide a compressed log-odd vector. It uses one byte to code the log value for one of the log-odds vectors for one position. Example : my $strA=$self->get_compressed_logs('A'); Returns : String Args : char =cut sub get_compressed_logs { my $self=shift; my $base=shift; my $string=''; my @prob; BASE: { if ($base eq 'A') {@prob= @{$self->{logA}} unless (!defined($self->{logA})); last BASE; } if ($base eq 'C') {@prob= @{$self->{logC}} unless (!defined($self->{logC})); last BASE; } if ($base eq 'G') {@prob= @{$self->{logG}} unless (!defined($self->{logG})); last BASE; } if ($base eq 'T') {@prob= @{$self->{logT}} unless (!defined($self->{logT})); last BASE; } $self->throw ("No such base: $base!\n"); } return _compress_array(\@prob,1000,2); } =head2 sequence_match_weight Title : sequence_match_weight Usage : Function: This method will calculate the score of a match, based on the PWM if such is associated with the matrix object. Returns undef if no PWM data is available. Throws : if the length of the sequence is different from the matrix width Example : my $score=$matrix->sequence_match_weight('ACGGATAG'); Returns : Floating point Args : string =cut sub sequence_match_weight { my ($self,$seq)=@_; return unless ($self->{logA}); my $width=$self->width; $self->throw ("I can calculate the score only for sequence which are exactly my size for $seq, my width is $width\n") unless (length($seq)==@{$self->{logA}}); $seq = uc($seq); my @seq=split(//,$seq); my $score = 0; my $i=0; foreach my $pos (@seq) { my $tv = 'log'.$pos; $self->warn("Position ".($i+1)." of input sequence has unknown (ambiguity?) character '$pos': scores will be wrong") unless defined $self->{$tv}; $score += defined $self->{$tv} ? $self->{$tv}->[$i] : 0; $i++; } return $score; } =head2 get_all_vectors Title : get_all_vectors Usage : Function: returns all possible sequence vectors to satisfy the PFM under a given threshold Throws : If threshold outside of 0..1 (no sense to do that) Example : my @vectors=$self->get_all_vectors(4); Returns : Array of strings Args : (optional) floating =cut sub get_all_vectors { my $self=shift; my $thresh=shift; $self->throw("Out of range. Threshold should be >0 and 1<.\n") if (($thresh<0) || ($thresh>1)); my @seq=split(//,$self->consensus($thresh*10)); my @perm; for my $i (0..@{$self->{probA}}) { push @{$perm[$i]},'A' if ($self->{probA}->[$i]>$thresh); push @{$perm[$i]},'C' if ($self->{probC}->[$i]>$thresh); push @{$perm[$i]},'G' if ($self->{probG}->[$i]>$thresh); push @{$perm[$i]},'T' if ($self->{probT}->[$i]>$thresh); push @{$perm[$i]},'N' if ($seq[$i] eq 'N'); } my $fpos=shift @perm; my @strings=@$fpos; foreach my $pos (@perm) { my @newstr; foreach my $let (@$pos) { foreach my $string (@strings) { my $newstring = $string . $let; push @newstr,$newstring; } } @strings=@newstr; } return @strings; } 1; BioPerl-1.007002/Bio/Matrix/PSM/SiteMatrixI.pm000444000766000024 3063413155576320 20715 0ustar00cjfieldsstaff000000000000 =head1 NAME Bio::Matrix::PSM::SiteMatrixI - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds =head1 SYNOPSIS # You cannot use this module directly; see Bio::Matrix::PSM::SiteMatrix # for an example implementation =head1 DESCRIPTION SiteMatrix is designed to provide some basic methods when working with position scoring (weight) matrices, such as transcription factor binding sites for example. A DNA PSM consists of four vectors with frequencies {A,C,G,T}. This is the minimum information you should provide to construct a PSM object. The vectors can be provided as strings with frequenciesx10 rounded to an int, going from {0..a} and 'a' represents the maximum (10). This is like MEME's compressed representation of a matrix and it is quite useful when working with relational DB. If arrays are provided as an input (references to arrays actually) they can be any number, real or integer (frequency or count). When creating the object you can ask the constructor to make a simple pseudo count correction by adding a number (typically 1) to all positions (with the -correction option). After adding the number the frequencies will be calculated. Only use correction when you supply counts, not frequencies. Throws an exception if: You mix as an input array and string (for example A matrix is given as array, C - as string). The position vector is (0,0,0,0). One of the probability vectors is shorter than the rest. Summary of the methods I use most frequently (details below): iupac - return IUPAC compliant consensus as a string score - Returns the score as a real number IC - information content. Returns a real number id - identifier. Returns a string accession - accession number. Returns a string next_pos - return the sequence probably for each letter, IUPAC symbol, IUPAC probability and simple sequence consenus letter for this position. Rewind at the end. Returns a hash. pos - current position get/set. Returns an integer. regexp - construct a regular expression based on IUPAC consensus. For example AGWV will be [Aa][Gg][AaTt][AaCcGg] width - site width get_string - gets the probability vector for a single base as a string. get_array - gets the probability vector for a single base as an array. get_logs_array - gets the log-odds vector for a single base as an array. New methods, which might be of interest to anyone who wants to store PSM in a relational database without creating an entry for each position is the ability to compress the PSM vector into a string with losing usually less than 1% of the data. this can be done with: my $str=$matrix->get_compressed_freq('A'); or my $str=$matrix->get_compressed_logs('A'); Loading from a database should be done with new, but is not yest implemented. However you can still uncompress such string with: my @arr=Bio::Matrix::PSM::_uncompress_string ($str,1,1); for PSM or my @arr=Bio::Matrix::PSM::_uncompress_string ($str,1000,2); for log odds =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::SiteMatrixI; # use strict; use base qw(Bio::Root::RootI); =head2 calc_weight Title : calc_weight Usage : $self->calc_weight({A=>0.2562,C=>0.2438,G=>0.2432,T=>0.2568}); Function: Recalculates the PSM (or weights) based on the PFM (the frequency matrix) and user supplied background model. Throws : if no model is supplied Example : Returns : Args : reference to a hash with background frequencies for A,C,G and T =cut sub calc_weight { my $self = shift; $self->throw_not_implemented(); } =head2 next_pos Title : next_pos Usage : my %base=$site->next_pos; Function: Retrieves the next position features: frequencies and weights for A,C,G,T, the main letter (as in consensus) and the probabilty for this letter to occur at this position and the current position Throws : Example : Returns : hash (pA,pC,pG,pT,lA,lC,lG,lT,base,prob,rel) Args : none =cut sub next_pos { my $self = shift; $self->throw_not_implemented(); } =head2 curpos Title : curpos Usage : my $pos=$site->curpos; Function: Gets/sets the current position. Converts to 0 if argument is minus and to width if greater than width Throws : Example : Returns : integer Args : integer =cut sub curpos { my $self = shift; $self->throw_not_implemented(); } =head2 e_val Title : e_val Usage : my $score=$site->e_val; Function: Gets/sets the e-value Throws : Example : Returns : real number Args : real number =cut sub e_val { my $self = shift; $self->throw_not_implemented(); } =head2 consensus Title : consensus Usage : Function: Returns the consensus Returns : string Args : (optional) threshold value 1 to 10, default 5 '5' means the returned characters had a 50% or higher presence at their position =cut sub consensus { my $self = shift; $self->throw_not_implemented(); } =head2 accession_number Title : accession_number Usage : Function: accession number, this will be unique id for the SiteMatrix object as well for any other object, inheriting from SiteMatrix Throws : Example : Returns : string Args : string =cut sub accession_number { my $self = shift; $self->throw_not_implemented(); } =head2 width Title : width Usage : my $width=$site->width; Function: Returns the length of the site Throws : Example : Returns : number Args : =cut sub width { my $self = shift; $self->throw_not_implemented(); } =head2 IUPAC Title : IUPAC Usage : my $iupac_consensus=$site->IUPAC; Function: Returns IUPAC compliant consensus Throws : Example : Returns : string Args : =cut sub IUPAC { my $self = shift; $self->throw_not_implemented(); } =head2 IC Title : IC Usage : my $ic=$site->IC; Function: Information content Throws : Example : Returns : real number Args : none =cut sub IC { my $self=shift; $self->throw_not_implemented(); } =head2 get_string Title : get_string Usage : my $freq_A=$site->get_string('A'); Function: Returns given probability vector as a string. Useful if you want to store things in a rel database, where arrays are not first choice Throws : If the argument is outside {A,C,G,T} Example : Returns : string Args : character {A,C,G,T} =cut sub get_string { my $self=shift; $self->throw_not_implemented(); } =head2 id Title : id Usage : my $id=$site->id; Function: Gets/sets the site id Throws : Example : Returns : string Args : string =cut sub id { my $self = shift; $self->throw_not_implemented(); } =head2 regexp Title : regexp Usage : my $regexp=$site->regexp; Function: Returns a regular expression which matches the IUPAC convention. N will match X, N, - and . Throws : Example : Returns : string Args : =cut sub regexp { my $self=shift; $self->throw_not_implemented(); } =head2 regexp_array Title : regexp_array Usage : my @regexp=$site->regexp; Function: Returns a regular expression which matches the IUPAC convention. N will match X, N, - and . Throws : Example : Returns : array Args : To do : I have separated regexp and regexp_array, but maybe they can be rewritten as one - just check what should be returned =cut sub regexp_array { my $self=shift; $self->throw_not_implemented(); } =head2 get_array Title : get_array Usage : my @freq_A=$site->get_array('A'); Function: Returns an array with frequencies for a specified base Throws : Example : Returns : array Args : char =cut sub get_array { my $self=shift; $self->throw_not_implemented(); } =head2 _to_IUPAC Title : _to_IUPAC Usage : Function: Converts a single position to IUPAC compliant symbol and returns its probability. For rules see the implementation. Throws : Example : Returns : char, real number Args : real numbers for A,C,G,T (positional) =cut sub _to_IUPAC { my $self = shift; $self->throw_not_implemented(); } =head2 _to_cons Title : _to_cons Usage : Function: Converts a single position to simple consensus character and returns its probability. For rules see the implementation, Throws : Example : Returns : char, real number Args : real numbers for A,C,G,T (positional) =cut sub _to_cons { my $self = shift; $self->throw_not_implemented(); } =head2 _calculate_consensus Title : _calculate_consensus Usage : Function: Internal stuff Throws : Example : Returns : Args : =cut sub _calculate_consensus { my $self = shift; $self->throw_not_implemented(); } =head2 _compress_array Title : _compress_array Usage : Function: Will compress an array of real signed numbers to a string (ie vector of bytes) -127 to +127 for bi-directional(signed) and 0..255 for unsigned ; Throws : Example : Internal stuff Returns : String Args : array reference, followed by an max value and direction (optional, default 1-unsigned),1 unsigned, any other is signed. =cut sub _compress_array { my $self = shift; $self->throw_not_implemented(); } =head2 _uncompress_string Title : _uncompress_string Usage : Function: Will uncompress a string (vector of bytes) to create an array of real signed numbers (opposite to_compress_array) Throws : Example : Internal stuff Returns : string, followed by an max value and direction (optional, default 1-unsigned), 1 unsigned, any other is signed. Args : array =cut sub _uncompress_string { my $self = shift; $self->throw_not_implemented(); } =head2 get_compressed_freq Title : get_compressed_freq Usage : Function: A method to provide a compressed frequency vector. It uses one byte to code the frequence for one of the probability vectors for one position. Useful for relational database. Improvement of the previous 0..a coding. Throws : Example : my $strA=$self->get_compressed_freq('A'); Returns : String Args : char =cut sub get_compressed_freq { my $self = shift; $self->throw_not_implemented(); } =head2 get_compressed_logs Title : get_compressed_logs Usage : Function: A method to provide a compressed log-odd vector. It uses one byte to code the log value for one of the log-odds vectors for one position. Throws : Example : my $strA=$self->get_compressed_logs('A'); Returns : String Args : char =cut sub get_compressed_logs { my $self = shift; $self->throw_not_implemented(); } =head2 sequence_match_weight Title : sequence_match_weight Usage : Function: This method will calculate the score of a match, based on the PWM if such is associated with the matrix object. Returns undef if no PWM data is available. Throws : if the length of the sequence is different from the matrix width Example : my $score=$matrix->sequence_match_weight('ACGGATAG'); Returns : Floating point Args : string =cut sub sequence_match_weight { my $self = shift; $self->throw_not_implemented(); } =head2 get_all_vectors Title : get_all_vectors Usage : Function: returns all possible sequence vectors to satisfy the PFM under a given threshold Throws : If threshold outside of 0..1 (no sense to do that) Example : my @vectors=$self->get_all_vectors(4); Returns : Array of strings Args : (optional) floating =cut sub get_all_vectors { my $self = shift; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Matrix/PSM/IO000755000766000024 013155576320 16301 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Matrix/PSM/IO/mast.pm000444000766000024 2125213155576320 17762 0ustar00cjfieldsstaff000000000000 =head1 NAME Bio::Matrix::PSM::IO::mast - PSM mast parser implementation =head1 SYNOPSIS See Bio::Matrix::PSM::IO for detailed documentation on how to use PSM parsers =head1 DESCRIPTION Parser for mast. This driver unlike meme or transfac for example is dedicated more to PSM sequence matches, than to PSM themselves. =head1 TO DO Section III should be parsed too, otherwise no real sequence is available, so we supply 'NNNNN....' as a seq which is not right. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Matrix::PSM::IO::mast; use Bio::Matrix::PSM::InstanceSite; use Bio::Matrix::PSM::Psm; use Bio::Root::Root; use strict; use base qw(Bio::Matrix::PSM::PsmHeader Bio::Matrix::PSM::IO); =head2 new Title : new Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'mast', -file=>$file); Function: Associates a file with the appropriate parser Throws : Throws if the file passed is in HTML format or if some criteria for the file format are not met. Example : Returns : psm object, associated with a file with matrix file Args : hash return : "Bio::Matrix::PSM::$format"->new(@args); =cut sub new { my($class, @args)=@_; my $self = $class->SUPER::new(@args); my (%instances,@header,$n); my ($file)=$self->_rearrange(['FILE'], @args); $self->{file} = $file; $self->{_factor}=1; $self->_initialize_io(@args) || warn "Did you intend to use STDIN?"; #Read only for now $self->{_end}=0; undef $self->{hid}; return $self if ($file=~/^>/);#Just writing my $buf=$self->_readline; $self->throw('Cannot parse HTML format yet') if ($buf =~/^/); # this should probably be moved to its own function while ( defined($buf=$self->_readline)) { chomp($buf); if ($buf=~/DATABASE AND MOTIFS/) { while ($buf=$self->_readline) { if ($buf=~/DATABASE/) { $buf=~s/^[\s\t]+//; chomp $buf; ($n,$self->{_dbname},$self->{_dbtype})=split(/\s/,$buf); $self->{_dbtype}=~s/[\(\)]//g; } if ($buf=~/MOTIFS/) { $buf=~s/^[\s\t]+//; chomp $buf; ($n,$self->{_mrsc},$self->{_msrctype})=split(/\s/,$buf); $self->{_msrctype}=~s/[\(\)]//g; last; } } if ($self->{_msrctype} ne $self->{_dbtype}) {#Assume we have protein motifs, nuc DB (not handling opp.) $self->{_factor}=3; $self->{_mixquery}=1; } } if ($buf=~m/MOTIF WIDTH BEST POSSIBLE MATCH/) { $self->_readline; while (defined($buf=$self->_readline)) { last if ($buf!~/\w/); $buf=~s/\t+//g; $buf=~s/^\s+//g; my ($id,$width,$seq)=split(/\s+/,$buf); push @{$self->{hid}},$id; $self->{length}->{$id}=$width; $self->{seq}->{$id}=$seq; } next; } if ($buf=~m/section i:/i) { $self->_readline; $self->_readline; $self->_readline; %instances=_get_genes($self); $self->{instances}=\%instances; if (!(%instances)) { $self->warn ("Your MAST analysis did not find any matches satisfying the current threshold.\nSee MAST documentation for more information.\n"); return $self; #The header might be useful so we return the object, not undef } next; } if ($buf=~m/section ii:/i) { $self->_readline; $self->_readline; $self->_readline; last; } $buf=~s/[\t+\s+]/ /g; push @header,$buf unless (($buf=~/\*{10,}/)||($buf!~/\w/)); } $self->throw('Could not read Section I, probably wrong format, make sure it is not HTML, giving up...') if !(%instances); $self->warn( "This file might be an unreadable version, proceed with caution!\n") if (!grep(/\s+MAST\s+version\s+3/,@header)); $self->{unstructured} = \@header; $self->_initialize; return $self; } # Get the file header and put store it as a hash, which later we'll use to create # the header for each Psm. See Bio::Matrix::PSM::PsmI for header function. sub _get_genes { my $self=shift; my %llid; my $ok=0; my $i=0; my %instances; while (my $line=$self->_readline) { last if ($line=~/^[\s\t*]/); # Well, ids can be nearly anything...??? chomp($line); $i++; next if ($line eq ''); $line=~s/\s+/,/g; my ($id,$key,$eval,$len)=split(/,/,$line); unless ($len) { warn "Malformed data found: $line\n"; next; } $instances{$id}=Bio::Matrix::PSM::InstanceSite->new(-id=>$id, -desc=>$key, -score=>$eval, -width=>$len, -seq=>'ACGT'); } return %instances; } =head2 next_psm Title : next_psm Usage : my $psm=$psmIO->next_psm(); Function: Reads the next PSM from the input file, associated with this object Throws : Throws if there ara format violations in the input file (checking is not very strict with all drivers). Example : Returns : Bio::Matrix::PSM::Psm object Args : none =cut sub next_psm { my $self=shift; return if ($self->{_end}==1); my (@lmotifsm,%index,$eval,$scheme,$sid); %index= %{$self->{length}}; my (@instances,%instances); my $line=$self->_readline; $line=~s/[\t\n]//; if ($line =~ /\*{10,}/) { #Endo of Section II if we do only section II $self->{_end}=1; return ; } do { if ($line!~/^\s/) { ($sid,$eval,$scheme)=split(/\s+/,$line,3); } else { $scheme .=$line; } $line=$self->_readline; $line=~s/[\t\n]//; } until ($line!~/^\s/); my $pos=1; $scheme=~s/\s+//g; $scheme=~s/\n//g; my @motifs=split(/_/,$scheme); while (@motifs) { my $next=shift(@motifs); if (!($next=~/\D/)) { last if (!@motifs); $pos+=$next; next; } my $id=$next; my $score= $id=~m/\[/ ? 'strong' : 'weak' ; my $frame; my $strand = $id =~ m/\-\d/ ? -1 : 1 ; if ($self->{_mixquery}) { $frame = 0 if $id =~ m/\d+a/ ; $frame = 1 if $id =~ m/\d+b/ ; $frame = 2 if $id =~ m/\d+c/ ; } $id=~s/\D+//g; my @s; my $width=$index{$id}; #We don't know the sequence, but we know the length my $seq='N' x ($width*$self->{_factor}); #Future version will have to parse Section tree nad get the real seq my $instance=Bio::Matrix::PSM::InstanceSite->new ( -id=>"$id\@$sid", -mid=>$id, -accession_number=>$sid, -desc=>"Motif $id occurrance in $sid", -score=>$score, -seq=>$seq, -alphabet => 'dna', -start=>$pos, -strand=>$strand); $instance->frame($frame) if ($self->{_mixquery}); push @instances,$instance; $pos+=$index{$id}*$self->{_factor}; } my $psm= Bio::Matrix::PSM::Psm->new(-instances=> \@instances, -e_val => $eval, -id => $sid); $self->_pushback($line); return $psm; } =head2 write_psm Title : write_psm Usage : #Get SiteMatrix object somehow (see Bio::Matrix::PSM::SiteMatrix) my $matrix=$psmin->next_matrix; #Create the stream my $psmio=new(-file=>">psms.mast",-format=>'mast'); $psmio->write_psm($matrix); #Will warn if only PFM data is contained in $matrix, recalculate the PWM #based on normal distribution (A=>0.25, C=>0.25, etc) Function: writes pwm in mast format Throws : Example : Args : SiteMatrix object Returns : =cut sub write_psm { my ($self,$matrix)=@_; # my $idline=">". $matrix->id . "\n"; my $w=$matrix->width; my $header="ALPHABET= ACGT\nlog-odds matrix: alength= 4 w= $w\n"; $self->_print($header); unless ($matrix->get_logs_array('A')) { warn "No log-odds data, available, using normal distribution to recalculate the PWM"; $matrix->calc_weight({A=>0.25, C=>0.25, G=>0.25,T=>0.25}); } while (my %h=$matrix->next_pos) { $self->_print (join("\t",$h{lA},$h{lC},$h{lG},$h{lT},"\n")); } } 1; BioPerl-1.007002/Bio/Matrix/PSM/IO/masta.pm000555000766000024 2035413155576320 20130 0ustar00cjfieldsstaff000000000000#--------------------------------------------------------- =head1 NAME Bio::Matrix::PSM::IO::masta - motif fasta format parser =head1 SYNOPSIS MASTA is a position frequency matrix format similar to fasta. It contains one ID row just like fasta and then the actual data, which is tab delimited: 0.1 0.62 .017 0.11 0.22 0.13 0.54 0.11 Or A,C,G and T could be horizontally positioned (positioning is automatically detected). Please note masta will parse only DNA at the moment. It will also convert a set of aligned sequences: ACATGCAT ACAGGGAT ACAGGCAT ACCGGCAT to a PFM (SiteMatrix object). When writing if you supply SEQ it will write 10 random instances, which represent correctly the frequency and can be used as an input for weblogo creation purposes. See Bio::Matrix::PSM::IO for detailed documentation on how to use masta parser =head1 DESCRIPTION Parser for meme. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::IO::masta; use Bio::Matrix::PSM::SiteMatrix; use vars qw(@HEADER); use strict; use base qw(Bio::Matrix::PSM::IO Bio::Root::Root); =head2 new Title : new Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=> 'masta', -file => $file, -mtype => 'PWM'); Function: Associates a file with the appropriate parser Throws : Example : Args : hash Returns : "Bio::Matrix::PSM::$format"->new(@args); =cut sub new { my($class, @args)=@_; my $self = $class->SUPER::new(@args); my ($file)=$self->_rearrange(['FILE'], @args); my ($query,$tr1)=split(/\./,$file,2); $self->{file} = $file; $self->{_end} = 0; $self->{mtype} = uc($self->_rearrange(['MTYPE'], @args) || "PFM"); $self->_initialize_io(@args) || $self->warn("Did you intend to use STDIN?"); #Read only for now return $self; } =head2 write_psm Title : write_psm Usage : Function: writes a pfm/pwm/raw sequence in a simple masta format Throws : Example : Args : SiteMatrix object, type (optional string: PWM, SEQ or PFM) Returns : =cut sub write_psm { my ($self,$matrix,$type)=@_; $self->{mtype} = uc($type) if ($type); my $idline=">". $matrix->id . "\n"; $self->_print($idline); unless ($self->{mtype} eq 'SEQ') { while (my %h=$matrix->next_pos) { my $row=$self->{mtype} eq 'PWM' ? join("\t",$h{lA},$h{lC},$h{lG},$h{lT},"\n"):join("\t",$h{pA},$h{pC},$h{pG},$h{pT},"\n"); $self->_print ($row); } } else { my @seq; while (my %h=$matrix->next_pos) { my ($a,$c,$g,$t)=_freq_to_count(\%h); $self->throw("Could not convert from frequency to count\n") if (($a+$c+$g+$t) !=10); for my $i (0..$a-1) {$seq[$i].='A';} my $m=$a+$c; for my $i ($a..$m-1) {$seq[$i].='C';} my $n=$a+$c+$g; for my $i ($m..$n-1) {$seq[$i].='G';} for my $i ($n..9) {$seq[$i].='T';} } foreach my $s (@seq) { $s.="\n"; $self->_print ($s); } } } =head2 next_matrix Title : next_matrix Usage : my $matrix = $psmio->next_matrix; Function: Alias of next_psm function =cut sub next_matrix { shift->next_psm(@_); } =head2 next_psm Title : next_psm Usage : my $matrix=$psmio->next_psm; Function: returns the next matrix in the stream Throws : If there is you mix different types, for example weights and frequencies occur in the same entry You can mix weights, but these should be designated by different ID lines Example : Args : Returns : Bio::Matrix::PSM::SiteMatrix =cut sub next_psm { my $self=shift; return if ($self->{_end}); my $line=$self->_readline; $self->throw("No ID line- wrong format\n") unless ($line=~/^>/); my ($id,$desc)=split(/[\t\s]+/,$line,2); $id=~s/>//; my ($mtype,$format,@mdata,$len); $self->{_mtype} = 0; while ($line=$self->_readline) { next if $line =~ /^\s+$/;# There should not be empty lines, but just in case... chomp $line; if ($line =~ /^>/) { $self->_pushback($line); last; } if ($line !~ /[^ACGTacgt]/g) { # This is a set of aligned sequences $self->throw("Mixing between types is not allowed or a parsing error occurred\n") if (($self->{_mtype} != 3) && ($mtype)) ; $self->throw("Bad sequence- different length: $line\n") if (($len) && ($len!=length($line))); $len=length($line) unless ($len); push @mdata,$line; $self->{_mtype}=3; } else { # do not strip 'e's since they are part of number notation for small/big numbers $line=~s/[a-df-zA-DF-Z]//g; #Well we may wanna do a hash and auto check for letter order if there is a really boring talk... $line=~s/^[\s\t]+//; $line=~s/[\s\t]+/\t/g; my @data=split(/[\s\t]+/,$line); if ($#data==3) { $self->throw("Mixing between types is not allowed or a parsing error occurred\n") if (($mtype)&&($self->{_mtype} !=1)) ; $self->{_mtype}=1; $mtype=1; } else { $self->throw("Mixing between types is not allowedor a parsing error occurred\n") if (($mtype)&&($self->{_mtype} !=2)) ; $self->{_mtype}=2; $mtype=1; } push @mdata,\@data; } } $self->{_end} = 1 if (!defined $line || $line !~ /^>/); return _make_matrix(\@mdata,$self->{_mtype},$id,$desc); } sub _make_matrix { my ($mdata,$type,$id,$desc)=@_; if ($type==1) { my @rearr=_rearrange_matrix($mdata); $mdata=\@rearr; } #Auto recognition for what type is this entry (PFM, PWM or simple count) #A bit dangerous, I hate too much auto stuff, but I want to be able to mix different #types in a single file my $mformat='count'; my ($a,$c,$g,$t); if ($type == 3 ) { ($a,$c,$g,$t)= &_count_positions($mdata); } else { ($a,$c,$g,$t)=@{$mdata}; my $k=$a->[0]+$c->[0]+$g->[0]+$t->[0]; my $l= ($a->[0]+$c->[0]+$g->[0]+$t->[0]) - (abs($a->[0])+abs($c->[0])+abs($g->[0])+abs($t->[0])); $mformat='freq' if (($k==1) && ($l==0)); $mformat='pwm' if ($l!=0); } my (@fa,@fc,@fg,@ft,%mparam); if ($mformat eq 'pwm') { foreach my $i (0..$#{$a}) { my $ca=exp $a->[$i]; my $cc=exp $c->[$i]; my $cg=exp $g->[$i]; my $ct=exp $t->[$i]; my $all=$ca+$cc+$cg+$ct; push @fa,($ca/$all)*100; push @fc,($cc/$all)*100; push @fg,($cg/$all)*100; push @ft,($ct/$all)*100; } } $desc.=", source is $mformat"; if ($mformat eq 'pwm') { $desc=~s/^pwm//; %mparam=(-pA=>\@fa,-pC=>\@fc,-pG=>\@fg,-pT=>\@ft,-id=>$id,-desc=>$desc, -lA=>$a,-lC=>$c,-lG=>$g,-lT=>$t); } else { %mparam=(-pA=>$a,-pC=>$c,-pG=>$g,-pT=>$t,-id=>$id,-desc=>$desc); } return new Bio::Matrix::PSM::SiteMatrix(%mparam); } sub _rearrange_matrix { my $mdata=shift; my (@a,@c,@g,@t); foreach my $entry (@{$mdata}) { my ($a,$c,$g,$t)=@$entry; push @a,$a; push @c,$c; push @g,$g; push @t,$t; } return \@a,\@c,\@g,\@t; } sub _count_positions { my $seq=shift; my %pos; my $l=length($seq->[0])-1; for( my $i = 0; $i <= $l; $i++ ) { for ( qw(A C G T) ) { $pos{$_}->[$i] = 0; } } foreach my $sequence (@{$seq}) { my @let= split(//,$sequence); for my $i (0..$#let) { $pos{uc($let[$i])}->[$i]++; } } return $pos{A},$pos{C},$pos{G},$pos{T}; } sub _freq_to_count { my $h=shift; my $a=int(10*$h->{pA}+0.5); my $c=int(10*$h->{pC}+0.5); my $g=int(10*$h->{pG}+0.5); my $t=int(10*$h->{pT}+0.5); return ($a,$c,$g,$t); } 1; BioPerl-1.007002/Bio/Matrix/PSM/IO/meme.pm000444000766000024 2261613155576320 17746 0ustar00cjfieldsstaff000000000000#--------------------------------------------------------- =head1 NAME Bio::Matrix::PSM::IO::meme - PSM meme parser implementation =head1 SYNOPSIS See Bio::Matrix::PSM::IO for detailed documentation on how to use PSM parsers =head1 DESCRIPTION Parser for meme. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::IO::meme; use Bio::Matrix::PSM::InstanceSite; use Bio::Matrix::PSM::SiteMatrix; use Bio::Matrix::PSM::Psm; use vars qw(@HEADER); use strict; use base qw(Bio::Matrix::PSM::PsmHeader Bio::Matrix::PSM::IO); @Bio::Matrix::PSM::IO::meme::HEADER = qw(e_val sites IC width); =head2 new Title : new Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'meme', -file=>$file); Function: Associates a file with the appropriate parser Throws : Throws if the file passed is in HTML format or if the MEME header cannot be found. Example : Args : hash Returns : "Bio::Matrix::PSM::$format"->new(@args); =cut sub new { my($class, @args)=@_; my $self = $class->SUPER::new(@args); my ($file)=$self->_rearrange(['FILE'], @args); my ($query,$tr1)=split(/\./,$file,2); $self->{file} = $file; $self->{query}= $query; $self->{end} = 0; $self->{_strand}=0; #This we'll need to see if revcom option is used $self->_initialize_io(@args) || warn "Did you intend to use STDIN?"; #Read only for now #Skip header my $line; while (my $line=$self->_readline) { $self->throw('Cannot parse HTML, please use text output\n') if ($line=~//); #Should start parsing HTML output, not a bug deal chomp($line); if ($line=~"^ALPHABET") { $self=_parse_coordinates($self); last; } push @{$self->{unstructured}},$line unless (($line=~/\*{10,}/) || ($line eq '')); } $self->_initialize; return $self; } =head2 _parse_coordinates Title : _parse_coordinates Usage : Function: Throws : Example : Internal stuff Returns : Args : =cut sub _parse_coordinates { my $self=shift; $self->_readline; $self->_readline; my $line=$self->_readline; while ($line !~ /^\*{10,}/ ) { chomp $line; $line =~ s/\s+/,/g; my ($id1,$w1,$l1,$id2,$w2,$l2)=split(/,/,$line); push @{$self->{hid}},$id1; $self->{weight}->{$id1}=$w1; $self->{length}->{$id1}=$l1; if ($id2) { push @{$self->{hid}},$id2; $self->{weight}->{$id2}=$w2; $self->{length}->{$id2}=$l2; } $line=$self->_readline; } return $self; } =head2 header Title : header Usage : my %header=$psmIO->header; Function: Returns the header for the MEME file Throws : Example : Fetching all the sequences included in the MEME analysis, being parsed my %header=$psmIO->header; foreach my $seqid (@{$header{instances}}) { my $seq=$db->get_Seq_by_acc($id); #Do something with the sequence } where $db might be Bio::DB:GenBank object, see Returns : Hash with three keys: instances, weights and lengths, which should be self-explenatory. Each value is an array reference. Each array element corresponds to the same element in the other two arrays. So $header{instances}->[$i] will refer to the same sequence in the motif file as $header{weights}->[$i] and $header{lengths}->[$i] Args : none Notes : OBSOLETE! =cut sub header { my $self=shift; my @instances=@{$self->{_inst_name}}; my @weights=@{$self->{_inst_weight}}; my @lengths=@{$self->{_inst_coord}}; return (instances=>\@instances,weights=>\@weights,lengths=>\@lengths); } =head2 next_psm Title : next_psm Usage : my $psm=$psmIO->next_psm(); Function: Reads the next PSM from the input file, associated with this object Throws : Throws if the format is inconsistent with the rules for MEME 3.0.4: no SUMMARY Section present or some keywords are missing/altered. Example : Returns : Bio::Matrix::PSM::Psm object Args : none =cut sub next_psm { #Parses the next prediction and returns a psm objects my $self=shift; return if ($self->{end}); my ($endm,$line,$instances,$tr,$width,$motif_id,$sites,$e_val,$id,$ic,$lA,$lC,$lG,$lT); while (defined( $line = $self->_readline) ) { #Check if revcom is enabled, not very original check.... $self->{_strand}=1 if (($line=~/^Sequence name/) && ($line=~/Strand/)); if ($line=~ m/\sSite\s/) { $instances= $self->_parseInstance; } #Here starts the next motif if ( ($line=~/width/) && ($line=~/sites/)) { chomp($line); $line=~s/[\t\s=]+/,/g; $line=~s/\t/,/g; #Parsing the general information for this prediction ($tr,$motif_id,$tr,$width,$tr,$sites, $tr,$tr,$tr,$e_val)=split(/,/,$line); $self->{id}=$self->{query} . $motif_id; } if ($line =~ /content/i) { $line=$self->_readline; chomp($line); $line=~s/[\)\(]//g; ($ic)=split(/\s/,$line); } #Last info-prob matrix data if ($line=~/position-specific\s+scoring matrix/) { ($lA,$lC,$lG,$lT)=_parse_logs($self); } if ($line=~/^letter-probability\smatrix/) { my %matrix_dat=$self->_parseMatrix($motif_id); my $psm= Bio::Matrix::PSM::Psm->new(%matrix_dat, -instances=>$instances, -e_val=>$e_val, -IC=>$ic, -width=>$width, -sites=>$sites, -lA=>$lA, -lC=>$lC, -lG=>$lG, -lT=>$lT, ); return $psm; } if ($line=~"SUMMARY OF MOTIFS") { $self->{end}=1; return; } $endm=1 if ($line=~/^Time\s/); } if ($endm) { #End of file found, end of current motif too, but not all predictions were made as requested (No summary) $self->{end}=1; warn "This MEME analysis was terminated prematurely, you may have less motifs than you requested\n"; return; } $self->throw("Wrong format\n"); # Multiple keywords not found, probably wrong format } =head2 _parseMatrix Title : _parseMatrix Usage : Function: Parses the next site matrix information in the meme file Throws : Example : Internal stuff Returns : hash as for constructing a SiteMatrix object (see SiteMatrixI) Args : string =cut sub _parseMatrix { my ($self,$id)=@_; my (@pA,@pC,@pG,@pT); my $i=0; my $line = $self->_readline; #Most important part- the probability matrix do { chomp $line; last if ($line eq ''); $line=~s/^\s+//; $line=~s/\s+/,/g; ($pA[$i],$pC[$i],$pG[$i],$pT[$i])=split(/,/,$line); $i++; $line=$self->_readline; } until $line =~ /\-{10,}/; return (-pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT,-id=>$id); } =head2 _parse_logs Title : _parse_logs Usage : Function: Parses the next site matrix log values in the meme file Throws : Example : Internal stuff Returns : array of array refs Args : string =cut sub _parse_logs { my $self=shift; my (@lA,@lC,@lG,@lT); my $i=0; $self->_readline; $self->_readline; my $line = $self->_readline; #Most important part- the probability matrix do { chomp $line; last if ($line eq ''); $line=~s/^\s+//; $line=~s/\s+/,/g; ($lA[$i],$lC[$i],$lG[$i],$lT[$i])=split(/,/,$line); $i++; $line=$self->_readline; } until $line =~ /\-{10,}/; return (\@lA,\@lC,\@lG,\@lT); } =head2 _parseInstance Title : _parseInstance Usage : Function: Parses the next sites instances from the meme file Throws : Example : Internal stuff Returns : Bio::Matrix::PSM::InstanceSite object Args : none =cut sub _parseInstance { my $self = shift; my $i=0; $self->_readline; my ($line,@instance); while (defined($line=$self->_readline) ) { last if ($line =~ /\-{5}/ ); chomp($line); my @comp=split(/\s+/,$line); my ($id,$start,$score,$strand,$s1,$s2,$s3); if ( $self->{_strand}) { ($id,$strand,$start,$score,$s1,$s2,$s3)=@comp; } else { ($id,$start,$score,$s1,$s2,$s3)=@comp; $strand=1; } my $seq= $s1.$s2.$s3; if ($seq =~ /[^ACGTacgtNnXx\-\.]/) { my $col=$#comp; $self->throw("I have not been able to parse the correct instance sequence: $seq, $col columns\n"); } my $sid = $self->{id} . '@' . $id; $instance[$i] = Bio::Matrix::PSM::InstanceSite->new (-mid => $self->{id}, -start => $start, -score => $score, -seq => $seq, -strand => $strand, -accession_number => $id, -primary_id => $sid, -desc => 'Bioperl MEME parser object' ); $i++; } $self->{instances} = \@instance; return \@instance; } 1; BioPerl-1.007002/Bio/Matrix/PSM/IO/psiblast.pm000444000766000024 722613155576320 20624 0ustar00cjfieldsstaff000000000000#--------------------------------------------------------- =head1 NAME Bio::Matrix::PSM::IO::psiblast - PSM psiblast parser =head1 SYNOPSIS See Bio::Matrix::PSM::IO for documentation =head1 DESCRIPTION Parser for ASCII matrices from PSI-BLAST (blastpgp program in BLAST distribution). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - James Thompson Email tex@biosysadmin.com =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::IO::psiblast; use Bio::Matrix::PSM::Psm; use Bio::Matrix::PSM::ProtMatrix; use strict; use base qw(Bio::Matrix::PSM::PsmHeader Bio::Matrix::PSM::IO); # define the order in which amino acids are listed in the psiblast matrix file our @ordered_alphabet = qw/A R N D C Q E G H I L K M F P S T W Y V/; =head2 new Title : new Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'psiblast', -file=>$file); Function: Associates a file with the appropriate parser Throws : Example : Args : Returns : Bio::Matrix::PSM::ProtMatrix->new(@args); =cut sub new { my ($class,@args)=@_; my $line; my $self = $class->SUPER::new(@args); my ($file) = $self->_rearrange(['FILE'], @args); $self->_initialize_io(@args) || warn "Did you intend to use STDIN?"; # Read only for now $self->_initialize; $self->{_ordered_alphabet} = \@ordered_alphabet; return $self; } =head2 next_psm Title : next_psm Usage : my $psm = $psmIO->next_psm(); Function: Reads the next PSM from the input file, associated with this object Throws : None Returns : Bio::Matrix::PSM::ProtPsm object Args : none =cut sub next_psm { my $self = shift; my $line; return if ($self->{_end}); my %args; my @ordered_alphabet = @{$self->{_ordered_alphabet}}; while ( defined( $line = $self->_readline) ) { # remove leading and trailing whitespace chomp $line; $line =~ s/^\s+//g; $line =~ s/\s+$//g; if ( $line =~ /^(\d+)\s+(\w{1})/ ) { # match reference aa and position number my @elements = split /\s+/, $line; my $position = shift @elements; my $letter = shift @elements; my $ratio = pop @elements; my $ic = pop @elements; # put the next 20 elements into the correct array in %args for ( 0 .. 19 ) { push @{$args{'l'.$ordered_alphabet[$_]}}, shift @elements; } for ( 0 .. 19 ) { push @{$args{'p'.$ordered_alphabet[$_]}}, shift @elements; } push @{$args{'ic'}}, $ic; } } $self->{_end} = 1; # psiblast matrix files currently only hold one PSM per file my $psm = Bio::Matrix::PSM::ProtMatrix->new( %args ); return $psm; } sub DESTROY { my $self=shift; $self->close; } 1; BioPerl-1.007002/Bio/Matrix/PSM/IO/transfac.pm000444000766000024 1544313155576320 20624 0ustar00cjfieldsstaff000000000000#--------------------------------------------------------- =head1 NAME Bio::Matrix::PSM::IO::transfac - PSM transfac parser =head1 SYNOPSIS See Bio::Matrix::PSM::IO for documentation =head1 DESCRIPTION # =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::IO::transfac; use Bio::Matrix::PSM::Psm; use Bio::Root::Root; use Bio::Annotation::Reference; use Bio::Annotation::Comment; use Bio::Annotation::DBLink; use strict; use base qw(Bio::Matrix::PSM::PsmHeader Bio::Matrix::PSM::IO); =head2 new Title : new Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'transfac', -file=>$file); Function: Associates a file with the appropriate parser Throws : Example : Args : Returns : "Bio::Matrix::PSM::$format"->new(@args); =cut sub new { my ($class,@args)=@_; my $line; my $self = $class->SUPER::new(@args); my ($file)=$self->_rearrange(['FILE'], @args); $self->_initialize_io(@args) || warn "Did you intend to use STDIN?"; #Read only for now #Remove header do { $line=$self->_readline; chomp $line; push @{$self->{unstructured}},$line if (length($line)>2); } until ($line =~ m{^//}) || (!defined($line)); #Unstructured header $self->_initialize; return $self; } =head2 next_psm Title : next_psm Usage : my $psm=$psmIO->next_psm(); Function: Reads the next PSM from the input file, associated with this object Throws : Upon finding a line, defining the matrix, where one or more positions are not defined, see _make_matrix Returns : Bio::Matrix::PSM::Psm object Args : none =cut sub next_psm { my $self=shift; my $line; return if ($self->{end}); my (@a,@c,@g,@t, $id, $tr1, @refs,$accn, $bf, $sites); my $i=0; while (defined( $line=$self->_readline)) { chomp($line); if ($line=~/^\d{2}/) { #Begining of the frequency data ($a[$i],$c[$i],$g[$i],$t[$i])=_parse_matrix($line); $i++; } ($tr1,$accn)=split(/\s{2}/,$line) if ($line=~/^AC\s/); ($tr1,$bf)=split(/\s{2}/,$line) if ($line=~/^BF\s/); ($tr1,$id)=split(/\s{2}/,$line) if ($line=~/^ID\s/); last if (($line=~/^XX/) && ($i>0)); } if (!(defined($id) && defined($accn))) { $self->{end}=1; return; } while (defined( $line=$self->_readline)) { #How many sites? if ($line=~/^BA\s/) { my ($tr1,$ba)=split(/\s{2}/,$line); ($sites)=split(/\s/,$ba); } if ($line=~/^RN/) { #Adding a reference as Bio::Annotation object (self) # not interested in RN line itself, since has only transfac-specific # reference id? - no push back of line my $ref=_parse_ref($self); push @refs,$ref } last if ($line=~m{^//}); } # We have the frequencies, let's create a SiteMatrix object my %matrix = &_make_matrix($self,\@a,\@c,\@g,\@t,$id, $accn); $matrix{-sites}=$sites if ($sites); $matrix{-width}=@a; my $psm=Bio::Matrix::PSM::Psm->new(%matrix); foreach my $ref (@refs) { $psm->add_Annotation('reference',$ref); } return $psm; } =head2 _parseMatrix Title : _parseMatrix Usage : Function: Parses a line Throws : Example : Internal stuff Returns : array (frequencies for A,C,G,T in this order). Args : string =cut sub _parse_matrix { my $line=shift; $line=~s/\s+/,/g; my ($tr,$a,$c,$g,$t)=split(/,/,$line); return $a,$c,$g,$t; } =head2 _make_matrix Title : _make_matrix Usage : Function: Throws : If a position is undefined, for example if you have line like this in the file you are parsing: 08 4,7,,9 Example : Internal stuff Returns : Args : =cut sub _make_matrix { my ($a, $c, $g, $t, @fa, @fc,@fg, @ft, @a,@c,@g,@t); my $ave=0; my ($self,$cA,$cC,$cG,$cT, $id, $accn)= @_; for (my $i=0; $i < @{$cA};$i++) { #No value can be undefined -throw an exception, since setting to 0 probably would be wrong #If this happens it would indicate most probably that the file, being parsed is in a different format map { $self->throw('Parsing error, a position is not defined') unless defined(${$_}[$i]) } ($cA, $cG, $cC, $cT); if ( (${$cA}[$i] + ${$cC}[$i] + ${$cG}[$i] + ${$cT}[$i] ) ==0 ) { push @a,$ave; push @c,$ave; push @g,$ave; push @t,$ave; } else { push @a,${$cA}[$i]; push @c,${$cC}[$i]; push @g,${$cG}[$i]; push @t,${$cT}[$i]; $ave = ((${$cA}[$i]+${$cC}[$i]+ ${$cG}[$i]+${$cT}[$i]) / 4 +$ave)/2; } } for (my $i=0; $i<@a;$i++) { my $zero=($a[$i]+$c[$i]+$g[$i]+$t[$i]); next if ($zero==0); push @fa, $a[$i]; push @fc, $c[$i]; push @fg, $g[$i]; push @ft, $t[$i]; } return (-pA=>\@fa,-pC=>\@fc,-pG=>\@fg,-pT=>\@ft, -id=>$id, -accession_number=>$accn) } sub _parse_ref { my $self=shift; my ($authors,$title,$loc,@refs,$tr,$db,$dbid); while (my $refline=$self->_readline) { #Poorely designed, should go through an array with fields chomp $refline; my ($field,$arg)=split(/\s+/,$refline,2); last if ($field=~/XX/); $field.=' '; REF: { if ($field=~/RX/) { #DB Reference $refline=~s/[;\.]//g; ($tr, $db, $dbid)=split(/\s+/,$refline); last REF; } if ($field=~/RT/) { #Title $title .= $arg; last REF; } if ($field=~/RA/) { #Author $authors .= $arg; last REF; } if ($field=~/RL/) { #Journal $loc .= $arg; last REF; } } } my $reference=Bio::Annotation::Reference->new(-authors=>$authors, -title=>$title, -location=>$loc); if ($db eq 'MEDLINE') { # does it ever equal medline? $reference->medline($dbid); } elsif ($dbid) { $reference->pubmed($dbid); } return $reference; } sub DESTROY { my $self=shift; $self->close; } 1; BioPerl-1.007002/Bio/MolEvol000755000766000024 013155576320 15444 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/MolEvol/CodonModel.pm000444000766000024 26415113155576320 20233 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::MolEvol::CodonModel # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::MolEvol::CodonModel - Codon Evolution Models =head1 SYNOPSIS use Bio::MolEvol::CodonModel; my $codon_path = Bio::MolEvol::CodonModel->codon_path; my ($ns, $syn) = $codon_path->{'AATAAC'}; print "AAT -> AAC: $ns ns mutations, $syn syn mutations\n"; =head1 DESCRIPTION This object is intended to group Codon Evolution Models. Currently it has one method codon_path that returns a hash reference representing the number of mutations it takes to mutate from one codon to another. Some more description of how this is generated will follow later. Additional codon evolution models and substitution matricies could be represented here as well. Some of this may not be optimally named so this can change before the next stable release of the BioPerl code. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org This is based on code and work from Alisha Holloway at UC Davis and Corbin Jones at UNC-Chapel Hill. See Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans http://dx.doi.org/http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050310 and http://www.dpgp.org/ =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::MolEvol::CodonModel; =head2 codon_path Title : codon_path Usage : return a matrix of edit paths between codons Example : my $codon_path = Bio::MolEvol::CodonModel->codon_path; Returns : Hash reference, the array values for each codon path are num of Nonsyn & syn changes respectively. Args : none =cut sub codon_path { return { 'AAAAAA' => [0,0], 'AAAAAC' => [1,0], 'AAAAAG' => [0,1], 'AAAAAT' => [1,0], 'AAAACA' => [1,0], 'AAAACC' => [1,1], 'AAAACG' => [1,1], 'AAAACT' => [1,1], 'AAAAGA' => [1,0], 'AAAAGC' => [2,0], 'AAAAGG' => [1,1], 'AAAAGT' => [2,0], 'AAAATA' => [1,0], 'AAAATC' => [1,1], 'AAAATG' => [1,1], 'AAAATT' => [1,1], 'AAACAA' => [1,0], 'AAACAC' => [2,0], 'AAACAG' => [1,1], 'AAACAT' => [2,0], 'AAACCA' => [2,0], 'AAACCC' => [2,1], 'AAACCG' => [2,1], 'AAACCT' => [2,1], 'AAACGA' => [1,1], 'AAACGC' => [1,2], 'AAACGG' => [1,2], 'AAACGT' => [1,2], 'AAACTA' => [2,0], 'AAACTC' => [2,1], 'AAACTG' => [2,1], 'AAACTT' => [2,1], 'AAAGAA' => [1,0], 'AAAGAC' => [2,0], 'AAAGAG' => [1,1], 'AAAGAT' => [2,0], 'AAAGCA' => [2,0], 'AAAGCC' => [2,1], 'AAAGCG' => [2,1], 'AAAGCT' => [2,1], 'AAAGGA' => [2,0], 'AAAGGC' => [2,1], 'AAAGGG' => [2,1], 'AAAGGT' => [2,1], 'AAAGTA' => [2,0], 'AAAGTC' => [2,1], 'AAAGTG' => [2,1], 'AAAGTT' => [2,1], 'AAATAC' => [2,0], 'AAATAT' => [2,0], 'AAATCA' => [2,0], 'AAATCC' => [2,1], 'AAATCG' => [2,1], 'AAATCT' => [2,1], 'AAATGC' => [3,0], 'AAATGG' => [2,1], 'AAATGT' => [3,0], 'AAATTA' => [2,0], 'AAATTC' => [2,1], 'AAATTG' => [2,1], 'AAATTT' => [2,1], 'AACAAA' => [1,0], 'AACAAC' => [0,0], 'AACAAG' => [1,0], 'AACAAT' => [0,1], 'AACACA' => [1,1], 'AACACC' => [1,0], 'AACACG' => [1,1], 'AACACT' => [1,1], 'AACAGA' => [2,0], 'AACAGC' => [1,0], 'AACAGG' => [2,0], 'AACAGT' => [1,1], 'AACATA' => [1,1], 'AACATC' => [1,0], 'AACATG' => [2,0], 'AACATT' => [1,1], 'AACCAA' => [2,0], 'AACCAC' => [1,0], 'AACCAG' => [2,0], 'AACCAT' => [1,1], 'AACCCA' => [2,1], 'AACCCC' => [2,0], 'AACCCG' => [2,1], 'AACCCT' => [2,1], 'AACCGA' => [2,1], 'AACCGC' => [2,0], 'AACCGG' => [2,1], 'AACCGT' => [2,1], 'AACCTA' => [2,1], 'AACCTC' => [2,0], 'AACCTG' => [2,1], 'AACCTT' => [2,1], 'AACGAA' => [2,0], 'AACGAC' => [1,0], 'AACGAG' => [2,0], 'AACGAT' => [1,1], 'AACGCA' => [2,1], 'AACGCC' => [2,0], 'AACGCG' => [2,1], 'AACGCT' => [2,1], 'AACGGA' => [2,1], 'AACGGC' => [2,0], 'AACGGG' => [2,1], 'AACGGT' => [2,1], 'AACGTA' => [2,1], 'AACGTC' => [2,0], 'AACGTG' => [2,1], 'AACGTT' => [2,1], 'AACTAC' => [1,0], 'AACTAT' => [1,1], 'AACTCA' => [2,1], 'AACTCC' => [2,0], 'AACTCG' => [2,1], 'AACTCT' => [2,1], 'AACTGC' => [2,0], 'AACTGG' => [3,0], 'AACTGT' => [2,1], 'AACTTA' => [2,1], 'AACTTC' => [2,0], 'AACTTG' => [3,0], 'AACTTT' => [2,1], 'AAGAAA' => [0,1], 'AAGAAC' => [1,0], 'AAGAAG' => [0,0], 'AAGAAT' => [1,0], 'AAGACA' => [1,1], 'AAGACC' => [1,1], 'AAGACG' => [1,0], 'AAGACT' => [1,1], 'AAGAGA' => [1,1], 'AAGAGC' => [2,0], 'AAGAGG' => [1,0], 'AAGAGT' => [2,0], 'AAGATA' => [1,1], 'AAGATC' => [2,0], 'AAGATG' => [1,0], 'AAGATT' => [2,0], 'AAGCAA' => [1,1], 'AAGCAC' => [2,0], 'AAGCAG' => [1,0], 'AAGCAT' => [2,0], 'AAGCCA' => [2,1], 'AAGCCC' => [2,1], 'AAGCCG' => [2,0], 'AAGCCT' => [2,1], 'AAGCGA' => [1,2], 'AAGCGC' => [1,2], 'AAGCGG' => [1,1], 'AAGCGT' => [1,2], 'AAGCTA' => [2,1], 'AAGCTC' => [2,1], 'AAGCTG' => [2,0], 'AAGCTT' => [2,1], 'AAGGAA' => [1,1], 'AAGGAC' => [2,0], 'AAGGAG' => [1,0], 'AAGGAT' => [2,0], 'AAGGCA' => [2,1], 'AAGGCC' => [2,1], 'AAGGCG' => [2,0], 'AAGGCT' => [2,1], 'AAGGGA' => [2,1], 'AAGGGC' => [2,1], 'AAGGGG' => [2,0], 'AAGGGT' => [2,1], 'AAGGTA' => [2,1], 'AAGGTC' => [2,1], 'AAGGTG' => [2,0], 'AAGGTT' => [2,1], 'AAGTAC' => [2,0], 'AAGTAT' => [2,0], 'AAGTCA' => [2,1], 'AAGTCC' => [2,1], 'AAGTCG' => [2,0], 'AAGTCT' => [2,1], 'AAGTGC' => [3,0], 'AAGTGG' => [2,0], 'AAGTGT' => [3,0], 'AAGTTA' => [2,1], 'AAGTTC' => [3,0], 'AAGTTG' => [2,0], 'AAGTTT' => [3,0], 'AATAAA' => [1,0], 'AATAAC' => [0,1], 'AATAAG' => [1,0], 'AATAAT' => [0,0], 'AATACA' => [1,1], 'AATACC' => [1,1], 'AATACG' => [1,1], 'AATACT' => [1,0], 'AATAGA' => [2,0], 'AATAGC' => [1,1], 'AATAGG' => [2,0], 'AATAGT' => [1,0], 'AATATA' => [1,1], 'AATATC' => [1,1], 'AATATG' => [2,0], 'AATATT' => [1,0], 'AATCAA' => [2,0], 'AATCAC' => [1,1], 'AATCAG' => [2,0], 'AATCAT' => [1,0], 'AATCCA' => [2,1], 'AATCCC' => [2,1], 'AATCCG' => [2,1], 'AATCCT' => [2,0], 'AATCGA' => [2,1], 'AATCGC' => [2,1], 'AATCGG' => [2,1], 'AATCGT' => [2,0], 'AATCTA' => [2,1], 'AATCTC' => [2,1], 'AATCTG' => [2,1], 'AATCTT' => [2,0], 'AATGAA' => [2,0], 'AATGAC' => [1,1], 'AATGAG' => [2,0], 'AATGAT' => [1,0], 'AATGCA' => [2,1], 'AATGCC' => [2,1], 'AATGCG' => [2,1], 'AATGCT' => [2,0], 'AATGGA' => [2,1], 'AATGGC' => [2,1], 'AATGGG' => [2,1], 'AATGGT' => [2,0], 'AATGTA' => [2,1], 'AATGTC' => [2,1], 'AATGTG' => [2,1], 'AATGTT' => [2,0], 'AATTAC' => [1,1], 'AATTAT' => [1,0], 'AATTCA' => [2,1], 'AATTCC' => [2,1], 'AATTCG' => [2,1], 'AATTCT' => [2,0], 'AATTGC' => [2,1], 'AATTGG' => [3,0], 'AATTGT' => [2,0], 'AATTTA' => [2,1], 'AATTTC' => [2,1], 'AATTTG' => [3,0], 'AATTTT' => [2,0], 'ACAAAA' => [1,0], 'ACAAAC' => [1,1], 'ACAAAG' => [1,1], 'ACAAAT' => [1,1], 'ACAACA' => [0,0], 'ACAACC' => [0,1], 'ACAACG' => [0,1], 'ACAACT' => [0,1], 'ACAAGA' => [1,0], 'ACAAGC' => [1,1], 'ACAAGG' => [1,1], 'ACAAGT' => [1,1], 'ACAATA' => [1,0], 'ACAATC' => [1,1], 'ACAATG' => [1,1], 'ACAATT' => [1,1], 'ACACAA' => [2,0], 'ACACAC' => [2,1], 'ACACAG' => [2,1], 'ACACAT' => [2,1], 'ACACCA' => [1,0], 'ACACCC' => [1,1], 'ACACCG' => [1,1], 'ACACCT' => [1,1], 'ACACGA' => [1,1], 'ACACGC' => [1,2], 'ACACGG' => [1,2], 'ACACGT' => [1,2], 'ACACTA' => [2,0], 'ACACTC' => [2,1], 'ACACTG' => [2,1], 'ACACTT' => [2,1], 'ACAGAA' => [2,0], 'ACAGAC' => [2,1], 'ACAGAG' => [2,1], 'ACAGAT' => [2,1], 'ACAGCA' => [1,0], 'ACAGCC' => [1,1], 'ACAGCG' => [1,1], 'ACAGCT' => [1,1], 'ACAGGA' => [2,0], 'ACAGGC' => [2,1], 'ACAGGG' => [2,1], 'ACAGGT' => [2,1], 'ACAGTA' => [2,0], 'ACAGTC' => [2,1], 'ACAGTG' => [2,1], 'ACAGTT' => [2,1], 'ACATAC' => [2,1], 'ACATAT' => [2,1], 'ACATCA' => [1,0], 'ACATCC' => [1,1], 'ACATCG' => [1,1], 'ACATCT' => [1,1], 'ACATGC' => [2,1], 'ACATGG' => [2,1], 'ACATGT' => [2,1], 'ACATTA' => [2,0], 'ACATTC' => [2,1], 'ACATTG' => [2,1], 'ACATTT' => [2,1], 'ACCAAA' => [1,1], 'ACCAAC' => [1,0], 'ACCAAG' => [1,1], 'ACCAAT' => [1,1], 'ACCACA' => [0,1], 'ACCACC' => [0,0], 'ACCACG' => [0,1], 'ACCACT' => [0,1], 'ACCAGA' => [1,1], 'ACCAGC' => [1,0], 'ACCAGG' => [1,1], 'ACCAGT' => [1,1], 'ACCATA' => [1,1], 'ACCATC' => [1,0], 'ACCATG' => [1,1], 'ACCATT' => [1,1], 'ACCCAA' => [2,1], 'ACCCAC' => [2,0], 'ACCCAG' => [2,1], 'ACCCAT' => [2,1], 'ACCCCA' => [1,1], 'ACCCCC' => [1,0], 'ACCCCG' => [1,1], 'ACCCCT' => [1,1], 'ACCCGA' => [1,2], 'ACCCGC' => [2,0], 'ACCCGG' => [1,2], 'ACCCGT' => [2,1], 'ACCCTA' => [2,1], 'ACCCTC' => [2,0], 'ACCCTG' => [2,1], 'ACCCTT' => [2,1], 'ACCGAA' => [2,1], 'ACCGAC' => [2,0], 'ACCGAG' => [2,1], 'ACCGAT' => [2,1], 'ACCGCA' => [1,1], 'ACCGCC' => [1,0], 'ACCGCG' => [1,1], 'ACCGCT' => [1,1], 'ACCGGA' => [2,1], 'ACCGGC' => [2,0], 'ACCGGG' => [2,1], 'ACCGGT' => [2,1], 'ACCGTA' => [2,1], 'ACCGTC' => [2,0], 'ACCGTG' => [2,1], 'ACCGTT' => [2,1], 'ACCTAC' => [2,0], 'ACCTAT' => [2,1], 'ACCTCA' => [1,1], 'ACCTCC' => [1,0], 'ACCTCG' => [1,1], 'ACCTCT' => [1,1], 'ACCTGC' => [2,0], 'ACCTGG' => [2,1], 'ACCTGT' => [2,1], 'ACCTTA' => [2,1], 'ACCTTC' => [2,0], 'ACCTTG' => [2,1], 'ACCTTT' => [2,1], 'ACGAAA' => [1,1], 'ACGAAC' => [1,1], 'ACGAAG' => [1,0], 'ACGAAT' => [1,1], 'ACGACA' => [0,1], 'ACGACC' => [0,1], 'ACGACG' => [0,0], 'ACGACT' => [0,1], 'ACGAGA' => [1,1], 'ACGAGC' => [1,1], 'ACGAGG' => [1,0], 'ACGAGT' => [1,1], 'ACGATA' => [1,1], 'ACGATC' => [1,1], 'ACGATG' => [1,0], 'ACGATT' => [1,1], 'ACGCAA' => [2,1], 'ACGCAC' => [2,1], 'ACGCAG' => [2,0], 'ACGCAT' => [2,1], 'ACGCCA' => [1,1], 'ACGCCC' => [1,1], 'ACGCCG' => [1,0], 'ACGCCT' => [1,1], 'ACGCGA' => [1,2], 'ACGCGC' => [1,2], 'ACGCGG' => [1,1], 'ACGCGT' => [1,2], 'ACGCTA' => [2,1], 'ACGCTC' => [2,1], 'ACGCTG' => [2,0], 'ACGCTT' => [2,1], 'ACGGAA' => [2,1], 'ACGGAC' => [2,1], 'ACGGAG' => [2,0], 'ACGGAT' => [2,1], 'ACGGCA' => [1,1], 'ACGGCC' => [1,1], 'ACGGCG' => [1,0], 'ACGGCT' => [1,1], 'ACGGGA' => [2,1], 'ACGGGC' => [2,1], 'ACGGGG' => [2,0], 'ACGGGT' => [2,1], 'ACGGTA' => [2,1], 'ACGGTC' => [2,1], 'ACGGTG' => [2,0], 'ACGGTT' => [2,1], 'ACGTAC' => [2,1], 'ACGTAT' => [2,1], 'ACGTCA' => [1,1], 'ACGTCC' => [1,1], 'ACGTCG' => [1,0], 'ACGTCT' => [1,1], 'ACGTGC' => [2,1], 'ACGTGG' => [2,0], 'ACGTGT' => [2,1], 'ACGTTA' => [2,1], 'ACGTTC' => [2,1], 'ACGTTG' => [2,0], 'ACGTTT' => [2,1], 'ACTAAA' => [1,1], 'ACTAAC' => [1,1], 'ACTAAG' => [1,1], 'ACTAAT' => [1,0], 'ACTACA' => [0,1], 'ACTACC' => [0,1], 'ACTACG' => [0,1], 'ACTACT' => [0,0], 'ACTAGA' => [1,1], 'ACTAGC' => [1,1], 'ACTAGG' => [1,1], 'ACTAGT' => [1,0], 'ACTATA' => [1,1], 'ACTATC' => [1,1], 'ACTATG' => [1,1], 'ACTATT' => [1,0], 'ACTCAA' => [2,1], 'ACTCAC' => [2,1], 'ACTCAG' => [2,1], 'ACTCAT' => [2,0], 'ACTCCA' => [1,1], 'ACTCCC' => [1,1], 'ACTCCG' => [1,1], 'ACTCCT' => [1,0], 'ACTCGA' => [1,2], 'ACTCGC' => [2,1], 'ACTCGG' => [1,2], 'ACTCGT' => [2,0], 'ACTCTA' => [2,1], 'ACTCTC' => [2,1], 'ACTCTG' => [2,1], 'ACTCTT' => [2,0], 'ACTGAA' => [2,1], 'ACTGAC' => [2,1], 'ACTGAG' => [2,1], 'ACTGAT' => [2,0], 'ACTGCA' => [1,1], 'ACTGCC' => [1,1], 'ACTGCG' => [1,1], 'ACTGCT' => [1,0], 'ACTGGA' => [2,1], 'ACTGGC' => [2,1], 'ACTGGG' => [2,1], 'ACTGGT' => [2,0], 'ACTGTA' => [2,1], 'ACTGTC' => [2,1], 'ACTGTG' => [2,1], 'ACTGTT' => [2,0], 'ACTTAC' => [2,1], 'ACTTAT' => [2,0], 'ACTTCA' => [1,1], 'ACTTCC' => [1,1], 'ACTTCG' => [1,1], 'ACTTCT' => [1,0], 'ACTTGC' => [2,1], 'ACTTGG' => [2,1], 'ACTTGT' => [2,0], 'ACTTTA' => [2,1], 'ACTTTC' => [2,1], 'ACTTTG' => [2,1], 'ACTTTT' => [2,0], 'AGAAAA' => [1,0], 'AGAAAC' => [2,0], 'AGAAAG' => [1,1], 'AGAAAT' => [2,0], 'AGAACA' => [1,0], 'AGAACC' => [1,1], 'AGAACG' => [1,1], 'AGAACT' => [1,1], 'AGAAGA' => [0,0], 'AGAAGC' => [1,0], 'AGAAGG' => [0,1], 'AGAAGT' => [1,0], 'AGAATA' => [1,0], 'AGAATC' => [1,1], 'AGAATG' => [1,1], 'AGAATT' => [1,1], 'AGACAA' => [1,1], 'AGACAC' => [1,2], 'AGACAG' => [1,2], 'AGACAT' => [1,2], 'AGACCA' => [1,1], 'AGACCC' => [1,2], 'AGACCG' => [1,2], 'AGACCT' => [1,2], 'AGACGA' => [0,1], 'AGACGC' => [0,2], 'AGACGG' => [0,2], 'AGACGT' => [0,2], 'AGACTA' => [1,1], 'AGACTC' => [1,2], 'AGACTG' => [1,2], 'AGACTT' => [1,2], 'AGAGAA' => [2,0], 'AGAGAC' => [2,1], 'AGAGAG' => [2,1], 'AGAGAT' => [2,1], 'AGAGCA' => [2,0], 'AGAGCC' => [2,1], 'AGAGCG' => [2,1], 'AGAGCT' => [2,1], 'AGAGGA' => [1,0], 'AGAGGC' => [1,1], 'AGAGGG' => [1,1], 'AGAGGT' => [1,1], 'AGAGTA' => [2,0], 'AGAGTC' => [2,1], 'AGAGTG' => [2,1], 'AGAGTT' => [2,1], 'AGATAC' => [3,0], 'AGATAT' => [3,0], 'AGATCA' => [2,0], 'AGATCC' => [2,1], 'AGATCG' => [2,1], 'AGATCT' => [2,1], 'AGATGC' => [2,0], 'AGATGG' => [1,1], 'AGATGT' => [2,0], 'AGATTA' => [2,0], 'AGATTC' => [2,1], 'AGATTG' => [2,1], 'AGATTT' => [2,1], 'AGCAAA' => [2,0], 'AGCAAC' => [1,0], 'AGCAAG' => [2,0], 'AGCAAT' => [1,1], 'AGCACA' => [1,1], 'AGCACC' => [1,0], 'AGCACG' => [1,1], 'AGCACT' => [1,1], 'AGCAGA' => [1,0], 'AGCAGC' => [0,0], 'AGCAGG' => [1,0], 'AGCAGT' => [0,1], 'AGCATA' => [1,1], 'AGCATC' => [1,0], 'AGCATG' => [2,0], 'AGCATT' => [1,1], 'AGCCAA' => [2,1], 'AGCCAC' => [2,0], 'AGCCAG' => [2,1], 'AGCCAT' => [2,1], 'AGCCCA' => [2,1], 'AGCCCC' => [2,0], 'AGCCCG' => [2,1], 'AGCCCT' => [2,1], 'AGCCGA' => [1,1], 'AGCCGC' => [1,0], 'AGCCGG' => [1,1], 'AGCCGT' => [1,1], 'AGCCTA' => [2,1], 'AGCCTC' => [2,0], 'AGCCTG' => [2,1], 'AGCCTT' => [2,1], 'AGCGAA' => [2,1], 'AGCGAC' => [2,0], 'AGCGAG' => [2,1], 'AGCGAT' => [2,1], 'AGCGCA' => [2,1], 'AGCGCC' => [2,0], 'AGCGCG' => [2,1], 'AGCGCT' => [2,1], 'AGCGGA' => [1,1], 'AGCGGC' => [1,0], 'AGCGGG' => [1,1], 'AGCGGT' => [1,1], 'AGCGTA' => [2,1], 'AGCGTC' => [2,0], 'AGCGTG' => [2,1], 'AGCGTT' => [2,1], 'AGCTAC' => [2,0], 'AGCTAT' => [2,1], 'AGCTCA' => [2,1], 'AGCTCC' => [2,0], 'AGCTCG' => [2,1], 'AGCTCT' => [2,1], 'AGCTGC' => [1,0], 'AGCTGG' => [2,0], 'AGCTGT' => [1,1], 'AGCTTA' => [2,1], 'AGCTTC' => [2,0], 'AGCTTG' => [3,0], 'AGCTTT' => [2,1], 'AGGAAA' => [1,1], 'AGGAAC' => [2,0], 'AGGAAG' => [1,0], 'AGGAAT' => [2,0], 'AGGACA' => [1,1], 'AGGACC' => [1,1], 'AGGACG' => [1,0], 'AGGACT' => [1,1], 'AGGAGA' => [0,1], 'AGGAGC' => [1,0], 'AGGAGG' => [0,0], 'AGGAGT' => [1,0], 'AGGATA' => [1,1], 'AGGATC' => [2,0], 'AGGATG' => [1,0], 'AGGATT' => [2,0], 'AGGCAA' => [1,2], 'AGGCAC' => [1,2], 'AGGCAG' => [1,1], 'AGGCAT' => [1,2], 'AGGCCA' => [1,2], 'AGGCCC' => [1,2], 'AGGCCG' => [1,1], 'AGGCCT' => [1,2], 'AGGCGA' => [0,2], 'AGGCGC' => [0,2], 'AGGCGG' => [0,1], 'AGGCGT' => [0,2], 'AGGCTA' => [1,2], 'AGGCTC' => [1,2], 'AGGCTG' => [1,1], 'AGGCTT' => [1,2], 'AGGGAA' => [2,1], 'AGGGAC' => [2,1], 'AGGGAG' => [2,0], 'AGGGAT' => [2,1], 'AGGGCA' => [2,1], 'AGGGCC' => [2,1], 'AGGGCG' => [2,0], 'AGGGCT' => [2,1], 'AGGGGA' => [1,1], 'AGGGGC' => [1,1], 'AGGGGG' => [1,0], 'AGGGGT' => [1,1], 'AGGGTA' => [2,1], 'AGGGTC' => [2,1], 'AGGGTG' => [2,0], 'AGGGTT' => [2,1], 'AGGTAC' => [3,0], 'AGGTAT' => [3,0], 'AGGTCA' => [2,1], 'AGGTCC' => [2,1], 'AGGTCG' => [2,0], 'AGGTCT' => [2,1], 'AGGTGC' => [2,0], 'AGGTGG' => [1,0], 'AGGTGT' => [2,0], 'AGGTTA' => [2,1], 'AGGTTC' => [3,0], 'AGGTTG' => [2,0], 'AGGTTT' => [3,0], 'AGTAAA' => [2,0], 'AGTAAC' => [1,1], 'AGTAAG' => [2,0], 'AGTAAT' => [1,0], 'AGTACA' => [1,1], 'AGTACC' => [1,1], 'AGTACG' => [1,1], 'AGTACT' => [1,0], 'AGTAGA' => [1,0], 'AGTAGC' => [0,1], 'AGTAGG' => [1,0], 'AGTAGT' => [0,0], 'AGTATA' => [1,1], 'AGTATC' => [1,1], 'AGTATG' => [2,0], 'AGTATT' => [1,0], 'AGTCAA' => [2,1], 'AGTCAC' => [2,1], 'AGTCAG' => [2,1], 'AGTCAT' => [2,0], 'AGTCCA' => [2,1], 'AGTCCC' => [2,1], 'AGTCCG' => [2,1], 'AGTCCT' => [2,0], 'AGTCGA' => [1,1], 'AGTCGC' => [1,1], 'AGTCGG' => [1,1], 'AGTCGT' => [1,0], 'AGTCTA' => [2,1], 'AGTCTC' => [2,1], 'AGTCTG' => [2,1], 'AGTCTT' => [2,0], 'AGTGAA' => [2,1], 'AGTGAC' => [2,1], 'AGTGAG' => [2,1], 'AGTGAT' => [2,0], 'AGTGCA' => [2,1], 'AGTGCC' => [2,1], 'AGTGCG' => [2,1], 'AGTGCT' => [2,0], 'AGTGGA' => [1,1], 'AGTGGC' => [1,1], 'AGTGGG' => [1,1], 'AGTGGT' => [1,0], 'AGTGTA' => [2,1], 'AGTGTC' => [2,1], 'AGTGTG' => [2,1], 'AGTGTT' => [2,0], 'AGTTAC' => [2,1], 'AGTTAT' => [2,0], 'AGTTCA' => [2,1], 'AGTTCC' => [2,1], 'AGTTCG' => [2,1], 'AGTTCT' => [2,0], 'AGTTGC' => [1,1], 'AGTTGG' => [2,0], 'AGTTGT' => [1,0], 'AGTTTA' => [2,1], 'AGTTTC' => [2,1], 'AGTTTG' => [3,0], 'AGTTTT' => [2,0], 'ATAAAA' => [1,0], 'ATAAAC' => [1,1], 'ATAAAG' => [1,1], 'ATAAAT' => [1,1], 'ATAACA' => [1,0], 'ATAACC' => [1,1], 'ATAACG' => [1,1], 'ATAACT' => [1,1], 'ATAAGA' => [1,0], 'ATAAGC' => [1,1], 'ATAAGG' => [1,1], 'ATAAGT' => [1,1], 'ATAATA' => [0,0], 'ATAATC' => [0,1], 'ATAATG' => [1,0], 'ATAATT' => [0,1], 'ATACAA' => [2,0], 'ATACAC' => [2,1], 'ATACAG' => [2,1], 'ATACAT' => [2,1], 'ATACCA' => [2,0], 'ATACCC' => [2,1], 'ATACCG' => [2,1], 'ATACCT' => [2,1], 'ATACGA' => [1,1], 'ATACGC' => [1,2], 'ATACGG' => [1,2], 'ATACGT' => [1,2], 'ATACTA' => [1,0], 'ATACTC' => [1,1], 'ATACTG' => [1,1], 'ATACTT' => [1,1], 'ATAGAA' => [2,0], 'ATAGAC' => [2,1], 'ATAGAG' => [2,1], 'ATAGAT' => [2,1], 'ATAGCA' => [2,0], 'ATAGCC' => [2,1], 'ATAGCG' => [2,1], 'ATAGCT' => [2,1], 'ATAGGA' => [2,0], 'ATAGGC' => [2,1], 'ATAGGG' => [2,1], 'ATAGGT' => [2,1], 'ATAGTA' => [1,0], 'ATAGTC' => [1,1], 'ATAGTG' => [1,1], 'ATAGTT' => [1,1], 'ATATAC' => [2,1], 'ATATAT' => [2,1], 'ATATCA' => [2,0], 'ATATCC' => [2,1], 'ATATCG' => [2,1], 'ATATCT' => [2,1], 'ATATGC' => [2,1], 'ATATGG' => [2,1], 'ATATGT' => [2,1], 'ATATTA' => [1,0], 'ATATTC' => [1,1], 'ATATTG' => [1,1], 'ATATTT' => [1,1], 'ATCAAA' => [1,1], 'ATCAAC' => [1,0], 'ATCAAG' => [2,0], 'ATCAAT' => [1,1], 'ATCACA' => [1,1], 'ATCACC' => [1,0], 'ATCACG' => [1,1], 'ATCACT' => [1,1], 'ATCAGA' => [1,1], 'ATCAGC' => [1,0], 'ATCAGG' => [2,0], 'ATCAGT' => [1,1], 'ATCATA' => [0,1], 'ATCATC' => [0,0], 'ATCATG' => [1,0], 'ATCATT' => [0,1], 'ATCCAA' => [2,1], 'ATCCAC' => [2,0], 'ATCCAG' => [2,1], 'ATCCAT' => [2,1], 'ATCCCA' => [2,1], 'ATCCCC' => [2,0], 'ATCCCG' => [2,1], 'ATCCCT' => [2,1], 'ATCCGA' => [1,2], 'ATCCGC' => [2,0], 'ATCCGG' => [2,1], 'ATCCGT' => [2,1], 'ATCCTA' => [1,1], 'ATCCTC' => [1,0], 'ATCCTG' => [1,1], 'ATCCTT' => [1,1], 'ATCGAA' => [2,1], 'ATCGAC' => [2,0], 'ATCGAG' => [2,1], 'ATCGAT' => [2,1], 'ATCGCA' => [2,1], 'ATCGCC' => [2,0], 'ATCGCG' => [2,1], 'ATCGCT' => [2,1], 'ATCGGA' => [2,1], 'ATCGGC' => [2,0], 'ATCGGG' => [2,1], 'ATCGGT' => [2,1], 'ATCGTA' => [1,1], 'ATCGTC' => [1,0], 'ATCGTG' => [1,1], 'ATCGTT' => [1,1], 'ATCTAC' => [2,0], 'ATCTAT' => [2,1], 'ATCTCA' => [2,1], 'ATCTCC' => [2,0], 'ATCTCG' => [2,1], 'ATCTCT' => [2,1], 'ATCTGC' => [2,0], 'ATCTGG' => [3,0], 'ATCTGT' => [2,1], 'ATCTTA' => [1,1], 'ATCTTC' => [1,0], 'ATCTTG' => [2,0], 'ATCTTT' => [1,1], 'ATGAAA' => [1,1], 'ATGAAC' => [2,0], 'ATGAAG' => [1,0], 'ATGAAT' => [2,0], 'ATGACA' => [1,1], 'ATGACC' => [1,1], 'ATGACG' => [1,0], 'ATGACT' => [1,1], 'ATGAGA' => [1,1], 'ATGAGC' => [2,0], 'ATGAGG' => [1,0], 'ATGAGT' => [2,0], 'ATGATA' => [1,0], 'ATGATC' => [1,0], 'ATGATG' => [0,0], 'ATGATT' => [1,0], 'ATGCAA' => [2,1], 'ATGCAC' => [2,1], 'ATGCAG' => [2,0], 'ATGCAT' => [2,1], 'ATGCCA' => [2,1], 'ATGCCC' => [2,1], 'ATGCCG' => [2,0], 'ATGCCT' => [2,1], 'ATGCGA' => [1,2], 'ATGCGC' => [1,2], 'ATGCGG' => [1,1], 'ATGCGT' => [1,2], 'ATGCTA' => [1,1], 'ATGCTC' => [1,1], 'ATGCTG' => [1,0], 'ATGCTT' => [1,1], 'ATGGAA' => [2,1], 'ATGGAC' => [2,1], 'ATGGAG' => [2,0], 'ATGGAT' => [2,1], 'ATGGCA' => [2,1], 'ATGGCC' => [2,1], 'ATGGCG' => [2,0], 'ATGGCT' => [2,1], 'ATGGGA' => [2,1], 'ATGGGC' => [2,1], 'ATGGGG' => [2,0], 'ATGGGT' => [2,1], 'ATGGTA' => [1,1], 'ATGGTC' => [1,1], 'ATGGTG' => [1,0], 'ATGGTT' => [1,1], 'ATGTAC' => [3,0], 'ATGTAT' => [3,0], 'ATGTCA' => [2,1], 'ATGTCC' => [2,1], 'ATGTCG' => [2,0], 'ATGTCT' => [2,1], 'ATGTGC' => [3,0], 'ATGTGG' => [2,0], 'ATGTGT' => [3,0], 'ATGTTA' => [1,1], 'ATGTTC' => [2,0], 'ATGTTG' => [1,0], 'ATGTTT' => [2,0], 'ATTAAA' => [1,1], 'ATTAAC' => [1,1], 'ATTAAG' => [2,0], 'ATTAAT' => [1,0], 'ATTACA' => [1,1], 'ATTACC' => [1,1], 'ATTACG' => [1,1], 'ATTACT' => [1,0], 'ATTAGA' => [1,1], 'ATTAGC' => [1,1], 'ATTAGG' => [2,0], 'ATTAGT' => [1,0], 'ATTATA' => [0,1], 'ATTATC' => [0,1], 'ATTATG' => [1,0], 'ATTATT' => [0,0], 'ATTCAA' => [2,1], 'ATTCAC' => [2,1], 'ATTCAG' => [2,1], 'ATTCAT' => [2,0], 'ATTCCA' => [2,1], 'ATTCCC' => [2,1], 'ATTCCG' => [2,1], 'ATTCCT' => [2,0], 'ATTCGA' => [1,2], 'ATTCGC' => [2,1], 'ATTCGG' => [2,1], 'ATTCGT' => [2,0], 'ATTCTA' => [1,1], 'ATTCTC' => [1,1], 'ATTCTG' => [1,1], 'ATTCTT' => [1,0], 'ATTGAA' => [2,1], 'ATTGAC' => [2,1], 'ATTGAG' => [2,1], 'ATTGAT' => [2,0], 'ATTGCA' => [2,1], 'ATTGCC' => [2,1], 'ATTGCG' => [2,1], 'ATTGCT' => [2,0], 'ATTGGA' => [2,1], 'ATTGGC' => [2,1], 'ATTGGG' => [2,1], 'ATTGGT' => [2,0], 'ATTGTA' => [1,1], 'ATTGTC' => [1,1], 'ATTGTG' => [1,1], 'ATTGTT' => [1,0], 'ATTTAC' => [2,1], 'ATTTAT' => [2,0], 'ATTTCA' => [2,1], 'ATTTCC' => [2,1], 'ATTTCG' => [2,1], 'ATTTCT' => [2,0], 'ATTTGC' => [2,1], 'ATTTGG' => [3,0], 'ATTTGT' => [2,0], 'ATTTTA' => [1,1], 'ATTTTC' => [1,1], 'ATTTTG' => [2,0], 'ATTTTT' => [1,0], 'CAAAAA' => [1,0], 'CAAAAC' => [2,0], 'CAAAAG' => [1,1], 'CAAAAT' => [2,0], 'CAAACA' => [2,0], 'CAAACC' => [2,1], 'CAAACG' => [2,1], 'CAAACT' => [2,1], 'CAAAGA' => [1,1], 'CAAAGC' => [2,1], 'CAAAGG' => [1,2], 'CAAAGT' => [2,1], 'CAAATA' => [2,0], 'CAAATC' => [2,1], 'CAAATG' => [2,1], 'CAAATT' => [2,1], 'CAACAA' => [0,0], 'CAACAC' => [1,0], 'CAACAG' => [0,1], 'CAACAT' => [1,0], 'CAACCA' => [1,0], 'CAACCC' => [1,1], 'CAACCG' => [1,1], 'CAACCT' => [1,1], 'CAACGA' => [1,0], 'CAACGC' => [1,1], 'CAACGG' => [1,1], 'CAACGT' => [1,1], 'CAACTA' => [1,0], 'CAACTC' => [1,1], 'CAACTG' => [1,1], 'CAACTT' => [1,1], 'CAAGAA' => [1,0], 'CAAGAC' => [2,0], 'CAAGAG' => [1,1], 'CAAGAT' => [2,0], 'CAAGCA' => [2,0], 'CAAGCC' => [2,1], 'CAAGCG' => [2,1], 'CAAGCT' => [2,1], 'CAAGGA' => [2,0], 'CAAGGC' => [2,1], 'CAAGGG' => [2,1], 'CAAGGT' => [2,1], 'CAAGTA' => [2,0], 'CAAGTC' => [2,1], 'CAAGTG' => [2,1], 'CAAGTT' => [2,1], 'CAATAC' => [2,0], 'CAATAT' => [2,0], 'CAATCA' => [2,0], 'CAATCC' => [2,1], 'CAATCG' => [2,1], 'CAATCT' => [2,1], 'CAATGC' => [2,1], 'CAATGG' => [2,1], 'CAATGT' => [2,1], 'CAATTA' => [1,1], 'CAATTC' => [2,1], 'CAATTG' => [1,2], 'CAATTT' => [2,1], 'CACAAA' => [2,0], 'CACAAC' => [1,0], 'CACAAG' => [2,0], 'CACAAT' => [1,1], 'CACACA' => [2,1], 'CACACC' => [2,0], 'CACACG' => [2,1], 'CACACT' => [2,1], 'CACAGA' => [1,2], 'CACAGC' => [2,0], 'CACAGG' => [1,2], 'CACAGT' => [2,1], 'CACATA' => [2,1], 'CACATC' => [2,0], 'CACATG' => [2,1], 'CACATT' => [2,1], 'CACCAA' => [1,0], 'CACCAC' => [0,0], 'CACCAG' => [1,0], 'CACCAT' => [0,1], 'CACCCA' => [1,1], 'CACCCC' => [1,0], 'CACCCG' => [1,1], 'CACCCT' => [1,1], 'CACCGA' => [1,1], 'CACCGC' => [1,0], 'CACCGG' => [1,1], 'CACCGT' => [1,1], 'CACCTA' => [1,1], 'CACCTC' => [1,0], 'CACCTG' => [1,1], 'CACCTT' => [1,1], 'CACGAA' => [2,0], 'CACGAC' => [1,0], 'CACGAG' => [2,0], 'CACGAT' => [1,1], 'CACGCA' => [2,1], 'CACGCC' => [2,0], 'CACGCG' => [2,1], 'CACGCT' => [2,1], 'CACGGA' => [2,1], 'CACGGC' => [2,0], 'CACGGG' => [2,1], 'CACGGT' => [2,1], 'CACGTA' => [2,1], 'CACGTC' => [2,0], 'CACGTG' => [2,1], 'CACGTT' => [2,1], 'CACTAC' => [1,0], 'CACTAT' => [1,1], 'CACTCA' => [2,1], 'CACTCC' => [2,0], 'CACTCG' => [2,1], 'CACTCT' => [2,1], 'CACTGC' => [2,0], 'CACTGG' => [2,1], 'CACTGT' => [2,1], 'CACTTA' => [1,2], 'CACTTC' => [2,0], 'CACTTG' => [1,2], 'CACTTT' => [2,1], 'CAGAAA' => [1,1], 'CAGAAC' => [2,0], 'CAGAAG' => [1,0], 'CAGAAT' => [2,0], 'CAGACA' => [2,1], 'CAGACC' => [2,1], 'CAGACG' => [2,0], 'CAGACT' => [2,1], 'CAGAGA' => [1,2], 'CAGAGC' => [2,1], 'CAGAGG' => [1,1], 'CAGAGT' => [2,1], 'CAGATA' => [2,1], 'CAGATC' => [2,1], 'CAGATG' => [2,0], 'CAGATT' => [2,1], 'CAGCAA' => [0,1], 'CAGCAC' => [1,0], 'CAGCAG' => [0,0], 'CAGCAT' => [1,0], 'CAGCCA' => [1,1], 'CAGCCC' => [1,1], 'CAGCCG' => [1,0], 'CAGCCT' => [1,1], 'CAGCGA' => [1,1], 'CAGCGC' => [1,1], 'CAGCGG' => [1,0], 'CAGCGT' => [1,1], 'CAGCTA' => [1,1], 'CAGCTC' => [1,1], 'CAGCTG' => [1,0], 'CAGCTT' => [1,1], 'CAGGAA' => [1,1], 'CAGGAC' => [2,0], 'CAGGAG' => [1,0], 'CAGGAT' => [2,0], 'CAGGCA' => [2,1], 'CAGGCC' => [2,1], 'CAGGCG' => [2,0], 'CAGGCT' => [2,1], 'CAGGGA' => [2,1], 'CAGGGC' => [2,1], 'CAGGGG' => [2,0], 'CAGGGT' => [2,1], 'CAGGTA' => [2,1], 'CAGGTC' => [2,1], 'CAGGTG' => [2,0], 'CAGGTT' => [2,1], 'CAGTAC' => [2,0], 'CAGTAT' => [2,0], 'CAGTCA' => [2,1], 'CAGTCC' => [2,1], 'CAGTCG' => [2,0], 'CAGTCT' => [2,1], 'CAGTGC' => [2,1], 'CAGTGG' => [2,0], 'CAGTGT' => [2,1], 'CAGTTA' => [1,2], 'CAGTTC' => [2,1], 'CAGTTG' => [1,1], 'CAGTTT' => [2,1], 'CATAAA' => [2,0], 'CATAAC' => [1,1], 'CATAAG' => [2,0], 'CATAAT' => [1,0], 'CATACA' => [2,1], 'CATACC' => [2,1], 'CATACG' => [2,1], 'CATACT' => [2,0], 'CATAGA' => [1,2], 'CATAGC' => [2,1], 'CATAGG' => [1,2], 'CATAGT' => [2,0], 'CATATA' => [2,1], 'CATATC' => [2,1], 'CATATG' => [2,1], 'CATATT' => [2,0], 'CATCAA' => [1,0], 'CATCAC' => [0,1], 'CATCAG' => [1,0], 'CATCAT' => [0,0], 'CATCCA' => [1,1], 'CATCCC' => [1,1], 'CATCCG' => [1,1], 'CATCCT' => [1,0], 'CATCGA' => [1,1], 'CATCGC' => [1,1], 'CATCGG' => [1,1], 'CATCGT' => [1,0], 'CATCTA' => [1,1], 'CATCTC' => [1,1], 'CATCTG' => [1,1], 'CATCTT' => [1,0], 'CATGAA' => [2,0], 'CATGAC' => [1,1], 'CATGAG' => [2,0], 'CATGAT' => [1,0], 'CATGCA' => [2,1], 'CATGCC' => [2,1], 'CATGCG' => [2,1], 'CATGCT' => [2,0], 'CATGGA' => [2,1], 'CATGGC' => [2,1], 'CATGGG' => [2,1], 'CATGGT' => [2,0], 'CATGTA' => [2,1], 'CATGTC' => [2,1], 'CATGTG' => [2,1], 'CATGTT' => [2,0], 'CATTAC' => [1,1], 'CATTAT' => [1,0], 'CATTCA' => [2,1], 'CATTCC' => [2,1], 'CATTCG' => [2,1], 'CATTCT' => [2,0], 'CATTGC' => [2,1], 'CATTGG' => [2,1], 'CATTGT' => [2,0], 'CATTTA' => [1,2], 'CATTTC' => [2,1], 'CATTTG' => [1,2], 'CATTTT' => [2,0], 'CCAAAA' => [2,0], 'CCAAAC' => [2,1], 'CCAAAG' => [2,1], 'CCAAAT' => [2,1], 'CCAACA' => [1,0], 'CCAACC' => [1,1], 'CCAACG' => [1,1], 'CCAACT' => [1,1], 'CCAAGA' => [1,1], 'CCAAGC' => [2,1], 'CCAAGG' => [1,2], 'CCAAGT' => [2,1], 'CCAATA' => [2,0], 'CCAATC' => [2,1], 'CCAATG' => [2,1], 'CCAATT' => [2,1], 'CCACAA' => [1,0], 'CCACAC' => [1,1], 'CCACAG' => [1,1], 'CCACAT' => [1,1], 'CCACCA' => [0,0], 'CCACCC' => [0,1], 'CCACCG' => [0,1], 'CCACCT' => [0,1], 'CCACGA' => [1,0], 'CCACGC' => [1,1], 'CCACGG' => [1,1], 'CCACGT' => [1,1], 'CCACTA' => [1,0], 'CCACTC' => [1,1], 'CCACTG' => [1,1], 'CCACTT' => [1,1], 'CCAGAA' => [2,0], 'CCAGAC' => [2,1], 'CCAGAG' => [2,1], 'CCAGAT' => [2,1], 'CCAGCA' => [1,0], 'CCAGCC' => [1,1], 'CCAGCG' => [1,1], 'CCAGCT' => [1,1], 'CCAGGA' => [2,0], 'CCAGGC' => [2,1], 'CCAGGG' => [2,1], 'CCAGGT' => [2,1], 'CCAGTA' => [2,0], 'CCAGTC' => [2,1], 'CCAGTG' => [2,1], 'CCAGTT' => [2,1], 'CCATAC' => [2,1], 'CCATAT' => [2,1], 'CCATCA' => [1,0], 'CCATCC' => [1,1], 'CCATCG' => [1,1], 'CCATCT' => [1,1], 'CCATGC' => [2,1], 'CCATGG' => [2,1], 'CCATGT' => [2,1], 'CCATTA' => [1,1], 'CCATTC' => [2,1], 'CCATTG' => [1,2], 'CCATTT' => [2,1], 'CCCAAA' => [2,1], 'CCCAAC' => [2,0], 'CCCAAG' => [2,1], 'CCCAAT' => [2,1], 'CCCACA' => [1,1], 'CCCACC' => [1,0], 'CCCACG' => [1,1], 'CCCACT' => [1,1], 'CCCAGA' => [1,2], 'CCCAGC' => [2,0], 'CCCAGG' => [1,2], 'CCCAGT' => [2,1], 'CCCATA' => [2,1], 'CCCATC' => [2,0], 'CCCATG' => [2,1], 'CCCATT' => [2,1], 'CCCCAA' => [1,1], 'CCCCAC' => [1,0], 'CCCCAG' => [1,1], 'CCCCAT' => [1,1], 'CCCCCA' => [0,1], 'CCCCCC' => [0,0], 'CCCCCG' => [0,1], 'CCCCCT' => [0,1], 'CCCCGA' => [1,1], 'CCCCGC' => [1,0], 'CCCCGG' => [1,1], 'CCCCGT' => [1,1], 'CCCCTA' => [1,1], 'CCCCTC' => [1,0], 'CCCCTG' => [1,1], 'CCCCTT' => [1,1], 'CCCGAA' => [2,1], 'CCCGAC' => [2,0], 'CCCGAG' => [2,1], 'CCCGAT' => [2,1], 'CCCGCA' => [1,1], 'CCCGCC' => [1,0], 'CCCGCG' => [1,1], 'CCCGCT' => [1,1], 'CCCGGA' => [2,1], 'CCCGGC' => [2,0], 'CCCGGG' => [2,1], 'CCCGGT' => [2,1], 'CCCGTA' => [2,1], 'CCCGTC' => [2,0], 'CCCGTG' => [2,1], 'CCCGTT' => [2,1], 'CCCTAC' => [2,0], 'CCCTAT' => [2,1], 'CCCTCA' => [1,1], 'CCCTCC' => [1,0], 'CCCTCG' => [1,1], 'CCCTCT' => [1,1], 'CCCTGC' => [2,0], 'CCCTGG' => [2,1], 'CCCTGT' => [2,1], 'CCCTTA' => [1,2], 'CCCTTC' => [2,0], 'CCCTTG' => [1,2], 'CCCTTT' => [2,1], 'CCGAAA' => [2,1], 'CCGAAC' => [2,1], 'CCGAAG' => [2,0], 'CCGAAT' => [2,1], 'CCGACA' => [1,1], 'CCGACC' => [1,1], 'CCGACG' => [1,0], 'CCGACT' => [1,1], 'CCGAGA' => [1,2], 'CCGAGC' => [2,1], 'CCGAGG' => [1,1], 'CCGAGT' => [2,1], 'CCGATA' => [2,1], 'CCGATC' => [2,1], 'CCGATG' => [2,0], 'CCGATT' => [2,1], 'CCGCAA' => [1,1], 'CCGCAC' => [1,1], 'CCGCAG' => [1,0], 'CCGCAT' => [1,1], 'CCGCCA' => [0,1], 'CCGCCC' => [0,1], 'CCGCCG' => [0,0], 'CCGCCT' => [0,1], 'CCGCGA' => [1,1], 'CCGCGC' => [1,1], 'CCGCGG' => [1,0], 'CCGCGT' => [1,1], 'CCGCTA' => [1,1], 'CCGCTC' => [1,1], 'CCGCTG' => [1,0], 'CCGCTT' => [1,1], 'CCGGAA' => [2,1], 'CCGGAC' => [2,1], 'CCGGAG' => [2,0], 'CCGGAT' => [2,1], 'CCGGCA' => [1,1], 'CCGGCC' => [1,1], 'CCGGCG' => [1,0], 'CCGGCT' => [1,1], 'CCGGGA' => [2,1], 'CCGGGC' => [2,1], 'CCGGGG' => [2,0], 'CCGGGT' => [2,1], 'CCGGTA' => [2,1], 'CCGGTC' => [2,1], 'CCGGTG' => [2,0], 'CCGGTT' => [2,1], 'CCGTAC' => [2,1], 'CCGTAT' => [2,1], 'CCGTCA' => [1,1], 'CCGTCC' => [1,1], 'CCGTCG' => [1,0], 'CCGTCT' => [1,1], 'CCGTGC' => [2,1], 'CCGTGG' => [2,0], 'CCGTGT' => [2,1], 'CCGTTA' => [1,2], 'CCGTTC' => [2,1], 'CCGTTG' => [1,1], 'CCGTTT' => [2,1], 'CCTAAA' => [2,1], 'CCTAAC' => [2,1], 'CCTAAG' => [2,1], 'CCTAAT' => [2,0], 'CCTACA' => [1,1], 'CCTACC' => [1,1], 'CCTACG' => [1,1], 'CCTACT' => [1,0], 'CCTAGA' => [1,2], 'CCTAGC' => [2,1], 'CCTAGG' => [1,2], 'CCTAGT' => [2,0], 'CCTATA' => [2,1], 'CCTATC' => [2,1], 'CCTATG' => [2,1], 'CCTATT' => [2,0], 'CCTCAA' => [1,1], 'CCTCAC' => [1,1], 'CCTCAG' => [1,1], 'CCTCAT' => [1,0], 'CCTCCA' => [0,1], 'CCTCCC' => [0,1], 'CCTCCG' => [0,1], 'CCTCCT' => [0,0], 'CCTCGA' => [1,1], 'CCTCGC' => [1,1], 'CCTCGG' => [1,1], 'CCTCGT' => [1,0], 'CCTCTA' => [1,1], 'CCTCTC' => [1,1], 'CCTCTG' => [1,1], 'CCTCTT' => [1,0], 'CCTGAA' => [2,1], 'CCTGAC' => [2,1], 'CCTGAG' => [2,1], 'CCTGAT' => [2,0], 'CCTGCA' => [1,1], 'CCTGCC' => [1,1], 'CCTGCG' => [1,1], 'CCTGCT' => [1,0], 'CCTGGA' => [2,1], 'CCTGGC' => [2,1], 'CCTGGG' => [2,1], 'CCTGGT' => [2,0], 'CCTGTA' => [2,1], 'CCTGTC' => [2,1], 'CCTGTG' => [2,1], 'CCTGTT' => [2,0], 'CCTTAC' => [2,1], 'CCTTAT' => [2,0], 'CCTTCA' => [1,1], 'CCTTCC' => [1,1], 'CCTTCG' => [1,1], 'CCTTCT' => [1,0], 'CCTTGC' => [2,1], 'CCTTGG' => [2,1], 'CCTTGT' => [2,0], 'CCTTTA' => [1,2], 'CCTTTC' => [2,1], 'CCTTTG' => [1,2], 'CCTTTT' => [2,0], 'CGAAAA' => [1,1], 'CGAAAC' => [2,1], 'CGAAAG' => [1,2], 'CGAAAT' => [2,1], 'CGAACA' => [1,1], 'CGAACC' => [1,2], 'CGAACG' => [1,2], 'CGAACT' => [1,2], 'CGAAGA' => [0,1], 'CGAAGC' => [1,1], 'CGAAGG' => [0,2], 'CGAAGT' => [1,1], 'CGAATA' => [1,1], 'CGAATC' => [1,2], 'CGAATG' => [1,2], 'CGAATT' => [1,2], 'CGACAA' => [1,0], 'CGACAC' => [1,1], 'CGACAG' => [1,1], 'CGACAT' => [1,1], 'CGACCA' => [1,0], 'CGACCC' => [1,1], 'CGACCG' => [1,1], 'CGACCT' => [1,1], 'CGACGA' => [0,0], 'CGACGC' => [0,1], 'CGACGG' => [0,1], 'CGACGT' => [0,1], 'CGACTA' => [1,0], 'CGACTC' => [1,1], 'CGACTG' => [1,1], 'CGACTT' => [1,1], 'CGAGAA' => [2,0], 'CGAGAC' => [2,1], 'CGAGAG' => [2,1], 'CGAGAT' => [2,1], 'CGAGCA' => [2,0], 'CGAGCC' => [2,1], 'CGAGCG' => [2,1], 'CGAGCT' => [2,1], 'CGAGGA' => [1,0], 'CGAGGC' => [1,1], 'CGAGGG' => [1,1], 'CGAGGT' => [1,1], 'CGAGTA' => [2,0], 'CGAGTC' => [2,1], 'CGAGTG' => [2,1], 'CGAGTT' => [2,1], 'CGATAC' => [2,1], 'CGATAT' => [2,1], 'CGATCA' => [2,0], 'CGATCC' => [2,1], 'CGATCG' => [2,1], 'CGATCT' => [2,1], 'CGATGC' => [1,1], 'CGATGG' => [1,1], 'CGATGT' => [1,1], 'CGATTA' => [1,1], 'CGATTC' => [2,1], 'CGATTG' => [1,2], 'CGATTT' => [2,1], 'CGCAAA' => [1,2], 'CGCAAC' => [2,0], 'CGCAAG' => [1,2], 'CGCAAT' => [2,1], 'CGCACA' => [1,2], 'CGCACC' => [2,0], 'CGCACG' => [1,2], 'CGCACT' => [2,1], 'CGCAGA' => [0,2], 'CGCAGC' => [1,0], 'CGCAGG' => [0,2], 'CGCAGT' => [1,1], 'CGCATA' => [1,2], 'CGCATC' => [2,0], 'CGCATG' => [1,2], 'CGCATT' => [2,1], 'CGCCAA' => [1,1], 'CGCCAC' => [1,0], 'CGCCAG' => [1,1], 'CGCCAT' => [1,1], 'CGCCCA' => [1,1], 'CGCCCC' => [1,0], 'CGCCCG' => [1,1], 'CGCCCT' => [1,1], 'CGCCGA' => [0,1], 'CGCCGC' => [0,0], 'CGCCGG' => [0,1], 'CGCCGT' => [0,1], 'CGCCTA' => [1,1], 'CGCCTC' => [1,0], 'CGCCTG' => [1,1], 'CGCCTT' => [1,1], 'CGCGAA' => [2,1], 'CGCGAC' => [2,0], 'CGCGAG' => [2,1], 'CGCGAT' => [2,1], 'CGCGCA' => [2,1], 'CGCGCC' => [2,0], 'CGCGCG' => [2,1], 'CGCGCT' => [2,1], 'CGCGGA' => [1,1], 'CGCGGC' => [1,0], 'CGCGGG' => [1,1], 'CGCGGT' => [1,1], 'CGCGTA' => [2,1], 'CGCGTC' => [2,0], 'CGCGTG' => [2,1], 'CGCGTT' => [2,1], 'CGCTAC' => [2,0], 'CGCTAT' => [2,1], 'CGCTCA' => [2,1], 'CGCTCC' => [2,0], 'CGCTCG' => [2,1], 'CGCTCT' => [2,1], 'CGCTGC' => [1,0], 'CGCTGG' => [1,1], 'CGCTGT' => [1,1], 'CGCTTA' => [1,2], 'CGCTTC' => [2,0], 'CGCTTG' => [1,2], 'CGCTTT' => [2,1], 'CGGAAA' => [1,2], 'CGGAAC' => [2,1], 'CGGAAG' => [1,1], 'CGGAAT' => [2,1], 'CGGACA' => [1,2], 'CGGACC' => [1,2], 'CGGACG' => [1,1], 'CGGACT' => [1,2], 'CGGAGA' => [0,2], 'CGGAGC' => [1,1], 'CGGAGG' => [0,1], 'CGGAGT' => [1,1], 'CGGATA' => [1,2], 'CGGATC' => [2,1], 'CGGATG' => [1,1], 'CGGATT' => [2,1], 'CGGCAA' => [1,1], 'CGGCAC' => [1,1], 'CGGCAG' => [1,0], 'CGGCAT' => [1,1], 'CGGCCA' => [1,1], 'CGGCCC' => [1,1], 'CGGCCG' => [1,0], 'CGGCCT' => [1,1], 'CGGCGA' => [0,1], 'CGGCGC' => [0,1], 'CGGCGG' => [0,0], 'CGGCGT' => [0,1], 'CGGCTA' => [1,1], 'CGGCTC' => [1,1], 'CGGCTG' => [1,0], 'CGGCTT' => [1,1], 'CGGGAA' => [2,1], 'CGGGAC' => [2,1], 'CGGGAG' => [2,0], 'CGGGAT' => [2,1], 'CGGGCA' => [2,1], 'CGGGCC' => [2,1], 'CGGGCG' => [2,0], 'CGGGCT' => [2,1], 'CGGGGA' => [1,1], 'CGGGGC' => [1,1], 'CGGGGG' => [1,0], 'CGGGGT' => [1,1], 'CGGGTA' => [2,1], 'CGGGTC' => [2,1], 'CGGGTG' => [2,0], 'CGGGTT' => [2,1], 'CGGTAC' => [2,1], 'CGGTAT' => [2,1], 'CGGTCA' => [2,1], 'CGGTCC' => [2,1], 'CGGTCG' => [2,0], 'CGGTCT' => [2,1], 'CGGTGC' => [1,1], 'CGGTGG' => [1,0], 'CGGTGT' => [1,1], 'CGGTTA' => [1,2], 'CGGTTC' => [2,1], 'CGGTTG' => [1,1], 'CGGTTT' => [2,1], 'CGTAAA' => [1,2], 'CGTAAC' => [2,1], 'CGTAAG' => [1,2], 'CGTAAT' => [2,0], 'CGTACA' => [1,2], 'CGTACC' => [2,1], 'CGTACG' => [1,2], 'CGTACT' => [2,0], 'CGTAGA' => [0,2], 'CGTAGC' => [1,1], 'CGTAGG' => [0,2], 'CGTAGT' => [1,0], 'CGTATA' => [1,2], 'CGTATC' => [2,1], 'CGTATG' => [1,2], 'CGTATT' => [2,0], 'CGTCAA' => [1,1], 'CGTCAC' => [1,1], 'CGTCAG' => [1,1], 'CGTCAT' => [1,0], 'CGTCCA' => [1,1], 'CGTCCC' => [1,1], 'CGTCCG' => [1,1], 'CGTCCT' => [1,0], 'CGTCGA' => [0,1], 'CGTCGC' => [0,1], 'CGTCGG' => [0,1], 'CGTCGT' => [0,0], 'CGTCTA' => [1,1], 'CGTCTC' => [1,1], 'CGTCTG' => [1,1], 'CGTCTT' => [1,0], 'CGTGAA' => [2,1], 'CGTGAC' => [2,1], 'CGTGAG' => [2,1], 'CGTGAT' => [2,0], 'CGTGCA' => [2,1], 'CGTGCC' => [2,1], 'CGTGCG' => [2,1], 'CGTGCT' => [2,0], 'CGTGGA' => [1,1], 'CGTGGC' => [1,1], 'CGTGGG' => [1,1], 'CGTGGT' => [1,0], 'CGTGTA' => [2,1], 'CGTGTC' => [2,1], 'CGTGTG' => [2,1], 'CGTGTT' => [2,0], 'CGTTAC' => [2,1], 'CGTTAT' => [2,0], 'CGTTCA' => [2,1], 'CGTTCC' => [2,1], 'CGTTCG' => [2,1], 'CGTTCT' => [2,0], 'CGTTGC' => [1,1], 'CGTTGG' => [1,1], 'CGTTGT' => [1,0], 'CGTTTA' => [1,2], 'CGTTTC' => [2,1], 'CGTTTG' => [1,2], 'CGTTTT' => [2,0], 'CTAAAA' => [2,0], 'CTAAAC' => [2,1], 'CTAAAG' => [2,1], 'CTAAAT' => [2,1], 'CTAACA' => [2,0], 'CTAACC' => [2,1], 'CTAACG' => [2,1], 'CTAACT' => [2,1], 'CTAAGA' => [1,1], 'CTAAGC' => [2,1], 'CTAAGG' => [1,2], 'CTAAGT' => [2,1], 'CTAATA' => [1,0], 'CTAATC' => [1,1], 'CTAATG' => [1,1], 'CTAATT' => [1,1], 'CTACAA' => [1,0], 'CTACAC' => [1,1], 'CTACAG' => [1,1], 'CTACAT' => [1,1], 'CTACCA' => [1,0], 'CTACCC' => [1,1], 'CTACCG' => [1,1], 'CTACCT' => [1,1], 'CTACGA' => [1,0], 'CTACGC' => [1,1], 'CTACGG' => [1,1], 'CTACGT' => [1,1], 'CTACTA' => [0,0], 'CTACTC' => [0,1], 'CTACTG' => [0,1], 'CTACTT' => [0,1], 'CTAGAA' => [2,0], 'CTAGAC' => [2,1], 'CTAGAG' => [2,1], 'CTAGAT' => [2,1], 'CTAGCA' => [2,0], 'CTAGCC' => [2,1], 'CTAGCG' => [2,1], 'CTAGCT' => [2,1], 'CTAGGA' => [2,0], 'CTAGGC' => [2,1], 'CTAGGG' => [2,1], 'CTAGGT' => [2,1], 'CTAGTA' => [1,0], 'CTAGTC' => [1,1], 'CTAGTG' => [1,1], 'CTAGTT' => [1,1], 'CTATAC' => [2,1], 'CTATAT' => [2,1], 'CTATCA' => [1,1], 'CTATCC' => [1,2], 'CTATCG' => [1,2], 'CTATCT' => [1,2], 'CTATGC' => [2,1], 'CTATGG' => [1,2], 'CTATGT' => [2,1], 'CTATTA' => [0,1], 'CTATTC' => [1,1], 'CTATTG' => [0,2], 'CTATTT' => [1,1], 'CTCAAA' => [2,1], 'CTCAAC' => [2,0], 'CTCAAG' => [2,1], 'CTCAAT' => [2,1], 'CTCACA' => [2,1], 'CTCACC' => [2,0], 'CTCACG' => [2,1], 'CTCACT' => [2,1], 'CTCAGA' => [1,2], 'CTCAGC' => [2,0], 'CTCAGG' => [1,2], 'CTCAGT' => [2,1], 'CTCATA' => [1,1], 'CTCATC' => [1,0], 'CTCATG' => [1,1], 'CTCATT' => [1,1], 'CTCCAA' => [1,1], 'CTCCAC' => [1,0], 'CTCCAG' => [1,1], 'CTCCAT' => [1,1], 'CTCCCA' => [1,1], 'CTCCCC' => [1,0], 'CTCCCG' => [1,1], 'CTCCCT' => [1,1], 'CTCCGA' => [1,1], 'CTCCGC' => [1,0], 'CTCCGG' => [1,1], 'CTCCGT' => [1,1], 'CTCCTA' => [0,1], 'CTCCTC' => [0,0], 'CTCCTG' => [0,1], 'CTCCTT' => [0,1], 'CTCGAA' => [2,1], 'CTCGAC' => [2,0], 'CTCGAG' => [2,1], 'CTCGAT' => [2,1], 'CTCGCA' => [2,1], 'CTCGCC' => [2,0], 'CTCGCG' => [2,1], 'CTCGCT' => [2,1], 'CTCGGA' => [2,1], 'CTCGGC' => [2,0], 'CTCGGG' => [2,1], 'CTCGGT' => [2,1], 'CTCGTA' => [1,1], 'CTCGTC' => [1,0], 'CTCGTG' => [1,1], 'CTCGTT' => [1,1], 'CTCTAC' => [2,0], 'CTCTAT' => [2,1], 'CTCTCA' => [1,2], 'CTCTCC' => [2,0], 'CTCTCG' => [1,2], 'CTCTCT' => [2,1], 'CTCTGC' => [2,0], 'CTCTGG' => [1,2], 'CTCTGT' => [2,1], 'CTCTTA' => [0,2], 'CTCTTC' => [1,0], 'CTCTTG' => [0,2], 'CTCTTT' => [1,1], 'CTGAAA' => [2,1], 'CTGAAC' => [2,1], 'CTGAAG' => [2,0], 'CTGAAT' => [2,1], 'CTGACA' => [2,1], 'CTGACC' => [2,1], 'CTGACG' => [2,0], 'CTGACT' => [2,1], 'CTGAGA' => [1,2], 'CTGAGC' => [2,1], 'CTGAGG' => [1,1], 'CTGAGT' => [2,1], 'CTGATA' => [1,1], 'CTGATC' => [1,1], 'CTGATG' => [1,0], 'CTGATT' => [1,1], 'CTGCAA' => [1,1], 'CTGCAC' => [1,1], 'CTGCAG' => [1,0], 'CTGCAT' => [1,1], 'CTGCCA' => [1,1], 'CTGCCC' => [1,1], 'CTGCCG' => [1,0], 'CTGCCT' => [1,1], 'CTGCGA' => [1,1], 'CTGCGC' => [1,1], 'CTGCGG' => [1,0], 'CTGCGT' => [1,1], 'CTGCTA' => [0,1], 'CTGCTC' => [0,1], 'CTGCTG' => [0,0], 'CTGCTT' => [0,1], 'CTGGAA' => [2,1], 'CTGGAC' => [2,1], 'CTGGAG' => [2,0], 'CTGGAT' => [2,1], 'CTGGCA' => [2,1], 'CTGGCC' => [2,1], 'CTGGCG' => [2,0], 'CTGGCT' => [2,1], 'CTGGGA' => [2,1], 'CTGGGC' => [2,1], 'CTGGGG' => [2,0], 'CTGGGT' => [2,1], 'CTGGTA' => [1,1], 'CTGGTC' => [1,1], 'CTGGTG' => [1,0], 'CTGGTT' => [1,1], 'CTGTAC' => [2,1], 'CTGTAT' => [2,1], 'CTGTCA' => [1,2], 'CTGTCC' => [1,2], 'CTGTCG' => [1,1], 'CTGTCT' => [1,2], 'CTGTGC' => [2,1], 'CTGTGG' => [1,1], 'CTGTGT' => [2,1], 'CTGTTA' => [0,2], 'CTGTTC' => [1,1], 'CTGTTG' => [0,1], 'CTGTTT' => [1,1], 'CTTAAA' => [2,1], 'CTTAAC' => [2,1], 'CTTAAG' => [2,1], 'CTTAAT' => [2,0], 'CTTACA' => [2,1], 'CTTACC' => [2,1], 'CTTACG' => [2,1], 'CTTACT' => [2,0], 'CTTAGA' => [1,2], 'CTTAGC' => [2,1], 'CTTAGG' => [1,2], 'CTTAGT' => [2,0], 'CTTATA' => [1,1], 'CTTATC' => [1,1], 'CTTATG' => [1,1], 'CTTATT' => [1,0], 'CTTCAA' => [1,1], 'CTTCAC' => [1,1], 'CTTCAG' => [1,1], 'CTTCAT' => [1,0], 'CTTCCA' => [1,1], 'CTTCCC' => [1,1], 'CTTCCG' => [1,1], 'CTTCCT' => [1,0], 'CTTCGA' => [1,1], 'CTTCGC' => [1,1], 'CTTCGG' => [1,1], 'CTTCGT' => [1,0], 'CTTCTA' => [0,1], 'CTTCTC' => [0,1], 'CTTCTG' => [0,1], 'CTTCTT' => [0,0], 'CTTGAA' => [2,1], 'CTTGAC' => [2,1], 'CTTGAG' => [2,1], 'CTTGAT' => [2,0], 'CTTGCA' => [2,1], 'CTTGCC' => [2,1], 'CTTGCG' => [2,1], 'CTTGCT' => [2,0], 'CTTGGA' => [2,1], 'CTTGGC' => [2,1], 'CTTGGG' => [2,1], 'CTTGGT' => [2,0], 'CTTGTA' => [1,1], 'CTTGTC' => [1,1], 'CTTGTG' => [1,1], 'CTTGTT' => [1,0], 'CTTTAC' => [2,1], 'CTTTAT' => [2,0], 'CTTTCA' => [1,2], 'CTTTCC' => [2,1], 'CTTTCG' => [1,2], 'CTTTCT' => [2,0], 'CTTTGC' => [2,1], 'CTTTGG' => [1,2], 'CTTTGT' => [2,0], 'CTTTTA' => [0,2], 'CTTTTC' => [1,1], 'CTTTTG' => [0,2], 'CTTTTT' => [1,0], 'GAAAAA' => [1,0], 'GAAAAC' => [2,0], 'GAAAAG' => [1,1], 'GAAAAT' => [2,0], 'GAAACA' => [2,0], 'GAAACC' => [2,1], 'GAAACG' => [2,1], 'GAAACT' => [2,1], 'GAAAGA' => [2,0], 'GAAAGC' => [2,1], 'GAAAGG' => [2,1], 'GAAAGT' => [2,1], 'GAAATA' => [2,0], 'GAAATC' => [2,1], 'GAAATG' => [2,1], 'GAAATT' => [2,1], 'GAACAA' => [1,0], 'GAACAC' => [2,0], 'GAACAG' => [1,1], 'GAACAT' => [2,0], 'GAACCA' => [2,0], 'GAACCC' => [2,1], 'GAACCG' => [2,1], 'GAACCT' => [2,1], 'GAACGA' => [2,0], 'GAACGC' => [2,1], 'GAACGG' => [2,1], 'GAACGT' => [2,1], 'GAACTA' => [2,0], 'GAACTC' => [2,1], 'GAACTG' => [2,1], 'GAACTT' => [2,1], 'GAAGAA' => [0,0], 'GAAGAC' => [1,0], 'GAAGAG' => [0,1], 'GAAGAT' => [1,0], 'GAAGCA' => [1,0], 'GAAGCC' => [1,1], 'GAAGCG' => [1,1], 'GAAGCT' => [1,1], 'GAAGGA' => [1,0], 'GAAGGC' => [1,1], 'GAAGGG' => [1,1], 'GAAGGT' => [1,1], 'GAAGTA' => [1,0], 'GAAGTC' => [1,1], 'GAAGTG' => [1,1], 'GAAGTT' => [1,1], 'GAATAC' => [2,0], 'GAATAT' => [2,0], 'GAATCA' => [2,0], 'GAATCC' => [2,1], 'GAATCG' => [2,1], 'GAATCT' => [2,1], 'GAATGC' => [2,1], 'GAATGG' => [2,1], 'GAATGT' => [2,1], 'GAATTA' => [2,0], 'GAATTC' => [2,1], 'GAATTG' => [2,1], 'GAATTT' => [2,1], 'GACAAA' => [2,0], 'GACAAC' => [1,0], 'GACAAG' => [2,0], 'GACAAT' => [1,1], 'GACACA' => [2,1], 'GACACC' => [2,0], 'GACACG' => [2,1], 'GACACT' => [2,1], 'GACAGA' => [2,1], 'GACAGC' => [2,0], 'GACAGG' => [2,1], 'GACAGT' => [2,1], 'GACATA' => [2,1], 'GACATC' => [2,0], 'GACATG' => [2,1], 'GACATT' => [2,1], 'GACCAA' => [2,0], 'GACCAC' => [1,0], 'GACCAG' => [2,0], 'GACCAT' => [1,1], 'GACCCA' => [2,1], 'GACCCC' => [2,0], 'GACCCG' => [2,1], 'GACCCT' => [2,1], 'GACCGA' => [2,1], 'GACCGC' => [2,0], 'GACCGG' => [2,1], 'GACCGT' => [2,1], 'GACCTA' => [2,1], 'GACCTC' => [2,0], 'GACCTG' => [2,1], 'GACCTT' => [2,1], 'GACGAA' => [1,0], 'GACGAC' => [0,0], 'GACGAG' => [1,0], 'GACGAT' => [0,1], 'GACGCA' => [1,1], 'GACGCC' => [1,0], 'GACGCG' => [1,1], 'GACGCT' => [1,1], 'GACGGA' => [1,1], 'GACGGC' => [1,0], 'GACGGG' => [1,1], 'GACGGT' => [1,1], 'GACGTA' => [1,1], 'GACGTC' => [1,0], 'GACGTG' => [1,1], 'GACGTT' => [1,1], 'GACTAC' => [1,0], 'GACTAT' => [1,1], 'GACTCA' => [2,1], 'GACTCC' => [2,0], 'GACTCG' => [2,1], 'GACTCT' => [2,1], 'GACTGC' => [2,0], 'GACTGG' => [2,1], 'GACTGT' => [2,1], 'GACTTA' => [2,1], 'GACTTC' => [2,0], 'GACTTG' => [2,1], 'GACTTT' => [2,1], 'GAGAAA' => [1,1], 'GAGAAC' => [2,0], 'GAGAAG' => [1,0], 'GAGAAT' => [2,0], 'GAGACA' => [2,1], 'GAGACC' => [2,1], 'GAGACG' => [2,0], 'GAGACT' => [2,1], 'GAGAGA' => [2,1], 'GAGAGC' => [2,1], 'GAGAGG' => [2,0], 'GAGAGT' => [2,1], 'GAGATA' => [2,1], 'GAGATC' => [2,1], 'GAGATG' => [2,0], 'GAGATT' => [2,1], 'GAGCAA' => [1,1], 'GAGCAC' => [2,0], 'GAGCAG' => [1,0], 'GAGCAT' => [2,0], 'GAGCCA' => [2,1], 'GAGCCC' => [2,1], 'GAGCCG' => [2,0], 'GAGCCT' => [2,1], 'GAGCGA' => [2,1], 'GAGCGC' => [2,1], 'GAGCGG' => [2,0], 'GAGCGT' => [2,1], 'GAGCTA' => [2,1], 'GAGCTC' => [2,1], 'GAGCTG' => [2,0], 'GAGCTT' => [2,1], 'GAGGAA' => [0,1], 'GAGGAC' => [1,0], 'GAGGAG' => [0,0], 'GAGGAT' => [1,0], 'GAGGCA' => [1,1], 'GAGGCC' => [1,1], 'GAGGCG' => [1,0], 'GAGGCT' => [1,1], 'GAGGGA' => [1,1], 'GAGGGC' => [1,1], 'GAGGGG' => [1,0], 'GAGGGT' => [1,1], 'GAGGTA' => [1,1], 'GAGGTC' => [1,1], 'GAGGTG' => [1,0], 'GAGGTT' => [1,1], 'GAGTAC' => [2,0], 'GAGTAT' => [2,0], 'GAGTCA' => [2,1], 'GAGTCC' => [2,1], 'GAGTCG' => [2,0], 'GAGTCT' => [2,1], 'GAGTGC' => [2,1], 'GAGTGG' => [2,0], 'GAGTGT' => [2,1], 'GAGTTA' => [2,1], 'GAGTTC' => [2,1], 'GAGTTG' => [2,0], 'GAGTTT' => [2,1], 'GATAAA' => [2,0], 'GATAAC' => [1,1], 'GATAAG' => [2,0], 'GATAAT' => [1,0], 'GATACA' => [2,1], 'GATACC' => [2,1], 'GATACG' => [2,1], 'GATACT' => [2,0], 'GATAGA' => [2,1], 'GATAGC' => [2,1], 'GATAGG' => [2,1], 'GATAGT' => [2,0], 'GATATA' => [2,1], 'GATATC' => [2,1], 'GATATG' => [2,1], 'GATATT' => [2,0], 'GATCAA' => [2,0], 'GATCAC' => [1,1], 'GATCAG' => [2,0], 'GATCAT' => [1,0], 'GATCCA' => [2,1], 'GATCCC' => [2,1], 'GATCCG' => [2,1], 'GATCCT' => [2,0], 'GATCGA' => [2,1], 'GATCGC' => [2,1], 'GATCGG' => [2,1], 'GATCGT' => [2,0], 'GATCTA' => [2,1], 'GATCTC' => [2,1], 'GATCTG' => [2,1], 'GATCTT' => [2,0], 'GATGAA' => [1,0], 'GATGAC' => [0,1], 'GATGAG' => [1,0], 'GATGAT' => [0,0], 'GATGCA' => [1,1], 'GATGCC' => [1,1], 'GATGCG' => [1,1], 'GATGCT' => [1,0], 'GATGGA' => [1,1], 'GATGGC' => [1,1], 'GATGGG' => [1,1], 'GATGGT' => [1,0], 'GATGTA' => [1,1], 'GATGTC' => [1,1], 'GATGTG' => [1,1], 'GATGTT' => [1,0], 'GATTAC' => [1,1], 'GATTAT' => [1,0], 'GATTCA' => [2,1], 'GATTCC' => [2,1], 'GATTCG' => [2,1], 'GATTCT' => [2,0], 'GATTGC' => [2,1], 'GATTGG' => [2,1], 'GATTGT' => [2,0], 'GATTTA' => [2,1], 'GATTTC' => [2,1], 'GATTTG' => [2,1], 'GATTTT' => [2,0], 'GCAAAA' => [2,0], 'GCAAAC' => [2,1], 'GCAAAG' => [2,1], 'GCAAAT' => [2,1], 'GCAACA' => [1,0], 'GCAACC' => [1,1], 'GCAACG' => [1,1], 'GCAACT' => [1,1], 'GCAAGA' => [2,0], 'GCAAGC' => [2,1], 'GCAAGG' => [2,1], 'GCAAGT' => [2,1], 'GCAATA' => [2,0], 'GCAATC' => [2,1], 'GCAATG' => [2,1], 'GCAATT' => [2,1], 'GCACAA' => [2,0], 'GCACAC' => [2,1], 'GCACAG' => [2,1], 'GCACAT' => [2,1], 'GCACCA' => [1,0], 'GCACCC' => [1,1], 'GCACCG' => [1,1], 'GCACCT' => [1,1], 'GCACGA' => [2,0], 'GCACGC' => [2,1], 'GCACGG' => [2,1], 'GCACGT' => [2,1], 'GCACTA' => [2,0], 'GCACTC' => [2,1], 'GCACTG' => [2,1], 'GCACTT' => [2,1], 'GCAGAA' => [1,0], 'GCAGAC' => [1,1], 'GCAGAG' => [1,1], 'GCAGAT' => [1,1], 'GCAGCA' => [0,0], 'GCAGCC' => [0,1], 'GCAGCG' => [0,1], 'GCAGCT' => [0,1], 'GCAGGA' => [1,0], 'GCAGGC' => [1,1], 'GCAGGG' => [1,1], 'GCAGGT' => [1,1], 'GCAGTA' => [1,0], 'GCAGTC' => [1,1], 'GCAGTG' => [1,1], 'GCAGTT' => [1,1], 'GCATAC' => [2,1], 'GCATAT' => [2,1], 'GCATCA' => [1,0], 'GCATCC' => [1,1], 'GCATCG' => [1,1], 'GCATCT' => [1,1], 'GCATGC' => [2,1], 'GCATGG' => [2,1], 'GCATGT' => [2,1], 'GCATTA' => [2,0], 'GCATTC' => [2,1], 'GCATTG' => [2,1], 'GCATTT' => [2,1], 'GCCAAA' => [2,1], 'GCCAAC' => [2,0], 'GCCAAG' => [2,1], 'GCCAAT' => [2,1], 'GCCACA' => [1,1], 'GCCACC' => [1,0], 'GCCACG' => [1,1], 'GCCACT' => [1,1], 'GCCAGA' => [2,1], 'GCCAGC' => [2,0], 'GCCAGG' => [2,1], 'GCCAGT' => [2,1], 'GCCATA' => [2,1], 'GCCATC' => [2,0], 'GCCATG' => [2,1], 'GCCATT' => [2,1], 'GCCCAA' => [2,1], 'GCCCAC' => [2,0], 'GCCCAG' => [2,1], 'GCCCAT' => [2,1], 'GCCCCA' => [1,1], 'GCCCCC' => [1,0], 'GCCCCG' => [1,1], 'GCCCCT' => [1,1], 'GCCCGA' => [2,1], 'GCCCGC' => [2,0], 'GCCCGG' => [2,1], 'GCCCGT' => [2,1], 'GCCCTA' => [2,1], 'GCCCTC' => [2,0], 'GCCCTG' => [2,1], 'GCCCTT' => [2,1], 'GCCGAA' => [1,1], 'GCCGAC' => [1,0], 'GCCGAG' => [1,1], 'GCCGAT' => [1,1], 'GCCGCA' => [0,1], 'GCCGCC' => [0,0], 'GCCGCG' => [0,1], 'GCCGCT' => [0,1], 'GCCGGA' => [1,1], 'GCCGGC' => [1,0], 'GCCGGG' => [1,1], 'GCCGGT' => [1,1], 'GCCGTA' => [1,1], 'GCCGTC' => [1,0], 'GCCGTG' => [1,1], 'GCCGTT' => [1,1], 'GCCTAC' => [2,0], 'GCCTAT' => [2,1], 'GCCTCA' => [1,1], 'GCCTCC' => [1,0], 'GCCTCG' => [1,1], 'GCCTCT' => [1,1], 'GCCTGC' => [2,0], 'GCCTGG' => [2,1], 'GCCTGT' => [2,1], 'GCCTTA' => [2,1], 'GCCTTC' => [2,0], 'GCCTTG' => [2,1], 'GCCTTT' => [2,1], 'GCGAAA' => [2,1], 'GCGAAC' => [2,1], 'GCGAAG' => [2,0], 'GCGAAT' => [2,1], 'GCGACA' => [1,1], 'GCGACC' => [1,1], 'GCGACG' => [1,0], 'GCGACT' => [1,1], 'GCGAGA' => [2,1], 'GCGAGC' => [2,1], 'GCGAGG' => [2,0], 'GCGAGT' => [2,1], 'GCGATA' => [2,1], 'GCGATC' => [2,1], 'GCGATG' => [2,0], 'GCGATT' => [2,1], 'GCGCAA' => [2,1], 'GCGCAC' => [2,1], 'GCGCAG' => [2,0], 'GCGCAT' => [2,1], 'GCGCCA' => [1,1], 'GCGCCC' => [1,1], 'GCGCCG' => [1,0], 'GCGCCT' => [1,1], 'GCGCGA' => [2,1], 'GCGCGC' => [2,1], 'GCGCGG' => [2,0], 'GCGCGT' => [2,1], 'GCGCTA' => [2,1], 'GCGCTC' => [2,1], 'GCGCTG' => [2,0], 'GCGCTT' => [2,1], 'GCGGAA' => [1,1], 'GCGGAC' => [1,1], 'GCGGAG' => [1,0], 'GCGGAT' => [1,1], 'GCGGCA' => [0,1], 'GCGGCC' => [0,1], 'GCGGCG' => [0,0], 'GCGGCT' => [0,1], 'GCGGGA' => [1,1], 'GCGGGC' => [1,1], 'GCGGGG' => [1,0], 'GCGGGT' => [1,1], 'GCGGTA' => [1,1], 'GCGGTC' => [1,1], 'GCGGTG' => [1,0], 'GCGGTT' => [1,1], 'GCGTAC' => [2,1], 'GCGTAT' => [2,1], 'GCGTCA' => [1,1], 'GCGTCC' => [1,1], 'GCGTCG' => [1,0], 'GCGTCT' => [1,1], 'GCGTGC' => [2,1], 'GCGTGG' => [2,0], 'GCGTGT' => [2,1], 'GCGTTA' => [2,1], 'GCGTTC' => [2,1], 'GCGTTG' => [2,0], 'GCGTTT' => [2,1], 'GCTAAA' => [2,1], 'GCTAAC' => [2,1], 'GCTAAG' => [2,1], 'GCTAAT' => [2,0], 'GCTACA' => [1,1], 'GCTACC' => [1,1], 'GCTACG' => [1,1], 'GCTACT' => [1,0], 'GCTAGA' => [2,1], 'GCTAGC' => [2,1], 'GCTAGG' => [2,1], 'GCTAGT' => [2,0], 'GCTATA' => [2,1], 'GCTATC' => [2,1], 'GCTATG' => [2,1], 'GCTATT' => [2,0], 'GCTCAA' => [2,1], 'GCTCAC' => [2,1], 'GCTCAG' => [2,1], 'GCTCAT' => [2,0], 'GCTCCA' => [1,1], 'GCTCCC' => [1,1], 'GCTCCG' => [1,1], 'GCTCCT' => [1,0], 'GCTCGA' => [2,1], 'GCTCGC' => [2,1], 'GCTCGG' => [2,1], 'GCTCGT' => [2,0], 'GCTCTA' => [2,1], 'GCTCTC' => [2,1], 'GCTCTG' => [2,1], 'GCTCTT' => [2,0], 'GCTGAA' => [1,1], 'GCTGAC' => [1,1], 'GCTGAG' => [1,1], 'GCTGAT' => [1,0], 'GCTGCA' => [0,1], 'GCTGCC' => [0,1], 'GCTGCG' => [0,1], 'GCTGCT' => [0,0], 'GCTGGA' => [1,1], 'GCTGGC' => [1,1], 'GCTGGG' => [1,1], 'GCTGGT' => [1,0], 'GCTGTA' => [1,1], 'GCTGTC' => [1,1], 'GCTGTG' => [1,1], 'GCTGTT' => [1,0], 'GCTTAC' => [2,1], 'GCTTAT' => [2,0], 'GCTTCA' => [1,1], 'GCTTCC' => [1,1], 'GCTTCG' => [1,1], 'GCTTCT' => [1,0], 'GCTTGC' => [2,1], 'GCTTGG' => [2,1], 'GCTTGT' => [2,0], 'GCTTTA' => [2,1], 'GCTTTC' => [2,1], 'GCTTTG' => [2,1], 'GCTTTT' => [2,0], 'GGAAAA' => [2,0], 'GGAAAC' => [2,1], 'GGAAAG' => [2,1], 'GGAAAT' => [2,1], 'GGAACA' => [2,0], 'GGAACC' => [2,1], 'GGAACG' => [2,1], 'GGAACT' => [2,1], 'GGAAGA' => [1,0], 'GGAAGC' => [1,1], 'GGAAGG' => [1,1], 'GGAAGT' => [1,1], 'GGAATA' => [2,0], 'GGAATC' => [2,1], 'GGAATG' => [2,1], 'GGAATT' => [2,1], 'GGACAA' => [2,0], 'GGACAC' => [2,1], 'GGACAG' => [2,1], 'GGACAT' => [2,1], 'GGACCA' => [2,0], 'GGACCC' => [2,1], 'GGACCG' => [2,1], 'GGACCT' => [2,1], 'GGACGA' => [1,0], 'GGACGC' => [1,1], 'GGACGG' => [1,1], 'GGACGT' => [1,1], 'GGACTA' => [2,0], 'GGACTC' => [2,1], 'GGACTG' => [2,1], 'GGACTT' => [2,1], 'GGAGAA' => [1,0], 'GGAGAC' => [1,1], 'GGAGAG' => [1,1], 'GGAGAT' => [1,1], 'GGAGCA' => [1,0], 'GGAGCC' => [1,1], 'GGAGCG' => [1,1], 'GGAGCT' => [1,1], 'GGAGGA' => [0,0], 'GGAGGC' => [0,1], 'GGAGGG' => [0,1], 'GGAGGT' => [0,1], 'GGAGTA' => [1,0], 'GGAGTC' => [1,1], 'GGAGTG' => [1,1], 'GGAGTT' => [1,1], 'GGATAC' => [2,1], 'GGATAT' => [2,1], 'GGATCA' => [2,0], 'GGATCC' => [2,1], 'GGATCG' => [2,1], 'GGATCT' => [2,1], 'GGATGC' => [1,1], 'GGATGG' => [1,1], 'GGATGT' => [1,1], 'GGATTA' => [2,0], 'GGATTC' => [2,1], 'GGATTG' => [2,1], 'GGATTT' => [2,1], 'GGCAAA' => [2,1], 'GGCAAC' => [2,0], 'GGCAAG' => [2,1], 'GGCAAT' => [2,1], 'GGCACA' => [2,1], 'GGCACC' => [2,0], 'GGCACG' => [2,1], 'GGCACT' => [2,1], 'GGCAGA' => [1,1], 'GGCAGC' => [1,0], 'GGCAGG' => [1,1], 'GGCAGT' => [1,1], 'GGCATA' => [2,1], 'GGCATC' => [2,0], 'GGCATG' => [2,1], 'GGCATT' => [2,1], 'GGCCAA' => [2,1], 'GGCCAC' => [2,0], 'GGCCAG' => [2,1], 'GGCCAT' => [2,1], 'GGCCCA' => [2,1], 'GGCCCC' => [2,0], 'GGCCCG' => [2,1], 'GGCCCT' => [2,1], 'GGCCGA' => [1,1], 'GGCCGC' => [1,0], 'GGCCGG' => [1,1], 'GGCCGT' => [1,1], 'GGCCTA' => [2,1], 'GGCCTC' => [2,0], 'GGCCTG' => [2,1], 'GGCCTT' => [2,1], 'GGCGAA' => [1,1], 'GGCGAC' => [1,0], 'GGCGAG' => [1,1], 'GGCGAT' => [1,1], 'GGCGCA' => [1,1], 'GGCGCC' => [1,0], 'GGCGCG' => [1,1], 'GGCGCT' => [1,1], 'GGCGGA' => [0,1], 'GGCGGC' => [0,0], 'GGCGGG' => [0,1], 'GGCGGT' => [0,1], 'GGCGTA' => [1,1], 'GGCGTC' => [1,0], 'GGCGTG' => [1,1], 'GGCGTT' => [1,1], 'GGCTAC' => [2,0], 'GGCTAT' => [2,1], 'GGCTCA' => [2,1], 'GGCTCC' => [2,0], 'GGCTCG' => [2,1], 'GGCTCT' => [2,1], 'GGCTGC' => [1,0], 'GGCTGG' => [1,1], 'GGCTGT' => [1,1], 'GGCTTA' => [2,1], 'GGCTTC' => [2,0], 'GGCTTG' => [2,1], 'GGCTTT' => [2,1], 'GGGAAA' => [2,1], 'GGGAAC' => [2,1], 'GGGAAG' => [2,0], 'GGGAAT' => [2,1], 'GGGACA' => [2,1], 'GGGACC' => [2,1], 'GGGACG' => [2,0], 'GGGACT' => [2,1], 'GGGAGA' => [1,1], 'GGGAGC' => [1,1], 'GGGAGG' => [1,0], 'GGGAGT' => [1,1], 'GGGATA' => [2,1], 'GGGATC' => [2,1], 'GGGATG' => [2,0], 'GGGATT' => [2,1], 'GGGCAA' => [2,1], 'GGGCAC' => [2,1], 'GGGCAG' => [2,0], 'GGGCAT' => [2,1], 'GGGCCA' => [2,1], 'GGGCCC' => [2,1], 'GGGCCG' => [2,0], 'GGGCCT' => [2,1], 'GGGCGA' => [1,1], 'GGGCGC' => [1,1], 'GGGCGG' => [1,0], 'GGGCGT' => [1,1], 'GGGCTA' => [2,1], 'GGGCTC' => [2,1], 'GGGCTG' => [2,0], 'GGGCTT' => [2,1], 'GGGGAA' => [1,1], 'GGGGAC' => [1,1], 'GGGGAG' => [1,0], 'GGGGAT' => [1,1], 'GGGGCA' => [1,1], 'GGGGCC' => [1,1], 'GGGGCG' => [1,0], 'GGGGCT' => [1,1], 'GGGGGA' => [0,1], 'GGGGGC' => [0,1], 'GGGGGG' => [0,0], 'GGGGGT' => [0,1], 'GGGGTA' => [1,1], 'GGGGTC' => [1,1], 'GGGGTG' => [1,0], 'GGGGTT' => [1,1], 'GGGTAC' => [2,1], 'GGGTAT' => [2,1], 'GGGTCA' => [2,1], 'GGGTCC' => [2,1], 'GGGTCG' => [2,0], 'GGGTCT' => [2,1], 'GGGTGC' => [1,1], 'GGGTGG' => [1,0], 'GGGTGT' => [1,1], 'GGGTTA' => [2,1], 'GGGTTC' => [2,1], 'GGGTTG' => [2,0], 'GGGTTT' => [2,1], 'GGTAAA' => [2,1], 'GGTAAC' => [2,1], 'GGTAAG' => [2,1], 'GGTAAT' => [2,0], 'GGTACA' => [2,1], 'GGTACC' => [2,1], 'GGTACG' => [2,1], 'GGTACT' => [2,0], 'GGTAGA' => [1,1], 'GGTAGC' => [1,1], 'GGTAGG' => [1,1], 'GGTAGT' => [1,0], 'GGTATA' => [2,1], 'GGTATC' => [2,1], 'GGTATG' => [2,1], 'GGTATT' => [2,0], 'GGTCAA' => [2,1], 'GGTCAC' => [2,1], 'GGTCAG' => [2,1], 'GGTCAT' => [2,0], 'GGTCCA' => [2,1], 'GGTCCC' => [2,1], 'GGTCCG' => [2,1], 'GGTCCT' => [2,0], 'GGTCGA' => [1,1], 'GGTCGC' => [1,1], 'GGTCGG' => [1,1], 'GGTCGT' => [1,0], 'GGTCTA' => [2,1], 'GGTCTC' => [2,1], 'GGTCTG' => [2,1], 'GGTCTT' => [2,0], 'GGTGAA' => [1,1], 'GGTGAC' => [1,1], 'GGTGAG' => [1,1], 'GGTGAT' => [1,0], 'GGTGCA' => [1,1], 'GGTGCC' => [1,1], 'GGTGCG' => [1,1], 'GGTGCT' => [1,0], 'GGTGGA' => [0,1], 'GGTGGC' => [0,1], 'GGTGGG' => [0,1], 'GGTGGT' => [0,0], 'GGTGTA' => [1,1], 'GGTGTC' => [1,1], 'GGTGTG' => [1,1], 'GGTGTT' => [1,0], 'GGTTAC' => [2,1], 'GGTTAT' => [2,0], 'GGTTCA' => [2,1], 'GGTTCC' => [2,1], 'GGTTCG' => [2,1], 'GGTTCT' => [2,0], 'GGTTGC' => [1,1], 'GGTTGG' => [1,1], 'GGTTGT' => [1,0], 'GGTTTA' => [2,1], 'GGTTTC' => [2,1], 'GGTTTG' => [2,1], 'GGTTTT' => [2,0], 'GTAAAA' => [2,0], 'GTAAAC' => [2,1], 'GTAAAG' => [2,1], 'GTAAAT' => [2,1], 'GTAACA' => [2,0], 'GTAACC' => [2,1], 'GTAACG' => [2,1], 'GTAACT' => [2,1], 'GTAAGA' => [2,0], 'GTAAGC' => [2,1], 'GTAAGG' => [2,1], 'GTAAGT' => [2,1], 'GTAATA' => [1,0], 'GTAATC' => [1,1], 'GTAATG' => [1,1], 'GTAATT' => [1,1], 'GTACAA' => [2,0], 'GTACAC' => [2,1], 'GTACAG' => [2,1], 'GTACAT' => [2,1], 'GTACCA' => [2,0], 'GTACCC' => [2,1], 'GTACCG' => [2,1], 'GTACCT' => [2,1], 'GTACGA' => [2,0], 'GTACGC' => [2,1], 'GTACGG' => [2,1], 'GTACGT' => [2,1], 'GTACTA' => [1,0], 'GTACTC' => [1,1], 'GTACTG' => [1,1], 'GTACTT' => [1,1], 'GTAGAA' => [1,0], 'GTAGAC' => [1,1], 'GTAGAG' => [1,1], 'GTAGAT' => [1,1], 'GTAGCA' => [1,0], 'GTAGCC' => [1,1], 'GTAGCG' => [1,1], 'GTAGCT' => [1,1], 'GTAGGA' => [1,0], 'GTAGGC' => [1,1], 'GTAGGG' => [1,1], 'GTAGGT' => [1,1], 'GTAGTA' => [0,0], 'GTAGTC' => [0,1], 'GTAGTG' => [0,1], 'GTAGTT' => [0,1], 'GTATAC' => [2,1], 'GTATAT' => [2,1], 'GTATCA' => [2,0], 'GTATCC' => [2,1], 'GTATCG' => [2,1], 'GTATCT' => [2,1], 'GTATGC' => [2,1], 'GTATGG' => [2,1], 'GTATGT' => [2,1], 'GTATTA' => [1,0], 'GTATTC' => [1,1], 'GTATTG' => [1,1], 'GTATTT' => [1,1], 'GTCAAA' => [2,1], 'GTCAAC' => [2,0], 'GTCAAG' => [2,1], 'GTCAAT' => [2,1], 'GTCACA' => [2,1], 'GTCACC' => [2,0], 'GTCACG' => [2,1], 'GTCACT' => [2,1], 'GTCAGA' => [2,1], 'GTCAGC' => [2,0], 'GTCAGG' => [2,1], 'GTCAGT' => [2,1], 'GTCATA' => [1,1], 'GTCATC' => [1,0], 'GTCATG' => [1,1], 'GTCATT' => [1,1], 'GTCCAA' => [2,1], 'GTCCAC' => [2,0], 'GTCCAG' => [2,1], 'GTCCAT' => [2,1], 'GTCCCA' => [2,1], 'GTCCCC' => [2,0], 'GTCCCG' => [2,1], 'GTCCCT' => [2,1], 'GTCCGA' => [2,1], 'GTCCGC' => [2,0], 'GTCCGG' => [2,1], 'GTCCGT' => [2,1], 'GTCCTA' => [1,1], 'GTCCTC' => [1,0], 'GTCCTG' => [1,1], 'GTCCTT' => [1,1], 'GTCGAA' => [1,1], 'GTCGAC' => [1,0], 'GTCGAG' => [1,1], 'GTCGAT' => [1,1], 'GTCGCA' => [1,1], 'GTCGCC' => [1,0], 'GTCGCG' => [1,1], 'GTCGCT' => [1,1], 'GTCGGA' => [1,1], 'GTCGGC' => [1,0], 'GTCGGG' => [1,1], 'GTCGGT' => [1,1], 'GTCGTA' => [0,1], 'GTCGTC' => [0,0], 'GTCGTG' => [0,1], 'GTCGTT' => [0,1], 'GTCTAC' => [2,0], 'GTCTAT' => [2,1], 'GTCTCA' => [2,1], 'GTCTCC' => [2,0], 'GTCTCG' => [2,1], 'GTCTCT' => [2,1], 'GTCTGC' => [2,0], 'GTCTGG' => [2,1], 'GTCTGT' => [2,1], 'GTCTTA' => [1,1], 'GTCTTC' => [1,0], 'GTCTTG' => [1,1], 'GTCTTT' => [1,1], 'GTGAAA' => [2,1], 'GTGAAC' => [2,1], 'GTGAAG' => [2,0], 'GTGAAT' => [2,1], 'GTGACA' => [2,1], 'GTGACC' => [2,1], 'GTGACG' => [2,0], 'GTGACT' => [2,1], 'GTGAGA' => [2,1], 'GTGAGC' => [2,1], 'GTGAGG' => [2,0], 'GTGAGT' => [2,1], 'GTGATA' => [1,1], 'GTGATC' => [1,1], 'GTGATG' => [1,0], 'GTGATT' => [1,1], 'GTGCAA' => [2,1], 'GTGCAC' => [2,1], 'GTGCAG' => [2,0], 'GTGCAT' => [2,1], 'GTGCCA' => [2,1], 'GTGCCC' => [2,1], 'GTGCCG' => [2,0], 'GTGCCT' => [2,1], 'GTGCGA' => [2,1], 'GTGCGC' => [2,1], 'GTGCGG' => [2,0], 'GTGCGT' => [2,1], 'GTGCTA' => [1,1], 'GTGCTC' => [1,1], 'GTGCTG' => [1,0], 'GTGCTT' => [1,1], 'GTGGAA' => [1,1], 'GTGGAC' => [1,1], 'GTGGAG' => [1,0], 'GTGGAT' => [1,1], 'GTGGCA' => [1,1], 'GTGGCC' => [1,1], 'GTGGCG' => [1,0], 'GTGGCT' => [1,1], 'GTGGGA' => [1,1], 'GTGGGC' => [1,1], 'GTGGGG' => [1,0], 'GTGGGT' => [1,1], 'GTGGTA' => [0,1], 'GTGGTC' => [0,1], 'GTGGTG' => [0,0], 'GTGGTT' => [0,1], 'GTGTAC' => [2,1], 'GTGTAT' => [2,1], 'GTGTCA' => [2,1], 'GTGTCC' => [2,1], 'GTGTCG' => [2,0], 'GTGTCT' => [2,1], 'GTGTGC' => [2,1], 'GTGTGG' => [2,0], 'GTGTGT' => [2,1], 'GTGTTA' => [1,1], 'GTGTTC' => [1,1], 'GTGTTG' => [1,0], 'GTGTTT' => [1,1], 'GTTAAA' => [2,1], 'GTTAAC' => [2,1], 'GTTAAG' => [2,1], 'GTTAAT' => [2,0], 'GTTACA' => [2,1], 'GTTACC' => [2,1], 'GTTACG' => [2,1], 'GTTACT' => [2,0], 'GTTAGA' => [2,1], 'GTTAGC' => [2,1], 'GTTAGG' => [2,1], 'GTTAGT' => [2,0], 'GTTATA' => [1,1], 'GTTATC' => [1,1], 'GTTATG' => [1,1], 'GTTATT' => [1,0], 'GTTCAA' => [2,1], 'GTTCAC' => [2,1], 'GTTCAG' => [2,1], 'GTTCAT' => [2,0], 'GTTCCA' => [2,1], 'GTTCCC' => [2,1], 'GTTCCG' => [2,1], 'GTTCCT' => [2,0], 'GTTCGA' => [2,1], 'GTTCGC' => [2,1], 'GTTCGG' => [2,1], 'GTTCGT' => [2,0], 'GTTCTA' => [1,1], 'GTTCTC' => [1,1], 'GTTCTG' => [1,1], 'GTTCTT' => [1,0], 'GTTGAA' => [1,1], 'GTTGAC' => [1,1], 'GTTGAG' => [1,1], 'GTTGAT' => [1,0], 'GTTGCA' => [1,1], 'GTTGCC' => [1,1], 'GTTGCG' => [1,1], 'GTTGCT' => [1,0], 'GTTGGA' => [1,1], 'GTTGGC' => [1,1], 'GTTGGG' => [1,1], 'GTTGGT' => [1,0], 'GTTGTA' => [0,1], 'GTTGTC' => [0,1], 'GTTGTG' => [0,1], 'GTTGTT' => [0,0], 'GTTTAC' => [2,1], 'GTTTAT' => [2,0], 'GTTTCA' => [2,1], 'GTTTCC' => [2,1], 'GTTTCG' => [2,1], 'GTTTCT' => [2,0], 'GTTTGC' => [2,1], 'GTTTGG' => [2,1], 'GTTTGT' => [2,0], 'GTTTTA' => [1,1], 'GTTTTC' => [1,1], 'GTTTTG' => [1,1], 'GTTTTT' => [1,0], 'TACAAA' => [2,0], 'TACAAC' => [1,0], 'TACAAG' => [2,0], 'TACAAT' => [1,1], 'TACACA' => [2,1], 'TACACC' => [2,0], 'TACACG' => [2,1], 'TACACT' => [2,1], 'TACAGA' => [3,0], 'TACAGC' => [2,0], 'TACAGG' => [3,0], 'TACAGT' => [2,1], 'TACATA' => [2,1], 'TACATC' => [2,0], 'TACATG' => [3,0], 'TACATT' => [2,1], 'TACCAA' => [2,0], 'TACCAC' => [1,0], 'TACCAG' => [2,0], 'TACCAT' => [1,1], 'TACCCA' => [2,1], 'TACCCC' => [2,0], 'TACCCG' => [2,1], 'TACCCT' => [2,1], 'TACCGA' => [2,1], 'TACCGC' => [2,0], 'TACCGG' => [2,1], 'TACCGT' => [2,1], 'TACCTA' => [2,1], 'TACCTC' => [2,0], 'TACCTG' => [2,1], 'TACCTT' => [2,1], 'TACGAA' => [2,0], 'TACGAC' => [1,0], 'TACGAG' => [2,0], 'TACGAT' => [1,1], 'TACGCA' => [2,1], 'TACGCC' => [2,0], 'TACGCG' => [2,1], 'TACGCT' => [2,1], 'TACGGA' => [2,1], 'TACGGC' => [2,0], 'TACGGG' => [2,1], 'TACGGT' => [2,1], 'TACGTA' => [2,1], 'TACGTC' => [2,0], 'TACGTG' => [2,1], 'TACGTT' => [2,1], 'TACTAC' => [0,0], 'TACTAT' => [0,1], 'TACTCA' => [1,1], 'TACTCC' => [1,0], 'TACTCG' => [1,1], 'TACTCT' => [1,1], 'TACTGC' => [1,0], 'TACTGG' => [2,0], 'TACTGT' => [1,1], 'TACTTA' => [2,0], 'TACTTC' => [1,0], 'TACTTG' => [2,0], 'TACTTT' => [1,1], 'TATAAA' => [2,0], 'TATAAC' => [1,1], 'TATAAG' => [2,0], 'TATAAT' => [1,0], 'TATACA' => [2,1], 'TATACC' => [2,1], 'TATACG' => [2,1], 'TATACT' => [2,0], 'TATAGA' => [3,0], 'TATAGC' => [2,1], 'TATAGG' => [3,0], 'TATAGT' => [2,0], 'TATATA' => [2,1], 'TATATC' => [2,1], 'TATATG' => [3,0], 'TATATT' => [2,0], 'TATCAA' => [2,0], 'TATCAC' => [1,1], 'TATCAG' => [2,0], 'TATCAT' => [1,0], 'TATCCA' => [2,1], 'TATCCC' => [2,1], 'TATCCG' => [2,1], 'TATCCT' => [2,0], 'TATCGA' => [2,1], 'TATCGC' => [2,1], 'TATCGG' => [2,1], 'TATCGT' => [2,0], 'TATCTA' => [2,1], 'TATCTC' => [2,1], 'TATCTG' => [2,1], 'TATCTT' => [2,0], 'TATGAA' => [2,0], 'TATGAC' => [1,1], 'TATGAG' => [2,0], 'TATGAT' => [1,0], 'TATGCA' => [2,1], 'TATGCC' => [2,1], 'TATGCG' => [2,1], 'TATGCT' => [2,0], 'TATGGA' => [2,1], 'TATGGC' => [2,1], 'TATGGG' => [2,1], 'TATGGT' => [2,0], 'TATGTA' => [2,1], 'TATGTC' => [2,1], 'TATGTG' => [2,1], 'TATGTT' => [2,0], 'TATTAC' => [0,1], 'TATTAT' => [0,0], 'TATTCA' => [1,1], 'TATTCC' => [1,1], 'TATTCG' => [1,1], 'TATTCT' => [1,0], 'TATTGC' => [1,1], 'TATTGG' => [2,0], 'TATTGT' => [1,0], 'TATTTA' => [2,0], 'TATTTC' => [1,1], 'TATTTG' => [2,0], 'TATTTT' => [1,0], 'TCAAAA' => [2,0], 'TCAAAC' => [2,1], 'TCAAAG' => [2,1], 'TCAAAT' => [2,1], 'TCAACA' => [1,0], 'TCAACC' => [1,1], 'TCAACG' => [1,1], 'TCAACT' => [1,1], 'TCAAGA' => [2,0], 'TCAAGC' => [2,1], 'TCAAGG' => [2,1], 'TCAAGT' => [2,1], 'TCAATA' => [2,0], 'TCAATC' => [2,1], 'TCAATG' => [2,1], 'TCAATT' => [2,1], 'TCACAA' => [2,0], 'TCACAC' => [2,1], 'TCACAG' => [2,1], 'TCACAT' => [2,1], 'TCACCA' => [1,0], 'TCACCC' => [1,1], 'TCACCG' => [1,1], 'TCACCT' => [1,1], 'TCACGA' => [2,0], 'TCACGC' => [2,1], 'TCACGG' => [2,1], 'TCACGT' => [2,1], 'TCACTA' => [1,1], 'TCACTC' => [1,2], 'TCACTG' => [1,2], 'TCACTT' => [1,2], 'TCAGAA' => [2,0], 'TCAGAC' => [2,1], 'TCAGAG' => [2,1], 'TCAGAT' => [2,1], 'TCAGCA' => [1,0], 'TCAGCC' => [1,1], 'TCAGCG' => [1,1], 'TCAGCT' => [1,1], 'TCAGGA' => [2,0], 'TCAGGC' => [2,1], 'TCAGGG' => [2,1], 'TCAGGT' => [2,1], 'TCAGTA' => [2,0], 'TCAGTC' => [2,1], 'TCAGTG' => [2,1], 'TCAGTT' => [2,1], 'TCATAC' => [1,1], 'TCATAT' => [1,1], 'TCATCA' => [0,0], 'TCATCC' => [0,1], 'TCATCG' => [0,1], 'TCATCT' => [0,1], 'TCATGC' => [1,1], 'TCATGG' => [1,1], 'TCATGT' => [1,1], 'TCATTA' => [1,0], 'TCATTC' => [1,1], 'TCATTG' => [1,1], 'TCATTT' => [1,1], 'TCCAAA' => [2,1], 'TCCAAC' => [2,0], 'TCCAAG' => [2,1], 'TCCAAT' => [2,1], 'TCCACA' => [1,1], 'TCCACC' => [1,0], 'TCCACG' => [1,1], 'TCCACT' => [1,1], 'TCCAGA' => [2,1], 'TCCAGC' => [2,0], 'TCCAGG' => [2,1], 'TCCAGT' => [2,1], 'TCCATA' => [2,1], 'TCCATC' => [2,0], 'TCCATG' => [2,1], 'TCCATT' => [2,1], 'TCCCAA' => [2,1], 'TCCCAC' => [2,0], 'TCCCAG' => [2,1], 'TCCCAT' => [2,1], 'TCCCCA' => [1,1], 'TCCCCC' => [1,0], 'TCCCCG' => [1,1], 'TCCCCT' => [1,1], 'TCCCGA' => [2,1], 'TCCCGC' => [2,0], 'TCCCGG' => [2,1], 'TCCCGT' => [2,1], 'TCCCTA' => [1,2], 'TCCCTC' => [2,0], 'TCCCTG' => [1,2], 'TCCCTT' => [2,1], 'TCCGAA' => [2,1], 'TCCGAC' => [2,0], 'TCCGAG' => [2,1], 'TCCGAT' => [2,1], 'TCCGCA' => [1,1], 'TCCGCC' => [1,0], 'TCCGCG' => [1,1], 'TCCGCT' => [1,1], 'TCCGGA' => [2,1], 'TCCGGC' => [2,0], 'TCCGGG' => [2,1], 'TCCGGT' => [2,1], 'TCCGTA' => [2,1], 'TCCGTC' => [2,0], 'TCCGTG' => [2,1], 'TCCGTT' => [2,1], 'TCCTAC' => [1,0], 'TCCTAT' => [1,1], 'TCCTCA' => [0,1], 'TCCTCC' => [0,0], 'TCCTCG' => [0,1], 'TCCTCT' => [0,1], 'TCCTGC' => [1,0], 'TCCTGG' => [1,1], 'TCCTGT' => [1,1], 'TCCTTA' => [1,1], 'TCCTTC' => [1,0], 'TCCTTG' => [1,1], 'TCCTTT' => [1,1], 'TCGAAA' => [2,1], 'TCGAAC' => [2,1], 'TCGAAG' => [2,0], 'TCGAAT' => [2,1], 'TCGACA' => [1,1], 'TCGACC' => [1,1], 'TCGACG' => [1,0], 'TCGACT' => [1,1], 'TCGAGA' => [2,1], 'TCGAGC' => [2,1], 'TCGAGG' => [2,0], 'TCGAGT' => [2,1], 'TCGATA' => [2,1], 'TCGATC' => [2,1], 'TCGATG' => [2,0], 'TCGATT' => [2,1], 'TCGCAA' => [2,1], 'TCGCAC' => [2,1], 'TCGCAG' => [2,0], 'TCGCAT' => [2,1], 'TCGCCA' => [1,1], 'TCGCCC' => [1,1], 'TCGCCG' => [1,0], 'TCGCCT' => [1,1], 'TCGCGA' => [2,1], 'TCGCGC' => [2,1], 'TCGCGG' => [2,0], 'TCGCGT' => [2,1], 'TCGCTA' => [1,2], 'TCGCTC' => [1,2], 'TCGCTG' => [1,1], 'TCGCTT' => [1,2], 'TCGGAA' => [2,1], 'TCGGAC' => [2,1], 'TCGGAG' => [2,0], 'TCGGAT' => [2,1], 'TCGGCA' => [1,1], 'TCGGCC' => [1,1], 'TCGGCG' => [1,0], 'TCGGCT' => [1,1], 'TCGGGA' => [2,1], 'TCGGGC' => [2,1], 'TCGGGG' => [2,0], 'TCGGGT' => [2,1], 'TCGGTA' => [2,1], 'TCGGTC' => [2,1], 'TCGGTG' => [2,0], 'TCGGTT' => [2,1], 'TCGTAC' => [1,1], 'TCGTAT' => [1,1], 'TCGTCA' => [0,1], 'TCGTCC' => [0,1], 'TCGTCG' => [0,0], 'TCGTCT' => [0,1], 'TCGTGC' => [1,1], 'TCGTGG' => [1,0], 'TCGTGT' => [1,1], 'TCGTTA' => [1,1], 'TCGTTC' => [1,1], 'TCGTTG' => [1,0], 'TCGTTT' => [1,1], 'TCTAAA' => [2,1], 'TCTAAC' => [2,1], 'TCTAAG' => [2,1], 'TCTAAT' => [2,0], 'TCTACA' => [1,1], 'TCTACC' => [1,1], 'TCTACG' => [1,1], 'TCTACT' => [1,0], 'TCTAGA' => [2,1], 'TCTAGC' => [2,1], 'TCTAGG' => [2,1], 'TCTAGT' => [2,0], 'TCTATA' => [2,1], 'TCTATC' => [2,1], 'TCTATG' => [2,1], 'TCTATT' => [2,0], 'TCTCAA' => [2,1], 'TCTCAC' => [2,1], 'TCTCAG' => [2,1], 'TCTCAT' => [2,0], 'TCTCCA' => [1,1], 'TCTCCC' => [1,1], 'TCTCCG' => [1,1], 'TCTCCT' => [1,0], 'TCTCGA' => [2,1], 'TCTCGC' => [2,1], 'TCTCGG' => [2,1], 'TCTCGT' => [2,0], 'TCTCTA' => [1,2], 'TCTCTC' => [2,1], 'TCTCTG' => [1,2], 'TCTCTT' => [2,0], 'TCTGAA' => [2,1], 'TCTGAC' => [2,1], 'TCTGAG' => [2,1], 'TCTGAT' => [2,0], 'TCTGCA' => [1,1], 'TCTGCC' => [1,1], 'TCTGCG' => [1,1], 'TCTGCT' => [1,0], 'TCTGGA' => [2,1], 'TCTGGC' => [2,1], 'TCTGGG' => [2,1], 'TCTGGT' => [2,0], 'TCTGTA' => [2,1], 'TCTGTC' => [2,1], 'TCTGTG' => [2,1], 'TCTGTT' => [2,0], 'TCTTAC' => [1,1], 'TCTTAT' => [1,0], 'TCTTCA' => [0,1], 'TCTTCC' => [0,1], 'TCTTCG' => [0,1], 'TCTTCT' => [0,0], 'TCTTGC' => [1,1], 'TCTTGG' => [1,1], 'TCTTGT' => [1,0], 'TCTTTA' => [1,1], 'TCTTTC' => [1,1], 'TCTTTG' => [1,1], 'TCTTTT' => [1,0], 'TGCAAA' => [3,0], 'TGCAAC' => [2,0], 'TGCAAG' => [3,0], 'TGCAAT' => [2,1], 'TGCACA' => [2,1], 'TGCACC' => [2,0], 'TGCACG' => [2,1], 'TGCACT' => [2,1], 'TGCAGA' => [2,0], 'TGCAGC' => [1,0], 'TGCAGG' => [2,0], 'TGCAGT' => [1,1], 'TGCATA' => [2,1], 'TGCATC' => [2,0], 'TGCATG' => [3,0], 'TGCATT' => [2,1], 'TGCCAA' => [2,1], 'TGCCAC' => [2,0], 'TGCCAG' => [2,1], 'TGCCAT' => [2,1], 'TGCCCA' => [2,1], 'TGCCCC' => [2,0], 'TGCCCG' => [2,1], 'TGCCCT' => [2,1], 'TGCCGA' => [1,1], 'TGCCGC' => [1,0], 'TGCCGG' => [1,1], 'TGCCGT' => [1,1], 'TGCCTA' => [2,1], 'TGCCTC' => [2,0], 'TGCCTG' => [2,1], 'TGCCTT' => [2,1], 'TGCGAA' => [2,1], 'TGCGAC' => [2,0], 'TGCGAG' => [2,1], 'TGCGAT' => [2,1], 'TGCGCA' => [2,1], 'TGCGCC' => [2,0], 'TGCGCG' => [2,1], 'TGCGCT' => [2,1], 'TGCGGA' => [1,1], 'TGCGGC' => [1,0], 'TGCGGG' => [1,1], 'TGCGGT' => [1,1], 'TGCGTA' => [2,1], 'TGCGTC' => [2,0], 'TGCGTG' => [2,1], 'TGCGTT' => [2,1], 'TGCTAC' => [1,0], 'TGCTAT' => [1,1], 'TGCTCA' => [1,1], 'TGCTCC' => [1,0], 'TGCTCG' => [1,1], 'TGCTCT' => [1,1], 'TGCTGC' => [0,0], 'TGCTGG' => [1,0], 'TGCTGT' => [0,1], 'TGCTTA' => [2,0], 'TGCTTC' => [1,0], 'TGCTTG' => [2,0], 'TGCTTT' => [1,1], 'TGGAAA' => [2,1], 'TGGAAC' => [3,0], 'TGGAAG' => [2,0], 'TGGAAT' => [3,0], 'TGGACA' => [2,1], 'TGGACC' => [2,1], 'TGGACG' => [2,0], 'TGGACT' => [2,1], 'TGGAGA' => [1,1], 'TGGAGC' => [2,0], 'TGGAGG' => [1,0], 'TGGAGT' => [2,0], 'TGGATA' => [2,1], 'TGGATC' => [3,0], 'TGGATG' => [2,0], 'TGGATT' => [3,0], 'TGGCAA' => [2,1], 'TGGCAC' => [2,1], 'TGGCAG' => [2,0], 'TGGCAT' => [2,1], 'TGGCCA' => [2,1], 'TGGCCC' => [2,1], 'TGGCCG' => [2,0], 'TGGCCT' => [2,1], 'TGGCGA' => [1,1], 'TGGCGC' => [1,1], 'TGGCGG' => [1,0], 'TGGCGT' => [1,1], 'TGGCTA' => [1,2], 'TGGCTC' => [1,2], 'TGGCTG' => [1,1], 'TGGCTT' => [1,2], 'TGGGAA' => [2,1], 'TGGGAC' => [2,1], 'TGGGAG' => [2,0], 'TGGGAT' => [2,1], 'TGGGCA' => [2,1], 'TGGGCC' => [2,1], 'TGGGCG' => [2,0], 'TGGGCT' => [2,1], 'TGGGGA' => [1,1], 'TGGGGC' => [1,1], 'TGGGGG' => [1,0], 'TGGGGT' => [1,1], 'TGGGTA' => [2,1], 'TGGGTC' => [2,1], 'TGGGTG' => [2,0], 'TGGGTT' => [2,1], 'TGGTAC' => [2,0], 'TGGTAT' => [2,0], 'TGGTCA' => [1,1], 'TGGTCC' => [1,1], 'TGGTCG' => [1,0], 'TGGTCT' => [1,1], 'TGGTGC' => [1,0], 'TGGTGG' => [0,0], 'TGGTGT' => [1,0], 'TGGTTA' => [1,1], 'TGGTTC' => [2,0], 'TGGTTG' => [1,0], 'TGGTTT' => [2,0], 'TGTAAA' => [3,0], 'TGTAAC' => [2,1], 'TGTAAG' => [3,0], 'TGTAAT' => [2,0], 'TGTACA' => [2,1], 'TGTACC' => [2,1], 'TGTACG' => [2,1], 'TGTACT' => [2,0], 'TGTAGA' => [2,0], 'TGTAGC' => [1,1], 'TGTAGG' => [2,0], 'TGTAGT' => [1,0], 'TGTATA' => [2,1], 'TGTATC' => [2,1], 'TGTATG' => [3,0], 'TGTATT' => [2,0], 'TGTCAA' => [2,1], 'TGTCAC' => [2,1], 'TGTCAG' => [2,1], 'TGTCAT' => [2,0], 'TGTCCA' => [2,1], 'TGTCCC' => [2,1], 'TGTCCG' => [2,1], 'TGTCCT' => [2,0], 'TGTCGA' => [1,1], 'TGTCGC' => [1,1], 'TGTCGG' => [1,1], 'TGTCGT' => [1,0], 'TGTCTA' => [2,1], 'TGTCTC' => [2,1], 'TGTCTG' => [2,1], 'TGTCTT' => [2,0], 'TGTGAA' => [2,1], 'TGTGAC' => [2,1], 'TGTGAG' => [2,1], 'TGTGAT' => [2,0], 'TGTGCA' => [2,1], 'TGTGCC' => [2,1], 'TGTGCG' => [2,1], 'TGTGCT' => [2,0], 'TGTGGA' => [1,1], 'TGTGGC' => [1,1], 'TGTGGG' => [1,1], 'TGTGGT' => [1,0], 'TGTGTA' => [2,1], 'TGTGTC' => [2,1], 'TGTGTG' => [2,1], 'TGTGTT' => [2,0], 'TGTTAC' => [1,1], 'TGTTAT' => [1,0], 'TGTTCA' => [1,1], 'TGTTCC' => [1,1], 'TGTTCG' => [1,1], 'TGTTCT' => [1,0], 'TGTTGC' => [0,1], 'TGTTGG' => [1,0], 'TGTTGT' => [0,0], 'TGTTTA' => [2,0], 'TGTTTC' => [1,1], 'TGTTTG' => [2,0], 'TGTTTT' => [1,0], 'TTAAAA' => [2,0], 'TTAAAC' => [2,1], 'TTAAAG' => [2,1], 'TTAAAT' => [2,1], 'TTAACA' => [2,0], 'TTAACC' => [2,1], 'TTAACG' => [2,1], 'TTAACT' => [2,1], 'TTAAGA' => [2,0], 'TTAAGC' => [2,1], 'TTAAGG' => [2,1], 'TTAAGT' => [2,1], 'TTAATA' => [1,0], 'TTAATC' => [1,1], 'TTAATG' => [1,1], 'TTAATT' => [1,1], 'TTACAA' => [1,1], 'TTACAC' => [1,2], 'TTACAG' => [1,2], 'TTACAT' => [1,2], 'TTACCA' => [1,1], 'TTACCC' => [1,2], 'TTACCG' => [1,2], 'TTACCT' => [1,2], 'TTACGA' => [1,1], 'TTACGC' => [1,2], 'TTACGG' => [1,2], 'TTACGT' => [1,2], 'TTACTA' => [0,1], 'TTACTC' => [0,2], 'TTACTG' => [0,2], 'TTACTT' => [0,2], 'TTAGAA' => [2,0], 'TTAGAC' => [2,1], 'TTAGAG' => [2,1], 'TTAGAT' => [2,1], 'TTAGCA' => [2,0], 'TTAGCC' => [2,1], 'TTAGCG' => [2,1], 'TTAGCT' => [2,1], 'TTAGGA' => [2,0], 'TTAGGC' => [2,1], 'TTAGGG' => [2,1], 'TTAGGT' => [2,1], 'TTAGTA' => [1,0], 'TTAGTC' => [1,1], 'TTAGTG' => [1,1], 'TTAGTT' => [1,1], 'TTATAC' => [2,0], 'TTATAT' => [2,0], 'TTATCA' => [1,0], 'TTATCC' => [1,1], 'TTATCG' => [1,1], 'TTATCT' => [1,1], 'TTATGC' => [2,0], 'TTATGG' => [1,1], 'TTATGT' => [2,0], 'TTATTA' => [0,0], 'TTATTC' => [1,0], 'TTATTG' => [0,1], 'TTATTT' => [1,0], 'TTCAAA' => [2,1], 'TTCAAC' => [2,0], 'TTCAAG' => [3,0], 'TTCAAT' => [2,1], 'TTCACA' => [2,1], 'TTCACC' => [2,0], 'TTCACG' => [2,1], 'TTCACT' => [2,1], 'TTCAGA' => [2,1], 'TTCAGC' => [2,0], 'TTCAGG' => [3,0], 'TTCAGT' => [2,1], 'TTCATA' => [1,1], 'TTCATC' => [1,0], 'TTCATG' => [2,0], 'TTCATT' => [1,1], 'TTCCAA' => [2,1], 'TTCCAC' => [2,0], 'TTCCAG' => [2,1], 'TTCCAT' => [2,1], 'TTCCCA' => [2,1], 'TTCCCC' => [2,0], 'TTCCCG' => [2,1], 'TTCCCT' => [2,1], 'TTCCGA' => [2,1], 'TTCCGC' => [2,0], 'TTCCGG' => [2,1], 'TTCCGT' => [2,1], 'TTCCTA' => [1,1], 'TTCCTC' => [1,0], 'TTCCTG' => [1,1], 'TTCCTT' => [1,1], 'TTCGAA' => [2,1], 'TTCGAC' => [2,0], 'TTCGAG' => [2,1], 'TTCGAT' => [2,1], 'TTCGCA' => [2,1], 'TTCGCC' => [2,0], 'TTCGCG' => [2,1], 'TTCGCT' => [2,1], 'TTCGGA' => [2,1], 'TTCGGC' => [2,0], 'TTCGGG' => [2,1], 'TTCGGT' => [2,1], 'TTCGTA' => [1,1], 'TTCGTC' => [1,0], 'TTCGTG' => [1,1], 'TTCGTT' => [1,1], 'TTCTAC' => [1,0], 'TTCTAT' => [1,1], 'TTCTCA' => [1,1], 'TTCTCC' => [1,0], 'TTCTCG' => [1,1], 'TTCTCT' => [1,1], 'TTCTGC' => [1,0], 'TTCTGG' => [2,0], 'TTCTGT' => [1,1], 'TTCTTA' => [1,0], 'TTCTTC' => [0,0], 'TTCTTG' => [1,0], 'TTCTTT' => [0,1], 'TTGAAA' => [2,1], 'TTGAAC' => [3,0], 'TTGAAG' => [2,0], 'TTGAAT' => [3,0], 'TTGACA' => [2,1], 'TTGACC' => [2,1], 'TTGACG' => [2,0], 'TTGACT' => [2,1], 'TTGAGA' => [2,1], 'TTGAGC' => [3,0], 'TTGAGG' => [2,0], 'TTGAGT' => [3,0], 'TTGATA' => [1,1], 'TTGATC' => [2,0], 'TTGATG' => [1,0], 'TTGATT' => [2,0], 'TTGCAA' => [1,2], 'TTGCAC' => [1,2], 'TTGCAG' => [1,1], 'TTGCAT' => [1,2], 'TTGCCA' => [1,2], 'TTGCCC' => [1,2], 'TTGCCG' => [1,1], 'TTGCCT' => [1,2], 'TTGCGA' => [1,2], 'TTGCGC' => [1,2], 'TTGCGG' => [1,1], 'TTGCGT' => [1,2], 'TTGCTA' => [0,2], 'TTGCTC' => [0,2], 'TTGCTG' => [0,1], 'TTGCTT' => [0,2], 'TTGGAA' => [2,1], 'TTGGAC' => [2,1], 'TTGGAG' => [2,0], 'TTGGAT' => [2,1], 'TTGGCA' => [2,1], 'TTGGCC' => [2,1], 'TTGGCG' => [2,0], 'TTGGCT' => [2,1], 'TTGGGA' => [2,1], 'TTGGGC' => [2,1], 'TTGGGG' => [2,0], 'TTGGGT' => [2,1], 'TTGGTA' => [1,1], 'TTGGTC' => [1,1], 'TTGGTG' => [1,0], 'TTGGTT' => [1,1], 'TTGTAC' => [2,0], 'TTGTAT' => [2,0], 'TTGTCA' => [1,1], 'TTGTCC' => [1,1], 'TTGTCG' => [1,0], 'TTGTCT' => [1,1], 'TTGTGC' => [2,0], 'TTGTGG' => [1,0], 'TTGTGT' => [2,0], 'TTGTTA' => [0,1], 'TTGTTC' => [1,0], 'TTGTTG' => [0,0], 'TTGTTT' => [1,0], 'TTTAAA' => [2,1], 'TTTAAC' => [2,1], 'TTTAAG' => [3,0], 'TTTAAT' => [2,0], 'TTTACA' => [2,1], 'TTTACC' => [2,1], 'TTTACG' => [2,1], 'TTTACT' => [2,0], 'TTTAGA' => [2,1], 'TTTAGC' => [2,1], 'TTTAGG' => [3,0], 'TTTAGT' => [2,0], 'TTTATA' => [1,1], 'TTTATC' => [1,1], 'TTTATG' => [2,0], 'TTTATT' => [1,0], 'TTTCAA' => [2,1], 'TTTCAC' => [2,1], 'TTTCAG' => [2,1], 'TTTCAT' => [2,0], 'TTTCCA' => [2,1], 'TTTCCC' => [2,1], 'TTTCCG' => [2,1], 'TTTCCT' => [2,0], 'TTTCGA' => [2,1], 'TTTCGC' => [2,1], 'TTTCGG' => [2,1], 'TTTCGT' => [2,0], 'TTTCTA' => [1,1], 'TTTCTC' => [1,1], 'TTTCTG' => [1,1], 'TTTCTT' => [1,0], 'TTTGAA' => [2,1], 'TTTGAC' => [2,1], 'TTTGAG' => [2,1], 'TTTGAT' => [2,0], 'TTTGCA' => [2,1], 'TTTGCC' => [2,1], 'TTTGCG' => [2,1], 'TTTGCT' => [2,0], 'TTTGGA' => [2,1], 'TTTGGC' => [2,1], 'TTTGGG' => [2,1], 'TTTGGT' => [2,0], 'TTTGTA' => [1,1], 'TTTGTC' => [1,1], 'TTTGTG' => [1,1], 'TTTGTT' => [1,0], 'TTTTAC' => [1,1], 'TTTTAT' => [1,0], 'TTTTCA' => [1,1], 'TTTTCC' => [1,1], 'TTTTCG' => [1,1], 'TTTTCT' => [1,0], 'TTTTGC' => [1,1], 'TTTTGG' => [2,0], 'TTTTGT' => [1,0], 'TTTTTA' => [1,0], 'TTTTTC' => [0,1], 'TTTTTG' => [1,0], 'TTTTTT' => [0,0], }; } 1; BioPerl-1.007002/Bio/Nexml000755000766000024 013155576320 15152 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Nexml/Factory.pm000444000766000024 6333513155576320 17306 0ustar00cjfieldsstaff000000000000# $Id: Util.pm 15875 2009-07-21 19:20:00Z chmille4 $ # # BioPerl module for Bio::Nexml::Factory # # Please direct questions and support issues to # # Cared for by Chase Miller # # Copyright Chase Miller # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Nexml::Factory - A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents =head1 SYNOPSIS Do not use this module directly. It shoulde be used through Bio::NexmlIO, Bio::SeqIO::nexml, Bio::AlignIO::nexml, or Bio::TreeIO::nexml =head1 DESCRIPTION This is a factory/utility module in the Nexml namespace. It contains methods that are needed by multiple modules. This module handles the creation of BioPerl objects from Bio::Phylo objects and vice versa, which is used to read and write nexml documents to and from BioPerl objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chase Miller Email chmille4@gmail.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #Let the code begin package Bio::Nexml::Factory; use strict; BEGIN { use Bio::Root::Root; unless (eval "require Bio::Phylo; 1") { Bio::Root::Root->throw("Bio::Phylo package required; see http://www.nexml.org for download details"); } } use Bio::Phylo::Factory; use Bio::Phylo::Matrices; use Bio::Phylo::Matrices::Matrix; use Bio::Phylo::Matrices::Datum; use Bio::Phylo::Forest::Tree; use Bio::Phylo::Matrices; use Bio::Phylo::IO; use Bio::SeqFeature::Generic; use base qw(Bio::Root::Root); my $fac = Bio::Phylo::Factory->new(); =head2 new Title : new Usage : my $obj = Bio::Nexml::Factory->new(); Function: Builds a new L object Returns : L object Args : none =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); } #should all these creates be private methods? # naah./maj =head2 create_bperl_aln Title : create_bperl_aln Usage : my @alns = $factory->create_bperl_aln($objIO); Function: Converts Bio::Phylo::Matrices::Matrix objects into L objects Returns : an array of L objects Args : Bio::NexmlIO, Bio::SeqIO, Bio::AlignIO, or Bio::TreeIO see [http://search.cpan.org/~rvosa/Bio-Phylo/lib/Bio/Phylo/Project.pm Bio::Phylo::Project] =cut sub create_bperl_aln { my ($self, $caller) = @_; my ($start, $end, $seq, $desc); my $matrices = $caller->doc->get_matrices(); my @alns; foreach my $matrix (@$matrices) { #check if mol_type is something that makes sense to be an aln my $mol_type = lc($matrix->get_type()); unless ($mol_type eq 'dna' || $mol_type eq 'rna' || $mol_type eq 'protein') { next; # something for the back-burner: BioPerl has objects # to handle arbitrary genotypes; might be cool to # be able to create something besides alignments # here .../maj } #continue creating an aln my $aln = Bio::SimpleAlign->new(); my $taxa = $matrix->get_taxa(); # TODO: should $caller->{_ID} always be defined? # ATM, this is a Bio::AlignIO::nexml stream... $aln->{_Nexml_ID} = $caller->{_ID}? $caller->{_ID} . $taxa->get_xml_id : $taxa->get_xml_id; my $aln_feats = Bio::SeqFeature::Generic->new(); $aln_feats->add_tag_value('NexmlIO_ID', $caller->{_ID}); #check if there is a taxa associated with this alignment if ($taxa) { $aln_feats->add_tag_value('taxa_id', $taxa->get_xml_id()); $aln_feats->add_tag_value('taxa_label', $taxa->get_name()) if $taxa->get_name(); my $taxon = $taxa->first; while ($taxon) { $aln_feats->add_tag_value('taxon', $taxon->get_name); $taxon = $taxa->next; } } $aln->add_SeqFeature($aln_feats); my $basename = $matrix->get_name(); $aln->id($basename); my $seqNum = 0; my$row = $matrix->first; while ($row) { my $newSeq = $row->get_char(); my $rowlabel; $seqNum++; #constuct seqID based on matrix label and row id my $seqID = "$basename.row_$seqNum"; #Check if theres a row label and if not default to seqID if( !defined($rowlabel = $row->get_name())) {$rowlabel = $seqID;} $seq = Bio::LocatableSeq->new( -seq => $newSeq, -display_id => "$rowlabel", #-description => $desc, -alphabet => $mol_type, ); my $seq_feats; #check if there is a taxa associated w/ this alignment if($taxa) { if (my $taxon = $taxa->get_by_name($row->get_taxon->get_name())) { #attach taxon to each sequence by using the sequenceID because #LocatableSeq does not support features my $taxon_name = $taxon->get_name(); $seq_feats = Bio::SeqFeature::Generic->new(); $seq_feats->add_tag_value('taxon', "$taxon_name"); $seq_feats->add_tag_value('id', "$rowlabel"); } } $aln->add_seq($seq); $aln->add_SeqFeature($seq_feats); $self->debug("Reading r$rowlabel\n"); $row = $matrix->next(); } push (@alns, $aln); } return \@alns; } =head2 create_bperl_tree Title : create_bperl_tree Usage : my @trees = $factory->create_bperl_seq($objIO); Function: Converts Bio::Phylo::Forest::Tree objects into L objects Returns : an array of L objects Args : Bio::NexmlIO, Bio::SeqIO, Bio::AlignIO, or Bio::TreeIO see [http://search.cpan.org/~rvosa/Bio-Phylo/lib/Bio/Phylo/Project.pm Bio::Phylo::Project] =cut sub create_bperl_tree { my($self, $caller) = @_; my @trees; my $forests = $caller->doc->get_forests(); foreach my $forest (@$forests) { my $basename = $forest->get_name() || ''; my $taxa = $forest->get_taxa(); my $taxa_label = $taxa->get_name(); my $taxa_id = $taxa->get_xml_id(); my $t = $forest->first(); while ($t) { my %created_nodes; my $tree_id = $t->get_name(); my $tree = Bio::Tree::Tree->new(-id => "$basename.$tree_id"); #set the taxa info of the tree $tree->add_tag_value('taxa_label', $taxa_label) if defined($taxa_label); $tree->add_tag_value('taxa_id', $taxa_id) if defined($taxa_id); # TODO: should $caller->{_ID} always be defined? # ATM, this is a Bio::TreeIO::nexml stream... $tree->add_tag_value('_NexmlIO_ID', $caller->{_ID}) if $caller->{_ID}; my $taxon = $taxa->first; while($taxon) { $tree->add_tag_value('taxon', $taxon->get_name()) if defined($taxon->get_name); $taxon = $taxa->next; } #process terminals only, removing terminals as they get processed #which inturn creates new terminals to process until the entire tree has been processed my $terminals = $t->get_terminals(); # for(my $i=0; $i<@$terminals; $i++) while (my $terminal = shift @$terminals) { # my $terminal = $$terminals[$i]; my $new_node_id = $terminal->get_name(); my $newNode; if(exists $created_nodes{$new_node_id}) { $newNode = $created_nodes{$new_node_id}; } else { $newNode = Bio::Tree::Node->new(); $new_node_id ||= 'internal_'.$newNode->_creation_id; $newNode->id($new_node_id); $created_nodes{$new_node_id} = $newNode; } #check if taxa data exists for the current node ($terminal) if($taxa) { my $taxon = $terminal->get_taxon(); $newNode->add_tag_value("taxon", $taxon->get_name()) if $taxon && $taxon->get_name; } #check if you've reached the root of the tree and if so, stop. if($terminal->is_root()) { $tree->set_root_node($newNode); last; } #transfer attributes that apply to non-root only nodes $newNode->branch_length($terminal->get_branch_length()); my $parent = $terminal->get_parent(); my $parentID = $parent->get_name(); if(exists $created_nodes{$parentID}) { $created_nodes{$parentID}->add_Descendent($newNode); } else { my $parent_node = Bio::Tree::Node->new(); $parentID ||= 'internal_'.$parent_node->_creation_id; $parent_node->id($parentID); $parent_node->add_Descendent($newNode); $created_nodes{$parentID} = $parent_node; } #remove processed node from tree $parent->prune_child($terminal); #check if the parent of the removed node is now a terminal node and should be added for processing if($parent->is_terminal()) { push(@$terminals, $terminal->get_parent()) if $terminal->get_parent; } } push @trees, $tree; $t = $forest->next(); } } return \@trees; } =head2 create_bperl_seq Title : create_bperl_seq Usage : my @seqs = $factory->create_bperl_seq($objIO); Function: Converts Bio::Phylo::Matrices::Datum objects into L objects Returns : an array of L objects Args : Bio::NexmlIO, Bio::SeqIO, Bio::AlignIO, or Bio::TreeIO see [http://search.cpan.org/~rvosa/Bio-Phylo/lib/Bio/Phylo/Project.pm Bio::Phylo::Project] =cut sub create_bperl_seq { my($self, $caller) = @_; my $matrices = $caller->doc->get_matrices(); my @seqs; foreach my $matrix (@$matrices) { #check if mol_type is something that makes sense to be a seq my $mol_type = lc($matrix->get_type()); unless ($mol_type eq 'dna' || $mol_type eq 'rna' || $mol_type eq 'protein') { next; } my $taxa = $matrix->get_taxa(); my $seqnum = 0; my $taxa_id = $taxa->get_xml_id(); my $taxa_label = $taxa->get_name(); my $basename = $matrix->get_name(); my $row = $matrix->first; while ($row) { my $newSeq = $row->get_char(); my $feat = Bio::SeqFeature::Generic->new(); $feat->add_tag_value('matrix_label', $matrix->get_name()) if defined($matrix->get_name); $feat->add_tag_value('matrix_id', $matrix->get_xml_id()); $feat->add_tag_value('NexmlIO_ID', $caller->{_ID}); $feat->add_tag_value('taxa_id', $taxa_id) if defined($taxa_id); $feat->add_tag_value('taxa_label', $taxa_label) if defined($taxa_label); $seqnum++; #construct full sequence id by using bio::phylo "matrix label" and "row id" my $seqID = "$basename.seq_$seqnum"; my $rowlabel; #check if there is a label for the row, if not default to seqID if (!defined ($rowlabel = $row->get_name())) {$rowlabel = $seqID;} else {$seqID = $rowlabel;} #build the seq object using the factory create method my $seqbuilder = Bio::Seq::SeqFactory->new('-type' => 'Bio::Seq'); my $seq = $seqbuilder->create( -seq => $newSeq, -id => $rowlabel, -primary_id => $seqID, #-desc => $fulldesc, -alphabet => $mol_type, -direct => 1, ); # TODO: should $caller->{_ID} always be defined? # ATM, this is a Bio::SeqIO::nexml stream... $seq->{_Nexml_ID} = $caller->{_ID} ? $caller->{_ID} . $taxa_id : $taxa_id; $seq->{_Nexml_matrix_ID} = $caller->{_ID} ? $caller->{_ID} . $matrix->get_xml_id() : $matrix->get_xml_id(); #check if taxon linked to sequence if so create feature to attach to alignment if ($taxa) { my $taxon = $taxa->first; while ($taxon) { $feat->add_tag_value('taxon', $taxon->get_name) if defined($taxon->get_name); if($taxon eq $row->get_taxon) { my $taxon_name = $taxon->get_name(); $feat->add_tag_value('my_taxon', "$taxon_name") if defined($taxon_name); $feat->add_tag_value('id', $rowlabel); } $taxon = $taxa->next; } } $seq->add_SeqFeature($feat); push (@seqs, $seq); $row = $matrix->next; } } return \@seqs; } =head2 create_bphylo_tree Title : create_bphylo_tree Usage : my $bphylo_tree = $factory->create_bphylo_tree($bperl_tree); Function: Converts a L object into Bio::Phylo::Forest::Tree object Returns : a Bio::Phylo::Forest::Tree object Args : Bio::Tree::Tree object =cut sub create_bphylo_tree { my ($self, $bptree, $taxa) = @_; #most of the code below ripped form Bio::Phylo::Forest::Tree::new_from_bioperl()d my $tree = $fac->create_tree; my $class = 'Bio::Phylo::Forest::Tree'; if ( ref $bptree && $bptree->isa('Bio::Tree::TreeI') ) { bless $tree, $class; ($tree) = _copy_tree( $tree, $bptree->get_root_node, "", $taxa); # copy name my $name = $bptree->id; $tree->set_name( $name ) if defined $name; # copy score my $score = $bptree->score; $tree->set_score( $score ) if defined $score; } else { $self->throw('Not a bioperl tree!'); } return $tree; } sub _copy_tree { my ( $tree, $bpnode, $parent, $taxa ) = @_; my $node = create_bphylo_node($bpnode); my $taxon; if ($parent) { $parent->set_child($node); } if (my $bptaxon_name = $bpnode->get_tag_values('taxon')) { $node->set_taxon($taxa->get_by_name($bptaxon_name)); } $tree->insert($node); foreach my $bpchild ( $bpnode->each_Descendent ) { _copy_tree( $tree, $bpchild, $node, $taxa ); } return $tree; } =head2 create_bphylo_node Title : create_bphylo_node Usage : my $bphylo_node = $factory->create_bphylo_node($bperl_node); Function: Converts a L object into Bio::Phylo::Forest::Node object Returns : a Bio::Phylo::Forest::Node object Args : L object =cut sub create_bphylo_node { my ($bpnode) = @_; my $node = Bio::Phylo::Forest::Node->new(); #mostly ripped from Bio::Phylo::Forest::Node->new_from_bioperl() # copy name my $name = $bpnode->id; $node->set_name( $name ) if defined $name; # copy branch length my $branch_length = $bpnode->branch_length; $node->set_branch_length( $branch_length ) if defined $branch_length; # copy description my $desc = $bpnode->description; $node->set_desc( $desc ) if defined $desc; # copy bootstrap my $bootstrap = $bpnode->bootstrap; $node->set_score( $bootstrap ) if defined $bootstrap and looks_like_number $bootstrap; # copy other tags for my $tag ( $bpnode->get_all_tags ) { my @values = $bpnode->get_tag_values( $tag ); $node->set_generic( $tag => \@values ); } return $node; } =head2 create_bphylo_aln Title : create_bphylo_aln Usage : my $bphylo_aln = $factory->create_bphylo_aln($bperl_aln); Function: Converts a L object into Bio::Phylo::Matrices::Matrix object Returns : a Bio::Phylo::Matrices::Matrix object Args : Bio::SimpleAlign object =cut sub create_bphylo_aln { my ($self, $aln, $taxa, @args) = @_; #most of the code below ripped from Bio::Phylo::Matrices::Matrix::new_from_bioperl() if ( $aln->isa('Bio::Align::AlignI') ) { $aln->unmatch; $aln->map_chars('\.','-'); my @seqs = $aln->each_seq; my ( $type, $missing, $gap, $matchchar ); if ( $seqs[0] ) { $type = $seqs[0]->alphabet || $seqs[0]->_guess_alphabet || 'dna'; } else { $type = 'dna'; } my $matrix = $fac->create_matrix( '-type' => $type, '-special_symbols' => { '-missing' => $aln->missing_char || '?', '-matchchar' => $aln->match_char || '.', '-gap' => $aln->gap_char || '-', }, @args ); # XXX create raw getter/setter pairs for annotation, accession, consensus_meta source for my $field ( qw(description accession id annotation consensus_meta score source) ) { $matrix->$field( $aln->$field ); } my $to = $matrix->get_type_object; my @feats = $aln->get_all_SeqFeatures(); for my $seq ( @seqs ) { #create datum linked to taxa my $datum = create_bphylo_datum($seq, $taxa, \@feats, '-type_object' => $to); $matrix->insert($datum); } return $matrix; } else { $self->throw('Not a bioperl alignment!'); } } =head2 create_bphylo_seq Title : create_bphylo_seq Usage : my $bphylo_seq = $factory->create_bphylo_seq($bperl_seq); Function: Converts a L object into Bio::Phylo::Matrices::Matrix object Returns : a Bio::Phylo::Matrices::Matrix object Args : Bio::Seq object =cut sub create_bphylo_seq { my ($self, $seq, $taxa, @args) = @_; my $type = $seq->alphabet || $seq->_guess_alphabet || 'dna'; $type = uc($type); my $dat = create_bphylo_datum($seq, $taxa, '-type' => $type); # copy seq string my $seqstring = $seq->seq; if ( $seqstring and $seqstring =~ /\S/ ) { eval { $dat->set_char( $seqstring ) }; if ( $@ and UNIVERSAL::isa($@,'Bio::Phylo::Util::Exceptions::InvalidData') ) { $self->throw("\n\nThe BioPerl sequence object contains invalid data ($seqstring)\n"); } } # copy name my $name = $seq->display_id; #$dat->set_name( $name ) if defined $name; # copy desc my $desc = $seq->desc; $dat->set_desc( $desc ) if defined $desc; #get features from SeqFeatureI for my $field ( qw(start end strand) ) { $dat->$field( $seq->$field ) if $seq->can($field); } return $dat; } =head2 create_bphylo_taxa Title : create_bphylo_seq Usage : my $taxa = $factory->create_bphylo_taxa($bperl_obj); Function: creates a taxa object from the data attached to a bioperl object Returns : a Bio::Phylo::Taxa object Args : L object, or L object, or L object =cut sub create_bphylo_taxa { my $self = shift @_; my ($obj) = @_; #check if tree or aln object if ( UNIVERSAL::isa( $obj, 'Bio::Align::AlignI' ) || UNIVERSAL::isa( $obj, 'Bio::Seq')) { return $self->_create_bphylo_matrix_taxa(@_); } elsif ( UNIVERSAL::isa( $obj, 'Bio::Tree::TreeI' ) ) { return $self->_create_bphylo_tree_taxa(@_); } } sub _create_bphylo_tree_taxa { my ($self, $tree) = @_; my $taxa = $fac->create_taxa(); my $taxon; #check if taxa exists unless ($tree->has_tag('taxa_id')) { return 0; } #copy taxa details $taxa->set_xml_id(($tree->get_tag_values('taxa_id'))[0]); $taxa->set_name(($tree->get_tag_values('taxa_label'))[0]); foreach my $taxon_name ($tree->get_tag_values('taxon')) { $taxon = $fac->create_taxon(-name => $taxon_name); $taxa->insert($taxon); } return $taxa; } sub _create_bphylo_matrix_taxa { my ($self, $aln) = @_; my $taxa = $fac->create_taxa(); my $taxon; my @feats = $aln->get_all_SeqFeatures(); foreach my $feat (@feats) { if (my $taxa_id = ($feat->get_tag_values('taxa_id'))[0]) { my $taxa_label = ($feat->get_tag_values('taxa_label'))[0]; $taxa->set_name($taxa_label) if defined $taxa_label; $taxa->set_xml_id($taxa_id) if defined $taxa_label; my @taxa_bp = $feat->get_tag_values('taxon'); foreach my $taxon_name (@taxa_bp) { $taxon = $fac->create_taxon(-name => $taxon_name); $taxa->insert($taxon); } last; } } return $taxa } =head2 create_bphylo_datum Title : create_bphylo_datum Usage : my $bphylo_datum = $factory->create_bphylo_datum($bperl_datum); Function: Converts a L object into Bio::Phylo::Matrices::datum object Returns : a Bio::Phylo::Matrices::datum object Args : Bio::Seq object, Bio::Phylo::Taxa object, [optional] arrayref to SeqFeatures, [optional] key => value pairs to pass to Bio::Phylo constructor =cut sub create_bphylo_datum { #mostly ripped from Bio::Phylo::Matrices::Datum::new_from_bioperl() my ( $seq, $taxa, @args ) = @_; my $class = 'Bio::Phylo::Matrices::Datum'; my $feats; # want $seq type-check here? Allowable: is-a Bio::PrimarySeq, # Bio::LocatableSeq /maj if (@args % 2) { # odd $feats = shift @args; unless (ref($feats) eq 'ARRAY') { Bio::Root::Root->throw("Third argument must be array of SeqFeatures"); } } my $type = $seq->alphabet || $seq->_guess_alphabet || 'dna'; my $self = $class->new( '-type' => $type, @args ); # copy seq string my $seqstring = $seq->seq; if ( $seqstring and $seqstring =~ /\S/ ) { eval { $self->set_char( $seqstring ) }; if ( $@ and UNIVERSAL::isa($@,'Bio::Phylo::Util::Exceptions::InvalidData') ) { $self->throw("\n\nThe BioPerl sequence object contains invalid data ($seqstring)\n"); } } # copy name my $name = $seq->display_id; $self->set_name( $name ) if defined $name; my $taxon; my @feats = (defined $feats ? @$feats : $seq->get_all_SeqFeatures); # convert taxa foreach my $feat (@feats) { #get sequence id associated with taxa to compare my $taxa_id = ($feat->get_tag_values('id'))[0] if $feat->has_tag('id'); if ($taxa_id && $name eq $taxa_id) { my $taxon_name; if($feat->has_tag('my_taxon')) { $taxon_name = ($feat->get_tag_values('my_taxon'))[0] } else { $taxon_name = ($feat->get_tag_values('taxon'))[0]; } $self->set_taxon($taxa->get_by_name($taxon_name)); } } # copy desc my $desc = $seq->desc; $self->set_desc( $desc ) if defined $desc; # only Bio::LocatableSeq objs have these fields... for my $field ( qw(start end strand) ) { $self->$field( $seq->$field ) if $seq->can($field); } return $self; } =head2 CREATOR =cut =head1 bioperl_create Title : bioperl_create Usage : $bioperl_obj = $fac->bioperl_create($obj_type, $biophylo_proj); Function: Create a specified bioperl object using a Bio::Phylo project Args : scalar string ('aln', 'tree', 'seq') type designator Bio::Phylo::Project object Returns : Appropriate BioPerl object =cut sub bioperl_create { my $self = shift; my ($type, @args) = @_; unless (grep /^type/,qw( seq aln tree )) { $self->throw("Unrecognized type for argument 1"); } my $call = 'create_bioperl_'.$type; return $self->$call(@args); } 1; BioPerl-1.007002/Bio/Ontology000755000766000024 013155576320 15701 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Ontology/DocumentRegistry.pm000444000766000024 1146113155576320 21726 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Ontology::DocumentRegistry # # Please direct questions and support issues to # # Cared for by Allen Day # # Copyright Allen Day # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Ontology::DocumentRegistry - Keep track of where to find ontologies. Allows lookups by name. =head1 SYNOPSIS my $registry = Bio::Ontology::DocumentRegistry->get_instance(); my($ont,$def,$fmt) = $registry->documents('Sequence Ontology'); my $io = Bio::OntologyIO->new(-url => $ont, -defs_url => $def, -format => $fmt); my $so = $io->next_ontology(); #... =head1 DESCRIPTION Do not use this directly, use Bio::Ontology::OntologyStore instead. Bio::Ontology::OntologyStore uses Bio::Ontology::DocumentRegistry to load and cache ontologies as object graphs, you can just ask it for what you want by name. See L for details. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Allen Day Email allenday@ucla.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::DocumentRegistry; use strict; use base qw(Bio::Root::Root); use Data::Dumper; my $instance; BEGIN { $instance = { 'Sequence Ontology' => { ontology => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.ontology?rev=HEAD", definitions => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.definition?rev=HEAD", format => 'soflat', }, 'Sequence Ontology OBO' => { ontology => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD", definitions => "http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.definition?rev=HEAD", format => 'obo', }, #### TODO Server http://umn.dl.sourceforge.net/ does not respond, are there #### alternative sources? 'Sequence Ontology Feature Annotation' => { ontology => 'http://umn.dl.sourceforge.net/sourceforge/song/sofa.ontology', definitions =>'http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition', format => 'soflat', }, 'Gene Ontology' => { ontology => [ 'http://www.geneontology.org/ontology/function.ontology', 'http://www.geneontology.org/ontology/process.ontology', 'http://www.geneontology.org/ontology/component.ontology' ], definitions => 'http://www.geneontology.org/ontology/GO.defs', format => 'soflat', }, }; #aliases $instance->{Gene_Ontology} = $instance->{'Gene Ontology'}; bless $instance, __PACKAGE__; } sub new { return shift->get_instance(@_); } =head2 get_instance Title : get_instance Usage : my $singleton = Bio::Ontology::DocumentRegistry->get_instance(); Function: constructor Returns : The Bio::Ontology::DocumentRegistry singleton. Args : None Usage =cut sub get_instance { return $instance; } =head2 documents Title : documents Usage : my($ontology_url, $definitions_url, $format) = $obj->documents('Sequence Ontology'); Function: Maps an ontology name to a list of (local or) remote URIs where the files can be located. Returns : A 3-item list: (1) URI for the ontology file (2) URI for the ontology definitions file (3) format of the files (dagedit, obo, etc) Args : Name of an ontology, e.g. 'Sequence Ontology', or 'Cellular Component (Gene Ontology)' =cut sub documents { my($self,$name) = @_; if(defined($self->{$name})){ return ($self->{$name}{ontology} , $self->{$name}{definitions}, $self->{$name}{format}); } else { return (); } } 1; BioPerl-1.007002/Bio/Ontology/GOterm.pm000444000766000024 2230613155576320 17614 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Ontology::GOterm # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Ontology::GOterm - representation of GO terms =head1 SYNOPSIS $term = Bio::Ontology::GOterm->new ( -go_id => "GO:0016847", -name => "1-aminocyclopropane-1-carboxylate synthase", -definition => "Catalysis of ...", -is_obsolete => 0, -comment => "" ); $term->add_definition_references( @refs ); $term->add_secondary_GO_ids( @ids ); $term->add_aliases( @aliases ); foreach my $dr ( $term->each_definition_reference() ) { print $dr, "\n"; } # etc. =head1 DESCRIPTION This is "dumb" class for GO terms (it provides no functionality related to graphs). Implements Bio::Ontology::TermI. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 APPENDIX The rest of the documentation details each of the object methods. =cut # Let the code begin... package Bio::Ontology::GOterm; use strict; use constant GOID_DEFAULT => "GO:0000000"; use constant TRUE => 1; use constant FALSE => 0; use base qw(Bio::Ontology::Term); =head2 new Title : new Usage : $term = Bio::Ontology::GOterm->new( -go_id => "GO:0016847", -name => "1-aminocyclopropane-1-carboxylate synthase", -definition => "Catalysis of ...", -is_obsolete => 0, -comment => "" ); Function: Creates a new Bio::Ontology::GOterm. Returns : A new Bio::Ontology::GOterm object. Args : -go_id => the goid of this GO term [GO:nnnnnnn] or [nnnnnnn] (nnnnnnn is a zero-padded integer of seven digits) -name => the name of this GO term [scalar] -definition => the definition of this GO term [scalar] -ontology => the ontology for this term (a Bio::Ontology::OntologyI compliant object) -version => version information [scalar] -is_obsolete => the obsoleteness of this GO term [0 or 1] -comment => a comment [scalar] =cut sub new { my( $class,@args ) = @_; my $self = $class->SUPER::new( @args ); my ( $GO_id ) = $self->_rearrange( [ qw( GO_ID ) ], @args ); $GO_id && $self->GO_id( $GO_id ); return $self; } # new =head2 init Title : init() Usage : $term->init(); Function: Initializes this GOterm to all "" and empty lists. Returns : Args : =cut sub init { my $self = shift; # first call the inherited version to properly chain up the hierarchy $self->SUPER::init(@_); # then only initialize what we implement ourselves here #$self->GO_id( GOID_DEFAULT ); } # init =head2 GO_id Title : GO_id Usage : $term->GO_id( "GO:0003947" ); or print $term->GO_id(); Function: Set/get for the goid of this GO term. This is essentially an alias to identifier(), with added format checking. Returns : The goid [GO:nnnnnnn]. Args : The goid [GO:nnnnnnn] or [nnnnnnn] (nnnnnnn is a zero-padded integer of seven digits) (optional). =cut sub GO_id { my $self = shift; my $value; if ( @_ ) { $value = $self->_check_go_id( shift ); unshift(@_, $value); } return $self->identifier( @_ ); } # GO_id =head2 get_secondary_GO_ids Title : get_secondary_GO_ids Usage : @ids = $term->get_secondary_GO_ids(); Function: Returns a list of secondary goids of this Term. This is aliased to remove_secondary_ids(). Returns : A list of secondary goids [array of [GO:nnnnnnn]] (nnnnnnn is a zero-padded integer of seven digits). Args : =cut sub get_secondary_GO_ids { return shift->get_secondary_ids(@_); } # get_secondary_GO_ids =head2 add_secondary_GO_id Title : add_secondary_GO_id Usage : $term->add_secondary_GO_id( @ids ); or $term->add_secondary_GO_id( $id ); Function: Pushes one or more secondary goids into the list of secondary goids. This is aliased to remove_secondary_ids(). Returns : Args : One secondary goid [GO:nnnnnnn or nnnnnnn] or a list of secondary goids [array of [GO:nnnnnnn or nnnnnnn]] (nnnnnnn is a zero-padded integer of seven digits). =cut sub add_secondary_GO_id { return shift->add_secondary_id(@_); } # add_secondary_GO_id =head2 remove_secondary_GO_ids Title : remove_secondary_GO_ids() Usage : $term->remove_secondary_GO_ids(); Function: Deletes (and returns) the secondary goids of this Term. This is aliased to remove_secondary_ids(). Returns : A list of secondary goids [array of [GO:nnnnnnn]] (nnnnnnn is a zero-padded integer of seven digits). Args : =cut sub remove_secondary_GO_ids { return shift->remove_secondary_ids(@_); } # remove_secondary_GO_ids =head2 to_string Title : to_string() Usage : print $term->to_string(); Function: to_string method for GO terms. Returns : A string representation of this GOterm. Args : =cut sub to_string { my( $self ) = @_; my $s = ""; $s .= "-- GO id:\n"; $s .= ($self->GO_id() || '')."\n"; $s .= "-- Name:\n"; $s .= ($self->name() || '') ."\n"; $s .= "-- Definition:\n"; $s .= ($self->definition() || '') ."\n"; $s .= "-- Category:\n"; if ( defined( $self->ontology() ) ) { $s .= $self->ontology()->name()."\n"; } else { $s .= "\n"; } $s .= "-- Version:\n"; $s .= ($self->version() || '') ."\n"; $s .= "-- Is obsolete:\n"; $s .= $self->is_obsolete()."\n"; $s .= "-- Comment:\n"; $s .= ($self->comment() || '') ."\n"; $s .= "-- Definition references:\n"; $s .= $self->_array_to_string( $self->get_dbxrefs() )."\n"; $s .= "-- Secondary GO ids:\n"; $s .= $self->_array_to_string( $self->get_secondary_GO_ids() )."\n"; $s .= "-- Aliases:\n"; $s .= $self->_array_to_string( $self->get_synonyms() ); return $s; } # to_string # Title : _check_go_id # Function: Checks whether the argument is [GO:nnnnnnn]. # If "GO:" is not present, it adds it. # Returns : The canonical GO id. # Args : The value to be checked. sub _check_go_id { my ( $self, $value ) = @_; unless ( $value =~ /^(GO:)?\d{7}$/ || $value eq GOID_DEFAULT ) { $self->throw( "Found [" . $value . "] where [GO:nnnnnnn] or [nnnnnnn] expected" ); } unless ( $value =~ /^GO:/ ) { $value = "GO:".$value; } return $value; } # _check_go_id # Title : _array_to_string # Function: # Returns : # Args : sub _array_to_string { my( $self, @value ) = @_; my $s = ""; for ( my $i = 0; $i < scalar( @value ); ++$i ) { if ( ! ref( $value[ $i ] ) ) { $s .= "#" . $i . "\n-- " . $value[ $i ] . "\n"; } } return $s; } # _array_to_string ################################################################# # aliases or forwards to maintain backward compatibility ################################################################# *each_secondary_GO_id = \&get_secondary_GO_ids; *add_secondary_GO_ids = \&add_secondary_GO_id; 1; BioPerl-1.007002/Bio/Ontology/InterProTerm.pm000444000766000024 3547213155576320 21021 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Ontology::InterProTerm # # Please direct questions and support issues to # # Cared for by Peter Dimitrov # # Copyright Peter Dimitrov # (c) Peter Dimitrov, dimitrov@gnf.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Ontology::InterProTerm - Implementation of InterProI term interface =head1 SYNOPSIS my $term = Bio::Ontology::InterProTerm->new( -interpro_id => "IPR000001", -name => "Kringle", -definition => "Kringles are autonomous structural domains ...", -ontology => "Domain" ); print $term->interpro_id(), "\n"; print $term->name(), "\n"; print $term->definition(), "\n"; print $term->is_obsolete(), "\n"; print $term->ontology->name(), "\n"; =head1 DESCRIPTION This is a simple extension of L for InterPro terms. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Peter Dimitrov Email dimitrov@gnf.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::InterProTerm; use strict; use Bio::Annotation::Reference; use constant INTERPRO_ID_DEFAULT => "IPR000000"; use base qw(Bio::Ontology::Term); =head2 new Title : new Usage : $term = Bio::Ontology::InterProTerm->new( -interpro_id => "IPR000002", -name => "Cdc20/Fizzy", -definition => "The Cdc20/Fizzy region is almost always ...", -ontology => "Domain" ); Function: Creates a new Bio::Ontology::InterProTerm. Example : Returns : A new Bio::Ontology::InterProTerm object. Args : -interpro_id => the InterPro ID of the term. Has the form IPRdddddd, where dddddd is a zero-padded six digit number -name => the name of this InterPro term [scalar] -definition => the definition/abstract of this InterPro term [scalar] -ontology => ontology of InterPro terms [Bio::Ontology::OntologyI] -comment => a comment [scalar] =cut sub new{ my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ( $interpro_id, $short_name) = $self->_rearrange( [qw( INTERPRO_ID SHORT_NAME ) ], @args ); $interpro_id && $self->interpro_id( $interpro_id ); $short_name && $self->short_name( $short_name ); return $self; } =head2 init Title : init Usage : $term->init(); Function: Initializes this InterProTerm to all "" and empty lists. Example : Returns : Args : =cut sub init{ my $self = shift; # first call the inherited version to properly chain up the hierarchy $self->SUPER::init(@_); # then only initialize what we implement ourselves here $self->interpro_id( INTERPRO_ID_DEFAULT ); $self->short_name(""); } =head2 _check_interpro_id Title : _check_interpro_id Usage : Function: Performs simple check in order to validate that its argument has the form IPRdddddd, where dddddd is a zero-padded six digit number. Example : Returns : Returns its argument if valid, otherwise throws exception. Args : String =cut sub _check_interpro_id{ my ($self, $value) = @_; $self->throw( "InterPro ID ".$value." is incorrect\n" ) unless ( $value =~ /^IPR\d{6}$/ || $value eq INTERPRO_ID_DEFAULT ); return $value; } =head2 interpro_id Title : interpro_id Usage : $obj->interpro_id($newval) Function: Set/get for the interpro_id of this InterProTerm Example : Returns : value of interpro_id (a scalar) Args : new value (a scalar, optional) =cut sub interpro_id{ my ($self, $value) = @_; if( defined $value) { $value = $self->_check_interpro_id($value); return $self->identifier($value); } return $self->identifier(); } =head2 short_name Title : short_name Usage : $obj->short_name($newval) Function: Set/get for the short name of this InterProTerm. Example : Returns : value of short_name (a scalar) Args : new value (a scalar, optional) =cut sub short_name{ my ($self, $value) = @_; if( defined $value) { $self->{'short_name'} = $value ? $value : undef; } return $self->{'short_name'}; } =head2 protein_count Title : protein_count Usage : $obj->protein_count($newval) Function: Set/get for the protein count of this InterProTerm. Example : Returns : value of protein_count (a scalar) Args : new value (a scalar, optional) =cut sub protein_count{ my ($self,$value) = @_; if( defined $value) { $self->{'protein_count'} = $value ? $value : undef; } return $self->{'protein_count'}; } =head2 get_references Title : get_references Usage : Function: Get the references for this InterPro term. Example : Returns : An array of L objects Args : =cut # Defined in parent class #sub get_references{ # my $self = shift; # # return @{$self->{"_references"}} if exists($self->{"_references"}); # return (); #} =head2 add_reference Title : add_reference Usage : Function: Add one or more references to this InterPro term. Example : Returns : Args : One or more L objects. =cut # Defined in parent class #sub add_reference{ # my $self = shift; # # $self->{"_references"} = [] unless exists($self->{"_references"}); # push(@{$self->{"_references"}}, @_); #} =head2 remove_references Title : remove_references Usage : Function: Remove all references for this InterPro term. Example : Returns : The list of previous references as an array of L objects. Args : =cut # Defined in parent class #sub remove_references{ # my $self = shift; # # my @arr = $self->get_references(); # $self->{"_references"} = []; # return @arr; #} =head2 get_members Title : get_members Usage : @arr = get_members() Function: Get the list of member(s) for this object. Example : Returns : An array of Bio::Annotation::DBLink objects Args : =cut sub get_members{ my $self = shift; return $self->get_dbxrefs('member_list'); } =head2 add_member Title : add_member Usage : Function: Add one or more member(s) to this object. Example : Returns : Args : One or more Bio::Annotation::DBLink objects. =cut sub add_member{ my $self = shift; $self->add_dbxref(-dbxrefs => \@_, -context => 'member_list'); } =head2 remove_members Title : remove_members Usage : Function: Remove all members for this class. Example : Returns : The list of previous members as an array of Bio::Annotation::DBLink objects. Args : =cut sub remove_members{ my $self = shift; return $self->remove_dbxrefs('member_list'); } =head2 get_examples Title : get_examples Usage : @arr = get_examples() Function: Get the list of example(s) for this object. This is an element of the InterPro xml schema. Example : Returns : An array of Bio::Annotation::DBLink objects Args : =cut sub get_examples{ my $self = shift; return $self->get_dbxrefs('example_list'); } =head2 add_example Title : add_example Usage : Function: Add one or more example(s) to this object. This is an element of the InterPro xml schema. Example : Returns : Args : One or more Bio::Annotation::DBLink objects. =cut sub add_example{ my $self = shift; return $self->add_dbxref(-dbxrefs => \@_, -context => 'example_list'); } =head2 remove_examples Title : remove_examples Usage : Function: Remove all examples for this class. This is an element of the InterPro xml schema. Example : Returns : The list of previous examples as an array of Bio::Annotation::DBLink objects. Args : =cut sub remove_examples{ my $self = shift; return $self->remove_dbxrefs('example_list'); } =head2 get_external_documents Title : get_external_documents Usage : @arr = get_external_documents() Function: Get the list of external_document(s) for this object. This is an element of the InterPro xml schema. Example : Returns : An array of Bio::Annotation::DBLink objects Args : =cut sub get_external_documents{ my $self = shift; return $self->get_dbxrefs('external_doc_list'); } =head2 add_external_document Title : add_external_document Usage : Function: Add one or more external_document(s) to this object. This is an element of the InterPro xml schema. Example : Returns : Args : One or more Bio::Annotation::DBLink objects. =cut sub add_external_document{ my $self = shift; return $self->add_dbxref(-dbxrefs => \@_, -context => 'external_doc_list'); } =head2 remove_external_documents Title : remove_external_documents Usage : Function: Remove all external_documents for this class. This is an element of the InterPro xml schema. Example : Returns : The list of previous external_documents as an array of Bio::Annotation::DBLink objects. Args : =cut sub remove_external_documents{ my $self = shift; return $self->remove_dbxrefs('external_doc_list'); } =head2 class_list Title : class_list Usage : $obj->class_list($newval) Function: Set/get for class list element of the InterPro xml schema Example : Returns : reference to an array of Bio::Annotation::DBLink objects Args : reference to an array of Bio::Annotation::DBLink objects =cut # this is inconsistent with the above, but we work around it and hope nothing # breaks sub class_list{ my ($self, $value) = @_; if( defined $value && ref $value eq 'ARRAY') { if (!@$value) { # passing an empty array ref is essentially same as remove_dbxrefs, # so do that $self->remove_dbxrefs('class_list'); } else { $self->add_dbxref(-dbxrefs => $value, -context => 'class_list'); } } return [$self->get_dbxrefs('class_list')]; } =head2 to_string Title : to_string() Usage : print $term->to_string(); Function: to_string method for InterPro terms. Returns : A string representation of this InterPro term. Args : =cut sub to_string { my ($self) = @_; my $s = ""; $s .= "-- InterPro id:\n"; $s .= $self->interpro_id() . "\n"; if ( defined $self->name ) { $s .= "-- Name:\n"; $s .= $self->name() . "\n"; $s .= "-- Definition:\n"; $s .= ( $self->definition() || '' ) . "\n"; $s .= "-- Category:\n"; if ( defined( $self->ontology() ) ) { $s .= $self->ontology()->name() . "\n"; } else { $s .= "\n"; } $s .= "-- Version:\n"; $s .= ( $self->version() || '' ) . "\n"; $s .= "-- Is obsolete:\n"; $s .= $self->is_obsolete() . "\n"; $s .= "-- Comment:\n"; $s .= ( $self->comment() || '' ) . "\n"; if ( defined $self->get_references ) { $s .= "-- References:\n"; foreach my $ref ( $self->get_references ) { $s .= $ref->authors . "\n" . $ref->title . "\n" . $ref->location . "\n\n"; } $s .= "\n"; } if ( defined $self->get_members ) { $s .= "-- Member List:\n"; foreach my $ref ( $self->get_members ) { $s .= $ref->database . "\t" . $ref->primary_id . "\n"; } $s .= "\n"; } if ( defined $self->get_external_documents ) { $s .= "-- External Document List:\n"; foreach my $ref ( $self->get_external_documents ) { $s .= $ref->database . "\t" . $ref->primary_id . "\n"; } $s .= "\n"; } if ( defined $self->get_examples ) { $s .= "-- Examples:\n"; foreach my $ref ( $self->get_examples ) { $s .= join( "\t", map { $ref->$_ || '' } qw(database primary_id comment) ) . "\n"; } $s .= "\n"; } if ( defined $self->class_list ) { $s .= "-- Class List:\n"; foreach my $ref ( @{ $self->class_list } ) { $s .= $ref->primary_id . "\n"; } $s .= "\n"; } if ( $self->get_secondary_ids ) { $s .= "-- Secondary IDs:\n"; foreach my $ref ( $self->get_secondary_ids() ) { # TODO: getting undef here in some cases, needs to be checked next unless defined ($ref); $s .= $ref . "\n"; } $s .= "\n"; } } else { $s .= "InterPro term not fully instantiated\n"; } return $s; } =head1 Deprecated methods These are here for backwards compatibility. =cut =head2 secondary_ids Title : secondary_ids Usage : $obj->secondary_ids($newval) Function: This is deprecated. Use get_secondary_ids() or add_secondary_id() instead. Example : Returns : reference to an array of strings Args : reference to an array of strings =cut sub secondary_ids{ my $self = shift; my @ids; $self->warn("secondary_ids is deprecated. Use ". "get_secondary_ids/add_secondary_id instead."); # set mode? if(@_) { my $sids = shift; if($sids) { $self->add_secondary_id(@$sids); @ids = @$sids; } else { # we interpret setting to undef as removing the array $self->remove_secondary_ids(); } } else { # no; get mode @ids = $self->get_secondary_ids(); } return \@ids; } 1; BioPerl-1.007002/Bio/Ontology/OBOEngine.pm000444000766000024 7023413155576320 20167 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Ontology::OBOEngine # # POD documentation - main docs before the code =head1 NAME Bio::Ontology::OBOEngine - An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium =head1 SYNOPSIS use Bio::Ontology::OBOEngine; my $parser = Bio::Ontology::OBOEngine->new ( -file => "gene_ontology.obo" ); my $engine = $parser->parse(); =head1 DESCRIPTION Needs Graph.pm from CPAN. This module replaces SimpleGOEngine.pm, which is deprecated. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Sohel Merchant Email: s-merchant@northwestern.edu Address: Northwestern University Center for Genetic Medicine (CGM), dictyBase Suite 1206, 676 St. Clair st Chicago IL 60611 =head2 CONTRIBUTOR Hilmar Lapp, hlapp at gmx.net Chris Mungall, cjm at fruitfly.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Ontology::OBOEngine; use Bio::Ontology::SimpleGOEngine::GraphAdaptor; use strict; use Bio::Ontology::RelationshipType; use Bio::Ontology::RelationshipFactory; use Data::Dumper; use constant TRUE => 1; use constant FALSE => 0; use constant IS_A => "IS_A"; use constant PART_OF => "PART_OF"; use constant RELATED_TO => "RELATED_TO"; use constant TERM => "TERM"; use constant TYPE => "TYPE"; use constant ONTOLOGY => "ONTOLOGY"; use constant REGULATES => "REGULATES"; use constant POSITIVELY_REGULATES => "POSITIVELY_REGULATES"; use constant NEGATIVELY_REGULATES => "NEGATIVELY_REGULATES"; use base qw(Bio::Root::Root Bio::Ontology::OntologyEngineI); =head2 new Title : new Usage : $engine = Bio::Ontology::OBOEngine->new() Function: Creates a new OBOEngine Returns : A new OBOEngine object Args : =cut sub new { my( $class, @args ) = @_; my $self = $class->SUPER::new( @args ); $self->init(); return $self; } # new =head2 init Title : init() Usage : $engine->init(); Function: Initializes this Engine. Returns : Args : =cut sub init { my ( $self ) = @_; $self->{ "_is_a_relationship" } = Bio::Ontology::RelationshipType->get_instance( IS_A ); $self->{ "_part_of_relationship" } = Bio::Ontology::RelationshipType->get_instance( PART_OF ); $self->{ "_related_to_relationship" } = Bio::Ontology::RelationshipType->get_instance( RELATED_TO ); $self->{'_regulates_relationship'} = Bio::Ontology::RelationshipType->get_instance(REGULATES); $self->{'_positively_regulate'} = Bio::Ontology::RelationshipType->get_instance(POSITIVELY_REGULATES); $self->{'_negatively_regulate'} = Bio::Ontology::RelationshipType->get_instance(NEGATIVELY_REGULATES); $self->graph( Bio::Ontology::SimpleGOEngine::GraphAdaptor->new() ); # NG 05-02-16 # set defaults for the factories $self->relationship_factory(Bio::Ontology::RelationshipFactory->new( -type => "Bio::Ontology::Relationship")); } # init =head2 is_a_relationship Title : is_a_relationship() Usage : $IS_A = $engine->is_a_relationship(); Function: Returns a Bio::Ontology::RelationshipType object for "is-a" relationships Returns : Bio::Ontology::RelationshipType set to "IS_A" Args : =cut sub is_a_relationship { my ( $self, $value ) = @_; if ( defined $value ) { $self->throw( "Attempted to change immutable field" ); } return $self->{ "_is_a_relationship" }; } # is_a_relationship =head2 part_of_relationship Title : part_of_relationship() Usage : $PART_OF = $engine->part_of_relationship(); Function: Returns a Bio::Ontology::RelationshipType object for "part-of" relationships Returns : Bio::Ontology::RelationshipType set to "PART_OF" Args : =cut sub part_of_relationship { my ( $self, $value ) = @_; if ( defined $value ) { $self->throw( "Attempted to change immutable field" ); } return $self->{ "_part_of_relationship" }; } # part_of_relationship =head2 related_to_relationship Title : related_to_relationship() Usage : $RELATED_TO = $engine->related_to_relationship(); Function: Returns a Bio::Ontology::RelationshipType object for "related-to" relationships Returns : Bio::Ontology::RelationshipType set to "RELATED_TO" Args : =cut sub related_to_relationship { my ( $self, $value ) = @_; if ( defined $value ) { $self->throw( "Attempted to change immutable field" ); } return $self->{ "_related_to_relationship" }; } # related_to_relationship =head2 regulates_relationship Title : regulates_relationship() Usage : $REGULATES = $engine->regulates_relationship(); Function: Returns a Bio::Ontology::RelationshipType object for "regulates" relationships Returns : Bio::Ontology::RelationshipType set to "REGULATES" Args : =cut sub regulates_relationship { my ( $self, $value ) = @_; if ( defined $value ) { $self->throw( "Attempted to change immutable field" ); } return $self->{ "_regulates_relationship" }; } # is_a_relationship =head2 positively_regulates_relationship Title : positively_regulates_relationship() Usage : $REGULATES = $engine->positively_regulates_relationship(); Function: Returns a Bio::Ontology::RelationshipType object for "positively_regulates" relationships Returns : Bio::Ontology::RelationshipType set to "POSITIVELY_REGULATES" Args : =cut sub positively_regulates_relationship { my ( $self, $value ) = @_; if ( defined $value ) { $self->throw( "Attempted to change immutable field" ); } return $self->{ "_positively_regulate" }; } =head2 negatively_regulates_relationship Title : negatively_regulates_relationship() Usage : $REGULATES = $engine->negatively_regulates_relationship(); Function: Returns a Bio::Ontology::RelationshipType object for "negatively_regulates" relationships Returns : Bio::Ontology::RelationshipType set to "POSITIVELY_REGULATES" Args : =cut sub negatively_regulates_relationship { my ( $self, $value ) = @_; if ( defined $value ) { $self->throw( "Attempted to change immutable field" ); } return $self->{ "_negatively_regulate" }; } =head2 add_term Title : add_term Usage : $engine->add_term( $term_obj ); Function: Adds a Bio::Ontology::TermI to this engine Returns : true if the term was added and false otherwise (e.g., if the term already existed in the ontology engine) Args : Bio::Ontology::TermI` =cut sub add_term { my ( $self, $term ) = @_; return FALSE if $self->has_term( $term ); my $goid = $self->_get_id($term); $self->graph()->add_vertex( $goid ); $self->graph()->set_vertex_attribute( $goid, TERM, $term ); # NG 05-02-16 return TRUE; } # add_term =head2 has_term Title : has_term Usage : $engine->has_term( $term ); Function: Checks whether this engine contains a particular term Returns : true or false Args : Bio::Ontology::TermI or Term identifier (e.g. "GO:0012345") =cut sub has_term { my ( $self, $term ) = @_; $term = $self->_get_id( $term ); if ( $self->graph()->has_vertex( $term ) ) { return TRUE; } else { return FALSE; } } # has_term =head2 add_relationship_type Title : add_relationship_type Usage : $engine->add_relationship_type( $type_name, $ont ); Function: Adds a new relationship type to the engine. Use get_relationship_type($type_name) to retrieve. Returns : true if successfully added, false otherwise Args : relationship type name to add (scalar) ontology to which to assign the relationship type =cut sub add_relationship_type{ my ($self,@args) = @_; if(scalar(@_) == 3){ my $type_name = $args[0]; my $ont = $args[1]; $self->{ "_extra_relationship_types" }{$type_name} = Bio::Ontology::RelationshipType->get_instance($type_name,$ont); #warn Dumper($self->{"_extra_relationship_types"}{$type_name}); return 1; } return 0; } =head2 get_relationship_type Title : get_relationship_type Usage : $engine->get_relationship_type( $type_name ); Function: Gets a Bio::Ontology::RelationshipI object corresponding to $type_name Returns : a Bio::Ontology::RelationshipI object Args : =cut sub get_relationship_type{ my ($self,$type_name) = @_; return $self->{ "_extra_relationship_types" }{$type_name}; } =head2 add_relationship Title : add_relationship Usage : $engine->add_relationship( $relationship ); $engine->add_relatioship( $subject_term, $predicate_term, $object_term, $ontology ); $engine->add_relatioship( $subject_id, $predicate_id, $object_id, $ontology); Function: Adds a relationship to this engine Returns : true if successfully added, false otherwise Args : The relationship in one of three ways: a) subject (or child) term id, Bio::Ontology::TermI (rel.type), object (or parent) term id, ontology or b) subject Bio::Ontology::TermI, predicate Bio::Ontology::TermI (rel.type), object Bio::Ontology::TermI, ontology or c) Bio::Ontology::RelationshipI-compliant object =cut # term objs or term ids sub add_relationship { my ( $self, $child, $type, $parent, $ont ) = @_; if ( scalar( @_ ) == 2 ) { $self->_check_class( $child, "Bio::Ontology::RelationshipI" ); $type = $child->predicate_term(); $parent = $child->object_term(); $ont = $child->ontology(); $child = $child->subject_term(); } $self->_check_class( $type, "Bio::Ontology::TermI" ); my $parentid = $self->_get_id( $parent ); my $childid = $self->_get_id( $child ); my $g = $self->graph(); $self->add_term($child) unless $g->has_vertex( $childid ); $self->add_term($parent) unless $g->has_vertex( $parentid ); # This prevents multi graphs. if ( $g->has_edge( $parentid, $childid ) ) { return FALSE; } $g->add_edge( $parentid, $childid ); $g->set_edge_attribute( $parentid, $childid, TYPE, $type ); # NG 05-02-16 $g->set_edge_attribute( $parentid, $childid, ONTOLOGY, $ont ); # NG 05-02-16 return TRUE; } # add_relationship =head2 get_relationships Title : get_relationships Usage : $engine->get_relationships( $term ); Function: Returns all relationships of a term, or all relationships in the graph if no term is specified. Returns : Relationship Args : term id or Bio::Ontology::TermI =cut sub get_relationships { my ( $self, $term ) = @_; my $g = $self->graph(); # obtain the ID if term provided my $termid; if($term) { $termid = $self->_get_id( $term ); # check for presence in the graph if ( ! $g->has_vertex( $termid ) ) { $self->throw( "no term with identifier \"$termid\" in ontology" ); } } # now build the relationships my $relfact = $self->relationship_factory(); # we'll build the relationships from edges my @rels = (); my @edges = $termid ? $g->edges_at( $termid ) : $g->edges(); # NG 05-02-13 while(@edges) { my ( $startid, $endid ) = @{ shift @edges }; # NG 05-02-16 my $rel = $relfact->create_object (-subject_term => $self->get_terms($endid), -object_term => $self->get_terms($startid), -predicate_term => $g->get_edge_attribute($startid, $endid, TYPE), -ontology => $g->get_edge_attribute($startid, $endid, ONTOLOGY)); push( @rels, $rel ); } return @rels; } # get_relationships =head2 get_all_relationships Title : get_all_relationships Usage : @rels = $engine->get_all_relationships(); Function: Returns all relationships in the graph. Returns : Relationship Args : =cut sub get_all_relationships { return shift->get_relationships(@_); } # get_all_relationships =head2 get_predicate_terms Title : get_predicate_terms Usage : $engine->get_predicate_terms(); Function: Returns the types of relationships this engine contains Returns : Bio::Ontology::RelationshipType Args : =cut sub get_predicate_terms { my ( $self ) = @_; my @a = ( $self->is_a_relationship(), $self->part_of_relationship(), $self->related_to_relationship(), $self->regulates_relationship(), $self->positively_regulates_relationship(), $self->negatively_regulates_relationship(), ); foreach my $termname (keys %{$self->{ "_extra_relationship_types" }}){ push @a, $self->{ "_extra_relationship_types" }{ $termname }; } return @a; } # get_predicate_terms =head2 get_child_terms Title : get_child_terms Usage : $engine->get_child_terms( $term_obj, @rel_types ); $engine->get_child_terms( $term_id, @rel_types ); Function: Returns the children of this term Returns : Bio::Ontology::TermI Args : Bio::Ontology::TermI, Bio::Ontology::RelationshipType or term id, Bio::Ontology::RelationshipType if NO Bio::Ontology::RelationshipType is indicated: children of ALL types are returned =cut sub get_child_terms { my ( $self, $term, @types ) = @_; return $self->_get_child_parent_terms_helper( $term, TRUE, @types ); } # get_child_terms =head2 get_descendant_terms Title : get_descendant_terms Usage : $engine->get_descendant_terms( $term_obj, @rel_types ); $engine->get_descendant_terms( $term_id, @rel_types ); Function: Returns the descendants of this term Returns : Bio::Ontology::TermI Args : Bio::Ontology::TermI, Bio::Ontology::RelationshipType or term id, Bio::Ontology::RelationshipType if NO Bio::Ontology::RelationshipType is indicated: descendants of ALL types are returned =cut sub get_descendant_terms { my ( $self, $term, @types ) = @_; my %ids = (); my @ids = (); $term = $self->_get_id( $term ); if ( ! $self->graph()->has_vertex( $term ) ) { $self->throw( "Ontology does not contain a term with an identifier of \"$term\"" ); } $self->_get_descendant_terms_helper( $term, \%ids, \@types ); while( ( my $id ) = each ( %ids ) ) { push( @ids, $id ); } return $self->get_terms( @ids ); } # get_descendant_terms =head2 get_parent_terms Title : get_parent_terms Usage : $engine->get_parent_terms( $term_obj, @rel_types ); $engine->get_parent_terms( $term_id, @rel_types ); Function: Returns the parents of this term Returns : Bio::Ontology::TermI Args : Bio::Ontology::TermI, Bio::Ontology::RelationshipType or term id, Bio::Ontology::RelationshipType if NO Bio::Ontology::RelationshipType is indicated: parents of ALL types are returned =cut sub get_parent_terms { my ( $self, $term, @types ) = @_; return $self->_get_child_parent_terms_helper( $term, FALSE, @types ); } # get_parent_terms =head2 get_ancestor_terms Title : get_ancestor_terms Usage : $engine->get_ancestor_terms( $term_obj, @rel_types ); $engine->get_ancestor_terms( $term_id, @rel_types ); Function: Returns the ancestors of this term Returns : Bio::Ontology::TermI Args : Bio::Ontology::TermI, Bio::Ontology::RelationshipType or term id, Bio::Ontology::RelationshipType if NO Bio::Ontology::RelationshipType is indicated: ancestors of ALL types are returned =cut sub get_ancestor_terms { my ( $self, $term, @types ) = @_; my %ids = (); my @ids = (); $term = $self->_get_id( $term ); if ( ! $self->graph()->has_vertex( $term ) ) { $self->throw( "Ontology does not contain a term with an identifier of \"$term\"" ); } $self->_get_ancestor_terms_helper( $term, \%ids, \@types ); while( ( my $id ) = each ( %ids ) ) { push( @ids, $id ); } return $self->get_terms( @ids ); } # get_ancestor_terms =head2 get_leaf_terms Title : get_leaf_terms Usage : $engine->get_leaf_terms(); Function: Returns the leaf terms Returns : Bio::Ontology::TermI Args : =cut sub get_leaf_terms { my ( $self ) = @_; my @a = $self->graph()->sink_vertices(); return $self->get_terms( @a ); } =head2 get_root_terms() Title : get_root_terms Usage : $engine->get_root_terms(); Function: Returns the root terms Returns : Bio::Ontology::TermI Args : =cut sub get_root_terms { my ( $self ) = @_; my @a = $self->graph()->source_vertices(); return $self->get_terms( @a ); } =head2 get_terms Title : get_terms Usage : @terms = $engine->get_terms( "GO:1234567", "GO:2234567" ); Function: Returns term objects with given identifiers Returns : Bio::Ontology::TermI, or the term corresponding to the first identifier if called in scalar context Args : term ids =cut sub get_terms { my ( $self, @ids ) = @_; my @terms = (); foreach my $id ( @ids ) { if ( $self->graph()->has_vertex( $id ) ) { push( @terms, $self->graph()->get_vertex_attribute( $id, TERM ) ); # NG 05-02-16 } } return wantarray ? @terms : shift(@terms); } # get_terms =head2 get_all_terms Title : get_all_terms Usage : $engine->get_all_terms(); Function: Returns all terms in this engine Returns : Bio::Ontology::TermI Args : =cut sub get_all_terms { my ( $self ) = @_; return( $self->get_terms( $self->graph()->vertices() ) ); } # get_all_terms =head2 find_terms Title : find_terms Usage : ($term) = $oe->find_terms(-identifier => "SO:0000263"); Function: Find term instances matching queries for their attributes. This implementation can efficiently resolve queries by identifier. Example : Returns : an array of zero or more Bio::Ontology::TermI objects Args : Named parameters. The following parameters should be recognized by any implementations: -identifier query by the given identifier -name query by the given name =cut sub find_terms{ my ($self,@args) = @_; my @terms; my ($id,$name) = $self->_rearrange([qw(IDENTIFIER NAME)],@args); if(defined($id)) { @terms = $self->get_terms($id); } else { @terms = $self->get_all_terms(); } if(defined($name)) { @terms = grep { $_->name() eq $name; } @terms; } return @terms; } =head2 find_identically_named_terms Title : find_identically_named_terms Usage : ($term) = $oe->find_identically_named_terms($term0); Function: Find term instances where names match the query term name exactly Example : Returns : an array of zero or more Bio::Ontology::TermI objects Args : a Bio::Ontology::TermI object =cut sub find_identically_named_terms{ my ($self,$qterm) = @_; $self->throw("Argument doesn't implement Bio::Ontology::TermI. " . "Bummer." ) unless defined $qterm and $qterm->isa("Bio::Ontology::TermI"); my %matching_terms; foreach my $term ($self->get_all_terms) { $matching_terms{$term->identifier} = $term and next if $term->name eq $qterm->name; } return values %matching_terms; } =head2 find_identical_terms Title : find_identical_terms Usage : ($term) = $oe->find_identical_terms($term0); Function: Find term instances where name or synonym matches the query exactly Example : Returns : an array of zero or more Bio::Ontology::TermI objects Args : a Bio::Ontology::TermI object =cut sub find_identical_terms{ my ($self,$qterm) = @_; $self->throw("Argument doesn't implement Bio::Ontology::TermI. " . "Bummer." ) unless defined $qterm and $qterm->isa("Bio::Ontology::TermI"); my %matching_terms; foreach my $qstring ($qterm->name, $qterm->each_synonym) { foreach my $term ($self->get_all_terms) { foreach my $string ( $term->name, $term->each_synonym() ) { $matching_terms{$term->identifier} = $term and next if $string eq $qstring; } } } return values %matching_terms; } =head2 find_similar_terms Title : find_similar_terms Usage : ($term) = $oe->find_similar_terms($term0); Function: Find term instances where name or synonym, or part of one, matches the query. Example : Returns : an array of zero or more Bio::Ontology::TermI objects Args : a Bio::Ontology::TermI object =cut sub find_similar_terms{ my ($self,$qterm) = @_; $self->throw("Argument doesn't implement Bio::Ontology::TermI. " . "Bummer." ) unless defined $qterm and $qterm->isa("Bio::Ontology::TermI"); my %matching_terms; foreach my $qstring ($qterm->name, $qterm->each_synonym) { foreach my $term ($self->get_all_terms) { foreach my $string ( $term->name, $term->each_synonym() ) { $matching_terms{$term->identifier} = $term and next if $string =~ /\Q$qstring\E/ or $qstring =~ /\Q$string\E/; } } } return values %matching_terms; } =head2 relationship_factory Title : relationship_factory Usage : $fact = $obj->relationship_factory() Function: Get/set the object factory to be used when relationship objects are created by the implementation on-the-fly. Example : Returns : value of relationship_factory (a Bio::Factory::ObjectFactoryI compliant object) Args : on set, a Bio::Factory::ObjectFactoryI compliant object =cut sub relationship_factory{ my $self = shift; return $self->{'relationship_factory'} = shift if @_; return $self->{'relationship_factory'}; } =head2 term_factory Title : term_factory Usage : $fact = $obj->term_factory() Function: Get/set the object factory to be used when term objects are created by the implementation on-the-fly. Note that this ontology engine implementation does not create term objects on the fly, and therefore setting this attribute is meaningless. Example : Returns : value of term_factory (a Bio::Factory::ObjectFactoryI compliant object) Args : on set, a Bio::Factory::ObjectFactoryI compliant object =cut sub term_factory{ my $self = shift; if(@_) { $self->warn("setting term factory, but ".ref($self). " does not create terms on-the-fly"); return $self->{'term_factory'} = shift; } return $self->{'term_factory'}; } =head2 graph Title : graph() Usage : $engine->graph(); Function: Returns the Graph this engine is based on Returns : Graph Args : =cut sub graph { my ( $self, $value ) = @_; if ( defined $value ) { $self->_check_class( $value, 'Bio::Ontology::SimpleGOEngine::GraphAdaptor' ); # NG 05-02-16 $self->{ "_graph" } = $value; } return $self->{ "_graph" }; } # graph # Internal methods # ---------------- # Checks the correct format of a GOBO-formatted id # Gets the id out of a term or id string sub _get_id { my ( $self, $term ) = @_; my $id = $term; if ( ref($term) ) { # use TermI standard API $self->throw( "Object doesn't implement Bio::Ontology::TermI" ) unless $term->isa("Bio::Ontology::TermI"); $id = $term->identifier(); # if there is no ID, we need to fake one from ontology name and name # in order to achieve uniqueness if ( !$id ) { $id = $term->ontology->name() if $term->ontology(); $id = $id ? $id . '|' : ''; $id .= $term->name(); } } # if $term->isa("Bio::Ontology::GOterm")||($id =~ /^[A-Z_]{1,8}:\d{1,}$/); return $id if $term->isa("Bio::Ontology::OBOterm") || ( $id =~ /^\w+:\w+$/ ); # prefix with something if only numbers # if($id =~ /^\d+$/) { # $self->warn(ref($self).": identifier [$id] is only numbers - ". # "prefixing with 'GO:'"); # return "GO:" . $id; # } # we shouldn't have gotten here if it's at least a remotely decent ID $self->throw( ref($self) . ": non-standard identifier '$id'\n" ) unless $id =~ /\|/; return $id; } # Helper for getting children and parent terms sub _get_child_parent_terms_helper { my ( $self, $term, $do_get_child_terms, @types ) = @_; foreach my $type ( @types ) { $self->_check_class( $type, "Bio::Ontology::TermI" ); } my @relative_terms = (); $term = $self->_get_id( $term ); if ( ! $self->graph()->has_vertex( $term ) ) { $self->throw( "Ontology does not contain a term with an identifier of \"$term\"" ); } my @all_relative_terms = (); if ( $do_get_child_terms ) { @all_relative_terms = $self->graph()->successors( $term ); } else { @all_relative_terms = $self->graph()->predecessors( $term ); } foreach my $relative ( @all_relative_terms ) { if ( scalar( @types ) > 0 ) { foreach my $type ( @types ) { my $relative_type; if ( $do_get_child_terms ) { $relative_type = $self->graph()->get_edge_attribute ($term, $relative, TYPE ); # NG 05-02-16 } else { $relative_type = $self->graph()->get_edge_attribute ($relative, $term, TYPE ); # NG 05-02-16 } if ( $relative_type->equals( $type ) ) { push( @relative_terms, $relative ); } } } else { push( @relative_terms, $relative ); } } return $self->get_terms( @relative_terms ); } # get_child_terms # Recursive helper sub _get_descendant_terms_helper { my ( $self, $term, $ids_ref, $types_ref ) = @_; my @child_terms = $self->get_child_terms( $term, @$types_ref ); if ( scalar( @child_terms ) < 1 ) { return; } foreach my $child_term ( @child_terms ) { my $child_term_id = $self->_get_id($child_term->identifier()); $ids_ref->{ $child_term_id } = 0; $self->_get_descendant_terms_helper( $child_term_id, $ids_ref, $types_ref ); } } # _get_descendant_terms_helper # Recursive helper sub _get_ancestor_terms_helper { my ( $self, $term, $ids_ref, $types_ref ) = @_; my @parent_terms = $self->get_parent_terms( $term, @$types_ref ); if ( scalar( @parent_terms ) < 1 ) { return; } foreach my $parent_term ( @parent_terms ) { my $parent_term_id = $self->_get_id($parent_term->identifier()); $ids_ref->{ $parent_term_id } = 0; $self->_get_ancestor_terms_helper( $parent_term_id, $ids_ref, $types_ref ); } } # get_ancestor_terms_helper sub _check_class { my ( $self, $value, $expected_class ) = @_; if ( ! defined( $value ) ) { $self->throw( "Found [undef] where [$expected_class] expected" ); } elsif ( ! ref( $value ) ) { $self->throw( "Found [scalar] where [$expected_class] expected" ); } elsif ( ! $value->isa( $expected_class ) ) { $self->throw( "Found [" . ref( $value ) . "] where [$expected_class] expected" ); } } # _check_class ################################################################# # aliases ################################################################# *get_relationship_types = \&get_predicate_terms; 1; BioPerl-1.007002/Bio/Ontology/OBOterm.pm000444000766000024 604113155576320 17704 0ustar00cjfieldsstaff000000000000 =head1 NAME Bio::Ontology::OBOterm - representation of OBO terms =head1 SYNOPSIS $term = Bio::Ontology::OBOterm->new ( -identifier => "GO:0005623", -name => "Cell", -definition => "The basic structural and functional unit ...", -is_obsolete => 0, -comment => "" ); $term->add_reference( @refs ); $term->add_secondary_id( @ids ); $term->add_synonym( @synonym ); # etc. =head1 DESCRIPTION This is data holder class for OBO terms. It is currently a dummy class since we anticipate that the OBO term will become more richer with more features being added to OBO flat-file format. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Sohel Merchant Email: s-merchant@northwestern.edu Address: Northwestern University Center for Genetic Medicine (CGM), dictyBase Suite 1206, 676 St. Clair st Chicago IL 60611 =head1 APPENDIX The rest of the documentation details each of the object methods. =cut # Let the code begin... package Bio::Ontology::OBOterm; use strict; use constant TRUE => 1; use constant FALSE => 0; use base qw(Bio::Ontology::Term); =head2 new Title : new Usage : $term = Bio::Ontology::OBOterm->new ( -identifier => "GO:0005623", -name => "Cell", -definition => "The basic structural and functional unit ...", -is_obsolete => 0, -comment => "" ); Function: Creates a new Bio::Ontology::OBOterm. Returns : A new Bio::Ontology::OBOterm object. Args : -identifier => the id of this OBO term [GO:nnnnnnn] integer of seven digits) -name => the name of this OBO term [scalar] -definition => the definition of this OBO term [scalar] -ontology => the ontology for this term (a Bio::Ontology::OntologyI compliant object) -version => version information [scalar] -is_obsolete => the obsoleteness of this OBO term [0 or 1] -comment => a comment [scalar] =cut sub new { my ( $class, @args ) = @_; my $self = $class->SUPER::new(@args); return $self; } # new 1;BioPerl-1.007002/Bio/Ontology/Ontology.pm000444000766000024 5564213155576320 20242 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Ontology::Ontology # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2003. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Ontology::Ontology - standard implementation of an Ontology =head1 SYNOPSIS use Bio::Ontology::Ontology; use Bio::Ontology::Term; # create ontology object my $ont = Bio::Ontology::Ontology->new(-name => "OBF"); # add terms, relationships ... my $bp = Bio::Ontology::Term->new(-identifier => '02', -name => "Bioperl"); my $obf = Bio::Ontology::Term->new(-identifier => '01', -name => "OBF"); my $partof = Bio::Ontology::RelationshipType->get_instance("PART_OF"); $ont->add_term($bp); $ont->add_term($obf); $ont->add_relationship($bp, $obf, $partof); # then query my @terms = $ont->get_root_terms(); # "OBF" my @desc = $ont->get_descendant_terms($terms[0], $partof); # "Bioperl" # ... see methods for other ways to query # for advanced users, you can re-use the query engine outside of an # ontology to let one instance manage multiple ontologies my $ont2 = Bio::Ontology::Ontology->new(-name => "Foundations", -engine => $ont->engine()); =head1 DESCRIPTION This is a no-frills implementation of L. The query functions are implemented by delegation to an OntologyEngineI implementation. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::Ontology; use strict; # Object preamble - inherits from Bio::Root::Root #use Bio::Ontology::SimpleOntologyEngine; # loaded dynamically now! use base qw(Bio::Root::Root Bio::Ontology::OntologyI Bio::AnnotatableI); =head2 new Title : new Usage : my $obj = Bio::Ontology::Ontology->new(); Function: Builds a new Bio::Ontology::Ontology object Returns : an instance of Bio::Ontology::Ontology Args : any number of named arguments. The following names will be recognized by this module: -name the name of the ontology -authority the name of the authority for the ontology -identifier an identifier for the ontology, if any -engine the Bio::Ontology::OntologyEngineI implementation that this instance should use; default is Bio::Ontology::SimpleOntologyEngine See the corresponding get/set methods for further documentation on individual properties. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($name,$auth,$def,$id,$engine) = $self->_rearrange([qw(NAME AUTHORITY DEFINITION IDENTIFIER ENGINE) ], @args); defined($name) && $self->name($name); defined($auth) && $self->authority($auth); defined($def) && $self->definition($def); defined($id) && $self->identifier($id); defined($engine) && $self->engine($engine); return $self; } =head1 Methods from L =cut =head2 name Title : name Usage : $obj->name($newval) Function: Get/set the name of the ontology. Example : Returns : value of name (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub name{ my $self = shift; return $self->{'name'} = shift if @_; return $self->{'name'}; } =head2 authority Title : authority Usage : $obj->authority($newval) Function: Get/set the authority for this ontology, for instance the DNS base for the organization granting the name of the ontology and identifiers for the terms. This attribute is optional and should not generally expected by applications to have been set. It is here to follow the rules for namespaces, which ontologies serve as for terms. Example : Returns : value of authority (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub authority{ my $self = shift; return $self->{'authority'} = shift if @_; return $self->{'authority'}; } =head2 definition Title : definition Usage : $obj->definition($newval) Function: Get/set a descriptive definition of the ontology. Example : Returns : value of definition (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub definition{ my $self = shift; return $self->{'definition'} = shift if @_; return $self->{'definition'}; } =head2 identifier Title : identifier Usage : $id = $obj->identifier() Function: Get an identifier for this ontology. This is primarily intended for look-up purposes. The value is not modifiable and is determined automatically by the implementation. Also, the identifier's uniqueness will only hold within the scope of a particular application's run time since it is derived from a memory location. Example : Returns : value of identifier (a scalar) Args : =cut sub identifier{ my $self = shift; if(@_) { $self->throw("cannot modify identifier for ".ref($self)) if exists($self->{'identifier'}); my $id = shift; $self->{'identifier'} = $id if $id; } if(! exists($self->{'identifier'})) { ($self->{'identifier'}) = "$self" =~ /(0x[0-9a-fA-F]+)/; } return $self->{'identifier'}; } =head2 close Title : close Usage : Function: Release any resources this ontology may occupy. In order to efficiently release unused memory or file handles, you should call this method once you are finished with an ontology. Example : Returns : TRUE on success and FALSE otherwise Args : none =cut sub close{ my $self = shift; # if it is in the ontology store, remove it from there my $store = Bio::Ontology::OntologyStore->get_instance(); $store->remove_ontology($self); # essentially we need to dis-associate from the engine here $self->engine(undef); return 1; } =head1 Implementation-specific public methods =cut =head2 engine Title : engine Usage : $engine = $obj->engine() Function: Get/set the ontology engine to which all the query methods delegate. Example : Returns : an object implementing Bio::Ontology::OntologyEngineI Args : on set, new value (an object implementing Bio::Ontology::OntologyEngineI, or undef) See L. =cut sub engine{ my $self = shift; if (@_) { my $engine = shift; if($engine && (! (ref($engine) && $engine->isa("Bio::Ontology::OntologyEngineI")))) { $self->throw("object of class ".ref($engine)." does not implement". " Bio::Ontology::OntologyEngineI. Bummer!"); } $self->{'engine'} = $engine; } elsif (! exists($self->{'engine'})) { # instantiate on demand eval { # this introduces a dependency on Graph.pm, so load dynamically require Bio::Ontology::SimpleOntologyEngine; }; if ($@) { $self->throw("failed to load SimpleOntologyEngine, possibly " ."Graph.pm is not installed; either install or supply " ."another OntologyEngineI implementation:\n" .$@); } $self->{'engine'} = Bio::Ontology::SimpleOntologyEngine->new(); } return $self->{'engine'}; } =head1 Methods defined in L =cut =head2 add_term Title : add_term Usage : add_term(TermI term): TermI Function: Adds TermI object to the ontology engine term store If the ontology property of the term object was not set, this implementation will set it to itself upon adding the term. Example : $oe->add_term($term) Returns : its argument. Args : object of class TermI. =cut sub add_term{ my $self = shift; my $term = shift; # set ontology if not set already $term->ontology($self) if $term && (! $term->ontology()); return $self->engine->add_term($term,@_); } =head2 add_relationship Title : add_relationship Usage : add_relationship(RelationshipI relationship): RelationshipI add_relatioship(TermI subject, TermI predicate, TermI object) Function: Adds a relationship object to the ontology engine. Example : Returns : Its argument. Args : A RelationshipI object. =cut sub add_relationship { my $self = shift; my $rel = shift; if($rel && $rel->isa("Bio::Ontology::TermI")) { # we need to construct the relationship object on the fly my ($predicate,$object) = @_; $rel = Bio::Ontology::Relationship->new( -subject_term => $rel, -object_term => $object, -predicate_term => $predicate, -ontology => $self, ); } # set ontology if not set already $rel->ontology($self) unless $rel->ontology(); return $self->engine->add_relationship($rel); } =head2 get_relationship_type Title : get_relationship_type Usage : get_relationship_type(scalar): RelationshipTypeI Function: Get a relationshiptype object from the ontology engine. Example : Returns : A RelationshipTypeI object. Args : The name (scalar) of the RelationshipTypeI object desired. =cut sub get_relationship_type{ my $self = shift; return $self->engine->get_relationship_type(@_); } =head2 get_relationships Title : get_relationships Usage : get_relationships(TermI term): RelationshipI[] Function: Retrieves all relationship objects in the ontology, or all relationships of a given term. Example : Returns : Array of Bio::Ontology::RelationshipI objects Args : Optionally, a Bio::Ontology::TermI compliant object =cut sub get_relationships { my $self = shift; my $term = shift; if($term) { # we don't need to filter in this case return $self->engine->get_relationships($term); } # else we need to filter by ontology return grep { my $ont = $_->ontology; # the first condition is a superset of the second, but # we add it here for efficiency reasons, as many times # it will short-cut to true and is supposedly faster than # string comparison ($ont == $self) || ($ont->name eq $self->name); } $self->engine->get_relationships(@_); } =head2 get_predicate_terms Title : get_predicate_terms Usage : get_predicate_terms(): TermI Function: Retrieves all relationship types. Example : Returns : Array of TermI objects Args : =cut sub get_predicate_terms{ my $self = shift; # skipped Bio::Ontology::Relationship w/o defined Ontology (bug 2573) return grep { $_->ontology && ($_->ontology->name eq $self->name) } $self->engine->get_predicate_terms(@_); } =head2 get_child_terms Title : get_child_terms Usage : get_child_terms(TermI term, TermI predicate_terms): TermI Function: Retrieves all child terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. get_child_terms is a special case of get_descendant_terms, limiting the search to the direct descendants. Note that a returned term may possibly be in another ontology than this one, because the underlying engine may manage multiple ontologies and the relationships of terms between them. If you only want descendants within this ontology, you need to filter the returned array. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut sub get_child_terms{ return shift->engine->get_child_terms(@_); } =head2 get_descendant_terms Title : get_descendant_terms Usage : get_descendant_terms(TermI term, TermI rel_types): TermI Function: Retrieves all descendant terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. Note that a returned term may possibly be in another ontology than this one, because the underlying engine may manage multiple ontologies and the relationships of terms between them. If you only want descendants within this ontology, you need to filter the returned array. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut sub get_descendant_terms{ return shift->engine->get_descendant_terms(@_); } =head2 get_parent_terms Title : get_parent_terms Usage : get_parent_terms(TermI term, TermI predicate_terms): TermI Function: Retrieves all parent terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. get_parent_terms is a special case of get_ancestor_terms, limiting the search to the direct ancestors. Note that a returned term may possibly be in another ontology than this one, because the underlying engine may manage multiple ontologies and the relationships of terms between them. If you only want descendants within this ontology, you need to filter the returned array. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut sub get_parent_terms{ return shift->engine->get_parent_terms(@_); } =head2 get_ancestor_terms Title : get_ancestor_terms Usage : get_ancestor_terms(TermI term, TermI predicate_terms): TermI Function: Retrieves all ancestor terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. Note that a returned term may possibly be in another ontology than this one, because the underlying engine may manage multiple ontologies and the relationships of terms between them. If you only want descendants within this ontology, you need to filter the returned array. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut sub get_ancestor_terms{ return shift->engine->get_ancestor_terms(@_); } =head2 get_leaf_terms Title : get_leaf_terms Usage : get_leaf_terms(): TermI Function: Retrieves all leaf terms from the ontology. Leaf term is a term w/o descendants. Example : @leaf_terms = $obj->get_leaf_terms() Returns : Array of TermI objects. Args : =cut sub get_leaf_terms{ my $self = shift; return grep { my $ont = $_->ontology; # the first condition is a superset of the second, but # we add it here for efficiency reasons, as many times # it will short-cut to true and is supposedly faster than # string comparison ($ont == $self) || ($ont->name eq $self->name); } $self->engine->get_leaf_terms(@_); } =head2 get_root_terms() Title : get_root_terms Usage : get_root_terms(): TermI Function: Retrieves all root terms from the ontology. Root term is a term w/o parents. Example : @root_terms = $obj->get_root_terms() Returns : Array of TermI objects. Args : =cut sub get_root_terms{ my $self = shift; return grep { my $ont = $_->ontology; # the first condition is a superset of the second, but # we add it here for efficiency reasons, as many times # it will short-cut to true and is supposedly faster than # string comparison ($ont == $self) || ($ont->name eq $self->name); } $self->engine->get_root_terms(@_); } =head2 get_all_terms Title : get_all_terms Usage : get_all_terms: TermI Function: Retrieves all terms from the ontology. We do not mandate an order here in which the terms are returned. In fact, the default implementation will return them in unpredictable order. Example : @terms = $obj->get_all_terms() Returns : Array of TermI objects. Args : =cut sub get_all_terms{ my $self = shift; return grep { my $ont = $_->ontology; # the first condition is a superset of the second, but # we add it here for efficiency reasons, as many times # it will short-cut to true and is supposedly faster than # string comparison ($ont == $self) || ($ont->name eq $self->name); } $self->engine->get_all_terms(@_); } =head2 find_terms Title : find_terms Usage : ($term) = $oe->find_terms(-identifier => "SO:0000263"); Function: Find term instances matching queries for their attributes. An implementation may not support querying for arbitrary attributes, but can generally be expected to accept -identifier and -name as queries. If both are provided, they are implicitly intersected. Example : Returns : an array of zero or more Bio::Ontology::TermI objects Args : Named parameters. The following parameters should be recognized by any implementations: -identifier query by the given identifier -name query by the given name =cut sub find_terms{ my $self = shift; return grep { $_->ontology->name eq $self->name; } $self->engine->find_terms(@_); } =head2 find_identical_terms Title : find_identical_terms Usage : ($term) = $oe->find_identical_terms($term0); Function: Find term instances where name or synonym matches the query exactly Example : Returns : an array of zero or more Bio::Ontology::TermI objects Args : a Bio::Ontology::TermI object =cut sub find_identical_terms{ my $self = shift; return grep { $_->ontology->name eq $self->name; } $self->engine->find_identical_terms(@_); } =head2 find_similar_terms Title : find_similar_terms Usage : ($term) = $oe->find_similar_terms($term0); Function: Find term instances where name or synonym, or part of one, matches the query. Example : Returns : an array of zero or more Bio::Ontology::TermI objects Args : a Bio::Ontology::TermI object =cut sub find_similar_terms{ my $self = shift; return grep { $_->ontology->name eq $self->name; } $self->engine->find_similar_terms(@_); } =head2 find_identically_named_terms Title : find_identically_named_terms Usage : ($term) = $oe->find_identically_named_terms($term0); Function: Find term instances where names match the query term name exactly Example : Returns : an array of zero or more Bio::Ontology::TermI objects Args : a Bio::Ontology::TermI object =cut sub find_identically_named_terms{ my $self = shift; return grep { $_->ontology->name eq $self->name } $self->engine->find_identically_named_terms(@_); } =head1 Factory for relationships and terms =cut =head2 relationship_factory Title : relationship_factory Usage : $fact = $obj->relationship_factory() Function: Get (and set, if the engine supports it) the object factory to be used when relationship objects are created by the implementation on-the-fly. Example : Returns : value of relationship_factory (a Bio::Factory::ObjectFactoryI compliant object) Args : =cut sub relationship_factory{ return shift->engine->relationship_factory(@_); } =head2 term_factory Title : term_factory Usage : $fact = $obj->term_factory() Function: Get (and set, if the engine supports it) the object factory to be used when term objects are created by the implementation on-the-fly. Example : Returns : value of term_factory (a Bio::Factory::ObjectFactoryI compliant object) Args : =cut sub term_factory{ return shift->engine->term_factory(@_); } =head2 annotation Title : annotation Usage : $annos = $obj->annotation() Function: Get/Set the Bio::Annotation::Collection object The collection contains Bio::Annotation::SimpleValue objects to store header information like the version and date present in the header section of an Ontology file. Example : Returns : value of annotation (a Bio::Annotation::Collection compliant object) Args : A Bio::Annotation::Collection object (Optional) =cut sub annotation{ my $self = shift; $self->{'annotation'} = shift if @_; return $self->{'annotation'}; } ################################################################# # aliases ################################################################# *get_relationship_types = \&get_predicate_terms; 1; BioPerl-1.007002/Bio/Ontology/OntologyEngineI.pm000444000766000024 3407113155576320 21472 0ustar00cjfieldsstaff000000000000# # BioPerl module for OntologyEngineI # # Please direct questions and support issues to # # Cared for by Peter Dimitrov # # (c) Peter Dimitrov # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Ontology::OntologyEngineI - Interface a minimal Ontology implementation should satisfy =head1 SYNOPSIS # see documentation of methods =head1 DESCRIPTION This describes the minimal interface an ontology query engine should provide. It intentionally does not make explicit references to the ontology being a DAG, nor does it mandate that the ontology be a vocabulary. Rather, it tries to generically express what should be accessible (queriable) about an ontology. The idea is to allow for different implementations for different purposes, which may then differ as to which operations are efficient and which are not, and how much richer the functionality is on top of this minimalistic set of methods. Check modules in the Bio::Ontology namespace to find out which implementations exist. At the time of writing, there is a SimpleOntologyEngine (which does not use Graph.pm), and a Graph.pm-based implementation in SimpleGOEngine. Ontology parsers in Bio::OntologyIO are required to return an implementation of this interface. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Peter Dimitrov Email dimitrov@gnf.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::OntologyEngineI; use strict; use Carp; use base qw(Bio::Root::RootI); =head2 add_term Title : add_term Usage : add_term(TermI term): TermI Function: Adds TermI object to the ontology engine term store Example : $oe->add_term($term) Returns : its argument. Args : object of class TermI. =cut sub add_term{ shift->throw_not_implemented(); } =head2 add_relationship Title : add_relationship Usage : add_relationship(RelationshipI relationship): RelationshipI Function: Adds a relationship object to the ontology engine. Example : Returns : Its argument. Args : A RelationshipI object. =cut sub add_relationship{ shift->throw_not_implemented(); } =head2 add_relationship_type Title : add_relationship_type Usage : add_relationship_type(scalar,OntologyI ontology) Function: Adds a relationshiptype object to the ontology engine. Example : Returns : 1 on success, undef on failure Args : The name(scalar) of the relationshiptype, and the OntologyI it is to be added to. =cut sub add_relationship_type{ shift->throw_not_implemented(); } =head2 get_relationship_type Title : get_relationship_type Usage : get_relationship_type(scalar): RelationshipTypeI Function: Get a relationshiptype object from the ontology engine. Example : Returns : A RelationshipTypeI object. Args : The name (scalar) of the RelationshipTypeI object desired. =cut sub get_relationship_type{ shift->throw_not_implemented(); } =head2 get_relationships Title : get_relationships Usage : get_relationships(TermI term): RelationshipI Function: Retrieves all relationship objects from this ontology engine, or all relationships of a term if a term is supplied. Example : Returns : Array of Bio::Ontology::RelationshipI objects Args : None, or a Bio::Ontology::TermI compliant object for which to retrieve the relationships. =cut sub get_relationships{ shift->throw_not_implemented(); } =head2 get_predicate_terms Title : get_predicate_terms Usage : get_predicate_terms(): TermI Function: Example : Returns : Args : =cut sub get_predicate_terms{ shift->throw_not_implemented(); } =head2 get_child_terms Title : get_child_terms Usage : get_child_terms(TermI term, TermI predicate_terms): TermI Function: Retrieves all child terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. get_child_terms is a special case of get_descendant_terms, limiting the search to the direct descendants. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut sub get_child_terms{ shift->throw_not_implemented(); } =head2 get_descendant_terms Title : get_descendant_terms Usage : get_descendant_terms(TermI term, TermI rel_types): TermI Function: Retrieves all descendant terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut sub get_descendant_terms{ shift->throw_not_implemented(); } =head2 get_parent_terms Title : get_parent_terms Usage : get_parent_terms(TermI term, TermI predicate_terms): TermI Function: Retrieves all parent terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. get_parent_terms is a special case of get_ancestor_terms, limiting the search to the direct ancestors. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut sub get_parent_terms{ shift->throw_not_implemented(); } =head2 get_ancestor_terms Title : get_ancestor_terms Usage : get_ancestor_terms(TermI term, TermI predicate_terms): TermI Function: Retrieves all ancestor terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut sub get_ancestor_terms{ shift->throw_not_implemented(); } =head2 get_leaf_terms Title : get_leaf_terms Usage : get_leaf_terms(): TermI Function: Retrieves all leaf terms from the ontology. Leaf term is a term w/o descendants. Example : @leaf_terms = $obj->get_leaf_terms() Returns : Array of TermI objects. Args : =cut sub get_leaf_terms{ shift->throw_not_implemented(); } =head2 get_root_terms Title : get_root_terms Usage : get_root_terms(): TermI Function: Retrieves all root terms from the ontology. Root term is a term w/o ancestors. Example : @root_terms = $obj->get_root_terms() Returns : Array of TermI objects. Args : =cut sub get_root_terms{ shift->throw_not_implemented(); } =head1 Factory for relationships and terms =cut =head2 relationship_factory Title : relationship_factory Usage : $fact = $obj->relationship_factory() Function: Get (and set, if the implementation supports it) the object factory to be used when relationship objects are created by the implementation on-the-fly. Example : Returns : value of relationship_factory (a Bio::Factory::ObjectFactory compliant object) Args : =cut sub relationship_factory{ return shift->throw_not_implemented(); } =head2 term_factory Title : term_factory Usage : $fact = $obj->term_factory() Function: Get (and set, if the implementation supports it) the object factory to be used when term objects are created by the implementation on-the-fly. Example : Returns : value of term_factory (a Bio::Factory::ObjectFactory compliant object) Args : =cut sub term_factory{ return shift->throw_not_implemented(); } =head1 Decorator Methods These methods come with a default implementation that uses the abstract methods defined for this interface. This may not be very efficient, and hence implementors are encouraged to override these methods if they can provide more efficient implementations. =cut =head2 get_all_terms Title : get_all_terms Usage : get_all_terms: TermI Function: Retrieves all terms from the ontology. This is more a decorator method. We provide a default implementation here that loops over all root terms and gets all descendants for each root term. The overall union of terms is then made unique by name and ontology. We do not mandate an order here in which the terms are returned. In fact, the default implementation will return them in unpredictable order. Engine implementations that can provide a more efficient method for obtaining all terms should definitely override this. Example : @terms = $obj->get_all_terms() Returns : Array of TermI objects. Args : =cut sub get_all_terms{ my $self = shift; # get all root nodes my @roots = $self->get_root_terms(); # accumulate all descendants for each root term my @terms = map { $self->get_descendant_terms($_); } @roots; # add on the root terms themselves push(@terms, @roots); # make unique by name and ontology my %name_map = map { ($_->name."@".$_->ontology->name, $_); } @terms; # done return values %name_map; } =head2 find_terms Title : find_terms Usage : ($term) = $oe->find_terms(-identifier => "SO:0000263"); Function: Find term instances matching queries for their attributes. An implementation may not support querying for arbitrary attributes, but can generally be expected to accept -identifier and -name as queries. If both are provided, they are implicitly intersected. Example : Returns : an array of zero or more Bio::Ontology::TermI objects Args : Named parameters. The following parameters should be recognized by any implementation: -identifier query by the given identifier -name query by the given name =cut sub find_terms{ my $self = shift; my %params = @_; @params{ map { lc $_; } keys %params } = values %params; # lowercase keys my @terms = grep { my $ok = exists($params{-identifier}) ? $_->identifier() eq $params{-identifier} : 1; $ok && ((! exists($params{-name})) || ($_->name() eq $params{-name})); } $self->get_all_terms(); return @terms; } =head1 Experimental API method proposals Ontologies are a very new domain in bioperl, and we are not sure yet what we will want to do on and with ontologies in which situation. The methods from here on downwards are solely API descriptions to solicit comment and feedback; the chance of any of those being actually implemented already is very slim. Disclaimer: As long as an API method stays in this section, it is subject to change, possibly even radical change or complete deletion. If it's not implemented yet (most likely it isn't), implement yourself at your own risk. So far for the disclaimer. The reason the API description is here, however, is to solicit feedback. Please feel encouraged to share your opinion, regardless of what it is (a notable difference of this API method to others is that there is actually no working code behind it - so the defense line is non-existent for practical purposes). =cut =head2 common_ancestor_path Title : common_ancestor_path Usage : Function: Get the paths from two terms A and B to term C, such that there is no other term D to which A and B would have a shorter path, provided there is a term C to which both A and B are connected by a path. Note that the path to the common ancestor between A and A exists, has distance zero, and predicate "identity". The search for the common ancestor C can be further constrained by supplying a predicate term. If supplied, the predicates of the two paths (A,C) and (B,C) must have a common ancestor identical to the predicate, or that has a path to the predicate. Example : Returns : The path of the first term to the common ancestor in scalar context, and both paths in list context. Paths are Bio::Ontology::PathI compliant objects. Args : The two terms (Bio::Ontology::TermI objects), and optionally a constraining common predicate (Bio::Ontology::TermI object). The latter may also be given as a scalar, in which case it is treated as a boolean that, if TRUE, means that the two paths must have identical predicates in order to be returned. =cut sub common_ancestor_path{ return shift->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Ontology/OntologyI.pm000444000766000024 2556513155576320 20354 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Ontology::OntologyI # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2003. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Ontology::OntologyI - Interface for an ontology implementation =head1 SYNOPSIS # see method documentation =head1 DESCRIPTION This describes the minimal interface an ontology implementation must provide. In essence, it represents a namespace with description on top of the query interface OntologyEngineI. This interface inherits from L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::OntologyI; use strict; use base qw(Bio::Ontology::OntologyEngineI); =head1 Methods defined in this interface. =cut =head2 name Title : name Usage : $obj->name($newval) Function: Get/set the name of this ontology. Example : Returns : value of name (a scalar) Args : =cut sub name{ shift->throw_not_implemented(); } =head2 authority Title : authority Usage : $auth = $obj->authority() Function: Get/set the authority for this ontology, for instance the DNS base for the organization granting the name of the ontology and identifiers for the terms. This attribute is optional and should not generally expected by applications to have been set. It is here to follow the rules for namespaces, which ontologies serve as for terms. Example : Returns : value of authority (a scalar) Args : =cut sub authority{ shift->throw_not_implemented(); } =head2 identifier Title : identifier Usage : $id = $obj->identifier() Function: Get an identifier for this ontology. This is primarily intended for look-up purposes. Clients should not expect the value to be modifiable, and it may not be allowed to set its value from outside. Also, the identifier's uniqueness may only hold within the scope of a particular application's run time, i.e., it may be a memory location. Example : Returns : value of identifier (a scalar) Args : =cut sub identifier{ shift->throw_not_implemented(); } =head2 definition Title : definition Usage : $def = $obj->definition() Function: Get a descriptive definition for this ontology. Example : Returns : value of definition (a scalar) Args : =cut sub definition{ shift->throw_not_implemented(); } =head2 close Title : close Usage : Function: Release any resources this ontology may occupy. In order to efficiently release used memory or file handles, you should call this method once you are finished with an ontology. Example : Returns : TRUE on success and FALSE otherwise Args : none =cut sub close{ shift->throw_not_implemented(); } =head1 Methods inherited from L Their documentations are copied here for completeness. In most use cases, you will want to access the query methods of an ontology, not just the name and description ... =cut =head2 add_term Title : add_term Usage : add_term(TermI term): TermI Function: Adds TermI object to the ontology engine term store. For ease of use, if the ontology property of the term object was not set, an implementation is encouraged to set it to itself upon adding the term. Example : $oe->add_term($term) Returns : its argument. Args : object of class TermI. =cut =head2 add_relationship Title : add_relationship Usage : add_relationship(RelationshipI relationship): RelationshipI Function: Adds a relationship object to the ontology engine. Example : Returns : Its argument. Args : A RelationshipI object. =cut =head2 get_relationships Title : get_relationships Usage : get_relationships(TermI term): RelationshipI Function: Retrieves all relationship objects from this ontology engine, or all relationships of a term if a term is supplied. Example : Returns : Array of Bio::Ontology::RelationshipI objects Args : None, or a Bio::Ontology::TermI compliant object for which to retrieve the relationships. =cut =head2 get_predicate_terms Title : get_predicate_terms Usage : get_predicate_terms(): TermI[] Function: Example : Returns : Args : =cut =head2 get_child_terms Title : get_child_terms Usage : get_child_terms(TermI term, TermI predicate_terms): TermI Function: Retrieves all child terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. get_child_terms is a special case of get_descendant_terms, limiting the search to the direct descendants. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut =head2 get_descendant_terms Title : get_descendant_terms Usage : get_descendant_terms(TermI term, TermI rel_types): TermI Function: Retrieves all descendant terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut =head2 get_parent_terms Title : get_parent_terms Usage : get_parent_terms(TermI term, TermI predicate_terms): TermI Function: Retrieves all parent terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. get_parent_terms is a special case of get_ancestor_terms, limiting the search to the direct ancestors. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut =head2 get_ancestor_terms Title : get_ancestor_terms Usage : get_ancestor_terms(TermI term, TermI predicate_terms): TermI Function: Retrieves all ancestor terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut =head2 get_leaf_terms Title : get_leaf_terms Usage : get_leaf_terms(): TermI Function: Retrieves all leaf terms from the ontology. Leaf term is a term w/o descendants. Example : @leaf_terms = $obj->get_leaf_terms() Returns : Array of TermI objects. Args : =cut =head2 get_root_terms() Title : get_root_terms Usage : get_root_terms(): TermI Function: Retrieves all root terms from the ontology. Root term is a term w/o descendants. Example : @root_terms = $obj->get_root_terms() Returns : Array of TermI objects. Args : =cut =head2 get_all_terms Title : get_all_terms Usage : get_all_terms: TermI Function: Retrieves all terms from the ontology. We do not mandate an order here in which the terms are returned. In fact, the default implementation will return them in unpredictable order. Example : @terms = $obj->get_all_terms() Returns : Array of TermI objects. Args : =cut =head2 find_terms Title : find_terms Usage : ($term) = $oe->find_terms(-identifier => "SO:0000263"); Function: Find term instances matching queries for their attributes. An implementation may not support querying for arbitrary attributes, but can generally be expected to accept -identifier and -name as queries. If both are provided, they are implicitly intersected. Example : Returns : an array of zero or more Bio::Ontology::TermI objects Args : Named parameters. The following parameters should be recognized by any implementation: -identifier query by the given identifier -name query by the given name =cut =head1 Factory for relationships and terms =cut =head2 relationship_factory Title : relationship_factory Usage : $fact = $obj->relationship_factory() Function: Get (and set, if the implementation supports it) the object factory to be used when relationship objects are created by the implementation on-the-fly. Example : Returns : value of relationship_factory (a Bio::Factory::ObjectFactoryI compliant object) Args : =cut sub relationship_factory{ return shift->throw_not_implemented(); } =head2 term_factory Title : term_factory Usage : $fact = $obj->term_factory() Function: Get (and set, if the implementation supports it) the object factory to be used when term objects are created by the implementation on-the-fly. Example : Returns : value of term_factory (a Bio::Factory::ObjectFactoryI compliant object) Args : =cut sub term_factory{ return shift->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Ontology/OntologyStore.pm000444000766000024 2375313155576320 21255 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Ontology::OntologyStore # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Ontology::OntologyStore - A repository of ontologies =head1 SYNOPSIS #---------- #SCENARIO 1 #---------- #make an ontology object manually. via OntologyIO my $io = Bio::OntologyIO->new( #params to fetch Cell Ontology here ); my $cell_ontology = $io->next_ontology; #this is a singleton that caches the fact that you've created #a 'Cell Ontology' instance... my $store = Bio::Ontology::OntologyStore->get_instance(); #...and it can hand you back a copy of it at any time. my $cell_ontology_copy = $store->get_ontology('Cell Ontology'); #---------- #SCENARIO 2 #---------- my $store = Bio::Ontology::OntologyStore->get_instance(); #this use case allows the construction of an ontology on #demand just by supplying the name. my $ontology = $store->get_ontology('Sequence Ontology'); =head1 DESCRIPTION The primary purpose of this module is that of a singleton repository of L instances from which an Ontology instance can be retrieved by name or identifier. This enables TermI implementations to return their corresponding OntologyI through using this singleton store instead of storing a direct reference to the Ontology object. The latter would almost inevitably lead to memory cycles, and would therefore potentially blow up an application. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Hilmar Lapp Ehlapp@gmx.netE Allen Day Eallenday@ucla.eduE =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::OntologyStore; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Ontology::DocumentRegistry; use Bio::OntologyIO; use FileHandle; use File::Spec::Functions; use base qw(Bio::Root::Root); # these are the static ontology stores by name and by identifier - there is # only one of each in any application my %ont_store_by_name = (); my %ont_store_by_id = (); my %ont_aliases = ( 'Gene Ontology' => 'Gene_Ontology' ); # also, this is really meant as a singleton object, so we try to enforce it my $instance = undef; =head2 new Title : new Usage : my $obj = Bio::Ontology::OntologyStore->new(); Function: Returns the Bio::Ontology::OntologyStore object. Unlike usual implementations of new, this implementation will try to return a previously instantiated store, if there is any. It is just a synonym for get_instance. In order to avoid ambiguities in your code, you may rather want to call rather get_instance explicitly, which also usually is better associated with this kind of behaviour. Returns : an instance of Bio::Ontology::OntologyStore Args : =cut sub new { return shift->get_instance(@_); } =head2 get_instance Title : get_instance Usage : Function: Get an instance of this class for perusal. Since by design this class is meant to be used as a singleton, the implementation will return a previously instantianted store if there is one, and instantiate a new one otherwise. In order to use this class by means of an instance, call this method for added code clarity, not new(). Example : Returns : an instance of this class Args : named parameters, if any (currently, there are no class-specific parameters other than those accepted by Bio::Root::Root. See L. =cut sub get_instance{ my ($self,@args) = @_; if(! $instance) { $instance = $self->SUPER::new(@args); } return $instance; } =head2 get_ontology Title : get_ontology Usage : Function: Get a previously instantiated and registered instance of this class by name or by identifier. One of the main purposes of this class is to enable TermI implementations to return their respective ontology without keeping a strong reference to the respective ontology object. Only objects previously registered objects can be retrieved. This is a class method, hence you can call it on the class name, without dereferencing an object. Example : Returns : a Bio::Ontology::OntologyI implementing object, or undef if the query could not be satisfied Args : Named parameters specifying the query. The following parameters are recognized: -name query the store for an ontology with the given name -id query for an ontology with the given identifier If both are specified, an implicit AND logical operator is assumed. See L. =cut sub get_ontology{ my ($self,@args) = @_; my $ont; my ($name,$id) = $self->_rearrange([qw(NAME ID)], @args); if($id) { $ont = $ont_store_by_id{$id}; return unless $ont; # no AND can be satisfied in this case } if($name) { my $o = $ont_store_by_name{$name}; if(!$o){ my $doc_registry = Bio::Ontology::DocumentRegistry->get_instance(); my($url,$def,$fmt) = $doc_registry->documents($name); if(ref($url) eq 'ARRAY'){ my $io = Bio::OntologyIO->new(-url => $url, -defs_url => $def, -format => $fmt, ); $o = $io->next_ontology(); $ont_store_by_name{$name} = $o; } elsif($url){ my $io = Bio::OntologyIO->new(-url => $url, -defs_url => $def, -format => $fmt, ); $o = $io->next_ontology; $ont_store_by_name{$name} = $o; } } if((! $ont) || ($ont->identifier() eq $o->identifier())) { $ont = $o; } else { $ont = undef; } } return $ont; } =head2 register_ontology Title : register_ontology Usage : Function: Registers the given Ontology object for later retrieval by name and identifier. Example : Returns : TRUE on success and FALSE otherwise Args : the Bio::Ontology::OntologyI object(s) to register See L. =cut sub register_ontology { my ($self,@args) = @_; my $ret = 1; foreach my $ont (@args) { if(ref($ont) && $ont->isa('Bio::Ontology::OntologyI')){ $ont_store_by_name{$ont->name()} = $ont if $ont->name; next; } if(! (ref($ont) && $ont->isa("Bio::Ontology::OntologyI"))) { $self->throw((ref($ont) ? ref($ont) : $ont)." does not implement ". "Bio::Ontology::OntologyI or is not an object"); } if($self->get_ontology(-name => $ont->name())) { $self->warn("ontology with name \"".$ont->name(). "\" already exists in the store, ignoring new one"); $ret = 0; next; } if($self->get_ontology(-id => $ont->identifier())) { $self->warn("ontology with id \"".$ont->identifier(). "\" already exists in the store, ignoring new one"); $ret = 0; next; } $ont_store_by_name{$ont->name()} = $ont; $ont_store_by_id{$ont->identifier()} = $ont; } return $ret; } =head2 remove_ontology Title : remove_ontology Usage : Function: Remove the specified ontology from the store. Example : Returns : TRUE on success and FALSE otherwise Args : the Bio::Ontology::OntologyI implementing object(s) to be removed from the store See L. =cut sub remove_ontology{ my $self = shift; my $ret = 1; foreach my $ont (@_) { $self->throw(ref($ont)." does not implement Bio::Ontology::OntologyI") unless $ont && ref($ont) && $ont->isa("Bio::Ontology::OntologyI"); # remove it from both the id hash and the name hash delete $ont_store_by_id{$ont->identifier()}; delete $ont_store_by_name{$ont->name()} if $ont->name(); } return 1; } =head2 guess_ontology() Usage : my $ontology = Bio::Ontology::OntologyStore->guess_ontology('GO:0000001'); Function: tries to guess which ontology a term identifier comes from, loads it as necessary, and returns it as a Bio::Ontology::Ontology object. Example : Returns : a Bio::Ontology::Ontology object, or warns and returns undef Args : an ontology term identifier in XXXX:DDDDDDD format. Guessing is based on the XXXX string before the colon. =cut sub guess_ontology { my ($self,$id) = @_; my($prefix) = $id =~ /^(.+?):.+$/; my %prefix = ( SO => 'Sequence Ontology', SOFA => 'Sequence Ontology Feature Annotation', GO => 'Gene Ontology', ); return $prefix{$prefix} || undef; } 1; BioPerl-1.007002/Bio/Ontology/Path.pm000444000766000024 1211313155576320 17306 0ustar00cjfieldsstaff000000000000# # BioPerl module for Path # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # (c) Hilmar Lapp, hlapp at gmx.net, 2003. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Ontology::Path - a path for an ontology term graph =head1 SYNOPSIS $path = Bio::Ontology::Path->new( -identifier => "16847", -subject_term => $subj, -object_term => $obj, -predicate_term => $pred, -distance => 3 ); =head1 DESCRIPTION This is a basic implementation of Bio::Ontology::PathI. Essiantially this is a very thin extension of L. It basically adds a method distance(). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Hilmar Lapp =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::Path; use strict; use base qw(Bio::Ontology::Relationship Bio::Ontology::PathI); =head2 new Title : new Usage : $rel = Bio::Ontology::Path->new(-identifier => "16847", -subject_term => $subject, -object_term => $object, -predicate_term => $type ); -distance => 3 ); Function: Creates a new Bio::Ontology::Path. Returns : A new Bio::Ontology::Path object. Args : -identifier => the identifier of this relationship [scalar] -subject_term => the subject term [Bio::Ontology::TermI] -object_term => the object term [Bio::Ontology::TermI] -predicate_term => the predicate term [Bio::Ontology::TermI] -distance => the distance between subject and object =cut sub new { my( $class, @args ) = @_; my $self = $class->SUPER::new( @args ); my ( $distance ) = $self->_rearrange( [qw( DISTANCE) ], @args ); $distance && $self->distance($distance); return $self; } # new =head2 init Title : init() Usage : $rel->init(); Function: Initializes this Path to all undef. Returns : Args : =cut sub init { my $self = shift; $self->SUPER::init(@_); $self->{ "_distance" } = undef; } # init =head2 distance Title : distance Usage : $obj->distance($newval) Function: Get/set the distance between the two terms connected by this path. Note that modifying the distance may not be meaningful. The implementation here is not connected to any graph engine, so changing an existing value may simply render the attribute's value wrong. Example : Returns : value of distance (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub distance{ my $self = shift; return $self->{'_distance'} = shift if @_; return $self->{'_distance'}; } =head2 to_string Title : to_string() Usage : print $rel->to_string(); Function: to_string method for Path. Returns : A string representation of this Path. Args : =cut sub to_string { my( $self ) = @_; my $s = $self->SUPER::to_string(); $s .= "-- Distance:\n"; $s .= $self->distance() if defined($self->distance()); $s .= "\n"; return $s; } # to_string 1; BioPerl-1.007002/Bio/Ontology/PathI.pm000444000766000024 1113613155576320 17423 0ustar00cjfieldsstaff000000000000# # BioPerl module for PathI # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # (c) Hilmar Lapp, hlapp at gmx.net, 2003. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Ontology::PathI - Interface for a path between ontology terms =head1 SYNOPSIS # see documentation of methods and an implementation, e.g., # Bio::Ontology::Path =head1 DESCRIPTION This is the minimal interface for a path between two terms in an ontology. Ontology engines may use this. Essentially this is a very thin extension of the L interface. It basically adds an attribute distance(). For a RelationshipI, you can think of distance as equal to zero (subject == object) or 1 (subject != object). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::PathI; use strict; use base qw(Bio::Ontology::RelationshipI); =head2 distance Title : distance Usage : $obj->distance($newval) Function: Get (and set if the implementation allows it) the distance between the two terms connected by this path. Example : Returns : value of distance (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub distance{ return shift->throw_not_implemented(); } =head1 Bio::Ontology::RelationshipI Methods =cut =head2 subject_term Title : subject_term Usage : $subj = $rel->subject_term(); Function: Set/get for the subject term of this Relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The subject term [Bio::Ontology::TermI]. Args : =cut =head2 object_term Title : object_term Usage : $object = $rel->object_term(); Function: Set/get for the object term of this Relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The object term [Bio::Ontology::TermI]. Args : =cut =head2 predicate_term Title : predicate_term Usage : $type = $rel->predicate_term(); Function: Set/get for the predicate of this relationship. For a path the predicate (relationship type) is defined as the greatest common denominator of all predicates (relationship types) encountered along the path. I.e., if predicate A is-a predicate B, the greatest common denominator for a path containing both predicates A and B is B Returns : The predicate term [Bio::Ontology::TermI]. Args : =cut =head2 ontology Title : ontology Usage : $ont = $obj->ontology() Function: Get the ontology that defined this relationship. Example : Returns : an object implementing Bio::Ontology::OntologyI Args : See L. =cut 1; BioPerl-1.007002/Bio/Ontology/Relationship.pm000444000766000024 2541113155576320 21060 0ustar00cjfieldsstaff000000000000# # BioPerl module for Relationship # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Ontology::Relationship - a relationship for an ontology =head1 SYNOPSIS $rel = Bio::Ontology::Relationship->new( -identifier => "16847", -subject_term => $subj, -object_term => $obj, -predicate_term => $pred ); =head1 DESCRIPTION This is a basic implementation of Bio::Ontology::RelationshipI. The terminology we use here is the one commonly used for ontologies, namely the triple of (subject, predicate, object), which in addition is scoped in a namespace (ontology). It is called triple because it is a tuple of three ontology terms. There are other terminologies in use for expressing relationships. For those who it helps to better understand the concept, the triple of (child, relationship type, parent) would be equivalent to the terminology chosen here, disregarding the question whether the notion of parent and child is sensible in the context of the relationship type or not. Especially in the case of ontologies with a wide variety of predicates the parent/child terminology and similar ones can quickly become ambiguous (e.g., A synthesises B), meaningless (e.g., A binds B), or even conflicting (e.g., A is-parent-of B), and are therefore strongly discouraged. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 CONTRIBUTORS Hilmar Lapp, email: hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::Relationship; use strict; use Bio::Ontology::TermI; use base qw(Bio::Root::Root Bio::Ontology::RelationshipI); =head2 new Title : new Usage : $rel = Bio::Ontology::Relationship->new(-identifier => "16847", -subject_term => $subject, -object_term => $object, -predicate_term => $type ); Function: Creates a new Bio::Ontology::Relationship. Returns : A new Bio::Ontology::Relationship object. Args : -identifier => the identifier of this relationship [scalar] -subject_term => the subject term [Bio::Ontology::TermI] -object_term => the object term [Bio::Ontology::TermI] -predicate_term => the predicate term [Bio::Ontology::TermI] =cut sub new { my( $class, @args ) = @_; my $self = $class->SUPER::new( @args ); my ( $identifier, $subject_term, $child, # for backwards compatibility $object_term, $parent, # for backwards compatibility $predicate_term, $reltype, # for backwards compatibility $ont) = $self->_rearrange( [qw( IDENTIFIER SUBJECT_TERM CHILD_TERM OBJECT_TERM PARENT_TERM PREDICATE_TERM RELATIONSHIP_TYPE ONTOLOGY) ], @args ); $self->init(); $self->identifier( $identifier ); $subject_term = $child unless $subject_term; $object_term = $parent unless $object_term; $predicate_term = $reltype unless $predicate_term; $self->subject_term( $subject_term) if $subject_term; $self->object_term( $object_term) if $object_term; $self->predicate_term( $predicate_term ) if $predicate_term; $self->ontology($ont) if $ont; return $self; } # new =head2 init Title : init() Usage : $rel->init(); Function: Initializes this Relationship to all undef. Returns : Args : =cut sub init { my( $self ) = @_; $self->{ "_identifier" } = undef; $self->{ "_subject_term" } = undef; $self->{ "_object_term" } = undef; $self->{ "_predicate_term" } = undef; $self->ontology(undef); } # init =head2 identifier Title : identifier Usage : $rel->identifier( "100050" ); or print $rel->identifier(); Function: Set/get for the identifier of this Relationship. Returns : The identifier [scalar]. Args : The identifier [scalar] (optional). =cut sub identifier { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_identifier" } = $value; } return $self->{ "_identifier" }; } # identifier =head2 subject_term Title : subject_term Usage : $rel->subject_term( $subject ); or $subject = $rel->subject_term(); Function: Set/get for the subject term of this Relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The subject term [Bio::Ontology::TermI]. Args : The subject term [Bio::Ontology::TermI] (optional). =cut sub subject_term { my ( $self, $term ) = @_; if ( defined $term ) { $self->_check_class( $term, "Bio::Ontology::TermI" ); $self->{ "_subject_term" } = $term; } return $self->{ "_subject_term" }; } # subject_term =head2 object_term Title : object_term Usage : $rel->object_term( $object ); or $object = $rel->object_term(); Function: Set/get for the object term of this Relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The object term [Bio::Ontology::TermI]. Args : The object term [Bio::Ontology::TermI] (optional). =cut sub object_term { my ( $self, $term ) = @_; if ( defined $term ) { $self->_check_class( $term, "Bio::Ontology::TermI" ); $self->{ "_object_term" } = $term; } return $self->{ "_object_term" }; } =head2 predicate_term Title : predicate_term Usage : $rel->predicate_term( $type ); or $type = $rel->predicate_term(); Function: Set/get for the predicate (relationship type) of this relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The predicate term [Bio::Ontology::TermI]. Args : The predicate term [Bio::Ontology::TermI] (optional). =cut sub predicate_term { my ( $self, $term ) = @_; if ( defined $term ) { $self->_check_class( $term, "Bio::Ontology::TermI" ); $self->{ "_predicate_term" } = $term; } return $self->{ "_predicate_term" }; } =head2 ontology Title : ontology Usage : $ont = $obj->ontology() Function: Get/set the ontology that defined this relationship. Example : Returns : an object implementing L Args : on set, undef or an object implementing Bio::Ontology::OntologyI (optional) See L. =cut sub ontology{ my $self = shift; my $ont; if(@_) { $ont = shift; if($ont) { $ont = Bio::Ontology::Ontology->new(-name => $ont) if ! ref($ont); if(! $ont->isa("Bio::Ontology::OntologyI")) { $self->throw(ref($ont)." does not implement ". "Bio::Ontology::OntologyI. Bummer."); } } return $self->{"_ontology"} = $ont; } return $self->{"_ontology"}; } =head2 to_string Title : to_string() Usage : print $rel->to_string(); Function: to_string method for Relationship. Returns : A string representation of this Relationship. Args : =cut sub to_string { my( $self ) = @_; local $^W = 0; my $s = ""; $s .= "-- Identifier:\n"; $s .= $self->identifier()."\n"; $s .= "-- Subject Term Identifier:\n"; $s .= $self->subject_term()->identifier()."\n"; $s .= "-- Object Term Identifier:\n"; $s .= $self->object_term()->identifier()."\n"; $s .= "-- Relationship Type Identifier:\n"; $s .= $self->predicate_term()->identifier(); return $s; } # to_string sub _check_class { my ( $self, $value, $expected_class ) = @_; if ( ! defined( $value ) ) { $self->throw( "Found [undef] where [$expected_class] expected" ); } elsif ( ! ref( $value ) ) { $self->throw( "Found [scalar] where [$expected_class] expected" ); } elsif ( ! $value->isa( $expected_class ) ) { $self->throw( "Found [" . ref( $value ) . "] where [$expected_class] expected" ); } } # _check_type ################################################################# # aliases for backwards compatibility ################################################################# =head1 Deprecated Methods These methods are deprecated and defined here solely to preserve backwards compatibility. =cut *child_term = \&subject_term; *parent_term = \&object_term; *relationship_type = \&predicate_term; 1; BioPerl-1.007002/Bio/Ontology/RelationshipFactory.pm000444000766000024 706313155576320 22373 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Ontology::RelationshipFactory # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Ontology::RelationshipFactory - Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory =head1 SYNOPSIS use Bio::Ontology::RelationshipFactory; # the default type is Bio::Ontology::Relationship my $factory = Bio::Ontology::RelationshipFactory->new( -type => 'Bio::Ontology::GOterm'); my $clu = $factory->create_object(-name => 'peroxisome', -ontology => 'Gene Ontology', -identifier => 'GO:0005777'); =head1 DESCRIPTION This object will build L objects generically. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::RelationshipFactory; use strict; use Bio::Root::Root; use base qw(Bio::Factory::ObjectFactory); =head2 new Title : new Usage : my $obj = Bio::Ontology::RelationshipFactory->new(); Function: Builds a new Bio::Ontology::RelationshipFactory object Returns : Bio::Ontology::RelationshipFactory Args : -type => string, name of a Bio::Ontology::RelationshipI derived class. The default is Bio::Ontology::Relationship. See L, L. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); # make sure this matches our requirements $self->interface("Bio::Ontology::RelationshipI"); $self->type($self->type() || "Bio::Ontology::Relationship"); return $self; } 1; BioPerl-1.007002/Bio/Ontology/RelationshipI.pm000444000766000024 1244613155576320 21175 0ustar00cjfieldsstaff000000000000# # BioPerl module for RelationshipI # # Please direct questions and support issues to # # Cared for by Peter Dimitrov # # (c) Peter Dimitrov # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Ontology::RelationshipI - Interface for a relationship between ontology terms =head1 SYNOPSIS # see documentation of methods and an implementation, e.g., # Bio::Ontology::Relationship =head1 DESCRIPTION This is the minimal interface for a relationship between two terms in an ontology. Ontology engines will use this. The terminology we use here is the one commonly used for ontologies, namely the triple of (subject, predicate, object), which in addition is scoped in a namespace (ontology). It is called triple because it is a tuple of three ontology terms. There are other terminologies in use for expressing relationships. For those who it helps to better understand the concept, the triple of (child, relationship type, parent) would be equivalent to the terminology chosen here, disregarding the question whether the notion of parent and child is sensible in the context of the relationship type or not. Especially in the case of ontologies with a wide variety of predicates the parent/child terminology and similar ones can quickly become ambiguous (e.g., A synthesises B), meaningless (e.g., A binds B), or even conflicting (e.g., A is-parent-of B), and are therefore strongly discouraged. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Peter Dimitrov Email dimitrov@gnf.org =head1 CONTRIBUTORS Hilmar Lapp, email: hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::RelationshipI; use strict; use base qw(Bio::Root::RootI); =head2 identifier Title : identifier Usage : print $rel->identifier(); Function: Set/get for the identifier of this Relationship. Note that this may not necessarily be used by a particular ontology. Returns : The identifier [scalar]. Args : =cut sub identifier{ shift->throw_not_implemented(); } =head2 subject_term Title : subject_term Usage : $subj = $rel->subject_term(); Function: Set/get for the subject term of this Relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The subject term [Bio::Ontology::TermI]. Args : =cut sub subject_term{ shift->throw_not_implemented(); } =head2 object_term Title : object_term Usage : $object = $rel->object_term(); Function: Set/get for the object term of this Relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The object term [Bio::Ontology::TermI]. Args : =cut sub object_term{ shift->throw_not_implemented(); } =head2 predicate_term Title : predicate_term Usage : $type = $rel->predicate_term(); Function: Set/get for the relationship type of this relationship. The common convention for ontologies is to express relationships between terms as triples (subject, predicate, object). Returns : The relationship type [Bio::Ontology::TermI]. Args : =cut sub predicate_term{ shift->throw_not_implemented(); } =head2 ontology Title : ontology Usage : $ont = $obj->ontology() Function: Get the ontology that defined (is the scope for) this relationship. Example : Returns : an object implementing Bio::Ontology::OntologyI Args : See L. =cut sub ontology{ shift->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/Ontology/RelationshipType.pm000444000766000024 2653713155576320 21734 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Ontology::RelationshipType # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Ontology::RelationshipType - a relationship type for an ontology =head1 SYNOPSIS # =head1 DESCRIPTION This class can be used to model various types of relationships (such as "IS_A", "PART_OF", "CONTAINS", "FOUND_IN", "RELATED_TO"). This class extends L, so it essentially is-a L. In addition, all methods are overridden such as to make the object immutable. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::RelationshipType; use strict; use constant PART_OF => "PART_OF"; use constant RELATED_TO => "RELATED_TO"; use constant IS_A => "IS_A"; use constant CONTAINS => "CONTAINS"; use constant FOUND_IN => "FOUND_IN"; use constant REGULATES => "REGULATES"; use constant POSITIVELY_REGULATES => "POSITIVELY_REGULATES"; use constant NEGATIVELY_REGULATES => "NEGATIVELY_REGULATES"; use base qw(Bio::Ontology::Term); # # cache for terms # my %term_name_map = (); =head2 get_instance Title : get_instance Usage : $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" ); $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" ); $RELATED_TO = Bio::Ontology::RelationshipType->get_instance( "RELATED_TO" ); $CONTAINS = Bio::Ontology::RelationshipType->get_instance( "CONTAINS" ); $FOUND_IN = Bio::Ontology::RelationshipType->get_instance( "FOUND_IN" ); Function: Factory method to create instances of RelationshipType Returns : [Bio::Ontology::RelationshipType] Args : "IS_A" or "PART_OF" or "CONTAINS" or "FOUND_IN" or "RELATED_TO" [scalar] the ontology [Bio::Ontology::OntologyI] (optional) =cut sub get_instance { my ( $class, $name, $ont ) = @_; $class->throw("must provide predicate name") unless $name; # is one in the cache? my $reltype = $term_name_map{$name}; if($reltype && # check whether ontologies match (($ont && $reltype->ontology() && ($ont->name() eq $reltype->ontology->name())) || (! ($reltype->ontology() || $ont)))) { # we're done, return cached type return $reltype; } # valid relationship type? # #see the cell ontology. this code is too strict, even for dag-edit files. -allen # # if ( ! (($name eq IS_A) || ($name eq PART_OF) || # ($name eq CONTAINS) || ( $name eq FOUND_IN ))) { # my $msg = "Found unknown type of relationship: [" . $name . "]\n"; # $msg .= "Known types are: [" . IS_A . "], [" . PART_OF . "], [" . CONTAINS . "], [" . FOUND_IN . "]"; # $class->throw( $msg ); # } # if we get here we need to create the rel.type $reltype = $class->new(-name => $name, -ontology => $ont); # cache it (FIXME possibly overrides one from another ontology) $term_name_map{$name} = $reltype; return $reltype; } # get_instance =head2 init Title : init() Usage : $type->init(); Function: Initializes this to all undef and empty lists. Returns : Args : =cut sub init { my $self = shift; $self->SUPER::init(); # at this point we don't really need to do anything special for us } # init =head2 equals Title : equals Usage : if ( $type->equals( $other_type ) ) { ... Function: Compares this type to another one, based on string "eq" of the "identifier" field, if at least one of the two types has the identifier set, or string eq of the name otherwise. Returns : true or false Args : [Bio::Ontology::RelationshipType] =cut sub equals { my( $self, $type ) = @_; $self->_check_class( $type, "Bio::Ontology::RelationshipType" ); if ( $self->identifier() xor $type->identifier() ) { $self->warn("comparing relationship types when only ". "one has an identifier will always return false" ); } return ($self->identifier() || $type->identifier()) ? $self->identifier() eq $type->identifier() : $self->name() eq $type->name(); } # equals =head2 identifier Title : identifier Usage : $term->identifier( "IS_A" ); or print $term->identifier(); Function: Set/get for the immutable identifier of this Type. Returns : The identifier [scalar]. Args : The identifier [scalar] (optional). =cut sub identifier { my $self = shift; my $ret = $self->SUPER::identifier(); if(@_) { $self->throw($self->veto_change("identifier",$ret,$_[0])) if $ret && ($ret ne $_[0]); $ret = $self->SUPER::identifier(@_); } return $ret; } # identifier =head2 name Title : name Usage : $term->name( "is a type" ); or print $term->name(); Function: Set/get for the immutable name of this Type. Returns : The name [scalar]. Args : The name [scalar] (optional). =cut sub name { my $self = shift; my $ret = $self->SUPER::name(); if(@_) { $self->throw($self->veto_change("name",$ret,$_[0])) if $ret && ($ret ne $_[0]); $ret = $self->SUPER::name(@_); } return $ret; } # name =head2 definition Title : definition Usage : $term->definition( "" ); or print $term->definition(); Function: Set/get for the immutable definition of this Type. Returns : The definition [scalar]. Args : The definition [scalar] (optional). =cut sub definition { my $self = shift; my $ret = $self->SUPER::definition(); if(@_) { $self->veto_change("definition",$ret,$_[0]) if $ret && ($ret ne $_[0]); $ret = $self->SUPER::definition(@_); } # let's be nice and return something readable here return $ret if $ret; return $self->name()." relationship predicate (type)" if $self->name(); } # definition =head2 ontology Title : ontology Usage : $term->ontology( $top ); or $top = $term->ontology(); Function: Set/get for the ontology this relationship type lives in. Returns : The ontology [Bio::Ontology::OntologyI]. Args : On set, the ontology [Bio::Ontology::OntologyI] (optional). =cut sub ontology { my $self = shift; my $ret = $self->SUPER::ontology(); if(@_) { my $ont = shift; if($ret) { $self->throw($self->veto_change("ontology",$ret->name, $ont ? $ont->name : $ont)) unless $ont && ($ont->name() eq $ret->name()); } $ret = $self->SUPER::ontology($ont,@_); } return $ret; } # category =head2 version Title : version Usage : $term->version( "1.00" ); or print $term->version(); Function: Set/get for immutable version information. Returns : The version [scalar]. Args : The version [scalar] (optional). =cut sub version { my $self = shift; my $ret = $self->SUPER::version(); if(@_) { $self->throw($self->veto_change("version",$ret,$_[0])) if $ret && ($ret ne $_[0]); $ret = $self->SUPER::version(@_); } return $ret; } # version =head2 is_obsolete Title : is_obsolete Usage : $term->is_obsolete( 1 ); or if ( $term->is_obsolete() ) Function: Set/get for the immutable obsoleteness of this Type. Returns : the obsoleteness [0 or 1]. Args : the obsoleteness [0 or 1] (optional). =cut sub is_obsolete { my $self = shift; my $ret = $self->SUPER::is_obsolete(); if(@_) { $self->throw($self->veto_change("is_obsolete",$ret,$_[0])) if $ret && ($ret != $_[0]); $ret = $self->SUPER::is_obsolete(@_); } return $ret; } # is_obsolete =head2 comment Title : comment Usage : $term->comment( "..." ); or print $term->comment(); Function: Set/get for an arbitrary immutable comment about this Type. Returns : A comment. Args : A comment (optional). =cut sub comment { my $self = shift; my $ret = $self->SUPER::comment(); if(@_) { $self->throw($self->veto_change("comment",$ret,$_[0])) if $ret && ($ret ne $_[0]); $ret = $self->SUPER::comment(@_); } return $ret; } # comment =head1 Private methods May be overridden in a derived class, but should never be called from outside. =cut sub _check_class { my ( $self, $value, $expected_class ) = @_; if ( ! defined( $value ) ) { $self->throw( "Found [undef] where [$expected_class] expected" ); } elsif ( ! ref( $value ) ) { $self->throw( "Found [scalar] where [$expected_class] expected" ); } elsif ( ! $value->isa( $expected_class ) ) { $self->throw( "Found [" . ref( $value ) . "] where [$expected_class] expected" ); } } # _check_type =head2 veto_change Title : veto_change Usage : Function: Called if an attribute is changed. Setting an attribute is considered a change if it had a value before and the attempt to set it would change the value. This method returns the message to be printed in the exception. Example : Returns : A string Args : The name of the attribute that was attempted to change. Optionally, the old value and the new value for reporting purposes only. =cut sub veto_change{ my ($self,$attr,$old,$new) = @_; my $changetype = $old ? ($new ? "change" : "unset") : "change"; my $msg = "attempt to $changetype attribute $attr in ".ref($self). ", which is immutable"; $msg .= " (\"$old\" to \"$new\")" if $old && $new; return $msg; } 1; BioPerl-1.007002/Bio/Ontology/SimpleOntologyEngine.pm000444000766000024 6646413155576320 22546 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Ontology::SimpleOntologyEngine # # Please direct questions and support issues to # # Cared for by Peter Dimitrov # # Copyright Peter Dimitrov # (c) Peter Dimitrov, dimitrov@gnf.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Ontology::SimpleOntologyEngine - Implementation of OntologyEngineI interface =head1 SYNOPSIS my $soe = Bio::Ontology::SimpleOntologyEngine->new; =head1 DESCRIPTION This is a "simple" implementation of Bio::Ontology::OntologyEngineI. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Peter Dimitrov Email dimitrov@gnf.org =head1 CONTRIBUTORS Hilmar Lapp, hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::SimpleOntologyEngine; use strict; use Carp; use Bio::Ontology::RelationshipFactory; use Data::Dumper; use base qw(Bio::Root::Root Bio::Ontology::OntologyEngineI); =head2 new Title : new Usage : $soe = Bio::Ontology::SimpleOntologyEngine->new; Function: Initializes the ontology engine. Example : $soe = Bio::Ontology::SimpleOntologyEngine->new; Returns : Object of class SimpleOntologyEngine. Args : =cut sub new { my ( $class, @args ) = @_; my $self = $class->SUPER::new(@args); # my %param = @args; $self->_term_store( {} ); $self->_relationship_store( {} ); $self->_inverted_relationship_store( {} ); $self->_relationship_type_store( {} ); $self->_instantiated_terms_store( {} ); # set defaults for the factories $self->relationship_factory( Bio::Ontology::RelationshipFactory->new( -type => "Bio::Ontology::Relationship" ) ); return $self; } =head2 _instantiated_terms_store Title : _instantiated_terms_store Usage : $obj->_instantiated_terms_store($newval) Function: Example : Returns : hash Args : empty hash =cut sub _instantiated_terms_store { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_instantiated_terms_store'} = $value; } return $self->{'_instantiated_terms_store'}; } =head2 mark_instantiated Title : mark_instantiated Usage : $self->mark_instantiated(TermI terms): TermI Function: Marks TermI objects as fully instantiated, allowing for proper counting of the number of terms in the term store. The TermI objects has to be already stored in the term store in order to be marked. Example : $self->mark_instantiated($term); Returns : its argument or throws an exception if a term is not in the term store. Args : array of objects of class TermI. =cut sub mark_instantiated { my ( $self, @terms ) = @_; foreach my $term (@terms) { $self->throw( "term " . $term->identifier . " not in the term store\n" ) if !defined $self->_term_store->{ $term->identifier }; $self->_instantiated_terms_store->{ $term->identifier } = 1; } return @terms; } =head2 mark_uninstantiated Title : mark_uninstantiated Usage : $self->mark_uninstantiated(TermI terms): TermI Function: Marks TermI objects as not fully instantiated, Example : $self->mark_uninstantiated($term); Returns : its argument or throws an exception if a term is not in the term store(if the term is not marked it does nothing). Args : array of objects of class TermI. =cut sub mark_uninstantiated { my ( $self, @terms ) = @_; foreach my $term (@terms) { $self->throw( "term " . $term->identifier . " not in the term store\n" ) if !defined $self->_term_store->{ $term->identifier }; delete $self->_instantiated_terms_store->{ $term->identifier } if defined $self->_instantiated_terms_store->{ $term->identifier }; } return @terms; } =head2 _term_store Title : term_store Usage : $obj->_term_store($newval) Function: Example : Returns : reference to an array of Bio::Ontology::TermI objects Args : reference to an array of Bio::Ontology::TermI objects =cut sub _term_store { my ( $self, $value ) = @_; if ( defined $value ) { if ( defined $self->{'_term_store'} ) { $self->throw("_term_store already defined\n"); } else { $self->{'_term_store'} = $value; } } return $self->{'_term_store'}; } =head2 add_term Title : add_term Usage : add_term(TermI term): TermI Function: Adds TermI object to the ontology engine term store. Marks the term fully instantiated by default. Example : $soe->add_term($term) Returns : its argument. Args : object of class TermI. =cut sub add_term { my ( $self, $term ) = @_; my $term_store = $self->_term_store; if ( defined $term_store->{ $term->identifier } && $self->_instantiated_terms_store->{ $term->identifier }) { $self->throw( "term " . $term->identifier . " already defined\n" ); } else { $term_store->{ $term->identifier } = $term; $self->_instantiated_terms_store->{ $term->identifier } = 1; } return $term; } =head2 get_term_by_identifier Title : get_term_by_identifier Usage : get_term_by_identifier(String id): TermI Function: Retrieves terms from the term store by their identifier field, or an empty list if not there. Example : $term = $soe->get_term_by_identifier("IPR000001"); Returns : An array of zero or more Bio::Ontology::TermI objects. Args : An array of identifier strings =cut sub get_term_by_identifier { my ( $self, @ids ) = @_; my @ans = (); foreach my $id (@ids) { my $term = $self->_term_store->{$id}; push @ans, $term if defined $term; } return @ans; } =head2 _get_number_rels Title : get_number_rels Usage : Function: Example : Returns : Args : =cut sub _get_number_rels { my ($self) = @_; my $num_rels = 0; foreach my $entry ( $self->_relationship_store ) { $num_rels += scalar keys %$entry; } return $num_rels; } =head2 _get_number_terms Title : _get_number_terms Usage : Function: Example : Returns : Args : =cut sub _get_number_terms { my ($self) = @_; return scalar $self->_filter_unmarked( values %{ $self->_term_store } ); } =head2 _relationship_store Title : _storerelationship_store Usage : $obj->relationship_store($newval) Function: Example : Returns : reference to an array of Bio::Ontology::TermI objects Args : reference to an array of Bio::Ontology::TermI objects =cut sub _relationship_store { my ( $self, $value ) = @_; if ( defined $value ) { if ( defined $self->{'_relationship_store'} ) { $self->throw("_relationship_store already defined\n"); } else { $self->{'_relationship_store'} = $value; } } return $self->{'_relationship_store'}; } =head2 _inverted_relationship_store Title : _inverted_relationship_store Usage : Function: Example : Returns : reference to an array of Bio::Ontology::TermI objects Args : reference to an array of Bio::Ontology::TermI objects =cut sub _inverted_relationship_store { my ( $self, $value ) = @_; if ( defined $value ) { if ( defined $self->{'_inverted_relationship_store'} ) { $self->throw("_inverted_relationship_store already defined\n"); } else { $self->{'_inverted_relationship_store'} = $value; } } return $self->{'_inverted_relationship_store'}; } =head2 _relationship_type_store Title : _relationship_type_store Usage : $obj->_relationship_type_store($newval) Function: Example : Returns : reference to an array of Bio::Ontology::RelationshipType objects Args : reference to an array of Bio::Ontology::RelationshipType objects =cut sub _relationship_type_store { my ( $self, $value ) = @_; if ( defined $value ) { if ( defined $self->{'_relationship_type_store'} ) { $self->throw("_relationship_type_store already defined\n"); } else { $self->{'_relationship_type_store'} = $value; } } return $self->{'_relationship_type_store'}; } =head2 _add_relationship_simple Title : _add_relationship_simple Usage : Function: Example : Returns : Args : =cut sub _add_relationship_simple { my ( $self, $store, $rel, $inverted ) = @_; my $subject = $rel->subject_term or $self->throw('cannot add relationship, relationship has no subject_term'); my $object = $rel->object_term or $self->throw('cannot add relationship, relationship has no object_term'); my ( $parent_id, $child_id ) = ( $object->identifier, $subject->identifier ); ( $parent_id, $child_id ) = ( $child_id, $parent_id ) if $inverted; if ( defined $store->{$parent_id} && defined $store->{$parent_id}->{$child_id} && $store->{$parent_id}->{$child_id}->name ne $rel->predicate_term->name ) { $self->throw( "relationship " . $rel->predicate_term->name . " between " . $parent_id . " and " . $child_id . " already defined as " . $store->{$parent_id}->{$child_id}->name . "\n" ); } # all is well if we get here $store->{$parent_id}->{$child_id} = $rel->predicate_term; } =head2 add_relationship Title : add_relationship Usage : add_relationship(RelationshipI relationship): RelationshipI Function: Adds a relationship object to the ontology engine. Example : Returns : Its argument. Args : A RelationshipI object. =cut sub add_relationship { my ( $self, $rel ) = @_; $self->_add_relationship_simple( $self->_relationship_store, $rel, 0 ); $self->_add_relationship_simple( $self->_inverted_relationship_store, $rel, 1 ); $self->_relationship_type_store->{ $self->_unique_termid( $rel->predicate_term ) } = $rel->predicate_term; return $rel; } =head2 get_relationships Title : get_relationships Usage : get_relationships(): RelationshipI Function: Retrieves all relationship objects. Example : Returns : Array of RelationshipI objects Args : =cut sub get_relationships { my $self = shift; my $term = shift; my @rels; my $store = $self->_relationship_store; my $relfact = $self->relationship_factory(); my @parent_ids = $term ? # if a term is supplied then only get the term's parents ( map { $_->identifier(); } $self->get_parent_terms($term) ) : # otherwise use all parent ids ( keys %{$store} ); # add the term as a parent too if one is supplied push( @parent_ids, $term->identifier ) if $term; foreach my $parent_id (@parent_ids) { my $parent_entry = $store->{$parent_id}; # if a term is supplied, add a relationship for the parent to the term # except if the parent is the term itself (we added that one before) if ( $term && ( $parent_id ne $term->identifier() ) ) { my @parent_terms = $self->get_term_by_identifier($parent_id); foreach my $parent_term (@parent_terms) { push( @rels, $relfact->create_object( -object_term => $parent_term, -subject_term => $term, -predicate_term => $parent_entry->{ $term->identifier }, -ontology => $term->ontology() ) ); } } else { # otherwise, i.e., no term supplied, or the parent equals the # supplied term my @parent_terms = $term ? ($term) : $self->get_term_by_identifier($parent_id); foreach my $child_id ( keys %$parent_entry ) { my $rel_info = $parent_entry->{$child_id}; my ($subj_term) = $self->get_term_by_identifier($child_id); foreach my $parent_term (@parent_terms) { push( @rels, $relfact->create_object( -object_term => $parent_term, -subject_term => $subj_term, -predicate_term => $rel_info, -ontology => $parent_term->ontology ) ); } } } } return @rels; } =head2 get_all_relationships Title : get_all_relationships Usage : get_all_relationships(): RelationshipI Function: Retrieves all relationship objects. Example : Returns : Array of RelationshipI objects Args : =cut sub get_all_relationships { return shift->get_relationships(); } =head2 get_predicate_terms Title : get_predicate_terms Usage : get_predicate_terms(): TermI Function: Retrieves all relationship types stored in the engine Example : Returns : reference to an array of Bio::Ontology::RelationshipType objects Args : =cut sub get_predicate_terms { my ($self) = @_; return values %{ $self->_relationship_type_store }; } =head2 _is_rel_type Title : _is_rel_type Usage : Function: Example : Returns : Args : =cut sub _is_rel_type { my ( $self, $term, @rel_types ) = @_; foreach my $rel_type (@rel_types) { if ( $rel_type->identifier || $term->identifier ) { return 1 if $rel_type->identifier eq $term->identifier; } else { return 1 if $rel_type->name eq $term->name; } } return 0; } =head2 _typed_traversal Title : _typed_traversal Usage : Function: Example : Returns : Args : =cut sub _typed_traversal { my ( $self, $rel_store, $level, $term_id, @rel_types ) = @_; return if !defined( $rel_store->{$term_id} ); my %parent_entry = %{ $rel_store->{$term_id} }; my @children = keys %parent_entry; my @ans; if ( @rel_types > 0 ) { @ans = (); foreach my $child_id (@children) { push @ans, $child_id if $self->_is_rel_type( $rel_store->{$term_id}->{$child_id}, @rel_types ); } } else { @ans = @children; } if ( $level < 1 ) { my @ans1 = (); foreach my $child_id (@ans) { push @ans1, $self->_typed_traversal( $rel_store, $level - 1, $child_id, @rel_types ) if defined $rel_store->{$child_id}; } push @ans, @ans1; } return @ans; } =head2 get_child_terms Title : get_child_terms Usage : get_child_terms(TermI term, TermI predicate_terms): TermI get_child_terms(TermI term, RelationshipType predicate_terms): TermI Function: Retrieves all child terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. get_child_terms is a special case of get_descendant_terms, limiting the search to the direct descendants. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut sub get_child_terms { my ( $self, $term, @relationship_types ) = @_; $self->throw("must provide TermI compliant object") unless defined($term) && $term->isa("Bio::Ontology::TermI"); return $self->_filter_unmarked( $self->get_term_by_identifier( $self->_typed_traversal( $self->_relationship_store, 1, $term->identifier, @relationship_types ) ) ); } =head2 get_descendant_terms Title : get_descendant_terms Usage : get_descendant_terms(TermI term, TermI rel_types): TermI get_child_terms(TermI term, RelationshipType predicate_terms): TermI Function: Retrieves all descendant terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. Uses _typed_traversal to find all descendants. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut sub get_descendant_terms { my ( $self, $term, @relationship_types ) = @_; $self->throw("must provide TermI compliant object") unless defined($term) && $term->isa("Bio::Ontology::TermI"); return $self->_filter_unmarked( $self->_filter_repeated( $self->get_term_by_identifier( $self->_typed_traversal( $self->_relationship_store, 0, $term->identifier, @relationship_types ) ) ) ); } =head2 get_parent_terms Title : get_parent_terms Usage : get_parent_terms(TermI term, TermI predicate_terms): TermI get_child_terms(TermI term, RelationshipType predicate_terms): TermI Function: Retrieves all parent terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. get_parent_terms is a special case of get_ancestor_terms, limiting the search to the direct ancestors. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut sub get_parent_terms { my ( $self, $term, @relationship_types ) = @_; $self->throw("term must be a valid object, not undef") unless defined $term; return $self->_filter_unmarked( $self->get_term_by_identifier( $self->_typed_traversal( $self->_inverted_relationship_store, 1, $term->identifier, @relationship_types ) ) ); } =head2 get_ancestor_terms Title : get_ancestor_terms Usage : get_ancestor_terms(TermI term, TermI predicate_terms): TermI get_child_terms(TermI term, RelationshipType predicate_terms): TermI Function: Retrieves all ancestor terms of a given term, that satisfy a relationship among those that are specified in the second argument or undef otherwise. Uses _typed_traversal to find all ancestors. Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms. =cut sub get_ancestor_terms { my ( $self, $term, @relationship_types ) = @_; $self->throw("term must be a valid object, not undef") unless defined $term; return $self->_filter_unmarked( $self->_filter_repeated( $self->get_term_by_identifier( $self->_typed_traversal( $self->_inverted_relationship_store, 0, $term->identifier, @relationship_types ) ) ) ); } =head2 get_leaf_terms Title : get_leaf_terms Usage : get_leaf_terms(): TermI Function: Retrieves all leaf terms from the ontology. Leaf term is a term w/o descendants. Example : @leaf_terms = $obj->get_leaf_terms() Returns : Array of TermI objects. Args : =cut sub get_leaf_terms { my ($self) = @_; my @leaf_terms; foreach my $term ( values %{ $self->_term_store } ) { push @leaf_terms, $term if !defined $self->_relationship_store->{ $term->identifier } && defined $self->_instantiated_terms_store->{ $term->identifier }; } return @leaf_terms; } =head2 get_root_terms Title : get_root_terms Usage : get_root_terms(): TermI Function: Retrieves all root terms from the ontology. Root term is a term w/o descendants. Example : @root_terms = $obj->get_root_terms() Returns : Array of TermI objects. Args : =cut sub get_root_terms { my ($self) = @_; my @root_terms; foreach my $term ( values %{ $self->_term_store } ) { push @root_terms, $term if !defined $self->_inverted_relationship_store->{ $term->identifier } && defined $self->_instantiated_terms_store->{ $term->identifier }; } return @root_terms; } =head2 _filter_repeated Title : _filter_repeated Usage : @lst = $self->_filter_repeated(@old_lst); Function: Removes repeated terms Example : Returns : List of unique TermI objects Args : List of TermI objects =cut sub _filter_repeated { my ( $self, @args ) = @_; my %h; foreach my $element (@args) { $h{ $element->identifier } = $element if !defined $h{ $element->identifier }; } return values %h; } =head2 get_all_terms Title : get_all_terms Usage : get_all_terms(): TermI Function: Retrieves all terms currently stored in the ontology. Example : @all_terms = $obj->get_all_terms() Returns : Array of TermI objects. Args : =cut sub get_all_terms { my ($self) = @_; return $self->_filter_unmarked( values %{ $self->_term_store } ); } =head2 find_terms Title : find_terms Usage : ($term) = $oe->find_terms(-identifier => "SO:0000263"); Function: Find term instances matching queries for their attributes. This implementation can efficiently resolve queries by identifier. Example : Returns : an array of zero or more Bio::Ontology::TermI objects Args : Named parameters. The following parameters should be recognized by any implementations: -identifier query by the given identifier -name query by the given name =cut sub find_terms { my ( $self, @args ) = @_; my @terms; my ( $id, $name ) = $self->_rearrange( [qw(IDENTIFIER NAME)], @args ); if ( defined($id) ) { @terms = $self->get_term_by_identifier($id); } else { @terms = $self->get_all_terms(); } if ( defined($name) ) { @terms = grep { $_->name() eq $name; } @terms; } return @terms; } =head2 relationship_factory Title : relationship_factory Usage : $fact = $obj->relationship_factory() Function: Get/set the object factory to be used when relationship objects are created by the implementation on-the-fly. Example : Returns : value of relationship_factory (a Bio::Factory::ObjectFactoryI compliant object) Args : on set, a Bio::Factory::ObjectFactoryI compliant object =cut sub relationship_factory { my $self = shift; return $self->{'relationship_factory'} = shift if @_; return $self->{'relationship_factory'}; } =head2 term_factory Title : term_factory Usage : $fact = $obj->term_factory() Function: Get/set the object factory to be used when term objects are created by the implementation on-the-fly. Note that this ontology engine implementation does not create term objects on the fly, and therefore setting this attribute is meaningless. Example : Returns : value of term_factory (a Bio::Factory::ObjectFactoryI compliant object) Args : on set, a Bio::Factory::ObjectFactoryI compliant object =cut sub term_factory { my $self = shift; if (@_) { $self->warn( "setting term factory, but " . ref($self) . " does not create terms on-the-fly" ); return $self->{'term_factory'} = shift; } return $self->{'term_factory'}; } =head2 _filter_unmarked Title : _filter_unmarked Usage : _filter_unmarked(TermI terms): TermI Function: Removes the uninstantiated terms from the list of terms Example : Returns : array of fully instantiated TermI objects Args : array of TermI objects =cut sub _filter_unmarked { my ( $self, @terms ) = @_; my @filtered_terms = (); if ( scalar(@terms) >= 1 ) { foreach my $term (@terms) { push @filtered_terms, $term if defined $self->_instantiated_terms_store->{ $term->identifier }; } } return @filtered_terms; } =head2 remove_term_by_id Title : remove_term_by_id Usage : remove_term_by_id(String id): TermI Function: Removes TermI object from the ontology engine using the string id as an identifier. Current implementation does not enforce consistency of the relationships using that term. Example : $term = $soe->remove_term_by_id($id); Returns : Object of class TermI or undef if not found. Args : The string identifier of a term. =cut sub remove_term_by_id { my ( $self, $id ) = @_; if ( $self->get_term_by_identifier($id) ) { my $term = $self->{_term_store}->{$id}; delete $self->{_term_store}->{$id}; return $term; } else { $self->warn("Term with id '$id' is not in the term store"); return; } } =head2 to_string Title : to_string Usage : print $sv->to_string(); Function: Currently returns formatted string containing the number of terms and number of relationships from the ontology engine. Example : print $sv->to_string(); Returns : Args : =cut sub to_string { my ($self) = @_; my $s = ""; $s .= "-- # Terms:\n"; $s .= scalar( $self->get_all_terms ) . "\n"; $s .= "-- # Relationships:\n"; $s .= $self->_get_number_rels . "\n"; return $s; } =head2 _unique_termid Title : _unique_termid Usage : Function: Returns a string that can be used as ID using fail-over approaches. If the identifier attribute is not set, it uses the combination of name and ontology name, provided both are set. If they are not, it returns the name alone. Note that this is a private method. Call from inheriting classes but not from outside. Example : Returns : a string Args : a Bio::Ontology::TermI compliant object =cut sub _unique_termid { my $self = shift; my $term = shift; return $term->identifier() if $term->identifier(); my $id = $term->ontology->name() if $term->ontology(); if ($id) { $id .= '|'; } else { $id = ''; } $id .= $term->name(); } ################################################################# # aliases ################################################################# *get_relationship_types = \&get_predicate_terms; 1; BioPerl-1.007002/Bio/Ontology/Term.pm000444000766000024 6304113155576320 17327 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Ontology::Term # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Ontology::Term - implementation of the interface for ontology terms =head1 SYNOPSIS #get Bio::Ontology::TermI somehow. print $term->identifier(), "\n"; print $term->name(), "\n"; print $term->definition(), "\n"; print $term->is_obsolete(), "\n"; print $term->comment(), "\n"; foreach my $synonym ( $term->each_synonym() ) { print $synonym, "\n"; } =head1 DESCRIPTION This is a simple implementation for ontology terms providing basic methods (it provides no functionality related to graphs). It implements the L interface. This class also implements L and L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 APPENDIX The rest of the documentation details each of the object methods. =cut # Let the code begin... package Bio::Ontology::Term; use strict; use Bio::Ontology::Ontology; use Bio::Ontology::OntologyStore; use Bio::Annotation::DBLink; use Data::Dumper; use constant TRUE => 1; use constant FALSE => 0; use base qw(Bio::Root::Root Bio::Ontology::TermI Bio::IdentifiableI Bio::DescribableI); =head2 new Title : new Usage : $term = Bio::Ontology::Term->new( -identifier => "16847", -name => "1-aminocyclopropane-1-carboxylate synthase", -definition => "Catalysis of ...", -is_obsolete => 0, -comment => "" ); Function: Creates a new Bio::Ontology::Term. Returns : A new Bio::Ontology::Term object. Args : -identifier => the identifier of this term [scalar] -name => the name of this term [scalar] -definition => the definition of this term [scalar] -ontology => the ontology this term lives in (a Bio::Ontology::OntologyI object) -version => version information [scalar] -is_obsolete => the obsoleteness of this term [0 or 1] -comment => a comment [scalar] -dblinks => Bio::Annotation::DBLink objects [reference to array] -references => Bio::Annotation::Reference objects [reference to array] See L, L, L. =cut sub new { my( $class,@args ) = @_; my $self = $class->SUPER::new( @args ); my ( $identifier, $name, $definition, $category, $ont, $version, $is_obsolete, $comment, $dblinks, $dbxrefs, $references) = $self->_rearrange( [ qw(IDENTIFIER NAME DEFINITION CATEGORY ONTOLOGY VERSION IS_OBSOLETE COMMENT DBLINKS DBXREFS REFERENCES) ], @args ); $self->init(); defined($identifier) && $self->identifier( $identifier ); defined($name) && $self->name( $name ); defined($definition) && $self->definition( $definition ); defined($category) && $self->category( $category ); defined($ont) && $self->ontology( $ont ); defined($version) && $self->version( $version ); defined($is_obsolete) && $self->is_obsolete( $is_obsolete ); defined($comment) && $self->comment( $comment ); defined($dbxrefs) && $self->add_dbxref(-dbxrefs => $dbxrefs); # deprecated methods, allow one to pass on to get the dep. notification ref($dblinks) && $self->add_dblink(@$dblinks); ref($references) && $self->add_reference(@$references); return $self; } # new sub init { my $self = shift; $self->identifier(undef); $self->name(undef); $self->comment(undef); $self->definition(undef); $self->ontology(undef); $self->is_obsolete(0); $self->remove_synonyms(); $self->remove_dbxrefs(); $self->remove_references; $self->remove_secondary_ids(); } # init =head2 identifier Title : identifier Usage : $term->identifier( "GO:0003947" ); or print $term->identifier(); Function: Set/get for the identifier of this Term. Returns : The identifier [scalar]. Args : The identifier [scalar] (optional). =cut sub identifier { my $self = shift; return $self->{'identifier'} = shift if @_; return $self->{'identifier'}; } # identifier =head2 name Title : name Usage : $term->name( "N-acetylgalactosaminyltransferase" ); or print $term->name(); Function: Set/get for the name of this Term. Returns : The name [scalar]. Args : The name [scalar] (optional). =cut sub name { my $self = shift; return $self->{'name'} = shift if @_; return $self->{'name'}; } # name =head2 definition Title : definition Usage : $term->definition( "Catalysis of ..." ); or print $term->definition(); Function: Set/get for the definition of this Term. Returns : The definition [scalar]. Args : The definition [scalar] (optional). =cut sub definition { my $self = shift; return $self->{'definition'} = shift if @_; return $self->{'definition'}; } # definition =head2 ontology Title : ontology Usage : $ont = $term->ontology(); or $term->ontology( $ont ); Function: Get the ontology this term is in. Note that with the ontology in hand you can query for all related terms etc. Returns : The ontology of this Term as a Bio::Ontology::OntologyI implementing object. Args : On set, the ontology of this Term as a Bio::Ontology::OntologyI implementing object or a string representing its name. See L. =cut sub ontology { my $self = shift; my $ont; if(@_) { $ont = shift; if($ont) { $ont = Bio::Ontology::Ontology->new(-name => $ont) if ! ref($ont); if(! $ont->isa("Bio::Ontology::OntologyI")) { $self->throw(ref($ont)." does not implement ". "Bio::Ontology::OntologyI. Bummer."); } } return $self->{"_ontology"} = $ont; } return $self->{"_ontology"}; } # ontology =head2 version Title : version Usage : $term->version( "1.00" ); or print $term->version(); Function: Set/get for version information. Returns : The version [scalar]. Args : The version [scalar] (optional). =cut sub version { my $self = shift; return $self->{'version'} = shift if @_; return $self->{'version'}; } # version =head2 is_obsolete Title : is_obsolete Usage : $term->is_obsolete( 1 ); or if ( $term->is_obsolete() ) Function: Set/get for the obsoleteness of this Term. Returns : the obsoleteness [0 or 1]. Args : the obsoleteness [0 or 1] (optional). =cut sub is_obsolete{ my $self = shift; return $self->{'is_obsolete'} = shift if @_; return $self->{'is_obsolete'}; } # is_obsolete =head2 comment Title : comment Usage : $term->comment( "Consider the term ..." ); or print $term->comment(); Function: Set/get for an arbitrary comment about this Term. Returns : A comment. Args : A comment (optional). =cut sub comment{ my $self = shift; return $self->{'comment'} = shift if @_; return $self->{'comment'}; } # comment =head2 get_synonyms Title : get_synonyms Usage : @aliases = $term->get_synonyms; Function: Returns a list of aliases of this Term. Returns : A list of aliases [array of [scalar]]. Args : =cut sub get_synonyms { my $self = shift; return @{ $self->{ "_synonyms" } } if exists($self->{ "_synonyms" }); return (); } # get_synonyms =head2 add_synonym Title : add_synonym Usage : $term->add_synonym( @asynonyms ); or $term->add_synonym( $synonym ); Function: Pushes one or more synonyms into the list of synonyms. Returns : Args : One synonym [scalar] or a list of synonyms [array of [scalar]]. =cut sub add_synonym { my ( $self, @values ) = @_; return unless( @values ); # avoid duplicates foreach my $syn (@values) { next if grep { $_ eq $syn; } @{$self->{ "_synonyms" }}; push( @{ $self->{ "_synonyms" } }, $syn ); } } # add_synonym =head2 remove_synonyms Title : remove_synonyms() Usage : $term->remove_synonyms(); Function: Deletes (and returns) the synonyms of this Term. Returns : A list of synonyms [array of [scalar]]. Args : =cut sub remove_synonyms { my ( $self ) = @_; my @a = $self->get_synonyms(); $self->{ "_synonyms" } = []; return @a; } # remove_synonyms =head2 get_dblinks Title : get_dblinks() Usage : @ds = $term->get_dblinks(); Function: Returns a list of each dblinks of this GO term. Returns : A list of dblinks [array of [scalars]]. Args : A scalar indicating the context (optional). If omitted, all dblinks will be returned. Note : deprecated method due to past use of mixed data types; use get_dbxrefs() instead, which handles both strings and DBLink instances =cut sub get_dblinks { my ($self, $context) = @_; $self->deprecated("Use of get_dblinks is deprecated. Note that prior use\n". "of this method could return either simple scalar values\n". "or Bio::Annotation::DBLink instances; only \n". "Bio::Annotation::DBLink is now supported.\n ". "Use get_dbxrefs() instead"); $self->get_dbxrefs($context); } # get_dblinks =head2 get_dbxrefs Title : get_dbxrefs() Usage : @ds = $term->get_dbxrefs(); Function: Returns a list of each link for this term. If an implementor of this interface permits modification of this array property, the class should define at least methods add_dbxref() and remove_dbxrefs(), with obvious functionality. Returns : A list of L instances Args : [optional] string which specifies context (default : returns all dbxrefs) =cut sub get_dbxrefs { my ($self, $context) = shift; my @dbxrefs; if (defined($context)) { if (exists($self->{_dblinks}->{$context})) { @dbxrefs = @{$self->{_dblinks}->{$context}}; } } else { @dbxrefs = map { @$_ } values %{$self->{_dblinks}} ; } return @dbxrefs; } # get_dbxrefs =head2 get_dblink_context Title : get_dblink_context Usage : @context = $term->get_dblink_context; Function: Return all context existing in Term Returns : a list of scalar Args : [none] Note : deprecated method due to past use of mixed data types; use get_dbxref_context() instead =cut sub get_dblink_context { my $self=shift; $self->deprecated("Use of get_dblink_context() is deprecated; use get_dbxref_context() instead"); return $self->get_dbxref_context(@_); } =head2 get_dbxref_context Title : get_dbxref_context Usage : @context = $term->get_dbxref_context; Function: Return all context strings existing in Term Returns : a list of scalars Args : [none] =cut sub get_dbxref_context { my $self=shift; return keys %{$self->{_dblinks}}; } =head2 add_dblink Title : add_dblink Usage : $term->add_dblink( @dbls ); or $term->add_dblink( $dbl ); Function: Pushes one or more dblinks onto the list of dblinks. Returns : Args : One or more L instances Note : deprecated method due to past use of mixed data types; use add_dbxref() instead, which handles both strings and DBLink instances =cut sub add_dblink { my $self = shift; $self->deprecated("Use of simple strings and add_dblink() is deprecated; use\n". "Bio::Annotation::DBLink instances and add_dbxref() instead"); # here we're assuming the data is in a simple DB:ID format my @dbxrefs; for my $string (@_) { my ($db, $id) = split(':',$string); push @dbxrefs, Bio::Annotation::DBLink->new(-database => $db, -primary_id => $id); } return $self->add_dbxref(-dbxrefs => \@dbxrefs, -context => '_default'); } # add_dblink =head2 add_dbxref Title : add_dbxref Usage : $term->add_dbxref( @dbls ); or $term->add_dbxref( $dbl ); Function: Pushes one or more dblinks onto the list of dblinks. Returns : Args : -dbxrefs : array ref of Bio::Annotation::DBLink instances -context : string designating the context for the DBLink (default : '_default' - contextless) =cut sub add_dbxref { my $self = shift; my ($links, $context) = $self->_rearrange([qw(DBXREFS CONTEXT)],@_); return unless defined $links; $context ||= '_default'; $self->throw("DBLinks must be passed as an array reference") if ref $links ne 'ARRAY'; foreach my $dbxref (@{$links}) { $self->throw("$dbxref is not a DBLink") unless ref $dbxref && $dbxref->isa('Bio::Annotation::DBLink'); $self->throw("'all' is a reserved word for context.") if $context eq 'all'; if (! exists($self->{_dblinks}->{$context})) { $self->{_dblinks}->{$context} = []; } my $linktext = ref $dbxref ? $dbxref->display_text : $dbxref; if (grep {$_->display_text eq $linktext} @{$self->{_dblinks}->{$context}}) { $self->warn("DBLink exists in the dblink of $context"); } push @{$self->{_dblinks}->{$context}}, $dbxref; } } # add_dbxref # alias, for consistency *add_dbxrefs = \&add_dbxref; =head2 has_dblink Title : has_dblink Usage : $term->has_dblink($dblink); Function: Checks if a DBXref is already existing in the OBOterm object Return : TRUE/FALSE Args : [arg1] A DBxref identifier Note : deprecated method due to past use of mixed data types; use has_dbxref() instead, which handles both strings and DBLink instances =cut sub has_dblink { my ( $self, $value ) = @_; $self->deprecated("use of has_dblink() is deprecated; use has_dbxref() instead"); return $self->has_dbxref($value); } =head2 has_dbxref Title : has_dbxref Usage : $term->has_dbxref($dbxref); Function: Checks if a dbxref string is already existing in the OBOterm object Return : TRUE/FALSE Args : [arg1] A DBxref identifier (string). Bio::Annotation::DBLink::display_text() is used for comparison against the string. =cut sub has_dbxref { my ( $self, $value ) = @_; return unless defined $value; my $context = "_default"; $self->throw("'all' is a reserved word for context.") if $context eq 'all'; $context ||= '_default'; if ( ( $self->{_dblinks}->{$context} ) && grep { $_->display_text eq $value } @{ $self->{_dblinks}->{$context} } ) { return TRUE; } else { return FALSE; } } =head2 add_dblink_context Title : add_dblink_context Usage : $term->add_dblink_context($db, $context); Function: add a dblink with its context Return : [none] Args : [arg1] a Bio::Annotation::DBLink instance [arg2] a string for context; if omitted, the default/context-less one will be used. Note : deprecated method due to past use of mixed data types; use add_dbxref() instead =cut sub add_dblink_context { my ($self, $value, $context) = @_; $self->deprecated("Use of simple strings and add_dblink_context() is deprecated; use\n Bio::Annotation::DBLink instances and add_dbxref() instead"); return $self->add_dbxref([$value],$context); } =head2 remove_dblinks Title : remove_dblinks() Usage : $term->remove_dblinks(); Function: Deletes (and returns) the definition references of this GO term. Returns : A list of definition references [array of [scalars]]. Args : Context. If omitted or equal to 'all', all dblinks will be removed. Note : deprecated method due to past use of mixed data types; use remove_dblinks() instead, which handles both strings and DBLink instances =cut sub remove_dblinks { my ($self, $context) = @_; $self->deprecated("use of remove_dblinks() is deprecated; use remove_dbxrefs() instead"); return $self->remove_dbxrefs(@_); } # remove_dblinks =head2 remove_dbxrefs Title : remove_dbxrefs() Usage : $term->remove_dbxrefs(); Function: Deletes (and returns) the definition references of this GO term. Returns : A list of definition references [array of [scalars]]. Args : Context. If omitted or equal to 'all', all dblinks will be removed. =cut sub remove_dbxrefs { my ($self, $context) = @_; $context = undef if $context && ($context eq "all"); my @old = $self->get_dbxrefs($context); if (defined($context)) { $self->{_dblinks}->{$context}=[]; } else { $self->{_dblinks} = {}; } return @old; } # remove_dbxrefs =head2 get_references Title : get_references Usage : @references = $self->get_references Fuctnion: Returns a list of references Return : A list of objects Args : [none] =cut sub get_references { my $self=shift; return @{$self->{_references}} if exists $self->{_references}; return (); } =head2 add_reference Title : add_reference Usage : $self->add_reference($reference); $self->add_reference($reference1, $reference2); Fuctnion: Add one or more references Returns : [none] =cut sub add_reference { my ($self, @values) =@_; return unless @values; # avoid duplicates and undefs foreach my $reference (@values){ $self->throw("Passed data not an Bio::Annotation::Reference") unless ref $reference && $reference->isa('Bio::AnnotationI'); next unless defined $reference; next if grep{$_ eq $reference} @{$self->{_references}}; push @{$self->{_references}}, $reference; } } =head2 remove_references Title : remove_references Usage : $self->remove_references; Function: Deletes (and returns) all references Returns : A list of references Args : [none] =cut sub remove_references { my $self=shift; my @references=$self->get_references; $self->{_references}=[]; return @references; } =head2 get_secondary_ids Title : get_secondary_ids Usage : @ids = $term->get_secondary_ids(); Function: Returns a list of secondary identifiers of this Term. Secondary identifiers mostly originate from merging terms, or possibly also from splitting terms. Returns : A list of secondary identifiers [array of [scalar]] Args : =cut sub get_secondary_ids { my $self = shift; return @{$self->{"_secondary_ids"}} if exists($self->{"_secondary_ids"}); return (); } # get_secondary_ids =head2 add_secondary_id Title : add_secondary_id Usage : $term->add_secondary_id( @ids ); or $term->add_secondary_id( $id ); Function: Adds one or more secondary identifiers to this term. Returns : Args : One or more secondary identifiers [scalars] =cut sub add_secondary_id { my $self = shift; return unless @_; # avoid duplicates foreach my $id (@_) { next if grep { !$_ or $_ eq $id; } @{$self->{ "_secondary_ids" }}; push( @{ $self->{ "_secondary_ids" } }, $id ); } } # add_secondary_id =head2 remove_secondary_ids Title : remove_secondary_ids Usage : $term->remove_secondary_ids(); Function: Deletes (and returns) the secondary identifiers of this Term. Returns : The previous list of secondary identifiers [array of [scalars]] Args : =cut sub remove_secondary_ids { my $self = shift; my @a = $self->get_secondary_ids(); $self->{ "_secondary_ids" } = []; return @a; } # remove_secondary_ids # Title :_is_true_or_false # Function: Checks whether the argument is TRUE or FALSE. # Returns : # Args : The value to be checked. sub _is_true_or_false { my ( $self, $value ) = @_; unless ( $value !~ /\D/ && ( $value == TRUE || $value == FALSE ) ) { $self->throw( "Found [" . $value . "] where " . TRUE . " or " . FALSE . " expected" ); } } # _is_true_or_false =head1 Methods implementing L and L =cut =head2 object_id Title : object_id Usage : $string = $obj->object_id() Function: a string which represents the stable primary identifier in this namespace of this object. This is a synonym for identifier(). Returns : A scalar =cut sub object_id { return shift->identifier(@_); } =head2 authority Title : authority Usage : $authority = $obj->authority() Function: a string which represents the organisation which granted the namespace, written as the DNS name for organisation (eg, wormbase.org) This forwards to ontology()->authority(). Note that you cannot set the authority before having set the ontology or the namespace (which will set the ontology). Returns : A scalar Args : on set, the new value (a scalar) =cut sub authority { my $self = shift; my $ont = $self->ontology(); return $ont->authority(@_) if $ont; $self->throw("cannot manipulate authority prior to ". "setting the namespace or ontology") if @_; return; } =head2 namespace Title : namespace Usage : $string = $obj->namespace() Function: A string representing the name space this identifier is valid in, often the database name or the name describing the collection. This forwards to ontology() (set mode) and ontology()->name() (get mode). I.e., setting the namespace will set the ontology to one matching that name in the ontology store, or to one newly created. Returns : A scalar Args : on set, the new value (a scalar) =cut sub namespace { my $self = shift; $self->ontology(@_) if(@_); my $ont = $self->ontology(); return defined($ont) ? $ont->name() : undef; } =head2 display_name Title : display_name Usage : $string = $obj->display_name() Function: A string which is what should be displayed to the user. The definition in Bio::DescribableI states that the string should not contain spaces. As this is not very sensible for ontology terms, we relax this here. The implementation just forwards to name(). Returns : A scalar Args : on set, the new value (a scalar) =cut sub display_name { return shift->name(@_); } =head2 description Title : description Usage : $string = $obj->description() Function: A text string suitable for displaying to the user a description. This string is likely to have spaces, but should not have any newlines or formatting - just plain text. This forwards to definition(). The caveat is that the text will often be longer for ontology term definitions than the 255 characters stated in the definition in Bio::DescribableI. Returns : A scalar Args : on set, the new value (a scalar) =cut sub description { return shift->definition(@_); } ################################################################# # aliases or forwards to maintain backward compatibility ################################################################# =head1 Deprecated methods Used for looking up the methods that supersedes them. =cut sub each_dblink {shift->throw("use of each_dblink() is deprecated; use get_dbxrefs() instead")} sub add_dblinks {shift->throw("use of add_dblinks() is deprecated; use add_dbxref() instead")} *each_synonym = \&get_synonyms; *add_synonyms = \&add_synonym; 1; BioPerl-1.007002/Bio/Ontology/TermFactory.pm000444000766000024 1007413155576320 20655 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Ontology::TermFactory # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Ontology::TermFactory - Instantiates a new Bio::Ontology::TermI (or derived class) through a factory =head1 SYNOPSIS use Bio::Ontology::TermFactory; # the default type is Bio::Ontology::Term my $factory = Bio::Ontology::TermFactory->new( -type => 'Bio::Ontology::GOterm'); my $term = $factory->create_object(-name => 'peroxisome', -ontology => 'Gene Ontology', -identifier => 'GO:0005777'); =head1 DESCRIPTION This object will build L objects generically. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::TermFactory; use strict; use Bio::Root::Root; use base qw(Bio::Factory::ObjectFactory); =head2 new Title : new Usage : my $obj = Bio::Ontology::TermFactory->new(); Function: Builds a new Bio::Ontology::TermFactory object Returns : Bio::Ontology::TermFactory Args : -type => string, name of a Bio::Ontology::TermI derived class. The default is Bio::Ontology::Term. See L, L. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); # make sure this matches our requirements $self->interface("Bio::Ontology::TermI"); $self->type($self->type() || "Bio::Ontology::Term"); return $self; } =head2 create_object Title : create_object Usage : my $term = $factory->create_object(); Function: Instantiates new Bio::Ontology::TermI (or one of its child classes) This object allows us to genericize the instantiation of Term objects. Returns : Bio::Ontology::TermI compliant object The return type is configurable using new(-type =>"..."). Args : initialization parameters specific to the type of term object we want. Typically -name => $name -identifier => identifier for the term -ontology => ontology for the term See L. =cut 1; BioPerl-1.007002/Bio/Ontology/TermI.pm000444000766000024 2244613155576320 17444 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Ontology::Term # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Ontology::TermI - interface for ontology terms =head1 SYNOPSIS #get Bio::Ontology::TermI somehow. print $term->identifier(), "\n"; print $term->name(), "\n"; print $term->definition(), "\n"; print $term->is_obsolete(), "\n"; print $term->comment(), "\n"; foreach my $synonym ( $term->get_synonyms() ) { print $synonym, "\n"; } =head1 DESCRIPTION This is "dumb" interface for ontology terms providing basic methods (it provides no functionality related to graphs). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 APPENDIX The rest of the documentation details each of the object methods. =cut # Let the code begin... package Bio::Ontology::TermI; use strict; use base qw(Bio::Root::RootI); =head2 identifier Title : identifier Usage : $term->identifier( "0003947" ); or print $term->identifier(); Function: Set/get for the identifier of this Term. Returns : The identifier [scalar]. Args : The identifier [scalar] (optional). =cut sub identifier { shift->throw_not_implemented(); } # identifier =head2 name Title : name Usage : $term->name( "N-acetylgalactosaminyltransferase" ); or print $term->name(); Function: Set/get for the name of this Term. Returns : The name [scalar]. Args : The name [scalar] (optional). =cut sub name { shift->throw_not_implemented(); } # name =head2 definition Title : definition Usage : $term->definition( "Catalysis of ..." ); or print $term->definition(); Function: Set/get for the definition of this Term. Returns : The definition [scalar]. Args : The definition [scalar] (optional). =cut sub definition { shift->throw_not_implemented(); } # definition =head2 ontology Title : ontology Usage : $ont = $term->ontology(); or $term->ontology( $ont ); Function: Get the ontology this term is in. An implementation may not permit the value of this attribute to be changed once it is set, since that may have serious consequences (note that with the ontology in hand you can query for all related terms etc). Note for implementors: you will almost certainly have to take special precaution in order not to create cyclical references in memory. Returns : The ontology of this Term as a Bio::Ontology::OntologyI implementing object. Args : On set, the ontology of this Term as a Bio::Ontology::OntologyI implementing object or a string representing its name. See L. =cut sub ontology { shift->throw_not_implemented(); } # ontology =head2 version Title : version Usage : $term->version( "1.00" ); or print $term->version(); Function: Set/get for version information. Returns : The version [scalar]. Args : The version [scalar] (optional). =cut sub version { shift->throw_not_implemented(); } # version =head2 is_obsolete Title : is_obsolete Usage : $term->is_obsolete( 1 ); or if ( $term->is_obsolete() ) Function: Set/get for the obsoleteness of this Term. Returns : the obsoleteness [0 or 1]. Args : the obsoleteness [0 or 1] (optional). =cut sub is_obsolete { shift->throw_not_implemented(); } # is_obsolete =head2 comment Title : comment Usage : $term->comment( "Consider the term ..." ); or print $term->comment(); Function: Set/get for an arbitrary comment about this Term. Returns : A comment. Args : A comment (optional). =cut sub comment { shift->throw_not_implemented(); } # comment =head2 get_synonyms Title : get_synonyms Usage : @aliases = $term->get_synonyms(); Function: Returns a list of aliases of this Term. If an implementor of this interface permits modification of this array property, the class should define at least methods add_synonym() and remove_synonyms(), with obvious functionality. Returns : A list of aliases [array of [scalar]]. Args : =cut sub get_synonyms { shift->throw_not_implemented(); } # get_synonyms =head2 get_dblinks Title : get_dblinks() Usage : @ds = $term->get_dblinks(); Function: Returns a list of each dblink of this term. If an implementor of this interface permits modification of this array property, the class should define at least methods add_dblink() and remove_dblinks(), with obvious functionality. Returns : A list of dblinks [array of [scalars]]. Args : Note : This has been deprecated in favor of get_dbxrefs() =cut sub get_dblinks { shift->throw('get_dblinks() is deprecated, use get_dbxrefs() instead'); } # get_dblinks =head2 get_dbxrefs Title : get_dbxrefs() Usage : @ds = $term->get_dbxrefs(); Function: Returns a list of each link for this term. If an implementor of this interface permits modification of this array property, the class should define at least methods add_dbxref() and remove_dbxrefs(), with obvious functionality. Returns : A list of dblinks. This can return a mixed 'bag' of scalars and L instances, or specific subgroups can be returned based on passed arguments Args : implementation-specific =cut sub get_dbxrefs { shift->throw_not_implemented(); } # get_dblinks =head2 get_secondary_ids Title : get_secondary_ids Usage : @ids = $term->get_secondary_ids(); Function: Returns a list of secondary identifiers of this Term. Secondary identifiers mostly originate from merging terms, or possibly also from splitting terms. If an implementor of this interface permits modification of this array property, the class should define at least methods add_secondary_id() and remove_secondary_ids(), with obvious functionality. Returns : A list of secondary identifiers [array of [scalar]] Args : =cut sub get_secondary_ids { shift->throw_not_implemented(); } # get_secondary_ids =head1 Deprecated methods Used for looking up the methods that supersedes them. =cut =head2 category Title : category Usage : Function: This method is deprecated. Use ontology() instead. We provide an implementation here that preserves backwards compatibility, but if you do not have legacy code using it you should not be calling this method. Example : Returns : Args : =cut sub category { my $self = shift; $self->warn("TermI::category is deprecated and being phased out. ". "Use TermI::ontology instead."); # called in set mode? if(@_) { # yes; what is incompatible with ontology() is if we were given # a TermI object my $arg = shift; $arg = $arg->name() if ref($arg) && $arg->isa("Bio::Ontology::TermI"); return $self->ontology($arg,@_); } else { # No, called in get mode. This is always incompatible with ontology() # since category is supposed to return a TermI. my $ont = $self->ontology(); my $term; if(defined($ont)) { $term = Bio::Ontology::Term->new(-name => $ont->name(), -identifier =>$ont->identifier()); } return $term; } } # category 1; BioPerl-1.007002/Bio/Ontology/SimpleGOEngine000755000766000024 013155576320 20506 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm000444000766000024 1614613155576320 23605 0ustar00cjfieldsstaff000000000000# $Id: GraphAdaptor.pm 10525 2006-09-26 22:03:22Z sendu $ # # BioPerl Graph adaptor for Bio::Ontology::SimpleGOEngine # # Please direct questions and support issues to # # Cared for by Nat Goodman # # (c) Nathan Goodman natg@shore.net 2005 # (c) ISB, Institute for Systems Biology 2005 # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph adaptor for Bio::Ontology::SimpleGOEngine =head1 SYNOPSIS use Bio::Ontology::SimpleGOEngine::GraphAdaptor; my $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor; =head1 DESCRIPTION This is an adaptor to simplify use of versions of the standard CPAN Graph module (old is versions 0.2x; new is 0.5x and beyond) within Bio::Ontology::SimpleGOEngine. Prior versions of this module supported Graph version older than 0.5, however we are removing support for these older version post BioPerl 1.6.901. If you absolutely require an old version of Graph, please use an older version of BioPerl. This module implements only those Graph methods used by SimpleGOEngine. It is far from a complete compatibility layer! It also implements workarounds for certain performance problems in the current versions of Graph v0.5x. This class provides implementations for the required graph methods using the new version of Graph. In most cases, these are simple pass-throughs The methods implemented here or in the subclasses are listed below. In all cases, we implemented the Graph v0.5x interface. Consult the Graph v0.5x man page for details. add_vertex has_vertex add_edge has_edge vertices edges edges_at predecessors successors set_vertex_attribute get_vertex_attribute set_edge_attribute get_edge_attribute source_vertices sink_vertices =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Nat Goodman Email: natg at shore.net Address: Institute for Systems Biology 1441 N 34th St Seattle, WA 98103-8904 =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Ontology::SimpleGOEngine::GraphAdaptor; use Graph::Directed; use strict; use base qw(Bio::Root::Root); =head2 new Title : new Usage : $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor->new() Function: Creates a new graph Returns : Bio::Ontology::SimpleGOEngine::GraphAdaptor02 or Bio::Ontology::SimpleGOEngine::GraphAdaptor05 object, depending on which Graph version is available Args : none =cut sub new { my( $class ) = @_; $class = ref $class || $class; my $self= bless( {}, $class ); $self->{_graph}=Graph::Directed->new(); $self->{_vertex_attributes}={}; $self->{_edge_attributes}={}; return $self; } # Here are the main methods sub add_vertex { my $self=shift; $self->_graph->add_vertex(@_); } sub has_vertex { my $self=shift; $self->_graph->has_vertex(@_); } sub add_edge { my $self=shift; $self->_graph->add_edge(@_); } sub has_edge { my $self=shift; $self->_graph->has_edge(@_); } sub vertices { my $self=shift; $self->_graph->vertices(@_); } sub edges { my $self=shift; $self->_graph->edges(@_); } sub edges_at { my $self=shift; $self->_graph->edges_at(@_); } sub predecessors { my $self=shift; $self->_graph->predecessors(@_); } sub successors { my $self=shift; $self->_graph->successors(@_); } sub source_vertices { my $self=shift; $self->_graph->source_vertices(); } sub sink_vertices { my $self=shift; $self->_graph->sink_vertices(); } # The following methods workaround a performance problem in Graph v0.5x # when attributes are attached to the graph sub set_vertex_attribute { my($self,$v,$attribute,$value)=@_; $self->_vertex2attributes($v)->{$attribute}=$value; } sub get_vertex_attribute { my($self,$v,$attribute)=@_; $self->_vertex2attributes($v)->{$attribute}; } sub set_edge_attribute { my($self,$u,$v,$attribute,$value)=@_; $self->_edge2attributes($u,$v)->{$attribute}=$value; } sub get_edge_attribute { my($self,$u,$v,$attribute)=@_; $self->_edge2attributes($u,$v)->{$attribute}; } =head2 _graph Title : _graph Usage : $self->_graph(); Function: Internal method to access 'real' graph Returns : Graph::Directed object Args : none =cut sub _graph {$_[0]->{_graph}; } =head2 _vertex_attributes Title : _vertex_attributes Usage : $self->vertex_attributes(); Function: Internal method to access HASH used to store vertex attributes Returns : Graph::Directed object Args : none =cut sub _vertex_attributes {$_[0]->{_vertex_attributes}; } =head2 _edge_attributes Title : _edge_attributes Usage : $self->edge_attributes(); Function: Internal method to access HASH used to store edge attributes Returns : Graph::Directed object Args : none =cut sub _edge_attributes {$_[0]->{_edge_attributes}; } =head2 _vertex2attributes Title : _vertex2attributes Usage : $value=$graph->_vertex2attributes($v_->{ATTRIBUTE}; $graph->_vertex2attributes($v)->{ATTRIBUTE}=$value; Function: Internal method to access attributes for a specific vertex Returns : HASH Args : none =cut sub _vertex2attributes { my($self,$vertex)=@_; $self->_vertex_attributes->{$vertex} or $self->_vertex_attributes->{$vertex}={}; } =head2 _edge2attributes Title : _edge2attributes Usage : $value=$graph->_edge2attributes($u,$v)->{ATTRIBUTE}; $graph->_edge2attributes($u,$v)->{ATTRIBUTE}=$value; Function: Internal method to access HASH used to store edge attributes Returns : HASH Args : none =cut sub _edge2attributes { my($self,$u,$v)=@_; $self->_edge_attributes->{$u,$v} or $self->_edge_attributes->{$u,$v}={}; } 1; BioPerl-1.007002/Bio/OntologyIO000755000766000024 013155576320 16131 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/OntologyIO/InterProParser.pm000444000766000024 1603513155576320 21570 0ustar00cjfieldsstaff000000000000# # BioPerl module for InterProParser # # Please direct questions and support issues to # # Cared for by Peter Dimitrov # # Copyright Peter Dimitrov # (c) Peter Dimitrov, dimitrov@gnf.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::OntologyIO::InterProParser - Parser for InterPro xml files. =head1 SYNOPSIS # don't use this module directly - use Bio::OntologyIO with instead my $ipp = Bio::OntologyIO->new( -format => 'interpro', -file => 't/data/interpro.xml', -ontology_engine => 'simple' ); =head1 DESCRIPTION Use InterProParser to parse InterPro files in xml format. Typical use is the interpro.xml file published by EBI. The xml records should follow the format described in interpro.dtd, although the dtd file is not needed, and the XML file will not be validated against it. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Peter Dimitrov Email dimitrov@gnf.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::OntologyIO::InterProParser; use strict; #use Carp; use XML::Parser::PerlSAX; use Bio::Ontology::SimpleOntologyEngine; use Bio::Ontology::TermFactory; use Bio::OntologyIO::Handlers::InterProHandler; use base qw(Bio::OntologyIO); =head2 new Title : new Usage : Function: Initializes objects needed for parsing. Example : $ipp = Bio::OntologyIO::InterProParser->new( -file => 't/data/interpro.xml', -ontology_engine => 'simple' ) Returns : Object of class Bio::OntologyIO::InterProParser. Args : -file - file name -ontology_engine - type of ontology engine. Should satisfy the OntologyEngine interface requirements. Currently the only option is 'simple'. In the future Graph.pm based engine will be added to the choices. =cut # in reality we let OntologyIO handle the first pass initialization # and instead override _initialize(). sub _initialize{ my $self = shift; $self->SUPER::_initialize(@_); my ($eng,$eng_type,$name) = $self->_rearrange([qw(ENGINE ONTOLOGY_ENGINE ONTOLOGY_NAME) ], @_); my $ip_h = Bio::OntologyIO::Handlers::InterProHandler->new( -ontology_name => $name); if(! $eng) { $eng_type = 'simple' unless $eng_type; if(lc($eng_type) eq 'simple') { $eng = Bio::Ontology::SimpleOntologyEngine->new(); } else { $self->throw("ontology engine type '$eng_type' ". "not implemented yet"); } } if($eng->isa("Bio::Ontology::OntologyI")) { $ip_h->ontology($eng); $eng = $eng->engine() if $eng->can('engine'); } $self->{_ontology_engine} = $eng; $ip_h->ontology_engine($eng); $self->{_parser} = XML::Parser::PerlSAX->new( Handler => $ip_h ); $self->{_interpro_handler} = $ip_h; # default term object factory $self->term_factory(Bio::Ontology::TermFactory->new( -type => "Bio::Ontology::InterProTerm")) unless $self->term_factory(); $ip_h->term_factory($self->term_factory()); } =head2 parse Title : parse Usage : Function: Performs the actual parsing. Example : $ipp->parse(); Returns : Args : =cut sub parse{ my $self = shift; my $ret; if ($self->file()) { $ret = $self->{_parser}->parse( Source => { SystemId => $self->file() } ); } elsif ($self->_fh()) { $ret = $self->{_parser}->parse( Source => { ByteStream => $self->_fh() } ); } else { $ret = undef; $self->throw("Only filenames and filehandles are understood here.\n"); } $self->_is_parsed(1); return $ret; } =head2 next_ontology Title : next_ontology Usage : $ipp->next_ontology() Function: Parses the input file and returns the next InterPro ontology available. Usually there will be only one ontology returned from an InterPro XML input. Example : $ipp->next_ontology(); Returns : Returns the ontology as a Bio::Ontology::OntologyEngineI compliant object. Args : See L. =cut sub next_ontology{ my $self = shift; $self->parse() unless $self->_is_parsed(); # there is only one ontology in an InterPro source file if(exists($self->{'_ontology_engine'})) { my $ont = $self->{_interpro_handler}->ontology(); delete $self->{_ontology_engine}; return $ont; } return; } =head2 _is_parsed Title : _is_parsed Usage : $obj->_is_parsed($newval) Function: Example : Returns : value of _is_parsed (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub _is_parsed{ my $self = shift; return $self->{'_is_parsed'} = shift if @_; return $self->{'_is_parsed'}; } =head2 secondary_accessions_map Title : secondary_accessions_map Usage : $obj->secondary_accessions_map() Function: This method is merely for convenience, and one should normally use the InterProTerm secondary_ids method to access the secondary accessions. Example : $map = $interpro_parser->secondary_accessions_map; Returns : Reference to a hash that maps InterPro identifier to an array reference of secondary accessions following the InterPro xml schema. Args : Empty hash reference =cut sub secondary_accessions_map{ my ($self) = @_; return $self->{_interpro_handler}->{secondary_accessions_map}; } 1; BioPerl-1.007002/Bio/OntologyIO/dagflat.pm000444000766000024 6271413155576320 20260 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::OntologyIO::dagflat # # Please direct questions and support issues to # # Cared for by Hilmar Lapp, hlapp at gmx.net # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) Hilmar Lapp, hlapp at gmx.net, 2003. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::OntologyIO::dagflat - a base class parser for GO flat-file type formats =head1 SYNOPSIS use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO # e.g., the GO parser is a simple extension of this class my $parser = Bio::OntologyIO->new ( -format => "go", -defs_file => "/home/czmasek/GO/GO.defs", -files => ["/home/czmasek/GO/component.ontology", "/home/czmasek/GO/function.ontology", "/home/czmasek/GO/process.ontology"] ); my $go_ontology = $parser->next_ontology(); my $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" ); my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" ); my $RELATED_TO = Bio::Ontology::RelationshipType->get_instance( "RELATED_TO" ); =head1 DESCRIPTION Needs Graph.pm from CPAN. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head2 CONTRIBUTOR Hilmar Lapp, hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::OntologyIO::dagflat; use strict; use Bio::Root::IO; use Bio::Ontology::OBOEngine; use Bio::Ontology::Ontology; use Bio::Ontology::OntologyStore; use Bio::Ontology::TermFactory; use Bio::Annotation::DBLink; use constant TRUE => 1; use constant FALSE => 0; use base qw(Bio::OntologyIO); =head2 new Title : new Usage : $parser = Bio::OntologyIO->new( -format => "go", -defs_file => "/path/to/GO.defs", -files => ["/path/to/component.ontology", "/path/to/function.ontology", "/path/to/process.ontology"] ); Function: Creates a new dagflat parser. Returns : A new dagflat parser object, implementing Bio::OntologyIO. Args : -defs_file => the name of the file holding the term definitions -files => a single ontology flat file holding the term relationships, or an array ref holding the file names (for GO, there will usually be 3 files: component.ontology, function.ontology, process.ontology) -file => if there is only a single flat file, it may also be specified via the -file parameter -ontology_name => the name of the ontology; if not specified the parser will auto-discover it by using the term that starts with a $, and converting underscores to spaces -engine => the Bio::Ontology::OntologyEngineI object to be reused (will be created otherwise); note that every Bio::Ontology::OntologyI will qualify as well since that one inherits from the former. See L. =cut # in reality, we let OntologyIO::new do the instantiation, and override # _initialize for all initialization work sub _initialize { my ($self, %arg) = @_; my ( $defs_file_name,$files,$defs_url,$url,$name,$eng ) = $self->_rearrange([qw( DEFS_FILE FILES DEFS_URL URL ONTOLOGY_NAME ENGINE) ], %arg ); delete($arg{-url}); #b/c GO has 3 files... $self->SUPER::_initialize( %arg ); $self->_done( FALSE ); $self->_not_first_record( FALSE ); $self->_term( "" ); delete $self->{'_ontologies'}; # ontology engine (and possibly name if it's an OntologyI) $eng = Bio::Ontology::OBOEngine->new() unless $eng; if($eng->isa("Bio::Ontology::OntologyI")) { $self->ontology_name($eng->name()); $eng = $eng->engine() if $eng->can('engine'); } $self->_ont_engine($eng); # flat files to parse if(defined($defs_file_name) && defined($defs_url)){ $self->throw('cannot provide both -defs_file and -defs_url'); } else { defined($defs_file_name) && $self->defs_file( $defs_file_name ); defined($defs_url) && $self->defs_url( $defs_url ); } if(defined($files) && defined($url)){ } elsif(defined($files)){ $self->{_flat_files} = $files ? ref($files) ? $files : [$files] : []; } elsif(defined($url)){ $self->url($url); } # ontology name (overrides implicit one through OntologyI engine) $self->ontology_name($name) if $name; } # _initialize =head2 ontology_name Title : ontology_name Usage : $obj->ontology_name($newval) Function: Get/set the name of the ontology parsed by this module. Example : Returns : value of ontology_name (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub ontology_name{ my $self = shift; return $self->{'ontology_name'} = shift if @_; return $self->{'ontology_name'}; } =head2 parse Title : parse() Usage : $parser->parse(); Function: Parses the files set with "new" or with methods defs_file and _flat_files. Normally you should not need to call this method as it will be called automatically upon the first call to next_ontology(). Returns : [Bio::Ontology::OntologyEngineI] Args : =cut sub parse { my $self = shift; #warn "PARSING"; # setup the default term factory if not done by anyone yet $self->term_factory(Bio::Ontology::TermFactory->new( -type => "Bio::Ontology::Term")) unless $self->term_factory(); # create the ontology object itself my $ont = Bio::Ontology::Ontology->new(-name => $self->ontology_name(), -engine => $self->_ont_engine()); # parse definitions while( my $term = $self->_next_term() ) { $self->_add_term( $term, $ont ); } # set up the ontology of the relationship types foreach ($self->_part_of_relationship(), $self->_is_a_relationship(), $self->_related_to_relationship()) { $_->ontology($ont); } # pre-seed the IO system with the first flat file if -file wasn't provided if(! $self->_fh) { if($self->url){ if(ref($self->url) eq 'ARRAY'){ #warn "BA"; foreach my $url (@{ $self->url }){ #warn $url; #warn $ont; #warn scalar($ont->get_all_terms()); $self->_initialize_io(-url => $url); $self->_parse_flat_file($ont); } $self->close(); } else { $self->_initialize_io(-url => $self->url); } } elsif($self->_flat_files){ $self->_initialize_io(-file => shift(@{$self->_flat_files()})); } } while($self->_fh) { $self->_parse_flat_file($ont); # advance to next flat file if more are available if(@{$self->_flat_files()}) { $self->close(); $self->_initialize_io(-file => shift(@{$self->_flat_files()})); } else { last; # nothing else to parse so terminate the loop } } $self->_add_ontology($ont); # not needed anywhere, only because of backward compatibility return $self->_ont_engine(); } # parse =head2 next_ontology Title : next_ontology Usage : Function: Get the next available ontology from the parser. This is the method prescribed by Bio::OntologyIO. Example : Returns : An object implementing Bio::Ontology::OntologyI, and undef if there is no more ontology in the input. Args : =cut sub next_ontology { my $self = shift; # parse if not done already $self->parse() unless exists($self->{'_ontologies'}); # return next available ontology if(exists($self->{'_ontologies'})){ my $ont = shift (@{$self->{'_ontologies'}}); if($ont){ my $store = Bio::Ontology::OntologyStore->new(); $store->register_ontology($ont); return $ont; } } return; } =head2 defs_file Title : defs_file Usage : $parser->defs_file( "GO.defs" ); Function: Set/get for the term definitions filename. Returns : The term definitions file name [string]. Args : On set, the term definitions file name [string] (optional). =cut sub defs_file { my $self = shift; if ( @_ ) { my $f = shift; $self->{ "_defs_file_name" } = $f; $self->_defs_io->close() if $self->_defs_io(); if(defined($f)) { $self->_defs_io( Bio::Root::IO->new( -input => $f ) ); } } return $self->{ "_defs_file_name" }; } # defs_file sub defs_url { my $self = shift; my $val = shift; if(defined($val)){ $self->{'_defs_url'} = $val; $self->_defs_io->close() if $self->_defs_io(); $self->_defs_io( Bio::Root::IO->new( -url => $val ) ); } return $self->{'_defs_url'}; } sub url { my $self = shift; my $val = shift; if(defined($val)){ $self->{'_url'} = $val; } return $self->{'_url'}; } =head2 close Title : close Usage : Function: Closes this ontology stream and associated file handles. Clients should call this method especially when they write ontologies. We need to override this here in order to close the file handle for the term definitions file. Example : Returns : none Args : none =cut sub close{ my $self = shift; # first call the inherited implementation $self->SUPER::close(); # then close the defs file io (if there is one) $self->_defs_io->close() if $self->_defs_io(); } =head2 _flat_files Title : _flat_files Usage : $files_to_parse = $parser->_flat_files(); Function: Get the array of ontology flat files that need to be parsed. Note that this array will decrease in elements over the parsing process. Therefore, it\'s value outside of this module will be limited. Also, be careful not to alter the array unless you know what you are doing. Returns : a reference to an array of zero or more strings Args : none =cut sub _flat_files { my $self = shift; $self->{_flat_files} = [] unless exists($self->{_flat_files}); return $self->{_flat_files}; } # INTERNAL METHODS # ---------------- =head2 _defs_io Title : _defs_io Usage : $obj->_defs_io($newval) Function: Get/set the Bio::Root::IO instance representing the definition file, if provided (see defs_file()). Example : Returns : value of _defs_io (a Bio::Root::IO object) Args : on set, new value (a Bio::Root::IO object or undef, optional) =cut sub _defs_io{ my $self = shift; return $self->{'_defs_io'} = shift if @_; return $self->{'_defs_io'}; } sub _add_ontology { my $self = shift; $self->{'_ontologies'} = [] unless exists($self->{'_ontologies'}); foreach my $ont (@_) { $self->throw(ref($ont)." does not implement Bio::Ontology::OntologyI") unless ref($ont) && $ont->isa("Bio::Ontology::OntologyI"); # the ontology name may have been auto-discovered while parsing # the file $ont->name($self->ontology_name) unless $ont->name(); push(@{$self->{'_ontologies'}}, $ont); } } # This simply delegates. See SimpleGOEngine. sub _add_term { my ( $self, $term, $ont ) = @_; $term->ontology($ont) if $ont && (! $term->ontology); $self->_ont_engine()->add_term( $term ); } # _add_term # This simply delegates. See SimpleGOEngine sub _part_of_relationship { my $self = shift; return $self->_ont_engine()->part_of_relationship(@_); } # _part_of_relationship # This simply delegates. See SimpleGOEngine sub _is_a_relationship { my $self = shift; return $self->_ont_engine()->is_a_relationship(@_); } # _is_a_relationship # This simply delegates. See SimpleGOEngine sub _related_to_relationship { my $self = shift; return $self->_ont_engine()->related_to_relationship(@_); } # _is_a_relationship # This simply delegates. See SimpleGOEngine sub _add_relationship { my ( $self, $parent, $child, $type, $ont ) = @_; # note the triple terminology (subject,predicate,object) corresponds to # (child,type,parent) $self->_ont_engine()->add_relationship( $child, $type, $parent, $ont ); } # _add_relationship # This simply delegates. See SimpleGOEngine sub _has_term { my $self = shift; return $self->_ont_engine()->has_term( @_ ); } # _add_term # This parses the relationships files sub _parse_flat_file { my $self = shift; my $ont = shift; my @stack = (); my $prev_spaces = -1; my $prev_term = ""; while ( my $line = $self->_readline() ) { if ( $line =~ /^!/ ) { next; } # split into term specifications my @termspecs = split(/ (?=[%<])/, $line); # the first element is whitespace only shift(@termspecs) if $termspecs[0] =~ /^\s*$/; # parse out the focus term my $current_term = $self->_get_first_termid( $termspecs[0] ); my @syns = $self->_get_synonyms( $termspecs[0] ); my @sec_go_ids = $self->_get_secondary_termids( $termspecs[0] ); my @cross = $self->_get_db_cross_refs( $termspecs[0] ); my @cross_refs; foreach my $cross_ref (@cross) { $cross_ref eq $current_term && next; push(@cross_refs, $cross_ref); } # parse out the parents of the focus term shift(@termspecs); my @isa_parents = (); my @partof_parents = (); foreach my $parent (@termspecs) { if (index($parent, "%") == 0) { push(@isa_parents, $self->_get_first_termid($parent)); } elsif (index($parent, "<") == 0) { push(@partof_parents, $self->_get_first_termid($parent)); } else { $self->warn("unhandled relationship type in '".$parent."'"); } } if ( ! $self->_has_term( $current_term ) ) { my $term =$self->_create_ont_entry($self->_get_name($line, $current_term), $current_term ); $self->_add_term( $term, $ont ); } my $current_term_object = $self->_ont_engine()->get_terms( $current_term ); my $anno = $self->_to_annotation(\@cross_refs); $current_term_object->add_dbxref(-dbxrefs => $anno); $current_term_object->add_secondary_id( @sec_go_ids ); $current_term_object->add_synonym( @syns ); unless ( $line =~ /^\$/ ) { $current_term_object->ontology( $ont ); } foreach my $parent ( @isa_parents ) { if ( ! $self->_has_term( $parent ) ) { my $term = $self->_create_ont_entry($self->_get_name($line, $parent), $parent ); $self->_add_term( $term, $ont ); } $self->_add_relationship( $parent, $current_term, $self->_is_a_relationship(), $ont); } foreach my $parent ( @partof_parents ) { if ( ! $self->_has_term( $parent ) ) { my $term = $self->_create_ont_entry($self->_get_name($line, $parent), $parent ); $self->_add_term( $term, $ont ); } $self->_add_relationship( $parent, $current_term, $self->_part_of_relationship(), $ont); } my $current_spaces = $self->_count_spaces( $line ); if ( $current_spaces != $prev_spaces ) { if ( $current_spaces == $prev_spaces + 1 ) { push( @stack, $prev_term ); } elsif ( $current_spaces < $prev_spaces ) { my $n = $prev_spaces - $current_spaces; for ( my $i = 0; $i < $n; ++$i ) { pop( @stack ); } } else { $self->throw( "format error (file ".$self->file.")" ); } } my $parent = $stack[ @stack - 1 ]; # add a relationship if the line isn\'t the one with the root term # of the ontology (which is also the name of the ontology) if ( index($line,'$') != 0 ) { #adding @reltype@ syntax if ( $line !~ /^\s*([<%~]|\@\w+?\@)/ ) { $self->throw( "format error (file ".$self->file.") offending line:\n$line" ); } my($relstring) = $line =~ /^\s*([<%~]|\@[^\@]+?\@)/; my $reltype; if ($relstring eq '<') { $reltype = $self->_part_of_relationship; } elsif ($relstring eq '%') { $reltype = $self->_is_a_relationship; } elsif ($relstring eq '~') { $reltype = $self->_related_to_relationship; } else { $relstring =~ s/\@//g; if ($self->_ont_engine->get_relationship_type($relstring)) { $reltype = $self->_ont_engine->get_relationship_type($relstring); } else { $self->_ont_engine->add_relationship_type($relstring, $ont); $reltype = $self->_ont_engine->get_relationship_type($relstring); } } #my $reltype = ($line =~ /^\s*_part_of_relationship() : #$self->_is_a_relationship(); $self->_add_relationship( $parent, $current_term, $reltype, $ont); } $prev_spaces = $current_spaces; $prev_term = $current_term; } return $ont; } # _parse_relationships_file # Parses the 1st term id number out of line. sub _get_first_termid { my ( $self, $line ) = @_; if ( $line =~ /;\s*([A-Z_]{1,8}:\d{1,})/ ) { # if ( $line =~ /;\s*(\w+:\w+)/ ) { return $1; } else { $self->throw( "format error: no term id in line \"$line\"" ); } } # _get_first_termid # Parses the name out of line. sub _get_name { my ( $self, $line, $termid ) = @_; if ( $line =~ /([^;<%~]+);\s*$termid/ ) { my $name = $1; # remove trailing and leading whitespace $name =~ s/\s+$//; $name =~ s/^\s+//; $name =~ s/\@.+?\@//; # remove leading dollar character; also we default the name of the # ontology to this name unless it is preset to something else if(index($name,'$') == 0) { $name = substr($name,1); # replace underscores by spaces for setting the ontology name $self->ontology_name(join(" ",split(/_/,$name))) unless $self->ontology_name(); } return $name; } else { return; } } # _get_name # Parses the synonyms out of line. sub _get_synonyms { my ( $self, $line ) = @_; my @synonyms = (); while ( $line =~ /synonym\s*:\s*([^;<%~]+)/g ) { my $syn = $1; $syn =~ s/\s+$//; $syn =~ s/^\s+//; push( @synonyms, $syn ); } return @synonyms; } # _get_synonyms # Parses the db cross refs out of line. sub _get_db_cross_refs { my ( $self, $line ) = @_; my @refs = (); while ( $line =~ /;([^;<%~:]+:[^;<%~:]+)/g ) { my $ref = $1; if ( $ref =~ /synonym/ || $ref =~ /[A-Z]{1,8}:\d{3,}/ ) { next; } $ref =~ s/\s+$//; $ref =~ s/^\s+//; $ref = $self->unescape( $ref ); push( @refs, $ref ) if defined $ref; } return @refs; } # Parses the secondary go ids out of a line sub _get_secondary_termids { my ( $self, $line ) = @_; my @secs = (); # while ( $line =~ /,\s*([A-Z]{1,8}:\d{3,})/g ) { while ( $line =~ /,\s*(\w+:\w+)/g ) { my $sec = $1; push( @secs, $sec ); } return @secs; } # _get_secondary_termids # Counts the spaces at the beginning of a line in the relationships files sub _count_spaces { my ( $self, $line ) = @_; if ( $line =~ /^(\s+)/ ) { return length( $1 ); } else { return 0; } } # _count_spaces # "next" method for parsing the defintions file sub _next_term { my ( $self ) = @_; if ( ($self->_done() == TRUE) || (! $self->_defs_io())) { return; } my $line = ""; my $termid = ""; my $next_term = $self->_term(); my $def = ""; my $comment = ""; my @def_refs = (); my $isobsolete; while( $line = ( $self->_defs_io->_readline() ) ) { if ( $line !~ /\S/ || $line =~ /^\s*!/ ) { next; } elsif ( $line =~ /^\s*term:\s*(.+)/ ) { $self->_term( $1 ); last if $self->_not_first_record(); $next_term = $1; $self->_not_first_record( TRUE ); } elsif ( $line =~ /^\s*[a-z]{0,8}id:\s*(.+)/ ) { $termid = $1; } elsif ( $line =~ /^\s*definition:\s*(.+)/ ) { $def = $self->unescape($1); $isobsolete = 1 if index($def,"OBSOLETE") == 0; } elsif ( $line =~ /^\s*definition_reference:\s*(.+)/ ) { push( @def_refs, $self->unescape($1) ); } elsif ( $line =~ /^\s*comment:\s*(.+)/ ) { $comment = $self->unescape($1); } } $self->_done( TRUE ) unless $line; # we'll come back until done return $self->_create_ont_entry( $next_term, $termid, $def, $comment, \@def_refs, $isobsolete); } # _next_term # Holds the GO engine to be parsed into sub _ont_engine { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_ont_engine" } = $value; } return $self->{ "_ont_engine" }; } # _ont_engine # Used to create ontology terms. # Arguments: name, id sub _create_ont_entry { my ( $self, $name, $termid, $def, $cmt, $dbxrefs, $obsolete ) = @_; if((!defined($obsolete)) && (index(lc($name),"obsolete") == 0)) { $obsolete = 1; } my $anno = $self->_to_annotation($dbxrefs); my $term = $self->term_factory->create_object(-name => $name, -identifier => $termid, -definition => $def, -comment => $cmt, -dbxrefs => $anno, -is_obsolete => $obsolete); return $term; } # _create_ont_entry # Holds whether first record or not sub _not_first_record { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_not_first_record" } = $value; } return $self->{ "_not_first_record" }; } # _not_first_record # Holds whether done or not sub _done { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_done" } = $value; } return $self->{ "_done" }; } # _done # Holds a term. sub _term { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_term" } = $value; } return $self->{ "_term" }; } # _term # convert simple strings to Bio::Annotation::DBLinks sub _to_annotation { my ($self , $links) = @_; return unless $links; my @dbxrefs; for my $string (@{$links}) { my ($db, $id) = split(':',$string); push @dbxrefs, Bio::Annotation::DBLink->new(-database => $db, -primary_id => $id); } return \@dbxrefs; } 1; BioPerl-1.007002/Bio/OntologyIO/goflat.pm000444000766000024 1245313155576320 20125 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::OntologyIO::goflat # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::OntologyIO::goflat - a parser for the Gene Ontology flat-file format =head1 SYNOPSIS use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO my $parser = Bio::OntologyIO->new ( -format => "go", -defs_file => "/home/czmasek/GO/GO.defs", -files => ["/home/czmasek/GO/component.ontology", "/home/czmasek/GO/function.ontology", "/home/czmasek/GO/process.ontology"] ); my $go_ontology = $parser->next_ontology(); my $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" ); my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" ); =head1 DESCRIPTION Needs Graph.pm from CPAN. This is essentially a very thin derivation of the dagflat parser. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head2 CONTRIBUTOR Hilmar Lapp, hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::OntologyIO::goflat; use strict; use Bio::Ontology::TermFactory; use constant TRUE => 1; use constant FALSE => 0; use base qw(Bio::OntologyIO::dagflat); =head2 new Title : new Usage : $parser = Bio::OntologyIO->new( -format => "go", -defs_file => "/path/to/GO.defs", -files => ["/path/to/component.ontology", "/path/to/function.ontology", "/path/to/process.ontology"] ); Function: Creates a new goflat parser. Returns : A new goflat parser object, implementing Bio::OntologyIO. Args : -defs_file => the name of the file holding the term definitions -files => a single ontology flat file holding the term relationships, or an array ref holding the file names (for GO, there will usually be 3 files: component.ontology, function.ontology, process.ontology) -file => if there is only a single flat file, it may also be specified via the -file parameter -ontology_name => the name of the ontology; if not specified the parser will auto-discover it by using the term that starts with a $, and converting underscores to spaces -engine => the Bio::Ontology::OntologyEngineI object to be reused (will be created otherwise); note that every Bio::Ontology::OntologyI will qualify as well since that one inherits from the former. See L. =cut # in reality, we let OntologyIO::new do the instantiation, and override # _initialize for all initialization work sub _initialize { my ($self, @args) = @_; $self->SUPER::_initialize( @args ); # default term object factory $self->term_factory(Bio::Ontology::TermFactory->new( -type => "Bio::Ontology::GOterm")) unless $self->term_factory(); } # _initialize 1; BioPerl-1.007002/Bio/OntologyIO/obo.pm000444000766000024 5747713155576320 17447 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::OntologyIO::obo # # Please direct questions and support issues to # # Cared for by Sohel Merchant, s-merchant at northwestern.edu # # Copyright Sohel Merchant # # You may distribute this module under the same terms as perl itself =head1 NAME Bio::OntologyIO::obo - parser for OBO flat-file format =head1 SYNOPSIS use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO my $parser = Bio::OntologyIO->new ( -format => "obo", -file => "gene_ontology.obo"); while(my $ont = $parser->next_ontology()) { print "read ontology ",$ont->name()," with ", scalar($ont->get_root_terms), " root terms, and ", scalar($ont->get_all_terms), " total terms, and ", scalar($ont->get_leaf_terms), " leaf terms\n"; } =head1 DESCRIPTION Parser for OBO flat-file format. 'obo' example: format-version: 1.2 ontology: so/dev/externalDerived property_value: owl:versionInfo "$Revision: 80 $" xsd:string default-namespace: SO [Term] id: SO_0000343 name: match def: "A region of sequence, aligned to another sequence." [] [Term] id: SO_0000039 name: match_part def: "A part of a match." [] is_a: SO_0000343 Specification: L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Sohel Merchant Email: s-merchant@northwestern.edu Address: Northwestern University Center for Genetic Medicine (CGM), dictyBase Suite 1206, 676 St. Clair st Chicago IL 60611 =head2 CONTRIBUTOR Hilmar Lapp, hlapp at gmx.net Chris Mungall, cjm at fruitfly.org Brian Osborne, briano@bioteam.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::OntologyIO::obo; use strict; use Bio::Root::IO; use Bio::Ontology::OBOEngine; use Bio::Ontology::Ontology; use Bio::Ontology::OntologyStore; use Bio::Ontology::TermFactory; use Bio::Annotation::Collection; use Text::Balanced qw(extract_quotelike extract_bracketed); use constant TRUE => 1; use constant FALSE => 0; use base qw(Bio::OntologyIO); =head2 new Title : new Usage : $parser = Bio::OntologyIO->new( -format => "obo", -file => "gene_ontology.obo"); Function: Creates a new dagflat parser. Returns : A new dagflat parser object, implementing Bio::OntologyIO. Args : -file => a single ontology flat file holding the terms, descriptions and relationships -ontology_name => the name of the ontology; if not specified the parser will assign the name of the ontology as the default-namespace header value from the OBO file. -engine => the Bio::Ontology::OntologyEngineI object to be reused (will be created otherwise); note that every Bio::Ontology::OntologyI will qualify as well since that one inherits from the former. See L. =cut # Let OntologyIO::new() do the instantiation, and override # _initialize for all initialization work sub _initialize { my ( $self, %arg ) = @_; my ( $file, $name, $eng ) = $self->_rearrange( [ qw( FILE ONTOLOGY_NAME ENGINE) ], %arg ); $self->SUPER::_initialize(%arg); delete $self->{'_ontologies'}; # Ontology engine (and possibly name if it's an OntologyI) $eng = Bio::Ontology::OBOEngine->new() unless $eng; if ( $eng->isa("Bio::Ontology::OntologyI") ) { $self->ontology_name( $eng->name() ); $eng = $eng->engine() if $eng->can('engine'); } $self->_ont_engine($eng); $self->ontology_name($name) if $name; } =head2 ontology_name Title : ontology_name Usage : $obj->ontology_name($newval) Function: Get/set the name of the ontology parsed by this module. Example : Returns : value of ontology_name (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub ontology_name { my $self = shift; return $self->{'ontology_name'} = shift if @_; return $self->{'ontology_name'}; } =head2 parse Title : parse() Usage : $parser->parse(); Function: Parses the files set with "new" or with methods defs_file and _flat_files. Normally you should not need to call this method as it will be called automatically upon the first call to next_ontology(). Returns : Bio::Ontology::OntologyEngineI Args : =cut sub parse { my $self = shift; # Setup the default term factory if not done by anyone yet $self->term_factory(Bio::Ontology::TermFactory->new( -type => "Bio::Ontology::OBOterm" ) ) unless $self->term_factory(); # Parse the file header my $annotations_collection = $self->_header(); # Create the default ontology object itself my $ont = Bio::Ontology::Ontology->new( -name => $self->ontology_name(), -engine => $self->_ont_engine() ); # Assign the file headers $ont->annotation($annotations_collection); # Set up the ontology of the relationship types for ( $self->_part_of_relationship(), $self->_is_a_relationship(), $self->_related_to_relationship(), $self->_regulates_relationship(), $self->_positively_regulates_relationship(), $self->_negatively_regulates_relationship(), ) { $_->ontology($ont); } $self->_add_ontology($ont); # Adding new terms while ( my $term = $self->_next_term() ) { # Check if the terms has a valid ID and NAME otherwise ignore the term if ( !$term->identifier() || !$term->name() ) { $self->throw( "OBO File Format Error on line " . $self->{'_current_line_no'} . "\nThe term does not have a id/name tag. This term will be ignored." ); next; } my $new_ontology_flag = 1; my $ontologies_array_ref = $self->{'_ontologies'}; for my $ontology ( @$ontologies_array_ref ) { my ($oname, $t_ns) = ( $ontology->name, $term->namespace ); next unless ( defined($oname) && defined($t_ns) ); if ( $oname eq $t_ns ) { # No need to create new ontology $new_ontology_flag = 0; $ont = $ontology; } } if ( $new_ontology_flag && $term->namespace ) { my $new_ont = Bio::Ontology::Ontology->new( -name => $term->namespace, -engine => $self->_ont_engine ); $new_ont->annotation($annotations_collection); $self->_add_ontology($new_ont); $ont = $new_ont; } $self->_add_term( $term, $ont ); # Adding the IS_A relationship for my $parent_term ( @{$self->{'_isa_parents'}} ) { # Check if parent exists, if not then add the term to the graph. if ( ! $self->_has_term($parent_term) ) { $self->_add_term( $parent_term, $ont ); # ! } $self->_add_relationship( $parent_term, $term, $self->_is_a_relationship(), $ont ); } # Adding the other relationships like part_of, related_to, develops_from for my $relationship ( keys %{$self->{'_relationships'}} ) { my $reltype; # Check if relationship exists, if not add it if ( $self->_ont_engine->get_relationship_type($relationship) ) { $reltype = $self->_ont_engine->get_relationship_type($relationship); } else { $self->_ont_engine->add_relationship_type( $relationship, $ont ); $reltype = $self->_ont_engine->get_relationship_type($relationship); } # Check if the id already exists in the graph for my $id ( @{$self->{'_relationships'}->{$relationship}} ) { my $parent_term = $self->_create_term_object(); $parent_term->identifier($id); $parent_term->ontology($ont); if ( ! $self->_has_term($parent_term) ) { $self->_add_term( $parent_term, $ont ); } $self->_add_relationship( $parent_term, $term, $reltype, $ont ); } } } return $self->_ont_engine(); } =head2 next_ontology Title : next_ontology Usage : Function: Get the next available ontology from the parser. This is the method prescribed by Bio::OntologyIO. Example : Returns : An object implementing Bio::Ontology::OntologyI, and nothing if there is no more ontology in the input. Args : =cut sub next_ontology { my $self = shift; # Parse if not done already $self->parse() unless exists( $self->{'_ontologies'} ); # Return next available ontology if ( exists( $self->{'_ontologies'} ) ) { my $ont = shift( @{ $self->{'_ontologies'} } ); if ($ont) { my $store = Bio::Ontology::OntologyStore->new(); $store->register_ontology($ont); return $ont; } } return; } =head2 close Title : close Usage : Function: Closes this ontology stream and associated file handles. Clients should call this method especially when they write ontologies. We need to override this here in order to close the file handle for the term definitions file. Example : Returns : none Args : none =cut sub close { my $self = shift; # first call the inherited implementation $self->SUPER::close(); } # INTERNAL METHODS sub _add_ontology { my $self = shift; $self->{'_ontologies'} = [] unless exists( $self->{'_ontologies'} ); for my $ont (@_) { $self->throw( ref($ont) . " does not implement Bio::Ontology::OntologyI" ) unless ref($ont) && $ont->isa("Bio::Ontology::OntologyI"); # The ontology name may have been auto-discovered while parsing # the file $ont->name( $self->ontology_name ) unless $ont->name(); push( @{ $self->{'_ontologies'} }, $ont ); } } # This simply delegates. See Ontology::OBOEngine::add_term. sub _add_term { my ( $self, $term, $ont ) = @_; $term->ontology($ont) if $ont && ( !$term->ontology ); $self->_ont_engine()->add_term($term); } # This simply delegates. See OBOEngine sub _part_of_relationship { my $self = shift; return $self->_ont_engine()->part_of_relationship(@_); } # This simply delegates. See OBOEngine sub _is_a_relationship { my $self = shift; return $self->_ont_engine()->is_a_relationship(@_); } # This simply delegates. See OBOEngine sub _related_to_relationship { my $self = shift; return $self->_ont_engine()->related_to_relationship(@_); } # This simply delegates. See OBOEngine sub _regulates_relationship { my $self = shift; return $self->_ont_engine()->regulates_relationship(@_); } # This simply delegates. See OBOEngine sub _positively_regulates_relationship { my $self = shift; return $self->_ont_engine()->positively_regulates_relationship(@_); } # This simply delegates. See OBOEngine sub _negatively_regulates_relationship { my $self = shift; return $self->_ont_engine()->negatively_regulates_relationship(@_); } # This simply delegates. See OBOEngine sub _add_relationship { my ( $self, $parent, $child, $type, $ont ) = @_; # Note the triple terminology (subject,predicate,object) corresponds to # (child,type,parent) $self->_ont_engine()->add_relationship( $child, $type, $parent, $ont ); } # This simply delegates. See OBOEngine sub _has_term { my $self = shift; return $self->_ont_engine()->has_term(@_); } # Holds the OBO engine to be parsed into sub _ont_engine { my ( $self, $value ) = @_; if ( defined $value ) { $self->{"_ont_engine"} = $value; } $self->{"_ont_engine"}; } # Removes the escape characters from the file sub _filter_line { my ( $self, $line ) = @_; chomp($line); $line =~ tr [\200-\377] [\000-\177]; # see 'man perlop', section on tr/ # weird ascii characters should be excluded $line =~ tr/\0-\10//d; # remove weird characters; ascii 0-8 # preserve \11 (9 - tab) and \12 (10-linefeed) $line =~ tr/\13\14//d; # remove weird characters; 11,12 # preserve \15 (13 - carriage return) $line =~ tr/\16-\37//d; # remove 14-31 (all rest before space) $line =~ tr/\177//d; # remove DEL character $line =~ s/^\!.*//; $line =~ s/[^\\]\!.*//; $line =~ s/[^\\]\#.*//; $line =~ s/^\s+//; $line =~ s/\s+$//; return $line; } # Parses the header sub _header { my $self = shift; my $annotation_collection = Bio::Annotation::Collection->new(); my ( $tag, $value ); my $line_counter = 0; $self->{'_current_line_no'} = 0; my $format_version_header_flag = 0; my $default_namespace_header_flag = 0; while ( my $line = $self->_readline() ) { ++$line_counter; my $line = $self->_filter_line($line); if ( !$line ) { if ( !$format_version_header_flag ) { $self->throw("Format Error - Cannot find tag format-version." . "This is required in header" ); } $self->{'_current_line_no'} = $line_counter; return $annotation_collection; } # Check if there is a header if ( $line =~ /\[\w*\]/ ) { $self->throw("Format Error - Cannot find tag format-version." . "This is required in header." ); } # If the line is not null, check it contains at least one colon $self->_check_colon( $line, $line_counter ); # These are the allowed headers. Any other headers will be ignored if ( $line =~ /^(\[|format-version: |data-version: |typeref: |version: |date: |saved-by: |auto-generated-by: |default-namespace: |remark: |subsetdef: |import: |synonymtypedef: |idspace: |default-relationship-id-prefix: |id-mapping: )/x ) { if ( $line =~ /^([\w\-]+)\:\s*(.*)/ ) { ( $tag, $value ) = ( $1, $2 ); } if ( $tag =~ /format-version/) { $format_version_header_flag = 1; }elsif( $tag =~ /default-namespace/ ) { $default_namespace_header_flag = 1; } my $header = Bio::Annotation::SimpleValue->new( -value => $value ); $annotation_collection->add_Annotation( $tag, $header ); # Assign the Ontology name as the value of the default-namespace header if ( $tag =~ /default-namespace/i ) { $self->ontology_name($value); } } } } # Parses each stanza of the file sub _next_term { my $self = shift; my $term; my $skip_stanza_flag = 1; my $line_counter = $self->{'_current_line_no'}; while ( my $line = $self->_readline() ) { ++$line_counter; my $line = $self->_filter_line($line); if ( !$line && $term ) { $self->{'_current_line_no'} = $line_counter; return $term; } if ( ( $line =~ /^\[(\w+)\]\s*(.*)/ ) ) { # New stanza if ( uc($1) eq "TERM" ) { $term = $self->_create_term_object; $skip_stanza_flag = 0; # Reset the relationships after each stanza $self->{'_relationships'} = {}; $self->{'_isa_parents'} = undef; } elsif ( uc($1) eq "TYPEDEF" ) { $skip_stanza_flag = 1; # Check if this typedef is already defined by the relationship } else { $skip_stanza_flag = 1; $self->warn("OBO File Format Warning on line $line_counter $line\n" . "Unrecognized stanza type found. Skipping this stanza." ); } next; } # If the line is not null, check it contains at least one colon $self->_check_colon( $line, $line_counter ); # If there is any tag value other than the list below move to the next tag next if (( $line !~ /^(\[|id: |is_anonymous: |name: |namespace: |alt_id: |def: |comment: |subset: |synonym: |xref: |is_a: |intersection_of: |union_of: |disjoint_from: |relationship: |is_obsolete: |replaced_by: |consider: |created_by: |creation_date: )/x ) || $skip_stanza_flag ); # Tag/value pair if ( $line =~ /^([\w\-]+)\:\s*(.*)/ ) { my ( $tag, $val ) = ( $1, $2 ); # If no value for the tag throw a warning if ( !$val ) { $self->warn("OBO File Format Warning on line $line_counter $line\n" . "Tag has no value." ); } my $qh; ( $val, $qh ) = $self->_extract_quals($val); my $val2 = $val; $val2 =~ s/\\,/,/g; $tag = uc($tag); if ( $tag eq "ID" ) { $term->identifier($val); if ( $self->_has_term($term) ) { $term = $self->_ont_engine()->get_terms($val); } } elsif ( $tag eq "NAME" ) { $term->name($val); } elsif ( $tag eq "XREF_ANALOG" ) { if ( !$term->has_dbxref($val) ) { $term->add_dbxref(-dbxrefs => $self->_to_annotation( [$val] ) ); } } elsif ( $tag eq "XREF_UNKNOWN" ) { $term->add_dbxref(-dbxrefs => $self->_to_annotation( [$val] ) ); } elsif ( $tag eq "NAMESPACE" ) { $term->namespace($val); } elsif ( $tag eq "DEF" ) { my ( $defstr, $parts ) = $self->_extract_qstr($val); $term->definition($defstr); my $ann = $self->_to_annotation($parts); $term->add_dbxref( -dbxrefs => $ann ); } elsif ( $tag eq "SYNONYM" ) { $term->add_synonym($val); } elsif ( $tag eq "ALT_ID" ) { $term->add_secondary_id($val); } elsif ( $tag =~ /XREF/i ) { $term->add_secondary_id($val); } elsif ( $tag eq "IS_OBSOLETE" ) { if ( $val eq 'true' ) { $val = 1; } elsif ( $val eq 'false' ) { $val = 0; } $term->is_obsolete($val); } elsif ( $tag eq "COMMENT" ) { $term->comment($val); } elsif ( $tag eq "RELATIONSHIP" ) { $self->_handle_relationship_tag($val); } elsif ( $tag eq "IS_A" ) { $val =~ s/ //g; my $parent_term = $self->_create_term_object(); $parent_term->identifier($val); push @{ $self->{'_isa_parents'} }, $parent_term; } } } $term; } # Creates a Bio::Ontology::OBOterm object sub _create_term_object { my ($self) = @_; my $term = $self->term_factory->create_object(); $term; } sub _extract_quals { my ( $self, $str ) = @_; my %q = (); if ( $str =~ /(.*)\s+(\{.*\})\s*$/ ) { my $return_str = $1; my $extr = $2; if ($extr) { my @qparts = $self->_split_on_comma($extr); foreach (@qparts) { if (/(\w+)=\"(.*)\"/) { $q{$1} = $2; } elsif (/(\w+)=\'(.*)\'/) { $q{$1} = $2; } else { warn("$_ in $str"); } } } return ( $return_str, \%q ); } else { return ( $str, {} ); } } sub _extract_qstr { my ( $self, $str ) = @_; my ( $extr, $rem, $prefix ) = extract_quotelike($str); my $txt = $extr; $txt =~ s/^\"//; $txt =~ s/\"$//; if ($prefix) { warn("illegal prefix: $prefix in: $str"); } my @extra = (); # e.g. synonym: "foo" EXACT [...] if ( $rem =~ /(\w+)\s+(\[.*)/ ) { $rem = $2; push( @extra, split( ' ', $1 ) ); } my @parts = (); while ( ( $extr, $rem, $prefix ) = extract_bracketed( $rem, '[]' ) ) { last unless $extr; $extr =~ s/^\[//; $extr =~ s/\]$//; push( @parts, $extr ) if $extr; } @parts = map { $self->_split_on_comma($_) } @parts; $txt =~ s/\\//g; ( $txt, \@parts, \@extra ); } sub _split_on_comma { my ( $self, $str ) = @_; my @parts = (); while ( $str =~ /(.*[^\\],\s*)(.*)/ ) { $str = $1; my $part = $2; unshift( @parts, $part ); $str =~ s/,\s*$//; } unshift( @parts, $str ); return map { s/\\//g; $_ } @parts; } # This method checks for an existing colon in a line sub _check_colon { my ( $self, $line, $line_no ) = @_; if ( $line && !( $line =~ /:/ ) ) { $self->throw("OBO File Format Error on line $line_no $line\n" . "Cannot find key-terminating colon" ); } } # This method handles relationship tags sub _handle_relationship_tag { my ( $self, $val ) = @_; my @parts = split( / /, $val ); my $relationship = uc($parts[0]); my $id = $parts[1] =~ /\^(w+)\s+\!/ ? $1 : $parts[1]; push @{$self->{_relationships}->{$relationship}}, $id; } # Convert simple strings to Bio::Annotation::DBLinks sub _to_annotation { my ($self , $links) = @_; return unless $links; my @dbxrefs; for my $string (@{$links}) { my ($db, $id) = split(':',$string,2); push @dbxrefs, Bio::Annotation::DBLink->new(-database => $db, -primary_id => $id); } \@dbxrefs; } 1; BioPerl-1.007002/Bio/OntologyIO/simplehierarchy.pm000555000766000024 4711013155576320 22042 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::OntologyIO::simplehierarchy # # Please direct questions and support issues to # # Cared for by Allen Day, allenday@ucla.edu # # (c) Allen Day, allenday@ucla.edu, 2003. # (c) Department of Human Genetics, UCLA Medical School, 2003. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::OntologyIO::simplehierarchy - a base class parser for simple hierarchy-by-indentation type formats =head1 SYNOPSIS use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO my $parser = Bio::OntologyIO->new ( -format => "simplehierarchy", -file => "pathology_terms.csv", -indent_string => ",", -ontology_name => "eVOC", -term_factory => $fact, ); my $ontology = $parser->next_ontology(); =head1 DESCRIPTION Needs Graph.pm from CPAN. This class is nearly identical to OntologyIO::dagflat, see L for details. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Allen Day Email: allenday@ucla.edu =head2 CONTRIBUTOR Christian Zmasek =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::OntologyIO::simplehierarchy; use strict; use Data::Dumper; use File::Basename; use Bio::Root::IO; use Bio::Ontology::OBOEngine; use Bio::Ontology::Ontology; use Bio::Ontology::TermFactory; use constant TRUE => 1; use constant FALSE => 0; use base qw(Bio::OntologyIO); =head2 new Title : new Usage : see SYNOPSIS Function: Creates a new simplehierarchy parser. Returns : A new simplehierarchy parser object, implementing Bio::OntologyIO. Args : -files => a single ontology flat file holding the term relationships, or an array ref holding the file names -file => if there is only a single flat file, it may also be specified via the -file parameter -ontology_name => the name of the ontology, defaults to "Gene Ontology" -file_is_root => Boolean indicating whether a virtual root term is to be added, the name of which will be derived from the file name. Default is false. Enabling this allows one to parse multiple input files into the same ontology and still have separately rooted. -engine => the L object to be reused (will be created otherwise); note that every L will qualify as well since that one inherits from the former. -indent_string => the string used to indent hierarchical levels in the file. For a file like this: term0 subterm1A subterm2A subterm1B subterm1C indent_string would be " ". Defaults to one space (" "). -comment_char => Allows specification of a regular expression string to indicate a comment line. Currently defaults to "[\|\-]". Note: this is not yet implemented. See L. =cut # in reality, we let OntologyIO::new do the instantiation, and override # _initialize for all initialization work sub _initialize { my ($self, @args) = @_; $self->SUPER::_initialize( @args ); my ( $indent,$files,$fileisroot,$name,$eng ) = $self->_rearrange([qw(INDENT_STRING FILES FILE_IS_ROOT ONTOLOGY_NAME ENGINE) ], @args); $self->_done( FALSE ); $self->_not_first_record( FALSE ); $self->_term( "" ); $self->file_is_root($fileisroot) if defined($fileisroot); $indent = ' ' unless defined($indent); #reasonable default? # the indentation string may have escaped chars if (($indent =~ /\\/) && ($indent !~ /[\$\`]/)) { $indent = "\$indent = \"$indent\""; eval $indent; } $self->indent_string($indent); delete $self->{'_ontologies'}; # ontology engine (and possibly name if it's an OntologyI) $eng = Bio::Ontology::OBOEngine->new() unless $eng; if($eng->isa("Bio::Ontology::OntologyI")) { $self->ontology_name($eng->name()); $eng = $eng->engine() if $eng->can('engine'); } $self->_ont_engine($eng); # flat files to parse $self->{_flat_files} = $files ? ref($files) ? $files : [$files] : []; # ontology name (overrides implicit one through OntologyI engine) $self->ontology_name($name) if $name; } # _initialize =head2 ontology_name Title : ontology_name Usage : $obj->ontology_name($newval) Function: Get/set the name of the ontology parsed by this module. Example : Returns : value of ontology_name (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub ontology_name{ my $self = shift; return $self->{'ontology_name'} = shift if @_; return $self->{'ontology_name'}; } =head2 parse Title : parse() Usage : $parser->parse(); Function: Parses the files set with "new" or with methods defs_file and _flat_files. Normally you should not need to call this method as it will be called automatically upon the first call to next_ontology(). Returns : [Bio::Ontology::OntologyEngineI] Args : =cut sub parse { my $self = shift; # setup the default term factory if not done by anyone yet $self->term_factory(Bio::Ontology::TermFactory->new( -type => "Bio::Ontology::Term")) unless $self->term_factory(); # create the ontology object itself my $ont = Bio::Ontology::Ontology->new(-name => $self->ontology_name(), -engine => $self->_ont_engine()); # set up the ontology of the relationship types foreach ($self->_part_of_relationship(), $self->_is_a_relationship(), $self->_related_to_relationship()) { $_->ontology($ont); } # pre-seed the IO system with the first flat file if -file wasn't provided if(! $self->_fh) { $self->_initialize_io(-file => shift(@{$self->_flat_files()})); } while($self->_fh) { $self->_parse_flat_file($ont); # advance to next flat file if more are available if(@{$self->_flat_files()}) { $self->close(); # reset the virtual root so that the next one is generated from # the next file $self->_virtual_root(undef); # now re-initialize the IO object $self->_initialize_io(-file => shift(@{$self->_flat_files()})); } else { last; # nothing else to parse so terminate the loop } } $self->_add_ontology($ont); # not needed anywhere, only because of backward compatibility return $self->_ont_engine(); } # parse =head2 next_ontology Title : next_ontology Usage : Function: Get the next available ontology from the parser. This is the method prescribed by Bio::OntologyIO. Example : Returns : An object implementing Bio::Ontology::OntologyI, and undef if there is no more ontology in the input. Args : =cut sub next_ontology{ my $self = shift; # parse if not done already $self->parse() unless exists($self->{'_ontologies'}); # return next available ontology return shift(@{$self->{'_ontologies'}}) if exists($self->{'_ontologies'}); return; } =head2 _flat_files Title : _flat_files Usage : $files_to_parse = $parser->_flat_files(); Function: Get the array of ontology flat files that need to be parsed. Note that this array will decrease in elements over the parsing process. Therefore, it\'s value outside of this module will be limited. Also, be careful not to alter the array unless you know what you are doing. Returns : a reference to an array of zero or more strings Args : none =cut sub _flat_files { my $self = shift; $self->{_flat_files} = [] unless exists($self->{_flat_files}); return $self->{_flat_files}; } # INTERNAL METHODS # ---------------- =head2 _defs_io Title : _defs_io Usage : $obj->_defs_io($newval) Function: Get/set the Bio::Root::IO instance representing the definition file, if provided (see defs_file()). Example : Returns : value of _defs_io (a Bio::Root::IO object) Args : on set, new value (a Bio::Root::IO object or undef, optional) =cut sub _defs_io{ my $self = shift; return $self->{'_defs_io'} = shift if @_; return $self->{'_defs_io'}; } sub _add_ontology { my $self = shift; $self->{'_ontologies'} = [] unless exists($self->{'_ontologies'}); foreach my $ont (@_) { $self->throw(ref($ont)." does not implement Bio::Ontology::OntologyI") unless ref($ont) && $ont->isa("Bio::Ontology::OntologyI"); push(@{$self->{'_ontologies'}}, $ont); } } # This simply delegates. See SimpleGOEngine. sub _add_term { my ( $self, $term, $ont ) = @_; $term->ontology($ont) if $ont && (! $term->ontology); $self->_ont_engine()->add_term( $term ); } # _add_term # This simply delegates. See SimpleGOEngine sub _part_of_relationship { my ( $self, $term ) = @_; return $self->_ont_engine()->part_of_relationship(); } # _part_of_relationship # This simply delegates. See SimpleGOEngine sub _is_a_relationship { my ( $self, $term ) = @_; return $self->_ont_engine()->is_a_relationship(); } # _is_a_relationship # This simply delegates. See SimpleGOEngine sub _related_to_relationship { my ( $self, $term ) = @_; return $self->_ont_engine()->related_to_relationship(); } # _is_a_relationship # This simply delegates. See SimpleGOEngine sub _add_relationship { my ( $self, $parent, $child, $type, $ont ) = @_; # note the triple terminology (subject,predicate,object) corresponds to # (child,type,parent) $self->_ont_engine()->add_relationship( $child, $type, $parent, $ont ); } # _add_relationship # This simply delegates. See SimpleGOEngine sub _has_term { my ( $self, $term ) = @_; $term = $self->ontology_name() .'|'. $term unless ref($term) || !$self->ontology_name(); return $self->_ont_engine()->has_term( $term ); } # _add_term # This simply delegates after prefixing the namespace name if it is just a # base identifier. See SimpleGOEngine sub _get_terms{ my $self = shift; my @args = (); while(@_) { unshift(@args, pop(@_)); # this actually does preserve the order $args[0] = $self->ontology_name() .'|'. $args[0] unless ref($args[0]) || !$self->ontology_name(); } return $self->_ont_engine->get_terms(@args); } # This parses the relationships files sub _parse_flat_file { my $self = shift; my $ont = shift; my @stack = (); my $prev_indent = -1; my $parent = ""; my $prev_term = ""; my $indent_string = $self->indent_string; while ( my $line = $self->_readline() ) { if ( $line =~ /^[$indent_string]*[\|\-]/ ) { #this is not yet generalized next; } my ($current_term) = $line =~ /^[$indent_string]*(.*)/; my $current_indent = $self->_count_indents( $line ); chomp $current_term; # remove extraneous delimiter characters at the end of the name if any $current_term =~ s/[$indent_string]+$//; # remove double quotes surrounding the entry, if any $current_term =~ s/^\"(.*)\"$/$1/; # also, the name might contain a synonym my $syn = $current_term =~ s/\s+{([^}]+)}// ? $1 : undef; if ( ! $self->_has_term( $current_term ) ) { my $term = $self->_create_ont_entry($current_term); # add synonym(s) if any $term->add_synonym(split(/[;,]\s*/,$syn)) if $syn; # add to the machine $self->_add_term( $term, $ont ); #go on to the next term if a root node. if($current_indent == 0) { # add the virtual root as parent if there is one if($self->_virtual_root()) { $self->_add_relationship($self->_virtual_root(), $term, $self->_is_a_relationship(), $ont); } $prev_indent = $current_indent; $prev_term = $current_term; push @stack, $current_term; next; } } # note: we are ensured to see the parent first in this type of file, # so we never need to possibly insert the parent here if ( $current_indent != $prev_indent ) { if ( $current_indent == $prev_indent + 1 ) { push( @stack, $prev_term ); } elsif ( $current_indent < $prev_indent ) { my $n = $prev_indent - $current_indent; for ( my $i = 0; $i < $n; ++$i ) { pop( @stack ); } } else { $self->throw("format error: indentation level $current_indent " ."is more than one higher than the previous " ."level $prev_indent ('$current_term', " ."file ".$self->file.")" ); } } $parent = $stack[-1]; if($parent ne $current_term) { #this prevents infinite recursion from a parent linking to itself $self->_add_relationship($self->_get_terms($parent), $self->_get_terms($current_term), $self->_is_a_relationship(), $ont); } $prev_indent = $current_indent; $prev_term = $current_term; } return $ont; } # _parse_relationships_file # Parses the 1st term id number out of line. sub _get_first_termid { my ( $self, $line ) = @_; if ( $line =~ /;\s*([A-Z]{1,8}:\d{7})/ ) { return $1; } else { $self->throw( "format error: no term id in line \"$line\"" ); } } # _get_first_termid # Counts the indents at the beginning of a line in the relationships files sub _count_indents { my ( $self, $line ) = @_; my $indent = $self->indent_string; if ( $line =~ /^($indent+)/ ) { return (length($1)/length($indent)); } else { return 0; } } # _count_indents # Holds the GO engine to be parsed into sub _ont_engine { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_ont_engine" } = $value; } return $self->{ "_ont_engine" }; } # _ont_engine # Used to create ontology terms. # Arguments: name, id sub _create_ont_entry { my ( $self, $name, $termid ) = @_; my $term = $self->term_factory->create_object(-name => $name, -identifier => $termid); return $term; } # _create_ont_entry # Holds whether first record or not sub _not_first_record { my ( $self, $value ) = @_; if ( defined $value ) { unless ( $value == FALSE || $value == TRUE ) { $self->throw( "Argument to method \"_not_first_record\" must be either ".TRUE." or ".FALSE ); } $self->{ "_not_first_record" } = $value; } return $self->{ "_not_first_record" }; } # _not_first_record # Holds whether done or not sub _done { my ( $self, $value ) = @_; if ( defined $value ) { unless ( $value == FALSE || $value == TRUE ) { $self->throw( "Found [$value] where [" . TRUE ." or " . FALSE . "] expected" ); } $self->{ "_done" } = $value; } return $self->{ "_done" }; } # _done # Holds a term. sub _term { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_term" } = $value; } return $self->{ "_term" }; } # _term =head2 indent_string Title : indent_string Usage : $obj->indent_string($newval) Function: Example : Returns : value of indent_string (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub indent_string{ my $self = shift; return $self->{'indent_string'} = shift if @_; return $self->{'indent_string'}; } =head2 file_is_root Title : file_is_root Usage : $obj->file_is_root($newval) Function: Boolean indicating whether a virtual root term is to be added, the name of which will be derived from the file name. Enabling this allows one to parse multiple input files into the same ontology and still have separately rooted. Example : Returns : value of file_is_root (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub file_is_root{ my $self = shift; return $self->{'file_is_root'} = shift if @_; return $self->{'file_is_root'}; } =head2 _virtual_root Title : _virtual_root Usage : $obj->_virtual_root($newval) Function: Example : Returns : value of _virtual_root (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub _virtual_root{ my $self = shift; return $self->{'_virtual_root'} = shift if @_; # don't return anything if not in file_is_root mode, or if we don't # have a file to derive the root node from return unless $self->file_is_root() && $self->file(); # construct it if we haven't done this before if(! $self->{'_virtual_root'}) { my ($rt,undef,undef) = fileparse($self->file(), '\..*'); $rt =~ s/_/ /g; $rt = $self->_create_ont_entry($rt); $self->_add_term($rt, $self->ontology_name()); $self->{'_virtual_root'} = $rt; } return $self->{'_virtual_root'}; } 1; BioPerl-1.007002/Bio/OntologyIO/soflat.pm000444000766000024 1163413155576320 20141 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::OntologyIO::soflat # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) Hilmar Lapp, hlapp at gnf.org, 2003. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002-3. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::OntologyIO::soflat - a parser for the Sequence Ontology flat-file format =head1 SYNOPSIS use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO my $parser = Bio::OntologyIO->new ( -format => "so", # or soflat -defs_file => "/home/czmasek/SO/SO.defs", -file => "/home/czmasek/SO/sofa.ontology" ); my $sofa_ontology = $parser->next_ontology(); my $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" ); my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" ); =head1 DESCRIPTION Needs Graph.pm from CPAN. This is essentially a very thin derivation of the dagflat base-parser. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head2 CONTRIBUTOR Hilmar Lapp, hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::OntologyIO::soflat; use strict; use Bio::Ontology::TermFactory; use constant TRUE => 1; use constant FALSE => 0; use base qw(Bio::OntologyIO::dagflat); =head2 new Title : new Usage : $parser = Bio::OntologyIO->new( -format => "soflat", -files => ["/path/to/sofa.ontology"] ); Function: Creates a new soflat parser. Returns : A new soflat parser object, implementing Bio::OntologyIO. Args : -defs_file => the name of the file holding the term definitions -files => a single ontology flat file holding the term relationships, or an array ref holding the file names -file => if there is only a single flat file, it may also be specified via the -file parameter -ontology_name => the name of the ontology; if not specified the parser will auto-discover it by using the term that starts with a $, and converting underscores to spaces -engine => the Bio::Ontology::OntologyEngineI object to be reused (will be created otherwise); note that every Bio::Ontology::OntologyI will qualify as well since that one inherits from the former. See L. =cut # in reality, we let OntologyIO::new do the instantiation, and override # _initialize for all initialization work sub _initialize { my ($self, @args) = @_; $self->SUPER::_initialize( @args ); # default term object factory $self->term_factory(Bio::Ontology::TermFactory->new( -type => "Bio::Ontology::GOterm")) unless $self->term_factory(); } # _initialize 1; BioPerl-1.007002/Bio/OntologyIO/Handlers000755000766000024 013155576320 17671 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/OntologyIO/Handlers/BaseSAXHandler.pm000444000766000024 1320213155576320 23126 0ustar00cjfieldsstaff000000000000# # BioPerl module for BaseSAXHandler # # Please direct questions and support issues to # # Cared for by Juguang Xiao, juguang@tll.org.sg # # Copyright Juguang Xiao # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::OntologyIO::Handlers::BaseSAXHandler - base class for SAX Handlers =head1 SYNOPSIS See description. =head1 DESCRIPTION This module is an abstract module, serving as the base of any SAX Handler implementation. It tries to offer the framework that SAX handlers generally need, such as tag_stack, char_store, etc. In the implementation handler, you can take advantage of this based module by the following suggestions. 1) In start_element, sub start_element { my $self=shift; my $tag=$_[0]->{Name}; my %args=%{$_[0]->{Attributes}}; # Your code here. # Before you conclude the method, write these 2 line. $self->_visited_count_inc($tag); $self->_push_tag($tag); } 2) In end_element, sub end_element { my $self=shift; my $tag=shift->{Name}; # Your code here. # Before you conclude the method, write these 2 lines. $self->_visited_count_dec($tag); $self->_pop_tag; } 3) In characters, or any other methods where you may use the tag stack or count sub characters { my $self=shift; my $text=shift->{Data}; $self->_chars_hash->{$self->_top_tag} .= $text; } $count = $self->_visited_count('myTag'); $tag = $self->_top_tag; =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Juguang Xiao, juguang@tll.org.sg =head2 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::OntologyIO::Handlers::BaseSAXHandler; use strict; use base qw(Bio::Root::Root); sub new { my ($class, @args) = @_; my $self=$class->SUPER::new(@args); $self->_initialize(@args); return $self; } sub _initialize { my $self = shift; $self->{_tag_stack} = []; $self->{_visited_count} = {}; $self->{_chars_hash} = {}; $self->{_current_hash} = {}; } =head2 _tag_stack Title : _tag_stack Usage : @tags = $self->_tag_stack; Function: Get an array of tags that have been accessed but not enclosed. Return : Args : =cut sub _tag_stack { return @{shift->{_tag_stack}}; } =head2 _push_tag =cut sub _push_tag { my($self,$tag)=@_; push @{$self->{_tag_stack}}, $tag; } =head2 _pop_tag =cut sub _pop_tag { my $self=shift; return pop @{$self->{_tag_stack}}; } =head2 _top_tag Title : _top_tag Usage : $top = $self->_top_tag; Function: get the top tag in the tag stack. Return : a tag name Args : [none] =cut sub _top_tag { my $self = shift; my @stack=@{$self->{_tag_stack}}; return $stack[-1]; # get the last element in an array while remaining it in. There are few ways # 1) $stack[-1] # 2) $stack[$#stack] # 3) $stack[@stack-1] } =head2 _chars_hash Title : _chars_hash Usage : $hash= $self->_chars_hash; Function: return the character cache for the specific tag Return : a hash reference, which is intent for character storage for tags Args : [none] =cut sub _chars_hash { return shift->{_chars_hash}; } =head2 _current_hash =cut sub _current_hash { return shift->{_current_hash}; } =head2 _visited_count_inc Title : _vistied_count_inc Usage : $self->vistied_count_inc($tag); # the counter for the tag increase Function: the counter for the tag increase Return : the current count after this increment Args : the tag name [scalar] =cut sub _visited_count_inc { my ($self, $tag) = @_; my $visited_count=$self->{_visited_count}; if(exists $visited_count->{$tag}){ $visited_count->{$tag}++; }else{ $visited_count->{$tag}=1; } return $visited_count->{$tag}; } =head2 _visited_count_dec Title : _visited_count_dec Usage : $self->_visited_count_dec($tag); Function: the counter for the tag decreases by one Return : the current count for the specific tag after the decrement Args : the tag name [scalar] =cut sub _visited_count_dec { my ($self, $tag) = @_; my $visited_count=$self->{_visited_count}; if(exists $visited_count->{$tag}){ $visited_count->{$tag}--; }else{ $self->throw("'$tag' has not been visited yet. How to decrease it?!"); } return $visited_count->{$tag}; } =head2 _visited_count Title : _visited_count Usage : $count = $self->_visited_count Function: return the counter for the tag Return : the current counter for the specific tag Args : the tag name [scalar] =cut sub _visited_count { my ($self, $tag) = @_; return $self->{_visited_count}->{$tag}; } 1; BioPerl-1.007002/Bio/OntologyIO/Handlers/InterProHandler.pm000444000766000024 5334213155576320 23453 0ustar00cjfieldsstaff000000000000# # BioPerl module for InterProHandler # # Please direct questions and support issues to # # Cared for by Peter Dimitrov # # Copyright Peter Dimitrov # (c) Peter Dimitrov, dimitrov@gnf.org, 2003. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::OntologyIO::Handlers::InterProHandler - XML handler class for InterProParser =head1 SYNOPSIS # do not use directly - used and instantiated by InterProParser =head1 DESCRIPTION Handles xml events generated by InterProParser when parsing InterPro XML files. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Peter Dimitrov Email dimitrov@gnf.org =head1 CONTRIBUTORS Juguang Xiao, juguang@tll.org.sg =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::OntologyIO::Handlers::InterProHandler; use strict; use Carp; use Bio::Ontology::Ontology; use Bio::Ontology::RelationshipType; use Bio::Ontology::SimpleOntologyEngine; use Bio::Annotation::Reference; use Data::Dumper; use base qw(Bio::Root::Root); my ( $record_count, $processed_count, $is_a_rel, $contains_rel, $found_in_rel ); =head2 new Title : new Usage : $h = Bio::OntologyIO::Handlers::InterProHandler->new; Function: Initializes global variables Example : Returns : an InterProHandler object Args : =cut sub new { my ( $class, @args ) = @_; my $self = $class->SUPER::new(@args); my ( $eng, $ont, $name, $fact ) = $self->_rearrange( [qw[ ENGINE ONTOLOGY ONTOLOGY_NAME TERM_FACTORY ]], @args ); if ( defined($ont) ) { $self->ontology($ont); } else { $name = "InterPro" unless $name; $self->ontology( Bio::Ontology::Ontology->new( -name => $name ) ); } $self->ontology_engine($eng) if $eng; $self->term_factory($fact) if $fact; $is_a_rel = Bio::Ontology::RelationshipType->get_instance("IS_A"); $contains_rel = Bio::Ontology::RelationshipType->get_instance("CONTAINS"); $found_in_rel = Bio::Ontology::RelationshipType->get_instance("FOUND_IN"); $is_a_rel->ontology( $self->ontology() ); $contains_rel->ontology( $self->ontology() ); $found_in_rel->ontology( $self->ontology() ); $self->_cite_skip(0); $self->secondary_accessions_map( {} ); return $self; } =head2 ontology_engine Title : ontology_engine Usage : $obj->ontology_engine($newval) Function: Get/set ontology engine. Can be initialized only once. Example : Returns : value of ontology_engine (a scalar) Args : new value (a scalar, optional) =cut sub ontology_engine { my ( $self, $value ) = @_; if ( defined $value ) { if ( defined $self->{'ontology_engine'} ) { $self->throw("ontology_engine already defined"); } else { $self->throw( ref($value) . " does not implement " . "Bio::Ontology::OntologyEngineI. Bummer." ) unless $value->isa("Bio::Ontology::OntologyEngineI"); $self->{'ontology_engine'} = $value; # don't forget to set this as the engine of the ontology, otherwise # those two might not point to the same object my $ont = $self->ontology(); if ( $ont && $ont->can("engine") && ( !$ont->engine() ) ) { $ont->engine($value); } $self->debug( ref($self) . "::ontology_engine: registering ontology engine (" . ref($value) . "):\n" . $value->to_string . "\n" ); } } return $self->{'ontology_engine'}; } =head2 ontology Title : ontology Usage : Function: Get the ontology to add the InterPro terms to. The value is determined automatically once ontology_engine has been set and if it hasn't been set before. Example : Returns : A L implementing object. Args : On set, a L implementing object. =cut sub ontology { my ( $self, $ont ) = @_; if ( defined($ont) ) { $self->throw( ref($ont) . " does not implement Bio::Ontology::OntologyI" . ". Bummer." ) unless $ont->isa("Bio::Ontology::OntologyI"); $self->{'_ontology'} = $ont; } return $self->{'_ontology'}; } =head2 term_factory Title : term_factory Usage : $obj->term_factory($newval) Function: Get/set the ontology term object factory Example : Returns : value of term_factory (a Bio::Factory::ObjectFactory instance) Args : on set, new value (a Bio::Factory::ObjectFactory instance or undef, optional) =cut sub term_factory { my $self = shift; return $self->{'term_factory'} = shift if @_; return $self->{'term_factory'}; } =head2 _cite_skip Title : _cite_skip Usage : $obj->_cite_skip($newval) Function: Example : Returns : value of _cite_skip (a scalar) Args : new value (a scalar, optional) =cut sub _cite_skip { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_cite_skip'} = $value; } return $self->{'_cite_skip'}; } =head2 _hash Title : _hash Usage : $obj->_hash($newval) Function: Example : Returns : value of _hash (a scalar) Args : new value (a scalar, optional) =cut sub _hash { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_hash'} = $value; } return $self->{'_hash'}; } =head2 _stack Title : _stack Usage : $obj->_stack($newval) Function: Example : Returns : value of _stack (a scalar) Args : new value (a scalar, optional) =cut sub _stack { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_stack'} = $value; } return $self->{'_stack'}; } =head2 _top Title : _top Usage : Function: Example : Returns : Args : =cut sub _top { my ( $self, $_stack ) = @_; my @stack = @{$_stack}; return ( @stack >= 1 ) ? $stack[ @stack - 1 ] : undef; } =head2 _term Title : _term Usage : $obj->_term($newval) Function: Get/set method for the term currently processed. Example : Returns : value of term (a scalar) Args : new value (a scalar, optional) =cut sub _term { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_term'} = $value; } return $self->{'_term'}; } =head2 _clear_term Title : _clear_term Usage : Function: Removes the current term from the handler Example : Returns : Args : =cut sub _clear_term { my ($self) = @_; delete $self->{'_term'}; } =head2 _names Title : _names Usage : $obj->_names($newval) Function: Example : Returns : value of _names (a scalar) Args : new value (a scalar, optional) =cut sub _names { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_names'} = $value; } return $self->{'_names'}; } =head2 _create_relationship Title : _create_relationship Usage : Function: Helper function. Adds relationships to one of the relationship stores. Example : Returns : Args : =cut { my %relationship_cache; sub _clear_cache { %relationship_cache = () } sub _create_relationship { my ( $self, $ref_id, $rel_type_term ) = @_; my $ont = $self->ontology(); my $fact = $self->term_factory(); my $term_temp = ( $ont->engine->get_term_by_identifier($ref_id) )[0]; if ( !defined $term_temp ) { $term_temp = $ont->engine->add_term( $fact->create_object( -InterPro_id => $ref_id, -name => $ref_id, -ontology => $ont ) ); $ont->engine->mark_uninstantiated($term_temp); } my $marshalled = join(':', (sort $self->_term->identifier, $ref_id)); # check cache to see if the two have been seen before, using marshalled IDs if ($relationship_cache{$marshalled}++) { # TODO: should check that the relationship type for these terms is the # inverse of the stored relationship type return; } my $rel_type_name = $self->_top( $self->_names ); my $rel = Bio::Ontology::Relationship->new( -predicate_term => $rel_type_term ); if ( $rel_type_name eq 'parent_list' || $rel_type_name eq 'found_in' ) { $rel->object_term($term_temp); $rel->subject_term( $self->_term ); } else { $rel->object_term( $self->_term ); $rel->subject_term($term_temp); } $rel->ontology($ont); $ont->add_relationship($rel); } } =head2 start_element Title : start_element Usage : Function: This is a method that is derived from XML::SAX::Base and has to be overridden for processing start of xml element events. Used internally only. Example : Returns : Args : =cut sub start_element { my ( $self, $element ) = @_; my $ont = $self->ontology(); my $fact = $self->term_factory(); if ( $element->{Name} eq 'interprodb' ) { $ont->add_term( $fact->create_object( -identifier => "Active_site", -name => "Active Site" ) ); $ont->add_term( $fact->create_object( -identifier => "Conserved_site", -name => "Conserved Site" ) ); $ont->add_term( $fact->create_object( -identifier => "Binding_site", -name => "Binding Site" ) ); $ont->add_term( $fact->create_object( -identifier => "Family", -name => "Family" ) ); $ont->add_term( $fact->create_object( -identifier => "Domain", -name => "Domain" ) ); $ont->add_term( $fact->create_object( -identifier => "Repeat", -name => "Repeat" ) ); $ont->add_term( $fact->create_object( -identifier => "PTM", -name => "post-translational modification" ) ); $ont->add_term( $fact->create_object( -identifier => "Region", -name => "Region" ) ); } elsif ( $element->{Name} eq 'interpro' ) { my %record_args = %{ $element->{Attributes} }; my $id = $record_args{"id"}; # this sets the current term my $term = ( $ont->engine->get_term_by_identifier($id) )[0] || $fact->create_object( -InterPro_id => $id, -name => $id ); $self->_term($term); $term->ontology($ont); $term->short_name( $record_args{"short_name"} ); $term->protein_count( $record_args{"protein_count"} ); $self->_increment_record_count(); $self->_stack( [ { interpro => undef } ] ); $self->_names( ["interpro"] ); ## Adding a relationship between the newly created InterPro term ## and the term describing its type my $rel = Bio::Ontology::Relationship->new( -predicate_term => $is_a_rel ); my ($object_term) = $ont->find_terms( -identifier => $record_args{"type"} ) or $self->throw( "when processing interpro ID '$id', no term found for interpro type '$record_args{type}'" ); $rel->object_term($object_term); $rel->subject_term( $self->_term ); $rel->ontology($ont); $ont->add_relationship($rel); $ont->add_term($term); } elsif ( defined $self->_stack ) { my %hash = (); if ( keys %{ $element->{Attributes} } > 0 ) { foreach my $key ( keys %{ $element->{Attributes} } ) { $hash{$key} = $element->{Attributes}->{$key}; } } push @{ $self->_stack }, \%hash; if ( $element->{Name} eq 'rel_ref' ) { my $ref_id = $element->{Attributes}->{"ipr_ref"}; my $parent = $self->_top( $self->_names ); if ( $parent eq 'parent_list' || $parent eq 'child_list' ) { $self->_create_relationship( $ref_id, $is_a_rel ); } if ( $parent eq 'contains' ) { $self->_create_relationship( $ref_id, $contains_rel ); } if ( $parent eq 'found_in' ) { $self->_create_relationship( $ref_id, $found_in_rel ); } } elsif ( $element->{Name} eq 'abstract' ) { $self->_cite_skip(1); } push @{ $self->_names }, $element->{Name}; } } =head2 _char_storage Title : _char_storage Usage : $obj->_char_storage($newval) Function: Example : Returns : value of _char_storage (a scalar) Args : new value (a scalar, optional) =cut sub _char_storage { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_char_storage'} = $value; } return $self->{'_char_storage'}; } =head2 characters Title : characters Usage : Function: This is a method that is derived from XML::SAX::Base and has to be overridden for processing xml characters events. Used internally only. Example : Returns : Args : =cut sub characters { my ( $self, $characters ) = @_; my $text = $characters->{Data}; chomp $text; $text =~ s/^(\s+)//; $self->{_char_storage} .= $text; } =head2 end_element Title : end_element Usage : Function: This is a method that is derived from XML::SAX::Base and has to be overridden for processing end of xml element events. Used internally only. Example : Returns : Args : =cut sub end_element { my ( $self, $element ) = @_; if ( $element->{Name} eq 'interprodb' ) { $self->debug( "Interpro DB Parser Finished: $record_count read, $processed_count processed\n"); $self->_clear_cache(); } elsif ( $element->{Name} eq 'interpro' ) { $self->_clear_term; $self->_increment_processed_count(); } elsif ( $element->{Name} ne 'cite' ) { $self->{_char_storage} =~ s/<\/?p>//g; if ( ( defined $self->_stack ) ) { my $current_hash = pop @{ $self->_stack }; my $parent_hash = $self->_top( $self->_stack ); my $current_hash_key = pop @{ $self->_names }; if ( keys %{$current_hash} > 0 && $self->_char_storage ne "" ) { $current_hash->{comment} = $self->_char_storage; push @{ $parent_hash->{$current_hash_key} }, $current_hash; } elsif ( $self->_char_storage ne "" ) { push @{ $parent_hash->{$current_hash_key} }, { 'accumulated_text_12345' => $self->_char_storage }; } elsif ( keys %{$current_hash} > 0 ) { push @{ $parent_hash->{$current_hash_key} }, $current_hash; } if ( $element->{Name} eq 'pub_list' ) { my @refs = (); foreach my $pub_record ( @{ $current_hash->{publication} } ) { my $ref = Bio::Annotation::Reference->new; my $loc = $pub_record->{location}->[0]; # TODO: Getting unset stuff here; should this be an error? $ref->location( sprintf("%s, %s-%s, %s, %s", $pub_record->{journal}->[0]->{accumulated_text_12345} || '', $loc->{firstpage} || '', $loc->{lastpage} || '', $loc->{volume} || '', $pub_record->{year}->[0]->{accumulated_text_12345} || '') ); $ref->title( $pub_record->{title}->[0]->{accumulated_text_12345} ); my $ttt = $pub_record->{author_list}->[0]; $ref->authors( $ttt->{accumulated_text_12345} ); $ref->medline( scalar( $ttt->{dbkey} ) ) if exists( $ttt->{db} ) && $ttt->{db} eq "MEDLINE"; push @refs, $ref; } $self->_term->add_reference(@refs); } elsif ( $element->{Name} eq 'name' ) { $self->_term->name( $self->_char_storage ); } elsif ( $element->{Name} eq 'abstract' ) { $self->_term->definition( $self->_char_storage ); $self->_cite_skip(0); } elsif ( $element->{Name} eq 'member_list' ) { my @refs = (); foreach my $db_xref ( @{ $current_hash->{db_xref} } ) { push @refs, Bio::Annotation::DBLink->new( -database => $db_xref->{db}, -primary_id => $db_xref->{dbkey} ); } $self->_term->add_dbxref(-dbxrefs => \@refs, -context => 'member_list'); } elsif ( $element->{Name} eq 'sec_list' ) { my @refs = (); foreach my $sec_ac ( @{ $current_hash->{sec_ac} } ) { push @refs, $sec_ac->{sec_ac}; } $self->_term->add_secondary_id(@refs); $self->secondary_accessions_map->{ $self->_term->identifier } = \@refs; } elsif ( $element->{Name} eq 'example_list' ) { my @refs = (); foreach my $example ( @{ $current_hash->{examples} } ) { push @refs, Bio::Annotation::DBLink->new( -database => $example->{db_xref}->[0]->{db}, -primary_id => $example->{db_xref}->[0]->{dbkey}, -comment => $example->{comment} ); } $self->_term->add_dbxref(-dbxrefs => \@refs, -context => 'example_list'); } elsif ( $element->{Name} eq 'external_doc_list' ) { my @refs = (); foreach my $db_xref ( @{ $current_hash->{db_xref} } ) { push @refs, Bio::Annotation::DBLink->new( -database => $db_xref->{db}, -primary_id => $db_xref->{dbkey} ); } $self->_term->add_dbxref(-dbxrefs => \@refs, -context => 'external_doc_list'); } elsif ( $element->{Name} eq 'class_list' ) { my @refs = (); foreach my $classification ( @{ $current_hash->{classification} } ) { push @refs, Bio::Annotation::DBLink->new( -database => $classification->{class_type}, -primary_id => $classification->{id} ); } $self->_term->add_dbxref(-dbxrefs => \@refs, -context => 'class_list'); } elsif ( $element->{Name} eq 'deleted_entries' ) { my @refs = (); foreach my $del_ref ( @{ $current_hash->{del_ref} } ) { my $term = ( $self->ontology_engine->get_term_by_identifier( $del_ref->{id} ) )[0]; $term->is_obsolete(1) if defined $term; } } } $self->_char_storage('') if !$self->_cite_skip; } } =head2 secondary_accessions_map Title : secondary_accessions_map Usage : $obj->secondary_accessions_map($newval) Function: Example : $map = $interpro_handler->secondary_accessions_map(); Returns : Reference to a hash that maps InterPro identifier to an array reference of secondary accessions following the InterPro xml schema. Args : Empty hash reference =cut sub secondary_accessions_map { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'secondary_accessions_map'} = $value; } return $self->{'secondary_accessions_map'}; } =head2 _increment_record_count Title : _increment_record_count Usage : Function: Example : Returns : Args : =cut sub _increment_record_count { $record_count++; } =head2 _increment_processed_count Title : _increment_processed_count Usage : Function: Example : Returns : Args : =cut sub _increment_processed_count { my $self = shift; $processed_count++; $self->debug("$processed_count\n") if $processed_count % 100 == 0; } 1; BioPerl-1.007002/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm000444000766000024 4605213155576320 24763 0ustar00cjfieldsstaff000000000000# # BioPerl module for InterPro_BioSQL_Handler # # Please direct questions and support issues to # # Cared for by Juguang Xiao, juguang@tll.org.sg # # Copyright Juguang Xiao # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler - parse an InterPro XML file and persist the resulting terms to a Biosql database =head1 SYNOPSIS # see load_interpro.pl in bioperl-db/scripts/biosql/ =head1 DESCRIPTION This module is for parsing an InterPro XML file and persist the resulting terms to a Biosql database as soon as the term is complete as signaled by the appropriate xml tag. This parser takes advantage of SAX, a stream-based XML parser technology, to keep the used memory as small as possible. The alternative parser for InterPro, module InterProHandler, builds up the entire ontology in memory, which given the size of the latest InterPro releases requires a huge amount of memory. This module takes the following non-standard arguments upon instantiation. -db the adaptor factory as returned by a call to Bio::DB::BioDB->new() -version the InterPro version (not available as property!) -term_factory the object factory to use for creating terms Note that there are two alternatives for how to persist the terms and relationships to the database. The default is using the adaptor factory passed as -db or set as a property to create persistent objects and store them in the database. The alternative is to specify a term persistence and a relationship persistence handler; if one or both have been set, the respective handler will be called with each term and relationship that is to be stored. See properties persist_term_handler and persist_relationship_handler. =head1 AUTHOR Juguang Xiao, juguang@tll.org.sg =head1 Contributors Hilmar Lapp, hlapp at gmx.net =head2 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler; use strict; use Bio::Ontology::Ontology; use Bio::Ontology::Term; use Bio::Ontology::TermFactory; use Bio::Ontology::RelationshipType; use Bio::Ontology::Relationship; use Bio::Annotation::DBLink; use Bio::Annotation::Reference; use base qw(Bio::OntologyIO::Handlers::BaseSAXHandler); my $is_a_rel; my $count=0; sub _initialize { my($self,@args)=@_; $self->SUPER::_initialize(@args); my ($db, $version, $fact) = $self->_rearrange( [qw(DB VERSION TERM_FACTORY)], @args); $self->db($db) if $db; # this is now a property and may be set later if (!$fact) { $fact = Bio::Ontology::TermFactory->new(-type=>"Bio::Ontology::Term"); } $self->term_factory($fact); my $ontology = Bio::Ontology::Ontology->new(-name => 'InterPro'); if (defined($version)) { $version = "InterPro version $version"; $ontology->definition($version); } $self->_ontology($ontology); $is_a_rel = Bio::Ontology::RelationshipType->get_instance('IS_A'); $is_a_rel->ontology($ontology); } =head2 term_factory Title : term_factory Usage : $obj->term_factory($newval) Function: Get/set the ontology term factory to use. As a user of this module it is not necessary to call this method as there will be default. In order to change the default, the easiest way is to instantiate L with the proper -type argument. Most if not all parsers will actually use this very implementation, so even easier than the aforementioned way is to simply call $ontio->term_factory->type("Bio::Ontology::MyTerm"). Example : Returns : value of term_factory (a Bio::Factory::ObjectFactoryI object) Args : on set, new value (a Bio::Factory::ObjectFactoryI object, optional) =cut sub term_factory{ my $self = shift; return $self->{'term_factory'} = shift if @_; return $self->{'term_factory'}; } =head2 db Title : db Usage : $obj->db($newval) Function: Sets or retrieves the database adaptor factory. The adaptor factory is a Bio::DB::DBAdaptorI compliant object and will be used to obtain the persistence adaptors necessary to serialize terms and relationships to the database. Usually, you will obtain such an object from a call to Bio::DB::BioDB. You *must* set this property before starting the parse. Note that this property is immutable once set, except that you may set it to undef. Therefore, be careful not to set to undef before setting the desired real value. Example : Returns : value of db (a Bio::DB::DBAdaptorI compliant object) Args : on set, new value (a Bio::DB::DBAdaptorI compliant object or undef, optional) =cut sub db { my $self=shift; if(@_){ my $db = shift; if ($db && exists($self->{_db}) && ($self->{_db} != $db)) { $self->throw('db may not be modified once set'); } $self->{_db}=$db; } return $self->{_db}; } =head2 persist_term_handler Title : persist_term_handler Usage : $obj->persist_term_handler($handler,@args) Function: Sets or retrieves the persistence handler for terms along with the constant set of arguments to be passed to the handler. If set, the first argument will be treated as a closure and be called for each term to persist to the database. The term will be passed as a named parameter (-term), followed by the other arguments passed to this setter. Note that this allows one to pass an arbitrary configuration to the handler. If not set, terms will be persisted along with their relationships using the respective persistence adaptor returned by the adaptor factory (see property db). Example : Returns : an array reference with the values passed on set, or an empty array if never set Args : On set, an array of values. The first value is the handler as a closure; all other values will be passed to the handler as constant argument. =cut sub persist_term_handler{ my $self = shift; return $self->{'persist_term_handler'} = [@_] if @_; return $self->{'persist_term_handler'} || []; } =head2 persist_relationship_handler Title : persist_relationship_handler Usage : $obj->persist_relationship_handler($handler,@args) Function: Sets or retrieves the persistence handler for relationships along with the constant set of arguments to be passed to the handler. If set, the first argument will be treated as a closure and be called for each relationship to persist to the database. The relationship will be passed as a named parameter (-rel), followed by the other arguments passed to this setter. Note that this allows one to pass an arbitrary configuration to the handler. If not set, relationships will be persisted along with their relationships using the respective persistence adaptor returned by the adaptor factory (see property db). Example : Returns : an array reference with the values passed on set, or an empty array if never set Args : On set, an array of values. The first value is the handler as a closure; all other values will be passed to the handler as constant argument. =cut sub persist_relationship_handler{ my $self = shift; return $self->{'persist_relationship_handler'} = [@_] if @_; return $self->{'persist_relationship_handler'} || []; } =head2 _persist_term Title : _persist_term Usage : Function: Persists a term to the database, using either a previously set persistence handler, or the adaptor factory directly. Example : Returns : Args : the ontology term to persist =cut sub _persist_term { my $self = shift; my $term = shift; my ($handler,@args) = @{$self->persist_term_handler}; if ($handler) { &$handler('-term' => $term, @args); } else { # no handler; we'll do this ourselves straight and simple my $db = $self->db(); my $pterm = $db->create_persistent($term); eval { $pterm->create(); $pterm->commit(); }; if ($@) { $pterm->rollback(); $self->warn("failed to store term '".$term->name."': ".$@); } } } =head2 _persist_relationship Title : _persist_relationship Usage : Function: Persists a relationship to the database, using either a previously set persistence handler, or the adaptor factory directly. Example : Returns : Args : the term relationship to persist =cut sub _persist_relationship { my $self = shift; my $rel = shift; my ($handler,@args) = @{$self->persist_relationship_handler}; if ($handler) { &$handler('-rel' => $rel, @args); } else { # no handler; we'll do this ourselves straight and simple my $db = $self->db(); my $prel = $db->create_persistent($rel); eval { $prel->create(); $prel->commit(); }; if ($@) { $prel->rollback(); $self->warn("failed to store relationship of subject '" .$rel->subject_term->name."' to object '" .$rel->object_term->name.": ".$@); } } } =head2 _persist_ontology Title : _persist_ontology Usage : Function: Perists the ontology itself to the database, by either inserting or updating it. Note that this will only create or update the ontology as an entity, not any of its terms, relationships, or relationship types. Example : Returns : the ontology as a persistent object with primary key Args : the ontology to persist as a Bio::Ontology::OntologyI compliant object =cut sub _persist_ontology{ my $self = shift; my $ont = shift; my $db = $self->db(); # do a lookup first; chances are we have this already in the database my $adp = $db->get_object_adaptor($ont); # to avoid clobbering this ontology's properties with possibly older ones # from the database we'll need an object factory my $ontfact = Bio::Factory::ObjectFactory->new(-type=>"Bio::Ontology::Ontology"); # do the lookup: my $found = $adp->find_by_unique_key($ont, '-obj_factory' => $ontfact); # make a persistent object of the ontology $ont = $db->create_persistent($ont); # transfer primary key if found in the lookup $ont->primary_key($found->primary_key) if $found; # insert or update my $result; eval { $result = $ont->store(); }; if ($@ || !$result) { $adp->rollback(); $self->throw("failed to update ontology '" .$ont->name."' in database".($@ ? ": $@" : "")); } # done - we don't commit here return ref($result) ? $result : $ont; } sub start_document { my $self = shift; my $ont = $self->_ontology; my @iprtypes = ( $self->create_term(-identifier=>'IPR:Family', -name=>'Family', -ontology => $ont), $self->create_term(-identifier=>'IPR:Domain', -name=>'Domain', -ontology => $ont), $self->create_term(-identifier=>'IPR:Repeat', -name=>'Repeat', -ontology => $ont), $self->create_term(-identifier=>'IPR:PTM', -name=>'post-translational modification', -ontology => $ont), $self->create_term(-identifier=>'IPR:Active_site', -name=>'Active_site', -ontology => $ont), $self->create_term(-identifier=>'IPR:Binding_site', -name=>'Binding_site', -ontology => $ont), ); foreach my $iprtype (@iprtypes) { $self->_persist_term($iprtype); $ont->add_term($iprtype); } } sub start_element { my $self=shift; my $tag=$_[0]->{Name}; my %args=%{$_[0]->{Attributes}}; my $ont = $self->_ontology; if($tag eq 'interpro'){ my $id = $args{id}; my $term = $self->create_term(-identifier=>$id); $term->ontology($ont); $term->add_synonym($args{short_name}); #$term->definition(); my ($object_term) = ($ont->engine->get_term_by_identifier("IPR:".$args{type})); my $rel = Bio::Ontology::Relationship->new( -subject_term => $term, -predicate_term => $is_a_rel, -object_term => $object_term, -ontology => $ont ); $self->_relationship($rel); }elsif($tag eq 'example'){ my $example = Bio::Annotation::DBLink->new; $self->_current_hash->{example} = $example; }elsif($tag eq 'db_xref'){ my $top = $self->_top_tag; if($top eq 'example'){ my $example = $self->_current_hash->{example}; $example->database($args{db}); $example->primary_id($args{dbkey}); #print "EXAmPLE:\t", $example->database, '|', $example->primary_id, "\n"; }elsif($top eq 'child'){ ; }elsif($top eq 'member_list'){ my $dblink=Bio::Annotation::DBLink->new( -dbname => $args{id}, -primary_id => $args{dbkey}, -comment => $args{name} ); }elsif($top eq 'external_doc_list'){ ; }elsif($top eq 'publication'){ if($args{db} eq 'MEDLINE'){ $self->_current_hash->{medline} =$args{dbkey}; } elsif($args{db} eq 'PUBMED'){ $self->_current_hash->{pubmed} =$args{dbkey}; }else{ $self->warn("'".$args{dbkey}."' is not a MEDLINE publication, " ."don't know how to handle"); } }elsif($top eq 'structure_db_links'){ ; }elsif($top eq 'abstract'){ ; } #else{ # $self->warn("unrecognized element '$top' in element '$tag', ignoring"); #} }elsif($tag eq 'publication'){ my $publication = Bio::Annotation::Reference->new(); $self->_current_hash->{publication} = $publication; }elsif($tag eq 'author_list'){ ; }elsif($tag eq 'journal'){ ; }elsif($tag eq 'location'){ ; }elsif($tag eq 'year'){ ; } elsif (($tag eq 'dbinfo') && ($self->_top_tag eq 'release')) { my $entrydate = $args{file_date} || ''; $entrydate =~ s/ \d{2}:\d{2}:\d{2}//; my $def = $ont->definition() || ''; $def .= "\n" if length($def) > 0; $def .= $args{dbname}." version ".$args{version}.", " .$args{entry_count}." entries, ".$entrydate; $ont->definition($def); } #else{ # $self->warn("unrecognized element '$tag', ignoring"); #} $self->_visited_count_inc($tag); $self->_push_tag($tag); } sub end_element { my $self=shift; my $tag=shift->{Name}; my $chars_in=$self->_chars_hash->{$tag}; if($tag eq 'interpro'){ my $rel = $self->_relationship; # store subject term first in order to give the handler a chance to # apply whatever custom behaviour # (note that the object term is the InterPro type and has been stored # at the start of the whole document) $self->_persist_term($rel->subject_term); # the store the relationship to the InterPro type $self->_persist_relationship($rel); }elsif($tag eq 'name'){ my $rel = $self->_relationship; $rel->subject_term->name($self->_chars_hash->{name}); $self->_chars_hash->{name}=''; }elsif($tag eq 'abstract'){ my $rel = $self->_relationship; my $abstract = $self->_chars_hash->{abstract}; $abstract =~ s/\n/ /g; $rel->subject_term->definition($abstract); $self->_chars_hash->{abstract} = ''; }elsif($tag eq 'example'){ my $example = $self->_current_hash->{example}; my $comment = $self->_chars_hash->{example}; $comment =~ s/^(\s+)//; $comment =~ s/(\s+)$//; $example->comment($comment); $self->_relationship->subject_term->add_dbxref(-dbxrefs => [$example]); $self->_chars_hash->{example}=''; }elsif($tag eq 'publication'){ my $publication = $self->_create_publication; $self->_relationship->subject_term->add_reference($publication); }elsif($tag eq 'author_list'){ $self->_current_hash->{author} =$chars_in; }elsif($tag eq 'title'){ $self->_current_hash->{title}=$chars_in; } elsif ($tag eq 'release') { my $ont = $self->_persist_ontology($self->_ontology); $self->_ontology($ont) if $ont; } $self->_pop_tag; $self->_visited_count_dec($tag); } sub characters { my $self=shift; my $text = shift->{Data}; my $top_tag =$self->_top_tag; $self->_chars_hash->{$top_tag} .= $text; # $self->_chars_hash->{abstract} .= $text if $self->_visited_count('abstract'); } sub create_term { return shift->term_factory->create_object(@_); } sub _ontology { my $self = shift; return $self->{_ontology}=shift if @_; return $self->{_ontology}; } sub _relationship { my $self =shift; $self->{_relationship}=shift if @_; return $self->{_relationship}; } sub _create_publication { my $self=shift; my $publ = $self->_current_hash->{publication}; my $journal = $self->_current_hash->{journal} || ''; my $year = $self->_current_hash->{year} || ''; my $page_location = $self->_current_hash->{page_location} || ''; my $volumn = $self->_current_hash->{volumn} || ''; my $medline = $self->_current_hash->{medline} || $self->_current_hash->{pubmed}; $publ->authors($self->_current_hash->{author}); $publ->location("$journal, $year, V $volumn, $page_location"); $publ->title($self->_current_hash->{title}); $publ->medline($medline); if ($self->_current_hash->{pubmed} && ($self->_current_hash->{pubmed} != $medline)) { $publ->pubmed($self->_current_hash->{pubmed}); } # Clear the above in current hash $self->_current_hash->{publication} = undef; $self->_current_hash->{author} = undef; $self->_current_hash->{journal} = undef; $self->_current_hash->{year} = undef; $self->_current_hash->{page_location}=undef; $self->_current_hash->{volumn} = undef; $self->_current_hash->{title} = undef; $self->_current_hash->{medline} = undef; $self->_current_hash->{pubmed} = undef; } 1; BioPerl-1.007002/Bio/Phenotype000755000766000024 013155576320 16042 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Phenotype/Correlate.pm000444000766000024 2140613155576320 20500 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Phenotype::Correlate # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Phenotype::Correlate - Representation of a correlating phenotype in a given species =head1 SYNOPSIS use Bio::Phenotype::Correlate; $co = Bio::Phenotype::Correlate->new( -name => "4(Tas1r3)", -description => "mouse correlate of human phenotype MIM 605865", -species => $mouse, -type => "homolog", -comment => "type=homolog is putative" ); print $co->name(); print $co->description(); print $co->species()->binomial(); print $co->type(); print $co->comment(); print $co->to_string(); =head1 DESCRIPTION This class models correlating phenotypes. Its creation was inspired by the OMIM database where many human phenotypes have a correlating mouse phenotype. Therefore, this class is intended to be used together with a phenotype class. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 APPENDIX The rest of the documentation details each of the object methods. =cut # Let the code begin... package Bio::Phenotype::Correlate; use strict; use Bio::Species; use base qw(Bio::Root::Root); =head2 new Title : new Usage : $co = Bio::Phenotype::Correlate->new( -name => "4(Tas1r3)", -description => "mouse correlate of human phenotype MIM 605865", -species => $mouse, -type => "homolog", -comment => "type=homolog is putative" ); Function: Creates a new Correlate object. Returns : A new Correlate object. Args : -name => a name or id -description => a description -species => the species of this correlating phenotype [Bio::Species] -type => the type of correlation -comment => a comment =cut sub new { my( $class, @args ) = @_; my $self = $class->SUPER::new( @args ); my ( $name, $desc, $species, $type, $comment ) = $self->_rearrange( [ qw( NAME DESCRIPTION SPECIES TYPE COMMENT ) ], @args ); $self->init(); $name && $self->name( $name ); $desc && $self->description( $desc ); $species && $self->species( $species ); $type && $self->type( $type ); $comment && $self->comment( $comment ); return $self; } # new =head2 init Title : init() Usage : $co->init(); Function: Initializes this Correlate to all "". Returns : Args : =cut sub init { my( $self ) = @_; $self->name( "" ); $self->description( "" ); my $species = Bio::Species->new(); $species->classification( qw( species Undetermined ) ); $self->species( $species ); $self->type( "" ); $self->comment( "" ); } # init =head2 name Title : name Usage : $co->name( "4(Tas1r3)" ); or print $co->name(); Function: Set/get for the name or id of this Correlate. Returns : The name or id of this Correlate. Args : The name or id of this Correlate (optional). =cut sub name { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_name" } = $value; } return $self->{ "_name" }; } # name =head2 description Title : description Usage : $co->description( "mouse correlate of human phenotype MIM 03923" ); or print $co->description(); Function: Set/get for the description of this Correlate. Returns : A description of this Correlate. Args : A description of this Correlate (optional). =cut sub description { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_description" } = $value; } return $self->{ "_description" }; } # description =head2 species Title : species Usage : $co->species( $species ); or $species = $co->species(); Function: Set/get for the species of this Correlate. Returns : The Bio::Species of this Correlate [Bio::Species]. Args : The Bio::Species of this Correlate [Bio::Species] (optional). =cut sub species { my ( $self, $value ) = @_; if ( defined $value ) { $self->_check_ref_type( $value, "Bio::Species" ); $self->{ "_species" } = $value; } return $self->{ "_species" }; } # species =head2 type Title : type Usage : $co->type( "homolog" ); or print $co->type(); Function: Set/get for the type of this Correlate. Returns : The type of this Correlate. Args : The type of this Correlate (optional). =cut sub type { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_type" } = $value; } return $self->{ "_type" }; } # type =head2 comment Title : comment Usage : $co->comment( "doubtful" ); or print $co->comment(); Function: Set/get for an arbitrary comment about this Correlate. Returns : A comment. Args : A comment (optional). =cut sub comment { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_comment" } = $value; } return $self->{ "_comment" }; } # comment =head2 to_string Title : to_string() Usage : print $co->to_string(); Function: To string method for Correlate objects. Returns : A string representations of this Correlate. Args : =cut sub to_string { my ( $self ) = @_; my $s = ""; $s .= "-- Name:\n"; $s .= $self->name()."\n"; $s .= "-- Description:\n"; $s .= $self->description()."\n"; $s .= "-- Species:\n"; $s .= $self->species()->binomial()."\n"; $s .= "-- Type of correlation:\n"; $s .= $self->type()."\n"; $s .= "-- Comment:\n"; $s .= $self->comment(); return $s; } # to_string # Title : _check_ref_type # Function: Checks for the correct type. # Returns : # Args : The value to be checked, the expected class. sub _check_ref_type { my ( $self, $value, $expected_class ) = @_; if ( ! defined( $value ) ) { $self->throw( ( caller( 1 ) )[ 3 ] .": Found [undef" ."] where [$expected_class] expected" ); } elsif ( ! ref( $value ) ) { $self->throw( ( caller( 1 ) )[ 3 ] .": Found scalar" ." where [$expected_class] expected" ); } elsif ( ! $value->isa( $expected_class ) ) { $self->throw( ( caller( 1 ) )[ 3 ] .": Found [". ref( $value ) ."] where [$expected_class] expected" ); } } # _check_ref_type 1; BioPerl-1.007002/Bio/Phenotype/Measure.pm000444000766000024 2030313155576320 20154 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Phenotype::Measure # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Phenotype::Measure - Representation of context/value(-range)/unit triplets =head1 SYNOPSIS use Bio::Phenotype::Measure; my $measure = Bio::Phenotype::Measure->new( -context => "length", -description => "reduced length in 4(Tas1r3)", -start => 0, -end => 15, -unit => "mm", -comment => "see also Miller et al" ); print $measure->context(); print $measure->description(); print $measure->start(); print $measure->end(); print $measure->unit(); print $measure->comment(); print $measure->to_string(); =head1 DESCRIPTION Measure is for biochemically defined phenotypes or any other types of measures. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 APPENDIX The rest of the documentation details each of the object methods. =cut # Let the code begin... package Bio::Phenotype::Measure; use strict; use base qw(Bio::Root::Root); =head2 new Title : new Usage : my $me = Bio::Phenotype::Measure->new( -context => "length", -description => "reduced length in 4(Tas1r3)", -start => 0, -end => 15, -unit => "mm", -comment => "see Miller also et al" ); Function: Creates a new Measure object. Returns : A new Measure object. Args : -context => the context -description => a description -start => the start value -end => the end value -unit => the unit -comment => a comment =cut sub new { my( $class, @args ) = @_; my $self = $class->SUPER::new( @args ); my ( $con, $desc, $start, $end, $unit, $comment ) = $self->_rearrange( [ qw( CONTEXT DESCRIPTION START END UNIT COMMENT ) ], @args ); $self->init(); $con && $self->context( $con ); $desc && $self->description( $desc ); $start && $self->start( $start ); $end && $self->end( $end ); $unit && $self->unit( $unit ); $comment && $self->comment( $comment ); return $self; } # new =head2 init Title : init() Usage : $measure->init(); Function: Initializes this Measure to all "". Returns : Args : =cut sub init { my( $self ) = @_; $self->context( "" ); $self->description( "" ); $self->start( "" ); $self->end( "" ); $self->unit( "" ); $self->comment( "" ); } # init =head2 context Title : context Usage : $measure->context( "Ca-conc" ); or print $measure->context(); Function: Set/get for the context of this Measure. Returns : The context. Args : The context (optional). =cut sub context { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_context" } = $value; } return $self->{ "_context" }; } # context =head2 description Title : description Usage : $measure->description( "reduced in 4(Tas1r3)" ); or print $measure->description(); Function: Set/get for the description of this Measure. Returns : A description. Args : A description (optional). =cut sub description { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_description" } = $value; } return $self->{ "_description" }; } # description =head2 start Title : start Usage : $measure->start( 330 ); or print $measure->start(); Function: Set/get for the start value of this Measure. Returns : The start value. Args : The start value (optional). =cut sub start { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_start" } = $value; } return $self->{ "_start" }; } # start =head2 end Title : end Usage : $measure->end( 459 ); or print $measure->end(); Function: Set/get for the end value of this Measure. Returns : The end value. Args : The end value (optional). =cut sub end { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_end" } = $value; } return $self->{ "_end" }; } # end =head2 unit Title : unit Usage : $measure->unit( "mM" ); or print $measure->unit(); Function: Set/get for the unit of this Measure. Returns : The unit. Args : The unit (optional). =cut sub unit { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_unit" } = $value; } return $self->{ "_unit" }; } # unit =head2 comment Title : comment Usage : $measure->comment( "see also Miller et al" ); or print $measure->comment(); Function: Set/get for an arbitrary comment about this Measure. Returns : A comment. Args : A comment (optional). =cut sub comment { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_comment" } = $value; } return $self->{ "_comment" }; } # comment =head2 to_string Title : to_string() Usage : print $measure->to_string(); Function: To string method for Measure objects. Returns : A string representations of this Measure. Args : =cut sub to_string { my ( $self ) = @_; my $s = ""; $s .= "-- Context:\n"; $s .= $self->context()."\n"; $s .= "-- Description:\n"; $s .= $self->description()."\n"; $s .= "-- Start:\n"; $s .= $self->start()."\n"; $s .= "-- End:\n"; $s .= $self->end()."\n"; $s .= "-- Unit:\n"; $s .= $self->unit()."\n"; $s .= "-- Comment:\n"; $s .= $self->comment(); return $s; } # to_string 1; BioPerl-1.007002/Bio/Phenotype/Phenotype.pm000444000766000024 5322513155576320 20537 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Phenotype::Phenotype # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Phenotype::Phenotype - A class for modeling phenotypes =head1 SYNOPSIS #get Bio::Phenotype::PhenotypeI somehow print $phenotype->name(), "\n"; print $phenotype->description(), "\n"; my @keywords = ( "achondroplasia", "dwarfism" ); $phenotype->add_keywords( @keywords ); foreach my $keyword ( $phenotype->each_keyword() ) { print $keyword, "\n"; } $phenotype->remove_keywords(); foreach my $gene_symbol ( $phenotype->each_gene_symbol() ) { print $gene_symbol, "\n"; } foreach my $corr ( $phenotype->each_Correlate() ) { # Do something with $corr } foreach my $var ( $phenotype->each_Variant() ) { # Do something with $var (mutation) } foreach my $measure ( $phenotype->each_Measure() ) { # Do something with $measure } =head1 DESCRIPTION This superclass implements common methods for classes modelling phenotypes. Bio::Phenotype::OMIM::OMIMentry is an example of an instantiable phenotype class (the design of this interface was partially guided by the need to model OMIM entries). Please note. This class provides methods to associate mutations (methods "each_Variant", ...) and genotypes (methods "each_Genotype", ...) with phenotypes. Yet, these aspects might need some future enhancements, especially since there is no "genotype" class yet. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Phenotype::Phenotype; use strict; use Bio::Species; use Bio::Variation::VariantI; use Bio::Annotation::DBLink; use Bio::Annotation::Reference; use Bio::Phenotype::Measure; use Bio::Phenotype::Correlate; use Bio::Map::CytoPosition; use Bio::Range; use base qw(Bio::Root::Root Bio::Phenotype::PhenotypeI); =head2 new Title : new Usage : $obj = Bio::Phenotype::Phenotype->new( -name => "XY", -description => "This is ..." ); Function: Creates a new Phenotype object. Returns : A new Phenotype object. Args : -name => the name -description => the description of this phenotype -species => ref to the the species -comment => a comment =cut sub new { my( $class,@args ) = @_; my $self = $class->SUPER::new( @args ); my ( $name, $description, $species, $comment ) = $self->_rearrange( [ qw( NAME DESCRIPTION SPECIES COMMENT ) ], @args ); $self->init(); $name && $self->name( $name ); $description && $self->description( $description ); $species && $self->species( $species ); $comment && $self->comment( $comment ); return $self; } # new =head2 init Title : init() Usage : $obj->init(); Function: Initializes this OMIMentry to all "" and empty lists. Returns : Args : =cut sub init { my( $self ) = @_; $self->name( "" ); $self->description( "" ); my $species = Bio::Species->new(); $species->classification( qw( sapiens Homo ) ); $self->species( $species ); $self->comment( "" ); $self->remove_Correlates(); $self->remove_References(); $self->remove_CytoPositions(); $self->remove_gene_symbols(); $self->remove_Genotypes(); $self->remove_DBLinks(); $self->remove_keywords(); $self->remove_Variants(); $self->remove_Measures(); } # init =head2 name Title : name Usage : $obj->name( "r1" ); or print $obj->name(); Function: Set/get for the name or id of this phenotype. Returns : A name or id [scalar]. Args : A name or id [scalar] (optional). =cut sub name { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_name" } = $value; } return $self->{ "_name" }; } # name =head2 description Title : description Usage : $obj->description( "This is ..." ); or print $obj->description(); Function: Set/get for the description of this phenotype. Returns : A description [scalar]. Args : A description [scalar] (optional). =cut sub description { my $self = shift; return $self->{ "_description" } = shift if(@_); return $self->{ "_description" }; } =head2 species Title : species Usage : $obj->species( $species ); or $species = $obj->species(); Function: Set/get for the species of this phenotype. Returns : A species [Bio::Species]. Args : A species [Bio::Species] (optional). =cut sub species { my ( $self, $value ) = @_; if ( defined $value ) { $self->_check_ref_type( $value, "Bio::Species" ); $self->{ "_species" } = $value; } return $self->{ "_species" }; } # species =head2 comment Title : comment Usage : $obj->comment( "putative" ); or print $obj->comment(); Function: Set/get for a comment about this phenotype. Returns : A comment [scalar]. Args : A comment [scalar] (optional). =cut sub comment { my $self = shift; return $self->{ "_comment" } = shift if(@_); return $self->{ "_comment" }; } # comment =head2 each_gene_symbol Title : each_gene_symbol() Usage : @gs = $obj->each_gene_symbol(); Function: Returns a list of gene symbols [scalars, most likely Strings] associated with this phenotype. Returns : A list of scalars. Args : =cut sub each_gene_symbol { my ( $self ) = @_; return @{$self->{"_gene_symbols"}} if exists($self->{"_gene_symbols"}); return (); } # each_gene_symbol =head2 add_gene_symbols Title : add_gene_symbols Usage : $obj->add_gene_symbols( @gs ); or $obj->add_gene_symbols( $gs ); Function: Pushes one or more gene symbols [scalars, most likely Strings] into the list of gene symbols. Returns : Args : scalar(s). =cut sub add_gene_symbols { my ( $self, @values ) = @_; return unless( @values ); push( @{ $self->{ "_gene_symbols" } }, @values ); } # add_gene_symbols =head2 remove_gene_symbols Usage : $obj->remove_gene_symbols(); Function: Deletes (and returns) the list of gene symbols [scalars, most likely Strings] associated with this phenotype. Returns : A list of scalars. Args : =cut sub remove_gene_symbols { my ( $self ) = @_; my @a = $self->each_gene_symbol(); $self->{ "_gene_symbols" } = []; return @a; } # remove_gene_symbols =head2 each_Variant Title : each_Variant() Usage : @vs = $obj->each_Variant(); Function: Returns a list of Bio::Variation::VariantI implementing objects associated with this phenotype. This is for representing the actual mutation(s) causing this phenotype. {* The "variants" data member and its methods will/might need to be changed/improved in one way or another, CZ 09/06/02 *} Returns : A list of Bio::Variation::VariantI implementing objects. Args : =cut sub each_Variant { my ( $self ) = @_; return @{ $self->{ "_variants" } } if exists($self->{ "_variants" }); return (); } # each_Variant =head2 add_Variants Usage : $obj->add_Variants( @vs ); or $obj->add_Variants( $v ); Function: Pushes one or more Bio::Variation::VariantI implementing objects into the list of Variants. Returns : Args : Bio::Variation::VariantI implementing object(s). =cut sub add_Variants { my ( $self, @values ) = @_; return unless( @values ); foreach my $value ( @values ) { $self->_check_ref_type( $value, "Bio::Variation::VariantI" ); } push( @{ $self->{ "_variants" } }, @values ); } # add_Variants =head2 remove_Variants Title : remove_Variants Usage : $obj->remove_Variants(); Function: Deletes (and returns) the list of Bio::Variation::VariantI implementing objects associated with this phenotype. Returns : A list of Bio::Variation::VariantI implementing objects. Args : =cut sub remove_Variants { my ( $self ) = @_; my @a = $self->each_Variant(); $self->{ "_variants" } = []; return @a; } # remove_Variants =head2 each_Reference Title : each_Reference() Usage : @refs = $obj->each_Reference(); Function: Returns a list of Bio::Annotation::Reference objects associated with this phenotype. Returns : A list of Bio::Annotation::Reference objects. Args : =cut sub each_Reference { my ( $self ) = @_; return @{ $self->{ "_references" } } if exists($self->{ "_references" }); return (); } # each_Reference =head2 add_References Title : add_References Usage : $obj->add_References( @refs ); or $obj->add_References( $ref ); Function: Pushes one or more Bio::Annotation::Reference objects into the list of References. Returns : Args : Bio::Annotation::Reference object(s). =cut sub add_References { my ( $self, @values ) = @_; return unless( @values ); foreach my $value ( @values ) { $self->_check_ref_type( $value, "Bio::Annotation::Reference" ); } push( @{ $self->{ "_references" } }, @values ); } # add_References =head2 remove_References Title : remove_References() Usage : $obj->remove_References(); Function: Deletes (and returns) the list of Bio::Annotation::Reference objects associated with this phenotype. Returns : A list of Bio::Annotation::Reference objects. Args : =cut sub remove_References { my ( $self ) = @_; my @a = $self->each_Reference(); $self->{ "_references" } = []; return @a; } # remove_References =head2 each_CytoPosition Title : each_CytoPosition() Usage : @cps = $obj->each_CytoPosition(); Function: Returns a list of Bio::Map::CytoPosition objects associated with this phenotype. Returns : A list of Bio::Map::CytoPosition objects. Args : =cut sub each_CytoPosition { my ( $self ) = @_; return @{$self->{"_cyto_positions"}} if exists($self->{"_cyto_positions"}); return (); } # each_CytoPosition =head2 add_CytoPositions Title : add_CytoPositions Usage : $obj->add_CytoPositions( @cps ); or $obj->add_CytoPositions( $cp ); Function: Pushes one or more Bio::Map::CytoPosition objects into the list of CytoPositions. Returns : Args : Bio::Map::CytoPosition object(s). =cut sub add_CytoPositions { my ( $self, @values ) = @_; return unless( @values ); foreach my $value ( @values ) { $self->_check_ref_type( $value, "Bio::Map::CytoPosition" ); } push( @{ $self->{ "_cyto_positions" } }, @values ); } # add_CytoPositions =head2 remove_CytoPositions Title : remove_CytoPositions Usage : $obj->remove_CytoPositions(); Function: Deletes (and returns) the list o fBio::Map::CytoPosition objects associated with this phenotype. Returns : A list of Bio::Map::CytoPosition objects. Args : =cut sub remove_CytoPositions { my ( $self ) = @_; my @a = $self->each_CytoPosition(); $self->{ "_cyto_positions" } = []; return @a; } # remove_CytoPositions =head2 each_Correlate Title : each_Correlate() Usage : @corrs = $obj->each_Correlate(); Function: Returns a list of Bio::Phenotype::Correlate objects associated with this phenotype. (Correlates are correlating phenotypes in different species; inspired by mouse correlates of human phenotypes in the OMIM database.) Returns : A list of Bio::Phenotype::Correlate objects. Args : =cut sub each_Correlate { my ( $self ) = @_; return @{ $self->{ "_correlates" } } if exists($self->{ "_correlates" }); return (); } # each_Correlate =head2 add_Correlates Title : add_Correlates Usage : $obj->add_Correlates( @corrs ); or $obj->add_Correlates( $corr ); Function: Pushes one or more Bio::Phenotype::Correlate objects into the list of Correlates. Returns : Args : Bio::Phenotype::Correlate object(s). =cut sub add_Correlates { my ( $self, @values ) = @_; return unless( @values ); foreach my $value ( @values ) { $self->_check_ref_type( $value, "Bio::Phenotype::Correlate" ); } push( @{ $self->{ "_correlates" } }, @values ); } # add_Correlates =head2 remove_Correlates Title : remove_Correlates Usage : $obj->remove_Correlates(); Function: Deletes (and returns) the list of Bio::Phenotype::Correlate objects associated with this phenotype. Returns : A list of Bio::Phenotype::Correlate objects. Args : =cut sub remove_Correlates { my ( $self ) = @_; my @a = $self->each_Correlate(); $self->{ "_correlates" } = []; return @a; } # remove_Correlates =head2 each_Measure Title : each_Measure() Usage : @ms = $obj->each_Measure(); Function: Returns a list of Bio::Phenotype::Measure objects associated with this phenotype. (Measure is for biochemically defined phenotypes or any other types of measures.) Returns : A list of Bio::Phenotype::Measure objects. Args : =cut sub each_Measure { my ( $self ) = @_; return @{ $self->{ "_measures" } } if exists($self->{ "_measures" }); return (); } # each_Measure =head2 add_Measures Title : add_Measures Usage : $obj->add_Measures( @ms ); or $obj->add_Measures( $m ); Function: Pushes one or more Bio::Phenotype::Measure objects into the list of Measures. Returns : Args : Bio::Phenotype::Measure object(s). =cut sub add_Measures { my ( $self, @values ) = @_; return unless( @values ); foreach my $value ( @values ) { $self->_check_ref_type( $value, "Bio::Phenotype::Measure" ); } push( @{ $self->{ "_measures" } }, @values ); } # add_Measures =head2 remove_Measures Title : remove_Measures Usage : $obj->remove_Measures(); Function: Deletes (and returns) the list of Bio::Phenotype::Measure objects associated with this phenotype. Returns : A list of Bio::Phenotype::Measure objects. Args : =cut sub remove_Measures { my ( $self ) = @_; my @a = $self->each_Measure(); $self->{ "_measures" } = []; return @a; } # remove_Measures =head2 each_keyword Title : each_keyword() Usage : @kws = $obj->each_keyword(); Function: Returns a list of key words [scalars, most likely Strings] associated with this phenotype. Returns : A list of scalars. Args : =cut sub each_keyword { my ( $self ) = @_; return @{ $self->{ "_keywords" } } if exists($self->{ "_keywords" }); return (); } # each_keyword =head2 add_keywords Title : add_keywords Usage : $obj->add_keywords( @kws ); or $obj->add_keywords( $kw ); Function: Pushes one or more keywords [scalars, most likely Strings] into the list of key words. Returns : Args : scalar(s). =cut sub add_keywords { my ( $self, @values ) = @_; return unless( @values ); push( @{ $self->{ "_keywords" } }, @values ); } # add_keywords =head2 remove_keywords Title : remove_keywords Usage : $obj->remove_keywords(); Function: Deletes (and returns) the list of key words [scalars, most likely Strings] associated with this phenotype. Returns : A list of scalars. Args : =cut sub remove_keywords { my ( $self ) = @_; my @a = $self->each_keyword(); $self->{ "_keywords" } = []; return @a; } # remove_keywords =head2 each_DBLink Title : each_DBLink() Usage : @dbls = $obj->each_DBLink(); Function: Returns a list of Bio::Annotation::DBLink objects associated with this phenotype. Returns : A list of Bio::Annotation::DBLink objects. Args : =cut sub each_DBLink { my ( $self ) = @_; return @{ $self->{ "_db_links" } } if exists($self->{ "_db_links" }); return (); } =head2 add_DBLinks Title : add_DBLinks Usage : $obj->add_DBLinks( @dbls ); or $obj->add_DBLinks( $dbl ); Function: Pushes one or more Bio::Annotation::DBLink objects into the list of DBLinks. Returns : Args : Bio::Annotation::DBLink object(s). =cut sub add_DBLinks { my ( $self, @values ) = @_; return unless( @values ); foreach my $value ( @values ) { $self->_check_ref_type( $value, "Bio::Annotation::DBLink" ); } push( @{ $self->{ "_db_links" } }, @values ); } # add_DBLinks =head2 remove_DBLinks Title : remove_DBLinks Usage : $obj->remove_DBLinks(); Function: Deletes (and returns) the list of Bio::Annotation::DBLink objects associated with this phenotype. Returns : A list of Bio::Annotation::DBLink objects. Args : =cut sub remove_DBLinks { my ( $self ) = @_; my @a = $self->each_DBLink(); $self->{ "_db_links" } = []; return @a; } # remove_DBLinks =head2 each_Genotype Title : each_Reference() Usage : @gts = $obj->each_Reference(); Function: Returns a list of "Genotype" objects associated with this phenotype. {* the "genotypes" data member and its methods certainly will/needs to be changed/improved in one way or another since there is no "Genotype" class yet, CZ 09/06/02 *} Returns : A list of "Genotype" objects. Args : =cut sub each_Genotype { my ( $self ) = @_; return @{ $self->{ "_genotypes" } } if exists($self->{ "_genotypes" }); return (); } # each_Genotype =head2 add_Genotypes Title : add_Genotypes Usage : $obj->add_Genotypes( @gts ); or $obj->add_Genotypes( $gt ); Function: Pushes one or more "Genotypes" into the list of "Genotypes". Returns : Args : "Genotypes(s)". =cut sub add_Genotypes { my ( $self, @values ) = @_; return unless( @values ); #foreach my $value ( @values ) { # $self->_check_ref_type( $value, "Bio::GenotypeI" ); #} push( @{ $self->{ "_genotypes" } }, @values ); } # add_Genotypes =head2 remove_Genotypes Title : remove_Genotypes Usage : $obj->remove_Genotypes(); Function: Deletes (and returns) the list of "Genotype" objects associated with this phenotype. Returns : A list of "Genotype" objects. Args : =cut sub remove_Genotypes { my ( $self ) = @_; my @a = $self->each_Genotype(); $self->{ "_genotypes" } = []; return @a; } # remove_Genotypes =head2 _check_ref_type Title : _check_ref_type Usage : $self->_check_ref_type( $value, "Bio::Annotation::DBLink" ); Function: Checks for the correct type. Returns : Args : The value to be checked, the expected class. =cut sub _check_ref_type { my ( $self, $value, $expected_class ) = @_; if ( ! defined( $value ) ) { $self->throw( ( caller( 1 ) )[ 3 ] .": Found [undef" ."] where [$expected_class] expected" ); } elsif ( ! ref( $value ) ) { $self->throw( ( caller( 1 ) )[ 3 ] .": Found scalar" ." where [$expected_class] expected" ); } elsif ( ! $value->isa( $expected_class ) ) { $self->throw( ( caller( 1 ) )[ 3 ] .": Found [". ref( $value ) ."] where [$expected_class] expected" ); } } # _check_ref_type 1; BioPerl-1.007002/Bio/Phenotype/PhenotypeI.pm000444000766000024 4055113155576320 20646 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Phenotype::PhenotypeI # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Phenotype::PhenotypeI - An interface for classes modeling phenotypes =head1 SYNOPSIS #get Bio::Phenotype::PhenotypeI somehow print $phenotype->name(), "\n"; print $phenotype->description(), "\n"; my @keywords = ( "achondroplasia", "dwarfism" ); $phenotype->add_keywords( @keywords ); foreach my $keyword ( $phenotype->each_keyword() ) { print $keyword, "\n"; } $phenotype->remove_keywords(); foreach my $gene_symbol ( $phenotype->each_gene_symbol() ) { print $gene_symbol, "\n"; } foreach my $corr ( $phenotype->each_Correlate() ) { # Do something with $corr } foreach my $var ( $phenotype->each_Variant() ) { # Do something with $var (mutation) } foreach my $measure ( $phenotype->each_Measure() ) { # Do something with $measure } =head1 DESCRIPTION This superclass defines common methods for classes modelling phenotypes. Bio::Phenotype::OMIM::OMIMentry is an example of an instantiable phenotype class (the design of this interface was partially guided by the need to model OMIM entries). Please note. This interface provides methods to associate mutations (methods "each_Variant", ...) and genotypes (methods "each_Genotype", ...) with phenotypes. Yet, these aspects might need some future enhancements, especially since there is no "genotype" class yet. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Phenotype::PhenotypeI; use base qw(Bio::Root::RootI); =head2 name Title : name Usage : $obj->name( "r1" ); or print $obj->name(); Function: Set/get for the name or id of this phenotype. Returns : A name or id [scalar]. Args : A name or id [scalar] (optional). =cut sub name { my ( $self ) = @_; $self->throw_not_implemented(); } # name =head2 description Title : description Usage : $obj->description( "This is ..." ); or print $obj->description(); Function: Set/get for the description of this phenotype. Returns : A description [scalar]. Args : A description [scalar] (optional). =cut sub description { my ( $self ) = @_; $self->throw_not_implemented(); } # description =head2 species Title : species Usage : $obj->species( $species ); or $species = $obj->species(); Function: Set/get for the species of this phenotype. Returns : A species [Bio::Species]. Args : A species [Bio::Species] (optional). =cut sub species { my ( $self ) = @_; $self->throw_not_implemented(); } # species =head2 comment Title : comment Usage : $obj->comment( "putative" ); or print $obj->comment(); Function: Set/get for a comment about this phenotype. Returns : A comment [scalar]. Args : A comment [scalar] (optional). =cut sub comment { my ( $self ) = @_; $self->throw_not_implemented(); } # comment =head2 each_gene_symbol Title : each_gene_symbol() Usage : @gs = $obj->each_gene_symbol(); Function: Returns a list of gene symbols [scalars, most likely Strings] associated with this phenotype. Returns : A list of scalars. Args : =cut sub each_gene_symbol { my ( $self ) = @_; $self->throw_not_implemented(); } # each_gene_symbol =head2 add_gene_symbols Title : add_gene_symbols Usage : $obj->add_gene_symbols( @gs ); or $obj->add_gene_symbols( $gs ); Function: Pushes one or more gene symbols [scalars, most likely Strings] into the list of gene symbols. Returns : Args : scalar(s). =cut sub add_gene_symbols { my ( $self ) = @_; $self->throw_not_implemented(); } # add_gene_symbols =head2 remove_gene_symbols Usage : $obj->remove_gene_symbols(); Function: Deletes (and returns) the list of gene symbols [scalars, most likely Strings] associated with this phenotype. Returns : A list of scalars. Args : =cut sub remove_gene_symbols { my ( $self ) = @_; $self->throw_not_implemented(); } # remove_gene_symbols =head2 each_Variant Title : each_Variant() Usage : @vs = $obj->each_Variant(); Function: Returns a list of Bio::Variation::VariantI implementing objects associated with this phenotype. This is for representing the actual mutation(s) causing this phenotype. {* The "variants" data member and its methods will/might need to be changed/improved in one way or another, CZ 09/06/02 *} Returns : A list of Bio::Variation::VariantI implementing objects. Args : =cut sub each_Variant { my ( $self ) = @_; $self->throw_not_implemented(); } # each_Variant =head2 add_Variants Usage : $obj->add_Variants( @vs ); or $obj->add_Variants( $v ); Function: Pushes one or more Bio::Variation::VariantI implementing objects into the list of Variants. Returns : Args : Bio::Variation::VariantI implementing object(s). =cut sub add_Variants { my ( $self ) = @_; $self->throw_not_implemented(); } # add_Variants =head2 remove_Variants Title : remove_Variants Usage : $obj->remove_Variants(); Function: Deletes (and returns) the list of Bio::Variation::VariantI implementing objects associated with this phenotype. Returns : A list of Bio::Variation::VariantI implementing objects. Args : =cut sub remove_Variants { my ( $self ) = @_; $self->throw_not_implemented(); } # remove_Variants =head2 each_Reference Title : each_Reference() Usage : @refs = $obj->each_Reference(); Function: Returns a list of Bio::Annotation::Reference objects associated with this phenotype. Returns : A list of Bio::Annotation::Reference objects. Args : =cut sub each_Reference { my ( $self ) = @_; $self->throw_not_implemented(); } # each_Reference =head2 add_References Title : add_References Usage : $obj->add_References( @refs ); or $obj->add_References( $ref ); Function: Pushes one or more Bio::Annotation::Reference objects into the list of References. Returns : Args : Bio::Annotation::Reference object(s). =cut sub add_References { my ( $self ) = @_; $self->throw_not_implemented(); } # add_References =head2 remove_References Title : remove_References() Usage : $obj->remove_References(); Function: Deletes (and returns) the list of Bio::Annotation::Reference objects associated with this phenotype. Returns : A list of Bio::Annotation::Reference objects. Args : =cut sub remove_References { my ( $self ) = @_; $self->throw_not_implemented(); } # remove_References =head2 each_CytoPosition Title : each_CytoPosition() Usage : @cps = $obj->each_CytoPosition(); Function: Returns a list of Bio::Map::CytoPosition objects associated with this phenotype. Returns : A list of Bio::Map::CytoPosition objects. Args : =cut sub each_CytoPosition { my ( $self ) = @_; $self->throw_not_implemented(); } # each_CytoPosition =head2 add_CytoPositions Title : add_CytoPositions Usage : $obj->add_CytoPositions( @cps ); or $obj->add_CytoPositions( $cp ); Function: Pushes one or more Bio::Map::CytoPosition objects into the list of CytoPositions. Returns : Args : Bio::Map::CytoPosition object(s). =cut sub add_CytoPositions { my ( $self ) = @_; $self->throw_not_implemented(); } # add_CytoPositions =head2 remove_CytoPositions Title : remove_CytoPositions Usage : $obj->remove_CytoPositions(); Function: Deletes (and returns) the list o fBio::Map::CytoPosition objects associated with this phenotype. Returns : A list of Bio::Map::CytoPosition objects. Args : =cut sub remove_CytoPositions { my ( $self ) = @_; $self->throw_not_implemented(); } # remove_CytoPositions =head2 each_Correlate Title : each_Correlate() Usage : @corrs = $obj->each_Correlate(); Function: Returns a list of Bio::Phenotype::Correlate objects associated with this phenotype. (Correlates are correlating phenotypes in different species; inspired by mouse correlates of human phenotypes in the OMIM database.) Returns : A list of Bio::Phenotype::Correlate objects. Args : =cut sub each_Correlate { my ( $self ) = @_; $self->throw_not_implemented(); } # each_Correlate =head2 add_Correlates Title : add_Correlates Usage : $obj->add_Correlates( @corrs ); or $obj->add_Correlates( $corr ); Function: Pushes one or more Bio::Phenotype::Correlate objects into the list of Correlates. Returns : Args : Bio::Phenotype::Correlate object(s). =cut sub add_Correlates { my ( $self ) = @_; $self->throw_not_implemented(); } # add_Correlates =head2 remove_Correlates Title : remove_Correlates Usage : $obj->remove_Correlates(); Function: Deletes (and returns) the list of Bio::Phenotype::Correlate objects associated with this phenotype. Returns : A list of Bio::Phenotype::Correlate objects. Args : =cut sub remove_Correlates { my ( $self ) = @_; $self->throw_not_implemented(); } # remove_Correlates =head2 each_Measure Title : each_Measure() Usage : @ms = $obj->each_Measure(); Function: Returns a list of Bio::Phenotype::Measure objects associated with this phenotype. (Measure is for biochemically defined phenotypes or any other types of measures.) Returns : A list of Bio::Phenotype::Measure objects. Args : =cut sub each_Measure { my ( $self ) = @_; $self->throw_not_implemented(); } # each_Measure =head2 add_Measures Title : add_Measures Usage : $obj->add_Measures( @ms ); or $obj->add_Measures( $m ); Function: Pushes one or more Bio::Phenotype::Measure objects into the list of Measures. Returns : Args : Bio::Phenotype::Measure object(s). =cut sub add_Measures { my ( $self ) = @_; $self->throw_not_implemented(); } # add_Measures =head2 remove_Measures Title : remove_Measures Usage : $obj->remove_Measures(); Function: Deletes (and returns) the list of Bio::Phenotype::Measure objects associated with this phenotype. Returns : A list of Bio::Phenotype::Measure objects. Args : =cut sub remove_Measures { my ( $self ) = @_; $self->throw_not_implemented(); } # remove_Measures =head2 each_keyword Title : each_keyword() Usage : @kws = $obj->each_keyword(); Function: Returns a list of key words [scalars, most likely Strings] associated with this phenotype. Returns : A list of scalars. Args : =cut sub each_keyword { my ( $self ) = @_; $self->throw_not_implemented(); } # each_keyword =head2 add_keywords Title : add_keywords Usage : $obj->add_keywords( @kws ); or $obj->add_keywords( $kw ); Function: Pushes one or more keywords [scalars, most likely Strings] into the list of key words. Returns : Args : scalar(s). =cut sub add_keywords { my ( $self ) = @_; $self->throw_not_implemented(); } # add_keywords =head2 remove_keywords Title : remove_keywords Usage : $obj->remove_keywords(); Function: Deletes (and returns) the list of key words [scalars, most likely Strings] associated with this phenotype. Returns : A list of scalars. Args : =cut sub remove_keywords { my ( $self ) = @_; $self->throw_not_implemented(); } # remove_keywords =head2 each_DBLink Title : each_DBLink() Usage : @dbls = $obj->each_DBLink(); Function: Returns a list of Bio::Annotation::DBLink objects associated with this phenotype. Returns : A list of Bio::Annotation::DBLink objects. Args : =cut sub each_DBLink { my ( $self ) = @_; $self->throw_not_implemented(); } =head2 add_DBLinks Title : add_DBLinks Usage : $obj->add_DBLinks( @dbls ); or $obj->add_DBLinks( $dbl ); Function: Pushes one or more Bio::Annotation::DBLink objects into the list of DBLinks. Returns : Args : Bio::Annotation::DBLink object(s). =cut sub add_DBLinks { my ( $self ) = @_; $self->throw_not_implemented(); } # add_DBLinks =head2 remove_DBLinks Title : remove_DBLinks Usage : $obj->remove_DBLinks(); Function: Deletes (and returns) the list of Bio::Annotation::DBLink objects associated with this phenotype. Returns : A list of Bio::Annotation::DBLink objects. Args : =cut sub remove_DBLinks { my ( $self ) = @_; $self->throw_not_implemented(); } # remove_DBLinks =head2 each_Genotype Title : each_Reference() Usage : @gts = $obj->each_Reference(); Function: Returns a list of "Genotype" objects associated with this phenotype. {* the "genotypes" data member and its methods certainly will/needs to be changed/improved in one way or another since there is no "Genotype" class yet, CZ 09/06/02 *} Returns : A list of "Genotype" objects. Args : =cut sub each_Genotype { my ( $self ) = @_; $self->throw_not_implemented(); } # each_Genotype =head2 add_Genotypes Title : add_Genotypes Usage : $obj->add_Genotypes( @gts ); or $obj->add_Genotypes( $gt ); Function: Pushes one or more "Genotypes" into the list of "Genotypes". Returns : Args : "Genotypes(s)". =cut sub add_Genotypes { my ( $self ) = @_; $self->throw_not_implemented(); } # add_Genotypes =head2 remove_Genotypes Title : remove_Genotypes Usage : $obj->remove_Genotypes(); Function: Deletes (and returns) the list of "Genotype" objects associated with this phenotype. Returns : A list of "Genotype" objects. Args : =cut sub remove_Genotypes { my ( $self ) = @_; $self->throw_not_implemented(); } # remove_Genotypes 1; BioPerl-1.007002/Bio/Phenotype/MeSH000755000766000024 013155576320 16636 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Phenotype/MeSH/Term.pm000444000766000024 1505313155576320 20264 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Phenotype::MeSH::Term # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho, heikki-at-bioperl-dot-org # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Phenotype::MeSH::Term - A MeSH term =head1 SYNOPSIS use Bio::Phenotype::MeSH::Term; # create a term object my $term = Bio::Phenotype::MeSH::Term->new (-id => 'D000001', -name => 'Dietary Fats', -description => 'dietary fats are...' ); # get a Bio::Phenotype::MeSH::Twig somehow... $term->add_twig($twig1); =head1 DESCRIPTION This class keeps information about MeSH terms. MeSH stands for Medical Subject Headings and is one of the ways for annotaing biomedical literature. The terminology is maintained by National Library of Medicine of USA . See http://www.nlm.nih.gov/mesh/meshhome.html. In addition to id, name and description a term can know about its surrounding terms (Bio::Phenotype::MeSH::Twig) in the term hierarchy. This class is mainly used from Bio::DB::MeSH which retrieves terms over the Web. =head1 SEE ALSO L, L =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Phenotype::MeSH::Term; use strict; use base qw(Bio::Root::Root); sub new { my( $class,@args ) = @_; my $self = $class->SUPER::new( @args ); my ( $id, $name, $description, $comment ) = $self->_rearrange ( [ qw( ID NAME DESCRIPTION SPECIES COMMENT ) ], @args ); $self->{"_twigs"} = []; $id && $self->id( $id ); $name && $self->name( $name ); $description && $self->description( $description ); return $self; } =head2 id Title : id Usage : $obj->id( "r1" ); or print $obj->id(); Function: Set/get for the id. Returns : A id [scalar]. Args : A id [scalar] (optional). =cut sub id { my ( $self, $value ) = @_; $self->{ "_id" } = $value if defined $value; return $self->{ "_id" }; } =head2 name Title : name Usage : $obj->name( "r1" ); or print $obj->name(); Function: Set/get for the name. Returns : A name [scalar]. Args : A name [scalar] (optional). =cut sub name { my ( $self, $value ) = @_; $self->{ "_name" } = $value if defined $value; return $self->{ "_name" }; } =head2 description Title : description Usage : $obj->description( "r1" ); or print $obj->description(); Function: Set/get for the description. Returns : A description [scalar]. Args : A description [scalar] (optional). =cut sub description { my ( $self, $value ) = @_; $self->{ "_description" } = $value if defined $value; return $self->{ "_description" }; } =head2 add_synonym Title : add_synonym Usage : $obj->add_synonym( @synonyms ); or $obj->add_synonym( $synonym ); Function: Pushes one or more synonyms for the term term into the list of synonyms. Returns : Args : scalar(s). =cut sub add_synonym { my ( $self, @values ) = @_; push( @{ $self->{ "_synonyms" } }, @values ); } =head2 each_synonym Title : each_synonym() Usage : @gs = $obj->each_synonym(); Function: Returns a list of gene symbols [scalars, most likely Strings] associated with this phenotype. Returns : A list of scalars. Args : =cut sub each_synonym { my ( $self ) = shift; return @{ $self->{ "_synonyms" } }; } =head2 purge_synonyms Usage : $obj->purge_synonym(); Function: Deletes the list of synonyms to this term. Returns : A list of scalars. Args : =cut sub purge_synonyms { my ( $self ) = @_; $self->{ "_synonyms" } = []; } =head2 Twig management Each MeSH term belongs to a complex tree like hierarchy of terms where each term can appear multiple times. The immediately surrounding nodes of the tree are modelled in twigs. See: L. =cut =head2 add_twig Title : add_twig Usage : $obj->add_twig( @twigs ); or $obj->add_twig( $twig ); Function: Pushes one or more twig term names [scalars, most likely Strings] into the list of twigs. Returns : Args : scalar(s). =cut sub add_twig { my ( $self, @values ) = @_; foreach my $twig (@values) { $self->warn ("Not a MeSH twig [$twig]") unless $twig->isa('Bio::Phenotype::MeSH::Twig'); $twig->term($self); push( @{ $self->{ "_twigs" } }, $twig ); } 1; } =head2 each_twig Title : each_twig() Usage : @gs = $obj->each_twig(); Function: Returns a list of gene symbols [scalars, most likely Strings] associated with this phenotype. Returns : A list of scalars. Args : =cut sub each_twig { my ( $self ) = shift; return @{ $self->{ "_twigs" } }; } =head2 purge_twigs Usage : $obj->purge_twig(); Function: Deletes the list of twigs associated with this term. Returns : A list of scalars. Args : =cut sub purge_twigs { my ( $self ) = @_; $self->{ "_twigs" } = []; } =head2 each_parent Title : each_parent() Usage : @gs = $obj->each_parent(); Function: Returns a list of names of parents for this term Returns : A list of scalars. Args : =cut sub each_parent { my ( $self ) = shift; return map {$_->parent()} @{ $self->{ "_twigs" } }; } 1; BioPerl-1.007002/Bio/Phenotype/MeSH/Twig.pm000444000766000024 1373613155576320 20275 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Phenotype::MeSH::Twig # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho, heikki-at-bioperl-dot-org # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Phenotype::MeSH::Twig - Context for a MeSH term =head1 SYNOPSIS use Bio::Phenotype::MeSH::Twig # create a twig object my $twig = Bio::Phenotype::MeSH::Twig->new(); # the term has only one parent in any twig $twig->parent('Fats'); # a twig makeas sense only in the context of a term # which is a Bio::Phenotype::MeSH::Term object # a term can have many twigs i.e. it can appear in many places in # the hierarchy # $ term->add_twig($twig); # adding the twig into a term adds a link into into it $twig->term eq $term; # a twig can know about other terms under the parant node $twig->add_sister('Bread', 'Candy', 'Cereals'); print join ( ', ', $twig->each_sister()), "\n"; # a twig can know about other terms under this term $twig->add_child('Butter', 'Margarine'); print join ( ', ', $twig->each_child()), "\n"; =head1 DESCRIPTION This class represents the immediate surrounding of a MeSH term. It keeps track on nodes names above the current node ('parent') other nodes at the same level ('sisters') and nodes under it ('children'). Note that these are name strings, not objects. Each twig can be associated with only one term, but term can have multiple twigs. (Twigs can be though to be roles for a term.) =head1 SEE ALSO L =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Phenotype::MeSH::Twig; use strict; use base qw(Bio::Root::Root); sub new { my( $class,@args ) = @_; my $self = $class->SUPER::new( @args ); my ($term, $parent ) = $self->_rearrange ( [ qw( TERM PARENT ) ], @args ); $self->{"_children"} = []; $self->{"_sisters"} = []; $term && $self->term($term ); $parent && $self->parent($parent ); return $self; } =head2 parent Title : parent Usage : $obj->parent( "r1" ); or print $obj->parent(); Function: Set/get for the parent. Returns : A parent [scalar]. Args : A parent [scalar] (optional). =cut sub parent { my ( $self, $value ) = @_; $self->{ "_parent" } = $value if defined $value; return $self->{ "_parent" }; } =head2 term Title : term Usage : $obj->term( "r1" ); or print $obj->term(); Function: Set/get for the term. Returns : A term [scalar]. Args : A term [scalar] (optional). =cut sub term { my ( $self, $value ) = @_; if (defined $value) { $self->throw ("Not a MeSH term [$value]") unless $value->isa('Bio::Phenotype::MeSH::Term'); $self->{ "_term" } = $value } return $self->{ "_term" }; } =head2 add_child Title : add_child Usage : $obj->add_child( @children ); or $obj->add_child( $child ); Function: Pushes one or more child term names [scalars, most likely Strings] into the list of children. Returns : Args : scalar(s). =cut sub add_child { my ( $self, @values ) = @_; push( @{ $self->{ "_children" } }, @values ); return scalar @values; } =head2 each_child Title : each_child() Usage : @gs = $obj->each_child(); Function: Returns a list of gene symbols [scalars, most likely Strings] associated with this phenotype. Returns : A list of scalars. Args : =cut sub each_child { my ( $self ) = shift; return @{ $self->{ "_children" } }; } =head2 purge_children Usage : $obj->purge_child(); Function: Deletes the list of children associated with this term. Returns : A list of scalars. Args : =cut sub purge_children { my ( $self ) = @_; $self->{ "_children" } = []; } =head2 add_sister Title : add_sister Usage : $obj->add_sister( @sisters ); or $obj->add_sister( $sister ); Function: Pushes one or more sister term names [scalars, most likely Strings] into the list of sisters. Returns : Args : scalar(s). =cut sub add_sister { my ( $self, @values ) = @_; push( @{ $self->{ "_sisters" } }, @values ); return scalar @values; } =head2 each_sister Title : each_sister() Usage : @gs = $obj->each_sister(); Function: Returns a list of gene symbols [scalars, most likely Strings] associated with this phenotype. Returns : A list of scalars. Args : =cut sub each_sister { my ( $self ) = shift; return @{ $self->{ "_sisters" } }; } =head2 purge_sisters Usage : $obj->purge_sister(); Function: Deletes the list of sisters associated with this term. Returns : A list of scalars. Args : =cut sub purge_sisters { my ( $self ) = @_; $self->{'_sisters'} = []; } 1; BioPerl-1.007002/Bio/Phenotype/OMIM000755000766000024 013155576320 16603 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Phenotype/OMIM/MiniMIMentry.pm000444000766000024 1621513155576320 21644 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Phenotype::OMIM::MiniMIMentry # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Phenotype::OMIM::MiniMIMentry - Representation of a Mini MIM entry =head1 SYNOPSIS use Bio::Phenotype::OMIM::MiniMIMentry; $mm = Bio::Phenotype::OMIM::MiniMIMentry->new( -description => "The central form of ...", -created => "Victor A. McKusick: 6/4/1986", -contributors => "Kelly A. Przylepa - revised: 03/18/2002", -edited => "alopez: 06/03/1997" ); =head1 DESCRIPTION This class representats of Mini MIM entries. This class is intended to be used together with a OMIM entry class. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 APPENDIX The rest of the documentation details each of the object methods. =cut # Let the code begin... package Bio::Phenotype::OMIM::MiniMIMentry; use strict; use base qw(Bio::Root::Root); =head2 new Title : new Usage : $mm = Bio::Phenotype::OMIM::MiniMIMentry->new( -description => "The central form of ...", -created => "Victor A. McKusick: 6/4/1986", -contributors => "Kelly A. Przylepa - revised: 03/18/2002", -edited => "alopez: 06/03/1997" ); Function: Creates a new MiniMIMentry object. Returns : A new MiniMIMentry object. Args : -description => a description -created => name(s) and date(s) (free form) -contributors => name(s) and date(s) (free form) -edited => name(s) and date(s) (free form) =cut sub new { my( $class, @args ) = @_; my $self = $class->SUPER::new( @args ); my ( $desc, $created, $contributors, $edited ) = $self->_rearrange( [ qw( DESCRIPTION CREATED CONTRIBUTORS EDITED ) ], @args ); $self->init(); $desc && $self->description( $desc ); $created && $self->created( $created ); $contributors && $self->contributors( $contributors ); $edited && $self->edited( $edited ); return $self; } # new =head2 init Title : init() Usage : $mm->init(); Function: Initializes this MiniMIMentry to all "". Returns : Args : =cut sub init { my( $self ) = @_; $self->description( "" ); $self->created( "" ); $self->contributors( "" ); $self->edited( "" ); } # init =head2 description Title : description Usage : $mm->description( "The central form of ..." ); or print $mm->description(); Function: Set/get for the description field of the Mini MIM database. Returns : The description. Args : The description (optional). =cut sub description { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_description" } = $value; } return $self->{ "_description" }; } # description =head2 created Title : created Usage : $mm->created( "Victor A. McKusick: 6/4/1986" ); or print $mm->created(); Function: Set/get for the created field of the Mini MIM database. Returns : Name(s) and date(s) [scalar - free form]. Args : Name(s) and date(s) [scalar - free form] (optional). =cut sub created { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_created" } = $value; } return $self->{ "_created" }; } # created =head2 contributors Title : contributors Usage : $mm->contributors( "Kelly A. Przylepa - revised: 03/18/2002" ); or print $mm->contributors(); Function: Set/get for the contributors field of the Mini MIM database. Returns : Name(s) and date(s) [scalar - free form]. Args : Name(s) and date(s) [scalar - free form] (optional). =cut sub contributors { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_contributors" } = $value; } return $self->{ "_contributors" }; } # contributors =head2 edited Title : edited Usage : $mm->edited( "alopez: 06/03/1997" ); or print $mm->edited(); Function: Set/get for the edited field of the Mini MIM database. Returns : Name(s) and date(s) [scalar - free form]. Args : Name(s) and date(s) [scalar - free form] (optional). =cut sub edited { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_edited" } = $value; } return $self->{ "_edited" }; } # edited =head2 to_string Title : to_string() Usage : print $mm->to_string(); Function: To string method for MiniMIMentry objects. Returns : A string representations of this MiniMIMentry. Args : =cut sub to_string { my ( $self ) = @_; my $s = ""; $s .= "-- Description:\n"; $s .= $self->description()."\n"; $s .= "-- Created:\n"; $s .= $self->created()."\n"; $s .= "-- Contributors:\n"; $s .= $self->contributors()."\n"; $s .= "-- Edited:\n"; $s .= $self->edited(); return $s; } # to_string 1; BioPerl-1.007002/Bio/Phenotype/OMIM/OMIMentry.pm000444000766000024 5752613155576320 21160 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Phenotype::OMIM::OMIMentry # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Phenotype::OMIM::OMIMentry - represents OMIM (Online Mendelian Inheritance in Man) database entries =head1 SYNOPSIS $obj = Bio::Phenotype::OMIM::OMIMentry->new( -mim_number => 200000, -description => "This is ...", -more_than_two_genes => 1 ); =head1 DESCRIPTION Inherits from Bio::Phenotype::PhenotypeI. Bio::Phenotype::OMIM::OMIMparser parses the flat file representation of OMIM (i.e. files "omim.txt" and "genemap") returning OMIMentry objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Phenotype::OMIM::OMIMentry; use strict; use Bio::Phenotype::OMIM::MiniMIMentry; use Bio::Phenotype::OMIM::OMIMentryAllelicVariant; use constant TRUE => 1; use constant FALSE => 0; use constant DEFAULT_MIM_NUMER => 0; use base qw(Bio::Phenotype::Phenotype); =head2 new Title : new Usage : $obj = Bio::Phenotype::OMIM::OMIMentry->new( -mim_number => 200000, -description => "This is ...", -more_than_two_genes => 1 ); Function: Creates a new OMIMentry object. Returns : A new OMIMentry object. Args : -mim_number => the MIM number -title => the title or name -alternative_titles_and_symbols => the "alternative titles and symbols" -more_than_two_genes => can phenotype can be caused by mutation in any of two or more genes? -is_separate => is this phenotype separate from those represented by other entries -description => the description of this phenotype -mapping_method => the mapping method -gene_status => the gene status of this -comment => a comment -species => ref to the the species (human) -created => created by whom/when -edited => edited by whom/when -contributors => contributed by whom/when -additional_references => "see also" -clinical_symptoms => the clinical symptoms -minimim => the Mini MIM associated with this OMIM antry =cut sub new { my( $class,@args ) = @_; my $self = $class->SUPER::new( @args ); my ( $mim_number, $title, $alternative_titles_and_symbols, $more_than_two_genes, $is_separate, $description, $mapping_method, $gene_status, $comment, $species, $created, $edited, $contributors, $additional_references, $clinical_symptoms, $miniMIM ) = $self->_rearrange( [ qw( MIM_NUMBER TITLE ALTERNATIVE_TITLES_AND_SYMBOLS MORE_THAN_TWO_GENES IS_SEPARATE DESCRIPTION MAPPING_METHOD GENE_STATUS COMMENT SPECIES CREATED EDITED CONTRIBUTORS ADDITIONAL_REFERENCES CLINICAL_SYMPTOMS MINIMIM ) ], @args ); $self->init(); $mim_number && $self->MIM_number( $mim_number ); $title && $self->title( $title ); $alternative_titles_and_symbols && $self->alternative_titles_and_symbols( $alternative_titles_and_symbols ); $more_than_two_genes && $self->more_than_two_genes( $more_than_two_genes ); $is_separate && $self->is_separate( $is_separate ); $description && $self->description( $description ); $mapping_method && $self->mapping_method( $mapping_method ); $gene_status && $self->gene_status( $gene_status ); $comment && $self->comment( $comment ); $species && $self->species( $species ); $created && $self->created( $created ); $edited && $self->edited( $edited ); $contributors && $self->contributors( $contributors ); $additional_references && $self->additional_references( $additional_references ); $clinical_symptoms && $self->clinical_symptoms_raw( $clinical_symptoms ); $miniMIM && $self->miniMIM( $miniMIM ); return $self; } # new =head2 init Title : init() Usage : $obj->init(); Function: Initializes this OMIMentry to all "" and empty lists. Returns : Args : =cut sub init { my( $self ) = @_; $self->MIM_number( DEFAULT_MIM_NUMER ); $self->title( "" ); $self->alternative_titles_and_symbols( "" ); $self->more_than_two_genes( FALSE ); $self->is_separate( FALSE ); $self->description( "" ); $self->mapping_method( "" ); $self->gene_status( "" ); $self->comment( "" ); my $species = Bio::Species->new(); $species->classification( qw( sapiens Homo ) ); $self->species( $species ); $self->created( "" ); $self->edited( "" ); $self->contributors( "" ); $self->additional_references( "" ); $self->clinical_symptoms( {} ); $self->remove_Correlates(); $self->remove_References(); $self->remove_AllelicVariants(); $self->remove_CytoPositions(); $self->remove_gene_symbols(); $self->remove_Genotypes(); $self->remove_DBLinks(); $self->remove_keywords(); $self->remove_Variants(); $self->remove_Measures(); $self->miniMIM( Bio::Phenotype::OMIM::MiniMIMentry->new() ); } # init sub to_string { my( $self ) = @_; my $s = ""; $s .= "-- MIM number:\n"; $s .= $self->MIM_number()."\n\n"; $s .= "-- Title:\n"; $s .= $self->title()."\n\n"; $s .= "-- Alternative Titles and Symbols:\n"; $s .= $self->alternative_titles_and_symbols()."\n\n"; $s .= "-- Can be caused by Mutation in any of two or more Genes:\n"; $s .= $self->more_than_two_genes()."\n\n"; $s .= "-- Phenotype is separate:\n"; $s .= $self->is_separate()."\n\n"; $s .= "-- Description:\n"; $s .= $self->description()."\n\n"; $s .= "-- Species:\n"; $s .= $self->species()->binomial()."\n\n"; $s .= "-- Clinical Symptoms:\n"; $s .= $self->clinical_symptoms()."\n\n"; $s .= "-- Allelic Variants:\n"; $s .= $self->_array_to_string( $self->each_AllelicVariant() )."\n"; $s .= "-- Cyto Positions:\n"; $s .= $self->_array_to_string( $self->each_CytoPosition() )."\n"; $s .= "-- Gene Symbols:\n"; $s .= $self->_array_to_string( $self->each_gene_symbol() )."\n"; $s .= "-- Correlates:\n"; $s .= $self->_array_to_string( $self->each_Correlate() )."\n"; $s .= "-- References:\n"; $s .= $self->_array_to_string( $self->each_Reference() )."\n"; $s .= "-- Additional References:\n"; $s .= $self->additional_references()."\n\n"; $s .= "-- Mapping Method:\n"; $s .= $self->mapping_method()."\n\n"; $s .= "-- Gene status:\n"; $s .= $self->gene_status()."\n\n"; $s .= "-- Created:\n"; $s .= $self->created()."\n\n"; $s .= "-- Contributors:\n"; $s .= $self->contributors()."\n\n"; $s .= "-- Edited:\n"; $s .= $self->edited()."\n\n"; $s .= "-- Comment:\n"; $s .= $self->comment()."\n\n"; $s .= "-- MiniMIM:\n"; $s .= $self->miniMIM()->to_string()."\n\n"; return $s; } # to_string =head2 MIM_number Title : MIM_number Usage : $omim->MIM_number( "100050" ); or print $omim->MIM_number(); Function: Set/get for the MIM number of this OMIM entry. Returns : The MIM number [an integer larger than 100000]. Args : The MIM number [an integer larger than 100000] (optional). =cut sub MIM_number { my ( $self, $value ) = @_; if ( defined $value ) { if ( $value =~ /\D/ || ( $value < 100000 && $value != DEFAULT_MIM_NUMER ) ) { $self->throw( "Found [$value]" . " where [integer larger than 100000] expected" ); } $self->{ "_MIM_number" } = $value; } return $self->{ "_MIM_number" }; } # MIM_number =head2 title Title : title Usage : $omim->title( "AARSKOG SYNDROME" ); or print $omim->title(); Function: Set/get for the title or name of this OMIM entry. This method is an alias to the method "name" of Bio::Phenotype::PhenotypeI. Returns : The title [scalar]. Args : The title [scalar] (optional). =cut sub title { my $self = shift; $self->name(@_); } # title =head2 alternative_titles_and_symbols Title : alternative_titles_and_symbols Usage : $omim->alternative_titles_and_symbols( "AORTIC ANEURYSM, ABDOMINAL" ); or print $omim->alternative_titles_and_symbols(); Function: Set/get for the "alternative titles and symbols" of this OMIM entry. Currently, everything after the first line of title (TI) field is considered "alternative titles and symbols". Returns : "alternative titles and symbols" [scalar]. Args : "alternative titles and symbols" [scalar] (optional). =cut sub alternative_titles_and_symbols { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_alternative_titles_and_symbols" } = $value; } return $self->{ "_alternative_titles_and_symbols" }; } # alternative_titles_and_symbols =head2 more_than_two_genes Title : more_than_two_genes Usage : $omim->more_than_two_genes( 1 ); or print $omim->more_than_two_genes(); Function: This is true if this phenotype can be caused by mutation in any of two or more genes. In OMIM, this is indicated by a number symbol (#) before an entry number (e.g. #114480 -- BREAST CANCER). Returns : [1 or 0]. Args : [1 or 0] (optional). =cut sub more_than_two_genes { my ( $self, $value ) = @_; if ( defined $value ) { $self->_is_true_or_false( $value ); $self->{ "_more_than_two_genes" } = $value; } return $self->{ "_more_than_two_genes" }; } # more_than_two_genes =head2 is_separate Title : is_separate Usage : $omim->is_separate( 1 ); or print $omim->is_separate(); Function: This is true if the phenotype determined by the gene at the given locus is separate from those represented by other entries where "is_separate" is true and if the mode of inheritance of the phenotype has been proved (in the judgment of the authors and editors). In OMIM, this is indicated by a asterisk (*) before an entry number (e.g. *113705 BREAST CANCER, TYPE 1; BRCA1). Returns : [1 or 0]. Args : [1 or 0] (optional). =cut sub is_separate { my ( $self, $value ) = @_; if ( defined $value ) { $self->_is_true_or_false( $value ); $self->{ "_is_separate" } = $value; } return $self->{ "_is_separate" }; } # is_separate =head2 mapping_method Title : mapping_method Usage : $omim->mapping_method( "PCR of somatic cell hybrid DNA" ); or print $omim->mapping_method(); Function: Set/get for the mapping method of this OMIM entry. Returns : The mapping method [scalar]. Args : The mapping method [scalar] (optional). =cut sub mapping_method { my $self = shift; return $self->{ "_mapping_method" } = shift if(@_); return $self->{ "_mapping_method" }; } # mapping_method =head2 gene_status Title : gene_status Usage : $omim->gene_status( "C" ); or print $omim->gene_status(); Function: Set/get for the gene status of this OMIM entry. The certainty with which assignment of loci to chromosomes or the linkage between two loci has been established has been graded into the following classes: C = confirmed - observed in at least two laboratories or in several families. P = provisional - based on evidence from one laboratory or one family. I = inconsistent - results of different laboratories disagree. L = limbo - evidence not as strong as that provisional, but included for heuristic reasons. (Same as `tentative'.) Returns : [C, P, I, or L]. Args : [C, P, I, or L] (optional). =cut sub gene_status { my ( $self, $value ) = @_; if ( defined $value ) { #unless ( $value eq "C" # || $value eq "P" # || $value eq "I" # || $value eq "L" # || $value eq "A" # !? # || $value eq "H" # !? # || $value eq "U" # !? # || $value eq "" ) { # $self->throw( "Found [$value]" # . " where [C, P, I, or L] expected" ); #} unless ( $value eq "C" || $value eq "P" || $value eq "I" || $value eq "L" || $value eq "" ) { $value = ""; } $self->{ "_gene_status" } = $value; } return $self->{ "_gene_status" }; } # gene_status =head2 clinical_symptoms Title : clinical_symptoms Usage : $omim->clinical_symptoms({}); Function: Set/get for the clinical symptoms of this OMIM entry. Returns : [hash reference]. Args : [hash reference]. Suggested not to assign alone. Parser will do. =cut sub clinical_symptoms { my ( $self, $value ) = @_; if ( defined $value ) { unless(ref($value) eq 'HASH'){ $self->throw('a hash referenced needed'); } $self->{ "_clinical_symptoms" } = $value; } return $self->{ "_clinical_symptoms" }; } # clinical_symptoms =head2 clinical_symptoms_raw Title : clinical_symptoms_raw Usage : $omim->clinical_symptoms( "Patients with ..." ); print $omim->clinical_symptoms(); Functions : Get/set for text information of clinical symptoms Returns : The clinical symptoms [scalar]. Args : The clinical symptoms [scalar] (optional). =cut sub clinical_symptoms_raw { my $self = shift; return $self->{_clinical_symptoms_raw} = shift if @_; return $self->{_clinical_symptoms_raw}; } =head2 add_clinical_symptoms Title : add_clinical_symptoms Usage : $entry->add_clinical_symptoms('Ears', 'Floppy ears', 'Lop-ears'); Function : add one or more symptoms on one part of body. Returns : [none] Args : ($part, @symptoms) $part, the text name of part/organism of human @symptoms, an array of text description =cut sub add_clinical_symptoms { my ($self, $part, @symptoms) = @_; unless(defined $part){ $self->throw('a part/organism must be assigned'); } $self->{_clinical_symptoms} = {} unless $self->{_clinical_symptoms}; $self->{_clinical_symptoms}->{$part} = [] unless $self->{_clinical_symptoms}->{$part}; push @{$self->{_clinical_symptoms}->{$part}}, @symptoms; } =head2 query_clinical_symptoms Title : get_clinical_symptoms Usage : @symptoms = $self->query_clinical_symptoms('Ears'); Function : get all symptoms specific to one part/organism. Returns : an array of text Args : $organ =cut sub query_clinical_symptoms { my ($self, $organ)=@_; my $symptoms=$self->{_clinical_symptoms}->{$organ}; @$symptoms; } sub get_clinical_symptom_organs { my ($self)=@_; keys %{$self->{_clinical_symptoms}}; } =head2 created Title : created Usage : $omim->created( "Victor A. McKusick: 6/4/1986" ); or print $omim->created(); Function: Set/get for the created field of the OMIM database. Returns : Name(s) and date(s) [scalar - free form]. Args : Name(s) and date(s) [scalar - free form] (optional). =cut sub created { my $self = shift; return $self->{ "_created" } = shift if(@_); return $self->{ "_created" }; } # created =head2 contributors Title : contributors Usage : $omim->contributors( "Kelly A. Przylepa - revised: 03/18/2002" ); or print $omim->contributors(); Function: Set/get for the contributors field of the OMIM database. Returns : Name(s) and date(s) [scalar - free form]. Args : Name(s) and date(s) [scalar - free form] (optional). =cut sub contributors { my $self = shift; $self->{ "_contributors" } = shift if(@_); return $self->{ "_contributors" }; } # contributors =head2 edited Title : edited Usage : $omim->edited( "alopez: 06/03/1997" ); or print $omim->edited(); Function: Set/get for the edited field of the OMIM database. Returns : Name(s) and date(s) [scalar - free form]. Args : Name(s) and date(s) [scalar - free form] (optional). =cut sub edited { my $self = shift; return $self->{ "_edited" } = shift if(@_); return $self->{ "_edited" }; } # edited =head2 additional_references Title : additional_references Usage : $omim->additional_references( "Miller er al." ); or print $omim->additional_references(); Function: Set/get for the additional references of this OMIM antry (see also). Returns : additional reference [scalar]. Args : additional reference [scalar] (optional). =cut sub additional_references { my $self = shift; return $self->{ "_additional_references" } = shift if(@_); return $self->{ "_additional_references" }; } # additional_references =head2 miniMIM Title : miniMIM Usage : $omim->miniMIM( $MM ); or $MM = $omim->miniMIM(); Function: Set/get for the Mini MIM associated with this OMIM antry (see also). Returns : [Bio::Phenotype::OMIM::MiniMIMentry]. Args : [Bio::Phenotype::OMIM::MiniMIMentry] (optional). =cut sub miniMIM { my ( $self, $value ) = @_; if ( defined $value ) { $self->_check_ref_type( $value, "Bio::Phenotype::OMIM::MiniMIMentry" ); $self->{ "_mini_mim" } = $value; } return $self->{ "_mini_mim" }; } =head2 each_AllelicVariant Title : each_AllelicVariant() Usage : @avs = $obj->each_AllelicVariant(); Function: Returns a list of Bio::Phenotype::OMIM::OMIMentryAllelicVariant objects associated with this OMIM entry. Returns : A list of Bio::Phenotype::OMIM::OMIMentryAllelicVariant objects. Args : =cut sub each_AllelicVariant { my ( $self ) = @_; return @{$self->{"_allelic_variants"}} if exists($self->{"_allelic_variants"}); return (); } # each_AllelicVariant =head2 add_AllelicVariants Title : add_AllelicVariants Usage : $obj->add_AllelicVariants( @avs ); or $obj->add_AllelicVariants( $av ); Function: Pushes one or more OMIMentryAllelicVariant into the list of OMIMentryAllelicVariants. Returns : Args : Bio::Phenotype::OMIM::OMIMentryAllelicVariant object(s). =cut sub add_AllelicVariants { my ( $self, @values ) = @_; return unless( @values ); foreach my $value ( @values ) { $self->_check_ref_type( $value, "Bio::Phenotype::OMIM::OMIMentryAllelicVariant" ); } push( @{ $self->{ "_allelic_variants" } }, @values ); } # add_AllelicVariants =head2 remove_AllelicVariants Title : remove_AllelicVariants Usage : $obj->remove_AllelicVariants(); Function: Deletes (and returns) the list of OMIMentryAllelicVariant objects associated with this OMIM entry. Returns : A list of OMIMentryAllelicVariant objects. Args : =cut sub remove_AllelicVariants { my ( $self ) = @_; my @a = $self->each_AllelicVariant(); $self->{ "_allelic_variants" } = []; return @a; } # remove_AllelicVariants # Title : _array_to_string # Function: # Returns : # Args : sub _array_to_string { my( $self, @value ) = @_; my $s = ""; for ( my $i = 0; $i < scalar( @value ); ++$i ) { if ( ! ref( $value[ $i ] ) ) { $s .= "#" . $i . "\n-- Value:\n" . $value[ $i ] . "\n"; } elsif ( $value[ $i ]->isa( "Bio::Phenotype::OMIM::OMIMentryAllelicVariant" ) || $value[ $i ]->isa( "Bio::Phenotype::Correlate" ) ) { $s .= "#" . $i . "\n" . ( $value[ $i ] )->to_string() . "\n"; } elsif ( $value[ $i ]->isa( "Bio::Annotation::Reference" ) ) { $s .= "#".$i."\n-- Authors:\n".( $value[ $i ] )->authors()."\n"; $s .= "-- Title:\n".( $value[ $i ] )->title()."\n"; $s .= "-- Location:\n".( $value[ $i ] )->location()."\n"; } elsif ( $value[ $i ]->isa( "Bio::Map::CytoPosition" ) ) { $s .= "#" . $i . "\n-- Value:\n" . ( $value[ $i ] )->value() . "\n"; } } return $s; } # _array_to_string # Title :_is_true_or_false # Function: Checks whether the argument is 1 or 0. # Returns : # Args : The value to be checked. sub _is_true_or_false { my ( $self, $value ) = @_; unless ( $value !~ /\D/ && ( $value == TRUE || $value == FALSE ) ) { $self->throw( "Found [" . $value . "] where " . TRUE . " or " . FALSE . " expected" ); } } # _is_true_or_false 1; BioPerl-1.007002/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm000444000766000024 2522713155576320 23764 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Phenotype::OMIM::OMIMentryAllelicVariant # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Phenotype::OMIM::OMIMentryAllelicVariant - Representation of a allelic variant of the OMIM database =head1 SYNOPSIS use Bio::Phenotype::OMIM::OMIMentryAllelicVariant; $av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new( -number => ".0001", -title => "ALCOHOL INTOLERANCE", -symbol => "ALDH2*2", -description => "The ALDH2*2-encoded ...", -aa_ori => "GLU", -aa_mut => "LYS", -position => 487, -additional_mutations => "IVS4DS, G-A, +1" ); =head1 DESCRIPTION This class models the allelic variant of the OMIM database. This class is intended to be used together with a OMIM entry class. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 APPENDIX The rest of the documentation details each of the object methods. =cut # Let the code begin... package Bio::Phenotype::OMIM::OMIMentryAllelicVariant; use strict; use base qw(Bio::Root::Root); =head2 new Title : new Usage : $av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new( -number => ".0001", -title => "ALCOHOL INTOLERANCE", -symbol => "ALDH2*2", -description => "The ALDH2*2-encoded ...", -aa_ori => "GLU", -aa_mut => "LYS", -position => 487, -additional_mutations => "IVS4DS, G-A, +1" ); Function: Creates a new OMIMentryAllelicVariant object. Returns : A new OMIMentryAllelicVariant object. Args : -number => the OMIM allelic variant number -title => the title -symbol => a symbol -description => a description -aa_ori => the original amino acid -aa_mut => the mutated amino acid -position => the position of the mutation -additional_mutations => free form description of additional mutations =cut sub new { my( $class, @args ) = @_; my $self = $class->SUPER::new( @args ); my ( $number, $title, $symbol, $desc, $ori, $mut, $pos, $am ) = $self->_rearrange( [ qw( NUMBER TITLE SYMBOL DESCRIPTION AA_ORI AA_MUT POSITION ADDITIONAL_MUTATIONS ) ], @args ); $self->init(); $number && $self->number( $number ); $title && $self->title( $title ); $symbol && $self->symbol( $symbol ); $desc && $self->description( $desc ); $ori && $self->aa_ori( $ori ); $mut && $self->aa_mut( $mut ); $pos && $self->position( $pos ); $am && $self->additional_mutations( $am ); return $self; } # new =head2 init Title : init() Usage : $av->init(); Function: Initializes this OMIMentryAllelicVariant to all "". Returns : Args : =cut sub init { my( $self ) = @_; $self->number( "" ); $self->title( "" ); $self->symbol( "" ); $self->description( "" ); $self->aa_ori( "" ); $self->aa_mut( "" ); $self->position( "" ); $self->additional_mutations( "" ); } # init =head2 number Title : number Usage : $av->number( ".0001" ); or print $av->number(); Function: Set/get for the OMIM allelic variant number of this OMIMentryAllelicVariant. Returns : The OMIM allelic variant number. Args : The OMIM allelic variant number (optional). =cut sub number { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_number" } = $value; } return $self->{ "_number" }; } # number =head2 title Title : title Usage : $av->title( "ALCOHOL INTOLERANCE" ); or print $av->title(); Function: Set/get for the title of this OMIMentryAllelicVariant. Returns : The title. Args : The title (optional). =cut sub title { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_title" } = $value; } return $self->{ "_title" }; } # title =head2 symbol Title : symbol Usage : $av->symbol( "ALDH2*2" ); or print $av->symbol(); Function: Set/get for the symbol of this OMIMentryAllelicVariant. Returns : A symbol. Args : A symbol (optional). =cut sub symbol { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_symbol" } = $value; } return $self->{ "_symbol" }; } # symbol =head2 description Title : description Usage : $av->description( "The ALDH2*2-encoded protein has a change ..." ); or print $av->description(); Function: Set/get for the description of this OMIMentryAllelicVariant. Returns : A description. Args : A description (optional). =cut sub description { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_description" } = $value; } return $self->{ "_description" }; } # description =head2 aa_ori Title : aa_ori Usage : $av->aa_ori( "GLU" ); or print $av->aa_ori(); Function: Set/get for the original amino acid(s). Returns : The original amino acid(s). Args : The original amino acid(s) (optional). =cut sub aa_ori { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_aa_ori" } = $value; } return $self->{ "_aa_ori" }; } # aa_ori =head2 aa_mut Title : aa_mut Usage : $av->aa_mut( "LYS" ); or print $av->aa_mut(); Function: Set/get for the mutated amino acid(s). Returns : The mutated amino acid(s). Args : The mutated amino acid(s) (optional). =cut sub aa_mut { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_aa_mut" } = $value; } return $self->{ "_aa_mut" }; } # aa_mut =head2 position Title : position Usage : $av->position( 487 ); or print $av->position(); Function: Set/get for the position of the mutation. Returns : The position of the mutation. Args : The position of the mutation (optional). =cut sub position { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_position" } = $value; } return $self->{ "_position" }; } # position =head2 additional_mutations Title : additional_mutations Usage : $av->additional_mutations( "1-BP DEL, 911T" ); or print $av->additional_mutations(); Function: Set/get for free form description of (additional) mutation(s). Returns : description of (additional) mutation(s). Args : description of (additional) mutation(s) (optional). =cut sub additional_mutations { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_additional_mutations" } = $value; } return $self->{ "_additional_mutations" }; } # additional_mutations =head2 to_string Title : to_string() Usage : print $av->to_string(); Function: To string method for OMIMentryAllelicVariant objects. Returns : A string representations of this OMIMentryAllelicVariant. Args : =cut sub to_string { my( $self ) = @_; my $s = ""; $s .= "-- Number:\n"; $s .= $self->number()."\n"; $s .= "-- Title:\n"; $s .= $self->title()."\n"; $s .= "-- Symbol:\n"; $s .= $self->symbol()."\n"; $s .= "-- Description:\n"; $s .= $self->description()."\n"; $s .= "-- Original AA(s):\n"; $s .= $self->aa_ori()."\n"; $s .= "-- Mutated AA(s):\n"; $s .= $self->aa_mut()."\n"; $s .= "-- Position:\n"; $s .= $self->position()."\n"; $s .= "-- Additional Mutation(s):\n"; $s .= $self->additional_mutations(); return $s; } # to_string 1; BioPerl-1.007002/Bio/Phenotype/OMIM/OMIMparser.pm000444000766000024 6552013155576320 21304 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Phenotype::OMIM::OMIMparser # # Please direct questions and support issues to # # Cared for by Christian M. Zmasek or # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Phenotype::OMIM::OMIMparser - parser for the OMIM database =head1 SYNOPSIS use Bio::Phenotype::OMIM::OMIMparser; # The OMIM database is available as textfile at: # ftp://ncbi.nlm.nih.gov/repository/OMIM/omim.txt.Z # The genemap is available as textfile at: # ftp://ncbi.nlm.nih.gov/repository/OMIM/genemap $omim_parser = Bio::Phenotype::OMIM::OMIMparser->new( -genemap => "/path/to/genemap", -omimtext => "/path/to/omim.txt" ); while ( my $omim_entry = $omim_parser->next_phenotype() ) { # This prints everything. print( $omim_entry->to_string() ); print "\n\n"; # This gets individual data (some of them object-arrays) # (and illustrates the relevant methods of OMIMentry). my $numb = $omim_entry->MIM_number(); # *FIELD* NO my $title = $omim_entry->title(); # *FIELD* TI - first line my $alt = $omim_entry->alternative_titles_and_symbols(); # *FIELD* TI - additional lines my $mtt = $omim_entry->more_than_two_genes(); # "#" before title my $sep = $omim_entry->is_separate(); # "*" before title my $desc = $omim_entry->description(); # *FIELD* TX my $mm = $omim_entry->mapping_method(); # from genemap my $gs = $omim_entry->gene_status(); # from genemap my $cr = $omim_entry->created(); # *FIELD* CD my $cont = $omim_entry->contributors(); # *FIELD* CN my $ed = $omim_entry->edited(); # *FIELD* ED my $sa = $omim_entry->additional_references(); # *FIELD* SA my $cs = $omim_entry->clinical_symptoms_raw(); # *FIELD* CS my $comm = $omim_entry->comment(); # from genemap my $mini_mim = $omim_entry->miniMIM(); # *FIELD* MN # A Bio::Phenotype::OMIM::MiniMIMentry object. # class Bio::Phenotype::OMIM::MiniMIMentry # provides the following: # - description() # - created() # - contributors() # - edited() # # Prints the contents of the MINI MIM entry (most OMIM entries do # not have MINI MIM entries, though). print $mini_mim->description()."\n"; print $mini_mim->created()."\n"; print $mini_mim->contributors()."\n"; print $mini_mim->edited()."\n"; my @corrs = $omim_entry->each_Correlate(); # from genemap # Array of Bio::Phenotype::Correlate objects. # class Bio::Phenotype::Correlate # provides the following: # - name() # - description() (not used) # - species() (always mouse) # - type() ("OMIM mouse correlate") # - comment() my @refs = $omim_entry->each_Reference(); # *FIELD* RF # Array of Bio::Annotation::Reference objects. my @avs = $omim_entry->each_AllelicVariant(); # *FIELD* AV # Array of Bio::Phenotype::OMIM::OMIMentryAllelicVariant objects. # class Bio::Phenotype::OMIM::OMIMentryAllelicVariant # provides the following: # - number (e.g ".0001" ) # - title (e.g "ALCOHOL INTOLERANCE" ) # - symbol (e.g "ALDH2*2" ) # - description (e.g "The ALDH2*2-encoded protein has a change ..." ) # - aa_ori (used if information in the form "LYS123ARG" is found) # - aa_mut (used if information in the form "LYS123ARG" is found) # - position (used if information in the form "LYS123ARG" is found) # - additional_mutations (used for e.g. "1-BP DEL, 911T") my @cps = $omim_entry->each_CytoPosition(); # from genemap # Array of Bio::Map::CytoPosition objects. my @gss = $omim_entry->each_gene_symbol(); # from genemap # Array of strings. # do something ... } =head1 DESCRIPTION This parser returns Bio::Phenotype::OMIM::OMIMentry objects (which inherit from Bio::Phenotype::PhenotypeI). It parses the OMIM database available as ftp://ncbi.nlm.nih.gov/repository/OMIM/omim.txt.Z together with (optionally) the gene map file at ftp://ncbi.nlm.nih.gov/repository/OMIM/genemap. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Phenotype::OMIM::OMIMparser; use strict; use Bio::Root::IO; use Bio::Species; use Bio::Annotation::Reference; use Bio::Map::CytoPosition; use Bio::Phenotype::OMIM::OMIMentry; use Bio::Phenotype::OMIM::OMIMentryAllelicVariant; use Bio::Phenotype::Correlate; use base qw(Bio::Root::Root); use constant DEFAULT_STATE => 0; use constant MIM_NUMBER_STATE => 1; use constant TITLE_STATE => 2; use constant TEXT_STATE => 3; use constant MINI_MIM_TEXT_STATE => 4; use constant ALLELIC_VARIANT_STATE => 5; use constant SEE_ALSO_STATE => 6; use constant REF_STATE => 7; use constant SYMPT_STATE => 8; use constant CONTRIBUTORS_STATE => 9; use constant CREATED_BY_STATE => 10; use constant EDITED_BY_STATE => 11; use constant MINI_MIM_EDITED_BY_STATE => 12; use constant MINI_MIM_CREATED_BY_STATE => 13; use constant MINI_MIM_CONTRIBUTORS_STATE => 14; use constant TRUE => 1; use constant FALSE => 0; =head2 new Title : new Usage : $omim_parser = Bio::Phenotype::OMIM::OMIMparser->new( -genemap => "/path/to/genemap", -omimtext => "/path/to/omim.txt" ); Function: Creates a new OMIMparser. Returns : A new OMIMparser object. Args : -genemap => the genemap file name (optional) -omimtext => the omim text file name =cut sub new { my( $class, @args ) = @_; my $self = $class->SUPER::new( @args ); my ( $genemap_file_name, $omimtxt_file_name ) = $self->_rearrange( [ qw( GENEMAP OMIMTEXT ) ], @args ); $self->init(); $genemap_file_name && $self->genemap_file_name( $genemap_file_name ); $omimtxt_file_name && $self->omimtxt_file_name( $omimtxt_file_name); return $self; } =head2 next_phenotype Title : next_phenotype() Usage : while ( my $omim_entry = $omim_parser->next_phenotype() ) { # do something with $omim_entry } Function: Returns an Bio::Phenotype::OMIM::OMIMentry or undef once the end of the omim text file is reached. Returns : A Bio::Phenotype::OMIM::OMIMentry. Args : =cut sub next_phenotype { my ( $self ) = @_; unless( defined( $self->_OMIM_text_file() ) ) { $self->_no_OMIM_text_file_provided_error(); } if ( $self->_done() == TRUE ) { return; } my $fieldtag = ""; my $contents = ""; my $line = ""; my $state = DEFAULT_STATE; my $saw_mini_min_flag = FALSE; my %record = (); while( $line = ( $self->_OMIM_text_file )->_readline() ) { if ( $line =~ /^\s*\*RECORD\*/ ) { if ( $self->_is_not_first_record() == TRUE ) { $self->_add_to_hash( $state, $contents,\%record ); my $omim_entry = $self->_createOMIMentry( \%record ); return $omim_entry; } else { $self->_is_not_first_record( TRUE ); } } elsif ( $line =~ /^\s*\*FIELD\*\s*(\S+)/ ) { $fieldtag = $1; if ( $state != DEFAULT_STATE ) { $self->_add_to_hash( $state, $contents,\%record ); } $contents = ""; if ( $fieldtag eq "NO" ) { $state = MIM_NUMBER_STATE; $saw_mini_min_flag = FALSE; } elsif ( $fieldtag eq "TI" ) { $state = TITLE_STATE; $saw_mini_min_flag = FALSE; } elsif ( $fieldtag eq "TX" ) { $state = TEXT_STATE; $saw_mini_min_flag = FALSE; } elsif ( $fieldtag eq "MN" ) { $state = MINI_MIM_TEXT_STATE; $saw_mini_min_flag = TRUE; } elsif ( $fieldtag eq "AV" ) { $state = ALLELIC_VARIANT_STATE; $saw_mini_min_flag = FALSE; } elsif ( $fieldtag eq "SA" ) { $state = SEE_ALSO_STATE; $saw_mini_min_flag = FALSE; } elsif ( $fieldtag eq "RF" ) { $state = REF_STATE; $saw_mini_min_flag = FALSE; } elsif ( $fieldtag eq "CS" ) { $state = SYMPT_STATE; $saw_mini_min_flag = FALSE; } elsif ( $fieldtag eq "CN" ) { if ( $saw_mini_min_flag == TRUE ) { $state = MINI_MIM_CONTRIBUTORS_STATE; } else { $state = CONTRIBUTORS_STATE; } } elsif ( $fieldtag eq "CD" ) { if ( $saw_mini_min_flag == TRUE ) { $state = MINI_MIM_CREATED_BY_STATE; } else { $state = CREATED_BY_STATE; } } elsif ( $fieldtag eq "ED" ) { if ( $saw_mini_min_flag == TRUE ) { $state = MINI_MIM_EDITED_BY_STATE; } else { $state = EDITED_BY_STATE; } } else { print "Warning: Unknown tag: $fieldtag\n"; } } else { $contents .= $line; } } $self->_OMIM_text_file()->close(); $self->_done( TRUE ); unless( %record ) { $self->_not_a_OMIM_text_file_error(); } $self->_add_to_hash( $state, $contents,\%record ); my $omim_entry = $self->_createOMIMentry( \%record ); return $omim_entry; } # next_phenotype =head2 init Title : init() Usage : $omim_parser->init(); Function: Initializes this OMIMparser to all "". Returns : Args : =cut sub init { my ( $self ) = @_; $self->genemap_file_name( "" ); $self->omimtxt_file_name( "" ); $self->_genemap_hash( {} ); $self->_OMIM_text_file( undef ); $self->_is_not_first_record( FALSE ); $self->_done( FALSE ); } # init =head2 genemap_file_name Title : genemap_file_name Usage : $omimparser->genemap_file_name( "genemap" ); Function: Set/get for the genemap file name. Returns : The genemap file name [string]. Args : The genemap file name [string] (optional). =cut sub genemap_file_name { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_genemap_file_name" } = $value; $self->_genemap_hash( $self->_read_genemap( $value ) ); } return $self->{ "_genemap_file_name" }; } # genemap_file_name =head2 omimtxt_file_name Title : omimtxt_file_name Usage : $omimparser->omimtxt_file_name( "omim.txt" ); Function: Set/get for the omim text file name. Returns : The the omim text file name [string]. Args : The the omim text file name [string] (optional). =cut sub omimtxt_file_name { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_omimtxt_file_name" } = $value; if ( $value =~ /\W/ ) { $self->_OMIM_text_file( Bio::Root::IO->new->new( -file => $value ) ); } } return $self->{ "_omimtxt_file_name" }; } # omimtxt_file_name sub _createOMIMentry { my ( $self, $record_ref ) = @_; my $omim_entry = Bio::Phenotype::OMIM::OMIMentry->new(); my $mini_mim = Bio::Phenotype::OMIM::MiniMIMentry->new(); while ( ( my $key, my $val ) = each( %$record_ref ) ) { $val =~ s/^\s+//; $val =~ s/\s+$//; if ( $key == MIM_NUMBER_STATE ) { $val =~ s/\s+//g; $val =~ s/\D//g; $omim_entry->MIM_number( $val ); my $gm = $self->_genemap_hash(); if ( exists( $$gm{ $val } ) ) { $self->_parse_genemap( $omim_entry, $val ); } } elsif ( $key == TITLE_STATE ) { my ( $title, $alt_titles ) = $self->_parse_title( $val ); $omim_entry->title( $title ); $omim_entry->alternative_titles_and_symbols( $alt_titles ); if ( $title =~ /^\*/ ) { $omim_entry->is_separate( TRUE ); } elsif ( $title =~ /^#/ ) { $omim_entry->more_than_two_genes( TRUE ); } } elsif ( $key == TEXT_STATE ) { $val = undef if($val =~ /DESCRIPTION1\nDESCRIPTION2/); $omim_entry->description( $val ); } elsif ( $key == ALLELIC_VARIANT_STATE ) { my @allelic_variants = $self->_parse_allelic_variants( $val ); $omim_entry->add_AllelicVariants( @allelic_variants ); } elsif ( $key == SEE_ALSO_STATE ) { $omim_entry->additional_references( $val ); } elsif ( $key == REF_STATE ) { my @refs = $self->_parse_references( $val ); $omim_entry->add_References( @refs ); } elsif ( $key == SYMPT_STATE ) { $val = '' if($val eq 'clinical symptoms'); $omim_entry->clinical_symptoms_raw( $val ); } elsif ( $key == CONTRIBUTORS_STATE ) { $val = undef if($val =~ /cn1\ncn2\ncn3/); $omim_entry->contributors( $val ); } elsif ( $key == CREATED_BY_STATE ) { $val = undef if($val =~ /cd1\ncd2\ncd3/); $omim_entry->created( $val ); } elsif ( $key == EDITED_BY_STATE ) { $val = undef if($val =~ /ed1\ned2\ned3/); $omim_entry->edited( $val ); } elsif ( $key == MINI_MIM_TEXT_STATE ) { $mini_mim->description( $val ); } elsif ( $key == MINI_MIM_CONTRIBUTORS_STATE ) { $mini_mim->contributors( $val ); } elsif ( $key == MINI_MIM_CREATED_BY_STATE ) { $mini_mim->created( $val ); } elsif ( $key == MINI_MIM_EDITED_BY_STATE ) { $mini_mim->edited( $val ); } } my $man = Bio::Species->new(); $man->classification( qw( sapiens Homo ) ); $man->common_name( "man" ); $omim_entry->species( $man ); $omim_entry->miniMIM( $mini_mim ); # parse the symptoms text into a hash-based structure. $self->_finer_parse_symptoms($omim_entry); return $omim_entry; } # _createOMIMentry sub _finer_parse_symptoms { my ($self, $omim_entry) = @_; my $text = $omim_entry->clinical_symptoms_raw; if( $text ) { my $part; for my $line (split /\n/, $text){ if ($line =~ /^([\w\s,]+)\:\s*$/) { $part = $1; } elsif( $line =~ /^\s+$/ ) { } elsif($line =~ /^(\s+)([^;]+)\;?\s*$/){ my $symptom = $2; if( ! $part ) { # $self->warn("$text\nline='$line'\n"); next; } $omim_entry->add_clinical_symptoms($part, $symptom); } } } $omim_entry->clinical_symptoms_raw(''); } sub _parse_genemap { my ( $self, $omim_entry, $val ) = @_; my $genemap_line = ${ $self->_genemap_hash() }{ $val }; my @a = split( /\|/, $genemap_line ); my $locations = $a[ 4 ]; if ( defined ( $locations ) ) { $locations =~ s/\s+//g; my @ls = split( /[,;]/, $locations ); my @cps; foreach my $l ( @ls ) { my $cp = Bio::Map::CytoPosition->new( -value => $l ); push( @cps, $cp ); } $omim_entry->add_CytoPositions( @cps ); } my $gene_symbols = $a[ 5 ]; if ( defined ( $gene_symbols ) ) { $gene_symbols =~ s/\s+//g; my @gss = split( /[,;]/, $gene_symbols ); $omim_entry->add_gene_symbols( @gss ); } my $mouse_correlates = $a[ 16 ]; if ( defined ( $mouse_correlates ) ) { $mouse_correlates =~ s/\s+//g; my @mcs = split( /[,;]/, $mouse_correlates ); my @cs; foreach my $mc ( @mcs ) { my $mouse = Bio::Species->new(); $mouse->classification( qw( musculus Mus ) ); $mouse->common_name( "mouse" ); my $c = Bio::Phenotype::Correlate->new(); $c->name( $mc ); $c->species( $mouse ); $c->type( "OMIM mouse correlate" ); push( @cs, $c ); } $omim_entry->add_Correlates( @cs ); } $omim_entry->gene_status( $a[ 6 ] ) if defined $a[ 6 ]; $omim_entry->mapping_method( $a[ 10 ] ) if defined $a[ 10 ]; $omim_entry->comment( $a[ 11 ] ) if defined $a[ 11 ]; } # _parse_genemap sub _parse_allelic_variants { my ( $self, $text ) = @_; my @allelic_variants; my $number = ""; my $title = ""; my $symbol_mut_line = ""; my $prev_line = ""; my $description = ""; my $saw_empty_line = FALSE; my @lines = split( /\n/, $text ); foreach my $line ( @lines ) { if ( $line !~ /\w/ ) { $saw_empty_line = TRUE; } elsif ( $line =~ /^\s*(\.\d+)/ ) { my $current_number = $1; if ( $number ne "" ) { my $allelic_variant = $self->_create_allelic_variant( $number, $title, $symbol_mut_line, $description ); push( @allelic_variants, $allelic_variant ); } $number = $current_number; $title = ""; $prev_line = ""; $symbol_mut_line = ""; $description = ""; $saw_empty_line = FALSE; } elsif ( $title eq "" ) { $title = $line; } elsif ( $saw_empty_line == FALSE ) { $prev_line = $line; } elsif ( $saw_empty_line == TRUE ) { if ( $prev_line ne "" ) { $symbol_mut_line = $prev_line; $prev_line = ""; } if ( $description ne "" ) { $description .= "\n" . $line; } else { $description = $line; } } } my $allelic_variant = $self->_create_allelic_variant( $number, $title, $symbol_mut_line, $description ); push( @allelic_variants, $allelic_variant ); return @allelic_variants; } # _parse_allelic_variants sub _create_allelic_variant { my ( $self, $number, $title, $symbol_mut_line, $description ) = @_; my $symbol = ""; my $mutation = ""; my $aa_ori = ""; my $aa_mut = ""; my $position = ""; if ( $symbol_mut_line =~ /\s*(.+?)\s*,\s*([a-z]{3})(\d+)([a-z]{3})/i ) { $symbol = $1; $aa_ori = $2; $aa_mut = $4; $position = $3; } elsif ( $symbol_mut_line =~ /\s*(.+?)\s*,\s*(.+)/ ) { $symbol = $1; $mutation = $2; } else { $symbol = $symbol_mut_line; } if ( ! defined( $description ) ) { $self->throw("undef desc"); } if ( ! defined( $mutation ) ) { $self->throw("undef mutation"); } my $allelic_variant = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new(); $allelic_variant->number( $number ); $allelic_variant->aa_ori( $aa_ori ); $allelic_variant->aa_mut( $aa_mut ); $allelic_variant->position( $position ); $allelic_variant->title( $title ); $allelic_variant->symbol( $symbol ); $allelic_variant->description( $description ); $allelic_variant->additional_mutations( $mutation ); return $allelic_variant; } # _create_allelic_variant sub _parse_title { my ( $self, $text ) = @_; my $title = ""; if ( $text =~ /^(.+)\n/ ) { $title = $1; $text =~ s/^.+\n//; } else { $title = $text; $text = ""; } return ( $title, $text ); } # _parse_title sub _parse_references { my ( $self, $text ) = @_; $text =~ s/\A\s+//; $text =~ s/\s+\z//; $text =~ s/\A\d+\.\s*//; my @references; my @texts = split( /\s*\n\s*\n\s*\d+\.\s*/, $text ); foreach my $t ( @texts ) { my $authors = ""; my $title = ""; my $location = ""; $t =~ s/\s+/ /g; if ( $t =~ /(.+?)\s*:\s*(.+?[.?!])\s+(.+?)\s+(\S+?)\s*:\s*(\w?\d+.*)\s*,\s*(\d+)/ ) { $authors = $1; $title = $2; my $journal = $3; my $volume = $4; my $fromto = $5; my $year = $6; my $from = "", my $to = ""; if ( $fromto =~ /(\d+)-+(\d+)/ ) { $from = $1; $to = "-".$2; } elsif ( $fromto =~ /\A(\w+)/ ) { $from = $1; } $location = $journal." ".$volume." ".$from.$to." (".$year.")"; } elsif ( $t =~ /(.+?)\s*:\s*(.+?[.?!])\s*(.+?)\z/ ) { $authors = $1; $title = $2; $location = $3; } else { $title = $t; } my $ref = Bio::Annotation::Reference->new( -title => $title, -location => $location, -authors => $authors ); push( @references, $ref ); } return @references; } # _parse_references sub _genemap_hash { my ( $self, $value ) = @_; if ( defined $value ) { unless ( ref( $value ) eq "HASH" ) { $self->throw( "Argument to method \"_genemap_hash\" is not a reference to an Hash" ); } $self->{ "_genemap_hash" } = $value; } return $self->{ "_genemap_hash" }; } # _genemap_hash sub _is_not_first_record { my ( $self, $value ) = @_; if ( defined $value ) { unless ( $value == FALSE || $value == TRUE ) { $self->throw( "Found [$value] where [" . TRUE ." or " . FALSE . "] expected" ); } $self->{ "_not_first_record" } = $value; } return $self->{ "_not_first_record" }; } # _is_not_first_record sub _done { my ( $self, $value ) = @_; if ( defined $value ) { unless ( $value == FALSE || $value == TRUE ) { $self->throw( "Found [$value] where [" . TRUE ." or " . FALSE . "] expected" ); } $self->{ "_done" } = $value; } return $self->{ "_done" }; } # _done sub _OMIM_text_file { my ( $self, $value ) = @_; if ( defined $value ) { unless ( $value->isa( "Bio::Root::IO" ) ) { $self->throw( "[$value] is not a valid \"Bio::Root::IO\"" ); } $self->{ "_omimtxt_file" } = $value; } return $self->{ "_omimtxt_file" }; } # _OMIM_text_file sub _read_genemap { my ( $self, $genemap_file_name ) = @_; my $line = ""; my %genemap_hash = (); my $genemap_file = Bio::Root::IO->new( -file => $genemap_file_name ); my @a = (); my %gm = (); while( $line = $genemap_file->_readline() ) { @a = split( /\|/, $line ); unless( scalar( @a ) == 18 ) { $self->throw( "Gene map file \"".$self->genemap_file_name() . "\" is not in the expected format." . " Make sure there is a linebreak after the final line." ); } $gm{ $a[ 9 ] } = $line; } $genemap_file->close(); $self->_genemap_hash( \%gm ); } #_read_genemap sub _no_OMIM_text_file_provided_error { my ( $self ) = @_; my $msg = "Need to indicate a OMIM text file to read from with\n"; $msg .= "either \"OMIMparser->new( -omimtext => \"path/to/omim.txt\" );\"\n"; $msg .= "or \"\$omim_parser->omimtxt_file_name( \"path/to/omim.txt\" );\""; $self->throw( $msg ); } # _no_OMIM_text_file_provided_error sub _not_a_OMIM_text_file_error { my ( $self ) = @_; my $msg = "File \"".$self->omimtxt_file_name() . "\" appears not to be a OMIM text file"; $self->throw( $msg ); } # _not_a_OMIM_text_file_error sub _add_to_hash { my ( $self, $state, $contents, $record_ref ) = @_; if ( exists( $record_ref->{ $state } ) ) { chomp( $record_ref->{ $state } ); $record_ref->{ $state } = $record_ref->{ $state } . $contents; } else { $record_ref->{ $state } = $contents; } } # _add_to_hash 1; BioPerl-1.007002/Bio/PhyloNetwork000755000766000024 013155576320 16534 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/PhyloNetwork/Factory.pm000444000766000024 1243113155576320 20657 0ustar00cjfieldsstaff000000000000# # Module for Bio::PhyloNetwork::Factory # # Please direct questions and support issues to # # Cared for by Gabriel Cardona # # Copyright Gabriel Cardona # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PhyloNetwork::Factory - Module to sequentially generate Phylogenetic Networks =head1 SYNOPSIS use strict; use warnings; use Bio::PhyloNetwork; use Bio::PhyloNetwork::Factory; # Will generate sequentially all the 4059 binary tree-child phylogenetic # networks with 4 leaves my $factory=Bio::PhyloNetwork::Factory->new(-numleaves=>4); my @nets; while (my $net=$factory->next_network()) { push @nets,$net; print "".(scalar @nets).": ".$net->eNewick()."\n"; } =head1 DESCRIPTION Sequentially builds a (binary tree-child) phylogenetic network each time next_network is called. =head1 AUTHOR Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es =head1 SEE ALSO L =head1 APPENDIX The rest of the documentation details each of the object methods. =cut package Bio::PhyloNetwork::Factory; use strict; use warnings; use base qw(Bio::Root::Root); use Bio::PhyloNetwork; use Bio::PhyloNetwork::TreeFactory; =head2 new Title : new Usage : my $factory = new Bio::PhyloNetwork::Factory(); Function: Creates a new Bio::PhyloNetwork::Factory Returns : Bio::PhyloNetwork::RandomFactory Args : -numleaves => integer OR -leaves => reference to an array (of leaves names) -numhybrids => integer [default = numleaves -1] -recurse => boolean [optional] Returns a Bio::PhyloNetwork::Factory object. Such an object will sequentially create binary tree-child phylogenetic networks each time next_network is called. If the parameter -leaves=E\@leaves is given, then the set of leaves of these networks will be @leaves. If it is given the parameter -numleaves=E$numleaves, then the set of leaves will be "l1"..."l$numleaves". If the parameter -numhybrids=E$numhybrids is given, then the generated networks will have at most $numhybrids hybrid nodes. Note that, necessarily, $numhybrids E $numleaves. If the parameter -recurse=E1 is given, then all networks with number of hybrid nodes less or equal to $numhybrids will be given; otherwise only those with exactly $numhybrids hybrid nodes. =cut sub new { my ($pkg,@args)=@_; my $self=$pkg->SUPER::new(@args); my ($leavesR,$numleaves,$numhybrids,$recurse)= $self->_rearrange([qw(LEAVES NUMLEAVES NUMHYBRIDS RECURSE)],@args); my @leaves; if ((! defined $leavesR) && (defined $numleaves)) { @leaves=map {"l$_"} (1..$numleaves); $leavesR=\@leaves; } if (! defined $leavesR) { $self->throw("No leaves set neither numleaves given"); } @leaves=@$leavesR; $self->{leaves}=$leavesR; $numleaves=@leaves; $self->{numleaves}=$numleaves; $recurse ||= 0; if (! defined $numhybrids) { $numhybrids=$numleaves-1; $recurse=1; } $self->{recurse}=$recurse; $self->{numhybrids}=$numhybrids; if ($numhybrids ==0) { return Bio::PhyloNetwork::TreeFactory->new(-leaves=>\@leaves); } my $parent; if ($numhybrids > 1) { $parent=new($pkg,'-leaves'=>\@leaves, '-numhybrids'=>($numhybrids-1), '-recurse'=>($recurse)); } else { $parent=Bio::PhyloNetwork::TreeFactory->new(-leaves=>\@leaves); } $self->{parent}=$parent; my $oldnet=$parent->next_network(); $self->{oldnet}=$oldnet; $self->update(); $self->{found}=[]; bless($self,$pkg); } sub update { my ($self)=@_; my @candidates=$self->{oldnet}->edges(); $self->{candidates}=\@candidates; $self->{numcandidates}=(scalar @candidates); $self->{index1}=-$self->{recurse}; $self->{index2}=0; } =head2 next_network Title : next_network Usage : my $net=$factory->next_network() Function: returns a network Returns : Bio::PhyloNetwork Args : none =cut sub next_network { my ($self)=@_; my $numleaves=$self->{numleaves}; my $numhybrids=$self->{numhybrids}; START: if ($self->{index1}==-1) { $self->{index1}++; return $self->{oldnet}; } if ($self->{index1} >= $self->{numcandidates}) { $self->{index2}++; $self->{index1}=0; } if ($self->{index2} >= $self->{numcandidates}) { my $oldnet=$self->{parent}->next_network(); if (! $oldnet) { return 0; } $self->{oldnet}=$oldnet; $self->update(); goto START; } if ((scalar $self->{oldnet}->hybrid_nodes())< $self->{numhybrids}-1) { $self->{candidates}=[]; $self->{numcandidates}=0; goto START; } my $u1=$self->{candidates}->[$self->{index1}]->[0]; my $v1=$self->{candidates}->[$self->{index1}]->[1]; my $u2=$self->{candidates}->[$self->{index2}]->[0]; my $v2=$self->{candidates}->[$self->{index2}]->[1]; my $lbl=$self->{numhybrids}; if ($self->{oldnet}->is_attackable($u1,$v1,$u2,$v2)) { my $net=Bio::PhyloNetwork->new(-graph=>$self->{oldnet}->graph); $net->do_attack($u1,$v1,$u2,$v2,$lbl); $self->{index1}++; my @found=@{$self->{found}}; foreach my $netant (@found) { if ($net->is_mu_isomorphic($netant) ) { goto START; } } push @found,$net; $self->{found}=\@found; return $net; } else { $self->{index1}++; goto START; } } 1; BioPerl-1.007002/Bio/PhyloNetwork/FactoryX.pm000444000766000024 1432313155576320 21011 0ustar00cjfieldsstaff000000000000# # Module for Bio::PhyloNetwork::FactoryX # # Please direct questions and support issues to # # Cared for by Gabriel Cardona # # Copyright Gabriel Cardona # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PhyloNetwork::FactoryX - Module to sequentially generate Phylogenetic Networks =head1 SYNOPSIS use strict; use warnings; use Bio::PhyloNetwork; use Bio::PhyloNetwork::Factory; # Will generate sequentially all the 4059 binary tree-child phylogenetic # networks with 4 leaves my $factory=Bio::PhyloNetwork::Factory->new(-numleaves=>4); my @nets; while (my $net=$factory->next_network()) { push @nets,$net; print "".(scalar @nets).": ".$net->eNewick()."\n"; } =head1 DESCRIPTION Sequentially builds a (binary tree-child) phylogenetic network each time next_network is called. =head1 AUTHOR Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es =head1 SEE ALSO L =head1 APPENDIX The rest of the documentation details each of the object methods. =cut package Bio::PhyloNetwork::FactoryX; use strict; use warnings; use Data::Dumper; use base qw(Bio::Root::Root); use Bio::PhyloNetwork; use Bio::PhyloNetwork::TreeFactoryX; =head2 new Title : new Usage : my $factory = new Bio::PhyloNetwork::Factory(); Function: Creates a new Bio::PhyloNetwork::Factory Returns : Bio::PhyloNetwork::RandomFactory Args : -numleaves => integer OR -leaves => reference to an array (of leaves names) -numhybrids => integer [default = numleaves -1] -recurse => boolean [optional] Returns a Bio::PhyloNetwork::Factory object. Such an object will sequentially create binary tree-child phylogenetic networks each time next_network is called. If the parameter -leaves=E\@leaves is given, then the set of leaves of these networks will be @leaves. If it is given the parameter -numleaves=E$numleaves, then the set of leaves will be "l1"..."l$numleaves". If the parameter -numhybrids=E$numhybrids is given, then the generated networks will have at most $numhybrids hybrid nodes. Note that, necessarily, $numhybrids E $numleaves. If the parameter -recurse=E1 is given, then all networks with number of hybrid nodes less or equal to $numhybrids will be given; otherwise only those with exactly $numhybrids hybrid nodes. =cut sub new { my ($pkg,@args)=@_; my $self=$pkg->SUPER::new(@args); my ($leavesR,$numleaves,$numhybrids)= $self->_rearrange([qw(LEAVES NUMLEAVES NUMHYBRIDS)],@args); my @leaves; if ((! defined $leavesR) && (defined $numleaves)) { @leaves=map {"l$_"} (1..$numleaves); $leavesR=\@leaves; } if (! defined $leavesR) { $self->throw("No leaves set neither numleaves given"); } @leaves=@$leavesR; $self->{leaves}=$leavesR; $numleaves=@leaves; $self->{numleaves}=$numleaves; if (! defined $numhybrids) { $numhybrids=$numleaves-1; } $self->{numhybrids}=$numhybrids; if ($numhybrids ==0) { return Bio::PhyloNetwork::TreeFactoryX->new(-leaves=>\@leaves); } my $parent; if ($numhybrids > 1) { $parent=new($pkg,'-leaves'=>\@leaves, '-numhybrids'=>($numhybrids-1) ); my @subfactories=@{$parent->{subfactories}}; push @subfactories,$parent; # print "$numhybrids : ".(scalar @subfactories); # print "\n"; $self->{subfactories}=\@subfactories; # print "$numhybrids: ".(scalar @subfactories)."\n"; } else { $parent=Bio::PhyloNetwork::TreeFactoryX->new(-leaves=>\@leaves); $self->{subfactories}=[$parent]; } $self->{parent}=$parent; $self->update(); $self->{found}=[]; $self->{thrown}=0; $self->{hybnow}=0; bless($self,$pkg); } sub update { my ($self)=@_; if (defined $self->{oldnet}) { my @candidates=$self->{oldnet}->edges(); $self->{candidates}=\@candidates; $self->{numcandidates}=(scalar @candidates); $self->{index1}=0; $self->{index2}=0; } else { $self->{candidates}=[]; $self->{numcandidates}=0; $self->{index1}=0; $self->{index2}=0; } } sub next_network_repeated { my ($self)=@_; return 0 if ($self->{thrown} >= (scalar @{$self->{found}})); $self->{thrown}=$self->{thrown}+1; return $self->{found}->[$self->{thrown}-1]; } sub next_network_new { my ($self)=@_; START: # print $self->{index1}.",".$self->{index2}.":".$self->{numcandidates}."\n"; if ($self->{index1} >= $self->{numcandidates}) { $self->{index2}++; $self->{index1}=0; } # print $self->{index1}.",".$self->{index2}.":".$self->{numcandidates}."\n"; if ($self->{index2} >= $self->{numcandidates}) { my $oldnet=$self->{parent}->next_network_repeated(); if (! $oldnet) { # print "notoldnet\n"; return 0; } $self->{oldnet}=$oldnet; $self->update(); } my $u1=$self->{candidates}->[$self->{index1}]->[0]; my $v1=$self->{candidates}->[$self->{index1}]->[1]; my $u2=$self->{candidates}->[$self->{index2}]->[0]; my $v2=$self->{candidates}->[$self->{index2}]->[1]; my $lbl=$self->{numhybrids}; if ($self->{oldnet}->is_attackable($u1,$v1,$u2,$v2)) { my $net=Bio::PhyloNetwork->new(-graph=>$self->{oldnet}->graph); $net->do_attack($u1,$v1,$u2,$v2,$lbl); $self->{index1}++; my @found=@{$self->{found}}; foreach my $netant (@found) { if ($net->is_mu_isomorphic($netant) ) { goto START; } } push @found,$net; $self->{found}=\@found; return $net; } else { $self->{index1}++; goto START; } } =head2 next_network Title : next_network Usage : my $net=$factory->next_network() Function: returns a network Returns : Bio::PhyloNetwork Args : none =cut sub next_network { my ($self)=@_; my $hybnow; WTF: $hybnow=$self->{hybnow}; # print $hybnow; # print Dumper($self->{subfactories}->[$hybnow]); # print "$hybnow\n"; # print (scalar @{$self->{subfactories}}); # print "\n"; my $net; if ($hybnow < $self->{numhybrids}) { $net=$self->{subfactories}->[$hybnow]->next_network_new(); } else { $net=$self->next_network_new(); } if (! $net) { if ($hybnow < $self->{numhybrids}) { $self->{hybnow}=$self->{hybnow}+1; goto WTF; } return 0; } return $net; } 1; BioPerl-1.007002/Bio/PhyloNetwork/GraphViz.pm000444000766000024 750113155576320 20764 0ustar00cjfieldsstaff000000000000# # Module for Bio::PhyloNetwork::GraphViz # # Please direct questions and support issues to # # Cared for by Gabriel Cardona # # Copyright Gabriel Cardona # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PhyloNetwork::GraphViz - Interface between PhyloNetwork and GraphViz =head1 SYNOPSIS use Bio::PhyloNetwork; use Bio::PhyloNetwork::GraphViz; my $net=Bio::PhyloNetwork->new( -eNewick=>'((H1,(H1,(H2,l))),H2)t0; (some long label)H1; ("quoted label")H2;' ); my $gv=Bio::PhyloNetwork::GraphViz->new(-net=>$net,-short_labels=>1); foreach my $u ($net->nodes()) { print "$u:".$gv->nodePN_to_nodeGV->{$u}."\n"; } print $gv->as_text; open my $PS, '>', "net.ps" or die "Could not write file 'net.ps': $!\n"; print $PS $gv->as_ps; close $PS; =head1 DESCRIPTION This is a module to create GraphViz objects representing phylogenetic networks. =head1 AUTHOR Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es =head1 SEE ALSO L, L =head1 APPENDIX The rest of the documentation details each of the object methods. =cut package Bio::PhyloNetwork::GraphViz; use strict; use warnings; use base qw(Bio::Root::Root GraphViz); use Bio::PhyloNetwork; =head2 new Title : new Usage : my $graphv = new Bio::PhyloNetwork::GraphViz(); Function: Creates a new Bio::PhyloNetwork::GraphViz object Returns : Bio::PhyloNetwork::GraphViz Args : -net => Bio::PhyloNetwork object -short_labels => boolean (optional) Returns a Bio::PhyloNetwork::GraphViz object, which is an extension of a GraphViz object. The GraphViz object is a representation of the phylogenetic network given. The extra information the created object holds is a hash table with keys the nodes of the PhyloNetwork object and values the nodes of the GraphViz object. If the optional argument -short_labels=E1 is given, the labels of the nodes in GraphViz are shortened to a maximum of 3 letters. =cut sub new { my ($pkg,@args)=@_; my $self=$pkg->SUPER::new(@args); my ($net,$short_labels)= $self->_rearrange([qw(NET SHORT_LABELS)],@args); if (! defined $short_labels) { $short_labels=0; } my $gv=GraphViz->new(); my $nodePN_to_nodeGV={}; my @nodes=$net->nodes(); foreach my $node (@nodes) { # my $namenode=generate_name($node); # $names->{$node}=$namenode; ### my $labelnodeint=$net->{labels}->{$node}; ### my $labelnode=($short_labels ? find_short_label($labelnodeint) : find_label($labelnodeint)); my $nodeGV= $gv->add_node(#$namenode, label=>$labelnode, shape=>($net->is_tree_node($node) ? 'circle' : 'box')); $nodePN_to_nodeGV->{$node}=$nodeGV; } my @edges=$net->edges(); foreach my $edge (@edges) { my $node1=$edge->[0]; # my $namenode1=generate_name($node1); my $node2=$edge->[1]; # my $namenode2=generate_name($node2); $gv->add_edge($nodePN_to_nodeGV->{$node1},$nodePN_to_nodeGV->{$node2}); } $self=$gv; $self->{nodePN_to_nodeGV}=$nodePN_to_nodeGV; bless($self,$pkg); } #sub generate_name { # my ($var)=@_; # if ($var =~ /\D/) { # print "$var contains a number.\b"; # return $var; # } # return "N$var"; #} sub find_short_label { my ($str)=@_; return substr(find_label($str),0,3); } sub find_label { my ($str)=@_; $str =~ tr/A-Za-z0-9//cd; return $str; } =head2 nodePN_to_nodeGV Title : nodePN_to_nodeGV Usage : my $hashR=$graphv->nodePN_to_nodeGV() Function: returns (a reference to) a hash holding the translation between nodes of the Bio::PhyloNetwork object and nodes of the GraphViz object Returns : reference to hash Args : none =cut sub nodePN_to_nodeGV { my ($self)=@_; return $self->{nodePN_to_nodeGV}; } 1; BioPerl-1.007002/Bio/PhyloNetwork/RandomFactory.pm000444000766000024 1047013155576320 22021 0ustar00cjfieldsstaff000000000000# # Module for Bio::PhyloNetwork::RandomFactory # # Please direct questions and support issues to # # Cared for by Gabriel Cardona # # Copyright Gabriel Cardona # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PhyloNetwork::RandomFactory - Module to generate random Phylogenetic Networks =head1 SYNOPSIS use strict; use warnings; use Bio::PhyloNetwork; use Bio::PhyloNetwork::RandomFactory; # Will generate at random all the 66 binary tree-child phylogenetic # networks with 3 leaves my $factory=Bio::PhyloNetwork::RandomFactory->new(-numleaves=>3,-norepeat=>1); my @nets; for (my $i=0; $i<66; $i++) { my $net=$factory->next_network(); push @nets,$net; print "".(scalar @nets).": ".$net->eNewick()."\n"; } =head1 DESCRIPTION Builds a random (binary tree-child) phylogenetic network each time next_network is called. =head1 AUTHOR Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es =head1 SEE ALSO L =head1 APPENDIX The rest of the documentation details each of the object methods. =cut package Bio::PhyloNetwork::RandomFactory; use strict; use warnings; use base qw(Bio::Root::Root); use Bio::PhyloNetwork; use Bio::Tree::RandomFactory; =head2 new Title : new Usage : my $factory = new Bio::PhyloNetwork::RandomFactory(); Function: Creates a new Bio::PhyloNetwork::RandomFactory Returns : Bio::PhyloNetwork::RandomFactory Args : -numleaves => integer OR -leaves => reference to an array (of leaves names) -numhybrids => integer [optional] -norepeat => boolean [optional] Returns a Bio::PhyloNetwork::RandomFactory object. Such an object will create random binary tree-child phylogenetic networks each time next_network is called. If the parameter -leaves=E\@leaves is given, then the set of leaves of these networks will be @leaves. If it is given the parameter -numleaves=E$numleaves, then the set of leaves will be "l1"..."l$numleaves". If the parameter -numhybrids=E$numhybrids is given, then the generated networks will have exactly $numhybrids hybrid nodes. Note that, necessarily, $numhybrids E $numleaves. Otherwise, the number of hybrid nodes will be chosen at random for each call of next_network. If the parameter -norepeat=E1 is given, then successive calls of next_network will give non-isomorphic networks. =cut sub new { my ($pkg,@args)=@_; my $self=$pkg->SUPER::new(@args); my ($leavesR,$numleaves,$numhybrids,$norepeat)= $self->_rearrange([qw(LEAVES NUMLEAVES NUMHYBRIDS NOREPEAT)],@args); my @leaves; if ((! defined $leavesR) && (defined $numleaves)) { @leaves=map {"l$_"} (1..$numleaves); $leavesR=\@leaves; } if (! defined $leavesR) { $self->throw("No leaves set neither numleaves given"); } $norepeat ||= 0; $self->{leaves}=\@leaves; $self->{numleaves}=$numleaves; $self->{numhybrids}=$numhybrids if defined $numhybrids; $self->{norepeat}=$norepeat; $self->{found}=[]; $self->{tree_factory}=Bio::Tree::RandomFactory->new(-taxa => \@leaves); bless($self,$pkg); } =head2 next_network Title : next_network Usage : my $net=$factory->next_network() Function: returns a random network Returns : Bio::PhyloNetwork Args : none =cut sub next_network { my ($self)=@_; my $numleaves=$self->{numleaves}; my @found=@{$self->{found}}; my $numhybrids; START: if (! defined $self->{numhybrids}) { $numhybrids=int(rand($numleaves)); } else { $numhybrids=$self->{numhybrids}; } my $tf=$self->{tree_factory}; my $tree=$tf->next_tree; my $net=Bio::PhyloNetwork->new(-tree=>$tree); for (my $i=1; $i<=$numhybrids; $i++) { $net=random_attack($net,$i); } if ($self->{norepeat}) { foreach my $ant (@found) { goto START if $net->is_mu_isomorphic($ant); } push @found,$net; $self->{found}=\@found; } return $net; } sub random_attack { my ($net,$lbl)=@_; my $graph=$net->{graph}; my ($u1,$v1,$u2,$v2); do { my $e1=$graph->random_edge; my $e2=$graph->random_edge; $u1=$e1->[0]; $v1=$e1->[1]; $u2=$e2->[0]; $v2=$e2->[1]; } while (! $net->is_attackable($u1,$v1,$u2,$v2,$lbl)); $net->do_attack($u1,$v1,$u2,$v2,$lbl); return $net; } 1; BioPerl-1.007002/Bio/PhyloNetwork/TreeFactory.pm000444000766000024 776113155576320 21471 0ustar00cjfieldsstaff000000000000# # Module for Bio::PhyloNetwork::TreeFactory # # Please direct questions and support issues to # # Cared for by Gabriel Cardona # # Copyright Gabriel Cardona # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PhyloNetwork::TreeFactory - Module to sequentially generate Phylogenetic Trees =head1 SYNOPSIS use strict; use warnings; use Bio::PhyloNetwork; use Bio::PhyloNetwork::TreeFactory; # Will generate sequentially all the 15 binary phylogetic # trees with 4 leaves my $factory=Bio::PhyloNetwork::TreeFactory->new(-numleaves=>4); my @nets; while (my $net=$factory->next_network()) { push @nets,$net; print "".(scalar @nets).": ".$net->eNewick()."\n"; } =head1 DESCRIPTION Sequentially builds a (binary) phylogenetic tree each time next_network is called. =head1 AUTHOR Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es =head1 SEE ALSO L =head1 APPENDIX The rest of the documentation details each of the object methods. =cut package Bio::PhyloNetwork::TreeFactory; use strict; use warnings; use base qw(Bio::Root::Root); use Bio::PhyloNetwork; =head2 new Title : new Usage : my $factory = new Bio::PhyloNetwork::TreeFactory(); Function: Creates a new Bio::PhyloNetwork::TreeFactory Returns : Bio::PhyloNetwork::RandomFactory Args : -numleaves => integer OR -leaves => reference to an array (of leaves names) Returns a Bio::PhyloNetwork::TreeFactory object. Such an object will sequentially create binary phylogenetic trees each time next_network is called. If the parameter -leaves=E\@leaves is given, then the set of leaves of these networks will be @leaves. If it is given the parameter -numleaves=E$numleaves, then the set of leaves will be "l1"..."l$numleaves". =cut sub new { my ($pkg,@args)=@_; my $self=$pkg->SUPER::new(@args); my ($leavesR,$numleaves,$numhybrids)= $self->_rearrange([qw(LEAVES NUMLEAVES NUMHYBRIDS)],@args); my @leaves; if ((! defined $leavesR) && (defined $numleaves)) { @leaves=map {"l$_"} (1..$numleaves); $leavesR=\@leaves; } if (! defined $leavesR) { $self->throw("No leaves set neither numleaves given"); } @leaves=@$leavesR; $self->{leaves}=$leavesR; $numleaves=@leaves; $self->{numleaves}=$numleaves; if ($numleaves > 2) { my @leavesparent=@leaves; my $newleaf=pop @leavesparent; $self->{newleaf}=$newleaf; $self->{parent}= new($pkg,-leaves=>\@leavesparent); my $oldnet=$self->{parent}->next_network(); $self->{oldnet}=$oldnet; my @candidates=$oldnet->nodes(); $self->{candidates}=\@candidates; } $self->{index}=0; bless($self,$pkg); } =head2 next_network Title : next_network Usage : my $net=$factory->next_network() Function: returns a tree Returns : Bio::PhyloNetwork Args : none =cut sub next_network { my ($self)=@_; my $n=$self->{numleaves}; if ($self->{numleaves} == 2) { if ($self->{index} == 0) { my $graph=Graph::Directed->new(); $graph->add_edges("t0",$self->{leaves}->[0],"t0",$self->{leaves}->[1]); my $net=Bio::PhyloNetwork->new(-graph=>$graph); $self->{index}++; return $net; } else { return 0; } } else { if ($self->{index} == (scalar @{$self->{candidates}})) { my $oldnet=$self->{parent}->next_network(); if (! $oldnet) { return 0; } $self->{oldnet}=$oldnet; my @candidates=$oldnet->nodes(); $self->{candidates}=\@candidates; $self->{index}=0; } my $graph=$self->{oldnet}->{graph}->copy(); my $u=$self->{candidates}->[$self->{index}]; foreach my $w ($graph->predecessors($u)) { $graph->delete_edge($w,$u); $graph->add_edge($w,"t$n"); } $graph->add_edge("t$n",$u); $graph->add_edge("t$n",$self->{newleaf}); my $net=Bio::PhyloNetwork->new(-graph=>$graph); $self->{index}++; return $net; } } 1; BioPerl-1.007002/Bio/PhyloNetwork/TreeFactoryMulti.pm000444000766000024 1163313155576320 22515 0ustar00cjfieldsstaff000000000000# # Module for Bio::PhyloNetwork::TreeFactoryMulti # # Please direct questions and support issues to # # Cared for by Gabriel Cardona # # Copyright Gabriel Cardona # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PhyloNetwork::TreeFactoryMulti - Module to sequentially generate Phylogenetic Trees =head1 SYNOPSIS use strict; use warnings; use Bio::PhyloNetwork; use Bio::PhyloNetwork::TreeFactory; # Will generate sequentially all the 15 binary phylogetic # trees with 4 leaves my $factory=Bio::PhyloNetwork::TreeFactory->new(-numleaves=>4); my @nets; while (my $net=$factory->next_network()) { push @nets,$net; print "".(scalar @nets).": ".$net->eNewick()."\n"; } =head1 DESCRIPTION Sequentially builds a (binary) phylogenetic tree each time next_network is called. =head1 AUTHOR Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es =head1 SEE ALSO L =head1 APPENDIX The rest of the documentation details each of the object methods. =cut package Bio::PhyloNetwork::TreeFactoryMulti; use strict; use warnings; use base qw(Bio::Root::Root); use Bio::PhyloNetwork; =head2 new Title : new Usage : my $factory = new Bio::PhyloNetwork::TreeFactory(); Function: Creates a new Bio::PhyloNetwork::TreeFactory Returns : Bio::PhyloNetwork::RandomFactory Args : -numleaves => integer OR -leaves => reference to an array (of leaves names) Returns a Bio::PhyloNetwork::TreeFactory object. Such an object will sequentially create binary phylogenetic trees each time next_network is called. If the parameter -leaves=E\@leaves is given, then the set of leaves of these networks will be @leaves. If it is given the parameter -numleaves=E$numleaves, then the set of leaves will be "l1"..."l$numleaves". =cut sub new { my ($pkg,@args)=@_; my $self=$pkg->SUPER::new(@args); my ($leavesR,$numleaves,$numhybrids)= $self->_rearrange([qw(LEAVES NUMLEAVES NUMHYBRIDS)],@args); my @leaves; if ((! defined $leavesR) && (defined $numleaves)) { @leaves=map {"l$_"} (1..$numleaves); $leavesR=\@leaves; } if (! defined $leavesR) { $self->throw("No leaves set neither numleaves given"); } @leaves=@$leavesR; $self->{leaves}=$leavesR; $numleaves=@leaves; $self->{numleaves}=$numleaves; if ($numleaves > 2) { my @leavesparent=@leaves; my $newleaf=pop @leavesparent; $self->{newleaf}=$newleaf; $self->{parent}= new($pkg,-leaves=>\@leavesparent); my $oldnet=$self->{parent}->next_network(); $self->{oldnet}=$oldnet; my @candidates=$oldnet->nodes(); $self->{candidates}=\@candidates; my @candidatesbis=$oldnet->internal_nodes(); $self->{candidatesbis}=\@candidatesbis; $self->{processbis}=0; } $self->{index}=0; bless($self,$pkg); } =head2 next_network Title : next_network Usage : my $net=$factory->next_network() Function: returns a tree Returns : Bio::PhyloNetwork Args : none =cut sub next_network { my ($self)=@_; my $n=$self->{numleaves}; if ($self->{numleaves} == 2) { if ($self->{index} == 0) { my $graph=Graph::Directed->new(); $graph->add_edges("t0",$self->{leaves}->[0],"t0",$self->{leaves}->[1]); my $net=Bio::PhyloNetwork->new(-graph=>$graph); $self->{index}++; return $net; } else { return 0; } } else { if (($self->{index} == (scalar @{$self->{candidatesbis}})) && $self->{processbis} ) { my $oldnet=$self->{parent}->next_network(); if (! $oldnet) { return 0; } $self->{oldnet}=$oldnet; my @candidates=$oldnet->nodes(); $self->{candidates}=\@candidates; my @candidatesbis=$oldnet->internal_nodes(); $self->{candidatesbis}=\@candidatesbis; $self->{processbis}=0; $self->{index}=0; my $n1=scalar @candidates; my $n2=scalar @candidatesbis; print $oldnet->eNewick()."(".$self->{numleaves}.")($n1,$n2):\n"; } if (($self->{index} == (scalar @{$self->{candidates}})) && $self->{processbis}==0 ) { $self->{processbis}=1; $self->{index}=0; print "--\n"; } if ($self->{processbis}==0) { my $graph=$self->{oldnet}->{graph}->copy(); my $u=$self->{candidates}->[$self->{index}]; foreach my $w ($graph->predecessors($u)) { $graph->delete_edge($w,$u); $graph->add_edge($w,"t$n"); } $graph->add_edge("t$n",$u); $graph->add_edge("t$n",$self->{newleaf}); my $net=Bio::PhyloNetwork->new(-graph=>$graph); $self->{index}++; return $net; } else { my $graph=$self->{oldnet}->{graph}->copy(); my $u=$self->{candidatesbis}->[$self->{index}]; # print "<<$u\n"; $graph->add_edge($u,$self->{newleaf}); my $net=Bio::PhyloNetwork->new(-graph=>$graph); $self->{index}++; return $net; } } } 1; BioPerl-1.007002/Bio/PhyloNetwork/TreeFactoryX.pm000444000766000024 1064713155576320 21636 0ustar00cjfieldsstaff000000000000# # Module for Bio::PhyloNetwork::TreeFactoryX # # Please direct questions and support issues to # # Cared for by Gabriel Cardona # # Copyright Gabriel Cardona # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PhyloNetwork::TreeFactoryX - Module to sequentially generate Phylogenetic Trees =head1 SYNOPSIS use strict; use warnings; use Bio::PhyloNetwork; use Bio::PhyloNetwork::TreeFactory; # Will generate sequentially all the 15 binary phylogetic # trees with 4 leaves my $factory=Bio::PhyloNetwork::TreeFactory->new(-numleaves=>4); my @nets; while (my $net=$factory->next_network()) { push @nets,$net; print "".(scalar @nets).": ".$net->eNewick()."\n"; } =head1 DESCRIPTION Sequentially builds a (binary) phylogenetic tree each time next_network is called. =head1 AUTHOR Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es =head1 SEE ALSO L =head1 APPENDIX The rest of the documentation details each of the object methods. =cut package Bio::PhyloNetwork::TreeFactoryX; use strict; use warnings; use base qw(Bio::Root::Root); use Bio::PhyloNetwork; =head2 new Title : new Usage : my $factory = new Bio::PhyloNetwork::TreeFactory(); Function: Creates a new Bio::PhyloNetwork::TreeFactory Returns : Bio::PhyloNetwork::RandomFactory Args : -numleaves => integer OR -leaves => reference to an array (of leaves names) Returns a Bio::PhyloNetwork::TreeFactory object. Such an object will sequentially create binary phylogenetic trees each time next_network is called. If the parameter -leaves=E\@leaves is given, then the set of leaves of these networks will be @leaves. If it is given the parameter -numleaves=E$numleaves, then the set of leaves will be "l1"..."l$numleaves". =cut sub new { my ($pkg,@args)=@_; my $self=$pkg->SUPER::new(@args); my ($leavesR,$numleaves,$numhybrids)= $self->_rearrange([qw(LEAVES NUMLEAVES NUMHYBRIDS)],@args); my @leaves; if ((! defined $leavesR) && (defined $numleaves)) { @leaves=map {"l$_"} (1..$numleaves); $leavesR=\@leaves; } if (! defined $leavesR) { $self->throw("No leaves set neither numleaves given"); } @leaves=@$leavesR; $self->{leaves}=$leavesR; $numleaves=@leaves; $self->{numleaves}=$numleaves; if ($numleaves > 2) { my @leavesparent=@leaves; my $newleaf=pop @leavesparent; $self->{newleaf}=$newleaf; $self->{parent}= new($pkg,-leaves=>\@leavesparent); my $oldnet=$self->{parent}->next_network_new(); $self->{oldnet}=$oldnet; my @candidates=$oldnet->nodes(); $self->{candidates}=\@candidates; } $self->{index}=0; $self->{found}=[]; $self->{thrown}=0; bless($self,$pkg); } =head2 next_network Title : next_network Usage : my $net=$factory->next_network() Function: returns a tree Returns : Bio::PhyloNetwork Args : none =cut sub next_network_new { my ($self)=@_; my $n=$self->{numleaves}; if ($self->{numleaves} == 2) { if ($self->{index} == 0) { my $graph=Graph::Directed->new(); $graph->add_edges("t0",$self->{leaves}->[0],"t0",$self->{leaves}->[1]); my $net=Bio::PhyloNetwork->new(-graph=>$graph); $self->{index}++; $self->{found}=[$net]; return $net; } else { return 0; } } else { if ($self->{index} == (scalar @{$self->{candidates}})) { my $oldnet=$self->{parent}->next_network_new(); if (! $oldnet) { return 0; } $self->{oldnet}=$oldnet; my @candidates=$oldnet->nodes(); $self->{candidates}=\@candidates; $self->{index}=0; } my $graph=$self->{oldnet}->{graph}->copy(); my $u=$self->{candidates}->[$self->{index}]; foreach my $w ($graph->predecessors($u)) { $graph->delete_edge($w,$u); $graph->add_edge($w,"t$n"); } $graph->add_edge("t$n",$u); $graph->add_edge("t$n",$self->{newleaf}); my $net=Bio::PhyloNetwork->new(-graph=>$graph); $self->{index}++; my @found=@{$self->{found}}; push @found,$net; $self->{found}=\@found; return $net; } } sub next_network_repeated { my ($self)=@_; return 0 if ($self->{thrown} >= (scalar @{$self->{found}})); $self->{thrown}=$self->{thrown}+1; return $self->{found}->[$self->{thrown}-1]; } sub next_network { my ($self)=@_; return $self->next_network_new(); } 1; BioPerl-1.007002/Bio/PhyloNetwork/muVector.pm000444000766000024 1516413155576320 21062 0ustar00cjfieldsstaff000000000000# # Module for Bio::PhyloNetwork::muVector # # Please direct questions and support issues to # # Cared for by Gabriel Cardona # # Copyright Gabriel Cardona # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PhyloNetwork::muVector - Module to compute with vectors of arbitrary dimension =head1 SYNOPSIS use strict; use warnings; use Bio::PhyloNetwork::muVector; my $vec1=Bio::PhyloNetwork::muVector->new(4); my $vec2=Bio::PhyloNetwork::muVector->new([1,2,3,4]); my $vec3=Bio::PhyloNetwork::muVector->new([10,20,30,40]); my $vec4=$vec3-10*$vec2; if (($vec4 cmp $vec1) == 0) { print "$vec4 is zero\n"; } my $vec5=Bio::PhyloNetwork::muVector->new([8,2,2,4]); my $vec6=Bio::PhyloNetwork::muVector->new([1,2,3,4]); print "Test poset $vec5 > $vec6: ".$vec5->geq_poset($vec6)."\n"; print "Test lex $vec5 > $vec6: ".($vec5 cmp $vec6)."\n"; =head1 DESCRIPTION This is a module to work with vectors. It creates vectors of arbitrary length, defines its basic arithmetic operations, its lexicographic ordering and the natural structure of poset. =head1 AUTHOR Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es =head1 APPENDIX The rest of the documentation details each of the object methods. =cut package Bio::PhyloNetwork::muVector; use strict; use warnings; use base qw(Bio::Root::Root); =head2 new Title : new Usage : my $mu = new Bio::PhyloNetwork::muVector(); Function: Creates a new Bio::PhyloNetwork::muVector object Returns : Bio::PhyloNetwork::muVector Args : integer or (reference to) an array If given an integer as argument, returns a Bio::PhyloNetwork::muVector object with dimension the integer given and initialized to zero. If it is an anonimous array, then the vector is initialized with the values in the array and with the corresponding dimension. =cut sub new { my ($pkg,$cont)=@_; my $self=$pkg->SUPER::new(); my @arr=(); if (!ref($cont)) { #$cont is a number; initialize to a zero-vector for (my $i=0; $i < $cont; $i++) { $arr[$i]=0; } $self->{arr}=\@arr; } else { #$cont points to an array @arr=@{$cont}; } $self->{dim}=scalar @arr; $self->{arr}=\@arr; bless($self,$pkg); return $self; } sub dim { return shift->{dim} } use overload "+" => \&add, "-" => \&substract, "*" => \&scalarproduct, "<=>" => \&comparelex, "cmp" => \&comparelex, '""' => \&display, '@{}' => \&as_array; sub as_array { return shift->{arr}; } =head2 display Title : display Usage : my $str=$mu->display() Function: returns an string displaying its contents Returns : string Args : none This function is also overloaded to the "" operator. =cut sub display { my ($self)=@_; my @arr=@{$self->{arr}}; return "(@arr)"; } =head2 add Title : add Usage : $mu->add($mu2) Function: returns the sum of $mu and $mu2 Returns : Bio::PhyloNetwork::muVector Args : Bio::PhyloNetwork::muVector This function is also overloaded to the + operator. =cut sub add { my ($v1,$v2)=@_; $v1->throw("Vectors not the same size") unless ($v1->{dim} == $v2->{dim}); my $dim=$v1->{dim}; my @sum=(); for (my $i=0; $i<$dim; $i++) { $sum[$i]=$v1->[$i]+$v2->[$i]; } my $result=Bio::PhyloNetwork::muVector->new(\@sum); return $result; } =head2 substract Title : substract Usage : $mu->substract($mu2) Function: returns the difference of $mu and $mu2 Returns : Bio::PhyloNetwork::muVector Args : Bio::PhyloNetwork::muVector This function is also overloaded to the - operator. =cut sub substract { my ($v1,$v2)=@_; $v1->throw("Vectors not the same size") unless ($v1->{dim} == $v2->{dim}); my $dim=$v1->{dim}; my @sum=(); for (my $i=0; $i<$dim; $i++) { $sum[$i]=$v1->{arr}->[$i]-$v2->{arr}->[$i]; } my $result=Bio::PhyloNetwork::muVector->new(\@sum); return $result; } =head2 scalarproduct Title : scalarproduct Usage : $mu->scalarproduct($ct) Function: returns the scalar product of $ct and $mu Returns : Bio::PhyloNetwork::muVector Args : scalar This function is also overloaded to the * operator. =cut sub scalarproduct { my ($v1,$num,$swapped)=@_; my $dim=$v1->{dim}; my @sum=(); for (my $i=0; $i<$dim; $i++) { $sum[$i]=$num*$v1->{arr}->[$i]; } my $result=Bio::PhyloNetwork::muVector->new(\@sum); return $result; return $result; } =head2 comparelex Title : comparelex Usage : $mu1->comparelex($mu2) Function: compares $mu and $mu2 w.r.t. the lexicographic ordering Returns : scalar (-1 if $mu1<$mu2, 0 if $mu1=$mu2, 1 if $mu1>$mu2) Args : Bio::PhyloNetwork::muVector This function is also overloaded to the E=E and cmp operator. =cut sub comparelex { my ($v1,$v2)=@_; $v1->throw("Vectors not the same size") unless ($v1->{dim} == $v2->{dim}); my $dim=$v1->{dim}; for (my $i=0; $i<$dim; $i++) { return -1 if $v1->{arr}->[$i] < $v2->{arr}->[$i]; return 1 if $v1->{arr}->[$i] > $v2->{arr}->[$i]; } return 0; } =head2 geq_poset Title : geq_poset Usage : $mu1->geq_poset($mu2) Function: compares $mu and $mu2 w.r.t. the natural partial ordering Returns : boolean (1 if $mu >= $mu2, 0 otherwise) Args : Bio::PhyloNetwork::muVector =cut sub geq_poset { my ($v1,$v2)=@_; $v1->throw("Vectors not the same size") unless ($v1->{dim} == $v2->{dim}); my $dim=$v1->{dim}; for (my $i=0; $i<$dim; $i++) { return 0 unless $v1->[$i] >= $v2->[$i]; } return 1; } =head2 is_positive Title : is_positive Usage : $mu->is_positive() Function: tests if all components of $mu are positive (or zero) Returns : boolean Args : none =cut sub is_positive { my ($v1)=@_; my $dim=$v1->{dim}; for (my $i=0; $i<$dim; $i++) { return 0 unless $v1->[$i] >= 0; } return 1; } =head2 hamming Title : hamming Usage : $mu1->hamming($mu2) Function: returns the Hamming distance between $mu1 and $mu2 Returns : scalar Args : Bio::PhyloNetwork::muVector =cut sub hamming { my ($v1,$v2)=@_; $v1->throw("Vectors not the same size") unless ($v1->{dim} == $v2->{dim}); my $dim=$v1->{dim}; my $w=0; for (my $i=0; $i<$dim; $i++) { $w++ unless $v1->[$i] == $v2->[$i]; } return $w; } =head2 manhattan Title : manhattan Usage : $mu1->manhattan($mu2) Function: returns the Manhattan distance between $mu1 and $mu2 Returns : scalar Args : Bio::PhyloNetwork::muVector =cut sub manhattan { my ($v1,$v2)=@_; $v1->throw("Vectors not the same size") unless ($v1->{dim} == $v2->{dim}); my $dim=$v1->{dim}; my $w=0; for (my $i=0; $i<$dim; $i++) { $w+= abs($v1->[$i] - $v2->[$i]); } return $w; } 1; BioPerl-1.007002/Bio/PopGen000755000766000024 013155576320 15257 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/PopGen/Genotype.pm000444000766000024 1520513155576320 17567 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::Genotype # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::Genotype - An implementation of GenotypeI which is just an allele container =head1 SYNOPSIS use Bio::PopGen::Genotype; my $genotype = Bio::PopGen::Genotype->new(-marker_name => $name, -individual_id => $indid, -alleles => \@alleles); =head1 DESCRIPTION This object will contain alleles for a given marker for a given individual. The class variable BlankAlleles (accessible through $Bio::PopGen::Genotype::BlankAlleles = 'somepattern') can be set to a regexp pattern for identifying blank alleles which should no be counted (they are effectively missing data). By default it set to match white space, '-', 'N' or 'n', and '?' as blank alleles which are skipped. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Matthew Hahn, matthew.hahn-at-duke.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::Genotype; use vars qw($BlankAlleles); use strict; $BlankAlleles = '[\s\-Nn\?]'; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root Bio::PopGen::GenotypeI); =head2 new Title : new Usage : my $obj = Bio::PopGen::Genotype->new(); Function: Builds a new Bio::PopGen::Genotype object Returns : an instance of Bio::PopGen::Genotype Args : -marker_name => string representing name of the marker -individual_id => string representing individual id (optional) -alleles => arrayref with each item in the array being an allele =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($marker_name, $marker_type, $ind_id, $alleles) = $self->_rearrange([qw(MARKER_NAME MARKER_TYPE INDIVIDUAL_ID ALLELES)],@args); defined $marker_name && $self->marker_name($marker_name); defined $marker_type && $self->marker_type($marker_type); defined $ind_id && $self->individual_id($ind_id); if( defined $alleles ) { if( ref($alleles) =~ /array/i ) { $self->add_Allele(@$alleles); } else { $self->warn("Could not initialize with -alleles value, it is not an array ref"); } } return $self; } =head2 marker_name Title : marker_name Usage : my $name = $genotype->marker_name(); Function: Get the marker name for a genotype result Returns : string Args : [optional] marker name value to store =cut sub marker_name{ my ($self) = shift; return $self->{'_marker_name'} = shift if @_; return $self->{'_marker_name'}; } =head2 marker_type Title : marker_type Usage : my $name = $genotype->marker_type(); Function: Get the marker type for a genotype result Returns : M (microsatellite, or other multi-allelic locus) or S (biallelic/SNP locus) Args : [optional] marker type value to store =cut sub marker_type{ my ($self) = shift; return $self->{'_marker_type'} = shift if @_; return $self->{'_marker_type'}; } =head2 individual_id Title : individual_id Usage : my $indid = $genotype->individual_id(); Function: Gets the individual id associated with a genotype This is effectively a back reference since we will typically associate a genotype with an individual with an individual HAS-A genotype relationship. Returns : unique id string for an individual Args : none =cut sub individual_id { my ($self) = shift; return $self->{'_individual_id'} = shift if @_; return $self->{'_individual_id'}; } =head2 get_Alleles Title : get_Alleles Usage : my @alleles = $genotype->get_Alleles(); Function: Get the alleles for a given marker and individual Returns : array of alleles (strings in this implementation) Args : $showblank - boolean flag to indicate return ALL alleles not skipping the coded EMPTY alleles Note : Uses the class variable $BlankAlleles to test if alleles should be skipped or not. =cut sub get_Alleles{ my ($self) = shift; if( @_ && $_[0] ) { return @{$self->{'_alleles'} || []}; } else { if( defined $self->{'_cached_noblank'} ) { return @{$self->{'_cached_noblank'}} } # one liners - woo hoo. $self->{'_cached_noblank'} = [ grep { ! /^\s*$BlankAlleles\s*$/o } @{$self->{'_alleles'} || []}]; return @{$self->{'_cached_noblank'}}; } } =head2 add_Allele Title : add_Allele Usage : $genotype->add_Allele(@alleles); Function: Add alleles to the genotype, at this point there is no verification to insure that haploid individuals only have 1 allele or that diploids only have 2 - we assume that is done by the user creating these objects Returns : count of the number of alleles in genotype Args : Array of alleles to store =cut sub add_Allele { my ($self) = shift; $self->{'_cached_noblank'} = undef; push @{$self->{'_alleles'}}, @_; return scalar @{$self->{'_alleles'}}; } =head2 reset_Alleles Title : reset_Alleles Usage : $genotype->reset_Alleles; Function: Resets the stored alleles so the list is empty Returns : None Args : None =cut sub reset_Alleles{ my ($self,@args) = @_; $self->{'_cached_noblank'} = undef; $self->{'_alleles'} = []; return 0; } 1; BioPerl-1.007002/Bio/PopGen/GenotypeI.pm000444000766000024 620013155576320 17653 0ustar00cjfieldsstaff000000000000# $Id $ # # BioPerl module for Bio::PopGen::GenotypeI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::GenotypeI - A marker and alleles for a specific individual =head1 SYNOPSIS Give standard usage here =head1 DESCRIPTION Describe the interface here =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::GenotypeI; use strict; use base qw(Bio::Root::RootI); =head2 marker_name Title : marker_name Usage : my $name = $genotype->marker_name(); Function: Get the marker name for a genotype result Returns : string Args : none =cut sub marker_name{ my ($self) = @_; $self->throw_not_implemented(); } =head2 individual_id Title : individual_id Usage : my $indid = $genotype->individual_id(); Function: Gets the individual id associated with a genotype This is effectively a back reference since we will typically associate a genotype with an individual with an individual HAS-A genotype relationship. Returns : unique id string for an individual Args : none =cut sub individual_id{ my ($self) = @_; $self->throw_not_implemented(); } =head2 annotation Title : annotation Usage : my $annotation_collection = $genotype->annotation; Function: Get/set a Bio::AnnotationCollectionI for this genotype Returns : Bio::AnnotationCollectionI object Args : [optional set] Bio::AnnotationCollectionI object =cut sub annotation{ my ($self) = @_; $self->throw_not_implemented(); } =head2 get_Alleles Title : get_Alleles Usage : my @alleles = $genotype->get_Alleles(); Function: Get the alleles for a given marker and individual Returns : array of alleles (strings in many implementations) Args : none =cut sub get_Alleles{ my ($self) = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/PopGen/HtSNP.pm000444000766000024 12506613155576320 16760 0ustar00cjfieldsstaff000000000000# module Bio::PopGen::HtSNP.pm # cared by Pedro M. Gomez-Fabre # # =head1 NAME Bio::PopGen::HtSNP.pm- Select htSNP from a haplotype set =head1 SYNOPSIS use Bio::PopGen::HtSNP; my $obj = Bio::PopGen::HtSNP->new($hap,$snp,$pop); =head1 DESCRIPTION Select the minimal set of SNP that contains the full information about the haplotype without redundancies. Take as input the followin values: =over 4 =item - the haplotype block (array of array). =item - the snp id (array). =item - family information and frequency (array of array). =back The final haplotype is generated in a numerical format and the SNP's sets can be retrieve from the module. B - If you force to include a family with indetermination, the SNP's with indetermination will be removed from the analysis, so consider before to place your data set what do you really want to do. - If two families have the same information (identical haplotype), one of them will be removed and the removed files will be stored classify as removed. - Only are accepted for calculation A, C, G, T and - (as deletion) and their combinations. Any other value as n or ? will be considered as degenerations due to lack of information. =head2 RATIONALE On a haplotype set is expected that some of the SNP and their variations contribute in the same way to the haplotype. Eliminating redundancies will produce a minimal set of SNP's that can be used as input for a taging selection process. On the process SNP's with the same variation are clustered on the same group. The idea is that because the tagging haplotype process is exponential. All redundant information we could eliminate on the tagging process will help to find a quick result. =head2 CONSTRUCTORS my $obj = Bio::PopGen::HtSNP->new (-haplotype_block => \@haplotype_patterns, -snp_ids => \@snp_ids, -pattern_freq => \@pattern_name_and_freq); where $hap, $snp and $pop are in the format: my $hap = [ 'acgt', 'agtc', 'cgtc' ]; # haplotype patterns' id my $snp = [qw/s1 s2 s3 s4/]; # snps' Id's my $pop = [ [qw/ uno 0.20/], [qw/ dos 0.20/], [qw/ tres 0.15/], ]; # haplotype_pattern_id Frequency =head2 OBJECT METHODS See Below for more detailed summaries. =head1 DETAILS =head2 How the process is working with one example Let's begin with one general example of the code. Input haplotype: acgtcca-t cggtagtgc cccccgtgc cgctcgtgc The first thing to to is to B into characters. a c g t c c a - t c g g t a g t g c c c c c c g t g c c g c t c g t g c Now we have to B the haplotype to B. This will produce the same SNP if we have input a or A. A C G T C C A - T C G G T A G T G C C C C C C G T G C C G C T C G T G C The program admit as values any combination of ACTG and - (deletions). The haplotype is B, considering the first variation as zero and the alternate value as 1 (see expanded description below). 0 0 0 0 0 0 0 0 0 1 1 0 0 1 1 1 1 1 1 0 1 1 0 1 1 1 1 1 1 1 0 0 1 1 1 1 Once we have the haplotype converted to numbers we have to generate the snp type information for the haplotype. B where: SUM is the sum of the values for the SNP value is the SNP number code (0 [generally for the mayor allele], 1 [for the minor allele]. position is the position on the block. For this example the code is: 0 0 0 0 0 0 0 0 0 1 1 0 0 1 1 1 1 1 1 0 1 1 0 1 1 1 1 1 1 1 0 0 1 1 1 1 ------------------------------------------------------------------ 14 10 12 4 2 14 14 14 14 14 = 0*2^0 + 1*2^1 + 1*2^2 + 1*2^3 12 = 0*2^0 + 1*2^1 + 0*2^2 + 1*2^3 .... Once we have the families classify. We will B just the SNP's B. 14 10 12 4 2 This information will be B is you want to tag the htSNP. Whatever it happens to one SNPs of a class will happen to a SNP of the same class. Therefore you don't need to scan redundancies =head2 Working with fuzzy data. This module is designed to work with fuzzy data. As the source of the haplotype is diverse. The program assume that some haplotypes can be generated using different values. If there is any indetermination (? or n) or any other degenerated value or invalid. The program will take away This SNP and will leave that for a further analysis. On a complex situation: a c g t ? c a c t a c g t ? c a - t c g ? t a g ? g c c a c t c g t g c c g c t c g t g c c g g t a g ? g c a c ? t ? c a c t On this haplotype everything is happening. We have a multialelic variance. We have indeterminations. We have deletions and we have even one SNP which is not a real SNP. The buiding process will be the same on this situation. Convert the haplotype to uppercase. A C G T ? C A C T A C G T ? C A - T C G ? T A G ? G C C A C T C G T G C C G C T C G T G C C G G T A G ? G C A C ? T ? C A C T All columns that present indeterminations will be removed from the analysis on this Step. hapotype after remove columns: A C T C C T A C T C - T C G T G G C C A T G G C C G T G G C C G T G G C A C T C C T All changes made on the haplotype matrix, will be also made on the SNP list. snp_id_1 snp_id_2 snp_id_4 snp_id_6 snp_id_8 snp_id_9 now the SNP that is not one SNP will be removed from the analysis. SNP with Id snp_id_4 (the one with all T's). because of the removing. Some of the families will become the same and will be clustered. A posteriori analysis will diference these families. but because of the indetermination can not be distinguish. A C C C T A C C - T C G G G C C A G G C C G G G C C G G G C A C C C T The result of the mergering will go like: A C C C T A C C - T C G G G C C A G G C Once again the changes made on the families and we merge the frequency (I) Before to convert the haplotype into numbers we consider how many variations we have on the set. On this case the variations are 3. The control code will use on this situation base three as mutiplicity 0 0 0 0 0 0 0 0 1 0 1 1 1 2 1 1 2 1 2 1 ----------------------------------- 36 63 36 75 36 And the minimal set for this combination is 0 0 0 0 0 1 1 1 2 1 2 2 B this second example is a remote example an on normal conditions. This conditions makes no sense, but as the haplotypes, can come from many sources we have to be ready for all kind of combinations. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Pedro M. Gomez-Fabre Email pgf18872-at-gsk-dot-com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::HtSNP; use Data::Dumper; use Storable qw(dclone); use vars qw (); use strict; use base qw(Bio::Root::Root); my $USAGE = 'Usage: Bio::PopGen::HtSNP->new(-haplotype_block -ids -pattern_freq) '; =head2 new Title : new Function: constructor of the class. Usage : $obj-> Bio::PopGen::HtSNP->new(-haplotype_block -snp_ids -pattern_freq) Returns : self hash Args : input haplotype (array of array) snp_ids (array) pop_freq (array of array) Status : public =cut sub new { my($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($haplotype_block, $snp_ids, $pattern_freq ) = $self->_rearrange([qw(HAPLOTYPE_BLOCK SNP_IDS PATTERN_FREQ)],@args); if ($haplotype_block){ $self->haplotype_block($haplotype_block); } else{ $self->throw("Haplotype block has not been defined. \n$USAGE"); } if ($snp_ids){ $self->snp_ids($snp_ids); } else{ $self->throw("Array with ids has not been defined. \n$USAGE"); } if ($pattern_freq){ $self->pattern_freq($pattern_freq); } else{ $self->throw("Array with pattern id and frequency has not been defined. \n$USAGE"); } # if the input values are not well formed complained and exit. _check_input($self); _do_it($self); return $self; } =head2 haplotype_block Title : haplotype_block Usage : my $haplotype_block = $HtSNP->haplotype_block(); Function: Get the haplotype block for a haplotype tagging selection Returns : reference of array Args : reference of array with haplotype pattern =cut sub haplotype_block{ my ($self) =shift; return $self->{'_haplotype_block'} = shift if @_; return $self->{'_haplotype_block'}; } =head2 snp_ids Title : snp_ids Usage : my $snp_ids = $HtSNP->$snp_ids(); Function: Get the ids for a haplotype tagging selection Returns : reference of array Args : reference of array with SNP ids =cut sub snp_ids{ my ($self) =shift; return $self->{'_snp_ids'} = shift if @_; return $self->{'_snp_ids'}; } =head2 pattern_freq Title : pattern_freq Usage : my $pattern_freq = $HtSNP->pattern_freq(); Function: Get the pattern id and frequency for a haplotype tagging selection Returns : reference of array Args : reference of array with SNP ids =cut sub pattern_freq{ my ($self) =shift; return $self->{'_pattern_freq'} = shift if @_; return $self->{'_pattern_freq'}; } =head2 _check_input Title : _check_input Usage : _check_input($self) Function: check for errors on the input Returns : self hash Args : self Status : internal =cut #------------------------ sub _check_input{ #------------------------ my $self = shift; _haplotype_length_error($self); _population_error($self); } =head2 _haplotype_length_error Title : _haplotype_length_error Usage : _haplotype_length_error($self) Function: check if the haplotype length is the same that the one on the SNP id list. If not break and exit Returns : self hash Args : self Status : internal =cut #------------------------ sub _haplotype_length_error{ #------------------------ my $self = shift; my $input_block = $self->haplotype_block(); my $snp_ids = $self->snp_ids(); ############################# # define error list ############################# my $different_haplotype_length = 0; ############################## # get parameters used to find # the errors ############################## my $snp_number = scalar @$snp_ids; my $number_of_families = scalar @$input_block; my $h = 0; # haplotype position ############################ # haplotype length # # if the length differs from the number of ids ############################ for ($h=0; $h<$#$input_block+1 ; $h++){ if (length $input_block->[$h] != $snp_number){ $different_haplotype_length = 1; last; } } # haploytypes does not have the same length if ($different_haplotype_length){ $self->throw("The number of snp ids is $snp_number and ". "the length of the family (". ($h+1) .") [". $input_block->[$h]."] is ". length $input_block->[$h], "\n"); } } =head2 _population_error Title : _population_error Usage : _population_error($self) Function: use input_block and pop_freq test if the number of elements match. If doesn't break and quit. Returns : self hash Args : self Status : internal =cut #------------------------ sub _population_error{ #------------------------ my $self = shift; my $input_block = $self->haplotype_block(); my $pop_freq = $self->pattern_freq(); ############################# # define error list ############################# my $pop_freq_elements_error = 0; # matrix bad formed ############################## # get parameters used to find # the errors ############################## my $number_of_families = scalar @$input_block; my $pf = 0; # number of elements on population frequency my $frequency = 0; # population frequency my $p_f_length = 0; # check if the pop_freq array is well formed and if the number # of elements fit with the number of families ############################# # check population frequency # # - population frequency matrix need to be well formed # - get the frequency # - calculate number of families on pop_freq ############################# for ($pf=0; $pf<$#$pop_freq+1; $pf++){ $frequency += $pop_freq->[$pf]->[1]; if ( scalar @{$pop_freq->[$pf]} !=2){ $p_f_length = scalar @{$pop_freq->[$pf]}; $pop_freq_elements_error = 1; last; } } ########################### ## error processing ########################### # The frequency shouldn't be greater than 1 if ($frequency >1) { $self->warn("The frequency for this set is $frequency (greater than 1)\n"); } # the haplotype matix is not well formed if ($pop_freq_elements_error){ $self->throw("the frequency matrix is not well formed\n". "\nThe number of elements for pattern ".($pf+1)." is ". "$p_f_length\n". "It should be 2 for pattern \"@{$pop_freq->[$pf]}\"\n". "\nFormat should be:\n". "haplotype_id\t frequency\n" ); } # the size does not fit on pop_freq array # with the one in haplotype (input_block) if ($pf != $number_of_families) { $self->throw("The number of patterns on frequency array ($pf)\n". "does not fit with the number of haplotype patterns on \n". "haplotype array ($number_of_families)\n"); } } =head2 _do_it Title : _do_it Usage : _do_it($self) Function: Process the input generating the results. Returns : self hash Args : self Status : internal =cut #------------------------ sub _do_it{ #------------------------ my $self = shift; # first we are goinf to define here all variables we are going to use $self -> {'w_hap'} = []; $self -> {'w_pop_freq'} = dclone ( $self ->pattern_freq() ); $self -> {'deg_pattern'} = {}; $self -> {'snp_type'} = {}; # type of snp on the set. see below $self -> {'alleles_number'} = 0; # number of variations (biallelic,...) $self -> {'snp_type_code'} = []; $self -> {'ht_type'} = []; # store the snp type used on the htSet $self -> {'split_hap'} = []; $self -> {'snp_and_code'} = []; # we classify the SNP under snp_type $self->{snp_type}->{useful_snp} = dclone ( $self ->snp_ids() ); $self->{snp_type}->{deg_snp} = []; # deg snp $self->{snp_type}->{silent_snp} = []; # not a real snp # split the haplotype _split_haplo ($self); # first we convert to upper case the haplotype # to make A the same as a for comparison _to_upper_case( $self -> {w_hap} ); ####################################################### # check if any SNP has indetermination. If any SNP has # indetermination this value will be removed. ####################################################### _remove_deg ( $self ); ####################################################### # depending of the families you use some SNPs can be # silent. This silent SNP's are not used on the # creation of tags and has to be skipped from the # analysis. ####################################################### _rem_silent_snp ( $self ); ####################################################### # for the remaining SNP's we have to check if two # families have the same value. If this is true, the families # will produce the same result and therefore we will not find # any pattern. So, the redundant families need to be take # away from the analysis. But also considered for a further # run. # # When we talk about a normal haplotype blocks this situation # makes no sense but if we remove one of the snp because the # degeneration two families can became the same. # these families may be analised on a second round ####################################################### _find_deg_pattern ( $self ); ################################################################# # if the pattern list length is different to the lenght of the w_hap # we can tell that tow columns have been considered as the same one # and therefore we have to start to remove the values. # remove all columns with degeneration # # For this calculation we don't use the pattern frequency. # All patterns are the same, This selection makes # sense when you have different frequency. # # Note: on this version we don't classify the haplotype by frequency # but if you need to do it. This is the place to do it!!!! # # In reality you don't need to sort the values because you will remove # the values according to their values. # # But as comes from a hash, the order could be different and as a # consequence the code generate on every run of the same set could # differ. That is not important. In fact, does not matter but could # confuse people. ################################################################# my @tmp =sort { $a <=> $b} keys %{$self -> {deg_pattern}}; # just count the families # if the size of the list is different to the size of the degenerated # family. There is degeneration. And the redundancies will be # removed. if($#tmp != $#{$self -> { w_hap } } ){ _keep_these_patterns($self->{w_hap}, \@tmp); _keep_these_patterns($self->{w_pop_freq}, \@tmp); } ################################################################# # the steps made before about removing snp and cluster families # are just needed pre-process the haplotype before. # # Now is when the fun starts. # # # once we have the this minimal matrix, we have to calculate the # max multipliticy for the values. The max number of alleles found # on the set. A normal haplotype is biallelic but we can not # reject multiple variations. ################################################################## _alleles_number ( $self ); ################################################################## # Now we have to convert the haplotype into number # # A C C - T # C A G G C # A C C C T # C G G G C # # one haplotype like this transformed into number produce this result # # 0 0 0 0 0 # 1 1 1 1 1 # 0 0 0 2 0 # 1 2 1 1 1 # ################################################################## _convert_to_numbers( $self ); ################################################################### # The next step is to calculate the type of the SNP. # This process is made based on the position of the SNP, the value # and its multiplicity. ################################################################### _snp_type_code( $self ); ################################################################### # now we have all information we need to calculate the haplotype # tagging SNP htSNP ################################################################### _htSNP( $self ); ################################################################### # patch: # # all SNP have a code. but if the SNP is not used this code must # be zero in case of silent SNP. This looks not to informative # because all the information is already there. But this method # compile the full set. ################################################################### _snp_and_code_summary( $self ); } =head2 input_block Title : input_block Usage : $obj->input_block() Function: returns input block Returns : reference to array of array Args : none Status : public =cut #------------------------ sub input_block{ #------------------------ my $self = shift; return $self -> {input_block}; } =head2 hap_length Title : hap_length Usage : $obj->hap_length() Function: get numbers of SNP on the haplotype Returns : scalar Args : none Status : public =cut #------------------------ sub hap_length{ #------------------------ my $self = shift; return scalar @{$self -> {'_snp_ids'}}; } =head2 pop_freq Title : pop_freq Usage : $obj->pop_freq() Function: returns population frequency Returns : reference to array Args : none Status : public =cut #------------------------ sub pop_freq{ #------------------------ my $self = shift; return $self -> {pop_freq} } =head2 deg_snp Title : deg_snp Usage : $obj->deg_snp() Function: returns snp_removes due to indetermination on their values Returns : reference to array Args : none Status : public =cut #------------------------ sub deg_snp{ #------------------------ my $self = shift; return $self -> {snp_type} ->{deg_snp}; } =head2 snp_type Title : snp_type Usage : $obj->snp_type() Function: returns hash with SNP type Returns : reference to hash Args : none Status : public =cut #------------------------ sub snp_type{ #------------------------ my $self = shift; return $self -> {snp_type}; } =head2 silent_snp Title : silent_snp Usage : $obj->silent_snp() Function: some SNP's are silent (not contibuting to the haplotype) and are not considering for this analysis Returns : reference to a array Args : none Status : public =cut #------------------------ sub silent_snp{ #------------------------ my $self = shift; return $self -> {snp_type} ->{silent_snp}; } =head2 useful_snp Title : useful_snp Usage : $obj->useful_snp() Function: returns list of SNP's that are can be used as htSNP. Some of them can produce the same information. But this is not considered here. Returns : reference to a array Args : none Status : public =cut #------------------------ sub useful_snp{ #------------------------ my $self = shift; return $self -> {snp_type} ->{useful_snp}; } =head2 ht_type Title : ht_type Usage : $obj->ht_type() Function: every useful SNP has a numeric code dependending of its value and position. For a better description see description of the module. Returns : reference to a array Args : none Status : public =cut #------------------------ sub ht_type{ #------------------------ my $self = shift; return $self -> {ht_type}; } =head2 ht_set Title : ht_set Usage : $obj->ht_set() Function: returns the minimal haplotype in numerical format. This haplotype contains the maximal information about the haplotype variations but with no redundancies. It's the minimal set that describes the haplotype. Returns : reference to an array of arrays Args : none Status : public =cut #------------------------ sub ht_set{ #------------------------ my $self = shift; return $self -> {w_hap}; } =head2 snp_type_code Title : snp_type_code Usage : $obj->snp_type_code() Function: returns the numeric code of the SNPs that need to be tagged that correspond to the SNP's considered in ht_set. Returns : reference to an array Args : none Status : public =cut #------------------------ sub snp_type_code{ #------------------------ my $self = shift; return $self -> {snp_type_code}; } =head2 snp_and_code Title : snp_and_code Usage : $obj->snp_and_code() Function: Returns the full list of SNP's and the code associate to them. If the SNP belongs to the group useful_snp it keep this code. If the SNP is silent the code is 0. And if the SNP is degenerated the code is -1. Returns : reference to an array of array Args : none Status : public =cut #------------------------ sub snp_and_code{ #------------------------ my $self = shift; return $self -> {'snp_and_code'}; } =head2 deg_pattern Title : deg_pattern Usage : $obj->deg_pattern() Function: Returns the a list with the degenerated haplotype. Sometimes due to degeneration some haplotypes looks the same and if we don't remove them it won't find any tag. Returns : reference to a hash of array Args : none Status : public =cut #------------------------ sub deg_pattern{ #------------------------ my $self = shift; return $self -> {'deg_pattern'}; } =head2 split_hap Title : split_hap Usage : $obj->split_hap() Function: simple representation of the haplotype base by base Same information that input haplotype but base based. Returns : reference to an array of array Args : none Status : public =cut #------------------------ sub split_hap{ #------------------------ my $self = shift; return $self -> {'split_hap'}; } =head2 _split_haplo Title : _split_haplo Usage : _split_haplo($self) Function: Take a haplotype and split it into bases Returns : self Args : none Status : internal =cut #------------------------ sub _split_haplo { #------------------------ my $self = shift; my $in = $self ->{'_haplotype_block'}; my $out = $self ->{'w_hap'}; # split every haplotype and store the result into $out foreach (@$in){ push @$out, [split (//,$_)]; } $self -> {'split_hap'} = dclone ($out); } # internal method to convert the haplotype to uppercase =head2 _to_upper_case Title : _to_upper_case Usage : _to_upper_case() Function: make SNP or in-dels Upper case Returns : self Args : an AoA ref Status : private =cut #------------------------ sub _to_upper_case { #------------------------ my ($arr) =@_; foreach my $aref (@$arr){ foreach my $value (@{$aref} ){ $value = uc $value; } } } =head2 _remove_deg Title : _remove_deg Usage : _remove_deg() Function: when have a indetermination or strange value this SNP is removed Returns : haplotype family set and degeneration list Args : ref to an AoA and a ref to an array Status : internal =cut #------------------------ sub _remove_deg { #------------------------ my $self = shift; my $hap = $self->{w_hap}; my $snp = $self->{snp_type}->{useful_snp}; my $deg_snp = $self->{snp_type}->{deg_snp}; my $rem = []; # take the position of the array to be removed # first we work on the columns we have void values $rem = _find_indet($hap,$rem); # find degenerated columns if (@$rem){ # remove column on haplotype _remove_col($hap,$rem); # remove list # now remove the values from SNP id _remove_snp_id($snp,$deg_snp,$rem); # remove list } } =head2 _rem_silent_snp Title : _rem_silent_snp Usage : _rem_silent_snp() Function: there is the remote possibility that one SNP won't be a real SNP on this situation we have to remove this SNP, otherwise the program won't find any tag Returns : nonthing Args : ref to an AoA and a ref to an array Status : internal =cut #------------------------ sub _rem_silent_snp { #------------------------ my $self = shift; my $hap = $self->{w_hap}; my $snp = $self->{snp_type}->{useful_snp}; my $silent_snp = $self->{snp_type}->{silent_snp}; my $rem = []; # store the positions to be removed #find columns with no variation on the SNP, Real snp? $rem = _find_silent_snps($hap); if (@$rem){ # remove column on haplotype _remove_col($hap,$rem); # remove the values from SNP id _remove_snp_id($snp,$silent_snp,$rem); } } =head2 _find_silent_snps Title : _find_silent_snps Usage : Function: list of snps that are not SNPs. All values for that SNPs on the set is the same one. Look stupid but can happened and if this happend you will not find any tag Returns : nothing Args : Status : =cut #------------------------ sub _find_silent_snps{ #------------------------ my ($arr)=@_; my $list =[]; # no snp list; # determine the number of snp by the length of the first row. # we assume that the matrix is squared. my $colsn= @{$arr->[0]}; for (my $i=0;$i<$colsn;$i++){ my $different =0; # check degeneration for my $r (1..$#$arr){ if($arr->[0][$i] ne $arr->[$r][$i]){ $different =1; last; } } if(!$different){ push (@$list, $i); } } return $list; } =head2 _find_indet Title : _find_indet Usage : Function: find column (SNP) with invalid or degenerated values and store this values into the second parameter supplied. Returns : nothing Args : ref to AoA and ref to an array Status : internal =cut #------------------------ sub _find_indet{ #------------------------ my ($arr, $list)=@_; foreach my $i(0..$#$arr){ foreach my $j(0..$#{$arr->[$i]}){ unless ($arr->[$i][$j] =~ /[ACTG-]/){ if ($#$list<0){ push(@$list,$j); } else{ my $found =0; # check if already exist the value foreach my $k(0..$#$list){ $found =1 if ($list->[$k] eq $j); last if ($found); } if(!$found){ push(@$list,$j); } } } } } @$list = sort { $a <=> $b} @$list; return $list; } =head2 _remove_col Title : _remove_col Usage : Function: remove columns contained on the second array from the first arr Returns : nothing Args : array of array reference and array reference Status : internal =cut #------------------------ sub _remove_col{ #------------------------ my ($arr,$rem)=@_; foreach my $col (reverse @$rem){ splice @$_, $col, 1 for @$arr; } } =head2 _remove_snp_id Title : _remove_snp_id Usage : Function: remove columns contained on the second array from the first arr Returns : nothing Args : array of array reference and array reference Status : internal =cut #------------------------ sub _remove_snp_id{ #------------------------ my ($arr,$removed,$rem_list)=@_; push @$removed, splice @$arr, $_, 1 foreach reverse @$rem_list; } =head2 _find_deg_pattern Title : _find_deg_pattern Usage : Function: create a list with the degenerated patterns Returns : @array Args : a ref to AoA Status : public =cut #------------------------ sub _find_deg_pattern{ #------------------------ my $self = shift; my $arr = $self ->{w_hap}; # the working haplotype my $list = $self ->{'deg_pattern'}; # degenerated patterns # we have to check all elements foreach my $i(0..$#$arr){ # is the element has not been used create a key unless ( _is_on_hash ($list,\$i) ) { $list->{$i}=[$i]; }; foreach my $j($i+1..$#$arr){ my $comp = compare_arrays($arr->[$i],$arr->[$j]); if($comp){ # as we have no elements we push this into the list # check for the first element my $key = _key_for_value($list,\$i); push (@{$list->{$key}},$j); last; } } } } #------------------------ sub _key_for_value{ #------------------------ my($hash,$value)=@_; foreach my $key (keys %$hash){ if( _is_there(\@{$hash->{$key}},$value)){ return $key; } } } #------------------------ sub _is_on_hash{ #------------------------ my($hash,$value)=@_; foreach my $key (keys %$hash){ if( _is_there(\@{$hash->{$key}},$value)){ return 1; } } } #------------------------ sub _is_there{ #------------------------ my($arr,$value)=@_; foreach my $el (@$arr){ if ($el eq $$value){ return 1; } } } =head2 _keep_these_patterns Title : _keep_these_patterns Usage : Function: this is a basic approach, take a LoL and a list, keep just the columns included on the list Returns : nothing Args : an AoA and an array Status : public =cut #------------------------ sub _keep_these_patterns{ #------------------------ my ($arr,$list)=@_; # by now we just take one of the repetitions but you can weight # the values by frequency my @outValues=(); foreach my $k (@$list){ push @outValues, $arr->[$k]; } #make arr to hold the new values @$arr= @{dclone(\@outValues)}; } =head2 compare_arrays Title : compare_arrays Usage : Function: take two arrays and compare their values Returns : 1 if the two values are the same 0 if the values are different Args : an AoA and an array Status : public =cut #------------------------ sub compare_arrays { #------------------------ my ($first, $second) = @_; return 0 unless @$first == @$second; for (my $i = 0; $i < @$first; $i++) { return 0 if $first->[$i] ne $second->[$i]; } return 1; } =head2 _convert_to_numbers Title : _convert_to_numbers Usage : _convert_to_numbers() Function: transform the haplotype into numbers. before to do that we have to consider the variation on the set. Returns : nonthing Args : ref to an AoA and a ref to an array Status : internal =cut #------------------------ sub _convert_to_numbers{ #------------------------ my $self = shift; my $hap_ref = $self->{w_hap}; my $mm = $self->{alleles_number}; # the first element is considered as zero. The first modification # is consider as one and so on. my $length = @{ @$hap_ref[0]}; #length of the haplotype for (my $c = 0; $c<$length;$c++){ my @al=(); for my $r (0..$#$hap_ref){ push @al,$hap_ref->[$r][$c] unless _is_there(\@al,\$hap_ref->[$r][$c]); $hap_ref->[$r][$c] = get_position(\@al,\$hap_ref->[$r][$c]); } } } =head2 _snp_type_code Title : _snp_type_code Usage : Function: we have to create the snp type code for each version. The way the snp type is created is the following: we take the number value for every SNP and do the following calculation let be a SNP set as follow: 0 0 1 1 1 2 and multiplicity 3 on this case the situation is: sum (value * multiplicity ^ position) for each SNP 0 * 3 ^ 0 + 1 * 3 ^ 1 + 1 * 3 ^ 2 = 12 0 * 3 ^ 0 + 1 * 3 ^ 1 + 2 * 3 ^ 2 = 21 Returns : nothing Args : $self Status : private =cut #------------------------ sub _snp_type_code{ #------------------------ my $self = shift; my $hap = $self->{w_hap}; my $arr = $self->{snp_type_code}; my $al = $self->{alleles_number}; my $length = @{ $hap->[0]}; #length of the haplotype for (my $c=0; $c<$length; $c++){ for my $r (0..$#$hap){ $arr->[$c] += $hap->[$r][$c] * $al ** $r; } } } ################################################# # return the position of an element in one array # The element is always present on the array ################################################# #------------------------ sub get_position{ #------------------------ my($array, $value)=@_; for my $i(0..$#$array) { if ($array->[$i] eq $$value){ return $i; } } } =head2 _alleles_number Title : _alleles_number Usage : Function: calculate the max number of alleles for a haplotype and if the number. For each SNP the number is stored and the max number of alleles for a SNP on the set is returned Returns : max number of alleles (a scalar storing a number) Args : ref to AoA Status : public =cut #------------------------ sub _alleles_number{ #------------------------ my $self = shift; my $hap_ref = $self ->{w_hap}; # working haplotype my $length = @{ @$hap_ref[0]}; # length of the haplotype for (my $c = 0; $c<$length;$c++){ my %alleles=(); for my $r (0..$#$hap_ref){ $alleles{ $hap_ref->[$r][$c] } =1; # new key for every new snp } # if the number of alleles for this column is # greater than before set $m value as allele number if ($self->{alleles_number} < keys %alleles) { $self->{alleles_number} = keys %alleles; } } } =head2 _htSNP Title : _htSNP Usage : _htSNP() Function: calculate the minimal set that contains all information of the haplotype. Returns : nonthing Args : ref to an AoA and a ref to an array Status : internal =cut #------------------------ sub _htSNP{ #------------------------ my $self = shift; my $hap = $self->{'w_hap'}; my $type = $self->{'snp_type_code'}; my $set = $self->{'ht_type'}; my $out = []; # store the minimal set my $nc=0; # new column for the output values # pass for every value of the snp_type_code for my $c (0..$#$type){ my $exist =0; # every new value (not present) is pushed into set if ( ! _is_there( $set,\$type->[$c] ) ){ push @$set, $type->[$c]; $exist =1; for my $r(0..$#$hap){ #save value of the snp for every SNP $out->[$r][$nc]= $hap->[$r][$c]; } } if ($exist){ $nc++ }; } @$hap = @{dclone $out}; } =head2 _snp_and_code_summary Title : _snp_and_code_summary Usage : _snp_and_code_summary() Function: compile on a list all SNP and the code for each. This information can be also obtained combining snp_type and snp_type_code but on these results the information about the rest of SNP's are not compiled as table. 0 will be silent SNPs -1 are degenerated SNPs and the rest of positive values are the code for useful SNP Returns : nonthing Args : ref to an AoA and a ref to an array Status : internal =cut #------------------------ sub _snp_and_code_summary{ #------------------------ my $self = shift; my $snp_type_code = $self->{'snp_type_code'}; my $useful_snp = $self->{'snp_type'}->{'useful_snp'}; my $silent_snp = $self->{'snp_type'}->{'silent_snp'}; my $deg_snp = $self->{'snp_type'}->{'deg_snp'}; my $snp_ids = $self->snp_ids(); my $snp_and_code = $self->{'snp_and_code'}; # walk all SNP's and generate code for each # do a practical thing. Consider all snp silent foreach my $i (0..$#$snp_ids){ # assign zero to silent my $value=0; # active SNPs foreach my $j (0..$#$useful_snp){ if ($snp_ids->[$i] eq $useful_snp->[$j]){ $value = $snp_type_code->[$j]; last; } } # assign -1 to degenerated foreach my $j (0..$#$deg_snp){ if ($snp_ids->[$i] eq $deg_snp->[$j]){ $value = -1; last; } } push @$snp_and_code, [$snp_ids->[$i], $value]; } } 1; BioPerl-1.007002/Bio/PopGen/IO.pm000444000766000024 1700613155576320 16305 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::IO # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::IO - Input individual,marker,allele information =head1 SYNOPSIS use Bio::PopGen::IO; my $io = Bio::PopGen::IO->new(-format => 'csv', -file => 'data.csv'); # Some IO might support reading in a population at a time my @population; while( my $ind = $io->next_individual ) { push @population, $ind; } =head1 DESCRIPTION This is a generic interface to reading in population genetic data (of which there really isn't too many standard formats). This implementation makes it easy to provide your own parser for the data. You need to only implement one function next_individual. You can also implement next_population if your data has explicit information about population memberhsip for the indidviduals. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... #TODO # Set the Individual creation as a factory rather than # hardcoded package Bio::PopGen::IO; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Root::Root; use base qw(Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::PopGen::IO->new(); Function: Builds a new Bio::PopGen::IO object Returns : an instance of Bio::PopGen::IO Args : =cut sub new { my($class,@args) = @_; if( $class =~ /Bio::PopGen::IO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $format = $param{'-format'} || $class->_guess_format( $param{'-file'} || $ARGV[0] ) || 'csv'; # normalize capitalization to lower case $format = "\L$format"; return unless( $class->_load_format_module($format) ); return "Bio::PopGen::IO::${format}"->new(@args); } } =head2 format Title : format Usage : $format = $stream->format() Function: Get the PopGen format Returns : PopGen format Args : none =cut # format() method inherited from Bio::Root::IO # _initialize is chained for all PopGen::IO classes sub _initialize { my($self, @args) = @_; # my ($indfact, $popfact) = $self->_rearrange([qw(INDIVIDUAL_FACTORY # POPULATION_FACTORY)], # @args); # $indfact = Bio::PopGen::IndividualBuilder->new() unless $indfact; # $indfact = Bio::PopGen::PopulationBuilder->new() unless $indfact; # initialize the IO part $self->_initialize_io(@args); return 1; } =head2 next_individual Title : next_individual Usage : my $ind = $popgenio->next_individual; Function: Retrieve the next individual from a dataset Returns : L object Args : none =cut sub next_individual{ my ($self) = @_; $self->throw_not_implemented(); } =head2 next_population Title : next_population Usage : my $pop = $popgenio->next_population; Function: Retrieve the next population from a dataset Returns : L object Args : none Note : Many implementation will not implement this =cut sub next_population{ my ($self) = @_; $self->throw_not_implemented(); } =head2 write_individual Title : write_individual Usage : $popgenio->write_individual($ind); Function: Write an individual out in the implementation format Returns : none Args : L object(s) =cut sub write_individual{ my ($self) = @_; $self->throw_not_implemented(); } =head2 write_population Title : write_population Usage : $popgenio->write_population($pop); Function: Write a population out in the implementation format Returns : none Args : L object(s) Note : Many implementation will not implement this =cut sub write_population{ my ($self) = @_; $self->throw_not_implemented(); } =head2 newFh Title : newFh Usage : $fh = Bio::SeqIO->newFh(-file=>$filename,-format=>'Format') Function: does a new() followed by an fh() Example : $fh = Bio::SeqIO->newFh(-file=>$filename,-format=>'Format') $sequence = <$fh>; # read a sequence object print $fh $sequence; # write a sequence object Returns : filehandle tied to the Bio::SeqIO::Fh class Args : See L =cut sub newFh { my $class = shift; return unless my $self = $class->new(@_); return $self->fh; } =head2 fh Title : fh Usage : $obj->fh Function: Example : $fh = $obj->fh; # make a tied filehandle $sequence = <$fh>; # read a sequence object print $fh $sequence; # write a sequence object Returns : filehandle tied to Bio::SeqIO class Args : none =cut sub fh { my $self = shift; my $class = ref($self) || $self; my $s = Symbol::gensym; tie $$s,$class,$self; return $s; } =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL Bio::PopGen::IO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($self,$format) = @_; my $module = "Bio::PopGen::IO::" . $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args : =cut sub _guess_format { my $class = shift; return unless $_ = shift; return 'csv' if (/csv/i or /\.dat\w$/i); } sub close { my $self = shift; $self->SUPER::close(@_); } sub DESTROY { my $self = shift; $self->close(); } sub TIEHANDLE { my $class = shift; return bless {processor => shift}, $class; } sub READLINE { my $self = shift; return $self->{'processor'}->next_result() || undef unless wantarray; my (@list, $obj); push @list, $obj while $obj = $self->{'processor'}->next_result(); return @list; } sub PRINT { my $self = shift; $self->{'processor'}->write_result(@_); } 1; BioPerl-1.007002/Bio/PopGen/Individual.pm000444000766000024 1675313155576320 20076 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::Individual # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::Individual - An implementation of an Individual who has Genotype or Sequence Results =head1 SYNOPSIS use Bio::PopGen::Individual; my $ind = Bio::PopGen::Individual->new(-unique_id => $id, -genotypes => \@genotypes); =head1 DESCRIPTION This object is a container for genotypes. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Matthew Hahn, matthew.hahn-at-duke.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::Individual; use vars qw($UIDCOUNTER); use strict; BEGIN { $UIDCOUNTER = 1 } # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root Bio::PopGen::IndividualI); =head2 new Title : new Usage : my $obj = Bio::PopGen::Individual->new(); Function: Builds a new Bio::PopGen::Individual object Returns : an instance of Bio::PopGen::Individual Args : -unique_id => $id, -genotypes => \@genotypes =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_genotypes'} = {}; my ($uid,$genotypes) = $self->_rearrange([qw(UNIQUE_ID GENOTYPES)],@args); unless( defined $uid ) { $uid = $UIDCOUNTER++; } $self->unique_id($uid); if( defined $genotypes ) { if( ref($genotypes) =~ /array/i ) { $self->add_Genotype(@$genotypes); } else { $self->warn("Must provide a valid array reference to set the genotypes value in the constructor"); } } return $self; } =head2 unique_id Title : unique_id Usage : my $id = $individual->unique_id Function: Unique Identifier Returns : string representing unique identifier Args : string =cut sub unique_id{ my ($self) = shift; return $self->{'_unique_id'} = shift if @_; return $self->{'_unique_id'}; } =head2 num_of_results Title : num_of_results Usage : my $count = $person->num_results; Function: returns the count of the number of Results for a person Returns : integer Args : none =cut sub num_of_results { return scalar keys %{shift->{'_genotypes'}}; } =head2 annotation Title : annotation Usage : my $annotation_collection = $ind->annotation; Function: Get/set a Bio::AnnotationCollectionI for this individual Returns : Bio::AnnotationCollectionI object Args : [optional set] Bio::AnnotationCollectionI object =cut sub annotation{ my ($self, $arg) = @_; return $self->{_annotation} unless $arg; $self->throw("Bio::AnnotationCollectionI required for argument") unless ref($arg) && $arg->isa('Bio::AnnotationCollectionI'); return $self->{_annotation} = $arg; } =head2 add_Genotype Title : add_Genotype Usage : $individual->add_Genotype Function: add a genotype value Returns : count of the number of genotypes associated with this individual Args : @genotypes - L object(s) containing alleles plus a marker name =cut sub add_Genotype { my ($self,@genotypes) = @_; foreach my $g ( @genotypes ) { if( !ref($g) || ! $g->isa('Bio::PopGen::GenotypeI') ) { $self->warn("cannot add $g as a genotype skipping"); next; } my $mname = $g->marker_name; if( ! defined $mname || ! length($mname) ) { # can't just say ! name b/c '0' wouldn't be valid $self->warn("cannot add genotype because marker name is not defined or is an empty string"); next; } if( $self->verbose > 0 && defined $self->{'_genotypes'}->{$mname} ) { # a warning when we have verbosity cranked up $self->debug("Overwriting the previous value for $mname for this individual"); } # this will force Genotype individual_id to be set to # the Individual it has been added for $g->individual_id($self->unique_id); $self->{'_genotypes'}->{$mname} = $g; } return scalar keys %{$self->{'_genotypes'}}; } =head2 reset_Genotypes Title : reset_Genotypes Usage : $individual->reset_Genotypes; Function: Reset the genotypes stored for this individual Returns : none Args : none =cut sub reset_Genotypes{ shift->{'_genotypes'} = {}; } =head2 remove_Genotype Title : remove_Genotype Usage : $individual->remove_Genotype(@names) Function: Removes the genotypes for the requested markers Returns : none Args : Names of markers =cut sub remove_Genotype{ my ($self,@mkrs) = @_; foreach my $m ( @mkrs ) { delete($self->{'_genotypes'}->{$m}); } } =head2 get_Genotypes Title : get_Genotypes Usage : my @genotypes = $ind->get_Genotypes(-marker => $markername); Function: Get the genotypes for an individual, based on a criteria Returns : Array of genotypes Args : either none (return all genotypes) or -marker => name of marker to return (exact match, case matters) =cut sub get_Genotypes{ my ($self,@args) = @_; if( @args ) { unshift @args, '-marker' if( @args == 1 ); # deal with single args my ($name) = $self->_rearrange([qw(MARKER)], @args); if( ! defined($name) ) { $self->warn("Only know how to process the -marker field currently"); return(); } my $v = $self->{'_genotypes'}->{$name}; return $v; } return values %{$self->{'_genotypes'} || {}}; } =head2 has_Marker Title : has_Marker Usage : if( $ind->has_Marker($name) ) {} Function: Boolean test to see if an Individual has a genotype for a specific marker Returns : Boolean (true or false) Args : String representing a marker name =cut sub has_Marker{ my ($self,$name) = @_; return 0 if ! defined $name; $name = $name->name if ref($name) && $name->isa('Bio::PopGen::MarkerI'); if( ref($name) ) { $self->warn("Passed in a ".ref($name). " to has_Marker, expecting either a string or a Bio::PopGen::MarkerI"); return 0; } return defined $self->{'_genotypes'}->{$name}; } =head2 get_marker_names Title : get_marker_names Usage : my @names = $individual->get_marker_names; Function: Returns the list of known marker names Returns : List of strings Args : none =cut sub get_marker_names{ my ($self) = @_; return keys %{$self->{'_genotypes'}}; } 1; BioPerl-1.007002/Bio/PopGen/IndividualI.pm000444000766000024 1003613155576320 20173 0ustar00cjfieldsstaff000000000000# $Id $ # # BioPerl module for Bio::PopGen::IndividualI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::IndividualI - An individual who has Genotype or Sequence Results =head1 SYNOPSIS # Get a Bio::PopGen::IndividualI somehow # test if it has alleles/genotypes for a given marker if( $ind->has_marker($markername) ) { } # get the unique id print $ind->unique_id, "\n"; # get the number of results (genotypes) print $ind->num_results; =head1 DESCRIPTION Describe the interface here =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::IndividualI; use strict; use base qw(Bio::Root::RootI); =head2 unique_id Title : unique_id Usage : my $id = $individual->unique_id Function: Unique Identifier Returns : string representing unique identifier Args : string =cut sub unique_id{ my ($self) = @_; $self->throw_not_implemented(); } =head2 num_genotypes Title : num_genotypes Usage : my $count = $person->num_results; Function: returns the count of the number of Results for a person Returns : integer Args : none =cut sub num_genotypes { shift->throw_not_implemented; } sub num_of_results{ my $self = shift; $self->deprecated("num_of_results is deprecated, use num_genotypes instead"); $self->num_genotypes; } =head2 annotation Title : annotation Usage : my $annotation_collection = $ind->annotation; Function: Get/set a Bio::AnnotationCollectionI for this individual Returns : Bio::AnnotationCollectionI object Args : [optional set] Bio::AnnotationCollectionI object =cut sub annotation{ my ($self, $arg) = @_; $self->throw_not_implemented(); } =head2 get_Genotypes Title : get_Genotypes Usage : my @genotypes = $ind->get_Genotypes(-marker => $markername); Function: Get the genotypes for an individual, based on a criteria Returns : Array of genotypes Args : either none (return all genotypes) or -marker => name of marker to return (exact match, case matters) =cut sub get_Genotypes{ my ($self) = @_; $self->throw_not_implemented(); } =head2 has_Marker Title : has_Marker Usage : if( $ind->has_Marker($name) ) {} Function: Boolean test to see if an Individual has a genotype for a specific marker Returns : Boolean (true or false) Args : String representing a marker name =cut sub has_Marker{ my ($self,$name) = @_; $self->throw_not_implemented(); } =head2 get_marker_names Title : get_marker_names Usage : my @names = $individual->get_marker_names; Function: Returns the list of known marker names Returns : List of strings Args : none =cut sub get_marker_names{ my ($self) = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/PopGen/Marker.pm000444000766000024 1672313155576320 17224 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::Marker # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::Marker - A genetic marker which one uses to generate genotypes =head1 SYNOPSIS my $name = $marker->name(); # marker name my $description = $marker->description(); # description my $type = $marker->type(); # coded type of the marker my $unique_id = $marker->unique_id; # optional unique ID my @alleles = $marker->get_Alleles(); # the known alleles my %allele_freqs = $marker->get_Allele_Frequencies(); # keys are marker names # vals are frequencies # may change to handle multiple populations =head1 DESCRIPTION This object will not contain genotype information pertaining to an individual, but rather population level statistics and descriptive information about a marker. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Matthew Hahn, matthew.hahn-at-duke.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::Marker; use strict; # Object preamble - inherits from Bio::Root::Root use vars qw($UniqueCounter); $UniqueCounter = 0; use base qw(Bio::Root::Root Bio::PopGen::MarkerI); =head2 new Title : new Usage : my $obj = Bio::PopGen::Marker->new(); Function: Builds a new Bio::PopGen::Marker object Returns : an instance of Bio::PopGen::Marker Args : -name => [string] marker name -description => [string] marker description -type => [string] marker type -unique_id => [string/int] unique id -allele_freq => [hash ref] allele frequencies =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($name,$desc,$type,$uid,$af) = $self->_rearrange([qw(NAME DESCRIPTION TYPE UNIQUE_ID ALLELE_FREQ)],@args); $self->{'_allele_freqs'} = {}; if( ! defined $uid ) { $uid = $UniqueCounter++; } if( defined $name) { $self->name($name); } else { $self->throw("Must provide a name when initializing a Marker"); } defined $desc && $self->description($desc); defined $type && $self->type($type); $self->unique_id($uid); if( defined $af) { if( ref($af) !~ /HASH/i ) { $self->warn("Must provide valid Hash reference for allele_freq method"); } else { foreach my $allele ( keys %$af ) { $self->add_Allele_Frequency($allele, $af->{$allele}); } } } return $self; } =head2 name Title : name Usage : my $name = $marker->name(); Function: Get the name of the marker Returns : string representing the name of the marker Args : [optional] name =cut sub name{ my $self = shift; return $self->{'_name'} = shift if @_; return $self->{'_name'}; } =head2 description Title : description Usage : my $desc = $marker->description Function: Get the marker description free text Returns : string Args : [optional] string =cut sub description{ my $self = shift; return $self->{'_description'} = shift if @_; return $self->{'_description'}; } =head2 type Title : type Usage : my $type = $marker->type; Function: Get coded string for marker type Returns : string Args : [optional] string =cut sub type{ my $self = shift; return $self->{'_type'} = shift if @_; return $self->{'_type'}; } =head2 unique_id Title : unique_id Usage : my $id = $marker->unique_id; Function: Get the unique marker ID Returns : unique ID string Args : [optional ] string =cut sub unique_id{ my $self = shift; return $self->{'_uniqueid'} = shift if @_; return $self->{'_uniqueid'}; } =head2 annotation Title : annotation Usage : my $annotation_collection = $marker->annotation; Function: Get/set a Bio::AnnotationCollectionI for this marker Returns : Bio::AnnotationCollectionI object Args : [optional set] Bio::AnnotationCollectionI object =cut sub annotation{ my ($self, $arg) = @_; return $self->{_annotation} unless $arg; $self->throw("Bio::AnnotationCollectionI required for argument") unless ref($arg) && $arg->isa('Bio::AnnotationCollectionI'); return $self->{_annotation} = $arg; } =head2 get_Alleles Title : get_Alleles Usage : my @alleles = $marker->get_Alleles(); Function: Get the available marker alleles Returns : Array of strings Args : none =cut sub get_Alleles{ my $self = shift; my (@numeric,@alpha); for ( keys %{$self->{'_allele_freqs'}} ) { if( /[^\d\.\-e]/ ) { push @alpha, $_ } else { push @numeric, $_ } } @numeric = sort { $b <=> $a } @numeric; @alpha = sort { $b cmp $a } @alpha; return @numeric,@alpha; } =head2 get_Allele_Frequencies Title : get_Allele_Frequencies Usage : my %allele_freqs = $marker->get_Allele_Frequencies; Function: Get the alleles and their frequency (set relative to a given population - you may want to create different markers with the same name for different populations with this current implementation Returns : Associative array where keys are the names of the alleles Args : none =cut sub get_Allele_Frequencies{ return %{$_[0]->{'_allele_freqs'}}; } =head2 add_Allele_Frequency Title : add_Allele_Frequency Usage : $marker->add_Allele_Frequency($allele,$freq) Function: Adds an allele frequency Returns : None Args : $allele - allele name $freq - frequency value =cut sub add_Allele_Frequency{ my ($self,$allele,$freq) = @_; $self->{'_allele_freqs'}->{$allele} = $freq; } =head2 reset_alleles Title : reset_alleles Usage : $marker->reset_alleles(); Function: Reset the alleles for a marker Returns : None Args : None =cut sub reset_alleles{ my ($self) = @_; $self->{'_allele_freqs'} = {}; } =head2 marker_coverage Title : marker_coverage Usage : $marker->marker_coverage(); Function: Get marker coverage, that is, the number of individuals where the marker is present excluding missing or ambiguous alleles Returns : integer, representing marker coverage Args : =cut sub marker_coverage{ my ($self) = @_; return $self->{_marker_coverage}; } 1; BioPerl-1.007002/Bio/PopGen/MarkerI.pm000444000766000024 1117313155576320 17327 0ustar00cjfieldsstaff000000000000# $Id $ # # BioPerl module for Bio::PopGen::MarkerI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::MarkerI - A Population Genetic conceptual marker =head1 SYNOPSIS # Get a Bio::PopGen::MarkerI somehow - like using a Bio::PopGen::Marker my $name = $marker->name(); # marker name my $description = $marker->description(); # description my $type = $marker->type(); # coded type of the marker my $unique_id = $marker->unique_id; # optional unique ID my @alleles = $marker->get_Alleles(); # the known alleles my %allele_freqs = $marker->get_Allele_Frequencies(); # keys are marker names # vals are frequencies # may change to handle multiple populations =head1 DESCRIPTION This is the basic interface for Markers which one can associate alleles with for calculating Theta and Pi. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Matthew Hahn, matthew.hahn-at-duke.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::MarkerI; use strict; use base qw(Bio::Root::RootI Bio::AnnotatableI); =head2 name Title : name Usage : my $name = $marker->name(); Function: Get the name of the marker Returns : string representing the name of the marker Args : =cut sub name{ $_[0]->throw_not_implemented(); } =head2 description Title : description Usage : my $desc = $marker->description Function: Get the marker description free text Returns : string Args : [optional] string =cut sub description{ $_[0]->throw_not_implemented(); } =head2 type Title : type Usage : my $type = $marker->type; Function: Get coded string for marker type Returns : string Args : [optional] string =cut sub type{ my ($self) = @_; $self->throw_not_implemented(); } =head2 unique_id Title : unique_id Usage : my $id = $marker->unique_id; Function: Get the unique marker ID Returns : unique ID string Args : [optional ] string =cut sub unique_id{ my ($self) = @_; $self->throw_not_implemented(); } =head2 annotation Title : annotation Usage : $obj->annotation($seq_obj) Function: retrieve the attached annotation object Returns : Bio::AnnotationCollectionI or none; See L and L for more information. This method comes through extension from L. =cut sub annotation{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_Alleles Title : get_Alleles Usage : my @alleles = $marker->get_Alleles(); Function: Get the available marker alleles if they are known and stored Returns : Array of strings Args : none =cut sub get_Alleles{ my ($self) = @_; $self->throw_not_implemented(); } =head2 get_Allele_Frequencies Title : get_Allele_Frequencies Usage : my %allele_freqs = $marker->get_Allele_Frequencies; Function: Get the alleles and their frequency (set relative to a given population - you may want to create different markers with the same name for different populations with this current implementation Returns : Associative array (hash) where keys are the names of the alleles Args : none =cut sub get_Allele_Frequencies{ my ($self) = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/PopGen/PopStats.pm000444000766000024 2072513155576320 17555 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::PopStats # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::PopStats - A collection of methods for calculating statistics about a population or sets of populations =head1 SYNOPSIS use Bio::PopGen::PopStats; my $stats = Bio::PopGen::PopStats->new(); # add -haploid => 1 # to process haploid data =head1 DESCRIPTION Calculate various population structure statistics, most notably Wright's Fst. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Matthew Hahn, matthew.hahn-at-duke.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::PopStats; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root); =head2 new Title : new Usage : my $obj = Bio::PopGen::PopStats->new(); Function: Builds a new Bio::PopGen::PopStats object Returns : an instance of Bio::PopGen::PopStats Args : -haploid => 1 (if want to use haploid calculations) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($haploid) = $self->_rearrange([qw(HAPLOID)],@args); if( $haploid ) { $self->haploid_status(1) } return $self; } =head2 haploid_status Title : haploid_status Usage : $obj->haploid_status($newval) Function: Boolean value for whether or not to do haploid or diploid calculations, where appropriate Returns : Boolean Args : on set, new boolean value optional) =cut sub haploid_status{ my $self = shift; return $self->{'haploid_status'} = shift if @_; return $self->{'haploid_status'}; } # Implementation provided my Matthew Hahn, massaged by Jason Stajich =head2 Fst Title : Fst Usage : my $fst = $stats->Fst(\@populations,\@markernames) Function: Calculate Wright's Fst based on a set of sub-populations and specific markers Returns : Fst value (a value between 0 and 1) Args : Arrayref of populations to process Arrayref of marker names to process Note : Based on diploid method in Weir BS, Genetics Data Analysis II, 1996 page 178. =cut #' make emacs happy here sub Fst { my ($self,$populations,$markernames) = @_; if( ! defined $populations || ref($populations) !~ /ARRAY/i ) { $self->warn("Must provide a valid arrayref for populations"); return; } elsif( ! defined $markernames || ref($markernames) !~ /ARRAY/i ) { $self->warn("Must provide a valid arrayref for marker names"); return; } my $num_sub_pops = scalar @$populations; if( $num_sub_pops < 2 ) { $self->warn("Must provide at least 2 populations for this test, you provided $num_sub_pops"); return; } # This code assumes that pop 1 contains at least one of all the # alleles - need to do some more work to insure that the complete # set of alleles is seen. my $Fst; my ($TS_sub1,$TS_sub2); foreach my $marker ( @$markernames ) { # Get all the alleles from all the genotypes in all subpopulations my %allAlleles; foreach my $allele ( map { $_->get_Alleles() } map { $_->get_Genotypes($marker) } @$populations ){ $allAlleles{$allele}++; } my @alleles = keys %allAlleles; foreach my $allele_name ( @alleles ) { my $avg_samp_size = 0; # n-bar my $avg_allele_freq = 0; # p-tilda-A-dot my $total_samples_squared = 0; # my $sum_heterozygote = 0; my @marker_freqs; # Walk through each population, get the calculated allele frequencies # for the marker, do some bookkeeping foreach my $pop ( @$populations ) { my $s = $pop->get_number_individuals($marker); $avg_samp_size += $s; $total_samples_squared += $s**2; my $markerobj = $pop->get_Marker($marker); if( ! defined $markerobj ) { $self->warn("Could not derive Marker for $marker ". "from population ". $pop->name); return; } my $freq_homozygotes = $pop->get_Frequency_Homozygotes($marker,$allele_name); my %af = $markerobj->get_Allele_Frequencies(); my $all_freq = ( ($af{$allele_name} || 0)); $avg_allele_freq += $s * $all_freq; $sum_heterozygote += (2 * $s)*( $all_freq - $freq_homozygotes); push @marker_freqs, \%af; } my $total_samples = $avg_samp_size; # sum of n over i sub-populations $avg_samp_size /= $num_sub_pops; $avg_allele_freq /= $total_samples; # n-sub-c my $adj_samp_size = ( 1/ ($num_sub_pops - 1)) * ( $total_samples - ( $total_samples_squared/$total_samples)); my $variance = 0; # s-squared-sub-A my $sum_variance = 0; my $i = 0; # we have cached the marker info foreach my $pop ( @$populations ) { my $s = $pop->get_number_individuals($marker); my %af = %{$marker_freqs[$i++]}; $sum_variance += $s * (( ($af{$allele_name} || 0) - $avg_allele_freq)**2); } $variance = ( 1 / (( $num_sub_pops-1)*$avg_samp_size))*$sum_variance; # H-tilda-A-dot my $freq_heterozygote = ($sum_heterozygote / $total_samples); if( $self->haploid_status ) { # Haploid calculations my $T_sub1 = $variance - ( ( 1/($avg_samp_size-1))* ( ($avg_allele_freq*(1-$avg_allele_freq))- ( (($num_sub_pops-1)/$num_sub_pops)*$variance))); my $T_sub2 = ( (($adj_samp_size-1)/($avg_samp_size-1))* $avg_allele_freq*(1-$avg_allele_freq) ) + ( 1 + ( (($num_sub_pops-1)* ($avg_samp_size-$adj_samp_size))/ ($avg_samp_size - 1))) * ($variance/$num_sub_pops); #to get total Fst from all alleles (if more than two) or all #loci (if more than one), we need to calculate $T_sub1 and #$T_sub2 for all alleles for all loci, sum, and then divide #again to get Fst. $TS_sub1 += $T_sub1; $TS_sub2 += $T_sub2; } else { my $S_sub1 = $variance - ( (1/($avg_samp_size-1))* ( ($avg_allele_freq* (1-$avg_allele_freq)) - ((($num_sub_pops-1)/$num_sub_pops)* $variance)-0.25*$freq_heterozygote ) ); my $S_sub2 = ($avg_allele_freq*(1-$avg_allele_freq)) - ( ($avg_samp_size/($num_sub_pops*($avg_samp_size-1)))* ( ((($num_sub_pops*($avg_samp_size- $adj_samp_size))/ $avg_samp_size)*$avg_allele_freq* (1-$avg_allele_freq)) - ( (1/$avg_samp_size)* (($avg_samp_size-1)+ ($num_sub_pops-1)* ($avg_samp_size- $adj_samp_size) )*$variance ) - ( (($num_sub_pops*($avg_samp_size-$adj_samp_size))/ (4*$avg_samp_size*$adj_samp_size))* $freq_heterozygote ) ) ); my $S_sub3 = ($adj_samp_size/(2*$avg_samp_size))* $freq_heterozygote; #Again, to get the average over many alleles or many loci, #we will have to run the above for each and then sum the $S #variables and recalculate the F statistics $TS_sub1 += $S_sub1; $TS_sub2 += $S_sub2; } } } # $Fst_diploid = $S_sub1/$S_sub2; #my $Fit_diploid = 1 - ($S_sub3/$S_sub2); #my $Fis_diploid = ($Fit_diploid-$Fst_diploid)/(1-$Fst_diploid); $Fst = $TS_sub1 / $TS_sub2; return $Fst; } 1; BioPerl-1.007002/Bio/PopGen/Population.pm000444000766000024 4200413155576320 20124 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::Population # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::Population - A population of individuals =head1 SYNOPSIS use Bio::PopGen::Population; use Bio::PopGen::Individual; my $population = Bio::PopGen::Population->new(); my $ind = Bio::PopGen::Individual->new(-unique_id => 'id'); $population->add_Individual($ind); for my $ind ( $population->get_Individuals ) { # iterate through the individuals } for my $name ( $population->get_marker_names ) { my $marker = $population->get_Marker($name); } my $num_inds = $population->get_number_individuals; my $homozygote_f = $population->get_Frequency_Homozygotes; my $heterozygote_f = $population->get_Frequency_Heterozygotes; # make a population haploid by making fake chromosomes through # haplotypes -- ala allele 1 is on chrom 1 and allele 2 is on chrom 2 # the number of individuals created will thus be 2 x number in # population my $happop = $population->haploid_population; =head1 DESCRIPTION This is a collection of individuals. We'll have ways of generating L objects out so we can calculate allele_frequencies for implementing the various statistical tests. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Matthew Hahn, matthew.hahn-at-duke.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::Population; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::PopGen::Marker; use Bio::PopGen::Genotype; our $CheckISA = 1; use base qw(Bio::Root::Root Bio::PopGen::PopulationI); =head2 new Title : new Usage : my $obj = Bio::PopGen::Population->new(); Function: Builds a new Bio::PopGen::Population object Returns : an instance of Bio::PopGen::Population Args : -individuals => array ref of individuals (optional) -name => population name (optional) -source => a source tag (optional) -description => a short description string of the population (optional) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_individuals'} = []; my ($name,$source,$description, $inds,$checkisa) = $self->_rearrange([qw(NAME SOURCE DESCRIPTION INDIVIDUALS CHECKISA)], @args); if( defined $inds ) { if( ref($inds) !~ /ARRAY/i ) { $self->warn("Need to provide a value array ref for the -individuals initialization flag"); } else { $self->add_Individual(@$inds); } } defined $name && $self->name($name); defined $source && $self->source($source); defined $description && $self->description($description); $self->{'_checkisa'} = defined $checkisa ? $checkisa : $CheckISA; return $self; } =head2 name Title : name Usage : my $name = $pop->name Function: Get the population name Returns : string representing population name Args : [optional] string representing population name =cut sub name{ my $self = shift; return $self->{'_name'} = shift if @_; return $self->{'_name'}; } =head2 description Title : description Usage : my $description = $pop->description Function: Get the population description Returns : string representing population description Args : [optional] string representing population description =cut sub description{ my $self = shift; return $self->{'_description'} = shift if @_; return $self->{'_description'}; } =head2 source Title : source Usage : my $source = $pop->source Function: Get the population source Returns : string representing population source Args : [optional] string representing population source =cut sub source{ my $self = shift; return $self->{'_source'} = shift if @_; return $self->{'_source'}; } =head2 annotation Title : annotation Usage : my $annotation_collection = $pop->annotation; Function: Get/set a Bio::AnnotationCollectionI for this population Returns : Bio::AnnotationCollectionI object Args : [optional set] Bio::AnnotationCollectionI object =cut sub annotation{ my ($self, $arg) = @_; return $self->{_annotation} unless $arg; $self->throw("Bio::AnnotationCollectionI required for argument") unless ref($arg) && $arg->isa('Bio::AnnotationCollectionI'); return $self->{_annotation} = $arg; } =head2 set_Allele_Frequency Title : set_Allele_Frequency Usage : $population->set_Allele_Frequency('marker' => { 'allele1' => 0.1}); Function: Sets an allele frequency for a Marker for this Population This allows the Population to not have individual individual genotypes but rather a set of overall allele frequencies Returns : Count of the number of markers Args : -name => (string) marker name -allele => (string) allele name -frequency => (double) allele frequency - must be between 0 and 1 OR -frequencies => { 'marker1' => { 'allele1' => 0.01, 'allele2' => 0.99}, 'marker2' => ... } =cut sub set_Allele_Frequency { my ($self,@args) = @_; my ($name,$allele, $frequency, $frequencies) = $self->_rearrange([qw(NAME ALLELE FREQUENCY FREQUENCIES )], @args); if( defined $frequencies ) { # this supersedes the res if( ref($frequencies) =~ /HASH/i ) { my ($markername,$alleles); while( ($markername,$alleles) = each %$frequencies ) { $self->{'_allele_freqs'}->{$markername} = Bio::PopGen::Marker->new(-name => $markername, -allele_freq => $alleles); } } else { $self->throw("Must provide a valid hashref for the -frequencies option"); } } else { unless( defined $self->{'_allele_freqs'}->{$name} ) { $self->{'_allele_freqs'}->{$name} = Bio::PopGen::Marker->new(-name => $name); } $self->{'_allele_freqs'}->{$name}->add_Allele_Frequency($allele,$frequency); } return scalar keys %{$self->{'_allele_freqs'}}; } =head2 add_Individual Title : add_Individual Usage : $population->add_Individual(@individuals); Function: Add individuals to a population Returns : count of the current number in the object Args : Array of Individuals =cut sub add_Individual{ my ($self,@inds) = @_; foreach my $i ( @inds ) { next if ! defined $i; unless( $self->{'_checkisa'} ? $i->isa('Bio::PopGen::IndividualI') : 1 ) { $self->warn("cannot add an individual ($i) which is not a Bio::PopGen::IndividualI"); next; } } push @{$self->{'_individuals'}}, @inds; $self->{'_cached_markernames'} = undef; $self->{'_allele_freqs'} = {}; return scalar @{$self->{'_individuals'} || []}; } =head2 remove_Individuals Title : remove_Individuals Usage : $population->remove_Individuals(@ids); Function: Remove individual(s) to a population Returns : count of the current number in the object Args : Array of ids =cut sub remove_Individuals { my ($self,@names) = @_; my $i = 0; my %namehash; # O(1) lookup will be faster I think foreach my $n ( @names ) { $namehash{$n}++ } my @tosplice; foreach my $ind ( @{$self->{'_individuals'} || []} ) { unshift @tosplice, $i if( $namehash{$ind->unique_id} ); $i++; } foreach my $index ( @tosplice ) { splice(@{$self->{'_individuals'}}, $index,1); } $self->{'_cached_markernames'} = undef; $self->{'_allele_freqs'} = {}; return scalar @{$self->{'_individuals'} || []}; } =head2 get_Individuals Title : get_Individuals Usage : my @inds = $pop->get_Individuals(); Function: Return the individuals, alternatively restrict by a criteria Returns : Array of Bio::PopGen::IndividualI objects Args : none if want all the individuals OR, -unique_id => To get an individual with a specific id -marker => To only get individuals which have a genotype specific for a specific marker name =cut sub get_Individuals{ my ($self,@args) = @_; my @inds = @{$self->{'_individuals'} || []}; return unless @inds; if( @args ) { # save a little time here if @args is empty my ($id,$marker) = $self->_rearrange([qw(UNIQUE_ID MARKER)], @args); if( defined $id ) { @inds = grep { $_->unique_id eq $id } @inds; } elsif (defined $marker) { @inds = grep { $_->has_Marker($marker) } @inds; } } return @inds; } =head2 get_Genotypes Title : get_Genotypes Usage : my @genotypes = $pop->get_Genotypes(-marker => $name) Function: Get the genotypes for all the individuals for a specific marker name Returns : Array of Bio::PopGen::GenotypeI objects Args : -marker => name of the marker =cut sub get_Genotypes{ my ($self,@args) = @_; my ($name) = $self->_rearrange([qw(MARKER)],@args); if( defined $name ) { return grep { defined $_ } map { $_->get_Genotypes(-marker => $name) } @{$self->{'_individuals'} || []} } $self->warn("You needed to have provided a valid -marker value"); return (); } =head2 get_marker_names Title : get_marker_names Usage : my @names = $pop->get_marker_names; Function: Get the names of the markers Returns : Array of strings Args : [optional] boolean flag to ignore internal cache status =cut sub get_marker_names { my ($self,$force) = @_; return @{$self->{'_cached_markernames'} || []} if( ! $force && defined $self->{'_cached_markernames'}); my %unique; foreach my $n ( map { $_->get_marker_names } $self->get_Individuals() ) { $unique{$n}++; } my @nms = keys %unique; if( $nms[0] =~ /^(Site|Codon)/ ) { # sort by site or codon number and do it in # a schwartzian transformation baby! @nms = map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [$_ =~ /^(?:Codon|Site)-(\d+)/, $_] } @nms; } $self->{'_cached_markernames'} = [ @nms ]; return @{$self->{'_cached_markernames'} || []}; } =head2 get_Marker Title : get_Marker Usage : my $marker = $population->get_Marker($name) Function: Get a Bio::PopGen::Marker object based on this population Returns : Bio::PopGen::MarkerI object Args : name of the marker =cut sub get_Marker{ my ($self,$markername) = @_; my $marker; # setup some caching too if( defined $self->{'_allele_freqs'} && defined ($marker = $self->{'_allele_freqs'}->{$markername}) ) { # marker is now set to the stored value } else { my @genotypes = $self->get_Genotypes(-marker => $markername); $marker = Bio::PopGen::Marker->new(-name => $markername); if( ! @genotypes ) { $self->warn("No genotypes for Marker $markername in the population"); } else { my %alleles; my $count; for my $al ( map { $_->get_Alleles} @genotypes ) { next if($al eq '?'); $count++; $alleles{$al}++ } foreach my $allele ( keys %alleles ) { $marker->add_Allele_Frequency($allele, $alleles{$allele}/$count); $marker->{_marker_coverage} = $count/2; } } $self->{'_allele_freqs'}->{$markername} = $marker; } return $marker; } =head2 get_number_individuals Title : get_number_individuals Usage : my $count = $pop->get_number_individuals; Function: Get the count of the number of individuals Returns : integer >= 0 Args : none =cut sub get_number_individuals{ my ($self,$markername) = @_; if( $self->{'_forced_set_individuals'} ) { return $self->{'_forced_set_individuals'}; } unless( defined $markername ) { return scalar @{$self->{'_individuals'} || []}; } else { my $number =0; foreach my $individual ( @{$self->{'_individuals'} || []} ) { $number++ if( $individual->has_Marker($markername)); } return $number; } } =head2 set_number_individuals Title : set_number_individuals Usage : $pop->set_number_individuals($num); Function: Fixes the number of individuals, call this with 0 to unset. Only use this if you know what you are doing, this is only relevant when you are just adding allele frequency data for a population and want to calculate something like theta Returns : none Args : individual count, calling it with undef or 0 will reset the value to return a number calculated from the number of individuals stored for this population. =cut sub set_number_individuals{ my ($self,$indcount) = @_; return $self->{'_forced_set_individuals'} = $indcount; } =head2 get_Frequency_Homozygotes Title : get_Frequency_Homozygotes Usage : my $freq = $pop->get_Frequency_Homozygotes; Function: Calculate the frequency of homozygotes in the population Returns : fraction between 0 and 1 Args : $markername =cut sub get_Frequency_Homozygotes{ my ($self,$marker,$allelename) = @_; my ($homozygote_count) = 0; return 0 if ! defined $marker || ! defined $allelename; $marker = $marker->name if( defined $marker && ref($marker) && ( $self->{'_checkisa'} ? $marker->isa('Bio::PopGen::MarkerI') : 1)); my $total = $self->get_number_individuals($marker); foreach my $genotype ( $self->get_Genotypes($marker) ) { my %alleles = map { $_ => 1} $genotype->get_Alleles(); # what to do for non-diploid situations? if( $alleles{$allelename} ) { $homozygote_count++ if( keys %alleles == 1); } } return $total ? $homozygote_count / $total : 0; } =head2 get_Frequency_Heterozygotes Title : get_Frequency_Heterozygotes Usage : my $freq = $pop->get_Frequency_Homozygotes; Function: Calculate the frequency of homozygotes in the population Returns : fraction between 0 and 1 Args : $markername =cut sub get_Frequency_Heterozygotes{ my ($self,$marker,$allelename) = @_; my ($heterozygote_count) = 0; return 0 if ! defined $marker || ! defined $allelename; $marker = $marker->name if( defined $marker && ref($marker) && ($self->{'_checkisa'} ? $marker->isa('Bio::PopGen::MarkerI') : 1)); if( ref($marker) ) { $self->warn("Passed in a ".ref($marker). " to has_Marker, expecting either a string or a Bio::PopGen::MarkerI"); return 0; } my $total = $self->get_number_individuals($marker); foreach my $genotype ( $self->get_Genotypes($marker) ) { my %alleles = map { $_ => 1} $genotype->get_Alleles(); # what to do for non-diploid situations? if( $alleles{$allelename} ) { $heterozygote_count++ if( keys %alleles == 2); } } return $total ? $heterozygote_count / $total : 0; } =head2 haploid_population Title : haploid_population Usage : my $pop = $population->haploid_population; Function: Make a new population where all the individuals are haploid - effectively an individual out of each chromosome an individual has. Returns : L Args : None =cut sub haploid_population{ my ($self) = @_; my @inds; my @marker_names = $self->get_marker_names; for my $ind ( $self->get_Individuals ) { my @chromosomes; my $id = $ind->unique_id; # separate genotypes into 'chromosomes' for my $marker_name( @marker_names ) { my ($genotype) = $ind->get_Genotypes(-marker => $marker_name); my $i =0; for my $allele ( $genotype->get_Alleles ) { push @{$chromosomes[$i]}, Bio::PopGen::Genotype->new(-marker_name => $marker_name, -individual_id => $id.".$i", -alleles => [$allele]); $i++; } } for my $chrom ( @chromosomes ) { my $copyind = ref($ind)->new(-unique_id => $id.".1", -genotypes => $chrom); push @inds, $ind; } } my $population = ref($self)->new(-name => $self->name, -source => $self->source, -description => $self->description, -individuals => \@inds); } 1; BioPerl-1.007002/Bio/PopGen/PopulationI.pm000444000766000024 1433713155576320 20245 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::PopulationI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::PopulationI - Interface for Populations =head1 SYNOPSIS # Get Bio::PopGen::PopulationI object somehow, like # from Bio::Population::Population print "name is ", $population->name(), "\n"; print "source is ", $population->source(), "\n"; print "description is ", $population->description(), "\n"; print "For marker $markername:\n"; foreach my $genotype ( $population->get_Genotypes(-marker => $markername) ) { print "Individual ", $genotype->individual_id, " genotype alleles are ", join(',', $genotype->get_Alleles()), "\n"; } # get a marker with allele frequencies calculated from the population my $marker = $population->get_Marker($markername); my %af = $marker->get_Allele_Frequencies; foreach my $allele ( keys %af ) { print "$allele $af{$allele}\n"; } =head1 DESCRIPTION This interface describes the basics of a population. One can use this object to get the genotypes of specific individuals, only those individuals which have a certain marker, or create a marker with allele frequency information. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Matthew Hahn, matthew.hahn-at-duke.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::PopulationI; use strict; use Carp; use base qw(Bio::Root::RootI); =head2 name Title : name Usage : my $name = $pop->name Function: Get the population name Returns : string representing population name Args : [optional] string representing population name =cut sub name{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 description Title : description Usage : my $description = $pop->description Function: Get the population description Returns : string representing population description Args : [optional] string representing population description =cut sub description{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 source Title : source Usage : my $source = $pop->source Function: Get the population source Returns : string representing population source Args : [optional] string representing population source =cut sub source{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 annotation Title : annotation Usage : my $annotation_collection = $pop->annotation; Function: Get/set a Bio::AnnotationCollectionI for this population Returns : Bio::AnnotationCollectionI object Args : [optional set] Bio::AnnotationCollectionI object =cut sub annotation{ my ($self) = @_; $self->throw_not_implemented(); } =head2 get_Individuals Title : get_Individuals Usage : my @inds = $pop->get_Individuals(); Function: Return the individuals, alternatively restrict by a criteria Returns : Array of L objects Args : none if want all the individuals OR, -unique_id => To get an individual with a specific id -marker => To only get individuals which have a genotype specific for a specific marker name =cut sub get_Individuals{ shift->throw_not_implemented(); } =head2 get_Genotypes Title : get_Genotypes Usage : my @genotypes = $pop->get_Genotypes(-marker => $name) Function: Get the genotypes for all the individuals for a specific marker name Returns : Array of L objects Args : -marker => name of the marker =cut sub get_Genotypes{ shift->throw_not_implemented; } =head2 get_Marker Title : get_Marker Usage : my $marker = $population->get_Marker($name) Function: Get a Bio::PopGen::Marker object based on this population Returns : L object Args : name of the marker =cut sub get_Marker{ shift->throw_not_implemented(); } =head2 get_marker_names Title : get_marker_names Usage : my @names = $pop->get_marker_names; Function: Get the names of the markers Returns : Array of strings Args : none =cut sub get_marker_names{ my ($self) = @_; $self->throw_not_implemented(); } =head2 get_Markers Title : get_Markers Usage : my @markers = $pop->get_Markers(); Function: Will retrieve a list of instantiated MarkerI objects for a population. This is a convience method combining get_marker_names with get_Marker Returns : List of array of Bio::PopGen::MarkerI objects Args : none =cut sub get_Markers{ my ($self) = shift; return map { $self->get_Marker($_) } $self->get_marker_names(); } =head2 get_number_individuals Title : get_number_individuals Usage : my $count = $pop->get_number_individuals; Function: Get the count of the number of individuals Returns : integer >= 0 Args : [optional] marker name, will return a count of the number of individuals which have this marker =cut sub get_number_individuals{ my ($self) = @_; $self->throw_not_implemented(); } 1; BioPerl-1.007002/Bio/PopGen/Statistics.pm000444000766000024 14475013155576320 20157 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::Statistics # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::Statistics - Population Genetics statistical tests =head1 SYNOPSIS use Bio::PopGen::Statistics; use Bio::AlignIO; use Bio::PopGen::IO; use Bio::PopGen::Simulation::Coalescent; my $sim = Bio::PopGen::Simulation::Coalescent->new( -sample_size => 12); my $tree = $sim->next_tree; $sim->add_Mutations($tree,20); my $stats = Bio::PopGen::Statistics->new(); my $individuals = [ $tree->get_leaf_nodes]; my $pi = $stats->pi($individuals); my $D = $stats->tajima_D($individuals); # Alternatively to do this on input data from # See the tests in t/PopGen.t for more examples my $parser = Bio::PopGen::IO->new(-format => 'prettybase', -file => 't/data/popstats.prettybase'); my $pop = $parser->next_population; # Note that you can also call the stats as a class method if you like # the only reason to instantiate it (as above) is if you want # to set the verbosity for debugging $pi = Bio::PopGen::Statistics->pi($pop); $theta = Bio::PopGen::Statistics->theta($pop); # Pi and Theta also take additional arguments, # see the documentation for more information use Bio::PopGen::Utilities; use Bio::AlignIO; my $in = Bio::AlignIO->new(-file => 't/data/t7.aln', -format => 'clustalw'); my $aln = $in->next_aln; # get a population, each sequence is an individual and # for the default case, every site which is not monomorphic # is a 'marker'. Each individual will have a 'genotype' for the # site which will be the specific base in the alignment at that # site my $pop = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln); =head1 DESCRIPTION This object is intended to provide implementations some standard population genetics statistics about alleles in populations. This module was previously named Bio::Tree::Statistics. This object is a place to accumulate routines for calculating various statistics from the coalescent simulation, marker/allele, or from aligned sequence data given that you can calculate alleles, number of segregating sites. Currently implemented: Fu and Li's D (fu_and_li_D) Fu and Li's D* (fu_and_li_D_star) Fu and Li's F (fu_and_li_F) Fu and Li's F* (fu_and_li_F_star) Tajima's D (tajima_D) Watterson's theta (theta) pi (pi) - number of pairwise differences composite_LD (composite_LD) McDonald-Kreitman (mcdonald_kreitman or MK) Count based methods also exist in case you have already calculated the key statistics (seg sites, num individuals, etc) and just want to compute the statistic. In all cases where a the method expects an arrayref of L objects and L object will also work. =head2 REFERENCES Fu Y.X and Li W.H. (1993) "Statistical Tests of Neutrality of Mutations." Genetics 133:693-709. Fu Y.X. (1996) "New Statistical Tests of Neutrality for DNA samples from a Population." Genetics 143:557-570. McDonald J, Kreitman M. Tajima F. (1989) "Statistical method for testing the neutral mutation hypothesis by DNA polymorphism." Genetics 123:585-595. =head2 CITING THIS WORK Please see this reference for use of this implementation. Stajich JE and Hahn MW "Disentangling the Effects of Demography and Selection in Human History." (2005) Mol Biol Evol 22(1):63-73. If you use these Bio::PopGen modules please cite the Bioperl publication (see FAQ) and the above reference. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich, Matthew Hahn Email jason-at-bioperl-dot-org Email matthew-dot-hahn-at-duke-dot-edu McDonald-Kreitman implementation based on work by Alisha Holloway at UC Davis. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::Statistics; use strict; use constant { in_label => 'ingroup', out_label => 'outgroup', non_syn => 'non_synonymous', syn => 'synonymous', default_codon_table => 1, # Standard Codon table }; use Bio::MolEvol::CodonModel; use List::Util qw(sum); use base qw(Bio::Root::Root); our $codon_table => default_codon_table; our $has_twotailed => 0; BEGIN { eval { require Text::NSP::Measures::2D::Fisher2::twotailed }; if( $@ ) { $has_twotailed = 0; } else { $has_twotailed = 1; } } =head2 new Title : new Usage : my $obj = Bio::PopGen::Statistics->new(); Function: Builds a new Bio::PopGen::Statistics object Returns : an instance of Bio::PopGen::Statistics Args : none =cut =head2 fu_and_li_D Title : fu_and_li_D Usage : my $D = $statistics->fu_and_li_D(\@ingroup,\@outgroup); OR my $D = $statistics->fu_and_li_D(\@ingroup,$extmutations); Function: Fu and Li D statistic for a list of individuals given an outgroup and the number of external mutations (either provided or calculated from list of outgroup individuals) Returns : decimal Args : $individuals - array reference which contains ingroup individuals (L or derived classes) $extmutations - number of external mutations OR arrayref of outgroup individuals =cut sub fu_and_li_D { my ($self,$ingroup,$outgroup) = @_; my ($seg_sites,$n,$ancestral,$derived) = (0,0,0,0); if( ref($ingroup) =~ /ARRAY/i ) { $n = scalar @$ingroup; # pi - all pairwise differences $seg_sites = $self->segregating_sites_count($ingroup); } elsif( ref($ingroup) && $ingroup->isa('Bio::PopGen::PopulationI')) { $n = $ingroup->get_number_individuals; $seg_sites = $self->segregating_sites_count($ingroup); } else { $self->throw("expected an array reference of a list of Bio::PopGen::IndividualI OR a Bio::PopGen::PopulationI object to fu_and_li_D"); return 0; } if( $seg_sites <= 0 ) { $self->warn("mutation total was not > 0, cannot calculate a Fu and Li D"); return 0; } if( ! defined $outgroup ) { $self->warn("Need to provide either an array ref to the outgroup individuals or the number of external mutations"); return 0; } elsif( ref($outgroup) ) { ($ancestral,$derived) = $self->derived_mutations($ingroup,$outgroup); $ancestral = 0 unless defined $ancestral; } else { $ancestral = $outgroup; } return $self->fu_and_li_D_counts($n,$seg_sites, $ancestral,$derived); } =head2 fu_and_li_D_counts Title : fu_li_D_counts Usage : my $D = $statistics->fu_and_li_D_counts($samps,$sites, $external); Function: Fu and Li D statistic for the raw counts of the number of samples, sites, external and internal mutations Returns : decimal number Args : number of samples (N) number of segregating sites (n) number of external mutations (n_e) =cut sub fu_and_li_D_counts { my ($self,$n,$seg_sites, $external_mut) = @_; my $a_n = 0; if( $n <= 3 ) { $self->warn("n is $n, too small, must be > 3\n"); return; } for(my $k= 1; $k < $n; $k++ ) { $a_n += ( 1 / $k ); } my $b = 0; for(my $k= 1; $k < $n; $k++ ) { $b += ( 1 / $k**2 ); } my $c = 2 * ( ( ( $n * $a_n ) - (2 * ( $n -1 ))) / ( ( $n - 1) * ( $n - 2 ) ) ); my $v = 1 + ( ( $a_n**2 / ( $b + $a_n**2 ) ) * ( $c - ( ( $n + 1) / ( $n - 1) ) )); my $u = $a_n - 1 - $v; ($seg_sites - $a_n * $external_mut) / sqrt( ($u * $seg_sites) + ($v * $seg_sites*$seg_sites)); } =head2 fu_and_li_D_star Title : fu_and_li_D_star Usage : my $D = $statistics->fu_an_li_D_star(\@individuals); Function: Fu and Li's D* statistic for a set of samples Without an outgroup Returns : decimal number Args : array ref of L objects OR L object =cut #' # fu_and_li_D* sub fu_and_li_D_star { my ($self,$individuals) = @_; my ($seg_sites,$n,$singletons); if( ref($individuals) =~ /ARRAY/i ) { $n = scalar @$individuals; $seg_sites = $self->segregating_sites_count($individuals); $singletons = $self->singleton_count($individuals); } elsif( ref($individuals) && $individuals->isa('Bio::PopGen::PopulationI')) { my $pop = $individuals; $n = $pop->get_number_individuals; $seg_sites = $self->segregating_sites_count($pop); $singletons = $self->singleton_count($pop); } else { $self->throw("expected an array reference of a list of Bio::PopGen::IndividualI OR a Bio::PopGen::PopulationI object to fu_and_li_D_star"); return 0; } return $self->fu_and_li_D_star_counts($n,$seg_sites, $singletons); } =head2 fu_and_li_D_star_counts Title : fu_li_D_star_counts Usage : my $D = $statistics->fu_and_li_D_star_counts($samps,$sites, $singletons); Function: Fu and Li D statistic for the raw counts of the number of samples, sites, external and internal mutations Returns : decimal number Args : number of samples (N) number of segregating sites (n) singletons (n_s) =cut sub fu_and_li_D_star_counts { my ($self,$n,$seg_sites, $singletons) = @_; my $a_n; for(my $k = 1; $k < $n; $k++ ) { $a_n += ( 1 / $k ); } my $a1 = $a_n + 1 / $n; my $b = 0; for(my $k= 1; $k < $n; $k++ ) { $b += ( 1 / $k**2 ); } my $c = 2 * ( ( ( $n * $a_n ) - (2 * ( $n -1 ))) / ( ( $n - 1) * ( $n - 2 ) ) ); my $d = $c + ($n -2) / ($n - 1)**2 + 2 / ($n -1) * ( 1.5 - ( (2*$a1 - 3) / ($n -2) ) - 1 / $n ); my $v_star = ( ( ($n/($n-1) )**2)*$b + (($a_n**2)*$d) - (2*( ($n*$a_n*($a_n+1)) )/(($n-1)**2)) ) / (($a_n**2) + $b); my $u_star = ( ($n/($n-1))* ($a_n - ($n/ ($n-1)))) - $v_star; return (($n / ($n - 1)) * $seg_sites - $a_n * $singletons) / sqrt( ($u_star * $seg_sites) + ($v_star * $seg_sites*$seg_sites)); } =head2 fu_and_li_F Title : fu_and_li_F Usage : my $F = Bio::PopGen::Statistics->fu_and_li_F(\@ingroup,$ext_muts); Function: Calculate Fu and Li's F on an ingroup with either the set of outgroup individuals, or the number of external mutations Returns : decimal number Args : array ref of L objects for the ingroup OR a L object number of external mutations OR list of individuals for the outgroup =cut #' sub fu_and_li_F { my ($self,$ingroup,$outgroup) = @_; my ($seg_sites,$pi,$n,$external,$internal); if( ref($ingroup) =~ /ARRAY/i ) { $n = scalar @$ingroup; # pi - all pairwise differences $pi = $self->pi($ingroup); $seg_sites = $self->segregating_sites_count($ingroup); } elsif( ref($ingroup) && $ingroup->isa('Bio::PopGen::PopulationI')) { $n = $ingroup->get_number_individuals; $pi = $self->pi($ingroup); $seg_sites = $self->segregating_sites_count($ingroup); } else { $self->throw("expected an array reference of a list of Bio::PopGen::IndividualI OR a Bio::PopGen::PopulationI object to Fu and Li's F"); return 0; } if( ! defined $outgroup ) { $self->warn("Need to provide either an array ref to the outgroup individuals or the number of external mutations"); return 0; } elsif( ref($outgroup) ) { ($external,$internal) = $self->derived_mutations($ingroup,$outgroup); } else { $external = $outgroup; } $self->fu_and_li_F_counts($n,$pi,$seg_sites,$external); } =head2 fu_and_li_F_counts Title : fu_li_F_counts Usage : my $F = $statistics->fu_and_li_F_counts($samps,$pi, $sites, $external); Function: Fu and Li F statistic for the raw counts of the number of samples, sites, external and internal mutations Returns : decimal number Args : number of samples (N) average pairwise differences (pi) number of segregating sites (n) external mutations (n_e) =cut sub fu_and_li_F_counts { my ($self,$n,$pi,$seg_sites, $external) = @_; my $a_n = 0; for(my $k= 1; $k < $n; $k++ ) { $a_n += ( 1 / $k ); } my $a1 = $a_n + (1 / $n ); my $b = 0; for(my $k= 1; $k < $n; $k++ ) { $b += ( 1 / $k**2 ); } my $c = 2 * ( ( ( $n * $a_n ) - (2 * ( $n -1 ))) / ( ( $n - 1) * ( $n - 2 ) ) ); my $v_F = ( $c + ( (2*(($n**2)+$n+3)) / ( (9*$n)*($n-1) ) ) - (2/($n-1)) ) / ( ($a_n**2)+$b ); my $u_F = ( 1 + ( ($n+1)/(3*($n-1)) )- ( 4*( ($n+1)/(($n-1)**2) ))* ($a1 - ((2*$n)/($n+1))) ) / $a_n - $v_F; # warn("$v_F vf $u_F uf n = $n\n"); my $F = ($pi - $external) / ( sqrt( ($u_F*$seg_sites) + ($v_F*($seg_sites**2)) ) ); return $F; } =head2 fu_and_li_F_star Title : fu_and_li_F_star Usage : my $F = Bio::PopGen::Statistics->fu_and_li_F_star(\@ingroup); Function: Calculate Fu and Li's F* on an ingroup without an outgroup It uses count of singleton alleles instead Returns : decimal number Args : array ref of L objects for the ingroup OR L object =cut #' keep my emacs happy sub fu_and_li_F_star { my ($self,$individuals) = @_; my ($seg_sites,$pi,$n,$singletons); if( ref($individuals) =~ /ARRAY/i ) { $n = scalar @$individuals; # pi - all pairwise differences $pi = $self->pi($individuals); $seg_sites = $self->segregating_sites_count($individuals); $singletons = $self->singleton_count($individuals); } elsif( ref($individuals) && $individuals->isa('Bio::PopGen::PopulationI')) { my $pop = $individuals; $n = $pop->get_number_individuals; $pi = $self->pi($pop); $seg_sites = $self->segregating_sites_count($pop); $singletons = $self->singleton_count($pop); } else { $self->throw("expected an array reference of a list of Bio::PopGen::IndividualI OR a Bio::PopGen::PopulationI object to fu_and_li_F_star"); return 0; } return $self->fu_and_li_F_star_counts($n, $pi, $seg_sites, $singletons); } =head2 fu_and_li_F_star_counts Title : fu_li_F_star_counts Usage : my $F = $statistics->fu_and_li_F_star_counts($samps, $pi,$sites, $singletons); Function: Fu and Li F statistic for the raw counts of the number of samples, sites, external and internal mutations Returns : decimal number Args : number of samples (N) average pairwise differences (pi) number of segregating sites (n) singleton mutations (n_s) =cut sub fu_and_li_F_star_counts { my ($self,$n,$pi,$seg_sites, $singletons) = @_; if( $n <= 1 ) { $self->warn("N must be > 1\n"); return; } if( $n == 2) { return 0; } my $a_n = 0; my $b = 0; for(my $k= 1; $k < $n; $k++ ) { $b += (1 / ($k**2)); $a_n += ( 1 / $k ); # Eq (2) } my $a1 = $a_n + (1 / $n ); # warn("a_n is $a_n a1 is $a1 n is $n b is $b\n"); # From Simonsen et al (1995) instead of Fu and Li 1993 my $v_F_star = ( (( 2 * $n ** 3 + 110 * $n**2 - (255 * $n) + 153)/ (9 * ($n ** 2) * ( $n - 1))) + ((2 * ($n - 1) * $a_n ) / $n ** 2) - (8 * $b / $n) ) / ( ($a_n ** 2) + $b ); my $u_F_star = ((( (4* ($n**2)) + (19 * $n) + 3 - (12 * ($n + 1)* $a1)) / (3 * $n * ( $n - 1))) / $a_n) - $v_F_star; # warn("vf* = $v_F_star uf* = $u_F_star n = $n\n"); my $F_star = ( $pi - ($singletons*( ( $n-1) / $n)) ) / sqrt ( $u_F_star*$seg_sites + $v_F_star*$seg_sites**2); return $F_star; } =head2 tajima_D Title : tajima_D Usage : my $D = Bio::PopGen::Statistics->tajima_D(\@samples); Function: Calculate Tajima's D on a set of samples Returns : decimal number Args : array ref of L objects OR L object =cut #' sub tajima_D { my ($self,$individuals) = @_; my ($seg_sites,$pi,$n); if( ref($individuals) =~ /ARRAY/i ) { $n = scalar @$individuals; # pi - all pairwise differences $pi = $self->pi($individuals); $seg_sites = $self->segregating_sites_count($individuals); } elsif( ref($individuals) && $individuals->isa('Bio::PopGen::PopulationI')) { my $pop = $individuals; $n = $pop->get_number_individuals; $pi = $self->pi($pop); $seg_sites = $self->segregating_sites_count($pop); } else { $self->throw("expected an array reference of a list of Bio::PopGen::IndividualI OR a Bio::PopGen::PopulationI object to tajima_D"); return 0; } $self->tajima_D_counts($n,$seg_sites,$pi); } =head2 tajima_D_counts Title : tajima_D_counts Usage : my $D = $statistics->tajima_D_counts($samps,$sites,$pi); Function: Tajima's D statistic for the raw counts of the number of samples, sites, and avg pairwise distances (pi) Returns : decimal number Args : number of samples (N) number of segregating sites (n) average pairwise differences (pi) =cut #' sub tajima_D_counts { my ($self,$n,$seg_sites,$pi) = @_; my $a1 = 0; for(my $k= 1; $k < $n; $k++ ) { $a1 += ( 1 / $k ); } my $a2 = 0; for(my $k= 1; $k < $n; $k++ ) { $a2 += ( 1 / $k**2 ); } my $b1 = ( $n + 1 ) / ( 3* ( $n - 1) ); my $b2 = ( 2 * ( $n ** 2 + $n + 3) ) / ( ( 9 * $n) * ( $n - 1) ); my $c1 = $b1 - ( 1 / $a1 ); my $c2 = $b2 - ( ( $n + 2 ) / ( $a1 * $n))+( $a2 / $a1 ** 2); my $e1 = $c1 / $a1; my $e2 = $c2 / ( $a1**2 + $a2 ); my $denom = sqrt ( ($e1 * $seg_sites) + (( $e2 * $seg_sites) * ( $seg_sites - 1))); return if $denom == 0; my $D = ( $pi - ( $seg_sites / $a1 ) ) / $denom; return $D; } =head2 pi Title : pi Usage : my $pi = Bio::PopGen::Statistics->pi(\@inds) Function: Calculate pi (average number of pairwise differences) given a list of individuals which have the same number of markers (also called sites) as available from the get_Genotypes() call in L Returns : decimal number Args : Arg1= array ref of L objects which have markers/mutations. We expect all individuals to have a marker - we will deal with missing data as a special case. OR Arg1= L object. In the event that only allele frequency data is available, storing it in Population object will make this available. num sites [optional], an optional second argument (integer) which is the number of sites, then pi returned is pi/site. =cut sub pi { my ($self,$individuals,$numsites) = @_; my (%data,%marker_total,@marker_names,$n); if( ref($individuals) =~ /ARRAY/i ) { # one possible argument is an arrayref of Bio::PopGen::IndividualI objs @marker_names = $individuals->[0]->get_marker_names; $n = scalar @$individuals; # Here we are calculating the allele frequencies foreach my $ind ( @$individuals ) { if( ! $ind->isa('Bio::PopGen::IndividualI') ) { $self->warn("Expected an arrayref of Bio::PopGen::IndividualI objects, this is a ".ref($ind)."\n"); return 0; } foreach my $m ( @marker_names ) { foreach my $allele (map { $_->get_Alleles} $ind->get_Genotypes($m) ) { $data{$m}->{$allele}++; $marker_total{$m}++; } } } # while( my ($marker,$count) = each %marker_total ) { # foreach my $c ( values %{$data{$marker}} ) { # $c /= $count; # } # } # %data will contain allele frequencies for each marker, allele } elsif( ref($individuals) && $individuals->isa('Bio::PopGen::PopulationI') ) { my $pop = $individuals; $n = $pop->get_number_individuals; foreach my $marker( $pop->get_Markers ) { push @marker_names, $marker->name; #$data{$marker->name} = {$marker->get_Allele_Frequencies}; my @genotypes = $pop->get_Genotypes(-marker => $marker->name); for my $al ( map { $_->get_Alleles} @genotypes ) { $data{$marker->name}->{$al}++; $marker_total{$marker->name}++; } } } else { $self->throw("expected an array reference of a list of Bio::PopGen::IndividualI to pi"); } # based on Kevin Thornton's code: # http://molpopgen.org/software/libsequence/doc/html/PolySNP_8cc-source.html#l00152 # For now we assume that all individuals have the same markers my ($diffcount,$totalcompare) = (0,0); my $pi = 0; while ( my ($marker,$markerdat) = each %data ) { my $sampsize = $marker_total{$marker}; my $ssh = 0; my @alleles = keys %$markerdat; if ( $sampsize > 1 ) { my $denom = $sampsize * ($sampsize - 1.0); foreach my $al ( @alleles ) { $ssh += ($markerdat->{$al} * ($markerdat->{$al} - 1)) / $denom; } $pi += 1.0 - $ssh; } } $self->debug( "pi=$pi\n"); if( $numsites ) { return $pi / $numsites; } else { return $pi; } } =head2 theta Title : theta Usage : my $theta = Bio::PopGen::Statistics->theta($sampsize,$segsites); Function: Calculates Watterson's theta from the sample size and the number of segregating sites. Providing the third parameter, total number of sites will return theta per site. This is also known as K-hat = K / a_n Returns : decimal number Args : sample size (integer), num segregating sites (integer) total sites (integer) [optional] (to calculate theta per site) OR provide an arrayref of the L objects total sites (integer) [optional] (to calculate theta per site) OR provide an L object total sites (integer)[optional] =cut #' sub theta { my $self = shift; my ( $n, $seg_sites,$totalsites) = @_; if( ref($n) =~ /ARRAY/i ) { my $samps = $n; $totalsites = $seg_sites; # only 2 arguments if one is an array my %data; my @marker_names = $samps->[0]->get_marker_names; # we need to calculate number of polymorphic sites $seg_sites = $self->segregating_sites_count($samps); $n = scalar @$samps; } elsif(ref($n) && $n->isa('Bio::PopGen::PopulationI') ) { # This will handle the case when we pass in a PopulationI object my $pop = $n; $totalsites = $seg_sites; # shift the arguments over by one $n = $pop->haploid_population->get_number_individuals; $seg_sites = $self->segregating_sites_count($pop); } my $a1 = 0; for(my $k= 1; $k < $n; $k++ ) { $a1 += ( 1 / $k ); } if( $totalsites ) { # 0 and undef are the same can't divide by them $seg_sites /= $totalsites; } if( $a1 == 0 ) { return 0; } return $seg_sites / $a1; } =head2 singleton_count Title : singleton_count Usage : my ($singletons) = Bio::PopGen::Statistics->singleton_count(\@inds) Function: Calculate the number of mutations/alleles which only occur once in a list of individuals for all sites/markers Returns : (integer) number of alleles which only occur once (integer) Args : arrayref of L objects OR L object =cut sub singleton_count { my ($self,$individuals) = @_; my @inds; if( ref($individuals) =~ /ARRAY/ ) { @inds = @$individuals; } elsif( ref($individuals) && $individuals->isa('Bio::PopGen::PopulationI') ) { my $pop = $individuals; @inds = $pop->get_Individuals(); unless( @inds ) { $self->warn("Need to provide a population which has individuals loaded, not just a population with allele frequencies"); return 0; } } else { $self->warn("Expected either a PopulationI object or an arrayref of IndividualI objects"); return 0; } # find number of sites where a particular allele is only seen once my ($singleton_allele_ct,%sites) = (0); # first collect all the alleles into a hash structure foreach my $n ( @inds ) { if( ! $n->isa('Bio::PopGen::IndividualI') ) { $self->warn("Expected an arrayref of Bio::PopGen::IndividualI objects, this is a ".ref($n)."\n"); return 0; } foreach my $g ( $n->get_Genotypes ) { my ($nm,@alleles) = ($g->marker_name, $g->get_Alleles); foreach my $allele (@alleles ) { $sites{$nm}->{$allele}++; } } } foreach my $site ( values %sites ) { # don't really care what the name is foreach my $allelect ( values %$site ) { # # find the sites which have an allele with only 1 copy $singleton_allele_ct++ if( $allelect == 1 ); } } return $singleton_allele_ct; } # Yes I know that singleton_count and segregating_sites_count are # basically processing the same data so calling them both is # redundant, something I want to fix later but want to make things # correct and simple first =head2 segregating_sites_count Title : segregating_sites_count Usage : my $segsites = Bio::PopGen::Statistics->segregating_sites_count Function: Gets the number of segregating sites (number of polymorphic sites) Returns : (integer) number of segregating sites Args : arrayref of L objects OR L object =cut # perhaps we'll change this in the future # to return the actual segregating sites # so one can use this to pull in the names of those sites. # Would be trivial if it is useful. sub segregating_sites_count { my ($self,$individuals) = @_; my $type = ref($individuals); my $seg_sites = 0; if( $type =~ /ARRAY/i ) { my %sites; foreach my $n ( @$individuals ) { if( ! $n->isa('Bio::PopGen::IndividualI') ) { $self->warn("Expected an arrayref of Bio::PopGen::IndividualI objects, this is a ".ref($n)."\n"); return 0; } foreach my $g ( $n->get_Genotypes ) { my ($nm,@alleles) = ($g->marker_name, $g->get_Alleles); foreach my $allele (@alleles ) { $sites{$nm}->{$allele}++; } } } foreach my $site ( values %sites ) { # use values b/c we don't # really care what the name is # find the sites which >1 allele $seg_sites++ if( keys %$site > 1 ); } } elsif( $type && $individuals->isa('Bio::PopGen::PopulationI') ) { foreach my $marker ( $individuals->haploid_population->get_Markers ) { my @alleles = $marker->get_Alleles; $seg_sites++ if ( scalar @alleles > 1 ); } } else { $self->warn("segregating_sites_count expects either a PopulationI object or a list of IndividualI objects"); return 0; } return $seg_sites; } =head2 heterozygosity Title : heterozygosity Usage : my $het = Bio::PopGen::Statistics->heterozygosity($sampsize,$freq1); Function: Calculate the heterozgosity for a sample set for a set of alleles Returns : decimal number Args : sample size (integer) frequency of one allele (fraction - must be less than 1) [optional] frequency of another allele - this is only needed in a non-binary allele system Note : p^2 + 2pq + q^2 =cut sub heterozygosity { my ($self,$samp_size, $freq1,$freq2) = @_; if( ! $freq2 ) { $freq2 = 1 - $freq1 } if( $freq1 > 1 || $freq2 > 1 ) { $self->warn("heterozygosity expects frequencies to be less than 1"); } my $sum = ($freq1**2) + (($freq2)**2); my $h = ( $samp_size*(1- $sum) ) / ($samp_size - 1) ; return $h; } =head2 derived_mutations Title : derived_mutations Usage : my $ext = Bio::PopGen::Statistics->derived_mutations($ingroup,$outgroup); Function: Calculate the number of alleles or (mutations) which are ancestral and the number which are derived (occurred only on the tips) Returns : array of 2 items - number of external and internal derived mutation Args : ingroup - Ls arrayref OR L outgroup- Ls arrayref OR L OR a single L =cut sub derived_mutations { my ($self,$ingroup,$outgroup) = @_; my (%indata,%outdata,@marker_names); # basically we have to do some type checking # if that perl were typed... my ($itype,$otype) = (ref($ingroup),ref($outgroup)); return $outgroup unless( $otype ); # we expect arrayrefs or objects, nums # are already the value we # are searching for # pick apart the ingroup # get the data if( ref($ingroup) =~ /ARRAY/i ) { if( ! ref($ingroup->[0]) || ! $ingroup->[0]->isa('Bio::PopGen::IndividualI') ) { $self->warn("Expected an arrayref of Bio::PopGen::IndividualI objects or a Population for ingroup in external_mutations"); return 0; } # we assume that all individuals have the same markers # i.e. that they are aligned @marker_names = $ingroup->[0]->get_marker_names; for my $ind ( @$ingroup ) { for my $m ( @marker_names ) { for my $allele ( map { $_->get_Alleles } $ind->get_Genotypes($m) ) { $indata{$m}->{$allele}++; } } } } elsif( ref($ingroup) && $ingroup->isa('Bio::PopGen::PopulationI') ) { @marker_names = $ingroup->get_marker_names; for my $ind ( $ingroup->haploid_population->get_Individuals() ) { for my $m ( @marker_names ) { for my $allele ( map { $_->get_Alleles} $ind->get_Genotypes($m) ) { $indata{$m}->{$allele}++; } } } } else { $self->warn("Need an arrayref of Bio::PopGen::IndividualI objs or a Bio::PopGen::Population for ingroup in external_mutations"); return 0; } if( $otype =~ /ARRAY/i ) { if( ! ref($outgroup->[0]) || ! $outgroup->[0]->isa('Bio::PopGen::IndividualI') ) { $self->warn("Expected an arrayref of Bio::PopGen::IndividualI objects or a Population for outgroup in external_mutations"); return 0; } for my $ind ( @$outgroup ) { for my $m ( @marker_names ) { for my $allele ( map { $_->get_Alleles } $ind->get_Genotypes($m) ) { $outdata{$m}->{$allele}++; } } } } elsif( $otype->isa('Bio::PopGen::PopulationI') ) { for my $ind ( $outgroup->haploid_population->get_Individuals() ) { for my $m ( @marker_names ) { for my $allele ( map { $_->get_Alleles} $ind->get_Genotypes($m) ) { $outdata{$m}->{$allele}++; } } } } else { $self->warn("Need an arrayref of Bio::PopGen::IndividualI objs or a Bio::PopGen::Population for outgroup in external_mutations"); return 0; } # derived mutations are defined as # # ingroup (G A T) # outgroup (A) # derived mutations are G and T, A is the external mutation # ingroup (A T) # outgroup (C) # derived mutations A,T no external/ancestral mutations # ingroup (G A T) # outgroup (A T) # cannot determine my ($internal,$external); foreach my $marker ( @marker_names ) { my @outalleles = keys %{$outdata{$marker}}; my @in_alleles = keys %{$indata{$marker}}; next if( @outalleles > 1 || @in_alleles == 1); for my $allele ( @in_alleles ) { if( ! exists $outdata{$marker}->{$allele} ) { if( $indata{$marker}->{$allele} == 1 ) { $external++; } else { $internal++; } } } } return ($external, $internal); } =head2 composite_LD Title : composite_LD Usage : %matrix = Bio::PopGen::Statistics->composite_LD($population); Function: Calculate the Linkage Disequilibrium This is for calculating LD for unphased data. Other methods will be appropriate for phased haplotype data. Returns : Hash of Hashes - first key is site 1,second key is site 2 and value is LD for those two sites. my $LDarrayref = $matrix{$site1}->{$site2}; my ($ldval, $chisquared) = @$LDarrayref; Args : L or arrayref of Ls Reference: Weir B.S. (1996) "Genetic Data Analysis II", Sinauer, Sunderlanm MA. =cut sub composite_LD { my ($self,$pop) = @_; if( ref($pop) =~ /ARRAY/i ) { if( ref($pop->[0]) && $pop->[0]->isa('Bio::PopGen::IndividualI') ) { $pop = Bio::PopGen::Population->new(-individuals => @$pop); } else { $self->warn("composite_LD expects a Bio::PopGen::PopulationI or an arrayref of Bio::PopGen::IndividualI objects"); return (); } } elsif( ! ref($pop) || ! $pop->isa('Bio::PopGen::PopulationI') ) { $self->warn("composite_LD expects a Bio::PopGen::PopulationI or an arrayref of Bio::PopGen::IndividualI objects"); return (); } my @marker_names = $pop->get_marker_names; my @inds = $pop->get_Individuals; my $num_inds = scalar @inds; my (%lookup); # calculate allele frequencies for each marker from the population # use the built-in get_Marker to get the allele freqs # we still need to calculate the genotype frequencies foreach my $marker_name ( @marker_names ) { my(%allelef); foreach my $ind ( @inds ) { my ($genotype) = $ind->get_Genotypes(-marker => $marker_name); if( ! defined $genotype ) { $self->warn("no genotype for marker $marker_name for individual ". $ind->unique_id. "\n"); next; } my @alleles = sort $genotype->get_Alleles; next if( scalar @alleles != 2); my $genostr = join(',', @alleles); $allelef{$alleles[0]}++; $allelef{$alleles[1]}++; } # we should check for cases where there > 2 alleles or # only 1 allele and throw out those markers. my @alleles = sort keys %allelef; my $allele_count = scalar @alleles; # test if site is polymorphic if( $allele_count != 2) { # only really warn if we're seeing multi-allele $self->warn("Skipping $marker_name because it has $allele_count alleles (".join(',',@alleles)."), \ncomposite_LD will currently only work for biallelic markers") if $allele_count > 2; next; # skip this marker } # Need to do something here to detect alleles which aren't # a single character if( length($alleles[0]) != 1 || length($alleles[1]) != 1 ) { $self->warn("An individual has an allele which is not a single base, this is currently not supported in composite_LD - consider recoding the allele as a single character"); next; } # fix the call for allele 1 (A or B) and # allele 2 (a or b) in terms of how we'll do the # N square from Weir p.126 $self->debug( "$alleles[0] is 1, $alleles[1] is 2 for $marker_name\n"); $lookup{$marker_name}->{'1'} = $alleles[0]; $lookup{$marker_name}->{'2'} = $alleles[1]; } @marker_names = sort keys %lookup; my $site_count = scalar @marker_names; # where the final data will be stored my %stats_for_sites; # standard way of generating pairwise combos # LD is done by comparing all the pairwise site (marker) # combinations and keeping track of the genotype and # pairwise genotype (ie genotypes of the 2 sites) frequencies for( my $i = 0; $i < $site_count - 1; $i++ ) { my $site1 = $marker_names[$i]; for( my $j = $i+1; $j < $site_count ; $j++) { my (%genotypes, %total_genotype_count,$total_pairwisegeno_count, %pairwise_genotypes); my $site2 = $marker_names[$j]; my (%allele_count,%allele_freqs) = (0,0); foreach my $ind ( @inds ) { # build string of genotype at site 1 my ($genotype1) = $ind->get_Genotypes(-marker => $site1); my @alleles1 = sort $genotype1->get_Alleles; # if an individual has only one available allele # (has a blank or N for one of the chromosomes) # we don't want to use it in our calculation next unless( scalar @alleles1 == 2); my $genostr1 = join(',', @alleles1); # build string of genotype at site 2 my ($genotype2) = $ind->get_Genotypes(-marker => $site2); my @alleles2 = sort $genotype2->get_Alleles; my $genostr2 = join(',', @alleles2); next unless( scalar @alleles2 == 2); for (@alleles1) { $allele_count{$site1}++; $allele_freqs{$site1}->{$_}++; } $genotypes{$site1}->{$genostr1}++; $total_genotype_count{$site1}++; for (@alleles2) { $allele_count{$site2}++; $allele_freqs{$site2}->{$_}++; } $genotypes{$site2}->{$genostr2}++; $total_genotype_count{$site2}++; # We are using the $site1,$site2 to signify # a unique key $pairwise_genotypes{"$genostr1,$genostr2"}++; # some individuals $total_pairwisegeno_count++; } for my $site ( %allele_freqs ) { for my $al ( keys %{ $allele_freqs{$site} } ) { $allele_freqs{$site}->{$al} /= $allele_count{$site}; } } my $n = $total_pairwisegeno_count; # number of pairs of comparisons # 'A' and 'B' are two loci or in our case site1 and site2 my $allele1_site1 = $lookup{$site1}->{'1'}; # this is the BigA allele my $allele1_site2 = $lookup{$site2}->{'1'}; # this is the BigB allele my $allele2_site1 = $lookup{$site1}->{'2'}; # this is the LittleA allele my $allele2_site2 = $lookup{$site2}->{'2'}; # this is the LittleB allele # AABB my $N1genostr = join(",",( $allele1_site1, $allele1_site1, $allele1_site2, $allele1_site2)); $self->debug(" [$site1,$site2](AABB) N1genostr=$N1genostr\n"); # AABb my $N2genostr = join(",",( $allele1_site1, $allele1_site1, $allele1_site2, $allele2_site2)); $self->debug(" [$site1,$site2](AABb) N2genostr=$N2genostr\n"); # AaBB my $N4genostr = join(",",( $allele1_site1, $allele2_site1, $allele1_site2, $allele1_site2)); $self->debug(" [$site1,$site2](AaBB) N4genostr=$N4genostr\n"); # AaBb my $N5genostr = join(",",( $allele1_site1, $allele2_site1, $allele1_site2, $allele2_site2)); $self->debug(" [$site1,$site2](AaBb) N5genostr=$N5genostr\n"); # count of AABB in my $n1 = $pairwise_genotypes{$N1genostr} || 0; # count of AABb in my $n2 = $pairwise_genotypes{$N2genostr} || 0; # count of AaBB in my $n4 = $pairwise_genotypes{$N4genostr} || 0; # count of AaBb in my $n5 = $pairwise_genotypes{$N5genostr} || 0; my $homozA_site1 = join(",", ($allele1_site1,$allele1_site1)); my $homozB_site2 = join(",", ($allele1_site2,$allele1_site2)); my $p_AA = ($genotypes{$site1}->{$homozA_site1} || 0) / $n; my $p_BB = ($genotypes{$site2}->{$homozB_site2} || 0) / $n; my $p_A = $allele_freqs{$site1}->{$allele1_site1} || 0; # an individual allele freq my $p_a = 1 - $p_A; my $p_B = $allele_freqs{$site2}->{$allele1_site2} || 0; # an individual allele freq my $p_b = 1 - $p_B; # variance of allele frequencies my $pi_A = $p_A * $p_a; my $pi_B = $p_B * $p_b; # hardy weinberg my $D_A = $p_AA - $p_A**2; my $D_B = $p_BB - $p_B**2; my $n_AB = 2*$n1 + $n2 + $n4 + 0.5 * $n5; $self->debug("n_AB=$n_AB -- n1=$n1, n2=$n2 n4=$n4 n5=$n5\n"); my $delta_AB = (1 / $n ) * ( $n_AB ) - ( 2 * $p_A * $p_B ); $self->debug("delta_AB=$delta_AB -- n=$n, n_AB=$n_AB p_A=$p_A, p_B=$p_B\n"); $self->debug(sprintf(" (%d * %.4f) / ( %.2f + %.2f) * ( %.2f + %.2f) \n", $n,$delta_AB**2, $pi_A, $D_A, $pi_B, $D_B)); my $chisquared; eval { $chisquared = ( $n * ($delta_AB**2) ) / ( ( $pi_A + $D_A) * ( $pi_B + $D_B) ); }; if( $@ ) { $self->debug("Skipping the site because the denom is 0.\nsite1=$site1, site2=$site2 : pi_A=$pi_A, pi_B=$pi_B D_A=$D_A, D_B=$D_B\n"); next; } # this will be an upper triangular matrix $stats_for_sites{$site1}->{$site2} = [$delta_AB,$chisquared]; } } return %stats_for_sites; } =head2 mcdonald_kreitman Title : mcdonald_kreitman Usage : $Fstat = mcdonald_kreitman($ingroup, $outgroup); Function: Calculates McDonald-Kreitman statistic based on a set of ingroup individuals and an outgroup by computing the number of differences at synonymous and non-synonymous sites for intraspecific comparisons and with the outgroup Returns : 2x2 table, followed by a hash reference indicating any warning messages about the status of the alleles or codons Args : -ingroup => L object or arrayref of Ls -outgroup => L object or arrayef of Ls -polarized => Boolean, to indicate if this should be a polarized test. Must provide two individuals as outgroups. =cut sub mcdonald_kreitman { my ($self,@args) = @_; my ($ingroup, $outgroup,$polarized) = $self->_rearrange([qw(INGROUP OUTGROUP POLARIZED)],@args); my $verbose = $self->verbose; my $outgroup_count; my $gapchar = '\-'; if( ref($outgroup) =~ /ARRAY/i ) { $outgroup_count = scalar @$outgroup; } elsif( UNIVERSAL::isa($outgroup,'Bio::PopGen::PopulationI') ) { $outgroup_count = $outgroup->get_number_individuals; } else { $self->throw("Expected an ArrayRef of Individuals OR a Bio::PopGen::PopulationI"); } if( $polarized ) { if( $outgroup_count < 2 ) { $self->throw("Need 2 outgroups with polarized option\n"); } } elsif( $outgroup_count > 1 ) { $self->warn(sprintf("%s outgroup sequences provided, but only first will be used",$outgroup_count )); } elsif( $outgroup_count == 0 ) { $self->throw("No outgroup sequence provided"); } my $codon_path = Bio::MolEvol::CodonModel->codon_path; my (%marker_names,%unique,@inds); for my $p ( $ingroup, $outgroup) { if( ref($p) =~ /ARRAY/i ) { push @inds, @$p; } else { push @inds, $p->get_Individuals; } } for my $i ( @inds ) { if( $unique{$i->unique_id}++ ) { $self->warn("Individual ". $i->unique_id. " is seen more than once in the ingroup or outgroup set\n"); } for my $n ( $i->get_marker_names ) { $marker_names{$n}++; } } my @marker_names = keys %marker_names; if( $marker_names[0] =~ /^(Site|Codon)/ ) { # sort by site or codon number and do it in # a schwartzian transformation baby! @marker_names = map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [$_ =~ /^(?:Codon|Site)-(\d+)/, $_] } @marker_names; } my $num_inds = scalar @inds; my %vals = ( 'ingroup' => $ingroup, 'outgroup' => $outgroup, ); # Make the Codon Table type a parameter! my $table = Bio::Tools::CodonTable->new(-id => $codon_table); my @vt = qw(outgroup ingroup); my %changes; my %status; my %two_by_two = ( 'fixed_N' => 0, 'fixed_S' => 0, 'poly_N' => 0, 'poly_S' => 0); for my $codon ( @marker_names ) { my (%codonvals); my %all_alleles; for my $t ( @vt ) { my $outcount = 1; for my $ind ( @{$vals{$t}} ) { my @alleles = $ind->get_Genotypes($codon)->get_Alleles; if( @alleles > 2 ) { warn("Codon $codon saw ", scalar @alleles, " alleles for ind ", $ind->unique_id, "\n"); die; } else { my ($allele) = shift @alleles; $all_alleles{$ind->unique_id} = $allele; my $AA = $table->translate($allele); next if( $AA eq 'X' || $AA eq '*' || $allele =~ /N/i); my $label = $t; if( $t eq 'outgroup' ) { $label = $t.$outcount++; } $codonvals{$label}->{$allele}++; $codonvals{all}->{$allele}++; } } } my $total = sum ( values %{$codonvals{'ingroup'}} ); next if( $total && $total < 2 ); # skip sites with < alleles # process all the seen alleles (codons) # this is a vertical slide through the alignment if( keys %{$codonvals{all}} <= 1 ) { # no changes or no VALID codons - monomorphic } else { # grab only the first outgroup codon (what to do with rest?) my ($outcodon) = keys %{$codonvals{'outgroup1'}}; if( ! $outcodon ) { $status{"no outgroup codon $codon"}++; next; } my $out_AA = $table->translate($outcodon); my ($outcodon2) = keys %{$codonvals{'outgroup2'}}; if( ($polarized && ($outcodon ne $outcodon2)) || $out_AA eq 'X' || $out_AA eq '*' ) { # skip if outgroup codons are different # (when polarized option is on) # or skip if the outcodon is STOP or 'NNN' if( $verbose > 0 ) { $self->debug("skipping $out_AA and $outcodon $outcodon2\n"); } $status{'outgroup codons different'}++; next; } # check if ingroup is actually different from outgroup - # if there are the same number of alleles when considering # ALL or just the ingroup, then there is nothing new seen # in the outgroup so it must be a shared allele (codon) # so we just count how many total alleles were seen # if this is the same as the number of alleles seen for just # the ingroup then the outgroup presents no new information my @ingroup_codons = keys %{$codonvals{'ingroup'}}; my $diff_from_out = ! exists $codonvals{'ingroup'}->{$outcodon}; if( $verbose > 0 ) { $self->debug("alleles are in: ", join(",", @ingroup_codons), " out: ", join(",", keys %{$codonvals{outgroup1}}), " diff_from_out=$diff_from_out\n"); for my $ind ( sort keys %all_alleles ) { $self->debug( "$ind\t$all_alleles{$ind}\n"); } } # are all the ingroup alleles the same and diferent from outgroup? # fixed differences between species if( $diff_from_out ) { if( scalar @ingroup_codons == 1 ) { # fixed differences if( $outcodon =~ /^$gapchar/ ) { $status{'outgroup codons with gaps'}++; next; } elsif( $ingroup_codons[0] =~ /$gapchar/) { $status{'ingroup codons with gaps'}++; next; } my $path = $codon_path->{uc $ingroup_codons[0].$outcodon}; $two_by_two{fixed_N} += $path->[0]; $two_by_two{fixed_S} += $path->[1]; if( $verbose > 0 ) { $self->debug("ingroup is @ingroup_codons outcodon is $outcodon\n"); $self->debug("path is ",join(",",@$path),"\n"); $self->debug (sprintf("%-15s fixeddiff - %s;%s(%s) %d,%d\tNfix=%d Sfix=%d Npoly=%d Spoly=%s\n",$codon,$ingroup_codons[0], $outcodon,$out_AA, @$path, map { $two_by_two{$_} } qw(fixed_N fixed_S poly_N poly_S))); } } else { # polymorphic and all are different from outgroup # Here we find the minimum number of NS subst my ($Ndiff,$Sdiff) = (3,0); # most different path for my $c ( @ingroup_codons ) { next if( $c =~ /$gapchar/ || $outcodon =~ /$gapchar/); my $path = $codon_path->{uc $c.$outcodon}; my ($tNdiff,$tSdiff) = @$path; if( $path->[0] < $Ndiff || ($tNdiff == $Ndiff && $tSdiff <= $Sdiff)) { ($Ndiff,$Sdiff) = ($tNdiff,$tSdiff); } } $two_by_two{fixed_N} += $Ndiff; $two_by_two{fixed_S} += $Sdiff; if( @ingroup_codons > 2 ) { $status{"more than 2 ingroup codons $codon"}++; warn("more than 2 ingroup codons (@ingroup_codons)\n"); } else { my $path = $codon_path->{uc join('',@ingroup_codons)}; $two_by_two{poly_N} += $path->[0]; $two_by_two{poly_S} += $path->[1]; if( $verbose > 0 ) { $self->debug(sprintf("%-15s polysite_all - %s;%s(%s) %d,%d\tNfix=%d Sfix=%d Npoly=%d Spoly=%s\n",$codon,join(',',@ingroup_codons), $outcodon,$out_AA,@$path, map { $two_by_two{$_} } qw(fixed_N fixed_S poly_N poly_S))); } } } } else { my %unq = map { $_ => 1 } @ingroup_codons; delete $unq{$outcodon}; my @unique_codons = keys %unq; # calc path for diff add to poly # Here we find the minimum number of subst bw # codons my ($Ndiff,$Sdiff) = (3,0); # most different path for my $c ( @unique_codons ) { my $path = $codon_path->{uc $c.$outcodon }; if( ! defined $path ) { die " cannot get path for ", $c.$outcodon, "\n"; } my ($tNdiff,$tSdiff) = @$path; if( $path->[0] < $Ndiff || ($tNdiff == $Ndiff && $tSdiff <= $Sdiff)) { ($Ndiff,$Sdiff) = ($tNdiff,$tSdiff); } } if( @unique_codons == 2 ) { my $path = $codon_path->{uc join('',@unique_codons)}; if( ! defined $path ) { $self->throw("no path for @unique_codons\n"); } $Ndiff += $path->[0]; $Sdiff += $path->[1]; } $two_by_two{poly_N} += $Ndiff; $two_by_two{poly_S} += $Sdiff; if( $verbose > 0 ) { $self->debug(sprintf("%-15s polysite - %s;%s(%s) %d,%d\tNfix=%d Sfix=%d Npoly=%d Spoly=%s\n",$codon,join(',',@ingroup_codons), $outcodon,$out_AA, $Ndiff, $Sdiff, map { $two_by_two{$_} } qw(fixed_N fixed_S poly_N poly_S))); } } } } return ( $two_by_two{'poly_N'}, $two_by_two{'fixed_N'}, $two_by_two{'poly_S'}, $two_by_two{'fixed_S'}, {%status}); } *MK = \&mcdonald_kreitman; =head2 mcdonald_kreitman_counts Title : mcdonald_kreitman_counts Usage : my $MK = $statistics->mcdonald_kreitman_counts( N_poly -> integer of count of non-syn polymorphism N_fix -> integer of count of non-syn fixed substitutions S_poly -> integer of count of syn polymorphism S_fix -> integer of count of syn fixed substitutions ); Function: Returns : decimal number Args : =cut sub mcdonald_kreitman_counts { my ($self,$Npoly,$Nfix,$Spoly,$Sfix) = @_; if( $has_twotailed ) { return &Text::NSP::Measures::2D::Fisher2::twotailed::calculateStatistic (n11=>$Npoly, n1p=>$Npoly+$Spoly, np1=>$Npoly+$Nfix, npp=>$Npoly+$Nfix+$Spoly+$Sfix); } else { $self->warn("cannot call mcdonald_kreitman_counts because no Fisher's exact is available - install Text::NSP::Measures::2D::Fisher2::twotailed"); return 0; } } 1; BioPerl-1.007002/Bio/PopGen/TagHaplotype.pm000444000766000024 2451113155576320 20376 0ustar00cjfieldsstaff000000000000# module Bio::PopGen::TagHaplotype.pm # # Please direct questions and support issues to # # Cared for by Pedro M. Gomez-Fabre # # Copyright Pedro M. Gomez-Fabre # # You may distribute this module under the same term as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::PopGen::TagHaplotype.pm - Haplotype tag object. =head1 SYNOPSIS use Bio::PopGen::TagHaplotype; my $obj = Bio::PopGen::TagHaplotype -> new($hap); =head1 DESCRIPTION This module take as input a haplotype and try toe get the minimal set of SNP that define the haplotype. This module can be use alone. But due to the tagging haplotype process is exponential one. My suggestion is that before to use this module you pass your data under Select.mp module also on this folder. In any case if, you provide an haplotype the module will try to find the answer to your question. =head1 CONSTRUCTORS my $obj = Bio::PopGen::TagHaplotype -> new($hap); were $hap is the reference to an array of array with the haplotype. $hap= [[0, 0, 0], [1, 0, 0], [0, 1, 1] ]; =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Pedro M. Gomez-Fabre Email pgf18872-at-gsk-dot-com =cut # Let the code begin... package Bio::PopGen::TagHaplotype; use strict; use Data::Dumper; use Storable qw(dclone); use base qw(Bio::Root::Root); my $USAGE = <new(-haplotype_block => \$hapblockref) EOF ; =head2 new Title : new Function: constructor of the class. Returns : self hash Args : input haplotype (array of array) Status : public =cut #------------------------ sub new{ #------------------------ my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($haplotype_block) = $self->_rearrange([qw(HAPLOTYPE_BLOCK)],@args); if ($haplotype_block) { $self->haplotype_block($haplotype_block); } else{ $self->throw("haplotype has not been supplied\n$USAGE"); } # check that the haplotype block is well formed. for (my $i=0; $i<$#$haplotype_block+1; $i++){ if ( $#{$haplotype_block->[0]} != $#{$haplotype_block->[$i]} ){ $self->throw("The haplotype matrix is not well formed (Not squared)"); } } # make the calculation my $tag_list = _scan_snp( $self ->haplotype_block ); if ($tag_list){ $self ->tag_list($tag_list); } else { $self ->tag_list(undef); } if ( defined $self->tag_list){ $self ->tag_length(scalar @{$self->tag_list}); } else { $self ->tag_length(0); #"NO TAGS FOUND!" } return $self; } =head2 haplotype_block Title : haplotype_block Usage : my $haplotype_block = $TagHaplotype->haplotype_block(); Function: Get the haplotype block for a haplotype tagging selection Returns : reference of array Args : reference of array with haplotype pattern =cut sub haplotype_block{ my ($self) =shift; return $self->{'_haplotype_block'} = shift if @_; return $self->{'_haplotype_block'}; } =head2 input_block Title : input_block Usage : $obj->input_block() Function: returns haplotype block. By now will produce the same output than $self->haplotype_block. but for compatibility, this method is kept. This method is deprecated. Returns : reference to array of array with the haplotype input value Args : none Status : public =cut #------------------------ sub input_block{ #------------------------ my $self = shift; $self->warn(ref($self). "::input_block - deprecated method. Use haplotype_block() instead."); return $self->haplotype_block; } =head2 tag_list Title : tag_list Usage : $obj->tag_list() Function: returns the list of SNPs combination that identify the haplotype. All combinations are displayed as arrays Returns : reference to array of array. Args : none Status : public =cut #------------------------ sub tag_list{ #------------------------ my ($self) = shift; return $self->{'_tag_list'}= shift if @_; return $self->{'_tag_list'}; } =head2 tag_length Title : tag_length Usage : $obj->tag_length() Function: returns the length of the tag. Returns : scalar Args : none Status : public =cut #------------------------ sub tag_length{ #------------------------ my ($self) =shift; return $self ->{'_tag_length'} = shift if @_; return $self ->{'_tag_length'}; } =head2 _scan_snp Title : _scan_snp Usage : internal Function: scan sets increasing the length until find a non degenerated pattern. Returns : scalar Args : none Status : private =cut #------------------------ sub _scan_snp{ #------------------------ my ($hap)=@_; my $hap_length = scalar @{$hap->[0]}; ## store the haplotype length for my $i(1..$hap_length){ my $list = _gen_comb($hap_length, $i); my $snp_collection = _scan_combinations($hap, $list); # if there is any element on the collection. # We have reached our goal and # we can stop the calculation. if($#$snp_collection>-1){ return $snp_collection; } } } =head2 _gen_comb Title : _gen_comb Usage : internal Function: we supply the length of the haplotype and the length of the word we need to find and the functions returns the possible list of combinations. Returns : scalar Args : none Status : private =cut #------------------------ sub _gen_comb{ #------------------------ my ($hap_length,$n) = @_; my @array = (); # list with all elements we have to combine for(0..$hap_length-1){ push @array, $_ }; # # we need some parameters to create the combination list. # This parameters can be changed if we can modify the list values # my $m = -1; # this parameter start the calculation at value # m+1 on the recursive cicle. my $value = []; ## seems to have not too much sense here, but is ## needed on the recursion and need to be started ## from here my $list = []; _generateCombinations ( \@array, \$m, \$n, $value, $list); return $list; } =head2 _generateCombinations Title : _generateCombinations Usage : internal Function: Recursive function that produce all combinations for a set i.e.: 1, 2, 3, 4 and word of B<3> will produce: 1, 2, 3 1, 2, 4 1, 3, 4 2, 3, 4 Returns : Args : none Status : private =cut #------------------------ sub _generateCombinations{ #------------------------ my ($rarr, $rm, $rn, $rvalue,$rlist)=@_; for (my $i = ($$rm+1); $i[$i]); if (scalar @value2<$$rn){ _generateCombinations($rarr,\$i, $rn, \@value2, $rlist); } if (scalar @value2==$$rn){ push @$rlist, [@value2]; } if(scalar @value2>$$rn){ last; } } } # take the list of combinations # i.e.: 1 2 3 # 1 2 4 # 1 3 4 # 2 3 4 # # generate a sub array from the haplotype with the snp tag for the combination # and check all haplotypes for these columns. # if two haplotypes have the same value. we can not define the haplotype # without ambiguity. # Will return a list of valid combinations (SNP Tags) # =head2 _scan_combinations Title : _scan_combinations Usage : internal Function: take the haplotype and a list of possible combination for that length. Generate a subset and scan it to find if the information is enough to define the haplotype set. Returns : Args : none Status : private =cut #------------------------ sub _scan_combinations { #------------------------ my($hap,$list) = @_; my $valid_combination = undef; # we have to check every snp combinations from the list for my $i (0..$#$list){ # extract from the big array the one we will use for tag calculations my $subArray = _get_subArray ($hap, $list->[$i]); my $degeneration = _deg_test($subArray); if(!$degeneration){ push @$valid_combination, [@{$list->[$i]}]; } } return $valid_combination; } # return 1 if two arrays are degenerated (same haplotype) #------------------------ sub _deg_test{ #------------------------ my ($hap)= @_; # for every sub array we compare each element with the rest for my $c1(0..$#$hap){ for my $c2($c1+1..$#$hap){ my $degeneration = compare_arrays($hap->[$c1], $hap->[$c2]); if ($degeneration){ # if the two arrays are the same return 1; } } } } #------------------------ sub _get_subArray { #------------------------ my($hap, $combination) =@_; my $out = []; # output array to be tested for my $i (0..$#$hap){ foreach(@$combination){ push @{$out->[$i]}, $hap->[$i][$_]; } } return $out; } # # take two arrays and compare their values # Returns : 1 if the two values are the same # 0 if the values are different # #------------------------ sub compare_arrays { #------------------------ my ($first, $second) = @_; return 0 unless @$first == @$second; for (my $i = 0; $i < @$first; $i++) { return 0 if $first->[$i] ne $second->[$i]; } return 1; } 1; BioPerl-1.007002/Bio/PopGen/Utilities.pm000444000766000024 2036313155576320 17751 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::Utilities # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::Utilities - Utilities for working with PopGen data and objects =head1 SYNOPSIS use Bio::PopGen::Utilities; use Bio::AlignIO; my $in = Bio::AlignIO->new(-file => 't/data/t7.aln', -format => 'clustalw'); my $aln = $in->next_aln; # get a population, each sequence is an individual and # for the default case, every site which is not monomorphic # is a 'marker'. Each individual will have a 'genotype' for the # site which will be the specific base in the alignment at that # site my $pop = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln); # get the synonymous sites from the alignemt only as the 'genotypes' # for the population my $synpop = Bio::PopGen::Utilities->aln_to_population(-site_model => 'cod', -alignment => $aln); =head1 DESCRIPTION This object provides some convience function to turn sequence alignments into usable objects for the Population genetics modules (Bio::PopGen). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::Utilities; use strict; use Bio::Align::DNAStatistics; use Bio::PopGen::Population; use Bio::PopGen::Individual; use base qw(Bio::Root::Root); use constant CodonLen => 3; =head2 aln_to_population Title : aln_to_population Usage : my $pop = Bio::PopGen::Utilities->aln_to_population($aln); Function: Turn and alignment into a set of L objects grouped in a L object Sites are treated as 'Markers' in the Bioperl PopGen object model in the sense that a site is a unique location for which an individual will have a genotype (a set of alleles). In this implementation we are assuming that each individual has a single entry in the alignment file. Specify a site model as one of those listed 'all' -- every base in the alignment is considered a site 'cod' -- codons The option -site_model for All sites : 'all' Codon sites : 'cod' or 'codon' To see all sites, including those which are fixed in the population add -include_monomorphic => 1 to the arguments Returns : Args : -include_monomorphic => 1 to specify all sites, even those which are monomorphic in the population (useful for HKA test mostly) [default is false] -phase => specify a phase for the data, this is only used if the site_mode is codon [default is 0] -site_model => one-of 'all', 'codon' to specify a site model for the data extraction from the alignment [default is all] -alignment => provide a L object [required] =cut sub aln_to_population{ my ($self,@args) = @_; my ($aln, $sitemodel,$phase, $includefixed,$checkisa) = $self->_rearrange([qw(ALIGNMENT SITE_MODEL PHASE INCLUDE_MONOMORPHIC CHECKISA)], @args); my %ambig_code = ('?' => ['?','?'], 'N' => ['?','?'], '-' => ['?','?'], 'G' => ['G','G'], 'A' => ['A','A'], 'T' => ['T','T'], 'C' => ['C','C'], 'R' => ['A','G'], 'Y' => ['C','T'], 'W' => ['T','A'], 'M' => ['C','A'], 'S' => ['C','G'], 'K' => ['G','T']); if( ! defined $aln ) { $self->warn("Must provide a valid Bio::SimpleAlign object to run aln_to_population"); return; } if( ! $aln->is_flush ) { $self->warn("Must provide a Bio::SimpleAlign object with aligned sequences to aln_to_population!"); return; } $phase = 0 unless defined $phase; if( $phase != 0 && $phase != 1 && $phase != 2 ) { warn("phase must be 0,1, or 2"); return; } my $alength = $aln->length; my @inds; if( ! defined $sitemodel || $sitemodel =~ /all/i ) { my $ct = 0; my @seqs; for my $seq ( $aln->each_seq ) { push @seqs, $seq->seq; push @inds, Bio::PopGen::Individual->new(-unique_id => $seq->display_id); } for( my $i = 0; $i < $alength; $i++ ) { my (@genotypes,%set); # do we skip indels? # slicing vertically for my $seq ( @seqs ) { my $site = uc(substr($seq,$i,1)); push @genotypes, $ambig_code{$site}; $set{$site}++; } if( keys %set > 1 || $includefixed ) { my $genoct = scalar @genotypes; for( my $j = 0; $j < $genoct; $j++ ) { $inds[$j]->add_Genotype(Bio::PopGen::Genotype->new (-marker_name => ($i+1), -individual_id=> $inds[$j]->unique_id, -alleles => $genotypes[$j])); } } } } elsif( $sitemodel =~ /cod(on)?/i ) { my $ct = 0; my @seqs; for my $seq ( $aln->each_seq ) { push @seqs, $seq->seq; push @inds, Bio::PopGen::Individual->new(-unique_id => $seq->display_id); } my $codonct = 0; for( my $i = $phase; $i < $alength; $i += CodonLen ) { my (@genotypes,%set,$genoct); for my $seq ( @seqs ) { my @unambig_site; my $site = uc(substr($seq,$i,CodonLen)); if( length($site) < CodonLen ) { # at end of alignment and this is not in phase $self->debug("phase was $phase, but got to end of alignment with overhang of $site"); next; } # do we check for gaps/indels here? for (my $pos=0; $pos 1 || $includefixed ) { for( my $j = 0; $j < $genoct; $j++ ) { $inds[$j]->add_Genotype(Bio::PopGen::Genotype->new (-marker_name => ($i/CodonLen), -individual_id=> $inds[$j]->unique_id, -alleles => $genotypes[$j])); } $codonct++; } } } else { $self->throw("Can only build sites based on all the data right now!"); } return Bio::PopGen::Population->new(-checkisa => 0, -source => 'alignment', -individuals=> \@inds); } 1; BioPerl-1.007002/Bio/PopGen/IO000755000766000024 013155576320 15566 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/PopGen/IO/csv.pm000444000766000024 2356313155576320 17105 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::IO::csv # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::IO::csv -Extract individual allele data from a CSV parser =head1 SYNOPSIS #Do not use directly, use through the Bio::PopGen::IO driver use Bio::PopGen::IO; my $io = Bio::PopGen::IO->new(-format => 'csv', -file => 'data.csv'); # Some IO might support reading in a population at a time my @population; while( my $ind = $io->next_individual ) { push @population, $ind; } =head1 DESCRIPTION This object will parse comma delimited format (CSV) or whatever delimiter you specify. It currently doesn't handle the more complex quote escaped CSV format. There are 3 initialization parameters, the delimiter (-field_delimiter) [default ','], (-allele_delimiter) [default ' ']. The third initialization parameter is a boolean -no_header which specifies if there is no header line to read in. All lines starting with '#' will be skipped When no_header is not specific the data is assumed to be of the following form. Having a header line this SAMPLE,MARKERNAME1,MARKERNAME2,... and each data line having the form (diploid data) SAMP1,101 102,100 90,a b or for haploid data SAMP1,101,100,a =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Matthew Hahn, matthew.hahn-at-duke.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::IO::csv; use vars qw($FieldDelim $AlleleDelim $NoHeader); use strict; ($FieldDelim,$AlleleDelim,$NoHeader) =( ',', '\s+',0); # Object preamble - inherits from Bio::Root::Root use Bio::PopGen::Individual; use Bio::PopGen::Population; use Bio::PopGen::Genotype; use base qw(Bio::PopGen::IO); =head2 new Title : new Usage : my $obj = Bio::PopGen::IO::csv->new(); Function: Builds a new Bio::PopGen::IO::csv object Returns : an instance of Bio::PopGen::IO::csv Args : [optional, these are the current defaults] -field_delimiter => ',' -allele_delimiter=> '\s+' -no_header => 0, =cut sub _initialize { my($self, @args) = @_; my ($fieldsep,$all_sep, $noheader) = $self->_rearrange([qw(FIELD_DELIMITER ALLELE_DELIMITER NO_HEADER)],@args); $self->flag('no_header', defined $noheader ? $noheader : $NoHeader); $self->flag('field_delimiter',defined $fieldsep ? $fieldsep : $FieldDelim); $self->flag('allele_delimiter',defined $all_sep ? $all_sep : $AlleleDelim); $self->{'_header'} = undef; return 1; } =head2 flag Title : flag Usage : $obj->flag($flagname,$newval) Function: Get/Set the flag value Returns : value of a flag (a boolean) Args : A flag name, currently we expect 'no_header', 'field_delimiter', or 'allele_delimiter' on set, new value (a boolean or undef, optional) =cut sub flag{ my $self = shift; my $fieldname = shift; return unless defined $fieldname; return $self->{'_flag'}->{$fieldname} = shift if @_; return $self->{'_flag'}->{$fieldname}; } =head2 next_individual Title : next_individual Usage : my $ind = $popgenio->next_individual; Function: Retrieve the next individual from a dataset Returns : L object Args : none =cut sub next_individual{ my ($self) = @_; while( defined( $_ = $self->_readline) ) { next if( /^\s*\#/ || /^\s+$/ || ! length($_) ); last; } return if ! defined $_; if( $self->flag('no_header') || defined $self->{'_header'} ) { #########new (allows field delim to be the same as the allele delim my ($samp,@marker_results); if($self->flag('field_delimiter') ne $self->flag('allele_delimiter')){ ($samp,@marker_results) = split($self->flag('field_delimiter'),$_); } else{ my $fielddelim = $self->flag('field_delimiter'); my $alleledelim = $self->flag('allele_delimiter'); ($samp) = /(^.+?)$fielddelim/; s/^.+?$fielddelim//; (@marker_results) = /([\d|\w]+$alleledelim[\d|\w]+)/g; } #########end new my $i = 1; foreach my $m ( @marker_results ) { $m =~ s/^\s+//; $m =~ s/\s+$//; my $markername; if( defined $self->{'_header'} ) { $markername = $self->{'_header'}->[$i]; } else { $markername = "Marker$i"; } $self->debug( "markername is $markername alleles are $m\n"); my @alleles = split($self->flag('allele_delimiter'), $m); $m = Bio::PopGen::Genotype->new(-alleles => \@alleles, -marker_name => $markername, -individual_id=> $samp); $i++; } return Bio::PopGen::Individual->new(-unique_id => $samp, -genotypes => \@marker_results); } else { chomp; $self->{'_header'} = [split($self->flag('field_delimiter'),$_)]; return $self->next_individual; # rerun loop again } return; } =head2 next_population Title : next_population Usage : my $ind = $popgenio->next_population; Function: Retrieve the next population from a dataset Returns : L object Args : none Note : Many implementation will not implement this =cut # Plan is to just return the whole dataset as a single population by # default I think - people would then have each population in a separate # file. sub next_population{ my ($self) = @_; my @inds; while( my $ind = $self->next_individual ) { push @inds, $ind; } Bio::PopGen::Population->new(-individuals => \@inds); } =head2 write_individual Title : write_individual Usage : $popgenio->write_individual($ind); Function: Write an individual out in the file format Returns : none Args : L object(s) =cut sub write_individual{ my ($self,@inds) = @_; my $fielddelim = $self->flag('field_delimiter'); my $alleledelim= $self->flag('allele_delimiter'); foreach my $ind ( @inds ) { if (! ref($ind) || ! $ind->isa('Bio::PopGen::IndividualI') ) { $self->warn("Cannot write an object that is not a Bio::PopGen::IndividualI object ($ind)"); next; } # we'll go ahead and sort these until # we have a better way to insure a consistent order my @marker_names = sort $ind->get_marker_names; if( ! $self->flag('no_header') && ! $self->flag('header_written') ) { $self->_print(join($fielddelim, ('SAMPLE', @marker_names)), "\n"); $self->flag('header_written',1); } $self->_print( join($fielddelim, $ind->unique_id, # we're chaining map here, pay attention and read # starting with the last map # we'll turn genotypes into allele pairs # which will be separated by the allele delimiter map { join($alleledelim,$_->get_Alleles) } # marker names will be sorted so we don't # have to worry about this between individuals # unless the individual set you pass in has # a mixed set of markers... # this will turn marker names into Genotypes map {$ind->get_Genotypes(-marker => $_)} @marker_names), "\n") } } =head2 write_population Title : write_population Usage : $popgenio->write_population($pop); Function: Write a population out in the file format Returns : none Args : L object(s) Note : Many implementation will not implement this =cut sub write_population{ my ($self,@pops) = @_; my $fielddelim = $self->flag('field_delimiter'); # my $alleledelim= $self->flag('allele_delimiter'); my $alleledelim = ' '; foreach my $pop ( @pops ) { if (! ref($pop) || ! $pop->isa('Bio::PopGen::PopulationI') ) { $self->warn("Cannot write an object that is not a Bio::PopGen::PopulationI object"); next; } # we'll go ahead and sort these until # we have a better way to insure a consistent order my @marker_names = sort $pop->get_marker_names; if( ! $self->flag('no_header') && ! $self->flag('header_written') ) { $self->_print( join($fielddelim, ('SAMPLE', @marker_names)), "\n"); $self->flag('header_written',1); } foreach my $ind ( $pop->get_Individuals ) { $self->_print( join($fielddelim, $ind->unique_id, # we're chaining map here, pay attention # and read starting with the last map # we'll turn genotypes into allele pairs # which will be separated by the allele # delimiter map { join($alleledelim,$_->get_Alleles) } # marker names will be sorted so we don't # have to worry about this between individuals # unless the individual set you pass in has # a mixed set of markers... # this will turn marker names into Genotypes map {$ind->get_Genotypes(-marker => $_)} @marker_names), "\n"); } } } 1; BioPerl-1.007002/Bio/PopGen/IO/hapmap.pm000444000766000024 1747713155576320 17567 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::IO::hapmap # # Please direct questions and support issues to # # Cared for by Rich Dobson # # Copyright Rich Dobson # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::IO::hapmap - A parser for HapMap output data =head1 SYNOPSIS # Do not use directly, use through the Bio::PopGen::IO driver use Bio::PopGen::IO; my $io = Bio::PopGen::IO->new(-format => 'hapmap', -file => 'data.hapmap'); # Some IO might support reading in a population at a time my @population; while( my $ind = $io->next_individual ) { push @population, $ind; } =head1 DESCRIPTION A driver module for Bio::PopGen::IO for parsing hapmap data. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Rich Dobson Email r.j.dobson-at-qmul.ac.uk =head1 CONTRIBUTORS Jason Stajich, jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::IO::hapmap; use vars qw($FieldDelim $AlleleDelim $NoHeader $StartingCol); use strict; ($FieldDelim,$AlleleDelim,$NoHeader,$StartingCol) =( '\s+','',0,11); use Bio::PopGen::Individual; use Bio::PopGen::Population; use Bio::PopGen::Genotype; use base qw(Bio::PopGen::IO); =head2 new Title : new Usage : my $obj = Bio::PopGen::IO::hapmap->new(); Function: Builds a new Bio::PopGen::IO::hapmap object Returns : an instance of Bio::PopGen::IO::hapmap Args : [optional, these are the current defaults] -field_delimiter => ',' -allele_delimiter=> '\s+' -no_header => 0, -starting_column => 11 =cut sub _initialize { my($self, @args) = @_; $Bio::PopGen::Genotype::BlankAlleles=''; my ($fieldsep,$all_sep, $noheader, $start_col) = $self->_rearrange([qw(FIELD_DELIMITER ALLELE_DELIMITER NO_HEADER STARTING_COLUMN)], @args); $self->flag('no_header', defined $noheader ? $noheader : $NoHeader); $self->flag('field_delimiter',defined $fieldsep ? $fieldsep : $FieldDelim); $self->flag('allele_delimiter',defined $all_sep ? $all_sep : $AlleleDelim); $self->starting_column(defined $start_col ? $start_col : $StartingCol ); $self->{'_header'} = undef; return 1; } =head2 flag Title : flag Usage : $obj->flag($flagname,$newval) Function: Get/Set the flag value Returns : value of a flag (a boolean) Args : A flag name, currently we expect 'no_header', 'field_delimiter', or 'allele_delimiter' on set, new value (a boolean or undef, optional) =cut sub flag { my $self = shift; my $fieldname = shift; return unless defined $fieldname; return $self->{'_flag'}->{$fieldname} = shift if @_; return $self->{'_flag'}->{$fieldname}; } sub _pivot { my ($self) = @_; my (@cols,@rows,@idheader); while ($_ = $self->_readline){ chomp($_); next if( /^\s*\#/ || /^\s+$/ || ! length($_) ); if( /^rs\#\s+alleles\s+chrom\s+pos\s+strand/ ) { @idheader = split $self->flag('field_delimiter'); } else { push @cols, [split $self->flag('field_delimiter')]; } } my $startingcol = $self->starting_column; $self->{'_header'} = [ map { $_->[0] } @cols]; for my $n ($startingcol.. $#{ $cols[ 0 ]}) { my $column = [ $idheader[$n], map{ $_->[ $n ] } @cols ]; push (@rows, $column); } $self->{'_pivot'} = [@rows]; $self->{'_i'} = 0; } =head2 next_individual Title : next_individual Usage : my $ind = $popgenio->next_individual; Function: Retrieve the next individual from a dataset Returns : A Bio::PopGen::IndividualI object Args : none See L =cut sub next_individual { my ($self) = @_; unless($self->{'_pivot'}){ #if it's the first time then pivot the table and store. #Lines will now be read from the stored pivot version of the input file $self->_pivot; } $_ = $self->{'_pivot'}->[$self->{'_i'}++]; return unless defined $_; # Store all the marker related info. Now that the pivot has taken # place this is in the first few lines of the file Maybe this # should be put in a marker object. Doesn't seem to fit too well # though my ($samp,@marker_results) = @$_; # at some point use all this info my $i = 1; foreach my $m ( @marker_results ) { $m =~ s/^\s+//; $m =~ s/\s+$//; my $markername; if( defined $self->{'_header'} ) { $markername = $self->{'_header'}->[$i-1]; } else { $markername = "Marker$i"; } my @alleles = split($self->flag('allele_delimiter'), $m); if( @alleles != 2 ) { $self->warn("$m for $samp\n"); } else { $m = Bio::PopGen::Genotype->new(-alleles => \@alleles, -marker_name => $markername, -marker_type => 'S', # Guess hapmap only has SNP data -individual_id => $samp); } $i++; } return new Bio::PopGen::Individual(-unique_id => $samp, -genotypes => \@marker_results); } =head2 next_population Title : next_population Usage : my $ind = $popgenio->next_population; Function: Retrieve the next population from a dataset Returns : Bio::PopGen::PopulationI object Args : none Note : Many implementation will not implement this See L =cut sub next_population { my ($self) = @_; my @inds; while( my $ind = $self->next_individual ) { push @inds, $ind; } Bio::PopGen::Population->new(-individuals => \@inds); } =head2 write_individual Title : write_individual Usage : $popgenio->write_individual($ind); Function: Write an individual out in the file format NOT SUPPORTED BY hapmap format Returns : none Args : Bio::PopGen::PopulationI object(s) See L =cut sub write_individual { my ($self,@inds) = @_; # data from hapmap is output, not input, so # we don't need a method for writing and input file $self->throw_not_implemented(); } =head2 write_population Title : write_population Usage : $popgenio->write_population($pop); Function: Write a population out in the file format NOT SUPPORTED BY hapmap format Returns : none Args : Bio::PopGen::PopulationI object(s) Note : Many implementation will not implement this See L =cut sub write_population { my ($self,@inds) = @_; $self->throw_not_implemented(); } =head2 starting_column Title : starting_column Usage : $obj->starting_column($newval) Function: Column where data starts Example : Returns : value of starting_column (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub starting_column{ my $self = shift; return $self->{'starting_column'} = shift if @_; return $self->{'starting_column'}; } 1; BioPerl-1.007002/Bio/PopGen/IO/phase.pm000444000766000024 2476713155576320 17421 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::IO::phase # # Please direct questions and support issues to # # Cared for by Rich Dobson # # Copyright Rich Dobson # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::IO::phase - A parser for Phase format data =head1 SYNOPSIS # Do not use directly, use through the Bio::PopGen::IO driver use Bio::PopGen::IO; my $io = Bio::PopGen::IO->new(-format => 'phase', -file => 'data.phase'); # Some IO might support reading in a population at a time my @population; while( my $ind = $io->next_individual ) { push @population, $ind; } =head1 DESCRIPTION A driver module for Bio::PopGen::IO for parsing phase data. PHASE is defined in http://www.stat.washington.edu/stephens/instruct2.1.pdf =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Rich Dobson Email r.j.dobson-at-qmul.ac.uk =head1 CONTRIBUTORS Jason Stajich, jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::IO::phase; use vars qw($FieldDelim $AlleleDelim $NoHeader); use strict; ($FieldDelim, $AlleleDelim, $NoHeader) = (' ', '\s+', 1); use Bio::PopGen::Individual; use Bio::PopGen::Population; use Bio::PopGen::Genotype; use base qw(Bio::PopGen::IO); =head2 new Title : new Usage : my $obj = Bio::PopGen::IO::hapmap->new(); Function: Builds a new Bio::PopGen::IO::hapmap object Returns : an instance of Bio::PopGen::IO::hapmap Args : [optional, these are the current defaults] -field_delimiter => ' ' -allele_delimiter=> '\s+' -no_header => 0, =cut sub _initialize { my($self, @args) = @_; $Bio::PopGen::Genotype::BlankAlleles=''; my ($fieldsep,$all_sep, $noheader) = $self->_rearrange([qw(FIELD_DELIMITER ALLELE_DELIMITER NO_HEADER)],@args); $self->flag('no_header', defined $noheader ? $noheader : $NoHeader); $self->flag('field_delimiter',defined $fieldsep ? $fieldsep : $FieldDelim); $self->flag('allele_delimiter',defined $all_sep ? $all_sep : $AlleleDelim); $self->{'_header'} = undef; return 1; } =head2 flag Title : flag Usage : $obj->flag($flagname,$newval) Function: Get/Set the flag value Returns : value of a flag (a boolean) Args : A flag name, currently we expect 'no_header', 'field_delimiter', or 'allele_delimiter' on set, new value (a boolean or undef, optional) =cut sub flag { my $self = shift; my $fieldname = shift; return unless defined $fieldname; return $self->{'_flag'}->{$fieldname} = shift if @_; return $self->{'_flag'}->{$fieldname}; } =head2 next_individual Title : next_individual Usage : my $ind = $popgenio->next_individual; Function: Retrieve the next individual from a dataset Returns : L object Args : none =cut sub next_individual { my ($self) = @_; my ($sam,@marker_results,$number_of_ids,$number_of_markers, $marker_positions,$micro_snp); while( defined( $_ = $self->_readline) ) { chomp; next if( /^\s+$/ || ! length($_) ); last; } return unless defined $_; if( $self->flag('no_header') || defined $self->{'_header'} ) { ####### sometimes there is some marker info at the start of a phase input file ####### we collect it in the next few lines if there is. Should this info be held in a marker object? if(!$self->{'_count'} && /^\s*\d+$/){ $self->flag('number_of_ids',$_); #print "number_of_ids : $number_of_ids\n"; $self->{'_count'}++; return $self->next_individual; } elsif($self->{'_count'} == 1 && /^\s*\d+$/){ $self->flag('number_of_markers',$_); #print "number_of_markers : $number_of_markers\n"; $self->{'_count'}++; return $self->next_individual; } elsif($self->{'_count'} == 2 && /^\s*P\s\d/){ $self->flag('marker_positions',$_); #print "marker_position : $marker_positions\n"; $self->{'_count'}++; return $self->next_individual; } elsif($self->{'_count'} == 3 && /^\s*(M|S)+\s*$/i){ $self->flag('micro_snp',$_); #print "microsat or snp : $micro_snp\n"; $self->{'_count'}++; return $self->next_individual; } elsif(/^\s*\#/){ ($self->{'_sam'}) = /^\s*\#(.+)/; #print "sample : $self->{'_sam'}\n"; $self->{'_count'}++; return $self->next_individual; } else { if( $self->{'_row1'} ) { # if we are looking at the 2nd row of alleles for this id @{$self->{'_second_row'}} = split($self->flag('field_delimiter'),$_); for my $i(0 .. $#{$self->{'_first_row'}}){ push(@{$self->{'_marker_results'}}, $self->{'_first_row'}->[$i]. $self->flag('field_delimiter'). $self->{'_second_row'}->[$i]); } $self->{'_row1'} = 0; } else { # if we are looking at the first row of alleles for this id @{$self->{'_marker_results'}} = (); @{$self->{'_first_row'}} = split($self->flag('field_delimiter'),$_); $self->{'_row1'} = 1; return $self->next_individual; } } my $i = 1; foreach my $m ( @{$self->{'_marker_results'}} ) { $m =~ s/^\s+//; $m =~ s/\s+$//; my $markername; if( defined($self->flag('marker_positions')) ) { $markername = (split($self->flag('field_delimiter'), $self->flag('marker_positions')))[$i]; } elsif( defined $self->{'_header'} ) { $markername = $self->{'_header'}->[$i] || "$i"; } else { $markername = "$i"; } my $markertype; if( defined($self->flag('marker_positions')) ) { $markertype = (split('', $self->flag('micro_snp')))[$i-1]; } else { $markertype = "S"; } $self->debug( "markername is $markername alleles are $m\n"); my @alleles = split($self->flag('allele_delimiter'), $m); $m = Bio::PopGen::Genotype->new(-alleles =>\@alleles, -marker_name => $markername, -marker_type => $markertype, -individual_id => $self->{'_sam'}); $i++; } return Bio::PopGen::Individual->new(-unique_id => $self->{'_sam'}, -genotypes =>\@{$self->{'_marker_results'}}, ); } else { $self->{'_header'} = [split($self->flag('field_delimiter'),$_)]; return $self->next_individual; # rerun loop again } return; } =head2 next_population Title : next_population Usage : my $ind = $popgenio->next_population; Function: Retrieve the next population from a dataset Returns : L object Args : none Note : Many implementation will not implement this =cut sub next_population{ my ($self) = @_; my @inds; while( my $ind = $self->next_individual ) { push @inds, $ind; } Bio::PopGen::Population->new(-individuals => \@inds); } =head2 write_individual Title : write_individual Usage : $popgenio->write_individual($ind); Function: Write an individual out in the file format Returns : none Args : L object(s) =cut sub write_individual { my ($self,@inds) = @_; my $fielddelim = $self->flag('field_delimiter'); my $alleledelim = $self->flag('allele_delimiter'); # For now capture print_header flag from @inds my $header = 1; $header = pop(@inds) if($inds[-1] =~ m/^[01]$/); foreach my $ind ( @inds ) { if (! ref($ind) || ! $ind->isa('Bio::PopGen::IndividualI') ) { $self->warn("Cannot write an object that is not a Bio::PopGen::IndividualI object ($ind)"); next; } # sort lexically until we have a better way to insure a consistent order my @marker_names = sort $ind->get_marker_names; if ($header) { my $n_markers = scalar(@marker_names); $self->_print( "1\n"); $self->_print( $n_markers, "\n"); if( $self->flag('no_header') && ! $self->flag('header_written') ) { $self->_print(join($fielddelim, ('P', @marker_names)), "\n"); $self->flag('header_written',1); } foreach my $geno ($ind->get_Genotypes()) { $self->_print($geno->marker_type); } $self->_print("\n"); } my(@row1,@row2); for (@marker_names){ my $geno = $ind->get_Genotypes(-marker => $_); my @alleles = $geno->get_Alleles(1); push(@row1,$alleles[0]); push(@row2,$alleles[1]); } $self->_print("#",$ind->unique_id,"\n", join($fielddelim,@row1),"\n", join($fielddelim,@row2),"\n"); } } =head2 write_population Title : write_population Usage : $popgenio->write_population($pop); Function: Write a population out in the file format Returns : none Args : L object(s) Note : Many implementation will not implement this =cut sub write_population { my ($self,@pops) = @_; my $fielddelim = $self->flag('field_delimiter'); my $alleledelim = $self->flag('allele_delimiter'); foreach my $pop ( @pops ) { if (! ref($pop) || ! $pop->isa('Bio::PopGen::PopulationI') ) { $self->warn("Cannot write an object that is not a Bio::PopGen::PopulationI object"); next; } # sort lexically until we have a better way to insure a consistent order my @marker_names = sort $pop->get_marker_names; my $n_markers = scalar(@marker_names); $self->_print( $pop->get_number_individuals, "\n"); $self->_print( $n_markers, "\n"); if( $self->flag('no_header') && ! $self->flag('header_written') ) { $self->_print( join($fielddelim, ('P', @marker_names)), "\n"); $self->flag('header_written',1); } foreach (@marker_names) { $self->_print(($pop->get_Genotypes($_))[0]->marker_type); } $self->_print("\n"); $self->write_individual( $pop->get_Individuals, 0 ); } } 1; BioPerl-1.007002/Bio/PopGen/IO/prettybase.pm000444000766000024 1760613155576320 20475 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::IO::prettybase # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::IO::prettybase - Extract individual allele data from PrettyBase format =head1 SYNOPSIS Do not use directly, use through the Bio::PopGen::IO driver =head1 DESCRIPTION This object will parse comma delimited PrettyBase output. PrettyBase is defined by the SeattleSNPs http://pga.gs.washington.edu/ This is expected to be tab delimited (you can vary with the field_delimiter flag SITE SAMPLE ALLELE1 ALLELE2 There are 2 initialization parameters, the delimiter (-field_delimiter) [default 'tab'] and a boolean -no_header which specifies if there is no header line to read in. All lines starting with '#' will be skipped =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Matthew Hahn, matthew.hahn-at-duke.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::IO::prettybase; use vars qw($FieldDelim $Header); use strict; ($FieldDelim,$Header) =( '\t',0); use Bio::PopGen::Individual; use Bio::PopGen::Population; use Bio::PopGen::Genotype; use base qw(Bio::PopGen::IO); =head2 new Title : new Usage : my $obj = Bio::PopGen::IO::prettybase->new(); Function: Builds a new Bio::PopGen::IO::prettybase object Returns : an instance of Bio::PopGen::IO::prettybase Args : -field_delimiter => a field delimiter character or regexp (default is /\t/ ) -header => boolean if the file will have a header and parser should skip first line in the file (default is false) -convert_indel_states => convert alleles which are longer than one character to an 'I' meaning insert state, and alleles which are '-' to a delete state. (default is false) =cut sub _initialize { my($self, @args) = @_; my ($fieldsep, $conv_indels, $header) = $self->_rearrange([qw(FIELD_DELIMITER CONVERT_INDEL_STATES HEADER)],@args); $self->flag('header', defined $header ? $header : $Header); $self->flag('field_delimiter',defined $fieldsep ? $fieldsep : $FieldDelim); $self->{'_header'} = undef; $self->{'_parsed_individiuals'} = []; $self->{'_parsed'} = 0; $self->flag('convert_indel',$conv_indels || 0); return 1; } =head2 flag Title : flag Usage : $obj->flag($flagname,$newval) Function: Get/Set the flag value Returns : value of a flag (a boolean) Args : A flag name, currently we expect 'header', 'field_delimiter', or 'allele_delimiter' on set, new value (a boolean or undef, optional) =cut sub flag{ my $self = shift; my $fieldname = shift; return unless defined $fieldname; return $self->{'_flag'}->{$fieldname} = shift if @_; return $self->{'_flag'}->{$fieldname}; } =head2 next_individual Title : next_individual Usage : my $ind = $popgenio->next_individual; Function: Retrieve the next individual from a dataset Returns : Bio::PopGen::IndividualI object Args : none =cut sub next_individual { my ($self) = @_; unless( $self->{'_parsed'} ) { $self->_parse_prettybase; } return $self->{'_parsed_individiuals'}->[$self->{'_iterator'}++]; } =head2 next_population Title : next_population Usage : my $ind = $popgenio->next_population; Function: Retrieve the next population from a dataset Returns : Bio::PopGen::PopulationI object Args : none Note : Many implementation will not implement this =cut # Plan is to just return the whole dataset as a single population by # default I think - people would then have each population in a separate # file. sub next_population{ my ($self) = @_; my @inds; while( my $ind = $self->next_individual ) { push @inds, $ind; } return unless @inds; Bio::PopGen::Population->new(-individuals => \@inds); } sub _parse_prettybase { my $self = shift; my %inds; my $convert_indels = $self->flag('convert_indel'); while( defined( $_ = $self->_readline) ) { next if( /^\s*\#/ || /^\s+$/ || ! length($_) ); my ($site,$sample,@alleles) = split($self->flag('field_delimiter'),$_); if( ! defined $sample ) { warn("sample id is undefined for $_"); next; } for my $allele ( @alleles ) { $allele =~ s/^\s+//; $allele =~ s/\s+$//; if( $convert_indels ) { if( length($allele) > 1 ) { # we have an insert state $allele = 'I'; } elsif( $allele eq '-' ) { # have a delete state $allele = 'D'; } } } my $g = Bio::PopGen::Genotype->new(-alleles => \@alleles, -marker_name => $site, -individual_id=> $sample); if( ! defined $inds{$sample} ) { $inds{$sample} = Bio::PopGen::Individual->new(-unique_id => $sample); } $inds{$sample}->add_Genotype($g); } $self->{'_parsed_individiuals'} = [ values %inds ]; $self->{'_parsed'} = 1; return; } =head2 write_individual Title : write_individual Usage : $popgenio->write_individual($ind); Function: Write an individual out in the file format Returns : none Args : L object(s) =cut sub write_individual{ my ($self,@inds) = @_; foreach my $ind ( @inds ) { if (! ref($ind) || ! $ind->isa('Bio::PopGen::IndividualI') ) { $self->warn("Cannot write an object that is not a Bio::PopGen::IndividualI object"); next; } foreach my $marker ( $ind->get_marker_names ) { my $g = $ind->get_Genotypes(-marker=> $marker); next unless defined $g; $self->_print( join("\t", $marker, $ind->unique_id, $g->get_Alleles), "\n"); } } } =head2 write_population Title : write_population Usage : $popgenio->write_population($pop); Function: Write a population out in the file format Returns : none Args : L object(s) Note : Many implementation will not implement this =cut sub write_population{ my ($self,@pops) = @_; foreach my $pop ( @pops ) { if (! ref($pop) || ! $pop->isa('Bio::PopGen::PopulationI') ) { $self->warn("Cannot write an object that is not a Bio::PopGen::PopulationI object"); next; } my @mnames = $pop->get_marker_names; foreach my $ind ( $pop->get_Individuals ) { if (! ref($ind) || ! $ind->isa('Bio::PopGen::IndividualI') ) { $self->warn("Cannot write an object that is not a Bio::PopGen::IndividualI object"); next; } foreach my $marker ( @mnames ) { my $g = $ind->get_Genotypes(-marker=> $marker); next unless defined $g; $self->_print( join("\t", $marker, $ind->unique_id, $g->get_Alleles), "\n"); } } } } 1; BioPerl-1.007002/Bio/PopGen/Simulation000755000766000024 013155576320 17403 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/PopGen/Simulation/Coalescent.pm000444000766000024 2642613155576320 22210 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::Simulation::Coalescent # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::Simulation::Coalescent - A Coalescent simulation factory =head1 SYNOPSIS use Bio::PopGen::Simulation::Coalescent; my @taxonnames = qw(SpeciesA SpeciesB SpeciesC SpeciesD); my $sim1 = Bio::PopGen::Simulation::Coalescent->new(-samples => \@taxonnames); my $tree = $sim1->next_tree; # add 20 mutations randomly to the tree $sim1->add_Mutations($tree,20); # or for anonymous samples my $sim2 = Bio::PopGen::Simulation::Coalescent->new( -sample_size => 6, -maxcount => 50); my $tree2 = $sim2->next_tree; # add 20 mutations randomly to the tree $sim2->add_Mutations($tree2,20); =head1 DESCRIPTION Builds a random tree every time next_tree is called or up to -maxcount times with branch lengths and provides the ability to randomly add mutations onto the tree with a probabilty proportional to the branch lengths. This algorithm is based on the make_tree algorithm from Richard Hudson 1990. Hudson, R. R. 1990. Gene genealogies and the coalescent process. Pp. 1-44 in D. Futuyma and J. Antonovics, eds. Oxford surveys in evolutionary biology. Vol. 7. Oxford University Press, New York. This module was previously named Bio::Tree::RandomTree =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich, Matthew Hahn Email jason-at-bioperl-dot-org Email matthew-dot-hahn-at-duke-dot-edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::Simulation::Coalescent; use vars qw($PRECISION_DIGITS); use strict; $PRECISION_DIGITS = 3; # Precision for the branchlength use Bio::Tree::AlleleNode; use Bio::PopGen::Genotype; use Bio::Tree::Tree; use base qw(Bio::Root::Root Bio::Factory::TreeFactoryI); =head2 new Title : new Usage : my $obj = Bio::PopGen::Simulation::Coalescent->new(); Function: Builds a new Bio::PopGen::Simulation::Coalescent object Returns : an instance of Bio::PopGen::Simulation::Coalescent Args : -samples => arrayref of sample names OR -sample_size=> number of samples (samps will get a systematic name) -maxcount => [optional] maximum number of trees to provide =cut sub new{ my ($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_treecounter'} = 0; $self->{'_maxcount'} = 0; my ($maxcount, $samps,$samplesize ) = $self->_rearrange([qw(MAXCOUNT SAMPLES SAMPLE_SIZE)], @args); my @samples; if( ! defined $samps ) { if( ! defined $samplesize || $samplesize <= 0 ) { $self->throw("Must specify a valid samplesize if parameter -SAMPLE is not specified (sampsize is $samplesize)"); } foreach ( 1..$samplesize ) { push @samples, "Samp$_"; } } else { if( ref($samps) !~ /ARRAY/i ) { $self->throw("Must specify a valid ARRAY reference to the parameter -SAMPLES, did you forget a leading '\\'?"); } @samples = @$samps; } $self->samples(\@samples); $self->sample_size(scalar @samples); defined $maxcount && $self->maxcount($maxcount); return $self; } =head2 next_tree Title : next_tree Usage : my $tree = $factory->next_tree Function: Returns a random tree based on the initialized number of nodes NOTE: if maxcount is not specified on initialization or set to a valid integer, subsequent calls to next_tree will continue to return random trees and never return undef Returns : Bio::Tree::TreeI object Args : none =cut sub next_tree{ my ($self) = @_; # If maxcount is set to something non-zero then next tree will # continue to return valid trees until maxcount is reached # otherwise will always return trees return if( $self->maxcount && $self->{'_treecounter'}++ >= $self->maxcount ); my $size = $self->sample_size; my $in; my @tree = (); my @list = (); for($in=0;$in < 2*$size -1; $in++ ) { push @tree, { 'nodenum' => "Node$in" }; } # in C we would have 2 arrays # an array of nodes (tree) # and array of pointers to these nodes (list) # and we just shuffle the list items to do the # tree topology generation # instead in perl, we will have a list of hashes (nodes) called @tree # and a list of integers representing the indexes in tree called @list for($in=0;$in < $size;$in++) { $tree[$in]->{'time'} = 0; $tree[$in]->{'desc1'} = undef; $tree[$in]->{'desc2'} = undef; push @list, $in; } my $t=0; # generate times for the nodes for($in = $size; $in > 1; $in-- ) { $t+= -2.0 * log(1 - $self->random(1)) / ( $in * ($in-1) ); $tree[2 * $size - $in]->{'time'} =$t; } # topology generation for ($in = $size; $in > 1; $in-- ) { my $pick = int $self->random($in); my $nodeindex = $list[$pick]; my $swap = 2 * $size - $in; $tree[$swap]->{'desc1'} = $nodeindex; $list[$pick] = $list[$in-1]; $pick = int rand($in - 1); $nodeindex = $list[$pick]; $tree[$swap]->{'desc2'} = $nodeindex; $list[$pick] = $swap; } # Let's convert the hashes into nodes my @nodes = (); foreach my $n ( @tree ) { push @nodes, Bio::Tree::AlleleNode->new(-id => $n->{'nodenum'}, -branch_length => $n->{'time'}); } my $ct = 0; foreach my $node ( @nodes ) { my $n = $tree[$ct++]; if( defined $n->{'desc1'} ) { $node->add_Descendent($nodes[$n->{'desc1'}]); } if( defined $n->{'desc2'} ) { $node->add_Descendent($nodes[$n->{'desc2'}]); } } my $T = Bio::Tree::Tree->new(-root => pop @nodes ); return $T; } =head2 add_Mutations Title : add_Mutations Usage : $factory->add_Mutations($tree, $mutcount); Function: Adds mutations to a tree via a random process weighted by branch length (it is a poisson distribution as part of a coalescent process) Returns : none Args : $tree - Bio::Tree::TreeI $nummut - number of mutations $precision - optional # of digits for precision =cut sub add_Mutations{ my ($self,$tree, $nummut,$precision) = @_; $precision ||= $PRECISION_DIGITS; $precision = 10**$precision; my @branches; my @lens; my $branchlen = 0; my $last = 0; my @nodes = $tree->get_nodes(); my $i = 0; # Jason's somewhat simplistics way of doing a poission # distribution for a fixed number of mutations # build an array and put the node number in a slot # representing the branch to put a mutation on # but weight the number of slots per branch by the # length of the branch ( ancestor's time - node time) foreach my $node ( @nodes ) { if( $node->ancestor ) { my $len = int ( ($node->ancestor->branch_length - $node->branch_length) * $precision); if ( $len > 0 ) { for( my $j =0;$j < $len;$j++) { push @branches, $i; } $last += $len; } $branchlen += $len; } if( ! $node->isa('Bio::Tree::AlleleNode') ) { bless $node, 'Bio::Tree::AlleleNode'; # rebless it to the right node } # This let's us reset the stored genotypes so we can keep reusing the # same tree topology, but throw down mutations multiple times $node->reset_Genotypes; $i++; } # sanity check $self->throw("branch len is $branchlen arraylen is $last") unless ( $branchlen == $last ); my @mutations; for( my $j = 0; $j < $nummut; $j++) { my $index = int(rand($branchlen)); my $branch = $branches[$index]; # We're using an infinite sites model so every new # mutation is a new site my $g = Bio::PopGen::Genotype->new(-marker_name => "Mutation$j", -alleles => [1]); $nodes[$branch]->add_Genotype($g); push @mutations, "Mutation$j"; # Let's add this mutation to all the children (push it down # the branches to the tips) foreach my $child ( $nodes[$branch]->get_all_Descendents ) { $child->add_Genotype($g); } } # Insure that everyone who doesn't have the mutation # has the ancestral state, which is '0' foreach my $node ( @nodes ) { foreach my $m ( @mutations ) { if( ! $node->has_Marker($m) ) { my $emptyg = Bio::PopGen::Genotype->new(-marker_name => $m, -alleles => [0]); $node->add_Genotype($emptyg); } } } } =head2 maxcount Title : maxcount Usage : $obj->maxcount($newval) Function: Returns : Maxcount value Args : newvalue (optional) =cut sub maxcount{ my ($self,$value) = @_; if( defined $value) { if( $value =~ /^(\d+)/ ) { $self->{'maxcount'} = $1; } else { $self->warn("Must specify a valid Positive integer to maxcount"); $self->{'maxcount'} = 0; } } return $self->{'_maxcount'}; } =head2 samples Title : samples Usage : $obj->samples($newval) Function: Example : Returns : value of samples Args : newvalue (optional) =cut sub samples{ my ($self,$value) = @_; if( defined $value) { if( ref($value) !~ /ARRAY/i ) { $self->warn("Must specify a valid array ref to the method 'samples'"); $value = []; } $self->{'samples'} = $value; } return $self->{'samples'}; } =head2 sample_size Title : sample_size Usage : $obj->sample_size($newval) Function: Example : Returns : value of sample_size Args : newvalue (optional) =cut sub sample_size{ my ($self,$value) = @_; if( defined $value) { $self->{'sample_size'} = $value; } return $self->{'sample_size'}; } =head2 random Title : random Usage : my $rfloat = $node->random($size) Function: Generates a random number between 0 and $size This is abstracted so that someone can override and provide their own special RNG. This is expected to be a uniform RNG. Returns : Floating point random Args : $maximum size for random number (defaults to 1) =cut sub random{ my ($self,$max) = @_; return rand($max); } 1; BioPerl-1.007002/Bio/PopGen/Simulation/GeneticDrift.pm000444000766000024 2035113155576320 22466 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::PopGen::Simulation::GeneticDrift # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::Simulation::GeneticDrift - A simple genetic drift simulation =head1 SYNOPSIS use Bio::PopGen::Simulation::GeneticDrift; my $sim = Bio::PopGen::Simulation::GeneticDrift->new(-popsize => 40, -alleles => {A => 0.2, B => 0.8}); for(my $i =0 ;$i < 10; $i++ ) { my %f = $sim->next_generation; # get the freqs for each generation } for(my $i =0 ;$i < 10; $i++ ) { # get the allele freqs as part of a Bio::PopGen::Population object my $pop = $sim->next_generation('population'); } =head1 DESCRIPTION A very simple 1 locus multi-allele random drift module, start with an initial set of allele frequency and simulate what happens over time. This isn't really useful for anything in particular yet but will be built upon. See Gillespie JH. (1998) "Population Genetics: a Concise guide." The Johns Hopkins University Press, Baltimore, USA. pp.19-47. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::Simulation::GeneticDrift; use strict; use Bio::PopGen::Population; use base qw(Bio::Root::Root); =head2 new Title : new Usage : my $obj = Bio::PopGen::Simulation::GeneticDrift->new(); Function: Builds a new Bio::PopGen::Simulation::GeneticDrift object Returns : an instance of Bio::PopGen::Simulation::GeneticDrift Args : -popsize => starting N -haploid => boolean if we should simulate haploids -alleles => arrayref of the allele names OR -population => L object to initialize from some previously defined Population object (or result from a previous simulation) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($population, $popsize, $haploid, $alleles) = $self->_rearrange([qw(POPULATION POPSIZE HAPLOID ALLELES)],@args); if( defined $population && ref($population) && $population->isa('Bio::PopGen::PopulationI') ) { $self->population_size($population->get_number_individuals || $popsize); my %f = $population->get_Allele_Frequencies; while( my ($allele,$freq) = each %f ) { $self->add_Allele_Frequency($allele,$freq); } } else { $self->population_size($popsize); if( ! defined $alleles || ref($alleles) !~ /HASH/i ) { $self->throw("Must provide a valid set of initial allele frequencies to $class as an hashref"); } while( my ($allele,$freq) = each %$alleles ) { $self->add_Allele_Frequency($allele,$freq); } } unless( $self->validate_Frequencies ) { $self->throw("You specified allele frequencies which summed to more than 1"); } return $self; } =head2 next_generation Title : next_generation Usage : my %generation = $sim->next_generation Function: Get the next generation of allele frequencies based on the current generation Returns : Hash of allele frequencies Args : 'allelefreqs' or 'population' to get back a hash of allele frequencies (default) OR a L object =cut sub next_generation{ my ($self,$rettype) = @_; my %initial = $self->get_Allele_Frequencies; my $popsize = $self->population_size || $self->throw("Need to have set a valid population size when running the simulation"); # we're going to construct a mapping of the rational space from 0->1 # which will map to a particular allele and be proportional to it # frequency my ($last,@mapping) = (0); # we'll make ranges that cover from >= left and < right in terms of the # order doesn't matter - 'distance' does # range that we're going to try and match # since rand() goes from 0 up to 1 (not including 1) foreach my $a ( keys %initial ) { push @mapping, [$last,$initial{$a}+$last,$a]; $last += $initial{$a}; } my %f; for( my $i =0; $i < $popsize; $i++ ) { my $rand = rand(1); foreach my $val ( @mapping ) { if( $rand >= $val->[0] && $rand < $val->[1] ) { $f{$val->[2]}++; last; } } } foreach my $f ( values %f ) { $f /= $popsize; } %{$self->{'_allele_freqs'}} = %f; if( defined $rettype && $rettype =~ /population/i) { return Bio::PopGen::Poulation->new(-frequencies => \%f); } else { return %f; } } =head2 population_size Title : population_size Usage : $obj->population_size($newval) Function: Example : Returns : value of population_size (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub population_size{ my $self = shift; return $self->{'_population_size'} = shift if @_; return $self->{'_population_size'}; } =head2 set_Frequencies_Equivalent Title : set_Frequencies_Equivalent Usage : $sim->set_Frequencies_Equivalent Function: Reset the allele frequencies so they are all even Returns : none Args : none =cut sub set_Frequencies_Equivalent{ my ($self) = @_; my @alleles = keys %{$self->{'_allele_freqs'}}; my $eqfreq = 1 / scalar @alleles; for ( @alleles ) { $self->{'_allele_freqs'}->{$_} = $eqfreq } return; } =head2 get_Allele_Frequencies Title : get_Allele_Frequencies Usage : my %allele_freqs = $marker->get_Allele_Frequencies; Function: Get the alleles and their frequency (set relative to a given population - you may want to create different markers with the same name for different populations with this current implementation Returns : Associative array where keys are the names of the alleles Args : none =cut sub get_Allele_Frequencies{ return %{$_[0]->{'_allele_freqs'}}; } =head2 add_Allele_Frequency Title : add_Allele_Frequency Usage : $marker->add_Allele_Frequency($allele,$freq) Function: Adds an allele frequency Returns : None Args : $allele - allele name $freq - frequency value =cut sub add_Allele_Frequency{ my ($self,$allele,$freq) = @_; $self->{'_allele_freqs'}->{$allele} = $freq; } =head2 reset_alleles Title : reset_alleles Usage : $marker->reset_alleles(); Function: Reset the alleles for a marker Returns : None Args : None =cut sub reset_alleles{ my ($self) = @_; $self->{'_allele_freqs'} = {}; } =head2 validate_Frequencies Title : validate_Frequencies Usage : if( $sim->validate_Frequencies) {} Function: Sanity checker that allele frequencies sum to 1 or less Returns : boolean Args : -strict => 1 boolean if you want to insure that sum of freqs is 1 =cut sub validate_Frequencies{ my ($self,@args) = @_; my ($strict) = $self->_rearrange([qw(STRICT)], @args); my $sum = 0; my %freq = $self->get_Allele_Frequencies; foreach my $f ( values %freq ) { $sum += $f; } return ($strict) ? $sum == 1 : $sum <= 1; } 1; BioPerl-1.007002/Bio/Restriction000755000766000024 013155576320 16374 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Restriction/Analysis.pm000444000766000024 12031013155576320 20707 0ustar00cjfieldsstaff000000000000# # BioPerl module Bio::Restriction::Analysis # # Please direct questions and support issues to # # Cared for by Rob Edwards # # You may distribute this module under the same terms as perl itself ## POD Documentation: =head1 NAME Bio::Restriction::Analysis - cutting sequences with restriction enzymes =head1 SYNOPSIS # analyze a DNA sequence for restriction enzymes use Bio::Restriction::Analysis; use Bio::PrimarySeq; use Data::Dumper; # get a DNA sequence from somewhere my $seq = Bio::PrimarySeq->new (-seq =>'AGCTTAATTCATTAGCTCTGACTGCAACGGGCAATATGTCTC', -primary_id => 'synopsis', -molecule => 'dna'); # now start an analysis. # this is using the default set of enzymes my $ra = Bio::Restriction::Analysis->new(-seq=>$seq); # find unique cutters. This returns a # Bio::Restriction::EnzymeCollection object my $enzymes = $ra->unique_cutters; print "Unique cutters: ", join (', ', map {$_->name} $enzymes->unique_cutters), "\n"; # AluI is one them. Where does it cut? # This is will return an array of the sequence strings my $enz = 'AluI'; my @frags = $ra->fragments($enz); # how big are the fragments? print "AluI fragment lengths: ", join(' & ', map {length $_} @frags), "\n"; # You can also bypass fragments and call sizes directly: # to see all the fragment sizes print "All sizes: ", join " ", $ra->sizes($enz), "\n"; # to see all the fragment sizes sorted by size like on a gel print "All sizes, sorted ", join (" ", $ra->sizes($enz, 0, 1)), "\n"; # how many times does each enzyme cut my $cuts = $ra->cuts_by_enzyme('BamHI'); print "BamHI cuts $cuts times\n"; # How many enzymes do not cut at all? print "There are ", scalar $ra->zero_cutters->each_enzyme, " enzymes that do not cut\n"; # what about enzymes that cut twice? my $two_cutters = $ra->cutters(2); print join (" ", map {$_->name} $two_cutters->each_enzyme), " cut the sequence twice\n"; # what are all the enzymes that cut, and how often do they cut printf "\n%-10s%s\n", 'Enzyme', 'Number of Cuts'; my $all_cutters = $ra->cutters; map { printf "%-10s%s\n", $_->name, $ra->cuts_by_enzyme($_->name) } $all_cutters->each_enzyme; # Finally, we can interact the restriction enzyme object by # retrieving it from the collection object see the docs for # Bio::Restriction::Enzyme.pm my $enzobj = $enzymes->get_enzyme($enz); =head1 DESCRIPTION Bio::Restriction::Analysis describes the results of cutting a DNA sequence with restriction enzymes. To use this module you can pass a sequence object and optionally a Bio::Restriction::EnzymeCollection that contains the enzyme(s) to cut the sequences with. There is a default set of enzymes that will be loaded if you do not pass in a Bio::Restriction::EnzymeCollection. To cut a sequence, set up a Restriction::Analysis object with a sequence like this: use Bio::Restriction::Analysis; my $ra = Bio::Restriction::Analysis->new(-seq=>$seqobj); or my $ra = Bio::Restriction::Analysis->new (-seq=>$seqobj, -enzymes=>$enzs); Then, to get the fragments for a particular enzyme use this: @fragments = $ra->fragments('EcoRI'); Note that the naming of restriction enzymes is that the last numbers are usually Roman numbers (I, II, III, etc). You may want to use something like this: # get a reference to an array of unique (single) cutters $singles = $re->unique_cutters; foreach my $enz ($singles->each_enzyme) { @fragments = $re->fragments($enz); ... do something here ... } Note that if your sequence is circular, the first and last fragment will be joined so that they are the appropriate length and sequence for further analysis. This fragment will also be checked for cuts by the enzyme(s). However, this will change the start of the sequence! There are two separate algorithms used depending on whether your enzyme has ambiguity. The non-ambiguous algorithm is a lot faster, and if you are using very large sequences you should try and use this algorithm. If you have a large sequence (e.g. genome) and want to use ambgiuous enzymes you may want to make separate Bio::Restriction::Enzyme objects for each of the possible alternatives and make sure that you do not set is_ambiguous! This version should correctly deal with overlapping cut sites in both ambiguous and non-ambiguous enzymes. I have tried to write this module with speed and memory in mind so that it can be effectively used for large (e.g. genome sized) sequence. This module only stores the cut positions internally, and calculates everything else on an as-needed basis. Therefore when you call fragment_maps (for example), there may be another delay while these are generated. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Rob Edwards, redwards@utmem.edu, Steve Chervitz, sac@bioperl.org =head1 CONTRIBUTORS Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Mark A. Jensen, maj-at-fortinbras-dot-us =head1 COPYRIGHT Copyright (c) 2003 Rob Edwards. Some of this work is Copyright (c) 1997-2002 Steve A. Chervitz. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 SEE ALSO L, L =head1 APPENDIX Methods beginning with a leading underscore are considered private and are intended for internal use by this module. They are not considered part of the public interface and are described here for documentation purposes only. =cut package Bio::Restriction::Analysis; use Bio::Restriction::EnzymeCollection; use strict; use Data::Dumper; use base qw(Bio::Root::Root); use Scalar::Util qw(blessed); =head1 new Title : new Function : Initializes the restriction enzyme object Returns : The Restriction::Analysis object Arguments : $re_anal->new(-seq=$seqobj, -enzymes=>Restriction::EnzymeCollection object) -seq requires a Bio::PrimarySeq object -enzymes is optional. If omitted it will use the default set of enzymes This is the place to start. Pass in a sequence, and you will be able to get the fragments back out. Several other things are available like the number of zero cutters or single cutters. =cut sub new { my($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($seq,$enzymes) = $self->_rearrange([qw( SEQ ENZYMES )], @args); $seq && $self->seq($seq); $enzymes ? $self->enzymes($enzymes) : ($self->{'_enzymes'} = Bio::Restriction::EnzymeCollection->new ); # keep track of status $self->{'_cut'} = 0; # left these here because we want to reforce a _cut if someone # just calls new $self->{maximum_cuts} = 0; $self->{'_number_of_cuts_by_enzyme'} = {}; $self->{'_number_of_cuts_by_cuts'} = {}; $self->{'_fragments'} = {}; $self->{'_cut_positions'} = {}; # cut position is the real position $self->{'_frag_map_list'} = {}; return $self; } =head1 Methods to set parameters =cut =head2 seq Title : seq Usage : $ranalysis->seq($newval); Function : get/set method for the sequence to be cut Example : $re->seq($seq); Returns : value of seq Args : A Bio::PrimarySeqI dna object (optional) =cut sub seq { my $self = shift; if (@_) { my $seq = shift; $self->throw('Need a sequence object ['. ref $seq. ']') unless $seq->isa('Bio::PrimarySeqI'); $self->throw('Need a DNA sequence object ['. $seq->alphabet. ']') unless $seq->alphabet eq 'dna'; $self->{'_seq'} = $seq; $self->{'_cut'} = 0; } return $self->{'_seq'}; } =head2 enzymes Title : enzymes Usage : $re->enzymes($newval) Function : gets/Set the restriction enzyme enzymes Example : $re->enzymes('EcoRI') Returns : reference to the collection Args : an array of Bio::Restriction::EnzymeCollection and/or Bio::Restriction::Enzyme objects The default object for this method is Bio::Restriction::EnzymeCollection. However, you can also pass it a list of Bio::Restriction::Enzyme objects - even mixed with Collection objects. They will all be stored into one collection. =cut sub enzymes { my $self = shift; if (@_) { $self->{'_enzymes'} = Bio::Restriction::EnzymeCollection->new (-empty => 1) unless $self->{'_enzymes'}; $self->{'_enzymes'}->enzymes(@_); $self->{'_cut'} = 0; } return $self->{'_enzymes'}; } =head1 Perform the analysis =cut =head2 cut Title : cut Usage : $re->cut() Function : Cut the sequence with the enzymes Example : $re->cut(); $re->cut('single'); or $re->cut('multiple', $enzymecollection); Returns : $self Args : 'single' (optional), 'multiple' with enzyme collection. An explicit cut method is needed to pass arguments to it. There are two varieties of cut. Single is the default, and need not be explicitly called. This cuts the sequence with each enzyme separately. Multiple cuts a sequence with more than one enzyme. You must pass it a Bio::Restriction::EnzymeCollection object of the set of enzymes that you want to use in the double digest. The results will be stored as an enzyme named "multiple_digest", so you can use all the retrieval methods to get the data. If you want to use the default setting there is no need to call cut directly. Every method in the class that needs output checks the object's internal status and recalculates the cuts if needed. Note: cut doesn't now re-initialize everything before figuring out cuts. This is so that you can do multiple digests, or add more data or whatever. You'll have to use new to reset everything. See also the comments in above about ambiguous and non-ambiguous sequences. =cut sub cut { my ($self, $opt, $ec) = @_; # for the moment I have left this as a separate routine so # the user calls cut rather than _cuts. This also initializes # some stuff we need to use. $self->throw("A sequence must be supplied") unless $self->seq; if ($opt && uc($opt) eq "MULTIPLE") { $self->throw("You must supply a separate enzyme collection for multiple digests") unless $ec; $self->_multiple_cuts($ec); # multiple digests } else { # reset some of the things that we save $self->{maximum_cuts} = 0; $self->{'_number_of_cuts_by_enzyme'} = {}; $self->{'_number_of_cuts_by_cuts'} = {}; $self->{'_fragments'} = {}; $self->{'_cut_positions'} = {}; # cut position is the real position $self->{'_frag_map_list'} = {}; $self->_cuts; } $self->{'_cut'} = 1; return $self; } =head2 multiple_digest Title : multiple_digest Function : perform a multiple digest on a sequence Returns : $self so you can go and get any of the other methods Arguments : An enzyme collection Multiple digests can use 1 or more enzymes, and the data is stored in as if it were an enzyme called multiple_digest. You can then retrieve information about multiple digests from any of the other methods. You can use this method in place of $re->cut('multiple', $enz_coll); =cut sub multiple_digest { my ($self, $ec)=@_; return $self->cut('multiple', $ec); } =head1 Query the results of the analysis =cut =head2 positions Title : positions Function : Retrieve the positions that an enzyme cuts at Returns : An array of the positions that an enzyme cuts at : or an empty array if the enzyme doesn't cut Arguments: An enzyme name to retrieve the positions for Comments : The cut occurs after the base specified. =cut sub positions { my ($self, $enz) = @_; $self->cut unless $self->{'_cut'}; $self->throw('no enzyme selected to get positions for') unless $enz; return defined $self->{'_cut_positions'}->{$enz} ? @{$self->{'_cut_positions'}->{$enz}} : (); } =head2 fragments Title : fragments Function : Retrieve the fragments that we cut Returns : An array of the fragments retrieved. Arguments: An enzyme name to retrieve the fragments for For example this code will retrieve the fragments for all enzymes that cut your sequence my $all_cutters = $analysis->cutters; foreach my $enz ($$all_cutters->each_enzyme}) { @fragments=$analysis->fragments($enz); } =cut sub fragments { my ($self, $enz) = @_; $self->cut unless $self->{'_cut'}; $self->throw('no enzyme selected to get fragments for') unless $enz; my @fragments; for ($self->fragment_maps($enz)) {push @fragments, $_->{seq}} return @fragments; } =head2 fragment_maps Title : fragment_maps Function : Retrieves fragment sequences with start and end points. Useful for feature construction. Returns : An array containing a hash reference for each fragment, containing the start point, end point and DNA sequence. The hash keys are 'start', 'end' and 'seq'. Returns an empty array if not defined. Arguments : An enzyme name, enzyme object, or enzyme collection to retrieve the fragments for. If passes an enzyme collection it will return the result of a multiple digest. This : will also cause the special enzyme 'multiple_digest' to be created so you can get : other information about this multiple digest. (TMTOWTDI). There is a minor problem with this and $self-Efragments that I haven't got a good answer for (at the moment). If the sequence is not cut, do we return undef, or the whole sequence? For linear fragments it would be good to return the whole sequence. For circular fragments I am not sure. At the moment it returns the whole sequence with start of 1 and end of length of the sequence. For example: use Bio::Restriction::Analysis; use Bio::Restriction::EnzymeCollection; use Bio::PrimarySeq; my $seq = Bio::PrimarySeq->new (-seq =>'AGCTTAATTCATTAGCTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATCCAAAAAAGAGTGAGCTTCTGAT', -primary_id => 'synopsis', -molecule => 'dna'); my $ra = Bio::Restriction::Analysis->new(-seq=>$seq); my @gel; my @bam_maps = $ra->fragment_maps('BamHI'); foreach my $i (@bam_maps) { my $start = $i->{start}; my $end = $i->{end}; my $sequence = $i->{seq}; push @gel, "$start--$sequence--$end"; @gel = sort {length $b <=> length $a} @gel; } print join("\n", @gel) . "\n"; =cut sub fragment_maps { my ($self, $enz) = @_; $self->cut unless $self->{'_cut'}; $self->throw('no enzyme selected to get fragment maps for') unless $enz; # we are going to generate this on an as-needed basis rather than # for every enzyme this should cut down on the amount of # duplicated data we are trying to save in memory and make this # faster and easier for large sequences, e.g. genome analysis my @cut_positions; if (ref $enz eq '' && exists $self->{'_cut_positions'}->{$enz}) { @cut_positions=@{$self->{'_cut_positions'}->{$enz}}; } elsif ($enz->isa("Bio::Restriction::EnzymeI")) { @cut_positions=@{$self->{'_cut_positions'}->{$enz->name}}; } elsif ($enz->isa("Bio::Restriction::EnzymeCollection")) { $self->cut('multiple', $enz); @cut_positions=@{$self->{'_cut_positions'}->{'multiple_digest'}}; } unless (defined($cut_positions[0])) { # it doesn't cut # return the whole sequence # this should probably have the is_circular command my %map=( 'start' => 1, 'end' => $self->{'_seq'}->length, 'seq' => $self->{'_seq'}->seq ); push (@{$self->{'_frag_map_list'}->{$enz}}, \%map); return defined $self->{'_frag_map_list'}->{$enz} ? @{$self->{'_frag_map_list'}->{$enz}} : (); } @cut_positions=sort {$a <=> $b} @cut_positions; push my @cuts, $cut_positions[0]; foreach my $i (@cut_positions) { push @cuts, $i if $i != $cuts[$#cuts]; } my $start=1; my $stop; my %seq; my %stop; foreach $stop (@cuts) { next if !$stop; # cuts at beginning of sequence $seq{$start}=$self->{'_seq'}->subseq($start, $stop); $stop{$start}=$stop; $start=$stop+1; } $stop=$self->{'_seq'}->length; if ($start > $stop) { # borderline case. The enzyme cleaved at the end of the sequence # what do I do now? } else { $seq{$start}=$self->{'_seq'}->subseq($start, $stop); $stop{$start}=$stop; } if ($self->{'_seq'}->is_circular) { # join the first and last fragments $seq{$start}.=$seq{'1'}; delete $seq{'1'}; $stop{$start}=$stop{'1'}; delete $stop{'1'}; } foreach my $start (sort {$a <=> $b} keys %seq) { my %map=( 'start' => $start, 'end' => $stop{$start}, 'seq' => $seq{$start} ); push (@{$self->{'_frag_map_list'}->{$enz}}, \%map); } return defined $self->{'_frag_map_list'}->{$enz} ? @{$self->{'_frag_map_list'}->{$enz}} : (); } =head2 sizes Title : sizes Function : Retrieves an array with the sizes of the fragments Returns : Array that has the sizes of the fragments ordered from largest to smallest like they would appear in a gel. Arguments: An enzyme name to retrieve the sizes for is required and kilobases to the nearest 0.1 kb, else it will be in bp. If the optional third entry is set the results will be sorted. This is designed to make it easy to see what fragments you should get on a gel! You should be able to do these: # to see all the fragment sizes, print join "\n", $re->sizes($enz), "\n"; # to see all the fragment sizes sorted print join "\n", $re->sizes($enz, 0, 1), "\n"; # to see all the fragment sizes in kb sorted print join "\n", $re->sizes($enz, 1, 1), "\n"; =cut sub sizes { my ($self, $enz, $kb, $sort) = @_; $self->throw('no enzyme selected to get fragments for') unless $enz; if (blessed($enz)) { $self->throw("Enzyme must be enzyme name or a Bio::Restriction::EnzymeI, not ".ref($enz)) if !$enz->isa('Bio::Restriction::EnzymeI'); $enz = $enz->name; } $self->cut unless $self->{'_cut'}; my @frag; my $lastsite=0; foreach my $site (@{$self->{'_cut_positions'}->{$enz}}) { $kb ? push (@frag, (int($site-($lastsite))/100)/10) : push (@frag, $site-($lastsite)); $lastsite=$site; } $kb ? push (@frag, (int($self->{'_seq'}->length-($lastsite))/100)/10) : push (@frag, $self->{'_seq'}->length-($lastsite)); if ($self->{'_seq'}->is_circular) { my $first=shift @frag; my $last=pop @frag; push @frag, ($first+$last); } $sort ? @frag = sort {$b <=> $a} @frag : 1; return @frag; } =head1 How many times does enzymes X cut? =cut =head2 cuts_by_enzyme Title : cuts_by_enzyme Function : Return the number of cuts for an enzyme Returns : An integer with the number of times each enzyme cuts. Returns 0 if doesn't cut or undef if not defined Arguments : An enzyme name string =cut sub cuts_by_enzyme { my ($self, $enz)=@_; $self->throw("Need an enzyme name") unless defined $enz; $self->cut unless $self->{'_cut'}; return $self->{'_number_of_cuts_by_enzyme'}->{$enz}; } =head1 Which enzymes cut the sequence N times? =cut =head2 cutters Title : cutters Function : Find enzymes that cut a given number of times Returns : a Bio::Restriction::EnzymeCollection Arguments : 1. exact time or lower limit, non-negative integer, optional 2. upper limit, non-negative integer, larger or equalthan first, optional If no arguments are given, the method returns all enzymes that do cut the sequence. The argument zero, '0', is same as method zero_cutters(). The argument one, '1', corresponds to unique_cutters. If either of the limits is larger than number of cuts any enzyme cuts the sequence, the that limit is automagically lowered. The method max_cuts() gives the largest number of cuts. See Also : L, L, L =cut sub cutters { my ($self, $a, $z) = @_; $self->cut unless $self->{'_cut'}; my ($start, $end); if (defined $a) { $self->throw("Need a non-zero integer [$a]") unless $a =~ /^[+]?\d+$/; $start = $a; } else { $start = 1; } $start = $self->{'maximum_cuts'} if $start > $self->{'maximum_cuts'}; if (defined $z) { $self->throw("Need a non-zero integer no smaller than start [0]") unless $z =~ /^[+]?\d+$/ and $z >= $a; $end = $z; } elsif (defined $a) { $end = $start; } else { $end = $self->{'maximum_cuts'}; } $end = $self->{'maximum_cuts'} if $end > $self->{'maximum_cuts'}; my $set = Bio::Restriction::EnzymeCollection->new(-empty => 1); #return an empty set if nothing cuts return $set unless $self->{'maximum_cuts'}; for (my $i=$start; $i<=$end; $i++) { $set->enzymes( @{$self->{_number_of_cuts_by_cuts}->{$i}} ) if defined $self->{_number_of_cuts_by_cuts}->{$i}; } return $set; } =head2 unique_cutters Title : unique_cutters Function : A special case if cutters() where enzymes only cut once Returns : a Bio::Restriction::EnzymeCollection Arguments : - See also: L, L =cut sub unique_cutters { shift->cutters(1); } =head2 zero_cutters Title : zero_cutters Function : A special case if cutters() where enzymes don't cut the sequence Returns : a Bio::Restriction::EnzymeCollection Arguments : - See also: L, L =cut sub zero_cutters { shift->cutters(0); } =head2 max_cuts Title : max_cuts Function : Find the most number of cuts Returns : The number of times the enzyme that cuts most cuts. Arguments : None This is not a very practical method, but if you are curious... =cut sub max_cuts { return shift->{maximum_cuts} } =head1 Internal methods =cut =head2 _cuts Title : _cuts Function : Figures out which enzymes we know about and cuts the sequence. Returns : Nothing. Arguments : None. Comments : An internal method. This will figure out where the sequence should be cut, and provide the appropriate results. =cut sub _cuts { my $self = shift; my $target_seq=uc $self->{'_seq'}->seq; # I have been burned on this before :) # first, find out all the enzymes that we have foreach my $enz ($self->{'_enzymes'}->each_enzyme) { my @all_cuts; my @others = $enz->others if $enz->can("others"); foreach my $enzyme ($enz, @others) { # cut the sequence # _make_cuts handles all cases (amibiguous, non-ambiguous) X # (palindromic X non-palindromic) # my $cut_positions = $self->_make_cuts($target_seq, $enzyme); push @all_cuts, @$cut_positions; #### need to refactor circular handling.... #### # deal with is_circular sequences if ($self->{'_seq'}->is_circular) { $cut_positions=$self->_circular($target_seq, $enzyme); push @all_cuts, @$cut_positions; } # non-symmetric cutters (most external cutters, e.g.) need # special handling unless ($enzyme->is_symmetric) { # do all of above with explicit use of the # enzyme's 'complementary_cut'... $cut_positions = $self->_make_cuts($target_seq, $enzyme, 'COMP'); push @all_cuts, @$cut_positions; # deal with is_circular sequences if ($self->{'_seq'}->is_circular) { $cut_positions=$self->_circular($target_seq, $enzyme, 'COMP'); push @all_cuts, @$cut_positions; } } } if (defined $all_cuts[0]) { # now just remove any duplicate cut sites @all_cuts = sort {$a <=> $b} @all_cuts; push @{$self->{'_cut_positions'}->{$enz->name}}, $all_cuts[0]; foreach my $i (@all_cuts) { push @{$self->{'_cut_positions'}->{$enz->name}}, $i if $i != ${$self->{'_cut_positions'}->{$enz->name}}[$#{$self->{'_cut_positions'}->{$enz->name}}]; } } else { # this just fixes an eror when @all_cuts is not defined! @{$self->{'_cut_positions'}->{$enz->name}}=(); } # note I have removed saving any other information except the # cut_positions this should significantly decrease the amount # of memory that is required for large sequences. It should # also speed things up dramatically, because fragments and # fragment maps are only calculated for those enzymes they are # needed for. # finally, save minimal information about each enzyme my $number_of_cuts=scalar @{$self->{'_cut_positions'}->{$enz->name}}; # now just store the number of cuts $self->{_number_of_cuts_by_enzyme}->{$enz->name}=$number_of_cuts; push (@{$self->{_number_of_cuts_by_cuts}->{$number_of_cuts}}, $enz); if ($number_of_cuts > $self->{maximum_cuts}) { $self->{maximum_cuts}=$number_of_cuts; } } } =head2 _enzyme_sites Title : _enzyme_sites Function : An internal method to figure out the two sides of an enzyme Returns : The sequence before the cut and the sequence after the cut Arguments : A Bio::Restriction::Enzyme object, $comp : boolean, calculate based on $enz->complementary_cut() if true, $enz->cut() if false Status : NOW DEPRECATED - maj =cut sub _enzyme_sites { my ($self, $enz, $comp )=@_; # get the cut site # I have reworked this so that it uses $enz->cut to get the site my $site= ( $comp ? $enz->complementary_cut : $enz->cut ); # split it into the two fragments for the sequence before and after. $site=0 unless defined $site; # the default values just stop an error from an undefined # string. But they don't affect the split. my ($beforeseq, $afterseq)= ('.', '.'); # extra-site cutting # the before seq is going to be the entire site # the after seq is empty # BUT, need to communicate how to cut within the sample sequence # relative to the end of the site (do through $enz->cut), and # ALSO, need to check length of sample seq so that if cut falls # outside the input sequence, we have a warning/throw. /maj # pre-site cutting # need to handle negative site numbers if ($site <= 0) { # <= to handle pre-site cutting $afterseq=$enz->string; } elsif ($site >= $enz->seq->length) { # >= to handle extrasite cutters/maj $beforeseq=$enz->string; } else { # $site < $enz->seq->length $beforeseq=$enz->seq->subseq(1, $site); $afterseq=$enz->seq->subseq($site+1, $enz->seq->length); } # if the enzyme is ambiguous we need to convert this into a perl string if ($enz->is_ambiguous) { $beforeseq=$self->_expanded_string($beforeseq); $afterseq =$self->_expanded_string($afterseq); } return ($beforeseq, $afterseq); } =head2 _non_pal_enz Title : _non_pal_enz Function : Analyses non_palindromic enzymes for cuts in both ways (in fact, delivers only minus strand cut positions in the plus strand coordinates/maj) Returns : A reference to an array of cut positions Arguments: The sequence to check and the enzyme object NOW DEPRECATED/maj =cut sub _non_pal_enz { my ($self, $target_seq, $enz) =@_; # add support for non-palindromic sequences # the enzyme is not the same forwards and backwards my $site=$enz->complementary_cut; # complementary_cut is in plus strand coordinates # we are going to rc the sequence, so complementary_cut becomes length-complementary_cut # I think this is wrong; cut sites are a matter of position with respect # to the plus strand: the recognition site is double stranded and # directly identifiable on the plus strand sequence. /maj # what really needs doing is to keep track of plus strand and minus strand # nicks separately./maj my ($beforeseq, $afterseq)=('.', '.'); # now, for extra-site cuts, $site > length...so...?/maj my $new_left_cut=$enz->seq->length-$site; # there is a problem when this is actually zero if ($new_left_cut == 0) {$afterseq=$enz->seq->revcom->seq} elsif ($new_left_cut == $enz->seq->length) {$beforeseq=$enz->seq->revcom->seq} else { # this can't be right./maj $beforeseq=$enz->seq->revcom->subseq(1, ($enz->seq->length-$site)); $afterseq=$enz->seq->revcom->subseq(($enz->seq->length-$site), $enz->seq->length); } # do this correctly, in the context of the current code design, # by providing a "complement" argument to _ambig_cuts and _nonambig_cuts, # use these explicitly rather than this wrapper./maj my $results=[]; if ($enz->is_ambiguous) { $results= $self->_ambig_cuts($beforeseq, $afterseq, $target_seq, $enz); } else { $results= $self->_nonambig_cuts($beforeseq, $afterseq, $target_seq, $enz); } # deal with is_circular my $more_results=[]; $more_results=$self->_circular($beforeseq, $afterseq, $enz) if ($self->{'_seq'}->is_circular); return [@$more_results, @$results]; } =head2 _ambig_cuts Title : _ambig_cuts Function : An internal method to localize the cuts in the sequence Returns : A reference to an array of cut positions Arguments : The separated enzyme site, the target sequence, and the enzyme object Comments : This is a slow implementation but works for ambiguous sequences. Whenever possible, _nonambig_cuts should be used as it is a lot faster. =cut # we have problems here when the cut is extrasite: $beforeseq/$afterseq do # not define the cut site then! I am renaming this to _ambig_cuts_depr, # providing a more compact method that correctly handles extrasite cuts # below /maj sub _ambig_cuts_depr { my ($self, $beforeseq, $afterseq, $target_seq, $enz) = @_; # cut the sequence. This is done with split so we can use # regexp. $target_seq = uc $target_seq; my @cuts = split /($beforeseq)($afterseq)/i, $target_seq; # now the array has extra elements --- the before and after! # we have: # element 0 sequence # element 1 3' end # element 2 5' end of next sequence # element 3 sequence # .... # we need to loop through the array and add the ends to the # appropriate parts of the sequence my $i=0; my @re_frags; if ($#cuts) { # there is >1 element while ($i<$#cuts) { my $joinedseq; # the first sequence is a special case if ($i == 0) { $joinedseq=$cuts[$i].$cuts[$i+1]; } else { $joinedseq=$cuts[$i-1].$cuts[$i].$cuts[$i+1]; } # now deal with overlapping sequences # we can do this through a regular regexp as we only # have a short fragment to look through while ($joinedseq =~ /$beforeseq$afterseq/) { $joinedseq =~ s/^(.*?$beforeseq)($afterseq)/$2/; push @re_frags, $1; } push @re_frags, $joinedseq; $i+=3; } # I don't think we want the last fragment in. It is messing up the _circular # part of things. So I deleted this part of the code :) } else { # if we don't cut, leave the array empty return []; } # the sequence was not cut. # now @re_frags has the fragments of all the sequences # but some people want to have this return the lengths # of the fragments. # in theory the actual cut sites should be the length # of the fragments in @re_frags # note, that now this is the only data that we are saving. We # will have to go back add regenerate re_frags. The reason is # that we can use this in _circular easier my @cut_positions = map {length($_)} @re_frags; # the cut positions are right now the lengths of the sequence, but # we need to add them all onto each other for (my $i=1; $i<=$#cut_positions; $i++) { $cut_positions[$i]+=$cut_positions[$i-1]; } # in one of those oddities in life, 2 fragments mean an enzyme cut once # so $#re_frags is the number of cuts return \@cut_positions; } # new version/maj sub _ambig_cuts { my ($self, $before, $after, $target, $enz, $comp) = @_; my $cut_site = ($comp ? $enz->complementary_cut : $enz->cut); local $_ = uc $target; my @cuts; my $recog = $enz->recog; my $site_re = qr/($recog)/; push @cuts, pos while (/$site_re/g); $_ = $_ - length($enz->recog) + $cut_site for @cuts; return [@cuts]; } =head2 _nonambig_cuts Title : _nonambig_cuts Function : Figures out which enzymes we know about and cuts the sequence. Returns : Nothing. Arguments : The separated enzyme site, the target sequence, and the enzyme object An internal method. This will figure out where the sequence should be cut, and provide the appropriate results. This is a much faster implementation because it doesn't use a regexp, but it can not deal with ambiguous sequences =cut # now, DO want the enzyme object.../maj sub _nonambig_cuts { my ($self, $beforeseq, $afterseq, $target_seq, $enz, $comp) = @_; my $cut_site = ($comp ? $enz->complementary_cut : $enz->cut); if ($beforeseq eq ".") {$beforeseq = ''} if ($afterseq eq ".") {$afterseq = ''} $target_seq = uc $target_seq; # my $index_posn=index($target_seq, $beforeseq.$afterseq); my $index_posn=index($target_seq, $enz->recog); return [] if ($index_posn == -1); # there is no match to the sequence # there is at least one cut site my @cuts; while ($index_posn > -1) { # extrasite cutting issue here... # think we want $index_posn+$enz->cut # push (@cuts, $index_posn+length($beforeseq)); push (@cuts, $index_posn+$cut_site); # $index_posn=index($target_seq, $beforeseq.$afterseq, $index_posn+1); $index_posn=index($target_seq, $enz->recog, $index_posn+1); } return \@cuts; } =head2 _make_cuts Title : _make_cuts Usage : $an->_make_cuts( $target_sequence, $enzyme, $complement_q ) Function: Returns an array of cut sites on target seq, using enzyme on the plus strand ($complement_q = 0) or minus strand ($complement_q = 1); follows Enzyme objects in $enzyme->others() Returns : array of scalar integers Args : sequence string, B:R:Enzyme object, boolean =cut sub _make_cuts { no warnings qw( uninitialized ); my ($self, $target, $enz, $comp) = @_; local $_ = uc $target; my @cuts; my @enzs = map { $_ || () } ($enz, $enz->can('others') ? $enz->others : ()); ENZ: foreach $enz (@enzs) { my $recog = $enz->recog; my $cut_site = ($comp ? $enz->complementary_cut : $enz->cut); my @these_cuts; if ( $recog =~ /[^\w]/ ) { # "ambig" my $site_re = qr/($recog)/; push @these_cuts, pos while (/$site_re/g); $_ = $_ - length($enz->string) + $cut_site for @these_cuts; if (!$enz->is_palindromic) { pos = 0; my @these_rev_cuts; $recog = $enz->revcom_recog; $cut_site = length($enz->string) - ($comp ? $enz->cut : $enz->complementary_cut); $site_re = qr/($recog)/; push @these_rev_cuts, pos while (/$site_re/g); $_ = $_ - length($enz->string) + $cut_site for @these_rev_cuts; push @these_cuts, @these_rev_cuts; } } else { # "nonambig" my $index_posn=index($_, $recog); while ($index_posn > -1) { push (@these_cuts, $index_posn+$cut_site); $index_posn=index($_, $recog, $index_posn+1); } if (!$enz->is_palindromic) { $recog = $enz->revcom_recog; $cut_site = length($enz->string) - ($comp ? $enz->cut : $enz->complementary_cut); $index_posn=index($_, $recog); while ($index_posn > -1) { push @these_cuts, $index_posn+$cut_site; $index_posn=index($_, $recog, $index_posn+1); } } } push @cuts, @these_cuts; } return [@cuts]; } =head2 _multiple_cuts Title : _multiple_cuts Function : Figures out multiple digests Returns : An array of the cut sites for multiply digested DNA Arguments : A Bio::Restriction::EnzymeCollection object Comments : Double digests is one subset of this, but you can use as many enzymes as you want. =cut sub _multiple_cuts { my ($self, $ec)=@_; $self->cut unless $self->{'_cut'}; # now that we are using positions rather than fragments # this is really easy my @cuts; foreach my $enz ($ec->each_enzyme) { push @cuts, @{$self->{'_cut_positions'}->{$enz->name}} if defined $self->{'_cut_positions'}->{$enz->name}; } @{$self->{'_cut_positions'}->{'multiple_digest'}}=sort {$a <=> $b} @cuts; my $number_of_cuts; $number_of_cuts=scalar @{$self->{'_cut_positions'}->{'multiple_digest'}}; $self->{_number_of_cuts_by_enzyme}->{'multiple_digest'}=$number_of_cuts; push (@{$self->{_number_of_cuts_by_cuts}->{$number_of_cuts}}, 'multiple_digest'); if ($number_of_cuts > $self->{maximum_cuts}) { $self->{maximum_cuts}=$number_of_cuts; } } =head2 _circular Title : _circular Function : Identifies cuts at the join of the end of the target with the beginning of the target Returns : array of scalar integers ( cut sites near join, if any ) Arguments : scalar string (target sequence), Bio::Restriction::Enzyme obj =cut sub _circular { my ($self, $target, $enz, $comp) = @_; $target=uc $target; my $patch_len = ( length $target > 20 ? 10 : int( length($target)/2 ) ); my ($first, $last) = (substr($target, 0, $patch_len),substr($target, -$patch_len)); my $patch=$last.$first; # now find the cut sites my $cut_positions = $self->_make_cuts($patch, $enz, $comp); # the enzyme doesn't cut in the new fragment return [] if (!$cut_positions); # now we are going to add things to _cut_positions # in this shema it doesn't matter if the site is there twice - # we will take care of that later. Because we are using position # rather than frag or anything else, we can just # remove duplicates. my @circ_cuts; foreach my $cut (@$cut_positions) { if ($cut == length($last)) { # the cut is actually at position 0, but we're going to call this the # length of the sequence so we don't confuse no cuts with a 0 cut # push (@circ_cuts, $self->{'_seq'}->length); push (@circ_cuts, 0); } elsif ($cut < length($last)) { # the cut is before the end of the sequence #check push (@circ_cuts, $self->{'_seq'}->length - (length($last) - $cut)); } else { # the cut is at the start of the sequence (position >=1) # note, we put this at the beginning of the array rather than the end! unshift (@circ_cuts, $cut-length($last)); } } return \@circ_cuts; } =head2 _expanded_string Title : _expanded_string Function : Expand nucleotide ambiguity codes to their representative letters Returns : The full length string Arguments : The string to be expanded. Stolen from the original RestrictionEnzyme.pm =cut sub _expanded_string { my ($self, $str) = @_; $str =~ s/N|X/\./g; $str =~ s/R/\[AG\]/g; $str =~ s/Y/\[CT\]/g; $str =~ s/S/\[GC\]/g; $str =~ s/W/\[AT\]/g; $str =~ s/M/\[AC\]/g; $str =~ s/K/\[TG\]/g; $str =~ s/B/\[CGT\]/g; $str =~ s/D/\[AGT\]/g; $str =~ s/H/\[ACT\]/g; $str =~ s/V/\[ACG\]/g; return $str; } 1; BioPerl-1.007002/Bio/Restriction/Enzyme.pm000444000766000024 13353413155576320 20407 0ustar00cjfieldsstaff000000000000#------------------------------------------------------------------ # # BioPerl module Bio::Restriction::Enzyme # # Please direct questions and support issues to # # Cared for by Rob Edwards # # You may distribute this module under the same terms as perl itself #------------------------------------------------------------------ ## POD Documentation: =head1 NAME Bio::Restriction::Enzyme - A single restriction endonuclease (cuts DNA at specific locations) =head1 SYNOPSIS # set up a single restriction enzyme. This contains lots of # information about the enzyme that is generally parsed from a # rebase file and can then be read back use Bio::Restriction::Enzyme; # define a new enzyme with the cut sequence my $re=Bio::Restriction::Enzyme->new (-enzyme=>'EcoRI', -seq=>'G^AATTC'); # once the sequence has been defined a bunch of stuff is calculated # for you: #### PRECALCULATED # find where the enzyme cuts after ... my $ca=$re->cut; # ... and where it cuts on the opposite strand my $oca = $re->complementary_cut; # get the cut sequence string back. # Note that site will return the sequence with a caret my $with_caret=$re->site; #returns 'G^AATTC'; # but it is also a Bio::PrimarySeq object .... my $without_caret=$re->seq; # returns 'GAATTC'; # ... and so does string $without_caret=$re->string; #returns 'GAATTC'; # what is the reverse complement of the cut site my $rc=$re->revcom; # returns 'GAATTC'; # now the recognition length. There are two types: # recognition_length() is the length of the sequence # cutter() estimate of cut frequency my $recog_length = $re->recognition_length; # returns 6 # also returns 6 in this case but would return # 4 for GANNTC and 5 for RGATCY (BstX2I)! $recog_length=$re->cutter; # is the sequence a palindrome - the same forwards and backwards my $pal= $re->palindromic; # this is a boolean # is the sequence blunt (i.e. no overhang - the forward and reverse # cuts are the same) print "blunt\n" if $re->overhang eq 'blunt'; # Overhang can have three values: "5'", "3'", "blunt", and undef # Direction is very important if you use Klenow! my $oh=$re->overhang; # what is the overhang sequence my $ohseq=$re->overhang_seq; # will return 'AATT'; # is the sequence ambiguous - does it contain non-GATC bases? my $ambig=$re->is_ambiguous; # this is boolean print "Stuff about the enzyme\nCuts after: $ca\n", "Complementary cut: $oca\nSite:\n\t$with_caret or\n", "\t$without_caret\n"; print "Reverse of the sequence: $rc\nRecognition length: $recog_length\n", "Is it palindromic? $pal\n"; print "The overhang is $oh with sequence $ohseq\n", "And is it ambiguous? $ambig\n\n"; ### THINGS YOU CAN SET, and get from rich REBASE file # get or set the isoschizomers (enzymes that recognize the same # site) $re->isoschizomers('PvuII', 'SmaI'); # not really true :) print "Isoschizomers are ", join " ", $re->isoschizomers, "\n"; # get or set the methylation sites $re->methylation_sites(2); # not really true :) print "Methylated at ", join " ", keys %{$re->methylation_sites},"\n"; #Get or set the source microbe $re->microbe('E. coli'); print "It came from ", $re->microbe, "\n"; # get or set the person who isolated it $re->source("Rob"); # not really true :) print $re->source, " sent it to us\n"; # get or set whether it is commercially available and the company # that it can be bought at $re->vendors('NEB'); # my favorite print "Is it commercially available :"; print $re->vendors ? "Yes" : "No"; print " and it can be got from ", join " ", $re->vendors, "\n"; # get or set a reference for this $re->reference('Edwards et al. J. Bacteriology'); print "It was not published in ", $re->reference, "\n"; # get or set the enzyme name $re->name('BamHI'); print "The name of EcoRI is not really ", $re->name, "\n"; =head1 DESCRIPTION This module defines a single restriction endonuclease. You can use it to make custom restriction enzymes, and it is used by Bio::Restriction::IO to define enzymes in the New England Biolabs REBASE collection. Use Bio::Restriction::Analysis to figure out which enzymes are available and where they cut your sequence. =head1 RESTRICTION MODIFICATION SYSTEMS At least three geneticaly and biochamically distinct restriction modification systems exist. The cutting components of them are known as restriction endonuleases. The three systems are known by roman numerals: Type I, II, and III restriction enzymes. REBASE format 'cutzymes'(#15) lists enzyme type in its last field. The categories there do not always match the the following short descriptions of the enzymes types. See http://it.stlawu.edu/~tbudd/rmsyst.html for a better overview. =head2 TypeI Type I systems recognize a bipartite asymetrical sequence of 5-7 bp: ---TGA*NnTGCT--- * = methylation sites ---ACTNnA*CGA--- n = 6 for EcoK, n = 8 for EcoB The cleavage site is roughly 1000 (400-7000) base pairs from the recognition site. =head2 TypeII The simplest and most common (at least commercially). Site recognition is via short palindromic base sequences that are 4-6 base pairs long. Cleavage is at the recognition site (but may occasionally be just adjacent to the palindromic sequence, usually within) and may produce blunt end termini or staggered, "sticky end" termini. =head2 TypeIII The recognition site is a 5-7 bp asymmetrical sequence. Cleavage is ATP dependent 24-26 base pairs downstream from the recognition site and usually yields staggered cuts 2-4 bases apart. =head1 COMMENTS I am trying to make this backwards compatible with Bio::Tools::RestrictionEnzyme. Undoubtedly some things will break, but we can fix things as we progress.....! I have added another comments section at the end of this POD that discusses a couple of areas I know are broken (at the moment) =head1 TO DO =over 2 =item * Convert vendors touse full names of companies instead of code =item * Add regular expression based matching to vendors =item * Move away from the archaic ^ notation for cut sites. Ideally I'd totally like to remove this altogether, or add a method that adds it in if someone really wants it. We should be fixed on a sequence, number notation. =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Rob Edwards, redwards@utmem.edu =head1 CONTRIBUTORS Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Peter Blaiklock, pblaiklo@restrictionmapper.org Mark A. Jensen, maj-at-fortinbras-dot-us =head1 COPYRIGHT Copyright (c) 2003 Rob Edwards. Some of this work is Copyright (c) 1997-2002 Steve A. Chervitz. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 SEE ALSO L, L, L =head1 APPENDIX Methods beginning with a leading underscore are considered private and are intended for internal use by this module. They are not considered part of the public interface and are described here for documentation purposes only. =cut package Bio::Restriction::Enzyme; use strict; use Bio::PrimarySeq; use Data::Dumper; use Tie::RefHash; use vars qw (%TYPE); use base qw(Bio::Root::Root Bio::Restriction::EnzymeI); BEGIN { my %TYPE = (I => 1, II => 1, III => 1); } =head2 new Title : new Function Function : Initializes the Enzyme object Returns : The Restriction::Enzyme object Argument : A standard definition can have several formats. For example: $re->new(-enzyme='EcoRI', -seq->'GAATTC' -cut->'1') Or, you can define the cut site in the sequence, for example $re->new(-enzyme='EcoRI', -seq->'G^AATTC'), but you must use a caret Or, a sequence can cut outside the recognition site, for example $re->new(-enzyme='AbeI', -seq->'CCTCAGC' -cut->'-5/-2') Other arguments: -isoschizomers=>\@list a reference to an array of known isoschizomers -references=>$ref a reference to the enzyme -source=>$source the source (person) of the enzyme -commercial_availability=>@companies a list of companies that supply the enzyme -methylation_site=>\%sites a reference to hash that has the position as the key and the type of methylation as the value -xln_sub => sub { ($self,$cut) = @_; ...; return $xln_cut }, a coderef to a routine that translates the input cut value into Bio::Restriction::Enzyme coordinates ( e.g., for withrefm format, this might be -xln_sub => sub { length( shift()->string ) + shift } ) A Restriction::Enzyme object manages its recognition sequence as a Bio::PrimarySeq object. The minimum requirement is for a name and a sequence. This will create the restriction enzyme object, and define several things about the sequence, such as palindromic, size, etc. =cut # do all cut/comp cut setting within the constructor # new args sub new { my($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($name,$enzyme,$site,$seq,$precut, $postcut,$cut,$complementary_cut, $is_prototype, $prototype, $isoschizomers, $meth, $microbe, $source, $vendors, $references, $neo, $recog, $xln_sub) = $self->_rearrange([qw( NAME ENZYME SITE SEQ PRECUT POSTCUT CUT COMPLEMENTARY_CUT IS_PROTOTYPE PROTOTYPE ISOSCHIZOMERS METHYLATION_SITES MICROBE SOURCE VENDORS REFERENCES IS_NEOSCHIZOMER RECOG XLN_SUB )], @args); $self->throw('At the minimum, you must define a name and '. 'recognition site for the restriction enzyme') unless (($name || $enzyme) && ($site || $recog || $seq)); $self->{_isoschizomers} = []; $self->{_methylation_sites} = {}; $self->{_vendors} = []; $self->{_references} = []; # squelch warnings $postcut ||=''; # enzyme name $enzyme && $self->name($enzyme); $name && $self->name($name); # site # # note that the site() setter will automatically set # cut(), complementary_cut(), if the cut site is indicated # in $site with '^' /maj # create the cut site if appropriate/this is a kludge due to # the base.pm format in the new B:R order... if ( $cut and $cut <= length $site) { $site = substr($site, 0, $cut).'^'.substr($site, $cut); } if ($site) { $self->site($site); } else { $seq && $self->site($seq); } if ($recog) { $self->recog($recog); } else { $seq && $self->recog($seq); $site && $self->recog($site); } # call revcom_site to initialize it and revcom_recog: $self->revcom_site(); $recog = $self->string; # for length calculations below if ($xln_sub) { $self->warn("Translation subroutine is not a coderef; ignoring") unless ref($xln_sub) eq 'CODE'; } # cut coordinates my ($pc_cut, $pc_comp_cut) = ( $postcut =~ /(-?\d+)\/(-?\d+)/ ); # cut definitions in constructor override any autoset in # site() # definitions in site conform to withrefm coords, translation # happens here if (defined $cut) { $self->cut( $xln_sub ? $xln_sub->($self, $cut) : $cut ); } elsif ( defined $pc_cut ) { $self->cut( $xln_sub ? $xln_sub->($self, $pc_cut) : $pc_cut ); } if (defined $complementary_cut) { $self->complementary_cut($xln_sub ? $xln_sub->($self,$complementary_cut) : $complementary_cut); } elsif (defined $pc_comp_cut) { $self->complementary_cut($xln_sub ? $xln_sub->($self,$pc_comp_cut) : $pc_comp_cut); } $is_prototype && $self->is_prototype($is_prototype); $prototype && $self->prototype($prototype); $isoschizomers && $self->isoschizomers($isoschizomers); $meth && $self->methylation_sites($meth); $microbe && $self->microbe($microbe); $source && $self->source($source); $vendors && $self->vendors($vendors); $references && $self->references($references); $neo && $self->is_neoschizomer($neo); # create multicut enzymes here if $precut defined if (defined $precut) { bless $self, 'Bio::Restriction::Enzyme::MultiCut'; my ($pc_cut, $pc_comp_cut) = $precut =~ /(-?\d+)\/(-?\d+)/; my $re2 = $self->clone; $re2->cut($xln_sub ? $xln_sub->($self, -$pc_cut) : -$pc_cut); $re2->complementary_cut($xln_sub ? $xln_sub->($self, -$pc_comp_cut) : -$pc_comp_cut); $self->others($re2); } return $self; } =head1 Essential methods =cut =head2 name Title : name Usage : $re->name($newval) Function : Gets/Sets the restriction enzyme name Example : $re->name('EcoRI') Returns : value of name Args : newvalue (optional) This will also clean up the name. I have added this because some people get confused about restriction enzyme names. The name should be One upper case letter, and two lower case letters (because it is derived from the organism name, eg. EcoRI is from E. coli). After that it is all confused, but the numbers should be roman numbers not numbers, therefore we'll correct those. At least this will provide some standard, I hope. =cut sub name{ my ($self, $name)=@_; if ($name) { # correct and set the name my $old_name = $name; # remove spaces. Some people write HindIII as Hind III $name =~ s/\s+//g; # change TAILING ones to I's if ($name =~ m/(1+)$/) { my $i = 'I' x length($1); $name =~ s/1+$/$i/; } # make the first letter upper case $name =~ s/^(\w)/uc($1)/e; unless ($name eq $old_name) { # we have changed the name, so send a warning $self->warn("The enzyme name $old_name was changed to $name"); } $self->{'_name'} = $name; } return $self->{'_name'}; } =head2 site Title : site Usage : $re->site(); Function : Gets/sets the recognition sequence for the enzyme. Example : $seq_string = $re->site(); Returns : String containing recognition sequence indicating : cleavage site as in 'G^AATTC'. Argument : n/a Throws : n/a Side effect: the sequence is always converted to upper case. The cut site can also be set by using methods L and L. This will pad out missing sequence with N's. For example the enzyme Acc36I cuts at ACCTGC(4/8). This will be returned as ACCTGCNNNN^ Note that the common notation ACCTGC(4/8) means that the forward strand cut is four nucleotides after the END of the recognition site. The forward cut() in the coordinates used here in Acc36I ACCTGC(4/8) is at 6+4 i.e. 10. ** This is the main setable method for the recognition site. =cut sub site { my ( $self, $site ) = @_; if ($site) { $self->throw("Unrecognized characters in site: [$site]") if $site =~ /[^ATGCMRWSYKVHDBN\^]/i; # we may have to redefine this if there is a ^ in the sequence # first, check and see if we have a cut site in the sequence # if so, find the position, and set the target sequence and cut site $self->{'_site'} = $site; my ( $first, $second ) = $site =~ /(.*)\^(.*)/; $site = "$1$2" if defined $first; $self->{'_site'} = $site; # now set the recognition site as a new Bio::PrimarySeq object # we need it before calling cut() and complementary_cut() $self->{_seq} = Bio::PrimarySeq->new( -id => $self->name, -seq => $site, -verbose => $self->verbose, -alphabet => 'dna' ); if ( defined $first ) { $self->cut( length $first ); $self->complementary_cut( length $second ); $self->revcom_site(); } } return $self->{'_site'}; } =head2 revcom_site Title : revcom_site Usage : $re->revcom_site(); Function : Gets/sets the complementary recognition sequence for the enzyme. Example : $seq_string = $re->revcom_site(); Returns : String containing recognition sequence indicating : cleavage site as in 'G^AATTC'. Argument : none (sets on first call) Throws : n/a This is the same as site, except it returns the revcom site. For palindromic enzymes these two are identical. For non-palindromic enzymes they are not! On set, this also handles setting the revcom_recog attribute. See also L above. =cut sub revcom_site { my $self = shift; # getter return $self->{'_revcom_site'} unless !$self->{'_revcom_site'}; # setter my $site = $self->{'_site'}; if ($self->is_palindromic) { $self->{'_revcom_site'}=$self->{'_site'}; $self->revcom_recog( $self->string ); return $self->{'_revcom_site'}; } $self->throw("Unrecognized characters in revcom site: [$site]") if $site =~ /[^ATGCMRWSYKVHDBN\^]/i; if ($site =~ /\^/) { # first, check and see if we have a cut site indicated in the sequence # if so, find the position, and set the target sequence and cut site $site = $self->revcom; $self->revcom_recog( $site ); my $c = length($site)-$self->cut; $site = substr($site, 0, $c).'^'.substr($site,$c); $self->{'_revcom_site'} = $site; } else { my $revcom=$self->revcom; $self->revcom_recog( $revcom ); # my $cc=$self->complementary_cut; # my $hat=length($revcom)-$cc+1; # we need it on the other strand! # if ($cc > length($revcom)) { # my $pad= "N" x ($cc-length($revcom)); # $revcom = $pad. $revcom; # $hat=length($revcom)-$cc+1; # } # elsif ($cc < 0) { # my $pad = "N" x -$cc; # $revcom .= $pad; # $hat=length($revcom); # } # $revcom =~ s/(.{$hat})/$1\^/; $self->{'_revcom_site'}=$revcom; } return $self->{'_revcom_site'}; } =head2 cut Title : cut Usage : $num = $re->cut(1); Function : Sets/gets an integer indicating the position of cleavage relative to the 5' end of the recognition sequence in the forward strand. For type II enzymes, sets the symmetrically positioned reverse strand cut site by calling complementary_cut(). Returns : Integer, 0 if not set Argument : an integer for the forward strand cut site (optional) Note that the common notation ACCTGC(4/8) means that the forward strand cut is four nucleotides after the END of the recognition site. The forward cut in the coordinates used here in Acc36I ACCTGC(4/8) is at 6+4 i.e. 10. Note that REBASE uses notation where cuts within symmetic sites are marked by '^' within the forward sequence but if the site is asymmetric the parenthesis syntax is used where numbering ALWAYS starts from last nucleotide in the forward strand. That's why AciI has a site usually written as CCGC(-3/-1) actualy cuts in C^C G C G G C^G In our notation, these locations are 1 and 3. The cuts locations in the notation used are relative to the first (non-N) nucleotide of the reported forward strand of the recognition sequence. The following diagram numbers the phosphodiester bonds (marked by + ) which can be cut by the restriction enzymes: 1 2 3 4 5 6 7 8 ... N + N + N + N + N + G + A + C + T + G + G + N + N + N ... -5 -4 -3 -2 -1 =cut sub cut { my ($self, $value) = @_; if (defined $value) { $self->throw("The cut position needs to be an integer [$value]") unless $value =~ /[-+]?\d+/; $self->{'_cut'} = $value; # add the caret to the site attribute only if internal /maj if ( ($self->{_site} !~ /\^/) && ($value <= length ($self->{_site}))) { $self->{_site} = substr($self->{_site}, 0, $value). '^'. substr($self->{_site}, $value); } # auto-set comp cut only if cut site is inside the recog site./maj $self->complementary_cut(length ($self->seq->seq) - $value ) if (($self->{_site} =~ /\^/) && ($self->type eq 'II')); } # return undef if not defined yet, not 0 /maj return $self->{'_cut'}; } =head2 cuts_after Title : cuts_after Usage : Alias for cut() =cut sub cuts_after { shift->cut(@_); } =head2 complementary_cut Title : complementary_cut Usage : $num = $re->complementary_cut('1'); Function : Sets/Gets an integer indicating the position of cleavage : on the reverse strand of the restriction site. Returns : Integer Argument : An integer (optional) Throws : Exception if argument is non-numeric. This method determines the cut on the reverse strand of the sequence. For most enzymes this will be within the sequence, and will be set automatically based on the forward strand cut, but it need not be. B that the returned location indicates the location AFTER the first non-N site nucleotide in the FORWARD strand. =cut sub complementary_cut { my ($self, $num)=@_; if (defined $num) { $self->throw("The cut position needs to be an integer [$num]") unless $num =~ /[-+]?\d+/; $self->{'_rc_cut'} = $num; } # return undef, not 0, if not yet defined /maj return $self->{'_rc_cut'}; } =head1 Read only (usually) recognition site descriptive methods =cut =head2 type Title : type Usage : $re->type(); Function : Get/set the restriction system type Returns : Argument : optional type: ('I'|II|III) Restriction enzymes have been catezorized into three types. Some REBASE formats give the type, but the following rules can be used to classify the known enzymes: =over 4 =item 1 Bipartite site (with 6-8 Ns in the middle and the cut site is E 50 nt away) =E type I =item 2 Site length E 3 =E type I =item 3 5-6 asymmetric site and cuts E20 nt away =E type III =item 4 All other =E type II =back There are some enzymes in REBASE which have bipartite recognition site and cat far from the site but are still classified as type I. I've no idea if this is really so. =cut sub type { my ($self, $value) = @_; if ($value) { $self->throw("Not a valid value [$value], needs to one of : ". join (', ', sort keys %TYPE) ) unless $TYPE{$value}; return $self->{'_type'} = $value; } # pre set #return $self->{'_type'} if $self->{'_type'}; # bipartite return $self->{'_type'} = 'I' if $self->{'_seq'}->seq =~ /N*[^N]+N{6,8}[^N]/ and abs($self->cut) > 50 ; # 3 nt site return $self->{'_type'} = 'I' if $self->{'_seq'}->length == 3; # asymmetric and cuts > 20 nt return $self->{'_type'} = 'III' if (length $self->string == 5 or length $self->string == 6 ) and not $self->palindromic and abs($self->cut) > 20; return $self->{'_type'} = 'II'; } =head2 seq Title : seq Usage : $re->seq(); Function : Get the Bio::PrimarySeq.pm object representing : the recognition sequence Returns : A Bio::PrimarySeq object representing the enzyme recognition site Argument : n/a Throws : n/a =cut sub seq { shift->{'_seq'}; } =head2 string Title : string Usage : $re->string(); Function : Get a string representing the recognition sequence. Returns : String. Does NOT contain a '^' representing the cut location as returned by the site() method. Argument : n/a Throws : n/a =cut sub string { shift->{'_seq'}->seq; } =head2 recog Title : recog Usage : $enz->recog($recognition_sequence) Function: Gets/sets the pure recognition site. Sets as regexp if appropriate. As for string(), the cut indicating carets (^) are expunged. Example : Returns : value of recog (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub recog{ my $self = shift; my $recog = shift; return $self->{'recog'} unless $recog; $recog =~ s/\^//g; $recog = _expand($recog) if $recog =~ /[^ATGC]/; return $self->{'recog'} = $recog; } =head2 revcom_recog Title : revcom_recog Usage : $enz->revcom_recog($recognition_sequence) Function: Gets/sets the pure reverse-complemented recognition site. Sets as regexp if appropriate. As for string(), the cut indicating carets (^) are expunged. Example : Returns : value of recog (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub revcom_recog{ my $self = shift; my $recog = shift; unless ($recog) { $self->throw( "revcom recognition site not set; call \$enz->revcom_site to initialize" ) unless $self->{'revcom_recog'}; return $self->{'revcom_recog'}; } $recog =~ s/\^//g; $recog = _expand($recog) if $recog =~ /[^ATGC]/; return $self->{'revcom_recog'} = $recog; } =head2 revcom Title : revcom Usage : $re->revcom(); Function : Get a string representing the reverse complement of : the recognition sequence. Returns : String Argument : n/a Throws : n/a =cut sub revcom { shift->{'_seq'}->revcom->seq(); } =head2 recognition_length Title : recognition_length Usage : $re->recognition_length(); Function : Get the length of the RECOGNITION sequence. This is the total recognition sequence, inluding the ambiguous codes. Returns : An integer Argument : Nothing See also: L =cut sub recognition_length { my $self = shift; return length($self->string); } =head2 cutter Title : cutter Usage : $re->cutter Function : Returns the "cutter" value of the recognition site. This is a value relative to site length and lack of ambiguity codes. Hence: 'RCATGY' is a five (5) cutter site and 'CCTNAGG' a six cutter This measure correlates to the frequency of the enzyme cuts much better than plain recognition site length. Example : $re->cutter Returns : integer or float number Args : none Why is this better than just stripping the ambiguos codes? Think about it like this: You have a random sequence; all nucleotides are equally probable. You have a four nucleotide re site. The probability of that site finding a match is one out of 4^4 or 256, meaning that on average a four cutter finds a match every 256 nucleotides. For a six cutter, the average fragment length is 4^6 or 4096. In the case of ambiguity codes the chances are finding the match are better: an R (A|T) has 1/2 chance of finding a match in a random sequence. Therefore, for RGCGCY the probability is one out of (2*4*4*4*4*2) which exactly the same as for a five cutter! Cutter, although it can have non-integer values turns out to be a useful and simple measure. From bug 2178: VHDB are ambiguity symbols that match three different nucleotides, so they contribute less to the effective recognition sequence length than e.g. Y which matches only two nucleotides. A symbol which matches n of the 4 nucleotides has an effective length of 1 - log(n) / log(4). =cut sub cutter { my ($self)=@_; $_ = uc $self->string; my $cutter = tr/[ATGC]//d; my $count = tr/[MRWSYK]//d; $cutter += $count/2; $count = tr/[VHDB]//d; $cutter += $count * (1 - log(3) / log(4)); return $cutter; } =head2 is_palindromic Title : is_palindromic Alias : palindromic Usage : $re->is_palindromic(); Function : Determines if the recognition sequence is palindromic : for the current restriction enzyme. Returns : Boolean Argument : n/a Throws : n/a A palindromic site (EcoRI): 5-GAATTC-3 3-CTTAAG-5 =cut sub is_palindromic { my $self = shift; return $self->{_palindromic} if defined $self->{_palindromic}; if ($self->string eq $self->revcom) { return $self->{_palindromic}=1; } return $self->{_palindromic} = 0; } sub palindromic { shift->is_palindromic(@_) } =head2 is_symmetric Title : is_symmetric Alias : symmetric Usage : $re->is_symmetric(); Function : Determines if the enzyme is a symmetric cutter Returns : Boolean Argument : none A symmetric but non-palindromic site (HindI): v 5-C A C-3 3-G T G-5 ^ =cut sub is_symmetric { no warnings qw( uninitialized ); my $self = shift; return $self->{_symmetric} if defined $self->{_symmetric}; if ($self->is_palindromic) { return $self->{_symmetric} = 1; } if ($self->cut == length($self->string) - $self->complementary_cut) { return $self->{_symmetric}=1; } return $self->{_symmetric} = 0; } sub symmetric { shift->is_symmetric(@_) } =head2 overhang Title : overhang Usage : $re->overhang(); Function : Determines the overhang of the restriction enzyme Returns : "5'", "3'", "blunt" of undef Argument : n/a Throws : n/a A blunt site in SmaI returns C 5' C C C^G G G 3' 3' G G G^C C C 5' A 5' overhang in EcoRI returns C<5'> 5' G^A A T T C 3' 3' C T T A A^G 5' A 3' overhang in KpnI returns C<3'> 5' G G T A C^C 3' 3' C^C A T G G 5' =cut sub overhang { my $self = shift; unless ($self->{'_cut'} && $self->{'_rc_cut'}) { return "unknown"; } if ($self->{_cut} < $self->{_rc_cut}) { $self->{_overhang}="5'"; } elsif ($self->{_cut} == $self->{_rc_cut}) { $self->{_overhang}="blunt"; } elsif ($self->{_cut} > $self->{_rc_cut}) { $self->{_overhang}="3'"; } else { $self->{_overhang}="unknown"; } return $self->{_overhang} } =head2 overhang_seq Title : overhang_seq Usage : $re->overhang_seq(); Function : Determines the overhang sequence of the restriction enzyme Returns : a Bio::LocatableSeq Argument : n/a Throws : n/a I do not think it is necessary to create a seq object of these. (Heikki) Note: returns empty string for blunt sequences and undef for ones that we don't know. Compare these: A blunt site in SmaI returns empty string 5' C C C^G G G 3' 3' G G G^C C C 5' A 5' overhang in EcoRI returns C 5' G^A A T T C 3' 3' C T T A A^G 5' A 3' overhang in KpnI returns C 5' G G T A C^C 3' 3' C^C A T G G 5' Note that you need to use method L to decide whether it is a 5' or 3' overhang!!! Note: The overhang stuff does not work if the site is asymmetric! Rethink! =cut sub overhang_seq { my $self = shift; # my $overhang->Bio::PrimarySeq(-id=>$self->name . '-overhang', # -verbose=>$self->verbose, # -alphabet=>'dna'); return '' if $self->overhang eq 'blunt' ; unless ($self->{_cut} && $self->{_rc_cut}) { # lets just check that we really can't figure it out $self->cut; $self->complementary_cut; unless ($self->{_cut} && $self->{_rc_cut}) { return; } } # this is throwing an error for sequences outside the restriction # site (eg ^NNNNGATCNNNN^) # So if this is the case we need to fake these guys if (($self->{_cut}<0) || ($self->{_rc_cut}<0) || ($self->{_cut}>$self->seq->length) || ($self->{_rc_cut}>$self->seq->length)) { my $tempseq=$self->site; my ($five, $three)=split /\^/, $tempseq; if ($self->{_cut} > $self->{_rc_cut}) { return substr($five, $self->{_rc_cut}) } elsif ($self->{_cut} < $self->{_rc_cut}) { return substr($three, 0, $self->{_rc_cut}) } else { return ''; } } if ($self->{_cut} > $self->{_rc_cut}) { return $self->seq->subseq($self->{_rc_cut}+1,$self->{_cut}); } elsif ($self->{_cut} < $self->{_rc_cut}) { return $self->seq->subseq($self->{_cut}+1, $self->{_rc_cut}); } else { return ''; } } =head2 compatible_ends Title : compatible_ends Usage : $re->compatible_ends($re2); Function : Determines if the two restriction enzyme cut sites have compatible ends. Returns : 0 if not, 1 if only one pair ends match, 2 if both ends. Argument : a Bio::Restriction::Enzyme Throws : unless the argument is a Bio::Resriction::Enzyme and if there are Ns in the ovarhangs In case of type II enzymes which which cut symmetrically, this function can be considered to return a boolean value. =cut sub compatible_ends { my ($self, $re) = @_; $self->throw("Need a Bio::Restriction::Enzyme as an argument, [$re]") unless $re->isa('Bio::Restriction::Enzyme'); # $self->throw("Only type II enzymes work now") # unless $self->type eq 'II'; $self->debug("N(s) in overhangs. Can not compare") if $self->overhang_seq =~ /N/ or $re->overhang_seq =~ /N/; return 2 if $self->overhang_seq eq $re->overhang_seq and $self->overhang eq $re->overhang; return 0; } =head2 is_ambiguous Title : is_ambiguous Usage : $re->is_ambiguous(); Function : Determines if the restriction enzyme contains ambiguous sequences Returns : Boolean Argument : n/a Throws : n/a =cut sub is_ambiguous { my $self = shift; return $self->string =~ m/[^AGCT]/ ? 1 : 0 ; } =head2 Additional methods from Rebase =cut =head2 is_prototype Title : is_prototype Usage : $re->is_prototype Function : Get/Set method for finding out if this enzyme is a prototype Example : $re->is_prototype(1) Returns : Boolean Args : none Prototype enzymes are the most commonly available and usually first enzymes discoverd that have the same recognition site. Using only prototype enzymes in restriction analysis avoids redundancy and speeds things up. =cut sub is_prototype { my ($self, $value) = @_; if (defined $value) { return $self->{'_is_prototype'} = $value ; } if (defined $self->{'_is_prototype'}) { return $self->{'_is_prototype'} } else { $self->warn("Can't unequivocally assign prototype based on input format alone"); return } } =head2 is_neoschizomer Title : is_neoschizomer Usage : $re->is_neoschizomer Function : Get/Set method for finding out if this enzyme is a neoschizomer Example : $re->is_neoschizomer(1) Returns : Boolean Args : none Neoschizomers are distinguishable from the prototype enzyme by having a different cleavage pattern. Note that not all formats report this =cut sub is_neoschizomer { my ($self, $value) = @_; if (defined $value) { return $self->{'_is_neoschizomer'} = $value ; } if (defined $self->{'_is_neoschizomer'}) { return $self->{'_is_neoschizomer'} } else { $self->warn("Can't unequivocally assign neoschizomer based on input format alone"); return } } =head2 prototype_name Title : prototype_name Alias : prototype Usage : $re->prototype_name Function : Get/Set method for the name of prototype for this enzyme's recognition site Example : $re->prototype_name(1) Returns : prototype enzyme name string or an empty string Args : optional prototype enzyme name string If the enzyme itself is the prototype, its own name is returned. Not to confuse the negative result with an unset value, use method L. This method is called I rather than I, because it returns a string rather than on object. =cut sub prototype_name { my $self = shift; $self->{'_prototype'} = shift if @_; return $self->name if $self->{'_is_prototype'}; return $self->{'_prototype'} || ''; } sub prototype { shift->prototype_name(@_) } =head2 isoschizomers Title : isoschizomers Alias : isos Usage : $re->isoschizomers(@list); Function : Gets/Sets a list of known isoschizomers (enzymes that recognize the same site, but don't necessarily cut at the same position). Arguments : A reference to an array that contains the isoschizomers Returns : A reference to an array of the known isoschizomers or 0 if not defined. This has to be the hardest name to spell, so now you can use the alias 'isos'. Added for compatibility to REBASE =cut sub isoschizomers { my ($self) = shift; push @{$self->{_isoschizomers}}, @_ if @_; # make sure that you don't dereference if null # chad believes quite strongly that you should return # a reference to an array anyway. don't bother dereferencing. # i'll post that to the list. if ($self->{'_isoschizomers'}) { return @{$self->{_isoschizomers}}; } } sub isos { shift->isoschizomers(@_) } =head2 purge_isoschizomers Title : purge_isoschizomers Alias : purge_isos Usage : $re->purge_isoschizomers(); Function : Purges the set of isoschizomers for this enzyme Arguments : Returns : 1 =cut sub purge_isoschizomers { my ($self) = shift; $self->{_isoschizomers} = []; } sub purge_isos { shift->purge_isoschizomers(@_) } =head2 methylation_sites Title : methylation_sites Usage : $re->methylation_sites(\%sites); Function : Gets/Sets known methylation sites (positions on the sequence that get modified to promote or prevent cleavage). Arguments : A reference to a hash that contains the methylation sites Returns : A reference to a hash of the methylation sites or an empty string if not defined. There are three types of methylation sites: =over 3 =item * (6) = N6-methyladenosine =item * (5) = 5-methylcytosine =item * (4) = N4-methylcytosine =back These are stored as 6, 5, and 4 respectively. The hash has the sequence position as the key and the type of methylation as the value. A negative number in the sequence position indicates that the DNA is methylated on the complementary strand. Note that in REBASE, the methylation positions are given Added for compatibility to REBASE. =cut sub methylation_sites { my $self = shift; while (@_) { my $key = shift; $self->{'_methylation_sites'}->{$key} = shift; } return %{$self->{_methylation_sites}}; } =head2 purge_methylation_sites Title : purge_methylation_sites Usage : $re->purge_methylation_sites(); Function : Purges the set of methylation_sites for this enzyme Arguments : Returns : =cut sub purge_methylation_sites { my ($self) = shift; $self->{_methylation_sites} = {}; } =head2 microbe Title : microbe Usage : $re->microbe($microbe); Function : Gets/Sets microorganism where the restriction enzyme was found Arguments : A scalar containing the microbes name Returns : A scalar containing the microbes name or 0 if not defined Added for compatibility to REBASE =cut sub microbe { my ($self, $microbe) = @_; if ($microbe) { $self->{_microbe}=$microbe; } return $self->{_microbe} || ''; } =head2 source Title : source Usage : $re->source('Rob Edwards'); Function : Gets/Sets the person who provided the enzyme Arguments : A scalar containing the persons name Returns : A scalar containing the persons name or 0 if not defined Added for compatibility to REBASE =cut sub source { my ($self, $source) = @_; if ($source) { $self->{_source}=$source; } return $self->{_source} || ''; } =head2 vendors Title : vendors Usage : $re->vendor(@list_of_companies); Function : Gets/Sets the a list of companies that you can get the enzyme from. Also sets the commercially_available boolean Arguments : A reference to an array containing the names of companies that you can get the enzyme from Returns : A reference to an array containing the names of companies that you can get the enzyme from Added for compatibility to REBASE =cut sub vendors { my $self = shift; push @{$self->{_vendors}}, @_ if @_; if ($self->{'_vendors'}) { return @{$self->{'_vendors'}}; } } =head2 purge_vendors Title : purge_vendors Usage : $re->purge_references(); Function : Purges the set of references for this enzyme Arguments : Returns : =cut sub purge_vendors { my ($self) = shift; $self->{_vendors} = []; } =head2 vendor Title : vendor Usage : $re->vendor(@list_of_companies); Function : Gets/Sets the a list of companies that you can get the enzyme from. Also sets the commercially_available boolean Arguments : A reference to an array containing the names of companies that you can get the enzyme from Returns : A reference to an array containing the names of companies that you can get the enzyme from Added for compatibility to REBASE =cut sub vendor { my $self = shift; return push @{$self->{_vendors}}, @_; return $self->{_vendors}; } =head2 references Title : references Usage : $re->references(string); Function : Gets/Sets the references for this enzyme Arguments : an array of string reference(s) (optional) Returns : an array of references Use L to reset the list of references This should be a L object, but its not (yet) =cut sub references { my ($self) = shift; push @{$self->{_references}}, @_ if @_; return @{$self->{_references}}; } =head2 purge_references Title : purge_references Usage : $re->purge_references(); Function : Purges the set of references for this enzyme Arguments : Returns : 1 =cut sub purge_references { my ($self) = shift; $self->{_references} = []; } =head2 clone Title : clone Usage : $re->clone Function : Deep copy of the object Arguments : - Returns : new Bio::Restriction::EnzymeI object This works as long as the object is a clean in-memory object using scalars, arrays and hashes. You have been warned. If you have module Storable, it is used, otherwise local code is used. Todo: local code cuts circular references. =cut # there's some issue here; deprecating and rolling another below/maj sub clone_depr { my ($self, $this) = @_; eval { require Storable; }; return Storable::dclone($self) unless $@; # modified from deep_copy() @ http://www.stonehenge.com/merlyn/UnixReview/col30.html unless ($this) { my $new; foreach my $k (keys %$self) { if (not ref $self->{$k}) { $new->{$k} = $self->{$k}; } else { $new->{$k} = $self->clone($self->{$k}); } #print Dumper $new; } bless $new, ref($self); return $new; } if (not ref $this) { $this; } elsif (ref $this eq "ARRAY") { [map $self->clone($_), @$this]; } elsif (ref $this eq "HASH") { +{map { $_ => $self->clone($this->{$_}) } keys %$this}; } else { # objects return if $this->isa('Bio::Restriction::EnzymeI'); return $this->clone if $this->can('clone'); my $obj; foreach my $k (keys %$this) { if (not ref $this->{$k}) { $obj->{$k} = $this->{$k}; } else { $obj->{$k} = $this->clone($this->{$k}); } } bless $obj, ref($this); return $obj; } } sub clone { my $self = shift; my ($this, $visited) = @_; unless (defined $this) { my %h; tie %h, 'Tie::RefHash'; my $visited = \%h; return $self->clone($self, $visited); } my $thing; for ($this) { if (ref) { return $visited->{$this} if $visited->{$this}; } # scalar (!ref) && do { $thing = $this; last; }; # object (ref =~ /^Bio::/) && do { $thing = {}; bless($thing, ref); $visited->{$this} = $thing; foreach my $attr (keys %{$_}) { $thing->{$attr} = (defined $_->{$attr} ? $self->clone($_->{$attr},$visited) : undef ); } last; }; (ref eq 'ARRAY') && do { $thing = []; $visited->{$this} = $thing; foreach my $elt (@{$_}) { push @$thing, (defined $elt ? $self->clone($elt,$visited) : undef); } last; }; (ref eq 'HASH') && do { $thing = {}; $visited->{$this} = $thing; no warnings qw( uninitialized ); # avoid 'uninitialized value' warning against $key foreach my $key (%{$_}) { $thing->{$key} = (defined $_->{key} ? $self->clone( $_->{$key},$visited) : undef ); } use warnings; last; }; (ref eq 'SCALAR') && do { $thing = ${$_}; $visited->{$this} = $thing; $thing = \$thing; last; }; } return $thing; } =head2 _expand Title : _expand Function : Expand nucleotide ambiguity codes to their representative letters Returns : The full length string Arguments : The string to be expanded. Stolen from the original RestrictionEnzyme.pm =cut sub _expand { my $str = shift; $str =~ s/N|X/\./g; $str =~ s/R/\[AG\]/g; $str =~ s/Y/\[CT\]/g; $str =~ s/S/\[GC\]/g; $str =~ s/W/\[AT\]/g; $str =~ s/M/\[AC\]/g; $str =~ s/K/\[TG\]/g; $str =~ s/B/\[CGT\]/g; $str =~ s/D/\[AGT\]/g; $str =~ s/H/\[ACT\]/g; $str =~ s/V/\[ACG\]/g; return $str; } 1; BioPerl-1.007002/Bio/Restriction/EnzymeCollection.pm000444000766000024 2703513155576320 22401 0ustar00cjfieldsstaff000000000000#------------------------------------------------------------------------------- # # BioPerl module Bio::Restriction::EnzymeCollection # # Please direct questions and support issues to # # Cared for by Rob Edwards # # You may distribute this module under the same terms as perl itself #------------------------------------------------------------------------------- ## POD Documentation: =head1 NAME Bio::Restriction::EnzymeCollection - Set of restriction endonucleases =head1 SYNOPSIS use Bio::Restriction::EnzymeCollection; # Create a collection with the default enzymes. my $default_collection = Bio::Restriction::EnzymeCollection->new(); # Or create a collection from a REBASE 'withrefm' file obtained from # ftp://ftp.neb.com/pub/rebase/. (See Bio::Restriction::IO for more # information.) my $rebase = Bio::Restriction::IO->new( -file => 'withrefm.610', -format => 'withrefm' ); my $rebase_collection = $rebase->read(); # Or create an empty collection and set the enzymes later. See # 'CUSTOM COLLECTIONS' below for more information. my $empty_collection = Bio::Restriction::EnzymeCollection->new( -empty => 1 ); # Get an array of Bio::Restriction::Enzyme objects from the collection. my @enzymes = $default_collection->each_enzyme(); # Get a Bio::Restriction::Enzyme object for a particular enzyme by name. my $enz = $default_collection->get_enzyme( 'EcoRI' ); # Get a Bio::Restriction::EnzymeCollection object containing the enzymes # that have the equivalent of 6-bp recognition sequences. my $six_cutters = $default_collection->cutters( 6 ); # Get a Bio::Restriction::EnzymeCollection object containing the enzymes # that are rare cutters. my $rare_cutters = $default_collection->cutters( -start => 6, -end => 8 ); # Get a Bio::Restriction::EnzymeCollection object that contains enzymes # that generate blunt ends: my $blunt_cutters = $default_collection->blunt_enzymes(); # See 'CUSTOM COLLECTIONS' below for an example of creating a # Bio::Restriction::EnzymeCollection object with a specified subset of # enzymes using methods provided by the Bio::RestrictionEnzyme class. =head1 DESCRIPTION Bio::Restriction::EnzymeCollection represents a collection of restriction enzymes. If you create a new collection directly rather than from a REBASE file using L, it will be populated by a default set of enzymes with site and cut information only. Use L to figure out which enzymes are available and where they cut your sequence. =head1 CUSTOM COLLECTIONS Note that the underlying L objects have a rich variety of methods that allow more complicated selections than the methods that are defined by Bio::Restriction::EnzymeCollection. For example, the way to create a custom collection of Type II enzymes is as follows: my $complete_collection = Bio::Restriction::EnzymeCollection->new(); my $type_ii_collection = Bio::Restriction::EnzymeCollection->new( -empty => 1 ); $type_ii_collection->enzymes( grep { $_->type() eq 'II' } $complete_collection->each_enzyme() ); =head1 SEE ALSO L - read in enzymes from REBASE files L - figure out what enzymes cut a sequence L - define a single restriction enzyme =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Rob Edwards, redwards@utmem.edu =head1 CONTRIBUTORS Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 COPYRIGHT Copyright (c) 2003 Rob Edwards. Some of this work is Copyright (c) 1997-2002 Steve A. Chervitz. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 APPENDIX Methods beginning with a leading underscore are considered private and are intended for internal use by this module. They are not considered part of the public interface and are described here for documentation purposes only. =cut package Bio::Restriction::EnzymeCollection; use strict; use Bio::Restriction::Enzyme; use Bio::Restriction::IO; use Data::Dumper; use base qw(Bio::Root::Root); =head2 new Title : new Function : Initializes the Restriction::EnzymeCollection object Returns : The Restriction::EnzymeCollection object Arguments : optional named parameter -empty Set parameter -empty to true if you do NOT want the collection be populated by the default set of prototype type II enzymes. Alternatively, pass an array of enzymes to -enzymes parameter. =cut sub new { my($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($empty, $enzymes) = $self->_rearrange([qw( EMPTY ENZYMES )], @args); $self->{'_all_enzymes'} = []; $self->{'_enzymes'} = {}; return $self if $empty; if ($enzymes) { # as advertised in pod/maj $self->throw( "Arg to -enzymes must be an arrayref to Bio::Restriction::Enzyme objects") unless ref($enzymes) eq 'ARRAY'; $self->enzymes(@$enzymes); return $self; } else { # the default set of enzymes my $in = Bio::Restriction::IO->new(-verbose => $self->verbose); return $in->read; } } =head2 Manipulate the enzymes within the collection =cut =head2 enzymes Title : enzyme Function : add/get method for enzymes and enzyme collections Returns : object itself Arguments : array of Bio::Restriction::Enzyme and Bio::Restriction::EnzymeCollection objects =cut sub enzymes { my ($self, @enzs)=@_; foreach my $e (@enzs) { if ( ref $e eq '') { print "|$e|\n"; } elsif ($e->isa('Bio::Restriction::EnzymeI')) { push(@{$self->{'_all_enzymes'}},$e); $self->{'_enzymes'}->{$e->name} = $e; } elsif ($e->isa('Bio::Restriction::EnzymeCollection')) { $self->enzymes($e->each_enzyme); } else { my $r = 1; $self->warn("EnzymeCollection can not deal with ". ref($e)." objects"); } } return $self; } # # method to remove duplicates? # =head2 each_enzyme Title : each_enzyme Function : get an array of enzymes Returns : array of Bio::Restriction::Enzyme objects Arguments : - =cut sub each_enzyme { my $self = shift; return @{$self->{'_all_enzymes'}}; } =head2 get_enzyme Title : get_enzyme Function : Gets a Bio::Restriction::Enzyme object for the enzyme name Returns : A Bio::Restriction::Enzyme object or undef Arguments : An enzyme name that is in the collection =cut sub get_enzyme { my ($self, $name)=@_; return $self->{'_enzymes'}->{$name}; } =head2 available_list Title : available_list Function : Gets a list of all the enzymes that we know about Returns : A reference to an array with all the enzyme names that we have defined or 0 if none are defined Arguments : Nothing Comments : Note, I maintain this for backwards compatibility, but I don't like the name as it is very ambiguous =cut sub available_list { my ($self, $size)=@_; my @keys = sort keys %{$self->{'_enzymes'}}; return @keys; } =head2 longest_cutter Title : longest_cutter Function : Gets the enzyme with the longest recognition site Returns : A Bio::Restriction::Enzyme object Arguments : Nothing Comments : Note, this is used by Bio::Restriction::Analysis to figure out what to do with circular sequences =cut sub longest_cutter { my ($self)=@_; my $longest=0; my $longest_enz='.'; foreach my $enz ($self->each_enzyme) { my $len=$enz->recognition_length; if ($len > $longest) {$longest=$len; $longest_enz=$enz} } return $longest_enz; } =head2 Filter enzymes =cut =head2 blunt_enzymes Title : blunt_enzymes Function : Gets a list of all the enzymes that are blunt cutters Returns : A reference to an array with all the enzyme names that are blunt cutters or 0 if none are defined Arguments : Nothing Comments : This is an example of the kind of filtering better done by the scripts using the rich collection of methods in Bio::Restriction::Enzyme. =cut sub blunt_enzymes { my $self=shift; my $bs = Bio::Restriction::EnzymeCollection->new(-empty => 1); return $bs->enzymes( grep { $_->overhang eq 'blunt' } $self->each_enzyme ); } =head2 cutters Title : cutters Function : Gets a list of all the enzymes that recognize a certain size, e.g. 6-cutters Usage : $cutters = $collection->cutters(6); Returns : A reference to an array with all the enzyme names that are x cutters or 0 if none are defined Arguments : A positive number for the size of cutters to return OR A range: (-start => 6, -end => 8, -inclusive => 1, -exclusive = 0 ) The default for a range is 'inclusive' =cut sub cutters { my ($self) = shift; return unless @_; # no argument if (scalar @_ == 1 ) { my $size = shift; my @sizes; (ref $size eq 'ARRAY') ? push @sizes, @{$size} : push @sizes, $size; my $bs = Bio::Restriction::EnzymeCollection->new(-empty => 1); for my $size (@sizes) { $self->throw("Need a positive number [$size]") unless $size =~ /[+]?[\d\.]+/; foreach my $e ($self->each_enzyme) { ##print $e->name, ": ", $e->cutter, "\n" if $e->cutter == $size; $bs->enzymes($e) if $e->cutter == $size; } } return $bs; } else { # named arguments my ($start, $end, $inclusive, $exclusive ) = $self->_rearrange([qw( START END INCLUSIVE EXCLUSIVE )], @_); $self->throw("Start needs a positive number [$start]") unless $start =~ /[+]?[\d\.]+/; $self->throw("End needs a positive number [$end]") unless $end =~ /[+]?[\d\.]+/; my $limits; $inclusive = 1 if $inclusive or not $exclusive; $inclusive = 0 if $exclusive; my $bs = Bio::Restriction::EnzymeCollection->new(-empty => 1); if ($inclusive) { foreach my $e ($self->each_enzyme) { $bs->enzymes($e) if $e->cutter >= $start and $e->cutter <= $end; } } else { foreach my $e ($self->each_enzyme) { $bs->enzymes($e) if $e->cutter > $start and $e->cutter < $end; } } return $bs; } } 1; BioPerl-1.007002/Bio/Restriction/EnzymeI.pm000444000766000024 4701413155576320 20475 0ustar00cjfieldsstaff000000000000#------------------------------------------------------------------ # # BioPerl module Bio::Restriction::EnzymeI # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho, heikki-at-bioperl-dot-org # # You may distribute this module under the same terms as perl itself #------------------------------------------------------------------ ## POD Documentation: =head1 NAME Bio::Restriction::EnzymeI - Interface class for restriction endonuclease =head1 SYNOPSIS # do not run this class directly =head1 DESCRIPTION This module defines methods for a single restriction endonuclease. For an implementation, see L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 CONTRIBUTORS Rob Edwards, redwards@utmem.edu =head1 SEE ALSO L =head1 APPENDIX Methods beginning with a leading underscore are considered private and are intended for internal use by this module. They are not considered part of the public interface and are described here for documentation purposes only. =cut package Bio::Restriction::EnzymeI; use strict; use base qw(Bio::Root::RootI); =head1 Essential methods =cut =head2 name Title : name Usage : $re->name($newval) Function : Gets/Sets the restriction enzyme name Example : $re->name('EcoRI') Returns : value of name Args : newvalue (optional) This will also clean up the name. I have added this because some people get confused about restriction enzyme names. The name should be One upper case letter, and two lower case letters (because it is derived from the organism name, eg. EcoRI is from E. coli). After that it is all confused, but the numbers should be roman numbers not numbers, therefore we'll correct those. At least this will provide some standard, I hope. =cut sub name { shift->throw_not_implemented; } =head2 site Title : site Usage : $re->site(); Function : Gets/sets the recognition sequence for the enzyme. Example : $seq_string = $re->site(); Returns : String containing recognition sequence indicating : cleavage site as in 'G^AATTC'. Argument : n/a Throws : n/a Side effect: the sequence is always converted to upper case. The cut site can also be set by using methods L and L. This will pad out missing sequence with N's. For example the enzyme Acc36I cuts at ACCTGC(4/8). This will be returned as ACCTGCNNNN^ Note that the common notation ACCTGC(4/8) means that the forward strand cut is four nucleotides after the END of the recognition site. The forward cut() in the coordinates used here in Acc36I ACCTGC(4/8) is at 6+4 i.e. 10. ** This is the main setable method for the recognition site. =cut sub site { shift->throw_not_implemented; } =head2 revcom_site Title : revcom_site Usage : $re->revcom_site(); Function : Gets/sets the complementary recognition sequence for the enzyme. Example : $seq_string = $re->revcom_site(); Returns : String containing recognition sequence indicating : cleavage site as in 'G^AATTC'. Argument : Sequence of the site Throws : n/a This is the same as site, except it returns the revcom site. For palindromic enzymes these two are identical. For non-palindromic enzymes they are not! See also L above. =cut sub cuts_after { shift->throw_not_implemented; } =head2 cut Title : cut Usage : $num = $re->cut(1); Function : Sets/gets an integer indicating the position of cleavage relative to the 5' end of the recognition sequence in the forward strand. For type II enzymes, sets the symmetrically positioned reverse strand cut site by calling complementary_cut(). Returns : Integer, 0 if not set Argument : an integer for the forward strand cut site (optional) Note that the common notation ACCTGC(4/8) means that the forward strand cut is four nucleotides after the END of the recognition site. The forward cut in the coordinates used here in Acc36I ACCTGC(4/8) is at 6+4 i.e. 10. Note that REBASE uses notation where cuts within symmetic sites are marked by '^' within the forward sequence but if the site is asymmetric the parenthesis syntax is used where numbering ALWAYS starts from last nucleotide in the forward strand. That's why AciI has a site usually written as CCGC(-3/-1) actualy cuts in C^C G C G G C^G In our notation, these locations are 1 and 3. The cuts locations in the notation used are relative to the first (non-N) nucleotide of the reported forward strand of the recognition sequence. The following diagram numbers the phosphodiester bonds (marked by + ) which can be cut by the restriction enzymes: 1 2 3 4 5 6 7 8 ... N + N + N + N + N + G + A + C + T + G + G + N + N + N ... -5 -4 -3 -2 -1 =cut sub cut { shift->throw_not_implemented; } =head2 complementary_cut Title : complementary_cut Usage : $num = $re->complementary_cut('1'); Function : Sets/Gets an integer indicating the position of cleavage : on the reverse strand of the restriction site. Returns : Integer Argument : An integer (optional) Throws : Exception if argument is non-numeric. This method determines the cut on the reverse strand of the sequence. For most enzymes this will be within the sequence, and will be set automatically based on the forward strand cut, but it need not be. B that the returned location indicates the location AFTER the first non-N site nucleotide in the FORWARD strand. =cut sub complementary_cut { shift->throw_not_implemented; } =head1 Read only (usually) recognition site descriptive methods =cut =head2 type Title : type Usage : $re->type(); Function : Get/set the restriction system type Returns : Argument : optional type: ('I'|II|III) Restriction enzymes have been catezorized into three types. Some REBASE formats give the type, but the following rules can be used to classify the known enzymes: =over 4 =item 1 Bipartite site (with 6-8 Ns in the middle and the cut site is E 50 nt away) =E type I =item 2 Site length E 3 =E type I =item 3 5-6 asymmetric site and cuts E20 nt away =E type III =item 4 All other =E type II =back There are some enzymes in REBASE which have bipartite recognition site and cat far from the site but are still classified as type I. I've no idea if this is really so. =cut sub type { shift->throw_not_implemented; } =head2 seq Title : seq Usage : $re->seq(); Function : Get the Bio::PrimarySeq.pm object representing : the recognition sequence Returns : A Bio::PrimarySeq object representing the enzyme recognition site Argument : n/a Throws : n/a =cut sub seq { shift->throw_not_implemented; } =head2 string Title : string Usage : $re->string(); Function : Get a string representing the recognition sequence. Returns : String. Does NOT contain a '^' representing the cut location as returned by the site() method. Argument : n/a Throws : n/a =cut sub string { shift->throw_not_implemented; } =head2 revcom Title : revcom Usage : $re->revcom(); Function : Get a string representing the reverse complement of : the recognition sequence. Returns : String Argument : n/a Throws : n/a =cut sub revcom { shift->throw_not_implemented; } =head2 recognition_length Title : recognition_length Usage : $re->recognition_length(); Function : Get the length of the RECOGNITION sequence. This is the total recognition sequence, inluding the ambiguous codes. Returns : An integer Argument : Nothing See also: L =cut sub recognition_length { shift->throw_not_implemented; } =head2 non_ambiguous_length Title : non_ambiguous_length Usage : $re->non_ambiguous_length(); Function : Get the nonambiguous length of the RECOGNITION sequence. This is the total recognition sequence, excluding the ambiguous codes. Returns : An integer Argument : Nothing See also: L =cut sub non_ambiguous_length { shift->throw_not_implemented; } =head2 cutter Title : cutter Usage : $re->cutter Function : Returns the "cutter" value of the recognition site. This is a value relative to site length and lack of ambiguity codes. Hence: 'RCATGY' is a five (5) cutter site and 'CCTNAGG' a six cutter This measure correlates to the frequency of the enzyme cuts much better than plain recognition site length. Example : $re->cutter Returns : integer or float number Args : none Why is this better than just stripping the ambiguous codes? Think about it like this: You have a random sequence; all nucleotides are equally probable. You have a four nucleotide re site. The probability of that site finding a match is one out of 4^4 or 256, meaning that on average a four cutter finds a match every 256 nucleotides. For a six cutter, the average fragment length is 4^6 or 4096. In the case of ambiguity codes the chances are finding the match are better: an R (A|T) has 1/2 chance of finding a match in a random sequence. Therefore, for RGCGCY the probability is one out of (2*4*4*4*4*2) which exactly the same as for a five cutter! Cutter, although it can have non-integer values turns out to be a useful and simple measure. From bug 2178: VHDB are ambiguity symbols that match three different nucleotides, so they contribute less to the effective recognition sequence length than e.g. Y which matches only two nucleotides. A symbol which matches n of the 4 nucleotides has an effective length of 1 - log(n) / log(4). =cut sub cutter { shift->throw_not_implemented; } =head2 is_palindromic Title : is_palindromic Usage : $re->is_palindromic(); Function : Determines if the recognition sequence is palindromic : for the current restriction enzyme. Returns : Boolean Argument : n/a Throws : n/a A palindromic site (EcoRI): 5-GAATTC-3 3-CTTAAG-5 =cut sub is_palindromic { shift->throw_not_implemented; } =head2 overhang Title : overhang Usage : $re->overhang(); Function : Determines the overhang of the restriction enzyme Returns : "5'", "3'", "blunt" of undef Argument : n/a Throws : n/a A blunt site in SmaI returns C 5' C C C^G G G 3' 3' G G G^C C C 5' A 5' overhang in EcoRI returns C<5'> 5' G^A A T T C 3' 3' C T T A A^G 5' A 3' overhang in KpnI returns C<3'> 5' G G T A C^C 3' 3' C^C A T G G 5' =cut sub overhang { shift->throw_not_implemented; } =head2 overhang_seq Title : overhang_seq Usage : $re->overhang_seq(); Function : Determines the overhang sequence of the restriction enzyme Returns : a Bio::LocatableSeq Argument : n/a Throws : n/a I do not think it is necessary to create a seq object of these. (Heikki) Note: returns empty string for blunt sequences and undef for ones that we don't know. Compare these: A blunt site in SmaI returns empty string 5' C C C^G G G 3' 3' G G G^C C C 5' A 5' overhang in EcoRI returns C 5' G^A A T T C 3' 3' C T T A A^G 5' A 3' overhang in KpnI returns C 5' G G T A C^C 3' 3' C^C A T G G 5' Note that you need to use method L to decide whether it is a 5' or 3' overhang!!! Note: The overhang stuff does not work if the site is asymmetric! Rethink! =cut sub overhang_seq { shift->throw_not_implemented; } =head2 compatible_ends Title : compatible_ends Usage : $re->compatible_ends($re2); Function : Determines if the two restriction enzyme cut sites have compatible ends. Returns : 0 if not, 1 if only one pair ends match, 2 if both ends. Argument : a Bio::Restriction::Enzyme Throws : unless the argument is a Bio::Resriction::Enzyme and if there are Ns in the ovarhangs In case of type II enzymes which which cut symmetrically, this function can be considered to return a boolean value. =cut sub compatible_ends {shift->throw_not_implemented;} =head2 is_ambiguous Title : is_ambiguous Usage : $re->is_ambiguous(); Function : Determines if the restriction enzyme contains ambiguous sequences Returns : Boolean Argument : n/a Throws : n/a =cut sub is_ambiguous { shift->throw_not_implemented; } =head2 Additional methods from Rebase =cut =head2 is_prototype Title : is_prototype Usage : $re->is_prototype Function : Get/Set method for finding out if this enzyme is a prototype Example : $re->is_prototype(1) Returns : Boolean Args : none Prototype enzymes are the most commonly available and usually first enzymes discoverd that have the same recognition site. Using only prototype enzymes in restriciton analysis avoids redundacy and speeds things up. =cut sub is_prototype { shift->throw_not_implemented; } =head2 prototype_name Title : prototype_name Usage : $re->prototype_name Function : Get/Set method for the name of prototype for this enzyme's recognition site Example : $re->prototype_name(1) Returns : prototype enzyme name string or an empty string Args : optional prototype enzyme name string If the enzyme itself is the protype, its own name is returned. Not to confuse the negative result with an unset value, use method L. This method is called I rather than I, because it returns a string rather than on object. =cut sub prototype_name { shift->throw_not_implemented; } =head2 isoschizomers Title : isoschizomers Usage : $re->isoschizomers(@list); Function : Gets/Sets a list of known isoschizomers (enzymes that recognize the same site, but don't necessarily cut at the same position). Arguments : A reference to an array that contains the isoschizomers Returns : A reference to an array of the known isoschizomers or 0 if not defined. Added for compatibility to REBASE =cut sub isoschizomers { shift->throw_not_implemented; } =head2 purge_isoschizomers Title : purge_isoschizomers Usage : $re->purge_isoschizomers(); Function : Purges the set of isoschizomers for this enzyme Arguments : Returns : 1 =cut sub purge_isoschizomers { shift->throw_not_implemented; } =head2 methylation_sites Title : methylation_sites Usage : $re->methylation_sites(\%sites); Function : Gets/Sets known methylation sites (positions on the sequence that get modified to promote or prevent cleavage). Arguments : A reference to a hash that contains the methylation sites Returns : A reference to a hash of the methylation sites or an empty string if not defined. There are three types of methylation sites: =over 3 =item * (6) = N6-methyladenosine =item * (5) = 5-methylcytosine =item * (4) = N4-methylcytosine =back These are stored as 6, 5, and 4 respectively. The hash has the sequence position as the key and the type of methylation as the value. A negative number in the sequence position indicates that the DNA is methylated on the complementary strand. Note that in REBASE, the methylation positions are given Added for compatibility to REBASE. =cut sub methylation_sites { shift->throw_not_implemented; } =head2 purge_methylation_sites Title : purge_methylation_sites Usage : $re->purge_methylation_sites(); Function : Purges the set of methylation_sites for this enzyme Arguments : Returns : =cut sub purge_methylation_sites { shift->throw_not_implemented; } =head2 microbe Title : microbe Usage : $re->microbe($microbe); Function : Gets/Sets microorganism where the restriction enzyme was found Arguments : A scalar containing the microbes name Returns : A scalar containing the microbes name or 0 if not defined Added for compatibility to REBASE =cut sub microbe { shift->throw_not_implemented; } =head2 source Title : source Usage : $re->source('Rob Edwards'); Function : Gets/Sets the person who provided the enzyme Arguments : A scalar containing the persons name Returns : A scalar containing the persons name or 0 if not defined Added for compatibility to REBASE =cut sub source { shift->throw_not_implemented; } =head2 vendors Title : vendors Usage : $re->vendor(@list_of_companies); Function : Gets/Sets the a list of companies that you can get the enzyme from. Also sets the commercially_available boolean Arguments : A reference to an array containing the names of companies that you can get the enzyme from Returns : A reference to an array containing the names of companies that you can get the enzyme from Added for compatibility to REBASE =cut sub vendors { shift->throw_not_implemented; } =head2 purge_vendors Title : purge_vendors Usage : $re->purge_references(); Function : Purges the set of references for this enzyme Arguments : Returns : =cut sub purge_vendors { shift->throw_not_implemented; } =head2 vendor Title : vendor Usage : $re->vendor(@list_of_companies); Function : Gets/Sets the a list of companies that you can get the enzyme from. Also sets the commercially_available boolean Arguments : A reference to an array containing the names of companies that you can get the enzyme from Returns : A reference to an array containing the names of companies that you can get the enzyme from Added for compatibility to REBASE =cut sub vendor { shift->throw_not_implemented; } =head2 references Title : references Usage : $re->references(string); Function : Gets/Sets the references for this enzyme Arguments : an array of string reference(s) (optional) Returns : an array of references Use L to reset the list of references This should be a L or L object, but its not (yet) =cut sub references { shift->throw_not_implemented; } =head2 purge_references Title : purge_references Usage : $re->purge_references(); Function : Purges the set of references for this enzyme Arguments : Returns : 1 =cut sub purge_references { shift->throw_not_implemented; } =head2 clone Title : clone Usage : $re->clone Function : Deep copy of the object Arguments : - Returns : new Bio::Restriction::EnzymeI object This works as long as the object is a clean in-memory object using scalars, arrays and hashes. You have been warned. If you have module Storable, it is used, otherwise local code is used. Todo: local code cuts circular references. =cut sub clone { shift->throw_not_implemented; } 1; BioPerl-1.007002/Bio/Restriction/IO.pm000444000766000024 1506413155576320 17424 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Restriction::IO # # Please direct questions and support issues to # # Cared for by Rob Edwards # # Copyright Rob Edwards # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Restriction::IO - Handler for sequence variation IO Formats =head1 SYNOPSIS use Bio::Restriction::IO; $in = Bio::Restriction::IO->new(-file => "inputfilename" , -format => 'withrefm'); my $res = $in->read; # a Bio::Restriction::EnzymeCollection =head1 DESCRIPTION L is a handler module for the formats in the Restriction IO set, e.g. C. It is the officially sanctioned way of getting at the format objects, which most people should use. The structure, conventions and most of the code is inherited from L. The main difference is that instead of using methods C, you drop C<_seq> from the method name. Also, instead of dealing only with individual L objects, C will slurp in all enzymes into a L object. For more details, see documentation in L. =head1 TO DO At the moment, these can be use mainly to get a custom set if enzymes in C or C formats into L or L objects. Using C format is highly experimental and is not recommmended at this time. This class inherits from L for convenience sake, though this should inherit from L. Get rid of L inheritance by copying relevant methods in. C methods are currently not implemented for any format except C. Using C even with C format is not recommended as it does not support multicut/multisite enzyme output. Should additional formats be supported (such as XML)? =head1 SEE ALSO L, L, L =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Rob Edwards, redwards@utmem.edu =head1 CONTRIBUTORS Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Restriction::IO; use strict; use vars qw(%FORMAT); use base qw(Bio::SeqIO); %FORMAT = ( 'itype2' => 'itype2', '8' => 'itype2', 'withrefm' => 'withrefm', '31' => 'withrefm', 'base' => 'base', '0' => 'base', 'bairoch' => 'bairoch', '19' => 'bairoch', 'macvector' => 'bairoch', 'vectorNTI' => 'bairoch', 'neo' => 'prototype', 'prototype' => 'prototype' ); =head2 new Title : new Usage : $stream = Bio::Restriction::IO->new(-file => $filename, -format => 'Format') Function: Returns a new seqstream Returns : A Bio::Restriction::IO::Handler initialised with the appropriate format Args : -file => $filename -format => format -fh => filehandle to attach to =cut sub new { my ($class, %param) = @_; my ($format); @param{ map { lc $_ } keys %param } = values %param; # lowercase keys $format = $FORMAT{$param{'-format'}} if defined $param{'-format'}; $format ||= $class->_guess_format( $param{-file} || $ARGV[0] ) || 'base'; $format = "\L$format"; # normalize capitalization to lower case return unless $class->_load_format_module($format); return "Bio::Restriction::IO::$format"->new(%param); } =head2 format Title : format Usage : $format = $stream->format() Function: Get the restriction format Returns : restriction format Args : none =cut # format() method inherited from Bio::Root::IO sub _load_format_module { my ($class, $format) = @_; my $module = "Bio::Restriction::IO::" . $format; my $ok; eval { $ok = $class->_load_module($module); }; if ( $@ ) { print STDERR <read Function: reads all the restrction enzymes from the stream Returns : a Bio::Restriction::EnzymeCollection object Args : =cut sub read { my ($self, $seq) = @_; $self->throw_not_implemented(); } sub next { my ($self, $seq) = @_; $self->throw_not_implemented(); } sub next_seq { my ($self, $seq) = @_; $self->throw_not_implemented(); } =head2 write Title : write Usage : $stream->write($seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Restriction::EnzymeCollection object =cut sub write { my ($self, $seq) = @_; $self->throw("Sorry, you cannot write to a generic ". "Bio::Restricion::IO object."); } sub write_seq { my ($self, $seq) = @_; $self->warn("These are not sequence objects. ". "Use method 'write' instead of 'write_seq'."); $self->write($seq); } =head2 _guess_format Title : _guess_format Usage : $obj->_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args : =cut sub _guess_format { my $class = shift; return unless $_ = shift; return 'flat' if /\.dat$/i; return 'xml' if /\.xml$/i; } 1; BioPerl-1.007002/Bio/Restriction/Enzyme000755000766000024 013155576320 17643 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Restriction/Enzyme/MultiCut.pm000444000766000024 1020413155576320 22121 0ustar00cjfieldsstaff000000000000#------------------------------------------------------------------ # # BioPerl module Bio::Restriction::Enzyme::MultiCut # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho, heikki-at-bioperl-dot-org # # You may distribute this module under the same terms as perl itself #------------------------------------------------------------------ ## POD Documentation: =head1 NAME Bio::Restriction::Enzyme::MultiCut - A single restriction endonuclease =head1 SYNOPSIS # set up a single restriction enzyme. This contains lots of # information about the enzyme that is generally parsed from a # rebase file and can then be read back use Bio::Restriction::Enzyme; =head1 DESCRIPTION This module defines a restriction endonuclease class where one object represents one of the distinct recognition sites for that enzyme. The method L stores references to other objects with alternative sites. In this schema each object within an EnzymeCollection can be checked for matching a sequence. REBASE report notation C means: Bsp24I 5' ^NNNNNNNNGACNNNNNNTGGNNNNNNNNNNNN^ 3' 3' ^NNNNNNNNNNNNNCTGNNNNNNACCNNNNNNN^ 5' =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 CONTRIBUTORS Rob Edwards, redwards@utmem.edu =head1 COPYRIGHT Copyright (c) 2003 Rob Edwards. Some of this work is Copyright (c) 1997-2002 Steve A. Chervitz. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 SEE ALSO L, L, L =head1 APPENDIX Methods beginning with a leading underscore are considered private and are intended for internal use by this module. They are not considered part of the public interface and are described here for documentation purposes only. =cut package Bio::Restriction::Enzyme::MultiCut; use strict; use Data::Dumper; use vars qw (); use base qw(Bio::Restriction::Enzyme); =head2 new Title : new Function Function : Initializes the enzyme object Returns : The Restriction::Enzyme::MultiCut object Argument : =cut sub new { my($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($others) = $self->_rearrange([qw( OTHERS )], @args); $others && $self->others($others); return $self; } =head2 others Title : others Usage : $re->others(@enz_obj_array); Function : Stores auxiliary Enzyme::MultiCut objects for multicutting enzymes Arguments : optional array of Enzyme::MultiCut objects Returns : array of Enzyme objects Added for compatibility to REBASE =cut sub others { my $self = shift; push @{$self->{_others}}, @_ if @_; return unless $self->{_others}; return @{$self->{'_others'}}; } =head2 purge_others Title : purge_others Usage : $re->purge_references(); Function : Purges the set of references for this enzyme Arguments : Returns : =cut sub purge_others { my ($self) = shift; $self->{_others} = []; } 1; BioPerl-1.007002/Bio/Restriction/Enzyme/MultiSite.pm000444000766000024 1040413155576320 22274 0ustar00cjfieldsstaff000000000000#------------------------------------------------------------------ # # BioPerl module Bio::Restriction::Enzyme::MultiSite # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho, heikki-at-bioperl-dot-org # # You may distribute this module under the same terms as perl itself #------------------------------------------------------------------ ## POD Documentation: =head1 NAME Bio::Restriction::Enzyme::MultiSite - A single restriction endonuclease =head1 SYNOPSIS # set up a single restriction enzyme. This contains lots of # information about the enzyme that is generally parsed from a # rebase file and can then be read back use Bio::Restriction::Enzyme; =head1 DESCRIPTION This module is used for restriction enzymes that recogonize more than one site. There are some enzymes that recognize sites that cannot be represented by the ambiguous genetic code. For example, M.PhiBssHII recognizes the sites: ACGCGT,CCGCGG,RGCGCY,RCCGGY, and GCGCGC Each site gets its own object that Bio::Restriction::Enzyme will refer to. Each also correlates with the other sites using the method L which stores references to other objects with alternative sites. In this schema each object within an EnzymeCollection can be checked for matching a sequence. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 CONTRIBUTORS Rob Edwards, redwards@utmem.edu =head1 COPYRIGHT Copyright (c) 2003 Rob Edwards. Some of this work is Copyright (c) 1997-2002 Steve A. Chervitz. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 SEE ALSO L, L, L =head1 APPENDIX Methods beginning with a leading underscore are considered private and are intended for internal use by this module. They are not considered part of the public interface and are described here for documentation purposes only. =cut package Bio::Restriction::Enzyme::MultiSite; use strict; use Data::Dumper; use vars qw (); use base qw(Bio::Restriction::Enzyme); =head2 new Title : new Function Function : Initializes the enzyme object Returns : The Restriction::Enzyme::MultiSite object Argument : =cut sub new { my($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($others) = $self->_rearrange([qw( OTHERS )], @args); $others && $self->others($others); return $self; } =head2 others Title : others Usage : $re->others(@others); Function : Gets/Sets the a list of other sites that this enzyme recoginizes Arguments : An array containing the other Bio::Restriction::Enzyme::MultiSite objects. Returns : An array containing the other Bio::Restriction::Enzyme::MultiSite objects. =cut sub others { my $self = shift; push @{$self->{_others}}, @_ if @_; return unless $self->{_others}; return @{$self->{'_others'}}; } =head2 purge_others Title : purge_others Usage : $re->purge_references(); Function : Purges the set of references for this enzyme Arguments : Returns : =cut sub purge_others { my ($self) = shift; $self->{_others} = []; } 1; BioPerl-1.007002/Bio/Restriction/IO000755000766000024 013155576320 16703 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Restriction/IO/bairoch.pm000444000766000024 1540113155576320 21026 0ustar00cjfieldsstaff000000000000# BioPerl module for Bio::Restriction::IO::withrefm # # Please direct questions and support issues to # # Cared for by Rob Edwards # # Copyright Rob Edwards # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Restriction::IO::bairoch - bairoch enzyme set =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::Restriction::IO class. =head1 DESCRIPTION This is the most complete format of the REBASE files, and basically includes all the data on each of the restriction enzymes. This parser is for the Bairoch format (aka MacVector, Vector NTI, PC/Gene (Bairoch) format), REBASE format #19 =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Rob Edwards, redwards@utmem.edu =head1 CONTRIBUTORS Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Restriction::IO::bairoch; use vars qw(%WITH_REFM_FIELD); use strict; use Bio::Restriction::Enzyme; use Bio::Restriction::Enzyme::MultiCut; use Bio::Restriction::Enzyme::MultiSite; use Bio::Restriction::EnzymeCollection; use Data::Dumper; use base qw(Bio::Restriction::IO::base); =head2 read Title : read Usage : $renzs = $stream->read Function: reads all the restrction enzymes from the stream Returns : a Bio::Restriction::Restriction object Args : none =cut sub read { my $self = shift; my $renzs = Bio::Restriction::EnzymeCollection->new(-empty => 1); local $/ = '//'; while (defined(my $entry=$self->_readline()) ) { $self->debug("|$entry|\n"); # # Minimal information # my ($name) = $entry =~ /ID\s+(\S+)/; my ($site) = $entry =~ /RS\s+([^\n]+)/; next unless ($name && $site); # the standard sequence format for these guys is: # GATC, 2; # or, for enzymes that cut more than once # GATC, 2; GTAC, 2; # there are a couple of sequences that have multiple # recognition sites. my @sequences; if ($site =~ /\;/) { @sequences = split /\;/, $site; $self->debug(@sequences,"\n"); $site=shift @sequences; } my ($seq, $cut)=split /,\s+/, $site; $self->debug("SITE: |$site| GAVE: |$seq| and |$cut|\n"); if ($seq eq '?') { $self->warn("$name: no site. Skipping") if $self->verbose > 1; next; } # this is mainly an error check to make sure that I am adding what I think I am! if ($seq !~ /[NGATC]/i) { $self->throw("Sequence $name has weird sequence: |$seq|"); } my $re; if ($cut eq "?") { $re = Bio::Restriction::Enzyme->new(-name=>$name, -seq => $seq); } else { if ($cut !~ /^-?\d+$/) { $self->throw("Cut site from $name is weird: |$cut|\n"); } $re = Bio::Restriction::Enzyme->new(-name=>$name, -cut => $cut, -seq => $seq ); } $renzs->enzymes($re); # # prototype / isoschizomers # my ($prototype) = $entry =~ /PT\s+([^\n]+)/; if ($prototype) { #$re->isoschizomers(split /\,/, $isoschizomers); #NOTE: Need to add a method so that we can add isoschosomers to enzymes that may not exist! $re->is_prototype(0); } else { $re->is_prototype(1); } # # methylation # my ($meth) = $entry =~ /MS\s+([^\n]+)/; my @meths; if ($meth) { # this can be either X(Y) or X(Y),X2(Y2) # where X is the base and y is the type of methylation if ( $meth =~ /(\S+)\((\d+)\),(\S+)\((\d+)\)/ ) { # two msites per site #my ($p1, $m1, $p2, $m2) = ($1, $2, $3, $4); $re->methylation_sites($self->_meth($re,$1, $2), $self->_meth($re,$3,$4)); } elsif ($meth =~ /(\S+)\((\d+)\)/ ) { # one msite per site or more sites #print Dumper $meth; $re->methylation_sites( $self->_meth($re,$1,$2) ); @meths = split /, /, $meth; $meth=shift @meths; } else { $self->warn("Unknown methylation format [$meth]") if $self->verbose >0; } } # # microbe # my ($microbe) = $entry =~ /OS\s+([^\n]+)/; $re->microbe($microbe) if $microbe; # # source # #my ($source) = $entry =~ /<6>([^\n]+)/; #$re->source($source) if $source; # # vendors # my ($vendors) = $entry =~ /CR\s+([^\n]+)/; $re->vendors(split /,\s*/, $vendors) if $vendors; # # references # #my ($refs) = $entry =~ /<8>(.+)/s; #$re->references(map {split /\n+/} $refs) if $refs; # # create special types of Enzymes # $self->warn("Current issues with multisite enzymes using bairoch format\n". "Recommend using itype2 or withrefm formats for now") if @sequences; #$self->_make_multisites($renzs, $re, \@sequences, \@meths) if @sequences; } return $renzs; } =head2 write Title : write Usage : $stream->write($renzs) Function: writes restriction enzymes into the stream Returns : 1 for success and 0 for error Args : a Bio::Restriction::Enzyme or a Bio::Restriction::EnzymeCollection object =cut sub write { my ($self,@h) = @_; $self->throw_not_implemented; } 1; BioPerl-1.007002/Bio/Restriction/IO/base.pm000444000766000024 5245513155576320 20343 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Restriction::IO::base # # Please direct questions and support issues to # # Cared for by Rob Edwards # # Copyright Rob Edwards # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Restriction::IO::base - base enzyme set =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::Restriction::IO class. =head1 DESCRIPTION This class defines some base methods for restriction enzyme input and at the same time gives a base list of common enzymes. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Rob Edwards, redwards@utmem.edu =head1 CONTRIBUTORS Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Mark A. Jensen, maj-at-fortinbras-dot-us =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Restriction::IO::base; use strict; use Bio::Restriction::Enzyme; use Bio::Restriction::EnzymeCollection; use Bio::Restriction::Enzyme::MultiCut; use Bio::Restriction::Enzyme::MultiSite; use base qw(Bio::Restriction::IO); my $offset; # class variable sub new { my($class, @args) = @_; $class = ref $class ? ref $class : $class; my $self = bless {}, $class; $self->_initialize(@args); return $self; } { my %FILE_FORMAT = ( #'itype2' => 'itype2', # itype2 format doesn't work with 'current' #'8' => 'itype2', 'withrefm' => 'withrefm', '31' => 'withrefm', #'bairoch' => 'bairoch', # bairoch format doesn't work with 'current' #'19' => 'bairoch', #'macvector' => 'bairoch', #'vectorNTI' => 'bairoch', 'neo' => 'neos', 'prototype' => 'proto' ); sub _initialize { my($self,@args) = @_; my ($current, $url, $file, $fh, $format, $verbose) = $self->_rearrange([qw(CURRENT URL FILE FH FORMAT VERBOSE)],@args); $verbose || 0; $self->verbose($verbose); if ($current && $format) { $self->throw("Can't use -current with file, fh, or url set") if ($url || $file || $fh); $self->throw("Format $format not retrievable using 'current'") if (!exists $FILE_FORMAT{$format}); my $io = $self->new(-url => 'ftp://ftp.neb.com/pub/rebase/VERSION'); chomp (my $version = $io->_readline); push @args, (-url => "ftp://ftp.neb.com/pub/rebase/$FILE_FORMAT{$format}.$version", -retries => 1); } $self->_companies; return unless $self->SUPER::_initialize(@args); } } =head2 read Title : read Usage : $renzs = $stream->read Function: reads all the restrction enzymes from the stream Returns : a Bio::Restriction::Restriction object Args : none =cut sub read { my $self = shift; my $renzs = Bio::Restriction::EnzymeCollection->new(-empty => 1); seek DATA,($offset||=tell DATA), 0; while () { chomp; next if /^\s*$/; my ($name, $site, $cut) = split /\s+/; my $re = Bio::Restriction::Enzyme->new(-name => $name, -site => $site, -cut => $cut); $renzs->enzymes($re); } return $renzs; } =head2 _xln_sub Title : _xln_sub Function: Translates withrefm coords to Bio::Restriction coords Args : Bio::Restriction::Enzyme object, scalar integer (cut posn) Note : Used internally; pass as a coderef to the B:R::Enzyme constructor Note : It is convenient for each format module to have its own version of this; not currently demanded by the interface. =cut sub _xln_sub { # for base.pm, a no-op my ($z,$c) = @_; return $c; } =head2 write Title : write Usage : $stream->write($renzs) Function: writes restriction enzymes into the stream Returns : 1 for success and 0 for error Args : a Bio::Restriction::Enzyme or a Bio::Restriction::EnzymeCollection object =cut sub write { my $self = shift; foreach (@_) { map { printf "%s\t%s\t%s\n", $_->name, $_->string, $_->cut } sort {$a->name cmp $b->name} $_->each_enzyme if $_->isa('Bio::Restriction::EnzymeCollection'); printf "%s\t%s\t%s\n", $_->name, $_->string, $_->cut if $_->isa('Bio::Restriction::Enzyme'); } } =head2 verify_prototype Title : verify_prototype Purpose : checks enzyme against current prototype list (retrieved remotely) Returns : returns TRUE if enzyme is prototype Argument : Bio::Restriction::EnzymeI Comments : This is an auxiliary method to retrieve and check an enzyme as a prototype. It retrieves the current list, stores it as a singleton instance, then uses it to check the prototype and modify is_prototype() to true or false. Use as follows: my $col = $io->read; for my $enz ($col->each_enzyme) { print $enz->name.":".$enz->site."\n"; print "\t".$io->verify_prototype($enz)."\n"; } =cut my $protodb; sub verify_prototype { my ($self, $enz) = @_; $self->throw("Must pass a Bio::Restriction::EnzymeI") unless $enz && ref $enz && $enz->isa("Bio::Restriction::EnzymeI"); if (!defined $protodb) { my $io = Bio::Restriction::IO->new(-format => 'prototype', -current => 1); $protodb = $io->read; } if ($protodb->get_enzyme($enz->name)) { $enz->is_prototype(1); } else { $enz->is_prototype(0); } $enz->is_prototype; } =head2 Common REBASE parsing methods The rest of the methods in this file are to be used by other REBASE parsers. They are not to be used outside subclasses of this base class. (They are 'protected' in the sense the word is used in Java.) =cut =head2 _cuts_from_site Title : _cuts_from_site Usage : ($site, $cut, $comp_cut) = _cuts_from_site('ACGCGT(4/5)'); Function: Separates cut positions from a single site string. Does nothing to site if it does not have the cut string Returns : array of site_string, forward_cut_position, reverse_cut_position Args : recognition site string Note : Not used in withrefm refactor/maj =cut sub _cuts_from_site { my ($self, $site) = @_; my ($cut, $comp_cut) = $site =~ /\((-?\d+)\/(-?\d+)\)/; $site =~ s/\(.*\)$//; return ($site, $cut, $comp_cut); } =head2 _meth Title : _meth Usage : ($pos, $meth) = $self->_meth('2(5)'); Function: Separates methylation position and coce from a string. Adjusts the position depending on enzyme site length and symmetry Returns : array of position and methylation code Args : 1. reference to Enzyme object 2. methylation description string =cut sub _meth { my ($self, $re, $meth) = @_; $meth =~ /(\S+)\((\d+)\)/; my ($pos, $m) = ($1, $2); $pos = 0 if $pos eq '?'; $pos = $re->seq->length + $pos if $pos and ! $re->palindromic; return ($pos, $m); $self->warn("Unknown methylation format [$meth]") if $self->verbose >0; } =head2 _coordinate_shift_to_cut Title : _coordinate_shift_to_cut Usage : $cut = $self->_coordinate_shift_to_cut($oricut, offset); Function: Adjust cut position coordinates to start from the first nucleotides of site Returns : Cut position in correct coordinates Args : 1. Original cut position 2. Length of the recognition site Note : Not used in withrefm.pm refactor/maj =cut sub _coordinate_shift_to_cut { my ($self, $cut, $site_length) = @_; return $cut + $site_length; } =head2 _make_multisites Title : _make_multisites Usage : $self->_make_multisites($first_enzyme, \@sites, \@mets) Function: Bless a Bio::Restriction::Enzyme into Bio::Restriction::Enzyme::MultiSite and clone it as many times as there are alternative sites. Returns : nothing, does in place editing Args : 1. a Bio::Restriction::Enzyme 2. reference to an array of recognition site strings 3. reference to an array of methylation code strings, optional =cut # removed the enzyme collection from arg list /maj sub _make_multisites { my ($self, $re, $sites, $meths, $xln_sub) = @_; bless $re, 'Bio::Restriction::Enzyme::MultiSite'; my $count = 0; while ($count < scalar @{$sites}) { # this should probably be refactored to use the constructor # too, rather than the clone/accessor method /maj # my $re2 = $re->clone; # my $re2; my $site = @{$sites}[$count]; my ($precut, $recog, $postcut) = ( $site =~ m/^(?:\((\w+\/\w+)\))?([\w^]+)(?:\((\w+\/\w+)\))?/ ); # set the site attribute # $re2->site($recog); # set the recog attribute (which will make the regexp transformation # if necessary: # $re2->recog($recog); # $recog = $re2->string; # no warnings; # avoid 'uninitialized value' warning against $postcut # my ($cut, $comp_cut) = ( $postcut =~ /(-?\d+)\/(-?\d+)/ ); # use warnings; # note the following hard codes the coordinate transformation # used for rebase/itype2 : this method will break on the # base.pm format. # if ($cut) { # $re2->cut($cut + length $recog); # $re2->complementary_cut($comp_cut + length $recog); # } my $re2 = Bio::Restriction::Enzyme::MultiSite->new( -name => $re->name, -site => $recog, -recog => $recog, -precut => $precut, -postcut => $postcut, -xln_sub => $xln_sub ); if ($meths and @$meths) { $re2->purge_methylation_sites; $re2->methylation_sites($self->_meth($re2, @{$meths}[$count])); } $re->others($re2); $count++; } foreach my $enz ($re->others) { $enz->others($re, grep {$_ ne $enz} $re->others); } 1; } =head2 _make_multicuts Title : _make_multicuts Usage : $self->_make_multicuts($first_enzyme, $precuts) Function: Bless a Bio::Restriction::Enzyme into Bio::Restriction::Enzyme::MultiCut and clone it. The precut string is processed to replase the cut sites in the cloned object. Both objects refer to each other through others() method. Returns : nothing, does in place editing Args : 1. a Bio::Restriction::Enzyme 2. precut string, e.g. '12/7' The examples we have of multiply cutting enzymes cut only four times. This protected method deals only with a string of two integers separated with a slash, e.g. '12/7'. The numbers represent the positions BEFORE the start of the recognition site, i.e. negative positions. =cut # removed the enzyme collection from arg list /maj sub _make_multicuts { my ($self, $re, $precut) = @_; bless $re, 'Bio::Restriction::Enzyme::MultiCut'; my ($cut, $comp_cut) = $precut =~ /(-?\d+)\/(-?\d+)/; my $re2 = $re->clone; $re2->cut("-$cut"); $re2->complementary_cut("-$comp_cut"); $re->others($re2); 1; } =head2 _companies Title : _companies Purpose : Defines the companies that we know about Returns : A hash Argument : Nothing Comments : An internal method to define the companies that we know about REBASE uses a code, and this converts the code to the real name (e.g. A = Amersham Pharmacia Biotech) =cut sub _companies { # this is just so it is easy to set up the codes that REBASE uses my $self=shift; my %companies=( 'A'=>'Amersham Pharmacia Biotech (1/03)', 'C'=>'Minotech Biotechnology (6/01)', 'E'=>'Stratagene (1/03)', 'F'=>'Fermentas AB (1/03)', 'G'=>'Qbiogene (1/03)', 'H'=>'American Allied Biochemical, Inc. (10/98)', 'I'=>'SibEnzyme Ltd. (1/03)', 'J'=>'Nippon Gene Co., Ltd. (6/00)', 'K'=>'Takara Shuzo Co. Ltd. (1/03)', 'M'=>'Roche Applied Science (1/03)', 'N'=>'New England Biolabs (1/03)', 'O'=>'Toyobo Biochemicals (11/98)', 'P'=>'Megabase Research Products (5/99)', 'Q'=>'CHIMERx (1/03)', 'R'=>'Promega Corporation (1/03)', 'S'=>'Sigma Chemical Corporation (1/03)', 'U'=>'Bangalore Genei (1/03)', 'V'=>'MRC-Holland (1/03)', 'X'=>'EURx Ltd. (1/03)'); $self->{company}=\%companies; } 1; __DATA__ AasI GACNNNNNNGTC 7 AatI AGGCCT 3 AccII CGCG 2 AatII GACGTC 5 AauI TGTACA 1 Acc113I AGTACT 3 Acc16I TGCGCA 3 Acc65I GGTACC 1 AccB1I GGYRCC 1 AccB7I CCANNNNNTGG 7 AccI GTMKAC 2 AccIII TCCGGA 1 AciI CCGC 1 AclI AACGTT 2 AcsI RAATTY 1 AcvI CACGTG 3 AcyI GRCGYC 2 AdeI CACNNNGTG 6 AfaI GTAC 2 AfeI AGCGCT 3 AflI GGWCC 1 AflII CTTAAG 1 AflIII ACRYGT 1 AgeI ACCGGT 1 AhaIII TTTAAA 3 AhdI GACNNNNNGTC 6 AhlI ACTAGT 1 AleI CACNNNNGTG 5 AluI AGCT 2 Alw21I GWGCWC 5 Alw44I GTGCAC 1 AlwNI CAGNNNCTG 6 Ama87I CYCGRG 1 AocI CCTNAGG 2 Aor51HI AGCGCT 3 ApaBI GCANNNNNTGC 8 ApaI GGGCCC 5 ApaLI GTGCAC 1 ApoI RAATTY 1 AscI GGCGCGCC 2 AseI ATTAAT 2 AsiAI ACCGGT 1 AsiSI GCGATCGC 5 AsnI ATTAAT 2 Asp700I GAANNNNTTC 5 Asp718I GGTACC 1 AspEI GACNNNNNGTC 6 AspHI GWGCWC 5 AspI GACNNNGTC 4 AspLEI GCGC 3 AspS9I GGNCC 1 AsuC2I CCSGG 2 AsuI GGNCC 1 AsuII TTCGAA 2 AsuNHI GCTAGC 1 AvaI CYCGRG 1 AvaII GGWCC 1 AviII TGCGCA 3 AvrII CCTAGG 1 AxyI CCTNAGG 2 BalI TGGCCA 3 BamHI GGATCC 1 BanI GGYRCC 1 BanII GRGCYC 5 BanIII ATCGAT 2 BbeI GGCGCC 5 BbrPI CACGTG 3 BbuI GCATGC 5 Bbv12I GWGCWC 5 BclI TGATCA 1 BcnI CCSGG 2 BcoI CYCGRG 1 BcuI ACTAGT 1 BetI WCCGGW 1 BfaI CTAG 1 BfmI CTRYAG 1 BfrBI ATGCAT 3 BfrI CTTAAG 1 BfuCI GATC 0 BglI GCCNNNNNGGC 7 BglII AGATCT 1 BlnI CCTAGG 1 BloHII CTGCAG 5 BlpI GCTNAGC 2 Bme1390I CCNGG 2 Bme1580I GKGCMC 5 Bme18I GGWCC 1 BmtI GCTAGC 5 BmyI GDGCHC 5 BoxI GACNNNNGTC 5 Bpu1102I GCTNAGC 2 Bpu14I TTCGAA 2 Bsa29I ATCGAT 2 BsaAI YACGTR 3 BsaBI GATNNNNATC 5 BsaHI GRCGYC 2 BsaJI CCNNGG 1 BsaOI CGRYCG 4 BsaWI WCCGGW 1 Bsc4I CCNNNNNNNGG 7 BscBI GGNNCC 3 BscFI GATC 0 BscI ATCGAT 2 Bse118I RCCGGY 1 Bse21I CCTNAGG 2 Bse8I GATNNNNATC 5 BseAI TCCGGA 1 BseBI CCWGG 2 BseCI ATCGAT 2 BseDI CCNNGG 1 BseJI GATNNNNATC 5 BseLI CCNNNNNNNGG 7 BsePI GCGCGC 1 BseSI GKGCMC 5 BseX3I CGGCCG 1 Bsh1236I CGCG 2 Bsh1285I CGRYCG 4 BshFI GGCC 2 BshI GGCC 2 BshNI GGYRCC 1 BshTI ACCGGT 1 BsiBI GATNNNNATC 5 BsiCI TTCGAA 2 BsiEI CGRYCG 4 BsiHKAI GWGCWC 5 BsiHKCI CYCGRG 1 BsiLI CCWGG 2 BsiMI TCCGGA 1 BsiQI TGATCA 1 BsiSI CCGG 1 BsiWI CGTACG 1 BsiXI ATCGAT 2 BsiYI CCNNNNNNNGG 7 BsiZI GGNCC 1 BslI CCNNNNNNNGG 7 BsoBI CYCGRG 1 Bsp106I ATCGAT 2 Bsp119I TTCGAA 2 Bsp120I GGGCCC 1 Bsp1286I GDGCHC 5 Bsp13I TCCGGA 1 Bsp1407I TGTACA 1 Bsp143I GATC 0 Bsp143II RGCGCY 5 Bsp1720I GCTNAGC 2 Bsp19I CCATGG 1 Bsp68I TCGCGA 3 BspA2I CCTAGG 1 BspCI CGATCG 4 BspDI ATCGAT 2 BspEI TCCGGA 1 BspHI TCATGA 1 BspLI GGNNCC 3 BspLU11I ACATGT 1 BspMII TCCGGA 1 BspT104I TTCGAA 2 BspT107I GGYRCC 1 BspTI CTTAAG 1 BspXI ATCGAT 2 BsrBRI GATNNNNATC 5 BsrFI RCCGGY 1 BsrGI TGTACA 1 BssAI RCCGGY 1 BssECI CCNNGG 1 BssHI CTCGAG 1 BssHII GCGCGC 1 BssKI CCNGG 0 BssNAI GTATAC 3 BssT1I CCWWGG 1 Bst1107I GTATAC 3 Bst2UI CCWGG 2 Bst4CI ACNGT 3 Bst98I CTTAAG 1 BstACI GRCGYC 2 BstAPI GCANNNNNTGC 7 BstBAI YACGTR 3 BstBI TTCGAA 2 BstC8I GCNNGC 3 BstDEI CTNAG 1 BstDSI CCRYGG 1 BstEII GGTNACC 1 BstENI CCTNNNNNAGG 5 BstENII GATC 0 BstFNI CGCG 2 BstH2I RGCGCY 5 BstHHI GCGC 3 BstHPI GTTAAC 3 BstKTI GATC 3 BstMAI CTGCAG 5 BstMCI CGRYCG 4 BstMWI GCNNNNNNNGC 7 BstNI CCWGG 2 BstNSI RCATGY 5 BstOI CCWGG 2 BstPAI GACNNNNGTC 5 BstPI GGTNACC 1 BstSCI CCNGG 0 BstSFI CTRYAG 1 BstSNI TACGTA 3 BstUI CGCG 2 BstX2I RGATCY 1 BstXI CCANNNNNNTGG 8 BstYI RGATCY 1 BstZ17I GTATAC 3 BstZI CGGCCG 1 Bsu15I ATCGAT 2 Bsu36I CCTNAGG 2 BsuRI GGCC 2 BsuTUI ATCGAT 2 BtgI CCRYGG 1 BthCI GCNGC 4 Cac8I GCNNGC 3 CaiI CAGNNNCTG 6 CauII CCSGG 2 CciNI GCGGCCGC 2 CelII GCTNAGC 2 CfoI GCGC 3 Cfr10I RCCGGY 1 Cfr13I GGNCC 1 Cfr42I CCGCGG 4 Cfr9I CCCGGG 1 CfrI YGGCCR 1 ChaI GATC 4 ClaI ATCGAT 2 CpoI CGGWCCG 2 Csp45I TTCGAA 2 Csp6I GTAC 1 CspAI ACCGGT 1 CspI CGGWCCG 2 CviAII CATG 1 CviJI RGCY 2 CviRI TGCA 2 CviTI RGCY 2 CvnI CCTNAGG 2 DdeI CTNAG 1 DpnI GATC 2 DpnII GATC 0 DraI TTTAAA 3 DraII RGGNCCY 2 DraIII CACNNNGTG 6 DrdI GACNNNNNNGTC 7 DsaI CCRYGG 1 DseDI GACNNNNNNGTC 7 EaeI YGGCCR 1 EagI CGGCCG 1 Eam1105I GACNNNNNGTC 6 Ecl136II GAGCTC 3 EclHKI GACNNNNNGTC 6 EclXI CGGCCG 1 Eco105I TACGTA 3 Eco130I CCWWGG 1 Eco147I AGGCCT 3 Eco24I GRGCYC 5 Eco32I GATATC 3 Eco47I GGWCC 1 Eco47III AGCGCT 3 Eco52I CGGCCG 1 Eco72I CACGTG 3 Eco81I CCTNAGG 2 Eco88I CYCGRG 1 Eco91I GGTNACC 1 EcoHI CCSGG 0 EcoICRI GAGCTC 3 EcoNI CCTNNNNNAGG 5 EcoO109I RGGNCCY 2 EcoO65I GGTNACC 1 EcoRI GAATTC 1 EcoRII CCWGG 0 EcoRV GATATC 3 EcoT14I CCWWGG 1 EcoT22I ATGCAT 5 EcoT38I GRGCYC 5 EgeI GGCGCC 3 EheI GGCGCC 3 ErhI CCWWGG 1 EsaBC3I TCGA 2 EspI GCTNAGC 2 FatI CATG 0 FauNDI CATATG 2 FbaI TGATCA 1 FblI GTMKAC 2 FmuI GGNCC 4 Fnu4HI GCNGC 2 FnuDII CGCG 2 FriOI GRGCYC 5 FseI GGCCGGCC 6 Fsp4HI GCNGC 2 FspAI RTGCGCAY 4 FspI TGCGCA 3 FunI AGCGCT 3 FunII GAATTC 1 HaeI WGGCCW 3 HaeII RGCGCY 5 HaeIII GGCC 2 HapII CCGG 1 HgiAI GWGCWC 5 HgiCI GGYRCC 1 HgiJII GRGCYC 5 HhaI GCGC 3 Hin1I GRCGYC 2 Hin6I GCGC 1 HinP1I GCGC 1 HincII GTYRAC 3 HindI CAC 2 HindII GTYRAC 3 HindIII AAGCTT 1 HinfI GANTC 1 HpaI GTTAAC 3 HpaII CCGG 1 Hpy178III TCNNGA 2 Hpy188I TCNGA 3 Hpy188III TCNNGA 2 Hpy8I GTNNAC 3 Hpy99I CGWCG 5 HpyCH4I CATG 3 HpyCH4III ACNGT 3 HpyCH4IV ACGT 1 HpyCH4V TGCA 2 HpyF10VI GCNNNNNNNGC 8 Hsp92I GRCGYC 2 Hsp92II CATG 4 HspAI GCGC 1 ItaI GCNGC 2 KasI GGCGCC 1 Kpn2I TCCGGA 1 KpnI GGTACC 5 Ksp22I TGATCA 1 KspAI GTTAAC 3 KspI CCGCGG 4 Kzo9I GATC 0 LpnI RGCGCY 3 LspI TTCGAA 2 MabI ACCWGGT 1 MaeI CTAG 1 MaeII ACGT 1 MaeIII GTNAC 0 MamI GATNNNNATC 5 MboI GATC 0 McrI CGRYCG 4 MfeI CAATTG 1 MflI RGATCY 1 MhlI GDGCHC 5 MlsI TGGCCA 3 MluI ACGCGT 1 MluNI TGGCCA 3 Mly113I GGCGCC 2 Mph1103I ATGCAT 5 MroI TCCGGA 1 MroNI GCCGGC 1 MroXI GAANNNNTTC 5 MscI TGGCCA 3 MseI TTAA 1 MslI CAYNNNNRTG 5 Msp20I TGGCCA 3 MspA1I CMGCKG 3 MspCI CTTAAG 1 MspI CCGG 1 MspR9I CCNGG 2 MssI GTTTAAAC 4 MstI TGCGCA 3 MunI CAATTG 1 MvaI CCWGG 2 MvnI CGCG 2 MwoI GCNNNNNNNGC 7 NaeI GCCGGC 3 NarI GGCGCC 2 NciI CCSGG 2 NcoI CCATGG 1 NdeI CATATG 2 NdeII GATC 0 NgoAIV GCCGGC 1 NgoMIV GCCGGC 1 NheI GCTAGC 1 NlaIII CATG 4 NlaIV GGNNCC 3 Nli3877I CYCGRG 5 NmuCI GTSAC 0 NotI GCGGCCGC 2 NruGI GACNNNNNGTC 6 NruI TCGCGA 3 NsbI TGCGCA 3 NsiI ATGCAT 5 NspBII CMGCKG 3 NspI RCATGY 5 NspIII CYCGRG 1 NspV TTCGAA 2 OliI CACNNNNGTG 5 PacI TTAATTAA 5 PaeI GCATGC 5 PaeR7I CTCGAG 1 PagI TCATGA 1 PalI GGCC 2 PauI GCGCGC 1 PceI AGGCCT 3 PciI ACATGT 1 PdiI GCCGGC 3 PdmI GAANNNNTTC 5 Pfl23II CGTACG 1 PflBI CCANNNNNTGG 7 PflFI GACNNNGTC 4 PflMI CCANNNNNTGG 7 PfoI TCCNGGA 1 PinAI ACCGGT 1 Ple19I CGATCG 4 PmaCI CACGTG 3 PmeI GTTTAAAC 4 PmlI CACGTG 3 Ppu10I ATGCAT 1 PpuMI RGGWCCY 2 PpuXI RGGWCCY 2 PshAI GACNNNNGTC 5 PshBI ATTAAT 2 PsiI TTATAA 3 Psp03I GGWCC 4 Psp124BI GAGCTC 5 Psp1406I AACGTT 2 Psp5II RGGWCCY 2 Psp6I CCWGG 0 PspAI CCCGGG 1 PspEI GGTNACC 1 PspGI CCWGG 0 PspLI CGTACG 1 PspN4I GGNNCC 3 PspOMI GGGCCC 1 PspPI GGNCC 1 PspPPI RGGWCCY 2 PssI RGGNCCY 5 PstI CTGCAG 5 PsuI RGATCY 1 PsyI GACNNNGTC 4 PvuI CGATCG 4 PvuII CAGCTG 3 RcaI TCATGA 1 RsaI GTAC 2 Rsr2I CGGWCCG 2 RsrII CGGWCCG 2 SacI GAGCTC 5 SacII CCGCGG 4 SalI GTCGAC 1 SanDI GGGWCCC 2 SatI GCNGC 2 Sau3AI GATC 0 Sau96I GGNCC 1 SauI CCTNAGG 2 SbfI CCTGCAGG 6 ScaI AGTACT 3 SciI CTCGAG 3 ScrFI CCNGG 2 SdaI CCTGCAGG 6 SduI GDGCHC 5 SecI CCNNGG 1 SelI CGCG 0 SexAI ACCWGGT 1 SfcI CTRYAG 1 SfeI CTRYAG 1 SfiI GGCCNNNNNGGCC 8 SfoI GGCGCC 3 Sfr274I CTCGAG 1 Sfr303I CCGCGG 4 SfuI TTCGAA 2 SgfI GCGATCGC 5 SgrAI CRCCGGYG 2 SgrBI CCGCGG 4 SinI GGWCC 1 SlaI CTCGAG 1 SmaI CCCGGG 3 SmiI ATTTAAAT 4 SmiMI CAYNNNNRTG 5 SmlI CTYRAG 1 SnaBI TACGTA 3 SpaHI GCATGC 5 SpeI ACTAGT 1 SphI GCATGC 5 SplI CGTACG 1 SrfI GCCCGGGC 4 Sse232I CGCCGGCG 2 Sse8387I CCTGCAGG 6 Sse8647I AGGWCCT 2 Sse9I AATT 0 SseBI AGGCCT 3 SspBI TGTACA 1 SspI AATATT 3 SstI GAGCTC 5 SstII CCGCGG 4 StuI AGGCCT 3 StyI CCWWGG 1 SunI CGTACG 1 SwaI ATTTAAAT 4 TaaI ACNGT 3 TaiI ACGT 4 TaqI TCGA 1 TasI AATT 0 TatI WGTACW 1 TauI GCSGC 4 TelI GACNNNGTC 4 TfiI GAWTC 1 ThaI CGCG 2 TliI CTCGAG 1 Tru1I TTAA 1 Tru9I TTAA 1 TscI ACGT 4 TseI GCWGC 1 Tsp45I GTSAC 0 Tsp4CI ACNGT 3 Tsp509I AATT 0 TspEI AATT 0 Tth111I GACNNNGTC 4 TthHB8I TCGA 1 UnbI GGNCC 0 Van91I CCANNNNNTGG 7 Vha464I CTTAAG 1 VneI GTGCAC 1 VpaK11AI GGWCC 0 VpaK11BI GGWCC 1 VspI ATTAAT 2 XagI CCTNNNNNAGG 5 XapI RAATTY 1 XbaI TCTAGA 1 XceI RCATGY 5 XcmI CCANNNNNNNNNTGG 8 XhoI CTCGAG 1 XhoII RGATCY 1 XmaCI CCCGGG 1 XmaI CCCGGG 1 XmaIII CGGCCG 1 XmaJI CCTAGG 1 XmiI GTMKAC 2 XmnI GAANNNNTTC 5 XspI CTAG 1 ZhoI ATCGAT 2 ZraI GACGTC 3 Zsp2I ATGCAT 5 BioPerl-1.007002/Bio/Restriction/IO/itype2.pm000444000766000024 1465613155576320 20646 0ustar00cjfieldsstaff000000000000# BioPerl module for Bio::Restriction::IO::itype2 # # Please direct questions and support issues to # # Cared for by Rob Edwards # # Copyright Rob Edwards # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Restriction::IO::itype2 - itype2 enzyme set =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::Restriction::IO class. =head1 DESCRIPTION This is tab delimited, entry per line format which is fast to process. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Rob Edwards, redwards@utmem.edu =head1 CONTRIBUTORS Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Mark A. Jensen, maj-at-fortinbras-dot-us =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Restriction::IO::itype2; use strict; use Bio::Restriction::Enzyme; use Bio::Restriction::EnzymeCollection; use Data::Dumper; use base qw(Bio::Restriction::IO::base); =head2 read Title : read Usage : $renzs = $stream->read Function: reads all the restrction enzymes from the stream Returns : a Bio::Restriction::IO object Args : none Internally creates a hash of enzyme information which is passed on to L. =cut sub read { my $self = shift; my $renzs = Bio::Restriction::EnzymeCollection->new(-empty => 1); # read until start of data while (defined( my $line = $self->_readline()) ) { next if $line =~ /^[ R]/; $self->_pushback($line); last; } # enzyme name [tab] prototype [tab] recognition sequence with # cleavage site [tab] methylation site and type [tab] commercial # source [tab] references while (defined(my $line = $self->_readline()) ) { $self->debug($line); chomp $line; my ($name, $prototype, $site, $meth, $vendor, $refs) = split /\t/, $line; # we need minimum name and site unless ($site) { $self->warn("Can not parse line with name [$name]") if $self->verbose > 0; next; } next unless $name; # # four cut enzymes are not in this format # my $precut; # if ($site =~ m/^\((\d+\/\d+)\)[ATGCN]+/) { # $precut=$1; # $site =~ s/\($precut\)//; # } # -------------- cut --------------- # this regexp now parses all possible components # $1 : (s/t) or undef # $2 : [site] # $3 : (m/n) or undef /maj my ($precut, $recog, $postcut) = ( $site =~ m/^(?:\((\w+\/\w+)\))?([\w^]+)(?:\((\w+\/\w+)\))?/ ); my @sequences; if ($site =~ /\,/) { @sequences = split( /\,/, $site); $site=shift @sequences; } # # prototype # # presence of a name means the prototype isoschizomer, absence means # this enzyme is the prototype my $is_prototype = ($prototype ? 1 : 0); # # vendors # my @vendors; @vendors = ( split / */, $vendor) if $vendor; # # references # my @refs; @refs = map {split /\n+/} $refs if $refs; # when enz is constructed, site() will contain original characters, # but recog() will contain a regexp if required.../maj my $re = Bio::Restriction::Enzyme->new( -name => $name, -site => $recog, -recog => $recog, -precut => $precut, -postcut => $postcut, -is_prototype => $is_prototype, -prototype => $prototype, -vendors => [@vendors], -references => [@refs], -xln_sub => \&_xln_sub ); # # methylation # # [easier to set here during parsing than in constructor] /maj my @meths; if ($meth) { # this can be either X(Y) or X(Y),X2(Y2) # where X is the base and y is the type of methylation if ( $meth =~ /(\S+)\((\d+)\),(\S+)\((\d+)\)/ ) { # two msites per site #my ($p1, $m1, $p2, $m2) = ($1, $2, $3, $4); $re->methylation_sites($self->_meth($re,$1, $2), $self->_meth($re,$3,$4)); } elsif ($meth =~ /(\S+)\((\d+)\)/ ) { # one msite per site or more sites #print Dumper $meth; $re->methylation_sites( $self->_meth($re,$1,$2) ); @meths = split (/, /, $meth); $meth=shift @meths; } else { $self->warn("Unknown methylation format [$meth]") if $self->verbose >0; } } # # create special types of Enzymes # $self->_make_multisites( $re, \@sequences, \@meths) if @sequences; $renzs->enzymes($re); } return $renzs; } =head2 _xln_sub Title : _xln_sub Function: Translates withrefm coords to Bio::Restriction coords Args : Bio::Restriction::Enzyme object, scalar integer (cut posn) Note : Used internally; pass as a coderef to the B:R::Enzyme constructor =cut sub _xln_sub { my ($z,$c) = @_; return ($c < 0 ? $c : length($z->string)+$c); } =head2 write Title : write Usage : $stream->write($renzs) Function: writes restriction enzymes into the stream Returns : 1 for success and 0 for error Args : a Bio::Restriction::Enzyme or a Bio::Restriction::EnzymeCollection object =cut sub write { my ($self,@h) = @_; $self->throw_not_implemented; } 1; BioPerl-1.007002/Bio/Restriction/IO/prototype.pm000444000766000024 1044713155576320 21471 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Restriction::IO::prototype # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Restriction::IO::prototype - prototype enzyme set =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::Restriction::IO class. =head1 DESCRIPTION This is a parser for the proto/neo file REBASE format, which contains prototype information as well as (in the neo file) neoschizomer data. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Rob Edwards, redwards@utmem.edu =head1 CONTRIBUTORS Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Restriction::IO::prototype; use vars qw(%WITH_REFM_FIELD); use strict; use Bio::Restriction::Enzyme; use Bio::Restriction::EnzymeCollection; use Data::Dumper; use base qw(Bio::Restriction::IO::base); =head2 read Title : read Usage : $renzs = $stream->read Function: reads all the restrction enzymes from the stream Returns : a Bio::Restriction::Restriction object Args : none =cut sub read { my $self = shift; my $coll = Bio::Restriction::EnzymeCollection->new(-empty => 1); my ($seentop, $last_type); ENZYME: while (defined (my $line = $self->_readline)) { chomp $line; next unless $line; if ($line =~ /TYPE\s+(I)+/) { $last_type = $1; $seentop ||= 1; next; } next unless $seentop; my @data = split /\s+/,$line,2; next if $data[0] =~ /^[-\s]*$/; # neo my ($enzyme, $is_neo, $is_proto, $site); if ($data[0] =~ /^\s+(\S+)\s+(\S+)/) { ($enzyme, $site, $is_proto, $is_neo) = ($1, $2, 0, 1); } else { ($enzyme, $site, $is_proto, $is_neo) = ($data[0], $data[1], 1, 0); } $site =~ s/\s+//g; my $precut; if ($site =~ /,/) { $self->warn("Split site support not available for Bio::Restriction::Enzyme yet, ". "skipping $enzyme [$site]"); next ENZYME; } if ($site =~ m/^\((\d+\/\d+)\)[RYATGCN]+/) { $precut=$1; $site =~ s/\($precut\)//; } my ($cut, $comp_cut); ($site, $cut, $comp_cut) = $self->_cuts_from_site($site); my $re = Bio::Restriction::Enzyme->new( -type => $last_type, -site => $site, -name => $enzyme, -is_prototype => $is_proto, -is_neoschizomer => $is_neo); if ($cut) { $re->cut($self->_coordinate_shift_to_cut(length($site), $cut)); $re->complementary_cut($self->_coordinate_shift_to_cut(length($site), $comp_cut)); } $coll->enzymes($re); } return $coll->enzymes; } =head2 write Title : write Usage : $stream->write($renzs) Function: writes restriction enzymes into the stream Returns : 1 for success and 0 for error Args : a Bio::Restriction::Enzyme or a Bio::Restriction::EnzymeCollection object =cut sub write { my ($self,@h) = @_; $self->throw_not_implemented; } 1; BioPerl-1.007002/Bio/Restriction/IO/withrefm.pm000444000766000024 1600613155576320 21246 0ustar00cjfieldsstaff000000000000# BioPerl module for Bio::Restriction::IO::withrefm # # Please direct questions and support issues to # # Cared for by Rob Edwards # # Copyright Rob Edwards # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Restriction::IO::withrefm - withrefm enzyme set =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::Restriction::IO class. =head1 DESCRIPTION This is the most complete format of the REBASE files, and basically includes all the data on each of the restriction enzymes. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Rob Edwards, redwards@utmem.edu =head1 CONTRIBUTORS Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Mark A. Jensen, maj-at-fortinbras-dot-us =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Restriction::IO::withrefm; use vars qw(%WITH_REFM_FIELD); use strict; #use Bio::Restriction::IO; use Bio::Restriction::Enzyme; use Bio::Restriction::EnzymeCollection; use Data::Dumper; use base qw(Bio::Restriction::IO::base); =head2 read Title : read Usage : $renzs = $stream->read Function: reads all the restrction enzymes from the stream Returns : a Bio::Restriction::Restriction object Args : none =cut sub read { my $self = shift; my $renzs = Bio::Restriction::EnzymeCollection->new(-empty => 1); local $/ = '<1>'; while (defined(my $entry=$self->_readline()) ) { # not an entry. next unless $entry =~ /<2>/; #$self->debug("|$entry|\n"); # # Minimal information # my ($name) = $entry =~ /^(\S+)/; my ($site) = $entry =~ /\<3\>([^\n]+)/; if ( ! defined $site || $site eq '' or $site eq '?') { $self->warn("$name: no site. Skipping") if $self->verbose > 1; next; } # there are a couple of sequences that have multiple # recognition sites eg M.PhiBssHII: ACGCGT,CCGCGG,RGCGCY,RCCGGY,GCGCGC # TaqII : GACCGA(11/9),CACCCA(11/9) my @sequences; if ($site =~ /\,/) { @sequences = split (/\,/, $site); $site=shift @sequences; } # this regexp now parses all possible components # $1 : (s/t) or undef # $2 : [site] # $3 : (m/n) or undef /maj no warnings; # avoid faulty 'uninitialized value' warnings # occurring against the variables set by # regexp matching (unless anyone has other ideas...) my ($precut, $recog, $postcut) = ( $site =~ m/^(?:\((-?\w+\/-?\w+)\))?([\w^]+)(?:\((-?\w+\/-?\w+)\))?/ ); # # prototype / isoschizomers # my ($isoschizomers) = $entry =~ /<2>([^\n]+)/; my @isos = split(/\,/,$isoschizomers); my $is_prototype = (@isos ? 1 : 0); # # microbe # my ($microbe) = $entry =~ /<5>([^\n]+)/; # # source # my ($source) = $entry =~ /<6>([^\n]+)/; # # vendors # my ($vendors) = $entry =~ /<7>([^\n]+)/; my @vendors = split(/ */, $vendors); # # references # my ($refs) = $entry =~ /<8>(.+)<1>/s; my @refs = map {split /\n+/} $refs; use warnings; # when enz is constructed, site() will contain original characters, # but recog() will contain a regexp if required.../maj my $re = Bio::Restriction::Enzyme->new( -name => $name, -site => $recog, -recog => $recog, -precut => $precut, -postcut => $postcut, -is_prototype => $is_prototype, -isoschizomers => [@isos], -source => $source, -vendors => [@vendors], -references => [@refs], -xln_sub => \&_xln_sub ); # # methylation: easier to set here during parsing/maj # my ($meth) = $entry =~ /<4>([^\n]+)/; my @meths; if ($meth) { # this can be either X(Y) or X(Y),X2(Y2) # where X is the base and y is the type of methylation if ( $meth =~ /(\S+)\((\d+)\),(\S+)\((\d+)\)/ ) { # two msites per site #my ($p1, $m1, $p2, $m2) = ($1, $2, $3, $4); $re->methylation_sites($self->_meth($re,$1, $2), $self->_meth($re,$3,$4)); } elsif ($meth =~ /(\S+)\((\d+)\)/ ) { # one msite per site or more sites $re->methylation_sites( $self->_meth($re,$1,$2) ); @meths = split (/\, /, $meth); $meth=shift @meths; } else { $self->warn("Unknown methylation format [$meth]") if $self->verbose >0; } } # the _make_multicuts function now takes place in the # Enzyme constructor / maj # # create special types of Enzymes # (because of object cloning in _make_multisites, this happens # after everything else is set /maj) # (with the removal of the collection from the arglist, this # call (or its code) could now be placed in the constructor, # which is safer (since this has to happen last), # but it requires the methylation info, which # is more natural to get out here in the parsing./maj $self->_make_multisites($re, \@sequences, \@meths, \&_xln_sub) if @sequences; $renzs->enzymes($re); } return $renzs; } =head2 _xln_sub Title : _xln_sub Function: Translates withrefm coords to Bio::Restriction coords Args : Bio::Restriction::Enzyme object, scalar integer (cut posn) Note : Used internally; pass as a coderef to the B:R::Enzyme constructor =cut sub _xln_sub { my ($z,$c) = @_; return ($c < 0 ? $c : length($z->string)+$c); } =head2 write Title : write Usage : $stream->write($renzs) Function: writes restriction enzymes into the stream Returns : 1 for success and 0 for error Args : a Bio::Restriction::Enzyme or a Bio::Restriction::EnzymeCollection object =cut sub write { my ($self,@h) = @_; $self->throw_not_implemented; } 1; BioPerl-1.007002/Bio/Root000755000766000024 013155576320 15012 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Root/Build.pm000444000766000024 3542313155576320 16573 0ustar00cjfieldsstaff000000000000package Bio::Root::Build; use Bio::Root::Version; use strict; use warnings; =head1 SYNOPSIS ...TO BE ADDED =head1 DESCRIPTION This is a subclass of Module::Build so we can override certain methods and do fancy stuff It was first written against Module::Build::Base v0.2805. Many of the methods here are copy/pasted from there in their entirety just to change one or two minor things, since for the most part Module::Build::Base code is hard to cleanly override. B: per bug 3196, the majority of the code in this module has been revised or commented out to bring it in line with the Module::Build API. In particular, 'requires/recommends' tags in the Build.PL file were not of the same format as those for Module::Build, and so caused serious issues with newer versions (including giving incorrect meta data). Other problematic methods involving automatic installation of prereq modules via CPAN were also removed as they do not work with more modern perl tools such as perlbrew and cpanm. =head1 AUTHOR Sendu Bala =cut BEGIN { # we really need Module::Build to be installed eval "use base 'Module::Build'; 1" or die "This package requires Module::Build v0.42 or greater to install itself.\n$@"; # ensure we'll be able to reload this module later by adding its path to inc use Cwd; use lib Cwd::cwd(); } our @extra_types = qw(options excludes_os feature_requires test); # test must always be last in the list! our $checking_types = "requires|conflicts|".join("|", @extra_types); our $VERSION = $Bio::Root::Version::VERSION; =head2 find_pm_files Our modules are in Bio, not lib =cut sub find_pm_files { my $self = shift; foreach my $pm (@{$self->rscan_dir('Bio', qr/\.pm$/)}) { $self->{properties}{pm_files}->{$pm} = File::Spec->catfile('lib', $pm); } $self->_find_file_by_type('pm', 'lib'); } =head2 choose_scripts Ask what scripts to install (this method is unique to bioperl) =cut sub choose_scripts { my $self = shift; my $accept = shift; # we can offer interactive installation by groups only if we have subdirs # in scripts and no .PLS files there opendir(my $scripts_dir, 'scripts') or die "Can't open directory 'scripts': $!\n"; my $int_ok = 0; my @group_dirs; # only retain top-level script directories (the 'categories') while (my $thing = readdir($scripts_dir)) { next if $thing =~ /^\./; $thing = File::Spec->catfile('scripts', $thing); if (-d $thing) { $int_ok = 1; push(@group_dirs, $thing); } } closedir($scripts_dir); my $question = $int_ok ? "Install [a]ll BioPerl scripts, [n]one, ". "or choose groups [i]nteractively?" : "Install [a]ll BioPerl scripts ". "or [n]one?"; my $prompt = $accept ? 'a' : $self->prompt($question, 'a'); if ($prompt =~ /^[aA]/) { $self->log_info(" - will install all scripts\n"); $self->notes(chosen_scripts => 'all'); } elsif ($prompt =~ /^[iI]/) { $self->log_info(" - will install interactively:\n"); my @chosen_scripts; foreach my $group_dir (@group_dirs) { my $group = File::Basename::basename($group_dir); print " * group '$group' has:\n"; my @script_files = @{$self->rscan_dir($group_dir, qr/\.PLS$|\.pl$/)}; foreach my $script_file (@script_files) { my $script = File::Basename::basename($script_file); print " $script\n"; } my $result = $self->prompt(" Install scripts for group '$group'? [y]es [n]o [q]uit", 'n'); die if $result =~ /^[qQ]/; if ($result =~ /^[yY]/) { $self->log_info(" + will install group '$group'\n"); push(@chosen_scripts, @script_files); } else { $self->log_info(" - will not install group '$group'\n"); } } my $chosen_scripts = @chosen_scripts ? join("|", @chosen_scripts) : 'none'; $self->notes(chosen_scripts => $chosen_scripts); } else { $self->log_info(" - won't install any scripts\n"); $self->notes(chosen_scripts => 'none'); } print "\n"; } =head2 script_files Our version of script_files doesn't take args but just installs those scripts requested by the user after choose_scripts() is called. If it wasn't called, installs all scripts in scripts directory =cut sub script_files { my $self = shift; unless (-d 'scripts') { return {}; } my $chosen_scripts = $self->notes('chosen_scripts'); if ($chosen_scripts) { return if $chosen_scripts eq 'none'; return { map {$_, 1} split(/\|/, $chosen_scripts) } unless $chosen_scripts eq 'all'; } return $_ = { map {$_,1} @{$self->rscan_dir('scripts', qr/\.PLS$|\.pl$/)} }; } =head2 prompt Overridden simply to not print the default answer if chosen by hitting return =cut sub prompt { my $self = shift; my $mess = shift or die "prompt() called without a prompt message"; my $def; if ( $self->_is_unattended && !@_ ) { die <_readline(); if ( !defined($ans) # Ctrl-D or unattended or !length($ans) ) { # User hit return #print "$def\n"; didn't like this! $ans = $def; } return $ans; } =head2 ACTION_manifest We always generate a new MANIFEST instead of allowing existing files to remain MANIFEST.SKIP is left alone =cut sub ACTION_manifest { my ($self) = @_; if ( -e 'MANIFEST' || -e 'MANIFEST.SKIP' ) { $self->log_warn("MANIFEST files already exist, will overwrite them\n"); unlink('MANIFEST'); } require ExtUtils::Manifest; # ExtUtils::Manifest is not warnings clean. local ($^W, $ExtUtils::Manifest::Quiet) = (0,1); ExtUtils::Manifest::mkmanifest(); } =head2 ACTION_install Extended to run scripts post-installation =cut sub ACTION_install { my ($self) = @_; require ExtUtils::Install; $self->depends_on('build'); ExtUtils::Install::install($self->install_map, !$self->quiet, 0, $self->{args}{uninst} || 0); #$self->run_post_install_scripts; } =head2 test_internet For use with auto_features, which should require LWP::UserAgent as one of its reqs Note: as of 4-11-11, this is no longer called - if someone wants to run network tests (off by default) w/o a network, then they are hanging themselves by their own shoelaces. =cut sub test_internet { eval {require LWP::UserAgent;}; if ($@) { # ideally this won't happen because auto_feature already specified # LWP::UserAgent, so this sub wouldn't get called if LWP not installed return "LWP::UserAgent not installed"; } my $ua = LWP::UserAgent->new; $ua->timeout(10); $ua->env_proxy; my $response = $ua->get('http://search.cpan.org/'); unless ($response->is_success) { return "Could not connect to the internet (http://search.cpan.org/)"; } return; } =head2 ACTION_ppmdist Don't copy across man3 docs since they're of little use under Windows and have bad filenames =cut sub ACTION_ppmdist { my $self = shift; my @types = $self->install_types(1); $self->SUPER::ACTION_ppmdist(@_); $self->install_types(0); } =head2 install_types When supplied a true value, pretends libdoc doesn't exist (preventing man3 installation for ppmdist). when supplied false, they exist again =cut sub install_types { my ($self, $no_libdoc) = @_; $self->{no_libdoc} = $no_libdoc if defined $no_libdoc; my @types = $self->SUPER::install_types; if ($self->{no_libdoc}) { my @altered_types; foreach my $type (@types) { push(@altered_types, $type) unless $type eq 'libdoc'; } return @altered_types; } return @types; } =head2 ACTION_dist We make all archive formats we want, not just .tar.gz we also auto-run manifest action, since we always want to re-create MANIFEST and MANIFEST.SKIP just-in-time =cut sub ACTION_dist { my ($self) = @_; $self->depends_on('manifest'); $self->depends_on('distdir'); my $dist_dir = $self->dist_dir; $self->make_zip($dist_dir); $self->make_tarball($dist_dir); $self->delete_filetree($dist_dir); } =head2 ACTION_clean Define custom clean/realclean actions to rearrange config file cleanup =cut sub ACTION_clean { my ($self) = @_; $self->log_info("Cleaning up build files\n"); foreach my $item (map glob($_), $self->cleanup) { $self->delete_filetree($item); } $self->log_info("Cleaning up configuration files\n"); $self->delete_filetree($self->config_dir); } =head2 ACTION_realclean Define custom clean/realclean actions to rearrange config file cleanup =cut sub ACTION_realclean { my ($self) = @_; $self->depends_on('clean'); for my $method (qw(mymetafile mymetafile2 build_script)) { if ($self->can($method)) { $self->delete_filetree($self->$method); $self->log_info("Cleaning up $method data\n"); } } } =head2 get_metadata This wraps the base metafile method to add in version information from Bio::Root::Version to META.json and META.yml if it isn't already present. Note this should be compliant with meta_add and meta_merge, but occurs after those steps. If a version is already set and dist_version differs from the set one, a warning is printed. =cut sub get_metadata { my ($self, %args) = @_; my $metadata = $self->SUPER::get_metadata(%args); if (exists $metadata->{provides}) { my $ver = $self->dist_version; my $pkgs = $metadata->{provides}; for my $p (keys %{$pkgs}) { if (!exists($pkgs->{$p}->{'version'})) { $pkgs->{$p}->{'version'} = $ver; } else { $self->log_warn("Note: Module $p has a set version: ".$pkgs->{$p}->{'version'}."\n") if $pkgs->{$p}->{'version'} ne $ver; } } } return $metadata; } =head2 make_zip Makes zip file for windows users and bzip2 files as well =cut sub make_zip { my ($self, $dir, $file) = @_; $file ||= $dir; $self->log_info("Creating $file.zip\n"); my $zip_flags = $self->verbose ? '-r' : '-rq'; $self->do_system($self->split_like_shell("zip"), $zip_flags, "$file.zip", $dir); $self->log_info("Creating $file.bz2\n"); require Archive::Tar; # Archive::Tar versions >= 1.09 use the following to enable a compatibility # hack so that the resulting archive is compatible with older clients. $Archive::Tar::DO_NOT_USE_PREFIX = 0; my $files = $self->rscan_dir($dir); Archive::Tar->create_archive("$file.tar", 0, @$files); $self->do_system($self->split_like_shell("bzip2"), "-k", "$file.tar"); } =head2 prompt_for_network A method that can be called in a Build.PL script to ask the user if they want internet tests. Should only be called if you have tested for yourself that $build->feature('Network Tests') is true =cut sub prompt_for_network { my ($self, $accept) = @_; my $proceed = $accept ? 0 : $self->y_n( "Do you want to run tests that require connection to servers across the internet\n" . "(likely to cause some failures)? y/n", 'n'); if ($proceed) { $self->notes('network' => 1); $self->log_info(" - will run internet-requiring tests\n"); my $use_email = $self->y_n("Do you want to run tests requiring a valid email address? y/n",'n'); if ($use_email) { my $address = $self->prompt("Enter email address:"); $self->notes(email => $address); } } else { $self->notes(network => 0); $self->log_info(" - will not run internet-requiring tests\n"); } } =head2 print_build_script Override the build script warnings flag =cut sub print_build_script { my ($self, $fh) = @_; my $build_package = $self->build_class; my $closedata=""; my $config_requires; if ( -f $self->metafile ) { my $meta = eval { $self->read_metafile( $self->metafile ) }; $config_requires = $meta && $meta->{configure_requires}{'Module::Build'}; } $config_requires ||= 0; my %q = map {$_, $self->$_()} qw(config_dir base_dir); $q{base_dir} = Win32::GetShortPathName($q{base_dir}) if $self->is_windowsish; $q{magic_numfile} = $self->config_file('magicnum'); my @myINC = $self->_added_to_INC; @myINC = map { $_ = File::Spec->canonpath( $_ ); $_ =~ s/([\\\'])/\\$1/g; $_; } @myINC; # Remove duplicates @myINC = sort {$a cmp $b} keys %{ { map { $_ => 1 } @myINC } }; foreach my $key (keys %q) { $q{$key} = File::Spec->canonpath( $q{$key} ); $q{$key} =~ s/([\\\'])/\\$1/g; } my $quoted_INC = join ",\n", map " '$_'", @myINC; my $shebang = $self->_startperl; my $magic_number = $self->magic_number; # unique to bioperl, shut off overly verbose warnings on windows, bug 3215 my $w = $^O =~ /win/i ? '# no warnings (win)' : '$^W = 1; # Use warnings'; print $fh <; close \$FH; return \$filenum == $magic_number; } my \$progname; my \$orig_dir; BEGIN { $w \$progname = basename(\$0); \$orig_dir = Cwd::cwd(); my \$base_dir = '$q{base_dir}'; if (!magic_number_matches()) { unless (chdir(\$base_dir)) { die ("Could not chdir '\$base_dir', aborting\\n"); } unless (magic_number_matches()) { die ("Configuration seems to be out of date, please re-run 'perl Build.PL' again.\\n"); } } unshift \@INC, ( $quoted_INC ); } close(*DATA) unless eof(*DATA); # ensure no open handles to this script use $build_package; Module::Build->VERSION(q{$config_requires}); # Some platforms have problems setting \$^X in shebang contexts, fix it up here \$^X = Module::Build->find_perl_interpreter; if (-e 'Build.PL' and not $build_package->up_to_date('Build.PL', \$progname)) { warn "Warning: Build.PL has been altered. You may need to run 'perl Build.PL' again.\\n"; } # This should have just enough arguments to be able to bootstrap the rest. my \$build = $build_package->resume( properties => { config_dir => '$q{config_dir}', orig_dir => \$orig_dir, }, ); \$build->dispatch; EOF } 1; BioPerl-1.007002/Bio/Root/Exception.pm000444000766000024 3172013155576320 17466 0ustar00cjfieldsstaff000000000000package Bio::Root::Exception; use strict; =head1 SYNOPSIS =head2 Throwing exceptions using L: use Bio::Root::Exception; use Error; # Set Error::Debug to include stack trace data in the error messages $Error::Debug = 1; $file = shift; open my $IN, '<', $file or Bio::Root::FileOpenException->throw("Could not read file '$file': $!"); =head2 Throwing exceptions using L: # Here we have an object that ISA Bio::Root::Root, so it inherits throw(). open my $IN, '<', $file or $object->throw(-class => 'Bio::Root::FileOpenException', -text => "Could not read file '$file'", -value => $!); =head2 Catching and handling exceptions using L: use Bio::Root::Exception; use Error qw(:try); # Note that we need to import the 'try' tag from Error.pm # Set Error::Debug to include stack trace data in the error messages $Error::Debug = 1; my $file = shift; my $IN; try { open $IN, '<', $file or Bio::Root::FileOpenException->throw("Could not read file '$file': $!"); } catch Bio::Root::FileOpenException with { my $err = shift; print STDERR "Using default input file: $default_file\n"; open $IN, '<', $default_file or die "Could not read file '$default_file': $!"; } otherwise { my $err = shift; print STDERR "An unexpected exception occurred: \n$err"; # By placing an the error object reference within double quotes, # you're invoking its stringify() method. } finally { # Any code that you want to execute regardless of whether or not # an exception occurred. }; # the ending semicolon is essential! =head2 Defining a new Exception type as a subclass of Bio::Root::Exception: @Bio::TestException::ISA = qw( Bio::Root::Exception ); =head1 DESCRIPTION =head2 Exceptions defined in L These are generic exceptions for typical problem situations that could arise in any module or script. =for :list * C * C * C * C * C * C * C * C Using defined exception classes like these is a good idea because it indicates the basic nature of what went wrong in a convenient, computable way. If there is a type of exception that you want to throw that is not covered by the classes listed above, it is easy to define a new one that fits your needs. Just write a line like the following in your module or script where you want to use it (or put it somewhere that is accessible to your code): @NoCanDoException::ISA = qw( Bio::Root::Exception ); All of the exceptions defined in this module inherit from a common base class exception, Bio::Root::Exception. This allows a user to write a handler for all Bioperl-derived exceptions as follows: use Bio::Whatever; use Error qw(:try); try { # some code that depends on Bioperl } catch Bio::Root::Exception with { my $err = shift; print "A Bioperl exception occurred:\n$err\n"; }; So if you do create your own exceptions, just be sure they inherit from Bio::Root::Exception directly, or indirectly by inheriting from a Bio::Root::Exception subclass. The exceptions in Bio::Root::Exception are extensions of Graham Barr's L module available from CPAN. Despite this dependency, the L module does not explicitly C. This permits Bio::Root::Exception to be loaded even when Error.pm is not available. =head2 Throwing exceptions within Bioperl modules Error.pm is not part of the Bioperl distribution, and may not be present within any given perl installation. So, when you want to throw an exception in a Bioperl module, the safe way to throw it is to use L which can use Error.pm when it's available. See documentation in Bio::Root::Root for details. =head1 SEE ALSO See the C directory of the Bioperl distribution for working demo code. L for information about throwing L-based exceptions. L (available from CPAN, author: GBARR) Error.pm is helping to guide the design of exception handling in Perl 6. See these RFC's: http://dev.perl.org/rfc/63.pod http://dev.perl.org/rfc/88.pod =head1 EXCEPTIONS =head1 AUTHOR Steve Chervitz =cut my $debug = $Error::Debug; # Prevents the "used only once" warning. my $DEFAULT_VALUE = "__DUMMY__"; # Permits eval{} based handlers to work =head2 L Purpose : A generic base class for all BioPerl exceptions. By including a "catch Bio::Root::Exception" block, you should be able to trap all BioPerl exceptions. Example : throw Bio::Root::Exception("A generic exception", $!); =cut #--------------------------------------------------------- @Bio::Root::Exception::ISA = qw( Error ); #--------------------------------------------------------- =head1 Methods defined by Bio::Root::Exception =head2 new Purpose : Guarantees that -value is set properly before calling Error::new(). Arguments: key-value style arguments same as for Error::new() You can also specify plain arguments as ($message, $value) where $value is optional. -value, if defined, must be non-zero and not an empty string in order for eval{}-based exception handlers to work. These require that if($@) evaluates to true, which will not be the case if the Error has no value (Error overloads numeric operations to the Error::value() method). It is OK to create Bio::Root::Exception objects without specifying -value. In this case, an invisible dummy value is used. If you happen to specify a -value of zero (0), it will be replaced by the string "The number zero (0)". If you happen to specify a -value of empty string (""), it will be replaced by the string "An empty string ("")". =cut sub new { my ($class, @args) = @_; my ($value, %params); if( @args % 2 == 0 && $args[0] =~ /^-/) { %params = @args; $value = $params{'-value'}; } else { $params{-text} = $args[0]; $value = $args[1]; } if( defined $value ) { $value = "The number zero (0)" if $value =~ /^\d+$/ && $value == 0; $value = "An empty string (\"\")" if $value eq ""; } else { $value ||= $DEFAULT_VALUE; } $params{-value} = $value; my $self = $class->SUPER::new( %params ); return $self; } =head2 pretty_format() Purpose : Get a nicely formatted string containing information about the exception. Format is similar to that produced by Bio::Root::Root::throw(), with the addition of the name of the exception class in the EXCEPTION line and some other data available via the Error object. Example : print $error->pretty_format; =cut sub pretty_format { my $self = shift; my $msg = $self->text; my $stack = ''; if( $Error::Debug ) { $stack = $self->_reformat_stacktrace(); } my $value_string = $self->value ne $DEFAULT_VALUE ? "VALUE: ".$self->value."\n" : ""; my $class = ref($self); my $title = "------------- EXCEPTION: $class -------------"; my $footer = "\n" . '-' x CORE::length($title); my $out = "\n$title\n" . "MSG: $msg\n". $value_string. $stack. $footer . "\n"; return $out; } =head2 _reformat_stacktrace Reformatting of the stack performed by _reformat_stacktrace: for :list 1. Shift the file:line data in line i to line i+1. 2. change xxx::__ANON__() to "try{} block" 3. skip the "require" and "Error::subs::try" stack entries (boring) This means that the first line in the stack won't have any file:line data But this isn't a big issue since it's for a Bio::Root::-based method that doesn't vary from exception to exception. =cut sub _reformat_stacktrace { my $self = shift; my $msg = $self->text; my $stack = $self->stacktrace(); $stack =~ s/\Q$msg//; my @stack = split( /\n/, $stack); my @new_stack = (); my ($method, $file, $linenum, $prev_file, $prev_linenum); my $stack_count = 0; foreach my $i( 0..$#stack ) { # print "STACK-ORIG: $stack[$i]\n"; if( ($stack[$i] =~ /^\s*([^(]+)\s*\(.*\) called at (\S+) line (\d+)/) || ($stack[$i] =~ /^\s*(require 0) called at (\S+) line (\d+)/)) { ($method, $file, $linenum) = ($1, $2, $3); $stack_count++; } else{ next; } if( $stack_count == 1 ) { push @new_stack, "STACK: $method"; ($prev_file, $prev_linenum) = ($file, $linenum); next; } if( $method =~ /__ANON__/ ) { $method = "try{} block"; } if( ($method =~ /^require/ and $file =~ /Error\.pm/ ) || ($method =~ /^Error::subs::try/ ) ) { last; } push @new_stack, "STACK: $method $prev_file:$prev_linenum"; ($prev_file, $prev_linenum) = ($file, $linenum); } push @new_stack, "STACK: $prev_file:$prev_linenum"; return join "\n", @new_stack; } =head2 stringify() Purpose : Overrides Error::stringify() to call pretty_format(). This is called automatically when an exception object is placed between double quotes. Example : catch Bio::Root::Exception with { my $error = shift; print "$error"; } See Also: L =cut sub stringify { my ($self, @args) = @_; return $self->pretty_format( @args ); } =head1 Subclasses of Bio::Root::Exception =head2 L Purpose : Indicates that a method has not been implemented. Example : throw Bio::Root::NotImplemented( -text => "Method \"foo\" not implemented in module FooBar.", -value => "foo" ); =cut #--------------------------------------------------------- @Bio::Root::NotImplemented::ISA = qw( Bio::Root::Exception ); #--------------------------------------------------------- =head2 L Purpose : Indicates that some input/output-related trouble has occurred. Example : throw Bio::Root::IOException( -text => "Can't save data to file $file.", -value => $! ); =cut #--------------------------------------------------------- @Bio::Root::IOException::ISA = qw( Bio::Root::Exception ); #--------------------------------------------------------- =head2 L Purpose : Indicates that a file could not be opened. Example : throw Bio::Root::FileOpenException( -text => "Can't open file $file for reading.", -value => $! ); =cut #--------------------------------------------------------- @Bio::Root::FileOpenException::ISA = qw( Bio::Root::IOException ); #--------------------------------------------------------- =head2 L Purpose : Indicates that a system call failed. Example : unlink($file) or throw Bio::Root::SystemException( -text => "Can't unlink file $file.", -value => $! ); =cut #--------------------------------------------------------- @Bio::Root::SystemException::ISA = qw( Bio::Root::Exception ); #--------------------------------------------------------- =head2 L Purpose : Indicates that one or more parameters supplied to a method are invalid, unspecified, or conflicting. Example : throw Bio::Root::BadParameter( -text => "Required parameter \"-foo\" was not specified", -value => "-foo" ); =cut #--------------------------------------------------------- @Bio::Root::BadParameter::ISA = qw( Bio::Root::Exception ); #--------------------------------------------------------- =head2 L Purpose : Indicates that a specified (start,end) range or an index to an array is outside the permitted range. Example : throw Bio::Root::OutOfRange( -text => "Start coordinate ($start) cannot be less than zero.", -value => $start ); =cut #--------------------------------------------------------- @Bio::Root::OutOfRange::ISA = qw( Bio::Root::Exception ); #--------------------------------------------------------- =head2 L Purpose : Indicates that a requested thing cannot be located and therefore could possibly be bogus. Example : throw Bio::Root::NoSuchThing( -text => "Accession M000001 could not be found.", -value => "M000001" ); =cut #--------------------------------------------------------- @Bio::Root::NoSuchThing::ISA = qw( Bio::Root::Exception ); #--------------------------------------------------------- 1; BioPerl-1.007002/Bio/Root/HTTPget.pm000444000766000024 2722313155576320 17012 0ustar00cjfieldsstaff000000000000# # BioPerl module for fallback HTTP get operations. # # Module is proxy-aware # # Please direct questions and support issues to # # Cared for by Chris Dagdigian # but all of the good stuff was written by # Lincoln Stein. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Root::HTTPget - module for fallback HTTP get operations when LWP:: is unavailable =head1 SYNOPSIS use Bio::Root::HTTPget; my $web = Bio::Root::HTTPget->new(); my $response = $web->get('http://localhost'); $response = $web->get('http://localhost/images'); $response = eval { $web->get('http://fred:secret@localhost/ladies_only/') } or warn $@; $response = eval { $web->get('http://jeff:secret@localhost/ladies_only/') } or warn $@; $response = $web->get('http://localhost/images/navauthors.gif'); $response = $web->get(-url=>'http://www.google.com', -proxy=>'http://www.modperl.com'); =head1 DESCRIPTION This is basically an last-chance module for doing network HTTP get requests in situations where more advanced external CPAN modules such as LWP:: are not installed. The particular reason this module was developed was so that the Open Bio Database Access code can fallback to fetching the default registry files from http://open-bio.org/registry/ without having to depend on external dependencies like Bundle::LWP for network HTTP access. The core of this module was written by Lincoln Stein. It can handle proxies and HTTP-based proxy authentication. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Lincoln Stein # Please direct questions and support issues to I Cared for by Chris Dagdigian =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Root::HTTPget; use strict; use warnings; use IO::Socket qw(:DEFAULT :crlf); use base qw(Bio::Root::Root); { # default attributes, in case used as a class/sub call my %attributes; =head2 get Title : get Usage : my $resp = get(-url => $url); Function: Returns : string Args : -url => URL to HTTPGet -proxy => proxy to use -user => username for proxy or authentication -pass => password for proxy or authentication -timeout => timeout =cut sub get { my $self; if($_[0] && (ref($_[0]) or $_[0] =~ /^Bio::/)) { $self = shift; } my ($url,$proxy,$timeout,$auth_user,$auth_pass) = __PACKAGE__->_rearrange([qw(URL PROXY TIMEOUT USER PASS)],@_); my $dest = $proxy || $url; my ($host,$port,$path,$user,$pass) = _http_parse_url($dest) or __PACKAGE__->throw("invalid URL $url"); $auth_user ||= $user; $auth_pass ||= $pass; if ($self) { unless ($proxy) { $proxy = $self->proxy; } unless ($auth_user) { ($auth_user, $auth_pass) = $self->authentication; } } $path = $url if $proxy; # set up the connection my $socket = _http_connect($host,$port) or __PACKAGE__->throw("can't connect: $@"); # the request print $socket "GET $path HTTP/1.0$CRLF"; print $socket "User-Agent: Bioperl fallback fetcher/1.0$CRLF"; # Support virtual hosts print $socket "HOST: $host$CRLF"; if ($auth_user && $auth_pass) { # authentication information my $token = _encode_base64("$auth_user:$auth_pass"); print $socket "Authorization: Basic $token$CRLF"; } print $socket "$CRLF"; # read the response my $response; { local $/ = "$CRLF$CRLF"; $response = <$socket>; } my ($status_line,@other_lines) = split $CRLF,$response; my ($stat_code,$stat_msg) = $status_line =~ m!^HTTP/1\.[01] (\d+) (.+)! or __PACKAGE__->throw("invalid response from web server: got $response"); my %headers = map {/^(\S+): (.+)/} @other_lines; if ($stat_code == 302 || $stat_code == 301) { # redirect my $location = $headers{Location} or __PACKAGE__->throw("invalid redirect: no Location header"); return get(-url => $location, -proxy => $proxy, -timeout => $timeout, -user => $auth_user, -pass => $auth_pass); # recursive call } elsif ($stat_code == 401) { # auth required my $auth_required = $headers{'WWW-Authenticate'}; $auth_required =~ /^Basic realm="([^\"]+)"/ or __PACKAGE__->throw("server requires unknown type of". " authentication: $auth_required"); __PACKAGE__->throw("request failed: $status_line, realm = $1"); } elsif ($stat_code != 200) { __PACKAGE__->throw("request failed: $status_line"); } $response = ''; while (1) { my $bytes = read($socket,$response,2048,length $response); last unless $bytes > 0; } $response; } =head2 getFH Title : getFH Usage : Function: Example : Returns : string Args : =cut sub getFH { my $self; if($_[0] && (ref($_[0]) or $_[0] =~ /^Bio::/)) { $self = shift; } my ($url,$proxy,$timeout,$auth_user,$auth_pass) = __PACKAGE__->_rearrange([qw(URL PROXY TIMEOUT USER PASS)],@_); my $dest = $proxy || $url; my ($host,$port,$path,$user,$pass) = _http_parse_url($dest) or __PACKAGE__->throw("invalid URL $url"); $auth_user ||= $user; $auth_pass ||= $pass; $path = $url if $proxy; # set up the connection my $socket = _http_connect($host,$port) or __PACKAGE__->throw("can't connect: $@"); # the request print $socket "GET $path HTTP/1.0$CRLF"; print $socket "User-Agent: Bioperl fallback fetcher/1.0$CRLF"; # Support virtual hosts print $socket "HOST: $host$CRLF"; if ($auth_user && $auth_pass) { # authentication information my $token = _encode_base64("$auth_user:$auth_pass"); print $socket "Authorization: Basic $token$CRLF"; } print $socket "$CRLF"; # read the response my $response; { local $/ = "$CRLF$CRLF"; $response = <$socket>; } my ($status_line,@other_lines) = split $CRLF,$response; my ($stat_code,$stat_msg) = $status_line =~ m!^HTTP/1\.[01] (\d+) (.+)! or __PACKAGE__->throw("invalid response from web server: got $response"); my %headers = map {/^(\S+): (.+)/} @other_lines; if ($stat_code == 302 || $stat_code == 301) { # redirect my $location = $headers{Location} or __PACKAGE__->throw("invalid redirect: no Location header"); return getFH(-url => $location, -proxy => $proxy, -timeout => $timeout, -user => $auth_user, -pass => $auth_pass); # recursive call } elsif ($stat_code == 401) { # auth required my $auth_required = $headers{'WWW-Authenticate'}; $auth_required =~ /^Basic realm="([^\"]+)"/ or __PACKAGE__->throw("server requires unknown type of ". "authentication: $auth_required"); __PACKAGE__->throw("request failed: $status_line, realm = $1"); } elsif ($stat_code != 200) { __PACKAGE__->throw("request failed: $status_line"); } # Now that we are reasonably sure the socket and request # are OK we pass the socket back as a filehandle so it can # be processed by the caller... $socket; } =head2 _http_parse_url Title : Usage : Function: Example : Returns : Args : =cut sub _http_parse_url { my $self; if($_[0] && (ref($_[0]) or $_[0] =~ /^Bio::/)) { $self = shift; } my $url = shift; my ($user,$pass,$hostent,$path) = $url =~ m!^http://(?:([^:]+):([^:]+)@)?([^/]+)(/?[^\#]*)! or return; $path ||= '/'; my ($host,$port) = split(':',$hostent); return ($host,$port||80,$path,$user,$pass); } =head2 _http_connect Title : Usage : Function: Example : Returns : Args : =cut sub _http_connect { my ($host,$port,$timeout) = @_; my $sock = IO::Socket::INET->new(Proto => 'tcp', Type => SOCK_STREAM, PeerHost => $host, PeerPort => $port, Timeout => $timeout, ); $sock; } =head2 _encode_base64 Title : Usage : Function: Example : Returns : Args : =cut sub _encode_base64 { my $self; if($_[0] && (ref($_[0]) or $_[0] =~ /^Bio::/)) { $self = shift; } my $res = ""; my $eol = $_[1]; $eol = "\n" unless defined $eol; pos($_[0]) = 0; # ensure start at the beginning $res = join '', map( pack('u',$_)=~ /^.(\S*)/, ($_[0]=~/(.{1,45})/gs)); $res =~ tr|` -_|AA-Za-z0-9+/|; # `# help emacs # fix padding at the end my $padding = (3 - length($_[0]) % 3) % 3; $res =~ s/.{$padding}$/'=' x $padding/e if $padding; # break encoded string into lines of no more than 76 characters each if (length $eol) { $res =~ s/(.{1,76})/$1$eol/g; } return $res; } =head2 proxy Title : proxy Usage : $httpproxy = $db->proxy('http') or $db->proxy(['http','ftp'], 'http://myproxy' ) Function: Get/Set a proxy for use of proxy. Defaults to environment variable http_proxy if present. Returns : a string indicating the proxy Args : $protocol : string for the protocol to set/get $proxyurl : url of the proxy to use for the specified protocol $username : username (if proxy requires authentication) $password : password (if proxy requires authentication) =cut sub proxy { my $self; if($_[0] && (ref($_[0]) or $_[0] =~ /^Bio::/)) { $self = shift; } my ($protocol,$proxy,$username,$password) = @_; my $atts = ref($self) ? $self : \%attributes; $protocol ||= 'http'; if (!$proxy) { if (defined $ENV{http_proxy}) { $proxy = $ENV{http_proxy}; if ($proxy =~ /\@/) { ($username, $password, $proxy) = $proxy =~ m{http://(\S+):(\S+)\@(\S+)}; $proxy = 'http://'.$proxy; } } } if (defined $proxy) { # default to class method call __PACKAGE__->authentication($username, $password) if ($username && $password); $atts->{'_proxy'}->{$protocol} = $proxy; } return $atts->{'_proxy'}->{$protocol}; } =head2 clear_proxy Title : clear_proxy Usage : my $old_prozy = $db->clear_proxy('http') Function: Unsets (clears) the proxy for the protocol indicated Returns : a string indicating the old proxy value Args : $protocol : string for the protocol to clear =cut sub clear_proxy { my $self; if($_[0] && (ref($_[0]) or $_[0] =~ /^Bio::/)) { $self = shift; } my ($protocol) = @_; my $atts = ref($self) ? $self : \%attributes; $protocol ||= 'http'; delete $atts->{'_proxy'}->{$protocol}; } =head2 authentication Title : authentication Usage : $db->authentication($user,$pass) Function: Get/Set authentication credentials Returns : Array of user/pass Args : Array or user/pass =cut sub authentication { my $self; if($_[0] && (ref($_[0]) or $_[0] =~ /^Bio::/)) { $self = shift; } my $atts = ref($self) ? $self : \%attributes; if (@_) { my ($u,$p) = @_; my $atts = ref($self) ? $self : \%attributes; $atts->{'_authentication'} = [ $u,$p]; } return @{$atts->{'_authentication'} || []}; } } 1; BioPerl-1.007002/Bio/Root/IO.pm000444000766000024 10760113155576320 16061 0ustar00cjfieldsstaff000000000000package Bio::Root::IO; use strict; use Symbol; use IO::Handle; use File::Copy; use Fcntl; use base qw(Bio::Root::Root); # as of 2016, worked on most systems, but will test this in a RC my %modes = ( 0 => 'r', 1 => 'w', 2 => 'rw' ); =head1 SYNOPSIS # Use stream I/O in your module $self->{'io'} = Bio::Root::IO->new(-file => "myfile"); $self->{'io'}->_print("some stuff"); my $line = $self->{'io'}->_readline(); $self->{'io'}->_pushback($line); $self->{'io'}->close(); # obtain platform-compatible filenames $path = Bio::Root::IO->catfile($dir, $subdir, $filename); # obtain a temporary file (created in $TEMPDIR) ($handle) = $io->tempfile(); =head1 DESCRIPTION This module provides methods that will usually be needed for any sort of file- or stream-related input/output, e.g., keeping track of a file handle, transient printing and reading from the file handle, a close method, automatically closing the handle on garbage collection, etc. To use this for your own code you will either want to inherit from this module, or instantiate an object for every file or stream you are dealing with. In the first case this module will most likely not be the first class off which your class inherits; therefore you need to call _initialize_io() with the named parameters in order to set file handle, open file, etc automatically. Most methods start with an underscore, indicating they are private. In OO speak, they are not private but protected, that is, use them in your module code, but a client code of your module will usually not want to call them (except those not starting with an underscore). In addition this module contains a couple of convenience methods for cross-platform safe tempfile creation and similar tasks. There are some CPAN modules related that may not be available on all platforms. At present, File::Spec and File::Temp are attempted. This module defines $PATHSEP, $TEMPDIR, and $ROOTDIR, which will always be set, and $OPENFLAGS, which will be set if either of File::Spec or File::Temp fails. The -noclose boolean (accessed via the noclose method) prevents a filehandle from being closed when the IO object is cleaned up. This is special behavior when a object like a parser might share a filehandle with an object like an indexer where it is not proper to close the filehandle as it will continue to be reused until the end of the stream is reached. In general you won't want to play with this flag. =head1 AUTHOR Hilmar Lapp =cut our ($FILESPECLOADED, $FILETEMPLOADED, $FILEPATHLOADED, $TEMPDIR, $PATHSEP, $ROOTDIR, $OPENFLAGS, $VERBOSE, $ONMAC, $HAS_EOL, ); my $TEMPCOUNTER; my $HAS_WIN32 = 0; BEGIN { $TEMPCOUNTER = 0; $FILESPECLOADED = 0; $FILETEMPLOADED = 0; $FILEPATHLOADED = 0; $VERBOSE = 0; # try to load those modules that may cause trouble on some systems eval { require File::Path; $FILEPATHLOADED = 1; }; if( $@ ) { print STDERR "Cannot load File::Path: $@" if( $VERBOSE > 0 ); # do nothing } # If on Win32, attempt to find Win32 package if($^O =~ /mswin/i) { eval { require Win32; $HAS_WIN32 = 1; }; } # Try to provide a path separator. Why doesn't File::Spec export this, # or did I miss it? if ($^O =~ /mswin/i) { $PATHSEP = "\\"; } elsif($^O =~ /macos/i) { $PATHSEP = ":"; } else { # unix $PATHSEP = "/"; } eval { require File::Spec; $FILESPECLOADED = 1; $TEMPDIR = File::Spec->tmpdir(); $ROOTDIR = File::Spec->rootdir(); require File::Temp; # tempfile creation $FILETEMPLOADED = 1; }; if( $@ ) { if(! defined($TEMPDIR)) { # File::Spec failed # determine tempdir if (defined $ENV{'TEMPDIR'} && -d $ENV{'TEMPDIR'} ) { $TEMPDIR = $ENV{'TEMPDIR'}; } elsif( defined $ENV{'TMPDIR'} && -d $ENV{'TMPDIR'} ) { $TEMPDIR = $ENV{'TMPDIR'}; } if($^O =~ /mswin/i) { $TEMPDIR = 'C:\TEMP' unless $TEMPDIR; $ROOTDIR = 'C:'; } elsif($^O =~ /macos/i) { $TEMPDIR = "" unless $TEMPDIR; # what is a reasonable default on Macs? $ROOTDIR = ""; # what is reasonable?? } else { # unix $TEMPDIR = "/tmp" unless $TEMPDIR; $ROOTDIR = "/"; } if (!( -d $TEMPDIR && -w $TEMPDIR )) { $TEMPDIR = '.'; # last resort } } # File::Temp failed (alone, or File::Spec already failed) # determine open flags for tempfile creation using Fcntl $OPENFLAGS = O_CREAT | O_EXCL | O_RDWR; for my $oflag (qw/FOLLOW BINARY LARGEFILE EXLOCK NOINHERIT TEMPORARY/){ my ($bit, $func) = (0, "Fcntl::O_" . $oflag); no strict 'refs'; $OPENFLAGS |= $bit if eval { $bit = &$func(); 1 }; } } $ONMAC = "\015" eq "\n"; } =head2 new Title : new Usage : my $io = Bio::Root::IO->new( -file => 'data.txt' ); Function: Create new class instance. It automatically calls C<_initialize_io>. Args : Same named parameters as C<_initialize_io>. Returns : A Bio::Root::IO object =cut sub new { my ($caller, @args) = @_; my $self = $caller->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 _initialize_io Title : _initialize_io Usage : $io->_initialize_io(@params); Function: Initializes filehandle and other properties from the parameters. Args : The following named parameters are currently recognized: -file name of file to read or write to -fh file handle to read or write to (mutually exclusive with -file and -string) -input name of file, or filehandle (GLOB or IO::Handle object) to read of write to -string string to read from (will be converted to filehandle) -url name of URL to open -flush boolean flag to autoflush after each write -noclose boolean flag, when set to true will not close a filehandle (must explicitly call close($io->_fh) -retries number of times to try a web fetch before failure -ua_parms when using -url, hashref of key => value parameters to pass to LWP::UserAgent->new(). A useful value might be, for example, {timeout => 60 } (ua defaults to 180s) Returns : True =cut sub _initialize_io { my($self, @args) = @_; $self->_register_for_cleanup(\&_io_cleanup); my ($input, $noclose, $file, $fh, $string, $flush, $url, $retries, $ua_parms) = $self->_rearrange([qw(INPUT NOCLOSE FILE FH STRING FLUSH URL RETRIES UA_PARMS)], @args); my $mode; if ($url) { $retries ||= 5; require LWP::UserAgent; my $ua = LWP::UserAgent->new(%$ua_parms); my $http_result; my ($handle, $tempfile) = $self->tempfile(); CORE::close($handle); for (my $try = 1 ; $try <= $retries ; $try++) { $http_result = $ua->get($url, ':content_file' => $tempfile); $self->warn("[$try/$retries] tried to fetch $url, but server ". "threw ". $http_result->code . ". retrying...") if !$http_result->is_success; last if $http_result->is_success; } $self->throw("Failed to fetch $url, server threw ".$http_result->code) if !$http_result->is_success; $file = $tempfile; $mode = '>'; } delete $self->{'_readbuffer'}; delete $self->{'_filehandle'}; $self->noclose( $noclose) if defined $noclose; # determine whether the input is a file(name) or a stream if ($input) { if (ref(\$input) eq 'SCALAR') { # we assume that a scalar is a filename if ($file && ($file ne $input)) { $self->throw("Input file given twice: '$file' and '$input' disagree"); } $file = $input; } elsif (ref($input) && ((ref($input) eq 'GLOB') || $input->isa('IO::Handle'))) { # input is a stream $fh = $input; } else { # let's be strict for now $self->throw("Unable to determine type of input $input: ". "not string and not GLOB"); } } if (defined($file) && defined($fh)) { $self->throw("Providing both a file and a filehandle for reading - ". "only one please!"); } if ($string) { if (defined($file) || defined($fh)) { $self->throw("File or filehandle provided with -string, ". "please unset if you are using -string as a file"); } open $fh, '<', \$string or $self->throw("Could not read string: $!"); } if (defined($file) && ($file ne '')) { $self->file($file); ($mode, $file) = $self->cleanfile; $mode ||= '<'; my $action = ($mode =~ m/>/) ? 'write' : 'read'; $fh = Symbol::gensym(); open $fh, $mode, $file or $self->throw("Could not $action file '$file': $!"); } if (defined $fh) { # check filehandle to ensure it's one of: # a GLOB reference, as in: open(my $fh, "myfile"); # an IO::Handle or IO::String object # the UNIVERSAL::can added to fix Bug2863 unless ( ( ref $fh and ( ref $fh eq 'GLOB' ) ) or ( ref $fh and ( UNIVERSAL::can( $fh, 'can' ) ) and ( $fh->isa('IO::Handle') or $fh->isa('IO::String') ) ) ) { $self->throw("Object $fh does not appear to be a file handle"); } if ($HAS_EOL) { binmode $fh, ':raw:eol(LF-Native)'; } $self->_fh($fh); # if $fh not provided, defaults to STDIN and STDOUT } $self->_flush_on_write(defined $flush ? $flush : 1); return 1; } =head2 _fh Title : _fh Usage : $io->_fh($newval); Function: Get or set the file handle for the stream encapsulated. Args : Optional filehandle to use Returns : Filehandle for the stream =cut sub _fh { my ($self, $value) = @_; if ( defined $value) { $self->{'_filehandle'} = $value; } return $self->{'_filehandle'}; } =head2 mode Title : mode Usage : $io->mode(); $io->mode(-force => 1); Function: Determine if the object was opened for reading or writing Args : -force: Boolean. Once mode() has been called, the mode is cached for further calls to mode(). Use this argument to override this behavior and re-check the object's mode. Returns : Mode of the object: 'r' for readable 'w' for writable 'rw' for readable and writable '?' if mode could not be determined (e.g. for a -url) =cut sub mode { my ($self, %arg) = @_; # Method 1: IO::Handle::fdopen # my $iotest = new IO::Handle; # $iotest->fdopen( dup(fileno($fh)) , 'r' ); # if ($iotest->error == 0) { ... } # It did not actually seem to work under any platform, since there would no # error if the filehandle had been opened writable only. It could not be # hacked around when dealing with unseekable (piped) filehandles. # Method 2: readline, a.k.a. the <> operator # no warnings "io"; # my $line = <$fh>; # if (defined $line) { # $self->{'_mode'} = 'r'; # ... # It did not work well either because <> returns undef, i.e. querying the # mode() after having read an entire file returned 'w'. if ( $arg{-force} || not exists $self->{'_mode'} ) { # Determine stream mode my $mode; my $fh = $self->_fh; if (defined $fh) { # use fcntl if not Windows-based if ($^O !~ /MSWin32/) { my $m = fcntl($fh, F_GETFL, 0); $mode = exists $modes{$m & 3} ? $modes{$m & 3} : '?'; } else { # Determine read/write status of filehandle no warnings 'io'; if ( defined( read $fh, my $content, 0 ) ) { # Successfully read 0 bytes $mode = 'r' } if ( defined( syswrite $fh, '') ) { # Successfully wrote 0 bytes $mode ||= ''; $mode .= 'w'; } } } else { # Stream does not have a filehandle... cannot determine mode $mode = '?'; } # Save mode for future use $self->{'_mode'} = $mode; } return $self->{'_mode'}; } =head2 file Title : file Usage : $io->file('>'.$file); my $file = $io->file; Function: Get or set the name of the file to read or write. Args : Optional file name (including its mode, e.g. '<' for reading or '>' for writing) Returns : A string representing the filename and its mode. =cut sub file { my ($self, $value) = @_; if ( defined $value) { $self->{'_file'} = $value; } return $self->{'_file'}; } =head2 cleanfile Title : cleanfile Usage : my ($mode, $file) = $io->cleanfile; Function: Get the name of the file to read or write, stripped of its mode ('>', '<', '+>', '>>', etc). Args : None Returns : In array context, an array of the mode and the clean filename. =cut sub cleanfile { my ($self) = @_; return ($self->{'_file'} =~ m/^ (\+?[><]{1,2})?\s*(.*) $/x); } =head2 format Title : format Usage : $io->format($newval) Function: Get the format of a Bio::Root::IO sequence file or filehandle. Every object inheriting Bio::Root::IO is guaranteed to have a format. Args : None Returns : Format of the file or filehandle, e.g. fasta, fastq, genbank, embl. =cut sub format { my ($self) = @_; my $format = (split '::', ref($self))[-1]; return $format; } =head2 variant Title : format Usage : $io->format($newval) Function: Get the variant of a Bio::Root::IO sequence file or filehandle. The format variant depends on the specific format used. Note that not all formats have variants. Also, the Bio::Root::IO-implementing modules that require access to variants need to define a global hash that has the allowed variants as its keys. Args : None Returns : Variant of the file or filehandle, e.g. sanger, solexa or illumina for the fastq format, or undef for formats that do not have variants. =cut sub variant { my ($self, $variant) = @_; if (defined $variant) { $variant = lc $variant; my $var_name = '%'.ref($self).'::variant'; my %ok_variants = eval $var_name; # e.g. %Bio::Assembly::IO::ace::variant if (scalar keys %ok_variants == 0) { $self->throw("Could not validate variant because global variant ". "$var_name was not set or was empty\n"); } if (not exists $ok_variants{$variant}) { $self->throw("$variant is not a valid variant of the " . $self->format . ' format'); } $self->{variant} = $variant; } return $self->{variant}; } =head2 _print Title : _print Usage : $io->_print(@lines) Function: Print lines of text to the IO stream object. Args : List of strings to print Returns : True on success, undef on failure =cut sub _print { my $self = shift; my $fh = $self->_fh() || \*STDOUT; my $ret = print $fh @_; return $ret; } =head2 _insert Title : _insert Usage : $io->_insert($string,1) Function: Insert some text in a file at the given line number (1-based). Args : * string to write in file * line number to insert the string at Returns : True =cut sub _insert { my ($self, $string, $line_num) = @_; # Line number check if ($line_num < 1) { $self->throw("Could not insert text at line $line_num: the minimum ". "line number possible is 1."); } # File check my ($mode, $file) = $self->cleanfile; if (not defined $file) { $self->throw('Could not insert a line: IO object was initialized with '. 'something else than a file.'); } # Everything that needs to be written is written before we read it $self->flush; # Edit the file line by line (no slurping) $self->close; my $temp_file; my $number = 0; while (-e "$file.$number.temp") { $number++; } $temp_file = "$file.$number.temp"; copy($file, $temp_file); open my $fh1, '<', $temp_file or $self->throw("Could not read temporary file '$temp_file': $!"); open my $fh2, '>', $file or $self->throw("Could not write file '$file': $!"); while (my $line = <$fh1>) { if ($. == $line_num) { # right line for new data print $fh2 $string . $line; } else { print $fh2 $line; } } CORE::close $fh1; CORE::close $fh2; unlink $temp_file or $self->throw("Could not delete temporary file '$temp_file': $!"); # Line number check (again) if ( $. > 0 && $line_num > $. ) { $self->throw("Could not insert text at line $line_num: there are only ". "$. lines in file '$file'"); } # Re-open the file in append mode to be ready to add text at the end of it # when the next _print() statement comes open my $new_fh, '>>', $file or $self->throw("Could not append to file '$file': $!"); $self->_fh($new_fh); # If file is empty and we're inserting at line 1, simply append text to file if ( $. == 0 && $line_num == 1 ) { $self->_print($string); } return 1; } =head2 _readline Title : _readline Usage : local $Bio::Root::IO::HAS_EOL = 1; my $io = Bio::Root::IO->new(-file => 'data.txt'); my $line = $io->_readline(); $io->close; Function: Read a line of input and normalize all end of line characters. End of line characters are typically "\n" on Linux platforms, "\r\n" on Windows and "\r" on older Mac OS. By default, the _readline() method uses the value of $/, Perl's input record separator, to detect the end of each line. This means that you will not get the expected lines if your input has Mac-formatted end of line characters. Also, note that the current implementation does not handle pushed back input correctly unless the pushed back input ends with the value of $/. For each line parsed, its line ending, e.g. "\r\n" is converted to "\n", unless you provide the -raw argument. Altogether it is easier to let the PerlIO::eol module automatically detect the proper end of line character and normalize it to "\n". Do so by setting $Bio::Root::IO::HAS_EOL to 1. Args : -raw : Avoid converting end of line characters to "\n" This option has no effect when using $Bio::Root::IO::HAS_EOL = 1. Returns : Line of input, or undef when there is nothing to read anymore =cut sub _readline { my ($self, %param) = @_; my $fh = $self->_fh or return; my $line; # if the buffer been filled by _pushback then return the buffer # contents, rather than read from the filehandle if( @{$self->{'_readbuffer'} || [] } ) { $line = shift @{$self->{'_readbuffer'}}; } else { $line = <$fh>; } # Note: In Windows the "-raw" parameter has no effect, because Perl already discards # the '\r' from the line when reading in text mode from the filehandle # ($line = <$fh>), and put it back automatically when printing if( !$HAS_EOL && !$param{-raw} && (defined $line) ) { # don't strip line endings if -raw or $HAS_EOL is specified $line =~ s/\015\012/\012/g; # Change all CR/LF pairs to LF $line =~ tr/\015/\n/ unless $ONMAC; # Change all single CRs to NEWLINE } return $line; } =head2 _pushback Title : _pushback Usage : $io->_pushback($newvalue) Function: Puts a line previously read with _readline back into a buffer. buffer can hold as many lines as system memory permits. Note that this is only supported for pushing back data ending with the current, localized value of $/. Using this method to push modified data back onto the buffer stack is not supported; see bug 843. Args : newvalue Returns : True =cut # fix for bug 843, this reveals some unsupported behavior #sub _pushback { # my ($self, $value) = @_; # if (index($value, $/) >= 0) { # push @{$self->{'_readbuffer'}}, $value; # } else { # $self->throw("Pushing modifed data back not supported: $value"); # } #} sub _pushback { my ($self, $value) = @_; return unless $value; unshift @{$self->{'_readbuffer'}}, $value; return 1; } =head2 close Title : close Usage : $io->close() Function: Closes the file handle associated with this IO instance, excepted if -noclose was specified. Args : None Returns : True =cut sub close { my ($self) = @_; # do not close if we explicitly asked not to return if $self->noclose; if( defined( my $fh = $self->{'_filehandle'} )) { $self->flush; return if ref $fh eq 'GLOB' && ( \*STDOUT == $fh || \*STDERR == $fh || \*STDIN == $fh ); # don't close IO::Strings CORE::close $fh unless ref $fh && $fh->isa('IO::String'); } $self->{'_filehandle'} = undef; delete $self->{'_readbuffer'}; return 1; } =head2 flush Title : flush Usage : $io->flush() Function: Flushes the filehandle Args : None Returns : True =cut sub flush { my ($self) = shift; if( !defined $self->{'_filehandle'} ) { $self->throw("Flush failed: no filehandle was active"); } if( ref($self->{'_filehandle'}) =~ /GLOB/ ) { my $oldh = select($self->{'_filehandle'}); $| = 1; select($oldh); } else { $self->{'_filehandle'}->flush(); } return 1; } =head2 noclose Title : noclose Usage : $io->noclose($newval) Function: Get or set the NOCLOSE flag - setting this to true will prevent a filehandle from being closed when an object is cleaned up or explicitly closed. Args : Optional new value (a scalar or undef) Returns : Value of noclose (a scalar) =cut sub noclose { my $self = shift; return $self->{'_noclose'} = shift if @_; return $self->{'_noclose'}; } =head2 _io_cleanup =cut sub _io_cleanup { my ($self) = @_; $self->close(); my $v = $self->verbose; # we are planning to cleanup temp files no matter what if ( exists($self->{'_rootio_tempfiles'}) and ref($self->{'_rootio_tempfiles'}) =~ /array/i and not $self->save_tempfiles ) { if( $v > 0 ) { warn( "going to remove files ", join(",", @{$self->{'_rootio_tempfiles'}}), "\n"); } unlink (@{$self->{'_rootio_tempfiles'}} ); } # cleanup if we are not using File::Temp if ( $self->{'_cleanuptempdir'} and exists($self->{'_rootio_tempdirs'}) and ref($self->{'_rootio_tempdirs'}) =~ /array/i and not $self->save_tempfiles ) { if( $v > 0 ) { warn( "going to remove dirs ", join(",", @{$self->{'_rootio_tempdirs'}}), "\n"); } $self->rmtree( $self->{'_rootio_tempdirs'}); } } =head2 exists_exe Title : exists_exe Usage : $exists = $io->exists_exe('clustalw'); $exists = Bio::Root::IO->exists_exe('clustalw') $exists = Bio::Root::IO::exists_exe('clustalw') Function: Determines whether the given executable exists either as file or within the path environment. The latter requires File::Spec to be installed. On Win32-based system, .exe is automatically appended to the program name unless the program name already ends in .exe. Args : Name of the executable Returns : 1 if the given program is callable as an executable, and 0 otherwise =cut sub exists_exe { my ($self, $exe) = @_; $self->throw("Must pass a defined value to exists_exe") unless defined $exe; $exe = $self if (!(ref($self) || $exe)); $exe .= '.exe' if(($^O =~ /mswin/i) && ($exe !~ /\.(exe|com|bat|cmd)$/i)); return $exe if ( -f $exe && -x $exe ); # full path and exists # Ewan's comment. I don't think we need this. People should not be # asking for a program with a pathseparator starting it # $exe =~ s/^$PATHSEP//; # Not a full path, or does not exist. Let's see whether it's in the path. if($FILESPECLOADED) { for my $dir (File::Spec->path()) { my $f = Bio::Root::IO->catfile($dir, $exe); return $f if( -f $f && -x $f ); } } return 0; } =head2 tempfile Title : tempfile Usage : my ($handle,$tempfile) = $io->tempfile(); Function: Create a temporary filename and a handle opened for reading and writing. Caveats: If you do not have File::Temp on your system you should avoid specifying TEMPLATE and SUFFIX. Args : Named parameters compatible with File::Temp: DIR (defaults to $Bio::Root::IO::TEMPDIR), TEMPLATE, SUFFIX. Returns : A 2-element array, consisting of temporary handle and temporary file name. =cut sub tempfile { my ($self, @args) = @_; my ($tfh, $file); my %params = @args; # map between naming with and without dash for my $key (keys(%params)) { if( $key =~ /^-/ ) { my $v = $params{$key}; delete $params{$key}; $params{uc(substr($key,1))} = $v; } else { # this is to upper case my $v = $params{$key}; delete $params{$key}; $params{uc($key)} = $v; } } $params{'DIR'} = $TEMPDIR if(! exists($params{'DIR'})); unless (exists $params{'UNLINK'} && defined $params{'UNLINK'} && ! $params{'UNLINK'} ) { $params{'UNLINK'} = 1; } else { $params{'UNLINK'} = 0; } if($FILETEMPLOADED) { if(exists($params{'TEMPLATE'})) { my $template = $params{'TEMPLATE'}; delete $params{'TEMPLATE'}; ($tfh, $file) = File::Temp::tempfile($template, %params); } else { ($tfh, $file) = File::Temp::tempfile(%params); } } else { my $dir = $params{'DIR'}; $file = $self->catfile( $dir, (exists($params{'TEMPLATE'}) ? $params{'TEMPLATE'} : sprintf( "%s.%s.%s", $ENV{USER} || 'unknown', $$, $TEMPCOUNTER++)) ); # sneakiness for getting around long filenames on Win32? if( $HAS_WIN32 ) { $file = Win32::GetShortPathName($file); } # Try to make sure this will be marked close-on-exec # XXX: Win32 doesn't respect this, nor the proper fcntl, # but may have O_NOINHERIT. This may or may not be in Fcntl. local $^F = 2; # Store callers umask my $umask = umask(); # Set a known umaskr umask(066); # Attempt to open the file if ( sysopen($tfh, $file, $OPENFLAGS, 0600) ) { # Reset umask umask($umask); } else { $self->throw("Could not write temporary file '$file': $!"); } } if( $params{'UNLINK'} ) { push @{$self->{'_rootio_tempfiles'}}, $file; } return wantarray ? ($tfh,$file) : $tfh; } =head2 tempdir Title : tempdir Usage : my ($tempdir) = $io->tempdir(CLEANUP=>1); Function: Creates and returns the name of a new temporary directory. Note that you should not use this function for obtaining "the" temp directory. Use $Bio::Root::IO::TEMPDIR for that. Calling this method will in fact create a new directory. Args : args - ( key CLEANUP ) indicates whether or not to cleanup dir on object destruction, other keys as specified by File::Temp Returns : The name of a new temporary directory. =cut sub tempdir { my ($self, @args) = @_; if ($FILETEMPLOADED && File::Temp->can('tempdir')) { return File::Temp::tempdir(@args); } # we have to do this ourselves, not good # we are planning to cleanup temp files no matter what my %params = @args; print "cleanup is " . $params{CLEANUP} . "\n"; $self->{'_cleanuptempdir'} = ( defined $params{CLEANUP} && $params{CLEANUP} == 1); my $tdir = $self->catfile( $TEMPDIR, sprintf("dir_%s-%s-%s", $ENV{USER} || 'unknown', $$, $TEMPCOUNTER++)); mkdir($tdir, 0755); push @{$self->{'_rootio_tempdirs'}}, $tdir; return $tdir; } =head2 catfile Title : catfile Usage : $path = Bio::Root::IO->catfile(@dirs, $filename); Function: Constructs a full pathname in a cross-platform safe way. If File::Spec exists on your system, this routine will merely delegate to it. Otherwise it tries to make a good guess. You should use this method whenever you construct a path name from directory and filename. Otherwise you risk cross-platform compatibility of your code. You can call this method both as a class and an instance method. Args : components of the pathname (directories and filename, NOT an extension) Returns : a string =cut sub catfile { my ($self, @args) = @_; return File::Spec->catfile(@args) if $FILESPECLOADED; # this is clumsy and not very appealing, but how do we specify the # root directory? if($args[0] eq '/') { $args[0] = $ROOTDIR; } return join($PATHSEP, @args); } =head2 rmtree Title : rmtree Usage : Bio::Root::IO->rmtree($dirname ); Function: Remove a full directory tree If File::Path exists on your system, this routine will merely delegate to it. Otherwise it runs a local version of that code. You should use this method to remove directories which contain files. You can call this method both as a class and an instance method. Args : roots - rootdir to delete or reference to list of dirs verbose - a boolean value, which if TRUE will cause C to print a message each time it examines a file, giving the name of the file, and indicating whether it's using C or C to remove it, or that it's skipping it. (defaults to FALSE) safe - a boolean value, which if TRUE will cause C to skip any files to which you do not have delete access (if running under VMS) or write access (if running under another OS). This will change in the future when a criterion for 'delete permission' under OSs other than VMS is settled. (defaults to FALSE) Returns : number of files successfully deleted =cut # taken straight from File::Path VERSION = "1.0403" sub rmtree { my ($self, $roots, $verbose, $safe) = @_; if ( $FILEPATHLOADED ) { return File::Path::rmtree ($roots, $verbose, $safe); } my $force_writable = ($^O eq 'os2' || $^O eq 'dos' || $^O eq 'MSWin32' || $^O eq 'amigaos' || $^O eq 'cygwin'); my $Is_VMS = $^O eq 'VMS'; my @files; my $count = 0; $verbose ||= 0; $safe ||= 0; if ( defined($roots) && length($roots) ) { $roots = [$roots] unless ref $roots; } else { $self->warn("No root path(s) specified\n"); return 0; } my $root; for $root (@{$roots}) { $root =~ s#/\z##; (undef, undef, my $rp) = lstat $root or next; $rp &= 07777; # don't forget setuid, setgid, sticky bits if ( -d _ ) { # notabene: 0777 is for making readable in the first place, # it's also intended to change it to writable in case we have # to recurse in which case we are better than rm -rf for # subtrees with strange permissions chmod(0777, ($Is_VMS ? VMS::Filespec::fileify($root) : $root)) or $self->warn("Could not make directory '$root' read+writable: $!") unless $safe; if (opendir DIR, $root){ @files = readdir DIR; closedir DIR; } else { $self->warn("Could not read directory '$root': $!"); @files = (); } # Deleting large numbers of files from VMS Files-11 filesystems # is faster if done in reverse ASCIIbetical order @files = reverse @files if $Is_VMS; ($root = VMS::Filespec::unixify($root)) =~ s#\.dir\z## if $Is_VMS; @files = map("$root/$_", grep $_!~/^\.{1,2}\z/s,@files); $count += $self->rmtree([@files],$verbose,$safe); if ($safe && ($Is_VMS ? !&VMS::Filespec::candelete($root) : !-w $root)) { print "skipped '$root'\n" if $verbose; next; } chmod 0777, $root or $self->warn("Could not make directory '$root' writable: $!") if $force_writable; print "rmdir '$root'\n" if $verbose; if (rmdir $root) { ++$count; } else { $self->warn("Could not remove directory '$root': $!"); chmod($rp, ($Is_VMS ? VMS::Filespec::fileify($root) : $root)) or $self->warn("and can't restore permissions to " . sprintf("0%o",$rp) . "\n"); } } else { if ( $safe and ($Is_VMS ? !&VMS::Filespec::candelete($root) : !(-l $root || -w $root)) ) { print "skipped '$root'\n" if $verbose; next; } chmod 0666, $root or $self->warn( "Could not make file '$root' writable: $!") if $force_writable; warn "unlink '$root'\n" if $verbose; # delete all versions under VMS for (;;) { unless (unlink $root) { $self->warn("Could not unlink file '$root': $!"); if ($force_writable) { chmod $rp, $root or $self->warn("and can't restore permissions to " . sprintf("0%o",$rp) . "\n"); } last; } ++$count; last unless $Is_VMS && lstat $root; } } } return $count; } =head2 _flush_on_write Title : _flush_on_write Usage : $io->_flush_on_write($newval) Function: Boolean flag to indicate whether to flush the filehandle on writing when the end of a component is finished (Sequences, Alignments, etc) Args : Optional new value Returns : Value of _flush_on_write =cut sub _flush_on_write { my ($self, $value) = @_; if (defined $value) { $self->{'_flush_on_write'} = $value; } return $self->{'_flush_on_write'}; } =head2 save_tempfiles Title : save_tempfiles Usage : $io->save_tempfiles(1) Function: Boolean flag to indicate whether to retain tempfiles/tempdir Args : Value evaluating to TRUE or FALSE Returns : Boolean value : 1 = save tempfiles/tempdirs, 0 = remove (default) =cut sub save_tempfiles { my $self = shift; if (@_) { my $value = shift; $self->{save_tempfiles} = $value ? 1 : 0; } return $self->{save_tempfiles} || 0; } 1; BioPerl-1.007002/Bio/Root/Root.pm000444000766000024 4105713155576320 16457 0ustar00cjfieldsstaff000000000000package Bio::Root::Root; use strict; use Bio::Root::IO; use Bio::Root::Version; use Scalar::Util qw(blessed reftype); use base qw(Bio::Root::RootI); our $VERSION = eval "$VERSION"; =head1 SYNOPSIS # Any Bioperl-compliant object is a RootI compliant object # Here's how to throw and catch an exception using the eval-based syntax. $obj->throw("This is an exception"); eval { $obj->throw("This is catching an exception"); }; if( $@ ) { print "Caught exception"; } else { print "no exception"; } # Alternatively, using the new typed exception syntax in the throw() call: $obj->throw( -class => 'Bio::Root::BadParameter', -text => "Can not open file $file", -value => $file ); # Want to see debug() outputs for this object my $obj = Bio::Object->new(-verbose=>1); my $obj = Bio::Object->new(%args); $obj->verbose(2); # Print debug messages which honour current verbosity setting $obj->debug("Boring output only to be seen if verbose > 0\n"); # Deep-object copy my $clone = $obj->clone; =head1 DESCRIPTION This is a hashref-based implementation of the Bio::Root::RootI interface. Most Bioperl objects should inherit from this. See the documentation for L for most of the methods implemented by this module. Only overridden methods are described here. =head2 Throwing Exceptions One of the functionalities that L provides is the ability to L() exceptions with pretty stack traces. Bio::Root::Root enhances this with the ability to use L (available from CPAN) if it has also been installed. If L has been installed, L() will use it. This causes an Error.pm-derived object to be thrown. This can be caught within a C block, from which you can extract useful bits of information. If L is not installed, it will use the L-based exception throwing facilty. =head2 Typed Exception Syntax The typed exception syntax of L() has the advantage of plainly indicating the nature of the trouble, since the name of the class is included in the title of the exception output. To take advantage of this capability, you must specify arguments as named parameters in the L() call. Here are the parameters: =over 4 =item -class name of the class of the exception. This should be one of the classes defined in L, or a custom error of yours that extends one of the exceptions defined in L. =item -text a sensible message for the exception =item -value the value causing the exception or $!, if appropriate. =back Note that Bio::Root::Exception does not need to be imported into your module (or script) namespace in order to throw exceptions via Bio::Root::Root::throw(), since Bio::Root::Root imports it. =head2 Try-Catch-Finally Support In addition to using an eval{} block to handle exceptions, you can also use a try-catch-finally block structure if L has been installed in your system (available from CPAN). See the documentation for Error for more details. Here's an example. See the L module for other pre-defined exception types: my $IN; try { open $IN, '<', $file or $obj->throw( -class => 'Bio::Root::FileOpenException', -text => "Cannot read file '$file'", -value => $!); } catch Bio::Root::BadParameter with { my $err = shift; # get the Error object # Perform specific exception handling code for the FileOpenException } catch Bio::Root::Exception with { my $err = shift; # get the Error object # Perform general exception handling code for any Bioperl exception. } otherwise { # A catch-all for any other type of exception } finally { # Any code that you want to execute regardless of whether or not # an exception occurred. }; # the ending semicolon is essential! =head1 AUTHOR Steve Chervitz Ewan Birney, Lincoln Stein =cut our ($DEBUG, $ID, $VERBOSITY, $ERRORLOADED, $CLONE_CLASS); BEGIN { $ID = 'Bio::Root::Root'; $DEBUG = 0; $VERBOSITY = 0; $ERRORLOADED = 0; # Check whether or not Error.pm is available. # $main::DONT_USE_ERROR is intended for testing purposes and also # when you don't want to use the Error module, even if it is installed. # Just put a INIT { $DONT_USE_ERROR = 1; } at the top of your script. if( not $main::DONT_USE_ERROR ) { if ( eval "require Error; 1;" ) { import Error qw(:try); require Bio::Root::Exception; $ERRORLOADED = 1; $Error::Debug = 1; # enable verbose stack trace } } if( !$ERRORLOADED ) { require Carp; import Carp qw( confess ); } # set up _dclone() for my $class (qw(Clone Storable)) { eval "require $class; 1;"; if (!$@) { $CLONE_CLASS = $class; if ($class eq 'Clone') { *Bio::Root::Root::_dclone = sub {shift; return Clone::clone(shift)}; } else { *Bio::Root::Root::_dclone = sub { shift; local $Storable::Deparse = 1; local $Storable::Eval = 1; return Storable::dclone(shift); }; } last; } } if (!defined $CLONE_CLASS) { *Bio::Root::Root::_dclone = sub { my ($self, $orig, $level) = @_; my $class = Scalar::Util::blessed($orig) || ''; my $reftype = Scalar::Util::reftype($orig) || ''; my $data; if (!$reftype) { $data = $orig } elsif ($reftype eq "ARRAY") { $data = [map $self->_dclone($_), @$orig]; } elsif ($reftype eq "HASH") { $data = { map { $_ => $self->_dclone($orig->{$_}) } keys %$orig }; } elsif ($reftype eq 'CODE') { # nothing, maybe shallow copy? $self->throw("Code reference cloning not supported; install Clone or Storable from CPAN"); } else { $self->throw("What type is $_?")} if ($class) { bless $data, $class; } $data; } } $main::DONT_USE_ERROR; # so that perl -w won't warn "used only once" } =head2 new Purpose : generic instantiation function can be overridden if special needs of a module cannot be done in _initialize =cut sub new { # my ($class, %param) = @_; my $class = shift; my $self = {}; bless $self, ref($class) || $class; if(@_ > 1) { # if the number of arguments is odd but at least 3, we'll give # it a try to find -verbose shift if @_ % 2; my %param = @_; ## See "Comments" above regarding use of _rearrange(). $self->verbose($param{'-VERBOSE'} || $param{'-verbose'}); } return $self; } =head2 clone Title : clone Usage : my $clone = $obj->clone(); or my $clone = $obj->clone( -start => 110 ); Function: Deep recursion copying of any object via Storable dclone() Returns : A cloned object. Args : Any named parameters provided will be set on the new object. Unnamed parameters are ignored. Comments: Where possible, faster clone methods are used, in order: Clone::Fast::clone(), Clone::clone(), Storable::dclone. If neither is present, a pure perl fallback (not very well tested) is used instead. Storable dclone() cannot clone CODE references. Therefore, any CODE reference in your original object will remain, but will not exist in the cloned object. This should not be used for anything other than cloning of simple objects. Developers of subclasses are encouraged to override this method with one of their own. =cut sub clone { my ($orig, %named_params) = @_; __PACKAGE__->throw("Can't call clone() as a class method") unless ref $orig && $orig->isa('Bio::Root::Root'); # Can't dclone CODE references... # Should we shallow copy these? Should be harmless for these specific # methods... my %put_these_back = ( _root_cleanup_methods => $orig->{'_root_cleanup_methods'}, ); delete $orig->{_root_cleanup_methods}; # call the proper clone method, set lazily above my $clone = __PACKAGE__->_dclone($orig); $orig->{_root_cleanup_methods} = $put_these_back{_root_cleanup_methods}; foreach my $key (grep { /^-/ } keys %named_params) { my $method = $key; $method =~ s/^-//; if ($clone->can($method)) { $clone->$method($named_params{$key}) } else { $orig->warn("Parameter $method is not a method for ".ref($clone)); } } return $clone; } =head2 _dclone Title : clone Usage : my $clone = $obj->_dclone($ref); or my $clone = $obj->_dclone($ref); Function: Returns a copy of the object passed to it (a deep clone) Returns : clone of passed argument Args : Anything NOTE : This differs from clone significantly in that it does not clone self, but the data passed to it. This code may need to be optimized or overridden as needed. Comments: This is set in the BEGIN block to take advantage of optimized cloning methods if Clone or Storable is present, falling back to a pure perl kludge. May be moved into a set of modules if the need arises. At the moment, code ref cloning is not supported. =cut =head2 verbose Title : verbose Usage : $self->verbose(1) Function: Sets verbose level for how ->warn behaves -1 = no warning 0 = standard, small warning 1 = warning with stack trace 2 = warning becomes throw Returns : The current verbosity setting (integer between -1 to 2) Args : -1,0,1 or 2 =cut sub verbose { my ($self,$value) = @_; # allow one to set global verbosity flag return $DEBUG if $DEBUG; return $VERBOSITY unless ref $self; if (defined $value || ! defined $self->{'_root_verbose'}) { $self->{'_root_verbose'} = $value || 0; } return $self->{'_root_verbose'}; } =head2 _register_for_cleanup =cut sub _register_for_cleanup { my ($self,$method) = @_; if ($method) { if(! exists($self->{'_root_cleanup_methods'})) { $self->{'_root_cleanup_methods'} = []; } push(@{$self->{'_root_cleanup_methods'}},$method); } } =head2 _unregister_for_cleanup =cut sub _unregister_for_cleanup { my ($self,$method) = @_; my @methods = grep {$_ ne $method} $self->_cleanup_methods; $self->{'_root_cleanup_methods'} = \@methods; } =head2 _cleanup_methods =cut sub _cleanup_methods { my $self = shift; return unless ref $self && $self->isa('HASH'); my $methods = $self->{'_root_cleanup_methods'} or return; @$methods; } =head2 throw Title : throw Usage : $obj->throw("throwing exception message"); or $obj->throw( -class => 'Bio::Root::Exception', -text => "throwing exception message", -value => $bad_value ); Function: Throws an exception, which, if not caught with an eval or a try block will provide a nice stack trace to STDERR with the message. If Error.pm is installed, and if a -class parameter is provided, Error::throw will be used, throwing an error of the type specified by -class. If Error.pm is installed and no -class parameter is provided (i.e., a simple string is given), A Bio::Root::Exception is thrown. Returns : n/a Args : A string giving a descriptive error message, optional Named parameters: '-class' a string for the name of a class that derives from Error.pm, such as any of the exceptions defined in Bio::Root::Exception. Default class: Bio::Root::Exception '-text' a string giving a descriptive error message '-value' the value causing the exception, or $! (optional) Thus, if only a string argument is given, and Error.pm is available, this is equivalent to the arguments: -text => "message", -class => Bio::Root::Exception Comments : If Error.pm is installed, and you don't want to use it for some reason, you can block the use of Error.pm by Bio::Root::Root::throw() by defining a scalar named $main::DONT_USE_ERROR (define it in your main script and you don't need the main:: part) and setting it to a true value; you must do this within a BEGIN subroutine. =cut sub throw { my ($self, @args) = @_; my ($text, $class, $value) = $self->_rearrange( [qw(TEXT CLASS VALUE)], @args); $text ||= $args[0] if @args == 1; if ($ERRORLOADED) { # Enable re-throwing of Error objects. # If the error is not derived from Bio::Root::Exception, # we can't guarantee that the Error's value was set properly # and, ipso facto, that it will be catchable from an eval{}. # But chances are, if you're re-throwing non-Bio::Root::Exceptions, # you're probably using Error::try(), not eval{}. # TODO: Fix the MSG: line of the re-thrown error. Has an extra line # containing the '----- EXCEPTION -----' banner. if (ref($args[0])) { if( $args[0]->isa('Error')) { my $class = ref $args[0]; $class->throw( @args ); } else { my $text .= "\nWARNING: Attempt to throw a non-Error.pm object: " . ref$args[0]; my $class = "Bio::Root::Exception"; $class->throw( '-text' => $text, '-value' => $args[0] ); } } else { $class ||= "Bio::Root::Exception"; my %args; if( @args % 2 == 0 && $args[0] =~ /^-/ ) { %args = @args; $args{-text} = $text; $args{-object} = $self; } $class->throw( scalar keys %args > 0 ? %args : @args ); # (%args || @args) puts %args in scalar context! } } else { $class ||= ''; $class = ': '.$class if $class; my $std = $self->stack_trace_dump(); my $title = "------------- EXCEPTION$class -------------"; my $footer = ('-' x CORE::length($title))."\n"; $text ||= ''; die "\n$title\n", "MSG: $text\n", $std, $footer, "\n"; } } =head2 debug Title : debug Usage : $obj->debug("This is debugging output"); Function: Prints a debugging message when verbose is > 0 Returns : none Args : message string(s) to print to STDERR =cut sub debug { my ($self, @msgs) = @_; # using CORE::warn doesn't give correct backtrace information; we want the # line from the previous call in the call stack, not this call (similar to # cluck). For now, just add a stack trace dump and simple comment under the # correct conditions. if (defined $self->verbose && $self->verbose > 0) { if (!@msgs || $msgs[-1] !~ /\n$/) { push @msgs, "Debugging comment:" if !@msgs; push @msgs, sprintf("%s %s:%s", @{($self->stack_trace)[2]}[3,1,2])."\n"; } CORE::warn @msgs; } } =head2 _load_module Title : _load_module Usage : $self->_load_module("Bio::SeqIO::genbank"); Function: Loads up (like use) the specified module at run time on demand. Example : Returns : TRUE on success. Throws an exception upon failure. Args : The module to load (_without_ the trailing .pm). =cut sub _load_module { my ($self, $name) = @_; my ($module, $load, $m); $module = "_<$name.pm"; return 1 if $main::{$module}; # untaint operation for safe web-based running (modified after # a fix by Lincoln) HL if ($name !~ /^([\w:]+)$/) { $self->throw("$name is an illegal perl package name"); } else { $name = $1; } $load = "$name.pm"; my $io = Bio::Root::IO->new(); # catfile comes from IO $load = $io->catfile((split(/::/,$load))); eval { require $load; }; if ( $@ ) { $self->throw("Failed to load module $name. ".$@); } return 1; } =head2 DESTROY =cut sub DESTROY { my $self = shift; my @cleanup_methods = $self->_cleanup_methods or return; for my $method (@cleanup_methods) { $method->($self); } } 1; BioPerl-1.007002/Bio/Root/RootI.pm000444000766000024 6551213155576320 16572 0ustar00cjfieldsstaff000000000000package Bio::Root::RootI; use strict; use Carp 'confess','carp'; =head1 SYNOPSIS # any bioperl or bioperl compliant object is a RootI # compliant object $obj->throw("This is an exception"); eval { $obj->throw("This is catching an exception"); }; if( $@ ) { print "Caught exception"; } else { print "no exception"; } # Using throw_not_implemented() within a RootI-based interface module: package Foo; use base qw(Bio::Root::RootI); sub foo { my $self = shift; $self->throw_not_implemented; } =head1 DESCRIPTION This is just a set of methods which do not assume B about the object they are on. The methods provide the ability to throw exceptions with nice stack traces. This is what should be inherited by all Bioperl compliant interfaces, even if they are exotic XS/CORBA/Other perl systems. =head2 Using throw_not_implemented() The method L should be called by all methods within interface modules that extend RootI so that if an implementation fails to override them, an exception will be thrown. For example, say there is an interface module called C that provides a method called C. Since this method is considered abstract within FooI and should be implemented by any module claiming to implement C, the C method should consist of the following: sub foo { my $self = shift; $self->throw_not_implemented; } So, if an implementer of C forgets to implement C and a user of the implementation calls C, a L exception will result. Unfortunately, failure to implement a method can only be determined at run time (i.e., you can't verify that an implementation is complete by running C on it). So it should be standard practice for a test of an implementation to check each method and verify that it doesn't throw a L. =head1 AUTHOR Steve Chervitz Ewan Birney, Lincoln Stein, Steve Chervitz, Sendu Bala, Jason Stajich =cut use vars qw($DEBUG $ID $VERBOSITY); BEGIN { $ID = 'Bio::Root::RootI'; $DEBUG = 0; $VERBOSITY = 0; } =head2 new =cut sub new { my $class = shift; my @args = @_; unless ( $ENV{'BIOPERLDEBUG'} ) { carp("Use of new in Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead"); } eval "require Bio::Root::Root"; return Bio::Root::Root->new(@args); } # for backwards compatibility sub _initialize { my($self,@args) = @_; return 1; } =head2 throw Title : throw Usage : $obj->throw("throwing exception message") Function: Throws an exception, which, if not caught with an eval brace will provide a nice stack trace to STDERR with the message Returns : nothing Args : A string giving a descriptive error message =cut sub throw{ my ($self,$string) = @_; my $std = $self->stack_trace_dump(); my $out = "\n-------------------- EXCEPTION --------------------\n" . "MSG: " . $string . "\n" . $std."-------------------------------------------\n"; die $out; } =head2 warn Title : warn Usage : $object->warn("Warning message"); Function: Places a warning. What happens now is down to the verbosity of the object (value of $obj->verbose) verbosity 0 or not set => small warning verbosity -1 => no warning verbosity 1 => warning with stack trace verbosity 2 => converts warnings into throw Returns : n/a Args : string (the warning message) =cut sub warn { my ($self,$string) = @_; my $verbose = $self->verbose; my $header = "\n--------------------- WARNING ---------------------\nMSG: "; my $footer = "---------------------------------------------------\n"; if ($verbose >= 2) { $self->throw($string); } elsif ($verbose <= -1) { return; } elsif ($verbose == 1) { CORE::warn $header, $string, "\n", $self->stack_trace_dump, $footer; return; } CORE::warn $header, $string, "\n", $footer; } =head2 deprecated Title : deprecated Usage : $obj->deprecated("Method X is deprecated"); $obj->deprecated("Method X is deprecated", 1.007); $obj->deprecated(-message => "Method X is deprecated"); $obj->deprecated(-message => "Method X is deprecated", -version => 1.007); Function: Prints a message about deprecation unless verbose is < 0 (which means be quiet) Returns : none Args : Message string to print to STDERR Version of BioPerl where use of the method results in an exception Notes : The method can be called two ways, either by positional arguments: $obj->deprecated('This module is deprecated', 1.006); or by named arguments: $obj->deprecated( -message => 'use of the method foo() is deprecated, use bar() instead', -version => 1.006 # throw if $VERSION is >= this version ); or timed to go off at a certain point: $obj->deprecated( -message => 'use of the method foo() is deprecated, use bar() instead', -warn_version => 1.006 # warn if $VERSION is >= this version -throw_version => 1.007 # throw if $VERSION is >= this version ); Using the last two named argument versions is suggested and will likely be the only supported way of calling this method in the future Yes, we see the irony of deprecating that particular usage of deprecated(). The main difference between usage of the two named argument versions is that by designating a 'warn_version' one indicates the functionality is officially deprecated beginning in a future version of BioPerl (so warnings are issued only after that point), whereas setting either 'version' or 'throw_version' (synonyms) converts the deprecation warning to an exception. For proper comparisons one must use a version in lines with the current versioning scheme for Perl and BioPerl, (i.e. where 1.006000 indicates v1.6.0, 5.010000 for v5.10.0, etc.). =cut sub deprecated{ my ($self) = shift; my $class = ref $self || $self; my $class_version = do { no strict 'refs'; ${"${class}::VERSION"} }; if( $class_version && $class_version =~ /set by/ ) { $class_version = 0.0001; } my ($msg, $version, $warn_version, $throw_version) = $self->_rearrange([qw(MESSAGE VERSION WARN_VERSION THROW_VERSION)], @_); $throw_version ||= $version; $warn_version ||= $class_version; $throw_version =~ s/_//g; $warn_version =~ s/_//g; for my $v ( $warn_version, $throw_version) { no warnings 'numeric'; $self->throw("Version must be numerical, such as 1.006000 for v1.6.0, not $v") unless !defined $v || $v + 0 == $v; } # below default insinuates we're deprecating a method and not a full module # but it's the most common use case $msg ||= "Use of ".(caller(1))[3]."() is deprecated."; if( $throw_version && $class_version && $class_version >= $throw_version ) { $self->throw($msg) } elsif( $warn_version && $class_version && $class_version >= $warn_version ) { $msg .= "\nTo be removed in $throw_version." if $throw_version; # passing this on to warn() should deal properly with verbosity issues $self->warn($msg); } } =head2 stack_trace_dump Title : stack_trace_dump Usage : Function: Example : Returns : Args : =cut sub stack_trace_dump{ my ($self) = @_; my @stack = $self->stack_trace(); shift @stack; shift @stack; shift @stack; my $out; my ($module,$function,$file,$position); foreach my $stack ( @stack) { ($module,$file,$position,$function) = @{$stack}; $out .= "STACK $function $file:$position\n"; } return $out; } =head2 stack_trace Title : stack_trace Usage : @stack_array_ref= $self->stack_trace Function: gives an array to a reference of arrays with stack trace info each coming from the caller(stack_number) call Returns : array containing a reference of arrays Args : none =cut sub stack_trace{ my ($self) = @_; my $i = 0; my @out = (); my $prev = []; while( my @call = caller($i++)) { # major annoyance that caller puts caller context as # function name. Hence some monkeying around... $prev->[3] = $call[3]; push(@out,$prev); $prev = \@call; } $prev->[3] = 'toplevel'; push(@out,$prev); return @out; } =head2 _rearrange Usage : $object->_rearrange( array_ref, list_of_arguments) Purpose : Rearranges named parameters to requested order. Example : $self->_rearrange([qw(SEQUENCE ID DESC)],@param); : Where @param = (-sequence => $s, : -desc => $d, : -id => $i); Returns : @params - an array of parameters in the requested order. : The above example would return ($s, $i, $d). : Unspecified parameters will return undef. For example, if : @param = (-sequence => $s); : the above _rearrange call would return ($s, undef, undef) Argument : $order : a reference to an array which describes the desired : order of the named parameters. : @param : an array of parameters, either as a list (in : which case the function simply returns the list), : or as an associative array with hyphenated tags : (in which case the function sorts the values : according to @{$order} and returns that new array.) : The tags can be upper, lower, or mixed case : but they must start with a hyphen (at least the : first one should be hyphenated.) Source : This function was taken from CGI.pm, written by Dr. Lincoln : Stein, and adapted for use in Bio::Seq by Richard Resnick and : then adapted for use in Bio::Root::Object.pm by Steve Chervitz, : then migrated into Bio::Root::RootI.pm by Ewan Birney. Comments : : Uppercase tags are the norm, : (SAC) : This method may not be appropriate for method calls that are : within in an inner loop if efficiency is a concern. : : Parameters can be specified using any of these formats: : @param = (-name=>'me', -color=>'blue'); : @param = (-NAME=>'me', -COLOR=>'blue'); : @param = (-Name=>'me', -Color=>'blue'); : @param = ('me', 'blue'); : A leading hyphenated argument is used by this function to : indicate that named parameters are being used. : Therefore, the ('me', 'blue') list will be returned as-is. : : Note that Perl will confuse unquoted, hyphenated tags as : function calls if there is a function of the same name : in the current namespace: : -name => 'foo' is interpreted as -&name => 'foo' : : For ultimate safety, put single quotes around the tag: : ('-name'=>'me', '-color' =>'blue'); : This can be a bit cumbersome and I find not as readable : as using all uppercase, which is also fairly safe: : (-NAME=>'me', -COLOR =>'blue'); : : Personal note (SAC): I have found all uppercase tags to : be more manageable: it involves less single-quoting, : the key names stand out better, and there are no method naming : conflicts. : The drawbacks are that it's not as easy to type as lowercase, : and lots of uppercase can be hard to read. : : Regardless of the style, it greatly helps to line : the parameters up vertically for long/complex lists. : : Note that if @param is a single string that happens to start with : a dash, it will be treated as a hash key and probably fail to : match anything in the array_ref, so not be returned as normally : happens when @param is a simple list and not an associative array. =cut sub _rearrange { my ($self, $order, @args) = @_; return @args unless $args[0] && $args[0] =~ /^\-/; push @args, undef unless $#args % 2; my %param; for( my $i = 0; $i < @args; $i += 2 ) { (my $key = $args[$i]) =~ tr/a-z\055/A-Z/d; #deletes all dashes! $param{$key} = $args[$i+1]; } return @param{map uc, @$order}; } =head2 _set_from_args Usage : $object->_set_from_args(\%args, -methods => \@methods) Purpose : Takes a hash of user-supplied args whose keys match method names, : and calls the method supplying it the corresponding value. Example : $self->_set_from_args(\%args, -methods => [qw(sequence id desc)]); : Where %args = (-sequence => $s, : -description => $d, : -ID => $i); : : the above _set_from_args calls the following methods: : $self->sequence($s); : $self->id($i); : ( $self->description($i) is not called because 'description' wasn't : one of the given methods ) Argument : \%args | \@args : a hash ref or associative array ref of arguments : where keys are any-case strings corresponding to : method names but optionally prefixed with : hyphens, and values are the values the method : should be supplied. If keys contain internal : hyphens (eg. to separate multi-word args) they : are converted to underscores, since method names : cannot contain dashes. : -methods => [] : (optional) only call methods with names in this : array ref. Can instead supply a hash ref where : keys are method names (of real existing methods : unless -create is in effect) and values are array : refs of synonyms to allow access to the method : using synonyms. If there is only one synonym it : can be supplied as a string instead of a single- : element array ref : -force => bool : (optional, default 0) call methods that don't : seem to exist, ie. let AUTOLOAD handle them : -create => bool : (optional, default 0) when a method doesn't : exist, create it as a simple getter/setter : (combined with -methods it would create all the : supplied methods that didn't exist, even if not : mentioned in the supplied %args) : -code => '' | {}: (optional) when creating methods use the supplied : code (a string which will be evaulated as a sub). : The default code is a simple get/setter. : Alternatively you can supply a hash ref where : the keys are method names and the values are : code strings. The variable '$method' will be : available at evaluation time, so can be used in : your code strings. Beware that the strict pragma : will be in effect. : -case_sensitive => bool : require case sensitivity on the part of : user (ie. a() and A() are two different : methods and the user must be careful : which they use). Comments : : The \%args argument will usually be the args received during new() : from the user. The user is allowed to get the case wrong, include : 0 or more than one hyphens as a prefix, and to include hyphens as : multi-word arg separators: '--an-arg' => 1, -an_arg => 1 and : An_Arg => 1 are all equivalent, calling an_arg(1). However, in : documentation users should only be told to use the standard form : -an_arg to avoid confusion. A possible exception to this is a : wrapper module where '--an-arg' is what the user is used to : supplying to the program being wrapped. : : Another issue with wrapper modules is that there may be an : argument that has meaning both to Bioperl and to the program, eg. : -verbose. The recommended way of dealing with this is to leave : -verbose to set the Bioperl verbosity whilst requesting users use : an invented -program_verbose (or similar) to set the program : verbosity. This can be resolved back with : Bio::Tools::Run::WrapperBase's _setparams() method and code along : the lines of: : my %methods = map { $_ => $_ } @LIST_OF_ALL_ALLOWED_PROGRAM_ARGS : delete $methods{'verbose'}; : $methods{'program_verbose'} = 'verbose'; : my $param_string = $self->_setparams(-methods => \%methods); : system("$exe $param_string"); =cut sub _set_from_args { my ($self, $args, @own_args) = @_; $self->throw("a hash/array ref of arguments must be supplied") unless ref($args); my ($methods, $force, $create, $code, $case); if (@own_args) { ($methods, $force, $create, $code, $case) = $self->_rearrange([qw(METHODS FORCE CREATE CODE CASE_SENSITIVE)], @own_args); } my $default_code = 'my $self = shift; if (@_) { $self->{\'_\'.$method} = shift } return $self->{\'_\'.$method};'; my %method_names = (); my %syns = (); if ($methods) { my @names; if (ref($methods) eq 'HASH') { @names = keys %{$methods}; %syns = %{$methods}; } else { @names = @{$methods}; %syns = map { $_ => $_ } @names; } %method_names = map { $case ? $_ : lc($_) => $_ } @names; } # deal with hyphens my %orig_args = ref($args) eq 'HASH' ? %{$args} : @{$args}; my %args; while (my ($method, $value) = each %orig_args) { $method =~ s/^-+//; $method =~ s/-/_/g; $args{$method} = $value; } # create non-existing methods on request if ($create) { unless ($methods) { %syns = map { $_ => $case ? $_ : lc($_) } keys %args; } foreach my $method (keys %syns) { $self->can($method) && next; my $string = $code || $default_code; if (ref($code) && ref($code) eq 'HASH') { $string = $code->{$method} || $default_code; } my $sub = eval "sub { $string }"; $self->throw("Compilation error for $method : $@") if $@; no strict 'refs'; *{ref($self).'::'.$method} = $sub; } } # create synonyms of existing methods while (my ($method, $syn_ref) = each %syns) { my $method_ref = $self->can($method) || next; foreach my $syn (@{ ref($syn_ref) ? $syn_ref : [$syn_ref] }) { next if $syn eq $method; $method_names{$case ? $syn : lc($syn)} = $syn; next if $self->can($syn); no strict 'refs'; *{ref($self).'::'.$syn} = $method_ref; } } # set values for methods while (my ($method, $value) = each %args) { $method = $method_names{$case ? $method : lc($method)} || ($methods ? next : $method); $self->can($method) || next unless $force; $self->$method($value); } } =head2 _rearrange_old =cut #----------------' sub _rearrange_old { #---------------- my($self,$order,@param) = @_; # JGRG -- This is wrong, because we don't want # to assign empty string to anything, and this # code is actually returning an array 1 less # than the length of @param: ## If there are no parameters, we simply wish to return ## an empty array which is the size of the @{$order} array. #return ('') x $#{$order} unless @param; # ...all we need to do is return an empty array: # return unless @param; # If we've got parameters, we need to check to see whether # they are named or simply listed. If they are listed, we # can just return them. # The mod test fixes bug where a single string parameter beginning with '-' gets lost. # This tends to happen in error messages such as: $obj->throw("-id not defined") return @param unless (defined($param[0]) && $param[0]=~/^-/o && ($#param % 2)); # Tester # print "\n_rearrange() named parameters:\n"; # my $i; for ($i=0;$i<@param;$i+=2) { printf "%20s => %s\n", $param[$i],$param[$i+1]; }; ; # Now we've got to do some work on the named parameters. # The next few lines strip out the '-' characters which # preceed the keys, and capitalizes them. for (my $i=0;$i<@param;$i+=2) { $param[$i]=~s/^\-//; $param[$i]=~tr/a-z/A-Z/; } # Now we'll convert the @params variable into an associative array. # local($^W) = 0; # prevent "odd number of elements" warning with -w. my(%param) = @param; # my(@return_array); # What we intend to do is loop through the @{$order} variable, # and for each value, we use that as a key into our associative # array, pushing the value at that key onto our return array. # my($key); #foreach (@{$order}) { # my($value) = $param{$key}; # delete $param{$key}; #push(@return_array,$param{$_}); #} return @param{@{$order}}; # print "\n_rearrange() after processing:\n"; # my $i; for ($i=0;$i<@return_array;$i++) { printf "%20s => %s\n", ${$order}[$i], $return_array[$i]; } ; # return @return_array; } =head2 _register_for_cleanup Title : _register_for_cleanup Usage : -- internal -- Function: Register a method to be called at DESTROY time. This is useful and sometimes essential in the case of multiple inheritance for classes coming second in the sequence of inheritance. Returns : Args : a code reference The code reference will be invoked with the object as the first argument, as per a method. You may register an unlimited number of cleanup methods. =cut sub _register_for_cleanup { my ($self,$method) = @_; $self->throw_not_implemented(); } =head2 _unregister_for_cleanup Title : _unregister_for_cleanup Usage : -- internal -- Function: Remove a method that has previously been registered to be called at DESTROY time. If called with a method to be called at DESTROY time. Has no effect if the code reference has not previously been registered. Returns : nothing Args : a code reference =cut sub _unregister_for_cleanup { my ($self,$method) = @_; $self->throw_not_implemented(); } =head2 _cleanup_methods Title : _cleanup_methods Usage : -- internal -- Function: Return current list of registered cleanup methods. Returns : list of coderefs Args : none =cut sub _cleanup_methods { my $self = shift; unless ( $ENV{'BIOPERLDEBUG'} || $self->verbose > 0 ) { carp("Use of Bio::Root::RootI is deprecated. Please use Bio::Root::Root instead"); } return; } =head2 throw_not_implemented Purpose : Throws a Bio::Root::NotImplemented exception. Intended for use in the method definitions of abstract interface modules where methods are defined but are intended to be overridden by subclasses. Usage : $object->throw_not_implemented(); Example : sub method_foo { $self = shift; $self->throw_not_implemented(); } Returns : n/a Args : n/a Throws : A Bio::Root::NotImplemented exception. The message of the exception contains - the name of the method - the name of the interface - the name of the implementing class If this object has a throw() method, $self->throw will be used. If the object doesn't have a throw() method, Carp::confess() will be used. =cut #' sub throw_not_implemented { my $self = shift; # Bio::Root::Root::throw() knows how to check for Error.pm and will # throw an Error-derived object of the specified class (Bio::Root::NotImplemented), # which is defined in Bio::Root::Exception. # If Error.pm is not available, the name of the class is just included in the # error message. my $message = $self->_not_implemented_msg; if ( $self->can('throw') ) { my @args; if ( $self->isa('Bio::Root::Root') ) { # Use Root::throw() hash-based arguments instead of RootI::throw() # single string argument whenever possible @args = ( -text => $message, -class => 'Bio::Root::NotImplemented' ); } else { @args = ( $message ); } $self->throw(@args); } else { confess $message; } } =head2 warn_not_implemented Purpose : Generates a warning that a method has not been implemented. Intended for use in the method definitions of abstract interface modules where methods are defined but are intended to be overridden by subclasses. Generally, throw_not_implemented() should be used, but warn_not_implemented() may be used if the method isn't considered essential and convenient no-op behavior can be provided within the interface. Usage : $object->warn_not_implemented( method-name-string ); Example : $self->warn_not_implemented( "get_foobar" ); Returns : Calls $self->warn on this object, if available. If the object doesn't have a warn() method, Carp::carp() will be used. Args : n/a =cut #' sub warn_not_implemented { my $self = shift; my $message = $self->_not_implemented_msg; if( $self->can('warn') ) { $self->warn( $message ); }else { carp $message ; } } =head2 _not_implemented_msg Unify 'not implemented' message. -Juguang =cut sub _not_implemented_msg { my $self = shift; my $package = ref $self; my $meth = (caller(2))[3]; my $msg =<new(); # Store/retrieve using class retriever my $token = $storable->store(); my $storable2 = Bio::Root::Storable->retrieve( $token ); # Store/retrieve using object retriever my $storable2 = $storable->new_retrievable(); $storable2->retrieve(); =head1 DESCRIPTION Generic module that allows objects to be safely stored/retrieved from disk. Can be inhereted by any BioPerl object. As it will not usually be the first class in the inheretence list, _initialise_storable() should be called during object instantiation. Object storage is recursive; If the object being stored contains other storable objects, these will be stored separately, and replaced by a skeleton object in the parent hierarchy. When the parent is later retrieved, its children remain in the skeleton state until explicitly retrieved by the parent. This lazy-retrieve approach has obvious memory efficiency benefits for certain applications. By default, objects are stored in binary format (using the Perl Storable module). Earlier versions of Perl5 do not include Storable as a core module. If this is the case, ASCII object storage (using the Perl Data::Dumper module) is used instead. ASCII storage can be enabled by default by setting the value of $Bio::Root::Storable::BINARY to false. =head1 AUTHOR Will Spooner =cut use vars qw( $BINARY ); BEGIN{ if( eval "require Storable" ){ Storable->import( 'freeze', 'thaw' ); $BINARY = 1; } } #---------------------------------------------------------------------- =head2 new Arg [1] : -workdir => filesystem path, -template => tmpfile template, -suffix => tmpfile suffix, Function : Builds a new Bio::Root::Storable inhereting object Returntype: Bio::Root::Storable inhereting object Exceptions: Caller : Example : $storable = Bio::Root::Storable->new() =cut sub new { my ($caller, @args) = @_; my $self = $caller->SUPER::new(@args); $self->_initialise_storable; return $self; } #---------------------------------------------------------------------- =head2 _initialise_storable Arg [1] : See 'new' method Function : Initialises storable-specific attributes Returntype: boolean Exceptions: Caller : Example : =cut sub _initialise_storable { my $self = shift; my( $workdir, $template, $suffix ) = $self->_rearrange([qw(WORKDIR TEMPLATE SUFFIX)], @_ ); $workdir && $self->workdir ( $workdir ); $template && $self->template( $template ); $suffix && $self->suffix ( $suffix ); return 1; } #---------------------------------------------------------------------- =head2 statefile Arg [1] : string (optional) Function : Accessor for the file to write state into. Should not normally use as a setter - let Root::IO do this for you. Returntype: string Exceptions: Caller : Bio::Root::Storable->store Example : my $statefile = $obj->statefile(); =cut sub statefile{ my $key = '_statefile'; my $self = shift; if( @_ ){ $self->{$key} = shift } if( ! $self->{$key} ){ # Create a new statefile my $workdir = $self->workdir; my $template = $self->template; my $suffix = $self->suffix; # TODO: add cleanup and unlink methods. For now, we'll keep the # statefile hanging around. my @args = ( CLEANUP=>0, UNLINK=>0 ); if( $template ){ push( @args, 'TEMPLATE' => $template )}; if( $workdir ){ push( @args, 'DIR' => $workdir )}; if( $suffix ){ push( @args, 'SUFFIX' => $suffix )}; my( $fh, $file ) = Bio::Root::IO->new->tempfile( @args ); # If filehandle is not stored, don't leave it open $fh->close; $self->{$key} = $file; } return $self->{$key}; } #---------------------------------------------------------------------- =head2 workdir Arg [1] : string (optional) (TODO - convert to array for x-platform) Function : Accessor for the statefile directory. Defaults to File::Spec->tmpdir Returntype: string Exceptions: Caller : Example : $obj->workdir('/tmp/foo'); =cut sub workdir { my $key = '_workdir'; my $self = shift; if( @_ ){ my $caller = join( ', ', (caller(0))[1..2] ); $self->{$key} && $self->debug("Overwriting workdir: probably bad!"); $self->{$key} = shift } #$self->{$key} ||= $Bio::Root::IO::TEMPDIR; $self->{$key} ||= File::Spec->tmpdir(); return $self->{$key}; } #---------------------------------------------------------------------- =head2 template Arg [1] : string (optional) Function : Accessor for the statefile template. Defaults to XXXXXXXX Returntype: string Exceptions: Caller : Example : $obj->workdir('RES_XXXXXXXX'); =cut sub template { my $key = '_template'; my $self = shift; if( @_ ){ $self->{$key} = shift } $self->{$key} ||= 'XXXXXXXX'; return $self->{$key}; } #---------------------------------------------------------------------- =head2 suffix Arg [1] : string (optional) Function : Accessor for the statefile template. Returntype: string Exceptions: Caller : Example : $obj->suffix('.state'); =cut sub suffix { my $key = '_suffix'; my $self = shift; if( @_ ){ $self->{$key} = shift } return $self->{$key}; } #---------------------------------------------------------------------- =head2 new_retrievable Arg [1] : Same as for 'new' Function : Similar to store, except returns a 'skeleton' of the calling object, rather than the statefile. The skeleton can be repopulated by calling 'retrieve'. This will be a clone of the original object. Returntype: Bio::Root::Storable inhereting object Exceptions: Caller : Example : my $skel = $obj->new_retrievable(); # skeleton $skel->retrieve(); # clone =cut sub new_retrievable{ my $self = shift; my @args = @_; $self->_initialise_storable( @args ); if( $self->retrievable ){ return $self->clone } # Clone retrievable return bless( { _statefile => $self->store(@args), _workdir => $self->workdir, _suffix => $self->suffix, _template => $self->template, _retrievable => 1 }, ref( $self ) ); } #---------------------------------------------------------------------- =head2 retrievable Arg [1] : none Function : Reports whether the object is in 'skeleton' state, and the 'retrieve' method can be called. Returntype: boolean Exceptions: Caller : Example : if( $obj->retrievable ){ $obj->retrieve } =cut sub retrievable { my $self = shift; if( @_ ){ $self->{_retrievable} = shift } return $self->{_retrievable}; } #---------------------------------------------------------------------- =head2 token Arg [1] : None Function : Accessor for token attribute Returntype: string. Whatever retrieve needs to retrieve. This base implementation returns the statefile Exceptions: Caller : Example : my $token = $obj->token(); =cut sub token{ my $self = shift; return $self->statefile; } #---------------------------------------------------------------------- =head2 store Arg [1] : none Function : Saves a serialised representation of the object structure to disk. Returns the name of the file that the object was saved to. Returntype: string Exceptions: Caller : Example : my $token = $obj->store(); =cut sub store{ my $self = shift; my $statefile = $self->statefile; my $store_obj = $self->serialise; my $io = Bio::Root::IO->new( ">$statefile" ); $io->_print( $store_obj ); $self->debug( "STORING $self to $statefile\n" ); # If filehandle is not stored, don't leave it open $io->close; return $statefile; } #---------------------------------------------------------------------- =head2 serialise Arg [1] : none Function : Prepares the the serialised representation of the object. Object attribute names starting with '__' are skipped. This is useful for those that do not serialise too well (e.g. filehandles). Attributes are examined for other storable objects. If these are found they are serialised separately using 'new_retrievable' Returntype: string Exceptions: Caller : Example : my $serialised = $obj->serialise(); =cut sub serialise{ my $self = shift; # Create a new object of same class that is going to be serialised my $store_obj = bless( {}, ref( $self ) ); my %retargs = ( -workdir =>$self->workdir, -suffix =>$self->suffix, -template=>$self->template ); # Assume that other storable bio objects held by this object are # only 1-deep. foreach my $key( keys( %$self ) ){ if( $key =~ /^__/ ){ next } # Ignore keys starting with '__' my $value = $self->{$key}; # Scalar value if( ! ref( $value ) ){ $store_obj->{$key} = $value; } # Bio::Root::Storable obj: save placeholder elsif( ref($value) =~ /^Bio::/ and $value->isa('Bio::Root::Storable') ){ # Bio::Root::Storable $store_obj->{$key} = $value->new_retrievable( %retargs ); next; } # Arrayref value. Look for Bio::Root::Storable objs elsif( ref( $value ) eq 'ARRAY' ){ my @ary; foreach my $val( @$value ){ if( ref($val) =~ /^Bio::/ and $val->isa('Bio::Root::Storable') ){ push( @ary, $val->new_retrievable( %retargs ) ); } else{ push( @ary, $val ) } } $store_obj->{$key} = \@ary; } # Hashref value. Look for Bio::Root::Storable objs elsif( ref( $value ) eq 'HASH' ){ my %hash; foreach my $k2( keys %$value ){ my $val = $value->{$k2}; if( ref($val) =~ /^Bio::/ and $val->isa('Bio::Root::Storable') ){ $hash{$k2} = $val->new_retrievable( %retargs ); } else{ $hash{$k2} = $val } } $store_obj->{$key} = \%hash; } # Unknown, just add to the store object regardless else{ $store_obj->{$key} = $value } } $store_obj->retrievable(0); # Once deserialised, obj not retrievable return $self->_freeze( $store_obj ); } #---------------------------------------------------------------------- =head2 retrieve Arg [1] : string; filesystem location of the state file to be retrieved Function : Retrieves a stored object from disk. Note that the retrieved object will be blessed into its original class, and not the Returntype: Bio::Root::Storable inhereting object Exceptions: Caller : Example : my $obj = Bio::Root::Storable->retrieve( $token ); =cut sub retrieve{ my( $caller, $statefile ) = @_; my $self = {}; my $class = ref( $caller ) || $caller; # Is this a call on a retrievable object? if ( ref( $caller ) and $caller->retrievable ){ $self = $caller; $statefile = $self->statefile; } bless( $self, $class ); # Recover serialised object if( ! -f $statefile ){ $self->throw( "Token $statefile is not found" ); } my $io = Bio::Root::IO->new( $statefile ); local $/ = undef; my $state_str = $io->_readline('-raw'=>1); # If filehandle is not stored, don't leave it open $io->close; # Dynamic-load modules required by stored object my $stored_obj; my $success; for( my $i=0; $i<10; $i++ ){ eval{ $stored_obj = $self->_thaw( $state_str ) }; if( ! $@ ){ $success = 1; last; } my $package; if( $@ =~ /Cannot restore overloading(.*)/i ){ my $postmatch = $1; #' if( $postmatch =~ /\(package +([\w\:]+)\)/ ) { $package = $1; } } if( $package ){ eval "require $package"; $self->throw($@) if $@; } else{ $self->throw($@) } } if( ! $success ){ $self->throw("maximum number of requires exceeded" ) } if( ! ref( $stored_obj ) ){ $self->throw( "Token $statefile returned no data" ); } map{ $self->{$_} = $stored_obj->{$_} } keys %$stored_obj; # Copy hasheys $self->retrievable(0); # Maintain class of stored obj return $self; } #---------------------------------------------------------------------- =head2 clone Arg [1] : none Function : Returns a clone of the calling object Returntype: Bio::Root::Storable inhereting object Exceptions: Caller : Example : my $clone = $obj->clone(); =cut sub clone { my $self = shift; my $frozen = $self->_freeze( $self ); return $self->_thaw( $frozen ); } #---------------------------------------------------------------------- =head2 remove Arg [1] : none Function : Clears the stored object from disk Returntype: boolean Exceptions: Caller : Example : $obj->remove(); =cut sub remove { my $self = shift; if( -e $self->statefile ){ unlink( $self->statefile ); } return 1; } #---------------------------------------------------------------------- =head2 _freeze Arg [1] : variable Function : Converts whatever is in the the arg into a string. Uses either Storable::freeze or Data::Dumper::Dump depending on the value of $Bio::Root::BINARY Returntype: Exceptions: Caller : Example : =cut sub _freeze { my $self = shift; my $data = shift; if( $BINARY ){ return freeze( $data ); } else{ $Data::Dumper::Purity = 1; return Data::Dumper->Dump( [\$data],["*code"] ); } } #---------------------------------------------------------------------- =head2 _thaw Arg [1] : string Function : Converts the string into a perl 'whatever'. Uses either Storable::thaw or eval depending on the value of $Bio::Root::BINARY. Note; the string arg should have been created with the _freeze method, or strange things may occur! Returntype: variable Exceptions: Caller : Example : =cut sub _thaw { my $self = shift; my $data = shift; if( $BINARY ){ return thaw( $data ) } else{ my $code; $code = eval( $data ) ; if($@) { $self->throw( "eval: $@" ); } ref( $code ) eq 'REF' or $self->throw( "Serialised string was not a scalar ref" ); return $$code; } } 1; BioPerl-1.007002/Bio/Root/Test.pm000444000766000024 4301413155576320 16446 0ustar00cjfieldsstaff000000000000package Bio::Root::Test; use strict; use warnings; # According to Ovid, 'use base' can override signal handling, so use # old-fashioned way. This should be a Test::Builder::Module subclass # for consistency (as are any Test modules) use Test::Most; use Test::Builder; use Test::Builder::Module; use File::Temp qw(tempdir); use File::Spec; our @ISA = qw(Test::Builder::Module); =head1 SYNOPSIS use lib '.'; # (for core package tests only) use Bio::Root::Test; test_begin(-tests => 20, -requires_modules => [qw(IO::String XML::Parser)], -requires_networking => 1); my $do_network_tests = test_network(); my $output_debugging = test_debug(); # Bio::Root::Test rewraps Test::Most, so one can carry out tests with # Test::More, Test::Exception, Test::Warn, Test::Deep, Test::Diff syntax SKIP: { # these tests need version 2.6 of Optional::Module to work test_skip(-tests => 10, -requires_module => 'Optional::Module 2.6'); use_ok('Optional::Module'); # 9 other optional tests that need Optional::Module } SKIP: { test_skip(-tests => 10, -requires_networking => 1); # 10 optional tests that require internet access (only makes sense in the # context of a script that doesn't use -requires_networking in the call to # &test_begin) } # in unix terms, we want to test with a file t/data/input_file.txt my $input_file = test_input_file('input_file.txt'); # we want the name of a file we can write to, that will be automatically # deleted when the test script finishes my $output_file = test_output_file(); # we want the name of a directory we can store files in, that will be # automatically deleted when the test script finishes my $output_dir = test_output_dir(); =head1 DESCRIPTION This provides a common base for all BioPerl test scripts. It safely handles the loading of Test::Most, itself a simple wrapper around several highly used test modules: Test::More, Test::Exception, Test::Warn, Test::Deep, and Test::Diff. It also presents an interface to common needs such as skipping all tests if required modules aren't present or if network tests haven't been enabled. See test_begin(). In the same way, it allows you to skip just a subset of tests for those same reasons, in addition to requiring certain executables and environment variables. See test_skip(). It also has two further methods that let you decide if network tests should be run, and if debugging information should be printed. See test_network() and test_debug(). Finally, it presents a consistent way of getting the path to input and output files. See test_input_file(), test_output_file() and test_output_dir(). =head1 AUTHOR Sendu Bala Chris Fields =cut # TODO: Evil magic ahead; can we clean this up? { my $Tester = Test::Builder->new; no warnings 'redefine'; sub Test::Warn::_canonical_got_warning { my ( $called_from, $msg ) = @_; my $warn_kind = $called_from eq 'Carp' ? 'carped' : ( $called_from =~ /Bio::/ ? 'Bioperl' : 'warn' ); my $warning; if ( $warn_kind eq 'Bioperl' ) { ($warning) = $msg =~ /\n--------------------- WARNING ---------------------\nMSG: (.+)\n---------------------------------------------------\n$/m; $warning ||= $msg; # shouldn't ever happen } else { my @warning_stack = split /\n/, $msg; # some stuff of uplevel is included $warning = $warning_stack[0]; } return { $warn_kind => $warning }; # return only the real message } sub Test::Warn::_diag_found_warning { my @warns = @_; foreach my $warn (@warns) { if ( ref($warn) eq 'HASH' ) { ${$warn}{carped} ? $Tester->diag("found carped warning: ${$warn}{carped}") : ( ${$warn}{Bioperl} ? $Tester->diag( "found Bioperl warning: ${$warn}{Bioperl}") : $Tester->diag("found warning: ${$warn}{warn}") ); } else { $Tester->diag("found warning: $warn"); } } $Tester->diag("didn't find a warning") unless @warns; } sub Test::Warn::_cmp_got_to_exp_warning { my ( $got_kind, $got_msg ) = %{ shift() }; my ( $exp_kind, $exp_msg ) = %{ shift() }; return 0 if ( $got_kind eq 'warn' ) && ( $exp_kind eq 'carped' ); my $cmp; if ( $got_kind eq 'Bioperl' ) { $cmp = $got_msg =~ /^\Q$exp_msg\E$/; } else { $cmp = $got_msg =~ /^\Q$exp_msg\E at \S+ line \d+\.?$/; } return $cmp; } } our @EXPORT = ( @Test::Most::EXPORT, #@Bio::Root::Test::Warn::EXPORT, # Test::Warn method wrappers # BioPerl-specific qw( test_begin test_skip test_output_file test_output_dir test_input_file test_network test_email test_debug float_is ) ); our $GLOBAL_FRAMEWORK = 'Test::Most'; our @TEMP_FILES; =head2 test_begin Title : test_begin Usage : test_begin(-tests => 20); Function: Begin your test script, setting up the plan (skip all tests, or run them all) Returns : True if tests should be run. Args : -tests => int (REQUIRED, the number of tests that will be run) -requires_modules => [] (array ref of module names that are required; if any don't load, all tests will be skipped. To specify a required version of a module, include the version number after the module name, separated by a space) -requires_module => str (as above, but for just one module) -requires_networking => 1|0 (default 0, if true all tests will be skipped if network tests haven't been enabled in Build.PL) -requires_email => 1 (if true the desired number of tests will be skipped if either network tests haven't been enabled in Build.PL or an email hasn't been entered) -excludes_os => str (default none, if OS supplied, all tests will skip if running on that OS (eg. 'mswin')) -framework => str (default 'Test::Most', the Test module to load. NB: experimental, avoid using) Note, supplying -tests => 0 is possible, allowing you to skip all tests in the case that a test script is testing deprecated modules that have yet to be removed from the distribution =cut sub test_begin { my ( $skip_all, $tests, $framework ) = _skip(@_); $GLOBAL_FRAMEWORK = $framework; if ( $framework eq 'Test::Most' ) { # ideally we'd delay loading Test::Most until this point, but see BEGIN # block if ($skip_all) { eval "plan skip_all => '$skip_all';"; } elsif ( defined $tests && $tests == 0 ) { eval "plan skip_all => 'These modules are now probably deprecated';"; } elsif ($tests) { eval "plan tests => $tests;"; } return 1; } # go ahead and add support for other frameworks here else { die "Only Test::Most is supported at the current time\n"; } return 0; } =head2 test_skip Title : test_skip Usage : SKIP: { test_skip(-tests => 10, -requires_module => 'Optional::Module 2.01'); # 10 tests that need v2.01 of Optional::Module } Function: Skip a subset of tests for one of several common reasons: missing one or more optional modules, network tests haven't been enabled, a required binary isn't present, or an environmental variable isn't set Returns : n/a Args : -tests => int (REQUIRED, the number of tests that are to be skipped in the event one of the following options isn't satisfied) -requires_modules => [] (array ref of module names that are required; if any don't load, the desired number of tests will be skipped. To specify a required version of a module, include the version number after the module name, separated by a space) -requires_module => str (as above, but for just one module) -requires_executable => Bio::Tools::Run::WrapperBase instance (checks WrapperBase::executable for the presence of a binary, skips if absent) -requires_env => str (checks %ENV for a specific env. variable, skips if absent) -excludes_os => str (default none, if OS supplied, desired num of tests will skip if running on that OS (eg. 'mswin')) -requires_networking => 1 (if true the desired number of tests will be skipped if network tests haven't been enabled in Build.PL) -requires_email => 1 (if true the desired number of tests will be skipped if either network tests haven't been enabled in Build.PL or an email hasn't been entered) =cut sub test_skip { my ( $skip, $tests, $framework ) = _skip(@_); $tests || die "-tests must be a number greater than 0"; if ( $framework eq 'Test::Most' ) { if ($skip) { eval "skip('$skip', $tests);"; } } # go ahead and add support for other frameworks here else { die "Only Test::Most is supported at the current time\n"; } } =head2 test_output_file Title : test_output_file Usage : my $output_file = test_output_file(); Function: Get the full path of a file suitable for writing to. When your test script ends, the file will be automatically deleted. Returns : string (file path) Args : none =cut sub test_output_file { die "test_output_file takes no args\n" if @_; # RT 48813 my $tmp = File::Temp->new(); push( @TEMP_FILES, $tmp ); close($tmp); # Windows needs this return $tmp->filename; } =head2 test_output_dir Title : test_output_dir Usage : my $output_dir = test_output_dir(); Function: Get the full path of a directory suitable for storing temporary files in. When your test script ends, the directory and its contents will be automatically deleted. Returns : string (path) Args : none =cut sub test_output_dir { die "test_output_dir takes no args\n" if @_; return tempdir( CLEANUP => 1 ); } =head2 test_input_file Title : test_input_file Usage : my $input_file = test_input_file(); Function: Get the path of a desired input file stored in the standard location (currently t/data), but correct for all platforms. Returns : string (file path) Args : list of strings (ie. at least the input filename, preceded by the names of any subdirectories within t/data) eg. for the file t/data/in.file pass 'in.file', for the file t/data/subdir/in.file, pass ('subdir', 'in.file') =cut sub test_input_file { return File::Spec->catfile( 't', 'data', @_ ); } =head2 test_network Title : test_network Usage : my $do_network_tests = test_network(); Function: Ask if network tests should be run. Returns : boolean Args : none =cut sub test_network { require Module::Build; my $build = Module::Build->current(); return $build->notes('network') || $ENV{AUTHOR_TESTING} || $ENV{RELEASE_TESTING}; } =head2 test_email Title : test_email Usage : my $do_network_tests = test_email(); Function: Ask if email address provided Returns : boolean Args : none =cut sub test_email { require Module::Build; my $build = Module::Build->current(); # this should not be settable unless the network tests work return $build->notes('email') || $ENV{AUTHOR_TESTING} || $ENV{RELEASE_TESTING}; } =head2 test_debug Title : test_debug Usage : my $output_debugging = test_debug(); Function: Ask if debugging information should be output. Returns : boolean Args : none =cut sub test_debug { return $ENV{'BIOPERLDEBUG'} || 0; } =head2 float_is Title : float_is Usage : float_is($val1, $val2); Function: test two floating point values for equality Returns : Boolean based on test (can use in combination with diag) Args : two scalar values (floating point numbers) (required via prototype) test message (optional) =cut sub float_is ($$;$) { my ( $val1, $val2, $message ) = @_; # catch any potential undefined values and directly compare if ( ! defined $val1 || ! defined $val2 ) { is( $val1, $val2, $message ); } else { is( sprintf( "%g", $val1 ), sprintf( "%g", $val2 ), $message ); } } =head2 _skip Decide if should skip and generate skip message =cut sub _skip { my %args = @_; # handle input strictly my $tests = $args{'-tests'}; #(defined $tests && $tests =~ /^\d+$/) || die "-tests must be supplied and be an int\n"; delete $args{'-tests'}; my $req_mods = $args{'-requires_modules'}; delete $args{'-requires_modules'}; my @req_mods; if ($req_mods) { ref($req_mods) eq 'ARRAY' || die "-requires_modules takes an array ref\n"; @req_mods = @{$req_mods}; } my $req_mod = $args{'-requires_module'}; delete $args{'-requires_module'}; if ($req_mod) { ref($req_mod) && die "-requires_module takes a string\n"; push( @req_mods, $req_mod ); } my $req_net = $args{'-requires_networking'}; delete $args{'-requires_networking'}; my $req_email = $args{'-requires_email'}; delete $args{'-requires_email'}; my $req_env = $args{'-requires_env'}; delete $args{'-requires_env'}; # strip any leading $ in case someone passes $FOO instead of 'FOO' $req_env =~ s{^\$}{} if $req_env; my $req_exe = $args{'-requires_executable'}; delete $args{'-requires_executable'}; if ($req_exe && ( ! ref($req_exe) || ! $req_exe->isa('Bio::Tools::Run::WrapperBase') ) ) { die "-requires_exe takes an argument of type Bio::Tools::Run::WrapperBase"; } my $os = $args{'-excludes_os'}; delete $args{'-excludes_os'}; my $framework = $args{'-framework'} || $GLOBAL_FRAMEWORK; delete $args{'-framework'}; # catch user mistakes while ( my ( $key, $val ) = each %args ) { die "unknown argument '$key' supplied, did you mistake 'required...' for 'requires...'?\n"; } # test user requirements and return if ($os) { if ( $^O =~ /$os/i ) { return ( 'Not compatible with your Operating System', $tests, $framework ); } } foreach my $mod (@req_mods) { my $skip = _check_module($mod); if ($skip) { return ( $skip, $tests, $framework ); } } if ( $req_net && ! test_network() ) { return ( 'Network tests have not been requested', $tests, $framework ); } if ( $req_email && ! test_email() ) { return ( 'Valid email not provided; required for tests', $tests, $framework ); } if ($req_exe) { my $eval = eval { $req_exe->executable }; if ( $@ or not defined $eval ) { my $msg = 'Required executable for ' . ref($req_exe) . ' is not present'; diag($msg); return ( $msg, $tests, $framework ); } } if ( $req_env && ! exists $ENV{$req_env} ) { my $msg = 'Required environment variable $' . $req_env . ' is not set'; diag($msg); return ( $msg, $tests, $framework ); } return ( '', $tests, $framework ); } =head2 _check_module =cut sub _check_module { my $mod = shift; my $desired_version; if ( $mod =~ /(\S+)\s+(\S+)/ ) { $mod = $1; $desired_version = $2; } eval "require $mod;"; if ($@) { if ( $@ =~ /Can't locate/ ) { return "The optional module $mod (or dependencies thereof) was not installed"; } else { return "The optional module $mod generated the following error: \n$@"; } } elsif ($desired_version) { no strict 'refs'; unless ( defined ${"${mod}::VERSION"} ) { return "The optional module $mod didn't have a version, but we want v$desired_version"; } elsif ( ${"${mod}::VERSION"} < $desired_version ) { return "The optional module $mod was out of date (wanted v$desired_version)"; } } return; } 1; BioPerl-1.007002/Bio/Root/TestObject.pm000444000766000024 333313155576320 17555 0ustar00cjfieldsstaff000000000000=head1 NAME TestObject - An implementation of TestInterface =head1 DESCRIPTION This module attempts to provide an implementation of TestInterface and is used for illustrating exception throwing using Graham Barr's Error.pm object. =head1 AUTHOR Steve Chervitz Esac@bioperl.orgE =cut package Bio::Root::TestObject; use strict; # Define a special type of error "Bio::TestException" as a subclass of Error. # Note two things: # 1. The ISA declaration effectively defines our new Exception object. # 2. This declaration doesn't have to be located in the Bio directory. # 3. We don't have to use Bio::Root::Exception in this module. # 4. If Error.pm isn't available this statement doesn't matter. @Bio::TestException::ISA = qw( Bio::Root::Exception ); use base qw( Bio::Root::Root ); # Note that we're not implementing foo(), so calling it # will result in a Bio::Root::NotImplemented exception. sub data { my ($self, $data) = @_; print "Setting test data ($data)\n" if $data && $self->verbose; $self->{'data'} = $data if $data; return $self->{'data'} } sub bar { my $self = shift; print "\nExecuting method bar() in TestObject\n" if $self->verbose; print "Throwing a Bio::TestException\n" if $self->verbose; my $message = "A Test error"; # Bio::Root::Root::throw() will make use of Error.pm if present. # The type of Error is specified with a -class parameter. # If -class is not supplied, a Bio::Root::Exception is throw. # In this case, the argument can consist of a simple string. $self->throw( -class => 'Bio::TestException', -text => $message ); print "Code within bar() below the throw that shouldn't be executed.\n" if $self->verbose; } 1; BioPerl-1.007002/Bio/Root/Utilities.pm000444000766000024 13050613155576320 17525 0ustar00cjfieldsstaff000000000000package Bio::Root::Utilities; use strict; use Bio::Root::IO; use Bio::Root::Exception; use base qw(Bio::Root::Root Exporter); =head1 SYNOPSIS =head2 Object Creation # Using the supplied singleton object: use Bio::Root::Utilities qw(:obj); $Util->some_method(); # Create an object manually: use Bio::Root::Utilities; my $util = Bio::Root::Utilities->new(); $util->some_method(); $date_stamp = $Util->date_format('yyy-mm-dd'); $clean = $Util->untaint($dirty); $compressed = $Util->compress('/home/me/myfile.txt') my ($mean, $stdev) = $Util->mean_stdev( @data ); $Util->authority("me@example.com"); $Util->mail_authority("Something you should know about..."); ...and a host of other methods. See below. =head1 DESCRIPTION Provides general-purpose utilities of potential interest to any Perl script. The C<:obj> tag is a convenience that imports a $Util symbol into your namespace representing a Bio::Root::Utilities object. This saves you from creating your own Bio::Root::Utilities object via Cnew()> or from prefixing all method calls with C, though feel free to do these things if desired. Since there should normally not be a need for a script to have more than one Bio::Root::Utilities object, this module thus comes with it's own singleton. =head1 INSTALLATION This module is included with the central Bioperl distribution: http://www.bioperl.org/wiki/Getting_BioPerl ftp://bio.perl.org/pub/DIST Follow the installation instructions included in the README file. =head1 DEPENDENCIES Inherits from L, and uses L and L. Relies on external executables for file compression/uncompression and sending mail. No paths to these are hard coded but are located as needed. =head1 SEE ALSO http://bioperl.org - Bioperl Project Homepage =head1 ACKNOWLEDGEMENTS This module was originally developed under the auspices of the Saccharomyces Genome Database: http://www.yeastgenome.org/ =head1 AUTHOR Steve Chervitz =cut use vars qw(@EXPORT_OK %EXPORT_TAGS); @EXPORT_OK = qw($Util); %EXPORT_TAGS = ( obj => [qw($Util)], std => [qw($Util)],); use vars qw($ID $Util $GNU_PATH $TIMEOUT_SECS @COMPRESSION_UTILS @UNCOMPRESSION_UTILS $DEFAULT_NEWLINE $NEWLINE $AUTHORITY @MONTHS @DAYS $BASE_YEAR $DEFAULT_CENTURY ); $ID = 'Bio::Root::Utilities'; # Number of seconds to wait before timing out when reading input (taste_file()) $TIMEOUT_SECS = 30; $NEWLINE = $ENV{'NEWLINE'} || undef; $BASE_YEAR = 1900; # perl's localtime() assumes this for it's year data. # TODO: update this every hundred years. Y2K-sensitive code. $DEFAULT_CENTURY = $BASE_YEAR + 100; @MONTHS = qw(Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec); @DAYS = qw(Sun Mon Tue Wed Thu Fri Sat); # Sets the preference for compression utilities to be used by compress(). # The first executable in this list to be found in the current PATH will be used, # unless overridden in the call to that function. See docs for details. @COMPRESSION_UTILS = qw(gzip bzip2 zip compress); @UNCOMPRESSION_UTILS = qw(gunzip gzip bunzip2 unzip uncompress); # Default person to receive feedback from users and possibly automatic error messages. $AUTHORITY = ''; # Note: $GNU_PATH is now deprecated, shouldn't be needed since now this module # will automatically locate the compression utility in the current PATH. # Retaining $GNU_PATH for backward compatibility. # # $GNU_PATH points to the directory containing the gzip and gunzip # executables. It may be required for executing gzip/gunzip # in some situations (e.g., when $ENV{PATH} doesn't contain this dir. # Customize $GNU_PATH for your site if the compress() or # uncompress() functions are generating exceptions. $GNU_PATH = ''; #$GNU_PATH = '/tools/gnu/bin/'; $DEFAULT_NEWLINE = "\012"; # \n (used if get_newline() fails for some reason) ## Static UTIL object. $Util = Bio::Root::Root->new(); =head2 date_format Title : date_format Usage : $Util->date_format( [FMT], [DATE]) Purpose : -- Get a string containing the formatted date or time : taken when this routine is invoked. : -- Provides a way to avoid using `date`. : -- Provides an interface to localtime(). : -- Interconverts some date formats. : : (For additional functionality, use Date::Manip or : Date::DateCalc available from CPAN). Example : $Util->date_format(); : $date = $Util->date_format('yyyy-mmm-dd', '11/22/92'); Returns : String (unless 'list' is provided as argument, see below) : : 'yyyy-mm-dd' = 1996-05-03 # default format. : 'yyyy-dd-mm' = 1996-03-05 : 'yyyy-mmm-dd' = 1996-May-03 : 'd-m-y' = 3-May-1996 : 'd m y' = 3 May 1996 : 'dmy' = 3may96 : 'mdy' = May 3, 1996 : 'ymd' = 96may3 : 'md' = may3 : 'year' = 1996 : 'hms' = 23:01:59 # when not converting a format, 'hms' can be : # tacked on to any of the above options : # to add the time stamp: eg 'dmyhms' : 'full' | 'unix' = UNIX-style date: Tue May 5 22:00:00 1998 : 'list' = the contents of localtime(time) in an array. Argument : (all are optional) : FMT = yyyy-mm-dd | yyyy-dd-mm | yyyy-mmm-dd | : mdy | ymd | md | d-m-y | hms | hm : ('hms' may be appended to any of these to : add a time stamp) : : DATE = String containing date to be converted. : Acceptable input formats: : 12/1/97 (for 1 December 1997) : 1997-12-01 : 1997-Dec-01 Throws : Comments : If you don't care about formatting or using backticks, you can : always use: $date = `date`; : : For more features, use Date::Manip.pm, (which I should : probably switch to...) See Also : L, L =cut #---------------' sub date_format { #--------------- my $self = shift; my $option = shift; my $date = shift; # optional date to be converted. my($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst); $option ||= 'yyyy-mm-dd'; my ($month_txt, $day_txt, $month_num, $fullYear); my ($converting, @date); # Load a supplied date for conversion: if(defined($date) && ($date =~ /[\D-]+/)) { $converting = 1; if( $date =~ m{/}) { ($mon,$mday,$year) = split(m{/}, $date); } elsif($date =~ /(\d{4})-(\d{1,2})-(\d{1,2})/) { ($year,$mon,$mday) = ($1, $2, $3); } elsif($date =~ /(\d{4})-(\w{3,})-(\d{1,2})/) { ($year,$mon,$mday) = ($1, $2, $3); $mon = $self->month2num($2); } else { print STDERR "\n*** Unsupported input date format: $date\n"; } if(length($year) == 4) { $fullYear = $year; $year = substr $year, 2; } else { # Heuristics to guess what century was intended when a 2-digit year is given # If number is over 50, assume it's for prev century; under 50 = default century. # TODO: keep an eye on this Y2K-sensitive code if ($year > 50) { $fullYear = $DEFAULT_CENTURY + $year - 100; } else { $fullYear = $DEFAULT_CENTURY + $year; } } $mon -= 1; } else { ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = @date = localtime(($date ? $date : time())); return @date if $option =~ /list/i; $fullYear = $BASE_YEAR+$year; } $month_txt = $MONTHS[$mon]; $day_txt = $DAYS[$wday] if defined $wday; $month_num = $mon+1; # print "sec: $sec, min: $min, hour: $hour, month: $mon, m-day: $mday, year: $year\nwday: $wday, yday: $yday, dst: $isdst";; if( $option =~ /yyyy-mm-dd/i ) { $date = sprintf "%4d-%02d-%02d",$fullYear,$month_num,$mday; } elsif( $option =~ /yyyy-dd-mm/i ) { $date = sprintf "%4d-%02d-%02d",$fullYear,$mday,$month_num; } elsif( $option =~ /yyyy-mmm-dd/i ) { $date = sprintf "%4d-%3s-%02d",$fullYear,$month_txt,$mday; } elsif( $option =~ /full|unix/i ) { $date = sprintf "%3s %3s %2d %02d:%02d:%02d %d",$day_txt, $month_txt, $mday, $hour, $min, $sec, $fullYear; } elsif( $option =~ /mdy/i ) { $date = "$month_txt $mday, $fullYear"; } elsif( $option =~ /ymd/i ) { $date = $year."\l$month_txt$mday"; } elsif( $option =~ /dmy/i ) { $date = $mday."\l$month_txt$year"; } elsif( $option =~ /md/i ) { $date = "\l$month_txt$mday"; } elsif( $option =~ /d-m-y/i ) { $date = "$mday-$month_txt-$fullYear"; } elsif( $option =~ /d m y/i ) { $date = "$mday $month_txt $fullYear"; } elsif( $option =~ /year/i ) { $date = $fullYear; } elsif( $option =~ /dmy/i ) { $date = $mday.'-'.$month_txt.'-'.$fullYear; } elsif($option and $option !~ /hms/i) { print STDERR "\n*** Unrecognized date format request: $option\n"; } if( $option =~ /hms/i and not $converting) { $date .= " $hour:$min:$sec" if $date; $date ||= "$hour:$min:$sec"; } return $date || join(" ", @date); } =head2 month2num Title : month2num Purpose : Converts a string containing a name of a month to integer : representing the number of the month in the year. Example : $Util->month2num("march"); # returns 3 Argument : The string argument must contain at least the first : three characters of the month's name. Case insensitive. Throws : Exception if the conversion fails. =cut #--------------' sub month2num { #-------------- my ($self, $str) = @_; # Get string in proper format for conversion. $str = substr($str, 0, 3); for my $month (0..$#MONTHS) { return $month+1 if $str =~ /$MONTHS[$month]/i; } $self->throw("Invalid month name: $str"); } =head2 num2month Title : num2month Purpose : Does the opposite of month2num. : Converts a number into a string containing a name of a month. Example : $Util->num2month(3); # returns 'Mar' Throws : Exception if supplied number is out of range. =cut #------------- sub num2month { #------------- my ($self, $num) = @_; $self->throw("Month out of range: $num") if $num < 1 or $num > 12; return $MONTHS[$num-1]; } =head2 compress Title : compress Usage : $Util->compress(full-path-filename); : $Util->compress(); Purpose : Compress a file. Example : $Util->compress("/usr/people/me/data.txt"); : $Util->compress(-file=>"/usr/people/me/data.txt", : -tmp=>1, : -outfile=>"/usr/people/share/data.txt.gz", : -exe=>"/usr/local/bin/fancyzip"); Returns : String containing full, absolute path to compressed file Argument : Named parameters (case-insensitive): : -FILE => String (name of file to be compressed, full path). : If the supplied filename ends with '.gz' or '.Z', : that extension will be removed before attempting to compress. : Optional: : -TMP => boolean. If true, (or if user is not the owner of the file) : the file is compressed to a temp file. If false, file may be : clobbered with the compressed version (if using a utility like : gzip, which is the default) : -OUTFILE => String (name of the output compressed file, full path). : -EXE => Name of executable for compression utility to use. : Will supersede those in @COMPRESSION_UTILS defined by : this module. If the absolute path to the executable is not provided, : it will be searched in the PATH env variable. Throws : Exception if file cannot be compressed. : If user is not owner of the file, generates a warning and compresses to : a tmp file. To avoid this warning, use the -o file test operator : and call this function with -TMP=>1. Comments : Attempts to compress using utilities defined in the @COMPRESSION_UTILS : defined by this module, in the order defined. The first utility that is : found to be executable will be used. Any utility defined in optional -EXE param : will be tested for executability first. : To minimize security risks, the -EXE parameter value is untained using : the untaint() method of this module (in 'relaxed' mode to permit path separators). See Also : L =cut #------------' sub compress { #------------ my ($self, @args) = @_; # This method formerly didn't use named params and expected fileName, tmp # in that order. This should be backward compatibile. my ($fileName, $tmp, $outfile, $exe) = $self->_rearrange([qw(FILE TMP OUTFILE EXE)], @args); my ($file, $get, $fmt); # in case the supplied name already has a compressed extension if($fileName =~ /(\.gz|\.Z|\.bz2|\.zip)$/) { $fileName =~ s/$1$//; }; $self->debug("compressing file $fileName"); my @util_to_use = @COMPRESSION_UTILS; if (defined $exe){ $exe = $self->untaint($exe, 1); unshift @util_to_use, $exe; } my @checked = @util_to_use; $exe ||= ''; while (not -x $exe and scalar(@util_to_use)) { $exe = $self->find_exe(shift @util_to_use); } unless (-x $exe) { $self->throw("Can't find compression utility. Looked for @checked"); } my ($compressed, @cmd, $handle); if(defined($outfile) or $tmp or not -o $fileName) { if (defined $outfile) { $compressed = $outfile; } else { # obtain a temporary file name (not using the handle) # and insert some special text to flag it as a bioperl-based temp file my $io = Bio::Root::IO->new(); ($handle, $compressed) = $io->tempfile(); $compressed .= '.tmp.bioperl.gz'; } # Use double quotes if executable path have empty spaces if ($exe =~ m/ /) { $exe = "\"$exe\""; } if ($exe =~ /gzip|bzip2|compress/) { @cmd = ("$exe -f < \"$fileName\" > \"$compressed\""); } elsif ($exe eq 'zip') { @cmd = ("$exe -r \"$fileName.zip\" \"$fileName\""); } not $tmp and $self->warn("Not owner of file $fileName. Compressing to temp file $compressed."); $tmp = 1; } else { # Need to compute the compressed name based on exe since we're returning it. $compressed = $fileName; if ($exe =~ /gzip/) { $compressed .= '.gz'; } elsif ($exe =~ /bzip2/) { $compressed .= '.bz2'; } elsif ($exe =~ /zip/) { $compressed .= '.zip'; } elsif ($exe =~ /compress/) { $compressed .= '.Z'; } if ($exe =~ /gzip|bzip2|compress/) { @cmd = ($exe, '-f', $fileName); } elsif ($exe eq 'zip') { @cmd = ($exe, '-r', "$compressed", $fileName); } } if(system(@cmd) != 0) { $self->throw( -class => 'Bio::Root::SystemException', -text => "Failed to compress file $fileName using $exe: $!"); } return $compressed; } =head2 uncompress Title : uncompress Usage : $Util->uncompress(full-path-filename); : $Util->uncompress(); Purpose : Uncompress a file. Example : $Util->uncompress("/usr/people/me/data.txt"); : $Util->uncompress(-file=>"/usr/people/me/data.txt.gz", : -tmp=>1, : -outfile=>"/usr/people/share/data.txt", : -exe=>"/usr/local/bin/fancyzip"); Returns : String containing full, absolute path to uncompressed file Argument : Named parameters (case-insensitive): : -FILE => String (name of file to be uncompressed, full path). : If the supplied filename ends with '.gz' or '.Z', : that extension will be removed before attempting to uncompress. : Optional: : -TMP => boolean. If true, (or if user is not the owner of the file) : the file is uncompressed to a temp file. If false, file may be : clobbered with the uncompressed version (if using a utility like : gzip, which is the default) : -OUTFILE => String (name of the output uncompressed file, full path). : -EXE => Name of executable for uncompression utility to use. : Will supersede those in @UNCOMPRESSION_UTILS defined by : this module. If the absolute path to the executable is not provided, : it will be searched in the PATH env variable. Throws : Exception if file cannot be uncompressed. : If user is not owner of the file, generates a warning and uncompresses to : a tmp file. To avoid this warning, use the -o file test operator : and call this function with -TMP=>1. Comments : Attempts to uncompress using utilities defined in the @UNCOMPRESSION_UTILS : defined by this module, in the order defined. The first utility that is : found to be executable will be used. Any utility defined in optional -EXE param : will be tested for executability first. : To minimize security risks, the -EXE parameter value is untained using : the untaint() method of this module (in 'relaxed' mode to permit path separators). See Also : L =cut #------------' sub uncompress { #------------ my ($self, @args) = @_; # This method formerly didn't use named params and expected fileName, tmp # in that order. This should be backward compatibile. my ($fileName, $tmp, $outfile, $exe) = $self->_rearrange([qw(FILE TMP OUTFILE EXE)], @args); my ($file, $get, $fmt); # in case the supplied name lacks a compressed extension if(not $fileName =~ /(\.gz|\.Z|\.bz2|\.zip)$/) { $fileName .= $1; }; $self->debug("uncompressing file $fileName"); my @util_to_use = @UNCOMPRESSION_UTILS; if (defined $exe){ $exe = $self->untaint($exe, 1); unshift @util_to_use, $exe; } $exe ||= ''; while (not -x $exe and scalar(@util_to_use)) { $exe = $self->find_exe(shift @util_to_use); } unless (-x $exe) { $self->throw("Can't find compression utility. Looked for @util_to_use"); } my ($uncompressed, @cmd, $handle); $uncompressed = $fileName; $uncompressed =~ s/\.\w+$//; if(defined($outfile) or $tmp or not -o $fileName) { if (defined $outfile) { $uncompressed = $outfile; } else { # obtain a temporary file name (not using the handle) my $io = Bio::Root::IO->new(); ($handle, $uncompressed) = $io->tempfile(); # insert some special text to flag it as a bioperl-based temp file $uncompressed .= '.tmp.bioperl'; } # Use double quotes if executable path have empty spaces if ($exe =~ m/ /) { $exe = "\"$exe\""; } if ($exe =~ /gunzip|bunzip2|uncompress/) { @cmd = ("$exe -f < \"$fileName\" > \"$uncompressed\""); } elsif ($exe =~ /gzip/) { @cmd = ("$exe -df < \"$fileName\" > \"$uncompressed\""); } elsif ($exe eq 'unzip') { @cmd = ("$exe -p \"$fileName\" > \"$uncompressed\""); } not $tmp and $self->warn("Not owner of file $fileName. Uncompressing to temp file $uncompressed."); $tmp = 1; } else { if ($exe =~ /gunzip|bunzip2|uncompress/) { @cmd = ($exe, '-f', $fileName); } elsif ($exe =~ /gzip/) { @cmd = ($exe, '-df', $fileName); } elsif ($exe eq 'zip') { @cmd = ($exe, $fileName); } } if(system(@cmd) != 0) { $self->throw( -class => 'Bio::Root::SystemException', -text => "Failed to uncompress file $fileName using $exe: $!"); } return $uncompressed; } =head2 file_date Title : file_date Usage : $Util->file_date( filename [,date_format]) Purpose : Obtains the date of a given file. : Provides flexible formatting via date_format(). Returns : String = date of the file as: yyyy-mm-dd (e.g., 1997-10-15) Argument : filename = string, full path name for file : date_format = string, desired format for date (see date_format()). : Default = yyyy-mm-dd Thows : Exception if no file is provided or does not exist. Comments : Uses the mtime field as obtained by stat(). =cut #-------------- sub file_date { #-------------- my ($self, $file, $fmt) = @_; $self->throw("No such file: $file") if not $file or not -e $file; $fmt ||= 'yyyy-mm-dd'; my @file_data = stat($file); return $self->date_format($fmt, $file_data[9]); # mtime field } =head2 untaint Title : untaint Purpose : To remove nasty shell characters from untrusted data : and allow a script to run with the -T switch. : Potentially dangerous shell meta characters: &;`'\"|*?!~<>^()[]{}$\n\r : Accept only the first block of contiguous characters: : Default allowed chars = "-\w.', ()" : If $relax is true = "-\w.', ()\/=%:^<>*" Usage : $Util->untaint($value, $relax) Returns : String containing the untained data. Argument: $value = string : $relax = boolean Comments: This general untaint() function may not be appropriate for every situation. To allow only a more restricted subset of special characters (for example, untainting a regular expression), then using a custom untainting mechanism would permit more control. Note that special trusted vars (like $0) require untainting. =cut #------------` sub untaint { #------------ my($self,$value,$relax) = @_; $relax ||= 0; my $untainted; $self->debug("\nUNTAINT: $value\n"); unless (defined $value and $value ne '') { return $value; } if( $relax ) { $value =~ /([-\w.\', ()\/=%:^<>*]+)/; $untainted = $1 # } elsif( $relax == 2 ) { # Could have several degrees of relax. # $value =~ /([-\w.\', ()\/=%:^<>*]+)/; # $untainted = $1 } else { $value =~ /([-\w.\', ()]+)/; $untainted = $1 } $self->debug("UNTAINTED: $untainted\n"); $untainted; } =head2 mean_stdev Title : mean_stdev Usage : ($mean, $stdev) = $Util->mean_stdev( @data ) Purpose : Calculates the mean and standard deviation given a list of numbers. Returns : 2-element list (mean, stdev) Argument : list of numbers (ints or floats) Thows : n/a =cut #--------------- sub mean_stdev { #--------------- my ($self, @data) = @_; return (undef, undef) if not @data; # case of empty @data list my $mean = 0; my $N = 0; foreach my $num (@data) { $mean += $num; $N++ } $mean /= $N; my $sum_diff_sqd = 0; foreach my $num (@data) { $sum_diff_sqd += ($mean - $num) * ($mean - $num); } # if only one element in @data list, unbiased stdev is undefined my $stdev = $N <= 1 ? undef : sqrt( $sum_diff_sqd / ($N-1) ); return ($mean, $stdev); } =head2 count_files Title : count_files Purpose : Counts the number of files/directories within a given directory. : Also reports the number of text and binary files in the dir : as well as names of these files and directories. Usage : count_files(\%data) : $data{-DIR} is the directory to be analyzed. Default is ./ : $data{-PRINT} = 0|1; if 1, prints results to STDOUT, (default=0). Argument : Hash reference (empty) Returns : n/a; : Modifies the hash ref passed in as the sole argument. : $$href{-TOTAL} scalar : $$href{-NUM_TEXT_FILES} scalar : $$href{-NUM_BINARY_FILES} scalar : $$href{-NUM_DIRS} scalar : $$href{-T_FILE_NAMES} array ref : $$href{-B_FILE_NAMES} array ref : $$href{-DIRNAMES} array ref =cut #---------------- sub count_files { #---------------- my $self = shift; my $href = shift; # Reference to an empty hash. my( $name, @fileLine); my $dir = $$href{-DIR} || './'; # THIS IS UNIX SPECIFIC? FIXME/TODO my $print = $$href{-PRINT} || 0; ### Make sure $dir ends with / $dir !~ m{/$} and do{ $dir .= '/'; $$href{-DIR} = $dir; }; open ( my $PIPE, "ls -1 $dir |" ) || $self->throw("Can't open input pipe: $!"); ### Initialize the hash data. $$href{-TOTAL} = 0; $$href{-NUM_TEXT_FILES} = $$href{-NUM_BINARY_FILES} = $$href{-NUM_DIRS} = 0; $$href{-T_FILE_NAMES} = []; $$href{-B_FILE_NAMES} = []; $$href{-DIR_NAMES} = []; while( my $line = <$PIPE> ) { chomp(); $$href{-TOTAL}++; if( -T $dir.$line ) { $$href{-NUM_TEXT_FILES}++; push @{$$href{-T_FILE_NAMES}}, $line; } if( -B $dir.$line and not -d $dir.$line) { $$href{-NUM_BINARY_FILES}++; push @{$$href{-B_FILE_NAMES}}, $line; } if( -d $dir.$line ) { $$href{-NUM_DIRS}++; push @{$$href{-DIR_NAMES}}, $line; } } close $PIPE; if( $print) { printf( "\n%4d %s\n", $$href{-TOTAL}, "total files+dirs in $dir"); printf( "%4d %s\n", $$href{-NUM_TEXT_FILES}, "text files"); printf( "%4d %s\n", $$href{-NUM_BINARY_FILES}, "binary files"); printf( "%4d %s\n", $$href{-NUM_DIRS}, "directories"); } } =head2 file_info Title : file_info Purpose : Obtains a variety of date for a given file. : Provides an interface to Perl's stat(). Status : Under development. Not ready. Don't use! =cut #-------------- sub file_info { #-------------- my ($self, %param) = @_; my ($file, $get, $fmt) = $self->_rearrange([qw(FILE GET FMT)], %param); $get ||= 'all'; $fmt ||= 'yyyy-mm-dd'; my($dev, $ino, $mode, $nlink, $uid, $gid, $rdev, $size, $atime, $mtime, $ctime, $blksize, $blocks) = stat $file; if($get =~ /date/i) { ## I can get the elapsed time since the file was modified but ## it's not so straightforward to get the date in a nice format... ## Think about using a standard CPAN module for this, like ## Date::Manip or Date::DateCalc. my $date = $mtime; my $elsec = time - $mtime; printf "\nFile age: %.0f sec %.0f hrs %.0f days", $elsec, $elsec/3600, $elsec/(3600*24);; my $days = sprintf "%.0f", $elsec/(3600*24); } elsif($get eq 'all') { return stat $file; } } =head2 delete Title : delete Purpose : =cut #------------ sub delete { #------------ my $self = shift; my $fileName = shift; if(not -e $fileName) { $self->throw("Could not delete file '$fileName': Does not exist."); } elsif(not -o $fileName) { $self->throw("Could not delete file '$fileName': Not owner."); } my $ulval = unlink($fileName) > 0 or $self->throw("Failed to delete file '$fileName': $!"); } =head2 create_filehandle Usage : $object->create_filehandle(); Purpose : Create a FileHandle object from a file or STDIN. : Mainly used as a helper method by read() and get_newline(). Example : $data = $object->create_filehandle(-FILE =>'usr/people/me/data.txt') Argument : Named parameters (case-insensitive): : (all optional) : -CLIENT => object reference for the object submitting : the request. Default = $Util. : -FILE => string (full path to file) or a reference : to a FileHandle object or typeglob. This is an : optional parameter (if not defined, STDIN is used). Returns : Reference to a FileHandle object. Throws : Exception if cannot open a supplied file or if supplied with a : reference that is not a FileHandle ref. Comments : If given a FileHandle reference, this method simply returns it. : This method assumes the user wants to read ascii data. So, if : the file is binary, it will be treated as a compressed (gzipped) : file and access it using gzip -ce. The problem here is that not : all binary files are necessarily compressed. Therefore, : this method should probably have a -mode parameter to : specify ascii or binary. See Also : L =cut #--------------------- sub create_filehandle { #--------------------- my($self, @param) = @_; my($client, $file, $handle) = $self->_rearrange([qw( CLIENT FILE HANDLE )], @param); if(not ref $client) { $client = $self; } $file ||= $handle; if( $client->can('file')) { $file = $client->file($file); } my $FH; my ($handle_ref); if($handle_ref = ref($file)) { if($handle_ref eq 'FileHandle') { $FH = $file; $client->{'_input_type'} = "FileHandle"; } elsif($handle_ref eq 'GLOB') { $FH = $file; $client->{'_input_type'} = "Glob"; } else { $self->throw(-class => 'Bio::Root::IOException', -text => "Could not read file '$file': Not a FileHandle or GLOB ref."); } $self->verbose > 0 and printf STDERR "$ID: reading data from FileHandle\n"; } elsif($file) { $client->{'_input_type'} = "FileHandle for $file"; # Use gzip -cd to access compressed data. if( -B $file ) { $client->{'_input_type'} .= " (compressed)"; my $gzip = $self->find_exe('gzip'); $file = "$gzip -cd $file |" } require FileHandle; $FH = FileHandle->new(); open ($FH, $file) || $self->throw(-class=>'Bio::Root::FileOpenException', -text =>"Could not access data file '$file': $!"); $self->verbose > 0 and printf STDERR "$ID: reading data from file '$file'\n"; } else { # Read from STDIN. $FH = \*STDIN; $self->verbose > 0 and printf STDERR "$ID: reading data from STDIN\n"; $client->{'_input_type'} = "STDIN"; } return $FH; } =head2 get_newline Usage : $object->get_newline(); Purpose : Determine the character(s) used for newlines in a given file or : input stream. Delegates to Bio::Root::Utilities::get_newline() Example : $data = $object->get_newline(-CLIENT => $anObj, : -FILE =>'usr/people/me/data.txt') Argument : Same arguemnts as for create_filehandle(). Returns : Reference to a FileHandle object. Throws : Propagates any exceptions thrown by Bio::Root::Utilities::get_newline(). See Also : L, L =cut #----------------- sub get_newline { #----------------- my($self, @param) = @_; return $NEWLINE if defined $NEWLINE; my($client ) = $self->_rearrange([qw( CLIENT )], @param); my $FH = $self->create_filehandle(@param); if(not ref $client) { $client = $self; } if($client->{'_input_type'} =~ /STDIN|Glob|compressed/) { # Can't taste from STDIN since we can't seek 0 on it. # Are other non special Glob refs seek-able? # Attempt to guess newline based on platform. # Not robust since we could be reading Unix files on a Mac, e.g. if(defined $ENV{'MACPERL'}) { $NEWLINE = "\015"; # \r } else { $NEWLINE = "\012"; # \n } } else { $NEWLINE = $self->taste_file($FH); } close ($FH) unless ($client->{'_input_type'} eq 'STDIN' || $client->{'_input_type'} eq 'FileHandle' || $client->{'_input_type'} eq 'Glob' ); delete $client->{'_input_type'}; return $NEWLINE || $DEFAULT_NEWLINE; } =head2 taste_file Usage : $object->taste_file( ); : Mainly a utility method for get_newline(). Purpose : Sample a filehandle to determine the character(s) used for a newline. Example : $char = $Util->taste_file($FH) Argument : Reference to a FileHandle object. Returns : String containing an octal represenation of the newline character string. : Unix = "\012" ("\n") : Win32 = "\012\015" ("\r\n") : Mac = "\015" ("\r") Throws : Exception if no input is read within $TIMEOUT_SECS seconds. : Exception if argument is not FileHandle object reference. : Warning if cannot determine neewline char(s). Comments : Based on code submitted by Vicki Brown (vlb@deltagen.com). See Also : L =cut #--------------- sub taste_file { #--------------- my ($self, $FH) = @_; my $BUFSIZ = 256; # Number of bytes read from the file handle. my ($buffer, $octal, $str, $irs, $i); ref($FH) eq 'FileHandle' or $self->throw("Can't taste file: not a FileHandle ref"); $buffer = ''; # this is a quick hack to check for availability of alarm(); just copied # from Bio/Root/IOManager.pm HL 02/19/01 my $alarm_available = 1; eval { alarm(0); }; if($@) { # alarm() not available (ActiveState perl for win32 doesn't have it. # See jitterbug PR#98) $alarm_available = 0; } $SIG{ALRM} = sub { die "Timed out!"; }; my $result; eval { $alarm_available && alarm( $TIMEOUT_SECS ); $result = read($FH, $buffer, $BUFSIZ); # read the $BUFSIZ characters of file $alarm_available && alarm(0); }; if($@ =~ /Timed out!/) { $self->throw( "Timed out while waiting for input.", "Timeout period = $TIMEOUT_SECS seconds.\n" ."For longer time before timing out, edit \$TIMEOUT_SECS in Bio::Root::Utilities.pm."); } elsif(not $result) { my $err = $@; $self->throw("read taste failed to read from FileHandle.", $err); } elsif($@ =~ /\S/) { my $err = $@; $self->throw("Unexpected error during read: $err"); } seek($FH, 0, 0) or $self->throw("seek failed to seek 0 on FileHandle."); my @chars = split(//, $buffer); my $flavor; for ($i = 0; $i <$BUFSIZ; $i++) { if (($chars[$i] eq "\012")) { unless ($chars[$i-1] eq "\015") { $flavor='Unix'; $octal = "\012"; $str = '\n'; $irs = "^J"; last; } } elsif (($chars[$i] eq "\015") && ($chars[$i+1] eq "\012")) { $flavor='DOS'; $octal = "\015\012"; $str = '\r\n'; $irs = "^M^J"; last; } elsif (($chars[$i] eq "\015")) { $flavor='Mac'; $octal = "\015"; $str = '\r'; $irs = "^M"; last; } } if (not $octal) { $self->warn("Could not determine newline char. Using '\012'"); $octal = "\012"; } else { #print STDERR "FLAVOR=$flavor, NEWLINE CHAR = $irs\n"; } return($octal); } =head2 file_flavor Usage : $object->file_flavor( ); Purpose : Returns the 'flavor' of a given file (unix, dos, mac) Example : print "$file has flavor: ", $Util->file_flavor($file); Argument : filename = string, full path name for file Returns : String describing flavor of file and handy info about line endings. : One of these is returned: : unix (\n or 012 or ^J) : dos (\r\n or 015,012 or ^M^J) : mac (\r or 015 or ^M) : unknown Throws : Exception if argument is not a file : Propagates any exceptions thrown by Bio::Root::Utilities::get_newline(). See Also : L, L =cut #--------------- sub file_flavor { #--------------- my ($self, $file) = @_; my %flavors=("\012" =>'unix (\n or 012 or ^J)', "\015\012" =>'dos (\r\n or 015,012 or ^M^J)', "\015" =>'mac (\r or 015 or ^M)' ); -f $file or $self->throw("Could not determine flavor: arg '$file' is either non existant or is not a file.\n"); my $octal = $self->get_newline($file); my $flavor = $flavors{$octal} || "unknown"; return $flavor; } ###################################### ##### Mail Functions ######## ###################################### =head2 mail_authority Title : mail_authority Usage : $Util->mail_authority( $message ) Purpose : Syntactic sugar to send email to $Bio::Root::Global::AUTHORITY See Also : L =cut #--------------- sub mail_authority { #--------------- my( $self, $message ) = @_; my $script = $self->untaint($0,1); my $email = $self->{'_auth_email'} || $AUTHORITY; if (defined $email) { $self->send_mail( -TO=>$AUTHORITY, -SUBJ=>$script, -MSG=>$message); } else { $self->throw("Can't email authority. No email defined."); } } =head2 authority Title : authority Usage : $Util->authority('admin@example.com'); Purpose : Set/get the email address that should be notified by mail_authority() See Also : L =cut #------------- sub authority { #------------- my( $self, $email ) = @_; $self->{'_auth_email'} = $email if defined $email; return $self->{'_auth_email'}; } =head2 send_mail Title : send_mail Usage : $Util->send_mail( named_parameters ) Purpose : Provides an interface to mail or sendmail, if available Returns : n/a Argument : Named parameters: (case-insensitive) : -TO => e-mail address to send to : -SUBJ => subject for message (optional) : -MSG => message to be sent (optional) : -CC => cc: e-mail address (optional) Thows : Exception if TO: address appears bad or is missing. : Exception if mail cannot be sent. Comments : Based on TomC's tip at: : http://www.perl.com/CPAN/doc/FMTEYEWTK/safe_shellings : : Using default 'From:' information. : sendmail options used: : -t: ignore the address given on the command line and : get To:address from the e-mail header. : -oi: prevents send_mail from ending the message if it : finds a period at the start of a line. See Also : L =cut #------------- sub send_mail { #------------- my( $self, @param) = @_; my($recipient,$subj,$message,$cc) = $self->_rearrange([qw(TO SUBJ MSG CC)],@param); $self->throw("Invalid or missing e-mail address: $recipient") if not $recipient =~ /\S+\@\S+/; $subj ||= 'empty subject'; $message ||= ''; # Best to use mail rather than sendmail. Permissions on sendmail in # linux distros have been significantly locked down in recent years, # due to the perception that it is insecure. my ($exe, $ccinfo); if ($exe = $self->find_exe('mail')) { if (defined $cc) { $ccinfo = "-c $cc"; } $self->debug("send_mail: $exe -s '$subj' $ccinfo $recipient\n"); open (MAIL, "| $exe -s '$subj' $ccinfo $recipient") || $self->throw("Can't send email: mail cannot fork: $!"); print MAIL <warn("mail didn't exit nicely: $?"); close(MAIL); } elsif ($exe = $self->find_exe('sendmail')) { open (SENDMAIL, "| $exe -oi -t") || $self->throw("Can't send email: sendmail cannot fork: $!"); print SENDMAIL <warn("sendmail didn't exit nicely: $?"); close(SENDMAIL); } else { $self->throw("Can't find executable for mail or sendmail."); } } =head2 find_exe Title : find_exe Usage : $Util->find_exe(name); Purpose : Locate an executable (for use in a system() call, e.g.)) Example : $Util->find_exe("gzip"); Returns : String containing executable that passes the -x test. Returns undef if an executable of the supplied name cannot be found. Argument : Name of executable to be found. : Can be a full path. If supplied name is not executable, an executable : of that name will be searched in all directories in the currently : defined PATH environment variable. Throws : No exceptions, but issues a warning if multiple paths are found : for a given name. The first one is used. Comments : TODO: Confirm functionality on all bioperl-supported platforms. May get tripped up by variation in path separator character used for splitting ENV{PATH}. See Also : =cut #------------ sub find_exe { #------------ my ($self, $name) = @_; my @bindirs; if ($^O =~ m/mswin/i) { @bindirs = split ';', $ENV{'PATH'}; # Add usual executable extension if missing or -x won't work $name.= '.exe' if ($name !~ m/\.exe$/i); } else { @bindirs = split ':', $ENV{'PATH'}; } my $exe = $name; unless (-x $exe) { undef $exe; my @exes; foreach my $d (@bindirs) { # Note: Windows also understand '/' as folder separator, # so there is no need to use a conditional with '\' push(@exes, "$d/$name") if -x "$d/$name"; } if (scalar @exes) { $exe = $exes[0]; if (defined $exes[1]) { $self->warn("find_exe: Multiple paths to '$name' found. Using $exe."); } } } return $exe; } ###################################### ### Interactive Functions ##### ###################################### =head2 yes_reply Title : yes_reply() Usage : $Util->yes_reply( [query_string]); Purpose : To test an STDIN input value for affirmation. Example : print +( $Util->yes_reply('Are you ok') ? "great!\n" : "sorry.\n" ); : $Util->yes_reply('Continue') || die; Returns : Boolean, true (1) if input string begins with 'y' or 'Y' Argument: query_string = string to be used to prompt user (optional) : If not provided, 'Yes or no' will be used. : Question mark is automatically appended. =cut #------------- sub yes_reply { #------------- my $self = shift; my $query = shift; my $reply; $query ||= 'Yes or no'; print "\n$query? (y/n) [n] "; chomp( $reply = ); $reply =~ /^y/i; } =head2 request_data Title : request_data() Usage : $Util->request_data( [value_name]); Purpose : To request data from a user to be entered via keyboard (STDIN). Example : $name = $Util->request_data('Name'); : # User will see: % Enter Name: Returns : String, (data entered from keyboard, sans terminal newline.) Argument: value_name = string to be used to prompt user. : If not provided, 'data' will be used, (not very helpful). : Question mark is automatically appended. =cut #---------------- sub request_data { #---------------- my $self = shift; my $data = shift || 'data'; print "Enter $data: "; # Remove the terminal newline char. chomp($data = ); $data; } =head2 quit_reply Title : quit_reply Usage : Purpose : =cut sub quit_reply { # Not much used since you can use request_data() # and test for an empty string. my $self = shift; my $reply; chop( $reply = ); $reply =~ /^q.*/i; } =head2 verify_version Purpose : Checks the version of Perl used to invoke the script. : Aborts program if version is less than the given argument. Usage : verify_version('5.000') =cut #------------------ sub verify_version { #------------------ my $self = shift; my $reqVersion = shift; $] < $reqVersion and do { printf STDERR ( "\a\n%s %0.3f.\n", "** Sorry. This Perl script requires at least version", $reqVersion); printf STDERR ( "%s %0.3f %s\n\n", "You are running Perl version", $], "Please update your Perl!\n\n" ); exit(1); } } 1; __END__ BioPerl-1.007002/Bio/Root/Version.pm000444000766000024 237413155576320 17140 0ustar00cjfieldsstaff000000000000package Bio::Root::Version; use strict; =head1 SYNOPSIS package Bio::Tools::NiftyFeature; require Bio::Root::RootI; # later, in client code: package main; use Bio::Tools::NiftyFeature 3.14; ## alternative usage: NiftyFeature defines own $VERSION: package Bio::Tools::NiftyFeature; my $VERSION = 9.8; # later in client code: package main; # ensure we're using an up-to-date BioPerl distribution use Bio::Perl 3.14; # NiftyFeature has its own versioning scheme: use Bio::Tools::NiftyFeature 9.8; =head1 DESCRIPTION This module provides a mechanism by which all other BioPerl modules can share the same $VERSION, without manually synchronizing each file. Bio::Root::RootI itself uses this module, so any module that directly (or indirectly) uses Bio::Root::RootI will get a global $VERSION variable set if it's not already. =head1 AUTHOR Aaron Mackey =cut our $VERSION = '1.007002'; sub import { # try to handle multiple levels of inheritance: my $i = 0; my $pkg = caller($i); no strict 'refs'; while ($pkg) { if ( $pkg =~ m/^Bio::/o and not defined ${$pkg . "::VERSION"} ) { ${$pkg . "::VERSION"} = $VERSION; } $pkg = caller(++$i); } } 1; __END__ BioPerl-1.007002/Bio/Search000755000766000024 013155576320 15274 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Search/BlastStatistics.pm000555000766000024 604213155576320 21114 0ustar00cjfieldsstaff000000000000# # # BioPerl module for wrapping Blast statistics # # Please direct questions and support issues to # # Cared for by Chad Matsalla (bioinformatics1 at dieselwurks dot com) # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::BlastStatistics - An object for Blast statistics =head1 SYNOPSIS # this is a wrapper to hold the statistics from a Blast report my $bs = $result->get_statistics(); # you can get a statistic generically, like this: my $kappa = $bs->get_statistic("kappa"); # or specifically, like this: my $kappa2 = $bs->get_kappa(); =head1 DESCRIPTION This is a basic container to hold the statistics returned from a Blast. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics1 at dieselwurks dot com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::BlastStatistics; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::RootI Bio::Search::StatisticsI); sub new { my ($class, @args) = @_; # really, don't bother with any initial initialization my $self = $class->SUPER::new(@args); return $self; } =head2 get_statistic Title : get_statistic Usage : $statistic_object->get_statistic($statistic_name); Function: Get the value of a statistic named $statistic_name Returns : A scalar that should be a string Args : A scalar that should be a string =cut sub get_statistic { my ($self,$arg) = @_; return $self->{$arg}; } =head2 set_statistic Title : set_statistic Usage : $statistic_object->set_statistic($statistic_name => $statistic_value); Function: Set the value of a statistic named $statistic_name to $statistic_value Returns : Void Args : A hash containing name=>value pairs =cut sub set_statistic { my ($self,%args) = @_; foreach (keys %args) { $self->{$_} = $args{$_}; } } 1; BioPerl-1.007002/Bio/Search/BlastUtils.pm000444000766000024 4660113155576320 20104 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::Search::BlastUtils - Utility functions for Bio::Search:: BLAST objects =head1 SYNOPSIS # This module is just a collection of subroutines, not an object. See L. =head1 DESCRIPTION The BlastUtils.pm module is a collection of subroutines used primarily by Bio::Search::Hit::BlastHit objects for some of the additional functionality, such as HSP tiling. Right now, the BlastUtils is just a collection of methods, not an object, and it's tightly coupled to Bio::Search::Hit::BlastHit. A goal for the future is to generalize it to work based on the Bio::Search interfaces, then it can work with any objects that implements them. =head1 AUTHOR Steve Chervitz Esac@bioperl.orgE =cut #' package Bio::Search::BlastUtils; use Bio::Root::Version; =head2 tile_hsps Usage : tile_hsps( $sbjct ); : This is called automatically by Bio::Search::Hit::BlastHit : during object construction or : as needed by methods that rely on having tiled data. Purpose : Collect statistics about the aligned sequences in a set of HSPs. : Calculates the following data across all HSPs: : -- total alignment length : -- total identical residues : -- total conserved residues Returns : n/a Argument : A Bio::Search::Hit::BlastHit object Throws : n/a Comments : : This method is *strongly* coupled to Bio::Search::Hit::BlastHit : (it accesses BlastHit data members directly). : TODO: Re-write this to the Bio::Search::Hit::HitI interface. : : This method performs more careful summing of data across : all HSPs in the Sbjct object. Only HSPs that are in the same strand : and frame are tiled. Simply summing the data from all HSPs : in the same strand and frame will overestimate the actual : length of the alignment if there is overlap between different HSPs : (often the case). : : The strategy is to tile the HSPs and sum over the : contigs, collecting data separately from overlapping and : non-overlapping regions of each HSP. To facilitate this, the : HSP.pm object now permits extraction of data from sub-sections : of an HSP. : : Additional useful information is collected from the results : of the tiling. It is possible that sub-sequences in : different HSPs will overlap significantly. In this case, it : is impossible to create a single unambiguous alignment by : concatenating the HSPs. The ambiguity may indicate the : presence of multiple, similar domains in one or both of the : aligned sequences. This ambiguity is recorded using the : ambiguous_aln() method. : : This method does not attempt to discern biologically : significant vs. insignificant overlaps. The allowable amount of : overlap can be set with the overlap() method or with the -OVERLAP : parameter used when constructing the Blast & Sbjct objects. : : For a given hit, both the query and the sbjct sequences are : tiled independently. : : -- If only query sequence HSPs overlap, : this may suggest multiple domains in the sbjct. : -- If only sbjct sequence HSPs overlap, : this may suggest multiple domains in the query. : -- If both query & sbjct sequence HSPs overlap, : this suggests multiple domains in both. : -- If neither query & sbjct sequence HSPs overlap, : this suggests either no multiple domains in either : sequence OR that both sequences have the same : distribution of multiple similar domains. : : This method can deal with the special case of when multiple : HSPs exactly overlap. : : Efficiency concerns: : Speed will be an issue for sequences with numerous HSPs. : Bugs : Currently, tile_hsps() does not properly account for : the number of non-tiled but overlapping HSPs, which becomes a problem : as overlap() grows. Large values overlap() may thus lead to : incorrect statistics for some hits. For best results, keep overlap() : below 5 (DEFAULT IS 2). For more about this, see the "HSP Tiling and : Ambiguous Alignments" section in L. See Also : L<_adjust_contigs>(), L =cut #-------------- sub tile_hsps { #-------------- my $sbjct = shift; $sbjct->{'_tile_hsps'} = 1; $sbjct->{'_gaps_query'} = 0; $sbjct->{'_gaps_sbjct'} = 0; ## Simple summation scheme. Valid if there is only one HSP. if((defined($sbjct->{'_n'}) and $sbjct->{'_n'} == 1) or $sbjct->num_hsps == 1) { my $hsp = $sbjct->hsp; $sbjct->{'_length_aln_query'} = $hsp->length('query'); $sbjct->{'_length_aln_sbjct'} = $hsp->length('sbjct'); $sbjct->{'_length_aln_total'} = $hsp->length('total'); ($sbjct->{'_totalIdentical'},$sbjct->{'_totalConserved'}) = $hsp->matches(); $sbjct->{'_gaps_query'} = $hsp->gaps('query'); $sbjct->{'_gaps_sbjct'} = $hsp->gaps('sbjct'); # print "_tile_hsps(): single HSP, easy stats.\n"; return; } else { # print STDERR "Sbjct: _tile_hsps: summing multiple HSPs\n"; $sbjct->{'_length_aln_query'} = 0; $sbjct->{'_length_aln_sbjct'} = 0; $sbjct->{'_length_aln_total'} = 0; $sbjct->{'_totalIdentical'} = 0; $sbjct->{'_totalConserved'} = 0; } ## More than one HSP. Must tile HSPs. # print "\nTiling HSPs for $sbjct\n"; my($hsp, $qstart, $qstop, $sstart, $sstop); my($frame, $strand, $qstrand, $sstrand); my(@qcontigs, @scontigs); my $qoverlap = 0; my $soverlap = 0; my $max_overlap = $sbjct->{'_overlap'}; foreach $hsp ($sbjct->hsps()) { # printf " HSP: %s\n%s\n",$hsp->name, $hsp->str('query'); # printf " Length = %d; Identical = %d; Conserved = %d; Conserved(1-10): %d",$hsp->length, $hsp->length(-TYPE=>'iden'), $hsp->length(-TYPE=>'cons'), $hsp->length(-TYPE=>'cons',-START=>0,-STOP=>10); ($qstart, $qstop) = $hsp->range('query'); ($sstart, $sstop) = $hsp->range('sbjct'); $frame = $hsp->frame('hit'); $frame = -1 unless defined $frame; ($qstrand, $sstrand) = $hsp->strand; my ($qgaps, $sgaps) = $hsp->gaps(); $sbjct->{'_gaps_query'} += $qgaps; $sbjct->{'_gaps_sbjct'} += $sgaps; $sbjct->{'_length_aln_total'} += $hsp->length; ## Collect contigs in the query sequence. $qoverlap = &_adjust_contigs('query', $hsp, $qstart, $qstop, \@qcontigs, $max_overlap, $frame, $qstrand); ## Collect contigs in the sbjct sequence (needed for domain data and gapped Blast). $soverlap = &_adjust_contigs('sbjct', $hsp, $sstart, $sstop, \@scontigs, $max_overlap, $frame, $sstrand); ## Collect overall start and stop data for query and sbjct over all HSPs. if(not defined $sbjct->{'_queryStart'}) { $sbjct->{'_queryStart'} = $qstart; $sbjct->{'_queryStop'} = $qstop; $sbjct->{'_sbjctStart'} = $sstart; $sbjct->{'_sbjctStop'} = $sstop; } else { $sbjct->{'_queryStart'} = ($qstart < $sbjct->{'_queryStart'} ? $qstart : $sbjct->{'_queryStart'}); $sbjct->{'_queryStop'} = ($qstop > $sbjct->{'_queryStop'} ? $qstop : $sbjct->{'_queryStop'}); $sbjct->{'_sbjctStart'} = ($sstart < $sbjct->{'_sbjctStart'} ? $sstart : $sbjct->{'_sbjctStart'}); $sbjct->{'_sbjctStop'} = ($sstop > $sbjct->{'_sbjctStop'} ? $sstop : $sbjct->{'_sbjctStop'}); } } ## Collect data across the collected contigs. # print "\nQUERY CONTIGS:\n"; # print " gaps = $sbjct->{'_gaps_query'}\n"; # TODO: Account for strand/frame issue! # Strategy: collect data on a per strand+frame basis and save the most significant one. my (%qctg_dat); foreach(@qcontigs) { # print " query contig: $_->{'start'} - $_->{'stop'}\n"; # print " iden = $_->{'iden'}; cons = $_->{'cons'}\n"; ($frame, $strand) = ($_->{'frame'}, $_->{'strand'}); $qctg_dat{ "$frame$strand" }->{'length_aln_query'} += $_->{'stop'} - $_->{'start'} + 1; $qctg_dat{ "$frame$strand" }->{'totalIdentical'} += $_->{'iden'}; $qctg_dat{ "$frame$strand" }->{'totalConserved'} += $_->{'cons'}; $qctg_dat{ "$frame$strand" }->{'qstrand'} = $strand; } # Find longest contig. my @sortedkeys = reverse sort { $qctg_dat{ $a }->{'length_aln_query'} <=> $qctg_dat{ $b }->{'length_aln_query'} } keys %qctg_dat; # Save the largest to the sbjct: my $longest = $sortedkeys[0]; $sbjct->{'_length_aln_query'} = $qctg_dat{ $longest }->{'length_aln_query'}; $sbjct->{'_totalIdentical'} = $qctg_dat{ $longest }->{'totalIdentical'}; $sbjct->{'_totalConserved'} = $qctg_dat{ $longest }->{'totalConserved'}; $sbjct->{'_qstrand'} = $qctg_dat{ $longest }->{'qstrand'}; ## Collect data for sbjct contigs. Important for gapped Blast. ## The totalIdentical and totalConserved numbers will be the same ## as determined for the query contigs. # print "\nSBJCT CONTIGS:\n"; # print " gaps = $sbjct->{'_gaps_sbjct'}\n"; my (%sctg_dat); foreach(@scontigs) { # print " sbjct contig: $_->{'start'} - $_->{'stop'}\n"; # print " iden = $_->{'iden'}; cons = $_->{'cons'}\n"; ($frame, $strand) = ($_->{'frame'}, $_->{'strand'}); $sctg_dat{ "$frame$strand" }->{'length_aln_sbjct'} += $_->{'stop'} - $_->{'start'} + 1; $sctg_dat{ "$frame$strand" }->{'frame'} = $frame; $sctg_dat{ "$frame$strand" }->{'sstrand'} = $strand; } @sortedkeys = reverse sort { $sctg_dat{ $a }->{'length_aln_sbjct'} <=> $sctg_dat{ $b }->{'length_aln_sbjct'} } keys %sctg_dat; # Save the largest to the sbjct: $longest = $sortedkeys[0]; $sbjct->{'_length_aln_sbjct'} = $sctg_dat{ $longest }->{'length_aln_sbjct'}; $sbjct->{'_frame'} = $sctg_dat{ $longest }->{'frame'}; $sbjct->{'_sstrand'} = $sctg_dat{ $longest }->{'sstrand'}; if($qoverlap) { if($soverlap) { $sbjct->ambiguous_aln('qs'); # print "\n*** AMBIGUOUS ALIGNMENT: Query and Sbjct\n\n"; } else { $sbjct->ambiguous_aln('q'); # print "\n*** AMBIGUOUS ALIGNMENT: Query\n\n"; } } elsif($soverlap) { $sbjct->ambiguous_aln('s'); # print "\n*** AMBIGUOUS ALIGNMENT: Sbjct\n\n"; } # Adjust length based on BLAST flavor. my $prog = $sbjct->algorithm; if($prog eq 'TBLASTN') { $sbjct->{'_length_aln_sbjct'} /= 3; } elsif($prog eq 'BLASTX' ) { $sbjct->{'_length_aln_query'} /= 3; } elsif($prog eq 'TBLASTX') { $sbjct->{'_length_aln_query'} /= 3; $sbjct->{'_length_aln_sbjct'} /= 3; } } =head2 _adjust_contigs Usage : n/a; called automatically during object construction. Purpose : Builds HSP contigs for a given BLAST hit. : Utility method called by _tile_hsps() Returns : Argument : Throws : Exceptions propagated from Bio::Search::Hit::BlastHSP::matches() : for invalid sub-sequence ranges. Status : Experimental Comments : This method does not currently support gapped alignments. : Also, it does not keep track of the number of HSPs that : overlap within the amount specified by overlap(). : This will lead to significant tracking errors for large : overlap values. See Also : L(), L =cut #------------------- sub _adjust_contigs { #------------------- my ($seqType, $hsp, $start, $stop, $contigs_ref, $max_overlap, $frame, $strand) = @_; my $overlap = 0; my ($numID, $numCons); # print STDERR "Testing $seqType data: HSP (${\$hsp->name}); $start, $stop, strand=$strand, frame=$frame\n"; foreach(@$contigs_ref) { # print STDERR " Contig: $_->{'start'} - $_->{'stop'}, strand=$_->{'strand'}, frame=$_->{'frame'}, iden= $_->{'iden'}, cons= $_->{'cons'}\n"; # Don't merge things unless they have matching strand/frame. next unless ($_->{'frame'} == $frame and $_->{'strand'} == $strand); ## Test special case of a nested HSP. Skip it. if($start >= $_->{'start'} and $stop <= $_->{'stop'}) { # print STDERR "----> Nested HSP. Skipping.\n"; $overlap = 1; next; } ## Test for overlap at beginning of contig. if($start < $_->{'start'} and $stop > ($_->{'start'} + $max_overlap)) { # print STDERR "----> Overlaps beg: existing beg,end: $_->{'start'},$_->{'stop'}, new beg,end: $start,$stop\n"; # Collect stats over the non-overlapping region. eval { ($numID, $numCons) = $hsp->matches(-SEQ =>$seqType, -START =>$start, -STOP =>$_->{'start'}-1); }; if($@) { warn "\a\n$@\n"; } else { $_->{'start'} = $start; # Assign a new start coordinate to the contig $_->{'iden'} += $numID; # and add new data to #identical, #conserved. $_->{'cons'} += $numCons; $overlap = 1; } } ## Test for overlap at end of contig. if($stop > $_->{'stop'} and $start < ($_->{'stop'} - $max_overlap)) { # print STDERR "----> Overlaps end: existing beg,end: $_->{'start'},$_->{'stop'}, new beg,end: $start,$stop\n"; # Collect stats over the non-overlapping region. eval { ($numID,$numCons) = $hsp->matches(-SEQ =>$seqType, -START =>$_->{'stop'}, -STOP =>$stop); }; if($@) { warn "\a\n$@\n"; } else { $_->{'stop'} = $stop; # Assign a new stop coordinate to the contig $_->{'iden'} += $numID; # and add new data to #identical, #conserved. $_->{'cons'} += $numCons; $overlap = 1; } } $overlap && do { # print STDERR " New Contig data:\n"; # print STDERR " Contig: $_->{'start'} - $_->{'stop'}, iden= $_->{'iden'}, cons= $_->{'cons'}\n"; last; }; } ## If there is no overlap, add the complete HSP data. !$overlap && do { # print STDERR "No overlap. Adding new contig.\n"; ($numID,$numCons) = $hsp->matches(-SEQ=>$seqType); push @$contigs_ref, {'start'=>$start, 'stop'=>$stop, 'iden'=>$numID, 'cons'=>$numCons, 'strand'=>$strand, 'frame'=>$frame}; }; $overlap; } =head2 get_exponent Usage : &get_exponent( number ); Purpose : Determines the power of 10 exponent of an integer, float, : or scientific notation number. Example : &get_exponent("4.0e-206"); : &get_exponent("0.00032"); : &get_exponent("10."); : &get_exponent("1000.0"); : &get_exponent("e+83"); Argument : Float, Integer, or scientific notation number Returns : Integer representing the exponent part of the number (+ or -). : If argument == 0 (zero), return value is "-999". Comments : Exponents are rounded up (less negative) if the mantissa is >= 5. : Exponents are rounded down (more negative) if the mantissa is <= -5. =cut #------------------ sub get_exponent { #------------------ my $data = shift; my($num, $exp) = split /[eE]/, $data; if( defined $exp) { $num = 1 if not $num; $num >= 5 and $exp++; $num <= -5 and $exp--; } elsif( $num == 0) { $exp = -999; } elsif( not $num =~ /\./) { $exp = CORE::length($num) -1; } else { $exp = 0; $num .= '0' if $num =~ /\.$/; my ($c); my $rev = 0; if($num !~ /^0/) { $num = reverse($num); $rev = 1; } do { $c = chop($num); $c == 0 && $exp++; } while( $c ne '.'); $exp = -$exp if $num == 0 and not $rev; $exp -= 1 if $rev; } return $exp; } =head2 collapse_nums Usage : @cnums = collapse_nums( @numbers ); Purpose : Collapses a list of numbers into a set of ranges of consecutive terms: : Useful for condensing long lists of consecutive numbers. : EXPANDED: : 1 2 3 4 5 6 10 12 13 14 15 17 18 20 21 22 24 26 30 31 32 : COLLAPSED: : 1-6 10 12-15 17 18 20-22 24 26 30-32 Argument : List of numbers sorted numerically. Returns : List of numbers mixed with ranges of numbers (see above). Throws : n/a See Also : L =cut #------------------ sub collapse_nums { #------------------ # This is probably not the slickest connectivity algorithm, but will do for now. my @a = @_; my ($from, $to, $i, @ca, $consec); $consec = 0; for($i=0; $i < @a; $i++) { not $from and do{ $from = $a[$i]; next; }; if($a[$i] == $a[$i-1]+1) { $to = $a[$i]; $consec++; } else { if($consec == 1) { $from .= ",$to"; } else { $from .= $consec>1 ? "\-$to" : ""; } push @ca, split(',', $from); $from = $a[$i]; $consec = 0; $to = undef; } } if(defined $to) { if($consec == 1) { $from .= ",$to"; } else { $from .= $consec>1 ? "\-$to" : ""; } } push @ca, split(',', $from) if $from; @ca; } =head2 strip_blast_html Usage : $boolean = &strip_blast_html( string_ref ); : This method is exported. Purpose : Removes HTML formatting from a supplied string. : Attempts to restore the Blast report to enable : parsing by Bio::SearchIO::blast.pm Returns : Boolean: true if string was stripped, false if not. Argument : string_ref = reference to a string containing the whole Blast : report containing HTML formatting. Throws : Croaks if the argument is not a scalar reference. Comments : Based on code originally written by Alex Dong Li : (ali@genet.sickkids.on.ca). : This method does some Blast-specific stripping : (adds back a '>' character in front of each HSP : alignment listing). : : THIS METHOD IS VERY SENSITIVE TO BLAST FORMATTING CHANGES! : : Removal of the HTML tags and accurate reconstitution of the : non-HTML-formatted report is highly dependent on structure of : the HTML-formatted version. For example, it assumes that first : line of each alignment section (HSP listing) starts with a : anchor tag. This permits the reconstruction of the : original report in which these lines begin with a ">". : This is required for parsing. : : If the structure of the Blast report itself is not intended to : be a standard, the structure of the HTML-formatted version : is even less so. Therefore, the use of this method to : reconstitute parsable Blast reports from HTML-format versions : should be considered a temporary solution. =cut #-------------------- sub strip_blast_html { #-------------------- # This may not best way to remove html tags. However, it is simple. # it won't work under following conditions: # 1) if quoted > appears in a tag (does this ever happen?) # 2) if a tag is split over multiple lines and this method is # used to process one line at a time. my ($string_ref) = shift; ref $string_ref eq 'SCALAR' or croak ("Can't strip HTML: ". "Argument is should be a SCALAR reference not a ${\ref $string_ref}\n"); my $str = $$string_ref; my $stripped = 0; # Removing "" and adding the '>' character for # HSP alignment listings. $str =~ s/(\A|\n)]+> ?/>/sgi and $stripped = 1; # Removing all "<>" tags. $str =~ s/<[^>]+>| //sgi and $stripped = 1; # Re-uniting any lone '>' characters. $str =~ s/(\A|\n)>\s+/\n\n>/sgi and $stripped = 1; $$string_ref = $str; $stripped; } 1; BioPerl-1.007002/Bio/Search/DatabaseI.pm000444000766000024 651713155576320 17615 0ustar00cjfieldsstaff000000000000#----------------------------------------------------------------- # # BioPerl module Bio::Search::DatabaseI # # Please direct questions and support issues to # # Cared for by Steve Chervitz # # You may distribute this module under the same terms as perl itself #----------------------------------------------------------------- # POD documentation - main docs before the code =head1 NAME Bio::Search::DatabaseI - Interface for a database used in a sequence search =head1 SYNOPSIS Bio::Search::DatabaseI objects should not be instantiated since this module defines a pure interface. Given an object that implements the Bio::Search::DatabaseI interface, you can do the following things with it: $name = $db->name(); $date = $db->date(); $num_letters = $db->letters(); $num_entries = $db->entries(); =head1 DESCRIPTION This module defines methods for an object that provides metadata information about a database used for sequence searching. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Steve Chervitz Esac@bioperl.orgE See L for where to send bug reports and comments. =head1 COPYRIGHT Copyright (c) 2001 Steve Chervitz. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =cut =head1 APPENDIX The rest of the documentation details each of the object methods. =cut # Let the code begin... package Bio::Search::DatabaseI; use strict; use base qw(Bio::Root::RootI); =head2 name Usage : $name = $db->name(); Purpose : Get the name of the database searched. Returns : String Argument : n/a =cut sub name { my $self = shift; $self->throw_not_implemented; } =head2 date Usage : $date = $db->date(); Purpose : Get the creation date of the queried database. Returns : String Argument : n/a =cut sub date { my $self = shift; $self->throw_not_implemented; } =head2 letters Usage : $num_letters = $db->letters(); Purpose : Get the number of letters in the queried database. Returns : Integer Argument : n/a =cut sub letters { my $self = shift; $self->throw_not_implemented; } =head2 entries Usage : $num_entries = $db->entries(); Purpose : Get the number of entries in the queried database. Returns : Integer Argument : n/a =cut sub entries { my $self = shift; $self->throw_not_implemented; } 1; BioPerl-1.007002/Bio/Search/GenericDatabase.pm000444000766000024 775713155576320 21010 0ustar00cjfieldsstaff000000000000#----------------------------------------------------------------- # # BioPerl module Bio::Search::GenericDatabase # # Please direct questions and support issues to # # Cared for by Steve Chervitz # # You may distribute this module under the same terms as perl itself #----------------------------------------------------------------- # POD documentation - main docs before the code =head1 NAME Bio::Search::GenericDatabase - Generic implementation of Bio::Search::DatabaseI =head1 SYNOPSIS use Bio::Search::GenericDatabase; $db = Bio::Search::GenericDatabase->new( -name => 'my Blast db', -date => '2001-03-13', -length => 2352511, -entries => 250000 ); $name = $db->name(); $date = $db->date(); $num_letters = $db->letters(); $num_entries = $db->entries(); =head1 DESCRIPTION This module provides a basic implementation of L. See documentation in that module for more information. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Steve Chervitz Esac@bioperl.orgE See L for where to send bug reports and comments. =head1 COPYRIGHT Copyright (c) 2001 Steve Chervitz. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =cut =head1 APPENDIX The rest of the documentation details each of the object methods. =cut # Let the code begin... package Bio::Search::GenericDatabase; use strict; use base qw(Bio::Root::Root Bio::Search::DatabaseI); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($name, $date, $length, $ents) = $self->_rearrange( [qw(NAME DATE LENGTH ENTRIES)], @args); $name && $self->name($name); $date && $self->date($date); $length && $self->letters($length); $ents && $self->entries($ents); return $self; } =head2 name See L() for documentation This implementation is a combined set/get accessor. =cut #--------------- sub name { #--------------- my $self = shift; if(@_) { my $name = shift; $name =~ s/(^\s+|\s+$)//g; $self->{'_db'} = $name; } $self->{'_db'}; } =head2 date See L() for documentation This implementation is a combined set/get accessor. =cut #----------------------- sub date { #----------------------- my $self = shift; if(@_) { $self->{'_dbDate'} = shift; } $self->{'_dbDate'}; } =head2 letters See L() for documentation This implementation is a combined set/get accessor. =cut #---------------------- sub letters { #---------------------- my $self = shift; if(@_) { $self->{'_dbLetters'} = shift; } $self->{'_dbLetters'}; } =head2 entries See L() for documentation This implementation is a combined set/get accessor. =cut #------------------ sub entries { #------------------ my $self = shift; if(@_) { $self->{'_dbEntries'} = shift; } $self->{'_dbEntries'}; } 1; BioPerl-1.007002/Bio/Search/GenericStatistics.pm000555000766000024 615113155576320 21424 0ustar00cjfieldsstaff000000000000# # # BioPerl module for wrapping statistics # # Please direct questions and support issues to # # Cared for by Chad Matsalla (bioinformatics1 at dieselwurks dot com) # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::GenericStatistics - An object for statistics =head1 SYNOPSIS my $void = $obj->set_statistic("statistic_name","statistic_value"); my $value = $obj->get_statistic("statistic_name"); =head1 DESCRIPTION This is a basic container to hold the statistics returned from a program. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics1 at dieselwurks dot com =head1 CONTRIBUTORS Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::GenericStatistics; use strict; use base qw(Bio::Root::Root Bio::Search::StatisticsI); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); return $self; } =head2 get_statistic Title : get_statistic Usage : $statistic_object->get_statistic($statistic_name); Function: Get the value of a statistic named $statistic_name Returns : A scalar that should be a string Args : A scalar that should be a string =cut sub get_statistic { my ($self,$arg) = @_; return $self->{stats}->{$arg}; } =head2 set_statistic Title : set_statistic Usage : $statistic_object->set_statistic($statistic_name => $statistic_value); Function: Set the value of a statistic named $statistic_name to $statistic_value Returns : Void Args : A hash containing name=>value pairs =cut sub set_statistic { my ($self,$name,$value) = @_; $self->{stats}->{$name} = $value; } =head2 available_statistics Title : available_statistics Usage : my @statnames = $statistic_object->available_statistics Function: Returns the names of the available statistics Returns : list of available statistic names Args : none =cut sub available_statistics { my $self = shift; return keys %{$self->{stats}}; } 1; BioPerl-1.007002/Bio/Search/Processor.pm000444000766000024 573013155576320 17753 0ustar00cjfieldsstaff000000000000 # # BioPerl module for Bio::Search::Processor # # Please direct questions and support issues to # # Cared for by Aaron Mackey # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Processor - DESCRIPTION of Object =head1 SYNOPSIS Give standard usage here =head1 DESCRIPTION Describe the object here =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Aaron Mackey Email amackey@virginia.edu Describe contact details here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Processor; use strict; use Bio::Root::Version; =head2 new Title : new Usage : $proc = Bio::Search::Processor->new -file => $filename, -algorithm => 'Algorithm' ; Function: Used to specify and initialize a data processor of search algorithm results. Returns : A processor specific to the algorithm type, if it exists. Args : -file => filename -algorithm => algorithm specifier -fh => filehandle to attach to (file or fh required) =cut sub new { my $type = shift; my $proc; my ($module, $load, $algorithm); my %args = @_; exists $args{'-algorithm'} or do { print STDERR "Must supply an algorithm!"; return; }; $algorithm = $args{'-algorithm'} || $args{'-ALGORITHM'}; $module = "_new(@_); return $proc; } 1; BioPerl-1.007002/Bio/Search/SearchUtils.pm000444000766000024 7500613155576320 20245 0ustar00cjfieldsstaff000000000000=head1 NAME Bio::Search::SearchUtils - Utility functions for Bio::Search:: objects =head1 SYNOPSIS # This module is just a collection of subroutines, not an object. =head1 DESCRIPTION The SearchUtils.pm module is a collection of subroutines used primarily by Bio::Search::Hit::HitI objects for some of the additional functionality, such as HSP tiling. Right now, the SearchUtils is just a collection of methods, not an object. =head1 AUTHOR Steve Chervitz Esac@bioperl.orgE =head1 CONTRIBUTORS Sendu Bala, bix@sendu.me.uk =cut package Bio::Search::SearchUtils; use Bio::Root::Version; use strict; =head2 tile_hsps Usage : tile_hsps( $sbjct ); : This is called automatically by methods in Bio::Search::Hit::GenericHit : that rely on having tiled data. : : If you are interested in getting data about the constructed HSP contigs: : my ($qcontigs, $scontigs) = Bio::Search::SearchUtils::tile_hsps($hit); : if (ref $qcontigs) { : print STDERR "Query contigs:\n"; : foreach (@{$qcontigs}) { : print "contig start is $_->{'start'}\n"; : print "contig stop is $_->{'stop'}\n"; : } : } : See below for more information about the contig data structure. : Purpose : Collect statistics about the aligned sequences in a set of HSPs. : Calculates the following data across all HSPs: : -- total alignment length : -- total identical residues : -- total conserved residues Returns : If there was only a single HSP (so no tiling was necessary) tile_hsps() returns a list of two non-zero integers. If there were multiple HSP, tile_hsps() returns a list of two array references containin HSP contig data. The first array ref contains a list of HSP contigs on the query sequence. The second array ref contains a list of HSP contigs on the subject sequence. Each contig is a hash reference with the following data fields: 'start' => start coordinate of the contig 'stop' => start coordinate of the contig 'iden' => number of identical residues in the contig 'cons' => number of conserved residues in the contig 'strand'=> strand of the contig 'frame' => frame of the contig Argument : A Bio::Search::Hit::HitI object Throws : n/a Comments : : This method performs more careful summing of data across : all HSPs in the Sbjct object. Only HSPs that are in the same strand : and frame are tiled. Simply summing the data from all HSPs : in the same strand and frame will overestimate the actual : length of the alignment if there is overlap between different HSPs : (often the case). : : The strategy is to tile the HSPs and sum over the : contigs, collecting data separately from overlapping and : non-overlapping regions of each HSP. To facilitate this, the : HSP.pm object now permits extraction of data from sub-sections : of an HSP. : : Additional useful information is collected from the results : of the tiling. It is possible that sub-sequences in : different HSPs will overlap significantly. In this case, it : is impossible to create a single unambiguous alignment by : concatenating the HSPs. The ambiguity may indicate the : presence of multiple, similar domains in one or both of the : aligned sequences. This ambiguity is recorded using the : ambiguous_aln() method. : : This method does not attempt to discern biologically : significant vs. insignificant overlaps. The allowable amount of : overlap can be set with the overlap() method or with the -OVERLAP : parameter used when constructing the Hit object. : : For a given hit, both the query and the sbjct sequences are : tiled independently. : : -- If only query sequence HSPs overlap, : this may suggest multiple domains in the sbjct. : -- If only sbjct sequence HSPs overlap, : this may suggest multiple domains in the query. : -- If both query & sbjct sequence HSPs overlap, : this suggests multiple domains in both. : -- If neither query & sbjct sequence HSPs overlap, : this suggests either no multiple domains in either : sequence OR that both sequences have the same : distribution of multiple similar domains. : : This method can deal with the special case of when multiple : HSPs exactly overlap. : : Efficiency concerns: : Speed will be an issue for sequences with numerous HSPs. : Bugs : Currently, tile_hsps() does not properly account for : the number of non-tiled but overlapping HSPs, which becomes a problem : as overlap() grows. Large values overlap() may thus lead to : incorrect statistics for some hits. For best results, keep overlap() : below 5 (DEFAULT IS 2). For more about this, see the "HSP Tiling and : Ambiguous Alignments" section in L. See Also : L<_adjust_contigs>(), L =cut #-------------- sub tile_hsps { #-------------- my $sbjct = shift; #print STDERR "Calling tile_hsps(): $sbjct\n"; #$sbjct->verbose(1); # to activate debugging $sbjct->tiled_hsps(1); # changed to not rely on n() (which is unreliable here) --cjfields 4/6/10 if( $sbjct->num_hsps == 0) { #print STDERR "_tile_hsps(): no hsps, nothing to tile! (", $sbjct->num_hsps, ")\n"; _warn_about_no_hsps($sbjct); return (undef, undef); } elsif($sbjct->num_hsps == 1) { ## Simple summation scheme. Valid if there is only one HSP. #print STDERR "_tile_hsps(): single HSP, easy stats.\n"; my $hsp = $sbjct->hsp; $sbjct->length_aln('query', $hsp->length('query')); $sbjct->length_aln('hit', $hsp->length('sbjct')); $sbjct->length_aln('total', $hsp->length('total')); $sbjct->matches( $hsp->matches() ); $sbjct->gaps('query', $hsp->gaps('query')); $sbjct->gaps('sbjct', $hsp->gaps('sbjct')); _adjust_length_aln($sbjct); return (1, 1); } else { #print STDERR "Sbjct: _tile_hsps: summing multiple HSPs\n"; $sbjct->length_aln('query', 0); $sbjct->length_aln('sbjct', 0); $sbjct->length_aln('total', 0); $sbjct->matches( 0, 0); $sbjct->gaps('query', 0); $sbjct->gaps('hit', 0); } ## More than one HSP. Must tile HSPs. # print "\nTiling HSPs for $sbjct\n"; my($hsp, $qstart, $qstop, $sstart, $sstop); my($frame, $strand, $qstrand, $sstrand); my(@qcontigs, @scontigs); my $qoverlap = 0; my $soverlap = 0; my $max_overlap = $sbjct->overlap; my $hit_qgaps = 0; my $hit_sgaps = 0; my $hit_len_aln = 0; my %start_stop; my $v = $sbjct->verbose; foreach $hsp ( $sbjct->hsps() ) { #$sbjct->debug( sprintf(" HSP: %s %d..%d\n",$hsp->query->seq_id, $hsp->query->start, $hsp->hit->end)) if $v > 0; #$hsp->str('query'); # printf " Length = %d; Identical = %d; Conserved = %d; Conserved(1-10): %d",$hsp->length, $hsp->length(-TYPE=>'iden'), # $hsp->length(-TYPE=>'cons'), # $hsp->length(-TYPE=>'cons', # -START=>0,-STOP=>10); ($qstart, $qstop) = $hsp->range('query'); ($sstart, $sstop) = $hsp->range('sbjct'); $frame = $hsp->frame('hit'); $frame = -1 unless defined $frame; ($qstrand, $sstrand) = ($hsp->query->strand, $hsp->hit->strand); # Note: No correction for overlap. my ($qgaps, $sgaps) = ($hsp->gaps('query'), $hsp->gaps('hit')); $hit_qgaps += $qgaps; $hit_sgaps += $sgaps; $hit_len_aln += $hsp->length; ## Collect contigs in the query sequence. $qoverlap += &_adjust_contigs('query', $hsp, $qstart, $qstop, \@qcontigs, $max_overlap, $frame, $qstrand); ## Collect contigs in the sbjct sequence # (needed for domain data and gapped Blast). $soverlap += &_adjust_contigs('sbjct', $hsp, $sstart, $sstop, \@scontigs, $max_overlap, $frame, $sstrand); ## Collect overall start and stop data for query and # sbjct over all HSPs. unless ( defined $start_stop{'qstart'} ) { $start_stop{'qstart'} = $qstart; $start_stop{'qstop'} = $qstop; $start_stop{'sstart'} = $sstart; $start_stop{'sstop'} = $sstop; } else { $start_stop{'qstart'} = ($qstart < $start_stop{'qstart'} ? $qstart : $start_stop{'qstart'} ); $start_stop{'qstop'} = ($qstop > $start_stop{'qstop'} ? $qstop : $start_stop{'qstop'} ); $start_stop{'sstart'} = ($sstart < $start_stop{'sstart'} ? $sstart : $start_stop{'sstart'} ); $start_stop{'sstop'} = ($sstop > $start_stop{'sstop'} ? $sstop : $start_stop{'sstop'} ); } } # Store the collected data in the Hit object $sbjct->gaps('query', $hit_qgaps); $sbjct->gaps('hit', $hit_sgaps); $sbjct->length_aln('total', $hit_len_aln); $sbjct->start('query',$start_stop{'qstart'}); $sbjct->end('query', $start_stop{'qstop'}); $sbjct->start('hit', $start_stop{'sstart'}); $sbjct->end('hit', $start_stop{'sstop'}); ## Collect data across the collected contigs. #$sbjct->debug( "\nQUERY CONTIGS:\n"." gaps = $sbjct->{'_gaps_query'}\n"); # Account for strand/frame. # Strategy: collect data on a per strand+frame basis and # save the most significant one. my (%qctg_dat); foreach (@qcontigs) { ($frame, $strand) = ($_->{'frame'}, $_->{'strand'}); if( $v > 0 ) { #$sbjct->debug(sprintf( "$frame/$strand len is getting %d for %d..%d\n", # ($_->{'stop'} - $_->{'start'} + 1), $_->{'start'}, $_->{'stop'})); } $qctg_dat{ "$frame$strand" }->{'length_aln_query'} += $_->{'stop'} - $_->{'start'} + 1; $qctg_dat{ "$frame$strand" }->{'totalIdentical'} += $_->{'iden'}; $qctg_dat{ "$frame$strand" }->{'totalConserved'} += $_->{'cons'}; $qctg_dat{ "$frame$strand" }->{'qstrand'} = $strand; } # Find longest contig. my @sortedkeys = sort { $qctg_dat{$b}->{'length_aln_query'} <=> $qctg_dat{$a}->{'length_aln_query'} } keys %qctg_dat; # Save the largest to the sbjct: my $longest = $sortedkeys[0]; #$sbjct->debug( "longest is ". $qctg_dat{ $longest }->{'length_aln_query'}. "\n"); $sbjct->length_aln('query', $qctg_dat{ $longest }->{'length_aln_query'}); $sbjct->matches($qctg_dat{ $longest }->{'totalIdentical'}, $qctg_dat{ $longest }->{'totalConserved'}); $sbjct->strand('query', $qctg_dat{ $longest }->{'qstrand'}); ## Collect data for sbjct contigs. Important for gapped Blast. ## The totalIdentical and totalConserved numbers will be the same ## as determined for the query contigs. #$sbjct->debug( "\nSBJCT CONTIGS:\n"." gaps = ". $sbjct->gaps('sbjct'). "\n"); my (%sctg_dat); foreach(@scontigs) { #$sbjct->debug(" sbjct contig: $_->{'start'} - $_->{'stop'}\n". # " iden = $_->{'iden'}; cons = $_->{'cons'}\n"); ($frame, $strand) = ($_->{'frame'}, $_->{'strand'}); $sctg_dat{ "$frame$strand" }->{'length_aln_sbjct'} += $_->{'stop'} - $_->{'start'} + 1; $sctg_dat{ "$frame$strand" }->{'frame'} = $frame; $sctg_dat{ "$frame$strand" }->{'sstrand'} = $strand; } @sortedkeys = sort { $sctg_dat{ $b }->{'length_aln_sbjct'} <=> $sctg_dat{ $a }->{'length_aln_sbjct'} } keys %sctg_dat; # Save the largest to the sbjct: $longest = $sortedkeys[0]; $sbjct->length_aln('sbjct', $sctg_dat{ $longest }->{'length_aln_sbjct'}); $sbjct->frame( $sctg_dat{ $longest }->{'frame'} ); $sbjct->strand('hit', $sctg_dat{ $longest }->{'sstrand'}); if($qoverlap) { if($soverlap) { $sbjct->ambiguous_aln('qs'); #$sbjct->debug("\n*** AMBIGUOUS ALIGNMENT: Query and Sbjct\n\n"); } else { $sbjct->ambiguous_aln('q'); #$sbjct->debug( "\n*** AMBIGUOUS ALIGNMENT: Query\n\n"); } } elsif($soverlap) { $sbjct->ambiguous_aln('s'); #$sbjct->debug( "\n*** AMBIGUOUS ALIGNMENT: Sbjct\n\n"); } _adjust_length_aln($sbjct); return ( [@qcontigs], [@scontigs] ); } # Title : _adjust_length_aln # Usage : n/a; internal use only; called by tile_hsps. # Purpose : Adjust length of aligment based on BLAST flavor. # Comments : See comments in logica_length() sub _adjust_length_aln { my $sbjct = shift; my $algo = $sbjct->algorithm; my $hlen = $sbjct->length_aln('sbjct'); my $qlen = $sbjct->length_aln('query'); $sbjct->length_aln('sbjct', logical_length($algo, 'sbjct', $hlen)); $sbjct->length_aln('query', logical_length($algo, 'query', $qlen)); } =head2 logical_length Usage : logical_length( $alg_name, $seq_type, $length ); Purpose : Determine the logical length of an aligned sequence based on : algorithm name and sequence type. Returns : integer representing the logical aligned length. Argument : $alg_name = name of algorigthm (e.g., blastx, tblastn) : $seq_type = type of sequence (e.g., query or hit) : $length = physical length of the sequence in the alignment. Throws : n/a Comments : This function is used to account for the fact that number of identities and conserved residues is reported in peptide space while the query length (in the case of BLASTX and TBLASTX) and/or the hit length (in the case of TBLASTN and TBLASTX) are in nucleotide space. The adjustment affects the values reported by the various frac_XXX methods in GenericHit and GenericHSP. =cut sub logical_length { my ($algo, $type, $len) = @_; my $logical = $len; if($algo =~ /^(?:PSI)?T(?:BLASTN|FAST(?:X|Y|XY))/oi ) { $logical = $len/3 if $type =~ /sbjct|hit|tot/i; } elsif($algo =~ /^(?:BLASTX|FAST(?:X|Y|XY))/oi ) { $logical = $len/3 if $type =~ /query|tot/i; } elsif($algo =~ /^TBLASTX/oi ) { $logical = $len/3; } return $logical; } #=head2 _adjust_contigs # # Usage : n/a; internal function called by tile_hsps # Purpose : Builds HSP contigs for a given BLAST hit. # : Utility method called by _tile_hsps() # Returns : # Argument : # Throws : Exceptions propagated from Bio::Search::Hit::BlastHSP::matches() # : for invalid sub-sequence ranges. # Status : Experimental # Comments : This method supports gapped alignments through a patch by maj # : to B:S:HSP:HSPI::matches(). # : It does not keep track of the number of HSPs that # : overlap within the amount specified by overlap(). # : This will lead to significant tracking errors for large # : overlap values. # #See Also : L(), L # #=cut sub _adjust_contigs { my ($seqType, $hsp, $start, $stop, $contigs_ref, $max_overlap, $frame, $strand) = @_; my $overlap = 0; my ($numID, $numCons); foreach (@$contigs_ref) { # Don't merge things unless they have matching strand/frame. next unless ($_->{'frame'} == $frame && $_->{'strand'} == $strand); # Test special case of a nested HSP. Skip it. if ($start >= $_->{'start'} && $stop <= $_->{'stop'}) { $overlap = 1; next; } # Test for overlap at beginning of contig, or precedes consecutively if ($start < $_->{'start'} && $stop >= ($_->{'start'} + $max_overlap - 1)) { eval { ($numID, $numCons) = $hsp->matches(-SEQ =>$seqType, -START => $start, -STOP => $_->{'start'} - 1); if ($numID eq '') { $hsp->warn("\$hsp->matches() returned '' for number identical; setting to 0"); $numID = 0; } if ($numCons eq '') { $hsp->warn("\$hsp->matches() returned '' for number conserved; setting to 0"); $numCons = 0; } }; if($@) { warn "\a\n$@\n"; } else { $_->{'start'} = $start; # Assign a new start coordinate to the contig $_->{'iden'} += $numID; # and add new data to #identical, #conserved. $_->{'cons'} += $numCons; push(@{$_->{hsps}}, $hsp); $overlap = 1; } } # Test for overlap at end of contig, or follows consecutively if ($stop > $_->{'stop'} and $start <= ($_->{'stop'} - $max_overlap + 1)) { eval { ($numID,$numCons) = $hsp->matches(-SEQ =>$seqType, -START => $_->{'stop'} + 1, -STOP => $stop); if ($numID eq '') { $hsp->warn("\$hsp->matches() returned '' for number identical; setting to 0"); $numID = 0; } if ($numCons eq '') { $hsp->warn("\$hsp->matches() returned '' for number conserved; setting to 0"); $numCons = 0; } }; if($@) { warn "\a\n$@\n"; } else { $_->{'stop'} = $stop; # Assign a new stop coordinate to the contig $_->{'iden'} += $numID; # and add new data to #identical, #conserved. $_->{'cons'} += $numCons; push(@{$_->{hsps}}, $hsp); $overlap = 1; } } last if $overlap; } if ($overlap && @$contigs_ref > 1) { ## Merge any contigs that now overlap my $max = $#{$contigs_ref}; for my $i (0..$max) { ${$contigs_ref}[$i] || next; my ($i_start, $i_stop) = (${$contigs_ref}[$i]->{start}, ${$contigs_ref}[$i]->{stop}); for my $u ($i+1..$max) { ${$contigs_ref}[$u] || next; my ($u_start, $u_stop) = (${$contigs_ref}[$u]->{start}, ${$contigs_ref}[$u]->{stop}); if ($u_start < $i_start && $u_stop >= ($i_start + $max_overlap - 1)) { # find the hsps within the contig that have sequence # extending before $i_start my ($ids, $cons) = (0, 0); my $use_start = $i_start; foreach my $hsp (sort { $b->end($seqType) <=> $a->end($seqType) } @{${$contigs_ref}[$u]->{hsps}}) { my $hsp_start = $hsp->start($seqType); $hsp_start < $use_start || next; my ($these_ids, $these_cons); eval { ($these_ids, $these_cons) = $hsp->matches(-SEQ => $seqType, -START => $hsp_start, -STOP => $use_start - 1); if ($these_ids eq '') { $hsp->warn("\$hsp->matches() returned '' for number identical; setting to 0"); $these_ids = 0; } if ($these_cons eq '') { $hsp->warn("\$hsp->matches() returned '' for number conserved; setting to 0"); $these_cons = 0; } }; if($@) { warn "\a\n$@\n"; } else { $ids += $these_ids; $cons += $these_cons; } last if $hsp_start == $u_start; $use_start = $hsp_start; } ${$contigs_ref}[$i]->{start} = $u_start; ${$contigs_ref}[$i]->{'iden'} += $ids; ${$contigs_ref}[$i]->{'cons'} += $cons; push(@{${$contigs_ref}[$i]->{hsps}}, @{${$contigs_ref}[$u]->{hsps}}); ${$contigs_ref}[$u] = undef; } elsif ($u_stop > $i_stop && $u_start <= ($i_stop - $max_overlap + 1)) { # find the hsps within the contig that have sequence # extending beyond $i_stop my ($ids, $cons) = (0, 0); my $use_stop = $i_stop; foreach my $hsp (sort { $a->start($seqType) <=> $b->start($seqType) } @{${$contigs_ref}[$u]->{hsps}}) { my $hsp_end = $hsp->end($seqType); $hsp_end > $use_stop || next; my ($these_ids, $these_cons); eval { ($these_ids, $these_cons) = $hsp->matches(-SEQ => $seqType, -START => $use_stop + 1, -STOP => $hsp_end); if ($these_ids eq '') { $hsp->warn("\$hsp->matches() returned '' for number identical; setting to 0"); $these_ids = 0; } if ($these_cons eq '') { $hsp->warn("\$hsp->matches() returned '' for number conserved; setting to 0"); $these_cons = 0; } }; if($@) { warn "\a\n$@\n"; } else { $ids += $these_ids; $cons += $these_cons; } last if $hsp_end == $u_stop; $use_stop = $hsp_end; } ${$contigs_ref}[$i]->{'stop'} = $u_stop; ${$contigs_ref}[$i]->{'iden'} += $ids; ${$contigs_ref}[$i]->{'cons'} += $cons; push(@{${$contigs_ref}[$i]->{hsps}}, @{${$contigs_ref}[$u]->{hsps}}); ${$contigs_ref}[$u] = undef; } elsif ($u_start >= $i_start && $u_stop <= $i_stop) { # nested, drop this contig #*** ideally we might do some magic to keep the stats of the # better hsp... ${$contigs_ref}[$u] = undef; } } } my @merged; foreach (@$contigs_ref) { push(@merged, $_ || next); } @{$contigs_ref} = @merged; } elsif (! $overlap) { ## If there is no overlap, add the complete HSP data. ($numID,$numCons) = $hsp->matches(-SEQ=>$seqType); if ($numID eq '') { $hsp->warn("\$hsp->matches() returned '' for number identical; setting to 0"); $numID = 0; } if ($numCons eq '') { $hsp->warn("\$hsp->matches() returned '' for number conserved; setting to 0"); $numCons = 0; } push @$contigs_ref, {'start' =>$start, 'stop' =>$stop, 'iden' =>$numID, 'cons' =>$numCons, 'strand'=>$strand,'frame'=>$frame,'hsps'=>[$hsp]}; } return $overlap; } =head2 get_exponent Usage : &get_exponent( number ); Purpose : Determines the power of 10 exponent of an integer, float, : or scientific notation number. Example : &get_exponent("4.0e-206"); : &get_exponent("0.00032"); : &get_exponent("10."); : &get_exponent("1000.0"); : &get_exponent("e+83"); Argument : Float, Integer, or scientific notation number Returns : Integer representing the exponent part of the number (+ or -). : If argument == 0 (zero), return value is "-999". Comments : Exponents are rounded up (less negative) if the mantissa is >= 5. : Exponents are rounded down (more negative) if the mantissa is <= -5. =cut sub get_exponent { my $data = shift; my($num, $exp) = split /[eE]/, $data; if( defined $exp) { $num = 1 if not $num; $num >= 5 and $exp++; $num <= -5 and $exp--; } elsif( $num == 0) { $exp = -999; } elsif( not $num =~ /\./) { $exp = CORE::length($num) -1; } else { $exp = 0; $num .= '0' if $num =~ /\.$/; my ($c); my $rev = 0; if($num !~ /^0/) { $num = reverse($num); $rev = 1; } do { $c = chop($num); $c == 0 && $exp++; } while( $c ne '.'); $exp = -$exp if $num == 0 and not $rev; $exp -= 1 if $rev; } return $exp; } =head2 collapse_nums Usage : @cnums = collapse_nums( @numbers ); Purpose : Collapses a list of numbers into a set of ranges of consecutive terms: : Useful for condensing long lists of consecutive numbers. : EXPANDED: : 1 2 3 4 5 6 10 12 13 14 15 17 18 20 21 22 24 26 30 31 32 : COLLAPSED: : 1-6 10 12-15 17 18 20-22 24 26 30-32 Argument : List of numbers sorted numerically. Returns : List of numbers mixed with ranges of numbers (see above). Throws : n/a See Also : L =cut sub collapse_nums { # This is probably not the slickest connectivity algorithm, but will do for now. my @a = @_; my ($from, $to, $i, @ca, $consec); $consec = 0; for($i=0; $i < @a; $i++) { not $from and do{ $from = $a[$i]; next; }; # pass repeated positions (gap inserts) next if $a[$i] == $a[$i-1]; if($a[$i] == $a[$i-1]+1) { $to = $a[$i]; $consec++; } else { if($consec == 1) { $from .= ",$to"; } else { $from .= $consec>1 ? "\-$to" : ""; } push @ca, split(',', $from); $from = $a[$i]; $consec = 0; $to = undef; } } if(defined $to) { if($consec == 1) { $from .= ",$to"; } else { $from .= $consec>1 ? "\-$to" : ""; } } push @ca, split(',', $from) if $from; @ca; } =head2 strip_blast_html Usage : $boolean = &strip_blast_html( string_ref ); : This method is exported. Purpose : Removes HTML formatting from a supplied string. : Attempts to restore the Blast report to enable : parsing by Bio::SearchIO::blast.pm Returns : Boolean: true if string was stripped, false if not. Argument : string_ref = reference to a string containing the whole Blast : report containing HTML formatting. Throws : Croaks if the argument is not a scalar reference. Comments : Based on code originally written by Alex Dong Li : (ali@genet.sickkids.on.ca). : This method does some Blast-specific stripping : (adds back a '>' character in front of each HSP : alignment listing). : : THIS METHOD IS VERY SENSITIVE TO BLAST FORMATTING CHANGES! : : Removal of the HTML tags and accurate reconstitution of the : non-HTML-formatted report is highly dependent on structure of : the HTML-formatted version. For example, it assumes that first : line of each alignment section (HSP listing) starts with a : anchor tag. This permits the reconstruction of the : original report in which these lines begin with a ">". : This is required for parsing. : : If the structure of the Blast report itself is not intended to : be a standard, the structure of the HTML-formatted version : is even less so. Therefore, the use of this method to : reconstitute parsable Blast reports from HTML-format versions : should be considered a temporary solution. =cut sub strip_blast_html { # This may not best way to remove html tags. However, it is simple. # it won't work under following conditions: # 1) if quoted > appears in a tag (does this ever happen?) # 2) if a tag is split over multiple lines and this method is # used to process one line at a time. my ($string_ref) = shift; ref $string_ref eq 'SCALAR' or croak ("Can't strip HTML: ". "Argument is should be a SCALAR reference not a ${\ref $string_ref}\n"); my $str = $$string_ref; my $stripped = 0; # Removing "" and adding the '>' character for # HSP alignment listings. $str =~ s/(\A|\n)]+> ?/>/sgi and $stripped = 1; # Removing all "<>" tags. $str =~ s/<[^>]+>| //sgi and $stripped = 1; # Re-uniting any lone '>' characters. $str =~ s/(\A|\n)>\s+/\n\n>/sgi and $stripped = 1; $$string_ref = $str; $stripped; } =head2 result2hash Title : result2hash Usage : my %data = &Bio::Search::SearchUtils($result) Function : converts ResultI data to simple hash Returns : hash Args : ResultI Note : used mainly as a utility for running SearchIO tests =cut sub result2hash { my ($result) = @_; my %hash; $hash{'query_name'} = $result->query_name; my $hitcount = 1; my $hspcount = 1; foreach my $hit ( $result->hits ) { $hash{"hit$hitcount\_name"} = $hit->name; # only going to test order of magnitude # too hard as these don't always match # $hash{"hit$hitcount\_signif"} = # ( sprintf("%.0e",$hit->significance) =~ /e\-?(\d+)/ ); $hash{"hit$hitcount\_bits"} = sprintf("%d",$hit->bits); foreach my $hsp ( $hit->hsps ) { $hash{"hsp$hspcount\_bits"} = sprintf("%d",$hsp->bits); # only going to test order of magnitude # too hard as these don't always match # $hash{"hsp$hspcount\_evalue"} = # ( sprintf("%.0e",$hsp->evalue) =~ /e\-?(\d+)/ ); $hash{"hsp$hspcount\_qs"} = $hsp->query->start; $hash{"hsp$hspcount\_qe"} = $hsp->query->end; $hash{"hsp$hspcount\_qstr"} = $hsp->query->strand; $hash{"hsp$hspcount\_hs"} = $hsp->hit->start; $hash{"hsp$hspcount\_he"} = $hsp->hit->end; $hash{"hsp$hspcount\_hstr"} = $hsp->hit->strand; #$hash{"hsp$hspcount\_pid"} = sprintf("%d",$hsp->percent_identity); #$hash{"hsp$hspcount\_fid"} = sprintf("%.2f",$hsp->frac_identical); $hash{"hsp$hspcount\_gaps"} = $hsp->gaps('total'); $hspcount++; } $hitcount++; } return %hash; } sub _warn_about_no_hsps { my $hit = shift; my $prev_func=(caller(1))[3]; $hit->warn("There is no HSP data for hit '".$hit->name."'.\n". "You have called a method ($prev_func)\n". "that requires HSP data and there was no HSP data for this hit,\n". "most likely because it was absent from the BLAST report.\n". "Note that by default, BLAST lists alignments for the first 250 hits,\n". "but it lists descriptions for 500 hits. If this is the case,\n". "and you care about these hits, you should re-run BLAST using the\n". "-b option (or equivalent if not using blastall) to increase the number\n". "of alignments.\n" ); } 1; BioPerl-1.007002/Bio/Search/StatisticsI.pm000555000766000024 536713155576320 20250 0ustar00cjfieldsstaff000000000000# # # BioPerl module for wrapping runtime parameters # # Please direct questions and support issues to # # Cared for by Chad Matsalla (bioinformatics1 at dieselwurks dot com) # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::StatisticsI - A Base object for statistics =head1 SYNOPSIS # do not use this object directly, it provides the following methods # for its subclasses my $void = $obj->set_statistic("statistic_name","statistic_value"); my $value = $obj->get_statistic("statistic_name"); =head1 DESCRIPTION This is a basic container to hold the statistics returned from a program. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics1 at dieselwurks dot com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::StatisticsI; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::RootI); =head2 get_statistic Title : get_statistic Usage : $statistic_object->get_statistic($statistic_name); Function: Get the value of a statistic named $statistic_name Returns : A scalar that should be a string Args : A scalar that should be a string =cut sub get_statistic { my ($self,$arg) = @_; $self->throw_not_implemented; } =head2 set_statistic Title : set_statistic Usage : $statistic_object->set_statistic($statistic_name => $statistic_value); Function: Set the value of a statistic named $statistic_name to $statistic_value Returns : Void Args : A hash containing name=>value pairs =cut sub set_statistic { my ($self,$name,$value) = @_; $self->throw_not_implemented; } 1; BioPerl-1.007002/Bio/Search/HSP000755000766000024 013155576320 15726 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Search/HSP/BlastHSP.pm000444000766000024 15446713155576320 20122 0ustar00cjfieldsstaff000000000000#----------------------------------------------------------------- # # BioPerl module Bio::Search::HSP::BlastHSP # # (This module was originally called Bio::Tools::Blast::HSP) # # Please direct questions and support issues to # # Cared for by Steve Chervitz # # You may distribute this module under the same terms as perl itself #----------------------------------------------------------------- ## POD Documentation: =head1 NAME Bio::Search::HSP::BlastHSP - Bioperl BLAST High-Scoring Pair object =head1 SYNOPSIS See L. =head1 DESCRIPTION A Bio::Search::HSP::BlastHSP object provides an interface to data obtained in a single alignment section of a Blast report (known as a "High-scoring Segment Pair"). This is essentially a pairwise alignment with score information. BlastHSP objects are accessed via L objects after parsing a BLAST report using the L system. The construction of BlastHSP objects is performed by Bio::Factory::BlastHitFactory in a process that is orchestrated by the Blast parser (L). The resulting BlastHSPs are then accessed via L). Therefore, you do not need to use L) directly. If you need to construct BlastHSPs directly, see the new() function for details. For L BLAST parsing usage examples, see the C directory of the Bioperl distribution. =head2 Start and End coordinates Sequence endpoints are swapped so that start is always less than end. This affects For TBLASTN/X hits on the minus strand. Strand information can be recovered using the strand() method. This normalization step is standard Bioperl practice. It also facilitates use of range information by methods such as match(). =over 1 =item * Supports BLAST versions 1.x and 2.x, gapped and ungapped. =back Bio::Search::HSP::BlastHSP.pm has the ability to extract a list of all residue indices for identical and conservative matches along both query and sbjct sequences. Since this degree of detail is not always needed, this behavior does not occur during construction of the BlastHSP object. These data will automatically be collected as necessary as the BlastHSP.pm object is used. =head1 DEPENDENCIES Bio::Search::HSP::BlastHSP.pm is a concrete class that inherits from L and L. L and L are employed for creating sequence and alignment objects, respectively. =head2 Relationship to SimpleAlign.pm & Seq.pm BlastHSP.pm can provide the query or sbjct sequence as a L object via the L method. The BlastHSP.pm object can also create a two-sequence L alignment object using the the query and sbjct sequences via the L method. Creation of alignment objects is not automatic when constructing the BlastHSP.pm object since this level of functionality is not always required and would generate a lot of extra overhead when crunching many reports. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Steve Chervitz Esac-at-bioperl.orgE See L for where to send bug reports and comments. =head1 ACKNOWLEDGEMENTS This software was originally developed in the Department of Genetics at Stanford University. I would also like to acknowledge my colleagues at Affymetrix for useful feedback. =head1 SEE ALSO Bio::Search::Hit::BlastHit.pm - Blast hit object. Bio::Search::Result::BlastResult.pm - Blast Result object. Bio::Seq.pm - Biosequence object =head2 Links: http://bio.perl.org/ - Bioperl Project Homepage =head1 COPYRIGHT Copyright (c) 1996-2001 Steve Chervitz. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =cut # END of main POD documentation. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::HSP::BlastHSP; use strict; use Bio::SeqFeature::Similarity; use vars qw($GAP_SYMBOL %STRAND_SYMBOL); use overload '""' => \&to_string; use base qw(Bio::SeqFeature::SimilarityPair Bio::Search::HSP::HSPI); $GAP_SYMBOL = '-'; # Need a more general way to handle gap symbols. %STRAND_SYMBOL = ('Plus' => 1, 'Minus' => -1 ); =head2 new Usage : $hsp = Bio::Search::HSP::BlastHSP->new( %named_params ); : Bio::Search::HSP::BlastHSP objects are constructed : automatically by Bio::SearchIO::BlastHitFactory, : so there is no need for direct instantiation. Purpose : Constructs a new BlastHSP object and Initializes key variables : for the HSP. Returns : A Bio::Search::HSP::BlastHSP object Argument : Named parameters: : Parameter keys are case-insensitive. : -RAW_DATA => array ref containing raw BLAST report data for : for a single HSP. This includes all lines : of the HSP alignment from a traditional BLAST or PSI-BLAST (non-XML) report, : -RANK => integer (1..n). : -PROGRAM => string ('TBLASTN', 'BLASTP', etc.). : -QUERY_NAME => string, id of query sequence : -HIT_NAME => string, id of hit sequence : Comments : Having the raw data allows this object to do lazy parsing of : the raw HSP data (i.e., not parsed until needed). : : Note that there is a fair amount of basic parsing that is : currently performed in this module that would be more appropriate : to do within a separate factory object. : This parsing code will likely be relocated and more initialization : parameters will be added to new(). : See Also : L, L =cut #---------------- sub new { #---------------- my ($class, @args ) = @_; my $self = $class->SUPER::new( @args ); # Initialize placeholders $self->{'_queryGaps'} = $self->{'_sbjctGaps'} = 0; my ($raw_data, $qname, $hname, $qlen, $hlen); ($self->{'_prog'}, $self->{'_rank'}, $raw_data, $qname, $hname) = $self->_rearrange([qw( PROGRAM RANK RAW_DATA QUERY_NAME HIT_NAME )], @args ); # _set_data() does a fair amount of parsing. # This will likely change (see comment above.) $self->_set_data( @{$raw_data} ); # Store the aligned query as sequence feature my ($qb, $hb) = ($self->start()); my ($qe, $he) = ($self->end()); my ($qs, $hs) = ($self->strand()); my ($qf,$hf) = ($self->query->frame(), $self->hit->frame); $self->query( Bio::SeqFeature::Similarity->new (-start =>$qb, -end =>$qe, -strand =>$qs, -bits =>$self->bits, -score =>$self->score, -frame =>$qf, -seq_id => $qname, -source =>$self->{'_prog'} )); $self->hit( Bio::SeqFeature::Similarity->new (-start =>$hb, -end =>$he, -strand =>$hs, -bits =>$self->bits, -score =>$self->score, -frame =>$hf, -seq_id => $hname, -source =>$self->{'_prog'} )); # set lengths $self->query->seqlength($qlen); # query $self->hit->seqlength($hlen); # subject $self->query->frac_identical($self->frac_identical('query')); $self->hit->frac_identical($self->frac_identical('hit')); return $self; } # Title : _id_str; # Purpose : Intended for internal use only to provide a string for use # within exception messages to help users figure out which # query/hit caused the problem. # Returns : Short string with name of query and hit seq sub _id_str { my $self = shift; if( not defined $self->{'_id_str'}) { my $qname = $self->query->seq_id; my $hname = $self->hit->seq_id; $self->{'_id_str'} = "QUERY=\"$qname\" HIT=\"$hname\""; } return $self->{'_id_str'}; } #================================================= # Begin Bio::Search::HSP::HSPI implementation #================================================= =head2 algorithm Title : algorithm Usage : $alg = $hsp->algorithm(); Function: Gets the algorithm specification that was used to obtain the hsp For BLAST, the algorithm denotes what type of sequence was aligned against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated dna-prt, TBLASTN prt-translated dna, TBLASTX translated dna-translated dna). Returns : a scalar string Args : none =cut #---------------- sub algorithm { #---------------- my ($self,@args) = @_; return $self->{'_prog'}; } =head2 signif() Usage : $hsp_obj->signif() Purpose : Get the P-value or Expect value for the HSP. Returns : Float (0.001 or 1.3e-43) : Returns P-value if it is defined, otherwise, Expect value. Argument : n/a Throws : n/a Comments : Provided for consistency with BlastHit::signif() : Support for returning the significance data in different : formats (e.g., exponent only), is not provided for HSP objects. : This is only available for the BlastHit or Blast object. See Also : L

, L, L =cut #----------- sub signif { #----------- my $self = shift; my $val ||= defined($self->{'_p'}) ? $self->{'_p'} : $self->{'_expect'}; $val; } =head2 evalue Usage : $hsp_obj->evalue() Purpose : Get the Expect value for the HSP. Returns : Float (0.001 or 1.3e-43) Argument : n/a Throws : n/a Comments : Support for returning the expectation data in different : formats (e.g., exponent only), is not provided for HSP objects. : This is only available for the BlastHit or Blast object. See Also : L

=cut #---------- sub evalue { shift->{'_expect'} } #---------- =head2 p Usage : $hsp_obj->p() Purpose : Get the P-value for the HSP. Returns : Float (0.001 or 1.3e-43) or undef if not defined. Argument : n/a Throws : n/a Comments : P-value is not defined with NCBI Blast2 reports. : Support for returning the expectation data in different : formats (e.g., exponent only) is not provided for HSP objects. : This is only available for the BlastHit or Blast object. See Also : L =cut #----- sub p { my $self = shift; $self->{'_p'}; } #----- # alias sub pvalue { shift->p(@_); } =head2 length Usage : $hsp->length( [seq_type] ) Purpose : Get the length of the aligned portion of the query or sbjct. Example : $hsp->length('query') Returns : integer Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total' (default = 'total') ('sbjct' is synonymous with 'hit') Throws : n/a Comments : 'total' length is the full length of the alignment : as reported in the denominators in the alignment section: : "Identical = 34/120 Positives = 67/120". See Also : L =cut #----------- sub length { #----------- ## Developer note: when using the built-in length function within ## this module, call it as CORE::length(). my( $self, $seqType,$data ) = @_; $seqType ||= 'total'; $seqType = 'sbjct' if $seqType eq 'hit'; $seqType ne 'total' and $self->_set_seq_data() unless $self->{'_set_seq_data'}; ## Sensitive to member name format. $seqType = "_\L$seqType\E"; if( defined $data ) { $self->{$seqType.'Length'} = $data; } $self->{$seqType.'Length'}; } =head2 gaps Usage : $hsp->gaps( [seq_type] ) Purpose : Get the number of gap characters in the query, sbjct, or total alignment. : Also can return query gap chars and sbjct gap chars as a two-element list : when in array context. Example : $total_gaps = $hsp->gaps(); : ($qgaps, $sgaps) = $hsp->gaps(); : $qgaps = $hsp->gaps('query'); Returns : scalar context: integer : array context without args: (int, int) = ('queryGaps', 'sbjctGaps') Argument : seq_type: 'query' or 'hit' or 'sbjct' or 'total' : ('sbjct' is synonymous with 'hit') : (default = 'total', scalar context) : Array context can be "induced" by providing an argument of 'list' or 'array'. Throws : n/a See Also : L, L =cut #--------- sub gaps { #--------- my( $self, $seqType ) = @_; $self->_set_seq_data() unless $self->{'_set_seq_data'}; $seqType ||= (wantarray ? 'list' : 'total'); $seqType = 'sbjct' if $seqType eq 'hit'; if($seqType =~ /list|array/i) { return (($self->{'_queryGaps'} || 0), ($self->{'_sbjctGaps'} || 0)); } if($seqType eq 'total') { return ($self->{'_queryGaps'} + $self->{'_sbjctGaps'}) || 0; } else { ## Sensitive to member name format. $seqType = "_\L$seqType\E"; return $self->{$seqType.'Gaps'} || 0; } } =head2 frac_identical Usage : $hsp_object->frac_identical( [seq_type] ); Purpose : Get the fraction of identical positions within the given HSP. Example : $frac_iden = $hsp_object->frac_identical('query'); Returns : Float (2-decimal precision, e.g., 0.75). Argument : seq_type: 'query' or 'hit' or 'sbjct' or 'total' : ('sbjct' is synonymous with 'hit') : default = 'total' (but see comments below). Throws : n/a Comments : Different versions of Blast report different values for the total : length of the alignment. This is the number reported in the : denominators in the stats section: : "Identical = 34/120 Positives = 67/120". : NCBI-BLAST uses the total length of the alignment (with gaps) : WU-BLAST uses the length of the query sequence (without gaps). : Therefore, when called without an argument or an argument of 'total', : this method will report different values depending on the : version of BLAST used. : : To get the fraction identical among only the aligned residues, : ignoring the gaps, call this method with an argument of 'query' : or 'sbjct' ('sbjct' is synonymous with 'hit'). See Also : L, L, L =cut #------------------- sub frac_identical { #------------------- # The value is calculated as opposed to storing it from the parsed results. # This saves storage and also permits flexibility in determining for which # sequence (query or sbjct) the figure is to be calculated. my( $self, $seqType ) = @_; $seqType ||= 'total'; $seqType = 'sbjct' if $seqType eq 'hit'; if($seqType ne 'total') { $self->_set_seq_data() unless $self->{'_set_seq_data'}; } ## Sensitive to member name format. $seqType = "_\L$seqType\E"; sprintf( "%.2f", $self->{'_numIdentical'}/$self->{$seqType.'Length'}); } =head2 frac_conserved Usage : $hsp_object->frac_conserved( [seq_type] ); Purpose : Get the fraction of conserved positions within the given HSP. : (Note: 'conservative' positions are called 'positives' in the : Blast report.) Example : $frac_cons = $hsp_object->frac_conserved('query'); Returns : Float (2-decimal precision, e.g., 0.75). Argument : seq_type: 'query' or 'hit' or 'sbjct' or 'total' : ('sbjct' is synonymous with 'hit') : default = 'total' (but see comments below). Throws : n/a Comments : Different versions of Blast report different values for the total : length of the alignment. This is the number reported in the : denominators in the stats section: : "Identical = 34/120 Positives = 67/120". : NCBI-BLAST uses the total length of the alignment (with gaps) : WU-BLAST uses the length of the query sequence (without gaps). : Therefore, when called without an argument or an argument of 'total', : this method will report different values depending on the : version of BLAST used. : : To get the fraction conserved among only the aligned residues, : ignoring the gaps, call this method with an argument of 'query' : or 'sbjct'. See Also : L, L, L =cut #-------------------- sub frac_conserved { #-------------------- # The value is calculated as opposed to storing it from the parsed results. # This saves storage and also permits flexibility in determining for which # sequence (query or sbjct) the figure is to be calculated. my( $self, $seqType ) = @_; $seqType ||= 'total'; $seqType = 'sbjct' if $seqType eq 'hit'; if($seqType ne 'total') { $self->_set_seq_data() unless $self->{'_set_seq_data'}; } ## Sensitive to member name format. $seqType = "_\L$seqType\E"; sprintf( "%.2f", $self->{'_numConserved'}/$self->{$seqType.'Length'}); } =head2 query_string Title : query_string Usage : my $qseq = $hsp->query_string; Function: Retrieves the query sequence of this HSP as a string Returns : string Args : none =cut #---------------- sub query_string{ shift->seq_str('query'); } #---------------- =head2 hit_string Title : hit_string Usage : my $hseq = $hsp->hit_string; Function: Retrieves the hit sequence of this HSP as a string Returns : string Args : none =cut #---------------- sub hit_string{ shift->seq_str('hit'); } #---------------- =head2 homology_string Title : homology_string Usage : my $homo_string = $hsp->homology_string; Function: Retrieves the homology sequence for this HSP as a string. : The homology sequence is the string of symbols in between the : query and hit sequences in the alignment indicating the degree : of conservation (e.g., identical, similar, not similar). Returns : string Args : none =cut #---------------- sub homology_string{ shift->seq_str('match'); } #---------------- #================================================= # End Bio::Search::HSP::HSPI implementation #================================================= # Older method delegating to method defined in HSPI. =head2 expect See L =cut #---------- sub expect { shift->evalue( @_ ); } #---------- =head2 rank Usage : $hsp->rank( [string] ); Purpose : Get the rank of the HSP within a given Blast hit. Example : $rank = $hsp->rank; Returns : Integer (1..n) corresponding to the order in which the HSP appears in the BLAST report. =cut #' #---------- sub rank { shift->{'_rank'} } #---------- # For backward compatibility #---------- sub name { shift->rank } #---------- =head2 to_string Title : to_string Usage : print $hsp->to_string; Function: Returns a string representation for the Blast HSP. Primarily intended for debugging purposes. Example : see usage Returns : A string of the form: [BlastHSP] e.g.: [BlastHit] 1 Args : None =cut #---------- sub to_string { #---------- my $self = shift; return "[BlastHSP] " . $self->rank(); } =head2 _set_data Usage : called automatically during object construction. Purpose : Parses the raw HSP section from a flat BLAST report and sets the query sequence, sbjct sequence, and the "match" data : which consists of the symbols between the query and sbjct lines : in the alignment. Argument : Array (all lines for a single, complete HSP, from a raw, flat (i.e., non-XML) BLAST report) Throws : Propagates any exceptions from the methods called ("See Also") See Also : L, L, L =cut #-------------- sub _set_data { #-------------- my $self = shift; my @data = @_; my @queryList = (); # 'Query' = SEQUENCE USED TO QUERY THE DATABASE. my @sbjctList = (); # 'Sbjct' = HOMOLOGOUS SEQUENCE FOUND IN THE DATABASE. my @matchList = (); my $matchLine = 0; # Alternating boolean: when true, load 'match' data. my @linedat = (); #print STDERR "BlastHSP: set_data()\n"; my($line, $aln_row_len, $length_diff); $length_diff = 0; # Collecting data for all lines in the alignment # and then storing the collections for possible processing later. # # Note that "match" lines may not be properly padded with spaces. # This loop now properly handles such cases: # Query: 1141 PSLVELTIRDCPRLEVGPMIRSLPKFPMLKKLDLAVANIIEEDLDVIGSLEELVIXXXXX 1200 # PSLVELTIRDCPRLEVGPMIRSLPKFPMLKKLDLAVANIIEEDLDVIGSLEELVI # Sbjct: 1141 PSLVELTIRDCPRLEVGPMIRSLPKFPMLKKLDLAVANIIEEDLDVIGSLEELVILSLKL 1200 foreach $line( @data ) { next if $line =~ /^\s*$/; if( $line =~ /^ ?Score/ ) { $self->_set_score_stats( $line ); } elsif( $line =~ /^ ?(Identities|Positives|Strand)/ ) { $self->_set_match_stats( $line ); } elsif( $line =~ /^ ?Frame = ([\d+-]+)/ ) { # Version 2.0.8 has Frame information on a separate line. # Storing frame according to SeqFeature::Generic::frame() # which does not contain strand info (use strand()). my $frame = abs($1) - 1; $self->frame( $frame ); } elsif( $line =~ /^(Query:?[\s\d]+)([^\s\d]+)/ ) { push @queryList, $line; $self->{'_match_indent'} = CORE::length $1; $aln_row_len = (CORE::length $1) + (CORE::length $2); $matchLine = 1; } elsif( $matchLine ) { # Pad the match line with spaces if necessary. $length_diff = $aln_row_len - CORE::length $line; $length_diff and $line .= ' 'x $length_diff; push @matchList, $line; $matchLine = 0; } elsif( $line =~ /^Sbjct/ ) { push @sbjctList, $line; } } # Storing the query and sbjct lists in case they are needed later. # We could make this conditional to save memory. $self->{'_queryList'} = \@queryList; $self->{'_sbjctList'} = \@sbjctList; # Storing the match list in case it is needed later. $self->{'_matchList'} = \@matchList; if(not defined ($self->{'_numIdentical'})) { my $id_str = $self->_id_str; $self->throw( -text => "Can't parse match statistics. Possibly a new or unrecognized Blast format. ($id_str)"); } if(!scalar @queryList or !scalar @sbjctList) { my $id_str = $self->_id_str; $self->throw( "Can't find query or sbjct alignment lines. Possibly unrecognized Blast format. ($id_str)"); } } =head2 _set_score_stats Usage : called automatically by _set_data() Purpose : Sets various score statistics obtained from the HSP listing. Argument : String with any of the following formats: : blast2: Score = 30.1 bits (66), Expect = 9.2 : blast2: Score = 158.2 bits (544), Expect(2) = e-110 : blast1: Score = 410 (144.3 bits), Expect = 1.7e-40, P = 1.7e-40 : blast1: Score = 55 (19.4 bits), Expect = 5.3, Sum P(3) = 0.99 Throws : Exception if the stats cannot be parsed, probably due to a change : in the Blast report format. See Also : L =cut #-------------------- sub _set_score_stats { #-------------------- my ($self, $data) = @_; my ($expect, $p); if($data =~ /Score = +([\d.e+-]+) bits \(([\d.e+-]+)\), +Expect = +([\d.e+-]+)/) { # blast2 format n = 1 $self->bits($1); $self->score($2); $expect = $3; } elsif($data =~ /Score = +([\d.e+-]+) bits \(([\d.e+-]+)\), +Expect\((\d+)\) = +([\d.e+-]+)/) { # blast2 format n > 1 $self->bits($1); $self->score($2); $self->{'_n'} = $3; $expect = $4; } elsif($data =~ /Score = +([\d.e+-]+) \(([\d.e+-]+) bits\), +Expect = +([\d.e+-]+), P = +([\d.e-]+)/) { # blast1 format, n = 1 $self->score($1); $self->bits($2); $expect = $3; $p = $4; } elsif($data =~ /Score = +([\d.e+-]+) \(([\d.e+-]+) bits\), +Expect = +([\d.e+-]+), +Sum P\((\d+)\) = +([\d.e-]+)/) { # blast1 format, n > 1 $self->score($1); $self->bits($2); $expect = $3; $self->{'_n'} = $4; $p = $5; } else { my $id_str = $self->_id_str; $self->throw(-class => 'Bio::Root::Exception', -text => "Can't parse score statistics: unrecognized format. ($id_str)", -value => $data); } $expect = "1$expect" if $expect =~ /^e/i; $p = "1$p" if defined $p and $p=~ /^e/i; $self->{'_expect'} = $expect; $self->{'_p'} = $p || undef; $self->significance( $p || $expect ); } =head2 _set_match_stats Usage : Private method; called automatically by _set_data() Purpose : Sets various matching statistics obtained from the HSP listing. Argument : blast2: Identities = 23/74 (31%), Positives = 29/74 (39%), Gaps = 17/74 (22%) : blast2: Identities = 57/98 (58%), Positives = 74/98 (75%) : blast1: Identities = 87/204 (42%), Positives = 126/204 (61%) : blast1: Identities = 87/204 (42%), Positives = 126/204 (61%), Frame = -3 : WU-blast: Identities = 310/553 (56%), Positives = 310/553 (56%), Strand = Minus / Plus Throws : Exception if the stats cannot be parsed, probably due to a change : in the Blast report format. Comments : The "Gaps = " data in the HSP header has a different meaning depending : on the type of Blast: for BLASTP, this number is the total number of : gaps in query+sbjct; for TBLASTN, it is the number of gaps in the : query sequence only. Thus, it is safer to collect the data : separately by examining the actual sequence strings as is done : in _set_seq(). See Also : L, L =cut #-------------------- sub _set_match_stats { #-------------------- my ($self, $data) = @_; if($data =~ m!Identities = (\d+)/(\d+)!) { # blast1 or 2 format $self->{'_numIdentical'} = $1; $self->{'_totalLength'} = $2; } if($data =~ m!Positives = (\d+)/(\d+)!) { # blast1 or 2 format $self->{'_numConserved'} = $1; $self->{'_totalLength'} = $2; } if($data =~ m!Frame = ([\d+-]+)!) { $self->frame($1); } # Strand data is not always present in this line. # _set_seq() will also set strand information. if($data =~ m!Strand = (\w+) / (\w+)!) { $self->{'_queryStrand'} = $1; $self->{'_sbjctStrand'} = $2; } # if($data =~ m!Gaps = (\d+)/(\d+)!) { # $self->{'_totalGaps'} = $1; # } else { # $self->{'_totalGaps'} = 0; # } } =head2 _set_seq_data Usage : called automatically when sequence data is requested. Purpose : Sets the HSP sequence data for both query and sbjct sequences. : Includes: start, stop, length, gaps, and raw sequence. Argument : n/a Throws : Propagates any exception thrown by _set_match_seq() Comments : Uses raw data stored by _set_data() during object construction. : These data are not always needed, so it is conditionally : executed only upon demand by methods such as gaps(), _set_residues(), : etc. _set_seq() does the dirty work. See Also : L =cut #----------------- sub _set_seq_data { #----------------- my $self = shift; $self->_set_seq('query', @{$self->{'_queryList'}}); $self->_set_seq('sbjct', @{$self->{'_sbjctList'}}); # Liberate some memory. @{$self->{'_queryList'}} = @{$self->{'_sbjctList'}} = (); undef $self->{'_queryList'}; undef $self->{'_sbjctList'}; $self->{'_set_seq_data'} = 1; } =head2 _set_seq Usage : called automatically by _set_seq_data() : $hsp_obj->($seq_type, @data); Purpose : Sets sequence information for both the query and sbjct sequences. : Directly counts the number of gaps in each sequence (if gapped Blast). Argument : $seq_type = 'query' or 'sbjct' : @data = all seq lines with the form: : Query: 61 SPHNVKDRKEQNGSINNAISPTATANTSGSQQINIDSALRDRSSNVAAQPSLSDASSGSN 120 Throws : Exception if data strings cannot be parsed, probably due to a change : in the Blast report format. Comments : Uses first argument to determine which data members to set : making this method sensitive data member name changes. : Behavior is dependent on the type of BLAST analysis (TBLASTN, BLASTP, etc). Warning : Sequence endpoints are normalized so that start < end. This affects HSPs : for TBLASTN/X hits on the minus strand. Normalization facilitates use : of range information by methods such as match(). See Also : L, L, L, L, L =cut #------------- sub _set_seq { #------------- my $self = shift; my $seqType = shift; my @data = @_; my @ranges = (); my @sequence = (); my $numGaps = 0; foreach( @data ) { if( m/(\d+) *([^\d\s]+) *(\d+)/) { push @ranges, ( $1, $3 ) ; push @sequence, $2; #print STDERR "_set_seq found sequence \"$2\"\n"; } else { $self->warn("Bad sequence data: $_"); } } if( !(scalar(@sequence) and scalar(@ranges))) { my $id_str = $self->_id_str; $self->throw("Can't set sequence: missing data. Possibly unrecognized Blast format. ($id_str) $seqType"); } # Sensitive to member name changes. $seqType = "_\L$seqType\E"; $self->{$seqType.'Start'} = $ranges[0]; $self->{$seqType.'Stop'} = $ranges[ $#ranges ]; $self->{$seqType.'Seq'} = \@sequence; $self->{$seqType.'Length'} = abs($ranges[ $#ranges ] - $ranges[0]) + 1; # Adjust lengths for BLASTX, TBLASTN, TBLASTX sequences # Converting nucl coords to amino acid coords. my $prog = $self->algorithm; if($prog eq 'TBLASTN' and $seqType eq '_sbjct') { $self->{$seqType.'Length'} /= 3; } elsif($prog eq 'BLASTX' and $seqType eq '_query') { $self->{$seqType.'Length'} /= 3; } elsif($prog eq 'TBLASTX') { $self->{$seqType.'Length'} /= 3; } if( $prog ne 'BLASTP' ) { $self->{$seqType.'Strand'} = 'Plus' if $prog =~ /BLASTN/; $self->{$seqType.'Strand'} = 'Plus' if ($prog =~ /BLASTX/ and $seqType eq '_query'); # Normalize sequence endpoints so that start < end. # Reverse complement or 'minus strand' HSPs get flipped here. if($self->{$seqType.'Start'} > $self->{$seqType.'Stop'}) { ($self->{$seqType.'Start'}, $self->{$seqType.'Stop'}) = ($self->{$seqType.'Stop'}, $self->{$seqType.'Start'}); $self->{$seqType.'Strand'} = 'Minus'; } } ## Count number of gaps in each seq. Only need to do this for gapped Blasts. # if($self->{'_gapped'}) { my $seqstr = join('', @sequence); $seqstr =~ s/\s//g; my $num_gaps = CORE::length($seqstr) - $self->{$seqType.'Length'}; $self->{$seqType.'Gaps'} = $num_gaps if $num_gaps > 0; # } } =head2 _set_residues Usage : called automatically when residue data is requested. Purpose : Sets the residue numbers representing the identical and : conserved positions. These data are obtained by analyzing the : symbols between query and sbjct lines of the alignments. Argument : n/a Throws : Propagates any exception thrown by _set_seq_data() and _set_match_seq(). Comments : These data are not always needed, so it is conditionally : executed only upon demand by methods such as seq_inds(). : Behavior is dependent on the type of BLAST analysis (TBLASTN, BLASTP, etc). See Also : L, L, L =cut #------------------ sub _set_residues { #------------------ my $self = shift; my @sequence = (); $self->_set_seq_data() unless $self->{'_set_seq_data'}; # Using hashes to avoid saving duplicate residue numbers. my %identicalList_query = (); my %identicalList_sbjct = (); my %conservedList_query = (); my %conservedList_sbjct = (); my $aref = $self->_set_match_seq() if not ref $self->{'_matchSeq'}; $aref ||= $self->{'_matchSeq'}; my $seqString = join('', @$aref ); my $qseq = join('',@{$self->{'_querySeq'}}); my $sseq = join('',@{$self->{'_sbjctSeq'}}); my $resCount_query = $self->{'_queryStop'} || 0; my $resCount_sbjct = $self->{'_sbjctStop'} || 0; my $prog = $self->algorithm; if($prog !~ /^BLASTP|^BLASTN/) { if($prog eq 'TBLASTN') { $resCount_sbjct /= 3; } elsif($prog eq 'BLASTX') { $resCount_query /= 3; } elsif($prog eq 'TBLASTX') { $resCount_query /= 3; $resCount_sbjct /= 3; } } my ($mchar, $schar, $qchar); while( $mchar = chop($seqString) ) { ($qchar, $schar) = (chop($qseq), chop($sseq)); if( $mchar eq '+' ) { $conservedList_query{ $resCount_query } = 1; $conservedList_sbjct{ $resCount_sbjct } = 1; } elsif( $mchar ne ' ' ) { $identicalList_query{ $resCount_query } = 1; $identicalList_sbjct{ $resCount_sbjct } = 1; } $resCount_query-- if $qchar ne $GAP_SYMBOL; $resCount_sbjct-- if $schar ne $GAP_SYMBOL; } $self->{'_identicalRes_query'} = \%identicalList_query; $self->{'_conservedRes_query'} = \%conservedList_query; $self->{'_identicalRes_sbjct'} = \%identicalList_sbjct; $self->{'_conservedRes_sbjct'} = \%conservedList_sbjct; } =head2 _set_match_seq Usage : $hsp_obj->_set_match_seq() Purpose : Set the 'match' sequence for the current HSP (symbols in between : the query and sbjct lines.) Returns : Array reference holding the match sequences lines. Argument : n/a Throws : Exception if the _matchList field is not set. Comments : The match information is not always necessary. This method : allows it to be conditionally prepared. : Called by _set_residues>() and seq_str(). See Also : L, L =cut #------------------- sub _set_match_seq { #------------------- my $self = shift; if( ! ref($self->{'_matchList'}) ) { my $id_str = $self->_id_str; $self->throw("Can't set HSP match sequence: No data ($id_str)"); } my @data = @{$self->{'_matchList'}}; my(@sequence); foreach( @data ) { chomp($_); ## Remove leading spaces; (note: aln may begin with a space ## which is why we can't use s/^ +//). s/^ {$self->{'_match_indent'}}//; push @sequence, $_; } # Liberate some memory. @{$self->{'_matchList'}} = undef; $self->{'_matchList'} = undef; $self->{'_matchSeq'} = \@sequence; return $self->{'_matchSeq'}; } =head2 n Usage : $hsp_obj->n() Purpose : Get the N value (num HSPs on which P/Expect is based). : This value is not defined with NCBI Blast2 with gapping. Returns : Integer or null string if not defined. Argument : n/a Throws : n/a Comments : The 'N' value is listed in parenthesis with P/Expect value: : e.g., P(3) = 1.2e-30 ---> (N = 3). : Not defined in NCBI Blast2 with gaps. : This typically is equal to the number of HSPs but not always. : To obtain the number of HSPs, use Bio::Search::Hit::BlastHit::num_hsps(). See Also : L =cut #----- sub n { my $self = shift; $self->{'N'} || ''; } #----- =head2 matches Usage : $hsp->matches([seq_type], [start], [stop]); Purpose : Get the total number of identical and conservative matches : in the query or sbjct sequence for the given HSP. Optionally can : report data within a defined interval along the seq. : (Note: 'conservative' matches are called 'positives' in the : Blast report.) Example : ($id,$cons) = $hsp_object->matches('hit'); : ($id,$cons) = $hsp_object->matches('query',300,400); Returns : 2-element array of integers Argument : (1) seq_type = 'query' or 'hit' or 'sbjct' (default = query) : ('sbjct' is synonymous with 'hit') : (2) start = Starting coordinate (optional) : (3) stop = Ending coordinate (optional) Throws : Exception if the supplied coordinates are out of range. Comments : Relies on seq_str('match') to get the string of alignment symbols : between the query and sbjct lines which are used for determining : the number of identical and conservative matches. See Also : L, L, L, L =cut #----------- sub matches { #----------- my( $self, %param ) = @_; my(@data); my($seqType, $beg, $end) = ($param{-SEQ}, $param{-START}, $param{-STOP}); $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; my($start,$stop); if(!defined $beg && !defined $end) { ## Get data for the whole alignment. push @data, ($self->{'_numIdentical'}, $self->{'_numConserved'}); } else { ## Get the substring representing the desired sub-section of aln. $beg ||= 0; $end ||= 0; ($start,$stop) = $self->range($seqType); if($beg == 0) { $beg = $start; $end = $beg+$end; } elsif($end == 0) { $end = $stop; $beg = $end-$beg; } if($end >= $stop) { $end = $stop; } ##ML changed from if (end >stop) else { $end += 1;} ##ML moved from commented position below, makes ##more sense here # if($end > $stop) { $end = $stop; } if($beg < $start) { $beg = $start; } # else { $end += 1;} # my $seq = substr($self->seq_str('match'), $beg-$start, ($end-$beg)); ## ML: START fix for substr out of range error ------------------ my $seq = ""; my $prog = $self->algorithm; if (($prog eq 'TBLASTN') and ($seqType eq 'sbjct')) { $seq = substr($self->seq_str('match'), int(($beg-$start)/3), int(($end-$beg+1)/3)); } elsif (($prog eq 'BLASTX') and ($seqType eq 'query')) { $seq = substr($self->seq_str('match'), int(($beg-$start)/3), int(($end-$beg+1)/3)); } else { $seq = substr($self->seq_str('match'), $beg-$start, ($end-$beg)); } ## ML: End of fix for substr out of range error ----------------- ## ML: debugging code ## This is where we get our exception. Try printing out the values going ## into this: ## # print STDERR # qq(*------------MY EXCEPTION --------------------\nSeq: ") , # $self->seq_str("$seqType"), qq("\n),$self->rank,",( index:"; # print STDERR $beg-$start, ", len: ", $end-$beg," ), (HSPRealLen:", # CORE::length $self->seq_str("$seqType"); # print STDERR ", HSPCalcLen: ", $stop - $start +1 ," ), # ( beg: $beg, end: $end ), ( start: $start, stop: stop )\n"; ## ML: END DEBUGGING CODE---------- if(!CORE::length $seq) { my $id_str = $self->_id_str; $self->throw("Undefined $seqType sub-sequence ($beg,$end). Valid range = $start - $stop ($id_str)"); } ## Get data for a substring. # printf "Collecting HSP subsection data: beg,end = %d,%d; start,stop = %d,%d\n%s<---\n", $beg, $end, $start, $stop, $seq; # printf "Original match seq:\n%s\n",$self->seq_str('match'); $seq =~ s/ //g; # remove space (no info). my $len_cons = CORE::length $seq; $seq =~ s/\+//g; # remove '+' characters (conservative substitutions) my $len_id = CORE::length $seq; push @data, ($len_id, $len_cons); # printf " HSP = %s\n id = %d; cons = %d\n", $self->rank, $len_id, $len_cons; ; } @data; } =head2 num_identical Usage : $hsp_object->num_identical(); Purpose : Get the number of identical positions within the given HSP. Example : $num_iden = $hsp_object->num_identical(); Returns : integer Argument : n/a Throws : n/a See Also : L, L =cut #------------------- sub num_identical { #------------------- my( $self) = shift; $self->{'_numIdentical'}; } =head2 num_conserved Usage : $hsp_object->num_conserved(); Purpose : Get the number of conserved positions within the given HSP. Example : $num_iden = $hsp_object->num_conserved(); Returns : integer Argument : n/a Throws : n/a See Also : L, L =cut #------------------- sub num_conserved { #------------------- my( $self) = shift; $self->{'_numConserved'}; } =head2 range Usage : $hsp->range( [seq_type] ); Purpose : Gets the (start, end) coordinates for the query or sbjct sequence : in the HSP alignment. Example : ($query_beg, $query_end) = $hsp->range('query'); : ($hit_beg, $hit_end) = $hsp->range('hit'); Returns : Two-element array of integers Argument : seq_type = string, 'query' or 'hit' or 'sbjct' (default = 'query') : ('sbjct' is synonymous with 'hit') Throws : n/a See Also : L, L =cut #---------- sub range { #---------- my ($self, $seqType) = @_; $self->_set_seq_data() unless $self->{'_set_seq_data'}; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; return ($self->{$seqType.'Start'},$self->{$seqType.'Stop'}); } =head2 start Usage : $hsp->start( [seq_type] ); Purpose : Gets the start coordinate for the query, sbjct, or both sequences : in the HSP alignment. : NOTE: Start will always be less than end. : To determine strand, use $hsp->strand() Example : $query_beg = $hsp->start('query'); : $hit_beg = $hsp->start('hit'); : ($query_beg, $hit_beg) = $hsp->start(); Returns : scalar context: integer : array context without args: list of two integers Argument : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default= 'query') : ('sbjct' is synonymous with 'hit') : Array context can be "induced" by providing an argument of 'list' or 'array'. Throws : n/a See Also : L, L =cut #---------- sub start { #---------- my ($self, $seqType) = @_; $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; $self->_set_seq_data() unless $self->{'_set_seq_data'}; if($seqType =~ /list|array/i) { return ($self->{'_queryStart'}, $self->{'_sbjctStart'}); } else { ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; return $self->{$seqType.'Start'}; } } =head2 end Usage : $hsp->end( [seq_type] ); Purpose : Gets the end coordinate for the query, sbjct, or both sequences : in the HSP alignment. : NOTE: Start will always be less than end. : To determine strand, use $hsp->strand() Example : $query_end = $hsp->end('query'); : $hit_end = $hsp->end('hit'); : ($query_end, $hit_end) = $hsp->end(); Returns : scalar context: integer : array context without args: list of two integers Argument : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default= 'query') : ('sbjct' is synonymous with 'hit') : Array context can be "induced" by providing an argument of 'list' or 'array'. Throws : n/a See Also : L, L, L =cut #---------- sub end { #---------- my ($self, $seqType) = @_; $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; $self->_set_seq_data() unless $self->{'_set_seq_data'}; if($seqType =~ /list|array/i) { return ($self->{'_queryStop'}, $self->{'_sbjctStop'}); } else { ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; return $self->{$seqType.'Stop'}; } } =head2 strand Usage : $hsp_object->strand( [seq_type] ) Purpose : Get the strand of the query or sbjct sequence. Example : print $hsp->strand('query'); : ($query_strand, $hit_strand) = $hsp->strand(); Returns : -1, 0, or 1 : -1 = Minus strand, +1 = Plus strand : Returns 0 if strand is not defined, which occurs : for BLASTP reports, and the query of TBLASTN : as well as the hit if BLASTX reports. : In scalar context without arguments, returns queryStrand value. : In array context without arguments, returns a two-element list : of strings (queryStrand, sbjctStrand). : Array context can be "induced" by providing an argument of 'list' or 'array'. Argument : seq_type: 'query' or 'hit' or 'sbjct' or undef : ('sbjct' is synonymous with 'hit') Throws : n/a See Also : L, L =cut #----------- sub strand { #----------- my( $self, $seqType ) = @_; $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; ## Sensitive to member name format. $seqType = "_\L$seqType\E"; # $seqType could be '_list'. $self->{'_queryStrand'} or $self->_set_seq_data() unless $self->{'_set_seq_data'}; my $prog = $self->algorithm; if($seqType =~ /list|array/i) { my ($qstr, $hstr); if( $prog eq 'BLASTP') { $qstr = 0; $hstr = 0; } elsif( $prog eq 'TBLASTN') { $qstr = 0; $hstr = $STRAND_SYMBOL{$self->{'_sbjctStrand'}}; } elsif( $prog eq 'BLASTX') { $qstr = $STRAND_SYMBOL{$self->{'_queryStrand'}}; $hstr = 0; } else { $qstr = $STRAND_SYMBOL{$self->{'_queryStrand'}} if defined $self->{'_queryStrand'}; $hstr = $STRAND_SYMBOL{$self->{'_sbjctStrand'}} if defined $self->{'_sbjctStrand'}; } $qstr ||= 0; $hstr ||= 0; return ($qstr, $hstr); } local $^W = 0; $STRAND_SYMBOL{$self->{$seqType.'Strand'}} || 0; } =head2 seq Usage : $hsp->seq( [seq_type] ); Purpose : Get the query or sbjct sequence as a Bio::Seq.pm object. Example : $seqObj = $hsp->seq('query'); Returns : Object reference for a Bio::Seq.pm object. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query'). : ('sbjct' is synonymous with 'hit') Throws : Propagates any exception that occurs during construction : of the Bio::Seq.pm object. Comments : The sequence is returned in an array of strings corresponding : to the strings in the original format of the Blast alignment. : (i.e., same spacing). See Also : L, L, L =cut #------- sub seq { #------- my($self,$seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; my $str = $self->seq_str($seqType); require Bio::Seq; Bio::Seq->new(-ID => $self->to_string, -SEQ => $str, -DESC => "$seqType sequence", ); } =head2 seq_str Usage : $hsp->seq_str( seq_type ); Purpose : Get the full query, sbjct, or 'match' sequence as a string. : The 'match' sequence is the string of symbols in between the : query and sbjct sequences. Example : $str = $hsp->seq_str('query'); Returns : String Argument : seq_Type = 'query' or 'hit' or 'sbjct' or 'match' : ('sbjct' is synonymous with 'hit') Throws : Exception if the argument does not match an accepted seq_type. Comments : Calls _set_seq_data() to set the 'match' sequence if it has : not been set already. See Also : L, L, L =cut #------------ sub seq_str { #------------ my($self,$seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; $self->_set_seq_data() unless $self->{'_set_seq_data'}; if($seqType =~ /sbjct|query/) { my $seq = join('',@{$self->{$seqType.'Seq'}}); $seq =~ s/\s+//g; return $seq; } elsif( $seqType =~ /match/i) { # Only need to call _set_match_seq() if the match seq is requested. my $aref = $self->_set_match_seq() unless ref $self->{'_matchSeq'}; $aref = $self->{'_matchSeq'}; return join('',@$aref); } else { my $id_str = $self->_id_str; $self->throw(-class => 'Bio::Root::BadParameter', -text => "Invalid or undefined sequence type: $seqType ($id_str)\n" . "Valid types: query, sbjct, match", -value => $seqType); } } =head2 seq_inds Usage : $hsp->seq_inds( seq_type, class, collapse ); Purpose : Get a list of residue positions (indices) for all identical : or conserved residues in the query or sbjct sequence. Example : @s_ind = $hsp->seq_inds('query', 'identical'); : @h_ind = $hsp->seq_inds('hit', 'conserved'); : @h_ind = $hsp->seq_inds('hit', 'conserved', 1); Returns : List of integers : May include ranges if collapse is true. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = query) : ('sbjct' is synonymous with 'hit') : class = 'identical' or 'conserved' (default = identical) : (can be shortened to 'id' or 'cons') : (actually, anything not 'id' will evaluate to 'conserved'). : collapse = boolean, if true, consecutive positions are merged : using a range notation, e.g., "1 2 3 4 5 7 9 10 11" : collapses to "1-5 7 9-11". This is useful for : consolidating long lists. Default = no collapse. Throws : n/a. Comments : Calls _set_residues() to set the 'match' sequence if it has : not been set already. See Also : L, L, L, L =cut #--------------- sub seq_inds { #--------------- my ($self, $seqType, $class, $collapse) = @_; $seqType ||= 'query'; $class ||= 'identical'; $collapse ||= 0; $seqType = 'sbjct' if $seqType eq 'hit'; $self->_set_residues() unless defined $self->{'_identicalRes_query'}; $seqType = ($seqType !~ /^q/i ? 'sbjct' : 'query'); $class = ($class !~ /^id/i ? 'conserved' : 'identical'); ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; $class = "_\L$class\E"; my @ary = sort { $a <=> $b } keys %{ $self->{"${class}Res$seqType"}}; require Bio::Search::BlastUtils if $collapse; return $collapse ? &Bio::Search::BlastUtils::collapse_nums(@ary) : @ary; } =head2 get_aln Usage : $hsp->get_aln() Purpose : Get a Bio::SimpleAlign object constructed from the query + sbjct : sequences of the present HSP object. Example : $aln_obj = $hsp->get_aln(); Returns : Object reference for a Bio::SimpleAlign.pm object. Argument : n/a. Throws : Propagates any exception ocurring during the construction of : the Bio::SimpleAlign object. Comments : Requires Bio::SimpleAlign. : The Bio::SimpleAlign object is constructed from the query + sbjct : sequence objects obtained by calling seq(). : Gap residues are included (see $GAP_SYMBOL). See Also : L, L =cut #------------ sub get_aln { #------------ my $self = shift; require Bio::SimpleAlign; require Bio::LocatableSeq; my $qseq = $self->seq('query'); my $sseq = $self->seq('sbjct'); my $type = $self->algorithm =~ /P$|^T/ ? 'amino' : 'dna'; my $aln = Bio::SimpleAlign->new(); $aln->add_seq(Bio::LocatableSeq->new(-seq => $qseq->seq(), -id => 'query_'.$qseq->display_id(), -start => 1, -end => CORE::length($qseq))); $aln->add_seq(Bio::LocatableSeq->new(-seq => $sseq->seq(), -id => 'hit_'.$sseq->display_id(), -start => 1, -end => CORE::length($sseq))); return $aln; } 1; __END__ =head1 FOR DEVELOPERS ONLY =head2 Data Members Information about the various data members of this module is provided for those wishing to modify or understand the code. Two things to bear in mind: =over 4 =item 1 Do NOT rely on these in any code outside of this module. All data members are prefixed with an underscore to signify that they are private. Always use accessor methods. If the accessor doesn't exist or is inadequate, create or modify an accessor (and let me know, too!). =item 2 This documentation may be incomplete and out of date. It is easy for these data member descriptions to become obsolete as this module is still evolving. Always double check this info and search for members not described here. =back An instance of Bio::Search::HSP::BlastHSP.pm is a blessed reference to a hash containing all or some of the following fields: FIELD VALUE -------------------------------------------------------------- (member names are mostly self-explanatory) _score : _bits : _p : _n : Integer. The 'N' value listed in parenthesis with P/Expect value: : e.g., P(3) = 1.2e-30 ---> (N = 3). : Not defined in NCBI Blast2 with gaps. : To obtain the number of HSPs, use Bio::Search::Hit::BlastHit::num_hsps(). _expect : _queryLength : _queryGaps : _queryStart : _queryStop : _querySeq : _sbjctLength : _sbjctGaps : _sbjctStart : _sbjctStop : _sbjctSeq : _matchSeq : String. Contains the symbols between the query and sbjct lines which indicate identical (letter) and conserved ('+') matches or a mismatch (' '). _numIdentical : _numConserved : _identicalRes_query : _identicalRes_sbjct : _conservedRes_query : _conservedRes_sbjct : _match_indent : The number of leading space characters on each line containing the match symbols. _match_indent is 13 in this example: Query: 285 QNSAPWGLARISHRERLNLGSFNKYLYDDDAG Q +APWGLARIS G+ + Y YD+ AG ^^^^^^^^^^^^^ =cut 1; BioPerl-1.007002/Bio/Search/HSP/BlastPullHSP.pm000444000766000024 3720013155576320 20720 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::HSP::BlastPullHSP # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::HSP::BlastPullHSP - A parser and HSP object for BlastN hsps =head1 SYNOPSIS # generally we use Bio::SearchIO to build these objects use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer_pull', -file => 'result.blast'); while (my $result = $in->next_result) { while (my $hit = $result->next_hit) { print $hit->name, "\n"; print $hit->score, "\n"; print $hit->significance, "\n"; while (my $hsp = $hit->next_hsp) { # process HSPI objects } } } =head1 DESCRIPTION This object implements a parser for BlastN hsp output. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::HSP::BlastPullHSP; use strict; use base qw(Bio::Search::HSP::PullHSPI); =head2 new Title : new Usage : my $obj = Bio::Search::HSP::BlastNHSP->new(); Function: Builds a new Bio::Search::HSP::BlastNHSP object. Returns : Bio::Search::HSP::BlastNHSP Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent) -parent => Bio::PullParserI object (required if no -chunk) where the array ref provided to -chunk contains an IO object for a filehandle to something representing the raw data of the hsp, and $start and $end define the tell() position within the filehandle that the hsp data starts and ends (optional; defaults to start and end of the entire thing described by the filehandle) =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->_setup(@args); my $fields = $self->_fields; foreach my $field (qw( header alignment query_strand hit_strand )) { $fields->{$field} = undef; } $self->_dependencies( { ( score => 'header', bits => 'header', evalue => 'header', total_gaps => 'header', query_strand => 'header', hit_strand => 'header', alignment => 'header', query_string => 'alignment', hit_string => 'alignment', homology_string => 'alignment', query_start => 'alignment', query_end => 'alignment', hit_start => 'alignment', hit_end => 'alignment', hit_identical_inds => 'seq_inds', hit_conserved_inds => 'seq_inds', hit_nomatch_inds => 'seq_inds', hit_gap_inds => 'seq_inds', query_identical_inds => 'seq_inds', query_conserved_inds => 'seq_inds', query_nomatch_inds => 'seq_inds', query_gap_inds => 'seq_inds' ) } ); return $self; } # # PullParserI discovery methods so we can answer all HitI questions # sub _discover_header { my $self = shift; $self->_chunk_seek(0); my $header = $self->_get_chunk_by_end("\nQuery"); $self->{_after_header} = $self->_chunk_tell; ($self->_fields->{bits}, $self->_fields->{score}, $self->_fields->{evalue}, $self->_fields->{total_gaps}, $self->_fields->{query_strand}, $self->_fields->{hit_strand}) = $header =~ /^\s*(\S+) bits \((\d+)\),\s+Expect = (\S+)(?:\s+.+Gaps = (\d+))?(?:.+Strand\s*=\s*(\w+)\s*\/\s*(\w+))?/sm; if ($self->_fields->{query_strand}) { # protein blasts don't have strand for my $strand_type ('query_strand', 'hit_strand') { $self->_fields->{$strand_type} = $self->_fields->{$strand_type} eq 'Plus' ? 1 : -1; } } else { $self->_fields->{query_strand} = 0; $self->_fields->{hit_strand} = 0; } if ($self->_fields->{evalue} =~ /^e/) { $self->_fields->{evalue} = '1'.$self->_fields->{evalue}; } # query_gaps isn't always given $self->_fields->{total_gaps} = '[unset]' unless $self->_fields->{total_gaps}; $self->_fields->{header} = 1; } sub _discover_alignment { my $self = shift; $self->_chunk_seek($self->{_after_header}); # work out various basic fields for the hsp # (quicker to do this all at once instead of each method working on # alignment itself) my ($query_string, $hit_string, $homology_string, $q_start, $h_start, $q_end, $h_end); while (my $strip = $self->_get_chunk_by_end("\nQuery") || $self->_get_chunk_by_nol(4)) { $strip =~ /\s+(\d+)\s+(\S+)\s+(\d+)\s+(\S.+)\nSbjct:?\s+(\d+)\s+(\S+)\s+(\d+)/gm || last; my $q1 = $1; $query_string .= $2; my $q2 = $3; my $hom = $4; my $h1 = $5; $hit_string .= $6; my $h2 = $7; $hom = ' 'x(length($6) - length($hom)).$hom; $homology_string .= $hom; for my $q ($q1, $q2) { if (! defined $q_start || $q < $q_start) { $q_start = $q; } if (! defined $q_end || $q > $q_end) { $q_end = $q; } } for my $h ($h1, $h2) { if (! defined $h_start || $h < $h_start) { $h_start = $h; } if (! defined $h_end || $h > $h_end) { $h_end = $h; } } } $self->_fields->{query_string} = $query_string; $self->_fields->{hit_string} = $hit_string; $self->_fields->{homology_string} = $homology_string; $self->_fields->{query_start} = $q_start; $self->_fields->{query_end} = $q_end; $self->_fields->{hit_start} = $h_start; $self->_fields->{hit_end} = $h_end; ($self->{_query_gaps}) = $query_string =~ tr/-//; ($self->{_hit_gaps}) = $hit_string =~ tr/-//; ($self->{_total_gaps}) = $self->{_query_gaps} + $self->{_hit_gaps}; $self->_fields->{alignment} = 1; # stop this method being called again } # seq_inds related methods, all just need seq_inds field to have been gotten sub _discover_seq_inds { my $self = shift; my ($seqString, $qseq, $sseq) = ( $self->get_field('homology_string'), $self->get_field('query_string'), $self->get_field('hit_string') ); # (code largely lifted from GenericHSP) # Using hashes to avoid saving duplicate residue numbers. my %identicalList_query = (); my %identicalList_sbjct = (); my %conservedList_query = (); my %conservedList_sbjct = (); my @gapList_query = (); my @gapList_sbjct = (); my %nomatchList_query = (); my %nomatchList_sbjct = (); my $resCount_query = $self->get_field('query_end'); my $resCount_sbjct = $self->get_field('hit_end'); my ($mchar, $schar, $qchar); while ($mchar = chop($seqString) ) { ($qchar, $schar) = (chop($qseq), chop($sseq)); if ($mchar eq '+' || $mchar eq '.' || $mchar eq ':') { $conservedList_query{ $resCount_query } = 1; $conservedList_sbjct{ $resCount_sbjct } = 1; } elsif ($mchar eq ' ') { $nomatchList_query{ $resCount_query } = 1; $nomatchList_sbjct{ $resCount_sbjct } = 1; } else { $identicalList_query{ $resCount_query } = 1; $identicalList_sbjct{ $resCount_sbjct } = 1; } if ($qchar eq '-') { push(@gapList_query, $resCount_query); } else { $resCount_query -= 1; } if ($schar eq '-') { push(@gapList_sbjct, $resCount_sbjct); } else { $resCount_sbjct -= 1; } } my $fields = $self->_fields; $fields->{hit_identical_inds} = [ sort { $a <=> $b } keys %identicalList_sbjct ]; $fields->{hit_conserved_inds} = [ sort { $a <=> $b } keys %conservedList_sbjct ]; $fields->{hit_nomatch_inds} = [ sort { $a <=> $b } keys %nomatchList_sbjct ]; $fields->{hit_gap_inds} = [ reverse @gapList_sbjct ]; $fields->{query_identical_inds} = [ sort { $a <=> $b } keys %identicalList_query ]; $fields->{query_conserved_inds} = [ sort { $a <=> $b } keys %conservedList_query ]; $fields->{query_nomatch_inds} = [ sort { $a <=> $b } keys %nomatchList_query ]; $fields->{query_gap_inds} = [ reverse @gapList_query ]; $fields->{seq_inds} = 1; } =head2 query Title : query Usage : my $query = $hsp->query Function: Returns a SeqFeature representing the query in the HSP Returns : L Args : none =cut sub query { my $self = shift; unless ($self->{_created_query}) { $self->SUPER::query( new Bio::SeqFeature::Similarity ('-primary' => $self->primary_tag, '-start' => $self->get_field('query_start'), '-end' => $self->get_field('query_end'), '-expect' => $self->get_field('evalue'), '-score' => $self->get_field('score'), '-strand' => $self->get_field('query_strand'), '-seq_id' => $self->get_field('query_name'), '-seqlength'=> $self->get_field('query_length'), '-source' => $self->get_field('algorithm'), '-seqdesc' => $self->get_field('query_description'), '-frame' => 0 # not known? ) ); $self->{_created_query} = 1; } return $self->SUPER::query(@_); } =head2 hit Title : hit Usage : my $hit = $hsp->hit Function: Returns a SeqFeature representing the hit in the HSP Returns : L Args : [optional] new value to set =cut sub hit { my $self = shift; unless ($self->{_created_hit}) { $self->SUPER::hit( new Bio::SeqFeature::Similarity ('-primary' => $self->primary_tag, '-start' => $self->get_field('hit_start'), '-end' => $self->get_field('hit_end'), '-expect' => $self->get_field('evalue'), '-score' => $self->get_field('score'), '-strand' => $self->get_field('hit_strand'), '-seq_id' => $self->get_field('name'), '-seqlength'=> $self->get_field('length'), '-source' => $self->get_field('algorithm'), '-seqdesc' => $self->get_field('description'), '-frame' => 0 # not known? ) ); $self->{_created_hit} = 1; } return $self->SUPER::hit(@_); } =head2 gaps Title : gaps Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); Function : Get the number of gap characters in the query, hit, or total alignment. Returns : Integer, number of gap characters or 0 if none Args : 'query' = num conserved / length of query seq (without gaps) 'hit' = num conserved / length of hit seq (without gaps) 'total' = num conserved / length of alignment (with gaps) default = 'total' =cut sub gaps { my ($self, $type) = @_; $type = lc $type if defined $type; $type = 'total' if (! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/); $type = 'hit' if $type =~ /sbjct|subject/; if ($type eq 'total') { my $answer = $self->get_field('total_gaps'); return $answer unless $answer eq '[unset]'; } $self->get_field('alignment'); # make sure gaps have been calculated return $self->{'_'.$type.'_gaps'}; } =head2 strand Title : strand Usage : $hsp->strand('query') Function: Retrieves the strand for the HSP component requested Returns : +1 or -1 (0 if unknown) Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject 'query' to retrieve the query strand (default) 'list' or 'array' to retrieve both query and hit together =cut sub strand { my $self = shift; my $val = shift; $val = 'query' unless defined $val; $val =~ s/^\s+//; if ($val =~ /^q/i) { return $self->get_field('query_strand'); } elsif ($val =~ /^hi|^s/i) { return $self->get_field('hit_strand'); } elsif ($val =~ /^list|array/i) { return ($self->get_field('query_strand'), $self->get_field('hit_strand')); } else { $self->warn("unrecognized component '$val' requested\n"); } return 0; } =head2 start Title : start Usage : $hsp->start('query') Function: Retrieves the start for the HSP component requested Returns : integer, or list of two integers (query start and subject start) in list context Args : 'hit' or 'subject' or 'sbjct' to retrieve the start of the subject 'query' to retrieve the query start (default) =cut sub start { my $self = shift; my $val = shift; $val = (wantarray ? 'list' : 'query') unless defined $val; $val =~ s/^\s+//; if ($val =~ /^q/i) { return $self->get_field('query_start'); } elsif ($val =~ /^(hi|s)/i) { return $self->get_field('hit_start'); } elsif ($val =~ /^list|array/i) { return ($self->get_field('query_start'), $self->get_field('hit_start') ); } else { $self->warn("unrecognized component '$val' requested\n"); } return 0; } =head2 end Title : end Usage : $hsp->end('query') Function: Retrieves the end for the HSP component requested Returns : integer, or list of two integers (query end and subject end) in list context Args : 'hit' or 'subject' or 'sbjct' to retrieve the end of the subject 'query' to retrieve the query end (default) =cut sub end { my $self = shift; my $val = shift; $val = (wantarray ? 'list' : 'query') unless defined $val; $val =~ s/^\s+//; if ($val =~ /^q/i) { return $self->get_field('query_end'); } elsif ($val =~ /^(hi|s)/i) { return $self->get_field('hit_end'); } elsif ($val =~ /^list|array/i) { return ($self->get_field('query_end'), $self->get_field('hit_end')); } else { $self->warn("unrecognized end component '$val' requested\n"); } return 0; } =head2 pvalue Title : pvalue Usage : my $pvalue = $hsp->pvalue(); Function: Returns the P-value for this HSP Returns : undef (Hmmpfam reports do not have p-values) Args : none =cut sub pvalue { } 1; BioPerl-1.007002/Bio/Search/HSP/FastaHSP.pm000444000766000024 1340013155576320 20050 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::HSP::FastaHSP # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data =head1 SYNOPSIS # get a FastaHSP from a SearchIO stream my $in = Bio::SearchIO->new(-format => 'fasta', -file => 'filename.fasta'); while( my $r = $in->next_result) { while( my $hit = $r->next_result ) { while( my $hsp = $hit->next_hsp ) { print "smith-waterman score (if available): ", $hsp->sw_score(),"\n"; } } } =head1 DESCRIPTION Describe the object here =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::HSP::FastaHSP; use strict; use base qw(Bio::Search::HSP::GenericHSP); =head2 new Title : new Usage : my $obj = Bio::Search::HSP::FastaHSP->new(); Function: Builds a new Bio::Search::HSP::FastaHSP object Returns : Bio::Search::HSP::FastaHSP Args : -swscore => smith-waterman score =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($swscore, $evalue2) = $self->_rearrange([qw(SWSCORE EVALUE2)], @args); defined $swscore && $self->sw_score($swscore); defined $evalue2 && $self->evalue2($evalue2); return $self; } =head2 sw_score Title : sw_score Usage : $obj->sw_score($newval) Function: Get/Set Smith-Waterman score Returns : value of sw_score Args : newvalue (optional) =cut sub sw_score{ my ($self,$value) = @_; if( defined $value || ! defined $self->{'_sw_score'} ) { $value = 0 unless defined $value; # default value $self->{'_sw_score'} = $value; } return $self->{'_sw_score'}; } =head2 evalue2 Title : evalue2 Usage : $obj->evalue2($newval) Function: Get/Set E2() expectation value Returns : value of evalue2 Args : newvalue (optional) =cut sub evalue2{ my ($self,$value) = @_; if( defined $value || ! defined $self->{'_evalue2'} ) { $value = 0 unless defined $value; # default value $self->{'_evalue2'} = $value; } return $self->{'_evalue2'}; } sub get_aln { my ($self) = @_; require Bio::LocatableSeq; require Bio::SimpleAlign; my $aln = Bio::SimpleAlign->new(); my $hs = $self->hit_string(); my $qs = $self->query_string(); # fasta reports some extra 'regional' sequence information # we need to clear out first # this seemed a bit insane to me at first, but it appears to # work --jason # modified to deal with LocatableSeq's end point verification and to deal # with frameshifts (which shift the end points in translated sequences). # we infer the end of the regional sequence where the first # non space is in the homology string # then we use the HSP->length to tell us how far to read # to cut off the end of the sequence my ($start, $rest) = (0, 0); if( $self->homology_string() =~ /^(\s+)?(.*?)\s*$/ ) { ($start, $rest) = ($1 ? CORE::length($1) : 0, CORE::length($2)); } $self->debug("hs seq is '$hs'\n"); $self->debug("qs seq is '$qs'\n"); $hs = substr($hs, $start,$rest); $qs = substr($qs, $start,$rest); my $seqonly = $qs; $seqonly =~ s/\s+//g; my ($q_nm,$s_nm) = ($self->query->seq_id(), $self->hit->seq_id()); unless( defined $q_nm && CORE::length ($q_nm) ) { $q_nm = 'query'; } unless( defined $s_nm && CORE::length ($s_nm) ) { $s_nm = 'hit'; } $self->_calculate_seq_positions; my $query = Bio::LocatableSeq->new('-seq' => $seqonly, '-id' => $q_nm, '-start' => $self->query->start, '-end' => $self->query->end, '-frameshifts' => (exists $self->{seqinds}{_frameshiftRes_query}) ? $self->{seqinds}{_frameshiftRes_query} : undef, '-mapping' => [1, $self->{_query_mapping}], -verbose => $self->verbose ); $seqonly = $hs; $seqonly =~ s/\s+//g; my $hit = Bio::LocatableSeq->new('-seq' => $seqonly, '-id' => $s_nm, '-start' => $self->hit->start, '-end' => $self->hit->end, '-frameshifts' => exists $self->{seqinds}{_frameshiftRes_sbjct} ? $self->{seqinds}{_frameshiftRes_sbjct} : undef, '-mapping' => [1, $self->{_hit_mapping}], -verbose => $self->verbose ); $aln->add_seq($query); $aln->add_seq($hit); return $aln; } 1; BioPerl-1.007002/Bio/Search/HSP/GenericHSP.pm000444000766000024 16025213155576320 20416 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::HSP::GenericHSP # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair =head1 SYNOPSIS my $hsp = Bio::Search::HSP::GenericHSP->new( -algorithm => 'blastp', -evalue => '1e-30', ); $r_type = $hsp->algorithm; $pvalue = $hsp->p(); $evalue = $hsp->evalue(); $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] ); $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] ); $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); $qseq = $hsp->query_string; $hseq = $hsp->hit_string; $homo_string = $hsp->homology_string; $len = $hsp->length( ['query'|'hit'|'total'] ); $len = $hsp->length( ['query'|'hit'|'total'] ); $rank = $hsp->rank; # TODO: Describe how to configure a SearchIO stream so that it generates # GenericHSP objects. =head1 DESCRIPTION This implementation is "Generic", meaning it is is suitable for holding information about High Scoring pairs from most Search reports such as BLAST and FastA. Specialized objects can be derived from this. Unless you're writing a parser, you won't ever need to create a GenericHSP or any other HSPI-implementing object. If you use the SearchIO system, HSPI objects are created automatically from a SearchIO stream which returns Bio::Search::Result::ResultI objects and you get the HSPI objects via the ResultI API. For documentation on what you can do with GenericHSP (and other HSPI objects), please see the API documentation in L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich and Steve Chervitz Email jason-at-bioperl.org Email sac-at-bioperl.org =head1 CONTRIBUTORS Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::HSP::GenericHSP; use strict; use Bio::Root::Root; use Bio::SeqFeature::Similarity; use base qw(Bio::Search::HSP::HSPI); =head2 new Title : new Usage : my $obj = Bio::Search::HSP::GenericHSP->new(); Function: Builds a new Bio::Search::HSP::GenericHSP object Returns : Bio::Search::HSP::GenericHSP Args : -algorithm => algorithm used (BLASTP, TBLASTX, FASTX, etc) -evalue => evalue -pvalue => pvalue -bits => bit value for HSP -score => score value for HSP (typically z-score but depends on analysis) -hsp_length=> Length of the HSP (including gaps) -identical => # of residues that that matched identically -percent_identity => (optional) percent identity -conserved => # of residues that matched conservatively (only protein comparisons; conserved == identical in nucleotide comparisons) -hsp_gaps => # of gaps in the HSP -query_gaps => # of gaps in the query in the alignment -hit_gaps => # of gaps in the subject in the alignment -query_name => HSP Query sequence name (if available) -query_start => HSP Query start (in original query sequence coords) -query_end => HSP Query end (in original query sequence coords) -query_length=> total length of the query sequence -query_seq => query sequence portion of the HSP -query_desc => textual description of the query -hit_name => HSP Hit sequence name (if available) -hit_start => HSP Hit start (in original hit sequence coords) -hit_end => HSP Hit end (in original hit sequence coords) -hit_length => total length of the hit sequence -hit_seq => hit sequence portion of the HSP -hit_desc => textual description of the hit -homology_seq=> homology sequence for the HSP -hit_frame => hit frame (only if hit is translated protein) -query_frame => query frame (only if query is translated protein) -rank => HSP rank -links => HSP links information (WU-BLAST only) -hsp_group => HSP Group informat (WU-BLAST only) -gap_symbol => symbol representing a gap (default = '-') -hit_features=> string of features found in or near HSP hit region (reported in some BLAST text output, v. 2.2.13 and up) -stranded => If the algorithm isn't known (i.e. defaults to 'generic'), setting this will indicate start/end coordinates are to be used to determine the strand for 'query', 'subject', 'hit', 'both', or 'none' (default = 'none') =cut sub new { my($class,%args) = @_; # don't pass anything to SUPER; complex hierarchy results in lots of work # for nothing my $self = $class->SUPER::new(); # for speed, don't use _rearrange and just store all input data directly # with no method calls and no work done. work can be carried # out just-in-time later if desired while (my ($arg, $value) = each %args) { $arg =~ tr/a-z\055/A-Z/d; $self->{$arg} = $value; } my $bits = $self->{BITS}; defined $self->{VERBOSE} && $self->verbose($self->{VERBOSE}); if (exists $self->{GAP_SYMBOL}) { # not checking anything else but the length (must be 1 as only one gap # symbol allowed currently); can add in support for symbol checks or # multiple symbols later if needed $self->throw("Gap symbol must be of length 1") if CORE::length($self->{GAP_SYMBOL}) != 1; } else { # dafault $self->{GAP_SYMBOL} = '-'; } $self->{ALGORITHM} ||= 'GENERIC'; $self->{STRANDED} ||= 'NONE'; if (! defined $self->{QUERY_LENGTH} || ! defined $self->{HIT_LENGTH}) { $self->throw("Must define hit and query length"); } $self->{'_sequenceschanged'} = 1; $self->{_finished_new} = 1; return $self; } sub _logical_length { my ($self, $type) = @_; if (!defined($self->{_sbjct_offset}) || !defined($self->{_query_offset})) { $self->_calculate_seq_offsets(); } my $key = $type =~ /sbjct|hit|tot/i ? 'sbjct' : 'query'; my $offset = $self->{"_${key}_offset"}; return $self->length($type) / $offset ; } =head2 L methods Implementation of L methods follow =head2 algorithm Title : algorithm Usage : my $r_type = $hsp->algorithm Function: Obtain the name of the algorithm used to obtain the HSP Returns : string (e.g., BLASTP) Args : [optional] scalar string to set value =cut sub algorithm{ my ($self,$value) = @_; my $previous = $self->{'ALGORITHM'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'ALGORITHM'} = $value; } return $previous; } =head2 pvalue Title : pvalue Usage : my $pvalue = $hsp->pvalue(); Function: Returns the P-value for this HSP or undef Returns : float or exponential (2e-10) P-value is not defined with NCBI Blast2 reports. Args : [optional] numeric to set value =cut sub pvalue { my ($self,$value) = @_; my $previous = $self->{'PVALUE'}; if( defined $value ) { $self->{'PVALUE'} = $value; } return $previous; } =head2 evalue Title : evalue Usage : my $evalue = $hsp->evalue(); Function: Returns the e-value for this HSP Returns : float or exponential (2e-10) Args : [optional] numeric to set value =cut sub evalue { my ($self,$value) = @_; my $previous = $self->{'EVALUE'}; if( defined $value ) { $self->{'EVALUE'} = $value; } return $previous; } =head2 frac_identical Title : frac_identical Usage : my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] ); Function: Returns the fraction of identitical positions for this HSP Returns : Float in range 0.0 -> 1.0 Args : arg 1: 'query' = num identical / length of query seq (without gaps) 'hit' = num identical / length of hit seq (without gaps) synonyms: 'sbjct', 'subject' 'total' = num identical / length of alignment (with gaps) synonyms: 'hsp' default = 'total' arg 2: [optional] frac identical value to set for the type requested Note : for translated sequences, this adjusts the length accordingly =cut sub frac_identical { my ($self, $type,$value) = @_; unless ($self->{_did_prefrac}) { $self->_pre_frac; } $type = lc $type if defined $type; $type = 'hit' if( defined $type && $type =~ /subject|sbjct/); $type = 'total' if( ! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/); my $previous = $self->{'_frac_identical'}->{$type}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; if( $type eq 'hit' || $type eq 'query' ) { $self->$type()->frac_identical( $value); } $self->{'_frac_identical'}->{$type} = $value; } return $previous; } =head2 frac_conserved Title : frac_conserved Usage : my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] ); Function : Returns the fraction of conserved positions for this HSP. This is the fraction of symbols in the alignment with a positive score. Returns : Float in range 0.0 -> 1.0 Args : arg 1: 'query' = num conserved / length of query seq (without gaps) 'hit' = num conserved / length of hit seq (without gaps) synonyms: 'sbjct', 'subject' 'total' = num conserved / length of alignment (with gaps) synonyms: 'hsp' default = 'total' arg 2: [optional] frac conserved value to set for the type requested =cut sub frac_conserved { my ($self, $type,$value) = @_; unless ($self->{_did_prefrac}) { $self->_pre_frac; } $type = lc $type if defined $type; $type = 'hit' if( defined $type && $type =~ /subject|sbjct/); $type = 'total' if( ! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/); my $previous = $self->{'_frac_conserved'}->{$type}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_frac_conserved'}->{$type} = $value; } return $previous; } =head2 gaps Title : gaps Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); Function : Get the number of gap characters in the query, hit, or total alignment. Returns : Integer, number of gaps or 0 if none Args : arg 1: 'query' = num gap characters in query seq 'hit' = num gap characters in hit seq; synonyms: 'sbjct', 'subject' 'total' = num gap characters in whole alignment; synonyms: 'hsp' default = 'total' arg 2: [optional] integer gap value to set for the type requested =cut sub gaps { my ($self, $type, $value) = @_; unless ($self->{_did_pregaps}) { $self->_pre_gaps; } $type = lc $type if defined $type; $type = 'total' if( ! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/); $type = 'hit' if $type =~ /sbjct|subject/; my $previous = $self->{'_gaps'}->{$type}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_gaps'}->{$type} = $value; } return $previous || 0; } =head2 query_string Title : query_string Usage : my $qseq = $hsp->query_string; Function: Retrieves the query sequence of this HSP as a string Returns : string Args : [optional] string to set for query sequence =cut sub query_string{ my ($self,$value) = @_; my $previous = $self->{QUERY_SEQ}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{QUERY_SEQ} = $value; # do some housekeeping so we know when to # re-run _calculate_seq_positions $self->{'_sequenceschanged'} = 1; } return $previous; } =head2 hit_string Title : hit_string Usage : my $hseq = $hsp->hit_string; Function: Retrieves the hit sequence of this HSP as a string Returns : string Args : [optional] string to set for hit sequence =cut sub hit_string{ my ($self,$value) = @_; my $previous = $self->{HIT_SEQ}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{HIT_SEQ} = $value; # do some housekeeping so we know when to # re-run _calculate_seq_positions $self->{'_sequenceschanged'} = 1; } return $previous; } =head2 homology_string Title : homology_string Usage : my $homo_string = $hsp->homology_string; Function: Retrieves the homology sequence for this HSP as a string. : The homology sequence is the string of symbols in between the : query and hit sequences in the alignment indicating the degree : of conservation (e.g., identical, similar, not similar). Returns : string Args : [optional] string to set for homology sequence =cut sub homology_string{ my ($self,$value) = @_; my $previous = $self->{HOMOLOGY_SEQ}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{HOMOLOGY_SEQ} = $value; # do some housekeeping so we know when to # re-run _calculate_seq_positions $self->{'_sequenceschanged'} = 1; } return $previous; } =head2 consensus_string Title : consensus_string Usage : my $cs_string = $hsp->consensus_string; Function: Retrieves the consensus structure line for this HSP as a string (HMMER). : If the model had any consensus structure or reference line annotation : that it inherited from a multiple alignment (#=GC SS cons, : #=GC RF annotation in Stockholm files), that information is shown : as CS or RF annotation line. Returns : string Args : [optional] string to set for consensus structure =cut sub consensus_string { my ($self,$value) = @_; my $previous = $self->{CS_SEQ}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{CS_SEQ} = $value; # do some housekeeping so we know when to # re-run _calculate_seq_positions $self->{'_sequenceschanged'} = 1; } return $previous; } =head2 posterior_string Title : posterior_string Usage : my $pp_string = $hsp->posterior_string; Function: Retrieves the posterior probability line for this HSP as a string (HMMer3). : The posterior probability is the string of symbols at the bottom : of the alignment indicating the expected accuracy of each aligned residue. : A 0 means 0-5%, 1 means 5-15%, and so on; 9 means 85-95%, : and a * means 95-100% posterior probability. Returns : string Args : [optional] string to set for posterior probability =cut sub posterior_string { my ($self,$value) = @_; my $previous = $self->{PP_SEQ}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{PP_SEQ} = $value; # do some housekeeping so we know when to # re-run _calculate_seq_positions $self->{'_sequenceschanged'} = 1; } return $previous; } =head2 length Title : length Usage : my $len = $hsp->length( ['query'|'hit'|'total'] ); Function : Returns the length of the query or hit in the alignment (without gaps) or the aggregate length of the HSP (including gaps; this may be greater than either hit or query ) Returns : integer Args : arg 1: 'query' = length of query seq (without gaps) 'hit' = length of hit seq (without gaps) (synonyms: sbjct, subject) 'total' = length of alignment (with gaps) default = 'total' arg 2: [optional] integer length value to set for specific type =cut sub length { my $self = shift; my $type = shift; $type = 'total' unless defined $type; $type = lc $type; if( $type =~ /^q/i ) { return $self->query()->length(shift); } elsif( $type =~ /^(hit|subject|sbjct)/ ) { return $self->hit()->length(shift); } else { my $v = shift; if( defined $v ) { $self->{HSP_LENGTH} = $v; } return $self->{HSP_LENGTH}; } return 0; # should never get here } =head2 hsp_length Title : hsp_length Usage : my $len = $hsp->hsp_length() Function: shortcut length('hsp') Returns : floating point between 0 and 100 Args : none =cut sub hsp_length { return shift->length('hsp', shift); } =head2 percent_identity Title : percent_identity Usage : my $percentid = $hsp->percent_identity() Function: Returns the calculated percent identity for an HSP Returns : floating point between 0 and 100 Args : none =cut sub percent_identity { my $self = shift; unless ($self->{_did_prepi}) { $self->_pre_pi; } return $self->SUPER::percent_identity(@_); } =head2 frame Title : frame Usage : my ($qframe, $hframe) = $hsp->frame('list',$queryframe,$subjectframe) Function: Set the Frame for both query and subject and insure that they agree. This overrides the frame() method implementation in FeaturePair. Returns : array of query and subject frame if return type wants an array or query frame if defined or subject frame if not defined Args : 'hit' or 'subject' or 'sbjct' to retrieve the frame of the subject (default) 'query' to retrieve the query frame 'list' or 'array' to retrieve both query and hit frames together Note : Frames are stored in the GFF way (0-2) not 1-3 as they are in BLAST (negative frames are deduced by checking the strand of the query or hit) =cut # Note: changed 4/19/08 - bug 2485 # # frame() is supposed to be a getter/setter (as is implied by the Function desc # above; this is also consistent with Bio::SeqFeature::SimilarityPair). Also, # the API is not consistent with the other HSP/SimilarityPair methods such as # strand(), start(), end(), etc. # # In order to make this consistent with other methods all work is now done # when the features are instantiated and not delayed. We compromise by # defaulting back 'to hit' w/o passed args. Setting is now allowed. sub frame { my $self = shift; my $val = shift; if (!defined $val) { # unfortunately, w/o args we need to warn about API changes $self->warn("API for frame() has changed.\n". "Please refer to documentation for Bio::Search::HSP::GenericHSP;\n". "returning query frame"); $val = 'query'; } $val =~ s/^\s+//; if( $val =~ /^q/i ) { return $self->query->frame(@_); } elsif( $val =~ /^hi|^s/i ) { return $self->hit->frame(@_); } elsif ( $val =~ /^list|array/i ) { return ($self->query->frame($_[0]), $self->hit->frame($_[1]) ); } elsif ( $val =~ /^\d+$/) { # old API i.e. frame($query_frame, $hit_frame). This catches all but one # case, where no arg is passed (so the hit is wanted). $self->warn("API for frame() has changed.\n". "Please refer to documentation for Bio::Search::HSP::GenericHSP"); wantarray ? return ($self->query->frame($val), $self->hit->frame(@_) ) : return $self->hit->frame($val,@_); } else { $self->warn("unrecognized component '$val' requested\n"); } return 0; } =head2 get_aln Title : get_aln Usage : my $aln = $hsp->gel_aln Function: Returns a L object representing the HSP alignment Returns : L Args : none =cut sub get_aln { my ($self) = @_; require Bio::LocatableSeq; require Bio::SimpleAlign; my $aln = Bio::SimpleAlign->new(); my $hs = $self->hit_string(); my $qs = $self->query_string(); # FASTA specific stuff moved to the FastaHSP object my $seqonly = $qs; $seqonly =~ s/[\-\s]//g; my ($q_nm,$s_nm) = ($self->query->seq_id(), $self->hit->seq_id()); # Should we silently change the name of the query or hit if it isn't # defined? May need revisiting... cjfields 2008-12-3 (commented out below) #unless( defined $q_nm && CORE::length ($q_nm) ) { # $q_nm = 'query'; #} #unless( defined $s_nm && CORE::length ($s_nm) ) { # $s_nm = 'hit'; #} # mapping: 1 residues for every x coordinate positions my $query = Bio::LocatableSeq->new( -seq => $qs, -id => $q_nm, -start => $self->query->start, -end => $self->query->end, -strand => $self->query->strand, -force_nse => $q_nm ? 0 : 1, -mapping => [ 1, $self->{_query_mapping} ] ); $seqonly = $hs; $seqonly =~ s/[\-\s]//g; my $hit = Bio::LocatableSeq->new( -seq => $hs, -id => $s_nm, -start => $self->hit->start, -end => $self->hit->end, -strand => $self->hit->strand, -force_nse => $s_nm ? 0 : 1, -mapping => [ 1, $self->{_hit_mapping} ] ); $aln->add_seq($query); $aln->add_seq($hit); return $aln; } =head2 num_conserved Title : num_conserved Usage : $obj->num_conserved($newval) Function: returns the number of conserved residues in the alignment Returns : integer Args : integer (optional) =cut sub num_conserved{ my ($self,$value) = @_; unless ($self->{_did_presimilar}) { $self->_pre_similar_stats; } if (defined $value) { $self->{CONSERVED} = $value; } return $self->{CONSERVED}; } =head2 num_identical Title : num_identical Usage : $obj->num_identical($newval) Function: returns the number of identical residues in the alignment Returns : integer Args : integer (optional) =cut sub num_identical{ my ($self,$value) = @_; unless ($self->{_did_presimilar}) { $self->_pre_similar_stats; } if( defined $value) { $self->{IDENTICAL} = $value; } return $self->{IDENTICAL}; } =head2 rank Usage : $hsp->rank( [string] ); Purpose : Get the rank of the HSP within a given Blast hit. Example : $rank = $hsp->rank; Returns : Integer (1..n) corresponding to the order in which the HSP appears in the BLAST report. =cut sub rank { my ($self,$value) = @_; if( defined $value) { $self->{RANK} = $value; } return $self->{RANK}; } =head2 seq_inds Title : seq_inds Purpose : Get a list of residue positions (indices) for all identical : or conserved residues in the query or sbjct sequence. Example : @s_ind = $hsp->seq_inds('query', 'identical'); : @h_ind = $hsp->seq_inds('hit', 'conserved'); : @h_ind = $hsp->seq_inds('hit', 'conserved-not-identical'); : @h_ind = $hsp->seq_inds('hit', 'conserved', 1); Returns : List of integers : May include ranges if collapse is true. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = query) : ('sbjct' is synonymous with 'hit') : class = 'identical' - identical positions : 'conserved' - conserved positions : 'nomatch' - mismatched residue or gap positions : 'mismatch' - mismatched residue positions (no gaps) : 'gap' - gap positions only : 'frameshift'- frameshift positions only : 'conserved-not-identical' - conserved positions w/o : identical residues : The name can be shortened to 'id' or 'cons' unless : the name is . The default value is : 'identical' : : collapse = boolean, if true, consecutive positions are merged : using a range notation, e.g., "1 2 3 4 5 7 9 10 11" : collapses to "1-5 7 9-11". This is useful for : consolidating long lists. Default = no collapse. : Throws : n/a. Comments : For HSPs partially or completely derived from translated sequences : (TBLASTN, BLASTX, TBLASTX, or similar), some positional data : cannot easily be attributed to a single position (i.e. the : positional data is ambiguous). In these cases all three codon : positions are reported. Under these conditions you can check : ambiguous_seq_inds() to determine whether the query, subject, : or both are ambiguous. : See Also : L, L =cut sub seq_inds{ my ($self, $seqType, $class, $collapse) = @_; # prepare the internal structures - this is cached so # if the strings have not changed we're okay $self->_calculate_seq_positions(); $seqType ||= 'query'; $class ||= 'identical'; $collapse ||= 0; $seqType = 'sbjct' if $seqType eq 'hit'; my $t = lc(substr($seqType,0,1)); if( $t eq 'q' ) { $seqType = 'query'; } elsif ( $t eq 's' || $t eq 'h' ) { $seqType = 'sbjct'; } else { $self->warn("unknown seqtype $seqType using 'query'"); $seqType = 'query'; } $t = lc(substr($class,0,1)); if( $t eq 'c' ) { if( $class =~ /conserved\-not\-identical/ ) { $class = 'conserved'; } else { $class = 'conservedall'; } } elsif( $t eq 'i' ) { $class = 'identical'; } elsif( $t eq 'n' ) { $class = 'nomatch'; } elsif( $t eq 'm' ) { $class = 'mismatch'; } elsif( $t eq 'g' ) { $class = 'gap'; } elsif( $t eq 'f' ) { $class = 'frameshift'; } else { $self->warn("unknown sequence class $class using 'identical'"); $class = 'identical'; } ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; $class = "_\L$class\E"; my @ary; if( $class eq '_gap' ) { # this means that we are remapping the gap length that is stored # in the hash (for example $self->{'_gapRes_query'} ) # so we'll return an array which has the values of the position of the # of the gap (the key in the hash) + the gap length (value in the # hash for this key - 1. # changing this; since the index is the position prior to the insertion, # repeat the position based on the number of gaps inserted @ary = map { my @tmp; # position holds number of gaps inserted for my $g (1..$self->{seqinds}{"${class}Res$seqType"}->{$_}) { push @tmp, $_ ; } @tmp} sort { $a <=> $b } keys %{ $self->{seqinds}{"${class}Res$seqType"}}; } elsif( $class eq '_conservedall' ) { @ary = sort { $a <=> $b } keys %{ $self->{seqinds}{"_conservedRes$seqType"}}, keys %{ $self->{seqinds}{"_identicalRes$seqType"}}, } else { @ary = sort { $a <=> $b } keys %{ $self->{seqinds}{"${class}Res$seqType"}}; } require Bio::Search::BlastUtils if $collapse; return $collapse ? &Bio::Search::SearchUtils::collapse_nums(@ary) : @ary; } =head2 ambiguous_seq_inds Title : ambiguous_seq_inds Purpose : returns a string denoting whether sequence indices for query, : subject, or both are ambiguous Returns : String; 'query', 'subject', 'query/subject', or empty string '' Argument : none Comments : For HSPs partially or completely derived from translated sequences : (TBLASTN, BLASTX, TBLASTX, or similar), some positional data : cannot easily be attributed to a single position (i.e. the : positional data is ambiguous). In these cases all three codon : positions are reported when using seq_inds(). Under these : conditions you can check ambiguous_seq_inds() to determine whether : the query, subject, or both are ambiguous. See Also : L =cut sub ambiguous_seq_inds { my $self = shift; $self->_calculate_seq_positions(); my $type = ($self->{_query_offset} == 3 && $self->{_sbjct_offset} == 3) ? 'query/subject' : ($self->{_query_offset} == 3) ? 'query' : ($self->{_sbjct_offset} == 3) ? 'subject' : ''; return $type; } =head2 Inherited from L These methods come from L =head2 query Title : query Usage : my $query = $hsp->query Function: Returns a SeqFeature representing the query in the HSP Returns : L Args : [optional] new value to set =cut sub query { my $self = shift; unless ($self->{_created_qff}) { $self->_query_seq_feature; } return $self->SUPER::query(@_); } sub feature1 { my $self = shift; if (! $self->{_finished_new} || $self->{_making_qff}) { return $self->{_sim1} if $self->{_sim1}; $self->{_sim1} = Bio::SeqFeature::Similarity->new(); return $self->{_sim1}; } unless ($self->{_created_qff}) { $self->_query_seq_feature; } return $self->SUPER::feature1(@_); } =head2 hit Title : hit Usage : my $hit = $hsp->hit Function: Returns a SeqFeature representing the hit in the HSP Returns : L Args : [optional] new value to set =cut sub hit { my $self = shift; unless ($self->{_created_sff}) { $self->_subject_seq_feature; } return $self->SUPER::hit(@_); } sub feature2 { my $self = shift; if (! $self->{_finished_new} || $self->{_making_sff}) { return $self->{_sim2} if $self->{_sim2}; $self->{_sim2} = Bio::SeqFeature::Similarity->new(); return $self->{_sim2}; } unless ($self->{_created_sff}) { $self->_subject_seq_feature; } return $self->SUPER::feature2(@_); } =head2 significance Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Get/Set the significance value Returns : numeric Args : [optional] new value to set =cut # Override significance to return the e-value or, if this is # not defined (WU-BLAST), return the p-value. sub significance { my ($self, $val) = @_; if (!defined $self->{SIGNIFICANCE} || defined $val) { $self->{SIGNIFICANCE} = defined $val ? $val : defined $self->evalue ? $self->evalue : defined $self->pvalue ? $$self->pvalue : undef; $self->query->significance($self->{SIGNIFICANCE}); } return $self->{SIGNIFICANCE}; } =head2 strand Title : strand Usage : $hsp->strand('query') Function: Retrieves the strand for the HSP component requested Returns : +1 or -1 Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject, 'query' to retrieve the query strand (default) =cut sub strand { my ($self,$type) = @_; if( $type =~ /^q/i && defined $self->{'QUERY_STRAND'} ) { return $self->{'QUERY_STRAND'}; } elsif( $type =~ /^(hit|subject|sbjct)/i && defined $self->{'HIT_STRAND'} ) { return $self->{'HIT_STRAND'}; } return $self->SUPER::strand($type) } =head2 score Title : score Usage : $score = $obj->score(); $obj->score($value); Function: Get/Set the score value Returns : numeric Args : [optional] new value to set =head2 bits Title : bits Usage : $bits = $obj->bits(); $obj->bits($value); Function: Get/Set the bits value Returns : numeric Args : [optional] new value to set =head1 Private methods =cut =head2 _calculate_seq_positions Title : _calculate_seq_positions Usage : $self->_calculate_seq_positions Function: Internal function Returns : Args : =cut sub _calculate_seq_positions { my ($self,@args) = @_; return unless ( $self->{'_sequenceschanged'} ); $self->{'_sequenceschanged'} = 0; my ($seqString, $qseq,$sseq) = ( $self->homology_string(), $self->query_string(), $self->hit_string() ); my ($mlen, $qlen, $slen) = (CORE::length($seqString), CORE::length($qseq), CORE::length($sseq)); my $qdir = $self->query->strand || 1; my $sdir = $self->hit->strand || 1; my ($resCount_query, $endpoint_query) = ($qdir <=0) ? ($self->query->end, $self->query->start) : ($self->query->start, $self->query->end); my ($resCount_sbjct, $endpoint_sbjct) = ($sdir <=0) ? ($self->hit->end, $self->hit->start) : ($self->hit->start, $self->hit->end); my $prog = $self->algorithm; if( $prog =~ /FAST|SSEARCH|SMITH-WATERMAN/i ) { # we infer the end of the regional sequence where the first and last # non spaces are in the homology string # then we use the HSP->length to tell us how far to read # to cut off the end of the sequence my ($start, $rest) = (0,0); if( $seqString =~ /^(\s+)?(.*?)\s*$/ ) { ($start, $rest) = ($1 ? CORE::length($1) : 0, CORE::length($2)); } $seqString = substr($seqString, $start, $rest); $qseq = substr($qseq, $start, $rest); $sseq = substr($sseq, $start, $rest); # commented out 10/29/08 # removing frameshift symbols doesn't take into account the following: # 1) does not remove the same point in the homology string (get # positional errors) # 2) adjustments to the overall position in the string due to the # frameshift must be taken into consideration (get balancing errors) # # Frameshifts will be handled directly in the main loop. # --chris # fasta reports some extra 'regional' sequence information # we need to clear out first # this seemed a bit insane to me at first, but it appears to # work --jason #$qseq =~ s![\\\/]!!g; #$sseq =~ s![\\\/]!!g; } if (!defined($self->{_sbjct_offset}) || !defined($self->{_query_offset})) { $self->_calculate_seq_offsets(); } my ($qfs, $sfs) = (0,0); CHAR_LOOP: for my $pos (0..CORE::length($seqString)-1) { my @qrange = (0 - $qfs)..($self->{_query_offset} - 1); my @srange = (0 - $sfs)..($self->{_sbjct_offset} - 1); # $self->debug("QRange:@qrange SRange:@srange\n") if ($qfs || $sfs); ($qfs, $sfs) = (0,0); my ($mchar, $qchar, $schar) = ( unpack("x$pos A1",$seqString) || ' ', $pos < CORE::length($qseq) ? unpack("x$pos A1",$qseq) : '-', $pos < CORE::length($sseq) ? unpack("x$pos A1",$sseq) : '-' ); my $matchtype = ''; my ($qgap, $sgap) = (0,0); if( $mchar eq '+' || $mchar eq '.') { # conserved $self->{seqinds}{_conservedRes_query}{ $resCount_query + ($_ * $qdir) } = 1 for @qrange; $self->{seqinds}{_conservedRes_sbjct}{ $resCount_sbjct + ($_ * $sdir) } = 1 for @srange; $matchtype = 'conserved'; } elsif( $mchar eq ':' || $mchar ne ' ' ) { # identical $self->{seqinds}{_identicalRes_query}{ $resCount_query + ($_ * $qdir) } = 1 for @qrange; $self->{seqinds}{_identicalRes_sbjct}{ $resCount_sbjct + ($_ * $sdir) } = 1 for @srange; $matchtype = 'identical'; } elsif( $mchar eq ' ' ) { # possible mismatch/nomatch/frameshift $qfs = $qchar eq '/' ? -1 : # base inserted to match frame $qchar eq '\\' ? 1 : # base deleted to match frame 0; $sfs = $schar eq '/' ? -1 : $schar eq '\\' ? 1 : 0; if ($qfs) { # Frameshifts are tricky. # '/' indicates that the next residue is shifted back one # (-1) frame position and is a deletion of one base (so to # correctly align, a base is inserted). That residue should only # occupy two sequence positions instead of three. # '\' indicates that the next residue is shifted forward # one (+1) frame position and is an insertion of one base (so to # correctly align, a base is removed). That residue should # occupy four sequence positions instead of three. # Note that gaps are not counted across from frameshifts. # Frameshift indices are a range of positions starting in the # previous sequence position in which the frameshift occurs; # they are ambiguous by nature. $self->{seqinds}{_frameshiftRes_query}{ $resCount_query - ($_ * $qdir * $qfs) } = $qfs for @qrange; $matchtype = "$qfs frameshift-query"; $sgap = $qgap = 1; } elsif ($sfs) { $self->{seqinds}{_frameshiftRes_sbjct}{ $resCount_sbjct - ($_ * $sdir * $sfs) } = $sfs for @srange; $matchtype = "$sfs frameshift-sbcjt"; $sgap = $qgap = 1; } elsif ($qchar eq $self->{GAP_SYMBOL}) { # gap are counted as being in the immediately preceeding residue # position; for translated sequences this is not the start of # the previous codon, but the third codon position $self->{seqinds}{_gapRes_query}{ $resCount_query - $qdir }++ for @qrange; $matchtype = 'gap-query'; $qgap++; } elsif ($schar eq $self->{GAP_SYMBOL}) { $self->{seqinds}{_gapRes_sbjct}{ $resCount_sbjct - $sdir }++ for @srange; $matchtype = 'gap-sbjct'; $sgap++; } else { # if not a gap or frameshift in either seq, must be mismatch $self->{seqinds}{_mismatchRes_query}{ $resCount_query + ($_ * $qdir) } = 1 for @qrange; $self->{seqinds}{_mismatchRes_sbjct}{ $resCount_sbjct + ($_ * $sdir) } = 1 for @srange; $matchtype = 'mismatch'; } # always add a nomatch unless the current position in the seq is a gap if (!$sgap) { $self->{seqinds}{_nomatchRes_sbjct}{ $resCount_sbjct + ($_ * $sdir) } = 1 for @srange; } if (!$qgap) { $self->{seqinds}{_nomatchRes_query}{ $resCount_query + ($_ * $qdir) } = 1 for @qrange; } } else { $self->warn("Unknown midline character: [$mchar]"); } # leave in and uncomment for future debugging #$self->debug(sprintf("%7d %1s[%1s]%1s %-7d Type: %-20s QOff:%-2d SOff:%-2d\n", # $resCount_query, # $qchar, # $mchar, # $schar, # $resCount_sbjct, # $matchtype, # ($self->{_query_offset} * $qdir), # ($self->{_sbjct_offset} * $sdir))); $resCount_query += ($qdir * (scalar(@qrange) + $qfs)) if !$qgap; $resCount_sbjct += ($sdir * (scalar(@srange) + $sfs)) if !$sgap; } return 1; } sub _calculate_seq_offsets { my $self = shift; my $prog = $self->algorithm; ($self->{_sbjct_offset}, $self->{_query_offset}) = (1,1); if($prog =~ /^(?:PSI)?T(BLAST|FAST)(N|X|Y)/oi ) { $self->{_sbjct_offset} = 3; if ($1 eq 'BLAST' && $2 eq 'X') { #TBLASTX $self->{_query_offset} = 3; } } elsif($prog =~ /^(BLAST|FAST)(X|Y|XY)/oi ) { $self->{_query_offset} = 3; } 1; } =head2 n See documentation in L =cut sub n { my $self = shift; if(@_) { $self->{'N'} = shift; } # note that returning 1 is completely an assumption defined $self->{'N'} ? $self->{'N'} : 1; } =head2 range See documentation in L =cut sub range { my ($self, $seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; my ($start, $end); if( $seqType eq 'query' ) { $start = $self->query->start; $end = $self->query->end; } else { $start = $self->hit->start; $end = $self->hit->end; } return ($start, $end); } =head2 links Title : links Usage : $obj->links($newval) Function: Get/Set the Links value (from WU-BLAST) Indicates the placement of the alignment in the group of HSPs Returns : Value of links Args : On set, new value (a scalar or undef, optional) =cut sub links{ my $self = shift; return $self->{LINKS} = shift if @_; return $self->{LINKS}; } =head2 hsp_group Title : hsp_group Usage : $obj->hsp_group($newval) Function: Get/Set the Group value (from WU-BLAST) Indicates a grouping of HSPs Returns : Value of group Args : On set, new value (a scalar or undef, optional) =cut sub hsp_group { my $self = shift; return $self->{HSP_GROUP} = shift if @_; return $self->{HSP_GROUP}; } =head2 hit_features Title : hit_features Usage : $obj->hit_features($newval) Function: Get/Set the HSP hit feature string (from some BLAST 2.2.13 text output), which is a string of overlapping or nearby features in HSP hit Returns : Value of hit features, if present Args : On set, new value (a scalar or undef, optional) =cut sub hit_features { my $self = shift; return $self->{HIT_FEATURES} = shift if @_; return $self->{HIT_FEATURES}; } # The cigar string code is written by Juguang Xiao =head1 Brief introduction on cigar string NOTE: the concept is originally from EnsEMBL docs at http://may2005.archive.ensembl.org/Docs/wiki/html/EnsemblDocs/CigarFormat.html Please append to these docs if you have a better definition. Sequence alignment hits can be stored in a database as ungapped alignments. This imposes 2 major constraints on alignments: a) alignments for a single hit record require multiple rows in the database, and b) it is not possible to accurately retrieve the exact original alignment. Alternatively, sequence alignments can be stored as gapped alignments using the CIGAR line format (where CIGAR stands for Concise Idiosyncratic Gapped Alignment Report). In the cigar line format alignments are stored as follows: M: Match D: Deletion I: Insertion An example of an alignment for a hypthetical protein match is shown below: Query: 42 PGPAGLP----GSVGLQGPRGLRGPLP-GPLGPPL... PG P G GP R PLGP Sbjct: 1672 PGTP*TPLVPLGPWVPLGPSSPR--LPSGPLGPTD... protein_align_feature table as the following cigar line: 7M4D12M2I2MD7M =head2 cigar_string Name: cigar_string Usage: $cigar_string = $hsp->cigar_string Function: Generate and return cigar string for this HSP alignment Args: No input needed Return: a cigar string =cut sub cigar_string { my ($self, $arg) = @_; $self->warn("this is not a setter") if(defined $arg); unless(defined $self->{_cigar_string}){ # generate cigar string my $cigar_string = $self->generate_cigar_string($self->query_string, $self->hit_string); $self->{_cigar_string} = $cigar_string; } # end of unless return $self->{_cigar_string}; } =head2 generate_cigar_string Name: generate_cigar_string Usage: my $cigar_string = Bio::Search::HSP::GenericHSP::generate_cigar_string ($qstr, $hstr); Function: generate cigar string from a simple sequence of alignment. Args: the string of query and subject Return: cigar string =cut sub generate_cigar_string { my ($self, $qstr, $hstr) = @_; my @qchars = split //, $qstr; my @hchars = split //, $hstr; unless(scalar(@qchars) == scalar(@hchars)){ $self->throw("two sequences are not equal in lengths"); } $self->{_count_for_cigar_string} = 0; $self->{_state_for_cigar_string} = 'M'; my $cigar_string = ''; for(my $i=0; $i <= $#qchars; $i++){ my $qchar = $qchars[$i]; my $hchar = $hchars[$i]; if($qchar ne $self->{GAP_SYMBOL} && $hchar ne $self->{GAP_SYMBOL}){ # Match $cigar_string .= $self->_sub_cigar_string('M'); }elsif($qchar eq $self->{GAP_SYMBOL}){ # Deletion $cigar_string .= $self->_sub_cigar_string('D'); }elsif($hchar eq $self->{GAP_SYMBOL}){ # Insertion $cigar_string .= $self->_sub_cigar_string('I'); }else{ $self->throw("Impossible state that 2 gaps on each seq aligned"); } } $cigar_string .= $self->_sub_cigar_string('X'); # not forget the tail. return $cigar_string; } # an internal method to help generate cigar string sub _sub_cigar_string { my ($self, $new_state) = @_; my $sub_cigar_string = ''; if($self->{_state_for_cigar_string} eq $new_state){ $self->{_count_for_cigar_string} += 1; # Remain the state and increase the counter }else{ $sub_cigar_string .= $self->{_count_for_cigar_string} unless $self->{_count_for_cigar_string} == 1; $sub_cigar_string .= $self->{_state_for_cigar_string}; $self->{_count_for_cigar_string} = 1; $self->{_state_for_cigar_string} = $new_state; } return $sub_cigar_string; } # needed before seqfeatures can be made sub _pre_seq_feature { my $self = shift; my $algo = $self->{ALGORITHM}; my ($queryfactor, $hitfactor) = (0,0); my ($hitmap, $querymap) = (1,1); if( $algo =~ /^(?:PSI)?T(?:BLAST|FAST|SW)[NY]/oi ) { $hitfactor = 1; $hitmap = 3; } elsif ($algo =~ /^(?:FAST|BLAST)(?:X|Y|XY)/oi || $algo =~ /^P?GENEWISE/oi ) { $queryfactor = 1; $querymap = 3; } elsif ($algo =~ /^T(BLAST|FAST|SW)(X|Y|XY)/oi || $algo =~ /^(BLAST|FAST|SW)N/oi || $algo =~ /^WABA|AXT|BLAT|BLASTZ|PSL|MEGABLAST|EXONERATE|SW|SSEARCH|SMITH\-WATERMAN|SIM4$/){ if ($2) { $hitmap = $querymap = 3; } $hitfactor = 1; $queryfactor = 1; } elsif ($algo =~ /^RPS-BLAST/) { if ($algo =~ /^RPS-BLAST\(BLASTX\)/) { $queryfactor = 1; $querymap = 3; } $hitfactor = 0; } else { my $stranded = lc substr($self->{STRANDED}, 0,1); $queryfactor = ($stranded eq 'q' || $stranded eq 'b') ? 1 : 0; $hitfactor = ($stranded eq 'h' || $stranded eq 's' || $stranded eq 'b') ? 1 : 0; } $self->{_query_factor} = $queryfactor; $self->{_hit_factor} = $hitfactor; $self->{_hit_mapping} = $hitmap; $self->{_query_mapping} = $querymap; } # make query seq feature sub _query_seq_feature { my $self = shift; $self->{_making_qff} = 1; my $qs = $self->{QUERY_START}; my $qe = $self->{QUERY_END}; unless (defined $self->{_query_factor}) { $self->_pre_seq_feature; } my $queryfactor = $self->{_query_factor}; unless( defined $qe && defined $qs ) { $self->throw("Did not specify a Query End or Query Begin"); } my $strand; if ($qe > $qs) { # normal query: start < end if ($queryfactor) { $strand = 1; } else { $strand = undef; } } else { if ($queryfactor) { $strand = -1; } else { $strand = undef; } ($qs,$qe) = ($qe,$qs); } # Note: many of these data are not query- and hit-specific. # Only start, end, name, length are. # We could be more efficient by only storing this info once. # steve chervitz --- Sat Apr 5 00:55:07 2003 my $sim1 = $self->{_sim1} || Bio::SeqFeature::Similarity->new(); $sim1->start($qs); $sim1->end($qe); $sim1->significance($self->{EVALUE}); $sim1->bits($self->{BITS}); $sim1->score($self->{SCORE}); $sim1->strand($strand); $sim1->seq_id($self->{QUERY_NAME}); $sim1->seqlength($self->{QUERY_LENGTH}); $sim1->source_tag($self->{ALGORITHM}); $sim1->seqdesc($self->{QUERY_DESC}); $sim1->add_tag_value('meta', $self->{META}) if $self->can('meta'); # to determine frame from something like FASTXY which doesn't # report the frame my $qframe = $self->{QUERY_FRAME}; if (defined $strand && !defined $qframe && $queryfactor) { $qframe = ( $qs % 3 ) * $strand; } elsif (!defined $strand) { $qframe = 0; } if( $qframe =~ /^([+-])?([0-3])/ ) { my $dir = $1 || '+'; if($qframe && (($dir eq '-' && $strand >= 0) || ($dir eq '+' && $strand <= 0)) ) { $self->warn("Query frame ($qframe) did not match strand of query ($strand)"); } $qframe = $2 != 0 ? $2 - 1 : $2; } else { $self->warn("Unknown query frame ($qframe)"); $qframe = 0; } $sim1->frame($qframe); $self->SUPER::feature1($sim1); $self->{_created_qff} = 1; $self->{_making_qff} = 0; } # make subject seq feature sub _subject_seq_feature { my $self = shift; $self->{_making_sff} = 1; my $hs = $self->{HIT_START}; my $he = $self->{HIT_END}; unless (defined $self->{_hit_factor}) { $self->_pre_seq_feature; } my $hitfactor = $self->{_hit_factor}; unless( defined $he && defined $hs ) { $self->throw("Did not specify a Hit End or Hit Begin"); } my $strand; if ($he > $hs) { # normal subject if ($hitfactor) { $strand = 1; } else { $strand = undef; } } else { if ($hitfactor) { $strand = -1; } else { $strand = undef; } ($hs,$he) = ( $he,$hs); # reverse subject: start bigger than end } my $sim2 = $self->{_sim2} || Bio::SeqFeature::Similarity->new(); $sim2->start($hs); $sim2->end($he); $sim2->significance($self->{EVALUE}); $sim2->bits($self->{BITS}); $sim2->score($self->{SCORE}); $sim2->strand($strand); $sim2->seq_id($self->{HIT_NAME}); $sim2->seqlength($self->{HIT_LENGTH}); $sim2->source_tag($self->{ALGORITHM}); $sim2->seqdesc($self->{HIT_DESC}); $sim2->add_tag_value('meta', $self->{META}) if $self->can('meta'); my $hframe = $self->{HIT_FRAME}; if (defined $strand && !defined $hframe && $hitfactor) { $hframe = ( $hs % 3 ) * $strand; } elsif (!defined $strand) { $hframe = 0; } if( $hframe =~ /^([+-])?([0-3])/ ) { my $dir = $1 || '+'; if($hframe && (($dir eq '-' && $strand >= 0) || ($dir eq '+' && $strand <= 0)) ) { $self->warn("Subject frame ($hframe) did not match strand of subject ($strand)"); } $hframe = $2 != 0 ? $2 - 1 : $2; } else { $self->warn("Unknown subject frame ($hframe)"); $hframe = 0; } $sim2->frame($hframe); $self->SUPER::feature2($sim2); $self->{_created_sff} = 1; $self->{_making_sff} = 0; } # before calling the num_* methods sub _pre_similar_stats { my $self = shift; my $identical = $self->{IDENTICAL}; my $conserved = $self->{CONSERVED}; my $percent_id = $self->{PERCENT_IDENTITY}; if (! defined $identical) { if (! defined $percent_id) { $self->warn("Did not defined the number of identical matches or overall percent identity in the HSP; assuming 0"); $identical = 0; } else { $identical = sprintf("%.0f",$percent_id * $self->{HSP_LENGTH}); } } if (! defined $conserved) { $self->warn("Did not define the number of conserved matches in the HSP; assuming conserved == identical ($identical)") if( $self->{ALGORITHM} !~ /^((FAST|BLAST)N)|EXONERATE|SIM4|AXT|PSL|BLAT|BLASTZ|WABA/oi); $conserved = $identical; } $self->{IDENTICAL} = $identical; $self->{CONSERVED} = $conserved; $self->{_did_presimilar} = 1; } # before calling the frac_* methods sub _pre_frac { my $self = shift; my $hsp_len = $self->{HSP_LENGTH}; my $hit_len = $self->{HIT_LENGTH}; my $query_len = $self->{QUERY_LENGTH}; my $identical = $self->num_identical; my $conserved = $self->num_conserved; $self->{_did_prefrac} = 1; my $logical; if( $hsp_len ) { $self->length('total', $hsp_len); $logical = $self->_logical_length('total'); $self->frac_identical( 'total', $identical / $hsp_len); $self->frac_conserved( 'total', $conserved / $hsp_len); } if( $hit_len ) { $logical = $self->_logical_length('hit'); $self->frac_identical( 'hit', $identical / $logical); $self->frac_conserved( 'hit', $conserved / $logical); } if( $query_len ) { $logical = $self->_logical_length('query'); $self->frac_identical( 'query', $identical / $logical) ; $self->frac_conserved( 'query', $conserved / $logical); } } # before calling gaps() # This relies first on passed parameters (parser-dependent), then on gaps # calculated by seq_inds() (if set), then falls back to directly checking # for '-' or '.' as a last resort sub _pre_gaps { my $self = shift; my $query_gaps = $self->{QUERY_GAPS}; my $query_seq = $self->{QUERY_SEQ}; my $hit_gaps = $self->{HIT_GAPS}; my $hit_seq = $self->{HIT_SEQ}; my $gaps = $self->{HSP_GAPS}; $self->{_did_pregaps} = 1; # well, we're in the process; avoid recursion if( defined $query_gaps ) { $self->gaps('query', $query_gaps); } elsif( defined $query_seq ) { my $qg = (defined $self->{'_query_offset'}) ? $self->seq_inds('query','gaps') : ($self->algorithm eq 'ERPIN') ? scalar( $hit_seq =~ tr/\-//) : scalar( $query_seq =~ tr/\-\.// ); # HMMER3 and Infernal uses '.' and '-' my $offset = $self->{'_query_offset'} || 1; $self->gaps('query', $qg/$offset); } if( defined $hit_gaps ) { $self->gaps('hit', $hit_gaps); } elsif( defined $hit_seq ) { my $hg = (defined $self->{'_sbjct_offset'}) ? $self->seq_inds('hit','gaps') : ($self->algorithm eq 'ERPIN') ? scalar( $hit_seq =~ tr/\-//) : scalar( $hit_seq =~ tr/\-\.// ); # HMMER3 and Infernal uses '.' and '-' my $offset = $self->{'_sbjct_offset'} || 1; $self->gaps('hit', $hg/$offset); } if( ! defined $gaps ) { $gaps = $self->gaps("query") + $self->gaps("hit"); } $self->gaps('total', $gaps); } # before percent_identity sub _pre_pi { my $self = shift; $self->{_did_prepi} = 1; $self->percent_identity($self->{PERCENT_IDENTITY} || $self->frac_identical('total')*100) if( $self->{HSP_LENGTH} > 0 ); } 1; BioPerl-1.007002/Bio/Search/HSP/HMMERHSP.pm000444000766000024 2743413155576320 17676 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::HSP::HMMERHSP # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::HSP::HMMERHSP - A HSP object for HMMER results =head1 SYNOPSIS use Bio::Search::HSP::HMMERHSP; # use it just like a Bio::Search::HSP::GenericHSP object =head1 DESCRIPTION This object is a specialization of L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::HSP::HMMERHSP; use strict; use base qw(Bio::Search::HSP::GenericHSP); =head2 new Title : new Usage : my $obj = Bio::Search::HSP::HMMERHSP->new(); Function: Builds a new Bio::Search::HSP::HMMERHSP object Returns : Bio::Search::HSP::HMMERHSP Args : Plus Bio::Search::HSP::GenericHSP methods -algorithm => algorithm used (BLASTP, TBLASTX, FASTX, etc) -evalue => evalue -pvalue => pvalue -bits => bit value for HSP -score => score value for HSP (typically z-score but depends on analysis) -hsp_length => Length of the HSP (including gaps) -identical => # of residues that that matched identically -conserved => # of residues that matched conservatively (only protein comparisons - conserved == identical in nucleotide comparisons) -hsp_gaps => # of gaps in the HSP -query_gaps => # of gaps in the query in the alignment -hit_gaps => # of gaps in the subject in the alignment -query_name => HSP Query sequence name (if available) -query_start => HSP Query start (in original query sequence coords) -query_end => HSP Query end (in original query sequence coords) -hit_name => HSP Hit sequence name (if available) -hit_start => HSP Hit start (in original hit sequence coords) -hit_end => HSP Hit end (in original hit sequence coords) -hit_length => total length of the hit sequence -query_length => total length of the query sequence -query_seq => query sequence portion of the HSP -hit_seq => hit sequence portion of the HSP -homology_seq => homology sequence for the HSP -hit_frame => hit frame (only if hit is translated protein) -query_frame => query frame (only if query is translated protein) =cut =head2 Bio::Search::HSP::HSPI methods Implementation of Bio::Search::HSP::HSPI methods follow =head2 algorithm Title : algorithm Usage : my $r_type = $hsp->algorithm Function: Obtain the name of the algorithm used to obtain the HSP Returns : string (e.g., BLASTP) Args : [optional] scalar string to set value =cut =head2 pvalue Title : pvalue Usage : my $pvalue = $hsp->pvalue(); Function: Returns the P-value for this HSP or undef Returns : float or exponential (2e-10) P-value is not defined with NCBI Blast2 reports. Args : [optional] numeric to set value =cut =head2 evalue Title : evalue Usage : my $evalue = $hsp->evalue(); Function: Returns the e-value for this HSP Returns : float or exponential (2e-10) Args : [optional] numeric to set value =cut =head2 frac_identical Title : frac_identical Usage : my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] ); Function: Returns the fraction of identitical positions for this HSP Returns : Float in range 0.0 -> 1.0 Args : arg 1: 'query' = num identical / length of query seq (without gaps) 'hit' = num identical / length of hit seq (without gaps) 'total' = num identical / length of alignment (with gaps) default = 'total' arg 2: [optional] frac identical value to set for the type requested =cut =head2 frac_conserved Title : frac_conserved Usage : my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] ); Function : Returns the fraction of conserved positions for this HSP. This is the fraction of symbols in the alignment with a positive score. Returns : Float in range 0.0 -> 1.0 Args : arg 1: 'query' = num conserved / length of query seq (without gaps) 'hit' = num conserved / length of hit seq (without gaps) 'total' = num conserved / length of alignment (with gaps) default = 'total' arg 2: [optional] frac conserved value to set for the type requested =cut =head2 gaps Title : gaps Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); Function : Get the number of gaps in the query, hit, or total alignment. Returns : Integer, number of gaps or 0 if none Args : arg 1: 'query' = num gaps in query seq 'hit' = num gaps in hit seq 'total' = num gaps in whole alignment default = 'total' arg 2: [optional] integer gap value to set for the type requested =cut =head2 query_string Title : query_string Usage : my $qseq = $hsp->query_string; Function: Retrieves the query sequence of this HSP as a string Returns : string Args : [optional] string to set for query sequence =cut =head2 hit_string Title : hit_string Usage : my $hseq = $hsp->hit_string; Function: Retrieves the hit sequence of this HSP as a string Returns : string Args : [optional] string to set for hit sequence =cut =head2 homology_string Title : homology_string Usage : my $homo_string = $hsp->homology_string; Function: Retrieves the homology sequence for this HSP as a string. : The homology sequence is the string of symbols in between the : query and hit sequences in the alignment indicating the degree : of conservation (e.g., identical, similar, not similar). Returns : string Args : [optional] string to set for homology sequence =cut =head2 length Title : length Usage : my $len = $hsp->length( ['query'|'hit'|'total'] ); Function : Returns the length of the query or hit in the alignment (without gaps) or the aggregate length of the HSP (including gaps; this may be greater than either hit or query ) Returns : integer Args : arg 1: 'query' = length of query seq (without gaps) 'hit' = length of hit seq (without gaps) 'total' = length of alignment (with gaps) default = 'total' arg 2: [optional] integer length value to set for specific type =cut =head2 percent_identity Title : percent_identity Usage : my $percentid = $hsp->percent_identity() Function: Returns the calculated percent identity for an HSP Returns : floating point between 0 and 100 Args : none =cut =head2 frame Title : frame Usage : my ($qframe, $hframe) = $hsp->frame('list',$queryframe,$subjectframe) Function: Set the Frame for both query and subject and insure that they agree. This overrides the frame() method implementation in FeaturePair. Returns : array of query and subject frame if return type wants an array or query frame if defined or subject frame if not defined Args : 'hit' or 'subject' or 'sbjct' to retrieve the frame of the subject (default) 'query' to retrieve the query frame 'list' or 'array' to retrieve both query and hit frames together Note : Frames are stored in the GFF way (0-2) not 1-3 as they are in BLAST (negative frames are deduced by checking the strand of the query or hit) =cut =head2 get_aln Title : get_aln Usage : my $aln = $hsp->gel_aln Function: Returns a Bio::SimpleAlign representing the HSP alignment Returns : Bio::SimpleAlign Args : none =cut sub get_aln { my ($self) = shift; $self->warn("Inappropriate to build a Bio::SimpleAlign from a HMMER HSP object"); return; } =head2 num_conserved Title : num_conserved Usage : $obj->num_conserved($newval) Function: returns the number of conserved residues in the alignment Returns : inetger Args : integer (optional) =cut =head2 num_identical Title : num_identical Usage : $obj->num_identical($newval) Function: returns the number of identical residues in the alignment Returns : integer Args : integer (optional) =cut =head2 seq_inds Title : seq_inds Purpose : Get a list of residue positions (indices) for all identical : or conserved residues in the query or sbjct sequence. Example : @s_ind = $hsp->seq_inds('query', 'identical'); : @h_ind = $hsp->seq_inds('hit', 'conserved'); : @h_ind = $hsp->seq_inds('hit', 'conserved', 1); Returns : List of integers : May include ranges if collapse is true. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = query) : ('sbjct' is synonymous with 'hit') : class = 'identical' or 'conserved' or 'nomatch' or 'gap' : (default = identical) : (can be shortened to 'id' or 'cons') : : collapse = boolean, if true, consecutive positions are merged : using a range notation, e.g., "1 2 3 4 5 7 9 10 11" : collapses to "1-5 7 9-11". This is useful for : consolidating long lists. Default = no collapse. Throws : n/a. Comments : See Also : L, L =cut =head2 Inherited from Bio::SeqFeature::SimilarityPair These methods come from Bio::SeqFeature::SimilarityPair =head2 query Title : query Usage : my $query = $hsp->query Function: Returns a SeqFeature representing the query in the HSP Returns : Bio::SeqFeature::Similarity Args : [optional] new value to set =head2 hit Title : hit Usage : my $hit = $hsp->hit Function: Returns a SeqFeature representing the hit in the HSP Returns : Bio::SeqFeature::Similarity Args : [optional] new value to set =head2 significance Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Get/Set the significance value Returns : numeric Args : [optional] new value to set =head2 score Title : score Usage : my $score = $hsp->score(); Function: Returns the score for this HSP or undef Returns : numeric Args : [optional] numeric to set value =cut =head2 bits Title : bits Usage : my $bits = $hsp->bits(); Function: Returns the bit value for this HSP or undef Returns : numeric Args : none =cut sub bits { return 0; } 1; BioPerl-1.007002/Bio/Search/HSP/HSPFactory.pm000444000766000024 706513155576320 20413 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::HSP::HSPFactory # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::HSP::HSPFactory - A factory to create Bio::Search::HSP::HSPI objects =head1 SYNOPSIS use Bio::Search::HSP::HSPFactory; my $factory = Bio::Search::HSP::HSPFactory->new(); my $resultobj = $factory->create(@args); =head1 DESCRIPTION This is a general way of hiding the object creation process so that we can dynamically change the objects that are created by the SearchIO parser depending on what format report we are parsing. This object is for creating new HSPs. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::HSP::HSPFactory; use vars qw($DEFAULT_TYPE); use strict; use base qw(Bio::Root::Root Bio::Factory::ObjectFactoryI); BEGIN { $DEFAULT_TYPE = 'Bio::Search::HSP::GenericHSP'; } =head2 new Title : new Usage : my $obj = Bio::Search::HSP::HSPFactory->new(); Function: Builds a new Bio::Search::HSP::HSPFactory object Returns : Bio::Search::HSP::HSPFactory Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($type) = $self->_rearrange([qw(TYPE)],@args); $self->type($type) if defined $type; return $self; } =head2 create Title : create Usage : $factory->create(%args) Function: Create a new L object Returns : L Args : hash of initialization parameters =cut sub create{ my ($self,@args) = @_; my $type = $self->type; eval { $self->_load_module($type) }; if( $@ ) { $self->throw("Unable to load module $type"); } return $type->new(@args); } =head2 type Title : type Usage : $factory->type('Bio::Search::HSP::GenericHSP'); Function: Get/Set the HSP creation type Returns : string Args : [optional] string to set =cut sub type{ my ($self,$type) = @_; if( defined $type ) { # redundancy with the create method which also calls _load_module # I know - but this is not a highly called object so I am going # to leave it in eval {$self->_load_module($type) }; if( $@ ){ $self->warn("Cannot find module $type, unable to set type. $@") } else { $self->{'_type'} = $type; } } return $self->{'_type'} || $DEFAULT_TYPE; } 1; BioPerl-1.007002/Bio/Search/HSP/HSPI.pm000444000766000024 5353613155576320 17220 0ustar00cjfieldsstaff000000000000#----------------------------------------------------------------- # # BioPerl module for Bio::Search::HSP::HSPI # # Please direct questions and support issues to # # Cared for by Steve Chervitz # and Jason Stajich # # You may distribute this module under the same terms as perl itself #----------------------------------------------------------------- # POD documentation - main docs before the code =head1 NAME Bio::Search::HSP::HSPI - Interface for a High Scoring Pair in a similarity search result =head1 SYNOPSIS # Bio::Search::HSP::HSPI objects cannot be instantiated since this # module defines a pure interface. # Given an object that implements the Bio::Search::HSP::HSPI interface, # you can do the following things with it: $r_type = $hsp->algorithm; $pvalue = $hsp->pvalue(); $evalue = $hsp->evalue(); $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] ); $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] ); $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); $qseq = $hsp->query_string; $hseq = $hsp->hit_string; $homology_string = $hsp->homology_string; $len = $hsp->length( ['query'|'hit'|'total'] ); $rank = $hsp->rank; =head1 DESCRIPTION Bio::Search::HSP::HSPI objects cannot be instantiated since this module defines a pure interface. Given an object that implements the L interface, you can do the following things with it: =head1 SEE ALSO This interface inherits methods from these other modules: L, L L Please refer to these modules for documentation of the many additional inherited methods. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Steve Chervitz, Jason Stajich Email sac-at-bioperl.org Email jason-at-bioperl.org =head1 COPYRIGHT Copyright (c) 2001 Steve Chervitz, Jason Stajich. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::HSP::HSPI; use strict; use Carp; use base qw(Bio::SeqFeature::SimilarityPair Bio::Root::RootI); =head2 algorithm Title : algorithm Usage : my $r_type = $hsp->algorithm Function: Obtain the name of the algorithm used to obtain the HSP Returns : string (e.g., BLASTP) Args : none =cut sub algorithm{ my ($self,@args) = @_; $self->throw_not_implemented; } =head2 pvalue Title : pvalue Usage : my $pvalue = $hsp->pvalue(); Function: Returns the P-value for this HSP or undef Returns : float or exponential (2e-10) P-value is not defined with NCBI Blast2 reports. Args : none =cut sub pvalue { my ($self) = @_; $self->throw_not_implemented; } =head2 evalue Title : evalue Usage : my $evalue = $hsp->evalue(); Function: Returns the e-value for this HSP Returns : float or exponential (2e-10) Args : none =cut sub evalue { my ($self) = @_; $self->throw_not_implemented; } =head2 frac_identical Title : frac_identical Usage : my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] ); Function: Returns the fraction of identitical positions for this HSP Returns : Float in range 0.0 -> 1.0 Args : 'query' = num identical / length of query seq (without gaps) 'hit' = num identical / length of hit seq (without gaps) 'total' = num identical / length of alignment (with gaps) default = 'total' =cut sub frac_identical { my ($self, $type) = @_; $self->throw_not_implemented; } =head2 frac_conserved Title : frac_conserved Usage : my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] ); Function : Returns the fraction of conserved positions for this HSP. This is the fraction of symbols in the alignment with a positive score. Returns : Float in range 0.0 -> 1.0 Args : 'query' = num conserved / length of query seq (without gaps) 'hit' = num conserved / length of hit seq (without gaps) 'total' = num conserved / length of alignment (with gaps) default = 'total' =cut sub frac_conserved { my ($self, $type) = @_; $self->throw_not_implemented; } =head2 num_identical Title : num_identical Usage : $obj->num_identical($newval) Function: returns the number of identical residues in the alignment Returns : integer Args : integer (optional) =cut sub num_identical{ shift->throw_not_implemented; } =head2 num_conserved Title : num_conserved Usage : $obj->num_conserved($newval) Function: returns the number of conserved residues in the alignment Returns : inetger Args : integer (optional) =cut sub num_conserved{ shift->throw_not_implemented(); } =head2 gaps Title : gaps Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); Function : Get the number of gap characters in the query, hit, or total alignment. Returns : Integer, number of gap characters or 0 if none Args : 'query' = num conserved / length of query seq (without gaps) 'hit' = num conserved / length of hit seq (without gaps) 'total' = num conserved / length of alignment (with gaps) default = 'total' =cut sub gaps { my ($self, $type) = @_; $self->throw_not_implemented; } =head2 query_string Title : query_string Usage : my $qseq = $hsp->query_string; Function: Retrieves the query sequence of this HSP as a string Returns : string Args : none =cut sub query_string{ my ($self) = @_; $self->throw_not_implemented; } =head2 hit_string Title : hit_string Usage : my $hseq = $hsp->hit_string; Function: Retrieves the hit sequence of this HSP as a string Returns : string Args : none =cut sub hit_string{ my ($self) = @_; $self->throw_not_implemented; } =head2 homology_string Title : homology_string Usage : my $homo_string = $hsp->homology_string; Function: Retrieves the homology sequence for this HSP as a string. : The homology sequence is the string of symbols in between the : query and hit sequences in the alignment indicating the degree : of conservation (e.g., identical, similar, not similar). Returns : string Args : none =cut sub homology_string{ my ($self) = @_; $self->throw_not_implemented; } =head2 length Title : length Usage : my $len = $hsp->length( ['query'|'hit'|'total'] ); Function : Returns the length of the query or hit in the alignment (without gaps) or the aggregate length of the HSP (including gaps; this may be greater than either hit or query ) Returns : integer Args : 'query' = length of query seq (without gaps) 'hit' = length of hit seq (without gaps) 'total' = length of alignment (with gaps) default = 'total' Args : none =cut sub length{ shift->throw_not_implemented(); } =head2 percent_identity Title : percent_identity Usage : my $percentid = $hsp->percent_identity() Function: Returns the calculated percent identity for an HSP Returns : floating point between 0 and 100 Args : none =cut sub percent_identity{ my ($self) = @_; return $self->frac_identical('hsp') * 100; } =head2 get_aln Title : get_aln Usage : my $aln = $hsp->get_aln Function: Returns a Bio::SimpleAlign representing the HSP alignment Returns : Bio::SimpleAlign Args : none =cut sub get_aln { my ($self) = @_; $self->throw_not_implemented; } =head2 seq_inds Title : seq_inds Purpose : Get a list of residue positions (indices) for all identical : or conserved residues in the query or sbjct sequence. Example : @s_ind = $hsp->seq_inds('query', 'identical'); : @h_ind = $hsp->seq_inds('hit', 'conserved'); : @h_ind = $hsp->seq_inds('hit', 'conserved', 1); Returns : List of integers : May include ranges if collapse is true. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = query) ('sbjct' is synonymous with 'hit') class = 'identical' or 'conserved' or 'nomatch' or 'gap' (default = identical) (can be shortened to 'id' or 'cons') collapse = boolean, if true, consecutive positions are merged using a range notation, e.g., "1 2 3 4 5 7 9 10 11" collapses to "1-5 7 9-11". This is useful for consolidating long lists. Default = no collapse. Throws : n/a. Comments : See Also : L, L =cut sub seq_inds { shift->throw_not_implemented(); } =head2 Inherited from L These methods come from L =head2 query Title : query Usage : my $query = $hsp->query Function: Returns a SeqFeature representing the query in the HSP Returns : Bio::SeqFeature::Similarity Args : [optional] new value to set =head2 hit Title : hit Usage : my $hit = $hsp->hit Function: Returns a SeqFeature representing the hit in the HSP Returns : Bio::SeqFeature::Similarity Args : [optional] new value to set =head2 significance Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Get/Set the significance value (see Bio::SeqFeature::SimilarityPair) Returns : significance value (scientific notation string) Args : significance value (sci notation string) =head2 score Title : score Usage : my $score = $hsp->score(); Function: Returns the score for this HSP or undef Returns : numeric Args : [optional] numeric to set value =head2 bits Title : bits Usage : my $bits = $hsp->bits(); Function: Returns the bit value for this HSP or undef Returns : numeric Args : none =cut # override =head2 strand Title : strand Usage : $hsp->strand('query') Function: Retrieves the strand for the HSP component requested Returns : +1 or -1 (0 if unknown) Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject 'query' to retrieve the query strand (default) 'list' or 'array' to retrieve both query and hit together =cut sub strand { my $self = shift; my $val = shift; $val = 'query' unless defined $val; $val =~ s/^\s+//; if ( $val =~ /^q/i ) { return $self->query->strand(@_); } elsif ( $val =~ /^hi|^s/i ) { return $self->hit->strand(@_); } elsif ( $val =~ /^list|array/i ) { # Do we really need to pass on additional arguments here? HL # (formerly this was strand(shift) which is really bad coding because # it breaks if the callee allows setting to undef) return ( $self->query->strand(@_), $self->hit->strand(@_) ); } else { $self->warn("unrecognized component '$val' requested\n"); } return 0; } =head2 start Title : start Usage : $hsp->start('query') Function: Retrieves the start for the HSP component requested Returns : integer Args : 'hit' or 'subject' or 'sbjct' to retrieve the start of the subject 'query' to retrieve the query start (default) =cut sub start { my $self = shift; my $val = shift; $val = 'query' unless defined $val; $val =~ s/^\s+//; if( $val =~ /^q/i ) { return $self->query->start(@_); } elsif( $val =~ /^(hi|s)/i ) { return $self->hit->start(@_); } elsif ( $val =~ /^list|array/i ) { # do we really need to pass on additional arguments here? HL # (formerly this was strand(shift) which is really bad coding because # it breaks if the callee allows setting to undef) return ($self->query->start(@_), $self->hit->start(@_) ); } else { $self->warn("unrecognized component '$val' requested\n"); } return 0; } =head2 end Title : end Usage : $hsp->end('query') Function: Retrieves the end for the HSP component requested Returns : integer Args : 'hit' or 'subject' or 'sbjct' to retrieve the end of the subject 'query' to retrieve the query end (default) =cut sub end { my $self = shift; my $val = shift; $val = 'query' unless defined $val; $val =~ s/^\s+//; if( $val =~ /^q/i ) { return $self->query->end(@_); } elsif( $val =~ /^(hi|s)/i ) { return $self->hit->end(@_); } elsif ( $val =~ /^list|array/i ) { # do we really need to pass on additional arguments here? HL # (formerly this was strand(shift) which is really bad coding because # it breaks if the callee allows setting to undef) return ($self->query->end(@_), $self->hit->end(@_) ); } else { $self->warn("unrecognized end component '$val' requested\n"); } return 0; } =head2 seq Usage : $hsp->seq( [seq_type] ); Purpose : Get the query or sbjct sequence as a Bio::Seq.pm object. Example : $seqObj = $hsp->seq('query'); Returns : Object reference for a Bio::Seq.pm object. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query'). : ('sbjct' is synonymous with 'hit') : default is 'query' Throws : Propagates any exception that occurs during construction : of the Bio::Seq.pm object. Comments : The sequence is returned in an array of strings corresponding : to the strings in the original format of the Blast alignment. : (i.e., same spacing). See Also : L, L, L =cut sub seq { my($self,$seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; my $str = $self->seq_str($seqType); if( $seqType =~ /^(m|ho)/i ) { $self->throw("cannot call seq on the homology match string, it isn't really a sequence, use get_aln to convert the HSP to a Bio::AlignIO and generate a consensus from that."); } require Bio::LocatableSeq; my $id = $seqType =~ /^q/i ? $self->query->seq_id : $self->hit->seq_id; return Bio::LocatableSeq->new( -ID => $id, -SEQ => $str, -START => $self->start($seqType), -END => $self->end($seqType), -STRAND => $self->strand($seqType), -FORCE_NSE => $id ? 0 : 1, -DESC => "$seqType sequence " ); } =head2 seq_str Usage : $hsp->seq_str( seq_type ); Purpose : Get the full query, sbjct, or 'match' sequence as a string. : The 'match' sequence is the string of symbols in between the : query and sbjct sequences. Example : $str = $hsp->seq_str('query'); Returns : String Argument : seq_Type = 'query' or 'hit' or 'sbjct' or 'match' : ('sbjct' is synonymous with 'hit') : default is 'query' Throws : Exception if the argument does not match an accepted seq_type. Comments : See Also : L, L, C<_set_match_seq> =cut sub seq_str { my $self = shift; my $type = shift || 'query'; if( $type =~ /^q/i ) { return $self->query_string(@_) } elsif( $type =~ /^(s)|(hi)/i ) { return $self->hit_string(@_)} elsif ( $type =~ /^(ho)|(ma)/i ) { return $self->homology_string(@_) } else { $self->warn("unknown sequence type $type"); } return ''; } =head2 rank Usage : $hsp->rank( [string] ); Purpose : Get the rank of the HSP within a given Blast hit. Example : $rank = $hsp->rank; Returns : Integer (1..n) corresponding to the order in which the HSP appears in the BLAST report. =cut sub rank { shift->throw_not_implemented } =head2 matches Usage : $hsp->matches(-seq => 'hit'|'query', -start => $start, -stop => $stop); Purpose : Get the total number of identical and conservative matches : in the query or sbjct sequence for the given HSP. Optionally can : report data within a defined interval along the seq. : (Note: 'conservative' matches are called 'positives' in the : Blast report.) Example : ($id,$cons) = $hsp_object->matches(-seq => 'hit'); : ($id,$cons) = $hsp_object->matches(-seq => 'query', -start => 300, -stop => 400); Returns : 2-element array of integers Argument : (1) seq_type = 'query' or 'hit' or 'sbjct' (default = query) : ('sbjct' is synonymous with 'hit') : (2) start = Starting coordinate (optional) : (3) stop = Ending coordinate (optional) Throws : Exception if the supplied coordinates are out of range. Comments : Relies on seq_str('match') to get the string of alignment symbols : between the query and sbjct lines which are used for determining : the number of identical and conservative matches. See Also : L, L, L, L =cut #----------- sub matches { #----------- my( $self, %param ) = @_; my(@data); my($seqType, $beg, $end) = ($param{-SEQ}, $param{-START}, $param{-STOP}); $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; if( (!defined $beg && !defined $end) || ! $self->seq_str('match') ) { ## Get data for the whole alignment. push @data, ($self->num_identical, $self->num_conserved); } else { ## Get the substring representing the desired sub-section of aln. $beg ||= 0; $end ||= 0; my($start,$stop) = $self->range($seqType); if($beg == 0) { $beg = $start; $end = $beg+$end; } # sane? elsif($end == 0) { $end = $stop; $beg = $end-$beg; } # sane? if($end > $stop) { $end = $stop; } if($beg < $start) { $beg = $start; } # now with gap handling! /maj my $match_str = $self->seq_str('match'); if ($self->gaps) { # strip the homology string of gap positions relative # to the target type $match_str = $self->seq_str('match'); my $tgt = $self->seq_str($seqType); my $encode = $match_str ^ $tgt; my $zap = '-'^' '; $encode =~ s/$zap//g; $tgt =~ s/-//g; $match_str = $tgt ^ $encode; } ## ML: START fix for substr out of range error ------------------ my $seq = ""; if (($self->algorithm =~ /TBLAST[NX]/) && ($seqType eq 'sbjct')) { $seq = substr($match_str, int(($beg-$start)/3), int(($end-$beg+1)/3)); } elsif (($self->algorithm =~ /T?BLASTX/) && ($seqType eq 'query')) { $seq = substr($match_str, int(($beg-$start)/3), int(($end-$beg+1)/3)); } else { $seq = substr($match_str, $beg-$start, ($end-$beg+1)); } ## ML: End of fix for substr out of range error ----------------- if(!CORE::length $seq) { $self->throw("Undefined sub-sequence ($beg,$end). Valid range = $start - $stop"); } $seq =~ s/ //g; # remove space (no info). my $len_cons = CORE::length $seq; $seq =~ s/\+//g; # remove '+' characters (conservative substitutions) my $len_id = CORE::length $seq; push @data, ($len_id, $len_cons); } @data; } =head2 n Usage : $hsp_obj->n() Purpose : Get the N value (num HSPs on which P/Expect is based). : This value is not defined with NCBI Blast2 with gapping. Returns : Integer or null string if not defined. Argument : n/a Throws : n/a Comments : The 'N' value is listed in parenthesis with P/Expect value: : e.g., P(3) = 1.2e-30 ---> (N = 3). : Not defined in NCBI Blast2 with gaps. : This typically is equal to the number of HSPs but not always. : To obtain the number of HSPs, use Bio::Search::Hit::HitI::num_hsps(). See Also : L =cut sub n { shift->throw_not_implemented } =head2 range Usage : $hsp->range( [seq_type] ); Purpose : Gets the (start, end) coordinates for the query or sbjct sequence : in the HSP alignment. Example : ($query_beg, $query_end) = $hsp->range('query'); : ($hit_beg, $hit_end) = $hsp->range('hit'); Returns : Two-element array of integers Argument : seq_type = string, 'query' or 'hit' or 'sbjct' (default = 'query') : ('sbjct' is synonymous with 'hit') Throws : n/a Comments : This is a convenience method for constructions such as ($hsp->query->start, $hsp->query->end) =cut sub range { shift->throw_not_implemented } sub expect { shift->evalue(@_) } 1; BioPerl-1.007002/Bio/Search/HSP/HmmpfamHSP.pm000555000766000024 2663313155576320 20416 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::HSP::HmmpfamHSP # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::HSP::HmmpfamHSP - A parser and HSP object for hmmpfam hsps =head1 SYNOPSIS # generally we use Bio::SearchIO to build these objects use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer_pull', -file => 'result.hmmer'); while (my $result = $in->next_result) { while (my $hit = $result->next_hit) { print $hit->name, "\n"; print $hit->score, "\n"; print $hit->significance, "\n"; while (my $hsp = $hit->next_hsp) { # process HSPI objects } } } =head1 DESCRIPTION This object implements a parser for hmmpfam hsp output, a program in the HMMER package. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::HSP::HmmpfamHSP; use strict; use base qw(Bio::Search::HSP::PullHSPI); =head2 new Title : new Usage : my $obj = Bio::Search::HSP::HmmpfamHSP->new(); Function: Builds a new Bio::Search::HSP::HmmpfamHSP object. Returns : Bio::Search::HSP::HmmpfamHSP Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent) -parent => Bio::PullParserI object (required if no -chunk) -hsp_data => array ref with [rank query_start query_end hit_start hit_end score evalue] where the array ref provided to -chunk contains an IO object for a filehandle to something representing the raw data of the hsp, and $start and $end define the tell() position within the filehandle that the hsp data starts and ends (optional; defaults to start and end of the entire thing described by the filehandle) =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->_setup(@args); my $fields = $self->_fields; foreach my $field (qw( alignment )) { $fields->{$field} = undef; } my $hsp_data = $self->_raw_hsp_data; if ($hsp_data && ref($hsp_data) eq 'ARRAY') { my @hsp_data = @{$hsp_data}; # don't alter the reference foreach my $field (qw(rank query_start query_end hit_start hit_end score evalue)) { $fields->{$field} = shift(@hsp_data); } } $self->_dependencies( { ( query_string => 'alignment', hit_string => 'alignment', homology_string => 'alignment', hit_identical_inds => 'seq_inds', hit_conserved_inds => 'seq_inds', hit_nomatch_inds => 'seq_inds', hit_gap_inds => 'seq_inds', query_identical_inds => 'seq_inds', query_conserved_inds => 'seq_inds', query_nomatch_inds => 'seq_inds', query_gap_inds => 'seq_inds' ) } ); return $self; } # # PullParserI discovery methods so we can answer all HitI questions # sub _discover_alignment { my $self = shift; my $alignments_hash = $self->get_field('alignments'); my $identifier = $self->get_field('name').'~~~~'.$self->get_field('rank'); while (! defined $alignments_hash->{$identifier}) { last unless $self->parent->parent->_next_alignment; } my $alignment = $alignments_hash->{$identifier}; if ($alignment) { # work out query, hit and homology strings, and some stats # (quicker to do this all at once instead of each method working on # $alignment string itself) my ($query_string, $hit_string, $homology_string); while ($alignment =~ /\s+(\S+)\n\s+(\S.+)\n\s+\S+\s+\d+\s+(\S+)\s+\d/gm) { my $hi = $1; my $ho = $2; $query_string .= $3; $hi =~ s/\*\-\>//; $ho = ' 'x(length($hi) - length($ho)).$ho; $hi =~ s/\<\-\*//; $hit_string .= $hi; $homology_string .= $ho; } $self->_fields->{query_string} = $query_string; $self->_fields->{hit_string} = $hit_string; $homology_string =~ s/ $//; $self->_fields->{homology_string} = $homology_string; ($self->{_query_gaps}) = $query_string =~ tr/-//; ($self->{_hit_gaps}) = $hit_string =~ tr/.//; ($self->{_total_gaps}) = $self->{_query_gaps} + $self->{_hit_gaps}; } $self->_fields->{alignment} = 1; # stop this method being called again } # seq_inds related methods, all just need seq_inds field to have been gotten sub _discover_seq_inds { my $self = shift; my ($seqString, $qseq, $sseq) = ( $self->get_field('homology_string'), $self->get_field('query_string'), $self->get_field('hit_string') ); # (code largely lifted from GenericHSP) # Using hashes to avoid saving duplicate residue numbers. my %identicalList_query = (); my %identicalList_sbjct = (); my %conservedList_query = (); my %conservedList_sbjct = (); my @gapList_query = (); my @gapList_sbjct = (); my %nomatchList_query = (); my %nomatchList_sbjct = (); my $resCount_query = $self->get_field('query_end'); my $resCount_sbjct = $self->get_field('hit_end'); my ($mchar, $schar, $qchar); while ($mchar = chop($seqString) ) { ($qchar, $schar) = (chop($qseq), chop($sseq)); if ($mchar eq '+' || $mchar eq '.' || $mchar eq ':') { $conservedList_query{ $resCount_query } = 1; $conservedList_sbjct{ $resCount_sbjct } = 1; } elsif ($mchar eq ' ') { $nomatchList_query{ $resCount_query } = 1; $nomatchList_sbjct{ $resCount_sbjct } = 1; } else { $identicalList_query{ $resCount_query } = 1; $identicalList_sbjct{ $resCount_sbjct } = 1; } if ($qchar eq '-') { push(@gapList_query, $resCount_query); } else { $resCount_query -= 1; } if ($schar eq '.') { push(@gapList_sbjct, $resCount_sbjct); } else { $resCount_sbjct -= 1; } } my $fields = $self->_fields; $fields->{hit_identical_inds} = [ sort { $a <=> $b } keys %identicalList_sbjct ]; $fields->{hit_conserved_inds} = [ sort { $a <=> $b } keys %conservedList_sbjct ]; $fields->{hit_nomatch_inds} = [ sort { $a <=> $b } keys %nomatchList_sbjct ]; $fields->{hit_gap_inds} = [ reverse @gapList_sbjct ]; $fields->{query_identical_inds} = [ sort { $a <=> $b } keys %identicalList_query ]; $fields->{query_conserved_inds} = [ sort { $a <=> $b } keys %conservedList_query ]; $fields->{query_nomatch_inds} = [ sort { $a <=> $b } keys %nomatchList_query ]; $fields->{query_gap_inds} = [ reverse @gapList_query ]; $fields->{seq_inds} = 1; } =head2 query Title : query Usage : my $query = $hsp->query Function: Returns a SeqFeature representing the query in the HSP Returns : L Args : none =cut sub query { my $self = shift; unless ($self->{_created_query}) { $self->SUPER::query( new Bio::SeqFeature::Similarity ('-primary' => $self->primary_tag, '-start' => $self->get_field('query_start'), '-end' => $self->get_field('query_end'), '-expect' => $self->get_field('evalue'), '-score' => $self->get_field('score'), '-strand' => 1, '-seq_id' => $self->get_field('query_name'), #'-seqlength'=> $self->get_field('query_length'), (not known) '-source' => $self->get_field('algorithm'), '-seqdesc' => $self->get_field('query_description') ) ); $self->{_created_query} = 1; } return $self->SUPER::query(@_); } =head2 hit Title : hit Usage : my $hit = $hsp->hit Function: Returns a SeqFeature representing the hit in the HSP Returns : L Args : [optional] new value to set =cut sub hit { my $self = shift; unless ($self->{_created_hit}) { # the full length isn't always known (given in the report), but don't # warn about the missing info all the time my $verbose = $self->parent->parent->parent->verbose; $self->parent->parent->parent->verbose(-1); my $seq_length = $self->get_field('length'); $self->parent->parent->parent->verbose($verbose); $self->SUPER::hit( new Bio::SeqFeature::Similarity ('-primary' => $self->primary_tag, '-start' => $self->get_field('hit_start'), '-end' => $self->get_field('hit_end'), '-expect' => $self->get_field('evalue'), '-score' => $self->get_field('score'), '-strand' => 1, '-seq_id' => $self->get_field('name'), $seq_length ? ('-seqlength' => $seq_length) : (), '-source' => $self->get_field('algorithm'), '-seqdesc' => $self->get_field('description') ) ); $self->{_created_hit} = 1; } return $self->SUPER::hit(@_); } =head2 gaps Title : gaps Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); Function : Get the number of gaps in the query, hit, or total alignment. Returns : Integer, number of gaps or 0 if none Args : 'query' = num conserved / length of query seq (without gaps) 'hit' = num conserved / length of hit seq (without gaps) 'total' = num conserved / length of alignment (with gaps) default = 'total' =cut sub gaps { my ($self, $type) = @_; $type = lc $type if defined $type; $type = 'total' if (! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/); $type = 'hit' if $type =~ /sbjct|subject/; $self->get_field('alignment'); # make sure gaps have been calculated return $self->{'_'.$type.'_gaps'}; } =head2 pvalue Title : pvalue Usage : my $pvalue = $hsp->pvalue(); Function: Returns the P-value for this HSP Returns : undef (Hmmpfam reports do not have p-values) Args : none =cut # noop sub pvalue { } 1; BioPerl-1.007002/Bio/Search/HSP/ModelHSP.pm000444000766000024 4310013155576320 20052 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::HSP::ModelHSP # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::HSP::ModelHSP - A HSP object for model-based searches =head1 SYNOPSIS use Bio::Search::HSP::ModelHSP; # us it just like a Bio::Search::HSP::ModelHSP object =head1 DESCRIPTION This object is a specialization of L and is used for searches which involve a query model, such as a Hidden Markov Model (HMM), covariance model (CM), descriptor, or anything else besides a sequence. Note that results from any HSPI class methods which rely on the query being a sequence are unreliable and have thus been overridden with warnings indicating they have not been implemented at this time. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Fields Email cjfields at bioperl dot org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::HSP::ModelHSP; use strict; use Bio::Seq::Meta; use base qw(Bio::Search::HSP::GenericHSP); =head2 new Title : new Usage : my $obj = Bio::Search::HSP::ModelHSP->new(); Function: Builds a new Bio::Search::HSP::ModelHSP object Returns : Bio::Search::HSP::ModelHSP Args : Plus Bio::Seach::HSP::ModelHSP methods -algorithm => algorithm used (Infernal, RNAMotif, ERPIN, etc) -evalue => evalue -pvalue => pvalue -bits => bit value for HSP -score => score value for HSP (typically z-score but depends on analysis) -hsp_length=> Length of the HSP (including gaps) -identical => # of residues that that matched identically -conserved => # of residues that matched conservatively (only protein comparisons; conserved == identical in nucleotide comparisons) -hsp_gaps => # of gaps in the HSP -query_gaps => # of gaps in the query in the alignment -hit_gaps => # of gaps in the subject in the alignment -query_name => HSP Query sequence name (if available) -query_start => HSP Query start (in original query sequence coords) -query_end => HSP Query end (in original query sequence coords) -hit_name => HSP Hit sequence name (if available) -hit_start => HSP Hit start (in original hit sequence coords) -hit_end => HSP Hit end (in original hit sequence coords) -hit_length => total length of the hit sequence -query_length=> total length of the query sequence -query_seq => query sequence portion of the HSP -hit_seq => hit sequence portion of the HSP -homology_seq=> homology sequence for the HSP -hit_frame => hit frame (only if hit is translated protein) -query_frame => query frame (only if query is translated protein) -meta => optional meta data (sec structure, markup, etc) -custom_score=> custom score data =cut =head2 meta Title : meta Usage : my $meta = $hsp->meta(); Function: Returns meta data for this HSP or undef Returns : string of meta data or undef Args : [optional] string to set value Note : At some point very soon this will likely be a Bio::AnnotationI. Don't get used to a simple string! =cut sub meta { my ($self,$value) = @_; my $previous = $self->{'META'}; if( defined $value ) { $self->{'META'} = $value; } return $previous; } =head2 noncanonical_string Title : noncanonical_string Usage : my $nc_seq = $hsp->noncanonical_string(); Function: Returns noncanonical string (NC) data for this HSP or undef Returns : string of noncanonical data or undef Args : [optional] string to set value =cut sub noncanonical_string { my ($self,$value) = @_; my $previous = $self->{'NC_SEQ'}; if( defined $value ) { $self->{'NC_SEQ'} = $value; } return $previous; } =head2 custom_score Title : custom_score Usage : my $data = $hsp->custom_score(); Function: Returns custom_score data for this HSP, or undef Returns : custom_score data or undef Args : [optional] custom_score Note : This is a Get/Set used to deal with odd score-like data generated from RNAMotif (and other programs) where the score section can be customized to include non-standard data, including sequence data, user-based scores, and other values. =cut sub custom_score { my ($self,$value) = @_; my $previous = $self->{'CUSTOMSCORE'}; if( defined $value ) { $self->{'CUSTOMSCORE'} = $value; } return $previous; } =head2 Bio::Search::HSP::HSPI methods Implementation of Bio::Search::HSP::HSPI methods follow =head2 algorithm Title : algorithm Usage : my $r_type = $hsp->algorithm Function: Obtain the name of the algorithm used to obtain the HSP Returns : string (e.g., BLASTP) Args : [optional] scalar string to set value =cut =head2 strand Title : strand Usage : $hsp->strand('hit') Function: Retrieves the strand for the HSP component requested Returns : +1 or -1 (0 if unknown) Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject. There is no strand available for 'query', as the query is a model and not a true sequence. =cut # overrides HSPI::seq() =head2 seq Usage : $hsp->seq( [seq_type] ); Purpose : Get the query or sbjct sequence as a Bio::Seq.pm object. Example : $seqObj = $hsp->seq('sbjct'); Returns : Object reference for a Bio::Seq.pm object. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'sbjct'). : ('sbjct' is synonymous with 'hit') : default is 'sbjct' : Note: if there is no sequence available (eg for a model-based : search), this returns a LocatableSeq object w/o a sequence Throws : Propagates any exception that occurs during construction : of the Bio::Seq.pm object. Comments : The sequence is returned in an array of strings corresponding : to the strings in the original format of the Blast alignment. : (i.e., same spacing). See Also : L, L =cut #------- sub seq { #------- my($self,$seqType) = @_; $seqType ||= 'sbjct'; $seqType = 'sbjct' if $seqType eq 'hit'; my $str = $self->seq_str($seqType); if( $seqType =~ /^(m|ho)/i ) { $self->throw("cannot call seq on the homology match string, it isn't really a sequence, use get_aln to convert the HSP to a Bio::AlignIO and generate a consensus from that."); } require Bio::LocatableSeq; my $id = $seqType =~ /^q/i ? $self->query->seq_id : $self->hit->seq_id; $str =~ s{\*\[\s*(\d+)\s*\]\*}{'N' x $1}ge; $str =~ s{\s+}{}g; my $seq = Bio::LocatableSeq->new (-ID => $id, -START => $self->start($seqType), -END => $self->end($seqType), -STRAND=> $self->strand($seqType), -DESC => "$seqType sequence ", ); $seq->seq($str) if $str; $seq; } =head2 pvalue Title : pvalue Usage : my $pvalue = $hsp->pvalue(); Function: Returns the P-value for this HSP or undef Returns : float or exponential (2e-10) P-value is not defined with NCBI Blast2 reports. Args : [optional] numeric to set value =cut =head2 evalue Title : evalue Usage : my $evalue = $hsp->evalue(); Function: Returns the e-value for this HSP Returns : float or exponential (2e-10) Args : [optional] numeric to set value =cut =head2 gaps Title : gaps Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); Function : Get the number of gaps in the query, hit, or total alignment. Returns : Integer, number of gaps or 0 if none Args : arg 1: 'query' = num gaps in query seq 'hit' = num gaps in hit seq 'total' = num gaps in whole alignment default = 'total' arg 2: [optional] integer gap value to set for the type requested =cut =head2 query_string Title : query_string Usage : my $qseq = $hsp->query_string; Function: Retrieves the query sequence of this HSP as a string Returns : string Args : [optional] string to set for query sequence =cut =head2 hit_string Title : hit_string Usage : my $hseq = $hsp->hit_string; Function: Retrieves the hit sequence of this HSP as a string Returns : string Args : [optional] string to set for hit sequence =cut =head2 homology_string Title : homology_string Usage : my $homo_string = $hsp->homology_string; Function: Retrieves the homology sequence for this HSP as a string. : The homology sequence is the string of symbols in between the : query and hit sequences in the alignment indicating the degree : of conservation (e.g., identical, similar, not similar). Returns : string Args : [optional] string to set for homology sequence =cut =head2 length Title : length Usage : my $len = $hsp->length( ['query'|'hit'|'total'] ); Function : Returns the length of the query or hit in the alignment (without gaps) or the aggregate length of the HSP (including gaps; this may be greater than either hit or query ) Returns : integer Args : arg 1: 'query' = length of query seq (without gaps) 'hit' = length of hit seq (without gaps) 'total' = length of alignment (with gaps) default = 'total' arg 2: [optional] integer length value to set for specific type =cut =head2 frame Title : frame Usage : my ($qframe, $hframe) = $hsp->frame('list',$queryframe,$subjectframe) Function: Set the Frame for both query and subject and insure that they agree. This overrides the frame() method implementation in FeaturePair. Returns : array of query and subject frame if return type wants an array or query frame if defined or subject frame if not defined Args : 'hit' or 'subject' or 'sbjct' to retrieve the frame of the subject (default) 'query' to retrieve the query frame 'list' or 'array' to retrieve both query and hit frames together Note : Frames are stored in the GFF way (0-2) not 1-3 as they are in BLAST (negative frames are deduced by checking the strand of the query or hit) =cut =head2 get_aln Title : get_aln Usage : my $aln = $hsp->gel_aln Function: Returns a Bio::SimpleAlign representing the HSP alignment Returns : Bio::SimpleAlign Args : none =cut sub get_aln { my ($self) = @_; require Bio::LocatableSeq; require Bio::SimpleAlign; my $aln = Bio::SimpleAlign->new; my %hsp = (hit => $self->hit_string, midline => $self->homology_string, query => $self->query_string, meta => $self->meta); # this takes care of infernal issues if ($hsp{meta} && $hsp{meta} =~ m{~+}) { $self->_postprocess_hsp(\%hsp); } if (!$hsp{query}) { $self->warn("Missing query string, can't build alignment"); return; } my $seqonly = $hsp{query}; $seqonly =~ s/[\-\s]//g; my ($q_nm,$s_nm) = ($self->query->seq_id(), $self->hit->seq_id()); unless( defined $q_nm && CORE::length ($q_nm) ) { $q_nm = 'query'; } unless( defined $s_nm && CORE::length ($s_nm) ) { $s_nm = 'hit'; } my $query = Bio::LocatableSeq->new('-seq' => $hsp{query}, '-id' => $q_nm, '-start' => $self->query->start, '-end' => $self->query->end, ); $seqonly = $hsp{hit}; $seqonly =~ s/[\-\s]//g; my $hit = Bio::LocatableSeq->new('-seq' => $hsp{hit}, '-id' => $s_nm, '-start' => $self->hit->start, '-end' => $self->hit->end, ); $aln->add_seq($query); $aln->add_seq($hit); if ($hsp{meta}) { my $meta_obj = Bio::Seq::Meta->new(); $meta_obj->named_meta('ss_cons', $hsp{meta}); $aln->consensus_meta($meta_obj); } return $aln; } =head2 Inherited from Bio::SeqFeature::SimilarityPair These methods come from Bio::SeqFeature::SimilarityPair =head2 query Title : query Usage : my $query = $hsp->query Function: Returns a SeqFeature representing the query in the HSP Returns : Bio::SeqFeature::Similarity Args : [optional] new value to set =head2 hit Title : hit Usage : my $hit = $hsp->hit Function: Returns a SeqFeature representing the hit in the HSP Returns : Bio::SeqFeature::Similarity Args : [optional] new value to set =head2 significance Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Get/Set the significance value Returns : numeric Args : [optional] new value to set =head2 score Title : score Usage : my $score = $hsp->score(); Function: Returns the score for this HSP or undef Returns : numeric Args : [optional] numeric to set value =cut =head2 bits Title : bits Usage : my $bits = $hsp->bits(); Function: Returns the bit value for this HSP or undef Returns : numeric Args : none =cut =head1 ModelHSP methods overridden in ModelHSP The following methods have been overridden due to their current reliance on sequence-based queries. They may be implemented in future versions of this class. =head2 seq_inds =cut sub seq_inds { my $self = shift; $self->warn('$hsp->seq_inds not implemented for Model-based searches'); return; } =head2 frac_identical =cut sub frac_identical { my $self = shift; $self->warn('$hsp->frac_identical not implemented for Model-based searches'); return; } =head2 frac_conserved =cut sub frac_conserved { my $self = shift; $self->warn('$hsp->frac_conserved not implemented for Model-based searches'); return; } =head2 matches =cut sub matches { my $self = shift; $self->warn('$hsp->matches not implemented for Model-based searches'); return; } =head2 num_conserved =cut sub num_conserved { my $self = shift; $self->warn('$hsp->num_conserved not implemented for Model-based searches'); return; } =head2 num_identical =cut sub num_identical { my $self = shift; $self->warn('$hsp->num_identical not implemented for Model-based searches'); return; } =head2 cigar_string =cut sub cigar_string { my $self = shift; $self->warn('$hsp->cigar_string not implemented for Model-based searches'); return; } =head2 generate_cigar_string =cut sub generate_cigar_string { my $self = shift; $self->warn('$hsp->generate_cigar_string not implemented for Model-based searches'); return; } =head2 percent_identity =cut sub percent_identity { my $self = shift; $self->warn('$hsp->percent_identity not implemented for Model-based searches'); return; } ############## PRIVATE ############## # the following method postprocesses HSP data in cases where the sequences # aren't complete (which can trigger a validation error) { my $SEQ_REGEX = qr/\*\[\s*(\d+)\s*\]\*/; my $META_REGEX = qr/(~+)/; sub _postprocess_hsp { my ($self, $hsp) = @_; $self->throw('Must pass a hash ref for HSP processing') unless ref($hsp) eq 'HASH'; my @ins; for my $type (qw(query hit meta)) { $hsp->{$type} =~ s{\s+$}{}; my $str = $hsp->{$type}; my $regex = $type eq 'meta' ? $META_REGEX : $SEQ_REGEX; my $ind = 0; while ($str =~ m{$regex}g) { $ins[$ind]->{$type} = {pos => pos($str) - length($1), str => $1}; $ind++; } } for my $chunk (reverse @ins) { my ($max, $min) = ($chunk->{hit}->{str} >= $chunk->{query}->{str}) ? ('hit', 'query') : ('query', 'hit'); my %rep; $rep{$max} = 'N' x $chunk->{$max}->{str}; $rep{$min} = 'N' x $chunk->{$min}->{str}. ('-'x($chunk->{$max}->{str}-$chunk->{$min}->{str})); $rep{'meta'} = '~' x $chunk->{$max}->{str}; $rep{'midline'} = ' ' x $chunk->{$max}->{str}; for my $t (qw(hit query meta midline)) { substr($hsp->{$t}, $chunk->{meta}->{pos}, length($chunk->{meta}->{str}) , $rep{$t}); } } } } 1; BioPerl-1.007002/Bio/Search/HSP/PSLHSP.pm000444000766000024 714613155576320 17442 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::HSP::PSLHSP # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::HSP::PSLHSP - A HSP for PSL output =head1 SYNOPSIS # get a PSLHSP somehow (SearchIO::psl) =head1 DESCRIPTION This is a HSP for PSL output so we can handle seq_inds differently. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::HSP::PSLHSP; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Search::HSP::GenericHSP); =head2 new Title : new Usage : my $obj = Bio::Search::HSP::PSLHSP->new(); Function: Builds a new Bio::Search::HSP::PSLHSP object Returns : an instance of Bio::Search::HSP::PSLHSP Args : -gapblocks => arrayref of gap locations which are [start,length] of gaps =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($qgaplocs, $hgaplocs, $mismatches) = $self->_rearrange([qw(QUERY_GAPBLOCKS HIT_GAPBLOCKS MISMATCHES)], @args); $self->gap_blocks('query',$qgaplocs) if defined $qgaplocs; $self->gap_blocks('hit', $hgaplocs) if defined $hgaplocs; $self->mismatches($mismatches) if defined $mismatches; return $self; } =head2 gap_blocks Title : gap_blocks Usage : $obj->gap_blocks($seqtype,$blocks) Function: Get/Set the gap blocks Returns : value of gap_blocks (a scalar) Args : sequence type - 'query' or 'hit' blocks - arrayref of block start,length =cut sub gap_blocks { my ($self,$seqtype,$blocks) = @_; if( ! defined $seqtype ) { $seqtype = 'query' } $seqtype = lc($seqtype); $seqtype = 'hit' if $seqtype eq 'sbjct'; if( $seqtype !~ /query|hit/i ) { $self->warn("Expect either 'query' or 'hit' as argument 1 for gap_blocks"); } unless( defined $blocks ) { return $self->{'_gap_blocks'}->{$seqtype}; } else { return $self->{'_gap_blocks'}->{$seqtype} = $blocks; } } =head2 mismatches Title : mismatches Usage : $obj->mismatches($newval) Function: Get/Set the number of mismatches Returns : value of mismatches (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub mismatches{ my $self = shift; return $self->{'mismatches'} = shift if @_; return $self->{'mismatches'}; } 1; BioPerl-1.007002/Bio/Search/HSP/PsiBlastHSP.pm000444000766000024 16102013155576320 20555 0ustar00cjfieldsstaff000000000000#----------------------------------------------------------------- # # BioPerl module Bio::Search::HSP::PsiBlastHSP # # (This module was originally called Bio::Tools::Blast::HSP) # # Please direct questions and support issues to # # Cared for by Steve Chervitz # # You may distribute this module under the same terms as perl itself #----------------------------------------------------------------- ## POD Documentation: =head1 NAME Bio::Search::HSP::PsiBlastHSP - Bioperl BLAST High-Scoring Pair object =head1 SYNOPSIS See L. =head1 DESCRIPTION A Bio::Search::HSP::PsiBlastHSP object provides an interface to data obtained in a single alignment section of a Blast report (known as a "High-scoring Segment Pair"). This is essentially a pairwise alignment with score information. PsiBlastHSP objects are accessed via L objects after parsing a BLAST report using the L system. The construction of PsiBlastHSP objects is performed by Bio::Factory::BlastHitFactory in a process that is orchestrated by the Blast parser (L). The resulting PsiBlastHSPs are then accessed via L). Therefore, you do not need to use L) directly. If you need to construct PsiBlastHSPs directly, see the new() function for details. For L BLAST parsing usage examples, see the C directory of the Bioperl distribution. =head2 Start and End coordinates Sequence endpoints are swapped so that start is always less than end. This affects For TBLASTN/X hits on the minus strand. Strand information can be recovered using the strand() method. This normalization step is standard Bioperl practice. It also facilitates use of range information by methods such as match(). =over 1 =item * Supports BLAST versions 1.x and 2.x, gapped and ungapped. =back Bio::Search::HSP::PsiBlastHSP.pm has the ability to extract a list of all residue indices for identical and conservative matches along both query and sbjct sequences. Since this degree of detail is not always needed, this behavior does not occur during construction of the PsiBlastHSP object. These data will automatically be collected as necessary as the PsiBlastHSP.pm object is used. =head1 DEPENDENCIES Bio::Search::HSP::PsiBlastHSP.pm is a concrete class that inherits from L and L. L and L are employed for creating sequence and alignment objects, respectively. =head2 Relationship to L and L PsiBlastHSP.pm can provide the query or sbjct sequence as a L object via the L method. The PsiBlastHSP.pm object can also create a two-sequence L alignment object using the the query and sbjct sequences via the L method. Creation of alignment objects is not automatic when constructing the PsiBlastHSP.pm object since this level of functionality is not always required and would generate a lot of extra overhead when crunching many reports. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Steve Chervitz Esac-at-bioperl.orgE See L for where to send bug reports and comments. =head1 ACKNOWLEDGEMENTS This software was originally developed in the Department of Genetics at Stanford University. I would also like to acknowledge my colleagues at Affymetrix for useful feedback. =head1 SEE ALSO Bio::Search::Hit::BlastHit.pm - Blast hit object. Bio::Search::Result::BlastResult.pm - Blast Result object. Bio::Seq.pm - Biosequence object =head2 Links: http://bio.perl.org/ - Bioperl Project Homepage =head1 COPYRIGHT Copyright (c) 1996-2001 Steve Chervitz. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =cut # END of main POD documentation. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::HSP::PsiBlastHSP; use strict; use Bio::SeqFeature::Similarity; use vars qw($GAP_SYMBOL %STRAND_SYMBOL); use overload '""' => \&to_string; use base qw(Bio::SeqFeature::SimilarityPair Bio::Search::HSP::HSPI); $GAP_SYMBOL = '-'; # Need a more general way to handle gap symbols. %STRAND_SYMBOL = ('Plus' => 1, 'Minus' => -1 ); =head2 new Usage : $hsp = Bio::Search::HSP::PsiBlastHSP->new( %named_params ); : Bio::Search::HSP::PsiBlastHSP.pm objects are constructed : automatically by Bio::SearchIO::BlastHitFactory.pm, : so there is no need for direct instantiation. Purpose : Constructs a new PsiBlastHSP object and Initializes key variables : for the HSP. Returns : A Bio::Search::HSP::PsiBlastHSP object Argument : Named parameters: : Parameter keys are case-insensitive. : -RAW_DATA => array ref containing raw BLAST report data for : for a single HSP. This includes all lines : of the HSP alignment from a traditional BLAST or PSI-BLAST (non-XML) report, : -RANK => integer (1..n). : -PROGRAM => string ('TBLASTN', 'BLASTP', etc.). : -QUERY_NAME => string, id of query sequence : -HIT_NAME => string, id of hit sequence : Comments : Having the raw data allows this object to do lazy parsing of : the raw HSP data (i.e., not parsed until needed). : : Note that there is a fair amount of basic parsing that is : currently performed in this module that would be more appropriate : to do within a separate factory object. : This parsing code will likely be relocated and more initialization : parameters will be added to new(). : See Also : L, L =cut #---------------- sub new { #---------------- my ($class, @args ) = @_; my $self = $class->SUPER::new( @args ); # Initialize placeholders $self->{'_queryGaps'} = $self->{'_sbjctGaps'} = 0; my ($raw_data, $qname, $hname, $qlen, $hlen); ($self->{'_prog'}, $self->{'_rank'}, $raw_data, $qname, $hname) = $self->_rearrange([qw( PROGRAM RANK RAW_DATA QUERY_NAME HIT_NAME )], @args ); # _set_data() does a fair amount of parsing. # This will likely change (see comment above.) $self->_set_data( @{$raw_data} ); # Store the aligned query as sequence feature my ($qb, $hb) = ($self->start()); my ($qe, $he) = ($self->end()); my ($qs, $hs) = ($self->strand()); my ($qf,$hf) = ($self->query->frame(), $self->hit->frame); $self->query( Bio::SeqFeature::Similarity->new (-start =>$qb, -end =>$qe, -strand =>$qs, -bits =>$self->bits, -score =>$self->score, -frame =>$qf, -seq_id => $qname, -source =>$self->{'_prog'} )); $self->hit( Bio::SeqFeature::Similarity->new (-start =>$hb, -end =>$he, -strand =>$hs, -bits =>$self->bits, -score =>$self->score, -frame =>$hf, -seq_id => $hname, -source =>$self->{'_prog'} )); # set lengths $self->query->seqlength($qlen); # query $self->hit->seqlength($hlen); # subject $self->query->frac_identical($self->frac_identical('query')); $self->hit->frac_identical($self->frac_identical('hit')); return $self; } #sub DESTROY { # my $self = shift; # #print STDERR "--->DESTROYING $self\n"; #} # Title : _id_str; # Purpose : Intended for internal use only to provide a string for use # within exception messages to help users figure out which # query/hit caused the problem. # Returns : Short string with name of query and hit seq sub _id_str { my $self = shift; if( not defined $self->{'_id_str'}) { my $qname = $self->query->seqname; my $hname = $self->hit->seqname; $self->{'_id_str'} = "QUERY=\"$qname\" HIT=\"$hname\""; } return $self->{'_id_str'}; } #================================================= # Begin Bio::Search::HSP::HSPI implementation #================================================= =head2 algorithm Title : algorithm Usage : $alg = $hsp->algorithm(); Function: Gets the algorithm specification that was used to obtain the hsp For BLAST, the algorithm denotes what type of sequence was aligned against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated dna-prt, TBLASTN prt-translated dna, TBLASTX translated dna-translated dna). Returns : a scalar string Args : none =cut #---------------- sub algorithm { #---------------- my ($self,@args) = @_; return $self->{'_prog'}; } =head2 signif() Usage : $hsp_obj->signif() Purpose : Get the P-value or Expect value for the HSP. Returns : Float (0.001 or 1.3e-43) : Returns P-value if it is defined, otherwise, Expect value. Argument : n/a Throws : n/a Comments : Provided for consistency with BlastHit::signif() : Support for returning the significance data in different : formats (e.g., exponent only), is not provided for HSP objects. : This is only available for the BlastHit or Blast object. See Also : L

, L, L =cut #----------- sub signif { #----------- my $self = shift; my $val ||= defined($self->{'_p'}) ? $self->{'_p'} : $self->{'_expect'}; $val; } =head2 evalue Usage : $hsp_obj->evalue() Purpose : Get the Expect value for the HSP. Returns : Float (0.001 or 1.3e-43) Argument : n/a Throws : n/a Comments : Support for returning the expectation data in different : formats (e.g., exponent only), is not provided for HSP objects. : This is only available for the BlastHit or Blast object. See Also : L

=cut #---------- sub evalue { shift->{'_expect'} } #---------- =head2 p Usage : $hsp_obj->p() Purpose : Get the P-value for the HSP. Returns : Float (0.001 or 1.3e-43) or undef if not defined. Argument : n/a Throws : n/a Comments : P-value is not defined with NCBI Blast2 reports. : Support for returning the expectation data in different : formats (e.g., exponent only) is not provided for HSP objects. : This is only available for the BlastHit or Blast object. See Also : L =cut #----- sub p { my $self = shift; $self->{'_p'}; } #----- # alias sub pvalue { shift->p(@_); } =head2 length Usage : $hsp->length( [seq_type] ) Purpose : Get the length of the aligned portion of the query or sbjct. Example : $hsp->length('query') Returns : integer Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total' (default = 'total') ('sbjct' is synonymous with 'hit') Throws : n/a Comments : 'total' length is the full length of the alignment : as reported in the denominators in the alignment section: : "Identical = 34/120 Positives = 67/120". See Also : L =cut #----------- sub length { #----------- ## Developer note: when using the built-in length function within ## this module, call it as CORE::length(). my( $self, $seqType ) = @_; $seqType ||= 'total'; $seqType = 'sbjct' if $seqType eq 'hit'; $seqType ne 'total' and $self->_set_seq_data() unless $self->{'_set_seq_data'}; ## Sensitive to member name format. $seqType = "_\L$seqType\E"; $self->{$seqType.'Length'}; } =head2 gaps Usage : $hsp->gaps( [seq_type] ) Purpose : Get the number of gap characters in the query, sbjct, or total alignment. : Also can return query gap chars and sbjct gap chars as a two-element list : when in array context. Example : $total_gaps = $hsp->gaps(); : ($qgaps, $sgaps) = $hsp->gaps(); : $qgaps = $hsp->gaps('query'); Returns : scalar context: integer : array context without args: (int, int) = ('queryGaps', 'sbjctGaps') Argument : seq_type: 'query' or 'hit' or 'sbjct' or 'total' : ('sbjct' is synonymous with 'hit') : (default = 'total', scalar context) : Array context can be "induced" by providing an argument of 'list' or 'array'. Throws : n/a See Also : L, L =cut #--------- sub gaps { #--------- my( $self, $seqType ) = @_; $self->_set_seq_data() unless $self->{'_set_seq_data'}; $seqType ||= (wantarray ? 'list' : 'total'); $seqType = 'sbjct' if $seqType eq 'hit'; if($seqType =~ /list|array/i) { return (($self->{'_queryGaps'} || 0), ($self->{'_sbjctGaps'} || 0)); } if($seqType eq 'total') { return ($self->{'_queryGaps'} + $self->{'_sbjctGaps'}) || 0; } else { ## Sensitive to member name format. $seqType = "_\L$seqType\E"; return $self->{$seqType.'Gaps'} || 0; } } =head2 frac_identical Usage : $hsp_object->frac_identical( [seq_type] ); Purpose : Get the fraction of identical positions within the given HSP. Example : $frac_iden = $hsp_object->frac_identical('query'); Returns : Float (2-decimal precision, e.g., 0.75). Argument : seq_type: 'query' or 'hit' or 'sbjct' or 'total' : ('sbjct' is synonymous with 'hit') : default = 'total' (but see comments below). Throws : n/a Comments : Different versions of Blast report different values for the total : length of the alignment. This is the number reported in the : denominators in the stats section: : "Identical = 34/120 Positives = 67/120". : NCBI-BLAST uses the total length of the alignment (with gaps) : WU-BLAST uses the length of the query sequence (without gaps). : Therefore, when called without an argument or an argument of 'total', : this method will report different values depending on the : version of BLAST used. : : To get the fraction identical among only the aligned residues, : ignoring the gaps, call this method with an argument of 'query' : or 'sbjct' ('sbjct' is synonymous with 'hit'). See Also : L, L, L =cut #------------------- sub frac_identical { #------------------- # The value is calculated as opposed to storing it from the parsed results. # This saves storage and also permits flexibility in determining for which # sequence (query or sbjct) the figure is to be calculated. my( $self, $seqType ) = @_; $seqType ||= 'total'; $seqType = 'sbjct' if $seqType eq 'hit'; if($seqType ne 'total') { $self->_set_seq_data() unless $self->{'_set_seq_data'}; } ## Sensitive to member name format. $seqType = "_\L$seqType\E"; sprintf( "%.2f", $self->{'_numIdentical'}/$self->{$seqType.'Length'}); } =head2 frac_conserved Usage : $hsp_object->frac_conserved( [seq_type] ); Purpose : Get the fraction of conserved positions within the given HSP. : (Note: 'conservative' positions are called 'positives' in the : Blast report.) Example : $frac_cons = $hsp_object->frac_conserved('query'); Returns : Float (2-decimal precision, e.g., 0.75). Argument : seq_type: 'query' or 'hit' or 'sbjct' or 'total' : ('sbjct' is synonymous with 'hit') : default = 'total' (but see comments below). Throws : n/a Comments : Different versions of Blast report different values for the total : length of the alignment. This is the number reported in the : denominators in the stats section: : "Identical = 34/120 Positives = 67/120". : NCBI-BLAST uses the total length of the alignment (with gaps) : WU-BLAST uses the length of the query sequence (without gaps). : Therefore, when called without an argument or an argument of 'total', : this method will report different values depending on the : version of BLAST used. : : To get the fraction conserved among only the aligned residues, : ignoring the gaps, call this method with an argument of 'query' : or 'sbjct'. See Also : L, L, L =cut #-------------------- sub frac_conserved { #-------------------- # The value is calculated as opposed to storing it from the parsed results. # This saves storage and also permits flexibility in determining for which # sequence (query or sbjct) the figure is to be calculated. my( $self, $seqType ) = @_; $seqType ||= 'total'; $seqType = 'sbjct' if $seqType eq 'hit'; if($seqType ne 'total') { $self->_set_seq_data() unless $self->{'_set_seq_data'}; } ## Sensitive to member name format. $seqType = "_\L$seqType\E"; sprintf( "%.2f", $self->{'_numConserved'}/$self->{$seqType.'Length'}); } =head2 query_string Title : query_string Usage : my $qseq = $hsp->query_string; Function: Retrieves the query sequence of this HSP as a string Returns : string Args : none =cut #---------------- sub query_string{ shift->seq_str('query'); } #---------------- =head2 hit_string Title : hit_string Usage : my $hseq = $hsp->hit_string; Function: Retrieves the hit sequence of this HSP as a string Returns : string Args : none =cut #---------------- sub hit_string{ shift->seq_str('hit'); } #---------------- =head2 homology_string Title : homology_string Usage : my $homo_string = $hsp->homology_string; Function: Retrieves the homology sequence for this HSP as a string. : The homology sequence is the string of symbols in between the : query and hit sequences in the alignment indicating the degree : of conservation (e.g., identical, similar, not similar). Returns : string Args : none =cut #---------------- sub homology_string{ shift->seq_str('match'); } #---------------- #================================================= # End Bio::Search::HSP::HSPI implementation #================================================= # Older method delegating to method defined in HSPI. =head2 expect See L =cut #---------- sub expect { shift->evalue( @_ ); } #---------- =head2 rank Usage : $hsp->rank( [string] ); Purpose : Get the rank of the HSP within a given Blast hit. Example : $rank = $hsp->rank; Returns : Integer (1..n) corresponding to the order in which the HSP appears in the BLAST report. =cut #' #---------- sub rank { shift->{'_rank'} } #---------- # For backward compatibility #---------- sub name { shift->rank } #---------- =head2 to_string Title : to_string Usage : print $hsp->to_string; Function: Returns a string representation for the Blast HSP. Primarily intended for debugging purposes. Example : see usage Returns : A string of the form: [PsiBlastHSP] e.g.: [BlastHit] 1 Args : None =cut #---------- sub to_string { #---------- my $self = shift; return "[PsiBlastHSP] " . $self->rank(); } =head2 _set_data Usage : called automatically during object construction. Purpose : Parses the raw HSP section from a flat BLAST report and sets the query sequence, sbjct sequence, and the "match" data : which consists of the symbols between the query and sbjct lines : in the alignment. Argument : Array (all lines for a single, complete HSP, from a raw, flat (i.e., non-XML) BLAST report) Throws : Propagates any exceptions from the methods called ("See Also") See Also : L, L, L =cut #-------------- sub _set_data { #-------------- my $self = shift; my @data = @_; my @queryList = (); # 'Query' = SEQUENCE USED TO QUERY THE DATABASE. my @sbjctList = (); # 'Sbjct' = HOMOLOGOUS SEQUENCE FOUND IN THE DATABASE. my @matchList = (); my $matchLine = 0; # Alternating boolean: when true, load 'match' data. my @linedat = (); #print STDERR "PsiBlastHSP: set_data()\n"; my($line, $aln_row_len, $length_diff); $length_diff = 0; # Collecting data for all lines in the alignment # and then storing the collections for possible processing later. # # Note that "match" lines may not be properly padded with spaces. # This loop now properly handles such cases: # Query: 1141 PSLVELTIRDCPRLEVGPMIRSLPKFPMLKKLDLAVANIIEEDLDVIGSLEELVIXXXXX 1200 # PSLVELTIRDCPRLEVGPMIRSLPKFPMLKKLDLAVANIIEEDLDVIGSLEELVI # Sbjct: 1141 PSLVELTIRDCPRLEVGPMIRSLPKFPMLKKLDLAVANIIEEDLDVIGSLEELVILSLKL 1200 foreach $line( @data ) { next if $line =~ /^\s*$/; if( $line =~ /^ ?Score/ ) { $self->_set_score_stats( $line ); } elsif( $line =~ /^ ?(Identities|Positives|Strand)/ ) { $self->_set_match_stats( $line ); } elsif( $line =~ /^ ?Frame = ([\d+-]+)/ ) { # Version 2.0.8 has Frame information on a separate line. # Storing frame according to SeqFeature::Generic::frame() # which does not contain strand info (use strand()). my $frame = abs($1) - 1; $self->frame( $frame ); } elsif( $line =~ /^(Query:?[\s\d]+)([^\s\d]+)/ ) { push @queryList, $line; $self->{'_match_indent'} = CORE::length $1; $aln_row_len = (CORE::length $1) + (CORE::length $2); $matchLine = 1; } elsif( $matchLine ) { # Pad the match line with spaces if necessary. $length_diff = $aln_row_len - CORE::length $line; $length_diff and $line .= ' 'x $length_diff; push @matchList, $line; $matchLine = 0; } elsif( $line =~ /^Sbjct/ ) { push @sbjctList, $line; } } # Storing the query and sbjct lists in case they are needed later. # We could make this conditional to save memory. $self->{'_queryList'} = \@queryList; $self->{'_sbjctList'} = \@sbjctList; # Storing the match list in case it is needed later. $self->{'_matchList'} = \@matchList; if(not defined ($self->{'_numIdentical'})) { my $id_str = $self->_id_str; $self->throw( -text => "Can't parse match statistics. Possibly a new or unrecognized Blast format. ($id_str)"); } if(!scalar @queryList or !scalar @sbjctList) { my $id_str = $self->_id_str; $self->throw( "Can't find query or sbjct alignment lines. Possibly unrecognized Blast format. ($id_str)"); } } =head2 _set_score_stats Usage : called automatically by _set_data() Purpose : Sets various score statistics obtained from the HSP listing. Argument : String with any of the following formats: : blast2: Score = 30.1 bits (66), Expect = 9.2 : blast2: Score = 158.2 bits (544), Expect(2) = e-110 : blast1: Score = 410 (144.3 bits), Expect = 1.7e-40, P = 1.7e-40 : blast1: Score = 55 (19.4 bits), Expect = 5.3, Sum P(3) = 0.99 Throws : Exception if the stats cannot be parsed, probably due to a change : in the Blast report format. See Also : L =cut #-------------------- sub _set_score_stats { #-------------------- my ($self, $data) = @_; my ($expect, $p); if($data =~ /Score = +([\d.e+-]+) bits \(([\d.e+-]+)\), +Expect = +([\d.e+-]+)/) { # blast2 format n = 1 $self->bits($1); $self->score($2); $expect = $3; } elsif($data =~ /Score = +([\d.e+-]+) bits \(([\d.e+-]+)\), +Expect\((\d+)\) = +([\d.e+-]+)/) { # blast2 format n > 1 $self->bits($1); $self->score($2); $self->{'_n'} = $3; $expect = $4; } elsif($data =~ /Score = +([\d.e+-]+) \(([\d.e+-]+) bits\), +Expect = +([\d.e+-]+), P = +([\d.e-]+)/) { # blast1 format, n = 1 $self->score($1); $self->bits($2); $expect = $3; $p = $4; } elsif($data =~ /Score = +([\d.e+-]+) \(([\d.e+-]+) bits\), +Expect = +([\d.e+-]+), +Sum P\((\d+)\) = +([\d.e-]+)/) { # blast1 format, n > 1 $self->score($1); $self->bits($2); $expect = $3; $self->{'_n'} = $4; $p = $5; } else { my $id_str = $self->_id_str; $self->throw(-class => 'Bio::Root::Exception', -text => "Can't parse score statistics: unrecognized format. ($id_str)", -value => $data); } $expect = "1$expect" if $expect =~ /^e/i; $p = "1$p" if defined $p and $p=~ /^e/i; $self->{'_expect'} = $expect; $self->{'_p'} = $p || undef; $self->significance( $p || $expect ); } =head2 _set_match_stats Usage : Private method; called automatically by _set_data() Purpose : Sets various matching statistics obtained from the HSP listing. Argument : blast2: Identities = 23/74 (31%), Positives = 29/74 (39%), Gaps = 17/74 (22%) : blast2: Identities = 57/98 (58%), Positives = 74/98 (75%) : blast1: Identities = 87/204 (42%), Positives = 126/204 (61%) : blast1: Identities = 87/204 (42%), Positives = 126/204 (61%), Frame = -3 : WU-blast: Identities = 310/553 (56%), Positives = 310/553 (56%), Strand = Minus / Plus Throws : Exception if the stats cannot be parsed, probably due to a change : in the Blast report format. Comments : The "Gaps = " data in the HSP header has a different meaning depending : on the type of Blast: for BLASTP, this number is the total number of : gaps in query+sbjct; for TBLASTN, it is the number of gaps in the : query sequence only. Thus, it is safer to collect the data : separately by examining the actual sequence strings as is done : in _set_seq(). See Also : L, L =cut #-------------------- sub _set_match_stats { #-------------------- my ($self, $data) = @_; if($data =~ m!Identities = (\d+)/(\d+)!) { # blast1 or 2 format $self->{'_numIdentical'} = $1; $self->{'_totalLength'} = $2; } if($data =~ m!Positives = (\d+)/(\d+)!) { # blast1 or 2 format $self->{'_numConserved'} = $1; $self->{'_totalLength'} = $2; } if($data =~ m!Frame = ([\d+-]+)!) { $self->frame($1); } # Strand data is not always present in this line. # _set_seq() will also set strand information. if($data =~ m!Strand = (\w+) / (\w+)!) { $self->{'_queryStrand'} = $1; $self->{'_sbjctStrand'} = $2; } # if($data =~ m!Gaps = (\d+)/(\d+)!) { # $self->{'_totalGaps'} = $1; # } else { # $self->{'_totalGaps'} = 0; # } } =head2 _set_seq_data Usage : called automatically when sequence data is requested. Purpose : Sets the HSP sequence data for both query and sbjct sequences. : Includes: start, stop, length, gaps, and raw sequence. Argument : n/a Throws : Propagates any exception thrown by _set_match_seq() Comments : Uses raw data stored by _set_data() during object construction. : These data are not always needed, so it is conditionally : executed only upon demand by methods such as gaps(), _set_residues(), : etc. _set_seq() does the dirty work. See Also : L =cut #----------------- sub _set_seq_data { #----------------- my $self = shift; $self->_set_seq('query', @{$self->{'_queryList'}}); $self->_set_seq('sbjct', @{$self->{'_sbjctList'}}); # Liberate some memory. @{$self->{'_queryList'}} = @{$self->{'_sbjctList'}} = (); undef $self->{'_queryList'}; undef $self->{'_sbjctList'}; $self->{'_set_seq_data'} = 1; } =head2 _set_seq Usage : called automatically by _set_seq_data() : $hsp_obj->($seq_type, @data); Purpose : Sets sequence information for both the query and sbjct sequences. : Directly counts the number of gaps in each sequence (if gapped Blast). Argument : $seq_type = 'query' or 'sbjct' : @data = all seq lines with the form: : Query: 61 SPHNVKDRKEQNGSINNAISPTATANTSGSQQINIDSALRDRSSNVAAQPSLSDASSGSN 120 Throws : Exception if data strings cannot be parsed, probably due to a change : in the Blast report format. Comments : Uses first argument to determine which data members to set : making this method sensitive data member name changes. : Behavior is dependent on the type of BLAST analysis (TBLASTN, BLASTP, etc). Warning : Sequence endpoints are normalized so that start < end. This affects HSPs : for TBLASTN/X hits on the minus strand. Normalization facilitates use : of range information by methods such as match(). See Also : L, L, L, L, L =cut #------------- sub _set_seq { #------------- my $self = shift; my $seqType = shift; my @data = @_; my @ranges = (); my @sequence = (); my $numGaps = 0; foreach( @data ) { if( m/(\d+) *([^\d\s]+) *(\d+)/) { push @ranges, ( $1, $3 ) ; push @sequence, $2; #print STDERR "_set_seq found sequence \"$2\"\n"; } else { $self->warn("Bad sequence data: $_"); } } if( !(scalar(@sequence) and scalar(@ranges))) { my $id_str = $self->_id_str; $self->throw("Can't set sequence: missing data. Possibly unrecognized Blast format. ($id_str)"); } # Sensitive to member name changes. $seqType = "_\L$seqType\E"; $self->{$seqType.'Start'} = $ranges[0]; $self->{$seqType.'Stop'} = $ranges[ $#ranges ]; $self->{$seqType.'Seq'} = \@sequence; $self->{$seqType.'Length'} = abs($ranges[ $#ranges ] - $ranges[0]) + 1; # Adjust lengths for BLASTX, TBLASTN, TBLASTX sequences # Converting nucl coords to amino acid coords. my $prog = $self->algorithm; if($prog eq 'TBLASTN' and $seqType eq '_sbjct') { $self->{$seqType.'Length'} /= 3; } elsif($prog eq 'BLASTX' and $seqType eq '_query') { $self->{$seqType.'Length'} /= 3; } elsif($prog eq 'TBLASTX') { $self->{$seqType.'Length'} /= 3; } if( $prog ne 'BLASTP' ) { $self->{$seqType.'Strand'} = 'Plus' if $prog =~ /BLASTN/; $self->{$seqType.'Strand'} = 'Plus' if ($prog =~ /BLASTX/ and $seqType eq '_query'); # Normalize sequence endpoints so that start < end. # Reverse complement or 'minus strand' HSPs get flipped here. if($self->{$seqType.'Start'} > $self->{$seqType.'Stop'}) { ($self->{$seqType.'Start'}, $self->{$seqType.'Stop'}) = ($self->{$seqType.'Stop'}, $self->{$seqType.'Start'}); $self->{$seqType.'Strand'} = 'Minus'; } } ## Count number of gaps in each seq. Only need to do this for gapped Blasts. # if($self->{'_gapped'}) { my $seqstr = join('', @sequence); $seqstr =~ s/\s//g; my $num_gaps = CORE::length($seqstr) - $self->{$seqType.'Length'}; $self->{$seqType.'Gaps'} = $num_gaps if $num_gaps > 0; # } } =head2 _set_residues Usage : called automatically when residue data is requested. Purpose : Sets the residue numbers representing the identical and : conserved positions. These data are obtained by analyzing the : symbols between query and sbjct lines of the alignments. Argument : n/a Throws : Propagates any exception thrown by _set_seq_data() and _set_match_seq(). Comments : These data are not always needed, so it is conditionally : executed only upon demand by methods such as seq_inds(). : Behavior is dependent on the type of BLAST analysis (TBLASTN, BLASTP, etc). See Also : L, L, L =cut #------------------ sub _set_residues { #------------------ my $self = shift; my @sequence = (); $self->_set_seq_data() unless $self->{'_set_seq_data'}; # Using hashes to avoid saving duplicate residue numbers. my %identicalList_query = (); my %identicalList_sbjct = (); my %conservedList_query = (); my %conservedList_sbjct = (); my $aref = $self->_set_match_seq() if not ref $self->{'_matchSeq'}; $aref ||= $self->{'_matchSeq'}; my $seqString = join('', @$aref ); my $qseq = join('',@{$self->{'_querySeq'}}); my $sseq = join('',@{$self->{'_sbjctSeq'}}); my $resCount_query = $self->{'_queryStop'} || 0; my $resCount_sbjct = $self->{'_sbjctStop'} || 0; my $prog = $self->algorithm; if($prog !~ /^BLASTP|^BLASTN/) { if($prog eq 'TBLASTN') { $resCount_sbjct /= 3; } elsif($prog eq 'BLASTX') { $resCount_query /= 3; } elsif($prog eq 'TBLASTX') { $resCount_query /= 3; $resCount_sbjct /= 3; } } my ($mchar, $schar, $qchar); while( $mchar = chop($seqString) ) { ($qchar, $schar) = (chop($qseq), chop($sseq)); if( $mchar eq '+' ) { $conservedList_query{ $resCount_query } = 1; $conservedList_sbjct{ $resCount_sbjct } = 1; } elsif( $mchar ne ' ' ) { $identicalList_query{ $resCount_query } = 1; $identicalList_sbjct{ $resCount_sbjct } = 1; } $resCount_query-- if $qchar ne $GAP_SYMBOL; $resCount_sbjct-- if $schar ne $GAP_SYMBOL; } $self->{'_identicalRes_query'} = \%identicalList_query; $self->{'_conservedRes_query'} = \%conservedList_query; $self->{'_identicalRes_sbjct'} = \%identicalList_sbjct; $self->{'_conservedRes_sbjct'} = \%conservedList_sbjct; } =head2 _set_match_seq Usage : $hsp_obj->_set_match_seq() Purpose : Set the 'match' sequence for the current HSP (symbols in between : the query and sbjct lines.) Returns : Array reference holding the match sequences lines. Argument : n/a Throws : Exception if the _matchList field is not set. Comments : The match information is not always necessary. This method : allows it to be conditionally prepared. : Called by _set_residues>() and seq_str(). See Also : L, L =cut #------------------- sub _set_match_seq { #------------------- my $self = shift; if( ! ref($self->{'_matchList'}) ) { my $id_str = $self->_id_str; $self->throw("Can't set HSP match sequence: No data ($id_str)"); } my @data = @{$self->{'_matchList'}}; my(@sequence); foreach( @data ) { chomp($_); ## Remove leading spaces; (note: aln may begin with a space ## which is why we can't use s/^ +//). s/^ {$self->{'_match_indent'}}//; push @sequence, $_; } # Liberate some memory. @{$self->{'_matchList'}} = undef; $self->{'_matchList'} = undef; $self->{'_matchSeq'} = \@sequence; return $self->{'_matchSeq'}; } =head2 n Usage : $hsp_obj->n() Purpose : Get the N value (num HSPs on which P/Expect is based). : This value is not defined with NCBI Blast2 with gapping. Returns : Integer or null string if not defined. Argument : n/a Throws : n/a Comments : The 'N' value is listed in parenthesis with P/Expect value: : e.g., P(3) = 1.2e-30 ---> (N = 3). : Not defined in NCBI Blast2 with gaps. : This typically is equal to the number of HSPs but not always. : To obtain the number of HSPs, use Bio::Search::Hit::BlastHit::num_hsps(). See Also : L =cut #----- sub n { my $self = shift; $self->{'_n'} || ''; } #----- =head2 matches Usage : $hsp->matches([seq_type], [start], [stop]); Purpose : Get the total number of identical and conservative matches : in the query or sbjct sequence for the given HSP. Optionally can : report data within a defined interval along the seq. : (Note: 'conservative' matches are called 'positives' in the : Blast report.) Example : ($id,$cons) = $hsp_object->matches('hit'); : ($id,$cons) = $hsp_object->matches('query',300,400); Returns : 2-element array of integers Argument : (1) seq_type = 'query' or 'hit' or 'sbjct' (default = query) : ('sbjct' is synonymous with 'hit') : (2) start = Starting coordinate (optional) : (3) stop = Ending coordinate (optional) Throws : Exception if the supplied coordinates are out of range. Comments : Relies on seq_str('match') to get the string of alignment symbols : between the query and sbjct lines which are used for determining : the number of identical and conservative matches. See Also : L, L, L, L =cut #----------- sub matches { #----------- my( $self, %param ) = @_; my(@data); my($seqType, $beg, $end) = ($param{-SEQ}, $param{-START}, $param{-STOP}); $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; my($start,$stop); if(!defined $beg && !defined $end) { ## Get data for the whole alignment. push @data, ($self->{'_numIdentical'}, $self->{'_numConserved'}); } else { ## Get the substring representing the desired sub-section of aln. $beg ||= 0; $end ||= 0; ($start,$stop) = $self->range($seqType); if($beg == 0) { $beg = $start; $end = $beg+$end; } elsif($end == 0) { $end = $stop; $beg = $end-$beg; } if($end >= $stop) { $end = $stop; } ##ML changed from if (end >stop) else { $end += 1;} ##ML moved from commented position below, makes ##more sense here # if($end > $stop) { $end = $stop; } if($beg < $start) { $beg = $start; } # else { $end += 1;} # my $seq = substr($self->seq_str('match'), $beg-$start, ($end-$beg)); ## ML: START fix for substr out of range error ------------------ my $seq = ""; my $prog = $self->algorithm; if (($prog eq 'TBLASTN') and ($seqType eq 'sbjct')) { $seq = substr($self->seq_str('match'), int(($beg-$start)/3), int(($end-$beg+1)/3)); } elsif (($prog eq 'BLASTX') and ($seqType eq 'query')) { $seq = substr($self->seq_str('match'), int(($beg-$start)/3), int(($end-$beg+1)/3)); } else { $seq = substr($self->seq_str('match'), $beg-$start, ($end-$beg)); } ## ML: End of fix for substr out of range error ----------------- ## ML: debugging code ## This is where we get our exception. Try printing out the values going ## into this: ## # print STDERR # qq(*------------MY EXCEPTION --------------------\nSeq: ") , # $self->seq_str("$seqType"), qq("\n),$self->rank,",( index:"; # print STDERR $beg-$start, ", len: ", $end-$beg," ), (HSPRealLen:", # CORE::length $self->seq_str("$seqType"); # print STDERR ", HSPCalcLen: ", $stop - $start +1 ," ), # ( beg: $beg, end: $end ), ( start: $start, stop: stop )\n"; ## ML: END DEBUGGING CODE---------- if(!CORE::length $seq) { my $id_str = $self->_id_str; $self->throw("Undefined $seqType sub-sequence ($beg,$end). Valid range = $start - $stop ($id_str)"); } ## Get data for a substring. # printf "Collecting HSP subsection data: beg,end = %d,%d; start,stop = %d,%d\n%s<---\n", $beg, $end, $start, $stop, $seq; # printf "Original match seq:\n%s\n",$self->seq_str('match'); $seq =~ s/ //g; # remove space (no info). my $len_cons = CORE::length $seq; $seq =~ s/\+//g; # remove '+' characters (conservative substitutions) my $len_id = CORE::length $seq; push @data, ($len_id, $len_cons); # printf " HSP = %s\n id = %d; cons = %d\n", $self->rank, $len_id, $len_cons; ; } @data; } =head2 num_identical Usage : $hsp_object->num_identical(); Purpose : Get the number of identical positions within the given HSP. Example : $num_iden = $hsp_object->num_identical(); Returns : integer Argument : n/a Throws : n/a See Also : L, L =cut #------------------- sub num_identical { #------------------- my( $self) = shift; $self->{'_numIdentical'}; } =head2 num_conserved Usage : $hsp_object->num_conserved(); Purpose : Get the number of conserved positions within the given HSP. Example : $num_iden = $hsp_object->num_conserved(); Returns : integer Argument : n/a Throws : n/a See Also : L, L =cut #------------------- sub num_conserved { #------------------- my( $self) = shift; $self->{'_numConserved'}; } =head2 range Usage : $hsp->range( [seq_type] ); Purpose : Gets the (start, end) coordinates for the query or sbjct sequence : in the HSP alignment. Example : ($query_beg, $query_end) = $hsp->range('query'); : ($hit_beg, $hit_end) = $hsp->range('hit'); Returns : Two-element array of integers Argument : seq_type = string, 'query' or 'hit' or 'sbjct' (default = 'query') : ('sbjct' is synonymous with 'hit') Throws : n/a See Also : L, L =cut #---------- sub range { #---------- my ($self, $seqType) = @_; $self->_set_seq_data() unless $self->{'_set_seq_data'}; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; return ($self->{$seqType.'Start'},$self->{$seqType.'Stop'}); } =head2 start Usage : $hsp->start( [seq_type] ); Purpose : Gets the start coordinate for the query, sbjct, or both sequences : in the HSP alignment. : NOTE: Start will always be less than end. : To determine strand, use $hsp->strand() Example : $query_beg = $hsp->start('query'); : $hit_beg = $hsp->start('hit'); : ($query_beg, $hit_beg) = $hsp->start(); Returns : scalar context: integer : array context without args: list of two integers Argument : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default= 'query') : ('sbjct' is synonymous with 'hit') : Array context can be "induced" by providing an argument of 'list' or 'array'. Throws : n/a See Also : L, L =cut #---------- sub start { #---------- my ($self, $seqType) = @_; $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; $self->_set_seq_data() unless $self->{'_set_seq_data'}; if($seqType =~ /list|array/i) { return ($self->{'_queryStart'}, $self->{'_sbjctStart'}); } else { ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; return $self->{$seqType.'Start'}; } } =head2 end Usage : $hsp->end( [seq_type] ); Purpose : Gets the end coordinate for the query, sbjct, or both sequences : in the HSP alignment. : NOTE: Start will always be less than end. : To determine strand, use $hsp->strand() Example : $query_end = $hsp->end('query'); : $hit_end = $hsp->end('hit'); : ($query_end, $hit_end) = $hsp->end(); Returns : scalar context: integer : array context without args: list of two integers Argument : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default= 'query') : ('sbjct' is synonymous with 'hit') : Array context can be "induced" by providing an argument of 'list' or 'array'. Throws : n/a See Also : L, L, L =cut #---------- sub end { #---------- my ($self, $seqType) = @_; $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; $self->_set_seq_data() unless $self->{'_set_seq_data'}; if($seqType =~ /list|array/i) { return ($self->{'_queryStop'}, $self->{'_sbjctStop'}); } else { ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; return $self->{$seqType.'Stop'}; } } =head2 strand Usage : $hsp_object->strand( [seq_type] ) Purpose : Get the strand of the query or sbjct sequence. Example : print $hsp->strand('query'); : ($query_strand, $hit_strand) = $hsp->strand(); Returns : -1, 0, or 1 : -1 = Minus strand, +1 = Plus strand : Returns 0 if strand is not defined, which occurs : for BLASTP reports, and the query of TBLASTN : as well as the hit if BLASTX reports. : In scalar context without arguments, returns queryStrand value. : In array context without arguments, returns a two-element list : of strings (queryStrand, sbjctStrand). : Array context can be "induced" by providing an argument of 'list' or 'array'. Argument : seq_type: 'query' or 'hit' or 'sbjct' or undef : ('sbjct' is synonymous with 'hit') Throws : n/a See Also : L, L =cut #----------- sub strand { #----------- my( $self, $seqType ) = @_; $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; ## Sensitive to member name format. $seqType = "_\L$seqType\E"; # $seqType could be '_list'. $self->{'_queryStrand'} or $self->_set_seq_data() unless $self->{'_set_seq_data'}; my $prog = $self->algorithm; if($seqType =~ /list|array/i) { my ($qstr, $hstr); if( $prog eq 'BLASTP') { $qstr = 0; $hstr = 0; } elsif( $prog eq 'TBLASTN') { $qstr = 0; $hstr = $STRAND_SYMBOL{$self->{'_sbjctStrand'}}; } elsif( $prog eq 'BLASTX') { $qstr = $STRAND_SYMBOL{$self->{'_queryStrand'}}; $hstr = 0; } else { $qstr = $STRAND_SYMBOL{$self->{'_queryStrand'}} if defined $self->{'_queryStrand'}; $hstr = $STRAND_SYMBOL{$self->{'_sbjctStrand'}} if defined $self->{'_sbjctStrand'}; } $qstr ||= 0; $hstr ||= 0; return ($qstr, $hstr); } local $^W = 0; $STRAND_SYMBOL{$self->{$seqType.'Strand'}} || 0; } =head2 seq Usage : $hsp->seq( [seq_type] ); Purpose : Get the query or sbjct sequence as a Bio::Seq.pm object. Example : $seqObj = $hsp->seq('query'); Returns : Object reference for a Bio::Seq.pm object. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query'). : ('sbjct' is synonymous with 'hit') Throws : Propagates any exception that occurs during construction : of the Bio::Seq.pm object. Comments : The sequence is returned in an array of strings corresponding : to the strings in the original format of the Blast alignment. : (i.e., same spacing). See Also : L, L, L =cut #------- sub seq { #------- my($self,$seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; my $str = $self->seq_str($seqType); require Bio::Seq; Bio::Seq->new(-ID => $self->to_string, -SEQ => $str, -DESC => "$seqType sequence", ); } =head2 seq_str Usage : $hsp->seq_str( seq_type ); Purpose : Get the full query, sbjct, or 'match' sequence as a string. : The 'match' sequence is the string of symbols in between the : query and sbjct sequences. Example : $str = $hsp->seq_str('query'); Returns : String Argument : seq_Type = 'query' or 'hit' or 'sbjct' or 'match' : ('sbjct' is synonymous with 'hit') Throws : Exception if the argument does not match an accepted seq_type. Comments : Calls _set_seq_data() to set the 'match' sequence if it has : not been set already. See Also : L, L, L =cut #------------ sub seq_str { #------------ my($self,$seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; $self->_set_seq_data() unless $self->{'_set_seq_data'}; if($seqType =~ /sbjct|query/) { my $seq = join('',@{$self->{$seqType.'Seq'}}); $seq =~ s/\s+//g; return $seq; } elsif( $seqType =~ /match/i) { # Only need to call _set_match_seq() if the match seq is requested. my $aref = $self->_set_match_seq() unless ref $self->{'_matchSeq'}; $aref = $self->{'_matchSeq'}; return join('',@$aref); } else { my $id_str = $self->_id_str; $self->throw(-class => 'Bio::Root::BadParameter', -text => "Invalid or undefined sequence type: $seqType ($id_str)\n" . "Valid types: query, sbjct, match", -value => $seqType); } } =head2 seq_inds Usage : $hsp->seq_inds( seq_type, class, collapse ); Purpose : Get a list of residue positions (indices) for all identical : or conserved residues in the query or sbjct sequence. Example : @s_ind = $hsp->seq_inds('query', 'identical'); : @h_ind = $hsp->seq_inds('hit', 'conserved'); : @h_ind = $hsp->seq_inds('hit', 'conserved', 1); Returns : List of integers : May include ranges if collapse is true. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = query) : ('sbjct' is synonymous with 'hit') : class = 'identical' or 'conserved' (default = identical) : (can be shortened to 'id' or 'cons') : (actually, anything not 'id' will evaluate to 'conserved'). : collapse = boolean, if true, consecutive positions are merged : using a range notation, e.g., "1 2 3 4 5 7 9 10 11" : collapses to "1-5 7 9-11". This is useful for : consolidating long lists. Default = no collapse. Throws : n/a. Comments : Calls _set_residues() to set the 'match' sequence if it has : not been set already. See Also : L, L, L, L =cut #--------------- sub seq_inds { #--------------- my ($self, $seqType, $class, $collapse) = @_; $seqType ||= 'query'; $class ||= 'identical'; $collapse ||= 0; $seqType = 'sbjct' if $seqType eq 'hit'; $self->_set_residues() unless defined $self->{'_identicalRes_query'}; $seqType = ($seqType !~ /^q/i ? 'sbjct' : 'query'); $class = ($class !~ /^id/i ? 'conserved' : 'identical'); ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; $class = "_\L$class\E"; my @ary = sort { $a <=> $b } keys %{ $self->{"${class}Res$seqType"}}; require Bio::Search::BlastUtils if $collapse; return $collapse ? &Bio::Search::BlastUtils::collapse_nums(@ary) : @ary; } =head2 get_aln Usage : $hsp->get_aln() Purpose : Get a Bio::SimpleAlign object constructed from the query + sbjct : sequences of the present HSP object. Example : $aln_obj = $hsp->get_aln(); Returns : Object reference for a Bio::SimpleAlign.pm object. Argument : n/a. Throws : Propagates any exception ocurring during the construction of : the Bio::SimpleAlign object. Comments : Requires Bio::SimpleAlign. : The Bio::SimpleAlign object is constructed from the query + sbjct : sequence objects obtained by calling seq(). : Gap residues are included (see $GAP_SYMBOL). See Also : L, L =cut #------------ sub get_aln { #------------ my $self = shift; require Bio::SimpleAlign; require Bio::LocatableSeq; my $qseq = $self->seq('query'); my $sseq = $self->seq('sbjct'); my $type = $self->algorithm =~ /P$|^T/ ? 'amino' : 'dna'; my $aln = Bio::SimpleAlign->new(); $aln->add_seq(Bio::LocatableSeq->new(-seq => $qseq->seq(), -id => 'query_'.$qseq->display_id(), -start => 1, -end => CORE::length($qseq))); $aln->add_seq(Bio::LocatableSeq->new(-seq => $sseq->seq(), -id => 'hit_'.$sseq->display_id(), -start => 1, -end => CORE::length($sseq))); return $aln; } 1; __END__ =head1 FOR DEVELOPERS ONLY =head2 Data Members Information about the various data members of this module is provided for those wishing to modify or understand the code. Two things to bear in mind: =over 4 =item 1 Do NOT rely on these in any code outside of this module. All data members are prefixed with an underscore to signify that they are private. Always use accessor methods. If the accessor doesn't exist or is inadequate, create or modify an accessor (and let me know, too!). =item 2 This documentation may be incomplete and out of date. It is easy for these data member descriptions to become obsolete as this module is still evolving. Always double check this info and search for members not described here. =back An instance of Bio::Search::HSP::PsiBlastHSP.pm is a blessed reference to a hash containing all or some of the following fields: FIELD VALUE -------------------------------------------------------------- (member names are mostly self-explanatory) _score : _bits : _p : _n : Integer. The 'N' value listed in parenthesis with P/Expect value: : e.g., P(3) = 1.2e-30 ---> (N = 3). : Not defined in NCBI Blast2 with gaps. : To obtain the number of HSPs, use Bio::Search::Hit::BlastHit::num_hsps(). _expect : _queryLength : _queryGaps : _queryStart : _queryStop : _querySeq : _sbjctLength : _sbjctGaps : _sbjctStart : _sbjctStop : _sbjctSeq : _matchSeq : String. Contains the symbols between the query and sbjct lines which indicate identical (letter) and conserved ('+') matches or a mismatch (' '). _numIdentical : _numConserved : _identicalRes_query : _identicalRes_sbjct : _conservedRes_query : _conservedRes_sbjct : _match_indent : The number of leading space characters on each line containing the match symbols. _match_indent is 13 in this example: Query: 285 QNSAPWGLARISHRERLNLGSFNKYLYDDDAG Q +APWGLARIS G+ + Y YD+ AG ^^^^^^^^^^^^^ =cut 1; BioPerl-1.007002/Bio/Search/HSP/PullHSPI.pm000555000766000024 6300613155576320 20051 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::HSP::PullHSPI # # Please direct questions and support issues to # # Cared for by Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::HSP::PullHSPI - Bio::Search::HSP::HSPI interface for pull parsers. =head1 SYNOPSIS # This is an interface and cannot be instantiated # generally we use Bio::SearchIO to build these objects use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer_pull', -file => 'result.hmmer'); while (my $result = $in->next_result) { while (my $hit = $result->next_hit) { while (my $hsp = $hit->next_hsp) { $r_type = $hsp->algorithm; $pvalue = $hsp->p(); $evalue = $hsp->evalue(); $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] ); $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] ); $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); $qseq = $hsp->query_string; $hseq = $hsp->hit_string; $homo_string = $hsp->homology_string; $len = $hsp->length( ['query'|'hit'|'total'] ); $len = $hsp->length( ['query'|'hit'|'total'] ); $rank = $hsp->rank; } } } =head1 DESCRIPTION PullHSP is for fast implementations that only do parsing work on the hsp data when you actually request information by calling one of the HSPI methods. Many methods of HSPI are implemented in a way suitable for inheriting classes that use Bio::PullParserI. It only really makes sense for PullHSP modules to be created by (and have as a -parent) PullHit modules. In addition to the usual -chunk and -parent, -hsp_data is all you should supply when making a PullHSP object. This will store that data and make it accessible via _raw_hsp_data, which you can access in your subclass. It would be best to simply provide the data as the input -chunk instead, if the raw data is large enough. =head1 SEE ALSO This module inherits methods from these other modules: L, L L Please refer to these modules for documentation of the many additional inherited methods. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 COPYRIGHT Copyright (c) 2006 Sendu Bala. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::HSP::PullHSPI; use strict; use base qw(Bio::Search::HSP::HSPI Bio::PullParserI); =head2 _setup Title : _setup Usage : $self->_setup(@args) Function: Implementers should call this to setup common fields and deal with common arguments to new(). Returns : n/a Args : @args received in new(). =cut sub _setup { my ($self, @args) = @_; # fields most subclasses probably will want $self->_fields( { ( hsp_length => undef, identical => undef, percent_identity => undef, conserved => undef, hsp_gaps => undef, query_gaps => undef, hit_gaps => undef, evalue => undef, pvalue => undef, score => undef, query_start => undef, query_end => undef, query_string => undef, hit_start => undef, hit_end => undef, hit_string => undef, homology_string => undef, rank => undef, seq_inds => undef, hit_identical_inds => undef, hit_conserved_inds => undef, hit_nomatch_inds => undef, hit_gap_inds => undef, query_identical_inds => undef, query_conserved_inds => undef, query_nomatch_inds => undef, query_gap_inds => undef ) } ); my ($parent, $chunk, $hsp_data) = $self->_rearrange([qw(PARENT CHUNK HSP_DATA)], @args); $self->throw("Need -parent or -chunk to be defined") unless defined $parent || $chunk; $self->parent($parent) if $parent; if ($chunk) { my ($io, $start, $end) = (undef, 0, undef); if (ref($chunk) eq 'ARRAY') { ($io, $start, $end) = @{$chunk}; } else { $io = $chunk; } $self->chunk($io, -start => $start, -end => $end); } $self->_raw_hsp_data($hsp_data) if $hsp_data; return $self; } sub _raw_hsp_data { my $self = shift; if (@_) { $self->{_raw_hsp_data} = shift; } return $self->{_raw_hsp_data}; } # # Some of these methods are written explitely to avoid HSPI throwing not # implemented or the wrong ancestor class being used to answer the method; # if it didn't do that then PullParserI AUTOLOAD would have cought them. # =head2 algorithm Title : algorithm Usage : my $r_type = $hsp->algorithm Function: Obtain the name of the algorithm used to obtain the HSP Returns : string (e.g., BLASTP) Args : none =cut sub algorithm { return shift->get_field('algorithm'); } =head2 pvalue Title : pvalue Usage : my $pvalue = $hsp->pvalue(); Function: Returns the P-value for this HSP or undef Returns : float or exponential (2e-10) Args : none =cut sub pvalue { return shift->get_field('pvalue'); } =head2 evalue Title : evalue Usage : my $evalue = $hsp->evalue(); Function: Returns the e-value for this HSP Returns : float or exponential (2e-10) Args : none =cut sub evalue { return shift->get_field('evalue'); } *expect = \&evalue; =head2 frac_identical Title : frac_identical Usage : my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] ); Function: Returns the fraction of identitical positions for this HSP Returns : Float in range 0.0 -> 1.0 Args : 'query' = num identical / length of query seq (without gaps) 'hit' = num identical / length of hit seq (without gaps) 'total' = num identical / length of alignment (with gaps) default = 'total' =cut sub frac_identical { my ($self, $type) = @_; $type = lc $type if defined $type; $type = 'hit' if (defined $type && $type =~ /subject|sbjct/); $type = 'total' if (! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/); my $ratio = $self->num_identical($type) / $self->length($type); return sprintf( "%.4f", $ratio); } =head2 frac_conserved Title : frac_conserved Usage : my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] ); Function : Returns the fraction of conserved positions for this HSP. This is the fraction of symbols in the alignment with a positive score. Returns : Float in range 0.0 -> 1.0 Args : 'query' = num conserved / length of query seq (without gaps) 'hit' = num conserved / length of hit seq (without gaps) 'total' = num conserved / length of alignment (with gaps) default = 'total' =cut sub frac_conserved { my ($self, $type) = @_; $type = lc $type if defined $type; $type = 'hit' if (defined $type && $type =~ /subject|sbjct/); $type = 'total' if (! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/); my $ratio = $self->num_conserved($type) / $self->length($type); return sprintf( "%.4f", $ratio); } =head2 num_identical Title : num_identical Usage : $obj->num_identical($newval) Function: returns the number of identical residues in the alignment Returns : integer Args : integer (optional) =cut sub num_identical { my $self = shift; return scalar($self->seq_inds('hit', 'identical')); } =head2 num_conserved Title : num_conserved Usage : $obj->num_conserved($newval) Function: returns the number of conserved residues in the alignment Returns : inetger Args : integer (optional) =cut sub num_conserved { my $self = shift; return scalar($self->seq_inds('hit', 'conserved-not-identical')); } =head2 gaps Title : gaps Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); Function : Get the number of gap characters in the query, hit, or total alignment. Returns : Integer, number of gap characters or 0 if none Args : 'query', 'hit' or 'total'; default = 'total' =cut sub gaps { my ($self, $type) = @_; $type = lc $type if defined $type; $type = 'total' if (! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/); $type = 'hit' if $type =~ /sbjct|subject/; if ($type eq 'total') { return scalar($self->seq_inds('hit', 'gap')) + scalar($self->seq_inds('query', 'gap')); } return scalar($self->seq_inds($type, 'gap')); } =head2 query_string Title : query_string Usage : my $qseq = $hsp->query_string; Function: Retrieves the query sequence of this HSP as a string Returns : string Args : none =cut sub query_string { return shift->get_field('query_string'); } =head2 hit_string Title : hit_string Usage : my $hseq = $hsp->hit_string; Function: Retrieves the hit sequence of this HSP as a string Returns : string Args : none =cut sub hit_string { return shift->get_field('hit_string'); } =head2 homology_string Title : homology_string Usage : my $homo_string = $hsp->homology_string; Function: Retrieves the homology sequence for this HSP as a string. : The homology sequence is the string of symbols in between the : query and hit sequences in the alignment indicating the degree : of conservation (e.g., identical, similar, not similar). Returns : string Args : none =cut sub homology_string { return shift->get_field('homology_string'); } =head2 length Title : length Usage : my $len = $hsp->length( ['query'|'hit'|'total'] ); Function : Returns the length of the query or hit in the alignment (without gaps) or the aggregate length of the HSP (including gaps; this may be greater than either hit or query ) Returns : integer Args : 'query' = length of query seq (without gaps) 'hit' = length of hit seq (without gaps) 'total' = length of alignment (with gaps) default = 'total' Args : none =cut sub length { my ($self, $type) = @_; $type = 'total' unless defined $type; $type = lc $type; if ($type =~ /^q/i) { return $self->query->length; } elsif ($type =~ /^(hit|subject|sbjct)/) { return $self->hit->length; } else { return $self->hit->length + $self->gaps('hit'); } } =head2 hsp_length Title : hsp_length Usage : my $len = $hsp->hsp_length() Function: shortcut length('hsp') Returns : floating point between 0 and 100 Args : none =cut sub hsp_length { return shift->length('total'); } =head2 percent_identity Title : percent_identity Usage : my $percentid = $hsp->percent_identity() Function: Returns the calculated percent identity for an HSP Returns : floating point between 0 and 100 Args : none =cut sub percent_identity{ my ($self) = @_; return $self->frac_identical('hsp') * 100; } =head2 get_aln Title : get_aln Usage : my $aln = $hsp->get_aln Function: Returns a Bio::SimpleAlign representing the HSP alignment Returns : Bio::SimpleAlign Args : none =cut sub get_aln { my $self = shift; require Bio::LocatableSeq; require Bio::SimpleAlign; my $aln = Bio::SimpleAlign->new(); my $hs = $self->seq('hit'); my $qs = $self->seq('query'); if ($hs && $qs) { $aln->add_seq($hs); $aln->add_seq($qs); return $aln; } return; } =head2 seq_inds Title : seq_inds Purpose : Get a list of residue positions (indices) for all identical : or conserved residues in the query or sbjct sequence. Example : @s_ind = $hsp->seq_inds('query', 'identical'); : @h_ind = $hsp->seq_inds('hit', 'conserved'); : @h_ind = $hsp->seq_inds('hit', 'conserved', 1); Returns : List of integers : May include ranges if collapse is true. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = query) ('sbjct' is synonymous with 'hit') class = 'identical' or 'conserved' or 'nomatch' or 'gap' (default = identical) (can be shortened to 'id' or 'cons') Note that 'conserved' includes identical unless you use 'conserved-not-identical' collapse = boolean, if true, consecutive positions are merged using a range notation, e.g., "1 2 3 4 5 7 9 10 11" collapses to "1-5 7 9-11". This is useful for consolidating long lists. Default = no collapse. Throws : n/a. Comments : See Also : L, L =cut sub seq_inds { my ($self, $seqType, $class, $collapse) = @_; $seqType ||= 'query'; $class ||= 'identical'; $collapse ||= 0; $seqType = lc($seqType); $class = lc($class); $seqType = 'hit' if $seqType eq 'sbjct'; my $t = substr($seqType,0,1); if ($t eq 'q') { $seqType = 'query'; } elsif ($t eq 's' || $t eq 'h') { $seqType = 'hit'; } else { $self->warn("unknown seqtype $seqType using 'query'"); $seqType = 'query'; } $t = substr($class,0,1); if ($t eq 'c') { if ($class eq 'conserved-not-identical') { $class = 'conserved'; } else { $class = 'conservedall'; } } elsif ($t eq 'i') { $class = 'identical'; } elsif ($t eq 'n') { $class = 'nomatch'; } elsif ($t eq 'g') { $class = 'gap'; } else { $self->warn("unknown sequence class $class using 'identical'"); $class = 'identical'; } $seqType .= '_'; $class .= '_inds'; my @ary; if ($class eq 'conservedall_inds') { my %tmp = map { $_, 1 } @{$self->get_field($seqType.'conserved_inds')}, @{$self->get_field($seqType.'identical_inds')}; @ary = sort {$a <=> $b} keys %tmp; } else { @ary = @{$self->get_field($seqType.$class)}; } return $collapse ? &Bio::Search::SearchUtils::collapse_nums(@ary) : @ary; } =head2 Inherited from L These methods come from L =head2 query Title : query Usage : my $query = $hsp->query Function: Returns a SeqFeature representing the query in the HSP Returns : Bio::SeqFeature::Similarity Args : [optional] new value to set =head2 hit Title : hit Usage : my $hit = $hsp->hit Function: Returns a SeqFeature representing the hit in the HSP Returns : Bio::SeqFeature::Similarity Args : [optional] new value to set =head2 significance Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Get/Set the significance value (see Bio::SeqFeature::SimilarityPair) Returns : significance value (scientific notation string) Args : significance value (sci notation string) =cut sub significance { return shift->get_field('evalue'); } =head2 score Title : score Usage : my $score = $hsp->score(); Function: Returns the score for this HSP or undef Returns : numeric Args : [optional] numeric to set value =cut sub score { return shift->get_field('score'); } =head2 bits Title : bits Usage : my $bits = $hsp->bits(); Function: Returns the bit value for this HSP or undef Returns : numeric Args : none =cut sub bits { return shift->get_field('bits'); } # override =head2 strand Title : strand Usage : $hsp->strand('query') Function: Retrieves the strand for the HSP component requested Returns : +1 or -1 (0 if unknown) Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject 'query' to retrieve the query strand (default) 'list' or 'array' to retrieve both query and hit together =cut sub strand { my $self = shift; my $val = shift; $val = 'query' unless defined $val; $val =~ s/^\s+//; if ($val =~ /^q/i) { return $self->query->strand(@_); } elsif ($val =~ /^hi|^s/i) { return $self->hit->strand(@_); } elsif ($val =~ /^list|array/i) { return ($self->query->strand(@_), $self->hit->strand(@_) ); } else { $self->warn("unrecognized component '$val' requested\n"); } return 0; } =head2 start Title : start Usage : $hsp->start('query') Function: Retrieves the start for the HSP component requested Returns : integer, or list of two integers (query start and subject start) in list context Args : 'hit' or 'subject' or 'sbjct' to retrieve the start of the subject 'query' to retrieve the query start (default) =cut sub start { my $self = shift; my $val = shift; $val = (wantarray ? 'list' : 'query') unless defined $val; $val =~ s/^\s+//; if ($val =~ /^q/i) { return $self->query->start(@_); } elsif ($val =~ /^(hi|s)/i) { return $self->hit->start(@_); } elsif ($val =~ /^list|array/i) { return ($self->query->start(@_), $self->hit->start(@_) ); } else { $self->warn("unrecognized component '$val' requested\n"); } return 0; } =head2 end Title : end Usage : $hsp->end('query') Function: Retrieves the end for the HSP component requested Returns : integer, or list of two integers (query end and subject end) in list context Args : 'hit' or 'subject' or 'sbjct' to retrieve the end of the subject 'query' to retrieve the query end (default) =cut sub end { my $self = shift; my $val = shift; $val = (wantarray ? 'list' : 'query') unless defined $val; $val =~ s/^\s+//; if ($val =~ /^q/i) { return $self->query->end(@_); } elsif ($val =~ /^(hi|s)/i) { return $self->hit->end(@_); } elsif ($val =~ /^list|array/i) { return ($self->query->end(@_), $self->hit->end(@_) ); } else { $self->warn("unrecognized end component '$val' requested\n"); } return 0; } =head2 seq Usage : $hsp->seq( [seq_type] ); Purpose : Get the query or sbjct sequence as a Bio::Seq.pm object. Example : $seqObj = $hsp->seq('query'); Returns : Object reference for a Bio::LocatableSeq object. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query'). : ('sbjct' is synonymous with 'hit') : default is 'query' =cut sub seq { my ($self, $seqType) = @_; $seqType ||= 'query'; $seqType = 'hit' if $seqType eq 'sbjct'; if ($seqType =~ /^(m|ho)/i ) { $self->throw("cannot call seq on the homology match string, it isn't really a sequence, use get_aln to convert the HSP to a Bio::AlignIO and generate a consensus from that."); } my $str = $self->seq_str($seqType) || return; require Bio::LocatableSeq; my $id = ($seqType =~ /^q/i) ? $self->query->seq_id : $self->hit->seq_id; return Bio::LocatableSeq->new( -ID => $id, -SEQ => $str, -START => $self->start($seqType), -END => $self->end($seqType), -STRAND => $self->strand($seqType), -FORCE_NSE => $id ? 0 : 1, -DESC => "$seqType sequence " ); } =head2 seq_str Usage : $hsp->seq_str( seq_type ); Purpose : Get the full query, sbjct, or 'match' sequence as a string. : The 'match' sequence is the string of symbols in between the : query and sbjct sequences. Example : $str = $hsp->seq_str('query'); Returns : String Argument : seq_Type = 'query' or 'hit' or 'sbjct' or 'match' : ('sbjct' is synonymous with 'hit') : default is 'query' Throws : Exception if the argument does not match an accepted seq_type. Comments : See Also : L, L, B<_set_match_seq()> =cut sub seq_str { my $self = shift; my $type = shift || 'query'; if ($type =~ /^q/i) { return $self->query_string(@_); } elsif ($type =~ /^(s)|(hi)/i) { return $self->hit_string(@_); } elsif ($type =~ /^(ho)|(ma)/i) { return $self->homology_string(@_); } else { $self->warn("unknown sequence type $type"); } return ''; } =head2 rank Usage : $hsp->rank( [string] ); Purpose : Get the rank of the HSP within a given Blast hit. Example : $rank = $hsp->rank; Returns : Integer (1..n) corresponding to the order in which the HSP appears in the BLAST report. =cut sub rank { return shift->get_field('rank'); } =head2 matches Usage : $hsp->matches(-seq => 'hit'|'query', -start => $start, -stop => $stop); Purpose : Get the total number of identical and conservative matches : in the query or sbjct sequence for the given HSP. Optionally can : report data within a defined interval along the seq. Example : ($id,$cons) = $hsp_object->matches(-seq => 'hit'); : ($id,$cons) = $hsp_object->matches(-seq => 'query', -start => 300, -stop => 400); Returns : 2-element array of integers Argument : (1) seq_type = 'query' or 'hit' or 'sbjct' (default = query) : ('sbjct' is synonymous with 'hit') : (2) start = Starting coordinate (optional) : (3) stop = Ending coordinate (optional) =cut sub matches { my ($self, @args) = @_; my($seqType, $beg, $end) = $self->_rearrange([qw(SEQ START STOP)], @args); $seqType ||= 'query'; $seqType = 'hit' if $seqType eq 'sbjct'; my @data; if ((!defined $beg && !defined $end) || ! $self->seq_str('match')) { push @data, ($self->num_identical, $self->num_conserved); } else { $beg ||= 0; $end ||= 0; my ($start, $stop) = $self->range($seqType); if ($beg == 0) { $beg = $start; $end = $beg+$end; } elsif ($end == 0) { $end = $stop; $beg = $end-$beg; } if ($end >= $stop) { $end = $stop; } else { $end += 1; } if ($beg < $start) { $beg = $start; } my $seq = substr($self->seq_str('homology'), $beg-$start, ($end-$beg)); if (!CORE::length $seq) { $self->throw("Undefined sub-sequence ($beg,$end). Valid range = $start - $stop"); } ## Get data for a substring. $seq =~ s/ //g; # remove space (no info). my $len_cons = CORE::length $seq; $seq =~ s/\+//g; # remove '+' characters (conservative substitutions) my $len_id = CORE::length $seq; push @data, ($len_id, $len_cons); } return @data; } =head2 n Usage : $hsp_obj->n() Purpose : Get the N value (num HSPs on which P/Expect is based). Returns : Integer or null string if not defined. Argument : n/a Throws : n/a Comments : The 'N' value is listed in parenthesis with P/Expect value: : e.g., P(3) = 1.2e-30 ---> (N = 3). : Not defined in NCBI Blast2 with gaps. : This typically is equal to the number of HSPs but not always. =cut sub n { return shift->get_field('num_hsps'); } =head2 range Usage : $hsp->range( [seq_type] ); Purpose : Gets the (start, end) coordinates for the query or sbjct sequence : in the HSP alignment. Example : ($query_beg, $query_end) = $hsp->range('query'); : ($hit_beg, $hit_end) = $hsp->range('hit'); Returns : Two-element array of integers Argument : seq_type = string, 'query' or 'hit' or 'sbjct' (default = 'query') : ('sbjct' is synonymous with 'hit') Throws : n/a Comments : This is a convenience method for constructions such as ($hsp->query->start, $hsp->query->end) =cut sub range { my ($self, $seqType) = @_; $seqType ||= 'query'; my ($start, $end); if ($seqType eq 'query') { $start = $self->query->start; $end = $self->query->end; } else { $start = $self->hit->start; $end = $self->hit->end; } return ($start, $end); } #*** would want cigar stuff from GenericHSP - move to HSPI? 1; BioPerl-1.007002/Bio/Search/HSP/WABAHSP.pm000444000766000024 1025013155576320 17524 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::HSP::WABAHSP # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::HSP::WABAHSP - HSP object suitable for describing WABA alignments =head1 SYNOPSIS # use this object as you would a GenericHSP # a few other methods have been added including state =head1 DESCRIPTION This object implements a few of the extra methods such as hmmstate_string which returns the HMM state representation for the WABA alignment. We also must implement a method to calculate homology_string since it is not returned by the algorithm in the machine readable format. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::HSP::WABAHSP; use strict; use Bio::Root::RootI; use base qw(Bio::Search::HSP::GenericHSP); =head2 new Title : new Usage : my $obj = Bio::Search::HSP::WABAHSP->new(); Function: Builds a new Bio::Search::HSP::WABAHSP object Returns : Bio::Search::HSP::WABAHSP Args : -hmmstate_seq => the string representing the state output from WABA =cut sub new { my($class,@args) = @_; # gotta do some preprocessing before we send the arguments to the superclass my ($len,$qs,$hs) = Bio::Root::RootI->_rearrange([qw(HSP_LENGTH QUERY_SEQ HIT_SEQ)],@args); if( $len != length($qs) ) { Bio::Root::RootI->warn("HSP_LENGTH must equal length of query_seq string, using value from QUERY_SEQ\n"); $len = length($qs); } my( $homol_seq,$gapct,$identical) = ('',0,0); for(my $i=0;$i<$len;$i++) { my $q = substr($qs,$i,1); my $h = substr($hs,$i,1); if( $q eq '-' || $h eq '-' ) { $homol_seq .= ' '; $gapct ++; } elsif( $q eq $h ) { $homol_seq .= '|'; $identical++; } else { $homol_seq .= ' '; } } my $self = $class->SUPER::new('-conserved' => $identical, '-identical' => $identical, '-gaps' => $gapct, '-homology_seq' => $homol_seq, @args); my ($hmmst) = $self->_rearrange([qw(HMMSTATE_SEQ)],@args); defined $hmmst && $self->hmmstate_string($hmmst); $self->add_tag_value('Target' , join(" ","Sequence:".$self->hit->seq_id, $self->hit->start, $self->hit->end)); return $self; } =head2 hmmstate_string Title : hmmstate_string Usage : my $hmmseq = $wabahsp->hmmstate_string(); Function: Get/Set the WABA HMM stateseq Returns : string Args : [optional] string =cut sub hmmstate_string{ my ($self,$val) = @_; if( defined $val ) { $self->{'_hmmstate_string'} = $val; } return $self->{'_hmmstate_string'}; } =head2 homology_string Title : homolgy_string Usage : my $homology_str = $hsp->homology_string(); Function: Homology string must be calculated for a WABA HSP so we can do so here and cache the result so it is only done once Returns : string Args : none =cut sub homology_string{ my ($self) = @_; return ''; } 1; BioPerl-1.007002/Bio/Search/Hit000755000766000024 013155576320 16020 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Search/Hit/BlastHit.pm000444000766000024 1177213155576320 20255 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Hit::GenericHit # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Hit::BlastHit - Blast-specific subclass of Bio::Search::Hit::GenericHit =head1 SYNOPSIS use Bio::Search::Hit::BlastHit; my $hit = Bio::Search::Hit::BlastHit->new(-algorithm => 'blastp'); # See Bio::Search::Hit::GenericHit for information about working with Hits. # TODO: Describe how to configure a SearchIO stream so that it generates # GenericHit objects. =head1 DESCRIPTION This object is a subclass of Bio::Search::Hit::GenericHit and provides some operations that facilitate working with BLAST and PSI-BLAST Hits. For general information about working with Hits, see Bio::Search::Hit::GenericHit. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich and Steve Chervitz Email jason@bioperl.org Email sac@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Hit::BlastHit; use strict; use Bio::Search::SearchUtils; use base qw(Bio::Search::Hit::GenericHit); =head2 new Title : new Usage : my $obj = Bio::Search::Hit::GenericHit->new(); Function: Builds a new Bio::Search::Hit::GenericHit object Returns : Bio::Search::Hit::GenericHit Args : See Bio::Search::Hit::GenericHit() for other args. Here are the BLAST-specific args that can be used when creating BlastHit objects: -iteration => integer for the PSI-Blast iteration number -found_again => boolean, true if hit appears in a "previously found" section of a PSI-Blast report. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($iter,$found) = $self->_rearrange([qw(ITERATION FOUND_AGAIN )], @args); defined $iter && $self->iteration($iter); defined $found && $self->found_again($found); return $self; } =head2 iteration Usage : $hit->iteration( $iteration_num ); Purpose : Gets the iteration number in which the Hit was found. Example : $iteration_num = $sbjct->iteration(); Returns : Integer greater than or equal to 1 Non-PSI-BLAST reports will report iteration as 1, but this number is only meaningful for PSI-BLAST reports. Argument : iteration_num (optional, used when setting only) Throws : none See Also : L =cut sub iteration{ my ($self,$value) = @_; if( defined $value) { $self->{'_psiblast_iteration'} = $value; } return $self->{'_psiblast_iteration'}; } =head2 found_again Title : found_again Usage : $hit->found_again; $hit->found_again(1); Purpose : Gets a boolean indicator whether or not the hit has been found in a previous iteration. This is only applicable to PSI-BLAST reports. This method indicates if the hit was reported in the "Sequences used in model and found again" section of the PSI-BLAST report or if it was reported in the "Sequences not found previously or not previously below threshold" section of the PSI-BLAST report. Only for hits in iteration > 1. Example : if( $hit->found_again()) { ... }; Returns : Boolean, true (1) if the hit has been found in a previous PSI-BLAST iteration. Returns false (0 or undef) for hits that have not occurred in a previous PSI-BLAST iteration. Argument : Boolean (1 or 0). Only used for setting. Throws : none See Also : L =cut sub found_again { my $self = shift; return $self->{'_found_again'} = shift if @_; return $self->{'_found_again'}; } sub expect { shift->significance(@_) } 1; BioPerl-1.007002/Bio/Search/Hit/BlastPullHit.pm000444000766000024 2167213155576320 21112 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Hit::BlastPullHit # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Hit::BlastPullHit - A parser and hit object for BLASTN hits =head1 SYNOPSIS # generally we use Bio::SearchIO to build these objects use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'blast_pull', -file => 'result.blast'); while (my $result = $in->next_result) { while (my $hit = $result->next_hit) { print $hit->name, "\n"; print $hit->score, "\n"; print $hit->significance, "\n"; while (my $hsp = $hit->next_hsp) { # process HSPI objects } } } =head1 DESCRIPTION This object implements a parser for BLASTN hit output. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Hit::BlastPullHit; use strict; use Bio::Search::HSP::BlastPullHSP; use base qw(Bio::Root::Root Bio::Search::Hit::PullHitI); =head2 new Title : new Usage : my $obj = Bio::Search::Hit::BlastNHit->new(); Function: Builds a new Bio::Search::Hit::BlastNHit object. Returns : Bio::Search::Hit::BlastNHit Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent) -parent => Bio::PullParserI object (required if no -chunk) -hit_data => array ref with [name description score significance] where the array ref provided to -chunk contains an IO object for a filehandle to something representing the raw data of the hit, and $start and $end define the tell() position within the filehandle that the hit data starts and ends (optional; defaults to start and end of the entire thing described by the filehandle) =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->_setup(@args); my $fields = $self->_fields; foreach my $field (qw( header start_end )) { $fields->{$field} = undef; } my $hit_data = $self->_raw_hit_data; if ($hit_data && ref($hit_data) eq 'ARRAY') { foreach my $field (qw(name description score significance)) { $fields->{$field} = shift(@{$hit_data}); } } $self->_dependencies( { ( name => 'header', length => 'header', description => 'header', accession => 'header', next_hsp => 'header', query_start => 'start_end', query_end => 'start_end', hit_start => 'start_end', hit_end => 'start_end' ) } ); return $self; } # # PullParserI discovery methods so we can answer all HitI questions # sub _discover_header { my $self = shift; $self->_chunk_seek(0); my $header = $self->_get_chunk_by_end("\n Score = "); unless ($header) { # no alignment or other data; all information was in the hit table of # the result $self->_calculate_accession_from_name; $self->_fields->{header} = 1; return; } $self->{_after_header} = $self->_chunk_tell; ($self->_fields->{name}, $self->_fields->{description}, $self->_fields->{length}) = $header =~ /^(\S+)\s+(\S.+?)?\s+Length\s*=\s*(\d+)/sm; if ($self->_fields->{description}) { $self->_fields->{description} =~ s/\n//g; } else { $self->_fields->{description} = ''; } $self->_calculate_accession_from_name; $self->_fields->{header} = 1; } sub _calculate_accession_from_name { my $self = shift; my $name = $self->get_field('name'); if ($name =~ /.+?\|.+?\|.+?\|(\w+)/) { $self->_fields->{accession} = $1; } elsif ($self->_fields->{name} =~ /.+?\|(\w+)?\./) { # old form? $self->_fields->{accession} = $1; } else { $self->_fields->{accession} = $name; } } sub _discover_start_end { my $self = shift; my ($q_start, $q_end, $h_start, $h_end); foreach my $hsp ($self->hsps) { my ($this_q_start, $this_h_start) = $hsp->start; my ($this_q_end, $this_h_end) = $hsp->end; if (! defined $q_start || $this_q_start < $q_start) { $q_start = $this_q_start; } if (! defined $h_start || $this_h_start < $h_start) { $h_start = $this_h_start; } if (! defined $q_end || $this_q_end > $q_end) { $q_end = $this_q_end; } if (! defined $h_end || $this_h_end > $h_end) { $h_end = $this_h_end; } } $self->_fields->{query_start} = $q_start; $self->_fields->{query_end} = $q_end; $self->_fields->{hit_start} = $h_start; $self->_fields->{hit_end} = $h_end; } sub _discover_next_hsp { my $self = shift; my $pos = $self->{_end_of_previous_hsp} || $self->{_after_header}; return unless $pos; $self->_chunk_seek($pos); my ($start, $end) = $self->_find_chunk_by_end("\n Score = "); if ((defined $end && ($end + $self->_chunk_true_start) > $self->_chunk_true_end) || ! $end) { $start = $self->{_end_of_previous_hsp} || $self->{_after_header}; $end = $self->_chunk_true_end; } else { $end += $self->_chunk_true_start; } $start += $self->_chunk_true_start; return if $start >= $self->_chunk_true_end; $self->{_end_of_previous_hsp} = $end - $self->_chunk_true_start; #*** needs to inherit piped_behaviour, and we need to deal with _sequential # ourselves $self->_fields->{next_hsp} = Bio::Search::HSP::BlastPullHSP->new(-parent => $self, -chunk => [$self->chunk, $start, $end]); } sub _discover_num_hsps { my $self = shift; $self->_fields->{num_hsps} = $self->hsps; } =head2 next_hsp Title : next_hsp Usage : while( $hsp = $obj->next_hsp()) { ... } Function : Returns the next available High Scoring Pair Example : Returns : L object or null if finished Args : none =cut sub next_hsp { my $self = shift; my $hsp = $self->get_field('next_hsp'); undef $self->_fields->{next_hsp}; return $hsp; } =head2 hsps Usage : $hit_object->hsps(); Purpose : Get a list containing all HSP objects. Example : @hsps = $hit_object->hsps(); Returns : list of L objects. Argument : none =cut sub hsps { my $self = shift; my $old = $self->{_end_of_previous_hsp}; $self->rewind; my @hsps; while (defined(my $hsp = $self->next_hsp)) { push(@hsps, $hsp); } $self->{_end_of_previous_hsp} = $old; return @hsps; } =head2 hsp Usage : $hit_object->hsp( [string] ); Purpose : Get a single HSPI object for the present HitI object. Example : $hspObj = $hit_object->hsp; # same as 'best' : $hspObj = $hit_object->hsp('best'); : $hspObj = $hit_object->hsp('worst'); Returns : Object reference for a L object. Argument : String (or no argument). : No argument (default) = highest scoring HSP (same as 'best'). : 'best' = highest scoring HSP. : 'worst' = lowest scoring HSP. Throws : Exception if an unrecognized argument is used. See Also : L, L() =cut sub hsp { my ($self, $type) = @_; $type ||= 'best'; $self->throw_not_implemented; } =head2 rewind Title : rewind Usage : $result->rewind; Function: Allow one to reset the HSP iterator to the beginning, so that next_hsp() will subsequently return the first hsp and so on. Returns : n/a Args : none =cut sub rewind { my $self = shift; delete $self->{_end_of_previous_hsp}; } # have p() a synonym of significance() sub p { return shift->significance; } 1; BioPerl-1.007002/Bio/Search/Hit/Fasta.pm000444000766000024 621413155576320 17554 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Hit::Fasta # # Please direct questions and support issues to # # Cared for by Aaron Mackey # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Hit::Fasta - Hit object specific for Fasta-generated hits =head1 SYNOPSIS # You wouldn't normally create these manually; # instead they would be produced by Bio::SearchIO::fasta use Bio::Search::Hit::Fasta; my $hit = Bio::Search::Hit::Fasta->new(id=>'LBL_6321', desc=>'lipoprotein', e_val=>0.01); =head1 DESCRIPTION L objects are data structures that contain information about specific hits obtained during a library search. Some information will be algorithm-specific, but others will be generally defined, such as the ability to obtain alignment objects corresponding to each hit. =head1 SEE ALSO L, L, L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Aaron Mackey Email amackey-at-virginia.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::Search::Hit::Fasta; use vars qw($AUTOLOAD); use strict; use base qw(Bio::Search::Hit::HitI); my @AUTOLOAD_OK = qw(_ID _DESC _SIZE _INITN _INIT1 _OPT _ZSC _E_VAL); my %AUTOLOAD_OK = (); @AUTOLOAD_OK{@AUTOLOAD_OK} = (1) x @AUTOLOAD_OK; =head2 _initialize Function: where the heavy stuff will happen when new is called =cut sub _initialize { my($self, %args) = @_; my $make = $self->SUPER::_initialize(%args); while (my ($key, $val) = each %args) { $key = '_' . uc($key); $self->$key($val); } return $make; # success - we hope! } =head2 AUTOLOAD Function: Provide getter/setters for ID,DESC,SIZE,INITN,INIT1,OPT,ZSC,E_VAL =cut sub AUTOLOAD { my ($self, $val) = @_; $AUTOLOAD =~ s/.*:://; if ( $AUTOLOAD_OK{$AUTOLOAD} ) { $self->{$AUTOLOAD} = $val if defined $val; return $self->{$AUTOLOAD}; } else { $self->throw("Unallowed accessor: $AUTOLOAD !"); } } 1; BioPerl-1.007002/Bio/Search/Hit/GenericHit.pm000444000766000024 16573313155576320 20613 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Hit::GenericHit # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Hit::GenericHit - A generic implementation of the Bio::Search::Hit::HitI interface =head1 SYNOPSIS use Bio::Search::Hit::GenericHit; my $hit = Bio::Search::Hit::GenericHit->new(-algorithm => 'blastp'); # typically one gets HitI objects from a SearchIO stream via a ResultI use Bio::SearchIO; my $parser = Bio::SearchIO->new(-format => 'blast', -file => 'result.bls'); my $result = $parser->next_result; my $hit = $result->next_hit; # TODO: Describe how to configure a SearchIO stream so that it generates # GenericHit objects. =head1 DESCRIPTION This object handles the hit data from a Database Sequence Search such as FASTA or BLAST. Unless you're writing a parser, you won't ever need to create a GenericHit or any other HitI-implementing object. If you use the SearchIO system, HitI objects are created automatically from a SearchIO stream which returns Bio::Search::Hit::HitI objects. For documentation on what you can do with GenericHit (and other HitI objects), please see the API documentation in L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich and Steve Chervitz Email jason-at-bioperl-dot-org Email sac-at-bioperl-dot-org =head1 CONTRIBUTORS Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Hit::GenericHit; use strict; use Bio::Search::SearchUtils; use base qw(Bio::Root::Root Bio::Search::Hit::HitI); =head2 new Title : new Usage : my $obj = Bio::Search::Hit::GenericHit->new(); Function: Builds a new Bio::Search::Hit::GenericHit object Returns : Bio::Search::Hit::GenericHit Args : -name => Name of Hit (required) -description => Description (optional) -accession => Accession number (optional) -ncbi_gi => NCBI GI UID (optional) -length => Length of the Hit (optional) -score => Raw Score for the Hit (optional) -bits => Bit Score for the Hit (optional) -significance => Significance value for the Hit (optional) -algorithm => Algorithm used (BLASTP, FASTX, etc...) -hsps => Array ref of HSPs for this Hit. -found_again => boolean, true if hit appears in a "previously found" section of a PSI-Blast report. -hsp_factory => Bio::Factory::ObjectFactoryI able to create HSPI objects. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($hsps, $name,$query_len,$desc, $acc, $locus, $length, $score,$algo,$signif,$bits, $p, $rank, $hsp_factory, $gi, $iter, $found) = $self->_rearrange([qw(HSPS NAME QUERY_LEN DESCRIPTION ACCESSION LOCUS LENGTH SCORE ALGORITHM SIGNIFICANCE BITS P RANK HSP_FACTORY NCBI_GI ITERATION FOUND_AGAIN)], @args); defined $query_len && $self->query_length($query_len); if( ! defined $name ) { $self->throw("Must have defined a valid name for Hit"); } else { $self->name($name); } defined $acc && $self->accession($acc); defined $locus && $self->locus($locus); defined $desc && $self->description($desc); defined $length && $self->length($length); defined $algo && $self->algorithm($algo); defined $signif && $self->significance($signif); defined $score && $self->raw_score($score); defined $bits && $self->bits($bits); defined $rank && $self->rank($rank); defined $hsp_factory && $self->hsp_factory($hsp_factory); defined $gi && $self->ncbi_gi($gi); defined $iter && $self->iteration($iter); defined $found && $self->found_again($found); # p() has a weird interface, so this is a hack workaround if (defined $p) { $self->{_p} = $p; } $self->{'_iterator'} = 0; if( defined $hsps ) { if( ref($hsps) !~ /array/i ) { $self->warn("Did not specify a valid array ref for the param HSPS ($hsps)"); } else { my $hspcount=0; while( @{$hsps} ) { $hspcount++; $self->add_hsp(shift @{$hsps} ); } $self->{'_hsps'} = undef if $hspcount == 0; } } else { $self->{'_hsps'} = undef; } return $self; } =head2 add_hsp Title : add_hsp Usage : $hit->add_hsp($hsp) Function: Add a HSP to the collection of HSPs for a Hit Returns : number of HSPs in the Hit Args : Bio::Search::HSP::HSPI object, OR hash ref containing data suitable for creating a HSPI object (&hsp_factory must be set to get it back) =cut sub add_hsp { my ($self,$hsp) = @_; if (!defined $hsp || (ref($hsp) ne 'HASH' && !$hsp->isa('Bio::Search::HSP::HSPI'))) { $self->throw("Must provide a valid Bio::Search::HSP::HSPI object or hash ref to object: $self method: add_hsp value: $hsp"); return; } push @{$self->{'_hsps'}}, $hsp; if (ref($hsp) eq 'HASH') { $self->{_hashes}->{$#{$self->{'_hsps'}}} = 1; } return scalar @{$self->{'_hsps'}}; } =head2 hsp_factory Title : hsp_factory Usage : $hit->hsp_factory($hsp_factory) Function: Get/set the factory used to build HSPI objects if necessary. Returns : Bio::Factory::ObjectFactoryI Args : Bio::Factory::ObjectFactoryI =cut sub hsp_factory { my $self = shift; if (@_) { $self->{_hsp_factory} = shift } return $self->{_hsp_factory} || return; } =head2 Bio::Search::Hit::HitI methods Implementation of Bio::Search::Hit::HitI methods =head2 name Title : name Usage : $hit_name = $hit->name(); Function: returns the name of the Hit sequence Returns : a scalar string Args : [optional] scalar string to set the name =cut sub name { my ($self,$value) = @_; my $previous = $self->{'_name'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_name'} = $value; } return $previous; } =head2 accession Title : accession Usage : $acc = $hit->accession(); Function: Retrieve the accession (if available) for the hit Returns : a scalar string (empty string if not set) Args : none =cut sub accession { my ($self,$value) = @_; my $previous = $self->{'_accession'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_accession'} = $value; } return $previous; } =head2 description Title : description Usage : $desc = $hit->description(); Function: Retrieve the description for the hit Returns : a scalar string Args : [optional] scalar string to set the description =cut sub description { my ($self,$value) = @_; my $previous = $self->{'_description'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_description'} = $value; } return $previous; } =head2 length Title : length Usage : my $len = $hit->length Function: Returns the length of the hit Returns : integer Args : [optional] integer to set the length =cut sub length { my ($self,$value) = @_; my $previous = $self->{'_length'}; if( defined $value || ! defined $previous ) { $value = $previous = 0 unless defined $value; $self->{'_length'} = $value; } return $previous; } =head2 algorithm Title : algorithm Usage : $alg = $hit->algorithm(); Function: Gets the algorithm specification that was used to obtain the hit For BLAST, the algorithm denotes what type of sequence was aligned against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated dna-prt, TBLASTN prt-translated dna, TBLASTX translated dna-translated dna). Returns : a scalar string Args : [optional] scalar string to set the algorithm =cut sub algorithm { my ($self,$value) = @_; my $previous = $self->{'_algorithm'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_algorithm'} = $value; } return $previous; } =head2 raw_score Title : raw_score Usage : $score = $hit->raw_score(); Function: Gets the "raw score" generated by the algorithm. What this score is exactly will vary from algorithm to algorithm, returning undef if unavailable. Returns : a scalar value Args : [optional] scalar value to set the raw score =cut sub raw_score { my ($self,$value) = @_; my $previous = $self->{'_score'}; if( defined $value ) { $self->{'_score'} = $value; } elsif ( ! defined $previous ) { # Set the bits of the Hit to that of the top HSP. unless( defined $self->{'_hsps'}->[0] ) { $self->warn("No HSPs for this minimal Hit (".$self->name.")\n". "If using NCBI BLAST, check bits() instead"); return; } # use 'score' if available if ( defined( ($self->hsps)[0]->score ) ) { $previous = $self->{'_score'} = ($self->hsps)[0]->score; } # otherwise use 'bits' elsif ( defined( ($self->hsps)[0]->bits ) ) { $previous = $self->{'_score'} = ($self->hsps)[0]->bits; } } return $previous; } =head2 score Equivalent to L =cut sub score { shift->raw_score(@_); } =head2 significance Title : significance Usage : $significance = $hit->significance(); Function: Used to obtain the E or P value of a hit, i.e. the probability that this particular hit was obtained purely by random chance. If information is not available (nor calculatable from other information sources), return undef. Returns : a scalar value or undef if unavailable Args : [optional] scalar value to set the significance =cut sub significance { my ($self,$value) = @_; my $previous = $self->{'_significance'}; if( defined $value ) { $self->{'_significance'} = $value; } elsif ( ! defined $previous ) { unless( defined $self->{'_hsps'}->[0] ) { $self->warn("No HSPs for this Hit (".$self->name.")"); return; } # Set the significance of the Hit to that of the top HSP. $previous = $self->{'_significance'} = ($self->hsps)[0]->significance; } return $previous; } =head2 bits Usage : $hit_object->bits(); Purpose : Gets the bit score of the best HSP for the current hit. Example : $bits = $hit_object->bits(); Returns : Integer or undef if bit score is not set Argument : n/a Comments : For BLAST1, the non-bit score is listed in the summary line. See Also : L =cut sub bits { my ($self,$value) = @_; my $previous = $self->{'_bits'}; if( defined $value ) { $self->{'_bits'} = $value; } elsif ( ! defined $previous ) { # Set the bits of the Hit to that of the top HSP. unless( defined $self->{'_hsps'}->[0] ) { $self->warn("No HSPs for this minimal Hit (".$self->name.")\n". "If using WU-BLAST, check raw_score() instead"); return; } $previous = $self->{'_bits'} = ($self->hsps)[0]->bits; } return $previous; } =head2 next_hsp Title : next_hsp Usage : while( $hsp = $obj->next_hsp()) { ... } Function : Returns the next available High Scoring Pair Example : Returns : Bio::Search::HSP::HSPI object or null if finished Args : none =cut sub next_hsp { my $self = shift; $self->{'_iterator'} = 0 unless defined $self->{'_iterator'}; return unless defined($self->{'_hsps'}) && $self->{'_iterator'} <= scalar @{$self->{'_hsps'}}; my $iterator = $self->{'_iterator'}++; my $hsp = $self->{'_hsps'}->[$iterator] || return; if (ref($hsp) eq 'HASH') { my $factory = $self->hsp_factory || $self->throw("Tried to get a HSP, but it was a hash ref and we have no hsp factory"); $hsp = $factory->create_object(%{$hsp}); $self->{'_hsps'}->[$iterator] = $hsp; delete $self->{_hashes}->{$iterator}; } return $hsp; } =head2 hsps Usage : $hit_object->hsps(); Purpose : Get a list containing all HSP objects. : Get the numbers of HSPs for the current hit. Example : @hsps = $hit_object->hsps(); : $num = $hit_object->hsps(); # alternatively, use num_hsps() Returns : Array context : list of Bio::Search::HSP::BlastHSP.pm objects. : Scalar context: integer (number of HSPs). : (Equivalent to num_hsps()). Argument : n/a. Relies on wantarray Throws : Exception if the HSPs have not been collected. See Also : L, L =cut sub hsps { my $self = shift; foreach my $i (keys %{$self->{_hashes} || {}}) { my $factory = $self->hsp_factory || $self->throw("Tried to get a HSP, but it was a hash ref and we have no hsp factory"); $self->{'_hsps'}->[$i] = $factory->create_object(%{$self->{'_hsps'}->[$i]}); delete $self->{_hashes}->{$i}; } return wantarray() ? @{$self->{'_hsps'} || []} : scalar(@{$self->{'_hsps'} || []}); } =head2 num_hsps Usage : $hit_object->num_hsps(); Purpose : Get the number of HSPs for the present hit. Example : $nhsps = $hit_object->num_hsps(); Returns : Integer or '-' if HSPs have not been callected Argument : n/a See Also : L =cut sub num_hsps { my $self = shift; unless ($self->{'_hsps'}) { return '-'; } return scalar(@{$self->{'_hsps'}}); } =head2 rewind Title : rewind Usage : $hit->rewind; Function: Allow one to reset the HSP iterator to the beginning Since this is an in-memory implementation Returns : none Args : none =cut sub rewind{ my ($self) = @_; $self->{'_iterator'} = 0; } =head2 ambiguous_aln Usage : $ambig_code = $hit_object->ambiguous_aln(); Purpose : Sets/Gets ambiguity code data member. Example : (see usage) Returns : String = 'q', 's', 'qs', '-' : 'q' = query sequence contains overlapping sub-sequences : while sbjct does not. : 's' = sbjct sequence contains overlapping sub-sequences : while query does not. : 'qs' = query and sbjct sequence contains overlapping sub-sequences : relative to each other. : '-' = query and sbjct sequence do not contains multiple domains : relative to each other OR both contain the same distribution : of similar domains. Argument : n/a Throws : n/a Comment : Note: "sbjct" is synonymous with "hit" =cut sub ambiguous_aln { my $self = shift; if(@_) { $self->{'_ambiguous_aln'} = shift; } $self->{'_ambiguous_aln'} || '-'; } =head2 overlap See documentation in L =cut sub overlap { my $self = shift; if(@_) { $self->{'_overlap'} = shift; } defined $self->{'_overlap'} ? $self->{'_overlap'} : 0; } =head2 n Usage : $hit_object->n(); Purpose : Gets the N number for the current hit. : This is the number of HSPs in the set which was ascribed : the lowest P-value (listed on the description line). : This number is not the same as the total number of HSPs. : To get the total number of HSPs, use num_hsps(). Example : $n = $hit_object->n(); Returns : Integer Argument : n/a Throws : Exception if HSPs have not been set (BLAST2 reports). Comments : Note that the N parameter is not reported in gapped BLAST2. : Calling n() on such reports will result in a call to num_hsps(). : The num_hsps() method will count the actual number of : HSPs in the alignment listing, which may exceed N in : some cases. See Also : L =cut sub n { my $self = shift; # The check for $self->{'_n'} is a remnant from the 'query' mode days # in which the sbjct object would collect data from the description # line only. my ($n); if(not defined($self->{'_n'})) { if( $self->hsp ) { $n = $self->hsp->n; } } else { $n = $self->{'_n'}; } $n ||= $self->num_hsps; return $n; } =head2 p Usage : $hit_object->p( [format] ); Purpose : Get the P-value for the best HSP of the given BLAST hit. : (Note that P-values are not provided with NCBI Blast2 reports). Example : $p = $sbjct->p; : $p = $sbjct->p('exp'); # get exponent only. : ($num, $exp) = $sbjct->p('parts'); # split sci notation into parts Returns : Float or scientific notation number (the raw P-value, DEFAULT). : Integer if format == 'exp' (the magnitude of the base 10 exponent). : 2-element list (float, int) if format == 'parts' and P-value : is in scientific notation (See Comments). Argument : format: string of 'raw' | 'exp' | 'parts' : 'raw' returns value given in report. Default. (1.2e-34) : 'exp' returns exponent value only (34) : 'parts' returns the decimal and exponent as a : 2-element list (1.2, -34) (See Comments). Throws : Warns if no P-value is defined. Uses expect instead. Comments : Using the 'parts' argument is not recommended since it will not : work as expected if the P-value is not in scientific notation. : That is, floats are not converted into sci notation before : splitting into parts. See Also : L, L, L =cut sub p { # Some duplication of logic for p(), expect() and signif() for the sake of performance. my ($self, $fmt) = @_; my $val = $self->{'_p'}; # $val can be zero. if(!defined $val) { # P-value not defined, must be a NCBI Blast2 report. # Use expect instead. $self->warn( "P-value not defined. Using significance() instead."); $val = $self->significance(); } return $val if not $fmt or $fmt =~ /^raw/i; ## Special formats: exponent-only or as list. return &Bio::Search::SearchUtils::get_exponent($val) if $fmt =~ /^exp/i; return (split (/eE/, $val)) if $fmt =~ /^parts/i; ## Default: return the raw P-value. return $val; } =head2 hsp Usage : $hit_object->hsp( [string] ); Purpose : Get a single HSPI object for the present HitI object. Example : $hspObj = $hit_object->hsp; # same as 'best' : $hspObj = $hit_object->hsp('best'); : $hspObj = $hit_object->hsp('worst'); Returns : Object reference for a Bio::Search::HSP::BlastHSP.pm object. Argument : String (or no argument). : No argument (default) = highest scoring HSP (same as 'best'). : 'best' or 'first' = highest scoring HSP. : 'worst' or 'last' = lowest scoring HSP. Throws : Exception if the HSPs have not been collected. : Exception if an unrecognized argument is used. See Also : L, L() =cut sub hsp { my( $self, $option ) = @_; $option ||= 'best'; if (not ref $self->{'_hsps'}) { $self->throw("Can't get HSPs: data not collected."); } my @hsps = $self->hsps; return $hsps[0] if $option =~ /best|first|1/i; return $hsps[$#hsps] if $option =~ /worst|last/i; $self->throw("Can't get HSP for: $option\n" . "Valid arguments: 'best', 'worst'"); } =head2 logical_length Usage : $hit_object->logical_length( [seq_type] ); : (mostly intended for internal use). Purpose : Get the logical length of the hit sequence. : This is necessary since the number of identical/conserved residues : can be in terms of peptide sequence space, yet the query and/or hit : sequence are in nucleotide space. Example : $len = $hit_object->logical_length(); Returns : Integer Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is synonymous with 'hit') Throws : n/a Comments : : In the case of BLAST flavors: : For TBLASTN reports, the length of the aligned portion of the : nucleotide hit sequence is divided by 3; for BLASTX reports, : the length of the aligned portion of the nucleotide query : sequence is divided by 3. For TBLASTX reports, the length of : both hit and query sequence are converted. : : This is important for functions like frac_aligned_query() : which need to operate in amino acid coordinate space when dealing : with [T]BLAST[NX] type reports. See Also : L, L, L =cut sub logical_length { my $self = shift; my $seqType = shift || 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; my ($length, $logical); my $algo = $self->algorithm; # For the sbjct, return logical sbjct length if( $seqType eq 'sbjct' ) { $length = $self->length; } else { # Otherwise, return logical query length $length = $self->query_length(); } $logical = Bio::Search::SearchUtils::logical_length($algo, $seqType, $length); return int($logical); } =head2 length_aln Usage : $hit_object->length_aln( [seq_type] ); Purpose : Get the total length of the aligned region for query or sbjct seq. : This number will include all HSPs Example : $len = $hit_object->length_aln(); # default = query : $lenAln = $hit_object->length_aln('query'); Returns : Integer Argument : seq_Type = 'query' or 'hit' or 'sbjct' (Default = 'query') ('sbjct' is synonymous with 'hit') Throws : Exception if the argument is not recognized. Comments : This method will report the logical length of the alignment, : meaning that for TBLAST[NX] reports, the length is reported : using amino acid coordinate space (i.e., nucleotides / 3). : : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically.. : If you don't want the tiled data, iterate through each HSP : calling length() on each (use hsps() to get all HSPs). See Also : L, L, L, L, L, L =cut sub length_aln { my( $self, $seqType, $num ) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; # Setter: if( defined $num) { return $self->{'_length_aln_'.$seqType} = $num; } unless ($self->{'_hsps'}) { #return wantarray ? ('-','-') : '-'; Bio::Search::SearchUtils::_warn_about_no_hsps($self); return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; my $data = $self->{'_length_aln_'.$seqType}; ## If we don't have data, figure out what went wrong. if(!$data) { $self->throw("Can't get length aln for sequence type \"$seqType\". " . "Valid types are 'query', 'hit', 'sbjct' ('sbjct' = 'hit')"); } return $data; } =head2 gaps Usage : $hit_object->gaps( [seq_type] ); Purpose : Get the number of gaps in the aligned query, hit, or both sequences. : Data is summed across all HSPs. Example : $qgaps = $hit_object->gaps('query'); : $hgaps = $hit_object->gaps('hit'); : $tgaps = $hit_object->gaps(); # default = total (query + hit) Returns : scalar context: integer : array context without args: two-element list of integers : (queryGaps, hitGaps) : Array context can be forced by providing an argument of 'list' or 'array'. : : CAUTION: Calling this method within printf or sprintf is arrray context. : So this function may not give you what you expect. For example: : printf "Total gaps: %d", $hit->gaps(); : Actually returns a two-element array, so what gets printed : is the number of gaps in the query, not the total : Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total' | 'list' (default = 'total') ('sbjct' is synonymous with 'hit') Throws : n/a Comments : If you need data for each HSP, use hsps() and then interate : through each HSP object. : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically.. : Not relying on wantarray since that will fail in situations : such as printf "%d", $hit->gaps() in which you might expect to : be printing the total gaps, but evaluates to array context. See Also : L =cut sub gaps { my( $self, $seqType, $num ) = @_; $seqType ||= (wantarray ? 'list' : 'total'); $seqType = 'sbjct' if $seqType eq 'hit'; unless ($self->{'_hsps'}) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); return wantarray ? ('-','-') : '-'; #return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; $seqType = lc($seqType); if( defined $num ) { $self->throw("Can't set gaps for seqType '$seqType'. Must be 'query' or 'hit'\n") unless ($seqType eq 'sbjct' or $seqType eq 'query'); return $self->{'_gaps_'.$seqType} = $num; } elsif($seqType =~ /list|array/i) { return ($self->{'_gaps_query'}, $self->{'_gaps_sbjct'}); } elsif($seqType eq 'total') { return ($self->{'_gaps_query'} + $self->{'_gaps_sbjct'}) || 0; } else { return $self->{'_gaps_'.$seqType} || 0; } } =head2 matches See documentation in L =cut sub matches { my( $self, $arg1, $arg2) = @_; my(@data,$data); unless ($self->{'_hsps'}) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); return wantarray ? ('-','-') : '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; unless( $arg1 ) { @data = ($self->{'_totalIdentical'}, $self->{'_totalConserved'}); return @data; } else { if( defined $arg2 ) { $self->{'_totalIdentical'} = $arg1; $self->{'_totalConserved'} = $arg2; return ( $arg1, $arg2 ); } elsif($arg1 =~ /^id/i) { $data = $self->{'_totalIdentical'}; } else { $data = $self->{'_totalConserved'}; } #print STDERR "\nmatches(): id=$self->{'_totalIdentical'}, cons=$self->{'_totalConserved'}\n\n"; return $data; } ## If we make it to here, it is likely the case that ## the parser constructed a minimal hit object from the summary line only. ## It either delibrately skipped parsing the alignment section, ## or was not able to because it was absent (due to blast executable parameter ## setting such as -b 0 (B=0 for WU-BLAST) ) #$self->throw("Can't get identical or conserved data: no data."); } =head2 start Usage : $sbjct->start( [seq_type] ); Purpose : Gets the start coordinate for the query, sbjct, or both sequences : in the BlastHit object. If there is more than one HSP, the lowest start : value of all HSPs is returned. Example : $qbeg = $sbjct->start('query'); : $sbeg = $sbjct->start('hit'); : ($qbeg, $sbeg) = $sbjct->start(); Returns : scalar context: integer : array context without args: list of two integers (queryStart, sbjctStart) : Array context can be "induced" by providing an argument of 'list' or 'array'. Argument : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is synonymous with 'hit') Throws : n/a See Also : L, L, L, L =cut sub start { my ($self, $seqType, $num) = @_; unless ($self->{'_hsps'}) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); return wantarray ? ('-','-') : '-'; } $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; if( defined $num ) { $seqType = "_\L$seqType\E"; return $self->{$seqType.'Start'} = $num; } # If there is only one HSP, defer this call to the solitary HSP. if($self->num_hsps == 1) { return $self->hsp->start($seqType); } else { # Tiling normally generates $self->{'_queryStart'} and # $self->{'_sbjctStart'}, but is very slow. If we haven't tiled, # find the answer quickly without tiling. unless (defined $self->{'_queryStart'}) { my $earliest_query_start; my $earliest_sbjct_start; foreach my $hsp ($self->hsps) { my $this_query_start = $hsp->start('query'); if (! defined $earliest_query_start || $this_query_start < $earliest_query_start) { $earliest_query_start = $this_query_start; } my $this_sbjct_start = $hsp->start('sbjct'); if (! defined $earliest_sbjct_start || $this_sbjct_start < $earliest_sbjct_start) { $earliest_sbjct_start = $this_sbjct_start; } } $self->{'_queryStart'} = $earliest_query_start; $self->{'_sbjctStart'} = $earliest_sbjct_start; } if ($seqType =~ /list|array/i) { return ($self->{'_queryStart'}, $self->{'_sbjctStart'}); } else { ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; return $self->{$seqType.'Start'}; } } } =head2 end Usage : $sbjct->end( [seq_type] ); Purpose : Gets the end coordinate for the query, sbjct, or both sequences : in the BlastHit object. If there is more than one HSP, the largest end : value of all HSPs is returned. Example : $qend = $sbjct->end('query'); : $send = $sbjct->end('hit'); : ($qend, $send) = $sbjct->end(); Returns : scalar context: integer : array context without args: list of two integers : (queryEnd, sbjctEnd) : Array context can be "induced" by providing an argument : of 'list' or 'array'. Argument : In scalar context: seq_type = 'query' or 'sbjct' : (case insensitive). If not supplied, 'query' is used. Throws : n/a See Also : L, L, L =cut sub end { my ($self, $seqType, $num) = @_; unless ($self->{'_hsps'}) { return wantarray ? ('-','-') : '-'; } $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; if( defined $num ) { $seqType = "_\L$seqType\E"; return $self->{$seqType.'Stop'} = $num; } # If there is only one HSP, defer this call to the solitary HSP. if($self->num_hsps == 1) { return $self->hsp->end($seqType); } else { # Tiling normally generates $self->{'_queryStop'} and # $self->{'_sbjctStop'}, but is very slow. If we haven't tiled, # find the answer quickly without tiling. unless (defined $self->{'_queryStop'}) { my $latest_query_end; my $latest_sbjct_end; foreach my $hsp ($self->hsps) { my $this_query_end = $hsp->end('query'); if (! defined $latest_query_end || $this_query_end > $latest_query_end) { $latest_query_end = $this_query_end; } my $this_sbjct_end = $hsp->end('sbjct'); if (! defined $latest_sbjct_end || $this_sbjct_end > $latest_sbjct_end) { $latest_sbjct_end = $this_sbjct_end; } } $self->{'_queryStop'} = $latest_query_end; $self->{'_sbjctStop'} = $latest_sbjct_end; } if($seqType =~ /list|array/i) { return ($self->{'_queryStop'}, $self->{'_sbjctStop'}); } else { ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; return $self->{$seqType.'Stop'}; } } } =head2 range Usage : $sbjct->range( [seq_type] ); Purpose : Gets the (start, end) coordinates for the query or sbjct sequence : in the HSP alignment. Example : ($qbeg, $qend) = $sbjct->range('query'); : ($sbeg, $send) = $sbjct->range('hit'); Returns : Two-element array of integers Argument : seq_type = string, 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is synonymous with 'hit') Throws : n/a See Also : L, L =cut sub range { my ($self, $seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; return ($self->start($seqType), $self->end($seqType)); } =head2 frac_identical Usage : $hit_object->frac_identical( [seq_type] ); Purpose : Get the overall fraction of identical positions across all HSPs. : The number refers to only the aligned regions and does not : account for unaligned regions in between the HSPs, if any. Example : $frac_iden = $hit_object->frac_identical('query'); Returns : Float (2-decimal precision, e.g., 0.75). Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total' : default = 'query' (but see comments below). : ('sbjct' is synonymous with 'hit') Throws : n/a Comments : : To compute the fraction identical, the logical length of the : aligned portion of the sequence is used, meaning that : in the case of BLAST flavors, for TBLASTN reports, the length of : the aligned portion of the : nucleotide hit sequence is divided by 3; for BLASTX reports, : the length of the aligned portion of the nucleotide query : sequence is divided by 3. For TBLASTX reports, the length of : both hit and query sequence are converted. : This is necessary since the number of identical residues is : in terms of peptide sequence space. : : Different versions of Blast report different values for the total : length of the alignment. This is the number reported in the : denominators in the stats section: : "Identical = 34/120 Positives = 67/120". : NCBI BLAST uses the total length of the alignment (with gaps) : WU-BLAST uses the length of the query sequence (without gaps). : : Therefore, when called with an argument of 'total', : this method will report different values depending on the : version of BLAST used. Total does NOT take into account HSP : tiling, so it should not be used. : : To get the fraction identical among only the aligned residues, : ignoring the gaps, call this method without an argument or : with an argument of 'query' or 'hit'. : : If you need data for each HSP, use hsps() and then iterate : through the HSP objects. : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically. See Also : L, L, L, L =cut sub frac_identical { my ($self, $seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; ## Sensitive to member name format. $seqType = lc($seqType); unless ($self->{'_hsps'}) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); #return wantarray ? ('-','-') : '-'; return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; my $ident = $self->matches('id'); my $total = $self->length_aln($seqType); my $ratio = $ident / $total; my $ratio_rounded = sprintf( "%.3f", $ratio); # Round down iff normal rounding yields 1 (just like blast) $ratio_rounded = 0.999 if (($ratio_rounded == 1) && ($ratio < 1)); return $ratio_rounded; } =head2 frac_conserved Usage : $hit_object->frac_conserved( [seq_type] ); Purpose : Get the overall fraction of conserved positions across all HSPs. : The number refers to only the aligned regions and does not : account for unaligned regions in between the HSPs, if any. Example : $frac_cons = $hit_object->frac_conserved('hit'); Returns : Float (2-decimal precision, e.g., 0.75). Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total' : default = 'query' (but see comments below). : ('sbjct' is synonymous with 'hit') Throws : n/a Comments : : To compute the fraction conserved, the logical length of the : aligned portion of the sequence is used, meaning that : in the case of BLAST flavors, for TBLASTN reports, the length of : the aligned portion of the : nucleotide hit sequence is divided by 3; for BLASTX reports, : the length of the aligned portion of the nucleotide query : sequence is divided by 3. For TBLASTX reports, the length of : both hit and query sequence are converted. : This is necessary since the number of conserved residues is : in terms of peptide sequence space. : : Different versions of Blast report different values for the total : length of the alignment. This is the number reported in the : denominators in the stats section: : "Positives = 34/120 Positives = 67/120". : NCBI BLAST uses the total length of the alignment (with gaps) : WU-BLAST uses the length of the query sequence (without gaps). : : Therefore, when called with an argument of 'total', : this method will report different values depending on the : version of BLAST used. Total does NOT take into account HSP : tiling, so it should not be used. : : To get the fraction conserved among only the aligned residues, : ignoring the gaps, call this method without an argument or : with an argument of 'query' or 'hit'. : : If you need data for each HSP, use hsps() and then interate : through the HSP objects. : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically. See Also : L, L, L =cut sub frac_conserved { my ($self, $seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; ## Sensitive to member name format. $seqType = lc($seqType); unless ($self->{'_hsps'}) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); #return wantarray ? ('-','-') : '-'; return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; my $consv = $self->matches('cons'); my $total = $self->length_aln($seqType); my $ratio = $consv / $total; my $ratio_rounded = sprintf( "%.3f", $ratio); # Round down iff normal rounding yields 1 (just like blast) $ratio_rounded = 0.999 if (($ratio_rounded == 1) && ($ratio < 1)); return $ratio_rounded; } =head2 frac_aligned_query Usage : $hit_object->frac_aligned_query(); Purpose : Get the fraction of the query sequence which has been aligned : across all HSPs (not including intervals between non-overlapping : HSPs). Example : $frac_alnq = $hit_object->frac_aligned_query(); Returns : Float (2-decimal precision, e.g., 0.75), : or undef if query length is unknown to avoid division by 0. Argument : n/a Throws : n/a Comments : If you need data for each HSP, use hsps() and then interate : through the HSP objects. : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically. See Also : L, L, L, L =cut sub frac_aligned_query { my $self = shift; unless ($self->{'_hsps'}) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); #return wantarray ? ('-','-') : '-'; return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; my $qry_len = $self->logical_length('query'); return undef if $qry_len == 0; # Avoid division by 0 crash sprintf( "%.2f", $self->length_aln('query') / $qry_len); } =head2 frac_aligned_hit Usage : $hit_object->frac_aligned_hit(); Purpose : Get the fraction of the hit (sbjct) sequence which has been aligned : across all HSPs (not including intervals between non-overlapping : HSPs). Example : $frac_alnq = $hit_object->frac_aligned_hit(); Returns : Float (2-decimal precision, e.g., 0.75), : or undef if hit length is unknown to avoid division by 0. Argument : n/a Throws : n/a Comments : If you need data for each HSP, use hsps() and then interate : through the HSP objects. : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically. See Also : L, L, , L, L, L =cut sub frac_aligned_hit { my $self = shift; unless ($self->{'_hsps'}) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); #return wantarray ? ('-','-') : '-'; return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; my $sbjct_len = $self->logical_length('sbjct'); return undef if $sbjct_len == 0; # Avoid division by 0 crash sprintf( "%.2f", $self->length_aln('sbjct') / $sbjct_len); } ## These methods are being maintained for backward compatibility. =head2 frac_aligned_sbjct Same as L =cut *frac_aligned_sbjct = \&frac_aligned_hit; =head2 num_unaligned_sbjct Same as L =cut *num_unaligned_sbjct = \&num_unaligned_hit; =head2 num_unaligned_hit Usage : $hit_object->num_unaligned_hit(); Purpose : Get the number of the unaligned residues in the hit sequence. : Sums across all all HSPs. Example : $num_unaln = $hit_object->num_unaligned_hit(); Returns : Integer Argument : n/a Throws : n/a Comments : See notes regarding logical lengths in the comments for frac_aligned_hit(). : They apply here as well. : If you need data for each HSP, use hsps() and then interate : through the HSP objects. : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically.. See Also : L, L, L =cut sub num_unaligned_hit { my $self = shift; unless ($self->{'_hsps'}) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); #return wantarray ? ('-','-') : '-'; return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; my $num = $self->logical_length('sbjct') - $self->length_aln('sbjct'); ($num < 0 ? 0 : $num ); } =head2 num_unaligned_query Usage : $hit_object->num_unaligned_query(); Purpose : Get the number of the unaligned residues in the query sequence. : Sums across all all HSPs. Example : $num_unaln = $hit_object->num_unaligned_query(); Returns : Integer Argument : n/a Throws : n/a Comments : See notes regarding logical lengths in the comments for frac_aligned_query(). : They apply here as well. : If you need data for each HSP, use hsps() and then interate : through the HSP objects. : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically.. See Also : L, L, L =cut sub num_unaligned_query { my $self = shift; unless ($self->{'_hsps'}) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); #return wantarray ? ('-','-') : '-'; return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; my $num = $self->logical_length('query') - $self->length_aln('query'); ($num < 0 ? 0 : $num ); } =head2 seq_inds Usage : $hit->seq_inds( seq_type, class, collapse ); Purpose : Get a list of residue positions (indices) across all HSPs : for identical or conserved residues in the query or sbjct sequence. Example : @s_ind = $hit->seq_inds('query', 'identical'); : @h_ind = $hit->seq_inds('hit', 'conserved'); : @h_ind = $hit->seq_inds('hit', 'conserved', 1); Returns : Array of integers : May include ranges if collapse is non-zero. Argument : [0] seq_type = 'query' or 'hit' or 'sbjct' (default = 'query') : ('sbjct' is synonymous with 'hit') : [1] class = 'identical' or 'conserved' (default = 'identical') : (can be shortened to 'id' or 'cons') : (actually, anything not 'id' will evaluate to 'conserved'). : [2] collapse = boolean, if non-zero, consecutive positions are merged : using a range notation, e.g., "1 2 3 4 5 7 9 10 11" : collapses to "1-5 7 9-11". This is useful for : consolidating long lists. Default = no collapse. Throws : n/a. See Also : L =cut sub seq_inds { my ($self, $seqType, $class, $collapse) = @_; $seqType ||= 'query'; $class ||= 'identical'; $collapse ||= 0; $seqType = 'sbjct' if $seqType eq 'hit'; my (@inds, $hsp); foreach $hsp ($self->hsps) { # This will merge data for all HSPs together. push @inds, $hsp->seq_inds($seqType, $class); } # Need to remove duplicates and sort the merged positions. if(@inds) { my %tmp = map { $_, 1 } @inds; @inds = sort {$a <=> $b} keys %tmp; } $collapse ? &Bio::Search::SearchUtils::collapse_nums(@inds) : @inds; } =head2 strand See documentation in L =cut sub strand { my ($self, $seqType, $strnd) = @_; unless ($self->{'_hsps'}) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); return wantarray ? ('-','-') : '-'; #return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; $seqType = lc($seqType); if( defined $strnd ) { $self->throw("Can't set strand for seqType '$seqType'. Must be 'query' or 'hit'\n") unless ($seqType eq 'sbjct' or $seqType eq 'query'); return $self->{'_strand_'.$seqType} = $strnd; } my ($qstr, $hstr); # If there is only one HSP, defer this call to the solitary HSP. if($self->num_hsps == 1) { return $self->hsp->strand($seqType); } elsif( defined $self->{'_strand_query'}) { # Get the data computed during hsp tiling. $qstr = $self->{'_strand_query'}; $hstr = $self->{'_strand_sbjct'} } else { # otherwise, iterate through all HSPs collecting strand info. # This will return the string "-1/1" if there are HSPs on different strands. # NOTE: This was the pre-10/21/02 procedure which will no longer be used, # (unless the above elsif{} is commented out). my (%qstr, %hstr); foreach my $hsp( $self->hsps ) { my ( $q, $h ) = $hsp->strand(); $qstr{ $q }++; $hstr{ $h }++; } $qstr = join( '/', sort keys %qstr); $hstr = join( '/', sort keys %hstr); } if($seqType =~ /list|array/i) { return ($qstr, $hstr); } elsif( $seqType eq 'query' ) { return $qstr; } else { return $hstr; } } =head2 frame See documentation in L =cut sub frame { my( $self, $frm ) = @_; unless ($self->{'_hsps'}) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); #return wantarray ? ('-','-') : '-'; return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; if( defined $frm ) { return $self->{'_frame'} = $frm; } # The check for $self->{'_frame'} is a remnant from the 'query' mode days # in which the sbjct object would collect data from the description line only. my ($frame); if(not defined($self->{'_frame'})) { $frame = $self->hsp->frame('hit'); } else { $frame = $self->{'_frame'}; } return $frame; } =head2 rank Title : rank Usage : $obj->rank($newval) Function: Get/Set the rank of this Hit in the Query search list i.e. this is the Nth hit for a specific query Returns : value of rank Args : newvalue (optional) =cut sub rank { my $self = shift; return $self->{'_rank'} = shift if @_; return $self->{'_rank'} || 1; } =head2 locus Title : locus Usage : $locus = $hit->locus(); Function: Retrieve the locus (if available) for the hit Returns : a scalar string (empty string if not set) Args : none =cut sub locus { my ($self,$value) = @_; my $previous = $self->{'_locus'}; if( defined $value || ! defined $previous ) { unless (defined $value) { if ($self->{'_name'} =~/(gb|emb|dbj|ref)\|(.*)\|(.*)/) { $value = $previous = $3; } else { $value = $previous = ''; } } $self->{'_locus'} = $value; } return $previous; } =head2 each_accession_number Title : each_accession_number Usage : @each_accession_number = $hit->each_accession_number(); Function: Get each accession number listed in the description of the hit. If there are no alternatives, then only the primary accession will be given Returns : list of all accession numbers in the description Args : none =cut sub each_accession_number { my ($self,$value) = @_; my $desc = $self->{'_description'}; #put primary accnum on the list my @accnums; push (@accnums,$self->{'_accession'}); if( defined $desc ) { while ($desc =~ /(\b\S+\|\S*\|\S*\s?)/g) { my $id = $1; my ($acc, $version); if ($id =~ /(gb|emb|dbj|sp|pdb|bbs|ref|tp[gde])\|(.*)\|(.*)/) { ($acc, $version) = split /\./, $2; } elsif ($id =~ /(pir|prf|pat|gnl)\|(.*)\|(.*)/) { ($acc, $version) = split /\./, $3; } elsif( $id =~ /(gim|gi|bbm|bbs|lcl)\|(\d*)/) { $acc = $id; } elsif( $id =~ /(oth)\|(.*)\|(.*)\|(.*)/ ) { # discontinued... ($acc,$version) = ($2); } else { #punt, not matching the db's at ftp://ftp.ncbi.nih.gov/blast/db/README #Database Name Identifier Syntax #============================ ======================== #GenBank gb|accession|locus #EMBL Data Library emb|accession|locus #DDBJ, DNA Database of Japan dbj|accession|locus #NBRF PIR pir||entry #Protein Research Foundation prf||name #SWISS-PROT sp|accession|entry name #Brookhaven Protein Data Bank pdb|entry|chain #Patents pat|country|number #GenInfo Backbone Id bbs|number #General database identifier gnl|database|identifier #NCBI Reference Sequence ref|accession|locus #Local Sequence identifier lcl|identifier $acc=$id; } push(@accnums, $acc); } } return @accnums; } =head2 tiled_hsps See documentation in L =cut sub tiled_hsps { my $self = shift; return $self->{'_tiled_hsps'} = shift if @_; return $self->{'_tiled_hsps'}; } =head2 query_length Title : query_length Usage : $obj->query_length($newval) Function: Get/Set the query_length Returns : value of query_length (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub query_length { my ($self,$value) = @_; my $previous = $self->{'_query_length'}; if( defined $value || ! defined $previous ) { $value = $previous = 0 unless defined $value; $self->{'_query_length'} = $value; } return $previous; } =head2 ncbi_gi Title : ncbi_gi Usage : $acc = $hit->ncbi_gi(); Function: Retrieve the NCBI Unique ID (aka the GI #), if available, for the hit Returns : a scalar string (empty string if not set) Args : none Note : As of Sept. 2016 NCBI records will no longer have a GI; this attributue will remain in place for older records =cut sub ncbi_gi { my ($self,$value) = @_; if( defined $value ) { $self->{'_ncbi_gi'} = $value; } else { $self->{'_ncbi_gi'} = $self->name =~ m{^gi\|(\d+)} ? $1 : ''; } return $self->{'_ncbi_gi'}; } # sort method for HSPs =head2 sort_hits Title : sort_hsps Usage : $result->sort_hsps(\&sort_function) Function : Sorts the available HSP objects by a user-supplied function. Defaults to sort by descending score. Returns : n/a Args : A coderef for the sort function. See the documentation on the Perl sort() function for guidelines on writing sort functions. Note : To access the special variables $a and $b used by the Perl sort() function the user function must access Bio::Search::Hit::HitI namespace. For example, use : $hit->sort_hsps( sub{$Bio::Search::Result::HitI::a->length <=> $Bio::Search::Result::HitI::b->length}); NOT $hit->sort_hsps($a->length <=> $b->length); =cut sub sort_hsps { my ($self, $coderef) = @_; my @sorted_hsps; if ($coderef) { $self->throw('sort_hsps requires a sort function passed as a subroutine reference') unless (ref($coderef) eq 'CODE'); } else { $coderef = \&_default_sort_hsps; # throw a warning? } my @hsps = $self->hsps(); eval {@sorted_hsps = sort $coderef @hsps }; if ($@) { $self->throw("Unable to sort hsps: $@"); } else { $self->{'_hsps'} = \@sorted_hsps; 1; } } =head2 iteration Usage : $hit->iteration( $iteration_num ); Purpose : Gets the iteration number in which the Hit was found. Example : $iteration_num = $sbjct->iteration(); Returns : Integer greater than or equal to 1 Non-PSI-BLAST reports may report iteration as 1, but this number is only meaningful for PSI-BLAST reports. Argument : iteration_num (optional, used when setting only) Throws : none See Also : L =cut sub iteration{ my ($self,$value) = @_; if( defined $value) { $self->{'_psiblast_iteration'} = $value; } return $self->{'_psiblast_iteration'}; } =head2 found_again Title : found_again Usage : $hit->found_again; $hit->found_again(1); Purpose : Gets a boolean indicator whether or not the hit has been found in a previous iteration. This is only applicable to PSI-BLAST reports. This method indicates if the hit was reported in the "Sequences used in model and found again" section of the PSI-BLAST report or if it was reported in the "Sequences not found previously or not previously below threshold" section of the PSI-BLAST report. Only for hits in iteration > 1. Example : if( $hit->found_again()) { ... }; Returns : Boolean, true (1) if the hit has been found in a previous PSI-BLAST iteration. Returns false (0 or undef) for hits that have not occurred in a previous PSI-BLAST iteration. Argument : Boolean (1 or 0). Only used for setting. Throws : none See Also : L =cut sub found_again { my $self = shift; return $self->{'_found_again'} = shift if @_; return $self->{'_found_again'}; } 1; BioPerl-1.007002/Bio/Search/Hit/HMMERHit.pm000444000766000024 1673413155576320 20063 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Hit::HMMERHit # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Hit::HMMERHit - A Hit module for HMMER hits =head1 SYNOPSIS use Bio::Search::Hit::HMMERHit; my $hit = Bio::Search::Hit::HMMERHit->new(); # use it in the same way as Bio::Search::Hit::GenericHit =head1 DESCRIPTION This is a specialization of L. There are a few news methods L and L. Note that L and L make no sense for this object and will return 0. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Hit::HMMERHit; use strict; use base qw(Bio::Search::Hit::GenericHit); =head2 new Title : new Usage : my $obj = Bio::Search::Hit::HMMERHit->new(); Function: Builds a new Bio::Search::Hit::HMMERHit object Returns : Bio::Search::Hit::HMMERHit Args : Plus the Bio::Search::Hit::GenericHit inherited params -name => Name of Hit (required) -description => Description (optional) -accession => Accession number (optional) -length => Length of the Hit (optional) -score => Raw Score for the Hit (optional) -significance => Significance value for the Hit (optional) -algorithm => Algorithm used (BLASTP, FASTX, etc...) -hsps => Array ref of HSPs for this Hit. =cut =head2 next_domain Title : next_domain Usage : my $domain = $hit->next_domain(); Function: An alias for L, this will return the next HSP Returns : L object Args : none =cut sub next_domain{ shift->next_hsp } =head2 domains Title : domains Usage : my @domains = $hit->domains(); Function: An alias for L, this will return the full list of hsps Returns : array of L objects Args : none =cut sub domains{ shift->hsps() } =head2 inherited Bio::Search::Hit::GenericHit methods =cut =head2 add_hsp Title : add_hsp Usage : $hit->add_hsp($hsp) Function: Add a HSP to the collection of HSPs for a Hit Returns : number of HSPs in the Hit Args : Bio::Search::HSP::HSPI object =cut =head2 Bio::Search::Hit::HitI methods =cut =head2 name Title : name Usage : $hit_name = $hit->name(); Function: returns the name of the Hit sequence Returns : a scalar string Args : [optional] scalar string to set the name =cut =head2 accession Title : accession Usage : $acc = $hit->accession(); Function: Retrieve the accession (if available) for the hit Returns : a scalar string (empty string if not set) Args : none =cut =head2 description Title : description Usage : $desc = $hit->description(); Function: Retrieve the description for the hit Returns : a scalar string Args : [optional] scalar string to set the description =cut =head2 length Title : length Usage : my $len = $hit->length Function: Returns the length of the hit Returns : integer Args : [optional] integer to set the length =cut =head2 algorithm Title : algorithm Usage : $alg = $hit->algorithm(); Function: Gets the algorithm specification that was used to obtain the hit For BLAST, the algorithm denotes what type of sequence was aligned against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated dna-prt, TBLASTN prt-translated dna, TBLASTX translated dna-translated dna). Returns : a scalar string Args : [optional] scalar string to set the algorithm =cut =head2 raw_score Title : raw_score Usage : $score = $hit->raw_score(); Function: Gets the "raw score" generated by the algorithm. What this score is exactly will vary from algorithm to algorithm, returning undef if unavailable. Returns : a scalar value Args : [optional] scalar value to set the raw score =cut =head2 significance Title : significance Usage : $significance = $hit->significance(); Function: Used to obtain the E or P value of a hit, i.e. the probability that this particular hit was obtained purely by random chance. If information is not available (nor calculatable from other information sources), return undef. Returns : a scalar value or undef if unavailable Args : [optional] scalar value to set the significance =cut =head2 bits Usage : $hit_object->bits(); Purpose : Gets the bit score of the best HSP for the current hit. Example : $bits = $hit_object->bits(); Returns : Integer or undef if bit score is not set Argument : n/a See Also : L =cut sub bits { return 0 } =head2 next_hsp Title : next_hsp Usage : while( $hsp = $obj->next_hsp()) { ... } Function : Returns the next available High Scoring Pair Example : Returns : Bio::Search::HSP::HSPI object or null if finished Args : none =cut =head2 hsps Usage : $hit_object->hsps(); Purpose : Get a list containing all HSP objects. : Get the numbers of HSPs for the current hit. Example : @hsps = $hit_object->hsps(); : $num = $hit_object->hsps(); # alternatively, use num_hsps() Returns : Array context : list of Bio::Search::HSP::BlastHSP.pm objects. : Scalar context: integer (number of HSPs). : (Equivalent to num_hsps()). Argument : n/a. Relies on wantarray Throws : Exception if the HSPs have not been collected. See Also : L, L =cut =head2 num_hsps Usage : $hit_object->num_hsps(); Purpose : Get the number of HSPs for the present Blast hit. Example : $nhsps = $hit_object->num_hsps(); Returns : Integer Argument : n/a Throws : Exception if the HSPs have not been collected. See Also : L =cut =head2 rewind Title : rewind Usage : $hit->rewind; Function: Allow one to reset the HSP iteration to the beginning Since this is an in-memory implementation Returns : none Args : none =cut =head2 iteration Title : iteration Usage : $obj->iteration($newval) Function: PSI-BLAST iteration Returns : value of iteration Args : newvalue (optional) =cut sub iteration { return 0 } 1; BioPerl-1.007002/Bio/Search/Hit/HitFactory.pm000444000766000024 712413155576320 20573 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Hit::HitFactory # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Hit::HitFactory - A factory to create Bio::Search::Hit::HitI objects =head1 SYNOPSIS use Bio::Search::Hit::HitFactory; my $factory = Bio::Search::Hit::HitFactory->new(); my $resultobj = $factory->create(@args); =head1 DESCRIPTION This is a general way of hiding the object creation process so that we can dynamically change the objects that are created by the SearchIO parser depending on what format report we are parsing. This object is for creating new Hits. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Hit::HitFactory; use vars qw($DEFAULT_TYPE); use strict; use base qw(Bio::Root::Root Bio::Factory::ObjectFactoryI); BEGIN { $DEFAULT_TYPE = 'Bio::Search::Hit::GenericHit'; } =head2 new Title : new Usage : my $obj = Bio::Search::Hit::HitFactory->new(); Function: Builds a new Bio::Search::Hit::HitFactory object Returns : Bio::Search::Hit::HitFactory Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($type) = $self->_rearrange([qw(TYPE)],@args); $self->type($type) if defined $type; return $self; } =head2 create Title : create Usage : $factory->create(%args) Function: Create a new L object Returns : L Args : hash of initialization parameters =cut sub create{ my ($self,@args) = @_; my $type = $self->type; eval { $self->_load_module($type) }; if( $@ ) { $self->throw("Unable to load module $type"); } return $type->new(@args); } =head2 type Title : type Usage : $factory->type('Bio::Search::Hit::GenericHit'); Function: Get/Set the Hit creation type Returns : string Args : [optional] string to set =cut sub type{ my ($self,$type) = @_; if( defined $type ) { # redundancy with the create method which also calls _load_module # I know - but this is not a highly called object so I am going # to leave it in eval {$self->_load_module($type) }; if( $@ ){ $self->warn("Cannot find module $type, unable to set type"); } else { $self->{'_type'} = $type; } } return $self->{'_type'} || $DEFAULT_TYPE; } 1; BioPerl-1.007002/Bio/Search/Hit/HitI.pm000444000766000024 5320213155576320 17372 0ustar00cjfieldsstaff000000000000#----------------------------------------------------------------- # # BioPerl module Bio::Search::Hit::HitI # # Please direct questions and support issues to # # Cared for by Steve Chervitz # # Originally created by Aaron Mackey # # You may distribute this module under the same terms as perl itself #----------------------------------------------------------------- # POD documentation - main docs before the code =head1 NAME Bio::Search::Hit::HitI - Interface for a hit in a similarity search result =head1 SYNOPSIS # Bio::Search::Hit::HitI objects should not be instantiated since this # module defines a pure interface. # Given an object that implements the Bio::Search::Hit::HitI interface, # you can do the following things with it: # Get a HitI object from a SearchIO stream: use Bio::SeachIO; my $searchio = Bio::SearchIO->new(-format => 'blast', -file => 'result.bls'); my $result = $searchio->next_result; my $hit = $result->next_hit; $hit_name = $hit->name(); $desc = $hit->description(); $len = $hit->length $alg = $hit->algorithm(); $score = $hit->raw_score(); $significance = $hit->significance(); $rank = $hit->rank(); # the Nth hit for a specific query while( $hsp = $obj->next_hsp()) { ... } # process in iterator fashion for my $hsp ( $obj->hsps()()) { ... } # process in list fashion =head1 DESCRIPTION Bio::Search::Hit::* objects are data structures that contain information about specific hits obtained during a library search. Some information will be algorithm-specific, but others will be generally defined. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Aaron Mackey, Steve Chervitz Email amackey@virginia.edu (original author) Email sac@bioperl.org =head1 COPYRIGHT Copyright (c) 1999-2001 Aaron Mackey, Steve Chervitz. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Hit::HitI; use strict; use base qw(Bio::Root::RootI); =head2 name Title : name Usage : $hit_name = $hit->name(); Function: returns the name of the Hit sequence Returns : a scalar string Args : none The B of a hit is unique within a Result or within an Iteration. =cut sub name { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 description Title : description Usage : $desc = $hit->description(); Function: Retrieve the description for the hit Returns : a scalar string Args : none =cut sub description { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 accession Title : accession Usage : $acc = $hit->accession(); Function: Retrieve the accession (if available) for the hit Returns : a scalar string (empty string if not set) Args : none =cut sub accession { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 locus Title : locus Usage : $acc = $hit->locus(); Function: Retrieve the locus(if available) for the hit Returns : a scalar string (empty string if not set) Args : none =cut sub locus { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 length Title : length Usage : my $len = $hit->length Function: Returns the length of the hit Returns : integer Args : none =cut sub length { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 algorithm Title : algorithm Usage : $alg = $hit->algorithm(); Function: Gets the algorithm specification that was used to obtain the hit For BLAST, the algorithm denotes what type of sequence was aligned against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated dna-prt, TBLASTN prt-translated dna, TBLASTX translated dna-translated dna). Returns : a scalar string Args : none =cut sub algorithm { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 raw_score Title : raw_score Usage : $score = $hit->raw_score(); Function: Gets the "raw score" generated by the algorithm. What this score is exactly will vary from algorithm to algorithm, returning undef if unavailable. Returns : a scalar value Args : none =cut sub raw_score { $_[0]->throw_not_implemented; } =head2 score Equivalent to L =cut sub score { shift->raw_score(@_); } =head2 significance Title : significance Usage : $significance = $hit->significance(); Function: Used to obtain the E or P value of a hit, i.e. the probability that this particular hit was obtained purely by random chance. If information is not available (nor calculatable from other information sources), return undef. Returns : a scalar value or undef if unavailable Args : none =cut sub significance { $_[0]->throw_not_implemented; } =head2 bits Usage : $hit_object->bits(); Purpose : Gets the bit score of the best HSP for the current hit. Example : $bits = $hit_object->bits(); Returns : Integer or double for FASTA reports Argument : n/a Comments : For BLAST1, the non-bit score is listed in the summary line. See Also : L =cut #--------- sub bits { #--------- $_[0]->throw_not_implemented(); } =head2 next_hsp Title : next_hsp Usage : while( $hsp = $obj->next_hsp()) { ... } Function : Returns the next available High Scoring Pair Example : Returns : L object or null if finished Args : none =cut sub next_hsp { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 hsps Usage : $hit_object->hsps(); Purpose : Get a list containing all HSP objects. : Get the numbers of HSPs for the current hit. Example : @hsps = $hit_object->hsps(); : $num = $hit_object->hsps(); # alternatively, use num_hsps() Returns : Array context : list of L objects. : Scalar context: integer (number of HSPs). : (Equivalent to num_hsps()). Argument : n/a. Relies on wantarray Throws : Exception if the HSPs have not been collected. See Also : L, L =cut #--------- sub hsps { #--------- my $self = shift; $self->throw_not_implemented(); } =head2 num_hsps Usage : $hit_object->num_hsps(); Purpose : Get the number of HSPs for the present Blast hit. Example : $nhsps = $hit_object->num_hsps(); Returns : Integer Argument : n/a Throws : Exception if the HSPs have not been collected. See Also : L =cut #------------- sub num_hsps { #------------- shift->throw_not_implemented(); } =head2 seq_inds Usage : $hit->seq_inds( seq_type, class, collapse ); Purpose : Get a list of residue positions (indices) across all HSPs : for identical or conserved residues in the query or sbjct sequence. Example : @s_ind = $hit->seq_inds('query', 'identical'); : @h_ind = $hit->seq_inds('hit', 'conserved'); : @h_ind = $hit->seq_inds('hit', 'conserved', 1); Returns : Array of integers : May include ranges if collapse is non-zero. Argument : [0] seq_type = 'query' or 'hit' or 'sbjct' (default = 'query') : ('sbjct' is synonymous with 'hit') : [1] class = 'identical' or 'conserved' (default = 'identical') : (can be shortened to 'id' or 'cons') : (actually, anything not 'id' will evaluate to 'conserved'). : [2] collapse = boolean, if non-zero, consecutive positions are merged : using a range notation, e.g., "1 2 3 4 5 7 9 10 11" : collapses to "1-5 7 9-11". This is useful for : consolidating long lists. Default = no collapse. Throws : n/a. See Also : L =cut #------------- sub seq_inds { #------------- my ($self, $seqType, $class, $collapse) = @_; $seqType ||= 'query'; $class ||= 'identical'; $collapse ||= 0; $seqType = 'sbjct' if $seqType eq 'hit'; my (@inds, $hsp); foreach $hsp ($self->hsps) { # This will merge data for all HSPs together. push @inds, $hsp->seq_inds($seqType, $class); } # Need to remove duplicates and sort the merged positions. if(@inds) { my %tmp = map { $_, 1 } @inds; @inds = sort {$a <=> $b} keys %tmp; } $collapse ? &Bio::Search::BlastUtils::collapse_nums(@inds) : @inds; } =head2 rewind Title : rewind Usage : $hit->rewind; Function: Allow one to reset the HSP iterator to the beginning if possible Returns : none Args : none =cut sub rewind{ my ($self) = @_; $self->throw_not_implemented(); } =head2 overlap Usage : $hit_object->overlap( [integer] ); Purpose : Gets/Sets the allowable amount overlap between different HSP sequences. Example : $hit_object->overlap(5); : $overlap = $hit_object->overlap; Returns : Integer. Argument : integer. Throws : n/a Status : Experimental Comments : Any two HSPs whose sequences overlap by less than or equal : to the overlap() number of resides will be considered separate HSPs : and will not get tiled by L. See Also : L, L =cut #------------- sub overlap { shift->throw_not_implemented } =head2 n Usage : $hit_object->n(); Purpose : Gets the N number for the current Blast hit. : This is the number of HSPs in the set which was ascribed : the lowest P-value (listed on the description line). : This number is not the same as the total number of HSPs. : To get the total number of HSPs, use num_hsps(). Example : $n = $hit_object->n(); Returns : Integer Argument : n/a Throws : Exception if HSPs have not been set (BLAST2 reports). Comments : Note that the N parameter is not reported in gapped BLAST2. : Calling n() on such reports will result in a call to num_hsps(). : The num_hsps() method will count the actual number of : HSPs in the alignment listing, which may exceed N in : some cases. See Also : L =cut #----- sub n { shift->throw_not_implemented } =head2 p Usage : $hit_object->p( [format] ); Purpose : Get the P-value for the best HSP of the given BLAST hit. : (Note that P-values are not provided with NCBI Blast2 reports). Example : $p = $sbjct->p; : $p = $sbjct->p('exp'); # get exponent only. : ($num, $exp) = $sbjct->p('parts'); # split sci notation into parts Returns : Float or scientific notation number (the raw P-value, DEFAULT). : Integer if format == 'exp' (the magnitude of the base 10 exponent). : 2-element list (float, int) if format == 'parts' and P-value : is in scientific notation (See Comments). Argument : format: string of 'raw' | 'exp' | 'parts' : 'raw' returns value given in report. Default. (1.2e-34) : 'exp' returns exponent value only (34) : 'parts' returns the decimal and exponent as a : 2-element list (1.2, -34) (See Comments). Throws : Warns if no P-value is defined. Uses expect instead. Comments : Using the 'parts' argument is not recommended since it will not : work as expected if the P-value is not in scientific notation. : That is, floats are not converted into sci notation before : splitting into parts. See Also : L, L, L =cut #-------- sub p { shift->throw_not_implemented() } =head2 hsp Usage : $hit_object->hsp( [string] ); Purpose : Get a single HSPI object for the present HitI object. Example : $hspObj = $hit_object->hsp; # same as 'best' : $hspObj = $hit_object->hsp('best'); : $hspObj = $hit_object->hsp('worst'); Returns : Object reference for a L object. Argument : String (or no argument). : No argument (default) = highest scoring HSP (same as 'best'). : 'best' or 'first' = highest scoring HSP. : 'worst' or 'last' = lowest scoring HSP. Throws : Exception if the HSPs have not been collected. : Exception if an unrecognized argument is used. See Also : L, L() =cut #---------- sub hsp { shift->throw_not_implemented } =head2 logical_length Usage : $hit_object->logical_length( [seq_type] ); : (mostly intended for internal use). Purpose : Get the logical length of the hit sequence. : If the Blast is a TBLASTN or TBLASTX, the returned length : is the length of the would-be amino acid sequence (length/3). : For all other BLAST flavors, this function is the same as length(). Example : $len = $hit_object->logical_length(); Returns : Integer Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is synonymous with 'hit') Throws : n/a Comments : This is important for functions like frac_aligned_query() : which need to operate in amino acid coordinate space when dealing : with [T]BLAST[NX] type reports. See Also : L, L, L =cut #-------------------- sub logical_length { shift->throw_not_implemented() } =head2 rank Title : rank Usage : $obj->rank($newval) Function: Get/Set the rank of this Hit in the Query search list i.e. this is the Nth hit for a specific query Returns : value of rank Args : newvalue (optional) =cut sub rank{ my ($self,$value) = @_; $self->throw_not_implemented(); } =head2 each_accession_number Title : each_accession_number Usage : $obj->each_accession_number Function: Get each accession number listed in the description of the hit. If there are no alternatives, then only the primary accession will be given Returns : list of all accession numbers in the description Args : none =cut sub each_accession_number{ my ($self,$value) = @_; $self->throw_not_implemented(); } =head2 tiled_hsps Usage : $hit_object->tiled_hsps( [integer] ); Purpose : Gets/Sets an indicator for whether or not the HSPs in this Hit : have been tiled. : Methods that rely on HSPs being tiled should check this : and then call SearchUtils::tile_hsps() if not. Example : $hit_object->tiled_hsps(1); : if( $hit_object->tiled_hsps ) { # do something } Returns : Boolean (1 or 0) Argument : integer (optional) Throws : n/a =cut sub tiled_hsps { shift->throw_not_implemented } =head2 strand Usage : $sbjct->strand( [seq_type] ); Purpose : Gets the strand(s) for the query, sbjct, or both sequences : in the best HSP of the BlastHit object after HSP tiling. : Only valid for BLASTN, TBLASTX, BLASTX-query, TBLASTN-hit. Example : $qstrand = $sbjct->strand('query'); : $sstrand = $sbjct->strand('hit'); : ($qstrand, $sstrand) = $sbjct->strand(); Returns : scalar context: integer '1', '-1', or '0' : array context without args: list of two strings (queryStrand, sbjctStrand) : Array context can be "induced" by providing an argument of 'list' or 'array'. Argument : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is synonymous with 'hit') Throws : n/a Comments : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically.. : If you don't want the tiled data, iterate through each HSP : calling strand() on each (use hsps() to get all HSPs). : : Formerly (prior to 10/21/02), this method would return the : string "-1/1" for hits with HSPs on both strands. : However, now that strand and frame is properly being accounted : for during HSP tiling, it makes more sense for strand() : to return the strand data for the best HSP after tiling. : : If you really want to know about hits on opposite strands, : you should be iterating through the HSPs using methods on the : HSP objects. : : A possible use case where knowing whether a hit has HSPs : on both strands would be when filtering via SearchIO for hits with : this property. However, in this case it would be better to have a : dedicated method such as $hit->hsps_on_both_strands(). Similarly : for frame. This could be provided if there is interest. See Also : L() =cut #---------' sub strand { shift->throw_not_implemented } =head2 frame Usage : $hit_object->frame(); Purpose : Gets the reading frame for the best HSP after HSP tiling. : This is only valid for BLASTX and TBLASTN/X type reports. Example : $frame = $hit_object->frame(); Returns : Integer (-2 .. +2) Argument : n/a Throws : Exception if HSPs have not been set. Comments : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically.. : If you don't want the tiled data, iterate through each HSP : calling frame() on each (use hsps() to get all HSPs). See Also : L =cut #---------' sub frame { shift->throw_not_implemented } =head2 matches Usage : $hit_object->matches( [class] ); Purpose : Get the total number of identical or conserved matches : (or both) across all HSPs. : (Note: 'conservative' matches are indicated as 'positives' : in BLAST reports.) Example : ($id,$cons) = $hit_object->matches(); # no argument : $id = $hit_object->matches('id'); : $cons = $hit_object->matches('cons'); Returns : Integer or a 2-element array of integers Argument : class = 'id' | 'cons' OR none. : If no argument is provided, both identical and conservative : numbers are returned in a two element list. : (Other terms can be used to refer to the conservative : matches, e.g., 'positive'. All that is checked is whether or : not the supplied string starts with 'id'. If not, the : conservative matches are returned.) Throws : Exception if the requested data cannot be obtained. Comments : This method requires that all HSPs be tiled. If there is more than one : HSP and they have not already been tiled, they will be tiled first automatically.. : : If you need data for each HSP, use hsps() and then interate : through the HSP objects. : Does not rely on wantarray to return a list. Only checks for : the presence of an argument (no arg = return list). See Also : L, L =cut sub matches { shift->throw_not_implemented } # aliasing for Steve's method names sub hit_description { shift->description(@_) } # aliasing for Steve's method names sub hit_length { shift->length(@_) } # sort method for HSPs =head2 sort_hits Title : sort_hsps Usage : $result->sort_hsps(\&sort_function) Function : Sorts the available HSP objects by a user-supplied function. Defaults to sort by descending score. Returns : n/a Args : A coderef for the sort function. See the documentation on the Perl sort() function for guidelines on writing sort functions. Note : To access the special variables $a and $b used by the Perl sort() function the user function must access Bio::Search::Hit::HitI namespace. For example, use : $hit->sort_hsps( sub{$Bio::Search::Result::HitI::a->length <=> $Bio::Search::Result::HitI::b->length}); NOT $hit->sort_hsps($a->length <=> $b->length); =cut sub sort_hsps {shift->throw_not_implemented } =head2 _default sort_hsps Title : _default_sort_hsps Usage : Do not call directly. Function : Sort hsps in ascending order by evalue Args : None Returns: 1 on success Note : Used by $hit->sort_hsps() =cut sub _default_sort_hsps { $Bio::Search::Hit::HitI::a->evalue <=> $Bio::Search::Hit::HitI::a->evalue; } 1; BioPerl-1.007002/Bio/Search/Hit/HmmpfamHit.pm000555000766000024 2343613155576320 20600 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Hit::HmmpfamHit # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Hit::HmmpfamHit - A parser and hit object for hmmpfam hits =head1 SYNOPSIS # generally we use Bio::SearchIO to build these objects use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer_pull', -file => 'result.hmmer'); while (my $result = $in->next_result) { while (my $hit = $result->next_hit) { print $hit->name, "\n"; print $hit->score, "\n"; print $hit->significance, "\n"; while (my $hsp = $hit->next_hsp) { # process HSPI objects } } } =head1 DESCRIPTION This object implements a parser for hmmpfam hit output, a program in the HMMER package. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Hit::HmmpfamHit; use strict; use Bio::Search::HSP::HmmpfamHSP; use base qw(Bio::Root::Root Bio::Search::Hit::PullHitI); =head2 new Title : new Usage : my $obj = Bio::Search::Hit::HmmpfamHit->new(); Function: Builds a new Bio::Search::Hit::HmmpfamHit object. Returns : Bio::Search::Hit::HmmpfamHit Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent) -parent => Bio::PullParserI object (required if no -chunk) -hit_data => array ref with [name description score significance num_hsps rank] where the array ref provided to -chunk contains an IO object for a filehandle to something representing the raw data of the hit, and $start and $end define the tell() position within the filehandle that the hit data starts and ends (optional; defaults to start and end of the entire thing described by the filehandle) =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->_setup(@args); my $fields = $self->_fields; foreach my $field (qw( next_domain domains hsp_data )) { $fields->{$field} = undef; } my $hit_data = $self->_raw_hit_data; if ($hit_data && ref($hit_data) eq 'ARRAY') { foreach my $field (qw(name description score significance num_hsps rank)) { $fields->{$field} = shift(@{$hit_data}); } } $fields->{hit_start} = 1; delete $self->_fields->{accession}; $self->_dependencies( { ( length => 'hsp_data' ) } ); return $self; } # # PullParserI discovery methods so we can answer all HitI questions # sub _discover_description { # this should be set when this object is created, but if it was undef as is # possible, this _discover method will be called: just return and keep the # return value undef return; } sub _discover_hsp_data { my $self = shift; my $hsp_table = $self->get_field('hsp_table'); my $hsp_data = $hsp_table->{$self->get_field('name')} || undef; if ($hsp_data) { if (defined $hsp_data->{hit_length}) { $self->_fields->{length} = $hsp_data->{hit_length}; } # rank query_start query_end hit_start hit_end score evalue $self->_fields->{hsp_data} = $hsp_data->{hsp_data}; } } sub _discover_query_start { my $self = shift; my $hsp_data = $self->get_field('hsp_data') || return; my ($this_hsp) = sort { $a->[1] <=> $b->[1] } @{$hsp_data}; $self->_fields->{query_start} = $this_hsp->[1]; } sub _discover_query_end { my $self = shift; my $hsp_data = $self->get_field('hsp_data') || return; my ($this_hsp) = sort { $b->[2] <=> $a->[2] } @{$hsp_data}; $self->_fields->{query_end} = $this_hsp->[2]; } sub _discover_hit_start { my $self = shift; my $hsp_data = $self->get_field('hsp_data') || return; my ($this_hsp) = sort { $a->[3] <=> $b->[3] } @{$hsp_data}; $self->_fields->{hit_start} = $this_hsp->[3]; } sub _discover_hit_end { my $self = shift; my $hsp_data = $self->get_field('hsp_data') || return; my ($this_hsp) = sort { $b->[4] <=> $a->[4] } @{$hsp_data}; $self->_fields->{hit_end} = $this_hsp->[4]; } sub _discover_next_hsp { my $self = shift; my $hsp_data = $self->get_field('hsp_data') || return; unless (defined $self->{_next_hsp_index}) { $self->{_next_hsp_index} = 0; } return if $self->{_next_hsp_index} == -1; $self->_fields->{next_hsp} = Bio::Search::HSP::HmmpfamHSP->new(-parent => $self, -hsp_data => $hsp_data->[$self->{_next_hsp_index}++]); if ($self->{_next_hsp_index} > $#{$hsp_data}) { $self->{_next_hsp_index} = -1; } } =head2 next_hsp Title : next_hsp Usage : while( $hsp = $obj->next_hsp()) { ... } Function : Returns the next available High Scoring Pair Example : Returns : L object or null if finished Args : none =cut sub next_hsp { my $self = shift; my $hsp = $self->get_field('next_hsp'); undef $self->_fields->{next_hsp}; return $hsp; } =head2 next_domain Title : next_domain Usage : my $domain = $hit->next_domain(); Function: An alias for L, this will return the next HSP Returns : L object Args : none =cut *next_domain = \&next_hsp; =head2 hsps Usage : $hit_object->hsps(); Purpose : Get a list containing all HSP objects. Example : @hsps = $hit_object->hsps(); Returns : list of L objects. Argument : none =cut sub hsps { my $self = shift; my $old = $self->{_next_hsp_index} || 0; $self->rewind; my @hsps; while (defined(my $hsp = $self->next_hsp)) { push(@hsps, $hsp); } $self->{_next_hsp_index} = @hsps > 0 ? $old : -1; return @hsps; } =head2 domains Title : domains Usage : my @domains = $hit->domains(); Function: An alias for L, this will return the full list of hsps Returns : array of L objects Args : none =cut *domains = \&hsps; =head2 hsp Usage : $hit_object->hsp( [string] ); Purpose : Get a single HSPI object for the present HitI object. Example : $hspObj = $hit_object->hsp; # same as 'best' : $hspObj = $hit_object->hsp('best'); : $hspObj = $hit_object->hsp('worst'); Returns : Object reference for a L object. Argument : String (or no argument). : No argument (default) = highest scoring HSP (same as 'best'). : 'best' = highest scoring HSP. : 'worst' = lowest scoring HSP. Throws : Exception if an unrecognized argument is used. See Also : L, L() =cut sub hsp { my ($self, $type) = @_; $type ||= 'best'; my $hsp_data = $self->get_field('hsp_data') || return; my $sort; if ($type eq 'best') { $sort = sub { $a->[6] <=> $b->[6] }; } elsif ($type eq 'worst') { $sort = sub { $b->[6] <=> $a->[6] }; } else { $self->throw("Unknown arg '$type' given to hsp()"); } my ($this_hsp) = sort $sort @{$hsp_data}; return Bio::Search::HSP::HmmpfamHSP->new(-parent => $self, -hsp_data => $this_hsp); } =head2 rewind Title : rewind Usage : $result->rewind; Function: Allow one to reset the Hit iterator to the beginning, so that next_hit() will subsequently return the first hit and so on. Returns : n/a Args : none =cut sub rewind { my $self = shift; my $hsp_data = $self->get_field('hsp_data') || return; $self->{_next_hsp_index} = @{$hsp_data} > 0 ? 0 : -1; } # have p() a synonym of significance() sub p { return shift->significance; } =head2 strand Usage : $sbjct->strand( [seq_type] ); Purpose : Gets the strand(s) for the query, sbjct, or both sequences. : For hmmpfam, the answers are always 1 (forward strand). Example : $qstrand = $sbjct->strand('query'); : $sstrand = $sbjct->strand('hit'); : ($qstrand, $sstrand) = $sbjct->strand(); Returns : scalar context: integer '1' : array context without args: list of two strings (1, 1) : Array context can be "induced" by providing an argument of 'list' : or 'array'. Argument : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default : = 'query') ('sbjct' is synonymous with 'hit') =cut sub strand { my ($self, $type) = @_; $type ||= (wantarray ? 'list' : 'query'); $type = lc($type); if ($type eq 'list' || $type eq 'array') { return (1, 1); } return 1; } =head2 frac_aligned_query Usage : $hit_object->frac_aligned_query(); Purpose : Get the fraction of the query sequence which has been aligned : across all HSPs (not including intervals between non-overlapping : HSPs). Example : $frac_alnq = $hit_object->frac_aligned_query(); Returns : undef (the length of query sequences is unknown in Hmmpfam reports) Argument : none =cut # noop sub frac_aligned_query { } 1; BioPerl-1.007002/Bio/Search/Hit/ModelHit.pm000444000766000024 4734713155576320 20257 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Hit::ModelHit # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Hit::ModelHit - A model-based implementation of the Bio::Search::Hit::HitI interface =head1 SYNOPSIS use Bio::Search::Hit::ModelHit; my $hit = Bio::Search::Hit::ModelHit->new(-algorithm => 'rnamotif'); # typically one gets HitI objects from a SearchIO stream via a ResultI use Bio::SearchIO; my $parser = Bio::SearchIO->new(-format => 'infernal', -file => 'trap.inf'); my $result = $parser->next_result; my $hit = $result->next_hit; =head1 DESCRIPTION This object handles the hit data from a database search using models or descriptors instead of sequences, such as Infernal, HMMER, RNAMotif, etc. Unless you're writing a parser, you won't ever need to create a ModelHit or any other HitI-implementing object. If you use the SearchIO system, HitI objects are created automatically from a SearchIO stream which returns Bio::Search::Hit::HitI objects. Note that several HitI-based methods have been overridden from ModelHit due to their unreliability when dealing with queries that aren't sequence-based. It may be possible to reimplement these at a later point, but for the time being they will throw warnings and return w/o results. For documentation on what you can do with ModelHit (and other HitI objects), please see the API documentation in L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Fields Email cjfields at bioperl dot org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Hit::ModelHit; use strict; use base qw(Bio::Search::Hit::GenericHit); =head1 HitI methods implemented in parent class Bio::Search::Hit::ModelHit =head2 new Title : new Usage : my $obj = Bio::Search::Hit::ModelHit->new(); Function: Builds a new Bio::Search::Hit::ModelHit object Returns : Bio::Search::Hit::ModelHit Args : -name => Name of Hit (required) -description => Description (optional) -accession => Accession number (optional) -ncbi_gi => NCBI GI UID (optional) -length => Length of the Hit (optional) -score => Raw Score for the Hit (optional) -bits => Bit Score for the Hit (optional) -significance => Significance value for the Hit (optional) -algorithm => Algorithm used (BLASTP, FASTX, etc...) -hsps => Array ref of HSPs for this Hit. -found_again => boolean, true if hit appears in a "previously found" section of a PSI-Blast report. -hsp_factory => Bio::Factory::ObjectFactoryI able to create HSPI objects. =cut =head2 add_hsp Title : add_hsp Usage : $hit->add_hsp($hsp) Function: Add a HSP to the collection of HSPs for a Hit Returns : number of HSPs in the Hit Args : Bio::Search::HSP::HSPI object, OR hash ref containing data suitable for creating a HSPI object (&hsp_factory must be set to get it back) =cut =head2 hsp_factory Title : hsp_factory Usage : $hit->hsp_factory($hsp_factory) Function: Get/set the factory used to build HSPI objects if necessary. Returns : Bio::Factory::ObjectFactoryI Args : Bio::Factory::ObjectFactoryI =cut =head2 Bio::Search::Hit::HitI methods Implementation of Bio::Search::Hit::HitI methods =head2 name Title : name Usage : $hit_name = $hit->name(); Function: returns the name of the Hit sequence Returns : a scalar string Args : [optional] scalar string to set the name =cut =head2 accession Title : accession Usage : $acc = $hit->accession(); Function: Retrieve the accession (if available) for the hit Returns : a scalar string (empty string if not set) Args : none =cut =head2 description Title : description Usage : $desc = $hit->description(); Function: Retrieve the description for the hit Returns : a scalar string Args : [optional] scalar string to set the description =cut =head2 length Title : length Usage : my $len = $hit->length Function: Returns the length of the hit Returns : integer Args : [optional] integer to set the length =cut =head2 algorithm Title : algorithm Usage : $alg = $hit->algorithm(); Function: Gets the algorithm specification that was used to obtain the hit For BLAST, the algorithm denotes what type of sequence was aligned against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated dna-prt, TBLASTN prt-translated dna, TBLASTX translated dna-translated dna). Returns : a scalar string Args : [optional] scalar string to set the algorithm =cut =head2 raw_score Title : raw_score Usage : $score = $hit->raw_score(); Function: Gets the "raw score" generated by the algorithm. What this score is exactly will vary from algorithm to algorithm, returning undef if unavailable. Returns : a scalar value Args : [optional] scalar value to set the raw score =cut =head2 score Equivalent to L =cut =head2 significance Title : significance Usage : $significance = $hit->significance(); Function: Used to obtain the E or P value of a hit, i.e. the probability that this particular hit was obtained purely by random chance. If information is not available (nor calculatable from other information sources), return undef. Returns : a scalar value or undef if unavailable Args : [optional] scalar value to set the significance =cut =head2 bits Usage : $hit_object->bits(); Purpose : Gets the bit score of the best HSP for the current hit. Example : $bits = $hit_object->bits(); Returns : Integer or undef if bit score is not set Argument : n/a Comments : For BLAST1, the non-bit score is listed in the summary line. See Also : L =cut =head2 next_hsp Title : next_hsp Usage : while( $hsp = $obj->next_hsp()) { ... } Function : Returns the next available High Scoring Pair Example : Returns : Bio::Search::HSP::HSPI object or null if finished Args : none =cut =head2 hsps Usage : $hit_object->hsps(); Purpose : Get a list containing all HSP objects. : Get the numbers of HSPs for the current hit. Example : @hsps = $hit_object->hsps(); : $num = $hit_object->hsps(); # alternatively, use num_hsps() Returns : Array context : list of Bio::Search::HSP::BlastHSP.pm objects. : Scalar context: integer (number of HSPs). : (Equivalent to num_hsps()). Argument : n/a. Relies on wantarray Throws : Exception if the HSPs have not been collected. See Also : L, L =cut =head2 num_hsps Usage : $hit_object->num_hsps(); Purpose : Get the number of HSPs for the present hit. Example : $nhsps = $hit_object->num_hsps(); Returns : Integer or '-' if HSPs have not been callected Argument : n/a See Also : L =cut =head2 rewind Title : rewind Usage : $hit->rewind; Function: Allow one to reset the HSP iterator to the beginning Since this is an in-memory implementation Returns : none Args : none =cut =head2 ambiguous_aln Usage : $ambig_code = $hit_object->ambiguous_aln(); Purpose : Sets/Gets ambiguity code data member. Example : (see usage) Returns : String = 'q', 's', 'qs', '-' : 'q' = query sequence contains overlapping sub-sequences : while sbjct does not. : 's' = sbjct sequence contains overlapping sub-sequences : while query does not. : 'qs' = query and sbjct sequence contains overlapping sub-sequences : relative to each other. : '-' = query and sbjct sequence do not contains multiple domains : relative to each other OR both contain the same distribution : of similar domains. Argument : n/a Throws : n/a Comment : Note: "sbjct" is synonymous with "hit" =cut =head2 overlap See documentation in L =cut sub overlap { my $self = shift; $self->{'_overlap'} = shift if @_; return exists $self->{'_overlap'} ? $self->{'_overlap'} : 0; } =head2 n Usage : $hit_object->n(); Purpose : Gets the N number for the current hit. : This is the number of HSPs in the set which was ascribed : the lowest P-value (listed on the description line). : This number is not the same as the total number of HSPs. : To get the total number of HSPs, use num_hsps(). Example : $n = $hit_object->n(); Returns : Integer Argument : n/a Throws : Exception if HSPs have not been set. Comments : Calling n() on such reports will result in a call to num_hsps(). : The num_hsps() method will count the actual number of : HSPs in the alignment listing, which may exceed N in : some cases. See Also : L =cut sub n { my $self = shift; $self->{'_n'} = shift if @_; return exists $self->{'_n'} ? $self->{'_n'} : $self->num_hsps; } =head2 p Usage : $hit_object->p( [format] ); Purpose : Get the P-value for the best HSP Example : $p = $sbjct->p; : $p = $sbjct->p('exp'); # get exponent only. : ($num, $exp) = $sbjct->p('parts'); # split sci notation into parts Returns : Float or scientific notation number (the raw P-value, DEFAULT). : Integer if format == 'exp' (the magnitude of the base 10 exponent). : 2-element list (float, int) if format == 'parts' and P-value : is in scientific notation (See Comments). Argument : format: string of 'raw' | 'exp' | 'parts' : 'raw' returns value given in report. Default. (1.2e-34) : 'exp' returns exponent value only (34) : 'parts' returns the decimal and exponent as a : 2-element list (1.2, -34) (See Comments). Throws : Warns if no P-value is defined. Uses expect instead. Comments : Using the 'parts' argument is not recommended since it will not : work as expected if the P-value is not in scientific notation. : That is, floats are not converted into sci notation before : splitting into parts. See Also : L, L, L =cut =head2 hsp Usage : $hit_object->hsp( [string] ); Purpose : Get a single HSPI object for the present HitI object. Example : $hspObj = $hit_object->hsp; # same as 'best' : $hspObj = $hit_object->hsp('best'); : $hspObj = $hit_object->hsp('worst'); Returns : Object reference for a Bio::Search::HSP::BlastHSP.pm object. Argument : String (or no argument). : No argument (default) = highest scoring HSP (same as 'best'). : 'best' or 'first' = highest scoring HSP. : 'worst' or 'last' = lowest scoring HSP. Throws : Exception if the HSPs have not been collected. : Exception if an unrecognized argument is used. See Also : L, L() =cut sub hsp { my( $self, $option ) = @_; $option ||= 'best'; if (not ref $self->{'_hsps'}) { $self->throw("Can't get HSPs: data not collected."); } my @hsps = $self->hsps; return $hsps[0] if $option =~ /best|first|1/i; return $hsps[$#hsps] if $option =~ /worst|last/i; $self->throw("Can't get HSP for: $option\n" . "Valid arguments: 'best', 'worst'"); } =head2 rank Title : rank Usage : $obj->rank($newval) Function: Get/Set the rank of this Hit in the Query search list i.e. this is the Nth hit for a specific query Returns : value of rank Args : newvalue (optional) =cut sub rank { my $self = shift; return $self->{'_rank'} = shift if @_; return $self->{'_rank'} || 1; } =head2 locus Title : locus Usage : $locus = $hit->locus(); Function: Retrieve the locus (if available) for the hit Returns : a scalar string (empty string if not set) Args : none =cut sub locus { my ($self,$value) = @_; my $previous = $self->{'_locus'}; if( defined $value || ! defined $previous ) { unless (defined $value) { if ($self->{'_name'} =~/(gb|emb|dbj|ref)\|(.*)\|(.*)/) { $value = $previous = $3; } else { $value = $previous = ''; } } $self->{'_locus'} = $value; } return $previous; } =head2 each_accession_number Title : each_accession_number Usage : @each_accession_number = $hit->each_accession_number(); Function: Get each accession number listed in the description of the hit. If there are no alternatives, then only the primary accession will be given Returns : list of all accession numbers in the description Args : none =cut sub each_accession_number { my ($self,$value) = @_; my $desc = $self->{'_description'}; #put primary accnum on the list my @accnums; push (@accnums,$self->{'_accession'}); if( defined $desc ) { while ($desc =~ /(\b\S+\|\S*\|\S*\s?)/g) { my $id = $1; my ($acc, $version); if ($id =~ /(gb|emb|dbj|sp|pdb|bbs|ref|tp[gde])\|(.*)\|(.*)/) { ($acc, $version) = split /\./, $2; } elsif ($id =~ /(pir|prf|pat|gnl)\|(.*)\|(.*)/) { ($acc, $version) = split /\./, $3; } elsif( $id =~ /(gim|gi|bbm|bbs|lcl)\|(\d*)/) { $acc = $id; } elsif( $id =~ /(oth)\|(.*)\|(.*)\|(.*)/ ) { # discontinued... ($acc,$version) = ($2); } else { #punt, not matching the db's at ftp://ftp.ncbi.nih.gov/blast/db/README #Database Name Identifier Syntax #============================ ======================== #GenBank gb|accession|locus #EMBL Data Library emb|accession|locus #DDBJ, DNA Database of Japan dbj|accession|locus #NBRF PIR pir||entry #Protein Research Foundation prf||name #SWISS-PROT sp|accession|entry name #Brookhaven Protein Data Bank pdb|entry|chain #Patents pat|country|number #GenInfo Backbone Id bbs|number #General database identifier gnl|database|identifier #NCBI Reference Sequence ref|accession|locus #Local Sequence identifier lcl|identifier $acc=$id; } push(@accnums, $acc); } } return @accnums; } =head2 tiled_hsps See documentation in L =cut =head2 query_length Title : query_length Usage : $obj->query_length($newval) Function: Get/Set the query_length Returns : value of query_length (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub query_length { my $self = shift; return $self->{'_query_length'} = shift if @_; return $self->{'_query_length'}; } =head2 ncbi_gi Title : ncbi_gi Usage : $acc = $hit->ncbi_gi(); Function: Retrieve the NCBI Unique ID (aka the GI #), if available, for the hit Returns : a scalar string (empty string if not set) Args : none Note : As of Sept. 2016 NCBI records will no longer have a GI; this attributue will remain in place for older records =cut sub ncbi_gi { my ($self,$value) = @_; my $previous = $self->{'_ncbi_gi'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_ncbi_gi'} = $value; } return $previous; } =head1 ModelHit methods overridden in ModelHit The following methods have been overridden due to their current reliance on sequence-based queries. They may be implemented in future versions of this class. =head2 length_aln =cut sub length_aln { my $self = shift; $self->warn('$hit->length_aln not implemented for Model-based searches'); return; } =head2 gaps =cut sub gaps { my $self = shift; $self->warn('$hit->gaps not implemented for Model-based searches'); return; } =head2 matches =cut sub matches { my $self = shift; $self->warn('$hit->matches not implemented for Model-based searches'); return; } =head2 start =cut sub start { my $self = shift; $self->warn('$hit->start not implemented for Model-based searches'); return; } =head2 end =cut sub end { my $self = shift; $self->warn('$hit->end not implemented for Model-based searches'); return; } =head2 range =cut sub range { my $self = shift; $self->warn('$hit->range not implemented for Model-based searches'); return; } =head2 frac_identical =cut sub frac_identical { my $self = shift; $self->warn('$hit->frac_identical not implemented for Model-based searches'); return; } =head2 frac_conserved =cut sub frac_conserved { my $self = shift; $self->warn('$hit->frac_conserved not implemented for Model-based searches'); return; } =head2 frac_aligned_query =cut sub frac_aligned_query { my $self = shift; $self->warn('$hit->frac_aligned_query not implemented for Model-based searches'); return; } =head2 frac_aligned_hit =cut sub frac_aligned_hit { my $self = shift; $self->warn('$hit->frac_aligned_hit not implemented for Model-based searches'); return; } =head2 num_unaligned_hit =cut *num_unaligned_sbjct = \&num_unaligned_hit; sub num_unaligned_hit { my $self = shift; $self->warn('$hit->num_unaligned_hit/num_unaligned_sbjct not implemented for Model-based searches'); return; } =head2 num_unaligned_query =cut sub num_unaligned_query { my $self = shift; $self->warn('$hit->num_unaligned_query not implemented for Model-based searches'); return; } =head2 seq_inds =cut sub seq_inds { my $self = shift; $self->warn('$hit->seq_inds not implemented for Model-based searches'); return; } =head2 strand =cut sub strand { my $self = shift; $self->warn('$hit->strand not implemented for Model-based searches'); return; } =head2 frame =cut sub frame { my $self = shift; $self->warn('$hit->frame not implemented for Model-based searches'); return; } =head2 logical_length =cut sub logical_length { my $self = shift; $self->warn('$hit->logical_length not implemented for Model-based searches'); return; } 1; BioPerl-1.007002/Bio/Search/Hit/PsiBlastHit.pm000444000766000024 20775313155576320 20757 0ustar00cjfieldsstaff000000000000#----------------------------------------------------------------- # # BioPerl module Bio::Search::Hit::PsiBlastHit # # (This module was originally called Bio::Tools::Blast::Sbjct) # # Please direct questions and support issues to # # Cared for by Steve Chervitz # # You may distribute this module under the same terms as perl itself #----------------------------------------------------------------- ## POD Documentation: =head1 NAME Bio::Search::Hit::PsiBlastHit - Bioperl BLAST Hit object =head1 SYNOPSIS See L. =head1 DESCRIPTION The Bio::Search::Hit::PsiBlastHit.pm module encapsulates data and methods for manipulating "hits" from a BLAST report. A BLAST hit is a collection of HSPs along with other metadata such as sequence name and score information. Hit objects are accessed via L objects after parsing a BLAST report using the L system. In Blast lingo, the "sbjct" sequences are all the sequences in a target database which were compared against a "query" sequence. The terms "sbjct" and "hit" will be used interchangeably in this module. All methods that take 'sbjct' as an argument also support 'hit' as a synonym. This module supports BLAST versions 1.x and 2.x, gapped and ungapped, and PSI-BLAST. The construction of PsiBlastHit objects is performed by Bio::SearchIO::blast::PsiBlastHitFactory in a process that is orchestrated by the Blast parser (L). The resulting PsiBlastHits are then accessed via L). Therefore, you do not need to use L) directly. If you need to construct PsiBlastHits directly, see the C function for details. For L BLAST parsing usage examples, see the C directory of the Bioperl distribution. =head2 HSP Tiling and Ambiguous Alignments If a Blast hit has more than one HSP, the Bio::Search::Hit::PsiBlastHit.pm object has the ability to merge overlapping HSPs into contiguous blocks. This permits the PsiBlastHit object to sum data across all HSPs without counting data in the overlapping regions multiple times, which would happen if data from each overlapping HSP are simply summed. HSP tiling is performed automatically when methods of the PsiBlastHit object that rely on tiled data are invoked. These include L, L, L, L, L, L, L. It also permits the assessment of an "ambiguous alignment" if the query (or sbjct) sequences from different HSPs overlap (see L). The existence of an overlap could indicate a biologically interesting region in the sequence, such as a repeated domain. The PsiBlastHit object uses the C<-OVERLAP> parameter to determine when two sequences overlap; if this is set to 2 -- the default -- then any two sbjct or query HSP sequences must overlap by more than two residues to get merged into the same contig and counted as an overlap. See the L section below for "issues" with HSP tiling. The results of the HSP tiling is reported with the following ambiguity codes: 'q' = Query sequence contains multiple sub-sequences matching a single region in the sbjct sequence. 's' = Subject (PsiBlastHit) sequence contains multiple sub-sequences matching a single region in the query sequence. 'qs' = Both query and sbjct sequences contain more than one sub-sequence with similarity to the other sequence. For addition information about ambiguous BLAST alignments, see L =head1 DEPENDENCIES Bio::Search::Hit::PsiBlastHit.pm is a concrete class that inherits from L and L. and relies on L. =head1 BUGS One consequence of the HSP tiling is that methods that rely on HSP tiling such as L, L, L etc. may report misleading numbers when C<-OVERLAP> is set to a large number. For example, say we have two HSPs and the query sequence tile as follows: 1 8 22 30 40 60 Full seq: ------------------------------------------------------------ * ** * ** HSP1: --------------- (6 identical matches) ** ** ** HSP2: ------------- (6 identical matches) If C<-OVERLAP> is set to some number over 4, HSP1 and HSP2 will not be tiled into a single contig and their numbers of identical matches will be added, giving a total of 12, not 10 if they had be combined into one contig. This can lead to number greater than 1.0 for methods L and L. This is less of an issue with gapped Blast since it tends to combine HSPs that would be listed separately without gapping. (Fractions E1.0 can be viewed as a signal for an interesting alignment that warrants further inspection, thus turning this bug into a feature :-). Using large values for C<-OVERLAP> can lead to incorrect numbers reported by methods that rely on HSP tiling but can be useful if you care more about detecting ambiguous alignments. Setting C<-OVERLAP> to zero will lead to the most accurate numbers for the tiling-dependent methods but will be useless for detecting overlapping HSPs since all HSPs will appear to overlap. =head1 SEE ALSO Bio::Search::HSP::BlastHSP.pm - Blast HSP object. Bio::Search::Result::BlastResult.pm - Blast Result object. Bio::Search::Hit::HitI.pm - Interface implemented by PsiBlastHit.pm Bio::Root::Root.pm - Base class for PsiBlastHit.pm Links: http://bio.perl.org/ - Bioperl Project Homepage =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Steve Chervitz Esac@bioperl.orgE See L for where to send bug reports and comments. =head1 ACKNOWLEDGEMENTS This software was originally developed in the Department of Genetics at Stanford University. I would also like to acknowledge my colleagues at Affymetrix for useful feedback. =head1 COPYRIGHT Copyright (c) 1996-2001 Steve Chervitz. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Hit::PsiBlastHit; use strict; use Bio::Search::BlastUtils; use vars qw(%SUMMARY_OFFSET); use overload '""' => \&to_string; use base qw(Bio::Root::Root Bio::Search::Hit::HitI); =head2 new Usage : $hit = Bio::Search::Hit::PsiBlastHit->new( %named_params ); : Bio::Search::Hit::PsiBlastHit.pm objects are constructed : automatically by Bio::SearchIO::PsiBlastHitFactory.pm, : so there is no need for direct instantiation. Purpose : Constructs a new PsiBlastHit object and Initializes key variables : for the hit. Returns : A Bio::Search::Hit::PsiBlastHit object Argument : Named Parameters: : Parameter keys are case-insensitive. : -RAW_DATA => array reference holding raw BLAST report data : for a single hit. This includes all lines : within the HSP alignment listing section of a : traditional BLAST or PSI-BLAST (non-XML) report, : starting at (or just after) the leading '>'. : -HOLD_RAW_DATA => boolean, should -RAW_DATA be saved within the object. : -QUERY_LEN => Length of the query sequence : -ITERATION => integer (PSI-BLAST iteration number in which hit was found) : -OVERLAP => integer (maximum overlap between adjacent : HSPs when tiling) : -PROGRAM => string (type of Blast: BLASTP, BLASTN, etc) : -SIGNIF => significance : -IS_PVAL => boolean, true if -SIGNIF contains a P-value : -SCORE => raw BLAST score : -FOUND_AGAIN => boolean, true if this was a hit from the : section of a PSI-BLAST with iteration > 1 : containing sequences that were also found : in iteration 1. Comments : This object accepts raw Blast report data not because it : is required for parsing, but in order to retrieve it : (only available if -HOLD_RAW_DATA is set to true). See Also : L, L =cut #------------------- sub new { #------------------- my ($class, @args ) = @_; my $self = $class->SUPER::new( @args ); my ($raw_data, $signif, $is_pval, $hold_raw); ($self->{'_blast_program'}, $self->{'_query_length'}, $raw_data, $hold_raw, $self->{'_overlap'}, $self->{'_iteration'}, $signif, $is_pval, $self->{'_score'}, $self->{'_found_again'} ) = $self->_rearrange( [qw(PROGRAM QUERY_LEN RAW_DATA HOLD_RAW_DATA OVERLAP ITERATION SIGNIF IS_PVAL SCORE FOUND_AGAIN )], @args ); # TODO: Handle this in parser. Just pass in name parameter. $self->_set_id( $raw_data->[0] ); if($is_pval) { $self->{'_p'} = $signif; } else { $self->{'_expect'} = $signif; } if( $hold_raw ) { $self->{'_hit_data'} = $raw_data; } return $self; } sub DESTROY { my $self=shift; #print STDERR "-->DESTROYING $self\n"; } #================================================= # Begin Bio::Search::Hit::HitI implementation #================================================= =head2 algorithm Title : algorithm Usage : $alg = $hit->algorithm(); Function: Gets the algorithm specification that was used to obtain the hit For BLAST, the algorithm denotes what type of sequence was aligned against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated dna-prt, TBLASTN prt-translated dna, TBLASTX translated dna-translated dna). Returns : a scalar string Args : none =cut #---------------- sub algorithm { #---------------- my ($self,@args) = @_; return $self->{'_blast_program'}; } =head2 name Usage : $hit->name([string]); Purpose : Set/Get a string to identify the hit. Example : $name = $hit->name; : $hit->name('M81707'); Returns : String consisting of the hit's name or undef if not set. Comments : The name is parsed out of the "Query=" line as the first chunk of non-whitespace text. If you want the rest of the line, use $hit->description(). See Also: L =cut #' #---------------- sub name { #---------------- my $self = shift; if (@_) { my $name = shift; $name =~ s/^\s+|(\s+|,)$//g; $self->{'_name'} = $name; } return $self->{'_name'}; } =head2 description Usage : $hit_object->description( [integer] ); Purpose : Set/Get a description string for the hit. This is parsed out of the "Query=" line as everything after the first chunk of non-whitespace text. Use $hit->name() to get the first chunk (the ID of the sequence). Example : $description = $hit->description; : $desc_60char = $hit->description(60); Argument : Integer (optional) indicating the desired length of the : description string to be returned. Returns : String consisting of the hit's description or undef if not set. =cut #' #---------------- sub description { #---------------- my( $self, $len ) = @_; $len = (defined $len) ? $len : (CORE::length $self->{'_description'}); return substr( $self->{'_description'}, 0 ,$len ); } =head2 accession Title : accession Usage : $acc = $hit->accession(); Function: Retrieve the accession (if available) for the hit Returns : a scalar string (empty string if not set) Args : none Comments: Accession numbers are extracted based on the assumption that they are delimited by | characters (NCBI-style). If this is not the case, use the name() method and parse it as necessary. See Also: L =cut #-------------------- sub accession { #-------------------- my $self = shift; if(@_) { $self->{'_accession'} = shift; } $self->{'_accession'} || ''; } =head2 raw_score Usage : $hit_object->raw_score(); Purpose : Gets the BLAST score of the best HSP for the current Blast hit. Example : $score = $hit_object->raw_score(); Returns : Integer Argument : n/a Throws : n/a See Also : L =cut #---------- sub raw_score { #---------- my $self = shift; # The check for $self->{'_score'} is a remnant from the 'query' mode days # in which the sbjct object would collect data from the description line only. my ($score); if(not defined($self->{'_score'})) { $score = $self->hsp->score; } else { $score = $self->{'_score'}; } return $score; } =head2 length Usage : $hit_object->length(); Purpose : Get the total length of the hit sequence. Example : $len = $hit_object->length(); Returns : Integer Argument : n/a Throws : n/a Comments : Developer note: when using the built-in length function within : this module, call it as CORE::length(). See Also : L, L =cut #----------- sub length { #----------- my $self = shift; return $self->{'_length'}; } =head2 significance Equivalent to L =cut #---------------- sub significance { shift->signif( @_ ); } #---------------- =head2 next_hsp Title : next_hsp Usage : $hsp = $obj->next_hsp(); Function : returns the next available High Scoring Pair object Example : Returns : Bio::Search::HSP::BlastHSP or undef if finished Args : none =cut #---------------- sub next_hsp { #---------------- my $self = shift; unless($self->{'_hsp_queue_started'}) { $self->{'_hsp_queue'} = [$self->hsps()]; $self->{'_hsp_queue_started'} = 1; } pop @{$self->{'_hsp_queue'}}; } #================================================= # End Bio::Search::Hit::HitI implementation #================================================= # Providing a more explicit method for getting name of hit # (corresponds with column name in HitTableWriter) #---------------- sub hit_name { #---------------- my $self = shift; $self->name( @_ ); } # Older method Delegates to description() #---------------- sub desc { #---------------- my $self = shift; return $self->description( @_ ); } # Providing a more explicit method for getting description of hit # (corresponds with column name in HitTableWriter) #---------------- sub hit_description { #---------------- my $self = shift; return $self->description( @_ ); } =head2 score Equivalent to L =cut #---------------- sub score { shift->raw_score( @_ ); } #---------------- =head2 hit_length Equivalent to L =cut # Providing a more explicit method for getting length of hit #---------------- sub hit_length { shift->length( @_ ); } #---------------- =head2 signif Usage : $hit_object->signif( [format] ); Purpose : Get the P or Expect value for the best HSP of the given BLAST hit. : The value returned is the one which is reported in the description : section of the Blast report. For Blast1 and WU-Blast2, this : is a P-value, for Blast2, it is an Expect value. Example : $obj->signif() # returns 1.3e-34 : $obj->signif('exp') # returns -34 : $obj->signif('parts') # returns (1.3, -34) Returns : Float or scientific notation number (the raw P/Expect value, DEFAULT). : Integer if format == 'exp' (the magnitude of the base 10 exponent). : 2-element list (float, int) if format == 'parts' and P/Expect value : is in scientific notation (see Comments). Argument : format: string of 'raw' | 'exp' | 'parts' : 'raw' returns value given in report. Default. (1.2e-34) : 'exp' returns exponent value only (34) : 'parts' returns the decimal and exponent as a : 2-element list (1.2, -34) (see Comments). Throws : n/a Comments : The signif() method provides a way to deal with the fact that : Blast1 and Blast2 formats (and WU- vs. NCBI-BLAST) differ in : what is reported in the description lines of each hit in the : Blast report. The signif() method frees any client code from : having to know if this is a P-value or an Expect value, : making it easier to write code that can process both : Blast1 and Blast2 reports. This is not necessarily a good thing, : since one should always know when one is working with P-values or : Expect values (hence the deprecated status). : Use of expect() is recommended since all hits will have an Expect value. : : Using the 'parts' argument is not recommended since it will not : work as expected if the expect value is not in scientific notation. : That is, floats are not converted into sci notation before : splitting into parts. See Also : L, L, L =cut #------------- sub signif { #------------- # Some duplication of logic for p(), expect() and signif() for the sake of performance. my ($self, $fmt) = @_; my $val = defined($self->{'_p'}) ? $self->{'_p'} : $self->{'_expect'}; # $val can be zero. defined($val) or $self->throw("Can't get P- or Expect value: HSPs may not have been set."); return $val if not $fmt or $fmt =~ /^raw/i; ## Special formats: exponent-only or as list. return &Bio::Search::BlastUtils::get_exponent($val) if $fmt =~ /^exp/i; return (split (/eE/, $val)) if $fmt =~ /^parts/i; ## Default: return the raw P/Expect-value. return $val; } #---------------- sub raw_hit_data { #---------------- my $self = shift; my $data = '>'; # Need to add blank lines where we've removed them. foreach( @{$self->{'_hit_data'}} ) { if( $_ eq 'end') { $data .= "\n"; } else { $data .= /^\s*(Score|Query)/ ? "\n$_" : $_; } } return $data; } #=head2 _set_length # # Usage : $hit_object->_set_length( "233" ); # Purpose : Set the total length of the hit sequence. # Example : $hit_object->_set_length( $len ); # Returns : n/a # Argument : Integer (only when setting). Any commas will be stripped out. # Throws : n/a # #=cut #----------- sub _set_length { #----------- my ($self, $len) = @_; $len =~ s/,//g; # get rid of commas $self->{'_length'} = $len; } #=head2 _set_description # # Usage : Private method; called automatically during construction # Purpose : Sets the description of the hit sequence. # : For sequence without descriptions, does not set any description. # Argument : Array containing description (multiple lines). # Comments : Processes the supplied description: # 1. Join all lines into one string. # 2. Remove sequence id at the beginning of description. # 3. Removes junk charactes at begin and end of description. # #=cut #-------------- sub _set_description { #-------------- my( $self, @desc ) = @_; my( $desc); # print STDERR "PsiBlastHit: RAW DESC:\n@desc\n"; $desc = join(" ", @desc); my $name = $self->name; if($desc) { $desc =~ s/^\s*\S+\s+//; # remove the sequence ID(s) # This won't work if there's no description. $desc =~ s/^\s*$name//; # ...but this should. $desc =~ s/^[\s!]+//; $desc =~ s/ \d+$//; $desc =~ s/\.+$//; $self->{'_description'} = $desc; } # print STDERR "PsiBlastHit: _set_description = $desc\n"; } =head2 to_string Title : to_string Usage : print $hit->to_string; Function: Returns a string representation for the Blast Hit. Primarily intended for debugging purposes. Example : see usage Returns : A string of the form: [PsiBlastHit] e.g.: [PsiBlastHit] emb|Z46660|SC9725 S.cerevisiae chromosome XIII cosmid Args : None =cut #---------------- sub to_string { #---------------- my $self = shift; return "[PsiBlastHit] " . $self->name . " " . $self->description; } #=head2 _set_id # # Usage : Private method; automatically called by new() # Purpose : Sets the name of the PsiBlastHit sequence from the BLAST summary line. # : The identifier is assumed to be the first # : chunk of non-whitespace characters in the description line # : Does not assume any semantics in the structure of the identifier # : (Formerly, this method attempted to extract database name from # : the seq identifiers, but this was prone to break). # Returns : n/a # Argument : String containing description line of the hit from Blast report # : or first line of an alignment section (with or without the leading '>'). # Throws : Warning if cannot locate sequence ID. # #See Also : L, L # #=cut #--------------- sub _set_id { #--------------- my( $self, $desc ) = @_; # New strategy: Assume only that the ID is the first white space # delimited chunk. Not attempting to extract accession & database name. # Clients will have to interpret it as necessary. if($desc =~ /^>?(\S+)\s*(.*)/) { my ($name, $desc) = ($1, $2); $self->name($name); $self->{'_description'} = $desc; # Note that this description comes from the summary section of the # BLAST report and so may be truncated. The full description will be # set from the alignment section. We're setting description here in case # the alignment section isn't being parsed. # Assuming accession is delimited with | symbols (NCBI-style) my @pieces = split(/\|/,$name); my $acc = pop @pieces; $self->accession( $acc ); } else { $self->warn("Can't locate sequence identifier in summary line.", "Line = $desc"); $desc = 'Unknown sequence ID' if not $desc; $self->name($desc); } } =head2 ambiguous_aln Usage : $ambig_code = $hit_object->ambiguous_aln(); Purpose : Sets/Gets ambiguity code data member. Example : (see usage) Returns : String = 'q', 's', 'qs', '-' : 'q' = query sequence contains overlapping sub-sequences : while sbjct does not. : 's' = sbjct sequence contains overlapping sub-sequences : while query does not. : 'qs' = query and sbjct sequence contains overlapping sub-sequences : relative to each other. : '-' = query and sbjct sequence do not contains multiple domains : relative to each other OR both contain the same distribution : of similar domains. Argument : n/a Throws : n/a Status : Experimental See Also : L, L =cut #-------------------- sub ambiguous_aln { #-------------------- my $self = shift; if(@_) { $self->{'_ambiguous_aln'} = shift; } $self->{'_ambiguous_aln'} || '-'; } =head2 overlap Usage : $blast_object->overlap( [integer] ); Purpose : Gets/Sets the allowable amount overlap between different HSP sequences. Example : $blast_object->overlap(5); : $overlap = $blast_object->overlap; Returns : Integer. Argument : integer. Throws : n/a Status : Experimental Comments : Any two HSPs whose sequences overlap by less than or equal : to the overlap() number of resides will be considered separate HSPs : and will not get tiled by Bio::Search::BlastUtils::_adjust_contigs(). See Also : L, L =cut #------------- sub overlap { #------------- my $self = shift; if(@_) { $self->{'_overlap'} = shift; } defined $self->{'_overlap'} ? $self->{'_overlap'} : 0; } =head2 bits Usage : $hit_object->bits(); Purpose : Gets the BLAST bit score of the best HSP for the current Blast hit. Example : $bits = $hit_object->bits(); Returns : Integer Argument : n/a Throws : Exception if bit score is not set. Comments : For BLAST1, the non-bit score is listed in the summary line. See Also : L =cut #--------- sub bits { #--------- my $self = shift; # The check for $self->{'_bits'} is a remnant from the 'query' mode days # in which the sbjct object would collect data from the description line only. my ($bits); if(not defined($self->{'_bits'})) { $bits = $self->hsp->bits; } else { $bits = $self->{'_bits'}; } return $bits; } =head2 n Usage : $hit_object->n(); Purpose : Gets the N number for the current Blast hit. : This is the number of HSPs in the set which was ascribed : the lowest P-value (listed on the description line). : This number is not the same as the total number of HSPs. : To get the total number of HSPs, use num_hsps(). Example : $n = $hit_object->n(); Returns : Integer Argument : n/a Throws : Exception if HSPs have not been set (BLAST2 reports). Comments : Note that the N parameter is not reported in gapped BLAST2. : Calling n() on such reports will result in a call to num_hsps(). : The num_hsps() method will count the actual number of : HSPs in the alignment listing, which may exceed N in : some cases. See Also : L =cut #----- sub n { #----- my $self = shift; # The check for $self->{'_n'} is a remnant from the 'query' mode days # in which the sbjct object would collect data from the description line only. my ($n); if(not defined($self->{'_n'})) { $n = $self->hsp->n; } else { $n = $self->{'_n'}; } $n ||= $self->num_hsps; return $n; } =head2 frame Usage : $hit_object->frame(); Purpose : Gets the reading frame for the best HSP after HSP tiling. : This is only valid for BLASTX and TBLASTN/X reports. Example : $frame = $hit_object->frame(); Returns : Integer (-2 .. +2) Argument : n/a Throws : Exception if HSPs have not been set (BLAST2 reports). Comments : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically.. : If you don't want the tiled data, iterate through each HSP : calling frame() on each (use hsps() to get all HSPs). See Also : L =cut #----------' sub frame { #---------- my $self = shift; Bio::Search::BlastUtils::tile_hsps($self) if not $self->{'_tile_hsps'}; # The check for $self->{'_frame'} is a remnant from the 'query' mode days # in which the sbjct object would collect data from the description line only. my ($frame); if(not defined($self->{'_frame'})) { $frame = $self->hsp->frame('hit'); } else { $frame = $self->{'_frame'}; } return $frame; } =head2 p Usage : $hit_object->p( [format] ); Purpose : Get the P-value for the best HSP of the given BLAST hit. : (Note that P-values are not provided with NCBI Blast2 reports). Example : $p = $sbjct->p; : $p = $sbjct->p('exp'); # get exponent only. : ($num, $exp) = $sbjct->p('parts'); # split sci notation into parts Returns : Float or scientific notation number (the raw P-value, DEFAULT). : Integer if format == 'exp' (the magnitude of the base 10 exponent). : 2-element list (float, int) if format == 'parts' and P-value : is in scientific notation (See Comments). Argument : format: string of 'raw' | 'exp' | 'parts' : 'raw' returns value given in report. Default. (1.2e-34) : 'exp' returns exponent value only (34) : 'parts' returns the decimal and exponent as a : 2-element list (1.2, -34) (See Comments). Throws : Warns if no P-value is defined. Uses expect instead. Comments : Using the 'parts' argument is not recommended since it will not : work as expected if the P-value is not in scientific notation. : That is, floats are not converted into sci notation before : splitting into parts. See Also : L, L, L =cut #-------- sub p { #-------- # Some duplication of logic for p(), expect() and signif() for the sake of performance. my ($self, $fmt) = @_; my $val = $self->{'_p'}; # $val can be zero. if(not defined $val) { # P-value not defined, must be a NCBI Blast2 report. # Use expect instead. $self->warn( "P-value not defined. Using expect() instead."); $val = $self->{'_expect'}; } return $val if not $fmt or $fmt =~ /^raw/i; ## Special formats: exponent-only or as list. return &Bio::Search::BlastUtils::get_exponent($val) if $fmt =~ /^exp/i; return (split (/eE/, $val)) if $fmt =~ /^parts/i; ## Default: return the raw P-value. return $val; } =head2 expect Usage : $hit_object->expect( [format] ); Purpose : Get the Expect value for the best HSP of the given BLAST hit. Example : $e = $sbjct->expect; : $e = $sbjct->expect('exp'); # get exponent only. : ($num, $exp) = $sbjct->expect('parts'); # split sci notation into parts Returns : Float or scientific notation number (the raw expect value, DEFAULT). : Integer if format == 'exp' (the magnitude of the base 10 exponent). : 2-element list (float, int) if format == 'parts' and Expect : is in scientific notation (see Comments). Argument : format: string of 'raw' | 'exp' | 'parts' : 'raw' returns value given in report. Default. (1.2e-34) : 'exp' returns exponent value only (34) : 'parts' returns the decimal and exponent as a : 2-element list (1.2, -34) (see Comments). Throws : Exception if the Expect value is not defined. Comments : Using the 'parts' argument is not recommended since it will not : work as expected if the expect value is not in scientific notation. : That is, floats are not converted into sci notation before : splitting into parts. See Also : L, L, L =cut #----------- sub expect { #----------- # Some duplication of logic for p(), expect() and signif() for the sake of performance. my ($self, $fmt) = @_; my $val; # For Blast reports that list the P value on the description line, # getting the expect value requires fully parsing the HSP data. # For NCBI blast, there's no problem. if(not defined($self->{'_expect'})) { if( defined $self->{'_hsps'}) { $self->{'_expect'} = $val = $self->hsp->expect; } else { # If _expect is not set and _hsps are not set, # then this must be a P-value-based report that was # run without setting the HSPs (shallow parsing). $self->throw("Can't get expect value. HSPs have not been set."); } } else { $val = $self->{'_expect'}; } # $val can be zero. defined($val) or $self->throw("Can't get Expect value."); return $val if not $fmt or $fmt =~ /^raw/i; ## Special formats: exponent-only or as list. return &Bio::Search::BlastUtils::get_exponent($val) if $fmt =~ /^exp/i; return (split (/eE/, $val)) if $fmt =~ /^parts/i; ## Default: return the raw Expect-value. return $val; } =head2 hsps Usage : $hit_object->hsps(); Purpose : Get a list containing all HSP objects. : Get the numbers of HSPs for the current hit. Example : @hsps = $hit_object->hsps(); : $num = $hit_object->hsps(); # alternatively, use num_hsps() Returns : Array context : list of Bio::Search::HSP::BlastHSP.pm objects. : Scalar context: integer (number of HSPs). : (Equivalent to num_hsps()). Argument : n/a. Relies on wantarray Throws : Exception if the HSPs have not been collected. See Also : L, L =cut #--------- sub hsps { #--------- my $self = shift; if (not ref $self->{'_hsps'}) { $self->throw("Can't get HSPs: data not collected."); } return wantarray # returning list containing all HSPs. ? @{$self->{'_hsps'}} # returning number of HSPs. : scalar(@{$self->{'_hsps'}}); } =head2 hsp Usage : $hit_object->hsp( [string] ); Purpose : Get a single BlastHSP.pm object for the present PsiBlastHit.pm object. Example : $hspObj = $hit_object->hsp; # same as 'best' : $hspObj = $hit_object->hsp('best'); : $hspObj = $hit_object->hsp('worst'); Returns : Object reference for a Bio::Search::HSP::BlastHSP.pm object. Argument : String (or no argument). : No argument (default) = highest scoring HSP (same as 'best'). : 'best' or 'first' = highest scoring HSP. : 'worst' or 'last' = lowest scoring HSP. Throws : Exception if the HSPs have not been collected. : Exception if an unrecognized argument is used. See Also : L, L() =cut #---------- sub hsp { #---------- my( $self, $option ) = @_; $option ||= 'best'; if (not ref $self->{'_hsps'}) { $self->throw("Can't get HSPs: data not collected."); } my @hsps = @{$self->{'_hsps'}}; return $hsps[0] if $option =~ /best|first|1/i; return $hsps[$#hsps] if $option =~ /worst|last/i; $self->throw("Can't get HSP for: $option\n" . "Valid arguments: 'best', 'worst'"); } =head2 num_hsps Usage : $hit_object->num_hsps(); Purpose : Get the number of HSPs for the present Blast hit. Example : $nhsps = $hit_object->num_hsps(); Returns : Integer Argument : n/a Throws : Exception if the HSPs have not been collected. See Also : L =cut #------------- sub num_hsps { #------------- my $self = shift; if (not defined $self->{'_hsps'}) { $self->throw("Can't get HSPs: data not collected."); } return scalar(@{$self->{'_hsps'}}); } =head2 logical_length Usage : $hit_object->logical_length( [seq_type] ); : (mostly intended for internal use). Purpose : Get the logical length of the hit sequence. : For query sequence of BLASTX and TBLASTX reports and the hit : sequence of TBLASTN and TBLASTX reports, the returned length : is the length of the would-be amino acid sequence (length/3). : For all other BLAST flavors, this function is the same as length(). Example : $len = $hit_object->logical_length(); Returns : Integer Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is synonymous with 'hit') Throws : n/a Comments : This is important for functions like frac_aligned_query() : which need to operate in amino acid coordinate space when dealing : with T?BLASTX type reports. See Also : L, L, L =cut #-------------------- sub logical_length { #-------------------- my $self = shift; my $seqType = shift || 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; my $length; # For the sbjct, return logical sbjct length if( $seqType eq 'sbjct' ) { $length = $self->{'_logical_length'} || $self->{'_length'}; } else { # Otherwise, return logical query length $length = $self->{'_query_length'}; # Adjust length based on BLAST flavor. if($self->{'_blast_program'} =~ /T?BLASTX/ ) { $length /= 3; } } return $length; } =head2 length_aln Usage : $hit_object->length_aln( [seq_type] ); Purpose : Get the total length of the aligned region for query or sbjct seq. : This number will include all HSPs Example : $len = $hit_object->length_aln(); # default = query : $lenAln = $hit_object->length_aln('query'); Returns : Integer Argument : seq_Type = 'query' or 'hit' or 'sbjct' (Default = 'query') ('sbjct' is synonymous with 'hit') Throws : Exception if the argument is not recognized. Comments : This method will report the logical length of the alignment, : meaning that for TBLAST[NX] reports, the length is reported : using amino acid coordinate space (i.e., nucleotides / 3). : : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically.. : If you don't want the tiled data, iterate through each HSP : calling length() on each (use hsps() to get all HSPs). See Also : L, L, L, L, L, L =cut #---------------' sub length_aln { #--------------- my( $self, $seqType ) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; Bio::Search::BlastUtils::tile_hsps($self) if not $self->{'_tile_hsps'}; my $data = $self->{'_length_aln_'.$seqType}; ## If we don't have data, figure out what went wrong. if(!$data) { $self->throw("Can't get length aln for sequence type \"$seqType\"" . "Valid types are 'query', 'hit', 'sbjct' ('sbjct' = 'hit')"); } $data; } =head2 gaps Usage : $hit_object->gaps( [seq_type] ); Purpose : Get the number of gaps in the aligned query, sbjct, or both sequences. : Data is summed across all HSPs. Example : $qgaps = $hit_object->gaps('query'); : $hgaps = $hit_object->gaps('hit'); : $tgaps = $hit_object->gaps(); # default = total (query + hit) Returns : scalar context: integer : array context without args: two-element list of integers : (queryGaps, sbjctGaps) : Array context can be forced by providing an argument of 'list' or 'array'. : : CAUTION: Calling this method within printf or sprintf is arrray context. : So this function may not give you what you expect. For example: : printf "Total gaps: %d", $hit->gaps(); : Actually returns a two-element array, so what gets printed : is the number of gaps in the query, not the total : Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total' | 'list' (default = 'total') ('sbjct' is synonymous with 'hit') Throws : n/a Comments : If you need data for each HSP, use hsps() and then interate : through each HSP object. : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically.. : Not relying on wantarray since that will fail in situations : such as printf "%d", $hit->gaps() in which you might expect to : be printing the total gaps, but evaluates to array context. See Also : L =cut #---------- sub gaps { #---------- my( $self, $seqType ) = @_; $seqType ||= (wantarray ? 'list' : 'total'); $seqType = 'sbjct' if $seqType eq 'hit'; Bio::Search::BlastUtils::tile_hsps($self) if not $self->{'_tile_hsps'}; $seqType = lc($seqType); if($seqType =~ /list|array/i) { return ($self->{'_gaps_query'}, $self->{'_gaps_sbjct'}); } if($seqType eq 'total') { return ($self->{'_gaps_query'} + $self->{'_gaps_sbjct'}) || 0; } else { return $self->{'_gaps_'.$seqType} || 0; } } =head2 matches Usage : $hit_object->matches( [class] ); Purpose : Get the total number of identical or conserved matches : (or both) across all HSPs. : (Note: 'conservative' matches are indicated as 'positives' : in the Blast report.) Example : ($id,$cons) = $hit_object->matches(); # no argument : $id = $hit_object->matches('id'); : $cons = $hit_object->matches('cons'); Returns : Integer or a 2-element array of integers Argument : class = 'id' | 'cons' OR none. : If no argument is provided, both identical and conservative : numbers are returned in a two element list. : (Other terms can be used to refer to the conservative : matches, e.g., 'positive'. All that is checked is whether or : not the supplied string starts with 'id'. If not, the : conservative matches are returned.) Throws : Exception if the requested data cannot be obtained. Comments : If you need data for each HSP, use hsps() and then interate : through the HSP objects. : Does not rely on wantarray to return a list. Only checks for : the presence of an argument (no arg = return list). See Also : L, L =cut #--------------- sub matches { #--------------- my( $self, $arg) = @_; my(@data,$data); if(!$arg) { @data = ($self->{'_totalIdentical'}, $self->{'_totalConserved'}); return @data if @data; } else { if($arg =~ /^id/i) { $data = $self->{'_totalIdentical'}; } else { $data = $self->{'_totalConserved'}; } return $data if $data; } ## Something went wrong if we make it to here. $self->throw("Can't get identical or conserved data: no data."); } =head2 start Usage : $sbjct->start( [seq_type] ); Purpose : Gets the start coordinate for the query, sbjct, or both sequences : in the PsiBlastHit object. If there is more than one HSP, the lowest start : value of all HSPs is returned. Example : $qbeg = $sbjct->start('query'); : $sbeg = $sbjct->start('hit'); : ($qbeg, $sbeg) = $sbjct->start(); Returns : scalar context: integer : array context without args: list of two integers (queryStart, sbjctStart) : Array context can be "induced" by providing an argument of 'list' or 'array'. Argument : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is synonymous with 'hit') Throws : n/a Comments : This method requires that all HSPs be tiled. If there is more than one : HSP and they have not already been tiled, they will be tiled first automatically.. : Remember that the start and end coordinates of all HSPs are : normalized so that start < end. Strand information can be : obtained by calling $hit->strand(). See Also : L, L, L, L, L =cut #---------- sub start { #---------- my ($self, $seqType) = @_; $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; # If there is only one HSP, defer this call to the solitary HSP. if($self->num_hsps == 1) { return $self->hsp->start($seqType); } else { Bio::Search::BlastUtils::tile_hsps($self) if not $self->{'_tile_hsps'}; if($seqType =~ /list|array/i) { return ($self->{'_queryStart'}, $self->{'_sbjctStart'}); } else { ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; return $self->{$seqType.'Start'}; } } } =head2 end Usage : $sbjct->end( [seq_type] ); Purpose : Gets the end coordinate for the query, sbjct, or both sequences : in the PsiBlastHit object. If there is more than one HSP, the largest end : value of all HSPs is returned. Example : $qend = $sbjct->end('query'); : $send = $sbjct->end('hit'); : ($qend, $send) = $sbjct->end(); Returns : scalar context: integer : array context without args: list of two integers (queryEnd, sbjctEnd) : Array context can be "induced" by providing an argument of 'list' or 'array'. Argument : In scalar context: seq_type = 'query' or 'sbjct' : (case insensitive). If not supplied, 'query' is used. Throws : n/a Comments : This method requires that all HSPs be tiled. If there is more than one : HSP and they have not already been tiled, they will be tiled first automatically.. : Remember that the start and end coordinates of all HSPs are : normalized so that start < end. Strand information can be : obtained by calling $hit->strand(). See Also : L, L, L, L, L =cut #---------- sub end { #---------- my ($self, $seqType) = @_; $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; # If there is only one HSP, defer this call to the solitary HSP. if($self->num_hsps == 1) { return $self->hsp->end($seqType); } else { Bio::Search::BlastUtils::tile_hsps($self) if not $self->{'_tile_hsps'}; if($seqType =~ /list|array/i) { return ($self->{'_queryStop'}, $self->{'_sbjctStop'}); } else { ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; return $self->{$seqType.'Stop'}; } } } =head2 range Usage : $sbjct->range( [seq_type] ); Purpose : Gets the (start, end) coordinates for the query or sbjct sequence : in the HSP alignment. Example : ($qbeg, $qend) = $sbjct->range('query'); : ($sbeg, $send) = $sbjct->range('hit'); Returns : Two-element array of integers Argument : seq_type = string, 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is synonymous with 'hit') Throws : n/a See Also : L, L =cut #---------- sub range { #---------- my ($self, $seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; return ($self->start($seqType), $self->end($seqType)); } =head2 frac_identical Usage : $hit_object->frac_identical( [seq_type] ); Purpose : Get the overall fraction of identical positions across all HSPs. : The number refers to only the aligned regions and does not : account for unaligned regions in between the HSPs, if any. Example : $frac_iden = $hit_object->frac_identical('query'); Returns : Float (2-decimal precision, e.g., 0.75). Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total' : default = 'query' (but see comments below). : ('sbjct' is synonymous with 'hit') Throws : n/a Comments : Different versions of Blast report different values for the total : length of the alignment. This is the number reported in the : denominators in the stats section: : "Identical = 34/120 Positives = 67/120". : NCBI BLAST uses the total length of the alignment (with gaps) : WU-BLAST uses the length of the query sequence (without gaps). : : Therefore, when called with an argument of 'total', : this method will report different values depending on the : version of BLAST used. Total does NOT take into account HSP : tiling, so it should not be used. : : To get the fraction identical among only the aligned residues, : ignoring the gaps, call this method without an argument or : with an argument of 'query' or 'hit'. : : If you need data for each HSP, use hsps() and then iterate : through the HSP objects. : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically. See Also : L, L, L, L =cut #------------------ sub frac_identical { #------------------ my ($self, $seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; ## Sensitive to member name format. $seqType = lc($seqType); Bio::Search::BlastUtils::tile_hsps($self) if not $self->{'_tile_hsps'}; sprintf( "%.2f", $self->{'_totalIdentical'}/$self->{'_length_aln_'.$seqType}); } =head2 frac_conserved Usage : $hit_object->frac_conserved( [seq_type] ); Purpose : Get the overall fraction of conserved positions across all HSPs. : The number refers to only the aligned regions and does not : account for unaligned regions in between the HSPs, if any. Example : $frac_cons = $hit_object->frac_conserved('hit'); Returns : Float (2-decimal precision, e.g., 0.75). Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total' : default = 'query' (but see comments below). : ('sbjct' is synonymous with 'hit') Throws : n/a Comments : Different versions of Blast report different values for the total : length of the alignment. This is the number reported in the : denominators in the stats section: : "Positives = 34/120 Positives = 67/120". : NCBI BLAST uses the total length of the alignment (with gaps) : WU-BLAST uses the length of the query sequence (without gaps). : : Therefore, when called with an argument of 'total', : this method will report different values depending on the : version of BLAST used. Total does NOT take into account HSP : tiling, so it should not be used. : : To get the fraction conserved among only the aligned residues, : ignoring the gaps, call this method without an argument or : with an argument of 'query' or 'hit'. : : If you need data for each HSP, use hsps() and then interate : through the HSP objects. : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically. See Also : L, L, L =cut #-------------------- sub frac_conserved { #-------------------- my ($self, $seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; ## Sensitive to member name format. $seqType = lc($seqType); Bio::Search::BlastUtils::tile_hsps($self) if not $self->{'_tile_hsps'}; sprintf( "%.2f", $self->{'_totalConserved'}/$self->{'_length_aln_'.$seqType}); } =head2 frac_aligned_query Usage : $hit_object->frac_aligned_query(); Purpose : Get the fraction of the query sequence which has been aligned : across all HSPs (not including intervals between non-overlapping : HSPs). Example : $frac_alnq = $hit_object->frac_aligned_query(); Returns : Float (2-decimal precision, e.g., 0.75). Argument : n/a Throws : n/a Comments : If you need data for each HSP, use hsps() and then interate : through the HSP objects. : To compute the fraction aligned, the logical length of the query : sequence is used, meaning that for [T]BLASTX reports, the : full length of the query sequence is converted into amino acids : by dividing by 3. This is necessary because of the way : the lengths of aligned sequences are computed. : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically. See Also : L, L, L, L =cut #---------------------- sub frac_aligned_query { #---------------------- my $self = shift; Bio::Search::BlastUtils::tile_hsps($self) if not $self->{'_tile_hsps'}; sprintf( "%.2f", $self->{'_length_aln_query'}/$self->logical_length('query')); } =head2 frac_aligned_hit Usage : $hit_object->frac_aligned_hit(); Purpose : Get the fraction of the hit (sbjct) sequence which has been aligned : across all HSPs (not including intervals between non-overlapping : HSPs). Example : $frac_alnq = $hit_object->frac_aligned_hit(); Returns : Float (2-decimal precision, e.g., 0.75). Argument : n/a Throws : n/a Comments : If you need data for each HSP, use hsps() and then interate : through the HSP objects. : To compute the fraction aligned, the logical length of the sbjct : sequence is used, meaning that for TBLAST[NX] reports, the : full length of the sbjct sequence is converted into amino acids : by dividing by 3. This is necessary because of the way : the lengths of aligned sequences are computed. : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically. See Also : L, L, , L, L, L =cut #-------------------- sub frac_aligned_hit { #-------------------- my $self = shift; Bio::Search::BlastUtils::tile_hsps($self) if not $self->{'_tile_hsps'}; sprintf( "%.2f", $self->{'_length_aln_sbjct'}/$self->logical_length('sbjct')); } ## These methods are being maintained for backward compatibility. =head2 frac_aligned_sbjct Same as L =cut #---------------- sub frac_aligned_sbjct { my $self=shift; $self->frac_aligned_hit(@_); } #---------------- =head2 num_unaligned_sbjct Same as L =cut #---------------- sub num_unaligned_sbjct { my $self=shift; $self->num_unaligned_hit(@_); } #---------------- =head2 num_unaligned_hit Usage : $hit_object->num_unaligned_hit(); Purpose : Get the number of the unaligned residues in the hit sequence. : Sums across all all HSPs. Example : $num_unaln = $hit_object->num_unaligned_hit(); Returns : Integer Argument : n/a Throws : n/a Comments : See notes regarding logical lengths in the comments for frac_aligned_hit(). : They apply here as well. : If you need data for each HSP, use hsps() and then interate : through the HSP objects. : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically.. See Also : L, L, L =cut #--------------------- sub num_unaligned_hit { #--------------------- my $self = shift; Bio::Search::BlastUtils::tile_hsps($self) if not $self->{'_tile_hsps'}; my $num = $self->logical_length('sbjct') - $self->{'_length_aln_sbjct'}; ($num < 0 ? 0 : $num ); } =head2 num_unaligned_query Usage : $hit_object->num_unaligned_query(); Purpose : Get the number of the unaligned residues in the query sequence. : Sums across all all HSPs. Example : $num_unaln = $hit_object->num_unaligned_query(); Returns : Integer Argument : n/a Throws : n/a Comments : See notes regarding logical lengths in the comments for frac_aligned_query(). : They apply here as well. : If you need data for each HSP, use hsps() and then interate : through the HSP objects. : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically.. See Also : L, L, L =cut #----------------------- sub num_unaligned_query { #----------------------- my $self = shift; Bio::Search::BlastUtils::tile_hsps($self) if not $self->{'_tile_hsps'}; my $num = $self->logical_length('query') - $self->{'_length_aln_query'}; ($num < 0 ? 0 : $num ); } =head2 seq_inds Usage : $hit->seq_inds( seq_type, class, collapse ); Purpose : Get a list of residue positions (indices) across all HSPs : for identical or conserved residues in the query or sbjct sequence. Example : @s_ind = $hit->seq_inds('query', 'identical'); : @h_ind = $hit->seq_inds('hit', 'conserved'); : @h_ind = $hit->seq_inds('hit', 'conserved', 1); Returns : Array of integers : May include ranges if collapse is non-zero. Argument : [0] seq_type = 'query' or 'hit' or 'sbjct' (default = 'query') : ('sbjct' is synonymous with 'hit') : [1] class = 'identical' or 'conserved' (default = 'identical') : (can be shortened to 'id' or 'cons') : (actually, anything not 'id' will evaluate to 'conserved'). : [2] collapse = boolean, if non-zero, consecutive positions are merged : using a range notation, e.g., "1 2 3 4 5 7 9 10 11" : collapses to "1-5 7 9-11". This is useful for : consolidating long lists. Default = no collapse. Throws : n/a. Comments : Note that HSPs are not tiled for this. This could be a problem : for hits containing mutually exclusive HSPs. : TODO: Consider tiling and then reporting seq_inds for the : best HSP contig. See Also : L =cut #------------- sub seq_inds { #------------- my ($self, $seqType, $class, $collapse) = @_; $seqType ||= 'query'; $class ||= 'identical'; $collapse ||= 0; $seqType = 'sbjct' if $seqType eq 'hit'; my (@inds, $hsp); foreach $hsp ($self->hsps) { # This will merge data for all HSPs together. push @inds, $hsp->seq_inds($seqType, $class); } # Need to remove duplicates and sort the merged positions. if(@inds) { my %tmp = map { $_, 1 } @inds; @inds = sort {$a <=> $b} keys %tmp; } $collapse ? &Bio::Search::BlastUtils::collapse_nums(@inds) : @inds; } =head2 iteration Usage : $sbjct->iteration( ); Purpose : Gets the iteration number in which the Hit was found. Example : $iteration_num = $sbjct->iteration(); Returns : Integer greater than or equal to 1 Non-PSI-BLAST reports will report iteration as 1, but this number is only meaningful for PSI-BLAST reports. Argument : none Throws : none See Also : L =cut #---------------- sub iteration { shift->{'_iteration'} } #---------------- =head2 found_again Usage : $sbjct->found_again; Purpose : Gets a boolean indicator whether or not the hit has been found in a previous iteration. This is only applicable to PSI-BLAST reports. This method indicates if the hit was reported in the "Sequences used in model and found again" section of the PSI-BLAST report or if it was reported in the "Sequences not found previously or not previously below threshold" section of the PSI-BLAST report. Only for hits in iteration > 1. Example : if( $sbjct->found_again()) { ... }; Returns : Boolean (1 or 0) for PSI-BLAST report iterations greater than 1. Returns undef for PSI-BLAST report iteration 1 and non PSI_BLAST reports. Argument : none Throws : none See Also : L =cut #---------------- sub found_again { shift->{'_found_again'} } #---------------- =head2 strand Usage : $sbjct->strand( [seq_type] ); Purpose : Gets the strand(s) for the query, sbjct, or both sequences : in the best HSP of the PsiBlastHit object after HSP tiling. : Only valid for BLASTN, TBLASTX, BLASTX-query, TBLASTN-hit. Example : $qstrand = $sbjct->strand('query'); : $sstrand = $sbjct->strand('hit'); : ($qstrand, $sstrand) = $sbjct->strand(); Returns : scalar context: integer '1', '-1', or '0' : array context without args: list of two strings (queryStrand, sbjctStrand) : Array context can be "induced" by providing an argument of 'list' or 'array'. Argument : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is synonymous with 'hit') Throws : n/a Comments : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically.. : If you don't want the tiled data, iterate through each HSP : calling strand() on each (use hsps() to get all HSPs). : : Formerly (prior to 10/21/02), this method would return the : string "-1/1" for hits with HSPs on both strands. : However, now that strand and frame is properly being accounted : for during HSP tiling, it makes more sense for strand() : to return the strand data for the best HSP after tiling. : : If you really want to know about hits on opposite strands, : you should be iterating through the HSPs using methods on the : HSP objects. : : A possible use case where knowing whether a hit has HSPs : on both strands would be when filtering via SearchIO for hits with : this property. However, in this case it would be better to have a : dedicated method such as $hit->hsps_on_both_strands(). Similarly : for frame. This could be provided if there is interest. See Also : L() =cut #----------' sub strand { #---------- my ($self, $seqType) = @_; Bio::Search::BlastUtils::tile_hsps($self) if not $self->{'_tile_hsps'}; $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; my ($qstr, $hstr); # If there is only one HSP, defer this call to the solitary HSP. if($self->num_hsps == 1) { return $self->hsp->strand($seqType); } elsif( defined $self->{'_qstrand'}) { # Get the data computed during hsp tiling. $qstr = $self->{'_qstrand'}; $hstr = $self->{'_sstrand'}; } else { # otherwise, iterate through all HSPs collecting strand info. # This will return the string "-1/1" if there are HSPs on different strands. # NOTE: This was the pre-10/21/02 procedure which will no longer be used, # (unless the above elsif{} is commented out). my (%qstr, %hstr); foreach my $hsp( $self->hsps ) { my ( $q, $h ) = $hsp->strand(); $qstr{ $q }++; $hstr{ $h }++; } $qstr = join( '/', sort keys %qstr); $hstr = join( '/', sort keys %hstr); } if($seqType =~ /list|array/i) { return ($qstr, $hstr); } elsif( $seqType eq 'query' ) { return $qstr; } else { return $hstr; } } 1; __END__ ##################################################################################### # END OF CLASS # ##################################################################################### =head1 FOR DEVELOPERS ONLY =head2 Data Members Information about the various data members of this module is provided for those wishing to modify or understand the code. Two things to bear in mind: =over 4 =item 1 Do NOT rely on these in any code outside of this module. All data members are prefixed with an underscore to signify that they are private. Always use accessor methods. If the accessor doesn't exist or is inadequate, create or modify an accessor (and let me know, too!). (An exception to this might be for BlastHSP.pm which is more tightly coupled to PsiBlastHit.pm and may access PsiBlastHit data members directly for efficiency purposes, but probably should not). =item 2 This documentation may be incomplete and out of date. It is easy for these data member descriptions to become obsolete as this module is still evolving. Always double check this info and search for members not described here. =back An instance of Bio::Search::Hit::PsiBlastHit.pm is a blessed reference to a hash containing all or some of the following fields: FIELD VALUE -------------------------------------------------------------- _hsps : Array ref for a list of Bio::Search::HSP::BlastHSP.pm objects. : _db : Database identifier from the summary line. : _desc : Description data for the hit from the summary line. : _length : Total length of the hit sequence. : _score : BLAST score. : _bits : BLAST score (in bits). Matrix-independent. : _p : BLAST P value. Obtained from summary section. (Blast1/WU-Blast only) : _expect : BLAST Expect value. Obtained from summary section. : _n : BLAST N value (number of HSPs) (Blast1/WU-Blast2 only) : _frame : Reading frame for TBLASTN and TBLASTX analyses. : _totalIdentical: Total number of identical aligned monomers. : _totalConserved: Total number of conserved aligned monomers (a.k.a. "positives"). : _overlap : Maximum number of overlapping residues between adjacent HSPs : before considering the alignment to be ambiguous. : _ambiguous_aln : Boolean. True if the alignment of all HSPs is ambiguous. : _length_aln_query : Length of the aligned region of the query sequence. : _length_aln_sbjct : Length of the aligned region of the sbjct sequence. =cut 1; BioPerl-1.007002/Bio/Search/Hit/PullHitI.pm000555000766000024 10572613155576320 20263 0ustar00cjfieldsstaff000000000000# # BioPerl module Bio::Search::Hit::PullHitI # # Please direct questions and support issues to # # Cared for by Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Hit::PullHitI - Bio::Search::Hit::HitI interface for pull parsers. =head1 SYNOPSIS # This is an interface and cannot be instantiated # typically one gets HitI objects from a SearchIO stream via a ResultI use Bio::SearchIO; my $parser = Bio::SearchIO->new(-format => 'hmmer_pull', -file => 't/data/hmmpfam.out'); my $result = $parser->next_result; my $hit = $result->next_hit; $hit_name = $hit->name(); $desc = $hit->description(); $len = $hit->length $alg = $hit->algorithm(); $score = $hit->raw_score(); $significance = $hit->significance(); $rank = $hit->rank(); # the Nth hit for a specific query while( $hsp = $obj->next_hsp()) { ... } # process in iterator fashion for my $hsp ( $obj->hsps()()) { ... } # process in list fashion =head1 DESCRIPTION This object handles the hit data from a database sequence search. PullHitI is for fast implementations that only do parsing work on the hit data when you actually request information by calling one of the HitI methods. Many methods of HitI are implemented in a way suitable for inheriting classes that use Bio::PullParserI. It only really makes sense for PullHit modules to be created by (and have as a -parent) PullResult modules. In addition to the usual -chunk and -parent, -hit_data is all you should supply when making a PullHit object. This will store that data and make it accessible via _raw_hit_data, which you can access in your subclass. It would be best to simply provide the data as the input -chunk instead, if the raw data is large enough. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 COPYRIGHT Copyright (c) 2006 Sendu Bala. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Hit::PullHitI; use Bio::Search::SearchUtils; use strict; use base qw(Bio::PullParserI Bio::Search::Hit::HitI); =head2 _setup Title : _setup Usage : $self->_setup(@args) Function: Implementers should call this to setup common fields and deal with common arguments to new(). Returns : n/a Args : @args received in new(). =cut sub _setup { my ($self, @args) = @_; # fields most subclasses probably will want $self->_fields( { ( next_hsp => undef, num_hsps => undef, hsps => undef, hit_start => undef, query_start => undef, hit_end => undef, query_end => undef, length => undef, name => undef , accession => undef ) } ); my ($parent, $chunk, $hit_data) = $self->_rearrange([qw(PARENT CHUNK HIT_DATA)], @args); $self->throw("Need -parent or -chunk to be defined") unless $parent || $chunk; $self->parent($parent) if $parent; if ($chunk) { my ($io, $start, $end) = (undef, 0, undef); if (ref($chunk) eq 'ARRAY') { ($io, $start, $end) = @{$chunk}; } else { $io = $chunk; } $self->chunk($io, -start => $start, -end => $end); } $self->_raw_hit_data($hit_data) if $hit_data; } sub _raw_hit_data { my $self = shift; if (@_) { $self->{_raw_hit_data} = shift; } return $self->{_raw_hit_data}; } # # Some of these methods are written explitely to avoid HitI throwing not # implemented; if it didn't do that then PullParserI AUTOLOAD would have # cought them. # =head2 name Title : name Usage : $hit_name = $hit->name(); Function: returns the name of the Hit sequence Returns : a scalar string Args : none The B of a hit is unique within a Result or within an Iteration. =cut sub name { return shift->get_field('name'); } =head2 description Title : description Usage : $desc = $hit->description(); Function: Retrieve the description for the hit Returns : a scalar string Args : none =cut sub description { return shift->get_field('description'); } =head2 accession Title : accession Usage : $acc = $hit->accession(); Function: Retrieve the accession (if available) for the hit Returns : a scalar string (empty string if not set) Args : none =cut sub accession { return shift->get_field('accession'); } =head2 locus Title : locus Usage : $acc = $hit->locus(); Function: Retrieve the locus(if available) for the hit Returns : a scalar string (empty string if not set) Args : none =cut sub locus { return shift->get_field('locus'); } =head2 length Title : length Usage : my $len = $hit->length Function: Returns the length of the hit Returns : integer Args : none =cut sub length { return shift->get_field('length'); } =head2 algorithm Title : algorithm Usage : $alg = $hit->algorithm(); Function: Gets the algorithm specification that was used to obtain the hit For BLAST, the algorithm denotes what type of sequence was aligned against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated dna-prt, TBLASTN prt-translated dna, TBLASTX translated dna-translated dna). Returns : a scalar string Args : none =cut sub algorithm { return shift->get_field('algorithm'); } =head2 raw_score Title : raw_score Usage : $score = $hit->raw_score(); Function: Gets the "raw score" generated by the algorithm. What this score is exactly will vary from algorithm to algorithm, returning undef if unavailable. Returns : a scalar value Args : none =cut sub raw_score { return shift->get_field('score'); } =head2 score Equivalent to L =cut sub score { return shift->get_field('score'); } =head2 significance Title : significance Usage : $significance = $hit->significance(); Function: Used to obtain the E or P value of a hit, i.e. the probability that this particular hit was obtained purely by random chance. If information is not available (nor calculatable from other information sources), return undef. Returns : a scalar value or undef if unavailable Args : none =cut sub significance { return shift->get_field('significance'); } =head2 bits Usage : $hit_object->bits(); Purpose : Gets the bit score of the best HSP for the current hit. Example : $bits = $hit_object->bits(); Returns : Integer or double for FASTA reports Argument : n/a Comments : For BLAST1, the non-bit score is listed in the summary line. See Also : L =cut sub bits { return shift->get_field('bits'); } =head2 next_hsp Title : next_hsp Usage : while( $hsp = $obj->next_hsp()) { ... } Function : Returns the next available High Scoring Pair Example : Returns : L object or null if finished Args : none =cut sub next_hsp { return shift->get_field('next_hsp'); } =head2 hsps Usage : $hit_object->hsps(); Purpose : Get a list containing all HSP objects. : Get the numbers of HSPs for the current hit. Example : @hsps = $hit_object->hsps(); : $num = $hit_object->hsps(); # alternatively, use num_hsps() Returns : Array context : list of L objects. : Scalar context: integer (number of HSPs). : (Equivalent to num_hsps()). Argument : n/a. Relies on wantarray Throws : Exception if the HSPs have not been collected. See Also : L, L =cut sub hsps { return shift->get_field('hsps'); } =head2 num_hsps Usage : $hit_object->num_hsps(); Purpose : Get the number of HSPs for the present Blast hit. Example : $nhsps = $hit_object->num_hsps(); Returns : Integer Argument : n/a Throws : Exception if the HSPs have not been collected. See Also : L =cut sub num_hsps { return shift->get_field('num_hsps'); } # # HitI/ GenericHit methods that are unrelated to simply parsing information # directly out of a file, but need more complex calculation; mostly not # implemented here. # =head2 seq_inds Usage : $hit->seq_inds( seq_type, class, collapse ); Purpose : Get a list of residue positions (indices) across all HSPs : for identical or conserved residues in the query or sbjct sequence. Example : @s_ind = $hit->seq_inds('query', 'identical'); : @h_ind = $hit->seq_inds('hit', 'conserved'); : @h_ind = $hit->seq_inds('hit', 'conserved', 1); Returns : Array of integers : May include ranges if collapse is non-zero. Argument : [0] seq_type = 'query' or 'hit' or 'sbjct' (default = 'query') : ('sbjct' is synonymous with 'hit') : [1] class = 'identical' or 'conserved' or 'nomatch' or 'gap' : (default = 'identical') : (can be shortened to 'id' or 'cons') : Note that 'conserved' includes identical unless you use : 'conserved-not-identical' : [2] collapse = boolean, if non-zero, consecutive positions are : merged using a range notation, e.g., : "1 2 3 4 5 7 9 10 11" collapses to "1-5 7 9-11". This : is useful for consolidating long lists. Default = no : collapse. Throws : n/a. See Also : L =cut sub seq_inds { my ($self, $seqType, $class, $collapse) = @_; $seqType ||= 'query'; $class ||= 'identical'; $collapse ||= 0; $seqType = 'hit' if $seqType eq 'sbjct'; my $storage_name = '_seq_inds_'.$seqType.'_'.$class; unless (defined $self->{$storage_name}) { my @inds; foreach my $hsp ($self->hsps) { # This will merge data for all HSPs together. push @inds, $hsp->seq_inds($seqType, $class); } # Need to remove duplicates and sort the merged positions, unless gaps. if (@inds && $class ne 'gap') { my %tmp = map { $_, 1 } @inds; @inds = sort {$a <=> $b} keys %tmp; } $self->{$storage_name} = \@inds; } my @inds = @{$self->{$storage_name}}; $collapse ? &Bio::Search::SearchUtils::collapse_nums(@inds) : @inds; } =head2 rewind Title : rewind Usage : $hit->rewind; Function: Allow one to reset the HSP iterator to the beginning if possible Returns : none Args : none =cut sub rewind { shift->throw_not_implemented(); } =head2 overlap Usage : $hit_object->overlap( [integer] ); Purpose : Gets/Sets the allowable amount overlap between different HSP sequences. Example : $hit_object->overlap(5); : $overlap = $hit_object->overlap; Returns : Integer. Argument : integer. Throws : n/a Status : Deprecated Comments : This value isn't used for anything =cut sub overlap { my $self = shift; if (@_) { $self->{_overlap} = shift } return $self->{_overlap} || 0; } =head2 n Usage : $hit_object->n(); Purpose : Gets the N number for the current Blast hit. : This is the number of HSPs in the set which was ascribed : the lowest P-value (listed on the description line). : This number is not the same as the total number of HSPs. : To get the total number of HSPs, use num_hsps(). Example : $n = $hit_object->n(); Returns : Integer Argument : n/a Throws : Exception if HSPs have not been set (BLAST2 reports). Comments : Note that the N parameter is not reported in gapped BLAST2. : Calling n() on such reports will result in a call to num_hsps(). : The num_hsps() method will count the actual number of : HSPs in the alignment listing, which may exceed N in : some cases. See Also : L =cut sub n { return shift->get_field('num_hsps'); } =head2 p Usage : $hit_object->p( [format] ); Purpose : Get the P-value for the best HSP of the given BLAST hit. : (Note that P-values are not provided with NCBI Blast2 reports). Example : $p = $sbjct->p; : $p = $sbjct->p('exp'); # get exponent only. : ($num, $exp) = $sbjct->p('parts'); # split sci notation into parts Returns : Float or scientific notation number (the raw P-value, DEFAULT). : Integer if format == 'exp' (the magnitude of the base 10 exponent). : 2-element list (float, int) if format == 'parts' and P-value : is in scientific notation (See Comments). Argument : format: string of 'raw' | 'exp' | 'parts' : 'raw' returns value given in report. Default. (1.2e-34) : 'exp' returns exponent value only (34) : 'parts' returns the decimal and exponent as a : 2-element list (1.2, -34) (See Comments). Throws : Warns if no P-value is defined. Uses expect instead. Comments : Using the 'parts' argument is not recommended since it will not : work as expected if the P-value is not in scientific notation. : That is, floats are not converted into sci notation before : splitting into parts. See Also : L, L, L =cut sub p { shift->throw_not_implemented; } =head2 hsp Usage : $hit_object->hsp( [string] ); Purpose : Get a single HSPI object for the present HitI object. Example : $hspObj = $hit_object->hsp; # same as 'best' : $hspObj = $hit_object->hsp('best'); : $hspObj = $hit_object->hsp('worst'); Returns : Object reference for a L object. Argument : String (or no argument). : No argument (default) = highest scoring HSP (same as 'best'). : 'best' = highest scoring HSP. : 'worst' = lowest scoring HSP. Throws : Exception if an unrecognized argument is used. See Also : L, L() =cut sub hsp { shift->throw_not_implemented; } =head2 logical_length Usage : $hit_object->logical_length( [seq_type] ); : (mostly intended for internal use). Purpose : Get the logical length of the hit sequence. : If the Blast is a TBLASTN or TBLASTX, the returned length : is the length of the would-be amino acid sequence (length/3). : For all other BLAST flavors, this function is the same as length(). Example : $len = $hit_object->logical_length(); Returns : Integer Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is synonymous with 'hit') Throws : n/a Comments : This is important for functions like frac_aligned_query() : which need to operate in amino acid coordinate space when dealing : with [T]BLAST[NX] type reports. See Also : L, L, L =cut sub logical_length { my ($self, $type) = @_; $type ||= 'query'; $type = lc($type); $type = 'hit' if $type eq 'sbjct'; if ($type eq 'query') { return $self->get_field('query_length'); } elsif ($type eq 'hit') { return $self->get_field('length'); } } =head2 rank Title : rank Usage : $obj->rank($newval) Function: Get/Set the rank of this Hit in the Query search list i.e. this is the Nth hit for a specific query Returns : value of rank Args : newvalue (optional) =cut sub rank { return shift->get_field('rank'); } =head2 each_accession_number Title : each_accession_number Usage : $obj->each_accession_number Function: Get each accession number listed in the description of the hit. If there are no alternatives, then only the primary accession will be given (if there is one). Returns : list of all accession numbers in the description Args : none =cut sub each_accession_number { my $self = shift; my $accession = $self->get_field('accession') if $self->has_field('accession'); my $desc = $self->get_field('description') if $self->has_field('description'); return unless $accession || $desc; my @accnums; push (@accnums, $accession) if $accession; if (defined $desc) { while ($desc =~ /(\b\S+\|\S*\|\S*\s?)/g) { my $id = $1; my $acc; if ($id =~ /(?:gb|emb|dbj|sp|pdb|bbs|ref|tp[gde])\|(.*)\|(?:.*)/) { ($acc) = split /\./, $1; } elsif ($id =~ /(?:pir|prf|pat|gnl)\|(?:.*)\|(.*)/) { ($acc) = split /\./, $1; } elsif ($id =~ /(?:gim|gi|bbm|bbs|lcl)\|(?:\d*)/) { $acc = $id; } elsif ($id =~ /(?:oth)\|(.*)\|(?:.*)\|(?:.*)/ ) { # discontinued... $acc = $1; } else { $acc = $id; } push(@accnums, $acc); } } return @accnums; } =head2 tiled_hsps Usage : $hit_object->tiled_hsps( [integer] ); Purpose : Gets/Sets an indicator for whether or not the HSPs in this Hit : have been tiled. Example : $hit_object->tiled_hsps(1); : if( $hit_object->tiled_hsps ) { # do something } Returns : Boolean (1 or 0) Argument : integer (optional) Throws : n/a Status : Deprecated Notes : This value is not used for anything =cut sub tiled_hsps { my $self = shift; if (@_) { $self->{_hsps_are_tiled} = shift } return $self->{_hsps_are_tiled} || 0; } =head2 strand Usage : $sbjct->strand( [seq_type] ); Purpose : Gets the strand(s) for the query, sbjct, or both sequences : in the best HSP of the BlastHit object after HSP tiling. : Only valid for BLASTN, TBLASTX, BLASTX-query, TBLASTN-hit. Example : $qstrand = $sbjct->strand('query'); : $sstrand = $sbjct->strand('hit'); : ($qstrand, $sstrand) = $sbjct->strand(); Returns : scalar context: integer '1', '-1', or '0' : array context without args: list of two strings (queryStrand, sbjctStrand) : Array context can be "induced" by providing an argument of 'list' or 'array'. Argument : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is synonymous with 'hit') Throws : n/a Comments : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically.. : If you don't want the tiled data, iterate through each HSP : calling strand() on each (use hsps() to get all HSPs). : : Formerly (prior to 10/21/02), this method would return the : string "-1/1" for hits with HSPs on both strands. : However, now that strand and frame is properly being accounted : for during HSP tiling, it makes more sense for strand() : to return the strand data for the best HSP after tiling. : : If you really want to know about hits on opposite strands, : you should be iterating through the HSPs using methods on the : HSP objects. : : A possible use case where knowing whether a hit has HSPs : on both strands would be when filtering via SearchIO for hits with : this property. However, in this case it would be better to have a : dedicated method such as $hit->hsps_on_both_strands(). Similarly : for frame. This could be provided if there is interest. See Also : L() =cut sub strand { shift->throw_not_implemented; } =head2 frame Usage : $hit_object->frame(); Purpose : Gets the reading frame for the best HSP after HSP tiling. : This is only valid for BLASTX and TBLASTN/X type reports. Example : $frame = $hit_object->frame(); Returns : Integer (-2 .. +2) Argument : n/a Throws : Exception if HSPs have not been set. Comments : This method requires that all HSPs be tiled. If they have not : already been tiled, they will be tiled first automatically.. : If you don't want the tiled data, iterate through each HSP : calling frame() on each (use hsps() to get all HSPs). See Also : L =cut sub frame { shift->throw_not_implemented; } =head2 length_aln Usage : $hit_object->length_aln( [seq_type] ); Purpose : Get the total length of the aligned region for query or sbjct seq. : This number will include all HSPs, and excludes gaps. Example : $len = $hit_object->length_aln(); # default = query : $lenAln = $hit_object->length_aln('query'); Returns : Integer Argument : seq_Type = 'query' or 'hit' or 'sbjct' (Default = 'query') ('sbjct' is synonymous with 'hit') Throws : Exception if the argument is not recognized. Comments : This method will report the logical length of the alignment, : meaning that for TBLAST[NX] reports, the length is reported : using amino acid coordinate space (i.e., nucleotides / 3). See Also : L, L, L, L, L, L =cut sub length_aln { my ($self, $seqType) = @_; $seqType ||= 'query'; $seqType = 'hit' if $seqType eq 'sbjct'; my %non_gaps = map { $_, 1 } $self->seq_inds($seqType, 'conserved'), $self->seq_inds($seqType, 'no_match'); return scalar(keys %non_gaps); } =head2 gaps Usage : $hit_object->gaps( [seq_type] ); Purpose : Get the number of gaps in the aligned query, hit, or both sequences. : Data is summed across all HSPs. Example : $qgaps = $hit_object->gaps('query'); : $hgaps = $hit_object->gaps('hit'); : $tgaps = $hit_object->gaps(); # default = total (query + hit) Returns : scalar context: integer : array context without args: two-element list of integers : (queryGaps, hitGaps) : Array context can be forced by providing an argument of 'list' or : 'array'. : : CAUTION: Calling this method within printf or sprintf is arrray : context. : So this function may not give you what you expect. For example: : printf "Total gaps: %d", $hit->gaps(); : Actually returns a two-element array, so what gets printed : is the number of gaps in the query, not the total : Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total' | 'list' : (default = 'total') ('sbjct' is synonymous with 'hit') Comments : If you need data for each HSP, use hsps() and then interate : through each HSP object. =cut sub gaps { my ($self, $seqType) = @_; $seqType ||= (wantarray ? 'list' : 'total'); $seqType = 'hit' if $seqType eq 'sbjct'; if ($seqType =~ /list|array/i) { return (scalar($self->seq_inds('query', 'gap')), scalar($self->seq_inds('hit', 'gap'))); } elsif ($seqType eq 'total') { return (scalar($self->seq_inds('query', 'gap')) + scalar($self->seq_inds('hit', 'gap'))) || 0; } else { return scalar($self->seq_inds($seqType, 'gap')) || 0; } } =head2 matches Usage : $hit_object->matches( [class] ); Purpose : Get the total number of identical or conserved matches : (or both) across all HSPs. : (Note: 'conservative' matches are indicated as 'positives' : in BLAST reports.) Example : ($id,$cons) = $hit_object->matches(); # no argument : $id = $hit_object->matches('id'); : $cons = $hit_object->matches('cons'); Returns : Integer or a 2-element array of integers Argument : [0] class = 'id' | 'cons' OR none. : [1] seq_type = 'query' or 'hit' or 'sbjct' (default = 'query') : ('sbjct' is synonymous with 'hit') : If no argument is provided, both identical and conservative : numbers are returned in a two element list. : (Other terms can be used to refer to the conservative : matches, e.g., 'positive'. All that is checked is whether or : not the supplied string starts with 'id'. If not, the : conservative matches are returned.) =cut sub matches { my ($self, $class, $seqType) = @_; # no query/hit choice? The answer differs depending on sequence, since # hsps could overlap on one sequence and not the other. Added an option, # but otherwise will assume 'hit' $seqType ||= 'hit'; $seqType = 'hit' if $seqType eq 'sbjct'; unless (exists $self->{_id_matches}) { $self->{_id_matches}->{hit} = scalar($self->seq_inds('hit', 'identical')); $self->{_id_matches}->{query} = scalar($self->seq_inds('query', 'identical')); } unless (exists $self->{_con_matches}) { foreach my $type ('hit', 'query') { # 'conserved-not-identical' can give us 'identical' matches if hsps # overlapped so have to get the difference my %identicals = map { $_ => 1 } $self->seq_inds($type, 'identical'); my @conserved = $self->seq_inds($type, 'conserved-not-identical'); my $real_conserved; foreach (@conserved) { unless (exists $identicals{$_}) { $real_conserved++; } } $self->{_con_matches}->{$type} = $real_conserved; } } unless ($class) { return ($self->{_id_matches}->{$seqType}, $self->{_con_matches}->{$seqType}); } else { if ($class =~ /^id/i) { return $self->{_id_matches}->{$seqType}; } else { return $self->{_con_matches}->{$seqType}; } } return; } =head2 start Usage : $sbjct->start( [seq_type] ); Purpose : Gets the start coordinate for the query, sbjct, or both sequences : in the object. If there is more than one HSP, the lowest start : value of all HSPs is returned. Example : $qbeg = $sbjct->start('query'); : $sbeg = $sbjct->start('hit'); : ($qbeg, $sbeg) = $sbjct->start(); Returns : scalar context: integer : array context without args: list of two integers (queryStart, : sbjctStart) : Array context can be "induced" by providing an argument of 'list' : or 'array'. Argument : 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is synonymous with 'hit') =cut sub start { my ($self, $seqType) = @_; unless ($self->get_field('num_hsps')) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); return; } $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'hit' if $seqType eq 'sbjct'; if ($seqType =~ /list|array/i) { return ($self->get_field('query_start'), $self->get_field('hit_start')); } elsif ($seqType eq 'hit') { return $self->get_field('hit_start'); } elsif ($seqType eq 'query') { return $self->get_field('query_start'); } else { $self->throw("Unknown sequence type '$seqType'"); } } =head2 end Usage : $sbjct->end( [seq_type] ); Purpose : Gets the end coordinate for the query, sbjct, or both sequences : in the object. If there is more than one HSP, the largest end : value of all HSPs is returned. Example : $qend = $sbjct->end('query'); : $send = $sbjct->end('hit'); : ($qend, $send) = $sbjct->end(); Returns : scalar context: integer : array context without args: list of two integers : (queryEnd, sbjctEnd) : Array context can be "induced" by providing an argument : of 'list' or 'array'. Argument : 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is synonymous with 'hit') =cut sub end { my ($self, $seqType) = @_; unless ($self->get_field('num_hsps')) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); return; } $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'hit' if $seqType eq 'sbjct'; if ($seqType =~ /list|array/i) { return ($self->get_field('query_end'), $self->get_field('hit_end')); } elsif ($seqType eq 'hit') { return $self->get_field('hit_end'); } elsif ($seqType eq 'query') { return $self->get_field('query_end'); } else { $self->throw("Unknown sequence type '$seqType'"); } } =head2 range Usage : $sbjct->range( [seq_type] ); Purpose : Gets the (start, end) coordinates for the query or sbjct sequence : in the HSP alignment. Example : ($qbeg, $qend) = $sbjct->range('query'); : ($sbeg, $send) = $sbjct->range('hit'); Returns : Two-element array of integers Argument : seq_type = string, 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is synonymous with 'hit') Throws : n/a See Also : L, L =cut sub range { my ($self, $seqType) = @_; $seqType ||= 'query'; $seqType = 'hit' if $seqType eq 'sbjct'; return ($self->start($seqType), $self->end($seqType)); } =head2 frac_identical Usage : $hit_object->frac_identical( [seq_type] ); Purpose : Get the overall fraction of identical positions across all HSPs. : The number refers to only the aligned regions and does not : account for unaligned regions in between the HSPs, if any. Example : $frac_iden = $hit_object->frac_identical('query'); Returns : Float (2-decimal precision, e.g., 0.75). Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total' : default = 'query' (but see comments below). : ('sbjct' is synonymous with 'hit') =cut sub frac_identical { my ($self, $seqType) = @_; $seqType ||= 'query'; $seqType = lc($seqType); $seqType = 'hit' if $seqType eq 'sbjct'; my $ident = $self->matches('id', $seqType); my $total = $self->length_aln($seqType); my $ratio = $ident / $total; my $ratio_rounded = sprintf( "%.3f", $ratio); # Round down if normal rounding yields 1 (just like blast) $ratio_rounded = 0.999 if (($ratio_rounded == 1) && ($ratio < 1)); return $ratio_rounded; } =head2 frac_conserved Usage : $hit_object->frac_conserved( [seq_type] ); Purpose : Get the overall fraction of conserved positions across all HSPs. : The number refers to only the aligned regions and does not : account for unaligned regions in between the HSPs, if any. Example : $frac_cons = $hit_object->frac_conserved('hit'); Returns : Float (2-decimal precision, e.g., 0.75). Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total' : default = 'query' (but see comments below). : ('sbjct' is synonymous with 'hit') =cut sub frac_conserved { my ($self, $seqType) = @_; $seqType ||= 'query'; $seqType = lc($seqType); $seqType = 'hit' if $seqType eq 'sbjct'; my $consv = $self->matches('cons'); my $total = $self->length_aln($seqType); my $ratio = $consv / $total; my $ratio_rounded = sprintf( "%.3f", $ratio); # Round down iff normal rounding yields 1 (just like blast) $ratio_rounded = 0.999 if (($ratio_rounded == 1) && ($ratio < 1)); return $ratio_rounded; } =head2 frac_aligned_query Usage : $hit_object->frac_aligned_query(); Purpose : Get the fraction of the query sequence which has been aligned : across all HSPs (not including intervals between non-overlapping : HSPs). Example : $frac_alnq = $hit_object->frac_aligned_query(); Returns : Float (2-decimal precision, e.g., 0.75). Argument : none Comments : If you need data for each HSP, use hsps() and then interate : through the HSP objects. =cut sub frac_aligned_query { my $self = shift; return sprintf("%.2f", $self->length_aln('query') / $self->logical_length('query')); } =head2 frac_aligned_hit Usage : $hit_object->frac_aligned_hit(); Purpose : Get the fraction of the hit (sbjct) sequence which has been aligned : across all HSPs (not including intervals between non-overlapping : HSPs). Example : $frac_alnq = $hit_object->frac_aligned_hit(); Returns : Float (2-decimal precision, e.g., 0.75). Argument : none Comments : If you need data for each HSP, use hsps() and then interate : through the HSP objects. =cut sub frac_aligned_hit { my $self = shift; return sprintf( "%.2f", $self->length_aln('sbjct') / $self->logical_length('sbjct')); } =head2 num_unaligned_hit Usage : $hit_object->num_unaligned_hit(); Purpose : Get the number of the unaligned residues in the hit sequence. : Sums across all all HSPs. Example : $num_unaln = $hit_object->num_unaligned_hit(); Returns : Integer Argument : none Comments : If you need data for each HSP, use hsps() and then interate : through the HSP objects. =cut sub num_unaligned_hit { my $self = shift; # why does this method even exist?! return $self->gaps('hit'); } =head2 num_unaligned_query Usage : $hit_object->num_unaligned_query(); Purpose : Get the number of the unaligned residues in the query sequence. : Sums across all all HSPs. Example : $num_unaln = $hit_object->num_unaligned_query(); Returns : Integer Argument : none Comments : If you need data for each HSP, use hsps() and then interate : through the HSP objects. =cut sub num_unaligned_query { my $self = shift; # why does this method even exist?! return $self->gaps('query'); } # aliasing for Steve's method names *hit_description = \&description; *hit_length = \&length; 1; BioPerl-1.007002/Bio/Search/Hit/hmmer3Hit.pm000444000766000024 712213155576320 20355 0ustar00cjfieldsstaff000000000000# $Id: bioperl.lisp 15559 2009-02-23 12:11:20Z maj $ # # BioPerl module for Bio::Search::Hit::hmmer3Hit # # Please direct questions and support issues to # # Cared for by Thomas Sharpton # # Copyright Thomas Sharpton # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Hit::hmmer3Hit - DESCRIPTION of Object =head1 SYNOPSIS Give standard usage here =head1 DESCRIPTION Describe the object here =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: L rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Thomas Sharpton Email thomas.sharpton@gmail.com Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Hit::hmmer3Hit; use strict; use base qw(Bio::Search::Hit::GenericHit); =head2 new Title : new Usage : my $obj = Bio::Search::Hit::HMMERHit->new(); Function: Builds a new Bio::Search::Hit::HMMERHit object Returns : Bio::Search::Hit::HMMERHit Args : Plus the Bio::Search::Hit::GenericHit inherited params -name => Name of Hit (required) -description => Description (optional) -accession => Accession number (optional) -length => Length of the Hit (optional) -score => Raw Score for the Hit (optional) -significance => Significance value for the Hit (optional) -algorithm => Algorithm used (BLASTP, FASTX, etc...) -hsps => Array ref of HSPs for this Hit. =cut =head2 next_domain Title : next_domain Usage : my $domain = $hit->next_domain(); Function: An alias for L, this will return the next HSP Returns : L object Args : none =cut sub next_domain{ shift->next_hsp } =head2 domains Title : domains Usage : my @domains = $hit->domains(); Function: An alias for L, this will return the full list of hsps Returns : array of L objects Args : none =cut sub domains{ shift->hsps() } =head2 bits Usage : $hit_object->bits(); Purpose : Gets the bit score of the best HSP for the current hit. Example : $bits = $hit_object->bits(); Returns : Integer or undef if bit score is not set Argument : n/a See Also : L =cut sub bits { return 0 } =head2 iteration Title : iteration Usage : $obj->iteration($newval) Function: PSI-BLAST iteration Returns : value of iteration Args : newvalue (optional) =cut sub iteration { return 0 } 1; BioPerl-1.007002/Bio/Search/Iteration000755000766000024 013155576320 17232 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Search/Iteration/GenericIteration.pm000444000766000024 5201213155576320 23200 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Iteration::GenericIteration # # Please direct questions and support issues to # # Cared for by Steve Chervitz # # Copyright Steve Chervitz # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code # TODO: Consider calling this BlastIteration (strongly) and maybe simplifying IterationI. =head1 NAME Bio::Search::Iteration::GenericIteration - A generic implementation of the Bio::Search::Iteration::IterationI interface. =head1 SYNOPSIS use Bio::Search::Iteration::GenericIteration; my $it = Bio::Search::GenericIteration->new( -number => 1, -converged => 0, -newhits_unclassified => [@newhits_unclass], -newhits_below => [@newhits_below_threshold], -newhits_not_below => [@newhits_not_below_threshold], -oldhits_below => [@oldhits_below_threshold], -oldhits_newly_below => [@oldhits_newly_below_threshold], -oldhits_not_below => [@oldhits_not_below_threshold], ); # TODO: Describe how to configure a SearchIO stream so that it generates # GenericIteration objects. =head1 DESCRIPTION This module acts as a container for Bio::Search::Hit::HitI objects, allowing a Search::Result::ResultI object to partition its hits based on which iteration the hit occurred in (e.g., a PSI-BLAST round). Unless you're writing a parser, you won't ever need to create a GenericIteration or any other IterationI-implementing object. If you use the SearchIO system, IterationI objects are created automatically from a SearchIO stream which returns Bio::Search::Result::ResultI objects and you get the IterationI objects via the ResultI API. For documentation on what you can do with GenericIteration (and other IterationI objects), please see the API documentation in L. Bio::Search::Iteration::GenericIteration is similar in spirit to the deprecated Bio::Tools::BPlite::Iteration modules in bioperl releases prior to 1.6, except that Bio::Search::Iteration::GenericIteration is a pure container, without any parsing functionality as is in Bio::Tools::BPlite::Iteration. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Steve Chervitz Email sac@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Iteration::GenericIteration; use strict; use base qw(Bio::Root::Root Bio::Search::Iteration::IterationI); =head2 new Title : new Usage : my $obj = Bio::Search::Iteration->new(%args); Function: Builds a new Bio::Search::Iteration object Returns : Bio::Search::Iteration::GenericIteration object Args : -number => integer for the number of this iteration (required) -converged => boolean value whether or not the iteration converged -newhits_unclassified => array reference to hits that were not found in a previous iteration for the iteration and have not been classified with regard to the inclusion threshold # The following are only used for PSI-BLAST reports: -newhits_below => array reference to hits were not found in a previous iteration and are below the inclusion threshold. -newhits_not_below => array reference to hits that were not found in a previous iteration below threshold that and are not below the inclusion threshold threshold. -oldhits_below => array reference to hits that were found in a previous iteration below inclusion threshold and are still below threshold in the current iteration. -oldhits_newly_below => array reference to hits that were found in a previous iteration above threshold but are below threshold in the current iteration. -oldhits_not_below => array reference to hits that were found in a previous iteration above threshold that and are still above the inclusion threshold threshold. -hit_factory => Bio::Factory::ObjectFactoryI capable of making Bio::Search::Hit::HitI objects =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($number, $newhits_unclassified, $newhits_below, $newhits_not_below, $oldhits_below, $oldhits_newly_below, $oldhits_not_below, $converged, $h_f) = $self->_rearrange([qw(NUMBER NEWHITS_UNCLASSIFIED NEWHITS_BELOW NEWHITS_NOT_BELOW OLDHITS_BELOW OLDHITS_NEWLY_BELOW OLDHITS_NOT_BELOW CONVERGED HIT_FACTORY )], @args); if( ! defined $number ) { $self->throw(-class=>'Bio::Root::BadParameter', -text=>"Iteration number not specified."); } else { $self->number($number); } defined $converged && $self->converged($converged); # TODO: Performance optimization test calling add_hit() vs. simple assignment: # push @{$self->{'_hits_new'}}, @{$newhits}; # vs. # foreach(@{$newhits_below}) {$self->add_hit(-hit=>$_, -old=>0, -below=>1);} if(defined $newhits_unclassified ) { if( ref($newhits_unclassified) =~ /ARRAY/i) { push @{$self->{'_newhits_unclassified'}}, @{$newhits_unclassified}; } else { $self->throw(-class=>'Bio::Root::BadParameter', -text=>"Parameter NEWHITS is not an array ref: $newhits_unclassified"); } } else { $self->{'_newhits_unclassified'} = []; } if(defined $newhits_below ) { if( ref($newhits_below) =~ /ARRAY/i) { push @{$self->{'_newhits_below_threshold'}}, @{$newhits_below}; } else { $self->throw(-class=>'Bio::Root::BadParameter', -text=>"Parameter NEWHITS_BELOW is not an array ref: $newhits_below"); } } else { $self->{'_newhits_below_threshold'} = []; } if(defined $newhits_not_below ) { if( ref($newhits_not_below) =~ /ARRAY/i) { push @{$self->{'_newhits_not_below_threshold'}}, @{$newhits_not_below}; } else { $self->throw(-class=>'Bio::Root::BadParameter', -text=>"Parameter NEWHITS_NOT_BELOW is not an array ref: $newhits_not_below"); } } else { $self->{'_newhits_not_below_threshold'} = []; } if(defined $oldhits_below ) { if( ref($oldhits_below) =~ /ARRAY/i) { push @{$self->{'_oldhits_below_threshold'}}, @{$oldhits_below}; } else { $self->throw(-class=>'Bio::Root::BadParameter', -text=>"Parameter OLDHITS_BELOW is not an array ref: $oldhits_below"); } } else { $self->{'_oldhits_below_threshold'} = []; } if(defined $oldhits_newly_below ) { if( ref($oldhits_newly_below) =~ /ARRAY/i) { push @{$self->{'_oldhits_newly_below_threshold'}}, @{$oldhits_newly_below}; } else { $self->throw(-class=>'Bio::Root::BadParameter', -text=>"Parameter OLDHITS_NEWLY_BELOW is not an array ref: $oldhits_newly_below"); } } else { $self->{'_oldhits_newly_below_threshold'} = []; } if(defined $oldhits_not_below ) { if( ref($oldhits_not_below) =~ /ARRAY/i) { push @{$self->{'_oldhits_not_below_threshold'}}, @{$oldhits_not_below}; } else { $self->throw(-class=>'Bio::Root::BadParameter', -text=>"Parameter OLDHITS_NOT_BELOW is not an array ref: $oldhits_not_below"); } } else { $self->{'_oldhits_not_below_threshold'} = []; } $self->hit_factory($h_f) if $h_f; return $self; } =head2 number See documentation in Bio::Search::Iteration::IterationI. =cut sub number { my ($self,$value) = @_; my $previous = $self->{'_number'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_number'} = $value; } return $previous; } =head2 converged See documentation in Bio::Search::Iteration::IterationI. =cut sub converged { my ($self,$value) = @_; my $previous = $self->{'_converged'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_converged'} = $value; } return $previous; } =head2 hit_factory Title : hit_factory Usage : $hit->hit_factory($hit_factory) Function: Get/set the factory used to build HitI objects if necessary. Returns : Bio::Factory::ObjectFactoryI Args : Bio::Factory::ObjectFactoryI =cut sub hit_factory { my $self = shift; if (@_) { $self->{_hit_factory} = shift } return $self->{_hit_factory} || return; } =head2 next_hit This iterates through all old hits as returned by L followed by all new hits as returned by L. For more documentation see L. =cut sub next_hit { my ($self) = @_; unless($self->{'_hit_queue_started'}) { $self->{'_hit_queue'} = ( [$self->oldhits(), $self->newhits()] ); $self->{'_hit_queue_started'} = 1; } return shift @{$self->{'_hit_queue'}}; } =head2 next_hit_new See documentation in L. =cut sub next_hit_new { my ($self) = @_; unless($self->{'_hit_queue_new_started'}) { $self->{'_hit_queue_new'} = [$self->newhits()]; $self->{'_hit_queue_new_started'} = 1; } return shift @{$self->{'_hit_queue_new'}}; } =head2 next_hit_old See documentation in L. =cut sub next_hit_old { my ($self,$found_again) = @_; unless($self->{'_hit_queue_old_started'}) { $self->{'_hit_queue_old'} = [$self->oldhits()]; $self->{'_hit_queue_old_started'} = 1; } return shift @{$self->{'_hit_queue_old'}}; } =head2 rewind Title : rewind Usage : $iteration->rewind; Function: Allow one to reset the Hit iterators to the beginning Since this is an in-memory implementation Returns : none Args : none =cut sub rewind { my $self = shift; $self->{'_hit_queue_started'} = 0; $self->{'_hit_queue_new_started'} = 0; $self->{'_hit_queue_old_started'} = 0; foreach ($self->hits) { $_->rewind; } } =head2 num_hits See documentation in L. =cut sub num_hits { my $self = shift; return $self->num_hits_old + $self->num_hits_new; } =head2 num_hits_new See documentation in L. =cut sub num_hits_new { my $self = shift; return scalar $self->newhits(); } =head2 num_hits_old See documentation in L. =cut sub num_hits_old { my ($self,$found_again) = @_; return scalar $self->oldhits(); } =head2 add_hit See documentation in L. =cut sub add_hit { my ($self,@args) = @_; my( $hit, $old, $below, $newly_below ) = $self->_rearrange([qw(HIT OLD BELOW_THRESHOLD NEWLY_BELOW )], @args); my $count = 0; unless( ref($hit) eq 'HASH' || $hit->isa('Bio::Search::Hit::HitI') ) { $self->throw(-class=>'Bio::Root::BadParameter', -text=>"Passed in " .ref($hit). " as a Hit which is not a Bio::Search::Hit::HitI."); } if($old) { if ($newly_below) { push @{$self->{'_oldhits_newly_below_threshold'}}, $hit; $count = scalar @{$self->{'_oldhits_newly_below_threshold'}}; } elsif ($below) { push @{$self->{'_oldhits_below_threshold'}}, $hit; $count = scalar @{$self->{'_oldhits_below_threshold'}}; } else { push @{$self->{'_oldhits_not_below_threshold'}}, $hit; $count = scalar @{$self->{'_oldhits_not_below_threshold'}}; } } elsif (defined $old) { # -old is defined but false, so this is a new PSI-BLAST hit if ($below) { push @{$self->{'_newhits_below_threshold'}}, $hit; $count = scalar @{$self->{'_newhits_below_threshold'}}; } elsif (defined $below) { push @{$self->{'_newhits_not_below_threshold'}}, $hit; $count = scalar @{$self->{'_newhits_not_below_threshold'}}; } else { # -below not defined, PSI-BLAST threshold may not be known push @{$self->{'_newhits_unclassified'}}, $hit; $count = scalar @{$self->{'_newhits_unclassified'}}; } } else { # -old not defined, so it's non-PSI-BLAST push @{$self->{'_newhits_unclassified'}}, $hit; $count = scalar @{$self->{'_newhits_unclassified'}}; } return $count; } =head2 hits See Documentation in InterfaceI. =cut sub hits { my $self = shift; # print STDERR "Called GenericIteration::hits()\n"; my @new = $self->newhits; my @old = $self->oldhits; return ( @new, @old ); } =head2 newhits Returns a list containing all newhits in this order: newhits_below_threshold newhits_not_below_threshold newhits_unclassified See more documentation in InterfaceI. =cut sub newhits { my $self = shift; my @hits = $self->newhits_below_threshold; push @hits, $self->newhits_not_below_threshold; push @hits, $self->newhits_unclassified; return @hits; } =head2 newhits_below_threshold See documentation in L. =cut sub newhits_below_threshold { my $self = shift; if (ref $self->{'_newhits_below_threshold'} ) { my $factory = $self->hit_factory || return @{$self->{'_newhits_below_threshold'}}; for (0..$#{$self->{'_newhits_below_threshold'}}) { ref(${$self->{'_newhits_below_threshold'}}[$_]) eq 'HASH' || next; ${$self->{'_newhits_below_threshold'}}[$_] = $factory->create_object(%{${$self->{'_newhits_below_threshold'}}[$_]}); } return @{$self->{'_newhits_below_threshold'}}; } return; } =head2 newhits_not_below_threshold See documentation in L. =cut sub newhits_not_below_threshold { my $self = shift; if (ref $self->{'_newhits_not_below_threshold'} ) { my $factory = $self->hit_factory || return @{$self->{'_newhits_not_below_threshold'}}; for (0..$#{$self->{'_newhits_not_below_threshold'}}) { ref(${$self->{'_newhits_not_below_threshold'}}[$_]) eq 'HASH' || next; ${$self->{'_newhits_not_below_threshold'}}[$_] = $factory->create_object(%{${$self->{'_newhits_not_below_threshold'}}[$_]}); } return @{$self->{'_newhits_not_below_threshold'}}; } return; } =head2 newhits_unclassified Title : newhits_unclassified Usage : foreach( $iteration->hits_unclassified ) {...} Function: Gets all newhits that have not been partitioned into sets relative to the inclusion threshold. Returns : Array of Bio::Search::Hit::HitI objects. Args : none =cut sub newhits_unclassified { my $self = shift; if (ref $self->{'_newhits_unclassified'} ) { my $factory = $self->hit_factory || return @{$self->{'_newhits_unclassified'}}; for (0..$#{$self->{'_newhits_unclassified'}}) { ref(${$self->{'_newhits_unclassified'}}[$_]) eq 'HASH' || next; ${$self->{'_newhits_unclassified'}}[$_] = $factory->create_object(%{${$self->{'_newhits_unclassified'}}[$_]}); } return @{$self->{'_newhits_unclassified'}}; } return; } =head2 oldhits Returns a list containing all oldhits in this order: oldhits_below_threshold oldhits_newly_below_threshold oldhits_not_below_threshold See more documentation in InterfaceI. =cut sub oldhits { my $self = shift; my @hits = $self->oldhits_below_threshold; push @hits, $self->oldhits_newly_below_threshold; push @hits, $self->oldhits_not_below_threshold; return @hits; } =head2 oldhits_below_threshold See documentation in L. =cut sub oldhits_below_threshold { my $self = shift; if (ref $self->{'_oldhits_below_threshold'} ) { my $factory = $self->hit_factory || return @{$self->{'_oldhits_below_threshold'}}; for (0..$#{$self->{'_oldhits_below_threshold'}}) { ref(${$self->{'_oldhits_below_threshold'}}[$_]) eq 'HASH' || next; ${$self->{'_oldhits_below_threshold'}}[$_] = $factory->create_object(%{${$self->{'_oldhits_below_threshold'}}[$_]}); } return @{$self->{'_oldhits_below_threshold'}}; } return; } =head2 oldhits_newly_below_threshold See documentation in L. =cut sub oldhits_newly_below_threshold { my $self = shift; if (ref $self->{'_oldhits_newly_below_threshold'} ) { my $factory = $self->hit_factory || return @{$self->{'_oldhits_newly_below_threshold'}}; for (0..$#{$self->{'_oldhits_newly_below_threshold'}}) { ref(${$self->{'_oldhits_newly_below_threshold'}}[$_]) eq 'HASH' || next; ${$self->{'_oldhits_newly_below_threshold'}}[$_] = $factory->create_object(%{${$self->{'_oldhits_newly_below_threshold'}}[$_]}); } return @{$self->{'_oldhits_newly_below_threshold'}}; } return; } =head2 oldhits_not_below_threshold See documentation in L. =cut sub oldhits_not_below_threshold { my $self = shift; if (ref $self->{'_oldhits_not_below_threshold'} ) { my $factory = $self->hit_factory || return @{$self->{'_oldhits_not_below_threshold'}}; for (0..$#{$self->{'_oldhits_not_below_threshold'}}) { ref(${$self->{'_oldhits_not_below_threshold'}}[$_]) eq 'HASH' || next; ${$self->{'_oldhits_not_below_threshold'}}[$_] = $factory->create_object(%{${$self->{'_oldhits_not_below_threshold'}}[$_]}); } return @{$self->{'_oldhits_not_below_threshold'}}; } return; } =head2 hits_below_threshold See documentation in L. =cut sub hits_below_threshold { my $self = shift; my @hits = $self->newhits_below_threshold; push @hits, $self->oldhits_newly_below_threshold; return @hits; } =head2 get_hit See documentation in L. To free up the memory used by the get_hit() functionality, call free_hit_lookup(). This functionality might be useful at the Result level, too. BlastResult::get_hit() would return a list of HitI objects for hits that occur in multiple iterations. =cut sub get_hit { my ($self,$name) = @_; $self->_create_hit_lookup() unless defined $self->{'_hit_lookup'}; return $self->{'_hit_lookup'}->{"\U$name"}; } # Internal method. sub _create_hit_lookup { my $self = shift; foreach ($self->hits) { my $hname = $_->name; $self->{'_hit_lookup'}->{"\U$hname"} = $_; } } =head2 free_hit_lookup Purpose : Frees up the memory used by the get_hit() functionality. For the memory-conscious. =cut sub free_hit_lookup { my $self = shift; undef $self->{'_hit_lookup'}; } 1; BioPerl-1.007002/Bio/Search/Iteration/IterationI.pm000444000766000024 5303213155576320 22017 0ustar00cjfieldsstaff000000000000#----------------------------------------------------------------- # # BioPerl module Bio::Search::Iteration::IterationI # # Please direct questions and support issues to # # Cared for by Steve Chervitz # # You may distribute this module under the same terms as perl itself #----------------------------------------------------------------- # POD documentation - main docs before the code =head1 NAME Bio::Search::Iteration::IterationI - Abstract interface to an iteration from an iterated search result, such as PSI-BLAST. =head1 SYNOPSIS # Bio::Search::Iteration::IterationI objects cannot be # instantiated since this module defines a pure interface. # Given an object that implements the # Bio::Search::Iteration::IterationI interface, # you can do the following things with it: # First, open up a SearchIO stream use Bio::SearchIO; my $file = shift or die "Usage: $0 \n"; my $in = Bio::SearchIO->new(-format => 'blast', -file => $file # comment out this line to read STDIN ); # Iterate over all results in the input stream while (my $result = $in->next_result) { printf "Result #%d: %s\n", $in->result_count, $result->to_string; printf "Total Iterations: %d\n", $result->num_iterations(); # Iterate over all iterations and process old and new hits # separately. while( my $it = $result->next_iteration) { printf "\nIteration %d\n", $it->number; printf "Converged: %d\n", $it->converged; # Print out the hits not found in previous iteration printf "New hits: %d\n", $it->num_hits_new; while( my $hit = $it->next_hit_new ) { printf " %s, Expect=%g\n", $hit->name, $hit->expect; } # Print out the hits found in previous iteration printf "Old hits: %d\n", $it->num_hits_old; while( my $hit = $it->next_hit_old ) { printf " %s, Expect=%g\n", $hit->name, $hit->expect; } } printf "%s\n\n", '-' x 50; } printf "Total Reports processed: %d: %s\n", $in->result_count; __END__ # NOTE: The following functionality is just proposed # (does not yet exist but might, given sufficient hew and cry): # Zero-in on the new hits found in last iteration. # By default, iteration() returns the last one. my $last_iteration = $result->iteration(); while( my $hit = $last_iteration->next_hit) { # Do something with new hit... } # Get the first iteration my $first_iteration = $result->iteration(1); =head1 DESCRIPTION Bio::Search::Result::ResultI objects are data structures containing the results from the execution of a search algorithm. As such, it may contain various algorithm specific information as well as details of the execution, but will contain a few fundamental elements, including the ability to return Bio::Search::Hit::HitI objects. =head2 Classification of Hits Within a given iteration, the hits can be classified into a number of useful subsets based on whether or not the hit appeard in a previous iteration and whether or not the hit is below the threshold E-value for inclusion in the score matrix model. All hits (A) _______________|_________________ | | New hits Old hits (B) (C) _________|________ _______|_________ | | | | Below Above Below Above threshold threshold threshold threshold (D) (E) (F) (G) _________|___________ | | Occurred in a Occurred in a previous iteration previous iteration below threshold above threshold (H) (I) Notes: The term I in the diagram and descriptions below refer to this inclusion threshold. I actually means I. The IterationI interface defines a number of methods for extracting these subsets of hits. =over 4 =item * newhits_below_threshold() [subset D] Hits that did not appear in a previous iteration and are below threshold in the current iteration. =item * newhits_not_below_threshold() [subset E] Hits that did not appear in a previous iteration and are not below threshold in the current iteration. =item * newhits() [subset B] All newly found hits, below and above the inclusion threshold. This is the union of newhits_below_threshold() + newhits_not_below_threshold() [subset D + subset E]. =item * oldhits_below_threshold() [subset H] Hits that appeared in a previous iteration below threshold and are still below threshold in the current iteration. =item * oldhits_newly_below_threshold() [subset I] Hits that appeared in a previous iteration above threshold but are below threshold in the current iteration. (Not applicable to the first iteration.) =item * oldhits_not_below_threshold() [subset G] Hits that appeared in a previous iteration not below threshold and are still not below threshold in the current iteration. =item * oldhits() [subset C] All hits that occurred in a previous iteration, whether below or above threshold in the current iteration. Union of oldhits_below_threshold() + oldhits_newly_below_threshold() + oldhits_not_below_threshold() [subset H + subset I + subset G]. (Not applicable to the first iteration.) =item * hits_below_threshold() [subset D + subset F] All hits, old and new, that are below the inclusion threshold in this iteration. This is the union of newhits_below_threshold() + oldhits_below_threshold() + oldhits_newly_below_threshold() [subset D + subset H + subset I]. =item * hits() [subset A] The union of newhits() and oldhits() [subset B + subset C]. =back For the first iteration, the methods L, L, L, and oldhits_not_below_threshold() will return empty lists. Iterator and numbers-of-hit methods are provided for subsets A, B, and C: =over 4 =item * next_hit_new(), num_hits_new() [subset B] =item * next_hit_old(), num_hits_old() [subset C] =item * next_hit(), num_hits() [subset A] =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Steve Chervitz Esac@bioperl.orgE See L for where to send bug reports and comments. =head1 COPYRIGHT Copyright (c) 2003 Steve Chervitz. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::Search::Iteration::IterationI; use strict; use base qw(Bio::Root::RootI); =head2 number Title : number Usage : $it_number = $iteration->number(); Purpose : returns the number of the iteration (a.k.a "round") within the Result. Returns : integer Args : [optional] integer to set the number of the iteration =cut sub number { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 converged Title : converged Usage : $it_converged = $iteration->converged(); Purpose : Indicates whether or not the iteration has converged Returns : boolean Args : [optional] boolean value to set the converged of the iteration =cut sub converged { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 next_hit Title : next_hit Usage : while( $hit = $iteration->next_hit( [$found_again]) ) { ... } Purpose : Iterates through all of the HitI objects including new hits and old hits found in a previous iteration and both below and above the inclusion threshold. Corresponds to subset A in the "Classification of Hits" documentation section of this module. Returns : A Bio::Search::Hit::HitI object or undef if there are no more. Hits will be returned in the order in which they occur in the report unless otherwise specified. Args : none See Also: L, L next_hit() iterates through all hits, including the new ones for this iteration and those found in previous iterations. You can interrogate each hit using L to determine whether it is new or old. To get just the new hits, use L. To get just the old hits, use L. =cut sub next_hit { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 next_hit_new Title : next_hit_new Usage : while( $hit = $iteration->next_hit_new() ) { ... } Purpose : Iterates through all newly found hits (did not occur in a previous iteration) and are either below or above the inclusion threshold. Corresponds to subset B in the "Classification of Hits" documentation section of this module. Returns : A Bio::Search::Hit::HitI object or undef if there are no more. Hits will be returned in the order in which they occur in the report unless otherwise specified. Args : none See Also: L, L, L, L =cut sub next_hit_new { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 next_hit_old Title : next_hit_old Usage : while( $hit = $iteration->next_hit_old() ) { ... } Purpose : Iterates through the Hit objects representing just the hits that have been found in a previous iteration, whether below or above the inclusion threshold. Corresponds to subset C in the "Classification of Hits" documentation section of this module. Returns : A Bio::Search::Hit::HitI object or undef if there are no more. Hits will be returned in the order in which they occur in the report unless otherwise specified. Args : none See Also: L, L, L, L =cut sub next_hit_old { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 num_hits Title : num_hits Usage : my $hitcount_total = $iteration->num_hits Purpose : Returns the total number of hits for this query result, including new and old below and above inclusion threshold. Returns : integer Args : none See Also: L, L, L =cut sub num_hits { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 num_hits_new Title : num_hits_new Usage : my $hitcount_new = $result->num_hits_new; : my $hitcount_new_below_thresh = $result->num_hits_new( 1 ); Purpose : Returns the number of new hits in this iteration that were not found in a previous iteration and are either below or above the the inclusion threshold. Corresponds to subset B in the "Classification of Hits" documentation section of this module. Returns : integer Args : (optional) boolean, true if you want to get a count of just the new hits that are below the inclusion threshold. See Also: L, L, L =cut sub num_hits_new { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 num_hits_old Title : num_hits_old Usage : my $hitcount_old = $result->num_hits_old; : my $hitcount_old_below_thresh = $result->num_hits_old( 1 ); Purpose : Returns the number of new hits in this iteration that were found in a previous iteration and are either below or above the the inclusion threshold. Corresponds to subset C in the "Classification of Hits" documentation section of this module. Returns : integer Args : (optional) boolean, true if you want to get a count of just the old hits that are below the inclusion threshold. See Also: L, L, L =cut sub num_hits_old { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 hits Title : hits Usage : foreach( $obj->hits() ) { ... }; Purpose : Provides access to all hits, both new and old, and either below or above the inclusion threshold. Corresponds to subset A in the "Classification of Hits" documentation section of this module. Returns : An array containing all HitI objects. Hits will be ordered according to their occurrence in the report unless otherwise specified. Args : none See Also: L, L, L =cut sub hits { shift->throw_not_implemented(); } =head2 newhits Title : newhits Usage : foreach( $obj->newhits() ) { ... }; Purpose : Provides access to hits that were not found in a previous iteration and may be either below or above the inclusion threshold. Corresponds to subset B in the "Classification of Hits" documentation section of this module. Returns : An array containing Bio::Search::Hit::HitI objects. Hits will be ordered according to their occurrence in the report unless otherwise specified. Args : none See Also: L, L, L + L, L =cut sub newhits { shift->throw_not_implemented(); } =head2 oldhits Title : oldhits Usage : foreach( $obj->oldhits() ) { ... }; Purpose : Provides access to hits that were found in a previous iteration and are either below or above the inclusion threshold in the current iteration. Corresponds to subset C in the "Classification of Hits" documentation section of this module. Returns : An array containing Bio::Search::Hit::HitI objects. Hits will be ordered according to their occurrence in the report unless otherwise specified. Args : none See Also: L, L, L, L, L, L =cut sub oldhits { shift->throw_not_implemented(); } =head2 newhits_below_threshold Title : newhits_below_threshold Usage : foreach( $obj->newhits_below_threshold() ) { ... }; Purpose : Provides access to hits that did not appear in a previous iteration and are below threshold. Corresponds to subset D in the "Classification of Hits" documentation section of this module. Returns : An array containing Bio::Search::Hit::HitI objects. Hits will be returned in the order in which they occur in the report unless otherwise specified. Args : none See Also: L, L, L, L =cut sub newhits_below_threshold { shift->throw_not_implemented(); } =head2 oldhits_below_threshold Title : oldhits_below_threshold Usage : foreach( $obj->oldhits_below_threshold() ) { ... }; Purpose : Provides access to hits that appeared in a previous iteration below inclusion threshold and are still below threshold. Corresponds to subset H in the "Classification of Hits" documentation section of this module. Returns : An array containing Bio::Search::Hit::HitI objects. Hits will be returned in the order in which they occur in the report unless otherwise specified. Args : none See Also: L, L, L, L =cut sub oldhits_below_threshold { shift->throw_not_implemented(); } =head2 oldhits_newly_below_threshold Title : oldhits_newly_below_threshold Usage : foreach( $obj->oldhits_newly_below_threshold() ) { ... }; Purpose : Provides access to hits that appeared in a previous iteration above threshold but are below threshold in the current iteration. Not applicable to the first iteration. Corresponds to subset I in the "Classification of Hits" documentation section of this module. Returns : An array containing Bio::Search::Hit::HitI objects. Hits will be returned in the order in which they occur in the report unless otherwise specified. Args : none See Also: L, L, L =cut sub oldhits_newly_below_threshold { shift->throw_not_implemented(); } =head2 oldhits_not_below_threshold Title : oldhits_not_below_threshold Usage : foreach( $obj->oldhits_not_below_threshold() ) { ... }; Purpose : Provides access to hits that appeared in a previous iteration not below threshold and are still not below threshold. Corresponds to subset G in the "Classification of Hits" documentation section of this module. Returns : An array containing Bio::Search::Hit::HitI objects. Hits will be returned in the order in which they occur in the report unless otherwise specified. Args : none See Also: L, L, L =cut sub oldhits_not_below_threshold { shift->throw_not_implemented(); } =head2 newhits_not_below_threshold Title : newhits_not_below_threshold Usage : foreach( $obj->newhits_not_below_threshold() ) { ... }; Purpose : Provides access to hits that did not appear in a previous iteration and are not below threshold in the current iteration. Corresponds to subset E in the "Classification of Hits" documentation section of this module. Returns : An array containing Bio::Search::Hit::HitI objects. Hits will be returned in the order in which they occur in the report unless otherwise specified. Args : none See Also: L, L, L =cut sub newhits_not_below_threshold { shift->throw_not_implemented(); } =head2 hits_below_threshold Title : hits_below_threshold Usage : foreach( $obj->hits_below_threshold() ) { ... }; Purpose : Provides access to all hits, old and new, that are below the inclusion threshold. Corresponds to the union of subset D and subset F in the "Classification of Hits" documentation section of this module. Returns : An array containing Bio::Search::Hit::HitI objects. Hits will be returned in the order in which they occur in the report unless otherwise specified. Args : none See Also: L, L, L, L =cut sub hits_below_threshold { shift->throw_not_implemented(); } =head2 add_hit Title : add_hit Usage : $report->add_hit(-hit =>$hit_obj, -old =>$boolean, -below_threshold =>$boolean, -newly_below =>$boolean ) Purpose : Adds a HitI to the stored list of hits Returns : Number of HitI currently stored for the class of the added hit. Args : Tagged values, the only required one is -hit. All others are used only for PSI-BLAST reports. -hit => Bio::Search::Hit::HitI object -old => boolean, true indicates that the hit was found in a previous iteration. Default=false. -below_threshold => boolean, true indicates that the hit is below the inclusion threshold. -newly_below => boolean, true indicates that the hit is below the inclusion threshold in this iteration but was above the inclusion threshold in a previous iteration. Only appropriate for old hits. Default=false. Throws : Bio::Root::BadParameter if the hit is not a Bio::Search::Hit::HitI. Bio::Root::BadParameter if -old=>false and -newly_below=>true. =cut sub add_hit { shift->throw_not_implemented } =head2 get_hit Title : get_hit Usage : $hit = $report->get_hit( $hit_name ) Purpose : Gets a HitI object given its name if a hit with this name exists within this Iteration. Returns : Bio::Search::Hit::HitI object or undef if there is no such hit. Args : $hit_name = string containing name of the hit Throws : n/a The name string must be the same as that returned by Bio::Search::Hit::HitI::name(). The lookup should be case-insensitive. =cut sub get_hit { shift->throw_not_implemented } 1; BioPerl-1.007002/Bio/Search/Result000755000766000024 013155576320 16552 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Search/Result/BlastPullResult.pm000444000766000024 2700413155576320 22371 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Result::BlastPullResult # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::BlastPullResult - A parser and result object for BLASTN results =head1 SYNOPSIS # generally we use Bio::SearchIO to build these objects use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'blast_pull', -file => 'result.blast'); while (my $result = $in->next_result) { print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n"; } =head1 DESCRIPTION This object implements a parser for NCBI BLASTN result output. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Result::BlastPullResult; use strict; use Bio::Search::Hit::BlastPullHit; use base qw(Bio::Root::Root Bio::Search::Result::PullResultI); =head2 new Title : new Usage : my $obj = Bio::SearchIO::Result::hmmpfam->new(); Function: Builds a new Bio::SearchIO::Result::hmmpfam object Returns : Bio::SearchIO::Result::hmmpfam Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent) -parent => Bio::PullParserI object (required if no -chunk) -parameters => hash ref of search parameters (key => value), optional -statistics => hash ref of search statistics (key => value), optional where the array ref provided to -chunk contains an IO object for a filehandle to something representing the raw data of the result, and $start and $end define the tell() position within the filehandle that the result data starts and ends (optional; defaults to start and end of the entire thing described by the filehandle) =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->_setup(@args); foreach my $field (qw( header hit_table hsp_table alignments next_model models query_length stats_and_params)) { $self->_fields->{$field} = undef; } $self->_dependencies( { ( query_name => 'header', query_accession => 'header', query_description => 'header', query_length => 'header', hit_table => 'header', num_hits => 'hit_table', no_hits_found => 'hit_table' ) } ); return $self; } # # PullParserI discovery methods so we can answer all ResultI questions # sub _discover_header { my $self = shift; $self->_chunk_seek(0); my $header = $self->_get_chunk_by_end("Value\n"); if (!$header) { $header = $self->_get_chunk_by_end("***** No hits found ******\n"); $self->{_no_hits_found} = 1; } $self->throw("Invalid header returned") unless $header; $self->{_after_header} = $self->_chunk_tell; ($self->_fields->{query_name}) = $header =~ /^\s*(\S+)/; $self->_fields->{query_accession} = ''; $self->_fields->{query_description} = ''; if ($header =~ /^Length=(\d+)/m) { $self->_fields->{query_length} = $1; } elsif ($header =~ /\((\d+) letters\)/) { # older form? $self->_fields->{query_length} = $1; if ($header =~ /^\s*\(\d+ letters/) { # there wasn't a query sequence name $self->_fields->{query_name} = ''; } } $self->_fields->{header} = 1; } sub _discover_hit_table { my $self = shift; $self->_chunk_seek($self->{_after_header}); my $table = $self->_get_chunk_by_end("\n>"); if (!$table && !$self->{_no_hits_found}) { # no alignments, presumably; hit table comprises the remainder of this # result while (my $line = $self->_get_chunk_by_nol(1)) { $table .= $line; } } $table ||= ''; $self->{_after_hit_table} = $self->_chunk_tell; my $evalue_cutoff = $self->get_field('evalue_cutoff'); undef $evalue_cutoff if $evalue_cutoff eq '[unset]'; my $score_cutoff = $self->get_field('score_cutoff'); undef $score_cutoff if $score_cutoff eq '[unset]'; my @table; my $no_hit = 1; while ($table =~ /^(\S+)\s+(\S.*?)?\s+(\S+)\s+([\de]\S*)\s*\n/gm) { $no_hit = 0; my ($name, $desc, $score, $evalue) = ($1, $2, $3, $4); $desc ||= ''; if ($evalue =~ /^e/) { $evalue = '1'.$evalue; } next if ($evalue_cutoff && $evalue > $evalue_cutoff); next if ($score_cutoff && $score < $score_cutoff); push(@table, [$name, $desc, $score, $evalue]); } $self->_fields->{hit_table} = \@table; $self->{_next_hit_index} = @table > 0 ? 0 : -1; $self->_fields->{no_hits_found} = $no_hit; $self->_fields->{num_hits} = @table; } sub _discover_next_hit { my $self = shift; my $hit_table = $self->get_field('hit_table'); return if $self->{_next_hit_index} == -1; my $hit_row = ${$hit_table}[$self->{_next_hit_index}]; $self->_chunk_seek($self->{_end_of_previous_hit} || $self->{_after_hit_table}); my ($start, $end) = $self->_find_chunk_by_end("\n>"); unless ($end) { $start = $self->{_end_of_previous_hit} || $self->{_after_hit_table}; $end = $self->_chunk_true_end; } else { $end += $self->_chunk_true_start; } $start += $self->_chunk_true_start; $self->{_end_of_previous_hit} = $end - $self->_chunk_true_start; #*** needs to inherit piped_behaviour, and we need to deal with _sequential # ourselves $self->_fields->{next_hit} = Bio::Search::Hit::BlastPullHit->new(-parent => $self, -chunk => [$self->chunk, $start, $end], -hit_data => $hit_row); $self->{_next_hit_index}++; if ($self->{_next_hit_index} > $#{$hit_table}) { $self->{_next_hit_index} = -1; } } sub _discover_stats_and_params { my $self = shift; $self->_chunk_seek(0); my ($start, $end) = $self->_find_chunk_by_end("\n Database: "); $self->_chunk_seek($end); my $gapped = 0; while ($self->_get_chunk_by_nol(1)) { if (/Number of letters in database:\s+(\S+)/) { my $stat = $1; $stat =~ s/,//g; $self->add_statistic('dbletters', $stat); } elsif (/Number of sequences in database:\s+(\S+)/) { my $stat = $1; $stat =~ s/,//g; $self->add_statistic('dbentries', $stat); } elsif (/^Lambda/) { my $line = $self->_get_chunk_by_nol(1); $line =~ /\s+(\S+)\s+(\S+)\s+(\S+)/; $self->add_statistic($gapped ? 'lambda_gapped' : 'lambda', $1); $self->add_statistic($gapped ? 'kappa_gapped' : 'kappa', $2); $self->add_statistic($gapped ? 'entropy_gapped' : 'entropy', $3); $gapped = 1; } elsif (/^Matrix: (.+)\n/) { $self->add_parameter('matrix', $1); } elsif (/^Gap Penalties: Existence: (\d+), Extension: (\d+)/) { $self->add_parameter('gapopen', $1); $self->add_parameter('gapext', $2); } elsif (/^Number of Hits to DB: (\d+)/) { $self->add_statistic('Hits_to_DB', $1); } elsif (/^Number of extensions: (\d+)/) { $self->add_statistic('num_extensions', $1); } elsif (/^Number of successful extensions: (\d+)/) { $self->add_statistic('num_successful_extensions', $1); } elsif (/^Number of sequences better than (\S+):/) { $self->add_parameter('expect', $1); } elsif (/^[Ll]ength of query: (\d+)/) { $self->add_statistic('querylength', $1); } elsif (/^[Ee]ffective HSP length: (\d+)/) { $self->add_statistic('effective_hsplength', $1); } elsif (/^[Ee]ffective length of database: (\d+)/) { $self->add_statistic('effectivedblength', $1); } elsif (/^[Ee]ffective search space: (\d+)/) { $self->add_statistic('effectivespace', $1); } elsif (/^[Ee]ffective search space used: (\d+)/) { $self->add_statistic('effectivespaceused', $1); } elsif (/^([TAXS]\d?): (\d+)(?: \((\S+))?/) { $self->add_statistic($1, $2); $self->add_statistic($1.'_bits', $3) if $3; } } $self->_fields->{stats_and_params} = 1; } =head2 next_hit Title : next_hit Usage : while( $hit = $result->next_hit()) { ... } Function: Returns the next available Hit object, representing potential matches between the query and various entities from the database. Returns : a Bio::Search::Hit::HitI object or undef if there are no more. Args : none =cut sub next_hit { my $self = shift; my $hit = $self->get_field('next_hit'); undef $self->_fields->{next_hit}; return $hit; } =head2 hits Title : hits Usage : my @hits = $result->hits Function: Returns the HitI objects contained within this Result Returns : Array of Bio::Search::Hit::HitI objects Args : none See Also: L =cut sub hits { my $self = shift; my $old = $self->{_next_hit_index} || 0; $self->rewind; my @hits; while (defined(my $hit = $self->next_hit)) { push(@hits, $hit); } $self->{_next_hit_index} = @hits > 0 ? $old : -1; return @hits; } =head2 sort_hits Title : sort_hits Usage : $result->sort_hits('throw("Not implemented yet"); } =head2 rewind Title : rewind Usage : $result->rewind; Function: Allow one to reset the Hit iterator to the beginning, so that next_hit() will subsequently return the first hit and so on. Returns : n/a Args : none =cut sub rewind { my $self = shift; unless ($self->_fields->{hit_table}) { $self->get_field('hit_table'); } $self->{_next_hit_index} = @{$self->_fields->{hit_table}} > 0 ? 0 : -1; } =head2 get_statistic Title : get_statistic Usage : my $gap_ext = $result->get_statistic('kappa') Function: Returns the value for a specific statistic available from this result Returns : string Args : name of statistic (string) =cut sub get_statistic { my $self = shift; $self->get_field('stats_and_params'); return $self->SUPER::get_statistic(@_); } =head2 get_parameter Title : get_parameter Usage : my $gap_ext = $result->get_parameter('gapext') Function: Returns the value for a specific parameter used when running this result Returns : string Args : name of parameter (string) =cut sub get_parameter { my $self = shift; $self->get_field('stats_and_params'); return $self->SUPER::get_parameter(@_); } 1; BioPerl-1.007002/Bio/Search/Result/BlastResult.pm000444000766000024 3554713155576320 21547 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Result::BlastResult # # Please direct questions and support issues to # # Cared for by Steve Chervitz # # Copyright Steve Chervitz # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::BlastResult - Blast-specific subclass of Bio::Search::Result::GenericResult =head1 SYNOPSIS # Working with iterations (PSI-BLAST results) $result->next_iteration(); $result->num_iterations(); $result->iteration(); $result->iterations(); # See Bio::Search::Result::GenericResult for information about working with Results. # See L # for details about working with iterations. # TODO: # * Show how to configure a SearchIO stream so that it generates # BlastResult objects. =head1 DESCRIPTION This object is a subclass of Bio::Search::Result::GenericResult and provides some operations that facilitate working with BLAST and PSI-BLAST results. For general information about working with Results, see Bio::Search::Result::GenericResult. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Steve Chervitz Email sac@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Result::BlastResult; use strict; use Bio::Search::BlastStatistics; use base qw(Bio::Search::Result::GenericResult); =head2 new Title : new Usage : my $obj = Bio::Search::Result::BlastResult->new(); Function: Builds a new Bio::Search::Result::BlastResult object Returns : Bio::Search::Result::BlastResult Args : See Bio::Search::Result::GenericResult(); The following parameters are specific to BlastResult: -iterations => array ref of Bio::Search::Iteration::IterationI objects -inclusion_threshold => e-value threshold for inclusion in the PSI-BLAST score matrix model (blastpgp) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_iterations'} = []; $self->{'_iteration_index'} = 0; $self->{'_iteration_count'} = 0; my( $iters, $ithresh ) = $self->_rearrange([qw(ITERATIONS INCLUSION_THRESHOLD)],@args); $self->{'_inclusion_threshold'} = $ithresh; # This is a read-only variable if( defined $iters ) { $self->throw("Must define arrayref of Iterations when initializing a $class\n") unless ref($iters) =~ /array/i; foreach my $i ( @{$iters} ) { $self->add_iteration($i); } } else { # This shouldn't get called with the new SearchIO::blast. print STDERR "BlastResult::new(): Not adding iterations.\n"; $self->{'_no_iterations'} = 1; } return $self; } =head2 hits Title : hits Usage : my @hits = $result->hits Function: Returns the available hits for this Result Returns : Array of L objects Args : none Note : This method overrides L to take into account the possibility of multiple iterations, as occurs in PSI-BLAST reports. If there are multiple iterations, all 'new' hits for all iterations are returned. These are the hits that did not occur in a previous iteration. See Also: L =cut sub hits { my ($self) = shift; if ($self->{'_no_iterations'}) { return $self->SUPER::hits; } my @hits = (); foreach my $it ($self->iterations) { push @hits, $it->hits; } return @hits; } =head2 next_hit Title : next_hit Usage : while( $hit = $result->next_hit()) { ... } Function: Returns the next available Hit object, representing potential matches between the query and various entities from the database. Returns : a Bio::Search::Hit::HitI object or undef if there are no more. Args : none Note : This method overrides L to take into account the possibility of multiple iterations, as occurs in PSI-BLAST reports. If there are multiple iterations, calling next_hit() traverses the all of the hits, old and new, for each iteration, calling next_hit() on each iteration. See Also: L =cut sub next_hit { my ($self,@args) = @_; if ($self->{'_no_iterations'}) { return $self->SUPER::next_hit(@args); } my $iter_index; if (not defined $self->{'_last_hit'}) { $iter_index = $self->{'_iter_index'} = $self->_next_iteration_index; } else { $iter_index = $self->{'_iter_index'}; } return if $iter_index >= scalar @{$self->{'_iterations'}}; my $it = $self->{'_iterations'}->[$iter_index]; my $hit = $self->{'_last_hit'} = $it->next_hit; return defined($hit) ? $hit : $self->next_hit; } =head2 num_hits Title : num_hits Usage : my $hitcount= $result->num_hits Function: returns the number of hits for this query result Returns : integer Args : none Note : This method overrides L to take into account the possibility of multiple iterations, as occurs in PSI-BLAST reports. If there are multiple iterations, calling num_hits() returns the number of 'new' hits for each iteration. These are the hits that did not occur in a previous iteration. See Also: L =cut sub num_hits{ my ($self) = shift; if ($self->{'_no_iterations'}) { return $self->SUPER::num_hits; } if (not defined $self->{'_iterations'}) { $self->throw("Can't get Hits: data not collected."); } return scalar( $self->hits ); } =head2 add_hit Title : add_hit Usage : $report->add_hit($hit) Function: Adds a HitI to the stored list of hits Returns : Number of HitI currently stored Args : Bio::Search::Hit::HitI =cut sub add_hit { my ($self,$hit) = @_; my $iter = $self->iteration; if( $hit->isa('Bio::Search::Hit::HitI') ) { return $iter->add_hit(-hit => $hit); } else { $self->throw("Passed in a " .ref($hit). " as a Iteration which is not a Bio::Search::Hit::HitI."); } return $iter->num_hits; } =head2 add_iteration Title : add_iteration Usage : $report->add_iteration($iteration) Function: Adds a IterationI to the stored list of iterations Returns : Number of IterationI currently stored Args : Bio::Search::Iteration::IterationI =cut sub add_iteration { my ($self,$i) = @_; if( $i->isa('Bio::Search::Iteration::IterationI') ) { push @{$self->{'_iterations'}}, $i; $self->{'_iteration_count'}++; } else { $self->throw("Passed in a " .ref($i). " as a Iteration which is not a Bio::Search::Iteration::IterationI."); } return scalar @{$self->{'_iterations'}}; } =head2 next_iteration Title : next_iteration Usage : while( $it = $result->next_iteration()) { ... } Function: Returns the next Iteration object, representing all hits found within a given PSI-Blast iteration. Returns : a Bio::Search::Iteration::IterationI object or undef if there are no more. Args : none =cut sub next_iteration { my ($self) = @_; unless($self->{'_iter_queue_started'}) { $self->{'_iter_queue'} = [$self->iterations()]; $self->{'_iter_queue_started'} = 1; } return shift @{$self->{'_iter_queue'}}; } =head2 iteration Usage : $iteration = $blast->iteration( $number ); Purpose : Get an IterationI object for the specified iteration in the search result (PSI-BLAST). Returns : Bio::Search::Iteration::IterationI object Throws : Bio::Root::NoSuchThing exception if $number is not within range of the number of iterations in this report. Argument : integer (optional, if not specified get the last iteration) First iteration = 1 =cut sub iteration { my ($self,$num) = @_; $num = scalar @{$self->{'_iterations'}} unless defined $num; unless ($num >= 1 and $num <= scalar $self->{'_iteration_count'}) { $self->throw(-class=>'Bio::Root::NoSuchThing', -text=>"No such iteration number: $num. Valid range=1-$self->{'_iteration_count'}", -value=>$num); } return $self->{'_iterations'}->[$num-1]; } =head2 num_iterations Usage : $num_iterations = $blast->num_iterations; Purpose : Get the number of iterations in the search result (PSI-BLAST). Returns : Total number of iterations in the report Argument : none (read-only) =cut sub num_iterations { shift->{'_iteration_count'} } # Methods provided for consistency with BPpsilite.pm (now deprecated); # these are now merely synonyms =head2 number_of_iterations Usage : $num_iterations = $blast->number_of_iterations; Purpose : Get the number of iterations in the search result (PSI-BLAST). Returns : Total number of iterations in the report Argument : none (read-only) Note : Alias of L. =cut sub number_of_iterations { shift->num_iterations } =head2 round Usage : $round = $blast->round( $number ); Purpose : Get an IterationI object for the specified iteration in the search result (PSI-BLAST). Returns : Bio::Search::Iteration::IterationI object Throws : Bio::Root::NoSuchThing exception if $number is not within range of the number of iterations in this report. Argument : integer (optional, if not specified get the last iteration) First iteration = 1 Note : Alias of L. =cut sub round { shift->iteration(@_) } =head2 iterations Title : iterations Usage : my @iterations = $result->iterations Function: Returns the IterationI objects contained within this Result Returns : Array of L objects Args : none =cut sub iterations { my $self = shift; my @its = (); if( ref($self->{'_iterations'}) =~ /ARRAY/i ) { @its = @{$self->{'_iterations'}}; } return @its; } =head2 psiblast Usage : if( $blast->psiblast ) { ... } Purpose : Set/get a boolean indicator whether or not the report is a PSI-BLAST report. Returns : 1 if PSI-BLAST, undef if not. Argument : 1 (when setting) =cut #---------------- sub psiblast { #---------------- my ($self, $val ) = @_; if( $val ) { $self->{'_psiblast'} = 1; } return $self->{'_psiblast'}; } =head2 no_hits_found Usage : $nohits = $blast->no_hits_found( $iteration_number ); Purpose : Get boolean indicator indicating whether or not any hits were present in the report. This is NOT the same as determining the number of hits via the hits() method, which will return zero hits if there were no hits in the report or if all hits were filtered out during the parse. Thus, this method can be used to distinguish these possibilities for hitless reports generated when filtering. Returns : Boolean Argument : (optional) integer indicating the iteration number (PSI-BLAST) If iteration number is not specified and this is a PSI-BLAST result, then this method will return true only if all iterations had no hits found. =cut sub no_hits_found { my ($self, $round) = @_; my $result = 0; # final return value of this method. # Watch the double negative! # result = 0 means "yes hits were found" # result = 1 means "no hits were found" (for the indicated iteration or all iterations) # If a iteration was not specified and there were multiple iterations, # this method should return true only if all iterations had no hits found. if( not defined $round ) { if( $self->{'_iterations'} > 1) { $result = 1; foreach my $i( 1..$self->{'_iterations'} ) { if( not defined $self->{"_iteration_$i"}->{'_no_hits_found'} ) { $result = 0; last; } } } else { $result = $self->{"_iteration_1"}->{'_no_hits_found'}; } } else { $result = $self->{"_iteration_$round"}->{'_no_hits_found'}; } return $result; } =head2 set_no_hits_found Usage : $blast->set_no_hits_found( $iteration_number ); Purpose : Set boolean indicator indicating whether or not any hits were present in the report. Returns : n/a Argument : (optional) integer indicating the iteration number (PSI-BLAST) =cut sub set_no_hits_found { my ($self, $round) = @_; $round ||= 1; $self->{"_iteration_$round"}->{'_no_hits_found'} = 1; } =head2 _next_iteration_index Title : _next_iteration_index Usage : private =cut sub _next_iteration_index{ my ($self,@args) = @_; return $self->{'_iteration_index'}++; } =head2 rewind Title : rewind Usage : $result->rewind; Function: Allow one to reset the Iteration iterator to the beginning Since this is an in-memory implementation Returns : none Args : none =cut sub rewind { my $self = shift; $self->SUPER::rewind(@_); $self->{'_iteration_index'} = 0; foreach ($self->iterations) { $_->rewind; } } =head2 inclusion_threshold Title : inclusion_threshold Usage : my $incl_thresh = $result->inclusion_threshold; (read-only) Function: Gets the e-value threshold for inclusion in the PSI-BLAST score matrix model (blastpgp) that was used for generating the report being parsed. Returns : number (real) or undef if not a PSI-BLAST report. Args : none =cut sub inclusion_threshold { my $self = shift; return $self->{'_inclusion_threshold'}; } 1; BioPerl-1.007002/Bio/Search/Result/CrossMatchResult.pm000444000766000024 3151413155576320 22536 0ustar00cjfieldsstaff000000000000package Bio::Search::Result::CrossMatchResult; # # BioPerl module for Bio::Search::Result::CrossMatchResult # # Please direct questions and support issues to # # Cared for by Shin Leong # # Copyright Shin Leong # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::CrossMatchResult - CrossMatch-specific subclass of Bio::Search::Result::GenericResult =head1 SYNOPSIS # Working with iterations (CrossMatch results) $result->next_iteration(); $result->num_iterations(); $result->iteration(); $result->iterations(); # See Bio::Search::Result::GenericResult for information about working with Results. # See L # for details about working with iterations. # TODO: # * Show how to configure a SearchIO stream so that it generates # CrossMatchResult objects. =head1 DESCRIPTION This object is a subclass of Bio::Search::Result::GenericResult and provides some operations that facilitate working with CrossMatch and CrossMatch results. For general information about working with Results, see Bio::Search::Result::GenericResult. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shin Leong Email sleong@watson.wustl.edu =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Result::CrossMatchResult; use strict; use Bio::Search::Result::GenericResult; use base qw(Bio::Search::Result::GenericResult); =head2 new Title : new Usage : my $obj = Bio::Search::Result::CrossMatchResult->new(); Function: Builds a new Bio::Search::Result::CrossMatchResult object Returns : Bio::Search::Result::CrossMatchResult Args : See Bio::Search::Result::GenericResult(); The following parameters are specific to CrossMatchResult: -iterations => array ref of Bio::Search::Iteration::IterationI objects -inclusion_threshold => e-value threshold for inclusion in the CrossMatch score matrix model (blastpgp) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_iterations'} = []; $self->{'_iteration_index'} = 0; $self->{'_iteration_count'} = 0; my( $iters, $ithresh ) = $self->_rearrange([qw(ITERATIONS INCLUSION_THRESHOLD)],@args); $self->{'_inclusion_threshold'} = $ithresh; # This is a read-only variable if( defined $iters ) { $self->throw("Must define arrayref of Iterations when initializing a $class\n") unless ref($iters) =~ /array/i; foreach my $i ( @{$iters} ) { $self->add_iteration($i); } } else { # This shouldn't get called with the new SearchIO::blast. #print STDERR "CrossMatchResult::new(): Not adding iterations.\n"; $self->{'_no_iterations'} = 1; } #$self->SUPER::algorithm('cross_match'); return $self; } =head2 hits This method overrides L to take into account the possibility of multiple iterations, as occurs in CrossMatch reports. If there are multiple iterations, all 'new' hits for all iterations are returned. These are the hits that did not occur in a previous iteration. See Also: L =cut sub hits { my ($self) = shift; if ($self->{'_no_iterations'}) { return $self->SUPER::hits; } my @hits = (); foreach my $it ($self->iterations) { push @hits, $it->hits; } return @hits; } =head2 next_hit This method overrides L to take into account the possibility of multiple iterations, as occurs in CrossMatch reports. If there are multiple iterations, calling next_hit() traverses the all of the hits, old and new, for each iteration, calling next_hit() on each iteration. See Also: L =cut sub next_hit { my ($self,@args) = @_; if ($self->{'_no_iterations'}) { return $self->SUPER::next_hit(@args); } my $iter_index; if (not defined $self->{'_last_hit'}) { $iter_index = $self->{'_iter_index'} = $self->_next_iteration_index; } else { $iter_index = $self->{'_iter_index'}; } return if $iter_index >= scalar @{$self->{'_iterations'}}; my $it = $self->{'_iterations'}->[$iter_index]; my $hit = $self->{'_last_hit'} = $it->next_hit; return defined($hit) ? $hit : $self->next_hit; } =head2 num_hits This method overrides L to take into account the possibility of multiple iterations, as occurs in CrossMatch reports. If there are multiple iterations, calling num_hits() returns the number of 'new' hits for each iteration. These are the hits that did not occur in a previous iteration. See Also: L =cut sub num_hits{ my ($self) = shift; if ($self->{'_no_iterations'}) { return $self->SUPER::num_hits; } if (not defined $self->{'_iterations'}) { $self->throw("Can't get Hits: data not collected."); } return scalar( $self->hits ); } =head2 add_iteration Title : add_iteration Usage : $report->add_iteration($iteration) Function: Adds a IterationI to the stored list of iterations Returns : Number of IterationI currently stored Args : Bio::Search::Iteration::IterationI =cut sub add_iteration { my ($self,$i) = @_; if( $i->isa('Bio::Search::Iteration::IterationI') ) { push @{$self->{'_iterations'}}, $i; $self->{'_iteration_count'}++; } else { $self->throw("Passed in a " .ref($i). " as a Iteration which is not a Bio::Search::IterationI."); } return scalar @{$self->{'_iterations'}}; } =head2 next_iteration Title : next_iteration Usage : while( $it = $result->next_iteration()) { ... } Function: Returns the next Iteration object, representing all hits found within a given CrossMatch iteration. Returns : a Bio::Search::Iteration::IterationI object or undef if there are no more. Args : none =cut sub next_iteration { my ($self) = @_; unless($self->{'_iter_queue_started'}) { $self->{'_iter_queue'} = [$self->iterations()]; $self->{'_iter_queue_started'} = 1; } return shift @{$self->{'_iter_queue'}}; } =head2 iteration Usage : $iteration = $blast->iteration( $number ); Purpose : Get an IterationI object for the specified iteration in the search result (CrossMatch). Returns : Bio::Search::Iteration::IterationI object Throws : Bio::Root::NoSuchThing exception if $number is not within range of the number of iterations in this report. Argument : integer (optional, if not specified get the last iteration) First iteration = 1 =cut sub iteration { my ($self,$num) = @_; $num = scalar @{$self->{'_iterations'}} unless defined $num; unless ($num >= 1 and $num <= scalar $self->{'_iteration_count'}) { $self->throw(-class=>'Bio::Root::NoSuchThing', -text=>"No such iteration number: $num. Valid range=1-$self->{'_iteration_count'}", -value=>$num); } return $self->{'_iterations'}->[$num-1]; } =head2 num_iterations Usage : $num_iterations = $blast->num_iterations; Purpose : Get the number of iterations in the search result (CrossMatch). Returns : Total number of iterations in the report Argument : none (read-only) =cut sub num_iterations { shift->{'_iteration_count'} } # Methods provided for consistency with BPpsilite.pm (now deprecated); # these are now merely synonyms =head2 number_of_iterations Same as L. =cut sub number_of_iterations { shift->num_iterations } =head2 round Same as L. =cut sub round { shift->iteration(@_) } =head2 iterations Title : iterations Usage : my @iterations = $result->iterations Function: Returns the IterationI objects contained within this Result Returns : Array of L objects Args : none =cut sub iterations { my $self = shift; my @its = (); if( ref($self->{'_iterations'}) =~ /ARRAY/i ) { @its = @{$self->{'_iterations'}}; } return @its; } =head2 no_hits_found Usage : $nohits = $blast->no_hits_found( $iteration_number ); Purpose : Get boolean indicator indicating whether or not any hits were present in the report. This is NOT the same as determining the number of hits via the hits() method, which will return zero hits if there were no hits in the report or if all hits were filtered out during the parse. Thus, this method can be used to distinguish these possibilities for hitless reports generated when filtering. Returns : Boolean Argument : (optional) integer indicating the iteration number (CrossMatch) If iteration number is not specified and this is a CrossMatch result, then this method will return true only if all iterations had no hits found. =cut sub no_hits_found { my ($self, $round) = @_; my $result = 0; # final return value of this method. # Watch the double negative! # result = 0 means "yes hits were found" # result = 1 means "no hits were found" (for the indicated iteration or all iterations) # If a iteration was not specified and there were multiple iterations, # this method should return true only if all iterations had no hits found. if( not defined $round ) { if( $self->{'_iterations'} > 1) { $result = 1; foreach my $i( 1..$self->{'_iterations'} ) { if( not defined $self->{"_iteration_$i"}->{'_no_hits_found'} ) { $result = 0; last; } } } else { $result = $self->{"_iteration_1"}->{'_no_hits_found'}; } } else { $result = $self->{"_iteration_$round"}->{'_no_hits_found'}; } return $result; } =head2 set_no_hits_found Usage : $blast->set_no_hits_found( $iteration_number ); Purpose : Set boolean indicator indicating whether or not any hits were present in the report. Returns : n/a Argument : (optional) integer indicating the iteration number (CrossMatch) =cut sub set_no_hits_found { my ($self, $round) = @_; $round ||= 1; $self->{"_iteration_$round"}->{'_no_hits_found'} = 1; } =head2 _next_iteration_index Title : _next_iteration_index Usage : private =cut sub _next_iteration_index{ my ($self,@args) = @_; return $self->{'_iteration_index'}++; } =head2 rewind Title : rewind Usage : $result->rewind; Function: Allow one to reset the Iteration iterator to the beginning Since this is an in-memory implementation Returns : none Args : none =cut sub rewind { my $self = shift; $self->SUPER::rewind(@_); $self->{'_iteration_index'} = 0; foreach ($self->iterations) { $_->rewind; } } =head2 inclusion_threshold Title : inclusion_threshold Usage : my $incl_thresh = $result->inclusion_threshold; (read-only) Function: Gets the e-value threshold for inclusion in the CrossMatch score matrix model (blastpgp) that was used for generating the report being parsed. Returns : number (real) or undef if not a CrossMatch report. Args : none =cut sub inclusion_threshold { my $self = shift; return $self->{'_inclusion_threshold'}; } sub algorithm_old { my $self = shift; my $value = shift; if($value) { print STDERR "Cannot set the algorightm on this class!\n"; return $self->SUPER::algorithm; } else { return $self->SUPER::algorithm; } } 1; #$Header$ BioPerl-1.007002/Bio/Search/Result/GenericResult.pm000444000766000024 5452013155576320 22046 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Result::GenericResult # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::GenericResult - Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. =head1 SYNOPSIS # typically one gets Results from a SearchIO stream use Bio::SearchIO; my $io = Bio::SearchIO->new(-format => 'blast', -file => 't/data/HUMBETGLOA.tblastx'); while( my $result = $io->next_result ) { # process all search results within the input stream while( my $hit = $result->next_hit ) { # insert code here for hit processing } } use Bio::Search::Result::GenericResult; my @hits = (); # would be a list of Bio::Search::Hit::HitI objects # typically these are created from a Bio::SearchIO stream my $result = Bio::Search::Result::GenericResult->new ( -query_name => 'HUMBETGLOA', -query_accession => '' -query_description => 'Human haplotype C4 beta-globin gene, complete cds.' -query_length => 3002 -database_name => 'ecoli.aa' -database_letters => 4662239, -database_entries => 400, -parameters => { 'e' => '0.001' }, -statistics => { 'kappa' => 0.731 }, -algorithm => 'blastp', -algorithm_version => '2.1.2', ); my $id = $result->query_name(); my $desc = $result->query_description(); my $name = $result->database_name(); my $size = $result->database_letters(); my $num_entries = $result->database_entries(); my $gap_ext = $result->get_parameter('e'); my @params = $result->available_parameters; my $kappa = $result->get_statistic('kappa'); my @statnames = $result->available_statistics; # TODO: Show how to configure a SearchIO stream so that it generates # GenericResult objects. =head1 DESCRIPTION This object is an implementation of the Bio::Search::Result::ResultI interface and provides a generic place to store results from a sequence database search. Unless you're writing a parser, you won't ever need to create a GenericResult or any other ResultI-implementing object. If you use the SearchIO system, ResultI objects are created automatically from a SearchIO stream which returns Bio::Search::Result::ResultI objects. For documentation on what you can do with GenericResult (and other ResultI objects), please see the API documentation in L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich and Steve Chervitz Email jason@bioperl.org Email sac@bioperl.org =head1 CONTRIBUTORS Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Result::GenericResult; use strict; use Bio::Search::GenericStatistics; use Bio::Tools::Run::GenericParameters; # bug #1420 #use overload # '""' => \&to_string; use base qw(Bio::Root::Root Bio::Search::Result::ResultI); =head2 new Title : new Usage : my $obj = Bio::Search::Result::GenericResult->new(); Function: Builds a new Bio::Search::Result::GenericResult object Returns : Bio::Search::Result::GenericResult Args : -query_name => Name of query Sequence -query_accession => Query accession number (if available) -query_description => Description of query sequence -query_length => Length of query sequence -database_name => Name of database -database_letters => Number of residues in database -database_entries => Number of entries in database -hits => array ref of Bio::Search::Hit::HitI objects -parameters => hash ref of search parameters (key => value) -statistics => hash ref of search statistics (key => value) -algorithm => program name (blastx) -algorithm_version => version of the algorithm (2.1.2) -algorithm_reference => literature reference string for this algorithm -rid => value of the BLAST Request ID (eg. RID: ZABJ4EA7014) -hit_factory => Bio::Factory::ObjectFactoryI capable of making Bio::Search::Hit::HitI objects =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_hits'} = []; $self->{'_hitindex'} = 0; $self->{'_statistics'} = Bio::Search::GenericStatistics->new(); $self->{'_parameters'} = Bio::Tools::Run::GenericParameters->new(); my ($qname,$qacc,$qdesc,$qlen, $qgi, $dbname,$dblet,$dbent,$params, $stats, $hits, $algo, $algo_v, $prog_ref, $algo_r, $rid, $hit_factory) = $self->_rearrange([qw(QUERY_NAME QUERY_ACCESSION QUERY_DESCRIPTION QUERY_LENGTH QUERY_GI DATABASE_NAME DATABASE_LETTERS DATABASE_ENTRIES PARAMETERS STATISTICS HITS ALGORITHM ALGORITHM_VERSION PROGRAM_REFERENCE ALGORITHM_REFERENCE RID HIT_FACTORY )],@args); $algo_r ||= $prog_ref; defined $algo && $self->algorithm($algo); defined $algo_v && $self->algorithm_version($algo_v); defined $algo_r && $self->algorithm_reference($algo_r); defined $rid && $self->rid($rid); defined $qname && $self->query_name($qname); defined $qacc && $self->query_accession($qacc); defined $qdesc && $self->query_description($qdesc); defined $qlen && $self->query_length($qlen); defined $qgi && $self->query_gi($qgi); defined $dbname && $self->database_name($dbname); defined $dblet && $self->database_letters($dblet); defined $dbent && $self->database_entries($dbent); defined $hit_factory && $self->hit_factory($hit_factory); if( defined $params ) { if( ref($params) !~ /hash/i ) { $self->throw("Must specify a hash reference with the parameter '-parameters"); } while( my ($key,$value) = each %{$params} ) { $self->{'_parameters'}->set_parameter($key => $value); # $self->add_parameter($key,$value); } } if( defined $stats ) { if( ref($stats) !~ /hash/i ) { $self->throw("Must specify a hash reference with the parameter '-statistics"); } while( my ($key,$value) = each %{$stats} ) { $self->{'_statistics'}->set_statistic($key => $value); # $self->add_statistic($key,$value); } } if( defined $hits ) { $self->throw("Must define arrayref of Hits when initializing a $class\n") unless ref($hits) =~ /array/i; foreach my $s ( @$hits ) { $self->add_hit($s); } } return $self; } =head2 algorithm Title : algorithm Usage : my $r_type = $hsp->algorithm Function: Obtain the name of the algorithm used to obtain the Result Returns : string (e.g., BLASTP) Args : [optional] scalar string to set value =cut sub algorithm{ my ($self,$value) = @_; my $previous = $self->{'_algorithm'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_algorithm'} = $value; } return $previous; } =head2 algorithm_version Title : algorithm_version Usage : my $r_version = $hsp->algorithm_version Function: Obtain the version of the algorithm used to obtain the Result Returns : string (e.g., 2.1.2) Args : [optional] scalar string to set algorithm version value =cut sub algorithm_version{ my ($self,$value) = @_; my $previous = $self->{'_algorithm_version'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_algorithm_version'} = $value; } return $previous; } =head2 Bio::Search::Result::ResultI interface methods Bio::Search::Result::ResultI implementation =head2 next_hit Title : next_hit Usage : while( $hit = $result->next_hit()) { ... } Function: Returns the next available Hit object, representing potential matches between the query and various entities from the database. Returns : a Bio::Search::Hit::HitI object or undef if there are no more. Args : none =cut sub next_hit { my ($self,@args) = @_; my $index = $self->_nexthitindex; return if $index > scalar @{$self->{'_hits'}}; my $hit = $self->{'_hits'}->[$index]; if (ref($hit) eq 'HASH') { my $factory = $self->hit_factory || $self->throw("Tried to get a Hit, but it was a hash ref and we have no hit factory"); $hit = $factory->create_object(%{$hit}); $self->{'_hits'}->[$index] = $hit; delete $self->{_hashes}->{$index}; } return $hit; } =head2 query_name Title : query_name Usage : $id = $result->query_name(); Function: Get the string identifier of the query used by the algorithm that performed the search. Returns : a string. Args : [optional] new string value for query name =cut sub query_name { my ($self,$value) = @_; my $previous = $self->{'_queryname'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_queryname'} = $value; } return $previous; } =head2 query_accession Title : query_accession Usage : $id = $result->query_accession(); Function: Get the accession (if available) for the query sequence Returns : a string Args : [optional] new string value for accession =cut sub query_accession { my ($self,$value) = @_; my $previous = $self->{'_queryacc'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_queryacc'} = $value; } return $previous; } =head2 query_gi Title : query_gi Usage : $acc = $hit->query_gi(); Function: Retrieve the NCBI Unique ID (aka the GI #), if available, for the query Returns : a scalar string (empty string if not set) Args : none =cut sub query_gi { my ($self,$value) = @_; if( defined $value ) { $self->{'_query_gi'} = $value; } else { $self->{'_query_gi'} = $self->query_name =~ m{^gi\|(\d+)} ? $1 : ''; } return $self->{'_query_gi'}; } =head2 query_length Title : query_length Usage : $id = $result->query_length(); Function: Get the length of the query sequence used in the search. Returns : a number Args : [optional] new integer value for query length =cut sub query_length { my ($self,$value) = @_; my $previous = $self->{'_querylength'}; if( defined $value || ! defined $previous ) { $value = $previous = 0 unless defined $value; $self->{'_querylength'} = $value; } return $previous; } =head2 query_description Title : query_description Usage : $id = $result->query_description(); Function: Get the description of the query sequence used in the search. Returns : a string Args : [optional] new string for the query description =cut sub query_description { my ($self,$value) = @_; my $previous = $self->{'_querydesc'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_querydesc'} = $value; } return $previous; } =head2 database_name Title : database_name Usage : $name = $result->database_name() Function: Used to obtain the name of the database that the query was searched against by the algorithm. Returns : a scalar string Args : [optional] new string for the db name =cut sub database_name { my ($self,$value) = @_; my $previous = $self->{'_dbname'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_dbname'} = $value; } return $previous; } =head2 database_letters Title : database_letters Usage : $size = $result->database_letters() Function: Used to obtain the size of database that was searched against. Returns : a scalar integer (units specific to algorithm, but probably the total number of residues in the database, if available) or undef if the information was not available to the Processor object. Args : [optional] new scalar integer for number of letters in db =cut sub database_letters { my ($self,$value) = @_; my $previous = $self->{'_dbletters'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_dbletters'} = $value; } return $previous; } =head2 database_entries Title : database_entries Usage : $num_entries = $result->database_entries() Function: Used to obtain the number of entries contained in the database. Returns : a scalar integer representing the number of entities in the database or undef if the information was not available. Args : [optional] new integer for the number of sequence entries in the db =cut sub database_entries { my ($self,$value) = @_; my $previous = $self->{'_dbentries'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_dbentries'} = $value; } return $previous; } =head2 get_parameter Title : get_parameter Usage : my $gap_ext = $report->get_parameter('gapext') Function: Returns the value for a specific parameter used when running this report Returns : string Args : name of parameter (string) =cut sub get_parameter { my ($self,$name) = @_; return $self->{'_parameters'}->get_parameter($name); } =head2 available_parameters Title : available_parameters Usage : my @params = $report->available_paramters Function: Returns the names of the available parameters Returns : Return list of available parameters used for this report Args : none =cut sub available_parameters{ my ($self) = @_; return $self->{'_parameters'}->available_parameters; } =head2 get_statistic Title : get_statistic Usage : my $gap_ext = $report->get_statistic('kappa') Function: Returns the value for a specific statistic available from this report Returns : string Args : name of statistic (string) =cut sub get_statistic{ my ($self,$key) = @_; return $self->{'_statistics'}->get_statistic($key); } =head2 available_statistics Title : available_statistics Usage : my @statnames = $report->available_statistics Function: Returns the names of the available statistics Returns : Return list of available statistics used for this report Args : none =cut sub available_statistics{ my ($self) = @_; return $self->{'_statistics'}->available_statistics; } =head2 Bio::Search::Report Bio::Search::Result::GenericResult specific methods =head2 add_hit Title : add_hit Usage : $report->add_hit($hit) Function: Adds a HitI to the stored list of hits Returns : Number of HitI currently stored Args : Bio::Search::Hit::HitI =cut sub add_hit { my ($self,$s) = @_; if (ref($s) eq 'HASH' || $s->isa('Bio::Search::Hit::HitI') ) { push @{$self->{'_hits'}}, $s; } else { $self->throw("Passed in " .ref($s)." as a Hit which is not a Bio::Search::HitI."); } if (ref($s) eq 'HASH') { $self->{_hashes}->{$#{$self->{'_hits'}}} = 1; } return scalar @{$self->{'_hits'}}; } =head2 hit_factory Title : hit_factory Usage : $hit->hit_factory($hit_factory) Function: Get/set the factory used to build HitI objects if necessary. Returns : Bio::Factory::ObjectFactoryI Args : Bio::Factory::ObjectFactoryI =cut sub hit_factory { my $self = shift; if (@_) { $self->{_hit_factory} = shift } return $self->{_hit_factory} || return; } =head2 rewind Title : rewind Usage : $result->rewind; Function: Allow one to reset the Hit iterator to the beginning Since this is an in-memory implementation Returns : none Args : none =cut sub rewind{ my ($self) = @_; $self->{'_hitindex'} = 0; } =head2 _nexthitindex Title : _nexthitindex Usage : private =cut sub _nexthitindex{ my ($self,@args) = @_; return $self->{'_hitindex'}++; } =head2 add_parameter Title : add_parameter Usage : $report->add_parameter('gapext', 11); Function: Adds a parameter Returns : none Args : key - key value name for this parama value - value for this parameter =cut sub add_parameter { my ($self,$key,$value) = @_; $self->{'_parameters'}->set_parameter($key => $value); } =head2 add_statistic Title : add_statistic Usage : $report->add_statistic('lambda', 2.3); Function: Adds a parameter Returns : none Args : key - key value name for this parama value - value for this parameter =cut sub add_statistic { my ($self,$key,$value) = @_; $self->{'_statistics'}->set_statistic($key => $value); return; } =head2 num_hits Title : num_hits Usage : my $hitcount= $result->num_hits Function: returns the number of hits for this query result Returns : integer Args : none =cut sub num_hits{ my ($self) = shift; if (not defined $self->{'_hits'}) { $self->throw("Can't get Hits: data not collected."); } return scalar(@{$self->{'_hits'}}); } =head2 hits Title : hits Usage : my @hits = $result->hits Function: Returns the available hits for this Result Returns : Array of L objects Args : none =cut sub hits { my ($self) = shift; foreach my $i (keys %{$self->{_hashes} || {}}) { my $factory = $self->hit_factory || $self->throw("Tried to get a Hit, but it was a hash ref and we have no hit factory"); $self->{'_hits'}->[$i] = $factory->create_object(%{$self->{'_hits'}->[$i]}); delete $self->{_hashes}->{$i}; } my @hits = (); if (ref $self->{'_hits'}) { @hits = @{$self->{'_hits'}}; } return @hits; } =head2 algorithm_reference Title : algorithm_reference Usage : $obj->algorithm_reference($newval) Function: Returns : string containing literature reference for the algorithm Args : newvalue string (optional) Comments: Formerly named program_reference(), which is still supported for backwards compatibility. =cut sub algorithm_reference{ my ($self,$value) = @_; if( defined $value) { $self->{'algorithm_reference'} = $value; } return $self->{'algorithm_reference'}; } =head2 program_reference Title : program_reference Usage : $obj->program_reference() Function: Returns : string containing literature reference for the algorithm Args : Comments: Deprecated - use algorithm_reference() instead. =cut sub program_reference { shift->algorithm_reference(@_); } =head2 rid Title : rid Usage : $obj->rid($newval) Function: Returns : value of the BLAST Request ID (eg. RID: ZABJ4EA7014) Args : newvalue (optional) Comments: The default implementation in ResultI returns an empty string rather than throwing a NotImplemented exception, since the RID may not always be available and is not critical. See: (1) https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/BLAST/rid.html (2) https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node63.html =cut sub rid{ my ($self,$value) = @_; if( defined $value) { $self->{'rid'} = $value; } return $self->{'rid'}; } =head2 no_hits_found See documentation in L =cut sub no_hits_found { my $self = shift; # Watch the double negative! # result = 0 means "yes hits were found" # result = 1 means "no hits were found" return $self->{'_no_hits_found'}; } =head2 set_no_hits_found See documentation in L =cut sub set_no_hits_found { my $self = shift; $self->{'_no_hits_found'} = 1; } =head2 to_string Title : to_string Usage : print $blast->to_string; Function: Returns a string representation for the Blast result. Primarily intended for debugging purposes. Example : see usage Returns : A string of the form: [GenericResult] query= db=query_description .", db=" . $self->database_name; return $str; } 1; BioPerl-1.007002/Bio/Search/Result/HMMERResult.pm000444000766000024 2535013155576320 21341 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Result::HMMERResult # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::HMMERResult - A Result object for HMMER results =head1 SYNOPSIS use Bio::Search::Result::HMMERResult; my $result = Bio::Search::Result::HMMERResult->new ( -hmm_name => 'pfam', -sequence_file => 'roa1.pep', -hits => \@hits); # generally we use Bio::SearchIO to build these objects use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer', -file => 'result.hmmer'); while( my $result = $in->next_result ) { print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n"; } =head1 DESCRIPTION This is a specialization of L. There are a few extra methods, specifically L, L, L, and L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Result::HMMERResult; use strict; use base qw(Bio::Search::Result::GenericResult); =head2 new Title : new Usage : my $obj = Bio::Search::Result::HMMERResult->new(); Function: Builds a new Bio::Search::Result::HMMERResult object Returns : Bio::Search::Result::HMMERResult Args : -hmm_name => string, name of hmm file -sequence_file => name of the sequence file plus Bio::Search::Result::GenericResult parameters -query_name => Name of query Sequence -query_accession => Query accession number (if available) -query_description => Description of query sequence -query_length => Length of query sequence -database_name => Name of database -database_letters => Number of residues in database -database_entries => Number of entries in database -parameters => hash ref of search parameters (key => value) -statistics => hash ref of search statistics (key => value) -algorithm => program name (blastx) -algorithm_version => version of the algorithm (2.1.2) -program_reference => literature reference string for this algorithm =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($hmm,$seqfile) = $self->_rearrange([qw(HMM_NAME SEQUENCE_FILE)], @args); defined( $seqfile) && $self->sequence_file($seqfile); defined( $hmm) && $self->hmm_name($hmm); return $self; } =head2 hmm_name Title : hmm_name Usage : $obj->hmm_name($newval) Function: Get/Set the value of hmm_name Returns : value of hmm_name Args : newvalue (optional) =cut sub hmm_name{ my ($self,$value) = @_; if( defined $value) { $self->{'_hmm_name'} = $value; } return $self->{'_hmm_name'}; } =head2 sequence_file Title : sequence_file Usage : $obj->sequence_file($newval) Function: Get/Set the value of sequence_file Returns : value of sequence_file Args : newvalue (optional) =cut sub sequence_file{ my ($self,$value) = @_; if( defined $value) { $self->{'_sequence_file'} = $value; } return $self->{'_sequence_file'}; } =head2 next_model Title : next_model Usage : my $domain = $result->next_model Function: Returns the next domain - this is an alias for next_hit Returns : L object Args : none =cut sub next_model{ shift->next_hit } =head2 models Title : models Usage : my @domains = $result->models; Function: Returns the list of HMM models seen - this is an alias for hits() Returns : Array of L objects Args : none =cut sub models{ shift->hits } =head2 Bio::Search::Result::GenericResult inherited methods =cut =head2 algorithm Title : algorithm Usage : my $r_type = $hsp->algorithm Function: Obtain the name of the algorithm used to obtain the Result Returns : string (e.g., BLASTP) Args : [optional] scalar string to set value =cut =head2 algorithm_version Title : algorithm_version Usage : my $r_version = $hsp->algorithm_version Function: Obtain the version of the algorithm used to obtain the Result Returns : string (e.g., 2.1.2) Args : [optional] scalar string to set algorithm version value =cut =head2 Bio::Search::Result::ResultI interface methods Bio::Search::Result::ResultI implementation =head2 next_hit Title : next_hit Usage : while( $hit = $result->next_hit()) { ... } Function: Returns the next available Hit object, representing potential matches between the query and various entities from the database. Returns : a Bio::Search::Hit::HitI object or undef if there are no more. Args : none =cut =head2 query_name Title : query_name Usage : $id = $result->query_name(); Function: Get the string identifier of the query used by the algorithm that performed the search. Returns : a string. Args : [optional] new string value for query name =cut =head2 query_accession Title : query_accession Usage : $id = $result->query_accession(); Function: Get the accession (if available) for the query sequence Returns : a string Args : [optional] new string value for accession =cut =head2 query_length Title : query_length Usage : $id = $result->query_length(); Function: Get the length of the query sequence used in the search. Returns : a number Args : [optional] new integer value for query length =cut =head2 query_description Title : query_description Usage : $id = $result->query_description(); Function: Get the description of the query sequence used in the search. Returns : a string Args : [optional] new string for the query description =cut =head2 database_name Title : database_name Usage : $name = $result->database_name() Function: Used to obtain the name of the database that the query was searched against by the algorithm. Returns : a scalar string Args : [optional] new string for the db name =cut =head2 database_letters Title : database_letters Usage : $size = $result->database_letters() Function: Used to obtain the size of database that was searched against. Returns : a scalar integer (units specific to algorithm, but probably the total number of residues in the database, if available) or undef if the information was not available to the Processor object. Args : [optional] new scalar integer for number of letters in db =cut =head2 database_entries Title : database_entries Usage : $num_entries = $result->database_entries() Function: Used to obtain the number of entries contained in the database. Returns : a scalar integer representing the number of entities in the database or undef if the information was not available. Args : [optional] new integer for the number of sequence entries in the db =cut =head2 get_parameter Title : get_parameter Usage : my $gap_ext = $report->get_parameter('gapext') Function: Returns the value for a specific parameter used when running this report Returns : string Args : name of parameter (string) =cut =head2 available_parameters Title : available_parameters Usage : my @params = $report->available_paramters Function: Returns the names of the available parameters Returns : Return list of available parameters used for this report Args : none =cut =head2 get_statistic Title : get_statistic Usage : my $gap_ext = $report->get_statistic('kappa') Function: Returns the value for a specific statistic available from this report Returns : string Args : name of statistic (string) =cut =head2 available_statistics Title : available_statistics Usage : my @statnames = $report->available_statistics Function: Returns the names of the available statistics Returns : Return list of available statistics used for this report Args : none =cut =head2 Bio::Search::Result::GenericResult specific methods =cut =head2 add_hit Title : add_hit Usage : $report->add_hit($hit) Function: Adds a HitI to the stored list of hits Returns : Number of HitI currently stored Args : Bio::Search::Hit::HitI =cut =head2 rewind Title : rewind Usage : $result->rewind; Function: Allow one to reset the Hit iteration to the beginning Since this is an in-memory implementation Returns : none Args : none =cut sub rewind{ my ($self) = @_; $self->{'_hitindex'} = 0; } =head2 add_parameter Title : add_parameter Usage : $report->add_parameter('gapext', 11); Function: Adds a parameter Returns : none Args : key - key value name for this parama value - value for this parameter =cut =head2 add_statistic Title : add_statistic Usage : $report->add_statistic('lambda', 2.3); Function: Adds a parameter Returns : none Args : key - key value name for this parama value - value for this parameter =cut =head2 num_hits Title : num_hits Usage : my $hitcount= $result->num_hits Function: returns the number of hits for this query result Returns : integer Args : none =cut =head2 hits Title : hits Usage : my @hits = $result->hits Function: Returns the available hits for this Result Returns : Array of L objects Args : none =cut =head2 program_reference Title : program_reference Usage : $obj->program_reference($newval) Function: Returns : value of the literature reference for the algorithm Args : newvalue (optional) =cut 1; BioPerl-1.007002/Bio/Search/Result/HmmpfamResult.pm000555000766000024 2662613155576320 22070 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Result::HmmpfamResult # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::HmmpfamResult - A parser and result object for hmmpfam results =head1 SYNOPSIS # generally we use Bio::SearchIO to build these objects use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer_pull', -file => 'result.hmmer'); while (my $result = $in->next_result) { print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n"; } =head1 DESCRIPTION This object implements a parser for hmmpfam result output, a program in the HMMER package. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Result::HmmpfamResult; use strict; use Bio::Search::Hit::HmmpfamHit; use base qw(Bio::Root::Root Bio::Search::Result::PullResultI); =head2 new Title : new Usage : my $obj = Bio::SearchIO::Result::hmmpfam->new(); Function: Builds a new Bio::SearchIO::Result::hmmpfam object Returns : Bio::SearchIO::Result::hmmpfam Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent) -parent => Bio::PullParserI object (required if no -chunk) -parameters => hash ref of search parameters (key => value), optional -statistics => hash ref of search statistics (key => value), optional where the array ref provided to -chunk contains an IO object for a filehandle to something representing the raw data of the result, and $start and $end define the tell() position within the filehandle that the result data starts and ends (optional; defaults to start and end of the entire thing described by the filehandle) =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->_setup(@args); foreach my $field (qw( header hit_table hsp_table alignments next_model models query_length )) { $self->_fields->{$field} = undef; } $self->_dependencies( { ( query_name => 'header', query_accession => 'header', query_description => 'header', hit_table => 'header', num_hits => 'hit_table', no_hits_found => 'hit_table', hsp_table => 'hit_table', next_alignment => 'hsp_table' ) } ); return $self; } # # PullParserI discovery methods so we can answer all ResultI questions # sub _discover_header { my $self = shift; $self->_chunk_seek(0); my $header = $self->_get_chunk_by_end("all domains):\n"); $self->{_after_header} = $self->_chunk_tell; $header || $self->throw("Could not find hmmer header, is file really hmmer format?"); ($self->_fields->{query_name}) = $header =~ /^Query(?:\s+sequence)?:\s+(\S+)/m; ($self->_fields->{query_accession}) = $header =~ /^Accession:\s+(\S+)/m; ($self->_fields->{query_description}) = $header =~ /^Description:\s+(\S.+)/m; $self->_fields->{query_accession} ||= ''; $self->_fields->{query_description} ||= ''; $self->_fields->{header} = 1; # stop this method being called again } sub _discover_hit_table { my $self = shift; $self->_chunk_seek($self->{_after_header}); my $table = $self->_get_chunk_by_end("for domains:\n"); $self->{_after_hit_table} = $self->_chunk_tell; my $evalue_cutoff = $self->get_field('evalue_cutoff'); undef $evalue_cutoff if $evalue_cutoff eq '[unset]'; my $score_cutoff = $self->get_field('score_cutoff'); undef $score_cutoff if $score_cutoff eq '[unset]'; my $hsps_cutoff = $self->get_field('hsps_cutoff'); undef $hsps_cutoff if $hsps_cutoff eq '[unset]'; my @table; my $no_hit = 1; while ($table =~ /^(\S+)\s+(\S.+?)?\s+(\S+)\s+(\S+)\s+(\d+)\n/gm) { $no_hit = 0; my $evalue = abs($4); # consistency for tests under Windows next if ($evalue_cutoff && $evalue > $evalue_cutoff); next if ($score_cutoff && $3 < $score_cutoff); next if ($hsps_cutoff && $5 < $hsps_cutoff); push(@table, [$1, $2, $3, $evalue, $5]); } $self->_fields->{hit_table} = \@table; $self->{_next_hit_index} = @table > 0 ? 0 : -1; $self->_fields->{no_hits_found} = $no_hit; $self->_fields->{num_hits} = @table; } sub _discover_hsp_table { my $self = shift; $self->_chunk_seek($self->{_after_hit_table}); my $table = $self->_get_chunk_by_end("top-scoring domains:\n"); $table ||= $self->_get_chunk_by_end("//\n"); # A0 reports $self->{_after_hsp_table} = $self->_chunk_tell; my %table; # can't save this regex work for the hsp object because the hit object needs # its length, so may as well just do all the work here while ($table =~ /^(\S+)\s+(\d+)\/\d+\s+(\d+)\s+(\d+)\s+\S\S\s+(\d+)\s+(\d+)\s+\S(\S)\s+(\S+)\s+(\S+)/gm) { # rank query_start query_end hit_start hit_end score evalue my $evalue = abs($9); # consistency for tests under Windows push(@{$table{$1}->{hsp_data}}, [$2, $3, $4, $5, $6, $8, $evalue]); if ($7 eq ']') { $table{$1}->{hit_length} = $6; } } $self->_fields->{hsp_table} = \%table; } sub _discover_alignments { my $self = shift; $self->_fields->{alignments} = { }; } sub _next_alignment { my $self = shift;; return if $self->{_no_more_alignments}; my $aligns = $self->_fields->{alignments}; unless (defined $self->{_after_previous_alignment}) { $self->_chunk_seek($self->{_after_hsp_table}); my $chunk = $self->_get_chunk_by_end(": domain"); unless ($chunk) { $self->{_no_more_alignments} = 1; return; } $self->{_after_previous_alignment} = $self->_chunk_tell; $self->{_next_alignment_start_text} = $chunk; return $self->_next_alignment; } $self->_chunk_seek($self->{_after_previous_alignment}); my $chunk = $self->_get_chunk_by_end(": domain"); unless ($chunk) { $self->_chunk_seek($self->{_after_previous_alignment}); $chunk = $self->_get_chunk_by_end("//"); unless ($chunk) { $self->{_no_more_alignments} = 1; return; } } $self->{_after_previous_alignment} = $self->_chunk_tell; if (defined $self->{_next_alignment_start_text}) { $chunk = $self->{_next_alignment_start_text}.$chunk; } $chunk =~ s/(\S+: domain)$//; $self->{_next_alignment_start_text} = $1; my ($name, $domain) = $chunk =~ /^(\S+): domain (\d+)/; $aligns->{$name.'~~~~'.$domain} = $chunk; return 1; } sub _discover_next_hit { my $self = shift; my @hit_table = @{$self->get_field('hit_table')}; return if $self->{_next_hit_index} == -1; #[name description score significance num_hsps rank] my @hit_data = (@{$hit_table[$self->{_next_hit_index}++]}, $self->{_next_hit_index}); $self->_fields->{next_hit} = Bio::Search::Hit::HmmpfamHit->new(-parent => $self, -hit_data => \@hit_data); if ($self->{_next_hit_index} > $#hit_table) { $self->{_next_hit_index} = -1; } } =head2 next_hit Title : next_hit Usage : while( $hit = $result->next_hit()) { ... } Function: Returns the next available Hit object, representing potential matches between the query and various entities from the database. Returns : a Bio::Search::Hit::HitI object or undef if there are no more. Args : none =cut sub next_hit { my $self = shift; my $hit = $self->get_field('next_hit'); undef $self->_fields->{next_hit}; return $hit; } =head2 next_model Title : next_model Usage : my $domain = $result->next_model Function: Returns the next domain - this is an alias for next_hit() Returns : L object Args : none =cut *next_model = \&next_hit; =head2 hits Title : hits Usage : my @hits = $result->hits Function: Returns the HitI objects contained within this Result Returns : Array of Bio::Search::Hit::HitI objects Args : none See Also: L =cut sub hits { my $self = shift; my $old = $self->{_next_hit_index} || 0; $self->rewind; my @hits; while (defined(my $hit = $self->next_hit)) { push(@hits, $hit); } $self->{_next_hit_index} = @hits > 0 ? $old : -1; return @hits; } =head2 models Title : models Usage : my @domains = $result->models; Function: Returns the list of HMM models seen - this is an alias for hits() Returns : Array of L objects Args : none =cut *models = \&hits; =head2 sort_hits Title : sort_hits Usage : $result->sort_hits('sort_hits( sub{$Bio::Search::Result::HmmpfamResult::a->[2] <=> $Bio::Search::Result::HmmpfamResult::b->[2]}); NOT $result->sort_hits($a->[2] <=> $b->[2]); =cut sub sort_hits { my ($self, $code_ref) = @_; $code_ref ||= sub { $a->[3] <=> $b->[3] }; # avoid creating hit objects just to sort, hence force user to sort on # the array references in hit table my $table_ref = $self->get_field('hit_table'); @{$table_ref} > 1 || return; my @sorted = sort $code_ref @{$table_ref}; @sorted == @{$table_ref} || $self->throw("Your sort routine failed to give back all hits!"); $self->_fields->{hit_table} = \@sorted; } =head2 rewind Title : rewind Usage : $result->rewind; Function: Allow one to reset the Hit iterator to the beginning, so that next_hit() will subsequently return the first hit and so on. Returns : n/a Args : none =cut sub rewind { my $self = shift; unless ($self->_fields->{hit_table}) { $self->get_field('hit_table'); } $self->{_next_hit_index} = @{$self->_fields->{hit_table}} > 0 ? 0 : -1; } 1; BioPerl-1.007002/Bio/Search/Result/INFERNALResult.pm000444000766000024 606313155576320 21647 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Result::INFERNALResult.pm # # Please direct questions and support issues to # # Cared for by Paul Cantalupo # # Copyright Paul Cantalupo # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::INFERNALResult - A Result object for INFERNAL results =head1 SYNOPSIS # typically one gets Results from a SearchIO stream use Bio::SearchIO; my $io = Bio::SearchIO->new(-format => 'infernal', -file => 't/data/cmsearch_output.txt'); while( my $result = $io->next_result ) { while( my $hit = $result->next_hit ) { print join(" ", $result->query_name, $result->algorithm, $result->num_hits), "\n"; } } =head1 DESCRIPTION This object is a specialization of L. There is one extra method called L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Paul Cantalupo =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Result::INFERNALResult; use strict; use warnings; use base qw(Bio::Search::Result::GenericResult); =head2 new Title : new Usage : my $obj = Bio::Search::Result::INFERNALResult->new(); Function: Builds a new Bio::Search::Result::INFERNALResult object Returns : Bio::Search::Result::INFERNALResult Args : -cm_name => string, name of covariance model (CM) file. plus Bio::Search::Result::GenericResult parameters =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($cm) = $self->_rearrange([qw(CM_NAME)], @args); if (defined $cm) { $self->cm_name($cm) } return $self; } =head2 cm_name Title : cm_name Usage : $obj->cm_name($newvalue) Function: Get/Set value of the covariance model file name (cm_name) Returns : value of cm_name Args : newvalue (optional) =cut sub cm_name { my ($self, $value) = @_; if (defined $value) { $self->{'_cm_name'} = $value; } return $self->{'_cm_name'}; } 1; BioPerl-1.007002/Bio/Search/Result/PullResultI.pm000555000766000024 3464313155576320 21526 0ustar00cjfieldsstaff000000000000# # BioPerl module Bio::Search::Result::PullResultI # # Please direct questions and support issues to # # Cared for by Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::PullResultI - Bio::Search::Result::ResultI interface for 'pull' parsers =head1 SYNOPSIS # This is an interface and cannot be instantiated # typically one gets Results from a SearchIO stream use Bio::SearchIO; my $io = Bio::SearchIO->new(-format => 'hmmer_pull', -file => 't/data/hmmpfam.out'); my $result = $io->next_result; while( $hit = $result->next_hit()) { # enter code here for hit processing } my $id = $result->query_name(); my $desc = $result->query_description(); my $dbname = $result->database_name(); my $size = $result->database_letters(); my $num_entries = $result->database_entries(); my $gap_ext = $result->get_parameter('gapext'); my @params = $result->available_parameters; my $kappa = $result->get_statistic('kappa'); my @statnames = $result->available_statistics; =head1 DESCRIPTION Bio::Search::Result::ResultI objects are data structures containing the results from the execution of a search algorithm. As such, it may contain various algorithm specific information as well as details of the execution, but will contain a few fundamental elements, including the ability to return Bio::Search::Hit::HitI objects. PullResultI is for fast implementations that only do parsing work on the result data when you actually request information by calling one of the ResultI methods. Many methods of ResultI are implemented in a way suitable for inheriting classes that use Bio::PullParserI. It only really makes sense for PullResult modules to be created by (and have as a -parent) SearchIO modules written using PullParserI. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Sendu Bala Email bix@sendu.me.uk =head1 COPYRIGHT Copyright (c) 2006 Sendu Bala. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Result::PullResultI; use strict; use Bio::Search::GenericStatistics; use Bio::Tools::Run::GenericParameters; use base qw(Bio::PullParserI Bio::Search::Result::ResultI); =head2 _setup Title : _setup Usage : $self->_setup(@args) Function: Implementers should call this to setup common fields and deal with common arguments to new(). Returns : n/a Args : @args received in new(). =cut sub _setup { my ($self, @args) = @_; # fields most subclasses probably will want $self->_fields( { ( next_hit => undef, num_hits => undef, hits => undef, no_hits_found => undef, query_name => undef, query_accession => undef, query_length => undef, query_description => undef ) } ); my ($parent, $chunk, $params, $stats) = $self->_rearrange([qw(PARENT CHUNK PARAMETERS STATISTICS)], @args); $self->throw("Need -parent or -chunk to be defined") unless $parent || $chunk; $self->parent($parent) if $parent; if ($chunk) { my ($io, $start, $end) = (undef, 0, undef); if (ref($chunk) eq 'ARRAY') { ($io, $start, $end) = @{$chunk}; } else { $io = $chunk; } $self->chunk($io, -start => $start, -end => $end); } if (defined $params) { if (ref($params) !~ /hash/i) { $self->throw("Must specify a hash reference with the the parameter '-parameters"); } while (my ($key,$value) = each %{$params}) { $self->add_parameter($key, $value); } } if (defined $stats) { if (ref($stats) !~ /hash/i) { $self->throw("Must specify a hash reference with the the parameter '-statistics"); } while (my ($key,$value) = each %{$stats}) { $self->add_statistic($key, $value); } } } # # Some of these methods are written explitely to avoid ResultI throwing not # implemented; if it didn't do that then PullParserI AUTOLOAD would have # cought all them. # =head2 next_hit Title : next_hit Usage : while( $hit = $result->next_hit()) { ... } Function: Returns the next available Hit object, representing potential matches between the query and various entities from the database. Returns : a Bio::Search::Hit::HitI object or undef if there are no more. Args : none =cut sub next_hit { return shift->get_field('next_hit'); } =head2 sort_hits Title : sort_hits Usage : $result->sort_hits(\&sort_function) Function : Sorts the available hit objects by a user-supplied function. Defaults to sort by descending score. Returns : n/a Args : A coderef for the sort function. See the documentation on the Perl sort() function for guidelines on writing sort functions. Note : To access the special variables $a and $b used by the Perl sort() function the user function must access Bio::Search::Result::ResultI namespace. For example, use : $result->sort_hits(sub{$Bio::Search::Result::ResultI::a->length <=> $Bio::Search::Result::ResultI::b->length}); NOT $result->sort_hits($a->length <=>$b->length); =cut # In ResultI. subclasses will probably want to override since sort_hits normally # calls hits(). =head2 query_name Title : query_name Usage : $id = $result->query_name(); Function: Get the string identifier of the query used by the algorithm that performed the search. Returns : a string. Args : none =cut sub query_name { return shift->get_field('query_name'); } =head2 query_accession Title : query_accession Usage : $id = $result->query_accession(); Function: Get the accession (if available) for the query sequence Returns : a string Args : none =cut sub query_accession { return shift->get_field('query_accession'); } =head2 query_length Title : query_length Usage : $id = $result->query_length(); Function: Get the length of the query sequence used in the search. Returns : a number Args : none =cut sub query_length { return shift->get_field('query_length'); } =head2 query_description Title : query_description Usage : $id = $result->query_description(); Function: Get the description of the query sequence used in the search. Returns : a string Args : none =cut sub query_description { return shift->get_field('query_description'); } =head2 database_name Title : database_name Usage : $name = $result->database_name() Function: Used to obtain the name of the database that the query was searched against by the algorithm. Returns : a scalar string Args : none =cut sub database_name { return shift->get_field('database_name'); } =head2 database_letters Title : database_letters Usage : $size = $result->database_letters() Function: Used to obtain the size of database that was searched against. Returns : a scalar integer (units specific to algorithm, but probably the total number of residues in the database, if available) or undef if the information was not available to the Processor object. Args : none =cut sub database_letters { return shift->get_field('database_letters'); } =head2 database_entries Title : database_entries Usage : $num_entries = $result->database_entries() Function: Used to obtain the number of entries contained in the database. Returns : a scalar integer representing the number of entities in the database or undef if the information was not available. Args : none =cut sub database_entries { return shift->get_field('database_entries'); } =head2 algorithm Title : algorithm Usage : my $r_type = $result->algorithm Function: Obtain the name of the algorithm used to obtain the Result Returns : string (e.g., BLASTP) Args : [optional] scalar string to set value =cut sub algorithm { return shift->get_field('algorithm'); } =head2 algorithm_version Title : algorithm_version Usage : my $r_version = $result->algorithm_version Function: Obtain the version of the algorithm used to obtain the Result Returns : string (e.g., 2.1.2) Args : [optional] scalar string to set algorithm version value =cut sub algorithm_version { return shift->get_field('algorithm_version'); } =head2 algorithm_reference Title : algorithm_reference Usage : $obj->algorithm_reference($newval) Function: Returns : value of the literature reference for the algorithm Args : newvalue (optional) Comments: The default implementation in ResultI returns an empty string rather than throwing a NotImplemented exception, since the ref may not always be available and is not critical. =cut sub algorithm_reference { my ($self) = @_; return ''; } =head2 num_hits Title : num_hits Usage : my $hitcount= $result->num_hits Function: returns the number of hits for this query result Returns : integer Args : none =cut sub num_hits { return shift->get_field('num_hits'); } =head2 hits Title : hits Usage : my @hits = $result->hits Function: Returns the HitI objects contained within this Result Returns : Array of Bio::Search::Hit::HitI objects Args : none See Also: L =cut sub hits { return shift->get_field('hits'); } =head2 no_hits_found Usage : $nohits = $blast->no_hits_found(); Function : Get boolean indicator indicating whether or not any hits were present in the report. This is NOT the same as determining the number of hits via the hits() method, which will return zero hits if there were no hits in the report or if all hits were filtered out during the parse. Thus, this method can be used to distinguish these possibilities for hitless reports generated when filtering. Returns : Boolean Args : none =cut sub no_hits_found { return shift->get_field('no_hits_found'); } =head2 rewind Title : rewind Usage : $result->rewind; Function: Allow one to reset the Hit iterator to the beginning Since this is an in-memory implementation Returns : none Args : none =cut sub rewind { shift->throw_not_implemented(); } =head2 get_parameter Title : get_parameter Usage : my $gap_ext = $result->get_parameter('gapext') Function: Returns the value for a specific parameter used when running this result Returns : string Args : name of parameter (string) =cut sub get_parameter { my ($self, $param) = @_; $param || return; return unless defined $self->{_parameters}; return $self->{_parameters}->get_parameter($param); } =head2 available_parameters Title : available_parameters Usage : my @params = $result->available_parameters Function: Returns the names of the available parameters Returns : Return list of available parameters used for this result Args : none =cut sub available_parameters { my $self = shift; return () unless defined $self->{_parameters}; return $self->{_parameters}->available_parameters; } =head2 add_parameter Title : add_parameter Usage : $result->add_parameter('gapext', 11); Function: Adds a parameter Returns : none Args : key - key value name for this parama value - value for this parameter =cut sub add_parameter { my ($self, $key, $value) = @_; unless (exists $self->{_parameters}) { $self->{_parameters} = Bio::Tools::Run::GenericParameters->new(); } $self->{_parameters}->set_parameter($key => $value); } =head2 get_statistic Title : get_statistic Usage : my $gap_ext = $result->get_statistic('kappa') Function: Returns the value for a specific statistic available from this result Returns : string Args : name of statistic (string) =cut sub get_statistic { my ($self, $stat) = @_; $stat || return; return unless defined $self->{_statistics}; return $self->{_statistics}->get_statistic($stat); } =head2 available_statistics Title : available_statistics Usage : my @statnames = $result->available_statistics Function: Returns the names of the available statistics Returns : Return list of available statistics used for this result Args : none =cut sub available_statistics { my $self = shift; return () unless defined $self->{_statistics}; return $self->{_statistics}->available_statistics; } =head2 add_statistic Title : add_statistic Usage : $result->add_statistic('lambda', 2.3); Function: Adds a statistic Returns : none Args : key - key value name for this statistic value - value for this statistic =cut sub add_statistic { my ($self, $key, $value) = @_; unless (exists $self->{_statistics}) { $self->{_statistics} = Bio::Search::GenericStatistics->new(); } $self->{_statistics}->set_statistic($key => $value); } 1; BioPerl-1.007002/Bio/Search/Result/ResultFactory.pm000444000766000024 725113155576320 22060 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Result::ResultFactory # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::ResultFactory - A factory to create Bio::Search::Result::ResultI objects =head1 SYNOPSIS use Bio::Search::Result::ResultFactory; my $factory = Bio::Search::Result::ResultFactory->new(); my $resultobj = $factory->create(@args); =head1 DESCRIPTION This is a general way of hiding the object creation process so that we can dynamically change the objects that are created by the SearchIO parser depending on what format report we are parsing. This object is for creating new Results. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Result::ResultFactory; use vars qw($DEFAULT_TYPE); use strict; use base qw(Bio::Root::Root Bio::Factory::ObjectFactoryI); BEGIN { $DEFAULT_TYPE = 'Bio::Search::Result::GenericResult'; } =head2 new Title : new Usage : my $obj = Bio::Search::Result::ResultFactory->new(); Function: Builds a new Bio::Search::Result::ResultFactory object Returns : Bio::Search::Result::ResultFactory Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($type) = $self->_rearrange([qw(TYPE)],@args); $self->type($type) if defined $type; return $self; } =head2 create Title : create Usage : $factory->create(%args) Function: Create a new L object Returns : L Args : hash of initialization parameters =cut sub create{ my ($self,@args) = @_; my $type = $self->type; eval { $self->_load_module($type) }; if( $@ ) { $self->throw("Unable to load module $type: $@"); } return $type->new(@args); } =head2 type Title : type Usage : $factory->type('Bio::Search::Result::GenericResult'); Function: Get/Set the Result creation type Returns : string Args : [optional] string to set =cut sub type{ my ($self,$type) = @_; if( defined $type ) { # redundancy with the create method which also calls _load_module # I know - but this is not a highly called object so I am going # to leave it in eval {$self->_load_module($type) }; if( $@ ){ $self->warn("Cannot find module $type, unable to set type"); } else { $self->{'_type'} = $type; } } return $self->{'_type'} || $DEFAULT_TYPE; } 1; BioPerl-1.007002/Bio/Search/Result/ResultI.pm000444000766000024 3104113155576320 20653 0ustar00cjfieldsstaff000000000000#----------------------------------------------------------------- # # BioPerl module Bio::Search::Result::ResultI # # Please direct questions and support issues to # # Cared for by Steve Chervitz # # Originally created by Aaron Mackey # # You may distribute this module under the same terms as perl itself #----------------------------------------------------------------- # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::ResultI - Abstract interface to Search Result objects =head1 SYNOPSIS # Bio::Search::Result::ResultI objects cannot be instantiated since this # module defines a pure interface. # Given an object that implements the Bio::Search::Result::ResultI interface, # you can do the following things with it: use Bio::SearchIO; my $io = Bio::SearchIO->new(-format => 'blast', -file => 't/data/HUMBETGLOA.tblastx'); my $result = $io->next_result; while( $hit = $result->next_hit()) { # enter code here for hit processing } my $id = $result->query_name(); my $desc = $result->query_description(); my $dbname = $result->database_name(); my $size = $result->database_letters(); my $num_entries = $result->database_entries(); my $gap_ext = $result->get_parameter('gapext'); my @params = $result->available_parameters; my $kappa = $result->get_statistic('kappa'); my @statnames = $result->available_statistics; =head1 DESCRIPTION Bio::Search::Result::ResultI objects are data structures containing the results from the execution of a search algorithm. As such, it may contain various algorithm specific information as well as details of the execution, but will contain a few fundamental elements, including the ability to return Bio::Search::Hit::HitI objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Aaron Mackey Eamackey@virginia.eduE (original author) Steve Chervitz Esac@bioperl.orgE See L for where to send bug reports and comments. =head1 COPYRIGHT Copyright (c) 1999-2001 Aaron Mackey, Steve Chervitz. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::Search::Result::ResultI; use strict; use base qw(Bio::AnalysisResultI); =head2 next_hit Title : next_hit Usage : while( $hit = $result->next_hit()) { ... } Function: Returns the next available Hit object, representing potential matches between the query and various entities from the database. Returns : a Bio::Search::Hit::HitI object or undef if there are no more. Args : none =cut sub next_hit { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 sort_hits Title : sort_hits Usage : $result->sort_hits(\&sort_function) Function : Sorts the available hit objects by a user-supplied function. Defaults to sort by descending score. Returns : n/a Args : A coderef for the sort function. See the documentation on the Perl sort() function for guidelines on writing sort functions. Note : To access the special variables $a and $b used by the Perl sort() function the user function must access Bio::Search::Result::ResultI namespace. For example, use : $result->sort_hits( sub{$Bio::Search::Result::ResultI::a->length <=> $Bio::Search::Result::ResultI::b->length}); NOT $result->sort_hits($a->length <=>$b->length); =cut sub sort_hits { my ($self, $coderef) = @_; my @sorted_hits; if ($coderef) { $self->throw('sort_hits requires a sort function passed as a subroutine reference') unless (ref($coderef) eq 'CODE'); } else { $coderef = \&_default_sort_hits; # throw a warning? } my @hits = $self->hits(); eval {@sorted_hits = sort $coderef @hits }; if ($@) { $self->throw("Unable to sort hits: $@"); } else { $self->{'_hits'} = \@sorted_hits; $self->{'_no_iterations'} = 1; # to bypass iteration checking in hits() method 1; } } =head2 _default sort_hits Title : _default_sort_hits Usage : Do not call directly. Function: Sort hits in descending order by score Args : None Returns: 1 on success Note : Used by $result->sort_hits() =cut sub _default_sort_hits { $Bio::Search::Result::ResultI::b->score <=> $Bio::Search::Result::ResultI::a->score; } =head2 query_name Title : query_name Usage : $id = $result->query_name(); Function: Get the string identifier of the query used by the algorithm that performed the search. Returns : a string. Args : none =cut sub query_name { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 query_accession Title : query_accession Usage : $id = $result->query_accession(); Function: Get the accession (if available) for the query sequence Returns : a string Args : none =cut sub query_accession { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 query_length Title : query_length Usage : $id = $result->query_length(); Function: Get the length of the query sequence used in the search. Returns : a number Args : none =cut sub query_length { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 query_description Title : query_description Usage : $id = $result->query_description(); Function: Get the description of the query sequence used in the search. Returns : a string Args : none =cut sub query_description { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 database_name Title : database_name Usage : $name = $result->database_name() Function: Used to obtain the name of the database that the query was searched against by the algorithm. Returns : a scalar string Args : none =cut sub database_name { my ($self,@args) = @_; $self->throw_not_implemented; } =head2 database_letters Title : database_letters Usage : $size = $result->database_letters() Function: Used to obtain the size of database that was searched against. Returns : a scalar integer (units specific to algorithm, but probably the total number of residues in the database, if available) or undef if the information was not available to the Processor object. Args : none =cut sub database_letters { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 database_entries Title : database_entries Usage : $num_entries = $result->database_entries() Function: Used to obtain the number of entries contained in the database. Returns : a scalar integer representing the number of entities in the database or undef if the information was not available. Args : none =cut sub database_entries { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_parameter Title : get_parameter Usage : my $gap_ext = $result->get_parameter('gapext') Function: Returns the value for a specific parameter used when running this result Returns : string Args : name of parameter (string) =cut sub get_parameter{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 available_parameters Title : available_parameters Usage : my @params = $result->available_parameters Function: Returns the names of the available parameters Returns : Return list of available parameters used for this result Args : none =cut sub available_parameters{ my ($self) = @_; $self->throw_not_implemented(); } =head2 get_statistic Title : get_statistic Usage : my $gap_ext = $result->get_statistic('kappa') Function: Returns the value for a specific statistic available from this result Returns : string Args : name of statistic (string) =cut sub get_statistic{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 available_statistics Title : available_statistics Usage : my @statnames = $result->available_statistics Function: Returns the names of the available statistics Returns : Return list of available statistics used for this result Args : none =cut sub available_statistics{ my ($self) = @_; $self->throw_not_implemented(); } =head2 algorithm Title : algorithm Usage : my $r_type = $result->algorithm Function: Obtain the name of the algorithm used to obtain the Result Returns : string (e.g., BLASTP) Args : [optional] scalar string to set value =cut sub algorithm{ my ($self) = @_; $self->throw_not_implemented(); } =head2 algorithm_version Title : algorithm_version Usage : my $r_version = $result->algorithm_version Function: Obtain the version of the algorithm used to obtain the Result Returns : string (e.g., 2.1.2) Args : [optional] scalar string to set algorithm version value =cut sub algorithm_version{ my ($self) = @_; $self->throw_not_implemented(); } =head2 algorithm_reference Title : algorithm_reference Usage : $obj->algorithm_reference($newval) Function: Returns : value of the literature reference for the algorithm Args : newvalue (optional) Comments: The default implementation in ResultI returns an empty string rather than throwing a NotImplemented exception, since the ref may not always be available and is not critical. =cut sub algorithm_reference{ my ($self) = @_; return ''; } =head2 rid Title : rid Usage : $obj->rid($newval) Function: Returns : value of the BLAST Request ID (eg. RID: ZABJ4EA7014) Args : newvalue (optional) Comments: The default implementation in ResultI returns an empty string rather than throwing a NotImplemented exception, since the RID may not always be available and is not critical. See: (1) https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/BLAST/rid.html (2) https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node63.html =cut sub rid{ my ($self) = @_; return ''; } =head2 num_hits Title : num_hits Usage : my $hitcount= $result->num_hits Function: returns the number of hits for this query result Returns : integer Args : none =cut sub num_hits{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 hits Title : hits Usage : my @hits = $result->hits Function: Returns the HitI objects contained within this Result Returns : Array of Bio::Search::Hit::HitI objects Args : none See Also: L =cut sub hits{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 no_hits_found Usage : $nohits = $blast->no_hits_found(); Purpose : Get boolean indicator indicating whether or not any hits were present in the report. This is NOT the same as determining the number of hits via the hits() method, which will return zero hits if there were no hits in the report or if all hits were filtered out during the parse. Thus, this method can be used to distinguish these possibilities for hitless reports generated when filtering. Returns : Boolean Argument : none =cut #----------- sub no_hits_found { shift->throw_not_implemented } =head2 set_no_hits_found Usage : $blast->set_no_hits_found(); Purpose : Set boolean indicator indicating whether or not any hits were present in the report. Returns : n/a Argument : none =cut sub set_no_hits_found { shift->throw_not_implemented } 1; BioPerl-1.007002/Bio/Search/Result/WABAResult.pm000444000766000024 640613155576320 21164 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Result::WABAResult # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::WABAResult - Result object for WABA alignment output =head1 SYNOPSIS # use this object exactly as you would a GenericResult # the only extra method is query_database which is the # name of the file where the query sequence came from =head1 DESCRIPTION This object is for WABA result output, there is little difference between this object and a GenericResult save the addition of one method query_database. Expect many of the fields for GenericResult to be empty however as WABA was not intended to provide a lot of extra information other than the alignment. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Result::WABAResult; use strict; use base qw(Bio::Search::Result::GenericResult); =head2 new Title : new Usage : my $obj = Bio::Search::Result::WABAResult->new(); Function: Builds a new Bio::Search::Result::WABAResult object Returns : Bio::Search::Result::WABAResult Args : -query_database => "name of the database where the query came from" =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($db) = $self->_rearrange([qw(QUERY_DATABASE)], @args); defined $db && $self->query_database($db); return $self; } =head2 query_database Title : query_database Usage : $obj->query_database($newval) Function: Data field for the database filename where the query sequence came from Returns : value of query_database Args : newvalue (optional) =cut sub query_database{ my ($self,$value) = @_; if( defined $value) { $self->{'query_database'} = $value; } return $self->{'query_database'}; } =head2 All other methods are inherited from Bio::Search::Result::GenericResult See the L for complete documentation of the rest of the methods that are available for this module. =cut 1; BioPerl-1.007002/Bio/Search/Result/hmmer3Result.pm000444000766000024 775413155576320 21654 0ustar00cjfieldsstaff000000000000# $Id: bioperl.lisp 15559 2009-02-23 12:11:20Z maj $ # # BioPerl module for Bio::Search::Result::hmmer3Result # # Please direct questions and support issues to # # Cared for by Thomas Sharpton # # Copyright Thomas Sharpton # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::hmmer3Result - DESCRIPTION of Object =head1 SYNOPSIS Give standard usage here =head1 DESCRIPTION Describe the object here =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: L rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Thomas Sharpton Email thomas.sharpton@gmail.com Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Result::hmmer3Result; use strict; use base qw(Bio::Search::Result::GenericResult); =head2 new Title : new Usage : my $obj = new Bio::Search::Result::hmmer3Result.pm(); Function: Builds a new Bio::Search::Result::hmmer3Result.pm object Returns : an instance of Bio::Search::Result::hmmer3Result.pm Args : -hmm_name => string, name of hmm file -sequence_file => name of the sequence file =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($hmm,$seqfile) = $self->_rearrange([qw(HMM_NAME SEQUENCE_FILE)], @args); defined( $seqfile ) && $self->sequence_file( $seqfile ); defined( $hmm ) && $self->hmm_name( $hmm ); return $self; } =head2 hmm_name Title : hmm_name Usage : $obj->hmm_name($newval) Function: Get/Set the value of hmm_name Returns : value of hmm_name Args : newvalue (optional) =cut sub hmm_name{ my ($self,$value) = @_; if( defined $value) { $self->{'_hmm_name'} = $value; } return $self->{'_hmm_name'}; } =head2 sequence_file Title : sequence_file Usage : $obj->sequence_file($newval) Function: Get/Set the value of sequence_file Returns : value of sequence_file Args : newvalue (optional) =cut sub sequence_file{ my ($self,$value) = @_; if( defined $value) { $self->{'_sequence_file'} = $value; } return $self->{'_sequence_file'}; } =head2 next_model Title : next_model Usage : my $domain = $result->next_model Function: Returns the next domain - this is an alias for next_hit Returns : L object Args : none =cut sub next_model{ shift->next_hit } =head2 models Title : models Usage : my @domains = $result->models; Function: Returns the list of HMM models seen - this is an alias for hits() Returns : Array of L objects Args : none =cut sub models{ shift->hits } =head2 rewind Title : rewind Usage : $result->rewind; Function: Allow one to reset the Hit iteration to the beginning Since this is an in-memory implementation Returns : none Args : none =cut sub rewind{ my ($self) = @_; $self->{'_hitindex'} = 0; } 1; BioPerl-1.007002/Bio/Search/Tiling000755000766000024 013155576320 16522 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/Search/Tiling/MapTileUtils.pm000555000766000024 5060613155576320 21623 0ustar00cjfieldsstaff000000000000#$Id$ package Bio::Search::Tiling::MapTileUtils; use strict; use warnings; use Exporter; BEGIN { our @ISA = qw( Exporter ); our @EXPORT = qw( get_intervals_from_hsps interval_tiling decompose_interval containing_hsps covering_groups _allowable_filters _set_attributes _mapping_coeff); } # tiling trials # assumed: intervals are [$a0, $a1], with $a0 <= $a1 =head1 NAME Bio::Search::Tiling::MapTileUtils - utilities for manipulating closed intervals for an HSP tiling algorithm =head1 SYNOPSIS Not used directly. =head1 DESCRIPTION Not used directly. =head1 NOTE An "interval" in this module is defined as an arrayref C<[$a0, $a1]>, where C<$a0, $a1> are scalar numbers satisfying C<$a0 E= $a1>. =head1 AUTHOR Mark A. Jensen - maj -at- fortinbras -dot- us =head1 APPENDIX =head2 interval_tiling Title : interval_tiling() Usage : @tiling = interval_tiling( \@array_of_intervals ) Function: Find minimal set of intervals covering the input set Returns : array of arrayrefs of the form ( [$interval => [ @indices_of_collapsed_input_intervals ]], ...) Args : arrayref of intervals =cut sub interval_tiling { return unless $_[0]; # no input my $n = scalar @{$_[0]}; my %input; @input{(0..$n-1)} = @{$_[0]}; my @active = (0..$n-1); my @hold; my @tiled_ints; my @ret; while (@active) { my $tgt = $input{my $tgt_i = shift @active}; push @tiled_ints, $tgt_i; my $tgt_not_disjoint = 1; while ($tgt_not_disjoint) { $tgt_not_disjoint = 0; while (my $try_i = shift @active) { my $try = $input{$try_i}; if ( !are_disjoint($tgt, $try) ) { $tgt = min_covering_interval($tgt,$try); push @tiled_ints, $try_i; $tgt_not_disjoint = 1; } else { push @hold, $try_i; } } if (!$tgt_not_disjoint) { push @ret, [ $tgt => [@tiled_ints] ]; @tiled_ints = (); } @active = @hold; @hold = (); } } return @ret; } =head2 decompose_interval Title : decompose_interval Usage : @decomposition = decompose_interval( \@overlappers ) Function: Calculate the disjoint decomposition of a set of overlapping intervals, each annotated with a list of covering intervals Returns : array of arrayrefs of the form ( [[@interval] => [@indices_of_coverers]], ... ) Args : arrayref of intervals (arrayrefs like [$a0, $a1], with Note : Each returned interval is associated with a list of indices of the original intervals that cover that decomposition component (scalar size of this list could be called the 'coverage coefficient') Note : Coverage: each component of the decomp is completely contained in the input intervals that overlap it, by construction. Caveat : This routine expects the members of @overlappers to overlap, but doesn't check this. =cut ### what if the input intervals don't overlap?? They MUST overlap; that's ### what interval_tiling() is for. sub decompose_interval { return unless $_[0]; # no input my @ints = @{$_[0]}; my (%flat,@flat); ### this is ok, but need to handle the case where a lh and rh endpoint ### coincide... # decomposition -- # flatten: # every lh endpoint generates (lh-1, lh) # every rh endpoint generates (rh, rh+) foreach (@ints) { $flat{$$_[0]-1}++; $flat{$$_[0]}++; $flat{$$_[1]}++; $flat{$$_[1]+1}++; } # sort, create singletons if nec. my @a; @a = sort {$a<=>$b} keys %flat; # throw out first and last (meeting a boundary condition) shift @a; pop @a; # look for singletons @flat = (shift @a, shift @a); if ( $flat[1]-$flat[0] == 1 ) { @flat = ($flat[0],$flat[0], $flat[1]); } while (my $a = shift @a) { if ($a-$flat[-2]==2) { push @flat, $flat[-1]; # create singleton interval } push @flat, $a; } if ($flat[-1]-$flat[-2]==1 and @flat % 2) { push @flat, $flat[-1]; } # component intervals are consecutive pairs my @decomp; while (my $a = shift @flat) { push @decomp, [$a, shift @flat]; } # for each component, return a list of the indices of the input intervals # that cover the component. my @coverage; foreach my $i (0..$#decomp) { foreach my $j (0..$#ints) { unless (are_disjoint($decomp[$i], $ints[$j])) { if (defined $coverage[$i]) { push @{$coverage[$i]}, $j; } else { $coverage[$i] = [$j]; } } } } return map { [$decomp[$_] => $coverage[$_]] } (0..$#decomp); } =head2 are_disjoint Title : are_disjoint Usage : are_disjoint( [$a0, $a1], [$b0, $b1] ) Function: Determine if two intervals are disjoint Returns : True if the intervals are disjoint, false if they overlap Args : array of two intervals =cut sub are_disjoint { my ($int1, $int2) = @_; return 1 if ( $$int1[1] < $$int2[0] ) || ( $$int2[1] < $$int1[0]); return 0; } =head2 min_covering_interval Title : min_covering_interval Usage : $interval = min_covering_interval( [$a0,$a1],[$b0,$b1] ) Function: Determine the minimal covering interval for two intervals Returns : an interval Args : two intervals =cut sub min_covering_interval { my ($int1, $int2) = @_; my @a = sort {$a <=> $b} (@$int1, @$int2); return [$a[0],$a[-1]]; } =head2 get_intervals_from_hsps Title : get_intervals_from_hsps Usage : @intervals = get_intervals_from_hsps($type, @hsp_objects) Function: Return array of intervals of the form [ $start, $end ], from an array of hsp objects Returns : an array of intervals Args : scalar $type, array of HSPI objects; where $type is one of 'hit', 'subject', 'query' =cut sub get_intervals_from_hsps { my $type = shift; my @hsps; if (ref($type) =~ /HSP/) { push @hsps, $type; $type = 'query'; } elsif ( !grep /^$type$/,qw( hit subject query ) ) { die "Unknown HSP type '$type'"; } $type = 'hit' if $type eq 'subject'; push @hsps, @_; my @ret; foreach (@hsps) { # push @ret, [ $_->start($type), $_->end($type)]; push @ret, [ $_->range($type) ]; } return @ret; } # fast, clear, nasty, brutish and short. # for _allowable_filters(), _set_mapping() # covers BLAST, FAST families # FASTA is ambiguous (nt or aa) based on alg name only my $alg_lookup = { 'N' => { 'mapping' => [1,1], 'def_context' => ['p_','p_'], 'has_strand' => [1, 1], 'has_frame' => [0, 0]}, 'P' => { 'mapping' => [1,1], 'def_context' => ['all','all'], 'has_strand' => [0, 0], 'has_frame' => [0, 0]}, 'X' => { 'mapping' => [3, 1], 'def_context' => [undef,'all'], 'has_strand' => [1, 0], 'has_frame' => [1, 0]}, 'Y' => { 'mapping' => [3, 1], 'def_context' => [undef,'all'], 'has_strand' => [1, 0], 'has_frame' => [1, 0]}, 'TA' => { 'mapping' => [1, 3], 'def_context' => ['all',undef], 'has_strand' => [0, 1], 'has_frame' => [0, 1]}, 'TN' => { 'mapping' => [1, 3], 'def_context' => ['p_',undef], 'has_strand' => [1,1], 'has_frame' => [0, 1]}, 'TX' => { 'mapping' => [3, 3], 'def_context' => [undef,undef], 'has_strand' => [1, 1], 'has_frame' => [1, 1]}, 'TY' => { 'mapping' => [3, 3], 'def_context' => [undef,undef], 'has_strand' => [1, 1], 'has_frame' => [1, 1]} }; =head2 _allowable_filters Title : _allowable_filters Usage : _allowable_filters($Bio_Search_Hit_HitI, $type) Function: Return the HSP filters (strand, frame) allowed, based on the reported algorithm Returns : String encoding allowable filters: s = strand, f = frame Empty string if no filters allowed undef if algorithm unrecognized Args : A Bio::Search::Hit::HitI object, scalar $type, one of 'hit', 'subject', 'query'; default is 'query' =cut sub _allowable_filters { my $hit = shift; my $type = shift; $type ||= 'q'; unless (grep /^$type$/, qw( h q s ) ) { warn("Unknown type '$type'; returning ''"); return ''; } $type = 'h' if $type eq 's'; my $alg = $hit->algorithm; # pretreat (i.e., kludge it) $alg =~ /^RPS/ and ($alg) = ($alg =~ /\(([^)]+)\)/); for ($hit->algorithm) { /MEGABLAST/i && do { return qr/[s]/; }; /(.?)BLAST(.?)/i && do { return $$alg_lookup{$1.$2}{$type}; }; /(.?)FAST(.?)/ && do { return $$alg_lookup{$1.$2}{$type}; }; do { # unrecognized last; }; } return; } =head2 _set_attributes Title : _set_attributes Usage : $tiling->_set_attributes() Function: Sets attributes for invocant that depend on algorithm name Returns : True on success Args : none Note : setting based on the configuration table %alg_lookup =cut sub _set_attributes { my $self = shift; my $alg = $self->hit->algorithm; # pretreat (i.e., kludge it) $alg =~ /^RPS/ and ($alg) = ($alg =~ /\(([^)]+)\)/); for ($alg) { /MEGABLAST/i && do { ($self->{_mapping_query},$self->{_mapping_hit}) = (1,1); ($self->{_def_context_query},$self->{_def_context_hit}) = ('p_','p_'); ($self->{_has_frame_query},$self->{_has_frame_hit}) = (0, 0); ($self->{_has_strand_query},$self->{_has_strand_hit}) = (1, 1); last; }; /(.?)BLAST(.?)/i && do { ($self->{_mapping_query},$self->{_mapping_hit}) = @{$$alg_lookup{$1.$2}{mapping}}; ($self->{_def_context_query},$self->{_def_context_hit}) = @{$$alg_lookup{$1.$2}{def_context}}; ($self->{_has_frame_query},$self->{_has_frame_hit}) = @{$$alg_lookup{$1.$2}{has_frame}}; ($self->{_has_strand_query},$self->{_has_strand_hit}) = @{$$alg_lookup{$1.$2}{has_strand}}; last; }; /(.?)FAST(.?)/ && do { ($self->{_mapping_query},$self->{_mapping_hit}) = @{$$alg_lookup{$1.$2}{mapping}}; ($self->{_def_context_query},$self->{_def_context_hit}) = @{$$alg_lookup{$1.$2}{def_context}}; ($self->{_has_frame_query},$self->{_has_frame_hit}) = @{$$alg_lookup{$1.$2}{has_frame}}; ($self->{_has_strand_query},$self->{_has_strand_hit}) = @{$$alg_lookup{$1.$2}{has_strand}}; last; }; do { # unrecognized $self->warn("Unrecognized algorithm '$alg'; defaults may not work"); ($self->{_mapping_query},$self->{_mapping_hit}) = (1,1); ($self->{_def_context_query},$self->{_def_context_hit}) = ('all','all'); ($self->{_has_frame_query},$self->{_has_frame_hit}) = (0,0); ($self->{_has_strand_query},$self->{_has_strand_hit}) = (0,0); return 0; last; }; } return 1; } sub _mapping_coeff { my $obj = shift; my $type = shift; my %type_i = ( 'query' => 0, 'hit' => 1 ); unless ( ref($obj) && $obj->can('algorithm') ) { $obj->warn("Object type unrecognized"); return undef; } $type ||= 'query'; unless ( grep(/^$type$/, qw( query hit subject ) ) ) { $obj->warn("Sequence type unrecognized"); return undef; } $type = 'hit' if $type eq 'subject'; my $alg = $obj->algorithm; # pretreat (i.e., kludge it) $alg =~ /^RPS/ and ($alg) = ($alg =~ /\(([^)]+)\)/); for ($alg) { /MEGABLAST/i && do { return 1; }; /(.?)BLAST(.?)/i && do { return $$alg_lookup{$1.$2}{'mapping'}[$type_i{$type}]; }; /(.?)FAST(.?)/ && do { return $$alg_lookup{$1.$2}{'mapping'}[$type_i{$type}]; }; do { # unrecognized last; }; } return; } # a graphical depiction of a set of intervals sub _ints_as_text { my $ints = shift; my @ints = @$ints; my %pos; for (@ints) { $pos{$$_[0]}++; $pos{$$_[1]}++; } my @pos = sort {$a<=>$b} keys %pos; @pos = map {sprintf("%03d",$_)} @pos; #header my $max=0; $max = (length > $max) ? length : $max for (@pos); for my $j (0..$max-1) { my $i = $max-1-$j; my @line = map { substr($_, $j, 1) || '0' } @pos; print join('', @line), "\n"; } print '-' x @pos, "\n"; undef %pos; @pos{map {sprintf("%d",$_)} @pos} = (0..@pos); foreach (@ints) { print ' ' x $pos{$$_[0]}, '[', ' ' x ($pos{$$_[1]}-$pos{$$_[0]}-1), ']', ' ' x (@pos-$pos{$$_[1]}), "\n"; } } =head2 containing_hsps() Title : containing_hsps Usage : @hsps = containing_hsps($interval, @hsps_to_search) Function: Return a list of hsps whose coordinates completely contain the given $interval Returns : Array of HSP objects Args : $interval : [$int1, $int2], array of HSP objects =cut # could be more efficient if hsps are assumed ordered... sub containing_hsps { my $intvl = shift; my @hsps = @_; my @ret; my ($beg, $end) = @$intvl; foreach my $hsp (@hsps) { my ($start, $stop) = ($hsp->start, $hsp->end); push @ret, $hsp if ( $start <= $beg and $end <= $stop ); } return @ret; } =head2 covering_groups() Title : covering_groups Usage : Function: divide a list of **ordered,disjoint** intervals (as from a coverage map) into a set of disjoint covering groups Returns : array of arrayrefs, each arrayref a covering set of intervals Args : array of intervals =cut sub covering_groups { my @intervals = @_; return unless @intervals; my (@groups, $grp); push @{$groups[0]}, shift @intervals; $grp = $groups[0]; for (my $intvl = shift @intervals; @intervals; $intvl = shift @intervals) { if ( $intvl->[0] - $grp->[-1][1] == 1 ) { # intervals are direcly adjacent push @$grp, $intvl; } else { $grp = [$intvl]; push @groups, $grp; } } return @groups; } 1; # need our own subsequencer for hsps. package Bio::Search::HSP::HSPI; use strict; use warnings; =head2 matches_MT Title : matches_MT Usage : $hsp->matches($type, $action, $start, $end) Purpose : Get the total number of identical or conserved matches in the query or sbjct sequence for the given HSP. Optionally can report data within a defined interval along the seq. Returns : scalar int Args : Comments : Relies on seq_str('match') to get the string of alignment symbols between the query and sbjct lines which are used for determining the number of identical and conservative matches. Note : Modeled on Bio::Search::HSP::HSPI::matches =cut sub matches_MT { use integer; my( $self, @args ) = @_; my($type, $action, $beg, $end) = $self->_rearrange( [qw(TYPE ACTION START END)], @args); my @actions = qw( identities conserved searchutils ); # prep $type $self->throw("Type not specified") if !defined $type; $self->throw("Type '$type' unrecognized") unless grep(/^$type$/,qw(query hit subject)); $type = 'hit' if $type eq 'subject'; # prep $action $self->throw("Action not specified") if !defined $action; $self->throw("Action '$action' unrecognized") unless grep(/^$action$/, @actions); my ($len_id, $len_cons); my $c = Bio::Search::Tiling::MapTileUtils::_mapping_coeff($self, $type); if ((defined $beg && !defined $end) || (!defined $beg && defined $end)) { $self->throw("Both start and end are required"); } elsif ( (!defined($beg) && !defined($end)) || !$self->seq_str('match') ) { ## Get data for the whole alignment. # the reported values x mapping $self->debug("Sequence data not present in report; returning data for entire HSP") unless $self->seq_str('match'); ($len_id, $len_cons) = map { $c*$_ } ($self->num_identical, $self->num_conserved); for ($action) { $_ eq 'identities' && do { return $len_id; }; $_ eq 'conserved' && do { return $len_cons; }; $_ eq 'searchutils' && do { return ($len_id, $len_cons); }; do { $self->throw("What are YOU doing here?"); }; } } else { ## Get the substring representing the desired sub-section of aln. my($start,$stop) = $self->range($type); if ( $beg < $start or $stop < $end ) { $self->throw("Start/stop out of range [$start, $stop]"); } # handle gaps my $match_str = $self->seq_str('match'); if ($self->gaps) { # strip the homology string of gap positions relative # to the target type $match_str = $self->seq_str('match'); my $tgt = $self->seq_str($type); my $encode = $match_str ^ $tgt; my $zap = '-'^' '; $encode =~ s/$zap//g; $tgt =~ s/-//g; $match_str = $tgt ^ $encode; # match string is now the correct length for substr'ing below, # given that start and end are gapless coordinates in the # blast report } my $seq = ""; $seq = substr( $match_str, int( ($beg-$start)/Bio::Search::Tiling::MapTileUtils::_mapping_coeff($self, $type) ), int( 1+($end-$beg)/Bio::Search::Tiling::MapTileUtils::_mapping_coeff($self, $type) ) ); if(!CORE::length $seq) { $self->throw("Undefined sub-sequence ($beg,$end). Valid range = $start - $stop"); } $seq =~ s/ //g; # remove space (no info). $len_cons = (CORE::length $seq)*(Bio::Search::Tiling::MapTileUtils::_mapping_coeff($self,$type)); $seq =~ s/\+//g; # remove '+' characters (conservative substitutions) $len_id = (CORE::length $seq)*(Bio::Search::Tiling::MapTileUtils::_mapping_coeff($self,$type)); for ($action) { $_ eq 'identities' && do { return $len_id; }; $_ eq 'conserved' && do { return $len_cons; }; $_ eq 'searchutils' && do { return ($len_id, $len_cons); }; do { $self->throw("What are YOU doing here?"); }; } } } 1; package Bio::LocatableSeq; use strict; use warnings; # mixin the Bio::FeatureHolderI implementation of # Bio::Seq -- for get_tiled_aln =head2 get_SeqFeatures Title : get_SeqFeatures Usage : Function: Get the feature objects held by this feature holder. Features which are not top-level are subfeatures of one or more of the returned feature objects, which means that you must traverse the subfeature arrays of each top-level feature object in order to traverse all features associated with this sequence. Top-level features can be obtained by tag, specified in the argument. Use get_all_SeqFeatures() if you want the feature tree flattened into one single array. Example : Returns : an array of Bio::SeqFeatureI implementing objects Args : [optional] scalar string (feature tag) =cut sub get_SeqFeatures{ my $self = shift; my $tag = shift; if( !defined $self->{'_as_feat'} ) { $self->{'_as_feat'} = []; } if ($tag) { return map { $_->primary_tag eq $tag ? $_ : () } @{$self->{'_as_feat'}}; } else { return @{$self->{'_as_feat'}}; } } =head2 feature_count Title : feature_count Usage : $seq->feature_count() Function: Return the number of SeqFeatures attached to a sequence Returns : integer representing the number of SeqFeatures Args : None =cut sub feature_count { my ($self) = @_; if (defined($self->{'_as_feat'})) { return ($#{$self->{'_as_feat'}} + 1); } else { return 0; } } =head2 add_SeqFeature Title : add_SeqFeature Usage : $seq->add_SeqFeature($feat); $seq->add_SeqFeature(@feat); Function: Adds the given feature object (or each of an array of feature objects to the feature array of this sequence. The object passed is required to implement the Bio::SeqFeatureI interface. Returns : 1 on success Args : A Bio::SeqFeatureI implementing object, or an array of such objects. =cut sub add_SeqFeature { my ($self,@feat) = @_; $self->{'_as_feat'} = [] unless $self->{'_as_feat'}; foreach my $feat ( @feat ) { if( !$feat->isa("Bio::SeqFeatureI") ) { $self->throw("$feat is not a SeqFeatureI and that's what we expect..."); } $feat->attach_seq($self); push(@{$self->{'_as_feat'}},$feat); } return 1; } =head2 remove_SeqFeatures Title : remove_SeqFeatures Usage : $seq->remove_SeqFeatures(); Function: Flushes all attached SeqFeatureI objects. To remove individual feature objects, delete those from the returned array and re-add the rest. Example : Returns : The array of Bio::SeqFeatureI objects removed from this seq. Args : None =cut sub remove_SeqFeatures { my $self = shift; return () unless $self->{'_as_feat'}; my @feats = @{$self->{'_as_feat'}}; $self->{'_as_feat'} = []; return @feats; } 1; BioPerl-1.007002/Bio/Search/Tiling/MapTiling.pm000555000766000024 13450713155576320 21156 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Tiling::MapTiling # # Please direct questions and support issues to # # Cared for by Mark A. Jensen # # Copyright Mark A. Jensen # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Tiling::MapTiling - An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics =head1 SYNOPSIS # get a BLAST $hit from somewhere, then $tiling = Bio::Search::Tiling::MapTiling->new($hit); # stats $numID = $tiling->identities(); $numCons = $tiling->conserved(); $query_length = $tiling->length('query'); $subject_length = $tiling->length('subject'); # or... $subject_length = $tiling->length('hit'); # get a visual on the coverage map print $tiling->coverage_map_as_text('query',$context,'LEGEND'); # tilings $context = $tiling->_context( -type => 'subject', -strand=> 1, -frame=>1); @covering_hsps_for_subject = $tiling->next_tiling('subject',$context); $context = $tiling->_context( -type => 'query', -strand=> -1, -frame=>0); @covering_hsps_for_query = $tiling->next_tiling('query', $context); =head1 DESCRIPTION Frequently, users want to use a set of high-scoring pairs (HSPs) obtained from a BLAST or other search to assess the overall level of identity, conservation, or coverage represented by matches between a subject and a query sequence. Because a set of HSPs frequently describes multiple overlapping sequence fragments, a simple summation of statistics over the HSPs will generally overestimate those statistics. To obtain an accurate estimate of global hit statistics, a 'tiling' of HSPs onto either the subject or the query sequence must be performed, in order to properly correct for this. This module will execute a tiling algorithm on a given hit based on an interval decomposition I'm calling the "coverage map". Internal object methods compute the various statistics, which are then stored in appropriately-named public object attributes. See L for more info on the algorithm. =head2 STRAND/FRAME CONTEXTS In BLASTX, TBLASTN, and TBLASTX reports, strand and frame information are reported for the query, subject, or query and subject, respectively, for each HSP. Tilings for these sequence types are only meaningful when they include HSPs in the same strand and frame, or "context". So, in these situations, the context must be specified in the method calls or the methods will throw. Contexts are specified as strings: C<[ 'all' | [m|p][_|0|1|2] ]>, where C = all HSPs (will throw if context must be specified), C = minus strand, C

= plus strand, and C<_> = no frame info, C<0,1,2> = respective (absolute) frame. The L method will convert a (strand, frame) specification to a context string, e.g.: $context = $self->_context(-type=>'query', -strand=>-1, -frame=>-2); returns C. The contexts present among the HSPs in a hit are identified and stored for convenience upon object construction. These are accessed off the object with the L method. If contexts don't apply for the given report, this returns C<('all')>. =head1 TILED ALIGNMENTS The experimental method L will use a tiling to concatenate tiled hsps into a series of L objects: @alns = $tiling->get_tiled_alns($type, $context); Each alignment contains two sequences with ids 'query' and 'subject', and consists of a concatenation of tiling HSPs which overlap or are directly adjacent. The alignment are returned in C<$type> sequence order. When HSPs overlap, the alignment sequence is taken from the HSP which comes first in the coverage map array. The sequences in each alignment contain features (even though they are L objects) which map the original query/subject coordinates to the new alignment sequence coordinates. You can determine the original BLAST fragments this way: $aln = ($tiling->get_tiled_alns)[0]; $qseq = $aln->get_seq_by_id('query'); $hseq = $aln->get_seq_by_id('subject'); foreach my $feat ($qseq->get_SeqFeatures) { $org_start = ($feat->get_tag_values('query_start'))[0]; $org_end = ($feat->get_tag_values('query_end'))[0]; # original fragment as represented in the tiled alignment: $org_fragment = $feat->seq; } foreach my $feat ($hseq->get_SeqFeatures) { $org_start = ($feat->get_tag_values('subject_start'))[0]; $org_end = ($feat->get_tag_values('subject_end'))[0]; # original fragment as represented in the tiled alignment: $org_fragment = $feat->seq; } =head1 DESIGN NOTE The major calculations are made just-in-time, and then memoized. So, for example, for a given MapTiling object, a coverage map would usually be calculated only once (for the query), and at most twice (if the subject perspective is also desired), and then only when a statistic is first accessed. Afterward, the map and/or any statistic is read from storage. So feel free to call the statistic methods frequently if it suits you. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Mark A. Jensen Email maj -at- fortinbras -dot- us =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Tiling::MapTiling; use strict; use warnings; # Object preamble - inherits from Bio::Root::Root #use lib '../../..'; use Bio::Root::Root; use Bio::Search::Tiling::TilingI; use Bio::Search::Tiling::MapTileUtils; use Bio::LocatableSeq; # use base qw(Bio::Root::Root Bio::Search::Tiling::TilingI); use base qw(Bio::Root::Root Bio::Search::Tiling::TilingI); =head1 CONSTRUCTOR =head2 new Title : new Usage : my $obj = new Bio::Search::Tiling::GenericTiling(); Function: Builds a new Bio::Search::Tiling::GenericTiling object Returns : an instance of Bio::Search::Tiling::GenericTiling Args : -hit => $a_Bio_Search_Hit_HitI_object general filter function: -hsp_filter => sub { my $this_hsp = shift; ...; return 1 if $wanted; return 0; } =cut sub new { my $class = shift; my @args = @_; my $self = $class->SUPER::new(@args); my($hit, $filter) = $self->_rearrange( [qw( HIT HSP_FILTER)],@args ); $self->throw("HitI object required") unless $hit; $self->throw("Argument must be HitI object") unless ( ref $hit && $hit->isa('Bio::Search::Hit::HitI') ); $self->{hit} = $hit; $self->_set_attributes(); $self->{"_algorithm"} = $hit->algorithm; my @hsps = $hit->hsps; # apply filter function if requested if ( defined $filter ) { if ( ref($filter) eq 'CODE' ) { @hsps = map { $filter->($_) ? $_ : () } @hsps; } else { $self->warn("-filter is not a coderef; ignoring"); } } # identify available contexts for my $t (qw( query hit )) { my %contexts; for my $i (0..$#hsps) { my $ctxt = $self->_context( -type => $t, -strand => $hsps[$i]->strand($t), -frame => $hsps[$i]->frame($t)); $contexts{$ctxt} ||= []; push @{$contexts{$ctxt}}, $i; } $self->{"_contexts_${t}"} = \%contexts; } $self->warn("No HSPs present in hit after filtering") unless (@hsps); $self->hsps(\@hsps); return $self; } # a tiling is based on the set of hsps contained in a single hit. # check all the boundaries - zero hsps, one hsp, all disjoint hsps =head1 TILING ITERATORS =head2 next_tiling Title : next_tiling Usage : @hsps = $self->next_tiling($type); Function: Obtain a tiling: a minimal set of HSPs covering the $type ('hit', 'subject', 'query') sequence Example : Returns : an array of HSPI objects Args : scalar $type: one of 'hit', 'subject', 'query', with 'subject' an alias for 'hit' =cut sub next_tiling{ my $self = shift; my ($type, $context) = @_; $self->_check_type_arg(\$type); $self->_check_context_arg($type, \$context); return $self->_tiling_iterator($type, $context)->(); } =head2 rewind_tilings Title : rewind_tilings Usage : $self->rewind_tilings($type) Function: Reset the next_tilings($type) iterator Example : Returns : True on success Args : scalar $type: one of 'hit', 'subject', 'query'; default is 'query' =cut sub rewind_tilings{ my $self = shift; my ($type,$context) = @_; $self->_check_type_arg(\$type); $self->_check_context_arg($type, \$context); return $self->_tiling_iterator($type, $context)->('REWIND'); } =head1 ALIGNMENTS =head2 get_tiled_alns() Title : get_tiled_alns Usage : @alns = $tiling->get_tiled_alns($type, $context) Function: Use a tiling to construct a minimal set of alignment objects covering the region specified by $type/$context by splicing adjacent HSP tiles Returns : an array of Bio::SimpleAlign objects; see Note below Args : scalar $type: one of 'hit', 'subject', 'query' default is 'query' scalar $context: strand/frame context string Following $type and $context, an array of ordered, tiled HSP objects can be specified; this is the tiling that will directly the alignment construction default -- the first tiling provided by a tiling iterator Notes : Each returned alignment is a concatenation of adjacent tiles. The set of alignments will cover all regions described by the $type/$context pair in the hit. The pair of sequences in each alignment have ids 'query' and 'subject', and each sequence possesses SeqFeatures that map the original query or subject coordinates to the sequence coordinates in the tiled alignment. =cut sub get_tiled_alns { my $self = shift; my ($type, $context) = @_; $self->_check_type_arg(\$type); $self->_check_context_arg($type, \$context); my $t = shift; # first arg after type/context, arrayref to a tiling my @tiling; if ($t && (ref($t) eq 'ARRAY')) { @tiling = @$t; } else { # otherwise, take the first tiling available @tiling = $self->_make_tiling_iterator($type,$context)->(); } my @ret; my @map = $self->coverage_map($type, $context); my @intervals = map {$_->[0]} @map; # disjoint decomp # divide into disjoint covering groups my @groups = covering_groups(@intervals); require Bio::SimpleAlign; require Bio::SeqFeature::Generic; # cut hsp aligns along the disjoint decomp # look for gaps...or add gaps? my ($q_start, $h_start, $q_strand, $h_strand); # build seqs for my $grp (@groups) { my $taln = Bio::SimpleAlign->new(); my (@qfeats, @hfeats); my $query_string = ''; my $hit_string = ''; my ($qlen,$hlen) = (0,0); my ($qinc, $hinc, $qstart, $hstart); for my $intvl (@$grp) { # following just chooses the first available hsp containing the # interval -- this is arbitrary, could be smarter. my $aln = ( containing_hsps($intvl, @tiling) )[0]->get_aln; my $qseq = $aln->get_seq_by_pos(1); my $hseq = $aln->get_seq_by_pos(2); $qstart ||= $qseq->start; $hstart ||= $hseq->start; # calculate the slice boundaries my ($beg, $end); for ($type) { /query/ && do { $beg = $aln->column_from_residue_number($qseq->id, $intvl->[0]); $end = $aln->column_from_residue_number($qseq->id, $intvl->[1]); last; }; /subject|hit/ && do { $beg = $aln->column_from_residue_number($hseq->id, $intvl->[0]); $end = $aln->column_from_residue_number($hseq->id, $intvl->[1]); last; }; } $aln = $aln->slice($beg, $end); $qseq = $aln->get_seq_by_pos(1); $hseq = $aln->get_seq_by_pos(2); $qinc = $qseq->length - $qseq->num_gaps($Bio::LocatableSeq::GAP_SYMBOLS); $hinc = $hseq->length - $hseq->num_gaps($Bio::LocatableSeq::GAP_SYMBOLS); push @qfeats, Bio::SeqFeature::Generic->new( -start => $qlen+1, -end => $qlen+$qinc, -strand => $qseq->strand, -primary => 'query', -source_tag => 'BLAST', -display_name => 'query coordinates', -tag => { query_id => $qseq->id, query_desc => $qseq->desc, query_start => $qstart + (($qseq->strand && $qseq->strand < 0) ? -1 : 1)*$qlen, query_end => $qstart + (($qseq->strand && $qseq->strand < 0) ? -1 : 1)*($qlen+$qinc-1), } ); push @hfeats, Bio::SeqFeature::Generic->new( -start => $hlen+1, -end => $hlen+$hinc, -strand => $hseq->strand, -primary => 'subject/hit', -source_tag => 'BLAST', -display_name => 'subject/hit coordinates', -tag => { subject_id => $hseq->id, subject_desc => $hseq->desc, subject_start => $hstart + (($hseq->strand && $hseq->strand < 0) ? -1 : 1)*$hlen, subject_end => $hstart + (($hseq->strand && $hseq->strand < 0) ? -1 : 1)*($hlen+$hinc-1) } ); $query_string .= $qseq->seq; $hit_string .= $hseq->seq; $qlen += $qinc; $hlen += $hinc; } # create the LocatableSeqs and add the features to each # then add the seqs to the new aln # note in MapTileUtils, Bio::FeatureHolderI methods have been # mixed into Bio::LocatableSeq my $qseq = Bio::LocatableSeq->new( -id => 'query', -seq => $query_string); $qseq->add_SeqFeature(@qfeats); my $hseq = Bio::LocatableSeq->new( -id => 'subject', -seq => $hit_string ); $hseq->add_SeqFeature(@hfeats); $taln->add_seq($qseq); $taln->add_seq($hseq); push @ret, $taln; } return @ret; } =head1 STATISTICS =head2 identities Title : identities Usage : $tiling->identities($type, $action, $context) Function: Retrieve the calculated number of identities for the invocant Example : Returns : value of identities (a scalar) Args : scalar $type: one of 'hit', 'subject', 'query' default is 'query' option scalar $action: one of 'exact', 'est', 'fast', 'max' default is 'exact' option scalar $context: strand/frame context string Note : getter only =cut sub identities{ my $self = shift; my ($type, $action, $context) = @_; $self->_check_type_arg(\$type); $self->_check_action_arg(\$action); $self->_check_context_arg($type, \$context); if (!defined $self->{"identities_${type}_${action}_${context}"}) { $self->_calc_stats($type, $action, $context); } return $self->{"identities_${type}_${action}_${context}"}; } =head2 conserved Title : conserved Usage : $tiling->conserved($type, $action) Function: Retrieve the calculated number of conserved sites for the invocant Example : Returns : value of conserved (a scalar) Args : scalar $type: one of 'hit', 'subject', 'query' default is 'query' option scalar $action: one of 'exact', 'est', 'fast', 'max' default is 'exact' option scalar $context: strand/frame context string Note : getter only =cut sub conserved{ my $self = shift; my ($type, $action, $context) = @_; $self->_check_type_arg(\$type); $self->_check_action_arg(\$action); $self->_check_context_arg($type, \$context); if (!defined $self->{"conserved_${type}_${action}_${context}"}) { $self->_calc_stats($type, $action, $context); } return $self->{"conserved_${type}_${action}_${context}"}; } =head2 length Title : length Usage : $tiling->length($type, $action, $context) Function: Retrieve the total length of aligned residues for the seq $type Example : Returns : value of length (a scalar) Args : scalar $type: one of 'hit', 'subject', 'query' default is 'query' option scalar $action: one of 'exact', 'est', 'fast', 'max' default is 'exact' option scalar $context: strand/frame context string Note : getter only =cut sub length{ my $self = shift; my ($type,$action,$context) = @_; $self->_check_type_arg(\$type); $self->_check_action_arg(\$action); $self->_check_context_arg($type, \$context); if (!defined $self->{"length_${type}_${action}_${context}"}) { $self->_calc_stats($type, $action, $context); } return $self->{"length_${type}_${action}_${context}"}; } =head2 frac Title : frac Usage : $tiling->frac($type, $denom, $action, $context, $method) Function: Return the fraction of sequence length consisting of desired kinds of pairs (given by $method), with respect to $denom Returns : scalar float Args : -type => one of 'hit', 'subject', 'query' -denom => one of 'total', 'aligned' -action => one of 'exact', 'est', 'fast', 'max' -context => strand/frame context string -method => one of 'identical', 'conserved' Note : $denom == 'aligned', return desired_stat/num_aligned $denom == 'total', return desired_stat/_reported_length (i.e., length of the original input sequences) Note : In keeping with the spirit of Bio::Search::HSP::HSPI, reported lengths of translated dna are reduced by a factor of 3, to provide fractions relative to amino acid coordinates. =cut sub frac { my $self = shift; my @args = @_; my ($type, $denom, $action, $context, $method) = $self->_rearrange([qw(TYPE DENOM ACTION CONTEXT METHOD)],@args); $self->_check_type_arg(\$type); $self->_check_action_arg(\$action); $self->_check_context_arg($type, \$context); unless ($method and grep(/^$method$/, qw( identical conserved ))) { $self->throw("-method must specified; one of ('identical', 'conserved')"); } $denom ||= 'total'; unless (grep /^$denom/, qw( total aligned )) { $self->throw("Denominator selection must be one of ('total', 'aligned'), not '$denom'"); } my $key = "frac_${method}_${type}_${denom}_${action}_${context}"; my $stat; for ($method) { $_ eq 'identical' && do { $stat = $self->identities($type, $action, $context); last; }; $_ eq 'conserved' && do { $stat = $self->conserved($type, $action, $context); last; }; do { $self->throw("What are YOU doing here?"); }; } if (!defined $self->{$key}) { for ($denom) { /total/ && do { $self->{$key} = $stat/$self->_reported_length($type); # need fudge fac?? last; }; /aligned/ && do { $self->{$key} = $stat/$self->length($type,$action,$context); last; }; do { $self->throw("What are YOU doing here?"); }; } } return $self->{$key}; } =head2 frac_identical Title : frac_identical Usage : $tiling->frac_identical($type, $denom, $action, $context) Function: Return the fraction of sequence length consisting of identical pairs, with respect to $denom Returns : scalar float Args : -type => one of 'hit', 'subject', 'query' -denom => one of 'total', 'aligned' -action => one of 'exact', 'est', 'fast', 'max' -context => strand/frame context string Note : $denom == 'aligned', return conserved/num_aligned $denom == 'total', return conserved/_reported_length (i.e., length of the original input sequences) Note : In keeping with the spirit of Bio::Search::HSP::HSPI, reported lengths of translated dna are reduced by a factor of 3, to provide fractions relative to amino acid coordinates. Note : This an alias that calls frac() =cut sub frac_identical{ my $self = shift; my @args = @_; my ($type, $denom, $action,$context) = $self->_rearrange( [qw[ TYPE DENOM ACTION CONTEXT]],@args ); $self->frac( -type=>$type, -denom=>$denom, -action=>$action, -method=>'identical', -context=>$context); } =head2 frac_conserved Title : frac_conserved Usage : $tiling->frac_conserved($type, $denom, $action, $context) Function: Return the fraction of sequence length consisting of conserved pairs, with respect to $denom Returns : scalar float Args : -type => one of 'hit', 'subject', 'query' -denom => one of 'total', 'aligned' -action => one of 'exact', 'est', 'fast', 'max' -context => strand/frame context string Note : $denom == 'aligned', return conserved/num_aligned $denom == 'total', return conserved/_reported_length (i.e., length of the original input sequences) Note : In keeping with the spirit of Bio::Search::HSP::HSPI, reported lengths of translated dna are reduced by a factor of 3, to provide fractions relative to amino acid coordinates. Note : This an alias that calls frac() =cut sub frac_conserved{ my $self = shift; my @args = @_; my ($type, $denom, $action, $context) = $self->_rearrange( [qw[ TYPE DENOM ACTION CONTEXT]],@args ); $self->frac( -type=>$type, -denom=>$denom, -action=>$action, -context=>$context, -method=>'conserved'); } =head2 frac_aligned Title : frac_aligned Aliases : frac_aligned_query - frac_aligned(-type=>'query',...) frac_aligned_hit - frac_aligned(-type=>'hit',...) Usage : $tiling->frac_aligned(-type=>$type, -action=>$action, -context=>$context) Function: Return the fraction of input sequence length that was aligned by the algorithm Returns : scalar float Args : -type => one of 'hit', 'subject', 'query' -action => one of 'exact', 'est', 'fast', 'max' -context => strand/frame context string =cut sub frac_aligned{ my ($self, @args) = @_; my ($type, $action, $context) = $self->_rearrange([qw(TYPE ACTION CONTEXT)],@args); $self->_check_type_arg(\$type); $self->_check_action_arg(\$action); $self->_check_context_arg($type, \$context); if (!$self->{"frac_aligned_${type}_${action}_${context}"}) { $self->{"frac_aligned_${type}_${action}_${context}"} = $self->num_aligned($type,$action,$context)/$self->_reported_length($type); } return $self->{"frac_aligned_${type}_${action}_${context}"}; } sub frac_aligned_query { shift->frac_aligned(-type=>'query', @_) } sub frac_aligned_hit { shift->frac_aligned(-type=>'hit', @_) } =head2 num_aligned Title : num_aligned Usage : $tiling->num_aligned(-type=>$type) Function: Return the number of residues of sequence $type that were aligned by the algorithm Returns : scalar int Args : -type => one of 'hit', 'subject', 'query' -action => one of 'exact', 'est', 'fast', 'max' -context => strand/frame context string Note : Since this is calculated from reported coordinates, not symbol string counts, it is already in terms of "logical length" Note : Aliases length() =cut sub num_aligned { shift->length( @_ ) }; =head2 num_unaligned Title : num_unaligned Usage : $tiling->num_unaligned(-type=>$type) Function: Return the number of residues of sequence $type that were left unaligned by the algorithm Returns : scalar int Args : -type => one of 'hit', 'subject', 'query' -action => one of 'exact', 'est', 'fast', 'max' -context => strand/frame context string Note : Since this is calculated from reported coordinates, not symbol string counts, it is already in terms of "logical length" =cut sub num_unaligned { my $self = shift; my ($type,$action,$context) = @_; my $ret; $self->_check_type_arg(\$type); $self->_check_action_arg(\$action); $self->_check_context_arg($type, \$context); if (!defined $self->{"num_unaligned_${type}_${action}_${context}"}) { $self->{"num_unaligned_${type}_${action}_${context}"} = $self->_reported_length($type)-$self->num_aligned($type,$action,$context); } return $self->{"num_unaligned_${type}_${action}_${context}"}; } =head2 range Title : range Usage : $tiling->range(-type=>$type) Function: Returns the extent of the longest tiling as ($min_coord, $max_coord) Returns : array of two scalar integers Args : -type => one of 'hit', 'subject', 'query' -context => strand/frame context string =cut sub range { my ($self, $type, $context) = @_; $self->_check_type_arg(\$type); $self->_check_context_arg($type, \$context); my @a = $self->_contig_intersection($type,$context); return ($a[0][0], $a[-1][1]); } =head1 ACCESSORS =head2 coverage_map Title : coverage_map Usage : $map = $tiling->coverage_map($type) Function: Property to contain the coverage map calculated by _calc_coverage_map() - see that for details Example : Returns : value of coverage_map_$type as an array Args : scalar $type: one of 'hit', 'subject', 'query' default is 'query' Note : getter =cut sub coverage_map{ my $self = shift; my ($type, $context) = @_; $self->_check_type_arg(\$type); $self->_check_context_arg($type, \$context); if (!defined $self->{"coverage_map_${type}_${context}"}) { # following calculates coverage maps in all strands/frames # if necessary $self->_calc_coverage_map($type, $context); } # if undef is returned, then there were no hsps for given strand/frame if (!defined $self->{"coverage_map_${type}_${context}"}) { $self->warn("No HSPS present for type '$type' in context '$context' for this hit"); return undef; } return @{$self->{"coverage_map_${type}_${context}"}}; } =head2 coverage_map_as_text Title : coverage_map_as_text Usage : $tiling->coverage_map_as_text($type, $legend_flag) Function: Format a text-graphic representation of the coverage map Returns : an array of scalar strings, suitable for printing Args : $type: one of 'query', 'hit', 'subject' $context: strand/frame context string $legend_flag: boolean; add a legend indicating the actual interval coordinates for each component interval and hsp (in the $type sequence context) Example : print $tiling->coverage_map_as_text('query',1); =cut sub coverage_map_as_text{ my $self = shift; my ($type, $context, $legend_q) = @_; $self->_check_type_arg(\$type); $self->_check_context_arg($type, \$context); my @map = $self->coverage_map($type, $context); my @ret; my @hsps = $self->hit->hsps; my %hsps_i; require Tie::RefHash; tie %hsps_i, 'Tie::RefHash'; @hsps_i{@hsps} = (0..$#hsps); my @mx; foreach (0..$#map) { my @hspx = ('') x @hsps; my @these_hsps = @{$map[$_]->[1]}; @hspx[@hsps_i{@these_hsps}] = ('*') x @these_hsps; $mx[$_] = \@hspx; } untie %hsps_i; push @ret, "\tIntvl\n"; push @ret, "HSPS\t", join ("\t", (0..$#map)), "\n"; foreach my $h (0..$#hsps) { push @ret, join("\t", $h, map { $mx[$_][$h] } (0..$#map) ),"\n"; } if ($legend_q) { push @ret, "Interval legend\n"; foreach (0..$#map) { push @ret, sprintf("%d\t[%d, %d]\n", $_, @{$map[$_][0]}); } push @ret, "HSP legend\n"; my @ints = get_intervals_from_hsps($type,@hsps); foreach (0..$#hsps) { push @ret, sprintf("%d\t[%d, %d]\n", $_, @{$ints[$_]}); } } return @ret; } =head2 hit Title : hit Usage : $tiling->hit Function: Example : Returns : The HitI object associated with the invocant Args : none Note : getter only =cut sub hit{ my $self = shift; $self->warn("Getter only") if @_; return $self->{'hit'}; } =head2 hsps Title : hsps Usage : $tiling->hsps() Function: Container for the HSP objects associated with invocant Example : Returns : an array of hsps associated with the hit Args : on set, new value (an arrayref or undef, optional) =cut sub hsps{ my $self = shift; return $self->{'hsps'} = shift if @_; return @{$self->{'hsps'}}; } =head2 contexts Title : contexts Usage : @contexts = $tiling->context($type) or @indices = $tiling->context($type, $context) Function: Retrieve the set of available contexts in the hit, or the indices of hsps having the given context (integer indices for the array returned by $self->hsps) Returns : array of scalar context strings or array of scalar positive integers undef if no hsps in given context Args : $type: one of 'query', 'hit', 'subject' optional $context: context string =cut sub contexts{ my $self = shift; my ($type, $context) = @_; $self->_check_type_arg(\$type); return keys %{$self->{"_contexts_$type"}} unless defined $context; return undef unless $self->{"_contexts_$type"}{$context}; return @{$self->{"_contexts_$type"}{$context}}; } =head2 mapping Title : mapping Usage : $tiling->mapping($type) Function: Retrieve the mapping coefficient for the sequence type based on the underlying algorithm Returns : scalar integer (mapping coefficient) Args : $type: one of 'query', 'hit', 'subject' Note : getter only (set in constructor) =cut sub mapping{ my $self = shift; my $type = shift; $self->_check_type_arg(\$type); return $self->{"_mapping_${type}"}; } =head2 default_context Title : default_context Usage : $tiling->default_context($type) Function: Retrieve the default strand/frame context string for the sequence type based on the underlying algorithm Returns : scalar string (context string) Args : $type: one of 'query', 'hit', 'subject' Note : getter only (set in constructor) =cut sub default_context{ my $self = shift; my $type = shift; $self->_check_type_arg(\$type); return $self->{"_def_context_${type}"}; } =head2 algorithm Title : algorithm Usage : $tiling->algorithm Function: Retrieve the algorithm name associated with the invocant's hit object Returns : scalar string Args : none Note : getter only (set in constructor) =cut sub algorithm{ my $self = shift; $self->warn("Getter only") if @_; return $self->{"_algorithm"}; } =head1 "PRIVATE" METHODS =head2 Calculators See L for lower level calculation methods. =head2 _calc_coverage_map Title : _calc_coverage_map Usage : $tiling->_calc_coverage_map($type) Function: Calculates the coverage map for the object's associated hit from the perspective of the desired $type (see Args:) and sets the coverage_map() property Returns : True on success Args : optional scalar $type: one of 'hit'|'subject'|'query' default is 'query' Note : The "coverage map" is an array with the following format: ( [ $component_interval => [ @containing_hsps ] ], ... ), where $component_interval is a closed interval (see DESCRIPTION) of the form [$a0, $a1] with $a0 <= $a1, and @containing_hsps is an array of all HspI objects in the hit which completely contain the $component_interval. The set of $component_interval's is a disjoint decomposition of the minimum set of minimal intervals that completely cover the hit's HSPs (from the perspective of the $type) Note : This calculates the map for all strand/frame contexts available in the hit =cut sub _calc_coverage_map { my $self = shift; my ($type) = @_; $self->_check_type_arg(\$type); # obtain the [start, end] intervals for all hsps in the hit (relative # to the type) unless ($self->{'hsps'}) { $self->warn("No HSPs for this hit"); return; } my (@map, @hsps, %filters, @intervals); # conversion here? my $c = $self->mapping($type); # create the possible maps for my $context ($self->contexts($type)) { @map = (); @hsps = ($self->hsps)[$self->contexts($type, $context)]; @intervals = get_intervals_from_hsps( $type, @hsps ); # the "frame" my $f = ($intervals[0]->[0] - 1) % $c; # convert interval endpoints... for (@intervals) { $$_[0] = ($$_[0] - $f + $c - 1)/$c; $$_[1] = ($$_[1] - $f)/$c; } # determine the minimal set of disjoint intervals that cover the # set of hsp intervals my @dj_set = interval_tiling(\@intervals); # decompose each disjoint interval into another set of disjoint # intervals, each of which is completely contained within the # original hsp intervals with which it overlaps my $i=0; my @decomp; for my $dj_elt (@dj_set) { my ($covering, $indices) = @$dj_elt; my @covering_hsps = @hsps[@$indices]; my @coverers = @intervals[@$indices]; @decomp = decompose_interval( \@coverers ); for (@decomp) { my ($component, $container_indices) = @{$_}; push @map, [ $component, [@covering_hsps[@$container_indices]] ]; } 1; } # unconvert the components: ##### foreach (@map) { $$_[0][0] = $c*$$_[0][0] - $c + 1 + $f; $$_[0][1] = $c*$$_[0][1] + $f; } foreach (@dj_set) { $$_[0][0] = $c*$$_[0][0] - $c + 1 + $f; $$_[0][1] = $c*$$_[0][1] + $f; } # sort the map on the interval left-ends @map = sort { $a->[0][0]<=>$b->[0][0] } @map; $self->{"coverage_map_${type}_${context}"} = [@map]; # set the _contig_intersection attribute here (side effect) $self->{"_contig_intersection_${type}_${context}"} = [map { $$_[0] } @map]; } return 1; # success } =head2 _calc_stats Title : _calc_stats Usage : $tiling->_calc_stats($type, $action, $context) Function: Calculates [estimated] tiling statistics (identities, conserved sites length) and sets the public accessors Returns : True on success Args : scalar $type: one of 'hit', 'subject', 'query' default is 'query' optional scalar $action: requests calculation method currently one of 'exact', 'est', 'fast', 'max' option scalar $context: strand/frame context string Note : Action: The statistics are calculated by summing quantities over the disjoint component intervals, taking into account coverage of those intervals by multiple HSPs. The action tells the algorithm how to obtain those quantities-- 'exact' will use Bio::Search::HSP::HSPI::matches to count the appropriate segment of the homology string; 'est' will estimate the statistics by multiplying the fraction of the HSP overlapped by the component interval (see MapTileUtils) by the BLAST-reported identities/postives (this may be convenient for BLAST summary report formats) * Both exact and est take the average over the number of HSPs that overlap the component interval. 'max' uses the exact method to calculate the statistics, and returns only the maximum identites/positives over overlapping HSP for the component interval. No averaging is involved here. 'fast' doesn't involve tiling at all (hence the name), but it seems like a very good estimate, and uses only reported values, and so does not require sequence data. It calculates an average of reported identities, conserved sites, and lengths, over unmodified hsps in the hit, weighted by the length of the hsps. =cut sub _calc_stats { my $self = shift; my ($type, $action, $context) = @_; # need to check args here, in case method is called internally. $self->_check_type_arg(\$type); $self->_check_action_arg(\$action); $self->_check_context_arg($type, \$context); my ($ident, $cons, $length) = (0,0,0); # fast : avoid coverage map altogether, get a pretty damn # good estimate with a weighted average of reported hsp # statistics ($action eq 'fast') && do { my @hsps = $self->hit->hsps; @hsps = @hsps[$self->contexts($type, $context)]; # weights for averages my @wt = map {$_->length($type)} @hsps; my $sum = eval( join('+',@wt) ); $_ /= $sum for (@wt); for (@hsps) { my $wt = shift @wt; $ident += $wt*$_->matches_MT($type,'identities'); $cons += $wt*$_->matches_MT($type,'conserved'); $length += $wt*$_->length($type); } }; # or, do tiling # calculate identities/conserved sites in tiling # estimate based on the fraction of the component interval covered # and ident/cons reported by the HSPs ($action ne 'fast') && do { foreach ($self->coverage_map($type, $context)) { my ($intvl, $hsps) = @{$_}; my $len = ($$intvl[1]-$$intvl[0]+1); my $ncover = ($action eq 'max') ? 1 : scalar @$hsps; my ($acc_i, $acc_c) = (0,0); foreach my $hsp (@$hsps) { for ($action) { ($_ eq 'est') && do { my ($inc_i, $inc_c) = $hsp->matches_MT( -type => $type, -action => 'searchutils', ); my $frac = $len/$hsp->length($type); $acc_i += $inc_i * $frac; $acc_c += $inc_c * $frac; last; }; ($_ eq 'max') && do { my ($inc_i, $inc_c) = $hsp->matches_MT( -type => $type, -action => 'searchutils', -start => $$intvl[0], -end => $$intvl[1] ); $acc_i = ($acc_i > $inc_i) ? $acc_i : $inc_i; $acc_c = ($acc_c > $inc_c) ? $acc_c : $inc_c; last; }; (!$_ || ($_ eq 'exact')) && do { my ($inc_i, $inc_c) = $hsp->matches_MT( -type => $type, -action => 'searchutils', -start => $$intvl[0], -end => $$intvl[1] ); $acc_i += $inc_i; $acc_c += $inc_c; last; }; } } $ident += ($acc_i/$ncover); $cons += ($acc_c/$ncover); $length += $len; } }; $self->{"identities_${type}_${action}_${context}"} = $ident; $self->{"conserved_${type}_${action}_${context}"} = $cons; $self->{"length_${type}_${action}_${context}"} = $length; return 1; } =head2 Tiling Helper Methods =cut # coverage_map is of the form # ( [ $interval, \@containing_hsps ], ... ) # so, for each interval, pick one of the containing hsps, # and return the union of all the picks. # use the combinatorial generating iterator, with # the urns containing the @containing_hsps for each # interval =head2 _make_tiling_iterator Title : _make_tiling_iterator Usage : $self->_make_tiling_iterator($type) Function: Create an iterator code ref that will step through all minimal combinations of HSPs that produce complete coverage of the $type ('hit', 'subject', 'query') sequence, and set the correct iterator property of the invocant Example : Returns : The iterator Args : scalar $type, one of 'hit', 'subject', 'query'; default is 'query' =cut sub _make_tiling_iterator { ### create the urns my $self = shift; my ($type, $context) = @_; $self->_check_type_arg(\$type); $self->_check_context_arg($type, \$context); # initialize the urns my @urns = map { [0, $$_[1]] } $self->coverage_map($type, $context); my $FINISHED = 0; my $iter = sub { # rewind? if (my $rewind = shift) { # reinitialize urn indices $$_[0] = 0 for (@urns); $FINISHED = 0; return 1; } # check if done... return if $FINISHED; my $finished_incrementing = 0; # @ret is the collector of urn choices my @ret; for my $urn (@urns) { my ($n, $hsps) = @$urn; push @ret, $$hsps[$n]; unless ($finished_incrementing) { if ($n == $#$hsps) { $$urn[0] = 0; } else { ($$urn[0])++; $finished_incrementing = 1 } } } # backstop... $FINISHED = 1 unless $finished_incrementing; # uniquify @ret # $hsp->rank is a unique identifier for an hsp in a hit. # preserve order in @ret my (%order, %uniq); @order{(0..$#ret)} = @ret; $uniq{$order{$_}->rank} = $_ for (0..$#ret); @ret = @order{ sort {$a<=>$b} values %uniq }; return @ret; }; return $iter; } =head2 _tiling_iterator Title : _tiling_iterator Usage : $tiling->_tiling_iterator($type,$context) Function: Retrieve the tiling iterator coderef for the requested $type ('hit', 'subject', 'query') Example : Returns : coderef to the desired iterator Args : scalar $type, one of 'hit', 'subject', 'query' default is 'query' option scalar $context: strand/frame context string Note : getter only =cut sub _tiling_iterator { my $self = shift; my ($type, $context) = @_; $self->_check_type_arg(\$type); $self->_check_context_arg($type, \$context); if (!defined $self->{"_tiling_iterator_${type}_${context}"}) { $self->{"_tiling_iterator_${type}_${context}"} = $self->_make_tiling_iterator($type,$context); } return $self->{"_tiling_iterator_${type}_${context}"}; } =head2 Construction Helper Methods See also L. =cut sub _check_type_arg { my $self = shift; my $typeref = shift; $$typeref ||= 'query'; $self->throw("Unknown type '$$typeref'") unless grep(/^$$typeref$/, qw( hit query subject )); $$typeref = 'hit' if $$typeref eq 'subject'; return 1; } sub _check_action_arg { my $self = shift; my $actionref = shift; if (!$$actionref) { $$actionref = ($self->_has_sequence_data ? 'exact' : 'est'); } else { $self->throw("Calc action '$$actionref' unrecognized") unless grep /^$$actionref$/, qw( est exact fast max ); if ($$actionref ne 'est' and !$self->_has_sequence_data) { $self->warn("Blast file did not possess sequence data; defaulting to 'est' action"); $$actionref = 'est'; } } return 1; } sub _check_context_arg { my $self = shift; my ($type, $contextref) = @_; if (!$$contextref) { $self->throw("Type '$type' requires strand/frame context for algorithm ".$self->algorithm) unless ($self->mapping($type) == 1); # set default according to default_context attrib $$contextref = $self->default_context($type); } else { ($$contextref =~ /^[mp]$/) && do { $$contextref .= '_' }; $self->throw("Context '$$contextref' unrecognized") unless $$contextref =~ /all|[mp][0-2_]/; } } =head2 _make_context_key Title : _make_context_key Alias : _context Usage : $tiling->_make_context_key(-strand => $strand, -frame => $frame) Function: create a string indicating strand/frame context; serves as component of memoizing hash keys Returns : scalar string Args : -type => one of ('query', 'hit', 'subject') -strand => one of (1,0,-1) -frame => one of (-2, 1, 0, 1, -2) called w/o args: returns 'all' =cut sub _make_context_key { my $self = shift; my @args = @_; my ($type, $strand, $frame) = $self->_rearrange([qw(TYPE STRAND FRAME)], @args); _check_type_arg(\$type); return 'all' unless (defined $strand or defined $frame); if ( defined $strand && $self->_has_strand($type) ) { if (defined $frame && $self->_has_frame($type)) { return ($strand >= 0 ? 'p' : 'm').abs($frame); } else { return ($strand >= 0 ? 'p_' : 'm_'); } } else { if (defined $frame && $self->_has_frame($type)) { $self->warn("Frame defined without strand; punting with plus strand"); return 'p'.abs($frame); } else { return 'all'; } } } =head2 _context Title : _context Alias : _make_context_key Usage : $tiling->_make_context_key(-strand => $strand, -frame => $frame) Function: create a string indicating strand/frame context; serves as component of memoizing hash keys Returns : scalar string Args : -type => one of ('query', 'hit', 'subject') -strand => one of (1,0,-1) -frame => one of (-2, 1, 0, 1, -2) called w/o args: returns 'all' =cut sub _context { shift->_make_context_key(@_) } =head2 Predicates Most based on a reading of the algorithm name with a configuration lookup. =over =item _has_sequence_data() =cut sub _has_sequence_data { my $self = shift; $self->throw("Hit attribute not yet set") unless defined $self->hit; return (($self->hit->hsps)[0]->seq_str('match') ? 1 : 0); } =item _has_logical_length() =cut sub _has_logical_length { my $self = shift; my $type = shift; $self->_check_type_arg(\$type); # based on mapping coeff $self->throw("Mapping coefficients not yet set") unless defined $self->mapping($type); return ($self->mapping($type) > 1); } =item _has_strand() =cut sub _has_strand { my $self = shift; my $type = shift; $self->_check_type_arg(\$type); return $self->{"_has_strand_${type}"}; } =item _has_frame() =cut sub _has_frame { my $self = shift; my $type = shift; $self->_check_type_arg(\$type); return $self->{"_has_frame_${type}"}; } =back =head1 Private Accessors =head2 _contig_intersection Title : _contig_intersection Usage : $tiling->_contig_intersection($type) Function: Return the minimal set of $type coordinate intervals covered by the invocant's HSPs Returns : array of intervals (2-member arrayrefs; see MapTileUtils) Args : scalar $type: one of 'query', 'hit', 'subject' =cut sub _contig_intersection { my $self = shift; my ($type, $context) = @_; $self->_check_type_arg(\$type); $self->_check_context_arg($type, \$context); if (!defined $self->{"_contig_intersection_${type}_${context}"}) { $self->_calc_coverage_map($type); } return @{$self->{"_contig_intersection_${type}_${context}"}}; } =head2 _reported_length Title : _reported_length Usage : $tiling->_reported_length($type) Function: Get the total length of the seq $type for the invocant's hit object, as reported by (not calculated from) the input data file Returns : scalar int Args : scalar $type: one of 'query', 'hit', 'subject' Note : This is kludgy; the hit object does not currently maintain accessors for these values, but the hsps possess these attributes. This is a wrapper that allows a consistent access method in the MapTiling code. Note : Since this number is based on a reported length, it is already a "logical length". =cut sub _reported_length { my $self = shift; my $type = shift; $self->_check_type_arg(\$type); my $key = uc( $type."_LENGTH" ); return ($self->hsps)[0]->{$key}; } 1; BioPerl-1.007002/Bio/Search/Tiling/TilingI.pm000555000766000024 2441313155576320 20603 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::Search::Tiling::TilingI # # Please direct questions and support issues to # # Cared for by Mark A. Jensen # # Copyright Mark A. Jensen # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Tiling::TilingI - Abstract interface for an HSP tiling module =head1 SYNOPSIS Not used directly. Useful POD here for developers, however. The interface is designed to make the following code conversion as simple as possible: From: # Bio::Search::SearchUtils-based while ( local $_ = $result->next_hit ) { printf( "E-value: %g; Fraction aligned: %f; Number identical: %d\n", $hit->significance, $hit->frac_aligned_query, $hit->num_identical); } To: # TilingI-based while ( local $_ = $result->next_hit ) { my $tiling = Bio::Search::Tiling::MyTiling($_); printf( "E-value: %g; Fraction aligned: %f; Number identical: %d\n", $hit->significance, $tiling->frac_aligned_query, $tiling->num_identical); } =head1 DESCRIPTION This module provides strong suggestions for any intended HSP tiling object implementation. An object subclassing TilingI should override the methods defined here according to their descriptions below. See the section STATISTICS METHODS for hints on implementing methods that are valid across different algorithms and report types. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Mark A. Jensen Email maj@fortinbras.us =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Tiling::TilingI; use strict; use warnings; # Object preamble - inherits from Bio::Root::Root use Bio::Root::Root; use base qw(Bio::Root::Root); =head2 STATISTICS METHODS The tiling statistics can be thought of as global counterparts to similar statistics defined for the individual HSPs. We therefore prescribe definitions for many of the synonymous methods defined in L. The tiling statistics must be able to keep track of the coordinate systems in which both the query and subject sequences exist; i.e., either nucleotide or amino acid. This information is typically inferred from the name of the algorithm used to perform the original search (contained in C<$hit_object-Ealgorithm>). Here is a table of algorithm information that may be useful (if you trust us). algorithm query on hit coordinates(q/h) --------- ------------ --------------- blastn dna on dna dna/dna blastp aa on aa aa/aa blastx xna on aa dna/aa tblastn aa on xna aa/dna tblastx xna on xna dna/dna fasta dna on dna dna/dna fasta aa on aa aa/aa fastx xna on aa dna/aa fasty xna on aa dna/aa tfasta aa on xna aa/dna tfasty aa on xna aa/dna megablast dna on dna dna/dna xna: translated nucleotide data Statistics methods must also be aware of differences in reporting among the algorithms. Hit attributes are not necessarily normalized over all algorithms. Devs, please feel free to add examples to the list below. =over =item NCBI BLAST vs WU-BLAST (AB-BLAST) lengths The total length of the alignment is reported differently between these two flavors. C<$hit_object-Elength()> will contain the number in the denominator of the stats line; i.e., 120 in Identical = 34/120 Positives = 67/120 NCBI BLAST uses the total length of the query sequence as input by the user (a.k.a. "with gaps"). WU-BLAST uses the length of the query sequence actually aligned by the algorithm (a.k.a. "without gaps"). =back Finally, developers should remember that sequence data may or may not be associated with the HSPs contained in the hit object. This will typically depend on whether a full report (e.g, C) or a summary (e.g., C) was parsed. Statistics methods that depend directly on the sequence data will need to check that that data is present. =head2 identities Title : identities Alias : num_identical Usage : $num_identities = $tiling->identities() Function: Return the estimated or exact number of identities in the tiling, accounting for overlapping HSPs Example : Returns : number of identical residue pairs Args : =cut sub identities{ my ($self,@args) = @_; $self->throw_not_implemented; } #HSPI synonym sub num_identical { shift->identities( @_ ) } =head2 conserved Title : conserved Alias : num_conserved Usage : $num_conserved = $tiling->conserved() Function: Return the estimated or exact number of conserved sites in the tiling, accounting for overlapping HSPs Example : Returns : number of conserved residue pairs Args : =cut sub conserved{ my ($self,@args) = @_; $self->throw_not_implemented; } #HSPI synonym sub num_conserved { shift->conserved( @_ ) } =head2 length Title : length Usage : $max_length = $tiling->length($type) Function: Return the total number of residues of the subject or query sequence covered by the tiling Returns : number of "logical" residues covered Args : scalar $type, one of 'hit', 'subject', 'query' =cut sub length{ my ($self, $type, @args) = @_; $self->throw_not_implemented; } =head2 frac_identical Title : frac_identical Usage : $tiling->frac_identical($type) Function: Return the fraction of sequence length consisting of identical pairs Returns : scalar float Args : scalar $type, one of 'hit', 'subject', 'query' Note : This method must take account of the $type coordinate system and the length reporting method (see STATISTICS METHODS above) =cut sub frac_identical { my ($self, $type, @args) = @_; $self->throw_not_implemented; } =head2 percent_identity Title : percent_identity Usage : $tiling->percent_identity($type) Function: Return the fraction of sequence length consisting of identical pairs as a percentage Returns : scalar float Args : scalar $type, one of 'hit', 'subject', 'query' =cut sub percent_identity { my ($self, $type, @args) = @_; return $self->frac_identical($type, @args) * 100; } =head2 frac_conserved Title : frac_conserved Usage : $tiling->frac_conserved($type) Function: Return the fraction of sequence length consisting of conserved pairs Returns : scalar float Args : scalar $type, one of 'hit', 'subject', 'query' Note : This method must take account of the $type coordinate system and the length reporting method (see STATISTICS METHODS above) =cut sub frac_conserved{ my ($self, $type, @args) = @_; $self->throw_not_implemented; } =head2 percent_conserved Title : percent_conserved Usage : $tiling->percent_conserved($type) Function: Return the fraction of sequence length consisting of conserved pairs as a percentage Returns : scalar float Args : scalar $type, one of 'hit', 'subject', 'query' =cut sub percent_conserved { my ($self, $type, @args) = @_; return $self->frac_conserved($type, @args) * 100; } =head2 frac_aligned Title : frac_aligned Usage : $tiling->frac_aligned($type) Function: Return the fraction of B sequence length consisting that was aligned by the algorithm Returns : scalar float Args : scalar $type, one of 'hit', 'subject', 'query' Note : This method must take account of the $type coordinate system and the length reporting method (see STATISTICS METHODS above) =cut sub frac_aligned{ my ($self, $type, @args) = @_; $self->throw_not_implemented; } # aliases for back compat sub frac_aligned_query { shift->frac_aligned('query', @_) } sub frac_aligned_hit { shift->frac_aligned('hit', @_) } =head2 range Title : range Usage : $tiling->range($type) Function: Returns the extent of the longest tiling as ($min_coord, $max_coord) Returns : array of two scalar integers Args : scalar $type, one of 'hit', 'subject', 'query' =cut sub range { my ($self, $type, @args) = @_; $self->throw_not_implemented; } =head1 TILING ITERATORS =head2 next_tiling Title : next_tiling Usage : @hsps = $self->next_tiling($type); Function: Obtain a tiling of HSPs over the $type ('hit', 'subject', 'query') sequence Example : Returns : an array of HSPI objects Args : scalar $type: one of 'hit', 'subject', 'query', with 'subject' an alias for 'hit' =cut sub next_tiling{ my ($self,$type,@args) = @_; $self->throw_not_implemented; } =head2 rewind_tilings Title : rewind_tilings Usage : $self->rewind_tilings($type) Function: Reset the next_tilings($type) iterator Example : Returns : True on success Args : scalar $type: one of 'hit', 'subject', 'query', with 'subject' an alias for 'hit' =cut sub rewind_tilings{ my ($self, $type, @args) = @_; $self->throw_not_implemented; } #alias sub rewind { shift->rewind_tilings(@_) } =head1 INFORMATIONAL ACCESSORS =head2 algorithm Title : algorithm Usage : $tiling->algorithm Function: Retrieve the algorithm name associated with the invocant's hit object Returns : scalar string Args : =cut sub algorithm{ my ($self, @args) = @_; $self->throw_not_implemented; } 1; BioPerl-1.007002/Bio/SearchIO000755000766000024 013155576320 15524 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/SearchIO/EventHandlerI.pm000444000766000024 1270313155576320 20732 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::EventHandlerI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing =head1 SYNOPSIS # do not use this object directly it is an interface # See Bio::SearchIO::SearchResultEventBuilder for an implementation use Bio::SearchIO::SearchResultEventBuilder; my $handler = Bio::SearchIO::SearchResultEventBuilder->new(); =head1 DESCRIPTION This interface describes the basic methods needed to handle Events thrown from parsing a Search Result such as FASTA, BLAST, or HMMer. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::EventHandlerI; use strict; use Carp; use base qw(Bio::Event::EventHandlerI); =head2 start_result Title : start_result Usage : $handler->start_result($data) Function: Begins a result event cycle Returns : none Args : Type of Result =cut sub start_result { my ($self) = @_; $self->throw_not_implemented(); } =head2 end_result Title : end_result Usage : $handler->end_result($data) Function: Ends a result event cycle Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_result{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 start_hsp Title : start_hsp Usage : $handler->start_hsp($data) Function: Start a HSP event cycle Returns : none Args : type of element associated hashref =cut sub start_hsp{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 end_hsp Title : end_hsp Usage : $handler->end_hsp() Function: Ends a HSP event cycle Returns : Bio::Search::HSP::HSPI object Args : type of event and associated hashref =cut sub end_hsp{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 start_hit Title : start_hit Usage : $handler->start_hit() Function: Starts a Hit event cycle Returns : none Args : type of event and associated hashref =cut sub start_hit { my ($self,@args) = @_; $self->throw_not_implemented } =head2 end_hit Title : end_hit Usage : $handler->end_hit() Function: Ends a Hit event cycle Returns : Bio::Search::Hit::HitI object Args : type of event and associated hashref =cut sub end_hit { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 start_iteration Title : start_iteration Usage : $handler->start_iteration() Function: Starts an Iteration event cycle Returns : none Args : type of event and associated hashref =cut sub start_iteration { my ($self,@args) = @_; $self->throw_not_implemented } =head2 end_iteration Title : end_iteration Usage : $handler->end_iteration() Function: Ends an Iterationevent cycle Returns : Bio::Search::Iteration::IterationI object Args : type of event and associated hashref =cut sub end_iteration { my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 register_factory Title : register_factory Usage : $handler->register_factory('TYPE',$factory); Function: Register a specific factory for a object type class Returns : none Args : string representing the class and Bio::Factory::ObjectFactoryI See L for more information =cut sub register_factory{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 factory Title : factory Usage : my $f = $handler->factory('TYPE'); Function: Retrieves the associated factory for requested 'TYPE' Returns : a Bio::Factory::ObjectFactoryI Throws : Bio::Root::BadParameter if none registered for the supplied type Args : name of factory class to retrieve See L for more information =cut sub factory{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 Bio::Event::EventHandlerI methods =cut =head2 will_handle Title : will_handle Usage : if( $handler->will_handle($event_type) ) { ... } Function: Tests if this event builder knows how to process a specific event Returns : boolean Args : event type name =cut =head2 SAX methods See L for the additional SAX methods. =cut 1; BioPerl-1.007002/Bio/SearchIO/FastHitEventBuilder.pm000444000766000024 1757513155576320 22131 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::FastHitEventBuilder # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::FastHitEventBuilder - Event Handler for SearchIO events. =head1 SYNOPSIS # Do not use this object directly, this object is part of the SearchIO # event based parsing system. # to use the FastHitEventBuilder do this use Bio::SearchIO::FastHitEventBuilder; my $searchio = Bio::SearchIO->new(-format => $format, -file => $file); $searchio->attach_EventHandler(Bio::SearchIO::FastHitEventBuilder->new()); while( my $r = $searchio->next_result ) { while( my $h = $r->next_hit ) { # note that Hits will NOT have HSPs } } =head1 DESCRIPTION This object handles Search Events generated by the SearchIO classes and build appropriate Bio::Search::* objects from them. This object is intended for lightweight parsers which only want Hits and not deal with the overhead of HSPs. It is a lot faster than the standard parser event handler but of course you are getting less information and less objects out. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::FastHitEventBuilder; use vars qw(%KNOWNEVENTS); use strict; use Bio::Search::HSP::HSPFactory; use Bio::Search::Hit::HitFactory; use Bio::Search::Result::ResultFactory; use base qw(Bio::Root::Root Bio::SearchIO::EventHandlerI); =head2 new Title : new Usage : my $obj = Bio::SearchIO::FastHitEventBuilder->new(); Function: Builds a new Bio::SearchIO::FastHitEventBuilder object Returns : Bio::SearchIO::FastHitEventBuilder Args : -hit_factory => Bio::Factory::ObjectFactoryI -result_factory => Bio::Factory::ObjectFactoryI See L for more information =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($hitF,$resultF) = $self->_rearrange([qw(HIT_FACTORY RESULT_FACTORY)],@args); $self->register_factory('hit', $hitF || Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Hit::GenericHit', -interface => 'Bio::Search::Hit::HitI')); $self->register_factory('result', $resultF || Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Result::GenericResult', -interface => 'Bio::Search::Result::ResultI')); return $self; } # new comes from the superclass =head2 will_handle Title : will_handle Usage : if( $handler->will_handle($event_type) ) { ... } Function: Tests if this event builder knows how to process a specific event Returns : boolean Args : event type name =cut sub will_handle{ my ($self,$type) = @_; # these are the events we recognize return ( $type eq 'hit' || $type eq 'result' ); } =head2 SAX methods =cut =head2 start_result Title : start_result Usage : $handler->start_result($resulttype) Function: Begins a result event cycle Returns : none Args : Type of Report =cut sub start_result { my ($self,$type) = @_; $self->{'_resulttype'} = $type; $self->{'_hits'} = []; return; } =head2 end_result Title : end_result Usage : my @results = $parser->end_result Function: Finishes a result handler cycle Returns : A Bio::Search::Result::ResultI Args : none =cut sub end_result { my ($self,$type,$data) = @_; if( defined $data->{'runid'} && $data->{'runid'} !~ /^\s+$/ ) { if( $data->{'runid'} !~ /^lcl\|/) { $data->{"RESULT-query_name"}= $data->{'runid'}; } else { ($data->{"RESULT-query_name"},$data->{"RESULT-query_description"}) = split(/\s+/,$data->{"RESULT-query_description"},2); } if( my @a = split(/\|/,$data->{'RESULT-query_name'}) ) { my $acc = pop @a ; # this is for accession |1234|gb|AAABB1.1|AAABB1 # this is for |123|gb|ABC1.1| $acc = pop @a if( ! defined $acc || $acc =~ /^\s+$/); $data->{"RESULT-query_accession"}= $acc; } delete $data->{'runid'}; } my %args = map { my $v = $data->{$_}; s/RESULT//; ($_ => $v); } grep { /^RESULT/ } keys %{$data}; $args{'-algorithm'} = uc( $args{'-algorithm_name'} || $type); $args{'-hits'} = $self->{'_hits'}; my $result = $self->factory('result')->create(%args); $self->{'_hits'} = []; return $result; } =head2 start_hit Title : start_hit Usage : $handler->start_hit() Function: Starts a Hit event cycle Returns : none Args : type of event and associated hashref =cut sub start_hit{ my ($self,$type) = @_; return; } =head2 end_hit Title : end_hit Usage : $handler->end_hit() Function: Ends a Hit event cycle Returns : Bio::Search::Hit::HitI object Args : type of event and associated hashref =cut sub end_hit{ my ($self,$type,$data) = @_; my %args = map { my $v = $data->{$_}; s/HIT//; ($_ => $v); } grep { /^HIT/ } keys %{$data}; $args{'-algorithm'} = uc( $args{'-algorithm_name'} || $type); $args{'-query_len'} = $data->{'RESULT-query_length'}; my ($hitrank) = scalar @{$self->{'_hits'}} + 1; $args{'-rank'} = $hitrank; my $hit = $self->factory('hit')->create(%args); push @{$self->{'_hits'}}, $hit; $self->{'_hsps'} = []; return $hit; } =head2 Factory methods =cut =head2 register_factory Title : register_factory Usage : $handler->register_factory('TYPE',$factory); Function: Register a specific factory for a object type class Returns : none Args : string representing the class and Bio::Factory::ObjectFactoryI See L for more information =cut sub register_factory{ my ($self, $type,$f) = @_; if( ! defined $f || ! ref($f) || ! $f->isa('Bio::Factory::ObjectFactoryI') ) { $self->throw("Cannot set factory to value $f".ref($f)."\n"); } $self->{'_factories'}->{lc($type)} = $f; } =head2 factory Title : factory Usage : my $f = $handler->factory('TYPE'); Function: Retrieves the associated factory for requested 'TYPE' Returns : a Bio::Factory::ObjectFactoryI or undef if none registered Args : name of factory class to retrieve See L for more information =cut sub factory{ my ($self,$type) = @_; return $self->{'_factories'}->{lc($type)} || $self->throw("No factory registered for $type"); } =head2 inclusion_threshold See L. =cut sub inclusion_threshold { my $self = shift; return $self->{'_inclusion_threshold'} = shift if @_; return $self->{'_inclusion_threshold'}; } 1; BioPerl-1.007002/Bio/SearchIO/IteratedSearchResultEventBuilder.pm000444000766000024 2712213155576320 24642 0ustar00cjfieldsstaff000000000000#------------------------------------------------------------------ # # BioPerl module for Bio::SearchIO::IteratedSearchResultEventBuilder # # Please direct questions and support issues to # # Cared for by Steve Chervitz and Jason Stajich # # Copyright Steve Chervitz # # You may distribute this module under the same terms as perl itself #------------------------------------------------------------------ # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::IteratedSearchResultEventBuilder - Event Handler for SearchIO events. =head1 SYNOPSIS # Do not use this object directly, this object is part of the SearchIO # event based parsing system. =head1 DESCRIPTION This object handles Search Events generated by the SearchIO classes and build appropriate Bio::Search::* objects from them. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Steve Chervitz Email sac-at-bioperl.org =head1 CONTRIBUTORS Parts of code based on SearchResultEventBuilder by Jason Stajich jason@bioperl.org Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::IteratedSearchResultEventBuilder; use strict; use Bio::Factory::ObjectFactory; use base qw(Bio::SearchIO::SearchResultEventBuilder); =head2 new Title : new Usage : my $obj = Bio::SearchIO::IteratedSearchResultEventBuilder->new(); Function: Builds a new Bio::SearchIO::IteratedSearchResultEventBuilder object Returns : Bio::SearchIO::IteratedSearchResultEventBuilder Args : -hsp_factory => Bio::Factory::ObjectFactoryI -hit_factory => Bio::Factory::ObjectFactoryI -result_factory => Bio::Factory::ObjectFactoryI -iteration_factory => Bio::Factory::ObjectFactoryI -inclusion_threshold => e-value threshold for inclusion in the PSI-BLAST score matrix model (blastpgp) -signif => float or scientific notation number to be used as a P- or Expect value cutoff -score => integer or scientific notation number to be used as a blast score value cutoff -bits => integer or scientific notation number to be used as a bit score value cutoff -hit_filter => reference to a function to be used for filtering hits based on arbitrary criteria. See L for more information =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($resultF, $iterationF, $hitF, $hspF) = $self->_rearrange([qw(RESULT_FACTORY ITERATION_FACTORY HIT_FACTORY HSP_FACTORY)],@args); $self->_init_parse_params(@args); # Note that we need to override the setting of result and factories here # so that we can set different default factories than are set by the super class. $self->register_factory('result', $resultF || Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Result::BlastResult', -interface => 'Bio::Search::Result::ResultI')); $self->register_factory('hit', $hitF || Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Hit::BlastHit', -interface => 'Bio::Search::Hit::HitI')); $self->register_factory('hsp', $hspF || Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::HSP::GenericHSP', -interface => 'Bio::Search::HSP::HSPI')); # TODO: Change this to BlastIteration (maybe) $self->register_factory('iteration', $iterationF || Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Iteration::GenericIteration', -interface => 'Bio::Search::Iteration::IterationI')); return $self; } =head2 will_handle Title : will_handle Usage : if( $handler->will_handle($event_type) ) { ... } Function: Tests if this event builder knows how to process a specific event Returns : boolean Args : event type name =cut sub will_handle{ my ($self,$type) = @_; # these are the events we recognize return ( $type eq 'hsp' || $type eq 'hit' || $type eq 'result' || $type eq 'iteration' || $type eq 'newhits' || $type eq 'oldhits' ); } =head2 SAX methods =cut =head2 start_result Title : start_result Usage : $handler->start_result($resulttype) Function: Begins a result event cycle Returns : none Args : Type of Report =cut sub start_result { my $self = shift; #print STDERR "ISREB: start_result()\n"; $self->SUPER::start_result(@_); $self->{'_iterations'} = []; $self->{'_iteration_count'} = 0; $self->{'_old_hit_names'} = undef; $self->{'_hit_names_below'} = undef; return; } =head2 start_iteration Title : start_iteration Usage : $handler->start_iteration() Function: Starts an Iteration event cycle Returns : none Args : type of event and associated hashref =cut sub start_iteration { my ($self,$type) = @_; #print STDERR "ISREB: start_iteration()\n"; $self->{'_iteration_count'}++; # Reset arrays for the various classes of hits. # $self->{'_newhits_unclassified'} = []; $self->{'_newhits_below'} = []; $self->{'_newhits_not_below'} = []; $self->{'_oldhits_below'} = []; $self->{'_oldhits_newly_below'} = []; $self->{'_oldhits_not_below'} = []; $self->{'_hitcount'} = 0; return; } =head2 end_iteration Title : end_iteration Usage : $handler->end_iteration() Function: Ends an Iteration event cycle Returns : Bio::Search::Iteration object Args : type of event and associated hashref =cut sub end_iteration { my ($self,$type,$data) = @_; # print STDERR "ISREB: end_iteration()\n"; my %args = map { my $v = $data->{$_}; s/ITERATION//; ($_ => $v); } grep { /^ITERATION/ } keys %{$data}; $args{'-number'} = $self->{'_iteration_count'}; $args{'-oldhits_below'} = $self->{'_oldhits_below'}; $args{'-oldhits_newly_below'} = $self->{'_oldhits_newly_below'}; $args{'-oldhits_not_below'} = $self->{'_oldhits_not_below'}; $args{'-newhits_below'} = $self->{'_newhits_below'}; $args{'-newhits_not_below'} = $self->{'_newhits_not_below'}; $args{'-hit_factory'} = $self->factory('hit'); my $it = $self->factory('iteration')->create_object(%args); push @{$self->{'_iterations'}}, $it; return $it; } # Title : _add_hit (private function for internal use only) # Purpose : Applies hit filtering and calls _store_hit if it passes filtering. # Argument: Bio::Search::Hit::HitI object sub _add_hit { my ($self, $hit) = @_; my $hit_name = uc($hit->{-name}); my $hit_signif = $hit->{-significance}; my $ithresh = $self->{'_inclusion_threshold'}; # Test significance using custom function (if supplied) my $add_hit = 1; my $hit_filter = $self->{'_hit_filter'}; if($hit_filter) { # since &hit_filter is out of our control and would expect a HitI object, # we're forced to make one for it $hit = $self->factory('hit')->create_object(%{$hit}); $add_hit = 0 unless &$hit_filter($hit); } else { if($self->{'_confirm_significance'}) { $add_hit = 0 unless $hit_signif <= $self->{'_max_significance'}; } if($self->{'_confirm_score'}) { my $hit_score = $hit->{-score} || $hit->{-hsps}->[0]->{-score}; $add_hit = 0 unless $hit_score >= $self->{'_min_score'}; } if($self->{'_confirm_bits'}) { my $hit_bits = $hit->{-bits} || $hit->{-hsps}->[0]->{-bits}; $add_hit = 0 unless $hit_bits >= $self->{'_min_bits'}; } } $add_hit && $self->_store_hit($hit, $hit_name, $hit_signif); # Building hit lookup hashes for determining if the hit is old/new and # above/below threshold. $self->{'_old_hit_names'}->{$hit_name}++; $self->{'_hit_names_below'}->{$hit_name}++ if $hit_signif <= $ithresh; } # Title : _store_hit (private function for internal use only) # Purpose : Collects hit objects into defined sets that are useful for # analyzing PSI-blast results. # These are ultimately added to the iteration object in end_iteration(). # # Strategy: # Primary split = old vs. new # Secondary split = below vs. above threshold # 1. Has this hit occurred in a previous iteration? # 1.1. If yes, was it below threshold? # 1.1.1. If yes, ---> [oldhits_below] # 1.1.2. If no, is it now below threshold? # 1.1.2.1. If yes, ---> [oldhits_newly_below] # 1.1.2.2. If no, ---> [oldhits_not_below] # 1.2. If no, is it below threshold? # 1.2.1. If yes, ---> [newhits_below] # 1.2.2. If no, ---> [newhits_not_below] # 1.2.3. If don't know (no inclusion threshold data), ---> [newhits_unclassified] # Note: As long as there's a default inclusion threshold, # there won't be an unclassified set. # # For the first iteration, it might be nice to detect non-PSI blast reports # and put the hits in the unclassified set. # However, it shouldn't matter where the hits get put for the first iteration # for non-PSI blast reports since they'll get flattened out in the # result and iteration search objects. sub _store_hit { my ($self, $hit, $hit_name, $hit_signif) = @_; my $ithresh = $self->{'_inclusion_threshold'}; # This is the assumption leading to Bug 1986. The assumption here is that # the hit name is unique (and thus new), therefore any subsequent encounters # with a hit containing the same name are filed as old hits. This isn't # always true (see the bug report for a few examples). Adding an explicit # check for the presence of iterations, adding to new hits otherwise. if (exists $self->{'_old_hit_names'}->{$hit_name} && scalar @{$self->{_iterations}}) { if (exists $self->{'_hit_names_below'}->{$hit_name}) { push @{$self->{'_oldhits_below'}}, $hit; } elsif ($hit_signif <= $ithresh) { push @{$self->{'_oldhits_newly_below'}}, $hit; } else { push @{$self->{'_oldhits_not_below'}}, $hit; } } else { if ($hit_signif <= $ithresh) { push @{$self->{'_newhits_below'}}, $hit; } else { push @{$self->{'_newhits_not_below'}}, $hit; } } $self->{'_hitcount'}++; } 1; BioPerl-1.007002/Bio/SearchIO/SearchResultEventBuilder.pm000444000766000024 5240313155576320 23160 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::SearchResultEventBuilder # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::SearchResultEventBuilder - Event Handler for SearchIO events. =head1 SYNOPSIS # Do not use this object directly, this object is part of the SearchIO # event based parsing system. =head1 DESCRIPTION This object handles Search Events generated by the SearchIO classes and build appropriate Bio::Search::* objects from them. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::SearchResultEventBuilder; use strict; use Bio::Factory::ObjectFactory; use base qw(Bio::Root::Root Bio::SearchIO::EventHandlerI); use vars qw($DEFAULT_INCLUSION_THRESHOLD $MAX_HSP_OVERLAP ); # e-value threshold for inclusion in the PSI-BLAST score matrix model (blastpgp) # NOTE: Executing `blastpgp -` incorrectly reports that the default is 0.005. # (version 2.2.2 [Jan-08-2002]) $DEFAULT_INCLUSION_THRESHOLD = 0.001; $MAX_HSP_OVERLAP = 2; # Used when tiling multiple HSPs. =head2 new Title : new Usage : my $obj = Bio::SearchIO::SearchResultEventBuilder->new(); Function: Builds a new Bio::SearchIO::SearchResultEventBuilder object Returns : Bio::SearchIO::SearchResultEventBuilder Args : -hsp_factory => Bio::Factory::ObjectFactoryI -hit_factory => Bio::Factory::ObjectFactoryI -result_factory => Bio::Factory::ObjectFactoryI -inclusion_threshold => e-value threshold for inclusion in the PSI-BLAST score matrix model (blastpgp) -signif => float or scientific notation number to be used as a P- or Expect value cutoff -score => integer or scientific notation number to be used as a blast score value cutoff -bits => integer or scientific notation number to be used as a bit score value cutoff -hit_filter => reference to a function to be used for filtering hits based on arbitrary criteria. See L for more information =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($resultF, $hitF, $hspF) = $self->_rearrange([qw(RESULT_FACTORY HIT_FACTORY HSP_FACTORY)],@args); $self->_init_parse_params(@args); $self->register_factory('result', $resultF || Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Result::GenericResult', -interface => 'Bio::Search::Result::ResultI')); $self->register_factory('hit', $hitF || Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Hit::GenericHit', -interface => 'Bio::Search::Hit::HitI')); $self->register_factory('hsp', $hspF || Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::HSP::GenericHSP', -interface => 'Bio::Search::HSP::HSPI')); return $self; } # Initializes parameters used during parsing of reports. sub _init_parse_params { my ($self, @args) = @_; # -FILT_FUNC has been replaced by -HIT_FILTER. # Leaving -FILT_FUNC in place for backward compatibility my($ithresh, $signif, $score, $bits, $hit_filter, $filt_func) = $self->_rearrange([qw(INCLUSION_THRESHOLD SIGNIF SCORE BITS HIT_FILTER FILT_FUNC )], @args); $self->inclusion_threshold( defined($ithresh) ? $ithresh : $DEFAULT_INCLUSION_THRESHOLD); my $hit_filt = $hit_filter || $filt_func; defined $hit_filter && $self->hit_filter($hit_filt); defined $signif && $self->max_significance($signif); defined $score && $self->min_score($score); defined $bits && $self->min_bits($bits); } =head2 will_handle Title : will_handle Usage : if( $handler->will_handle($event_type) ) { ... } Function: Tests if this event builder knows how to process a specific event Returns : boolean Args : event type name =cut sub will_handle{ my ($self,$type) = @_; # these are the events we recognize return ( $type eq 'hsp' || $type eq 'hit' || $type eq 'result' ); } =head2 SAX methods =cut =head2 start_result Title : start_result Usage : $handler->start_result($resulttype) Function: Begins a result event cycle Returns : none Args : Type of Report =cut sub start_result { my ($self,$type) = @_; $self->{'_resulttype'} = $type; $self->{'_hits'} = []; $self->{'_hsps'} = []; $self->{'_hitcount'} = 0; return; } =head2 end_result Title : end_result Usage : my @results = $parser->end_result Function: Finishes a result handler cycle Returns : A Bio::Search::Result::ResultI Args : none =cut # this is overridden by IteratedSearchResultEventBuilder # so keep that in mind when debugging sub end_result { my ($self,$type,$data) = @_; if( defined $data->{'runid'} && $data->{'runid'} !~ /^\s+$/ ) { if( $data->{'runid'} !~ /^lcl\|/) { $data->{"RESULT-query_name"} = $data->{'runid'}; } else { ($data->{"RESULT-query_name"}, $data->{"RESULT-query_description"}) = split(/\s+/,$data->{"RESULT-query_description"},2); } if( my @a = split(/\|/,$data->{'RESULT-query_name'}) ) { my $acc = pop @a ; # this is for accession |1234|gb|AAABB1.1|AAABB1 # this is for |123|gb|ABC1.1| $acc = pop @a if( ! defined $acc || $acc =~ /^\s+$/); $data->{"RESULT-query_accession"}= $acc; } delete $data->{'runid'}; } my %args = map { my $v = $data->{$_}; s/RESULT//; ($_ => $v); } grep { /^RESULT/ } keys %{$data}; $args{'-algorithm'} = uc( $args{'-algorithm_name'} || $data->{'RESULT-algorithm_name'} || $type); ($self->isa('Bio::SearchIO::IteratedSearchResultEventBuilder')) ? ( $args{'-iterations'} = $self->{'_iterations'} ) : ( $args{'-hits'} = $self->{'_hits'} ); my $result = $self->factory('result')->create_object(%args); $result->hit_factory($self->factory('hit')); ($self->isa('Bio::SearchIO::IteratedSearchResultEventBuilder')) ? ( $self->{'_iterations'} = [] ) : ( $self->{'_hits'} = [] ); return $result; } =head2 start_hsp Title : start_hsp Usage : $handler->start_hsp($name,$data) Function: Begins processing a HSP event Returns : none Args : type of element associated data (hashref) =cut sub start_hsp { my ($self,@args) = @_; return; } =head2 end_hsp Title : end_hsp Usage : $handler->end_hsp() Function: Finish processing a HSP event Returns : none Args : type of event and associated hashref =cut sub end_hsp { my ($self,$type,$data) = @_; if( defined $data->{'runid'} && $data->{'runid'} !~ /^\s+$/ ) { if( $data->{'runid'} !~ /^lcl\|/) { $data->{"RESULT-query_name"}= $data->{'runid'}; } else { ($data->{"RESULT-query_name"}, $data->{"RESULT-query_description"}) = split(/\s+/,$data->{"RESULT-query_description"},2); } if( my @a = split(/\|/,$data->{'RESULT-query_name'}) ) { my $acc = pop @a ; # this is for accession |1234|gb|AAABB1.1|AAABB1 # this is for |123|gb|ABC1.1| $acc = pop @a if( ! defined $acc || $acc =~ /^\s+$/); $data->{"RESULT-query_accession"}= $acc; } delete $data->{'runid'}; } # this code is to deal with the fact that Blast XML data # always has start < end and one has to infer strandedness # from the frame which is a problem for the Search::HSP object # which expect to be able to infer strand from the order of # of the begin/end of the query and hit coordinates if( defined $data->{'HSP-query_frame'} && # this is here to protect from undefs (( $data->{'HSP-query_frame'} < 0 && $data->{'HSP-query_start'} < $data->{'HSP-query_end'} ) || $data->{'HSP-query_frame'} > 0 && ( $data->{'HSP-query_start'} > $data->{'HSP-query_end'} ) ) ) { # swap ($data->{'HSP-query_start'}, $data->{'HSP-query_end'}) = ($data->{'HSP-query_end'}, $data->{'HSP-query_start'}); } if( defined $data->{'HSP-hit_frame'} && # this is here to protect from undefs ((defined $data->{'HSP-hit_frame'} && $data->{'HSP-hit_frame'} < 0 && $data->{'HSP-hit_start'} < $data->{'HSP-hit_end'} ) || defined $data->{'HSP-hit_frame'} && $data->{'HSP-hit_frame'} > 0 && ( $data->{'HSP-hit_start'} > $data->{'HSP-hit_end'} ) ) ) { # swap ($data->{'HSP-hit_start'}, $data->{'HSP-hit_end'}) = ($data->{'HSP-hit_end'}, $data->{'HSP-hit_start'}); } $data->{'HSP-query_frame'} ||= 0; $data->{'HSP-hit_frame'} ||= 0; # handle Blast 2.1.2 which did not support data member: hsp_align-len $data->{'HSP-query_length'} ||= $data->{'RESULT-query_length'}; $data->{'HSP-hit_length'} ||= $data->{'HIT-length'}; # If undefined lengths, calculate from alignment without gaps and separators if (not defined $data->{'HSP-query_length'}) { if (my $hsp_qry_seq = $data->{'HSP-query_seq'}) { $hsp_qry_seq =~ s/[-\.]//g; $data->{'HSP-query_length'} = length $hsp_qry_seq; } else { $data->{'HSP-query_length'} = 0; } } if (not defined $data->{'HSP-hit_length'}) { if (my $hsp_hit_seq = $data->{'HSP-hit_seq'}) { $hsp_hit_seq =~ s/[-\.]//g; $data->{'HSP-hit_length'} = length $hsp_hit_seq; } else { $data->{'HSP-hit_length'} = 0; } } $data->{'HSP-hsp_length'} ||= length ($data->{'HSP-homology_seq'} || ''); my %args = map { my $v = $data->{$_}; s/HSP//; ($_ => $v) } grep { /^HSP/ } keys %{$data}; $args{'-algorithm'} = uc( $args{'-algorithm_name'} || $data->{'RESULT-algorithm_name'} || $type); # copy this over from result $args{'-query_name'} = $data->{'RESULT-query_name'}; $args{'-hit_name'} = $data->{'HIT-name'}; my ($rank) = scalar @{$self->{'_hsps'} || []} + 1; $args{'-rank'} = $rank; $args{'-hit_desc'} = $data->{'HIT-description'}; $args{'-query_desc'} = $data->{'RESULT-query_description'}; my $bits = $args{'-bits'}; my $hsp = \%args; push @{$self->{'_hsps'}}, $hsp; return $hsp; } =head2 start_hit Title : start_hit Usage : $handler->start_hit() Function: Starts a Hit event cycle Returns : none Args : type of event and associated hashref =cut sub start_hit{ my ($self,$type) = @_; $self->{'_hsps'} = []; return; } =head2 end_hit Title : end_hit Usage : $handler->end_hit() Function: Ends a Hit event cycle Returns : Bio::Search::Hit::HitI object Args : type of event and associated hashref =cut sub end_hit{ my ($self,$type,$data) = @_; # Skip process unless there is HSP data or Hit Significance (e.g. a bl2seq with no similarity # gives a hit with the subject, but shows a "no hits found" message instead # of the alignment data and don't have a significance value). # This way, we avoid false positives my @hsp_data = grep { /^HSP/ } keys %{$data}; return unless (scalar @hsp_data > 0 or exists $data->{'HIT-significance'}); my %args = map { my $v = $data->{$_}; s/HIT//; ($_ => $v); } grep { /^HIT/ } keys %{$data}; # I hate special cases, but this is here because NCBI BLAST XML # doesn't play nice and is undergoing mutation -jason if(exists $args{'-name'} && $args{'-name'} =~ /BL_ORD_ID/ ) { ($args{'-name'}, $args{'-description'}) = split(/\s+/,$args{'-description'},2); } $args{'-algorithm'} = uc( $args{'-algorithm_name'} || $data->{'RESULT-algorithm_name'} || $type); $args{'-hsps'} = $self->{'_hsps'}; $args{'-query_len'} = $data->{'RESULT-query_length'}; $args{'-rank'} = $self->{'_hitcount'} + 1; unless( defined $args{'-significance'} ) { if( defined $args{'-hsps'} && $args{'-hsps'}->[0] ) { # use pvalue if present (WU-BLAST), otherwise evalue (NCBI BLAST) $args{'-significance'} = $args{'-hsps'}->[0]->{'-pvalue'} || $args{'-hsps'}->[0]->{'-evalue'}; } } my $hit = \%args; $hit->{'-hsp_factory'} = $self->factory('hsp'); $self->_add_hit($hit); $self->{'_hsps'} = []; return $hit; } # Title : _add_hit (private function for internal use only) # Purpose : Applies hit filtering and store it if it passes filtering. # Argument: Bio::Search::Hit::HitI object sub _add_hit { my ($self, $hit) = @_; my $hit_signif = $hit->{-significance}; # Test significance using custom function (if supplied) my $add_hit = 1; my $hit_filter = $self->{'_hit_filter'}; if($hit_filter) { # since &hit_filter is out of our control and would expect a HitI object, # we're forced to make one for it $hit = $self->factory('hit')->create_object(%{$hit}); $add_hit = 0 unless &$hit_filter($hit); } else { if($self->{'_confirm_significance'}) { $add_hit = 0 unless $hit_signif <= $self->{'_max_significance'}; } if($self->{'_confirm_score'}) { my $hit_score = $hit->{-score} || $hit->{-hsps}->[0]->{-score}; $add_hit = 0 unless $hit_score >= $self->{'_min_score'}; } if($self->{'_confirm_bits'}) { my $hit_bits = $hit->{-bits} || $hit->{-hsps}->[0]->{-bits} || 0; $add_hit = 0 unless $hit_bits >= $self->{'_min_bits'}; } } $add_hit && push @{$self->{'_hits'}}, $hit;; $self->{'_hitcount'} = scalar @{$self->{'_hits'}}; } =head2 Factory methods =cut =head2 register_factory Title : register_factory Usage : $handler->register_factory('TYPE',$factory); Function: Register a specific factory for a object type class Returns : none Args : string representing the class and Bio::Factory::ObjectFactoryI See L for more information =cut sub register_factory{ my ($self, $type,$f) = @_; if( ! defined $f || ! ref($f) || ! $f->isa('Bio::Factory::ObjectFactoryI') ) { $self->throw("Cannot set factory to value $f".ref($f)."\n"); } $self->{'_factories'}->{lc($type)} = $f; } =head2 factory Title : factory Usage : my $f = $handler->factory('TYPE'); Function: Retrieves the associated factory for requested 'TYPE' Returns : a Bio::Factory::ObjectFactoryI Throws : Bio::Root::BadParameter if none registered for the supplied type Args : name of factory class to retrieve See L for more information =cut sub factory{ my ($self,$type) = @_; return $self->{'_factories'}->{lc($type)} || $self->throw(-class=>'Bio::Root::BadParameter', -text=>"No factory registered for $type"); } =head2 inclusion_threshold See L. =cut sub inclusion_threshold { my $self = shift; return $self->{'_inclusion_threshold'} = shift if @_; return $self->{'_inclusion_threshold'}; } =head2 max_significance Usage : $obj->max_significance(); Purpose : Set/Get the P or Expect value used as significance screening cutoff. This is the value of the -signif parameter supplied to new(). Hits with P or E-value at HIT level above this are skipped. Returns : Scientific notation number with this format: 1.0e-05. Argument : Number (sci notation, float, integer) (when setting) Throws : Bio::Root::BadParameter exception if the supplied argument is : not a valid number. Comments : Screening of significant hits uses the data provided on the : description line. For NCBI BLAST1 and WU-BLAST, this data : is P-value. for NCBI BLAST2 it is an Expect value. =cut sub max_significance { my $self = shift; if (@_) { my $sig = shift; if( $sig =~ /[^\d.e-]/ or $sig <= 0) { $self->throw(-class => 'Bio::Root::BadParameter', -text => "Invalid significance value: $sig\n" . "Must be a number greater than zero.", -value => $sig); } $self->{'_confirm_significance'} = 1; $self->{'_max_significance'} = $sig; } sprintf "%.1e", $self->{'_max_significance'}; } =head2 signif Synonym for L =cut sub signif { shift->max_significance } =head2 min_score Usage : $obj->min_score(); Purpose : Gets the Blast score used as screening cutoff. This is the value of the -score parameter supplied to new(). Hits with scores at HIT level below this are skipped. Returns : Integer (or undef if not set) Argument : Integer (when setting) Throws : Bio::Root::BadParameter exception if the supplied argument is : not a valid number. Comments : Screening of significant hits uses the data provided on the : description line. =cut sub min_score { my $self = shift; if (@_) { my $score = shift; if( $score =~ /[^\de+]/ or $score <= 0) { $self->throw(-class => 'Bio::Root::BadParameter', -text => "Invalid score value: $score\n" . "Must be an integer greater than zero.", -value => $score); } $self->{'_confirm_score'} = 1; $self->{'_min_score'} = $score; } return $self->{'_min_score'}; } =head2 min_bits Usage : $obj->min_bits(); Purpose : Gets the Blast bit score used as screening cutoff. This is the value of the -bits parameter supplied to new(). Hits with bits score at HIT level below this are skipped. Returns : Integer (or undef if not set) Argument : Integer (when setting) Throws : Bio::Root::BadParameter exception if the supplied argument is : not a valid number. Comments : Screening of significant hits uses the data provided on the : description line. =cut sub min_bits { my $self = shift; if (@_) { my $bits = shift; if( $bits =~ /[^\de+]/ or $bits <= 0) { $self->throw(-class => 'Bio::Root::BadParameter', -text => "Invalid bits value: $bits\n" . "Must be an integer greater than zero.", -value => $bits); } $self->{'_confirm_bits'} = 1; $self->{'_min_bits'} = $bits; } return $self->{'_min_bits'}; } =head2 hit_filter Usage : $obj->hit_filter(); Purpose : Set/Get a function reference used for filtering out hits. This is the value of the -hit_filter parameter supplied to new(). Hits that fail to pass the filter at HIT level are skipped. Returns : Function ref (or undef if not set) Argument : Function ref (when setting) Throws : Bio::Root::BadParameter exception if the supplied argument is : not a function reference. =cut sub hit_filter { my $self = shift; if (@_) { my $func = shift; if(not ref $func eq 'CODE') { $self->throw(-class => 'Bio::Root::BadParameter', -text => "Not a function reference: $func\n" . "The -hit_filter parameter must be function reference.", -value => $func); } $self->{'_hit_filter'} = $func; } return $self->{'_hit_filter'}; } 1; BioPerl-1.007002/Bio/SearchIO/SearchWriterI.pm000444000766000024 653713155576320 20745 0ustar00cjfieldsstaff000000000000#----------------------------------------------------------------- # # BioPerl module Bio::SearchIO::SearchWriterI # # Please direct questions and support issues to # # Cared for by Steve Chervitz # # You may distribute this module under the same terms as perl itself #----------------------------------------------------------------- =head1 NAME Bio::SearchIO::SearchWriterI - Interface for outputting parsed Search results =head1 SYNOPSIS Bio::SearchIO::SearchWriterI objects cannot be instantiated since this module defines a pure interface. Given an object that implements the Bio::SearchIO::SearchWriterI interface, you can do the following things with it: print $writer->to_string( $result_obj, @args ); =head1 DESCRIPTION This module defines abstract methods that all subclasses must implement to be used for outputting results from L objects. =head1 AUTHOR Steve Chervitz Esac-at-bioperl.orgE =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX The rest of the documentation details each of the object methods. =cut package Bio::SearchIO::SearchWriterI; use base qw(Bio::Root::RootI); =head2 to_string Purpose : Produces data for each Search::Result::ResultI in a string. : This is an abstract method. For some useful implementations, : see ResultTableWriter.pm, HitTableWriter.pm, : and HSPTableWriter.pm. Usage : print $writer->to_string( $result_obj, @args ); Argument : $result_obj = A Bio::Search::Result::ResultI object : @args = any additional arguments used by your implementation. Returns : String containing data for each search Result or any of its : sub-objects (Hits and HSPs). Throws : n/a =cut sub to_string { my ($self, $result, @args) = @_; $self->throw_not_implemented; } =head2 start_report Title : start_report Usage : $self->start_report() Function: The method to call when starting a report. You can override it to make a custom header Returns : string Args : none =cut sub start_report { return '' } =head2 end_report Title : end_report Usage : $self->end_report() Function: The method to call when ending a report, this is mostly for cleanup for formats which require you to have something at the end of the document () for HTML Returns : string Args : none =cut sub end_report { return '' } =head2 filter Title : filter Usage : $writer->filter('hsp', \&hsp_filter); Function: Filter out either at HSP,Hit,or Result level Returns : none Args : string => data type, CODE reference =cut # yes this is an implementation in the interface, # yes it assumes that the underlying class is hash-based # yes that might not be a good idea, but until people # start extending the SearchWriterI interface I think # this is an okay way to go sub filter { my ($self,$method,$code) = @_; return unless $method; $method = uc($method); if( $method ne 'HSP' && $method ne 'HIT' && $method ne 'RESULT' ) { $self->warn("Unknown method $method"); return; } if( $code ) { $self->throw("Must provide a valid code reference") unless ref($code) =~ /CODE/; $self->{$method} = $code; } return $self->{$method}; } 1; BioPerl-1.007002/Bio/SearchIO/axt.pm000444000766000024 3124713155576320 17042 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::axt # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::axt - a parser for axt format reports =head1 SYNOPSIS use Bio::SearchIO; my $parser = Bio::SearchIO->new(-format => 'axt', -file => 't/data/report.blastz'); while( my $result = $parser->next_result ) { while( my $hit = $result->next_hit ) { while( my $hsp = $hit->next_hsp ) { } } } =head1 DESCRIPTION This is a parser and event-generator for AXT format reports. BLASTZ reports (Schwartz et al,(2003) Genome Research, 13:103-107) are normally in LAV format but are commonly post-processed to AXT format; many precomputed BLASTZ reports, such as those found in the UCSC Genome Browser, are in AXT format. This parser will also parse any AXT format produced from any lav report and directly out of BLAT. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::axt; use vars qw(%MODEMAP %MAPPING @STATES $GAPCHAR); use strict; use Bio::Search::Result::ResultFactory; use Bio::Search::HSP::HSPFactory; use base qw(Bio::SearchIO); use POSIX; BEGIN { # mapping of NCBI Blast terms to Bioperl hash keys %MODEMAP = ('AXTOutput' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); $GAPCHAR = '-'; %MAPPING = ( 'Hsp_score' => 'HSP-score', 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_positive' => 'HSP-conserved', 'Hsp_identity' => 'HSP-identical', 'Hsp_gaps' => 'HSP-hsp_gaps', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_midline' => 'HSP-homology_seq', # ignoring this for now 'Hsp_align-len' => 'HSP-hsp_length', 'Hit_id' => 'HIT-name', 'AXTOutput_query-def'=> 'RESULT-query_name', ); } =head2 new Title : new Usage : my $obj = Bio::SearchIO::axt->new(); Function: Builds a new Bio::SearchIO::axt object Returns : an instance of Bio::SearchIO::axt Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); return $self; } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result{ my ($self) = @_; local $/ = "\n"; local $_; my ($curquery,$curhit); $self->start_document(); my @hit_signifs; while( defined ($_ = $self->_readline )) { next if (/^\s+$/); if( m/^(\d+)\s+ # alignment number - we'll throw this away anyways (\S+)\s+ # Query name (\d+)\s+(\d+)\s+ # Query start Query end (always + strand, 0 based) (\S+)\s+ # Hit name (\d+)\s+(\d+)\s+ # Hit start Hit end (0 based) ([\-\+])\s+ # Hit strand ([\d\.\-]+)\s+ # Score /ox ) { my ($alnnum, $qname,$qstart,$qend, $hname, $hstart,$hend,$hstrand, $score) = ($1,$2,$3,$4,$5, $6,$7,$8,$9); $self->{'_reporttype'} = 'AXT'; # Jim's code is 0 based # yes, but axt format is one-based, see bug 3145 - cjfields 10-11-10 #$qstart++; $qend++; $hstart++; $hend++; if( defined $curquery && $curquery ne $qname ) { $self->end_element({'Name' => 'Hit'}); $self->_pushback($_); $self->end_element({'Name' => 'AXTOutput'}); return $self->end_document(); } if( defined $curhit && $curhit ne $hname) { # slight duplication here -- keep these in SYNC $self->end_element({'Name' => 'Hit'}); $self->start_element({'Name' => 'Hit'}); $self->element({'Name' => 'Hit_id', 'Data' => $hname}); } elsif ( ! defined $curquery ) { $self->start_element({'Name' => 'AXTOutput'}); $self->{'_result_count'}++; $self->element({'Name' => 'AXTOutput_query-def', 'Data' => $qname }); $self->start_element({'Name' => 'Hit'}); $self->element({'Name' => 'Hit_id', 'Data' => $hname}); } $self->start_element({'Name' => 'Hsp'}); my $queryalign = $self->_readline; my $hitalign = $self->_readline; chomp($queryalign); chomp($hitalign); my $alnlen = length($queryalign); my $qgapnum = ( $queryalign =~ s/\Q$GAPCHAR/$GAPCHAR/g); my $hgapnum = ( $hitalign =~ s/\Q$GAPCHAR/$GAPCHAR/g); my $totalgaps = ($qgapnum + $hgapnum); if( $hstrand eq '-' ) { # strand gets inferred by start/end ($hstart,$hend) = ($hend,$hstart); } $self->element({'Name' => 'Hsp_score', 'Data' => $score}); $self->element({'Name' => 'Hsp_query-from', 'Data' => $qstart}); $self->element({'Name' => 'Hsp_query-to', 'Data' => $qend}); $self->element({'Name' => 'Hsp_hit-from', 'Data' => $hstart}); $self->element({'Name' => 'Hsp_hit-to', 'Data' => $hend}); $self->element({'Name' => 'Hsp_gaps', 'Data' => $qgapnum + $hgapnum}); $self->element({'Name' => 'Hsp_querygaps', 'Data' => $qgapnum}); $self->element({'Name' => 'Hsp_hitgaps', 'Data' => $hgapnum}); $self->element({'Name' => 'Hsp_identity', 'Data' => $alnlen - $totalgaps}); $self->element({'Name' => 'Hsp_positive', 'Data' => $alnlen - $totalgaps}); $self->element({'Name' => 'Hsp_qseq', 'Data' => $queryalign}); $self->element({'Name' => 'Hsp_hseq', 'Data' => $hitalign}); $self->end_element({'Name' => 'Hsp'}); $curquery = $qname; $curhit = $hname; } } # fence post if( defined $curquery ) { $self->end_element({'Name' => 'Hit'}); $self->end_element({'Name' => 'AXTOutput'}); return $self->end_document(); } return; } sub _initialize { my ($self,@args) = @_; $self->SUPER::_initialize(@args); $self->_eventHandler->register_factory('result', Bio::Search::Result::ResultFactory->new(-type => 'Bio::Search::Result::GenericResult')); $self->_eventHandler->register_factory('hsp', Bio::Search::HSP::HSPFactory->new(-type => 'Bio::Search::HSP::GenericHSP')); } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element{ my ($self,$data) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; if( my $type = $MODEMAP{$nm} ) { $self->_mode($type); if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("start_%s",lc $type); $self->_eventHandler->$func($data->{'Attributes'}); } unshift @{$self->{'_elements'}}, $type; } if($nm eq 'AXTOutput') { $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_mode'} = ''; } } =head2 end_element Title : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub end_element { my ($self,$data) = @_; my $nm = $data->{'Name'}; my $rc; # Hsp are sort of weird, in that they end when another # object begins so have to detect this in end_element for now if( my $type = $MODEMAP{$nm} ) { if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("end_%s",lc $type); $rc = $self->_eventHandler->$func($self->{'_reporttype'}, $self->{'_values'}); } shift @{$self->{'_elements'}}; } elsif( $MAPPING{$nm} ) { if ( ref($MAPPING{$nm}) =~ /hash/i ) { my $key = (keys %{$MAPPING{$nm}})[0]; $self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'}; } else { $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'}; } } else { $self->warn( "unknown nm $nm ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if( $nm eq 'AXTOutput' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element{ my ($self,$data) = @_; $self->start_element($data); $self->characters($data); $self->end_element($data); } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters{ my ($self,$data) = @_; return unless ( defined $data->{'Data'} ); if( $data->{'Data'} =~ /^\s+$/ ) { return unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/; } if( $self->in_element('hsp') && $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) { $self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'}; } $self->{'_last_data'} = $data->{'Data'}; } =head2 _mode Title : _mode Usage : $obj->_mode($newval) Function: Example : Returns : value of _mode Args : newvalue (optional) =cut sub _mode{ my ($self,$value) = @_; if( defined $value) { $self->{'_mode'} = $value; } return $self->{'_mode'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub within_element{ my ($self,$name) = @_; return 0 if ( ! defined $name && ! defined $self->{'_elements'} || scalar @{$self->{'_elements'}} == 0) ; foreach ( @{$self->{'_elements'}} ) { if( $_ eq $name ) { return 1; } } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub in_element{ my ($self,$name) = @_; return 0 if ! defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name) } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handles a start document event Returns : none Args : none =cut sub start_document{ my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_mode'} = ''; $self->{'_elements'} = []; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document{ my ($self,@args) = @_; return $self->{'_result'}; } =head2 result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } sub report_count { shift->result_count } 1; BioPerl-1.007002/Bio/SearchIO/blast.pm000444000766000024 27145013155576320 17375 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::blast # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code # 20030409 - sac # PSI-BLAST full parsing support. Rollout of new # model which will remove Steve's old psiblast driver # 20030424 - jason # Megablast parsing fix as reported by Neil Saunders # 20030427 - jason # Support bl2seq parsing # 20031124 - jason # Parse more blast statistics, lambda, entropy, etc # from WU-BLAST in frame-specific manner # 20060216 - cjf - fixed blast parsing for BLAST v2.2.13 output # 20071104 - dmessina - added support for WUBLAST -echofilter # 20071121 - cjf - fixed several bugs (bugs 2391, 2399, 2409) =head1 NAME Bio::SearchIO::blast - Event generator for event based parsing of blast reports =head1 SYNOPSIS # Do not use this object directly - it is used as part of the # Bio::SearchIO system. use Bio::SearchIO; my $searchio = Bio::SearchIO->new(-format => 'blast', -file => 't/data/ecolitst.bls'); while( my $result = $searchio->next_result ) { while( my $hit = $result->next_hit ) { while( my $hsp = $hit->next_hsp ) { # ... } } } =head1 DESCRIPTION This object encapsulated the necessary methods for generating events suitable for building Bio::Search objects from a BLAST report file. Read the L for more information about how to use this. This driver can parse: =over 4 =item * NCBI produced plain text BLAST reports from blastall, this also includes PSIBLAST, PSITBLASTN, RPSBLAST, and bl2seq reports. NCBI XML BLAST output is parsed with the blastxml SearchIO driver =item * WU-BLAST all reports =item * Jim Kent's BLAST-like output from his programs (BLASTZ, BLAT) =item * BLAST-like output from Paracel BTK output =back =head2 bl2seq parsing Since I cannot differentiate between BLASTX and TBLASTN since bl2seq doesn't report the algorithm used - I assume it is BLASTX by default - you can supply the program type with -report_type in the SearchIO constructor i.e. my $parser = Bio::SearchIO->new(-format => 'blast', -file => 'bl2seq.tblastn.report', -report_type => 'tblastn'); This only really affects where the frame and strand information are put - they will always be on the $hsp-Equery instead of on the $hsp-Ehit part of the feature pair for blastx and tblastn bl2seq produced reports. Hope that's clear... =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email Jason Stajich jason-at-bioperl.org =head1 CONTRIBUTORS Steve Chervitz sac-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin...' package Bio::SearchIO::blast; use Bio::SearchIO::IteratedSearchResultEventBuilder; use strict; use vars qw(%MAPPING %MODEMAP $DEFAULT_BLAST_WRITER_CLASS $MAX_HSP_OVERLAP $DEFAULT_SIGNIF $DEFAULT_SCORE $DEFAULTREPORTTYPE ); use base qw(Bio::SearchIO); use Data::Dumper; BEGIN { # mapping of NCBI Blast terms to Bioperl hash keys %MODEMAP = ( 'BlastOutput' => 'result', 'Iteration' => 'iteration', 'Hit' => 'hit', 'Hsp' => 'hsp' ); # This should really be done more intelligently, like with # XSLT %MAPPING = ( 'Hsp_bit-score' => 'HSP-bits', 'Hsp_score' => 'HSP-score', 'Hsp_evalue' => 'HSP-evalue', 'Hsp_n', => 'HSP-n', 'Hsp_pvalue' => 'HSP-pvalue', 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_positive' => 'HSP-conserved', 'Hsp_identity' => 'HSP-identical', 'Hsp_gaps' => 'HSP-hsp_gaps', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_midline' => 'HSP-homology_seq', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_query-frame' => 'HSP-query_frame', 'Hsp_hit-frame' => 'HSP-hit_frame', 'Hsp_links' => 'HSP-links', 'Hsp_group' => 'HSP-hsp_group', 'Hsp_features' => 'HSP-hit_features', 'Hit_id' => 'HIT-name', 'Hit_len' => 'HIT-length', 'Hit_accession' => 'HIT-accession', 'Hit_def' => 'HIT-description', 'Hit_signif' => 'HIT-significance', # For NCBI blast, the description line contains bits. # For WU-blast, the description line contains score. 'Hit_score' => 'HIT-score', 'Hit_bits' => 'HIT-bits', 'Iteration_iter-num' => 'ITERATION-number', 'Iteration_converged' => 'ITERATION-converged', 'BlastOutput_program' => 'RESULT-algorithm_name', 'BlastOutput_version' => 'RESULT-algorithm_version', 'BlastOutput_algorithm-reference' => 'RESULT-algorithm_reference', 'BlastOutput_rid' => 'RESULT-rid', 'BlastOutput_query-def' => 'RESULT-query_name', 'BlastOutput_query-len' => 'RESULT-query_length', 'BlastOutput_query-acc' => 'RESULT-query_accession', 'BlastOutput_query-gi' => 'RESULT-query_gi', 'BlastOutput_querydesc' => 'RESULT-query_description', 'BlastOutput_db' => 'RESULT-database_name', 'BlastOutput_db-len' => 'RESULT-database_entries', 'BlastOutput_db-let' => 'RESULT-database_letters', 'BlastOutput_inclusion-threshold' => 'RESULT-inclusion_threshold', 'Parameters_matrix' => { 'RESULT-parameters' => 'matrix' }, 'Parameters_expect' => { 'RESULT-parameters' => 'expect' }, 'Parameters_include' => { 'RESULT-parameters' => 'include' }, 'Parameters_sc-match' => { 'RESULT-parameters' => 'match' }, 'Parameters_sc-mismatch' => { 'RESULT-parameters' => 'mismatch' }, 'Parameters_gap-open' => { 'RESULT-parameters' => 'gapopen' }, 'Parameters_gap-extend' => { 'RESULT-parameters' => 'gapext' }, 'Parameters_filter' => { 'RESULT-parameters' => 'filter' }, 'Parameters_allowgaps' => { 'RESULT-parameters' => 'allowgaps' }, 'Parameters_full_dbpath' => { 'RESULT-parameters' => 'full_dbpath' }, 'Statistics_db-len' => { 'RESULT-statistics' => 'dbentries' }, 'Statistics_db-let' => { 'RESULT-statistics' => 'dbletters' }, 'Statistics_hsp-len' => { 'RESULT-statistics' => 'effective_hsplength' }, 'Statistics_query-len' => { 'RESULT-statistics' => 'querylength' }, 'Statistics_eff-space' => { 'RESULT-statistics' => 'effectivespace' }, 'Statistics_eff-spaceused' => { 'RESULT-statistics' => 'effectivespaceused' }, 'Statistics_eff-dblen' => { 'RESULT-statistics' => 'effectivedblength' }, 'Statistics_kappa' => { 'RESULT-statistics' => 'kappa' }, 'Statistics_lambda' => { 'RESULT-statistics' => 'lambda' }, 'Statistics_entropy' => { 'RESULT-statistics' => 'entropy' }, 'Statistics_gapped_kappa' => { 'RESULT-statistics' => 'kappa_gapped' }, 'Statistics_gapped_lambda' => { 'RESULT-statistics' => 'lambda_gapped' }, 'Statistics_gapped_entropy' => { 'RESULT-statistics' => 'entropy_gapped' }, 'Statistics_framewindow' => { 'RESULT-statistics' => 'frameshiftwindow' }, 'Statistics_decay' => { 'RESULT-statistics' => 'decayconst' }, 'Statistics_hit_to_db' => { 'RESULT-statistics' => 'Hits_to_DB' }, 'Statistics_num_suc_extensions' => { 'RESULT-statistics' => 'num_successful_extensions' }, 'Statistics_length_adjustment' => { 'RESULT-statistics' => 'length_adjustment' }, 'Statistics_number_of_hsps_better_than_expect_value_cutoff_without_gapping' => { 'RESULT-statistics' => 'number_of_hsps_better_than_expect_value_cutoff_without_gapping' }, 'Statistics_number_of_hsps_gapped' => { 'RESULT-statistics' => 'number_of_hsps_gapped' }, 'Statistics_number_of_hsps_successfully_gapped' => { 'RESULT-statistics' => 'number_of_hsps_successfully_gapped' }, # WU-BLAST stats 'Statistics_DFA_states' => { 'RESULT-statistics' => 'num_dfa_states' }, 'Statistics_DFA_size' => { 'RESULT-statistics' => 'dfa_size' }, 'Statistics_noprocessors' => { 'RESULT-statistics' => 'no_of_processors' }, 'Statistics_neighbortime' => { 'RESULT-statistics' => 'neighborhood_generate_time' }, 'Statistics_starttime' => { 'RESULT-statistics' => 'start_time' }, 'Statistics_endtime' => { 'RESULT-statistics' => 'end_time' }, ); # add WU-BLAST Frame-Based Statistics for my $frame ( 0 .. 3 ) { for my $strand ( '+', '-' ) { for my $ind ( qw(length efflength E S W T X X_gapped E2 E2_gapped S2) ) { $MAPPING{"Statistics_frame$strand$frame\_$ind"} = { 'RESULT-statistics' => "Frame$strand$frame\_$ind" }; } for my $val (qw(lambda kappa entropy )) { for my $type (qw(used computed gapped)) { my $key = "Statistics_frame$strand$frame\_$val\_$type"; my $val = { 'RESULT-statistics' => "Frame$strand$frame\_$val\_$type" }; $MAPPING{$key} = $val; } } } } # add Statistics for my $stats ( qw(T A X1 X2 X3 S1 S2 X1_bits X2_bits X3_bits S1_bits S2_bits num_extensions num_successful_extensions seqs_better_than_cutoff posted_date search_cputime total_cputime search_actualtime total_actualtime no_of_processors ctxfactor) ) { my $key = "Statistics_$stats"; my $val = { 'RESULT-statistics' => $stats }; $MAPPING{$key} = $val; } # add WU-BLAST Parameters for my $param ( qw(span span1 span2 links warnings notes hspsepsmax hspsepqmax topcomboN topcomboE postsw cpus wordmask filter sort_by_pvalue sort_by_count sort_by_highscore sort_by_totalscore sort_by_subjectlength noseqs gi qtype qres V B Z Y M N) ) { my $key = "Parameters_$param"; my $val = { 'RESULT-parameters' => $param }; $MAPPING{$key} = $val; } $DEFAULT_BLAST_WRITER_CLASS = 'Bio::SearchIO::Writer::HitTableWriter'; $MAX_HSP_OVERLAP = 2; # Used when tiling multiple HSPs. $DEFAULTREPORTTYPE = 'BLASTP'; # for bl2seq } =head2 new Title : new Usage : my $obj = Bio::SearchIO::blast->new(%args); Function: Builds a new Bio::SearchIO::blast object Returns : Bio::SearchIO::blast Args : Key-value pairs: -fh/-file => filehandle/filename to BLAST file -format => 'blast' -report_type => 'blastx', 'tblastn', etc -- only for bl2seq reports when you want to distinguish between tblastn and blastx reports (this only controls where the frame information is put - on the query or subject object. -inclusion_threshold => e-value threshold for inclusion in the PSI-BLAST score matrix model (blastpgp) -signif => float or scientific notation number to be used as a P- or Expect value cutoff -score => integer or scientific notation number to be used as a blast score value cutoff -bits => integer or scientific notation number to be used as a bit score value cutoff -hit_filter => reference to a function to be used for filtering hits based on arbitrary criteria. All hits of each BLAST report must satisfy this criteria to be retained. If a hit fails this test, it is ignored. This function should take a Bio::Search::Hit::BlastHit.pm object as its first argument and return true if the hit should be retained. Sample filter function: -hit_filter => sub { $hit = shift; $hit->gaps == 0; }, (Note: -filt_func is synonymous with -hit_filter) -overlap => integer. The amount of overlap to permit between adjacent HSPs when tiling HSPs. A reasonable value is 2. Default = $Bio::SearchIO::blast::MAX_HSP_OVERLAP. The following criteria are not yet supported: (these are probably best applied within this module rather than in the event handler since they would permit the parser to take some shortcuts.) -check_all_hits => boolean. Check all hits for significance against significance criteria. Default = false. If false, stops processing hits after the first non-significant hit or the first hit that fails the hit_filter call. This speeds parsing, taking advantage of the fact that the hits are processed in the order they appear in the report. -min_query_len => integer to be used as a minimum for query sequence length. Reports with query sequences below this length will not be processed. Default = no minimum length. -best => boolean. Only process the best hit of each report; default = false. =cut sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); # Blast reports require a specialized version of the SREB due to the # possibility of iterations (PSI-BLAST). Forwarding all arguments to it. An # issue here is that we want to set new default object factories if none are # supplied. my $handler = Bio::SearchIO::IteratedSearchResultEventBuilder->new(@args); $self->attach_EventHandler($handler); # 2006-04-26 move this to the attach_handler function in this module so we # can really reset the handler # Optimization: caching # the EventHandler since it is used a lot during the parse. # $self->{'_handler_cache'} = $handler; my ($rpttype ) = $self->_rearrange( [ qw( REPORT_TYPE) ], @args ); defined $rpttype && ( $self->{'_reporttype'} = $rpttype ); } sub attach_EventHandler { my ($self,$handler) = @_; $self->SUPER::attach_EventHandler($handler); # Optimization: caching the EventHandler since it is used a lot # during the parse. $self->{'_handler_cache'} = $handler; return; } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result { my ($self) = @_; my $v = $self->verbose; my $data = ''; my $flavor = ''; $self->{'_seentop'} = 0; # start next report at top my ( $reporttype, $seenquery, $reportline, $reportversion ); my ( $seeniteration, $found_again ); my $incl_threshold = $self->inclusion_threshold; my $bl2seq_fix; $self->start_document(); # let the fun begin... my (@hit_signifs); my $gapped_stats = 0; # for switching between gapped/ungapped # lambda, K, H local $_ = "\n"; #consistency PARSER: while ( defined( $_ = $self->_readline ) ) { next if (/^\s+$/); # skip empty lines next if (/CPU time:/); next if (/^>\s*$/); next if (/[*]+\s+No hits found\s+[*]+/); if ( /^((?:\S+?)?BLAST[NPX]?)\s+(.+)$/i # NCBI BLAST, PSIBLAST # RPSBLAST, MEGABLAST || /^(P?GENEWISE|HFRAME|SWN|TSWN)\s+(.+)/i #Paracel BTK ) { ($reporttype, $reportversion) = ($1, $2); # need to keep track of whether this is WU-BLAST if ($reportversion && $reportversion =~ m{WashU$}) { $self->{'_wublast'}++; } $self->debug("blast.pm: Start of new report: $reporttype, $reportversion\n"); if ( $self->{'_seentop'} ) { # This handles multi-result input streams $self->_pushback($_); last PARSER; } $self->_start_blastoutput; if ($reporttype =~ /RPS-BLAST/) { $reporttype .= '(BLASTP)'; # default RPS-BLAST type } $reportline = $_; # to fix the fact that RPS-BLAST output is wrong $self->element( { 'Name' => 'BlastOutput_program', 'Data' => $reporttype } ); $self->element( { 'Name' => 'BlastOutput_version', 'Data' => $reportversion } ); $self->element( { 'Name' => 'BlastOutput_inclusion-threshold', 'Data' => $incl_threshold } ); } # parse the BLAST algorithm reference elsif(/^Reference:\s+(.*)$/) { # want to preserve newlines for the BLAST algorithm reference my $algorithm_reference = "$1\n"; $_ = $self->_readline; # while the current line, does not match an empty line, a RID:, a # Database:, or a query definition line (Query=) we are still # looking at the algorithm_reference, append it to what we parsed so # far while($_ !~ /^$/ && $_ !~ /^RID:/ && $_ !~ /^Database:/ && $_ !~ /^Query=/) { $algorithm_reference .= "$_"; $_ = $self->_readline; } # if we exited the while loop, we saw an empty line, a RID:, or a # Database:, so push it back $self->_pushback($_); $self->element( { 'Name' => 'BlastOutput_algorithm-reference', 'Data' => $algorithm_reference } ); } # parse BLAST RID (Request ID) elsif(/^RID:\s+(.*)$/) { my $rid = $1; $self->element( { 'Name' => 'BlastOutput_rid', 'Data' => $rid } ); } # added Windows workaround for bug 1985 elsif (/^(Searching|Results from round)/) { next unless $1 =~ /Results from round/; $self->debug("blast.pm: Possible psi blast iterations found...\n"); $self->in_element('hsp') && $self->end_element( { 'Name' => 'Hsp' } ); $self->in_element('hit') && $self->end_element( { 'Name' => 'Hit' } ); if ( defined $seeniteration ) { $self->within_element('iteration') && $self->end_element( { 'Name' => 'Iteration' } ); $self->start_element( { 'Name' => 'Iteration' } ); } else { $self->start_element( { 'Name' => 'Iteration' } ); } $seeniteration = 1; } elsif (/^Query=\s*(.*)$/) { my $q = $1; $self->debug("blast.pm: Query= found...$_\n"); my $size = 0; if ( defined $seenquery ) { $self->_pushback($_); $self->_pushback($reportline) if $reportline; last PARSER; } if ( !defined $reporttype ) { $self->_start_blastoutput; if ( defined $seeniteration ) { $self->in_element('iteration') && $self->end_element( { 'Name' => 'Iteration' } ); $self->start_element( { 'Name' => 'Iteration' } ); } else { $self->start_element( { 'Name' => 'Iteration' } ); } $seeniteration = 1; } $seenquery = $q; $_ = $self->_readline; while ( defined($_) ) { if (/^Database:/) { $self->_pushback($_); last; } # below line fixes length issue with BLAST v2.2.13; still works # with BLAST v2.2.12 if ( /\((\-?[\d,]+)\s+letters.*\)/ || /^Length=(\-?[\d,]+)/ ) { $size = $1; $size =~ s/,//g; last; } else { # bug 2391 $q .= ($q =~ /\w$/ && $_ =~ /^\w/) ? " $_" : $_; $q =~ s/\s+/ /g; # this catches the newline as well $q =~ s/^ | $//g; } $_ = $self->_readline; } chomp($q); my ( $nm, $desc ) = split( /\s+/, $q, 2 ); $self->element( { 'Name' => 'BlastOutput_query-def', 'Data' => $nm } ) if $nm; $self->element( { 'Name' => 'BlastOutput_query-len', 'Data' => $size } ); defined $desc && $desc =~ s/\s+$//; $self->element( { 'Name' => 'BlastOutput_querydesc', 'Data' => $desc } ); my ( $gi, $acc, $version ) = $self->_get_seq_identifiers($nm); $version = defined($version) && length($version) ? ".$version" : ""; $self->element( { 'Name' => 'BlastOutput_query-acc', 'Data' => "$acc$version" } ) if $acc; # these elements are dropped with some multiquery reports; add # back here $self->element( { 'Name' => 'BlastOutput_db-len', 'Data' => $self->{'_blsdb_length'} } ) if $self->{'_blsdb_length'}; $self->element( { 'Name' => 'BlastOutput_db-let', 'Data' => $self->{'_blsdb_letters'} } ) if $self->{'_blsdb_letters'}; $self->element( { 'Name' => 'BlastOutput_db', 'Data' => $self->{'_blsdb'} } ) if $self->{'_blsdb_letters'}; } # added check for WU-BLAST -echofilter option (bug 2388) elsif (/^>Unfiltered[+-]1$/) { # skip all of the lines of unfiltered sequence while($_ !~ /^Database:/) { $self->debug("Bypassing features line: $_"); $_ = $self->_readline; } $self->_pushback($_); } elsif (/Sequences producing significant alignments:/) { $self->debug("blast.pm: Processing NCBI-BLAST descriptions\n"); $flavor = 'ncbi'; # PSI-BLAST parsing needs to be fixed to specifically look # for old vs new per iteration, as sorting based on duplication # leads to bugs, see bug 1986 # The next line is not necessarily whitespace in psiblast reports. # Also note that we must look for the end of this section by testing # for a line with a leading >. Blank lines occur with this section # for psiblast. if ( !$self->in_element('iteration') ) { $self->start_element( { 'Name' => 'Iteration' } ); } # changed 8/28/2008 to exit hit table if blank line is found after an # appropriate line my $h_regex; my $seen_block; DESCLINE: while ( defined( my $descline = $self->_readline() ) ) { if ($descline =~ m{^\s*$}) { last DESCLINE if $seen_block; next DESCLINE; } # any text match is part of block... $seen_block++; # GCG multiline oddness... if ($descline =~ /^(\S+)\s+Begin:\s\d+\s+End:\s+\d+/xms) { my ($id, $nextline) = ($1, $self->_readline); $nextline =~ s{^!}{}; $descline = "$id $nextline"; } # NCBI style hit table (no N) if ($descline =~ /(?element( { 'Name' => 'Iteration_converged', 'Data' => 1 } ); } else { $self->_pushback($descline); # Catch leading > (end of section) last DESCLINE; } } } elsif (/Sequences producing High-scoring Segment Pairs:/) { # This block is for WU-BLAST, so we don't have to check for psi-blast stuff # skip the next line $self->debug("blast.pm: Processing WU-BLAST descriptions\n"); $_ = $self->_readline(); $flavor = 'wu'; if ( !$self->in_element('iteration') ) { $self->start_element( { 'Name' => 'Iteration' } ); } while ( defined( $_ = $self->_readline() ) && !/^\s+$/ ) { my @line = split; pop @line; # throw away first number which is for 'N'col # add the last 2 entries to array s.t. we can reconstruct # a minimal Hit object at the end of the day push @hit_signifs, [ pop @line, pop @line, shift @line, join( ' ', @line ) ]; } } elsif (/^Database:\s*(.+?)\s*$/) { $self->debug("blast.pm: Database: $1\n"); my $db = $1; while ( defined( $_ = $self->_readline ) ) { if ( /^\s+(\-?[\d\,]+|\S+)\s+sequences\; \s+(\-?[\d,]+|\S+)\s+ # Deal with NCBI 2.2.8 OSX problems total\s+letters/ox ) { my ( $s, $l ) = ( $1, $2 ); $s =~ s/,//g; $l =~ s/,//g; $self->element( { 'Name' => 'BlastOutput_db-len', 'Data' => $s } ); $self->element( { 'Name' => 'BlastOutput_db-let', 'Data' => $l } ); # cache for next round in cases with multiple queries $self->{'_blsdb'} = $db; $self->{'_blsdb_length'} = $s; $self->{'_blsdb_letters'} = $l; last; } else { chomp; $db .= $_; } } $self->element( { 'Name' => 'BlastOutput_db', 'Data' => $db } ); } # move inside of a hit elsif (/^(?:Subject=|>)\s*(\S+)\s*(.*)?/) { chomp; $self->debug("blast.pm: Hit: $1\n"); $self->in_element('hsp') && $self->end_element( { 'Name' => 'Hsp' } ); $self->in_element('hit') && $self->end_element( { 'Name' => 'Hit' } ); # special case when bl2seq reports don't have a leading # Query= if ( !$self->within_element('result') ) { $self->_start_blastoutput; $self->start_element( { 'Name' => 'Iteration' } ); } elsif ( !$self->within_element('iteration') ) { $self->start_element( { 'Name' => 'Iteration' } ); } $self->start_element( { 'Name' => 'Hit' } ); my $id = $1; my $restofline = $2; $self->debug("Starting a hit: $1 $2\n"); $self->element( { 'Name' => 'Hit_id', 'Data' => $id } ); my ($gi, $acc, $version ) = $self->_get_seq_identifiers($id); $self->element( { 'Name' => 'Hit_accession', 'Data' => $acc } ); # add hit significance (from the hit table) # this is where Bug 1986 went awry # Changed for Bug2409; hit->significance and hit->score/bits derived # from HSPs, not hit table unless necessary HITTABLE: while (my $v = shift @hit_signifs) { my $tableid = $v->[2]; if ($tableid !~ m{\Q$id\E}) { $self->debug("Hit table ID $tableid doesn't match current hit id $id, checking next hit table entry...\n"); next HITTABLE; } else { last HITTABLE; } } while ( defined( $_ = $self->_readline() ) ) { next if (/^\s+$/); chomp; if (/Length\s*=\s*([\d,]+)/) { my $l = $1; $l =~ s/\,//g; $self->element( { 'Name' => 'Hit_len', 'Data' => $l } ); last; } else { if ($restofline !~ /\s$/) { # bug #3235 s/^\s(?!\s)/\x01/; #new line to concatenate desc lines with } $restofline .= ($restofline =~ /\w$/ && $_ =~ /^\w/) ? " $_" : $_; $restofline =~ s/\s+/ /g; # this catches the newline as well $restofline =~ s/^ | $//g; } } $restofline =~ s/\s+/ /g; $self->element( { 'Name' => 'Hit_def', 'Data' => $restofline } ); } elsif (/\s+(Plus|Minus) Strand HSPs:/i) { next; } elsif ( ( $self->in_element('hit') || $self->in_element('hsp') ) && # paracel genewise BTK m/Score\s*=\s*(\S+)\s*bits\s* # Bit score (?:\((\d+)\))?, # Raw score \s+Log\-Length\sScore\s*=\s*(\d+) # Log-Length score /ox ) { $self->in_element('hsp') && $self->end_element( { 'Name' => 'Hsp' } ); $self->start_element( { 'Name' => 'Hsp' } ); $self->debug( "Got paracel genewise HSP score=$1\n"); # Some data clean-up so e-value will appear numeric to perl my ( $bits, $score, $evalue ) = ( $1, $2, $3 ); $evalue =~ s/^e/1e/i; $self->element( { 'Name' => 'Hsp_score', 'Data' => $score } ); $self->element( { 'Name' => 'Hsp_bit-score', 'Data' => $bits } ); $self->element( { 'Name' => 'Hsp_evalue', 'Data' => $evalue } ); } elsif ( ( $self->in_element('hit') || $self->in_element('hsp') ) && # paracel hframe BTK m/Score\s*=\s*([^,\s]+), # Raw score \s*Expect\s*=\s*([^,\s]+), # E-value \s*P(?:\(\S+\))?\s*=\s*([^,\s]+) # P-value /ox ) { $self->in_element('hsp') && $self->end_element( { 'Name' => 'Hsp' } ); $self->start_element( { 'Name' => 'Hsp' } ); $self->debug( "Got paracel hframe HSP score=$1\n"); # Some data clean-up so e-value will appear numeric to perl my ( $score, $evalue, $pvalue ) = ( $1, $2, $3 ); $evalue = "1$evalue" if $evalue =~ /^e/; $pvalue = "1$pvalue" if $pvalue =~ /^e/; $self->element( { 'Name' => 'Hsp_score', 'Data' => $score } ); $self->element( { 'Name' => 'Hsp_evalue', 'Data' => $evalue } ); $self->element( { 'Name' => 'Hsp_pvalue', 'Data' => $pvalue } ); } elsif ( ( $self->in_element('hit') || $self->in_element('hsp') ) && # wublast m/Score\s*=\s*(\S+)\s* # Bit score \(([\d\.]+)\s*bits\), # Raw score \s*Expect\s*=\s*([^,\s]+), # E-value \s*(?:Sum)?\s* # SUM P(?:\(\d+\))?\s*=\s*([^,\s]+) # P-value (?:\s*,\s+Group\s*\=\s*(\d+))? # HSP Group /ox ) { # wu-blast HSP parse $self->in_element('hsp') && $self->end_element( { 'Name' => 'Hsp' } ); $self->start_element( { 'Name' => 'Hsp' } ); # Some data clean-up so e-value will appear numeric to perl my ( $score, $bits, $evalue, $pvalue, $group ) = ( $1, $2, $3, $4, $5 ); $evalue =~ s/^e/1e/i; $pvalue =~ s/^e/1e/i; $self->element( { 'Name' => 'Hsp_score', 'Data' => $score } ); $self->element( { 'Name' => 'Hsp_bit-score', 'Data' => $bits } ); $self->element( { 'Name' => 'Hsp_evalue', 'Data' => $evalue } ); $self->element( { 'Name' => 'Hsp_pvalue', 'Data' => $pvalue } ); if ( defined $group ) { $self->element( { 'Name' => 'Hsp_group', 'Data' => $group } ); } } elsif ( ( $self->in_element('hit') || $self->in_element('hsp') ) && # ncbi blast, works with 2.2.17 m/^\sFeatures\s\w+\sthis\spart/xmso # If the line begins with "Features in/flanking this part of subject sequence:" ) { $self->in_element('hsp') && $self->end_element( { 'Name' => 'Hsp' } ); my $featline; $_ = $self->_readline; while($_ !~ /^\s*$/) { chomp; $featline .= $_; $_ = $self->_readline; } $self->_pushback($_); $featline =~ s{(?:^\s+|\s+^)}{}g; $featline =~ s{\n}{;}g; $self->start_element( { 'Name' => 'Hsp' } ); $self->element( { 'Name' => 'Hsp_features', 'Data' => $featline } ); $self->{'_seen_hsp_features'} = 1; } elsif ( ( $self->in_element('hit') || $self->in_element('hsp') ) && # ncbi blast, works with 2.2.17 m/Score\s*=\s*(\S+)\s*bits\s* # Bit score (?:\((\d+)\))?, # Missing for BLAT pseudo-BLAST fmt \s*Expect(?:\((\d+\+?)\))?\s*=\s*([^,\s]+) # E-value /ox ) { # parse NCBI blast HSP if( !$self->{'_seen_hsp_features'} ) { $self->in_element('hsp') && $self->end_element( { 'Name' => 'Hsp' } ); $self->start_element( { 'Name' => 'Hsp' } ); } # Some data clean-up so e-value will appear numeric to perl my ( $bits, $score, $n, $evalue ) = ( $1, $2, $3, $4 ); $evalue =~ s/^e/1e/i; $self->element( { 'Name' => 'Hsp_score', 'Data' => $score } ); $self->element( { 'Name' => 'Hsp_bit-score', 'Data' => $bits } ); $self->element( { 'Name' => 'Hsp_evalue', 'Data' => $evalue } ); $self->element( { 'Name' => 'Hsp_n', 'Data' => $n } ) if defined $n; $score = '' unless defined $score; # deal with BLAT which # has no score only bits $self->debug("Got NCBI HSP score=$score, evalue $evalue\n"); } elsif ( $self->in_element('hsp') && m/Identities\s*=\s*(\d+)\s*\/\s*(\d+)\s*[\d\%\(\)]+\s* (?:,\s*Positives\s*=\s*(\d+)\/(\d+)\s*[\d\%\(\)]+\s*)? # pos only valid for Protein alignments (?:\,\s*Gaps\s*=\s*(\d+)\/(\d+))? # Gaps /oxi ) { $self->element( { 'Name' => 'Hsp_identity', 'Data' => $1 } ); $self->element( { 'Name' => 'Hsp_align-len', 'Data' => $2 } ); if ( defined $3 ) { $self->element( { 'Name' => 'Hsp_positive', 'Data' => $3 } ); } else { $self->element( { 'Name' => 'Hsp_positive', 'Data' => $1 } ); } if ( defined $6 ) { $self->element( { 'Name' => 'Hsp_gaps', 'Data' => $5 } ); } $self->{'_Query'} = { 'begin' => 0, 'end' => 0 }; $self->{'_Sbjct'} = { 'begin' => 0, 'end' => 0 }; if (/(Frame\s*=\s*.+)$/) { # handle wu-blast Frame listing on same line $self->_pushback($1); } } elsif ( $self->in_element('hsp') && /Strand\s*=\s*(Plus|Minus)\s*\/\s*(Plus|Minus)/i ) { # consume this event ( we infer strand from start/end) if (!defined($reporttype)) { $self->{'_reporttype'} = $reporttype = 'BLASTN'; $bl2seq_fix = 1; # special case to resubmit the algorithm # reporttype } next; } elsif ( $self->in_element('hsp') && /Links\s*=\s*(\S+)/ox ) { $self->element( { 'Name' => 'Hsp_links', 'Data' => $1 } ); } elsif ( $self->in_element('hsp') && /Frame\s*=\s*([\+\-][1-3])\s*(\/\s*([\+\-][1-3]))?/ ) { my $frame1 = $1 || 0; my $frame2 = $2 || 0; # this is for bl2seq only if ( not defined $reporttype ) { $bl2seq_fix = 1; if ( $frame1 && $frame2 ) { $reporttype = 'TBLASTX' } else { # We can distinguish between BLASTX and TBLASTN from the report # (and assign $frame1 properly) by using the start/end from query. # If the report is BLASTX, the coordinates distance from query # will be 3 times the length of the alignment shown (coordinates in nt, # alignment in aa); if not then subject is the nucleotide sequence (TBLASTN). # Will have to fast-forward to query alignment line and then go back. my $fh = $self->_fh; my $file_pos = tell $fh; my $a_position = ''; my $ali_length = ''; my $b_position = ''; while (my $line = <$fh>) { if ($line =~ m/^(?:Query|Sbjct):?\s+(\-?\d+)?\s*(\S+)\s+(\-?\d+)?/) { $a_position = $1; my $alignment = $2; $b_position = $3; use Bio::LocatableSeq; my $gap_symbols = $Bio::LocatableSeq::GAP_SYMBOLS; $alignment =~ s/[$gap_symbols]//g; $ali_length = length($alignment); last; } } my $coord_length = ($a_position < $b_position) ? ($b_position - $a_position + 1) : ($a_position - $b_position + 1); ($coord_length == ($ali_length * 3)) ? ($reporttype = 'BLASTX') : ($reporttype = 'TBLASTN'); # Rewind filehandle to its original position to continue parsing seek $fh, $file_pos, 0; } $self->{'_reporttype'} = $reporttype; } my ( $queryframe, $hitframe ); if ( $reporttype eq 'TBLASTX' ) { ( $queryframe, $hitframe ) = ( $frame1, $frame2 ); $hitframe =~ s/\/\s*//g; } elsif ( $reporttype eq 'TBLASTN' || $reporttype eq 'PSITBLASTN') { ( $hitframe, $queryframe ) = ( $frame1, 0 ); } elsif ( $reporttype eq 'BLASTX' || $reporttype eq 'RPS-BLAST(BLASTP)') { ( $queryframe, $hitframe ) = ( $frame1, 0 ); # though NCBI doesn't report it, this is a special BLASTX-like # RPS-BLAST; should be handled differently if ($reporttype eq 'RPS-BLAST(BLASTP)') { $self->element( { 'Name' => 'BlastOutput_program', 'Data' => 'RPS-BLAST(BLASTX)' } ); } } $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => $queryframe } ); $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => $hitframe } ); } elsif (/^Parameters:/ || /^\s+Database:\s+?/ || /^\s+Subset/ || /^\s*Lambda/ || /^\s*Histogram/ || ( $self->in_element('hsp') && /WARNING|NOTE/ ) ) { # Note: Lambda check was necessary to parse # t/data/ecoli_domains.rpsblast AND to parse bl2seq $self->debug("blast.pm: found parameters section \n"); $self->in_element('hsp') && $self->end_element( { 'Name' => 'Hsp' } ); $self->in_element('hit') && $self->end_element( { 'Name' => 'Hit' } ); # This is for the case when we specify -b 0 (or B=0 for WU-BLAST) # and still want to construct minimal Hit objects $self->_cleanup_hits(\@hit_signifs) if scalar(@hit_signifs); $self->within_element('iteration') && $self->end_element( { 'Name' => 'Iteration' } ); next if /^\s+Subset/; my $blast = (/^(\s+Database\:)|(\s*Lambda)/) ? 'ncbi' : 'wublast'; if (/^\s*Histogram/) { $blast = 'btk'; } my $last = ''; # default is that gaps are allowed $self->element( { 'Name' => 'Parameters_allowgaps', 'Data' => 'yes' } ); while ( defined( $_ = $self->_readline ) ) { # If Lambda/Kappa/Entropy numbers appear first at this point, # pushback and add the header line to process it correctly if (/^\s+[\d+\.]+\s+[\d+\.]+\s+[\d+\.]/ and $last eq '') { $self->_pushback($_); $self->_pushback("Lambda K H\n"); next; } elsif ( /^((?:\S+)?BLAST[NPX]?)\s+(.+)$/i # NCBI BLAST, PSIBLAST # RPSBLAST, MEGABLAST || /^(P?GENEWISE|HFRAME|SWN|TSWN)\s+(.+)/i #Paracel BTK ) { $self->_pushback($_); # let's handle this in the loop last; } elsif (/^Query=/) { $self->_pushback($_); $self->_pushback($reportline) if $reportline; last PARSER; } # here is where difference between wublast and ncbiblast # is better handled by different logic if ( /Number of Sequences:\s+([\d\,]+)/i || /of sequences in database:\s+(\-?[\d,]+)/i ) { my $c = $1; $c =~ s/\,//g; $self->element( { 'Name' => 'Statistics_db-len', 'Data' => $c } ); } elsif (/letters in database:\s+(\-?[\d,]+)/i) { my $s = $1; $s =~ s/,//g; $self->element( { 'Name' => 'Statistics_db-let', 'Data' => $s } ); } elsif ( $blast eq 'btk' ) { next; } elsif ( $blast eq 'wublast' ) { # warn($_); if (/E=(\S+)/) { $self->element( { 'Name' => 'Parameters_expect', 'Data' => $1 } ); } elsif (/nogaps/) { $self->element( { 'Name' => 'Parameters_allowgaps', 'Data' => 'no' } ); } elsif (/ctxfactor=(\S+)/) { $self->element( { 'Name' => 'Statistics_ctxfactor', 'Data' => $1 } ); } elsif ( /(postsw|links|span[12]?|warnings|notes|gi|noseqs|qres|qype)/ ) { $self->element( { 'Name' => "Parameters_$1", 'Data' => 'yes' } ); } elsif (/(\S+)=(\S+)/) { $self->element( { 'Name' => "Parameters_$1", 'Data' => $2 } ); } elsif ( $last =~ /(Frame|Strand)\s+MatID\s+Matrix name/i ) { my $firstgapinfo = 1; my $frame = undef; while ( defined($_) && !/^\s+$/ ) { s/^\s+//; s/\s+$//; if ( $firstgapinfo && s/Q=(\d+),R=(\d+)\s+//x ) { $firstgapinfo = 0; $self->element( { 'Name' => 'Parameters_gap-open', 'Data' => $1 } ); $self->element( { 'Name' => 'Parameters_gap-extend', 'Data' => $2 } ); my @fields = split; for my $type ( qw(lambda_gapped kappa_gapped entropy_gapped) ) { next if $type eq 'n/a'; if ( !@fields ) { warn "fields is empty for $type\n"; next; } $self->element( { 'Name' => "Statistics_frame$frame\_$type", 'Data' => shift @fields } ); } } else { my ( $frameo, $matid, $matrix, @fields ) = split; if ( !defined $frame ) { # keep some sort of default feature I guess # even though this is sort of wrong $self->element( { 'Name' => 'Parameters_matrix', 'Data' => $matrix } ); $self->element( { 'Name' => 'Statistics_lambda', 'Data' => $fields[0] } ); $self->element( { 'Name' => 'Statistics_kappa', 'Data' => $fields[1] } ); $self->element( { 'Name' => 'Statistics_entropy', 'Data' => $fields[2] } ); } $frame = $frameo; my $ii = 0; for my $type ( qw(lambda_used kappa_used entropy_used lambda_computed kappa_computed entropy_computed) ) { my $f = $fields[$ii]; next unless defined $f; # deal with n/a if ( $f eq 'same' ) { $f = $fields[ $ii - 3 ]; } $ii++; $self->element( { 'Name' => "Statistics_frame$frame\_$type", 'Data' => $f } ); } } # get the next line $_ = $self->_readline; } $last = $_; } elsif ( $last =~ /(Frame|Strand)\s+MatID\s+Length/i ) { my $frame = undef; while ( defined($_) && !/^\s+/ ) { s/^\s+//; s/\s+$//; my @fields = split; if ( @fields <= 3 ) { for my $type (qw(X_gapped E2_gapped S2)) { last unless @fields; $self->element( { 'Name' => "Statistics_frame$frame\_$type", 'Data' => shift @fields } ); } } else { for my $type ( qw(length efflength E S W T X E2 S2) ) { $self->element( { 'Name' => "Statistics_frame$frame\_$type", 'Data' => shift @fields } ); } } $_ = $self->_readline; } $last = $_; } elsif (/(\S+\s+\S+)\s+DFA:\s+(\S+)\s+\((.+)\)/) { if ( $1 eq 'states in' ) { $self->element( { 'Name' => 'Statistics_DFA_states', 'Data' => "$2 $3" } ); } elsif ( $1 eq 'size of' ) { $self->element( { 'Name' => 'Statistics_DFA_size', 'Data' => "$2 $3" } ); } } elsif ( m/^\s+Time to generate neighborhood:\s+ (\S+\s+\S+\s+\S+)/x ) { $self->element( { 'Name' => 'Statistics_neighbortime', 'Data' => $1 } ); } elsif (/processors\s+used:\s+(\d+)/) { $self->element( { 'Name' => 'Statistics_noprocessors', 'Data' => $1 } ); } elsif ( m/^\s+(\S+)\s+cpu\s+time:\s+ # cputype (\S+\s+\S+\s+\S+) # cputime \s+Elapsed:\s+(\S+)/x ) { my $cputype = lc($1); $self->element( { 'Name' => "Statistics_$cputype\_cputime", 'Data' => $2 } ); $self->element( { 'Name' => "Statistics_$cputype\_actualtime", 'Data' => $3 } ); } elsif (/^\s+Start:/) { my ( $junk, $start, $stime, $end, $etime ) = split( /\s+(Start|End)\:\s+/, $_ ); chomp($stime); $self->element( { 'Name' => 'Statistics_starttime', 'Data' => $stime } ); chomp($etime); $self->element( { 'Name' => 'Statistics_endtime', 'Data' => $etime } ); } elsif (/^\s+Database:\s+(.+)$/) { $self->element( { 'Name' => 'Parameters_full_dbpath', 'Data' => $1 } ); } elsif (/^\s+Posted:\s+(.+)/) { my $d = $1; chomp($d); $self->element( { 'Name' => 'Statistics_posted_date', 'Data' => $d } ); } } elsif ( $blast eq 'ncbi' ) { if (m/^Matrix:\s+(.+)\s*$/oxi) { $self->element( { 'Name' => 'Parameters_matrix', 'Data' => $1 } ); } elsif (/^Gapped/) { $gapped_stats = 1; } elsif (/^Lambda/) { $_ = $self->_readline; s/^\s+//; my ( $lambda, $kappa, $entropy ) = split; if ($gapped_stats) { $self->element( { 'Name' => "Statistics_gapped_lambda", 'Data' => $lambda } ); $self->element( { 'Name' => "Statistics_gapped_kappa", 'Data' => $kappa } ); $self->element( { 'Name' => "Statistics_gapped_entropy", 'Data' => $entropy } ); } else { $self->element( { 'Name' => "Statistics_lambda", 'Data' => $lambda } ); $self->element( { 'Name' => "Statistics_kappa", 'Data' => $kappa } ); $self->element( { 'Name' => "Statistics_entropy", 'Data' => $entropy } ); } } elsif (m/effective\s+search\s+space\s+used:\s+(\d+)/oxi) { $self->element( { 'Name' => 'Statistics_eff-spaceused', 'Data' => $1 } ); } elsif (m/effective\s+search\s+space:\s+(\d+)/oxi) { $self->element( { 'Name' => 'Statistics_eff-space', 'Data' => $1 } ); } elsif ( m/Gap\s+Penalties:\s+Existence:\s+(\d+)\, \s+Extension:\s+(\d+)/ox ) { $self->element( { 'Name' => 'Parameters_gap-open', 'Data' => $1 } ); $self->element( { 'Name' => 'Parameters_gap-extend', 'Data' => $2 } ); } elsif (/effective\s+HSP\s+length:\s+(\d+)/) { $self->element( { 'Name' => 'Statistics_hsp-len', 'Data' => $1 } ); } elsif (/Number\s+of\s+HSP's\s+better\s+than\s+(\S+)\s+without\s+gapping:\s+(\d+)/) { $self->element( { 'Name' => 'Statistics_number_of_hsps_better_than_expect_value_cutoff_without_gapping', 'Data' => $2 } ); } elsif (/Number\s+of\s+HSP's\s+gapped:\s+(\d+)/) { $self->element( { 'Name' => 'Statistics_number_of_hsps_gapped', 'Data' => $1 } ); } elsif (/Number\s+of\s+HSP's\s+successfully\s+gapped:\s+(\d+)/) { $self->element( { 'Name' => 'Statistics_number_of_hsps_successfully_gapped', 'Data' => $1 } ); } elsif (/Length\s+adjustment:\s+(\d+)/) { $self->element( { 'Name' => 'Statistics_length_adjustment', 'Data' => $1 } ); } elsif (/effective\s+length\s+of\s+query:\s+([\d\,]+)/i) { my $c = $1; $c =~ s/\,//g; $self->element( { 'Name' => 'Statistics_query-len', 'Data' => $c } ); } elsif (/effective\s+length\s+of\s+database:\s+([\d\,]+)/i) { my $c = $1; $c =~ s/\,//g; $self->element( { 'Name' => 'Statistics_eff-dblen', 'Data' => $c } ); } elsif ( /^(T|A|X1|X2|X3|S1|S2):\s+(\d+(\.\d+)?)\s+(?:\(\s*(\d+\.\d+) bits\))?/ ) { my $v = $2; chomp($v); $self->element( { 'Name' => "Statistics_$1", 'Data' => $v } ); if ( defined $4 ) { $self->element( { 'Name' => "Statistics_$1_bits", 'Data' => $4 } ); } } elsif ( m/frameshift\s+window\, \s+decay\s+const:\s+(\d+)\,\s+([\.\d]+)/x ) { $self->element( { 'Name' => 'Statistics_framewindow', 'Data' => $1 } ); $self->element( { 'Name' => 'Statistics_decay', 'Data' => $2 } ); } elsif (m/^Number\s+of\s+Hits\s+to\s+DB:\s+(\S+)/ox) { $self->element( { 'Name' => 'Statistics_hit_to_db', 'Data' => $1 } ); } elsif (m/^Number\s+of\s+extensions:\s+(\S+)/ox) { $self->element( { 'Name' => 'Statistics_num_extensions', 'Data' => $1 } ); } elsif ( m/^Number\s+of\s+successful\s+extensions:\s+ (\S+)/ox ) { $self->element( { 'Name' => 'Statistics_num_suc_extensions', 'Data' => $1 } ); } elsif ( m/^Number\s+of\s+sequences\s+better\s+than\s+ (\S+):\s+(\d+)/ox ) { $self->element( { 'Name' => 'Parameters_expect', 'Data' => $1 } ); $self->element( { 'Name' => 'Statistics_seqs_better_than_cutoff', 'Data' => $2 } ); } elsif (/^\s+Posted\s+date:\s+(.+)/) { my $d = $1; chomp($d); $self->element( { 'Name' => 'Statistics_posted_date', 'Data' => $d } ); } elsif ( !/^\s+$/ ) { #$self->debug( "unmatched stat $_"); } } $last = $_; } } elsif ( $self->in_element('hsp') ) { $self->debug("blast.pm: Processing HSP\n"); # let's read 3 lines at a time; # bl2seq hackiness... Not sure I like $self->{'_reporttype'} ||= $DEFAULTREPORTTYPE; my %data = ( 'Query' => '', 'Mid' => '', 'Hit' => '' ); my $len; for ( my $i = 0 ; defined($_) && $i < 3 ; $i++ ) { # $self->debug("$i: $_") if $v; if ( ( $i == 0 && /^\s+$/) || /^\s*(?:Lambda|Minus|Plus|Score)/i ) { $self->_pushback($_) if defined $_; $self->end_element( { 'Name' => 'Hsp' } ); last; } chomp; if (/^((Query|Sbjct):?\s+(\-?\d+)?\s*)(\S+)\s+(\-?\d+)?/) { my ( $full, $type, $start, $str, $end ) = ( $1, $2, $3, $4, $5 ); if ( $str eq '-' ) { $i = 3 if $type eq 'Sbjct'; } else { $data{$type} = $str; } $len = length($full); $self->{"\_$type"}->{'begin'} = $start unless $self->{"_$type"}->{'begin'}; $self->{"\_$type"}->{'end'} = $end; } elsif (/^((Query|Sbjct):?\s+(\-?0+)\s*)/) { # Bug from NCBI's BLAST: unaligned output $_ = $self->_readline() for 0..1; last; } else { $self->throw("no data for midline $_") unless ( defined $_ && defined $len ); $data{'Mid'} = substr( $_, $len ); } $_ = $self->_readline(); } $self->characters( { 'Name' => 'Hsp_qseq', 'Data' => $data{'Query'} } ); $self->characters( { 'Name' => 'Hsp_hseq', 'Data' => $data{'Sbjct'} } ); $self->characters( { 'Name' => 'Hsp_midline', 'Data' => $data{'Mid'} } ); } else { #$self->debug("blast.pm: unrecognized line $_"); } } $self->debug("blast.pm: End of BlastOutput\n"); if ( $self->{'_seentop'} ) { $self->within_element('hsp') && $self->end_element( { 'Name' => 'Hsp' } ); $self->within_element('hit') && $self->end_element( { 'Name' => 'Hit' } ); # cleanup extra hits $self->_cleanup_hits(\@hit_signifs) if scalar(@hit_signifs); $self->within_element('iteration') && $self->end_element( { 'Name' => 'Iteration' } ); if ($bl2seq_fix) { $self->element( { 'Name' => 'BlastOutput_program', 'Data' => $reporttype } ); } $self->end_element( { 'Name' => 'BlastOutput' } ); } return $self->end_document(); } # Private method for internal use only. sub _start_blastoutput { my $self = shift; $self->start_element( { 'Name' => 'BlastOutput' } ); $self->{'_seentop'} = 1; $self->{'_result_count'}++; $self->{'_handler_rc'} = undef; } =head2 _will_handle Title : _will_handle Usage : Private method. For internal use only. if( $self->_will_handle($type) ) { ... } Function: Provides an optimized way to check whether or not an element of a given type is to be handled. Returns : Reference to EventHandler object if the element type is to be handled. undef if the element type is not to be handled. Args : string containing type of element. Optimizations: =over 2 =item 1 Using the cached pointer to the EventHandler to minimize repeated lookups. =item 2 Caching the will_handle status for each type that is encountered so that it only need be checked by calling handler-Ewill_handle($type) once. =back This does not lead to a major savings by itself (only 5-10%). In combination with other optimizations, or for large parse jobs, the savings good be significant. To test against the unoptimized version, remove the parentheses from around the third term in the ternary " ? : " operator and add two calls to $self-E_eventHandler(). =cut sub _will_handle { my ( $self, $type ) = @_; my $handler = $self->{'_handler_cache'}; my $will_handle = defined( $self->{'_will_handle_cache'}->{$type} ) ? $self->{'_will_handle_cache'}->{$type} : ( $self->{'_will_handle_cache'}->{$type} = $handler->will_handle($type) ); return $will_handle ? $handler : undef; } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element { my ( $self, $data ) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; if ($type) { my $handler = $self->_will_handle($type); if ($handler) { my $func = sprintf( "start_%s", lc $type ); $self->{'_handler_rc'} = $handler->$func( $data->{'Attributes'} ); } #else { #$self->debug( # changed 4/29/2006 to play nice with other event handlers # "Bio::SearchIO::InternalParserError ". # "\nCan't handle elements of type \'$type.\'" #); #} unshift @{ $self->{'_elements'} }, $type; if ( $type eq 'result' ) { $self->{'_values'} = {}; $self->{'_result'} = undef; } else { # cleanup some things if ( defined $self->{'_values'} ) { foreach my $k ( grep { /^\U$type\-/ } keys %{ $self->{'_values'} } ) { delete $self->{'_values'}->{$k}; } } } } } =head2 end_element Title : end_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : hashref with an element's worth of data Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub end_element { my ( $self, $data ) = @_; my $nm = $data->{'Name'}; my $type; my $rc; # cache these (TODO: we should probably cache all cross-report data) if ( $nm eq 'BlastOutput_program' ) { if ( $self->{'_last_data'} =~ /(t?blast[npx])/i ) { $self->{'_reporttype'} = uc $1; } $self->{'_reporttype'} ||= $DEFAULTREPORTTYPE; } if ( $nm eq 'BlastOutput_version' ) { $self->{'_reportversion'} = $self->{'_last_data'}; } # Hsps are sort of weird, in that they end when another # object begins so have to detect this in end_element for now if ( $nm eq 'Hsp' ) { foreach (qw(Hsp_qseq Hsp_midline Hsp_hseq Hsp_features)) { $self->element( { 'Name' => $_, 'Data' => $self->{'_last_hspdata'}->{$_} } ) if defined $self->{'_last_hspdata'}->{$_}; } $self->{'_last_hspdata'} = {}; $self->element( { 'Name' => 'Hsp_query-from', 'Data' => $self->{'_Query'}->{'begin'} } ); $self->element( { 'Name' => 'Hsp_query-to', 'Data' => $self->{'_Query'}->{'end'} } ); $self->element( { 'Name' => 'Hsp_hit-from', 'Data' => $self->{'_Sbjct'}->{'begin'} } ); $self->element( { 'Name' => 'Hsp_hit-to', 'Data' => $self->{'_Sbjct'}->{'end'} } ); # } elsif( $nm eq 'Iteration' ) { # Nothing special needs to be done here. } if ( $type = $MODEMAP{$nm} ) { my $handler = $self->_will_handle($type); if ($handler) { my $func = sprintf( "end_%s", lc $type ); $rc = $handler->$func( $self->{'_reporttype'}, $self->{'_values'} ); } shift @{ $self->{'_elements'} }; } elsif ( $MAPPING{$nm} ) { if ( ref( $MAPPING{$nm} ) =~ /hash/i ) { # this is where we shove in the data from the # hashref info about params or statistics my $key = ( keys %{ $MAPPING{$nm} } )[0]; $self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } = $self->{'_last_data'}; } else { $self->{'_values'}->{ $MAPPING{$nm} } = $self->{'_last_data'}; } } else { #$self->debug("blast.pm: unknown nm $nm, ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if ( defined $type && $type eq 'result' ); $self->{'_seen_hsp_features'} = 0; return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convenience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element { my ( $self, $data ) = @_; # Note that start element isn't needed for character data # Not too SAX-y, though #$self->start_element($data); $self->characters($data); $self->end_element($data); } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters { my ( $self, $data ) = @_; if ( $self->in_element('hsp') && $data->{'Name'} =~ /^Hsp\_(qseq|hseq|midline)$/ ) { $self->{'_last_hspdata'}->{ $data->{'Name'} } .= $data->{'Data'} if defined $data->{'Data'}; } return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ ); $self->{'_last_data'} = $data->{'Data'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name See Also: L =cut sub within_element { my ( $self, $name ) = @_; return 0 if ( !defined $name && !defined $self->{'_elements'} || scalar @{ $self->{'_elements'} } == 0 ); foreach ( @{ $self->{'_elements'} } ) { if ( $_ eq $name ) { return 1; } } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'within_element' because within can be tested for a whole block. Returns : boolean Args : string element name See Also: L =cut sub in_element { my ( $self, $name ) = @_; return 0 if !defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name ); } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handle a start document event Returns : none Args : none =cut sub start_document { my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'} = undef; $self->{'_elements'} = []; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document { my ( $self, @args ) = @_; #$self->debug("blast.pm: end_document\n"); return $self->{'_result'}; } sub write_result { my ( $self, $blast, @args ) = @_; if ( not defined( $self->writer ) ) { $self->warn("Writer not defined. Using a $DEFAULT_BLAST_WRITER_CLASS"); $self->writer( $DEFAULT_BLAST_WRITER_CLASS->new() ); } $self->SUPER::write_result( $blast, @args ); } sub result_count { my $self = shift; return $self->{'_result_count'}; } sub report_count { shift->result_count } =head2 inclusion_threshold Title : inclusion_threshold Usage : my $incl_thresh = $isreb->inclusion_threshold; : $isreb->inclusion_threshold(1e-5); Function: Get/Set the e-value threshold for inclusion in the PSI-BLAST score matrix model (blastpgp) that was used for generating the reports being parsed. Returns : number (real) Default value: $Bio::SearchIO::IteratedSearchResultEventBuilder::DEFAULT_INCLUSION_THRESHOLD Args : number (real) (e.g., 0.0001 or 1e-4 ) =cut =head2 max_significance Usage : $obj->max_significance(); Purpose : Set/Get the P or Expect value used as significance screening cutoff. This is the value of the -signif parameter supplied to new(). Hits with P or E-value above this are skipped. Returns : Scientific notation number with this format: 1.0e-05. Argument : Scientific notation number or float (when setting) Comments : Screening of significant hits uses the data provided on the : description line. For NCBI BLAST1 and WU-BLAST, this data : is P-value. for NCBI BLAST2 it is an Expect value. =cut =head2 signif Synonym for L =cut =head2 min_score Usage : $obj->min_score(); Purpose : Set/Get the Blast score used as screening cutoff. This is the value of the -score parameter supplied to new(). Hits with scores below this are skipped. Returns : Integer or scientific notation number. Argument : Integer or scientific notation number (when setting) Comments : Screening of significant hits uses the data provided on the : description line. =cut =head2 min_query_length Usage : $obj->min_query_length(); Purpose : Gets the query sequence length used as screening criteria. This is the value of the -min_query_len parameter supplied to new(). Hits with sequence length below this are skipped. Returns : Integer Argument : n/a =cut =head2 best_hit_only Title : best_hit_only Usage : print "only getting best hit.\n" if $obj->best_hit_only; Purpose : Set/Get the indicator for whether or not to process only : the best BlastHit. Returns : Boolean (1 | 0) Argument : Boolean (1 | 0) (when setting) =cut =head2 check_all_hits Title : check_all_hits Usage : print "checking all hits.\n" if $obj->check_all_hits; Purpose : Set/Get the indicator for whether or not to process all hits. : If false, the parser will stop processing hits after the : the first non-significance hit or the first hit that fails : any hit filter. Returns : Boolean (1 | 0) Argument : Boolean (1 | 0) (when setting) =cut # general private method used to make minimal hits from leftover # data in the hit table sub _cleanup_hits { my ($self, $hits) = @_; while ( my $v = shift @{ $hits }) { next unless defined $v; $self->start_element( { 'Name' => 'Hit' } ); my $id = $v->[2]; my $desc = $v->[3]; $self->element( { 'Name' => 'Hit_id', 'Data' => $id } ); my ($gi, $acc, $version ) = $self->_get_seq_identifiers($id); $self->element( { 'Name' => 'Hit_accession', 'Data' => $acc } ); if ( defined $v ) { $self->element( { 'Name' => 'Hit_signif', 'Data' => $v->[0] } ); if (exists $self->{'_wublast'}) { $self->element( { 'Name' => 'Hit_score', 'Data' => $v->[1] } ); } else { $self->element( { 'Name' => 'Hit_bits', 'Data' => $v->[1] } ); } } $self->element( { 'Name' => 'Hit_def', 'Data' => $desc } ); $self->end_element( { 'Name' => 'Hit' } ); } } 1; __END__ Developer Notes --------------- The following information is added in hopes of increasing the maintainability of this code. It runs the risk of becoming obsolete as the code gets updated. As always, double check against the actual source. If you find any discrepencies, please correct them. [ This documentation added on 3 Jun 2003. ] The logic is the brainchild of Jason Stajich, documented by Steve Chervitz. Jason: please check it over and modify as you see fit. Question: Elmo wants to know: How does this module unmarshall data from the input stream? (i.e., how does information from a raw input file get added to the correct Bioperl object?) Answer: This answer is specific to SearchIO::blast, but may apply to other SearchIO.pm subclasses as well. The following description gives the basic idea. The actual processing is a little more complex for certain types of data (HSP, Report Parameters). You can think of blast::next_result() as faking a SAX XML parser, making a non-XML document behave like its XML. The overhead to do this is quite substantial (~650 lines of code instead of ~80 in blastxml.pm). 0. First, add a key => value pair for the datum of interest to %MAPPING Example: 'Foo_bar' => 'Foo-bar', 1. next_result() collects the datum of interest from the input stream, and calls element(). Example: $self->element({ 'Name' => 'Foo_bar', 'Data' => $foobar}); 2. The element() method is a convenience method that calls start_element(), characters(), and end_element(). 3. start_element() checks to see if the event handler can handle a start_xxx(), where xxx = the 'Name' parameter passed into element(), and calls start_xxx() if so. Otherwise, start_element() does not do anything. Data that will have such an event handler are defined in %MODEMAP. Typically, there are only handler methods for the main parts of the search result (e.g., Result, Iteration, Hit, HSP), which have corresponding Bioperl modules. So in this example, there was an earlier call such as $self->element({'Name'=>'Foo'}) and the Foo_bar datum is meant to ultimately go into a Foo object. The start_foo() method in the handler will typically do any data initialization necessary to prepare for creating a new Foo object. Example: SearchResultEventBuilder::start_result() 4. characters() takes the value of the 'Data' key from the hashref argument in the elements() call and saves it in a local data member: Example: $self->{'_last_data'} = $data->{'Data'}; 5. end_element() is like start_element() in that it does the check for whether the event handler can handle end_xxx() and if so, calls it, passing in the data collected from all of the characters() calls that occurred since the start_xxx() call. If there isn't any special handler for the data type specified by 'Name', end_element() will place the data saved by characters() into another local data member that saves it in a hash with a key defined by %MAPPING. Example: $nm = $data->{'Name'}; $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'}; In this case, $MAPPING{$nm} is 'Foo-bar'. end_element() finishes by resetting the local data member used by characters(). (i.e., $self->{'_last_data'} = '';) 6. When the next_result() method encounters the end of the Foo element in the input stream. It will invoke $self->end_element({'Name'=>'Foo'}). end_element() then sends all of the data in the $self->{'_values'} hash. Note that $self->{'_values'} is cleaned out during start_element(), keeping it at a resonable size. In the event handler, the end_foo() method takes the hash from end_element() and creates a new hash containing the same data, but having keys lacking the 'Foo' prefix (e.g., 'Foo-bar' becomes '-bar'). The handler's end_foo() method then creates the Foo object, passing in this new hash as an argument. Example: SearchResultEventBuilder::end_result() 7. Objects created from the data in the search result are managed by the event handler which adds them to a ResultI object (using API methods for that object). The ResultI object gets passed back to SearchIO::end_element() when it calls end_result(). The ResultI object is then saved in an internal data member of the SearchIO object, which returns it at the end of next_result() by calling end_document(). (Technical Note: All objects created by end_xxx() methods in the event handler are returned to SearchIO::end_element(), but the SearchIO object only cares about the ResultI objects.) (Sesame Street aficionados note: This answer was NOT given by Mr. Noodle ;-P) BioPerl-1.007002/Bio/SearchIO/blast_pull.pm000444000766000024 2116713155576320 20407 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::blast_pull # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::blast_pull - A parser for BLAST output =head1 SYNOPSIS # do not use this class directly it is available through Bio::SearchIO use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'blast_pull', -file => 't/data/new_blastn.txt'); while (my $result = $in->next_result) { # this is a Bio::Search::Result::BlastPullResult object print "Results for ", $result->query_name(), "\n"; while (my $hit = $result->next_hit) { print $hit->name(), "\n"; while (my $hsp = $hit->next_hsp) { print "length is ", $hsp->length(), "\n"; } } } =head1 DESCRIPTION This object implements a pull-parser for BLAST output. It is fast since it only does work on request (hence 'pull'). Currently only NCBI BLASTN and BLASTP are supported. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::blast_pull; use strict; use Bio::Search::Result::BlastPullResult; use base qw(Bio::SearchIO Bio::PullParserI); =head2 new Title : new Usage : my $obj = Bio::SearchIO::blast_pull->new(); Function: Builds a new Bio::SearchIO::blast_pull object Returns : Bio::SearchIO::blast_pull Args : -fh/-file => BLAST output filename -format => 'blast_pull' -evalue => float or scientific notation number to be used as an evalue cutoff for hits -score => integer or scientific notation number to be used as a score value cutoff for hits -piped_behaviour => 'temp_file'|'memory'|'sequential_read' -piped_behaviour defines what the parser should do if the input is an unseekable filehandle (eg. piped input), see Bio::PullParserI::chunk for details. Default is 'memory'. =cut sub _initialize { my ($self, @args) = @_; # don't do normal SearchIO initialization my ($writer, $file, $fh, $piped_behaviour, $evalue, $score) = $self->_rearrange([qw(WRITER FILE FH PIPED_BEHAVIOUR EVALUE SCORE)], @args); $self->writer($writer) if $writer; $self->_fields( { ( header => undef, algorithm => undef, algorithm_version => undef, algorithm_reference => '', database_name => undef, database_letters => undef, database_entries => undef, next_result => undef, evalue_cutoff => '[unset]', score_cutoff => '[unset]' ) } ); $self->_fields->{evalue_cutoff} = $evalue if $evalue; $self->_fields->{score_cutoff} = $score if $score; $self->_dependencies( { ( algorithm => 'header', algorithm_version => 'header', database_name => 'header', database_letters => 'header', database_entries => 'header' ) } ); $self->chunk($file || $fh || $self->throw("-file or -fh must be supplied"), -piped_behaviour => $piped_behaviour || 'memory'); } sub _discover_header { my $self = shift; $self->_chunk_seek(0); my $header = $self->_get_chunk_by_end("\nQuery="); $self->{_after_header} = $self->_chunk_tell; #*** won't catch all types? only support blastn/p now anyway $header =~ /^(\S+) (\S+\s+\S+)/; $self->_fields->{algorithm} = $1; $self->_fields->{algorithm_version} = $2; my ($database) = $header =~ /^Database: (.+)/sm; unless ($database) { # earlier versions put query before database? my $header2 = $self->_get_chunk_by_end(".done\n"); ($database) = $header2 =~ /^Database: (.+)/sm; } $database =~ s/\s+(\d\S+) sequences; (\d\S+) total letters.*//s; my $entries = $1; my $letters = $2; $database =~ s/\n//g; $entries =~ s/,//g; $letters =~ s/,//g; $self->_fields->{database_name} = $database; $self->_fields->{database_entries} = $entries; $self->_fields->{database_letters} = $letters; $self->_fields->{header} = 1; } sub _discover_next_result { my $self = shift; return if $self->{_after_results}; my $type = $self->get_field('algorithm'); # also sets _after_header if not set if ($type eq 'BLASTN' || $type eq 'BLASTP') { unless ($self->_sequential) { $self->_chunk_seek($self->{_end_of_previous_result} || $self->{_after_header}); my ($start, $end) = $self->_find_chunk_by_end("\nQuery="); return if ($start == $end); unless ($end) { $start = $self->{_end_of_previous_result} || $self->{_after_header}; $end = undef; } $self->_fields->{next_result} = Bio::Search::Result::BlastPullResult->new(-chunk => [($self->chunk, $start, $end)], -parent => $self); $self->{_end_of_previous_result} = $end; } else { #*** doesn't work for the last result, needs fixing - try getting the database end chunk on failure?... $self->throw("sequential mode not yet implemented"); my $chunk = $self->_get_chunk_by_end("\nQuery="); $chunk || return; $self->_fields->{next_result} = Bio::Search::Result::BlastPullResult->new(-chunk => [$chunk], -parent => $self); } } else { $self->throw("Can only handle NCBI BLASTN and BLASTP right now"); } } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result { my $self = shift; my $result = $self->get_field('next_result') || return; undef $self->_fields->{next_result}; $self->{'_result_count'}++; return $result; } =head2 result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed. Returns : integer Args : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } =head2 rewind Title : rewind Usage : $searchio->rewind; Function: Allow one to reset the Result iterator to the beginning, so that next_result() will subsequently return the first result and so on. NB: result objects are not cached, so you will get new result objects each time you rewind. Also, note that result_count() counts the number of times you have called next_result(), so will not be able tell you how many results there were in the file if you use rewind(). Returns : n/a Args : none =cut sub rewind { my $self = shift; delete $self->{_end_of_previous_result}; } 1; BioPerl-1.007002/Bio/SearchIO/blasttable.pm000444000766000024 4320213155576320 20355 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::blasttable # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::blasttable - Driver module for SearchIO for parsing NCBI -m 8/9 format =head1 SYNOPSIS # do not use this module directly use Bio::SearchIO; my $parser = Bio::SearchIO->new(-file => $file, -format => 'blasttable'); while( my $result = $parser->next_result ) { } =head1 DESCRIPTION This module will support parsing NCBI -m 8 or -m 9 tabular output and WU-BLAST -mformat 2 or -mformat 3 tabular output. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::blasttable; use vars qw(%MAPPING %MODEMAP $DEFAULT_WRITER_CLASS $DefaultProgramName); use strict; use Bio::Search::Result::ResultFactory; use Bio::Search::Hit::HitFactory; use Bio::Search::HSP::HSPFactory; $DefaultProgramName = 'BLASTN'; $DEFAULT_WRITER_CLASS = 'Bio::SearchIO::Writer::HitTableWriter'; # mapping of terms to Bioperl hash keys %MODEMAP = ( 'Result' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); %MAPPING = ( 'Hsp_bit-score' => 'HSP-bits', 'Hsp_score' => 'HSP-score', 'Hsp_evalue' => 'HSP-evalue', 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_positive' => 'HSP-conserved', 'Hsp_identity' => 'HSP-identical', 'Hsp_mismatches' => 'HSP-mismatches', 'Hsp_qgapblocks' => 'HSP-query_gapblocks', 'Hsp_hgapblocks' => 'HSP-hit_gapblocks', 'Hsp_gaps' => 'HSP-hsp_gaps', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_query-frame'=> 'HSP-query_frame', 'Hsp_hit-frame' => 'HSP-hit_frame', 'Hit_id' => 'HIT-name', 'Hit_len' => 'HIT-length', 'Hit_accession' => 'HIT-accession', 'Hit_def' => 'HIT-description', 'Hit_signif' => 'HIT-significance', 'Hit_score' => 'HIT-score', 'Hit_bits' => 'HIT-bits', 'Result_program' => 'RESULT-algorithm_name', 'Result_version' => 'RESULT-algorithm_version', 'Result_query-def'=> 'RESULT-query_name', 'Result_query-len'=> 'RESULT-query_length', 'Result_query-acc'=> 'RESULT-query_accession', 'Result_querydesc'=> 'RESULT-query_description', 'Result_db' => 'RESULT-database_name', 'Result_db-len' => 'RESULT-database_entries', 'Result_db-let' => 'RESULT-database_letters', ); use base qw(Bio::SearchIO); =head2 new Title : new Usage : my $obj = Bio::SearchIO::blasttable->new(); Function: Builds a new Bio::SearchIO::blasttable object Returns : an instance of Bio::SearchIO::blasttable Args : =cut sub _initialize { my ($self,@args) = @_; $self->SUPER::_initialize(@args); my ($pname) = $self->_rearrange([qw(PROGRAM_NAME)], @args); $self->program_name($pname || $DefaultProgramName); $self->_eventHandler->register_factory('result', Bio::Search::Result::ResultFactory->new(-type => 'Bio::Search::Result::GenericResult')); $self->_eventHandler->register_factory('hit', Bio::Search::Hit::HitFactory->new(-type => 'Bio::Search::Hit::GenericHit')); $self->_eventHandler->register_factory('hsp', Bio::Search::HSP::HSPFactory->new(-type => 'Bio::Search::HSP::GenericHSP')); } =head2 next_result Title : next_result Usage : my $result = $parser->next_result Function: Parse the next result from the data stream Returns : L Args : none =cut sub next_result{ my ($self) = @_; my ($lastquery,$lasthit); local $/ = "\n"; local $_; my ($alg, $ver); while( defined ($_ = $self->_readline) ) { # WU-BLAST -mformat 3 only if(m{^#\s((?:\S+?)?BLAST[NPX])\s(\d+\.\d+.+\d{4}\])}) { ($alg, $ver) = ($1, $2); # only one header for whole file with WU-BLAST # so $alg and $ver won't get set properly for # each result $self->program_name($alg) if $alg; $self->element({'Name' => 'Result_version', 'Data' => $ver}) if $ver; next; } # -m 9 only elsif(m{^#\s+((?:\S+?)?BLAST[NPX])\s+(.+)}) { ($alg, $ver) = ($1, $2); next; } next if /^#/ || /^\s*$/; my @fields = split; next if @fields == 1; my ($qname,$hname, $percent_id, $hsp_len, $mismatches,$gapsm, $qstart,$qend,$hstart,$hend,$evalue,$bits); # WU-BLAST-specific my ($num_scores, $raw_score, $identities, $positives, $percent_pos, $qgap_blocks,$qgaps, $sgap_blocks, $sgaps, $qframe, $sframe); # NCBI -m8 and -m9 if (@fields == 12) { ($qname,$hname, $percent_id, $hsp_len, $mismatches,$gapsm, $qstart,$qend,$hstart,$hend,$evalue,$bits) = @fields; # NCBI -m8 and -m9, v 2.2.18+ } elsif (@fields == 13) { ($qname, $hname, $percent_id, $percent_pos, $hsp_len, $mismatches, $gapsm, $qstart,$qend,$hstart,$hend,$evalue,$bits) = @fields; } # WU-BLAST -mformat 2 and 3 elsif ((@fields == 22) or (@fields == 24)) { ($qname,$hname,$evalue,$num_scores, $bits, $raw_score, $hsp_len, $identities, $positives,$mismatches, $percent_id, $percent_pos, $qgap_blocks, $qgaps, $sgap_blocks, $sgaps, $qframe, $qstart, $qend, $sframe, $hstart,$hend,) = @fields; # we need total gaps in the alignment $gapsm=$qgaps+$sgaps; } if (@fields == 12 || @fields == 13) { # need to determine total gaps in the alignment for NCBI output # since NCBI reports number of gapopens and NOT total gaps my $qlen = abs($qstart - $qend) + 1; my $querygaps = $hsp_len - $qlen; my $hlen = abs($hstart - $hend) + 1; my $hitgaps = $hsp_len - $hlen; $gapsm = $querygaps + $hitgaps; } # Remember Jim's code is 0 based if( defined $lastquery && $lastquery ne $qname ) { $self->end_element({'Name' => 'Hit'}); $self->end_element({'Name' => 'Result'}); $self->_pushback($_); return $self->end_document; } elsif( ! defined $lastquery ) { $self->{'_result_count'}++; $self->start_element({'Name' => 'Result'}); $self->element({'Name' => 'Result_program', 'Data' => $alg || $self->program_name}); $self->element({'Name' => 'Result_version', 'Data' => $ver}) if $ver; $self->element({'Name' => 'Result_query-def', 'Data' => $qname}); $self->start_element({'Name' => 'Hit'}); $self->element({'Name' => 'Hit_id', 'Data' => $hname}); # we'll store the 1st hsp bits as the hit bits $self->element({'Name' => 'Hit_bits', 'Data' => $bits}); # we'll store the 1st hsp value as the hit evalue $self->element({'Name' => 'Hit_signif', 'Data' => $evalue}); } elsif( $lasthit ne $hname ) { if( $self->in_element('hit') ) { $self->end_element({'Name' => 'Hit'}); } $self->start_element({'Name' => 'Hit'}); $self->element({'Name' => 'Hit_id', 'Data' => $hname}); # we'll store the 1st hsp bits as the hit bits $self->element({'Name' => 'Hit_bits', 'Data' => $bits}); # we'll store the 1st hsp value as the hit evalue $self->element({'Name' => 'Hit_signif', 'Data' => $evalue}); } my $identical = $hsp_len - $mismatches - $gapsm; # If $positives value is absent, try to recover it from $percent_pos, # this is better than letting the program to assume "conserved == identical" if (not defined $positives and defined $percent_pos) { $positives = sprintf "%d", ($percent_pos * $hsp_len / 100); } $self->start_element({'Name' => 'Hsp'}); $self->element({'Name' => 'Hsp_evalue', 'Data' => $evalue}); $self->element({'Name' => 'Hsp_bit-score', 'Data' => $bits}); $self->element({'Name' => 'Hsp_identity', 'Data' => $identical}); $self->element({'Name' => 'Hsp_positive', 'Data' => $positives}); $self->element({'Name' => 'Hsp_gaps', 'Data' => $gapsm}); $self->element({'Name' => 'Hsp_query-from', 'Data' => $qstart}); $self->element({'Name' => 'Hsp_query-to', 'Data' => $qend}); $self->element({'Name' => 'Hsp_hit-from', 'Data' => $hstart }); $self->element({'Name' => 'Hsp_hit-to', 'Data' => $hend }); $self->element({'Name' => 'Hsp_align-len', 'Data' => $hsp_len}); $self->end_element({'Name' => 'Hsp'}); $lastquery = $qname; $lasthit = $hname; } # fencepost if( defined $lasthit && defined $lastquery ) { if( $self->in_element('hit') ) { $self->end_element({'Name' => 'Hit'}); } $self->end_element({'Name' => 'Result'}); return $self->end_document; } } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element{ my ($self,$data) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; if( my $type = $MODEMAP{$nm} ) { $self->_mode($type); if( $self->_will_handle($type) ) { my $func = sprintf("start_%s",lc $type); $self->_eventHandler->$func($data->{'Attributes'}); } unshift @{$self->{'_elements'}}, $type; } if($nm eq 'Result') { $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_mode'} = ''; } } =head2 end_element Title : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub end_element { my ($self,$data) = @_; my $nm = $data->{'Name'}; my $rc; # Hsp are sort of weird, in that they end when another # object begins so have to detect this in end_element for now if( my $type = $MODEMAP{$nm} ) { if( $self->_will_handle($type) ) { my $func = sprintf("end_%s",lc $type); $rc = $self->_eventHandler->$func($self->{'_reporttype'}, $self->{'_values'}); } shift @{$self->{'_elements'}}; } elsif( $MAPPING{$nm} ) { if ( ref($MAPPING{$nm}) =~ /hash/i ) { my $key = (keys %{$MAPPING{$nm}})[0]; $self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'}; } else { $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'}; } } else { $self->warn( "unknown nm $nm ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if( $nm eq 'Result' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element{ my ($self,$data) = @_; $self->start_element($data); $self->characters($data); $self->end_element($data); } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters{ my ($self,$data) = @_; # deep bug fix: set $self->{'_last_data'} to undef if $$data{Data} is # a valid slot, whose value is undef -- # allows an undef to be propagated to object constructors and # handled there as desired; in particular, when Hsp_postive => -conserved # is not defined (in BLASTN, e.g.), the value of hsp's {CONSERVED} property is # set to the value of {IDENTICAL}. #/maj # return unless ( defined $data->{'Data'} ); return unless ( grep /Data/, keys %$data ); if ( !defined $data->{'Data'} ) { $self->{'_last_data'} = undef; return; } if( $data->{'Data'} =~ /^\s+$/ ) { return unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/; } if( $self->in_element('hsp') && $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) { $self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'}; } $self->{'_last_data'} = $data->{'Data'}; } =head2 _mode Title : _mode Usage : $obj->_mode($newval) Function: Example : Returns : value of _mode Args : newvalue (optional) =cut sub _mode{ my ($self,$value) = @_; if( defined $value) { $self->{'_mode'} = $value; } return $self->{'_mode'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub within_element{ my ($self,$name) = @_; return 0 if ( ! defined $name && ! defined $self->{'_elements'} || scalar @{$self->{'_elements'}} == 0) ; foreach ( @{$self->{'_elements'}} ) { if( $_ eq $name ) { return 1; } } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub in_element{ my ($self,$name) = @_; return 0 if ! defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name) } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handles a start document event Returns : none Args : none =cut sub start_document{ my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_mode'} = ''; $self->{'_elements'} = []; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document{ my ($self,@args) = @_; return $self->{'_result'}; } =head2 result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } sub report_count { shift->result_count } =head2 program_name Title : program_name Usage : $obj->program_name($newval) Function: Get/Set the program name Returns : value of program_name (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub program_name{ my $self = shift; $self->{'program_name'} = shift if @_; return $self->{'program_name'} || $DefaultProgramName; } =head2 _will_handle Title : _will_handle Usage : Private method. For internal use only. if( $self->_will_handle($type) ) { ... } Function: Provides an optimized way to check whether or not an element of a given type is to be handled. Returns : Reference to EventHandler object if the element type is to be handled. undef if the element type is not to be handled. Args : string containing type of element. Optimizations: =over 2 =item 1 Using the cached pointer to the EventHandler to minimize repeated lookups. =item 2 Caching the will_handle status for each type that is encountered so that it only need be checked by calling handler-Ewill_handle($type) once. =back This does not lead to a major savings by itself (only 5-10%). In combination with other optimizations, or for large parse jobs, the savings good be significant. To test against the unoptimized version, remove the parentheses from around the third term in the ternary " ? : " operator and add two calls to $self-E_eventHandler(). =cut sub _will_handle { my ($self,$type) = @_; my $handler = $self->{'_handler'}; my $will_handle = defined($self->{'_will_handle_cache'}->{$type}) ? $self->{'_will_handle_cache'}->{$type} : ($self->{'_will_handle_cache'}->{$type} = $handler->will_handle($type)); return $will_handle ? $handler : undef; } 1; BioPerl-1.007002/Bio/SearchIO/cross_match.pm000444000766000024 2343213155576320 20550 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::cross_match # # Please direct questions and support issues to # # Cared for by Shin Leong # # Copyright Shin Leong # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::cross_match - CrossMatch-specific subclass of Bio::SearchIO =head1 SYNOPSIS # Working with iterations (CrossMatch results) my $searchIO = Bio::SearchIO->new( -format => 'cross_match', -file => "$file.screen.out" ) while(my $r = $searchIO->next_result) { while(my $hit = $r->next_hit) { while(my $hsp = $hit->next_hsp) { #Do the processing here. } } } See L for details about working with Bio::SearchIO. =head1 DESCRIPTION This object is a subclass of Bio::SearchIO and provides some operations that facilitate working with CrossMatch and CrossMatch results. For general information about working with Results, see L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shin Leong Email sleong@watson.wustl.edu =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::cross_match; use Bio::Search::Result::CrossMatchResult; use Bio::SearchIO; use Bio::Search::Hit::GenericHit; use Bio::Search::HSP::GenericHSP; use base qw(Bio::SearchIO); =head2 next_result Title : next_result Usage : $result = stream->next_result Function: Reads the next ResultI object from the stream and returns it. Certain driver modules may encounter entries in the stream that are either misformatted or that use syntax not yet understood by the driver. If such an incident is recoverable, e.g., by dismissing a feature of a feature table or some other non-mandatory part of an entry, the driver will issue a warning. In the case of a non-recoverable situation an exception will be thrown. Do not assume that you can resume parsing the same stream after catching the exception. Note that you can always turn recoverable errors into exceptions by calling $stream->verbose(2) (see Bio::Root::RootI POD page). Returns : A Bio::Search::Result::ResultI object Args : n/a See L =cut sub next_result { my ($self) = @_; my $start = 0; while ( defined( $_ = $self->_readline ) ) { return if ( $self->{'_end_document'} ); if (/^cross_match version\s+(.*?)$/) { $self->{_algorithm_version} = $1; } elsif (/^Maximal single base matches/) { $start = 1; } elsif (/^(\d+) matching entries/) { $self->{'_end_document'} = 1; return; } elsif ( ( $start || $self->{'_result_count'} ) && /^\s*(\d+)/xms ) { $self->{'_result_count'}++; return $self->_parse($_); } elsif ( !$self->{_parameters} ) { if (/.*?\s+(\-.*?)$/) { my $p = $1; my @pp = split /\s+/, $p; for ( my $i = 0 ; $i < @pp ; $i++ ) { if ( $pp[$i] =~ /^\-/ ) { if ( $pp[ $i + 1 ] && $pp[ $i + 1 ] !~ /^\-/ ) { $self->{_parameters}->{ $pp[$i] } = $pp[ $i + 1 ]; $i++; } else { $self->{_parameters}->{ $pp[$i] } = ""; } } } } } elsif (/^Query file(s):\s+(.*?)$/) { $self->{_query_name} = $1; } elsif (/^Subject file(s):\s+(.*?)$/) { $self->{_subject_name} = $2; } } } =head2 _alignment Title : _alignment Usage : private =cut sub _alignment { my $self = shift; # C H_EO-aaa01PCR02 243 CCTCTGAATGGCTGAAGACCCCTCTGCCGAGGGAGGTTGGGGATTGTGGG 194 # # 0284119_008.c1- 1 CCTCTGAATGGCTGAAGACCCCTCTGCCGAGGGAGGTTGGGGATTGTGGG 50 # # C H_EO-aaa01PCR02 193 ACAAGGTCCCTTGGTGCTGATGGCCTGAAGGGGCCTGAGCTGTGGGCAGA 144 # # 0284119_008.c1- 51 ACAAGGTCCCTTGGTGCTGATGGCCTGAAGGGGCCTGAGCTGTGGGCAGA 100 # # C H_EO-aaa01PCR02 143 TGCAGTTTTCTGTGGGCTTGGGGAACCTCTCACGTTGCTGTGTCCTGGTG 94 # # 0284119_008.c1- 101 TGCAGTTTTCTGTGGGCTTGGGGAACCTCTCACGTTGCTGTGTCCTGGTG 150 # # C H_EO-aaa01PCR02 93 AGCAGCCCGACCAATAAACCTGCTTTTCTAAAAGGATCTGTGTTTGATTG 44 # # 0284119_008.c1- 151 AGCAGCCCGACCAATAAACCTGCTTTTCTAAAAGGATCTGTGTTTGATTG 200 # # C H_EO-aaa01PCR02 43 TATTCTCTGAAGGCAGTTACATAGGGTTACAGAGG 9 # # 0284119_008.c1- 201 TATTCTCTGAAGGCAGTTACATAGGGTTACAGAGG 235 # LSF: Should be the blank line. Otherwise error. my $blank = $self->_readline; unless ( $blank =~ /^\s*$/ ) { return; } my @data; my @pad; $count = 0; while ( defined( $_ = $self->_readline ) ) { $count = 0 if ( $count >= 3 ); next if (/^$/); if (/^(C \S+.*?\d+ )(\S+) \d+$|^( \S+.*?\d+ )(\S+) \d+$$|^\s+$/) { $count++; if ( $1 || $3 ) { $pad[$count] = $1 ? $1 : $3; push @{ $data[$count] }, ( $2 ? $2 : $4 ); } else { if (/\s{$pad[0],$pad[0]}(.*?)$/) { push @{ $data[$count] }, $1; } else { $self->throw("Format error for the homology line [$_]."); } } } else { last; } } return @data; } =head2 _parse Title : _parse Usage : private =cut sub _parse { my $self = shift; my $line = shift; my $is_alignment = 0; my ( $hit_seq, $homology_seq, $query_seq ); # 32 5.13 0.00 0.00 H_DO-0065PCR0005792_034a.b1-1 327 365 (165) C 1111547847_forward (0) 39 1 #OR #ALIGNMENT 32 5.13 0.00 0.00 H_DO-0065PCR0005792_034a.b1-1 327 365 (165) C 1111547847_forward (0) 39 1 $line =~ s/^\s+|\s+$//g; my @r = split /\s+/, $line; if ( $r[0] eq "ALIGNMENT" ) { $is_alignment = 1; shift @r; ( $hit_seq, $homology_seq, $query_seq ) = $self->_alignment(); } my $subject_seq_id; my $query_seq_id = $r[4]; my $query_start = $r[5]; my $query_end = $r[6]; my $is_complement = 0; my $subject_start; my $subject_end; if ( $r[8] eq "C" && $r[9] !~ /^\(\d+\)$/ ) { $subject_seq_id = $r[9]; $is_complement = 1; $subject_start = $r[11]; $subject_end = $r[12]; } else { $subject_seq_id = $r[8]; $subject_start = $r[9]; $subject_end = $r[10]; } my $hit = Bio::Search::Hit::GenericHit->new( -name => $subject_seq_id, -hsps => [ Bio::Search::HSP::GenericHSP->new( -query_name => $query_seq_id, -query_start => $query_start, -query_end => $query_end, -hit_name => $subject_seq_id, -hit_start => $subject_start, -hit_end => $subject_end, -query_length => 0, -hit_length => 0, -identical => $r[0], -conserved => $r[0], -query_seq => $query_seq ? ( join "", @$query_seq ) : "", #query sequence portion of the HSP -hit_seq => $hit_seq ? ( join "", @$hit_seq ) : "", #hit sequence portion of the HSP -homology_seq => $homology_seq ? ( join "", @$homology_seq ) : "", #homology sequence for the HSP #LSF: Need the direction, just to fool the GenericHSP module. -algorithm => 'SW', ) ], ); my $result = Bio::Search::Result::CrossMatchResult->new( -query_name => $self->{_query_name}, -query_accession => '', -query_description => '', -query_length => 0, -database_name => $self->{_subject_name}, -database_letters => 0, -database_entries => 0, -parameters => $self->{_parameters}, -statistics => {}, -algorithm => 'cross_match', -algorithm_version => $self->{_algorithm_version}, ); $result->add_hit($hit); return $result; } =head2 result_count Title : result_count Usage : $num = $stream->result_count; Function: Gets the number of CrossMatch results that have been parsed. Returns : integer Args : none Throws : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } 1; #$Header$ BioPerl-1.007002/Bio/SearchIO/erpin.pm000444000766000024 4627413155576320 17371 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::erpin # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::erpin - SearchIO-based ERPIN parser =head1 SYNOPSIS # do not call this module directly. Use Bio::SearchIO. =head1 DESCRIPTION This is an experimental SearchIO-based parser for output from the erpin program. It currently parses erpin output for ERPIN versions 4.2.5 and above; older versions may work but will not be supported. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Fields Email cjfields-at-uiuc-dot-edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::erpin; use strict; use Data::Dumper; use base qw(Bio::SearchIO); my %MODEMAP = ( 'Result' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); my %MAPPING = ( 'Hsp_bit-score' => 'HSP-bits', 'Hsp_score' => 'HSP-score', 'Hsp_evalue' => 'HSP-evalue', # no evalues yet 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', # 'Hsp_hit-to' => 'HSP-hit_end', # 'Hsp_gaps' => 'HSP-hsp_gaps', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_midline' => 'HSP-homology_seq', 'Hsp_structure' => 'HSP-meta', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_stranded' => 'HSP-stranded', # not supported yet 'Hsp_positive' => 'HSP-conserved', 'Hsp_identity' => 'HSP-identical', 'Hit_id' => 'HIT-name', 'Hit_len' => 'HIT-length', 'Hit_gi' => 'HIT-ncbi_gi', 'Hit_accession' => 'HIT-accession', 'Hit_def' => 'HIT-description', 'Hit_signif' => 'HIT-significance', # none yet 'Hit_score' => 'HIT-score', # best HSP bit score 'Hit_bits' => 'HIT-bits', # best HSP bit score 'ERPIN_program' => 'RESULT-algorithm_name', # get/set 'ERPIN_version' => 'RESULT-algorithm_version', # get/set 'ERPIN_query-def'=> 'RESULT-query_name', # get/set 'ERPIN_query-len'=> 'RESULT-query_length', 'ERPIN_query-acc'=> 'RESULT-query_accession', # get/set 'ERPIN_querydesc'=> 'RESULT-query_description', # get/set 'ERPIN_db' => 'RESULT-database_name', # get/set 'ERPIN_db-len' => 'RESULT-database_entries', # none yet 'ERPIN_db-let' => 'RESULT-database_letters', # none yet 'Parameters_cutoff' => { 'RESULT-parameters' => 'cutoff' }, 'Parameters_expect' => { 'RESULT-parameters' => 'expect' }, 'Parameters_include' => { 'RESULT-parameters' => 'include' }, 'Parameters_sc-match' => { 'RESULT-parameters' => 'match' }, 'Parameters_sc-mismatch' => { 'RESULT-parameters' => 'mismatch' }, 'Parameters_gap-open' => { 'RESULT-parameters' => 'gapopen' }, 'Parameters_gap-extend' => { 'RESULT-parameters' => 'gapext' }, 'Parameters_filter' => { 'RESULT-parameters' => 'filter' }, 'Parameters_allowgaps' => { 'RESULT-parameters' => 'allowgaps' }, 'Parameters_full_dbpath' => { 'RESULT-parameters' => 'full_dbpath' }, 'Statistics_db-let' => { 'RESULT-statistics' => 'dbletters' }, ); my $MINSCORE = 0; my $DEFAULT_VERSION = '4.2.5'; my $DEFAULT_ALGORITHM = 'erpin'; =head2 new Title : new Usage : my $obj = Bio::SearchIO::infernal->new(); Function: Builds a new Bio::SearchIO::infernal object Returns : Bio::SearchIO::infernal Args : -fh/-file => cmsearch (infernal) filename -format => 'erpin' -algorithm => algorithm (default 'Infernal') -query_acc => query accession, eg. Rfam accession (default undef) -hsp_minscore => minimum HSP score cutoff -version => ERPIN version (not reported in output) =cut sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); my ($cutoff, $accession, $version) = $self->_rearrange([qw(HSP_MINSCORE QUERY_ACC VERSION)],@args); my $handler = $self->_eventHandler; $handler->register_factory( 'result', Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Result::GenericResult', -interface => 'Bio::Search::Result::ResultI', -verbose => $self->verbose() ) ); $handler->register_factory( 'hit', Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Hit::ModelHit', -interface => 'Bio::Search::Hit::HitI', -verbose => $self->verbose() ) ); $handler->register_factory( 'hsp', Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::HSP::ModelHSP', -interface => 'Bio::Search::HSP::HSPI', -verbose => $self->verbose() ) ); $accession && $self->query_accession($accession); $cutoff ||= $MINSCORE; $self->hsp_minscore($cutoff); $version ||= $DEFAULT_VERSION; $self->algorithm_version($version); } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result { my ($self) = @_; my $seentop = 0; local $/ = "\n"; local $_; my $accession = $self->query_accession; my $minscore = $self->hsp_minscore; my $version = $self->algorithm_version; my $verbose = $self->verbose; # cache for speed? $self->start_document(); my ($lasthit, $lastscore, $lastlen, $lasteval); #my $hitline; PARSER: while ( defined( my $line = $self->_readline ) ) { next if $line =~ m{^\s*$}; if ($line =~ m{^Training\sset:\s+"(.*)"}xmso) { if ($seentop) { $self->_pushback($line); last PARSER; } $self->start_element({'Name' => 'Result'}); $self->element_hash( { 'ERPIN_query-def' => $1, 'ERPIN_program' =>'erpin', 'ERPIN_version' => $version, 'ERPIN_query-acc' => $accession, }); $seentop = 1; # parse rest of header here HEADER: while (defined ($line = $self->_readline) ) { next if $line =~ m{^\s*$}; if (index($line, '>') == 0 || index($line, '-------- at level 1 --------') == 0) { $self->_pushback($line); last HEADER; } if ($line =~ m{^\s+(\d+\ssequences\sof\slength\s\d+)}xmso) { $self->element( {'Name' => 'ERPIN_querydesc', 'Data' => $1} ); } elsif ($line =~ m{^Cutoff:\s+(\S+)}xmso) { $self->element( {'Name' => 'Parameters_cutoff', 'Data' => $1} ); } elsif ($line =~ m{^Database:\s+"(.*)"}xmso) { $self->element( {'Name' => 'ERPIN_db', 'Data' => $1} ); } elsif ($line =~ m{^\s+(\d+)\snucleotides\sto\sbe\sprocessed\sin\s(\d+)\ssequences}xmso) { $self->element_hash( {'ERPIN_db-len' => $2, 'ERPIN_db-let' => $1} ); } elsif ($line =~ m{^E-value\sat\scutoff\s\S+\sfor\s\S+\sdouble\sstrand\sdata:\s+(\S+)}xmso) { $self->element( {'Name' => 'Parameters_expect', 'Data' => $1} ); } elsif ($line =~ m{^\s+(ATGC\sratios:\s+(?:\S+\s+\S+\s+\S+\s+\S+))}) { $self->element( {'Name' => 'Statistics_db-let', 'Data' => $1} ); } } } elsif ($line =~ m{^>(\S+)\s+(.*)}xmso ) { my ($id, $desc) = ($1, $2); chomp $desc; # desc line is repeated for each strand, so must check # prior to starting a new hit if (!$lasthit || $id ne $lasthit) { if ($self->within_element('hit') ) { $self->element_hash({ 'Hit_signif' => $lasteval, 'Hit_score' => $lastscore, 'Hit_bits' => $lastscore }); $self->end_element({'Name' => 'Hit'}); } $self->start_element({'Name' => 'Hit'}); my ($gi, $acc, $ver) = $self->_get_seq_identifiers($id); $self->element_hash({ 'Hit_id' => $id, 'Hit_gi' => $gi, 'Hit_accession' => $ver ? "$acc.$ver" : $acc ? $acc : $id, 'Hit_def' => $desc }); } $lasthit = $id; } elsif ( (index($line, 'FW') == 0) || (index($line, 'RC') == 0)) { my ($str, $hn, $pos, $score, $eval) = split ' ', $line; if ($minscore < $score) { $self->start_element({'Name' => 'Hsp'}); my ($start, $end) = split m{\.\.}, $pos, 2; ($start, $end) = ($end, $start) if ($str eq 'RC'); $line = $self->_readline; chomp $line; $self->element_hash({ 'Hsp_stranded' => 'HIT', 'Hsp_hit-from' => $start, 'Hsp_hit-to' => $end, 'Hsp_score' => $score, 'Hsp_bit-score' => $score, 'Hsp_evalue' => $eval, 'Hsp_query-from' => 1, 'Hsp_query-to' => length($line), 'Hsp_align-len' => length($line), 'Hsp_hseq' =>$line }); $self->end_element({'Name' => 'Hsp'}); $lastscore = $score if (!$lastscore || $lastscore < $score); $lasteval = $eval if (!$lasteval || $lasteval > $eval); } } else { #$self->debug("Dropped data: $line"); } } if ($seentop) { if ($self->within_element('hit')) { $self->element_hash({ 'Hit_signif' => $lasteval, 'Hit_score' => $lastscore, 'Hit_bits' => $lastscore }); $self->end_element({'Name' => 'Hit'}); } $self->end_element({'Name' => 'Result'}); } return $self->end_document(); } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element { my ( $self, $data ) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; if ($type) { if ( $self->_eventHandler->will_handle($type) ) { my $func = sprintf( "start_%s", lc $type ); $self->_eventHandler->$func( $data->{'Attributes'} ); } unshift @{ $self->{'_elements'} }, $type; } if ( defined $type && $type eq 'result' ) { $self->{'_values'} = {}; $self->{'_result'} = undef; } } =head2 end_element Title : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none Args : hashref with at least 2 keys, 'Data' and 'Name' =cut sub end_element { my ( $self, $data ) = @_; my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; my $rc; if ($type) { if ( $self->_eventHandler->will_handle($type) ) { my $func = sprintf( "end_%s", lc $type ); $rc = $self->_eventHandler->$func( $self->{'_reporttype'}, $self->{'_values'} ); } my $lastelem = shift @{ $self->{'_elements'} }; } elsif ( $MAPPING{$nm} ) { if ( ref( $MAPPING{$nm} ) =~ /hash/i ) { my $key = ( keys %{ $MAPPING{$nm} } )[0]; $self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } = $self->{'_last_data'}; } else { $self->{'_values'}->{ $MAPPING{$nm} } = $self->{'_last_data'}; } } else { $self->debug("unknown nm $nm, ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if ( defined $type && $type eq 'result' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convenience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element { my ( $self, $data ) = @_; # simple data calls (%MAPPING) do not need start_element $self->characters($data); $self->end_element($data); } =head2 element_hash Title : element Usage : $eventhandler->element_hash({'Hsp_hit-from' => $start, 'Hsp_hit-to' => $end, 'Hsp_score' => $lastscore}); Function: Convenience method that takes multiple simple data elements and maps to appropriate parameters Returns : none Args : Hash ref with the mapped key (in %MAPPING) and value =cut sub element_hash { my ($self, $data) = @_; $self->throw("Must provide data hash ref") if !$data || !ref($data); for my $nm (sort keys %{$data}) { next if $data->{$nm} && $data->{$nm} =~ m{^\s*$}o; if ( $MAPPING{$nm} ) { if ( ref( $MAPPING{$nm} ) =~ /hash/i ) { my $key = ( keys %{ $MAPPING{$nm} } )[0]; $self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } = $data->{$nm}; } else { $self->{'_values'}->{ $MAPPING{$nm} } = $data->{$nm}; } } } } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters { my ( $self, $data ) = @_; return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/o ); $self->{'_last_data'} = $data->{'Data'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub within_element { my ( $self, $name ) = @_; return 0 if ( !defined $name || !defined $self->{'_elements'} || scalar @{ $self->{'_elements'} } == 0 ); foreach ( @{ $self->{'_elements'} } ) { return 1 if ( $_ eq $name ); } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'within' because 'in' only tests its immediate parent. Returns : boolean Args : string element name =cut sub in_element { my ( $self, $name ) = @_; return 0 if !defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name ); } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handle a start document event Returns : none Args : none =cut sub start_document { my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'} = undef; $self->{'_elements'} = []; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document { my ($self) = @_; return $self->{'_result'}; } =head2 result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } =head2 query_accession Title : query_accession Usage : my $acc = $parser->query_accession(); Function: Get/Set query (model) accession; Infernal currently does not output the accession number (Rfam accession #) Returns : String (accession) Args : [optional] String (accession) =cut sub query_accession { my $self = shift; return $self->{'_query_accession'} = shift if @_; return $self->{'_query_accession'}; } =head2 hsp_minscore Title : hsp_minscore Usage : my $cutoff = $parser->hsp_minscore(); Function: Get/Set min bit score cutoff (for generating Hits/HSPs) Returns : score (number) Args : [optional] score (number) =cut sub hsp_minscore { my $self = shift; return $self->{'_hsp_minscore'} = shift if @_; return $self->{'_hsp_minscore'}; } =head2 algorithm_version Title : algorithm_version Usage : my $ver = $parser->algorithm_version(); Function: Get/Set algorithm version (not defined in RNAMotif output) Returns : String (accession) Args : [optional] String (accession) =cut sub algorithm_version { my $self = shift; return $self->{'_algorithm'} = shift if @_; return $self->{'_algorithm'}; } 1; BioPerl-1.007002/Bio/SearchIO/exonerate.pm000444000766000024 5414713155576320 20244 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::exonerate # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::exonerate - parser for Exonerate =head1 SYNOPSIS # do not use this module directly, it is a driver for SearchIO use Bio::SearchIO; my $searchio = Bio::SearchIO->new(-file => 'file.exonerate', -format => 'exonerate'); while( my $r = $searchio->next_result ) { print $r->query_name, "\n"; } =head1 DESCRIPTION This is a driver for the SearchIO system for parsing Exonerate (Guy Slater) output. You can get Exonerate at http://www.ebi.ac.uk/~guy/exonerate/ [until Guy puts up a Web reference,publication for it.]). An optional parameter -min_intron is supported by the L initialization method. This is if you run Exonerate with a different minimum intron length (default is 30) the parser will be able to detect the difference between standard deletions and an intron. Still some room to play with there that might cause this to get misinterpreted that has not been fully tested or explored. The VULGAR and CIGAR formats should be parsed okay now creating HSPs where appropriate (so merging match states where appropriate rather than breaking an HSP at each indel as it may have done in the past). The GFF that comes from exonerate is still probably a better way to go if you are doing protein2genome or est2genome mapping. For example you can see this script: ### TODO: Jason, this link is dead, do we have an updated one? http://fungal.genome.duke.edu/~jes12/software/scripts/process_exonerate_gff3.perl.txt If your report contains both CIGAR and VULGAR lines only the first one will processed for a given Query/Target pair. If you preferentially want to use VULGAR or CIGAR add one of these options when initializing the SearchIO object. -cigar => 1 OR -vulgar => 1 Or set them via these methods. $parser->cigar(1) OR $parser->vulgar(1) =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::exonerate; use strict; use vars qw(@STATES %MAPPING %MODEMAP $DEFAULT_WRITER_CLASS $MIN_INTRON); use base qw(Bio::SearchIO); %MODEMAP = ( 'ExonerateOutput' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); %MAPPING = ( 'Hsp_query-from'=> 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_midline' => 'HSP-homology_seq', 'Hsp_score' => 'HSP-score', 'Hsp_qlength' => 'HSP-query_length', 'Hsp_hlength' => 'HSP-hit_length', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_identity' => 'HSP-identical', 'Hsp_gaps' => 'HSP-hsp_gaps', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hit_id' => 'HIT-name', 'Hit_desc' => 'HIT-description', 'Hit_len' => 'HIT-length', 'Hit_score' => 'HIT-score', 'ExonerateOutput_program' => 'RESULT-algorithm_name', 'ExonerateOutput_query-def' => 'RESULT-query_name', 'ExonerateOutput_query-desc'=> 'RESULT-query_description', 'ExonerateOutput_query-len' => 'RESULT-query_length', ); $DEFAULT_WRITER_CLASS = 'Bio::SearchIO::Writer::HitTableWriter'; $MIN_INTRON=30; # This is the minimum intron size =head2 new Title : new Usage : my $obj = Bio::SearchIO::exonerate->new(); Function: Builds a new Bio::SearchIO::exonerate object Returns : an instance of Bio::SearchIO::exonerate Args : -min_intron => somewhat obsolete option, how to determine if a an indel is an intron or a local gap. Use VULGAR rather than CIGAR to avoid this heuristic,default 30. -cigar => 1 set this to 1 if you want to parse CIGAR exclusively. -vulgar => 1 set this to 1 if you want to parse VULGAR exclusively, setting both to 1 will revert to the default behavior of just parsing the first line that it sees. =cut sub new { my ($class) = shift; my $self = $class->SUPER::new(@_); my ($min_intron,$cigar, $vulgar) = $self->_rearrange([qw(MIN_INTRON CIGAR VULGAR)], @_); if( $min_intron ) { $MIN_INTRON = $min_intron; } if( $cigar && $vulgar ) { $self->warn("cannot get HSPs from both CIGAR and VULGAR lines, will just choose whichever comes first (same as if you had chosen neither"); $cigar = 0; $vulgar=0; } $self->cigar($cigar); $self->vulgar($vulgar); $self; } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result{ my ($self) = @_; local $/ = "\n"; local $_; $self->{'_last_data'} = ''; my ($reporttype,$seenquery,$reportline); $self->start_document(); my @hit_signifs; my $seentop; my (@q_ex, @m_ex, @h_ex); ## gc addition while( defined($_ = $self->_readline) ) { # warn( "Reading $_"); if( /^\s*Query:\s+(\S+)\s*(.+)?/ ) { if( $seentop ) { $self->end_element({'Name' => 'ExonerateOutput'}); $self->_pushback($_); return $self->end_document(); } $seentop = 1; my ($nm,$desc) = ($1,$2); chomp($desc) if defined $desc; $self->{'_result_count'}++; $self->start_element({'Name' => 'ExonerateOutput'}); $self->element({'Name' => 'ExonerateOutput_query-def', 'Data' => $nm }); $self->element({'Name' => 'ExonerateOutput_query-desc', 'Data' => $desc }); $self->element({'Name' => 'ExonerateOutput_program', 'Data' => 'Exonerate' }); $self->{'_seencigar'} = 0; $self->{'_vulgar'} = 0; } elsif ( /^Target:\s+(\S+)\s*(.+)?/ ) { my ($nm,$desc) = ($1,$2); chomp($desc) if defined $desc; $self->start_element({'Name' => 'Hit'}); $self->element({'Name' => 'Hit_id', 'Data' => $nm}); $self->element({'Name' => 'Hit_desc', 'Data' => $desc}); $self->{'_seencigar'} = 0; $self->{'_vulgar'} = 0; } elsif( s/^vulgar:\s+(\S+)\s+ # query sequence id (\d+)\s+(\d+)\s+([\-\+\.])\s+ # query start-end-strand (\S+)\s+ # target sequence id (\d+)\s+(\d+)\s+([\-\+])\s+ # target start-end-strand (-?\d+)\s+ # score //ox ) { next if( $self->cigar || $self->{'_seencigar'}); $self->{'_vulgar'}++; # # Note from Ewan. This is ugly - copy and paste from # cigar line parsing. Should unify somehow... # if( ! $self->within_element('result') ) { $self->start_element({'Name' => 'ExonerateOutput'}); $self->element({'Name' => 'ExonerateOutput_query-def', 'Data' => $1 }); } if( ! $self->within_element('hit') ) { $self->start_element({'Name' => 'Hit'}); $self->element({'Name' => 'Hit_id', 'Data' => $5}); } ## gc note: ## $qe and $he are no longer used for calculating the ends, ## just the $qs and $hs values and the alignment and insert lenghts my ($qs,$qe,$qstrand) = ($2,$3,$4); my ($hs,$he,$hstrand) = ($6,$7,$8); my $score = $9; # $self->element({'Name' => 'ExonerateOutput_query-len', # 'Data' => $qe}); # $self->element({'Name' => 'Hit_len', # 'Data' => $he}); ## gc note: ## add one because these values are zero-based ## this calculation was originally done lower in the code, ## but it's clearer to do it just once at the start my @rest = split; my ($qbegin,$qend) = ('query-from', 'query-to'); if( $qstrand eq '-' ) { $qstrand = -1; $qe++; } else { $qstrand = 1; $qs++; } my ($hbegin,$hend) = ('hit-from', 'hit-to'); if( $hstrand eq '-' ) { $hstrand = -1; $he++; } else { $hstrand = 1; $hs++; } # okay let's do this right and generate a set of HSPs # from the cigar line/home/bio1/jes12/bin/exonerate --model est2genome --bestn 1 t/data/exonerate_cdna.fa t/data/exonerate_genomic_rev.fa my ($aln_len,$inserts,$deletes) = (0,0,0); my ($laststate,@events,$gaps) =( '' ); while( @rest >= 3 ) { my ($state,$len1,$len2) = (shift @rest, shift @rest, shift @rest); # # HSPs are only the Match cases; otherwise we just # move the coordinates on by the correct amount # if( $state eq 'M' ) { if( $laststate eq 'G' ) { # merge gaps across Match states so the HSP # goes across $events[-1]->{$qend} = $qs + $len1*$qstrand - $qstrand; $events[-1]->{$hend} = $hs + $len2*$hstrand - $hstrand; $events[-1]->{'gaps'} = $gaps; } else { push @events, { 'score' => $score, 'align-len' => $len1, $qbegin => $qs, $qend => ($qs + $len1*$qstrand - $qstrand), $hbegin => $hs, $hend => ($hs + $len2*$hstrand - $hstrand), }; } $gaps = 0; } else { $gaps = $len1 + $len2 if $state eq 'G'; } $qs += $len1*$qstrand; $hs += $len2*$hstrand; $laststate= $state; } for my $event ( @events ) { $self->start_element({'Name' => 'Hsp'}); while( my ($key,$val) = each %$event ) { $self->element({'Name' => "Hsp_$key", 'Data' => $val}); } $self->element({'Name' => 'Hsp_identity', 'Data' => 0}); $self->end_element({'Name' => 'Hsp'}); } # end of hit $self->element({'Name' => 'Hit_score', 'Data' => $score}); # issued end... $self->end_element({'Name' => 'Hit'}); $self->end_element({'Name' => 'ExonerateOutput'}); return $self->end_document(); } elsif( s/^cigar:\s+(\S+)\s+ # query sequence id (\d+)\s+(\d+)\s+([\-\+])\s+ # query start-end-strand (\S+)\s+ # target sequence id (\d+)\s+(\d+)\s+([\-\+])\s+ # target start-end-strand (-?\d+)\s+ # score //ox ) { next if( $self->vulgar || $self->{'_seenvulgar'}); $self->{'_cigar'}++; if( ! $self->within_element('result') ) { $self->start_element({'Name' => 'ExonerateOutput'}); $self->element({'Name' => 'ExonerateOutput_query-def', 'Data' => $1 }); } if( ! $self->within_element('hit') ) { $self->start_element({'Name' => 'Hit'}); $self->element({'Name' => 'Hit_id', 'Data' => $5}); } ## gc note: ## $qe and $he are no longer used for calculating the ends, ## just the $qs and $hs values and the alignment and insert lenghts my ($qs,$qe,$qstrand) = ($2,$3,$4); my ($hs,$he,$hstrand) = ($6,$7,$8); my $score = $9; # $self->element({'Name' => 'ExonerateOutput_query-len', # 'Data' => $qe}); # $self->element({'Name' => 'Hit_len', # 'Data' => $he}); my @rest = split; if( $qstrand eq '-' ) { $qstrand = -1; ($qs,$qe) = ($qe,$qs); # flip-flop if we're on opp strand $qs--; $qe++; } else { $qstrand = 1; } if( $hstrand eq '-' ) { $hstrand = -1; ($hs,$he) = ($he,$hs); # flip-flop if we're on opp strand $hs--; $he++; } else { $hstrand = 1; } # okay let's do this right and generate a set of HSPs # from the cigar line ## gc note: ## add one because these values are zero-based ## this calculation was originally done lower in the code, ## but it's clearer to do it just once at the start $qs++; $hs++; my ($aln_len,$inserts,$deletes) = (0,0,0); while( @rest >= 2 ) { my ($state,$len) = (shift @rest, shift @rest); if( $state eq 'I' ) { $inserts+=$len; } elsif( $state eq 'D' ) { if( $len >= $MIN_INTRON ) { $self->start_element({'Name' => 'Hsp'}); $self->element({'Name' => 'Hsp_score', 'Data' => $score}); $self->element({'Name' => 'Hsp_align-len', 'Data' => $aln_len}); $self->element({'Name' => 'Hsp_identity', 'Data' => $aln_len - ($inserts + $deletes)}); # HSP ends where the other begins $self->element({'Name' => 'Hsp_query-from', 'Data' => $qs}); ## gc note: ## $qs is now the start of the next hsp ## the end of this hsp is 1 before this position ## (or 1 after in case of reverse strand) $qs += $aln_len*$qstrand; $self->element({'Name' => 'Hsp_query-to', 'Data' => $qs - ($qstrand*1)}); $hs += $deletes*$hstrand; $self->element({'Name' => 'Hsp_hit-from', 'Data' => $hs}); $hs += $aln_len*$hstrand; $self->element({'Name' => 'Hsp_hit-to', 'Data' => $hs-($hstrand*1)}); $self->element({'Name' => 'Hsp_align-len', 'Data' => $aln_len + $inserts + $deletes}); $self->element({'Name' => 'Hsp_identity', 'Data' => $aln_len }); $self->element({'Name' => 'Hsp_gaps', 'Data' => $inserts + $deletes}); $self->element({'Name' => 'Hsp_querygaps', 'Data' => $inserts}); $self->element({'Name' => 'Hsp_hitgaps', 'Data' => $deletes}); ## gc addition start $self->element({'Name' => 'Hsp_qseq', 'Data' => shift @q_ex, }); $self->element({'Name' => 'Hsp_hseq', 'Data' => shift @h_ex, }); $self->element({'Name' => 'Hsp_midline', 'Data' => shift @m_ex, }); ## gc addition end $self->end_element({'Name' => 'Hsp'}); $aln_len = $inserts = $deletes = 0; } $deletes+=$len; } else { $aln_len += $len; } } $self->start_element({'Name' => 'Hsp'}); ## gc addition start $self->element({'Name' => 'Hsp_qseq', 'Data' => shift @q_ex, }); $self->element({'Name' => 'Hsp_hseq', 'Data' => shift @h_ex, }); $self->element({'Name' => 'Hsp_midline', 'Data' => shift @m_ex, }); ## gc addition end $self->element({'Name' => 'Hsp_score', 'Data' => $score}); $self->element({'Name' => 'Hsp_query-from', 'Data' => $qs}); $qs += $aln_len*$qstrand; $self->element({'Name' => 'Hsp_query-to', 'Data' => $qs - ($qstrand*1)}); $hs += $deletes*$hstrand; $self->element({'Name' => 'Hsp_hit-from', 'Data' => $hs}); $hs += $aln_len*$hstrand; $self->element({'Name' => 'Hsp_hit-to', 'Data' => $hs -($hstrand*1)}); $self->element({'Name' => 'Hsp_align-len', 'Data' => $aln_len}); $self->element({'Name' => 'Hsp_identity', 'Data' => $aln_len - ($inserts + $deletes)}); $self->element({'Name' => 'Hsp_gaps', 'Data' => $inserts + $deletes}); $self->element({'Name' => 'Hsp_querygaps', 'Data' => $inserts}); $self->element({'Name' => 'Hsp_hitgaps', 'Data' => $deletes}); $self->end_element({'Name' => 'Hsp'}); $self->element({'Name' => 'Hit_score', 'Data' => $score}); $self->end_element({'Name' => 'Hit'}); $self->end_element({'Name' => 'ExonerateOutput'}); return $self->end_document(); } else { # skipping this line } } return $self->end_document() if( $seentop ); } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element{ my ($self,$data) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; if( $type ) { if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("start_%s",lc $type); $self->_eventHandler->$func($data->{'Attributes'}); } unshift @{$self->{'_elements'}}, $type; if($type eq 'result') { $self->{'_values'} = {}; $self->{'_result'}= undef; } } } =head2 end_element Title : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub end_element { my ($self,$data) = @_; my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; my $rc; if( $type = $MODEMAP{$nm} ) { if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("end_%s",lc $type); $rc = $self->_eventHandler->$func($self->{'_reporttype'}, $self->{'_values'}); } shift @{$self->{'_elements'}}; } elsif( $MAPPING{$nm} ) { if ( ref($MAPPING{$nm}) =~ /hash/i ) { my $key = (keys %{$MAPPING{$nm}})[0]; $self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'}; } else { $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'}; } } else { $self->debug( "unknown nm $nm, ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if( defined $type && $type eq 'result' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element{ my ($self,$data) = @_; $self->start_element($data); $self->characters($data); $self->end_element($data); } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters{ my ($self,$data) = @_; return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ ); $self->{'_last_data'} = $data->{'Data'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub within_element{ my ($self,$name) = @_; return 0 if ( ! defined $name && ! defined $self->{'_elements'} || scalar @{$self->{'_elements'}} == 0) ; foreach ( @{$self->{'_elements'}} ) { if( $_ eq $name ) { return 1; } } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub in_element{ my ($self,$name) = @_; return 0 if ! defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name) } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handle a start document event Returns : none Args : none =cut sub start_document{ my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_elements'} = []; $self->{'_reporttype'} = 'exonerate'; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document{ my ($self,@args) = @_; return $self->{'_result'}; } sub write_result { my ($self, $blast, @args) = @_; if( not defined($self->writer) ) { $self->warn("Writer not defined. Using a $DEFAULT_WRITER_CLASS"); $self->writer( $DEFAULT_WRITER_CLASS->new() ); } $self->SUPER::write_result( $blast, @args ); } sub result_count { my $self = shift; return $self->{'_result_count'}; } sub report_count { shift->result_count } =head2 vulgar Title : vulgar Usage : $obj->vulgar($newval) Function: Get/Set flag, do you want to build HSPs from VULGAR string? Returns : value of vulgar (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub vulgar{ my $self = shift; my $x = shift if @_; if( @_ ) { if( $_[0] && $self->{'_cigar'} ) { $self->warn("Trying to set vulgar and cigar both to 1, must be either or"); $self->{'_cigar'} = 0; return $self->{'_vulgar'} = 0; } } return $self->{'_vulgar'}; } =head2 cigar Title : cigar Usage : $obj->cigar($newval) Function: Get/Set boolean flag do you want to build HSPs from CIGAR strings? Returns : value of cigar (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub cigar{ my $self = shift; my $x = shift if @_; if( @_ ) { if( $_[0] && $self->{'_vulgar'} ) { $self->warn("Trying to set vulgar and cigar both to 1, must be either or"); $self->{'_vulgar'} = 0; return $self->{'_cigar'} = 0; } } return $self->{'_cigar'}; } 1; BioPerl-1.007002/Bio/SearchIO/fasta.pm000444000766000024 14766213155576320 17375 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::fasta # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::fasta - A SearchIO parser for FASTA results =head1 SYNOPSIS # Do not use this object directly, use it through the SearchIO system use Bio::SearchIO; my $searchio = Bio::SearchIO->new(-format => 'fasta', -file => 'report.FASTA'); while( my $result = $searchio->next_result ) { # ... do what you would normally doi with Bio::SearchIO. } =head1 DESCRIPTION This object contains the event based parsing code for FASTA format reports. It creates L objects instead of L for the HSP objects. This module will parse -m 9 -d 0 output as well as default m 1 output from FASTA as well as SSEARCH. Also see the SearchIO HOWTO: L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich, Aaron Mackey, William Pearson Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::fasta; use vars qw(%MODEMAP %MAPPING $IDLENGTH); use strict; # Object preamble - inherits from Bio::Root::RootI use Bio::Factory::ObjectFactory; BEGIN { # Set IDLENGTH to a new value if you have # compile FASTA with a different ID length # (actually newest FASTA allows the setting of this # via -C parameter, default is 6) $IDLENGTH = 6; # mapping of NCBI Blast terms to Bioperl hash keys %MODEMAP = ( 'FastaOutput' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); # This should really be done more intelligently, like with # XSLT %MAPPING = ( 'Hsp_bit-score' => 'HSP-bits', 'Hsp_score' => 'HSP-score', 'Hsp_sw-score' => 'HSP-swscore', 'Hsp_evalue' => 'HSP-evalue', 'Hsp_evalue2' => 'HSP-evalue2', 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_positive' => 'HSP-conserved', 'Hsp_identity' => 'HSP-identical', 'Hsp_gaps' => 'HSP-hsp_gaps', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_midline' => 'HSP-homology_seq', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_query-frame' => 'HSP-query_frame', 'Hsp_hit-frame' => 'HSP-hit_frame', 'Hit_id' => 'HIT-name', 'Hit_len' => 'HIT-length', 'Hit_accession' => 'HIT-accession', 'Hit_def' => 'HIT-description', 'Hit_signif' => 'HIT-significance', 'Hit_score' => 'HIT-score', 'FastaOutput_program' => 'RESULT-algorithm_name', 'FastaOutput_version' => 'RESULT-algorithm_version', 'FastaOutput_query-def' => 'RESULT-query_name', 'FastaOutput_querydesc' => 'RESULT-query_description', 'FastaOutput_query-len' => 'RESULT-query_length', 'FastaOutput_db' => 'RESULT-database_name', 'FastaOutput_db-len' => 'RESULT-database_entries', 'FastaOutput_db-let' => 'RESULT-database_letters', 'Parameters_matrix' => { 'RESULT-parameters' => 'matrix' }, 'Parameters_expect' => { 'RESULT-parameters' => 'expect' }, 'Parameters_include' => { 'RESULT-parameters' => 'include' }, 'Parameters_sc-match' => { 'RESULT-parameters' => 'match' }, 'Parameters_sc-mismatch' => { 'RESULT-parameters' => 'mismatch' }, 'Parameters_gap-open' => { 'RESULT-parameters' => 'gapopen' }, 'Parameters_gap-ext' => { 'RESULT-parameters' => 'gapext' }, 'Parameters_word-size' => { 'RESULT-parameters' => 'wordsize' }, 'Parameters_ktup' => { 'RESULT-parameters' => 'ktup' }, 'Parameters_filter' => { 'RESULT-parameters' => 'filter' }, 'Statistics_db-num' => { 'RESULT-statistics' => 'dbentries' }, 'Statistics_db-len' => { 'RESULT-statistics' => 'dbletters' }, 'Statistics_hsp-len' => { 'RESULT-statistics' => 'hsplength' }, 'Statistics_eff-space' => { 'RESULT-statistics' => 'effectivespace' }, 'Statistics_kappa' => { 'RESULT-statistics' => 'kappa' }, 'Statistics_lambda' => { 'RESULT-statistics' => 'lambda' }, 'Statistics_entropy' => { 'RESULT-statistics' => 'entropy' }, ); } use base qw(Bio::SearchIO); =head2 new Title : new Usage : my $obj = Bio::SearchIO::fasta->new(); Function: Builds a new Bio::SearchIO::fasta object Returns : Bio::SearchIO::fasta Args : -idlength - set ID length to something other than the default (6), this is only necessary if you have compiled FASTA with a new default id length to display in the HSP alignment blocks =cut sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); return unless @args; my ($idlength) = $self->_rearrange( [qw(IDLENGTH)], @args ); $self->idlength( $idlength || $IDLENGTH ); $self->_eventHandler->register_factory( 'hsp', Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::HSP::FastaHSP', -interface => 'Bio::Search::HSP::HSPI' ) ); return 1; } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result { my ($self) = @_; local $/ = "\n"; local $_; my $data = ''; my $seentop = 0; my $current_hsp; my $m9HSP = 0; $self->start_document(); my @hit_signifs; while ( defined( $_ = $self->_readline ) ) { next if ( !$self->in_element('hsp') && /^\s+$/ ); # skip empty lines if ( m/(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/oxi || /(\S+)\s+compares\s+a/ || /(\S+)\s+performs\s+a/ || /(\S+)\s+produces\s/ || /(\S+)\s+finds\s+/ # for lalign, but does not work because no "The best scores are:" || ( m/^\#\s+/ # has a command log line && ( $_ = $self->_readline ) && /(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/oxi || /(\S+)\s+compares\s+a/ || /(\S+)\s+performs\s+a/ || /(\S+)\s+produces\s/ || /(\S+)\s+finds\s+/ # for lalign, but does not work because no "The best scores are:" ) ) { if ($seentop) { $self->_pushback($_); $self->end_element( { 'Name' => 'FastaOutput' } ); return $self->end_document(); } $self->{'_reporttype'} = $1; $self->start_element( { 'Name' => 'FastaOutput' } ); $self->{'_result_count'}++; $seentop = 1; #$self->debug( "reporttype is " . $self->{'_reporttype'} . "\n" ); $self->element( { 'Name' => 'FastaOutput_program', 'Data' => $self->{'_reporttype'} } ); my $version; # version 35 version string on same line if (/version/) { ($version) = (/version\s+(\S+)/); } # earlier versions, it's on the next line else { $_ = $self->_readline(); ($version) = (/version\s+(\S+)/); } $version = '' unless defined $version; $self->{'_version'} = $version; $self->element( { 'Name' => 'FastaOutput_version', 'Data' => $version } ); my ( $last, $leadin, $type, $querylen, $querytype, $querydef ); while ( defined( $_ = $self->_readline() ) ) { if ( /^ ( (?:\s+>) | # fa33 lead-in (?:\s*\d+\s*>>>) # fa34 mlib lead-in ) (.*) /x ) { ( $leadin, $querydef ) = ( $1, $2 ); if ( $leadin =~ m/>>>/ ) { if ( $querydef =~ /^(.*?)\s+(?:\-\s+)?(\d+)\s+(aa|nt).*$/o ) { ( $querydef, $querylen, $querytype ) = ( $1, $2, $3 ); last; } } else { if ( $last =~ /(\S+)[:,]\s*(\d+)\s+(aa|nt)/ ) { ( $querylen, $querytype ) = ( $2, $3 ); $querydef ||= $1; last; } } } elsif (m/^\s*vs\s+\S+/o) { if ( $last =~ /(\S+)[,:]\s+(\d+)\s+(aa|nt)/o ) { ( $querydef, $querylen, $querytype ) = ( $1, $2, $3 ); last; } } $last = $_; } if ( $self->{'_reporttype'} && $self->{'_reporttype'} eq 'FASTA' ) { if ( $querytype eq 'nt' ) { $self->{'_reporttype'} = 'FASTN'; } elsif ( $querytype eq 'aa' ) { $self->{'_reporttype'} = 'FASTP'; } } my ( $name, $descr ) = $querydef =~ m/^(\S+)\s*(.*?)\s*$/o; $self->element( { 'Name' => 'FastaOutput_query-def', 'Data' => $name } ); $self->element( { 'Name' => 'FastaOutput_querydesc', 'Data' => $descr } ); if ($querylen) { $self->element( { 'Name' => 'FastaOutput_query-len', 'Data' => $querylen } ); } else { $self->warn("unable to find and set query length"); } if ( $last =~ /^\s*vs\s+(\S+)/ || ( $last =~ /^searching\s+(\S+)\s+library/ ) || ( $last =~ /^Library:\s+(\S+)\s+/ ) || ( defined $_ && ( /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)\s+/ ) ) || ( defined( $_ = $self->_readline() ) && ( /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)/ ) ) ) { $self->element( { 'Name' => 'FastaOutput_db', 'Data' => $1 } ); } elsif (m/^\s+opt(?:\s+E\(\))?$/o) { # histogram ... read over it more rapidly than the larger outer loop: while ( defined( $_ = $self->_readline ) ) { last if m/^>\d+/; } } } elsif (/(\d+)\s+residues\s+in\s+(\d+)\s+(?:library\s+)?sequences/) { $self->element( { 'Name' => 'FastaOutput_db-let', 'Data' => $1 } ); $self->element( { 'Name' => 'FastaOutput_db-len', 'Data' => $2 } ); $self->element( { 'Name' => 'Statistics_db-len', 'Data' => $1 } ); $self->element( { 'Name' => 'Statistics_db-num', 'Data' => $2 } ); } elsif (/Lambda=\s*(\S+)/) { $self->element( { 'Name' => 'Statistics_lambda', 'Data' => $1 } ); } elsif (/K=\s*(\S+)/) { $self->element( { 'Name' => 'Statistics_kappa', 'Data' => $1 } ); } elsif (/^\s*(Smith-Waterman)/) { $self->{'_reporttype'} = $1; m/\[\s*(\S+)\s+matrix \([^\)]+\)(xS)?\],/; $self->element( { 'Name' => 'Parameters_matrix', 'Data' => $1 } ); $self->element( { 'Name' => 'Parameters_filter', 'Data' => defined $2 ? 1 : 0, } ); if (/\s*gap\-penalty:\s*(\-?\d+)\/(\-?\d+)/) { $self->element( { 'Name' => 'Parameters_gap-open', 'Data' => $1, } ); $self->element( { 'Name' => 'Parameters_gap-ext', 'Data' => $2, } ); } elsif (/\s*open\/ext:\s*(\-?\d+)\/(\-?\d+)/) { $self->element( { 'Name' => 'Parameters_gap-open', 'Data' => $1, } ); $self->element( { 'Name' => 'Parameters_gap-ext', 'Data' => $2, } ); } $self->element( { 'Name' => 'FastaOutput_program', 'Data' => $self->{'_reporttype'} } ); } elsif (/The best( related| unrelated)? scores are:/) { my $rel = $1; my @labels = split; @labels = map { if ( $_ =~ m/^E\((\d+)\)$/o ) { $self->element( { 'Name' => 'Statistics_eff-space', 'Data' => $1 } ); "evalue"; } else { # canonicalize changed column headers if ($_ eq "gapl") { $_ = "lgaps"; } elsif ($_ eq "gapq") { $_ = "qgaps"; } elsif ($_ eq "E2()") { $_ = "evalue2"; } $_; } } @labels[ $rel ? 5 : 4 .. $#labels ]; while ( defined( $_ = $self->_readline() ) && !/^\s+$/ ) { my @line = split; if ( $line[-1] =~ m/\=/o && $labels[-1] ne 'aln_code' ) { # unlabelled alignment hit; push @labels, "aln_code"; } if ($line[0] eq "+-") { $m9HSP = 1; # parse HSP, add to last parsed Hit my %hspData; my @line = split; @hspData{@labels} = splice( @line, @line - @labels ); $hspData{lframe} = $hit_signifs[-1]->{lframe}; push @{$hit_signifs[-1]->{HSPs}}, \%hspData; next; } elsif ($line[0] eq '>>><<<') { last; } my (%data, %hspData); @data{@labels} = @hspData{@labels} = splice( @line, @line - @labels ); if ( $line[-1] =~ m/\[([1-6rf])\]/o ) { my $fr = $1; $hspData{lframe} = $data{lframe} = ( $fr =~ /\d/o ? ( $fr <= 3 ? "+$fr" : "-@{[$fr-3]}" ) : ( $fr eq 'f' ? '+1' : '-1' ) ); pop @line; } else { $hspData{lframe} = $data{lframe} = '0'; } if ( $line[-1] =~ m/^\(?(\d+)\)$/ ) { $data{hit_len} = $1; pop @line; if ( $line[-1] =~ m/^\($/ ) { pop @line; } } else { $data{hit_len} = 0; } # rebuild the first part of the line, preserving spaces: ($_) = m/^(\S+(?:\s+\S+){$#line})/; my ( $id, $desc ) = split( /\s+/, $_, 2 ); my @pieces = split( /\|/, $id ); my $acc = pop @pieces; $acc =~ s/\.\d+$//; @data{qw(id desc acc)} = ( $id, $desc, $acc ); $data{HSPs} = [ \%hspData ]; push @hit_signifs, \%data; } } elsif ( /^\s*([T]?FAST[XYAF]).+,\s*(\S+)\s*matrix[^\]]+?(xS)?\]\s*ktup:\s*(\d+)/ ) { $self->element( { 'Name' => 'Parameters_matrix', 'Data' => $2 } ); $self->element( { 'Name' => 'Parameters_filter', 'Data' => defined $3 ? 1 : 0, } ); $self->element( { 'Name' => 'Parameters_ktup', 'Data' => $4 } ); $self->{'_reporttype'} = $1 if ( $self->{'_reporttype'} !~ /FAST[PN]/i ); # # get gap-pen line for FASTA33, which is not on the matrix line # # FASTA (3.36 June 2000) function [optimized, BL50 matrix (15:-5)] ktup: 2 # join: 36, opt: 24, gap-pen: -12/ -2, width: 16 # $_ = $self->_readline(); if (/(?:gap\-pen|open\/ext):\s+([\-\+]?\d+)\s*\/\s*([\-\+]?\d+)/) { $self->element( { 'Name' => 'Parameters_gap-open', 'Data' => $1 } ); $self->element( { 'Name' => 'Parameters_gap-ext', 'Data' => $2 } ); } $self->element( { 'Name' => 'FastaOutput_program', 'Data' => $self->{'_reporttype'} } ); } elsif (/^Algorithm:\s+(\S+)\s+.*\s*\(([^)]+)\)\s+(\S+)/) { $self->{'_reporttype'} = $1 if ( $self->{'_reporttype'} !~ /FAST[PN]/i ); } elsif ( /^Parameters:/ ) { # FASTA 35.04/FASTA 36 m/Parameters:\s+(\S+)\s+matrix\s+\([^\)]+\)(xS)?,?\s/; $self->element( { 'Name' => 'Parameters_matrix', 'Data' => $1 } ); $self->element( { 'Name' => 'Parameters_filter', 'Data' => defined $2 ? $2 : 0, } ); if (/ktup:\s(\d+)/) { $self->element( { 'Name' => 'Parameters_ktup', 'Data' => $1 } ); if (/ktup:\s\d+$/) { $_ = $self->_readline(); } } if (/(?:gap\-pen|open\/ext):\s+([\-\+]?\d+)\s*\/\s*([\-\+]?\d+)/) { $self->element( { 'Name' => 'Parameters_gap-open', 'Data' => $1 } ); $self->element( { 'Name' => 'Parameters_gap-ext', 'Data' => $2 } ); } $self->element( { 'Name' => 'FastaOutput_program', 'Data' => $self->{'_reporttype'} } ); } elsif ( /^\s+ktup:\s*(\d+),/ ) { $self->element( { 'Name' => 'Parameters_ktup', 'Data' => $1 } ); } elsif (/^(>--)$/ || /^>>(?!>)(.+?)\s+(?:\((\d+)\s*(aa|nt)\))?$/) { if ( $self->in_element('hsp') ) { $self->end_element( { 'Name' => 'Hsp' } ); } my $firstHSP = 0; if ($1 ne ">--") { $firstHSP = 1; my ($hit_id, $len, $alphabet) = ($1, $2, $3); if (!$len || !$alphabet) { WRAPPED: while (defined($_ = $self->_readline)) { if (/(.*?)\s+\((\d+)\s*(aa|nt)\)/) { ($len, $alphabet) = ($2, $3); $hit_id .= $1 ? " ".$1 : ''; last WRAPPED; } if (/^>>(?!>)/) { # too far, throw $self->throw("Couldn't find length, bailing"); } } } if ( $self->in_element('hit') ) { $self->end_element( { 'Name' => 'Hit' } ); shift @hit_signifs if @hit_signifs; } $self->start_element( { 'Name' => 'Hit' } ); $self->element( { 'Name' => 'Hit_len', 'Data' => $len } ); my ( $id, $desc ) = split( /\s+/, $hit_id, 2 ); $self->element( { 'Name' => 'Hit_id', 'Data' => $id } ); #$self->debug("Hit ID is $id\n"); my @pieces = split( /\|/, $id ); my $acc = pop @pieces; $acc =~ s/\.\d+$//; $self->element( { 'Name' => 'Hit_accession', 'Data' => $acc } ); $self->element( { 'Name' => 'Hit_def', 'Data' => $desc } ); } else { # push @{$hit_signifs[0]->{HSPs}}, $current_hsp; } $_ = $self->_readline(); my ( $score, $bits, $e, $e2 ) = /Z-score: \s* (\S+) \s* (?: bits: \s* (\S+) \s+ )? (?: E|expect ) \s* \((?:\d+)?\) :? \s*(\S+) (?: \s* E2 \s* \(\) :? \s*(\S+) )? /ox; $bits = $score unless defined $bits; my ($v); if ($firstHSP && !$m9HSP) { $v = shift @{$hit_signifs[0]->{HSPs}} if (@hit_signifs && @{$hit_signifs[0]->{HSPs}}); $current_hsp = $v; } else { $v = $current_hsp; } if ( defined $v ) { @{$v}{qw(evalue evalue2 bits z-sc)} = ( $e, $e2, $bits, $score ); } if ($firstHSP) { $self->element( { 'Name' => 'Hit_signif', 'Data' => $v ? $v->{evalue} : $e } ); $self->element( { 'Name' => 'Hit_score', 'Data' => $v ? $v->{bits} : $bits } ); } $self->start_element( { 'Name' => 'Hsp' } ); $self->element( { 'Name' => 'Hsp_score', 'Data' => $v ? $v->{'z-sc'} : $score } ); $self->element( { 'Name' => 'Hsp_evalue', 'Data' => $v ? $v->{evalue} : $e } ); $self->element( { 'Name' => 'Hsp_evalue2', 'Data' => $v && exists($v->{evalue2}) ? $v->{evalue2} : $e2 } ) if (($v && exists($v->{evalue2})) || defined $e2); $self->element( { 'Name' => 'Hsp_bit-score', 'Data' => $v ? $v->{bits} : $bits } ); $_ = $self->_readline(); if (s/global\/.* score:\s*(\d+)\;?//) { $self->element( { 'Name' => 'Hsp_sw-score', 'Data' => $1 } ); } if (s/Smith-Waterman score:\s*(\d+)\;?//) { $self->element( { 'Name' => 'Hsp_sw-score', 'Data' => $1 } ); } if ( / (\d*\.?\d+)\% \s* identity (?:\s* \(\s*(\S+)\% \s* (?:ungapped|similar) \) )? \s* in \s* (\d+) \s+ (?:aa|nt) \s+ overlap \s* \( (\d+) \- (\d+) : (\d+) \- (\d+) \) /x ) { my ( $identper, $gapper, $len, $querystart, $queryend, $hitstart, $hitend ) = ( $1, $2, $3, $4, $5, $6, $7 ); my $ident = sprintf( "%.0f", ( $identper / 100 ) * $len ); my $positive = sprintf( "%.0f", ( $gapper / 100 ) * $len ); $self->element( { 'Name' => 'Hsp_identity', 'Data' => $ident } ); $self->element( { 'Name' => 'Hsp_positive', 'Data' => $positive } ); $self->element( { 'Name' => 'Hsp_align-len', 'Data' => $len } ); $self->element( { 'Name' => 'Hsp_query-from', 'Data' => $querystart } ); $self->element( { 'Name' => 'Hsp_query-to', 'Data' => $queryend } ); $self->element( { 'Name' => 'Hsp_hit-from', 'Data' => $hitstart } ); $self->element( { 'Name' => 'Hsp_hit-to', 'Data' => $hitend } ); } if ($v) { $self->element( { 'Name' => 'Hsp_querygaps', 'Data' => $v->{qgaps} } ) if exists $v->{qgaps}; $self->element( { 'Name' => 'Hsp_hitgaps', 'Data' => $v->{lgaps} } ) if exists $v->{lgaps}; if ( $self->{'_reporttype'} =~ m/^FAST[NXY]$/o ) { if ( 8 == scalar grep { exists $v->{$_} } qw(an0 ax0 pn0 px0 an1 ax1 pn1 px1) ) { if ( $v->{ax0} < $v->{an0} ) { $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => "-@{[(($v->{px0} - $v->{ax0}) % 3) + 1]}" } ); } else { $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => "+@{[(($v->{an0} - $v->{pn0}) % 3) + 1]}" } ); } if ( $v->{ax1} < $v->{an1} ) { $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => "-@{[(($v->{px1} - $v->{ax1}) % 3) + 1]}" } ); } else { $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => "+@{[(($v->{an1} - $v->{pn1}) % 3) + 1]}" } ); } } else { $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => $v->{lframe} } ); $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => 0 } ); } } else { $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => 0 } ); $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => $v->{lframe} } ); } } else { $self->warn("unable to parse FASTA score line: $_"); } } elsif (/\d+\s*residues\s*in\s*\d+\s*query\s*sequences/) { if ( $self->in_element('hsp') ) { $self->end_element( { 'Name' => 'Hsp' } ); } if ( $self->in_element('hit') ) { $self->end_element( { 'Name' => 'Hit' } ); shift @hit_signifs if @hit_signifs; } # $_ = $self->_readline(); # my ( $liblen,$libsize) = /(\d+)\s+residues\s*in(\d+)\s*library/; # fast forward to the end of the file as there is # nothing else left to do with this file and want to be sure and # reset it while ( defined( $_ = $self->_readline() ) ) { last if (/^Function used was/); if ( /(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)? sequence/oxi || /(\S+)\s+compares\s+a/oi ) { $self->_pushback($_); } } $self->_processHits(@hit_signifs) if @hit_signifs; $self->end_element( { 'Name' => 'FastaOutput' } ); return $self->end_document(); } elsif (/^\s*\d+\s*>>>/) { if ( $self->within_element('FastaOutput') ) { if ( $self->in_element('hsp') ) { $self->end_element( { 'Name' => 'Hsp' } ); } if ( $self->in_element('hit') ) { $self->end_element( { 'Name' => 'Hit' } ); shift @hit_signifs if @hit_signifs; } $self->_processHits(@hit_signifs) if (@hit_signifs); $self->end_element( { 'Name' => 'FastaOutput' } ); $self->_pushback($_); return $self->end_document(); } else { $self->start_element( { 'Name' => 'FastaOutput' } ); $self->{'_result_count'}++; $seentop = 1; $self->element( { 'Name' => 'FastaOutput_program', 'Data' => $self->{'_reporttype'} } ); $self->element( { 'Name' => 'FastaOutput_version', 'Data' => $self->{'_version'} } ); my ( $type, $querylen, $querytype, $querydef ); if (/^\s*\d+\s*>>>(.*)/) { $querydef = $1; if ( $querydef =~ /^(.*?)\s+(?:\-\s+)?(\d+)\s+(aa|nt).*$/o ) { ( $querydef, $querylen, $querytype ) = ( $1, $2, $3 ); } } if ( $self->{'_reporttype'} && $self->{'_reporttype'} eq 'FASTA' ) { if ( $querytype eq 'nt' ) { $self->{'_reporttype'} = 'FASTN'; } elsif ( $querytype eq 'aa' ) { $self->{'_reporttype'} = 'FASTP'; } } my ( $name, $descr ) = ( $querydef =~ m/^(\S+)(?:\s+(.*))?\s*$/o ); $self->element( { 'Name' => 'FastaOutput_query-def', 'Data' => $name } ); $self->element( { 'Name' => 'FastaOutput_querydesc', 'Data' => $descr } ); if ($querylen) { $self->element( { 'Name' => 'FastaOutput_query-len', 'Data' => $querylen } ); } else { $self->warn("unable to find and set query length"); } if ( defined( $_ = $self->_readline() ) && ( /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)/ ) ) { $self->element( { 'Name' => 'FastaOutput_db', 'Data' => $1 } ); } } } elsif ( $self->in_element('hsp') ) { my @data = ( [], [], [] ); my $count = 0; my $len = $self->idlength + 1; my ($seq1_id); while ( defined($_) ) { chomp; #$self->debug("$count $_\n"); if (/residues in \d+\s+query\s+sequences/o) { $self->_pushback($_); last; } elsif (/^>>>(\*\*\*|\/\/\/|<<<)/o) { $self->end_element( { Name => "Hsp" } ); last; } elsif (/^>>/o) { $self->_pushback($_); last; } elsif (/^\s*\d+\s*>>>/o) { $self->_pushback($_); last; } if ( $count == 0 ) { if (/^(\S+)\s+/) { $self->_pushback($_); $count = 2; } elsif ( /^\s+\d+/ || /^\s+$/ ) { # do nothing, this is really a 0 line } elsif ( length($_) == 0 ) { $count = -1; } else { $self->_pushback($_); $count = 0; } } elsif ( $count == 1 || $count == 3 ) { if (/^(\S+)\s+/) { $len = CORE::length($1) if $len < CORE::length($1); s/\s+$//; # trim trailing spaces,we don't want them push @{ $data[ $count - 1 ] }, substr( $_, $len ); } elsif (/^\s+(\d+)/) { $count = -1; $self->_pushback($_); } elsif ( /^\s+$/ || length($_) == 0 ) { $count = 5; # going to skip these } elsif ( /\s+\S+fasta3\d\s+/) { # this is something that looks like a path but contains # the fasta3x executable string, such as: # /usr/local/fasta3/bin/fasta35 -n -U -Q -H -A -E 2.0 -C 19 -m 0 -m 9i test.fa ../other_mirs.fa -O test.fasta35 last; } else { $self->throw( "Unrecognized alignment line ($count) '$_'"); } } elsif ( $count == 2 ) { if (/^\s+\d+\s+/) { $self->warn("$_\n") if $self->verbose > 0; # we are on a Subject part of the alignment # but we THOUGHT we were on the Query # move that last line to the proper place push @{ $data[2] }, pop @{ $data[0] }; $count = 4; } else { # toss the first IDLENGTH characters of the line if ( length($_) >= $len ) { push @{ $data[ $count - 1 ] }, substr( $_, $len ); } } } last if ( $count++ >= 5 ); $_ = $self->_readline(); } if ( @{ $data[0] } || @{ $data[2] } ) { $self->characters( { 'Name' => 'Hsp_qseq', 'Data' => join( '', @{ $data[0] } ) } ); $self->characters( { 'Name' => 'Hsp_midline', 'Data' => join( '', @{ $data[1] } ) } ); $self->characters( { 'Name' => 'Hsp_hseq', 'Data' => join( '', @{ $data[2] } ) } ); } } else { if ( !$seentop ) { $self->debug($_); #$self->warn("unrecognized FASTA Family report file!"); #return; } } } if ( $self->in_element('result') ) { if ( $self->in_element('hsp') ) { $self->end_element( { 'Name' => 'Hsp' } ); } if ( $self->in_element('hit') ) { $self->end_element( { 'Name' => 'Hit' } ); shift @hit_signifs if @hit_signifs; } $self->end_element( { 'Name' => 'FastaOutput' } ); } return $self->end_document(); } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element { my ( $self, $data ) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; if ( my $type = $MODEMAP{$nm} ) { $self->_mode($type); if ( my $handler = $self->_will_handle($type) ) { my $func = sprintf( "start_%s", lc $type ); $handler->$func( $data->{'Attributes'} ); } unshift @{ $self->{'_elements'} }, $type; } if ( $nm eq 'FastaOutput' ) { $self->{'_values'} = {}; $self->{'_result'} = undef; $self->{'_mode'} = ''; } } =head2 end_element Title : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub end_element { my ( $self, $data ) = @_; my $nm = $data->{'Name'}; my $rc; # Hsp are sort of weird, in that they end when another # object begins so have to detect this in end_element for now if ( $nm eq 'Hsp' ) { foreach (qw(Hsp_qseq Hsp_midline Hsp_hseq)) { $self->element( { 'Name' => $_, 'Data' => $self->{'_last_hspdata'}->{$_} } ); } $self->{'_last_hspdata'} = {}; } if ( my $type = $MODEMAP{$nm} ) { if ( my $handler = $self->_will_handle($type) ) { my $func = sprintf( "end_%s", lc $type ); $rc = $handler->$func( $self->{'_reporttype'}, $self->{'_values'} ); } shift @{ $self->{'_elements'} }; } elsif ( $MAPPING{$nm} ) { if ( ref( $MAPPING{$nm} ) =~ /hash/i ) { my $key = ( keys %{ $MAPPING{$nm} } )[0]; $self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } = $self->{'_last_data'}; } else { $self->{'_values'}->{ $MAPPING{$nm} } = $self->{'_last_data'}; } } else { $self->warn("unknown nm $nm, ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if ( $nm eq 'FastaOutput' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element { my ( $self, $data ) = @_; $self->start_element($data); $self->characters($data); $self->end_element($data); } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters { my ( $self, $data ) = @_; return unless ( defined $data->{'Data'} ); if ( $data->{'Data'} =~ /^\s+$/ ) { return unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/; } if ( $self->in_element('hsp') && $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) { $self->{'_last_hspdata'}->{ $data->{'Name'} } .= $data->{'Data'}; } $self->{'_last_data'} = $data->{'Data'}; } =head2 _mode Title : _mode Usage : $obj->_mode($newval) Function: Example : Returns : value of _mode Args : newvalue (optional) =cut sub _mode { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_mode'} = $value; } return $self->{'_mode'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub within_element { my ( $self, $name ) = @_; return 0 if (!defined $name && !defined $self->{'_elements'} || scalar @{ $self->{'_elements'} } == 0 ); foreach ( @{ $self->{'_elements'} } ) { if ( $_ eq $name || $_ eq $MODEMAP{$name} ) { return 1; } } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub in_element { my ( $self, $name ) = @_; return 0 if !defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name || ( exists $MODEMAP{$name} && $self->{'_elements'}->[0] eq $MODEMAP{$name} ) ); } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handles a start document event Returns : none Args : none =cut sub start_document { my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'} = undef; $self->{'_mode'} = ''; $self->{'_elements'} = []; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document { my ( $self, @args ) = @_; return $self->{'_result'}; } =head2 idlength Title : idlength Usage : $obj->idlength($newval) Function: Internal storage of the length of the ID desc in the HSP alignment blocks. Defaults to $IDLENGTH class variable value Returns : value of idlength Args : newvalue (optional) =cut sub idlength { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_idlength'} = $value; } return $self->{'_idlength'} || $IDLENGTH; } =head2 result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } sub attach_EventHandler { my ( $self, $handler ) = @_; $self->SUPER::attach_EventHandler($handler); # Optimization: caching the EventHandler since it is used a lot # during the parse. $self->{'_handler_cache'} = $handler; return; } =head2 _will_handle Title : _will_handle Usage : Private method. For internal use only. if( $self->_will_handle($type) ) { ... } Function: Provides an optimized way to check whether or not an element of a given type is to be handled. Returns : Reference to EventHandler object if the element type is to be handled. undef if the element type is not to be handled. Args : string containing type of element. Optimizations: =over 2 =item 1 Using the cached pointer to the EventHandler to minimize repeated lookups. =item 2 Caching the will_handle status for each type that is encountered so that it only need be checked by calling handler-Ewill_handle($type) once. =back This does not lead to a major savings by itself (only 5-10%). In combination with other optimizations, or for large parse jobs, the savings good be significant. To test against the unoptimized version, remove the parentheses from around the third term in the ternary " ? : " operator and add two calls to $self-E_eventHandler(). =cut sub _will_handle { my ( $self, $type ) = @_; my $handler = $self->{'_handler_cache'}; my $will_handle = defined( $self->{'_will_handle_cache'}->{$type} ) ? $self->{'_will_handle_cache'}->{$type} : ( $self->{'_will_handle_cache'}->{$type} = $handler->will_handle($type) ); return $will_handle ? $handler : undef; } =head2 _processHits Title : _processHits Usage : Private method. For internal use only. Function: Process/report any hits/hsps we saw in the top table, not in alignments. Returns : nothing. Args : array of hits to process. =cut sub _processHits { my ($self, @hit_signifs) = @_; # process remaining best hits for my $hit (@hit_signifs) { # Hsp_score Hsp_evalue Hsp_bit-score # Hsp_sw-score Hsp_gaps Hsp_identity Hsp_positive # Hsp_align-len Hsp_query-from Hsp_query-to # Hsp_hit-from Hsp_hit-to Hsp_qseq Hsp_midline $self->start_element( { 'Name' => 'Hit' } ); $self->element( { 'Name' => 'Hit_len', 'Data' => $hit->{hit_len} } ) if exists $hit->{hit_len}; $self->element( { 'Name' => 'Hit_id', 'Data' => $hit->{id} } ) if exists $hit->{id}; $self->element( { 'Name' => 'Hit_accession', 'Data' => $hit->{acc} } ) if exists $hit->{acc}; $self->element( { 'Name' => 'Hit_def', 'Data' => $hit->{desc} } ) if exists $hit->{desc}; $self->element( { 'Name' => 'Hit_signif', 'Data' => $hit->{evalue} } ) if exists $hit->{evalue}; $self->element( { 'Name' => 'Hit_score', 'Data' => $hit->{bits} } ) if exists $hit->{bits}; for my $hsp (@{$hit->{HSPs}}) { $self->start_element( { 'Name' => 'Hsp' } ); $self->element({'Name' => 'Hsp_score', 'Data' => $hsp->{'z-sc'}}) if exists $hsp->{'z-sc'}; $self->element({'Name' => 'Hsp_evalue', 'Data' => $hsp->{evalue} } ) if exists $hsp->{evalue}; $self->element({'Name' => 'Hsp_evalue2', 'Data' => $hsp->{evalue2} } ) if exists $hsp->{evalue2}; $self->element({'Name' => 'Hsp_bit-score', 'Data' => $hsp->{bits} } ) if exists $hsp->{bits}; $self->element({'Name' => 'Hsp_sw-score', 'Data' => $hsp->{'n-w'} } ) if exists $hsp->{'n-w'}; $self->element({'Name' => 'Hsp_sw-score', 'Data' => $hsp->{sw} } ) if exists $hsp->{sw}; $self->element({'Name' => 'Hsp_gaps', 'Data' => $hsp->{'%_gid'} } ) if exists $hsp->{'%_gid'}; $self->element({ 'Name' => 'Hsp_identity', 'Data' => sprintf( "%.0f", $hsp->{'%_id'} * $hsp->{alen} ) }) if ( exists $hsp->{'%_id'} && exists $hsp->{alen} ); if ( exists $hsp->{'%_gid'} ) { $self->element( { 'Name' => 'Hsp_positive', 'Data' => sprintf( "%.0f", $hsp->{'%_gid'} * $hsp->{alen} ) } ) if exists $hsp->{'%_gid'} && exists $hsp->{alen}; } else { $self->element( { 'Name' => 'Hsp_positive', 'Data' => sprintf( "%.0f", $hsp->{'%_id'} * $hsp->{alen} ) } ) if ( exists $hsp->{'%_id'} && exists $hsp->{alen} ); } $self->element( { 'Name' => 'Hsp_align-len', 'Data' => $hsp->{alen} } ) if exists $hsp->{alen}; $self->element( { 'Name' => 'Hsp_query-from', 'Data' => $hsp->{an0} } ) if exists $hsp->{an0}; $self->element( { 'Name' => 'Hsp_query-to', 'Data' => $hsp->{ax0} } ) if exists $hsp->{ax0}; $self->element( { 'Name' => 'Hsp_hit-from', 'Data' => $hsp->{an1} } ) if exists $hsp->{an1}; $self->element( { 'Name' => 'Hsp_hit-to', 'Data' => $hsp->{ax1} } ) if exists $hsp->{ax1}; $self->element( { 'Name' => 'Hsp_querygaps', 'Data' => $hsp->{qgaps} } ) if exists $hsp->{qgaps}; $self->element( { 'Name' => 'Hsp_hitgaps', 'Data' => $hsp->{lgaps} } ) if exists $hsp->{lgaps}; if ( $self->{'_reporttype'} =~ m/^FAST[NXY]$/o ) { if ( 8 == scalar grep { exists $hsp->{$_} } qw(an0 ax0 pn0 px0 an1 ax1 pn1 px1) ) { if ( $hsp->{ax0} < $hsp->{an0} ) { $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => "-@{[(($hsp->{px0} - $hsp->{ax0}) % 3) + 1]}" } ); } else { $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => "+@{[(($hsp->{an0} - $hsp->{pn0}) % 3) + 1]}" } ); } if ( $hsp->{ax1} < $hsp->{an1} ) { $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => "-@{[(($hsp->{px1} - $hsp->{ax1}) % 3) + 1]}" } ); } else { $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => "+@{[(($hsp->{an1} - $hsp->{pn1}) % 3) + 1]}" } ); } } else { $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => $hsp->{lframe} } ); $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => 0 } ); } } else { $self->element( { 'Name' => 'Hsp_query-frame', 'Data' => 0 } ); $self->element( { 'Name' => 'Hsp_hit-frame', 'Data' => $hsp->{lframe} } ); } $self->end_element( { 'Name' => 'Hsp' } ); } $self->end_element( { 'Name' => 'Hit' } ); } } 1; BioPerl-1.007002/Bio/SearchIO/gmap_f9.pm000444000766000024 2772313155576320 17574 0ustar00cjfieldsstaff000000000000# $Id: gmap_f9.pm 15987 2009-08-18 21:08:55Z lstein $ # # BioPerl module for Bio::SearchIO::gmap_f9 # # Cared for by George Hartzell # # Copyright George Hartzell # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::gmap_f9 - Event generator for parsing gmap reports (Z format) =head1 SYNOPSIS # Do not use this object directly - it is used as part of the # Bio::SearchIO system. use Bio::SearchIO; my $searchio = Bio::SearchIO->new(-format => 'gmap', -file => 't/data/her2.gmapz'); while( my $result = $searchio->next_result ) { while( my $hit = $result->next_hit ) { while( my $hsp = $hit->next_hsp ) { # ... } } } =head1 DESCRIPTION This object encapsulated the necessary methods for generating events suitable for building Bio::Search objects from a GMAP "compressed" report (from gmap run with -Z flag) Read the L for more information about how to use this. =head2 REVERSE STRAND AND BIOPERL COORDINATES I believe that I'm doing the correct thing when reporting hits on the negative strand of the genome. In particular, I've compared the "exons" this code generates with the set returned by ncbi's megablast web service. NCBI's hsp's are ordered differently and have a different genomic location (off by ~18,000,000 bases, padding?) but the starts, ends, and lengths were similar and my strand handling matches theirs. E.g. CDNA GENOME start end strand start end strand blast 1913 2989 1 86236731 86237808 -1 1 475 1 86260509 86260983 -1 1510 1727 1 86240259 86240476 -1 841 989 1 86243034 86243182 -1 1381 1514 1 86240630 86240763 -1 989 1122 1 86242457 86242590 -1 599 729 1 86247470 86247600 -1 473 608 1 86259972 86260107 -1 1255 1382 1 86240837 86240964 -1 730 842 1 86244040 86244152 -1 1813 1921 1 86238123 86238231 -1 1725 1814 1 86239747 86239836 -1 1167 1256 1 86241294 86241383 -1 1120 1188 1 86242319 86242387 -1 gmap 1 475 1 104330509 104330983 -1 476 600 1 104329980 104330104 -1 601 729 1 104317470 104317598 -1 730 841 1 104314041 104314152 -1 842 989 1 104313034 104313181 -1 990 1121 1 104312458 104312589 -1 1122 1187 1 104312320 104312385 -1 1188 1256 1 104311294 104311362 -1 1257 1382 1 104310837 104310962 -1 1383 1511 1 104310633 104310761 -1 1512 1726 1 104310260 104310474 -1 1727 1814 1 104309747 104309834 -1 1815 1917 1 104308127 104308229 -1 1918 2989 1 104306731 104307802 -1 =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - George Hartzell Email hartzell@alerce.com =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with an underscore (_). =cut # Let the code begin... package Bio::SearchIO::gmap_f9; use strict; use warnings; use Bio::Search::Hit::GenericHit; use Bio::Search::HSP::GenericHSP; use base qw(Bio::SearchIO ); use Data::Dumper; =head2 next_result Title : next_result Usage : $result = stream->next_result Function: Reads the next ResultI object from the stream and returns it. Returns : A Bio::Search::Result::ResultI object Args : n/a =cut sub next_result { my $self = shift; my $info = []; my $result; my $hit; my @hsp_info; my $previous_hit_pos; while ( $_ = $self->_readline ) { if ( $_ =~ /^>/ ) { # looking at the start of a result if ($result) { # and done if there's one in progress $self->_pushback($_); goto DONE; } else { # otherwise start a new one. my ($id, $desc, $md5) = m|>([^ ]*)\s*(.*)\s*(?:md5:(.*))?|; $result = Bio::Search::Result::GenericResult->new(); $result->algorithm('gmap'); $result->query_name($id); $result->query_accession($id); $result->query_description($desc); #$self->warn("Take care of MD5!\n"); $hit ||= Bio::Search::Hit::GenericHit->new( -name => "NONE_SPECIFIED"); } } else { # add another position to the hit/hsp # 468 H 1956 C -14:104307764 2298317517 C H # 468 1957 A -14:104307763 2298317516 A my $c; # info about a column ($c->{query_aa_pos}, $c->{query_aa}, $c->{query_pos}, $c->{query_base}, $c->{hit_strand}, $c->{hit_chromo}, $c->{hit_pos}, $c->{hit_concat_pos}, $c->{hit_base}, $c->{hit_aa}) = ($_ =~ m| (\d+)[ ]?(.)?[\t] (\d+)[ ]?(.)?[\t] # TODO chromosome isn't a number... X, Y, MT.... (\+\|\-)([\dxXyY]+\|MT):(\d+)[ ](\d+)[ ](.) [\t]?(.)? |xo ); if ($previous_hit_pos && (abs($c->{hit_pos} - $previous_hit_pos) > 1)) { $hit ||= Bio::Search::Hit::GenericHit->new( -name => "NONE_SPECIFIED", ); $hit->add_hsp( $self->_hsp_from_info(\@hsp_info) ); @hsp_info = (); } push @hsp_info, $c; $previous_hit_pos = $c->{hit_pos}; } } DONE: if ($result) { $hit->add_hsp( $self->_hsp_from_info(\@hsp_info) ) if (@hsp_info); my ($hit_length,$query_length); for my $hsp ($hit->hsps) { $hit_length += $hsp->length(); $query_length += $hsp->length('query'); } $hit->length($hit_length); $hit->query_length($query_length); # update this now that we actually know something useful.q $hit->name($hsp_info[0]->{hit_chromo}); $result->add_hit($hit) if ($hit); } return($result); } sub _hsp_from_info { my $self = shift; my $info = shift; my $a = {}; # args w/ which we'll create hsp my $hsp; my $identical; $a->{-algorithm} = 'GMAP'; for my $c (@{$info}) { $a->{-query_seq} .= $c->{query_base}; $a->{-hit_seq} .= $c->{hit_base}; $a->{-homology_seq} .= $c->{query_base} eq $c->{hit_base} ? $c->{hit_base} : ' '; $identical++ if ( $c->{query_base} eq $c->{hit_base} ); } $a->{-query_seq} =~ s| |\-|g; # switch to bioperl gaps. $a->{-hit_seq} =~ s| |\-|g; $a->{-conserved} = $a->{-identical} = $identical; # use the coordinates from from gmap's -f 9 output to # determine whether gmap revcomped the query sequence # to generate the alignment. Note that this is not # the same as the cDNA's sense/anti-sense-ness. $a->{-stranded} = 'both'; $a->{-query_start} = $info->[0]->{query_pos}; $a->{-query_end} = $info->[-1]->{query_pos}; $a->{-query_length} = $a->{-query_end} - $a->{-query_start} + 1; # hit can be either strand, -f 9 output tells us which. # we don't have to worry about it here, but telling the generichsp code # that this hit is 'stranded', it compares the start and end positions # sets it for us. $a->{-hit_start} = $info->[0]->{hit_pos}; $a->{-hit_end} = $info->[-1]->{hit_pos}; $a->{-hit_length} = abs($a->{-hit_end} - $a->{-hit_start}) + 1; $a->{-hsp_length} = $a->{-query_length} > $a->{-hit_length} ? $a->{-query_length} : $a->{-hit_length}; $hsp = Bio::Search::HSP::GenericHSP->new( %$a ); return $hsp; } # TODO (adjust regexp to swallow lines w/out md5 sig's. sub _parse_path_header { my $self = shift; my $path_line = shift; my $path = {}; ( $path->{query}, $path->{db}, $path->{path_num}, $path->{path_total_num}, $path->{query_length}, $path->{exon_count}, $path->{trimmed_coverage}, $path->{percent_identity}, $path->{query_start}, $path->{query_end}, $path->{whole_genome_start}, $path->{whole_genome_end}, $path->{chromosome}, $path->{chromo_start}, $path->{chromo_end}, $path->{strand}, $path->{sense}, $path->{md5}, ) = ($_ =~ qr| > ([^ ]*)[ ] # the query id}, followed by a space ([^ ]*)[ ] # the genome database, followed by a space (\d+)/(\d+)[ ] # path_num/path_total_num (e.g. 3/12) (\d+)[ ] # query length, followed by a space (\d+)[ ] # hsp/exon count, followed by a space (\d+\.\d*)[ ] # trimmed coverage (\d+\.\d*)[ ] # percent identity (\d+)\.\.(\d+)[ ] # query start .. query end, followed by space (\d+)\.\.(\d+)[ ] # whole genome s..e, followed by space (\d+): # chromosome number (\d+)\.\.(\d+)[ ] # chromo s..e, followed by a space ([+-])[ ] # strand, followed by a space dir:(.*) # dir:sense or dir:antisense [ ]md5:([\dabcdefg]+) # md5 signature |x ); $path->{query} or $self->throw("query was not found in path line."); $path->{db} or $self->throw("db was not found in path line."); $path->{path_num} or $self->throw("path_num was not found in path line."); $path->{path_total_num} or $self->throw("path_total_num was not found in path line."); $path->{query_length} or $self->throw("query_length was not found in path line."); $path->{exon_count} or $self->throw("exon_count was not found in path line."); $path->{trimmed_coverage} or $self->throw("trimmed_coverage was not found in path line."); $path->{percent_identity} or $self->throw("percent_identity was not found in path line."); $path->{query_start} or $self->throw("query_start was not found in path line."); $path->{query_end} or $self->throw("query_end was not found in path line."); $path->{whole_genome_start} or $self->throw("whole_genome_start was not found in path line."); $path->{whole_genome_end} or $self->throw("whole_genome_end was not found in path line."); $path->{chromosome} or $self->throw("chromosome was not found in path line."); $path->{chromo_start} or $self->throw("chromo_start was not found in path line."); $path->{chromo_end} or $self->throw("chromo_end was not found in path line."); $path->{strand} or $self->throw("strand was not found in path line."); $path->{sense} or $self->throw("sense was not found in path line."); return $path; } sub _parse_alignment_line { my $self = shift; my $a_line = shift; my $align = {}; ( $align->{chromo_start}, $align->{chromo_end}, $align->{query_start}, $align->{query_end}, $align->{percent_identity}, $align->{align_length}, $align->{intron_length}, ) = ($_ =~ qr| [\t] ([\d]+)[ ] # start in chromosome coord. ([\d]+)[ ] # end in chromosome coord. ([\d]+)[ ] # start in query coord. ([\d]+)[ ] # end in query coord. ([\d]+) # percent identity (as integer) [\t].*[\t] # skip the edit script ([\d]+) # length of alignment block. [\t]*([\d]+)* # length of following intron. |x ); $align->{chromo_start} or $self->throw("chromo_start missing in alignment line."); $align->{chromo_end}, or $self->throw("chromo_end was missing in alignment line."); $align->{query_start}, or $self->throw("query_start was missing in alignment line."); $align->{query_end}, or $self->throw("query_end was missing in alignment line."); $align->{percent_identity}, or $self->throw("percent_identity was missing in alignment line."); $align->{align_length}, or $self->throw("align_length was missing in alignment line."); return $align; } 1; BioPerl-1.007002/Bio/SearchIO/hmmer.pm000444000766000024 1002713155576320 17347 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::hmmer # # Please direct questions and support issues to # # Cared for by Kai Blin # # Copyright Kai Blin # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::hmmer - A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) =head1 SYNOPSIS # do not use this class directly it is available through Bio::SearchIO use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer', -file => 't/data/L77119.hmmer'); while( my $result = $in->next_result ) { # this is a Bio::Search::Result::HMMERResult object print $result->query_name(), " for HMM ", $result->hmm_name(), "\n"; while( my $hit = $result->next_hit ) { print $hit->name(), "\n"; while( my $hsp = $hit->next_hsp ) { print "length is ", $hsp->length(), "\n"; } } } =head1 DESCRIPTION This object implements a parser for HMMER output. It works with both HMMER2 and HMMER3 =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Kai Blin Email kai.blin-at-biotech.uni-tuebingen.de =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::hmmer; use strict; use Bio::Factory::ObjectFactory; use base qw(Bio::SearchIO); sub new { my ( $caller, @args ) = @_; my $class = ref($caller) || $caller; my $self = $class->SUPER::new(@args); $self->_initialize(@args); # Try to guess the hmmer format version if it's not specified. my $version; my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys # If the caller specified a version, go for that if (defined($param{"-version"})) { $version = $param{"-version"}; } else { # read second line of the file my $first_line = $self->_readline; $_ = $self->_readline; if ( m/HMMER\s3/ ) { $version = "3"; } else { $version = "2"; } $self->_pushback($_); $self->_pushback($first_line); } my $format = "hmmer$version"; return unless( $class->_load_format_module($format) ); bless($self, "Bio::SearchIO::$format"); return $self; } sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); my $handler = $self->_eventHandler; $handler->register_factory( 'result', Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Result::HMMERResult', -interface => 'Bio::Search::Result::ResultI' ) ); $handler->register_factory( 'hit', Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Hit::HMMERHit', -interface => 'Bio::Search::Hit::HitI' ) ); $handler->register_factory( 'hsp', Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::HSP::HMMERHSP', -interface => 'Bio::Search::HSP::HSPI' ) ); } 1; BioPerl-1.007002/Bio/SearchIO/hmmer2.pm000444000766000024 12017213155576320 17454 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::hmmer2 # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::hmmer2 - A parser for HMMER output (hmmpfam, hmmsearch) =head1 SYNOPSIS # do not use this class directly it is available through Bio::SearchIO use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer2', -file => 't/data/L77119.hmmer'); while( my $result = $in->next_result ) { # this is a Bio::Search::Result::HMMERResult object print $result->query_name(), " for HMM ", $result->hmm_name(), "\n"; while( my $hit = $result->next_hit ) { print $hit->name(), "\n"; while( my $hsp = $hit->next_hsp ) { print "length is ", $hsp->length(), "\n"; } } } =head1 DESCRIPTION This object implements a parser for HMMER output. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::hmmer2; use strict; use Bio::Factory::ObjectFactory; use vars qw(%MAPPING %MODEMAP ); use base qw(Bio::SearchIO::hmmer); BEGIN { # mapping of HMMER items to Bioperl hash keys %MODEMAP = ( 'HMMER_Output' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); %MAPPING = ( 'Hsp_bit-score' => 'HSP-bits', 'Hsp_score' => 'HSP-score', 'Hsp_evalue' => 'HSP-evalue', 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_positive' => 'HSP-conserved', 'Hsp_identity' => 'HSP-identical', 'Hsp_gaps' => 'HSP-hsp_gaps', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_csline' => 'HSP-cs_seq', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_midline' => 'HSP-homology_seq', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_query-frame' => 'HSP-query_frame', 'Hsp_hit-frame' => 'HSP-hit_frame', 'Hit_id' => 'HIT-name', 'Hit_len' => 'HIT-length', 'Hit_accession' => 'HIT-accession', 'Hit_desc' => 'HIT-description', 'Hit_signif' => 'HIT-significance', 'Hit_score' => 'HIT-score', 'HMMER_program' => 'RESULT-algorithm_name', 'HMMER_version' => 'RESULT-algorithm_version', 'HMMER_query-def' => 'RESULT-query_name', 'HMMER_query-len' => 'RESULT-query_length', 'HMMER_query-acc' => 'RESULT-query_accession', 'HMMER_querydesc' => 'RESULT-query_description', 'HMMER_hmm' => 'RESULT-hmm_name', 'HMMER_seqfile' => 'RESULT-sequence_file', 'HMMER_db' => 'RESULT-database_name', ); } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result { my ($self) = @_; my $seentop = 0; my $reporttype; my ( $buffer, $last, @hitinfo, @hspinfo, %hspinfo, %hitinfo ); local $/ = "\n"; my $verbose = $self->verbose; # cache for speed? $self->start_document(); while ( defined( $buffer = $self->_readline ) ) { my $lineorig = $buffer; chomp $buffer; if ($buffer =~ /^HMMER\s+(\S+)\s+\((.+)\)/o) { my ( $prog, $version ) = split( /\s+/, $buffer ); if ($seentop) { $self->_pushback($buffer); $self->end_element( { 'Name' => 'HMMER_Output' } ); return $self->end_document(); } $self->{'_hmmidline'} = $buffer; $self->start_element( { 'Name' => 'HMMER_Output' } ); $self->{'_result_count'}++; $seentop = 1; if ( defined $last ) { ($reporttype) = split( /\s+/, $last ); $reporttype = uc($reporttype) if defined $reporttype; $self->element( { 'Name' => 'HMMER_program', 'Data' => $reporttype } ); } $self->element( { 'Name' => 'HMMER_version', 'Data' => $version } ); } elsif ($buffer =~ s/^HMM file:\s+//o) { $self->{'_hmmfileline'} = $lineorig; $self->element( { 'Name' => 'HMMER_hmm', 'Data' => $buffer } ); } elsif ($buffer =~ s/^Sequence\s+(file|database):\s+//o) { $self->{'_hmmseqline'} = $lineorig; if ( $1 eq 'database' ) { $self->element( { 'Name' => 'HMMER_db', 'Data' => $buffer } ); } $self->element( { 'Name' => 'HMMER_seqfile', 'Data' => $buffer } ); } elsif ($buffer =~ s/^Query(?:\s+(?:sequence|HMM))?(?:\s+\d+)?:\s+//o) { if ( !$seentop ) { # we're in a multi-query report $self->_pushback($lineorig); $self->_pushback( $self->{'_hmmseqline'} ); $self->_pushback( $self->{'_hmmfileline'} ); $self->_pushback( $self->{'_hmmidline'} ); next; } $buffer =~ s/\s+$//; $self->element( { 'Name' => 'HMMER_query-def', 'Data' => $buffer } ); } elsif ($buffer =~ s/^Accession:\s+//o) { $buffer =~ s/\s+$//; $self->element( { 'Name' => 'HMMER_query-acc', 'Data' => $buffer } ); } elsif ($buffer =~ s/^Description:\s+//o) { $buffer =~ s/\s+$//; $self->element( { 'Name' => 'HMMER_querydesc', 'Data' => $buffer } ); } elsif ( defined $self->{'_reporttype'} && ( $self->{'_reporttype'} eq 'HMMSEARCH' || $self->{'_reporttype'} eq 'HMMPFAM' ) ) { # PROCESS RESULTS HERE if ($buffer =~ /^Scores for (?:complete sequences|sequence family)/o) { while ( defined( $buffer = $self->_readline ) ) { last if ($buffer =~ /^\s+$/); next if ( $buffer =~ /^Model\s+Description/o || $buffer =~ /^Sequence\s+Description/o || $buffer =~ /^\-\-\-/o ); chomp $buffer; my @line = split( /\s+/, $buffer ); my ( $name, $domaintotal, $evalue, $score ) = ( shift @line, pop @line, pop @line, pop @line ); my $desc = join( ' ', @line ); push @hitinfo, [ $name, $desc, $score, $evalue, $domaintotal ]; $hitinfo{$name} = $#hitinfo; } } elsif ($buffer =~ /^Parsed for domains:/o) { @hspinfo = (); while ( defined( $buffer = $self->_readline ) ) { last if ($buffer =~ /^\s+$/); if ($buffer =~ m!^//!) { $self->_pushback($buffer); last; } next if ( $buffer =~ /^(?:Model|Sequence)\s+Domain/ || $buffer =~ /^\-\-\-/ ); chomp $buffer; if ( my ( $name, $domainct, $domaintotal, $seq_start, $seq_end, $seq_cov, $hmm_start, $hmm_end, $hmm_cov, $score, $evalue ) = ( $buffer =~ m!^(\S+)\s+ # domain name (\d+)/(\d+)\s+ # domain num out of num (\d+)\s+(\d+)\s+ # seq start, end (\S+)\s+ # seq coverage (\d+)\s+(\d+)\s+ # hmm start, end (\S+)\s+ # hmm coverage (\S+)\s+ # score (\S+) # evalue \s*$!ox ) ) { my $hindex = $hitinfo{$name}; if ( !defined $hindex ) { push @hitinfo, [ $name, '', $score, $evalue, $domaintotal ]; $hitinfo{$name} = $#hitinfo; $hindex = $#hitinfo; } my $info = $hitinfo[$hindex]; if ( !defined $info ) { if ($self->{'_reporttype'} eq 'HMMSEARCH') { $self->warn( "Incomplete Sequence information, can't find $name hitinfo says $hitinfo{$name}" ); } elsif ($self->{'_reporttype'} eq 'HMMPFAM') { $self->warn( "Incomplete Domain information, can't find $name hitinfo says $hitinfo{$name}" ); } next; } # Try to get HMM and Sequence lengths from the alignment information if ($self->{'_reporttype'} eq 'HMMSEARCH') { # For Hmmsearch, if seq coverage ends in ']' it means that the alignment # runs until the end. In that case add the END coordinate to @hitinfo # to use it as Hit Length if ( $seq_cov =~ m/\]$/ and scalar @{ $hitinfo[$hindex] } == 5 ) { push @{ $hitinfo[$hindex] }, $seq_end ; } # For Hmmsearch, if hmm coverage ends in ']', it means that the alignment # runs until the end. In that case use the END coordinate as Query Length if ( $hmm_cov =~ m/\]$/ and not exists $self->{_values}->{'RESULT-query_length'} ) { $self->element( { 'Name' => 'HMMER_query-len', 'Data' => $hmm_end } ); } } elsif ($self->{'_reporttype'} eq 'HMMPFAM') { # For Hmmpfam, if hmm coverage ends in ']' it means that the alignment # runs until the end. In that case add the END coordinate to @hitinfo # to use it as Hit Length if ( $hmm_cov =~ m/\]$/ and scalar @{ $hitinfo[$hindex] } == 5 ) { push @{ $hitinfo[$hindex] }, $hmm_end ; } # For Hmmpfam, if seq coverage ends in ']', it means that the alignment # runs until the end. In that case use the END coordinate as Query Length if ( $seq_cov =~ m/\]$/ and not exists $self->{_values}->{'RESULT-query_length'} ) { $self->element( { 'Name' => 'HMMER_query-len', 'Data' => $seq_end } ); } } my @vals = ($seq_start, $seq_end, $hmm_start, $hmm_end, $score, $evalue); push @hspinfo, [ $name, @vals ]; } } } elsif ($buffer =~ /^Alignments of top/o) { my ( $prelength, $count, $width ); $count = 0; my %domaincounter; my $second_tier = 0; my $csline = ''; while ( defined( $buffer = $self->_readline ) ) { next if ( $buffer =~ /^Align/o ); if ( $buffer =~ m/^Histogram/o || $buffer =~ m!^//!o || $buffer =~ m/^Query(?:\s+(?:sequence|HMM))?(?:\s+\d+)?:/o ) { if ( $self->in_element('hsp') ) { $self->end_element( { 'Name' => 'Hsp' } ); } if ( $self->within_element('hit') ) { $self->end_element( { 'Name' => 'Hit' } ); } $self->_pushback($buffer); last; } chomp $buffer; if ( my ( $name, $domainct, $domaintotal, $from, $to ) = ( $buffer =~ m/^\s*(.+): \s+ domain \s+ (\d+) \s+ of \s+ (\d+) , \s+ from \s+ (\d+) \s+ to \s+ (\d+)/x ) ) { $domaincounter{$name}++; if ( $self->within_element('hit') ) { if ( $self->within_element('hsp') ) { $self->end_element( { 'Name' => 'Hsp' } ); } $self->end_element( { 'Name' => 'Hit' } ); } my $info = [ @{ $hitinfo[ $hitinfo{$name} ] } ]; if ( !defined $info || $info->[0] ne $name ) { $self->warn( "Somehow the Model table order does not match the order in the domains (got " . $info->[0] . ", expected $name). We're back loading this from the alignment information instead" ); $info = [ $name, '', $buffer =~ /score \s+ ([^,\s]+), \s+E\s+=\s+ (\S+)/ox, $domaintotal ]; push @hitinfo, $info; $hitinfo{$name} = $#hitinfo; } $self->start_element( { 'Name' => 'Hit' } ); $self->element( { 'Name' => 'Hit_id', 'Data' => shift @{$info} } ); $self->element( { 'Name' => 'Hit_desc', 'Data' => shift @{$info} } ); $self->element( { 'Name' => 'Hit_score', 'Data' => shift @{$info} } ); $self->element( { 'Name' => 'Hit_signif', 'Data' => shift @{$info} } ); my $dom_total = shift @{$info}; if (my $hit_end = shift @{$info}) { $self->element( { 'Name' => 'Hit_len', 'Data' => $hit_end } ); } $self->start_element( { 'Name' => 'Hsp' } ); my $HSPinfo = shift @hspinfo; my $id = shift @$HSPinfo; if ( $id ne $name ) { $self->throw( "Somehow the domain list details do not match " . "the table (got $id, expected $name)" ); } if ($self->{'_reporttype'} eq 'HMMSEARCH') { $self->element( { 'Name' => 'Hsp_hit-from', 'Data' => shift @$HSPinfo } ); $self->element( { 'Name' => 'Hsp_hit-to', 'Data' => shift @$HSPinfo } ); $self->element( { 'Name' => 'Hsp_query-from', 'Data' => shift @$HSPinfo } ); $self->element( { 'Name' => 'Hsp_query-to', 'Data' => shift @$HSPinfo } ); } elsif ($self->{'_reporttype'} eq 'HMMPFAM') { $self->element( { 'Name' => 'Hsp_query-from', 'Data' => shift @$HSPinfo } ); $self->element( { 'Name' => 'Hsp_query-to', 'Data' => shift @$HSPinfo } ); $self->element( { 'Name' => 'Hsp_hit-from', 'Data' => shift @$HSPinfo } ); $self->element( { 'Name' => 'Hsp_hit-to', 'Data' => shift @$HSPinfo } ); } $self->element( { 'Name' => 'Hsp_score', 'Data' => shift @$HSPinfo } ); $self->element( { 'Name' => 'Hsp_evalue', 'Data' => shift @$HSPinfo } ); if ( $domaincounter{$name} == $domaintotal ) { $hitinfo[ $hitinfo{$name} ] = undef; } } else { # Might want to change this so that it # accumulates all the of the alignment lines into # three array slots and then tests for the # end of the line if ($buffer =~ m/^\s+(?:CS|RF)\s+/o && $count == 0) { # Buffer the CS line now and process it later at # midline point, where $prelength and width will be known $csline = $buffer; next; } elsif ($buffer =~ /^(\s+ \*->) (\S+)/ox) { # start of domain $prelength = CORE::length($1); $width = 0; # deal with fact that start and stop is on same line my $data = $2; if ($data =~ s/<-?\*?\s*$//) { $width = CORE::length($data); } if ($self->{'_reporttype'} eq 'HMMSEARCH') { $self->element( { 'Name' => 'Hsp_qseq', 'Data' => $data } ); } elsif ($self->{'_reporttype'} eq 'HMMPFAM') { $self->element( { 'Name' => 'Hsp_hseq', 'Data' => $data } ); } $count = 0; $second_tier = 0; } elsif ($buffer =~ /^(\s+) (\S+) <-?\*? \s*$/ox) { # end of domain $prelength -= 3 unless ( $second_tier++ ); if ($self->{'_reporttype'} eq 'HMMSEARCH') { $self->element( { 'Name' => 'Hsp_qseq', 'Data' => $2 } ); } elsif ($self->{'_reporttype'} eq 'HMMPFAM') { $self->element( { 'Name' => 'Hsp_hseq', 'Data' => $2 } ); } $width = CORE::length($2); $count = 0; } elsif ( ( $count != 1 && $buffer =~ /^\s+$/o ) || CORE::length($buffer) == 0 || $buffer =~ /^\s+\-?\*\s*$/ || $buffer =~ /^\s+\S+\s+\-\s+\-\s*$/ ) { next; } elsif ( $count == 0 ) { $prelength -= 3 unless ( $second_tier++ ); unless ( defined $prelength ) { # $self->warn("prelength not set"); next; } if ($self->{'_reporttype'} eq 'HMMSEARCH') { $self->element( { 'Name' => 'Hsp_qseq', 'Data' => substr( $buffer, $prelength ) } ); } elsif ($self->{'_reporttype'} eq 'HMMPFAM') { $self->element( { 'Name' => 'Hsp_hseq', 'Data' => substr( $buffer, $prelength ) } ); } } elsif ( $count == 1 ) { if ( !defined $prelength ) { $self->warn("prelength not set"); } if ($width) { $self->element( { 'Name' => 'Hsp_midline', 'Data' => substr( $buffer, $prelength, $width ) } ); if ($csline ne '') { $self->element( { 'Name' => 'Hsp_csline', 'Data' => substr( $csline, $prelength, $width ) } ); $csline = ''; } } else { $self->element( { 'Name' => 'Hsp_midline', 'Data' => substr( $buffer, $prelength ) } ); if ($csline ne '') { $self->element( { 'Name' => 'Hsp_csline', 'Data' => substr( $csline, $prelength ) } ); $csline = ''; } } } elsif ( $count == 2 ) { if ( $buffer =~ /^\s+(\S+)\s+(\d+|\-)\s+(\S*)\s+(\d+|\-)/o ) { if ($self->{'_reporttype'} eq 'HMMSEARCH') { $self->element( { 'Name' => 'Hsp_hseq', 'Data' => $3 } ); } elsif ($self->{'_reporttype'} eq 'HMMPFAM') { $self->element( { 'Name' => 'Hsp_qseq', 'Data' => $3 } ); } } else { $self->warn("unrecognized line ($count): $buffer\n"); } } $count = 0 if $count++ >= 2; } } } elsif ( $buffer =~ /^Histogram/o || $buffer =~ m!^//!o ) { my %domaincounter; while ( my $HSPinfo = shift @hspinfo ) { my $id = shift @$HSPinfo; $domaincounter{$id}++; my $info = [ @{ $hitinfo[ $hitinfo{$id} ] } ]; next unless defined $info; $self->start_element( { 'Name' => 'Hit' } ); $self->element( { 'Name' => 'Hit_id', 'Data' => shift @{$info} } ); $self->element( { 'Name' => 'Hit_desc', 'Data' => shift @{$info} } ); $self->element( { 'Name' => 'Hit_score', 'Data' => shift @{$info} } ); $self->element( { 'Name' => 'Hit_signif', 'Data' => shift @{$info} } ); my $domaintotal = shift @{$info}; if (my $hit_end = shift @{$info}) { $self->element( { 'Name' => 'Hit_len', 'Data' => $hit_end } ); } # Histogram is exclusive of Hmmsearch, not found in Hmmpfam, # so just use Hmmsearch start/end order (first hit, then query) $self->start_element( { 'Name' => 'Hsp' } ); $self->element( { 'Name' => 'Hsp_hit-from', 'Data' => shift @$HSPinfo } ); $self->element( { 'Name' => 'Hsp_hit-to', 'Data' => shift @$HSPinfo } ); $self->element( { 'Name' => 'Hsp_query-from', 'Data' => shift @$HSPinfo } ); $self->element( { 'Name' => 'Hsp_query-to', 'Data' => shift @$HSPinfo } ); $self->element( { 'Name' => 'Hsp_score', 'Data' => shift @$HSPinfo } ); $self->element( { 'Name' => 'Hsp_evalue', 'Data' => shift @$HSPinfo } ); $self->end_element( { 'Name' => 'Hsp' } ); $self->end_element( { 'Name' => 'Hit' } ); if ( $domaincounter{$id} == $domaintotal ) { $hitinfo[ $hitinfo{$id} ] = undef; } } @hitinfo = (); %hitinfo = (); last; } # uncomment to see missed lines with verbose on #else { # $self->debug($buffer); #} } $last = $buffer; } $self->end_element( { 'Name' => 'HMMER_Output' } ) unless !$seentop; return $self->end_document(); } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element { my ( $self, $data ) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; if ($type) { if ( $self->_eventHandler->will_handle($type) ) { my $func = sprintf( "start_%s", lc $type ); $self->_eventHandler->$func( $data->{'Attributes'} ); } unshift @{ $self->{'_elements'} }, $type; } if ( defined $type && $type eq 'result' ) { $self->{'_values'} = {}; $self->{'_result'} = undef; } } =head2 end_element Title : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub end_element { my ( $self, $data ) = @_; my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; my $rc; if ( $nm eq 'HMMER_program' ) { if ( $self->{'_last_data'} =~ /(HMM\S+)/i ) { $self->{'_reporttype'} = uc $1; } } # Hsp are sort of weird, in that they end when another # object begins so have to detect this in end_element for now if ( $nm eq 'Hsp' ) { foreach my $line (qw(Hsp_csline Hsp_qseq Hsp_midline Hsp_hseq)) { my $data = $self->{'_last_hspdata'}->{$line}; if ($data && $line eq 'Hsp_hseq') { # replace hmm '.' gap symbol by '-' $data =~ s/\./-/g; } $self->element( { 'Name' => $line, 'Data' => $data } ); # Since HMMER doesn't print some data explicitly, # calculate it from the homology line (midline) if ($line eq 'Hsp_midline') { if ($data) { my $length = length $data; my $identical = ($data =~ tr/a-zA-Z//); my $positive = ($data =~ tr/+//) + $identical; $self->element( { 'Name' => 'Hsp_align-len', 'Data' => $length } ); $self->element( { 'Name' => 'Hsp_identity', 'Data' => $identical } ); $self->element( { 'Name' => 'Hsp_positive', 'Data' => $positive } ); } else { $self->element( { 'Name' => 'Hsp_identity', 'Data' => 0 } ); $self->element( { 'Name' => 'Hsp_positive', 'Data' => 0 } ); } } } $self->{'_last_hspdata'} = {}; } if ($type) { if ( $self->_eventHandler->will_handle($type) ) { my $func = sprintf( "end_%s", lc $type ); $rc = $self->_eventHandler->$func( $self->{'_reporttype'}, $self->{'_values'} ); } my $lastelem = shift @{ $self->{'_elements'} }; # Flush corresponding values from the {_values} buffer my $name = uc $type; foreach my $key (keys %{ $self->{_values} }) { delete $self->{_values}->{$key} if ($key =~ m/^$name-/); } } elsif ( $MAPPING{$nm} ) { if ( ref( $MAPPING{$nm} ) =~ /hash/i ) { my $key = ( keys %{ $MAPPING{$nm} } )[0]; $self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } = $self->{'_last_data'}; } else { $self->{'_values'}->{ $MAPPING{$nm} } = $self->{'_last_data'}; } } else { $self->debug("unknown nm $nm, ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if ( defined $type && $type eq 'result' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element { my ( $self, $data ) = @_; $self->start_element($data); $self->characters($data); $self->end_element($data); } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters { my ( $self, $data ) = @_; if ( $self->in_element('hsp') && $data->{'Name'} =~ /Hsp\_(?:qseq|hseq|csline|midline)/o && defined $data->{'Data'} ) { $self->{'_last_hspdata'}->{ $data->{'Name'} } .= $data->{'Data'}; } return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/o ); $self->{'_last_data'} = $data->{'Data'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub within_element { my ( $self, $name ) = @_; return 0 if ( !defined $name || !defined $self->{'_elements'} || scalar @{ $self->{'_elements'} } == 0 ); foreach my $element ( @{ $self->{'_elements'} } ) { return 1 if ( $element eq $name ); } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'within' because 'in' only tests its immediete parent. Returns : boolean Args : string element name =cut sub in_element { my ( $self, $name ) = @_; return 0 if !defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name ); } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handle a start document event Returns : none Args : none =cut sub start_document { my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'} = undef; $self->{'_elements'} = []; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document { my ($self) = @_; return $self->{'_result'}; } =head2 result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } 1; BioPerl-1.007002/Bio/SearchIO/hmmer3.pm000444000766000024 14045513155576320 17463 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::hmmer3 # # Please direct questions and support issues to # # Cared for by Thomas Sharpton # # Copyright Thomas Sharpton # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::hmmer3 =head1 SYNOPSIS use Bio::SearchIO; my $searchio = Bio::SearchIO->new( -format => 'hmmer', -version => 3, -file => 'hmmsearch.out' ); my $result = $searchio->next_result; my $hit = $result->next_hit; print $hit->name, $hit->description, $hit->significance, $hit->score, "\n"; my $hsp = $hit->next_hsp; print $hsp->start('hit'), $hsp->end('hit'), $hsp->start('query'), $hsp->end('query'), "\n"; =head1 DESCRIPTION Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with both version 2 and version 3 of the HMMER package from L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: L rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Thomas Sharpton Email thomas.sharpton@gmail.com Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here briano at bioteam.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::hmmer3; use strict; use Data::Dumper; use Bio::Factory::ObjectFactory; use Bio::Tools::IUPAC; use vars qw(%MAPPING %MODEMAP); use base qw(Bio::SearchIO::hmmer); BEGIN { # mapping of HMMER items to Bioperl hash keys %MODEMAP = ( 'HMMER_Output' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); %MAPPING = ( 'Hsp_bit-score' => 'HSP-bits', 'Hsp_score' => 'HSP-score', 'Hsp_evalue' => 'HSP-evalue', 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_query-strand' => 'HSP-query_strand', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_hit-strand' => 'HSP-hit_strand', 'Hsp_positive' => 'HSP-conserved', 'Hsp_identity' => 'HSP-identical', 'Hsp_gaps' => 'HSP-hsp_gaps', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_csline' => 'HSP-cs_seq', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_midline' => 'HSP-homology_seq', 'Hsp_pline' => 'HSP-pp_seq', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_query-frame' => 'HSP-query_frame', 'Hsp_hit-frame' => 'HSP-hit_frame', 'Hit_id' => 'HIT-name', 'Hit_len' => 'HIT-length', 'Hit_accession' => 'HIT-accession', 'Hit_desc' => 'HIT-description', 'Hit_signif' => 'HIT-significance', 'Hit_score' => 'HIT-score', 'HMMER_program' => 'RESULT-algorithm_name', 'HMMER_version' => 'RESULT-algorithm_version', 'HMMER_query-def' => 'RESULT-query_name', 'HMMER_query-len' => 'RESULT-query_length', 'HMMER_query-acc' => 'RESULT-query_accession', 'HMMER_querydesc' => 'RESULT-query_description', 'HMMER_hmm' => 'RESULT-hmm_name', 'HMMER_seqfile' => 'RESULT-sequence_file', 'HMMER_db' => 'RESULT-database_name', ); } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result { my ($self) = @_; my ( $buffer, $last, @hit_list, @hsp_list, %hspinfo, %hitinfo, %domaincounter ); local $/ = "\n"; my @ambiguous_nt = keys %Bio::Tools::IUPAC::IUB; my $ambiguous_nt = join '', @ambiguous_nt; my $verbose = $self->verbose; # cache for speed? JES's idea in hmmer.pm $self->start_document(); # This is here to ensure that next_result doesn't produce infinite loop if ( !defined( $buffer = $self->_readline ) ) { return undef; } else { $self->_pushback($buffer); } my $hit_counter = 0; # helper variable for non-unique hit IDs # Regex goes here for HMMER3 # Start with hmmsearch processing while ( defined( $buffer = $self->_readline ) ) { my $lineorig = $buffer; chomp $buffer; # Grab the program name if ( $buffer =~ m/^\#\s(\S+)\s\:\:\s/ ) { my $prog = $1; # TO DO: customize the above regex to adapt to other # program types (hmmscan, etc) $self->start_element( { 'Name' => 'HMMER_Output' } ); $self->{'_result_count'}++; #Might need to move to another block $self->element( { 'Name' => 'HMMER_program', 'Data' => uc($prog) } ); } # Get the HMMER package version and release date elsif ( $buffer =~ m/^\#\sHMMER\s+(\S+)\s+\((.+)\)/ ) { my $version = $1; my $versiondate = $2; $self->{'_hmmidline'} = $buffer; $self->element( { 'Name' => 'HMMER_version', 'Data' => $version } ); } # Get the query info elsif ( $buffer =~ /^\#\squery (?:\w+ )?file\:\s+(\S+)/ ) { if ( $self->{'_reporttype'} eq 'HMMSEARCH' || $self->{'_reporttype'} eq 'PHMMER' || $self->{'_reporttype'} eq 'NHMMER' ) { $self->{'_hmmfileline'} = $lineorig; $self->element( { 'Name' => 'HMMER_hmm', 'Data' => $1 } ); } elsif ( $self->{'_reporttype'} eq 'HMMSCAN' ) { $self->{'_hmmseqline'} = $lineorig; $self->element( { 'Name' => 'HMMER_seqfile', 'Data' => $1 } ); } } # If this is a report without alignments elsif ( $buffer =~ m/^\#\sshow\salignments\sin\soutput/ ) { $self->{'_alnreport'} = 0; } # Get the database info elsif ( $buffer =~ m/^\#\starget\s\S+\sdatabase\:\s+(\S+)/ ) { if ( $self->{'_reporttype'} eq 'HMMSEARCH' || $self->{'_reporttype'} eq 'PHMMER' || $self->{'_reporttype'} eq 'NHMMER' ) { $self->{'_hmmseqline'} = $lineorig; $self->element( { 'Name' => 'HMMER_seqfile', 'Data' => $1 } ); } elsif ( $self->{'_reporttype'} eq 'HMMSCAN' ) { $self->{'_hmmfileline'} = $lineorig; $self->element( { 'Name' => 'HMMER_hmm', 'Data' => $1 } ); } } # Get query data elsif ( $buffer =~ s/^Query:\s+// ) { # For multi-query reports if ( ( not exists $self->{_values}->{"RESULT-algorithm_name"} or not exists $self->{_values}->{"RESULT-algorithm_version"} ) and exists $self->{_hmmidline} ) { my ($version, $versiondate) = $self->{_hmmidline} =~ m/^\#\sHMMER\s+(\S+)\s+\((.+)\)/; $self->element( { 'Name' => 'HMMER_program', 'Data' => $self->{_reporttype} } ); $self->element( { 'Name' => 'HMMER_version', 'Data' => $version } ); } if ( ( not exists $self->{_values}->{"RESULT-hmm_name"} or not exists $self->{_values}->{"RESULT-sequence_file"} ) and ( exists $self->{_hmmfileline} or exists $self->{_hmmseqline} ) ) { if ( $self->{'_reporttype'} eq 'HMMSEARCH' or $self->{'_reporttype'} eq 'PHMMER' or $self->{'_reporttype'} eq 'NHMMER' ) { my ($qry_file) = $self->{_hmmfileline} =~ m/^\#\squery (?:\w+ )?file\:\s+(\S+)/; my ($target_file) = $self->{_hmmseqline} =~ m/^\#\starget\s\S+\sdatabase\:\s+(\S+)/; $self->element( { 'Name' => 'HMMER_hmm', 'Data' => $qry_file } ); $self->element( { 'Name' => 'HMMER_seqfile', 'Data' => $target_file } ); } elsif ( $self->{'_reporttype'} eq 'HMMSCAN' ) { my ($qry_file) = $self->{_hmmseqline} =~ m/^\#\squery \w+ file\:\s+(\S+)/; my ($target_file) = $self->{_hmmfileline} =~ m/^\#\starget\s\S+\sdatabase\:\s+(\S+)/; $self->element( { 'Name' => 'HMMER_seqfile', 'Data' => $qry_file } ); $self->element( { 'Name' => 'HMMER_hmm', 'Data' => $target_file } ); } } unless ($buffer =~ s/\s+\[[L|M]\=(\d+)\]$//) { warn "Error parsing length for query, offending line $buffer\n"; exit(0); } my $querylen = $1; $self->element( { 'Name' => 'HMMER_query-len', 'Data' => $querylen } ); $self->element( { 'Name' => 'HMMER_query-def', 'Data' => $buffer } ); } # Get Accession data elsif ( $buffer =~ s/^Accession:\s+// ) { $buffer =~ s/\s+$//; $self->element( { 'Name' => 'HMMER_query-acc', 'Data' => $buffer } ); } # Get description data elsif ( $buffer =~ s/^Description:\s+// ) { $buffer =~ s/\s+$//; $self->element( { 'Name' => 'HMMER_querydesc', 'Data' => $buffer } ); } # hmmsearch, nhmmer, and hmmscan-specific formatting here elsif ( defined $self->{'_reporttype'} && ( $self->{'_reporttype'} eq 'HMMSEARCH' || $self->{'_reporttype'} eq 'HMMSCAN' || $self->{'_reporttype'} eq 'PHMMER' || $self->{'_reporttype'} eq 'NHMMER' ) ) { # Complete sequence table data above inclusion threshold, # hmmsearch or hmmscan if ( $buffer =~ m/Scores for complete sequence/ ) { while ( defined( $buffer = $self->_readline ) ) { if ( $buffer =~ m/inclusion threshold/ || $buffer =~ m/Domain( and alignment)? annotation for each/ || $buffer =~ m/\[No hits detected/ || $buffer =~ m!^//! ) { $self->_pushback($buffer); last; } elsif ( $buffer =~ m/^\s+E-value\s+score/ || $buffer =~ m/\-\-\-/ || $buffer =~ m/^$/ ) { next; } # Grab table data $hit_counter++; my ($eval_full, $score_full, $bias_full, $eval_best, $score_best, $bias_best, $exp, $n, $hitid, $desc, @hitline ); @hitline = split( " ", $buffer ); $eval_full = shift @hitline; $score_full = shift @hitline; $bias_full = shift @hitline; $eval_best = shift @hitline; $score_best = shift @hitline; $bias_best = shift @hitline; $exp = shift @hitline; $n = shift @hitline; $hitid = shift @hitline; $desc = join " ", @hitline; $desc = '' if ( !defined($desc) ); push @hit_list, [ $hitid, $desc, $eval_full, $score_full ]; $hitinfo{"$hitid.$hit_counter"} = $#hit_list; } } # nhmmer elsif ( $buffer =~ /Scores for complete hits/ ) { while ( defined( $buffer = $self->_readline ) ) { if ( $buffer =~ /inclusion threshold/ || $buffer =~ /Annotation for each hit/ || $buffer =~ /\[No hits detected/ || $buffer =~ m!^//! ) { $self->_pushback($buffer); last; } elsif ( $buffer =~ m/^\s+E-value\s+score/ || $buffer =~ m/\-\-\-/ || $buffer =~ m/^$/ ) { next; } # Grab table data $hit_counter++; my ($eval, $score, $bias, $hitid, $start, $end, $desc, @hitline ); @hitline = split( " ", $buffer ); $eval = shift @hitline; $score = shift @hitline; $bias = shift @hitline; $hitid = shift @hitline; $start = shift @hitline; $end = shift @hitline; $desc = join ' ', @hitline; $desc = '' if ( !defined($desc) ); push @hit_list, [ $hitid, $desc, $eval, $score ]; $hitinfo{"$hitid.$hit_counter"} = $#hit_list; } } # Complete sequence table data below inclusion threshold elsif ( $buffer =~ /inclusion threshold/ ) { while ( defined( $buffer = $self->_readline ) ) { if ( $buffer =~ /Domain( and alignment)? annotation for each/ || $buffer =~ /Internal pipeline statistics summary/ || $buffer =~ /Annotation for each hit\s+\(and alignments\)/ ) { $self->_pushback($buffer); last; } elsif ( $buffer =~ m/inclusion threshold/ || $buffer =~ m/^$/ ) { next; } # Grab table data $hit_counter++; my ($eval_full, $score_full, $bias_full, $eval_best, $score_best, $bias_best, $exp, $n, $hitid, $desc, @hitline ); @hitline = split( " ", $buffer ); $eval_full = shift @hitline; $score_full = shift @hitline; $bias_full = shift @hitline; $eval_best = shift @hitline; $score_best = shift @hitline; $bias_best = shift @hitline; $exp = shift @hitline; $n = shift @hitline; $hitid = shift @hitline; $desc = join " ", @hitline; $desc = '' if ( !defined($desc) ); push @hit_list, [ $hitid, $desc, $eval_full, $score_full ]; $hitinfo{"$hitid.$hit_counter"} = $#hit_list; } } # Domain annotation for each sequence table data, # for hmmscan, hmmsearch & nhmmer elsif ( $buffer =~ /Domain( and alignment)? annotation for each/ or $buffer =~ /Annotation for each hit\s+\(and alignments\)/ ) { @hsp_list = (); # Here for multi-query reports my $name; my $annot_counter = 0; while ( defined( $buffer = $self->_readline ) ) { if ( $buffer =~ /\[No targets detected/ || $buffer =~ /Internal pipeline statistics/ ) { $self->_pushback($buffer); last; } if ( $buffer =~ m/^\>\>\s(\S*)\s+(.*)/ ) { $name = $1; my $desc = $2; $annot_counter++; $domaincounter{"$name.$annot_counter"} = 0; # The Hit Description from the Scores table can be truncated if # its too long, so use the '>>' line description when its longer if (length $hit_list[ $hitinfo{"$name.$annot_counter"} ] [1] < length $desc ) { $hit_list[ $hitinfo{"$name.$annot_counter"} ][1] = $desc; } while ( defined( $buffer = $self->_readline ) ) { if ( $buffer =~ m/Internal pipeline statistics/ || $buffer =~ m/Alignments for each domain/ || $buffer =~ m/^\s+Alignment:/ || $buffer =~ m/^\>\>/ ) { $self->_pushback($buffer); last; } elsif ( $buffer =~ m/^\s+score\s+bias/ || $buffer =~ m/^\s+\#\s+score/ || $buffer =~ m/^\s+------\s+/ || $buffer =~ m/^\s\-\-\-\s+/ || $buffer =~ m/^$/ ) { next; } # Grab hsp data from table, push into @hsp; if ($self->{'_reporttype'} =~ m/(?:HMMSCAN|HMMSEARCH|PHMMER|NHMMER)/) { my ( $domain_num, $score, $bias, $ceval, $ieval, $hmm_start, $hmm_stop, $hmm_cov, $seq_start, $seq_stop, $seq_cov, $env_start, $env_stop, $env_cov, $hitlength, $acc ); my @vals; if ( # HMMSCAN & HMMSEARCH ( $domain_num, $score, $bias, $ceval, $ieval, $hmm_start, $hmm_stop, $hmm_cov, $seq_start, $seq_stop, $seq_cov, $env_start, $env_stop, $env_cov, $acc ) = ( $buffer =~ m|^\s+(\d+)\s\!*\?*\s+ # domain number (\S+)\s+(\S+)\s+ # score, bias (\S+)\s+(\S+)\s+ # c-eval, i-eval (\d+)\s+(\d+)\s+(\S+)\s+ # hmm start, stop, coverage (\d+)\s+(\d+)\s+(\S+)\s+ # seq start, stop, coverage (\d+)\s+(\d+)\s+(\S+)\s+ # env start, stop, coverage (\S+) # posterior probability accuracy \s*$|ox ) ) { # Values assigned when IF succeeded # Try to get the Hit length from the alignment information $hitlength = 0; if ($self->{'_reporttype'} eq 'HMMSEARCH' || $self->{'_reporttype'} eq 'PHMMER') { # For Hmmsearch, if seq coverage ends in ']' it means that the alignment # runs until the end. In that case add the END coordinate to @hitinfo # to use it as Hit Length if ( $seq_cov =~ m/\]$/ ) { $hitlength = $seq_stop; } } elsif ($self->{'_reporttype'} eq 'HMMSCAN') { # For Hmmscan, if hmm coverage ends in ']' it means that the alignment # runs until the end. In that case add the END coordinate to @hitinfo # to use it as Hit Length if ( $hmm_cov =~ m/\]$/ ) { $hitlength = $hmm_stop; } } } elsif ( # NHMMER ( $score, $bias, $ceval, $hmm_start, $hmm_stop, $hmm_cov, $seq_start, $seq_stop, $seq_cov, $env_start, $env_stop, $env_cov, $hitlength, $acc ) = ( $buffer =~ m|^\s+[!?]\s+ (\S+)\s+(\S+)\s+(\S+)\s+ # score, bias, evalue (\d+)\s+(\d+)\s+(\S+)\s+ # hmm start, stop, coverage (\d+)\s+(\d+)\s+(\S+)\s+ # seq start, stop, coverage (\d+)\s+(\d+)\s+(\S+)\s+ # env start, stop, coverage (\d+)\s+(\S+) # target length, pp accuracy .*$|ox ) ) { # Values assigned when IF succeeded } else { print STDERR "Missed this line: $buffer\n"; next; } my $info = $hit_list[ $hitinfo{"$name.$annot_counter"} ]; if ( !defined $info ) { $self->warn( "Incomplete information: can't find HSP $name in list of hits\n" ); next; } $domaincounter{"$name.$annot_counter"}++; my $hsp_key = $name . "_" . $domaincounter{"$name.$annot_counter"}; # Keep it simple for now. let's customize later @vals = ( $hmm_start, $hmm_stop, $seq_start, $seq_stop, $score, $ceval, $hitlength, '', '', '', '', '' ); push @hsp_list, [ $name, @vals ]; $hspinfo{"$hsp_key.$annot_counter"} = $#hsp_list; } } } elsif ( $buffer =~ /Alignment(?:s for each domain)?:/ ) { #line counter my $count = 0; # There's an optional block, so we sometimes need to # count to 3, and sometimes to 4. my $max_count = 3; my $lastdomain; my $hsp; my ( $csline, $hline, $midline, $qline, $pline ); # To avoid deleting whitespaces from the homology line, # keep track of the position and length of the alignment # in each individual hline/qline, to take them as reference # and use them in the homology line my $align_offset = 0; my $align_length = 0; while ( defined( $buffer = $self->_readline ) ) { if ( $buffer =~ m/^\>\>/ || $buffer =~ m/Internal pipeline statistics/ ) { $self->_pushback($buffer); last; } elsif ($buffer =~ m/^$/ ) { # Reset these scalars on empty lines to help # distinguish between the consensus structure/reference # tracks (CS|RF lines) and homology lines ending in # CS or RF aminoacids $align_offset = 0; $align_length = 0; next; } if ( $buffer =~ /\s\s\=\=\sdomain\s(\d+)\s+/ or $buffer =~ /\s\sscore:\s\S+\s+/ ) { my $domainnum = $1 || 1; $count = 0; my $key = $name . "_" . $domainnum; $hsp = $hsp_list[ $hspinfo{"$key.$annot_counter"} ]; $csline = $$hsp[-5]; $hline = $$hsp[-4]; $midline = $$hsp[-3]; $qline = $$hsp[-2]; $pline = $$hsp[-1]; $lastdomain = $name; } # Consensus Structure or Reference track, some reports # don't have it. Since it appears on top of the alignment, # the reset of $align_length to 0 between alignment blocks # avoid confusing homology lines with it. elsif ( $buffer =~ m/\s+\S+\s(?:CS|RF)$/ and $align_length == 0 ) { my @data = split( " ", $buffer ); $csline .= $data[-2]; $max_count++; $count++; next; } # Query line and Hit line swaps positions # depending of the program elsif ( $count == $max_count - 3 or $count == $max_count - 1 ) { my @data = split( " ", $buffer ); my $line_offset = 0; # Use \Q\E on match to avoid errors on alignments # that include stop codons (*) while ($buffer =~ m/\Q$data[-2]\E/g) { $line_offset = pos $buffer; } if ($line_offset != 0) { $align_length = length $data[-2]; $align_offset = $line_offset - $align_length; } if ($self->{'_reporttype'} eq 'HMMSCAN') { # hit sequence $hline .= $data[-2] if ($count == $max_count - 3); # query sequence $qline .= $data[-2] if ($count == $max_count - 1); } else { # hmmsearch & nhmmer # hit sequence $hline .= $data[-2] if ($count == $max_count - 1); # query sequence $qline .= $data[-2] if ($count == $max_count - 3); } $count++; next; } # conservation track # storage isn't quite right - need to remove # leading/lagging whitespace while preserving # gap data (latter isn't done, former is) elsif ( $count == $max_count - 2 ) { $midline .= substr $buffer, $align_offset, $align_length; $count++; next; } # posterior probability track elsif ( $count == $max_count ) { my @data = split(" ", $buffer); $pline .= $data[-2]; $count = 0; $max_count = 3; $$hsp[-5] = $csline; $$hsp[-4] = $hline; $$hsp[-3] = $midline; $$hsp[-2] = $qline; $$hsp[-1] = $pline; next; } else { print STDERR "Missed this line: $buffer\n"; } } } } } # End of report elsif ( $buffer =~ m/Internal pipeline statistics/ || $buffer =~ m!^//! ) { # If within hit, hsp close; if ( $self->within_element('hit') ) { if ( $self->within_element('hsp') ) { $self->end_element( { 'Name' => 'Hsp' } ); } $self->end_element( { 'Name' => 'Hit' } ); } # Grab summary statistics of run while ( defined( $buffer = $self->_readline ) ) { last if ( $buffer =~ m/^\/\/$/ ); } # Do a lot of processing of hits and hsps here my $index = 0; while ( my $hit = shift @hit_list ) { $index++; my $hit_name = shift @$hit; my $hit_desc = shift @$hit; my $hit_signif = shift @$hit; my $hit_score = shift @$hit; my $num_domains = $domaincounter{"$hit_name.$index"} || 0; $self->start_element( { 'Name' => 'Hit' } ); $self->element( { 'Name' => 'Hit_id', 'Data' => $hit_name } ); $self->element( { 'Name' => 'Hit_desc', 'Data' => $hit_desc } ); $self->element( { 'Name' => 'Hit_signif', 'Data' => $hit_signif } ); $self->element( { 'Name' => 'Hit_score', 'Data' => $hit_score } ); for my $i ( 1 .. $num_domains ) { my $key = $hit_name . "_" . $i; my $hsp = $hsp_list[ $hspinfo{"$key.$index"} ]; if ( defined $hsp ) { my $hsp_name = shift @$hsp; $self->start_element( { 'Name' => 'Hsp' } ); # Since HMMER doesn't print some data explicitly, # calculate it from the homology line (midline) if ($$hsp[-3] ne '') { my $length = length $$hsp[-3]; my $identical = ($$hsp[-3] =~ tr/a-zA-Z//); my $positive = ($$hsp[-3] =~ tr/+//) + $identical; $self->element( { 'Name' => 'Hsp_align-len', 'Data' => $length } ); $self->element( { 'Name' => 'Hsp_identity', 'Data' => $identical } ); $self->element( { 'Name' => 'Hsp_positive', 'Data' => $positive } ); } else { $self->element( { 'Name' => 'Hsp_identity', 'Data' => 0 } ); $self->element( { 'Name' => 'Hsp_positive', 'Data' => 0 } ); } if ( $self->{'_reporttype'} eq 'HMMSCAN' ) { $self->element( { 'Name' => 'Hsp_hit-from', 'Data' => shift @$hsp } ); $self->element( { 'Name' => 'Hsp_hit-to', 'Data' => shift @$hsp } ); $self->element( { 'Name' => 'Hsp_query-from', 'Data' => shift @$hsp } ); $self->element( { 'Name' => 'Hsp_query-to', 'Data' => shift @$hsp } ); } elsif ( $self->{'_reporttype'} eq 'HMMSEARCH' or $self->{'_reporttype'} eq 'NHMMER' ) { $self->element( { 'Name' => 'Hsp_query-from', 'Data' => shift @$hsp } ); $self->element( { 'Name' => 'Hsp_query-to', 'Data' => shift @$hsp } ); $self->element( { 'Name' => 'Hsp_hit-from', 'Data' => shift @$hsp } ); $self->element( { 'Name' => 'Hsp_hit-to', 'Data' => shift @$hsp } ); } $self->element( { 'Name' => 'Hsp_score', 'Data' => shift @$hsp } ); $self->element( { 'Name' => 'Hsp_evalue', 'Data' => shift @$hsp } ); my $hitlength = shift @$hsp; if ( $hitlength != 0 ) { $self->element( { 'Name' => 'Hit_len', 'Data' => $hitlength } ); } $self->element( { 'Name' => 'Hsp_csline', 'Data' => shift @$hsp } ); $self->element( { 'Name' => 'Hsp_hseq', 'Data' => shift @$hsp } ); $self->element( { 'Name' => 'Hsp_midline', 'Data' => shift @$hsp } ); $self->element( { 'Name' => 'Hsp_qseq', 'Data' => shift @$hsp } ); $self->element( { 'Name' => 'Hsp_pline', 'Data' => shift @$hsp } ); # Only nhmmer output has strand information if ( $self->{'_reporttype'} eq 'NHMMER' ) { my $hstart = $self->get_from_element('HSP-hit_start'); my $hend = $self->get_from_element('HSP-hit_end'); my $hstrand = ( $hstart < $hend ) ? 1 : -1; my $qstart = $self->get_from_element('HSP-query_start'); my $qend = $self->get_from_element('HSP-query_end'); my $qstrand = ( $qstart < $qend ) ? 1 : -1; $self->element( { 'Name' => 'Hsp_query-strand', 'Data' => $qstrand } ); $self->element( { 'Name' => 'Hsp_hit-strand', 'Data' => $hstrand } ); } $self->end_element( { 'Name' => 'Hsp' } ); } } $self->end_element( { 'Name' => 'Hit' } ); } @hit_list = (); %hitinfo = (); last; } } else { print STDERR "Missed this line: $buffer\n"; $self->debug($buffer); } $last = $buffer; } $self->end_element( { 'Name' => 'HMMER_Output' } ); my $result = $self->end_document(); return $result; } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element { my ( $self, $data ) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; if ($type) { if ( $self->_eventHandler->will_handle($type) ) { my $func = sprintf( "start_%s", lc $type ); $self->_eventHandler->$func( $data->{'Attributes'} ); } unshift @{ $self->{'_elements'} }, $type; } if ( defined $type && $type eq 'result' ) { $self->{'_values'} = {}; $self->{'_result'} = undef; } } =head2 end_element Title : end_element Usage : $eventgeneartor->end_element Function: Handles and end element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub end_element { my ( $self, $data ) = @_; my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; my $rc; if ( $nm eq 'HMMER_program' ) { if ( $self->{'_last_data'} =~ /([NP]?HMM\S+)/i ) { $self->{'_reporttype'} = uc $1; } } # Hsp are sort of weird, in that they end when another # object begins so have to detect this in end_element for now if ( $nm eq 'Hsp' ) { foreach my $line (qw(Hsp_csline Hsp_qseq Hsp_midline Hsp_hseq Hsp_pline)) { my $data = $self->{'_last_hspdata'}->{$line}; if ( $data && $line eq 'Hsp_hseq' ) { # replace hmm '.' gap symbol by '-' $data =~ s/\./-/g; } $self->element( { 'Name' => $line, 'Data' => $data } ); } $self->{'_last_hspdata'} = {}; } if ($type) { if ( $self->_eventHandler->will_handle($type) ) { my $func = sprintf( "end_%s", lc $type ); $rc = $self->_eventHandler->$func( $self->{'_reporttype'}, $self->{'_values'} ); } my $lastelem = shift @{ $self->{'_elements'} }; # Flush corresponding values from the {_values} buffer my $name = uc $type; foreach my $key (keys %{ $self->{_values} }) { delete $self->{_values}->{$key} if ($key =~ m/^$name-/); } } elsif ( $MAPPING{$nm} ) { if ( ref( $MAPPING{$nm} ) =~ /hash/i ) { my $key = ( keys %{ $MAPPING{$nm} } )[0]; $self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } = $self->{'_last_data'}; } else { $self->{'_values'}->{ $MAPPING{$nm} } = $self->{'_last_data'}; # print "lastdata is " . $self->{'_last_data'} . "\n"; } } else { $self->debug("unknown nm $nm, ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if ( defined $type && $type eq 'result' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convenience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element { my ( $self, $data ) = @_; $self->start_element($data); $self->characters($data); $self->end_element($data); } =head2 get_from_element Title : get_from_element Usage : $self->get_from_element('HSP-hit_start'); Function: Convenience method to retrieve data from '_values' hash Returns : string Args : key =cut sub get_from_element { my ($self,$key) = @_; my $values = $self->{_values}; $values->{$key}; } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters { my ( $self, $data ) = @_; if ( $self->in_element('hsp') && $data->{'Name'} =~ /Hsp\_(?:qseq|hseq|csline|pline|midline)/o && defined $data->{'Data'} ) { $self->{'_last_hspdata'}->{ $data->{'Name'} } .= $data->{'Data'}; } return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/o ); $self->{'_last_data'} = $data->{'Data'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element( $element ) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block Returns : boolean Args : string element name =cut sub within_element { my ( $self, $name ) = @_; return 0 if ( !defined $name || !defined $self->{'_elements'} || scalar @{ $self->{'_elements'} } == 0 ); foreach my $element ( @{ $self->{'_elements'} } ) { return 1 if ( $element eq $name ); } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element( $element ) ) {} Function: Test if we are in a particular element This is different than 'within' because 'in' only tests its immediate parent Returns : boolean Args : string element name =cut sub in_element { my ( $self, $name ) = @_; return 0 if !defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name ); } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handle a start document event Returns : none Args : none =cut sub start_document { my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'} = undef; $self->{'_elements'} = []; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document { my ($self) = @_; return $self->{'_result'}; } =head2 result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results processed Returns : integer Args : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } 1; BioPerl-1.007002/Bio/SearchIO/hmmer_pull.pm000555000766000024 2205413155576320 20411 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::hmmer_pull # # Please direct questions and support issues to # # Cared for by Sendu Bala # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::hmmer_pull - A parser for HMMER output =head1 SYNOPSIS # do not use this class directly it is available through Bio::SearchIO use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer_pull', -file => 't/data/hmmpfam.bigout'); while (my $result = $in->next_result) { # this is a Bio::Search::Result::HmmpfamResult object print $result->query_name(), " for HMM ", $result->hmm_name(), "\n"; while (my $hit = $result->next_hit) { print $hit->name(), "\n"; while (my $hsp = $hit->next_hsp) { print "length is ", $hsp->length(), "\n"; } } } =head1 DESCRIPTION This object implements a pull-parser for HMMER output. It is fast since it only does work on request (hence 'pull'). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::hmmer_pull; use strict; use base qw(Bio::SearchIO Bio::PullParserI); =head2 new Title : new Usage : my $obj = Bio::SearchIO::hmmer_pull->new(); Function: Builds a new Bio::SearchIO::hmmer_pull object Returns : Bio::SearchIO::hmmer_pull Args : -fh/-file => HMMER output filename -format => 'hmmer_pull' -evalue => float or scientific notation number to be used as an evalue cutoff for hits -score => integer or scientific notation number to be used as a score value cutoff for hits -hsps => integer minimum number of hsps (domains) a hit must have -piped_behaviour => 'temp_file'|'memory'|'sequential_read' -piped_behaviour defines what the parser should do if the input is an unseekable filehandle (eg. piped input), see Bio::PullParserI::chunk for details. Default is 'sequential_read'. =cut sub _initialize { my ($self, @args) = @_; # don't do normal SearchIO initialization my ($writer, $file, $fh, $piped_behaviour, $evalue, $score, $hsps) = $self->_rearrange([qw(WRITER FILE FH PIPED_BEHAVIOUR EVALUE SCORE HSPS)], @args); $self->writer($writer) if $writer; $self->_fields( { ( header => undef, algorithm => undef, algorithm_version => undef, algorithm_reference => '', hmm_file => undef, hmm_name => undef, sequence_file => undef, sequence_database => undef, database_name => undef, database_letters => undef, database_entries => undef, next_result => undef, evalue_cutoff => '[unset]', score_cutoff => '[unset]', hsps_cutoff => '[unset]' ) } ); $self->_fields->{evalue_cutoff} = $evalue if $evalue; $self->_fields->{score_cutoff} = $score if $score; $self->_fields->{hsps_cutoff} = $hsps if $hsps; $self->_dependencies( { ( algorithm => 'header', algorithm_version => 'header', hmm_file => 'header', hmm_name => 'header', sequence_file => 'header', sequence_database => 'header' ) } ); $self->chunk($file || $fh || $self->throw("-file or -fh must be supplied"), -piped_behaviour => $piped_behaviour || 'sequential_read'); } sub _discover_header { my $self = shift; $self->_chunk_seek(0); my $header = $self->_get_chunk_by_nol(8); $self->{_after_header} = $self->_chunk_tell; my ($algo) = $header =~ /^(hmm\S+) - search/m; $self->_fields->{algorithm} = uc $algo; ($self->_fields->{algorithm_version}) = $header =~ /^HMMER\s+?(\S+)/m; ($self->_fields->{hmm_file}) = $header =~ /^HMM file:\s.+?(\S+)$/m; $self->_fields->{hmm_name} = $self->_fields->{hmm_file}; ($self->_fields->{sequence_file}) = $header =~ /^Sequence (?:file|database):\s.+?(\S+)$/m; $self->_fields->{sequence_database} = $self->_fields->{sequence_file}; $self->_fields->{header} = 1; } sub _discover_database_name { my $self = shift; my $type = $self->get_field('algorithm'); if ($type eq 'HMMPFAM') { $self->_fields->{database_name} = $self->get_field('hmm_file'); } elsif ($type eq 'HMMSEARCH') { $self->_fields->{database_name} = $self->get_field('sequence_file'); } } sub _discover_next_result { my $self = shift; my $type = $self->get_field('algorithm'); # also sets _after_header if not set if ($type eq 'HMMPFAM') { use Bio::Search::Result::HmmpfamResult; unless ($self->_sequential) { $self->_chunk_seek($self->{_end_of_previous_result} || $self->{_after_header}); my ($start, $end) = $self->_find_chunk_by_end("//\n"); return if $start == $end; $self->_fields->{next_result} = Bio::Search::Result::HmmpfamResult->new(-chunk => [($self->chunk, $start, $end)], -parent => $self); $self->{_end_of_previous_result} = $end; } else { # deliberatly don't cache these, which means rewind won't work; # if we cached we may as well have used 'memory' option to # -piped_behaviour my $chunk = $self->_get_chunk_by_end("//\n"); $chunk || return; $self->_fields->{next_result} = Bio::Search::Result::HmmpfamResult->new(-chunk => [$chunk], -parent => $self); } } elsif ($type eq 'HMMSEARCH') { $self->throw("Can't handle hmmsearch yet\n"); } else { $self->throw("Unknown report type"); } } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result { my $self = shift; my $result = $self->get_field('next_result') || return; undef $self->_fields->{next_result}; $self->{'_result_count'}++; return $result; } =head2 result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed. Returns : integer Args : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } =head2 rewind Title : rewind Usage : $searchio->rewind; Function: Allow one to reset the Result iterator to the beginning, so that next_result() will subsequently return the first result and so on. NB: result objects are not cached, so you will get new result objects each time you rewind. Also, note that result_count() counts the number of times you have called next_result(), so will not be able tell you how many results there were in the file if you use rewind(). Returns : n/a Args : none =cut sub rewind { my $self = shift; if ($self->_sequential) { $self->warn("rewind has no effect on piped input when you have chosen 'sequential_read' mode"); } delete $self->{_end_of_previous_result}; } 1; BioPerl-1.007002/Bio/SearchIO/infernal.pm000444000766000024 15257513155576320 20074 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::infernal # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::infernal - SearchIO-based Infernal parser =head1 SYNOPSIS my $parser = Bio::SearchIO->new(-format => 'infernal', -file => 'purine.inf'); while( my $result = $parser->next_result ) { # general result info, such as model used, Infernal version while( my $hit = $result->next_hit ) { while( my $hsp = $hit->next_hsp ) { # ... } } } =head1 DESCRIPTION This is a SearchIO-based parser for Infernal output from the cmsearch program. It currently parses cmsearch output for Infernal versions 0.7-1.1; older versions may work but will not be supported. The latest version of Infernal is 1.1. The output has changed substantially relative to version 1.0. Versions 1.x are stable releases (and output has stabilized) therefore it is highly recommended that users upgrade to using the latest Infernal release. Support for the older pre-v.1 developer releases will be dropped for future core 1.6 releases. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Fields Email cjfields-at-uiuc-dot-edu =head1 CONTRIBUTORS Jeffrey Barrick, Michigan State University Paul Cantalupo, University of Pittsburgh =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::infernal; use strict; use Data::Dumper; use base qw(Bio::SearchIO); our %MODEMAP = ( 'Result' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); our %MAPPING = ( 'Hsp_bit-score' => 'HSP-bits', 'Hsp_score' => 'HSP-score', 'Hsp_evalue' => 'HSP-evalue', # evalues only in v0.81, optional 'Hsp_pvalue' => 'HSP-pvalue', # pvalues only in v0.81, optional 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_query-strand'=> 'HSP-query_strand', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_hit-strand' => 'HSP-hit_strand', 'Hsp_gaps' => 'HSP-hsp_gaps', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_ncline' => 'HSP-nc_seq', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_midline' => 'HSP-homology_seq', 'Hsp_pline' => 'HSP-pp_seq', 'Hsp_structure' => 'HSP-meta', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_stranded' => 'HSP-stranded', 'Hit_id' => 'HIT-name', 'Hit_len' => 'HIT-length', 'Hit_gi' => 'HIT-ncbi_gi', 'Hit_accession' => 'HIT-accession', 'Hit_desc' => 'HIT-description', 'Hit_def' => 'HIT-description', 'Hit_signif' => 'HIT-significance', # evalues in v1.1 and v0.81, optional 'Hit_p' => 'HIT-p', # pvalues only in 1.0, optional 'Hit_score' => 'HIT-score', # best HSP bit score (in v1.1, the only HSP bit score) 'Hit_bits' => 'HIT-bits', # best HSP bit score (ditto) 'Infernal_program' => 'RESULT-algorithm_name', # get/set 'Infernal_version' => 'RESULT-algorithm_version', # get/set 'Infernal_query-def'=> 'RESULT-query_name', # get/set 'Infernal_query-len'=> 'RESULT-query_length', 'Infernal_query-acc'=> 'RESULT-query_accession', # get/set 'Infernal_querydesc'=> 'RESULT-query_description', # get/set 'Infernal_cm' => 'RESULT-cm_name', 'Infernal_db' => 'RESULT-database_name', # get/set 'Infernal_db-len' => 'RESULT-database_entries', # in v1.1 only 'Infernal_db-let' => 'RESULT-database_letters', # in v1.1 only ); my $MINSCORE = 0; my $DEFAULT_ALGORITHM = 'cmsearch'; my $DEFAULT_VERSION = '1.1'; my @VALID_SYMBOLS = qw(5-prime 3-prime single-strand unknown gap); my %STRUCTURE_SYMBOLS = ( '5-prime' => '<', '3-prime' => '>', 'single-strand' => ':', 'unknown' => '?', 'gap' => '.' ); =head2 new Title : new Usage : my $obj = Bio::SearchIO::infernal->new(); Function: Builds a new Bio::SearchIO::infernal object Returns : Bio::SearchIO::infernal Args : -fh/-file => cmsearch (infernal) filename -format => 'infernal' -model => query model (Rfam ID) (default undef) -database => database name (default undef) -query_acc => query accession, eg. Rfam accession RF#### -query_desc => query description, eg. Rfam description -hsp_minscore => minimum HSP score cutoff -convert_meta => boolean, set to convert meta string to simple WUSS format -symbols => hash ref of structure symbols to use (default symbols in %STRUCTURE_SYMBOLS hash) =cut sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); my ($model, $database, $convert, $symbols, $cutoff, $desc, $accession, $algorithm, $version) = $self->_rearrange([qw(MODEL DATABASE CONVERT_META SYMBOLS HSP_MINSCORE QUERY_DESC QUERY_ACC ALGORITHM VERSION)],@args); my $handler = $self->_eventHandler; $handler->register_factory( 'result', Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Result::INFERNALResult', -interface => 'Bio::Search::Result::ResultI', -verbose => $self->verbose ) ); $handler->register_factory( 'hit', Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Hit::ModelHit', -interface => 'Bio::Search::Hit::HitI', -verbose => $self->verbose ) ); $handler->register_factory( 'hsp', Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::HSP::ModelHSP', -interface => 'Bio::Search::HSP::HSPI', -verbose => $self->verbose ) ); defined $model && $self->model($model); defined $database && $self->database($database); defined $accession && $self->query_accession($accession); defined $convert && $self->convert_meta($convert); defined $desc && $self->query_description($desc); $version ||= $DEFAULT_VERSION; $self->version($version); $symbols ||= \%STRUCTURE_SYMBOLS; $self->structure_symbols($symbols); $cutoff ||= $MINSCORE; $self->hsp_minscore($cutoff); $algorithm ||= $DEFAULT_ALGORITHM; $self->algorithm($algorithm); } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result { my ($self) = @_; unless (exists $self->{'_handlerset'}) { my $line; while ($line = $self->_readline) { # advance to first line next if $line =~ m{^\s*$}; # newer output starts with model name if ($line =~ m{^\#\s+cmsearch\s}) { my $secondline = $self->_readline; if ($secondline =~ m{INFERNAL 1\.1}) { $self->{'_handlerset'} = '1.1'; } else { $self->{'_handlerset'} = 'latest'; # v1.0 } $self->_pushback($secondline); } elsif ($line =~ m{^CM\s\d+:}) { $self->{'_handlerset'} = 'pre-1.0'; } else { $self->{'_handlerset'} ='old'; } last; } $self->_pushback($line); #if ($self->{'_handlerset'} ne '1.0') { # $self->deprecated( # -message => "Parsing of Infernal pre-1.0 release is deprecated;\n". # "upgrading to Infernal 1.0 or above is highly recommended", # -version => 1.007); #} } return ($self->{'_handlerset'} eq '1.1') ? $self->_parse_v1_1 : ($self->{'_handlerset'} eq 'latest') ? $self->_parse_latest : ($self->{'_handlerset'} eq 'pre-1.0') ? $self->_parse_pre : $self->_parse_old; } sub _parse_v1_1 { my ($self) = @_; my $seentop = 0; local $/ = "\n"; my ($accession, $description) = ($self->query_accession, $self->query_description); my ($buffer, $last, %modelcounter, @hit_list, %hitindex, @hsp_list, %hspindex); $self->start_document(); $buffer = $self->_readline; if ( !defined $buffer || $buffer =~ m/^\[ok/ ) { # end of report return undef; } else { $self->_pushback($buffer); } PARSER: # Parse each line of report while ( defined( $buffer = $self->_readline ) ) { my $hit_counter = 0; my $lineorig = $buffer; chomp $buffer; # INFERNAL program name if ( $buffer =~ m/^\#\s(\S+)\s\:\:\s/ ) { $seentop = 1; my $prog = $1; $self->start_element( { 'Name' => 'Result' } ); $self->element_hash( { 'Infernal_program' => uc($prog) } ); } # INFERNAL version and release date elsif ( $buffer =~ m/^\#\sINFERNAL\s+(\S+)\s+\((.+)\)/ ) { my $version = $1; my $versiondate = $2; $self->{'_cmidline'} = $buffer; $self->element_hash( { 'Infernal_version' => $version } ); } # Query info elsif ( $buffer =~ /^\#\squery (?:\w+ )?file\:\s+(\S+)/ ) { $self->{'_cmfileline'} = $lineorig; $self->element_hash( { 'Infernal_cm' => $1 } ); } # Database info elsif ( $buffer =~ m/^\#\starget\s\S+\sdatabase\:\s+(\S+)/ ) { $self->{'_cmseqline'} = $lineorig; $self->element_hash( { 'Infernal_db' => $1 } ); } # Query data elsif ( $buffer =~ m/^Query:\s+(\S+)\s+\[CLEN=(\d+)\]$/ ) { $self->element_hash( { 'Infernal_query-def' => $1, 'Infernal_query-len' => $2, 'Infernal_query-acc' => $accession, 'Infernal_querydesc' => $description, } ); } # Get query accession elsif ( $buffer =~ s/^Accession:\s+// && ! $accession) { $buffer =~ s/\s+$//; $self->element_hash( { 'Infernal_query-acc' => $buffer } ); } # Get query description elsif ( $buffer =~ s/^Description:\s+// && ! $description) { $buffer =~ s/\s+$//; $self->element_hash( { 'Infernal_querydesc' => $buffer } ); } # Process hit table - including those below inclusion threshold elsif ( $buffer =~ m/^Hit scores:/) { @hit_list = (); # here is case there are multi-query reports while ( defined( $buffer = $self->_readline ) ) { if ( $buffer =~ m/^Hit alignments:/ ) { $self->_pushback($buffer); last; } elsif ( $buffer =~ m/^\s+rank\s+E-value/ || $buffer =~ m/\-\-\-/ || $buffer =~ m/^$/ || $buffer =~ m/No hits detected/ ) { next; } # Process hit $hit_counter++; my ($rank, $threshold, $eval, $score, $bias, $hitid, $start, $end, $strand, $mdl, $truc, $gc, @desc) = split( " ", $buffer ); my $desc = join " ", @desc; $desc = '' if ( !defined($desc) ); push @hit_list, [ $hitid, $desc, $eval, $score ]; $hitindex{ $hitid.$hit_counter } = $#hit_list; } } # Process hit alignments elsif ( $buffer =~ /^Hit alignments:/ ) { my $hitid; my $align_counter = 0; while ( defined( $buffer = $self->_readline ) ) { if ( $buffer =~ /^Internal CM pipeline statistics summary/ ) { $self->_pushback($buffer); last; } if ( $buffer =~ m/^\>\>\s(\S*)\s+(.*)/ ) { # defline of hit $hitid = $1; my $desc = $2; $align_counter++; my $hitid_alignctr = $hitid.$align_counter; $modelcounter{$hitid_alignctr} = 0; # The Hit Description from the Hit table can be truncated if # it is too long, so use the '>>' line description instead $hit_list[ $hitindex{$hitid_alignctr} ][1] = $desc; # Process hit information table while ( defined( $buffer = $self->_readline ) ) { if ( $buffer =~ m/^Internal CM pipeline statistics/ || $buffer =~ m/NC$/ || $buffer =~ m/^\>\>/ ) { $self->_pushback($buffer); last; } elsif ( $buffer =~ m/^\s+rank\s+E-value/ || $buffer =~ m/^\s----/ || $buffer =~ m/^$/ || $buffer =~ m/No hits detected/ ) { next; } # Get hsp data from table, push into @hsp; my ( $rank, $threshold, $eval, $score, $bias, $model, $cm_start, $cm_stop, $cm_cov, $seq_start, $seq_stop, $seq_strand, $seq_cov, $acc, $trunc, $gc, ) = split( " ", $buffer ); # Try to get the Hit Length from the alignment information. # For cmsearch, if sequence coverage ends in ']' it means that the # alignment runs full-length flush to the end of the target. my $hitlength = ( $seq_cov =~ m/\]$/ ) ? $seq_stop : 0; my $tmphit = $hit_list[ $hitindex{$hitid_alignctr} ]; if ( !defined $tmphit ) { $self->warn("Incomplete information: can't find HSP $hitid in list of hits\n"); next; } push @hsp_list, [ $hitid, $cm_start, $cm_stop, $seq_start, $seq_stop, $score, $eval, $hitlength]; $modelcounter{$hitid_alignctr}++; my $hsp_key = $hitid_alignctr . "_" . $modelcounter{$hitid_alignctr}; $hspindex{$hsp_key} = $#hsp_list; } } elsif ( $buffer =~ m/NC$/ ) { # start of HSP # need CS line to get number of spaces before structure data my $csline = $self->_readline; $csline =~ m/^(\s+)\S+ CS$/; my $offset = length($1); $self->_pushback($csline); $self->_pushback($buffer); # set up for loop my ($ct, $strln) = 0; my $hspdata; HSP: my %hspline = ('0' => 'nc', '1' => 'meta', '2' => 'query', '3' => 'midline', '4' => 'hit', '5' => 'pp'); HSP: while (defined ($buffer = $self->_readline)) { chomp $buffer; if ( $buffer =~ /^>>\s/ || $buffer =~ /^Internal CM pipeline statistics/) { $self->_pushback($buffer); last HSP; } elsif ( $ct % 6 == 0 && $buffer =~ /^$/ ) { next; } my $iterator = $ct % 6; # NC line ends with ' NC' so remove these from the strlen count $strln = ( length($buffer) - 3 ) if $iterator == 0; my $data = substr($buffer, $offset, $strln-$offset); $hspdata->{ $hspline{$iterator} } .= $data; $ct++; } # 'HSP' while loop my $strlen = 0; # catch any insertions and add them into the actual length while ($hspdata->{'query'} =~ m{\*\[\s*(\d+)\s*\]\*}g) { $strlen += $1; } # add on the actual residues $strlen += $hspdata->{'query'} =~ tr{A-Za-z}{A-Za-z}; my $metastr = ($self->convert_meta) ? ($self->simple_meta($hspdata->{'meta'})) : $hspdata->{'meta'}; my $hitid_alignctr = $hitid . $align_counter; my $hsp_key = $hitid_alignctr . "_" . $modelcounter{$hitid_alignctr}; my $hsp = $hsp_list[ $hspindex{$hsp_key} ]; push (@$hsp, $hspdata->{'nc'}, $metastr, $hspdata->{'query'}, $hspdata->{'midline'}, $hspdata->{'hit'}, $hspdata->{'pp'}); } } } # end of 'Hit alignments:' section of report # Process internal pipeline stats (end of report) elsif ( $buffer =~ m/Internal CM pipeline statistics summary:/ ) { while ( defined( $buffer = $self->_readline ) ) { last if ( $buffer =~ m!^//! ); if ( $buffer =~ /^Target sequences:\s+(\d+)\s+\((\d+) residues/ ) { $self->element_hash( { 'Infernal_db-len' => $1, 'Infernal_db-let' => $2, } ); } } last; # of the outer while defined $self->readline } # Leftovers else { #print STDERR "Missed line: $buffer\n"; $self->debug($buffer); } $last = $buffer; } # PARSER end # Final processing of hits and hsps my $hit_counter = 0; foreach my $hit ( @hit_list ) { $hit_counter++; my ($hit_name, $hit_desc, $hit_signif, $hit_score) = @$hit; my $num_hsp = $modelcounter{$hit_name . $hit_counter} || 0; $self->start_element( { 'Name' => 'Hit' } ); $self->element_hash( {'Hit_id' => $hit_name, 'Hit_desc' => $hit_desc, 'Hit_signif'=> $hit_signif, 'Hit_score' => $hit_score, 'Hit_bits' => $hit_score, } ); for my $i ( 1 .. $num_hsp ) { my $hsp_key = $hit_name . $hit_counter . "_" . $i; my $hsp = $hsp_list[ $hspindex{$hsp_key} ]; if ( defined $hsp ) { my $hspid = shift @$hsp; my ($cm_start, $cm_stop, $seq_start, $seq_stop, $score, $eval, $hitlength, $ncline, $csline, $qseq, $midline, $hseq, $pline) = @$hsp; if ( $hitlength != 0 ) { $self->element( { 'Name' => 'Hit_len', 'Data' => $hitlength } ); } $self->start_element( { 'Name' => 'Hsp' } ); $self->element_hash( { 'Hsp_stranded' => 'HIT', 'Hsp_query-from' => $cm_start, 'Hsp_query-to' => $cm_stop, 'Hsp_hit-from' => $seq_start, 'Hsp_hit-to' => $seq_stop, 'Hsp_score' => $score, 'Hsp_bit-score' => $score, 'Hsp_evalue' => $eval, 'Hsp_ncline' => $ncline, 'Hsp_structure' => $csline, 'Hsp_qseq' => $qseq, 'Hsp_midline' => $midline, 'Hsp_hseq' => $hseq, 'Hsp_pline' => $pline, } ); $self->end_element( { 'Name' => 'Hsp' } ); } } $self->end_element( { 'Name' => 'Hit' } ); } $self->end_element( { 'Name' => 'Result' } ); my $result = $self->end_document(); return $result; } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element { my ( $self, $data ) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; if ($type) { if ( $self->_eventHandler->will_handle($type) ) { my $func = sprintf( "start_%s", lc $type ); $self->_eventHandler->$func( $data->{'Attributes'} ); } unshift @{ $self->{'_elements'} }, $type; } if ( defined $type && $type eq 'result' ) { $self->{'_values'} = {}; $self->{'_result'} = undef; } } =head2 end_element Title : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none Args : hashref with at least 2 keys, 'Data' and 'Name' =cut sub end_element { my ( $self, $data ) = @_; my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; my $rc; if ($type) { if ( $self->_eventHandler->will_handle($type) ) { my $func = sprintf( "end_%s", lc $type ); $rc = $self->_eventHandler->$func( $self->{'_reporttype'}, $self->{'_values'} ); } my $lastelem = shift @{ $self->{'_elements'} }; # Infernal 1.1 allows one to know hit->length in some instances # so remove it so it doesn't carry over to next hit. Tried flushing # all 'type' values from {_values} buffer but it breaks legacy tests if ($type eq 'hit' ) { delete $self->{_values}{'HIT-length'}; delete $self->{_values}{'HSP-hit_length'}; } } elsif ( $MAPPING{$nm} ) { if ( ref( $MAPPING{$nm} ) =~ /hash/i ) { my $key = ( keys %{ $MAPPING{$nm} } )[0]; $self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } = $self->{'_last_data'}; } else { $self->{'_values'}->{ $MAPPING{$nm} } = $self->{'_last_data'}; } } else { $self->debug("unknown nm $nm, ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if ( defined $type && $type eq 'result' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convenience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element { my ( $self, $data ) = @_; # simple data calls (%MAPPING) do not need start_element $self->characters($data); $self->end_element($data); } =head2 element_hash Title : element Usage : $eventhandler->element_hash({'Hsp_hit-from' => $start, 'Hsp_hit-to' => $end, 'Hsp_score' => $lastscore}); Function: Convenience method that takes multiple simple data elements and maps to appropriate parameters Returns : none Args : Hash ref with the mapped key (in %MAPPING) and value =cut sub element_hash { my ($self, $data) = @_; $self->throw("Must provide data hash ref") if !$data || !ref($data); for my $nm (sort keys %{$data}) { next if $data->{$nm} && $data->{$nm} =~ m{^\s*$}o; if ( $MAPPING{$nm} ) { if ( ref( $MAPPING{$nm} ) =~ /hash/i ) { my $key = ( keys %{ $MAPPING{$nm} } )[0]; $self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } = $data->{$nm}; } else { $self->{'_values'}->{ $MAPPING{$nm} } = $data->{$nm}; } } } } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters { my ( $self, $data ) = @_; return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/o ); $self->{'_last_data'} = $data->{'Data'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub within_element { my ( $self, $name ) = @_; return 0 if ( !defined $name || !defined $self->{'_elements'} || scalar @{ $self->{'_elements'} } == 0 ); foreach ( @{ $self->{'_elements'} } ) { return 1 if ( $_ eq $name ); } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'within' because 'in' only tests its immediate parent. Returns : boolean Args : string element name =cut sub in_element { my ( $self, $name ) = @_; return 0 if !defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name ); } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handle a start document event Returns : none Args : none =cut sub start_document { my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'} = undef; $self->{'_elements'} = []; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document { my ($self) = @_; return $self->{'_result'}; } =head2 result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } =head2 model Title : model Usage : my $model = $parser->model(); Function: Get/Set model; Infernal currently does not output the model name (Rfam ID) Returns : String (name of model) Args : [optional] String (name of model) =cut sub model { my $self = shift; return $self->{'_model'} = shift if @_; return $self->{'_model'}; } =head2 database Title : database Usage : my $database = $parser->database(); Function: Get/Set database; pre-v.1 versions of Infernal do not output the database name Returns : String (database name) Args : [optional] String (database name) =cut sub database { my $self = shift; return $self->{'_database'} = shift if @_; return $self->{'_database'}; } =head2 algorithm Title : algorithm Usage : my $algorithm = $parser->algorithm(); Function: Get/Set algorithm; pre-v.1 versions of Infernal do not output the algorithm name Returns : String (algorithm name) Args : [optional] String (algorithm name) =cut sub algorithm { my $self = shift; return $self->{'_algorithm'} = shift if @_; return $self->{'_algorithm'}; } =head2 query_accession Title : query_accession Usage : my $acc = $parser->query_accession(); Function: Get/Set query (model) accession; pre-v1.1 Infernal does not output the accession number (Rfam accession #) Returns : String (accession) Args : [optional] String (accession) =cut sub query_accession { my $self = shift; return $self->{'_query_accession'} = shift if @_; return $self->{'_query_accession'}; } =head2 query_description Title : query_description Usage : my $acc = $parser->query_description(); Function: Get/Set query (model) description; pre-v1.1 Infernal does not output the Rfam description Returns : String (description) Args : [optional] String (description) =cut sub query_description { my $self = shift; return $self->{'_query_description'} = shift if @_; return $self->{'_query_description'}; } =head2 hsp_minscore Title : hsp_minscore Usage : my $cutoff = $parser->hsp_minscore(); Function: Get/Set min bit score cutoff (for generating Hits/HSPs) Returns : score (number) Args : [optional] score (number) =cut sub hsp_minscore { my $self = shift; return $self->{'_hsp_minscore'} = shift if @_; return $self->{'_hsp_minscore'}; } =head2 convert_meta Title : convert_meta Usage : $parser->convert_meta(1); Function: Get/Set boolean flag for converting Infernal WUSS format to a simple bracketed format (simple WUSS by default) Returns : boolean flag (TRUE or FALSE) Args : [optional] boolean (eval's to TRUE or FALSE) =cut sub convert_meta { my $self = shift; return $self->{'_convert_meta'} = shift if @_; return $self->{'_convert_meta'}; } =head2 version Title : version Usage : $parser->version(); Function: Set the Infernal cmsearch version Returns : version Args : [optional] version =cut sub version { my $self = shift; return $self->{'_version'} = shift if @_; return $self->{'_version'}; } =head2 structure_symbols Title : structure_symbols Usage : my $hashref = $parser->structure_symbols(); Function: Get/Set RNA structure symbols Returns : Hash ref of delimiters (5' stem, 3' stem, single-strand, etc) : default = < (5-prime) > (3-prime) : (single-strand) ? (unknown) . (gap) Args : Hash ref of substitute delimiters, using above keys. =cut sub structure_symbols { my ($self, $delim) = @_; if ($delim) { if (ref($delim) =~ m{HASH}) { my %data = %{ $delim }; for my $d (@VALID_SYMBOLS) { if ( exists $data{$d} ) { $self->{'_delimiter'}->{$d} = $data{$d}; } } } else { $self->throw("Args to helix_delimiters() should be in a hash reference"); } } return $self->{'_delimiter'}; } =head2 simple_meta Title : simple_meta Usage : my $string = $parser->simple_meta($str); Function: converts more complex WUSS meta format into simple bracket format using symbols defined in structure_symbols() Returns : converted string Args : [required] string to convert Note : This is a very simple conversion method to get simple bracketed format from Infernal data. If the convert_meta() flag is set, this is the method used to convert the strings. =cut sub simple_meta { my ($self, $str) = @_; $self->throw("No string arg sent!") if !$str; my $structs = $self->structure_symbols(); my ($ls, $rs, $ss, $unk, $gap) = ($structs->{'5-prime'}, $structs->{'3-prime'}, $structs->{'single-strand'}, $structs->{'unknown'}, $structs->{'gap'}); $str =~ s{[\(\<\[\{]}{$ls}g; $str =~ s{[\)\>\]\}]}{$rs}g; $str =~ s{[:,_-]}{$ss}g; $str =~ s{\.}{$gap}g; # unknown not handled yet return $str; } ## private methods # this is a hack which guesses the format and sets the handler for parsing in # an instance; it'll be taken out when infernal 1.0 is released sub _parse_latest { my ($self) = @_; my $seentop = 0; local $/ = "\n"; my ($accession, $description) = ($self->query_accession, $self->query_description); my ($maxscore, $mineval, $minpval); $self->start_document(); my ($lasthit, $lastscore, $lasteval, $lastpval, $laststart, $lastend); PARSER: while (my $line = $self->_readline) { next if $line =~ m{^\s+$}; # stats aren't parsed yet... if ($line =~ m{^\#\s+cmsearch}xms) { $seentop = 1; $self->start_element({'Name' => 'Result'}); $self->element_hash({ 'Infernal_program' => 'CMSEARCH' }); } elsif ($line =~ m{^\#\sINFERNAL\s+(\d+\.\d+)}xms) { $self->element_hash({ 'Infernal_version' => $1, }); } elsif ($line =~ m{^\#\scommand:.*?\s(\S+)$}xms) { $self->element_hash({ 'Infernal_db' => $1, }); } elsif ($line =~ m{^\#\s+dbsize\(Mb\):\s+(\d+\.\d+)}xms) { # store absolute DB length $self->element_hash({ 'Infernal_db-let' => $1 * 1e6 }); } elsif ($line =~ m{^CM(?:\s(\d+))?:\s*(\S+)}xms) { # not sure, but it's possible single reports may contain multiple # models; if so, they should be rolled over into a new ResultI #print STDERR "ACC: $accession\nDESC: $description\n"; $self->element_hash({ 'Infernal_query-def' => $2, # present in output now 'Infernal_query-acc' => $accession, 'Infernal_querydesc' => $description }); } elsif ($line =~ m{^>\s*(\S+)} ){ #$self->debug("Start Hit: Found hit:$1\n"); if ($self->in_element('hit')) { $self->element_hash({'Hit_score' => $maxscore, 'Hit_bits' => $maxscore}); ($maxscore, $minpval, $mineval) = undef; $self->end_element({'Name' => 'Hit'}); } $lasthit = $1; } elsif ($line =~ m{ ^\sQuery\s=\s\d+\s-\s\d+,\s # Query start/end Target\s=\s(\d+)\s-\s(\d+) # Target start/end }xmso) { # Query (model) start/end always the same, determined from # the HSP length ($laststart, $lastend) = ($1, $2); #$self->debug("Found hit coords:$laststart - $lastend\n"); } elsif ($line =~ m{ ^\sScore\s=\s([\d\.]+),\s # Score = Bitscore (for now) (?:E\s=\s([\d\.e-]+),\s # E-val optional P\s=\s([\d\.e-]+),\s)? # P-val optional GC\s= # GC not captured }xmso ) { ($lastscore, $lasteval, $lastpval) = ($1, $2, $3); #$self->debug(sprintf("Found hit data:Score:%s,Eval:%s,Pval:%s\n",$lastscore, $lasteval||'', $lastpval||'')); $maxscore ||= $lastscore; if ($lasteval && $lastpval) { $mineval ||= $lasteval; $minpval ||= $lastpval; $mineval = ($mineval > $lasteval) ? $lasteval : $mineval; $minpval = ($minpval > $lastpval) ? $lastpval : $minpval; } $maxscore = ($maxscore < $lastscore) ? $lastscore : $maxscore; if (!$self->within_element('hit')) { my ($gi, $acc, $ver) = $self->_get_seq_identifiers($lasthit); $self->start_element({'Name' => 'Hit'}); $self->element_hash({ 'Hit_id' => $lasthit, 'Hit_accession' => $ver ? "$acc.$ver" : $acc ? $acc : $lasthit, 'Hit_gi' => $gi }); } if (!$self->in_element('hsp')) { $self->start_element({'Name' => 'Hsp'}); } # hsp is similar to older output } elsif ($line =~ m{^(\s+)[<>\{\}\(\)\[\]:_,-\.]+}xms) { # start of HSP $self->_pushback($line); # set up for loop #$self->debug("Start HSP\n"); # what is length of the gap to the structure data? my $offset = length($1); my ($ct, $strln) = 0; my $hsp; HSP: my %hsp_key = ('0' => 'meta', '1' => 'query', '2' => 'midline', '3' => 'hit'); HSP: while (defined ($line = $self->_readline)) { chomp $line; next if (!$line); # toss empty lines # next if $line =~ m{^\s*$}; # toss empty lines # it is possible to have homology lines consisting # entirely of spaces if the subject has a large # insertion where nothing matches the model # exit loop if at end of file or upon next hit/HSP if ($line =~ m{^\s{0,2}\S+}) { $self->_pushback($line); last HSP; } # iterate to keep track of each line (4 lines per hsp block) my $iterator = $ct % 4; # strlen set only with structure lines (proper length) $strln = length($line) if $iterator == 0; # only grab the data needed (hit start and stop in hit line above) my $data = substr($line, $offset, $strln-$offset); $hsp->{ $hsp_key{$iterator} } .= $data; $ct++; } # query start, end are from the actual query length (entire hit is # mapped to CM data, so all CM data is represented) # works for now... if ($self->in_element('hsp')) { # In some cases with HSPs unaligned residues are present in # the hit or query (Ex: '*[ 8]*' is 8 unaligned residues). # This info needs to be passed on unmodifed to the HSP class # and handled there as it is subjectively changed based on # use. my $strlen = 0; # catch any insertions and add them into the actual length while ($hsp->{'query'} =~ m{\*\[\s*(\d+)\s*\]\*}g) { $strlen += $1; } # add on the actual residues $strlen += $hsp->{'query'} =~ tr{A-Za-z}{A-Za-z}; my $metastr = ($self->convert_meta) ? ($self->simple_meta($hsp->{'meta'})) : $hsp->{'meta'}; $self->element_hash( {'Hsp_stranded' => 'HIT', 'Hsp_qseq' => $hsp->{'query'}, 'Hsp_hseq' => $hsp->{'hit'}, 'Hsp_midline' => $hsp->{'midline'}, 'Hsp_structure' => $metastr, 'Hsp_query-from' => 1, 'Infernal_query-len' => $strlen, 'Hsp_query-to' => $strlen, 'Hsp_hit-from' => $laststart, 'Hsp_hit-to' => $lastend, 'Hsp_score' => $lastscore, 'Hsp_bit-score' => $lastscore, }); $self->element_hash( {'Hsp_evalue' => $lasteval, 'Hsp_pvalue' => $lastpval, }) if ($lasteval && $lastpval); $self->end_element({'Name' => 'Hsp'}); } # result now ends with // and 'Fin' } elsif ($line =~ m{^//}xms ) { if ($self->within_element('result') && $seentop) { if ($self->in_element('hit')) { $self->element_hash({'Hit_score' => $maxscore, 'Hit_bits' => $maxscore}); # don't know where to put minpval yet $self->element_hash({'Hit_signif' => $mineval}) if $mineval; $self->element_hash({'Hit_p' => $minpval}) if $minpval; $self->end_element({'Name' => 'Hit'}); } last PARSER; } } } $self->within_element('hit') && $self->end_element( { 'Name' => 'Hit' } ); $self->end_element( { 'Name' => 'Result' } ) if $seentop; return $self->end_document(); } # cmsearch 0.81 (pre-1.0) sub _parse_pre { my ($self) = @_; my $seentop = 0; local $/ = "\n"; my ($accession, $db, $algorithm, $description, $version) = ($self->query_accession, $self->database, $self->algorithm, $self->query_description, '0.81'); my ($maxscore, $mineval, $minpval); $self->start_document(); my ($lasthit, $lastscore, $lasteval, $lastpval, $laststart, $lastend); PARSER: while (my $line = $self->_readline) { next if $line =~ m{^\s+$}; # stats aren't parsed yet... if ($line =~ m{CM\s\d+:\s*(\S+)}xms) { #$self->debug("Start Result: Found model:$1\n"); if (!$self->within_element('result')) { $seentop = 1; $self->start_element({'Name' => 'Result'}); $self->element_hash({ 'Infernal_program' => $algorithm, 'Infernal_query-def' => $1, # present in output now 'Infernal_query-acc' => $accession, 'Infernal_querydesc' => $description, 'Infernal_db' => $db }); } } elsif ($line =~ m{^>\s*(\S+)} ){ #$self->debug("Start Hit: Found hit:$1\n"); if ($self->in_element('hit')) { $self->element_hash({'Hit_score' => $maxscore, 'Hit_bits' => $maxscore}); ($maxscore, $minpval, $mineval) = undef; $self->end_element({'Name' => 'Hit'}); } $lasthit = $1; } elsif ($line =~ m{ ^\sQuery\s=\s\d+\s-\s\d+,\s # Query start/end Target\s=\s(\d+)\s-\s(\d+) # Target start/end }xmso) { # Query (model) start/end always the same, determined from # the HSP length ($laststart, $lastend) = ($1, $2); #$self->debug("Found hit coords:$laststart - $lastend\n"); } elsif ($line =~ m{ ^\sScore\s=\s([\d\.]+),\s # Score = Bitscore (for now) (?:E\s=\s([\d\.e-]+),\s # E-val optional P\s=\s([\d\.e-]+),\s)? # P-val optional GC\s= # GC not captured }xmso ) { ($lastscore, $lasteval, $lastpval) = ($1, $2, $3); #$self->debug(sprintf("Found hit data:Score:%s,Eval:%s,Pval:%s\n",$lastscore, $lasteval||'', $lastpval||'')); $maxscore ||= $lastscore; if ($lasteval && $lastpval) { $mineval ||= $lasteval; $minpval ||= $lastpval; $mineval = ($mineval > $lasteval) ? $lasteval : $mineval; $minpval = ($minpval > $lastpval) ? $lastpval : $minpval; } $maxscore = ($maxscore < $lastscore) ? $lastscore : $maxscore; if (!$self->within_element('hit')) { my ($gi, $acc, $ver) = $self->_get_seq_identifiers($lasthit); $self->start_element({'Name' => 'Hit'}); $self->element_hash({ 'Hit_id' => $lasthit, 'Hit_accession' => $ver ? "$acc.$ver" : $acc ? $acc : $lasthit, 'Hit_gi' => $gi }); } if (!$self->in_element('hsp')) { $self->start_element({'Name' => 'Hsp'}); } # hsp is similar to older output } elsif ($line =~ m{^(\s+)[<>\{\}\(\)\[\]:_,-\.]+}xms) { # start of HSP $self->_pushback($line); # set up for loop #$self->debug("Start HSP\n"); # what is length of the gap to the structure data? my $offset = length($1); my ($ct, $strln) = 0; my $hsp; HSP: my %hsp_key = ('0' => 'meta', '1' => 'query', '2' => 'midline', '3' => 'hit'); HSP: while (defined ($line = $self->_readline)) { chomp $line; next if (!$line); # toss empty lines # next if $line =~ m{^\s*$}; # toss empty lines # it is possible to have homology lines consisting # entirely of spaces if the subject has a large # insertion where nothing matches the model # exit loop if at end of file or upon next hit/HSP if ($line =~ m{^\s{0,2}\S+}) { $self->_pushback($line); last HSP; } # iterate to keep track of each line (4 lines per hsp block) my $iterator = $ct%4; # strlen set only with structure lines (proper length) $strln = length($line) if $iterator == 0; # only grab the data needed (hit start and stop in hit line above) my $data = substr($line, $offset, $strln-$offset); $hsp->{ $hsp_key{$iterator} } .= $data; $ct++; } # query start, end are from the actual query length (entire hit is # mapped to CM data, so all CM data is represented) # works for now... if ($self->in_element('hsp')) { my $strlen = $hsp->{'query'} =~ tr{A-Za-z}{A-Za-z}; my $metastr; $metastr = ($self->convert_meta) ? ($self->simple_meta($hsp->{'meta'})) : ($hsp->{'meta'}); $self->element_hash( {'Hsp_stranded' => 'HIT', 'Hsp_qseq' => $hsp->{'query'}, 'Hsp_hseq' => $hsp->{'hit'}, 'Hsp_midline' => $hsp->{'midline'}, 'Hsp_structure' => $metastr, 'Hsp_query-from' => 1, 'Infernal_query-len' => $strlen, 'Hsp_query-to' => $strlen, 'Hsp_hit-from' => $laststart, 'Hsp_hit-to' => $lastend, 'Hsp_score' => $lastscore, 'Hsp_bit-score' => $lastscore, }); $self->element_hash( {'Hsp_evalue' => $lasteval, 'Hsp_pvalue' => $lastpval, }) if ($lasteval && $lastpval); $self->end_element({'Name' => 'Hsp'}); } # result now ends with // and 'Fin' } elsif ($line =~ m{^//}xms ) { if ($self->within_element('result') && $seentop) { $self->element( {'Name' => 'Infernal_version', 'Data' => $version} ); if ($self->in_element('hit')) { $self->element_hash({'Hit_score' => $maxscore, 'Hit_bits' => $maxscore}); # don't know where to put minpval yet $self->element_hash({'Hit_signif' => $mineval}) if $mineval; $self->end_element({'Name' => 'Hit'}); } last PARSER; } } } $self->within_element('hit') && $self->end_element( { 'Name' => 'Hit' } ); $self->end_element( { 'Name' => 'Result' } ) if $seentop; return $self->end_document(); } # cmsearch 0.72 and below; will likely be dropped when Infernal 1.0 is released sub _parse_old { my ($self) = @_; my $seentop = 0; local $/ = "\n"; my ($accession, $db, $algorithm, $model, $description, $version) = ($self->query_accession, $self->database, $self->algorithm, $self->model, $self->query_description, $self->version); my $maxscore; my $cutoff = $self->hsp_minscore; $self->start_document(); local ($_); my $line; my ($lasthit, $lastscore, $laststart, $lastend); my $hitline; PARSER: while ( defined( $line = $self->_readline ) ) { next if $line =~ m{^\s+$}; # bypass this for now... next if $line =~ m{^HMM\shit}; # pre-0.81 if ($line =~ m{^sequence:\s+(\S+)} ){ if (!$self->within_element('result')) { $seentop = 1; $self->start_element({'Name' => 'Result'}); $self->element_hash({ 'Infernal_program' => $algorithm, 'Infernal_query-def' => $model, 'Infernal_query-acc' => $accession, 'Infernal_querydesc' => $description, 'Infernal_db' => $db }); } if ($self->in_element('hit')) { $self->element_hash({'Hit_score' => $maxscore, 'Hit_bits' => $maxscore}); $maxscore = undef; $self->end_element({'Name' => 'Hit'}); } $lasthit = $1; } elsif ($line =~ m{^hit\s+\d+\s+:\s+(\d+)\s+(\d+)\s+(\d+\.\d+)\s+bits}xms) { ($laststart, $lastend, $lastscore) = ($1, $2, $3); $maxscore = $lastscore unless $maxscore; if ($lastscore > $cutoff) { if (!$self->within_element('hit')) { my ($gi, $acc, $ver) = $self->_get_seq_identifiers($lasthit); $self->start_element({'Name' => 'Hit'}); $self->element_hash({ 'Hit_id' => $lasthit, 'Hit_accession' => $ver ? "$acc.$ver" : $acc ? $acc : $lasthit, 'Hit_gi' => $gi }); } # necessary as infernal 0.71 has repeated hit line if (!$self->in_element('hsp')) { $self->start_element({'Name' => 'Hsp'}); } $maxscore = ($maxscore < $lastscore) ? $lastscore : $maxscore; } } elsif ($line =~ m{^(\s+)[<>\{\}\(\)\[\]:_,-\.]+}xms) { # start of HSP $self->_pushback($line); # set up for loop # what is length of the gap to the structure data? my $offset = length($1); my ($ct, $strln) = 0; my $hsp; HSP: my %hsp_key = ('0' => 'meta', '1' => 'query', '2' => 'midline', '3' => 'hit'); HSP: while ($line = $self->_readline) { next if $line =~ m{^\s*$}; # toss empty lines chomp $line; # exit loop if at end of file or upon next hit/HSP if (!defined($line) || $line =~ m{^\S+}) { $self->_pushback($line); last HSP; } # iterate to keep track of each line (4 lines per hsp block) my $iterator = $ct%4; # strlen set only with structure lines (proper length) $strln = length($line) if $iterator == 0; # only grab the data needed (hit start and stop in hit line above) my $data = substr($line, $offset, $strln-$offset); $hsp->{ $hsp_key{$iterator} } .= $data; $ct++; } # query start, end are from the actual query length (entire hit is # mapped to CM data, so all CM data is represented) # works for now... if ($self->in_element('hsp')) { my $strlen = $hsp->{'query'} =~ tr{A-Za-z}{A-Za-z}; my $metastr; # Ugh...these should be passed in a hash $metastr = ($self->convert_meta) ? ($self->simple_meta($hsp->{'meta'})) : ($hsp->{'meta'}); $self->element_hash( {'Hsp_stranded' => 'HIT', 'Hsp_qseq' => $hsp->{'query'}, 'Hsp_hseq' => $hsp->{'hit'}, 'Hsp_midline' => $hsp->{'midline'}, 'Hsp_structure' => $metastr, 'Hsp_query-from' => 1, 'Infernal_query-len' => $strlen, 'Hsp_query-to' => $strlen, 'Hsp_hit-from' => $laststart, 'Hsp_hit-to' => $lastend, 'Hsp_score' => $lastscore, 'Hsp_bit-score' => $lastscore }); $self->end_element({'Name' => 'Hsp'}); } } elsif ($line =~ m{^memory}xms || $line =~ m{^CYK\smemory}xms ) { if ($self->within_element('result') && $seentop) { $self->element( {'Name' => 'Infernal_version', 'Data' => $version} ); if ($self->in_element('hit')) { $self->element_hash({'Hit_score' => $maxscore, 'Hit_bits' => $maxscore}); $self->end_element({'Name' => 'Hit'}); } last PARSER; } } } $self->within_element('hit') && $self->end_element( { 'Name' => 'Hit' } ); $self->end_element( { 'Name' => 'Result' } ) if $seentop; return $self->end_document(); } 1; BioPerl-1.007002/Bio/SearchIO/megablast.pm000444000766000024 3203613155576320 20202 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::megablast # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::megablast - a driver module for Bio::SearchIO to parse megablast reports (format 0) =head1 SYNOPSIS # do not use this module directly use Bio::SearchIO; # for default format output from megablast my $in = Bio::SearchIO->new(-file => 'file.mbl', -format => 'megablast', -report_format => 0); while( my $r = $in->next_result ) { while( my $hit = $r->next_hit ) { while( my $hsp = $hit->next_hsp ) { } } } =head1 DESCRIPTION Beware! Because of the way megablast report format 0 is coded, realize that score means # gap characters + # mismatches for a HSP. The docs from NCBI regarding FORMAT 0 # 0: Produce one-line output for each alignment, in the form # # 'subject-id'=='[+-]query-id' (s_off q_off s_end q_end) score # # Here subject(query)-id is a gi number, an accession or some other type of # identifier found in the FASTA definition line of the respective sequence. # # + or - corresponds to same or different strand alignment. # # Score for non-affine gapping parameters means the total number of # differences (mismatches + gap characters). For affine case it is the # actual (raw) score of the alignment. FORMAT 1 parsing has not been implemented FORMAT 2 parsing should work with the SearchIO 'blast' parser =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::megablast; use strict; use vars qw(%MAPPING %MODEMAP $DEFAULT_BLAST_WRITER_CLASS); use base qw(Bio::SearchIO); BEGIN { # mapping of MegaBlast terms to Bioperl hash keys %MODEMAP = ('MegaBlastOutput' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); # This should really be done more intelligently, like with # XSLT %MAPPING = ( 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hit_score' => 'HIT-score', 'Hsp_score' => 'HSP-score', 'Hsp_identity' => 'HSP-identical', 'Hsp_positive' => 'HSP-conserved', 'Hit_id' => 'HIT-name', 'MegaBlastOutput_program' => 'RESULT-algorithm_name', 'MegaBlastOutput_query-def'=> 'RESULT-query_name', ); $DEFAULT_BLAST_WRITER_CLASS = 'Bio::SearchIO::Writer::HitTableWriter'; } =head2 new Title : new Usage : my $obj = Bio::SearchIO::blast->new(); Function: Builds a new Bio::SearchIO::blast object Returns : Bio::SearchIO::blast Args : -fh/-file => filehandle/filename to BLAST file -format => 'blast' =cut sub _initialize { my ($self,@args) = @_; $self->SUPER::_initialize(@args); my ($fmt) = $self->_rearrange([qw(REPORT_FORMAT)], @args); $self->throw("Must provide a value for -report_format when initializing a megablast parser") unless defined $fmt ; $self->report_format($fmt); return 1; } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result{ my ($self) = @_; local $/ = "\n"; local $_; my $fmt = $self->report_format; my ($lastquery,$lasthit); while( defined($_ = $self->_readline) ) { if( $fmt == 0 ) { if( /^\'(\S+)\'\=\=\'(\+|\-)(\S+)\'\s+ \((\d+)\s+(\d+)\s+(\d+)\s+(\d+)\)\s+ (\d+)/ox ) { my ($hit,$strand,$query, $h_start,$q_start,$h_end,$q_end, $score) = ($1,$2,$3,$4,$5,$6,$7,$8); if( ! defined $lastquery ) { $self->start_element({'Name' => 'MegaBlastOutput'}); $self->element({'Name' => 'MegaBlastOutput_program', 'Data' => 'MEGABLAST'}); $self->element({'Name' => 'MegaBlastOutput_query-def', 'Data' => $query}); } elsif( $lastquery ne $query ) { $self->_pushback($_); $self->end_element({'Name' => 'Hit'}) if( defined $lasthit); $self->end_element({ 'Name' => 'MegaBlastOutput'}); $lasthit = undef; $lastquery = undef; return $self->end_document(); } if( ! defined $lasthit || $lasthit ne $hit ) { $self->end_element({'Name' => 'Hit'}) if( defined $lasthit); $self->start_element({'Name' => 'Hit'}); $self->element({'Name' => 'Hit_id', 'Data' => $hit}); } $self->start_element({'Name' => 'Hsp'}); $self->element({'Name' => 'Hsp_score', 'Data' => $score}); # flip flop start/end if strand is < 0 # since strandedness is inferred from the query # because of the way it is coded all queries will # be on the forward strand and hits will be either # +/- # also the NCBI docs state: # 0: Produce one-line output for each alignment, in the form # # 'subject-id'=='[+-]query-id' (s_off q_off s_end q_end) score # # Here subject(query)-id is a gi number, an accession or some other type of # identifier found in the FASTA definition line of the respective sequence. # # + or - corresponds to same or different strand alignment. # # Score for non-affine gapping parameters means the total number of # differences (mismatches + gap characters). For affine case it is the # actual (raw) score of the alignment. # and yet when rev strand hits are made I see # (MBL 2.2.4) # 'Contig634'=='-503384' (1 7941 321 7620) 19 # so the query is on the rev strand and the # subject is on the fwd strand # so I am flip-flopping everything when I see a '-' if( $strand eq '-' ) { ($h_start,$h_end) = ( $h_end,$h_start); ($q_start,$q_end) = ( $q_end,$q_start); } $self->element({'Name' => 'Hsp_hit-from', 'Data' => $h_start}); $self->element({'Name' => 'Hsp_hit-to', 'Data' => $h_end}); $self->element({'Name' => 'Hsp_query-from', 'Data' => $q_start}); $self->element({'Name' => 'Hsp_query-to', 'Data' => $q_end}); # might not be quite right -- need to know length of the HSP my $numid = (abs($q_end - $q_start) - $score); $self->element({'Name' => 'Hsp_identity', 'Data' => $numid}); $self->element({'Name' => 'Hsp_positive', 'Data' => $numid}); $self->end_element({'Name' => 'Hsp'}); $lasthit = $hit; $lastquery = $query; } else { $self->debug("Unknown line in fmt0 parsing: $_"); } } } if( defined $lastquery && $fmt == 0 ) { $self->end_element({'Name' => 'Hit'}) if( defined $lasthit); $self->end_element({ 'Name' => 'MegaBlastOutput'}); return $self->end_document(); } return; } =head2 report_format Title : report_format Usage : $obj->report_format($newval) Function: Get/Set the report_format value Returns : value of report_format (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub report_format{ my $self = shift; return $self->{'_report_format'} = shift if @_; return $self->{'_report_format'}; } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element{ my ($self,$data) = @_; # we currently do not care about attributes my $nm = $data->{'Name'}; if( my $type = $MODEMAP{$nm} ) { $self->_mode($type); if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("start_%s",lc $type); $self->_eventHandler->$func($data->{'Attributes'}); } unshift @{$self->{'_elements'}}, $type; } if($nm eq 'MegaBlastOutput') { $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_mode'} = ''; } } =head2 end_element Title : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub end_element { my ($self,$data) = @_; my $nm = $data->{'Name'}; my $rc; if( my $type = $MODEMAP{$nm} ) { if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("end_%s",lc $type); $rc = $self->_eventHandler->$func($self->{'_reporttype'}, $self->{'_values'}); } shift @{$self->{'_elements'}}; } elsif( $MAPPING{$nm} ) { if ( ref($MAPPING{$nm}) =~ /hash/i ) { my $key = (keys %{$MAPPING{$nm}})[0]; $self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'}; } else { $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'}; } } else { $self->warn( "unknown nm $nm ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if( $nm eq 'MegaBlastOutput' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element{ my ($self,$data) = @_; $self->start_element($data); $self->characters($data); $self->end_element($data); } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters{ my ($self,$data) = @_; return unless defined $data->{'Data'}; $self->{'_last_data'} = $data->{'Data'}; } =head2 _mode Title : _mode Usage : $obj->_mode($newval) Function: Example : Returns : value of _mode Args : newvalue (optional) =cut sub _mode{ my ($self,$value) = @_; if( defined $value) { $self->{'_mode'} = $value; } return $self->{'_mode'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub within_element{ my ($self,$name) = @_; return 0 if ( ! defined $name && ! defined $self->{'_elements'} || scalar @{$self->{'_elements'}} == 0) ; foreach ( @{$self->{'_elements'}} ) { if( $_ eq $name ) { return 1; } } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub in_element{ my ($self,$name) = @_; return 0 if ! defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name) } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handles a start document event Returns : none Args : none =cut sub start_document{ my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_mode'} = ''; $self->{'_elements'} = []; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document{ my ($self,@args) = @_; return $self->{'_result'}; } =head2 result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } sub report_count { shift->result_count } 1; BioPerl-1.007002/Bio/SearchIO/psl.pm000444000766000024 4447413155576320 17052 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::psl # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::psl - A parser for PSL output (UCSC) =head1 SYNOPSIS use Bio::SearchIO; my $parser = Bio::SearchIO->new(-file => 'file.psl', -format => 'psl'); while( my $result = $parser->next_result ) { } =head1 DESCRIPTION This is a SearchIO driver for PSL format. PSL format is documented here: http://genome.ucsc.edu/goldenPath/help/customTrack.html#PSL By default it assumes PSL output came from BLAT you can override that by specifying -program_name =E 'BLASTZ' when initializing the SearchIO object. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::psl; use vars qw(%MAPPING %MODEMAP $DEFAULT_WRITER_CLASS $DefaultProgramName); use strict; use Bio::Search::HSP::HSPFactory; use Bio::Search::Hit::HitFactory; use Bio::Search::Result::ResultFactory; $DefaultProgramName = 'BLAT'; $DEFAULT_WRITER_CLASS = 'Bio::SearchIO::Writer::HitTableWriter'; # mapping of terms to Bioperl hash keys %MODEMAP = ( 'PSLOutput' => 'result', 'Result' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); %MAPPING = ( 'Hsp_bit-score' => 'HSP-bits', 'Hsp_score' => 'HSP-score', 'Hsp_evalue' => 'HSP-evalue', 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_positive' => 'HSP-conserved', 'Hsp_identity' => 'HSP-identical', 'Hsp_mismatches' => 'HSP-mismatches', 'Hsp_qgapblocks' => 'HSP-query_gapblocks', 'Hsp_hgapblocks' => 'HSP-hit_gapblocks', 'Hsp_gaps' => 'HSP-hsp_gaps', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_query-frame' => 'HSP-query_frame', 'Hsp_hit-frame' => 'HSP-hit_frame', 'Hit_id' => 'HIT-name', 'Hit_len' => 'HIT-length', 'Hit_accession' => 'HIT-accession', 'Hit_def' => 'HIT-description', 'Hit_signif' => 'HIT-significance', 'Hit_score' => 'HIT-score', 'Hit_bits' => 'HIT-bits', 'PSLOutput_program' => 'RESULT-algorithm_name', 'PSLOutput_version' => 'RESULT-algorithm_version', 'PSLOutput_query-def' => 'RESULT-query_name', 'PSLOutput_query-len' => 'RESULT-query_length', 'PSLOutput_query-acc' => 'RESULT-query_accession', 'PSLOutput_querydesc' => 'RESULT-query_description', 'PSLOutput_db' => 'RESULT-database_name', 'PSLOutput_db-len' => 'RESULT-database_entries', 'PSLOutput_db-let' => 'RESULT-database_letters', ); use base qw(Bio::SearchIO); =head2 new Title : new Usage : my $obj = Bio::SearchIO::psl->new(); Function: Builds a new Bio::SearchIO::psl object Returns : an instance of Bio::SearchIO::psl Args : =cut sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); my ($pname) = $self->_rearrange( [qw(PROGRAM_NAME)], @args ); $self->program_name( $pname || $DefaultProgramName ); $self->_eventHandler->register_factory( 'result', Bio::Search::Result::ResultFactory->new( -type => 'Bio::Search::Result::GenericResult' ) ); $self->_eventHandler->register_factory( 'hit', Bio::Search::Hit::HitFactory->new( -type => 'Bio::Search::Hit::GenericHit' ) ); $self->_eventHandler->register_factory( 'hsp', Bio::Search::HSP::HSPFactory->new( -type => 'Bio::Search::HSP::PSLHSP' ) ); } =head2 next_result Title : next_result Usage : my $result = $parser->next_result Function: Parse the next result from the data stream Returns : L or undef if no more results Args : none =cut sub next_result { my ($self) = @_; my ( $lastquery, $lasthit ); local $/ = "\n"; local $_; # skip over any header lines while( defined($_ = $self->_readline) and ! /^\d+\s+\d+\s+/ ) {} $self->_pushback($_); # now start the main parsing loop while ( defined( $_ = $self->_readline ) ) { my ( $matches, $mismatches, $rep_matches, $n_count, $q_num_insert, $q_base_insert, $t_num_insert, $t_base_insert, $strand, $q_name, $q_length, $q_start, $q_end, $t_name, $t_length, $t_start, $t_end, $block_count, $block_sizes, $q_starts, $t_starts ) = split; $q_length > 0 or $self->throw("parse error, invalid query length '$q_length'"); my $score = sprintf( "%.2f", 100 * ( $matches + $mismatches + $rep_matches ) / $q_length ); # this is overall percent identity... my $match_total = $matches + $mismatches + $rep_matches; $match_total > 0 or $self->throw("parse error, matches + mismatches + rep_matches must be > 0!"); my $percent_id = sprintf("%.2f", 100 * ( $matches + $rep_matches ) / $match_total ); # Remember Jim's code is 0 based if ( defined $lastquery && $lastquery ne $q_name ) { $self->end_element( { 'Name' => 'Hit' } ); $self->end_element( { 'Name' => 'PSLOutput' } ); $self->_pushback($_); return $self->end_document; } elsif ( !defined $lastquery ) { $self->{'_result_count'}++; $self->start_element( { 'Name' => 'PSLOutput' } ); $self->element( { 'Name' => 'PSLOutput_program', 'Data' => $self->program_name } ); $self->element( { 'Name' => 'PSLOutput_query-def', 'Data' => $q_name } ); $self->element( { 'Name' => 'PSLOutput_query-len', 'Data' => $q_length } ); $self->start_element( { 'Name' => 'Hit' } ); $self->element( { 'Name' => 'Hit_id', 'Data' => $t_name } ); $self->element( { 'Name' => 'Hit_len', 'Data' => $t_length } ); $self->element( { 'Name' => 'Hit_score', 'Data' => $score } ); } elsif ( $lasthit ne $t_name ) { $self->end_element( { 'Name' => 'Hit' } ); $self->start_element( { 'Name' => 'Hit' } ); $self->element( { 'Name' => 'Hit_id', 'Data' => $t_name } ); $self->element( { 'Name' => 'Hit_len', 'Data' => $t_length } ); $self->element( { 'Name' => 'Hit_score', 'Data' => $score } ); } my $identical = $matches + $rep_matches; $self->start_element( { 'Name' => 'Hsp' } ); $self->element( { 'Name' => 'Hsp_score', 'Data' => $score } ); $self->element( { 'Name' => 'Hsp_identity', 'Data' => $identical } ); $self->element( { 'Name' => 'Hsp_positive', 'Data' => $identical } ); $self->element( { 'Name' => 'Hsp_mismatches', 'Data' => $mismatches } ); $self->element( { 'Name' => 'Hsp_gaps', 'Data' => $q_base_insert + $t_base_insert } ); # query gaps are the number of target inserts and vice-versa $self->element( { 'Name' => 'Hsp_querygaps', 'Data' => $t_base_insert } ); $self->element( { 'Name' => 'Hsp_hitgaps', 'Data' => $q_base_insert } ); if ( $strand eq '+' ) { $self->element( { 'Name' => 'Hsp_query-from', 'Data' => $q_start + 1 } ); $self->element( { 'Name' => 'Hsp_query-to', 'Data' => $q_end } ); } else { $self->element( { 'Name' => 'Hsp_query-to', 'Data' => $q_start + 1 } ); $self->element( { 'Name' => 'Hsp_query-from', 'Data' => $q_end } ); } my $hsplen = ($q_base_insert + $t_base_insert + abs( $t_end - $t_start ) + abs( $q_end - $q_start ))/2; $self->element( { 'Name' => 'Hsp_hit-from', 'Data' => $t_start + 1 } ); $self->element( { 'Name' => 'Hsp_hit-to', 'Data' => $t_end } ); $self->element( { 'Name' => 'Hsp_align-len', 'Data' => $hsplen } ); # cleanup trailing commas in some output $block_sizes =~ s/\,$//; $q_starts =~ s/\,$//; $t_starts =~ s/\,$//; my @blocksizes = split( /,/, $block_sizes ); # block sizes my @qstarts = split( /,/, $q_starts ); # starting position of each block # in query my @tstarts = split( /,/, $t_starts ); # starting position of each block # in target my ( @qgapblocks, @hgapblocks ); for ( my $i = 0 ; $i < $block_count ; $i++ ) { if ( $strand eq '+' ) { push @qgapblocks, [ $qstarts[$i] + 1, $blocksizes[$i] ]; } else { push @qgapblocks, [ $q_length - $qstarts[$i], $blocksizes[$i] ]; } push @hgapblocks, [ $tstarts[$i] + 1, $blocksizes[$i] ]; } $self->element( { 'Name' => 'Hsp_qgapblocks', 'Data' => \@qgapblocks } ); $self->element( { 'Name' => 'Hsp_hgapblocks', 'Data' => \@hgapblocks } ); $self->end_element( { 'Name' => 'Hsp' } ); $lastquery = $q_name; $lasthit = $t_name; } if ( defined $lasthit || defined $lastquery ) { $self->end_element( { 'Name' => 'Hit' } ); $self->end_element( { 'Name' => 'Result' } ); return $self->end_document; } } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element { my ( $self, $data ) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; if ( my $type = $MODEMAP{$nm} ) { $self->_mode($type); if ( $self->_eventHandler->will_handle($type) ) { my $func = 'start_'.lc $type; $self->_eventHandler->$func( $data->{'Attributes'} ); } unshift @{ $self->{'_elements'} }, $type; } if ( $nm eq 'PSLOutput' ) { $self->{'_values'} = {}; $self->{'_result'} = undef; $self->{'_mode'} = ''; } } =head2 end_element Title : end_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : return value from the associated end_$type event handler Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub end_element { my ( $self, $data ) = @_; my $nm = $data->{'Name'}; my $rc; # Hsp are sort of weird, in that they end when another # object begins so have to detect this in end_element for now if ( my $type = $MODEMAP{$nm} ) { if ( $self->_eventHandler->will_handle($type) ) { my $func = 'end_'.lc $type; $rc = $self->_eventHandler->$func( $self->{'_reporttype'}, $self->{'_values'} ); } shift @{ $self->{'_elements'} }; } elsif ( $MAPPING{$nm} ) { if ( ref( $MAPPING{$nm} ) =~ /hash/i ) { my $key = ( keys %{ $MAPPING{$nm} } )[0]; $self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } = $self->{'_last_data'}; } else { $self->{'_values'}->{ $MAPPING{$nm} } = $self->{'_last_data'}; } } else { $self->warn( __PACKAGE__ . "::end_element: unknown nm '$nm', ignoring\n" ); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if ( defined $nm && defined $MODEMAP{$nm} && $MODEMAP{$nm} eq 'result' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element { my ( $self, $data ) = @_; $self->start_element($data); $self->characters($data); $self->end_element($data); } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters { my ( $self, $data ) = @_; return unless ( defined $data->{'Data'} ); if ( $data->{'Data'} =~ /^\s+$/ ) { return unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/; } if ( $self->in_element('hsp') && $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) { $self->{'_last_hspdata'}->{ $data->{'Name'} } .= $data->{'Data'}; } $self->{'_last_data'} = $data->{'Data'}; } =head2 _mode Title : _mode Usage : $obj->_mode($newval) Function: Example : Returns : value of _mode Args : newvalue (optional) =cut sub _mode { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_mode'} = $value; } return $self->{'_mode'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub within_element { my ( $self, $name ) = @_; return 0 if (!defined $name && !defined $self->{'_elements'} || scalar @{ $self->{'_elements'} } == 0 ); foreach ( @{ $self->{'_elements'} } ) { if ( $_ eq $name ) { return 1; } } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub in_element { my ( $self, $name ) = @_; return 0 if !defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name ); } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handles a start document event Returns : none Args : none =cut sub start_document { my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'} = undef; $self->{'_mode'} = ''; $self->{'_elements'} = []; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document { my ( $self, @args ) = @_; return $self->{'_result'}; } =head2 result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } sub report_count { shift->result_count } =head2 program_name Title : program_name Usage : $obj->program_name($newval) Function: Get/Set the program name Returns : value of program_name (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub program_name { my $self = shift; $self->{'program_name'} = shift if @_; return $self->{'program_name'} || $DefaultProgramName; } 1; BioPerl-1.007002/Bio/SearchIO/rnamotif.pm000444000766000024 6003013155576320 20055 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::rnamotif # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::rnamotif - SearchIO-based RNAMotif parser =head1 SYNOPSIS # do not call this module directly. Use Bio::SearchIO. =head1 DESCRIPTION This is a highly experimental SearchIO-based parser for output from the rnamotif program (one of the programs in the RNAMotif suite). It currently parses only raw rnamotif output for RNAMotif versions 3.0 and above; older versions may work but will not be supported. rmfmt output will not be supported at this time. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Fields Email cjfields-at-uiuc-dot-edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::rnamotif; use strict; use base qw(Bio::SearchIO); my %MODEMAP = ( 'Result' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); my %MAPPING = ( # commented out tags have not been assigned 'Hsp_score' => 'HSP-score', 'Hsp_custom-data' => 'HSP-custom_score', # rnamotif has no evalue # descriptor has no start, end; same as hit start, end 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', # descriptor has no start, end 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_align-len' => 'HSP-hsp_length', # build this from scratch, simple WUSS-format 'Hsp_structure' => 'HSP-meta', 'Hsp_stranded' => 'HSP-stranded', # not supported for RNAMotif 'Hit_id' => 'HIT-name', 'Hit_accession' => 'HIT-accession', 'Hit_gi' => 'HIT-ncbi_gi', 'Hit_def' => 'HIT-description', 'Hit_score' => 'HIT-score', # best HSP score 'RNAMotif_program' => 'RESULT-algorithm_name', # get/set 'RNAMotif_version' => 'RESULT-algorithm_version', # get/set 'RNAMotif_query-def'=> 'RESULT-query_name', # get/set # No length (query is a descriptor) 'RNAMotif_query-acc'=> 'RESULT-query_accession', # get/set 'RNAMotif_querydesc'=> 'RESULT-query_description', # get/set 'RNAMotif_db' => 'RESULT-database_name', # get/set ); # use structure_delimiters to set custom delimiters my @VALID_SYMBOLS = qw(5-prime 3-prime single-strand unknown); my %STRUCTURE_SYMBOLS = ( '5-prime' => '<', '3-prime' => '>', 'single-strand' => '.', 'unknown' => '?' # may add more for quartets, triplets ); my $DEFAULT_VERSION = '3.0.3'; =head2 new Title : new Usage : my $obj = Bio::SearchIO->new(); Function: Builds a new Bio::SearchIO::rnamotif object Returns : Bio::SearchIO::rnamotif parser Args : -fh/-file => RNAMotif filename -format => 'rnamotif' -model => query model (or descriptor, in this case) -database => database name (default undef) -query_acc => query accession (default undef) -hsp_minscore => minimum HSP score cutoff -hsp_maxscore => maximum HSP score cutoff -symbols => hash ref of structure symbols to use (default symbols in %STRUCTURE_SYMBOLS hash) =cut sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); my ($version, $model, $database, $maxcutoff, $mincutoff, $seqdistance, $accession, $symbols) = $self->_rearrange([qw(VERSION MODEL DATABASE HSP_MAXSCORE HSP_MINSCORE SEQ_DISTANCE QUERY_ACC SYMBOLS)],@args); my $handler = $self->_eventHandler; $handler->register_factory( 'result', Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Result::GenericResult', -interface => 'Bio::Search::Result::ResultI', -verbose => $self->verbose ) ); $handler->register_factory( 'hit', Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::Hit::ModelHit', -interface => 'Bio::Search::Hit::HitI', -verbose => $self->verbose ) ); $handler->register_factory( 'hsp', Bio::Factory::ObjectFactory->new( -type => 'Bio::Search::HSP::ModelHSP', -interface => 'Bio::Search::HSP::HSPI', -verbose => $self->verbose ) ); $model && $self->model($model); $database && $self->database($database); $accession && $self->query_accession($accession); $version ||= $DEFAULT_VERSION; $self->algorithm_version($version); $self->throw("Cannot define both a minimal and maximal cutoff") if (defined($mincutoff) && defined($maxcutoff)); defined($mincutoff) && $self->hsp_minscore($mincutoff); defined($maxcutoff) && $self->hsp_maxscore($maxcutoff); $symbols ||= \%STRUCTURE_SYMBOLS; $self->structure_symbols($symbols); } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result { my ($self) = @_; my $seentop = 0; local $/ = "\n"; local $_; my ($rm, $d, $descriptor, $file, $oktobuild); my ($hitid, $hitdesc, $hspid, $lastid, $lastscore); my $sprintf; # user-determined Result data my ($accession, $db, $model) = ($self->query_accession, $self->database, $self->model); # HSP building options my $hsp_min = $self->hsp_minscore; my $hsp_max = $self->hsp_maxscore; my $version = $self->algorithm_version; my $laststart; my $verbose = $self->verbose; # cache for speed? $self->start_document(); PARSER: while ( defined( my $line = $self->_readline ) ) { # start of report next if $line =~ m{^\s+$}; if (index($line,'#RM') == 0) { if (index($line,'#RM scored') == 0 ) { if ($seentop) { $self->_pushback($line); last PARSER; } $self->start_element({'Name' => 'Result'}); $self->element_hash({ 'RNAMotif_program' => 'rnamotif', 'RNAMotif_version' => $version, 'RNAMotif_query-acc' => $accession, 'RNAMotif_db' => $db }); $seentop = 1; #$self->debug("Start result\n"); } elsif (index($line,'#RM descr') == 0) { ($rm, $d, $descriptor) = split ' ', $line, 3; # toss $rm, $d; keep $descr chomp $descriptor; $self->{'_descriptor'} = $descriptor; $self->element( {'Name' => 'RNAMotif_querydesc', 'Data' => $descriptor} ); } elsif(index($line,'#RM dfile') == 0) { ($rm, $d, $file) = split ' ', $line, 3; # toss $rm, $d; keep $file chomp $file; $self->element( {'Name' => 'RNAMotif_query-def', 'Data' => $file} ); } else { $self->debug("Unrecognized line: $line"); } } elsif ($line =~ s{^>}{}) { chomp $line; ($hitid, $hitdesc) = split ' ',$line,2; if ($self->within_element('hit') && ($hitid ne $lastid)) { $self->element( {'Name' => 'Hit_score', 'Data' => $lastscore} ) if $lastscore; $self->end_element({'Name' => 'Hit'}); $self->start_element({'Name' => 'Hit'}); } elsif (!$self->within_element('hit')) { $self->start_element({'Name' => 'Hit'}); } my ($gi, $acc, $ver) = $self->_get_seq_identifiers($hitid); $self->element_hash({ 'Hit_id' => $hitid, 'Hit_gi' => $gi, 'Hit_accession' => $ver ? "$acc.$ver" : $acc ? $acc : $hitid, 'Hit_def' => $hitdesc} ); $lastid = $hitid; } elsif ($line =~ m{^(\S+)\s+(.+?)\s+(\d+)\s+(\d+)\s+(\d+)\s(.*)$}xm) { chomp $line; my $hspid = $1; my ($score, $strand, $start, $length , $seq) = ($2, $3, $4, $5, $6); $score *= 1; # implicitly cast any odd '0.000' to float # sanity check ids unless ($hitid eq $hspid) { $self->throw("IDs do not match!"); } # check score for possible sprintf data, mark as such, cache result if (!defined($sprintf)) { if ($score =~ m{[^0-9.-]+}gxms) { if (defined $hsp_min || defined $hsp_max ) { $self->warn("HSP data likely contains custom score; ". "ignoring min/maxscore"); } $sprintf = $oktobuild = 1; } else { $sprintf = 0; } } if (!$sprintf) { if (($hsp_min && $score <= $hsp_min) || ($hsp_max && ($score >= $hsp_max)) ) { # do not build HSP $oktobuild = 0; } else { $oktobuild = 1; # store best hit score based on the hsp min/maxscore only if (defined $hsp_min && $score > $hsp_min) { $lastscore = $score if !$lastscore || $score > $lastscore; } elsif (defined $hsp_max && $score < $hsp_max) { $lastscore = $score if !$lastscore || $score < $lastscore; } } } # build HSP if ($oktobuild) { my $end; # calculate start/end if( $strand==0 ) { $end = $start + $length -1; } else { $end = $start - $length + 1; } my ($rna, $meta) = $self->_motif2meta($seq, $descriptor); $self->start_element({'Name' => 'Hsp'}); my $rnalen = $rna =~ tr{ATGCatgc}{ATGCatgc}; $self->element_hash({ 'Hsp_stranded' => 'HIT', 'Hsp_hseq' => $rna, 'Hsp_query-from' => 1, 'Hsp_query-to' =>length($rna), 'Hsp_hit-from' => $start, 'Hsp_hit-to' => $end, 'Hsp_structure' => $meta, 'Hsp_align-len' => length($rna), 'Hsp_score' => $sprintf ? undef : $score, 'Hsp_custom-data' => $sprintf ? $score : undef, }); $self->end_element({'Name' => 'Hsp'}); $oktobuild = 0 if (!$sprintf); } } } if ($self->within_element('hit')) { $self->element( {'Name' => 'Hit_score', 'Data' => $lastscore} ) if $lastscore; $self->end_element( { 'Name' => 'Hit' } ); } if ($seentop) { $self->end_element( { 'Name' => 'Result' } ); } return $self->end_document(); } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element { my ( $self, $data ) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; if ($type) { if ( $self->_eventHandler->will_handle($type) ) { my $func = sprintf( "start_%s", lc $type ); $self->_eventHandler->$func( $data->{'Attributes'} ); } unshift @{ $self->{'_elements'} }, $type; } if ( defined $type && $type eq 'result' ) { $self->{'_values'} = {}; $self->{'_result'} = undef; } } =head2 end_element Title : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none Args : hashref with at least 2 keys, 'Data' and 'Name' =cut sub end_element { my ( $self, $data ) = @_; my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; my $rc; if ($type) { if ( $self->_eventHandler->will_handle($type) ) { my $func = sprintf( "end_%s", lc $type ); $rc = $self->_eventHandler->$func( $self->{'_reporttype'}, $self->{'_values'} ); } my $lastelem = shift @{ $self->{'_elements'} }; } elsif ( $MAPPING{$nm} ) { if ( ref( $MAPPING{$nm} ) =~ /hash/i ) { my $key = ( keys %{ $MAPPING{$nm} } )[0]; $self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } = $self->{'_last_data'}; } else { $self->{'_values'}->{ $MAPPING{$nm} } = $self->{'_last_data'}; } } else { $self->debug("unknown nm $nm, ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if ( defined $type && $type eq 'result' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convenience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element { my ( $self, $data ) = @_; # simple data calls (%MAPPING) do not need start_element $self->characters($data); $self->end_element($data); } =head2 element_hash Title : element Usage : $eventhandler->element_hash({'Hsp_hit-from' => $start, 'Hsp_hit-to' => $end, 'Hsp_score' => $lastscore}); Function: Convenience method that takes multiple simple data elements and maps to appropriate parameters Returns : none Args : Hash ref with the mapped key (in %MAPPING) and value =cut sub element_hash { my ($self, $data) = @_; $self->throw("Must provide data hash ref") if !$data || !ref($data); for my $nm (sort keys %{$data}) { next if $data->{$nm} && $data->{$nm} =~ m{^\s*$}o; if ( $MAPPING{$nm} ) { if ( ref( $MAPPING{$nm} ) =~ /hash/i ) { my $key = ( keys %{ $MAPPING{$nm} } )[0]; $self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } = $data->{$nm}; } else { $self->{'_values'}->{ $MAPPING{$nm} } = $data->{$nm}; } } } } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters { my ( $self, $data ) = @_; return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/o ); $self->{'_last_data'} = $data->{'Data'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub within_element { my ( $self, $name ) = @_; return 0 if ( !defined $name || !defined $self->{'_elements'} || scalar @{ $self->{'_elements'} } == 0 ); foreach ( @{ $self->{'_elements'} } ) { return 1 if ( $_ eq $name ); } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'within' because 'in' only tests its immediate parent. Returns : boolean Args : string element name =cut sub in_element { my ( $self, $name ) = @_; return 0 if !defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name ); } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handle a start document event Returns : none Args : none =cut sub start_document { my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'} = undef; $self->{'_elements'} = []; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document { my ($self) = @_; return $self->{'_result'}; } =head2 result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } =head2 descriptor Title : descriptor Usage : my $descr = $parser->descriptor(); Function: Get/Set descriptor name. Some versions of RNAMotif do not add the descriptor name to the output. This also overrides any name found while parsing. Returns : String (name of model) Args : [optional] String (name of model) =cut sub descriptor { my $self = shift; return $self->{'_descriptor'} = shift if @_; return $self->{'_descriptor'}; } =head2 model Title : model Usage : my $model = $parser->model(); Function: Get/Set model; Infernal currently does not output the model name (Rfam ID) Returns : String (name of model) Args : [optional] String (name of model) Note : this is a synonym for descriptor() =cut sub model { shift->descriptor(@_) } =head2 database Title : database Usage : my $database = $parser->database(); Function: Get/Set database; Infernal currently does not output the database name Returns : String (database name) Args : [optional] String (database name) =cut sub database { my $self = shift; return $self->{'_database'} = shift if @_; return $self->{'_database'}; } =head2 query_accession Title : query_accession Usage : my $acc = $parser->query_accession(); Function: Get/Set query (model) accession; RNAMotif currently does not output the accession number Returns : String (accession) Args : [optional] String (accession) =cut sub query_accession { my $self = shift; return $self->{'_query_accession'} = shift if @_; return $self->{'_query_accession'}; } =head2 algorithm_version Title : algorithm_version Usage : my $ver = $parser->algorithm_version(); Function: Get/Set algorithm version (not defined in RNAMotif output) Returns : String (accession) Args : [optional] String (accession) =cut sub algorithm_version { my $self = shift; return $self->{'_algorithm'} = shift if @_; return $self->{'_algorithm'}; } =head2 hsp_minscore Title : hsp_minscore Usage : my $cutoff = $parser->hsp_minscore(); Function: Get/Set min score cutoff (for generating Hits/HSPs). Returns : score (number) Args : [optional] score (number) Note : Cannot be set along with hsp_maxscore() =cut sub hsp_minscore { my ($self, $score) = shift; $self->throw('Minscore not set to a number') if ($score && $score !~ m{[0-9.]+}); return $self->{'_hsp_minscore'} = shift if @_; return $self->{'_hsp_minscore'}; } =head2 hsp_maxscore Title : hsp_maxscore Usage : my $cutoff = $parser->hsp_maxscore(); Function: Get/Set max score cutoff (for generating Hits/HSPs). Returns : score (number) Args : [optional] score (number) Note : Cannot be set along with hsp_minscore() =cut sub hsp_maxscore { my ($self, $score) = shift; $self->throw('Maxscore not set to a number') if ($score && $score !~ m{[0-9.]+}); return $self->{'_hsp_maxscore'} = shift if @_; return $self->{'_hsp_maxscore'}; } =head2 structure_symbols Title : structure_symbols Usage : my $hashref = $parser->structure_symbols(); Function: Get/Set RNA structure symbols Returns : Hash ref of delimiters (5' stem, 3' stem, single-strand, etc) : default = < (5-prime) > (3-prime) . (single-strand) ? (unknown) Args : Hash ref of substitute delimiters, using above keys. =cut sub structure_symbols { my ($self, $delim) = @_; if ($delim) { if (ref($delim) =~ m{HASH}) { my %data = %{ $delim }; for my $d (@VALID_SYMBOLS) { if ( exists $data{$d} ) { $self->{'_delimiter'}->{$d} = $data{$d}; } } } else { $self->throw("Args to helix_delimiters() should be in a hash reference"); } } return $self->{'_delimiter'}; } #Private methods =head2 _motif2meta Title : _motif2meta Usage : my ($rna, $meta) = $parser->_motif2meta($str, $descr); Function: Creates meta string from sequence and descriptor Returns : array of sequence, meta strings Args : Array of string data and descriptor data Note: This is currently a quick and simple way of making simple RNA structures (stem-loops, helices, etc) from RNAMotif descriptor data in the output file. It does not currently work with pseudoknots, triplets, G-quartets, or other more complex RNA structural motifs. =cut sub _motif2meta { my ($self, $str, $descriptor) = @_; my ($rna, $meta); my @desc_el = split ' ',$descriptor; my @seq_el = split ' ',$str; my $symbol = $self->structure_symbols(); if ($#desc_el != $#seq_el) { $self->throw("Descriptor elements and seq elements do not match"); } while (@desc_el) { my $struct; my ($seq, $motif) = (shift @seq_el, shift @desc_el); $struct = (index($motif,'h5') == 0) ? $symbol->{'5-prime'} : (index($motif,'h3') == 0) ? $symbol->{'3-prime'} : (index($motif,'ss') == 0) ? $symbol->{'single-strand'} : (index($motif,'ctx')== 0) ? $symbol->{'single-strand'} : $symbol->{'unknown'}; $meta .= $struct x (length($seq)); $rna .= $seq; } return ($rna, $meta); } 1; BioPerl-1.007002/Bio/SearchIO/sim4.pm000444000766000024 5247113155576320 17124 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::sim4 # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::sim4 - parser for Sim4 alignments =head1 SYNOPSIS # do not use this module directly, it is a driver for SearchIO use Bio::SearchIO; my $searchio = Bio::SearchIO->new(-file => 'results.sim4', -format => 'sim4'); while ( my $result = $searchio->next_result ) { while ( my $hit = $result->next_hit ) { while ( my $hsp = $hit->next_hsp ) { # ... } } } =head1 DESCRIPTION This is a driver for the SearchIO system for parsing Sim4. http://globin.cse.psu.edu/html/docs/sim4.html Cannot parse LAV or 'exon file' formats (A=2 or A=5) =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 CONTRIBUTORS Luc Gauthier (lgauthie@hotmail.com) =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::sim4; use strict; use vars qw($DEFAULTFORMAT %ALIGN_TYPES %MAPPING %MODEMAP $DEFAULT_WRITER_CLASS); use POSIX; use Bio::SearchIO::SearchResultEventBuilder; use base qw(Bio::SearchIO); $DEFAULTFORMAT = 'SIM4'; $DEFAULT_WRITER_CLASS = 'Bio::SearchIO::Writer::HitTableWriter'; %ALIGN_TYPES = ( 0 => 'Ruler', 1 => 'Query', 2 => 'Mid', 3 => 'Sbjct' ); %MODEMAP = ( 'Sim4Output' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); %MAPPING = ( 'Hsp_query-from'=> 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_qlength' => 'HSP-query_length', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_hlength' => 'HSP-hit_length', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_midline' => 'HSP-homology_seq', 'Hsp_score' => 'HSP-score', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_identity' => 'HSP-identical', 'Hit_id' => 'HIT-name', 'Hit_desc' => 'HIT-description', 'Hit_len' => 'HIT-length', 'Sim4Output_program' => 'RESULT-algorithm_name', 'Sim4Output_query-def' => 'RESULT-query_name', 'Sim4Output_query-desc'=> 'RESULT-query_description', 'Sim4Output_query-len' => 'RESULT-query_length', ); =head2 new Title : new Usage : my $obj = Bio::SearchIO::sim4->new(); Function: Builds a new Bio::SearchIO::sim4 object Returns : an instance of Bio::SearchIO::sim4 Args : =cut =head2 next_result Title : next_result Usage : my $result = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result { my ($self) = @_; local $/ = "\n"; local $_; # Declare/adjust needed variables $self->{'_last_data'} = ''; my ($seentop, $qfull, @hsps, %alignment, $format); my $hit_direction = 1; # Start document and main element $self->start_document(); $self->start_element({'Name' => 'Sim4Output'}); my $lastquery = ''; # Read output report until EOF while( defined($_ = $self->_readline) ) { # Skip empty lines, chomp filled ones next if( /^\s+$/); chomp; # Make sure sim4 output format is not 2 or 5 if (!$seentop) { if ( /^\#:lav/ ) { $format = 2; } elsif ( /^<|>/ ) { $format = 5; } $self->throw("Bio::SearchIO::sim4 module cannot parse 'type $format' outputs.") if $format; } # This line indicates the start of a new hit if( /^seq1\s*=\s*(\S+),\s+(\d+)/ ) { my ($nm,$desc) = ($1,$2); # First hit? Adjust some parameters if so if ( ! $seentop ) { $self->element( {'Name' => 'Sim4Output_query-def', 'Data' => $nm} ); $self->element( {'Name' => 'Sim4Output_query-len', 'Data' => $desc} ); $seentop = 1; } elsif( $nm ne $lastquery ) { $self->_pushback($_); last; } $lastquery = $nm; # A previous HSP may need to be ended $self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') ); # A previous hit exists? End it and reset needed variables if ( $self->in_element('hit') ) { foreach (@hsps) { $self->start_element({'Name' => 'Hsp'}); while (my ($name, $data) = each %$_) { $self->{'_currentHSP'}{$name} = $data; } $self->end_element({'Name' => 'Hsp'}); $self->{'_currentHSP'} = {}; } $format = 0 if @hsps; @hsps = (); %alignment = (); $qfull = 0; $hit_direction = 1; $self->end_element({'Name' => 'Hit'}); } # This line describes the current hit... so let's start it } elsif( /^seq2\s*=\s*(\S+)\s+\(>?(\S+)\s*\),\s*(\d+)/ ) { $self->start_element({'Name' => 'Hit'}); $self->element( {'Name' => 'Hit_id', 'Data' => $2} ); $self->element( {'Name' => 'Hit_desc', 'Data' => $1} ); $self->element( {'Name' => 'Hit_len', 'Data' => $3} ); # This line may give additional details about query or subject } elsif( /^>(\S+)\s*(.*)?/ ) { # Previous line was query details... this time subject details if( $qfull ) { $format = 4 if !$format; $self->element({'Name' => 'Hit_desc', 'Data' => $2}); # First line of this type is always query details for a given hit } else { $self->element({'Name' => 'Sim4Output_query-desc', 'Data' => $2}); $qfull = 1; } # This line indicates that subject is on reverse strand } elsif( /^\(complement\)/ ) { $hit_direction = -1; # This line describes the current HSP... so add it to @hsps array } elsif( /^\(?(\d+)\-(\d+)\)?\s+\(?(\d+)\-(\d+)\)?\s+(\d+)/ ) { my ($qs,$qe,$hs,$he,$pid) = ($1,$2,$3,$4,$5); push @hsps, { 'Hsp_query-from' => $qs, 'Hsp_query-to' => $qe, 'Hsp_hit-from' => $hit_direction >= 0 ? $hs : $he, 'Hsp_hit-to' => $hit_direction >= 0 ? $he : $hs, 'Hsp_identity' => 0, #can't determine correctly from raw pct 'Hsp_qlength' => abs($qe - $qs) + 1, 'Hsp_hlength' => abs($he - $hs) + 1, 'Hsp_align-len' => abs($qe - $qs) + 1, }; # This line indicates the start of an alignment block } elsif( /^\s+(\d+)\s/ ) { # Store the current alignment block in a hash for( my $i = 0; defined($_) && $i < 4; $i++ ) { my ($start, $string) = /^\s+(\d*)\s(.*)/; $alignment{$ALIGN_TYPES{$i}} = { start => $start, string => $i != 2 ? $string : (' ' x (length($alignment{$ALIGN_TYPES{$i-1}}{string}) - length($string))) . $string }; $_ = $self->_readline(); } # 'Ruler' line indicates the start of a new HSP if ($alignment{Ruler}{start} == 0) { $format = @hsps ? 3 : 1 if !$format; # A previous HSP may need to be ended $self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') ); # Start the new HSP and fill the '_currentHSP' property with available details $self->start_element({'Name' => 'Hsp'}); $self->{'_currentHSP'} = @hsps ? shift @hsps : { 'Hsp_query-from' => $alignment{Query}{start}, 'Hsp_hit-from' => $alignment{Sbjct}{start}, } } # Midline indicates a boundary between two HSPs if ( $alignment{Mid}{string} =~ /<|>/g ) { my ($hsp_start, $hsp_end); # Are we currently in an open HSP? if ( $self->in_element('hsp') ) { # Find end pos, adjust 'gaps', 'seq' and 'midline' properties... then close HSP $hsp_end = (pos $alignment{Mid}{string}) - 1; $self->{'_currentHSP'}{'Hsp_querygaps'} += ($self->{'_currentHSP'}{'Hsp_qseq'} .= substr($alignment{Query}{string}, 0, $hsp_end)) =~ s/ /-/g; $self->{'_currentHSP'}{'Hsp_hitgaps'} += ($self->{'_currentHSP'}{'Hsp_hseq'} .= substr($alignment{Sbjct}{string}, 0, $hsp_end)) =~ s/ /-/g; ($self->{'_currentHSP'}{'Hsp_midline'} .= substr($alignment{Mid}{string}, 0, $hsp_end)) =~ s/-/ /g; $self->end_element({'Name' => 'Hsp'}); # Does a new HSP start in the current alignment block? if ( $alignment{Mid}{string} =~ /\|/g ) { # Find start pos, start new HSP and fill it with available details $hsp_start = (pos $alignment{Mid}{string}) - 1; $self->start_element({'Name' => 'Hsp'}); $self->{'_currentHSP'} = @hsps ? shift @hsps : {}; $self->{'_currentHSP'}{'Hsp_querygaps'} += ($self->{'_currentHSP'}{'Hsp_qseq'} = substr($alignment{Query}{string}, $hsp_start)) =~ s/ /-/g; $self->{'_currentHSP'}{'Hsp_hitgaps'} += ($self->{'_currentHSP'}{'Hsp_hseq'} = substr($alignment{Sbjct}{string}, $hsp_start)) =~ s/ /-/g; ($self->{'_currentHSP'}{'Hsp_midline'} = substr($alignment{Mid}{string}, $hsp_start)) =~ s/-/ /g; } } # No HSP is currently open... else { # Find start pos, start new HSP and fill it with available # details then skip to next alignment block $hsp_start = index($alignment{Mid}{string}, '|'); $self->start_element({'Name' => 'Hsp'}); $self->{'_currentHSP'} = @hsps ? shift @hsps : { 'Hsp_query-from' => $alignment{Query}{start}, }; $self->{'_currentHSP'}{'Hsp_querygaps'} += ($self->{'_currentHSP'}{'Hsp_qseq'} = substr($alignment{Query}{string}, $hsp_start)) =~ s/ /-/g; $self->{'_currentHSP'}{'Hsp_hitgaps'} += ($self->{'_currentHSP'}{'Hsp_hseq'} = substr($alignment{Sbjct}{string}, $hsp_start)) =~ s/ /-/g; ($self->{'_currentHSP'}{'Hsp_midline'} = substr($alignment{Mid}{string}, $hsp_start)) =~ s/-/ /g; next; } } # Current alignment block does not contain HSPs boundary else { # Start a new HSP if none is currently open # (Happens if last boundary finished at the very end of previous block) if ( !$self->in_element('hsp') ) { $self->start_element({'Name' => 'Hsp'}); $self->{'_currentHSP'} = @hsps ? shift @hsps : { 'Hsp_query-from' => $alignment{Query}{start}, 'Hsp_hit-from' => $alignment{Sbjct}{start}, } } # Adjust details of the current HSP $self->{'_currentHSP'}{'Hsp_query-from'} ||= $alignment{Query}{start} - length($self->{'_currentHSP'}{'Hsp_qseq'} || ''); $self->{'_currentHSP'}{'Hsp_hit-from'} ||= $alignment{Sbjct}{start} - length($self->{'_currentHSP'}{'Hsp_hseq'} || ''); $self->{'_currentHSP'}{'Hsp_querygaps'} += ($self->{'_currentHSP'}{'Hsp_qseq'} .= $alignment{Query}{string}) =~ s/ /-/g; $self->{'_currentHSP'}{'Hsp_hitgaps'} += ($self->{'_currentHSP'}{'Hsp_hseq'} .= $alignment{Sbjct}{string}) =~ s/ /-/g; ($self->{'_currentHSP'}{'Hsp_midline'} .= $alignment{Mid}{string}) =~ s/-/ /g; } } } # We are done reading the sim4 report, end everything and return if( $seentop ) { # end HSP if needed $self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') ); # end Hit if needed if ( $self->in_element('hit') ) { foreach (@hsps) { $self->start_element({'Name' => 'Hsp'}); while (my ($name, $data) = each %$_) { $self->{'_currentHSP'}{$name} = $data; } $self->end_element({'Name' => 'Hsp'}); } $self->end_element({'Name' => 'Hit'}); } # adjust result's algorithm name, end output and return $self->element({'Name' => 'Sim4Output_program', 'Data' => $DEFAULTFORMAT . ' (A=' . (defined $format ? $format : '?') . ')'}); $self->end_element({'Name' => 'Sim4Output'}); return $self->end_document(); } return; } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element{ my ($self,$data) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; if( $type ) { if( $self->_will_handle($type) ) { my $func = sprintf("start_%s",lc $type); $self->_eventHandler->$func($data->{'Attributes'}); } unshift @{$self->{'_elements'}}, $type; if($type eq 'result') { $self->{'_values'} = {}; $self->{'_result'}= undef; } } } =head2 end_element Title : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub end_element { my ($self,$data) = @_; my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; my $rc; if( $nm eq 'Hsp' ) { $self->{'_currentHSP'}{'Hsp_midline'} ||= ''; $self->{'_currentHSP'}{'Hsp_query-to'} ||= $self->{'_currentHSP'}{'Hsp_query-from'} + length($self->{'_currentHSP'}{'Hsp_qseq'}) - 1 - $self->{'_currentHSP'}{'Hsp_querygaps'}; $self->{'_currentHSP'}{'Hsp_hit-to'} ||= $self->{'_currentHSP'}{'Hsp_hit-from'} + length($self->{'_currentHSP'}{'Hsp_hseq'}) - 1 - $self->{'_currentHSP'}{'Hsp_hitgaps'}; $self->{'_currentHSP'}{'Hsp_identity'} ||= ($self->{'_currentHSP'}{'Hsp_midline'} =~ tr/\|//); $self->{'_currentHSP'}{'Hsp_qlength'} ||= abs($self->{'_currentHSP'}{'Hsp_query-to'} - $self->{'_currentHSP'}{'Hsp_query-from'}) + 1; $self->{'_currentHSP'}{'Hsp_hlength'} ||= abs($self->{'_currentHSP'}{'Hsp_hit-to'} - $self->{'_currentHSP'}{'Hsp_hit-from'}) + 1; $self->{'_currentHSP'}{'Hsp_align-len'} ||= abs($self->{'_currentHSP'}{'Hsp_query-to'} - $self->{'_currentHSP'}{'Hsp_query-from'}) + 1; $self->{'_currentHSP'}{'Hsp_score'} ||= int(100 * ($self->{'_currentHSP'}{'Hsp_identity'} / $self->{'_currentHSP'}{'Hsp_align-len'})); foreach (keys %{$self->{'_currentHSP'}}) { $self->element({'Name' => $_, 'Data' => delete ${$self->{'_currentHSP'}}{$_}}); } } if( $type = $MODEMAP{$nm} ) { if( $self->_will_handle($type) ) { my $func = sprintf("end_%s",lc $type); $rc = $self->_eventHandler->$func($self->{'_reporttype'}, $self->{'_values'}); } shift @{$self->{'_elements'}}; } elsif( $MAPPING{$nm} ) { if ( ref($MAPPING{$nm}) =~ /hash/i ) { my $key = (keys %{$MAPPING{$nm}})[0]; $self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'}; } else { $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'}; } } else { $self->debug( "unknown nm $nm, ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if( defined $type && $type eq 'result' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element{ my ($self,$data) = @_; $self->start_element($data); $self->characters($data); $self->end_element($data); } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters{ my ($self,$data) = @_; return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ ); if( $self->in_element('hsp') && $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) { $self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'}; } $self->{'_last_data'} = $data->{'Data'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub within_element{ my ($self,$name) = @_; return 0 if ( ! defined $name && ! defined $self->{'_elements'} || scalar @{$self->{'_elements'}} == 0) ; foreach ( @{$self->{'_elements'}} ) { if( $_ eq $name ) { return 1; } } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub in_element{ my ($self,$name) = @_; return 0 if ! defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name) } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handle a start document event Returns : none Args : none =cut sub start_document{ my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_elements'} = []; $self->{'_reporttype'} = $DEFAULTFORMAT; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document{ my ($self,@args) = @_; return $self->{'_result'}; } sub write_result { my ($self, $blast, @args) = @_; if( not defined($self->writer) ) { $self->warn("Writer not defined. Using a $DEFAULT_WRITER_CLASS"); $self->writer( $DEFAULT_WRITER_CLASS->new() ); } $self->SUPER::write_result( $blast, @args ); } sub result_count { return 1; # can a sim4 report contain more than one result? } sub report_count { shift->result_count } =head2 _will_handle Title : _will_handle Usage : Private method. For internal use only. if( $self->_will_handle($type) ) { ... } Function: Provides an optimized way to check whether or not an element of a given type is to be handled. Returns : Reference to EventHandler object if the element type is to be handled. undef if the element type is not to be handled. Args : string containing type of element. Optimizations: 1. Using the cached pointer to the EventHandler to minimize repeated lookups. 2. Caching the will_handle status for each type that is encountered so that it only need be checked by calling handler->will_handle($type) once. This does not lead to a major savings by itself (only 5-10%). In combination with other optimizations, or for large parse jobs, the savings good be significant. To test against the unoptimized version, remove the parentheses from around the third term in the ternary " ? : " operator and add two calls to $self-E_eventHandler(). =cut sub _will_handle { my ($self,$type) = @_; my $handler = $self->{'_handler_cache'} ||= $self->_eventHandler; my $will_handle = defined($self->{'_will_handle_cache'}->{$type}) ? $self->{'_will_handle_cache'}->{$type} : ($self->{'_will_handle_cache'}->{$type} = $handler->will_handle($type)); return $will_handle ? $handler : undef; } 1; BioPerl-1.007002/Bio/SearchIO/waba.pm000444000766000024 3161113155576320 17153 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::waba # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::waba - SearchIO parser for Jim Kent WABA program alignment output =head1 SYNOPSIS # do not use this object directly, rather through Bio::SearchIO use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'waba', -file => 'output.wab'); while( my $result = $in->next_result ) { while( my $hit = $result->next_hit ) { while( my $hsp = $result->next_hsp ) { } } } =head1 DESCRIPTION This parser will process the waba output (NOT the human readable format). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::waba; use vars qw(%MODEMAP %MAPPING @STATES); use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Search::Result::ResultFactory; use Bio::Search::HSP::HSPFactory; use POSIX; BEGIN { # mapping of NCBI Blast terms to Bioperl hash keys %MODEMAP = ('WABAOutput' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); @STATES = qw(Hsp_qseq Hsp_hseq Hsp_stateseq); %MAPPING = ( 'Hsp_query-from'=> 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_midline' => 'HSP-homology_seq', 'Hsp_stateseq' => 'HSP-hmmstate_seq', 'Hsp_align-len' => 'HSP-hsp_length', 'Hit_id' => 'HIT-name', 'Hit_accession' => 'HIT-accession', 'WABAOutput_program' => 'RESULT-algorithm_name', 'WABAOutput_version' => 'RESULT-algorithm_version', 'WABAOutput_query-def'=> 'RESULT-query_name', 'WABAOutput_query-db' => 'RESULT-query_database', 'WABAOutput_db' => 'RESULT-database_name', ); } use base qw(Bio::SearchIO); =head2 new Title : new Usage : my $obj = Bio::SearchIO::waba->new(); Function: Builds a new Bio::SearchIO::waba object Returns : Bio::SearchIO::waba Args : see Bio::SearchIO =cut sub _initialize { my ($self,@args) = @_; $self->SUPER::_initialize(@args); $self->_eventHandler->register_factory('result', Bio::Search::Result::ResultFactory->new(-type => 'Bio::Search::Result::WABAResult')); $self->_eventHandler->register_factory('hsp', Bio::Search::HSP::HSPFactory->new(-type => 'Bio::Search::HSP::WABAHSP')); } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result{ my ($self) = @_; local $/ = "\n"; local $_; my ($curquery,$curhit); my $state = -1; $self->start_document(); my @hit_signifs; while( defined ($_ = $self->_readline )) { if( $state == -1 ) { my ($qid, $qhspid,$qpercent, $junk, $alnlen,$qdb,$qacc,$qstart,$qend,$qstrand, $hitdb,$hacc,$hstart,$hend, $hstrand) = ( /^(\S+)\.(\S+)\s+align\s+ # get the queryid (\d+(\.\d+)?)\%\s+ # get the percentage of\s+(\d+)\s+ # get the length of the alignment (\S+)\s+ # this is the query database (\S+):(\-?\d+)\-(\-?\d+) # The accession:start-end for query \s+([\-\+]) # query strand \s+(\S+)\. # hit db (\S+):(\-?\d+)\-(\-?\d+) # The accession:start-end for hit \s+([\-\+])\s*$ # hit strand /ox ); # Curses. Jim's code is 0 based, the following is to readjust if( $hstart < 0 ) { $hstart *= -1} if( $hend < 0 ) { $hend *= -1} if( $qstart < 0 ) { $qstart *= -1} if( $qend < 0 ) { $qend *= -1} $hstart++; $hend++; $qstart++; $qend++; if( ! defined $alnlen ) { $self->warn("Unable to parse the rest of the WABA alignment info for: '$_'"); last; } $self->{'_reporttype'} = 'WABA'; # hardcoded - only # one type of WABA AFAIK if( defined $curquery && $curquery ne $qid ) { $self->end_element({'Name' => 'Hit'}); $self->_pushback($_); $self->end_element({'Name' => 'WABAOutput'}); return $self->end_document(); } if( defined $curhit && $curhit ne $hacc) { # slight duplication here -- keep these in SYNC $self->end_element({'Name' => 'Hit'}); $self->start_element({'Name' => 'Hit'}); $self->element({'Name' => 'Hit_id', 'Data' => $hacc}); $self->element({'Name' => 'Hit_accession', 'Data' => $hacc}); } elsif ( ! defined $curquery ) { $self->start_element({'Name' => 'WABAOutput'}); $self->{'_result_count'}++; $self->element({'Name' => 'WABAOutput_query-def', 'Data' => $qid }); $self->element({'Name' => 'WABAOutput_program', 'Data' => 'WABA'}); $self->element({'Name' => 'WABAOutput_query-db', 'Data' => $qdb}); $self->element({'Name' => 'WABAOutput_db', 'Data' => $hitdb}); # slight duplication here -- keep these N'SYNC ;-) $self->start_element({'Name' => 'Hit'}); $self->element({'Name' => 'Hit_id', 'Data' => $hacc}); $self->element({'Name' => 'Hit_accession', 'Data' => $hacc}); } # strand is inferred by start,end values # in the Result Builder if( $qstrand eq '-' ) { ($qstart,$qend) = ($qend,$qstart); } if( $hstrand eq '-' ) { ($hstart,$hend) = ($hend,$hstart); } $self->start_element({'Name' => 'Hsp'}); $self->element({'Name' => 'Hsp_query-from', 'Data' => $qstart}); $self->element({'Name' => 'Hsp_query-to', 'Data' => $qend}); $self->element({'Name' => 'Hsp_hit-from', 'Data' => $hstart}); $self->element({'Name' => 'Hsp_hit-to', 'Data' => $hend}); $self->element({'Name' => 'Hsp_align-len', 'Data' => $alnlen}); $curquery = $qid; $curhit = $hacc; $state = 0; } elsif( ! defined $curquery ) { $self->warn("skipping because no Hit begin line was recognized\n$_") if( $_ !~ /^\s+$/ ); next; } else { chomp; $self->element({'Name' => $STATES[$state++], 'Data' => $_}); if( $state >= scalar @STATES ) { $state = -1; $self->end_element({'Name' => 'Hsp'}); } } } if( defined $curquery ) { $self->end_element({'Name' => 'Hit'}); $self->end_element({'Name' => 'WABAOutput'}); return $self->end_document(); } return; } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element{ my ($self,$data) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; if( my $type = $MODEMAP{$nm} ) { $self->_mode($type); if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("start_%s",lc $type); $self->_eventHandler->$func($data->{'Attributes'}); } unshift @{$self->{'_elements'}}, $type; } if($nm eq 'WABAOutput') { $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_mode'} = ''; } } =head2 end_element Title : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub end_element { my ($self,$data) = @_; my $nm = $data->{'Name'}; my $rc; # Hsp are sort of weird, in that they end when another # object begins so have to detect this in end_element for now if( $nm eq 'Hsp' ) { foreach ( qw(Hsp_qseq Hsp_midline Hsp_hseq) ) { $self->element({'Name' => $_, 'Data' => $self->{'_last_hspdata'}->{$_}}); } $self->{'_last_hspdata'} = {} } if( my $type = $MODEMAP{$nm} ) { if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("end_%s",lc $type); $rc = $self->_eventHandler->$func($self->{'_reporttype'}, $self->{'_values'}); } shift @{$self->{'_elements'}}; } elsif( $MAPPING{$nm} ) { if ( ref($MAPPING{$nm}) =~ /hash/i ) { my $key = (keys %{$MAPPING{$nm}})[0]; $self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'}; } else { $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'}; } } else { $self->warn( "unknown nm $nm ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if( $nm eq 'WABAOutput' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element{ my ($self,$data) = @_; $self->start_element($data); $self->characters($data); $self->end_element($data); } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters{ my ($self,$data) = @_; return unless ( defined $data->{'Data'} ); if( $data->{'Data'} =~ /^\s+$/ ) { return unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/; } if( $self->in_element('hsp') && $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) { $self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'}; } $self->{'_last_data'} = $data->{'Data'}; } =head2 _mode Title : _mode Usage : $obj->_mode($newval) Function: Example : Returns : value of _mode Args : newvalue (optional) =cut sub _mode{ my ($self,$value) = @_; if( defined $value) { $self->{'_mode'} = $value; } return $self->{'_mode'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub within_element{ my ($self,$name) = @_; return 0 if ( ! defined $name && ! defined $self->{'_elements'} || scalar @{$self->{'_elements'}} == 0) ; foreach ( @{$self->{'_elements'}} ) { if( $_ eq $name ) { return 1; } } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub in_element{ my ($self,$name) = @_; return 0 if ! defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name) } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handles a start document event Returns : none Args : none =cut sub start_document{ my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_mode'} = ''; $self->{'_elements'} = []; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document{ my ($self,@args) = @_; return $self->{'_result'}; } =head2 result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } sub report_count { shift->result_count } 1; BioPerl-1.007002/Bio/SearchIO/wise.pm000444000766000024 3051313155576320 17210 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::wise # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::wise - Parsing of wise output as alignments =head1 SYNOPSIS use Bio::SearchIO; my $parser = Bio::SearchIO->new(-file => 'file.genewise', -format => 'wise', -wisetype=> 'genewise'); while( my $result = $parser->next_result ) {} =head1 DESCRIPTION This object parsers Wise output using Bio::Tools::Genewise or Bio::Tools::Genomewise as a helper. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::wise; use vars qw(%MAPPING %MODEMAP $DEFAULT_WRITER_CLASS); use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::SearchIO); %MODEMAP = ('WiseOutput' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); %MAPPING = ( 'Hsp_query-from'=> 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_midline' => 'HSP-homology_seq', 'Hsp_score' => 'HSP-score', 'Hsp_qlength' => 'HSP-query_length', 'Hsp_hlength' => 'HSP-hit_length', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_positive' => 'HSP-conserved', 'Hsp_identity' => 'HSP-identical', #'Hsp_gaps' => 'HSP-hsp_gaps', #'Hsp_hitgaps' => 'HSP-hit_gaps', #'Hsp_querygaps' => 'HSP-query_gaps', 'Hit_id' => 'HIT-name', # 'Hit_desc' => 'HIT-description', # 'Hit_len' => 'HIT-length', 'Hit_score' => 'HIT-score', 'WiseOutput_program' => 'RESULT-algorithm_name', 'WiseOutput_query-def' => 'RESULT-query_name', 'WiseOutput_query-desc'=> 'RESULT-query_description', 'WiseOutput_query-len' => 'RESULT-query_length', ); $DEFAULT_WRITER_CLASS = 'Bio::SearchIO::Writer::HitTableWriter'; use Bio::Tools::Genewise; use Bio::Tools::Genomewise; =head2 new Title : new Usage : my $obj = Bio::SearchIO::wise->new(); Function: Builds a new Bio::SearchIO::wise object Returns : an instance of Bio::SearchIO::wise Args : -wise => a Bio::Tools::Genewise or Bio::Tools::Genomewise object =cut sub _initialize { my ($self,@args) = @_; my ( $wisetype, $file,$fh ) = $self->_rearrange([qw(WISETYPE FILE FH)], @args); my @newargs; while( @args ) { my $a = shift @args; if( $a =~ /FILE|FH/i ) { shift @args; next; } push @newargs, $a, shift @args; } $self->SUPER::_initialize(@newargs); # Optimization: caching the EventHandler # since it's use a lot during the parse. $self->{'_handler_cache'} = $self->_eventHandler; $self->wisetype($wisetype); my @ioargs; if( $fh ) { push @ioargs, ('-fh' => $fh); } elsif( $file ) { push @ioargs, ('-file' => $file); } if( $wisetype =~ /genewise/i ) { $self->wise(Bio::Tools::Genewise->new(@ioargs)); } elsif( $wisetype =~ /genomewise/i ) { $self->wise(Bio::Tools::Genomewise->new(@ioargs)); } else { $self->throw("Must supply a -wisetype to ".ref($self)." which is one of 'genomewise' 'genewise'\n"); } return $self; } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result{ my ($self) = @_; local $/ = "\n"; local $_; return unless $self->wise; my $prediction = $self->wise->next_prediction; return unless $prediction; $self->{'_reporttype'} = uc $self->wisetype; $self->start_element({'Name' => 'WiseOutput'}); $self->element({'Name' => 'WiseOutput_program', 'Data' => $self->wisetype}); $self->element({'Name' => 'WiseOutput_query-def', 'Data' => $self->wise->_prot_id}); my @transcripts = $prediction->transcripts; foreach my $transcript ( @transcripts ) { my @exons = $transcript->exons; my $protid; $self->start_element({'Name' => 'Hit'}); if( $exons[0]->has_tag('supporting_feature') ) { my ($supporting_feature) = $exons[0]->get_tag_values('supporting_feature'); $protid = $supporting_feature->feature2->seq_id; $self->element({'Name' => 'Hit_id', 'Data' => $self->wise->_target_id}); } $self->element({'Name' => 'Hit_score', 'Data' => $self->wise->_score}); foreach my $exon ( @exons ) { $self->start_element({'Name' => 'Hsp'}); if( $exon->strand < 0 ) { $self->element({'Name' => 'Hsp_query-from', 'Data' => $exon->end}); $self->element({'Name' => 'Hsp_query-to', 'Data' => $exon->start}); } else { $self->element({'Name' => 'Hsp_query-from', 'Data' => $exon->start}); $self->element({'Name' => 'Hsp_query-to', 'Data' => $exon->end}); } $self->element({'Name' => 'Hsp_score', 'Data' => $self->wise->_score}); if( $exon->has_tag('supporting_feature') ) { my ($sf) = $exon->get_tag_values('supporting_feature'); my $protein = $sf->feature2; if( $protein->strand < 0 ) { $self->element({'Name' => 'Hsp_hit-from', 'Data' => $protein->end}); $self->element({'Name' => 'Hsp_hit-to', 'Data' => $protein->start}); } else { $self->element({'Name' => 'Hsp_hit-from', 'Data' => $protein->start}); $self->element({'Name' => 'Hsp_hit-to', 'Data' => $protein->end}); } } $self->element({'Name' => 'Hsp_identity', 'Data' => 0}); $self->element({'Name' => 'Hsp_positive', 'Data' => 0}); $self->end_element({'Name' => 'Hsp'}); } $self->end_element({'Name' => 'Hit'}); } $self->end_element({'Name' => 'WiseOutput'}); return $self->end_document(); } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element{ my ($self,$data) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; if( $type ) { if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("start_%s",lc $type); $self->_eventHandler->$func($data->{'Attributes'}); } unshift @{$self->{'_elements'}}, $type; if($type eq 'result') { $self->{'_values'} = {}; $self->{'_result'}= undef; } } } =head2 end_element Title : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub end_element { my ($self,$data) = @_; my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; my $rc; if( $type = $MODEMAP{$nm} ) { if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("end_%s",lc $type); $rc = $self->_eventHandler->$func($self->{'_reporttype'}, $self->{'_values'}); } shift @{$self->{'_elements'}}; } elsif( $MAPPING{$nm} ) { if ( ref($MAPPING{$nm}) =~ /hash/i ) { my $key = (keys %{$MAPPING{$nm}})[0]; $self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'}; } else { $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'}; } } else { $self->debug( "unknown nm $nm, ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if( defined $type && $type eq 'result' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element{ my ($self,$data) = @_; $self->start_element($data); $self->characters($data); $self->end_element($data); } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters{ my ($self,$data) = @_; return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ ); $self->{'_last_data'} = $data->{'Data'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub within_element{ my ($self,$name) = @_; return 0 if ( ! defined $name && ! defined $self->{'_elements'} || scalar @{$self->{'_elements'}} == 0) ; foreach ( @{$self->{'_elements'}} ) { if( $_ eq $name ) { return 1; } } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub in_element{ my ($self,$name) = @_; return 0 if ! defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name) } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handle a start document event Returns : none Args : none =cut sub start_document{ my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_elements'} = []; $self->{'_reporttype'} = 'exonerate'; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document{ my ($self,@args) = @_; return $self->{'_result'}; } sub write_result { my ($self, $blast, @args) = @_; if( not defined($self->writer) ) { $self->warn("Writer not defined. Using a $DEFAULT_WRITER_CLASS"); $self->writer( $DEFAULT_WRITER_CLASS->new() ); } $self->SUPER::write_result( $blast, @args ); } sub result_count { my $self = shift; return $self->{'_result_count'}; } sub report_count { shift->result_count } =head2 wise Title : wise Usage : $obj->wise($newval) Function: Get/Set the Wise object parser Returns : value of wise (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub wise{ my $self = shift; return $self->{'wise'} = shift if @_; return $self->{'wise'}; } =head2 wisetype Title : wisetype Usage : $obj->wisetype($newval) Function: Wise program type Returns : value of wisetype (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub wisetype{ my $self = shift; return $self->{'wisetype'} = shift if @_; return $self->{'wisetype'}; } 1; BioPerl-1.007002/Bio/SearchIO/Writer000755000766000024 013155576320 17000 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/Bio/SearchIO/Writer/GbrowseGFF.pm000444000766000024 3753213155576320 21460 0ustar00cjfieldsstaff000000000000#----------------------------------------------------------------- # # BioPerl module Bio::SearchIO::Writer::GbrowseGFF.pm # # Please direct questions and support issues to # # Cared for by Mark Wilkinson # # You may distribute this module under the same terms as perl itself #----------------------------------------------------------------- =head1 NAME Bio::SearchIO::Writer::GbrowseGFF - Interface for outputting parsed search results in Gbrowse GFF format =head1 SYNOPSIS use Bio::SearchIO; my $in = Bio::SearchIO->new(-file => 'result.blast', -format => 'blast'); my $out = Bio::SearchIO->new(-output_format => 'GbrowseGFF', -output_cigar => 1, -output_signif => 1, -file => ">result.gff"); while( my $r = $in->next_result ) { $out->write_result($r); } =head1 DESCRIPTION This writer produces Gbrowse flavour GFF from a Search::Result object. =head1 AUTHOR Mark Wilkinson Email markw-at-illuminae-dot-com =head1 CONTRIBUTORS Susan Miller sjmiller at email-DOT-arizon-DOT-edu Jason Stajich jason at bioperl-dot-org =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SearchIO::Writer::GbrowseGFF; use vars qw(%Defaults); use strict; $Defaults{'Prefix'} = 'EST'; $Defaults{'HSPTag'} = 'HSP'; $Defaults{'MatchTag'} = 'match'; use base qw(Bio::Root::Root Bio::SearchIO::SearchWriterI); =head2 new Title : new Usage : my $obj = Bio::SearchIO::Writer::GbrowseGFF->new(@args); Function: Builds a new Bio::SearchIO::Writer::GbrowseGFF object Returns : an instance of Bio::SearchIO::Writer::GbrowseGFF Args : -e_value => 10 : set e_value parsing cutoff (default undef) (note the -e_value flag is deprecated.) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); ($self->{'_evalue'}, $self->{'_cigar'}, $self->{'_prefix'}, $self->{'_signif'} ) = $self->_rearrange([qw(E_VALUE OUTPUT_CIGAR PREFIX OUTPUT_SIGNIF)], @args); $self->{'_evalue'} && warn( "Use of the -e_value argument is deprecated.\nIn future, use \$writer->filter(\"type\", \&code) instead.\n\tparsing will proceed correctly with this e_value\n"); $self->{Gbrowse_HSPID} = 0; $self->{Gbrowse_HITID} = 0; $self->{'_prefix'} ||= $Defaults{'Prefix'}; return $self; } sub _incrementHSP { my ($self) = @_; return ++$self->{Gbrowse_HSPID}; } sub _incrementHIT { my ($self) = @_; return ++$self->{Gbrowse_HITID} } # according to the GFF3 spec: #"match". In addition to the generic "match" #type, there are the subclasses "cDNA_match," "EST_match," #"translated_nucleotide_match," "nucleotide_to_protein_match," and #"nucleotide_motif." =head2 to_string Purpose : Produce the Gbrowse format GFF lines for a Result Usage : print $writer->to_string( $result_obj, @args); Argument : $result_obj = A Bio::Search::Result::ResultI object -version => 1|2|2.5|3 ; the GFF format you want to output (default 3) -match_tag => match|cDNA_match|EST_match|translated_nucleotide_match nucleotide_to_protein_match|nucleotide_motif This is the SO term to be placed in GFF column 3. -prefix => String to prefix the group by, default is EST (see %Defaults class variable) A default can also be set on object init Returns : String containing data for each search Result or any of its : sub-objects (Hits and HSPs). Throws : n/a =cut #-reference => 'hit'|'query' ; whether the hit sequence name or the # query sequence name is used as the # 'reference' sequence (GFF column 1) sub to_string { my ($self, $result, @args) = @_; my ($format, $reference, $match_tag,$hsp_tag, $prefix) = $self->_rearrange([qw (VERSION REFERENCE MATCH_TAG HSP_TAG PREFIX)], @args); $self->warn($reference) if $reference; $reference ||='hit'; # default is that the hit sequence (db sequence) becomes the reference sequence. I think this is fairly typical... $match_tag ||= $Defaults{'MatchTag'}; # default is the generic 'match' tag. $hsp_tag ||= $Defaults{'HSPTag'}; # default is the generic 'hsp' tag. $prefix ||= $self->{'_prefix'}; $self->throw("$reference must be one of 'query', or 'hit'\n") unless $reference; #************* THIS IS WHERE I STOPPED **************** # ***************************************************** #************************************************* $format ||='3'; my $gffio = Bio::Tools::GFF->new(-gff_version => $format); # try to set it # just in case that behaviour changes (at the moment, an invalid format throws an exception, but it might return undef in the future return "" unless defined $gffio; # be kind and don't return undef in case the person is putting the output directly into a print statement without testing it # now $gffio is either false, or a valid GFF formatter my ($GFF,$cigar,$score); my ($resultfilter,$hitfilter,$hspfilter) = ( $self->filter('RESULT'), $self->filter('HIT'), $self->filter('HSP')); $result->can('rewind') && $result->rewind(); # ensure we're at the beginning next if (defined $resultfilter && ! (&{$resultfilter}($result)) ); while( my $hit = $result->next_hit ) { if (defined $self->{_evalue}){ next unless ($hit->significance < $self->{_evalue}); } next if( defined $hitfilter && ! &{$hitfilter}($hit) ); # test against filter code my $refseq = $reference eq 'hit' ? $hit->name : $result->query_name; my $seqname = $reference eq 'hit' ? $result->query_name : $hit->name; # hopefully this will be a simple identifier without a full description line!! if ($self->{_signif}) { $score = $hit->significance; } else { $score = $hit->raw_score; } $self->throw("No reference sequence name found in hit; required for GFF (this may not be your fault if your report type does not include reference sequence names)\n") unless $refseq; my $source = $hit->algorithm; $self->throw("No algorithm name found in hit; required for GFF (this may not be your fault if your report type does not include algorithm names)\n") unless $refseq; $self->throw("This module only works on BLASTN reports at this time. Sorry.\n") unless $source eq "BLASTN"; my @plus_hsps; my @minus_hsps; # pre-process the HSP's because we later need to know # the extents of the plus and munus strand # on both the subject and query strands individually my ($qpmin, $qpmax, $qmmin, $qmmax, $spmin, $spmax, $smmin, $smmax); # variables for the plus/minus strand min start and max end to know the full extents of the hit while( my $hsp = $hit->next_hsp ) { if ( defined $self->{_evalue} ) { # for backward compatibility only next unless ($hsp->significance < $self->{_evalue}); } next if( defined $hspfilter && ! &{$hspfilter}($hsp) ); # test against HSP filter if ($hsp->hit->strand >= 0 ){ push @plus_hsps, $hsp; if (defined $qpmin){ # set or reset the minimum and maximum extent of the plus-strand hit $qpmin = $hsp->query->start if $hsp->query->start < $qpmin; $qpmax = $hsp->query->end if $hsp->query->end > $qpmax; $spmin = $hsp->hit->start if $hsp->hit->start < $spmin; $spmax = $hsp->hit->end if $hsp->hit->end > $spmax; } else { $qpmin = $hsp->query->start; $qpmax = $hsp->query->end; $spmin = $hsp->hit->start; $spmax = $hsp->hit->end; } } if ($hsp->hit->strand < 0 ){ push @minus_hsps, $hsp; if (defined $qmmin){ # set or reset the minimum and maximum extent of the minus-strand hit $qmmin = $hsp->query->start if $hsp->query->start < $qmmin; $qmmax = $hsp->query->end if $hsp->query->end > $qmmax; $smmin = $hsp->hit->start if $hsp->hit->start < $smmin; $smmax = $hsp->hit->end if $hsp->hit->end > $smmax; } else { $qmmin = $hsp->query->start; $qmmax = $hsp->query->end; $smmin = $hsp->hit->start; $smmax = $hsp->hit->end; } } #else next if there is no strand, but that makes no sense..?? } next unless (scalar(@plus_hsps) + scalar(@minus_hsps)); # next if no hsps (??) my $ID = $self->_incrementHIT(); # okay, write out the index line for the entire hit before # processing HSP's # unfortunately (or not??), HitI objects do not implement # SeqFeatureI, so we can't just call ->gff_string # as a result, this module is quite brittle to changes # in the GFF format since we are hard-coding the GFF output here :-( if (scalar(@plus_hsps)){ my %tags = ( 'ID' => "match_sequence$ID"); if ($format==2.5) { $tags{'Target'} = "$prefix:$seqname"; $tags{'tstart'} = $qmmin; $tags{'tend'} = $qmmax; } else { $tags{'Target'} = "$prefix:$seqname $qpmin $qpmax"; } if ( $self->{'_cigar'} ) { $tags{'Gap'} = $cigar; } my $feat = Bio::SeqFeature::Generic->new( -seq_id => $refseq, -source_tag => $source, -primary_tag => $match_tag, -start => $spmin, -end => $spmax, -score => $score, -strand => '+', -frame => '.', -tag => \%tags ); my $formatter = Bio::Tools::GFF->new(-gff_version => $format); $GFF .= $feat->gff_string($formatter)."\n"; } if (scalar(@minus_hsps)){ my %tags = ( 'ID' => "match_sequence$ID"); if ($format==2.5) { $tags{'Target'} = "$prefix:$seqname"; $tags{'tstart'} = $qpmax; $tags{'tend'} = $qpmin; } else { $tags{'Target'} = "$prefix:$seqname $qpmax $qpmin"; } my $feat = Bio::SeqFeature::Generic->new( -seq_id => $refseq, -source_tag => $source, -primary_tag => $match_tag, -start => $smmin, -end => $smmax, -score => $score, -strand => '-', -frame => '.', -tag => \%tags ); my $formatter = Bio::Tools::GFF->new(-gff_version => $format); $GFF .= $feat->gff_string($formatter)."\n"; } # process + strand hsps foreach my $hsp (@plus_hsps){ my $hspID = $self->_incrementHSP(); my $qstart = $hsp->query->start; my $qend = $hsp->query->end; my $sstart = $hsp->hit->start; my $send = $hsp->hit->end; my $score = $hsp->score; my %tags = ( 'ID' => "match_hsp$hspID", 'Parent' => "match_sequence$ID" ); if ($format==2.5) { $tags{'Target'} = "$prefix:$seqname"; $tags{'tstart'} = $qstart; $tags{'tend'} = $qend; } else { $tags{'Target'} = "$prefix:$seqname $qstart $qend"; } if ( $self->{'_cigar'} ) { $tags{'Gap'} = $hsp->cigar_string; } my $feat = Bio::SeqFeature::Generic->new( -seq_id => $refseq, -source_tag => $source, -primary_tag => $hsp_tag, -start => $sstart, -end => $send, -score => $score, -strand => '+', -frame => '.', -tag => \%tags ); my $formatter = Bio::Tools::GFF->new(-gff_version => $format); $GFF .= $feat->gff_string($formatter)."\n"; } foreach my $hsp (@minus_hsps) { my $hspID = $self->_incrementHSP(); my $qstart = $hsp->query->start; my $qend = $hsp->query->end; my $sstart = $hsp->hit->start; my $send = $hsp->hit->end; my $score = $hsp->score; my %tags = ( 'ID' => "match_hsp$hspID", 'Parent' => "match_sequence$ID" ); if ($format==2.5) { $tags{'Target'} = "$prefix:$seqname"; $tags{'tstart'} = $qend; $tags{'tend'} = $qstart; } else { $tags{'Target'} = "$prefix:$seqname $qend $qstart"; } if ( $self->{'_cigar'} ) { $tags{'Gap'} = $hsp->cigar_string; } my $feat = Bio::SeqFeature::Generic->new( -seq_id => $refseq, -source_tag => $source, -primary_tag => $hsp_tag, -start => $sstart, -end => $send, -score => $score, -strand => '-', -frame => '.', -tag => \%tags ); my $formatter = Bio::Tools::GFF->new(-gff_version => $format); $GFF .= $feat->gff_string($formatter) ."\n"; } } return $GFF; } sub significance_filter { my ($self,$method,$code) = @_; return unless $method; $method = uc($method); if( $method ne 'HSP' && $method ne 'HIT' && $method ne 'RESULT' ) { $self->warn("Unknown method $method"); return; } if( $code ) { $self->throw("Must provide a valid code reference") unless ref($code) =~ /CODE/; $self->{$method} = $code; } return $self->{$method}; } =head2 start_report Title : start_report Usage : $self->start_report() Function: has no function, returns nothing Returns : empty string Args : none =cut sub start_report { return '' } =head2 end_report Title : end_report Usage : $self->end_report() Function: has no function, returns nothing Returns : empty string Args : none =cut sub end_report { return '' } =head2 filter Title : filter Usage : $writer->filter('hsp', \&hsp_filter); Function: Filter out either at HSP,Hit,or Result level Returns : none Args : string => data type, CODE reference Note : GbrowseGFF.pm makes no changes to the default filter code =cut 1; BioPerl-1.007002/Bio/SearchIO/Writer/HSPTableWriter.pm000444000766000024 3005513155576320 22315 0ustar00cjfieldsstaff000000000000 =head1 NAME Bio::SearchIO::Writer::HSPTableWriter - Tab-delimited data for Bio::Search::HSP::HSPI objects =head1 SYNOPSIS =head2 Example 1: Using the default columns use Bio::SearchIO; use Bio::SearchIO::Writer::HSPTableWriter; my $in = Bio::SearchIO->new(); my $writer = Bio::SearchIO::Writer::HSPTableWriter->new(); my $out = Bio::SearchIO->new( -writer => $writer ); while ( my $result = $in->next_result() ) { $out->write_result($result, ($in->report_count - 1 ? 0 : 1) ); } =head2 Example 2: Specifying a subset of columns use Bio::SearchIO; use Bio::SearchIO::Writer::HSPTableWriter; my $in = Bio::SearchIO->new(); my $writer = Bio::SearchIO::Writer::HSPTableWriter->new( -columns => [qw( query_name query_length hit_name hit_length rank frac_identical_query expect )] ); my $out = Bio::SearchIO->new( -writer => $writer, -file => ">searchio.out" ); while ( my $result = $in->next_result() ) { $out->write_result($result, ($in->report_count - 1 ? 0 : 1) ); } =head2 Custom Labels You can also specify different column labels if you don't want to use the defaults. Do this by specifying a C<-labels> hash reference parameter when creating the HSPTableWriter object. The keys of the hash should be the column number (left-most column = 1) for the label(s) you want to specify. Here's an example: my $writer = Bio::SearchIO::Writer::HSPTableWriter->new( -columns => [qw( query_name query_length hit_name hit_length )], -labels => { 1 => 'QUERY_GI', 3 => 'HIT_IDENTIFIER' } ); =head1 DESCRIPTION Bio::SearchIO::Writer::HSPTableWriter generates output at the finest level of granularity for data within a search result. Data for each HSP within each hit in a search result is output in tab-delimited format, one row per HSP. =head2 Available Columns Here are the columns that can be specified in the C<-columns> parameter when creating a HSPTableWriter object. If a C<-columns> parameter is not specified, this list, in this order, will be used as the default. query_name # Sequence identifier of the query. query_length # Full length of the query sequence hit_name # Sequence identifier of the hit hit_length # Full length of the hit sequence round # Round number for hit (PSI-BLAST) rank expect # Expect value for the alignment score # Score for the alignment (e.g., BLAST score) bits # Bit score for the alignment frac_identical_query # fraction of identical substitutions in query frac_identical_hit # fraction of identical substitutions in hit frac_conserved_query # fraction of conserved substitutions in query frac_conserved_hit # fraction of conserved substitutions in hit length_aln_query # Length of the aligned portion of the query sequence length_aln_hit # Length of the aligned portion of the hit sequence gaps_query # Number of gap characters in the aligned query sequence gaps_hit # Number of gap characters in the aligned hit sequence gaps_total # Number of gap characters in the aligned query and hit sequences start_query # Starting coordinate of the aligned portion of the query sequence end_query # Ending coordinate of the aligned portion of the query sequence start_hit # Starting coordinate of the aligned portion of the hit sequence end_hit # Ending coordinate of the aligned portion of the hit sequence strand_query # Strand of the aligned query sequence strand_hit # Strand of the aligned hit sequence frame # Reading frame of the aligned query sequence hit_description # Full description of the hit sequence query_description # Full description of the query sequence frac_identical_total # fraction of total identical substitutions frac_conserved_total # fraction of total conserved substitutions For more details about these columns, see the documentation for the corresponding method in Bio::Search::HSP::HSPI. =head1 TODO Figure out the best way to incorporate algorithm-specific score columns. The best route is probably to have algorith-specific subclasses (e.g., BlastHSPTableWriter, FastaHSPTableWriter). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Steve Chervitz Esac@bioperl.orgE See L for where to send bug reports and comments. =head1 COPYRIGHT Copyright (c) 2001 Steve Chervitz. All Rights Reserved. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 SEE ALSO Bio::SearchIO::Writer::HitTableWriter Bio::SearchIO::Writer::ResultTableWriter =head1 METHODS =cut package Bio::SearchIO::Writer::HSPTableWriter; use strict; use base qw(Bio::SearchIO::Writer::ResultTableWriter); # Array fields: column, object, method[/argument], printf format, column label # Methods for result object are defined in Bio::Search::Result::ResultI. # Methods for hit object are defined in Bio::Search::Hit::HitI. # Methods for hsp object are defined in Bio::Search::HSP::HSPI. # Tech note: If a bogus method is supplied, it will result in all values to be zero. # Don't know why this is. # TODO (maybe): Allow specification of signif_format (i.e., separate mantissa/exponent) my %column_map = ( 'query_name' => ['1', 'result', 'query_name', 's', 'QUERY' ], 'query_length' => ['2', 'result', 'query_length', 'd', 'LEN_Q'], 'hit_name' => ['3', 'hit', 'name', 's', 'HIT'], 'hit_length' => ['4', 'hit', 'hit_length', 'd', 'LEN_H'], 'round' => ['5', 'hit', 'iteration', 'd', 'ROUND', 'hit'], 'rank' => ['6', 'hsp', 'rank', 'd', 'RANK'], 'expect' => ['7', 'hsp', 'expect', '.1e', 'EXPCT'], 'score' => ['8', 'hsp', 'score', 'd', 'SCORE'], 'bits' => ['9', 'hsp', 'bits', 'd', 'BITS'], 'frac_identical_query' => ['10', 'hsp', 'frac_identical/query', '.2f', 'FR_IDQ'], 'frac_identical_hit' => ['11', 'hsp', 'frac_identical/hit', '.2f', 'FR_IDH'], 'frac_conserved_query' => ['12', 'hsp', 'frac_conserved/query', '.2f', 'FR_CNQ'], 'frac_conserved_hit' => ['13', 'hsp', 'frac_conserved/hit', '.2f', 'FR_CNH'], 'length_aln_query' => ['14', 'hsp', 'length/query', 'd', 'LN_ALQ'], 'length_aln_hit' => ['15', 'hsp', 'length/hit', 'd', 'LN_ALH'], 'gaps_query' => ['16', 'hsp', 'gaps/query', 'd', 'GAPS_Q'], 'gaps_hit' => ['17', 'hsp', 'gaps/hit', 'd', 'GAPS_H'], 'gaps_total' => ['18', 'hsp', 'gaps/total', 'd', 'GAPS_QH'], 'start_query' => ['19', 'hsp', 'start/query', 'd', 'START_Q'], 'end_query' => ['20', 'hsp', 'end/query', 'd', 'END_Q'], 'start_hit' => ['21', 'hsp', 'start/hit', 'd', 'START_H'], 'end_hit' => ['22', 'hsp', 'end/hit', 'd', 'END_H'], 'strand_query' => ['23', 'hsp', 'strand/query', 'd', 'STRND_Q'], 'strand_hit' => ['24', 'hsp', 'strand/hit', 'd', 'STRND_H'], 'frame_hit' => ['25', 'hsp', 'frame/hit', 's', 'FRAME_H'], 'frame_query' => ['26', 'hsp', 'frame/query', 's', 'FRAME_Q'], 'hit_description' => ['27', 'hit', 'hit_description', 's', 'DESC_H'], 'query_description' => ['28', 'result', 'query_description', 's', 'DESC_Q'], 'frac_identical_total' => ['29', 'hsp', 'frac_identical/total', '.2f', 'FR_IDT'], 'frac_conserved_total' => ['30', 'hsp', 'frac_conserved/total', '.2f', 'FR_CNT'], ); sub column_map { return %column_map } =head2 to_string() Note: this method is not intended for direct use. The SearchIO::write_result() method calls it automatically if the writer is hooked up to a SearchIO object as illustrated in L. Title : to_string() : Usage : print $writer->to_string( $result_obj, [$include_labels] ); : Argument : $result_obj = A Bio::Search::Result::ResultI object : $include_labels = boolean, if true column labels are included (default: false) : Returns : String containing tab-delimited set of data for each HSP : in each Hit of the supplied ResultI object. : Throws : n/a =cut sub to_string { my ($self, $result, $include_labels) = @_; my $str = $include_labels ? $self->column_labels() : ''; my ($resultfilter,$hitfilter, $hspfilter) = ( $self->filter('RESULT'), $self->filter('HIT'), $self->filter('HSP')); if( ! defined $resultfilter || &{$resultfilter}($result) ) { my $func_ref = $self->row_data_func; my $printf_fmt = $self->printf_fmt; $result->can('rewind') && $result->rewind(); # insure we're at the beginning while( my $hit = $result->next_hit) { next if( defined $hitfilter && ! &{$hitfilter}($hit) ); $hit->can('rewind') && $hit->rewind;# insure we're at the beginning while(my $hsp = $hit->next_hsp) { next if ( defined $hspfilter && ! &{$hspfilter}($hsp)); my @row_data = &{$func_ref}($result, $hit, $hsp); $str .= sprintf("$printf_fmt\n", map {$_ || ($printf_fmt eq 's' ? '' : 0)} @row_data); } } } $str =~ s/\t\n/\n/gs; return $str; } =head2 end_report Title : end_report Usage : $self->end_report() Function: The method to call when ending a report, this is mostly for cleanup for formats which require you to have something at the end of the document. Nothing for a text message. Returns : string Args : none =cut sub end_report { return ''; } =head2 filter Title : filter Usage : $writer->filter('hsp', \&hsp_filter); Function: Filter out either at HSP,Hit,or Result level Returns : none Args : string => data type, CODE reference =cut 1; BioPerl-1.007002/Bio/SearchIO/Writer/HTMLResultWriter.pm000444000766000024 7416013155576320 22663 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::Writer::HTMLResultWriter # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # Changes 2003-07-31 (jason) # Gary has cleaned up the code a lot to produce better looking HTML # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::Writer::HTMLResultWriter - write a Bio::Search::ResultI in HTML =head1 SYNOPSIS use Bio::SearchIO; use Bio::SearchIO::Writer::HTMLResultWriter; my $in = Bio::SearchIO->new(-format => 'blast', -file => shift @ARGV); my $writer = Bio::SearchIO::Writer::HTMLResultWriter->new(); my $out = Bio::SearchIO->new(-writer => $writer); $out->write_result($in->next_result); # to filter your output my $MinLength = 100; # need a variable with scope outside the method sub hsp_filter { my $hsp = shift; return 1 if $hsp->length('total') > $MinLength; } sub result_filter { my $result = shift; return $hsp->num_hits > 0; } my $writer = Bio::SearchIO::Writer::HTMLResultWriter->new (-filters => { 'HSP' => \&hsp_filter} ); my $out = Bio::SearchIO->new(-writer => $writer); $out->write_result($in->next_result); # can also set the filter via the writer object $writer->filter('RESULT', \&result_filter); =head1 DESCRIPTION This object implements the SearchWriterI interface which will produce a set of HTML for a specific L interface. See L for more info on the filter method. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 CONTRIBUTORS Gary Williams G.Williams@hgmp.mrc.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SearchIO::Writer::HTMLResultWriter; use strict; use vars qw(%RemoteURLDefault $MaxDescLen $DATE $AlignmentLineWidth $Revision); # Object preamble - inherits from Bio::Root::RootI BEGIN { $Revision = '$Id$'; $DATE = localtime(time); %RemoteURLDefault = ( 'PROTEIN' => 'https://www.ncbi.nlm.nih.gov/protein?term=%s', 'NUCLEOTIDE' => 'https://www.ncbi.nlm.nih.gov/nucleotide?term=%s' ); $MaxDescLen = 60; $AlignmentLineWidth = 60; } use base qw(Bio::Root::Root Bio::SearchIO::SearchWriterI); =head2 new Title : new Usage : my $obj = Bio::SearchIO::Writer::HTMLResultWriter->new(); Function: Builds a new Bio::SearchIO::Writer::HTMLResultWriter object Returns : Bio::SearchIO::Writer::HTMLResultWriter Args : -filters => hashref with any or all of the keys (HSP HIT RESULT) which have values pointing to a subroutine reference which will expect to get a -nucleotide_url => URL sprintf string base for the nt sequences -protein_url => URL sprintf string base for the aa sequences -no_wublastlinks => boolean. Do not display WU-BLAST lines even if they are parsed out. Links = (1) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($p,$n,$filters, $nowublastlinks) = $self->_rearrange([qw(PROTEIN_URL NUCLEOTIDE_URL FILTERS NO_WUBLASTLINKS)],@args); $self->remote_database_url('p',$p || $RemoteURLDefault{'PROTEIN'}); $self->remote_database_url('n',$n || $RemoteURLDefault{'NUCLEOTIDE'}); $self->no_wublastlinks(! $nowublastlinks); if( defined $filters ) { if( !ref($filters) =~ /HASH/i ) { $self->warn("Did not provide a hashref for the FILTERS option, ignoring."); } else { while( my ($type,$code) = each %{$filters} ) { $self->filter($type,$code); } } } return $self; } =head2 remote_database_url Title : remote_database_url Usage : $obj->remote_database_url($type,$newval) Function: This should return or set a string that contains a %s which can be filled in with sprintf. Returns : value of remote_database_url Args : $type - 'PROTEIN' or 'P' for protein URLS 'NUCLEOTIDE' or 'N' for nucleotide URLS $value - new value to set [optional] =cut sub remote_database_url{ my ($self,$type,$value) = @_; if( ! defined $type || $type !~ /^(P|N)/i ) { $self->warn("Must provide a type (PROTEIN or NUCLEOTIDE)"); return ''; } $type = uc $1; if( defined $value) { $self->{'remote_database_url'}->{$type} = $value; } return $self->{'remote_database_url'}->{$type}; } =head2 to_string Purpose : Produces data for each Search::Result::ResultI in a string. : This is an abstract method. For some useful implementations, : see ResultTableWriter.pm, HitTableWriter.pm, : and HSPTableWriter.pm. Usage : print $writer->to_string( $result_obj, @args ); Argument : $result_obj = A Bio::Search::Result::ResultI object : @args = any additional arguments used by your implementation. Returns : String containing data for each search Result or any of its : sub-objects (Hits and HSPs). Throws : n/a =cut sub to_string { my ($self,$result,$num) = @_; $num ||= 0; return unless defined $result; my $links = $self->no_wublastlinks; my ($resultfilter,$hitfilter, $hspfilter) = ( $self->filter('RESULT'), $self->filter('HIT'), $self->filter('HSP') ); return '' if( defined $resultfilter && ! &{$resultfilter}($result) ); my ($qtype,$dbtype,$dbseqtype,$type); my $alg = $result->algorithm; # This is actually wrong for the FASTAs I think if( $alg =~ /T(FAST|BLAST)([XY])/i ) { $qtype = $dbtype = 'translated'; $dbseqtype = $type = 'PROTEIN'; } elsif( $alg =~ /T(FAST|BLAST)N/i ) { $qtype = ''; $dbtype = 'translated'; $type = 'PROTEIN'; $dbseqtype = 'NUCLEOTIDE'; } elsif( $alg =~ /(FAST|BLAST)N/i || $alg =~ /(WABA|EXONERATE)/i ) { $qtype = $dbtype = ''; $type = $dbseqtype = 'NUCLEOTIDE'; } elsif( $alg =~ /(FAST|BLAST)P/ || $alg =~ /SSEARCH|HMM(PFAM|SEARCH)/i ) { $qtype = $dbtype = ''; $type = $dbseqtype = 'PROTEIN'; } elsif( $alg =~ /(FAST|BLAST)[XY]/i ) { $qtype = 'translated'; $dbtype = 'PROTEIN'; $dbseqtype = $type = 'PROTEIN'; } else { $self->warn("algorithm was ", $result->algorithm, " couldn't match\n"); } my %baselens = ( 'Sbjct:' => ( $dbtype eq 'translated' ) ? 3 : 1, 'Query:' => ( $qtype eq 'translated' ) ? 3 : 1); my $str; if( $num <= 1 ) { $str = &{$self->start_report}($result); } $str .= &{$self->title}($result); $str .= $result->algorithm_reference || $self->algorithm_reference($result); $str .= &{$self->introduction}($result); $str .= ""; my $hspstr = '

'; if( $result->can('rewind')) { $result->rewind(); # support stream based parsing routines } while( my $hit = $result->next_hit ) { next if( $hitfilter && ! &{$hitfilter}($hit) ); my $nm = $hit->name(); $self->debug( "no $nm for name (".$hit->description(). "\n") unless $nm; my ($gi,$acc) = &{$self->id_parser}($nm); my $p = "%-$MaxDescLen". "s"; my $descsub; if( length($hit->description) > ($MaxDescLen - 3) ) { $descsub = sprintf($p, substr($hit->description,0,$MaxDescLen-3) . "..."); } else { $descsub = sprintf($p,$hit->description); } my $url_desc = &{$self->hit_link_desc()}($self,$hit, $result); my $url_align = &{$self->hit_link_align()}($self,$hit, $result); my @hsps = $hit->hsps; if( ! @hsps ) { # no HSPs so no link $str .= sprintf('

'."\n", $url_desc, $descsub, ($hit->bits ? $hit->bits : (defined $hsps[0] ? $hsps[0]->bits : ' ')), ( $hit->significance ? $hit->significance : (defined $hsps[0] ? $hsps[0]->evalue : ' ')) ); } else { # failover to first HSP if the data does not contain a # bitscore/significance value for the Hit (NCBI XML data for one) $str .= sprintf(''."\n", $url_desc, $descsub, ($hit->bits ? $hit->bits : (defined $hsps[0] ? $hsps[0]->bits : ' ')), $acc, ( $hit->significance ? $hit->significance : (defined $hsps[0] ? $hsps[0]->evalue : ' ')) ); my $dline = &{$self->hit_desc_line}($self, $hit, $result); $hspstr .= "\n". sprintf(">%s %s
Length = %s

\n\n", $url_align, $dline , &_numwithcommas($hit->length)); my $ct = 0; foreach my $hsp (@hsps ) { next if( $hspfilter && ! &{$hspfilter}($hsp) ); $hspstr .= sprintf(" Score = %s bits (%s), Expect = %s", $hsp->bits || $hsp->score, $hsp->score || $hsp->bits, $hsp->evalue || ''); if( defined $hsp->pvalue ) { $hspstr .= ", P = ".$hsp->pvalue; } $hspstr .= "
\n"; $hspstr .= sprintf(" Identities = %d/%d (%d%%)", ( $hsp->frac_identical('total') * $hsp->length('total')), $hsp->length('total'), $hsp->frac_identical('total') * 100); if( $type eq 'PROTEIN' ) { $hspstr .= sprintf(", Positives = %d/%d (%d%%)", ( $hsp->frac_conserved('total') * $hsp->length('total')), $hsp->length('total'), $hsp->frac_conserved('total') * 100); } if( $hsp->gaps ) { $hspstr .= sprintf(", Gaps = %d/%d (%d%%)", $hsp->gaps('total'), $hsp->length('total'), (100 * $hsp->gaps('total') / $hsp->length('total'))); } my ($hframe,$qframe) = ( $hsp->hit->frame, $hsp->query->frame); my ($hstrand,$qstrand) = ($hsp->hit->strand,$hsp->query->strand); # so TBLASTX will have Query/Hit frames # BLASTX will have Query frame # TBLASTN will have Hit frame if( $hstrand || $qstrand ) { $hspstr .= ", Frame = "; my ($signq, $signh); unless( $hstrand ) { $hframe = undef; # if strand is null or 0 then it is protein # and this no frame } else { $signh = $hstrand < 0 ? '-' : '+'; } unless( $qstrand ) { $qframe = undef; # if strand is null or 0 then it is protein } else { $signq =$qstrand < 0 ? '-' : '+'; } # remember bioperl stores frames as 0,1,2 (GFF way) # BLAST reports reports as 1,2,3 so # we have to add 1 to the frame values if( defined $hframe && ! defined $qframe) { $hspstr .= "$signh".($hframe+1); } elsif( defined $qframe && ! defined $hframe) { $hspstr .= "$signq".($qframe+1); } else { $hspstr .= sprintf(" %s%d / %s%d", $signq,$qframe+1, $signh, $hframe+1); } } if($links && $hsp->can('links') && defined(my $lnks = $hsp->links) ) { $hspstr .= sprintf("
\nLinks = %s\n",$lnks); } $hspstr .= "

\n

";

		my @hspvals = ( {'name' => 'Query:',
				 'seq'  => $hsp->query_string,
				 'start' => ($qstrand >= 0 ? 
					     $hsp->query->start : 
					     $hsp->query->end),
					     'end'   => ($qstrand >= 0 ? 
							 $hsp->query->end : 
							 $hsp->query->start),
							 'index' => 0,
							 'direction' => $qstrand || 1
						     },
				{ 'name' => ' 'x6,
				  'seq'  => $hsp->homology_string,
				  'start' => undef,
				  'end'   => undef,
				  'index' => 0,
				  'direction' => 1
				  },
				{ 'name'  => 'Sbjct:',
				  'seq'   => $hsp->hit_string,
				  'start' => ($hstrand >= 0 ? 
					      $hsp->hit->start : 
					      $hsp->hit->end),
					      'end'   => ($hstrand >= 0 ? 
							  $hsp->hit->end : 
							  $hsp->hit->start),
							  'index' => 0, 
							  'direction' => $hstrand || 1
						      }
				);	    


		# let's set the expected length (in chars) of the starting number
		# in an alignment block so we can have things line up
		# Just going to try and set to the largest

		my ($numwidth) = sort { $b <=> $a }(length($hspvals[0]->{'start'}),
						    length($hspvals[0]->{'end'}),
						    length($hspvals[2]->{'start'}),
						    length($hspvals[2]->{'end'}));
		my $count = 0;
		while ( $count < $hsp->length('total') ) {
		    foreach my $v ( @hspvals ) {
			my $piece = substr($v->{'seq'}, $v->{'index'} + $count,
					   $AlignmentLineWidth);
			my $cp = $piece;
			my $plen = scalar ( $cp =~ tr/\-//);
			my ($start,$end) = ('','');
			if( defined $v->{'start'} ) { 
			    $start = $v->{'start'};
			    # since strand can be + or - use the direction
			    # to signify which whether to add or subtract from end
			    my $d = $v->{'direction'} * ( $AlignmentLineWidth - $plen )*
				$baselens{$v->{'name'}};
			    if( length($piece) < $AlignmentLineWidth ) {
				$d = (length($piece) - $plen) * $v->{'direction'} * 
				    $baselens{$v->{'name'}};
			    }
			    $end   = $v->{'start'} + $d - $v->{'direction'};
			    $v->{'start'} += $d;
			}
			$hspstr .= sprintf("%s %-".$numwidth."s %s %s\n",
					   $v->{'name'},
					   $start,
					   $piece,
					   $end
					   );
		    }
		    $count += $AlignmentLineWidth;
		    $hspstr .= "\n\n";
		}
		$hspstr .= "
\n"; } } # $hspstr .= "\n"; } $str .= "
Sequences producing significant alignments: Score
(bits)		E
value
%s %s%s%.2g
%s %s%s%.2g

\n".$hspstr; my ($pav, $sav) = ($result->available_parameters, $result->available_statistics); if ($pav || $sav) { # make table of search statistics and end the web page $str .= "

Search Parameters

"; if ($pav) { $str .= "\n"; foreach my $param ( sort $result->available_parameters ) { $str .= "\n"; } $str .= "
ParameterValue
$param". $result->get_parameter($param) ."
"; } if ($sav) { $str .= "

Search Statistics

\n"; foreach my $stat ( sort $result->available_statistics ) { $str .= "\n"; } $str .= "
StatisticValue
$stat". $result->get_statistic($stat). "
"; } } $str .= $self->footer() . "

\n"; return $str; } =head2 hit_link_desc Title : hit_link_desc Usage : $self->hit_link_desc(\&link_function); Function: Get/Set the function which provides an HTML link(s) for the given hit to be used within the description section at the top of the BLAST report. This allows a person reading the report within a web browser to go to one or more database entries for the given hit from the description section. Returns : Function reference Args : Function reference See Also: L =cut sub hit_link_desc{ my( $self, $code ) = @_; if ($code) { $self->{'_hit_link_desc'} = $code; } return $self->{'_hit_link_desc'} || \&default_hit_link_desc; } =head2 default_hit_link_desc Title : default_hit_link_desc Usage : $self->default_hit_link_desc($hit, $result) Function: Provides an HTML link(s) for the given hit to be used within the description section at the top of the BLAST report. This allows a person reading the report within a web browser to go to one or more database entries for the given hit from the description section. Returns : string containing HTML markup ", L, L =cut sub default_hit_link_desc { my($self, $hit, $result) = @_; my $type = ( $result->algorithm =~ /(P|X|Y)$/i ) ? 'PROTEIN' : 'NUCLEOTIDE'; my ($gi,$acc) = &{$self->id_parser}($hit->name); my $url = length($self->remote_database_url($type)) > 0 ? sprintf('%s', sprintf($self->remote_database_url($type),$gi || $acc), $hit->name()) : $hit->name(); return $url; } =head2 hit_link_align Title : hit_link_align Usage : $self->hit_link_align(\&link_function); Function: Get/Set the function which provides an HTML link(s) for the given hit to be used within the HSP alignment section of the BLAST report. This allows a person reading the report within a web browser to go to one or more database entries for the given hit from the alignment section. Returns : string containing HTML markup ", L, L =cut sub hit_link_align { my ($self,$code) = @_; if ($code) { $self->{'_hit_link_align'} = $code; } return $self->{'_hit_link_align'} || \&default_hit_link_desc; } =head2 hit_desc_line Title : hit_desc_line Usage : $self->hit_desc_line(\&link_function); Function: Get/Set the function which provides HTML for the description information from a hit. This allows one to parse the rest of the description and split up lines, add links, etc. Returns : Function reference Args : Function reference See Also: L =cut sub hit_desc_line{ my( $self, $code ) = @_; if ($code) { $self->{'_hit_desc_line'} = $code; } return $self->{'_hit_desc_line'} || \&default_hit_desc_line; } =head2 default_hit_desc_line Title : default_hit_desc_line Usage : $self->default_hit_desc_line($hit, $result) Function: Parses the description line information, splits based on the hidden \x01 between independent descriptions, checks the lines for possible web links, and adds HTML link(s) for the given hit to be used. Returns : string containing HTML markup ", L, L =cut sub default_hit_desc_line { my($self, $hit, $result) = @_; my $type = ( $result->algorithm =~ /(P|X|Y)$/i ) ? 'PROTEIN' : 'NUCLEOTIDE'; my @descs = split /\x01/, $hit->description; #my $descline = join("
",@descs)."
"; my $descline = ''; #return $descline; for my $sec (@descs) { my $url = ''; if ($sec =~ s/((?:gi\|(\d+)\|)? # optional GI (\w+)\|([A-Z\d\.\_]+) # main (\|[A-Z\d\_]+)?) # optional secondary ID//xms) { my ($name, $gi, $db, $acc) = ($1, $2, $3, $4); #$acc ||= ($rest) ? $rest : $gi; $acc =~ s/^\s+(\S+)/$1/; $acc =~ s/(\S+)\s+$/$1/; $url = length($self->remote_database_url($type)) > 0 ? sprintf('%s %s', sprintf($self->remote_database_url($type), $gi || $acc || $db), $name, $sec) : $sec; } else { $url = $sec; } $descline .= "$url
\n"; } return $descline; } =head2 start_report Title : start_report Usage : $index->start_report( CODE ) Function: Stores or returns the code to write the start of the block, the block and the start of the <BODY> block of HTML. Useful for (for instance) specifying alternative HTML if you are embedding the output in an HTML page which you have already started. (For example a routine returning a null string). Returns \&default_start_report (see below) if not set. Example : $index->start_report( \&my_start_report ) Returns : ref to CODE if called without arguments Args : CODE =cut sub start_report { my( $self, $code ) = @_; if ($code) { $self->{'_start_report'} = $code; } return $self->{'_start_report'} || \&default_start_report; } =head2 default_start_report Title : default_start_report Usage : $self->default_start_report($result) Function: The default method to call when starting a report. Returns : sting Args : First argument is a Bio::Search::Result::ResultI =cut sub default_start_report { my ($result) = @_; return sprintf( qq{<HTML> <HEAD> <CENTER><TITLE>Bioperl Reformatted HTML of %s output with Bioperl Bio::SearchIO system },$result->algorithm,$Revision); } =head2 title Title : title Usage : $self->title($CODE) Function: Stores or returns the code to provide HTML for the given BLAST report that will appear at the top of the BLAST report HTML output. Useful for (for instance) specifying alternative routines to write your own titles. Returns \&default_title (see below) if not set. Example : $index->title( \&my_title ) Returns : ref to CODE if called without arguments Args : CODE =cut sub title { my( $self, $code ) = @_; if ($code) { $self->{'_title'} = $code; } return $self->{'_title'} || \&default_title; } =head2 default_title Title : default_title Usage : $self->default_title($result) Function: Provides HTML for the given BLAST report that will appear at the top of the BLAST report HTML output. Returns : string containing HTML markup The default implementation returns

HTML containing text such as: "Bioperl Reformatted HTML of BLASTP Search Report for gi|1786183|gb|AAC73113.1|" Args : First argument is a Bio::Search::Result::ResultI =cut sub default_title { my ($result) = @_; return sprintf( qq{

Bioperl Reformatted HTML of %s Search Report
for %s

}, $result->algorithm, $result->query_name()); } =head2 introduction Title : introduction Usage : $self->introduction($CODE) Function: Stores or returns the code to provide HTML for the given BLAST report detailing the query and the database information. Useful for (for instance) specifying routines returning alternative introductions. Returns \&default_introduction (see below) if not set. Example : $index->introduction( \&my_introduction ) Returns : ref to CODE if called without arguments Args : CODE =cut sub introduction { my( $self, $code ) = @_; if ($code) { $self->{'_introduction'} = $code; } return $self->{'_introduction'} || \&default_introduction; } =head2 default_introduction Title : default_introduction Usage : $self->default_introduction($result) Function: Outputs HTML to provide the query and the database information Returns : string containing HTML Args : First argument is a Bio::Search::Result::ResultI Second argument is string holding literature citation =cut sub default_introduction { my ($result) = @_; return sprintf( qq{ Query= %s %s
(%s letters)

Database: %s

%s sequences; %s total letters

}, $result->query_name, $result->query_description, &_numwithcommas($result->query_length), $result->database_name(), &_numwithcommas($result->database_entries()), &_numwithcommas($result->database_letters()), ); } =head2 end_report Title : end_report Usage : $self->end_report() Function: The method to call when ending a report, this is mostly for cleanup for formats which require you to have something at the end of the document () for HTML Returns : string Args : none =cut sub end_report { return "\n\n"; } # copied from Bio::Index::Fasta # useful here as well =head2 id_parser Title : id_parser Usage : $index->id_parser( CODE ) Function: Stores or returns the code used by record_id to parse the ID for record from a string. Useful for (for instance) specifying a different parser for different flavours of FASTA file. Returns \&default_id_parser (see below) if not set. If you supply your own id_parser subroutine, then it should expect a fasta description line. An entry will be added to the index for each string in the list returned. Example : $index->id_parser( \&my_id_parser ) Returns : ref to CODE if called without arguments Args : CODE =cut sub id_parser { my( $self, $code ) = @_; if ($code) { $self->{'_id_parser'} = $code; } return $self->{'_id_parser'} || \&default_id_parser; } =head2 default_id_parser Title : default_id_parser Usage : $id = default_id_parser( $header ) Function: The default Fasta ID parser for Fasta.pm Returns $1 from applying the regexp /^>\s*(\S+)/ to $header. Returns : ID string The default implementation checks for NCBI-style identifiers in the given string ('gi|12345|AA54321'). For these IDs, it extracts the GI and accession and returns a two-element list of strings (GI, acc). Args : a fasta header line string =cut sub default_id_parser { my ($string) = @_; my ($gi,$acc); if( $string =~ s/gi\|(\d+)\|?// ) { $gi = $1; $acc = $1;} if( $string =~ /(\w+)\|([A-Z\d\.\_]+)(\|[A-Z\d\_]+)?/ ) { $acc = defined $2 ? $2 : $1; } else { $acc = $string; $acc =~ s/^\s+(\S+)/$1/; $acc =~ s/(\S+)\s+$/$1/; } return ($gi,$acc); } sub MIN { $a <=> $b ? $a : $b; } sub MAX { $a <=> $b ? $b : $a; } sub footer { my ($self) = @_; return "

Produced by Bioperl module ".ref($self)." on $DATE
Revision: $Revision
\n" } =head2 algorithm_reference Title : algorithm_reference Usage : my $reference = $writer->algorithm_reference($result); Function: Returns the appropriate Bibliographic reference for the algorithm format being produced Returns : String Args : L to reference =cut sub algorithm_reference { my ($self,$result) = @_; return '' if( ! defined $result || !ref($result) || ! $result->isa('Bio::Search::Result::ResultI')) ; if( $result->algorithm =~ /BLAST/i ) { my $res = $result->algorithm . ' ' . $result->algorithm_version . "

"; if( $result->algorithm_version =~ /WashU/i ) { return $res . "Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference: Gish, W. (1996-2000) http://blast.wustl.edu

"; } else { return $res . "Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
\"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs\", Nucleic Acids Res. 25:3389-3402.

"; } } elsif( $result->algorithm =~ /FAST/i ) { return $result->algorithm . " " . $result->algorithm_version . "
" . "\nReference: Pearson et al, Genomics (1997) 46:24-36

"; } else { return ''; } } # from Perl Cookbook 2.17 sub _numwithcommas { my $num = reverse( $_[0] ); $num =~ s/(\d{3})(?=\d)(?!\d*\.)/$1,/g; return scalar reverse $num; } =head2 Methods Bio::SearchIO::SearchWriterI L inherited methods. =head2 filter Title : filter Usage : $writer->filter('hsp', \&hsp_filter); Function: Filter out either at HSP,Hit,or Result level Returns : none Args : string => data type, CODE reference =cut =head2 no_wublastlinks Title : no_wublastlinks Usage : $obj->no_wublastlinks($newval) Function: Get/Set boolean value regarding whether or not to display Link = (1) type output in the report output (WU-BLAST only) Returns : boolean Args : on set, new boolean value (a scalar or undef, optional) =cut sub no_wublastlinks{ my $self = shift; return $self->{'no_wublastlinks'} = shift if @_; return $self->{'no_wublastlinks'}; } 1; BioPerl-1.007002/Bio/SearchIO/Writer/HitTableWriter.pm000444000766000024 3104613155576320 22410 0ustar00cjfieldsstaff000000000000 =head1 NAME Bio::SearchIO::Writer::HitTableWriter - Tab-delimited data for Bio::Search::Hit::HitI objects =head1 SYNOPSIS =head2 Example 1: Using the default columns use Bio::SearchIO; use Bio::SearchIO::Writer::HitTableWriter; my $in = Bio::SearchIO->new(); my $writer = Bio::SearchIO::Writer::HitTableWriter->new(); my $out = Bio::SearchIO->new( -writer => $writer ); while ( my $result = $in->next_result() ) { $out->write_result($result, ($in->report_count - 1 ? 0 : 1) ); } =head2 Example 2: Specifying a subset of columns use Bio::SearchIO; use Bio::SearchIO::Writer::HitTableWriter; my $in = Bio::SearchIO->new(); my $writer = Bio::SearchIO::Writer::HitTableWriter->new( -columns => [qw( query_name query_length hit_name hit_length frac_identical_query expect )] ); my $out = Bio::SearchIO->new( -writer => $writer, -file => ">searchio.out" ); while ( my $result = $in->next_result() ) { $out->write_result($result, ($in->report_count - 1 ? 0 : 1) ); } =head2 Custom Labels You can also specify different column labels if you don't want to use the defaults. Do this by specifying a C<-labels> hash reference parameter when creating the HitTableWriter object. The keys of the hash should be the column number (left-most column = 1) for the label(s) you want to specify. Here's an example: my $writer = Bio::SearchIO::Writer::HitTableWriter->new( -columns => [qw( query_name query_length hit_name hit_length )], -labels => { 1 => 'QUERY_GI', 3 => 'HIT_IDENTIFIER' } ); =head1 DESCRIPTION Bio::SearchIO::Writer::HitTableWriter outputs summary data for each Hit within a search result. Output is in tab-delimited format, one row per Hit. The reason why this is considered summary data is that if a hit contains multiple HSPs, the HSPs will be tiled and the data represents a summary across all HSPs. See below for which columns are affected. See the docs in L for more details on HSP tiling. =head2 Available Columns Here are the columns that can be specified in the C<-columns> parameter when creating a HitTableWriter object. If a C<-columns> parameter is not specified, this list, in this order, will be used as the default. query_name # Sequence identifier of the query. query_length # Full length of the query sequence hit_name # Sequence identifier of the hit hit_length # Full length of the hit sequence round # Round number for hit (PSI-BLAST) expect # Expect value for the alignment score # Score for the alignment (e.g., BLAST score) bits # Bit score for the alignment num_hsps # Number of HSPs (not the "N" value) frac_identical_query* # fraction of identical substitutions in query frac_identical_hit* # fraction of identical substitutions in hit frac_conserved_query* # fraction of conserved substitutions in query frac_conserved_hit* # fraction of conserved substitutions in hit frac_aligned_query* # fraction of the query sequence that is aligned frac_aligned_hit* # fraction of the hit sequence that is aligned length_aln_query* # Length of the aligned portion of the query sequence length_aln_hit* # Length of the aligned portion of the hit sequence gaps_query* # Number of gap characters in the aligned query sequence gaps_hit* # Number of gap characters in the aligned hit sequence gaps_total* # Number of gap characters in the aligned query and hit sequences start_query* # Starting coordinate of the aligned portion of the query sequence end_query* # Ending coordinate of the aligned portion of the query sequence start_hit* # Starting coordinate of the aligned portion of the hit sequence end_hit* # Ending coordinate of the aligned portion of the hit sequence strand_query # Strand of the aligned query sequence strand_hit # Strand of the aligned hit sequence frame # Frame of the alignment (0,1,2) ambiguous_aln # Ambiguous alignment indicator ('qs', 'q', 's') hit_description # Full description of the hit sequence query_description # Full description of the query sequence rank # The rank order of the hit num_hits # Number of hits for the query finding this hit Items marked with a C<*> report data summed across all HSPs after tiling them to avoid counting data from overlapping regions multiple times. For more details about these columns, see the documentation for the corresponding method in Bio::Search::Result::BlastHit. =head1 TODO Figure out the best way to incorporate algorithm-specific score columns. The best route is probably to have algorithm-specific subclasses (e.g., BlastHitTableWriter, FastaHitTableWriter). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Steve Chervitz Esac@bioperl.orgE See L for where to send bug reports and comments. =head1 COPYRIGHT Copyright (c) 2001, 2002 Steve Chervitz. All Rights Reserved. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 SEE ALSO L, L =head1 METHODS =cut package Bio::SearchIO::Writer::HitTableWriter; use strict; use base qw(Bio::SearchIO::Writer::ResultTableWriter); # Array fields: column, object, method[/argument], printf format, # column label Methods for result object are defined in # Bio::Search::Result::ResultI. Methods for hit object are defined in # Bio::Search::Hit::HitI. Tech note: If a bogus method is supplied, # it will result in all values to be zero. Don't know why this is. # TODO (maybe): Allow specification of separate mantissa/exponent for # significance data. my %column_map = ( 'query_name' => ['1', 'result', 'query_name', 's', 'QUERY' ], 'query_length' => ['2', 'result', 'query_length', 'd', 'LEN_Q'], 'hit_name' => ['3', 'hit', 'name', 's', 'HIT'], 'hit_length' => ['4', 'hit', 'length', 'd', 'LEN_H'], 'round' => ['5', 'hit', 'iteration', 'd', 'ROUND'], 'expect' => ['6', 'hit', 'significance', '.1e', 'EXPCT'], 'score' => ['7', 'hit', 'raw_score', 'd', 'SCORE'], 'bits' => ['8', 'hit', 'bits', 'd', 'BITS'], 'num_hsps' => ['9', 'hit', 'num_hsps', 'd', 'HSPS'], 'frac_identical_query' => ['10', 'hit', 'frac_identical/query', '.2f', 'FR_IDQ'], 'frac_identical_hit' => ['11', 'hit', 'frac_identical/hit', '.2f', 'FR_IDH'], 'frac_conserved_query' => ['12', 'hit', 'frac_conserved/query', '.2f', 'FR_CNQ'], 'frac_conserved_hit' => ['13', 'hit', 'frac_conserved/hit', '.2f', 'FR_CNH'], 'frac_aligned_query' => ['14', 'hit', 'frac_aligned_query', '.2f', 'FR_ALQ'], 'frac_aligned_hit' => ['15', 'hit', 'frac_aligned_hit', '.2f', 'FR_ALH'], 'length_aln_query' => ['16', 'hit', 'length_aln/query', 'd', 'LN_ALQ'], 'length_aln_hit' => ['17', 'hit', 'length_aln/hit', 'd', 'LN_ALH'], 'gaps_query' => ['18', 'hit', 'gaps/query', 'd', 'GAPS_Q'], 'gaps_hit' => ['19', 'hit', 'gaps/hit', 'd', 'GAPS_H'], 'gaps_total' => ['20', 'hit', 'gaps/total', 'd', 'GAPS_QH'], 'start_query' => ['21', 'hit', 'start/query', 'd', 'START_Q'], 'end_query' => ['22', 'hit', 'end/query', 'd', 'END_Q'], 'start_hit' => ['23', 'hit', 'start/hit', 'd', 'START_H'], 'end_hit' => ['24', 'hit', 'end/hit', 'd', 'END_H'], 'strand_query' => ['25', 'hit', 'strand/query', 's', 'STRND_Q'], 'strand_hit' => ['26', 'hit', 'strand/hit', 's', 'STRND_H'], 'frame' => ['27', 'hit', 'frame', 'd', 'FRAME'], 'ambiguous_aln' => ['28', 'hit', 'ambiguous_aln', 's', 'AMBIG'], 'hit_description' => ['29', 'hit', 'description', 's', 'DESC_H'], 'query_description' => ['30', 'result', 'query_description', 's', 'DESC_Q'], 'rank' => ['31', 'hit', 'rank', 's', 'RANK'], 'num_hits' => ['32', 'result', 'num_hits', 's', 'NUM_HITS'], ); sub column_map { return %column_map } =head2 to_string() Note: this method is not intended for direct use. The SearchIO::write_result() method calls it automatically if the writer is hooked up to a SearchIO object as illustrated in L. Title : to_string() : Usage : print $writer->to_string( $result_obj, [$include_labels] ); : Argument : $result_obj = A Bio::Search::Result::BlastResult object : $include_labels = boolean, if true column labels are included (default: false) : Returns : String containing tab-delimited set of data for each hit : in a BlastResult object. Some data is summed across multiple HSPs. : Throws : n/a =cut #---------------- sub to_string { #---------------- my ($self, $result, $include_labels) = @_; my $str = $include_labels ? $self->column_labels() : ''; my $func_ref = $self->row_data_func; my $printf_fmt = $self->printf_fmt; my ($resultfilter,$hitfilter) = ( $self->filter('RESULT'), $self->filter('HIT') ); if( ! defined $resultfilter || &{$resultfilter}($result) ) { $result->can('rewind') && $result->rewind(); # insure we're at the beginning foreach my $hit($result->hits) { next if( defined $hitfilter && ! &{$hitfilter}($hit)); my @row_data = map { defined $_ ? $_ : 0 } &{$func_ref}($result, $hit); $str .= sprintf "$printf_fmt\n", @row_data; } } $str =~ s/\t\n/\n/gs; return $str; } =head2 end_report Title : end_report Usage : $self->end_report() Function: The method to call when ending a report, this is mostly for cleanup for formats which require you to have something at the end of the document. Nothing for a text message. Returns : string Args : none =cut sub end_report { return ''; } =head2 filter Title : filter Usage : $writer->filter('hsp', \&hsp_filter); Function: Filter out either at HSP,Hit,or Result level Returns : none Args : string => data type, CODE reference =cut 1; BioPerl-1.007002/Bio/SearchIO/Writer/ResultTableWriter.pm000444000766000024 3241113155576320 23137 0ustar00cjfieldsstaff000000000000 =head1 NAME Bio::SearchIO::Writer::ResultTableWriter - Outputs tab-delimited data for each Bio::Search::Result::ResultI object. =head1 SYNOPSIS =head2 Example 1: Using the default columns use Bio::SearchIO; use Bio::SearchIO::Writer::ResultTableWriter; my $in = Bio::SearchIO->new(); my $writer = Bio::SearchIO::Writer::ResultTableWriter->new(); my $out = Bio::SearchIO->new( -writer => $writer ); while ( my $result = $in->next_result() ) { $out->write_result($result, ($in->report_count - 1 ? 0 : 1) ); } =head2 Example 2: Specifying a subset of columns use Bio::SearchIO; use Bio::SearchIO::Writer::ResultTableWriter; my $in = Bio::SearchIO->new(); my $writer = Bio::SearchIO::Writer::ResultTableWriter->new( -columns => [qw( query_name query_length num_hits )] ); my $out = Bio::SearchIO->new( -writer => $writer, -file => ">result.out" ); while ( my $result = $in->next_result() ) { $out->write_result($result, ($in->report_count - 1 ? 0 : 1) ); } =head2 Custom Labels You can also specify different column labels if you don't want to use the defaults. Do this by specifying a C<-labels> hash reference parameter when creating the ResultTableWriter object. The keys of the hash should be the column number (left-most column = 1) for the label(s) you want to specify. Here's an example: my $writer = Bio::SearchIO::Writer::ResultTableWriter->new( -columns => [qw( query_name query_length query_description num_hits)], -labels => { 1 => 'QUERY_GI', 2 => 'QUERY_LENGTH' } ); =head1 DESCRIPTION Bio::SearchIO::Writer::ResultTableWriter outputs data in tab-delimited format for each search result, one row per search result. This is a very coarse-grain level of information since it only includes data stored in the Bio::Search::Result::ResultI object itself and does not include any information about hits or HSPs. You most likely will never use this object but instead will use one of its subclasses: Bio::SearchIO::Writer::HitTableWriter or Bio::SearchIO::Writer::HSPTableWriter. =head2 Available Columns Here are the columns that can be specified in the C<-columns> parameter when creating a ResultTableWriter object. If a C<-columns> parameter is not specified, this list, in this order, will be used as the default. query_name query_length query_description For more details about these columns, see the documentation for the corresponding method in L. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Steve Chervitz Esac@bioperl.orgE See L for where to send bug reports and comments. =head1 COPYRIGHT Copyright (c) 2001 Steve Chervitz. All Rights Reserved. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 SEE ALSO L, L =head1 METHODS =cut package Bio::SearchIO::Writer::ResultTableWriter; use strict; use base qw(Bio::Root::Root Bio::SearchIO::SearchWriterI); # Array fields: column, object, method[/argument], printf format, column label # Methods are defined in Bio::Search::Result::ResultI. # Tech note: If a bogus method is supplied, it will result in all values to be zero. # Don't know why this is. my %column_map = ( 'query_name' => ['1', 'result', 'query_name', 's', 'QUERY' ], 'query_length' => ['2', 'result', 'query_length', 'd', 'LEN_Q'], 'query_description' => ['3', 'result', 'query_description', 's', 'DESC_Q'], 'num_hits' => ['4', 'result', 'num_hits', 'd', 'NUM_HITS'], ); sub column_map { return %column_map } sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my( $col_spec, $label_spec, $filters ) = $self->_rearrange( [qw(COLUMNS LABELS FILTERS)], @args); $self->_set_cols( $col_spec ); $self->_set_labels( $label_spec ) if $label_spec; $self->_set_printf_fmt(); $self->_set_row_data_func(); $self->_set_column_labels(); if( defined $filters ) { if( !ref($filters) =~ /HASH/i ) { $self->warn("Did not provide a hashref for the FILTERS option, ignoring."); } else { while( my ($type,$code) = each %{$filters} ) { $self->filter($type,$code); } } } return $self; } # Purpose : Stores the column spec internally. Also performs QC on the # user-supplied column specification. # sub _set_cols { my ($self, $col_spec_ref) = @_; return if defined $self->{'_cols'}; # only set columns once my %map = $self->column_map; if( not defined $col_spec_ref) { print STDERR "\nUsing default column map.\n"; $col_spec_ref = [ map { $_ } sort { $map{$a}->[0] <=> $map{$b}->[0] } keys %map ]; } if( ref($col_spec_ref) eq 'ARRAY') { # printf "%d columns to process\n", scalar(@$col_spec_ref); my @col_spec = @{$col_spec_ref}; while( my $item = shift @col_spec ) { $item = lc($item); if( not defined ($map{$item}) ) { $self->throw(-class =>'Bio::Root::BadParameter', -text => "Unknown column name: $item" ); } push @{$self->{'_cols'}}, $item; #print "pushing on to col $col_num, $inner: $item\n"; } } else { $self->throw(-class =>'Bio::Root::BadParameter', -text => "Can't set columns: not a ARRAY ref", -value => $col_spec_ref ); } } sub _set_printf_fmt { my ($self) = @_; my @cols = $self->columns(); my %map = $self->column_map; my $printf_fmt = ''; foreach my $col ( @cols ) { $printf_fmt .= "\%$map{$col}->[3]\t"; } $printf_fmt =~ s/\\t$//; $self->{'_printf_fmt'} = $printf_fmt; } sub printf_fmt { shift->{'_printf_fmt'} } # Sets the data to be used for the labels. sub _set_labels { my ($self, $label_spec) = @_; if( ref($label_spec) eq 'HASH') { foreach my $col ( sort { $a <=> $b } keys %$label_spec ) { # print "LABEL: $col $label_spec->{$col}\n"; $self->{'_custom_labels'}->{$col} = $label_spec->{$col}; } } else { $self->throw(-class =>'Bio::Root::BadParameter', -text => "Can't set labels: not a HASH ref: $label_spec" ); } } sub _set_column_labels { my $self = shift; my @cols = $self->columns; my %map = $self->column_map; my $printf_fmt = ''; my (@data, $label, @underbars); my $i = 0; foreach my $col( @cols ) { $i++; $printf_fmt .= "\%s\t"; if(defined $self->{'_custom_labels'}->{$i}) { $label = $self->{'_custom_labels'}->{$i}; } else { $label = $map{$col}->[4]; } push @data, $label; push @underbars, '-' x length($label); } $printf_fmt =~ s/\\t$//; my $str = sprintf "$printf_fmt\n", @data; $str =~ s/\t\n/\n/; $str .= sprintf "$printf_fmt\n", @underbars; $str =~ s/\t\n/\n/gs; $self->{'_column_labels'} = $str; } # Purpose : Generate a function that will call the appropriate # methods on the result, hit, and hsp objects to retrieve the column data # specified in the column spec. # # We should only have to go through the column spec once # for a given ResultTableWriter. To permit this, we'll generate code # for a method that returns an array of the data for a row of output # given a result, hit, and hsp object as arguments. # sub _set_row_data_func { my $self = shift; # Now we need to generate a string that can be eval'd to get the data. my @cols = $self->columns(); my %map = $self->column_map; my @data; while( my $col = shift @cols ) { my $object = $map{$col}->[1]; my $method = $map{$col}->[2]; my $arg = ''; if( $method =~ m!(\w+)/(\w+)! ) { $method = $1; $arg = "\"$2\""; } push @data, "\$$object->$method($arg)"; } my $code = join( ",", @data); if( $self->verbose > 0 ) { ## Begin Debugging $self->debug( "Data to print:\n"); foreach( 0..$#data) { $self->debug( " [". ($_+ 1) . "] $data[$_]\n");} $self->debug( "CODE:\n$code\n"); $self->debug("Printf format: ". $self->printf_fmt. "\n"); ## End Debugging } my $func = sub { my ($result, $hit, $hsp) = @_; my @r = eval $code; # This should reduce the occurrence of those opaque "all zeros" bugs. if( $@ ) { $self->throw("Trouble in ResultTableWriter::_set_row_data_func() eval: $@\n\n"); } return @r; }; $self->{'_row_data_func'} = $func; } sub row_data_func { shift->{'_row_data_func'} } =head2 to_string() Note: this method is not intended for direct use. The SearchIO::write_result() method calls it automatically if the writer is hooked up to a SearchIO object as illustrated in L. Title : to_string() : Usage : print $writer->to_string( $result_obj, [$include_labels] ); : Argument : $result_obj = A Bio::Search::Result::ResultI object : $include_labels = boolean, if true column labels are included (default: false) : Returns : String containing tab-delimited set of data for each hit : in a ResultI object. Some data is summed across multiple HSPs. : Throws : n/a =cut #---------------- sub to_string { #---------------- my ($self, $result, $include_labels) = @_; my $str = $include_labels ? $self->column_labels() : ''; my $resultfilter = $self->filter('RESULT'); if( ! defined $resultfilter || &{$resultfilter}($result) ) { my @row_data = &{$self->{'_row_data_func'}}( $result ); $str .= sprintf "$self->{'_printf_fmt'}\n", @row_data; $str =~ s/\t\n/\n/gs; } return $str; } sub columns { my $self = shift; my @cols; if( ref $self->{'_cols'} ) { @cols = @{$self->{'_cols'}}; } else { my %map = $self->column_map; @cols = sort { $map{$a}->[0] <=> $map{$b}->[0] } keys %map; } return @cols; } =head2 column_labels Usage : print $result_obj->column_labels(); Purpose : Get column labels for to_string(). Returns : String containing column labels. Tab-delimited. Argument : n/a Throws : n/a =cut sub column_labels { shift->{'_column_labels'} } =head2 end_report Title : end_report Usage : $self->end_report() Function: The method to call when ending a report, this is mostly for cleanup for formats which require you to have something at the end of the document. Nothing for a text message. Returns : string Args : none =cut sub end_report { return ''; } =head2 filter Title : filter Usage : $writer->filter('hsp', \&hsp_filter); Function: Filter out either at HSP,Hit,or Result level Returns : none Args : string => data type, CODE reference =cut # Is this really needed? #=head2 signif_format # # Usage : $writer->signif_format( [FMT] ); # Purpose : Allows retrieval of the P/Expect exponent values only # : or as a two-element list (mantissa, exponent). # Usage : $writer->signif_format('exp'); # : $writer->signif_format('parts'); # Returns : String or '' if not set. # Argument : String, FMT = 'exp' (return the exponent only) # : = 'parts'(return exponent + mantissa in 2-elem list) # : = undefined (return the raw value) # Comments : P/Expect values are still stored internally as the full, # : scientific notation value. # #=cut # ##------------- #sub signif_format { ##------------- # my $self = shift; # if(@_) { $self->{'_signif_format'} = shift; } # return $self->{'_signif_format'}; #} 1; BioPerl-1.007002/Bio/SearchIO/Writer/TextResultWriter.pm000444000766000024 5735413155576320 23051 0ustar00cjfieldsstaff000000000000# # BioPerl module for Bio::SearchIO::Writer::TextResultWriter # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::Writer::TextResultWriter - Object to implement writing a Bio::Search::ResultI in Text. =head1 SYNOPSIS use Bio::SearchIO; use Bio::SearchIO::Writer::TextResultWriter; my $in = Bio::SearchIO->new(-format => 'blast', -file => shift @ARGV); my $writer = Bio::SearchIO::Writer::TextResultWriter->new(); my $out = Bio::SearchIO->new(-writer => $writer); $out->write_result($in->next_result); =head1 DESCRIPTION This object implements the SearchWriterI interface which will produce a set of Text for a specific Bio::Search::Report::ReportI interface. You can also provide the argument -filters =E \%hash to filter the at the hsp, hit, or result level. %hash is an associative array which contains any or all of the keys (HSP, HIT, RESULT). The values pointed to by these keys would be references to a subroutine which expects to be passed an object - one of Bio::Search::HSP::HSPI, Bio::Search::Hit::HitI, and Bio::Search::Result::ResultI respectively. Each function needs to return a boolean value as to whether or not the passed element should be included in the output report - true if it is to be included, false if it to be omitted. For example to filter on sequences in the database which are too short for your criteria you would do the following. Define a hit filter method sub hit_filter { my $hit = shift; return $hit->length E 100; # test if length of the hit sequence # long enough } my $writer = Bio::SearchIO::Writer::TextResultWriter->new( -filters => { 'HIT' =E \&hit_filter } ); Another example would be to filter HSPs on percent identity, let's only include HSPs which are 75% identical or better. sub hsp_filter { my $hsp = shift; return $hsp->percent_identity E 75; } my $writer = Bio::SearchIO::Writer::TextResultWriter->new( -filters => { 'HSP' =E \&hsp_filter } ); See L for more info on the filter method. This module will use the module Text::Wrap if it is installed to wrap the Query description line. If you do not have Text::Wrap installed this module will work fine but you won't have the Query line wrapped. You will see a warning about this when you first instantiate a TextResultWriter - to avoid these warnings from showing up, simply set the verbosity upon initialization to -1 like this: my $writer = new Bio::SearchIO::Writer::TextResultWriter(-verbose =E -1); =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::Writer::TextResultWriter; use vars qw($MaxNameLen $MaxDescLen $AlignmentLineWidth $DescLineLen $TextWrapLoaded); use strict; # Object preamble - inherits from Bio::Root::RootI BEGIN { $MaxDescLen = 65; $AlignmentLineWidth = 60; eval { require Text::Wrap; $TextWrapLoaded = 1;}; if( $@ ) { $TextWrapLoaded = 0; } } use POSIX; use base qw(Bio::Root::Root Bio::SearchIO::SearchWriterI); =head2 new Title : new Usage : my $obj = Bio::SearchIO::Writer::TextResultWriter->new(); Function: Builds a new Bio::SearchIO::Writer::TextResultWriter object Returns : Bio::SearchIO::Writer::TextResultWriter Args : -filters => hashref with any or all of the keys (HSP HIT RESULT) which have values pointing to a subroutine reference which will expect to get a Hit,HSP, Result object respectively -no_wublastlinks => boolean. Do not display WU-BLAST lines even if they are parsed out Links = (1) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($filters,$nowublastlinks) = $self->_rearrange([qw(FILTERS NO_WUBLASTLINKS)], @args); if( defined $filters ) { if( !ref($filters) =~ /HASH/i ) { $self->warn("Did not provide a hashref for the FILTERS option, ignoring."); } else { while( my ($type,$code) = each %{$filters} ) { $self->filter($type,$code); } } } $self->no_wublastlinks(! $nowublastlinks); unless( $TextWrapLoaded ) { $self->warn("Could not load Text::Wrap - the Query Description will not be line wrapped\n"); } else { $Text::Wrap::columns = $MaxDescLen; } return $self; } =head2 to_string Purpose : Produces data for each Search::Result::ResultI in a string. : This is an abstract method. For some useful implementations, : see ResultTableWriter.pm, HitTableWriter.pm, : and HSPTableWriter.pm. Usage : print $writer->to_string( $result_obj, @args ); Argument : $result_obj = A Bio::Search::Result::ResultI object : @args = any additional arguments used by your implementation. Returns : String containing data for each search Result or any of its : sub-objects (Hits and HSPs). Throws : n/a =cut sub to_string { my ($self,$result,$num) = @_; $num ||= 0; return unless defined $result; my $links = $self->no_wublastlinks; my ($resultfilter,$hitfilter, $hspfilter) = ( $self->filter('RESULT'), $self->filter('HIT'), $self->filter('HSP') ); return '' if( defined $resultfilter && ! &{$resultfilter}($result) ); my ($qtype,$dbtype,$dbseqtype,$type); my $alg = $result->algorithm; my $wublast = ($result->algorithm_version =~ /WashU/) ? 1 : 0; # This is actually wrong for the FASTAs I think if( $alg =~ /T(FAST|BLAST)([XY])/i ) { $qtype = $dbtype = 'translated'; $dbseqtype = $type = 'PROTEIN'; } elsif( $alg =~ /T(FAST|BLAST)N/i ) { $qtype = ''; $dbtype = 'translated'; $type = 'PROTEIN'; $dbseqtype = 'NUCLEOTIDE'; } elsif( $alg =~ /(FAST|BLAST)N/i || $alg =~ /(WABA|EXONERATE)/i ) { $qtype = $dbtype = ''; $type = $dbseqtype = 'NUCLEOTIDE'; } elsif( $alg =~ /(FAST|BLAST)P/ || $alg =~ /SSEARCH|(HMM|SEARCH|PFAM)/i ) { $qtype = $dbtype = ''; $type = $dbseqtype = 'PROTEIN'; } elsif( $alg =~ /(FAST|BLAST)[XY]/i ) { $qtype = 'translated'; $dbtype = 'PROTEIN'; $dbseqtype = $type = 'PROTEIN'; } else { print STDERR "algorithm was ", $result->algorithm, " couldn't match\n"; } my %baselens = ( 'Sbjct:' => ( $dbtype eq 'translated' ) ? 3 : 1, 'Query:' => ( $qtype eq 'translated' ) ? 3 : 1); my $str; if( ! defined $num || $num <= 1 ) { $str = &{$self->start_report}($result); } $str .= &{$self->title}($result); $str .= $result->algorithm . " " . $result->algorithm_version . "\n\n\n"; $str .= $result->algorithm_reference || $self->algorithm_reference($result); $str .= &{$self->introduction}($result); $str .= qq{ Score E Sequences producing significant alignments: (bits) value }; my $hspstr = ''; if( $result->can('rewind')) { $result->rewind(); # support stream based parsing routines } while( my $hit = $result->next_hit ) { next if( defined $hitfilter && ! &{$hitfilter}($hit) ); my $nm = $hit->name(); $self->debug( "no $nm for name (".$hit->description(). "\n") unless $nm; my ($gi,$acc) = &{$self->id_parser}($nm); my $p = "%-$MaxDescLen". "s"; my $descsub; my $desc = sprintf("%s %s",$nm,$hit->description); if( length($desc) - 3 > $MaxDescLen) { $descsub = sprintf($p, substr($desc,0,$MaxDescLen-3) . "..."); } else { $descsub = sprintf($p,$desc); } $str .= $wublast ? sprintf("%s %-4s %s\n", $descsub, defined $hit->raw_score ? $hit->raw_score : ' ', defined $hit->significance ? $hit->significance : '?') : sprintf("%s %-4s %s\n", $descsub, defined $hit->bits ? $hit->bits: ' ', defined $hit->significance ? $hit->significance : '?'); my @hsps = $hit->hsps; if( @hsps ) { $hspstr .= sprintf(">%s %s\n%9sLength = %d\n\n", $hit->name, defined $hit->description ? $hit->description : '', '', # empty is for the %9s in the str formatting $hit->length); foreach my $hsp ( @hsps ) { next if( defined $hspfilter && ! &{$hspfilter}($hsp) ); $hspstr .= sprintf(" Score = %4s bits (%s), Expect = %s", $hsp->bits, $hsp->score, $hsp->evalue); if( $hsp->pvalue ) { $hspstr .= ", P = ".$hsp->pvalue; } $hspstr .= "\n"; $hspstr .= sprintf(" Identities = %d/%d (%d%%)", ( $hsp->frac_identical('total') * $hsp->length('total')), $hsp->length('total'), POSIX::floor($hsp->frac_identical('total') * 100)); if( $type eq 'PROTEIN' ) { $hspstr .= sprintf(", Positives = %d/%d (%d%%)", ( $hsp->frac_conserved('total') * $hsp->length('total')), $hsp->length('total'), POSIX::floor($hsp->frac_conserved('total') * 100)); } if( $hsp->gaps ) { $hspstr .= sprintf(", Gaps = %d/%d (%d%%)", $hsp->gaps('total'), $hsp->length('total'), POSIX::floor(100 * $hsp->gaps('total') / $hsp->length('total'))); } $hspstr .= "\n"; my ($hframe,$qframe) = ( $hsp->hit->frame, $hsp->query->frame); my ($hstrand,$qstrand) = ($hsp->hit->strand,$hsp->query->strand); # so TBLASTX will have Query/Hit frames # BLASTX will have Query frame # TBLASTN will have Hit frame if( $hstrand || $qstrand ) { $hspstr .= " Frame = "; my ($signq, $signh); unless( $hstrand ) { $hframe = undef; # if strand is null or 0 then it is protein # and this no frame } else { $signh = $hstrand < 0 ? '-' : '+'; } unless( $qstrand ) { $qframe = undef; # if strand is null or 0 then it is protein } else { $signq =$qstrand < 0 ? '-' : '+'; } # remember bioperl stores frames as 0,1,2 (GFF way) # BLAST reports reports as 1,2,3 so # we have to add 1 to the frame values if( defined $hframe && ! defined $qframe) { $hspstr .= "$signh".($hframe+1); } elsif( defined $qframe && ! defined $hframe) { $hspstr .= "$signq".($qframe+1); } else { $hspstr .= sprintf(" %s%d / %s%d", $signq,$qframe+1, $signh, $hframe+1); } } if( $links && $hsp->can('links') && defined(my $lnks = $hsp->links) ) { $hspstr .= sprintf(" Links = %s\n",$lnks); } $hspstr .= "\n\n"; my @hspvals = ( {'name' => 'Query:', 'seq' => $hsp->query_string, 'start' => ( $qstrand >= 0 ? $hsp->query->start : $hsp->query->end), 'end' => ($qstrand >= 0 ? $hsp->query->end : $hsp->query->start), 'index' => 0, 'direction' => $qstrand || 1 }, { 'name' => ' 'x6, # this might need to adjust for long coordinates?? 'seq' => $hsp->homology_string, 'start' => undef, 'end' => undef, 'index' => 0, 'direction' => 1 }, { 'name' => 'Sbjct:', 'seq' => $hsp->hit_string, 'start' => ($hstrand >= 0 ? $hsp->hit->start : $hsp->hit->end), 'end' => ($hstrand >= 0 ? $hsp->hit->end : $hsp->hit->start), 'index' => 0, 'direction' => $hstrand || 1 } ); # let's set the expected length (in chars) of the starting number # in an alignment block so we can have things line up # Just going to try and set to the largest my ($numwidth) = sort { $b <=> $a }(length($hspvals[0]->{'start'}), length($hspvals[0]->{'end'}), length($hspvals[2]->{'start'}), length($hspvals[2]->{'end'})); my $count = 0; while ( $count <= $hsp->length('total') ) { foreach my $v ( @hspvals ) { my $piece = substr($v->{'seq'}, $v->{'index'} +$count, $AlignmentLineWidth); my $cp = $piece; my $plen = scalar ( $cp =~ tr/\-//); my ($start,$end) = ('',''); if( defined $v->{'start'} ) { $start = $v->{'start'}; # since strand can be + or - use the direction # to signify which whether to add or subtract from end my $d = $v->{'direction'} * ( $AlignmentLineWidth - $plen )* $baselens{$v->{'name'}}; if( length($piece) < $AlignmentLineWidth ) { $d = (length($piece) - $plen) * $v->{'direction'} * $baselens{$v->{'name'}}; } $end = $v->{'start'} + $d - $v->{'direction'}; $v->{'start'} += $d; } $hspstr .= sprintf("%s %-".$numwidth."s %s %s\n", $v->{'name'}, $start, $piece, $end ); } $count += $AlignmentLineWidth; $hspstr .= "\n"; } } $hspstr .= "\n"; } } $str .= "\n\n".$hspstr; $str .= sprintf(qq{ Database: %s Posted date: %s Number of letters in database: %s Number of sequences in database: %s Matrix: %s }, $result->database_name(), $result->get_statistic('posted_date') || POSIX::strftime("%b %d, %Y %I:%M %p",localtime), &_numwithcommas($result->database_letters()), &_numwithcommas($result->database_entries()), $result->get_parameter('matrix') || ''); if( defined (my $open = $result->get_parameter('gapopen')) ) { $str .= sprintf("Gap Penalties Existence: %d, Extension: %d\n", $open || 0, $result->get_parameter('gapext') || 0); } # skip those params we've already output foreach my $param ( grep { ! /matrix|gapopen|gapext/i } $result->available_parameters ) { $str .= "$param: ". $result->get_parameter($param) ."\n"; } $str .= "Search Statistics\n"; # skip posted date, we already output it foreach my $stat ( sort grep { ! /posted_date/ } $result->available_statistics ) { my $expect = $result->get_parameter('expect'); my $v = $result->get_statistic($stat); if( $v =~ /^\d+$/ ) { $v = &_numwithcommas($v); } if( defined $expect && $stat eq 'seqs_better_than_cutoff' ) { $str .= "seqs_better_than_$expect: $v\n"; } else { my $v = $str .= "$stat: $v\n"; } } $str .= "\n\n"; return $str; } =head2 start_report Title : start_report Usage : $index->start_report( CODE ) Function: Stores or returns the code to write the start of the block, the block and the start of the <BODY> block of HTML. Useful for (for instance) specifying alternative HTML if you are embedding the output in an HTML page which you have already started. (For example a routine returning a null string). Returns \&default_start_report (see below) if not set. Example : $index->start_report( \&my_start_report ) Returns : ref to CODE if called without arguments Args : CODE =cut sub start_report { my( $self, $code ) = @_; if ($code) { $self->{'_start_report'} = $code; } return $self->{'_start_report'} || \&default_start_report; } =head2 default_start_report Title : default_start_report Usage : $self->default_start_report($result) Function: The default method to call when starting a report. Returns : sting Args : First argument is a Bio::Search::Result::ResultI =cut sub default_start_report { my ($result) = @_; return ""; } =head2 title Title : title Usage : $self->title($CODE) Function: Stores or returns the code to provide HTML for the given BLAST report that will appear at the top of the BLAST report HTML output. Useful for (for instance) specifying alternative routines to write your own titles. Returns \&default_title (see below) if not set. Example : $index->title( \&my_title ) Returns : ref to CODE if called without arguments Args : CODE =cut sub title { my( $self, $code ) = @_; if ($code) { $self->{'_title'} = $code; } return $self->{'_title'} || \&default_title; } =head2 default_title Title : default_title Usage : $self->default_title($result) Function: Provides HTML for the given BLAST report that will appear at the top of the BLAST report output. Returns : empty for text implementation Args : First argument is a Bio::Search::Result::ResultI =cut sub default_title { my ($result) = @_; return ""; # The HTML implementation # return sprintf( # qq{<CENTER><H1><a href="http://bioperl.org">Bioperl</a> Reformatted HTML of %s Search Report<br> for %s</H1></CENTER>}, # $result->algorithm, # $result->query_name()); } =head2 introduction Title : introduction Usage : $self->introduction($CODE) Function: Stores or returns the code to provide HTML for the given BLAST report detailing the query and the database information. Useful for (for instance) specifying routines returning alternative introductions. Returns \&default_introduction (see below) if not set. Example : $index->introduction( \&my_introduction ) Returns : ref to CODE if called without arguments Args : CODE =cut sub introduction { my( $self, $code ) = @_; if ($code) { $self->{'_introduction'} = $code; } return $self->{'_introduction'} || \&default_introduction; } =head2 default_introduction Title : default_introduction Usage : $self->default_introduction($result) Function: Outputs HTML to provide the query and the database information Returns : string containing HTML Args : First argument is a Bio::Search::Result::ResultI Second argument is string holding literature citation =cut sub default_introduction { my ($result) = @_; return sprintf( qq{ Query= %s (%s letters) Database: %s %s sequences; %s total letters }, &_linewrap($result->query_name . " " . $result->query_description), &_numwithcommas($result->query_length), $result->database_name(), &_numwithcommas($result->database_entries()), &_numwithcommas($result->database_letters()), ); } =head2 end_report Title : end_report Usage : $self->end_report() Function: The method to call when ending a report, this is mostly for cleanup for formats which require you to have something at the end of the document (</BODY></HTML>) for HTML Returns : string Args : none =cut sub end_report { return ""; } # copied from Bio::Index::Fasta # useful here as well =head2 id_parser Title : id_parser Usage : $index->id_parser( CODE ) Function: Stores or returns the code used by record_id to parse the ID for record from a string. Useful for (for instance) specifying a different parser for different flavours of FASTA file. Returns \&default_id_parser (see below) if not set. If you supply your own id_parser subroutine, then it should expect a fasta description line. An entry will be added to the index for each string in the list returned. Example : $index->id_parser( \&my_id_parser ) Returns : ref to CODE if called without arguments Args : CODE =cut sub id_parser { my( $self, $code ) = @_; if ($code) { $self->{'_id_parser'} = $code; } return $self->{'_id_parser'} || \&default_id_parser; } =head2 default_id_parser Title : default_id_parser Usage : $id = default_id_parser( $header ) Function: The default Fasta ID parser for Fasta.pm Returns $1 from applying the regexp /^>\s*(\S+)/ to $header. Returns : ID string Args : a fasta header line string =cut sub default_id_parser { my ($string) = @_; my ($gi,$acc); if( $string =~ s/gi\|(\d+)\|?// ) { $gi = $1; $acc = $1;} if( $string =~ /(\w+)\|([A-Z\d\.\_]+)(\|[A-Z\d\_]+)?/ ) { $acc = defined $2 ? $2 : $1; } else { $acc = $string; $acc =~ s/^\s+(\S+)/$1/; $acc =~ s/(\S+)\s+$/$1/; } return ($gi,$acc); } sub MIN { $a <=> $b ? $a : $b; } sub MAX { $a <=> $b ? $b : $a; } =head2 algorithm_reference Title : algorithm_reference Usage : my $reference = $writer->algorithm_reference($result); Function: Returns the appropriate Bibliographic reference for the algorithm format being produced Returns : String Args : L<Bio::Search::Result::ResultI> to reference =cut sub algorithm_reference{ my ($self,$result) = @_; return '' if( ! defined $result || !ref($result) || ! $result->isa('Bio::Search::Result::ResultI')) ; if( $result->algorithm =~ /BLAST/i ) { my $res = $result->algorithm . ' '. $result->algorithm_version. "\n"; if( $result->algorithm_version =~ /WashU/i ) { return $res .qq{ Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA. All Rights Reserved. Reference: Gish, W. (1996-2000) http://blast.wustl.edu }; } else { return $res . qq{ Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. }; } } elsif( $result->algorithm =~ /FAST/i ) { return $result->algorithm. " ". $result->algorithm_version . "\n". "\nReference: Pearson et al, Genomics (1997) 46:24-36\n"; } else { return ''; } } # from Perl Cookbook 2.17 sub _numwithcommas { my $num = reverse( $_[0] ); $num =~ s/(\d{3})(?=\d)(?!\d*\.)/$1,/g; return scalar reverse $num; } sub _linewrap { my ($str) = @_; if($TextWrapLoaded) { return Text::Wrap::wrap("","",$str); # use Text::Wrap } else { return $str; } # cannot wrap } =head2 Methods Bio::SearchIO::SearchWriterI L<Bio::SearchIO::SearchWriterI> inherited methods. =head2 filter Title : filter Usage : $writer->filter('hsp', \&hsp_filter); Function: Filter out either at HSP,Hit,or Result level Returns : none Args : string => data type, CODE reference =cut =head2 no_wublastlinks Title : no_wublastlinks Usage : $obj->no_wublastlinks($newval) Function: Get/Set boolean value regarding whether or not to display Link = (1) type output in the report output (WU-BLAST only) Returns : boolean Args : on set, new boolean value (a scalar or undef, optional) =cut sub no_wublastlinks{ my $self = shift; return $self->{'no_wublastlinks'} = shift if @_; return $self->{'no_wublastlinks'}; } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq����������������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 14617� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/BaseSeqProcessor.pm��������������������������������������������������������000444��000766��000024�� 20073�13155576320� 20557� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::BaseSeqProcessor # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp at gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Seq::BaseSeqProcessor - Base implementation for a SequenceProcessor =head1 SYNOPSIS # you need to derive your own processor from this one =head1 DESCRIPTION This provides just a basic framework for implementations of L<Bio::Factory::SequenceProcessorI>. Essentially what it does is support a parameter to new() to set sequence factory and source stream, and a next_seq() implementation that will use a queue to be filled by a class overriding process_seq(). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::BaseSeqProcessor; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root Bio::Factory::SequenceProcessorI); =head2 new Title : new Usage : my $obj = Bio::Seq::BaseSeqProcessor->new(); Function: Builds a new Bio::Seq::BaseSeqProcessor object Returns : an instance of Bio::Seq::BaseSeqProcessor Args : Named parameters. Currently supported are -seqfactory the Bio::Factory::SequenceFactoryI object to use -source_stream the Bio::Factory::SequenceStreamI object to which we are chained =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($stream,$fact) = $self->_rearrange([qw(SOURCE_STREAM SEQFACTORY)], @args); $self->{'_queue'} = []; $self->sequence_factory($fact) if $fact; $self->source_stream($stream) if $stream; return $self; } =head1 L<Bio::Factory::SequenceProcessorI> methods =cut =head2 source_stream Title : source_stream Usage : $obj->source_stream($newval) Function: Get/set the source sequence stream for this sequence processor. Example : Returns : A Bio::Factory::SequenceStreamI compliant object Args : on set, new value (a Bio::Factory::SequenceStreamI compliant object) =cut sub source_stream{ my $self = shift; if(@_) { my $stream = shift; my $fact = $stream->sequence_factory(); $self->sequence_factory($fact) unless $self->sequence_factory() || (! $fact); return $self->{'source_stream'} = $stream; } return $self->{'source_stream'}; } =head1 L<Bio::Factory::SequenceStreamI> methods =cut =head2 next_seq Title : next_seq Usage : $seq = stream->next_seq Function: Reads the next sequence object from the stream and returns it. This implementation will obtain objects from the source stream as necessary and pass them to process_seq() for processing. This method will return the objects one at a time that process_seq() returns. Returns : a Bio::Seq sequence object Args : none See L<Bio::Factory::SequenceStreamI::next_seq> =cut sub next_seq{ my $self = shift; my $seq; # if the queue is empty, fetch next from source and process it if(@{$self->{'_queue'}} == 0) { my @seqs = (); while($seq = $self->source_stream->next_seq()) { @seqs = $self->process_seq($seq); # we may get zero seqs returned last if @seqs; } push(@{$self->{'_queue'}}, @seqs) if @seqs; } # take next from the queue of seqs $seq = shift(@{$self->{'_queue'}}); return $seq; } =head2 write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: Writes the result(s) of processing the sequence object into the stream. You need to override this method in order not to alter (process) sequence objects before output. Returns : 1 for success and 0 for error. The method stops attempting to write objects after the first error returned from the source stream. Otherwise the return value is the value returned from the source stream from writing the last object resulting from processing the last sequence object given as argument. Args : Bio::SeqI object, or an array of such objects =cut sub write_seq{ my ($self, @seqs) = @_; my $ret; foreach my $seq (@seqs) { foreach my $processed ($self->process_seq($seq)) { $ret = $self->source_stream->write_seq($seq); return unless $ret; } } return $ret; } =head2 sequence_factory Title : sequence_factory Usage : $seqio->sequence_factory($seqfactory) Function: Get the Bio::Factory::SequenceFactoryI Returns : Bio::Factory::SequenceFactoryI Args : none =cut sub sequence_factory{ my $self = shift; return $self->{'sequence_factory'} = shift if @_; return $self->{'sequence_factory'}; } =head2 object_factory Title : object_factory Usage : $obj->object_factory($newval) Function: This is an alias to sequence_factory with a more generic name. Example : Returns : a L<Bio::Factory::ObjectFactoryI> compliant object Args : on set, new value (a L<Bio::Factory::ObjectFactoryI> compliant object or undef, optional) =cut sub object_factory{ return shift->sequence_factory(@_); } =head2 close Title : close Usage : Function: Closes the stream. We override this here in order to cascade to the source stream. Example : Returns : Args : none =cut sub close{ my $self = shift; return $self->source_stream() ? $self->source_stream->close(@_) : 1; } =head1 To be overridden by a derived class =cut =head2 process_seq Title : process_seq Usage : Function: This is the method that is supposed to do the actual processing. It needs to be overridden to do what you want it to do. Generally, you do not have to override or implement any other method to derive your own sequence processor. The implementation provided here just returns the unaltered input sequence and hence is not very useful other than serving as a neutral default processor. Example : Returns : An array of zero or more Bio::PrimarySeqI (or derived interface) compliant object as the result of processing the input sequence. Args : A Bio::PrimarySeqI (or derived interface) compliant object to be processed. =cut sub process_seq{ my ($self,$seq) = @_; return ($seq); } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/EncodedSeq.pm��������������������������������������������������������������000444��000766��000024�� 52327�13155576320� 17355� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::EncodedSeq # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Aaron Mackey # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::EncodedSeq - subtype of L<Bio::LocatableSeq|Bio::LocatableSeq> to store DNA that encodes a protein =head1 SYNOPSIS $obj = Bio::Seq::EncodedSeq->new( -seq => $dna, -encoding => "CCCCCCCIIIIICCCCC", -start => 1, -strand => 1, -length => 17 ); # splice out (and possibly revcomp) the coding sequence $cds = obj->cds; # obtain the protein translation of the sequence $prot = $obj->translate; # other access/inspection routines as with Bio::LocatableSeq and # Bio::SeqI; note that coordinates are relative only to the DNA # sequence, not it's implicit encoded protein sequence. =head1 DESCRIPTION Bio::Seq::EncodedSeq is a L<Bio::LocatableSeq|Bio::LocatableSeq> object that holds a DNA sequence as well as information about the coding potential of that DNA sequence. It is meant to be useful in an alignment context, where the DNA may contain frameshifts, gaps and/or introns, or in describing the transcript of a gene. An EncodedSeq provides the ability to access the "spliced" coding sequence, meaning that all introns and gaps are removed, and any frameshifts are adjusted to provide a "clean" CDS. In order to make simultaneous use of either the DNA or the implicit encoded protein sequence coordinates, please see L<Bio::Coordinate::EncodingPair>. =head1 ENCODING We use the term "encoding" here to refer to the series of symbols that we use to identify which residues of a DNA sequence are protein-coding (i.e. part of a codon), intronic, part of a 5' or 3', frameshift "mutations", etc. From this information, a Bio::Seq::EncodedSeq is able to "figure out" its translational CDS. There are two sets of coding characters, one termed "implicit" and one termed "explicit". The "implicit" encoding is a bit simpler than the "explicit" encoding: 'C' is used for any nucleotide that's part of a codon, 'U' for any UTR, etc. The full list is shown below: Code Meaning ---- ------- C coding I intronic U untranslated G gapped (for use in alignments) F a "forward", +1 frameshift B a "backward", -1 frameshift The "explicit" encoding is just an expansion of the "implicit" encoding, to denote phase: Code Meaning ---- ------- C coding, 1st codon position D coding, 2nd codon position E coding, 3rd codon position I intronic, phase 0 (relative to intron begin) J intronic, phase 1 K intronic, phase 2 U untranslated 3'UTR V untranslated 5'UTR G gapped (for use in alignments) F a "forward", +1 frameshift B a "backward", -1 frameshift Note that the explicit coding is meant to provide easy access to position/phase specific nucleotides: $obj = Bio::Seq::EncodedSeq->new(-seq => "ACAATCAGACTACG...", -encoding => "CCCCCCIII..." ); # fetch arrays of nucleotides at each codon position: my @pos1 = $obj->dnaseq(encoding => 'C', explicit => 1); my @pos2 = $obj->dnaseq(encoding => 'D'); my @pos3 = $obj->dnaseq(encoding => 'E'); # fetch arrays of "3-1" codon dinucleotides, useful for genomic # signature analyses without compounding influences of codon bias: my @pairs = $obj->dnaseq(encoding => 'EC'); =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Aaron Mackey Email amackey@virginia.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Seq::EncodedSeq; use strict; use base qw(Bio::LocatableSeq); =head2 new Title : new Usage : $obj = Bio::Seq::EncodedSeq->new(-seq => "AGTACGTGTCATG", -encoding => "CCCCCCFCCCCCC", -id => "myseq", -start => 1, -end => 13, -strand => 1 ); Function: creates a new Bio::Seq::EncodedSeq object from a supplied DNA sequence Returns : a new Bio::Seq::EncodedSeq object Args : seq - primary nucleotide sequence used to encode the protein; note that any positions involved in a gap ('G') or backward frameshift ('B') should have one or more gap characters; if the encoding specifies G or B, but no (or not enough) gap characters exist, *they'll be added*; similarly, if there are gap characters without a corresponding G or B encoding, G's will be inserted into the encoding. This allows some flexibility in specifying your sequence and coding without having to calculate a lot of the encoding for yourself. encoding - a string of characters (see Encoding Table) describing backwards frameshifts implied by the encoding but not present in the sequence will be added (as '-'s) to the sequence. If not supplied, it will be assumed that all positions are coding (C). Encoding may include either implicit phase encoding characters (i.e. "CCC") and/or explicit encoding characters (i.e. "CDE"). Additionally, prefixed numbers may be used to denote repetition (i.e. "27C3I28C"). Alternatively, encoding may be a hashref datastructure, with encoding characters as keys and Bio::LocationI objects (or arrayrefs of Bio::LocationI objects) as values, e.g.: { C => [ Bio::Location::Simple->new(1,9), Bio::Location::Simple->new(11,13) ], F => Bio::Location::Simple->new(10,10), } # same as "CCCCCCCCCFCCC" Note that if the location ranges overlap, the behavior of the encoding will be undefined (well, it will be defined, but only according to the order in which the hash keys are read, which is basically undefined ... just don't do that). id, start, end, strand - as with Bio::LocatableSeq; note that the coordinates are relative to the encoding DNA sequence, not the implicit protein sequence. If strand is reversed, then the encoding is assumed to be relative to the reverse strand as well. =cut sub new { my ($self, @args) = @_; $self = $self->SUPER::new(@args, -alphabet => 'dna'); my ($enc) = $self->_rearrange([qw(ENCODING)], @args); # set the real encoding: if ($enc) { $self->encoding($enc); } else { $self->_recheck_encoding; } return $self; } =head2 encoding Title : encoding Usage : $obj->encoding("CCCCCC"); $obj->encoding( -encoding => { I => $location } ); $enc = $obj->encoding(-explicit => 1); $enc = $obj->encoding("CCCCCC", -explicit => 1); $enc = $obj->encoding(-location => $location, -explicit => 1, -absolute => 1 ); Function: get/set the objects encoding, either globally or by location(s). Returns : the (possibly new) encoding string. Args : encoding - see the encoding argument to the new() function. explicit - whether or not to return explicit phase information in the coding (i.e. "CCC" becomes "CDE", "III" becomes "IJK", etc); defaults to 0. location - optional; location to get/set the encoding. Defaults to the entire sequence. absolute - whether or not the locational elements (either in the encoding hashref or the location argument) are relative to the absolute start/end of the Bio::LocatableSeq, or to the internal, relative coordinate system (beginning at 1); defaults to 0 (i.e. relative) =cut sub encoding { my ($self, @args) = @_; my ($enc, $loc, $exp, $abs) = $self->_rearrange([qw(ENCODING LOCATION EXPLICIT ABSOLUTE)], @args); if (!$enc) { # do nothing; _recheck_encoding will fix for us, if necessary } elsif (ref $enc eq 'HASH') { $self->throw( -class => 'Bio::Root::NotImplemented', -text => "Hashref functionality not yet implemented;\nplease email me if you really need this."); #TODO: finish all this while (my ($char, $locs) = each %$enc) { if (ref $locs eq 'ARRAY') { } elsif (UNIVERSAL::isa($locs, "Bio::LocationI")) { } else { $self->throw("Only a scalar or a ref to a hash; not a ref to a @{{lc ref $enc}}"); } } } elsif (! ref $enc) { $enc = uc $enc; $exp = 1 if (!defined $exp && $enc =~ m/[DEJKV]/o); if ($enc =~ m/\d/o) { # numerically "enhanced" encoding my $numenc = $enc; $enc = ''; while ($numenc =~ m/\G(\d*)([CDEIJKUVGFB])/g) { my ($num, $char) = ($1, $2); $num = 1 unless $num; $enc .= $char x $num; } } if (defined $exp && $exp == 0 && $enc =~ m/([^CIUGFB])/) { $self->throw("Unrecognized character '$1' in implicit encoding"); } elsif ($enc =~ m/[^CDEIJKUVGFB]/) { $self->throw("Unrecognized character '$1' in explicit encoding"); } if ($loc) { # a global location, over which to apply the specified encoding. # balk if too many non-gap characters present in encoding: my ($ct) = $enc =~ tr/GB/GB/; $ct = length($enc) - $ct; $self->throw("Location length doesn't match number of coding chars in encoding!") if ($loc->location_type eq 'EXACT' && $loc->length != $ct); my $start = $loc->start; my $end = $loc->end; # strip any encoding that hangs off the ends of the sequence: if ($start < $self->start) { my $diff = $self->start - $start; $start = $self->start; $enc = substr($enc, $diff); } if ($end > $self->end) { my $diff = $end - $self->end; $end = $self->end; $enc = substr($enc, -$diff); } my $currenc = $self->{_encoding}; my $currseq = $self->seq; my ($spanstart, $spanend) = ($self->column_from_residue_number($start), $self->column_from_residue_number($end) ); if ($currseq) { # strip any gaps in sequence spanned by this location: ($spanstart, $spanend) = ($spanend, $spanstart) if $self->strand < 0; my ($before, $in, $after) = $currseq =~ m/(.{@{[ $spanstart - ($loc->location_type eq 'IN-BETWEEN' ? 0 : 1) ]}}) (.{@{[ $spanend - $spanstart + ($loc->location_type eq 'IN-BETWEEN' ? -1 : 1) ]}}) (.*) /x; $in ||= ''; $in =~ s/[\.\-]+//g; $currseq = ($before||'') . $in. ($after||''); # change seq without changing the alphabet $self->seq($currseq,$self->alphabet()); } $currenc = reverse $currenc if $self->strand < 0; substr($currenc, $spanstart, $spanend - $spanstart + ($loc->location_type eq 'IN-BETWEEN' ? -1 : 1), $self->strand >= 0 ? $enc : reverse $enc); $currenc = reverse $currenc if $self->strand < 0; $self->{_encoding} = $currenc; $self->_recheck_encoding; $currenc = $self->{_encoding}; $currenc = reverse $currenc if $self->strand < 0; $enc = substr($currenc, $spanstart, length $enc); $enc = reverse $enc if $self->strand < 0; return $exp ? $enc: $self->_convert2implicit($enc); } else { # presume a global redefinition; strip any current gap # characters in the sequence so they don't corrupt the # encoding my $dna = $self->seq; $dna =~ s/[\.\-]//g; $self->seq($dna, 'dna'); $self->{_encoding} = $enc; } } else { $self->throw("Only a scalar or a ref to a hash; not a ref to a @{{lc ref $enc}}"); } $self->_recheck_encoding(); return $exp ? $self->{_encoding} : $self->_convert2implicit($self->{_encoding}); } sub _convert2implicit { my ($self, $enc) = @_; $enc =~ s/[DE]/C/g; $enc =~ s/[JK]/I/g; $enc =~ s/V/U/g; return $enc; } sub _recheck_encoding { my $self = shift; my @enc = split //, ($self->{_encoding} || ''); my @nt = split(//, $self->SUPER::seq); @nt = reverse @nt if $self->strand && $self->strand < 0; # make sure an encoding exists! @enc = ('C') x scalar grep { !/[\.\-]/o } @nt unless @enc; # check for gaps to be truly present in the sequence # and vice versa my $i; for ($i = 0 ; $i < @nt && $i < @enc ; $i++) { if ($nt[$i] =~ /[\.\-]/o && $enc[$i] !~ m/[GB]/o) { splice(@enc, $i, 0, 'G'); } elsif ($nt[$i] !~ /[\.\-]/o && $enc[$i] =~ m/[GB]/o) { splice(@nt, $i, 0, '-'); } } if ($i < @enc) { # extra encoding; presumably all gaps? for ( ; $i < @enc ; $i++) { if ($enc[$i] =~ m/[GB]/o) { push @nt, '-'; } else { $self->throw("Extraneous encoding info: " . join('', @enc[$i..$#enc])); } } } elsif ($i < @nt) { for ( ; $i < @nt ; $i++) { if ($nt[$i] =~ m/[\.\-]/o) { push @enc, 'G'; } else { push @enc, 'C'; } } } my @cde_array = qw(C D E); my @ijk_array = qw(I J K); # convert any leftover implicit coding into explicit coding my ($Cct, $Ict, $Uct, $Vct, $Vwarned) = (0, 0, 0, 0); for ($i = 0 ; $i < @enc ; $i++) { if ($enc[$i] =~ m/[CDE]/o) { my $temp_index = $Cct %3; $enc[$i] = $cde_array[$temp_index]; $Cct++; $Ict = 0; $Uct = 1; $self->warn("3' untranslated encoding (V) seen prior to other coding symbols") if ($Vct && !$Vwarned++); } elsif ($enc[$i] =~ m/[IJK]/o) { $enc[$i] = $ijk_array[$Ict % 3]; $Ict++; $Uct = 1; $self->warn("3' untranslated encoding (V) seen before other coding symbols") if ($Vct && !$Vwarned++); } elsif ($enc[$i] =~ m/[UV]/o) { if ($Uct == 1) { $enc[$i] = 'V'; $Vct = 1; } } elsif ($enc[$i] eq 'B') { $Cct++; $Ict++ } elsif ($enc[$i] eq 'G') { # gap; leave alone } } @nt = reverse @nt if $self->strand && $self->strand < 0; $self->seq(join('', @nt), 'dna'); $self->{_encoding} = join '', @enc; } =head2 cds Title : cds Usage : $cds = $obj->cds(-nogaps => 1); Function: obtain the "spliced" DNA sequence, by removing any nucleotides that participate in an UTR, forward frameshift or intron, and replacing any unknown nucleotide implied by a backward frameshift or gap with N's. Returns : a Bio::Seq::EncodedSeq object, with an encoding consisting only of "CCCC..". Args : nogaps - strip any gap characters (resulting from 'G' or 'B' encodings), rather than replacing them with N's. =cut sub cds { my ($self, @args) = @_; my ($nogaps, $loc) = $self->_rearrange([qw(NOGAPS LOCATION)], @args); $nogaps = 0 unless defined $nogaps; my @nt = split //, $self->strand < 0 ? $self->revcom->seq : $self->seq; my @enc = split //, $self->_convert2implicit($self->{_encoding}); my ($start, $end) = (0, scalar @nt); if ($loc) { $start = $loc->start; $start++ if $loc->location_type eq 'IN-BETWEEN'; $start = $self->column_from_residue_number($start); $start--; $end = $loc->end; $end = $self->column_from_residue_number($end); ($start, $end) = ($end, $start) if $self->strand < 0; $start--; } for (my $i = $start ; $i < $end ; $i++) { if ($enc[$i] eq 'I' || $enc[$i] eq 'U' || $enc[$i] eq 'F') { # remove introns, untranslated and forward frameshift nucleotides $nt[$i] = undef; } elsif ($enc[$i] eq 'G' || $enc[$i] eq 'B') { # replace gaps and backward frameshifts with N's, unless asked not to. $nt[$i] = $nogaps ? undef : 'N'; } } return ($self->can_call_new ? ref($self) : __PACKAGE__)->new( -seq => join('', grep { defined } @nt[$start..--$end]), -start => $self->start, -end => $self->end, -strand => 1, -alphabet => 'dna' ); } =head2 translate Title : translate Usage : $prot = $obj->translate(@args); Function: obtain the protein sequence encoded by the underlying DNA sequence; same as $obj->cds()->translate(@args). Returns : a Bio::PrimarySeq object. Args : same as the translate() function of Bio::PrimarySeqI =cut sub translate { shift->cds(-nogaps => 1, @_)->SUPER::translate(@_) }; =head2 protseq Title : seq Usage : $protseq = $obj->protseq(); Function: obtain the raw protein sequence encoded by the underlying DNA sequence; This is the same as calling $obj->translate()->seq(); Returns : a string of single-letter amino acid codes Args : same as the seq() function of Bio::PrimarySeq; note that this function may not be used to set the protein sequence; see the dnaseq() function for that. =cut sub protseq { shift->cds(-nogaps => 1, @_)->SUPER::translate(@_)->seq }; =head2 dnaseq Title : dnaseq Usage : $dnaseq = $obj->dnaseq(); $obj->dnaseq("ACGTGTCGT", "CCCCCCCCC"); $obj->dnaseq(-seq => "ATG", -encoding => "CCC", -location => $loc ); @introns = $obj->$dnaseq(-encoding => 'I') Function: get/set the underlying DNA sequence; will overwrite any current DNA and/or encoding information present. Returns : a string of single-letter nucleotide codes, including any gaps implied by the encoding. Args : seq - the DNA sequence to be used as a replacement encoding - the encoding of the DNA sequence (see the new() constructor); defaults to all 'C' if setting a new DNA sequence. If no new DNA sequence is being provided, then the encoding is used as a "filter" for which to return fragments of non-overlapping DNA that match the encoding. location - optional, the location of the DNA sequence to get/set; defaults to the entire sequence. =cut sub dnaseq { my ($self, @args) = @_; my ($seq, $enc, $loc) = $self->_rearrange([qw(DNASEQ ENCODING LOCATION)], @args); return $self; } # need to overload this so that we truncate both the seq and the encoding! sub trunc { my ($self, $start, $end) = @_; my $new = $self->SUPER::trunc($start, $end); $start--; my $enc = $self->{_encoding}; $enc = reverse $enc if $self->strand < 0; $enc = substr($enc, $start, $end - $start); $enc = reverse $enc if $self->strand < 0; $new->encoding($enc); return $new; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/LargeLocatableSeq.pm�������������������������������������������������������000444��000766��000024�� 20326�13155576320� 20647� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Seq::LargeLocatableSeq # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Albert Vilella # # based on the Bio::LargePrimarySeq module # by Ewan Birney <birney@sanger.ac.uk> # # and the Bio::LocatableSeq module # by Ewan Birney <birney@sanger.ac.uk> # # Copyright Albert Vilella # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::LargeLocatableSeq - LocatableSeq object that stores sequence as files in the tempdir =head1 SYNOPSIS # normal primary seq usage use Bio::Seq::LargeLocatableSeq; my $seq = Bio::Seq::LargeLocatableSeq->new(-seq => "CAGT-GGT", -id => "seq1", -start => 1, -end => 7); =head1 DESCRIPTION Bio::Seq::LargeLocatableSeq - object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. This object, unlike Bio::LocatableSeq, stores a sequence as a series of files in a temporary directory. The aim is to allow someone the ability to store very large sequences (eg, E<gt> 100MBases) in a file system without running out of memory (eg, on a 64 MB real memory machine!). Of course, to actually make use of this functionality, the programs which use this object B<must> not call $primary_seq-E<gt>seq otherwise the entire sequence will come out into memory and probably crash your machine. However, calls like $primary_seq-E<gt>subseq(10,100) will cause only 90 characters to be brought into real memory. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Albert Vilella Email avilella-AT-gmail-DOT-com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::LargeLocatableSeq; use vars qw($AUTOLOAD); use strict; use base qw(Bio::Seq::LargePrimarySeq Bio::LocatableSeq Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Seq::LargeLocatableSeq->new(); Function: Builds a new Bio::Seq::LargeLocatableSeq object Returns : an instance of Bio::Seq::LargeLocatableSeq Args : =cut sub new { my ($class, %params) = @_; # don't let PrimarySeq set seq until we have # opened filehandle my $seq = $params{'-seq'} || $params{'-SEQ'}; if($seq ) { delete $params{'-seq'}; delete $params{'-SEQ'}; } my $self = $class->SUPER::new(%params); my $mapping = exists $params{'-mapping'} ? $params{'-mapping'} : [1,1]; $self->mapping($mapping); $self->_initialize_io(%params); my $tempdir = $self->tempdir( CLEANUP => 1); my ($tfh,$file) = $self->tempfile( DIR => $tempdir ); $tfh && $self->_fh($tfh); $file && $self->_filename($file); $self->length(0); $seq && $self->seq($seq); return $self; } =head2 length Title : length Usage : Function: Example : Returns : Args : =cut sub length { my ($obj,$value) = @_; if( defined $value) { $obj->{'length'} = $value; } return (defined $obj->{'length'}) ? $obj->{'length'} : 0; } =head2 seq Title : seq Usage : Function: Example : Returns : Args : =cut sub seq { my ($self, $data) = @_; if( defined $data ) { if( $self->length() == 0) { $self->add_sequence_as_string($data); } else { $self->warn("Trying to reset the seq string, cannot do this with a LargeLocatableSeq - must allocate a new object"); } } return $self->subseq(1,$self->length); } =head2 subseq Title : subseq Usage : Function: Example : Returns : Args : =cut sub subseq{ my ($self,$start,$end) = @_; my $string; my $fh = $self->_fh(); if( ref($start) && $start->isa('Bio::LocationI') ) { my $loc = $start; if( $loc->length == 0 ) { $self->warn("Expect location lengths to be > 0"); return ''; } elsif( $loc->end < $loc->start ) { # what about circular seqs $self->warn("Expect location start to come before location end"); } my $seq = ''; if( $loc->isa('Bio::Location::SplitLocationI') ) { foreach my $subloc ( $loc->sub_Location ) { if(! seek($fh,$subloc->start() - 1,0)) { $self->throw("Unable to seek on file $start:$end $!"); } my $ret = read($fh, $string, $subloc->length()); if( !defined $ret ) { $self->throw("Unable to read $start:$end $!"); } if( $subloc->strand < 0 ) { # $string = Bio::PrimarySeq->new(-seq => $string)->revcom()->seq(); $string = Bio::Seq::LargePrimarySeq->new(-seq => $string)->revcom()->seq(); } $seq .= $string; } } else { if(! seek($fh,$loc->start()-1,0)) { $self->throw("Unable to seek on file ".$loc->start.":". $loc->end ." $!"); } my $ret = read($fh, $string, $loc->length()); if( !defined $ret ) { $self->throw("Unable to read ".$loc->start.":". $loc->end ." $!"); } $seq = $string; } if( defined $loc->strand && $loc->strand < 0 ) { # $seq = Bio::PrimarySeq->new(-seq => $string)->revcom()->seq(); $seq = Bio::Seq::LargePrimarySeq->new(-seq => $seq)->revcom()->seq(); } return $seq; } if( $start <= 0 || $end > $self->length ) { $self->throw("Attempting to get a subseq out of range $start:$end vs ". $self->length); } if( $end < $start ) { $self->throw("Attempting to subseq with end ($end) less than start ($start). To revcom use the revcom function with trunc"); } if(! seek($fh,$start-1,0)) { $self->throw("Unable to seek on file $start:$end $!"); } my $ret = read($fh, $string, $end-$start+1); if( !defined $ret ) { $self->throw("Unable to read $start:$end $!"); } return $string; } =head2 add_sequence_as_string Title : add_sequence_as_string Usage : $seq->add_sequence_as_string("CATGAT"); Function: Appends additional residues to an existing LargeLocatableSeq object. This allows one to build up a large sequence without storing entire object in memory. Returns : Current length of sequence Args : string to append =cut sub add_sequence_as_string{ my ($self,$str) = @_; my $len = $self->length + CORE::length($str); my $fh = $self->_fh(); if(! seek($fh,0,2)) { $self->throw("Unable to seek end of file: $!"); } $self->_print($str); $self->length($len); } =head2 _filename Title : _filename Usage : $obj->_filename($newval) Function: Example : Returns : value of _filename Args : newvalue (optional) =cut sub _filename{ my ($obj,$value) = @_; if( defined $value) { $obj->{'_filename'} = $value; } return $obj->{'_filename'}; } =head2 alphabet Title : alphabet Usage : $obj->alphabet($newval) Function: Example : Returns : value of alphabet Args : newvalue (optional) =cut sub alphabet{ my ($self,$value) = @_; if( defined $value) { $self->SUPER::alphabet($value); } return $self->SUPER::alphabet() || 'dna'; } sub DESTROY { my $self = shift; my $fh = $self->_fh(); close($fh) if( defined $fh ); # this should be handled by Tempfile removal, but we'll unlink anyways. unlink $self->_filename() if defined $self->_filename() && -e $self->_filename; $self->SUPER::DESTROY(); } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/LargePrimarySeq.pm���������������������������������������������������������000444��000766��000024�� 17170�13155576320� 20407� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::LargePrimarySeq # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # # updated to utilize File::Temp - jason 2000-12-12 # POD documentation - main docs before the code =head1 NAME Bio::Seq::LargePrimarySeq - PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root =head1 SYNOPSIS # normal primary seq usage =head1 DESCRIPTION This object stores a sequence as a series of files in a temporary directory. The aim is to allow someone the ability to store very large sequences (eg, E<gt> 100MBases) in a file system without running out of memory (eg, on a 64 MB real memory machine!). Of course, to actually make use of this functionality, the programs which use this object B<must> not call $primary_seq-E<gt>seq otherwise the entire sequence will come out into memory and probably paste your machine. However, calls $primary_seq-E<gt>subseq(10,100) will cause only 90 characters to be brought into real memory. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney, Jason Stajich Email birney@ebi.ac.uk Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::LargePrimarySeq; use vars qw($AUTOLOAD); use strict; use base qw(Bio::PrimarySeq Bio::Root::IO Bio::Seq::LargeSeqI); sub new { my ($class, %params) = @_; # don't let PrimarySeq set seq until we have # opened filehandle my $seq = $params{'-seq'} || $params{'-SEQ'}; if($seq ) { delete $params{'-seq'}; delete $params{'-SEQ'}; } my $self = $class->SUPER::new(%params); $self->_initialize_io(%params); my $tempdir = $self->tempdir( CLEANUP => 1); my ($tfh,$file) = $self->tempfile( DIR => $tempdir ); $self->{tempdir} = $tempdir; $tfh && $self->_fh($tfh); $file && $self->_filename($file); $self->length(0); $seq && $self->seq($seq); return $self; } =head2 length Title : length Usage : Function: Example : Returns : Args : =cut sub length { my ($obj,$value) = @_; if( defined $value) { $obj->{'length'} = $value; } return (defined $obj->{'length'}) ? $obj->{'length'} : 0; } =head2 seq Title : seq Usage : Function: Example : Returns : Args : =cut sub seq { my ($self, $data) = @_; if( defined $data ) { if( $self->length() == 0) { $self->add_sequence_as_string($data); } else { $self->warn("Trying to reset the seq string, cannot do this with a LargePrimarySeq - must allocate a new object"); } } return $self->subseq(1,$self->length); } =head2 subseq Title : subseq Usage : Function: Example : Returns : Args : =cut sub subseq{ my ($self,$start,$end) = @_; my $string; my $fh = $self->_fh(); if( ref($start) && $start->isa('Bio::LocationI') ) { my $loc = $start; if( $loc->length == 0 ) { $self->warn("Expect location lengths to be > 0"); return ''; } elsif( $loc->end < $loc->start ) { # what about circular seqs $self->warn("Expect location start to come before location end"); } my $seq = ''; if( $loc->isa('Bio::Location::SplitLocationI') ) { foreach my $subloc ( $loc->sub_Location ) { if(! seek($fh,$subloc->start() - 1,0)) { $self->throw("Unable to seek on file $start:$end $!"); } my $ret = read($fh, $string, $subloc->length()); if( !defined $ret ) { $self->throw("Unable to read $start:$end $!"); } if( $subloc->strand < 0 ) { $string = Bio::PrimarySeq->new(-seq => $string)->revcom()->seq(); } $seq .= $string; } } else { if(! seek($fh,$loc->start()-1,0)) { $self->throw("Unable to seek on file ".$loc->start.":". $loc->end ." $!"); } my $ret = read($fh, $string, $loc->length()); if( !defined $ret ) { $self->throw("Unable to read ".$loc->start.":". $loc->end ." $!"); } $seq = $string; } if( defined $loc->strand && $loc->strand < 0 ) { $seq = Bio::PrimarySeq->new(-seq => $seq)->revcom()->seq(); } return $seq; } if( $start <= 0 || $end > $self->length ) { $self->throw("Attempting to get a subseq out of range $start:$end vs ". $self->length); } if( $end < $start ) { $self->throw("Attempting to subseq with end ($end) less than start ($start). To revcom use the revcom function with trunc"); } if(! seek($fh,$start-1,0)) { $self->throw("Unable to seek on file $start:$end $!"); } my $ret = read($fh, $string, $end-$start+1); if( !defined $ret ) { $self->throw("Unable to read $start:$end $!"); } return $string; } =head2 add_sequence_as_string Title : add_sequence_as_string Usage : $seq->add_sequence_as_string("CATGAT"); Function: Appends additional residues to an existing LargePrimarySeq object. This allows one to build up a large sequence without storing entire object in memory. Returns : Current length of sequence Args : string to append =cut sub add_sequence_as_string{ my ($self,$str) = @_; my $len = $self->length + CORE::length($str); my $fh = $self->_fh(); if(! seek($fh,0,2)) { $self->throw("Unable to seek end of file: $!"); } $self->_print($str); $self->length($len); } =head2 _filename Title : _filename Usage : $obj->_filename($newval) Function: Example : Returns : value of _filename Args : newvalue (optional) =cut sub _filename{ my ($obj,$value) = @_; if( defined $value) { $obj->{'_filename'} = $value; } return $obj->{'_filename'}; } =head2 alphabet Title : alphabet Usage : $obj->alphabet($newval) Function: Example : Returns : value of alphabet Args : newvalue (optional) =cut sub alphabet{ my ($self,$value) = @_; if( defined $value) { $self->SUPER::alphabet($value); } return $self->SUPER::alphabet() || 'dna'; } sub DESTROY { my $self = shift; my $fh = $self->_fh(); close($fh) if( defined $fh ); # this should be handled by Tempfile removal, but we'll unlink anyways. unlink $self->_filename() if defined $self->_filename() && -e $self->_filename; # remove tempdirs as well rmdir $self->{tempdir} if defined $self->{tempdir} && -e $self->{tempdir}; $self->SUPER::DESTROY(); } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/LargeSeq.pm����������������������������������������������������������������000444��000766��000024�� 7225�13155576320� 17023� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::LargeSeq # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney, Jason Stajich # # Copyright Ewan Birney, Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp =head1 SYNOPSIS # normal primary seq usage =head1 DESCRIPTION This object stores a sequence as a series of files in a temporary directory. The aim is to allow someone the ability to store very large sequences (eg, E<gt> 100MBases) in a file system without running out of memory (eg, on a 64 MB real memory machine!). Of course, to actually make use of this functionality, the programs which use this object B<must> not call $primary_seq-E<gt>seq otherwise the entire sequence will come out into memory and probably paste your machine. However, calls $primary_seq-E<gt>subseq(10,100) will cause only 90 characters to be brought into real memory. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::LargeSeq; use vars qw($AUTOLOAD); use strict; # Object preamble use Bio::Seq::LargePrimarySeq; use base qw(Bio::Seq Bio::Seq::LargeSeqI); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($pseq) = $self->_rearrange([qw(PRIMARYSEQ)], @args); if( ! defined $pseq ) { $pseq = Bio::Seq::LargePrimarySeq->new(@args); } $self->primary_seq($pseq); return $self; } =head2 trunc Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence, Example : Returns : a fresh Bio::SeqI object Args : =cut sub trunc { my ($self, $s, $e) = @_; return new Bio::Seq::LargeSeq ('-display_id' => $self->display_id, '-accession_number' => $self->accession_number, '-desc' => $self->desc, '-alphabet' => $self->alphabet, -primaryseq => $self->primary_seq->trunc($s,$e)); } =head2 Bio::Seq::LargePrimarySeq methods =cut =head2 add_sequence_as_string Title : add_sequence_as_string Usage : $seq->add_sequence_as_string("CATGAT"); Function: Appends additional residues to an existing LargePrimarySeq object. This allows one to build up a large sequence without storing entire object in memory. Returns : Current length of sequence Args : string to append =cut sub add_sequence_as_string { my ($self,$str) = @_; return $self->primary_seq->add_sequence_as_string($str); } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/LargeSeqI.pm���������������������������������������������������������������000444��000766��000024�� 5457�13155576320� 17141� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::LargeSeqI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Albert Vilella # # Copyright Albert Vilella # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::LargeSeqI - Interface class for sequences that cache their residues in a temporary file =head1 SYNOPSIS # =head1 DESCRIPTION The interface class defines a group of sequence classes that do not keep their sequence information in memory but store it in a file. This makes it possible to work with very large files even with limited RAM. The most important consequence of file caching for sequences is that you do not want to inspect the sequence unless absolutely necessary. These sequences typically override the length() method not to check the sequence. The seq() method is not resetable, if you want to add to the end of the sequence you have to use add_sequence_as_string(), for any other sequence changes you'll have to create a new object. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Albert Vilella Email avilella-AT-gmail-DOT-com =head1 CONTRIBUTORS Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::LargeSeqI; use strict; use base qw(Bio::Root::RootI); =head2 add_sequence_as_string Title : add_sequence_as_string Usage : $seq->add_sequence_as_string("CATGAT"); Function: Appends additional residues to an existing object. This allows one to build up a large sequence without storing entire object in memory. Returns : Current length of sequence Args : string to append =cut sub add_sequence_as_string { my ($self) = @_; $self->throw_not_implemented(); } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/Meta.pm��������������������������������������������������������������������000444��000766��000024�� 46752�13155576320� 16236� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::Meta # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::Meta - Generic superclass for sequence objects with residue-based meta information =head1 SYNOPSIS use Bio::LocatableSeq; use Bio::Seq::Meta; use Bio::Tools::OddCodes; use Bio::SeqIO; my $seq = Bio::Seq::Meta->new(-id=>'test', -seq=>'ACTGCTAGCT', -start=>2434, -end=>2443, -strand=>1, -verbose=>1, # to see warnings ); # the existing sequence object can be a Bio::PrimarySeq, too # to test this is a meta seq object $seq->isa("Bio::Seq::Meta") || $seq->throw("$seq is not a Bio::Seq::Meta"); $seq->meta('1234567890'); $seq = Bio::Seq::Meta->new(-id=>'test', -seq=>'HACILMIFGT', -start=>2434, -end=>2443, -strand=>1, -meta=>'1234567890', -verbose=>1, # to see warnings ); # accessors $string = $seq->meta_text(); $substring = $seq->submeta_text(2,5); $unique_key = $seq->accession_number(); # storing output from Bio::Tools::OddCodes as meta data my $protcodes = Bio::Tools::OddCodes->new(-seq => $seq); my @codes = qw(structural chemical functional charge hydrophobic); map { $seq->named_meta($_, ${$protcodes->$_($seq) } )} @codes; my $out = Bio::SeqIO->new(-format=>'metafasta'); $out->write_seq($seq); =head1 DESCRIPTION This class implements generic methods for sequences with residue-based meta information. Meta sequences with meta data are Bio::LocatableSeq objects with additional methods to store that meta information. See L<Bio::LocatableSeq> and L<Bio::Seq::MetaI>. The meta information in this class is always one character per residue long and blank values are space characters (ASCII 32). After the latest rewrite, the meta information no longer covers all the residues automatically. Methods to check the length of meta information (L<meta_length>)and to see if the ends are flushed to the sequence have been added (L<is_flush>). To force the old functionality, set L<force_flush> to true. It is assumed that meta data values do not depend on the nucleotide sequence strand value. Application specific implementations should inherit from this class to override and add to these methods. L<Bio::Seq::Meta::Array> allows for more complex meta values (scalars or objects) to be used. =head2 Method naming Character based meta data is read and set by method meta() and its variants. These are the suffixes and prefixes used in the variants: [named_] [sub] meta [_text] =over 3 =item _text Suffix B<_text> guaranties that output is a string. Note that it does not limit the input. In this implementation, the output is always text, so these methods are redundant. =item sub Prefix B<sub>, like in subseq(), means that the method applies to sub region of the sequence range and takes start and end as arguments. Unlike subseq(), these methods are able to set values. If the range is not defined, it defaults to the complete sequence. =item named Prefix B<named_> in method names allows the used to attach multiple meta strings to one sequence by explicitly naming them. The name is always the first argument to the method. The "unnamed" methods use the class wide default name for the meta data and are thus special cases "named" methods. Note that internally names are keys in a hash and any misspelling of a name will silently store the data under a wrong name. The used names (keys) can be retrieved using method meta_names(). See L<meta_names>. =back =head1 NOTE This Bio::Seq::MetaI implementation inherits from Bio::LocatableSeq, which itself inherits from Bio::PrimarySeq. It is not a Bio::SeqI, so bless-ing objects of this class into a Bio::SeqI or vice versa and will not work as expected (see bug 2262). This may be addressed in a future refactor of Bio::LocatableSeq. =head1 SEE ALSO L<Bio::LocatableSeq>, L<Bio::Seq::MetaI>, L<Bio::Seq::Meta::Array> =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email heikki-at-bioperl-dot-org =head1 CONTRIBUTORS Chad Matsalla, bioinformatics@dieselwurks.com Aaron Mackey, amackey@virginia.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::Meta; use vars qw($DEFAULT_NAME $GAP $META_GAP); use strict; #use overload '""' => \&to_string; use base qw(Bio::LocatableSeq Bio::Seq::MetaI); BEGIN { $DEFAULT_NAME = 'DEFAULT'; $GAP = '-'; $META_GAP = ' '; } =head2 new Title : new Usage : $metaseq = Bio::Seq::Meta->new ( -meta => 'aaaaaaaabbbbbbbb', -seq => 'TKLMILVSHIVILSRM' -id => 'human_id', -accession_number => 'S000012', ); Function: Constructor for Bio::Seq::Meta class, meta data being in a string. Note that you can provide an empty quality string. Returns : a new Bio::Seq::Meta object =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my($meta, $forceflush, $nm) = $self->_rearrange([qw(META FORCE_FLUSH NAMED_META)], @args); #$self->{'_meta'} = {}; $self->{'_meta'}->{$DEFAULT_NAME} = ""; $meta && $self->meta($meta); if ($nm && ref($nm) eq 'HASH') { while (my ($name, $meta) = each %$nm) { $self->named_meta($name, $meta); } } $forceflush && $self->force_flush($forceflush); return $self; } =head2 meta Title : meta Usage : $meta_values = $obj->meta($values_string); Function: Get and set method for the meta data starting from residue position one. Since it is dependent on the length of the sequence, it needs to be manipulated after the sequence. The length of the returned value always matches the length of the sequence, if force_flush() is set. See L<force_flush>. Returns : meta data in a string Args : new value, string, optional =cut sub meta { shift->named_meta($DEFAULT_NAME, shift); } =head2 meta_text Title : meta_text Usage : $meta_values = $obj->meta_text($values_arrayref); Function: Variant of meta() guarantied to return a textual representation of meta data. For details, see L<meta>. Returns : a string Args : new value, optional =cut sub meta_text { shift->meta(shift); } =head2 named_meta Title : named_meta() Usage : $meta_values = $obj->named_meta($name, $values_arrayref); Function: A more general version of meta(). Each meta data set needs to be named. See also L<meta_names>. Returns : a string Args : scalar, name of the meta data set new value, optional =cut sub named_meta { my ($self, $name, $value) = @_; $name ||= $DEFAULT_NAME; if( defined $value) { $self->throw("I need a scalar value, not [". ref($value). "]") if ref($value); # test for length my $diff = $self->length - CORE::length($value); if ($diff > 0) { $value .= (" " x $diff); } $self->{'_meta'}->{$name} = $value; #$self->_test_gap_positions($name) if $self->verbose > 0; } return " " x $self->length if $self->force_flush && not defined $self->{'_meta'}->{$name}; $self->_do_flush if $self->force_flush; return $self->{'_meta'}->{$name}; } =head2 _test_gap_positions Title : _test_gap_positions Usage : $meta_values = $obj->_test_gap_positions($name); Function: Internal test for correct position of gap characters. Gap being only '-' this time. This method is called from named_meta() when setting meta data but only if verbose is positive as this can be an expensive process on very long sequences. Set verbose(1) to see warnings when gaps do not align in sequence and meta data and turn them into errors by setting verbose(2). Returns : true on success, prints warnings Args : none =cut sub _test_gap_positions { my $self = shift; my $name = shift; my $success = 1; $self->seq || return $success; my $len = CORE::length($self->seq); for (my $i=0; $i < $len; $i++) { my $s = substr $self->{seq}, $i, 1; my $m = substr $self->{_meta}->{$name}, $i, 1; $self->warn("Gap mismatch [$m/$s] in column [". ($i+1). "] of [$name] meta data in seq [". $self->id. "]") and $success = 0 if ($s eq $META_GAP) && $s ne $m; } return $success; } =head2 named_meta_text Title : named_meta_text() Usage : $meta_values = $obj->named_meta_text($name, $values_arrayref); Function: Variant of named_meta() guarantied to return a textual representation of the named meta data. For details, see L<meta>. Returns : a string Args : scalar, name of the meta data set new value, optional =cut sub named_meta_text { shift->named_meta(@_); } =head2 submeta Title : submeta Usage : $subset_of_meta_values = $obj->submeta(10, 20, $value_string); $subset_of_meta_values = $obj->submeta(10, undef, $value_string); Function: Get and set method for meta data for subsequences. Numbering starts from 1 and the number is inclusive, ie 1-2 are the first two residue of the sequence. Start cannot be larger than end but can be equal. If the second argument is missing the returned values should extend to the end of the sequence. The return value may be a string or an array reference, depending on the implementation. If in doubt, use submeta_text() which is a variant guarantied to return a string. See L<submeta_text>. Returns : A reference to an array or a string Args : integer, start position integer, end position, optional when a third argument present new value, optional =cut sub submeta { shift->named_submeta($DEFAULT_NAME, @_); } =head2 submeta_text Title : submeta_text Usage : $meta_values = $obj->submeta_text(20, $value_string); Function: Variant of submeta() guarantied to return a textual representation of meta data. For details, see L<meta>. Returns : a string Args : new value, optional =cut sub submeta_text { shift->submeta(@_); } =head2 named_submeta Title : named_submeta Usage : $subset_of_meta_values = $obj->named_submeta($name, 10, 20, $value_string); $subset_of_meta_values = $obj->named_submeta($name, 10); Function: Variant of submeta() guarantied to return a textual representation of meta data. For details, see L<meta>. Returns : A reference to an array or a string Args : scalar, name of the meta data set integer, start position integer, end position, optional when a third argument present new value, optional =cut sub named_submeta { my ($self, $name, $start, $end, $value) = @_; $name ||= $DEFAULT_NAME; $start ||=1; $start =~ /^[+]?\d+$/ and $start > 0 or $self->throw("Need at least a positive integer start value"); if ($value) { $end ||= $start+length($value)-1; $self->warn("You are setting meta values beyond the length of the sequence\n". "[$start > ". length($self->seq)."] in sequence ". $self->id) if $start > length $self->seq; # pad meta data if needed $self->{_meta}->{$name} = () unless defined $self->{_meta}->{$name}; if (length($self->{_meta}->{$name}) < $start) { $self->{'_meta'}->{$name} .= " " x ( $start - length($self->{'_meta'}->{$name}) -1); } my $tail = ''; $tail = substr ($self->{_meta}->{$name}, $start-1+length($value)) if length($self->{_meta}->{$name}) >= $start-1+length($value); substr ($self->{_meta}->{$name}, --$start) = $value; $self->{_meta}->{$name} .= $tail; return substr ($self->{_meta}->{$name}, $start, $end - $start + 1); } else { $end or $end = length $self->seq; # pad meta data if needed if (length($self->{_meta}->{$name}) < $end) { $self->{'_meta'}->{$name} .= " " x ( $start - length($self->{'_meta'}->{$name})); } return substr ($self->{_meta}->{$name}, $start-1, $end - $start + 1) } } =head2 named_submeta_text Title : named_submeta_text Usage : $meta_values = $obj->named_submeta_text($name, 20, $value_string); Function: Variant of submeta() guarantied to return a textual representation of meta data. For details, see L<meta>. Returns : a string Args : scalar, name of the meta data Args : integer, start position, optional integer, end position, optional new value, optional =cut sub named_submeta_text { shift->named_submeta(@_); } =head2 meta_names Title : meta_names Usage : @meta_names = $obj->meta_names() Function: Retrieves an array of meta data set names. The default (unnamed) set name is guarantied to be the first name. Returns : an array of names Args : none =cut sub meta_names { my ($self) = @_; my @r; foreach ( sort keys %{$self->{'_meta'}} ) { push (@r, $_) unless $_ eq $DEFAULT_NAME; } unshift @r, $DEFAULT_NAME if $self->{'_meta'}->{$DEFAULT_NAME}; return @r; } =head2 meta_length Title : meta_length() Usage : $meeta_len = $obj->meta_length(); Function: return the number of elements in the meta set Returns : integer Args : - =cut sub meta_length { my ($self) = @_; return $self->named_meta_length($DEFAULT_NAME); } =head2 named_meta_length Title : named_meta_length() Usage : $meta_len = $obj->named_meta_length($name); Function: return the number of elements in the named meta set Returns : integer Args : - =cut sub named_meta_length { my ($self, $name) = @_; $name ||= $DEFAULT_NAME; return length ($self->{'_meta'}->{$name}); } =head2 force_flush Title : force_flush() Usage : $force_flush = $obj->force_flush(1); Function: Automatically pad with empty values or truncate meta values to sequence length. Not done by default. Returns : boolean 1 or 0 Args : optional boolean value Note that if you turn this forced padding off, the previously padded values are not changed. =cut sub force_flush { my ($self, $value) = @_; if (defined $value) { if ($value) { $self->{force_flush} = 1; $self->_do_flush; } else { $self->{force_flush} = 0; } } return $self->{force_flush}; } =head2 _do_flush Title : _do_flush Usage : Function: internal method to do the force that meta values are same length as the sequence . Called from L<force_flush> Returns : Args : =cut sub _do_flush { my ($self) = @_; foreach my $name ( ('DEFAULT', $self->meta_names) ) { # elongnation if ($self->length > $self->named_meta_length($name)) { $self->{'_meta'}->{$name} .= $META_GAP x ($self->length - $self->named_meta_length($name)) ; } # truncation elsif ( $self->length < $self->named_meta_length($name) ) { $self->{_meta}->{$name} = substr($self->{_meta}->{$name}, 0, $self->length-1); } } } =head2 is_flush Title : is_flush Usage : $is_flush = $obj->is_flush() or $is_flush = $obj->is_flush($my_meta_name) Function: Boolean to tell if all meta values are in flush with the sequence length. Returns true if force_flush() is set Set verbosity to a positive value to see failed meta sets Returns : boolean 1 or 0 Args : optional name of the meta set =cut sub is_flush { my ($self, $name) = shift; return 1 if $self->force_flush; my $sticky = ''; if ($name) { $sticky .= "$name " if $self->length != $self->named_meta_length($name); } else { foreach my $m ($self->meta_names) { $sticky .= "$m " if ($self->named_meta_length($m) > 0) && ($self->length != $self->named_meta_length($m)); } } if ($sticky) { print "These meta set are not flush: $sticky\n" if $self->verbose; return 0; } return 1; } =head1 Bio::PrimarySeqI methods =head2 revcom Title : revcom Usage : $newseq = $seq->revcom(); Function: Produces a new Bio::Seq::MetaI implementing object where the order of residues and their meta information is reversed. Returns : A new (fresh) Bio::Seq::Meta object Args : none Throws : if the object returns false on is_flush() Note: The method does nothing to meta values, it reorders them, only. =cut sub revcom { my $self = shift; $self->throw("Can not get a reverse complement. The object is not flush.") unless $self->is_flush; my $new = $self->SUPER::revcom; foreach (keys %{$self->{_meta}}) { $new->named_meta($_, scalar reverse $self->{_meta}->{$_} ); }; return $new; } =head2 trunc Title : trunc Usage : $subseq = $seq->trunc(10,100); Function: Provides a truncation of a sequence together with meta data Returns : a fresh Bio::Seq::Meta implementing object Args : Two integers denoting first and last residue of the sub-sequence. =cut sub trunc { my ($self, $start, $end) = @_; # test arguments $start =~ /^[+]?\d+$/ and $start > 0 or $self->throw("Need at least a positive integer start value as start"); $end =~ /^[+]?\d+$/ and $end > 0 or $self->throw("Need at least a positive integer start value as end"); $end >= $start or $self->throw("End position has to be larger or equal to start"); $end <= $self->length or $self->throw("End position can not be larger than sequence length"); my $new = $self->SUPER::trunc($start, $end); $start--; foreach (keys %{$self->{_meta}}) { $new->named_meta($_, substr($self->{_meta}->{$_}, $start, $end - $start) ); }; return $new; } sub to_string { my ($self) = @_; my $out = Bio::SeqIO->new(-format=>'metafasta'); $out->write_seq($self); return 1; } 1; ����������������������BioPerl-1.007002/Bio/Seq/MetaI.pm�������������������������������������������������������������������000444��000766��000024�� 27420�13155576320� 16336� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::MetaI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::MetaI - Interface for sequence objects with residue-based meta information =head1 SYNOPSIS # get a Bio::Seq::MetaI compliant object somehow # to test this is a meta seq object $obj->isa("Bio::Seq::MetaI") || $obj->throw("$obj not a Bio::Seq::MetaI"); # accessors $string = $obj->meta; $string = $obj->meta_text; $substring = $obj->submeta(12,50); $unique_key = $obj->accession_number(); =head1 DESCRIPTION This class defines an abstract interface for basic residue-based meta information. Examples of this kind of meta data are secondary structures (RNA and protein), protein hydrophobicity assignments, or other alternative alphabets for polypeptides, sequence quality data and nucleotide alignments with translations. The length of the meta data sequence is not dependent on the amount of the meta information. The meta information always covers all the residues, but a blank value is used to denote unavailable information. If necessary the implementation quietly truncates or extends meta information with blank values. Definition of blank is implementation dependent. Gaps in MSAs should not have meta information. At this point a residue in a sequence object can have only one meta value. If you need more, use multiple copies of the sequence object. Meta data storage can be implemented in various ways, e.g: string, array of scalars, array of hashes, array of objects. If the implementation so chooses, there can be more then one meta values associated to each residue. See L<named_meta> and L<names_submeta>. Note that use of arbitrary names is very prone to typos leading to creation of additional copies of meta data sets. Bio::Seq::Meta provides basic, pure perl implementation of sequences with meta information. See L<Bio::Seq::Meta>. Application specific implementations will override and add to these methods. =head2 Method naming Character based meta data is read and set by method meta() and its variants. These are the suffixes and prefixes used in the variants: [named_] [sub] meta [_text] =over 3 =item _text Suffix B<_text> guaranties that output is a string. Note that it does not limit the input. =item sub Prefix B<sub>, like in subseq(), means that the method applies to sub region of the sequence range and takes start and end as arguments. Unlike subseq(), these methods are able to set values. If the range is not defined, it defaults to the complete sequence. =item named_ Prefix B<named_> in method names allows the used to attach multiple meta strings to one sequence by explicitly naming them. The name is always the first argument to the method. The "unnamed" methods use the class wide default name for the meta data and are thus special cases "named" methods. Note that internally names are keys in a hash and any misspelling of a name will silently store the data under a wrong name. The used names (keys) can be retrieved using method meta_names(). See L<meta_names>. =back =head1 SEE ALSO L<Bio::Seq::Meta>, L<Bio::Seq::Meta::Array>, L<Bio::Seq::EncodedSeq>, L<Bio::Tools::OddCodes>, L<Bio::Seq::Quality> =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email heikki-at-bioperl-dot-org =head1 CONTRIBUTORS Chad Matsalla, bioinformatics@dieselwurks.com; Aaron Mackey, amackey@virginia.edu; Peter Schattner schattner@alum.mit.edu; Richard Adams, Richard.Adams@ed.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::MetaI; use strict; use base qw(Bio::Root::RootI); =head2 meta Title : meta Usage : $meta_values = $obj->meta($values_string); Function: Get and set method for the unnamed meta data starting from residue position one. Since it is dependent on the length of the sequence, it needs to be manipulated after the sequence. The implementation may choose to accept argument values in a string or in an array (reference) or in a hash (reference). The return value may be a string or an array reference, depending on the implementation. If in doubt, use meta_text() which is a variant guarantied to return a string. See L<meta_text>. The length of the returned value always matches the length of the sequence. Returns : A reference to an array or a string Args : new value, optional =cut sub meta { shift->throw_not_implemented } =head2 meta_text Title : meta_text() Usage : $meta_values = $obj->meta_text($values_arrayref); Function: Variant of meta() guarantied to return a textual representation of the meta data. For details, see L<meta>. Returns : a string Args : new value, optional =cut sub meta_text { shift->throw_not_implemented } =head2 named_meta Title : named_meta() Usage : $meta_values = $obj->named_meta($name, $values_arrayref); Function: A more general version of meta(). Each meta data set needs to be named. See also L<meta_names>. Returns : a string Args : scalar, name of the meta data set new value, optional =cut sub named_meta { shift->throw_not_implemented } =head2 named_meta_text Title : named_meta_text() Usage : $meta_values = $obj->named_meta_text($name, $values_arrayref); Function: Variant of named_meta() guarantied to return a textual representation of the named meta data. For details, see L<meta>. Returns : a string Args : scalar, name of the meta data set new value, optional =cut sub named_meta_text { shift->throw_not_implemented } =head2 submeta Title : submeta Usage : $subset_of_meta_values = $obj->submeta(10, 20, $value_string); $subset_of_meta_values = $obj->submeta(10, undef, $value_string); Function: Get and set method for meta data for subsequences. Numbering starts from 1 and the number is inclusive, ie 1-2 are the first two residue of the sequence. Start cannot be larger than end but can be equal. If the second argument is missing the returned values should extend to the end of the sequence. If implementation tries to set values beyond the current sequence, they should be ignored. The return value may be a string or an array reference, depending on the implementation. If in doubt, use submeta_text() which is a variant guarantied to return a string. See L<submeta_text>. Returns : A reference to an array or a string Args : integer, start position, optional integer, end position, optional new value, optional =cut sub submeta { shift->throw_not_implemented } =head2 submeta_text Title : submeta_text Usage : $meta_values = $obj->submeta_text(20, $value_string); Function: Variant of submeta() guarantied to return a textual representation of meta data. For details, see L<meta>. Returns : a string Args : integer, start position, optional integer, end position, optional new value, optional =cut sub submeta_text { shift->throw_not_implemented } =head2 named_submeta Title : named_submeta Usage : $subset_of_meta_values = $obj->named_submeta($name, 10, 20, $value_string); $subset_of_meta_values = $obj->named_submeta($name, 10); Function: Variant of submeta() guarantied to return a textual representation of meta data. For details, see L<meta>. Returns : A reference to an array or a string Args : scalar, name of the meta data set integer, start position integer, end position, optional when a third argument present new value, optional =cut sub named_submeta { shift->throw_not_implemented } =head2 named_submeta_text Title : named_submeta_text Usage : $meta_values = $obj->named_submeta_text($name, 20, $value_string); Function: Variant of submeta() guarantied to return a textual representation of meta data. For details, see L<meta>. Returns : a string Args : scalar, name of the meta data Args : integer, start position, optional integer, end position, optional new value, optional =cut sub named_submeta_text { shift->throw_not_implemented } =head2 meta_names Title : meta_names Usage : @meta_names = $obj->meta_names() Function: Retrieves an array of meta data set names. The default (unnamed) set name is guarantied to be the first name. Returns : an array of names Args : none =cut sub meta_names { shift->throw_not_implemented } =head2 force_flush Title : force_flush() Usage : $force_flush = $obj->force_flush(1); Function: Automatically pad with empty values or truncate meta values to sequence length Returns : boolean 1 or 0 Args : optional boolean value =cut sub force_flush { shift->throw_not_implemented } =head2 is_flush Title : is_flush Usage : $is_flush = $obj->is_flush() or $is_flush = $obj->is_flush($my_meta_name) Function: Boolean to tell if all meta values are in flush with the sequence length. Returns true if force_flush() is set Set verbosity to a positive value to see failed meta sets Returns : boolean 1 or 0 Args : optional name of the meta set =cut sub is_flush { shift->throw_not_implemented } =head2 meta_length Title : meta_length() Usage : $meeta_len = $obj->meta_length(); Function: return the number of elements in the meta set Returns : integer Args : - =cut sub meta_length { shift->throw_not_implemented } =head2 named_meta_length Title : named_meta_length() Usage : $meeta_len = $obj->named_meta_length($name); Function: return the number of elements in the named meta set Returns : integer Args : - =cut sub named_meta_length { shift->throw_not_implemented } =head1 Bio::PrimarySeqI methods Implementing classes will need to rewrite these Bio::PrimaryI methods. =cut =head2 revcom Title : revcom Usage : $newseq = $seq->revcom(); Function: Produces a new Bio::Seq::MetaI implementing object where the order of residues and their meta information is reversed. Returns : A new (fresh) Bio::Seq::MetaI object Args : none =cut sub revcom { shift->throw_not_implemented } =head2 trunc Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence Returns : a fresh Bio::Seq::MetaI implementing object Args : Two integers denoting first and last residue of the sub-sequence. =cut sub trunc { shift->throw_not_implemented } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/PrimaryQual.pm�������������������������������������������������������������000444��000766��000024�� 33361�13155576320� 17606� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # bioperl module for Bio::PrimaryQual # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chad Matsalla <bioinformatics@dieselwurks.com> # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::PrimaryQual - Bioperl lightweight Quality Object =head1 SYNOPSIS use Bio::Seq::PrimaryQual; # you can use either a space-delimited string for quality my $string_quals = "10 20 30 40 50 40 30 20 10"; my $qualobj = Bio::Seq::PrimaryQual->new( -qual => $string_quals, -id => 'QualityFragment-12', -accession_number => 'X78121', ); # _or_ you can use an array of quality values my @q2 = split/ /,$string_quals; $qualobj = Bio::Seq::PrimaryQual->new( -qual => \@q2, -primary_id => 'chads primary_id', -desc => 'chads desc', -accession_number => 'chads accession_number', -id => 'chads id' ); # to get the quality values out: my @quals = @{$qualobj->qual()}; # to give _new_ quality values my $newqualstring = "50 90 1000 20 12 0 0"; $qualobj->qual($newqualstring); =head1 DESCRIPTION This module provides a mechanism for storing quality values. Much more useful as part of Bio::Seq::SeqWithQuality where these quality values are associated with the sequence information. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics@dieselwurks.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Seq::PrimaryQual; use strict; use base qw(Bio::Root::Root Bio::Seq::QualI); our $MATCHPATTERN = '0-9eE\.\s+-'; =head2 new() Title : new() Usage : $qual = Bio::Seq::PrimaryQual->new( -qual => '10 20 30 40 50 50 20 10', -id => 'human_id', -accession_number => 'AL000012', ); Function: Returns a new Bio::Seq::PrimaryQual object from basic constructors, being a string _or_ a reference to an array for the sequence and strings for id and accession_number. Note that you can provide an empty quality string. Returns : a new Bio::Seq::PrimaryQual object =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); # default: turn ON the warnings (duh) my($qual,$id,$acc,$pid,$desc,$given_id,$header) = $self->_rearrange([qw(QUAL DISPLAY_ID ACCESSION_NUMBER PRIMARY_ID DESC ID HEADER )], @args); if( defined $id && defined $given_id ) { if( $id ne $given_id ) { $self->throw("Provided both id and display_id constructor functions. [$id] [$given_id]"); } } if( defined $given_id ) { $id = $given_id; } # note: the sequence string may be empty $self->qual(defined($qual) ? $qual : []); $header && $self->header($header); $id && $self->display_id($id); $acc && $self->accession_number($acc); $pid && $self->primary_id($pid); $desc && $self->desc($desc); return $self; } =head2 qual() Title : qual() Usage : @quality_values = @{$obj->qual()}; Function: Get or set the quality as a reference to an array containing the quality values. An error is generated if the quality scores are invalid, see validate_qual(). Returns : A reference to an array. =cut sub qual { my ($self,$value) = @_; if( ! defined $value || length($value) == 0 ) { $self->{'qual'} ||= []; } elsif( ref($value) =~ /ARRAY/i ) { # if the user passed in a reference to an array $self->{'qual'} = $value; } else { $self->validate_qual($value, 1); $value =~ s/^\s+//; $self->{'qual'} = [split(/\s+/,$value)]; } return $self->{'qual'}; } =head2 seq() Title : seq() Usager : $sequence = $obj->seq(); Function : Returns the quality numbers as a space-separated string. Returns : Single string. Args : None. =cut sub seq { return join ' ', @{ shift->qual }; } =head2 validate_qual($qualstring) Title : validate_qual($qualstring) Usage : print("Valid.") if { &validate_qual($self, $quality_string); } Function: Test that the given quality string is valid. It is expected to contain space-delimited numbers that can be parsed using split /\d+/. However, this validation takes shortcuts and only tests that the string contains characters valid in numbers: 0-9 . eE +- Note that empty quality strings are valid too. Returns : 1 for a valid sequence, 0 otherwise Args : - Scalar containing the quality string to validate. - Boolean to optionally throw an error if validation failed =cut sub validate_qual { my ($self, $qualstr, $throw) = @_; if ( (defined $qualstr ) && ($qualstr !~ /^[$MATCHPATTERN]*$/) ) { if ($throw) { $self->throw("Failed validation of quality score from '". (defined($self->id)||'[unidentified sequence]')."'. No numeric ". "value found.\n"); } return 0; } return 1; } =head2 subqual($start,$end) Title : subqual($start,$end) Usage : @subset_of_quality_values = @{$obj->subqual(10,40)}; Function: returns the quality values from $start to $end, where the first value is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Start cannot be larger than end but can be equal. Returns : A reference to an array. Args : a start position and an end position =cut sub subqual { my ($self,$start,$end) = @_; if( $start > $end ){ $self->throw("in subqual, start [$start] has to be greater than end [$end]"); } if( $start <= 0 || $end > $self->length ) { $self->throw("You have to have start positive and length less than the total length of sequence [$start:$end] Total ".$self->length.""); } # remove one from start, and then length is end-start $start--; $end--; my @sub_qual_array = @{$self->{qual}}[$start..$end]; # return substr $self->seq(), $start, ($end-$start); return \@sub_qual_array; } =head2 display_id() Title : display_id() Usage : $id_string = $obj->display_id(); Function: returns the display id, aka the common name of the Quality object. The semantics of this is that it is the most likely string to be used as an identifier of the quality sequence, and likely to have "human" readability. The id is equivalent to the ID field of the GenBank/EMBL databanks and the id field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. Notice that $seq->id() maps to this function, mainly for legacy/convience issues Returns : A string Args : None =cut sub display_id { my ($obj,$value) = @_; if( defined $value) { $obj->{'display_id'} = $value; } return $obj->{'display_id'}; } =head2 header() Title : header() Usage : $header = $obj->header(); Function: Get/set the header that the user wants printed for this quality object. Returns : A string Args : None =cut sub header { my ($obj,$value) = @_; if( defined $value) { $obj->{'header'} = $value; } return $obj->{'header'}; } =head2 accession_number() Title : accession_number() Usage : $unique_biological_key = $obj->accession_number(); Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". Returns : A string Args : None =cut sub accession_number { my( $obj, $acc ) = @_; if (defined $acc) { $obj->{'accession_number'} = $acc; } else { $acc = $obj->{'accession_number'}; $acc = 'unknown' unless defined $acc; } return $acc; } =head2 primary_id() Title : primary_id() Usage : $unique_implementation_key = $obj->primary_id(); Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a way the implementation can control clients can expect one id to map to one object. For sequences with no accession number, this method should return a stringified memory location. Returns : A string Args : None =cut sub primary_id { my ($obj,$value) = @_; if( defined $value) { $obj->{'primary_id'} = $value; } return $obj->{'primary_id'}; } =head2 desc() Title : desc() Usage : $qual->desc($newval); $description = $qual->desc(); Function: Get/set description text for a qual object Example : Returns : Value of desc Args : newvalue (optional) =cut sub desc { my ($obj,$value) = @_; if( defined $value) { $obj->{'desc'} = $value; } return $obj->{'desc'}; } =head2 id() Title : id() Usage : $id = $qual->id(); Function: Return the ID of the quality. This should normally be (and actually is in the implementation provided here) just a synonym for display_id(). Returns : A string. Args : None. =cut sub id { my ($self,$value) = @_; if( defined $value ) { return $self->display_id($value); } return $self->display_id(); } =head2 length() Title : length() Usage : $length = $qual->length(); Function: Return the length of the array holding the quality values. Under most circumstances, this should match the number of quality values but no validation is done when the PrimaryQual object is constructed and non-digits could be put into this array. Is this a bug? Just enough rope... Returns : A scalar (the number of elements in the quality array). Args : None. =cut sub length { my $self = shift; if (ref($self->{qual}) ne "ARRAY") { $self->warn("{qual} is not an array here. Why? It appears to be ".ref($self->{qual})."(".$self->{qual}."). Good thing this can _never_ happen."); } return scalar(@{$self->{qual}}); } =head2 qualat() Title : qualat Usage : $quality = $obj->qualat(10); Function: Return the quality value at the given location, where the first value is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Start cannot be larger than end but can be equal. Returns : A scalar. Args : A position. =cut sub qualat { my ($self,$val) = @_; my @qualat = @{$self->subqual($val,$val)}; if (scalar(@qualat) == 1) { return $qualat[0]; } else { $self->throw("qualat() provided more than one quality."); } } =head2 to_string() Title : to_string() Usage : $quality = $obj->to_string(); Function: Return a textual representation of what the object contains. For this module, this function will return: qual display_id accession_number primary_id desc id length Returns : A scalar. Args : None. =cut sub to_string { my ($self,$out,$result) = shift; $out = "qual: ".join(',',@{$self->qual()}); foreach (qw(display_id accession_number primary_id desc id length)) { $result = $self->$_(); if (!$result) { $result = "<unset>"; } $out .= "$_: $result\n"; } return $out; } sub to_string_automatic { my ($self,$sub_result,$out) = shift; foreach (sort keys %$self) { print("Working on $_\n"); eval { $self->$_(); }; if ($@) { $sub_result = ref($_); } elsif (!($sub_result = $self->$_())) { $sub_result = "<unset>"; } if (ref($sub_result) eq "ARRAY") { print("This thing ($_) is an array!\n"); $sub_result = join(',',@$sub_result); } $out .= "$_: ".$sub_result."\n"; } return $out; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/PrimedSeq.pm���������������������������������������������������������������000444��000766��000024�� 34543�13155576320� 17234� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # This is the original copyright statement. I have relied on Chad's module # extensively for this module. # # Copyright (c) 1997-2001 bioperl, Chad Matsalla. All Rights Reserved. # This module is free software; you can redistribute it and/or # modify it under the same terms as Perl itself. # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code # # But I have modified lots of it, so I guess I should add: # # Copyright (c) 2003 bioperl, Rob Edwards. All Rights Reserved. # This module is free software; you can redistribute it and/or # modify it under the same terms as Perl itself. # # Copyright Rob Edwards # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::PrimedSeq - A sequence and a pair of primers matching on it =head1 SYNOPSIS use Bio::Seq; use Bio::Seq::PrimedSeq; my $template = Bio::Seq->new( -seq => 'AGCTTTTCATTCTGACTGCAAC' ); my $left = Bio::Seq->new( -seq => 'AGCT' ); my $right = Bio::Seq->new( -seq => 'GTTGC' ); my $primedseq = Bio::Seq::PrimedSeq->new( -seq => $template, # sequence object -left_primer => $left, # sequence or primer object -right_primer => $right # sequence or primer object ); # Get the primers as Bio::SeqFeature::Primer objects my @primer_objects = $primedseq->get_primer(); # Sequence object representing the PCR product, i.e. the section of the target # sequence contained between the primers (primers included) my $amplicon_seq = $primedseq->amplicon(); print 'Got amplicon sequence: '.$amplicon_seq->seq."\n"; # Amplicon should be: agctTTTCATTCTGACTgcaac =head1 DESCRIPTION This module was created to address the fact that a primer is more than a SeqFeature and that there is a need to represent the primer-sequence complex and the attributes that are associated with the complex. A PrimedSeq object is initialized with a target sequence and two primers. The location of the primers on the target sequence is calculated if needed so that one can then get the PCR product, or amplicon sequence. From the PrimedSeq object you can also retrieve information about melting temperatures and what not on each of the primers and the amplicon. The L<Bio::Tools::Primer3> module uses PrimedSeq objects extensively. Note that this module does not simulate PCR. It assumes that the primers will match in a single location on the target sequence and does not understand degenerate primers. =over =item * Providing primers as sequence objects If the primers are specified as sequence objects, e.g. L<Bio::PrimarySeq> or L<Bio::Seq>, they are first converted to L<Bio::SeqFeature::Primer> objects. Their location on the target sequence is then calculated and added to the L<Bio::SeqFeature::Primer> objects, which you can retrieve using the get_primer() method. =item * Providing primers as primer objects Because of the limitations of specifying primers as sequence objects, the recommended method is to provide L<Bio::SeqFeature::Primer> objects. If you did not record the location of the primers in the primer object, it will be calculated. =back L<Bio::Seq::PrimedSeq> was initially started by Chad Matsalla, and later improved on by Rob Edwards. =head1 RECIPES =over =item 1. Run Primer3 to get PrimedSeq objects: use Bio::SeqIO; use Bio::Tools::Run::Primer3; # Read a target sequences from a FASTA file my $file = shift || die "Need a file to read"; my $seqin = Bio::SeqIO->new(-file => $file); my $seq = $seqin->next_seq; # Use Primer3 to design some primers my $primer3 = Bio::Tools::Run::Primer3->new(-seq => $seq); my $results = $primer3->run; # default parameters # Write all the results in a Genbank file my $seqout = Bio::SeqIO->new(-file => ">primed_sequence.gbk", -format => 'genbank'); while (my $primedseq = $results->next_primer) { $seqout->write_seq( $primedseq->annotated_seq ); } =item 2. Create a genbank file for a sequence and its cognate primers: use Bio::SeqIO; use Bio::Seq::PrimedSeq; # Read a FASTA file that contains the target sequence and its two primers my $file = shift || die "$0 <file>"; my $seqin = Bio::SeqIO->new(-file => $file); my ($template, $leftprimer, $rightprimer) = ($seqin->next_seq, $seqin->next_seq, $seqin->next_seq); # Set up a PrimedSeq object my $primedseq = Bio::Seq::PrimedSeq->new(-seq => $template, -left_primer => $leftprimer, -right_primer => $rightprimer); # Write the sequences in an output Genbank file my $seqout = Bio::SeqIO->new(-file => ">primed_sequence.gbk", -format => 'genbank'); $seqout->write_seq($primedseq->annotated_sequence); =back =head1 FEEDBACK User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Rob Edwards, redwards@utmem.edu Based on a module written by Chad Matsalla, bioinformatics1@dieselwurks.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::PrimedSeq; use strict; use Bio::SeqFeature::Primer; use base qw(Bio::Root::Root Bio::SeqFeature::Generic); # Since this module occupies the Bio::Seq::* namespace, it should probably # inherit from Bio::Seq before it inherits from Bio::SeqFeature::Generic. But # then, Bio::SeqI and Bio::SeqFeatureI both request a seq() method that return # different things. So, being Bio::SeqI is incompatible with being Bio::SeqFeatureI =head2 new Title : new() Usage : my $primedseq = Bio::SeqFeature::Primer->new( -seq => $sequence, -left_primer => $left_primer, -right_primer => $right_primer ); Function: Construct a primed sequence. Returns : A Bio::Seq::PrimedSeq object Args : -seq => a Bio::Seq object (required) -left_primer => a Bio::SeqFeature::Primer or sequence object (required) -right_primer => a Bio::SeqFeature::Primer or sequence object (required) If you pass a sequence object to specify a primer, it will be used to construct a Bio::SeqFeature::Primer that you can retrieve with the L<get_primer> method. Many other parameters can be included including all of the output parameters from the primer3 program (see L<Bio::Tools::Primer3>). At the moment these parameters will simply be stored and do anything. =cut sub new { my($class,%args) = @_; my $self = $class->SUPER::new(%args); # Need an amplicon sequence $self->{seq} = delete $args{-seq} || delete $args{-target_sequence} || $self->throw("Need to provide a sequence during PrimedSeq object construction"); if (! ref($self->{seq}) || ! $self->{seq}->isa('Bio::SeqI') ) { $self->throw("The target_sequence must be a Bio::Seq to create this object."); } # Need a left and right primers for my $primer ( 'left', 'right' ) { $self->{$primer} = delete $args{'-'.$primer.'_primer'} || $self->throw("Need to provide both primers during PrimedSeq object construction"); if ( ref $self->{$primer} && $self->{$primer}->isa('Bio::PrimarySeqI') ) { # Convert Bio::Seq or Bio::PrimarySeq objects to Bio::SeqFeature::Primer $self->{$primer} = Bio::SeqFeature::Primer->new(-seq => $self->{$primer}); } if (not (ref $self->{$primer} && $self->{$primer}->isa("Bio::SeqFeature::Primer"))) { $self->throw("Primers must be Bio::SeqFeature::Primer objects but got a ".ref($self->{$primer})); } } # Save remaining arguments while (my ($arg, $val) = each %args) { $self->{$arg} = $val; } # Determine primer location on target if needed if ( not( $self->{'left'}->start && $self->{'left'}->end && $self->{'right'}->start && $self->{'right'}->end ) ) { $self->_place_primers(); } return $self; } =head2 get_primer Title : get_primer(); Usage : my @primers = $primedseq->get_primer(); or my $primer = $primedseq->get_primer('-left_primer'); Function: Get the primers associated with the PrimedSeq object. Returns : A Bio::SeqFeature::Primer object Args : For the left primer, use: l, left, left_primer or -left_primer For the right primer, use: r, right, right_primer or -right_primer For both primers [default], use: b, both, both_primers or -both_primers =cut sub get_primer { my ($self, $arg) = @_; if (! defined $arg ) { return ($self->{left}, $self->{right}); } elsif ( $arg =~ /^-?l/ ) { # What a cheat, I couldn't be bothered to write all the exact statements! # Hah, now you can write 'leprechaun' to get the left primer. return $self->{left} } elsif ( $arg =~ /^-?r/ ) { return $self->{right}; } elsif ( $arg =~ /^-?b/ ) { return ($self->{left}, $self->{right}); } } =head2 annotated_sequence Title : annotated_sequence Usage : my $annotated_sequence_object = $primedseq->annotate_sequence(); Function: Get an annotated sequence object containing the left and right primers Returns : An annotated sequence object or 0 if not defined. Args : Note : Use this method to return a sequence object that you can write out (e.g. in GenBank format). See the example above. =cut sub annotated_sequence { my $self = shift; my $seq = $self->{'seq'}; ### clone?? $seq->add_SeqFeature($self->{'left'}); $seq->add_SeqFeature($self->{'right'}); return $seq; } =head2 amplicon Title : amplicon Usage : my $amplicon = $primedseq->amplicon(); Function: Retrieve the amplicon as a sequence object. The amplicon sequnce is only the section of the target sequence between the primer matches (primers included). Returns : A Bio::Seq object. To get the sequence use $amplicon->seq Args : None Note : =cut sub amplicon { my ($self) = @_; my $left = $self->{left}; my $right = $self->{right}; my $target = $self->{seq}; return Bio::PrimarySeq->new( -id => 'Amplicon_from_'.($target->id || 'unidentified'), -seq => lc( $left->seq->seq ). uc( $target->subseq($left->end+1, $right->start-1) ). lc( $right->seq->revcom->seq ), ); } =head2 seq Title : seq Usage : my $seqobj = $primedseq->seq(); Function: Retrieve the target sequence as a sequence object Returns : A seq object. To get the sequence use $seqobj->seq Args : None Note : =cut sub seq { my $self = shift; return $self->{seq}; } =head2 _place_primers Title : _place_primers Usage : $self->_place_primers(); Function: An internal method to place the primers on the sequence and set up the ranges of the sequences Returns : Nothing Args : None Note : Internal use only =cut sub _place_primers { my $self = shift; # Get the target and primer sequence strings, all in uppercase my $left = $self->{left}; my $right = $self->{right}; my $target_seq = uc $self->{seq}->seq(); my $left_seq = uc $left->seq()->seq(); my $right_seq = uc $right->seq()->revcom()->seq(); # Locate primers on target sequence my ($before, $middle, $after) = ($target_seq =~ /^(.*)$left_seq(.*)$right_seq(.*)$/); if (not defined $before || not defined $middle || not defined $after) { if ($target_seq !~ /$left_seq/) { $self->throw("Could not place left primer on target"); } if ($target_seq !~ /$right_seq/) { $self->throw("Could not place right primer on target") } } # Save location information in primer object my $left_location = length($before) + 1; my $right_location = length($target_seq) - length($after); $left->start($left_location); $left->end($left_location + $left->seq->length - 1); $left->strand(1); $right->start($right_location - $right->seq->length + 1); $right->end($right_location); $right->strand(-1); # If Primer3 information was recorded, compare it to what we calculated if ( exists($left->{PRIMER_LEFT}) || exists($right->{PRIMER_RIGHT}) || exists($self->{PRIMER_PRODUCT_SIZE}) ) { # Bio::Seq::PrimedSeq positions my $amplicon_size = length($left_seq) + length($middle) + length($right_seq); $left_location = $left_location.','.length($left_seq); $right_location = $right_location.','.length($right_seq); # Primer3 positions my $primer_product = $self->{PRIMER_PRODUCT_SIZE}; my $primer_left = $left->{PRIMER_LEFT}; my $primer_right = $right->{PRIMER_RIGHT}; if ( defined($primer_left) && (not $primer_left eq $left_location) ) { $self->warn("Got |$primer_left| from primer3 but calculated ". "|$left_location| for the left primer."); } if ( defined($primer_right) && (not $primer_right eq $right_location) ) { $self->warn("Got |$primer_right| from primer3 but calculated ". "|$right_location| for the right primer."); } if ( defined($primer_product) && (not $primer_product eq $amplicon_size) ) { $self->warn("Got |$primer_product| from primer3 but calculated ". "|$amplicon_size| for the size."); } } } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/QualI.pm�������������������������������������������������������������������000444��000766��000024�� 41624�13155576320� 16354� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::QualI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chad Matsalla <bioinformatics@dieselwurks.com # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::QualI - Interface definition for a Bio::Seq::Qual =head1 SYNOPSIS # get a Bio::Seq::Qual compliant object somehow # to test this is a seq object $obj->isa("Bio::Seq::QualI") || $obj->throw("$obj does not implement the Bio::Seq::QualI interface"); # accessors $string = $obj->qual(); $substring = $obj->subqual(12,50); $display = $obj->display_id(); # for human display $id = $obj->primary_id(); # unique id for this object, # implementation defined $unique_key= $obj->accession_number(); # unique biological id =head1 DESCRIPTION This object defines an abstract interface to basic quality information. PrimaryQual is an object just for the quality and its name(s), nothing more. There is a pure perl implementation of this in Bio::Seq::PrimaryQual. If you just want to use Bio::Seq::PrimaryQual objects, then please read that module first. This module defines the interface, and is of more interest to people who want to wrap their own Perl Objects/RDBs/FileSystems etc in way that they "are" bioperl quality objects, even though it is not using Perl to store the sequence etc. This interface defines what bioperl consideres necessary to "be" a sequence of qualities, without providing an implementation of this. (An implementation is provided in Bio::Seq::PrimaryQual). If you want to provide a Bio::Seq::PrimaryQual 'compliant' object which in fact wraps another object/database/out-of-perl experience, then this is the correct thing to wrap, generally by providing a wrapper class which would inherit from your object and this Bio::Seq::QualI interface. The wrapper class then would have methods lists in the "Implementation Specific Functions" which would provide these methods for your object. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla This module is heavily based on Bio::Seq::PrimarySeq and is modeled after or outright copies sections of it. Thanks Ewan! Email bioinformatics@dieselwurks.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::QualI; use strict; use Carp; use base qw(Bio::Root::RootI); =head1 Implementation Specific Functions These functions are the ones that a specific implementation must define. =head2 qual() Title : qual() Usage : @quality_values = @{$obj->qual()}; Function: Returns the quality as a reference to an array containing the quality values. The individual elements of the quality array are not validated and can be any numeric value. Returns : A reference to an array. Status : =cut sub qual { my ($self) = @_; if( $self->can('throw') ) { $self->throw("Bio::Seq::QualI definition of qual - implementing class did not provide this method"); } else { confess("Bio::Seq::QualI definition of qual - implementing class did not provide this method"); } } =head2 subqual($start,$end) Title : subqual($start,$end) Usage : @subset_of_quality_values = @{$obj->subseq(10,40)}; Function: returns the quality values from $start to $end, where the first value is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Start cannot be larger than end but can be equal. Returns : A reference to an array. Args : a start position and an end position =cut sub subqual { my ($self) = @_; if( $self->can('throw') ) { $self->throw("Bio::Seq::QualI definition of subqual - implementing class did not provide this method"); } else { confess("Bio::Seq::QualI definition of subqual - implementing class did not provide this method"); } } =head2 display_id() Title : display_id() Usage : $id_string = $obj->display_id() _or_ $id_string = $obj->display_id($new_display_id); Function: Returns the display id, aka the common name of the Quality object. The semantics of this is that it is the most likely string to be used as an identifier of the quality sequence, and likely to have "human" readability. The id is equivalent to the ID field of the GenBank/EMBL databanks and the id field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. Notice that $seq->id() maps to this function, mainly for legacy/convience issues Returns : A string Args : If an arg is provided, it will replace the existing display_id in the object. =cut sub display_id { my ($self) = @_; if( $self->can('throw') ) { $self->throw("Bio::Seq::QualI definition of id - implementing class did not provide this method"); } else { confess("Bio::Seq::QualI definition of id - implementing class did not provide this method"); } } =head2 accession_number() Title : accession_number() Usage : $unique_biological_key = $obj->accession_number(); _or_ $unique_biological_key = $obj->accession_number($new_acc_num); Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". Returns : A string. Args : If an arg is provided, it will replace the existing accession_number in the object. =cut sub accession_number { my ($self,@args) = @_; if( $self->can('throw') ) { $self->throw("Bio::Seq::QualI definition of seq - implementing class did not provide this method"); } else { confess("Bio::Seq::QualI definition of seq - implementing class did not provide this method"); } } =head2 primary_id() Title : primary_id() Usage : $unique_implementation_key = $obj->primary_id(); _or_ $unique_implementation_key = $obj->primary_id($new_prim_id); Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a way the implementation can control clients can expect one id to map to one object. For sequences with no accession number, this method should return a stringified memory location. Returns : A string Args : If an arg is provided, it will replace the existing primary_id in the object. =cut sub primary_id { my ($self,@args) = @_; if( $self->can('throw') ) { $self->throw("Bio::Seq::QualI definition of qual - implementing class did not provide this method"); } else { confess("Bio::Seq::QualI definition of qual - implementing class did not provide this method"); } } =head2 can_call_new() Title : can_call_new() Usage : if( $obj->can_call_new ) { $newobj = $obj->new( %param ); } Function: can_call_new returns 1 or 0 depending on whether an implementation allows new constructor to be called. If a new constructor is allowed, then it should take the followed hashed constructor list. $myobject->new( -qual => $quality_as_string, -display_id => $id, -accession_number => $accession, ); Example : Returns : 1 or 0 Args : =cut sub can_call_new{ my ($self,@args) = @_; # we default to 0 here return 0; } =head2 qualat($position) Title : qualat($position) Usage : $quality = $obj->qualat(10); Function: Return the quality value at the given location, where the first value is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Start cannot be larger than end but can be equal. Returns : A scalar. Args : A position. =cut sub qualat { my ($self,$value) = @_; if( $self->can('warn') ) { $self->warn("Bio::Seq::QualI definition of qualat - implementing class did not provide this method"); } else { warn("Bio::Seq::QualI definition of qualat - implementing class did not provide this method"); } return ''; } =head1 Optional Implementation Functions The following functions rely on the above functions. A implementing class does not need to provide these functions, as they will be provided by this class, but is free to override these functions. All of revcom(), trunc(), and translate() create new sequence objects. They will call new() on the class of the sequence object instance passed as argument, unless can_call_new() returns FALSE. In the latter case a Bio::PrimarySeq object will be created. Implementors which really want to control how objects are created (eg, for object persistence over a database, or objects in a CORBA framework), they are encouraged to override these methods =head2 revcom Title : revcom Usage : @rev = @{$qual->revcom()}; Function: Produces a new Bio::Seq::QualI implementing object which is reversed from the original quality array. The id is the same id as the original sequence, and the accession number is also identical. If someone wants to track that this sequence has been reversed, it needs to define its own extensions To do an inplace edit of an object you can go: $qual = $qual->revcom(); This of course, causes Perl to handle the garbage collection of the old object, but it is roughly speaking as efficient as an inplace edit. Returns : A new (fresh) Bio::Seq::PrimaryQualI object Args : none =cut sub revcom{ my ($self) = @_; # this is the cleanest way my @qualities = @{$self->qual()}; my @reversed_qualities = reverse(@qualities); my $seqclass; if($self->can_call_new()) { $seqclass = ref($self); } else { $seqclass = 'Bio::Seq::PrimaryQual'; # Wassat? # $self->_attempt_to_load_Seq(); } # the \@reverse_qualities thing works simply because I will it to work. my $out = $seqclass->new( '-qual' => \@reversed_qualities, '-display_id' => $self->display_id, '-accession_number' => $self->accession_number, '-desc' => $self->desc() ); return $out; } =head2 trunc() Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence, Returns : a fresh Bio::Seq::QualI implementing object Args : Two integers denoting first and last base of the sub-sequence. =cut sub trunc { my ($self,$start,$end) = @_; if( !$end ) { if( $self->can('throw') ) { $self->throw("trunc start,end"); } else { confess("[$self] trunc start,end"); } } if( $end < $start ) { if( $self->can('throw') ) { $self->throw("$end is smaller than $start. if you want to truncated and reverse complement, you must call trunc followed by revcom. Sorry."); } else { confess("[$self] $end is smaller than $start. If you want to truncated and reverse complement, you must call trunc followed by revcom. Sorry."); } } my $r_qual = $self->subqual($start,$end); my $seqclass; if($self->can_call_new()) { $seqclass = ref($self); } else { $seqclass = 'Bio::Seq::PrimaryQual'; # wassat? # $self->_attempt_to_load_Seq(); } my $out = $seqclass->new( '-qual' => $r_qual, '-display_id' => $self->display_id, '-accession_number' => $self->accession_number, '-desc' => $self->desc() ); return $out; } =head2 translate() Title : translate() Usage : $protein_seq_obj = $dna_seq_obj->translate #if full CDS expected: $protein_seq_obj = $cds_seq_obj->translate(undef,undef,undef,undef,1); Function: Completely useless in this interface. Returns : Nothing. Args : Nothing. =cut sub translate { return 0; } =head2 id() Title : id() Usage : $id = $qual->id() Function: ID of the quality. This should normally be (and actually is in the implementation provided here) just a synonym for display_id(). Example : Returns : A string. Args : =cut sub id { my ($self)= @_; return $self->display_id(); } =head2 length() Title : length() Usage : $length = $qual->length(); Function: Return the length of the array holding the quality values. Under most circumstances, this should match the number of quality values but no validation is done when the PrimaryQual object is constructed and non-digits could be put into this array. Is this a bug? Just enough rope... Returns : A scalar (the number of elements in the quality array). Args : None. =cut sub length { my ($self)= @_; if( $self->can('throw') ) { $self->throw("Bio::Seq::QualI definition of length - implementing class did not provide this method"); } else { confess("Bio::Seq::QualI definition of length - implementing class did not provide this method"); } } =head2 desc() Title : desc() Usage : $qual->desc($newval); $description = $seq->desc(); Function: Get/set description text for a qual object Example : Returns : value of desc Args : newvalue (optional) =cut sub desc { my ($self,$value) = @_; if( $self->can('warn') ) { $self->warn("Bio::Seq::QualI definition of desc - implementing class did not provide this method"); } else { warn("Bio::Seq::QualI definition of desc - implementing class did not provide this method"); } return ''; } # These methods are here for backward compatibility with the old, 0.5 # Seq objects. They all throw warnings that someone is using a # deprecated method, and may eventually be removed completely from # this object. However, they are important to ease the transition from # the old system. =head1 Private functions These are some private functions for the PrimarySeqI interface. You do not need to implement these functions =head2 _attempt_to_load_Seq Title : _attempt_to_load_Seq Usage : Function: Example : Returns : Args : =cut sub _attempt_to_load_Seq{ my ($self) = @_; if( $main::{'Bio::Seq::PrimaryQual'} ) { return 1; } else { eval { require Bio::Seq::PrimaryQual; }; if( $@ ) { if( $self->can('throw') ) { $self->throw("Bio::Seq::PrimaryQual could not be loaded for $self\nThis indicates that you are using Bio::Seq::PrimaryQualI without Bio::Seq::PrimaryQual loaded and without providing a complete solution\nThe most likely problem is that there has been a misconfiguration of the bioperl environment\nActual exception\n\n$@\n"); } else { confess("Bio::Seq::PrimarySeq could not be loaded for $self\nThis indicates that you are usnig Bio::Seq::PrimaryQualI without Bio::Seq::PrimaryQual loaded and without providing a complete solution\nThe most likely problem is that there has been a misconfiguration of the bioperl environment\nActual exception\n\n$@\n"); } return 0; } return 1; } } =head2 qualtype() Title : qualtype() Usage : if( $obj->qualtype eq 'phd' ) { /Do Something/ } Function: At this time, this function is not used for Bio::Seq::PrimaryQual objects. In fact, now it is a month later and I just completed the Bio::Seq::SeqWithQuality object and this is definitely deprecated. Returns : Nothing. (not implemented) Args : none Status : Virtual =cut sub qualtype { my ($self,@args) = @_; if( $self->can('throw') ) { # $self->throw("Bio::Seq::QualI definition of qual - implementing class did not provide this method"); $self->throw("qualtypetype is not used with quality objects."); } else { # confess("Bio::Seq::QualI definition of qual - implementing class did not provide this method"); confess("qualtype is not used with quality objects."); } } 1; ������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/Quality.pm�����������������������������������������������������������������000444��000766��000024�� 51020�13155576320� 16760� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::Quality # # Please direct questions and support issues to # <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::Quality - Implementation of sequence with residue quality and trace values =head1 SYNOPSIS use Bio::Seq::Quality; # input can be space delimited string or array ref my $qual = '0 1 2 3 4 5 6 7 8 9 11 12'; my $trace = '0 5 10 15 20 25 30 35 40 45 50 55'; my $seq = Bio::Seq::Quality->new ( -qual => $qual, -trace_indices => $trace, -seq => 'atcgatcgatcg', -id => 'human_id', -accession_number => 'S000012', -verbose => -1 # to silence deprecated methods ); my $quals = $seq->qual; # array ref my $traces = $seq->trace; # array ref my $quals = $seq->qual_text; # string my $traces = $seq->trace_text; # string # get sub values $quals = $seq->subqual(2, 3); # array ref $traces = $seq->subtrace(2, 3); # array ref $quals = $seq->subqual_text(2, 3); # string $quals = $seq->subtrace_text(2, 3); # string # set sub values $seq->subqual(2, 3, "9 9"); $seq->subtrace(2, 3, "9 9"); =head1 DESCRIPTION This object stores base quality values together with the sequence string. It is a reimplementation of Chad Matsalla's Bio::Seq::SeqWithQuality module using Bio::Seq::MetaI. The implementation is based on Bio::Seq::Meta::Array. qual() and trace() are base methods to store and retrieve information that have extensions to retrieve values as a scalar (e.g. qual_text() ), or get or set subvalues (e.g. subqual() ). See L<Bio::Seq::MetaI> for more details. All the functional code is in Bio::Seq::Meta::Array. There deprecated methods that are included for compatibility with Bio::Seq::SeqWithQuality. These will print a warning unless verbosity of the object is set to be less than zero. =head2 Differences from Bio::Seq::SeqWithQuality It is not possible to fully follow the interface of Bio::Seq::SeqWithQuality since internally a Bio::Seq::SeqWithQuality object is a composite of two independent objects: a Bio::PrimarySeq object and Bio::Seq::PrimaryQual object. Both of these objects can be created separately and merged into Bio::Seq::SeqWithQuality. This implementation is based on Bio::Seq::Meta::Array that is a subclass of Bio::PrimarySeq that stores any number of meta information in unnamed arrays. Here we assume that two meta sets, called 'qual' and 'trace_indices' are attached to a sequence. (But there is nothing that prevents you to add as many named meta sets as you need using normal meta() methods). qual() is an alias to meta(), qualat($loc) is an alias to submeta($loc,$loc). trace_indices() in Bio::Seq::SeqWithQuality has been abbreviated to trace() and is an alias to named_meta('trace'). You can create an object without passing any arguments to the constructor (Bio::Seq::SeqWithQuality fails without alphabet). It will warn about not being able to set alphabet unless you set verbosity of the object to a negative value. After the latest rewrite, the meta information sets (quality and trace) no longer cover all the residues automatically. Methods to check the length of meta information (L<quality_length>, L<trace_length>)and to see if the ends are flushed to the sequence have been added (L<quality_is_flush>, L<trace_is_flush>). To force the old functinality, set L<force_flush> to true. qual_obj() and seq_obj() methods do not exist! Finally, there is only one set of descriptors (primary_id, display_id, accession_number) for the object. =head1 SEE ALSO L<Bio::Seq::MetaI>, L<Bio::Seq::Meta::Array> =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email heikki-at-bioperl-dot-org =head1 CONTRIBUTORS Chad Matsalla, bioinformatics at dieselwurks dot com Dan Bolser, dan dot bolser at gmail dot com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::Quality; use strict; use base qw(Bio::Seq::Meta::Array); ## Is this the right place (and way) to define this? our $MASK_CHAR = 'X'; our $DEFAULT_NAME = 'DEFAULT'; our $GAP = '-'; our $META_GAP = ' '; =head2 new Title : new Usage : $metaseq = Bio::Seq::Quality->new ( -qual => '0 1 2 3 4 5 6 7 8 9 11 12', -trace => '0 5 10 15 20 25 30 35 40 45 50 55', -seq => 'atcgatcgatcg', -id => 'human_id', -accession_number => 'S000012', ); Function: Constructor for Bio::Seq::Quality class. Note that you can provide an empty quality and trace strings. Returns : a new Bio::Seq::Quality object =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my($meta, $qual, $trace, $trace_indices, $trace_data) = $self->_rearrange([qw(META QUAL TRACE TRACE_INDICES TRACE_DATA)], @args); $self->{'_meta'}->{$DEFAULT_NAME} = []; $self->{'_meta'}->{'trace'} = []; $self->{trace_data} = $trace_data; $meta && $self->meta($meta); $qual && $self->qual($qual); $trace && $self->named_meta('trace', $trace); $trace_indices && $self->named_meta('trace', $trace_indices); return $self; } ## QUAL =head2 qual Title : qual Usage : $qual_values = $obj->qual($values_string); Function: Get and set method for the meta data starting from residue position one. Since it is dependent on the length of the sequence, it needs to be manipulated after the sequence. The length of the returned value always matches the length of the sequence. Returns : reference to an array of meta data Args : new value, string or array ref or Bio::Seq::PrimaryQual, optional Setting quality values resets the clear range. =cut sub qual { my $self = shift; my $value = shift; $value = $value->qual if ref($value) and ref($value) ne 'ARRAY' and $value->isa('Bio::Seq::PrimaryQual'); $self->_empty_cache if $value; return $self->named_meta($DEFAULT_NAME, $value); } =head2 qual_text Title : qual_text Usage : $qual_values = $obj->qual_text($values_arrayref); Function: Variant of meta() and qual() guarantied to return a string representation of meta data. For details, see L<meta>. Returns : a string Args : new value, optional =cut sub qual_text { return join ' ', @{shift->named_submeta($DEFAULT_NAME, @_)}; } =head2 subqual Title : subqual Usage : $subset_of_qual_values = $obj->subqual(10, 20, $value_string); $subset_of_qual_values = $obj->subqual(10, undef, $value_string); Function: Get and set method for meta data for subsequences. Numbering starts from 1 and the number is inclusive, ie 1-2 are the first two residue of the sequence. Start cannot be larger than end but can be equal. If the second argument is missing the returned values should extend to the end of the sequence. Returns : A reference to an array Args : integer, start position integer, end position, optional when a third argument present new value, optional =cut sub subqual { shift->named_submeta($DEFAULT_NAME, @_); } =head2 subqual_text Title : subqual_text Usage : $meta_values = $obj->subqual_text(20, $value_string); Function: Variant of subqual() returning a stringified representation of meta data. For details, see L<Bio::Seq::MetaI>. Returns : a string Args : new value, optional =cut sub subqual_text { return join ' ', @{shift->named_submeta($DEFAULT_NAME, @_)}; } =head2 quality_length Title : quality_length() Usage : $qual_len = $obj->quality_length(); Function: return the number of elements in the quality array Returns : integer Args : - =cut sub quality_length { my ($self) = @_; return $self->named_meta_length($DEFAULT_NAME); } =head2 quality_is_flush Title : quality_is_flush Usage : $quality_is_flush = $obj->quality_is_flush() Function: Boolean to tell if the trace length equals the sequence length. Returns true if force_flush() is set. Returns : boolean 1 or 0 Args : none =cut sub quality_is_flush { return shift->is_flush('quality'); } ## TRACE =head2 trace Title : trace Usage : $trace_values = $obj->trace($values_string); Function: Get and set method for the meta data starting from residue position one. Since it is dependent on the length of the sequence, it needs to be manipulated after the sequence. The length of the returned value always matches the length of the sequence. Returns : reference to an array of meta data Args : new value, string or array ref, optional =cut sub trace { my $self = shift; my $value = shift; return $self->named_meta('trace', $value); } =head2 trace_text Title : trace_text Usage : $trace_values = $obj->trace_text($values_arrayref); Function: Variant of meta() and trace() guarantied to return a string representation of meta data. For details, see L<meta>. Returns : a string Args : new value, optional =cut sub trace_text { return join ' ', @{shift->named_submeta('trace', @_)}; } =head2 subtrace Title : subtrace Usage : $subset_of_trace_values = $obj->subtrace(10, 20, $value_string); $subset_of_trace_values = $obj->subtrace(10, undef, $value_string); Function: Get and set method for meta data for subsequences. Numbering starts from 1 and the number is inclusive, ie 1-2 are the first two residue of the sequence. Start cannot be larger than end but can be equal. If the second argument is missing the returned values should extend to the end of the sequence. Returns : A reference to an array Args : integer, start position integer, end position, optional when a third argument present new value, optional =cut sub subtrace { return shift->named_submeta('trace', @_); } =head2 subtrace_text Title : subtrace_text Usage : $meta_values = $obj->subtrace_text(20, $value_string); Function: Variant of subtrace() returning a stringified representation of meta data. For details, see L<Bio::Seq::MetaI>. Returns : a string Args : new value, optional =cut sub subtrace_text { return join ' ', @{shift->named_submeta('trace', @_)}; } =head2 trace_length Title : trace_length() Usage : $trace_len = $obj->trace_length(); Function: return the number of elements in the trace set Returns : integer Args : - =cut sub trace_length { my ($self) = @_; return $self->named_meta_length('trace'); } =head2 trace_is_flush Title : trace_is_flush Usage : $trace_is_flush = $obj->trace_is_flush() Function: Boolean to tell if the trace length equals the sequence length. Returns true if force_flush() is set. Returns : boolean 1 or 0 Args : none =cut sub trace_is_flush { return shift->is_flush('trace'); } =head2 get_trace_graph Title : get_trace_graph Usage : @trace_values = $obj->get_trace_graph( -trace => 'a', -scale => 100) Function : Returns array of raw trace values for a trace file, or false if no trace data exists. Requires a value for trace to get either the a, g, c or t trace information, and an optional value for scale, which rescales the data between 0 and the provided value, a scale value of '0' performs no scaling Returns : Array or 0 Args : string, trace to retrieve, one of a, g, c or t integer, scale, for scaling of trace between 0 and scale, or 0 for no scaling, optional =cut sub get_trace_graph { my $self = shift; my($trace, $scale) = $self->_rearrange([qw(TRACE SCALE )], @_); unless (defined($self->{trace_data})) { return 0 } unless (grep { lc($trace) eq $_ } ('a', 'g', 'c', 't')) { return 0 } $trace = lc($trace) . "_trace"; my @trace_data = exists $self->{trace_data}->{$trace} && ref $self->{trace_data}->{$trace} eq 'ARRAY' ? @{$self->{trace_data}->{$trace}} : (); my $max = $self->{trace_data}->{max_height}; if (defined($scale) and $scale != 0) { @trace_data = map { $_ / $max * $scale } @trace_data; } return @trace_data; } =head2 threshold Title : threshold Usage : $qual->threshold($value); Function: Sets the quality threshold. Returns : an integer Args : new value, optional Value used by *clear_range* method below. =cut sub threshold { my $self = shift; my $value = shift; if (defined $value) { $self->throw("Threshold needs to be an integer [$value]") unless $value =~ /^[-+]?\d+$/; $self->_empty_cache if defined $self->{_threshold} and $self->{_threshold} ne $value; $self->{_threshold} = $value; } return $self->{_threshold}; } =head2 mask_below_threshold Title : mask_below_threshold Usage : $count = $obj->count_clear_ranges($threshold); Function: Counts number of ranges in the sequence where quality values are above the threshold Returns : count integer Args : threshold integer, optional Set threshold first using method L<threshold>. =cut sub mask_below_threshold { my $self = shift; my $threshold = shift; $self->threshold($threshold) if defined $threshold; # populate the cache if needed $self->_find_clear_ranges unless defined $self->{_ranges}; my $maskSeq = $self->seq; my $maskQual = $self->qual; ## There must be a more efficient way than this! for(my $i=0; $i<length($maskSeq); $i++){ #print join ("\t", $i, $maskQual->[$i]), "\n"; substr($maskSeq, $i, 1, $MASK_CHAR) if $maskQual->[$i] < $self->{_threshold}; } ## This is the *wrong* way to do it! #for my $r (@{$self->{_ranges}} ){ # substr($maskSeq, $r->{start}, $r->{length}, $MASK_CHAR x $r->{length}); #} return $maskSeq; } =head2 count_clear_ranges Title : count_clear_ranges Usage : $count = $obj->count_clear_ranges($threshold); Function: Counts number of ranges in the sequence where quality values are above the threshold Returns : count integer Args : threshold integer, optional Set threshold first using method L<threshold>. =cut sub count_clear_ranges { my $self = shift; my $threshold = shift; $self->threshold($threshold) if defined $threshold; # populate the cache if needed $self->_find_clear_ranges unless defined $self->{_ranges}; return scalar @{$self->{_ranges}}; } =head2 clear_ranges_length Title : clear_ranges_length Usage : $total_lenght = $obj->clear_ranges_length($threshold); Function: Return number of residues with quality values above the threshold in all clear ranges Returns : an integer Args : threshold, optional Set threshold first using method L<threshold>. I think this method needs a better name! count_high_quality_bases? or sum_clear_ranges? =cut sub clear_ranges_length { my $self = shift; my $threshold = shift; $self->threshold($threshold) if defined $threshold; # populate the cache if needed $self->_find_clear_ranges unless defined $self->{_ranges}; my $sum; map {$sum += $_->{length}} @{$self->{_ranges}}; return $sum; } =head2 get_clear_range Title : get_clear_range Usage : $newqualobj = $obj->get_clear_range($threshold); Function: Return longest subsequence that has quality values above the given threshold, or a default value of 13 Returns : a new Bio::Seq::Quality object Args : threshold, optional Set threshold first using method L<threshold>. Note, this method could be implemented using some gaussian smoothing of the quality scores. Currently one base below the threshold is enough to end the clear range. =cut sub get_clear_range { my $self = shift; my $threshold = shift; $self->threshold($threshold) if defined $threshold; # populate the cache if needed $self->_find_clear_ranges unless defined $self->{_ranges}; # fix for bug 2847 return unless defined $self->{_ranges}; # pick the longest for (sort {$b->{length} <=> $a->{length} } @{$self->{_ranges}} ){ my $newqualobj = Bio::Seq::Quality->new( -seq => $self->subseq( $_->{start}, $_->{end}), -qual => $self->subqual($_->{start}, $_->{end}), -id => $self->id); $newqualobj->threshold($threshold); return $newqualobj; } } =head2 get_all_clean_ranges Title : get_all_clean_ranges Usage : @ranges = $obj->get_all_clean_ranges($minlength); Function: Return all ranges where quality values are above the threshold. Original ordering. Returns : an ordered array of new Bio::Seq::Quality objects Args : minimum length , optional Set threshold first using method L<threshold>. =cut sub get_all_clean_ranges { my $self = shift; my $minl = shift || 0; $self->throw("Mimimum length needs to be zero or a positive integer [$minl]") unless $minl =~ /^\+?\d+$/; # populate the cache if needed $self->_find_clear_ranges unless defined $self->{_ranges}; # return in the order of occurrence my @ranges; for my $r (sort {$b->{start} <=> $a->{start} } @{$self->{_ranges}} ){ next if $r->{length} < $minl; ## Constructor should allow "-threshold => ..."! push @ranges, Bio::Seq::Quality->new ( -seq => $self->subseq( $r->{start}, $r->{end}), -qual => $self->subqual($r->{start}, $r->{end}), -id => $self->id ); } return @ranges; } # # _find_clear_ranges: where range/threshold calculations happen # sub _find_clear_ranges { my $self = shift; my $qual = $self->qual; $self->throw("You need to set the threshold value first") unless defined $self->threshold; my $threshold = $self->threshold; my $rangeFlag = 0; for(my $i=0; $i<@$qual; $i++){ ## Are we currently within a clear range or not? if($rangeFlag){ ## Did we just leave the clear range? if($qual->[$i]<$threshold){ ## Log the range my $range; $range->{end} = $i-1; $range->{start} = $rangeFlag; $range->{length} = $i - $rangeFlag; push @{$self->{_ranges}}, $range; ## and reset the range flag. $rangeFlag = 0; } ## else nothing changes } else{ ## Did we just enter a clear range? if($qual->[$i]>=$threshold){ ## then set the range flag! $rangeFlag = $i; } ## else nothing changes } } ## Did we exit the last clear range? if($rangeFlag){ my $i = scalar(@$qual); ## Log the range my $range; $range->{end} = $i-1; $range->{start} = $rangeFlag; $range->{length} = $i - $rangeFlag; push @{$self->{_ranges}}, $range; } 1; } sub _empty_cache { my $self = shift; undef $self->{_ranges}; } ################## deprecated methods ################## sub trace_indices { my $self = shift; return $self->named_meta('trace'); } sub trace_index_at { my ($self, $val) =@_; return shift @{$self->named_submeta('trace', $val, $val)}; } sub sub_trace_index { my $self = shift; return $self->named_submeta('trace', @_); } sub qualat { my ($self, $val) =@_; return shift @{$self->submeta($val, $val)}; } sub baseat { my ($self,$val) = @_; return $self->subseq($val,$val); } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/RichSeq.pm�����������������������������������������������������������������000444��000766��000024�� 24452�13155576320� 16677� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::RichSeq # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::RichSeq - Module implementing a sequence created from a rich sequence database entry =head1 SYNOPSIS See L<Bio::Seq::RichSeqI> and documentation of methods. =head1 DESCRIPTION This module implements Bio::Seq::RichSeqI, an interface for sequences created from or created for entries from/of rich sequence databanks, like EMBL, GenBank, and SwissProt. Methods added to the Bio::SeqI interface therefore focus on databank-specific information. Note that not every rich databank format may use all of the properties provided. For more information, please see the relevant =head1 Implemented Interfaces This class implementes the following interfaces. =over 4 =item L<Bio::Seq::RichSeqI> Note that this includes implementing L<Bio::PrimarySeqI> and L<Bio::SeqI>, specifically via L<Bio::Seq> and L<Bio::PrimarySeq>. Please review the documentation for those modules on implementation details relevant to those interfaces, as well as the ones below. =item L<Bio::IdentifiableI> =item L<Bio::DescribableI> =item L<Bio::AnnotatableI> =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::RichSeq; use vars qw($AUTOLOAD); use strict; use base qw(Bio::Seq Bio::Seq::RichSeqI); =head2 new Title : new Usage : $seq = Bio::Seq::RichSeq->new( -seq => 'ATGGGGGTGGTGGTACCCT', -id => 'human_id', -accession_number => 'AL000012', ); Function: Returns a new seq object from basic constructors, being a string for the sequence and strings for id and accession_number Returns : a new Bio::Seq::RichSeq object =cut sub new { # standard new call.. my($caller,@args) = @_; my $self = $caller->SUPER::new(@args); $self->{'_dates'} = []; $self->{'_secondary_accession'} = []; my ($dates, $xtra, $sv, $keywords, $pid, $mol, $division ) = $self->_rearrange([qw(DATES SECONDARY_ACCESSIONS SEQ_VERSION KEYWORDS PID MOLECULE DIVISION )], @args); defined $division && $self->division($division); defined $mol && $self->molecule($mol); if(defined($keywords)) { if(ref($keywords) && (ref($keywords) eq "ARRAY")) { $self->add_keyword(@$keywords); } else { # got a string - use the old API $self->keywords($keywords); } } defined $sv && $self->seq_version($sv); defined $pid && $self->pid($pid); if( defined $dates ) { if( ref($dates) eq "ARRAY" ) { foreach ( @$dates) { $self->add_date($_); } } else { $self->add_date($dates); } } if( defined $xtra ) { if( ref($xtra) eq "ARRAY" ) { foreach ( @$xtra) { $self->add_secondary_accession($_); } } else { $self->add_secondary_accession($xtra); } } return $self; } =head2 division Title : division Usage : $obj->division($newval) Function: Returns : value of division Args : newvalue (optional) =cut sub division { my $obj = shift; if( @_ ) { my $value = shift; $obj->{'_division'} = $value; } return $obj->{'_division'}; } =head2 molecule Title : molecule Usage : $obj->molecule($newval) Function: Returns : type of molecule (DNA, mRNA) Args : newvalue (optional) =cut sub molecule { my $obj = shift; if( @_ ) { my $value = shift; $obj->{'_molecule'} = $value; } return $obj->{'_molecule'}; } =head2 add_date Title : add_date Usage : $self->add_date($datestr) Function: adds one or more dates This implementation stores dates as keyed annotation, the key being 'date_changed'. You can take advantage of this fact when accessing the annotation collection directly. Example : Returns : Args : a date string or an array of such strings =cut sub add_date { return shift->_add_annotation_value('date_changed',@_); } =head2 get_dates Title : get_dates Usage : my @dates = $seq->get_dates; Function: Get the dates of the sequence (usually, when it was created and changed. Returns : an array of date strings Args : =cut sub get_dates{ return shift->_get_annotation_values('date_changed'); } =head2 pid Title : pid Usage : my $pid = $seq->pid(); Function: Get (and set, depending on the implementation) the PID property for the sequence. Returns : a string Args : =cut sub pid{ my $self = shift; return $self->{'_pid'} = shift if @_; return $self->{'_pid'}; } =head2 accession Title : accession Usage : $obj->accession($newval) Function: Whilst the underlying sequence object does not have an accession, so we need one here. In this implementation this is merely a synonym for accession_number(). Example : Returns : value of accession Args : newvalue (optional) =cut sub accession { my ($obj,@args) = @_; return $obj->accession_number(@args); } =head2 add_secondary_accession Title : add_secondary_accession Usage : $self->add_domment($ref) Function: adds a secondary_accession This implementation stores secondary accession numbers as keyed annotation, the key being 'secondary_accession'. You can take advantage of this fact when accessing the annotation collection directly. Example : Returns : Args : a string or an array of strings =cut sub add_secondary_accession { return shift->_add_annotation_value('secondary_accession',@_); } =head2 get_secondary_accessions Title : get_secondary_accessions Usage : my @acc = $seq->get_secondary_accessions(); Function: Get the secondary accession numbers as strings. Returns : An array of strings Args : none =cut sub get_secondary_accessions{ return shift->_get_annotation_values('secondary_accession'); } =head2 seq_version Title : seq_version Usage : $obj->seq_version($newval) Function: Get/set the sequence version Returns : value of seq_version (a scalar) Args : on set, new value (a scalar or undef, optional) Note : this differs from Bio::PrimarySeq version() in that this explicitly refers to the sequence record version one would find in a typical sequence file. =cut sub seq_version{ my $self = shift; return $self->{'_seq_version'} = shift if @_; return $self->{'_seq_version'}; } =head2 add_keyword Title : add_keyword Usage : $obj->add_keyword($newval) Function: Add a new keyword to the annotation of the sequence. This implementation stores keywords as keyed annotation, the key being 'keyword'. You can take advantage of this fact when accessing the annotation collection directly. Returns : Args : value to be added (optional) (a string) =cut sub add_keyword { return shift->_add_annotation_value('keyword',@_); } =head2 get_keywords Title : get_keywords Usage : $obj->get_keywords($newval) Function: Get the keywords for this sequence as an array of strings. Returns : an array of strings Args : =cut sub get_keywords { return shift->_get_annotation_values('keyword'); } =head1 Private methods and synonyms for backward compatibility =cut =head2 _add_annotation_value Title : _add_annotation_value Usage : Function: Adds a value to the annotation collection under the specified key. Note that this is not a public method. Returns : Args : key (a string), value(s) (one or more scalars) =cut sub _add_annotation_value{ my $self = shift; my $key = shift; foreach my $val (@_) { $self->annotation->add_Annotation( Bio::Annotation::SimpleValue->new(-tagname => $key, -value => $val) ); } } =head2 _get_annotation_values Title : _get_annotation_values Usage : Function: Gets the values of a specific annotation as identified by the key from the annotation collection. Note that this is not a public method. Example : Returns : an array of strings Args : the key (a string) =cut sub _get_annotation_values{ my $self = shift; return map { $_->value(); } $self->annotation->get_Annotations(shift); } # ## ### Deprecated methods kept for ease of transition ## # sub keywords { my $self = shift; # have we been called in set mode? if(@_) { # yes; translate to the new API foreach my $kwd (@_) { $self->add_keyword(split(/\s*;\s*/,$kwd)); } } else { # no; translate read-only to the new API return join("; ",$self->get_keywords()); } } sub each_date { my ($self) = @_; $self->warn("Deprecated method... please use get_dates"); return $self->get_dates; } sub each_secondary_accession { my ($self) = @_; $self->warn("each_secondary_accession - deprecated method. use get_secondary_accessions"); return $self->get_secondary_accessions; } sub sv { my ($obj,$value) = @_; $obj->warn("sv - deprecated method. use seq_version"); $obj->seq_version($value); } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/RichSeqI.pm����������������������������������������������������������������000444��000766��000024�� 12663�13155576320� 17011� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::RichSeqI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::RichSeqI - interface for sequences from rich data sources, mostly databases =head1 SYNOPSIS @secondary = $richseq->get_secondary_accessions; $division = $richseq->division; $mol = $richseq->molecule; @dates = $richseq->get_dates; $seq_version = $richseq->seq_version; $pid = $richseq->pid; @keywords = $richseq->get_keywords; =head1 DESCRIPTION This interface extends the L<Bio::SeqI> interface to give additional functionality to sequences with richer data sources, in particular from database sequences (EMBL, GenBank and Swissprot). For a general implementation, please see the documentation for L<Bio::Seq::RichSeq>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::RichSeqI; use strict; use base qw(Bio::SeqI); =head2 get_secondary_accessions Title : get_secondary_accessions Usage : Function: Get the secondary accessions for a sequence. An implementation that allows modification of this array property should provide the methods add_secondary_accession and remove_secondary_accessions, with obvious purpose. Example : Returns : an array of strings Args : none =cut sub get_secondary_accessions{ my ($self,@args) = @_; $self->throw("hit get_secondary_accessions in interface definition - error"); } =head2 division Title : division Usage : Function: Get (and set, depending on the implementation) the division for a sequence. Examples from GenBank are PLN (plants), PRI (primates), etc. Example : Returns : a string Args : =cut sub division{ my ($self,@args) = @_; $self->throw("hit division in interface definition - error"); } =head2 molecule Title : molecule Usage : Function: Get (and set, depending on the implementation) the molecule type for the sequence. This is not necessarily the same as Bio::PrimarySeqI::alphabet(), because it is databank-specific. Example : Returns : a string Args : =cut sub molecule{ my ($self,@args) = @_; $self->throw("hit molecule in interface definition - error"); } =head2 pid Title : pid Usage : Function: Get (and set, depending on the implementation) the PID property for the sequence. Example : Returns : a string Args : =cut sub pid { my ($self,@args) = @_; $self->throw("hit pid in interface definition - error"); } =head2 get_dates Title : get_dates Usage : Function: Get (and set, depending on the implementation) the dates the databank entry specified for the sequence An implementation that allows modification of this array property should provide the methods add_date and remove_dates, with obvious purpose. Example : Returns : an array of strings Args : =cut sub get_dates{ my ($self,@args) = @_; $self->throw("hit get_dates in interface definition - error"); } =head2 seq_version Title : seq_version Usage : Function: Get (and set, depending on the implementation) the version string of the sequence. Example : Returns : a string Args : Note : this differs from Bio::PrimarySeq version() in that this explicitly refers to the sequence record version one would find in a typical sequence file. It is up to the implementation whether this is set separately or falls back to the more generic Bio::Seq::version() =cut sub seq_version{ my ($self,@args) = @_; $self->throw("hit seq_version in interface definition - error"); } =head2 get_keywords Title : get_keywords Usage : $obj->get_keywords() Function: Get the keywords for this sequence object. An implementation that allows modification of this array property should provide the methods add_keyword and remove_keywords, with obvious purpose. Returns : an array of strings Args : =cut sub get_keywords { my ($self) = @_; $self->throw("hit keywords in interface definition - error"); } 1; �����������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/SeqBuilder.pm��������������������������������������������������������������000444��000766��000024�� 42367�13155576320� 17405� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::SeqBuilder # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp at gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Seq::SeqBuilder - Configurable object builder for sequence stream parsers =head1 SYNOPSIS use Bio::SeqIO; # usually you won't instantiate this yourself - a SeqIO object - # you will have one already my $seqin = Bio::SeqIO->new(-fh => \*STDIN, -format => "genbank"); my $builder = $seqin->sequence_builder(); # if you need only sequence, id, and description (e.g. for # conversion to FASTA format): $builder->want_none(); $builder->add_wanted_slot('display_id','desc','seq'); # if you want everything except the sequence and features $builder->want_all(1); # this is the default if it's untouched $builder->add_unwanted_slot('seq','features'); # if you want only human sequences shorter than 5kb and skip all # others $builder->add_object_condition(sub { my $h = shift; return 0 if $h->{'-length'} > 5000; return 0 if exists($h->{'-species'}) && ($h->{'-species'}->binomial() ne "Homo sapiens"); return 1; }); # when you are finished with configuring the builder, just use # the SeqIO API as you would normally while(my $seq = $seqin->next_seq()) { # do something } =head1 DESCRIPTION This is an implementation of L<Bio::Factory::ObjectBuilderI> used by parsers of rich sequence streams. It provides for a relatively easy-to-use configurator of the parsing flow. Configuring the parsing process may be for you if you need much less information, or much less sequence, than the stream actually contains. Configuration can in both cases speed up the parsing time considerably, because unwanted sections or the rest of unwanted sequences are skipped over by the parser. This configuration could also conserve memory if you're running out of available RAM. See the methods of the class-specific implementation section for further documentation of what can be configured. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::SeqBuilder; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root Bio::Factory::ObjectBuilderI); my %slot_param_map = ("add_SeqFeature" => "features", ); my %param_slot_map = ("features" => "add_SeqFeature", ); =head2 new Title : new Usage : my $obj = Bio::Seq::SeqBuilder->new(); Function: Builds a new Bio::Seq::SeqBuilder object Returns : an instance of Bio::Seq::SeqBuilder Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'wanted_slots'} = []; $self->{'unwanted_slots'} = []; $self->{'object_conds'} = []; $self->{'_objhash'} = {}; $self->want_all(1); return $self; } =head1 Methods for implementing L<Bio::Factory::ObjectBuilderI> =cut =head2 want_slot Title : want_slot Usage : Function: Whether or not the object builder wants to populate the specified slot of the object to be built. The slot can be specified either as the name of the respective method, or the initialization parameter that would be otherwise passed to new() of the object to be built. Note that usually only the parser will call this method. Use add_wanted_slots and add_unwanted_slots for configuration. Example : Returns : TRUE if the object builder wants to populate the slot, and FALSE otherwise. Args : the name of the slot (a string) =cut sub want_slot{ my ($self,$slot) = @_; my $ok = 0; $slot = substr($slot,1) if substr($slot,0,1) eq '-'; if($self->want_all()) { foreach ($self->get_unwanted_slots()) { # this always overrides in want-all mode return 0 if($slot eq $_); } if(! exists($self->{'_objskel'})) { $self->{'_objskel'} = $self->sequence_factory->create_object(); } if(exists($param_slot_map{$slot})) { $ok = $self->{'_objskel'}->can($param_slot_map{$slot}); } else { $ok = $self->{'_objskel'}->can($slot); } return $ok if $ok; # even if the object 'cannot' do this slot, it might have been # added to the list of wanted slot, so carry on } foreach ($self->get_wanted_slots()) { if($slot eq $_) { $ok = 1; last; } } return $ok; } =head2 add_slot_value Title : add_slot_value Usage : Function: Adds one or more values to the specified slot of the object to be built. Naming the slot is the same as for want_slot(). The object builder may further filter the content to be set, or even completely ignore the request. If this method reports failure, the caller should not add more values to the same slot. In addition, the caller may find it appropriate to abandon the object being built altogether. This implementation will allow the caller to overwrite the return value from want_slot(), because the slot is not checked against want_slot(). Note that usually only the parser will call this method, but you may call it from anywhere if you know what you are doing. A derived class may be used to further manipulate the value to be added. Example : Returns : TRUE on success, and FALSE otherwise Args : the name of the slot (a string) parameters determining the value to be set OR alternatively, a list of slotname/value pairs in the style of named parameters as they would be passed to new(), where each element at an even index is the parameter (slot) name starting with a dash, and each element at an odd index is the value of the preceding name. =cut sub add_slot_value{ my ($self,$slot,@args) = @_; my $h = $self->{'_objhash'}; return unless $h; # multiple named parameter variant of calling? if((@args > 1) && (@args % 2) && (substr($slot,0,1) eq '-')) { unshift(@args, $slot); while(@args) { my $key = shift(@args); $h->{$key} = shift(@args); } } else { if($slot eq 'add_SeqFeature') { $slot = '-'.$slot_param_map{$slot}; $h->{$slot} = [] unless $h->{$slot}; push(@{$h->{$slot}}, @args); } else { $slot = '-'.$slot unless substr($slot,0,1) eq '-'; $h->{$slot} = $args[0]; } } return 1; } =head2 want_object Title : want_object Usage : Function: Whether or not the object builder is still interested in continuing with the object being built. If this method returns FALSE, the caller should not add any more values to slots, or otherwise risks that the builder throws an exception. In addition, make_object() is likely to return undef after this method returned FALSE. Note that usually only the parser will call this method. Use add_object_condition for configuration. Example : Returns : TRUE if the object builder wants to continue building the present object, and FALSE otherwise. Args : none =cut sub want_object{ my $self = shift; my $ok = 1; foreach my $cond ($self->get_object_conditions()) { $ok = &$cond($self->{'_objhash'}); last unless $ok; } delete $self->{'_objhash'} unless $ok; return $ok; } =head2 make_object Title : make_object Usage : Function: Get the built object. This method is allowed to return undef if no value has ever been added since the last call to make_object(), or if want_object() returned FALSE (or would have returned FALSE) before calling this method. For an implementation that allows consecutive building of objects, a caller must call this method once, and only once, between subsequent objects to be built. I.e., a call to make_object implies 'end_object.' Example : Returns : the object that was built Args : none =cut sub make_object{ my $self = shift; my $obj; if(exists($self->{'_objhash'}) && %{$self->{'_objhash'}}) { $obj = $self->sequence_factory->create_object(%{$self->{'_objhash'}}); } $self->{'_objhash'} = {}; # reset return $obj; } =head1 Implementation specific methods These methods allow one to conveniently configure this sequence object builder as to which slots are desired, and under which circumstances a sequence object should be abandoned altogether. The default mode is want_all(1), which means the builder will report all slots as wanted that the object created by the sequence factory supports. You can add specific slots you want through add_wanted_slots(). In most cases, you will want to call want_none() before in order to relax zero acceptance through a list of wanted slots. Alternatively, you can add specific unwanted slots through add_unwanted_slots(). In this case, you will usually want to call want_all(1) before (which is the default if you never touched the builder) to restrict unrestricted acceptance. I.e., want_all(1) means want all slots except for the unwanted, and want_none() means only those explicitly wanted. If a slot is in both the unwanted and the wanted list, the following rules hold. In want-all mode, the unwanted list overrules. In want-none mode, the wanted list overrides the unwanted list. If this is confusing to you, just try to avoid having slots at the same time in the wanted and the unwanted lists. =cut =head2 get_wanted_slots Title : get_wanted_slots Usage : $obj->get_wanted_slots($newval) Function: Get the list of wanted slots Example : Returns : a list of strings Args : =cut sub get_wanted_slots{ my $self = shift; return @{$self->{'wanted_slots'}}; } =head2 add_wanted_slot Title : add_wanted_slot Usage : Function: Adds the specified slots to the list of wanted slots. Example : Returns : TRUE Args : an array of slot names (strings) =cut sub add_wanted_slot{ my ($self,@slots) = @_; my $myslots = $self->{'wanted_slots'}; foreach my $slot (@slots) { if(! grep { $slot eq $_; } @$myslots) { push(@$myslots, $slot); } } return 1; } =head2 remove_wanted_slots Title : remove_wanted_slots Usage : Function: Removes all wanted slots added previously through add_wanted_slots(). Example : Returns : the previous list of wanted slot names Args : none =cut sub remove_wanted_slots{ my $self = shift; my @slots = $self->get_wanted_slots(); $self->{'wanted_slots'} = []; return @slots; } =head2 get_unwanted_slots Title : get_unwanted_slots Usage : $obj->get_unwanted_slots($newval) Function: Get the list of unwanted slots. Example : Returns : a list of strings Args : none =cut sub get_unwanted_slots{ my $self = shift; return @{$self->{'unwanted_slots'}}; } =head2 add_unwanted_slot Title : add_unwanted_slot Usage : Function: Adds the specified slots to the list of unwanted slots. Example : Returns : TRUE Args : an array of slot names (strings) =cut sub add_unwanted_slot{ my ($self,@slots) = @_; my $myslots = $self->{'unwanted_slots'}; foreach my $slot (@slots) { if(! grep { $slot eq $_; } @$myslots) { push(@$myslots, $slot); } } return 1; } =head2 remove_unwanted_slots Title : remove_unwanted_slots Usage : Function: Removes the list of unwanted slots added previously through add_unwanted_slots(). Example : Returns : the previous list of unwanted slot names Args : none =cut sub remove_unwanted_slots{ my $self = shift; my @slots = $self->get_unwanted_slots(); $self->{'unwanted_slots'} = []; return @slots; } =head2 want_none Title : want_none Usage : Function: Disables all slots. After calling this method, want_slot() will return FALSE regardless of slot name. This is different from removed_wanted_slots() in that it also sets want_all() to FALSE. Note that it also resets the list of unwanted slots in order to avoid slots being in both lists. Example : Returns : TRUE Args : none =cut sub want_none{ my $self = shift; $self->want_all(0); $self->remove_wanted_slots(); $self->remove_unwanted_slots(); return 1; } =head2 want_all Title : want_all Usage : $obj->want_all($newval) Function: Whether or not this sequence object builder wants to populate all slots that the object has. Whether an object supports a slot is generally determined by what can() returns. You can add additional 'virtual' slots by calling add_wanted_slot. This will be ON by default. Call $obj->want_none() to disable all slots. Example : Returns : TRUE if this builder wants to populate all slots, and FALSE otherwise. Args : on set, new value (a scalar or undef, optional) =cut sub want_all{ my $self = shift; return $self->{'want_all'} = shift if @_; return $self->{'want_all'}; } =head2 get_object_conditions Title : get_object_conditions Usage : Function: Get the list of conditions an object must meet in order to be 'wanted.' See want_object() for where this is used. Conditions in this implementation are closures (anonymous functions) which are passed one parameter, a hash reference the keys of which are equal to initialization parameters. The closure must return TRUE to make the object 'wanted.' Conditions will be implicitly ANDed. Example : Returns : a list of closures Args : none =cut sub get_object_conditions{ my $self = shift; return @{$self->{'object_conds'}}; } =head2 add_object_condition Title : add_object_condition Usage : Function: Adds a condition an object must meet in order to be 'wanted.' See want_object() for where this is used. Conditions in this implementation must be closures (anonymous functions). These will be passed one parameter, which is a hash reference with the sequence object initialization parameters being the keys. Conditions are implicitly ANDed. If you want other operators, perform those tests inside of one closure instead of multiple. This will also be more efficient. Example : Returns : TRUE Args : the list of conditions =cut sub add_object_condition{ my ($self,@conds) = @_; if(grep { ref($_) ne 'CODE'; } @conds) { $self->throw("conditions against which to validate an object ". "must be anonymous code blocks"); } push(@{$self->{'object_conds'}}, @conds); return 1; } =head2 remove_object_conditions Title : remove_object_conditions Usage : Function: Removes the conditions an object must meet in order to be 'wanted.' Example : Returns : The list of previously set conditions (an array of closures) Args : none =cut sub remove_object_conditions{ my $self = shift; my @conds = $self->get_object_conditions(); $self->{'object_conds'} = []; return @conds; } =head1 Methods to control what type of object is built =cut =head2 sequence_factory Title : sequence_factory Usage : $obj->sequence_factory($newval) Function: Get/set the sequence factory to be used by this object builder. Example : Returns : the Bio::Factory::SequenceFactoryI implementing object to use Args : on set, new value (a Bio::Factory::SequenceFactoryI implementing object or undef, optional) =cut sub sequence_factory{ my $self = shift; if(@_) { delete $self->{'_objskel'}; return $self->{'sequence_factory'} = shift; } return $self->{'sequence_factory'}; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/SeqFactory.pm��������������������������������������������������������������000444��000766��000024�� 7663�13155576320� 17406� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::SeqFactory # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::SeqFactory - Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory =head1 SYNOPSIS use Bio::Seq::SeqFactory; my $factory = Bio::Seq::SeqFactory->new(); my $primaryseq = $factory->create( -seq => 'WYRAVLC', -id => 'name' ); # Create Bio::Seq instead of Bio::PrimarySeq objects: my $factory = Bio::Seq::SeqFactory->new( -type => 'Bio::Seq' ); =head1 DESCRIPTION This object will build L<Bio::PrimarySeqI> and L<Bio::SeqI> objects generically. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::SeqFactory; use strict; use base qw(Bio::Root::Root Bio::Factory::SequenceFactoryI); =head2 new Title : new Usage : my $obj = Bio::Seq::SeqFactory->new(); Function: Builds a new Bio::Seq::SeqFactory object Returns : Bio::Seq::SeqFactory Args : -type => string, name of a PrimarySeqI derived class This is optional. Default=Bio::PrimarySeq. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($type) = $self->_rearrange([qw(TYPE)], @args); if( ! defined $type ) { $type = 'Bio::PrimarySeq'; } $self->type($type); return $self; } =head2 create Title : create Usage : my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name'); Function: Instantiates new Bio::SeqI (or one of its child classes) This object allows us to genericize the instantiation of sequence objects. Returns : Bio::PrimarySeq object (default) The return type is configurable using new(-type =>"..."). Args : initialization parameters specific to the type of sequence object we want. Typically -seq => $str, -display_id => $name =cut sub create { my ($self,@args) = @_; return $self->type->new(-verbose => $self->verbose, @args); } =head2 type Title : type Usage : $obj->type($newval) Function: Returns : value of type Args : newvalue (optional) =cut sub type { my ($self, $value) = @_; if (defined $value) { eval "require $value"; if( $@ ) { $self->throw("$@: Unrecognized Sequence type for SeqFactory '$value'");} my $a = bless {},$value; unless( $a->isa('Bio::PrimarySeqI') || $a->isa('Bio::Seq::QualI' ) ) { $self->throw("Must provide a valid Bio::PrimarySeqI or Bio::Seq::QualI or child class to SeqFactory Not $value"); } $self->{'type'} = $value; } return $self->{'type'}; } 1; �����������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/SeqFastaSpeedFactory.pm����������������������������������������������������000444��000766��000024�� 7566�13155576320� 21350� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::SeqFastaSpeedFactory # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::SeqFastaSpeedFactory - Rapid creation of Bio::Seq objects through a factory =head1 SYNOPSIS use Bio::Seq::SeqFastaSpeedFactory; my $factory = Bio::Seq::SeqFastaSpeedFactory->new(); my $seq = $factory->create( -seq => 'WYRAVLC', -id => 'name' ); =head1 DESCRIPTION This factory was designed to build Bio::Seq objects as quickly as possible, but is not as generic as L<Bio::Seq::SeqFactory>. It can be used to create sequences from non-rich file formats. The L<Bio::SeqIO::fasta> sequence parser uses this factory. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::SeqFastaSpeedFactory; use strict; use Bio::Seq; use Bio::PrimarySeq; use base qw(Bio::Root::Root Bio::Factory::SequenceFactoryI); =head2 new Title : new Usage : my $obj = Bio::Seq::SeqFastaSpeedFactory->new(); Function: Builds a new Bio::Seq::SeqFastaSpeedFactory object Returns : Bio::Seq::SeqFastaSpeedFactory Args : None =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); return $self; } =head2 create Title : create Usage : my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name'); Function: Instantiates a new Bio::Seq object, correctly built but very fast, knowing stuff about Bio::PrimarySeq and Bio::Seq Returns : A Bio::Seq object Args : Initialization parameters for the sequence object we want: -id -primary_id -display_id -desc -seq -alphabet =cut sub create { my ($self,@args) = @_; my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $sequence = $param{'-seq'}; my $fulldesc = $param{'-desc'}; my $id = defined $param{'-id'} ? $param{'-id'} : $param{'-primary_id'}; my $alphabet = $param{'-alphabet'}; my $seq = bless {}, 'Bio::Seq'; my $t_pseq = $seq->{'primary_seq'} = bless {}, 'Bio::PrimarySeq'; $t_pseq->{'seq'} = $sequence; $t_pseq->{'length'} = CORE::length($sequence); $t_pseq->{'desc'} = $fulldesc; $t_pseq->{'display_id'} = $id; $t_pseq->{'primary_id'} = $id; $seq->{'primary_id'} = $id; # currently Bio::Seq does not delegate this if( $sequence and !$alphabet ) { $t_pseq->_guess_alphabet(); } elsif ( $sequence and $alphabet ) { $t_pseq->{'alphabet'} = $alphabet; } return $seq; } 1; ������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/SeqWithQuality.pm����������������������������������������������������������000444��000766��000024�� 73407�13155576320� 20302� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::QualI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chad Matsalla <bioinformatics@dieselwurks.com # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::SeqWithQuality - Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead! =head1 SYNOPSIS use Bio::PrimarySeq; use Bio::Seq::PrimaryQual; use Bio::Seq::SeqWithQuality; # make from memory my $qual = Bio::Seq::SeqWithQuality->new ( -qual => '10 20 30 40 50 50 20 10', -seq => 'ATCGATCG', -id => 'human_id', -accession_number => 'AL000012', ); # make from objects # first, make a PrimarySeq object my $seqobj = Bio::PrimarySeq->new ( -seq => 'atcgatcg', -id => 'GeneFragment-12', -accession_number => 'X78121', -alphabet => 'dna' ); # now make a PrimaryQual object my $qualobj = Bio::Seq::PrimaryQual->new ( -qual => '10 20 30 40 50 50 20 10', -id => 'GeneFragment-12', -accession_number => 'X78121', -alphabet => 'dna' ); # now make the SeqWithQuality object my $swqobj = Bio::Seq::SeqWithQuality->new ( -seq => $seqobj, -qual => $qualobj ); # done! $swqobj->id(); # the id of the SeqWithQuality object # may not match the the id of the sequence or # of the quality (check the pod, luke) $swqobj->seq(); # the sequence of the SeqWithQuality object $swqobj->qual(); # the quality of the SeqWithQuality object # to get out parts of the sequence. print "Sequence ", $seqobj->id(), " with accession ", $seqobj->accession, " and desc ", $seqobj->desc, "\n"; $string2 = $seqobj->subseq(1,40); =head1 DESCRIPTION This object stores base quality values together with the sequence string. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics@dieselwurks.com =head1 CONTRIBUTORS Jason Stajich, jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Seq::SeqWithQuality; use strict; use Bio::PrimarySeq; use Bio::Seq::PrimaryQual; use base qw(Bio::Root::Root Bio::PrimarySeqI Bio::Seq::QualI); =head2 new() Title : new() Usage : $qual = Bio::Seq::SeqWithQuality ->new ( -qual => '10 20 30 40 50 50 20 10', -seq => 'ATCGATCG', -id => 'human_id', -accession_number => 'AL000012', -trace_indices => '0 5 10 15 20 25 30 35' ); Function: Returns a new Bio::Seq::SeqWithQual object from basic constructors. Returns : a new Bio::Seq::PrimaryQual object Args : -qual can be a quality string (see Bio::Seq::PrimaryQual for more information on this) or a reference to a Bio::Seq::PrimaryQual object. -seq can be a sequence string (see Bio::PrimarySeq for more information on this) or a reference to a Bio::PrimaryQual object. -seq, -id, -accession_number, -primary_id, -desc, -id behave like this: 1. if they are provided on construction of the Bio::Seq::SeqWithQuality they will be set as the descriptors for the object unless changed by one of the following mechanisms: a) $obj->set_common_descriptors() is used and both the -seq and the -qual object have the same descriptors. These common descriptors will then become the descriptors for the Bio::Seq::SeqWithQual object. b) the descriptors are manually set using the seq(), id(), desc(), or accession_number(), primary_id(), 2. if no descriptors are provided, the new() constructor will see if the descriptor used in the PrimarySeq and in the PrimaryQual objects match. If they do, they will become the descriptors for the SeqWithQuality object. To eliminate ambiguity, I strongly suggest you set the descriptors manually on construction of the object. Really. -trace_indices : a space_delimited list of trace indices (where would the peaks be drawn if this list of qualities was to be plotted?) =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); # default: turn OFF the warnings $self->{suppress_warnings} = 1; my($qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet,$trace_indices) = $self->_rearrange([qw( QUAL SEQ DISPLAY_ID ACCESSION_NUMBER PRIMARY_ID DESC ID ALPHABET TRACE_INDICES )], @args); # Deal with the ID if ( defined $id && defined $given_id ) { if( $id ne $given_id ) { $self->throw("Provided both id and display_id constructor functions. [$id] [$given_id]"); } } if( defined $given_id ) { $self->display_id($given_id); $id = $given_id; } # Import sequence first if (!$seq) { my $id; unless ($self->{suppress_warnings} == 1) { $self->warn("You did not provide sequence information during the ". "construction of a Bio::Seq::SeqWithQuality object. Sequence ". "components for this object will be empty."); } if (!$alphabet) { $self->throw("If you want me to create a PrimarySeq object for your ". "empty sequence <boggle> you must specify a -alphabet to satisfy ". "the constructor requirements for a Bio::PrimarySeq object with no ". "sequence. Read the POD for it, luke."); } $self->{seq_ref} = Bio::PrimarySeq->new( -seq => "", -accession_number => $acc, -primary_id => $pid, -desc => $desc, -display_id => $id, -alphabet => $alphabet ); } elsif ($seq->isa('Bio::PrimarySeqI') || $seq->isa('Bio::SeqI')) { $self->{seq_ref} = $seq; } elsif (ref($seq)) { $self->throw("You passed a seq argument into a SeqWithQUality object and". " it was a reference ($seq) which did not inherit from Bio::SeqI or ". "Bio::PrimarySeqI. I don't know what to do with this!"); } else { my $seqobj = Bio::PrimarySeq->new( -seq => $seq, -accession_number => $acc, -primary_id => $pid, -desc => $desc, -display_id => $id ); $self->{seq_ref} = $seqobj; } # Then import the quality scores if (!defined($qual)) { $self->{qual_ref} = Bio::Seq::PrimaryQual->new( -qual => "", -accession_number => $acc, -primary_id => $pid, -desc => $desc, -display_id => $id, ); } elsif (ref($qual) eq "Bio::Seq::PrimaryQual") { $self->{qual_ref} = $qual; } else { my $qualobj = Bio::Seq::PrimaryQual->new( -qual => $qual, -accession_number => $acc, -primary_id => $pid, -desc => $desc, -display_id => $id, -trace_indices => $trace_indices ); $self->{qual_ref} = $qualobj; } # Now try to set the descriptors for this object $self->_set_descriptors($qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet); $self->length(); $self->deprecated("deprecated class - use Bio::Seq::Quality instead"); return $self; } =head2 _common_id() Title : _common_id() Usage : $common_id = $self->_common_id(); Function: Compare the display_id of {qual_ref} and {seq_ref}. Returns : Nothing if they don't match. If they do return {seq_ref}->display_id() Args : None. =cut #' sub _common_id { my $self = shift; return if (!$self->{seq_ref} || !$self->{qual_ref}); my $sid = $self->{seq_ref}->display_id(); return if (!$sid); return if (!$self->{qual_ref}->display_id()); return $sid if ($sid eq $self->{qual_ref}->display_id()); # should this become a warning? # print("ids $sid and $self->{qual_ref}->display_id() do not match. Bummer.\n"); } =head2 _common_display_id() Title : _common_id() Usage : $common_id = $self->_common_display_id(); Function: Compare the display_id of {qual_ref} and {seq_ref}. Returns : Nothing if they don't match. If they do return {seq_ref}->display_id() Args : None. =cut #' sub _common_display_id { my $self = shift; $self->common_id(); } =head2 _common_accession_number() Title : _common_accession_number() Usage : $common_id = $self->_common_accession_number(); Function: Compare the accession_number() of {qual_ref} and {seq_ref}. Returns : Nothing if they don't match. If they do return {seq_ref}->accession_number() Args : None. =cut #' sub _common_accession_number { my $self = shift; return if ($self->{seq_ref} || $self->{qual_ref}); my $acc = $self->{seq_ref}->accession_number(); # if (!$acc) { print("the seqref has no acc.\n"); } return if (!$acc); # if ($acc eq $self->{qual_ref}->accession_number()) { print("$acc matches ".$self->{qual_ref}->accession_number()."\n"); } return $acc if ($acc eq $self->{qual_ref}->accession_number()); # should this become a warning? # print("accession numbers $acc and $self->{qual_ref}->accession_number() do not match. Bummer.\n"); } =head2 _common_primary_id() Title : _common_primary_id() Usage : $common_primard_id = $self->_common_primary_id(); Function: Compare the primary_id of {qual_ref} and {seq_ref}. Returns : Nothing if they don't match. If they do return {seq_ref}->primary_id() Args : None. =cut #' sub _common_primary_id { my $self = shift; return if ($self->{seq_ref} || $self->{qual_ref}); my $pid = $self->{seq_ref}->primary_id(); return if (!$pid); return $pid if ($pid eq $self->{qual_ref}->primary_id()); # should this become a warning? # print("primary_ids $pid and $self->{qual_ref}->primary_id() do not match. Bummer.\n"); } =head2 _common_desc() Title : _common_desc() Usage : $common_desc = $self->_common_desc(); Function: Compare the desc of {qual_ref} and {seq_ref}. Returns : Nothing if they don't match. If they do return {seq_ref}->desc() Args : None. =cut #' sub _common_desc { my $self = shift; return if ($self->{seq_ref} || $self->{qual_ref}); my $des = $self->{seq_ref}->desc(); return if (!$des); return $des if ($des eq $self->{qual_ref}->desc()); # should this become a warning? # print("descriptions $des and $self->{qual_ref}->desc() do not match. Bummer.\n"); } =head2 set_common_descriptors() Title : set_common_descriptors() Usage : $self->set_common_descriptors(); Function: Compare the descriptors (id,accession_number,display_id, primary_id, desc) for the PrimarySeq and PrimaryQual objects within the SeqWithQuality object. If they match, make that descriptor the descriptor for the SeqWithQuality object. Returns : Nothing. Args : None. =cut sub set_common_descriptors { my $self = shift; return if ($self->{seq_ref} || $self->{qual_ref}); &_common_id(); &_common_display_id(); &_common_accession_number(); &_common_primary_id(); &_common_desc(); } =head2 alphabet() Title : alphabet(); Usage : $molecule_type = $obj->alphabet(); Function: Get the molecule type from the PrimarySeq object. Returns : What what PrimarySeq says the type of the sequence is. Args : None. =cut sub alphabet { my $self = shift; return $self->{seq_ref}->alphabet(); } =head2 display_id() Title : display_id() Usage : $id_string = $obj->display_id(); Function: Returns the display id, aka the common name of the Quality object. The semantics of this is that it is the most likely string to be used as an identifier of the quality sequence, and likely to have "human" readability. The id is equivalent to the ID field of the GenBank/EMBL databanks and the id field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. Notice that $seq->id() maps to this function, mainly for legacy/convience issues. This method sets the display_id for the SeqWithQuality object. Returns : A string Args : If a scalar is provided, it is set as the new display_id for the SeqWithQuality object. Status : Virtual =cut sub display_id { my ($obj,$value) = @_; if( defined $value) { $obj->{'display_id'} = $value; } return $obj->{'display_id'}; } =head2 accession_number() Title : accession_number() Usage : $unique_biological_key = $obj->accession_number(); Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". This method sets the accession_number for the SeqWithQuality object. Returns : A string (the value of accession_number) Args : If a scalar is provided, it is set as the new accession_number for the SeqWithQuality object. Status : Virtual =cut sub accession_number { my( $obj, $acc ) = @_; if (defined $acc) { $obj->{'accession_number'} = $acc; } else { $acc = $obj->{'accession_number'}; $acc = 'unknown' unless defined $acc; } return $acc; } =head2 primary_id() Title : primary_id() Usage : $unique_implementation_key = $obj->primary_id(); Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a way the implementation can control clients can expect one id to map to one object. For sequences with no accession number, this method should return a stringified memory location. This method sets the primary_id for the SeqWithQuality object. Returns : A string. (the value of primary_id) Args : If a scalar is provided, it is set as the new primary_id for the SeqWithQuality object. =cut sub primary_id { my ($obj,$value) = @_; if ($value) { $obj->{'primary_id'} = $value; } return $obj->{'primary_id'}; } =head2 desc() Title : desc() Usage : $qual->desc($newval); _or_ $description = $qual->desc(); Function: Get/set description text for this SeqWithQuality object. Returns : A string. (the value of desc) Args : If a scalar is provided, it is set as the new desc for the SeqWithQuality object. =cut sub desc { # a mechanism to set the disc for the SeqWithQuality object. # probably will be used most often by set_common_features() my ($obj,$value) = @_; if( defined $value) { $obj->{'desc'} = $value; } return $obj->{'desc'}; } =head2 id() Title : id() Usage : $id = $qual->id(); Function: Return the ID of the quality. This should normally be (and actually is in the implementation provided here) just a synonym for display_id(). Returns : A string. (the value of id) Args : If a scalar is provided, it is set as the new id for the SeqWithQuality object. =cut sub id { my ($self,$value) = @_; if (!$self) { $self->throw("no value for self in $value"); } if( defined $value ) { return $self->display_id($value); } return $self->display_id(); } =head2 seq Title : seq() Usage : $string = $obj->seq(); _or_ $obj->seq("atctatcatca"); Function: Returns the sequence that is contained in the imbedded in the PrimarySeq object within the SeqWithQuality object Returns : A scalar (the seq() value for the imbedded PrimarySeq object.) Args : If a scalar is provided, the SeqWithQuality object will attempt to set that as the sequence for the imbedded PrimarySeq object. Otherwise, the value of seq() for the PrimarySeq object is returned. Notes : This is probably not a good idea because you then should call length() to make sure that the sequence and quality are of the same length. Even then, how can you make sure that this sequence belongs with that quality? I provided this to give you rope to hang yourself with. Tie it to a strong device and use a good knot. =cut sub seq { my ($self,$value) = @_; if( defined $value) { $self->{seq_ref}->seq($value); $self->length(); } return $self->{seq_ref}->seq(); } =head2 qual() Title : qual() Usage : @quality_values = @{$obj->qual()}; _or_ $obj->qual("10 10 20 40 50"); Function: Returns the quality as imbedded in the PrimaryQual object within the SeqWithQuality object. Returns : A reference to an array containing the quality values in the PrimaryQual object. Args : If a scalar is provided, the SeqWithQuality object will attempt to set that as the quality for the imbedded PrimaryQual object. Otherwise, the value of qual() for the PrimaryQual object is returned. Notes : This is probably not a good idea because you then should call length() to make sure that the sequence and quality are of the same length. Even then, how can you make sure that this sequence belongs with that quality? I provided this to give you a strong board with which to flagellate yourself. =cut sub qual { my ($self,$value) = @_; if( defined $value) { $self->{qual_ref}->qual($value); # update the lengths $self->length(); } return $self->{qual_ref}->qual(); } =head2 trace_indices() Title : trace_indices() Usage : @trace_indice_values = @{$obj->trace_indices()}; _or_ $obj->trace_indices("10 10 20 40 50"); Function: Returns the trace_indices as imbedded in the Primaryqual object within the SeqWithQualiity object. Returns : A reference to an array containing the trace_indice values in the PrimaryQual object. Args : If a scalar is provided, the SeqWithuQuality object will attempt to set that as the trace_indices for the imbedded PrimaryQual object. Otherwise, the value of trace_indices() for the PrimaryQual object is returned. Notes : This is probably not a good idea because you then should call length() to make sure that the sequence and trace_indices are of the same length. Even then, how can you make sure that this sequence belongs with that trace_indicex? I provided this to give you a strong board with which to flagellate yourself. =cut sub trace_indices { my ($self,$value) = @_; if( defined $value) { $self->{qual_ref}->trace_indices($value); # update the lengths $self->length(); } return $self->{qual_ref}->trace_indices(); } =head2 length() Title : length() Usage : $length = $seqWqual->length(); Function: Get the length of the SeqWithQuality sequence/quality. Returns : Returns the length of the sequence and quality if they are both the same. Returns "DIFFERENT" if they differ. Args : None. =cut sub length { my $self = shift; if (!$self->{seq_ref}) { unless ($self->{suppress_warnings} == 1) { $self->warn("Can't find {seq_ref} here in length()."); } return; } if (!$self->{qual_ref}) { unless ($self->{suppress_warnings} == 1) { $self->warn("Can't find {qual_ref} here in length()."); } return; } my $seql = $self->{seq_ref}->length(); if ($seql != $self->{qual_ref}->length()) { unless ($self->{suppress_warnings} == 1) { $self->warn("Sequence length (".$seql.") is different from quality ". "length (".$self->{qual_ref}->length().") in the SeqWithQuality ". "object. This can only lead to problems later."); } $self->{'length'} = "DIFFERENT"; } else { $self->{'length'} = $seql; } return $self->{'length'}; } =head2 qual_obj Title : qual_obj($different_obj) Usage : $qualobj = $seqWqual->qual_obj(); _or_ $qualobj = $seqWqual->qual_obj($ref_to_primaryqual_obj); Function: Get the PrimaryQual object that is imbedded in the SeqWithQuality object or if a reference to a PrimaryQual object is provided, set this as the PrimaryQual object imbedded in the SeqWithQuality object. Returns : A reference to a Bio::Seq::SeqWithQuality object. =cut sub qual_obj { my ($self,$value) = @_; if (defined($value)) { if (ref($value) eq "Bio::Seq::PrimaryQual") { $self->{qual_ref} = $value; $self->debug("You successfully changed the PrimaryQual object within ". "a SeqWithQuality object. ID's for the SeqWithQuality object may ". "now not be what you expect. Use something like ". "set_common_descriptors() to fix them if you care,"); } else { $self->debug("You tried to change the PrimaryQual object within a ". "SeqWithQuality object but you passed a reference to an object that". " was not a Bio::Seq::PrimaryQual object. Thus your change failed. ". "Sorry.\n"); } } return $self->{qual_ref}; } =head2 seq_obj Title : seq_obj() Usage : $seqobj = $seqWqual->qual_obj(); _or_ $seqobj = $seqWqual->seq_obj($ref_to_primary_seq_obj); Function: Get the PrimarySeq object that is imbedded in the SeqWithQuality object or if a reference to a PrimarySeq object is provided, set this as the PrimarySeq object imbedded in the SeqWithQuality object. Returns : A reference to a Bio::PrimarySeq object. =cut sub seq_obj { my ($self,$value) = @_; if( defined $value) { if (ref($value) eq "Bio::PrimarySeq") { $self->debug("You successfully changed the PrimarySeq object within a". " SeqWithQuality object. ID's for the SeqWithQuality object may now". " not be what you expect. Use something like ". "set_common_descriptors() to fix them if you care,"); } else { $self->debug("You tried to change the PrimarySeq object within a ". "SeqWithQuality object but you passed a reference to an object that". " was not a Bio::PrimarySeq object. Thus your change failed. Sorry.\n"); } } return $self->{seq_ref}; } =head2 _set_descriptors Title : _set_descriptors() Usage : $seqWqual->_qual_obj($qual,$seq,$id,$acc,$pid,$desc,$given_id, $alphabet); Function: Set the descriptors for the SeqWithQuality object. Try to match the descriptors in the PrimarySeq object and in the PrimaryQual object if descriptors were not provided with construction. Returns : Nothing. Args : $qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet as found in the new() method. Notes : Really only intended to be called by the new() method. If you want to invoke a similar function try set_common_descriptors(). =cut sub _set_descriptors { my ($self,$qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet) = @_; my ($c_id,$c_acc,$c_pid,$c_desc); if (!$self->display_id()) { if ($c_id = $self->_common_id() ) { $self->display_id($c_id); } else { if ($self->{seq_ref}) { # print("Using seq_ref to set id to ".$self->{seq_ref}->display_id()."\n"); # ::dumpValue($self->{seq_ref}); $self->display_id($self->{seq_ref}->id()); } elsif ($self->{qual_ref}) { $self->display_id($self->{qual_ref}->id()); } } } if ($acc) { $self->accession_number($acc); } elsif ($c_acc = $self->_common_accession_number() ) { $self->accession_number($c_acc); } if ($pid) { $self->primary_id($pid); } elsif ($c_pid = $self->_common_primary_id() ) { $self->primary_id($c_pid); } if ($desc) { $self->desc($desc); } elsif ($c_desc = $self->_common_desc() ) { $self->desc($c_desc); } } =head2 subseq($start,$end) Title : subseq($start,$end) Usage : $subsequence = $obj->subseq($start,$end); Function: Returns the subseq from start to end, where the first base is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Returns : A string. Args : Two positions. =cut sub subseq { my ($self,@args) = @_; # does a single value work? return $self->{seq_ref}->subseq(@args); } =head2 baseat($position) Title : baseat($position) Usage : $base_at_position_6 = $obj->baseat("6"); Function: Returns a single base at the given position, where the first base is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Returns : A scalar. Args : A position. =cut sub baseat { my ($self,$val) = @_; return $self->{seq_ref}->subseq($val,$val); } =head2 subqual($start,$end) Title : subqual($start,$end) Usage : @qualities = @{$obj->subqual(10,20); Function: returns the quality values from $start to $end, where the first value is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Start cannot be larger than end but can be equal. Returns : A reference to an array. Args : a start position and an end position =cut sub subqual { my ($self,@args) = @_; return $self->{qual_ref}->subqual(@args); } =head2 qualat($position) Title : qualat($position) Usage : $quality = $obj->qualat(10); Function: Return the quality value at the given location, where the first value is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Start cannot be larger than end but can be equal. Returns : A scalar. Args : A position. =cut sub qualat { my ($self,$val) = @_; return $self->{qual_ref}->qualat($val); } =head2 sub_trace_index($start,$end) Title : sub_trace_index($start,$end) Usage : @trace_indices = @{$obj->sub_trace_index(10,20); Function: returns the trace index values from $start to $end, where the first value is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Start cannot be larger than end but can be e_trace_index. Returns : A reference to an array. Args : a start position and an end position =cut sub sub_trace_index { my ($self,@args) = @_; return $self->{qual_ref}->sub_trace_index(@args); } =head2 trace_index_at($position) Title : trace_index_at($position) Usage : $trace_index = $obj->trace_index_at(10); Function: Return the trace_index value at the given location, where the first value is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Start cannot be larger than end but can be etrace_index_. Returns : A scalar. Args : A position. =cut sub trace_index_at { my ($self,$val) = @_; return $self->{qual_ref}->trace_index_at($val); } =head2 to_string() Title : to_string() Usage : $quality = $obj->to_string(); Function: Return a textual representation of what the object contains. For this module, this function will return: qual seq display_id accession_number primary_id desc id length_sequence length_quality Returns : A scalar. Args : None. =cut sub to_string { my ($self,$out,$result) = shift; $out = "qual: ".join(',',@{$self->qual()})."\n"; foreach (qw(seq display_id accession_number primary_id desc id)) { $result = $self->$_(); if (!$result) { $result = "<unset>"; } $out .= "$_: $result\n"; } return $out; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/SequenceTrace.pm�����������������������������������������������������������000555��000766��000024�� 102015�13155576320� 20103� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::SequenceTrace # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chad Matsalla <bioinformatics@dieselwurks.com # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::SequenceTrace - Bioperl object packaging a sequence with its trace =head1 SYNOPSIS # example code here =head1 DESCRIPTION This object stores a sequence with its trace. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics@dieselwurks.com The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Seq::SequenceTrace; use strict; use Bio::Seq::QualI; use Bio::PrimarySeqI; use Bio::PrimarySeq; use Bio::Seq::PrimaryQual; use base qw(Bio::Root::Root Bio::Seq::Quality Bio::Seq::TraceI); =head2 new() Title : new() Usage : $st = Bio::Seq::SequenceTrace->new ( -swq => Bio::Seq::SequenceWithQuality, -trace_a => \@trace_values_for_a_channel, -trace_t => \@trace_values_for_t_channel, -trace_g => \@trace_values_for_g_channel, -trace_c => \@trace_values_for_c_channel, -accuracy_a => \@a_accuracies, -accuracy_t => \@t_accuracies, -accuracy_g => \@g_accuracies, -accuracy_c => \@c_accuracies, -peak_indices => '0 5 10 15 20 25 30 35' ); Function: Returns a new Bio::Seq::SequenceTrace object from basic constructors. Returns : a new Bio::Seq::SequenceTrace object Arguments: I think that these are all describes in the usage above. =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); # default: turn OFF the warnings $self->{suppress_warnings} = 1; my($swq,$peak_indices,$trace_a,$trace_t, $trace_g,$trace_c,$acc_a,$acc_t,$acc_g,$acc_c) = $self->_rearrange([qw( SWQ PEAK_INDICES TRACE_A TRACE_T TRACE_G TRACE_C ACCURACY_A ACCURACY_T ACCURACY_G ACCURACY_C )], @args); # first, deal with the sequence and quality information if ($swq && ref($swq) eq "Bio::Seq::Quality") { $self->{swq} = $swq; } else { $self->throw("A Bio::Seq::SequenceTrace object must be created with a Bio::Seq::Quality object. You provided this type of object: " .ref($swq)); } if (!$acc_a) { # this means that you probably did not provide traces and accuracies # and that they need to be synthesized $self->set_accuracies(); } else { $self->accuracies('a',$acc_a); $self->accuracies('t',$acc_t); $self->accuracies('g',$acc_g); $self->accuracies('c',$acc_c); } if (!$trace_a) { $self->_synthesize_traces(); } else { $self->trace('a',$trace_a); $self->trace('t',$trace_t); $self->trace('g',$trace_g); $self->trace('c',$trace_c); $self->peak_indices($peak_indices); } $self->id($self->seq_obj->id); return $self; } sub swq_obj { my $self = shift; $self->warn('swq_obj() is deprecated: use seq_obj()'); return $self->{swq}; } =head2 trace($base,\@new_values) Title : trace($base,\@new_values) Usage : @trace_Values = @{$obj->trace($base,\@new_values)}; Function: Returns the trace values as a reference to an array containing the trace values. The individual elements of the trace array are not validated and can be any numeric value. Returns : A reference to an array. Status : Arguments: $base : which color channel would you like the trace values for? - $base must be one of "A","T","G","C" \@new_values : a reference to an array of values containing trace data for this base =cut sub trace { my ($self,$base_channel,$values) = @_; if (!$base_channel) { $self->throw('You must provide a valid base channel (atgc) to use trace()'); } $base_channel =~ tr/A-Z/a-z/; if ($base_channel !~ /[acgt]/) { $self->throw('You must provide a valid base channel (atgc) to use trace()'); } if ($values) { if (ref($values) eq "ARRAY") { $self->{trace}->{$base_channel} = $values; } else { my @trace = split(' ',$values); $self->{trace}->{$base_channel} = \@trace; } } if ($self->{trace}->{$base_channel}) { return $self->{trace}->{$base_channel}; } else { return; } } =head2 peak_indices($new_indices) Title : peak_indices($new_indices) Usage : $indices = $obj->peak_indices($new_indices); Function: Return the trace index points for this object. Returns : A scalar Args : If used, the trace indices will be set to the provided value. =cut sub peak_indices { my ($self,$peak_indices)= @_; if ($peak_indices) { if (ref($peak_indices) eq "ARRAY") { $self->{peak_indices} = $peak_indices; } else { my @indices = split(' ',$peak_indices); $self->{peak_indices} = \@indices; } } if (!$self->{peak_indices}) { my @temp = (); $self->{peak_indices} = \@temp; } return $self->{peak_indices}; } =head2 _reset_peak_indices() Title : _rest_peak_indices() Usage : $obj->_reset_peak_indices(); Function: Reset the peak indices. Returns : Nothing. Args : None. Notes : When you create a sub_trace_object, the peak indices will still be pointing to the apporpriate location _in the original trace_. In order to fix this, the initial value must be subtracted from each value here. ie. The first peak index must be "1". =cut sub _reset_peak_indices { my $self = shift; my $length = $self->length(); my $subtractive = $self->peak_index_at(1); my ($original,$new); $self->peak_index_at(1,"null"); for (my $counter=2; $counter<= $length; $counter++) { my $original = $self->peak_index_at($counter); $new = $original - $subtractive; $self->peak_index_at($counter,$new); } return; } =head2 peak_index_at($position) Title : peak_index_at($position) Usage : $peak_index = $obj->peak_index_at($postition); Function: Return the trace iindex point at this position Returns : A scalar Args : If used, the trace index at this position will be set to the provided value. =cut sub peak_index_at { my ($self,$position,$value)= @_; if ($value) { if ($value eq "null") { $self->peak_indices->[$position-1] = "0"; } else { $self->peak_indices->[$position-1] = $value; } } return $self->peak_indices()->[$position-1]; } =head2 alphabet() Title : alphabet(); Usage : $molecule_type = $obj->alphabet(); Function: Get the molecule type from the PrimarySeq object. Returns : What what PrimarySeq says the type of the sequence is. Args : None. =cut sub alphabet { my $self = shift; return $self->{swq}->alphabet; } =head2 display_id() Title : display_id() Usage : $id_string = $obj->display_id(); Function: Returns the display id, aka the common name of the Quality object. The semantics of this is that it is the most likely string to be used as an identifier of the quality sequence, and likely to have "human" readability. The id is equivalent to the ID field of the GenBank/EMBL databanks and the id field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. Notice that $seq->id() maps to this function, mainly for legacy/convience issues. This method sets the display_id for the Quality object. Returns : A string Args : If a scalar is provided, it is set as the new display_id for the Quality object. Status : Virtual =cut sub display_id { my ($self,$value) = @_; if( defined $value) { $self->{swq}->display_id($value); } return $self->{swq}->display_id(); } =head2 accession_number() Title : accession_number() Usage : $unique_biological_key = $obj->accession_number(); Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". This method sets the accession_number for the Quality object. Returns : A string (the value of accession_number) Args : If a scalar is provided, it is set as the new accession_number for the Quality object. Status : Virtual =cut sub accession_number { my( $self, $acc ) = @_; if (defined $acc) { $self->{swq}->accession_number($acc); } else { $acc = $self->{swq}->accession_number(); $acc = 'unknown' unless defined $acc; } return $acc; } =head2 primary_id() Title : primary_id() Usage : $unique_implementation_key = $obj->primary_id(); Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a way the implementation can control clients can expect one id to map to one object. For sequences with no accession number, this method should return a stringified memory location. This method sets the primary_id for the Quality object. Returns : A string. (the value of primary_id) Args : If a scalar is provided, it is set as the new primary_id for the Quality object. =cut sub primary_id { my ($self,$value) = @_; if ($value) { $self->{swq}->primary_id($value); } return $self->{swq}->primary_id(); } =head2 desc() Title : desc() Usage : $qual->desc($newval); _or_ $description = $qual->desc(); Function: Get/set description text for this Quality object. Returns : A string. (the value of desc) Args : If a scalar is provided, it is set as the new desc for the Quality object. =cut sub desc { # a mechanism to set the desc for the Quality object. # probably will be used most often by set_common_features() my ($self,$value) = @_; if( defined $value) { $self->{swq}->desc($value); } return $self->{swq}->desc(); } =head2 id() Title : id() Usage : $id = $qual->id(); Function: Return the ID of the quality. This should normally be (and actually is in the implementation provided here) just a synonym for display_id(). Returns : A string. (the value of id) Args : If a scalar is provided, it is set as the new id for the Quality object. =cut sub id { my ($self,$value) = @_; if (!$self) { $self->throw("no value for self in $value"); } if( defined $value ) { $self->{swq}->display_id($value); } return $self->{swq}->display_id(); } =head2 seq Title : seq() Usage : $string = $obj->seq(); _or_ $obj->seq("atctatcatca"); Function: Returns the sequence that is contained in the imbedded in the PrimarySeq object within the Quality object Returns : A scalar (the seq() value for the imbedded PrimarySeq object.) Args : If a scalar is provided, the Quality object will attempt to set that as the sequence for the imbedded PrimarySeq object. Otherwise, the value of seq() for the PrimarySeq object is returned. Notes : This is probably not a good idea because you then should call length() to make sure that the sequence and quality are of the same length. Even then, how can you make sure that this sequence belongs with that quality? I provided this to give you rope to hang yourself with. Tie it to a strong device and use a good knot. =cut sub seq { my ($self,$value) = @_; if( defined $value) { $self->{swq}->seq($value); } return $self->{swq}->seq(); } =head2 qual() Title : qual() Usage : @quality_values = @{$obj->qual()}; _or_ $obj->qual("10 10 20 40 50"); Function: Returns the quality as imbedded in the PrimaryQual object within the Quality object. Returns : A reference to an array containing the quality values in the PrimaryQual object. Args : If a scalar is provided, the Quality object will attempt to set that as the quality for the imbedded PrimaryQual object. Otherwise, the value of qual() for the PrimaryQual object is returned. Notes : This is probably not a good idea because you then should call length() to make sure that the sequence and quality are of the same length. Even then, how can you make sure that this sequence belongs with that quality? I provided this to give you a strong board with which to flagellate yourself. =cut sub qual { my ($self,$value) = @_; if( defined $value) { $self->{swq}->qual($value); } return $self->{swq}->qual(); } =head2 length() Title : length() Usage : $length = $seqWqual->length(); Function: Get the length of the Quality sequence/quality. Returns : Returns the length of the sequence and quality Args : None. =cut sub length { my $self = shift; return $self->seq_obj->length; } =head2 qual_obj Title : qual_obj($different_obj) Usage : $qualobj = $seqWqual->qual_obj(); _or_ $qualobj = $seqWqual->qual_obj($ref_to_primaryqual_obj); Function: Get the Qualilty object that is imbedded in the Quality object or if a reference to a PrimaryQual object is provided, set this as the PrimaryQual object imbedded in the Quality object. Returns : A reference to a Bio::Seq::Quality object. Identical to L<seq_obj>. =cut sub qual_obj { my ($self,$value) = @_; # return $self->{swq}->qual_obj($value); return $self->{swq}; } =head2 seq_obj Title : seq_obj() Usage : $seqobj = $seqWqual->seq_obj(); _or_ $seqobj = $seqWqual->seq_obj($ref_to_primary_seq_obj); Function: Get the PrimarySeq object that is imbedded in the Quality object or if a reference to a PrimarySeq object is provided, set this as the PrimarySeq object imbedded in the Quality object. Returns : A reference to a Bio::PrimarySeq object. =cut sub seq_obj { my ($self,$value) = @_; return $self->{swq}; } =head2 _set_descriptors Title : _set_descriptors() Usage : $seqWqual->_qual_obj($qual,$seq,$id,$acc,$pid,$desc,$given_id, $alphabet); Function: Set the descriptors for the Quality object. Try to match the descriptors in the PrimarySeq object and in the PrimaryQual object if descriptors were not provided with construction. Returns : Nothing. Args : $qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet as found in the new() method. Notes : Really only intended to be called by the new() method. If you want to invoke a similar function try set_common_descriptors(). =cut sub _set_descriptors { my ($self,$qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet) = @_; $self->{swq}->_seq_descriptors($qual,$seq,$id,$acc,$pid, $desc,$given_id,$alphabet); } =head2 subseq($start,$end) Title : subseq($start,$end) Usage : $subsequence = $obj->subseq($start,$end); Function: Returns the subseq from start to end, where the first base is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Returns : A string. Args : Two positions. =cut sub subseq { my ($self,@args) = @_; # does a single value work? return $self->{swq}->subseq(@args); } =head2 baseat($position) Title : baseat($position) Usage : $base_at_position_6 = $obj->baseat("6"); Function: Returns a single base at the given position, where the first base is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Returns : A scalar. Args : A position. =cut sub baseat { my ($self,$val) = @_; return $self->{swq}->subseq($val,$val); } =head2 subqual($start,$end) Title : subqual($start,$end) Usage : @qualities = @{$obj->subqual(10,20); Function: returns the quality values from $start to $end, where the first value is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Start cannot be larger than end but can be equal. Returns : A reference to an array. Args : a start position and an end position =cut sub subqual { my ($self,@args) = @_; return $self->{swq}->subqual(@args); } =head2 qualat($position) Title : qualat($position) Usage : $quality = $obj->qualat(10); Function: Return the quality value at the given location, where the first value is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Start cannot be larger than end but can be equal. Returns : A scalar. Args : A position. =cut sub qualat { my ($self,$val) = @_; return $self->{swq}->qualat($val); } =head2 sub_peak_index($start,$end) Title : sub_peak_index($start,$end) Usage : @peak_indices = @{$obj->sub_peak_index(10,20); Function: returns the trace index values from $start to $end, where the first value is 1 and the number is inclusive, ie 1-2 are the first two trace indices for this channel. Returns : A reference to an array. Args : a start position and an end position =cut sub sub_peak_index { my ($self,$start,$end) = @_; if( $start > $end ){ $self->throw("in sub_peak_index, start [$start] has to be greater than end [$end]"); } if( $start <= 0 || $end > $self->length ) { $self->throw("You have to have start positive and length less than the total length of sequence [$start:$end] Total ".$self->length.""); } # remove one from start, and then length is end-start $start--; $end--; my @sub_peak_index_array = @{$self->{peak_indices}}[$start..$end]; # return substr $self->seq(), $start, ($end-$start); return \@sub_peak_index_array; } =head2 sub_trace($start,$end) Title : sub_trace($base_channel,$start,$end) Usage : @trace_values = @{$obj->sub_trace('a',10,20)}; Function: returns the trace values from $start to $end, where the first value is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Start cannot be larger than end but can be e_peak_index. Returns : A reference to an array. Args : a start position and an end position =cut sub sub_trace { my ($self,$base_channel,$start,$end) = @_; if( $start > $end ){ $self->throw("in sub_trace, start [$start] has to be greater than end [$end]"); } if( $start <= 0 || $end > $self->trace_length() ) { $self->throw("You have to have start positive and length less than the total length of traces [$start:$end] Total ".$self->trace_length.""); } # remove one from start, and then length is end-start $start--; $end--; my @sub_peak_index_array = @{$self->trace($base_channel)}[$start..$end]; # return substr $self->seq(), $start, ($end-$start); return \@sub_peak_index_array; } =head2 trace_length() Title : trace_length() Usage : $trace_length = $obj->trace_length(); Function: Return the length of the trace if all four traces (atgc) are the same. Otherwise, throw an error. Returns : A scalar. Args : none =cut sub trace_length { my $self = shift; if ( !$self->trace('a') || !$self->trace('t') || !$self->trace('g') || !$self->trace('c') ) { $self->warn("One or more of the trace channels are missing. Cannot give you a length."); } my $lengtha = scalar(@{$self->trace('a')}); my $lengtht = scalar(@{$self->trace('t')}); my $lengthg = scalar(@{$self->trace('g')}); my $lengthc = scalar(@{$self->trace('c')}); if (($lengtha == $lengtht) && ($lengtha == $lengthg) && ($lengtha == $lengthc) ) { return $lengtha; } $self->warn("Not all of the trace indices are the same length". " Here are their lengths: a: $lengtha t:$lengtht ". " g: $lengthg c: $lengthc"); } =head2 sub_trace_object($start,$end) Title : sub_trace_object($start,$end) Usage : $smaller_object = $object->sub_trace_object('1','100'); Function: Get a subset of the sequence, its quality, and its trace. Returns : A reference to a Bio::Seq::SequenceTrace object Args : a start position and an end position Notes : - the start and end position refer to the positions of _bases_. - for example, to get a sub SequenceTrace for bases 5-10, use this routine. - you will get the bases, qualities, and the trace values - you can then use this object to synthesize a new scf using seqIO::scf. =cut sub sub_trace_object { my ($self,$start,$end) = @_; my ($start2,$end2); my @subs = @{$self->sub_peak_index($start,$end)}; $start2 = shift(@subs); $end2 = pop(@subs); my $new_object = Bio::Seq::SequenceTrace->new( -swq => Bio::Seq::Quality->new( -seq => $self->subseq($start,$end), -qual => $self->subqual($start,$end), -id => $self->id() ), -trace_a => $self->sub_trace('a',$start2,$end2), -trace_t => $self->sub_trace('t',$start2,$end2), -trace_g => $self->sub_trace('g',$start2,$end2), -trace_c => $self->sub_trace('c',$start2,$end2), -peak_indices => $self->sub_peak_index($start,$end) ); $new_object->set_accuracies(); $new_object->_reset_peak_indices(); return $new_object; } =head2 _synthesize_traces() Title : _synthesize_traces() Usage : $obj->_synthesize_traces(); Function: Synthesize false traces for this object. Returns : Nothing. Args : None. Notes : This method is intended to be invoked when this object is created with a SWQ object- that is to say that there is a sequence and a set of qualities but there was no actual trace data. =cut sub _synthesize_traces { my ($self) = shift; $self->peak_indices(qw()); #ml my $version = 2; # the user should be warned if traces already exist # # #ml ( my $sequence = $self->seq() ) =~ tr/a-z/A-Z/; #ml my @quals = @{$self->qual()}; #ml my $info; # build the ramp for the first base. # a ramp looks like this "1 4 13 29 51 71 80 71 51 29 13 4 1" times the quality score. # REMEMBER: A C G T # note to self-> smooth this thing out a bit later my $ramp_data; @{$ramp_data->{'ramp'}} = qw( 1 4 13 29 51 75 80 75 51 29 13 4 1 ); # the width of the ramp $ramp_data->{'ramp_width'} = scalar(@{$ramp_data->{'ramp'}}); # how far should the peaks overlap? $ramp_data->{'ramp_overlap'} = 1; # where should the peaks be located? $ramp_data->{'peak_at'} = 7; $ramp_data->{'ramp_total_length'} = $self->seq_obj()->length() * $ramp_data->{'ramp_width'} - $self->seq_obj()->length() * $ramp_data->{'ramp_overlap'}; my $pos; my $total_length = $ramp_data->{ramp_total_length}; $self->initialize_traces("0",$total_length+2); # now populate them my ($current_base,$place_base_at,$peak_quality,$ramp_counter,$current_ramp,$ramp_position); #ml my $sequence_length = $self->length(); my $half_ramp = int($ramp_data->{'ramp_width'}/2); for ($pos = 0; $pos<$self->length();$pos++) { $current_base = uc $self->seq_obj()->subseq($pos+1,$pos+1); # print("Synthesizing the ramp for $current_base\n"); my $all_bases = "ATGC"; $peak_quality = $self->qual_obj()->qualat($pos+1); # where should the peak for this base be placed? Modeled after a mktrace scf $place_base_at = ($pos * $ramp_data->{'ramp_width'}) - ($pos * $ramp_data->{'ramp_overlap'}) - $half_ramp + $ramp_data->{'ramp_width'} - 1; # print("Placing this base at this position: $place_base_at\n"); push @{$self->peak_indices()},$place_base_at; $ramp_position = $place_base_at - $half_ramp; if ($current_base =~ "N" ) { $current_base = "A"; } for ($current_ramp = 0; $current_ramp < $ramp_data->{'ramp_width'}; $current_ramp++) { # print("Placing a trace value here: $current_base ".($ramp_position+$current_ramp+1)." ".$peak_quality*$ramp_data->{'ramp'}->[$current_ramp]."\n"); $self->trace_value_at($current_base,$ramp_position+$current_ramp+1,$peak_quality*$ramp_data->{'ramp'}->[$current_ramp]); } $self->peak_index_at($pos+1, $place_base_at+1 ); #ml my $other_bases = $self->_get_other_bases($current_base); # foreach ( split('',$other_bases) ) { # push @{$self->{'text'}->{"v3_base_accuracy"}->{$_}},0; #} } } =head2 _dump_traces($transformed) Title : _dump_traces("transformed") Usage : &_dump_traces($ra,$rc,$rg,$rt); Function: Used in debugging. Prints all traces one beside each other. Returns : Nothing. Args : References to the arrays containing the traces for A,C,G,T. Notes : Beats using dumpValue, I'll tell ya. Much better then using join' ' too. - if a scalar is included as an argument (any scalar), this procedure will dump the _delta'd trace. If you don't know what that means you should not be using this. =cut #' sub _dump_traces { my ($self) = @_; my (@sA,@sT,@sG,@sC); print ("Count\ta\tc\tg\tt\n"); my $length = $self->trace_length(); for (my $curr=1; $curr <= $length; $curr++) { print(($curr-1)."\t".$self->trace_value_at('a',$curr). "\t".$self->trace_value_at('c',$curr). "\t".$self->trace_value_at('g',$curr). "\t".$self->trace_value_at('t',$curr)."\n"); } return; } =head2 _initialize_traces() Title : _initialize_traces() Usage : $trace_object->_initialize_traces(); Function: Creates empty arrays to hold synthetic trace values. Returns : Nothing. Args : None. =cut sub initialize_traces { my ($self,$value,$length) = @_; foreach (qw(a t g c)) { my @temp; for (my $count=0; $count<$length; $count++) { $temp[$count] = $value; } $self->trace($_,\@temp); } } =head2 trace_value_at($channel,$position) Title : trace_value_at($channel,$position) Usage : $value = $trace_object->trace_value_at($channel,$position); Function: What is the value of the trace for this base at this position? Returns : A scalar represnting the trace value here. Args : a base channel (a,t,g,c) a position ( < $trace_object->trace_length() ) =cut sub trace_value_at { my ($self,$channel,$position,$value) = @_; if ($value) { $self->trace($channel)->[$position] = $value; } return $self->sub_trace($channel,($position),($position))->[0]; } sub _deprecated_get_scf_version_2_base_structure { # this sub is deprecated- check inside SeqIO::scf my $self = shift; my (@structure,$current); my $length = $self->length(); for ($current=1; $current <= $self->length() ; $current++) { my $base_here = $self->seq_obj()->subseq($current,$current); $base_here = lc($base_here); my $probabilities; $probabilities->{$base_here} = $self->qual_obj()->qualat($current); my $other_bases = "atgc"; my $empty = ""; $other_bases =~ s/$base_here/$empty/e; foreach ( split('',$other_bases) ) { $probabilities->{$_} = "0"; } @structure = ( @structure, $self->peak_index_at($current), $probabilities->{'a'}, $probabilities->{'t'}, $probabilities->{'g'}, $probabilities->{'c'} ); } return \@structure; } sub _deprecated_get_scf_version_3_base_structure { my $self = shift; my $structure; $structure = join('',$self->peak_indices()); return $structure; } =head2 accuracies($channel,$position) Title : trace_value_at($channel,$position) Usage : $value = $trace_object->trace_value_at($channel,$position); Function: What is the value of the trace for this base at this position? Returns : A scalar representing the trace value here. Args : a base channel (a,t,g,c) a position ( < $trace_object->trace_length() ) =cut sub accuracies { my ($self,$channel,$value) = @_; if ($value) { if (ref($value) eq "ARRAY") { $self->{accuracies}->{$channel} = $value; } else { my @acc = split(' ',$value); $self->{accuracies}->{$channel} = \@acc; } } return $self->{accuracies}->{$channel}; } =head2 set_accuracies() Title : set_sccuracies() Usage : $trace_object->set_accuracies(); Function: Take a sequence's quality and synthesize proper scf-style base accuracies that can then be accessed with accuracies("a") or something like it. Returns : Nothing. Args : None. =cut sub set_accuracies { my $self = shift; my $count = 0; my $length = $self->length(); for ($count=1; $count <= $length; $count++) { my $base_here = $self->seq_obj()->subseq($count,$count); my $qual_here = $self->qual_obj()->qualat($count); $self->accuracy_at($base_here,$count,$qual_here); my $other_bases = $self->_get_other_bases($base_here); foreach (split('',$other_bases)) { $self->accuracy_at($_,$count,"null"); } } } =head2 scf_dump() Title : scf_dump() Usage : $trace_object->scf_dump(); Function: Prints out the contents of the structures representing the SequenceTrace in a manner similar to io_lib's scf_dump. Returns : Nothing. Prints out the contents of the structures used to represent the sequence and its trace. Args : None. Notes : Used in debugging, obviously. =cut sub scf_dump { my $self = shift; my $count; for ($count=1;$count<=$self->length();$count++) { my $base_here = lc($self->seq_obj()->subseq($count,$count)); print($base_here." ".sprintf("%05d",$self->peak_index_at($count))."\t"); foreach (sort qw(a c g t)) { print(sprintf("%03d",$self->accuracy_at($_,$count))."\t"); } print("\n"); } $self->_dump_traces(); } =head2 _get_other_bases($this_base) Title : _get_other_bases($this_base) Usage : $other_bases = $trace_object->_get_other_bases($this_base); Function: A utility routine to return bases other then the one provided. I was doing this over and over so I put it here. Returns : Three of a,t,g and c. Args : A base (atgc) Notes : $obj->_get_other_bases("a") returns "tgc" =cut sub _get_other_bases { my ($self,$this_base) = @_; $this_base = lc($this_base); my $all_bases = "atgc"; my $empty = ""; $all_bases =~ s/$this_base/$empty/e; return $all_bases; } =head2 accuracy_at($base,$position) Title : accuracy_at($base,$position) Usage : $accuracy = $trace_object->accuracy_at($base,$position); Function: Returns : Returns the accuracy of finding $base at $position. Args : 1. a base channel (atgc) 2. a value to _set_ the accuracy Notes : $obj->_get_other_bases("a") returns "tgc" =cut sub accuracy_at { my ($self,$base,$position,$value) = @_; $base = lc($base); if ($value) { if ($value eq "null") { $self->{accuracies}->{$base}->[$position-1] = "0"; } else { $self->{accuracies}->{$base}->[$position-1] = $value; } } return $self->{accuracies}->{$base}->[$position-1]; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/SimulatedRead.pm�����������������������������������������������������������000444��000766��000024�� 54102�13155576320� 20057� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������package Bio::Seq::SimulatedRead; =head1 NAME Bio::Seq::SimulatedRead - Read with sequencing errors taken from a reference sequence =head1 SYNOPSIS use Bio::Seq::SimulatedRead; use Bio::PrimarySeq; # Create a reference sequence my $genome = Bio::PrimarySeq->new( -id => 'human_chr2', -seq => 'TAAAAAAACCCCTG', -desc => 'The human genome' ); # A 10-bp error-free read taken from a genome my $read = Bio::Seq::SimulatedRead->new( -reference => $genome , # sequence to generate the read from -id => 'read001', # read ID -start => 3 , # start of the read on the genome forward strand -end => 12 , # end of the read on the genome forward strand -strand => 1 , # genome strand that the read is on ); # Display the sequence of the read print $read->seq."\n"; # Add a tag or MID to the beginning of the read $read->mid('ACGT'); # Add sequencing errors (error positions are 1-based and relative to the # error-free MID-containing read) my $errors = {}; $errors->{'8'}->{'+'} = 'AAA'; # insertion of AAA after residue 8 $errors->{'1'}->{'%'} = 'G'; # substitution of residue 1 by a G $errors->{'4'}->{'-'} = undef; # deletion of residue 4 $read->errors($errors); # Display the sequence of the read with errors print $read->seq."\n"; # String representation of where the read came from and its errors print $read->desc."\n"; =head1 DESCRIPTION This object is a simulated read with sequencing errors. The user can provide a reference sequence to take a read from, the position and orientation of the read on the reference sequence, and the sequencing errors to generate. The sequence of the read is automatically calculated based on this information. By default, the description of the reads contain tracking information and will look like this (Bioperl-style): reference=human_chr2 start=3 end=12 strand=-1 mid=ACGT errors=1%G,4-,8+AAA description="The human genome" or Genbank-style: reference=human_chr2 position=complement(3..12) mid=ACGT errors=1%G,4-,8+AAA description="The human genome" Creating a simulated read follows these steps: 1/ Define the read start(), end(), strand() and qual_levels() if you want quality scores to be generated. Do not change these values once set because the read will not be updated. 2/ Specify the reference sequence that the read should be taken from. Once this is done, you have a fully functional read. Do not use the reference() method again after you have gone to the next step. 3/ Use mid() to input a MID (or tag or barcode) to add to the beginning of the read. You can change the MID until you go to next step. 4/ Give sequencing error specifications using errors() as the last step. You can do that as many times as you like, and the read will be updated. =head1 AUTHOR Florent E Angly E<lt>florent . angly @ gmail-dot-comE<gt>. Copyright (c) 2011 Florent E Angly. This library is free software; you can redistribute it under the GNU General Public License version 3. =cut use strict; use warnings; use Bio::LocatableSeq; use base qw( Bio::Seq::Quality Bio::LocatableSeq ); =head2 new Title : new Function : Create a new simulated read object Usage : my $read = Bio::Seq::SimulatedRead->new( -id => 'read001', -reference => $seq_obj , -errors => $errors , -start => 10 , -end => 135 , -strand => 1 , ); Arguments: -reference => Bio::SeqI, Bio::PrimarySeqI object representing the reference sequence to take the read from. See reference(). -errors => Hashref representing the position of errors in the read See errors(). -mid => String of a MID to prepend to the read. See mid(). -track => Track where the read came from in the read description? See track(). -coord_style => Define what coordinate system to use. See coord_style(). All other methods from Bio::LocatableSeq are available. Returns : new Bio::Seq::SimulatedRead object =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($qual_levels, $reference, $mid, $errors, $track, $coord_style) = $self->_rearrange([qw(QUAL_LEVELS REFERENCE MID ERRORS TRACK COORD_STYLE)], @args); $coord_style = defined $coord_style ? $coord_style : 'bioperl'; $self->coord_style($coord_style); $track = defined $track ? $track : 1; $self->track($track); $qual_levels = defined $qual_levels ? $qual_levels : []; $self->qual_levels($qual_levels) if defined $qual_levels; $self->reference($reference) if defined $reference; $self->mid($mid) if defined $mid; $self->{_mutated} = 0; $self->errors($errors) if defined $errors; return $self; } =head2 qual_levels Title : qual_levels Function : Get or set the quality scores to give to the read. By default, if your reference sequence does not have quality scores, no quality scores are generated for the simulated read. The generated quality scores are very basic. If a residue is error-free, it gets the quality score defined for good residues. If the residue has an error (is an addition or a mutation), the residue gets the quality score specified for bad residues. Call the qual_levels() method before using the reference() method. Usage : my $qual_levels = $read->qual_levels( ); Arguments: Array reference containing the quality scores to use for: 1/ good residues (e.g. 30) 2/ bad residues (e.g. 10) Returns : Array reference containing the quality scores to use. =cut sub qual_levels { my ($self, $qual_levels) = @_; if (defined $qual_levels) { if ( (scalar @$qual_levels != 0) && (scalar @$qual_levels != 2) ) { $self->throw("The quality score specification must define the score". " to use for good and for bad residues\n"); } $self->{qual_levels} = $qual_levels; } return $self->{qual_levels}; } =head2 reference Title : reference Function : Get or set the reference sequence that the read comes from. Once the reference has been set, you have a functional simulated read which supports all the Bio::LocatableSeq methods. This method must be called after qual_levels() but before mid() or errors(). Usage : my $seq_obj = $read->reference(); Arguments: Bio::SeqI or Bio::PrimarySeqI object Returns : Bio::SeqI or Bio::PrimarySeqI object =cut sub reference { my ($self, $reference) = @_; if (defined $reference) { # Sanity check 1 if ( (not $reference->isa('Bio::SeqI')) && (not $reference->isa('Bio::PrimarySeqI')) ) { $self->throw("Expected a Bio::SeqI object as reference, but got: $reference\n"); } # Sanity check 2 if ($self->{mid} || $self->{errors}) { $self->throw("Cannot change the reference sequence after an MID or ". "sequencing errors have been added to the read\n"); } # Use beginning of reference sequence as start default if (not defined $self->start) { $self->start(1); } # Use end of reference sequence as end default if (not defined $self->end) { $self->end($reference->length); } # Use strand 1 as strand default if (not defined $self->strand) { $self->strand(1); } # Set the reference sequence object $self->{reference} = $reference; # Create a sequence, quality scores and description from the reference $self->_create_seq; $self->_create_qual if scalar @{$self->qual_levels}; $self->_create_desc if $self->track; } return $self->{reference}; } sub _create_seq { my $self = shift; # Get a truncation of the reference sequence my $reference = $self->reference; my $read_obj = $reference->trunc( $self->start, $self->end ); # Reverse complement the read if needed if ($self->strand == -1) { $read_obj = $read_obj->revcom(); } $self->seq($read_obj->seq); return 1; } sub _create_qual { my $self = shift; $self->qual([ ($self->qual_levels->[0]) x ($self->end - $self->start + 1) ]); return 1; } sub _create_desc { # Create the read description of the error-free read my $self = shift; # Reference sequence ID my $desc_str = ''; my $ref_id = $self->reference->id; if (defined $ref_id) { $desc_str .= 'reference='.$ref_id.' '; } # Position of read on reference sequence: start, end and strand my $strand = $self->strand; if ($self->coord_style eq 'bioperl') { $desc_str .= 'start='.$self->start.' end='.$self->end.' '; if (defined $strand) { # Strand of the reference sequence that the read is on $strand = '+1' if $strand == 1; $desc_str .= 'strand='.$strand.' '; } } else { if ( (defined $strand) && ($strand == -1) ) { # Reverse complemented $desc_str .= 'position=complement('.$self->start.'..'.$self->end.') '; } else { # Regular (forward) orientation $desc_str .= 'position='.$self->start.'..'.$self->end.' '; } } # Description of the original sequence my $ref_desc = $self->reference->desc; if ( (defined $self->reference->desc) && ($self->reference->desc !~ m/^\s*$/) ) { $ref_desc =~ s/"/\\"/g; # escape double-quotes to \" $desc_str .= 'description="'.$ref_desc.'" '; } $desc_str =~ s/\s$//g; # Record new description $self->desc($desc_str); return 1; } =head2 mid Title : mid Function : Get or set a multiplex identifier (or MID, or tag, or barcode) to add to the read. By default, no MID is used. This method must be called after reference() but before errors(). Usage : my $mid = read->mid(); Arguments: MID sequence string (e.g. 'ACGT') Returns : MID sequence string =cut sub mid { my ($self, $mid) = @_; if (defined $mid) { # Sanity check 1 if (not defined $self->reference) { $self->throw("Cannot add MID because the reference sequence was not ". "set\n"); } # Sanity check 2 if ($self->{errors}) { $self->throw("Cannot add an MID after sequencing errors have been ". "introduced in the read\n"); } # Sanity check 3 if (not $self->validate_seq($mid)) { $self->throw("MID is not a valid DNA sequence\n"); } # Update sequence, quality scores and description with the MID $self->_update_seq_mid($mid); $self->_update_qual_mid($mid) if scalar @{$self->qual_levels}; $self->_update_desc_mid($mid) if $self->track; # Set the MID value $self->{mid} = $mid; } return $self->{mid} } sub _update_seq_mid { # Update the MID of a sequence my ($self, $mid) = @_; # Remove old MID my $seq = $self->seq; my $old_mid = $self->{mid}; if (defined $old_mid) { $seq =~ s/^$old_mid//; } # Add new MID $seq = $mid . $seq; $self->seq( $seq ); return 1; } sub _update_qual_mid { # Update the MID of a quality scores my ($self, $mid) = @_; # Remove old MID my $qual = $self->qual; my $old_mid = $self->{mid}; if (defined $old_mid) { splice @$qual, 0, length($old_mid); } $qual = [($self->qual_levels->[0]) x length($mid), @$qual]; $self->qual( $qual ); return 1; } sub _update_desc_mid { # Update MID specifications in the read description my ($self, $mid) = @_; if ($mid) { # Sequencing errors introduced in the read my $mid_str = "mid=".$mid; my $desc_str = $self->desc; $desc_str =~ s/((position|strand)=\S+)( mid=\S+)?/$1 $mid_str/g; $self->desc( $desc_str ); } return 1; } =head2 errors Title : errors Function : Get or set the sequencing errors and update the read. By default, no errors are made. This method must be called after the mid() method. Usage : my $errors = $read->errors(); Arguments: Reference to a hash of the position and nature of sequencing errors. The positions are 1-based relative to the error-free MID-containing read (not relative to the reference sequence). For example: $errors->{34}->{'%'} = 'T' ; # substitution of residue 34 by a T $errors->{23}->{'+'} = 'GG' ; # insertion of GG after residue 23 $errors->{45}->{'-'} = undef; # deletion of residue 45 Substitutions and deletions are for a single residue, but additions can be additions of several residues. An alternative way to specify errors is by using array references instead of scalar for the hash values. This allows one to specify redundant mutations. For example, the case presented above would result in the same read sequence as the example below: $errors->{34}->{'%'} = ['C', 'T'] ; # substitution by a C and then a T $errors->{23}->{'+'} = ['G', 'G'] ; # insertion of G and then a G $errors->{45}->{'-'} = [undef, undef]; # deletion of residue, and again Returns : Reference to a hash of the position and nature of sequencing errors. =cut sub errors { my ($self, $errors) = @_; if (defined $errors) { # Verify that we have a hashref if ( (not defined ref $errors) || (not ref $errors eq 'HASH') ) { $self->throw("Error specification has to be a hashref. Got: $errors\n"); } # Verify that we have a reference sequence if (not defined $self->reference) { $self->throw("Cannot add errors because the reference sequence was not set\n"); } # Convert scalar error specs to arrayref specs $errors = $self->_scalar_to_arrayref($errors); # Check validity of error specifications $errors = $self->_validate_error_specs($errors); # Set the error specifications $self->{errors} = $errors; # Need to recalculate the read from the reference if previously mutated if ($self->{_mutated}) { $self->_create_seq; $self->_create_qual if scalar @{$self->qual_levels}; $self->_create_desc if $self->track; } # Now mutate the read, quality score and description $self->_update_seq_errors; $self->_update_qual_errors if scalar @{$self->qual_levels}; $self->_update_desc_errors if $self->track; } return $self->{errors}; } sub _scalar_to_arrayref { # Replace the scalar values in the error specs by more versatile arrayrefs my ($self, $errors) = @_; while ( my ($pos, $ops) = each %$errors ) { while ( my ($op, $res) = each %$ops ) { if (ref $res eq '') { my $arr = [ split //, ($res || '') ]; $arr = [undef] if scalar @$arr == 0; $$errors{$pos}{$op} = $arr; } } } return $errors; } sub _validate_error_specs { # Clean error specifications and warn of any issues encountered my ($self, $errors) = @_; my %valid_ops = ('%' => undef, '-' => undef, '+' => undef); # valid operations # Calculate read length my $read_length = $self->length; while ( my ($pos, $ops) = each %$errors ) { # Position cannot be no longer than the read length if ( (defined $read_length) && ($pos > $read_length) ) { $self->warn("Position $pos is beyond end of read ($read_length ". "residues). Skipping errors specified at this position.\n"); delete $errors->{$pos}; } # Position has to be 0+ for addition, 1+ for substitution and deletion if ( $pos < 1 && (exists $ops->{'%'} || exists $ops->{'-'}) ) { $self->warn("Positions of substitutions and deletions have to be ". "strictly positive but got $pos. Skipping substitution or deletion". " at this position\n"); delete $ops->{'%'}; delete $ops->{'-'}; } if ( $pos < 0 && exists $ops->{'+'}) { $self->warn("Positions of additions have to be zero or more. ". "Skipping addition at position $pos.\n"); delete $ops->{'+'}; } # Valid operations are '%', '+' and '-' while ( my ($op, $res) = each %$ops ) { if (not exists $valid_ops{$op}) { $self->warn("Skipping unknown error operation '$op' at position". " $pos\n"); delete $ops->{$op}; } else { # Substitutions: have to have at least one residue to substitute if ( ($op eq '%') && (scalar @$res < 1) ) { $self->warn("At least one residue must be provided for substitutions,". "but got ".scalar(@$res)." at position $pos.\n"); } # Additions: have to have at least one residue to add if ( ($op eq '+') && (scalar @$res < 1) ) { $self->warn("At least one residue must be provided for additions,". "but got ".scalar(@$res)." at position $pos.\n"); } # Deletions if ( ($op eq '-') && (scalar @$res < 1) ) { $self->warn("At least one 'undef' must be provided for deletions,". "but got ".scalar(@$res)." at position $pos.\n"); } } } delete $errors->{$pos} unless scalar keys %$ops; } return $errors; } sub _update_seq_errors { my $self = shift; my $seq_str = $self->seq; my $errors = $self->errors; if (scalar keys %$errors > 0) { my $off = 0; for my $pos ( sort {$a <=> $b} (keys %$errors) ) { # Process sequencing errors at that position for my $type ( '%', '-', '+' ) { next if not exists $$errors{$pos}{$type}; my $arr = $$errors{$pos}{$type}; if ($type eq '%') { # Substitution at residue position. If there are multiple # substitutions to do, directly skip to the last one. substr $seq_str, $pos - 1 + $off, 1, $$arr[-1]; } elsif ($type eq '-') { # Deletion at residue position substr $seq_str, $pos - 1 + $off, 1, ''; $off--; } elsif ($type eq '+') { # Insertion after residue position substr $seq_str, $pos + $off, 0, join('', @$arr); $off += scalar @$arr; } } } $self->{_mutated} = 1; } else { $self->{_mutated} = 0; } $self->seq($seq_str); return 1; } sub _update_qual_errors { my $self = shift; my $qual = $self->qual; my $errors = $self->errors; my $bad_qual = $self->qual_levels->[1]; if (scalar keys %$errors > 0) { my $off = 0; for my $pos ( sort {$a <=> $b} (keys %$errors) ) { # Process sequencing errors at that position for my $type ( '%', '-', '+' ) { next if not exists $$errors{$pos}{$type}; my $arr = $$errors{$pos}{$type}; if ($type eq '%') { # Substitution at residue position splice @$qual, $pos - 1 + $off, 1, $bad_qual; } elsif ($type eq '-') { # Deletion at residue position splice @$qual, $pos - 1 + $off, 1; $off--; } elsif ($type eq '+') { # Insertion after residue position splice @$qual, $pos + $off, 0, ($bad_qual) x scalar(@$arr); $off += scalar @$arr; } } } } $self->qual($qual); return 1; } sub _update_desc_errors { # Add or update error specifications in the read description my $self = shift; my $errors = $self->errors; if (defined $errors and scalar keys %$errors > 0) { # Sequencing errors introduced in the read my $err_str = 'errors='; for my $pos ( sort {$a <=> $b} (keys %$errors) ) { # Process sequencing errors at that position for my $type ( '%', '-', '+' ) { next if not exists $$errors{$pos}{$type}; for my $val ( @{$$errors{$pos}{$type}} ) { $val = '' if not defined $val; $err_str .= $pos . $type . $val . ','; } } } $err_str =~ s/,$//; my $desc_str = $self->desc; $desc_str =~ s/((position|strand)=\S+( mid=\S+)?)( errors=\S+)?/$1 $err_str/g; $self->desc( $desc_str ); } return 1; } =head2 track Title : track Function : Get or set the tracking status in the read description. By default, tracking is on. This method can be called at any time. Usage : my $track = $read->track(); Arguments: 1 for tracking, 0 otherwise Returns : 1 for tracking, 0 otherwise =cut sub track { my ($self, $track) = @_; if (defined $track) { if (defined $self->reference) { if ($track == 1) { $self->_create_desc; $self->_update_desc_mid($self->mid); $self->_update_desc_errors; } else { $self->desc(undef); } } $self->{track} = $track; } return $self->{track}; } =head2 coord_style Title : coord_style Function : When tracking is on, define which 1-based coordinate system to use in the read description: * 'bioperl' uses the start, end and strand keywords (default), similarly to the GFF3 format. Example: start=1 end=10 strand=+1 start=1 end=10 strand=-1 * 'genbank' does only provide the position keyword. Example: position=1..10 position=complement(1..10) Usage : my $coord_style = $read->track(); Arguments: 'bioperl' or 'genbank' Returns : 'bioperl' or 'genbank' =cut sub coord_style { my ($self, $coord_style) = @_; my %styles = ( 'bioperl' => undef, 'genbank' => undef ); if (defined $coord_style) { if (not exists $styles{$coord_style}) { die "Error: Invalid coordinate style '$coord_style'\n"; } $self->{coord_style} = $coord_style; } return $self->{coord_style}; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/TraceI.pm������������������������������������������������������������������000555��000766��000024�� 16310�13155576320� 16505� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Seq::TraceI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chad Matsalla <bioinformatics@dieselwurks.com # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::TraceI - Interface definition for a Bio::Seq::Trace =head1 SYNOPSIS # get a Bio::Seq::Qual compliant object somehow $st = &get_object_somehow(); # to test this is a seq object $st->isa("Bio::Seq::TraceI") || $obj->throw("$obj does not implement the Bio::Seq::TraceI interface"); # set the trace for T to be @trace_points my $arrayref = $st->trace("T",\@trace_points); # get the trace points for "C" my $arrayref = $st->trace("C"); # get a subtrace for "G" from 10 to 100 $arrayref = $st->subtrace("G",10,100); # what is the trace value for "A" at position 355? my $trace_calue = $st->traceat("A",355); # create a false trace for "A" with $accuracy $arrayref = $st->false_trace("A",Bio::Seq::Quality, $accuracy); # does this trace have entries for each base? $bool = $st->is_complete(); # how many entries are there in this trace? $length = $st->length(); =head1 DESCRIPTION This object defines an abstract interface to basic trace information. This information may have come from an ABI- or scf- formatted file or may have been made up. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics@dieselwurks.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::TraceI; use strict; use Carp; use Dumpvalue; use Bio::Root::RootI; =head1 Implementation Specific Functions These functions are the ones that a specific implementation must define. =head2 trace($base,\@new_values) Title : trace($base,\@new_values) Usage : @trace_Values = @{$obj->trace($base,\@new_values)}; Function: Returns the trace values as a reference to an array containing the trace values. The individual elements of the trace array are not validated and can be any numeric value. Returns : A reference to an array. Status : Arguments: $base : which color channel would you like the trace values for? - $base must be one of "A","T","G","C" \@new_values : a reference to an array of values containing trace data for this base =cut sub trace { my ($self) = @_; if( $self->can('throw') ) { $self->throw("Bio::Seq::TraceI definition of trace - implementing class did not provide this method"); } else { confess("Bio::Seq::TraceI definition of trace - implementing class did not provide this method"); } } =head2 subtrace($base,$start,$end) Title : subtrace($base,$start,$end) Usage : @subset_of_traces = @{$obj->subtrace("A",10,40)}; Function: returns the trace values from $start to $end, where the first value is 1 and the number is inclusive, ie 1-2 are the first two trace values of this base. Start cannot be larger than end but can be equal. Returns : A reference to an array. Args : $base: "A","T","G" or "C" $start: a start position $end : an end position =cut sub subtrace { my ($self) = @_; if( $self->can('throw') ) { $self->throw("Bio::Seq::TraceI definition of subtrace - implementing class did not provide this method"); } else { confess("Bio::Seq::TraceI definition of subtrace - implementing class did not provide this method"); } } =head2 can_call_new() Title : can_call_new() Usage : if( $obj->can_call_new ) { $newobj = $obj->new( %param ); } Function: can_call_new returns 1 or 0 depending on whether an implementation allows new constructor to be called. If a new constructor is allowed, then it should take the followed hashed constructor list. $myobject->new( -qual => $quality_as_string, -display_id => $id, -accession_number => $accession, ); Example : Returns : 1 or 0 Args : =cut sub can_call_new{ my ($self,@args) = @_; # we default to 0 here return 0; } =head2 traceat($channel,$position) Title : qualat($channel,$position) Usage : $trace = $obj->traceat(500); Function: Return the trace value at the given location, where the first value is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence. Start cannot be larger than end but can be equal. Returns : A scalar. Args : A base and a position. =cut sub traceat { my ($self,$value) = @_; if( $self->can('warn') ) { $self->warn("Bio::Seq::TraceI definition of traceat - implementing class did not provide this method"); } else { warn("Bio::Seq::TraceI definition of traceat - implementing class did not provide this method"); } return ''; } =head2 length() Title : length() Usage : $length = $obj->length("A"); Function: Return the length of the array holding the trace values for the "A" channel. A check should be done to make sure that this Trace object is_complete() before doing this to prevent hazardous results. Returns : A scalar (the number of elements in the quality array). Args : If used, get the traces from that channel. Default to "A" =cut sub length { my ($self)= @_; if( $self->can('throw') ) { $self->throw("Bio::Seq::TraceI definition of length - implementing class did not provide this method"); } else { confess("Bio::Seq::TraceI definition of length - implementing class did not provide this method"); } } =head2 trace_indices($new_indices) Title : trace_indices($new_indices) Usage : $indices = $obj->trace_indices($new_indices); Function: Return the trace iindex points for this object. Returns : A scalar Args : If used, the trace indices will be set to the provided value. =cut sub trace_indices { my ($self)= @_; if( $self->can('throw') ) { $self->throw("Bio::Seq::TraceI definition of trace_indices - implementing class did not provide this method"); } else { confess("Bio::Seq::TraceI definition of trace_indices - implementing class did not provide this method"); } } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/Meta�����������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 15505� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Seq/Meta/Array.pm��������������������������������������������������������������000444��000766��000024�� 45556�13155576320� 17315� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Seq::Meta::Array # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::Meta::Array - array-based generic implementation of a sequence class with residue-based meta information =head1 SYNOPSIS use Bio::LocatableSeq; use Bio::Seq::Meta::Array; my $seq = Bio::Seq::Meta::Array->new(-id=>'test', -seq=>'ACTGCTAGCT', -start=>2434, -start=>2443, -strand=>1, -verbose=>1, # to see warnings ); # to test this is a meta seq object $seq->isa("Bio::Seq::Meta::Array") || $seq->throw("$seq is not a Bio::Seq::Meta::Array"); $seq->meta('1 2 3 4 5 6 7 8 9 10'); # or you could create the Meta object directly $seq = Bio::Seq::Meta::Array->new(-id=>'test', -seq=>'ACTGCTAGCT', -start=>2434, -start=>2443, -strand=>1, -meta=>'1 2 3 4 5 6 7 8 9 10', -verbose=>1, # to see warnings ); # accessors $arrayref = $seq->meta(); $string = $seq->meta_text(); $substring = $seq->submeta_text(2,5); $unique_key = $seq->accession_number(); =head1 DESCRIPTION This class implements generic methods for sequences with residue-based meta information. Meta sequences with meta data are Bio::LocatableSeq objects with additional methods to store that meta information. See L<Bio::LocatableSeq> and L<Bio::Seq::MetaI>. The meta information in this class can be a string of variable length and can be a complex structure. Blank values are undef or zero. Application specific implementations should inherit from this class to override and add to these methods. This class can be used for storing sequence quality values but Bio::Seq::Quality has named methods that make it easier. =head1 SEE ALSO L<Bio::LocatableSeq>, L<Bio::Seq::MetaI>, L<Bio::Seq::Meta>, L<Bio::Seq::Quality> =head1 NOTE This Bio::Seq::MetaI implementation inherits from Bio::LocatableSeq, which itself inherits from Bio::PrimarySeq. It is not a Bio::SeqI, so bless-ing objects of this class into a Bio::SeqI or vice versa and will not work as expected (see bug 2262). This may be addressed in a future refactor of Bio::LocatableSeq. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email heikki-at-bioperl-dot-org =head1 CONTRIBUTORS Chad Matsalla, bioinformatics@dieselwurks.com Aaron Mackey, amackey@virginia.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::Meta::Array; use strict; use base qw(Bio::LocatableSeq Bio::Seq Bio::Seq::MetaI); our $DEFAULT_NAME = 'DEFAULT'; our $GAP = '-'; our $META_GAP = 0; =head2 new Title : new Usage : $metaseq = Bio::Seq::Meta::Array->new ( -meta => 'aaaaaaaabbbbbbbb', -seq => 'TKLMILVSHIVILSRM' -id => 'human_id', -accession_number => 'S000012', ); Function: Constructor for Bio::Seq::Meta::Array class, meta data being in a string. Note that you can provide an empty quality string. Returns : a new Bio::Seq::Meta::Array object =cut sub new { my ($class, %args) = @_; # run-time modification of @ISA is extremely evil (you should't pick your # interface on the fly); this has no obvious effect on any tests so # commenting out - cjfields 2011-4-6 #defined inheritance according to stated baseclass, #if undefined then will be PrimarySeq #if (defined($args{'-baseclass'})) { # @ISA = ($args{'-baseclass'},"Bio::Seq::MetaI"); # } #else { # @ISA = qw( Bio::LocatableSeq Bio::Seq Bio::Seq::MetaI ); # } my $self = $class->SUPER::new(%args); my($meta, $forceflush) = $self->_rearrange([qw(META FORCE_FLUSH )], %args); $self->{'_meta'}->{$DEFAULT_NAME} = []; $meta && $self->meta($meta); $forceflush && $self->force_flush($forceflush); return $self; } =head2 meta Title : meta Usage : $meta_values = $obj->meta($values_string); Function: Get and set method for the meta data starting from residue position one. Since it is dependent on the length of the sequence, it needs to be manipulated after the sequence. The length of the returned value always matches the length of the sequence. Returns : reference to an array of meta data Args : new value, string or array ref, optional =cut sub meta { shift->named_meta($DEFAULT_NAME, shift); } =head2 meta_text Title : meta_text Usage : $meta_values = $obj->meta_text($values_arrayref); Function: Variant of meta() guarantied to return a string representation of meta data. For details, see L<meta>. Returns : a string Args : new value, string or array ref, optional =cut sub meta_text { return join ' ', map {0 unless $_} @{shift->meta(shift)}; } =head2 named_meta Title : named_meta() Usage : $meta_values = $obj->named_meta($name, $values_arrayref); Function: A more general version of meta(). Each meta data set needs to be named. See also L<meta_names>. Returns : reference to an array of meta data Args : scalar, name of the meta data set new value, string or array ref, optional =cut sub named_meta { my ($self, $name, $value) = @_; $name ||= $DEFAULT_NAME; if (defined $value) { my ($arrayref); if (ref $value eq 'ARRAY' ) { # array ref $arrayref = $value; } elsif (not ref($value)) { # scalar $arrayref = [split /\s+/, $value]; } else { $self->throw("I need a scalar or array ref, not [". ref($value). "]"); } # test for length my $diff = $self->length - @{$arrayref}; if ($diff > 0) { foreach (1..$diff) { push @{$arrayref}, 0;} } $self->{'_meta'}->{$name} = $arrayref; #$self->_test_gap_positions($name) if $self->verbose > 0; } $self->_do_flush if $self->force_flush; return $self->{'_meta'}->{$name} || (" " x $self->length); } =head2 _test_gap_positions Title : _test_gap_positions Usage : $meta_values = $obj->_test_gap_positions($name); Function: Internal test for correct position of gap characters. Gap being only '-' this time. This method is called from named_meta() when setting meta data but only if verbose is positive as this can be an expensive process on very long sequences. Set verbose(1) to see warnings when gaps do not align in sequence and meta data and turn them into errors by setting verbose(2). Returns : true on success, prints warnings Args : none =cut sub _test_gap_positions { my $self = shift; my $name = shift; my $success = 1; $self->seq || return $success; my $len = CORE::length($self->seq); for (my $i=0; $i < $len; $i++) { my $s = substr $self->{seq}, $i, 1; my $m = substr $self->{_meta}->{$name}, $i, 1; $self->warn("Gap mismatch in column [". ($i+1). "] of [$name] meta data in seq [". $self->id. "]") and $success = 0 if ($m eq '-') && $s ne $m; } return $success; } =head2 named_meta_text Title : named_meta_text() Usage : $meta_values = $obj->named_meta_text($name, $values_arrayref); Function: Variant of named_meta() guarantied to return a textual representation of the named meta data. For details, see L<meta>. Returns : a string Args : scalar, name of the meta data set new value, string or array ref, optional =cut sub named_meta_text { return join ' ', @{shift->named_meta(@_)}; } =head2 submeta Title : submeta Usage : $subset_of_meta_values = $obj->submeta(10, 20, $value_string); $subset_of_meta_values = $obj->submeta(10, undef, $value_string); Function: Get and set method for meta data for subsequences. Numbering starts from 1 and the number is inclusive, ie 1-2 are the first two residue of the sequence. Start cannot be larger than end but can be equal. If the second argument is missing the returned values should extend to the end of the sequence. The return value may be a string or an array reference, depending on the implementation. If in doubt, use submeta_text() which is a variant guarantied to return a string. See L<submeta_text>. Returns : A reference to an array or a string Args : integer, start position integer, end position, optional when a third argument present new value, string or array ref, optional =cut sub submeta { shift->named_submeta($DEFAULT_NAME, @_); } =head2 submeta_text Title : submeta_text Usage : $meta_values = $obj->submeta_text(20, $value_string); Function: Variant of submeta() guarantied to return a textual representation of meta data. For details, see L<meta>. Returns : a string Args : new value, string or array ref, optional =cut sub submeta_text { return join ' ', @{shift->named_submeta($DEFAULT_NAME, @_)}; } =head2 named_submeta Title : named_submeta Usage : $subset_of_meta_values = $obj->named_submeta($name, 10, 20, $value_string); $subset_of_meta_values = $obj->named_submeta($name, 10); Function: Variant of submeta() guarantied to return a textual representation of meta data. For details, see L<meta>. Returns : A reference to an array or a string Args : scalar, name of the meta data set integer, start position integer, end position, optional when a third argument present (can be undef) new value, string or array ref, optional =cut sub named_submeta { my ($self, $name, $start, $end, $value) = @_; $name ||= $DEFAULT_NAME; $start ||=1; $start =~ /^[+]?\d+$/ and $start > 0 or $self->throw("Need at least a positive integer start value"); $start--; my $meta_len = scalar(@{$self->{_meta}->{$name}}); if (defined $value) { my $arrayref; if (ref $value eq 'ARRAY' ) { # array ref $arrayref = $value; } elsif (not ref($value)) { # scalar $arrayref = [split /\s+/, $value]; } else { $self->throw("I need a space separated scalar or array ref, not [". ref($value). "]"); } $self->warn("You are setting meta values beyond the length of the sequence\n". "[$start > ". length($self->seq)."] in sequence ". $self->id) if $start + scalar @{$arrayref} -1 > $self->length; $end or $end = @{$arrayref} + $start; $end--; # test for length; pad if needed my $diff = $end - $start - scalar @{$arrayref}; if ($diff > 0) { foreach (1..$diff) { push @{$arrayref}, $META_GAP} } @{$self->{_meta}->{$name}}[$start..$end] = @{$arrayref}; $self->_do_flush if $self->force_flush; return $arrayref; } else { # don't set by seq length; use meta array length instead; bug 2478 $end ||= $meta_len; if ($end > $meta_len) { $self->warn("End is longer than meta sequence $name length; resetting to $meta_len"); $end = $meta_len; } # warn but don't reset (push use of trunc() instead) $self->warn("End is longer than sequence length; use trunc() \n". "if you want a fully truncated object") if $end > $self->length; $end--; return [@{$self->{_meta}->{$name}}[$start..$end]]; } } =head2 named_submeta_text Title : named_submeta_text Usage : $meta_values = $obj->named_submeta_text($name, 20, $value_string); Function: Variant of submeta() guarantied to return a textual representation of meta data. For details, see L<meta>. Returns : a string Args : scalar, name of the meta data Args : integer, start position, optional integer, end position, optional new value, string or array ref, optional =cut sub named_submeta_text { return join ' ', @{shift->named_submeta(@_)}; } =head2 meta_names Title : meta_names Usage : @meta_names = $obj->meta_names() Function: Retrieves an array of meta data set names. The default (unnamed) set name is guarantied to be the first name if it contains any data. Returns : an array of names Args : none =cut sub meta_names { my ($self) = @_; my @r; foreach ( sort keys %{$self->{'_meta'}} ) { push (@r, $_) unless $_ eq $DEFAULT_NAME; } unshift @r, $DEFAULT_NAME if $self->{'_meta'}->{$DEFAULT_NAME}; return @r; } =head2 meta_length Title : meta_length() Usage : $meta_len = $obj->meta_length(); Function: return the number of elements in the meta set Returns : integer Args : - =cut sub meta_length { my ($self) = @_; return $self->named_meta_length($DEFAULT_NAME); } =head2 named_meta_length Title : named_meta_length() Usage : $meeta_len = $obj->named_meta_length($name); Function: return the number of elements in the named meta set Returns : integer Args : - =cut sub named_meta_length { my ($self, $name) = @_; $name ||= $DEFAULT_NAME; return scalar @{$self->{'_meta'}->{$name}}; } =head2 force_flush Title : force_flush() Usage : $force_flush = $obj->force_flush(1); Function: Automatically pad with empty values or truncate meta values to sequence length. Not done by default. Returns : boolean 1 or 0 Args : optional boolean value Note that if you turn this forced padding off, the previously padded values are not changed. =cut sub force_flush { my ($self, $value) = @_; if (defined $value) { if ($value) { $self->{force_flush} = 1; $self->_do_flush; } else { $self->{force_flush} = 0; } } return $self->{force_flush}; } =head2 _do_flush Title : _do_flush Usage : Function: internal method to do the force that meta values are same length as sequence . Called from L<force_flush> Returns : Args : =cut sub _do_flush { my ($self) = @_; foreach my $name ($self->meta_names) { #print "seq: ", $self->length , " ", $name, ": ", $self->named_meta_length($name), "======\n"; # elongnation if ($self->length > $self->named_meta_length($name)) { my $diff = $self->length - $self->named_meta_length($name); foreach (1..$diff) { push @{$self->{'_meta'}->{$name}}, $META_GAP} } # truncation elsif ( $self->length < $self->named_meta_length($name) ) { $self->{_meta}->{$name} = [@{$self->{_meta}->{$name}}[0..($self->length-1)]] } } } =head2 is_flush Title : is_flush Usage : $is_flush = $obj->is_flush() or $is_flush = $obj->is_flush($my_meta_name) Function: Boolean to tell if all meta values are in flush with the sequence length. Returns true if force_flush() is set Set verbosity to a positive value to see failed meta sets Returns : boolean 1 or 0 Args : optional name of the meta set =cut sub is_flush { my ($self, $name) = shift; return 1 if $self->force_flush; my $sticky = ''; if ($name) { $sticky .= "$name " if $self->length != $self->named_meta_length($name); } else { foreach my $m ($self->meta_names) { $sticky .= "$m " if ($self->named_meta_length($m) > 0) && ($self->length != $self->named_meta_length($m)) ; } } if ($sticky) { print "These meta set are not flush: $sticky\n" if $self->verbose; return 0; } return 1; } =head1 Bio::PrimarySeqI methods =head2 revcom Title : revcom Usage : $newseq = $seq->revcom(); Function: Produces a new Bio::Seq::MetaI implementing object where the order of residues and their meta information is reversed. Returns : A new (fresh) Bio::Seq::Meta object Args : none Throws : if the object returns false on is_flush() Note: The method does nothing to meta values, it reorders them, only. =cut sub revcom { my $self = shift; $self->throw("Can not get a reverse complement. The object is not flush.") unless $self->is_flush; my $new = $self->SUPER::revcom; my $end = $self->length - 1; map { $new->{_meta}->{$_} = [ reverse @{$self->{_meta}->{$_}}[0..$end]] } keys %{$self->{_meta}}; return $new; } =head2 trunc Title : trunc Usage : $subseq = $seq->trunc(10,100); Function: Provides a truncation of a sequence together with meta data Returns : a fresh Bio::Seq::Meta implementing object Args : Two integers denoting first and last residue of the sub-sequence. =cut sub trunc { my ($self, $start, $end) = @_; # test arguments $start =~ /^[+]?\d+$/ and $start > 0 or $self->throw("Need at least a positive integer start value as start; got [$start]"); $end =~ /^[+]?\d+$/ and $end > 0 or $self->throw("Need at least a positive integer start value as end; got [$end]"); $end >= $start or $self->throw("End position has to be larger or equal to start; got [$start..$end]"); $end <= $self->length or $self->throw("End position can not be larger than sequence length; got [$end]"); my $new = $self->SUPER::trunc($start, $end); $start--; $end--; map { $new->{_meta}->{$_} = [@{$self->{_meta}->{$_}}[$start..$end]] } keys %{$self->{_meta}}; return $new; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqEvolution�������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16524� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqEvolution/DNAPoint.pm�������������������������������������������������������000444��000766��000024�� 24013�13155576320� 20653� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqEvolution::DNAPoint # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki at bioperl dot org> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqEvolution::DNAPoint - evolve a sequence by point mutations =head1 SYNOPSIS # $seq is a Bio::PrimarySeqI to mutate $evolve = Bio::SeqEvolution::Factory->new (-rate => 5, -seq => $seq, -identity => 50 ); $newseq = $evolve->next_seq; =head1 DESCRIPTION Bio::SeqEvolution::DNAPoint implements the simplest evolution model: nucleotides change by point mutations, only. Transition/transversion rate of the change, rate(), can be set. The new sequences are named with the id of the reference sequence added with a running number. Placing a new sequence into a factory to be evolved resets that counter. It can also be called directly with L<reset_sequence_counter>. The default sequence type returned is Bio::PrimarySeq. This can be changed to any Bio::PrimarySeqI compliant sequence class. Internally the probability of the change of one nucleotide is mapped to scale from 0 to 100. The probability of the transition occupies range from 0 to some value. The remaining range is divided equally among the two transversion nucleotides. A random number is then generated to pick up one change. Not that the default transition/transversion rate, 1:1, leads to observed transition/transversion ratio of 1:2 simply because there is only one transition nucleotide versus two transversion nucleotides. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt> =head1 CONTRIBUTORS Additional contributor's names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqEvolution::DNAPoint; use strict; use Bio::Root::Root; use Bio::SeqEvolution::Factory; use Bio::Variation::DNAMutation; use Bio::Variation::Allele; use Bio::SimpleAlign; use base qw(Bio::SeqEvolution::Factory); sub _initialize { my($self, @args) = @_; $self->SUPER::_initialize(@args); my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys exists $param{'-rate'} && $self->rate($param{'-rate'}); $self->_init_mutation_engine; } sub _init_mutation_engine { my $self = shift; # arrays of possible changes have transitions as first items my %changes; $self->{'_changes'}->{'a'} = ['t', 'c', 'g']; $self->{'_changes'}->{'t'} = ['a', 'c', 'g']; $self->{'_changes'}->{'c'} = ['g', 'a', 't']; $self->{'_changes'}->{'g'} = ['c', 'a', 't']; # given the desired rate, find out where cut off points need to be # when random numbers are generated from 0 to 100 # we are ignoring identical mutations (e.g. A->A) to speed things up my $bin_size = 100/($self->rate + 2); $self->{'_transition'} = 100 - (2*$bin_size); $self->{'_first_transversion'} = $self->{'_transition'} + $bin_size; $self->_init_alignment; } sub _init_alignment { my $self = shift; # put the initial sequence into the alignment object $self->{'_align'} = Bio::SimpleAlign->new(-verbose => -1); return unless $self->seq; $self->{'_ori_locatableseq'} = Bio::LocatableSeq->new(-id => 'ori', -seq=> $self->seq->seq); $self->{'_mut_locatableseq'} = Bio::LocatableSeq->new(-id => 'mut', -seq=> $self->seq->seq); $self->{'_align'}->add_seq($self->{'_ori_locatableseq'}); $self->{'_align'}->add_seq($self->{'_mut_locatableseq'}); } =head2 seq Title : seq Usage : $obj->seq($newval) Function: Set the sequence object for the original sequence Returns : The sequence object Args : newvalue (optional) Setting this will reset mutation and generated mutation counters. =cut sub seq{ my $self = shift; if (@_) { my $seq = shift; $self->throw('Need a valid Bio::PrimarySeqI, not [', ref($seq), ']') unless $seq->isa('Bio::PrimarySeqI'); $self->throw('Only nucleotide sequences are supported') if $seq->alphabet eq 'protein'; $self->throw('No ambiquos nucleotides allowed in the input sequence') if $seq->seq =~ m/[^acgt]/; $self->{'_seq'} = $seq; # unify the look of sequence strings and cache the information $self->{'_ori_string'} = lc $seq->seq; # lower case $self->{'_ori_string'} =~ s/u/t/; # simplyfy our life; modules should deal with the change anyway $self->{'_seq_length'} = $seq->length; $self->reset_sequence_counter; } return $self->{'_seq'}; } =head2 set_mutated_seq Title : seq_mutated_seq Usage : $obj->set_mutated_seq($newval) Function: In case of mutating a sequence with multiple evolvers, this Returns : set_mutated_seq Args : newvalue (optional) =cut sub set_mutated_seq { my $self = shift; if (@_) { my $seq = shift; $self->throw('Need a valid Bio::PrimarySeqI, not [', ref($seq), ']') unless $seq->isa('Bio::PrimarySeqI'); $self->throw('Only nucleotide sequences are supported') if $seq->alphabet eq 'protein'; $self->throw('No ambiquos nucleotides allowed in the input sequence') if $seq->seq =~ m/[^acgt]/; $self->{'_seq_mutated'} = $seq; # unify the look of sequence strings and cache the information $self->{'_mut_string'} = lc $seq->seq; # lower case $self->{'_mut_string'} =~ s/u/t/; # simplyfy our life; modules should deal with the change anyway $self->reset_sequence_counter; } #set returned sequence to be the last mutated string $self->{'_seq'}->seq($self->{'_mut_string'}); return $self->{'_seq'}; } =head2 rate Title : rate Usage : $obj->rate($newval) Function: Set the transition/transversion rate. Returns : value of rate Args : newvalue (optional) Transition/transversion ratio is an observed attribute of an sequence comparison. We are dealing here with the transition/transversion rate that we set for our model of sequence evolution. Note that we are using standard nucleotide alphabet and that there can there is only one transition versus two possible transversions. Rate 2 is needed to have an observed transition/transversion ratio of 1. =cut sub rate{ my $self = shift; if (@_) { $self->{'_rate'} = shift @_; $self->_init_mutation_engine; } return $self->{'_rate'} || 1; } =head2 next_seq Title : next_seq Usage : $obj->next_seq Function: Evolve the reference sequence to desired level Returns : A new sequence object mutated from the reference sequence Args : - =cut sub next_seq { my $self = shift; $self->{'_mut_string'} = $self->{'_ori_string'}; $self->reset_mutation_counter; $self->{'_mutations'} = []; while (1) { # find the location in the string to change my $loc = int (rand length($self->{'_mut_string'})) + 1; $self->mutate($loc); # for modularity # stop evolving if any of the limit has been reached last if $self->identity && $self->get_alignment_identity <= $self->identity; last if $self->pam && 100*$self->get_mutation_counter/$self->{'_seq_length'} >= $self->pam; last if $self->mutation_count && $self->get_mutation_counter >= $self->mutation_count; } $self->_increase_sequence_counter; my $type = $self->seq_type; return $type->new(-id => $self->seq->id. "-". $self->get_sequence_counter, -description => $self->seq->description, -seq => $self->{'_mut_string'} ) } =head2 mutate Title : mutate Usage : $obj->mutate Function: mutate the sequence at the given location according to the model Returns : true Args : integer, start location of the mutation, required argument Called from next_seq(). =cut sub mutate { my $self = shift; my $loc = shift; $self->throw('the first argument is the location of the mutation') unless $loc; # nucleotide to change my $oldnuc = substr $self->{'_mut_string'}, $loc-1, 1; my $newnuc; # find the nucleotide it is changed to my $choose = rand(100); # scale is 0-100 if ($choose < $self->{'_transition'} ) { $newnuc = $self->{'_changes'}->{$oldnuc}[0]; } elsif ($choose < $self->{'_first_transversion'} ) { $newnuc = $self->{'_changes'}->{$oldnuc}[1]; } else { $newnuc = $self->{'_changes'}->{$oldnuc}[2]; } # do the change substr $self->{'_mut_string'}, $loc-1, 1 , $newnuc; $self->_increase_mutation_counter; $self->{'_mut_locatableseq'}->seq($self->{'_mut_string'}); print STDERR "$loc$oldnuc>$newnuc\n" if $self->verbose > 0; push @{$self->{'_mutations'}}, "$loc$oldnuc>$newnuc"; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqEvolution/EvolutionI.pm�����������������������������������������������������000444��000766��000024�� 6370�13155576320� 21322� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqEvolution::EvolutionI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki at bioperl dot org> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqEvolution::EvolutionI - the interface for evolving sequences =head1 SYNOPSIS # not an instantiable class =head1 DESCRIPTION This is the interface that all classes that mutate sequence objects in constant fashion must implement. A good example is Bio::SeqEvolution::DNAPoint. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt> =head1 CONTRIBUTORS Additional contributor's names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqEvolution::EvolutionI; use strict; use base qw(Bio::Root::RootI); =head2 annotation Title : annotation Usage : $obj->annotation($newval) Function: Get the annotation collection for this annotatable object. Example : Returns : a Bio::AnnotationCollectionI implementing object, or undef Args : on set, new value (a Bio::AnnotationCollectionI implementing object, optional) (an implementation may not support changing the annotation collection) See L<Bio::AnnotationCollectionI> =cut =head2 seq Title : seq Usage : $obj->seq($newval) Function: Set the sequence object for the original sequence Returns : The sequence object Args : newvalue (optional) Setting this will reset mutation and generated mutation counters. =cut sub seq { shift->throw_not_implemented(); } =head2 next_seq Title : next_seq Usage : $obj->next_seq Function: Evolve the reference sequence to desired level Returns : A new sequence object mutated from the reference sequence Args : - =cut sub next_seq{ shift->throw_not_implemented(); } =head2 mutate Title : mutate Usage : $obj->mutate Function: mutate the sequence at the given location according to the model Returns : true Args : integer, start location of the mutation, required argument Called from next_seq(). =cut sub mutate { shift->throw_not_implemented(); } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqEvolution/Factory.pm��������������������������������������������������������000444��000766��000024�� 25071�13155576320� 20653� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqEvolution::Factory # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki at bioperl dot org> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqEvolution::Factory - Factory object to instantiate sequence evolving classes =head1 SYNOPSIS # not an instantiable class =head1 DESCRIPTION This is the factory class that can be used to call for a specific model to mutate a sequence. Bio::SeqEvolution::DNAPoint is the default for nucleotide sequences and the only implementation at this point. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt> =head1 CONTRIBUTORS Additional contributor's names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqEvolution::Factory; use strict; use Bio::Root::Root; use Bio::SeqEvolution::EvolutionI; use base qw(Bio::Root::Root Bio::SeqEvolution::EvolutionI); =head2 new Title : new Usage : my $obj = Bio::SeqEvolution::Factory->new(); Function: Builds a new Bio:SeqEvolution::EvolutionI object Returns : Bio:SeqEvolution::EvolutionI object Args : -type => class name See L<Bio:SeqEvolution::EvolutionI> =cut sub new { my($caller,@args) = @_; my $class = ref($caller) || $caller; my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys if ( $class eq 'Bio::SeqEvolution::Factory') { #my %param = @args; #@param{ map { lc $_ } keys %param } = values %param; # lowercase keys if (exists $param{'-type'}) { # $self->type($param{'-type'}); } else { $param{'-type'} = 'Bio::SeqEvolution::DNAPoint'; #$self->type('Bio::SeqEvolution::DNAPoint'} unless $seq->alphabet == 'protein' } my $type = $param{'-type'}; return unless( $class->_load_format_module($param{'-type'}) ); return $type->new(%param); } else { my ($self) = $class->SUPER::new(%param); $self->_initialize(%param); return $self; } } sub _initialize { my($self, @args) = @_; $self->SUPER::_initialize(@args); my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys exists $param{'-seq'} && $self->seq($param{'-seq'}); exists $param{'-set_mutated_seq'} && $self->set_mutated_seq($param{'-set_mutated_seq'}); exists $param{'-identity'} && $self->identity($param{'-identity'}); exists $param{'-pam'} && $self->pam($param{'-pam'}); exists $param{'-mutation_count'} && $self->mutation_count($param{'-mutation_count'}); } =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL SeqIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($self, $format) = @_; my $module = $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <<END; $self: $format cannot be found Exception $@ END ; } return $ok; } =head2 type Title : type Usage : $obj->type($newval) Function: Set used evolution model. It is set by giving a valid Bio::SeqEvolution::* class name Returns : value of type Args : newvalue (optional) Defaults to Bio::SeqEvolution::DNAPoint. =cut sub type{ my $self = shift; if (@_) { $self->{'_type'} = shift @_; $self->_load_module($self->{'_type'}); } return $self->{'_type'} || 'Bio::SeqEvolution::DNAPoint'; } =head1 mutation counters The next three methods set a value to limit the number of mutations introduced the the input sequence. =cut =head2 identity Title : identity Usage : $obj->identity($newval) Function: Set the desired identity between original and mutated sequence Returns : value of identity Args : newvalue (optional) =cut sub identity{ my $self = shift; $self->{'_identity'} = shift @_ if @_; return $self->{'_identity'}; } =head2 pam Title : pam Usage : $obj->pam($newval) Function: Set the wanted Percentage of Accepted Mutations, PAM Returns : value of PAM Args : newvalue (optional) When you are measuring sequence divergence, PAM needs to be estimated. When you are generating sequences, PAM is simply the count of mutations introduced to the reference sequence normalised to the original sequence length. =cut sub pam{ my $self = shift; $self->{'_pam'} = shift @_ if @_; return $self->{'_pam'}; } =head2 mutation_count Title : mutation_count Usage : $obj->mutation_count($newval) Function: Set the number of wanted mutations to the sequence Returns : value of mutation_count Args : newvalue (optional) =cut sub mutation_count{ my $self = shift; $self->{'_mutation_count'} = shift @_ if @_; return $self->{'_mutation_count'}; } =head2 seq Title : seq Usage : $obj->seq($newval) Function: Set the sequence object for the original sequence Returns : The sequence object Args : newvalue (optional) Setting this will reset mutation and generated mutation counters. =cut sub seq { my $self = shift; if (@_) { $self->{'_seq'} = shift @_ ; return $self->{'_seq'}; $self->reset_mutation_counter; $self->reset_sequence_counter; } return $self->{'_seq'}; } =head2 seq_type Title : seq_type Usage : $obj->seq_type($newval) Function: Set the returned seq_type to one needed Returns : value of seq_type Args : newvalue (optional) Defaults to Bio::PrimarySeq. =cut sub seq_type{ my $self = shift; if (@_) { $self->{'_seq_type'} = shift @_; $self->_load_module($self->{'_seq_type'}); } return $self->{'_seq_type'} || 'Bio::PrimarySeq'; } =head2 get_mutation_counter Title : get_mutation_counter Usage : $obj->get_mutation_counter() Function: Get the count of sequences created Returns : value of counter Args : - =cut sub get_mutation_counter{ return shift->{'_mutation_counter'}; } =head2 reset_mutation_counter Title : reset_mutation_counter Usage : $obj->reset_mutation_counter() Function: Resert the counter of mutations Returns : value of counter Args : - =cut sub reset_mutation_counter{ shift->{'_mutation_counter'} = 0; return 1; } =head2 get_sequence_counter Title : get_sequence_counter Usage : $obj->get_sequence_counter() Function: Get the count of sequences created Returns : value of counter Args : - =cut sub get_sequence_counter{ return shift->{'_sequence_counter'}; } =head2 reset_sequence_counter Title : reset_sequence_counter Usage : $obj->reset_sequence_counter() Function: Resert the counter of sequences created Returns : value of counter Args : - This is called when ever mutated sequences are reassigned new values using methods seq() and mutated_seq(). As a side affect, this method also recreates the intermal alignment that is used to calculate the sequence identity. =cut sub reset_sequence_counter{ my $self = shift; $self->{'_sequence_counter'} = 0; $self->_init_alignment; return 1; } =head2 each_seq Title : each_seq Usage : $obj->each_seq($int) Function: Returns : an array of sequences mutated from the reference sequence according to evolutionary parameters given Args : - =cut sub each_seq{ my $self = shift; my $number = shift; $self->throw("[$number] ". ' should be a positive integer') unless $number =~ /^[+\d]+$/; my @array; for (my $count=1; $count<$number; $count++) { push @array, $self->next_seq(); } return @array; } =head2 each_mutation Title : each_mutation Usage : $obj->each_mutation Function: return the mutations leading to the last generated sequence in objects Returns : an array of Bio::Variation::DNAMutation objects Args : optional argument to return an array of stringified names =cut sub each_mutation { my $self = shift; my $string = shift; return @{$self->{'_mutations'}} if $string; return map { /(\d+)(\w*)>(\w*)/; # print; my $dnamut = Bio::Variation::DNAMutation->new ('-start' => $1, '-end' => $1, '-length' => 1, '-isMutation' => 1 ); $dnamut->allele_ori( Bio::Variation::Allele->new(-seq => $2, -alphabet => 'dna') ); $dnamut->add_Allele( Bio::Variation::Allele->new(-seq => $3, -alphabet => 'dna') ); $dnamut; } @{$self->{'_mutations'}} } sub get_alignment_identity { my $self = shift; return $self->{'_align'}->overall_percentage_identity; } sub get_alignmet { my $self = shift; return $self->{'_align'}->remove_gaps('-', 'all-gaps'); } =head1 Internal methods =cut =head2 _increase_mutation_counter Title : _increase_mutation_counter Usage : $obj->_increase_mutation_counter() Function: Internal method to increase the counter of mutations performed Returns : value of counter Args : - =cut sub _increase_mutation_counter{ return shift->{'_mutation_counter'}++; } =head2 _increase_sequence_counter Title : _increase_sequence_counter Usage : $obj->_increase_sequence_counter() Function: Internal method to increase the counter of sequences created Returns : value of counter Args : - =cut sub _increase_sequence_counter{ return shift->{'_sequence_counter'}++; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature���������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16133� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Amplicon.pm���������������������������������������������������������000444��000766��000024�� 11453�13155576320� 20414� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Amplicon # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Copyright Florent Angly # # You may distribute this module under the same terms as perl itself =head1 NAME Bio::SeqFeature::Amplicon - Amplicon feature =head1 SYNOPSIS # Amplicon with explicit sequence use Bio::SeqFeature::Amplicon; my $amplicon = Bio::SeqFeature::Amplicon->new( -seq => $seq_object, -fwd_primer => $primer_object_1, -rev_primer => $primer_object_2, ); # Amplicon with implicit sequence use Bio::Seq; my $template = Bio::Seq->new( -seq => 'AAAAACCCCCGGGGGTTTTT' ); $amplicon = Bio::SeqFeature::Amplicon->new( -start => 6, -end => 15, ); $template->add_SeqFeature($amplicon); print "Amplicon start : ".$amplicon->start."\n"; print "Amplicon end : ".$amplicon->end."\n"; print "Amplicon sequence: ".$amplicon->seq->seq."\n"; # Amplicon sequence should be 'CCCCCGGGGG' =head1 DESCRIPTION Bio::SeqFeature::Amplicon extends L<Bio::SeqFeature::Subseq> to represent an amplicon sequence and optional primer sequences. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Florent Angly <florent.angly@gmail.com> =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqFeature::Amplicon; use strict; use base qw(Bio::SeqFeature::SubSeq); =head2 new Title : new() Usage : my $amplicon = Bio::SeqFeature::Amplicon( -seq => $seq_object ); Function: Instantiate a new Bio::SeqFeature::Amplicon object Args : -seq , the sequence object or sequence string of the amplicon (optional) -fwd_primer , a Bio::SeqFeature primer object with specified location on amplicon (optional) -rev_primer , a Bio::SeqFeature primer object with specified location on amplicon (optional) Returns : A Bio::SeqFeature::Amplicon object =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($fwd_primer, $rev_primer) = $self->_rearrange([qw(FWD_PRIMER REV_PRIMER)], @args); $fwd_primer && $self->fwd_primer($fwd_primer); $rev_primer && $self->rev_primer($rev_primer); return $self; } sub _primer { # Get or set a primer. Type is either 'fwd' or 'rev'. my ($self, $type, $primer) = @_; if (defined $primer) { if ( not(ref $primer) || not $primer->isa('Bio::SeqFeature::Primer') ) { $self->throw("Expected a primer object but got a '".ref($primer)."'\n"); } if ( not defined $self->location ) { $self->throw("Location of $type primer on amplicon is not known. ". "Use start(), end() or location() to set it."); } $primer->primary_tag($type.'_primer'); $self->add_SeqFeature($primer); } return (grep { $_->primary_tag eq $type.'_primer' } $self->get_SeqFeatures)[0]; } =head2 fwd_primer Title : fwd_primer Usage : my $primer = $feat->fwd_primer(); Function: Get or set the forward primer. When setting it, the primary tag 'fwd_primer' is added to the primer and its start, stop and strand attributes are set if needed, assuming that the forward primer is at the beginning of the amplicon and the reverse primer at the end. Args : A Bio::SeqFeature::Primer object (optional) Returns : A Bio::SeqFeature::Primer object =cut sub fwd_primer { my ($self, $primer) = @_; return $self->_primer('fwd', $primer); } =head2 rev_primer Title : rev_primer Usage : my $primer = $feat->rev_primer(); Function: Get or set the reverse primer. When setting it, the primary tag 'rev_primer' is added to the primer. Args : A Bio::SeqFeature::Primer object (optional) Returns : A Bio::SeqFeature::Primer object =cut sub rev_primer { my ($self, $primer) = @_; return $self->_primer('rev', $primer); } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/AnnotationAdaptor.pm������������������������������������������������000444��000766��000024�� 36431�13155576320� 22302� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::AnnotationAdaptor # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp at gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::AnnotationAdaptor - integrates SeqFeatureIs annotation =head1 SYNOPSIS use Bio::SeqFeature::Generic; use Bio::SeqFeature::AnnotationAdaptor; # obtain a SeqFeatureI implementing object somehow my $feat = Bio::SeqFeature::Generic->new(-start => 10, -end => 20); # add tag/value annotation $feat->add_tag_value("mytag", "value of tag mytag"); $feat->add_tag_value("mytag", "another value of tag mytag"); # Bio::SeqFeature::Generic also provides annotation(), which returns a # Bio::AnnotationCollectionI compliant object $feat->annotation->add_Annotation("dbxref", $dblink); # to integrate tag/value annotation with AnnotationCollectionI # annotation, use this adaptor, which also implements # Bio::AnnotationCollectionI my $anncoll = Bio::SeqFeature::AnnotationAdaptor->new(-feature => $feat); # this will now return tag/value pairs as # Bio::Annotation::SimpleValue objects my @anns = $anncoll->get_Annotations("mytag"); # other added before annotation is available too my @dblinks = $anncoll->get_Annotations("dbxref"); # also supports transparent adding of tag/value pairs in # Bio::AnnotationI flavor my $tagval = Bio::Annotation::SimpleValue->new(-value => "some value", -tagname => "some tag"); $anncoll->add_Annotation($tagval); # this is now also available from the feature's tag/value system my @vals = $feat->get_tag_values("some tag"); =head1 DESCRIPTION L<Bio::SeqFeatureI> defines light-weight annotation of features through tag/value pairs. Conversely, L<Bio::AnnotationCollectionI> together with L<Bio::AnnotationI> defines an annotation bag, which is better typed, but more heavy-weight because it contains every single piece of annotation as objects. The frequently used base implementation of Bio::SeqFeatureI, Bio::SeqFeature::Generic, defines an additional slot for AnnotationCollectionI-compliant annotation. This adaptor provides a L<Bio::AnnotationCollectionI> compliant, unified, and integrated view on the annotation of L<Bio::SeqFeatureI> objects, including tag/value pairs, and annotation through the annotation() method, if the object supports it. Code using this adaptor does not need to worry about the different ways of possibly annotating a SeqFeatureI object, but can instead assume that it strictly follows the AnnotationCollectionI scheme. The price to pay is that retrieving and adding annotation will always use objects instead of light-weight tag/value pairs. In other words, this adaptor allows us to keep the best of both worlds. If you create tens of thousands of feature objects, and your only annotation is tag/value pairs, you are best off using the features' native tag/value system. If you create a smaller number of features, but with rich and typed annotation mixed with tag/value pairs, this adaptor may be for you. Since its implementation is by double-composition, you only need to create one instance of the adaptor. In order to transparently annotate a feature object, set the feature using the feature() method. Every annotation you add will be added to the feature object, and hence will not be lost when you set feature() to the next object. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' Let the code begin... package Bio::SeqFeature::AnnotationAdaptor; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Annotation::SimpleValue; use base qw(Bio::Root::Root Bio::AnnotationCollectionI Bio::AnnotatableI); =head2 new Title : new Usage : my $obj = Bio::SeqFeature::AnnotationAdaptor->new(); Function: Builds a new Bio::SeqFeature::AnnotationAdaptor object Returns : an instance of Bio::SeqFeature::AnnotationAdaptor Args : Named parameters -feature the Bio::SeqFeatureI implementing object to adapt (mandatory to be passed here, or set via feature() before calling other methods) -annotation the Bio::AnnotationCollectionI implementing object for storing richer annotation (this will default to the $feature->annotation() if it supports it) -tagvalue_factory the object factory to use for creating tag/value pair representing objects =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($feat,$anncoll,$fact) = $self->_rearrange([qw(FEATURE ANNOTATION TAGVALUE_FACTORY)], @args); $self->feature($feat) if $feat; $self->annotation($anncoll) if $feat; $self->tagvalue_object_factory($fact) if $fact; return $self; } =head2 feature Title : feature Usage : $obj->feature($newval) Function: Get/set the feature that this object adapts to an AnnotationCollectionI. Example : Returns : value of feature (a Bio::SeqFeatureI compliant object) Args : new value (a Bio::SeqFeatureI compliant object, optional) =cut sub feature{ my ($self,$value) = @_; if( defined $value) { $self->{'feature'} = $value; } return $self->{'feature'}; } =head2 annotation Title : annotation Usage : $obj->annotation($newval) Function: Get/set the AnnotationCollectionI implementing object used by this adaptor to store additional annotation that cannot be stored by the SeqFeatureI itself. If requested before having been set, the value will default to the annotation object of the feature if it has one. Example : Returns : value of annotation (a Bio::AnnotationCollectionI compliant object) Args : new value (a Bio::AnnotationCollectionI compliant object, optional) =cut sub annotation{ my ($self,$value) = @_; if( defined $value) { $self->{'annotation'} = $value; } if((! exists($self->{'annotation'})) && $self->feature()->can('annotation')) { return $self->feature()->annotation(); } return $self->{'annotation'}; } =head1 AnnotationCollectionI implementing methods =cut =head2 get_all_annotation_keys Title : get_all_annotation_keys Usage : $ac->get_all_annotation_keys() Function: gives back a list of annotation keys, which are simple text strings Returns : list of strings Args : none =cut sub get_all_annotation_keys{ my ($self) = @_; my @keys = (); # get the tags from the feature object if ($self->feature()->can('get_all_tags')) { push(@keys, $self->feature()->get_all_tags()); } else { push(@keys, $self->feature()->all_tags()); } # ask the annotation implementation in addition, while avoiding duplicates if($self->annotation()) { push(@keys, grep { ! $self->feature->has_tag($_); } $self->annotation()->get_all_annotation_keys()); } # done return @keys; } =head2 get_Annotations Title : get_Annotations Usage : my @annotations = $collection->get_Annotations('key') Function: Retrieves all the Bio::AnnotationI objects for a specific key Returns : list of Bio::AnnotationI - empty if no objects stored for a key Args : string which is key for annotations =cut sub get_Annotations{ my ($self, @keys) = @_; my @anns = (); # we need a annotation object factory my $fact = $self->tagvalue_object_factory(); # get all tags if no keys have been provided @keys = $self->feature->all_tags() unless @keys; # build object for each value for each tag foreach my $key (@keys) { # protect against keys that aren't tags next unless $self->feature->has_tag($key); # add each tag/value pair as a SimpleValue object foreach my $val ($self->feature()->get_tag_values($key)) { my $ann; if($fact) { $ann = $fact->create_object(-value => $val, -tagname => $key); } else { $ann = Bio::Annotation::SimpleValue->new(-value => $val, -tagname => $key); } push(@anns, $ann); } } # add what is in the annotation implementation if any if($self->annotation()) { push(@anns, $self->annotation->get_Annotations(@keys)); } # done return @anns; } =head2 get_num_of_annotations Title : get_num_of_annotations Usage : my $count = $collection->get_num_of_annotations() Function: Returns the count of all annotations stored in this collection Returns : integer Args : none =cut sub get_num_of_annotations{ my ($self) = @_; # first, count the number of tags on the feature my $num_anns = 0; foreach ($self->feature()->all_tags()) { $num_anns += scalar( $self->feature()->get_tag_values($_)); } # add from the annotation implementation if any if($self->annotation()) { $num_anns += $self->annotation()->get_num_of_annotations(); } # done return $num_anns; } =head1 Implementation specific functions - to allow adding =cut =head2 add_Annotation Title : add_Annotation Usage : $self->add_Annotation('reference',$object); $self->add_Annotation($object,'Bio::MyInterface::DiseaseI'); $self->add_Annotation($object); $self->add_Annotation('disease',$object,'Bio::MyInterface::DiseaseI'); Function: Adds an annotation for a specific key. If the key is omitted, the object to be added must provide a value via its tagname(). If the archetype is provided, this and future objects added under that tag have to comply with the archetype and will be rejected otherwise. This implementation will add all Bio::Annotation::SimpleValue objects to the adapted features as tag/value pairs. Caveat: this may potentially result in information loss if a derived object is supplied. Returns : none Args : annotation key ('disease', 'dblink', ...) object to store (must be Bio::AnnotationI compliant) [optional] object archetype to map future storage of object of these types to =cut sub add_Annotation{ my ($self,$key,$object,$archetype) = @_; # if there's no key we use the tagname() as key if(ref($key) && $key->isa("Bio::AnnotationI") && (! ($object && ref($object)))) { $archetype = $object if $object; $object = $key; $key = $object->tagname(); $key = $key->name() if $key && ref($key); # OntologyTermI $self->throw("Annotation object must have a tagname if key omitted") unless $key; } if( !defined $object ) { $self->throw("Must have at least key and object in add_Annotation"); } if( ! (ref($object) && $object->isa("Bio::AnnotationI")) ) { $self->throw("object must be a Bio::AnnotationI compliant object, otherwise we won't add it!"); } # ready to add -- if it's a SimpleValue, we add to the feature's tags, # otherwise we'll add to the annotation collection implementation if($object->isa("Bio::Annotation::SimpleValue") && $self->feature()->can('add_tag_value')) { return $self->feature()->add_tag_value($key, $object->value()); } else { my $anncoll = $self->annotation(); if(! $anncoll) { $anncoll = Bio::Annotation::Collection->new(); $self->annotation($anncoll); } if($anncoll->can('add_Annotation')) { return $anncoll->add_Annotation($key,$object,$archetype); } $self->throw("Annotation implementation does not allow adding!"); } } =head2 remove_Annotations Title : remove_Annotations Usage : Function: Remove the annotations for the specified key from this collection. If the key happens to be a tag, then the tag is removed from the feature. Example : Returns : an array Bio::AnnotationI compliant objects which were stored under the given key(s) Args : the key(s) (tag name(s), one or more strings) for which to remove annotations (optional; if none given, flushes all annotations) =cut sub remove_Annotations{ my ($self, @keys) = @_; # set to all keys if none are supplied @keys = $self->get_all_annotation_keys() unless @keys; # collect existing annotation my @anns = $self->get_Annotations(@keys); # flush foreach my $key (@keys) { # delete the tag if it is one $self->feature->remove_tag($key) if $self->feature->has_tag($key); # and delegate to the annotation implementation my $anncoll = $self->annotation(); if($anncoll && $anncoll->can('remove_Annotations')) { $anncoll->remove_Annotations($key); } elsif($anncoll) { $self->warn("Annotation bundle implementation ".ref($anncoll). " does not allow remove!"); } } return @anns; } =head1 Additional methods =cut =head2 tagvalue_object_factory Title : tagvalue_object_factory Usage : $obj->tagval_object_factory($newval) Function: Get/set the object factory to use for creating objects that represent tag/value pairs (e.g., Bio::Annotation::SimpleValue). The object to be created is expected to follow Bio::Annotation::SimpleValue in terms of supported arguments at creation time, and the methods. Example : Returns : A Bio::Factory::ObjectFactoryI compliant object Args : new value (a Bio::Factory::ObjectFactoryI compliant object, optional) =cut sub tagvalue_object_factory{ my ($self,$value) = @_; if( defined $value) { $self->{'tagval_object_factory'} = $value; } return $self->{'tagval_object_factory'}; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Collection.pm�������������������������������������������������������000444��000766��000024�� 36220�13155576320� 20744� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Collection # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Collection - A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc. =head1 SYNOPSIS use Bio::SeqFeature::Collection; use Bio::Location::Simple; use Bio::Tools::GFF; use Bio::Root::IO; use File::Spec; # let's first input some features my $gffio = Bio::Tools::GFF->new(-file => File::Spec->catfile ("t","data","myco_sites.gff"), -gff_version => 2); my @features = (); # loop over the input stream while(my $feature = $gffio->next_feature()) { # do something with feature push @features, $feature; } $gffio->close(); # build the Collection object my $col = Bio::SeqFeature::Collection->new(); # add these features to the object my $totaladded = $col->add_features(\@features); my @subset = $col->features_in_range(-start => 1, -end => 25000, -strand => 1, -contain => 0); # subset should have 18 entries for this dataset print "size is ", scalar @subset, "\n"; @subset = $col->features_in_range(-range => Bio::Location::Simple->new (-start => 70000, -end => 150000, -strand => -1), -contain => 1, -strandmatch => 'strong'); # subset should have 22 entries for this dataset print "size is ", scalar @subset, "\n"; print "total number of features in collection is ", $col->feature_count(),"\n"; =head1 DESCRIPTION This object will efficiently allow one for query subsets of ranges within a large collection of sequence features (in fact the objects just have to be Bio::RangeI compliant). This is done by the creation of bins which are stored in order in a B-Tree data structure as provided by the DB_File interface to the Berkeley DB. This is based on work done by Lincoln for storage in a mysql instance - this is intended to be an embedded in-memory implementation for easily querying for subsets of a large range set. Collections can be made persistent by keeping the indexfile and passing in the -keep flag like this: my $collection = Bio::SeqFeature::Collection->new(-keep => 1, -file => 'col.idx'); $collaction->add_features(\@features); undef $collection; # To reuse this collection, next time you initialize a Collection object # specify the filename and the index will be reused. $collection = Bio::SeqFeature::Collection->new(-keep => 1, -file => 'col.idx'); =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 CONTRIBUTORS Using code and strategy developed by Lincoln Stein (lstein@cshl.org) in Bio::DB::GFF implementation. Credit also to Lincoln for suggesting using Storable to serialize features rather than my previous implementation which kept the features in memory. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Collection; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::DB::GFF::Util::Binning; use DB_File; use Bio::Location::Simple; use Bio::SeqFeature::Generic; use Storable qw(freeze thaw); use base qw(Bio::Root::Root Bio::SeqFeature::CollectionI); # This may need to get re-optimized for BDB usage as these # numbers were derived empirically by Lincoln on a mysql srv # running on his laptop # this is the largest that any reference sequence can be (100 megabases) use constant MAX_BIN => 100_000_000; # this is the smallest bin (1 K) use constant MIN_BIN => 1_000; =head2 new Title : new Usage : my $obj = Bio::SeqFeature::Collection->new(); Function: Builds a new Bio::SeqFeature::Collection object Returns : Bio::SeqFeature::Collection Args : -minbin minimum value to use for binning (default is 100,000,000) -maxbin maximum value to use for binning (default is 1,000) -file filename to store/read the BTREE from rather than an in-memory structure (default is false and in-memory). -keep boolean, will not remove index file on object destruction. -features Array ref of features to add initially =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($maxbin,$minbin, $file, $keep, $features) = $self->_rearrange([qw(MAXBIN MINBIN FILE KEEP FEATURES)],@args); defined $maxbin && $self->max_bin($maxbin); defined $minbin && $self->min_bin($minbin); defined $features && $self->add_features($features); $DB_BTREE->{'flags'} = R_DUP ; $DB_BTREE->{'compare'} = \&_compare; $self->{'_btreehash'} = {}; if( $file ) { $self->debug("using file $file"); $self->indexfile($file); } $self->keep($keep); $self->{'_btree'} = tie %{$self->{'_btreehash'}}, 'DB_File', $self->indexfile, O_RDWR|O_CREAT, 0640, $DB_BTREE; $self->{'_btree'} || $self->throw("Unable to tie DB_File handle"); return $self; } =head2 add_features Title : add_features Usage : $collection->add_features(\@features); Function: Returns : number of features added Args : arrayref of Bio::SeqFeatureI objects to index =cut sub add_features{ my ($self,$feats) = @_; if( ref($feats) !~ /ARRAY/i ) { $self->warn("Must provide a valid Array reference to add_features"); return 0; } my $count = 0; foreach my $f ( @$feats ) { if( ! $f || ! ref($f) || ! $f->isa('Bio::RangeI') ) { $self->warn("Must provide valid Bio::RangeI objects to add_features, skipping object '$f'\n"); next; } my $bin = bin($f->start,$f->end,$self->min_bin); my $serialized = &feature_freeze($f); $self->{'_btree'}->put($bin,$serialized); if( $f->isa('Bio::SeqFeature::Generic') ) { $self->debug( "$bin for ". $f->location->to_FTstring(). " matches ".$#{$self->{'_features'}}. "\n"); } $count++; } return $count; } =head2 features_in_range Title : features_in_range Usage : my @features = $collection->features_in_range($range) Function: Retrieves a list of features which were contained or overlap the the requested range (see Args for way to specify overlap or only those containe)d Returns : List of Bio::SeqFeatureI objects Args : -range => Bio::RangeI object defining range to search, OR -start => start, -end => end, -strand => strand -contain => boolean - true if feature must be completely contained with range OR false if should include features that simply overlap the range. Default: true. -strandmatch => 'strong', ranges must have the same strand 'weak', ranges must have the same strand or no strand 'ignore', ignore strand information Default. 'ignore'. =cut sub features_in_range{ my $self = shift; my (@args) = @_; my ($range, $contain, $strandmatch,$start,$end,$strand); if( @args == 1 ) { $range = shift @args; } else { ($start,$end,$strand,$range, $contain,$strandmatch) = $self->_rearrange([qw(START END STRAND RANGE CONTAIN STRANDMATCH)], @args); $contain = 1 unless defined $contain; } $strand = 1 unless defined $strand; if( $strand !~ /^([\-\+])$/ && $strand !~ /^[\-\+]?1$/ ) { $self->warn("must provide a valid numeric or +/- for strand"); return (); } if( defined $1 ) { $strand .= 1; } if( !defined $start && !defined $end ) { if( ! defined $range || !ref($range) || ! $range->isa("Bio::RangeI") ) { $self->warn("Must defined a valid Range for the method feature_in_range"); return (); } ($start,$end,$strand) = ($range->start,$range->end,$range->strand); } my $r = Bio::Location::Simple->new(-start => $start, -end => $end, -strand => $strand); my @features; my $maxbin = $self->max_bin; my $minbin = $self->min_bin; my $tier = $maxbin; my ($k,$v,@bins) = ("",undef); while ($tier >= $minbin) { my ($tier_start,$tier_stop) = (bin_bot($tier,$start), bin_top($tier,$end)); if( $tier_start == $tier_stop ) { my @vals = $self->{'_btree'}->get_dup($tier_start); if( scalar @vals > 0 ) { push @bins, map { thaw($_) } @vals; } } else { $k = $tier_start; my @vals; for( my $rc = $self->{'_btree'}->seq($k,$v,R_CURSOR); $rc == 0; $rc = $self->{'_btree'}->seq($k,$v, R_NEXT) ) { last if( $k > $tier_stop || $k < $tier_start); push @bins, thaw($v); } } $tier /= 10; } my %seen = (); foreach my $t ( map { ref($_) } @bins) { next if $seen{$t}++; eval "require $t"; if( $@ ) { $self->warn("Trying to thaw a stored feature $t which does not appear in your Perl library. $@"); next; } } $strandmatch = 'ignore' unless defined $strandmatch; return ( $contain ) ? grep { $r->contains($_,$strandmatch) } @bins : grep { $r->overlaps($_,$strandmatch)} @bins; } =head2 remove_features Title : remove_features Usage : $collection->remove_features(\@array) Function: Removes the requested sequence features (based on features which have the same location) Returns : Number of features removed Args : Arrayref of Bio::RangeI objects =cut sub remove_features{ my ($self,$feats) = @_; if( ref($feats) !~ /ARRAY/i ) { $self->warn("Must provide a valid Array reference to remove_features"); return 0; } my $countprocessed = 0; foreach my $f ( @$feats ) { next if ! ref($f) || ! $f->isa('Bio::RangeI'); my $bin = bin($f->start,$f->end,$self->min_bin); my @vals = $self->{'_btree'}->get_dup($bin); my $vcount = scalar @vals; foreach my $v ( @vals ) { # Once we have uniquely identifiable field # I think it will work better. if( $v eq &feature_freeze($f) ) { $self->{'_btree'}->del_dup($bin,$v); $vcount--; $countprocessed++; } } if( $vcount == 0 ) { $self->{'_btree'}->del($bin); } } $countprocessed; } =head2 get_all_features Title : get_all_features Usage : my @f = $col->get_all_features() Function: Return all the features stored in this collection (Could be large) Returns : Array of Bio::RangeI objects Args : None =cut sub get_all_features{ my ($self) = @_; my @features; my ($key,$value); for (my $status = $self->{'_btree'}->seq($key, $value, R_FIRST) ; $status == 0 ; $status = $self->{'_btree'}->seq($key, $value, R_NEXT) ) { next unless defined $value; push @features, &thaw($value); } if( scalar @features != $self->feature_count() ) { $self->warn("feature count does not match actual count\n"); } return @features; } =head2 min_bin Title : min_bin Usage : my $minbin= $self->min_bin; Function: Get/Set the minimum value to use for binning Returns : integer Args : [optional] minimum bin value =cut sub min_bin { my ($self,$min) = @_; if( defined $min ) { $self->{'_min_bin'} = $min; } return $self->{'_min_bin'} || MIN_BIN; } =head2 max_bin Title : max_bin Usage : my $maxbin= $self->max_bin; Function: Get/Set the maximum value to use for binning Returns : integer Args : [optional] maximum bin value =cut sub max_bin { my ($self,$max) = @_; if( defined $max ) { $self->{'_max_bin'} = $max; } return $self->{'max_bin'} || MAX_BIN; } =head2 feature_count Title : feature_count Usage : my $c = $col->feature_count() Function: Retrieve the total number of features in the collection Returns : integer Args : none =cut sub feature_count { my $self = shift; my $count = 0; for ( keys %{$self->{'_btreehash'}} ) { my $v = $self->{'_btreehash'}->{$_}; next unless defined $v; $count++; } $count; } =head2 indexfile Title : indexfile Usage : $obj->indexfile($newval) Function: Get/set the filename where index is kept Returns : value of indexfile (a filename string) Args : on set, new value (a filename string ) =cut sub indexfile{ my $self = shift; return $self->{'indexfile'} = shift if @_; return $self->{'indexfile'}; } =head2 keep Title : keep Usage : $obj->keep($newval) Function: Get/set boolean flag to keep the indexfile after exiting program Example : Returns : value of keep (boolean) Args : on set, new value (boolean) =cut sub keep{ my $self = shift; return $self->{'keep'} = shift if @_; return $self->{'keep'}; } sub _compare{ if( defined $_[0] && ! defined $_[1]) { return -1; } elsif ( defined $_[1] && ! defined $_[0]) { return 1; } $_[0] <=> $_[1]; } sub feature_freeze { my $obj = shift; _remove_cleanup_methods($obj); return freeze($obj); } sub _remove_cleanup_methods { my $obj = shift; # we have to remove any cleanup methods here for Storable for my $funcref ( $obj->_cleanup_methods ) { $obj->_unregister_for_cleanup($funcref); } # ... and the same for any contained features; hopefully any implementations # adhere to implementing Bio::SeqFeatureI::sub_SeqFeature for my $contained ($obj->sub_SeqFeature) { _remove_cleanup_methods($contained); } 1; } sub feature_thaw { return thaw(shift); } sub DESTROY { my $self = shift; $self->{'_btree'} = undef; untie(%{$self->{'_btreehash'}}); if( ! $self->keep && $self->indexfile ) { my $f = $self->indexfile; $self->debug( "unlinking ".$f. "\n"); close($f); unlink($f); } $self->SUPER::DESTROY(); } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/CollectionI.pm������������������������������������������������������000444��000766��000024�� 7342�13155576320� 21040� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::CollectionI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::CollectionI - An interface for a collection of SeqFeatureI objects. =head1 SYNOPSIS # get a Bio::SeqFeature::CollectionI somehow # perhaps a Bio::SeqFeature::Collection use Bio::SeqFeature::Collection; my $collection = Bio::SeqFeature::Collection->new(); $collection->add_features(\@featurelist); $collection->features(-attributes => [ { 'location' => Bio::Location::Simple->new (-start=> 1, -end => 300) , 'overlaps' }]); =head1 DESCRIPTION This interface describes the basic methods needed for a collection of Sequence Features. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::CollectionI; use strict; use Carp; use base qw(Bio::Root::RootI); =head2 add_features Title : add_features Usage : $collection->add_features(\@features); Function: Returns : number of features added Args : arrayref of Bio::SeqFeatureI objects to index =cut sub add_features{ shift->throw_not_implemented(); } =head2 features Title : features Usage : my @f = $collection->features(@args); Returns : a list of Bio::SeqFeatureI objects Args : see below Status : public This routine will retrieve features associated with this collection object. It can be used to return all features, or a subset based on their type, location, or attributes. -types List of feature types to return. Argument is an array of Bio::Das::FeatureTypeI objects or a set of strings that can be converted into FeatureTypeI objects. -callback A callback to invoke on each feature. The subroutine will be passed to each Bio::SeqFeatureI object in turn. -attributes A hash reference containing attributes to match. The -attributes argument is a hashref containing one or more attributes to match against: -attributes => { Gene => 'abc-1', Note => 'confirmed' } Attribute matching is simple exact string matching, and multiple attributes are ANDed together. See L<Bio::DB::ConstraintsI> for a more sophisticated take on this. If one provides a callback, it will be invoked on each feature in turn. If the callback returns a false value, iteration will be interrupted. When a callback is provided, the method returns undef. =cut sub features{ shift->throw_not_implemented(); } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Computation.pm������������������������������������������������������000444��000766��000024�� 35216�13155576320� 21157� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Generic # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by mark Fiers <m.w.e.j.fiers@plant.wag-ur.nl> # # Copyright Ewan Birney, Mark Fiers # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Computation - Computation SeqFeature =head1 SYNOPSIS $feat = Bio::SeqFeature::Computation->new( -start => 10, -end => 100, -strand => -1, -primary => 'repeat', -program_name => 'GeneMark', -program_date => '12-5-2000', -program_version => 'x.y', -database_name => 'Arabidopsis', -database_date => '12-dec-2000', -computation_id => 2231, -score => { no_score => 334 } ); =head1 DESCRIPTION Bio::SeqFeature::Computation extends the Generic seqfeature object with a set of computation related fields and a more flexible set of storing more types of score and subseqfeatures. It is compatible with the Generic SeqFeature object. The new way of storing score values is similar to the tag structure in the Generic object. For storing sets of subseqfeatures the array containing the subseqfeatures is now a hash which contains arrays of seqfeatures Both the score and subSeqfeature methods can be called in exactly the same way, the value's will be stored as a 'default' score or subseqfeature. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney, Mark Fiers Ewan Birney E<lt>birney@sanger.ac.ukE<gt> Mark Fiers E<lt>m.w.e.j.fiers@plant.wag-ur.nlE<gt> =head1 DEVELOPERS This class has been written with an eye out of inheritance. The fields the actual object hash are: _gsf_sub_hash = reference to a hash containing sets of sub arrays _gsf_score_hash= reference to a hash for the score values =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Computation; use strict; use base qw(Bio::SeqFeature::Generic); sub new { my ( $class, @args) = @_; my $self = $class->SUPER::new(@args); my ( $computation_id, $program_name, $program_date, $program_version, $database_name, $database_date, $database_version) = $self->_rearrange([qw( COMPUTATION_ID PROGRAM_NAME PROGRAM_DATE PROGRAM_VERSION DATABASE_NAME DATABASE_DATE DATABASE_VERSION )],@args); $program_name && $self->program_name($program_name); $program_date && $self->program_date($program_date); $program_version && $self->program_version($program_version); $database_name && $self->database_name($database_name); $database_date && $self->database_date($database_date); $database_version && $self->database_version($database_version); $computation_id && $self->computation_id($computation_id); return $self; } =head2 has_score Title : has_score Usage : $value = $self->has_score('some_score') Function: Tests whether a feature contains a score Returns : TRUE if the SeqFeature has the score, and FALSE otherwise. Args : The name of a score =cut sub has_score { my ($self, $score) = @_; return unless defined $score; return exists $self->{'_gsf_score_hash'}->{$score}; } =head2 add_score_value Title : add_score_value Usage : $self->add_score_value('P_value',224); Returns : TRUE on success Args : score (string) and value (any scalar) =cut sub add_score_value { my ($self, $score, $value) = @_; if( ! defined $score || ! defined $value ) { $self->warn("must specify a valid $score and $value to add_score_value"); return 0; } if ( !defined $self->{'_gsf_score_hash'}->{$score} ) { $self->{'_gsf_score_hash'}->{$score} = []; } push(@{$self->{'_gsf_score_hash'}->{$score}},$value); } =head2 score Title : score Usage : $value = $comp_obj->score() $comp_obj->score($value) Function: Returns the 'default' score or sets the 'default' score This method exist for compatibility options It would equal ($comp_obj->each_score_value('default'))[0]; Returns : A value Args : (optional) a new value for the 'default' score =cut sub score { my ($self, $value) = @_; my @v; if (defined $value) { if( ref($value) =~ /HASH/i ) { while( my ($t,$val) = each %{ $value } ) { $self->add_score_value($t,$val); } } else { @v = $value; $self->add_score_value('default', $value); } } else { @v = $self->each_score_value('default'); } return $v[0]; } =head2 each_score_value Title : each_score_value Usage : @values = $gsf->each_score_value('note'); Function: Returns a list of all the values stored under a particular score. Returns : A list of scalars Args : The name of the score =cut sub each_score_value { my ($self, $score) = @_; if ( ! exists $self->{'_gsf_score_hash'}->{$score} ) { $self->warn("asking for score value that does not exist $score"); return; } return @{$self->{'_gsf_score_hash'}->{$score}}; } =head2 all_scores Title : all_scores Usage : @scores = $feat->all_scores() Function: Get a list of all the scores in a feature Returns : An array of score names Args : none =cut sub all_scores { my ($self, @args) = @_; return keys %{$self->{'_gsf_score_hash'}}; } =head2 remove_score Title : remove_score Usage : $feat->remove_score('some_score') Function: removes a score from this feature Returns : nothing Args : score (string) =cut sub remove_score { my ($self, $score) = @_; if ( ! exists $self->{'_gsf_score_hash'}->{$score} ) { $self->warn("trying to remove a score that does not exist: $score"); } delete $self->{'_gsf_score_hash'}->{$score}; } =head2 computation_id Title : computation_id Usage : $computation_id = $feat->computation_id() $feat->computation_id($computation_id) Function: get/set on program name information Returns : string Args : none if get, the new value if set =cut sub computation_id { my ($self,$value) = @_; if (defined($value)) { $self->{'_gsf_computation_id'} = $value; } return $self->{'_gsf_computation_id'}; } =head2 program_name Title : program_name Usage : $program_name = $feat->program_name() $feat->program_name($program_name) Function: get/set on program name information Returns : string Args : none if get, the new value if set =cut sub program_name { my ($self,$value) = @_; if (defined($value)) { $self->{'_gsf_program_name'} = $value; } return $self->{'_gsf_program_name'}; } =head2 program_date Title : program_date Usage : $program_date = $feat->program_date() $feat->program_date($program_date) Function: get/set on program date information Returns : date (string) Args : none if get, the new value if set =cut sub program_date { my ($self,$value) = @_; if (defined($value)) { $self->{'_gsf_program_date'} = $value; } return $self->{'_gsf_program_date'}; } =head2 program_version Title : program_version Usage : $program_version = $feat->program_version() $feat->program_version($program_version) Function: get/set on program version information Returns : date (string) Args : none if get, the new value if set =cut sub program_version { my ($self,$value) = @_; if (defined($value)) { $self->{'_gsf_program_version'} = $value; } return $self->{'_gsf_program_version'}; } =head2 database_name Title : database_name Usage : $database_name = $feat->database_name() $feat->database_name($database_name) Function: get/set on program name information Returns : string Args : none if get, the new value if set =cut sub database_name { my ($self,$value) = @_; if (defined($value)) { $self->{'_gsf_database_name'} = $value; } return $self->{'_gsf_database_name'}; } =head2 database_date Title : database_date Usage : $database_date = $feat->database_date() $feat->database_date($database_date) Function: get/set on program date information Returns : date (string) Args : none if get, the new value if set =cut sub database_date { my ($self,$value) = @_; if (defined($value)) { $self->{'_gsf_database_date'} = $value; } return $self->{'_gsf_database_date'}; } =head2 database_version Title : database_version Usage : $database_version = $feat->database_version() $feat->database_version($database_version) Function: get/set on program version information Returns : date (string) Args : none if get, the new value if set =cut sub database_version { my ($self,$value) = @_; if (defined($value)) { $self->{'_gsf_database_version'} = $value; } return $self->{'_gsf_database_version'}; } =head2 get_SeqFeature_type Title : get_SeqFeature_type Usage : $SeqFeature_type = $feat->get_SeqFeature_type() $feat->get_SeqFeature_type($SeqFeature_type) Function: Get SeqFeature type which is automatically set when adding a computation (SeqFeature) to a computation object Returns : SeqFeature_type (string) Args : none if get, the new value if set =cut sub get_SeqFeature_type { my ($self, $value) = @_; if (defined($value)) { $self->{'_gsf_sub_SeqFeature_type'} = $value; } return $self->{'_gsf_sub_SeqFeature_type'}; } =head2 get_all_SeqFeature_types Title : get_all_SeqFeature_types Usage : @all_SeqFeature_types = $comp->get_all_SeqFeature_types(); Function: Returns an array with all subseqfeature types Returns : An array Args : none =cut sub get_all_SeqFeature_types { my ($self) = @_; return keys ( %{$self->{'gsf_sub_hash'}} ); } =head2 get_SeqFeatures Title : get_SeqFeatures('feature_type') Usage : @feats = $feat->get_SeqFeatures(); @feats = $feat->get_SeqFeatures('feature_type'); Function: Returns an array of sub Sequence Features of a specific type or, if the type is omitted, all sub Sequence Features Returns : An array Args : (optional) a SeqFeature type (ie exon, pattern) =cut sub get_SeqFeatures { my ($self, $ssf_type) = @_; my (@return_array) = (); if ($ssf_type eq '') { #return all SeqFeatures foreach (keys ( %{$self->{'gsf_sub_hash'}} )){ push @return_array, @{$self->{'gsf_sub_hash'}->{$_}}; } return @return_array; } else { if (defined ($self->{'gsf_sub_hash'}->{$ssf_type})) { return @{$self->{'gsf_sub_hash'}->{$ssf_type}}; } else { $self->warn("$ssf_type is not a valid sub SeqFeature type"); } } } =head2 add_SeqFeature Title : add_SeqFeature Usage : $feat->add_SeqFeature($subfeat); $feat->add_SeqFeature($subfeat,'seqfeature_type') $feat->add_SeqFeature($subfeat,'EXPAND') $feat->add_SeqFeature($subfeat,'EXPAND','seqfeature_type') Function: adds a SeqFeature into a specific subSeqFeature array. with no 'EXPAND' qualifer, subfeat will be tested as to whether it lies inside the parent, and throw an exception if not. If EXPAND is used, the parents start/end/strand will be adjusted so that it grows to accommodate the new subFeature, optionally a seqfeature type can be defined. Returns : nothing Args : An object which has the SeqFeatureI interface (optional) 'EXPAND' (optional) 'SeqFeature_type' =cut sub add_SeqFeature{ my ($self,$feat,$var1, $var2) = @_; $var1 = '' unless( defined $var1); $var2 = '' unless( defined $var2); my ($expand, $ssf_type) = ('', $var1 . $var2); $expand = 'EXPAND' if ($ssf_type =~ s/EXPAND//); if ( !$feat->isa('Bio::SeqFeatureI') ) { $self->warn("$feat does not implement Bio::SeqFeatureI. Will add it anyway, but beware..."); } if($expand eq 'EXPAND') { $self->_expand_region($feat); } else { if ( !$self->contains($feat) ) { $self->throw("$feat is not contained within parent feature, and expansion is not valid"); } } $ssf_type = 'default' if ($ssf_type eq ''); if (!(defined ($self->{'gsf_sub_hash'}->{$ssf_type}))) { @{$self->{'gsf_sub_hash'}->{$ssf_type}} = (); } $feat->get_SeqFeature_type($ssf_type); push @{$self->{'gsf_sub_hash'}->{$ssf_type}}, $feat; } =head2 remove_SeqFeatures Title : remove_SeqFeatures Usage : $sf->remove_SeqFeatures $sf->remove_SeqFeatures('SeqFeature_type'); Function: Removes all sub SeqFeature or all sub SeqFeatures of a specified type (if you want to remove a more specific subset, take an array of them all, flush them, and add back only the guys you want) Example : Returns : none Args : none =cut sub remove_SeqFeatures { my ($self, $ssf_type) = @_; if ($ssf_type) { if ((defined ($self->{'gsf_sub_hash'}->{$ssf_type}))) { delete $self->{'gsf_sub_hash'}->{$ssf_type}; } else { $self->warn("$ssf_type is not a valid sub SeqFeature type"); } } else { $self->{'_gsf_sub_hash'} = {}; # zap the complete hash implicitly. } } # Aliases to better match Bio::SeqFeature function names *sub_SeqFeature_type = \&get_SeqFeature_type; *all_sub_SeqFeature_types = \&get_all_SeqFeature_types; *sub_SeqFeature = \&get_SeqFeatures; *add_sub_SeqFeature = \&add_SeqFeature; *flush_sub_SeqFeatures = \&remove_SeqFeatures; *flush_sub_SeqFeature = \&remove_SeqFeatures; 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/FeaturePair.pm������������������������������������������������������000444��000766��000024�� 31726�13155576320� 21066� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::FeaturePair # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@sanger.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::FeaturePair - hold pair feature information e.g. blast hits =head1 SYNOPSIS my $feat = Bio::SeqFeature::FeaturePair->new( -feature1 => $f1, -feature2 => $f2, ); # Bio::SeqFeatureI methods can be used my $start = $feat->start; my $end = $feat->end; # Bio::FeaturePair methods can be used my $hstart = $feat->hstart; my $hend = $feat->hend; my $feature1 = $feat->feature1; # returns feature1 object =head1 DESCRIPTION A sequence feature object where the feature is itself a feature on another sequence - e.g. a blast hit where residues 1-40 of a protein sequence SW:HBA_HUMAN has hit to bases 100 - 220 on a genomic sequence HS120G22. The genomic sequence coordinates are used to create one sequence feature $f1 and the protein coordinates are used to create feature $f2. A FeaturePair object can then be made my $fp = Bio::SeqFeature::FeaturePair->new( -feature1 => $f1, # genomic -feature2 => $f2, # protein ); This object can be used as a standard Bio::SeqFeatureI in which case my $gstart = $fp->start # returns start coord on feature1 - genomic seq. my $gend = $fp->end # returns end coord on feature1. In general standard Bio::SeqFeatureI method calls return information in feature1. Data in the feature 2 object are generally obtained using the standard methods prefixed by h (for hit!) my $pstart = $fp->hstart # returns start coord on feature2 = protein seq. my $pend = $fp->hend # returns end coord on feature2. If you wish to swap feature1 and feature2 around : $feat->invert so... $feat->start # etc. returns data in $feature2 object No sub_SeqFeatures or tags can be stored in this object directly. Any features or tags are expected to be stored in the contained objects feature1, and feature2. =head1 CONTACT Ewan Birney E<lt>birney@sanger.ac.ukE<gt> =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::FeaturePair; use vars qw($AUTOLOAD); use strict; use Bio::SeqFeatureI; use Bio::Factory::ObjectFactory; use base qw(Bio::SeqFeature::Generic); =head2 new Title : new Usage : Function: Constructor for this module. Accepts the following parameters: -feature1 Bio::SeqFeatureI-compliant object -feature2 Bio::SeqFeatureI-compliant object -feature_factory Bio::Factory::ObjectFactoryI compliant object to be used when feature1 and/or feature2 are accessed without explicitly set before. This is mostly useful for derived classes who want to set their preferred class for feature objects. Example : Returns : Args : see above =cut sub new { my ($class, @args) = @_; # # We've got a certain problem here that somewhat relates to chicken and # eggs. The problem is, we override a lot of SeqFeatureI methods here # to delegate them to either feature1 or feature2. If we pass along # those attributes right away, we need feature1 or feature2 or the feature # factory in place, or there is no way around the dreaded default, which # is ugly too (as it necessitates subsequent copying if you wanted a # different feature object class). # # So I decided to go with the lesser of two evils here: we need to assume # here that we can set all attributes through set_attributes(), which we # assume is no different from setting them through the constructor. This # gives us a window to set the feature objects and the factory, such that # any derived class doesn't have to worry about this any more. # # I'm happy to hear a better solution, but I think this one isn't so bad. # my $self = $class->SUPER::new(); my ($feature1,$feature2,$featfact) = $self->_rearrange([qw( FEATURE1 FEATURE2 FEATURE_FACTORY )],@args); $self->_register_for_cleanup(\&cleanup_fp); # initialize the feature object factory if not provided if(! $featfact) { $featfact = Bio::Factory::ObjectFactory->new( -type => "Bio::SeqFeature::Generic", -interface => "Bio::SeqFeatureI" ); } $self->feature_factory($featfact); # Store the features in the object $feature1 && $self->feature1($feature1); $feature2 && $self->feature2($feature2); # OK. Now we're setup to store all the attributes, and they'll go right # away into the right objects. $self->set_attributes(@args); # done - we hope return $self; } =head2 feature1 Title : feature1 Usage : $f = $featpair->feature1 $featpair->feature1($feature) Function: Get/set for the query feature Returns : Bio::SeqFeatureI Args : Bio::SeqFeatureI =cut sub feature1 { my ($self,$arg) = @_; if ( defined($arg) || !defined $self->{'feature1'} ) { $self->throw("internal error: feature factory not set!") unless $self->feature_factory; $arg = $self->feature_factory->create_object() unless( defined $arg); $self->throw("Argument [$arg] must be a Bio::SeqFeatureI") unless (ref($arg) && $arg->isa("Bio::SeqFeatureI")); $self->{'feature1'} = $arg; } return $self->{'feature1'}; } =head2 feature2 Title : feature2 Usage : $f = $featpair->feature2 $featpair->feature2($feature) Function: Get/set for the hit feature Returns : Bio::SeqFeatureI Args : Bio::SeqFeatureI =cut sub feature2 { my ($self,$arg) = @_; if ( defined($arg) || ! defined $self->{'feature2'}) { $self->throw("internal error: feature factory not set!") unless $self->feature_factory; $arg = $self->feature_factory->create_object() unless( defined $arg); $self->throw("Argument [$arg] must be a Bio::SeqFeatureI") unless (ref($arg) && $arg->isa("Bio::SeqFeatureI")); $self->{'feature2'} = $arg; } return $self->{'feature2'}; } =head2 start Title : start Usage : $start = $featpair->start $featpair->start(20) Function: Get/set on the start coordinate of feature1 Returns : integer Args : [optional] beginning of feature =cut sub start { return shift->feature1->start(@_); } =head2 end Title : end Usage : $end = $featpair->end $featpair->end($end) Function: get/set on the end coordinate of feature1 Returns : integer Args : [optional] ending point of feature =cut sub end { return shift->feature1->end(@_); } =head2 strand Title : strand Usage : $strand = $feat->strand() $feat->strand($strand) Function: get/set on strand information, being 1,-1 or 0 Returns : -1,1 or 0 Args : [optional] strand information to set =cut sub strand { return shift->feature1->strand(@_); } =head2 location Title : location Usage : $location = $featpair->location $featpair->location($location) Function: Get/set location object (using feature1) Returns : Bio::LocationI object Args : [optional] LocationI to store =cut sub location { return shift->feature1->location(@_); } =head2 score Title : score Usage : $score = $feat->score() $feat->score($score) Function: get/set on score information Returns : float Args : none if get, the new value if set =cut sub score { return shift->feature1->score(@_); } =head2 frame Title : frame Usage : $frame = $feat->frame() $feat->frame($frame) Function: get/set on frame information Returns : 0,1,2 Args : none if get, the new value if set =cut sub frame { return shift->feature1->frame(@_); } =head2 primary_tag Title : primary_tag Usage : $ptag = $featpair->primary_tag Function: get/set on the primary_tag of feature1 Returns : 0,1,2 Args : none if get, the new value if set =cut sub primary_tag { return shift->feature1->primary_tag(@_); } =head2 source_tag Title : source_tag Usage : $tag = $feat->source_tag() $feat->source_tag('genscan'); Function: Returns the source tag for a feature, eg, 'genscan' Returns : a string Args : none =cut sub source_tag { return shift->feature1->source_tag(@_); } =head2 seqname Title : seqname Usage : $obj->seq_id($newval) Function: There are many cases when you make a feature that you do know the sequence name, but do not know its actual sequence. This is an attribute such that you can store the seqname. This attribute should *not* be used in GFF dumping, as that should come from the collection in which the seq feature was found. Returns : value of seqname Args : newvalue (optional) =cut sub seq_id { return shift->feature1->seq_id(@_); } =head2 hseqname Title : hseqname Usage : $featpair->hseqname($newval) Function: Get/set method for the name of feature2. Returns : value of $feature2->seq_id Args : newvalue (optional) =cut sub hseq_id { return shift->feature2->seq_id(@_); } =head2 hstart Title : hstart Usage : $start = $featpair->hstart $featpair->hstart(20) Function: Get/set on the start coordinate of feature2 Returns : integer Args : none =cut sub hstart { return shift->feature2->start(@_); } =head2 hend Title : hend Usage : $end = $featpair->hend $featpair->hend($end) Function: get/set on the end coordinate of feature2 Returns : integer Args : none =cut sub hend { return shift->feature2->end(@_); } =head2 hstrand Title : hstrand Usage : $strand = $feat->strand() $feat->strand($strand) Function: get/set on strand information, being 1,-1 or 0 Returns : -1,1 or 0 Args : none =cut sub hstrand { return shift->feature2->strand(@_); } =head2 hscore Title : hscore Usage : $score = $feat->score() $feat->score($score) Function: get/set on score information Returns : float Args : none if get, the new value if set =cut sub hscore { return shift->feature2->score(@_); } =head2 hframe Title : hframe Usage : $frame = $feat->frame() $feat->frame($frame) Function: get/set on frame information Returns : 0,1,2 Args : none if get, the new value if set =cut sub hframe { return shift->feature2->frame(@_); } =head2 hprimary_tag Title : hprimary_tag Usage : $ptag = $featpair->hprimary_tag Function: Get/set on the primary_tag of feature2 Returns : 0,1,2 Args : none if get, the new value if set =cut sub hprimary_tag { return shift->feature2->primary_tag(@_); } =head2 hsource_tag Title : hsource_tag Usage : $tag = $feat->hsource_tag() $feat->source_tag('genscan'); Function: Returns the source tag for a feature, eg, 'genscan' Returns : a string Args : none =cut sub hsource_tag { return shift->feature2->source_tag(@_); } =head2 invert Title : invert Usage : $tag = $feat->invert Function: Swaps feature1 and feature2 around Returns : Nothing Args : none =cut sub invert { my ($self) = @_; my $tmp = $self->feature1; $self->feature1($self->feature2); $self->feature2($tmp); return 1; } =head2 feature_factory Title : feature_factory Usage : $obj->feature_factory($newval) Function: Get/set the feature object factory for this feature pair. The feature object factory will be used to create a feature object if feature1() or feature2() is called in get mode without having been set before. The default is an instance of Bio::Factory::ObjectFactory and hence allows the type to be changed dynamically at any time. Example : Returns : The feature object factory in use (a Bio::Factory::ObjectFactoryI compliant object) Args : on set, a Bio::Factory::ObjectFactoryI compliant object =cut sub feature_factory { my $self = shift; return $self->{'feature_factory'} = shift if @_; return $self->{'feature_factory'}; } ################################################################# # aliases for backwards compatibility # ################################################################# # seqname() is already aliased in Generic.pm, and we overwrite seq_id sub hseqname { my $self = shift; $self->warn("SeqFeatureI::seqname() is deprecated. Please use seq_id() instead."); return $self->hseq_id(@_); } sub cleanup_fp { my $self = shift; $self->{'feature1'} = $self->{'feature2'} = undef; } 1; ������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Generic.pm����������������������������������������������������������000444��000766��000024�� 76031�13155576320� 20231� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Generic # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@sanger.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Generic - Generic SeqFeature =head1 SYNOPSIS $feat = Bio::SeqFeature::Generic->new( -start => 10, -end => 100, -strand => -1, -primary => 'repeat', # -primary_tag is a synonym -source_tag => 'repeatmasker', -display_name => 'alu family', -score => 1000, -tag => { new => 1, author => 'someone', sillytag => 'this is silly!' } ); $feat = Bio::SeqFeature::Generic->new( -gff_string => $string ); # if you want explicitly GFF1 $feat = Bio::SeqFeature::Generic->new( -gff1_string => $string ); # add it to an annotated sequence $annseq->add_SeqFeature($feat); =head1 DESCRIPTION Bio::SeqFeature::Generic is a generic implementation for the Bio::SeqFeatureI interface, providing a simple object to provide all the information for a feature on a sequence. For many Features, this is all you will need to use (for example, this is fine for Repeats in DNA sequence or Domains in protein sequence). For other features, which have more structure, this is a good base class to extend using inheritance to have new things: this is what is done in the L<Bio::SeqFeature::Gene>, L<Bio::SeqFeature::Transcript> and L<Bio::SeqFeature::Exon>, which provide well coordinated classes to represent genes on DNA sequence (for example, you can get the protein sequence out from a transcript class). For many Features, you want to add some piece of information, for example a common one is that this feature is 'new' whereas other features are 'old'. The tag system, which here is implemented using a hash can be used here. You can use the tag system to extend the L<Bio::SeqFeature::Generic> programmatically: that is, you know that you have read in more information into the tag 'mytag' which you can then retrieve. This means you do not need to know how to write inherited Perl to provide more complex information on a feature, and/or, if you do know but you do not want to write a new class every time you need some extra piece of information, you can use the tag system to easily store and then retrieve information. The tag system can be written in/out of GFF format, and also into EMBL format via the L<Bio::SeqIO> system =head1 Implemented Interfaces This class implements the following interfaces. =over 4 =item L<Bio::SeqFeatureI> Note that this includes implementing Bio::RangeI. =item L<Bio::AnnotatableI> =item L<Bio::FeatureHolderI> Features held by a feature are essentially sub-features. =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Ewan Birney E<lt>birney@sanger.ac.ukE<gt> =head1 DEVELOPERS This class has been written with an eye out for inheritance. The fields the actual object hash are: _gsf_tag_hash = reference to a hash for the tags _gsf_sub_array = reference to an array for subfeatures =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Generic; use strict; use Bio::Annotation::Collection; use Bio::Location::Simple; use Bio::Location::Split; use Bio::Tools::GFF; #use Tie::IxHash; use base qw(Bio::Root::Root Bio::SeqFeatureI Bio::FeatureHolderI Bio::AnnotatableI); sub new { my ( $caller, @args) = @_; my ($self) = $caller->SUPER::new(@args); $self->_register_for_cleanup(\&cleanup_generic); $self->{'_parse_h'} = {}; $self->{'_gsf_tag_hash'} = {}; # bulk-set attributes $self->set_attributes(@args); # done - we hope return $self; } =head2 set_attributes Title : set_attributes Usage : Function: Sets a whole array of parameters at once. Example : Returns : none Args : Named parameters, in the form as they would otherwise be passed to new(). Currently recognized are: -start start position -end end position -strand strand -phase the phase of the feature (0..2) -primary_tag primary tag -primary (synonym for -primary_tag) -source_tag source tag -source (synonym for -source_tag) -frame frame -score score value -tag a reference to a tag/value hash -gff_string GFF v.2 string to initialize from -gff1_string GFF v.1 string to initialize from -seq_id the display name of the sequence -annotation the AnnotationCollectionI object -location the LocationI object =cut sub set_attributes { my ($self,@args) = @_; my ($start, $end, $strand, $primary_tag, $source_tag, $primary, $source, $frame, $score, $tag, $gff_string, $gff1_string, $seqname, $seqid, $annot, $location, $display_name, $pid, $phase) = $self->_rearrange([qw(START END STRAND PRIMARY_TAG SOURCE_TAG PRIMARY SOURCE FRAME SCORE TAG GFF_STRING GFF1_STRING SEQNAME SEQ_ID ANNOTATION LOCATION DISPLAY_NAME PRIMARY_ID PHASE )], @args); $location && $self->location($location); $gff_string && $self->_from_gff_string($gff_string); $gff1_string && do { $self->gff_format(Bio::Tools::GFF->new('-gff_version' => 1)); $self->_from_gff_stream($gff1_string); }; $pid && $self->primary_id($pid); $primary_tag && $self->primary_tag($primary_tag); $source_tag && $self->source_tag($source_tag); $primary && $self->primary_tag($primary); $source && $self->source_tag($source); $annot && $self->annotation($annot); defined $start && $self->start($start); defined $end && $self->end($end); defined $strand && $self->strand($strand); defined $frame && $self->frame($frame); defined $display_name && $self->display_name($display_name); defined $score && $self->score($score); defined $phase && $self->phase($phase); if($seqname) { $self->warn("-seqname is deprecated. Please use -seq_id instead."); $seqid = $seqname unless $seqid; } $self->seq_id($seqid) if (defined($seqid)); $tag && do { foreach my $t ( keys %$tag ) { $self->add_tag_value($t, UNIVERSAL::isa($tag->{$t}, "ARRAY") ? @{$tag->{$t}} : $tag->{$t}); } }; } =head2 direct_new Title : direct_new Usage : my $feat = Bio::SeqFeature::Generic->direct_new; Function: create a blessed hash - for performance improvement in object creation Returns : Bio::SeqFeature::Generic object Args : none =cut sub direct_new { my ( $class) = @_; my ($self) = {}; bless $self,$class; return $self; } =head2 location Title : location Usage : my $location = $feat->location(); Function: returns a location object suitable for identifying location of feature on sequence or parent feature Returns : Bio::LocationI object Args : [optional] Bio::LocationI object to set the value to. =cut sub location { my($self, $value ) = @_; if (defined($value)) { unless (ref($value) and $value->isa('Bio::LocationI')) { $self->throw("object $value pretends to be a location but ". "does not implement Bio::LocationI"); } $self->{'_location'} = $value; } elsif (! $self->{'_location'}) { # guarantees a real location object is returned every time $self->{'_location'} = Bio::Location::Simple->new(); } return $self->{'_location'}; } =head2 start Title : start Usage : my $start = $feat->start; $feat->start(20); Function: Get/set on the start coordinate of the feature Returns : integer Args : none =cut sub start { my ($self, $value) = @_; # Return soon if setting value if (defined $value) { return $self->location->start($value); } return $self->location->start() if not defined $self->{'_gsf_seq'}; # Check circular sequences cut by origin my $start; if ( $self->{'_gsf_seq'}->is_circular and $self->location->isa('Bio::Location::SplitLocationI') ) { my $primary_seq_length = $self->{'_gsf_seq'}->length; my @sublocs = $self->location->sub_Location; my $cut_by_origin = 0; my ($a_end, $a_strand) = (0, 0); my ($b_start, $b_strand) = (0, 0); for (my $i = 1; $i < scalar @sublocs; $i++) { $a_end = $sublocs[$i-1]->end; $a_strand = $sublocs[$i-1]->strand; $b_start = $sublocs[$i]->start; $b_strand = $sublocs[$i]->strand; # cut by origin condition if ( $a_end == $primary_seq_length and $b_start == 1 and $a_strand == $b_strand ) { $cut_by_origin = 1; last; } } $start = ($cut_by_origin == 1) ? ($sublocs[0]->start) : ($self->location->start); } else { $start = $self->location->start; } return $start; } =head2 end Title : end Usage : my $end = $feat->end; $feat->end($end); Function: get/set on the end coordinate of the feature Returns : integer Args : none =cut sub end { my ($self, $value) = @_; # Return soon if setting value if (defined $value) { return $self->location->end($value); } return $self->location->end() if not defined $self->{'_gsf_seq'}; # Check circular sequences cut by origin my $end; if ( $self->{'_gsf_seq'}->is_circular and $self->location->isa('Bio::Location::SplitLocationI') ) { my $primary_seq_length = $self->{'_gsf_seq'}->length; my @sublocs = $self->location->sub_Location; my $cut_by_origin = 0; my ($a_end, $a_strand) = (0, 0); my ($b_start, $b_strand) = (0, 0); for (my $i = 1; $i < scalar @sublocs; $i++) { $a_end = $sublocs[$i-1]->end; $a_strand = $sublocs[$i-1]->strand; $b_start = $sublocs[$i]->start; $b_strand = $sublocs[$i]->strand; # cut by origin condition if ( $a_end == $primary_seq_length and $b_start == 1 and $a_strand == $b_strand ) { $cut_by_origin = 1; last; } } $end = ($cut_by_origin == 1) ? ($sublocs[-1]->end) : ($self->location->end); } else { $end = $self->location->end; } return $end; } =head2 length Title : length Usage : my $len = $feat->length; Function: Get the feature length computed as: $feat->end - $feat->start + 1 Returns : integer Args : none =cut sub length { my $self = shift; my $length = $self->end() - $self->start() + 1; # In circular sequences cut by origin $start > $end, # e.g., join(5075..5386,1..51)), $start = 5075, $end = 51, # then adjust using the primary_seq length (5386) if ($length < 0 and defined $self->{'_gsf_seq'}) { $length += $self->{'_gsf_seq'}->length; } return $length; } =head2 strand Title : strand Usage : my $strand = $feat->strand(); $feat->strand($strand); Function: get/set on strand information, being 1,-1 or 0 Returns : -1,1 or 0 Args : none =cut sub strand { my $self = shift; return $self->location->strand(@_); } =head2 score Title : score Usage : my $score = $feat->score(); $feat->score($score); Function: get/set on score information Returns : float Args : none if get, the new value if set =cut sub score { my $self = shift; if (@_) { my $value = shift; if ( defined $value && $value && $value !~ /^[A-Za-z]+$/ && $value !~ /^[+-]?\d+\.?\d*(e-\d+)?/ and $value != 0) { $self->throw(-class=>'Bio::Root::BadParameter', -text=>"'$value' is not a valid score", -value=>$value); } if ($self->has_tag('score')) { $self->warn("Removing score value(s)"); $self->remove_tag('score'); } $self->add_tag_value('score',$value); } my ($score) = $self->has_tag('score') ? $self->get_tag_values('score') : undef; return $score; } =head2 frame Title : frame Usage : my $frame = $feat->frame(); $feat->frame($frame); Function: get/set on frame information Returns : 0,1,2, '.' Args : none if get, the new value if set =cut sub frame { my $self = shift; if ( @_ ) { my $value = shift; if ( defined $value && $value !~ /^[0-2.]$/ ) { $self->throw("'$value' is not a valid frame"); } if( defined $value && $value eq '.' ) { $value = '.' } return $self->{'_gsf_frame'} = $value; } return $self->{'_gsf_frame'}; } =head2 primary_tag Title : primary_tag Usage : my $tag = $feat->primary_tag(); $feat->primary_tag('exon'); Function: get/set on the primary tag for a feature, eg 'exon' Returns : a string Args : none =cut sub primary_tag { my $self = shift; return $self->{'_primary_tag'} = shift if @_; return $self->{'_primary_tag'} || ''; } =head2 source_tag Title : source_tag Usage : my $tag = $feat->source_tag(); $feat->source_tag('genscan'); Function: Returns the source tag for a feature, eg, 'genscan' Returns : a string Args : none =cut sub source_tag { my $self = shift; return $self->{'_source_tag'} = shift if @_; return $self->{'_source_tag'} || ''; } =head2 has_tag Title : has_tag Usage : my $value = $feat->has_tag('some_tag'); Function: Tests whether a feature containings a tag Returns : TRUE if the SeqFeature has the tag, and FALSE otherwise. Args : The name of a tag =cut sub has_tag { my ($self, $tag) = @_; return exists $_[0]->{'_gsf_tag_hash'}->{$tag}; } =head2 add_tag_value Title : add_tag_value Usage : $feat->add_tag_value('note',"this is a note"); Returns : TRUE on success Args : tag (string) and one or more values (any scalar(s)) =cut sub add_tag_value { my $self = shift; my $tag = shift; $self->{'_gsf_tag_hash'}->{$tag} ||= []; push(@{$self->{'_gsf_tag_hash'}->{$tag}},@_); } =head2 get_tag_values Title : get_tag_values Usage : my @values = $feat->get_tag_values('note'); Function: Returns a list of all the values stored under a particular tag. Returns : A list of scalars Args : The name of the tag =cut sub get_tag_values { my ($self, $tag) = @_; if( ! defined $tag ) { return (); } if ( ! exists $self->{'_gsf_tag_hash'}->{$tag} ) { $self->throw("asking for tag value that does not exist $tag"); } return @{$self->{'_gsf_tag_hash'}->{$tag}}; } =head2 get_all_tags Title : get_all_tags Usage : my @tags = $feat->get_all_tags(); Function: Get a list of all the tags in a feature Returns : An array of tag names Args : none # added a sort so that tags will be returned in a predictable order # I still think we should be able to specify a sort function # to the object at some point # -js =cut sub get_all_tags { my ($self, @args) = @_; return sort keys %{ $self->{'_gsf_tag_hash'}}; } =head2 remove_tag Title : remove_tag Usage : $feat->remove_tag('some_tag'); Function: removes a tag from this feature Returns : the array of values for this tag before removing it Args : tag (string) =cut sub remove_tag { my ($self, $tag) = @_; if ( ! exists $self->{'_gsf_tag_hash'}->{$tag} ) { $self->throw("trying to remove a tag that does not exist: $tag"); } my @vals = @{$self->{'_gsf_tag_hash'}->{$tag}}; delete $self->{'_gsf_tag_hash'}->{$tag}; return @vals; } =head2 attach_seq Title : attach_seq Usage : $feat->attach_seq($seq); Function: Attaches a Bio::Seq object to this feature. This Bio::Seq object is for the *entire* sequence: ie from 1 to 10000 Example : Returns : TRUE on success Args : a Bio::PrimarySeqI compliant object =cut sub attach_seq { my ($self, $seq) = @_; if ( ! ($seq && ref($seq) && $seq->isa("Bio::PrimarySeqI")) ) { $self->throw("Must attach Bio::PrimarySeqI objects to SeqFeatures but got '".ref($seq)."'"); } $self->{'_gsf_seq'} = $seq; # attach to sub features if they want it foreach ( $self->sub_SeqFeature() ) { $_->attach_seq($seq); } return 1; } =head2 seq Title : seq Usage : my $tseq = $feat->seq(); Function: returns the truncated sequence (if there) for this Example : Returns : sub seq (a Bio::PrimarySeqI compliant object) on attached sequence bounded by start & end, or undef if there is no sequence attached. If the strand is defined and set to -1, the returned sequence is the reverse-complement of the region Args : none =cut sub seq { my ($self, $arg) = @_; if ( defined $arg ) { $self->throw("Calling SeqFeature::Generic->seq with an argument. You probably want attach_seq"); } if ( ! exists $self->{'_gsf_seq'} ) { return; } # assumming our seq object is sensible, it should not have to yank # the entire sequence out here. my $seq; my $start = $self->start; my $end = $self->end; # Check circular sequences cut by origin (e.g. join(2006035..2007700,1..257)) if ( $self->{'_gsf_seq'}->is_circular and $self->location->isa('Bio::Location::SplitLocationI') and $start > $end ) { my $primary_seq_length = $self->{'_gsf_seq'}->length; # Get duplicate object with the first sequence piece using trunc() $seq = $self->{'_gsf_seq'}->trunc($start, $primary_seq_length); # Get post-origin sequence and build the complete sequence my $post_origin = $self->{'_gsf_seq'}->subseq(1, $end); my $complete_seq = $seq->seq() . $post_origin; # Add complete sequence to object $seq->seq($complete_seq); } else { $seq = $self->{'_gsf_seq'}->trunc($start, $end); } if ( defined $self->strand && $self->strand == -1 ) { $seq = $seq->revcom; } return $seq; } =head2 entire_seq Title : entire_seq Usage : my $whole_seq = $feat->entire_seq(); Function: gives the entire sequence that this seqfeature is attached to Example : Returns : a Bio::PrimarySeqI compliant object, or undef if there is no sequence attached Args : =cut sub entire_seq { return shift->{'_gsf_seq'}; } =head2 seq_id Title : seq_id Usage : $feat->seq_id($newval) Function: There are many cases when you make a feature that you do know the sequence name, but do not know its actual sequence. This is an attribute such that you can store the ID (e.g., display_id) of the sequence. This attribute should *not* be used in GFF dumping, as that should come from the collection in which the seq feature was found. Returns : value of seq_id Args : newvalue (optional) =cut sub seq_id { my $obj = shift; return $obj->{'_gsf_seq_id'} = shift if @_; return $obj->{'_gsf_seq_id'}; } =head2 display_name Title : display_name Usage : my $featname = $feat->display_name; Function: Implements the display_name() method, which is a human-readable name for the feature. Returns : value of display_name (a string) Args : Optionally, on set the new value or undef =cut sub display_name { my $self = shift; return $self->{'display_name'} = shift if @_; return $self->{'display_name'} || ''; } =head1 Methods for implementing Bio::AnnotatableI =head2 annotation Title : annotation Usage : $feat->annotation($annot_obj); Function: Get/set the annotation collection object for annotating this feature. Example : Returns : A Bio::AnnotationCollectionI object Args : newvalue (optional) =cut sub annotation { my ($obj,$value) = @_; # we are smart if someone references the object and there hasn't been # one set yet if(defined $value || ! defined $obj->{'annotation'} ) { $value = Bio::Annotation::Collection->new() unless ( defined $value ); $obj->{'annotation'} = $value; } return $obj->{'annotation'}; } =head1 Methods to implement Bio::FeatureHolderI This includes methods for retrieving, adding, and removing features. Since this is already a feature, features held by this feature holder are essentially sub-features. =head2 get_SeqFeatures Title : get_SeqFeatures Usage : my @feats = $feat->get_SeqFeatures(); Function: Returns an array of sub Sequence Features Returns : An array Args : none =cut sub get_SeqFeatures { return @{ shift->{'_gsf_sub_array'} || []}; } =head2 add_SeqFeature Title : add_SeqFeature Usage : $feat->add_SeqFeature($subfeat); $feat->add_SeqFeature($subfeat,'EXPAND'); Function: Adds a SeqFeature into the subSeqFeature array. With no 'EXPAND' qualifer, subfeat will be tested as to whether it lies inside the parent, and throw an exception if not. If EXPAND is used, the parent's start/end/strand will be adjusted so that it grows to accommodate the new subFeature !IMPORTANT! The coordinates of the subfeature should not be relative to the parent feature it is attached to, but relative to the sequence the parent feature is located on. Returns : nothing Args : An object which has the SeqFeatureI interface =cut sub add_SeqFeature { my ($self,$feat,$expand) = @_; unless( defined $feat ) { $self->warn("Called add_SeqFeature with no feature, ignoring"); return; } if ( !$feat->isa('Bio::SeqFeatureI') ) { $self->warn("$feat does not implement Bio::SeqFeatureI. Will add it anyway, but beware..."); } if($expand && ($expand eq 'EXPAND')) { $self->_expand_region($feat); } else { if ( !$self->contains($feat) ) { $self->throw("$feat is not contained within parent feature, and expansion is not valid"); } } $self->{'_gsf_sub_array'} = [] unless exists($self->{'_gsf_sub_array'}); push(@{$self->{'_gsf_sub_array'}},$feat); } =head2 remove_SeqFeatures Title : remove_SeqFeatures Usage : $feat->remove_SeqFeatures; Function: Removes all SeqFeatures If you want to remove only a subset of features then remove that subset from the returned array, and add back the rest. Example : Returns : The array of Bio::SeqFeatureI implementing features that was deleted. Args : none =cut sub remove_SeqFeatures { my ($self) = @_; my @subfeats = @{$self->{'_gsf_sub_array'} || []}; $self->{'_gsf_sub_array'} = []; # zap the array implicitly. return @subfeats; } =head1 GFF-related methods =head2 gff_format Title : gff_format Usage : # get: my $gffio = $feat->gff_format(); # set (change the default version of GFF2): $feat->gff_format(Bio::Tools::GFF->new(-gff_version => 1)); Function: Get/set the GFF format interpreter. This object is supposed to format and parse GFF. See Bio::Tools::GFF for the interface. If this method is called as class method, the default for all newly created instances will be changed. Otherwise only this instance will be affected. Example : Returns : a Bio::Tools::GFF compliant object Args : On set, an instance of Bio::Tools::GFF or a derived object. =cut sub gff_format { my ($self, $gffio) = @_; if(defined($gffio)) { if(ref($self)) { $self->{'_gffio'} = $gffio; } else { $Bio::SeqFeatureI::static_gff_formatter = $gffio; } } return (ref($self) && exists($self->{'_gffio'}) ? $self->{'_gffio'} : $self->_static_gff_formatter); } =head2 gff_string Title : gff_string Usage : my $str = $feat->gff_string; my $str = $feat->gff_string($gff_formatter); Function: Provides the feature information in GFF format. We override this here from Bio::SeqFeatureI in order to use the formatter returned by gff_format(). Returns : A string Args : Optionally, an object implementing gff_string(). =cut sub gff_string { my ($self,$formatter) = @_; $formatter = $self->gff_format() unless $formatter; return $formatter->gff_string($self); } =head2 slurp_gff_file Title : slurp_file Usage : my @features = Bio::SeqFeature::Generic::slurp_gff_file(\*FILE); Function: Sneaky function to load an entire file as in memory objects. Beware of big files. This method is deprecated. Use Bio::Tools::GFF instead, which can also handle large files. Example : Returns : Args : =cut sub slurp_gff_file { my ($f) = @_; my @out; if ( !defined $f ) { Bio::Root::Root->throw("Must have a filehandle"); } Bio::Root::Root->deprecated( -message => "deprecated method slurp_gff_file() called in Bio::SeqFeature::Generic. Use Bio::Tools::GFF instead.", -warn_version => '1.005', -throw_version => '1.007', ); while(<$f>) { my $sf = Bio::SeqFeature::Generic->new('-gff_string' => $_); push(@out, $sf); } return @out; } =head2 _from_gff_string Title : _from_gff_string Usage : Function: Set feature properties from GFF string. This method uses the object returned by gff_format() for the actual interpretation of the string. Set a different GFF format interpreter first if you need a specific version, like GFF1. (The default is GFF2.) Example : Returns : Args : a GFF-formatted string =cut sub _from_gff_string { my ($self, $string) = @_; $self->gff_format()->from_gff_string($self, $string); } =head2 _expand_region Title : _expand_region Usage : $feat->_expand_region($feature); Function: Expand the total region covered by this feature to accommodate for the given feature. May be called whenever any kind of subfeature is added to this feature. add_SeqFeature() already does this. Returns : Args : A Bio::SeqFeatureI implementing object. =cut sub _expand_region { my ($self, $feat) = @_; if(! $feat->isa('Bio::SeqFeatureI')) { $self->warn("$feat does not implement Bio::SeqFeatureI"); } # if this doesn't have start set - forget it! # changed to reflect sanity checks for LocationI if(!$self->location->valid_Location) { $self->start($feat->start); $self->end($feat->end); $self->strand($feat->strand) unless $self->strand; } else { my ($start,$end,$strand) = $self->union($feat); $self->start($start); $self->end($end); $self->strand($strand); } } =head2 _parse Title : _parse Usage : Function: Parsing hints Example : Returns : Args : =cut sub _parse { my ($self) = @_; return $self->{'_parse_h'}; } =head2 _tag_value Title : _tag_value Usage : Function: For internal use only. Convenience method for those tags that may only have a single value. Returns : The first value under the given tag as a scalar (string) Args : The tag as a string. Optionally, the value on set. =cut sub _tag_value { my $self = shift; my $tag = shift; if(@_ || (! $self->has_tag($tag))) { $self->remove_tag($tag) if($self->has_tag($tag)); $self->add_tag_value($tag, @_); } return ($self->get_tag_values($tag))[0]; } ####################################################################### # aliases for methods that changed their names in an attempt to make # # bioperl names more consistent # ####################################################################### sub seqname { my $self = shift; $self->warn("SeqFeatureI::seqname() is deprecated. Please use seq_id() instead."); return $self->seq_id(@_); } sub display_id { my $self = shift; $self->warn("SeqFeatureI::display_id() is deprecated. Please use display_name() instead."); return $self->display_name(@_); } # this is towards consistent naming sub each_tag_value { return shift->get_tag_values(@_); } sub all_tags { return shift->get_all_tags(@_); } # we revamped the feature containing property to implementing # Bio::FeatureHolderI *sub_SeqFeature = \&get_SeqFeatures; *add_sub_SeqFeature = \&add_SeqFeature; *flush_sub_SeqFeatures = \&remove_SeqFeatures; # this one is because of inconsistent naming ... *flush_sub_SeqFeature = \&remove_SeqFeatures; sub cleanup_generic { my $self = shift; foreach my $f ( @{$self->{'_gsf_sub_array'} || []} ) { $f = undef; } $self->{'_gsf_seq'} = undef; foreach my $t ( keys %{$self->{'_gsf_tag_hash'} } ) { $self->{'_gsf_tag_hash'}->{$t} = undef; delete($self->{'_gsf_tag_hash'}->{$t}); # bug 1720 fix } } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Lite.pm�������������������������������������������������������������000444��000766��000024�� 60051�13155576320� 17545� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������package Bio::SeqFeature::Lite; =head1 NAME Bio::SeqFeature::Lite - Lightweight Bio::SeqFeatureI class =head1 SYNOPSIS # create a simple feature with no internal structure $f = Bio::SeqFeature::Lite->new(-start => 1000, -stop => 2000, -type => 'transcript', -name => 'alpha-1 antitrypsin', -desc => 'an enzyme inhibitor', ); # create a feature composed of multiple segments, all of type "similarity" $f = Bio::SeqFeature::Lite->new(-segments => [[1000,1100],[1500,1550],[1800,2000]], -name => 'ABC-3', -type => 'gapped_alignment', -subtype => 'similarity'); # build up a gene exon by exon $e1 = Bio::SeqFeature::Lite->new(-start=>1,-stop=>100,-type=>'exon'); $e2 = Bio::SeqFeature::Lite->new(-start=>150,-stop=>200,-type=>'exon'); $e3 = Bio::SeqFeature::Lite->new(-start=>300,-stop=>500,-type=>'exon'); $f = Bio::SeqFeature::Lite->new(-segments=>[$e1,$e2,$e3],-type=>'gene'); =head1 DESCRIPTION This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing. All methods are as described in L<Bio::SeqFeatureI> with the following additions: =head2 The new() Constructor $feature = Bio::SeqFeature::Lite->new(@args); This method creates a new feature object. You can create a simple feature that contains no subfeatures, or a hierarchically nested object. Arguments are as follows: -seq_id the reference sequence -start the start position of the feature -end the stop position of the feature -stop an alias for end -name the feature name (returned by seqname()) -type the feature type (returned by primary_tag()) -primary_tag the same as -type -source the source tag -score the feature score (for GFF compatibility) -desc a description of the feature -segments a list of subfeatures (see below) -subtype the type to use when creating subfeatures -strand the strand of the feature (one of -1, 0 or +1) -phase the phase of the feature (0..2) -seq a dna or protein sequence string to attach to feature -id an alias for -name -seqname an alias for -name -display_id an alias for -name -display_name an alias for -name (do you get the idea the API has changed?) -primary_id unique database ID -url a URL to link to when rendered with Bio::Graphics -attributes a hashref of tag value attributes, in which the key is the tag and the value is an array reference of values -factory a reference to a feature factory, used for compatibility with more obscure parts of Bio::DB::GFF The subfeatures passed in -segments may be an array of Bio::SeqFeature::Lite objects, or an array of [$start,$stop] pairs. Each pair should be a two-element array reference. In the latter case, the feature type passed in -subtype will be used when creating the subfeatures. If no feature type is passed, then it defaults to "feature". =head2 Non-SeqFeatureI methods A number of new methods are provided for compatibility with Ace::Sequence, which has a slightly different API from SeqFeatureI: =over 4 =item url() Get/set the URL that the graphical rendering of this feature will link to. =item add_segment(@segments) Add one or more segments (a subfeature). Segments can either be Feature objects, or [start,stop] arrays, as in the -segments argument to new(). The feature endpoints are automatically adjusted. =item segments() An alias for sub_SeqFeature(). =item get_SeqFeatures() Alias for sub_SeqFeature() =item get_all_SeqFeatures() Alias for sub_SeqFeature() =item merged_segments() Another alias for sub_SeqFeature(). =item stop() An alias for end(). =item name() An alias for seqname(). =item exons() An alias for sub_SeqFeature() (you don't want to know why!) =back =cut use strict; use base qw(Bio::Root::Root Bio::SeqFeatureI Bio::LocationI Bio::SeqI); *stop = \&end; *info = \&name; *seqname = \&name; *exons = *sub_SeqFeature = *merged_segments = \&segments; *get_all_SeqFeatures = *get_SeqFeatures = \&segments; *method = \&primary_tag; *source = \&source_tag; *get_tag_values = \&each_tag_value; *add_SeqFeature = \&add_segment; *get_all_tags = \&all_tags; *abs_ref = \&ref; # implement Bio::SeqI and FeatureHolderI interface sub primary_seq { return $_[0] } sub annotation { my ($obj,$value) = @_; if( defined $value ) { $obj->throw("object of class ".ref($value)." does not implement ". "Bio::AnnotationCollectionI. Too bad.") unless $value->isa("Bio::AnnotationCollectionI"); $obj->{'_annotation'} = $value; } elsif( ! defined $obj->{'_annotation'}) { $obj->{'_annotation'} = Bio::Annotation::Collection->new(); } return $obj->{'_annotation'}; } sub species { my ($self, $species) = @_; if ($species) { $self->{'species'} = $species; } else { return $self->{'species'}; } } sub is_remote { return } sub feature_count { return scalar @{shift->{segments} || []} } sub target { return; } sub hit { shift->target } sub type { my $self = shift; my $method = $self->primary_tag; my $source = $self->source_tag; return $source ne '' ? "$method:$source" : $method; } # usage: # Bio::SeqFeature::Lite->new( # -start => 1, # -end => 100, # -name => 'fred feature', # -strand => +1); # # Alternatively, use -segments => [ [start,stop],[start,stop]...] # to create a multisegmented feature. sub new { my $class= shift; $class = ref($class) if ref $class; my %arg = @_; my $self = bless {},$class; $arg{-strand} ||= 0; if ($arg{-strand} =~ /^[\+\-\.]$/){ ($arg{-strand} eq "+") && ($self->{strand} = '1'); ($arg{-strand} eq "-") && ($self->{strand} = '-1'); ($arg{-strand} eq ".") && ($self->{strand} = '0'); } else { $self->{strand} = $arg{-strand} ? ($arg{-strand} >= 0 ? +1 : -1) : 0; } $self->{name} = $arg{-name} || $arg{-seqname} || $arg{-display_id} || $arg{-display_name} || $arg{-id}; $self->{type} = $arg{-type} || $arg{-primary_tag} || 'feature'; $self->{subtype} = $arg{-subtype} if exists $arg{-subtype}; $self->{source} = $arg{-source} || $arg{-source_tag} || ''; $self->{score} = $arg{-score} if exists $arg{-score}; $self->{start} = $arg{-start}; $self->{stop} = exists $arg{-end} ? $arg{-end} : $arg{-stop}; $self->{ref} = $arg{-seq_id} || $arg{-ref}; $self->{attributes} = $arg{-attributes} || $arg{-tag}; for my $option (qw(class url seq phase desc primary_id)) { $self->{$option} = $arg{"-$option"} if exists $arg{"-$option"}; } # is_circular is needed for Bio::PrimarySeqI compliance $self->{is_circular} = $arg{-is_circular} || 0; # fix start, stop if (defined $self->{stop} && defined $self->{start} && $self->{stop} < $self->{start}) { @{$self}{'start','stop'} = @{$self}{'stop','start'}; $self->{strand} *= -1; } my @segments; if (my $s = $arg{-segments}) { # NB: when $self ISA Bio::DB::SeqFeature the following invokes # Bio::DB::SeqFeature::add_segment and not # Bio::DB::SeqFeature::add_segment (as might be expected?) $self->add_segment(@$s); } $self; } sub add_segment { my $self = shift; my $type = $self->{subtype} || $self->{type}; $self->{segments} ||= []; my $ref = $self->seq_id; my $name = $self->name; my $class = $self->class; my $source_tag = $self->source_tag; my $min_start = $self->start || 999_999_999_999; my $max_stop = $self->end || -999_999_999_999; my @segments = @{$self->{segments}}; for my $seg (@_) { if (ref($seg) eq 'ARRAY') { my ($start,$stop) = @{$seg}; next unless defined $start && defined $stop; # fixes an obscure bug somewhere above us my $strand = $self->{strand}; if ($start > $stop) { ($start,$stop) = ($stop,$start); $strand = -1; } push @segments,$self->new(-start => $start, -stop => $stop, -strand => $strand, -ref => $ref, -type => $type, -name => $name, -class => $class, -phase => $self->{phase}, -score => $self->{score}, -source_tag => $source_tag, -attributes => $self->{attributes}, ); $min_start = $start if $start < $min_start; $max_stop = $stop if $stop > $max_stop; } elsif (ref $seg) { push @segments,$seg; $min_start = $seg->start if ($seg->start && $seg->start < $min_start); $max_stop = $seg->end if ($seg->end && $seg->end > $max_stop); } } if (@segments) { local $^W = 0; # some warning of an uninitialized variable... $self->{segments} = \@segments; $self->{ref} ||= $self->{segments}[0]->seq_id; $self->{start} = $min_start; $self->{stop} = $max_stop; } } sub segments { my $self = shift; my $s = $self->{segments} or return wantarray ? () : 0; @$s; } sub score { my $self = shift; my $d = $self->{score}; $self->{score} = shift if @_; $d; } sub primary_tag { my $self = shift; my $d = $self->{type}; $self->{type} = shift if @_; $d; } sub name { my $self = shift; my $d = $self->{name}; $self->{name} = shift if @_; $d; } sub seq_id { shift->ref(@_) } sub ref { my $self = shift; my $d = $self->{ref}; $self->{ref} = shift if @_; $d; } sub start { my $self = shift; my $d = $self->{start}; $self->{start} = shift if @_; if (my $rs = $self->{refseq}) { my $strand = $rs->strand || 1; return $strand >= 0 ? ($d - $rs->start + 1) : ($rs->end - $d + 1); } else { return $d; } } sub end { my $self = shift; my $d = $self->{stop}; $self->{stop} = shift if @_; if (my $rs = $self->{refseq}) { my $strand = $rs->strand || 1; return $strand >= 0 ? ($d - $rs->start + 1) : ($rs->end - $d + 1); } $d; } sub strand { my $self = shift; my $d = $self->{strand}; $self->{strand} = shift if @_; if (my $rs = $self->{refseq}) { my $rstrand = $rs->strand; return 0 unless $d; return 1 if $rstrand == $d; return -1 if $rstrand != $d; } $d; } # this does nothing, but it is here for compatibility reasons sub absolute { my $self = shift; my $d = $self->{absolute}; $self->{absolute} = shift if @_; $d; } sub abs_start { my $self = shift; local $self->{refseq} = undef; $self->start(@_); } sub abs_end { my $self = shift; local $self->{refseq} = undef; $self->end(@_); } sub abs_strand { my $self = shift; local $self->{refseq} = undef; $self->strand(@_); } sub length { my $self = shift; return $self->end - $self->start + 1; } #is_circular is needed for Bio::PrimarySeqI sub is_circular { my $self = shift; my $d = $self->{is_circular}; $self->{is_circular} = shift if @_; $d; } sub seq { my $self = shift; my $seq = exists $self->{seq} ? $self->{seq} : ''; return $seq; } sub dna { my $seq = shift->seq; $seq = $seq->seq if CORE::ref($seq); return $seq; } =head2 display_name Title : display_name Usage : $id = $obj->display_name or $obj->display_name($newid); Function: Gets or sets the display id, also known as the common name of the Seq object. The semantics of this is that it is the most likely string to be used as an identifier of the sequence, and likely to have "human" readability. The id is equivalent to the LOCUS field of the GenBank/EMBL databanks and the ID field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. Notice that $seq->id() maps to this function, mainly for legacy/convenience issues. Returns : A string Args : None or a new id =cut sub display_name { shift->name(@_) } *display_id = \&display_name; =head2 accession_number Title : accession_number Usage : $unique_biological_key = $obj->accession_number; Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". Returns : A string Args : None =cut sub accession_number { return 'unknown'; } =head2 alphabet Title : alphabet Usage : if( $obj->alphabet eq 'dna' ) { /Do Something/ } Function: Returns the type of sequence being one of 'dna', 'rna' or 'protein'. This is case sensitive. This is not called <type> because this would cause upgrade problems from the 0.5 and earlier Seq objects. Returns : a string either 'dna','rna','protein'. NB - the object must make a call of the type - if there is no type specified it has to guess. Args : none Status : Virtual =cut sub alphabet{ return 'dna'; # no way this will be anything other than dna! } =head2 desc Title : desc Usage : $seqobj->desc($string) or $seqobj->desc() Function: Sets or gets the description of the sequence Example : Returns : The description Args : The description or none =cut sub desc { my $self = shift; my ($d) = $self->notes; $self->{desc} = shift if @_; $d; } sub attributes { my $self = shift; if (@_) { return $self->get_tag_values(@_); } else { return $self->{attributes} ? %{$self->{attributes}} : (); } } sub primary_id { my $self = shift; my $d = $self->{primary_id}; $self->{primary_id} = shift if @_; return $d; # return $d if defined $d; # return (overload::StrVal($self) =~ /0x([a-f0-9]+)/)[0]; } sub notes { my $self = shift; my $notes = $self->{desc}; return $notes if defined $notes; return $self->attributes('Note'); } sub aliases { my $self = shift; return $self->attributes('Alias'); } sub low { my $self = shift; return $self->start < $self->end ? $self->start : $self->end; } sub high { my $self = shift; return $self->start > $self->end ? $self->start : $self->end; } =head2 location Title : location Usage : my $location = $seqfeature->location() Function: returns a location object suitable for identifying location of feature on sequence or parent feature Returns : Bio::LocationI object Args : none =cut sub location { my $self = shift; require Bio::Location::Split unless Bio::Location::Split->can('new'); my $location; if (my @segments = $self->segments) { $location = Bio::Location::Split->new(); foreach (@segments) { $location->add_sub_Location($_); } } else { $location = $self; } $location; } sub each_Location { my $self = shift; require Bio::Location::Simple unless Bio::Location::Simple->can('new'); if (my @segments = $self->segments) { return map { Bio::Location::Simple->new(-start => $_->start, -end => $_->end, -strand => $_->strand); } @segments; } else { return Bio::Location::Simple->new(-start => $self->start, -end => $self->end, -strand => $self->strand); } } =head2 location_string Title : location_string Usage : my $string = $seqfeature->location_string() Function: Returns a location string in a format recognized by gbrowse Returns : a string Args : none This is a convenience function used by the generic genome browser. It returns the location of the feature and its subfeatures in the compact form "start1..end1,start2..end2,...". Use $seqfeature-E<gt>location()-E<gt>toFTString() to obtain a standard GenBank/EMBL location representation. =cut sub location_string { my $self = shift; my @segments = $self->segments or return $self->to_FTstring; join ',',map {$_->to_FTstring} @segments; } sub coordinate_policy { require Bio::Location::WidestCoordPolicy unless Bio::Location::WidestCoordPolicy->can('new'); return Bio::Location::WidestCoordPolicy->new(); } sub min_start { shift->low } sub max_start { shift->low } sub min_end { shift->high } sub max_end { shift->high} sub start_pos_type { 'EXACT' } sub end_pos_type { 'EXACT' } sub to_FTstring { my $self = shift; my $low = $self->min_start; my $high = $self->max_end; my $strand = $self->strand; my $str = defined $strand && $strand<0 ? "complement($low..$high)" : "$low..$high"; if (my $id = $self->seq_id()) { $str = $id . ":" . $str; } $str; } sub phase { my $self = shift; my $d = $self->{phase}; $self->{phase} = shift if @_; $d; } sub class { my $self = shift; my $d = $self->{class}; $self->{class} = shift if @_; return defined($d) ? $d : 'Sequence'; # acedb is still haunting me - LS } # set GFF dumping version sub version { my $self = shift; my $d = $self->{gff3_version} || 2; $self->{gff3_version} = shift if @_; $d; } sub gff_string { my $self = shift; if ($self->version == 3) { return $self->gff3_string(@_); } my $recurse = shift; my $name = $self->name; my $class = $self->class; my $group = "$class $name" if $name; my $strand = ('-','.','+')[$self->strand+1]; my $string; $string .= join("\t", $self->ref||'.',$self->source||'.',$self->method||'.', $self->start||'.',$self->stop||'.', defined($self->score) ? $self->score : '.', $strand||'.', defined($self->phase) ? $self->phase : '.', $group||'' ); $string .= "\n"; if ($recurse) { foreach ($self->sub_SeqFeature) { $string .= $_->gff_string($recurse); } } $string; } # Suggested strategy for dealing with the multiple parentage issue. # First recurse through object tree and record parent tree. # Then recurse again, skipping objects we've seen before. sub gff3_string { my ($self,$recurse,$parent_tree,$seenit,$force_id) = @_; $parent_tree ||= {}; $seenit ||= {}; my @rsf = (); my @parent_ids; if ($recurse) { $self->_traverse($parent_tree) unless %$parent_tree; # this will record parents of all children my $primary_id = defined $force_id ? $force_id : $self->_real_or_dummy_id; return if $seenit->{$primary_id}++; @rsf = $self->get_SeqFeatures; if (@rsf) { # Detect case in which we have a split location feature. In this case we # skip to the grandchildren and trick them into thinking that our parent is theirs. my %types = map {$_->primary_tag=>1} @rsf; my @types = keys %types; if (@types == 1 && $types[0] eq $self->primary_tag) { return join ("\n",map {$_->gff3_string(1,$parent_tree,{},$primary_id)} @rsf); } } @parent_ids = keys %{$parent_tree->{$primary_id}}; } my $group = $self->format_attributes(\@parent_ids,$force_id); my $name = $self->name; my $class = $self->class; my $strand = ('-','.','+')[$self->strand+1]; my $p = join("\t", $self->seq_id||'.', $self->source||'.', $self->method||'.', $self->start||'.', $self->stop||'.', defined($self->score) ? $self->score : '.', $strand||'.', defined($self->phase) ? $self->phase : '.', $group||''); return join("\n", $p, map {$_->gff3_string(1,$parent_tree,$seenit)} @rsf); } sub _real_or_dummy_id { my $self = shift; my $id = $self->primary_id; return $id if defined $id; return return (overload::StrVal($self) =~ /0x([a-f0-9]+)/)[0]; } sub _traverse { my $self = shift; my $tree = shift; # tree => {$child}{$parent} = 1 my $parent = shift; my $id = $self->_real_or_dummy_id; defined $id or return; $tree->{$id}{$parent->_real_or_dummy_id}++ if $parent; $_->_traverse($tree,$self) foreach $self->get_SeqFeatures; } sub db { return } sub source_tag { my $self = shift; my $d = $self->{source}; $self->{source} = shift if @_; $d; } # This probably should be deleted. Not sure why it's here, but might # have been added for Ace::Sequence::Feature-compliance. sub introns { my $self = shift; return; } sub has_tag { my $self = shift; my $tag = shift; return exists $self->{attributes}{$tag}; } sub escape { my $self = shift; my $toencode = shift; $toencode =~ s/([^a-zA-Z0-9_.:?^*\(\)\[\]@!+-])/uc sprintf("%%%02x",ord($1))/eg; $toencode; } sub all_tags { my $self = shift; return keys %{$self->{attributes}}; } sub add_tag_value { my $self = shift; my ($tag_name,@tag_values) = @_; push @{$self->{attributes}{$tag_name}},@tag_values; } sub remove_tag { my $self = shift; my $tag_name = shift; delete $self->{attributes}{$tag_name}; } sub each_tag_value { my $self = shift; my $tag = shift; my $value = $self->{attributes}{$tag} or return; my $ref = CORE::ref $value; return $ref && $ref eq 'ARRAY' ? @{$self->{attributes}{$tag}} : $self->{attributes}{$tag}; } sub get_Annotations { my $self = shift; my $tag = shift; my @values = $self->get_tag_values($tag); return $values[0] if @values == 1; return @values; } sub format_attributes { my $self = shift; my $parent = shift; my $fallback_id = shift; my @tags = $self->get_all_tags; my @result; for my $t (@tags) { my @values = $self->get_tag_values($t); push @result,join '=',$self->escape($t),join(',', map {$self->escape($_)} @values) if @values; } #my $id = $self->escape($self->_real_or_dummy_id) || $fallback_id; my $id = $fallback_id || $self->escape($self->_real_or_dummy_id); my $parent_id; if (@$parent) { $parent_id = join (',',map {$self->escape($_)} @$parent); } my $name = $self->display_name; unshift @result,"ID=".$id if defined $id; unshift @result,"Parent=".$parent_id if defined $parent_id; unshift @result,"Name=".$self->escape($name) if defined $name; return join ';',@result; } =head2 clone Title : clone Usage : my $feature = $seqfeature->clone Function: Create a deep copy of the feature Returns : A copy of the feature Args : none =cut sub clone { my $self = shift; my %clone = %$self; # overwrite attributes my $clone = bless \%clone,CORE::ref($self); $clone{attributes} = {}; for my $k (keys %{$self->{attributes}}) { @{$clone{attributes}{$k}} = @{$self->{attributes}{$k}}; } return $clone; } =head2 refseq Title : refseq Usage : $ref = $s->refseq([$newseq] [,$newseqclass]) Function: get/set reference sequence Returns : current reference sequence Args : new reference sequence and class (optional) Status : Public This method will get or set the reference sequence. Called with no arguments, it returns the current reference sequence. Called with any Bio::SeqFeatureI object that provides the seq_id(), start(), end() and strand() methods. The method will generate an exception if you attempt to set the reference sequence to a sequence that has a different seq_id from the current feature. =cut sub refseq { my $self = shift; my $d = $self->{refseq}; if (@_) { my $newref = shift; $self->throw("attempt to set refseq using a feature that does not share the same seq_id") unless $newref->seq_id eq $self->seq_id; $self->{refseq} = $newref; } return $d; } sub DESTROY { } 1; __END__ =head1 SEE ALSO L<Bio::Graphics::Feature> =head1 AUTHOR Lincoln Stein E<lt>lstein@cshl.eduE<gt>. Copyright (c) 2006 Cold Spring Harbor Laboratory This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. =cut ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/PositionProxy.pm����������������������������������������������������000444��000766��000024�� 22331�13155576320� 21515� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::PositionProxy # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::PositionProxy - handle features when truncation/revcom sequences span a feature =head1 SYNOPSIS $proxy = Bio::SeqFeature::PositionProxy->new( -loc => $loc, -parent => $basefeature); $seq->add_SeqFeature($feat); =head1 DESCRIPTION PositionProxy is a Proxy Sequence Feature to handle truncation and revcomp without duplicating all the data within the sequence features. It holds a new location for a sequence feature and the original feature it came from to provide the additional annotation information. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Ewan Birney E<lt>birney@sanger.ac.ukE<gt> =head1 DEVELOPERS This class has been written with an eye out of inheritance. The fields the actual object hash are: _gsf_tag_hash = reference to a hash for the tags _gsf_sub_array = reference to an array for sub arrays _gsf_start = scalar of the start point _gsf_end = scalar of the end point _gsf_strand = scalar of the strand =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::PositionProxy; use strict; use Bio::Tools::GFF; use base qw(Bio::Root::Root Bio::SeqFeatureI); sub new { my ($caller, @args) = @_; my $self = $caller->SUPER::new(@args); my ($feature,$location) = $self->_rearrange([qw(PARENT LOC)],@args); if( !defined $feature || !ref $feature || !$feature->isa('Bio::SeqFeatureI') ) { $self->throw("Must have a parent feature, not a [$feature]"); } if( $feature->isa("Bio::SeqFeature::PositionProxy") ) { $feature = $feature->parent(); } if( !defined $location || !ref $location || !$location->isa('Bio::LocationI') ) { $self->throw("Must have a location, not a [$location]"); } return $self; } =head2 location Title : location Usage : my $location = $seqfeature->location() Function: returns a location object suitable for identifying location of feature on sequence or parent feature Returns : Bio::LocationI object Args : none =cut sub location { my($self, $value ) = @_; if (defined($value)) { unless (ref($value) and $value->isa('Bio::LocationI')) { $self->throw("object $value pretends to be a location but ". "does not implement Bio::LocationI"); } $self->{'_location'} = $value; } elsif (! $self->{'_location'}) { # guarantees a real location object is returned every time $self->{'_location'} = Bio::Location::Simple->new(); } return $self->{'_location'}; } =head2 parent Title : parent Usage : my $sf = $proxy->parent() Function: returns the seqfeature parent of this proxy Returns : Bio::SeqFeatureI object Args : none =cut sub parent { my($self, $value ) = @_; if (defined($value)) { unless (ref($value) and $value->isa('Bio::SeqFeatureI')) { $self->throw("object $value pretends to be a location but ". "does not implement Bio::SeqFeatureI"); } $self->{'_parent'} = $value; } return $self->{'_parent'}; } =head2 start Title : start Usage : $start = $feat->start $feat->start(20) Function: Get Returns : integer Args : none =cut sub start { my ($self,$value) = @_; return $self->location->start($value); } =head2 end Title : end Usage : $end = $feat->end $feat->end($end) Function: get Returns : integer Args : none =cut sub end { my ($self,$value) = @_; return $self->location->end($value); } =head2 length Title : length Usage : Function: Example : Returns : Args : =cut sub length { my ($self) = @_; return $self->end - $self->start() + 1; } =head2 strand Title : strand Usage : $strand = $feat->strand() $feat->strand($strand) Function: get/set on strand information, being 1,-1 or 0 Returns : -1,1 or 0 Args : none =cut sub strand { my ($self,$value) = @_; return $self->location->strand($value); } =head2 attach_seq Title : attach_seq Usage : $sf->attach_seq($seq) Function: Attaches a Bio::Seq object to this feature. This Bio::Seq object is for the *entire* sequence: ie from 1 to 10000 Example : Returns : TRUE on success Args : =cut sub attach_seq { my ($self, $seq) = @_; if ( !defined $seq || !ref $seq || ! $seq->isa("Bio::PrimarySeqI") ) { $self->throw("Must attach Bio::PrimarySeqI objects to SeqFeatures"); } $self->{'_gsf_seq'} = $seq; # attach to sub features if they want it foreach my $sf ( $self->sub_SeqFeature() ) { if ( $sf->can("attach_seq") ) { $sf->attach_seq($seq); } } return 1; } =head2 seq Title : seq Usage : $tseq = $sf->seq() Function: returns the truncated sequence (if there) for this Example : Returns : sub seq on attached sequence bounded by start & end Args : none =cut sub seq { my ($self, $arg) = @_; if ( defined $arg ) { $self->throw("Calling SeqFeature::PositionProxy->seq with an argument. You probably want attach_seq"); } if ( ! exists $self->{'_gsf_seq'} ) { return; } # assumming our seq object is sensible, it should not have to yank # the entire sequence out here. my $seq = $self->{'_gsf_seq'}->trunc($self->start(), $self->end()); if ( $self->strand == -1 ) { $seq = $seq->revcom; } return $seq; } =head2 entire_seq Title : entire_seq Usage : $whole_seq = $sf->entire_seq() Function: gives the entire sequence that this seqfeature is attached to Example : Returns : Args : =cut sub entire_seq { my ($self) = @_; return unless exists($self->{'_gsf_seq'}); return $self->{'_gsf_seq'}; } =head2 seqname Title : seqname Usage : $obj->seq_id($newval) Function: There are many cases when you make a feature that you do know the sequence name, but do not know its actual sequence. This is an attribute such that you can store the seqname. This attribute should *not* be used in GFF dumping, as that should come from the collection in which the seq feature was found. Returns : value of seqname Args : newvalue (optional) =cut sub seqname { my ($obj,$value) = @_; if ( defined $value ) { $obj->{'_gsf_seqname'} = $value; } return $obj->{'_gsf_seqname'}; } =head2 Proxies These functions chain back to the parent for all non sequence related stuff. =cut =head2 primary_tag Title : primary_tag Usage : $tag = $feat->primary_tag() Function: Returns the primary tag for a feature, eg 'exon' Returns : a string Args : none =cut sub primary_tag { my ($self,@args) = @_; return $self->parent->primary_tag(); } =head2 source_tag Title : source_tag Usage : $tag = $feat->source_tag() Function: Returns the source tag for a feature, eg, 'genscan' Returns : a string Args : none =cut sub source_tag { my ($self) = @_; return $self->parent->source_tag(); } =head2 has_tag Title : has_tag Usage : $tag_exists = $self->has_tag('some_tag') Function: Returns : TRUE if the specified tag exists, and FALSE otherwise Args : =cut sub has_tag { my ($self,$tag) = @_; return $self->parent->has_tag($tag); } =head2 get_tag_values Title : get_tag_values Usage : @values = $self->get_tag_values('some_tag') Function: Returns : An array comprising the values of the specified tag. Args : =cut *each_tag_value = \&get_tag_values; sub get_tag_values { my ($self,$tag) = @_; return $self->parent->get_tag_values($tag); } =head2 get_all_tags Title : get_all_tags Usage : @tags = $feat->get_all_tags() Function: gives all tags for this feature Returns : an array of strings Args : none =cut *all_tags = \&get_all_tags; sub get_all_tags { my ($self) = @_; return $self->parent->all_tags(); } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Primer.pm�����������������������������������������������������������000444��000766��000024�� 30127�13155576320� 20107� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Primer # # This is the original copyright statement. I have relied on Chad's module # extensively for this module. # # Copyright (c) 1997-2001 bioperl, Chad Matsalla. All Rights Reserved. # This module is free software; you can redistribute it and/or # modify it under the same terms as Perl itself. # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code # # But I have modified lots of it, so I guess I should add: # # Copyright (c) 2003 bioperl, Rob Edwards. All Rights Reserved. # This module is free software; you can redistribute it and/or # modify it under the same terms as Perl itself. # # Copyright Rob Edwards # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Primer - Primer Generic SeqFeature =head1 SYNOPSIS use Bio::SeqFeature::Primer; # Primer object with explicitly-defined sequence object or sequence string my $primer = Bio::SeqFeature::Primer->new( -seq => 'ACGTAGCT' ); $primer->display_name('test_id'); print "These are the details of the primer:\n". "Name: ".$primer->display_name."\n". "Tag: ".$primer->primary_tag."\n". # always 'Primer' "Sequence: ".$primer->seq->seq."\n". "Tm: ".$primer->Tm."\n\n"; # melting temperature # Primer object with implicit sequence object # It is a lighter approach for when the primer location on a template is known use Bio::Seq; my $template = Bio::Seq->new( -seq => 'ACGTAGCTCTTTTCATTCTGACTGCAACG' ); $primer = Bio::SeqFeature::Primer->new( -start => 1, -end =>5, -strand => 1 ); $template->add_SeqFeature($primer); print "Primer sequence is: ".$primer->seq->seq."\n"; # Primer sequence is 'ACGTA' =head1 DESCRIPTION This module handles PCR primer sequences. The L<Bio::SeqFeature::Primer> object is a L<Bio::SeqFeature::Subseq> object that can additionally contain a primer sequence and its coordinates on a template sequence. The primary_tag() for this object is 'Primer'. A method is provided to calculate the melting temperature Tm of the primer. L<Bio::SeqFeature::Primer> objects are useful to build L<Bio::Seq::PrimedSeq> amplicon objects such as the ones returned by L<Bio::Tools::Primer3>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Rob Edwards, redwards@utmem.edu The original concept and much of the code was written by Chad Matsalla, bioinformatics1@dieselwurks.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqFeature::Primer; use strict; use Bio::PrimarySeq; use Bio::Tools::SeqStats; use base qw(Bio::SeqFeature::SubSeq); =head2 new() Title : new() Usage : my $primer = Bio::SeqFeature::Primer( -seq => $seq_object ); Function: Instantiate a new Bio::SeqFeature::Primer object Returns : A Bio::SeqFeature::Primer object Args : -seq , a sequence object or a sequence string (optional) -id , the ID to give to the primer sequence, not feature (optional) =cut sub new { my ($class, %args) = @_; # Legacy stuff my $sequence = delete $args{-sequence}; if ($sequence) { Bio::Root::Root->deprecated( -message => 'Creating a Bio::SeqFeature::Primer with -sequence is deprecated. Use -seq instead.', -warn_version => '1.006', -throw_version => '1.008', ); $args{-seq} = $sequence; } # Initialize Primer object my $self = $class->SUPER::new(%args); my ($id) = $self->_rearrange([qw(ID)], %args); $id && $self->seq->id($id); $self->primary_tag('Primer'); return $self; } # Bypass B::SF::Generic's location() when a string is passed (for compatibility) sub location { my ($self, $location) = @_; if ($location) { if ( not ref $location ) { # Use location as a string for backward compatibility Bio::Root::Root->deprecated( -message => 'Passing a string to location() is deprecated. Pass a Bio::Location::Simple object or use start() and end() instead.', -warn_version => '1.006', -throw_version => '1.008', ); $self->{'_location'} = $location; } else { $self->SUPER::location($location); } } return $self->SUPER::location; } =head2 Tm() Title : Tm() Usage : my $tm = $primer->Tm(-salt => 0.05, -oligo => 0.0000001); Function: Calculate the Tm (melting temperature) of the primer Returns : A scalar containing the Tm. Args : -salt : set the Na+ concentration on which to base the calculation (default=0.05 molar). : -oligo : set the oligo concentration on which to base the calculation (default=0.00000025 molar). Notes : Calculation of Tm as per Allawi et. al Biochemistry 1997 36:10581-10594. Also see documentation at http://www.idtdna.com/Scitools/Scitools.aspx as they use this formula and have a couple nice help pages. These Tm values will be about are about 0.5-3 degrees off from those of the idtdna web tool. I don't know why. This was suggested by Barry Moore (thanks!). See the discussion on the bioperl-l with the subject "Bio::SeqFeature::Primer Calculating the PrimerTM" =cut sub Tm { my ($self, %args) = @_; my $salt_conc = 0.05; # salt concentration (molar units) my $oligo_conc = 0.00000025; # oligo concentration (molar units) if ($args{'-salt'}) { # Accept object defined salt concentration $salt_conc = $args{'-salt'}; } if ($args{'-oligo'}) { # Accept object defined oligo concentration $oligo_conc = $args{'-oligo'}; } my $seqobj = $self->seq(); my $length = $seqobj->length(); my $sequence = uc $seqobj->seq(); my @dinucleotides; my $enthalpy; my $entropy; # Break sequence string into an array of all possible dinucleotides while ($sequence =~ /(.)(?=(.))/g) { push @dinucleotides, $1.$2; } # Build a hash with the thermodynamic values my %thermo_values = ('AA' => {'enthalpy' => -7.9, 'entropy' => -22.2}, 'AC' => {'enthalpy' => -8.4, 'entropy' => -22.4}, 'AG' => {'enthalpy' => -7.8, 'entropy' => -21}, 'AT' => {'enthalpy' => -7.2, 'entropy' => -20.4}, 'CA' => {'enthalpy' => -8.5, 'entropy' => -22.7}, 'CC' => {'enthalpy' => -8, 'entropy' => -19.9}, 'CG' => {'enthalpy' => -10.6, 'entropy' => -27.2}, 'CT' => {'enthalpy' => -7.8, 'entropy' => -21}, 'GA' => {'enthalpy' => -8.2, 'entropy' => -22.2}, 'GC' => {'enthalpy' => -9.8, 'entropy' => -24.4}, 'GG' => {'enthalpy' => -8, 'entropy' => -19.9}, 'GT' => {'enthalpy' => -8.4, 'entropy' => -22.4}, 'TA' => {'enthalpy' => -7.2, 'entropy' => -21.3}, 'TC' => {'enthalpy' => -8.2, 'entropy' => -22.2}, 'TG' => {'enthalpy' => -8.5, 'entropy' => -22.7}, 'TT' => {'enthalpy' => -7.9, 'entropy' => -22.2}, 'A' => {'enthalpy' => 2.3, 'entropy' => 4.1}, 'C' => {'enthalpy' => 0.1, 'entropy' => -2.8}, 'G' => {'enthalpy' => 0.1, 'entropy' => -2.8}, 'T' => {'enthalpy' => 2.3, 'entropy' => 4.1} ); # Loop through dinucleotides and calculate cumulative enthalpy and entropy values for (@dinucleotides) { $enthalpy += $thermo_values{$_}{enthalpy}; $entropy += $thermo_values{$_}{entropy}; } # Account for initiation parameters $enthalpy += $thermo_values{substr($sequence, 0, 1)}{enthalpy}; $entropy += $thermo_values{substr($sequence, 0, 1)}{entropy}; $enthalpy += $thermo_values{substr($sequence, -1, 1)}{enthalpy}; $entropy += $thermo_values{substr($sequence, -1, 1)}{entropy}; # Symmetry correction $entropy -= 1.4; my $r = 1.987; # molar gas constant my $tm = $enthalpy * 1000 / ($entropy + ($r * log($oligo_conc))) - 273.15 + (12* (log($salt_conc)/log(10))); return $tm; } =head2 Tm_estimate Title : Tm_estimate Usage : my $tm = $primer->Tm_estimate(-salt => 0.05); Function: Estimate the Tm (melting temperature) of the primer Returns : A scalar containing the Tm. Args : -salt set the Na+ concentration on which to base the calculation. Notes : This is only an estimate of the Tm that is kept in for comparative reasons. You should probably use Tm instead! This Tm calculations are taken from the Primer3 docs: They are based on Bolton and McCarthy, PNAS 84:1390 (1962) as presented in Sambrook, Fritsch and Maniatis, Molecular Cloning, p 11.46 (1989, CSHL Press). Tm = 81.5 + 16.6(log10([Na+])) + .41*(%GC) - 600/length where [Na+] is the molar sodium concentration, %GC is the %G+C of the sequence, and length is the length of the sequence. However.... I can never get this calculation to give me the same result as primer3 does. Don't ask why, I never figured it out. But I did want to include a Tm calculation here because I use these modules for other things besides reading primer3 output. The primer3 calculation is saved as 'PRIMER_LEFT_TM' or 'PRIMER_RIGHT_TM' and this calculation is saved as $primer->Tm so you can get both and average them! =cut sub Tm_estimate { # This should probably be put into seqstats as it is more generic, but what the heck. my ($self, %args) = @_; my $salt = 0.2; if ($args{'-salt'}) { $salt = $args{'-salt'} }; my $seqobj = $self->seq(); my $length = $seqobj->length(); my $seqdata = Bio::Tools::SeqStats->count_monomers($seqobj); my $gc=$$seqdata{'G'} + $$seqdata{'C'}; my $percent_gc = ($gc/$length)*100; my $tm = 81.5+(16.6*(log($salt)/log(10)))+(0.41*$percent_gc) - (600/$length); return $tm; } =head2 primary_tag, source_tag, location, start, end, strand... The documentation of L<Bio::SeqFeature::Generic> describes all the methods that L<Bio::SeqFeature::Primer> object inherit. =cut 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Similarity.pm�������������������������������������������������������000444��000766��000024�� 11015�13155576320� 20772� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Similarity # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp@gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Similarity - A sequence feature based on similarity =head1 SYNOPSIS # obtain a similarity feature somehow print "significance: ", $sim_fea->significance(), "\n"; print "bit score: ", $sim_fea->bits(), "\n"; print "score: ", $sim_fea->score(), "\n"; print "fraction of identical residues: ", $sim_fea->frac_identical(), "\n"; =head1 DESCRIPTION This module is basically a sequence features based on similarity, and therefore has support for measures assessing the similarity. Everything else is inherited from L<Bio::SeqFeature::Generic>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Similarity; use strict; use base qw(Bio::SeqFeature::Generic); sub new { my ( $caller, @args) = @_; my ($self) = $caller->SUPER::new(@args); my ($primary,$evalue, $bits, $frac,$seqlen,$seqdesc) = $self->_rearrange([qw(PRIMARY EXPECT BITS FRAC SEQLENGTH SEQDESC )],@args); defined $evalue && $self->significance($evalue); defined $bits && $self->bits($bits); defined $frac && $self->frac_identical($frac); defined $seqlen && $self->seqlength($seqlen); defined $seqdesc && $self->seqdesc($seqdesc); $primary = 'similarity' unless defined $primary; $self->primary_tag($primary) unless( defined $self->primary_tag() ); $self->strand(0) unless( defined $self->strand() ); return $self; } =head2 significance Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Returns : Args : =cut sub significance { return shift->_tag_value('signif', @_); } =head2 bits Title : bits Usage : $bits = $obj->bits(); $obj->bits($value); Function: Returns : Args : =cut sub bits { return shift->_tag_value('Bits', @_); } =head2 frac_identical Title : frac_identical Usage : $fracid = $obj->frac_identical(); $obj->frac_identical($value); Function: Returns : Args : =cut sub frac_identical { return shift->_tag_value('FracId', @_); } =head2 seqlength Title : seqlength Usage : $len = $obj->seqlength(); $obj->seqlength($len); Function: Returns : Args : =cut sub seqlength { return shift->_tag_value('SeqLength', @_); } =head2 seqdesc Title : seqdesc Usage : $desc = $obj->seqdesc(); $obj->seqdesc($desc); Function: At present this method is a shorthand for $obj->annotation()->description(). Note that this is not stored in the tag system and hence will not be included in the return value of gff_string(). Returns : Args : =cut sub seqdesc { my ( $self, $value ) = @_; if ( defined $value ) { my $v = Bio::Annotation::SimpleValue->new(); $v->value($value); $self->annotation->add_Annotation( 'description', $v ); } my ($v) = $self->annotation()->get_Annotations('description'); return defined $v ? $v->value : undef; } # # Everything else is just inherited from SeqFeature::Generic. # 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/SimilarityPair.pm���������������������������������������������������000444��000766��000024�� 16525�13155576320� 21621� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::SimilarityPair # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp@gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity of two sequences. =head1 SYNOPSIS $sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($blastHit); $sim = $sim_pair->query(); # a Bio::SeqFeature::Similarity object - the query $sim = $sim_pair->hit(); # dto - the hit. # some properties for the similarity pair $expect = $sim_pair->significance(); $score = $sim_pair->score(); $bitscore = $sim_pair->bits(); # this will not write the description for the sequence (only its name) print $sim_pair->query()->gff_string(), "\n"; =head1 DESCRIPTION Lightweight similarity search result as a pair of Similarity features. This class inherits off Bio::SeqFeature::FeaturePair and therefore implements Bio::SeqFeatureI, whereas the two features of the pair are descendants of Bio::SeqFeature::Generic, with better support for representing similarity search results in a cleaner way. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::SimilarityPair; use strict; use Bio::SeqFeature::Similarity; use Bio::Factory::ObjectFactory; use base qw(Bio::SeqFeature::FeaturePair); =head2 new Title : new Usage : my $similarityPair = Bio::SeqFeature::SimilarityPair->new (-hit => $hit, -query => $query, -source => 'blastp'); Function: Initializes a new SimilarityPair object Returns : Bio::SeqFeature::SimilarityPair Args : -query => The query in a Feature pair -hit => (formerly '-subject') the subject/hit in a Feature pair =cut sub new { my($class,@args) = @_; if(! grep { lc($_) eq "-feature_factory"; } @args) { # if no overriding factory is provided, provide our preferred one my $fact = Bio::Factory::ObjectFactory->new( -type => "Bio::SeqFeature::Similarity", -interface => "Bio::SeqFeatureI"); push(@args, '-feature_factory', $fact); } my $self = $class->SUPER::new(@args); my ($primary, $hit, $query, $fea1, $source,$sbjct) = $self->_rearrange([qw(PRIMARY HIT QUERY FEATURE1 SOURCE SUBJECT )],@args); if( $sbjct ) { # undeprecated by Jason before 1.1 release # $self->deprecated("use of -subject deprecated: SimilarityPair now uses 'hit'"); if(! $hit) { $hit = $sbjct } else { $self->warn("-hit and -subject were specified, using -hit and ignoring -subject"); } } # set the query and subject feature if provided $self->query( $query) if $query && ! $fea1; $hit && $self->hit($hit); # the following refer to feature1, which is guaranteed to exist if( defined $primary || ! defined $self->primary_tag) { $primary = 'similarity' unless defined $primary; $self->primary_tag($primary); } $source && $self->source_tag($source); return $self; } # # Everything else is just inherited from SeqFeature::FeaturePair. # =head2 query Title : query Usage : $query_feature = $obj->query(); $obj->query($query_feature); Function: The query object for this similarity pair Returns : Bio::SeqFeature::Similarity Args : [optional] Bio::SeqFeature::Similarity See L<Bio::SeqFeature::Similarity>, L<Bio::SeqFeature::FeaturePair> =cut sub query { return shift->feature1(@_); } =head2 subject Title : subject Usage : $sbjct_feature = $obj->subject(); $obj->subject($sbjct_feature); Function: Get/Set Subject for a SimilarityPair Returns : Bio::SeqFeature::Similarity Args : [optional] Bio::SeqFeature::Similarity Notes : Deprecated. Use the method 'hit' instead =cut sub subject { my $self = shift; # $self->deprecated("Method subject deprecated: use hit() instead"); $self->hit(@_); } =head2 hit Title : hit Usage : $sbjct_feature = $obj->hit(); $obj->hit($sbjct_feature); Function: Get/Set Hit for a SimilarityPair Returns : Bio::SeqFeature::Similarity Args : [optional] Bio::SeqFeature::Similarity =cut sub hit { return shift->feature2(@_); } =head2 source_tag Title : source_tag Usage : $source = $obj->source_tag(); # i.e., program $obj->source_tag($evalue); Function: Gets the source tag (program name typically) for a feature Returns : string Args : [optional] string =cut sub source_tag { my ($self, @args) = @_; if(@args) { $self->hit()->source_tag(@args); } return $self->query()->source_tag(@args); } =head2 significance Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Returns : Args : =cut sub significance { my ($self, @args) = @_; if(@args) { $self->hit()->significance(@args); } return $self->query()->significance(@args); } =head2 score Title : score Usage : $score = $obj->score(); $obj->score($value); Function: Returns : Args : =cut sub score { my ($self, @args) = @_; if(@args) { $self->hit()->score(@args); } # Note: You might think it's only getting set on the hit object. # Actually, it's getting set on both hit and query. return $self->query()->score(@args); } =head2 bits Title : bits Usage : $bits = $obj->bits(); $obj->bits($value); Function: Returns : Args : =cut sub bits { my ($self, @args) = @_; if(@args) { $self->hit()->bits(@args); } return $self->query()->bits(@args); } ################################################################# # aliases for backwards compatibility or convenience # ################################################################# *sbjct = \&subject; 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/SubSeq.pm�����������������������������������������������������������000444��000766��000024�� 14171�13155576320� 20054� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::SubSeq # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Copyright Florent Angly # # You may distribute this module under the same terms as perl itself =head1 NAME Bio::SeqFeature::SubSeq - Feature representing a subsequence =head1 SYNOPSIS # SubSeq with implicit sequence use Bio::Seq; my $template = Bio::Seq->new( -seq => 'AAAAACCCCCGGGGGTTTTT' ); $subseq = Bio::SeqFeature::Amplicon->new( -start => 6, -end => 15, -template => $template, ); print "Subsequence is: ".$amplicon->seq->seq."\n"; # Should be 'CCCCCGGGGG' # SubSeq with explicit sequence use Bio::SeqFeature::Subseq; my $subseq = Bio::SeqFeature::Amplicon->new( -seq => $seq_object, ); =head1 DESCRIPTION Bio::SeqFeature::SubSeq extends L<Bio::SeqFeature::Generic> features to represent a subsequence. When this feature is attached to a template sequence, the sequence of feature is the subsequence of the template at this location. The purpose of this class is to represent a sequence as a feature without having to explicitly store its sequence string. Of course, you might have reasons to explicitly set a sequence. In that case, note that the length of the sequence is allowed to not match the position of the feature. For example, you can set sequence of length 10 in a SubSeq feature that spans positions 30 to 50 of the template if you so desire. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Florent Angly <florent.angly@gmail.com> =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqFeature::SubSeq; use strict; use base qw(Bio::SeqFeature::Generic); =head2 new Title : new() Usage : my $subseq = Bio::SeqFeature::SubSeq( -start => 1, -end => 10, -strand => -1); Function: Instantiate a new Bio::SeqFeature::SubSeq feature object Args : -seq , the sequence object or sequence string of the feature (optional) -template , attach the feature to the provided parent template sequence or feature (optional). Note that you must specify the feature location to do this. -start, -end, -location, -strand and all other L<Bio::SeqFeature::Generic> argument can be used. Returns : A Bio::SeqFeature::SubSeq object =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($seq, $template) = $self->_rearrange([qw(SEQ TEMPLATE)], @args); if (defined $seq) { # Set the subsequence explicitly if (not ref $seq) { # Convert string to sequence object $seq = Bio::PrimarySeq->new( -seq => $seq ); } else { # Sanity check if (not $seq->isa('Bio::PrimarySeqI')) { $self->throw("Expected a sequence object but got a '".ref($seq)."'\n"); } } $self->seq($seq); } if ($template) { if ( not($self->start) || not($self->end) ) { $self->throw('Could not attach feature to template $template because'. ' the feature location was not specified.'); } # Need to attach to parent sequence and then add sequence feature my $template_seq; if ($template->isa('Bio::SeqFeature::Generic')) { $template_seq = $template->entire_seq; } elsif ($template->isa('Bio::SeqI')) { $template_seq = $template; } else { $self->throw("Expected a Bio::SeqFeature::Generic or Bio::SeqI object". " as template, but got '$template'."); } $self->attach_seq($template_seq); $template->add_SeqFeature($self); } return $self; } =head2 seq Title : seq() Usage : my $seq = $subseq->seq(); Function: Get or set the sequence object of this SubSeq feature. If no sequence was provided, but the subseq is attached to a sequence, get the corresponding subsequence. Returns : A sequence object or undef Args : None. =cut sub seq { my ($self, $value) = @_; if (defined $value) { # The sequence is explicit if ( not(ref $value) || not $value->isa('Bio::PrimarySeqI') ) { $self->throw("Expected a sequence object but got a '".ref($value)."'\n"); } $self->{seq} = $value; } my $seq = $self->{seq}; if (not defined $seq) { # The sequence is implied $seq = $self->SUPER::seq; } return $seq; } =head2 length Title : seq() Usage : my $length = $subseq->seq(); Function: Get the length of the SubSeq feature. It is similar to the length() method of L<Bio::Generic::SeqFeature>, which computes length based on the location of the feature. However, if the feature was not given a location, return the length of the subsequence if possible. Returns : integer or undef Args : None. =cut sub length { my ($self) = @_; # Try length from location first if ($self->start && $self->end) { return $self->SUPER::length(); } # Then try length from subsequence my $seq = $self->seq; if (defined $seq) { return length $seq->seq; } # We failed return undef; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/TypedSeqFeatureI.pm�������������������������������������������������000444��000766��000024�� 6312�13155576320� 22013� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::TypedSeqFeatureI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::TypedSeqFeatureI - a strongly typed SeqFeature =head1 SYNOPSIS # get Sequence Features in some manner, eg # from a Sequence object foreach $sf ( $seq->get_SeqFeatures() ) { # all sequence features must have primary_tag() return a string $type_as_string = $sf->primary_tag(); if( $sf->isa("Bio::SeqFeature::TypedSeqFeatureI") ) { $ot = $sf->ontology_term(); print "Ontology identifier:",$ot->identifier(), " name:",$ot->name(), " Description:",$ot->description(),"\n"; } else { print "Sequence Feature does not have an ontology type\n"; } } =head1 DESCRIPTION This interface describes the extension of SeqFeatureI to being a strongly typed SeqFeature. Bio::SeqFeature::TypedSeqFeatureI extends the Bio::SeqFeatureI interface (ie, a TypedSeqFeatureI feature must also implement all the Bio::SeqFeatureI interface as well). It is suggested that the primary_tag() method of SeqFeatureI return the same as the ontology_term()-E<gt>name() of the OntologyTypedI (ie, the "string" name of the ontology type is used as the primary tag), but this should not be assumed by client code as they are scenarios where one would like to maintain the difference. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email - please email the BioPerl mailing list above. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::TypedSeqFeatureI; use strict; use Bio::Root::RootI; use base qw(Bio::SeqFeatureI); =head2 ontology_term Title : ontology_term Usage : my $ot = $seqfeature->ontology_term() Returns : a Bio::Ontology::TermI compliant object Args : none Status : public This method returns the ontology term for a strongly typed sequence feature. =cut sub ontology_term { shift->throw_not_implemented(); } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Gene����������������������������������������������������������������000755��000766��000024�� 0�13155576320� 17011� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Gene/Exon.pm��������������������������������������������������������000444��000766��000024�� 14265�13155576320� 20445� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Gene::Exon # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp@gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Gene::Exon - a feature representing an exon =head1 SYNOPSIS # obtain an exon instance $exon somehow print "exon from ", $exon->start(), " to ", $exon->end(), " on seq ", $exon->seq_id(), ", strand ", $exon->strand(), ", encodes the peptide sequence ", $exon->cds()->translate()->seq(), "\n"; =head1 DESCRIPTION This module implements a feature representing an exon by implementing the Bio::SeqFeature::Gene::ExonI interface. By default an Exon is coding. Supply -is_coding =E<gt> 0 to the constructor or call $exon-E<gt>is_coding(0) otherwise. Apart from that, this class also implements Bio::SeqFeatureI by inheriting off Bio::SeqFeature::Generic. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Gene::Exon; use strict; use base qw(Bio::SeqFeature::Generic Bio::SeqFeature::Gene::ExonI); # # A list of allowed exon types. See primary_tag(). # my @valid_exon_types = ('initial', 'internal', 'terminal'); sub new { my ($caller, @args) = @_; my $self = $caller->SUPER::new(@args); my ($is_coding) = $self->_rearrange([qw(IS_CODING)],@args); $self->primary_tag('exon') unless $self->primary_tag(); $self->is_coding(defined($is_coding) ? $is_coding : 1); $self->strand(0) if(! defined($self->strand())); return $self; } =head2 is_coding Title : is_coding Usage : if($exon->is_coding()) { # do something } if($is_utr) { $exon->is_coding(0); } Function: Get/set whether or not the exon codes for amino acid. Returns : TRUE if the object represents a feature translated into protein, and FALSE otherwise. Args : A boolean value on set. =cut sub is_coding { my ($self,$val) = @_; if(defined($val)) { $self->{'_iscoding'} = $val; } return $self->{'_iscoding'}; } =head2 primary_tag Title : primary_tag Usage : $tag = $feat->primary_tag() $feat->primary_tag('exon') Function: Get/set the primary tag for the exon feature. This method is overridden here in order to allow only for tag values following a certain convention. For consistency reasons, the tag value must either contain the string 'exon' or the string 'utr' (both case-insensitive). In the case of 'exon', a string describing the type of exon may be appended or prefixed. Presently, the following types are allowed: initial, internal, and terminal (all case-insensitive). If the supplied tag value matches 'utr' (case-insensitive), is_coding() will automatically be set to FALSE, and to TRUE otherwise. Returns : A string. Args : A string on set. =cut # sub primary_tag { # my ($self,$value) = @_; # if(defined($value)) { # if((lc($value) =~ /utr/i) || (lc($value) eq "exon") || # ((lc($value) =~ /exon/i) && # (grep { $value =~ /$_/i; } @valid_exon_types))) { # $self->is_coding($value =~ /utr/i ? 0 : 1); # } else { # $self->throw("primary tag $value is invalid for object of class ". # ref($self)); # } # } # return $self->SUPER::primary_tag($value); # } =head2 location Title : location Usage : my $location = $exon->location() Function: Returns a location object suitable for identifying the location of the exon on the sequence or parent feature. This method is overridden here to restrict allowed location types to non-compound locations. Returns : Bio::LocationI object Args : none =cut sub location { my ($self,$value) = @_; if(defined($value) && $value->isa('Bio::Location::SplitLocationI')) { $self->throw("split or compound location is not allowed ". "for an object of type " . ref($self)); } return $self->SUPER::location($value); } =head2 cds Title : cds() Usage : $cds = $exon->cds(); Function: Get the coding sequence of the exon as a sequence object. The sequence of the returned object is prefixed by Ns (lower case) if the frame of the exon is defined and different from zero. The result is that the first base starts a codon (frame 0). This implementation returns undef if the particular exon is not translated to protein, i.e., is_coding() returns FALSE. Undef will also be returned if no sequence is attached to this exon feature. Returns : A Bio::PrimarySeqI implementing object. Args : =cut sub cds { my ($self) = @_; # UTR is not translated return if(! $self->is_coding()); my $seq = $self->seq(); if(defined($seq) && defined($self->frame()) && ($self->frame() != 0)) { my $prefix = "n" x $self->frame(); $seq->seq($prefix . $seq->seq()); } return $seq; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Gene/ExonI.pm�������������������������������������������������������000444��000766��000024�� 5447�13155576320� 20540� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Gene::ExonI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp@gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Gene::ExonI - Interface for a feature representing an exon =head1 SYNOPSIS See documentation of methods. =head1 DESCRIPTION A feature representing an exon. An exon in this definition is transcribed and at least for one particular transcript not spliced out of the pre-mRNA. However, it does not necessarily code for amino acid. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Gene::ExonI; use strict; use base qw(Bio::SeqFeatureI); =head2 is_coding Title : is_coding Usage : if($exon->is_coding()) { # do something } Function: Whether or not the exon codes for amino acid. Returns : TRUE if the object represents a feature translated into protein, and FALSE otherwise. Args : =cut sub is_coding { my ($self) = @_; $self->throw_not_implemented(); } =head2 cds Title : cds() Usage : $cds = $exon->cds(); Function: Get the coding sequence of the exon as a sequence object. The returned sequence object must be in frame 0, i.e., the first base starts a codon. An implementation may return undef, indicating that a coding sequence does not exist, e.g. for a UTR (untranslated region). Returns : A L<Bio::PrimarySeqI> implementing object. Args : =cut sub cds { my ($self) = @_; $self->throw_not_implemented(); } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Gene/GeneStructure.pm�����������������������������������������������000444��000766��000024�� 24552�13155576320� 22333� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Gene::GeneStructure # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp@gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Gene::GeneStructure - A feature representing an arbitrarily complex structure of a gene =head1 SYNOPSIS # See documentation of methods. =head1 DESCRIPTION A feature representing a gene structure. As of now, a gene structure really is only a collection of transcripts. See L<Bio::SeqFeature::Gene::TranscriptI> (interface) and L<Bio::SeqFeature::Gene::Transcript> (implementation) for the features of such objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp-at-gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Gene::GeneStructure; use vars qw($WeakRefs); use strict; BEGIN { eval "use Scalar::Util qw(weaken);"; if ($@) { $Bio::SeqFeature::Gene::GeneStructure::WeakRefs = 0; } else { $Bio::SeqFeature::Gene::GeneStructure::WeakRefs = 1; } } use base qw(Bio::SeqFeature::Generic Bio::SeqFeature::Gene::GeneStructureI); sub new { my ($caller, @args) = @_; my $self = $caller->SUPER::new(@args); $self->_register_for_cleanup(\&gene_cleanup); my ($primary) = $self->_rearrange([qw(PRIMARY )],@args); $primary = 'genestructure' unless $primary; $self->primary_tag($primary); $self->strand(0) if(! defined($self->strand())); return $self; } =head2 transcripts Title : transcripts Usage : @transcripts = $gene->transcripts(); Function: Get the transcripts of this gene structure. Many gene structures will have only one transcript. Returns : An array of Bio::SeqFeature::Gene::TranscriptI implementing objects. Args : =cut sub transcripts { return @{shift->{'_transcripts'} || []}; } =head2 add_transcript Title : add_transcript() Usage : $gene->add_transcript($transcript); Function: Add a transcript to this gene structure. Returns : Args : A Bio::SeqFeature::Gene::TranscriptI implementing object. =cut sub add_transcript { my ($self, $fea) = @_; if(!$fea || ! $fea->isa('Bio::SeqFeature::Gene::TranscriptI') ) { $self->throw("$fea does not implement Bio::SeqFeature::Gene::TranscriptI"); } unless( exists $self->{'_transcripts'} ) { $self->{'_transcripts'} = []; } $self->_expand_region($fea); if( $Bio::SeqFeature::Gene::GeneStructure::WeakRefs ) { $fea->parent(weaken $self); } else { $fea->parent($self); } push(@{$self->{'_transcripts'}}, $fea); } =head2 flush_transcripts Title : flush_transcripts() Usage : $gene->flush_transcripts(); Function: Remove all transcripts from this gene structure. Returns : Args : =cut sub flush_transcripts { my ($self) = @_; if( defined $self->{'_transcripts'} ) { foreach my $t ( grep {defined} @{$self->{'_transcripts'} || []} ) { $t->parent(undef); # remove bkwds pointers $t = undef; } delete($self->{'_transcripts'}); } } =head2 add_transcript_as_features Title : add_transcript_as_features Usage : $gene->add_transcript_as_features(@featurelist); Function: take a list of Bio::SeqFeatureI objects and turn them into a Bio::SeqFeature::Gene::Transcript object. Add that transcript to the gene. Returns : nothing Args : a list of Bio::SeqFeatureI compliant objects =cut sub add_transcript_as_features { my ($self,@features) = @_; my $transcript=Bio::SeqFeature::Gene::Transcript->new; foreach my $fea (@features) { if ($fea->primary_tag =~ /utr/i) { #UTR / utr/ 3' utr / utr5 etc. $transcript->add_utr($fea); } elsif ($fea->primary_tag =~ /promot/i) { #allow for spelling differences $transcript->add_promoter($fea); } elsif ($fea->primary_tag =~ /poly.*A/i) { #polyA, POLY_A, etc. $transcript->poly_A_site($fea); } else { #assume the rest are exons $transcript->add_exon($fea); } } $self->add_transcript($transcript); } =head2 promoters Title : promoters Usage : @prom_sites = $gene->promoters(); Function: Get the promoter features of this gene structure. This method basically merges the promoters returned by transcripts. Note that OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it. Returns : An array of Bio::SeqFeatureI implementing objects. Args : =cut sub promoters { my ($self) = @_; my @transcripts = $self->transcripts(); my @feas = (); foreach my $tr (@transcripts) { push(@feas, $tr->promoters()); } return @feas; } =head2 exons Title : exons() Usage : @exons = $gene->exons(); @inital_exons = $gene->exons('Initial'); Function: Get all exon features or all exons of a specified type of this gene structure. Exon type is treated as a case-insensitive regular expression and optional. For consistency, use only the following types: initial, internal, terminal, utr, utr5prime, and utr3prime. A special and virtual type is 'coding', which refers to all types except utr. This method basically merges the exons returned by transcripts. Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects. Args : An optional string specifying the type of exon. =cut sub exons { my ($self, @args) = @_; my @transcripts = $self->transcripts(); my @feas = (); foreach my $tr (@transcripts) { push(@feas, $tr->exons(@args)); } return @feas; } =head2 introns Title : introns() Usage : @introns = $gene->introns(); Function: Get all introns of this gene structure. Note that this class currently generates these features on-the-fly, that is, it simply treats all regions between exons as introns. It assumes that the exons in the transcripts do not overlap. This method basically merges the introns returned by transcripts. Returns : An array of Bio::SeqFeatureI implementing objects. Args : =cut sub introns { my ($self) = @_; my @transcripts = $self->transcripts(); my @feas = (); foreach my $tr (@transcripts) { push(@feas, $tr->introns()); } return @feas; } =head2 poly_A_sites Title : poly_A_sites() Usage : @polyAsites = $gene->poly_A_sites(); Function: Get the poly-adenylation sites of this gene structure. This method basically merges the poly-adenylation sites returned by transcripts. Returns : An array of Bio::SeqFeatureI implementing objects. Args : =cut sub poly_A_sites { my ($self) = @_; my @transcripts = $self->transcripts(); my @feas = (); foreach my $tr (@transcripts) { push(@feas, $tr->poly_A_site()); } return @feas; } =head2 utrs Title : utrs() Usage : @utr_sites = $gene->utrs('3prime'); @utr_sites = $gene->utrs('5prime'); @utr_sites = $gene->utrs(); Function: Get the features representing untranslated regions (UTR) of this gene structure. You may provide an argument specifying the type of UTR. Currently the following types are recognized: 5prime 3prime for UTR on the 5' and 3' end of the CDS, respectively. This method basically merges the UTRs returned by transcripts. Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects representing the UTR regions or sites. Args : Optionally, either 3prime, or 5prime for the the type of UTR feature. =cut sub utrs { my ($self,@args) = @_; my @transcripts = $self->transcripts(); my @feas = (); foreach my $tr (@transcripts) { push(@feas, $tr->utrs(@args)); } return @feas; } =head2 sub_SeqFeature Title : sub_SeqFeature Usage : @feats = $gene->sub_SeqFeature(); Function: Returns an array of all subfeatures. This method is defined in Bio::SeqFeatureI. We override this here to include the transcripts. Returns : An array Bio::SeqFeatureI implementing objects. Args : none =cut sub sub_SeqFeature { my ($self) = @_; my @feas = (); # get what the parent already has @feas = $self->SUPER::sub_SeqFeature(); push(@feas, $self->transcripts()); return @feas; } =head2 flush_sub_SeqFeature Title : flush_sub_SeqFeature Usage : $gene->flush_sub_SeqFeature(); $gene->flush_sub_SeqFeature(1); Function: Removes all subfeatures. This method is overridden from Bio::SeqFeature::Generic to flush all additional subfeatures, i.e., transcripts, which is almost certainly not what you want. To remove only features added through $gene->add_sub_SeqFeature($feature) pass any argument evaluating to TRUE. Example : Returns : none Args : Optionally, an argument evaluating to TRUE will suppress flushing of all gene structure-specific subfeatures (transcripts). =cut sub flush_sub_SeqFeature { my ($self,$fea_only) = @_; $self->SUPER::flush_sub_SeqFeature(); if(! $fea_only) { $self->flush_transcripts(); } } sub gene_cleanup { my $self = shift; $self->flush_transcripts; } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Gene/GeneStructureI.pm����������������������������������������������000444��000766��000024�� 11265�13155576320� 22441� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Gene::GeneStructureI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp@gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily complex structure of a gene =head1 SYNOPSIS #documentation needed =head1 DESCRIPTION A feature representing a gene structure. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Gene::GeneStructureI; use strict; use Carp; use base qw(Bio::SeqFeatureI); =head2 transcripts Title : transcripts() Usage : @transcripts = $gene->transcripts(); Function: Get the transcript features/sites of this gene structure. See Bio::SeqFeature::Gene::TranscriptI for properties of the returned objects. Returns : An array of Bio::SeqFeature::Gene::TranscriptI implementing objects representing the promoter regions or sites. Args : =cut sub transcripts { my ($self) = @_; $self->throw_not_implemented(); } =head2 promoters Title : promoters() Usage : @prom_sites = $gene->promoters(); Function: Get the promoter features/sites of this gene structure. Note that OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it. Returns : An array of Bio::SeqFeatureI implementing objects representing the promoter regions or sites. Args : =cut sub promoters { my ($self) = @_; $self->throw_not_implemented(); } =head2 exons Title : exons() Usage : @exons = $gene->exons(); @inital = $gene->exons('Initial'); Function: Get all exon features or all exons of specified type of this gene structure. Refer to the documentation of the class that produced this gene structure object for information about the possible types. See Bio::SeqFeature::Gene::ExonI for properties of the returned objects. Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects representing the exon regions. Args : An optional string specifying the type of the exon. =cut sub exons { my ($self, $type) = @_; $self->throw_not_implemented(); } =head2 introns Title : introns() Usage : @introns = $gene->introns(); Function: Get all introns of this gene structure. Returns : An array of Bio::SeqFeatureI implementing objects representing the introns. Args : =cut sub introns { my ($self) = @_; $self->throw_not_implemented(); } =head2 poly_A_sites Title : poly_A_sites() Usage : @polyAsites = $gene->poly_A_sites(); Function: Get the poly-adenylation features/sites of this gene structure. Returns : An array of Bio::SeqFeatureI implementing objects representing the poly-adenylation regions or sites. Args : =cut sub poly_A_sites { my ($self) = @_; $self->throw_not_implemented(); } =head2 utrs Title : utrs() Usage : @utr_sites = $gene->utrs(); Function: Get the UTR features/sites of this gene structure. See Bio::SeqFeature::Gene::ExonI for properties of the returned objects. Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects representing the UTR regions or sites. Args : =cut sub utrs { my ($self) = @_; $self->throw_not_implemented(); } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Gene/Intron.pm������������������������������������������������������000444��000766��000024�� 21636�13155576320� 21005� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Gene::Intron # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by David Block <dblock@gene.pbi.nrc.ca> # # Copyright David Block # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Gene::Intron - An intron feature =head1 SYNOPSIS Give standard usage here =head1 DESCRIPTION Describe the object here =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - David Block Email dblock@gene.pbi.nrc.ca =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Gene::Intron; use strict; use Bio::SeqFeature::Gene::Exon; use base qw(Bio::SeqFeature::Gene::NC_Feature); sub new { my($class,@args) = @_; # introns are non-coding by default if(! grep { lc($_) eq '-is_coding'; } @args) { push(@args, '-is_coding', 0); } my $self = $class->SUPER::new(@args); my ($primary, $prim) = $self->_rearrange([qw(PRIMARY PRIMARY_TAG)],@args); $self->primary_tag('intron') unless $primary || $prim; return $self; } =head2 upstream_Exon Title : upstream_Exon Usage : $intron->upstream_Exon() Function: exon upstream of the intron Returns : Bio::EnsEMBL::Exon Args : =cut sub upstream_Exon { my( $self, $exon ) = @_; if ($exon) { $self->{'_intron_location'} = undef; $self->throw("'$exon' is not a Bio::SeqFeature::Gene::ExonI") unless $exon->isa('Bio::SeqFeature::Gene::ExonI'); $self->{'_upstream_exon'} = $exon; } return $self->{'_upstream_exon'}; } =head2 downstream_Exon Title : downstream_Exon Usage : $intron->downstream_Exon() Function: exon downstream of the intron Returns : Bio::EnsEMBL::Exon Args : =cut sub downstream_Exon { my( $self, $exon ) = @_; if ($exon) { $self->{'_intron_location'} = undef; $self->throw("'$exon' is not a Bio::SeqFeature::Gene::ExonI") unless $exon->isa('Bio::SeqFeature::Gene::ExonI'); $self->{'_downstream_exon'} = $exon; } return $self->{'_downstream_exon'}; } =head2 phase Title : phase Usage : $intron->phase() Function: returns the phase of the intron(where it interrupts the codon) Returns : int(0,1,2) Args : =cut sub phase { my ($self) = @_; return $self->downstream_Exon->phase; } =head2 acceptor_splice_site Title : acceptor_splice_site Usage : $intron->acceptor_splice_site(21,3) Function: returns the sequence corresponding to the consensus acceptor splice site. If start and end are provided, it will number of base pairs left and right of the canonical AG. Here 21 means 21 bp into intron and 3 means 3 bp into the exon. --Intron--21----|AG|-3-----Exon Defaults to 21,3 Returns : Bio::Seq Args : start and end =cut sub acceptor_splice_site { my ($self,$ss_start,$ss_end) = @_; $ss_start = 21 unless defined $ss_start; $ss_end = 3 unless defined $ss_end; if($self->strand < 0){ my $tmp= $ss_start; $ss_start = $ss_end; $ss_end = $tmp; } my $intron_end= $self->location->end; my $down_exon = $self->downstream_Exon; my $acceptor; if($self->strand < 0){ $ss_start= $ss_start > $down_exon->length ? $down_exon->length: $ss_start; $ss_end= $ss_end > $self->length-2 ? $self->length-2 : $ss_end; $acceptor = Bio::SeqFeature::Generic->new(-start=>$self->start - ($ss_start) , -end=>$self->start + ($ss_end+1), -strand=>$self->strand, -primary_tag=>"donor splice site"); } else { $ss_start = $ss_start > $self->length-2 ? $self->length-2 : $ss_start; $ss_end = $ss_end > $down_exon->length ? $down_exon->length : $ss_end; $acceptor = Bio::SeqFeature::Generic->new(-start=>$self->end - ($ss_start + 1), -end=>$self->end + $ss_end, -strand=>$self->strand, -primary_tag=>"donor splice site"); } $acceptor->attach_seq($self->entire_seq); return $acceptor; } =head2 donor_splice_site Title : donor_splice_site Usage : $intron->donor_splice_site(3,6) Function: returns the sequence corresponding to the consensus donor splice site. If start and end are provided, it will number of base pairs left and right of the canonical GT. Here 3 means 3 bp into exon and 6 means 6 bp into the intron. --Exon-3--|GT|-6----Intron- Defaults to 3,6 Returns : Bio::Seq Args : start and end =cut sub donor_splice_site { my ($self,$ss_start,$ss_end) = @_; $ss_start = 3 unless defined $ss_start; $ss_end = 10 unless defined $ss_end; if($self->strand < 0){ my $tmp= $ss_start; $ss_start = $ss_end; $ss_end = $tmp; } my $up_exon = $self->upstream_Exon; my $donor; if($self->strand < 0){ $ss_end = $ss_end > $up_exon->length ? $up_exon->length : $ss_end; $ss_start = $ss_start> $self->length -2 ? $self->length -2 : $ss_start; $donor = Bio::SeqFeature::Generic->new(-start=>$self->end - ($ss_start+1), -end => $self->end + ($ss_end), -strand=>$self->strand, -primary_tag=>"acceptor splice site"); } else { $ss_start = $ss_start > $up_exon->length ? $up_exon->length : $ss_start; $ss_end = $ss_end > $self->length -2 ? $self->length -2 : $ss_end; $donor = Bio::SeqFeature::Generic->new(-start=>$self->start - $ss_start, -end => $self->start +($ss_end+1), -strand=>$self->strand, -primary_tag=>"acceptor splice site"); } $donor->attach_seq($self->entire_seq); return $donor; } sub location { my( $self ) = @_; unless ($self->{'_intron_location'}) { my $loc = Bio::Location::Simple->new; my $up_exon = $self->upstream_Exon; my $down_exon = $self->downstream_Exon; # Get the PrimarySeqs attached to both and check it is the same sequence my $up_seq = $up_exon ->entire_seq; my $down_seq = $down_exon->entire_seq; unless (ref($up_seq) eq ref($down_seq) ) { $self->throw("upstream and downstream exons are attached to different sequences\n'$up_seq' and '$down_seq'"); } # Check that the exons are on the same strand. (Do I need to bother?) my $up_strand = $up_exon ->strand; my $down_strand = $down_exon->strand; unless ($up_strand == $down_strand) { $self->throw("upstream and downstream exons are on different strands " . "('$up_strand' and '$down_strand')"); } $loc->strand($up_strand); # $exon_end is the end of the exon which is 5' of the intron on the genomic sequence. # $exon_start is the start of the exon which is 3' of the intron on the genomic sequence. my( $exon_end, $exon_start ); if ($up_strand == 1) { $exon_end = $up_exon ->end; $exon_start = $down_exon->start; } else { $exon_end = $down_exon->end; $exon_start = $up_exon ->start; } unless ($exon_end < $exon_start) { $self->throw("Intron gap begins after '$exon_end' and ends before '$exon_start'"); } $loc->start($exon_end + 1); $loc->end ($exon_start - 1); # Attach the sequence and location objects to the intron $self->{'_intron_location'} = $loc; } return $self->{'_intron_location'}; } 1; ��������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Gene/NC_Feature.pm��������������������������������������������������000444��000766��000024�� 5125�13155576320� 21462� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Gene::NC_Feature.pm # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by David Block <dblock@gene.pbi.nrc.ca> # # Copyright David Block # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Gene::NC_Feature.pm - superclass for non-coding features =head1 SYNOPSIS Give standard usage here =head1 DESCRIPTION Describe the object here =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - David Block Email dblock@gnf.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Gene::NC_Feature; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::SeqFeature::Generic); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($is_coding) = $self->_rearrange([qw(IS_CODING)],@args); # default is non-coding $self->is_coding(defined($is_coding) ? $is_coding : 0); return $self; } =head2 is_coding Title : is_coding Usage : if ($feature->is_coding()) { #do something } Function: Whether or not the feature codes for amino acid. Returns : FALSE Args : none =cut sub is_coding{ my $self = shift; return $self->{'is_coding'} = shift if @_; return $self->{'is_coding'}; } =head2 cds Title : cds Usage : $cds=$feature->cds(); Function: get the coding sequence of this feature Returns : undef Args : none =cut sub cds { my ($self,@args) = @_; return; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Gene/Poly_A_site.pm�������������������������������������������������000444��000766��000024�� 3614�13155576320� 21717� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Gene::Poly_A_site # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by David Block <dblock@gene.pbi.nrc.ca> # # Copyright David Block # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Gene::Poly_A_site - poly A feature =head1 SYNOPSIS Give standard usage here =head1 DESCRIPTION Inherits from L<Bio::SeqFeature::Gene::NC_Feature>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - David Block Email dblock@gene.pbi.nrc.ca =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Gene::Poly_A_site; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::SeqFeature::Gene::NC_Feature); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); } 1; ��������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Gene/Promoter.pm����������������������������������������������������000444��000766��000024�� 3565�13155576320� 21324� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Gene::Promoter # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by David Block <dblock@gene.pbi.nrc.ca> # # Copyright David Block # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Gene::Promoter - Describes a promoter =head1 SYNOPSIS Give standard usage here =head1 DESCRIPTION Describe the object here =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - David Block Email dblock@gene.pbi.nrc.ca =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Gene::Promoter; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::SeqFeature::Gene::NC_Feature); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); } 1; �������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Gene/Transcript.pm��������������������������������������������������000444��000766��000024�� 53724�13155576320� 21670� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Gene::Transcript # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp@gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Gene::Transcript - A feature representing a transcript =head1 SYNOPSIS # See documentation of methods. =head1 DESCRIPTION A feature representing a transcript. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Gene::Transcript; use strict; use Bio::PrimarySeq; use base qw(Bio::SeqFeature::Generic Bio::SeqFeature::Gene::TranscriptI); sub new { my ($caller, @args) = @_; my $self = $caller->SUPER::new(@args); $self->_register_for_cleanup(\&transcript_destroy); my ($primary) = $self->_rearrange([qw(PRIMARY)],@args); $primary = 'transcript' unless $primary; $self->primary_tag($primary); $self->strand(0) if(! defined($self->strand())); return $self; } =head2 promoters Title : promoters() Usage : @proms = $transcript->promoters(); Function: Get the promoter features/sites of this transcript. Note that OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it. Returns : An array of Bio::SeqFeatureI implementing objects representing the promoter regions or sites. Args : =cut sub promoters { my ($self) = @_; return $self->get_feature_type('Bio::SeqFeature::Gene::Promoter'); } =head2 add_promoter Title : add_promoter() Usage : $transcript->add_promoter($feature); Function: Add a promoter feature/site to this transcript. Note that OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it. Returns : Args : A Bio::SeqFeatureI implementing object. =cut sub add_promoter { my ($self, $fea) = @_; $self->_add($fea,'Bio::SeqFeature::Gene::Promoter'); } =head2 flush_promoters Title : flush_promoters() Usage : $transcript->flush_promoters(); Function: Remove all promoter features/sites from this transcript. Note that OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it. Returns : the removed features as a list Args : none =cut sub flush_promoters { my ($self) = @_; return $self->_flush('Bio::SeqFeature::Gene::Promoter'); } =head2 exons Title : exons() Usage : @exons = $gene->exons(); ($inital_exon) = $gene->exons('Initial'); Function: Get all exon features or all exons of specified type of this transcript. Exon type is treated as a case-insensitive regular expression and is optional. For consistency, use only the following types: initial, internal, terminal. Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects. Args : An optional string specifying the primary_tag of the feature. =cut sub exons { my ($self, $type) = @_; return $self->get_unordered_feature_type('Bio::SeqFeature::Gene::ExonI', $type); } =head2 exons_ordered Title : exons_ordered Usage : @exons = $gene->exons_ordered(); @exons = $gene->exons_ordered("Internal"); Function: Get an ordered list of all exon features or all exons of specified type of this transcript. Exon type is treated as a case-insensitive regular expression and is optional. For consistency, use only the following types: Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects. Args : An optional string specifying the primary_tag of the feature. =cut sub exons_ordered { my ($self,$type) = @_; return $self->get_feature_type('Bio::SeqFeature::Gene::ExonI', $type); } =head2 add_exon Title : add_exon() Usage : $transcript->add_exon($exon,'initial'); Function: Add a exon feature to this transcript. The second argument denotes the type of exon. Mixing exons with and without a type is likely to cause trouble in exons(). Either leave out the type for all exons or for none. Presently, the following types are known: initial, internal, terminal, utr, utr5prime, and utr3prime (all case-insensitive). UTR should better be added through utrs()/add_utr(). If you wish to use other or additional types, you will almost certainly have to call exon_type_sortorder() in order to replace the default sort order, or mrna(), cds(), protein(), and exons() may yield unexpected results. Returns : Args : A Bio::SeqFeature::Gene::ExonI implementing object. A string indicating the type of the exon (optional). =cut sub add_exon { my ($self, $fea, $type) = @_; if(! $fea->isa('Bio::SeqFeature::Gene::ExonI') ) { $self->throw("$fea does not implement Bio::SeqFeature::Gene::ExonI"); } $self->_add($fea,'Bio::SeqFeature::Gene::Exon', $type); } =head2 flush_exons Title : flush_exons() Usage : $transcript->flush_exons(); $transcript->flush_exons('terminal'); Function: Remove all or a certain type of exon features from this transcript. See add_exon() for documentation about types. Calling without a type will not flush UTRs. Call flush_utrs() for this purpose. Returns : the deleted features as a list Args : A string indicating the type of the exon (optional). =cut sub flush_exons { my ($self, $type) = @_; return $self->_flush('Bio::SeqFeature::Gene::Exon',$type); } =head2 introns Title : introns() Usage : @introns = $gene->introns(); Function: Get all intron features this gene structure. Note that this implementation generates these features on-the-fly, that is, it simply treats all regions between exons as introns, assuming that exons do not overlap. A consequence is that a consistent correspondence between the elements in the returned array and the array that exons() returns will exist only if the exons are properly sorted within their types (forward for plus- strand and reverse for minus-strand transcripts). To ensure correctness the elements in the array returned will always be sorted. Returns : An array of Bio::SeqFeature::Gene::Intron objects representing the intron regions. Args : =cut sub introns { my ($self) = @_; my @introns = (); my @exons = $self->exons(); my ($strand, $rev_order); # if there's 1 or less exons we're done return () unless($#exons > 0); # record strand and order (a minus-strand transcript is likely to have # the exons stacked in reverse order) foreach my $exon (@exons) { $strand = $exon->strand(); last if $strand; # we're done if we've got 1 or -1 } $rev_order = ($exons[0]->end() < $exons[1]->start() ? 0 : 1); # Make sure exons are sorted. Because we assume they don't overlap, we # simply sort by start position. if((! defined($strand)) || ($strand != -1) || (! $rev_order)) { # always sort forward for plus-strand transcripts, and for negative- # strand transcripts that appear to be unsorted or forward sorted @exons = map { $_->[0] } sort { $a->[1] <=> $b->[1] } map { [ $_, $_->start * ($_->strand || 1)] } @exons; } else { # sort in reverse order for transcripts on the negative strand and # found to be in reverse order @exons = map { $_->[0] } sort { $b->[1] <=> $a->[1] } map { [ $_, $_->start()] } @exons; } # loop over all intervening gaps while ((my $exonA = shift (@exons)) &&(my $exonB = shift(@exons))){ my $intron = Bio::SeqFeature::Gene::Intron->new(-primary=>'intron'); $intron->upstream_Exon($exonA); $intron->downstream_Exon($exonB); $intron->attach_seq($self->entire_seq) if $self->entire_seq; unshift(@exons,$exonB); push @introns,$intron; } return @introns; } =head2 poly_A_site Title : poly_A_site() Usage : $polyAsite = $transcript->poly_A_site(); Function: Get/set the poly-adenylation feature/site of this transcript. Returns : A Bio::SeqFeatureI implementing object representing the poly-adenylation region. Args : A Bio::SeqFeatureI implementing object on set, or FALSE to flush a previously set object. =cut sub poly_A_site { my ($self, $fea) = @_; if ($fea) { $self->_add($fea,'Bio::SeqFeature::Gene::Poly_A_site'); } return ($self->get_feature_type('Bio::SeqFeature::Gene::Poly_A_site'))[0]; } =head2 utrs Title : utrs() Usage : @utr_sites = $transcript->utrs('utr3prime'); @utr_sites = $transcript->utrs('utr5prime'); @utr_sites = $transcript->utrs(); Function: Get the features representing untranslated regions (UTR) of this transcript. You may provide an argument specifying the type of UTR. Currently the following types are recognized: utr5prime utr3prime for UTR on the 5' and 3' end of the CDS, respectively. Returns : An array of Bio::SeqFeature::Gene::UTR objects representing the UTR regions or sites. Args : Optionally, either utr3prime, or utr5prime for the the type of UTR feature. =cut sub utrs { my ($self, $type) = @_; return $self->get_feature_type('Bio::SeqFeature::Gene::UTR',$type); } =head2 add_utr Title : add_utr() Usage : $transcript->add_utr($utrobj, 'utr3prime'); $transcript->add_utr($utrobj); Function: Add a UTR feature/site to this transcript. The second parameter is optional and denotes the type of the UTR feature. Presently recognized types include 'utr5prime' and 'utr3prime' for UTR on the 5' and 3' end of a gene, respectively. Calling this method is the same as calling add_exon($utrobj, 'utr'.$type). In this sense a UTR object is a special exon object, which is transcribed, not spliced out, but not translated. Note that the object supplied should return FALSE for is_coding(). Otherwise cds() and friends will become confused. Returns : Args : A Bio::SeqFeature::Gene::UTR implementing object. =cut sub add_utr { my ($self, $fea, $type) = @_; $self->_add($fea,'Bio::SeqFeature::Gene::UTR',$type); } =head2 flush_utrs Title : flush_utrs() Usage : $transcript->flush_utrs(); $transcript->flush_utrs('utr3prime'); Function: Remove all or a specific type of UTR features/sites from this transcript. Cf. add_utr() for documentation about recognized types. Returns : a list of the removed features Args : Optionally a string denoting the type of UTR feature. =cut sub flush_utrs { my ($self, $type) = @_; return $self->_flush('Bio::SeqFeature::Gene::UTR',$type); } =head2 sub_SeqFeature Title : sub_SeqFeature Usage : @feats = $transcript->sub_SeqFeature(); Function: Returns an array of all subfeatures. This method is defined in Bio::SeqFeatureI. We override this here to include the exon etc features. Returns : An array Bio::SeqFeatureI implementing objects. Args : none =cut sub sub_SeqFeature { my ($self) = @_; my @feas; # get what the parent already has @feas = $self->SUPER::sub_SeqFeature(); # add the features we have in addition push(@feas, $self->exons()); # this includes UTR features push(@feas, $self->promoters()); push(@feas, $self->poly_A_site()) if($self->poly_A_site()); return @feas; } =head2 flush_sub_SeqFeature Title : flush_sub_SeqFeature Usage : $transcript->flush_sub_SeqFeature(); $transcript->flush_sub_SeqFeature(1); Function: Removes all subfeatures. This method is overridden from Bio::SeqFeature::Generic to flush all additional subfeatures like exons, promoters, etc., which is almost certainly not what you want. To remove only features added through $transcript->add_sub_SeqFeature($feature) pass any argument evaluating to TRUE. Example : Returns : none Args : Optionally, an argument evaluating to TRUE will suppress flushing of all transcript-specific subfeatures (exons etc.). =cut sub flush_sub_SeqFeature { my ($self,$fea_only) = @_; $self->SUPER::flush_sub_SeqFeature(); if(! $fea_only) { $self->flush_promoters(); $self->flush_exons(); $self->flush_utrs(); $self->poly_A_site(0); } } =head2 cds Title : cds Usage : $seq = $transcript->cds(); Function: Returns the CDS (coding sequence) as defined by the exons of this transcript and the attached sequence. If no sequence is attached this method will return false. Note that the implementation provided here returns a concatenation of all coding exons, thereby assuming that exons do not overlap. Note also that you cannot set the CDS via this method. Set a single CDS feature as a single exon, or derive your own class if you want to store a predicted CDS. Example : Returns : A Bio::PrimarySeqI implementing object. Args : =cut sub cds { my ($self) = @_; my @exons = $self->exons_ordered(); #this is always sorted properly according to strand my $strand; return unless(@exons); # record strand (a minus-strand transcript must have the exons sorted in # reverse order) foreach my $exon (@exons) { if(defined($exon->strand()) && (! $strand)) { $strand = $exon->strand(); } if($exon->strand() && (($exon->strand() * $strand) < 0)) { $self->throw("Transcript mixes coding exons on plus and minus ". "strand. This makes no sense."); } } my $cds = $self->_make_cds(@exons); return unless $cds; return Bio::PrimarySeq->new('-id' => $self->seq_id(), '-seq' => $cds, '-alphabet' => "dna"); } =head2 protein Title : protein() Usage : $protein = $transcript->protein(); Function: Get the protein encoded by the transcript as a sequence object. The implementation provided here simply calls translate() on the object returned by cds(). Returns : A Bio::PrimarySeqI implementing object. Args : =cut sub protein { my ($self) = @_; my $seq; $seq = $self->cds(); return $seq->translate() if $seq; return; } =head2 mrna Title : mrna() Usage : $mrna = $transcript->mrna(); Function: Get the mRNA of the transcript as a sequence object. The difference to cds() is that the sequence object returned by this methods will also include UTR and the poly-adenylation site, but not promoter sequence (TBD). HL: do we really need this method? Returns : A Bio::PrimarySeqI implementing object. Args : =cut sub mrna { my ($self) = @_; my ($seq, $mrna, $elem); # get the coding part $seq = $self->cds(); if(! $seq) { $seq = Bio::PrimarySeq->new('-id' => $self->seq_id(), '-alphabet' => "rna", '-seq' => ""); } # get and add UTR sequences $mrna = ""; foreach $elem ($self->utrs('utr5prime')) { $mrna .= $elem->seq()->seq(); } $seq->seq($mrna . $seq->seq()); $mrna = ""; foreach $elem ($self->utrs('utr3prime')) { $mrna .= $elem->seq()->seq(); } $seq->seq($seq->seq() . $mrna); if($self->poly_A_site()) { $seq->seq($seq->seq() . $self->poly_A_site()->seq()->seq()); } return if($seq->length() == 0); return $seq; } sub _get_typed_keys { my ($self, $keyprefix, $type) = @_; my @keys = (); my @feas = (); # make case-insensitive $type = ($type ? lc($type) : ""); # pull out all feature types that exist and match @keys = grep { /^_$keyprefix$type/i; } (keys(%{$self})); return @keys; } sub _make_cds { my ($self,@exons) = @_; my $cds = ""; foreach my $exon (@exons) { next if((! defined($exon->seq())) || (! $exon->is_coding())); my $phase = length($cds) % 3; # let's check the simple case if((! defined($exon->frame())) || ($phase == $exon->frame())) { # this one fits exactly, or frame of the exon is undefined (should # we warn about that?); we bypass the $exon->cds() here (hmm, # not very clean style, but I don't see where this screws up) $cds .= $exon->seq()->seq(); } else { # this one is probably from exon shuffling and needs some work my $seq = $exon->cds(); # now $seq is guaranteed to be in frame 0 next if(! $seq); $seq = $seq->seq(); # adjustment needed? if($phase > 0) { # how many Ns can we chop off the piece to be added? my $n_crop = 0; if($seq =~ /^(n+)/i) { $n_crop = length($1); } if($n_crop >= $phase) { # chop off to match the phase $seq = substr($seq, $phase); } else { # fill in Ns $seq = ("n" x (3-$phase)) . $seq; } } $cds .= $seq; } } return $cds; } =head2 features Title : features Usage : my @features=$transcript->features; Function: returns all the features associated with this transcript Returns : a list of SeqFeatureI implementing objects Args : none =cut sub features { my $self = shift; return grep { defined } @{$self->{'_features'} || []}; } =head2 features_ordered Title : features_ordered Usage : my @features=$transcript->features_ordered; Function: returns all the features associated with this transcript, in order by feature start, according to strand Returns : a list of SeqFeatureI implementing objects Args : none =cut sub features_ordered{ my ($self) = @_; return $self->_stranded_sort(@{$self->{'_features'} || []}); } sub get_unordered_feature_type{ my ($self, $type, $pri)=@_; my @list; foreach ( $self->features) { if ($_->isa($type)) { if ($pri && $_->primary_tag !~ /$pri/i) { next; } push @list,$_; } } return @list; } sub get_feature_type { my ($self)=shift; return $self->_stranded_sort($self->get_unordered_feature_type(@_)); } #This was fixed by Gene Cutler - the indexing on the list being reversed #fixed a bad bug. Thanks Gene! sub _flush { my ($self, $type, $pri)=@_; my @list=$self->features; my @cut; for (reverse (0..$#list)) { if (defined $list[$_] && $list[$_]->isa($type)) { if ($pri && $list[$_]->primary_tag !~ /$pri/i) { next; } push @cut, splice @list, $_, 1; #remove the element of $type from @list #and return each of them in @cut } } $self->{'_features'}=\@list; return reverse @cut; } sub _add { my ($self, $fea, $type, $pri)=@_; require Bio::SeqFeature::Gene::Promoter; require Bio::SeqFeature::Gene::UTR; require Bio::SeqFeature::Gene::Exon; require Bio::SeqFeature::Gene::Intron; require Bio::SeqFeature::Gene::Poly_A_site; if(! $fea->isa('Bio::SeqFeatureI') ) { $self->throw("$fea does not implement Bio::SeqFeatureI"); } if(! $fea->isa($type) || $pri) { $fea=$self->_new_of_type($fea,$type,$pri); } if (! $self->strand) { $self->strand($fea->strand); } else { if ($self->strand * $fea->strand == -1) { $self->throw("$fea is on opposite strand from $self"); } } $self->_expand_region($fea); if(defined($self->entire_seq()) && (! defined($fea->entire_seq())) && $fea->can('attach_seq')) { $fea->attach_seq($self->entire_seq()); } if (defined $self->parent) { $self->parent->_expand_region($fea); } push(@{$self->{'_features'}}, $fea); 1; } sub _stranded_sort { my ($self,@list)=@_; my $strand; foreach my $fea (@list) { if($fea->strand()) { # defined and != 0 $strand = $fea->strand() if(! $strand); if(($fea->strand() * $strand) < 0) { $strand = undef; last; } } } if (defined $strand && $strand == - 1) { #reverse strand return map { $_->[0] } sort {$b->[1] <=> $a->[1]} map { [$_, $_->start] } @list; } else { #undef or forward strand return map { $_->[0] } sort {$a->[1] <=> $b->[1]} map { [$_, $_->start] } @list; } } sub _new_of_type { my ($self, $fea, $type, $pri)= @_; my $primary; if ($pri) { $primary = $pri; #can set new primary tag if desired } else { ($primary) = $type =~ /.*::(.+)/; #or else primary is just end of type string } bless $fea,$type; $fea->primary_tag($primary); return $fea; } sub transcript_destroy { my $self = shift; # We're going to be really explicit to insure memory leaks # don't occur foreach my $f ( $self->features ) { $f = undef; } $self->parent(undef); } 1; ��������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Gene/TranscriptI.pm�������������������������������������������������000444��000766��000024�� 13230�13155576320� 21765� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Gene::TranscriptI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp@gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Gene::TranscriptI - Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. =head1 SYNOPSIS #documentation needed =head1 DESCRIPTION A feature representing a transcript. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Gene::TranscriptI; use strict; use Carp; use base qw(Bio::SeqFeatureI); =head2 promoters Title : promoters() Usage : @proms = $transcript->promoters(); Function: Get the promoter features of this transcript. Note that OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it. Returns : An array of Bio::SeqFeatureI implementing objects representing the promoter regions or sites. Args : =cut sub promoters { my ($self) = @_; $self->throw_not_implemented(); } =head2 exons Title : exons() Usage : @exons = $transcript->exons(); @inital = $transcript->exons('Initial'); Function: Get the individual exons this transcript comprises of, or all exons of a specified type. Refer to the documentation of the class that produced this transcript object for information about the possible types. See Bio::SeqFeature::Gene::ExonI for properties of the returned objects. Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects Args : An optional string specifying the type of the exon. =cut sub exons { my ($self, $type) = @_; $self->throw_not_implemented(); } =head2 introns Title : introns() Usage : @introns = $transcript->introns(); Function: Get all introns this transcript comprises of. Returns : An array of Bio::SeqFeatureI implementing objects representing the introns. Args : =cut sub introns { my ($self) = @_; $self->throw_not_implemented(); } =head2 poly_A_site Title : poly_A_site() Usage : $polyAsite = $transcript->poly_A_site(); Function: Get the poly-adenylation site of this transcript. Returns : A Bio::SeqFeatureI implementing object. Args : =cut sub poly_A_site { my ($self) = @_; $self->throw_not_implemented(); } =head2 utrs Title : utrs() Usage : @utr_sites = $transcript->utrs(); Function: Get the UTR regions this transcript comprises of. See Bio::SeqFeature::Gene::ExonI for properties of the returned objects. Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects Args : =cut sub utrs { my ($self) = @_; $self->throw_not_implemented(); } =head2 mrna Title : mrna() Usage : $mrna = $transcript->mrna(); Function: Get the mRNA of the transcript as a sequence object. Returns : A Bio::PrimarySeqI implementing object. Args : =cut sub mrna { my ($self) = @_; $self->throw_not_implemented(); } =head2 cds Title : cds() Usage : $cds = $transcript->cds(); Function: Get the CDS (coding sequence) of the transcript as a sequence object. Returns : A Bio::PrimarySeqI implementing object. Args : =cut sub cds { my ($self) = @_; $self->throw_not_implemented(); } =head2 protein Title : protein() Usage : $protein = $transcript->protein(); Function: Get the protein encoded by the transcript as a sequence object. Returns : A Bio::PrimarySeqI implementing object. Args : =cut sub protein { my ($self) = @_; $self->throw_not_implemented(); } =head2 parent Title : parent Usage : $obj->parent($newval) Function: get the parent gene of the transcript Returns : value of parent - a Bio::SeqFeature::Gene::GeneStructureI-compliant object Args : a Bio::SeqFeature::Gene::GeneStructureI-compliant object (optional) =cut sub parent{ my $self = shift; if( @_ ) { my $value = shift; # I really mean ! defined $value - # we will allow re-setting the parent to undef if (! defined $value || $value->isa("Bio::SeqFeature::Gene::GeneStructureI")) { $self->{'_parent'} = $value; } else { $self->throw("$value must be a Bio::SeqFeature::Gene::GeneStructureI") } } return $self->{'_parent'}; } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Gene/UTR.pm���������������������������������������������������������000444��000766��000024�� 6251�13155576320� 20162� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::Gene::UTR # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by David Block <dblock@gene.pbi.nrc.ca> # # Copyright David Block # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Gene::UTR - A feature representing an untranslated region that is part of a transcriptional unit =head1 SYNOPSIS See documentation of methods =head1 DESCRIPTION A UTR is a Bio::SeqFeature::Gene::ExonI compliant object that is non-coding, and can be either 5' or 3' in a transcript. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - David Block Email dblock@gene.pbi.nrc.ca =head1 CONTRIBUTORS This is based on the Gene Structure scaffolding erected by Hilmar Lapp (hlapp@gmx.net). =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Gene::UTR; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::SeqFeature::Gene::Exon); =head2 new Title : new Usage : Function: We override the constructor here to set is_coding to false unless explicitly overridden. Example : Returns : Args : =cut sub new{ my ($caller, @args) = @_; if(! grep { lc($_) eq '-is_coding'; } @args) { push(@args, '-is_coding', 0); } my $self = $caller->SUPER::new(@args); my ($primary, $prim) = $self->_rearrange([qw(PRIMARY PRIMARY_TAG)],@args); $self->primary_tag('utr') unless $primary || $prim; return $self; } =head2 primary_tag Title : primary_tag Usage : $tag = $feat->primary_tag() Function: Returns the primary tag for a feature, eg 'utr5prime'. This method insures that 5prime/3prime information is uniformly stored Returns : a string Args : none =cut sub primary_tag{ my $self = shift; if(@_ && defined($_[0])) { my $val = shift; if ($val =~ /(3|5)/ ) { $val = "utr$1prime"; } else { $self->warn("Primary tag should indicate if this is 3 or 5'. ". "Preferred text is 'utr3prime' or 'utr5prime'."); } unshift(@_,$val); } return $self->SUPER::primary_tag(@_); } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/SiRNA���������������������������������������������������������������000755��000766��000024�� 0�13155576320� 17047� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/SiRNA/Oligo.pm������������������������������������������������������000444��000766��000024�� 12214�13155576320� 20633� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::SiRNA::Pair # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Donald Jackson, donald.jackson@bms.com # # Copyright Donald Jackson # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::SiRNA::Oligo - Perl object for small inhibitory RNAs. =head1 SYNOPSIS use Bio::SeqFeature::SiRNA::Oligo; my $oligo = Bio::SeqFeature::SiRNA::Oligo-> new( -seq => 'AUGCCGAUUGCAAGUCAGATT', -start => 10, -end => 31, -strand => -1, -primary => 'SiRNA::Oligo', -source_tag => 'Bio::Tools::SiRNA', -tag => { note => 'A note' }, ); # normally two complementary Oligos are combined in an SiRNA::Pair # object $pair->antisense($oligo); =head1 DESCRIPTION Object methods for single SiRNA oligos - inherits L<Bio::SeqFeature::Generic>. Does B<not> include methods for designing SiRNAs - see L<Bio::Tools::SiRNA> for that. =head1 SEE ALSO L<Bio::Tools::SiRNA>, L<Bio::SeqFeature::SiRNA::Pair>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Donald Jackson (donald.jackson@bms.com) =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqFeature::SiRNA::Oligo; use strict; use warnings; use base qw(Bio::SeqFeature::Generic); our @ARGNAMES = qw(SEQ START END STRAND PRIMARY SOURCE_TAG SCORE TAG SEQ_ID ANNOTATION LOCATION); =head2 new Title : new Usage : my $sirna_oligo = Bio::SeqFeature::SiRNA::Oligo->new(); Function : Create a new SiRNA::Oligo object Returns : Bio::Tools::SiRNA object Args : -seq sequence of the RNAi oligo. Should be in RNA alphabet except for the final TT overhang. -start start position -end end position -strand strand -primary primary tag - defaults to 'SiRNA::Oligo' -source source tag -score score value -tag a reference to a tag/value hash -seq_id the display name of the sequence -annotation the AnnotationCollectionI object -location the LocationI object Currently passing arguments in gff_string or gff1_string is not supported. SiRNA::Oligo objects are typically created by a design algorithm such as Bio::Tools::SiRNA =cut sub new { my ($proto, @args) = @_; my $pkg = ref($proto) || $proto; my (%args); my $self = $pkg->SUPER::new(); @args{@ARGNAMES} = $self->_rearrange(\@ARGNAMES, @args); # default primary tag $args{'PRIMARY'} ||= 'SiRNA::Oligo'; $args{'PRIMARY'} && $self->primary_tag($args{'PRIMARY'}); $args{'SOURCE_TAG'} && $self->source_tag($args{'SOURCE_TAG'}); $args{'SEQNAME'} && $self->seqname($args{'SEQNAME'}); $args{'SEQ'} && $self->seq($args{'SEQ'}); $args{'ANNOTATION'} && $self->annotation($args{'ANNOTATION'}); $args{'LOCATION'} && $self->location($args{'LOCATION'}); defined($args{'START'}) && $self->start($args{'START'}); defined($args{'END'}) && $self->end($args{'END'}); defined($args{'STRAND'}) && $self->strand($args{'STRAND'}); defined($args{'SCORE'}) && $self->score($args{'SCORE'}); if ($args{'TAG'}) { foreach my $t ( keys %{ $args{'TAG'} } ) { $self->add_tag_value($t, $args{'TAG'}->{$t}); } } return $self; } =head2 seq Title : Seq Usage : my $oligo_sequence = $sirna_oligo->seq(); Purpose : Get/set the sequence of the RNAi oligo Returns : Sequence for the RNAi oligo Args : Sequence of the RNAi oligo (optional) Note : Overloads Bio::SeqFeature::Generic seq method - the oligo and parent sequences are different. Note that all but the last 2 nucleotides are RNA (per Tuschl and colleagues). SiRNA::Pair objects are typically created by a design algorithm such as Bio::Tools::SiRNA. =cut sub seq { my ($self, $seq) = @_; if ($seq) { # check alphabet if ($seq =~ /[^ACGTUacgtu]/ ) { warn "Sequence contains illegal characters"; return; } else { $self->{'seq'} = $seq; } } return $self->{'seq'}; } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/SiRNA/Pair.pm�������������������������������������������������������000444��000766��000024�� 17631�13155576320� 20465� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqFeature::SiRNA::Pair # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Donald Jackson, donald.jackson@bms.com # # Copyright Donald Jackson # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::SiRNA::Pair - Perl object for small inhibitory RNA (SiRNA) oligo pairs =head1 SYNOPSIS use Bio::SeqFeature::SiRNA::Pair; my $pair = Bio::SeqFeature::SiRNA::Pair-> new( -sense => $bio_seqfeature_sirna_oligo, # strand=1 -antisense => $bio_seqfeature_sirna_oligo, # strand= -1 -primary => 'SiRNA::Pair', -source_tag => 'Bio::Tools::SiRNA', -start => 8, -end => 31, -rank => 1, -fxgc => 0.5, -tag => { note => 'a note' } ); $target_sequence->add_SeqFeature($pair); =head1 DESCRIPTION Object methods for (complementary) pairs of L<Bio::SeqFeature::SiRNA::Oligo> objects - inherits L<Bio::SeqFeature::Generic>. See that package for information on inherited methods. Does B<not> include methods for designing SiRNAs -- see L<Bio::Tools::SiRNA> =head1 SEE ALSO L<Bio::SeqFeature::Oligo>, L<Bio::Tools::SiRNA>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Donald Jackson (donald.jackson@bms.com) =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqFeature::SiRNA::Pair; use strict; use warnings; use base qw(Bio::SeqFeature::Generic); # arguments to new(). Taken from Bio::SeqFeature Generic. # Omit frame (not relevant), GFF_STRING and GFF1_STRING # because I'm not sure how to handle them. Add RANK, FXGC, SENSE, ANTISENSE our @ARGNAMES = qw(RANK FXGC SENSE ANTISENSE START END STRAND PRIMARY SOURCE_TAG SCORE TAG SEQNAME ANNOTATION LOCATION); =head1 METHODS =head2 new Title : new Usage : my $sirna_pair = Bio::SeqFeature::SiRNA::Pair->new(); Purpose : Create a new SiRNA::Pair object Returns : Bio::Tools::SiRNA object Args : -start 10 -end 31 -rank 1 # 'Rank' in Tuschl group's rules -fxgc 0.5 # GC fraction for target sequence -primary 'SiRNA::Pair', # default value -source_tag 'Bio::Tools::SiRNA' -tag { note => 'A note' } -sense a Bio::SeqFeature::SiRNA::Oligo object with strand = 1 -antisense a Bio::SeqFeature::SiRNA::Oligo object with strand = -1 ); Note : SiRNA::Pair objects are typically created by a design algorithm such as Bio::Tools::SiRNA =cut sub new { my ($proto, @args) = @_; my $pkg = ref($proto) || $proto; my $self = $pkg->SUPER::new(); my %args; @args{@ARGNAMES} = $self->_rearrange(\@ARGNAMES, @args); # default primary tag $args{'PRIMARY'} ||= 'SiRNA::Pair'; $args{'PRIMARY'} && $self->primary_tag($args{'PRIMARY'}); $args{'SOURCE_TAG'} && $self->source_tag($args{'SOURCE_TAG'}); $args{'SEQNAME'} && $self->seqname($args{'SEQNAME'}); $args{'ANNOTATION'} && $self->annotation($args{'ANNOTATION'}); $args{'LOCATION'} && $self->location($args{'LOCATION'}); $args{'SENSE'} && $self->sense($args{'SENSE'}); $args{'ANTISENSE'} && $self->antisense($args{'ANTISENSE'}); defined($args{'START'}) && $self->start($args{'START'}); defined($args{'END'}) && $self->end($args{'END'}); defined($args{'STRAND'}) && $self->strand($args{'STRAND'}); defined($args{'SCORE'}) && $self->score($args{'SCORE'}); defined($args{'RANK'}) && $self->rank($args{'RANK'}); defined($args{'FXGC'}) && $self->fxGC($args{'FXGC'}); if ($args{'TAG'}) { foreach my $t (keys %{$args{'TAG'}}) { $self->add_tag_value($t, $args{'TAG'}->{$t}); } } return $self; } =head2 rank Title : rank Usage : my $pair_rank = $sirna_pair->rank() Purpose : Get/set the 'quality rank' for this pair. See Bio::Tools::SiRNA for a description of ranks. Returns : scalar Args : scalar (optional) indicating pair rank =cut sub rank { my ($self, $rank) = @_; if (defined $rank) { # first clear out old tags $self->remove_tag('rank') if ( $self->has_tag('rank') ); $self->add_tag_value('rank', $rank); } else { if ($self->has_tag('rank')) { my @ranks = $self->get_tag_values('rank'); return shift @ranks; } else { $self->throw("Rank not defined for this Pair\n"); return; } } } =head2 fxGC Title : fxGC Usage : my $fxGC = $sirna_pair->fxGC(); Purpose : Get/set the fraction of GC for this pair - based on TARGET sequence, not oligos. Returns : scalar between 0-1 Args : scalar between 0-1 (optional) =cut sub fxGC { my ($self, $fxGC) = @_; if (defined $fxGC) { # is this an integer? if ($fxGC =~ /[^.\d]/) { $self->throw( -class => 'Bio::Root::BadParameter', -text => "Fraction GC must be a number between 0, 1 - NOT <$fxGC>", -value => $fxGC ); } if ( $fxGC < 0 or $fxGC > 1 ) { $self->throw( -class => 'Bio::Root::BadParameter', -text => "Fraction GC must be a number between 0, 1 - NOT <$fxGC>", -value => $fxGC ); } # clear out old tags $self->remove_tag('fxGC') if ( $self->has_tag('fxGC') ); $self->add_tag_value('fxGC', $fxGC) or $self->throw("Unable to set fxGC"); } else { if ($self->has_tag('fxGC')) { my @fxGCs = $self->get_tag_values('fxGC'); return shift @fxGCs; } else { $self->throw("FxGC not defined for this Pair"); } } } =head2 sense Title : sense Usage : my $sense_oligo = $sirna_pair->sense() Purpose : Get/set the SiRNA::Oligo object corresponding to the sense strand Returns : Bio::SeqFeature::SiRNA::Oligo object Args : Bio::SeqFeature::SiRNA::Oligo object =cut sub sense { my ($self, $soligo) = @_; if ($soligo) { $self->_add_oligo($soligo, 1) or return; } else { return $self->_get_oligo(1); } } =head2 antisense Title : antisense Usage : my $antisense_oligo = $sirna_pair->antisense() Purpose : Get/set the SiRNA::Oligo object corresponding to the antisense strand Returns : Bio::SeqFeature::SiRNA::Oligo object Args : Bio::SeqFeature::SiRNA::Oligo object =cut sub antisense { my ($self, $asoligo) = @_; if ($asoligo) { $self->_add_oligo($asoligo, -1) or return; } else { return $self->_get_oligo(-1); } } sub _add_oligo { my ($self, $oligo, $strand) = @_; unless ($oligo->isa('Bio::SeqFeature::SiRNA::Oligo')) { $self->throw( -class => 'Bio::Root::BadParameter', -text => "Oligos must be passed as Bio::SeqFeature::SiRNA::Oligo objects\n"); } $oligo->strand($strand); return $self->add_sub_SeqFeature($oligo, 'EXPAND'); } sub _get_oligo { my ($self, $strand) = @_; my $feat; my @feats = $self->sub_SeqFeature; foreach $feat (@feats) { next unless ($feat->primary_tag eq 'SiRNA::Oligo'); next unless ($feat->strand == $strand); return $feat; } return; } 1; �������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Tools���������������������������������������������������������������000755��000766��000024�� 0�13155576320� 17233� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Tools/FeatureNamer.pm�����������������������������������������������000444��000766��000024�� 14066�13155576320� 22333� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # bioperl module for Bio::SeqFeature::Tools::FeatureNamer # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chris Mungall <cjm@fruitfly.org> # # Copyright Chris Mungall # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Tools::FeatureNamer - generates unique persistent names for features =head1 SYNOPSIS use Bio::SeqIO; use Bio::SeqFeature::Tools::FeatureNamer; # first fetch a genbank SeqI object $seqio = Bio::SeqIO->new(-file=>'AE003644.gbk', -format=>'GenBank'); $seq = $seqio->next_seq(); $namer = Bio::SeqFeature::Tools::FeatureNamer->new; my @features = $seq->get_SeqFeatures; foreach my $feature (@features) { $namer->name_feature($feature) unless $feature->display_name; } =head1 DESCRIPTION This is a helper class for providing names for SeqFeatures The L<Bio::SeqFeatureI> class provides a display_name method. Typically the display_name is not set when parsing formats such as genbank - instead properties such as B<label>, B<product> or B<gene> are set in a somewhat inconsistent manner. In addition, when generating subfeatures (for example, exons that are subfeatures of a transcript feature), it is often desirable to name these subfeatures before either exporting to another format or reporting to the user. This module is intended to help given uniform display_names to features and their subfeatures. =head1 TODO Currently the naming policy is hardcoded. It may be desirable to allow plugging in variations on naming policies; this could be done either by subclassing, anonymous subroutines (closures) or parameterization. Contact the author if you feel you have need for a different naming policy =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Mungall Email: cjm AT fruitfly DOT org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Tools::FeatureNamer; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root); =head2 new Title : new Usage : $unflattener = Bio::SeqFeature::Tools::FeatureNamer->new(); Function: constructor Example : Returns : a new Bio::SeqFeature::Tools::FeatureNamer Args : see below =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); # my($typemap) = # $self->_rearrange([qw(TYPEMAP # )], # @args);# # $typemap && $self->typemap($typemap); return $self; # success - we hope! } =head2 name_feature Title : name_feature Usage : $namer->name_feature($sf); Function: sets display_name Example : Returns : Args : L<Bio::SeqFeatureI> This method calls generate_feature_name() and uses the returned value to set the display_name of the feature =cut sub name_feature { my ($self, $sf) = @_; my $name = $self->generate_feature_name($sf); $sf->display_name($name); } =head2 name_contained_features Title : name_contained_features Usage : $namer->name_contained_features($sf); Function: sets display_name for all features contained by sf Example : Returns : Args : L<Bio::SeqFeatureI> iterates through all subfeatures of a certain feature (using get_all_SeqFeatures) and names each subfeatures, based on the generated name for the holder feature A subfeature is named by concatenating the generated name of the container feature with the type and a number. For example, if the containing feature is a gene with display name B<dpp>, subfeatures will be named dpp-mRNA-1 dpp-mRNA2 dpp-exon1 dpp-exon2 etc =cut sub name_contained_features{ my ($self,$sf) = @_; my $cname = $self->generate_feature_name($sf); my @subsfs = $sf->get_all_SeqFeatures; my %num_by_type = (); foreach my $ssf (@subsfs) { my $type = $ssf->primary_tag; my $num = $num_by_type{$type} || 0; $num++; $num_by_type{$type} = $num; $ssf->display_name("$cname-$type-$num"); } return; } =head2 generate_feature_name Title : generate_feature_name Usage : $name = $namer->generate_feature_name($sf); Function: derives a sensible human readable name for a $sf Example : Returns : str Args : L<Bio::SeqFeatureI> returns a generated name (but does not actually set display_name). If display_name is already set, the method will return this Otherwise, the name will depend on the property: =over =item label =item product =item gene =item locus_tag =back (in order of priority) =cut sub generate_feature_name { my ($self, $sf) = @_; my $name = $sf->display_name; if (!$name) { if ($sf->has_tag("label")) { ($name) = $sf->get_tag_values("label"); } elsif ($sf->has_tag("product")) { ($name) = $sf->get_tag_values("product"); } elsif ($sf->primary_tag eq 'gene' && $sf->has_tag("gene")) { ($name) = $sf->get_tag_values("gene"); } elsif ($sf->primary_tag eq 'gene' && $sf->has_tag("locus_tag")) { ($name) = $sf->get_tag_values("locus_tag"); } else { $name = $sf->display_name; } } return $name; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Tools/IDHandler.pm��������������������������������������������������000444��000766��000024�� 15666�13155576320� 21556� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # bioperl module for Bio::SeqFeature::Tools::IDHandler # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chris Mungall <cjm@fruitfly.org> # # Copyright Chris Mungall # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Tools::IDHandler - maps $seq_feature-E<gt>primary_tag =head1 SYNOPSIS use Bio::SeqIO; use Bio::SeqFeature::Tools::IDHandler; =head1 DESCRIPTION Class to map $seq_feature-E<gt>primary_tag =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Mungall Email: cjm@fruitfly.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Tools::IDHandler; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root); =head2 new Title : new Usage : $unflattener = Bio::SeqFeature::Tools::IDHandler->new(); Function: constructor Example : Returns : a new Bio::SeqFeature::Tools::IDHandler Args : see below =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my($generate_id_sub) = $self->_rearrange([qw(GENERATE_ID_SUB )], @args); return $self; # success - we hope! } =head2 set_ParentIDs_from_hierarchy() Title : set_ParentIDs_from_hierarchy() Usage : $idhandler->set_ParentIDs_from_hierarchy($fholder) Function: populates tags Parent and ID via holder hierarchy Example : Returns : Args : Bio::featureHolderI (either a SeqFeature or a Seq) This is mainly for GFF3 export GFF3 uses the tags ID and Parent to represent the feature containment hierarchy; it does NOT use the feature holder tree This method sets Parent (and ID for any parents not set) based on feature holder/containement hierarchy, ready for GFF3 output =cut # method author: cjm@fruitfly.org sub set_ParentIDs_from_hierarchy(){ my $self = shift; my ($featholder) = @_; # we will traverse the tree of contained seqfeatures # (a seqfeature is itself a holder) # start with the top-level features my @sfs = $featholder->get_SeqFeatures; # clear existing parent tags # (we assume this is the desired behaviour) my @all_sfs = $featholder->get_all_SeqFeatures; foreach (@all_sfs) { if ($_->has_tag('Parent')) { $_->remove_tag('Parent'); } } # iterate until entire tree traversed while (@sfs) { my $sf = shift @sfs; my @subsfs = $sf->get_SeqFeatures; # see if the ID tag my $id = $sf->primary_id; if (!$id) { # the skolem function feature(seq,start,end,type) # is presumed to uniquely identify this feature, and # to also be persistent $id = $sf->generate_unique_persistent_id; } foreach my $subsf (@subsfs) { $subsf->add_tag_value('Parent', $id); } # push children on to end of stack (breadth first search) push(@sfs, @subsfs); } return; } =head2 create_hierarchy_from_ParentIDs Title : create_hierarchy_from_ParentIDs Usage : $idhandler->set_ParentIDs_from_hierarchy($fholder) Function: inverse of set_ParentIDs_from_hierarchy Example : Returns : list of top SeqFeatures Args : =cut sub create_hierarchy_from_ParentIDs{ my ($self,$featholder,@args) = @_; my @sfs = $featholder->get_all_SeqFeatures; my %sf_by_ID = (); foreach (@sfs) { my $id = $_->primary_id; next unless $id; if ($sf_by_ID{$id}) { $featholder->throw("DUPLICATE ID: $id"); } $sf_by_ID{$id} = $_; $_->remove_SeqFeatures; # clear existing hierarchy (assume this is desired) } if (!%sf_by_ID) { # warn?? # this is actually expected behaviour for some kinds of data; # eg lists of STSs - no containment hierarchy return; } my @topsfs = grep { my @parents = $_->get_tagset_values('Parent'); foreach my $parent (@parents) { $sf_by_ID{$parent}->add_SeqFeature($_) if exists $sf_by_ID{$parent}; } !@parents; } @sfs; $featholder->remove_SeqFeatures; $featholder->add_SeqFeature($_) foreach @topsfs; return @topsfs; } =head2 generate_unique_persistent_id Title : generate_unique_persistent_id Usage : Function: generates a unique and persistent identifier for this Example : Returns : value of primary_id (a scalar) Args : Will generate an ID, B<and> set primary_id() (see above) The ID is a string generated from seq_id primary_tag start end There are three underlying assumptions: that all the above accessors are set; that seq_id is a persistent and unique identifier for the sequence containing this feature; and that (seq_id, primary_tag, start, end) is a "unique constraint" over features The ID is persistent, so long as none of these values change - if they do, it is considered a separate entity =cut # method author: cjm@fruitfly.org sub generate_unique_persistent_id{ my ($self,$sf,@args) = @_; my $id; if (!$sf->isa("Bio::SeqFeatureI")) { $sf->throw("not a Bio::SeqFeatureI"); } my $seq_id = $sf->seq_id || $sf->throw("seq_id must be set: ".$sf->display_name); #my $seq_id = $sf->seq_id || 'unknown_seq'; if ($sf->has_tag('transcript_id')) { ($id) = $sf->get_tag_values('transcript_id'); } elsif ($sf->has_tag('protein_id')) { ($id) = $sf->get_tag_values('protein_id'); } else { my $source = $sf->source_tag || $sf->throw("source tag must be set: ".$sf->display_name); #my $source = $sf->source_tag || 'unknown_source'; my $start = $sf->start || $sf->throw("start must be set or is zero: ".$sf->display_name); my $end = $sf->end || $sf->throw("end must be set"); my $type = $sf->primary_tag || $sf->throw("primary_tag/type must be set: ".$sf->display_name); $id = "$source:$type:$seq_id:$start:$end"; } $sf->primary_id($id); return $id; } 1; ��������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Tools/TypeMapper.pm�������������������������������������������������000444��000766��000024�� 34071�13155576320� 22041� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # bioperl module for Bio::SeqFeature::Tools::TypeMapper # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chris Mungall <cjm@fruitfly.org> # # Copyright Chris Mungall # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Tools::TypeMapper - maps $seq_feature-E<gt>primary_tag =head1 SYNOPSIS use Bio::SeqIO; use Bio::SeqFeature::Tools::TypeMapper; # first fetch a genbank SeqI object $seqio = Bio::SeqIO->new(-file=>'AE003644.gbk', -format=>'GenBank'); $seq = $seqio->next_seq(); $tm = Bio::SeqFeature::Tools::TypeMapper->new; # map all the types in the sequence $tm->map_types(-seq=>$seq, {CDS=>'ORF', variation=>sub { my $f = shift; $f->length > 1 ? 'variation' : 'SNP' }, }); # alternatively, use the hardcoded SO mapping $tm->map_types_to_SO(-seq=>$seq); =head1 DESCRIPTION This class implements an object for mapping between types; for example, the types in a genbank feature table, and the types specified in the Sequence Ontology. You can specify your own mapping, either as a simple hash index, or by providing your own subroutines. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Mungall Email: cjm@fruitfly.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Tools::TypeMapper; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root); =head2 new Title : new Usage : $unflattener = Bio::SeqFeature::Tools::TypeMapper->new(); Function: constructor Example : Returns : a new Bio::SeqFeature::Tools::TypeMapper Args : see below =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my($typemap) = $self->_rearrange([qw(TYPEMAP )], @args); $typemap && $self->typemap($typemap); return $self; # success - we hope! } =head2 typemap Title : typemap Usage : $obj->typemap($newval) Function: Example : Returns : value of typemap (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub typemap{ my $self = shift; return $self->{'typemap'} = shift if @_; return $self->{'typemap'}; } =head2 map_types Title : map_types Usage : Function: Example : Returns : Args : dgg: added -undefined => "region" option to produce all valid SO mappings. =cut sub map_types{ my ($self,@args) = @_; my($sf, $seq, $type_map, $undefmap) = $self->_rearrange([qw(FEATURE SEQ TYPE_MAP UNDEFINED )], @args); if (!$sf && !$seq) { $self->throw("you need to pass in either -feature or -seq"); } my @sfs = ($sf); if ($seq) { $seq->isa("Bio::SeqI") || $self->throw("$seq NOT A SeqI"); @sfs = $seq->get_all_SeqFeatures; } $type_map = $type_map || $self->typemap; # dgg: was type_map; foreach my $sf (@sfs) { $sf->isa("Bio::SeqFeatureI") || $self->throw("$sf NOT A SeqFeatureI"); $sf->isa("Bio::FeatureHolderI") || $self->throw("$sf NOT A FeatureHolderI"); my $type = $sf->primary_tag; my $mtype = $type_map->{$type}; if ($mtype) { if (ref($mtype)) { if (ref($mtype) eq 'CODE') { $mtype = $mtype->($sf); } else { $self->throw('type_map values must be scalar or CODE ref. You said: '.$mtype.' for type: '.$type); } } elsif ($undefmap && $mtype eq 'undefined') { # dgg $mtype= $undefmap; } $sf->primary_tag($mtype); } } return; } =head2 map_types_to_SO Title : map_types_to_SO Usage : Function: Example : Returns : Args : hardcodes the genbank to SO mapping Based on revision 1.22 of SO Please see the actual code for the mappings Taken from L<http://sequenceontology.org/resources/mapping/FT_SO.txt> dgg: separated out FT_SO_map for caller changes. Update with: open(FTSO,"curl -s http://sequenceontology.org/resources/mapping/FT_SO.txt|"); while(<FTSO>){ chomp; ($ft,$so,$sid,$ftdef,$sodef)= split"\t"; print " '$ft' => '$so',\n" if($ft && $so && $ftdef); } =cut sub FT_SO_map { # $self= shift; # note : some of the ft_so mappings are commented out and overriden... return { "-" => ["located_sequence_feature", "so:0000110"], "-10_signal" => ["minus_10_signal", "so:0000175"], "-35_signal" => ["minus_35_signal", "so:0000176"], "3'utr" => ["three_prime_utr", "so:0000205"], "3'clip" => ["three_prime_clip", "so:0000557"], "5'utr" => ["five_prime_utr", "so:0000204"], "5'clip" => ["five_prime_clip", "so:0000555"], "caat_signal" => ["caat_signal", "so:0000172"], "cds" => ["cds", "so:0000316"], "c_region" => ["undefined", ""], "d-loop" => ["d_loop", "so:0000297"], "d_segment" => ["d_gene", "so:0000458"], "gc_signal" => ["gc_rich_region", "so:0000173"], "j_segment" => ["undefined", ""], "ltr" => ["long_terminal_repeat", "so:0000286"], "n_region" => ["undefined", ""], "rbs" => ["ribosome_entry_site", "so:0000139"], "sts" => ["sts", "so:0000331"], "s_region" => ["undefined", ""], "tata_signal" => ["tata_box", "so:0000174"], "v_region" => ["undefined", ""], "v_segment" => ["undefined", ""], "attenuator" => ["attenuator", "so:0000140"], "conflict" => ["undefined", ""], "enhancer" => ["enhancer", "so:0000165"], "exon" => ["exon", "so:0000147"], "gap" => ["gap", "so:0000730"], "gene" => ["gene", "so:0000704"], "idna" => ["idna", "so:0000723"], "intron" => ["intron", "so:0000188"], "mRNA" => ["mRNA", "so:0000234"], "mat_peptide" => ["mature_protein_region", "so:0000419"], "mature_peptide" => ["mature_protein_region", "so:0000419"], #"misc_RNA" => ["transcript", "so:0000673"], "misc_binding" => ["binding_site", "so:0000409"], "misc_difference" => ["sequence_difference", "so:0000413"], "misc_feature" => ["region", undef], "misc_recomb" => ["recombination_feature", "so:0000298"], "misc_signal" => ["regulatory_region", "so:0005836"], "misc_structure" => ["sequence_secondary_structure", "so:0000002"], "modified_base" => ["modified_base_site", "so:0000305"], "old_sequence" => ["undefined", ""], "operon" => ["operon", "so:0000178"], "oriT" => ["origin_of_transfer", "so:0000724"], "polya_signal" => ["polyA_signal_sequence", "so:0000551"], "polya_site" => ["polyA_site", "so:0000553"], "precursor_RNA" => ["primary_transcript", "so:0000185"], "prim_transcript" => ["primary_transcript", "so:0000185"], "primer_bind" => ["primer_binding_site", "so:0005850"], "promoter" => ["promoter", "so:0000167"], "protein_bind" => ["protein_binding_site", "so:0000410"], "rRNA" => ["rRNA", "so:0000252"], "repeat_region" => ["repeat_region", "so:0000657"], "repeat_unit" => ["repeat_unit", "so:0000726"], "satellite" => ["satellite_dna", "so:0000005"], "scRNA" => ["scRNA", "so:0000013"], "sig_peptide" => ["signal_peptide", "so:0000418"], "snRNA" => ["snRNA", "so:0000274"], "snoRNA" => ["snoRNA", "so:0000275"], #"source" => ["databank_entry", "so:2000061"], "stem_loop" => ["stem_loop", "so:0000313"], "tRNA" => ["tRNA", "so:0000253"], "terminator" => ["terminator", "so:0000141"], "transit_peptide" => ["transit_peptide", "so:0000725"], "unsure" => "undefined", "variation" => ["sequence_variant", "so:0000109"], # manually added ## has parent = pseudogene ; dgg "pseudomRNA" => ["pseudogenic_transcript", "so:0000516"], ## from unflattener misc_rna ; dgg "pseudotranscript" => ["pseudogenic_transcript", "so:0000516"], "pseudoexon" => ["pseudogenic_exon", "so:0000507"], "pseudoCDS" => ["pseudogenic_exon", "so:0000507"], "pseudomisc_feature" => ["pseudogenic_region", "so:0000462"], "pseudointron" => ["pseudogenic_region", "so:0000462"], ## "undefined" => "region", # this is the most generic form for rnas; # we always represent the processed form of # the transcript misc_RNA => ['mature_transcript',"so:0000233"], # not sure about this one... source=>['contig', "SO:0000149"], rep_origin=>['origin_of_replication',"SO:0000296"], Protein=>['polypeptide',"SO:0000104"], }; # return { #"FT term" => "SO term", #"-" => "located_sequence_feature", #"-10_signal" => "minus_10_signal", #"-35_signal" => "minus_35_signal", #"3'UTR" => "three_prime_UTR", #"3'clip" => "three_prime_clip", #"5'UTR" => "five_prime_UTR", #"5'clip" => "five_prime_clip", #"CAAT_signal" => "CAAT_signal", #"CDS" => "CDS", #"C_region" => "undefined", #"D-loop" => "D_loop", #"D_segment" => "D_gene", #"GC_signal" => "GC_rich_region", #"J_segment" => "undefined", #"LTR" => "long_terminal_repeat", #"N_region" => "undefined", #"RBS" => "ribosome_entry_site", #"STS" => "STS", #"S_region" => "undefined", #"TATA_signal" => "TATA_box", #"V_region" => "undefined", #"V_segment" => "undefined", #"attenuator" => "attenuator", #"conflict" => "undefined", #"enhancer" => "enhancer", #"exon" => "exon", #"gap" => "gap", #"gene" => "gene", #"iDNA" => "iDNA", #"intron" => "intron", #"mRNA" => "mRNA", #"mat_peptide" => "mature_protein_region", #"mature_peptide" => "mature_protein_region", ## "misc_RNA" => "transcript", #"misc_binding" => "binding_site", #"misc_difference" => "sequence_difference", #"misc_feature" => "region", #"misc_recomb" => "recombination_feature", #"misc_signal" => "regulatory_region", #"misc_structure" => "sequence_secondary_structure", #"modified_base" => "modified_base_site", #"old_sequence" => "undefined", #"operon" => "operon", #"oriT" => "origin_of_transfer", #"polyA_signal" => "polyA_signal_sequence", #"polyA_site" => "polyA_site", #"precursor_RNA" => "primary_transcript", #"prim_transcript" => "primary_transcript", #"primer_bind" => "primer_binding_site", #"promoter" => "promoter", #"protein_bind" => "protein_binding_site", #"rRNA" => "rRNA", #"repeat_region" => "repeat_region", #"repeat_unit" => "repeat_unit", #"satellite" => "satellite_DNA", #"scRNA" => "scRNA", #"sig_peptide" => "signal_peptide", #"snRNA" => "snRNA", #"snoRNA" => "snoRNA", ## "source" => "databank_entry", #"stem_loop" => "stem_loop", #"tRNA" => "tRNA", #"terminator" => "terminator", #"transit_peptide" => "transit_peptide", #"unsure" => "undefined", #"variation" => "sequence_variant", #"pseudomRNA" => "pseudogenic_transcript", ## has parent = pseudogene ; dgg #"pseudotranscript" => "pseudogenic_transcript", ## from Unflattener misc_RNA ; dgg #"pseudoexon" => "pseudogenic_exon", #"pseudoCDS" => "pseudogenic_exon", #"pseudomisc_feature" => "pseudogenic_region", #"pseudointron" => "pseudogenic_region", ### "undefined" => "region", ## this is the most generic form for RNAs; ## we always represent the processed form of ## the transcript #misc_RNA=>'processed_transcript', ## not sure about this one... #source=>'contig', #rep_origin=>'origin_of_replication', #Protein=>'protein', #}; } sub map_types_to_SO{ my ($self,@args) = @_; push(@args, (-type_map=> $self->FT_SO_map() ) ); return $self->map_types(@args); } =head2 get_relationship_type_by_parent_child Title : get_relationship_type_by_parent_child Usage : $type = $tm->get_relationship_type_by_parent_child($parent_sf, $child_sf); Usage : $type = $tm->get_relationship_type_by_parent_child('mRNA', 'protein'); Function: given two features where the parent contains the child, will determine what the relationship between them in Example : Returns : Args : parent SeqFeature, child SeqFeature OR parent type string, child type string OR bioperl Seq::FeatureHolderI hierarchies are equivalent to unlabeled graphs (where parent nodes are the containers, and child nodes are the features being contained). For example, a feature of type mRNA can contain features of type exon. Some external representations (eg chadoxml or chaosxml) require that the edges in the feature relationship graph are labeled. For example, the type between mRNA and exon would be B<part_of>. Although it stretches the bioperl notion of containment, we could have a CDS contained by an mRNA (for example, the L<Bio::SeqFeature::Tools::Unflattener> module takes genbank records and makes these kind of links. The relationship here would be B<produced_by> In chado speak, the child is the B<subject> feature and the parent is the B<object> feature =cut sub get_relationship_type_by_parent_child { my ($self,$parent,$child) = @_; $parent = ref($parent) ? $parent->primary_tag : $parent; $child = ref($child) ? $child->primary_tag : $child; my $type = 'part_of'; # default # TODO - do this with metadata, or infer via SO itself if (lc($child) eq 'protein') { $type = 'derives_from'; } if (lc($child) eq 'polypeptide') { $type = 'derives_from'; } return $type; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqFeature/Tools/Unflattener.pm������������������������������������������������000444��000766��000024�� 262217�13155576320� 22267� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # bioperl module for Bio::SeqFeature::Tools::Unflattener # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chris Mungall <cjm@fruitfly.org> # # Copyright Chris Mungall # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::Tools::Unflattener - turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy =head1 SYNOPSIS # standard / generic use - unflatten a genbank record use Bio::SeqIO; use Bio::SeqFeature::Tools::Unflattener; # generate an Unflattener object $unflattener = Bio::SeqFeature::Tools::Unflattener->new; # first fetch a genbank SeqI object $seqio = Bio::SeqIO->new(-file=>'AE003644.gbk', -format=>'GenBank'); my $out = Bio::SeqIO->new(-format=>'asciitree'); while ($seq = $seqio->next_seq()) { # get top level unflattended SeqFeatureI objects $unflattener->unflatten_seq(-seq=>$seq, -use_magic=>1); $out->write_seq($seq); @top_sfs = $seq->get_SeqFeatures; foreach my $sf (@top_sfs) { # do something with top-level features (eg genes) } } =head1 DESCRIPTION Most GenBank entries for annotated genomic DNA contain a B<flat> list of features. These features can be parsed into an equivalent flat list of L<Bio::SeqFeatureI> objects using the standard L<Bio::SeqIO> classes. However, it is often desirable to B<unflatten> this list into something resembling actual B<gene models>, in which genes, mRNAs and CDSs are B<nested> according to the nature of the gene model. The BioPerl object model allows us to store these kind of associations between SeqFeatures in B<containment hierarchies> -- any SeqFeatureI object can contain nested SeqFeatureI objects. The Bio::SeqFeature::Tools::Unflattener object facilitates construction of these hierarchies from the underlying GenBank flat-feature-list representation. For example, if you were to look at a typical GenBank DNA entry, say, B<AE003644>, you would see a flat list of features: source gene CG4491 mRNA CG4491-RA CDS CG4491-PA gene tRNA-Pro tRNA tRNA-Pro gene CG32954 mRNA CG32954-RA mRNA CG32954-RC mRNA CG32954-RB CDS CG32954-PA CDS CG32954-PB CDS CG32954-PC These features have sequence locations, but it is not immediately clear how to write code such that each mRNA is linked to the appropriate CDS (other than relying on IDs which is very bad) We would like to convert the above list into the B<containment hierarchy>, shown below: source gene mRNA CG4491-RA CDS CG4491-PA exon exon gene tRNA tRNA-Pro exon gene mRNA CG32954-RA CDS CG32954-PA exon exon mRNA CG32954-RC CDS CG32954-PC exon exon mRNA CG32954-RB CDS CG32954-PB exon exon Where each feature is nested underneath its container. Note that exons have been automatically inferred (even for tRNA genes). We do this using a call on a L<Bio::SeqFeature::Tools::Unflattener> object @sfs = $unflattener->unflatten_seq(-seq=>$seq); This would return a list of the B<top level> (i.e. container) SeqFeatureI objects - in this case, genes. Other top level features are possible; for instance, the B<source> feature which is always present, and other features such as B<variation> or B<misc_feature> types. The containment hierarchy can be accessed using the get_SeqFeature() call on any feature object - see L<Bio::SeqFeature::FeatureHolderI>. The following code will traverse the containment hierarchy for a feature: sub traverse { $sf = shift; # $sf isa Bio::SeqfeatureI # ...do something with $sf! # depth first traversal of containment tree @contained_sfs = $sf->get_SeqFeatures; traverse($_) foreach @contained_sfs; } Once you have built the hierarchy, you can do neat stuff like turn the features into 'rich' feature objects (eg L<Bio::SeqFeature::Gene::GeneStructure>) or convert to a suitable format such as GFF3 or chadoxml (after mapping to the Sequence Ontology); this step is not described here. =head1 USING MAGIC Due to the quixotic nature of how features are stored in GenBank/EMBL/DDBJ, there is no guarantee that the default behaviour of this module will produce perfect results. Sometimes it is hard or impossible to build a correct containment hierarchy if the information provided is simply too lossy, as is often the case. If you care deeply about your data, you should always manually inspect the resulting containment hierarchy; you may have to customise the algorithm for building the hierarchy, or even manually tweak the resulting hierarchy. This is explained in more detail further on in the document. However, if you are satisfied with the default behaviour, then you do not need to read any further. Just make sure you set the parameter B<use_magic> - this will invoke incantations which will magically produce good results no matter what the idiosyncracies of the particular GenBank record in question. For example $unflattener->unflatten_seq(-seq=>$seq, -use_magic=>1); The success of this depends on the phase of the moon at the time the entry was submitted to GenBank. Note that the magical recipe is being constantly improved, so the results of invoking magic may vary depending on the bioperl release. If you are skeptical of magic, or you wish to exact fine grained control over how the entry is unflattened, or you simply wish to understand more about how this crazy stuff works, then read on! =head1 PROBLEMATIC DATA AND INCONSISTENCIES Occasionally the Unflattener will have problems with certain records. For example, the record may contain inconsistent data - maybe there is an B<exon> entry that has no corresponding B<mRNA> location. The default behaviour is to throw an exception reporting the problem, if the problem is relatively serious - for example, inconsistent data. You can exert more fine grained control over this - perhaps you want the Unflattener to do the best it can, and report any problems. This can be done - refer to the methods. error_threshold() get_problems() report_problems() ignore_problems() =head1 ALGORITHM This is the default algorithm; you should be able to override any part of it to customise. The core of the algorithm is in two parts =over =item Partitioning the flat feature list into groups =item Resolving the feature containment hierarchy for each group =back There are other optional steps after the completion of these two steps, such as B<inferring exons>; we now describe in more detail what is going on. =head2 Partitioning into groups First of all the flat feature list is partitioned into B<group>s. The default way of doing this is to use the B<gene> attribute; if we look at two features from GenBank accession AE003644.3: gene 20111..23268 /gene="noc" /locus_tag="CG4491" /note="last curated on Thu Dec 13 16:51:32 PST 2001" /map="35B2-35B2" /db_xref="FLYBASE:FBgn0005771" mRNA join(20111..20584,20887..23268) /gene="noc" /locus_tag="CG4491" /product="CG4491-RA" /db_xref="FLYBASE:FBgn0005771" Both these features share the same /gene tag which is "noc", so they correspond to the same gene model (the CDS feature is not shown, but this also has a tag-value /gene="noc"). Not all groups need to correspond to gene models, but this is the most common use case; later on we shall describe how to customise the grouping. Sometimes other tags have to be used; for instance, if you look at the entire record for AE003644.3 you will see you actually need the use the /locus_tag attribute. This attribute is actually B<not present> in most records! You can override this: $collection->unflatten_seq(-seq=>$seq, -group_tag=>'locus_tag'); Alternatively, if you B<-use_magic>, the object will try and make a guess as to what the correct group_tag should be. At the end of this step, we should have a list of groups - there is no structure within a group; the group just serves to partition the flat features. For the example data above, we would have the following groups. [ source ] [ gene mRNA CDS ] [ gene mRNA CDS ] [ gene mRNA CDS ] [ gene mRNA mRNA mRNA CDS CDS CDS ] =head3 Multicopy Genes Multicopy genes are usually rRNAs or tRNAs that are duplicated across the genome. Because they are functionally equivalent, and usually have the same sequence, they usually have the same group_tag (ie gene symbol); they often have a /note tag giving copy number. This means they will end up in the same group. This is undesirable, because they are spatially disconnected. There is another step, which involves splitting spatially disconnected groups into distinct groups this would turn this [gene-rrn3 rRNA-rrn3 gene-rrn3 rRNA-rrn3] into this [gene-rrn3 rRNA-rrn3] [gene-rrn3 rRNA-rrn3] based on the coordinates =head3 What next? The next step is to add some structure to each group, by making B<containment hierarchies>, trees that represent how the features interrelate =head2 Resolving the containment hierarchy After the grouping is done, we end up with a list of groups which probably contain features of type 'gene', 'mRNA', 'CDS' and so on. Singleton groups (eg the 'source' feature) are ignored at this stage. Each group is itself flat; we need to add an extra level of organisation. Usually this is because different spliceforms (represented by the 'mRNA' feature) can give rise to different protein products (indicated by the 'CDS' feature). We want to correctly associate mRNAs to CDSs. We want to go from a group like this: [ gene mRNA mRNA mRNA CDS CDS CDS ] to a containment hierarchy like this: gene mRNA CDS mRNA CDS mRNA CDS In which each CDS is nested underneath the correct corresponding mRNA. For entries that contain no alternate splicing, this is simple; we know that the group [ gene mRNA CDS ] Must resolve to the tree gene mRNA CDS How can we do this in entries with alternate splicing? The bad news is that there is no guaranteed way of doing this correctly for any GenBank entry. Occasionally the submission will have been done in such a way as to reconstruct the containment hierarchy. However, this is not consistent across databank entries, so no generic solution can be provided by this object. This module does provide the framework within which you can customise a solution for the particular dataset you are interested in - see later. The good news is that there is an inference we can do that should produce pretty good results the vast majority of the time. It uses splice coordinate data - this is the default behaviour of this module, and is described in detail below. =head2 Using splice site coordinates to infer containment If an mRNA is to be the container for a CDS, then the splice site coordinates (or intron coordinates, depending on how you look at it) of the CDS must fit inside the splice site coordinates of the mRNA. Ambiguities can still arise, but the results produced should still be reasonable and consistent at the sequence level. Look at this fake example: mRNA XXX---XX--XXXXXX--XXXX join(1..3,7..8,11..16,19..23) mRNA XXX-------XXXXXX--XXXX join(1..3,11..16,19..23) CDS XXXX--XX join(13..16,19..20) CDS XXXX--XX join(13..16,19..20) [obviously the positions have been scaled down] We cannot unambiguously match mRNA with CDS based on splice sites, since both CDS share the splice site locations 16^17 and 18^19. However, the consequences of making a wrong match are probably not very severe. Any annotation data attached to the first CDS is probably identical to the seconds CDS, other than identifiers. The default behaviour of this module is to make an arbitrary call where it is ambiguous (the mapping will always be bijective; i.e. one mRNA -E<gt> one CDS). [TODO: NOTE: not tested on EMBL data, which may not be bijective; ie two mRNAs can share the same CDS??] This completes the building of the containment hierarchy; other optional step follow =head1 POST-GROUPING STEPS =head2 Inferring exons from mRNAs This step always occurs if B<-use_magic> is invoked. In a typical GenBank entry, the exons are B<implicit>. That is they can be inferred from the mRNA location. For example: mRNA join(20111..20584,20887..23268) This tells us that this particular transcript has two exons. In bioperl, the mRNA feature will have a 'split location'. If we call $unflattener->feature_from_splitloc(-seq=>$seq); This will generate the necessary exon features, and nest them under the appropriate mRNAs. Note that the mRNAs will no longer have split locations - they will have simple locations spanning the extent of the exons. This is intentional, to avoid redundancy. Occasionally a GenBank entry will have both implicit exons (from the mRNA location) B<and> explicit exon features. In this case, exons will still be transferred. Tag-value data from the explicit exon will be transferred to the implicit exon. If exons are shared between mRNAs these will be represented by different objects. Any inconsistencies between implicit and explicit will be reported. =head3 tRNAs and other noncoding RNAs exons will also be generated from these features =head2 Inferring mRNAs from CDS Some GenBank entries represent gene models using features of type gene, mRNA and CDS; some entries just use gene and CDS. If we only have gene and CDS, then the containment hierarchies will look like this: gene CDS If we want the containment hierarchies to be uniform, like this gene mRNA CDS Then we must create an mRNA feature. This will have identical coordinates to the CDS. The assumption is that there is either no untranslated region, or it is unknown. To do this, we can call $unflattener->infer_mRNA_from_CDS(-seq=>$seq); This is taken care of automatically, if B<-use_magic> is invoked. =head1 ADVANCED =head2 Customising the grouping of features The default behaviour is suited mostly to building models of protein coding genes and noncoding genes from genbank genomic DNA submissions. You can change the tag used to partition the feature by passing in a different group_tag argument - see the unflatten_seq() method Other behaviour may be desirable. For example, even though SNPs (features of type 'variation' in GenBank) are not actually part of the gene model, it may be desirable to group SNPs that overlap or are nearby gene models. It should certainly be possible to extend this module to do this. However, I have yet to code this part!!! If anyone would find this useful let me know. In the meantime, you could write your own grouping subroutine, and feed the results into unflatten_groups() [see the method documentation below] =head2 Customising the resolution of the containment hierarchy Once the flat list of features has been partitioned into groups, the method unflatten_group() is called on each group to build a tree. The algorithm for doing this is described above; ambiguities are resolved by using splice coordinates. As discussed, this can be ambiguous. Some submissions may contain information in tags/attributes that hint as to the mapping that needs to be made between the features. For example, with the Drosophila Melanogaster release 3 submission, we see that CDS features in alternately spliced mRNAs have a form like this: CDS join(145588..145686,145752..146156,146227..146493) /locus_tag="CG32954" /note="CG32954 gene product from transcript CG32954-RA" ^^^^^^^^^^^^^^^^^^^^^^^^^^^ /codon_start=1 /product="CG32954-PA" /protein_id="AAF53403.1" /db_xref="GI:7298167" /db_xref="FLYBASE:FBgn0052954" /translation="MSFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENP..." Here the /note tag provides the clue we need to link CDS to mRNA (highlighted with ^^^^). We just need to find the mRNA with the tag /product="CG32954-RA" I have no idea how consistent this practice is across submissions; it is consistent for the fruitfly genome submission. We can customise the behaviour of unflatten_group() by providing our own resolver method. This obviously requires a bit of extra programming, but there is no way to get around this. Here is an example of how to pass in your own resolver; this example basically checks the parent (container) /product tag to see if it matches the required string in the child (contained) /note tag. $unflattener->unflatten_seq(-seq=>$seq, -group_tag=>'locus_tag', -resolver_method=>sub { my $self = shift; my ($sf, @candidate_container_sfs) = @_; if ($sf->has_tag('note')) { my @notes = $sf->get_tag_values('note'); my @trnames = map {/from transcript\s+(.*)/; $1} @notes; @trnames = grep {$_} @trnames; my $trname; if (@trnames == 0) { $self->throw("UNRESOLVABLE"); } elsif (@trnames == 1) { $trname = $trnames[0]; } else { $self->throw("AMBIGUOUS: @trnames"); } my @container_sfs = grep { my ($product) = $_->has_tag('product') ? $_->get_tag_values('product') : (''); $product eq $trname; } @candidate_container_sfs; if (@container_sfs == 0) { $self->throw("UNRESOLVABLE"); } elsif (@container_sfs == 1) { # we got it! return $container_sfs[0]; } else { $self->throw("AMBIGUOUS"); } } }); the resolver method is only called when there is more than one spliceform. =head2 Parsing mRNA records Some of the entries in sequence databanks are for mRNA sequences as well as genomic DNA. We may want to build models from these too. NOT YET DONE - IN PROGRESS!!! Open question - what would these look like? Ideally we would like a way of combining a mRNA record with the corresponding SeFeature entry from the appropriate genomic DNA record. This could be problemmatic in some cases - for example, the mRNA sequences may not match 100% (due to differences in strain, assembly problems, sequencing problems, etc). What then...? =head1 SEE ALSO Feature table description http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Mungall Email: cjm@fruitfly.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Tools::Unflattener; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Location::Simple; use Bio::SeqFeature::Generic; use Bio::Range; use base qw(Bio::Root::Root); =head2 new Title : new Usage : $unflattener = Bio::SeqFeature::Tools::Unflattener->new(); $unflattener->unflatten_seq(-seq=>$seq); Function: constructor Example : Returns : a new Bio::SeqFeature::Tools::Unflattener Args : see below Arguments -seq : A L<Bio::SeqI> object (optional) the sequence to unflatten; this can also be passed in when we call unflatten_seq() -group_tag : a string representing the /tag used to partition flat features (see discussion above) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my($seq, $group_tag, $trust_grouptag) = $self->_rearrange([qw(SEQ GROUP_TAG TRUST_GROUPTAG )], @args); $seq && $self->seq($seq); $group_tag && $self->group_tag($group_tag); # $self->{'trust_grouptag'}= $trust_grouptag if($trust_grouptag); #dgg suggestion return $self; # success - we hope! } sub DESTROY { my $self = shift; return if $self->{_reported_problems}; return if $self->{_ignore_problems}; my @probs = $self->get_problems; if (!$self->{_problems_reported} && scalar(@probs)) { $self->warn( "WARNING: There are UNREPORTED PROBLEMS.\n". "You may wish to use the method report_problems(), \n", "or ignore_problems() on the Unflattener object\n"); } return; } =head2 seq Title : seq Usage : $unflattener->seq($newval) Function: Example : Returns : value of seq (a Bio::SeqI) Args : on set, new value (a Bio::SeqI, optional) The Bio::SeqI object should hold a flat list of Bio::SeqFeatureI objects; this is the list that will be unflattened. The sequence object can also be set when we call unflatten_seq() =cut sub seq{ my $self = shift; return $self->{'seq'} = shift if @_; return $self->{'seq'}; } =head2 group_tag Title : group_tag Usage : $unflattener->group_tag($newval) Function: Example : Returns : value of group_tag (a scalar) Args : on set, new value (a scalar or undef, optional) This is the tag that will be used to collect elements from the flat feature list into groups; for instance, if we look at two typical GenBank features: gene 20111..23268 /gene="noc" /locus_tag="CG4491" /note="last curated on Thu Dec 13 16:51:32 PST 2001" /map="35B2-35B2" /db_xref="FLYBASE:FBgn0005771" mRNA join(20111..20584,20887..23268) /gene="noc" /locus_tag="CG4491" /product="CG4491-RA" /db_xref="FLYBASE:FBgn0005771" We can see that these comprise the same gene model because they share the same /gene attribute; we want to collect these together in groups. Setting group_tag is optional. The default is to use 'gene'. In the example above, we could also use /locus_tag =cut sub group_tag{ my $self = shift; return $self->{'group_tag'} = shift if @_; return $self->{'group_tag'}; } =head2 partonomy Title : partonomy Usage : $unflattener->partonomy({mRNA=>'gene', CDS=>'mRNA') Function: Example : Returns : value of partonomy (a scalar) Args : on set, new value (a scalar or undef, optional) A hash representing the containment structure that the seq_feature nesting should conform to; each key represents the contained (child) type; each value represents the container (parent) type. =cut sub partonomy{ my $self = shift; return $self->{'partonomy'} = shift if @_; if (!$self->{'partonomy'}) { $self->{'partonomy'} = $self->_default_partonomy; } return $self->{'partonomy'}; } sub _default_partonomy{ return { mRNA => 'gene', tRNA => 'gene', rRNA => 'gene', scRNA => 'gene', snRNA => 'gene', snoRNA => 'gene', misc_RNA => 'gene', CDS => 'mRNA', exon => 'mRNA', intron => 'mRNA', pseudoexon => 'pseudogene', pseudointron => 'pseudogene', pseudotranscript => 'pseudogene', }; } =head2 structure_type Title : structure_type Usage : $unflattener->structure_type($newval) Function: Example : Returns : value of structure_type (a scalar) Args : on set, new value (an int or undef, optional) GenBank entries conform to different flavours, or B<structure types>. Some have mRNAs, some do not. Right now there are only two base structure types defined. If you set the structure type, then appropriate unflattening action will be taken. The presence or absence of explicit exons does not affect the structure type. If you invoke B<-use_magic> then this will be set automatically, based on the content of the record. =over =item Type 0 (DEFAULT) typically contains source gene mRNA CDS with this structure type, we want the seq_features to be nested like this gene mRNA CDS exon exons and introns are implicit from the mRNA 'join' location to get exons from the mRNAs, you will need this call (see below) $unflattener->feature_from_splitloc(-seq=>$seq); =item Type 1 typically contains source gene CDS exon [optional] intron [optional] there are no mRNA features with this structure type, we want the seq_features to be nested like this gene CDS exon intron exon and intron may or may not be present; they may be implicit from the CDS 'join' location =back =cut sub structure_type{ my $self = shift; return $self->{'structure_type'} = shift if @_; return $self->{'structure_type'}; } =head2 get_problems Title : get_problems Usage : @probs = get_problems() Function: Get the list of problem(s) for this object. Example : Returns : An array of [severity, description] pairs Args : In the course of unflattening a record, problems may occur. Some of these problems are non-fatal, and can be ignored. Problems are represented as arrayrefs containing a pair [severity, description] severity is a number, the higher, the more severe the problem the description is a text string =cut sub get_problems{ my $self = shift; return @{$self->{'_problems'}} if exists($self->{'_problems'}); return (); } =head2 clear_problems Title : clear_problems Usage : Function: resets the problem list to empty Example : Returns : Args : =cut sub clear_problems{ my ($self,@args) = @_; $self->{'_problems'} = []; return; } # PRIVATE # see get_problems sub add_problem{ my $self = shift; $self->{'_problems'} = [] unless exists($self->{'_problems'}); if ($self->verbose > 0) { warn( "PROBLEM: $_\n") foreach @_; } push(@{$self->{'_problems'}}, @_); } # PRIVATE # see get_problems sub problem { my $self = shift; my ($severity, $desc, @sfs) = @_; if (@sfs) { foreach my $sf (@sfs) { $desc .= sprintf("\nSF [$sf]: ". $sf->location->to_FTstring . "; %s\n", join('; ', $sf->primary_tag, map { $sf->has_tag($_) ? $sf->get_tag_values($_) : () } qw(locus_tag gene product label))); } } my $thresh = $self->error_threshold; if ($severity > $thresh) { $self->{_problems_reported} = 1; $self->throw("PROBLEM, SEVERITY==$severity\n$desc"); } $self->add_problem([$severity, $desc]); return; } =head2 report_problems Title : report_problems Usage : $unflattener->report_problems(\*STDERR); Function: Example : Returns : Args : FileHandle (defaults to STDERR) =cut sub report_problems{ my ($self, $fh) = @_; if (!$fh) { $fh = \*STDERR; } foreach my $problem ($self->get_problems) { my ($sev, $desc) = @$problem; printf $fh "PROBLEM, SEVERITY==$sev\n$desc\n"; } $self->{_problems_reported} = 1; return; } =head2 ignore_problems Title : ignore_problems Usage : $obj->ignore_problems(); Function: Example : Returns : Args : Unflattener is very particular about problems it finds along the way. If you have set the error_threshold such that less severe problems do not cause exceptions, Unflattener still expects you to report_problems() at the end, so that the user of the module is aware of any inconsistencies or problems with the data. In fact, a warning will be produced if there are unreported problems. To silence, this warning, call the ignore_problems() method before the Unflattener object is destroyed. =cut sub ignore_problems{ my ($self) = @_; $self->{_ignore_problems} = 1; return; } =head2 error_threshold Title : error_threshold Usage : $obj->error_threshold($severity) Function: Example : Returns : value of error_threshold (a scalar) Args : on set, new value (an integer) Sets the threshold above which errors cause this module to throw an exception. The default is 0; all problems with a severity E<gt> 0 will cause an exception. If you raise the threshold to 1, then the unflattening process will be more lax; problems of severity==1 are generally non-fatal, but may indicate that the results should be inspected, for example, to make sure there is no data loss. =cut sub error_threshold{ my $self = shift; return $self->{'error_threshold'} = shift if @_; return $self->{'error_threshold'} || 0; } # PRIVATE # # given a type (eg mRNA), will return the container type (eg gene) sub get_container_type{ my ($self,$type) = @_; my @roots = $self->_get_partonomy_roots; if (grep {$_ eq $type} @roots) { # it is a root - no parents/containers return; } my $ch = $self->partonomy; my $ctype = $ch->{$type}; if (!$ctype) { # asterix acts as a wild card $ctype = $ch->{'*'}; } return $ctype; } # get root node of partonomy hierarchy (usually gene) sub _get_partonomy_roots { my $self = shift; my $ch = $self->partonomy; my @parents = values %$ch; # find parents that do not have parents themselves return grep {!$ch->{$_}} @parents; } =head2 unflatten_seq Title : unflatten_seq Usage : @sfs = $unflattener->unflatten_seq($seq); Function: turns a flat list of features into a list of holder features Example : Returns : list of Bio::SeqFeatureI objects Args : see below partitions a list of features then arranges them in a nested tree; see above for full explanation. note - the Bio::SeqI object passed in will be modified Arguments -seq : a Bio::SeqI object; must contain Bio::SeqFeatureI objects (this is optional if seq has already been set) -use_magic: if TRUE (ie non-zero) then magic will be invoked; see discussion above. -resolver_method: a CODE reference see the documentation above for an example of a subroutine that can be used to resolve hierarchies within groups. this is optional - if nothing is supplied, a default subroutine will be used (see below) -group_tag: a string [ see the group_tag() method ] this overrides the default group_tag which is 'gene' =cut sub unflatten_seq{ my ($self,@args) = @_; my($seq, $resolver_method, $group_tag, $partonomy, $structure_type, $resolver_tag, $use_magic, $noinfer) = $self->_rearrange([qw(SEQ RESOLVER_METHOD GROUP_TAG PARTONOMY STRUCTURE_TYPE RESOLVER_TAG USE_MAGIC NOINFER )], @args); # seq we want to unflatten $seq = $seq || $self->seq; if (!$self->seq) { $self->seq($seq); } # prevent bad argument combinations if ($partonomy && defined($structure_type)) { $self->throw("You cannot set both -partonomy and -structure_type\n". "(the former is implied by the latter)"); } # remember the current value of partonomy, to reset later my $old_partonomy = $self->partonomy; $self->partonomy($partonomy) if defined $partonomy; # remember old structure_type my $old_structure_type = $self->structure_type; $self->structure_type($structure_type) if defined $structure_type; # if we are sourcing our data from genbank, all the # features should be flat (eq no sub_SeqFeatures) my @flat_seq_features = $seq->get_SeqFeatures; my @all_seq_features = $seq->get_all_SeqFeatures; # sanity checks if (@all_seq_features > @flat_seq_features) { $self->throw("It looks as if this sequence has already been unflattened"); } if (@all_seq_features < @flat_seq_features) { $self->throw("ASSERTION ERROR: something is seriously wrong with your features"); } # tag for ungrouping; usually /gene or /locus_tag # for example: /gene="foo" $group_tag = $group_tag || $self->group_tag; if ($use_magic) { # use magic to guess the group tag my @sfs_with_locus_tag = grep {$_->has_tag("locus_tag")} @flat_seq_features; my @sfs_with_gene_tag = grep {$_->has_tag("gene")} @flat_seq_features; my @sfs_with_product_tag = grep {$_->has_tag("product")} @flat_seq_features; # if ($group_tag && $self->{'trust_grouptag'}) { # dgg suggestion # # } # elsif if (@sfs_with_locus_tag) { # dgg note: would like to -use_magic with -group_tag = 'gene' for ensembl genomes # where ensembl gene FT have both /locus_tag and /gene, but mRNA, CDS have /gene only if ($group_tag && $group_tag ne 'locus_tag') { $self->throw("You have explicitly set group_tag to be '$group_tag'\n". "However, I detect that some features use /locus_tag\n". "I believe that this is the correct group_tag to use\n". "You can resolve this by either NOT setting -group_tag\n". "OR you can unset -use_magic to regain control"); } # use /locus_tag instead of /gene tag for grouping # see GenBank entry AE003677 (version 3) for an example $group_tag = 'locus_tag'; if ($self->verbose > 0) { warn "Set group tag to: $group_tag\n"; } } # on rare occasions, records will have no /gene or /locus_tag # but it WILL have /product tags. These serve the same purpose # for grouping. For an example, see AY763288 (also in t/data) if (@sfs_with_locus_tag==0 && @sfs_with_gene_tag==0 && @sfs_with_product_tag>0 && !$group_tag) { $group_tag = 'product'; if ($self->verbose > 0) { warn "Set group tag to: $group_tag\n"; } } } if (!$group_tag) { $group_tag = 'gene'; } # ------------------------------ # GROUP FEATURES using $group_tag # collect features into unstructured groups # ------------------------------ # ------------- # we want to generate a list of groups; # each group is a list of SeqFeatures; this # group probably (but not necessarily) # corresponds to a gene model. # # this array will look something like this: # ([$f1], [$f2, $f3, $f4], ...., [$f97, $f98, $f99]) # # there are also 'singleton' groups, with one member. # for instance, the 'source' feature is in a singleton group; # the same with others such as 'misc_feature' my @groups = (); # ------------- # -------------------- # we hope that the genbank record allows us to group by some grouping # tag. # for instance, most of the time a gene model can be grouped using # the gene tag - that is where you see # /gene="foo" # in a genbank record # -------------------- # keep an index of groups by their # grouping tag my %group_by_tag = (); # iterate through all features, putting them into groups foreach my $sf (@flat_seq_features) { if (!$sf->has_tag($group_tag)) { # SINGLETON # this is an ungroupable feature; # add it to a group of its own push(@groups, [$sf]); } else { # NON-SINGLETON my @group_tagvals = $sf->get_tag_values($group_tag); if (@group_tagvals > 1) { # sanity check: # currently something can only belong to one group $self->problem(2, ">1 value for /$group_tag: @group_tagvals\n". "At this time this module is not equipped to handle this adequately", $sf); } # get value of group tag my $gtv = shift @group_tagvals; $gtv || $self->throw("Empty /$group_tag vals not allowed!"); # is this a new group? my $group = $group_by_tag{$gtv}; if ($group) { # this group has been encountered before - add current # sf to the end of the group push(@$group, $sf); } else { # new group; add to index and create new group $group = [$sf]; # currently one member; probably more to come $group_by_tag{$gtv} = $group; push(@groups, $group); } } } # as well as having the same group_tag, a group should be spatially # connected. if not, then the group should be split into subgroups. # this turns out to be necessary in the case of multicopy genes. # the standard way to represent these is as spatially disconnected # gene models (usually a 'gene' feature and some kind of RNA feature) # with the same group tag; the code below will split these into # seperate groups, one per copy. @groups = map { $self->_split_group_if_disconnected($_) } @groups; # remove any duplicates; most of the time the method below has # no effect. there are some unusual genbank records for which # duplicate removal is necessary. see the comments in the # _remove_duplicates_from_group() method if you want to know # the ugly details foreach my $group (@groups) { $self->_remove_duplicates_from_group($group); } # - # PSEUDOGENES, PSEUDOEXONS AND PSEUDOINTRONS # these are indicated with the /pseudo tag # these are mapped to a different type; they should NOT # be treated as normal genes foreach my $sf (@all_seq_features) { if ($sf->has_tag('pseudo')) { my $type = $sf->primary_tag; # SO type is typically the same as the normal # type but preceeded by "pseudo" if ($type eq 'misc_RNA' || $type eq 'mRNA') { # dgg: see TypeMapper; both pseudo mRNA,misc_RNA should be pseudogenic_transcript $sf->primary_tag("pseudotranscript"); } else { $sf->primary_tag("pseudo$type"); } } } # now some of the post-processing that follows which applies to # genes will NOT be applied to pseudogenes; this is deliberate # for example, gene models are normalised to be gene-transcript-exon # for pseudogenes we leave them as pseudogene-pseudoexon # --- MAGIC --- my $need_to_infer_exons = 0; my $need_to_infer_mRNAs = 0; my @removed_exons = (); if ($use_magic) { if (defined($structure_type)) { $self->throw("Can't combine use_magic AND setting structure_type"); } my $n_introns = scalar(grep {$_->primary_tag eq 'exon'} @flat_seq_features); my $n_exons = scalar(grep {$_->primary_tag eq 'exon'} @flat_seq_features); my $n_mrnas = scalar(grep {$_->primary_tag eq 'mRNA'} @flat_seq_features); my $n_mrnas_attached_to_gene = scalar(grep {$_->primary_tag eq 'mRNA' && $_->has_tag($group_tag)} @flat_seq_features); my $n_cdss = scalar(grep {$_->primary_tag eq 'CDS'} @flat_seq_features); my $n_rnas = scalar(grep {$_->primary_tag =~ /RNA/} @flat_seq_features); # Are there any CDS features in the record? if ($n_cdss > 0) { # YES # - a pc gene model should contain at the least a CDS # Are there any mRNA features in the record? if ($n_mrnas == 0) { # NO mRNAs: # looks like structure_type == 1 $structure_type = 1; $need_to_infer_mRNAs = 1; } elsif ($n_mrnas_attached_to_gene == 0) { # $n_mrnas > 0 # $n_mrnas_attached_to_gene = 0 # # The entries _do_ contain mRNA features, # but none of them are part of a group/gene, i.e. they # are 'floating' # this is an annoying weird file that has some floating # mRNA features; # eg ftp.ncbi.nih.gov/genomes/Schizosaccharomyces_pombe/ if ($self->verbose) { my @floating_mrnas = grep {$_->primary_tag eq 'mRNA' && !$_->has_tag($group_tag)} @flat_seq_features; printf STDERR "Unattached mRNAs:\n"; foreach my $mrna (@floating_mrnas) { $self->_write_sf_detail($mrna); } printf STDERR "Don't know how to deal with these; filter at source?\n"; } foreach (@flat_seq_features) { if ($_->primary_tag eq 'mRNA') { # what should we do?? # I think for pombe we just have to filter # out bogus mRNAs prior to starting } } # looks like structure_type == 2 $structure_type = 2; $need_to_infer_mRNAs = 1; } else { } # we always infer exons in magic mode $need_to_infer_exons = 1; } else { # this doesn't seem to be any kind of protein coding gene model if ( $n_rnas > 0 ) { $need_to_infer_exons = 1; } } $need_to_infer_exons = 0 if $noinfer; #NML if ($need_to_infer_exons) { # remove exons and introns from group - # we will infer exons later, and we # can always infer introns from exons foreach my $group (@groups) { @$group = grep { my $type = $_->primary_tag(); if ($type eq 'exon') { # keep track of all removed exons, # so we can do a sanity check later push(@removed_exons, $_); } $type ne 'exon' && $type ne 'intron' } @$group; } # get rid of any groups that have zero members @groups = grep {scalar(@$_)} @groups; } } # --- END OF MAGIC --- # LOGICAL ASSERTION if (grep {!scalar(@$_)} @groups) { $self->throw("ASSERTION ERROR: empty group"); } # LOGGING if ($self->verbose > 0) { printf STDERR "GROUPS:\n"; foreach my $group (@groups) { $self->_write_group($group, $group_tag); } } # - # --------- FINISHED GROUPING ------------- # TYPE CONTAINMENT HIERARCHY (aka partonomy) # set the containment hierarchy if desired # see docs for structure_type() method if ($structure_type) { if ($structure_type == 1) { $self->partonomy( {CDS => 'gene', exon => 'CDS', intron => 'CDS', } ); } else { $self->throw("structure_type $structure_type is currently unknown"); } } # see if we have an obvious resolver_tag if ($use_magic) { foreach my $sf (@all_seq_features) { if ($sf->has_tag('derived_from')) { $resolver_tag = 'derived_from'; } } } if ($use_magic) { # point all feature types without a container type to the root type. # # for example, if we have an unanticipated feature_type, say # 'aberration', this should by default point to the parent 'gene' foreach my $group (@groups) { my @sfs = @$group; if (@sfs > 1) { foreach my $sf (@sfs) { my $type = $sf->primary_tag; next if $type eq 'gene'; my $container_type = $self->get_container_type($type); if (!$container_type) { $self->partonomy->{$type} = 'gene'; } } } } } # we have done the first part of the unflattening. # we now have a list of groups; each group is a list of seqfeatures. # the actual group itself is flat; we may want to unflatten this further; # for instance, a gene model can contain multiple mRNAs and CDSs. We may want # to link the correct mRNA to the correct CDS via the bioperl sub_SeqFeature tree. # # what we would end up with would be # gene1 # mRNA-a # CDS-a # mRNA-b # CDS-b my @top_sfs = $self->unflatten_groups(-groups=>\@groups, -resolver_method=>$resolver_method, -resolver_tag=>$resolver_tag); # restore settings $self->partonomy($old_partonomy); # restore settings $self->structure_type($old_structure_type); # modify the original Seq object - the top seqfeatures are now # the top features from each group $seq->remove_SeqFeatures; $seq->add_SeqFeature($_) foreach @top_sfs; # --------- FINISHED UNFLATTENING ------------- # lets see if there are any post-unflattening tasks we need to do # INFERRING mRNAs if ($need_to_infer_mRNAs) { if ($self->verbose > 0) { printf STDERR "** INFERRING mRNA from CDS\n"; } $self->infer_mRNA_from_CDS(-seq=>$seq, -noinfer=>$noinfer); } # INFERRING exons if ($need_to_infer_exons) { # infer exons, one group/gene at a time foreach my $sf (@top_sfs) { my @sub_sfs = ($sf, $sf->get_all_SeqFeatures); $self->feature_from_splitloc(-features=>\@sub_sfs); } # some exons are stated explicitly; ie there is an "exon" feature # most exons are inferred; ie there is a "mRNA" feature with # split locations # # if there were exons explicitly stated in the entry, we need to # do two things: # # make sure these exons are consistent with the inferred exons # (you never know) # # transfer annotation (tag-vals) from the explicit exon to the # new inferred exon if (@removed_exons) { my @allfeats = $seq->get_all_SeqFeatures; # find all the inferred exons that are children of mRNA my @mrnas = grep {$_->primary_tag eq 'mRNA'} @allfeats; my @exons = grep {$_->primary_tag eq 'exon'} map {$_->get_SeqFeatures} @mrnas; my %exon_h = (); # index of exons by location; # there CAN be >1 exon at a location; we can represent these redundantly # (ie as a tree, not a graph) push(@{$exon_h{$self->_locstr($_)}}, $_) foreach @exons; my @problems = (); # list of problems; # each problem is a # [$severity, $description] pair my $problem = ''; my ($n_exons, $n_removed_exons) = (scalar(keys %exon_h), scalar(@removed_exons)); foreach my $removed_exon (@removed_exons) { my $locstr = $self->_locstr($removed_exon); my $inferred_exons = $exon_h{$locstr}; delete $exon_h{$locstr}; if ($inferred_exons) { my %exons_done = (); foreach my $exon (@$inferred_exons) { # make sure we don't move stuff twice next if $exons_done{$exon}; $exons_done{$exon} = 1; # we need to tranfer any tag-values from the explicit # exon to the implicit exon foreach my $tag ($removed_exon->get_all_tags) { my @vals = $removed_exon->get_tag_values($tag); if (!$exon->can("add_tag_value")) { # I'm puzzled as to what should be done here; # SeqFeatureIs are not necessarily mutable, # but we know that in practice the implementing # class is mutable $self->throw("The SeqFeature object does not ". "implement add_tag_value()"); } $exon->add_tag_value($tag, @vals); } } } else { # no exons inferred at $locstr push(@problems, [1, "there is a conflict with exons; there was an explicitly ". "stated exon with location $locstr, yet I cannot generate ". "this exon from the supplied mRNA locations\n"]); } } # do we have any inferred exons left over, that were not # covered in the explicit exons? if (keys %exon_h) { # TODO - we ignore this problem for now push(@problems, [1, sprintf("There are some inferred exons that are not in the ". "explicit exon list; they are the exons at locations:\n". join("\n", keys %exon_h)."\n")]); } # report any problems if (@problems) { my $thresh = $self->error_threshold; my @bad_problems = grep {$_->[0] > $thresh} @problems; if (@bad_problems) { printf STDERR "PROBLEM:\n"; $self->_write_hier(\@top_sfs); # TODO - allow more fine grained control over this $self->{_problems_reported} = 1; $self->throw(join("\n", map {"@$_"} @bad_problems)); } $self->problem(@$_) foreach @problems; } } } # --- end of inferring exons -- # return new top level features; this can also # be retrieved via # $seq->get_SeqFeatures(); # return @top_sfs; return $seq->get_SeqFeatures; } # _split_group_if_disconnected([@sfs]) # # as well as having the same group_tag, a group should be spatially # connected. if not, then the group should be split into subgroups. # this turns out to be necessary in the case of multicopy genes. # the standard way to represent these is as spatially disconnected # gene models (usually a 'gene' feature and some kind of RNA feature) # with the same group tag; the code below will split these into # seperate groups, one per copy. sub _split_group_if_disconnected { my $self = shift; my $group = shift; my @sfs = @$group; my @ranges = Bio::Range->disconnected_ranges(@sfs); my @groups; if (@ranges == 0) { $self->throw("ASSERTION ERROR"); } elsif (@ranges == 1) { # no need to split the group @groups = ($group); } else { # @ranges > 1 # split the group into disconnected ranges if ($self->verbose > 0) { printf STDERR "GROUP PRE-SPLIT:\n"; $self->_write_group($group, $self->group_tag); } @groups = map { my $range = $_; [grep { $_->intersection($range); } @sfs] } @ranges; if ($self->verbose > 0) { printf STDERR "SPLIT GROUPS:\n"; $self->_write_group($_, $self->group_tag) foreach @groups; } } return @groups; } sub _remove_duplicates_from_group { my $self = shift; my $group = shift; # ::: WEIRD BOUNDARY CASE CODE ::: # for some reason, there are some gb records with two gene # features for one gene; for example, see ATF14F8.gbk # in the t/data directory # # in this case, we get rid of one of the genes my @genes = grep {$_->primary_tag eq 'gene'} @$group; if (@genes > 1) { # OK, if we look at ATF14F8.gbk we see that some genes # just exist as a single location, some exist as a multisplit location; # # eg # gene 16790..26395 # /gene="F14F8_60" # ... # gene complement(join(16790..19855,20136..20912,21378..21497, # 21654..21876,22204..22400,22527..23158,23335..23448, # 23538..23938,24175..24536,24604..24715,24889..24984, # 25114..25171,25257..25329,25544..25589,25900..26018, # 26300..26395)) # /gene="F14F8_60" # the former is the 'standard' way of representing the gene in genbank; # the latter is redundant with the CDS entry. So we shall get rid of # the latter with the following filter if ($self->verbose > 0) { printf STDERR "REMOVING DUPLICATES:\n"; } @genes = grep { my $loc = $_->location; if ($loc->isa("Bio::Location::SplitLocationI")) { my @locs = $loc->each_Location; if (@locs > 1) { 0; } else { 1; } } else { 1; } } @genes; if (@genes > 1) { # OK, that didn't work. Our only resort is to just pick one at random @genes = ($genes[0]); } if (@genes) { @genes == 1 || $self->throw("ASSERTION ERROR"); @$group = ($genes[0], grep {$_->primary_tag ne 'gene'} @$group); } } # its a dirty job but someone's gotta do it return; } =head2 unflatten_groups Title : unflatten_groups Usage : Function: iterates over groups, calling unflatten_group() [see below] Example : Returns : list of Bio::SeqFeatureI objects that are holders Args : see below Arguments -groups: list of list references; inner list is of Bio::SeqFeatureI objects e.g. ( [$sf1], [$sf2, $sf3, $sf4], [$sf5, ...], ...) -resolver_method: a CODE reference see the documentation above for an example of a subroutine that can be used to resolve hierarchies within groups. this is optional - a default subroutine will be used NOTE: You should not need to call this method, unless you want fine grained control over how the unflattening process. =cut sub unflatten_groups{ my ($self,@args) = @_; my($groups, $resolver_method, $resolver_tag) = $self->_rearrange([qw(GROUPS RESOLVER_METHOD RESOLVER_TAG )], @args); # this is just a simple wrapper for unflatten_group() return map { $self->unflatten_group(-group=>$_, -resolver_method=>$resolver_method, -resolver_tag=>$resolver_tag) } @$groups; } =head2 unflatten_group Title : unflatten_group Usage : Function: nests a group of features into a feature containment hierarchy Example : Returns : Bio::SeqFeatureI objects that holds other features Args : see below Arguments -group: reference to list of Bio::SeqFeatureI objects -resolver_method: a CODE reference see the documentation above for an example of a subroutine that can be used to resolve hierarchies within groups this is optional - a default subroutine will be used NOTE: You should not need to call this method, unless you want fine grained control over how the unflattening process. =cut sub unflatten_group{ my ($self,@args) = @_; my($group, $resolver_method, $resolver_tag) = $self->_rearrange([qw(GROUP RESOLVER_METHOD RESOLVER_TAG )], @args); if ($self->verbose > 0) { printf STDERR "UNFLATTENING GROUP:\n"; $self->_write_group($group, $self->group_tag); } my @sfs = @$group; # we can safely ignore singletons (e.g. [source]) return $sfs[0] if @sfs == 1; my $partonomy = $self->partonomy; # $resolver_method is a reference to a SUB that will resolve # ambiguous parent/child containment; for example, determining # which mRNAs go with which CDSs $resolver_method = $resolver_method || \&_resolve_container_for_sf; # TAG BASED RESOLVING OF HIERARCHIES # # if the user specifies $resolver_tag, then we use this tag # to pair up ambiguous parents and children; # # for example, the CDS feature may have a resolver tag of /derives_from # which is a 'foreign key' into the /label tag of the mRNA feature # # this kind of tag-based resolution is possible for a certain subset # of genbank records # # if no resolver tag is specified, we revert to the normal # resolver_method if ($resolver_tag) { my $backup_resolver_method = $resolver_method; # closure: $resolver_tag is remembered by this sub my $sub = sub { my ($self, $sf, @possible_container_sfs) = @_; my @container_sfs = (); if ($sf->has_tag($resolver_tag)) { my ($resolver_tagval) = $sf->get_tag_values($resolver_tag); # if a feature has a resolver_tag (e.g. /derives_from) # this specifies the /product, /symbol or /label for the # parent feature @container_sfs = grep { my $match = 0; $self->_write_sf($_) if $self->verbose > 0; foreach my $tag (qw(product symbol label)) { if ($_->has_tag($tag)) { my @vals = $_->get_tag_values($tag); if (grep {$_ eq $resolver_tagval} @vals) { $match = 1; last; } } } $match; } @possible_container_sfs; } else { return $backup_resolver_method->($sf, @possible_container_sfs); } return map {$_=>0} @container_sfs; }; $resolver_method = $sub; } else { # CONDITION: $resolver_tag is NOT set $self->throw("assertion error") if $resolver_tag; } # we have now set $resolver_method to a subroutine for # disambiguatimng parent/child relationships. we will # now build the whole containment hierarchy for this group # FIND TOP/ROOT SEQFEATURES # # find all the features for which there is no # containing feature type (eg genes) my @top_sfs = grep { !$self->get_container_type($_->primary_tag); } @sfs; # CONDITION: there must be at most one root if (@top_sfs > 1) { $self->_write_group($group, $self->group_tag); printf STDERR "TOP SFS:\n"; $self->_write_sf($_) foreach @top_sfs; $self->throw("multiple top-sfs in group"); } my $top_sf = $top_sfs[0]; # CREATE INDEX OF SEQFEATURES BY TYPE my %sfs_by_type = (); foreach my $sf (@sfs) { push(@{$sfs_by_type{$sf->primary_tag}}, $sf); } # containment index; keyed by child; lookup parent # note: this index uses the stringified object reference of # the object as a surrogate lookup key my %container = (); # child -> parent # ALGORITHM: build containment graph # # find all possible containers for each SF; # for instance, for a CDS, the possible containers are all # the mRNAs in the same group. For a mRNA, the possible # containers are any SFs of type 'gene' (should only be 1). # (these container-type mappings can be overridden) # # contention is resolved by checking coordinates of splice sites # (this is the default, but can be overridden) # # most of the time, there is no problem identifying a unique # parent for every child; this can be ambiguous when constructing # CDS to mRNA relationships with lots of alternate splicing # # a hash of child->parent relationships is constructed (%container) # any mappings that need further resolution (eg CDS to mRNA) are # placed in %unresolved # %unresolved index # (keyed by stringified object reference of child seqfeature) my %unresolved = (); # child -> [parent,score] to be resolved # index of seqfeatures by their stringified object reference; # this is essentially a way of 'reviving' an object from its stringified # reference # (see NOTE ON USING OBJECTS AS KEYS IN HASHES, below) my %idxsf = map {$_=>$_} @sfs; foreach my $sf (@sfs) { my $type = $sf->primary_tag; # container type (e.g. the container type for CDS is usually mRNA) my $container_type = $self->get_container_type($type); if ($container_type) { my @possible_container_sfs = @{$sfs_by_type{$container_type} || []}; # we now have a list of possible containers # (eg for a CDS in an alternately spliced gene, this # would be a list of all the mRNAs for this gene) if (!@possible_container_sfs) { # root of hierarchy } else { if (@possible_container_sfs == 1) { # this is the easy situation, whereby the containment # hierarchy is unambiguous. this will probably be the # case if the genbank record has no alternate splicing # within it # ONE OPTION ONLY - resolved! $container{$sf} = $possible_container_sfs[0]; } else { # MULTIPLE CONTAINER CHOICES $self->throw("ASSERTION ERROR") unless @possible_container_sfs > 1; # push this onto the %unresolved graph, and deal with it # later # for now we hardcode things such that the only type # with ambiguous parents is a CDS; if this is violated, # it has a weak problem class of '1' so the API user # can easily set things to ignore these if ($sf->primary_tag ne 'CDS') { $self->problem(1, "multiple container choice for non-CDS; ". "CDS to mRNA should be the only ". "relationships requiring resolving", $sf); } # previously we set the SUB $resolver_method $self->throw("ASSERTION ERROR") unless $resolver_method; # $resolver_method will assign scores to # parent/child combinations; later on we # will use these scores to find the optimal # parent/child pairings # the default $resolver_method uses splice sites to # score possible parent/child matches my %container_sfh = $resolver_method->($self, $sf, @possible_container_sfs); if (!%container_sfh) { $self->problem(2, "no containers possible for SeqFeature of ". "type: $type; this SF is being placed at ". "root level", $sf); # RESOLVED! (sort of - placed at root/gene level) $container{$sf} = $top_sf; # this sort of thing happens if the record is # badly messed up and there is absolutely no indication # of where to put the CDS. Perhaps we should just # place it with a random mRNA? } foreach my $jsf (keys %container_sfh) { # add [score, parent] pairs to the %unresolved # lookup table/graph push(@{$unresolved{$sf}}, [$idxsf{$jsf}, $container_sfh{$jsf} || 0]); } } } } else { # CONDITION: # not container type for $sf->primary_tag # CONDITION: # $sf must be a root/top node (eg gene) } } if (0) { # CODE CURRENTLY DISABLED # we require a 1:1 mapping between mRNAs and CDSs; # create artificial duplicates if we can't do this... if (%unresolved) { my %childh = map {$_=>1} keys %unresolved; my %parenth = map {$_->[0]=>1} map {@$_} values %unresolved; if ($self->verbose > 0) { printf STDERR "MATCHING %d CHILDREN TO %d PARENTS\n", scalar(keys %childh), scalar(keys %parenth); } # 99.99% of the time in genbank genomic record of structure type 0, we # see one CDS for every mRNA; one exception is the S Pombe # genome, which is all CDS, bar a few spurious mRNAs; we have to # filter out the spurious mRNAs in this case # # another strange case is in the mouse genome, NT_078847.1 # for Pcdh13 you will notice there is 4 mRNAs and 5 CDSs. # most unusual! # I'm at a loss for a really clever thing to do here. I think the # best thing is to create duplicate features to preserve the 1:1 mapping # my $suffix_id = 1; # while (keys %childh > keys %parenth) { # # } } } # DEBUGGING CODE if ($self->verbose > 0 && scalar(keys %unresolved)) { printf STDERR "UNRESOLVED PAIRS:\n"; foreach my $childsf (keys %unresolved) { my @poss = @{$unresolved{$childsf}}; foreach my $p (@poss) { my $parentsf = $p->[0]; $childsf = $idxsf{$childsf}; my @clabels = ($childsf->get_tagset_values(qw(protein_id label product)), "?"); my @plabels = ($parentsf->get_tagset_values(qw(transcript_id label product)), "?"); printf STDERR (" PAIR: $clabels[0] => $plabels[0] (of %d)\n", scalar(@poss)); } } } # -- end of verbose # Now we have to fully resolve the containment hierarchy; remember, # the graph %container has the fully resolved child->parent links; # # the graph %unresolved is keyed by children missing parents; we # need to put all these orphans in the %container graph # # we do this using the scores in %unresolved, with the # find_best_matches() algorithm my $unresolved_problem_reported = 0; if (%unresolved) { my $new_pairs = $self->find_best_matches(\%unresolved, []); if (!$new_pairs) { my ($g) = $sfs[0]->get_tagset_values($self->group_tag || 'gene'); $self->problem(2, "Could not resolve hierarchy for $g"); $new_pairs = []; $unresolved_problem_reported = 1; } foreach my $pair (@$new_pairs) { if ($self->verbose > 0) { printf STDERR " resolved pair @$pair\n"; } $container{$pair->[0]} = $pair->[1]; delete $unresolved{$pair->[0]}; } } # CONDITION: containment hierarchy resolved if (%unresolved) { $self->throw("UNRESOLVED: %unresolved") unless $unresolved_problem_reported; } # make nested SeqFeature hierarchy from @containment_pairs # ie put child SeqFeatures into parent SeqFeatures my @top = (); foreach my $sf (@sfs) { my $container_sf = $container{$sf}; if ($container_sf) { # make $sf nested inside $container_sf # first check if the container spatially contains the containee if ($container_sf->contains($sf)) { # add containee $container_sf->add_SeqFeature($sf); } else { # weird case - the container does NOT spatially # contain the containee; # we expand and throw a warning # # for an example of this see ZFP91-CNTF dicistronic gene # in NCBI chrom 11 build 34.3 $self->problem(1, "Container feature does not spatially contain ". "subfeature. Perhaps this is a dicistronic gene? ". "I am expanding the parent feature", $container_sf, $sf); $container_sf->add_SeqFeature($sf, 'EXPAND'); } } else { push(@top, $sf); } } return @top; } # -- end of unflatten_group # ------- # A NOTE ON USING OBJECTS AS KEYS IN HASHES (stringified objects) # # Often we with to use seqfeatures as keys in a hashtable; because seqfeatures # in bioperl have no unique ID, we use a surrogate ID in the form of the # stringified object references - this is just what you get if you say # # print "$sf\n"; # # this is guaranteed to be unique (within a particular perl execution) # # often we want to 'revive' the objects used as keys in a hash - once the # objects are used as keys, remember it is the *strings* used as keys and # not the object itself, so the object needs to be revived using another # hashtable that looks like this # # %sfidx = map { $_ => $_ } @sfs # # ------- # recursively finds the best set of pairings from a matrix of possible pairings # # tries to make sure nothing is unpaired # # given a matrix of POSSIBLE matches # (matrix expressed as hash/lookup; keyed by child object; val = [parent, score] # # sub find_best_matches { my $self = shift; my $matrix = shift; my $pairs = shift; # [child,parent] pairs already selected my $verbose = $self->verbose; #################################print "I"; if ($verbose > 0) { printf STDERR "find_best_matches: (/%d)\n", scalar(@$pairs); } my %selected_children = map {($_->[0]=>1)} @$pairs; my %selected_parents = map {($_->[1]=>1)} @$pairs; # make a copy of the matrix with the portions still to be # resolved my %unresolved_parents = (); my %unresolved = map { if ($verbose > 0) { printf STDERR " $_ : %s\n", join("; ", map {"[@$_]"} @{$matrix->{$_}}); } if ($selected_children{$_}) { (); } else { my @parents = grep { !$selected_parents{$_->[0]} } @{$matrix->{$_}}; $unresolved_parents{$_} = 1 foreach @parents; # new parents ($_ => [@parents]); } } keys %$matrix; my @I = keys %unresolved; return $pairs if !scalar(keys %unresolved_parents); # NECESSARY CONDITION: # all possible parents have a child match return $pairs if !scalar(@I); # NECESSARY CONDITION: # all possible children have a parent match # give those with fewest choices highest priority @I = sort { # n possible parents scalar(@{$unresolved{$a}}) <=> scalar(@{$unresolved{$b}}) ; } @I; my $csf = shift @I; my @J = @{$unresolved{$csf}}; # array of [parent, score] # sort by score, highest first @J = sort { $b->[1] <=> $a->[1] } @J; # select pair(s) from remaining matrix of possible pairs # by iterating through possible parents my $successful_pairs; foreach my $j (@J) { my ($psf, $score) = @$j; # would selecting $csf, $psf as a pair # remove all choices from another? my $bad = 0; foreach my $sf (@I) { if (!grep {$_->[0] ne $psf} @{$unresolved{$sf}}) { # $psf was the only parent choice for $sf $bad = 1; last; } } if (!$bad) { my $pair = [$csf, $psf]; my $new_pairs = [@$pairs, $pair]; my $set = $self->find_best_matches($matrix, $new_pairs); if ($set) { $successful_pairs = $set; last; } } } # success return $successful_pairs if $successful_pairs; # fail return 0; } # ---------------------------------------------- # writes a group to stdout # # mostly for logging/debugging # ---------------------------------------------- sub _write_group { my $self = shift; my $group = shift; my $group_tag = shift || 'gene'; my $f = $group->[0]; my $label = '?'; if ($f->has_tag($group_tag)) { ($label) = $f->get_tag_values($group_tag); } if( $self->verbose > 0 ) { printf STDERR (" GROUP [%s]:%s\n", $label, join(' ', map { $_->primary_tag } @$group)); } } sub _write_sf { my $self = shift; my $sf = shift; printf STDERR "TYPE:%s\n", $sf->primary_tag; return; } sub _write_sf_detail { my $self = shift; my $sf = shift; printf STDERR "TYPE:%s\n", $sf->primary_tag; my @locs = $sf->location->each_Location; printf STDERR " %s,%s [%s]\n", $_->start, $_->end, $_->strand foreach @locs; return; } sub _write_hier { my $self = shift; my @sfs = @{shift || []}; my $indent = shift || 0; if( $self->verbose > 0 ) { foreach my $sf (@sfs) { my $label = '?'; if ($sf->has_tag('product')) { ($label) = $sf->get_tag_values('product'); } printf STDERR "%s%s $label\n", ' ' x $indent, $sf->primary_tag; my @sub_sfs = $sf->sub_SeqFeature; $self->_write_hier(\@sub_sfs, $indent+1); } } } # ----------------------------------------------- # # returns all possible containers for an SF based # on splice site coordinates; splice site coords # must be contained # ----------------------------------------------- sub _resolve_container_for_sf{ my ($self, $sf, @possible_container_sfs) = @_; my @coords = $self->_get_splice_coords_for_sf($sf); my $start = $sf->start; my $end = $sf->end; my $splice_uniq_str = "@coords"; my @sf_score_pairs = (); # a CDS is contained by a mRNA if the locations of the splice # coordinates are identical foreach (@possible_container_sfs) { my @container_coords = $self->_get_splice_coords_for_sf($_); my $inside = !$splice_uniq_str || index("@container_coords", $splice_uniq_str) > -1; if ($inside) { # the container cannot be smaller than the thing contained if ($_->start > $start || $_->end < $end) { $inside = 0; } } # SPECIAL CASE FOR /ribosomal_slippage # See: https://www.ncbi.nlm.nih.gov/collab/FT/ if (!$inside && $sf->has_tag('ribosomal_slippage')) { if ($self->verbose > 0) { printf STDERR " Checking for ribosomal_slippage\n"; } # TODO: rewrite this to match introns; # each slippage will be a "fake" small CDS exon my @transcript_splice_sites = @container_coords; my @cds_splice_sites = @coords; ##printf STDERR "xxTR SSs: @transcript_splice_sites :: %s\n", $_->get_tag_values('product'); ##printf STDERR "xxCD SSs: @cds_splice_sites :: %s\n\n", $sf->get_tag_values('product'); # find the the first splice site within the CDS while (scalar(@transcript_splice_sites) && $transcript_splice_sites[0] < $cds_splice_sites[0]) { shift @transcript_splice_sites; } ##print STDERR "TR SSs: @transcript_splice_sites\n"; ##print STDERR "CD SSs: @cds_splice_sites\n\n"; if (!(scalar(@transcript_splice_sites)) || $transcript_splice_sites[0] == $cds_splice_sites[0]) { # we will now try and align all splice remaining sites in the transcript and CDS; # any splice site that can't be aligned is assumed to be a ribosomal slippage my @slips = (); my $in_exon = 1; $inside = 1; # innocent until proven guilty.. while (@cds_splice_sites) { if (!@transcript_splice_sites) { # ribosomal slippage is after the last transcript splice site # Example: (NC_00007, isoform 3 of PEG10) # mRNA join(85682..85903,92646..99007) # mRNA join(85682..85903,92646..99007) # CDS join(85899..85903,92646..93825,93825..94994) # OR: None of the splice sites align; # may be a single CDS exon with one slippage inside it. # Example: (NC_00007, isoform 4 of PEG10) # mRNA join(85637..85892,92646..99007) # CDS join(92767..93825,93825..94994) # Yes, this code is repeated below... my $p1 = shift @cds_splice_sites; my $p2 = shift @cds_splice_sites; if ($self->verbose > 0) { printf STDERR " Found the ribosomal_slippage: $p1..$p2\n"; } push(@slips, ($p2-$p1)-1); } elsif ($cds_splice_sites[0] == $transcript_splice_sites[0]) { # splice sites align: this is not the slippage shift @cds_splice_sites; shift @transcript_splice_sites; ##print STDERR "MATCH\n"; } else { # mismatch if ($cds_splice_sites[0] < $transcript_splice_sites[0]) { # potential slippage # v # ---TTTTTTTTTT---- # ---CCCC--CCCC---- # ^ my $p1 = shift @cds_splice_sites; my $p2 = shift @cds_splice_sites; if ($self->verbose > 0) { printf STDERR " Found the ribosomal_slippage: $p1..$p2\n"; } push(@slips, ($p2-$p1)-1); } else { # not a potential ribosomal slippage $inside = 0; # guilty! ##print STDERR "FAIL\n"; last; } } } if ($inside) { # TODO: this is currently completely arbitrary. How many ribosomal slippages do we allow? # perhaps we need some mini-statistical model here....? if (@slips > 1) { $inside = 0; } # TODO: this is currently completely arbitrary. What is the maximum size of a ribosomal slippage? # perhaps we need some mini-statistical model here....? if (grep {$_ > 2} @slips) { $inside = 0; } } } else { # not a ribosomal_slippage, sorry } } if ($self->verbose > 0) { printf STDERR " Checking containment:[$inside] (@container_coords) IN ($splice_uniq_str)\n"; } if ($inside) { # SCORE: matching (ss-scoords+2)/(n-container-ss-coords+2) my $score = (scalar(@coords)+2)/(scalar(@container_coords)+2); push(@sf_score_pairs, $_=>$score); } } return @sf_score_pairs; } sub _get_splice_coords_for_sf { my $self = shift; my $sf = shift; my @locs = $sf->location; if ($sf->location->isa("Bio::Location::SplitLocationI")) { @locs = $sf->location->each_Location; } # get an ordered list of (start, end) positions # my @coords = # map { # $_->strand > 0 ? ($_->start, $_->end) : ($_->end, $_->start) # } @locs; my @coords = map {($_->start, $_->end)} @locs; # remove first and last leaving only splice sites pop @coords; shift @coords; return @coords; } =head2 feature_from_splitloc Title : feature_from_splitloc Usage : $unflattener->feature_from_splitloc(-features=>$sfs); Function: Example : Returns : Args : see below At this time all this method does is generate exons for mRNA or other RNA features Arguments: -feature: a Bio::SeqFeatureI object (that conforms to Bio::FeatureHolderI) -seq: a Bio::SeqI object that contains Bio::SeqFeatureI objects -features: an arrayref of Bio::SeqFeatureI object =cut sub feature_from_splitloc{ my ($self,@args) = @_; my($sf, $seq, $sfs) = $self->_rearrange([qw(FEATURE SEQ FEATURES )], @args); my @sfs = (@{$sfs || []}); push(@sfs, $sf) if $sf; if ($seq) { $seq->isa("Bio::SeqI") || $self->throw("$seq NOT A SeqI"); @sfs = $seq->get_all_SeqFeatures; } my @exons = grep {$_->primary_tag eq 'exon'} @sfs; if (@exons) { $self->problem(2, "There are already exons, so I will not infer exons"); } # index of features by type+location my %loc_h = (); # infer for every feature foreach my $sf (@sfs) { $sf->isa("Bio::SeqFeatureI") || $self->throw("$sf NOT A SeqFeatureI"); $sf->isa("Bio::FeatureHolderI") || $self->throw("$sf NOT A FeatureHolderI"); my $type = $sf->primary_tag; next unless $type eq 'mRNA' or $type =~ /RNA/; # an mRNA from genbank will have a discontinuous location, # with each sub-location being equivalent to an exon my @locs = $sf->location; if ($sf->location->isa("Bio::Location::SplitLocationI")) { @locs = $sf->location->each_Location; } if (!@locs) { use Data::Dumper; print Dumper $sf; $self->throw("ASSERTION ERROR: sf has no location objects"); } # make exons from locations my @subsfs = map { my $subsf = Bio::SeqFeature::Generic->new(-location=>$_, -primary_tag=>'exon'); ## Provide seq_id to new feature: $subsf->seq_id($sf->seq_id) if $sf->seq_id; $subsf->source_tag($sf->source_tag) if $sf->source_tag; ## Transfer /locus_tag and /gene tag values to inferred ## features. TODO: Perhaps? this should not be done ## indiscriminantly but rather by virtue of the setting ## of group_tag. foreach my $tag (grep /gene|locus_tag/, $sf->get_all_tags) { my @vals = $sf->get_tag_values($tag); $subsf->add_tag_value($tag, @vals); } my $locstr = 'exon::'.$self->_locstr($subsf); # re-use feature if type and location the same if ($loc_h{$locstr}) { $subsf = $loc_h{$locstr}; } else { $loc_h{$locstr} = $subsf; } $subsf; } @locs; # PARANOID CHECK $self->_check_order_is_consistent($sf->location->strand,@subsfs); #---- $sf->location(Bio::Location::Simple->new()); # we allow the exons to define the boundaries of the transcript $sf->add_SeqFeature($_, 'EXPAND') foreach @subsfs; if (!$sf->location->strand) { # correct weird bioperl bug in previous versions; # strand was not being set correctly $sf->location->strand($subsfs[0]->location->strand); } } return; } #sub merge_features_with_same_loc { # my ($self,@args) = @_; # my($sfs, $seq) = # $self->_rearrange([qw(FEATURES # SEQ # )], # @args); # my @sfs = (@$sfs); # if ($seq) { # $seq->isa("Bio::SeqI") || $self->throw("$seq NOT A SeqI"); # @sfs = $seq->get_all_SeqFeatures; # } # my %loc_h = (); # foreach my $sf (@sfs) { # my $type = $sf->primary_tag; # my $locstr = $self->_locstr($sf); ## $loc_h{$type.$locstr} # push(@{$exon_h{$self->_locstr($_)}}, $_) foreach @exons; # } #} =head2 infer_mRNA_from_CDS Title : infer_mRNA_from_CDS Usage : Function: Example : Returns : Args : given a "type 1" containment hierarchy gene CDS exon this will infer the uniform "type 0" containment hierarchy gene mRNA CDS exon all the children of the CDS will be moved to the mRNA a "type 2" containment hierarchy is mixed type "0" and "1" (for example, see ftp.ncbi.nih.gov/genomes/Schizosaccharomyces_pombe/) =cut sub infer_mRNA_from_CDS{ my ($self,@args) = @_; my($sf, $seq, $noinfer) = $self->_rearrange([qw(FEATURE SEQ NOINFER )], @args); my @sfs = ($sf); if ($seq) { $seq->isa("Bio::SeqI") || $self->throw("$seq NOT A SeqI"); @sfs = $seq->get_all_SeqFeatures; } foreach my $sf (@sfs) { $sf->isa("Bio::SeqFeatureI") || $self->throw("$sf NOT A SeqFeatureI"); $sf->isa("Bio::FeatureHolderI") || $self->throw("$sf NOT A FeatureHolderI"); if ($self->verbose > 0) { printf STDERR " Checking $sf %s\n", $sf->primary_tag; } if ($sf->primary_tag eq 'mRNA') { $self->problem(2, "Inferring mRNAs when there are already mRNAs present"); } my @cdsl = grep {$_->primary_tag eq 'CDS' } $sf->get_SeqFeatures; if (@cdsl) { my @children = grep {$_->primary_tag ne 'CDS'} $sf->get_SeqFeatures; my @mrnas = (); foreach my $cds (@cdsl) { if ($self->verbose > 0) { print " Inferring mRNA from CDS $cds\n"; } $self->_check_order_is_consistent($cds->location->strand,$cds->location->each_Location); my $loc = Bio::Location::Split->new; foreach my $cdsexonloc ($cds->location->each_Location) { my $subloc = Bio::Location::Simple->new(-start=>$cdsexonloc->start, -end=>$cdsexonloc->end, -strand=>$cdsexonloc->strand); $loc->add_sub_Location($subloc); } if ($noinfer) { push(@mrnas, $cds); } else { # share the same location my $mrna = Bio::SeqFeature::Generic->new(-location=>$loc, -primary_tag=>'mRNA'); ## Provide seq_id to new feature: $mrna->seq_id($cds->seq_id) if $cds->seq_id; $mrna->source_tag($cds->source_tag) if $cds->source_tag; $self->_check_order_is_consistent($mrna->location->strand,$mrna->location->each_Location); # make the mRNA hold the CDS; no EXPAND option, # the CDS cannot be wider than the mRNA $mrna->add_SeqFeature($cds); # mRNA steals children of CDS foreach my $subsf ($cds->get_SeqFeatures) { $mrna->add_SeqFeature($subsf); } $cds->remove_SeqFeatures; push(@mrnas, $mrna); } } # change gene/CDS to gene/mRNA $sf->remove_SeqFeatures; $sf->add_SeqFeature($_) foreach (@mrnas, @children); } } return; } =head2 remove_types Title : remove_types Usage : $unf->remove_types(-seq=>$seq, -types=>["mRNA"]); Function: Example : Returns : Args : removes features of a set type useful for pre-filtering a genbank record; eg to get rid of STSs also, there is no way to unflatten ftp.ncbi.nih.gov/genomes/Schizosaccharomyces_pombe/ UNLESS the bogus mRNAs in these records are removed (or changed to a different type) - they just confuse things too much =cut sub remove_types{ my ($self,@args) = @_; my($seq, $types) = $self->_rearrange([qw( SEQ TYPES )], @args); $seq->isa("Bio::SeqI") || $self->throw("$seq NOT A SeqI"); my @sfs = $seq->get_all_SeqFeatures; my %rh = map {$_=>1} @$types; @sfs = grep {!$rh{$_->primary_tag}} @sfs; $seq->remove_SeqFeatures; $seq->add_SeqFeature($_) foreach @sfs; return; } # _check_order_is_consistent($strand,$ranges) RETURNS BOOL # # note: the value of this test is moot - there are many valid, # if unusual cases where it would flag an anomaly. for example # transpliced genes such as mod(mdg4) in dmel on AE003744, and # the following spliced gene on NC_001284: # # mRNA complement(join(20571..20717,21692..22086,190740..190761, # 140724..141939,142769..142998)) # /gene="nad5" # /note="trans-splicing, RNA editing" # /db_xref="GeneID:814567" # # note how the exons are not in order # this will flag a level-3 warning, the user of this module # can ignore this and deal appropriately with the resulting # unordered exons sub _check_order_is_consistent { my $self = shift; my $parent_strand = shift; # this does nothing..? my @ranges = @_; return unless @ranges; my $rangestr = join(" ",map{sprintf("[%s,%s]",$_->start,$_->end)} @ranges); my $strand = $ranges[0]->strand; for (my $i=1; $i<@ranges;$i++) { if ($ranges[$i]->strand != $strand) { $self->problem(1,"inconsistent strands. Trans-spliced gene? Range: $rangestr"); return 1; # mixed ranges - autopass # some mRNAs have exons on both strands; for # example, the dmel mod(mdg4) gene which is # trans-spliced (in actual fact two mRNAs) } } my $pass = 1; for (my $i=1; $i<@ranges;$i++) { my $rangeP = $ranges[$i-1]; my $range = $ranges[$i]; if ($rangeP->start > $range->end) { if ($self->seq->is_circular) { # see for example NC_006578.gbk # we make exceptions for circular genomes here. # see Re: [Gmod-ajax] flatfile-to-json.pl error with GFF # 2010-07-26 } else { # failed - but still get one more chance.. $pass = 0; $self->problem(2,"Ranges not in correct order. Strange ensembl genbank entry? Range: $rangestr"); last; } } } if (!$pass) { # sometimes (eg ensembl flavour genbank files) # exons on reverse strand listed in reverse order # eg join(complement(R1),...,complement(Rn)) # where R1 > R2 for (my $i=1; $i<@ranges;$i++) { my $rangeP = $ranges[$i-1]; my $range = $ranges[$i]; if ($rangeP->end < $range->start) { $self->problem(3,"inconsistent order. Range: $rangestr"); return 0; } } } return 1; # pass } # PRIVATE METHOD: _locstr($sf) # # returns a location string for a feature; just the outer boundaries sub _locstr { my $self = shift; my $sf = shift; return sprintf("%d..%d", $sf->start, $sf->end); } sub iterate_containment_tree { my $self = shift; my $feature_holder = shift; my $sub = shift; $sub->($feature_holder); my @sfs = $feature_holder->get_SeqFeatures; $self->iterate_containment_tree($_) foreach @sfs; } sub find_best_pairs { my $matrix = shift; my $size = shift; my $i = shift || 0; for (my $j=0; $j < $size; $j++) { my $score = $matrix->[$i][$j]; if (!defined($score)) { next; } } } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO��������������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 15047� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/FTHelper.pm��������������������������������������������������������������000444��000766��000024�� 16650�13155576320� 17243� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::FTHelper # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::FTHelper - Helper class for EMBL/Genbank feature tables =head1 SYNOPSIS Used by Bio::SeqIO::EMBL,Bio::SeqIO::genbank, and Bio::SeqIO::swiss to help process the Feature Table =head1 DESCRIPTION Represents one particular Feature with the following fields key - the key of the feature loc - the location string of the feature <other fields> - other fields =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 CONTRIBUTORS Jason Stajich jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::FTHelper; use strict; use Bio::SeqFeature::Generic; use Bio::Location::Simple; use Bio::Location::Fuzzy; use Bio::Location::Split; use base qw(Bio::Root::Root); sub new { my ($class, @args) = @_; # no chained new because we make lots and lots of these. my $self = {}; bless $self,$class; $self->{'_field'} = {}; return $self; } =head2 _generic_seqfeature Title : _generic_seqfeature Usage : $fthelper->_generic_seqfeature($annseq, "GenBank") Function: processes fthelper into a generic seqfeature Returns : TRUE on success and otherwise FALSE Args : The Bio::Factory::LocationFactoryI object to use for parsing location strings. The ID (e.g., display_id) of the sequence on which this feature is located, optionally a string indicating the source (GenBank/EMBL/SwissProt) =cut sub _generic_seqfeature { my ($fth, $locfac, $seqid, $source) = @_; my ($sf); # set a default if not specified if(! defined($source)) { $source = "EMBL/GenBank/SwissProt"; } # initialize feature object $sf = Bio::SeqFeature::Generic->direct_new(); # parse location; this may cause an exception, in which case we gently # recover and ignore this feature my $loc; eval { $loc = $locfac->from_string($fth->loc); }; if(! $loc) { $fth->warn("exception while parsing location line [" . $fth->loc . "] in reading $source, ignoring feature " . $fth->key() . " (seqid=" . $seqid . "): " . $@); return; } # set additional location attributes if($seqid && (! $loc->is_remote())) { $loc->seq_id($seqid); # propagates if it is a split location } # set attributes of feature $sf->location($loc); $sf->primary_tag($fth->key); $sf->source_tag($source); $sf->seq_id($seqid); foreach my $key ( keys %{$fth->field} ){ foreach my $value ( @{$fth->field->{$key}} ) { $sf->add_tag_value($key,$value); } } return $sf; } =head2 from_SeqFeature Title : from_SeqFeature Usage : @fthelperlist = Bio::SeqIO::FTHelper::from_SeqFeature($sf, $context_annseq); Function: constructor of fthelpers from SeqFeatures : : The additional annseq argument is to allow the building of FTHelper : lines relevant to particular sequences (ie, when features are spread over : enteries, knowing how to build this) Returns : an array of FThelpers Args : seq features =cut sub from_SeqFeature { my ($sf, $context_annseq) = @_; my @ret; # # If this object knows how to make FThelpers, then let it # - this allows us to store *really* weird objects that can write # themselves to the EMBL/GenBank... # if ( $sf->can("to_FTHelper") ) { return $sf->to_FTHelper($context_annseq); } my $fth = Bio::SeqIO::FTHelper->new(); my $key = $sf->primary_tag(); my $locstr = $sf->location->to_FTstring; # ES 25/06/01 Commented out this code, Jason to double check #The location FT string for all simple subseqfeatures is already #in the Split location FT string # going into sub features #foreach my $sub ( $sf->sub_SeqFeature() ) { #my @subfth = &Bio::SeqIO::FTHelper::from_SeqFeature($sub); #push(@ret, @subfth); #} $fth->loc($locstr); $fth->key($key); $fth->field->{'note'} = []; # the lines below take specific tags (e.g. /score=23 ) and re-enter them as # new tags like /note="score=25" - if the file is round-tripped this creates # duplicate values #$sf->source_tag && do { push(@{$fth->field->{'note'}},"source=" . $sf->source_tag ); }; #($sf->can('score') && $sf->score) && do { push(@{$fth->field->{'note'}}, # "score=" . $sf->score ); }; #($sf->can('frame') && $sf->frame) && do { push(@{$fth->field->{'note'}}, # "frame=" . $sf->frame ); }; #$sf->strand && do { push(@{$fth->field->{'note'}},"strand=" . $sf->strand ); }; foreach my $tag ( $sf->get_all_tags ) { # Tags which begin with underscores are considered # private, and are therefore not printed next if $tag =~ /^_/; if ( !defined $fth->field->{$tag} ) { $fth->field->{$tag} = []; } foreach my $val ( $sf->get_tag_values($tag) ) { push(@{$fth->field->{$tag}},$val); } } push(@ret, $fth); unless (@ret) { $context_annseq->throw("Problem in processing seqfeature $sf - no fthelpers. Error!"); } foreach my $ft (@ret) { if ( !$ft->isa('Bio::SeqIO::FTHelper') ) { $sf->throw("Problem in processing seqfeature $sf - made a $fth!"); } } return @ret; } =head2 key Title : key Usage : $obj->key($newval) Function: Example : Returns : value of key Args : newvalue (optional) =cut sub key { my ($obj, $value) = @_; if ( defined $value ) { $obj->{'key'} = $value; } return $obj->{'key'}; } =head2 loc Title : loc Usage : $obj->loc($newval) Function: Example : Returns : value of loc Args : newvalue (optional) =cut sub loc { my ($obj, $value) = @_; if ( defined $value ) { $obj->{'loc'} = $value; } return $obj->{'loc'}; } =head2 field Title : field Usage : Function: Example : Returns : Args : =cut sub field { my ($self) = @_; return $self->{'_field'}; } =head2 add_field Title : add_field Usage : Function: Example : Returns : Args : =cut sub add_field { my ($self, $key, $val) = @_; if ( !exists $self->field->{$key} ) { $self->field->{$key} = []; } push( @{$self->field->{$key}} , $val); } 1; ����������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/MultiFile.pm�������������������������������������������������������������000444��000766��000024�� 11534�13155576320� 17460� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::MultiFile # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::MultiFile - Treating a set of files as a single input stream =head1 SYNOPSIS my $seqin = Bio::SeqIO::MultiFile->new( -format => 'Fasta', -files => ['file1','file2'] ); while (my $seq = $seqin->next_seq) { # do something with $seq } =head1 DESCRIPTION Bio::SeqIO::MultiFile provides a simple way of bundling a whole set of identically formatted sequence input files as a single stream. File format is automatically determined by C<Bio::SeqIO>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::MultiFile; use strict; use base qw(Bio::SeqIO); # _initialize is where the heavy stuff will happen when new is called sub _initialize { my($self, @args) = @_; $self->SUPER::_initialize(@args); my ($file_array, $format) = $self->_rearrange([qw(FILES FORMAT)], @args); if( !defined $file_array || ! ref $file_array ) { $self->throw("Must have an array files for MultiFile"); } $self->{'_file_array'} = []; $self->_set_file(@$file_array); $self->format($format) if defined $format; if( $self->_load_file() == 0 ) { $self->throw("Unable to initialise the first file"); } } =head2 next_seq Title : next_seq Usage : Function: Example : Returns : Args : =cut sub next_seq{ my ($self, @args) = @_; my $seq = $self->_current_seqio->next_seq(); if( !defined $seq ) { if( $self->_load_file() == 0) { return; } else { return $self->next_seq(); } } else { return $seq; } } =head2 next_primary_seq Title : next_primary_seq Usage : Function: Example : Returns : Args : =cut sub next_primary_seq{ my ($self, @args) = @_; my $seq = $self->_current_seqio->next_primary_seq(); if( !defined $seq ) { if( $self->_load_file() == 0) { return; } else { return $self->next_primary_seq(); } } else { return $seq; } } =head2 _load_file Title : _load_file Usage : Function: Example : Returns : Args : =cut sub _load_file{ my ($self, @args) = @_; my $file = shift @{$self->{'_file_array'}}; if( !defined $file ) { return 0; } my $seqio; my $format = $self->format; if ($format) { $seqio = Bio::SeqIO->new( -file => $file, -format => $format ); } else { $seqio = Bio::SeqIO->new( -file => $file ); $self->format($seqio->format) if not $format; } # should throw an exception - but if not... if( !defined $seqio) { $self->throw("Could not build SeqIO object for $file!"); } $self->_current_seqio($seqio); return 1; } =head2 _set_file Title : _set_file Usage : Function: Example : Returns : Args : =cut sub _set_file{ my ($self, @files) = @_; push @{$self->{'_file_array'}}, @files; } =head2 _current_seqio Title : _current_seqio Usage : $obj->_current_seqio($newval) Function: Example : Returns : value of _current_seqio Args : newvalue (optional) =cut sub _current_seqio{ my ($obj, $value) = @_; if( defined $value) { $obj->{'_current_seqio'} = $value; } return $obj->{'_current_seqio'}; } # We overload the format() method of Bio::Root::IO by a simple get/set sub format{ my ($obj, $value) = @_; if( defined $value) { $obj->{'_format'} = $value; } return $obj->{'_format'}; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/abi.pm�������������������������������������������������������������������000444��000766��000024�� 11323�13155576320� 16315� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::abi # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Aaron Mackey <amackey@virginia.edu> # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::abi - abi trace sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from abi trace files. To optionally read the trace graph data (which can be used to draw chromatographs, for instance), set the optional '-get_trace_data' flag or the get_trace_data method to a value evaluating to TRUE. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Aaron Mackey Email: amackey@virginia.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::abi; use vars qw(@ISA $READ_AVAIL); use strict; use Bio::SeqIO; use Bio::Seq::SeqFactory; push @ISA, qw( Bio::SeqIO ); sub BEGIN { eval { require Bio::SeqIO::staden::read; }; if ($@) { $READ_AVAIL = 0; } else { push @ISA, "Bio::SeqIO::staden::read"; $READ_AVAIL = 1; } } sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); my ($get_trace) = $self->_rearrange([qw(get_trace_data)],@args); $get_trace && $self->get_trace_data(1); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::Quality')); } unless ($READ_AVAIL) { Bio::Root::Root->throw( -class => 'Bio::Root::SystemException', -text => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!" ); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq::Quality object Args : NONE =cut sub next_seq { my ($self) = @_; my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'abi'); # create the seq object my ($base_locs, $a_trace, $c_trace, $g_trace, $t_trace, $points, $max_height); if ($self->get_trace_data) { ($base_locs, $a_trace, $c_trace, $g_trace, $t_trace, $points, $max_height) = $self->read_trace_with_graph($self->_fh, 'abi'); } else { $base_locs = []; } # create the seq object $seq = $self->sequence_factory->create(-seq => $seq, -id => $id, -primary_id => $id, -desc => $desc, -alphabet => 'DNA', -qual => $qual, -trace => join (" ", @{$base_locs}), -trace_data => { a_trace => $a_trace, c_trace => $c_trace, g_trace => $g_trace, t_trace => $t_trace, max_height => $max_height, num_points => $points } ); return $seq; } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object =cut sub write_seq { my ($self,@seq) = @_; my $fh = $self->_fh; foreach my $seq (@seq) { $self->write_trace($fh, $seq, 'abi'); } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 get_trace_data Title : get_trace_data Usage : $stream->get_trace_data(1) Function: set boolean flag to retrieve the trace data (possibly for output) Returns : bool value, TRUE = retrieve trace data (default FALSE) Args : bool value =cut sub get_trace_data { my ($self, $val) = @_; $self->{_get_trace_data} = $val ? 1 : 0 if (defined $val); $self->{_get_trace_data}; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/ace.pm�������������������������������������������������������������������000444��000766��000024�� 12453�13155576320� 16317� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::ace # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by James Gilbert <jgrg@sanger.ac.uk> # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::ace - ace sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from ace file format. It only parses a DNA or Peptide objects contained in the ace file, producing PrimarySeq objects from them. All other objects in the files will be ignored. It doesn't attempt to parse any annotation attached to the containing Sequence or Protein objects, which would probably be impossible, since everyone's ACeDB schema can be different. It won't parse ace files containing Timestamps correctly either. This can easily be added if considered necessary. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - James Gilbert Email: jgrg@sanger.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' # Let the code begin... package Bio::SeqIO::ace; use strict; use Bio::Seq; use Bio::Seq::SeqFactory; use base qw(Bio::SeqIO); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::PrimarySeq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : NONE =cut { my %bio_mol_type = ( 'dna' => 'dna', 'peptide' => 'protein', ); sub next_seq { my( $self ) = @_; local $/ = ""; # Split input on blank lines my $fh = $self->_filehandle; my( $type, $id ); while (<$fh>) { if (($type, $id) = /^(DNA|Peptide)[\s:]+(.+?)\s*\n/si) { s/^.+$//m; # Remove first line s/\s+//g; # Remove whitespace last; } } # Return if there weren't any DNA or peptide objects return unless $type; # Choose the molecule type my $mol_type = $bio_mol_type{lc $type} or $self->throw("Can't get Bio::Seq molecule type for '$type'"); # Remove quotes from $id $id =~ s/^"|"$//g; # Un-escape forward slashes, double quotes, percent signs, # semi-colons, tabs, and backslashes (if you're mad enough # to have any of these as part of object names in your acedb # database). $id =~ s/\\([\/"%;\t\\])/$1/g; #" # Called as next_seq(), so give back a Bio::Seq return $self->sequence_factory->create( -seq => $_, -primary_id => $id, -display_id => $id, -alphabet => $mol_type, ); } } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object(s) =cut sub write_seq { my ($self, @seq) = @_; foreach my $seq (@seq) { $self->throw("Did not provide a valid Bio::PrimarySeqI object") unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI'); my $mol_type = $seq->alphabet; my $id = $seq->display_id; # Escape special charachers in id $id =~ s/([\/"%;\t\\])/\\$1/g; #" # Print header for DNA or Protein object if ($mol_type eq 'dna') { $self->_print( qq{\nSequence : "$id"\nDNA "$id"\n}, qq{\nDNA : "$id"\n}, ); } elsif ($mol_type eq 'protein') { $self->_print( qq{\nProtein : "$id"\nPeptide "$id"\n}, qq{\nPeptide : "$id"\n}, ); } else { $self->throw("Don't know how to produce ACeDB output for '$mol_type'"); } # Print the sequence my $str = $seq->seq; my( $formatted_seq ); while ($str =~ /(.{1,60})/g) { $formatted_seq .= "$1\n"; } $self->_print($formatted_seq, "\n"); } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/agave.pm�����������������������������������������������������������������000444��000766��000024�� 157075�13155576320� 16704� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module: Bio::SeqIO::agave # # AGAVE: Architecture for Genomic Annotation, Visualization and Exchange. # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code # # The original version of the module can be found here: # http://www.agavexml.org/ # # ### TODO: live link for this anymore? # The DTD for AGAVE XML was once located here (dead link): # http://www.lifecde.com/products/agave/schema/v2_3/agave.dtd # # =head1 NAME Bio::SeqIO::agave - AGAVE sequence output stream. =head1 SYNOPSIS It is probably best not to use this object directly, but rather go through the SeqIO handler system. Go: $in = Bio::SeqIO->new('-file' => "$file_in", '-format' => 'EMBL'); $out = Bio::SeqIO->new('-file' => ">$file_out", '-format' => 'AGAVE'); while (my $seq = $in->next_seq){ $out->write_seq($seq); } =head1 DESCRIPTION This object can transform Bio::Seq objects to agave xml file and vice-versa. I (Simon) coded up this module because I needed a parser to extract data from AGAVE xml to be utitlized by the GenQuire genome annotation system (See http://www.bioinformatics.org/Genquire). ***NOTE*** At the moment, not all of the tags are implemented. In general, I followed the output format for the XEMBL project http://www.ebi.ac.uk/xembl/ =cut =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Simon K. Chan Email: =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # =================== # Let the code begin... package Bio::SeqIO::agave; use strict; use IO::File; use Bio::SeqFeature::Generic; use Bio::Seq; use Bio::PrimarySeq; use Bio::Seq::SeqFactory; use Bio::Annotation::Reference; use Bio::Species; use XML::Writer; use Data::Dumper; use base qw(Bio::SeqIO); # ================================================================================== sub _initialize { my ($self,@args) = @_; $self->SUPER::_initialize(@args); # Run the constructor of the parent class. my %tmp = @args ; $self->{'file'} = $tmp{'-file'}; if ($self->{'file'} !~ /^>/) { $self->_process; # Parse the thing, but only if it is the input file (ie not # outputing agave file, but reading it). $self->{'parsed'} = 1; # Set the flag to let the code know that the agave xml file # has been parsed. } $self->{'seqs_stored'} = 0; } # ================================================================================== =head2 _process Title : _process Usage : $self->_process Function : Parses the agave xml file. Args : None. Returns : Nothing. Note : Method(s) that call(s) this method : _initialize Method(s) that this method calls : _process_sciobj FIRST/START sub. =cut sub _process { my ($self) = @_; while (1) { my $line = $self->_readline; next unless $line; next if $line =~ /^\s*$/; if ($line =~ /<\?xml version/o) { # do nothing } elsif ($line =~ /\<!DOCTYPE (\w+) SYSTEM "([\w\.]+)"\>/) { $self->throw("Error: This xml file is not in AGAVE format! DOCTYPE: $1 , SYSTEM: $2\n\n") if $1 ne 'sciobj' || $2 ne 'sciobj.dtd'; } elsif ($line =~ /<sciobj (.*)>/) { push @{$self->{'sciobj'}}, $self->_process_sciobj($1); } elsif ($line =~ /<\/sciobj>/) { last; # It is finished. } else { # throw an error message. The above conditions should # take care all of the possible options...? # $self->throw("Error: Do not recognize this AGAVE xml # line: $line\n\n"); } } # close while loop return; } # ================================================================================== =head2 _process_sciobj Title : _process_sciobj Usage : $self->_process_sciobj Function : Parses the data between the <sciobj></sciobj> tags. Args : The string that holds the attributes for <sciobj>. Returns : Data structure holding the values parsed between the <sciobj></sciobj> tags. Note : Method(s) that call(s) this method : _process Method(s) that this method calls : _helper_store_attribute_list , _process_contig =cut sub _process_sciobj { my ($self, $attribute_line) = @_; my $sciobj; $self->_helper_store_attribute_list($attribute_line, \$sciobj); my $line = $self->_readline; # Zero or more <contig> while ($line =~ /<contig\s?(.*?)\s?>/) { my $contig = $self->_process_contig(\$line, $1); push @{$sciobj->{'contig'}}, $contig; # print "line in _process_sciobj: $line\n"; # $line changes value within the subs called in this sub (_process_contig). } return $sciobj; } # ================================================================================== =head2 _process_contig Title : _process_contig Usage : $self->_process_contig Function : Parses the data between the <contig></contig> tags. Args : 2 scalars: - reference to a scalar holding the line to be parsed. - scalar holding the attributes for the <contig> tag to be parsed. Returns : Data structure holding the values parsed between the <contig></contig> tags. Note : Method(s) that call(s) this method : _process_sciobj Method(s) that this method calls : _helper_store_attribute_list, _one_tag , _process_fragment_order =cut sub _process_contig { my ($self, $line, $attribute_line) = @_; my $contig; $self->_helper_store_attribute_list($attribute_line, \$contig); $$line = $self->_readline; # One <db_id>: $self->_one_tag($line, \$contig, 'db_id'); # Zero or more <fragment_order> $self->_process_fragment_order($line, \$contig); return $contig; } # ================================================================================== =head2 _process_fragment_order Title : _process_fragment_order Usage : $self->_process_fragment_order Function : Parses the data between the <fragment_order></fragment_order> tags. Args : 2 scalars: - reference to a scalar holding the value of the line to be parsed. - reference to a data structure to store the <fragment_order> data. Returns : Nothing. Note : Method(s) that call(s) this method : _process_contig Method(s) that this method calls : _helper_store_attribute_list , _process_fragment_orientation =cut sub _process_fragment_order { my ($self, $line, $data_structure) = @_; # Because I'm passing a reference to a data structure, I don't need to return it # after values have been added. while ($$line =~ /<fragment_order\s?(.*?)\s?>/) { my $fragment_order; $self->_helper_store_attribute_list($1, \$fragment_order); # Store the attribute(s) for <fragment_order> into the # $fragment_order data structure. $$line = $self->_readline; # One or more <fragment_orientation> $self->_process_fragment_orientation($line, \$fragment_order); # Don't forget: $line is a reference to a scalar. push @{$$data_structure->{'fragment_order'}}, $fragment_order; # Store the data between <fragment_order></fragment_order> # in $$data_structure. } return; } # ================================================================================== =head2 _process_fragment_orientation Title : _process_fragment_orientation Usage : $self->_process_fragment_orientation Function : Parses the data between the <fragment_orientation> and </fragment_orientation> tags. Args : 2 scalars: - reference to a scalar holding the value of the line to be parsed. - reference to a data structure to store the <fragment_orientation> data. Returns : Nothing. Note : Method(s) that call(s) this method : _process_fragment_order Method(s) that this method calls : _helper_store_attribute_list , _process_bio_sequence =cut sub _process_fragment_orientation { my ($self, $line, $data_structure) = @_; # counter to determine the number of iterations within this while loop. my $count = 0; # One or more <fragment_orientation> while ($$line =~ /<fragment_orientation\s?(.*?)\s?>/) { my $fragment_orientation; $self->_helper_store_attribute_list($1, \$fragment_orientation); $$line = $self->_readline; # One <bio_sequence> $$line =~ /<bio_sequence\s?(.*?)\s?>/; # Process the data between <bio_sequence></bio_sequence> my $bio_sequence = $self->_process_bio_sequence($line, $1); $fragment_orientation->{'bio_sequence'} = $bio_sequence; push @{$$data_structure->{'fragment_orientation'}}, $fragment_orientation; ++$count; } $self->throw("Error: Missing <fragment_orientation> tag. Got this: $$line\n\n") if $count == 0; return; } # ================================================================================== =head2 _process_bio_sequence Title : _process_bio_sequence Usage : $self->_process_bio_sequence Function : Parses the data between the <bio_sequence></bio_sequence> tags. Args : 2 scalars: - reference to a scalar holding the value of the line to be parsed. - scalar holding the value of the attributes for <bio_sequence> Returns : data structure holding the values between <bio_sequence></bio_sequence> Note : Method(s) that call(s) this method : _process_fragment_orientation Method(s) that this method calls : _helper_store_attribute_list , _one_tag , _question_mark_tag , _star_tag , _process_alt_ids , _process_xrefs , _process_sequence_map =cut sub _process_bio_sequence { my ($self, $line, $attribute_line) = @_; my $bio_sequence; $self->_helper_store_attribute_list($attribute_line, \$bio_sequence); $$line = $self->_readline; # One <db_id>. $self->_one_tag($line, \$bio_sequence, 'db_id'); # Zero or one <note>. $self->_question_mark_tag($line, \$bio_sequence, 'note'); # Zero or more <description> $self->_question_mark_tag($line, \$bio_sequence, 'description'); # Zero or more <keyword> $self->_star_tag($line, \$bio_sequence, 'keyword'); # Zero or one <sequence> $self->_question_mark_tag($line, \$bio_sequence, 'sequence'); # Zero or one <alt_ids> # NOT IMPLEMENTED!!!! #if ($line =~ /<alt_ids>/){ # NOT DONE YET! # my $alt_ids; # $bio_sequence->{'alt_ids'} = $self->_process_alt_ids(\$alt_ids); #} # Zero or one <xrefs> if ($$line =~ /<xrefs\s?(.*?)\s?>/) { my $xrefs = $self->_process_xrefs($line, \$bio_sequence); $bio_sequence->{'xrefs'} = $xrefs || 'null'; } # Zero or more <sequence_map> if ($$line =~ /<sequence_map\s?(.*?)\s?>/) { my $sequence_map = $self->_process_sequence_map($line); push @{$bio_sequence->{'sequence_map'}}, $sequence_map; } # print Data::Dumper->Dump([$bio_sequence]); exit; return $bio_sequence; } # ================================================================================== =head2 _process_xrefs Title : _process_xrefs Usage : $self->_process_xrefs Function : Parse the data between the <xrefs></xrefs> tags. Args : reference to a scalar holding the value of the line to be parsed. Return : Nothing. Note : Method(s) that call(s) this method: _process_bio_sequence Method(s) that this method calls: _one_tag , _process_xref =cut sub _process_xrefs { my ($self, $line) = @_; my $xrefs; $$line = $self->_readline; # One or more <db_id> or <xref> within <xrefs></xrefs>. Check if # to see if there's at least one. if ($$line =~ /<db_id|xref\s?(.*?)\s?>/) { while ($$line =~ /<(db_id|xref)\s?(.*?)\s?>/) { if ($1 eq "db_id") { my $db_id; $self->_one_tag($line, \$db_id, 'db_id'); push @{$xrefs->{'db_id'}}, $db_id; } elsif ($1 eq "xref") { my $xref; $self->_process_xref($line, \$xref); push @{$xrefs->{'xref'}}, $xref; } else { $self->throw("Error: Tag type should be one of db_id or xref! Got this: $$line\n\n"); } } # close while loop if ($$line =~ /<\/xrefs>/) { $$line = $self->_readline; # get the next line to be _processed by the next sub. return $xrefs; } else { $self->throw("Error: Missing </xrefs> tag. Got this: $$line\n\n"); } } else { $self->throw("Error: Missing <db_id> or <xref> tag. Got this: $$line\n\n"); } return; } # ================================================================================== =head2 _process_xref Title : _process_xref Usage : $self->_process_xref Function : Parses the data between the <xref></xref> tags. Args : 2 scalars: - reference to a scalar holding the value of the line to be parsed. - reference to a data structure to store the <xref> data. Returns : Nothing. Note : Method(s) that call(s) this method : _process_xrefs (note the 's' in 'xrefs') Method(s) that this method calls : _helper_store_attribute_list , _star_tag =cut sub _process_xref { my ($self, $line, $xref) = @_; $$line = $self->_readline; # One <db_id> if ($$line =~ /<db_id\s?(.*?)\s?>/) { $self->_helper_store_attribute_list($1, $xref); } else { $self->throw("Error: Missing <db_id> tag. Got this: $$line\n\n"); } # Zero or more <xref_property> $self->_star_tag($line, $xref, 'xref_propery'); return; } # ================================================================================== =head2 _process_sequence_map Title : _process_sequence_map Usage : $self->_process_sequence_map Function : Parses the data between the <sequence_map></sequence_map> tags. Args : Reference to scalar holding the line to be parsed. Returns : Data structure that holds the values that were parsed. Note : Method(s) that call(s) this method : _process_bio_sequence Method(s) that this method calls : _helper_store_attribute_list , _question_mark_tag , _process_annotations =cut sub _process_sequence_map { my ($self, $line) = @_; my $sequence_map; # Zero or more <sequence_map> while ($$line =~ /<sequence_map\s?(.*?)\s?>/) { $self->_helper_store_attribute_list($1, \$sequence_map) if defined $1; $$line = $self->_readline; # Zero or one <note> $self->_question_mark_tag($line, \$sequence_map, 'note'); # NOT IMPLEMENTED!!! #if ($$line =~ /<computations\?(.*?)\s?>/){ # # $self->_process_computations(); #} # Zero or one <annotations> if ($$line =~ /<annotations\s?(.*?)\s?>/) { my $annotations = $self->_process_annotations($line); $sequence_map->{'annotations'} = $annotations; } } # closes the while loop # Match closing tag: if ($$line =~ /<\/sequence_map>/) { return $sequence_map; } else { $self->throw("Error: Missing </sequence_map> tag. Got this: $$line\n\n"); } } # ================================================================================== =head2 _process_annotations Title : _process_annotations Usage : $self->_process_annotations Function : Parse the data between the <annotations></annotations> tags. Args : Reference to scalar holding the line to be parsed. Returns : Data structure that holds the values that were parsed. Note : Method(s) that call(s) this method : _process_sequence_map Method(s) that this method calls : _process_seq_feature =cut sub _process_annotations { my ($self, $line) = @_; # ( seq_feature | gene | comp_result )+ my $annotations; $$line = $self->_readline; my $count = 0; # counter to keep track of number of iterations in the loop. # One or more of these: while ($$line =~ /<(seq_feature|gene|comp_result)\s?(.*?)\s?>/) { if ($$line =~ /<seq_feature\s?(.*?)\s?>/) { my $seq_feature = $self->_process_seq_feature($line, $1); push @{$annotations->{'seq_feature'}}, $seq_feature; } elsif ($$line =~ /<gene\s?(.*?)\s?>/) { # gene } elsif ($$line =~ /<comp_result\s?(.*?)\s?>/) { # comp_result } ++$count; } # closes the while loop. $self->throw("Error: Missing <seq_feature> tag. Got: $$line\n\n") if $count == 0; # Match closing tag: if ($$line =~ /<\/annotations/) { $$line = $self->_readline; # get the next line to be _processed by the next sub. return $annotations; } else { $self->throw("Error: Missing </annotations> tag. Got this: $$line\n\n"); } } # ================================================================================== =head2 _process_seq_feature Title : _process_seq_feature Usage : $self->_process_seq_feature Function : Parses the data between the <seq_feature></seq_feature> tag. Args : 2 scalars: - Reference to scalar holding the line to be parsed. - Scalar holding the attributes for <seq_feature>. Returns : Data structure holding the values parsed. Note : Method(s) that call(s) this method: _process_annotations Method(s) that this method calls: _helper_store_attribute_list , _process_classification , _question_mark_tag , _one_tag , _process_evidence , _process_qualifier , _process_seq_feature , _process_related_annot =cut sub _process_seq_feature { my ($self, $line, $attribute_line) = @_; my $seq_feature; $self->_helper_store_attribute_list($attribute_line, \$seq_feature); $$line = $self->_readline; # Zero or more <classification> $self->_process_classification($line, \$seq_feature); # Zero or one <note> $self->_question_mark_tag($line, \$seq_feature, 'note'); # One <seq_location> $self->_one_tag($line, \$seq_feature, 'seq_location'); # Zero or one <xrefs> $self->_question_mark_tag($line, \$seq_feature, 'xrefs'); # Zero or one <evidence> $self->_process_evidence($line, \$seq_feature); # Zero or more <qualifier> $self->_process_qualifier($line, \$seq_feature); # Zero or more <seq_feature>. A <seq_feature> tag within a <seq_feature> tag? Oh, well. Whatever... while ($$line =~ /<seq_feature\s?(.*?)\s?>/) { $self->_process_seq_feature($line, $1); $$line = $self->_readline; } # Zero or more <related_annot> while ($$line =~ /<related_annot\s?(.*?)\s?>/) { $self->_process_related_annot($line, $1); $$line = $self->_readline; } # Match the closing tag: if ($$line =~ /<\/seq_feature>/) { $$line = $self->_readline; # for the next sub... return $seq_feature; } else { $self->throw("Error. Missing </seq_feature> tag. Got this: $$line\n"); } } # ================================================================================== =head2 _process_qualifier Title : _process_qualifier Usage : $self->_process_qualifier Function : Parse the data between the <qualifier></qualifier> tags. Args : 2 scalars: - reference to a scalar holding the value of the line to be parsed. - reference to a data structure to store the <qualifer> data. Returns : Nothing. Note : Method(s) that call(s) this method : _process_seq_feature Method(s) that this method calls : _star_tag =cut sub _process_qualifier { my ($self, $line, $data_structure) = @_; my $qualifier; $self->_star_tag($line, \$qualifier, 'qualifier'); push @{$$data_structure->{'qualifier'}},$qualifier; return; # No need to return the data structure since its reference was what was modified. } # ================================================================================== =head2 _process_classification Title : _process_classification Usage : $self->_process_classification Function: Parse the data between the <classification></classification> tags. Args : 2 scalars: - reference to a scalar holding the value of the line to be parsed. - reference to a data structure to store the <qualifer> data. Returns : Nothing. Note : Method(s) that call(s) this method: _process_seq_feature Method(s) that this method calls: _helper_store_attribute_list , _question_mark_tag , _star_tag, _process_evidence =cut sub _process_classification { # NOT IN USE. my ($self, $line, $data_structure) = @_; my $classification = $$data_structure->{'classification'}; while ($$line =~ /<classification\s?(.*?)\s?>/) { $self->_helper_store_attribute_list($1, \$classification); # Zero or one <description> $self->_question_mark_tag($line, \$classification, 'description'); # Zero or more <id_alias> $self->_star_tag($line, \$classification, 'id_alias'); # Zero or one <evidence> $self->_process_evidence($line, \$classification); } } # ================================================================================== sub _process_evidence { # NOT done. my ($self, $line, $data_structure) = @_; if ($$line =~ /<evidence>/) { $$line = $self->_readline; # One or more <element_id> OR One or more <comp_result> while ($$line =~ /<(element_id|comp_result)\s?(.*?)\s?>/) { if ($$line =~ /<element_id\s?(.*?)\s?>/) { my $element_id; $self->_plus_tag($line, \$element_id, 'element_id'); push @{$$data_structure->{'element_id'}}, $element_id; } elsif ($$line =~ /<comp_result\s?(.*?)\s?>/) { my $comp_result; $self->_process_comp_result($line, \$comp_result, $1); push @{$$data_structure->{'comp_result'}}, $comp_result; } $$line = $self->_readline; } } } # ================================================================================== sub _process_comp_result { # NOT IN USE. my ($self, $line, $comp_result, $attribute_line) = @_; $self->_helper_store_attribute_list($attribute_line, $comp_result); $$line = $self->_readline; # Zero or one <note> $self->_question_mark_tag($line, $comp_result, 'note'); # Zero or one <match_desc> $self->_question_mark_tag($line, $comp_result, 'match_desc'); # Zero or one <match_align> $self->_question_mark_tag($line, $comp_result, 'match_align'); # Zero or one <query_region> $self->_process_query_region($line, $comp_result); # Zero or one <match_region> $self->_process_match_region($line, $comp_result); # Zero or more <result_property> $self->_star_tag($line, $comp_result, 'result_property'); # Zero or more <result_group> $self->_process_result_group($line, $comp_result); # Zero or more <related_annot> $self->_process_related_annot($line, $comp_result); } # ================================================================================== sub _process_related_annot { # NOT IN USE. my ($self, $line, $data_structure) = @_; while ($$line =~ /<related_annot\s?(.*?)\s?>/) { my $related_annot; # Zero or one <related_annot> $self->_helper_store_attribute_list($1, \$related_annot); $$line = $self->_readline; # One or more <element_id> my $element_id_count = 0; while ($$line =~ /<element_id\s?(.*?)\s?>/) { my $element_id; $self->_helper_store_attribute_list($1, \$element_id); push @{$related_annot->{'element_id'}}, $element_id; $$line = $self->_readline; ++$element_id_count; } if ($element_id_count == 0) { $self->throw("Error. Missing <element_id> tag. Got: $$line"); } # Zero or more <sci_property> $self->_star_tag($line, \$related_annot, 'sci_property'); # while ($$line =~ /<sci_property\s?(.*?)\s?>/){ # # } push @{$data_structure->{'related_annot'}}, $related_annot; unless ($$line =~ /<\/related_annot>/){ $self->throw("Error. Missing </related_tag>. Got: $$line\n"); } } } # ================================================================================== sub _process_result_group { # NOT IN USE. my ($self, $line, $data_structure) = @_; while ($$line =~ /<result_group\s?(.*?)\s?>/) { my $result_group = $$data_structure->{'result_group'}; $self->_helper_store_attribute_list($1, \$result_group); my $count = 0; $$line = $self->_readline; while ($$line =~ /<comp_result\s?(.*?)\s?>/) { # one or more <comp_result> $self->_process_comp_result(\$line, \$result_group, $1); $$line = $self->_readline; ++$count; } $self->throw("Error. No <comp_result></comp_result> tag! Got this: $$line") if $count == 0; # in the last iteration in the inner while loop, $line will # have a value of the closing tag of 'result_group' if ($line =~ /<\/result_group>/) { $$line = $self->_readline; } else { $self->throw("Error. No </result_tag>! Got this: $$line"); } } } # ================================================================================== sub _process_match_region { # NOT IN USE. my ($self, $line, $data_structure) = @_; my $match_region = $data_structure->{'match_region'}; if ($$line =~ /<match_region\s?(.*?)\s?>(.*?)>/) { $self->_helper_store_attribute_line($1, \$match_region); $$line = $self->_readline; # Zero or one db_id | element_id | bio_sequence if ($$line =~ /<db_id\s?(.*?)\s?>(.*?)<\/db_id>/) { $self->_question_mark_tag($line, \$match_region, 'db_id'); } elsif ($$line =~ /<element_id\s?(.*?)\s?>/) { # empty... $self->_question_mark_tag($line, \$match_region, 'element_id'); } elsif ($$line =~ /<bio_sequence\s?(.*?)\s?>/) { $match_region->{'bio_sequence'} = $self->_process_bio_sequence($line, $1); } $$line = $self->_readline; if ($$line =~ /<\/match_region>/o) { $$line = $self->_readline; # get the next line to be _processed by the next sub return; } else { $self->throw("No closing tag </match_region>! Got this: $$line\n"); } } } # ================================================================================== sub _process_query_region { # NOT IN USE. my ($self, $line, $data_structure) = @_; my $query_region = $data_structure->{'query_region'}; if ($$line =~ /<query_region\s?(.*?)\s?>/) { $self->_helper_store_attribute_list($1, \$query_region); $$line = $self->_readline; # Zero or one <db_id> $self->_question_mark_tag($line, \$query_region, 'db_id'); if ($$line =~ /<\/query_region>/) { $$line = $self->_readline; # get the next line to _process. return; } else { $self->throw("No closing tag </query_region>. Got this: $$line\n"); } } } # ================================================================================== =head2 _tag_processing_helper Title : _tag_processing_helper Usage : $self->_tag_processing_helper Function : Stores the tag value within the data structure. Also calls _helper_store_attribute_list to store the attributes and their values in the data structure. Args : 5 scalars: - Scalar holding the value of the attributes - Reference to a data structure to store the data for <$tag_name> - Scalar holding the tag name. - Scalar holding the value of the tag. - Scalar holding the value of either 'star', 'plus', or 'question mark' which specifies what type of method called this method. Returns : Nothing. Note : Method(s) that call(s) this method: Method(s) that this method calls: _helper_store_attribute_list =cut sub _tag_processing_helper { my ($self, $attribute_list, $data_structure, $tag_name, $tag_value, $caller) = @_; # Add the attributes to the $$data_structure if they exist. # print "tag_name: $tag_name , attribute_list: $attribute_list\n"; if (defined $attribute_list) { $self->_helper_store_attribute_list($attribute_list, $data_structure); } if ($caller eq 'star' || $caller eq 'plus') { push @{$$data_structure->{$tag_name}}, $tag_value; # There's either zero or more tags (*) or one or more (+) } else { $$data_structure->{$tag_name} = $tag_value || 'null'; # There's zero or one tag (?) } return; } # ================================================================================== =head2 _one_tag Title : _one_tag Usage : $self->_one_tag Function : A method to store data from tags that occurs just once. Args : 2 scalars: - reference to a scalar holding the value of the line to be parsed. - reference to a data structure to store the data for <$tag_name> Returns : Nothing. Note : Method(s) that call(s) this method : many Method(s) that this method calls : _tag_processing_helper =cut sub _one_tag { my ($self, $line, $data_structure, $tag_name) = @_; $self->throw("Error: Missing <$tag_name></$tag_name>. Got: $$line\n\n") if $$line !~ /\<$tag_name/; # check to see if $$line is in correct format. if ($$line =~ /<$tag_name\s?(.*?)\s?\/?>(.*?)<\/$tag_name>/) { $self->_tag_processing_helper($1, $data_structure, $tag_name, $2, 'one'); # $1 = attributes $data_structure = to hold the parsed values # # $tag_name = name of the tag $2 = tag value 'one' = lets # _tag_processing_helper know that it was called from the # _one_tag method. } elsif ($$line =~ /<$tag_name\s?(.*?)\s?\/?>/) { $self->_tag_processing_helper($1, $data_structure, $tag_name, '', 'one'); } else { $self->throw("Error: Cannot parse this line: $$line\n\n"); } $$line = $self->_readline; # get the next line. return; } # ================================================================================== =head2 _question_mark_tag Title : _question_mark_tag Usage : $self->_question_mark_tag Function : Parses values from tags that occurs zero or one time. ie: tag_name? Args : 3 scalars: - reference to a scalar holding the value of the line to be parsed. - reference to a data structure to store the data for <$tag_name> - scalar holding the name of the tag. Returns : Nothing. Note : Method(s) that call(s) this method : many. Method(s) that this method calls : _tag_processing_helper =cut sub _question_mark_tag { my ($self, $line, $data_structure, $tag_name) = @_; if ($$line =~ /<$tag_name\s?(.*?)\s?>(.*?)<\/$tag_name>/) { $self->_tag_processing_helper($1, $data_structure, $tag_name, $2, 'question mark'); $$line = $self->_readline; } return; } # ================================================================================== =head2 _star_tag Title : _star_tag Usage : $self->_star_tag Function : Parses values from tags that occur zero or more times. ie: tag_name* Args : 3 scalars: - reference to a scalar holding the value of the line to be parsed. - reference to a data structure to store the data for <$tag_name> - scalar holding the name of the tag. Returns : Nothing. Note : Method(s) that call(s) this method : many. Method(s) that this method calls : _tag_processing_helper =cut sub _star_tag { my ($self, $line, $data_structure, $tag_name) = @_; #print "tag_name: $tag_name\n"; while ($$line =~ /<$tag_name\s?(.*?)\s?>(.*?)<\/$tag_name>/) { $self->_tag_processing_helper ($1, $data_structure, $tag_name, $2, 'star'); # The tag and attribute values are stored within # $$data_structure within the _tag_processing_helper method. $$line = $self->_readline; } #if ($tag_name eq 'qualifier'){ # print "this one:\n"; # print Data::Dumper->Dump([$data_structure]); exit; #} return; } # ================================================================================== =head2 _plus_tag Title : _plus_tag Usage : $self->_plus_tag Function : Handles 'plus' tags (tags that occur one or more times). tag_name+ Args : 3 scalars: - reference to a scalar holding the value of the line to be parsed. - reference to a data structure to store the data for <$tag_name> - scalar holding the name of the tag. Returns : Nothing. Note : Method(s) that call(s) this method : many. Method(s) that this method calls : _star_tag =cut sub _plus_tag { my ($self, $line, $data_structure, $tag_name) = @_; if ($$line =~ /<$tag_name\s?(.*?)\s?>(.*?)<\/$tag_name>/) { # Store value of the first occurence of $tag_name. # All subsequent values, if any, will be stored in the method _star_tag. $self->_tag_processing_helper($1, $data_structure, $tag_name, $2, 'plus'); # If the flow gets within this block, we've already determined # that there's at least one of <$tag_name> Are there more? To # answer this, we could just treat the tag as a * tag now # (zero or more). We've already determined that it's NOT # zero, so how many more? Thus, call _star_tag. $$line = $self->_readline; $self->_star_tag($line, $data_structure, $tag_name); } else { $self->throw("Error: Missing <$tag_name></$tag_name>. Got: $$line\n\n"); } return; } # ================================================================================== =head2 _helper_store_attribute_list Title : _helper_store_attribute_list Usage : $self->_helper_store_attribute_list Function : A helper method used to store the attributes from the tags into the data structure. Args : 2 scalars: - scalar holding the attribute values to be parsed. - reference to a data structure to store the data between the 2 tags. Returns : Nothing. Note : Method(s) that call(s) this method : Many. Method(s) that this method call(s) : None. =cut sub _helper_store_attribute_list { my ($self, $attribute_line, $data_structure) = @_; my %attribs = ($attribute_line =~ /(\w+)\s*=\s*"([^"]*)"/g); my $attribute_list; for my $key (keys %attribs) { # print "\tkey: $key , value: $attribs{$key}\n"; ###$$data_structure->{$key} = $attribs{$key}; # <- The ORIGINAL. push @{$$data_structure->{$key}}, $attribs{$key}; # Now, store them in an array because there may be > 1 tag, thus # > 1 attribute of the same name. # Doing this has made it necessary to change the _store_seqs method. # ie: Change $bio_sequence->{'molecule_type'}; # to # $bio_sequence->{'molecule_type'}->[0]; } return; } # ================================================================================== =head2 _store_seqs Title : _store_seqs Usage : $self->_store_seqs Function : This method is called once in the life time of the script. It stores the data parsed from the agave xml file into the Bio::Seq object. Args : None. Returns : Nothing. Note : Method(s) that call(s) this method : next_seq Method(s) that this method calls : None. =cut sub _store_seqs { my ($self) = @_; for my $sciobj (@{$self->{'sciobj'}}) { ### $sciobj = $self->{'sciobj'}; # The root node. for my $contig (@{$sciobj->{'contig'}}) { # Each contig has a fragment order. for my $fragment_order (@{$contig->{'fragment_order'}}) { # Each fragment order has a fragment_orientation. for my $fragment_orientation (@{$fragment_order->{'fragment_orientation'}}) { # Each fragment_orientation contain 1 bio sequence. my $bio_sequence = $fragment_orientation->{'bio_sequence'}; # <bio_sequence> contains all the # interesting stuff: my $sequence = $bio_sequence->{'sequence'}; my $accession_number = $bio_sequence->{'sequence_id'}->[0]; # also use for primary_id my $organism = $bio_sequence->{'organism'}; my $description = $bio_sequence->{'description'}; my $molecule_type = $bio_sequence->{'molecule_type'}->[0]; my $primary_seq = Bio::PrimarySeq->new( -id => $accession_number, -alphabet => $molecule_type, -seq => $sequence, -desc => $description, ); my $seq = Bio::Seq->new ( -display_id => $accession_number, -accession_number => $accession_number, -primary_seq => $primary_seq, -seq => $sequence, -description => $description, ); my $organism_name = $bio_sequence->{organism_name}->[0]; if (defined $organism_name) { my @classification = split(' ', $organism_name); my $species = Bio::Species->new(); $species->classification(@classification); $seq->species($species); } # Pull out the keywords: $keywords is an array ref. my $keywords = $bio_sequence->{keyword}; my %key_to_value; for my $keywords (@$keywords) { # print "keywords: $keywords\n"; my @words = split(':', $keywords); for (my $i = 0; $i < scalar @words - 1; $i++) { if ($i % 2 == 0) { my $j = $i; $j++; # print "$words[$i] , $words[$j]\n"; $key_to_value{$words[$i]} = $words[$j]; } } # print Data::Dumper->Dump([%key_to_value]); my $reference = Bio::Annotation::Reference-> new(-authors => $key_to_value{authors}, -title => $key_to_value{title}, -database => $key_to_value{database}, -pubmed => $key_to_value{pubmed}, ); $seq->annotation->add_Annotation('reference', $reference); } # close for my $keywords # print Data::Dumper->Dump([$bio_sequence]); print "here\n"; exit; if (defined $bio_sequence->{'sequence_map'}) { for my $sequence_map (@{$bio_sequence->{'sequence_map'}}) { # print Data::Dumper->Dump([$sequence_map]); print "here\n"; exit; my $label = $sequence_map->{label}; if (defined $sequence_map->{annotations} && ref($sequence_map->{annotations}) eq 'HASH') { # Get the sequence features (ie genes, exons, etc) from this $sequence_map for my $seq_feature (@{$sequence_map->{'annotations'}->{'seq_feature'}}) { # print Data::Dumper->Dump([$seq_feature]); exit; my $seq_location = $seq_feature->{'seq_location'}; my $start_coord = $seq_feature->{'least_start'}->[0]; my $feature_type = $seq_feature->{'feature_type'}->[0]; my $end_coord = $seq_feature->{'greatest_end'}->[0]; my $is_on_complement = $seq_feature->{'is_on_complement'}->[0]; # Specify the coordinates and the tag for this seq feature. # print "Primary Tag for this SeqFeature: $feature_type\n"; my $feat = Bio::SeqFeature::Generic-> new( -start => $start_coord, -end => $end_coord, -primary_tag => $feature_type, ); if (defined $seq_feature->{'qualifier'} && ref($seq_feature->{'qualifier'}) eq 'ARRAY') { for my $feature (@{$seq_feature->{'qualifier'}}) { my $value = $feature->{'qualifier'}; my $feature_type = $feature->{'qualifier_type'}; for (my $i = 0; $i < scalar @{$value}; $i++) { $feat->add_tag_value( $feature_type->[$i] => $value->[$i] ); } # close the for loop } } # close if (defined $seq_feature->... $seq->add_SeqFeature($feat); } # close for my $seq_feature (@{$sequence_map->... } # close if (defined $sequence_map->{annotations} && } # close for my $sequence_map (@{$bio_sequence->{'sequence_map'}}){ } # close if (defined $bio_sequence->{'sequence_map'}){ # This is where the Bio::Seq objects are stored: push @{$self->{'sequence_objects'}}, $seq; } # close for my $fragment_orientation } # close for my $fragment_order } # close for my $contig } # close for my $sciobj # Flag is set so that we know that the sequence objects are now stored in $self. $self->{'seqs_stored'} = 1; return; } # ================================================================================== =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function : Returns the next sequence in the stream. Args : None. Returns : Bio::Seq object Method is called from the script. Method(s) that this method calls: _store_seqs (only once throughout the life time of script execution). =cut sub next_seq { my ($self) = @_; # convert agave to genbank/fasta/embl whatever. $self->_store_seqs if $self->{'seqs_stored'} == 0; $self->throw("Error: No Bio::Seq objects stored yet!\n\n") if !defined $self->{'sequence_objects'}; # This should never occur... if (scalar @{$self->{'sequence_objects'}} > 0) { return shift @{$self->{'sequence_objects'}}; } else { # All done. Nothing more to parse. # print "returning nothing!\n"; return; } } # ================================================================================== =head2 next_primary_seq Title : next_primary_seq Usage : $seq = $stream->next_primary_seq() Function: returns the next primary sequence (ie no seq_features) in the stream Returns : Bio::PrimarySeq object Args : NONE =cut sub next_primary_seq { my $self=shift; return 0; } # ================================================================================== =head2 write_seq Title : write_seq Usage : Not Yet Implemented! $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object =cut sub write_seq { # Convert the Bio::Seq object(s) to AGAVE xml file. my ($self,@seqs) = @_; foreach my $seq ( @seqs ) { $self->_write_each_record( $seq ); # where most of the work actually takes place. } return; } # ================================================================================== =head2 _write_each_record Title : _write_each_record Usage : $agave->_write_each_record( $seqI ) Function: change data into agave format Returns : NONE Args : Bio::SeqI object =cut sub _write_each_record { my ($self,$seq) = @_; # $self->{'file'} =~ s/>//g; my $output = IO::File->new(">" . $self->{'file'}); my $writer = XML::Writer->new(OUTPUT => $output, NAMESPACES => 0, DATA_MODE => 1, DATA_INDENT => 2 ) ; $writer->xmlDecl("UTF-8"); $writer->doctype("sciobj", '', "sciobj.dtd"); $writer ->startTag('sciobj', 'version', '2', 'release', '2'); $writer->startTag('contig', 'length', $seq->length); my $annotation = $seq ->annotation; # print "annotation: $annotation\n"; exit; Bio::Annotation::Collection=HASH(0x8112e6c) if ( $annotation->get_Annotations('dblink') ) { # used to be $annotation->each_DBLink, but Bio::Annotation::Collection::each_DBLink # is now replaced with get_Annotations('dblink') my $dblink = $annotation->get_Annotations('dblink')->[0] ; $writer ->startTag('db_id', 'id', $dblink->primary_id , 'db_code', $dblink->database ); } else { $writer ->startTag('db_id', 'id', $seq->display_id , 'db_code', 'default' ); } $writer ->endTag('db_id') ; $writer->startTag('fragment_order'); $writer->startTag('fragment_orientation'); ##start bio_sequence ####my $organism = $seq->species->genus . " " . $seq->species->species; $writer ->startTag('bio_sequence', 'sequence_id', $seq->display_id, 'seq_length', $seq->length, # 'molecule_type', $seq->moltype, # deprecated 'molecule_type', $self->alphabet, #'organism_name', $organism ); # my $desc = $seq->{primary_seq}->{desc}; # print "desc: $desc\n"; exit; # print Data::Dumper->Dump([$seq]); exit; ##start db_id under bio_sequence $annotation = $seq ->annotation; # print "annotation: $annotation\n"; exit; Bio::Annotation::Collection=HASH(0x8112e6c) if ( $annotation->get_Annotations('dblink') ) { # used to be $annotation->each_DBLink, but Bio::Annotation::Collection::each_DBLink # is now replaced with get_Annotations('dblink') my $dblink = $annotation->get_Annotations('dblink')->[0] ; $writer ->startTag('db_id', 'id', $dblink->primary_id , 'db_code', $dblink->database ); } else { $writer ->startTag('db_id', 'id', $seq->display_id , 'db_code', 'default' ); } $writer ->endTag('db_id') ; ##start note my $note = "" ; foreach my $comment ( $annotation->get_Annotations('comment') ) { # used to be $annotations->each_Comment(), but that's now been replaced # with get_Annotations() # $comment is a Bio::Annotation::Comment object $note .= $comment->text() . "\n"; } $writer ->startTag('note'); $writer ->characters( $note ) ; $writer ->endTag('note'); ##start description $writer ->startTag('description'); # $writer ->characters( $annotation->get_Annotations('description') ) ; # used to be $annotations->each_description(), but that's now been # replaced with get_Annotations. # Simon added this: this is the primary_seq's desc (the DEFINITION tag in a genbank file) $writer->characters($seq->{primary_seq}->{desc}); $writer ->endTag('description'); ##start keywords foreach my $genename ( $annotation->get_Annotations('gene_name') ) { # used to be $annotations->each_gene_name, but that's now been # replaced with get_Annotations() $writer ->startTag('keyword'); $writer ->characters( $genename ) ; $writer ->endTag('keyword'); } foreach my $ref ( $annotation->get_Annotations('reference') ) { # used to be $annotation->each_Reference, but # that's now been replaced with get_Annotations('reference'); # link is a Bio::Annotation::Reference object $writer ->startTag('keyword'); # print Data::Dumper->Dump([$ref]); exit; my $medline = $ref->medline || 'null'; my $pubmed = $ref->pubmed || 'null'; my $database = $ref->database || 'null'; my $authors = $ref->authors || 'null'; my $title = $ref->title || 'null'; $writer ->characters( 'medline:' . "$medline" . ':' . 'pubmed:' . "$pubmed" . ':' . 'database:' . "$database" . ':' .'authors:' . "$authors" . ':' . 'title:' . "$title" ) ; $writer ->endTag('keyword'); } ## start sequence $writer ->startTag('sequence'); $writer ->characters( $seq->seq ) ; $writer ->endTag('sequence'); ## start xrefs $writer ->startTag('xrefs'); foreach my $link ( $annotation->get_Annotations('dblink') ) { # link is a Bio::Annotation::DBLink object $writer ->startTag('db_id', 'db_code', $link->database, 'id', $link->primary_id); $writer ->characters( $link->comment ) ; $writer ->endTag('db_id'); } $writer ->endTag('xrefs') ; ##start sequence map ##we can not use : my @feats = $seq->all_SeqFeatures; ##rather, we use top_SeqFeatures() to keep the tree structure my @feats = $seq->top_SeqFeatures ; my $features; ##now we need cluster top level seqfeature by algorithm my $maps; foreach my $feature (@feats) { my $map_type = $feature ->source_tag; push (@{$maps->{ $map_type }}, $feature); } ##now we enter each sequence_map foreach my $map_type (keys %$maps ) { $writer->startTag('sequence_map', 'label', $map_type ); $writer->startTag('annotations'); # the original author accidently entered 'annotation' instead of 'annotations' foreach my $feature ( @{$maps->{ $map_type }} ) { $self->_write_seqfeature( $feature, $writer ) ; } $writer->endTag('annotations'); $writer->endTag('sequence_map'); } $writer->endTag('bio_sequence'); $writer->endTag('fragment_orientation'); $writer->endTag('fragment_order'); $writer->endTag('contig'); $writer->endTag('sciobj'); } # ================================================================================== =head2 _write_seqfeature Usage : $agave->_write_each_record( $seqfeature, $write ) Function: change seeqfeature data into agave format Returns : NONE Args : Bio::SeqFeature object and XML::writer object =cut sub _write_seqfeature{ my ($self,$seqf, $writer) = @_; ##now enter seq feature $writer ->startTag('seq_feature', 'feature_type', $seqf->primary_tag() ); my $strand = $seqf->strand(); $strand = 0 if !defined $strand; # $strand == 1 ? 'false' : 'true'; my $is_on_complement; if ($strand == 1) { $is_on_complement = 'true'; } else { $is_on_complement = 'false'; } # die Data::Dumper->Dump([$seqf]) if !defined $strand; $writer ->startTag('seq_location', 'lease_start', $seqf->start(), 'greatest_end', $seqf->end(), # 'is_on_complement', $seqf->strand() == 1 ? 'false' : 'true') ; 'is_on_complement' , $is_on_complement); # is_on_complement: is the feature found on the complementary # strand (true) or not (false)? $writer ->endTag('seq_location'); ##enter qualifier foreach my $tag ( $seqf->all_tags() ) { $writer ->startTag('qualifier', 'qualifier_type', $tag); $writer ->characters( $seqf->each_tag_value($tag) ) ; $writer ->endTag('qualifier'); } ##now recursively travel the seqFeature foreach my $subfeat ( $seqf->sub_SeqFeature ) { $self->_write_seqfeature( $subfeat, $writer ) ; } $writer->endTag('seq_feature'); return; } # ================================================================================== =head2 _filehandle Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional) =cut sub _filehandle{ my ($obj,$value) = @_; if ( defined $value) { $obj->{'_filehandle'} = $value; } return $obj->{'_filehandle'}; } # ================================================================================== =head2 throw Title : throw Usage : $self->throw; Function : Throw's error message. Calls SeqIO's throw method. Args : Array of string(s), holding error message(s). Returns : Nothing. Note : Method(s) that call(s) this method: many. Method(s) that this method calls: Bio::SeqIO's throw method. =cut sub throw { my ($self, @s) = @_; my $string = "[$.]" . join('', @s); $self->SUPER::throw($string); return; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/alf.pm�������������������������������������������������������������������000444��000766��000024�� 6731�13155576320� 16313� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::alf # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Aaron Mackey <amackey@virginia.edu> # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::alf - alf trace sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from alf trace files. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Aaron Mackey Email: amackey@virginia.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::alf; use vars qw(@ISA $READ_AVAIL); use strict; use Bio::SeqIO; use Bio::Seq::SeqFactory; push @ISA, qw( Bio::SeqIO ); sub BEGIN { eval { require Bio::SeqIO::staden::read; }; if ($@) { $READ_AVAIL = 0; } else { push @ISA, "Bio::SeqIO::staden::read"; $READ_AVAIL = 1; } } sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::Quality')); } unless ($READ_AVAIL) { Bio::Root::Root->throw( -class => 'Bio::Root::SystemException', -text => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!" ); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq::Quality object Args : NONE =cut sub next_seq { my ($self) = @_; my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'alf'); # create the seq object $seq = $self->sequence_factory->create(-seq => $seq, -id => $id, -primary_id => $id, -desc => $desc, -alphabet => 'DNA', -qual => $qual ); return $seq; } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object =cut sub write_seq { my ($self,@seq) = @_; my $fh = $self->_fh; foreach my $seq (@seq) { $self->write_trace($fh, $seq, 'alf'); } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; ���������������������������������������BioPerl-1.007002/Bio/SeqIO/asciitree.pm�������������������������������������������������������������000444��000766��000024�� 12723�13155576320� 17537� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::asciitree # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chris Mungall <cjm@fruitfly.org> # # Copyright Chris Mungall # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::asciitree - asciitree sequence input/output stream =head1 SYNOPSIS # It is probably best not to use this object directly, but # rather go through the SeqIO handler system. Go: $instream = Bio::SeqIO->new(-file => $filename, -format => 'chadoxml'); $outstream = Bio::SeqIO->new(-file => $filename, -format => 'asciitree'); while ( my $seq = $instream->next_seq() ) { $outstream->write_seq(); } =head1 DESCRIPTION This is a WRITE-ONLY SeqIO module. It writes a Bio::SeqI object containing nested SeqFeature objects in such a way that the SeqFeature containment hierarchy is visible as a tree structure =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Mungall Email cjm@fruitfly.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::asciitree; use strict; use base qw(Bio::SeqIO); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); # hash for functions for decoding keys. } =head2 show_detail Title : show_detail Usage : $obj->show_detail($newval) Function: Example : Returns : value of show_detail (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub show_detail{ my $self = shift; return $self->{'show_detail'} = shift if @_; return $self->{'show_detail'}; } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : =cut sub next_seq { my ($self,@args) = @_; $self->throw("This is a WRITE-ONLY adapter"); } =head2 write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object (must be seq) to the stream Returns : 1 for success and 0 for error Args : array of 1 to n Bio::SeqI objects =cut sub write_seq { my ($self,@seqs) = @_; foreach my $seq ( @seqs ) { $self->throw("Attempting to write with no seq!") unless defined $seq; if( ! ref $seq || ! $seq->isa('Bio::SeqI') ) { $self->warn(" $seq is not a SeqI compliant module. Attempting to dump, but may fail!"); } $self->_print("Seq: ".$seq->accession_number); $self->_print("\n"); my @top_sfs = $seq->get_SeqFeatures; $self->write_indented_sf(1, @top_sfs); } } sub write_indented_sf { my $self = shift; my $indent = shift; my @sfs = @_; foreach my $sf (@sfs) { my $label = ''; if ($sf->has_tag('standard_name')) { ($label) = $sf->get_tag_values('standard_name'); } if ($sf->has_tag('product')) { ($label) = $sf->get_tag_values('product'); } my $COLS = 60; my $tab = ' ' x 10; my @lines = (); if ($self->show_detail) { my @tags = $sf->all_tags; foreach my $tag (@tags) { my @vals = $sf->get_tag_values($tag); foreach my $val (@vals) { $val = "\"$val\""; push(@lines, "$tab/$tag="); while (my $cut = substr($val, 0, $COLS - length($lines[-1]), '')) { $lines[-1] .= "$cut"; if ($val) { push(@lines, $tab); } } } } } my $detail = join("\n", @lines); my @sub_sfs = $sf->get_SeqFeatures; my $locstr = ''; if (!@sub_sfs) { $locstr = $self->_locstr($sf); } my $col1 = sprintf("%s%s $label", ' ' x $indent, $sf->primary_tag); my $line = sprintf("%-50s %s\n", substr($col1, 0, 50), $locstr); $self->_print($line); if ($detail) { $self->_print($detail."\n"); } $self->write_indented_sf($indent+1, @sub_sfs); } return; } sub _locstr { my $self = shift; my $sf = shift; my $strand = $sf->strand || 0; my $ss = '.'; $ss = '+' if $strand > 0; $ss = '-' if $strand < 0; my $splitlocstr = ''; if ($sf->isa("Bio::SeqFeatureI")) { my @locs = ($sf->location); if ($sf->location->isa("Bio::Location::SplitLocationI")) { @locs = $sf->location->each_Location; $splitlocstr = "; SPLIT: ".join(" ", map {$self->_locstr($_)} @locs); } } return sprintf("%d..%d[%s] $splitlocstr", $sf->start, $sf->end, $ss); } 1; ���������������������������������������������BioPerl-1.007002/Bio/SeqIO/bsml.pm������������������������������������������������������������������000444��000766��000024�� 137274�13155576320� 16555� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::bsml # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Charles Tilford (tilfordc@bms.com) # Copyright (C) Charles Tilford 2001 # # This library is free software; you can redistribute it and/or # modify it under the terms of the GNU Lesser General Public # License as published by the Free Software Foundation; either # version 2.1 of the License, or (at your option) any later version. # # This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public # License along with this library; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # Also at: http://www.gnu.org/copyleft/lesser.html # Much of the basic documentation in this module has been # cut-and-pasted from the embl.pm (Ewan Birney) SeqIO module. =head1 NAME Bio::SeqIO::bsml - BSML sequence input/output stream =head1 SYNOPSIS It is probably best not to use this object directly, but rather go through the SeqIO handler system. To read a BSML file: $stream = Bio::SeqIO->new( -file => $filename, -format => 'bsml'); while ( my $bioSeqObj = $stream->next_seq() ) { # do something with $bioSeqObj } To write a Seq object to the current file handle in BSML XML format: $stream->write_seq( -seq => $seqObj); If instead you would like a XML::DOM object containing the BSML, use: my $newXmlObject = $stream->to_bsml( -seq => $seqObj); =head1 DEPENDENCIES In addition to parts of the Bio:: hierarchy, this module uses: XML::DOM =head1 DESCRIPTION This object can transform Bio::Seq objects to and from BSML (XML) flatfiles. =head2 NOTE: 2/1/02 - I have changed the API to more closely match argument passing used by other BioPerl methods ( -tag => value ). Internal methods are using the same API, but you should not be calling those anyway... =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head2 Things Still to Do * The module now uses the new Collection.pm system. However, Annotations associated with a Feature object still seem to use the old system, so parsing with the old methods are included.. * Generate Seq objects with no sequence data but an assigned length. This appears to be an issue with Bio::Seq. It is possible (and reasonable) to make a BSML document with features but no sequence data. * Support <Seq-data-import>. Do not know how commonly this is used. * Some features are awaiting implementation in later versions of BSML. These include: * Nested feature support * Complex feature (ie joins) * Unambiguity in strand (ie -1,0,1, not just 'complement' ) * More friendly dblink structures * Location.pm (or RangeI::union?) appears to have a bug when 'expand' is used. * More intelligent hunting for sequence and feature titles? It is not terribly clear where the most appropriate field is located, better grepping (eg looking for a reasonable count for spaces and numbers) may allow for titles better than "AE008041". =head1 AUTHOR - Charles Tilford Bristol-Myers Squibb Bioinformatics Email tilfordc@bms.com I have developed the BSML specific code for this package, but have used code from other SeqIO packages for much of the nuts-and-bolts. In particular I have used code from the embl.pm module either directly or as a framework for many of the subroutines that are common to SeqIO modules. =cut package Bio::SeqIO::bsml; use strict; use Bio::SeqFeature::Generic; use Bio::Species; use XML::DOM; use Bio::Seq::SeqFactory; use Bio::Annotation::Collection; use Bio::Annotation::Comment; use Bio::Annotation::Reference; use Bio::Annotation::DBLink; use base qw(Bio::SeqIO); my $idcounter = {}; # Used to generate unique id values my $nvtoken = ": "; # The token used if a name/value pair has to be stuffed # into a single line =head1 METHODS =cut # LS: this seems to get overwritten on line 1317, generating a redefinition error. # Dead code? # CAT: This was inappropriately added in revision 1.10 - I added the check for # existence of a sequence factory to the actual _initialize # sub _initialize { # my($self,@args) = @_; # $self->SUPER::_initialize(@args); # if( ! defined $self->sequence_factory ) { # $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), # -type => 'Bio::Seq::RichSeq')); # } # } =head2 next_seq Title : next_seq Usage : my $bioSeqObj = $stream->next_seq Function: Retrieves the next sequence from a SeqIO::bsml stream. Returns : A reference to a Bio::Seq::RichSeq object Args : =cut sub next_seq { my $self = shift; my ($desc); my $bioSeq = $self->sequence_factory->create(-verbose =>$self->verbose()); unless (exists $self->{'domtree'}) { $self->throw("A BSML document has not yet been parsed."); return; } my $dom = $self->{'domtree'}; my $seqElements = $dom->getElementsByTagName ("Sequence"); if ($self->{'current_node'} == $seqElements->getLength ) { # There are no more <Sequence>s to process return; } my $xmlSeq = $seqElements->item($self->{'current_node'}); # Assume that title attribute contains the best display id if (my $val = $xmlSeq->getAttribute( "title")) { $bioSeq->display_id($val); } # Set the molecule type if (my $val = $xmlSeq->getAttribute( "molecule" )) { my %mol = ('dna' => 'DNA', 'rna' => 'RNA', 'aa' => 'protein'); $bioSeq->molecule($mol{ lc($val) }); } # Set the accession number if (my $val = $xmlSeq->getAttribute( "ic-acckey" )) { $bioSeq->accession_number($val); } # Get the sequence data for the element if (my $seqData = &FIRSTDATA($xmlSeq->getElementsByTagName("Seq-data") ->item(0) ) ) { # Sequence data exists, transfer to the Seq object # Remove white space and CRs (not neccesary?) $seqData =~ s/[\s\n\r]//g; $bioSeq->seq($seqData); } elsif (my $import = $xmlSeq->getElementsByTagName("Seq-dataimport") ->item(0) ) { #>>>> # What about <Seq-data-import> ?? } elsif (my $val = $xmlSeq->getAttribute("length")) { # No sequence defined, set the length directly #>>>> # This does not appear to work - length is apparently calculated # from the sequence. How to make a "virtual" sequence??? Such # creatures are common in BSML... $bioSeq->length($val); } my $species = Bio::Species->new(); my @classification = (); # Peruse the generic <Attributes> - those that are direct children of # the <Sequence> or the <Feature-tables> element # Sticky wicket here - data not controlled by schema, could be anything my @seqDesc = (); my %specs = ('common_name' => 'y', 'genus' => 'y', 'species' => 'y', 'sub_species' => 'y', ); my %seqMap = ( 'add_date' => [ qw(date date-created date-last-updated)], 'keywords' => [ 'keyword', ], 'seq_version' => [ 'version' ], 'division' => [ 'division' ], 'add_secondary_accession' => ['accession'], 'pid' => ['pid'], 'primary_id' => [ 'primary.id', 'primary_id' ], ); my @links; my $floppies = &GETFLOPPIES($xmlSeq); for my $attr (@{$floppies}) { # Don't want to get attributes from <Feature> or <Table> elements yet my $parent = $attr->getParentNode->getNodeName; next unless($parent eq "Sequence" || $parent eq "Feature-tables"); my ($name, $content) = &FLOPPYVALS($attr); $name = lc($name); if (exists $specs{$name}) { # It looks like part of species... $species->$name($content); next; } my $value = ""; # Cycle through the Seq methods: for my $method (keys %seqMap) { # Cycle through potential matching attributes: for my $match (@{$seqMap{$method}}) { # If the <Attribute> name matches one of the keys, # set $value, unless it has already been set $value ||= $content if ($name =~ /$match/i); } if ($value ne "") { if( $method eq 'seq_version'&& $value =~ /\S+\.(\d+)/ ) { # hack for the fact that data in version is actually # ACCESSION.VERSION ($value) = $1; } $bioSeq->$method($value); last; } } if( $name eq 'database-xref' ) { my ($link_id,$link_db) = split(/:/,$value); push @links, Bio::Annotation::DBLink->new(-primary_id => $link_id, -database => $link_db); } next if ($value ne ""); if ($name =~ /^species$/i) { # Uh, it's the species designation? if ($content =~ / /) { # Assume that a full species name has been provided # This will screw up if the last word is the subspecies... my @break = split " ", $content; @classification = reverse @break; } else { $classification[0] = $content; } next; } if ($name =~ /sub[_ ]?species/i) { # Should be the subspecies... $species->sub_species( $content ); next; } if ($name =~ /classification/i) { # Should be species classification # We will assume that there are spaces separating the terms: my @bits = split " ", $content; # Now make sure there is not other cruft as well (eg semi-colons) for my $i (0..$#bits) { $bits[$i] =~ /(\w+)/; $bits[$i] = $1; } $species->classification( @bits ); next; } if ($name =~ /comment/) { my $com = Bio::Annotation::Comment->new('-text' => $content); # $bioSeq->annotation->add_Comment($com); $bioSeq->annotation->add_Annotation('comment', $com); next; } # Description line - collect all descriptions for later assembly if ($name =~ /descr/) { push @seqDesc, $content; next; } # Ok, we have no idea what this attribute is. Dump to SimpleValue my $simp = Bio::Annotation::SimpleValue->new( -value => $content); $bioSeq->annotation->add_Annotation($name, $simp); } unless ($#seqDesc < 0) { $bioSeq->desc( join "; ", @seqDesc); } #>>>> This should be modified so that any IDREF associated with the # <Reference> is then used to associate the reference with the # appropriate Feature # Extract out <Reference>s associated with the sequence my @refs; my %tags = ( -title => "RefTitle", -authors => "RefAuthors", -location => "RefJournal", ); for my $ref ( $xmlSeq->getElementsByTagName ("Reference") ) { my %refVals; for my $tag (keys %tags) { my $rt = &FIRSTDATA($ref->getElementsByTagName($tags{$tag})->item(0)); next unless ($rt); $rt =~ s/^[\s\r\n]+//; # Kill leading space $rt =~ s/[\s\r\n]+$//; # Kill trailing space $rt =~ s/[\s\r\n]+/ /; # Collapse internal space runs $refVals{$tag} = $rt; } my $reference = Bio::Annotation::Reference->new( %refVals ); # Pull out any <Reference> information hidden in <Attributes> my %refMap = ( comment => [ 'comment', 'remark' ], medline => [ 'medline', ], pubmed => [ 'pubmed' ], start => [ 'start', 'begin' ], end => [ 'stop', 'end' ], ); my @refCom = (); my $floppies = &GETFLOPPIES($ref); for my $attr (@{$floppies}) { my ($name, $content) = &FLOPPYVALS($attr); my $value = ""; # Cycle through the Seq methods: for my $method (keys %refMap) { # Cycle through potential matching attributes: for my $match (@{$refMap{$method}}) { # If the <Attribute> name matches one of the keys, # set $value, unless it has already been set $value ||= $content if ($name =~ /$match/i); } if ($value ne "") { my $str = '$reference->' . $method . "($value)"; eval($str); next; } } next if ($value ne ""); # Don't know what the <Attribute> is, dump it to comments: push @refCom, $name . $nvtoken . $content; } unless ($#refCom < 0) { # Random stuff was found, tack it to the comment field my $exist = $reference->comment; $exist .= join ", ", @refCom; $reference->comment($exist); } push @refs, $reference; } $bioSeq->annotation->add_Annotation('reference' => $_) for @refs; my $ann_col = $bioSeq->annotation; # Extract the <Feature>s for this <Sequence> for my $feat ( $xmlSeq->getElementsByTagName("Feature") ) { $bioSeq->add_SeqFeature( $self->_parse_bsml_feature($feat) ); } $species->classification( @classification ); $bioSeq->species( $species ); $bioSeq->annotation->add_Annotation('dblink' => $_) for @links; $self->{'current_node'}++; return $bioSeq; } #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Get all the <Attribute> and <Qualifier> children for an object, and # return them as an array reference # ('floppy' since these elements have poor/no schema control) sub GETFLOPPIES { my $obj = shift; my @floppies; my $attributes = $obj->getElementsByTagName ("Attribute"); for (my $i = 0; $i < $attributes->getLength; $i++) { push @floppies, $attributes->item($i); } my $qualifiers = $obj->getElementsByTagName ("Qualifier"); for (my $i = 0; $i < $qualifiers->getLength; $i++) { push @floppies, $qualifiers->item($i); } return \@floppies; } #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Given a DOM <Attribute> or <Qualifier> object, return the [name, value] pair sub FLOPPYVALS { my $obj = shift; my ($name, $value); if ($obj->getNodeName eq "Attribute") { $name = $obj->getAttribute('name'); $value = $obj->getAttribute('content'); } elsif ($obj->getNodeName eq "Qualifier") { # Wheras <Attribute>s require both 'name' and 'content' attributes, # <Qualifier>s can technically have either blank (and sometimes do) my $n = $obj->getAttribute('value-type'); $name = $n if ($n ne ""); my $v = $obj->getAttribute('value'); $value = $v if ($v ne ""); } return ($name, $value); } #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Returns the value of the first TEXT_NODE encountered below an element # Rational - avoid grabbing a comment rather than the PCDATA. Not foolproof... sub FIRSTDATA { my $element = shift; return unless ($element); my $hopefuls = $element->getChildNodes; my $data; for (my $i = 0; $i < $hopefuls->getLength; $i++) { if ($hopefuls->item($i)->getNodeType == XML::DOM::Node::TEXT_NODE() ) { $data = $hopefuls->item($i)->getNodeValue; last; } } return $data; } #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Just collapses whitespace runs in a string sub STRIP { my $string = shift; $string =~ s/[\s\r\n]+/ /g; return $string; } =head2 to_bsml Title : to_bsml Usage : my $domDoc = $obj->to_bsml(@args) Function: Generates an XML structure for one or more Bio::Seq objects. If $seqref is an array ref, the XML tree generated will include all the sequences in the array. Returns : A reference to the XML DOM::Document object generated / modified Args : Argument array in form of -key => val. Recognized keys: -seq A Bio::Seq reference, or an array reference of many of them -xmldoc Specifies an existing XML DOM document to add the sequences to. If included, then only data (no page formatting) will be added. If not, a new XML::DOM::Document will be made, and will be populated with both <Sequence> data, as well as <Page> display elements. -nodisp Do not generate <Display> elements, or any children thereof, even if -xmldoc is not set. -skipfeat If set to 'all', all <Feature>s will be skipped. If it is a hash reference, any <Feature> with a class matching a key in the hash will be skipped - for example, to skip 'source' and 'score' features, use: -skipfeat => { source => 'Y', score => 'Y' } -skiptags As above: if set to 'all', no tags are included, and if a hash reference, those specific tags will be ignored. Skipping some or all tags and features can result in noticeable speed improvements. -nodata If true, then <Seq-data> will not be included. This may be useful if you just want annotations and do not care about the raw ACTG information. -return Default is 'xml', which will return a reference to the BSML XML object. If set to 'seq' will return an array ref of the <Sequence> objects added (rather than the whole XML object) -close Early BSML browsers will crash if an element *could* have children but does not, and is closed as an empty element e.g. <Styles/>. If -close is true, then such tags are given a comment child to explicitly close them e.g. <Styles><!-- --></Styles>. This is default true, set to "0" if you do not want this behavior. Examples : my $domObj = $stream->to_bsml( -seq => \@fourCoolSequenceObjects, -skipfeat => { source => 1 }, ); # Or add sequences to an existing BSML document: $stream->to_bsml( -seq => \@fourCoolSequenceObjects, -skipfeat => { source => 1 }, -xmldoc => $myBsmlDocumentInProgress, ); =cut sub to_bsml { my $self = shift; my $args = $self->_parseparams( -close => 1, -return => 'xml', @_); $args->{NODISP} ||= $args->{NODISPLAY}; my $seqref = $args->{SEQ}; $seqref = (ref($seqref) eq 'ARRAY') ? $seqref : [ $seqref ]; ############################# # Basic BSML XML Components # ############################# my $xml; my ($bsmlElem, $defsElem, $seqsElem, $dispElem); if ($args->{XMLDOC}) { # The user has provided an existing XML DOM object $xml = $args->{XMLDOC}; unless ($xml->isa("XML::DOM::Document")) { $self->throw('SeqIO::bsml.pm error:\n'. 'When calling ->to_bsml( { xmldoc => $myDoc }), $myDoc \n' . 'should be an XML::DOM::Document object, or an object that\n'. 'inherits from that class (like BsmlHelper.pm)'); } } else { # The user has not provided a new document, make one from scratch $xml = XML::DOM::Document->new(); $xml->setXMLDecl( $xml->createXMLDecl("1.0") ); my $url = "http://www.labbook.com/dtd/bsml2_2.dtd"; my $doc = $xml->createDocumentType("Bsml",$url); $xml->setDoctype($doc); $bsmlElem = $self->_addel( $xml, 'Bsml'); $defsElem = $self->_addel( $bsmlElem, 'Definitions'); $seqsElem = $self->_addel( $defsElem, 'Sequences'); unless ($args->{NODISP}) { $dispElem = $self->_addel( $bsmlElem, 'Display'); my $stylElem = $self->_addel( $dispElem, 'Styles'); my $style = $self->_addel( $stylElem, 'Style', { type => "text/css" }); my $styleText = qq(Interval-widget { display : "1"; }\n) . qq(Feature { display-auto : "1"; }); $style->appendChild( $xml->createTextNode($styleText) ); } } # Establish fundamental BSML elements, if they do not already exist $bsmlElem ||= $xml->getElementsByTagName("Bsml")->item(0); $defsElem ||= $xml->getElementsByTagName("Definitions")->item(0); $seqsElem ||= $xml->getElementsByTagName("Sequences")->item(0); ############### # <Sequences> # ############### # Map over Bio::Seq to BSML my %mol = ('dna' => 'DNA', 'rna' => 'RNA', 'protein' => 'AA'); my @xmlSequences; for my $bioSeq (@{$seqref}) { my $xmlSeq = $xml->createElement("Sequence"); my $FTs = $xml->createElement("Feature-tables"); # Array references to hold <Reference> objects: my $seqRefs = []; my $featRefs = []; # Array references to hold <Attribute> values (not objects): my $seqDesc = []; push @{$seqDesc}, [ "comment", "This file generated to BSML 2.2 standards - " . "joins will be collapsed to a single feature enclosing all members of the join" ]; push @{$seqDesc}, ["description" , eval{$bioSeq->desc}]; for my $kwd ( eval{$bioSeq->get_keywords} ) { push @{$seqDesc}, ["keyword" , $kwd]; } push @{$seqDesc}, ["keyword" , eval{$bioSeq->keywords}]; push @{$seqDesc}, ["version" , eval{ join(".", $bioSeq->accession_number, $bioSeq->seq_version); }]; push @{$seqDesc}, ["division" , eval{$bioSeq->division}]; push @{$seqDesc}, ["pid" , eval{$bioSeq->pid}]; # push @{$seqDesc}, ["bio_object" , ref($bioSeq)]; push @{$seqDesc}, ["primary_id" , eval{$bioSeq->primary_id}]; for my $dt (eval{$bioSeq->get_dates()} ) { push @{$seqDesc}, ["date" , $dt]; } for my $ac (eval{$bioSeq->get_secondary_accessions()} ) { push @{$seqDesc}, ["secondary_accession" , $ac]; } # Determine the accession number and a unique identifier my $acc = $bioSeq->accession_number eq "unknown" ? "" : $bioSeq->accession_number; my $id; my $pi = $bioSeq->primary_id; if ($pi && $pi !~ /Bio::/) { # Not sure I understand what primary_id is... It sometimes # is a string describing a reference to a BioSeq object... $id = "SEQ" . $bioSeq->primary_id; } else { # Nothing useful found, make a new unique ID $id = $acc || ("SEQ-io" . $idcounter->{Sequence}++); } # print "$id->",ref($bioSeq->primary_id),"\n"; # An id field with spaces is interpreted as an idref - kill the spaces $id =~ s/ /-/g; # Map over <Sequence> attributes my %attr = ( 'title' => $bioSeq->display_id, 'length' => $bioSeq->length, 'ic-acckey' => $acc, 'id' => $id, 'representation' => 'raw', ); $attr{molecule} = $mol{ lc($bioSeq->molecule) } if $bioSeq->can('molecule'); for my $a (keys %attr) { $xmlSeq->setAttribute($a, $attr{$a}) if (defined $attr{$a} && $attr{$a} ne ""); } # Orphaned Attributes: $xmlSeq->setAttribute('topology', 'circular') if ($bioSeq->is_circular); # <Sequence> strand, locus $self->_add_page($xml, $xmlSeq) if ($dispElem); ################ # <Attributes> # ################ # Check for Bio::Annotations on the * <Sequence> *. $self->_parse_annotation( -xml => $xml, -obj => $bioSeq, -desc => $seqDesc, -refs => $seqRefs); # Incorporate species data if (ref($bioSeq->species) eq 'Bio::Species') { # Need to peer into Bio::Species ... my @specs = ('common_name', 'genus', 'species', 'sub_species'); for my $sp (@specs) { next unless (my $val = $bioSeq->species()->$sp()); push @{$seqDesc}, [$sp , $val]; } push @{$seqDesc}, ['classification', (join " ", $bioSeq->species->classification) ]; # Species::binomial will return "genus species sub_species" ... } elsif (my $val = $bioSeq->species) { # Ok, no idea what it is, just dump it in there... push @{$seqDesc}, ["species", $val]; } # Add the description <Attribute>s for the <Sequence> for my $seqD (@{$seqDesc}) { $self->_addel($xmlSeq, "Attribute", { name => $seqD->[0], content => $seqD->[1]}) if ($seqD->[1]); } # If sequence references were added, make a Feature-table for them unless ($#{$seqRefs} < 0) { my $seqFT = $self->_addel($FTs, "Feature-table", { title => "Sequence References", }); for my $feat (@{$seqRefs}) { $seqFT->appendChild($feat); } } # This is the appropriate place to add <Feature-tables> $xmlSeq->appendChild($FTs); ############# # <Feature> # ############# #>>>> # Perhaps it is better to loop through top_Seqfeatures?... #>>>> # ...however, BSML does not have a hierarchy for Features if (defined $args->{SKIPFEAT} && $args->{SKIPFEAT} eq 'all') { $args->{SKIPFEAT} = { all => 1}; } else { $args->{SKIPFEAT} ||= {} } for my $class (keys %{$args->{SKIPFEAT}}) { $args->{SKIPFEAT}{lc($class)} = $args->{SKIPFEAT}{$class}; } # Loop through all the features my @features = $bioSeq->all_SeqFeatures(); if (@features && !$args->{SKIPFEAT}{all}) { my $ft = $self->_addel($FTs, "Feature-table", { title => "Features", }); for my $bioFeat (@features ) { my $featDesc = []; my $class = lc($bioFeat->primary_tag); # The user may have specified to ignore this type of feature next if ($args->{SKIPFEAT}{$class}); my $id = "FEAT-io" . $idcounter->{Feature}++; my $xmlFeat = $self->_addel( $ft, 'Feature', { 'id' => $id, 'class' => $class , 'value-type' => $bioFeat->source_tag }); # Check for Bio::Annotations on the * <Feature> *. $self->_parse_annotation( -xml => $xml, -obj => $bioFeat, -desc => $featDesc, -id => $id, -refs =>$featRefs, ); # Add the description stuff for the <Feature> for my $de (@{$featDesc}) { $self->_addel($xmlFeat, "Attribute", { name => $de->[0], content => $de->[1]}) if ($de->[1]); } $self->_parse_location($xml, $xmlFeat, $bioFeat); # loop through the tags, add them as <Qualifiers> next if (defined $args->{SKIPTAGS} && $args->{SKIPTAGS} =~ /all/i); # Tags can consume a lot of CPU cycles, and can often be # rather non-informative, so -skiptags can allow one total or # selective omission of tags. for my $tag ($bioFeat->all_tags()) { next if (exists $args->{SKIPTAGS}{$tag}); for my $val ($bioFeat->each_tag_value($tag)) { $self->_addel( $xmlFeat, 'Qualifier', { 'value-type' => $tag , 'value' => $val }); } } } } ############## # <Seq-data> # ############## # Add sequence data if ( (my $data = $bioSeq->seq) && !$args->{NODATA} ) { my $d = $self->_addel($xmlSeq, 'Seq-data'); $d->appendChild( $xml->createTextNode($data) ); } # If references were added, make a Feature-table for them unless ($#{$featRefs} < 0) { my $seqFT = $self->_addel($FTs, "Feature-table", { title => "Feature References", }); for my $feat (@{$featRefs}) { $seqFT->appendChild($feat); } } # Place the completed <Sequence> tree as a child of <Sequences> $seqsElem->appendChild($xmlSeq); push @xmlSequences, $xmlSeq; } # Prevent browser crashes by explicitly closing empty elements: if ($args->{CLOSE}) { my @problemChild = ('Sequences', 'Sequence', 'Feature-tables', 'Feature-table', 'Screen', 'View',); for my $kid (@problemChild) { for my $prob ($xml->getElementsByTagName($kid)) { unless ($prob->hasChildNodes) { $prob->appendChild( $xml->createComment(" Must close <$kid> explicitly ")); } } } } if (defined $args->{RETURN} && $args->{RETURN} =~ /seq/i) { return \@xmlSequences; } else { return $xml; } } =head2 write_seq Title : write_seq Usage : $obj->write_seq(@args) Function: Prints out an XML structure for one or more Bio::Seq objects. If $seqref is an array ref, the XML tree generated will include all the sequences in the array. This method is fairly simple, most of the processing is performed within to_bsml. Returns : A reference to the XML object generated / modified Args : Argument array. Recognized keys: -seq A Bio::Seq reference, or an array reference of many of them Alternatively, the method may be called simply as... $obj->write_seq( $bioseq ) ... if only a single argument is passed, it is assumed that it is the sequence object (can also be an array ref of many Seq objects ) -printmime If true prints "Content-type: $mimetype\n\n" at top of document, where $mimetype is the value designated by this key. For generic XML use text/xml, for BSML use text/x-bsml -return This option will be suppressed, since the nature of this method is to print out the XML document. If you wish to retrieve the <Sequence> objects generated, use the to_bsml method directly. =cut sub write_seq { my $self = shift; my $args = $self->_parseparams( @_); if ($#_ == 0 ) { # If only a single value is passed, assume it is the seq object unshift @_, "-seq"; } # Build a BSML XML DOM object based on the sequence(s) my $xml = $self->to_bsml( @_, -return => undef ); # Convert to a string my $out = $xml->toString; # Print after putting a return after each element - more readable $out =~ s/>/>\n/g; $self->_print("Content-type: " . $args->{PRINTMIME} . "\n\n") if ($args->{PRINTMIME}); $self->_print( $out ); # Return the DOM tree in case the user wants to do something with it $self->flush if $self->_flush_on_write && defined $self->_fh; return $xml; } =head1 INTERNAL METHODS #-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#- The following methods are used for internal processing, and should probably not be accessed by the user. =head2 _parse_location Title : _parse_location Usage : $obj->_parse_location($xmlDocument, $parentElem, $SeqFeatureObj) Function: Adds <Interval-loc> and <Site-loc> children to <$parentElem> based on locations / sublocations found in $SeqFeatureObj. If sublocations exist, the original location will be ignored. Returns : An array ref containing the elements added to the parent. These will have already been added to <$parentElem> Args : 0 The DOM::Document being modified 1 The DOM::Element parent that you want to add to 2 Reference to the Bio::SeqFeature being analyzed =cut ############################### # <Interval-loc> & <Site-loc> # ############################### sub _parse_location { my $self = shift; my ($xml, $xmlFeat, $bioFeat) = @_; my $bioLoc = $bioFeat->location; my @locations; if (ref($bioLoc) =~ /Split/) { @locations = $bioLoc->sub_Location; # BSML 2.2 does not recognize / support joins. For this reason, # we will just use the upper-level location. The line below can # be deleted or commented out if/when BSML 3 supports complex # interval deffinitions: @locations = ($bioLoc); } else { @locations = ($bioLoc); } my @added = (); # Add the site or interval positional information: for my $loc (@locations) { my ($start, $end) = ($loc->start, $loc->end); my %locAttr; # Strand information is not well described in BSML $locAttr{complement} = 1 if ($loc->strand == -1); if ($start ne "" && ($start == $end || $end eq "")) { $locAttr{sitepos} = $start; push @added, $self->_addel($xmlFeat,'Site-loc',\%locAttr); } elsif ($start ne "" && $end ne "") { if ($start > $end) { # The feature is on the complementary strand ($start, $end) = ($end, $start); $locAttr{complement} = 1; } $locAttr{startpos} = $start; $locAttr{endpos} = $end; push @added, $self->_addel($xmlFeat,'Interval-loc',\%locAttr); } else { warn "Failure to parse SeqFeature location. Start = '$start' & End = '$end'"; } } return \@added; } =head2 _parse_bsml_feature Title : _parse_bsml_feature Usage : $obj->_parse_bsml_feature($xmlFeature ) Function: Will examine the <Feature> element provided by $xmlFeature and return a generic seq feature. Returns : Bio::SeqFeature::Generic Args : 0 XML::DOM::Element <Feature> being analyzed. =cut sub _parse_bsml_feature { my $self = shift; my ($feat) = @_; my $basegsf = Bio::SeqFeature::Generic->new(); # score # frame # source_tag # Use the class as the primary tag value, if it is present if ( my $val = $feat->getAttribute("class") ) { $basegsf->primary_tag($val); } # Positional information is in <Interval-loc>s or <Site-loc>s # We need to grab these in order, to try to recreate joins... my @locations = (); for my $kid ($feat->getChildNodes) { my $nodeName = $kid->getNodeName; next unless ($nodeName eq "Interval-loc" || $nodeName eq "Site-loc"); push @locations, $kid; } if ($#locations == 0) { # There is only one location specified $self->_parse_bsml_location($locations[0], $basegsf); } elsif ($#locations > 0) { #>>>> # This is not working, I think the error is somewhere downstream # of add_sub_SeqFeature, probably in RangeI::union ? # The sub features are added fine, but the EXPANDed parent feature # location has a messed up start - Bio::SeqFeature::Generic ref # instead of an integer - and an incorrect end - the end of the first # sub feature added, not of the union of all of them. # Also, the SeqIO::genbank.pm output is odd - the sub features appear # to be listed with the *previous* feature, not this one. for my $location (@locations) { my $subgsf = $self->_parse_bsml_location($location); # print "start ", $subgsf->start,"\n"; # print "end ", $subgsf->end,"\n"; $basegsf->add_sub_SeqFeature($subgsf, 'EXPAND'); } # print $feat->getAttribute('id'),"\n"; # print $basegsf->primary_tag,"\n"; } else { # What to do if there are no locations? Nothing needed? } # Look at any <Attribute>s or <Qualifier>s that are present: my $floppies = &GETFLOPPIES($feat); for my $attr (@{$floppies}) { my ($name, $content) = &FLOPPYVALS($attr); # Don't know what the object is, dump it to a tag: $basegsf->add_tag_value(lc($name), $content); } # Mostly this helps with debugging, but may be of utility... # Add a tag holding the BSML id value if ( (my $val = $feat->getAttribute('id')) && !$basegsf->has_tag('bsml-id')) { # Decided that this got a little sloppy... # $basegsf->add_tag_value("bsml-id", $val); } return $basegsf; } =head2 _parse_bsml_location Title : _parse_bsml_location Usage : $obj->_parse_bsml_feature( $intOrSiteLoc, $gsfObject ) Function: Will examine the <Interval-loc> or <Site-loc> element provided Returns : Bio::SeqFeature::Generic Args : 0 XML::DOM::Element <Interval/Site-loc> being analyzed. 1 Optional SeqFeature::Generic to use =cut sub _parse_bsml_location { my $self = shift; my ($loc, $gsf) = @_; $gsf ||= Bio::SeqFeature::Generic->new(); my $type = $loc->getNodeName; my ($start, $end); if ($type eq 'Interval-loc') { $start = $loc->getAttribute('startpos'); $end = $loc->getAttribute('endpos'); } elsif ($type eq 'Site-loc') { $start = $end = $loc->getAttribute('sitepos'); } else { warn "Unknown location type '$type', could not make GSF\n"; return; } $gsf->start($start); $gsf->end($end); # BSML does not have an explicit method to set undefined strand if (my $s = $loc->getAttribute("complement")) { if ($s) { $gsf->strand(-1); } else { $gsf->strand(1); } } else { # We're setting "strand nonspecific" here - bad idea? # In most cases the user likely meant it to be on the + strand $gsf->strand(0); } return $gsf; } =head2 _parse_reference Title : _parse_reference Usage : $obj->_parse_reference(@args ) Function: Makes a new <Reference> object from a ::Reference, which is then stored in an array provide by -refs. It will be appended to the XML tree later. Returns : Args : Argument array. Recognized keys: -xml The DOM::Document being modified -refobj The Annotation::Reference Object -refs An array reference to hold the new <Reference> DOM object -id Optional. If the XML id for the 'calling' element is provided, it will be placed in any <Reference> refs attribute. =cut sub _parse_reference { my $self = shift; my $args = $self->_parseparams( @_); my ($xml, $ref, $refRef) = ($args->{XML}, $args->{REFOBJ}, $args->{REFS}); ############### # <Reference> # ############### my $xmlRef = $xml->createElement("Reference"); #>> This may not be the right way to make a BSML dbxref... if (my $link = $ref->medline) { $xmlRef->setAttribute('dbxref', $link); } # Make attributes for some of the characteristics my %stuff = ( start => $ref->start, end => $ref->end, rp => $ref->rp, comment => $ref->comment, pubmed => $ref->pubmed, ); for my $s (keys %stuff) { $self->_addel($xmlRef, "Attribute", { name => $s, content => $stuff{$s} }) if ($stuff{$s}); } $xmlRef->setAttribute('refs', $args->{ID}) if ($args->{ID}); # Add the basic information # Should probably check for content before creation... $self->_addel($xmlRef, "RefAuthors")-> appendChild( $xml->createTextNode(&STRIP($ref->authors)) ); $self->_addel($xmlRef, "RefTitle")-> appendChild( $xml->createTextNode(&STRIP($ref->title)) ); $self->_addel($xmlRef, "RefJournal")-> appendChild( $xml->createTextNode(&STRIP($ref->location)) ); # References will be added later in a <Feature-Table> push @{$refRef}, $xmlRef; } =head2 _parse_annotation Title : _parse_annotation Usage : $obj->_parse_annotation(@args ) Function: Will examine any Annotations found in -obj. Data found in ::Comment and ::DBLink structures, as well as Annotation description fields are stored in -desc for later generation of <Attribute>s. <Reference> objects are generated from ::References, and are stored in -refs - these will be appended to the XML tree later. Returns : Args : Argument array. Recognized keys: -xml The DOM::Document being modified -obj Reference to the Bio object being analyzed -descr An array reference for holding description text items -refs An array reference to hold <Reference> DOM objects -id Optional. If the XML id for the 'calling' element is provided, it will be placed in any <Reference> refs attribute. =cut sub _parse_annotation { my $self = shift; my $args = $self->_parseparams( @_); my ($xml, $obj, $descRef, $refRef) = ( $args->{XML}, $args->{OBJ}, $args->{DESC}, $args->{REFS} ); # No good place to put any of this (except for references). Most stuff # just gets dumped to <Attribute>s my $ann = $obj->annotation; return unless ($ann); # use BMS::Branch; my $debug = BMS::Branch->new( ); warn "$obj :"; $debug->branch($ann); unless (ref($ann) =~ /Collection/) { # Old style annotation. It seems that Features still use this # form of object $self->_parse_annotation_old(@_); return; } for my $key ($ann->get_all_annotation_keys()) { for my $thing ($ann->get_Annotations($key)) { if ($key eq 'description') { push @{$descRef}, ["description" , $thing->value]; } elsif ($key eq 'comment') { push @{$descRef}, ["comment" , $thing->text]; } elsif ($key eq 'dblink') { # DBLinks get dumped to attributes, too push @{$descRef}, ["db_xref" , $thing->database . ":" . $thing->primary_id ]; if (my $com = $thing->comment) { push @{$descRef}, ["link" , $com->text ]; } } elsif ($key eq 'reference') { $self->_parse_reference( @_, -refobj => $thing ); } elsif (ref($thing) =~ /SimpleValue/) { push @{$descRef}, [$key , $thing->value]; } else { # What is this?? push @{$descRef}, ["error", "bsml.pm did not understand ". "'$key' = '$thing'" ]; } } } } =head2 _parse_annotation_old Title : _parse_annotation_old Usage : $obj->_parse_annotation_old(@args) Function: As above, but for the old Annotation system. Apparently needed because Features are still using the old-style annotations? Returns : Args : Argument array. Recognized keys: -xml The DOM::Document being modified -obj Reference to the Bio object being analyzed -descr An array reference for holding description text items -refs An array reference to hold <Reference> DOM objects -id Optional. If the XML id for the 'calling' element is provided, it will be placed in any <Reference> refs attribute. =cut ############### # <Reference> # ############### sub _parse_annotation_old { my $self = shift; my $args = $self->_parseparams( @_); my ($xml, $obj, $descRef, $refRef) = ( $args->{XML}, $args->{OBJ}, $args->{DESC}, $args->{REFS} ); # No good place to put any of this (except for references). Most stuff # just gets dumped to <Attribute>s if (my $ann = $obj->annotation) { push @{$descRef}, ["annotation", $ann->description]; for my $com ($ann->each_Comment) { push @{$descRef}, ["comment" , $com->text]; } # Gene names just get dumped to <Attribute name="gene"> for my $gene ($ann->each_gene_name) { push @{$descRef}, ["gene" , $gene]; } # DBLinks get dumped to attributes, too for my $link ($ann->each_DBLink) { push @{$descRef}, ["db_xref" , $link->database . ":" . $link->primary_id ]; if (my $com = $link->comment) { push @{$descRef}, ["link" , $com->text ]; } } # References get produced and temporarily held for my $ref ($ann->each_Reference) { $self->_parse_reference( @_, -refobj => $ref ); } } } =head2 _add_page Title : _add_page Usage : $obj->_add_page($xmlDocument, $xmlSequenceObject) Function: Adds a simple <Page> and <View> structure for a <Sequence> Returns : a reference to the newly created <Page> Args : 0 The DOM::Document being modified 1 Reference to the <Sequence> object =cut sub _add_page { my $self = shift; my ($xml, $seq) = @_; my $disp = $xml->getElementsByTagName("Display")->item(0); my $page = $self->_addel($disp, "Page"); my ($width, $height) = ( 7.8, 5.5); my $screen = $self->_addel($page, "Screen", { width => $width, height => $height, }); # $screen->appendChild($xml->createComment("Must close explicitly")); my $view = $self->_addel($page, "View", { seqref => $seq->getAttribute('id'), title => $seq->getAttribute('title'), title1 => "{NAME}", title2 => "{LENGTH} {UNIT}", }); $self->_addel($view, "View-line-widget", { shape => 'horizontal', hcenter => $width/2 + 0.7, 'linear-length' => $width - 2, }); $self->_addel($view, "View-axis-widget"); return $page; } =head2 _addel Title : _addel Usage : $obj->_addel($parentElem, 'ChildName', { anAttr => 'someValue', anotherAttr => 'aValue',}) Function: Add an element with attribute values to a DOM tree Returns : a reference to the newly added element Args : 0 The DOM::Element parent that you want to add to 1 The name of the new child element 2 Optional hash reference containing attribute name => attribute value assignments =cut sub _addel { my $self = shift; my ($root, $name, $attr) = @_; # Find the DOM::Document for the parent my $doc = $root->getOwnerDocument || $root; my $elem = $doc->createElement($name); for my $a (keys %{$attr}) { $elem->setAttribute($a, $attr->{$a}); } $root->appendChild($elem); return $elem; } =head2 _show_dna Title : _show_dna Usage : $obj->_show_dna($newval) Function: (cut-and-pasted directly from embl.pm) Returns : value of _show_dna Args : newvalue (optional) =cut sub _show_dna { my $obj = shift; if( @_ ) { my $value = shift; $obj->{'_show_dna'} = $value; } return $obj->{'_show_dna'}; } =head2 _initialize Title : _initialize Usage : $dom = $obj->_initialize(@args) Function: Coppied from embl.pm, and augmented with initialization of the XML DOM tree Returns : Args : -file => the XML file to be parsed =cut sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); # hash for functions for decoding keys. $self->{'_func_ftunit_hash'} = {}; $self->_show_dna(1); # sets this to one by default. People can change it my %param = @args; # From SeqIO.pm @param{ map { lc $_ } keys %param } = values %param; # lowercase keys if ( exists $param{-file} && $param{-file} !~ /^>/) { # Is it blasphemy to add your own keys to an object in another package? # domtree => the parsed DOM tree retruned by XML::DOM $self->{'domtree'} = $self->_parse_xml( $param{-file} ); # current_node => the <Sequence> node next in line for next_seq $self->{'current_node'} = 0; } $self->sequence_factory( Bio::Seq::SeqFactory->new ( -verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')) if( ! defined $self->sequence_factory ); } =head2 _parseparams Title : _parseparams Usage : my $paramHash = $obj->_parseparams(@args) Function: Borrowed from Bio::Parse.pm, who borrowed it from CGI.pm Lincoln Stein -> Richard Resnick -> here Returns : A hash reference of the parameter keys (uppercase) pointing to their values. Args : An array of key, value pairs. Easiest to pass values as: -key1 => value1, -key2 => value2, etc Leading "-" are removed. =cut sub _parseparams { my $self = shift; my %hash = (); my @param = @_; # Hacked out from Parse.pm # The next few lines strip out the '-' characters which # preceed the keys, and capitalizes them. for (my $i=0;$i<@param;$i+=2) { $param[$i]=~s/^\-//; $param[$i]=~tr/a-z/A-Z/; } pop @param if @param %2; # not an even multiple %hash = @param; return \%hash; } =head2 _parse_xml Title : _parse_xml Usage : $dom = $obj->_parse_xml($filename) Function: uses XML::DOM to construct a DOM tree from the BSML document Returns : a reference to the parsed DOM tree Args : 0 Path to the XML file needing to be parsed =cut sub _parse_xml { my $self = shift; my $file = shift; unless (-e $file) { $self->throw("Could not parse non-existant XML file '$file'."); return; } my $parser = XML::DOM::Parser->new(); my $doc = $parser->parsefile ($file); return $doc; } sub DESTROY { my $self = shift; # Reports off the net imply that DOM::Parser will memory leak if you # do not explicitly dispose of it: # http://aspn.activestate.com/ASPN/Mail/Message/perl-xml/788458 my $dom = $self->{'domtree'}; # For some reason the domtree can get undef-ed somewhere... $dom->dispose if ($dom); } =head1 TESTING SCRIPT The following script may be used to test the conversion process. You will need a file of the format you wish to test. The script will convert the file to BSML, store it in /tmp/bsmltemp, read that file into a new SeqIO stream, and write it back as the original format. Comparison of this second file to the original input file will allow you to track where data may be lost or corrupted. Note that you will need to specify $readfile and $readformat. use Bio::SeqIO; # Tests preservation of details during round-trip conversion: # $readformat -> BSML -> $readformat my $tempspot = "/tmp/bsmltemp"; # temp folder to hold generated files my $readfile = "rps4y.embl"; # The name of the file you want to test my $readformat = "embl"; # The format of the file being tested system "mkdir $tempspot" unless (-d $tempspot); # Make Seq object from the $readfile my $biostream = Bio::SeqIO->new( -file => "$readfile" ); my $seq = $biostream->next_seq(); # Write BSML from SeqObject my $bsmlout = Bio::SeqIO->new( -format => 'bsml', -file => ">$tempspot/out.bsml"); warn "\nBSML written to $tempspot/out.bsml\n"; $bsmlout->write_seq($seq); # Need to kill object for following code to work... Why is this so? $bsmlout = ""; # Make Seq object from BSML my $bsmlin = Bio::SeqIO->new( -file => "$tempspot/out.bsml", -format => 'bsml'); my $seq2 = $bsmlin->next_seq(); # Write format back from Seq Object my $genout = Bio::SeqIO->new( -format => $readformat, -file => ">$tempspot/out.$readformat"); $genout->write_seq($seq2); warn "$readformat written to $tempspot/out.$readformat\n"; # BEING LOST: # Join information (not possible in BSML 2.2) # Sequence type (??) =cut 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/bsml_sax.pm��������������������������������������������������������������000444��000766��000024�� 17625�13155576320� 17405� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::bsml_sax # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich # =head1 NAME Bio::SeqIO::bsml_sax - BSML sequence input/output stream using SAX =head1 SYNOPSIS It is probably best not to use this object directly, but rather go through the SeqIO handler system. To read a BSML file: $stream = Bio::SeqIO->new( -file => $filename, -format => 'bsml'); while ( my $bioSeqObj = $stream->next_seq() ) { # do something with $bioSeqObj } To write a Seq object to the current file handle in BSML XML format: $stream->write_seq( -seq => $seqObj); If instead you would like a XML::DOM object containing the BSML, use: my $newXmlObject = $stream->to_bsml( -seq => $seqObj); =head1 DEPENDENCIES In addition to parts of the Bio:: hierarchy, this module uses: XML::SAX =head1 DESCRIPTION This object can transform Bio::Seq objects to and from BSML (XML) flatfiles. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =cut package Bio::SeqIO::bsml_sax; use vars qw($Default_Source); use strict; use Bio::SeqFeature::Generic; use Bio::Species; use XML::SAX; use Bio::Seq::SeqFactory; use Bio::Annotation::Collection; use Bio::Annotation::Comment; use Bio::Annotation::Reference; use Bio::Annotation::DBLink; use base qw(Bio::SeqIO XML::SAX::Base); $Default_Source = 'BSML'; sub _initialize { my ($self) = shift; $self->SUPER::_initialize(@_); $self->{'_parser'} = XML::SAX::ParserFactory->parser('Handler' => $self); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } return; } =head1 METHODS =cut =head2 next_seq Title : next_seq Usage : my $bioSeqObj = $stream->next_seq Function: Retrieves the next sequence from a SeqIO::bsml stream. Returns : A reference to a Bio::Seq::RichSeq object Args : =cut sub next_seq { my $self = shift; if( @{$self->{'_seendata'}->{'_seqs'} || []} || eof($self->_fh)) { return shift @{$self->{'_seendata'}->{'_seqs'}}; } $self->{'_parser'}->parse_file($self->_fh); return shift @{$self->{'_seendata'}->{'_seqs'}}; } # XML::SAX::Base methods sub start_document { my ($self,$doc) = @_; $self->{'_seendata'} = {'_seqs' => [], '_authors' => [], '_feats' => [] }; $self->SUPER::start_document($doc); } sub end_document { my ($self,$doc) = @_; $self->SUPER::end_document($doc); } sub start_element { my ($self,$ele) = @_; my $name = uc($ele->{'LocalName'}); my $attr = $ele->{'Attributes'}; my $seqid = defined $self->{'_seendata'}->{'_seqs'}->[-1] ? $self->{'_seendata'}->{'_seqs'}->[-1]->display_id : undef; for my $k ( keys %$attr ) { $attr->{uc $k} = $attr->{$k}; delete $attr->{$k}; } if( $name eq 'BSML' ) { } elsif( $name eq 'DEFINITIONS' ) { } elsif( $name eq 'SEQUENCES' ) { } elsif( $name eq 'SEQUENCE' ) { my ($id,$acc,$title, $desc,$length,$topology, $mol) = map { $attr->{'{}'.$_}->{'Value'} } qw(ID IC-ACCKEY TITLE COMMENT LENGTH TOPOLOGY MOLECULE); push @{$self->{'_seendata'}->{'_seqs'}}, $self->sequence_factory->create ( -display_id => $id, -accession_number => $acc, -description => $desc, -length => $length, -is_circular => ($topology =~ /^linear$/i) ? 0 : 1, -molecule => $mol, ); } elsif( $name eq 'FEATURE-TABLES' ) { } elsif( $name eq 'ATTRIBUTE' ) { my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1]; my ($name,$content) = map { $attr->{'{}'.$_}->{'Value'} } qw(NAME CONTENT); if($name =~ /^version$/i ) { my ($version); if($content =~ /^[^\.]+\.(\d+)/) { $version = $1; } else { $version = $content } $curseq->seq_version($version); } elsif( $name eq 'organism-species') { my ($genus,$species,$subsp) = split(/\s+/,$content,3); $curseq->species(Bio::Species->new(-sub_species => $subsp, -classification => [$species,$genus])); } elsif( $name eq 'organism-classification' ) { my (@class) =(split(/\s*;\s*/,$content),$curseq->species->species); $curseq->species->classification([reverse @class]); } elsif( $name eq 'database-xref' ) { my ($db,$id) = split(/:/,$content); $curseq->annotation->add_Annotation('dblink', Bio::Annotation::DBLink->new ( -database => $db, -primary_id=> $id)); } elsif( $name eq 'date-created' || $name eq 'date-last-updated' ) { $curseq->add_date($content); } } elsif( $name eq 'FEATURE' ) { my ($id,$class,$type,$title,$display_auto) = map { $attr->{'{}'.$_}->{'Value'} } qw(ID CLASS VALUE-TYPE TITLE DISPLAY-AUTO); push @{$self->{'_seendata'}->{'_feats'}}, Bio::SeqFeature::Generic->new ( -seq_id => $self->{'_seendata'}->{'_seqs'}->[-1]->display_id, -source_tag => $Default_Source, -primary_tag => $type, -tag => {'ID' => $id, }); } elsif( $name eq 'QUALIFIER') { my ($type,$value) = map { $attr->{'{}'.$_}->{'Value'} } qw(VALUE-TYPE VALUE); my $curfeat = $self->{'_seendata'}->{'_feats'}->[-1]; $curfeat->add_tag_value($type,$value); } elsif( $name eq 'INTERVAL-LOC' ) { my $curfeat = $self->{'_seendata'}->{'_feats'}->[-1]; my ($start,$end,$strand) = map { $attr->{'{}'.$_}->{'Value'} } qw(STARTPOS ENDPOS COMPLEMENT); $curfeat->start($start); $curfeat->end($end); $curfeat->strand(-1) if($strand); } elsif( $name eq 'REFERENCE' ) { push @{$self->{'_seendata'}->{'_annot'}}, Bio::Annotation::Reference->new(); } push @{$self->{'_state'}}, $name; $self->SUPER::start_element($ele); } sub end_element { my ($self,$ele) = @_; pop @{$self->{'_state'}}; my $name = uc $ele->{'LocalName'}; my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1]; if( $name eq 'REFERENCE') { my $ref = pop @{$self->{'_seendata'}->{'_annot'}}; $curseq->annotation->add_Annotation('reference',$ref); } elsif( $name eq 'FEATURE' ) { my $feat = pop @{$self->{'_seendata'}->{'_feats'}}; $curseq->add_SeqFeature($feat); } $self->SUPER::end_element($ele); } sub characters { my ($self,$data) = @_; if( ! @{$self->{'_state'}} ) { $self->warn("Calling characters with no previous start_element call. Ignoring data"); } else { my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1]; my $curfeat = $self->{'_seendata'}->{'_feats'}->[-1]; my $curannot = $self->{'_seendata'}->{'_annot'}->[-1]; my $name = $self->{'_state'}->[-1]; if( $name eq 'REFAUTHORS' ) { $curannot->authors($data->{'Data'}); } elsif( $name eq 'REFTITLE') { $curannot->title($data->{'Data'}); } elsif( $name eq 'REFJOURNAL') { $curannot->location($data->{'Data'}); } elsif( $name eq 'SEQ-DATA') { $data->{'Data'} =~ s/\s+//g; $curseq->seq($data->{'Data'}); } } $self->SUPER::characters($data); } 1; �����������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/chadoxml.pm��������������������������������������������������������������000444��000766��000024�� 203351�13155576320� 17405� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::chadoxml # # Peili Zhang <peili@morgan.harvard.edu> # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::chadoxml - chadoxml sequence output stream =head1 SYNOPSIS It is probably best not to use this object directly, but rather go through the SeqIO handler system: $writer = Bio::SeqIO->new(-file => ">chado.xml", -format => 'chadoxml'); # assume you already have Sequence or SeqFeature objects $writer->write_seq($seq_obj); #after writing all seqs $writer->close_chadoxml(); =head1 DESCRIPTION This object can transform Bio::Seq objects to chadoxml flat file databases (for chadoxml DTD, see http://gmod.cvs.sourceforge.net/gmod/schema/chado/dat/chado.dtd). This is currently a write-only module. $seqio = Bio::SeqIO->new(-file => '>outfile.xml', -format => 'chadoxml' -suppress_residues => 1, -allow_residues => 'chromosome', ); # we have a Bio::Seq object $seq which is a gene located on # chromosome arm 'X', to be written out to chadoxml # before converting to chadoxml, $seq object B<must> be transformed # so that all the coordinates in $seq are against the source # feature to be passed into Bio::SeqIO::chadoxml->write_seq() # -- chromosome arm X in the example below. $seqio->write_seq(-seq=>$seq, -genus => 'Homo', -species => 'sapiens', -seq_so_type=>'gene', -src_feature=>'X', -src_feat_type=>'chromosome_arm', -nounflatten=>1, -is_analysis=>'true', -data_source=>'GenBank'); The chadoxml output of Bio::SeqIO::chadoxml-E<gt>write_seq() method can be passed to the loader utility in XORT package (http://gmod.cvs.sourceforge.net/gmod/schema/XMLTools/XORT/) to be loaded into chado. This object is currently implemented to work with sequence and annotation data from whole genome projects deposited in GenBank. It may not be able to handle all different types of data from all different sources. In converting a Bio::Seq object into chadoxml, a top-level feature is created to represent the object and all sequence features inside the Bio::Seq object are treated as subfeatures of the top-level feature. The Bio::SeqIO::chadoxml object calls Bio::SeqFeature::Tools::Unflattener to unflatten the flat feature list contained in the subject Bio::Seq object, to build gene model containment hierarchy conforming to chado central dogma model: gene --E<gt> mRNA --E<gt> exons and protein. Destination of data in the subject Bio::Seq object $seq is as following: *$seq->display_id: name of the top-level feature; *$seq->accession_number: if defined, uniquename and feature_dbxref of the top-level feature if not defined, $seq->display_id is used as the uniquename of the top-level feature; *$seq->molecule: transformed to SO type, used as the feature type of the top-level feature if -seq_so_type argument is supplied, use the supplied SO type as the feature type of the top-level feature; *$seq->species: organism of the top-level feature; *$seq->seq: residues of the top-level feature; *$seq->is_circular, $seq->division: feature_cvterm; *$seq->keywords, $seq->desc, comments: featureprop; *references: pub and feature_pub; medline/pubmed ids: pub_dbxref; comments: pubprop; *feature "source" span: featureloc for top-level feature; *feature "source" db_xref: feature_dbxref for top-level feature; *feature "source" other tags: featureprop for top-level feature; *subfeature 'symbol' or 'label' tag: feature uniquename, if none of these is present, the chadoxml object generates feature uniquenames as: <gene>-<feature_type>-<span> (e.g. foo-mRNA--1000..3000); *gene model: feature_relationship built based on the containment hierarchy; *feature span: featureloc; *feature accession numbers: feature_dbxref; *feature tags (except db_xref, symbol and gene): featureprop; Things to watch out for: *chado schema change: this version works with the chado version tagged chado_1_01 in GMOD CVS. *feature uniquenames: especially important if using XORT loader to do incremental load into chado. may need pre-processing of the source data to put the correct uniquenames in place. *pub uniquenames: chadoxml->write_seq() has the FlyBase policy on pub uniquenames hard-coded, it assigns pub uniquenames in the following way: for journals and books, use ISBN number; for published papers, use MEDLINE ID; for everything else, use FlyBase unique identifier FBrf#. need to modify the code to implement your policy. look for the comments in the code. *for pubs possibly existing in chado but with no knowledge of its uniquename:put "op" as "match", then need to run the output chadoxml through a special filter that talks to chado database and tries to find the pub by matching with the provided information instead of looking up by the unique key. after matching, the filter also resets the "match" operation to either "force" (default), or "lookup", or "insert", or "update". the "match" operation is for a special FlyBase use case. please modify to work according to your rules. *chado initialization for loading: cv & cvterm: in the output chadoxml, all cv's and cvterm's are lookup only. Therefore, before using XORT loader to load the output into chado, chado must be pre-loaded with all necessary CVs and CVterms, including "SO" , "property type", "relationship type", "pub type", "pubprop type", "pub relationship type", "sequence topology", "GenBank feature qualifier", "GenBank division". A pub by the uniquename 'nullpub' of type 'null pub' needs to be inserted. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Peili Zhang Email peili@morgan.harvard.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::chadoxml; use strict; use English; use Carp; use Data::Dumper; use XML::Writer; use IO::File; use IO::Handle; use Bio::Seq; use Bio::Seq::RichSeq; use Bio::SeqIO::FTHelper; use Bio::Species; use Bio::Seq::SeqFactory; use Bio::Factory::SequenceStreamI; use Bio::SeqFeature::Generic; use Bio::Annotation::Collection; use Bio::Annotation::Comment; use Bio::Annotation::Reference; use Bio::Annotation::DBLink; use Bio::SeqFeature::Tools::Unflattener; #global variables undef(my %finaldatahash); #data from Bio::Seq object stored in a hash undef(my %datahash); #data from Bio::Seq object stored in a hash my $chadotables = 'feature featureprop feature_relationship featureloc feature_cvterm cvterm cv feature_pub pub pub_dbxref pub_author author pub_relationship pubprop feature_dbxref dbxref db synonym feature_synonym'; my %fkey = ( "cvterm.cv_id" => "cv", "cvterm.dbxref_id" => "dbxref", "dbxref.db_id" => "db", "feature.type_id" => "cvterm", "feature.organism_id" => "organism", "feature.dbxref_id" => "dbxref", "featureprop.type_id" => "cvterm", "feature_pub.pub_id" => "pub", "feature_cvterm.cvterm_id" => "cvterm", "feature_cvterm.pub_id" => "pub", "feature_cvterm.feature_id" => "feature", "feature_dbxref.dbxref_id" => "dbxref", "feature_relationship.object_id" => "feature", "feature_relationship.subject_id" => "feature", "feature_relationship.type_id" => "cvterm", "featureloc.srcfeature_id" => "feature", "pub.type_id" => "cvterm", "pub_dbxref.dbxref_id" => "dbxref", "pub_author.author_id" => "author", "pub_relationship.obj_pub_id" => "pub", "pub_relationship.subj_pub_id" => "pub", "pub_relationship.type_id" => "cvterm", "pubprop.type_id" => "cvterm", "feature_synonym.feature_id" => "feature", "feature_synonym.synonym_id" => "synonym", "feature_synonym.pub_id" => "pub", "synonym.type_id" => "cvterm", ); my %cv_name = ( 'relationship' => 'relationship', 'sequence' => 'sequence', 'feature_property' => 'feature_property', ); my %feattype_args2so = ( "aberr" => "aberration_junction", # "conflict" => "sequence_difference", # "polyA_signal" => "polyA_signal_sequence", "variation" => "sequence_variant", "mutation1" => "point_mutation", #for single-base mutation "mutation2" => "sequence_variant", #for multi-base mutation "rescue" => "rescue_fragment", # "rfrag" => "restriction_fragment", "protein_bind" => "protein_binding_site", "misc_feature" => "region", # "prim_transcript" => "primary_transcript", "CDS" => "polypeptide", "reg_element" => "regulatory_region", "seq_variant" => "sequence_variant", "mat_peptide" => "mature_peptide", "sig_peptide" => "signal_peptide", ); undef(my %organism); use base qw(Bio::SeqIO); sub _initialize { my($self,%args) = @_; $self->SUPER::_initialize(%args); unless( defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } #optional arguments that can be passed in $self->suppress_residues($args{'-suppress_residues'}) if defined $args{'-suppress_residues'}; $self->allow_residues($args{'-allow_residues'}) if defined $args{'-allow_residues'}; return; } =head2 write_seq Title : write_seq Usage : $stream->write_seq(-seq=>$seq, -seq_so_type=>$seqSOtype, -src_feature=>$srcfeature, -src_feat_type=>$srcfeattype, -nounflatten=>0 or 1, -is_analysis=>'true' or 'false', -data_source=>$datasource) Function: writes the $seq object (must be seq) into chadoxml. Returns : 1 for success and 0 for error Args : A Bio::Seq object $seq, optional $seqSOtype, $srcfeature, $srcfeattype, $nounflatten, $is_analysis and $data_source. When $srcfeature (a string, the uniquename of the source feature) is given, the location and strand information of the top-level feature against the source feature will be derived from the sequence feature called 'source' of the $seq object, a featureloc record is generated for the top -level feature on $srcfeature. when $srcfeature is given, $srcfeattype must also be present. All feature coordinates in $seq should be against $srcfeature. $seqSOtype is the optional SO term to use as the type of the top-level feature. For example, a GenBank data file for a Drosophila melanogaster genome scaffold has the molecule type of "DNA", when converting to chadoxml, a $seqSOtype argument of "golden_path_region" can be supplied to save the scaffold as a feature of type "golden_path_region" in chadoxml, instead of "DNA". a feature with primary tag of 'source' must be present in the sequence feature list of $seq, to describe the whole sequence record. In the current implementation: =over 3 =item * non-mRNA records A top-level feature of type $seq-E<gt>alphabet is generated for the whole GenBank record, features listed are unflattened for DNA records to build gene model feature graph, and for the other types of records all features in $seq are treated as subfeatures of the top-level feature. =item * mRNA records If a 'gene' feature is present, it B<must> have a /symbol or /label tag to contain the uniquename of the gene. a top-level feature of type 'gene' is generated. the mRNA is written as a subfeature of the top-level gene feature, and the other sequence features listed in $seq are treated as subfeatures of the mRNA feature. =back =cut sub write_seq { my $usage = <<EOUSAGE; Bio::SeqIO::chadoxml->write_seq() Usage : \$stream->write_seq(-seq=>\$seq, -seq_so_type=>\$SOtype, -src_feature=>\$srcfeature, -src_feat_type=>\$srcfeattype, -nounflatten=>0 or 1, -is_analysis=>'true' or 'false', -data_source=>\$datasource) Args : \$seq : a Bio::Seq object \$SOtype : the SO term to use as the feature type of the \$seq record, optional \$srcfeature : unique name of the source feature, a string containing at least one alphabetical letter (a-z, A-Z), optional \$srcfeattype : feature type of \$srcfeature. one of SO terms. optional when \$srcfeature is given, \$srcfeattype becomes mandatory, \$datasource : source of the sequence annotation data, e.g. 'GenBank' or 'GFF'. EOUSAGE my ($self,@args) = @_; my ($seq, $seq_so_type, $srcfeature, $srcfeattype, $nounflatten, $isanalysis, $datasource, $genus, $species) = $self->_rearrange([qw(SEQ SEQ_SO_TYPE SRC_FEATURE SRC_FEAT_TYPE NOUNFLATTEN IS_ANALYSIS DATA_SOURCE GENUS SPECIES )], @args); #print "$seq_so_type, $srcfeature, $srcfeattype\n"; if( !defined $seq ) { $self->throw("Attempting to write with no seq!"); } if( ! ref $seq || ! $seq->isa('Bio::Seq::RichSeqI') ) { ## FIXME $self->warn(" $seq is not a RichSeqI compliant module. Attempting to dump, but may fail!"); } # try to get the srcfeature from the seqFeature object # for this to work, the user has to pass in the srcfeature type if (!$srcfeature) { if ($seq->can('seq_id')) { $srcfeature=$seq->seq_id if ($seq->seq_id ne $seq->display_name); } } #$srcfeature, when provided, should contain at least one alphabetical letter if (defined $srcfeature) { if ($srcfeature =~ /[a-zA-Z]/) { chomp($srcfeature); } else { $self->throw( $usage ); } #check for mandatory $srcfeattype if (! defined $srcfeattype) { $self->throw( $usage ); #$srcfeattype must be a string of non-whitespace characters } else { if ($srcfeattype =~ /\S+/) { chomp($srcfeattype); } else { $self->throw( $usage ); } } } # variables local to write_seq() my $div = undef; my $hkey = undef; undef(my @top_featureprops); undef(my @featuresyns); undef(my @top_featurecvterms); my $name = $seq->display_id if $seq->can('display_id'); $name = $seq->display_name if $seq->can('display_name'); undef(my @feature_cvterms); undef(my %sthash); undef(my %dvhash); undef(my %h1); undef(my %h2); my $temp = undef; my $ann = undef; undef(my @references); undef(my @feature_pubs); my $ref = undef; my $location = undef; my $fbrf = undef; my $journal = undef; my $issue = undef; my $volume = undef; my $volumeissue = undef; my $pages = undef; my $year = undef; my $pubtype = undef; # my $miniref= undef; my $uniquename = undef; my $refhash = undef; my $feat = undef; my $tag = undef; my $tag_cv = undef; my $ftype = undef; my $subfeatcnt = undef; undef(my @top_featrels); undef (my %srcfhash); local($^W) = 0; # suppressing warnings about uninitialized fields. if (!$name && $seq->can('attributes') ) { ($name) = $seq->attributes('Alias'); } if ($seq->can('accession_number') && defined $seq->accession_number && $seq->accession_number ne 'unknown') { $uniquename = $seq->accession_number; } elsif ($seq->can('accession') && defined $seq->accession && $seq->accession ne 'unknown') { $uniquename = $seq->accession; } elsif ($seq->can('attributes')) { ($uniquename) = $seq->attributes('load_id'); } else { $uniquename = $name; } my $len = $seq->length(); if ($len == 0) { $len = undef; } undef(my $gb_type); if (!$seq->can('molecule') || ! defined ($gb_type = $seq->molecule()) ) { $gb_type = $seq->can('alphabet') ? $seq->alphabet : 'DNA'; } $gb_type = 'DNA' if $ftype eq 'dna'; $gb_type = 'RNA' if $ftype eq 'rna'; if(length $seq_so_type > 0) { if (defined $seq_so_type) { $ftype = $seq_so_type; } elsif ($seq->type) { $ftype = ($seq->type =~ /(.*):/) ? $1 : $seq->type; } else { $ftype = $gb_type; } } else { $ftype = $gb_type; } my %ftype_hash = $self->return_ftype_hash($ftype); if ($species) { %organism = ("genus"=>$genus, "species" => $species); } else { my $spec = $seq->species(); if (!defined $spec) { $self->throw("$seq does not know what organism it is from, which is required by chado. cannot proceed!\n"); } else { %organism = ("genus"=>$spec->genus(), "species" => $spec->species()); } } my $residues; if (!$self->suppress_residues || ($self->suppress_residues && $self->allow_residues eq $ftype)) { $residues = $seq->seq->isa('Bio::PrimarySeq') ? $seq->seq->seq : $seq->seq; } else { $residues = ''; } #set is_analysis flag for gene model features undef(my $isanal); if ($ftype eq 'gene' || $ftype eq 'mRNA' || $ftype eq 'exon' || $ftype eq 'protein' || $ftype eq 'polypeptide') { $isanal = $isanalysis; $isanal = 'false' if !defined $isanal; } %datahash = ( "name" => $name, "uniquename" => $uniquename, "seqlen" => $len, "residues" => $residues, "type_id" => \%ftype_hash, "organism_id" => \%organism, "is_analysis" => $isanal || 'false', ); if (defined $srcfeature) { %srcfhash = $self->_srcf_hash($srcfeature, $srcfeattype, \%organism); my ($phase,$strand); if ($seq->can('phase')) { $phase = $seq->phase; } if ($seq->can('strand')) { $strand = $seq->strand; } my %fl = ( "srcfeature_id" => \%srcfhash, "fmin" => $seq->start - 1, "fmax" => $seq->end, "strand" => $strand, "phase" => $phase, ); $datahash{'featureloc'} = \%fl; } #if $srcfeature is not given, use the Bio::Seq object itself as the srcfeature for featureloc's if (!defined $srcfeature) { $srcfeature = $uniquename; $srcfeattype = $ftype; } #default data source is 'GenBank' if (!defined $datasource) { $datasource = 'GenBank'; } if ($datasource =~ /GenBank/i) { #sequence topology as feature_cvterm if ($seq->can('is_circular') && $seq->is_circular) { %sthash = ( "cvterm_id" => {'name' => 'circular', 'cv_id' => { 'name' => 'sequence topology', }, }, "pub_id" => {'uniquename' => 'nullpub', 'type_id' => { 'name' => 'null pub', 'cv_id' => { 'name'=> 'pub type', }, }, }, ); } else { %sthash = ( "cvterm_id" => { 'name' => 'linear', 'cv_id' => { 'name' => 'sequence topology', } }, "pub_id" => {'uniquename' => 'nullpub', 'type_id' => { 'name' => 'null pub', 'cv_id' => { 'name'=> 'pub type', }, }, }, ); } push(@feature_cvterms, \%sthash); #division as feature_cvterm if ($seq->can('division') && defined $seq->division()) { $div = $seq->division(); %dvhash = ( "cvterm_id" => {'name' => $div, 'cv_id' => { 'name' => 'GenBank division'}}, "pub_id" => {'uniquename' => 'nullpub', 'type_id' => { 'name' => 'null pub', 'cv_id' => { 'name'=> 'pub type'}, }}, ); push(@feature_cvterms, \%dvhash); } $datahash{'feature_cvterm'} = \@feature_cvterms; } # closes if GenBank #featureprop's #DEFINITION if ($seq->can('desc') && defined $seq->desc()) { $temp = $seq->desc(); my %prophash = ( "type_id" => {'name' => 'description', 'cv_id' => { 'name' => $cv_name{'feature_property'} }, }, "value" => $temp, ); push(@top_featureprops, \%prophash); } #KEYWORDS if ($seq->can('keywords')) { $temp = $seq->keywords(); if (defined $temp && $temp ne '.' && $temp ne '') { my %prophash = ( "type_id" => {'name' => 'keywords', 'cv_id' => { 'name' => $cv_name{'feature_property'} } }, "value" => $temp, ); push(@top_featureprops, \%prophash); } } #COMMENT if ($seq->can('annotation')) { $ann = $seq->annotation(); foreach my $comment ($ann->get_Annotations('comment')) { $temp = $comment->as_text(); #print "fcomment: $temp\n"; my %prophash = ( "type_id" => {'name' => 'comment', 'cv_id' => { 'name' => $cv_name{'feature_property'} } }, "value" => $temp, ); push(@top_featureprops, \%prophash); } } my @top_dbxrefs = (); #feature object from Bio::DB::SeqFeature::Store if ($seq->can('attributes')) { my %attributes = $seq->attributes; for my $key (keys %attributes) { next if ($key eq 'parent_id'); next if ($key eq 'load_id'); if ($key eq 'Alias') { @featuresyns = $self->handle_Alias_tag($seq,@featuresyns); } ###FIXME deal with Dbxref, Ontology_term,source, elsif ($key eq 'Ontology_term') { @top_featurecvterms = $self->handle_Ontology_tag($seq,@top_featurecvterms); } elsif ($key eq 'dbxref' or $key eq 'Dbxref') { @top_dbxrefs = $self->handle_dbxref($seq, $key, @top_dbxrefs); } elsif ($key =~ /^[a-z]/) { @top_featureprops = $self->handle_unreserved_tags($seq,$key,@top_featureprops); } } } $datahash{'feature_synonym'} = \@featuresyns; if ($seq->can('source')) { @top_dbxrefs = $self->handle_source($seq,@top_dbxrefs); } #accession and version as feature_dbxref if ($seq->can('accession_number') && defined $seq->accession_number && $seq->accession_number ne 'unknown') { my $db = $self->_guess_acc_db($seq, $seq->accession_number); my %acchash = ( "db_id" => {'name' => $db}, "accession" => $seq->accession_number, "version" => $seq->seq_version, ); my %fdbx = ('dbxref_id' => \%acchash); push(@top_dbxrefs, \%fdbx); } if( $seq->isa('Bio::Seq::RichSeqI') && defined $seq->get_secondary_accessions() ) { my @secacc = $seq->get_secondary_accessions(); my $acc; foreach $acc (@secacc) { my %acchash = ( "db_id" => {'name' => 'GB'}, "accession" => $acc, ); my %fdbx = ('dbxref_id' => \%acchash); push(@top_dbxrefs, \%fdbx); } } #GI number if( $seq->isa('Bio::Seq::RichSeqI') && defined ($seq->pid)) { my $id = $seq->pid; #print "reftype: ", ref($id), "\n"; #if (ref($id) eq 'HASH') { my %acchash = ( "db_id" => {'name' => 'GI'}, "accession" => $id, ); my %fdbx = ('dbxref_id' => \%acchash); push (@top_dbxrefs, \%fdbx); } #REFERENCES as feature_pub if (defined $ann) { #get the references @references = $ann->get_Annotations('reference'); foreach $ref (@references) { undef(my %pubhash); $refhash = $ref->hash_tree(); $location = $ref->location || $refhash->{'location'}; #print "location: $location\n"; #get FBrf#, special for FlyBase SEAN loading if (index($location, ' ==') >= 0) { $location =~ /\s==/; #print "match: $MATCH\n"; #print "prematch: $PREMATCH\n"; #print "postmatch: $POSTMATCH\n"; $fbrf = $PREMATCH; $location = $POSTMATCH; $location =~ s/^\s//; } #print "location: $location\n"; #unpublished reference if ($location =~ /Unpublished/) { $pubtype = 'unpublished'; %pubhash = ( "title" => $ref->title || $refhash->{'title'}, #"miniref" => substr($location, 0, 255), #"uniquename" => $fbrf, "type_id" => {'name' => $pubtype, 'cv_id' => {'name' =>'pub type'}} ); } #submitted elsif ($location =~ /Submitted/) { $pubtype = 'submitted'; %pubhash = ( "title" => $ref->title || $refhash->{'title'}, #"miniref" => substr($location, 0, 255), #"uniquename" => $fbrf, "type_id" => {'name' => $pubtype, 'cv_id' => {'name' =>'pub type'}} ); undef(my $pyear); $pyear = $self->_getSubmitYear($location); if (defined $pyear) { $pubhash{'pyear'} = $pyear; } } #published journal paper elsif ($location =~ /\D+\s\d+\s\((\d+|\d+-\d+)\),\s(\d+-\d+|\d+--\d+)\s\(\d\d\d\d\)$/) { $pubtype = 'paper'; #parse location to get journal, volume, issue, pages & year $location =~ /\(\d\d\d\d\)$/; $year = $MATCH; my $stuff = $PREMATCH; $year =~ s/\(//; #remove the leading parenthesis $year =~ s/\)//; #remove the trailing parenthesis $stuff =~ /,\s(\d+-\d+|\d+--\d+)\s$/; $pages = $MATCH; $stuff = $PREMATCH; $pages =~ s/^, //; #remove the leading comma and space $pages =~ s/ $//; #remove the last space $stuff =~ /\s\d+\s\((\d+|\d+-\d+)\)$/; $volumeissue = $MATCH; $journal = $PREMATCH; $volumeissue =~ s/^ //; #remove the leading space $volumeissue =~ /\((\d+|\d+-\d+)\)$/; $issue = $MATCH; $volume = $PREMATCH; $issue =~ s/^\(//; #remove the leading parentheses $issue =~ s/\)$//; #remove the last parentheses $volume =~ s/^\s//; #remove the leading space $volume =~ s/\s$//; #remove the last space %pubhash = ( "title" => $ref->title || $refhash->{'title'}, "volume" => $volume, "issue" => $issue, "pyear" => $year, "pages" => $pages, #"miniref" => substr($location, 0, 255), #"miniref" => ' ', #"uniquename" => $fbrf, "type_id" => {'name' => $pubtype, 'cv_id' => {'name' =>'pub type'}}, "pub_relationship" => { 'obj_pub_id' => { 'uniquename' => $journal, 'title' => $journal, #'miniref' => substr($journal, 0, 255), 'type_id' =>{'name' => 'journal', 'cv_id' => {'name' => 'pub type' }, }, #'pubprop' =>{'value'=> $journal, # 'type_id'=>{'name' => 'abbreviation', 'cv_id' => {'name' => 'pubprop type'}}, # }, }, 'type_id' => { 'name' => 'published_in', 'cv_id' => { 'name' => 'pub relationship type'}, }, }, ); } #other references else { $pubtype = 'other'; %pubhash = ( "title" => $ref->title || $refhash->{'title'}, #"miniref" => $fbrf, "type_id" => { 'name' => $pubtype, 'cv_id' => {'name' =>'pub type'} } ); } #pub_author my $autref = $self->_getRefAuthors($ref); if (defined $autref) { $pubhash{'pub_author'} = $autref; } # if no author and is type 'submitted' and has submitter address, use the first 100 characters of submitter address as the author lastname. else { if ($pubtype eq 'submitted') { my $autref = $self->_getSubmitAddr($ref); if (defined $autref) { $pubhash{'pub_author'} = $autref; } } } #$ref->comment as pubprop #print "ref comment: ", $ref->comment, "\n"; #print "ref comment: ", $refhash->{'comment'}, "\n"; if (defined $ref->comment || defined $refhash->{'comment'}) { my $comnt = $ref->comment || $refhash->{'comment'}; #print "remark: ", $comnt, "\n"; $pubhash{'pubprop'} = { "type_id" => {'name' => 'comment', 'cv_id' => {'name' => 'pubprop type'}}, "value" => $comnt, }; } #pub_dbxref undef(my @pub_dbxrefs); if (defined $fbrf) { push(@pub_dbxrefs, {dbxref_id => {accession => $fbrf, db_id => {'name' => 'FlyBase'}}}); } if (defined ($temp = $ref->medline)) { push(@pub_dbxrefs, {dbxref_id => {accession => $temp, db_id => {'name' => 'MEDLINE'}}}); #use medline # as the pub's uniquename $pubhash{'uniquename'} = $temp; } if (defined ($temp = $ref->pubmed)) { push(@pub_dbxrefs, {dbxref_id => {accession => $temp, db_id => {'name' => 'PUBMED'}}}); } $pubhash{'pub_dbxref'} = \@pub_dbxrefs; #if the pub uniquename is not defined or blank, put its FBrf# as its uniquename #this is unique to FlyBase #USERS OF THIS MODULE: PLEASE MODIFY HERE TO IMPLEMENT YOUR POLICY # ON PUB UNIQUENAME!!! if (!defined $pubhash{'uniquename'} || $pubhash{'uniquename'} eq '') { if (defined $fbrf) { $pubhash{'uniquename'} = $fbrf; } #else { # $pubhash{'uniquename'} = $self->_CreatePubUname($ref); #} } #add to collection of references #if the pub covers the entire sequence of the top-level feature, add it to feature_pubs if (($ref->start == 1 && $ref->end == $len) || (!defined $ref->start && !defined $ref->end)) { push(@feature_pubs, {"pub_id" => \%pubhash}); } #the pub is about a sub-sequence of the top-level feature #create a feature for the sub-sequence and add pub as its feature_pub #featureloc of this sub-sequence is against the top-level feature, in interbase coordinates. else { my %parf = ( 'uniquename' => $uniquename . ':' . $ref->start . "\.\." . $ref->end, 'organism_id' =>\%organism, 'type_id' =>{'name' =>'region', 'cv_id' => {'name' => $cv_name{'sequence'} }}, ); my %parfsrcf = ( 'uniquename' => $uniquename, 'organism_id' =>\%organism, ); my %parfloc = ( 'srcfeature_id' => \%parfsrcf, 'fmin' => $ref->start - 1, 'fmax' => $ref->end, ); $parf{'featureloc'} = \%parfloc; $parf{'feature_pub'} = {'pub_id' => \%pubhash}; my %ffr = ( 'subject_id' => \%parf, 'type_id' => { 'name' => 'partof', 'cv_id' => { 'name' => $cv_name{'relationship'}}}, ); push(@top_featrels, \%ffr); } } $datahash{'feature_pub'} = \@feature_pubs; } ##construct srcfeature hash for use in featureloc if (defined $srcfeature) { %srcfhash = $self->_srcf_hash($srcfeature, $srcfeattype, \%organism); # my %fr = ( # "object_id" => \%srcfhash, # "type_id" => { 'name' => 'partof', 'cv_id' => { 'name' => 'relationship type'}}, # ); # push (@top_featrels, \%fr); } #unflatten the seq features in $seq if $seq is a gene or a DNA sequence if (($gb_type eq 'gene' || $gb_type eq 'DNA') && !$nounflatten) { my $u = Bio::SeqFeature::Tools::Unflattener->new; $u->unflatten_seq(-seq=>$seq, -use_magic=>1); } my @top_sfs = $seq->get_SeqFeatures; #print $#top_sfs, "\n"; #SUBFEATURES if ($datasource =~ /GenBank/i) { $tag_cv = 'GenBank feature qualifier'; } elsif ($datasource =~ /GFF/i) { $tag_cv = 'feature_property'; } else { $tag_cv = $cv_name{'feature_property'}; } my $si = 0; foreach $feat (@top_sfs) { #$feat = $top_sfs[$si]; #print "si: $si\n"; my $prim_tag = $feat->primary_tag; #print $prim_tag, "\n"; # get all qualifiers of the 'source' feature, load these as top_featureprops of the top level feature if ($prim_tag eq 'source') { foreach $tag ($feat->all_tags()) { #db_xref if ($tag eq 'db_xref' or $tag eq 'Dbxref' or $tag eq 'dbxref') { my @t1 = $feat->each_tag_value($tag); foreach $temp (@t1) { $temp =~ /([^:]*?):(.*)/; my $db = $1; my $xref = $2; #PRE/POST very inefficent #my $db = $PREMATCH; #my $xref = $POSTMATCH; my %acchash = ( "db_id" => {'name' => $db}, "accession" => $xref, ); my %fdbx = ('dbxref_id' => \%acchash); push (@top_dbxrefs, \%fdbx); } #Ontology_term } elsif ($tag eq 'Ontology_term') { my @t1 = $feat->each_tag_value($tag); foreach $temp (@t1) { ###FIXME } #other tags as featureprop } elsif ($tag ne 'gene') { my %prophash = undef; %prophash = ( "type_id" => {'name' => $tag, 'cv_id' => {'name' => $tag_cv}}, "value" => join(' ',$feat->each_tag_value($tag)), ); push(@top_featureprops, \%prophash); } } if ($feat->can('source')) { my $source = $feat->source(); @top_dbxrefs = $self->handle_source($feat, @top_dbxrefs); } #featureloc for the top-level feature my $fmin = undef; my $fmax = undef; my $strand = undef; my $phase = undef; my %fl = undef; $fmin = $feat->start - 1; $fmax = $feat->end; $strand = $feat->strand; if ($feat->can('phase')) { $phase = $feat->phase; } %fl = ( "srcfeature_id" => \%srcfhash, "fmin" => $fmin, "fmax" => $fmax, "strand" => $strand, "phase" => $phase, ); $datahash{'featureloc'} = \%fl; #delete 'source' feature from @top_sfs splice(@top_sfs, $si, 1); } $si ++; #close loop over top_sfs } #the top-level features other than 'source' foreach $feat (@top_sfs) { #print $feat->primary_tag, "\n"; my $r = $self->_subfeat2featrelhash($name, $ftype, $feat, \%srcfhash, $tag_cv, $isanalysis); if (!($ftype eq 'mRNA' && $feat->primary_tag eq 'gene')) { my %fr = %$r; push(@top_featrels, \%fr); } else { %finaldatahash = %$r; } } if (@top_dbxrefs) { $datahash{'feature_dbxref'} = \@top_dbxrefs; } if (@top_featureprops) { $datahash{'featureprop'} = \@top_featureprops; } if (@top_featrels) { $datahash{'feature_relationship'} = \@top_featrels; } if (@top_featurecvterms) { $datahash{'feature_cvterm'} = \@top_featurecvterms; } if ($ftype eq 'mRNA' && %finaldatahash) { $finaldatahash{'feature_relationship'} = { 'subject_id' => \%datahash, 'type_id' => { 'name' => 'partof', 'cv_id' => { 'name' => $cv_name{'relationship'} }}, }; } else { %finaldatahash = %datahash; } my $mainTag = 'feature'; $self->_hash2xml(undef, $mainTag, \%finaldatahash); return 1; } sub _hash2xml { my $self = shift; my $isMatch = undef; $isMatch = shift; my $ult = shift; my $ref = shift; my %mh = %$ref; my $key; my $v; my $sh; my $xx; my $yy; my $nt; my $ntref; my $output; my $root = shift if (@_); #print "ult: $ult\n"; if (!defined $self->{'writer'}) { $root = 1; $self->_create_writer(); } my $temp; my %subh = undef; #start opeing tag #if pub record of type 'journal', form the 'ref' attribute for special pub lookup #requires that the journal name itself is also stored as a pubprop record for the journal with value equal #to the journal name and type of 'abbreviation'. if ($ult eq 'pub' && $mh{'type_id'}->{'name'} eq 'journal') { $self->{'writer'}->startTag($ult, 'ref' => $mh{'title'} . ':journal:abbreviation'); } #special pub match if pub uniquename not known elsif ($ult eq 'pub' && !defined $mh{'uniquename'}) { $self->{'writer'}->startTag($ult, 'op' => 'match'); #set the match flag, all the sub tags should also have "op"="match" $isMatch = 1; } #if cvterm or cv, lookup only elsif (($ult eq 'cvterm') || ($ult eq 'cv')) { $self->{'writer'}->startTag($ult, 'op' => 'lookup'); } #if nested tables of match table, match too elsif ($isMatch) { $self->{'writer'}->startTag($ult, 'op' => 'match'); } else { $self->{'writer'}->startTag($ult); } #first loop to produce xml for all the table columns foreach $key (keys %mh) { #print "key: $key\n"; $xx = ' ' . $key; $yy = $key . ' '; if (index($chadotables, $xx) < 0 && index($chadotables, $yy) < 0) { if ($isMatch) { $self->{'writer'}->startTag($key, 'op' => 'match'); } else { $self->{'writer'}->startTag($key); } my $x = $ult . '.' . $key; #the column is a foreign key if (defined $fkey{$x}) { $nt = $fkey{$x}; $sh = $mh{$key}; $self->_hash2xml($isMatch, $nt, $sh, 0); } else { #print "$key: $mh{$key}\n"; $self->{'writer'}->characters($mh{$key}); } $self->{'writer'}->endTag($key); } } #second loop to produce xml for all the nested tables foreach $key (keys %mh) { #print "key: $key\n"; $xx = ' ' . $key; $yy = $key . ' '; #a nested table if (index($chadotables, $xx) > 0 || index($chadotables, $yy) > 0) { #$writer->startTag($key); $ntref = $mh{$key}; #print "$key: ", ref($ntref), "\n"; if (ref($ntref) =~ 'HASH') { $self->_hash2xml($isMatch, $key, $ntref, 0); } elsif (ref($ntref) =~ 'ARRAY') { #print "array dim: ", $#$ntref, "\n"; foreach $ref (@$ntref) { #print "\n"; $self->_hash2xml($isMatch, $key, $ref, 0); } } #$writer->endTag($key); } } #end tag $self->{'writer'}->endTag($ult); #if ($root == 1) { # $self->{'writer'}->endTag('chado'); # } } sub _guess_acc_db { my $self = shift; my $seq = shift; my $acc = shift; #print "acc: $acc\n"; if ($acc =~ /^NM_\d{6}/ || $acc =~ /^NP_\d{6}/ || $acc =~ /^NT_\d{6}/ || $acc =~ /^NC_\d{6}/) { return "RefSeq"; } elsif ($acc =~ /^XM_\d{6}/ || $acc =~ /^XP_\d{6}/ || $acc =~ /^XR_\d{6}/) { return "RefSeq"; } elsif ($acc =~ /^[a-zA-Z]{1,2}\d{5,6}/) { return "GB"; } elsif ($seq->molecule() eq 'protein' && $acc =~ /^[a-zA-z]\d{5}/) { return "PIR"; } elsif ($seq->molecule() eq 'protein' && $acc =~ /^\d{6,7}[a-zA-Z]/) { return "PRF"; } elsif ($acc =~ /\d+/ && $acc !~ /[a-zA-Z]/) { return "LocusID"; } elsif ($acc =~ /^CG\d+/ || $acc =~ /^FB[a-z][a-z]\d+/) { return "FlyBase"; } else { return "unknown"; } } sub _subfeat2featrelhash { my $self = shift; my $genename = shift; my $seqtype = shift; my $feat = shift; my $r = shift; my %srcf = %$r; #srcfeature hash for featureloc.srcfeature_id my $tag_cv = shift; my $isanalysis = shift; my $prim_tag = $feat->primary_tag; my $sfunique = undef; #subfeature uniquename my $sfname = undef; #subfeature name my $sftype = undef; #subfeature type if ($feat->has_tag('symbol')) { ($sfunique) = $feat->each_tag_value("symbol"); } elsif ($feat->has_tag('label')) { ($sfunique) = $feat->each_tag_value("label"); } else { #$self->throw("$prim_tag at " . $feat->start . "\.\." . $feat->end . " does not have symbol or label! To convert into chadoxml, a seq feature must have a /symbol or /label tag holding its unique name."); #generate feature unique name as <genename>-<feature-type>-<span> $sfunique = $self->_genFeatUniqueName($genename, $feat); } if ($feat->has_tag('Name')) { ($sfname) = $feat->each_tag_value("Name"); } #feature type translation if (defined $feattype_args2so{$prim_tag}) { $sftype = $feattype_args2so{$prim_tag}; } else { $sftype = $prim_tag; } if ($prim_tag eq 'mutation') { if ($feat->start == $feat->end) { $sftype = $feattype_args2so{'mutation1'}; } else { $sftype = $feattype_args2so{'mutation2'}; } } #set is_analysis flag for gene model features undef(my $isanal); if ($sftype eq 'gene' || $sftype eq 'mRNA' || $sftype eq 'exon' || $sftype eq 'protein' || $sftype eq 'polypeptide') { $isanal = $isanalysis; } my %sfhash = ( "name" => $sfname, "uniquename" => $sfunique, "organism_id" => \%organism, "type_id" => { 'name' => $sftype, 'cv_id' => { 'name' => $cv_name{'sequence'} }}, "is_analysis" => $isanal || 'false', ); #make a copy of %sfhash for passing to this method when recursively called #my %srcfeat = ( # "name" => $sfname, # "uniquename" => $sfunique, # "organism_id" => \%organism, # "type_id" => { 'name' => $sftype, 'cv_id' => { 'name' => 'SO'}}, # ); #featureloc for subfeatures undef(my $sfmin); undef(my $sfmax); undef(my $is_sfmin_partial); undef(my $is_sfmax_partial); undef(my $sfstrand); undef(my $sfphase); $sfmin = $feat->start - 1; $sfmax = $feat->end; $sfstrand = $feat->strand(); if ($feat->can('phase')) { $sfphase = $feat->phase; } #if the gene feature in an mRNA record, cannot use its coordinates, omit featureloc if ($seqtype eq 'mRNA' && $sftype eq 'gene') { } else { if ($feat->location->isa('Bio::Location::FuzzyLocationI')) { if ($feat->location->start_pos_type() ne 'EXACT') { $is_sfmin_partial = 'true'; } if ($feat->location->end_pos_type() ne 'EXACT') { $is_sfmax_partial = 'true'; } } my %sfl = ( "srcfeature_id" => \%srcf, "fmin" => $sfmin, "is_fmin_partial" => $is_sfmin_partial || 'false', "fmax" => $sfmax, "is_fmax_partial" => $is_sfmax_partial || 'false', "strand" => $sfstrand, "phase" => $sfphase, ); $sfhash{'featureloc'} = \%sfl; } #subfeature tags undef(my @sfdbxrefs); #subfeature dbxrefs undef(my @sub_featureprops); #subfeature props undef(my @sub_featuresyns); #subfeature synonyms undef(my @sub_featurecvterms); #subfeature cvterms foreach my $tag ($feat->all_tags()) { #feature_dbxref for features if ($tag eq 'db_xref' or $tag eq 'dbxref' or $tag eq 'Dbxref') { my @t1 = $feat->each_tag_value($tag); #print "# of dbxref: @t1\n"; for my $temp (@t1) { $temp =~ /:/; my $db = $PREMATCH; my $xref = $POSTMATCH; #print "db: $db; xref: $xref\n"; my %acchash = ( "db_id" => {'name' => $db}, "accession" => $xref, ); my %sfdbx = ('dbxref_id' => \%acchash); push (@sfdbxrefs, \%sfdbx); } #Alias tags } elsif ($tag eq 'Alias') { @sub_featuresyns = $self->handle_Alias_tag($feat, @sub_featuresyns); } elsif ($tag eq 'Ontology_term') { @sub_featurecvterms = $self->handle_Ontology_tag($feat, @sub_featurecvterms); #featureprop for features, excluding GFF Name & Parent tags } elsif ($tag ne 'gene' && $tag ne 'symbol' && $tag ne 'Name' && $tag ne 'Parent') { next if ($tag eq 'parent_id'); next if ($tag eq 'load_id'); foreach my $val ($feat->each_tag_value($tag)) { my %prophash = undef; %prophash = ( "type_id" => {'name' => $tag, 'cv_id' => {'name' => $tag_cv}}, "value" => $val, ); push(@sub_featureprops, \%prophash); } } } if ($feat->can('source')) { @sfdbxrefs = $self->handle_source($feat,@sfdbxrefs); } if (@sub_featureprops) { $sfhash{'featureprop'} = \@sub_featureprops; } if (@sfdbxrefs) { $sfhash{'feature_dbxref'} = \@sfdbxrefs; } if (@sub_featuresyns) { $sfhash{'feature_synonym'} = \@sub_featuresyns; } if (@sub_featurecvterms) { $sfhash{'feature_cvterm'} = \@sub_featurecvterms; } undef(my @ssfeatrel); if ($feat->has_tag('locus_tag')) { ($genename)= $feat->each_tag_value('locus_tag'); } elsif ($feat->has_tag('gene')) { ($genename)= $feat->each_tag_value('gene'); } foreach my $sf ($feat->get_SeqFeatures()) { #print $sf->primary_tag, "\n"; my $rref = $self->_subfeat2featrelhash($genename, $sftype, $sf, \%srcf, $tag_cv, $isanalysis); if (defined $rref) { push(@ssfeatrel, $rref); } } if (@ssfeatrel) { $sfhash{'feature_relationship'} = \@ssfeatrel; } #subj-obj relationship type undef(my $reltypename); $reltypename = return_reltypename($sftype); my %fr = ( "subject_id" => \%sfhash, "type_id" => { 'name' => $reltypename, 'cv_id' => { 'name' => $cv_name{'relationship'} }}, ); if ($seqtype eq 'mRNA' && $sftype eq 'gene') { return \%sfhash; } else { return \%fr; } } #generate uniquename for feature as: <genename>-<feature-type>-<span> (foo-mRNA-10..1000) sub _genFeatUniqueName { my $self = shift; my $genename = shift; my $feat = shift; undef(my $uniquename); my $ftype = $feat->primary_tag; my $start = $feat->start; my $end = $feat->end; if ($feat->has_tag('locus_tag')) { ($genename) = $feat->each_tag_value("locus_tag"); } elsif ($feat->has_tag('gene')) { ($genename) = $feat->each_tag_value("gene"); } $uniquename = $genename . '-' . $ftype . '-' . $start . "\.\." . $end; return $uniquename; } #create uniquename for pubs with no medline id and no FBrf# #use "<authors>, <year>, <type>" as the uniquename (same as miniref) #<authors> is <sole-author-surname> if one author, # or <first-author-surname> and <second-author-surname> if two, # or <first-author-surname> et al. if more #sub _CreatePubUname { # my $self = shift; # my $pub = shift; # undef(my $pubuname); # # return $pubuname; #} #get authors of a reference #returns ref to the array of author hashes sub _getRefAuthors { my $self = shift; my $ref = shift; my $temp = $ref->authors; undef(my @authors); undef(my @aut); #there are authors if ($temp ne '.') { if (index($temp, ' and ') > 0) { $temp =~ / and /; my $lastauthor = $POSTMATCH; @authors = split(/\, /, $PREMATCH); push (@authors, $lastauthor); } else { @authors = split(/\, /, $temp); } my $a; my $i = 0; foreach $a (@authors) { $i ++; #parse the author lastname and givennames undef(my $last); undef(my $given); if (index($a, ',') > 0) { #genbank format, last,f.m. ($last, $given) = split(/\,/, $a); } elsif (index($a, ' ') > 0) { #embl format, last f.m. ($last, $given) = split(/ /, $a); } my %au = ( 'surname' => $last, 'givennames' => $given, ); push(@aut, {author_id => \%au, arank => $i}); } return \@aut; } #no authors, Bio::SeqIO::genbank doesn't pick up 'CONSRTM' line. else { return; } } #extract submission year from the citation of the submitted reference #genbank format for the submitted citation: JOURNAL Submitted (DD-MON-YYYY) submitter address sub _getSubmitYear { my $self = shift; my $citation = shift; if ($citation !~ /Submitted/) { $self->warn("not citation for a submitted reference. cannot extract submission year."); return; } else { $citation =~ /Submitted \(\d\d-[a-zA-Z]{3}-\d{4}\)/; my $a = $MATCH; $a =~ /\d{4}/; my $year = $MATCH; return $year; } } sub _getSubmitAddr { my $self = shift; my $ref = shift; undef(my %author); my $citation = $ref->location; if ($citation !~ /Submitted/) { $self->warn("not citation for a submitted reference. cannot extract submission year."); return; } else { $citation =~ /Submitted \(\d\d-[a-zA-Z]{3}-\d{4}\)/; my $a = $POSTMATCH; if (defined $a) { $a =~ s/^\s//; %author = ( 'author_id' => {'surname' => substr($a, 0, 100)}, ); return \%author; } else { return; } } } =head2 suppress_residues Title : suppress_residues Usage : $obj->suppress_residues() #get existing value $obj->suppress_residues($newval) #set new value Function : Keep track of the flag to suppress printing of residues in the chadoxml file. The default it to allow all residues to go into the file. Returns : value of suppress_residues (a scalar) Args : new value of suppress_residues (to set) =cut sub suppress_residues { my $self = shift; my $suppress_residues = shift if @_; return $self->{'suppress_residues'} = $suppress_residues if defined($suppress_residues); return $self->{'suppress_residues'}; } =head2 allow_residues Title : allow_residues Usage : $obj->allow_residues() #get existing value $obj->allow_residues($feature_type) #set new value Function : Track the allow_residues type. This can be used in conjunction with the suppress_residues flag to only allow residues from a specific feature type to be printed in the xml file, for example, only printing chromosome residues. When suppress_residues is set to true, then only chromosome features would would go into the xml file. If suppress_residues is not set, this function has no effect (since the default is to put all residues in the xml file). Returns : value of allow_residues (string that corresponds to a feature type) Args : new value of allow_residues (to set) Status : =cut sub allow_residues { my $self = shift; my $allow_residues = shift if @_; return $self->{'allow_residues'} = $allow_residues if defined($allow_residues); return $self->{'allow_residues'}; } =head2 return_ftype_hash Title : return_ftype_hash Usage : $obj->return_ftype_hash() Function : A simple hash where returning it has be factored out of the main code to allow subclasses to override it. Returns : A hash that indicates what the name of the SO term is and what the name of the Sequence Ontology is in the cv table. Args : The string that represents the SO term. Status : =cut sub return_ftype_hash { my $self = shift; my $ftype = shift; my %ftype_hash = ( "name" => $ftype, "cv_id" => {"name" => $cv_name{'sequence'} }); return %ftype_hash; } =head2 return_reltypename Title : return_reltypename Usage : $obj->return_reltypename Function : Return the appropriate relationship type name depending on the feature type (typically part_of, but derives_from for polypeptide). Returns : A relationship type name. Args : A SO type name. Status : =cut sub return_reltypename { my $self = shift; my $sftype = shift; my $reltypename; if ($sftype eq 'protein' || $sftype eq 'polypeptide') { $reltypename = 'derives_from'; } else { $reltypename = 'part_of'; } return $reltypename; } =head2 next_seq Title : next_seq Usage : $obj->next_seq Function : Returns : Args : Status : Not implemented (write only adaptor) =cut sub next_seq { my ($self, %argv) = @_; $self->throw('next_seq is not implemented; this is a write-only adapter.'); } =head2 _create_writer Title : _create_writer Usage : $obj->_create_writer Function : Creates XML::Writer object and writes start tag Returns : Nothing, though the writer persists as part of the chadoxml object Args : None Status : =cut sub _create_writer { my $self = shift; $self->{'writer'} = XML::Writer->new(OUTPUT => $self->_fh, DATA_MODE => 1, DATA_INDENT => 3); #print header $self->{'writer'}->xmlDecl("UTF-8"); $self->{'writer'}->comment("created by Peili Zhang, Flybase, Harvard University\n". "and Scott Cain, GMOD, Cold Spring Harbor Laboratory"); #start chadoxml $self->{'writer'}->startTag('chado'); return; } =head2 close_chadoxml Title : close_chadoxml Usage : $obj->close_chadoxml Function : Writes the closing xml tag Returns : None Args : None Status : =cut sub close_chadoxml { my $self = shift; $self->{'writer'}->endTag('chado'); return; } =head2 handle_unreserved_tags Title : handle_unreserved_tags Usage : $obj->handle_unreserved_tags Function : Converts tag value pairs to xml-ready hashrefs Returns : The array containing the hashrefs Args : In order: the Seq or SeqFeature object, the key, and the hasharray Status : =cut sub handle_unreserved_tags { my $self = shift; my $seq = shift; my $key = shift; my @arr = @_; my @values = $seq->attributes($key); for my $value (@values) { my %prophash = ( "type_id" => {'name' => $key, 'cv_id' => { 'name' => $cv_name{'feature_property'} } }, "value" => $value, ); push(@arr, \%prophash); } return @arr; } =head2 handle_Alias_tag Title : handle_Alias_tag Usage : $obj->handle_Alias_tag Function : Convert Alias values to synonym hash refs Returns : An array of synonym hash tags Args : The seq or seqFeature object and the synonym hash array Status : =cut sub handle_Alias_tag { my $self = shift; my $seq = shift; my @arr = @_; my @Aliases = $seq->attributes('Alias'); for my $Alias (@Aliases) { my %synhash = ( "type_id" => { 'name' => 'exact', 'cv_id' => { 'name' => 'synonym_type' } }, "name" => $Alias, "synonym_sgml" => $Alias, ); push(@arr, {'synonym_id' => \%synhash, 'pub_id' => {'uniquename' => 'null', 'type_id' => { 'name' => 'null', 'cv_id' => { 'name' => 'null', }, }, }, }); } return @arr; } =head2 handle_Ontology_tag Title : handle_Ontology_tag Usage : $obj->handle_Ontology_tag Function : Convert Ontology_term values to ontology term hash refs Returns : An array of ontology term hash refs Args : The seq or seqFeature object and the ontology term array Status : =cut sub handle_Ontology_tag { my $self = shift; my $seq = shift; my @arr = @_; my @terms = $seq->attributes('Ontology_term'); for my $term (@terms) { my $hashref; if ($term =~ /(\S+):(\S+)/) { my $db = $1; my $acc = $2; $hashref = { 'cvterm_id' => { 'dbxref_id' => { 'db_id' => { 'name' => $db }, 'accession' => $acc }, }, }; } push(@arr, {cvterm_id => $hashref}); } return @arr; } =head2 handle_dbxref Title : handle_dbxref Usage : $obj->handle_dbxref Function : Convert Dbxref values to dbxref hashref Returns : An array of dbxref hashrefs Args : A seq or seqFeature object and the dbxref array Status : =cut sub handle_dbxref { my $self = shift; my $seq = shift; my $tag = shift; my @arr = @_; my @terms = $seq->attributes($tag); for my $term (@terms) { my $hashref; if ($term =~ /(\S+):(\S+)/) { my $db = $1; my $acc= $2; my $version = 1; if ($acc =~ /(\S+)\.(\S+)/) { $acc = $1; $version = $2; } $hashref = { 'dbxref_id' => { 'db_id' => { 'name' => $db }, 'accession' => $acc, 'version' => $version, }, }; } else { $self->throw("I don't know how to handle a dbxref like $term"); } push(@arr, {'dbxref_id' => $hashref}); } return @arr; } =head2 handle_source Title : handle_source Usage : $obj->handle_source Function : Returns : Args : Status : =cut sub handle_source { my $self = shift; my $seq = shift; my @arr = @_; my $source = $seq->source(); return @arr unless $source; my $hashref = { 'dbxref_id' => { 'db_id' => {'name' => 'GFF_source'}, 'accession' => $source, } }; push(@arr, {'dbxref_id' => $hashref}); return @arr; } =head2 _srcf_hash Title : _srcf_hash Usage : $obj->_srcf_hash Function : Creates the srcfeature hash for use in featureloc hashes Returns : The srcfeature hash Args : The srcfeature name, the srcfeature type and a reference to the organism hash. Status : =cut sub _srcf_hash { my $self = shift; my $srcf = shift; my $stype= shift; my $orgref = shift; my %hash = ('uniquename' => $srcf, 'organism_id' => $orgref, 'type_id' => {'name' => $stype, 'cv_id' => {'name' => $cv_name{'sequence'} }}, ); return %hash; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/chaos.pm�����������������������������������������������������������������000444��000766��000024�� 47700�13155576320� 16667� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::chaos # # Chris Mungall <cjm@fruitfly.org> # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::chaos - chaos sequence input/output stream =head1 SYNOPSIS #In general you will not want to use this module directly; #use the chaosxml format via SeqIO $outstream = Bio::SeqIO->new(-file => $filename, -format => 'chaosxml'); while ( my $seq = $instream->next_seq() ) { $outstream->write_seq($seq); } =head1 DESCRIPTION This is the guts of L<Bio::SeqIO::chaosxml> - please refer to the documentation for this module B<CURRENTLY WRITE ONLY> ChaosXML is an XML mapping of the chado relational database; for more information, see http://www.fruitfly.org/chaos-xml chaos can be represented in various syntaxes - XML, S-Expressions or indented text. You should see the relevant SeqIO file. You will probably want to use L<Bio::SeqIO::chaosxml>, which is a wrapper to this module. =head2 USING STAG OBJECTS B<non-standard bioperl stuff you don't necessarily need to know follows> This module (in write mode) is an B<event producer> - it generates XML events via the L<Data::Stag> module. If you only care about the final end-product xml, use L<Bio::SeqIO::chaosxml> You can treat the resulting chaos-xml stream as stag XML objects; $outstream = Bio::SeqIO->new(-file => $filename, -format => 'chaos'); while ( my $seq = $instream->next_seq() ) { $outstream->write_seq($seq); } my $chaos = $outstream->handler->stag; # stag provides get/set methods for xml elements # (these are chaos objects, not bioperl objects) my @features = $chaos->get_feature; my @feature_relationships = $chaos->get_feature_relationships; # stag objects can be queried with functional-programming # style queries my @features_in_range = $chaos->where('feature', sub { my $featureloc = shift->get_featureloc; $featureloc->strand == 1 && $featureloc->nbeg > 10000 && $featureloc->nend < 20000; }); foreach my $feature (@features_in_range) { my $featureloc = $feature->get_featureloc; printf "%s [%d->%d on %s]\n", $feature->sget_name, $featureloc->sget_nbeg, $featureloc->sget_end, $featureloc->sget_srcfeature_id; } =head1 MODULES REQUIRED L<Data::Stag> Downloadable from CPAN; see also http://stag.sourceforge.net =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Mungall Email cjm@fruitfly.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::chaos; use strict; use Bio::SeqFeature::Generic; use Bio::Species; use Bio::Seq::SeqFactory; use Bio::Annotation::Collection; use Bio::Annotation::Comment; use Bio::Annotation::Reference; use Bio::Annotation::DBLink; use Bio::SeqFeature::Tools::TypeMapper; use Bio::SeqFeature::Tools::FeatureNamer; use Bio::SeqFeature::Tools::IDHandler; use Data::Stag qw(:all); use base qw(Bio::SeqIO); our $TM = 'Bio::SeqFeature::Tools::TypeMapper'; our $FNAMER = 'Bio::SeqFeature::Tools::FeatureNamer'; our $IDH = 'Bio::SeqFeature::Tools::IDHandler'; sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } my $wclass = $self->default_handler_class; $self->handler($wclass); if ($self->_fh) { $self->handler->fh($self->_fh); } $self->{_end_of_data} = 0; $self->_type_by_id_h({}); my $t = time; my $ppt = localtime $t; $self->handler->S("chaos"); $self->handler->ev(chaos_metadata=>[ [chaos_version=>1], [chaos_flavour=>'bioperl'], [feature_unique_key=>'feature_id'], [equiv_chado_release=>'chado_1_01'], [export_unixtime=>$t], [export_localtime=>$ppt], [export_host=>$ENV{HOST}], [export_user=>$ENV{USER}], [export_perl5lib=>$ENV{PERL5LIB}], [export_program=>$0], [export_module=>'Bio::SeqIO::chaos'], [export_module_cvs_id=>'$Id$'], ]); return; } sub DESTROY { my $self = shift; $self->end_of_data(); $self->SUPER::DESTROY(); } sub end_of_data { my $self = shift; return if $self->{_end_of_data}; $self->{_end_of_data} = 1; $self->handler->E("chaos"); } sub default_handler_class { return Data::Stag->makehandler; } =head2 context_namespace Title : context_namespace Usage : $obj->context_namespace($newval) Function: Example : Returns : value of context_namespace (a scalar) Args : on set, new value (a scalar or undef, optional) IDs will be preceded with the context namespace =cut sub context_namespace{ my $self = shift; return $self->{'context_namespace'} = shift if @_; return $self->{'context_namespace'}; } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : =cut sub next_seq { my ($self,@args) = @_; my $seq = $self->sequence_factory->create ( # '-verbose' =>$self->verbose(), # %params, # -seq => $seqc, # -annotation => $annotation, # -features => \@features ); return $seq; } sub handler { my $self = shift; $self->{_handler} = shift if @_; return $self->{_handler}; } =head2 write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object (must be seq) to the stream Returns : 1 for success and 0 for error Args : Bio::Seq =cut sub write_seq { my ($self,$seq) = @_; if( !defined $seq ) { $self->throw("Attempting to write with no seq!"); } if( ! ref $seq || ! $seq->isa('Bio::SeqI') ) { $self->warn(" $seq is not a SeqI compliant module. Attempting to dump, but may fail!"); } # get a handler - must inherit from Data::Stag::BaseHandler; my $w = $self->handler; # start of data ### $w->S("chaos_block"); my $seq_chaos_feature_id; # different seq objects have different version accessors - # weird but true my $version = $seq->can('seq_version') ? $seq->seq_version : $seq->version; my $accversion = $seq->accession_number; if ($version) { $accversion .= ".$version"; } if ($accversion) { $seq_chaos_feature_id = $accversion; } else { $seq_chaos_feature_id = $self->get_chaos_feature_id($seq); $accversion = $seq_chaos_feature_id; } # All ids must have a namespace prefix if ($seq_chaos_feature_id !~ /:/) { $seq_chaos_feature_id = "GenericSeqDB:$seq_chaos_feature_id"; } # if ($seq->accession_number eq 'unknown') { # $seq_chaos_feature_id = $self->get_chaos_feature_id('contig', $seq); # } my $haplotype; if ($seq->desc =~ /haplotype(.*)/i) { # yikes, no consistent way to specify haplotype in gb $haplotype = $1; $haplotype =~ s/\s+/_/g; $haplotype =~ s/\W+//g; } my $OS; # Organism lines if (my $spec = $seq->species) { my ($species, $genus, @class) = $spec->classification(); $OS = "$genus $species"; if (my $ssp = $spec->sub_species) { $OS .= " $ssp"; } $self->genus_species($OS); if( $spec->common_name ) { my $common = $spec->common_name; # genbank parser sets species->common_name to # be "Genus Species (common name)" which is wrong; # we will correct for this; if common_name is set # correctly then carry on if ($common =~ /\((.*)\)/) { $common = $1; } $OS .= " (".$common.")"; } } if ($OS) { $self->organismstr($OS); } if ($haplotype) { # genus_species is part of uniquename - add haplotype # to make it genuinely unique $self->genus_species($self->genus_species .= " $haplotype"); } my $uname = $self->make_uniquename($self->genus_species, $accversion); # data structure representing the core sequence for this record my $seqnode = Data::Stag->new(feature=>[ [feature_id=>$seq_chaos_feature_id], [dbxrefstr=>'SEQDB:'.$accversion], [name=>$seq->display_name], [uniquename=>$uname], [residues=>$seq->seq], ]); # soft properties my %prop = (); $seqnode->set_type('databank_entry'); map { $prop{$_} = $seq->$_() if $seq->can($_); } qw(desc keywords division molecule is_circular); $prop{dates} = join("; ", $seq->get_dates) if $seq->can("get_dates"); local($^W) = 0; # suppressing warnings about uninitialized fields. # Reference lines my $count = 1; foreach my $ref ( $seq->annotation->get_Annotations('reference') ) { # TODO } # Comment lines $seqnode->add_featureprop([[type=>'haplotype'],[value=>$haplotype]]) if $haplotype; foreach my $comment ( $seq->annotation->get_Annotations('comment') ) { $seqnode->add_featureprop([[type=>'comment'],[value=>$comment->text]]); } if ($OS) { $seqnode->set_organismstr($OS); } my @sfs = $seq->get_SeqFeatures; # genbank usually includes a 'source' feature - we just # migrate the data from this to the actual source feature my @sources = grep {$_->primary_tag eq 'source'} @sfs; @sfs = grep {$_->primary_tag ne 'source'} @sfs; $self->throw(">1 source types") if @sources > 1; my $source = shift @sources; if ($source) { my $tempw = Data::Stag->makehandler; $self->write_sf($source, $seq_chaos_feature_id, $tempw); my $snode = $tempw->stag; $seqnode->add($_->name, $_->data) foreach ($snode->get_featureprop, $snode->get_feature_dbxref); } # throw the writer an event $w->ev(@$seqnode); $seqnode = undef; # free memory # make events for all the features within the record foreach my $sf ( @sfs ) { $FNAMER->name_feature($sf); $FNAMER->name_contained_features($sf); $self->write_sf($sf, $seq_chaos_feature_id); } # data end ### $w->E("chaos_block"); return 1; } sub organismstr{ my $self = shift; return $self->{'organismstr'} = shift if @_; return $self->{'organismstr'}; } sub genus_species{ my $self = shift; return $self->{'genus_species'} = shift if @_; return $self->{'genus_species'}; } # maps ID to type sub _type_by_id_h { my $self = shift; $self->{_type_by_id_h} = shift if @_; return $self->{_type_by_id_h}; } # ---- # writes a seq feature # ---- sub write_sf { my $self = shift; my $sf = shift; my $seq_chaos_feature_id = shift; my $w = shift || $self->handler; my %props = map { lc($_)=>[$sf->each_tag_value($_)] } $sf->all_tags; my $loc = $sf->location; my $name = $FNAMER->generate_feature_name($sf); my $type = $sf->primary_tag; # The CDS (eg in a genbank feature) implicitly represents # the protein $type =~ s/CDS/polypeptide/; my @subsfs = $sf->sub_SeqFeature; my @locnodes = (); my $sid = $loc->is_remote ? $loc->seq_id : $seq_chaos_feature_id; my $CREATE_SPLIT_SFS = 0; if($CREATE_SPLIT_SFS && $loc->isa("Bio::Location::SplitLocationI") ) { # turn splitlocs into subfeatures my $n = 1; push(@subsfs, map { my $ssf = Bio::SeqFeature::Generic->new( -start=>$_->start, -end=>$_->end, -strand=>$_->strand, -primary=>$self->subpartof($type), ); if ($_->is_remote) { $ssf->location->is_remote(1); $ssf->location->seq_id($_->seq_id); } $ssf; } $loc->each_Location); } elsif( $loc->isa("Bio::Location::RemoteLocationI") ) { # turn splitlocs into subfeatures my $n = 1; push(@subsfs, map { Bio::SeqFeature::Generic->new( # -name=>$name.'.'.$n++, -start=>$_->start, -end=>$_->end, -strand=>$_->strand, -primary=>$self->subpartof($type), ) } $loc->each_Location); } else { my ($beg, $end, $strand) = $self->bp2ib($loc); if (!$strand) { use Data::Dumper; print Dumper $sf, $loc; $self->throw("($beg, $end, $strand) - no strand\n"); } @locnodes = ( [featureloc=>[ [nbeg=>$beg], [nend=>$end], [strand=>$strand], [srcfeature_id=>$sid], [locgroup=>0], [rank=>0], ] ] ); } my $feature_id = $self->get_chaos_feature_id($sf); delete $props{id} if $props{id}; # do something with genbank stuff my $pid = $props{'protein_id'}; my $tn = $props{'translation'}; my @xrefs = @{$props{'db_xref'} || []}; if ($pid) { push(@xrefs, "protein:$pid->[0]"); } my $org = $props{organism} ? $props{organism}->[0] : undef; if (!$org && $self->organismstr) { $org = $self->organismstr; } my $uname = $name ? $name.'/'.$feature_id : $feature_id; if ($self->genus_species && $name) { $uname = $self->make_uniquename($self->genus_species, $name); } if (!$uname) { $self->throw("cannot make uniquename for $feature_id $name"); } $self->_type_by_id_h->{$feature_id} = $type; my $fnode = [feature=>[ [feature_id=>$feature_id], $name ? ([name=>$name]) : (), [uniquename=>$uname], [type=>$type], $tn ? ([residues=>$tn->[0]], [seqlen=>length($tn->[0])], #####[md5checksum=>md5checksum($tn->[0])], ) :(), $org ? ([organismstr=>$org]) : (), @locnodes, (map { [feature_dbxref=>[ [dbxrefstr=>$_] ] ] } @xrefs), (map { my $k = $_; my $rank=0; map { [featureprop=>[[type=>$k],[value=>$_],[rank=>$rank++]]] } @{$props{$k}} } keys %props), ]]; $w->ev(@$fnode); my $rank = 0; if (@subsfs) { # strand is always determined by FIRST feature listed # (see genbank entry for trans-spliced mod(mdg4) AE003734) my $strand = $subsfs[0]; # almost all the time, all features are on same strand my @sfs_on_main_strand = grep {$_->strand == $strand} @subsfs; my @sfs_on_other_strand = grep {$_->strand != $strand} @subsfs; sort_by_strand($strand, \@sfs_on_main_strand); sort_by_strand(0-$strand, \@sfs_on_other_strand); @subsfs = (@sfs_on_main_strand, @sfs_on_other_strand); foreach my $ssf (@subsfs) { my $ssfid = $self->write_sf($ssf, $sid); #my $rtype = 'part_of'; my $rtype = $TM->get_relationship_type_by_parent_child($sf,$ssf); if ($ssf->primary_tag eq 'CDS') { $rtype = 'derives_from'; } $w->ev(feature_relationship=>[ [subject_id=>$ssfid], [object_id=>$feature_id], [type=>$rtype], [rank=>$rank++], ] ); } } else { # parents not stored as bioperl containment hierarchy my @parent_ids = @{$props{parent} || []}; foreach my $parent_id (@parent_ids) { my $ptype = $self->_type_by_id_h->{$parent_id} || 'unknown'; my $rtype = $TM->get_relationship_type_by_parent_child($ptype,$type); $w->ev(feature_relationship=>[ [subject_id=>$feature_id], [object_id=>$parent_id], [type=>$rtype], [rank=>$rank++], ] ); } } return $feature_id; } sub sort_by_strand { my $strand = shift || 1; my $sfs = shift; @$sfs = sort { ($a->start <=> $b->start) * $strand } @$sfs; return; } sub make_uniquename { my $self = shift; my $org = shift; my $name = shift; my $os = $org; $os =~ s/\s+/_/g; $os =~ s/\(/_/g; $os =~ s/\)/_/g; $os =~ s/_+/_/g; $os =~ s/^_+//g; $os =~ s/_+$//g; return "$os:$name"; } sub get_chaos_feature_id { my $self = shift; my $ob = shift; my $id; if ($ob->isa("Bio::SeqI")) { $id = $ob->accession_number . '.' . ($ob->can('seq_version') ? $ob->seq_version : $ob->version); } else { $ob->isa("Bio::SeqFeatureI") || $self->throw("$ob must be either SeqI or SeqFeatureI"); if ($ob->primary_id) { $id = $ob->primary_id; } else { eval { $id = $IDH->generate_unique_persistent_id($ob); }; if ($@) { $self->warn($@); $id = "$ob"; # last resort - use memory pointer ref # will not be persistent, but will be unique } } } if (!$id) { if ($ob->isa("Bio::SeqFeatureI")) { $id = $IDH->generate_unique_persistent_id($ob); } else { $self->throw("Cannot generate a unique persistent ID for a Seq without either primary_id or accession"); } } if ($id) { $id = $self->context_namespace ? $self->context_namespace . ":" . $id : $id; } return $id; } # interbase and directional semantics sub bp2ib { my $self = shift; my $loc = shift; my ($s, $e, $str) = ref($loc) eq "ARRAY" ? (@$loc) : ($loc->start, $loc->end, $loc->strand); $s--; if ($str < 0) { ($s, $e) = ($e, $s); } return ($s, $e, $str || 1); } sub subpartof { my $self = shift; my $type = 'partof_'.shift; $type =~ s/partof_CDS/CDS_exon/; $type =~ s/partof_protein/CDS_exon/; $type =~ s/partof_polypeptide/CDS_exon/; $type =~ s/partof_\w*RNA/exon/; return $type; } 1; ����������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/chaosxml.pm��������������������������������������������������������������000444��000766��000024�� 4521�13155576320� 17362� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::chaosxml # # Chris Mungall <cjm@fruitfly.org> # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::chaosxml - chaosxml sequence input/output stream =head1 SYNOPSIS #In general you will not want to use this module directly; #use the chaosxml format via SeqIO $outstream = Bio::SeqIO->new(-file => $filename, -format => 'chaosxml'); while ( my $seq = $instream->next_seq() ) { $outstream->write_seq($seq); } =head1 DESCRIPTION This object can transform Bio::Seq objects to and from chaos files. B<CURRENTLY WRITE ONLY> ChaosXML is an XML mapping of the chado relational database; for more information, see http://www.fruitfly.org/chaos-xml Chaos can have other syntaxes than XML (eg S-Expressions, Indented text) See L<Bio::SeqIO::chaos> for a full description =head1 VERY VERY IMPORTANT !!!!!!!!!!!CHADO AND CHAOS USE INTERBASE COORDINATES!!!!!!!!!!!!!!!! =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Mungall Email cjm@fruitfly.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::chaosxml; use strict; use Data::Stag::XMLWriter; use base qw(Bio::SeqIO::chaos); sub default_handler_class { return Data::Stag->getformathandler('xml'); } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/ctf.pm�������������������������������������������������������������������000444��000766��000024�� 6731�13155576320� 16325� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::ctf # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Aaron Mackey <amackey@virginia.edu> # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::ctf - ctf trace sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from ctf trace files. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Aaron Mackey Email: amackey@virginia.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::ctf; use vars qw(@ISA $READ_AVAIL); use strict; use Bio::SeqIO; use Bio::Seq::SeqFactory; push @ISA, qw( Bio::SeqIO ); sub BEGIN { eval { require Bio::SeqIO::staden::read; }; if ($@) { $READ_AVAIL = 0; } else { push @ISA, "Bio::SeqIO::staden::read"; $READ_AVAIL = 1; } } sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::Quality')); } unless ($READ_AVAIL) { Bio::Root::Root->throw( -class => 'Bio::Root::SystemException', -text => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!" ); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq::Quality object Args : NONE =cut sub next_seq { my ($self) = @_; my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'ctf'); # create the seq object $seq = $self->sequence_factory->create(-seq => $seq, -id => $id, -primary_id => $id, -desc => $desc, -alphabet => 'DNA', -qual => $qual ); return $seq; } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object =cut sub write_seq { my ($self,@seq) = @_; my $fh = $self->_fh; foreach my $seq (@seq) { $self->write_trace($fh, $seq, 'ctf'); } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; ���������������������������������������BioPerl-1.007002/Bio/SeqIO/embl.pm������������������������������������������������������������������000444��000766��000024�� 144364�13155576320� 16535� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::EMBL # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::embl - EMBL sequence input/output stream =head1 SYNOPSIS It is probably best not to use this object directly, but rather go through the SeqIO handler system. Go: $stream = Bio::SeqIO->new(-file => $filename, -format => 'EMBL'); while ( (my $seq = $stream->next_seq()) ) { # do something with $seq } =head1 DESCRIPTION This object can transform Bio::Seq objects to and from EMBL flat file databases. There is a lot of flexibility here about how to dump things which should be documented more fully. There should be a common object that this and Genbank share (probably with Swissprot). Too much of the magic is identical. =head2 Optional functions =over 3 =item _show_dna() (output only) shows the dna or not =item _post_sort() (output only) provides a sorting func which is applied to the FTHelpers before printing =item _id_generation_func() This is function which is called as print "ID ", $func($annseq), "\n"; To generate the ID line. If it is not there, it generates a sensible ID line using a number of tools. If you want to output annotations in EMBL format they need to be stored in a Bio::Annotation::Collection object which is accessible through the Bio::SeqI interface method L<annotation()|annotation>. The following are the names of the keys which are polled from a L<Bio::Annotation::Collection> object. reference - Should contain Bio::Annotation::Reference objects comment - Should contain Bio::Annotation::Comment objects dblink - Should contain Bio::Annotation::DBLink objects =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::embl; use vars qw(%FTQUAL_NO_QUOTE); use strict; use Bio::SeqIO::FTHelper; use Bio::SeqFeature::Generic; use Bio::Species; use Bio::Seq::SeqFactory; use Bio::Annotation::Collection; use Bio::Annotation::Comment; use Bio::Annotation::Reference; use Bio::Annotation::DBLink; use base qw(Bio::SeqIO); # Note that a qualifier that exceeds one line (i.e. a long label) will # automatically be quoted regardless: %FTQUAL_NO_QUOTE=( 'anticodon'=>1, 'citation'=>1, 'codon'=>1, 'codon_start'=>1, 'cons_splice'=>1, 'direction'=>1, 'evidence'=>1, 'label'=>1, 'mod_base'=> 1, 'number'=> 1, 'rpt_type'=> 1, 'rpt_unit'=> 1, 'transl_except'=> 1, 'transl_table'=> 1, 'usedin'=> 1, ); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); # hash for functions for decoding keys. $self->{'_func_ftunit_hash'} = {}; # sets this to one by default. People can change it $self->_show_dna(1); if ( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : =cut sub next_seq { my ($self,@args) = @_; my ($pseq,$c,$line,$name,$desc,$acc,$seqc,$mol,$div, $date, $comment, @date_arr); my ($annotation, %params, @features) = Bio::Annotation::Collection->new(); $line = $self->_readline; # This needs to be before the first eof() test if ( !defined $line ) { return; # no throws - end of file } if ( $line =~ /^\s+$/ ) { while ( defined ($line = $self->_readline) ) { $line =~/^\S/ && last; } # return without error if the whole next sequence was just a single # blank line and then eof return unless $line; } # no ID as 1st non-blank line, need short circuit and exit routine $self->throw("EMBL stream with no ID. Not embl in my book") unless $line =~ /^ID\s+\S+/; # At this point we are sure that $line contains an ID header line my $alphabet; if ( $line =~ tr/;/;/ == 6) { # New style headers contain exactly six semicolons. # New style header (EMBL Release >= 87, after June 2006) my $topology; my $sv; # ID DQ299383; SV 1; linear; mRNA; STD; MAM; 431 BP. # This regexp comes from the new2old.pl conversion script, from EBI if ($line =~ m/^ID (\S+);\s+SV (\d+); (\w+); ([^;]+); (\w{3}); (\w{3}); (\d+) BP./) { ($name, $sv, $topology, $mol, $div) = ($1, $2, $3, $4, $6); } if (defined $sv) { $params{'-seq_version'} = $sv; $params{'-version'} = $sv; } if (defined $topology && $topology eq 'circular') { $params{'-is_circular'} = 1; } if (defined $mol ) { if ($mol =~ /DNA/) { $alphabet = 'dna'; } elsif ($mol =~ /RNA/) { $alphabet = 'rna'; } elsif ($mol =~ /AA/) { $alphabet = 'protein'; } } } else { # Old style header (EMBL Release < 87, before June 2006) if ($line =~ /^ID\s+(\S+)[^;]*;\s+(\S+)[^;]*;\s+(\S+)[^;]*;/) { ($name, $mol, $div) = ($1, $2, $3); } if ($mol) { if ( $mol =~ /circular/ ) { $params{'-is_circular'} = 1; $mol =~ s|circular ||; } if (defined $mol ) { if ($mol =~ /DNA/) { $alphabet='dna'; } elsif ($mol =~ /RNA/) { $alphabet='rna'; } elsif ($mol =~ /AA/) { $alphabet='protein'; } } } } unless( defined $name && length($name) ) { $name = "unknown_id"; } # $self->warn("not parsing upper annotation in EMBL file yet!"); my $buffer = $line; local $_; BEFORE_FEATURE_TABLE : my $ncbi_taxid; until ( !defined $buffer ) { $_ = $buffer; # Exit at start of Feature table if ( /^(F[HT]|SQ)/ ) { $self->_pushback($_) if( $1 eq 'SQ' || $1 eq 'FT'); last; } # Description line(s) if (/^DE\s+(\S.*\S)/) { $desc .= $desc ? " $1" : $1; } #accession number if ( /^AC\s+(.*)?/ || /^PA\s+(.*)?/) { my @accs = split(/[; ]+/, $1); # allow space in addition $params{'-accession_number'} = shift @accs unless defined $params{'-accession_number'}; push @{$params{'-secondary_accessions'}}, @accs; } #version number if ( /^SV\s+\S+\.(\d+);?/ ) { my $sv = $1; #$sv =~ s/\;//; $params{'-seq_version'} = $sv; $params{'-version'} = $sv; } #date (NOTE: takes last date line) if ( /^DT\s+(.+)$/ ) { my $line = $1; my ($date, $version) = split(' ', $line, 2); $date =~ tr/,//d; # remove comma if new version if ($version) { if ($version =~ /\(Rel\. (\d+), Created\)/ms ) { my $release = Bio::Annotation::SimpleValue->new( -tagname => 'creation_release', -value => $1 ); $annotation->add_Annotation($release); } elsif ($version =~ /\(Rel\. (\d+), Last updated, Version (\d+)\)/ms ) { my $release = Bio::Annotation::SimpleValue->new( -tagname => 'update_release', -value => $1 ); $annotation->add_Annotation($release); my $update = Bio::Annotation::SimpleValue->new( -tagname => 'update_version', -value => $2 ); $annotation->add_Annotation($update); } } push @{$params{'-dates'}}, $date; } #keywords if ( /^KW (.*)\S*$/ ) { my @kw = split(/\s*\;\s*/,$1); push @{$params{'-keywords'}}, @kw; } # Organism name and phylogenetic information elsif (/^O[SC]/) { # pass the accession number so we can give an informative throw message if necessary my $species = $self->_read_EMBL_Species(\$buffer, $params{'-accession_number'}); $params{'-species'}= $species; } # NCBI TaxID Xref elsif (/^OX/) { if (/NCBI_TaxID=(\d+)/) { $ncbi_taxid=$1; } my @links = $self->_read_EMBL_TaxID_DBLink(\$buffer); foreach my $dblink ( @links ) { $annotation->add_Annotation('dblink',$dblink); } } # References elsif (/^R/) { my @refs = $self->_read_EMBL_References(\$buffer); foreach my $ref ( @refs ) { $annotation->add_Annotation('reference',$ref); } } # DB Xrefs elsif (/^DR/) { my @links = $self->_read_EMBL_DBLink(\$buffer); foreach my $dblink ( @links ) { $annotation->add_Annotation('dblink',$dblink); } } # Comments elsif (/^CC\s+(.*)/) { $comment .= $1; $comment .= " "; while (defined ($_ = $self->_readline) ) { if (/^CC\s+(.*)/) { $comment .= $1; $comment .= " "; } else { last; } } my $commobj = Bio::Annotation::Comment->new(); $commobj->text($comment); $annotation->add_Annotation('comment',$commobj); $comment = ""; } # Get next line. $buffer = $self->_readline; } while ( defined ($_ = $self->_readline) ) { /^FT\s{3}\w/ && last; /^SQ / && last; /^CO / && last; } $buffer = $_; if (defined($buffer) && $buffer =~ /^FT /) { until ( !defined ($buffer) ) { my $ftunit = $self->_read_FTHelper_EMBL(\$buffer); # process ftunit my $feat = $ftunit->_generic_seqfeature($self->location_factory(), $name); # add taxon_id from source if available # Notice, this will override what is found in the OX line. # this is by design as this seems to be the official way # of specifying a TaxID if ($params{'-species'} && ($feat->primary_tag eq 'source') && $feat->has_tag('db_xref') && (! $params{'-species'}->ncbi_taxid())) { foreach my $tagval ($feat->get_tag_values('db_xref')) { if (index($tagval,"taxon:") == 0) { $params{'-species'}->ncbi_taxid(substr($tagval,6)); last; } } } # add feature to list of features push(@features, $feat); if ( $buffer !~ /^FT/ ) { last; } } } # Set taxid found in OX line if ($params{'-species'} && defined $ncbi_taxid && (! $params{'-species'}->ncbi_taxid())) { $params{'-species'}->ncbi_taxid($ncbi_taxid); } # skip comments while ( defined ($buffer) && $buffer =~ /^XX/ ) { $buffer = $self->_readline(); } if ( $buffer =~ /^CO/ ) { # bug#2982 # special : create contig as annotation while ( defined ($buffer) ) { $annotation->add_Annotation($_) for $self->_read_EMBL_Contig(\$buffer); if ( !$buffer || $buffer !~ /^CO/ ) { last; } } $buffer ||= ''; } if ($buffer !~ /^\/\//) { # if no SQ lines following CO (bug#2958) if ( $buffer !~ /^SQ/ ) { while ( defined ($_ = $self->_readline) ) { /^SQ/ && last; } } $seqc = ""; while ( defined ($_ = $self->_readline) ) { m{^//} && last; $_ = uc($_); s/[^A-Za-z]//g; $seqc .= $_; } } my $seq = $self->sequence_factory->create (-verbose => $self->verbose(), -division => $div, -seq => $seqc, -desc => $desc, -display_id => $name, -annotation => $annotation, -molecule => $mol, -alphabet => $alphabet, -features => \@features, %params); return $seq; } =head2 _write_ID_line Title : _write_ID_line Usage : $self->_write_ID_line($seq); Function: Writes the EMBL Release 87 format ID line to the stream, unless : there is a user-supplied ID line generation function in which : case that is used instead. : ( See Bio::SeqIO::embl::_id_generation_function(). ) Returns : nothing Args : Bio::Seq object =cut sub _write_ID_line { my ($self, $seq) = @_; my $id_line; # If there is a user-supplied ID generation function, use it. if ( $self->_id_generation_func ) { $id_line = "ID " . &{$self->_id_generation_func}($seq) . "\nXX\n"; } # Otherwise, generate a standard EMBL release 87 (June 2006) ID line. else { # The sequence name is supposed to be the primary accession number, my $name = $seq->accession_number(); if ( not(defined $name) || $name eq 'unknown') { # but if it is not present, use the sequence ID or the empty string $name = $seq->id() || ''; } $self->warn("No whitespace allowed in EMBL id [". $name. "]") if $name =~ /\s/; # Use the sequence version, or default to 1. my $version = $seq->version() || 1; my $len = $seq->length(); # Taxonomic division. my $div; if ( $seq->can('division') && defined($seq->division) && $self->_is_valid_division($seq->division) ) { $div = $seq->division(); } else { $div ||= 'UNC'; # 'UNC' is the EMBL division code for 'unclassified'. } my $mol; # If the molecule type is a valid EMBL type, use it. if ( $seq->can('molecule') && defined($seq->molecule) && $self->_is_valid_molecule_type($seq->molecule) ) { $mol = $seq->molecule(); } # Otherwise, choose unassigned DNA or RNA based on the alphabet. elsif ($seq->can('primary_seq') && defined $seq->primary_seq->alphabet) { my $alphabet =$seq->primary_seq->alphabet; if ($alphabet eq 'dna') { $mol ='unassigned DNA'; } elsif ($alphabet eq 'rna') { $mol='unassigned RNA'; } elsif ($alphabet eq 'protein') { $self->warn("Protein sequence found; EMBL is a nucleotide format."); $mol='AA'; # AA is not a valid EMBL molecule type. } } my $topology = 'linear'; if ($seq->is_circular) { $topology = 'circular'; } $mol ||= ''; # 'unassigned'; ? $id_line = "ID $name; SV $version; $topology; $mol; STD; $div; $len BP.\nXX\n"; } $self->_print($id_line); } =head2 _is_valid_division Title : _is_valid_division Usage : $self->_is_valid_division($div) Function: tests division code for validity Returns : true if $div is a valid EMBL release 87 taxonomic division. Args : taxonomic division code string =cut sub _is_valid_division { my ($self, $division) = @_; my %EMBL_divisions = ( "PHG" => 1, # Bacteriophage "ENV" => 1, # Environmental Sample "FUN" => 1, # Fungal "HUM" => 1, # Human "INV" => 1, # Invertebrate "MAM" => 1, # Other Mammal "VRT" => 1, # Other Vertebrate "MUS" => 1, # Mus musculus "PLN" => 1, # Plant "PRO" => 1, # Prokaryote "ROD" => 1, # Other Rodent "SYN" => 1, # Synthetic "UNC" => 1, # Unclassified "VRL" => 1 # Viral ); return exists($EMBL_divisions{$division}); } =head2 _is_valid_molecule_type Title : _is_valid_molecule_type Usage : $self->_is_valid_molecule_type($mol) Function: tests molecule type for validity Returns : true if $mol is a valid EMBL release 87 molecule type. Args : molecule type string =cut sub _is_valid_molecule_type { my ($self, $moltype) = @_; my %EMBL_molecule_types = ( "genomic DNA" => 1, "genomic RNA" => 1, "mRNA" => 1, "tRNA" => 1, "rRNA" => 1, "snoRNA" => 1, "snRNA" => 1, "scRNA" => 1, "pre-RNA" => 1, "other RNA" => 1, "other DNA" => 1, "unassigned DNA" => 1, "unassigned RNA" => 1 ); return exists($EMBL_molecule_types{$moltype}); } =head2 write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object (must be seq) to the stream Returns : 1 for success and undef for error Args : array of 1 to n Bio::SeqI objects =cut sub write_seq { my ($self,@seqs) = @_; foreach my $seq ( @seqs ) { $self->throw("Attempting to write with no seq!") unless defined $seq; unless ( ref $seq && $seq->isa('Bio::SeqI' ) ) { $self->warn("$seq is not a SeqI compliant sequence object!") if $self->verbose >= 0; unless ( ref $seq && $seq->isa('Bio::PrimarySeqI' ) ) { $self->throw("$seq is not a PrimarySeqI compliant sequence object!"); } } my $str = $seq->seq || ''; # Write the ID line. $self->_write_ID_line($seq); # Write the accession line if present my( $acc ); { if ( my $func = $self->_ac_generation_func ) { $acc = &{$func}($seq); } elsif ( $seq->isa('Bio::Seq::RichSeqI') && defined($seq->accession_number) ) { $acc = $seq->accession_number; $acc = join("; ", $acc, $seq->get_secondary_accessions); } elsif ( $seq->can('accession_number') ) { $acc = $seq->accession_number; } if (defined $acc) { $self->_print("AC $acc;\n", "XX\n") || return; } } # Date lines my $switch=0; if ( $seq->can('get_dates') ) { my @dates = $seq->get_dates(); my $ct = 1; my $date_flag = 0; my ($cr) = $seq->annotation->get_Annotations("creation_release"); my ($ur) = $seq->annotation->get_Annotations("update_release"); my ($uv) = $seq->annotation->get_Annotations("update_version"); unless ($cr && $ur && $ur) { $date_flag = 1; } foreach my $dt (@dates) { if (!$date_flag) { $self->_write_line_EMBL_regex("DT ","DT ", $dt." (Rel. ".($cr->value()).", Created)", '\s+|$',80) if $ct == 1; $self->_write_line_EMBL_regex("DT ","DT ", $dt." (Rel. ".($ur->value()).", Last updated, Version ".($uv->value()).")", '\s+|$',80) if $ct == 2; } else { # other formats? $self->_write_line_EMBL_regex("DT ","DT ", $dt,'\s+|$',80); } $switch =1; $ct++; } if ($switch == 1) { $self->_print("XX\n") || return; } } # Description lines $self->_write_line_EMBL_regex("DE ","DE ",$seq->desc(),'\s+|$',80) || return; #' $self->_print( "XX\n") || return; # if there, write the kw line { my( $kw ); if ( my $func = $self->_kw_generation_func ) { $kw = &{$func}($seq); } elsif ( $seq->can('keywords') ) { $kw = $seq->keywords; } if (defined $kw) { $self->_write_line_EMBL_regex("KW ", "KW ", $kw, '\s+|$', 80) || return; #' $self->_print( "XX\n") || return; } } # Organism lines if ($seq->can('species') && (my $spec = $seq->species)) { my @class = $spec->classification(); shift @class; # get rid of species name. Some embl files include # the species name in the OC lines, but this seems # more like an error than something we need to # emulate my $OS = $spec->scientific_name; if ($spec->common_name) { $OS .= ' ('.$spec->common_name.')'; } $self->_print("OS $OS\n") || return; my $OC = join('; ', reverse(@class)) .'.'; $self->_write_line_EMBL_regex("OC ","OC ",$OC,'; |$',80) || return; if ($spec->organelle) { $self->_write_line_EMBL_regex("OG ","OG ",$spec->organelle,'; |$',80) || return; } my $ncbi_taxid = $spec->ncbi_taxid; if ($ncbi_taxid) { $self->_print("OX NCBI_TaxID=$ncbi_taxid\n") || return; } $self->_print("XX\n") || return; } # Reference lines my $t = 1; if ( $seq->can('annotation') && defined $seq->annotation ) { foreach my $ref ( $seq->annotation->get_Annotations('reference') ) { $self->_print( "RN [$t]\n") || return; # Having no RP line is legal, but we need both # start and end for a valid location. if ($ref->comment) { $self->_write_line_EMBL_regex("RC ", "RC ", $ref->comment, '\s+|$', 80) || return; #' } my $start = $ref->start; my $end = $ref->end; if ($start and $end) { $self->_print( "RP $start-$end\n") || return; } elsif ($start or $end) { $self->throw("Both start and end are needed for a valid RP line.". " Got: start='$start' end='$end'"); } if (my $med = $ref->medline) { $self->_print( "RX MEDLINE; $med.\n") || return; } if (my $pm = $ref->pubmed) { $self->_print( "RX PUBMED; $pm.\n") || return; } my $authors = $ref->authors; $authors =~ s/([\w\.]) (\w)/$1#$2/g; # add word wrap protection char '#' $self->_write_line_EMBL_regex("RA ", "RA ", $authors . ";", '\s+|$', 80) || return; #' # If there is no title to the reference, it appears # as a single semi-colon. All titles must end in # a semi-colon. my $ref_title = $ref->title || ''; $ref_title =~ s/[\s;]*$/;/; $self->_write_line_EMBL_regex("RT ", "RT ", $ref_title, '\s+|$', 80) || return; #' $self->_write_line_EMBL_regex("RL ", "RL ", $ref->location, '\s+|$', 80) || return; #' $self->_print("XX\n") || return; $t++; } # DB Xref lines if (my @db_xref = $seq->annotation->get_Annotations('dblink') ) { for my $dr (@db_xref) { my $db_name = $dr->database; my $prim = $dr->primary_id; my $opt = $dr->optional_id || ''; my $line = $opt ? "$db_name; $prim; $opt." : "$db_name; $prim."; $self->_write_line_EMBL_regex("DR ", "DR ", $line, '\s+|$', 80) || return; #' } $self->_print("XX\n") || return; } # Comment lines foreach my $comment ( $seq->annotation->get_Annotations('comment') ) { $self->_write_line_EMBL_regex("CC ", "CC ", $comment->text, '\s+|$', 80) || return; #' $self->_print("XX\n") || return; } } # "\\s\+\|\$" ## FEATURE TABLE $self->_print("FH Key Location/Qualifiers\n") || return; $self->_print("FH\n") || return; my @feats = $seq->can('top_SeqFeatures') ? $seq->top_SeqFeatures : (); if ($feats[0]) { if ( defined $self->_post_sort ) { # we need to read things into an array. # Process. Sort them. Print 'em my $post_sort_func = $self->_post_sort(); my @fth; foreach my $sf ( @feats ) { push(@fth,Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq)); } @fth = sort { &$post_sort_func($a,$b) } @fth; foreach my $fth ( @fth ) { $self->_print_EMBL_FTHelper($fth) || return; } } else { # not post sorted. And so we can print as we get them. # lower memory load... foreach my $sf ( @feats ) { my @fth = Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq); foreach my $fth ( @fth ) { if ( $fth->key eq 'CONTIG') { $self->_show_dna(0); } $self->_print_EMBL_FTHelper($fth) || return; } } } } if ( $self->_show_dna() == 0 ) { $self->_print( "//\n") || return; return; } $self->_print( "XX\n") || return; # finished printing features. # print contig if present : bug#2982 if ( $seq->can('annotation') && defined $seq->annotation) { foreach my $ctg ( $seq->annotation->get_Annotations('contig') ) { if ($ctg->value) { $self->_write_line_EMBL_regex("CO ","CO ", $ctg->value, '[,]|$', 80) || return; } } } # print sequence lines only if sequence is present! bug#2982 if (length($str)) { $str =~ tr/A-Z/a-z/; # Count each nucleotide my $alen = $str =~ tr/a/a/; my $clen = $str =~ tr/c/c/; my $glen = $str =~ tr/g/g/; my $tlen = $str =~ tr/t/t/; my $len = $seq->length(); my $olen = $seq->length() - ($alen + $tlen + $clen + $glen); if ( $olen < 0 ) { $self->warn("Weird. More atgc than bases. Problem!"); } $self->_print("SQ Sequence $len BP; $alen A; $clen C; $glen G; $tlen T; $olen other;\n") || return; my $nuc = 60; # Number of nucleotides per line my $whole_pat = 'a10' x 6; # Pattern for unpacking a whole line my $out_pat = 'A11' x 6; # Pattern for packing a line my $length = length($str); # Calculate the number of nucleotides which fit on whole lines my $whole = int($length / $nuc) * $nuc; # Print the whole lines my( $i ); for ($i = 0; $i < $whole; $i += $nuc) { my $blocks = pack $out_pat, unpack $whole_pat, substr($str, $i, $nuc); $self->_print(sprintf(" $blocks%9d\n", $i + $nuc)) || return; } # Print the last line if (my $last = substr($str, $i)) { my $last_len = length($last); my $last_pat = 'a10' x int($last_len / 10) .'a'. $last_len % 10; my $blocks = pack $out_pat, unpack($last_pat, $last); $self->_print(sprintf(" $blocks%9d\n", $length)) || return; # Add the length to the end } } $self->_print( "//\n") || return; $self->flush if $self->_flush_on_write && defined $self->_fh; } return 1; } =head2 _print_EMBL_FTHelper Title : _print_EMBL_FTHelper Usage : Function: Internal function Returns : 1 if writing succeeded, otherwise undef Args : =cut sub _print_EMBL_FTHelper { my ($self,$fth) = @_; if ( ! ref $fth || ! $fth->isa('Bio::SeqIO::FTHelper') ) { $fth->warn("$fth is not a FTHelper class. Attempting to print, but there could be tears!"); } #$self->_print( "FH Key Location/Qualifiers\n"); #$self->_print( sprintf("FT %-15s %s\n",$fth->key,$fth->loc)); # let if ( $fth->key eq 'CONTIG' ) { $self->_print("XX\n") || return; $self->_write_line_EMBL_regex("CO ", "CO ",$fth->loc, '\,|$',80) || return; #' return 1; } $self->_write_line_EMBL_regex(sprintf("FT %-15s ",$fth->key), "FT ",$fth->loc, '\,|$',80) || return; #' foreach my $tag (sort keys %{$fth->field} ) { if ( ! defined $fth->field->{$tag} ) { next; } foreach my $value ( @{$fth->field->{$tag}} ) { $value =~ s/\"/\"\"/g; if ($value eq "_no_value") { $self->_write_line_EMBL_regex("FT ", "FT ", "/$tag",'.|$',80) || return; #' } # there are almost 3x more quoted qualifier values and they # are more common too so we take quoted ones first # # Long qualifiers, that will be line wrapped, are always quoted elsif (!$FTQUAL_NO_QUOTE{$tag} or length("/$tag=$value")>=60) { my $pat = $value =~ /\s+/ ? '\s+|\-|$' : '.|\-|$'; $self->_write_line_EMBL_regex("FT ", "FT ", "/$tag=\"$value\"",$pat,80) || return; } else { $self->_write_line_EMBL_regex("FT ", "FT ", "/$tag=$value",'.|$',80) || return; #' } } } return 1; } =head2 _read_EMBL_Contig() Title : _read_EMBL_Contig Usage : Function: convert CO lines into annotations Returns : Args : =cut sub _read_EMBL_Contig { my ($self, $buffer) = @_; my @ret; if ( $$buffer !~ /^CO/ ) { warn("Not parsing line '$$buffer' which maybe important"); } $self->_pushback($$buffer); while ( defined ($_ = $self->_readline) ) { /^C/ || last; /^CO\s+(.*)/ && do { push @ret, Bio::Annotation::SimpleValue->new( -tagname => 'contig', -value => $1); }; } $$buffer = $_; return @ret; } #' =head2 _read_EMBL_References Title : _read_EMBL_References Usage : Function: Reads references from EMBL format. Internal function really Example : Returns : Args : =cut sub _read_EMBL_References { my ($self,$buffer) = @_; my (@refs); # assume things are starting with RN if ( $$buffer !~ /^RN/ ) { warn("Not parsing line '$$buffer' which maybe important"); } my $b1; my $b2; my $title; my $loc; my $au; my $med; my $pm; my $com; while ( defined ($_ = $self->_readline) ) { /^R/ || last; /^RP (\d+)-(\d+)/ && do {$b1=$1;$b2=$2;}; /^RX MEDLINE;\s+(\d+)/ && do {$med=$1}; /^RX PUBMED;\s+(\d+)/ && do {$pm=$1}; /^RA (.*)/ && do { $au = $self->_concatenate_lines($au,$1); next; }; /^RT (.*)/ && do { $title = $self->_concatenate_lines($title,$1); next; }; /^RL (.*)/ && do { $loc = $self->_concatenate_lines($loc,$1); next; }; /^RC (.*)/ && do { $com = $self->_concatenate_lines($com,$1); next; }; } my $ref = Bio::Annotation::Reference->new(); $au =~ s/;\s*$//g; $title =~ s/;\s*$//g; $ref->start($b1); $ref->end($b2); $ref->authors($au); $ref->title($title); $ref->location($loc); $ref->medline($med); $ref->comment($com); $ref->pubmed($pm); push(@refs,$ref); $$buffer = $_; return @refs; } =head2 _read_EMBL_Species Title : _read_EMBL_Species Usage : Function: Reads the EMBL Organism species and classification lines. Example : Returns : A Bio::Species object Args : a reference to the current line buffer, accession number =cut sub _read_EMBL_Species { my( $self, $buffer, $acc ) = @_; my $org; $_ = $$buffer; my( $sub_species, $species, $genus, $common, $sci_name, $class_lines ); while (defined( $_ ||= $self->_readline )) { if (/^OS\s+(.+)/) { $sci_name .= ($sci_name) ? ' '.$1 : $1; } elsif (s/^OC\s+(.+)$//) { $class_lines .= $1; } elsif (/^OG\s+(.*)/) { $org = $1; } else { last; } $_ = undef; # Empty $_ to trigger read of next line } # $$buffer = $_; $self->_pushback($_); $sci_name =~ s{\.$}{}; $sci_name || return; # Convert data in classification lines into classification array. # only split on ';' or '.' so that classification that is 2 or more words # will still get matched, use map() to remove trailing/leading/intervening # spaces my @class = map { s/^\s+//; s/\s+$//; s/\s{2,}/ /g; $_; } split /(?<!subgen)[;\.]+/, $class_lines; # do we have a genus? my $possible_genus = $class[-1]; $possible_genus .= "|$class[-2]" if $class[-2]; if ($sci_name =~ /^($possible_genus)/) { $genus = $1; ($species) = $sci_name =~ /^$genus\s+(.+)/; } else { $species = $sci_name; } # Don't make a species object if it is "Unknown" or "None" if ($genus) { return if $genus =~ /^(Unknown|None)$/i; } # is this organism of rank species or is it lower? # (doesn't catch everything, but at least the guess isn't dangerous) if ($species =~ /subsp\.|var\./) { ($species, $sub_species) = $species =~ /(.+)\s+((?:subsp\.|var\.).+)/; } # sometimes things have common name in brackets, like # Schizosaccharomyces pombe (fission yeast), so get rid of the common # name bit. Probably dangerous if real scientific species name ends in # bracketed bit. unless ($class[-1] eq 'Viruses') { ($species, $common) = $species =~ /^(.+)\s+\((.+)\)$/; $sci_name =~ s/\s+\(.+\)$// if $common; } # Bio::Species array needs array in Species -> Kingdom direction unless ($class[-1] eq $sci_name) { push(@class, $sci_name); } @class = reverse @class; # do minimal sanity checks before we hand off to Bio::Species which won't # be able to give informative throw messages if it has to throw because # of problems here $self->throw("$acc seems to be missing its OS line: invalid.") unless $sci_name; my %names; foreach my $i (0..$#class) { my $name = $class[$i]; $names{$name}++; # this code breaks examples like: Xenopus (Silurana) tropicalis # commenting out, see bug 3158 #if ($names{$name} > 1 && ($name ne $class[$i - 1])) { # $self->warn("$acc seems to have an invalid species classification:$name ne $class[$i - 1]"); #} } my $make = Bio::Species->new(); $make->scientific_name($sci_name); $make->classification(@class); unless ($class[-1] eq 'Viruses') { $make->genus($genus) if $genus; $make->species($species) if $species; $make->sub_species($sub_species) if $sub_species; $make->common_name($common) if $common; } $make->organelle($org) if $org; return $make; } =head2 _read_EMBL_DBLink Title : _read_EMBL_DBLink Usage : Function: Reads the EMBL database cross reference ("DR") lines Example : Returns : A list of Bio::Annotation::DBLink objects Args : =cut sub _read_EMBL_DBLink { my( $self,$buffer ) = @_; my( @db_link ); $_ = $$buffer; while (defined( $_ ||= $self->_readline )) { if ( /^DR ([^\s;]+);\s*([^\s;]+);?\s*([^\s;]+)?\.$/) { my ($databse, $prim_id, $sec_id) = ($1,$2,$3); my $link = Bio::Annotation::DBLink->new(-database => $databse, -primary_id => $prim_id, -optional_id => $sec_id); push(@db_link, $link); } else { last; } $_ = undef; # Empty $_ to trigger read of next line } $$buffer = $_; return @db_link; } =head2 _read_EMBL_TaxID_DBLink Title : _read_EMBL_TaxID_DBLink Usage : Function: Reads the EMBL database cross reference to NCBI TaxID ("OX") lines Example : Returns : A list of Bio::Annotation::DBLink objects Args : =cut sub _read_EMBL_TaxID_DBLink { my( $self,$buffer ) = @_; my( @db_link ); $_ = $$buffer; while (defined( $_ ||= $self->_readline )) { if ( /^OX (\S+)=(\d+);$/ ) { my ($databse, $prim_id) = ($1,$2); my $link = Bio::Annotation::DBLink->new(-database => $databse, -primary_id => $prim_id,); push(@db_link, $link); } else { last; } $_ = undef; # Empty $_ to trigger read of next line } $$buffer = $_; return @db_link; } =head2 _filehandle Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional) =cut sub _filehandle{ my ($obj,$value) = @_; if ( defined $value) { $obj->{'_filehandle'} = $value; } return $obj->{'_filehandle'}; } =head2 _read_FTHelper_EMBL Title : _read_FTHelper_EMBL Usage : _read_FTHelper_EMBL($buffer) Function: reads the next FT key line Example : Returns : Bio::SeqIO::FTHelper object Args : filehandle and reference to a scalar =cut sub _read_FTHelper_EMBL { my ($self,$buffer) = @_; my ($key, # The key of the feature $loc, # The location line from the feature @qual, # An arrray of lines making up the qualifiers ); if ($$buffer =~ /^FT\s{3}(\S+)\s+(\S+)/ ) { $key = $1; $loc = $2; # Read all the lines up to the next feature while ( defined($_ = $self->_readline) ) { if (/^FT(\s+)(.+?)\s*$/) { # Lines inside features are preceeded by 19 spaces # A new feature is preceeded by 3 spaces if (length($1) > 4) { # Add to qualifiers if we're in the qualifiers if (@qual) { push(@qual, $2); } # Start the qualifier list if it's the first qualifier elsif (substr($2, 0, 1) eq '/') { @qual = ($2); } # We're still in the location line, so append to location else { $loc .= $2; } } else { # We've reached the start of the next feature last; } } else { # We're at the end of the feature table last; } } } elsif ( $$buffer =~ /^CO\s+(\S+)/) { $key = 'CONTIG'; $loc = $1; # Read all the lines up to the next feature while ( defined($_ = $self->_readline) ) { if (/^CO\s+(\S+)\s*$/) { $loc .= $1; } else { # We've reached the start of the next feature last; } } } else { # No feature key return; } # Put the first line of the next feature into the buffer $$buffer = $_; # Make the new FTHelper object my $out = Bio::SeqIO::FTHelper->new(); $out->verbose($self->verbose()); $out->key($key); $out->loc($loc); # Now parse and add any qualifiers. (@qual is kept # intact to provide informative error messages.) my $last_unquoted_qualifier; QUAL: for (my $i = 0; $i < @qual; $i++) { my $data = $qual[$i]; my ( $qualifier, $value ); unless (( $qualifier, $value ) = ($data =~ m{^/([^=]+)(?:=\s*(.*))?})) { if ( defined $last_unquoted_qualifier ) { # handle case of unquoted multiline - read up everything until the next qualifier do { # Protein sequence translations need to be joined without spaces, # other qualifiers need those. $value .= ' ' if $qualifier ne "translation"; $value .= $data; } while defined($data = $qual[++$i]) && $data !~ m[^/]; $i--; $out->field->{$last_unquoted_qualifier}->[-1] .= $value; $last_unquoted_qualifier = undef; next QUAL; } else { $self->throw("Can't see new qualifier in: $_\nfrom:\n" . join('', map "$_\n", @qual)); } } $qualifier = '' if not defined $qualifier; $last_unquoted_qualifier = undef; if (defined $value) { # Do we have a quoted value? if (substr($value, 0, 1) eq '"') { # Keep adding to value until we find the trailing quote # and the quotes are balanced QUOTES: while ($value !~ /"$/ or $value =~ tr/"/"/ % 2) { #" $i++; my $next = $qual[$i]; if (!defined($next)) { $self->warn("Unbalanced quote in:\n".join("\n", @qual). "\nAdding quote to close...". "Check sequence quality!"); $value .= '"'; last QUOTES; } # Protein sequence translations need to be joined without spaces, # other qualifiers need those. if ($qualifier eq "translation") { $value .= $next; } else { $value .= " $next"; } } # Trim leading and trailing quotes $value =~ s/^"|"$//g; # Undouble internal quotes $value =~ s/""/"/g; #" } else { $last_unquoted_qualifier = $qualifier; } } else { $value = '_no_value'; } # Store the qualifier $out->field->{$qualifier} ||= []; push(@{$out->field->{$qualifier}},$value); } return $out; } =head2 _write_line_EMBL Title : _write_line_EMBL Usage : Function: internal function Example : Returns : 1 if writing succeeded, else undef Args : =cut sub _write_line_EMBL { my ($self,$pre1,$pre2,$line,$length) = @_; $length || $self->throw("Miscalled write_line_EMBL without length. Programming error!"); my $subl = $length - length $pre2; my $linel = length $line; my $i; my $sub = substr($line,0,$length - length $pre1); $self->_print( "$pre1$sub\n") || return; for ($i= ($length - length $pre1);$i < $linel;) { $sub = substr($line,$i,($subl)); $self->_print( "$pre2$sub\n") || return; $i += $subl; } return 1; } =head2 _write_line_EMBL_regex Title : _write_line_EMBL_regex Usage : Function: internal function for writing lines of specified length, with different first and the next line left hand headers and split at specific points in the text Example : Returns : nothing Args : file handle, first header, second header, text-line, regex for line breaks, total line length =cut sub _write_line_EMBL_regex { my ($self,$pre1,$pre2,$line,$regex,$length) = @_; #print STDOUT "Going to print with $line!\n"; $length || $self->throw("Programming error - called write_line_EMBL_regex without length."); my $subl = $length - (length $pre1) -1 ; my( @lines ); CHUNK: while($line) { foreach my $pat ($regex, '[,;\.\/-]\s|'.$regex, '[,;\.\/-]|'.$regex) { if ($line =~ m/^(.{1,$subl})($pat)(.*)/ ) { my $l = $1.$2; $l =~ s/#/ /g # remove word wrap protection char '#' if $pre1 eq "RA "; my $newl = $3; $line = substr($line,length($l)); # be strict about not padding spaces according to # genbank format $l =~ s/\s+$//; next CHUNK if ($l eq ''); push(@lines, $l); next CHUNK; } } # if we get here none of the patterns matched $subl or less chars $self->warn("trouble dissecting \"$line\"\n into chunks ". "of $subl chars or less - this tag won't print right"); # insert a space char to prevent infinite loops $line = substr($line,0,$subl) . " " . substr($line,$subl); } my $s = shift @lines; ($self->_print("$pre1$s\n") || return) if $s; foreach my $s ( @lines ) { $self->_print("$pre2$s\n") || return; } return 1; } =head2 _post_sort Title : _post_sort Usage : $obj->_post_sort($newval) Function: Returns : value of _post_sort Args : newvalue (optional) =cut sub _post_sort{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_post_sort'} = $value; } return $obj->{'_post_sort'}; } =head2 _show_dna Title : _show_dna Usage : $obj->_show_dna($newval) Function: Returns : value of _show_dna Args : newvalue (optional) =cut sub _show_dna{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_show_dna'} = $value; } return $obj->{'_show_dna'}; } =head2 _id_generation_func Title : _id_generation_func Usage : $obj->_id_generation_func($newval) Function: Returns : value of _id_generation_func Args : newvalue (optional) =cut sub _id_generation_func{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_id_generation_func'} = $value; } return $obj->{'_id_generation_func'}; } =head2 _ac_generation_func Title : _ac_generation_func Usage : $obj->_ac_generation_func($newval) Function: Returns : value of _ac_generation_func Args : newvalue (optional) =cut sub _ac_generation_func{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_ac_generation_func'} = $value; } return $obj->{'_ac_generation_func'}; } =head2 _sv_generation_func Title : _sv_generation_func Usage : $obj->_sv_generation_func($newval) Function: Returns : value of _sv_generation_func Args : newvalue (optional) =cut sub _sv_generation_func{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_sv_generation_func'} = $value; } return $obj->{'_sv_generation_func'}; } =head2 _kw_generation_func Title : _kw_generation_func Usage : $obj->_kw_generation_func($newval) Function: Returns : value of _kw_generation_func Args : newvalue (optional) =cut sub _kw_generation_func{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_kw_generation_func'} = $value; } return $obj->{'_kw_generation_func'}; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/embldriver.pm������������������������������������������������������������000444��000766��000024�� 25023�13155576320� 17717� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::embldriver # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::embldriver - EMBL sequence input/output stream =head1 SYNOPSIS It is probably best not to use this object directly, but rather go through the SeqIO handler system. Go: $stream = Bio::SeqIO->new(-file => $filename, -format => 'embldriver'); while ( (my $seq = $stream->next_seq()) ) { # do something with $seq } =head1 DESCRIPTION This object can transform Bio::Seq objects to and from EMBL flat file databases. There is a lot of flexibility here about how to dump things which should be documented more fully. There should be a common object that this and Genbank share (probably with Swissprot). Too much of the magic is identical. =head2 Optional functions =over 3 =item _show_dna() (output only) shows the dna or not =item _post_sort() (output only) provides a sorting func which is applied to the FTHelpers before printing =item _id_generation_func() This is function which is called as print "ID ", $func($annseq), "\n"; To generate the ID line. If it is not there, it generates a sensible ID line using a number of tools. If you want to output annotations in EMBL format they need to be stored in a Bio::Annotation::Collection object which is accessible through the Bio::SeqI interface method L<annotation()|annotation>. The following are the names of the keys which are polled from a L<Bio::Annotation::Collection> object. reference - Should contain Bio::Annotation::Reference objects comment - Should contain Bio::Annotation::Comment objects dblink - Should contain Bio::Annotation::DBLink objects =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::embldriver; use vars qw(%FTQUAL_NO_QUOTE); use strict; use Bio::SeqIO::Handler::GenericRichSeqHandler; use Data::Dumper; use base qw(Bio::SeqIO); my %FTQUAL_NO_QUOTE = map {$_ => 1} qw( anticodon citation codon codon_start cons_splice direction evidence label mod_base number rpt_type rpt_unit transl_except transl_table usedin LOCATION ); my %DATA_KEY = ( ID => 'ID', AC => 'ACCESSION', DT => 'DATE', DE => 'DESCRIPTION', KW => 'KEYWORDS', OS => 'SOURCE', OC => 'CLASSIFICATION', OG => 'ORGANELLE', RN => 'REFERENCE', RA => 'AUTHORS', RC => 'COMMENT', RG => 'CONSRTM', RP => 'POSITION', RX => 'CROSSREF', RT => 'TITLE', RL => 'LOCATION', XX => 'SPACER', FH => 'FEATHEADER', FT => 'FEATURES', AH => 'TPA_HEADER', # Third party annotation AS => 'TPA_DATA', # Third party annotation DR => 'DBLINK', CC => 'COMMENT', CO => 'CO', CON => 'CON', WGS => 'WGS', ANN => 'ANN', TPA => 'TPA', SQ => 'SEQUENCE', ); my %SEC = ( OC => 'CLASSIFICATION', OH => 'HOST', # not currently handled, bundled with organism data for now OG => 'ORGANELLE', OX => 'CROSSREF', RA => 'AUTHORS', RC => 'COMMENT', RG => 'CONSRTM', RP => 'POSITION', RX => 'CROSSREF', RT => 'TITLE', RL => 'JOURNAL', AS => 'ASSEMBLYINFO', # Third party annotation ); my %DELIM = ( #CC => "\n", #DR => "\n", #DT => "\n", ); # signals to process what's in the hash prior to next round # these should be changed to map secondary data my %PRIMARY = map {$_ => 1} qw(ID AC DT DE SV KW OS RN AH DR FH CC SQ FT WGS CON ANN TPA //); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); my $handler = $self->_rearrange([qw(HANDLER)],@args); # hash for functions for decoding keys. $handler ? $self->seqhandler($handler) : $self->seqhandler(Bio::SeqIO::Handler::GenericRichSeqHandler->new( -format => 'embl', -verbose => $self->verbose, -builder => $self->sequence_builder )); # if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : =cut sub next_seq { my $self = shift; my $hobj = $self->seqhandler; local($/) = "\n"; my ($featkey, $qual, $annkey, $delim, $seqdata); my $lastann = ''; my $ct = 0; PARSER: while(defined(my $line = $self->_readline)) { next PARSER if $line =~ m{^\s*$}; chomp $line; my ($ann,$data) = split m{\s{2,3}}, $line , 2; next PARSER if ($ann eq 'XX' || $ann eq 'FH'); if ($ann) { $data ||=''; if ($ann eq 'FT') { # seqfeatures if ($data =~ m{^(\S+)\s+([^\n]+)}) { $hobj->data_handler($seqdata) if $seqdata; $seqdata = (); ($seqdata->{FEATURE_KEY}, $data) = ($1, $2); $seqdata->{NAME} = $ann; $qual = 'LOCATION'; } elsif ($data =~ m{^\s+/([^=]+)=?(.+)?}) { ($qual, $data) = ($1, $2 ||''); $ct = (exists $seqdata->{$qual}) ? ((ref($seqdata->{$qual})) ? scalar(@{ $seqdata->{$qual} }) : 1) : 0 ; } $data =~ s{^\s+}{}; $data =~ tr{"}{}d; # we don't care about quotes yet... my $delim = ($FTQUAL_NO_QUOTE{$qual}) ? '' : ' '; if ($ct == 0) { $seqdata->{$qual} .= ($seqdata->{$qual}) ? $delim.$data : $data; } else { if (!ref($seqdata->{$qual})) { $seqdata->{$qual} = [$seqdata->{$qual}]; } (exists $seqdata->{$qual}->[$ct]) ? (($seqdata->{$qual}->[$ct]) .= $delim.$data) : (($seqdata->{$qual}->[$ct]) .= $data); } } else { # simple annotations $data =~ s{;$}{}; last PARSER if $ann eq '//'; if ($ann ne $lastann) { if (!$SEC{$ann} && $seqdata) { $hobj->data_handler($seqdata); # can't use undef here; it can lead to subtle mem leaks $seqdata = (); } $annkey = (!$SEC{$ann}) ? 'DATA' : # primary data $SEC{$ann}; $seqdata->{'NAME'} = $ann if !$SEC{$ann}; } # toss the data for SQ lines; this needs to be done after the # call to the data handler next PARSER if $ann eq 'SQ'; my $delim = $DELIM{$ann} || ' '; $seqdata->{$annkey} .= ($seqdata->{$annkey}) ? $delim.$data : $data; $lastann = $ann; } } else { # this should only be sequence (fingers crossed!) SEQUENCE: while (defined ($line = $self->_readline)) { if (index($line, '//') == 0) { $data =~ tr{0-9 \n}{}d; $seqdata->{DATA} = $data; #$self->debug(Dumper($seqdata)); $hobj->data_handler($seqdata); $seqdata = (); last PARSER; } else { $data .= $line; $line = undef; } } } } $hobj->data_handler($seqdata) if $seqdata; $seqdata = (); return $hobj->build_sequence; } sub next_chunk { my $self = shift; my $ct = 0; PARSER: while(defined(my $line = $self->_readline)) { next if $line =~ m{^\s*$}; chomp $line; my ($ann,$data) = split m{\s{2,3}}, $line , 2; $data ||= ''; $self->debug("Ann: [$ann]\n\tData: [$data]\n"); last PARSER if $ann =~ m{//}; } } =head2 write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object (must be seq) to the stream Returns : 1 for success and 0 for error Args : array of 1 to n Bio::SeqI objects =cut sub write_seq { shift->throw("Use Bio::SeqIO::embl for output"); # maybe make a Writer class as well???? } =head2 seqhandler Title : seqhandler Usage : $stream->seqhandler($handler) Function: Get/Set the Bio::Seq::HandlerBaseI object Returns : Bio::Seq::HandlerBaseI Args : Bio::Seq::HandlerBaseI =cut sub seqhandler { my ($self, $handler) = @_; if ($handler) { $self->throw("Not a Bio::HandlerBaseI") unless ref($handler) && $handler->isa("Bio::HandlerBaseI"); $self->{'_seqhandler'} = $handler; } return $self->{'_seqhandler'}; } 1; __END__ �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/entrezgene.pm������������������������������������������������������������000444��000766��000024�� 126336�13155576320� 17763� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::entrezgene # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::entrezgene - Entrez Gene ASN1 parser =head1 SYNOPSIS use Bio::SeqIO; # don't instantiate directly - instead do my $seqio = Bio::SeqIO->new(-format => 'entrezgene', -file => $file); my $gene = $seqio->next_seq; =head1 DESCRIPTION This is EntrezGene ASN bioperl parser. It is built on top of L<Bio::ASN1::EntrezGene>, a low level ASN parser built by Mingyi Liu (L<http://sourceforge.net/projects/egparser>). The easiest way to use it is shown above. You will get most of the Entrez Gene annotation such as gene symbol, gene name and description, accession numbers associated with the gene, etc. Almost all of these are given as L<Bio::AnnotationI> objects. If you need all the data do: my $seqio = Bio::SeqIO->new(-format => 'entrezgene', -file => $file, -debug => 'on' ); my ($gene,$genestructure,$uncaptured) = $seqio->next_seq; The second variable returned, C<$genestructure>, is a L<Bio::Cluster::SequenceFamily> object. It contains all Refseqs and the genomic contigs that are associated with the particular gene. The third variable, C<$uncaptured>, is a reference to a plain array. You can also modify the output to allow back compatibility with the old LocusLink parser: my $seqio = Bio::SeqIO->new(-format => 'entrezgene', -file => $file, -locuslink => 'convert'); The C<-debug> and C<-locuslink> options slow down the parser. Example code which looks for ontology terms: my $eio = new Bio::SeqIO(-file => $file, -format => 'entrezgene', -service_record => 'yes'); while (my $seq = $eio->next_seq) { my $gid = $seq->accession_number; foreach my $ot ($ann->get_Annotations('OntologyTerm')) { next if ($ot->term->authority eq 'STS marker'); # No STS markers my $evid = $ot->comment; $evid =~ s/evidence: //i; my @ref = $ot->term->get_references; my $id = $ot->identifier; my $fid = 'GO:' . sprintf("%07u",$id); print join("\t",$gid, $ot->ontology->name, $ot->name, $evid, $fid, @ref?$ref[0]->medline:''), "\n"; } } =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Stefan Kirov Email skirov at utk.edu =head1 CONTRIBUTORS Hilmar Lapp, hlapp at gmx.net =head1 APPENDIX This parser is based on Bio::ASN1::EntrezGene module. The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqIO::entrezgene; use strict; use Bio::ASN1::EntrezGene; use Bio::Seq; use Bio::Species; use Bio::Annotation::SimpleValue; use Bio::Annotation::DBLink; use Bio::Annotation::Comment; use Bio::SeqFeature::Generic; use Bio::Annotation::Reference; use Bio::SeqFeature::Gene::Exon; use Bio::SeqFeature::Gene::Transcript; use Bio::SeqFeature::Gene::GeneStructure; use Bio::Cluster::SequenceFamily; #use Bio::Ontology::Ontology; Relationships.... later use Bio::Ontology::Term; use Bio::Annotation::OntologyTerm; use Data::Dumper; use base qw(Bio::SeqIO); %main::eg_to_ll = ( 'Official Full Name' => 'OFFICIAL_GENE_NAME', 'chromosome' => 'CHR', 'cyto' => 'MAP', 'Official Symbol' => 'OFFICIAL_SYMBOL' ); @main::egonly = keys %main::eg_to_ll; # We define $xval and some other variables so we don't have # to pass them as arguments my ( $seq, $ann, $xval, %seqcollection, $buf ); sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys $self->{_debug} = $param{-debug} || 'off'; $self->{_locuslink} = $param{-locuslink} || 'no'; $self->{_service_record} = $param{-service_record} || 'no'; $self->{_parser} = Bio::ASN1::EntrezGene->new( file => $param{-file} ); #Instantiate the low level parser here (it is -file in Bioperl #-should tell M.) #$self->{_parser}->next_seq; #First empty record- bug in Bio::ASN::Parser } sub next_seq { my $self = shift; my $value = $self->{_parser}->next_seq(1); # $value contains data structure for the # record being parsed. 2 indicates the recommended # trimming mode of the data structure #I use 1 as I prefer not to descend into size 0 arrays return unless ($value); my $debug = $self->{_debug}; $self->{_ann} = Bio::Annotation::Collection->new(); $self->{_currentann} = Bio::Annotation::Collection->new(); my @alluncaptured; # parse the entry #my @keys=keys %{$value}; obsolete $xval = $value->[0]; #return unless ($xval->{gene}->{desc} eq 'albumin'); #return new Bio::Seq (-id=>'Generif service record', -seq=>'') # unless ($xval->{'track-info'}{geneid}== 283); return Bio::Seq->new( -id => 'Generif service record', -seq => '' ) if ( ( $self->{_service_record} ne 'yes' ) && ( $xval->{gene}->{desc} =~ /record to support submission of generifs for a gene not in entrez/i ) ); #Basic data #$xval->{summary}=~s/\n//g; $seq = Bio::Seq->new( -display_id => $xval->{gene}{locus}, -accession_number => $xval->{'track-info'}{geneid}, -desc => $xval->{summary} ); #Source data here $self->_add_to_ann( $xval->{'track-info'}->{status}, 'Entrez Gene Status' ); my $lineage = $xval->{source}{org}{orgname}{lineage}; $lineage =~ s/[\s\n]//g; my ( $comp, @lineage ); while ($lineage) { ( $comp, $lineage ) = split( /;/, $lineage, 2 ); unshift @lineage, $comp; } unless ( exists( $xval->{source}{org}{orgname}{name}{binomial} ) ) { shift @lineage; my ( $gen, $sp ) = split( /\s/, $xval->{source}{org}{taxname} ); if ( ($sp) && ( $sp ne '' ) ) { if ( $gen =~ /plasmid/i ) { $sp = $gen . $sp; } unshift @lineage, $sp; } else { unshift @lineage, 'unknown'; } } else { my $sp = $xval->{source}{org}{orgname}{name}{binomial}{species}; if ( ($sp) && ( $sp ne '' ) ) { my ( $spc, $strain ) = split( 'sp.', $sp ); #Do we need strain? $spc =~ s/\s//g; if ( ($spc) && ( $spc ne '' ) ) { unshift @lineage, $spc; } else { unshift @lineage, 'unknown'; } } else { unshift @lineage, 'unknown'; } } #print Dumper($xval->{source}{org}); my $ncbiid; if ( ref( $xval->{source}{org}{db} ) eq 'ARRAY' ) { foreach my $taxonomy ( @{ $xval->{source}{org}{db} } ) { if ( lc( $taxonomy->{db} ) eq 'taxon' ) { $ncbiid = $taxonomy->{tag}{id}; } else { push @alluncaptured, $taxonomy; } delete $xval->{source}{org}{db}; } } $ncbiid = $ncbiid || $xval->{source}{org}{db}{tag}{id}; my $s1 = shift @lineage; my $s2 = shift @lineage; my $specie = Bio::Species->new( -classification => [ $s1, $s2 ], -ncbi_taxid => $ncbiid ); $specie->common_name( $xval->{source}{org}{common} ); if ( exists( $xval->{source}->{subtype} ) && ( $xval->{source}->{subtype} ) ) { if ( ref( $xval->{source}->{subtype} ) eq 'ARRAY' ) { foreach my $subtype ( @{ $xval->{source}->{subtype} } ) { $self->_add_to_ann( $subtype->{name}, $subtype->{subtype} ); } } else { $self->_add_to_ann( $xval->{source}->{subtype}->{name}, $xval->{source}->{subtype}->{subtype} ); } } #Synonyms if ( ref( $xval->{gene}->{syn} ) eq 'ARRAY' ) { foreach my $symsyn ( @{ $xval->{gene}->{syn} } ) { $self->_add_to_ann( $symsyn, 'ALIAS_SYMBOL' ); } } else { $self->_add_to_ann( $xval->{gene}->{syn}, 'ALIAS_SYMBOL' ) if ( $xval->{gene}->{syn} ); } #COMMENTS (STS not dealt with yet) if ( exists( $xval->{comments} ) ) { if ( ref( $xval->{comments} ) eq 'ARRAY' ) { for my $i ( 0 .. $#{ $xval->{comments} } ) { $self->{_current} = $xval->{comments}->[$i]; push @alluncaptured, $self->_process_all_comments(); } } else { $self->{_current} = $xval->{comments}; push @alluncaptured, $self->_process_all_comments(); } } #Gene if ( exists( $xval->{gene}->{db} ) ) { if ( ref( $xval->{gene}->{db} ) eq 'ARRAY' ) { foreach my $genedb ( @{ $xval->{gene}->{db} } ) { my $id = exists( $genedb->{tag}->{id} ) ? $genedb->{tag}->{id} : $genedb->{tag}->{str}; $self->_add_to_ann( $id, $genedb->{db} ); } } else { my $id = ( $xval->{gene}->{db}->{tag}->{id} ) ? $xval->{gene}->{db}->{tag}->{id} : $xval->{gene}->{db}->{tag}->{str}; $self->_add_to_ann( $id, $xval->{gene}->{db}->{db} ); } $self->_add_to_ann( $xval->{gene}->{'locus-tag'}, 'LOCUS_SYNONYM' ); delete $xval->{gene}->{db} unless ( $debug eq 'off' ); } #LOCATION To do: uncaptured stuff if ( exists( $xval->{location} ) ) { if ( ref( $xval->{location} ) eq 'ARRAY' ) { foreach my $loc ( @{ $xval->{location} } ) { $self->_add_to_ann( $loc->{'display-str'}, $loc->{method}->{'map-type'} ); } } else { $self->_add_to_ann( $xval->{location}->{'display-str'}, $xval->{location}->{method}->{'map-type'} ); } delete $xval->{location} unless ( $debug eq 'off' ); } #LOCUS if ( ref( $xval->{locus} ) eq 'ARRAY' ) { foreach my $locus ( @{ $xval->{locus} } ) { $self->{_current} = $locus; push @alluncaptured, $self->_process_locus(); } } else { push @alluncaptured, $self->_process_locus( $xval->{locus} ); } #Homology my @homologies; # Sometimes there are multiple entries if (ref $xval->{homology} eq 'ARRAY') { @homologies = @{ $xval->{homology} }; } else { push @homologies, $xval->{homology}; } foreach my $homology (@homologies) { my ( $uncapt, $hom, $anchor ) = _process_src( $homology->{source} ); foreach my $homann (@$hom) { $self->{_ann}->add_Annotation( 'dblink', $homann ); } push @alluncaptured, $uncapt; } #Index terms if ( ( exists( $xval->{'xtra-index-terms'} ) ) && ( $xval->{'xtra-index-terms'} ) ) { if ( ref( $xval->{'xtra-index-terms'} ) eq 'ARRAY' ) { foreach my $term ( @{ $xval->{'xtra-index-terms'} } ) { $self->_add_to_ann( $term, 'Index terms' ); } } else { $self->_add_to_ann( $xval->{'xtra-index-terms'}, 'Index terms' ); } } #PROPERTIES my @prop; if ( exists( $xval->{properties} ) ) { if ( ref( $xval->{properties} ) eq 'ARRAY' ) { foreach my $property ( @{ $xval->{properties} } ) { push @alluncaptured, $self->_process_prop($property); } } else { push @alluncaptured, $self->_process_prop( $xval->{properties} ); } } $seq->annotation( $self->{_ann} ); $seq->species($specie); my @seqs; foreach my $key ( keys %seqcollection ) { #Optimize this, no need to go through hash? push @seqs, @{ $seqcollection{$key} }; } my $cluster = Bio::Cluster::SequenceFamily->new( -family_id => $seq->accession_number, -description => "Entrez Gene " . $seq->accession_number, -members => \@seqs ); #Our EntrezGene object #clean unless ( $debug eq 'off' ) { delete $xval->{homology}->{source}; delete( $xval->{summary} ); delete( $xval->{'track-info'} ); delete( $xval->{gene}{locus} ); delete( $xval->{source}{org}{orgname}{lineage} ); delete $xval->{source}{org}{orgname}{name}{binomial}{species}; delete $xval->{gene}{syn}; delete $xval->{source}->{subtype}; delete $xval->{comments}; delete $xval->{properties}; delete $xval->{'xtra-index-terms'}; delete $xval->{status}; } push @alluncaptured, $xval; undef %seqcollection; $seq->annotation( _backcomp_ll( $self->{_ann} ) ) if ( $self->{_locuslink} eq 'convert' ); #Fix this! return wantarray ? ( $seq, $cluster, \@alluncaptured ) : $seq; #Hilmar's suggestion } sub _process_refseq { my $self = shift; my $products = shift; my $ns = shift; my $iter = shift; $iter++; my $pid; my ( @uncaptured, @products ); if ( ref($products) eq 'ARRAY' ) { @products = @{$products}; } else { push @products, $products; } foreach my $product (@products) { if ( ( ref($product) eq 'ARRAY' ) && ( $#{$product} > -1 ) ) { $self->_process_refseq( $product, $ns, $iter ); next; } if ( ( exists( $product->{products} ) && ( !exists( $product->{accession} ) ) ) ) { $self->_process_refseq( $product->{products}, $ns ); next; } #if ((exists($product->{products})&&($product->{products}))) { # $self->_process_refseq($product->{products},$ns,$iter); #} if ( ( exists( $product->{seqs}->{whole}->{gi} ) ) && ( ref( $product->{seqs}->{whole}->{gi} ) eq 'ARRAY' ) ) { $product->{seqs}->{whole}->{gi} = $product->{seqs}->{whole}->{gi}->[0]; } #Lose some data if ( ( exists( $product->{seqs}->{whole}->{gi} ) ) || ( exists( $product->{accession} ) ) ) { #Minimal data required my $cann = Bio::Annotation::Collection->new(); $pid = $product->{accession}; my $authority = exists( $product->{type} ) ? $product->{type} : $product->{heading}; my $nseq = Bio::Seq->new( -accession_number => $product->{seqs}->{whole}->{gi}, -display_id => $product->{accession}, -authority => $authority, -namespace => $ns ); if ( exists( $product->{source} ) && ( $product->{source} ) ) { if ( ( !defined( $nseq->authority ) ) && ( exists( $product->{source}->{src} ) ) && ( exists( $product->{source}->{src}->{db} ) ) ) { $nseq->authority( $product->{source}->{src}->{db} ); } my ( $uncapt, $allann ) = _process_src( $product->{source} ); push @uncaptured, $uncapt; delete $product->{source}; foreach my $annotation ( @{$allann} ) { $cann->add_Annotation( 'dblink', $annotation ); } } delete $product->{seqs}->{whole}->{gi}; delete $product->{accession}; delete $product->{source}; delete $product->{heading}; my ( $uncapt, $ann, $cfeat ) = $self->_process_comments( $product->{comment} ) if ( exists( $product->{comment} ) ); push @uncaptured, $uncapt; foreach my $feat ( @{$cfeat} ) { $nseq->add_SeqFeature($feat); } if ( exists( $product->{products} ) && ( $product->{products} ) ) { my ( $uncapt, $prodid ) = $self->_process_refseq( $product->{products} ); push @uncaptured, $uncapt; my $simann = Bio::Annotation::SimpleValue->new( -value => $prodid, -tagname => 'product' ); $cann->add_Annotation($simann); } foreach my $key ( keys %$ann ) { foreach my $val ( @{ $ann->{$key} } ) { $cann->add_Annotation( $key, $val ); } } $nseq->annotation($cann); push @{ $seqcollection{seq} }, $nseq; } } undef @products; undef $products; #my $ti2=new Benchmark; # my $td= timediff($ti2, $ti1); # print "\tITER $iter:",timestr($td),"\n"; return \@uncaptured, $pid, $seqcollection{seq}, $iter; } sub _process_links { my $self = shift; my $links = shift; my ( @annot, @uncapt ); if ( ref($links) eq 'ARRAY' ) { foreach my $link (@$links) { my ( $uncapt, $annot ) = _process_src( $link->{source} ) if ( exists( $link->{source} ) ); push @uncapt, $uncapt; foreach my $annotation (@$annot) { $self->{_ann}->add_Annotation( 'dblink', $annotation ); } } } else { my ( $uncapt, $annot ) = _process_src( $links->{source} ) if ( exists( $links->{source} ) ); push @uncapt, $uncapt; foreach my $annotation (@$annot) { $self->{_ann}->add_Annotation( 'dblink', $annotation ); } } return @uncapt; } sub _add_to_ann { #Highest level only my ( $self, $val, $tag ) = @_; # $val=~s/\n//g;#Low level EG parser leaves this so we take care of them here unless ($tag) { $self->warn( "No tagname for value $val, tag $tag " . $seq->id . "\n" ); return; } my $simann = Bio::Annotation::SimpleValue->new( -value => $val, -tagname => $tag ); $self->{_ann}->add_Annotation($simann); } sub _process_comments { my $self = shift; my $prod = shift; my ( %cann, @feat, @uncaptured, @comments, @sfann ); if ( ( ref($prod) eq 'HASH' ) && ( exists( $prod->{comment} ) ) ) { $prod = $prod->{comment}; } if ( ref($prod) eq 'ARRAY' ) { @comments = @{$prod}; } else { push @comments, $prod; } my $i = 0; for my $comm (@comments) { # Each comments is a hash reference $self->throw("Comment not a hash reference") unless ref($comm) eq 'HASH'; my ( $desc, $nfeat, $add, @ann, @comm ); # next unless (exists($comm->{comment}));#Should be more careful when calling _process_comment:To do my $heading = $comm->{heading} || 'description'; if ( !exists( $comm->{comment} ) ) { if ( ( exists( $comm->{type} ) ) && ( $comm->{type} ) && ( $self->{_current_heading} ) ) { $comm->{type} = $self->{_current_heading}; } if ( ( exists( $comm->{source} ) ) && ( exists( $comm->{type} ) ) && ( exists( $comm->{text} ) ) && ( $comm->{type} ne 'comment' ) ) { my ( $uncapt, $annot, $anchor ) = _process_src( $comm->{source} ); my $cann = shift(@$annot); if ( defined $cann ) { $cann->optional_id( $comm->{text} ); $cann->authority( $comm->{type} ); $cann->version( $comm->{version} ); push @sfann, $cann; } } } while (ref($comm) eq 'HASH' && ( exists( $comm->{comment} ) ) && ( $comm->{comment} ) ) { if ( ( exists( $comm->{source} ) ) && ( $comm->{source} ) ) { my ( $uncapt, $allann, $anchor ) = _process_src( $comm->{source} ); if ($allann) { delete $comm->{source}; push @uncaptured, $uncapt; foreach my $annotation ( @{$allann} ) { if ( $annotation->{_anchor} ) { $desc .= $annotation->{_anchor} . ' '; } $annotation->optional_id($heading); push @sfann, $annotation; push @{ $cann{'dblink'} }, $annotation; } } } $comm = $comm->{comment}; if ( ref($comm) eq 'ARRAY' ) { @comm = @{$comm}; } else { push @comm, $comm if ($comm); } foreach my $ccomm (@comm) { next unless ($ccomm); if ( exists( $ccomm->{source} ) ) { my ( $uncapt, $allann, $anchor ) = _process_src( $ccomm->{source} ); if ($allann) { @sfann = @{$allann}; delete $ccomm->{source}; push @uncaptured, $uncapt; } } $ccomm = $ccomm->{comment} if ( exists( $ccomm->{comment} ) ); #Alice in Wonderland??? my @loc; if ($ccomm) { if ( ref($ccomm) eq 'ARRAY' ) { @loc = @{$ccomm}; } else { push @loc, $ccomm; } } foreach my $loc (@loc) { if ( ( exists( $loc->{text} ) ) && ( $loc->{text} =~ /Location/i ) ) { my ( $l1, $rest ) = split( /-/, $loc->{text} ); $l1 =~ s/\D//g; $rest =~ s/^\s//; my ( $l2, $scorestr ) = split( /\s/, $rest, 2 ); my ( $scoresrc, $score ) = split( /:/, $scorestr ); $score =~ s/\D//g; my ( %tags, $tag ); unless ($l1) { next; } $nfeat = Bio::SeqFeature::Generic->new( -start => $l1, -end => $l2, -strand => $tags{strand}, -source => $loc->{type}, -seq_id => $desc, -primary => $heading, -score => $score, -tag => { score_src => $scoresrc } ); my $sfeatann = Bio::Annotation::Collection->new(); foreach my $sfann (@sfann) { $sfeatann->add_Annotation( 'dblink', $sfann ); } undef @sfann; $nfeat->annotation($sfeatann) ; #Thus the annotation will be available both in the seq and seqfeat? push @feat, $nfeat; delete $loc->{text}; delete $loc->{type}; } elsif ( exists( $loc->{label} ) ) { my $simann = Bio::Annotation::SimpleValue->new( -value => $loc->{text}, -tagname => $loc->{label} ); delete $loc->{text}; delete $loc->{label}; push @{ $cann{'simple'} }, $simann; push @uncaptured, $loc; } elsif ( exists( $loc->{text} ) ) { my $simann = Bio::Annotation::SimpleValue->new( -value => $loc->{text}, -tagname => $heading ); delete $loc->{text}; push @{ $cann{'simple'} }, $simann; push @uncaptured, $loc; } } } #Bit clumsy but that's what we get from the low level parser } $i++; } if (@sfann) { push @{ $cann{'dblink'} }, @sfann; } #Annotation that is not location specific, for example phenotype #undef $self->{_current_heading}; return \@uncaptured, \%cann, \@feat; } sub _process_src { my $src = shift; #Trick we do because sometimes we have an array ref my ( @ann, $anch, @uncapt ); if ( ref($src) eq 'ARRAY' ) { foreach my $msrc (@$src) { my ( $uncapt, $ann, $anchor ) = _process_src($msrc); push @ann, @$ann; push @uncapt, $uncapt; $anch = $anchor; } return \@uncapt, \@ann, $anch; } return unless ( exists( $src->{src}->{tag} ) ); #my $t0=new Benchmark my $db = $src->{src}->{db}; delete $src->{src}->{db}; my $anchor = $src->{anchor} || ''; delete $src->{anchor}; my $url; if ( exists( $src->{url} ) && ( $src->{url} ) ) { $url = $src->{url}; $url =~ s/\n//g; delete $src->{url}; } if ( ( exists( $src->{src}->{tag}->{str} ) ) && ( $src->{src}->{tag}->{str} ) ) { my @sq = split( /[,;]/, $src->{src}->{tag}->{str} ); delete $src->{src}->{tag}; foreach my $id (@sq) { $id =~ s/\n//g; undef $anchor if ( $anchor eq 'id' ); my $simann = Bio::Annotation::DBLink->new( -database => $db, -primary_id => $id, -authority => $src->{heading} ); $simann->url($url) if ($url); #DBLink should have URL! push @ann, $simann; } } else { my $id = $src->{src}->{tag}->{id} || ''; delete $src->{src}->{tag}; undef $anchor if ( $anchor eq 'id' ); $id =~ s/\n//g; my $simann = Bio::Annotation::DBLink->new( -database => $db, -primary_id => $id, -authority => $src->{heading} ); if ($anchor) { $simann->{_anchor} = $anchor; $simann->optional_id($anchor); } $simann->url($url) if ($url); #DBLink should have URL! push @ann, $simann; } #my $t1=new Benchmark; #my $td= timediff($t1, $t0); #print "\t\tSRC:",timestr($td),"\n"; return $src, \@ann, $anchor; } sub _add_references { my $self = shift; my $refs = shift; if ( ref($refs) eq 'ARRAY' ) { foreach my $ref (@$refs) { my $refan = Bio::Annotation::Reference->new( -database => 'Pubmed', -primary_id => $ref ); $self->{_ann}->add_Annotation( 'Reference', $refan ); } } else { my $refan = Bio::Annotation::Reference->new( -database => 'Pubmed', -primary_id => $refs ); $self->{_ann}->add_Annotation( 'Reference', $refan ); } } #Should we do this at all if no seq coord are present? sub _process_locus { my $self = shift; my @uncapt; return $self unless ( exists( $self->{_current}->{accession} ) && ( $self->{_current}->{accession} ) ); my $gseq = Bio::Seq->new( -display_id => $self->{_current}->{accession}, -version => $self->{_current}->{version}, -accession_number => $self->{_current}->{seqs}->{'int'}->{id}->{gi}, -authority => $self->{_current}->{type}, -namespace => $self->{_current}->{heading} ); delete $self->{_current}->{accession}; delete $self->{_current}->{version}; delete $self->{_current}->{'int'}->{id}->{gi}; my ( $start, $end, $strand ); if ( exists( $self->{_current}->{seqs}->{'int'}->{from} ) ) { $start = $self->{_current}->{seqs}->{'int'}->{from}; delete $self->{_current}->{seqs}->{'int'}->{from}; #unless ($start) {print $locus->{seqs}->{'int'}->{from},"\n",$locus,"\n";} $end = $self->{_current}->{seqs}->{'int'}->{to}; delete $self->{_current}->{seqs}->{'int'}->{to}; delete $self->{_current}->{seqs}->{'int'}->{strand}; $strand = $self->{_current}->{seqs}->{'int'}->{strand} eq 'minus' ? -1 : 1 if ( exists( $self->{_current}->{seqs}->{'int'}->{strand} ) ) ; #1 being default my $nfeat = Bio::SeqFeature::Generic->new( -start => $start, -end => $end, -strand => $strand, primary => 'gene location' ); $gseq->add_SeqFeature($nfeat); } my @products; if ( ref( $self->{_current}->{products} ) eq 'ARRAY' ) { @products = @{ $self->{_current}->{products} }; } else { push @products, $self->{_current}->{products}; } delete $self->{_current}->{products}; my $gstruct = Bio::SeqFeature::Gene::GeneStructure->new(); foreach my $product (@products) { my ( $tr, $uncapt ) = _process_products_coordinates( $product, $start, $end, $strand ); $gstruct->add_transcript($tr) if ($tr); undef $tr->{parent}; #Because of a cycleG push @uncapt, $uncapt; } $gseq->add_SeqFeature($gstruct); push @{ $seqcollection{genestructure} }, $gseq; return @uncapt; } =head1 _process_products_coordinates To do: =cut sub _process_products_coordinates { my $coord = shift; my $start = shift || 0; #In case it is not known: should there be an entry at all? my $end = shift || 1; my $strand = shift || 1; return unless ( exists( $coord->{accession} ) ); my ( @coords, @uncapt ); my $transcript = Bio::SeqFeature::Gene::Transcript->new( -primary => $coord->{accession}, #Desc is actually non functional... -start => $start, -end => $end, -strand => $strand, -desc => $coord->{type} ); if ( ( exists( $coord->{'genomic-coords'}->{mix}->{'int'} ) ) || ( exists( $coord->{'genomic-coords'}->{'packed-int'} ) ) ) { @coords = exists( $coord->{'genomic-coords'}->{mix}->{'int'} ) ? @{ $coord->{'genomic-coords'}->{mix}->{'int'} } : @{ $coord->{'genomic-coords'}->{'packed-int'} }; foreach my $exon (@coords) { next unless ( exists( $exon->{from} ) ); my $exonobj = Bio::SeqFeature::Gene::Exon->new( -start => $exon->{from}, -end => $exon->{to}, -strand => $strand ); $transcript->add_exon($exonobj); delete $exon->{from}; delete $exon->{to}; delete $exon->{strand}; push @uncapt, $exon; } } my ( $prot, $uncapt ); if ( exists( $coord->{products} ) ) { my @products; # Sometimes there are multiple entries if (ref $coord->{products} eq 'ARRAY') { @products = @{ $coord->{products} }; } else { push @products, $coord->{products}; } foreach my $product (@products) { my ( $prot, $uncapt ) = _process_products_coordinates( $product, $start, $end, $strand ); $transcript->add_SeqFeature($prot); push @uncapt, $uncapt; } } return $transcript, \@uncapt; } =head1 _process_prop To do: process GO =cut sub _process_prop { my $self = shift; my $prop = shift; my @uncapt; if ( exists( $prop->{properties} ) ) { #Iterate if ( ref( $prop->{properties} ) eq 'ARRAY' ) { foreach my $propn ( @{ $prop->{properties} } ) { push @uncapt, $self->_process_prop($propn); } } else { push @uncapt, $self->_process_prop( $prop->{properties} ); } } unless ( ( exists( $prop->{heading} ) ) && ( $prop->{heading} eq 'GeneOntology' ) ) { $self->_add_to_ann( $prop->{text}, $prop->{label} ) if ( exists( $prop->{text} ) ); delete $prop->{text}; delete $prop->{label}; push @uncapt, $prop; return \@uncapt; } #Will do GO later if ( exists( $prop->{comment} ) ) { push @uncapt, $self->_process_go( $prop->{comment} ); } } sub _process_all_comments { my $self = shift; my $product = $self->{_current}; #Better without copying my @alluncaptured; my $heading = $product->{heading} if ( exists( $product->{heading} ) ); if ($heading) { #my $tx1=new Benchmark; delete $product->{heading}; CLASS: { if ( $heading =~ 'RefSeq Status' ) { #IN case NCBI changes slightly the spacing:-) $self->_add_to_ann( $product->{label}, 'RefSeq status' ); last CLASS; } if ( $heading =~ 'NCBI Reference Sequences' ) { #IN case NCBI changes slightly the spacing:-) if ( ( exists( $product->{comment} ) ) && ( !exists( $product->{products} ) ) ) { $product->{products} = $product->{comment}; } #unless (($product->{products})&&(exists($product->{comment}))) { #if (ref ($product->{comment}) eq 'ARRAY') { # foreach my $pc (@{$product->{comment}}) { # push @{$product->{products}},$pc->{products}; # } #} #else { # $product->{products}=exists($product->{comments}->{products})?$product->{comments}->{products}:$product->{comment}; #} #} my @uncaptured = $self->_process_refseq( $product->{products}, 'refseq' ); push @alluncaptured, @uncaptured; last CLASS; } if ( ( $heading =~ 'Related Sequences' ) && ( exists( $product->{products} ) ) ) { #IN case NCBI changes slightly the spacing:-) my @uncaptured = $self->_process_refseq( $product->{products} ); push @alluncaptured, @uncaptured; last CLASS; } if ( ( $heading =~ 'Additional Links' ) && ( exists( $product->{comment} ) ) ) { #IN case NCBI changes slightly the spacing:-) push @alluncaptured, $self->_process_links( $product->{comment} ); last CLASS; } if ( $heading =~ 'LocusTagLink' ) { #IN case NCBI changes slightly the spacing:-) $self->_add_to_ann( $product->{source}->{src}->{tag}->{id}, $product->{source}->{src}->{db} ); last CLASS; } if ( ( $heading =~ 'Sequence Tagged Sites' ) && ( exists( $product->{comment} ) ) ) { #IN case NCBI changes slightly the spacing:-) push @alluncaptured, $self->_process_STS( $product->{comment} ); delete $product->{comment}; last CLASS; } if ( $heading =~ 'Pathways' ) { $self->{_current_heading} = 'Pathways'; last CLASS; } } # my $tx2=new Benchmark; # my $td= timediff($tx2, $tx1); #print "\t\t$heading:",timestr($td),"\n"; } if ( exists( $product->{type} ) && ( $product->{type} eq 'generif' ) ) { push @alluncaptured, $self->_process_grif($product); return @alluncaptured; #Maybe still process the comments? } if ( exists( $product->{refs} ) ) { $self->_add_references( $product->{refs}->{pmid} ); delete $product->{refs}->{pmid}; push @alluncaptured, $product; } if ( exists( $product->{comment} ) ) { my ( $uncapt, $allan, $allfeat ) = $self->_process_comments( $product->{comment} ); foreach my $key ( keys %$allan ) { foreach my $val ( @{ $allan->{$key} } ) { $self->{_ann}->add_Annotation( $key, $val ); } } delete $product->{refs}->{comment}; push @alluncaptured, $uncapt; } #if (exists($product->{source})) { # my ($uncapt,$ann,$anchor)=_process_src($product->{source}); # foreach my $dbl (@$ann) { # $self->{_ann}->add_Annotation('dblink',$dbl); # } #} return @alluncaptured; } sub _process_STS { my $self = shift; my $comment = shift; my @comm; push @comm, ( ref($comment) eq 'ARRAY' ) ? @{$comment} : $comment; foreach my $product (@comm) { my $sts = Bio::Ontology::Term->new( -identifier => $product->{source}->{src}->{tag}->{id}, -name => $product->{source}->{anchor}, -comment => $product->{source}->{'post-text'} ); $sts->namespace( $product->{source}->{src}->{db} ); $sts->authority('STS marker'); my @alt; if ( exists( $product->{comment} ) ) { push @alt, ( ref( $product->{comment} ) eq 'ARRAY' ) ? @{ $product->{comment} } : $product->{comment}; foreach my $alt (@alt) { $sts->add_synonym( $alt->{text} ); } } my $annterm = Bio::Annotation::OntologyTerm->new(); $annterm->term($sts); $self->{_ann}->add_Annotation( 'OntologyTerm', $annterm ); } } sub _process_go { my $self = shift; my $comm = shift; my @comm; push @comm, ( ref($comm) eq 'ARRAY' ) ? @{$comm} : $comm; foreach my $comp (@comm) { my $category = $comp->{label}; if ( ref( $comp->{comment} ) eq 'ARRAY' ) { foreach my $go ( @{ $comp->{comment} } ) { my $term = _get_go_term( $go, $category ); my $annterm = Bio::Annotation::OntologyTerm->new( -tagname => 'Gene Ontology' ); $annterm->term($term); $self->{_ann}->add_Annotation( 'OntologyTerm', $annterm ); } } else { my $term = _get_go_term( $comp->{comment}, $category ); my $annterm = Bio::Annotation::OntologyTerm->new( -tagname => 'Gene Ontology' ); $annterm->term($term); $self->{_ann}->add_Annotation( 'OntologyTerm', $annterm ); } } } sub _process_grif { my $self = shift; my $grif = shift; if ( ( exists( $grif->{comment} ) ) && ( ref( $grif->{comment} ) eq 'ARRAY' ) ) { my @uncapt; foreach my $product ( @{ $grif->{comment} } ) { next unless ( exists( $product->{text} ) ); my $uproduct = $self->_process_grif($product); #$self->{_ann->add_Annotation($type,$grifobj); push @uncapt, $uproduct; } return \@uncapt; } if ( exists( $grif->{comment}->{comment} ) ) { $grif = $grif->{comment}; } my $ref = ( ref( $grif->{refs} ) eq 'ARRAY' ) ? shift @{ $grif->{refs} } : $grif->{refs}; my $refergene = ''; my $refdb = ''; my ( $obj, $type ); if ( $ref->{pmid} ) { if ( exists( $grif->{source} ) ) { #unfortunatrely we cannot put yet everything in $refergene = $grif->{source}->{src}->{tag}->{id}; $refdb = $grif->{source}->{src}->{db}; } my $grifobj = Bio::Annotation::Comment->new( -text => $grif->{text} ); $obj = Bio::Annotation::DBLink->new( -database => 'generif', -primary_id => $ref->{pmid} , #The pubmed id (at least the first one) which is a base for the conclusion -version => $grif->{version}, -optional_id => $refergene, -authority => $refdb ); $obj->comment($grifobj); $type = 'dblink'; } else { $obj = Bio::Annotation::SimpleValue->new( $grif->{text}, 'generif' ); $type = 'generif'; } delete $grif->{text}; delete $grif->{version}; delete $grif->{type}; delete $grif->{refs}; $self->{_ann}->add_Annotation( $type, $obj ); return $grif; } sub _get_go_term { my $go = shift; my $category = shift; my $refan = Bio::Annotation::Reference->new( #We expect one ref per GO -medline => $go->{refs}->{pmid}, -title => 'no title' ); my $term = Bio::Ontology::Term->new( -identifier => $go->{source}->{src}->{tag}->{id}, -name => $go->{source}->{anchor}, -definition => $go->{source}->{anchor}, -comment => $go->{source}->{'post-text'}, -version => $go->{version} ); $term->add_reference($refan); $term->namespace($category); return $term; } sub _backcomp_ll { my $ann = shift; my $newann = Bio::Annotation::Collection->new(); #$newann->{_annotation}->{ALIAS_SYMBOL}=$ann->{_annotation}->{ALIAS_SYMBOL}; # $newann->{_annotation}->{CHR}=$ann->{_annotation}->{chromosome}; # $newann->{_annotation}->{MAP}=$ann->{_annotation}->{cyto}; foreach my $tagmap ( keys %{ $ann->{_typemap}->{_type} } ) { next if ( grep( /$tagmap/, @main::egonly ) ); $newann->{_annotation}->{$tagmap} = $ann->{_annotation}->{$tagmap}; } #$newann->{_annotation}->{Reference}=$ann->{_annotation}->{Reference}; #$newann->{_annotation}->{generif}=$ann->{_annotation}->{generif}; #$newann->{_annotation}->{comment}=$ann->{_annotation}->{comment}; # $newann->{_annotation}->{OFFICIAL_GENE_NAME}=$ann->{_annotation}->{'Official Full Name'}; $newann->{_typemap}->{_type} = $ann->{_typemap}->{_type}; foreach my $ftype ( keys %main::eg_to_ll ) { my $newkey = $main::eg_to_ll{$ftype}; $newann->{_annotation}->{$newkey} = $ann->{_annotation}->{$ftype}; $newann->{_typemap}->{_type}->{$newkey} = 'Bio::Annotation::SimpleValue'; delete $newann->{_typemap}->{_type}->{$ftype}; $newann->{_annotation}->{$newkey}->[0]->{tagname} = $newkey; } foreach my $dblink ( @{ $newann->{_annotation}->{dblink} } ) { next unless ( $dblink->{_url} ); my $simann = Bio::Annotation::SimpleValue->new( -value => $dblink->{_url}, -tagname => 'URL' ); $newann->add_Annotation($simann); } # my $simann=Bio::Annotation::SimpleValue->new(-value=>$seq->desc,-tagname=>'comment'); # $newann->add_Annotation($simann); return $newann; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/excel.pm�����������������������������������������������������������������000444��000766��000024�� 20306�13155576320� 16663� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::excel # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp at gmx.net> # # # (c) Hilmar Lapp, hlapp at gmx.net, 2005. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2005. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::excel - sequence input/output stream from a MSExcel-formatted table =head1 SYNOPSIS #It is probably best not to use this object directly, but #rather go through the SeqIO handler system. Go: $stream = Bio::SeqIO->new(-file => $filename, -format => 'excel'); while ( my $seq = $stream->next_seq() ) { # do something with $seq } =head1 DESCRIPTION This class transforms records in a MS Excel workbook file into Bio::Seq objects. It is derived from the table format module and merely defines additional properties and overrides the way to get data from the file and advance to the next record. The module permits specifying which columns hold which type of annotation. The semantics of certain attributes, if present, are pre-defined, e.g., accession number and sequence. Additional attributes may be added to the annotation bundle. See L<Bio::SeqIO::table> for a complete list of parameters and capabilities. You may also specify the worksheet from which to obtain the data, and after finishing one worksheet you may change the name to keep reading from another worksheet (in the same file). This module depends on Spreadsheet::ParseExcel to parse the underlying Excel file. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::excel; use strict; use Bio::SeqIO; use Spreadsheet::ParseExcel; #use Spreadsheet::ParseExcel::Workbook; use base qw(Bio::SeqIO::table); =head2 new Title : new Usage : $stream = Bio::SeqIO->new(-file => $filename, -format => 'excel') Function: Returns a new seqstream Returns : A Bio::SeqIO stream for a MS Excel format Args : Supports the same named parameters as Bio::SeqIO::table, except -delim, which obviously does not apply to a binary format. In addition, the following parameters are supported. -worksheet the name of the worksheet holding the table; if unspecified the first worksheet will be used =cut sub _initialize { my($self,@args) = @_; # chained initialization $self->SUPER::_initialize(@args); # our own parameters my ($worksheet) = $self->_rearrange([qw(WORKSHEET)], @args); # store options and apply defaults $self->worksheet($worksheet || 0); } =head2 worksheet Title : worksheet Usage : $obj->worksheet($newval) Function: Get/set the name of the worksheet holding the table. The worksheet name may also be a numeric index. You may change the value during parsing at any time in order to start reading from a different worksheet (in the same file). Example : Returns : value of worksheet (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub worksheet{ my $self = shift; if (@_) { my $sheetname = shift; # on set we reset the parser here in order to allow reading # from multiple worksheets in a row $self->_worksheet(undef) if defined($sheetname); return $self->{'worksheet'} = $sheetname; } return $self->{'worksheet'}; } =head2 close Title : close Usage : Function: Close and/or release the resources used by this parser instance. We override this here in order to free up the worksheet and other related objects. Example : Returns : Args : =cut sub close{ my $self = shift; $self->_worksheet(undef); # make sure we chain to the inherited method $self->SUPER::close(@_); } =head1 Internal methods All methods with a leading underscore are not meant to be part of the 'official' API. They are for use by this module only, consider them private unless you are a developer trying to modify this module. =cut =head2 _worksheet Title : _worksheet Usage : $obj->_worksheet($newval) Function: Get/set the worksheet object to be used for accessing cells. Example : Returns : value of _worksheet (a Spreadsheet::ParseExcel::Worksheet object) Args : on set, new value (a Spreadsheet::ParseExcel::Worksheet object or undef, optional) =cut sub _worksheet{ my $self = shift; return $self->{'_worksheet'} = shift if @_; return $self->{'_worksheet'}; } =head2 _next_record Title : _next_record Usage : Function: Navigates the underlying file to the next record. We override this here in order to adapt navigation to data in an Excel worksheet. Example : Returns : TRUE if the navigation was successful and FALSE otherwise. Unsuccessful navigation will usually be treated as an end-of-file condition. Args : =cut sub _next_record{ my $self = shift; my $wsheet = $self->_worksheet(); if (! defined($wsheet)) { # worksheet hasn't been initialized yet, do so now my $wbook = Spreadsheet::ParseExcel::Workbook->Parse($self->_fh); $wsheet = $wbook->Worksheet($self->worksheet); # store the result $self->_worksheet($wsheet); # re-initialize the current row $self->{'_row'} = -1; } # we need a valid worksheet to continue return unless defined($wsheet); # check whether we are at or beyond the last defined row my ($minrow, $maxrow) = $wsheet->RowRange(); return if $self->{'_row'} >= $maxrow; # we don't check for empty rows here as in order to do that we'd # have to know in which column to look # so, just advance to the next row $self->{'_row'}++; # done return 1; } =head2 _get_row_values Title : _get_row_values Usage : Function: Get the values for the current line (or row) as an array in the order of columns. We override this here in order to adapt access to column values to data contained in an Excel worksheet. Example : Returns : An array of column values for the current row. Args : =cut sub _get_row_values{ my $self = shift; # obtain the range of columns - we use all that are defined my $wsheet = $self->_worksheet(); my ($colmin,$colmax) = $wsheet->ColRange(); # build the array of columns for the current row my @cols = (); my $row = $self->{'_row'}; for (my $i = $colmin; $i <= $colmax; $i++) { my $cell = $wsheet->Cell($row, $i); push(@cols, defined($cell) ? $cell->Value : $cell); } # done return @cols; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/exp.pm�������������������������������������������������������������������000444��000766��000024�� 6724�13155576320� 16347� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::exp # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Aaron Mackey <amackey@virginia.edu> # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::exp - exp trace sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from exp trace files. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Aaron Mackey Email: amackey@virginia.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::exp; use vars qw(@ISA $READ_AVAIL); use strict; use Bio::SeqIO; use Bio::Seq::SeqFactory; push @ISA, qw( Bio::SeqIO ); sub BEGIN { eval { require Bio::SeqIO::staden::read; }; if ($@) { $READ_AVAIL = 0; } else { push @ISA, "Bio::SeqIO::staden::read"; $READ_AVAIL = 1; } } sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::Quality')); } unless ($READ_AVAIL) { Bio::Root::Root->throw( -class => 'Bio::Root::SystemException', -text => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!" ); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq::Quality object Args : NONE =cut sub next_seq { my ($self) = @_; my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'exp'); # create the seq object $seq = $self->sequence_factory->create(-seq => $seq, -id => $id, -primary_id => $id, -desc => $desc, -alphabet => 'DNA', -qual => $qual ); return $seq; } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object =cut sub write_seq { my ($self,@seq) = @_; my $fh = $self->_fh; foreach my $seq (@seq) { $self->write_trace($fh, $seq, 'exp'); } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; ��������������������������������������������BioPerl-1.007002/Bio/SeqIO/fasta.pm�����������������������������������������������������������������000444��000766��000024�� 24364�13155576320� 16671� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::fasta # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # and Lincoln Stein <lstein@cshl.org> # # Copyright Ewan Birney & Lincoln Stein # # You may distribute this module under the same terms as perl itself # _history # October 18, 1999 Largely rewritten by Lincoln Stein # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::fasta - fasta sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from fasta flat file databases. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Ewan Birney & Lincoln Stein Email: birney@ebi.ac.uk lstein@cshl.org =head1 CONTRIBUTORS Jason Stajich, jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::fasta; use strict; use warnings; use Bio::Seq::SeqFastaSpeedFactory; use parent qw(Bio::SeqIO); sub _initialize { my ($self, @args) = @_; $self->SUPER::_initialize(@args); ## Initialize fasta specific parameters ## There are some problems with _rearrange. If there's no value for one of ## the parameters, it will return an empty value (not undef). This means we ## can't just merge two hashes since the empty values would override the ## defaults anyway. my (%defs) = ( "width" => 60, "block" => "", # default is same as width "preferred_id_type" => "display", ); foreach my $param (keys %defs) { $self->$param( $self->_rearrange([$param], @args) || $defs{$param}); } unless ( defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFastaSpeedFactory->new()); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object, or nothing if no more available Args : NONE =cut sub next_seq { my( $self ) = @_; my $seq; my $alphabet; local $/ = "\n>"; return unless my $entry = $self->_readline; # Replacing chomp for s///, since chomp is not working in some cases $entry =~ s/\n$//; $entry =~ s/\r$//; if ($entry =~ m/\A\s*\Z/s) { # very first one return unless $entry = $self->_readline; chomp($entry); } # this just checks the initial input; beyond that, due to setting $/ above, # the > is part of the record separator and is removed $self->throw("The sequence does not appear to be FASTA format ". "(lacks a descriptor line '>')") if $. == 1 && $entry !~ /^>/; $entry =~ s/^>//; my ($top,$sequence) = split(/\n/,$entry,2); defined $sequence && $sequence =~ s/>//g; #my ($top,$sequence) = $entry =~ /^>?(.+?)\n+([^>]*)/s # or $self->throw("Can't parse fasta entry"); my ($id,$fulldesc); if( $top =~ /^\s*(\S+)\s*(.*)/ ) { ($id,$fulldesc) = ($1,$2); } if (defined $id && $id eq '') {$id=$fulldesc;} # FIX incase no space # between > and name \AE defined $sequence && $sequence =~ tr/ \t\n\r//d; # Remove whitespace # for empty sequences we need to know the mol.type $alphabet = $self->alphabet(); if(defined $sequence && length($sequence) == 0) { if(! defined($alphabet)) { # let's default to dna $alphabet = "dna"; } }# else { # we don't need it really, so disable # we want to keep this if SeqIO alphabet was set by user # not sure if this could break something #$alphabet = undef; #} $seq = $self->sequence_factory->create( -seq => $sequence, -id => $id, # Ewan's note - I don't think this healthy # but obviously to taste. #-primary_id => $id, -desc => $fulldesc, -alphabet => $alphabet, -direct => 1, ); # if there wasn't one before, set the guessed type #unless ( defined $alphabet ) { # don't assume that all our seqs are the same as the first one found #$self->alphabet($seq->alphabet()); #} return $seq; } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: Writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Array of 1 or more Bio::PrimarySeqI objects =cut sub write_seq { my ($self,@seq) = @_; my $width = $self->width; my $block = $self->block; ## take a reference for single string (the sequence) and add the whitespace local *format_str = sub { my $str = $_[0]; my @lines = unpack ("(A$width)*", $$str); if ($block >= $width) { $$str = join ("\n", @lines)."\n"; } else { $$str = ""; $$str .= join (" ", unpack ("(A$block)*", $_)) . "\n" foreach (@lines); } }; foreach my $seq (@seq) { $self->throw("Did not provide a valid Bio::PrimarySeqI object") unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI'); # Allow for different ids my $top; my $id_type = $self->preferred_id_type; if( $id_type =~ /^acc/i ) { $top = $seq->accession_number(); if( $id_type =~ /vers/i ) { $top .= "." . $seq->version(); } } elsif($id_type =~ /^displ/i ) { $self->warn("No whitespace allowed in FASTA ID [". $seq->display_id. "]") if defined $seq->display_id && $seq->display_id =~ /\s/; $top = $seq->display_id(); $top = '' unless defined $top; $self->warn("No whitespace allowed in FASTA ID [". $top. "]") if defined $top && $top =~ /\s/; } elsif($id_type =~ /^pri/i ) { $top = $seq->primary_id(); } if ($seq->can('desc') and my $desc = $seq->desc()) { $desc =~ s/\n//g; $top .= " $desc"; } if( $seq->isa('Bio::Seq::LargeSeqI') ) { $self->_print(">$top\n"); # for large seqs, don't call seq(), it defeats the # purpose of the largeseq functionality. instead get # chunks of the seq, $width at a time my $buff_max = 2000; my $buff_size = int($buff_max/$width)*$width; #< buffer is even multiple of widths my $seq_length = $seq->length; my $num_chunks = int($seq_length/$buff_size+1); for( my $c = 0; $c < $num_chunks; $c++ ) { my $buff_end = $buff_size*($c+1); $buff_end = $seq_length if $buff_end > $seq_length; my $buff = $seq->subseq($buff_size*$c+1,$buff_end); if($buff) { format_str (\$buff); $self->_print($buff); } else { $self->_print("\n"); } } } else { my $str = $seq->seq; if(defined $str && length($str) > 0) { format_str (\$str); } else { $str = "\n"; } $self->_print (">",$top,"\n",$str) or return; } } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 width Title : width Usage : $obj->width($newval) Function: Get/Set the line width for FASTA output (not counting whitespace). Returns : value of width Args : newvalue (optional) =cut sub width { my ($self,$value) = @_; if (defined $value) { $self->{'width'} = $value; } return $self->{'width'}; } =head2 block Title : block Usage : $obj->block($newval) Function: Get/Set the length of each block for FASTA output. Sequence blocks will be split with a space. Configuring block, to a value of 10 for example, allows one to easily identify a position in a sequence by eye. Default : same value used for width. Returns : value of block Args : newvalue (optional) =cut sub block { my ($self,$value) = @_; if (defined $value) { $self->{'block'} = $value; } return $self->{'block'} || $self->width; } =head2 preferred_id_type Title : preferred_id_type Usage : $obj->preferred_id_type('accession') Function: Get/Set the preferred type of identifier to use in the ">ID" position for FASTA output. Returns : string, one of values defined in @Bio::SeqIO::fasta::SEQ_ID_TYPES. Default : display Args : string when setting. This must be one of values defined in @Bio::SeqIO::fasta::SEQ_ID_TYPES. Allowable values: accession, accession.version, display, primary Throws : fatal exception if the supplied id type is not in @SEQ_ID_TYPES. =cut our @SEQ_ID_TYPES = qw(accession accession.version display primary); sub preferred_id_type { my ($self,$type) = @_; if (defined $type) { if( ! grep lc($type) eq $_, @SEQ_ID_TYPES) { $self->throw(-class=>'Bio::Root::BadParameter', -text=>"Invalid ID type \"$type\". Must be one of: @SEQ_ID_TYPES"); } $self->{'_seq_id_type'} = lc($type); } $self->{'_seq_id_type'}; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/fastq.pm�����������������������������������������������������������������000444��000766��000024�� 43435�13155576320� 16711� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# POD at __END__, let the code begin... package Bio::SeqIO::fastq; use strict; use Bio::Seq::SeqFactory; use base qw(Bio::SeqIO); our %variant = ( sanger => { 'offset' => 33, 'qual_start' => 0, 'qual_end' => 93 }, solexa => { 'offset' => 64, 'qual_start' => -5, 'qual_end' => 62 }, illumina => { 'offset' => 64, 'qual_start' => 0, 'qual_end' => 62 }, ); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); my ($variant, $validate, $header) = $self->_rearrange([qw(VARIANT VALIDATE QUALITY_HEADER)], @args); $variant ||= 'sanger'; $self->variant($variant); $self->_init_tables($variant); $validate = defined $validate ? $validate : 1; $self->validate($validate); $header && $self->quality_header($header); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new( -verbose => $self->verbose(), -type => 'Bio::Seq::Quality') ); } } sub next_seq { my( $self ) = @_; while (defined(my $data = $self->next_dataset)) { # Are FASTQ sequences w/o any sequence valid? Removing for now # -cjfields 6.22.09 my $seq = $self->sequence_factory->create(%$data); return $seq; } return; } # pure perl version sub next_dataset { my $self = shift; local $/ = "\n"; my $data; my $mode = '-seq'; # speed this up by directly accessing the filehandle and in-lining the # _readline stuff vs. making the repeated method calls. Tradeoff is speed # over repeated code. # we can probably normalize line endings using PerlIO::eol or # Encode::Newlines my $fh = $self->_fh; my $line = $self->{lastline} || <$fh>; FASTQ: while (defined $line) { $line =~ s/\015\012/\012/; $line =~ tr/\015/\n/; if ($mode eq '-seq' && $line =~ m{^@([^\n]+)$}xmso) { $data->{-descriptor} = $1; my ($id,$fulldesc); if ($data->{-descriptor} =~ /^\s*(\S+)\s*(.*)/) { ($id,$fulldesc) = ($1, $2); } else { $self->throw("Can't parse fastq header"); } $data->{-id} = $id; $data->{-desc} = $fulldesc; $data->{-namespace} = $self->variant; } elsif ($mode eq '-seq' && $line =~ m{^\+([^\n]*)}xmso) { my $desc = $1; $self->throw("No description line parsed") unless $data->{-descriptor}; if ($desc && $data->{-descriptor} ne $desc) { $self->throw("Quality descriptor [$desc] doesn't match seq ". "descriptor ".$data->{-descriptor}.", line: $." ); } $mode = '-raw_quality'; } else { if ($mode eq '-raw_quality' && defined($data->{-raw_quality}) && (length($data->{-raw_quality}) >= length($data->{-seq}))) { $self->{lastline} = $line; last FASTQ } chomp $line; if ($line =~ /^$/) { delete $self->{lastline}; last FASTQ; } $data->{$mode} .= $line } $line = <$fh>; if (!defined $line) { delete $self->{lastline}; last FASTQ; } } return unless $data; if (!$data->{-seq} || !defined($data->{-raw_quality})) { $self->throw("Missing sequence and/or quality data; line: $."); } # simple quality control tests if (length $data->{-seq} != length $data->{-raw_quality}) { $self->throw("Quality string [".$data->{-raw_quality}."] of length [". length($data->{-raw_quality})."]\ndoesn't match length of sequence ". $data->{-seq}."\n[".length($data->{-seq})."], line: $."); } $data->{-qual} = [map { if ($self->{_validate_qual} && !exists($self->{chr2qual}->{$_})) { $self->throw("Unknown symbol with ASCII value ".ord($_)." outside ". "of quality range") # TODO: fallback? } $self->variant eq 'solexa' ? $self->{sol2phred}->{$self->{chr2qual}->{$_}}: $self->{chr2qual}->{$_}; } unpack("A1" x length($data->{-raw_quality}), $data->{-raw_quality})]; return $data; } # This should be creating fastq output only. Bio::SeqIO::fasta and # Bio::SeqIO::qual should be used for that output sub write_seq { my ($self,@seq) = @_; my $var = $self->variant; foreach my $seq (@seq) { unless ($seq->isa("Bio::Seq::Quality")){ $self->warn("You can't write FASTQ without supplying a Bio::Seq::". "Quality object! ".ref($seq)."\n"); next; } my $str = $seq->seq || ''; my @qual = @{$seq->qual}; # this should be the origin of the sequence (illumina, solexa, sanger) my $ns= $seq->namespace; my $top = $seq->display_id(); if (my $desc = $seq->desc()) { $desc =~ s/\n//g; $top .= " $desc"; } my $qual = ''; my $qual_map = ($ns eq 'solexa' && $var eq 'solexa') ? $self->{phred_fp2chr} : ($var eq 'solexa') ? $self->{phred_int2chr} : $self->{qual2chr}; my %bad_qual; for my $q (@qual) { $q = sprintf("%.0f", $q) if ($var ne 'solexa' && $ns eq 'solexa'); if (exists $qual_map->{$q}) { $qual .= $qual_map->{$q}; next; } else { # fuzzy mapping, for edited qual scores my $qr = sprintf("%.0f",$q); my $bounds = sprintf("%.1f-%.1f",$qr-0.5, $qr+0.5); if (exists $self->{fuzzy_qual2chr}->{$bounds}) { $qual .= $self->{fuzzy_qual2chr}->{$bounds}; next; } else { my $rep = ($q <= $self->{qual_start}) ? $qual_map->{$self->{qual_start}} : $qual_map->{$self->{qual_end}}; $qual .= $rep; $bad_qual{$q}++; } } } if ($self->{_validate_qual} && %bad_qual) { $self->warn("Data loss for $var: following values not found\n". join(',',sort {$a <=> $b} keys %bad_qual)) } $self->_print("\@",$top,"\n",$str,"\n") or return; $self->_print("+",($self->{_quality_header} ? $top : ''),"\n",$qual,"\n") or return; } return 1; } sub write_fastq { my ($self,@seq) = @_; return $self->write_seq(@seq); } sub write_fasta { my ($self,@seq) = @_; if (!exists($self->{fasta_proxy})) { $self->{fasta_proxy} = Bio::SeqIO->new(-format => 'fasta', -fh => $self->_fh); } return $self->{fasta_proxy}->write_seq(@seq); } sub write_qual { my ($self,@seq) = @_; if (!exists($self->{qual_proxy})) { $self->{qual_proxy} = Bio::SeqIO->new(-format => 'qual', -fh => $self->_fh); } return $self->{qual_proxy}->write_seq(@seq); } # variant() method inherited from Bio::Root::IO sub _init_tables { my ($self, $var) = @_; # cache encode/decode values for quicker accession ($self->{qual_start}, $self->{qual_end}, $self->{qual_offset}) = @{ $variant{$var} }{qw(qual_start qual_end offset)}; if ($var eq 'solexa') { for my $q ($self->{qual_start} .. $self->{qual_end}) { my $char = chr($q + $self->{qual_offset}); $self->{chr2qual}->{$char} = $q; $self->{qual2chr}->{$q} = $char; my $s2p = 10 * log(1 + 10 ** ($q / 10.0)) / log(10); # solexa <=> solexa mapping speedup (retain floating pt precision) $self->{phred_fp2chr}->{$s2p} = $char; $self->{sol2phred}->{$q} = $s2p; # this is for mapping values fuzzily (fallback) $self->{fuzzy_qual2chr}->{sprintf("%.1f-%.1f",$q - 0.5, $q + 0.5)} = $char; next if $q < 0; # skip loop; PHRED scores greater than 0 my $p2s = sprintf("%.0f",($q <= 1) ? -5 : 10 * log(-1 + 10 ** ($q / 10.0)) / log(10)); # sanger/illumina PHRED <=> Solexa char mapping speedup $self->{phred_int2chr}->{$q} = chr($p2s + $self->{qual_offset}); } } else { for my $c ($self->{qual_start}..$self->{qual_end}) { # PHRED mapping my $char = chr($c + $self->{qual_offset}); $self->{chr2qual}->{$char} = $c; $self->{qual2chr}->{$c} = $char; # this is for mapping values not found with above $self->{fuzzy_qual2chr}->{sprintf("%.1f-%.1f",$c - 0.5, $c + 0.5)} = $char; } } } sub validate { my ($self, $val) = @_; if (defined $val) { $self->{_validate_qual} = $val; } return $self->{_validate_qual}; } sub quality_header{ my ($self, $val) = @_; if (defined $val) { $self->{_quality_header} = $val; } return $self->{_quality_header} || 0; } 1; __END__ # BioPerl module for Bio::SeqIO::fastq # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for Chris Fields # # Completely refactored from the original FASTQ parser # by Tony Cox <avc@sanger.ac.uk> # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # # _history # # October 29, 2001 incept data (Tony Cox) # June 20, 2009 updates for Illumina variant FASTQ formats for Solexa and later # Aug 26, 2009 fixed bugs and added tests for fastq.t # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::fastq - fastq sequence input/output stream =head1 SYNOPSIS ################## pertains to FASTQ parsing only ################## # grabs the FASTQ parser, specifies the Illumina variant my $in = Bio::SeqIO->new(-format => 'fastq-illumina', -file => 'mydata.fq'); # simple 'fastq' format defaults to 'sanger' variant my $out = Bio::SeqIO->new(-format => 'fastq', -file => '>mydata.fq'); # $seq is a Bio::Seq::Quality object while (my $seq = $in->next_seq) { $out->write_seq($seq); # convert Illumina 1.3 to Sanger format } # for 4x faster parsing, one can do something like this for raw data use Bio::Seq::Quality; # $data is a hash reference containing all arguments to be passed to # the Bio::Seq::Quality constructor while (my $data = $in->next_dataset) { # process $data, such as trim, etc my $seq = Bio::Seq::Quality->new(%$data); # for now, write_seq only accepts Bio::Seq::Quality, but may be modified # to allow raw hash references for speed $out->write_seq($data); } =head1 DESCRIPTION This object can transform Bio::Seq and Bio::Seq::Quality objects to and from FASTQ flat file databases. FASTQ is a file format used frequently at the Sanger Centre and in next-gen sequencing to bundle a FASTA sequence and its quality data. A typical FASTQ entry takes the form: @HCDPQ1D0501 GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT..... +HCDPQ1D0501 !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65..... where: @ = descriptor, followed by one or more sequence lines + = optional descriptor (if present, must match first one), followed by one or more qual lines When writing FASTQ output the redundant descriptor following the '+' is by default left off to save disk space. If needed, one can set the quality_header() flag in order for this to be printed. =head2 FASTQ and Bio::Seq::Quality mapping FASTQ files have sequence and quality data on single line or multiple lines, and the quality values are single-byte encoded. Data are mapped very simply to Bio::Seq::Quality instances: Data Bio::Seq::Quality method ------------------------------------------------------------------------ first non-whitespace chars in descriptor id^ descriptor line desc^ sequence lines seq quality qual* FASTQ variant namespace ^ first nonwhitespace chars are id(), everything else after (to end of line) is in desc() * Converted to PHRED quality scores where applicable ('solexa') =head2 FASTQ variants This parser supports all variants of FASTQ, including Illumina v 1.0 and 1.3: variant note ----------------------------------------------------------- sanger original solexa Solexa, Inc. (2004), aka Illumina 1.0 illumina Illumina 1.3 The variant can be specified by passing by either passing the additional -variant parameter to the constructor: my $in = Bio::SeqIO->new(-format => 'fastq', -variant => 'solexa', -file => 'mysol.fq'); or by passing the format and variant together (Bio::SeqIO will now handle this and convert it accordingly to the proper argument): my $in = Bio::SeqIO->new(-format => 'fastq-solexa', -file => 'mysol.fq'); Variants can be converted back and forth from one another; however, due to the difference in scaling for solexa quality reads, converting from 'illumina' or 'sanger' FASTQ to solexa is not recommended. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Chris Fields (taken over from Tony Cox) Email: cjfields at bioperl dot org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =head1 Bio::SeqIO interface methods =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function : returns the next sequence in the stream Returns : Bio::Seq::Quality object Args : NONE Status : Stable =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function : writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq::Quality Note : This now conforms to SeqIO spec (module output is same format as next_seq) Status : Stable =head2 variant Title : variant Usage : $format = $obj->variant(); Function: Get and set method for the quality sequence variant. This is important for indicating the encoding/decoding to be used for quality data. Current values accepted are: 'sanger' (original FASTQ) ASCII encoding from 33-126, PHRED quality score from 0 to 93 'solexa' (aka illumina1.0) ASCII encoding from 59-104, SOLEXA quality score from -5 to 40 'illumina' (aka illumina1.3) ASCII encoding from 64-104, PHRED quality score from 0 to 40 (Derived from the MAQ website): For 'solexa', scores are converted to PHRED qual scores using: $Q = 10 * log(1 + 10 ** (ord($sq) - 64) / 10.0)) / log(10) Returns : string Args : new value, string =head1 Plugin-specific methods =head2 next_dataset Title : next_dataset Usage : $obj->next_dataset Function : returns a hash reference containing the parsed data Returns : hash reference Args : none Status : Stable =head2 write_fastq Title : write_fastq Usage : $stream->write_fastq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq::Quality object Status : Deprecated (delegates to write_seq) =head2 write_fasta Title : write_fasta Usage : $stream->write_fasta(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object Note : This method does not currently delegate to Bio::SeqIO::fasta (maybe it should?). Not sure whether we should keep this as a convenience method. Status : Unstable =head2 write_qual Title : write_qual Usage : $stream->write_qual(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq::Quality object Note : This method does not currently delegate to Bio::SeqIO::qual (maybe it should?). Not sure whether we should keep this as a convenience method. Status : Unstable =head2 validate Title : validate Usage : $obj->validate(0) Function : flag for format/qual range validation - default is 1, validate Returns : Bool (0/1) Args : Bool (0/1) Status : Stable (may be moved to interface) =head2 quality_header Title : quality_header Usage : $obj->quality_header Function : flag for printing quality header - default is 0, no header Returns : Bool (0/1) Args : Bool (0/1) Status : Unstable (name may change dep. on feedback) =cut �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/flybase_chadoxml.pm������������������������������������������������������000444��000766��000024�� 10766�13155576320� 21100� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::flybase_chadoxml # # Peili Zhang <peili@morgan.harvard.edu> # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::flybase_chadoxml - FlyBase variant of chadoxml with sequence output stream =head1 SYNOPSIS It is probably best not to use this object directly, but rather go through the SeqIO handler system: $writer = Bio::SeqIO->new(-file => ">chado.xml", -format => 'flybase_chadoxml'); # assume you already have Sequence or SeqFeature objects $writer->write_seq($seq_obj); #after writing all seqs $writer->close_chadoxml(); =head1 DESCRIPTION This is a simple subclass of L<Bio::SeqIO::chadoxml>; please see its documentation for details. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Peili Zhang Email peili@morgan.harvard.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqIO::flybase_chadoxml; use strict; use base 'Bio::SeqIO::chadoxml'; sub _initialize { my($self,%args) = @_; $self->SUPER::_initialize(%args); #default for standard chado is polypeptide $Bio::SeqIO::chadoxml::feattype_args2so{'CDS'} = 'protein'; $Bio::SeqIO::chadoxml::cv_name{'sequence'} = 'SO'; $Bio::SeqIO::chadoxml::cv_name{'relationship'} = 'relationship type'; $Bio::SeqIO::chadoxml::cv_name{'feature_property'} = 'property type'; return; } =head2 return_ftype_hash Title : return_ftype_hash Usage : $obj->return_ftype_hash() Function : A simple hash where returning it has be factored out of the main code to allow subclasses to override it. Returns : A hash that indicates what the name of the SO term is and what the name of the Sequence Ontology is in the cv table. Args : The string that represents the SO term. Status : =cut sub return_ftype_hash { my $self = shift; my $ftype = shift; my %ftype_hash = ( "name" => $ftype, "cv_id" => {"name" => $Bio::SeqIO::chadoxml::cv_name{'sequence'} }); return %ftype_hash; } =head2 return_reltypename Title : return_reltypename Usage : $obj->return_reltypename Function : Return the appropriate relationship type name depending on the feature type (typically part_of, but derives_from for polypeptide). Returns : A relationship type name. Args : A SO type name. Status : =cut sub return_reltypename { my $self = shift; my $sftype = shift; my $reltypename; if ($sftype eq 'protein' || $sftype eq 'polypeptide') { $reltypename = 'producedby'; } else { $reltypename = 'partof'; } return $reltypename; } =head2 write_seq Title : write_seq Usage : $stream->write_seq(-seq=>$seq, -seq_so_type=>$seqSOtype, -src_feature=>$srcfeature, -src_feat_type=>$srcfeattype, -nounflatten=>0 or 1, -is_analysis=>'true' or 'false', -data_source=>$datasource) Function: writes the $seq object (must be seq) into chadoxml. Returns : 1 for success and 0 for error Args : A Bio::Seq object $seq, optional $seqSOtype, $srcfeature, $srcfeattype, $nounflatten, $is_analysis and $data_source. Overrides Bio::SeqIO::chadoxml's write_seq method just to add an internal close_chadoxml (mimics original use by FlyBase). =cut sub write_seq { my ($self, @argv) = @_; $self->SUPER::write_seq(@argv); $self->close_chadoxml; return 1; } 1; ����������BioPerl-1.007002/Bio/SeqIO/game.pm������������������������������������������������������������������000444��000766��000024�� 10556�13155576320� 16502� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::game # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Sheldon McKay <mckays@cshl.edu> # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::game -- a class for parsing and writing game-XML =head1 SYNOPSIS This module is not used directly, use SeqIO. use Bio::SeqIO; my $in = Bio::SeqIO->new ( -file => 'file.xml', -format => 'game', -verbose => 1 ); my $seq = $in->next_seq; =head1 DESCRIPTION Bio::SeqIO::game will parse game XML (version 1.2) or write game XML from a Bio::SeqI implementing object. The XML is readable by the genome annotation editor 'Apollo' (www.gmod.org). It is not backwards compatible with the previous version of game XML. The XML format currently used by Apollo contains a single 'main' annotated sequence, so we will only get a single annotated sequence in the stream when parsing a game-XML record. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sheldon McKay Email mckays@cshl.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqIO::game; use Bio::SeqIO::game::gameHandler; use Bio::SeqIO::game::gameWriter; use base qw(Bio::SeqIO); sub _initialize { my ($self, @args) = @_; $self->SUPER::_initialize(@args); } =head2 next_seq Title : next_seq Usage : my $seq = $seqio->next_seq; Function: get the main sequence object Returns : a Bio::Seq::RichSeq object Args : none =cut sub next_seq { my $self = shift; my $seq_l = $self->_getseqs; my $annseq = shift @{$seq_l}; my $seq = $annseq->[0]; my $feats = $annseq->[1]; for ( @{$feats} ) { $seq->add_SeqFeature( $_ ); } return $seq; } =head2 write_seq Title : write_seq Usage : $seqio->write_seq($seq) Function: writes a sequence object as game XML Returns : nothing Args : a Bio::SeqI compliant object =cut sub write_seq { my ($self, $seq) = @_; my $writer = Bio::SeqIO::game::gameWriter->new($seq); my $xml = $writer->write_to_game; $self->_print($xml); } =head2 _getseqs Title : _getseqs Usage : $self->_getseqs Function: An internal method to invoke the PerlSAX XML handler and get the sequence objects Returns : an reference to an array with sequence object and annotations Args : none =cut sub _getseqs { my $self = shift; if ( defined $self->{seq_l} ) { return $self->{seq_l}; } else { my $fh = $self->_fh; my $text = join '', <$fh>; $text || $self->throw("Input file is empty or does not exist"); my $source = $text =~ /type>(source|origin|\bregion\b)<\/type/gm ? 1 : 0; my $handler = Bio::SeqIO::game::gameHandler->new; $handler->{has_source} = $source if $source; $handler->{verbose} = 1 if $self->verbose; my $parser = XML::Parser::PerlSAX->new( Handler => $handler ); my $game = $parser->parse( $text ); $self->{seq_l} = $game->load; } } =head2 _hide_dna Title : _hide_dna Usage : $seqio->_hide_dna Function: Hide the DNA for really huge sequences Returns : nothing Args : none =cut sub _hide_dna { my $self = shift; my $annseqs = $self->_getseqs; for ( @{$annseqs} ) { my $seq = $_->[0]; $seq->seq(''); } return 0; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/gbdriver.pm��������������������������������������������������������������000444��000766��000024�� 37337�13155576320� 17403� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::gbdriver # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Bioperl project bioperl-l(at)bioperl.org # # Copyright Chris Fields and contributors see AUTHORS section # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::gbdriver - GenBank handler-based push parser =head1 SYNOPSIS #It is probably best not to use this object directly, but #rather go through the SeqIO handler: $stream = Bio::SeqIO->new(-file => $filename, -format => 'gbdriver'); while ( my $seq = $stream->next_seq() ) { # do something with $seq } =head1 DESCRIPTION This object can transform Bio::Seq objects to and from GenBank flat file databases. The key difference between this parser and the tried-and-true Bio::SeqIO::genbank parser is this version separates the parsing and data manipulation into a 'driver' method (next_seq) and separate object handlers which deal with the data passed to it. =head2 The Driver The main purpose of the driver routine, in this case next_seq(), is to carve out the data into meaningful chunks which are passed along to relevant handlers (see below). Each chunk of data in the has a NAME tag attached to it, similar to that for XML parsing. This designates the type of data passed (annotation type or seqfeature) and the handler to be called for processing the data. For GenBank annotations, the data is divided up and passed along to handlers according to whether the data is tagged with a field name (i.e. LOCUS) and whether the field name represents 'primary' annotation (in this case, is present at the beginning of the line, such as REFERENCE). If the field is primary, it is assigned to the NAME tag. Field names which aren't primary (have at least 2 spaces before the name, like ORGANISM) are appended to the preceding primary field name as additional tags. For feature table data each new feature name signals the beginning of a new chunk of data. 'FEATURES' is attached to NAME, the feature key ('CDS', 'gene', etc) is attached as the PRIMARY_ID, and the location is assigned to it's own tag name (LOCATION). Feature qualifiers are added as additional keys, with multiple keys included in an array. Once a particular event occurs (new primary tag, sequence, end of record), the data is passed along to be processed by a handler or (if no handler is defined) tossed away. Internally, the hash ref for a representative annotation (here a REFERENCE) looks like this: $VAR1 = { 'JOURNAL' => 'Unpublished (2003)', 'TITLE' => 'The DNA sequence of Homo sapiens', 'NAME' => 'REFERENCE', 'REFERENCE' => '1 (bases 1 to 10001)', 'AUTHORS' => 'International Human Genome Sequencing Consortium.' }; and a SeqFeature as this: $VAR1 = { 'db_xref' => [ 'GeneID:127086', 'InterimID:127086' ], 'LOCATION' => 'complement(3024..6641)', 'NAME' => 'FEATURES', 'FEATURE_KEY' => 'gene', 'gene' => 'LOC127086', 'note' => 'Derived by automated computational analysis using gene prediction method: GNOMON.' }; Note that any driver implementation would suffice as long as it fulfilled the requirements above. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Bioperl Project bioperl-l at bioperl.org Original author Elia Stupka, elia -at- tigem.it =head1 CONTRIBUTORS Ewan Birney birney at ebi.ac.uk Jason Stajich jason at bioperl.org Chris Mungall cjm at fruitfly.bdgp.berkeley.edu Lincoln Stein lstein at cshl.org Heikki Lehvaslaiho, heikki at ebi.ac.uk Hilmar Lapp, hlapp at gmx.net Donald G. Jackson, donald.jackson at bms.com James Wasmuth, james.wasmuth at ed.ac.uk Brian Osborne, bosborne at alum.mit.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # POD is at the end of the module # Let the code begin... package Bio::SeqIO::gbdriver; use strict; use warnings; use Data::Dumper; use Bio::SeqIO::Handler::GenericRichSeqHandler; use Bio::Seq::SeqFactory; use base qw(Bio::SeqIO); # map all annotation keys to consistent INSDC-based tags for all handlers my %FTQUAL_NO_QUOTE = map {$_ => 1} qw( anticodon citation codon codon_start cons_splice direction evidence label mod_base number rpt_type rpt_unit transl_except transl_table usedin ); # 1) change this to indicate what should be secondary, not primary, which allows # unknown or new stuff to be passed to handler automatically; current behavior # appends unknowns to previous data, which isn't good since it's subtly passing # by important data # 2) add mapping details about how to separate data using specific delimiters # Features are the only ones postprocessed for now # Uncomment relevant code in next_seq and add keys as needed... my %POSTPROCESS_DATA = map {$_ => 1} qw (FEATURES); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); my $handler = $self->_rearrange([qw(HANDLER)],@args); # hash for functions for decoding keys. $handler ? $self->seqhandler($handler) : $self->seqhandler(Bio::SeqIO::Handler::GenericRichSeqHandler->new( -format => 'genbank', -verbose => $self->verbose, -builder => $self->sequence_builder )); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : =cut # at this point there is minimal sequence validation, # but the parser seems to hold up nicely so far... sub next_seq { my $self = shift; local($/) = "\n"; my ($ann, $data, $annkey); my $endrec = my $seenfeat = 0; my $seqdata; my $seenlocus; my $hobj = $self->seqhandler; my $handlers = $self->seqhandler->handler_methods; #$self->debug(Dumper($handlers)); PARSER: while (defined(my $line = $self->_readline)) { next if $line =~ m{^\s*$}; # have to catch this at the top of the loop, then exit SEQ loop on // # The reason? The regex match for ann/feat keys also matches some lines # in the sequence; no easy way around it since some feature keys may # start with a number as well if ($ann && $ann eq 'ORIGIN') { SEQ: while (defined($line)) { last SEQ if index($line,'//') == 0; $seqdata->{DATA} .= uc $line; $line = $self->_readline; } $seqdata->{DATA} =~ tr{0-9 \n}{}d; } $endrec = 1 if (index($line,'//')==0); if ($line =~ m{^(\s{0,5})(\w+)\s+(.*)$}ox || $endrec) { ($ann, $data) = ($2, $3); unless ($seenlocus) { $self->throw("No LOCUS found. Not GenBank in my book!") if ($ann ne 'LOCUS'); $seenlocus = 1; } # use the spacer to determine the annotation type my $len = length($1 || ''); $annkey = ($len == 0 || $len > 4) ? 'DATA' : $ann; # Push off the previously cached data to the handler # whenever a new primary annotation or seqfeature is found # Note use of $endrec for catching end of record if (($annkey eq 'DATA') && $seqdata) { chomp $seqdata->{DATA}; # postprocessing for some data if ($seqdata->{NAME} eq 'FEATURES') { $self->_process_features($seqdata) } # using handlers directly, slightly faster #my $method = (exists $handlers->{ $seqdata->{NAME} }) ? # ($handlers->{$seqdata->{NAME}}) : # (exists $handlers->{'_DEFAULT_'}) ? # ($handlers->{'_DEFAULT_'}) : # undef; #($method) ? ($hobj->$method($seqdata) ) : # $self->debug("No handler defined for ",$seqdata->{NAME},"\n"); # using handler methods in the Handler object, more centralized #$self->debug(Dumper($seqdata)); $hobj->data_handler($seqdata); # bail here on // last PARSER if $endrec; # reset for next round $seqdata = undef; } $seqdata->{NAME} = ($len == 0) ? $ann : # primary ann ($len > 4 ) ? 'FEATURES': # sf feature key $seqdata->{NAME}; # all rest are sec. ann if ($seqdata->{NAME} eq 'FEATURES') { $seqdata->{FEATURE_KEY} = $ann; } # throw back to top if seq is found to avoid regex next PARSER if $ann eq 'ORIGIN'; } else { ($data = $line) =~ s{^\s+}{}; chomp $data; } my $delim = ($seqdata && $seqdata->{NAME} eq 'FEATURES') ? "\n" : ' '; $seqdata->{$annkey} .= ($seqdata->{$annkey}) ? $delim.$data : $data; } return $hobj->build_sequence; } sub next_chunk { my $self = shift; local($/) = "\n"; my ($ann, $data, $annkey); my $endrec = my $seenfeat = 0; my $seqdata; my $seenlocus; my $hobj = $self->seqhandler; PARSER: while (defined(my $line = $self->_readline)) { next if $line =~ m{^\s*$}; # have to catch this at the top of the loop, then exit SEQ loop on // # The reason? The regex match for ann/feat keys also matches some lines # in the sequence; no easy way around it since some feature keys may # start with a number as well if ($ann && $ann eq 'ORIGIN') { SEQ: while (defined($line)) { last SEQ if index($line,'//') == 0; $seqdata->{DATA} .= uc $line; $line = $self->_readline; } $seqdata->{DATA} =~ tr{0-9 \n}{}d; } $endrec = 1 if (index($line,'//')==0); if ($line =~ m{^(\s{0,5})(\w+)\s+(.*)$}ox || $endrec) { ($ann, $data) = ($2, $3); unless ($seenlocus) { $self->throw("No LOCUS found. Not GenBank in my book!") if ($ann ne 'LOCUS'); $seenlocus = 1; } # use the spacer to determine the annotation type my $len = length($1 || ''); $annkey = ($len == 0 || $len > 4) ? 'DATA' : $ann; # Push off the previously cached data to the handler # whenever a new primary annotation or seqfeature is found # Note use of $endrec for catching end of record if (($annkey eq 'DATA') && $seqdata) { chomp $seqdata->{DATA}; # postprocessing for some data if ($seqdata->{NAME} eq 'FEATURES') { $self->_process_features($seqdata) } # using handler methods in the Handler object, more centralized $hobj->data_handler($seqdata); # bail here on // last PARSER if $endrec; # reset for next round $seqdata = undef; } $seqdata->{NAME} = ($len == 0) ? $ann : # primary ann ($len > 4 ) ? 'FEATURES': # sf feature key $seqdata->{NAME}; # all rest are sec. ann if ($seqdata->{NAME} eq 'FEATURES') { $seqdata->{FEATURE_KEY} = $ann; } # throw back to top if seq is found to avoid regex next PARSER if $ann eq 'ORIGIN'; } else { ($data = $line) =~ s{^\s+}{}; chomp $data; } my $delim = ($seqdata && $seqdata->{NAME} eq 'FEATURES') ? "\n" : ' '; $seqdata->{$annkey} .= ($seqdata->{$annkey}) ? $delim.$data : $data; } } =head2 write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object (must be seq) to the stream Returns : 1 for success and 0 for error Args : array of 1 to n Bio::SeqI objects =cut sub write_seq { shift->throw("Use Bio::SeqIO::genbank for output"); # maybe make a Writer class as well???? } =head2 seqhandler Title : seqhandler Usage : $stream->seqhandler($handler) Function: Get/Set the Bio::Seq::HandlerBaseI object Returns : Bio::Seq::HandlerBaseI Args : Bio::Seq::HandlerBaseI =cut sub seqhandler { my ($self, $handler) = @_; if ($handler) { $self->throw("Not a Bio::HandlerBaseI") unless ref($handler) && $handler->isa("Bio::HandlerBaseI"); $self->{'_seqhandler'} = $handler; } return $self->{'_seqhandler'}; } #=head2 _process_features # # Title : _process_features # Usage : $self->_process_features($seqdata) # Function: Process feature data chunk into usable bits # Returns : # Args : data chunk # #=cut sub _process_features { my ($self, $seqdata) = @_; my @ftlines = split m{\n}, $seqdata->{DATA}; delete $seqdata->{DATA}; # don't deal with balancing quotes for now; just get rid of them... # Should we worry about checking whether these are balanced # for round-tripping tests? map { s{"}{}g } @ftlines; # all sfs start with the location... my $qual = 'LOCATION'; my $ct = 0; for my $qualdata (@ftlines) { if ($qualdata =~ m{^/([^=]+)=?(.+)?}) { ($qual, $qualdata) = ($1, $2); $qualdata ||= ''; # for those qualifiers that have no data, like 'pseudo' $ct = (exists $seqdata->{$qual}) ? ((ref($seqdata->{$qual})) ? scalar(@{ $seqdata->{$qual} }) : 1) : 0 ; } my $delim = ($qual eq 'translation' || exists $FTQUAL_NO_QUOTE{$qual}) ? '' : ' '; # if more than one, turn into an array ref and append if ($ct == 0) { (exists $seqdata->{$qual}) ? ($seqdata->{$qual}.= $delim.$qualdata || '') : ($seqdata->{$qual} .= $qualdata || ''); } else { if (!ref($seqdata->{$qual})) { $seqdata->{$qual} = [$seqdata->{$qual}]; } (exists $seqdata->{$qual}->[$ct]) ? (($seqdata->{$qual}->[$ct]) .= $delim.$qualdata) : (($seqdata->{$qual}->[$ct]) .= $qualdata); } } } 1; __END__ �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/gbxml.pm�����������������������������������������������������������������000444��000766��000024�� 31566�13155576320� 16706� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# $Id: gbxml.pm # # BioPerl module for Bio::SeqIO::gbxml # # Cared for by Ryan Golhar # NOTE: This module is implemented on an as needed basis. As features # are needed, they are implemented. Its very bare-bones. # # Based off http://www.insdc.org/page.php?page=documents&sid=105a8b52b69db9c36c82a2e0d923ca69 # # I tried to follow the genbank module to keep things as consistent as possible # Right now, I'm not respecting the want_slot parameters. This will need to be added. =head1 NAME Bio::SeqIO::gbxml - GenBank sequence input/output stream using SAX =head1 SYNOPSIS It is probably best not to use this object directly, but rather go through the SeqIO handler system. To read a GenBank XML file: $stream = Bio::SeqIO->new( -file => $filename, -format => 'gbxml'); while ( my $bioSeqObj = $stream->next_seq() ) { # do something with $bioSeqObj } To write a Seq object to the current file handle in GenBank XML format: $stream->write_seq( -seq => $seqObj); If instead you would like a XML::DOM object containing the GBXML, use: my $newXmlObject = $stream->to_bsml( -seq => $seqObj); =head1 DEPENDENCIES In addition to parts of the Bio:: hierarchy, this module uses: XML::SAX =head1 DESCRIPTION This object can transform Bio::Seq objects to and from GenBank XML flatfiles. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ryan Golhar Email golharam-at-umdnj-dot-edu =cut package Bio::SeqIO::gbxml; use vars qw($Default_Source); use strict; use Bio::SeqIO::FTHelper; use Bio::SeqFeature::Generic; use Bio::Species; use XML::SAX; use Bio::Seq::SeqFactory; use Bio::Annotation::Collection; use Bio::Annotation::Comment; use Bio::Annotation::Reference; use Bio::Annotation::DBLink; use base qw(Bio::SeqIO XML::SAX::Base); $Default_Source = 'GBXML'; sub _initialize { my ($self) = shift; $self->SUPER::_initialize(@_); $self->{'_parser'} = XML::SAX::ParserFactory->parser('Handler' => $self); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } return; } =head1 METHODS =cut =head2 next_seq Title : next_seq Usage : my $bioSeqObj = $stream->next_seq Function: Retrieves the next sequence from a SeqIO::gbxml stream. Returns : A reference to a Bio::Seq::RichSeq object Args : =cut sub next_seq { my $self = shift; if( @{$self->{'_seendata'}->{'_seqs'} || []} || eof($self->_fh)) { return shift @{$self->{'_seendata'}->{'_seqs'}}; } $self->{'_parser'}->parse_file($self->_fh); return shift @{$self->{'_seendata'}->{'_seqs'}}; } # XML::SAX::Base methods sub start_document { my ($self,$doc) = @_; $self->{'_seendata'} = {'_seqs' => [] #, # '_authors' => [], # '_feats' => [] }; $self->SUPER::start_document($doc); } sub end_document { my ($self,$doc) = @_; $self->SUPER::end_document($doc); } sub start_element { my ($self,$ele) = @_; my $name = uc($ele->{'LocalName'}); # my $attr = $ele->{'Attributes'}; # my $seqid = defined $self->{'_seendata'}->{'_seqs'}->[-1] ? # $self->{'_seendata'}->{'_seqs'}->[-1]->display_id : undef; # for my $k ( keys %$attr ) { # $attr->{uc $k} = $attr->{$k}; # delete $attr->{$k}; # } if( $name eq 'GBSET' ) { } elsif( $name eq 'GBSEQ' ) { # Initialize, we are starting a new sequence. push @{$self->{'_seendata'}->{'_seqs'}}, $self->sequence_factory->create(); } elsif( $name eq 'GBFEATURE' ) { my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1]; my $fthelper = Bio::SeqIO::FTHelper->new(); $fthelper->verbose($self->verbose()); push @{$self->{'_seendata'}->{'_feats'}}, $fthelper; } # } elsif( $name eq 'FEATURE-TABLES' ) { # } elsif( $name eq 'database-xref' ) { # my ($db,$id) = split(/:/,$content); # $curseq->annotation->add_Annotation('dblink', # Bio::Annotation::DBLink->new # ( -database => $db, # -primary_id=> $id)); # } elsif( $name eq 'INTERVAL-LOC' ) { # my $curfeat = $self->{'_seendata'}->{'_feats'}->[-1]; # my ($start,$end,$strand) = # map { $attr->{'{}'.$_}->{'Value'} } qw(STARTPOS # ENDPOS # COMPLEMENT); # $curfeat->start($start); # $curfeat->end($end); # $curfeat->strand(-1) if($strand); # } elsif( $name eq 'REFERENCE' ) { # push @{$self->{'_seendata'}->{'_annot'}}, # Bio::Annotation::Reference->new(); # } $self->{'_characters'} = ''; push @{$self->{'_state'}}, $name; $self->SUPER::start_element($ele); } sub end_element { my ($self,$ele) = @_; pop @{$self->{'_state'}}; my $name = uc $ele->{'LocalName'}; my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1]; my $curfeat = $self->{'_seendata'}->{'_feats'}->[-1]; if ($name eq 'GBSEQ_LOCUS') { $curseq->display_id($self->{'_characters'}); } elsif ($name eq 'GBSEQ_LENGTH' ) { $curseq->length($self->{'_characters'}); } elsif ($name eq 'GBSEQ_MOLTYPE' ) { if ($self->{'_characters'} =~ /mRNA|dna/) { $curseq->alphabet('dna'); } else { $curseq->alphabet('protein'); } $curseq->molecule($self->{'_characters'}); } elsif ($name eq 'GBSEQ_TOPOLOGY' ) { $curseq->is_circular(($self->{'_characters'} =~ /^linear$/i) ? 0 : 1); } elsif ($name eq 'GBSEQ_DIVISION' ) { $curseq->division($self->{'_characters'}); } elsif ($name =~ m/GBSEQ_UPDATE-DATE|GBSEQ_CREATE-DATE/ ) { my $date = $self->{'_characters'}; # This code was taken from genbank.pm if($date =~ s/\s*((\d{1,2})-(\w{3})-(\d{2,4})).*/$1/) { if( length($date) < 11 ) { # improperly formatted date # But we'll be nice and fix it for them my ($d,$m,$y) = ($2,$3,$4); $d = "0$d" if( length($d) == 1 ); # guess the century here if( length($y) == 2 ) { # arbitrarily guess that '60' means 1960 $y = ($y > 60) ? "19$y" : "20$y"; $self->warn("Date was malformed, guessing the century for $date to be $y\n"); } $date = [join('-',$d,$m,$y)]; } $curseq->add_date($date); } } elsif ($name eq 'GBSEQ_DEFINITION' ) { $curseq->description($self->{'_characters'}); } elsif ($name eq 'GBSEQ_PRIMARY-ACCESSION' ) { $curseq->accession_number($self->{'_characters'}); } elsif ($name eq 'GBSEQ_ACCESSION-VERSION' ) { # also taken from genbank.pm $self->{'_characters'} =~ m/^\w+\.(\d+)/; if ($1) { $curseq->version($1); $curseq->seq_version($1); } } elsif ($name eq 'GBSEQID' ) { if ($self->{'_characters'} =~ m/gi\|(\d+)/) { $curseq->primary_id($1); } } elsif ($name eq 'GBSEQ_SOURCE') { $self->{'_taxa'}->{'_common'} = $self->{'_characters'}; } elsif ($name eq 'GBSEQ_ORGANISM' ) { # taken from genbank.pm my @organell_names = ("chloroplast", "mitochondr"); my @spflds = split(' ', $self->{'_characters'}); $_ = $self->{'_characters'}; if (grep { $_ =~ /^$spflds[0]/i; } @organell_names) { $self->{'_taxa'}->{'_organelle'} = shift(@spflds); } $self->{'_taxa'}->{'_genus'} = shift(@spflds); $self->{'_taxa'}->{'_species'} = shift(@spflds) if (@spflds); $self->{'_taxa'}->{'_sub_species'} = shift(@spflds) if (@spflds); $self->{'_taxa'}->{'_ns_name'} = $self->{'_characters'}; } elsif ($name eq 'GBSEQ_TAXONOMY' ) { # taken from genbank.pm $_ = $self->{'_characters'}; my @class; push (@class, map { s/^\s+//; s/\s+$//; $_; } split /[;\.]+/, $_); next unless $self->{'_taxa'}->{'_genus'} and $self->{'_taxa'}->{'_genus'} !~ /^(unknown|None)$/oi; if ($class[0] eq 'Viruses') { push( @class, $self->{'_taxa'}->{'_ns_name'} ); } elsif ($class[$#class] eq $self->{'_taxa'}->{'_genus'}) { push( @class, $self->{'_taxa'}->{'_species'} ); } else { push( @class, $self->{'_taxa'}->{'_genus'}, $self->{'_taxa'}->{'_species'} ); } @class = reverse @class; my $make = Bio::Species->new(); $make->classification( \@class, "FORCE"); $make->common_name($self->{'_taxa'}->{'_common'}) if $self->{'_taxa'}->{'_common'}; unless ($class[-1] eq 'Viruses') { $make->sub_species( $self->{'_taxa'}->{'_sub_species'} ) if $self->{'_taxa'}->{'_sub_species'}; } $make->organelle( $self->{'_taxa'}->{'_organelle'} ) if $self->{'_taxa'}->{'_organelle'}; $curseq->species($make); delete $self->{'_taxa'}; } elsif( $name eq 'GBSEQ_COMMENT' ) { $curseq->annotation->add_Annotation('comment', Bio::Annotation::Comment->new(-text => $self->{'_characters'} )) if ($self->{'_characters'}); } elsif ($name eq 'GBFEATURE_KEY' ) { $curfeat->key($self->{'_characters'}); } elsif ($name eq 'GBFEATURE_LOCATION' ) { $curfeat->loc($self->{'_characters'}); } elsif ($name eq 'GBQUALIFIER_NAME' ) { $self->{'_feature'}->{"_qualifer_name"} = $self->{'_characters'}; } elsif ($name eq 'GBQUALIFIER_VALUE' ) { my $qualifier = $self->{'_feature'}->{"_qualifer_name"}; delete $self->{'_feature'}->{"_qualifer_name"}; $curfeat->field->{$qualifier} ||= []; push(@{$curfeat->field->{$qualifier}}, $self->{'_characters'}); } elsif ($name eq 'GBSEQ_SEQUENCE' ) { $curseq->seq($self->{'_characters'}); } elsif( $name eq 'GBFEATURE' ) { shift @{$self->{'_seendata'}->{'_feats'}}; # copied from genbank.pm if (!defined($curfeat)) { $self->warn("Unexpected error in feature table for ".$curseq->display_id." Skipping feature, attempting to recover"); } else { my $feat = $curfeat->_generic_seqfeature($self->location_factory(), $curseq->display_id); if ($curseq->species && ($feat->primary_tag eq 'source') && $feat->has_tag('db_xref') && (! $curseq->species->ncbi_taxid())) { foreach my $tagval ($feat->get_tag_values('db_xref')) { if (index($tagval,"taxon:") == 0) { $curseq->species->ncbi_taxid(substr($tagval,6)); } } } $curseq->add_SeqFeature($feat); } } # if( $name eq 'REFERENCE') { # my $ref = pop @{$self->{'_seendata'}->{'_annot'}}; # $curseq->annotation->add_Annotation('reference',$ref); # } $self->SUPER::end_element($ele); } # Characters should be buffered because we may not always get the entire string. Once the entire string is read # process it in end_element. sub characters { my ($self,$data) = @_; if( ! @{$self->{'_state'}} ) { $self->warn("Calling characters with no previous start_element call. Ignoring data"); } else { # my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1]; # my $curfeat = $self->{'_seendata'}->{'_feats'}->[-1]; # my $curannot = $self->{'_seendata'}->{'_annot'}->[-1]; # my $name = $self->{'_state'}->[-1]; # if ($name eq 'GBSEQ_LOCUS' ) { $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBSEQ_LENGTH' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBSEQ_MOLTYPE' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBSEQ_TOPOLOGY' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBSEQ_DIVISION' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name =~ m/GBSEQ_UPDATE-DATE|GBSEQ_CREATE-DATE/ ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBSEQ_DEFINITION' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBSEQ_PRIMARY-ACCESSION' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBSEQ_ACCESSION-VERSION' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBSEQID' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBSEQ_SOURCE') { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBSEQ_ORGANISM' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBSEQ_TAXONOMY' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBSEQ_COMMENT' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBFEATURE_KEY' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBFEATURE_LOCATION' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBQUALIFIER_NAME' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBQUALIFIER_VALUE' ) { # $self->{'_characters'} .= $data->{'Data'}; # } elsif ($name eq 'GBINTERVAL_FROM' ) { # $self->{'_feature'}->{'_interval_from'} = $data->{'Data'}; # } elsif ($name eq 'GBINTERVAL_TO' ) { # $self->{'_feature'}->{'_interval_to'} = $data->{'Data'}; # } elsif ($name eq 'GBINTERVAL_ACCESSION' ) { # $self->{'_feature'}->{'_interval_accession'} = $data->{'Data'}; # } elsif ($name eq 'GBSEQ_SEQUENCE' ) { # $self->{'_characters'} .= $data->{'Data'}; # } } $self->SUPER::characters($data); } 1; ������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/gcg.pm�������������������������������������������������������������������000444��000766��000024�� 17407�13155576320� 16333� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::gcg # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # and Lincoln Stein <lstein@cshl.org> # # Copyright Ewan Birney & Lincoln Stein # # You may distribute this module under the same terms as perl itself # # _history # October 18, 1999 Largely rewritten by Lincoln Stein # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::gcg - GCG sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from GCG flat file databases. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Ewan Birney & Lincoln Stein Email: E<lt>birney@ebi.ac.ukE<gt> E<lt>lstein@cshl.orgE<gt> =head1 CONTRIBUTORS Jason Stajich, jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::gcg; use strict; use Bio::Seq::SeqFactory; use base qw(Bio::SeqIO); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : =cut sub next_seq { my ($self,@args) = @_; my($id,$type,$desc,$line,$chksum,$sequence,$date,$len); while( defined($_ = $self->_readline()) ) { ## Get the descriptive info (anything before the line with '..') unless( /\.\.$/ ) { $desc.= $_; } ## Pull ID, Checksum & Type from the line containing '..' /\.\.$/ && do { $line = $_; chomp; if(/Check\:\s(\d+)\s/) { $chksum = $1; } if(/Type:\s(\w)\s/) { $type = $1; } if(/(\S+)\s+Length/) { $id = $1; } if(/Length:\s+(\d+)\s+(\S.+\S)\s+Type/ ) { $len = $1; $date = $2;} last; } } return if ( !defined $_); chomp($desc); # remove last "\n" while( defined($_ = $self->_readline()) ) { ## This is where we grab the sequence info. if( /\.\.$/ ) { $self->throw("Looks like start of another sequence. See documentation. "); } next if($_ eq "\n"); ## skip whitespace lines in formatted seq s/[\d\s\t]//g; ## remove anything that is not alphabet char: preserve anything that is not explicitly specified for removal (Stefan Kirov) # $_ = uc($_); ## uppercase sequence: NO. Keep the case. HL $sequence .= $_; } ##If we parsed out a checksum, we might as well test it if(defined $chksum) { unless(_validate_checksum(uc($sequence),$chksum)) { $self->throw("Checksum failure on parsed sequence."); } } ## Remove whitespace from identifier because the constructor ## will throw a warning otherwise... if(defined $id) { $id =~ s/\s+//g;} ## Turn our parsed "Type: N" or "Type: P" (if found) into the appropriate ## keyword that the constructor expects... if(defined $type) { if($type eq "N") { $type = "dna"; } if($type eq "P") { $type = "prot"; } } return $self->sequence_factory->create(-seq => $sequence, -id => $id, -desc => $desc, -type => $type, -dates => [ $date ] ); } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the formatted $seq object into the stream Returns : 1 for success and 0 for error Args : array of Bio::PrimarySeqI object =cut sub write_seq { my ($self,@seq) = @_; for my $seq (@seq) { $self->throw("Did not provide a valid Bio::PrimarySeqI object") unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI'); $self->warn("No whitespace allowed in GCG ID [". $seq->display_id. "]") if $seq->display_id =~ /\s/; my $str = $seq->seq; my $comment = $seq->desc || ''; my $id = $seq->id; my $type = ( $seq->alphabet() =~ /[dr]na/i ) ? 'N' : 'P'; my $timestamp; if( $seq->can('get_dates') ) { ($timestamp) = $seq->get_dates; } else { $timestamp = localtime(time); } my($sum,$offset,$len,$i,$j,$cnt,@out); $len = length($str); ## Set the offset if we have any non-standard numbering going on $offset=1; # checksum $sum = $self->GCG_checksum($seq); #Output the sequence header info push(@out,"$comment\n"); push(@out,"$id Length: $len $timestamp Type: $type Check: $sum ..\n\n"); #Format the sequence $i = $#out + 1; for($j = 0 ; $j < $len ; ) { if( $j % 50 == 0) { $out[$i] = sprintf("%8d ",($j+$offset)); #numbering } $out[$i] .= sprintf("%s",substr($str,$j,10)); $j += 10; if( $j < $len && $j % 50 != 0 ) { $out[$i] .= " "; }elsif($j % 50 == 0 ) { $out[$i++] .= "\n\n"; } } local($^W) = 0; if($j % 50 != 0 ) { $out[$i] .= "\n"; } $out[$i] .= "\n"; return unless $self->_print(@out); } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 GCG_checksum Title : GCG_checksum Usage : $cksum = $gcgio->GCG_checksum($seq); Function : returns a gcg checksum for the sequence specified This method can also be called as a class method. Example : Returns : a GCG checksum string Argument : a Bio::PrimarySeqI implementing object =cut sub GCG_checksum { my ($self,$seqobj) = @_; my $index = 0; my $checksum = 0; my $char; my $seq = $seqobj->seq(); $seq =~ tr/a-z/A-Z/; foreach $char ( split(/[\.\-]*/, $seq)) { $index++; $checksum += ($index * (unpack("c",$char) || 0) ); if( $index == 57 ) { $index = 0; } } return ($checksum % 10000); } =head2 _validate_checksum Title : _validate_checksum Usage : n/a - internal method Function: if parsed gcg sequence contains a checksum field : we compare it to a value computed here on the parsed : sequence. A checksum mismatch would indicate some : type of parsing failure occurred. : Returns : 1 for success, 0 for failure Args : string containing parsed seq, value of parsed checksum =cut sub _validate_checksum { my($seq,$parsed_sum) = @_; my($i,$len,$computed_sum,$cnt); $len = length($seq); #Generate the GCG Checksum value for($i=0; $i<$len ;$i++) { $cnt++; $computed_sum += $cnt * ord(substr($seq,$i,1)); ($cnt == 57) && ($cnt=0); } $computed_sum %= 10000; ## Compare and decide if success or failure if($parsed_sum == $computed_sum) { return 1; } else { return 0; } } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/genbank.pm���������������������������������������������������������������000444��000766��000024�� 214022�13155576320� 17210� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::genbank # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Bioperl project bioperl-l(at)bioperl.org # # Copyright Elia Stupka and contributors see AUTHORS section # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::genbank - GenBank sequence input/output stream =head1 SYNOPSIS It is probably best not to use this object directly, but rather go through the SeqIO handler: $stream = Bio::SeqIO->new(-file => $filename, -format => 'GenBank'); while ( my $seq = $stream->next_seq ) { # do something with $seq } =head1 DESCRIPTION This object can transform Bio::Seq objects to and from GenBank flat file databases. There is some flexibility here about how to write GenBank output that is not fully documented. =head2 Optional functions =over 3 =item _show_dna() (output only) shows the dna or not =item _post_sort() (output only) provides a sorting func which is applied to the FTHelpers before printing =item _id_generation_func() This is function which is called as print "ID ", $func($seq), "\n"; To generate the ID line. If it is not there, it generates a sensible ID line using a number of tools. If you want to output annotations in Genbank format they need to be stored in a Bio::Annotation::Collection object which is accessible through the Bio::SeqI interface method L<annotation()|annotation>. The following are the names of the keys which are pulled from a L<Bio::Annotation::Collection> object: reference - Should contain Bio::Annotation::Reference objects comment - Should contain Bio::Annotation::Comment objects dblink - Should contain a Bio::Annotation::DBLink object segment - Should contain a Bio::Annotation::SimpleValue object origin - Should contain a Bio::Annotation::SimpleValue object wgs - Should contain a Bio::Annotation::SimpleValue object =back =head1 Where does the data go? Data parsed in Bio::SeqIO::genbank is stored in a variety of data fields in the sequence object that is returned. Here is a partial list of fields. Items listed as RichSeq or Seq or PrimarySeq and then NAME() tell you the top level object which defines a function called NAME() which stores this information. Items listed as Annotation 'NAME' tell you the data is stored the associated Bio::AnnotationCollectionI object which is associated with Bio::Seq objects. If it is explicitly requested that no annotations should be stored when parsing a record of course they will not be available when you try and get them. If you are having this problem look at the type of SeqBuilder that is being used to construct your sequence object. Comments Annotation 'comment' References Annotation 'reference' Segment Annotation 'segment' Origin Annotation 'origin' Dbsource Annotation 'dblink' Accessions PrimarySeq accession_number() Secondary accessions RichSeq get_secondary_accessions() GI number PrimarySeq primary_id() LOCUS PrimarySeq display_id() Keywords RichSeq get_keywords() Dates RichSeq get_dates() Molecule RichSeq molecule() Seq Version RichSeq seq_version() PID RichSeq pid() Division RichSeq division() Features Seq get_SeqFeatures() Alphabet PrimarySeq alphabet() Definition PrimarySeq description() or desc() Version PrimarySeq version() Sequence PrimarySeq seq() There is more information in the Feature-Annotation HOWTO about each field and how it is mapped to the Sequence object L<http://bioperl.org/howtos/Features_and_Annotations_HOWTO.html>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Bioperl Project bioperl-l at bioperl.org Original author Elia Stupka, elia -at- tigem.it =head1 CONTRIBUTORS Ewan Birney birney at ebi.ac.uk Jason Stajich jason at bioperl.org Chris Mungall cjm at fruitfly.bdgp.berkeley.edu Lincoln Stein lstein at cshl.org Heikki Lehvaslaiho, heikki at ebi.ac.uk Hilmar Lapp, hlapp at gmx.net Donald G. Jackson, donald.jackson at bms.com James Wasmuth, james.wasmuth at ed.ac.uk Brian Osborne, bosborne at alum.mit.edu Chris Fields, cjfields at bioperl dot org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::genbank; use strict; use Bio::SeqIO::FTHelper; use Bio::SeqFeature::Generic; use Bio::Species; use Bio::Seq::SeqFactory; use Bio::Annotation::Collection; use Bio::Annotation::Comment; use Bio::Annotation::Reference; use Bio::Annotation::DBLink; use base qw(Bio::SeqIO); # Note that a qualifier that exceeds one line (i.e. a long label) will # automatically be quoted regardless: our $FTQUAL_LINE_LENGTH = 60; our %FTQUAL_NO_QUOTE = map {$_ => 1} qw( anticodon citation codon codon_start cons_splice direction evidence label mod_base number rpt_type rpt_unit transl_except transl_table usedin ); our %DBSOURCE = map {$_ => 1} qw( EchoBASE IntAct SWISS-2DPAGE ECO2DBASE ECOGENE TIGRFAMs TIGR GO InterPro Pfam PROSITE SGD GermOnline HSSP PhosSite Ensembl RGD AGD ArrayExpress KEGG H-InvDB HGNC LinkHub PANTHER PRINTS SMART SMR MGI MIM RZPD-ProtExp ProDom MEROPS TRANSFAC Reactome UniGene GlycoSuiteDB PIRSF HSC-2DPAGE PHCI-2DPAGE PMMA-2DPAGE Siena-2DPAGE Rat-heart-2DPAGE Aarhus/Ghent-2DPAGE Biocyc MetaCyc Biocyc:Metacyc GenomeReviews FlyBase TMHOBP COMPLUYEAST-2DPAGE OGP DictyBase HAMAP PhotoList Gramene WormBase WormPep Genew ZFIN PeroxiBase MaizeDB TAIR DrugBank REBASE HPA swissprot GenBank GenPept REFSEQ embl PDB UniProtKB DIP PeptideAtlas PRIDE CYGD HOGENOME Gene3D Project); our %VALID_MOLTYPE = map {$_ => 1} qw(NA DNA RNA tRNA rRNA cDNA cRNA ms-DNA mRNA uRNA ss-RNA ss-DNA snRNA snoRNA PRT); our %VALID_ALPHABET = ( 'bp' => 'dna', 'aa' => 'protein', 'rc' => '' # rc = release candidate; file has no sequences ); sub _initialize { my($self, @args) = @_; $self->SUPER::_initialize(@args); # hash for functions for decoding keys. $self->{'_func_ftunit_hash'} = {}; $self->_show_dna(1); # sets this to one by default. People can change it if ( not defined $self->sequence_factory ) { $self->sequence_factory (Bio::Seq::SeqFactory->new(-verbose => $self->verbose, -type => 'Bio::Seq::RichSeq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : =cut sub next_seq { my ($self, @args) = @_; my %args = @args; my $builder = $self->sequence_builder; my $seq; my %params; RECORDSTART: while (1) { my $buffer; my ( @acc, @features ); my ( $display_id, $annotation ); my $species; # initialize; we may come here because of starting over @features = (); $annotation = undef; @acc = (); $species = undef; %params = ( -verbose => $self->verbose ); # reset hash local ($/) = "\n"; while ( defined( $buffer = $self->_readline ) ) { last if index( $buffer, 'LOCUS ' ) == 0; } return unless defined $buffer; # end of file $buffer =~ /^LOCUS\s+(\S.*)$/o or $self->throw( "GenBank stream with bad LOCUS line. " . "Not GenBank in my book. Got '$buffer'"); my @tokens = split( ' ', $1 ); # this is important to have the id for display in e.g. FTHelper, # otherwise you won't know which entry caused an error $display_id = shift @tokens; $params{'-display_id'} = $display_id; # may still be useful if we don't want the seq my $seqlength = shift @tokens; if ( exists $VALID_ALPHABET{$seqlength} ) { # moved one token too far. No locus name? $self->warn( "Bad LOCUS name? Changing [$params{'-display_id'}] " . "to 'unknown' and length to '$display_id'" ); $params{'-display_id'} = 'unknown'; $params{'-length'} = $display_id; # add token back... unshift @tokens, $seqlength; } else { $params{'-length'} = $seqlength; } # the alphabet of the entry # shouldn't assign alphabet unless one # is specifically designated (such as for rc files) my $alphabet = lc( shift @tokens ); $params{'-alphabet'} = ( exists $VALID_ALPHABET{$alphabet} ) ? $VALID_ALPHABET{$alphabet} : $self->warn("Unknown alphabet: $alphabet"); # for aa there is usually no 'molecule' (mRNA etc) if ( $params{'-alphabet'} eq 'protein' ) { $params{'-molecule'} = 'PRT'; } else { $params{'-molecule'} = shift(@tokens); } # take care of lower case issues if ( $params{'-molecule'} eq 'dna' or $params{'-molecule'} eq 'rna' ) { $params{'-molecule'} = uc $params{'-molecule'}; } $self->debug( "Unrecognized molecule type: " . $params{'-molecule'} ) if not exists( $VALID_MOLTYPE{ $params{'-molecule'} } ); my $circ = shift @tokens; if ( $circ eq 'circular' ) { $params{'-is_circular'} = 1; $params{'-division'} = shift @tokens; } else { # 'linear' or 'circular' may actually be omitted altogether $params{'-division'} = ( CORE::length($circ) == 3 ) ? $circ : shift @tokens; } my $date = join( ' ', @tokens ); # we lump together the rest # this is per request bug #1513 # we can handle: # 9-10-2003 # 9-10-03 # 09-10-2003 # 09-10-03 if ( $date =~ s/\s*((\d{1,2})-(\w{3})-(\d{2,4})).*/$1/ ) { if ( length($date) < 11 ) { # improperly formatted date # But we'll be nice and fix it for them my ( $d, $m, $y ) = ( $2, $3, $4 ); if ( length($d) == 1 ) { $d = "0$d"; } # guess the century here if ( length($y) == 2 ) { if ( $y > 60 ) { # arbitrarily guess that '60' means 1960 $y = "19$y"; } else { $y = "20$y"; } $self->warn( "Date was malformed, guessing the " . "century for $date to be $y\n" ); } $params{'-dates'} = [ join( '-', $d, $m, $y ) ]; } else { $params{'-dates'} = [$date]; } } # set them all at once $builder->add_slot_value(%params); %params = (); # parse the rest if desired, otherwise start over if ( not $builder->want_object ) { $builder->make_object; next RECORDSTART; } # set up annotation depending on what the builder wants if ( $builder->want_slot('annotation') ) { $annotation = Bio::Annotation::Collection->new; } $buffer = $self->_readline; while ( defined( my $line = $buffer ) ) { # Description line(s) if ($line =~ /^DEFINITION\s+(\S.*\S)/) { my @desc = ($1); while ( defined( $line = $self->_readline ) ) { if ($line =~ /^\s+(.*)/) { push( @desc, $1 ); next; } last; } $builder->add_slot_value( -desc => join( ' ', @desc ) ); # we'll continue right here because DEFINITION # always comes at the top of the entry $buffer = $line; } # accession number (there can be multiple accessions) if ($line =~ /^ACCESSION\s+(\S.*\S)/) { push( @acc, split( /\s+/, $1 ) ); while ( defined( $line = $self->_readline ) ) { if ($line =~ /^\s+(.*)/) { push( @acc, split( /\s+/, $1 ) ); next; } last; } $buffer = $line; next; } # PID elsif ($line =~ /^PID\s+(\S+)/) { $params{'-pid'} = $1; } # Version number elsif ($line =~ /^VERSION\s+(\S.+)$/) { my ( $acc, $gi ) = split( ' ', $1 ); if ( $acc =~ /^\w+\.(\d+)/ ) { $params{'-version'} = $1; $params{'-seq_version'} = $1; } if ( $gi && ( index( $gi, "GI:" ) == 0 ) ) { $params{'-primary_id'} = substr( $gi, 3 ); } } # Keywords elsif ($line =~ /^KEYWORDS\s+(\S.*)/) { my @kw = split( /\s*\;\s*/, $1 ); while ( defined( $line = $self->_readline ) ) { chomp $line; if ($line =~ /^\s+(.*)/) { push( @kw, split( /\s*\;\s*/, $1 ) ); next; } last; } @kw && $kw[-1] =~ s/\.$//; $params{'-keywords'} = \@kw; $buffer = $line; next; } # Organism name and phylogenetic information elsif ($line =~ /^SOURCE\s+\S/) { if ( $builder->want_slot('species') ) { $species = $self->_read_GenBank_Species( \$buffer ); $builder->add_slot_value( -species => $species ); } else { while ( defined( $buffer = $self->_readline ) ) { last if substr( $buffer, 0, 1 ) ne ' '; } } next; } # References elsif ($line =~ /^REFERENCE\s+\S/) { if ($annotation) { my @refs = $self->_read_GenBank_References( \$buffer ); foreach my $ref (@refs) { $annotation->add_Annotation( 'reference', $ref ); } } else { while ( defined( $buffer = $self->_readline ) ) { last if substr( $buffer, 0, 1 ) ne ' '; } } next; } # Project elsif ($line =~ /^PROJECT\s+(\S.*)/) { if ($annotation) { my $project = Bio::Annotation::SimpleValue->new( -value => $1 ); $annotation->add_Annotation( 'project', $project ); } } # Comments may be plain text or Structured Comments. # Structured Comments are made up of tag/value pairs and have beginning # and end delimiters like ##*-Data-START## and ##*-Data-END## elsif ($line =~ /^COMMENT\s+(\S.*)/) { if ($annotation) { my $comment = $1; while ( defined( $line = $self->_readline ) ) { last if ($line =~ /^\S/); $comment .= $line; } $comment =~ s/ +/ /g; # Structured Comment, do not remove returns in the tabular section if ( my ( $text, $table )= $comment =~ /([^#]*)(##\S+Data-START##.+?##\S+Data-END##)/is ) { $text =~ s/\n/ /g if $text; $table =~ s/START##/START##\n/; $table =~ s/^\s+//gm; $comment = $text . "\n" . $table; } # Plain text, remove returns else { $comment =~ s/\n/ /g; } $annotation->add_Annotation( 'comment', Bio::Annotation::Comment->new( -text => $comment, -tagname => 'comment' ) ); $buffer = $line; } else { while ( defined( $buffer = $self->_readline ) ) { last if substr( $buffer, 0, 1 ) ne ' '; } } next; } # Corresponding Genbank nucleotide id, Genpept only elsif ($line =~ /^DB(?:SOURCE|LINK)\s+(\S.+)/) { if ($annotation) { my $dbsource = $1; while ( defined( $line = $self->_readline ) ) { last if ($line =~ /^\S/); $dbsource .= $line; } # deal with UniProKB dbsources if ( $dbsource =~ s/(UniProt(?:KB)?|swissprot):\s+locus\s+(\S+)\,.+\n// ) { $annotation->add_Annotation( 'dblink', Bio::Annotation::DBLink->new( -primary_id => $2, -database => $1, -tagname => 'dblink' ) ); if ( $dbsource =~ s/\s+created:\s+([^\.]+)\.\n// ) { $annotation->add_Annotation( 'swissprot_dates', Bio::Annotation::SimpleValue->new( -tagname => 'date_created', -value => $1 ) ); } while ( $dbsource =~ s/\s+(sequence|annotation)\s+updated:\s+([^\.]+)\.\n//g ) { $annotation->add_Annotation( 'swissprot_dates', Bio::Annotation::SimpleValue->new( -tagname => 'date_updated', -value => $2 ) ); } $dbsource =~ s/\n/ /g; if ( $dbsource =~ s/\s+xrefs:\s+((?:\S+,\s+)+\S+)\s+xrefs/xrefs/ ) { # will use $i to determine even or odd # for swissprot the accessions are paired my $i = 0; for my $dbsrc ( split( /,\s+/, $1 ) ) { if ( $dbsrc =~ /(\S+)\.(\d+)/ or $dbsrc =~ /(\S+)/ ) { my ( $id, $version ) = ( $1, $2 ); $version = '' unless defined $version; my $db = ( $id =~ /^\d\S{3}/ ) ? 'PDB' : ( $i++ % 2 ) ? 'GenPept' : 'GenBank'; $annotation->add_Annotation( 'dblink', Bio::Annotation::DBLink->new( -primary_id => $id, -version => $version, -database => $db, -tagname => 'dblink' ) ); } } } elsif ( $dbsource =~ s/\s+xrefs:\s+(.+)\s+xrefs/xrefs/i ) { # download screwed up and ncbi didn't put acc in for gi numbers my $i = 0; for my $id ( split( /\,\s+/, $1 ) ) { my ( $acc, $db ); if ( $id =~ /gi:\s+(\d+)/ ) { $acc = $1; $db = ( $i++ % 2 ) ? 'GenPept' : 'GenBank'; } elsif ( $id =~ /pdb\s+accession\s+(\S+)/ ) { $acc = $1; $db = 'PDB'; } else { $acc = $id; $db = ''; } $annotation->add_Annotation( 'dblink', Bio::Annotation::DBLink->new( -primary_id => $acc, -database => $db, -tagname => 'dblink' ) ); } } else { $self->debug("Cannot match $dbsource\n"); } if ( $dbsource =~ s/xrefs\s+ \(non\-sequence\s+databases\):\s+ ((?:\S+,\s+)+\S+)//x ) { for my $id ( split( /\,\s+/, $1 ) ) { my $db; # this is because GenBank dropped the spaces!!! # I'm sure we're not going to get this right ##if ( $id =~ s/^://i ) { ## $db = $1; ##} $db = substr( $id, 0, index( $id, ':' ) ); if ( not exists $DBSOURCE{$db} ) { $db = ''; # do we want 'GenBank' here? } $id = substr( $id, index( $id, ':' ) + 1 ); $annotation->add_Annotation( 'dblink', Bio::Annotation::DBLink->new( -primary_id => $id, -database => $db, -tagname => 'dblink' ) ); } } } else { if ( $dbsource =~ /^(\S*?):?\s*accession\s+(\S+)\.(\d+)/ ) { my ( $db, $id, $version ) = ( $1, $2, $3 ); $annotation->add_Annotation( 'dblink', Bio::Annotation::DBLink->new( -primary_id => $id, -version => $version, -database => $db || 'GenBank', -tagname => 'dblink' ) ); } elsif ( $dbsource =~ /^(\S*?):?\s*accession\s+(\S+)/ ) { my ( $db, $id ) = ( $1, $2 ); $annotation->add_Annotation( 'dblink', Bio::Annotation::DBLink->new( -primary_id => $id, -database => $db || 'GenBank', -tagname => 'dblink' ) ); } elsif ( $dbsource =~ /(\S+)([\.:])\s*(\S+)/ ) { my ( $db, $version ); my @ids = (); if ( $2 eq ':' ) { $db = $1; # Genbank 192 release notes say this: "The second # field can consist of multiple comma-separated # identifiers, if a sequence record has multiple # DBLINK cross-references of a given type." # For example: DBLINK Project:100,200,300" @ids = split( /,/, $3 ); } else { ( $db, $version ) = ( 'GenBank', $3 ); $ids[0] = $1; } foreach my $id (@ids) { $annotation->add_Annotation( 'dblink', Bio::Annotation::DBLink->new( -primary_id => $id, -version => $version, -database => $db, -tagname => 'dblink' ) ); } } else { $self->warn( "Unrecognized DBSOURCE data: $dbsource\n"); } } $buffer = $line; } else { while ( defined( $buffer = $self->_readline ) ) { last if substr( $buffer, 0, 1 ) ne ' '; } } next; } # Exit at start of Feature table, or start of sequence if ($line =~ /^(FEATURES|ORIGIN)/) { my $trap; } last if ($line =~ /^(FEATURES|ORIGIN)/); # Get next line and loop again $buffer = $self->_readline; } return unless defined $buffer; # add them all at once for efficiency $builder->add_slot_value( -accession_number => shift(@acc), -secondary_accessions => \@acc, %params ); $builder->add_slot_value( -annotation => $annotation ) if $annotation; %params = (); # reset before possible re-use to avoid setting twice # start over if we don't want to continue with this entry if ( not $builder->want_object ) { $builder->make_object; next RECORDSTART; } # some "minimal" formats may not necessarily have a feature table if ( $builder->want_slot('features') and defined $buffer and $buffer =~ /^FEATURES/o ) { # need to read the first line of the feature table $buffer = $self->_readline; # DO NOT read lines in the while condition -- this is done # as a side effect in _read_FTHelper_GenBank! # part of new circular spec: # commented out for now until kinks worked out #my $sourceEnd = 0; #$sourceEnd = $2 if ($buffer =~ /(\d+?)\.\.(\d+?)$/); while ( defined $buffer ) { # check immediately -- not at the end of the loop # note: GenPept entries obviously do not have a BASE line last if ( $buffer =~ /^BASE|ORIGIN|CONTIG|WGS/o ); # slurp in one feature at a time -- at return, the start of # the next feature will have been read already, so we need # to pass a reference, and the called method must set this # to the last line read before returning my $ftunit = $self->_read_FTHelper_GenBank( \$buffer ); # implement new circular spec: features that cross the origin are now # seamless instead of being 2 separate joined features # commented out until kinks get worked out #if ((! $args{'-nojoin'}) && $ftunit->{'loc'} =~ /^join\((\d+?)\.\.(\d+?),(\d+?)..(\d+?)\)$/ #&& $sourceEnd == $2 && $3 == 1) { #my $start = $1; #my $end = $2 + $4; #$ftunit->{'loc'} = "$start..$end"; #} # fix suggested by James Diggans if ( not defined $ftunit ) { # GRRRR. We have fallen over. Try to recover $self->warn( "Unexpected error in feature table for " . $params{'-display_id'} . " Skipping feature, attempting to recover" ); unless ( $buffer =~ /^\s{5,5}\S+/o or $buffer =~ /^\S+/o ) { $buffer = $self->_readline; } next; # back to reading FTHelpers } # process ftunit my $feat = $ftunit->_generic_seqfeature( $self->location_factory, $display_id ); # add taxon_id from source if available if ( $species and $feat->primary_tag eq 'source' and $feat->has_tag('db_xref') and ( not $species->ncbi_taxid or ( $species->ncbi_taxid and $species->ncbi_taxid =~ /^list/ ) ) ) { foreach my $tagval ( $feat->get_tag_values('db_xref') ) { if ( index( $tagval, "taxon:" ) == 0 ) { $species->ncbi_taxid( substr( $tagval, 6 ) ); last; } } } # add feature to list of features push( @features, $feat ); } $builder->add_slot_value( -features => \@features ); } if ( defined $buffer ) { # CONTIG lines: TODO, this needs to be cleaned up if ($buffer =~/^CONTIG\s+(.*)/o) { my $ctg = $1; while ( defined( $buffer = $self->_readline ) ) { last if $buffer =~ m{^ORIGIN|//}o; $buffer =~ s/\s+(.*)/$1/; $ctg .= $buffer; } if ($ctg) { $annotation->add_Annotation( Bio::Annotation::SimpleValue->new( -tagname => 'contig', -value => $ctg ) ); } } elsif ($buffer =~ /^WGS|WGS_SCAFLD\s+/o) { # catch WGS/WGS_SCAFLD lines while ( $buffer =~ s/(^WGS|WGS_SCAFLD)\s+// ) { # gulp lines chomp $buffer; $annotation->add_Annotation( Bio::Annotation::SimpleValue->new( -value => $buffer, -tagname => lc $1 ) ); $buffer = $self->_readline; } } elsif ( $buffer !~ m{^ORIGIN|//}o ) { # advance to the sequence, if any while ( defined( $buffer = $self->_readline ) ) { last if $buffer =~ m{^(ORIGIN|//)}; } } } if ( not $builder->want_object ) { $builder->make_object; # implicit end-of-object next RECORDSTART; } if ( $builder->want_slot('seq') ) { # the fact that we want a sequence does not necessarily mean that # there also is a sequence ... if ( defined $buffer and $buffer =~ s/^ORIGIN\s+// ) { if ( $annotation and length($buffer) > 0 ) { $annotation->add_Annotation( 'origin', Bio::Annotation::SimpleValue->new( -tagname => 'origin', -value => $buffer ) ); } my $seqc = ''; while ( defined( $buffer = $self->_readline ) ) { last if $buffer =~ m{^//}; $buffer = uc $buffer; $buffer =~ s/[^A-Za-z]//g; $seqc .= $buffer; } $builder->add_slot_value( -seq => $seqc ); } } elsif ( defined($buffer) and ( substr( $buffer, 0, 2 ) ne '//' ) ) { # advance to the end of the record while ( defined( $buffer = $self->_readline ) ) { last if substr( $buffer, 0, 2 ) eq '//'; } } # Unlikely, but maybe the sequence is so weird that we don't want it # anymore. We don't want to return undef if the stream's not exhausted # yet. $seq = $builder->make_object; next RECORDSTART unless $seq; last RECORDSTART; } # end while RECORDSTART return $seq; } =head2 write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object (must be seq) to the stream Returns : 1 for success and 0 for error Args : array of 1 to n Bio::SeqI objects =cut sub write_seq { my ($self,@seqs) = @_; foreach my $seq ( @seqs ) { $self->throw("Attempting to write with no seq!") unless defined $seq; if ( not ref $seq or not $seq->isa('Bio::SeqI') ) { $self->warn(" $seq is not a SeqI compliant module. Attempting to dump, but may fail!"); } my $str = $seq->seq; my $len = $seq->length; my $alpha = $seq->alphabet; my ($div, $mol); if ( not $seq->can('division') or not defined($div = $seq->division) ) { $div = 'UNK'; } if ( not $seq->can('molecule') or not defined ($mol = $seq->molecule) ) { $mol = $alpha || 'DNA'; } my $circular = ($seq->is_circular) ? 'circular' : 'linear '; local($^W) = 0; # suppressing warnings about uninitialized fields. my $temp_line; if ( $self->_id_generation_func ) { $temp_line = &{$self->_id_generation_func}($seq); } else { my $date = ''; if ( $seq->can('get_dates') ) { ($date) = $seq->get_dates; } $self->warn("No whitespace allowed in GenBank display id [". $seq->display_id. "]") if $seq->display_id =~ /\s/; my @data = ( lc($alpha) eq 'protein' ) ? ('aa', '', '') : ('bp', '', $mol); $temp_line = sprintf ("%-12s%-15s%13s %s%4s%-8s%-8s %3s %-s\n", 'LOCUS', $seq->id, $len, @data, $circular, $div, $date); } $self->_print($temp_line); $self->_write_line_GenBank_regex("DEFINITION ", " ", $seq->desc, "\\s\+\|\$",80); # if there, write the accession line if ( $self->_ac_generation_func ) { $temp_line = &{$self->_ac_generation_func}($seq); $self->_print("ACCESSION $temp_line\n"); } else { my @acc = (); push @acc, $seq->accession_number; if ( $seq->isa('Bio::Seq::RichSeqI') ) { push @acc, $seq->get_secondary_accessions; } $self->_print("ACCESSION ", join(" ", @acc), "\n"); # otherwise - cannot print <sigh> } # if PID defined, print it if ($seq->isa('Bio::Seq::RichSeqI') and $seq->pid) { $self->_print("PID ", $seq->pid, "\n"); } # if there, write the version line if ( defined $self->_sv_generation_func ) { $temp_line = &{$self->_sv_generation_func}($seq); if ( $temp_line ) { $self->_print("VERSION $temp_line\n"); } } elsif ($seq->isa('Bio::Seq::RichSeqI') and defined($seq->seq_version)) { my $id = $seq->primary_id; # this may be a GI number my $data = (defined $id and $id =~ /^\d+$/) ? " GI:$id" : ""; $self->_print("VERSION ", $seq->accession_number, ".", $seq->seq_version, $data, "\n"); } # if there, write the PROJECT line for my $proj ( $seq->annotation->get_Annotations('project') ) { $self->_print("PROJECT ".$proj->value."\n"); } # if there, write the DBSOURCE line foreach my $ref ( $seq->annotation->get_Annotations('dblink') ) { my ($db, $id) = ($ref->database, $ref->primary_id); my $prefix = $db eq 'Project' ? 'DBLINK' : 'DBSOURCE'; my $text = $db eq 'GenBank' ? '' : $db eq 'Project' ? "$db:$id" : "$db accession $id"; $self->_print(sprintf ("%-11s %s\n", $prefix, $text)); } # if there, write the keywords line if ( defined $self->_kw_generation_func ) { $temp_line = &{$self->_kw_generation_func}($seq); $self->_print("KEYWORDS $temp_line\n"); } elsif ( $seq->can('keywords') ) { my $kw = $seq->keywords; $kw .= '.' if ( $kw !~ /\.$/ ); $self->_print("KEYWORDS $kw\n"); } # SEGMENT if it exists foreach my $ref ( $seq->annotation->get_Annotations('segment') ) { $self->_print(sprintf ("%-11s %s\n",'SEGMENT', $ref->value)); } # Organism lines if (my $spec = $seq->species) { my ($on, $sn, $cn) = ($spec->can('organelle') ? $spec->organelle : '', $spec->scientific_name, $spec->common_name); my @classification; if ($spec->isa('Bio::Species')) { @classification = $spec->classification; shift @classification; } else { # Bio::Taxon should have a DB handle of some type attached, so # derive the classification from that my $node = $spec; while ($node) { $node = $node->ancestor || last; unshift @classification, $node->node_name; #$node eq $root && last; } @classification = reverse @classification; } my $abname = $spec->name('abbreviated') ? # from genbank file $spec->name('abbreviated')->[0] : $sn; my $sl = $on ? "$on " : ''; $sl .= $cn ? "$abname ($cn)" : $abname; $self->_write_line_GenBank_regex("SOURCE ", ' 'x12, $sl, "\\s\+\|\$", 80); $self->_print(" ORGANISM ", $spec->scientific_name, "\n"); my $OC = join('; ', reverse @classification) . '.'; $self->_write_line_GenBank_regex(' 'x12,' 'x12, $OC, "\\s\+\|\$", 80); } # Reference lines my $count = 1; foreach my $ref ( $seq->annotation->get_Annotations('reference') ) { $temp_line = "REFERENCE $count"; if ($ref->start) { $temp_line .= sprintf (" (%s %d to %d)", ($seq->alphabet() eq "protein" ? "residues" : "bases"), $ref->start, $ref->end); } elsif ($ref->gb_reference) { $temp_line .= sprintf (" (%s)", $ref->gb_reference); } $self->_print("$temp_line\n"); $self->_write_line_GenBank_regex(" AUTHORS ", ' 'x12, $ref->authors, "\\s\+\|\$", 80); $self->_write_line_GenBank_regex(" CONSRTM ", ' 'x12, $ref->consortium, "\\s\+\|\$", 80) if $ref->consortium; $self->_write_line_GenBank_regex(" TITLE ", ' 'x12, $ref->title, "\\s\+\|\$", 80); $self->_write_line_GenBank_regex(" JOURNAL ", ' 'x12, $ref->location, "\\s\+\|\$", 80); if ( $ref->medline) { $self->_write_line_GenBank_regex(" MEDLINE ", ' 'x12, $ref->medline, "\\s\+\|\$", 80); # I am assuming that pubmed entries only exist when there # are also MEDLINE entries due to the indentation } # This could be a wrong assumption if ( $ref->pubmed ) { $self->_write_line_GenBank_regex(" PUBMED ", ' 'x12, $ref->pubmed, "\\s\+\|\$", 80); } # put remark at the end if ($ref->comment) { $self->_write_line_GenBank_regex(" REMARK ", ' 'x12, $ref->comment, "\\s\+\|\$", 80); } $count++; } # Comment lines foreach my $comment ( $seq->annotation->get_Annotations('comment') ) { $self->_write_line_GenBank_regex("COMMENT ", ' 'x12, $comment->text, "\\s\+\|\$", 80); } # FEATURES section $self->_print("FEATURES Location/Qualifiers\n"); if ( defined $self->_post_sort ) { # we need to read things into an array. Process. Sort them. Print 'em my $post_sort_func = $self->_post_sort; my @fth; foreach my $sf ( $seq->top_SeqFeatures ) { push @fth, Bio::SeqIO::FTHelper::from_SeqFeature($sf, $seq); } @fth = sort { &$post_sort_func($a, $b) } @fth; foreach my $fth ( @fth ) { $self->_print_GenBank_FTHelper($fth); } } else { # not post sorted. And so we can print as we get them. # lower memory load... foreach my $sf ( $seq->top_SeqFeatures ) { my @fth = Bio::SeqIO::FTHelper::from_SeqFeature($sf, $seq); foreach my $fth ( @fth ) { if ( ! $fth->isa('Bio::SeqIO::FTHelper') ) { $sf->throw("Cannot process FTHelper... $fth"); } $self->_print_GenBank_FTHelper($fth); } } } # deal with WGS; WGS_SCAFLD present only if WGS is also present if ($seq->annotation->get_Annotations('wgs')) { foreach my $wgs (map {$seq->annotation->get_Annotations($_)} qw(wgs wgs_scaffold) ) { $self->_print(sprintf ("%-11s %s\n", uc($wgs->tagname), $wgs->value)); } $self->_show_dna(0); } if ($seq->annotation->get_Annotations('contig')) { my $ct = 0; my $cline; foreach my $contig ($seq->annotation->get_Annotations('contig')) { unless ($ct) { $cline = uc($contig->tagname) . " " . $contig->value . "\n"; } else { $cline = " " . $contig->value . "\n"; } $self->_print($cline); $ct++; } } if ( $seq->length == 0 ) { $self->_show_dna(0); } if ( $self->_show_dna == 0 ) { $self->_print("\n//\n"); return; } # finished printing features. $str =~ tr/A-Z/a-z/; my ($o) = $seq->annotation->get_Annotations('origin'); $self->_print(sprintf("%-12s%s\n", 'ORIGIN', $o ? $o->value : '')); # print out the sequence my $nuc = 60; # Number of nucleotides per line my $whole_pat = 'a10' x 6; # Pattern for unpacking a whole line my $out_pat = 'A11' x 6; # Pattern for packing a line my $length = length $str; # Calculate the number of nucleotides which fit on whole lines my $whole = int($length / $nuc) * $nuc; # Print the whole lines my $i; for ($i = 0; $i < $whole; $i += $nuc) { my $blocks = pack $out_pat, unpack $whole_pat, substr($str, $i, $nuc); chop $blocks; $self->_print(sprintf("%9d $blocks\n", $i + $nuc - 59)); } # Print the last line if (my $last = substr($str, $i)) { my $last_len = length($last); my $last_pat = 'a10' x int($last_len / 10) . 'a' . $last_len % 10; my $blocks = pack $out_pat, unpack($last_pat, $last); $blocks =~ s/ +$//; $self->_print(sprintf("%9d $blocks\n", $length - $last_len + 1)); } $self->_print("//\n"); $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } } =head2 _print_GenBank_FTHelper Title : _print_GenBank_FTHelper Usage : Function: Example : Returns : Args : =cut sub _print_GenBank_FTHelper { my ( $self, $fth ) = @_; if ( not ref $fth or not $fth->isa('Bio::SeqIO::FTHelper') ) { $fth->warn( "$fth is not a FTHelper class. Attempting to print but there could be issues" ); } my $spacer = ( length $fth->key >= 15 ) ? ' ' : ''; $self->_write_line_GenBank_regex( sprintf( " %-16s%s", $fth->key, $spacer ), " " x 21, $fth->loc, "\,\|\$", 80 ); foreach my $tag ( sort keys %{ $fth->field } ) { # Account for hash structure in Annotation::DBLink, not the expected array if ( $tag eq 'db_xref' and grep /HASH/, @{ $fth->field->{$tag} }) { for my $ref ( @{ $fth->field->{$tag} } ) { my $db = $ref->{'database'}; my $id = $ref->{'primary_id'}; $self->_write_line_GenBank_regex ( " " x 21, " " x 21, "/$tag=\"$db:$id\"", "\.\|\$", 80 ); } } # The usual case, where all values are found in an array else { foreach my $value ( @{ $fth->field->{$tag} } ) { $value =~ s/\"/\"\"/g; if ( $value eq "_no_value" ) { $self->_write_line_GenBank_regex ( " " x 21, " " x 21, "/$tag", "\.\|\$", 80 ); } # There are almost 3x more quoted qualifier values and they # are more common too so we take quoted ones first. # Long qualifiers, that will be line wrapped, are always quoted elsif ( not $FTQUAL_NO_QUOTE{$tag} or length("/$tag=$value") >= $FTQUAL_LINE_LENGTH ) { my ($pat) = ( $value =~ /\s/ ? '\s|$' : '.|$' ); $self->_write_line_GenBank_regex ( " " x 21, " " x 21, "/$tag=\"$value\"", $pat, 80 ); } else { $self->_write_line_GenBank_regex ( " " x 21, " " x 21, "/$tag=$value", "\.\|\$", 80 ); } } } } } =head2 _read_GenBank_References Title : _read_GenBank_References Usage : Function: Reads references from GenBank format. Internal function really Returns : Args : =cut sub _read_GenBank_References { my ($self, $buffer) = @_; my (@refs); my $ref; # assume things are starting with RN if ( $$buffer !~ /^REFERENCE/ ) { warn("Not parsing line '$$buffer' which maybe important"); } my $line = $$buffer; my (@title,@loc,@authors,@consort,@com,@medline,@pubmed); REFLOOP: while( defined($line) or defined($line = $self->_readline) ) { if ($line =~ /^\s{2}AUTHORS\s+(.*)/o) { push @authors, $1; while ( defined($line = $self->_readline) ) { if ($line =~ /^\s{9,}(.*)/o) { push @authors, $1; next; } last; } $ref->authors(join(' ', @authors)); } if ($line =~ /^\s{2}CONSRTM\s+(.*)/o) { push @consort, $1; while ( defined($line = $self->_readline) ) { if ($line =~ /^\s{9,}(.*)/o) { push @consort, $1; next; } last; } $ref->consortium(join(' ', @consort)); } if ($line =~ /^\s{2}TITLE\s+(.*)/o) { push @title, $1; while ( defined($line = $self->_readline) ) { if ($line =~ /^\s{9,}(.*)/o) { push @title, $1; next; } last; } $ref->title(join(' ', @title)); } if ($line =~ /^\s{2}JOURNAL\s+(.*)/o) { push @loc, $1; while ( defined($line = $self->_readline) ) { # we only match when there are at least 4 spaces # there is probably a better way to match this # as it assumes that the describing tag is short enough if ($line =~ /^\s{9,}(.*)/o) { push @loc, $1; next; } last; } $ref->location(join(' ', @loc)); redo REFLOOP; } if ($line =~ /^\s{2}REMARK\s+(.*)/o) { push @com, $1; while ( defined($line = $self->_readline) ) { if ($line =~ /^\s{9,}(.*)/o) { push @com, $1; next; } last; } $ref->comment(join(' ', @com)); redo REFLOOP; } if ( $line =~ /^\s{2}MEDLINE\s+(.*)/ ) { push @medline, $1; while ( defined($line = $self->_readline) ) { if ($line =~ /^\s{9,}(.*)/) { push @medline, $1; next; } last; } $ref->medline(join(' ', @medline)); redo REFLOOP; } if ( $line =~ /^\s{3}PUBMED\s+(.*)/ ) { push @pubmed, $1; while ( defined($line = $self->_readline) ) { if ($line =~ /^\s{9,}(.*)/) { push @pubmed, $1; next; } last; } $ref->pubmed(join(' ', @pubmed)); redo REFLOOP; } if ( $line =~ /^REFERENCE/o ) { # store current reference $self->_add_ref_to_array(\@refs,$ref) if defined $ref; # reset @authors = (); @title = (); @loc = (); @com = (); @pubmed = (); @medline = (); # create the new reference object $ref = Bio::Annotation::Reference->new(-tagname => 'reference'); # check whether start and end base is given if ($line =~ /^REFERENCE\s+\d+\s+\([a-z]+ (\d+) to (\d+)\)/){ $ref->start($1); $ref->end($2); } elsif ($line =~ /^REFERENCE\s+\d+\s+\((.*)\)/) { $ref->gb_reference($1); } } last if ($line =~ /^(FEATURES)|(COMMENT)/o); $line = undef; # Empty $line to trigger read of next line } # store last reference $self->_add_ref_to_array(\@refs, $ref) if defined $ref; $$buffer = $line; #print "\nnumber of references found: ", $#refs+1,"\n"; return @refs; } =head2 _add_ref_to_array Title: _add_ref_to_array Usage: Function: Adds a Reference object to an array of Reference objects, takes care of possible cleanups to be done (currently, only author and title will be chopped of trailing semicolons). Args: A reference to an array of Reference objects and the Reference object to be added Returns: nothing =cut sub _add_ref_to_array { my ($self, $refs, $ref) = @_; # first, polish author and title by removing possible trailing semicolons my $au = $ref->authors; my $title = $ref->title; $au =~ s/;\s*$//g if $au; $title =~ s/;\s*$//g if $title; $ref->authors($au); $ref->title($title); # the rest should be clean already, so go ahead and add it push @{$refs}, $ref; } =head2 _read_GenBank_Species Title : _read_GenBank_Species Usage : Function: Reads the GenBank Organism species and classification lines. Able to deal with unconvential Organism naming formats, and varietas in plants Example : ORGANISM unknown marine gamma proteobacterium NOR5 $genus = undef $species = unknown marine gamma proteobacterium NOR5 ORGANISM Drosophila sp. 'white tip scutellum' $genus = Drosophila $species = sp. 'white tip scutellum' (yes, this really is a species and that is its name) $subspecies = undef ORGANISM Ajellomyces capsulatus var. farciminosus $genus = Ajellomyces $species = capsulatus $subspecies = var. farciminosus ORGANISM Hepatitis delta virus $genus = undef (though this virus has a genus in its lineage, we cannot know that without a database lookup) $species = Hepatitis delta virus Returns : A Bio::Species object Args : A reference to the current line buffer =cut sub _read_GenBank_Species { my ($self, $buffer) = @_; my @unkn_names = ('other', 'unknown organism', 'not specified', 'not shown', 'Unspecified', 'Unknown', 'None', 'unclassified', 'unidentified organism', 'not supplied'); # dictionary of synonyms for taxid 32644 my @unkn_genus = ('unknown', 'unclassified', 'uncultured', 'unidentified'); # all above can be part of valid species name my $line = $$buffer; my( $sub_species, $species, $genus, $sci_name, $common, $class_lines, $source_flag, $abbr_name, $organelle, $sl ); my %source = map { $_ => 1 } qw(SOURCE ORGANISM CLASSIFICATION); # upon first entering the loop, we must not read a new line -- the SOURCE # line is already in the buffer (HL 05/10/2000) my ($ann, $tag, $data); while (defined($line) or defined($line = $self->_readline)) { # de-HTMLify (links that may be encountered here don't contain # escaped '>', so a simple-minded approach suffices) $line =~ s{<[^>]+>}{}g; if ($line =~ m{^(?:\s{0,2})(\w+)\s+(.+)?$}ox) { ($tag, $data) = ($1, $2 || ''); last if ($tag and not exists $source{$tag}); } else { return unless $tag; ($data = $line) =~ s{^\s+}{}; chomp $data; $tag = 'CLASSIFICATION' if ( $tag ne 'CLASSIFICATION' and $tag eq 'ORGANISM' # Don't match "str." or "var." (fix NC_021815), # and don't match ".1" (fix NC_021902) and $line =~ m{(?<!\bstr|\bvar)[;\.]+(?!\d)}); } (exists $ann->{$tag}) ? ($ann->{$tag} .= ' '.$data) : ($ann->{$tag} .= $data); $line = undef; } ($sl, $class_lines, $sci_name) = ($ann->{SOURCE}, $ann->{CLASSIFICATION}, $ann->{ORGANISM}); $$buffer = $line; $sci_name or return; # parse out organelle, common name, abbreviated name if present; # this should catch everything, but falls back to # entire SOURCE line just in case if ($sl =~ m{^(mitochondrion|chloroplast|plastid)? \s*(.*?) \s*(?: \( (.*?) \) )?\.? $ }xms ) { ($organelle, $abbr_name, $common) = ($1, $2, $3); # optional } else { $abbr_name = $sl; # nothing caught; this is a backup! } # Convert data in classification lines into classification array. # only split on ';' or '.' so that classification that is 2 or more words will # still get matched, use map() to remove trailing/leading/intervening spaces my @class = map { $_ =~ s/^\s+//; $_ =~ s/\s+$//; $_ =~ s/\s{2,}/ /g; $_; } split /(?<!subgen)[;\.]+/, $class_lines; # do we have a genus? my $possible_genus = quotemeta($class[-1]) . ($class[-2] ? "|" . quotemeta($class[-2]) : ''); if ($sci_name =~ /^($possible_genus)/) { $genus = $1; ($species) = $sci_name =~ /^$genus\s+(.+)/; } else { $species = $sci_name; } # is this organism of rank species or is it lower? # (we don't catch everything lower than species, but it doesn't matter - # this is just so we abide by previous behaviour whilst not calling a # species a subspecies) if ($species and $species =~ /(.+)\s+((?:subsp\.|var\.).+)/) { ($species, $sub_species) = ($1, $2); } # Don't make a species object if it's empty or "Unknown" or "None" # return unless $genus and $genus !~ /^(Unknown|None)$/oi; # Don't make a species object if it belongs to taxid 32644 # my $unkn = grep { $_ =~ /^\Q$sl\E$/; } @unkn_names; my $unkn = grep { $_ eq $sl } @unkn_names; return unless (defined $species or defined $genus) and $unkn == 0; # Bio::Species array needs array in Species -> Kingdom direction push @class, $sci_name; @class = reverse @class; my $make = Bio::Species->new; $make->scientific_name($sci_name); $make->classification(@class) if @class > 0; $make->common_name( $common ) if $common; $make->name('abbreviated', $abbr_name) if $abbr_name; $make->organelle($organelle) if $organelle; #$make->sub_species( $sub_species ) if $sub_species; return $make; } =head2 _read_FTHelper_GenBank Title : _read_FTHelper_GenBank Usage : _read_FTHelper_GenBank($buffer) Function: reads the next FT key line Example : Returns : Bio::SeqIO::FTHelper object Args : filehandle and reference to a scalar =cut sub _read_FTHelper_GenBank { my ($self, $buffer) = @_; my ($key, # The key of the feature $loc # The location line from the feature ); my @qual = (); # An array of lines making up the qualifiers if ($$buffer =~ /^\s{5}(\S+)\s+(.+?)\s*$/o) { $key = $1; $loc = $2; # Read all the lines up to the next feature while ( defined(my $line = $self->_readline) ) { if ($line =~ /^(\s+)(.+?)\s*$/o) { # Lines inside features are preceded by 21 spaces # A new feature is preceded by 5 spaces if (length($1) > 6) { # Add to qualifiers if we're in the qualifiers, or if it's # the first qualifier if (@qual or (index($2,'/') == 0)) { push @qual, $2; } # We're still in the location line, so append to location else { $loc .= $2; } } else { # We've reached the start of the next feature # Put the first line of the next feature into the buffer $$buffer = $line; last; } } else { # We're at the end of the feature table # Put the first line of the next feature into the buffer $$buffer = $line; last; } } } else { # No feature key $self->debug("no feature key!\n"); # change suggested by JDiggans to avoid infinite loop- # see bugreport 1062. # reset buffer to prevent infinite loop $$buffer = $self->_readline; return; } # Make the new FTHelper object my $out = Bio::SeqIO::FTHelper->new; $out->verbose($self->verbose); $out->key($key); $out->loc($loc); # Now parse and add any qualifiers. (@qual is kept # intact to provide informative error messages.) QUAL: for (my $i = 0; $i < @qual; $i++) { my $data = $qual[$i]; my ( $qualifier, $value ) = ($data =~ m{^/([^=]+)(?:=\s*(.+))?}) or $self->warn( "cannot see new qualifier in feature $key: " . $data); $qualifier = '' if not defined $qualifier; if (defined $value) { # Do we have a quoted value? if (substr($value, 0, 1) eq '"') { # Keep adding to value until we find the trailing quote # and the quotes are balanced while ($value !~ /\"$/ or $value =~ tr/"/"/ % 2) { if ($i >= $#qual) { $self->warn( "Unbalanced quote in:\n" . join("\n", @qual) . "No further qualifiers will " . "be added for this feature"); last QUAL; } # modifying a for-loop variable inside of the loop # is not the best programming style ... $i++; my $next = $qual[$i]; # add to value with a space unless the value appears # to be a sequence (translation for example) # if (($value.$next) =~ /[^A-Za-z\"\-]/o) { # changed to explicitly look for translation tag - cjf 06/8/29 if ($qualifier !~ /^translation$/i ) { $value .= " "; } $value .= $next; } # Trim leading and trailing quotes $value =~ s/^"|"$//g; # Undouble internal quotes $value =~ s/""/\"/g; } elsif ( $value =~ /^\(/ ) { # values quoted by ()s # Keep adding to value until we find the trailing bracket # and the ()s are balanced my $left = ($value =~ tr/\(/\(/); # count left parens my $right = ($value =~ tr/\)/\)/); # count right parens while( $left != $right ) { # was "$value !~ /\)$/ or $left != $right" if ( $i >= $#qual) { $self->warn( "Unbalanced parens in:\n" . join("\n", @qual) . "\nNo further qualifiers will " . "be added for this feature"); last QUAL; } $i++; my $next = $qual[$i]; $value .= $next; $left += ($next =~ tr/\(/\(/); $right += ($next =~ tr/\)/\)/); } } } else { $value = '_no_value'; } # Store the qualifier $out->field->{$qualifier} ||= []; push @{$out->field->{$qualifier}}, $value; } return $out; } =head2 _write_line_GenBank Title : _write_line_GenBank Usage : Function: internal function Example : Returns : Args : =cut sub _write_line_GenBank { my ($self, $pre1, $pre2, $line, $length) = @_; $length or $self->throw("Miscalled write_line_GenBank without length. Programming error!"); my $subl = $length - length $pre2; my $linel = length $line; my $i; my $subr = substr($line,0,$length - length $pre1); $self->_print("$pre1$subr\n"); for($i = ($length - length $pre1); $i < $linel; $i += $subl) { $subr = substr($line, $i, $subl); $self->_print("$pre2$subr\n"); } } =head2 _write_line_GenBank_regex Title : _write_line_GenBank_regex Usage : Function: internal function for writing lines of specified length, with different first and the next line left hand headers and split at specific points in the text Example : Returns : nothing Args : file handle, first header, second header, text-line, regex for line breaks, total line length =cut sub _write_line_GenBank_regex { my ($self, $pre1, $pre2, $line, $regex, $length) = @_; #print STDOUT "Going to print with $line!\n"; $length or $self->throw("Miscalled write_line_GenBank without length. Programming error!"); my $subl = $length - (length $pre1) - 2; my @lines = (); CHUNK: while ($line) { foreach my $pat ($regex, '[,;\.\/-]\s|'.$regex, '[,;\.\/-]|'.$regex) { if ($line =~ m/^(.{0,$subl})($pat)(.*)/ ) { my $l = $1 . $2; $line = substr($line, length $l); # be strict about not padding spaces according to # genbank format $l =~ s/\s+$//; next CHUNK if ($l eq ''); push @lines, $l; next CHUNK; } } # if we get here none of the patterns matched $subl or less chars $self->warn( "trouble dissecting \"$line\"\n into chunks " . "of $subl chars or less - this tag won't print right"); # insert a space char to prevent infinite loops $line = substr($line, 0, $subl) . " " . substr($line, $subl); } my $s = shift @lines; $self->_print("$pre1$s\n") if $s; foreach my $s ( @lines ) { $self->_print("$pre2$s\n"); } } =head2 _post_sort Title : _post_sort Usage : $obj->_post_sort($newval) Function: Returns : value of _post_sort Args : newvalue (optional) =cut sub _post_sort { my ($obj,$value) = @_; if ( defined $value) { $obj->{'_post_sort'} = $value; } return $obj->{'_post_sort'}; } =head2 _show_dna Title : _show_dna Usage : $obj->_show_dna($newval) Function: Returns : value of _show_dna Args : newvalue (optional) =cut sub _show_dna { my ($obj,$value) = @_; if ( defined $value) { $obj->{'_show_dna'} = $value; } return $obj->{'_show_dna'}; } =head2 _id_generation_func Title : _id_generation_func Usage : $obj->_id_generation_func($newval) Function: Returns : value of _id_generation_func Args : newvalue (optional) =cut sub _id_generation_func { my ($obj,$value) = @_; if ( defined $value ) { $obj->{'_id_generation_func'} = $value; } return $obj->{'_id_generation_func'}; } =head2 _ac_generation_func Title : _ac_generation_func Usage : $obj->_ac_generation_func($newval) Function: Returns : value of _ac_generation_func Args : newvalue (optional) =cut sub _ac_generation_func { my ($obj,$value) = @_; if ( defined $value ) { $obj->{'_ac_generation_func'} = $value; } return $obj->{'_ac_generation_func'}; } =head2 _sv_generation_func Title : _sv_generation_func Usage : $obj->_sv_generation_func($newval) Function: Returns : value of _sv_generation_func Args : newvalue (optional) =cut sub _sv_generation_func { my ($obj,$value) = @_; if ( defined $value ) { $obj->{'_sv_generation_func'} = $value; } return $obj->{'_sv_generation_func'}; } =head2 _kw_generation_func Title : _kw_generation_func Usage : $obj->_kw_generation_func($newval) Function: Returns : value of _kw_generation_func Args : newvalue (optional) =cut sub _kw_generation_func { my ($obj,$value) = @_; if ( defined $value ) { $obj->{'_kw_generation_func'} = $value; } return $obj->{'_kw_generation_func'}; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/interpro.pm��������������������������������������������������������������000444��000766��000024�� 21404�13155576320� 17425� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for interpro # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::interpro - InterProScan XML input/output stream =head1 SYNOPSIS # do not call this module directly, use Bio::SeqIO use strict; use Bio::SeqIO; my $io = Bio::SeqIO->new(-format => "interpro", -file => $interpro_file); while (my $seq = $io->next_seq) { # use the Sequence object } =head1 DESCRIPTION L<Bio::SeqIO::interpro> will parse Interpro scan XML (version 1.2) and create L<Bio::SeqFeature::Generic> objects based on the contents of the XML document. L<Bio::SeqIO::interpro> will also attach the annotation given in the XML file to the L<Bio::SeqFeature::Generic> objects that it creates. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jared Fox Email jaredfox@ucla.edu =head1 CONTRIBUTORS Allen Day allenday@ucla.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::interpro; use strict; use Bio::SeqFeature::Generic; use XML::DOM; use XML::DOM::XPath; use Bio::Seq::SeqFactory; use Bio::Annotation::Collection; use Bio::Annotation::DBLink; use base qw(Bio::SeqIO); my $idcounter = {}; # Used to generate unique id values my $nvtoken = ": "; # The token used if a name/value pair has to be stuffed # into a single line =head2 next_seq Title : next_seq Usage : my $seqobj = $stream->next_seq Function: Retrieves the next sequence from a SeqIO::interpro stream. Returns : A Bio::Seq::RichSeq object Args : =cut sub next_seq { my $self = shift; my ($desc); my $bioSeq = $self->_sequence_factory->create(-verbose =>$self->verbose()); my $zinc = "(\"zincins\")"; my $wing = "\"Winged helix\""; my $finger = "\"zinc finger\""; my $xml_fragment = undef; while(my $line = $self->_readline()){ my $where = index($line, $zinc); my $wherefinger = index($line, $finger); my $finishedline = $line; my $wingwhere = index($line, $wing); # the interpro XML is not fully formed, so we need to convert the # extra double quotes and ampersands into appropriate XML character codes if($where > 0){ my @linearray = split /$zinc/, $line; $finishedline = join ""zincins"", $linearray[0], $linearray[2]; } if(index($line, "&") > 0){ my @linearray = split /&/, $line; $finishedline = join "&", $linearray[0], $linearray[1]; } if($wingwhere > 0){ my @linearray = split /$wing/, $line; $finishedline = join ""Winged helix"", $linearray[0], $linearray[1]; } $xml_fragment .= $finishedline; last if $finishedline =~ m!</protein>!; } # Match <protein> but not other similar elements like <protein-matches> return unless $xml_fragment =~ /<protein[\s>]/; $self->_parse_xml($xml_fragment); my $dom = $self->_dom; my ($protein_node) = $dom->findnodes('/protein'); my @interproNodes = $protein_node->findnodes('/protein/interpro'); my @DBNodes = $protein_node->findnodes('/protein/interpro/match'); for(my $interpn=0; $interpn<scalar(@interproNodes); $interpn++){ my $ipnlevel = join "", "/protein/interpro[", $interpn + 1, "]"; my @matchNodes = $protein_node->findnodes($ipnlevel); for(my $match=0; $match<scalar(@matchNodes); $match++){ my $matlevel = join "", "/protein/interpro[", $interpn+1, "]/match[", $match+1, "]/location"; my @locNodes = $protein_node->findnodes($matlevel); my $class_level = join "", "/protein/interpro[",$interpn+1, "]/classification"; my @goNodes = $protein_node->findnodes($class_level); my @seqFeatures = map { Bio::SeqFeature::Generic->new( -start => $_->getAttribute('start'), -end => $_->getAttribute('end'), -score => $_->getAttribute('score'), -source_tag => 'IPRscan', -primary_tag => 'region', -display_name => $interproNodes[$interpn]->getAttribute('name'), -seq_id => $protein_node->getAttribute('id') ), } @locNodes; foreach my $seqFeature (@seqFeatures){ $bioSeq->add_SeqFeature($seqFeature); my $annotation1 = Bio::Annotation::DBLink->new; $annotation1->database($matchNodes[$match]->getAttribute('dbname')); $annotation1->primary_id($matchNodes[$match]->getAttribute('id')); $annotation1->comment($matchNodes[$match]->getAttribute('name')); $seqFeature->annotation->add_Annotation('dblink',$annotation1); my $annotation2 = Bio::Annotation::DBLink->new; $annotation2->database('INTERPRO'); $annotation2->primary_id($interproNodes[$interpn]->getAttribute('id')); $annotation2->comment($interproNodes[$interpn]->getAttribute('name')); $seqFeature->annotation->add_Annotation('dblink',$annotation2); # Bug 1908 (enhancement) my $annotation3 = Bio::Annotation::DBLink->new; $annotation3->database($DBNodes[$interpn]->getAttribute('dbname')); $annotation3->primary_id($DBNodes[$interpn]->getAttribute('id')); $annotation3->comment($DBNodes[$interpn]->getAttribute('name')); $seqFeature->annotation->add_Annotation('dblink',$annotation3); # need to put in the go annotation here! foreach my $g (@goNodes) { my $goid = $g->getAttribute('id'); my $go_annotation = Bio::Annotation::DBLink->new; $go_annotation->database('GO'); $go_annotation->primary_id($goid); $go_annotation->comment($goid); $seqFeature->annotation->add_Annotation('dblink', $go_annotation); } } } } my $accession = $protein_node->getAttribute('id'); my $displayname = $protein_node->getAttribute('name'); $bioSeq->accession($accession); $bioSeq->display_name($displayname); return $bioSeq; } =head2 _initialize Title : _initialize Usage : Function: Returns : Args : =cut sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); # hash for functions for decoding keys. $self->{'_func_ftunit_hash'} = {}; my %param = @args; # From SeqIO.pm @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $line = undef; # fast forward to first <protein/> record. while($line = $self->_readline()){ # Match <protein> but not other similar elements like <protein-matches> if($line =~ /<protein[\s>]/){ $self->_pushback($line); last; } } $self->_xml_parser( XML::DOM::Parser->new() ); $self->_sequence_factory( Bio::Seq::SeqFactory->new ( -verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')) if ( ! defined $self->sequence_factory ); } =head2 _sequence_factory Title : _sequence_factory Usage : Function: Returns : Args : =cut sub _sequence_factory { my $self = shift; my $val = shift; $self->{'sequence_factory'} = $val if defined($val); return $self->{'sequence_factory'}; } =head2 _xml_parser Title : _xml_parser Usage : Function: Returns : Args : =cut sub _xml_parser { my $self = shift; my $val = shift; $self->{'xml_parser'} = $val if defined($val); return $self->{'xml_parser'}; } =head2 _parse_xml Title : _parse_xml Usage : Function: Returns : Args : =cut sub _parse_xml { my ($self,$xml) = @_; $self->_dom( $self->_xml_parser->parse($xml) ); return 1; } =head2 _dom Title : _dom Usage : Function: Returns : Args : =cut sub _dom { my $self = shift; my $val = shift; $self->{'dom'} = $val if defined($val); return $self->{'dom'}; } 1; __END__ ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/kegg.pm������������������������������������������������������������������000444��000766��000024�� 20262�13155576320� 16501� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::kegg # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Allen Day <allenday@ucla.edu> # # Copyright Allen Day # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::kegg - KEGG sequence input/output stream =head1 SYNOPSIS # It is probably best not to use this object directly, but # rather go through the SeqIO handler system. Go: use Bio::SeqIO; $stream = Bio::SeqIO->new(-file => $filename, -format => 'KEGG'); while ( my $seq = $stream->next_seq() ) { # do something with $seq } =head1 DESCRIPTION This class transforms KEGG gene records into Bio::Seq objects. =head2 Mapping of record properties to object properties This section is supposed to document which sections and properties of a KEGG databank record end up where in the Bioperl object model. It is far from complete and presently focuses only on those mappings which may be non-obvious. $seq in the text refers to the Bio::Seq::RichSeqI implementing object returned by the parser for each record. =over 4 =item 'ENTRY' $seq->primary_id =item 'NAME' $seq->display_id =item 'DEFINITION' $seq->annotation->get_Annotations('description'); =item 'ORTHOLOG' grep {$_->database eq 'KO'} $seq->annotation->get_Annotations('dblink') =item 'CLASS' grep {$_->database eq 'PATH'} $seq->annotation->get_Annotations('dblink') =item 'POSITION' FIXME, NOT IMPLEMENTED =item 'PATHWAY' for my $pathway ( $seq->annotation->get_Annotations('pathway') ) { # } =item 'DBLINKS' $seq->annotation->get_Annotations('dblink') =item 'CODON_USAGE' FIXME, NOT IMPLEMENTED =item 'AASEQ' $seq->translate->seq =item 'NTSEQ' $seq-E<gt>seq =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Allen Day Email allenday@ucla.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::kegg; use strict; use Bio::SeqFeature::Generic; use Bio::Species; use Bio::Seq::SeqFactory; use Bio::Annotation::Collection; use Bio::Annotation::Comment; use Bio::Annotation::DBLink; use base qw(Bio::SeqIO); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); # hash for functions for decoding keys. $self->{'_func_ftunit_hash'} = {}; if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq::RichSeq object Args : =cut sub next_seq { my ($self,@args) = @_; my $builder = $self->sequence_builder(); my $seq; my %params; my $buffer; my (@acc, @features); my ($display_id, $annotation); my $species; # initialize; we may come here because of starting over @features = (); $annotation = undef; @acc = (); $species = undef; %params = (-verbose => $self->verbose); # reset hash local($/) = "///\n"; $buffer = $self->_readline(); return if( !defined $buffer ); # end of file $buffer =~ /^ENTRY/ || $self->throw("KEGG stream with bad ENTRY line. Not KEGG in my book. Got $buffer'"); my %FIELDS; my @chunks = split /\n(?=\S)/, $buffer; foreach my $chunk (@chunks){ my($key) = $chunk =~ /^(\S+)/; $FIELDS{$key} = $chunk; } # changing to split method to get entry_ids that include # sequence version like Whatever.1 my(undef,$entry_id,$entry_seqtype,$entry_species) = split(' ',$FIELDS{ENTRY}); my($name); if ($FIELDS{NAME}) { ($name) = $FIELDS{NAME} =~ /^NAME\s+(.+)$/; } my( $definition, $aa_length, $aa_seq, $nt_length, $nt_seq ); if(( exists $FIELDS{DEFINITION} ) and ( $FIELDS{DEFINITION} =~ /^DEFINITION/ )) { ($definition) = $FIELDS{DEFINITION} =~ /^DEFINITION\s+(.+)$/s; $definition =~ s/\s+/ /gs; } if(( exists $FIELDS{AASEQ} ) and ( $FIELDS{AASEQ} =~ /^AASEQ/ )) { ($aa_length,$aa_seq) = $FIELDS{AASEQ} =~ /^AASEQ\s+(\d+)\n(.+)$/s; $aa_seq =~ s/\s+//g; } if(( exists $FIELDS{NTSEQ} ) and ( $FIELDS{NTSEQ} =~ /^NTSEQ/ )) { ($nt_length,$nt_seq) = $FIELDS{NTSEQ} =~ /^NTSEQ\s+(\d+)\n(.+)$/s; $nt_seq =~ s/\s+//g; } $annotation = Bio::Annotation::Collection->new(); $annotation->add_Annotation('description', Bio::Annotation::Comment->new(-text => $definition)); $annotation->add_Annotation('aa_seq', Bio::Annotation::Comment->new(-text => $aa_seq)); my($ortholog_db,$ortholog_id,$ortholog_desc); if ($FIELDS{ORTHOLOG}) { ($ortholog_db,$ortholog_id,$ortholog_desc) = $FIELDS{ORTHOLOG} =~ /^ORTHOLOG\s+(\S+):\s+(\S+)\s+(.*?)$/; $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new( -database => $ortholog_db, -primary_id => $ortholog_id, -comment => $ortholog_desc) ); } if($FIELDS{MOTIF}){ $FIELDS{MOTIF} =~ s/^MOTIF\s+//; while($FIELDS{MOTIF} =~/\s*?(\S+):\s+(.+?)$/mg){ my $db = $1; my $ids = $2; foreach my $id (split(/\s+/, $ids)){ $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new( -database =>$db, -primary_id => $id, -comment => "") ); } } } if($FIELDS{PATHWAY}) { $FIELDS{PATHWAY} =~ s/^PATHWAY\s+//; while($FIELDS{PATHWAY} =~ /\s*PATH:\s+(.+)$/mg){ $annotation->add_Annotation('pathway', Bio::Annotation::Comment->new(-text => "$1")); } } if($FIELDS{POSITION}) { $FIELDS{POSITION} =~ s/^POSITION\s+//; $annotation->add_Annotation('position', Bio::Annotation::Comment->new(-text => $FIELDS{POSITION})); } if ($FIELDS{CLASS}) { $FIELDS{CLASS} =~ s/^CLASS\s+//; $FIELDS{'CLASS'} =~ s/\n//g; while($FIELDS{CLASS} =~ /(.*?)\[(\S+):(\S+)\]/g){ my ($pathway,$db,$id) = ($1,$2,$3); $pathway =~ s/\s+/ /g; $pathway =~ s/\s$//g; $pathway =~ s/^\s+//; $annotation->add_Annotation('pathway', Bio::Annotation::Comment->new(-text => $pathway)); $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new( -database => $db, -primary_id => $id)); } } if($FIELDS{DBLINKS}) { $FIELDS{DBLINKS} =~ s/^DBLINKS/ /; while($FIELDS{DBLINKS} =~ /\s+(\S+):\s+(\S+)\n?/gs){ ### modified $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new( -database => $1, -primary_id => $2)) if $1; } } $params{'-alphabet'} = 'dna'; $params{'-seq'} = $nt_seq; $params{'-display_id'} = $name; $params{'-accession_number'} = $entry_id; $params{'-species'} = Bio::Species->new( -common_name => $entry_species); $params{'-annotation'} = $annotation; $builder->add_slot_value(%params); $seq = $builder->make_object(); return $seq; } =head2 write_seq Title : write_seq Note : write_seq() is not implemented for KEGG format output. =cut sub write_seq { shift->throw("write_seq() not implemented for KEGG format output."); } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/largefasta.pm������������������������������������������������������������000444��000766��000024�� 11471�13155576320� 17677� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::largefasta # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # _history # # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::largefasta - method i/o on very large fasta sequence files =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from fasta flat file databases. This module handles very large sequence files by using the Bio::Seq::LargePrimarySeq module to store all the sequence data in a file. This can be a problem if you have limited disk space on your computer because this will effectively cause 2 copies of the sequence file to reside on disk for the life of the Bio::Seq::LargePrimarySeq object. The default location for this is specified by the L<File::Spec>-E<gt>tmpdir routine which is usually /tmp on UNIX. If a sequence file is larger than the swap space (capacity of the /tmp dir) this could cause problems for the machine. It is possible to set the directory where the temporary file is located by adding the following line to your code BEFORE calling next_seq. See L<Bio::Seq::LargePrimarySeq> for more information. $Bio::Seq::LargePrimarySeq::DEFAULT_TEMP_DIR = 'newdir'; =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Jason Stajich Email: jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::largefasta; use vars qw($FASTALINELEN); use strict; use Bio::Seq::SeqFactory; $FASTALINELEN = 60; use base qw(Bio::SeqIO); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::LargePrimarySeq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : A Bio::Seq::LargePrimarySeq object Args : NONE =cut sub next_seq { my ($self) = @_; # local $/ = "\n"; my $largeseq = $self->sequence_factory->create(); my ($id,$fulldesc,$entry); my $count = 0; my $seen = 0; while( defined ($entry = $self->_readline) ) { if( $seen == 1 && $entry =~ /^\s*>/ ) { $self->_pushback($entry); return $largeseq; } # if ( ($entry eq '>') || eof($self->_fh) ) { $seen = 1; next; } if ( ($entry eq '>') ) { $seen = 1; next; } elsif( $entry =~ /\s*>(.+?)$/ ) { $seen = 1; ($id,$fulldesc) = ($1 =~ /^\s*(\S+)\s*(.*)$/) or $self->warn("Can't parse fasta header"); $largeseq->display_id($id); $largeseq->primary_id($id); $largeseq->desc($fulldesc); } else { $entry =~ s/\s+//g; $largeseq->add_sequence_as_string($entry); } (++$count % 1000 == 0 && $self->verbose() > 0) && print "line $count\n"; } return unless $seen; return $largeseq; } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object =cut sub write_seq { my ($self,@seq) = @_; foreach my $seq (@seq) { my $top = $seq->id(); if ($seq->can('desc') and my $desc = $seq->desc()) { $desc =~ s/\n//g; $top .= " $desc"; } $self->_print (">",$top,"\n"); my $end = $seq->length(); my $start = 1; while( $start <= $end ) { my $stop = $start + $FASTALINELEN - 1; $stop = $end if( $stop > $end ); $self->_print($seq->subseq($start,$stop), "\n"); $start += $FASTALINELEN; } } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/lasergene.pm�������������������������������������������������������������000444��000766��000024�� 10111�13155576320� 17521� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������#-----------------------------------------5~------------------------------------ # PACKAGE : Bio::SeqIO::lasergene # AUTHOR : Malcolm Cook <mec@stowers-institute.org> # CREATED : Feb 16 1999 # # _History_ # # This code is based on the Bio::SeqIO::raw module with # the necessary minor tweaks necessary to get it to read (only) # Lasergene formatted sequences # # Cleaned up by Torsten Seemann June 2006 # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::lasergene - Lasergene sequence file input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L<Bio::SeqIO> class. =head1 DESCRIPTION This object can product Bio::Seq::RichSeq objects from Lasergene sequence files. IT DOES NOT PARSE ANY ATTRIBUTE VALUE PAIRS IN THE HEADER OF THE LASERGENE FORMATTED FILE. IT DOES NOT WRITE THESE FILES EITHER. =head1 REFERENCES https://www.dnastar.com/products/lasergene.php =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Torsten Seemann - torsten.seemann AT infotech.monash.edu.au Malcolm Cook - mec AT stowers-institute.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::lasergene; use strict; use base qw(Bio::SeqIO); =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : none =cut use Bio::Seq; use Bio::Annotation::Collection; use Bio::Annotation::Comment; sub next_seq { my ($self) = @_; my $state = 0; my @comment; my @sequence; while (my $line = $self->_readline) { $state = 1 if $state == 0; chomp $line; next if $line =~ m/^\s*$/; # skip blank lines if ($line eq '^^') { # end of a comment or sequence $state++; last if $state > 2; # we have comment and sequence so exit } elsif ($state == 1) { # another piece of comment push @comment, $line; } elsif ($state == 2) { # another piece of sequence push @sequence, $line } else { $self->throw("unreachable state reached, probable bug!"); } } # return quietly if there was nothing in the file return if $state == 0; # ensure we read some comment and some sequence if ($state < 2) { $self->throw("unexpected end of file"); } my $sequence = join('', @sequence); # print STDERR "SEQ=[[$sequence]]\n"; $sequence or $self->throw("empty sequence in lasergene file"); my $seq = Bio::Seq->new(-seq => $sequence); my $comment = join('; ', @comment); # print STDERR "COM=[[$comment]]\n"; my $anno = Bio::Annotation::Collection->new; $anno->add_Annotation('comment', Bio::Annotation::Comment->new(-text => $comment) ); $seq->annotation($anno); return $seq; } =head2 write_seq (NOT IMPLEMENTED) Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Array of Bio::PrimarySeqI objects =cut sub write_seq { my ($self, @seq) = @_; $self->throw("write_seq() is not implemented for the lasergene format."); } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/locuslink.pm�������������������������������������������������������������000444��000766��000024�� 36130�13155576320� 17570� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::locuslink # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Keith Ching <kching at gnf.org> # # Copyright Keith Ching # # You may distribute this module under the same terms as perl itself # # (c) Keith Ching, kching at gnf.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::locuslink - LocusLink input/output stream =head1 SYNOPSIS # don't instantiate directly - instead do my $seqio = Bio::SeqIO->new(-format => "locuslink", -file => \STDIN); =head1 DESCRIPTION This module parses LocusLink into Bio::SeqI objects with rich annotation, but no sequence. The input file has to be in the LL_tmpl format - the tabular format will not work. The way the current implementation populates the object is rather a draft work than a finished work of art. Note that at this stage the LocusLink entries cannot be round-tripped, because the parser loses certain information. For instance, most of the alternative transcript descriptions are not retained. The parser also misses any element that deals with visual representation (e.g., 'button') except for the URLs. Almost all of the pieces of the annotation are kept in a Bio::Annotation::Collection object, see L<Bio::Annotation::Collection> for more information. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Keith Ching Email kching at gnf.org =head1 CONTRIBUTORS Hilmar Lapp, hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqIO::locuslink; use strict; use Bio::Seq::SeqFactory; use Bio::Species; use Bio::Annotation::DBLink; #use Bio::Annotation::Reference; use Bio::Annotation::Comment; use Bio::Annotation::SimpleValue; use Bio::Annotation::OntologyTerm; use Bio::Annotation::Collection; use base qw(Bio::SeqIO); # list of all the field names in locuslink my @locuslink_keys = qw( ACCNUM ALIAS_PROT ALIAS_SYMBOL ASSEMBLY BUTTON CDD CHR COMP CONTIG CURRENT_LOCUSID DB_DESCR DB_LINK ECNUM EVID EXTANNOT GO GRIF LINK LOCUSID LOCUS_CONFIRMED LOCUS_TYPE MAP MAPLINK NC NG NM NP NR OFFICIAL_GENE_NAME OFFICIAL_SYMBOL OMIM ORGANISM PHENOTYPE PHENOTYPE_ID PMID PREFERRED_GENE_NAME PREFERRED_PRODUCT PREFERRED_SYMBOL PRODUCT PROT RELL STATUS STS SUMFUNC SUMMARY TRANSVAR TYPE UNIGENE XG XM XP XR ); # list of fields to make simple annotations from # fields not listed here or as a key in feature hash are ignored (lost). my %anntype_map = ( SimpleValue => [qw( ALIAS_PROT ALIAS_SYMBOL CDD CHR CURRENT_LOCUSID ECNUM EXTANNOT MAP NC NR OFFICIAL_GENE_NAME OFFICIAL_SYMBOL PHENOTYPE PREFERRED_GENE_NAME PREFERRED_PRODUCT PREFERRED_SYMBOL PRODUCT RELL SUMFUNC ) ], Comment => [qw( SUMMARY ) ], ); # certain fields are not named the same as the symgene database list my %dbname_map = ( pfam => 'Pfam', smart => 'SMART', NM => 'RefSeq', NP => 'RefSeq', XP => 'RefSeq', XM => 'RefSeq', NG => 'RefSeq', XG => 'RefSeq', XR => 'RefSeq', PROT => 'GenBank', ACCNUM => 'GenBank', CONTIG => 'GenBank', # certain fields are not named the same as the symgene # database list: rename the fields the symgene database name # key = field name in locuslink # value = database name in sym #GO => 'GO', OMIM => 'MIM', GRIF => 'GRIF', STS => 'STS', UNIGENE => 'UniGene', ); # certain CDD entries use the wrong prefix for the accession number # cddprefix will replace the key w/ the value for these entries my %cddprefix = ( pfam => 'PF', smart => 'SM', ); # alternate mappings if one field does not exist my %alternate_map = ( OFFICIAL_GENE_NAME => 'PREFERRED_GENE_NAME', OFFICIAL_SYMBOL => 'PREFERRED_SYMBOL', ); # for these field names, we only care about the first value X in value X|Y|Z my @ll_firstelements = qw( NM NP NG XG XM XP XR PROT STS ACCNUM CONTIG GRIF ); # these fields need to be flattened into a single string, using the given # join string my %flatten_tags = ( ASSEMBLY => ',', ORGANISM => '', # this should occur only once OFFICIAL_SYMBOL => '', # this should occur only once OFFICIAL_GENE_NAME => '', # this should occur only once LOCUSID => '', # this should occur only once PMID => ',', PREFERRED_SYMBOL => ', ', PREFERRED_GENE_NAME => ', ' ); # set the default search pattern for all the field names my %feature_pat_map = map { ($_ , "^$_: (.+)\n"); } @locuslink_keys; sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); # overwrite the search pattern w/ the first value pattern foreach my $key(@ll_firstelements){ $feature_pat_map{$key}="^$key: ([^|]+)"; } # special search pattern for cdd entries foreach my $key(keys %cddprefix) { $feature_pat_map{$key}='^CDD: .+\|'.$key.'(\d+)'; } # special patterns for specific fields $feature_pat_map{MAP} = '^MAP: (.+?)\|'; $feature_pat_map{MAPHTML} = '^MAP: .+\|(<.+>)\|'; $feature_pat_map{GO} = '^GO: .+\|.+\|\w+\|(GO:\d+)\|'; $feature_pat_map{GO_DESC} = '^GO: .+\|(.+)\|\w+\|GO:\d+\|'; $feature_pat_map{GO_CAT} = '^GO: (.+)\|.+\|\w+\|GO:\d+\|'; $feature_pat_map{EXTANNOT} = '^EXTANNOT: (.+)\|(.+)\|\w+\|.+\|\d+'; # set the sequence factory of none has been set already if(! $self->sequence_factory()) { $self->sequence_factory(Bio::Seq::SeqFactory->new( -type => 'Bio::Seq::RichSeq')); } } ######################### # sub search_pattern{ # ######################### my ($self, $entry, #text to search $searchconfirm, #to make sure you got the right thing $searchpattern, $searchtype) = @_; my @query = $entry=~/$searchpattern/gm; if ($searchconfirm ne "FALSE"){ $self->warn("No $searchtype found\n$entry\n") unless @query; foreach (@query){ if (!($_=~/$searchconfirm/)){ $self->throw("error\n$entry\n$searchtype parse $_ does not match $searchconfirm\n"); } }#endforeach }#endsearchconfirm return(@query); }#endsub ############ # sub read_species{ # ############ my ($spline)=@_; my $species; my $genus; ($genus,$species)=$spline=~/([^ ]+) ([^ ]+)/; my $make = Bio::Species->new(); $make->classification( ($species,$genus) ); return $make; } ################ # sub read_dblink{ # ################ my ($ann,$db,$ref)=@_; my @results=$ref ? @$ref : (); foreach my $id(@results){ if($id){ $ann->add_Annotation('dblink', Bio::Annotation::DBLink->new( -database =>$db , -primary_id =>$id)); } } return($ann); } ################ # sub read_reference{ # ################ my ($ann,$db,$results)=@_; if($results){ chomp($results); my @ids=split(/,/,$results); $ann = read_dblink($ann,$db,\@ids) if @ids; } return $ann; }#endsub ################ # sub add_annotation{ # ################ my ($ac,$type,$text,$anntype)=@_; my @args; $anntype = 'SimpleValue' unless $anntype; SWITCH : { $anntype eq 'SimpleValue' && do { push(@args, -value => $text, -tagname => $type); last SWITCH; }; $anntype eq 'Comment' && do { push(@args, -text => $text, -tagname => 'comment'); last SWITCH; }; } $ac->add_Annotation("Bio::Annotation::$anntype"->new(@args)); return($ac); }#endsub ################ # sub add_annotation_ref{ # ################ my ($ann,$type,$textref)=@_; my @text=$textref ? @$textref : (); foreach my $text(@text){ $ann->add_Annotation($type,Bio::Annotation::SimpleValue->new(-value => $text)); } return($ann); }#endsub ################ # sub make_unique{ # ############## my ($ann,$key) = @_; my %seen = (); foreach my $dbl ($ann->remove_Annotations($key)) { if(!exists($seen{$dbl->as_text()})) { $seen{$dbl->as_text()} = 1; $ann->add_Annotation($dbl); } } return $ann; } ################ # sub next_seq{ # ############## my ($self, @args)=@_; my (@results,$search,$ref,$cddref); # LOCUSLINK entries begin w/ >> local $/="\n>>"; # slurp in a whole entry and return if no more entries return unless my $entry = $self->_readline; # strip the leading '>>' if it's the first entry if (index($entry,'>>') == 0) { #first entry $entry = substr($entry,2); } # we aren't interested in obsoleted entries, so we need to loop # and skip those until we've found the next not obsoleted my %record = (); while($entry && ($entry =~ /\w/)) { if (!($entry=~/LOCUSID/)){ $self->throw("No LOCUSID in first line of record. ". "Not LocusLink in my book."); } # see whether it's an obsoleted entry, and if so jump to the next # one entry right away if($entry =~ /^CURRENT_LOCUSID:/m) { # read next entry and continue $entry = $self->_readline; %record = (); next; } # loop through list of features and get field values # place into record hash as array refs foreach my $key (keys %feature_pat_map){ $search=$feature_pat_map{$key}; @results=$self->search_pattern($entry,'FALSE',$search,$search); $record{$key} = @results ? [@results] : undef; }#endfor # terminate loop as this one hasn't been obsoleted last; } # we have reached the end-of-file ... return unless %record; # special processing for CDD entries like pfam and smart my ($PRESENT,@keep); foreach my $key(keys %cddprefix){ #print "check CDD $key\n"; if($record{$key}) { @keep=(); foreach my $list (@{$record{$key}}) { # replace AC with correct AC number push(@keep,$cddprefix{$key}.$list); } # replace CDD ref with correctly prefixed AC number $record{$key} = [@keep]; } } # modify CDD references @=(); if($record{CDD}) { @keep=(); foreach my $cdd (@{$record{CDD}}) { $PRESENT = undef; foreach my $key (keys %cddprefix) { if ($cdd=~/$key/){ $PRESENT = 1; last; } } push(@keep,$cdd) if(! $PRESENT); } $record{CDD} = [@keep]; } # create annotation collection - we'll need it now my $ann = Bio::Annotation::Collection->new(); foreach my $field(keys %dbname_map){ $ann=read_dblink($ann,$dbname_map{$field},$record{$field}); } # add GO link as an OntologyTerm annotation if($record{GO}) { for(my $j = 0; $j < @{$record{GO}}; $j++) { my $goann = Bio::Annotation::OntologyTerm->new( -identifier => $record{GO}->[$j], -name => $record{GO_DESC}->[$j], -ontology => $record{GO_CAT}->[$j]); $ann->add_Annotation($goann); } } $ann=add_annotation_ref($ann,'URL',$record{LINK}); $ann=add_annotation_ref($ann,'URL',$record{DB_LINK}); # everything else gets a simple tag or comment value annotation foreach my $anntype (keys %anntype_map) { foreach my $key (@{$anntype_map{$anntype}}){ if($record{$key}){ foreach (@{$record{$key}}){ #print "$key\t\t$_\n"; $ann=add_annotation($ann,$key,$_,$anntype); } } } } # flatten designated attributes into a scalar value foreach my $field (keys %flatten_tags) { if($record{$field}) { $record{$field} = join($flatten_tags{$field}, @{$record{$field}}); } } # annotation that expects the array flattened out $ann=read_reference($ann,'PUBMED',$record{PMID}); if($record{ASSEMBLY}) { my @assembly=split(/,/,$record{ASSEMBLY}); $ann=read_dblink($ann,'GenBank',\@assembly); } # replace fields w/ alternate if original does not exist foreach my $fieldval (keys %alternate_map){ if((! $record{$fieldval}) && ($record{$alternate_map{$fieldval}})){ $record{$fieldval}=$record{$alternate_map{$fieldval}}; } } # presently we can't store types or context of dblinks - therefore # we need to remove duplicates that only differ in context make_unique($ann,'dblink'); # create sequence object (i.e., let seq.factory create one) my $seq = $self->sequence_factory->create( -verbose => $self->verbose(), -accession_number => $record{LOCUSID}, -desc => $record{OFFICIAL_GENE_NAME}, -display_id => $record{OFFICIAL_SYMBOL}, -species => read_species($record{ORGANISM}), -annotation => $ann); # dump out object contents # show_obj([$seq]); return($seq); } ################ # sub show_obj{ # ################ my ($seqlistref)=@_; my @list=@$seqlistref; my $out = Bio::SeqIO->new('-fh' => \*STDOUT, -format => 'genbank' ); my ($ann,@values,$val); foreach my $seq(@list){ $out->write_seq($seq); $ann=$seq->annotation; foreach my $key ( $ann->get_all_annotation_keys() ) { @values = $ann->get_Annotations($key); foreach my $value ( @values ) { # value is an Bio::AnnotationI, and defines a "as_text" method $val=$value->as_text; print "Annotation ",$key,"\t\t",$val,"\n"; } } } }#endsub 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/mbsout.pm����������������������������������������������������������������000444��000766��000024�� 52106�13155576320� 17077� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# POD documentation - main docs before the code =head1 NAME Bio::SeqIO::mbsout - input stream for output by Teshima et al.'s mbs. =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION mbs (Teshima KM, Innan H (2009) mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection. BMC Bioinformatics 10: 166 ) can be found at http://www.biomedcentral.com/1471-2105/10/166/additional/. Currently this object can be used to read output from mbs into seq objects. However, because bioperl has no support for haplotypes created using an infinite sites model (where '1' identifies a derived allele and '0' identifies an ancestral allele), the sequences returned by mbsout are coded using A, T, C and G. To decode the bases, use the sequence conversion table (a hash) returned by get_base_conversion_table(). In the table, 4 and 5 are used when the ancestry is unclear. This should not ever happen when creating files with mbs, but it will be used when creating mbsOUT files from a collection of seq objects ( To be added later ). Alternatively, use get_next_hap() to get a string with 1's and 0's instead of a seq object. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Warren Kretzschmar This module was written by Warren Kretzschmar email: wkretzsch@gmail.com This module grew out of a parser written by Aida Andres. =head1 COPYRIGHT =head2 Public Domain Notice This software/database is ``United States Government Work'' under the terms of the United States Copyright Act. It was written as part of the authors' official duties for the United States Government and thus cannot be copyrighted. This software/database is freely available to the public for use without a copyright notice. Restrictions cannot be placed on its present or future use. Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the National Human Genome Research Institute (NHGRI) and the U.S. Government does not and cannot warrant the performance or results that may be obtained by using this software or data. NHGRI and the U.S. Government disclaims all warranties as to performance, merchantability or fitness for any particular purpose. =head1 METHODS =cut package Bio::SeqIO::mbsout; use version; our $API_VERSION = qv('1.1.3'); use strict; use base qw(Bio::SeqIO); # This ISA Bio::SeqIO object use Bio::Seq::SeqFactory; =head2 INTERNAL METHODS =head3 _initialize Title : _initialize Usage : $stream = Bio::SeqIO::mbsout->new($infile) Function: extracts basic information about the file. Returns : Bio::SeqIO object Args : no_og Details : include 'no_og' flag = 0 if the last population of an mbsout file contains only one haplotype and you want the last haplotype to be treated as the outgroup. =cut sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); unless ( defined $self->sequence_factory ) { $self->sequence_factory( Bio::Seq::SeqFactory->new() ); } # Don't expect mbs to create an outgroup my ($no_og) = $self->_rearrange( [qw(NO_OG)], @args ) || 1; my %initial_values = ( RUNS => undef, SEGSITES => undef, MBS_INFO_LINE => undef, TOT_RUN_HAPS => undef, NEXT_RUN_NUM => undef, # What run is the next hap from? undef = EOF LAST_READ_HAP_NUM => undef, # What did we just read from LAST_READ_POSITIONS => [], LAST_READ_SEGSITES => undef, BUFFER_HAP => undef, NO_OUTGROUP => $no_og, OPTIONS => {}, LAST_READ_ALLELES => [], LAST_READ_TRAJECTORY_FILE => undef, LAST_READ_REPLICATION_OF_TRAJECTORY_FILE => undef, BASE_CONVERSION_TABLE_HASH_REF => { 'A' => 0, 'T' => 1, 'C' => 4, 'G' => 5, }, ); foreach my $key ( keys %initial_values ) { $self->{$key} = $initial_values{$key}; } # If the filehandle is defined open it and read a few lines if ( ref( $self->{_filehandle} ) eq 'GLOB' ) { $self->_read_start(); return $self; } # Otherwise throw a warning else { $self->throw( "No filehandle defined. Please define a file handle through -file when calling mbsout with Bio::SeqIO" ); } } =head3 _read_start Title : _read_start Usage : $stream->_read_start() Function: reads from the filehandle $stream->{_filehandle} all information up to the first haplotype (sequence). Returns : void Args : none =cut sub _read_start { my $self = shift; my $fh_IN = $self->{_filehandle}; # get the first five lines and parse for important info my ($mbs_info_line) = $self->_get_next_clean_hap( $fh_IN, 1, 1 ); my @mbs_info_line = split( /\s+/, $mbs_info_line ); # Parsing the mbs header line shift @mbs_info_line; shift @mbs_info_line; my $tot_run_haps = shift @mbs_info_line; my $runs; # $pop_mut_param_per_site is the population mutation parameter per site. my $pop_mut_param_per_site; # $pop_recomb_param_per_site is the population recombination parameter per # site. my $pop_recomb_param_per_site; # $nsites is length of the simulated region. # $selpos is position of the target site of selection relative to the first # site of the simulated region. my $nsites; my $selpos; # $nfile is number of trajectory files. # $nrep is number of replications for each trajectory. # $traj_filename is initial part of the name of the trajectory files. my $nfiles; my $nreps; my $traj_filename; foreach my $word ( 0 .. $#mbs_info_line ) { if ( $mbs_info_line[$word] eq '-t' ) { $pop_mut_param_per_site = $mbs_info_line[ $word + 1 ]; } elsif ( $mbs_info_line[$word] eq '-r' ) { $pop_recomb_param_per_site = $mbs_info_line[ $word + 1 ]; $selpos = $mbs_info_line[ $word + 2 ]; } elsif ( $mbs_info_line[$word] eq '-s' ) { $nsites = $mbs_info_line[ $word + 1 ]; $selpos = $mbs_info_line[ $word + 2 ]; } elsif ( $mbs_info_line[$word] eq '-f' ) { $nfiles = $mbs_info_line[ $word + 1 ]; $nreps = $mbs_info_line[ $word + 2 ]; $traj_filename = $mbs_info_line[ $word + 3 ]; $runs = $nfiles * $nreps; } else { next; } } # Save mbs info data $self->{RUNS} = $runs; $self->{MBS_INFO_LINE} = $mbs_info_line; $self->{TOT_RUN_HAPS} = $tot_run_haps; $self->{POP_MUT_PARAM_PER_SITE} = $pop_mut_param_per_site; $self->{POP_RECOMB_PARAM_PER_SITE} = $pop_recomb_param_per_site; $self->{NSITES} = $nsites; $self->{SELPOS} = $selpos; $self->{NFILES} = $nfiles; $self->{NREPS} = $nreps; $self->{TRAJ_FILENAME} = $traj_filename; } =head2 Methods to retrieve mbsout data =head3 get_segsites Title : get_segsites Usage : $segsites = $stream->get_segsites() Function: returns the number segsites in the mbsout file (according to the mbsout header line). Returns : scalar Args : NONE =cut sub get_segsites { my $self = shift; if ( defined $self->{SEGSITES} ) { return $self->{SEGSITES}; } else { return $self->get_current_run_segsites; } } =head3 get_current_run_segsites Title : get_current_run_segsites Usage : $segsites = $stream->get_current_run_segsites() Function: returns the number of segsites in the run of the last read haplotype (sequence). Returns : scalar Args : NONE =cut sub get_current_run_segsites { my $self = shift; return $self->{LAST_READ_SEGSITES}; } =head3 get_pop_mut_param_per_site Title : get_pop_mut_param_per_site Usage : $pop_mut_param_per_site = $stream->get_pop_mut_param_per_site() Function: returns 4*N0*mu or the "population mutation parameter per site" Returns : scalar Args : NONE =cut sub get_pop_mut_param_per_site { my $self = shift; return $self->{POP_MUT_PARAM_PER_SITE}; } =head3 get_pop_recomb_param_per_site Title : get_pop_recomb_param_per_site Usage : $pop_recomb_param_per_site = $stream->get_pop_recomb_param_per_site() Function: returns 4*N0*r or the "population recombination parameter per site" Returns : scalar Args : NONE =cut sub get_pop_recomb_param_per_site { my $self = shift; return $self->{POP_RECOMB_PARAM_PER_SITE}; } =head3 get_nsites Title : get_nsites Usage : $nsites = $stream->get_nsites() Function: returns the number of sites simulated by mbs. Returns : scalar Args : NONE =cut sub get_nsites { my $self = shift; return $self->{NSITES}; } =head3 get_selpos Title : get_selpos Usage : $selpos = $stream->get_selpos() Function: returns the location on the chromosome where the allele is located that was selected for by mbs. Returns : scalar Args : NONE =cut sub get_selpos { my $self = shift; return $self->{SELPOS}; } =head3 get_nreps Title : get_nreps Usage : $nreps = $stream->get_nreps() Function: returns the number replications done by mbs on each trajectory file to create the mbsout file. Returns : scalar Args : NONE =cut sub get_nreps { my $self = shift; return $self->{NREPS}; } =head3 get_nfiles Title : get_nfiles Usage : $nfiles = $stream->get_nfiles() Function: returns the number of trajectory files used by mbs to create the mbsout file Returns : scalar Args : NONE =cut sub get_nfiles { my $self = shift; return $self->{NFILES}; } =head3 get_traj_filename Title : get_traj_filename Usage : $traj_filename = $stream->get_traj_filename() Function: returns the prefix of the trajectory files used by mbs to create the mbsout file Returns : scalar Args : NONE =cut sub get_traj_filename { my $self = shift; return $self->{TRAJ_FILENAME}; } =head3 get_runs Title : get_runs Usage : $runs = $stream->get_runs() Function: returns the number of runs in the mbsout file Returns : scalar Args : NONE =cut sub get_runs { my $self = shift; return $self->{RUNS}; } =head3 get_Positions Title : get_Positions Usage : @positions = $stream->get_Positions() Function: returns an array of the names of each segsite of the run of the last read hap. Returns : array Args : NONE =cut sub get_Positions { my $self = shift; return @{ $self->{LAST_READ_POSITIONS} }; } =head3 get_tot_run_haps Title : get_tot_run_haps Usage : $number_of_haps_per_run = $stream->get_tot_run_haps() Function: returns the number of haplotypes (sequences) in each run of the mbsout file. Returns : scalar >= 0 Args : NONE =cut sub get_tot_run_haps { my $self = shift; return $self->{TOT_RUN_HAPS}; } =head3 get_mbs_info_line Title : get_mbs_info_line Usage : $mbs_info_line = $stream->get_mbs_info_line() Function: returns the header line of the mbsout file. Returns : scalar Args : NONE =cut sub get_mbs_info_line { my $self = shift; return $self->{MBS_INFO_LINE}; } =head3 tot_haps Title : tot_haps Usage : $number_of_haplotypes_in_file = $stream->tot_haps() Function: returns the number of haplotypes (sequences) in the mbsout file. Information gathered from mbsout header line. Returns : scalar Args : NONE =cut sub get_tot_haps { my $self = shift; return ( $self->{TOT_RUN_HAPS} * $self->{RUNS} ); } =head3 next_run_num Title : next_run_num Usage : $next_run_number = $stream->next_run_num() Function: returns the number of the mbs run that the next haplotype (sequence) will be taken from (starting at 1). Returns undef if the complete file has been read. Returns : scalar > 0 or undef Args : NONE =cut sub get_next_run_num { my $self = shift; return $self->{NEXT_RUN_NUM}; } =head3 get_last_haps_run_num Title : get_last_haps_run_num Usage : $last_haps_run_number = $stream->get_last_haps_run_num() Function: returns the number of the ms run that the last haplotype (sequence) was taken from (starting at 1). Returns undef if no hap has been read yet. Returns : scalar > 0 or undef Args : NONE =cut sub get_last_haps_run_num { my $self = shift; return $self->{LAST_HAPS_RUN_NUM}; } =head3 get_last_read_hap_num Title : get_last_read_hap_num Usage : $last_read_hap_num = $stream->get_last_read_hap_num() Function: returns the number (starting with 1) of the last haplotype read from the mbs file Returns : scalar >= 0 Args : NONE Details : 0 means that no haplotype has been read yet. =cut sub get_last_read_hap_num { my $self = shift; return $self->{LAST_READ_HAP_NUM}; } =head3 outgroup Title : outgroup Usage : $outgroup = $stream->outgroup() Function: returns '1' if the mbsout object has an outgroup. Returns '0' otherwise. Returns : 1 or 0, currently always 0 Args : NONE Details : This method will return '1' only if the last population in the mbsout file contains only one haplotype. If the last population is not an outgroup then create the mbsout object using 'no_outgroup' as input parameter for new() (see mbsout->new()). Currently there exists no way of introducing an outgroup into an mbs file, so this function will always return '0'. =cut sub outgroup { my $self = shift; if ( $self->{NO_OUTGROUP} ) { return 0; } else { return 0; } } =head3 get_next_seq Title : get_next_seq Usage : $seq = $stream->get_next_seq() Function: reads and returns the next sequence (haplotype) in the stream Returns : Bio::Seq object Args : NONE Note : This function is included only to conform to convention. It only calls next_hap() and passes on that method's return value. Use next_hap() instead for better performance. =cut sub get_next_seq { my $self = shift; my $seqstring = $self->get_next_hap; return unless defined $seqstring; # Used to create unique ID; my $run = $self->get_last_haps_run_num; # Converting numbers to letters so that the haplotypes can be stored as a # seq object my $rh_base_conversion_table = $self->get_base_conversion_table; foreach my $base ( keys %{$rh_base_conversion_table} ) { $seqstring =~ s/($rh_base_conversion_table->{$base})/$base/g; } my $last_read_hap = $self->get_last_read_hap_num; my $id = 'Hap_' . $last_read_hap . '_Run_' . $run; my $description = 'Segsites ' . $self->get_current_run_segsites . "; Positions $self->positions; Haplotype " . $last_read_hap . '; Run ' . $run . ';'; my $seq = $self->sequence_factory->create( -seq => $seqstring, -id => $id, -desc => $description, -alphabet => q(dna), -direct => 1, ); return $seq; } =head3 get_next_hap Title : get_next_hap Usage : $seq = $stream->get_next_hap() Function: reads and returns the next sequence (haplotype) in the stream. Returns void if all sequences in stream have been read. Returns : Bio::Seq object Args : NONE Note : Use this instead of get_next_seq(). =cut sub get_next_hap { my $self = shift; # Let's figure out how many haps to read from the input file so that # we get back to the beginning of the next run. my $end_run = 0; if ( $self->{TOT_RUN_HAPS} == $self->{LAST_READ_HAP_NUM} + 1 ) { $end_run = 1; } # Setting last_haps_run_num $self->{LAST_HAPS_RUN_NUM} = $self->get_next_run_num; my $fh_IN = $self->{_filehandle}; my ($seqstring) = $self->_get_next_clean_hap( $self->{_filehandle}, 1, $end_run ); return $seqstring; } =head3 get_next_run Title : get_next_run Usage : @seqs = $stream->get_next_run() Function: reads and returns all the remaining sequences (haplotypes) in the mbs run of the next sequence. Returns : array of Bio::Seq objects Args : NONE =cut sub get_next_run { my $self = shift; # Let's figure out how many haps to read from the input file so that # we get back to the beginning of the next run. my $haps_to_pull = $self->{TOT_RUN_HAPS} - $self->{LAST_READ_HAP_NUM}; # Read those haps from the input file # Next hap read will be the first hap of the next run. my @seqs; for ( 1 .. $haps_to_pull ) { my $seq = $self->get_next_seq; next unless defined $seq; push @seqs, $seq; } return @seqs; } =head2 METHODS TO RETRIEVE CONSTANTS =head3 base_conversion_table Title : get_base_conversion_table Usage : $table_hash_ref = $stream->get_base_conversion_table() Function: returns a reference to a hash. The keys of the hash are the letters 'A','T','G','C'. The values associated with each key are the value that each letter in the sequence of a seq object returned by a Bio::SeqIO::mbsout stream should be translated to. Returns : reference to a hash Args : NONE Synopsis: # retrieve the Bio::Seq object's sequence my $haplotype = $seq->seq; my $rh_base_conversion_table = $stream->get_base_conversion_table(); # need to convert all letters to their corresponding numbers. foreach my $base (keys %{$rh_base_conversion_table}){ $haplotype =~ s/($base)/$rh_base_conversion_table->{$base}/g; } # $haplotype is now an ms style haplotype. (e.g. '100101101455') =cut sub get_base_conversion_table { my $self = shift; return $self->{BASE_CONVERSION_TABLE_HASH_REF}; } ############################################################################## ## subs for internal use only ############################################################################## sub _get_next_clean_hap { #By Warren Kretzschmar # return the next non-empty line from file handle (chomped line) # skipps to the next run if '//' is encountered my ( $self, $fh, $times, $end_run ) = @_; my @data; unless ( defined $fh ) { return; } unless ( defined $times && $times > 0 ) { $times = 1; } if ( defined $self->{BUFFER_HAP} ) { push @data, $self->{BUFFER_HAP}; $self->{BUFFER_HAP} = undef; $self->{LAST_READ_HAP_NUM}++; $times--; } while ( 1 <= $times-- ) { # Find next clean line my $data = <$fh>; last if !defined($data); chomp $data; while ( $data !~ /./ ) { $data = <$fh>; chomp $data; } # If the next run is encountered here, then we have a programming # or format error if ( $data eq '//' ) { $self->throw("'//' found when not expected\n") } $self->{LAST_READ_HAP_NUM}++; push @data, $data; } if ($end_run) { $self->_load_run_info($fh); } return (@data); } sub _load_run_info { my ( $self, $fh ) = @_; my $data = <$fh>; # In this case we are at EOF if ( !defined($data) ) { $self->{NEXT_RUN_NUM} = undef; return; } chomp $data; while ( $data !~ /./ ) { $data = <$fh>; # In this case we are at EOF if ( !defined($data) ) { $self->{NEXT_RUN_NUM} = undef; return; } chomp $data; } # If the next run is encountered, then skip to the next hap and save it in # the buffer. if ( $data =~ /^\/\// ) { $self->{NEXT_RUN_NUM}++; $self->{LAST_READ_HAP_NUM} = 0; my @data = split( /\s+/, $data ); my @temp = split( /\/\//, $data[0] ); @temp = split( /-/, $temp[0] ); $self->{LAST_READ_TRAJ_FILE} = $temp[0]; $self->{LAST_LEAD_TRAJ_FILE_REPLICATION} = $temp[1]; $self->{LAST_READ_ALLELES} = \@data[ 2 .. $#data ]; for ( 1 .. 3 ) { $data = <$fh>; while ( $data !~ /./ ) { $data = <$fh>; } chomp $data; @data = split( /\s+/, $data ); if ( $_ eq '1' ) { $self->{LAST_READ_SEGSITES} = $data[1]; } elsif ( $_ eq '2' ) { $self->{LAST_READ_POSITIONS} = [ @data[ 1 .. $#data ] ]; } else { if ( !defined($data) ) { $self->throw("run $self->{NEXT_RUN_NUM} has no haps./n"); } $self->{BUFFER_HAP} = $data; } } } else { $self->throw("'//' not encountered when expected\n") } } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/metafasta.pm�������������������������������������������������������������000444��000766��000024�� 14430�13155576320� 17531� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::metafasta # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::metafasta - metafasta sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. use Bio::SeqIO; # read the metafasta file $io = Bio::SeqIO->new(-file => "test.metafasta", -format => "metafasta" ); $seq = $io->next_seq; =head1 DESCRIPTION This object can transform Bio::Seq::Meta objects to and from metafasta flat file databases. For sequence part the code is an exact copy of Bio::SeqIO::fasta module. The only added bits deal with meta data IO. The format of a metafasta file is >test ABCDEFHIJKLMNOPQRSTUVWXYZ &charge NBNAANCNJCNNNONNCNNUNNXNZ &chemical LBSAARCLJCLSMOIMCHHULRXRZ where the sequence block is followed by one or several meta blocks. Each meta block starts with the ampersand character '&' in the first column and is immediately followed by the name of the meta data which continues until the new line. The meta data follows it. All characters, except new line, are important in meta data. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::metafasta; use vars qw($WIDTH); use strict; use Bio::Seq::SeqFactory; use Bio::Seq::SeqFastaSpeedFactory; use Bio::Seq::Meta; use base qw(Bio::SeqIO); BEGIN { $WIDTH = 60} sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); my ($width) = $self->_rearrange([qw(WIDTH)], @args); $width && $self->width($width); unless ( defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFastaSpeedFactory->new()); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : NONE =cut sub next_seq { my( $self ) = @_; my $seq; my $alphabet; local $/ = "\n>"; return unless my $entry = $self->_readline; chomp($entry); if ($entry =~ m/\A\s*\Z/s) { # very first one return unless $entry = $self->_readline; chomp($entry); } $entry =~ s/^>//; my ($top,$sequence) = split(/\n/,$entry,2); defined $sequence && $sequence =~ s/>//g; my @metas; ($sequence, @metas) = split /\n&/, $sequence; my ($id,$fulldesc); if( $top =~ /^\s*(\S+)\s*(.*)/ ) { ($id,$fulldesc) = ($1,$2); } if (defined $id && $id eq '') {$id=$fulldesc;} # FIX incase no space # between > and name \AE defined $sequence && $sequence =~ s/\s//g; # Remove whitespace # for empty sequences we need to know the mol.type $alphabet = $self->alphabet(); if(defined $sequence && length($sequence) == 0) { if(! defined($alphabet)) { # let's default to dna $alphabet = "dna"; } } else { # we don't need it really, so disable $alphabet = undef; } $seq = $self->sequence_factory->create( -seq => $sequence, -id => $id, # Ewan's note - I don't think this healthy # but obviously to taste. #-primary_id => $id, -desc => $fulldesc, -alphabet => $alphabet, -direct => 1, ); $seq = $seq->primary_seq; bless $seq, 'Bio::Seq::Meta'; foreach my $meta (@metas) { my ($name,$string) = split /\n/, $meta; # $split ||= ''; $string =~ s/\n//g; # Remove newlines, spaces are important $seq->named_meta($name, $string); } # if there wasn't one before, set the guessed type unless ( defined $alphabet ) { $self->alphabet($seq->alphabet()); } return $seq; } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : array of 1 to n Bio::PrimarySeqI objects =cut sub write_seq { my ($self,@seq) = @_; my $width = $self->width; foreach my $seq (@seq) { $self->throw("Did not provide a valid Bio::PrimarySeqI object") unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI'); my $str = $seq->seq; my $top = $seq->display_id(); if ($seq->can('desc') and my $desc = $seq->desc()) { $desc =~ s/\n//g; $top .= " $desc"; } if(length($str) > 0) { $str =~ s/(.{1,$width})/$1\n/g; } else { $str = "\n"; } $self->_print (">",$top,"\n",$str) or return; if ($seq->isa('Bio::Seq::MetaI')) { foreach my $meta ($seq->meta_names) { my $str = $seq->named_meta($meta); $str =~ s/(.{1,$width})/$1\n/g; $self->_print ("&",$meta,"\n",$str); } } } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 width Title : width Usage : $obj->width($newval) Function: Get/Set the line width for METAFASTA output Returns : value of width Args : newvalue (optional) =cut sub width{ my ($self,$value) = @_; if( defined $value) { $self->{'width'} = $value; } return $self->{'width'} || $WIDTH; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/msout.pm�����������������������������������������������������������������000444��000766��000024�� 62017�13155576320� 16737� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# POD documentation - main docs before the code =head1 NAME Bio::SeqIO::msout - input stream for output by Hudson's ms =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION ms ( Hudson, R. R. (2002) Generating samples under a Wright-Fisher neutral model. Bioinformatics 18:337-8 ) can be found at http://home.uchicago.edu/~rhudson1/source/mksamples.html. Currently, this object can be used to read output from ms into seq objects. However, because bioperl has no support for haplotypes created using an infinite sites model (where '1' identifies a derived allele and '0' identifies an ancestral allele), the sequences returned by msout are coded using A, T, C and G. To decode the bases, use the sequence conversion table (a hash) returned by get_base_conversion_table(). In the table, 4 and 5 are used when the ancestry is unclear. This should not ever happen when creating files with ms, but it will be used when creating msOUT files from a collection of seq objects ( To be added later ). Alternatively, use get_next_hap() to get a string with 1's and 0's instead of a seq object. =head2 Mapping to Finite Sites This object can now also be used to map haplotypes created using an infinite sites model to sequences of arbitrary finite length. See set_n_sites() for more detail. Thanks to Filipe G. Vieira <fgvieira@berkeley.edu> for the idea and code. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Warren Kretzschmar This module was written by Warren Kretzschmar email: wkretzsch@gmail.com This module grew out of a parser written by Aida Andres. =head1 COPYRIGHT =head2 Public Domain Notice This software/database is ``United States Government Work'' under the terms of the United States Copyright Act. It was written as part of the authors' official duties for the United States Government and thus cannot be copyrighted. This software/database is freely available to the public for use without a copyright notice. Restrictions cannot be placed on its present or future use. Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the National Human Genome Research Institute (NHGRI) and the U.S. Government does not and cannot warrant the performance or results that may be obtained by using this software or data. NHGRI and the U.S. Government disclaims all warranties as to performance, merchantability or fitness for any particular purpose. =head1 METHODS =cut package Bio::SeqIO::msout; use version; our $API_VERSION = qv('1.1.8'); use strict; use base qw(Bio::SeqIO); # This ISA Bio::SeqIO object use Bio::Seq::SeqFactory; =head2 Methods for Internal Use =head3 _initialize Title : _initialize Usage : $stream = Bio::SeqIO::msOUT->new($infile) Function: extracts basic information about the file. Returns : Bio::SeqIO object Args : no_og, gunzip, gzip, n_sites Details : - include 'no_og' flag if the last population of an msout file contains only one haplotype and you don't want the last haplotype to be treated as the outgroup ( suggested when reading data created by ms ). - including 'n_sites' (positive integer) causes all output haplotypes to be mapped to a sequence of length 'n_sites'. See set_n_sites() for more details. =cut sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); unless ( defined $self->sequence_factory ) { $self->sequence_factory( Bio::Seq::SeqFactory->new() ); } my ($no_og) = $self->_rearrange( [qw(NO_OG)], @args ); my ($n_sites) = $self->_rearrange( [qw(N_SITES)], @args ); my %initial_values = ( RUNS => undef, N_SITES => undef, SEGSITES => undef, SEEDS => [], MS_INFO_LINE => undef, TOT_RUN_HAPS => undef, POPS => [], NEXT_RUN_NUM => undef, # What run is the next hap from? undef = EOF LAST_READ_HAP_NUM => undef, # What did we just read from LAST_HAPS_RUN_NUM => undef, LAST_READ_POSITIONS => [], LAST_READ_SEGSITES => undef, BUFFER_HAP => undef, NO_OUTGROUP => $no_og, BASE_CONVERSION_TABLE_HASH_REF => { 'A' => 0, 'T' => 1, 'C' => 4, 'G' => 5, }, ); foreach my $key ( keys %initial_values ) { $self->{$key} = $initial_values{$key}; } $self->set_n_sites($n_sites); # If the filehandle is defined open it and read a few lines if ( ref( $self->{_filehandle} ) eq 'GLOB' ) { $self->_read_start(); return $self; } # Otherwise throw a warning else { $self->throw( "No filehandle defined. Please define a file handle through -file when calling msout with Bio::SeqIO" ); } } =head3 _read_start Title : _read_start Usage : $stream->_read_start() Function: reads from the filehandle $stream->{_filehandle} all information up to the first haplotype (sequence). Closes the filehandle if all lines have been read. Returns : void Args : none =cut sub _read_start { my $self = shift; my $fh_IN = $self->{_filehandle}; # get the first five lines and parse for important info my ( $ms_info_line, $seeds ) = $self->_get_next_clean_hap( $fh_IN, 2, 1 ); my @ms_info_line = split( /\s+/, $ms_info_line ); my ( $tot_pops, @pop_haplos ); # Parsing the ms header line shift @ms_info_line; my $tot_run_haps = shift @ms_info_line; my $runs = shift @ms_info_line; my $segsites; foreach my $word ( 0 .. $#ms_info_line ) { if ( $ms_info_line[$word] eq '-I' ) { $tot_pops = $ms_info_line[ $word + 1 ]; for my $pop_num ( 1 .. $tot_pops ) { push @pop_haplos, $ms_info_line[ $word + 1 + $pop_num ]; } # if @pop_haplos contains a non-digit, then there is an error in the msinfo line. if ( !defined $pop_haplos[-1] || $pop_haplos[-1] =~ /\D/ ) { $self->throw( "Incorrect number of populations in the ms info line (after the -I specifier)" ); } } elsif ( $ms_info_line[$word] eq '-s' ) { $segsites = $ms_info_line[ $word + 1 ]; } else { next; } } unless (@pop_haplos) { @pop_haplos = ($tot_run_haps) } my @seeds = split( /\s+/, $seeds ); # Save ms info data $self->{RUNS} = $runs; $self->{SEGSITES} = $segsites; $self->{SEEDS} = \@seeds; $self->{MS_INFO_LINE} = $ms_info_line; $self->{TOT_RUN_HAPS} = $tot_run_haps; $self->{POPS} = [@pop_haplos]; return; } =head2 Methods to Access Data =head3 get_segsites Title : get_segsites Usage : $segsites = $stream->get_segsites() Function: returns the number of segsites in the msOUT file (according to the msOUT header line's -s option), or the current run's segsites if -s was not specified in the command line (in this case the number of segsites varies from run to run). Returns : scalar Args : NONE =cut sub get_segsites { my $self = shift; if ( defined $self->{SEGSITES} ) { return $self->{SEGSITES}; } else { return $self->get_current_run_segsites; } } =head3 get_current_run_segsites Title : get_current_run_segsites Usage : $segsites = $stream->get_current_run_segsites() Function: returns the number of segsites in the run of the last read haplotype (sequence). Returns : scalar Args : NONE =cut sub get_current_run_segsites { my $self = shift; return $self->{LAST_READ_SEGSITES}; } =head3 get_n_sites Title : get_n_sites Usage : $n_sites = $stream->get_n_sites() Function: Gets the number of total sites (variable or not) to be output. Returns : scalar if n_sites option is defined at call time of new() Args : NONE Note : WARNING: Final sequence length might not be equal to n_sites if n_sites is too close to number of segregating sites in the msout file. =cut sub get_n_sites { my ($self) = @_; return $self->{N_SITES}; } =head3 set_n_sites Title : set_n_sites Usage : $n_sites = $stream->set_n_sites($value) Function: Sets the number of total sites (variable or not) to be output. Returns : 1 on success; throws an error if $value is not a positive integer or undef Args : positive integer Note : WARNING: Final sequence length might not be equal to n_sites if it is too close to number of segregating sites. - n_sites needs to be at least as large as the number of segsites of the next haplotype returned - n_sites may also be set to undef, in which case haplotypes are returned under the infinite sites model assumptions. =cut sub set_n_sites { my ( $self, $value ) = @_; # make sure $value is a positive integer if it is defined if ( defined $value ) { $self->throw( "first argument needs to be a positive integer. argument supplied: $value" ) unless ( $value =~ m/^\d+$/ && $value > 0 ); } $self->{N_SITES} = $value; return 1; } =head3 get_runs Title : get_runs Usage : $runs = $stream->get_runs() Function: returns the number of runs in the msOUT file (according to the msinfo line) Returns : scalar Args : NONE =cut sub get_runs { my $self = shift; return $self->{RUNS}; } =head3 get_Seeds Title : get_Seeds Usage : @seeds = $stream->get_Seeds() Function: returns an array of the seeds used in the creation of the msOUT file. Returns : array Args : NONE Details : In older versions, ms used three seeds. Newer versions of ms seem to use only one (longer) seed. This function will return all the seeds found. =cut sub get_Seeds { my $self = shift; return @{ $self->{SEEDS} }; } =head3 get_Positions Title : get_Positions Usage : @positions = $stream->get_Positions() Function: returns an array of the names of each segsite of the run of the last read hap. Returns : array Args : NONE Details : The Positions may or may not vary from run to run depending on the options used with ms. =cut sub get_Positions { my $self = shift; return @{ $self->{LAST_READ_POSITIONS} }; } =head3 get_tot_run_haps Title : get_tot_run_haps Usage : $number_of_haps_per_run = $stream->get_tot_run_haps() Function: returns the number of haplotypes (sequences) in each run of the msOUT file ( according to the msinfo line ). Returns : scalar >= 0 Args : NONE Details : This number should not vary from run to run. =cut sub get_tot_run_haps { my $self = shift; return $self->{TOT_RUN_HAPS}; } =head3 get_ms_info_line Title : get_ms_info_line Usage : $ms_info_line = $stream->get_ms_info_line() Function: returns the header line of the msOUT file. Returns : scalar Args : NONE =cut sub get_ms_info_line { my $self = shift; return $self->{MS_INFO_LINE}; } =head3 tot_haps Title : tot_haps Usage : $number_of_haplotypes_in_file = $stream->tot_haps() Function: returns the number of haplotypes (sequences) in the msOUT file. Information gathered from msOUT header line. Returns : scalar Args : NONE =cut sub get_tot_haps { my $self = shift; return ( $self->{TOT_RUN_HAPS} * $self->{RUNS} ); } =head3 get_Pops Title : get_Pops Usage : @pops = $stream->pops() Function: returns an array of population sizes (order taken from the -I flag in the msOUT header line). This array will include the last hap even if it looks like an outgroup. Returns : array of scalars > 0 Args : NONE =cut sub get_Pops { my $self = shift; return @{ $self->{POPS} }; } =head3 get_next_run_num Title : get_next_run_num Usage : $next_run_number = $stream->next_run_num() Function: returns the number of the ms run that the next haplotype (sequence) will be taken from (starting at 1). Returns undef if the complete file has been read. Returns : scalar > 0 or undef Args : NONE =cut sub get_next_run_num { my $self = shift; return $self->{NEXT_RUN_NUM}; } =head3 get_last_haps_run_num Title : get_last_haps_run_num Usage : $last_haps_run_number = $stream->get_last_haps_run_num() Function: returns the number of the ms run that the last haplotype (sequence) was taken from (starting at 1). Returns undef if no hap has been read yet. Returns : scalar > 0 or undef Args : NONE =cut sub get_last_haps_run_num { my $self = shift; return $self->{LAST_HAPS_RUN_NUM}; } =head3 get_last_read_hap_num Title : get_last_read_hap_num Usage : $last_read_hap_num = $stream->get_last_read_hap_num() Function: returns the number (starting with 1) of the last haplotype read from the ms file Returns : scalar >= 0 Args : NONE Details : 0 means that no haplotype has been read yet. Is reset to 0 every run. =cut sub get_last_read_hap_num { my $self = shift; return $self->{LAST_READ_HAP_NUM}; } =head3 outgroup Title : outgroup Usage : $outgroup = $stream->outgroup() Function: returns '1' if the msOUT stream has an outgroup. Returns '0' otherwise. Returns : '1' or '0' Args : NONE Details : This method will return '1' only if the last population in the msOUT file contains only one haplotype. If the last population is not an outgroup then create the msOUT object using 'no_og' as input flag. Also, return 0, if the run has only one population. =cut sub outgroup { my $self = shift; my @pops = $self->get_Pops; if ( $pops[$#pops] == 1 && !defined $self->{NO_OUTGROUP} && @pops > 1 ) { return 1; } else { return 0; } } =head3 get_next_haps_pop_num Title : get_next_haps_pop_num Usage : ($next_haps_pop_num, $num_haps_left_in_pop) = $stream->get_next_haps_pop_num() Function: First return value is the population number (starting with 1) the next hap will come from. The second return value is the number of haps left to read in the population from which the next hap will come. Returns : (scalar > 0, scalar > 0) Args : NONE =cut sub get_next_haps_pop_num { my $self = shift; my $last_read_hap = $self->get_last_read_hap_num; my @pops = $self->get_Pops; foreach my $pop_num ( 0 .. $#pops ) { if ( $last_read_hap < $pops[$pop_num] ) { return ( $pop_num + 1, $pops[$pop_num] - $last_read_hap ); } else { $last_read_hap -= $pops[$pop_num] } } # In this case we're at the beginning of the next run return ( 1, $pops[0] ); } =head3 get_next_seq Title : get_next_seq Usage : $seq = $stream->get_next_seq() Function: reads and returns the next sequence (haplotype) in the stream Returns : Bio::Seq object or void if end of file Args : NONE Note : This function is included only to conform to convention. The returned Bio::Seq object holds a halpotype in coded form. Use the hash returned by get_base_conversion_table() to convert 'A', 'T', 'C', 'G' back into 1,2,4 and 5. Use get_next_hap() to retrieve the halptoype as a string of 1,2,4 and 5s instead. =cut sub get_next_seq { my $self = shift; my $seqstring = $self->get_next_hap; return unless ($seqstring); # Used to create unique ID; my $run = $self->get_last_haps_run_num; # Converting numbers to letters so that the haplotypes can be stored as a # seq object my $rh_base_conversion_table = $self->get_base_conversion_table; foreach my $base ( keys %{$rh_base_conversion_table} ) { $seqstring =~ s/($rh_base_conversion_table->{$base})/$base/g; } # Fill in non-variable positions my $segsites = $self->get_current_run_segsites; my $n_sites = $self->get_n_sites; if ( defined($n_sites) ) { # make sure that n_sites is at least as large # as segsites for each run. Throw an exception otherwise. $self->throw( "n_sites:\t$n_sites" . "\nsegsites:\t$segsites" . "\nrun:\t$run" . "\nn_sites needs to be at least the number of segsites of every run" ) unless $segsites <= $n_sites; my $seq_len = 0; my @seq; my @pos = $self->get_Positions; for ( my $i = 0 ; $i <= $#pos ; $i++ ) { $pos[$i] *= $n_sites; push( @seq, "A" x ( $pos[$i] - 1 - $seq_len ) ); $seq_len += length( $seq[-1] ); push( @seq, substr( $seqstring, $i, 1 ) ); $seq_len += length( $seq[-1] ); } push( @seq, "A" x ( $n_sites - $seq_len ) ); $seqstring = join( "", @seq ); } my $last_read_hap = $self->get_last_read_hap_num; my $id = 'Hap_' . $last_read_hap . '_Run_' . $run; my $description = "Segsites $segsites;" . " Positions " . ( defined $n_sites ? $n_sites : $segsites ) . ";" . " Haplotype $last_read_hap;" . " Run $run;"; my $seq = $self->sequence_factory->create( -seq => $seqstring, -id => $id, -desc => $description, -alphabet => q(dna), -direct => 1, ); return $seq } =head3 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: Alias to get_next_seq() Returns : Bio::Seq object or void if end of file Args : NONE Note : This function is only included for convention. It calls get_next_seq(). See get_next_seq() for details. =cut sub next_seq { my $self = shift; return $self->get_next_seq(); } =head3 get_next_hap Title : get_next_hap Usage : $hap = $stream->next_hap() Function: reads and returns the next sequence (haplotype) in the stream. Returns undef if all sequences in stream have been read. Returns : Haplotype string (e.g. '110110000101101045454000101' Args : NONE Note : Use get_next_seq() if you want the halpotype returned as a Bio::Seq object. =cut sub get_next_hap { my $self = shift; # Let's figure out how many haps to read from the input file so that # we get back to the beginning of the next run. my $end_run = 0; if ( $self->{TOT_RUN_HAPS} == $self->{LAST_READ_HAP_NUM} + 1 ) { $end_run = 1; } # Setting last_haps_run_num $self->{LAST_HAPS_RUN_NUM} = $self->get_next_run_num; my $last_read_hap = $self->get_last_read_hap_num; my ($seqstring) = $self->_get_next_clean_hap( $self->{_filehandle}, 1, $end_run ); if ( !defined $seqstring && $last_read_hap < $self->get_tot_haps ) { $self->throw( "msout file has only $last_read_hap hap(s), which is less than indicated in msinfo line ( " . $self->get_tot_haps . " )" ); } return $seqstring; } =head3 get_next_pop Title : get_next_pop Usage : @seqs = $stream->next_pop() Function: reads and returns all the remaining sequences (haplotypes) in the population of the next sequence. Returns an empty list if no more haps remain to be read in the stream Returns : array of Bio::Seq objects Args : NONE =cut sub get_next_pop { my $self = shift; # Let's figure out how many haps to read from the input file so that # we get back to the beginning of the next run. my @pops = $self->get_Pops; my @seqs; # holds Bio::Seq objects to return # Determine number of the pop that the next hap will be taken from my ( $next_haps_pop_num, $haps_to_pull ) = $self->get_next_haps_pop_num; # If $haps_to_pull == 0, then we need to pull the whole population if ( $haps_to_pull == 0 ) { $haps_to_pull = $pops[ $next_haps_pop_num - 1 ]; } for ( 1 .. $haps_to_pull ) { my $seq = $self->get_next_seq; next unless defined $seq; # Add Population number information to description $seq->display_id(" Population number $next_haps_pop_num;"); push @seqs, $seq; } return @seqs; } =head3 next_run Title : next_run Usage : @seqs = $stream->next_run() Function: reads and returns all the remaining sequences (haplotypes) in the ms run of the next sequence. Returns an empty list if all haps have been read from the stream. Returns : array of Bio::Seq objects Args : NONE =cut sub get_next_run { my $self = shift; # Let's figure out how many haps to read from the input file so that # we get back to the beginning of the next run. my ( $next_haps_pop_num, $haps_to_pull ) = $self->get_next_haps_pop_num; my @seqs; my @pops = $self->get_Pops; foreach ( $next_haps_pop_num .. $#pops ) { $haps_to_pull += $pops[$_]; } # Read those haps from the input file # Next hap read will be the first hap of the first pop of the next run. for ( 1 .. $haps_to_pull ) { my $seq = $self->get_next_seq; next unless defined $seq; push @seqs, $seq; } return @seqs; } =head2 Methods to Retrieve Constants =head3 base_conversion_table Title : get_base_conversion_table Usage : $table_hash_ref = $stream->get_base_conversion_table() Function: returns a reference to a hash. The keys of the hash are the letters ' A','T','G','C'. The values associated with each key are the value that each letter in the sequence of a seq object returned by a Bio::SeqIO::msout stream should be translated to. Returns : reference to a hash Args : NONE Synopsis: # retrieve the Bio::Seq object's sequence my $haplotype = $seq->seq; # need to convert all letters to their corresponding numbers. foreach my $base (keys %{$rh_base_conversion_table}){ $haplotype =~ s/($base)/$rh_base_conversion_table->{$base}/g; } # $haplotype is now an ms style haplotype. (e.g. '100101101455') =cut sub get_base_conversion_table { my $self = shift; return $self->{BASE_CONVERSION_TABLE_HASH_REF}; } ############################################################################## ## subs for internal use only ############################################################################## sub _get_next_clean_hap { #By Warren Kretzschmar # return the next non-empty line from file handle (chomped line) # skipps to the next run if '//' is encountered my ( $self, $fh, $times, $end_run ) = @_; my @data; unless ( ref($fh) eq q(GLOB) ) { return; } unless ( defined $times && $times > 0 ) { $times = 1; } if ( defined $self->{BUFFER_HAP} ) { push @data, $self->{BUFFER_HAP}; $self->{BUFFER_HAP} = undef; $self->{LAST_READ_HAP_NUM}++; $times--; } while ( 1 <= $times-- ) { # Find next clean line my $data = <$fh>; last if !defined($data); chomp $data; while ( $data !~ /./ ) { $data = <$fh>; chomp $data; } # If the next run is encountered here, then we have a programming # or format error if ( $data eq '//' ) { $self->throw("'//' found when not expected\n") } $self->{LAST_READ_HAP_NUM}++; push @data, $data; } if ($end_run) { $self->_load_run_info($fh); } return (@data); } sub _load_run_info { my ( $self, $fh ) = @_; my $data = <$fh>; # getting rid of excess newlines while ( defined($data) && $data !~ /./ ) { $data = <$fh>; } # In this case we are at EOF if ( !defined($data) ) { $self->{NEXT_RUN_NUM} = undef; return; } while ( $data !~ /./ ) { $data = <$fh>; chomp $data; } chomp $data; # If the next run is encountered, then skip to the next hap and save it in # the buffer. if ( $data eq '//' ) { $self->{NEXT_RUN_NUM}++; $self->{LAST_READ_HAP_NUM} = 0; for ( 1 .. 3 ) { $data = <$fh>; while ( $data !~ /./ ) { $data = <$fh>; chomp $data; } chomp $data; if ( $_ eq '1' ) { my @sites = split( /\s+/, $data ); $self->{LAST_READ_SEGSITES} = $sites[1]; } elsif ( $_ eq '2' ) { my @positions = split( /\s+/, $data ); shift @positions; $self->{LAST_READ_POSITIONS} = \@positions; } else { if ( !defined($data) ) { $self->throw("run $self->{NEXT_RUN_NUM} has no haps./n"); } $self->{BUFFER_HAP} = $data; } } } else { $self->throw( "'//' not encountered when expected. There are more haplos in one of the msOUT runs than advertised in the msinfo line." ); } } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/nexml.pm�����������������������������������������������������������������000444��000766��000024�� 12052�13155576320� 16705� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::nexml # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chase Miller <chmille4@gmail.com> # # Copyright Chase Miller # # You may distribute this module under the same terms as perl itself # _history # May, 2009 Largely written by Chase Miller # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::nexml - NeXML sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from NeXML format. For more information on the NeXML standard, visit L<http://www.nexml.org>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Chase Miller Email: chmille4@gmail.com =head1 CONTRIBUTORS Mark Jensen, maj@fortinbras.us Rutger Vos, rutgeraldo@gmail.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::nexml; use strict; use lib '../..'; use Bio::Seq; use Bio::Seq::SeqFactory; use Bio::Nexml::Factory; use Bio::Phylo::IO qw (parse unparse); use base qw(Bio::SeqIO); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); $self->{_doc} = undef; } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : L<Bio::Seq> object Args : NONE =cut sub next_seq { my ($self) = @_; unless ( $self->{'_parsed'} ) { #use a parse function to load all the sequence objects found in the nexml file at once $self->_parse; } return $self->{'_seqs'}->[ $self->{'_seqiter'}++ ]; } =head2 rewind Title : rewind Usage : $seqio->rewind Function: Resets the stream Returns : none Args : none =cut sub rewind { my $self = shift; $self->{'_seqiter'} = 0; } =head2 doc Title : doc Usage : $treeio->doc Function: Returns the biophylo nexml document object Returns : Bio::Phylo::Project Args : none or Bio::Phylo::Project object =cut sub doc { my ($obj,$value) = @_; if( defined $value) { $obj->{'_doc'} = $value; } return $obj->{'_doc'}; } sub _parse { my ($self) = @_; $self->{'_parsed'} = 1; $self->{'_seqiter'} = 0; my $fac = Bio::Nexml::Factory->new(); # Only pass filename if filehandle is not available, # or "Bio::Phylo" will create a new filehandle that ends # out of scope and can't be closed directly, leaving 2 open # filehandles for the same file (so file can't be deleted) my $file_arg; my $file_value; if ( exists $self->{'_filehandle'} and defined $self->{'_filehandle'} ) { $file_arg = '-handle'; $file_value = $self->{'_filehandle'}; } else { $file_arg = '-file'; $file_value = $self->{'_file'}; } $self->doc(Bio::Phylo::IO->parse( $file_arg => $file_value, '-format' => 'nexml', '-as_project' => '1' ) ); $self->{'_seqs'} = $fac->create_bperl_seq($self); unless(@{ $self->{'_seqs'} } == 0) { # self->debug("no seqs in $self->{_file}"); } } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: Writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Array of 1 or more L<Bio::PrimarySeqI> objects =cut sub write_seq { my ($self, $bp_seq) = @_; my $fac = Bio::Nexml::Factory->new(); my $taxa = $fac->create_bphylo_taxa($bp_seq); my ($seq) = $fac->create_bphylo_seq($bp_seq, $taxa); my $matrix = Bio::Phylo::Factory->create_matrix('-type' => $seq->get_type()); $matrix->insert($seq); $matrix->set_taxa($taxa); #set matrix label my $feat = ($bp_seq->get_SeqFeatures())[0]; $matrix->set_name($feat->get_tag_values('matrix_label')); $self->doc(Bio::Phylo::Factory->create_project()); $self->doc->insert($matrix); my $ret = $self->_print($self->doc->to_xml()); $self->flush; return $ret } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/phd.pm�������������������������������������������������������������������000444��000766��000024�� 31141�13155576320� 16335� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # Copyright (c) 1997-2001 bioperl, Chad Matsalla. All Rights Reserved. # This module is free software; you can redistribute it and/or # modify it under the same terms as Perl itself. # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::phd - phd file input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L<Bio::SeqIO> class. =head1 DESCRIPTION This object can transform .phd files (from Phil Green's phred basecaller) to and from Bio::Seq::Quality objects. The phd format is described in section 10 at this url: http://www.phrap.org/phredphrap/phred.html =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Chad Matsalla Chad Matsalla bioinformatics@dieselwurks.com =head1 CONTRIBUTORS Jason Stajich, jason@bioperl.org Jean-Marc Frigerio, Frigerio@pierroton.inra.fr =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # 'Let the code begin... # package Bio::SeqIO::phd; use strict; use Bio::Seq::SeqFactory; use Bio::Seq::RichSeq; use Bio::Annotation::Collection; use Bio::Annotation::Comment; use Dumpvalue; my $dumper = Dumpvalue->new(); use base qw(Bio::SeqIO); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::Quality')); } } =head2 next_seq Title : next_seq() Usage : $swq = $stream->next_seq() Function: returns the next phred sequence in the stream Returns : Bio::Seq::Quality object Args : NONE =cut sub next_seq { my ($self,@args) = @_; my $seq; while (my $entry = $self->_readline) { chomp $entry; if ($entry =~ /^BEGIN_SEQUENCE\s+(\S+)/) { if (defined $seq) { # done with current sequence $self->_pushback($entry); last; } else { # start new sequence my $id = $1; $seq = $self->sequence_factory->create( -id => $id, -primary_id => $id, -display_id => $id, ); } } elsif ($entry =~ /^BEGIN_COMMENT/) { my $collection = Bio::Annotation::Collection->new; while ($entry = $self->_readline) { chomp $entry; if ($entry =~ /^(\w+):\s+(.+)$/) { my ($name, $content) = ($1, $2); my $comment = Bio::Annotation::Comment->new( -text => $content, -tagname => $name ); $collection->add_Annotation('header',$comment); } elsif ($entry =~ /^END_COMMENT/) { $seq->Bio::Seq::RichSeq::annotation($collection); last; } } } elsif ($entry =~ /^BEGIN_DNA/) { my $dna = ''; my @qualities = (); my @trace_indices = (); while ($entry = $self->_readline) { chomp $entry; if ( $entry =~ /(\S+)\s+(\S+)\s+(\S+)/ ) { # add nucleotide and quality scores to sequence $dna .= $1; push @qualities,$2; push(@trace_indices,$3) if defined $3; # required for phd file } elsif ($entry =~ /^END_DNA/) { # end of sequence, save it $seq->seq($dna); $seq->qual(\@qualities); $seq->trace(\@trace_indices); last; } } } elsif ($entry =~ /^END_SEQUENCE/) { # the sequence may be over, but some other info can come after next; } elsif ($entry =~ /^WR\{/) { # Whole-Read items # Programs like Consed or Autofinish add it to phd file. See doc: # http://www.phrap.org/consed/distributions/README.16.0.txt #my ($type, $nane, $date, $time) = split(' ',$self->_readline); #my $extra_info = ''; #while ($entry = $self->_readline) { # chomp $entry; # last if ($entry =~ /\}/); # $extra_info .= $entry; #} ### fea: save WR somewhere? but where? } } return $seq; } =head2 write_header Title : write_header() Usage : $seqio->write_header() Function: Write out the header (BEGIN_COMMENTS .. END_COMMENT) part of a phd file Returns : nothing Args : a Bio::Seq::Quality object Notes : These are the comments that reside in the header of a phd file at the present time. If not provided by the Bio::Seq::Quality object, the following default values will be used: CHROMAT_FILE : $swq->id() ABI_THUMBPRINT : 0 PHRED_VERSION : 0.980904.e CALL_METHOD : phred QUALITY_LEVELS : 99 TIME : <current time> TRACE_ARRAY_MIN_INDEX : 0 TRACE_ARRAY_MAX_INDEX : unknown CHEM : unknown DYE : unknown =cut sub write_header { my ($self, $swq) = @_; $self->_print("\nBEGIN_COMMENT\n\n"); #defaults my $time = localtime(); for ([CHROMAT_FILE =>$swq->attribute('CHROMAT_FILE')], [ABI_THUMBPRINT => 0], [PHRED_VERSION => '0.980904.e'], [CALL_METHOD => 'phred'], [QUALITY_LEVELS => '99'], [TIME => $time], [TRACE_ARRAY_MIN_INDEX => 0], [TRACE_ARRAY_MAX_INDEX => 'unknown'], [CHEM => 'unknown'], [DYE => 'unknown']) { $swq->attribute($_->[0],$_->[1]) unless $swq->attribute($_->[0]); } my @annot = $swq->annotation->get_Annotations('header'); for (@annot) { $self->_print($_->tagname,": ",$_->text,"\n"); } $self->_print("\nEND_COMMENT\n\n"); $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 write_seq Title : write_seq() Usage : $seqio->write_seq($swq); Function: Write out a phd file. Returns : Nothing. Args : a Bio::Seq::Quality object =cut sub write_seq { my ($self,$swq) = @_; $self->throw("You must pass a Bio::Seq::Quality object to write_seq") unless (ref($swq) eq "Bio::Seq::Quality"); $self->throw("Can't create the phd because the sequence and the quality in the Quality object are of different lengths.") unless $swq->length() ne 'DIFFERENT'; $self->_print("BEGIN_SEQUENCE ".$swq->id()."\n"); $self->write_header($swq); $self->_print("BEGIN_DNA\n"); for my $curr(1 .. $swq->length()) { $self->_print (sprintf("%s %s %s\n", uc($swq->baseat($curr)), $swq->qualat($curr), $swq->trace_index_at($curr))); } $self->_print ("END_DNA\n\nEND_SEQUENCE\n"); $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 attribute Title : attribute() Usage : swq->attribute(name[,value]); Function: Get/Set the name attribute. Returns : a string if 1 param, nothing else. Args : a name or a pair name, value =cut sub Bio::Seq::Quality::attribute { my ($self, $name, $value) = @_; my $collection = $self->annotation; my @annot = $collection->get_Annotations('header'); my %attribute; my $annot; for (@annot) { $attribute{$_->tagname} = $_->display_text; $annot = $_ if $_->tagname eq $name; } unless (defined $attribute{$name}) { #new comment my $comment = Bio::Annotation::Comment->new(-text => $value || 'unknown'); $comment->tagname($name); $collection->add_Annotation('header',$comment); return; } return $attribute{$name} unless (defined $value);#get #print "ATTRIBUTE ",$annot," $name $attribute{$name}\n"; $annot->text($value); #set return; } =head2 chromat_file Title : chromat_file Usage : swq->chromat_file([filename]); Function: Get/Set the CHROMAT_FILE attribute. Returns : a string if 1 param, nothing else. Args : none or a filename =cut sub Bio::Seq::Quality::chromat_file { my ($self,$arg) = @_; return $self->attribute('CHROMAT_FILE',$arg); } =head2 abi_thumbprint Title : abi_thumbprint Usage : swq->abi_thumbprint([value]); Function: Get/Set the ABI_THUMBPRINT attribute. Returns : a string if 1 param, nothing else. Args : none or a value =cut sub Bio::Seq::Quality::abi_thumbprint { my ($self,$arg) = @_; return $self->attribute('ABI_THUMBPRINT',$arg); } =head2 phred_version Title : phred_version Usage : swq->phred_version([value]); Function: Get/Set the PHRED_VERSION attribute. Returns : a string if 1 param, nothing else. Args : none or a value =cut sub Bio::Seq::Quality::phred_version { my ($self,$arg) = @_; return $self->attribute('PHRED_VERSION', $arg); } =head2 call_method Title : call_method Usage : swq->call_method([value]); Function: Get/Set the CALL_METHOD attribute. Returns : a string if 1 param, nothing else. Args : none or a value =cut sub Bio::Seq::Quality::call_method { my ($self,$arg) = @_; return $self->attribute('CALL_METHOD', $arg); } =head2 quality_levels Title : quality_levels Usage : swq->quality_levels([value]); Function: Get/Set the quality_levels attribute. Returns : a string if 1 param, nothing else. Args : none or a value =cut sub Bio::Seq::Quality::quality_levels { my ($self,$arg) = @_; return $self->attribute('QUALITY_LEVELS', $arg); } =head2 trace_array_min_index Title : trace_array_min_index Usage : swq->trace_array_min_index([value]); Function: Get/Set the trace_array_min_index attribute. Returns : a string if 1 param, nothing else. Args : none or a value =cut sub Bio::Seq::Quality::trace_array_min_index { my ($self,$arg) = @_; return $self->attribute('TRACE_ARRAY_MIN_INDEX', $arg); } =head2 trace_array_max_index Title : trace_array_max_index Usage : swq->trace_array_max_index([value]); Function: Get/Set the trace_array_max_index attribute. Returns : a string if 1 param, nothing else. Args : none or a value =cut sub Bio::Seq::Quality::trace_array_max_index { my ($self,$arg) = @_; return $self->attribute('TRACE_ARRAY_MAX_INDEX', $arg); } =head2 chem Title : chem Usage : swq->chem([value]); Function: Get/Set the chem attribute. Returns : a string if 1 param, nothing else. Args : none or a value =cut sub Bio::Seq::Quality::chem { my ($self,$arg) = @_; return $self->attribute('CHEM', $arg); } =head2 dye Title : dye Usage : swq->dye([value]); Function: Get/Set the dye attribute. Returns : a string if 1 param, nothing else. Args : none or a value =cut sub Bio::Seq::Quality::dye { my ($self,$arg) = @_; return $self->attribute('DYE', $arg); } =head2 time Title : time Usage : swq->time([value]); Function: Get/Set the time attribute. Returns : a string if 1 param, nothing else. Args : none or a value =cut sub Bio::Seq::Quality::time { my ($self,$arg) = @_; return $self->attribute('TIME', $arg); } =head2 touch Title : touch Usage : swq->touch(); Function: Set the time attribute to current time. Returns : nothing Args : none =cut sub Bio::Seq::Quality::touch { my $time = localtime(); shift->attribute('TIME',$time); return; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/pir.pm�������������������������������������������������������������������000444��000766��000024�� 11107�13155576320� 16354� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::PIR # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # # _history # October 18, 1999 Largely rewritten by Lincoln Stein # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::pir - PIR sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from pir flat file databases. Note: This does not completely preserve the PIR format - quality information about sequence is currently discarded since bioperl does not have a mechanism for handling these encodings in sequence data. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Aaron Mackey E<lt>amackey@virginia.eduE<gt> Lincoln Stein E<lt>lstein@cshl.orgE<gt> Jason Stajich E<lt>jason@bioperl.orgE<gt> =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::pir; use strict; use Bio::Seq::SeqFactory; use base qw(Bio::SeqIO); our %VALID_TYPE = map {$_ => 1} qw(P1 F1 DL DC RL RC XX); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : NONE =cut sub next_seq { my ($self) = @_; local $/ = "\n>"; return unless my $line = $self->_readline; if ( $line eq '>' ) { # handle the very first one having no comment return unless $line = $self->_readline; } my ( $top, $desc, $seq ) = ( $line =~ /^(.+?)\n(.*?)\n([^>]*)/s ) or $self->throw("Cannot parse entry PIR entry [$line]"); my ( $type, $id ); if ( $top =~ /^>?(\S{2});(\S+)\s*$/ ) { ( $type, $id ) = ( $1, $2 ); if ( ! exists $VALID_TYPE{$type} ) { $self->throw( "PIR stream read attempted without proper two-letter sequence code [ $type ]" ); } } else { $self->throw("Line does not match PIR format [ $line ]"); } # P - indicates complete protein # F - indicates protein fragment # not sure how to stuff these into a Bio object # suitable for writing out. $seq =~ s/\*//g; $seq =~ s/[\(\)\.\/\=\,]//g; $seq =~ s/\s+//g; # get rid of whitespace my ($alphabet) = ('protein'); # TODO - not processing SFS data return $self->sequence_factory->create( -seq => $seq, -primary_id => $id, -id => $id, -desc => $desc, -alphabet => $alphabet ); } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Array of Bio::PrimarySeqI objects =cut sub write_seq { my ($self, @seq) = @_; for my $seq (@seq) { $self->throw("Did not provide a valid Bio::PrimarySeqI object") unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI'); $self->warn("No whitespace allowed in PIR ID [". $seq->display_id. "]") if $seq->display_id =~ /\s/; my $str = $seq->seq(); return unless $self->_print(">P1;".$seq->id(), "\n", $seq->desc(), "\n", $str, "*\n"); } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/pln.pm�������������������������������������������������������������������000444��000766��000024�� 6731�13155576320� 16342� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::pln # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Aaron Mackey <amackey@virginia.edu> # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::pln - pln trace sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from pln trace files. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Aaron Mackey Email: amackey@virginia.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::pln; use vars qw(@ISA $READ_AVAIL); use strict; use Bio::SeqIO; use Bio::Seq::SeqFactory; push @ISA, qw( Bio::SeqIO ); sub BEGIN { eval { require Bio::SeqIO::staden::read; }; if ($@) { $READ_AVAIL = 0; } else { push @ISA, "Bio::SeqIO::staden::read"; $READ_AVAIL = 1; } } sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::Quality')); } unless ($READ_AVAIL) { Bio::Root::Root->throw( -class => 'Bio::Root::SystemException', -text => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!" ); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq::Quality object Args : NONE =cut sub next_seq { my ($self) = @_; my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'pln'); # create the seq object $seq = $self->sequence_factory->create(-seq => $seq, -id => $id, -primary_id => $id, -desc => $desc, -alphabet => 'DNA', -qual => $qual ); return $seq; } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object =cut sub write_seq { my ($self,@seq) = @_; my $fh = $self->_fh; foreach my $seq (@seq) { $self->write_trace($fh, $seq, 'pln'); } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; ���������������������������������������BioPerl-1.007002/Bio/SeqIO/qual.pm������������������������������������������������������������������000444��000766��000024�� 20314�13155576320� 16524� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # Copyright (c) 1997-9 bioperl, Chad Matsalla. All Rights Reserved. # This module is free software; you can redistribute it and/or # modify it under the same terms as Perl itself. # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::qual - .qual file input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class (see L<Bio::SeqIO> for details). my $in_qual = Bio::SeqIO->new(-file => $qualfile, -format => 'qual', -width => $width, -verbose => $verbose); =head1 DESCRIPTION This object can transform .qual (similar to fasta) objects to and from Bio::Seq::Quality objects. See L<Bio::Seq::Quality> for details. Like the fasta module, it can take an argument '-width' to change the number of values per line (defaults to 50). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Chad Matsalla Chad Matsalla bioinformatics@dieselwurks.com =head1 CONTRIBUTORS Jason Stajich, jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::qual; use strict; use Bio::Seq::SeqFactory; use Dumpvalue; my $dumper = Dumpvalue->new(); use base qw(Bio::SeqIO); our $WIDTH = 25; sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); my ($width) = $self->_rearrange([qw(WIDTH)], @args); $width && $self->width($width); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::PrimaryQual')); } } =head2 next_seq() Title : next_seq() Usage : $scf = $stream->next_seq() Function: returns the next scf sequence in the stream Returns : Bio::Seq::PrimaryQual object Notes : Get the next quality sequence from the stream. =cut sub next_seq { my ($self,@args) = @_; my ($qual,$seq); my $alphabet; local $/ = "\n>"; return unless my $entry = $self->_readline; if ($entry eq '>') { # very first one return unless $entry = $self->_readline; } # original: my ($top,$sequence) = $entry =~ /^(.+?)\n([^>]*)/s my ($top,$sequence) = $entry =~ /^(.+?)\n([^>]*)/s or $self->throw("Can't parse entry [$entry]"); my ($id,$fulldesc) = $top =~ /^\s*(\S+)\s*(.*)/ or $self->throw("Can't parse fasta header"); $id =~ s/^>//; # create the seq object $sequence =~ s/\n+/ /g; return $self->sequence_factory->create (-qual => $sequence, -id => $id, -primary_id => $id, -display_id => $id, -desc => $fulldesc ); } =head2 _next_qual Title : _next_qual Usage : $seq = $stream->_next_qual() (but do not do that. Use $stream->next_seq() instead) Function: returns the next quality in the stream Returns : Bio::Seq::PrimaryQual object Args : NONE Notes : An internal method. Gets the next quality in the stream. =cut sub _next_qual { my $qual = next_primary_qual( $_[0], 1 ); return $qual; } =head2 next_primary_qual() Title : next_primary_qual() Usage : $seq = $stream->next_primary_qual() Function: returns the next sequence in the stream Returns : Bio::PrimaryQual object Args : NONE =cut sub next_primary_qual { # print("CSM next_primary_qual!\n"); my( $self, $as_next_qual ) = @_; my ($qual,$seq); local $/ = "\n>"; return unless my $entry = $self->_readline; if ($entry eq '>') { # very first one return unless $entry = $self->_readline; } my ($top,$sequence) = $entry =~ /^(.+?)\n([^>]*)/s or $self->throw("Can't parse entry [$entry]"); my ($id,$fulldesc) = $top =~ /^\s*(\S+)\s*(.*)/ or $self->throw("Can't parse fasta header"); $id =~ s/^>//; # create the seq object $sequence =~ s/\n+/ /g; if ($as_next_qual) { $qual = Bio::Seq::PrimaryQual->new(-qual => $sequence, -id => $id, -primary_id => $id, -display_id => $id, -desc => $fulldesc ); } return $qual; } =head2 width Title : width Usage : $obj->width($newval) Function: Get/Set the number of values per line for FASTA-like output Returns : value of width Args : newvalue (optional) =cut sub width{ my ($self,$value) = @_; if( defined $value) { $self->{'width'} = $value; } return $self->{'width'} || $WIDTH; } =head2 write_seq Title : write_seq Usage : $obj->write_seq( -source => $source, -header => "some information" -oneline => 0); Function: Write out a list of quality values to a fasta-style file. Returns : Nothing. Args : Requires a reference to a Bio::Seq::Quality object or a PrimaryQual object as the -source. Option 1: information for the header. Option 2: whether the quality score should be on a single line or not Notes : If no -header is provided, $obj->id() will be used where $obj is a reference to either a Quality object or a PrimaryQual object. If $source->id() fails, "unknown" will be the header. If the Quality object has $source->length() of "DIFFERENT" (read the pod, luke), write_seq will use the length of the PrimaryQual object within the Quality object. =cut sub write_seq { my ($self,@args) = @_; my $width = $self->width; my ($source, $head, $oneline) = $self->_rearrange([qw(SOURCE HEADER ONELINE)], @args); if (!$source || ( !$source->isa('Bio::Seq::Quality') && !$source->isa('Bio::Seq::PrimaryQual') )) { $self->throw("You must pass a Bio::Seq::Quality or a Bio::Seq::PrimaryQual". " object to write_seq() as a parameter named \"source\""); } my $header = ($source->can("header") && $source->header) ? $source->header : ($source->can("id") && $source->id) ? $source->id : "unknown"; my @quals = $source->qual(); # ::dumpValue(\@quals); my $desc = $source->desc if $source->can('desc'); $desc ||= ''; $self->_print (">$header $desc\n"); my (@slice,$max,$length); $length = $source->length(); if ( not(defined($oneline)) || $oneline == 0) { # $width quality values per line for (my $count = 1; $count<=$length; $count+= $width) { if ($count+$width > $length) { $max = $length; } else { $max = $count+$width-1; } my @slice = @{$source->subqual($count,$max)}; $self->_print (join(' ',@slice), "\n"); } } else { # quality values on a single line my @slice = @{$source->qual}; $self->_print (join(' ',@slice), "\n"); } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; __END__ ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/raw.pm�������������������������������������������������������������������000444��000766��000024�� 13027�13155576320� 16356� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������#----------------------------------------------------------------------------- # PACKAGE : Bio::SeqIO::raw # AUTHOR : Ewan Birney <birney@ebi.ac.uk> # CREATED : Feb 16 1999 # # Copyright (c) 1997-9 bioperl, Ewan Birney. All Rights Reserved. # This module is free software; you can redistribute it and/or # modify it under the same terms as Perl itself. # # _History_ # # Ewan Birney <birney@ebi.ac.uk> developed the SeqIO # schema and the first prototype modules. # # This code is based on his Bio::SeqIO::Fasta module with # the necessary minor tweaks necessary to get it to read # and write raw formatted sequences made by # chris dagdigian <dag@sonsorol.org> # # October 18, 1999 Largely rewritten by Lincoln Stein # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::raw - raw sequence file input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L<Bio::SeqIO> class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from raw flat file databases. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Ewan Birney E<lt>birney@ebi.ac.ukE<gt> Lincoln Stein E<lt>lstein@cshl.orgE<gt> =head1 CONTRIBUTORS Jason Stajich E<lt>jason@bioperl.org<gt> =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::raw; use strict; use Bio::Seq::SeqFactory; use base qw(Bio::SeqIO); our %variant = ( 'multiple' => undef, # default 'single' => undef ); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); my ($variant) = $self->_rearrange([qw(VARIANT)], @args); $variant ||= 'multiple'; $self->variant($variant); $self->{record_separator} = $variant eq 'single' ? undef : $/; if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq')); } $self->variant; } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : =cut sub next_seq{ my ($self,@args) = @_; ## When its 1 sequence per line with no formatting at all, ## grabbing it should be easy :) ## adding an option to assume the file is one sequence local $/ = $self->{record_separator}; my $nextline = $self->_readline(); return unless defined $nextline; my $sequence = uc($nextline); $sequence =~ s/\W//g; return unless $sequence; return $self->sequence_factory->create(-seq => $sequence) if $sequence; } =head2 write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Array of Bio::PrimarySeqI objects =cut sub write_seq { my ($self,@seq) = @_; foreach my $seq (@seq) { $self->throw("Must provide a valid Bio::PrimarySeqI object") unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI'); $self->_print($seq->seq, "\n") or return; } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 write_qual Title : write_qual Usage : $stream->write_qual($seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq::Quality object =cut sub write_qual { my ($self,@seq) = @_; my @qual = (); foreach (@seq) { unless ($_->isa("Bio::Seq::Quality")){ warn("You cannot write raw qualities without supplying a Bio::Seq::". "Quality object! You passed a ".ref($_)."\n"); next; } @qual = @{$_->qual}; if(scalar(@qual) == 0) { $qual[0] = "\n"; } $self->_print (join " ", @qual,"\n") or return; } return 1; } =head2 variant Title : variant Usage : $format = $obj->variant(); Function: Get and set method for the sequence variant. For raw sequence, this indicates whether to treat the input as multiple sequences (the default) or as a single sequence. Current values accepted are: 'single' single sequence 'multiple' multiple sequences (default) Returns : string Args : new value, string =cut # variant() method inherited from Bio::Root::IO # private method for testing record separator sub _separator { shift->{record_separator}; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/scf.pm�������������������������������������������������������������������000444��000766��000024�� 133274�13155576320� 16367� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # Copyright (c) 1997-2001 bioperl, Chad Matsalla. All Rights Reserved. # This module is free software; you can redistribute it and/or # modify it under the same terms as Perl itself. # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::scf - .scf file input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class, see L<Bio::SeqIO> for more information. =head1 DESCRIPTION This object can transform .scf files to and from Bio::Seq::SequenceTrace objects. Mechanisms are present to retrieve trace data from scf files. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Chad Matsalla Chad Matsalla bioinformatics@dieselwurks.com =head1 CONTRIBUTORS Jason Stajich, jason@bioperl.org Tony Cox, avc@sanger.ac.uk Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Nancy Hansen, nhansen at mail.nih.gov =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::scf; use vars qw($DEFAULT_QUALITY); use strict; use Bio::Seq::SeqFactory; use Bio::Seq::SequenceTrace; use Bio::Annotation::Comment; use Dumpvalue; my $dumper = Dumpvalue->new(); $dumper->veryCompact(1); BEGIN { $DEFAULT_QUALITY= 10; } use base qw(Bio::SeqIO); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::Quality')); } binmode $self->_fh; # for the Win32/Mac crowds } =head2 next_seq() Title : next_seq() Usage : $scf = $stream->next_seq() Function: returns the next scf sequence in the stream Returns : a Bio::Seq::SequenceTrace object Args : NONE Notes : Fills the interface specification for SeqIO. The SCF specification does not provide for having more then one sequence in a given scf. So once the filehandle has been open and passed to SeqIO do not expect to run this function more then once on a given scf unless you embraced and extended the SCF standard. SCF comments are accessible through the Bio::SeqI interface method annotation(). =cut #' sub next_seq { my ($self) = @_; my ($seq, $seqc, $fh, $buffer, $offset, $length, $read_bytes, @read, %names); # set up a filehandle to read in the scf return if $self->{_readfile}; $fh = $self->_fh(); unless ($fh) { # simulate the <> function if ( !fileno(ARGV) or eof(ARGV) ) { return unless my $ARGV = shift; open(ARGV,$ARGV) or $self->throw("Could not open $ARGV for SCF stream reading $!"); } $fh = \*ARGV; } return unless read $fh, $buffer, 128; # no exception; probably end of file # now, the master data structure will be the creator my $creator; # he first thing to do is parse the header. This is common # among all versions of scf. # the rest of the the information is different between the # the different versions of scf. $creator->{header} = $self->_get_header($buffer); if ($creator->{header}->{'version'} lt "3.00") { $self->debug("scf.pm is working with a version 2 scf.\n"); # first gather the trace information $length = $creator->{header}->{'samples'} * $creator->{header}->{sample_size}*4; $buffer = $self->read_from_buffer($fh, $buffer, $length, $creator->{header}->{samples_offset}); # @read = unpack "n$length",$buffer; # these traces need to be split # returns a reference to a hash $creator->{traces} = $self->_parse_v2_traces( $buffer,$creator->{header}->{sample_size}); # now go and get the base information $offset = $creator->{header}->{bases_offset}; $length = ($creator->{header}->{bases} * 12); seek $fh,$offset,0; $buffer = $self->read_from_buffer($fh,$buffer,$length,$creator->{header}->{bases_offset}); # now distill the information into its fractions. # the old way : $self->_set_v2_bases($buffer); # ref to an array, ref to a hash, string ($creator->{peak_indices}, $creator->{qualities}, $creator->{sequence}, $creator->{accuracies}) = $self->_parse_v2_bases($buffer); } else { $self->debug("scf.pm is working with a version 3+ scf.\n"); my $transformed_read; my $current_read_position = $creator->{header}->{sample_offset}; $length = $creator->{header}->{'samples'}* $creator->{header}->{sample_size}; # $dumper->dumpValue($creator->{header}); foreach (qw(a c g t)) { $buffer = $self->read_from_buffer($fh,$buffer,$length,$current_read_position); my $byte = "n"; if ($creator->{header}->{sample_size} == 1) { $byte = "c"; } @read = unpack "${byte}${length}",$buffer; # this little spurt of nonsense is because # the trace values are given in the binary # file as unsigned shorts but they really # are signed deltas. 30000 is an arbitrary number # (will there be any traces with a given # point greater then 30000? I hope not. # once the read is read, it must be changed # from relative foreach (@read) { if ($_ > 30000) { $_ -= 65536; } } $transformed_read = $self->_delta(\@read,"backward"); # For 8-bit data we need to emulate a signed/unsigned # cast that is implicit in the C implementations..... if ($creator->{header}->{sample_size} == 1) { foreach (@{$transformed_read}) { $_ += 256 if ($_ < 0); } } $current_read_position += $length; $creator->{'traces'}->{$_} = join(' ',@{$transformed_read}); } # now go and get the peak index information $offset = $creator->{header}->{bases_offset}; $length = ($creator->{header}->{bases} * 4); $buffer = $self->read_from_buffer($fh,$buffer,$length,$offset); $creator->{peak_indices} = $self->_get_v3_peak_indices($buffer); $offset += $length; # now go and get the accuracy information $buffer = $self->read_from_buffer($fh,$buffer,$length,$offset); $creator->{accuracies} = $self->_get_v3_base_accuracies($buffer); # OK, now go and get the base information. $offset += $length; $length = $creator->{header}->{bases}; $buffer = $self->read_from_buffer($fh,$buffer,$length,$offset); $creator->{'sequence'} = unpack("a$length",$buffer); # now, finally, extract the calls from the accuracy information. $creator->{qualities} = $self->_get_v3_quality( $creator->{'sequence'},$creator->{accuracies}); } # now go and get the comment information $offset = $creator->{header}->{comments_offset}; seek $fh,$offset,0; $length = $creator->{header}->{comment_size}; $buffer = $self->read_from_buffer($fh,$buffer,$length); $creator->{comments} = $self->_get_comments($buffer); my @name_comments = grep {$_->tagname() eq 'NAME'} $creator->{comments}->get_Annotations('comment'); my $name_comment; if (@name_comments){ $name_comment = $name_comments[0]->as_text(); $name_comment =~ s/^Comment:\s+//; } my $swq = Bio::Seq::Quality->new( -seq => $creator->{'sequence'}, -qual => $creator->{'qualities'}, -id => $name_comment ); my $returner = Bio::Seq::SequenceTrace->new( -swq => $swq, -trace_a => $creator->{'traces'}->{'a'}, -trace_t => $creator->{'traces'}->{'t'}, -trace_g => $creator->{'traces'}->{'g'}, -trace_c => $creator->{'traces'}->{'c'}, -accuracy_a => $creator->{'accuracies'}->{'a'}, -accuracy_t => $creator->{'accuracies'}->{'t'}, -accuracy_g => $creator->{'accuracies'}->{'g'}, -accuracy_c => $creator->{'accuracies'}->{'c'}, -peak_indices => $creator->{'peak_indices'} ); $returner->annotation($creator->{'comments'}); # add SCF comments $self->{'_readfile'} = 1; return $returner; } =head2 _get_v3_quality() Title : _get_v3_quality() Usage : $self->_get_v3_quality() Function: Set the base qualities from version3 scf Returns : Nothing. Alters $self. Args : None. Notes : =cut #' sub _get_v3_quality { my ($self,$sequence,$accuracies) = @_; my @bases = split//,$sequence; my (@qualities,$currbase,$currqual,$counter); for ($counter=0; $counter <= $#bases ; $counter++) { $currbase = lc($bases[$counter]); if ($currbase eq "a") { $currqual = $accuracies->{'a'}->[$counter]; } elsif ($currbase eq "c") { $currqual = $accuracies->{'c'}->[$counter]; } elsif ($currbase eq "g") { $currqual = $accuracies->{'g'}->[$counter]; } elsif ($currbase eq "t") { $currqual = $accuracies->{'t'}->[$counter]; } else { $currqual = "unknown"; } push @qualities,$currqual; } return \@qualities; } =head2 _get_v3_peak_indices($buffer) Title : _get_v3_peak_indices($buffer) Usage : $self->_get_v3_peak_indices($buffer); Function: Unpacks the base accuracies for version3 scf Returns : Nothing. Alters $self Args : A scalar containing binary data. Notes : =cut sub _get_v3_peak_indices { my ($self,$buffer) = @_; my $length = length($buffer); my @read = unpack "N$length",$buffer; return join(' ',@read); } =head2 _get_v3_base_accuracies($buffer) Title : _get_v3_base_accuracies($buffer) Usage : $self->_get_v3_base_accuracies($buffer) Function: Set the base accuracies for version 3 scf's Returns : Nothing. Alters $self. Args : A scalar containing binary data. Notes : =cut #' sub _get_v3_base_accuracies { my ($self,$buffer) = @_; my $length = length($buffer); my $qlength = $length/4; my $offset = 0; my (@qualities,@sorter,$counter,$round,$last_base,$accuracies,$currbase); foreach $currbase (qw(a c g t)) { my @read; $last_base = $offset + $qlength; for (;$offset < $last_base; $offset += $qlength) { # a bioperler (perhaps me?) changed the unpack string to include 'n' rather than 'C' # on 040322 I think that 'C' is correct. please email chad if you would like to accuse me of being incorrect @read = unpack "C$qlength", substr($buffer,$offset,$qlength); $accuracies->{$currbase} = \@read; } } return $accuracies; } =head2 _get_comments($buffer) Title : _get_comments($buffer) Usage : $self->_get_comments($buffer); Function: Gather the comments section from the scf and parse it into its components. Returns : a Bio::Annotation::Collection object Args : The buffer. It is expected that the buffer contains a binary string for the comments section of an scf file according to the scf file specifications. Notes : =cut sub _get_comments { my ($self,$buffer) = @_; my $comments = Bio::Annotation::Collection->new(); my $size = length($buffer); my $comments_retrieved = unpack "a$size",$buffer; $comments_retrieved =~ s/\0//; my @comments_split = split/\n/,$comments_retrieved; if (@comments_split) { foreach (@comments_split) { /(\w+)=(.*)/; if ($1 && $2) { my ($tagname, $text) = ($1, $2); my $comment_obj = Bio::Annotation::Comment->new( -text => $text, -tagname => $tagname); $comments->add_Annotation('comment', $comment_obj); } } } $self->{'comments'} = $comments; return $comments; } =head2 _get_header() Title : _get_header($buffer) Usage : $self->_get_header($buffer); Function: Gather the header section from the scf and parse it into its components. Returns : Reference to a hash containing the header components. Args : The buffer. It is expected that the buffer contains a binary string for the header section of an scf file according to the scf file specifications. Notes : None. =cut sub _get_header { my ($self,$buffer) = @_; my $header; ($header->{'scf'}, $header->{'samples'}, $header->{'sample_offset'}, $header->{'bases'}, $header->{'bases_left_clip'}, $header->{'bases_right_clip'}, $header->{'bases_offset'}, $header->{'comment_size'}, $header->{'comments_offset'}, $header->{'version'}, $header->{'sample_size'}, $header->{'code_set'}, @{$header->{'header_spare'}} ) = unpack "a4 NNNNNNNN a4 NN N20", $buffer; $self->{'header'} = $header; return $header; } =head2 _parse_v2_bases($buffer) Title : _parse_v2_bases($buffer) Usage : $self->_parse_v2_bases($buffer); Function: Gather the bases section from the scf and parse it into its components. Returns : Args : The buffer. It is expected that the buffer contains a binary string for the bases section of an scf file according to the scf file specifications. Notes : None. =cut sub _parse_v2_bases { my ($self,$buffer) = @_; my $length = length($buffer); my ($offset2,$currbuff,$currbase,$currqual,$sequence,@qualities,@indices); my (@read,$harvester,$accuracies); for ($offset2=0;$offset2<$length;$offset2+=12) { @read = unpack "N C C C C a C3", substr($buffer,$offset2,$length); push @indices,$read[0]; $currbase = lc($read[5]); if ($currbase eq "a") { $currqual = $read[1]; } elsif ($currbase eq "c") { $currqual = $read[2]; } elsif ($currbase eq "g") { $currqual = $read[3]; } elsif ($currbase eq "t") { $currqual = $read[4]; } else { $currqual = "UNKNOWN"; } push @{$accuracies->{"a"}},$read[1]; push @{$accuracies->{"c"}},$read[2]; push @{$accuracies->{"g"}},$read[3]; push @{$accuracies->{"t"}},$read[4]; $sequence .= $currbase; push @qualities,$currqual; } return (\@indices,\@qualities,$sequence,$accuracies) } =head2 _parse_v2_traces(\@traces_array) Title : _pares_v2_traces(\@traces_array) Usage : $self->_parse_v2_traces(\@traces_array); Function: Parses an scf Version2 trace array into its base components. Returns : Nothing. Modifies $self. Args : A reference to an array of the unpacked traces section of an scf version2 file. =cut sub _parse_v2_traces { my ($self,$buffer,$sample_size) = @_; my $byte; if ($sample_size == 1) { $byte = "c"; } else { $byte = "n"; } my $length = CORE::length($buffer); my @read = unpack "${byte}${length}",$buffer; # this will be an array to the reference holding the array my $traces; my $array = 0; for (my $offset2 = 0; $offset2< scalar(@read); $offset2+=4) { push @{$traces->{'a'}},$read[$offset2]; push @{$traces->{'c'}},$read[$offset2+1]; push @{$traces->{'g'}},$read[$offset2+3]; push @{$traces->{'t'}},$read[$offset2+2]; } return $traces; } sub get_trace_deprecated_use_the_sequencetrace_object_instead { # my ($self,$base_channel,$traces) = @_; # $base_channel =~ tr/a-z/A-Z/; # if ($base_channel !~ /A|T|G|C/) { # $self->throw("You tried to ask for a base channel that wasn't A,T,G, or C. Ask for one of those next time."); ##} elsif ($base_channel) { # my @temp = split(' ',$self->{'traces'}->{$base_channel}); #return \@temp; #} } sub _deprecated_get_peak_indices_deprecated_use_the_sequencetrace_object_instead { my ($self) = shift; my @temp = split(' ',$self->{'parsed'}->{'peak_indices'}); return \@temp; } =head2 get_header() Title : get_header() Usage : %header = %{$obj->get_header()}; Function: Return the header for this scf. Returns : A reference to a hash containing the header for this scf. Args : None. Notes : =cut sub get_header { my ($self) = shift; return $self->{'header'}; } =head2 get_comments() Title : get_comments() Usage : %comments = %{$obj->get_comments()}; Function: Return the comments for this scf. Returns : A Bio::Annotation::Collection object Args : None. Notes : =cut sub get_comments { my ($self) = shift; return $self->{'comments'}; } sub _dump_traces_outgoing_deprecated_use_the_sequencetrace_object { my ($self,$transformed) = @_; my (@sA,@sT,@sG,@sC); if ($transformed) { @sA = @{$self->{'text'}->{'t_samples_a'}}; @sC = @{$self->{'text'}->{'t_samples_c'}}; @sG = @{$self->{'text'}->{'t_samples_g'}}; @sT = @{$self->{'text'}->{'t_samples_t'}}; } else { @sA = @{$self->{'text'}->{'samples_a'}}; @sC = @{$self->{'text'}->{'samples_c'}}; @sG = @{$self->{'text'}->{'samples_g'}}; @sT = @{$self->{'text'}->{'samples_t'}}; } print ("Count\ta\tc\tg\tt\n"); for (my $curr=0; $curr < scalar(@sG); $curr++) { print("$curr\t$sA[$curr]\t$sC[$curr]\t$sG[$curr]\t$sT[$curr]\n"); } return; } sub _dump_traces_incoming_deprecated_use_the_sequencetrace_object { # my ($self) = @_; # my (@sA,@sT,@sG,@sC); # @sA = @{$self->{'traces'}->{'A'}}; # @sC = @{$self->{'traces'}->{'C'}}; # @sG = @{$self->{'traces'}->{'G'}}; # @sT = @{$self->{'traces'}->{'T'}}; # @sA = @{$self->get_trace('A')}; # @sC = @{$self->get_trace('C')}; # @sG = @{$self->get_trace('G')}; # @sT = @{$self->get_trace('t')}; # print ("Count\ta\tc\tg\tt\n"); # for (my $curr=0; $curr < scalar(@sG); $curr++) { # print("$curr\t$sA[$curr]\t$sC[$curr]\t$sG[$curr]\t$sT[$curr]\n"); #} #return; } =head2 write_seq Title : write_seq(-target => $swq, <comments>) Usage : $obj->write_seq( -target => $swq, -version => 2, -CONV => "Bioperl-Chads Mighty SCF writer."); Function: Write out an scf. Returns : Nothing. Args : Requires: a reference to a Bio::Seq::Quality object to form the basis for the scf. if -version is provided, it should be "2" or "3". A SCF of that version will be written. Any other arguments are assumed to be comments and are put into the comments section of the scf. Read the specifications for scf to decide what might be good to put in here. Notes : For best results, use a SequenceTrace object. The things that you need to write an scf: a) sequence b) quality c) peak indices d) traces - You _can_ write an scf with just a and b by passing in a Bio::Seq::Quality object- false traces will be synthesized for you. =cut sub write_seq { my ($self,%args) = @_; my %comments; my ($label,$arg); my ($swq) = $self->_rearrange([qw(TARGET)], %args); my $writer_fodder; if (ref($swq) =~ /Bio::Seq::SequenceTrace|Bio::Seq::Quality/) { if (ref($swq) eq "Bio::Seq::Quality") { # this means that the object *has no trace data* # we might as well synthesize some now, ok? $swq = Bio::Seq::SequenceTrace->new( -swq => $swq ); } } else { $self->throw("You must pass a Bio::Seq::Quality or a Bio::Seq::SequenceTrace object to write_seq as a parameter named \"target\""); } # all of the rest of the arguments are comments for the scf foreach $arg (sort keys %args) { next if ($arg =~ /target/i); ($label = $arg) =~ s/^\-//; $writer_fodder->{comments}->{$label} = $args{$arg}; } if (!$comments{'NAME'}) { $comments{'NAME'} = $swq->id(); } # HA! Bwahahahaha. $writer_fodder->{comments}->{'CONV'} = "Bioperl-Chads Mighty SCF writer." unless defined $comments{'CONV'}; # now deal with the version of scf they want to write if ($writer_fodder->{comments}->{version}) { if ($writer_fodder->{comments}->{version} != 2 && $writer_fodder->{comments}->{version} != 3) { $self->warn("This module can only write version 2.0 or 3.0 scf's. Writing a version 2.0 scf by default."); $writer_fodder->{header}->{version} = "2.00"; } elsif ($writer_fodder->{comments}->{'version'} > 2) { $writer_fodder->{header}->{'version'} = "3.00"; } else { $writer_fodder->{header}->{version} = "2"; } } else { $writer_fodder->{header}->{'version'} = "3.00"; } # set a few things in the header $writer_fodder->{'header'}->{'magic'} = ".scf"; $writer_fodder->{'header'}->{'sample_size'} = "2"; $writer_fodder->{'header'}->{'bases'} = length($swq->seq()); $writer_fodder->{'header'}->{'bases_left_clip'} = "0"; $writer_fodder->{'header'}->{'bases_right_clip'} = "0"; $writer_fodder->{'header'}->{'sample_size'} = "2"; $writer_fodder->{'header'}->{'code_set'} = "9"; @{$writer_fodder->{'header'}->{'spare'}} = qw(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0); $writer_fodder->{'header'}->{'samples_offset'} = "128"; $writer_fodder->{'header'}->{'samples'} = $swq->trace_length(); # create the binary for the comments and file it in writer_fodder $writer_fodder->{comments} = $self->_get_binary_comments( $writer_fodder->{comments}); # create the binary and the strings for the traces, bases, # offsets (if necessary), and accuracies (if necessary) $writer_fodder->{traces} = $self->_get_binary_traces( $writer_fodder->{'header'}->{'version'}, $swq,$writer_fodder->{'header'}->{'sample_size'}); my ($b_base_offsets,$b_base_accuracies,$samples_size,$bases_size); # # version 2 # if ($writer_fodder->{'header'}->{'version'} == 2) { $writer_fodder->{bases} = $self->_get_binary_bases( 2, $swq, $writer_fodder->{'header'}->{'sample_size'}); $samples_size = CORE::length($writer_fodder->{traces}->{'binary'}); $bases_size = CORE::length($writer_fodder->{bases}->{binary}); $writer_fodder->{'header'}->{'bases_offset'} = 128 + $samples_size; $writer_fodder->{'header'}->{'comments_offset'} = 128 + $samples_size + $bases_size; $writer_fodder->{'header'}->{'comments_size'} = length($writer_fodder->{'comments'}->{binary}); $writer_fodder->{'header'}->{'private_size'} = "0"; $writer_fodder->{'header'}->{'private_offset'} = 128 + $samples_size + $bases_size + $writer_fodder->{'header'}->{'comments_size'}; $writer_fodder->{'header'}->{'binary'} = $self->_get_binary_header($writer_fodder->{header}); $dumper->dumpValue($writer_fodder) if $self->verbose > 0; $self->_print ($writer_fodder->{'header'}->{'binary'}) or print("Could not write binary header...\n"); $self->_print ($writer_fodder->{'traces'}->{'binary'}) or print("Could not write binary traces...\n"); $self->_print ($writer_fodder->{'bases'}->{'binary'}) or print("Could not write binary base structures...\n"); $self->_print ($writer_fodder->{'comments'}->{'binary'}) or print("Could not write binary comments...\n"); } else { ($writer_fodder->{peak_indices}, $writer_fodder->{accuracies}, $writer_fodder->{bases}, $writer_fodder->{reserved} ) = $self->_get_binary_bases( 3, $swq, $writer_fodder->{'header'}->{'sample_size'} ); $writer_fodder->{'header'}->{'bases_offset'} = 128 + length($writer_fodder->{'traces'}->{'binary'}); $writer_fodder->{'header'}->{'comments_size'} = length($writer_fodder->{'comments'}->{'binary'}); # this is: # bases_offset + base_offsets + accuracies + called_bases + # reserved $writer_fodder->{'header'}->{'private_size'} = "0"; $writer_fodder->{'header'}->{'comments_offset'} = 128+length($writer_fodder->{'traces'}->{'binary'})+ length($writer_fodder->{'peak_indices'}->{'binary'})+ length($writer_fodder->{'accuracies'}->{'binary'})+ length($writer_fodder->{'bases'}->{'binary'})+ length($writer_fodder->{'reserved'}->{'binary'}); $writer_fodder->{'header'}->{'private_offset'} = $writer_fodder->{'header'}->{'comments_offset'} + $writer_fodder->{'header'}->{'comments_size'}; $writer_fodder->{'header'}->{'spare'}->[1] = $writer_fodder->{'header'}->{'comments_offset'} + length($writer_fodder->{'comments'}->{'binary'}); $writer_fodder->{header}->{binary} = $self->_get_binary_header($writer_fodder->{header}); $self->_print ($writer_fodder->{'header'}->{'binary'}) or print("Couldn't write header\n"); $self->_print ($writer_fodder->{'traces'}->{'binary'}) or print("Couldn't write samples\n"); $self->_print ($writer_fodder->{'peak_indices'}->{'binary'}) or print("Couldn't write peak offsets\n"); $self->_print ($writer_fodder->{'accuracies'}->{'binary'}) or print("Couldn't write accuracies\n"); $self->_print ($writer_fodder->{'bases'}->{'binary'}) or print("Couldn't write called_bases\n"); $self->_print ($writer_fodder->{'reserved'}->{'binary'}) or print("Couldn't write reserved\n"); $self->_print ($writer_fodder->{'comments'}->{'binary'}) or print ("Couldn't write comments\n"); } # kinda unnecessary, given the close() below, but maybe that'll go # away someday. $self->flush if $self->_flush_on_write && defined $self->_fh; $self->close(); return 1; } =head2 _get_binary_header() Title : _get_binary_header(); Usage : $self->_get_binary_header(); Function: Provide the binary string that will be used as the header for a scfv2 document. Returns : A binary string. Args : None. Uses the entries in the $self->{'header'} hash. These are set on construction of the object (hopefully correctly!). Notes : =cut sub _get_binary_header { my ($self,$header) = @_; my $binary = pack "a4 NNNNNNNN a4 NN N20", ( $header->{'magic'}, $header->{'samples'}, $header->{'samples_offset'}, $header->{'bases'}, $header->{'bases_left_clip'}, $header->{'bases_right_clip'}, $header->{'bases_offset'}, $header->{'comments_size'}, $header->{'comments_offset'}, $header->{'version'}, $header->{'sample_size'}, $header->{'code_set'}, @{$header->{'spare'}} ); return $binary; } =head2 _get_binary_traces($version,$ref) Title : _set_binary_tracesbases($version,$ref) Usage : $self->_set_binary_tracesbases($version,$ref); Function: Constructs the trace and base strings for all scfs Returns : Nothing. Alters self. Args : $version - "2" or "3" $sequence - a scalar containing arbitrary sequence data $ref - a reference to either a SequenceTraces or a SequenceWithQuality object. Notes : This is a really complicated thing. =cut sub _get_binary_traces { my ($self,$version,$ref,$sample_size) = @_; # ref _should_ be a Bio::Seq::SequenceTrace, but might be a # Bio::Seq::Quality my $returner; my $sequence = $ref->seq(); my $sequence_length = length($sequence); # first of all, do we need to synthesize the trace? # if so, call synthesize_base my ($traceobj,@traces,$current); if ( ref($ref) eq "Bio::Seq::Quality" ) { $traceobj = Bio::Seq::Quality->new( -target => $ref ); $traceobj->_synthesize_traces(); } else { $traceobj = $ref; if ($version eq "2") { my $trace_length = $traceobj->trace_length(); for ($current = 1; $current <= $trace_length; $current++) { foreach (qw(a c g t)) { push @traces,$traceobj->trace_value_at($_,$current); } } } elsif ($version == 3) { foreach my $current_trace (qw(a c g t)) { my @trace = @{$traceobj->trace($current_trace)}; foreach (@trace) { if ($_ > 30000) { $_ -= 65536; } } my $transformed = $self->_delta(\@trace,"forward"); if($sample_size == 1){ foreach (@{$transformed}) { $_ += 256 if ($_ < 0); } } push @traces,@{$transformed}; } } } $returner->{version} = $version; $returner->{string} = \@traces; my $length_of_traces = scalar(@traces); my $byte; if ($sample_size == 1) { $byte = "c"; } else { $byte = "n"; } # an unsigned integer should be I, but this is too long # $returner->{binary} = pack "n${length_of_traces}",@traces; $returner->{length} = CORE::length($returner->{binary}); return $returner; } sub _get_binary_bases { my ($self,$version,$trace,$sample_size) = @_; my $byte; if ($sample_size == 1) { $byte = "c"; } else { $byte = "n"; } my ($returner,@current_row,$current_base,$string,$binary); my $length = $trace->length(); if ($version == 2) { $returner->{'version'} = "2"; for (my $current_base =1; $current_base <= $length; $current_base++) { my @current_row; push @current_row,$trace->peak_index_at($current_base); push @current_row,$trace->accuracy_at("a",$current_base); push @current_row,$trace->accuracy_at("c",$current_base); push @current_row,$trace->accuracy_at("g",$current_base); push @current_row,$trace->accuracy_at("t",$current_base); push @current_row,$trace->baseat($current_base); push @current_row,0,0,0; push @{$returner->{string}},@current_row; $returner->{binary} .= pack "N C C C C a C3",@current_row; } return $returner; } else { $returner->{'version'} = "3.00"; $returner->{peak_indices}->{string} = $trace->peak_indices(); my $length = scalar(@{$returner->{peak_indices}->{string}}); $returner->{peak_indices}->{binary} = pack "N$length",@{$returner->{peak_indices}->{string}}; $returner->{peak_indices}->{length} = CORE::length($returner->{peak_indices}->{binary}); my @accuracies; foreach my $base (qw(a c g t)) { $returner->{accuracies}->{$base} = $trace->accuracies($base); push @accuracies,@{$trace->accuracies($base)}; } $returner->{sequence} = $trace->seq(); $length = scalar(@accuracies); # this really is "c" for samplesize == 2 $returner->{accuracies}->{binary} = pack "C${length}",@accuracies; $returner->{accuracies}->{length} = CORE::length($returner->{accuracies}->{binary}); $length = $trace->seq_obj()->length(); for (my $count=0; $count< $length; $count++) { push @{$returner->{reserved}->{string}},0,0,0; } } $length = scalar(@{$returner->{reserved}->{string}}); # this _must_ be "c" $returner->{'reserved'}->{'binary'} = pack "c$length",@{$returner->{reserved}->{string}}; $returner->{'reserved'}->{'length'} = CORE::length($returner->{'reserved'}->{'binary'}); # $returner->{'bases'}->{'string'} = $trace->seq(); my @bases = split('',$trace->seq()); $length = $trace->length(); $returner->{'bases'}->{'binary'} = $trace->seq(); # print("Returning this:\n"); # $dumper->dumpValue($returner); return ($returner->{peak_indices}, $returner->{accuracies}, $returner->{bases}, $returner->{reserved}); } =head2 _make_trace_string($version) Title : _make_trace_string($version) Usage : $self->_make_trace_string($version) Function: Merges trace data for the four bases to produce an scf trace string. _requires_ $version Returns : Nothing. Alters $self. Args : $version - a version number. "2" or "3" Notes : =cut sub _make_trace_string { my ($self,$version) = @_; my @traces; my @traces_view; my @as = @{$self->{'text'}->{'samples_a'}}; my @cs = @{$self->{'text'}->{'samples_c'}}; my @gs = @{$self->{'text'}->{'samples_g'}}; my @ts = @{$self->{'text'}->{'samples_t'}}; if ($version == 2) { for (my $curr=0; $curr < scalar(@as); $curr++) { $as[$curr] = $DEFAULT_QUALITY unless defined $as[$curr]; $cs[$curr] = $DEFAULT_QUALITY unless defined $cs[$curr]; $gs[$curr] = $DEFAULT_QUALITY unless defined $gs[$curr]; $ts[$curr] = $DEFAULT_QUALITY unless defined $ts[$curr]; push @traces,($as[$curr],$cs[$curr],$gs[$curr],$ts[$curr]); } } elsif ($version == 3) { @traces = (@as,@cs,@gs,@ts); } else { $self->throw("No idea what version required to make traces here. You gave #$version# Bailing."); } my $length = scalar(@traces); $self->{'text'}->{'samples_all'} = \@traces; } =head2 _get_binary_comments(\@comments) Title : _get_binary_comments(\@comments) Usage : $self->_get_binary_comments(\@comments); Function: Provide a binary string that will be the comments section of the scf file. See the scf specifications for detailed specifications for the comments section of an scf file. Hint: CODE=something\nBODE=something\n\0 Returns : Args : A reference to an array containing comments. Notes : None. =cut sub _get_binary_comments { my ($self,$rcomments) = @_; my $returner; my $comments_string = ''; my %comments = %$rcomments; foreach my $key (sort keys %comments) { $comments{$key} ||= ''; $comments_string .= "$key=$comments{$key}\n"; } $comments_string .= "\n\0"; my $length = CORE::length($comments_string); $returner->{length} = $length; $returner->{string} = $comments_string; $returner->{binary} = pack "A$length",$comments_string; return $returner; } #=head2 _fill_missing_data($swq) # # Title : _fill_missing_data($swq) # Usage : $self->_fill_missing_data($swq); # Function: If the $swq with quality has no qualities, set all qualities # to 0. # If the $swq has no sequence, set the sequence to N's. # Returns : Nothing. Modifies the Bio::Seq::Quality that was passed as an # argument. # Args : A reference to a Bio::Seq::Quality # Notes : None. # #=cut # ##' #sub _fill_missing_data { # my ($self,$swq) = @_; # my $qual_obj = $swq->qual_obj(); # my $seq_obj = $swq->seq_obj(); # if ($qual_obj->length() == 0 && $seq_obj->length() != 0) { # my $fake_qualities = ("$DEFAULT_QUALITY ")x$seq_obj->length(); # $swq->qual($fake_qualities); # } # if ($seq_obj->length() == 0 && $qual_obj->length != 0) { # my $sequence = ("N")x$qual_obj->length(); # $swq->seq($sequence); # } #} =head2 _delta(\@trace_data,$direction) Title : _delta(\@trace_data,$direction) Usage : $self->_delta(\@trace_data,$direction); Function: Returns : A reference to an array containing modified trace values. Args : A reference to an array containing trace data and a string indicating the direction of conversion. ("forward" or "backward"). Notes : This code is taken from the specification for SCF3.2. http://www.mrc-lmb.cam.ac.uk/pubseq/manual/formats_unix_4.html =cut sub _delta { my ($self,$rsamples,$direction) = @_; my @samples = @$rsamples; # /* If job == DELTA_IT: # * change a series of sample points to a series of delta delta values: # * ie change them in two steps: # * first: delta = current_value - previous_value # * then: delta_delta = delta - previous_delta # * else # * do the reverse # */ # int i; # uint_2 p_delta, p_sample; my ($i,$num_samples,$p_delta,$p_sample,@samples_converted,$p_sample1,$p_sample2); my $SLOW_BUT_CLEAR = 0; $num_samples = scalar(@samples); # c-programmers are funny people with their single-letter variables if ( $direction eq "forward" ) { if($SLOW_BUT_CLEAR){ $p_delta = 0; for ($i=0; $i < $num_samples; $i++) { $p_sample = $samples[$i]; $samples[$i] = $samples[$i] - $p_delta; $p_delta = $p_sample; } $p_delta = 0; for ($i=0; $i < $num_samples; $i++) { $p_sample = $samples[$i]; $samples[$i] = $samples[$i] - $p_delta; $p_delta = $p_sample; } } else { for ($i = $num_samples-1; $i > 1; $i--){ $samples[$i] = $samples[$i] - 2*$samples[$i-1] + $samples[$i-2]; } $samples[1] = $samples[1] - 2*$samples[0]; } } elsif ($direction eq "backward") { if($SLOW_BUT_CLEAR){ $p_sample = 0; for ($i=0; $i < $num_samples; $i++) { $samples[$i] = $samples[$i] + $p_sample; $p_sample = $samples[$i]; } $p_sample = 0; for ($i=0; $i < $num_samples; $i++) { $samples[$i] = $samples[$i] + $p_sample; $p_sample = $samples[$i]; } } else { $p_sample1 = $p_sample2 = 0; for ($i = 0; $i < $num_samples; $i++){ $p_sample1 = $p_sample1 + $samples[$i]; $samples[$i] = $p_sample1 + $p_sample2; $p_sample2 = $samples[$i]; } } } else { $self->warn("Bad direction. Use \"forward\" or \"backward\"."); } return \@samples; } =head2 _unpack_magik($buffer) Title : _unpack_magik($buffer) Usage : $self->_unpack_magik($buffer) Function: What unpack specification should be used? Try them all. Returns : Nothing. Args : A buffer containing arbitrary binary data. Notes : Eliminate the ambiguity and the guesswork. Used in the adaptation of _delta(), mostly. =cut sub _unpack_magik { my ($self,$buffer) = @_; my $length = length($buffer); my (@read,$counter); foreach (qw(c C s S i I l L n N v V)) { @read = unpack "$_$length", $buffer; for ($counter=0; $counter < 20; $counter++) { print("$read[$counter]\n"); } } } =head2 read_from_buffer($filehandle,$buffer,$length) Title : read_from_buffer($filehandle,$buffer,$length) Usage : $self->read_from_buffer($filehandle,$buffer,$length); Function: Read from the buffer. Returns : $buffer, containing a read of $length Args : a filehandle, a buffer, and a read length Notes : I just got tired of typing "unless (length($buffer) == $length)" so I put it here. =cut sub read_from_buffer { my ($self,$fh,$buffer,$length,$start_position) = @_; # print("Reading from a buffer!!! length($length) "); if ($start_position) { # print(" startposition($start_position)(".sprintf("%X", $start_position).")\n"); } # print("\n"); if ($start_position) { # print("seeking to this position in the file: (".$start_position.")\n"); seek ($fh,$start_position,0); # print("done. here is where I am now: (".tell($fh).")\n"); } else { # print("You did not specify a start position. Going from this position (the current position) (".tell($fh).")\n"); } read $fh, $buffer, $length; unless (length($buffer) == $length) { $self->warn("The read was incomplete! Trying harder."); my $missing_length = $length - length($buffer); my $buffer2; read $fh,$buffer2,$missing_length; $buffer .= $buffer2; if (length($buffer) != $length) { $self->throw("Unexpected end of file while reading from SCF file. I should have read $length but instead got ".length($buffer)."! Current file position is ".tell($fh)."."); } } return $buffer; } =head2 _dump_keys() Title : _dump_keys() Usage : &_dump_keys($a_reference_to_some_hash) Function: Dump out the keys in a hash. Returns : Nothing. Args : A reference to a hash. Notes : A debugging method. =cut sub _dump_keys { my $rhash = shift; if ($rhash !~ /HASH/) { print("_dump_keys: that was not a hash.\nIt was #$rhash# which was this reference:".ref($rhash)."\n"); return; } print("_dump_keys: The keys for $rhash are:\n"); foreach (sort keys %$rhash) { print("$_\n"); } } =head2 _dump_base_accuracies() Title : _dump_base_accuracies() Usage : $self->_dump_base_accuracies(); Function: Dump out the v3 base accuracies in an easy to read format. Returns : Nothing. Args : None. Notes : A debugging method. =cut sub _dump_base_accuracies { my $self = shift; print("Dumping base accuracies! for v3\n"); print("There are this many elements in a,c,g,t:\n"); print(scalar(@{$self->{'text'}->{'v3_base_accuracy_a'}}).",".scalar(@{$self->{'text'}->{'v3_base_accuracy_c'}}).",".scalar(@{$self->{'text'}->{'v3_base_accuracy_g'}}).",".scalar(@{$self->{'text'}->{'v3_base_accuracy_t'}})."\n"); my $number_traces = scalar(@{$self->{'text'}->{'v3_base_accuracy_a'}}); for (my $counter=0; $counter < $number_traces; $counter++ ) { print("$counter\t"); print $self->{'text'}->{'v3_base_accuracy_a'}->[$counter]."\t"; print $self->{'text'}->{'v3_base_accuracy_c'}->[$counter]."\t"; print $self->{'text'}->{'v3_base_accuracy_g'}->[$counter]."\t"; print $self->{'text'}->{'v3_base_accuracy_t'}->[$counter]."\t"; print("\n"); } } =head2 _dump_peak_indices_incoming() Title : _dump_peak_indices_incoming() Usage : $self->_dump_peak_indices_incoming(); Function: Dump out the v3 peak indices in an easy to read format. Returns : Nothing. Args : None. Notes : A debugging method. =cut sub _dump_peak_indices_incoming { my $self = shift; print("Dump peak indices incoming!\n"); my $length = $self->{'bases'}; print("The length is $length\n"); for (my $count=0; $count < $length; $count++) { print("$count\t$self->{parsed}->{peak_indices}->[$count]\n"); } } =head2 _dump_base_accuracies_incoming() Title : _dump_base_accuracies_incoming() Usage : $self->_dump_base_accuracies_incoming(); Function: Dump out the v3 base accuracies in an easy to read format. Returns : Nothing. Args : None. Notes : A debugging method. =cut sub _dump_base_accuracies_incoming { my $self = shift; print("Dumping base accuracies! for v3\n"); # print("There are this many elements in a,c,g,t:\n"); # print(scalar(@{$self->{'parsed'}->{'v3_base_accuracy_a'}}).",".scalar(@{$self->{'text'}->{'v3_base_accuracy_c'}}).",".scalar(@{$self->{'text'}->{'v3_base_accuracy_g'}}).",".scalar(@{$self->{'text'}->{'v3_base_accuracy_t'}})."\n"); my $number_traces = $self->{'bases'}; for (my $counter=0; $counter < $number_traces; $counter++ ) { print("$counter\t"); foreach (qw(A T G C)) { print $self->{'parsed'}->{'base_accuracies'}->{$_}->[$counter]."\t"; } print("\n"); } } =head2 _dump_comments() Title : _dump_comments() Usage : $self->_dump_comments(); Function: Debug dump the comments section from the scf. Returns : Nothing. Args : Nothing. Notes : None. =cut sub _dump_comments { my ($self) = @_; warn ("SCF comments:\n"); foreach my $k (keys %{$self->{'comments'}}) { warn ("\t {$k} ==> ", $self->{'comments'}->{$k}, "\n"); } } 1; __END__ ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/seqxml.pm����������������������������������������������������������������000444��000766��000024�� 70574�13155576320� 17110� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::seqxml # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Dave Messina <dmessina@cpan.org> # # Copyright Dave Messina # # You may distribute this module under the same terms as perl itself # _history # December 2009 - initial version # July 2 2010 - updated for SeqXML v0.2 # November 11 2010 - added schemaLocation # December 9 2010 - SeqXML v0.3 # # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::seqxml - SeqXML sequence input/output stream =head1 SYNOPSIS # Do not use this module directly. Use it via the Bio::SeqIO class. use Bio::SeqIO; # read a SeqXML file my $seqio = Bio::SeqIO->new(-format => 'seqxml', -file => 'my_seqs.xml'); while (my $seq_object = $seqio->next_seq) { print join("\t", $seq_object->display_id, $seq_object->description, $seq_object->seq, ), "\n"; } # write a SeqXML file # # Note that you can (optionally) specify the source # (usually a database) and source version. my $seqwriter = Bio::SeqIO->new(-format => 'seqxml', -file => ">outfile.xml", -source => 'Ensembl', -sourceVersion => '56'); $seqwriter->write_seq($seq_object); # once you've written all of your seqs, you may want to do # an explicit close to get the closing </seqXML> tag $seqwriter->close; =head1 DESCRIPTION This object can transform Bio::Seq objects to and from SeqXML format. For more information on the SeqXML standard, visit L<http://www.seqxml.org>. In short, SeqXML is a lightweight sequence format that takes advantage of the validation capabilities of XML while not overburdening you with a strict and complicated schema. This module is based in part (particularly the XML-parsing part) on Bio::TreeIO::phyloxml by Mira Han. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Dave Messina Email: I<dmessina@cpan.org> =head1 CONTRIBUTORS =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::seqxml; use strict; use Bio::Seq; use Bio::Seq::SeqFactory; use Bio::Species; use Bio::Annotation::DBLink; use Bio::Annotation::SimpleValue; use XML::LibXML; use XML::LibXML::Reader; use XML::Writer; use base qw(Bio::SeqIO); # define seqXML header stuff # there's no API for XMLNS XMLNS_XSI; you must set them here. use constant SEQXML_VERSION => 0.3; use constant SCHEMA_LOCATION => 'http://www.seqxml.org/0.3/seqxml.xsd'; use constant XMLNS_XSI => 'http://www.w3.org/2001/XMLSchema-instance'; =head2 _initialize Title : _initialize Usage : $self->_initialize(@args) Function: constructor (for internal use only). Besides the usual SeqIO arguments (-file, -fh, etc.), Bio::SeqIO::seqxml accepts three arguments which are used when writing out a seqxml file. They are all optional. Returns : none Args : -source => source string (usually a database name) -sourceVersion => source version. The version number of the source -seqXMLversion => the version of seqXML that will be used Throws : Exception if XML::LibXML::Reader or XML::Writer is not initialized =cut sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); if ( !defined $self->sequence_factory ) { $self->sequence_factory( Bio::Seq::SeqFactory->new( -verbose => $self->verbose(), -type => 'Bio::Seq', ) ); } # holds version and source data $self->{'_seqxml_metadata'} = {}; # load any passed parameters my %params = @args; if ($params{'-sourceVersion'}) { $self->sourceVersion($params{'-sourceVersion'}); } if ($params{'-source'}) { $self->source($params{'-source'}); } if ($params{'-seqXMLversion'}) { $self->seqXMLversion($params{'-seqXMLversion'}); } # reading in SeqXML if ( $self->mode eq 'r' ) { if ( $self->_fh ) { $self->{'_reader'} = XML::LibXML::Reader->new( IO => $self->_fh, no_blanks => 1, ); } if ( !$self->{'_reader'} ) { $self->throw("XML::LibXML::Reader not initialized"); } # holds data temporarily during parsing $self->{'_current_entry_data'} = {}; $self->_initialize_seqxml_node_methods(); # read SeqXML header $self->parseHeader(); } # writing out SeqXML elsif ( $self->mode eq 'w' ) { if ( $self->_fh ) { $self->{'_writer'} = XML::Writer->new( OUTPUT => $self->_fh, DATA_MODE => 1, DATA_INDENT => 1, ); if ( !$self->{'_writer'} ) { $self->throw("XML::Writer not initialized"); } # write SeqXML header $self->{'_writer'}->xmlDecl("UTF-8"); if ($self->source || $self->sourceVersion) { $self->{'_writer'}->startTag( 'seqXML', 'seqXMLversion' => $self->seqXMLversion(SEQXML_VERSION), 'xmlns:xsi' => XMLNS_XSI, 'xsi:noNamespaceSchemaLocation' => $self->schemaLocation(SCHEMA_LOCATION), 'source' => $self->source, 'sourceVersion' => $self->sourceVersion, ); } else { $self->{'_writer'}->startTag( 'seqXML', 'seqXMLversion' => $self->seqXMLversion(SEQXML_VERSION), 'xmlns:xsi' => XMLNS_XSI, 'xsi:noNamespaceSchemaLocation' => $self->schemaLocation(SCHEMA_LOCATION), ); } } } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : L<Bio::Seq> object, or nothing if no more available Args : none =cut sub next_seq { my ($self) = @_; my $reader = $self->{'_reader'}; my $entry; while ( $reader->read ) { # we're done if we hit </entry> if ( $reader->nodeType == XML_READER_TYPE_END_ELEMENT ) { if ( $reader->name eq 'entry' ) { $entry = $self->end_element_entry(); last; } } $self->processXMLnode; } return $entry; } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: Writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Array of 1 or more L<Bio::PrimarySeqI> objects =cut sub write_seq { my ( $self, @seqs ) = @_; my $writer = $self->{'_writer'}; foreach my $seqobj (@seqs) { $self->throw("Trying to write with no seq!") unless defined $seqobj; if ( !ref $seqobj || !$seqobj->isa('Bio::SeqI') ) { $self->warn( " $seqobj is not a SeqI compliant module. Attempting to dump, but may fail!" ); } # opening tag, ID, and source (if present -- it's optional) my $id = $seqobj->display_id; my ($source_obj) = $seqobj->get_Annotations('source'); if (defined $source_obj && defined $id) { $writer->startTag( 'entry', 'id' => $id, 'source' => $source_obj->value ); } elsif (defined $id) { $writer->startTag( 'entry', 'id' => $id ); } else { $self->throw(" $seqobj has no ID!"); } # species and NCBI taxID if ( $seqobj->species ) { my $name = $seqobj->species->node_name; my $taxid = $seqobj->species->ncbi_taxid; if ( $name && ( $taxid =~ /[0-9]+/ ) ) { $writer->emptyTag( 'species', 'name' => $name, 'ncbiTaxID' => $taxid ); } else { $self->throw("$seqobj has malformed species data"); } } # description if ( $seqobj->desc ) { $writer->dataElement( 'description', $seqobj->desc ); } # sequence # - throws if seq is empty or missing because having a sequence # is a SeqXML requirement if ( $seqobj->seq ) { # check that there's actually sequence in there unless ( length($seqobj->seq) > 0 ) { $self->throw("sequence entry $id lacks a sequence!"); } my $alphabet = $seqobj->alphabet; my %seqtype = ( 'rna' => 'RNAseq', 'dna' => 'DNAseq', 'protein' => 'AAseq' ); unless ( exists( $seqtype{$alphabet} ) ) { $self->throw("invalid sequence alphabet $alphabet!"); } $writer->dataElement( $seqtype{$alphabet}, $seqobj->seq ); } else { $self->throw("sequence entry $id lacks a sequence!"); } # Database crossreferences my @dblinks = $seqobj->get_Annotations('dblink'); foreach my $dblink (@dblinks) { unless ( $dblink->database && $dblink->primary_id ) { $self->throw("dblink $dblink is malformed"); } if (defined($dblink->type)) { $writer->emptyTag( 'DBRef', 'type' => $dblink->type, 'source' => $dblink->database, 'id' => $dblink->primary_id, ); } else { $writer->emptyTag( 'DBRef', 'source' => $dblink->database, 'id' => $dblink->primary_id, ); } } # properties my @annotations = $seqobj->get_Annotations(); foreach my $annot_obj (@annotations) { next if ( $annot_obj->tagname eq 'dblink' ); next if ( $annot_obj->tagname eq 'source' ); # handled above # SeqXML doesn't support references next if ( $annot_obj->tagname eq 'reference' ); unless ( $annot_obj->tagname ) { $self->throw("property $annot_obj is missing a tagname"); } if ( $annot_obj->value ) { $writer->emptyTag( 'property', 'name' => $annot_obj->tagname, 'value' => $annot_obj->value, ); } else { $writer->emptyTag( 'property', 'name' => $annot_obj->tagname, ); } } # closing tag $writer->endTag('entry'); # make sure it gets written to the file $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } } =head2 _initialize_seqxml_node_methods Title : _initialize_seqxml_node_methods Usage : $self->_initialize_xml_node_methods Function: sets up code ref mapping of each seqXML node type to a method for processing that node type Returns : none Args : none =cut sub _initialize_seqxml_node_methods { my ($self) = @_; my %start_elements = ( 'seqXML' => \&element_seqXML, 'entry' => \&element_entry, 'species' => \&element_species, 'description' => \&element_description, 'RNAseq' => \&element_RNAseq, 'DNAseq' => \&element_DNAseq, 'AAseq' => \&element_AAseq, 'DBRef' => \&element_DBRef, 'property' => \&element_property, ); $self->{'_start_elements'} = \%start_elements; my %end_elements = ( 'seqXML' => \&end_element_default, 'entry' => \&end_element_entry, 'species' => \&end_element_default, 'description' => \&end_element_default, 'RNAseq' => \&end_element_RNAseq, 'DNAseq' => \&end_element_DNAseq, 'AAseq' => \&end_element_AAseq, 'DBRef' => \&end_element_default, 'property' => \&end_element_default, ); $self->{'_end_elements'} = \%end_elements; } =head2 schemaLocation Title : schemaLocation Usage : $self->schemaLocation Function: gets/sets the schema location in the <seqXML> header Returns : the schema location string Args : To set the schemaLocation, call with a schemaLocation as the argument. =cut sub schemaLocation { my ( $self, $value ) = @_; my $metadata = $self->{'_seqxml_metadata'}; # set if a value is supplied if ($value) { $metadata->{'schemaLocation'} = $value; } return $metadata->{'schemaLocation'}; } =head2 source Title : source Usage : $self->source Function: gets/sets the data source in the <seqXML> header Returns : the data source string Args : To set the source, call with a source string as the argument. =cut sub source { my ( $self, $value ) = @_; my $metadata = $self->{'_seqxml_metadata'}; # set if a value is supplied if ($value) { $metadata->{'source'} = $value; } return $metadata->{'source'}; } =head2 sourceVersion Title : sourceVersion Usage : $self->sourceVersion Function: gets/sets the data source version in the <seqXML> header Returns : the data source version string Args : To set the source version, call with a source version string as the argument. =cut sub sourceVersion { my ( $self, $value ) = @_; my $metadata = $self->{'_seqxml_metadata'}; # set if a value is supplied if ($value) { $metadata->{'sourceVersion'} = $value; } return $metadata->{'sourceVersion'}; } =head2 seqXMLversion Title : seqXMLversion Usage : $self->seqXMLversion Function: gets/sets the seqXML version in the <seqXML> header Returns : the seqXML version string. Args : To set the seqXML version, call with a seqXML version string as the argument. =cut sub seqXMLversion { my ( $self, $value ) = @_; my $metadata = $self->{'_seqxml_metadata'}; # set if a value is supplied if ($value) { $metadata->{'seqXMLversion'} = $value; } return $metadata->{'seqXMLversion'}; } =head1 Methods for parsing the XML document =cut =head2 processXMLNode Title : processXMLNode Usage : $seqio->processXMLNode Function: reads the XML node and processes according to the node type Returns : none Args : none Throws : Exception on unexpected XML node type, warnings on unexpected XML element names. =cut sub processXMLnode { my ($self) = @_; my $reader = $self->{'_reader'}; my $nodetype = $reader->nodeType; if ( $nodetype == XML_READER_TYPE_ELEMENT ) { $self->{'_current_element_name'} = $reader->name; if ( exists $self->{'_start_elements'}->{ $reader->name } ) { my $method = $self->{'_start_elements'}->{ $reader->name }; $self->$method(); } else { my $name = $reader->name; $self->warn("unexpected start element encountered: $name"); } } elsif ( $nodetype == XML_READER_TYPE_TEXT ) { # store key-value pair of element name and the corresponding text my $name = $self->{'_current_element_name'}; $self->{'_current_entry_data'}->{$name} = $reader->value; } elsif ( $nodetype == XML_READER_TYPE_END_ELEMENT ) { if ( exists $self->{'_end_elements'}->{ $reader->name } ) { my $method = $self->{'_end_elements'}->{ $reader->name }; $self->$method(); } else { my $name = $reader->name; $self->warn("unexpected end element encountered: $name"); } $self->{'_current_element_name'} = {}; # empty current element name } else { $self->throw( "unexpected node type " . $nodetype, " encountered (name: ", $reader->name, ")\n" ); } if ( $self->debug ) { printf "%d %d %s %d\n", ( $reader->depth, $reader->nodeType, $reader->name, $reader->isEmptyElement ); } } =head2 processAttribute Title : processAttribute Usage : $seqio->processAttribute(\%hash_for_attribute); Function: reads the attributes of the current element into a hash Returns : none Args : hash reference where the attributes will be stored. =cut sub processAttribute { my ( $self, $data ) = @_; my $reader = $self->{'_reader'}; # several ways of reading attributes: # read all attributes: if ( $reader->moveToFirstAttribute ) { do { $data->{ $reader->name() } = $reader->value; } while ( $reader->moveToNextAttribute ); $reader->moveToElement; } } =head2 parseHeader Title : parseHeader Usage : $self->parseHeader(); Function: reads the opening <seqXML> block and grabs the metadata from it, namely the source, sourceVersion, and seqXMLversion. Returns : none Args : none Throws : Exception if it hits an <entry> tag, because that means it's missed the <seqXML> tag and read too far into the file. =cut sub parseHeader { my ($self) = @_; my $reader = $self->{'_reader'}; while($reader->read) { # just read the header if ( $reader->nodeType == XML_READER_TYPE_ELEMENT ) { if ( $reader->name eq 'seqXML' ) { $self->element_seqXML(); last; } elsif ( $reader->name eq 'entry' ) { my $name = $reader->name; $self->throw("Missed the opening <seqXML> tag. Got $name instead."); } } } } =head2 element_seqXML Title : element_seqXML Usage : $self->element_seqXML Function: processes the opening <seqXML> node Returns : none Args : none =cut sub element_seqXML { my ($self) = @_; my $reader = $self->{'_reader'}; # reset for every new <seqXML> block $self->{'_seqxml_metadata'} = {}; if ( $reader->hasAttributes() ) { $self->processAttribute( $self->{'_seqxml_metadata'} ); } else { $self->throw("no SeqXML metadata!"); } } =head2 element_entry Title : element_entry Usage : $self->element_entry Function: processes a sequence <entry> node Returns : none Args : none Throws : Exception if sequence ID is not present in <entry> element =cut sub element_entry { my ($self) = @_; my $reader = $self->{'_reader'}; if ( $reader->hasAttributes() ) { $self->processAttribute( $self->{'_current_entry_data'} ); } else { $self->throw("no sequence ID!"); } } =head2 element_species Title : element_entry Usage : $self->element_entry Function: processes a <species> node, creating a Bio::Species object Returns : none Args : none Throws : Exception if <species> tag exists but is empty, or if the attributes 'name' or 'ncbiTaxID' are undefined =cut sub element_species { my ($self) = @_; my $reader = $self->{'_reader'}; my $data = $self->{'_current_entry_data'}; my $species_data = {}; my $species_obj; if ( $reader->hasAttributes() ) { $self->processAttribute($species_data); } else { $self->throw("no species information!"); } if ( defined $species_data->{'name'} && defined $species_data->{'ncbiTaxID'} ) { $species_obj = Bio::Species->new( -ncbi_taxid => $species_data->{'ncbiTaxID'}, ); $species_obj->node_name( $species_data->{'name'} ); $data->{'species'} = $species_obj; } else { $self->throw("<species> attributes name and ncbiTaxID are undefined"); } } =head2 element_description Title : element_description Usage : $self->element_description Function: processes a sequence <description> node; a no-op -- description text is read by processXMLnode Returns : none Args : none =cut sub element_description { my ($self) = @_; } =head2 element_RNAseq Title : element_RNAseq Usage : $self->element_RNAseq Function: processes a sequence <RNAseq> node Returns : none Args : none =cut sub element_RNAseq { my ($self) = @_; my $reader = $self->{'_reader'}; my $data = $self->{'_current_entry_data'}; $data->{'alphabet'} = 'rna'; $data->{'sequence'} = $data->{'RNAseq'}; } =head2 element_DNAseq Title : element_DNAseq Usage : $self->element_DNAseq Function: processes a sequence <DNAseq> node Returns : none Args : none =cut sub element_DNAseq { my ($self) = @_; my $reader = $self->{'_reader'}; my $data = $self->{'_current_entry_data'}; $data->{'alphabet'} = 'dna'; $data->{'sequence'} = $data->{'DNAseq'}; } =head2 element_AAseq Title : element_AAseq Usage : $self->element_AAseq Function: processes a sequence <AAseq> node Returns : none Args : none =cut sub element_AAseq { my ($self) = @_; my $reader = $self->{'_reader'}; my $data = $self->{'_current_entry_data'}; $data->{'alphabet'} = 'protein'; $data->{'sequence'} = $data->{'AAseq'}; } =head2 element_DBRef Title : element_DBRef Usage : $self->element_DBRef Function: processes a sequence <DBRef> node, creating a Bio::Annotation::DBLink object Returns : none Args : none =cut sub element_DBRef { my ($self) = @_; my $reader = $self->{'_reader'}; my $data = $self->{'_current_entry_data'}; my $DBRef = {}; my $annotation_obj; if ( $reader->hasAttributes() ) { $self->processAttribute($DBRef); } else { $self->throw("no DBRef data!"); } if ( defined $DBRef->{'source'} && defined $DBRef->{'id'} && defined $DBRef->{'type'}) { $annotation_obj = Bio::Annotation::DBLink->new( -primary_id => $DBRef->{'id'}, -database => $DBRef->{'source'}, -type => $DBRef->{'type'}, -tagname => 'dblink', ); push @{ $data->{'DBRefs'} }, $annotation_obj; } else { $self->throw("malformed DBRef data!"); } } =head2 element_property Title : element_property Usage : $self->element_property Function: processes a sequence <property> node, creating a Bio::Annotation::SimpleValue object Returns : none Args : none =cut sub element_property { my ($self) = @_; my $reader = $self->{'_reader'}; my $data = $self->{'_current_entry_data'}; my $property = {}; my $annotation_obj; if ( $reader->hasAttributes() ) { $self->processAttribute($property); } else { $self->throw("no property data!"); } if ( defined $property->{'name'} ) { $annotation_obj = Bio::Annotation::SimpleValue->new( -tagname => $property->{'name'} ); if ( defined $property->{'value'} ) { $annotation_obj->value( $property->{'value'} ); } push @{ $data->{'properties'} }, $annotation_obj; } else { $self->throw("malformatted property!"); } } =head2 end_element_RNAseq Title : end_element_RNAseq Usage : $self->end_element_RNAseq Function: processes a sequence <RNAseq> node Returns : none Args : none =cut sub end_element_RNAseq { my ($self) = @_; my $reader = $self->{'_reader'}; my $data = $self->{'_current_entry_data'}; $data->{'alphabet'} = 'rna'; $data->{'sequence'} = $data->{'RNAseq'}; } =head2 end_element_DNAseq Title : end_element_DNAseq Usage : $self->end_element_DNAseq Function: processes a sequence <DNAseq> node Returns : none Args : none =cut sub end_element_DNAseq { my ($self) = @_; my $reader = $self->{'_reader'}; my $data = $self->{'_current_entry_data'}; $data->{'alphabet'} = 'dna'; $data->{'sequence'} = $data->{'DNAseq'}; } =head2 end_element_AAseq Title : end_element_AAseq Usage : $self->end_element_AAseq Function: processes a sequence <AAseq> node Returns : none Args : none =cut sub end_element_AAseq { my ($self) = @_; my $reader = $self->{'_reader'}; my $data = $self->{'_current_entry_data'}; $data->{'alphabet'} = 'protein'; $data->{'sequence'} = $data->{'AAseq'}; } =head2 end_element_entry Title : end_element_entry Usage : $self->end_element_entry Function: processes the closing </entry> node, creating the Seq object Returns : a Bio::Seq object Args : none Throws : Exception if sequence, sequence ID, or alphabet are missing =cut sub end_element_entry { my ($self) = @_; my $reader = $self->{'_reader'}; my $data = $self->{'_current_entry_data'}; # make sure we've got at least a seq, an ID, and an alphabet unless ( $data->{'sequence'} && length($data->{'sequence'}) > 0) { $self->throw("this entry lacks a sequence"); } unless ( $data->{'id'} ) { $self->throw("this entry lacks an id"); } unless ( $data->{'alphabet'} ) { $self->throw("this entry lacks an alphabet"); } # create new sequence object with minimum necessary parameters my $seq_obj = $self->sequence_factory->create( -seq => $data->{'sequence'}, -alphabet => $data->{'alphabet'}, -id => $data->{'id'}, -primary_id => $data->{'id'}, ); # add additional parameters if available if ( $data->{'description'} ) { $seq_obj->desc( $data->{'description'} ); } if ( $data->{'species'} ) { $seq_obj->species( $data->{'species'} ); } if ( $data->{'DBRefs'} ) { foreach my $annotation_obj ( @{ $data->{'DBRefs'} } ) { $seq_obj->add_Annotation($annotation_obj); } } if ( $data->{'properties'} ) { foreach my $annotation_obj ( @{ $data->{'properties'} } ) { $seq_obj->add_Annotation($annotation_obj); } } if ( $data->{'source'} ) { my $annotation_obj = Bio::Annotation::SimpleValue->new( '-tagname' => 'source', '-value' => $data->{'source'}, ); $seq_obj->add_Annotation($annotation_obj); } # empty the temporary data store $self->{'_current_entry_data'} = {}; return $seq_obj; } =head2 end_element_default Title : end_element_default Usage : $self->end_element_default Function: processes all other closing tags; a no-op. Returns : none Args : none =cut sub end_element_default { my ($self) = @_; } =head2 DESTROY Title : DESTROY Usage : called automatically by Perl just before object goes out of scope Function: performs a write flush Returns : none Args : none =cut sub DESTROY { my $self = shift; $self->flush if $self->_flush_on_write && defined $self->_fh; $self->SUPER::DESTROY; } =head2 close Title : close Usage : $seqio_obj->close(). Function: writes closing </seqXML> tag. close() will be called automatically by Perl when your program exits, but if you want to use the seqXML file you've written before then, you'll need to do an explicit close first to get the final </seqXML> tag. Returns : none Args : none =cut sub close { my $self = shift; if ( $self->mode eq 'w' && $self->{'_writer'}->within_element('seqXML') ) { $self->{'_writer'}->endTag("seqXML"); $self->{'_writer'}->end(); } $self->SUPER::close(); } 1; ������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/strider.pm���������������������������������������������������������������000444��000766��000024�� 15617�13155576320� 17250� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::strider # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Malcolm Cook <mec@stowers-institute.org> # # You may distribute this module under the same terms as perl itself # # _history # April 7th, 2005 Malcolm Cook authored # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::strider - DNA strider sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from strider 'binary' format, as documented in the strider manual, in which the first 112 bytes are a header, following by the sequence, followed by a sequence description. Note: it does NOT assign any sequence identifier, since they are not contained in the byte stream of the file; the Strider application simply displays the name of the file on disk as the name of the sequence. The caller should set the id, probably based on the name of the file (after possibly cleaning up whitespace, which ought not to be used as the id in most applications). Note: the strider 'comment' is mapped to the BioPerl 'description' (since there is no other text field, and description maps to defline text). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Malcolm Cook Email: mec@stowers-institute.org =head1 CONTRIBUTORS Modelled after Bio::SeqIO::fasta by Ewan Birney E<lt>birney@ebi.ac.ukE<gt> and Lincoln Stein E<lt>lstein@cshl.orgE<gt> =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::strider; use strict; use warnings; use Bio::Seq::SeqFactory; use Convert::Binary::C; use base qw(Bio::SeqIO); my $c = Convert::Binary::C->new ( ByteOrder => 'BigEndian', Alignment => 2 ); my $headerdef; {local ($/); # See this file's __DATA__ section for the c structure definitions # for strider binary header data. Here we slurp it all into $headerdef. $headerdef = <DATA>}; $c->parse($headerdef); my $size_F_HEADER = 112; die "expected strider header structure size of $size_F_HEADER" unless $size_F_HEADER eq $c->sizeof('F_HEADER'); my %alphabet2type = ( # map between BioPerl alphabet and strider # sequence type code. # From Strider Documentation: the sequence type: # 1, 2, 3 and 4 for DNA, DNA Degenerate, RNA and # Protein sequence files, respectively. # TODO: determine 'DNA Degenerate' based on # sequence alphabet? dna => 1, rna => 3, protein => 4, ); my %type2alphabet = reverse %alphabet2type; sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); unless ( defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : NONE =cut sub next_seq { my( $self ) = @_; my $fh = $self->_fh; my ($header,$sequence,$fulldesc); eval {read $fh,$header,$size_F_HEADER}; $self->throw ("$@ while attempting to reading strider header from " . $self->{'_file'}) if $@; $self->throw("required $size_F_HEADER bytes while reading strider header in " . $self->{'_file'} . " but found: " . length($header)) unless $size_F_HEADER == length($header); my $headerdata = $c->unpack('F_HEADER',$header) or return; read $fh,$sequence,$headerdata->{nLength}; read $fh,$fulldesc,$headerdata->{com_length}; $fulldesc =~ s/\cM/ /g; # gratuitous replacement of mac # linefeed with space. my $seq = $self->sequence_factory->create( # -id => $main::ARGV, #might want to set this in caller to $ARGV. -seq => $sequence, -desc => $fulldesc, -alphabet => $type2alphabet{$headerdata->{type}} || 'dna', ); return $seq; } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : array of 1 to n Bio::PrimarySeqI objects =cut sub write_seq { my ($self,@seq) = @_; my $fh = $self->_fh() || *STDOUT; #die "could not determine filehandle in strider.pm"; foreach my $seq (@seq) { $self->throw("Did not provide a valid Bio::PrimarySeqI object") unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI'); my $headerdata = $c->pack('F_HEADER',{ versionNb => 0, type => $alphabet2type{$seq->alphabet} || $alphabet2type{dna}, topology => $seq->is_circular ? 1 : 0, nLength => $seq->length, nMinus => 0, com_length => length($seq->desc || ""), }); print $fh $headerdata, $seq->seq() || "" , $seq->desc || ""; } } 1; __DATA__ //The following was taken from the strider 1.4 release notes Appendix (with //some comments gleaned from other parts of manual) struct F_HEADER { char versionNb; // the format version number, currently it is set to 0 char type; // 1=DNA, 2=DNA Degenerate, 3=RNA or 4=Protein char topology; // linear or circular - 0 for a linear sequence, 1 for a circular one char reserved1; int reserved2; int reserved3; int reserved4; char reserved5; char filler1; short filler2; int filler3; int reserved6; int nLength; // Sequence length - the length the Sequence field (the number of char in the text, each being a base or an aa) int nMinus; // nb of "negative" bases, i.e. the number of bases numbered with negative numbers int reserved7; int reserved8; int reserved9; int reserved10; int reserved11; char reserved12[32]; short reserved13; short filler4; char reserved14; char reserved15; char reserved16; char filler5; int com_length; // the length the Comment field (the number of char in the text). int reserved17; int filler6; int filler7; }; �����������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/swiss.pm�����������������������������������������������������������������000444��000766��000024�� 145433�13155576320� 16764� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::swiss # # Copyright Elia Stupka # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::swiss - Swissprot sequence input/output stream =head1 SYNOPSIS It is probably best not to use this object directly, but rather go through the SeqIO handler system: use Bio::SeqIO; $stream = Bio::SeqIO->new(-file => $filename, -format => 'swiss'); while ( my $seq = $stream->next_seq() ) { # do something with $seq } =head1 DESCRIPTION This object can transform Bio::Seq objects to and from Swiss-Pprot flat file databases. There is a lot of flexibility here about how to dump things which needs to be documented. =head2 GN (Gene name) line management details A Uniprot/Swiss-Prot entry holds information on one protein sequence. If that sequence is identical across genes and species, they are all merged into one entry. This creates complex needs for several annotation fields in swiss-prot format. The latest syntax for GN line is described in the user manual: http://www.expasy.ch/sprot/userman.html#GN_line Each of the possibly multiple genes in an entry can have Name, Synonyms (only if there is a name), OrderedLocusNames (names from genomic sequences) and ORFNames (temporary or cosmid names). "Name" here really means "symbol". This complexity is now dealt with the following way: A new Bio::AnnotationI class was created in order to store the data in tag-value pairs. This class (Bio::Annotation::TagTree) is stored in the Bio::Annotation::Collection object and is accessed like all other annotations. The tag name is 'gene_name'. There is a single Bio::Annotation::TagTree per sequence record, which corresponds to the original class that stored this data (Bio::Annotation::StructuredValue). Depending on how we progress this may change to represent each group of gene names. For now, to access the gene name tree annotation, one uses the below method: my ($gene) = $seq->annotation->get_Annotations('gene_name'); If you are only interested in displaying the values, value() returns a string with similar formatting. There are several ways to get directly at the information you want if you know the element (tag) for the data. For gene names all data is stored with the element-tag pairs: "element1=tag1, tag2, tag3; element2=tag4, tag5;" This normally means the element will be 'Name', 'Synonyms', etc. and the gene names the values. Using findval(), you can do the following: # grab a flattened list of all gene names my @names = $ann->findval('Name'); # or iterated through the nodes and grab the name for each group for my $node ($ann->findnode('gene_name')) { my @names = $node->findval('Name'); } The current method for parsing gene name data (and reconstructing gene name output) is very generic. This is somewhat preemptive if, for instance, UniProt decides to update and add another element name to the current ones using the same formatting layout. Under those circumstances, one can iterate through the tag tree in a safe way and retrieve all node data like so. # retrieve the gene name nodes (groups like names, synonyms, etc). for my $ann ($seq->annotation->get_Annotations('gene_name')) { # each gene name group for my $node ($ann->findnode('gene_name')) { print "Gene name:\n"; # each gene name node (tag => value pair) for my $n ($node->children) { print "\t".$n->element.": ".$n->children."\n"; } } } For more uses see Bio::Annotation::TagTree. Since Uniprot/Swiss-Prot format have been around for quite some time, the parser is also able to read in the older GN line syntax where genes are separated by AND and various symbols by OR. The first symbol is taken to be the 'Name' and the remaining ones are stored as 'Synonyms'. Also, for UniProt output we support using other Bio::AnnotationI, but in this case we only use the stringified version of the annotation. This is to allow for backwards compatibility with code that previously used Bio::Annotation::SimpleValue or other Bio::AnnotationI classes. =head2 Optional functions =over 3 =item _show_dna() (output only) shows the dna or not =item _post_sort() (output only) provides a sorting func which is applied to the FTHelpers before printing =item _id_generation_func() This is function which is called as print "ID ", $func($seq), "\n"; To generate the ID line. If it is not there, it generates a sensible ID line using a number of tools. If you want to output annotations in Swissprot format they need to be stored in a Bio::Annotation::Collection object which is accessible through the Bio::SeqI interface method L<annotation()|annotation>. The following are the names of the keys which are polled from a L<Bio::Annotation::Collection> object. reference - Should contain Bio::Annotation::Reference objects comment - Should contain Bio::Annotation::Comment objects dblink - Should contain Bio::Annotation::DBLink objects gene_name - Should contain Bio::Annotation::SimpleValue object =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions, preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Elia Stupka Email elia@tll.org.sg =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::swiss; use vars qw(@Unknown_names @Unknown_genus); use strict; use Bio::SeqIO::FTHelper; use Bio::SeqFeature::Generic; use Bio::Species; use Bio::Tools::SeqStats; use Bio::Seq::SeqFactory; use Bio::Annotation::Collection; use Bio::Annotation::Comment; use Bio::Annotation::Reference; use Bio::Annotation::DBLink; use Bio::Annotation::SimpleValue; use Bio::Annotation::TagTree; use base qw(Bio::SeqIO); our $LINE_LENGTH = 76; # this is for doing species name parsing @Unknown_names=('other', 'unidentified', 'unknown organism', 'not specified', 'not shown', 'Unspecified', 'Unknown', 'None', 'unclassified', 'unidentified organism', 'not supplied' ); # dictionary of synonyms for taxid 32644 # all above can be part of valid species name @Unknown_genus = qw(unknown unclassified uncultured unidentified); # if there are any other gene name tags, they are added to the end our @GENE_NAME_ORDER = qw(Name Synonyms OrderedLocusNames ORFNames); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); # hash for functions for decoding keys. $self->{'_func_ftunit_hash'} = {}; # sets this to one by default. People can change it $self->_show_dna(1); if ( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : =cut sub next_seq { my ($self,@args) = @_; my ($pseq,$c,$line,$name,$desc,$acc,$seqc,$mol,$div, $sptr,$seq_div, $date,$comment,@date_arr); my $genename = ""; my ($annotation, %params, @features) = ( Bio::Annotation::Collection->new()); local $_; 1 while defined($_ = $self->_readline) && /^\s+$/; return unless defined $_ && /^ID\s/; # fixed to allow _DIVISION to be optional for bug #946 # see bug report for more information # # 9/6/06 Note: Swiss/TrEMBL sequences have no division acc. to UniProt # release notes; this is fixed to simplify the regex parsing # STANDARD (SwissProt) and PRELIMINARY (TrEMBL) added to namespace() unless( m{^ ID \s+ # (\S+) \s+ # $1 entryname ([^\s;]+); \s+ # $2 DataClass (?:PRT;)? \s+ # Molecule Type (optional) [0-9]+[ ]AA \. # Sequencelength (capture?) $ }ox ) { # I couldn't find any new current UniProt sequences # that matched this format: # || m/^ID\s+(\S+)\s+(_([^\s_]+))? /ox ) { $self->throw("swissprot stream with no ID. Not swissprot in my book"); } ($name, $seq_div) = ($1, $2); $params{'-namespace'} = ($seq_div eq 'Reviewed' || $seq_div eq 'STANDARD') ? 'Swiss-Prot' : ($seq_div eq 'Unreviewed' || $seq_div eq 'PRELIMINARY') ? 'TrEMBL' : $seq_div; # we shouldn't be setting the division, but for now... my ($junk, $division) = split q(_), $name; $params{'-division'} = $division; $params{'-alphabet'} = 'protein'; # this is important to have the id for display in e.g. FTHelper, otherwise # you won't know which entry caused an error $params{'-display_id'} = $name; BEFORE_FEATURE_TABLE : while ( defined($_ = $self->_readline) ) { # Exit at start of Feature table and at the sequence at the # latest HL 05/11/2000 last if( /^(FT|SQ)/ ); # Description line(s) if (/^DE\s+(\S.*\S)/) { $desc .= $desc ? " $1" : $1; } #Gene name elsif (/^GN\s+(.*)/) { $genename .= " " if $genename; $genename .= $1; } #accession number(s) elsif ( /^AC\s+(.+)/) { my @accs = split(/[; ]+/, $1); # allow space in addition $params{'-accession_number'} = shift @accs unless defined $params{'-accession_number'}; push @{$params{'-secondary_accessions'}}, @accs; } #date and sequence version elsif ( /^DT\s+(.*)/ ) { my $line = $1; my ($date, $version) = split(' ', $line, 2); $date =~ tr/,//d; # remove comma if new version if ($version =~ /\(Rel\. (\d+), Last sequence update\)/ || # old /sequence version (\d+)/) { #new my $update = Bio::Annotation::SimpleValue->new (-tagname => 'seq_update', -value => $1 ); $annotation->add_Annotation($update); } elsif ($version =~ /\(Rel\. (\d+), Last annotation update\)/ || #old /entry version (\d+)/) { #new $params{'-version'} = $1; } push @{$params{'-dates'}}, $date; } # Evidence level elsif ( /^PE\s+(.*)/ ) { my $line = $1; $line =~ s/;\s*//; # trim trailing semicolon and any spaces at the end of the line my $evidence = Bio::Annotation::SimpleValue->new (-tagname => 'evidence', -value => $line ); $annotation->add_Annotation($evidence); } # Organism name and phylogenetic information elsif (/^O[SCG]/) { my $species = $self->_read_swissprot_Species($_); $params{'-species'}= $species; # now we are one line ahead -- so continue without reading the next # line HL 05/11/2000 } # References elsif (/^R/) { my $refs = $self->_read_swissprot_References($_); foreach my $r (@$refs) { $annotation->add_Annotation('reference',$r); } } # Comments elsif (/^CC\s{3}(.*)/) { $comment .= $1; $comment .= "\n"; while (defined ($_ = $self->_readline) && /^CC\s{3}(.*)/ ) { $comment .= $1 . "\n"; } # note: don't try to process comments here -- they may contain # structure. LP 07/30/2000 my $commobj = Bio::Annotation::Comment->new(-tagname => 'comment', -text => $comment); $annotation->add_Annotation('comment',$commobj); $comment = ""; $self->_pushback($_); } #DBLinks # old regexp # /^DR\s+(\S+)\;\s+(\S+)\;\s+(\S+)[\;\.](.*)$/) { # new regexp from Andreas Kahari bug #1584 elsif (/^DR\s+(\S+)\;\s+(\S+)\;\s+([^;]+)[\;\.](.*)$/) { my ($database,$primaryid,$optional,$comment) = ($1,$2,$3,$4); # drop leading and training spaces and trailing . $comment =~ s/\.\s*$//; $comment =~ s/^\s+//; my $dblinkobj = Bio::Annotation::DBLink->new (-database => $database, -primary_id => $primaryid, -optional_id => $optional, -comment => $comment, -tagname => 'dblink', ); $annotation->add_Annotation('dblink',$dblinkobj); } #keywords elsif ( /^KW\s+(.*)$/ ) { my @kw = split(/\s*\;\s*/,$1); defined $kw[-1] && $kw[-1] =~ s/\.$//; push @{$params{'-keywords'}}, @kw; } } # process and parse the gene name line if there was one (note: we # can't do this above b/c GN may be multi-line and we can't # unequivocally determine whether we've seen the last GN line in # the new format) if ($genename) { my @stags; if ($genename =~ /\w=\w/) { # new format (e.g., Name=RCHY1; Synonyms=ZNF363, CHIMP) for my $n (split(m{\s+and\s+},$genename)) { my @genenames; for my $section (split(m{\s*;\s*},$n)) { my ($tag, $rest) = split("=",$section); $rest ||= ''; for my $val (split(m{\s*,\s*},$rest)) { push @genenames, [$tag => $val]; } } push @stags, ['gene_name' => \@genenames]; } } else { # old format for my $section (split(/ AND /, $genename)) { my @genenames; $section =~ s/[\(\)\.]//g; my @names = split(m{\s+OR\s+}, $section); push @genenames, ['Name' => shift @names]; push @genenames, map {['Synonyms' => $_]} @names; push @stags, ['gene_name' => \@genenames] } } #use Data::Dumper; print Dumper $gn, $genename;# exit; my $gn = Bio::Annotation::TagTree->new(-tagname => 'gene_name', -value => ['gene_names' => \@stags]); $annotation->add_Annotation('gene_name', $gn); } FEATURE_TABLE : # if there is no feature table, or if we've got beyond, exit loop or don't # even enter HL 05/11/2000 while (defined $_ && /^FT/ ) { my $ftunit = $self->_read_FTHelper_swissprot($_); # process ftunit # when parsing of the line fails we get undef returned if ($ftunit) { push(@features, $ftunit->_generic_seqfeature($self->location_factory(), $params{'-seqid'}, "SwissProt")); } else { $self->warn("failed to parse feature table line for seq " . $params{'-display_id'}. "\n$_"); } $_ = $self->_readline; } while ( defined($_) && ! /^SQ/ ) { $_ = $self->_readline; } $seqc = ""; while ( defined ($_ = $self->_readline) ) { last if m{^//}; s/[^A-Za-z]//g; $seqc .= uc($_); } my $seq= $self->sequence_factory->create (-verbose => $self->verbose, %params, -seq => $seqc, -desc => $desc, -features => \@features, -annotation => $annotation, ); # The annotation doesn't get added by the constructor $seq->annotation($annotation); return $seq; } =head2 write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object (must be seq) to the stream Returns : 1 for success and 0 for error Args : array of 1 to n Bio::SeqI objects =cut sub write_seq { my ($self,@seqs) = @_; foreach my $seq ( @seqs ) { $self->throw("Attempting to write with no seq!") unless defined $seq; if ( ! ref $seq || ! $seq->isa('Bio::SeqI') ) { $self->warn(" $seq is not a SeqI compliant module. Attempting to dump, but may fail!"); } my $i; my $str = $seq->seq; my $div; my $ns = ($seq->can('namespace')) && $seq->namespace(); my $len = $seq->length(); if ( !$seq->can('division') || ! defined ($div = $seq->division()) ) { $div = 'UNK'; } # namespace dictates database, takes precedent over division. Sorry! if (defined($ns) && $ns ne '') { $div = ($ns eq 'Swiss-Prot') ? 'Reviewed' : ($ns eq 'TrEMBL') ? 'Unreviewed' : $ns; } else { $ns = 'Swiss-Prot'; # division not reset; acts as fallback } $self->warn("No whitespace allowed in SWISS-PROT display id [". $seq->display_id. "]") if $seq->display_id =~ /\s/; my $temp_line; if ( $self->_id_generation_func ) { $temp_line = &{$self->_id_generation_func}($seq); } else { #$temp_line = sprintf ("%10s STANDARD; %3s; %d AA.", # $seq->primary_id()."_".$div,$mol,$len); # Reconstructing the ID relies heavily upon the input source having # been in a format that is parsed as this routine expects it -- that is, # by this module itself. This is bad, I think, and immediately breaks # if e.g. the Bio::DB::GenPept module is used as input. # Hence, switch to display_id(); _every_ sequence is supposed to have # this. HL 2000/09/03 # Changed to reflect ID line changes in UniProt # Oct 2006 - removal of molecule type - see bug 2134 $temp_line = sprintf ("%-24s%-12s%9d AA.", $seq->display_id(), $div.';', $len); } $self->_print( "ID $temp_line\n"); # if there, write the accession line local($^W) = 0; # suppressing warnings about uninitialized fields if ( $self->_ac_generation_func ) { $temp_line = &{$self->_ac_generation_func}($seq); $self->_print( "AC $temp_line\n"); } elsif ($seq->can('accession_number') ) { my $ac_line = $seq->accession_number; if ($seq->can('get_secondary_accessions') ) { foreach my $sacc ($seq->get_secondary_accessions) { $ac_line .= "; ". $sacc;; } $ac_line .= ";"; } $self->_write_line_swissprot_regex("AC ","AC ",$ac_line, "\\s\+\|\$",$LINE_LENGTH); } # otherwise - cannot print <sigh> # Date lines and sequence versions (changed 6/15/2006) # This is rebuilt from scratch using the current SwissProt/UniProt format if ( $seq->can('get_dates') ) { my @dates = $seq->get_dates(); my $ct = 1; my $seq_version = $seq->version; my ($update_version) = $seq->annotation->get_Annotations("seq_update"); foreach my $dt (@dates) { $self->_write_line_swissprot_regex("DT ","DT ", $dt.', integrated into UniProtKB/'.$ns.'.', "\\s\+\|\$",$LINE_LENGTH) if $ct == 1; $self->_write_line_swissprot_regex("DT ","DT ", $dt.", sequence version ".$update_version->display_text.'.', "\\s\+\|\$",$LINE_LENGTH) if $ct == 2; $self->_write_line_swissprot_regex("DT ","DT ", $dt.", entry version $seq_version.", "\\s\+\|\$",$LINE_LENGTH) if $ct == 3; $ct++; } } #Definition lines $self->_write_line_swissprot_regex("DE ","DE ",$seq->desc(),"\\s\+\|\$",$LINE_LENGTH); #Gene name; print out new format foreach my $gene ( my @genes = $seq->annotation->get_Annotations('gene_name') ) { # gene is a Bio::Annotation::TagTree; if ($gene->isa('Bio::Annotation::TagTree')) { my @genelines; for my $node ($gene->findnode('gene_name')) { # check for Name and Synonym first, then the rest get tagged on my $geneline = "GN "; my %genedata = $node->hash; for my $tag (@GENE_NAME_ORDER) { if (exists $genedata{$tag}) { $geneline .= (ref $genedata{$tag} eq 'ARRAY') ? "$tag=".join(', ',@{$genedata{$tag}})."; " : "$tag=$genedata{$tag}; "; delete $genedata{$tag}; } } # add rest for my $tag (sort keys %genedata) { $geneline .= (ref $genedata{$tag} eq 'ARRAY') ? "$tag=".join(', ',@{$genedata{$tag}})."; " : "$tag=$genedata{$tag}; "; delete $genedata{$tag}; } push @genelines, "$geneline\n"; } $self->_print(join("GN and\n",@genelines)); } else { # fall back to getting stringified output $self->_write_line_swissprot_regex("GN ","GN ", $gene->display_text, "\\s\+\|\$", $LINE_LENGTH); } } # Organism lines if ($seq->can('species') && (my $spec = $seq->species)) { my @class = $spec->classification(); shift(@class); my $species = $spec->species; my $genus = $spec->genus; my $OS = $spec->scientific_name; if ($class[-1] =~ /viruses/i) { $OS = $species; $OS .= " ". $spec->sub_species if $spec->sub_species; } foreach (($spec->variant, $spec->common_name)) { $OS .= " ($_)" if $_; } $self->_print( "OS $OS.\n"); my $OC = join('; ', reverse(@class)) .'.'; $self->_write_line_swissprot_regex("OC ","OC ",$OC,"\; \|\$",$LINE_LENGTH); if ($spec->organelle) { $self->_write_line_swissprot_regex("OG ","OG ",$spec->organelle,"\; \|\$",$LINE_LENGTH); } if ($spec->ncbi_taxid) { $self->_print("OX NCBI_TaxID=".$spec->ncbi_taxid.";\n"); } } # Reference lines my $t = 1; foreach my $ref ( $seq->annotation->get_Annotations('reference') ) { $self->_print( "RN [$t]\n"); # changed by lorenz 08/03/00 # j.gilbert and h.lapp agreed that the rp line in swissprot seems # more like a comment than a parseable value, so print it as is if ($ref->rp) { $self->_write_line_swissprot_regex("RP ","RP ",$ref->rp, "\\s\+\|\$",$LINE_LENGTH); } if ($ref->comment) { $self->_write_line_swissprot_regex("RC ","RC ",$ref->comment, "\\s\+\|\$",$LINE_LENGTH); } if ($ref->medline or $ref->pubmed or $ref->doi) { # new RX format in swissprot LP 09/17/00 # RX line can now have a DOI, Heikki 13 Feb 2008 my $line; $line .= "MEDLINE=". $ref->medline. '; ' if $ref->medline; $line .= "PubMed=". $ref->pubmed. '; ' if $ref->pubmed; $line .= "DOI=". $ref->doi. '; ' if $ref->doi; chop $line; $self->_write_line_swissprot_regex("RX ","RX ", $line, "\\s\+\|\$",$LINE_LENGTH); } my $author = $ref->authors .';' if($ref->authors); my $title = $ref->title .';' if( $ref->title); my $rg = $ref->rg . ';' if $ref->rg; $author =~ s/([\w\.]) (\w)/$1#$2/g; # add word wrap protection char '#' $self->_write_line_swissprot_regex("RG ","RG ",$rg,"\\s\+\|\$",$LINE_LENGTH) if $rg; $self->_write_line_swissprot_regex("RA ","RA ",$author,"\\s\+\|\$",$LINE_LENGTH) if $author; $self->_write_line_swissprot_regex("RT ","RT ",$title,'[\s\-]+|$',$LINE_LENGTH) if $title; $self->_write_line_swissprot_regex("RL ","RL ",$ref->location,"\\s\+\|\$",$LINE_LENGTH); $t++; } # Comment lines foreach my $comment ( $seq->annotation->get_Annotations('comment') ) { foreach my $cline (split ("\n", $comment->text)) { while (length $cline > 74) { $self->_print("CC ",(substr $cline,0,74),"\n"); $cline = substr $cline,74; } $self->_print("CC ",$cline,"\n"); } } # Database xref lines foreach my $dblink ( $seq->annotation->get_Annotations('dblink') ) { my ($primary_id) = $dblink->primary_id; if (defined($dblink->comment) && ($dblink->comment) ) { $self->_print("DR ",$dblink->database,"; ",$primary_id,"; ", $dblink->optional_id,"; ",$dblink->comment,".\n"); } elsif ($dblink->optional_id) { $self->_print("DR ",$dblink->database,"; ", $primary_id,"; ", $dblink->optional_id,".\n"); } else { $self->_print("DR ",$dblink->database, "; ",$primary_id,"; ","-.\n"); } } # Evidence lines foreach my $evidence ( $seq->annotation->get_Annotations('evidence') ) { $self->_print("PE ",$evidence->value,";\n"); } # if there, write the kw line { my $kw; if ( my $func = $self->_kw_generation_func ) { $kw = &{$func}($seq); } elsif ( $seq->can('keywords') ) { $kw = $seq->keywords; if ( ref($kw) =~ /ARRAY/i ) { $kw = join("; ", @$kw); } $kw .= '.' if $kw and $kw !~ /\.$/ ; } $kw =~ s/([\w\.]) (\w)/$1#$2/g; # add word wrap protection char '#' $self->_write_line_swissprot_regex("KW ","KW ", $kw, "\\s\+\|\$",$LINE_LENGTH) if $kw; } #Check if there is seqfeatures before printing the FT line my @feats = $seq->can('top_SeqFeatures') ? $seq->top_SeqFeatures : (); if ($feats[0]) { if ( defined $self->_post_sort ) { # we need to read things into an array. Process. Sort them. Print 'em my $post_sort_func = $self->_post_sort(); my @fth; foreach my $sf ( @feats ) { push(@fth,Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq)); } @fth = sort { &$post_sort_func($a,$b) } @fth; foreach my $fth ( @fth ) { $self->_print_swissprot_FTHelper($fth); } } else { # not post sorted. And so we can print as we get them. # lower memory load... foreach my $sf ( @feats ) { my @fth = Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq); foreach my $fth ( @fth ) { if ( ! $fth->isa('Bio::SeqIO::FTHelper') ) { $sf->throw("Cannot process FTHelper... $fth"); } $self->_print_swissprot_FTHelper($fth); } } } if ( $self->_show_dna() == 0 ) { return; } } # finished printing features. # molecular weight my $mw = ${Bio::Tools::SeqStats->get_mol_wt($seq->primary_seq)}[0]; # checksum # was crc32 checksum, changed it to crc64 my $crc64 = $self->_crc64(\$str); $self->_print( sprintf("SQ SEQUENCE %4d AA; %d MW; %16s CRC64;\n", $len,$mw,$crc64)); $self->_print( " "); my $linepos; for ($i = 0; $i < length($str); $i += 10) { $self->_print( " ", substr($str,$i,10)); $linepos += 11; if ( ($i+10)%60 == 0 && (($i+10) < length($str))) { $self->_print( "\n "); } } $self->_print( "\n//\n"); $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } } # Thanks to James Gilbert for the following two. LP 08/01/2000 =head2 _generateCRCTable Title : _generateCRCTable Usage : Function: Example : Returns : Args : =cut sub _generateCRCTable { # 10001000001010010010001110000100 # 32 my $poly = 0xEDB88320; my ($self) = shift; $self->{'_crcTable'} = []; foreach my $i (0..255) { my $crc = $i; for (my $j=8; $j > 0; $j--) { if ($crc & 1) { $crc = ($crc >> 1) ^ $poly; } else { $crc >>= 1; } } ${$self->{'_crcTable'}}[$i] = $crc; } } =head2 _crc32 Title : _crc32 Usage : Function: Example : Returns : Args : =cut sub _crc32 { my( $self, $str ) = @_; $self->throw("Argument to crc32() must be ref to scalar") unless ref($str) eq 'SCALAR'; $self->_generateCRCTable() unless exists $self->{'_crcTable'}; my $len = length($$str); my $crc = 0xFFFFFFFF; for (my $i = 0; $i < $len; $i++) { # Get upper case value of each letter my $int = ord uc substr $$str, $i, 1; $crc = (($crc >> 8) & 0x00FFFFFF) ^ ${$self->{'_crcTable'}}[ ($crc ^ $int) & 0xFF ]; } return $crc; } =head2 _crc64 Title : _crc64 Usage : Function: Example : Returns : Args : =cut sub _crc64{ my ($self, $sequence) = @_; my $POLY64REVh = 0xd8000000; my @CRCTableh = 256; my @CRCTablel = 256; my $initialized; my $seq = $$sequence; my $crcl = 0; my $crch = 0; if (!$initialized) { $initialized = 1; for (my $i=0; $i<256; $i++) { my $partl = $i; my $parth = 0; for (my $j=0; $j<8; $j++) { my $rflag = $partl & 1; $partl >>= 1; $partl |= (1 << 31) if $parth & 1; $parth >>= 1; $parth ^= $POLY64REVh if $rflag; } $CRCTableh[$i] = $parth; $CRCTablel[$i] = $partl; } } foreach (split '', $seq) { my $shr = ($crch & 0xFF) << 24; my $temp1h = $crch >> 8; my $temp1l = ($crcl >> 8) | $shr; my $tableindex = ($crcl ^ (unpack "C", $_)) & 0xFF; $crch = $temp1h ^ $CRCTableh[$tableindex]; $crcl = $temp1l ^ $CRCTablel[$tableindex]; } my $crc64 = sprintf("%08X%08X", $crch, $crcl); return $crc64; } =head2 _print_swissprot_FTHelper Title : _print_swissprot_FTHelper Usage : Function: Example : Returns : Args : =cut sub _print_swissprot_FTHelper { my ($self,$fth,$always_quote) = @_; $always_quote ||= 0; my ($start,$end) = ('?', '?'); if ( ! ref $fth || ! $fth->isa('Bio::SeqIO::FTHelper') ) { $fth->warn("$fth is not a FTHelper class. ". "Attempting to print, but there could be tears!"); } my $desc = ""; for my $tag ( qw(description gene note product) ) { if ( exists $fth->field->{$tag} ) { $desc = @{$fth->field->{$tag}}[0]."."; last; } } $desc =~ s/\.$//; my $ftid = ""; if ( exists $fth->field->{'FTId'} ) { $ftid = @{$fth->field->{'FTId'}}[0]. '.'; } my $key =substr($fth->key,0,8); my $loc = $fth->loc; if ( $loc =~ /(\?|\d+|\>\d+|<\d+)?\.\.(\?|\d+|<\d+|>\d+)?/ ) { $start = $1 if defined $1; $end = $2 if defined $2; # to_FTString only returns one value when start == end, #JB955 # so if no match is found, assume it is both start and end #JB955 } elsif ( $loc =~ /join\((\d+)((?:,\d+)+)?\)/) { my @y = ($1); if ( defined( my $m = $2) ) { $m =~ s/^\,//; push @y, split(/,/,$m); } for my $x ( @y ) { $self->_write_line_swissprot_regex( sprintf("FT %-8s %6s %6s ", $key, $x ,$x), "FT ", $desc.'.','\s+|$',$LINE_LENGTH); } return; } else { $start = $end = $fth->loc; } if ($desc) { $self->_write_line_swissprot_regex(sprintf("FT %-8s %6s %6s ", $key, $start ,$end), "FT ", $desc. '.', '\s+|$', $LINE_LENGTH); } else { #HELIX and STRAND do not have descriptions $self->_write_line_swissprot_regex(sprintf("FT %-8s %6s %6s", $key, $start ,$end), "FT ", ' ', '\s+|$', $LINE_LENGTH); } if ($ftid) { $self->_write_line_swissprot_regex("FT ", "FT ", "/FTId=$ftid",'.|$',$LINE_LENGTH); } } #' =head2 _read_swissprot_References Title : _read_swissprot_References Usage : Function: Reads references from swissprot format. Internal function really Example : Returns : Args : =cut sub _read_swissprot_References{ my ($self,$line) = @_; my ($b1, $b2, $rp, $rg, $title, $loc, $au, $med, $com, $pubmed, $doi); my @refs; local $_ = $line; while ( defined $_ ) { if ( /^[^R]/ || /^RN/ ) { if ( $rp ) { $rg =~ s/;\s*$//g if defined($rg); if (defined($au)) { $au =~ s/;\s*$//; } else { $au = $rg; } $title =~ s/;\s*$//g if defined($title); push @refs, Bio::Annotation::Reference->new (-title => $title, -start => $b1, -end => $b2, -authors => $au, -location=> $loc, -medline => $med, -pubmed => $pubmed, -doi => $doi, -comment => $com, -rp => $rp, -rg => $rg, -tagname => 'reference', ); # reset state for the next reference $rp = ''; } if (index($_,'R') != 0) { $self->_pushback($_); # want this line to go back on the list last; # may be the safest exit point HL 05/11/2000 } # don't forget to reset the state for the next reference $b1 = $b2 = $rg = $med = $com = $pubmed = $doi = undef; $title = $loc = $au = undef; } elsif ( /^RP\s{3}(.+? OF (\d+)-(\d+).*)/) { $rp .= $1; $b1 = $2; $b2 = $3; } elsif ( /^RP\s{3}(.*)/) { if ($rp) { $rp .= " ".$1; } else { $rp = $1; } } elsif (/^RX\s{3}(.*)/) { # each reference can have only one RX line my $line = $1; $med = $1 if $line =~ /MEDLINE=(\d+);/; $pubmed = $1 if $line =~ /PubMed=(\d+);/; $doi = $1 if $line =~ /DOI=(.+);/; } elsif ( /^RA\s{3}(.*)/ ) { $au .= $au ? " $1" : $1; } elsif ( /^RG\s{3}(.*)/ ) { $rg .= $rg ? " $1" : $1; } elsif ( /^RT\s{3}(.*)/ ) { if ($title) { my $tline = $1; $title .= ($title =~ /[\w;,:\?!]$/) ? " $tline" : $tline; } else { $title = $1; } } elsif (/^RL\s{3}(.*)/ ) { $loc .= $loc ? " $1" : $1; } elsif ( /^RC\s{3}(.*)/ ) { $com .= $com ? " $1" : $1; } $_ = $self->_readline; } return \@refs; } =head2 _read_swissprot_Species Title : _read_swissprot_Species Usage : Function: Reads the swissprot Organism species and classification lines. Able to deal with unconventional species names. Example : OS Unknown prokaryotic organism $genus = undef ; $species = Unknown prokaryotic organism Returns : A Bio::Species object Args : =cut sub _read_swissprot_Species { my( $self,$line ) = @_; my $org; local $_ = $line; my( $sub_species, $species, $genus, $common, $variant, $ncbi_taxid, $sci_name, $class_lines, $descr ); my $osline = ""; my $do_genus_check = 1; while ( defined $_ ) { last unless /^O[SCGX]/; # believe it or not, but OS may come multiple times -- at this time # we can't capture multiple species if (/^OS\s+(\S.+)/ && (! defined($sci_name))) { $osline .= " " if $osline; $osline .= $1; if ($osline =~ s/(,|, and|\.)$//) { # OS lines are usually like: # Homo sapiens (human) # where we have $sci_name followed by $descr (common name) in # brackets, but we can also have: # Venerupis (Ruditapes) philippinarum # where we have brackets but they don't indicate a $descr if ($osline =~ /[^\(\)]+\(.+\)[^\(\)]+$/) { #*** Danger! no idea if this will pick up some syntaxes for # common names as well) $sci_name = $osline; $sci_name =~ s/\.$//; $descr = ''; $do_genus_check = 0; } else { ($sci_name, $descr) = $osline =~ /(\S[^\(]+)(.*)/; } $sci_name =~ s/\s+$//; while ($descr =~ /\(([^\)]+)\)/g) { my $item = $1; # strain etc may not necessarily come first (yes, swissprot # is messy) if ((! defined($variant)) && (($item =~ /(^|[^\(\w])([Ss]train|isolate|serogroup|serotype|subtype|clone)\b/) || ($item =~ /^(biovar|pv\.|type\s+)/))) { $variant = $item; } elsif ($item =~ s/^subsp\.\s+//) { if (! $sub_species) { $sub_species = $item; } elsif (! $variant) { $variant = $item; } } elsif (! defined($common)) { # we're only interested in the first common name $common = $item; if ((index($common, '(') >= 0) && (index($common, ')') < 0)) { $common .= ')'; } } } } } elsif (s/^OC\s+(\S.+)$//) { $class_lines .= $1; } elsif (/^OG\s+(.*)/) { $org = $1; } elsif (/^OX\s+(.*)/ && (! defined($ncbi_taxid))) { my $taxstring = $1; # we only keep the first one and ignore all others if ($taxstring =~ /NCBI_TaxID=([\w\d]+)/) { $ncbi_taxid = $1; } else { $self->throw("$taxstring doesn't look like NCBI_TaxID"); } } $_ = $self->_readline; } $self->_pushback($_); # pushback the last line because we need it $sci_name || return; # if the organism belongs to taxid 32644 then no Bio::Species object. return if grep { $_ eq $sci_name } @Unknown_names; # Convert data in classification lines into classification array. # Remove trailing . then split on ';' or '.;' so that classification that is 2 # or more words will still get matched, use map() to remove trailing/leading/intervening # spaces $class_lines=~s/\.\s*$//; my @class = map { s/^\s+//; s/\s+$//; s/\s{2,}/ /g; $_; } split /[;\.]*;/, $class_lines; if ($class[0] =~ /viruses/i) { # viruses have different OS/OC syntax my @virusnames = split(/\s+/, $sci_name); $species = (@virusnames > 1) ? pop(@virusnames) : ''; $genus = join(" ", @virusnames); $sub_species = $descr; } elsif ($do_genus_check) { # do we have a genus? my $possible_genus = $class[-1]; $possible_genus .= "|$class[-2]" if $class[-2]; if ($sci_name =~ /^($possible_genus)/) { $genus = $1; ($species) = $sci_name =~ /^$genus\s+(.+)/; } else { $species = $sci_name; } # is this organism of rank species or is it lower? # (doesn't catch everything, but at least the guess isn't dangerous) if ($species && $species =~ /subsp\.|var\./) { ($species, $sub_species) = $species =~ /(.+)\s+((?:subsp\.|var\.).+)/; } } # Bio::Species array needs array in Species -> Kingdom direction unless ($class[-1] eq $sci_name) { push(@class, $sci_name); } @class = reverse @class; my $taxon = Bio::Species->new(); $taxon->scientific_name($sci_name); $taxon->classification(@class); $taxon->common_name($common) if $common; $taxon->sub_species($sub_species) if $sub_species; $taxon->organelle($org) if $org; $taxon->ncbi_taxid($ncbi_taxid) if $ncbi_taxid; $taxon->variant($variant) if $variant; # done return $taxon; } =head2 _filehandle Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional) =cut # inherited from SeqIO.pm ! HL 05/11/2000 =head2 _read_FTHelper_swissprot Title : _read_FTHelper_swissprot Usage : _read_FTHelper_swissprot(\$buffer) Function: reads the next FT key line Example : Returns : Bio::SeqIO::FTHelper object Args : =cut sub _read_FTHelper_swissprot { my ($self,$line ) = @_; # initial version implemented by HL 05/10/2000 # FIXME this may not be perfect, so please review # lots of cleaning up by JES 2004/07/01, still may not be perfect =) # FTId now sepated from description as a qualifier local $_ = $line; my ($key, # The key of the feature $loc, # The location line from the feature $desc, # The descriptive text $ftid, # feature Id is like a qualifier but there can be only one of them ); if ( m/^FT\s{3}(\w+)\s+([\d\?\<]+)\s+([\d\?\>]+)\s*(.*)$/ox) { $key = $1; my $loc1 = $2; my $loc2 = $3; $loc = "$loc1..$loc2"; if ($4 && (length($4) > 0)) { $desc = $4; chomp($desc); } else { $desc = ""; } } while ( defined($_ = $self->_readline) && /^FT\s{20,}(\S.*)$/ ) { my $continuation_line = $1; if ( $continuation_line =~ /.FTId=(.*)\./ ) { $ftid=$1; } elsif ( $desc) { $desc .= " $continuation_line"; } else { $desc = $continuation_line; } chomp $desc; } $self->_pushback($_); unless( $key ) { # No feature key. What's this? $self->warn("No feature key in putative feature table line: $line"); return; } # Make the new FTHelper object my $out = Bio::SeqIO::FTHelper->new(-verbose => $self->verbose()); $out->key($key); $out->loc($loc); # store the description if there is one if ( $desc && length($desc) ) { $desc =~ s/\.$//; push(@{$out->field->{"description"}}, $desc); } # Store the qualifier i.e. FTId if ( $ftid ) { push(@{$out->field->{"FTId"}}, $ftid); } return $out; } =head2 _write_line_swissprot Title : _write_line_swissprot Usage : Function: internal function Example : Returns : Args : =cut sub _write_line_swissprot{ my ($self,$pre1,$pre2,$line,$length) = @_; $length || $self->throw( "Miscalled write_line_swissprot without length. Programming error!"); my $subl = $length - length $pre2; my $linel = length $line; my $i; my $sub = substr($line,0,$length - length $pre1); $self->_print( "$pre1$sub\n"); for ($i= ($length - length $pre1);$i < $linel;) { $sub = substr($line,$i,($subl)); $self->_print( "$pre2$sub\n"); $i += $subl; } } =head2 _write_line_swissprot_regex Title : _write_line_swissprot_regex Usage : Function: internal function for writing lines of specified length, with different first and the next line left hand headers and split at specific points in the text Example : Returns : nothing Args : file handle, first header, second header, text-line, regex for line breaks, total line length =cut sub _write_line_swissprot_regex { my ($self,$pre1,$pre2,$line,$regex,$length) = @_; #print STDOUT "Going to print with $line!\n"; $length || $self->throw( "Miscalled write_line_swissprot without length. Programming error!"); if ( length $pre1 != length $pre2 ) { $self->warn( "len 1 is ". length ($pre1) . " len 2 is ". length ($pre2) . "\n"); $self->throw( "Programming error - cannot called write_line_swissprot_regex with different length \npre1 ($pre1) and \npre2 ($pre2) tags!"); } my $subl = $length - (length $pre1) -1 ; my $first_line = 1; while ($line =~ m/(.{1,$subl})($regex)/g) { my $s = $1.$2; $s =~ s/([\w\.])#(\w)/$1 $2/g # remove word wrap protection char '#' if $pre1 eq "RA " or $pre1 eq "KW "; # remove annoying extra spaces at the end of the wrapped lines substr($s, -1, 1, '') if substr($s, -1, 1) eq ' '; if ($first_line) { $self->_print( "$pre1$s\n"); $first_line = 0; } else { $self->_print( "$pre2$s\n"); } } } =head2 _post_sort Title : _post_sort Usage : $obj->_post_sort($newval) Function: Returns : value of _post_sort Args : newvalue (optional) =cut sub _post_sort{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_post_sort'} = $value; } return $obj->{'_post_sort'}; } =head2 _show_dna Title : _show_dna Usage : $obj->_show_dna($newval) Function: Returns : value of _show_dna Args : newvalue (optional) =cut sub _show_dna{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_show_dna'} = $value; } return $obj->{'_show_dna'}; } =head2 _id_generation_func Title : _id_generation_func Usage : $obj->_id_generation_func($newval) Function: Returns : value of _id_generation_func Args : newvalue (optional) =cut sub _id_generation_func{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_id_generation_func'} = $value; } return $obj->{'_id_generation_func'}; } =head2 _ac_generation_func Title : _ac_generation_func Usage : $obj->_ac_generation_func($newval) Function: Returns : value of _ac_generation_func Args : newvalue (optional) =cut sub _ac_generation_func{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_ac_generation_func'} = $value; } return $obj->{'_ac_generation_func'}; } =head2 _sv_generation_func Title : _sv_generation_func Usage : $obj->_sv_generation_func($newval) Function: Returns : value of _sv_generation_func Args : newvalue (optional) =cut sub _sv_generation_func{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_sv_generation_func'} = $value; } return $obj->{'_sv_generation_func'}; } =head2 _kw_generation_func Title : _kw_generation_func Usage : $obj->_kw_generation_func($newval) Function: Returns : value of _kw_generation_func Args : newvalue (optional) =cut sub _kw_generation_func{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_kw_generation_func'} = $value; } return $obj->{'_kw_generation_func'}; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/swissdriver.pm�����������������������������������������������������������000444��000766��000024�� 21376�13155576320� 20157� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::swissdriver # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Bioperl project bioperl-l(at)bioperl.org # # Copyright Chris Fields and contributors see AUTHORS section # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::swissdriver - SwissProt/UniProt handler-based push parser =head1 SYNOPSIS #It is probably best not to use this object directly, but #rather go through the SeqIO handler: $stream = Bio::SeqIO->new(-file => $filename, -format => 'swissdriver'); while ( my $seq = $stream->next_seq() ) { # do something with $seq } =head1 DESCRIPTION This object can transform Bio::Seq objects to and from UniProt flat file databases. The key difference between this parser and the tried-and-true Bio::SeqIO::swiss parser is this version separates the parsing and data manipulation into a 'driver' method (next_seq) and separate object handlers which deal with the data passed to it. =head2 The Driver The main purpose of the driver routine, in this case next_seq(), is to carve out the data into meaningful chunks which are passed along to relevant handlers (see below). Each chunk of data in the has a NAME tag attached to it, similar to that for XML parsing. This designates the type of data passed (annotation type or seqfeature) and the handler to be called for processing the data. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Bioperl Project bioperl-l at bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # POD is at the end of the module # Let the code begin... # Let the code begin... package Bio::SeqIO::swissdriver; use vars qw(%FTQUAL_NO_QUOTE); use strict; use Bio::SeqIO::Handler::GenericRichSeqHandler; use Data::Dumper; use base qw(Bio::SeqIO); # signals to process what's in the hash prior to next round, maps ann => names my %SEC = ( OC => 'CLASSIFICATION', OH => 'HOST', # not currently handled, bundled with organism data for now OG => 'ORGANELLE', OX => 'CROSSREF', RA => 'AUTHORS', RC => 'COMMENT', RG => 'CONSRTM', RP => 'POSITION', RX => 'CROSSREF', RT => 'TITLE', RL => 'JOURNAL', AS => 'ASSEMBLYINFO', # Third party annotation '//' => 'RECORDEND' ); # add specialized delimiters here for easier postprocessing my %DELIM = ( CC => "\n", DR => "\n", DT => "\n", ); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); my $handler = $self->_rearrange([qw(HANDLER)],@args); # hash for functions for decoding keys. $handler ? $self->seqhandler($handler) : $self->seqhandler(Bio::SeqIO::Handler::GenericRichSeqHandler->new( -format => 'swiss', -verbose => $self->verbose, -builder => $self->sequence_builder )); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : none =cut sub next_seq { my $self = shift; my $hobj = $self->seqhandler; local($/) = "\n"; # these contain values that need to carry over each round my ($featkey, $qual, $annkey, $seqdata, $location); my $lastann = ''; my $ct = 0; # main parser PARSER: while(defined(my $line = $self->_readline)) { chomp $line; my ($ann, $data) = split(m{\s+}, $line, 2); if ($ann) { if ($ann eq 'FT') { # sequence features if ($data =~ m{^(\w+)\s+([\d\?\<]+)\s+([\d\?\>]+)(?:\s+?(\S.*))?}ox) { # has location data and desc if ($seqdata) { $hobj->data_handler($seqdata); $seqdata = (); } ($seqdata->{FEATURE_KEY}, my $loc1, my $loc2, $data) = ($1, $2, $3, $4); $qual = 'description'; $seqdata->{$qual} = $data; $seqdata->{NAME} = $ann; $seqdata->{LOCATION} = "$loc1..$loc2" if defined $loc1; next PARSER; } elsif ($data =~ m{^\s+/([^=]+)(?:=(.+))?}ox) { # has qualifer ($qual, $data) = ($1, $2 || ''); $ct = ($seqdata->{$qual}) ? ((ref($seqdata->{$qual})) ? scalar(@{ $seqdata->{$qual} }) : 1) : 0 ; } $data =~ s{\.$}{}; if ($ct == 0) { $seqdata->{$qual} .= ($seqdata->{$qual}) ? ' '.$data : $data; } else { if (!ref($seqdata->{$qual})) { $seqdata->{$qual} = [$seqdata->{$qual}]; } ($seqdata->{$qual}->[$ct]) ? ($seqdata->{$qual}->[$ct] .= ' '.$data) : ($seqdata->{$qual}->[$ct] .= $data); } } else { # simple annotations if ($ann ne $lastann) { if (!$SEC{$ann} && $seqdata) { $hobj->data_handler($seqdata); # can't use undef here; it can lead to subtle mem leaks $seqdata = (); } $annkey = (!$SEC{$ann}) ? 'DATA' : # primary data $SEC{$ann}; $seqdata->{'NAME'} = $ann if !$SEC{$ann}; } last PARSER if $ann eq '//'; next PARSER if $ann eq 'SQ'; my $delim = $DELIM{$ann} || ' '; $seqdata->{$annkey} .= ($seqdata->{$annkey}) ? $delim.$data : $data; $lastann = $ann; } } else { # this should only be sequence (fingers crossed!) SEQUENCE: while (defined ($line = $self->_readline)) { if (index($line, '//') == 0) { $data =~ tr{0-9 \n}{}d; $seqdata->{DATA} = $data; #$self->debug(Dumper($seqdata)); $hobj->data_handler($seqdata); $seqdata = (); last PARSER; } else { $data .= $line; $line = undef; } } } } # some files have no // for the last file; this catches the last bit o' data $hobj->data_handler($seqdata) if $seqdata; return $hobj->build_sequence; } =head2 write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object (must be seq) to the stream Returns : 1 for success and 0 for error Args : array of 1 to n Bio::SeqI objects =cut sub write_seq { shift->throw("Use Bio::SeqIO::swiss write_seq() for output"); # maybe make a Writer class as well???? } =head2 seqhandler Title : seqhandler Usage : $stream->seqhandler($handler) Function: Get/Set the Bio::Seq::HandlerBaseI object Returns : Bio::Seq::HandlerBaseI Args : Bio::Seq::HandlerBaseI =cut sub seqhandler { my ($self, $handler) = @_; if ($handler) { $self->throw("Not a Bio::HandlerBaseI") unless ref($handler) && $handler->isa("Bio::HandlerBaseI"); $self->{'_seqhandler'} = $handler; } return $self->{'_seqhandler'}; } 1; __END__ ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/tab.pm�������������������������������������������������������������������000444��000766��000024�� 10530�13155576320� 16327� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������#----------------------------------------------------------------------------- # PACKAGE : Bio::SeqIO::tab # AUTHOR : Philip Lijnzaad <p.lijnzaad@med.uu.nl> # CREATED : Feb 6 2003 # # Copyright (c) This module is free software; you can redistribute it # and/or modify it under the same terms as Perl itself. # # _History_ # # Ewan Birney <birney@ebi.ac.uk> developed the SeqIO # schema and the first prototype modules. # # This code is based on his Bio::SeqIO::raw # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::tab - nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n" =head1 SYNOPSIS Do not use this module directly. Use it via the L<Bio::SeqIO> class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from tabbed flat file databases. It is very useful when doing large scale stuff using the Unix command line utilities (grep, sort, awk, sed, split, you name it). Imagine that you have a format converter 'seqconvert' along the following lines: my $in = Bio::SeqIO->newFh(-fh => \*STDIN , '-format' => $from); my $out = Bio::SeqIO->newFh(-fh=> \*STDOUT, '-format' => $to); print $out $_ while <$in>; then you can very easily filter sequence files for duplicates as: $ seqconvert < foo.fa -from fasta -to tab | sort -u |\ seqconvert -from tab -to fasta > foo-unique.fa Or grep [-v] for certain sequences with: $ seqconvert < foo.fa -from fasta -to tab | grep -v '^S[a-z]*control' |\ seqconvert -from tab -to fasta > foo-without-controls.fa Or chop up a huge file with sequences into smaller chunks with: $ seqconvert < all.fa -from fasta -to tab | split -l 10 - chunk- $ for i in chunk-*; do seqconvert -from tab -to fasta < $i > $i.fa; done # (this creates files chunk-aa.fa, chunk-ab.fa, ..., each containing 10 # sequences) =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Philip Lijnzaad, p.lijnzaad@med.uu.nl =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::tab; use strict; use Bio::Seq; use base qw(Bio::SeqIO); =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : =cut sub next_seq{ my ($self,@args) = @_; ## When its 1 sequence per line with no formatting at all, ## grabbing it should be easy :) my $nextline = $self->_readline(); chomp($nextline) if defined $nextline; return unless defined $nextline; if ($nextline =~ /^([^\t]*)\t(.*)/) { my ($id, $seq)=($1, uc($2)); $seq =~ s/\s+//g; return Bio::Seq->new(-display_id=> $id, -seq => $seq); } else { $self->throw("Can't parse tabbed sequence entry:'$nextline' around line $."); } } =head2 write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object =cut sub write_seq { my ($self,@seq) = @_; foreach (@seq) { if ($_->display_id() =~ /\t/) { $self->throw("display_id [".$_->display_id()."] contains TAB -- illegal in tab format"); } $self->_print($_->display_id(), "\t",$_->seq, "\n") or return; } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/table.pm�����������������������������������������������������������������000444��000766��000024�� 63672�13155576320� 16667� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::table # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::table - sequence input/output stream from a delimited table =head1 SYNOPSIS # Do not to use this object directly, use Bio::SeqIO, for example: $in = Bio::SeqIO->new(-file => $filename, -format => 'table'); while ( my $seq = $in->next_seq() ) { # do something with $seq } =head1 DESCRIPTION This class transforms records in a table-formatted text file into Bio::Seq objects. A table-formatted text file of sequence records for the purposes of this module is defined as a text file with each row corresponding to a sequence, and the attributes of the sequence being in different columns. Columns are delimited by a common delimiter, for instance tab or comma. The module permits specifying which columns hold which type of annotation. The semantics of certain attributes, if present, are pre-defined, e.g., accession number and sequence. Additional attributes may be added to the annotation bundle. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::table; use strict; use Bio::Species; use Bio::Seq::SeqFactory; use Bio::Annotation::Collection; use Bio::Annotation::SimpleValue; use base qw(Bio::SeqIO); =head2 new Title : new Usage : $stream = Bio::SeqIO->new(-file => $filename, -format => 'table') Function: Returns a new seqstream Returns : A Bio::SeqIO stream for a table format Args : Named parameters: -file Name of file to read -fh Filehandle to attach to -comment Leading character(s) introducing a comment line -header the number of header lines to skip; the first non-comment header line will be used to obtain column names; column names will be used as the default tags for attaching annotation. -delim The delimiter for columns as a regular expression; consecutive occurrences of the delimiter will not be collapsed. -display_id The one-based index of the column containing the display ID of the sequence -accession_number The one-based index of the column containing the accession number of the sequence -seq The one-based index of the column containing the sequence string of the sequence -desc The one-based index of the column containing the description of the sequence -species The one-based index of the column containing the species for the sequence record; if not a number, will be used as the static species common to all records -annotation If provided and a scalar (but see below), a flag whether or not all additional columns are to be preserved as annotation, the tags used will either be 'colX' if there is no column header and where X is the one-based column index, and otherwise the column headers will be used as tags; If a reference to an array, or a square bracket-enclosed string of comma-delimited values, only those columns (one-based index) will be preserved as annotation, tags as before; If a reference to a hash, or a curly braces-enclosed string of comma-delimited key and value pairs in alternating order, the keys are one-based column indexes to be preserved, and the values are the tags under which the annotation is to be attached; if not provided or supplied as undef, no additional annotation will be preserved. -colnames A reference to an array of column labels, or a string of comma-delimited labels, denoting the columns to be converted into annotation; this is an alternative to -annotation and will be ignored if -annotation is also supplied with a valid value. -trim Flag determining whether or not all values should be trimmed of leading and trailing white space and double quotes Additional arguments may be used to e.g. set factories and builders involved in the sequence object creation (see the POD of Bio::SeqIO). =cut sub _initialize { my($self,@args) = @_; # chained initialization $self->SUPER::_initialize(@args); # our own parameters my ($cmtchars, $header, $delim, $display_id, $desc, $accnr, $seq, $taxon, $useann, $colnames, $trim) = $self->_rearrange([qw(COMMENT HEADER DELIM DISPLAY_ID DESC ACCESSION_NUMBER SEQ SPECIES ANNOTATION COLNAMES TRIM) ], @args); # store options and apply defaults $self->comment_char(defined($cmtchars) ? $cmtchars : "#") if (!defined($self->comment_char)) || defined($cmtchars); $self->delimiter(defined($delim) ? $delim : "\t") if (!defined($self->delimiter)) || defined($delim); $self->header($header) if defined($header); $self->trim_values($trim) if defined($trim); # attribute columns my $attrs = {}; $attrs->{-display_id} = $display_id if defined($display_id); $attrs->{-accession_number} = $accnr if defined($accnr); $attrs->{-seq} = $seq if defined($seq); $attrs->{-desc} = $desc if defined($desc); if (defined($taxon)) { if (ref($taxon) || ($taxon =~ /^\d+$/)) { # either a static object, or a column reference $attrs->{-species} = $taxon; } else { # static species as a string $attrs->{-species} = Bio::Species->new( -classification => [reverse(split(' ',$taxon))]); } } $self->attribute_map($attrs); # annotation columns, if any if ($useann && !ref($useann)) { # it's a scalar; check whether this is in fact an array or # hash as a string rather than just a flag if ($useann =~ /^\[(.*)\]$/) { $useann = [split(/[,;]/,$1)]; } elsif ($useann =~ /^{(.*)}$/) { $useann = {split(/[,;]/,$1)}; } # else it is probably indeed just a flag } if (ref($useann)) { my $ann_map; if (ref($useann) eq "ARRAY") { my $has_header = ($self->header > 0); $ann_map = {}; foreach my $i (@$useann) { $ann_map->{$i} = $has_header ? undef : "col$i"; } } else { # no special handling necessary $ann_map = $useann; } $self->annotation_map($ann_map); } else { $self->keep_annotation($useann || $colnames); # annotation columns, if any if ($colnames && !ref($colnames)) { # an array as a string $colnames =~ s/^\[(.*)\]$/$1/; $colnames = [split(/[,;]/,$colnames)]; } $self->annotation_columns($colnames) if ref($colnames); } # make sure we have a factory defined if(!defined($self->sequence_factory)) { $self->sequence_factory( Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq::RichSeq object Args : =cut sub next_seq { my $self = shift; # skip until not a comment and not an empty line my $line_ok = $self->_next_record(); # if there is a header but we haven't read past it yet then do so now if ($line_ok && (! $self->_header_skipped) && $self->header) { $line_ok = $self->_parse_header(); $self->_header_skipped(1); } # return if we reached end-of-file return unless $line_ok; # otherwise, parse the record # split into columns my @cols = $self->_get_row_values(); # trim leading and trailing whitespace and quotes if desired if ($self->trim_values) { for(my $i = 0; $i < scalar(@cols); $i++) { if ($cols[$i]) { # trim off whitespace $cols[$i] =~ s/^\s+//; $cols[$i] =~ s/\s+$//; # trim off double quotes $cols[$i] =~ s/^"//; $cols[$i] =~ s/"$//; } } } # assign values for columns in the attribute map my $attrmap = $self->_attribute_map; my %params = (); foreach my $attr (keys %$attrmap) { if ((!ref($attrmap->{$attr})) && ($attrmap->{$attr} =~ /^\d+$/)) { # this is a column index, add to instantiation parameters $params{$attr} = $cols[$attrmap->{$attr}]; } else { # not a column index; we assume it's a static value $params{$attr} = $attrmap->{$attr}; } } # add annotation columns to the annotation bundle my $annmap = $self->_annotation_map; if ($annmap && %$annmap) { my $anncoll = Bio::Annotation::Collection->new(); foreach my $col (keys %$annmap) { next unless $cols[$col]; # skip empty columns! $anncoll->add_Annotation( Bio::Annotation::SimpleValue->new(-value => $cols[$col], -tagname=> $annmap->{$col})); } $params{'-annotation'} = $anncoll; } # ask the object builder to add the slots that we've gathered my $builder = $self->sequence_builder(); $builder->add_slot_value(%params); # and instantiate the object my $seq = $builder->make_object(); # done! return $seq; } =head2 comment_char Title : comment_char Usage : $obj->comment_char($newval) Function: Get/set the leading character(s) designating a line as a comment-line. Example : Returns : value of comment_char (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub comment_char{ my $self = shift; return $self->{'comment_char'} = shift if @_; return $self->{'comment_char'}; } =head2 header Title : header Usage : $obj->header($newval) Function: Get/set the number of header lines to skip before the rows containing actual sequence records. If set to zero or undef, means that there is no header and therefore also no column headers. Example : Returns : value of header (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub header{ my $self = shift; return $self->{'header'} = shift if @_; return $self->{'header'}; } =head2 delimiter Title : delimiter Usage : $obj->delimiter($newval) Function: Get/set the column delimiter. This will in fact be treated as a regular expression. Consecutive occurrences will not be collapsed to a single one. Example : Returns : value of delimiter (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub delimiter{ my $self = shift; return $self->{'delimiter'} = shift if @_; return $self->{'delimiter'}; } =head2 attribute_map Title : attribute_map Usage : $obj->attribute_map($newval) Function: Get/set the map of sequence object initialization attributes (keys) to one-based column index. Attributes will usually need to be prefixed by a dash, just as if they were passed to the new() method of the sequence class. Example : Returns : value of attribute_map (a reference to a hash) Args : on set, new value (a reference to a hash or undef, optional) =cut sub attribute_map{ my $self = shift; # internally we store zero-based maps - so we need to convert back # and forth here if (@_) { my $arg = shift; # allow for and protect against undef return delete $self->{'_attribute_map'} unless defined($arg); # copy to avoid side-effects my $attr_map = {%$arg}; foreach my $key (keys %$attr_map) { if ((!ref($attr_map->{$key})) && ($attr_map->{$key} =~ /^\d+$/)) { $attr_map->{$key}--; } } $self->{'_attribute_map'} = $attr_map; } # there may not be a map return unless exists($self->{'_attribute_map'}); # we need to copy in order not to override the stored map! my %attr_map = %{$self->{'_attribute_map'}}; foreach my $key (keys %attr_map) { if ((!ref($attr_map{$key})) && ($attr_map{$key} =~ /^\d+$/)) { $attr_map{$key}++; } } return \%attr_map; } =head2 annotation_map Title : annotation_map Usage : $obj->annotation_map($newval) Function: Get/set the mapping between one-based column indexes (keys) and annotation tags (values). Note that the map returned by this method may change after the first next_seq() call if the file contains a column header and no annotation keys have been predefined in the map, because upon reading the column header line the tag names will be set automatically. Note also that the map may reference columns that are used as well in the sequence attribute map. Example : Returns : value of annotation_map (a reference to a hash) Args : on set, new value (a reference to a hash or undef, optional) =cut sub annotation_map{ my $self = shift; # internally we store zero-based maps - so we need to convert back # and forth here if (@_) { my $arg = shift; # allow for and protect against undef return delete $self->{'_annotation_map'} unless defined($arg); # copy to avoid side-effects my $ann_map = {%$arg}; # make sure we sort the keys numerically or otherwise we may # clobber a key with a higher index foreach my $key (sort { $a <=> $b } keys(%$ann_map)) { $ann_map->{$key-1} = $ann_map->{$key}; delete $ann_map->{$key}; } $self->{'_annotation_map'} = $ann_map; # also make a note that we want to keep annotation $self->keep_annotation(1); } # there may not be a map return unless exists($self->{'_annotation_map'}); # we need to copy in order not to override the stored map! my %ann_map = %{$self->{'_annotation_map'}}; # here we need to sort numerically in reverse order ... foreach my $key (sort { $b <=> $a } keys(%ann_map)) { $ann_map{$key+1} = $ann_map{$key}; delete $ann_map{$key}; } return \%ann_map; } =head2 keep_annotation Title : keep_annotation Usage : $obj->keep_annotation($newval) Function: Get/set flag whether or not to keep values from additional columns as annotation. Additional columns are all those columns in the input file that aren't referenced in the attribute map. Example : Returns : value of keep_annotation (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub keep_annotation{ my $self = shift; return $self->{'keep_annotation'} = shift if @_; return $self->{'keep_annotation'}; } =head2 annotation_columns Title : annotation_columns Usage : $obj->annotation_columns($newval) Function: Get/set the names (labels) of the columns to be used for annotation. This is an alternative to using annotation_map. In order to have any effect, it must be set before the first call of next_seq(), and obviously there must be a header line (or row) too giving the column labels. Example : Returns : value of annotation_columns (a reference to an array) Args : on set, new value (a reference to an array of undef, optional) =cut sub annotation_columns{ my $self = shift; return $self->{'annotation_columns'} = shift if @_; return $self->{'annotation_columns'}; } =head2 trim_values Title : trim_values Usage : $obj->trim_values($newval) Function: Get/set whether or not to trim leading and trailing whitespace off all column values. Example : Returns : value of trim_values (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub trim_values{ my $self = shift; return $self->{'trim_values'} = shift if @_; return $self->{'trim_values'}; } =head2 write_seq Title: write_seq Usage: write_seq() is not implemented for table format output. =cut sub write_seq { shift->throw("write_seq() not implemented for 'table' format"); } =head1 Internal methods All methods with a leading underscore are not meant to be part of the 'official' API. They are for use by this module only, consider them private unless you are a developer trying to modify this module. =cut =head2 _attribute_map Title : _attribute_map Usage : $obj->_attribute_map($newval) Function: Get only. Same as attribute_map, but zero-based indexes. Note that any changes made to the returned map will change the map used by this instance. You should know what you are doing if you modify the returned value (or if you call this method in the first place). Example : Returns : value of _attribute_map (a reference to a hash) Args : none =cut sub _attribute_map{ my $self = shift; return $self->{'_attribute_map'}; } =head2 _annotation_map Title : _annotation_map Usage : $obj->_annotation_map($newval) Function: Get only. Same as annotation_map, but with zero-based indexes. Note that any changes made to the returned map will change the map used by this instance. You should know what you are doing if you modify the returned value (or if you call this method in the first place). Example : Returns : value of _annotation_map (a reference to a hash) Args : none =cut sub _annotation_map{ my $self = shift; return $self->{'_annotation_map'}; } =head2 _header_skipped Title : _header_skipped Usage : $obj->_header_skipped($newval) Function: Get/set the flag whether the header was already read (and skipped) or not. Example : Returns : value of _header_skipped (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub _header_skipped{ my $self = shift; return $self->{'_header_skipped'} = shift if @_; return $self->{'_header_skipped'}; } =head2 _next_record Title : _next_record Usage : Function: Navigates the underlying file to the next record. For row-based records in delimited text files, this will skip all empty lines and lines with a leading comment character. This method is here is to serve as a hook for other formats that conceptually also represent tables but aren't formatted as row-based text files. Example : Returns : TRUE if the navigation was successful and FALSE otherwise. Unsuccessful navigation will usually be treated as an end-of-file condition. Args : =cut sub _next_record{ my $self = shift; my $cmtcc = $self->comment_char; my $line = $self->_readline(); # skip until not a comment and not an empty line while (defined($line) && (($cmtcc && ($line =~ /^\s*$cmtcc/)) || ($line =~ /^\s*$/))) { $line = $self->_readline(); } return $self->{'_line'} = $line; } =head2 _parse_header Title : _parse_header Usage : Function: Parse the table header and navigate past it. This method is called if the number of header rows has been specified equal to or greater than one, and positioned at the first header line (row). By default the first header line (row) is used for setting column names, but additional lines (rows) may be skipped too. Empty lines and comment lines do not count as header lines (rows). This method will call _next_record() to navigate to the next header line (row), if there is more than one header line (row). Upon return, the file is presumed to be positioned at the first record after the header. This method is here is to serve as a hook for other formats that conceptually also represent tables but aren't formatted as row-based text files. Note however that the only methods used to access file content or navigate the position are _get_row_values() and _next_record(), so it should usually suffice to override those. Example : Returns : TRUE if navigation past the header was successful and FALSE otherwise. Unsuccessful navigation will usually be treated as an end-of-file condition. Args : =cut sub _parse_header{ my $self = shift; # the first header line contains the column headers, see whether # we need them if ($self->keep_annotation) { my @colnames = $self->_get_row_values(); # trim leading and trailing whitespace if desired if ($self->trim_values) { # trim off whitespace @colnames = map { $_ =~ s/^\s+//; $_ =~ s/\s+$//; $_; } @colnames; # trim off double quotes @colnames = map { $_ =~ s/^"//; $_ =~ s/"$//; $_; } @colnames; } # build or complete annotation column map my $annmap = $self->annotation_map || {}; if (! %$annmap) { # check whether columns have been defined by name rather than index if (my $anncols = $self->annotation_columns) { # first sanity check: all column names must map my %colmap = map { ($_,1); } @colnames; foreach my $col (@$anncols) { if (!exists($colmap{$col})) { $self->throw("no such column labeled '$col'"); } } # now map to the column indexes %colmap = map { ($_,1); } @$anncols; for (my $i = 0; $i < scalar(@colnames); $i++) { if (exists($colmap{$colnames[$i]})) { $annmap->{$i+1} = $colnames[$i]; } } } else { # no columns specified, default to all non-attribute columns for (my $i = 0; $i < scalar(@colnames); $i++) { $annmap->{$i+1} = $colnames[$i]; } # subtract all attribute-referenced columns foreach my $attrcol (values %{$self->attribute_map}) { if ((!ref($attrcol)) && ($attrcol =~ /^\d+$/)) { delete $annmap->{$attrcol}; } } } } else { # fill in where the tag names weren't pre-defined for (my $i = 0; $i < scalar(@colnames); $i++) { if (exists($annmap->{$i+1}) && ! defined($annmap->{$i+1})) { $annmap->{$i+1} = $colnames[$i]; } } } $self->annotation_map($annmap); } # now read past the header my $header_lines = $self->header; my $line_ok = 1; while (defined($line_ok) && ($header_lines > 0)) { $line_ok = $self->_next_record(); $header_lines--; } return $line_ok; } =head2 _get_row_values Title : _get_row_values Usage : Function: Get the values for the current line (or row) as an array in the order of columns. This method is here is to serve as a hook for other formats that conceptually also represent tables but aren't formatted as row-based text files. Example : Returns : An array of column values for the current row. Args : =cut sub _get_row_values{ my $self = shift; my $delim = $self->delimiter; my $line = $self->{'_line'}; chomp($line); my @cols = split(/$delim/,$line); return @cols; } 1; ����������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/tigr.pm������������������������������������������������������������������000444��000766��000024�� 100623�13155576320� 16551� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::tigr # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Josh Lauricha (laurichj@bioinfo.ucr.edu) # # Copyright Josh Lauricha # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::tigr - TIGR XML sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from efa flat file databases. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Josh Lauricha Email: laurichj@bioinfo.ucr.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # TODO: # - Clean up code # - Find and fix bugs ;) # Let the code begin... package Bio::SeqIO::tigr; use strict; use Bio::Seq::RichSeq; use Bio::Species; use Bio::Annotation::Comment; use Bio::SeqFeature::Generic; use Bio::Seq::SeqFactory; use Bio::Seq::RichSeq; use Data::Dumper; use Error qw/:try/; use base qw(Bio::SeqIO); sub _initialize { my($self, @args) = @_; $self->SUPER::_initialize(@args); $self->sequence_factory(Bio::Seq::SeqFactory->new( -type => 'Bio::Seq::RichSeq') ); # Parse the document $self->_process(); } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : NONE =cut sub next_seq() { my ($self) = @_; # Check for any more sequences return if !defined($self->{_sequences}) or scalar(@{$self->{_sequences}}) < 1; # get the next sequence my $seq = shift(@{ $self->{_sequences} } ); # Get the 5' and 3' ends my ($source) = grep { $_->primary_tag() eq 'source' } $seq->get_SeqFeatures(); my ($end5) = $source->get_tag_values('end5'); my ($end3) = $source->get_tag_values('end3'); # Sort the 5' and 3': my ($start, $end) = ( $end5 < $end3 ? ( $end5, $end3 ) : ( $end3, $end5 ) ); # make the start a perl index $start -= 1; # Figure out the length my $length = $end - $start; # check to make sure $start >= 0 and $end <= length(assembly_seq) if($start < 0) { throw Bio::Root::OutOfRange("the sequence start is $start < 0"); } elsif($end > length($self->{_assembly}->{seq})) { throw Bio::Root::OutOfRange("the sequence end is $end < " . length($self->{_assembly}->{seq})); } elsif($start >= $end) { throw Bio::Root::OutOfRange("the sequence start is after end $start >= $end"); } # Get and set the real sequence $seq->seq(substr($self->{_assembly}->{seq}, $start, $length)); if( $end5 > $end3 ) { # Reverse complement the sequence $seq->seq( $seq->primary_seq()->revcom()->seq() ); } # add the translation to each CDS foreach my $feat ($seq->get_SeqFeatures()) { next if $feat->primary_tag() ne "CDS"; # Check for an invalid protein try { # Get the subsq my $cds = Bio::PrimarySeq->new( -strand => 1, -id => $seq->accession_number(), -seq => $seq->subseq($feat->location()) ); # Translate it my $trans = $cds->translate(undef, undef, undef, undef, 1, 1)->seq(); # Add the tag $feat->add_tag_value(translation => $trans); } catch Bio::Root::Exception with { print STDERR 'TIGR strikes again, the CDS is not a valid protein: ', $seq->accession_number(), "\n" if $self->verbose() > 0; }; } # Set the display id to the accession number if there # is no display id $seq->display_id( $seq->accession_number() ) unless $seq->display_id(); return $seq; } sub _process { my($self) = @_; my $line; my $tu = undef; $line = $self->_readline(); do { if($line =~ /<\?xml\s+version\s+=\s+"\d+\.\d+"\?>/o) { # do nothing } elsif ($line =~ /<!DOCTYPE (\w+) SYSTEM "[\w\.]+">/o) { $self->throw("DOCTYPE of $1, not TIGR!") if $1 ne "TIGR" ; } elsif ($line =~ /<TIGR>/o) { $self->_pushback($line); $self->_process_tigr(); } elsif ($line =~ /<ASSEMBLY.*?>/o) { $self->_pushback($line); $self->_process_assembly(); } elsif ($line =~ /<\/TIGR>/o) { $self->{'eof'} = 1; return; } else { $self->throw("Unknown or Invalid process directive:", join('', ($line =~ /^\s*(<[^>]+>)/o))); } $line = $self->_readline(); } while( defined( $line ) ); } sub _process_tigr { my($self) = @_; my $line; $line = $self->_readline(); if($line !~ /<TIGR>/o) { $self->throw("Bio::SeqIO::tigr::_process_tigr called but no ", "<TIGR> found in stream"); } $line = $self->_readline(); if($line =~ /<PSEUDOCHROMOSOME>/o) { $self->_pushback($line); $self->_process_pseudochromosome(); } elsif ($line =~ /<ASSEMBLY.*?>/o) { $self->_pushback($line); $self->_process_assembly(); } } sub _process_pseudochromosome { my($self) = @_; my $line; $line = $self->_readline(); return if $line !~ /<PSEUDOCHROMOSOME>/o; $line = $self->_readline(); if($line =~ /<SCAFFOLD>/o) { $self->_pushback($line); $self->_process_scaffold(); $line = $self->_readline(); } else { $self->warn( "No Scaffold found in <PSUEDOCHROMOSOME> this " . "is a violation of the TIGR dtd, but we ignore " . "it so we are ignoring the error\n" ); } if($line =~ /<ASSEMBLY.*>/o) { $self->_pushback($line); $self->_process_assembly(); $line = $self->_readline(); } else { $self->throw("Missing required ASSEMBLY in <PSEUDOCHROMOSOME>"); } if($line =~ /<\/PSEUDOCHROMOSOME>/) { return; } $self->throw("Reached end of _process_pseudochromosome"); } sub _process_assembly { my($self) = @_; my $line; $line = $self->_readline(); if($line !~ /<ASSEMBLY([^>]*)>/o) { $self->throw("Bio::SeqIO::tigr::_process_assembly called ", "but no <ASSEMBLY> found in stream"); } my %attribs = ($1 =~ /(\w+)\s*=\s+"(.*?)"/og); $self->{_assembly}->{date} = $attribs{CURRENT_DATE}; $self->{_assembly}->{db} = $attribs{DATABASE}; $self->{_assembly}->{chromosome} = $attribs{CHROMOSOME}; $line = $self->_readline(); my($attr, $val); if(($attr, $val) = ($line =~ /<ASMBL_ID([^>]*)>([^<]*)<\/ASMBL_ID>/o)) { %attribs = ($attr =~ /(\w+)\s*=\s+"(.*?)"/og); $self->{_assembly}->{clone_name} = $attribs{CLONE_NAME}; $self->{_assembly}->{clone} = $val; $line = $self->_readtag(); } else { $self->throw("Required <ASMBL_ID> missing"); } if($line =~ /<COORDSET>/o) { $self->_pushback($line); my $cs = $self->_process_coordset(); $self->{_assembly}->{end5} = $cs->{end5}; $self->{_assembly}->{end3} = $cs->{end3}; $line = $self->_readline(); } else { $self->throw("Required <COORDSET> missing"); } if($line =~ /<HEADER>/o) { $self->_pushback($line); $self->_process_header(); $line = $self->_readline(); } else { $self->throw("Required <HEADER> missing"); } if($line =~ /<TILING_PATH>/o) { $self->_pushback($line); $self->_process_tiling_path(); $line = $self->_readline(); } if($line =~ /<GENE_LIST>/o) { $self->_pushback($line); $self->_process_gene_list(); $line = $self->_readline(); } else { $self->throw("Required <GENE_LIST> missing"); } if($line =~ /<MISC_INFO>/o) { $self->_pushback($line); $self->_process_misc_info(); $line = $self->_readline(); } if($line =~ /<REPEAT_LIST>/o) { $self->_pushback($line); $self->_process_repeat_list(); $line = $self->_readline(); } if($line =~ /<ASSEMBLY_SEQUENCE>/o) { $self->_pushback($line); $self->_process_assembly_seq(); $line = $self->_readline(); } else { $self->throw("Required <ASSEMBLY_SEQUENCE> missing"); } if($line =~ /<\/ASSEMBLY>/o) { return; } $self->throw("Reached the end of <ASSEMBLY>"); } sub _process_assembly_seq() { my ($self) = @_; my $line; $line = $self->_readline(); if($line !~ /<ASSEMBLY_SEQUENCE>/o) { $self->throw("Bio::SeqIO::tigr::_process_assembly_seq called ". "with no <ASSEMBLY_SEQUENCE> in the stream"); } # Protect against lots of smaller lines my @chunks; do { $line = $self->_readline(); last unless $line; my $seq; if (($seq) = ($line =~ /^\s*(\w+)\s*$/o)) { push(@chunks, $seq); } elsif( ($seq) = ( $line =~ /^\s*(\w+)<\/ASSEMBLY_SEQUENCE>\s*$/o) ) { push(@chunks, $seq); $self->{_assembly}->{seq} = join('', @chunks); return; } } while( $line ); $self->throw("Reached end of _proces_assembly"); } sub _process_coordset($) { my ($self) = @_; my $line; my $h; $line = $self->_readline(); if($line =~ /<COORDSET>/o) { $self->_pushback($line); $line = $self->_readtag(); ($h->{end5}, $h->{end3}) = ($line =~ /<COORDSET>\s*<END5>\s*(\d+)\s*<\/END5>\s*<END3>\s*(\d+)\s*<\/END3>/os); if(!defined($h->{end5}) or !defined($h->{end3})) { $self->throw("Invalid <COORDSET>: $line"); } return $h; } else { $self->throw("Bio::SeqIO::tigr::_process_coordset() called ", "but no <COORDSET> found in stream"); } } sub _process_header { my ($self) = @_; my $line = $self->_readline(); if($line !~ /<HEADER>/o) { $self->throw("Bio::SeqIO::tigr::_process_header called ", "but no <HEADER> found in stream"); } $line = $self->_readtag(); if($line =~ /<CLONE_NAME>([^>]+)<\/CLONE_NAME>/o) { $self->{_assembly}->{clone_name} = $1; $line = $self->_readtag(); } else { $self->throw("Required <CLONE_NAME> missing"); } if($line =~ /<SEQ_LAST_TOUCHED>/o) { # Ignored for now $line = $self->_readtag(); } else { $self->throw("Reqired <SEQ_LAST_TOUCHED> missing"); } if($line =~ /<GB_ACCESSION>([^<]*)<\/GB_ACCESSION>/o) { $self->{_assembly}->{gb} = $1; $line = $self->_readtag(); } else { $self->throw("Required <GB_ACCESSION> missing"); } if($line =~ /<ORGANISM>\s*(.+)\s*<\/ORGANISM>/o) { my( $genus, $species, @ss ) = split(/\s+/o, $1); $self->{_assembly}->{species} = Bio::Species->new(); $self->{_assembly}->{species}->genus($genus); $self->{_assembly}->{species}->species($species); $self->{_assembly}->{species}->sub_species(join(' ', @ss)) if scalar(@ss) > 0; $line = $self->_readtag(); } else { $self->throw("Required <ORGANISM> missing"); } if($line =~ /<LINEAGE>([^<]*)<\/LINEAGE>/o) { $self->{_assembly}->{species}->classification( $self->{_assembly}->{species}->species(), reverse(split(/\s*;\s*/o, $1)) ); $line = $self->_readtag(); } else { $self->throw("Required <LINEAGE> missing"); } if($line =~ /<SEQ_GROUP>([^<]*)<\/SEQ_GROUP>/o) { # ingnored $line = $self->_readtag(); } else { $self->throw("Required <SEQ_GROUP> missing"); } while($line =~ /<KEYWORDS>[^<]*<\/KEYWORDS>/o) { push(@{$self->{_assembly}->{keywords}}, $1); $line = $self->_readtag(); } while($line =~ /<GB_DESCRIPTION>([^<]+)<\/GB_DESCRIPTION>/o) { push(@{$self->{_assembly}->{gb_desc}},$1); $line = $self->_readtag(); } while($line =~ /<GB_COMMENT>([^<]+)<\/GB_COMMENT>/o) { push(@{$self->{_assembly}->{gb_comment}}, $1); $line = $self->_readtag(); } if(my %h = ($line =~ /<AUTHOR_LIST(?:\s*(\w+)\s*=\s*"([^"]+)"\s*)*>/o)) { #$header->{'AUTHOR_LIST'}=$h{'CONTACT'}; # Ignored while($line !~ /<\/AUTHOR_LIST>/o) { $self->_readtag(); } $line = $self->_readline(); } else { $self->throw("Required <AUTHOR_LIST> missing"); } if($line =~ /<\/HEADER>/o) { return; } $self->throw("Reached end of header\n"); } sub _process_gene_list { my($self) = @_; my $line; $line = $self->_readline(); if($line !~ /<GENE_LIST>/o) { $self->throw("Bio::SeqIO::tigr::_process_gene_list called ", "but no <GENE_LIST> in the stream"); } $line = $self->_readline(); if($line =~ /<PROTEIN_CODING>/o) { $self->_pushback($line); $self->_process_protein_coding(); $line = $self->_readline(); } else { $self->throw("Required <PROTEIN_CODING> missing"); } if($line =~ /<RNA_GENES>/o) { $self->_pushback($line); $self->_process_rna_genes(); $line = $self->_readline(); } else { $self->throw("Required <RNA_GENES> missing"); } if($line =~ /<\/GENE_LIST>/o) { return; } $self->throw("Reached end of _process_gene_list"); } sub _process_protein_coding { my ($self) = @_; my $line = $self->_readline(); if($line !~ /<PROTEIN_CODING>/o) { $self->throw("Bio::SeqIO::tigr::_process_protein_coding called" . "but no <GENE_LIST> in the stream"); } $line = $self->_readline(); while($line and $line =~ /<TU>/o) { $self->_pushback($line); $self->_process_tu(); $line = $self->_readline(); } # Sort the sequences @{$self->{_sequences}} = sort { my($one, $two) = ( $a, $b ); ($one) = grep { $_->primary_tag() eq 'source' } $one->get_SeqFeatures(); ($two) = grep { $_->primary_tag() eq 'source' } $two->get_SeqFeatures(); return 0 unless defined $one and defined $two; ($one) = sort { $a <=> $b } $one->get_tagset_values(qw/end5 end3/); ($two) = sort { $a <=> $b } $two->get_tagset_values(qw/end5 end3/); return $one <=> $two; } @{$self->{_sequences}}; if($line =~ /<\/PROTEIN_CODING>/o) { return; } $self->throw("Reached end of _process_protein_coding"); } sub _process_rna_genes { my ($self) = @_; my $line = $self->_readline(); if($line =~ /<RNA_GENES>/o) { while($line !~ /<\/RNA_GENES>/o) { $line = $self->_readline(); } } else { $self->throw("Bio::SeqIO::tigr::_process_rna_genes called ", "but no <RNA_GENES> in the stream"); } } sub _process_misc_info { my ($self) = @_; my $line = $self->_readline(); if($line =~ /<MISC_INFO>/o) { while($line !~ /<\/MISC_INFO>/o) { $line = $self->_readline(); } } else { $self->throw("Bio::SeqIO::tigr::_process_misc_info called ", "but no <MISC_INFO> in the stream"); } } sub _process_repeat_list { my ($self) = @_; my $line = $self->_readline(); if($line =~ /<REPEAT_LIST>/o) { while($line !~ /<\/REPEAT_LIST>/o) { $line = $self->_readline(); } } else { $self->throw("Bio::SeqIO::tigr::_process_repeat_list called ", "but no <MISC_INFO> in the stream"); } } sub _process_tiling_path { my($self) = @_; my $line = $self->_readline(); if($line =~ /<TILING_PATH>/o) { while($line !~ /<\/TILING_PATH>/o) { $line = $self->_readline(); } } else { $self->throw("Bio::SeqIO::tigr::_process_repeat_list called ", "but no <MISC_INFO> in the stream"); } } sub _process_scaffold { my ($self) = @_; my $line; # for now we just skip them $line = $self->_readline(); return if $line !~ /<SCAFFOLD>/o; do { $line = $self->_readline(); } while(defined($line) && $line !~ /<\/SCAFFOLD>/o); } sub _process_tu { my($self) = @_; my $line = $self->_readline(); try { my $tu = Bio::Seq::RichSeq->new(-strand => 1); $tu->species( $self->{_assembly}->{species} ); # Add the source tag, so we can add the GO annotations to it $tu->add_SeqFeature(Bio::SeqFeature::Generic->new(-source_tag => 'TIGR', -primary_tag => 'source')); if($line !~ /<TU>/o) { $self->throw("Process_tu called when no <TU> tag"); } $line = $self->_readtag(); if ($line =~ /<FEAT_NAME>([\w\.]+)<\/FEAT_NAME>/o) { $tu->accession_number($1); $tu->add_secondary_accession($1); $line = $self->_readtag(); } else { $self->throw("Invalid Feat_Name"); } while($line =~ /<GENE_SYNONYM>/o) { # ignore $line = $self->_readtag(); } while($line =~ /<CHROMO_LINK>\s*([\w\.]+)\s*<\/CHROMO_LINK>/o) { $tu->add_secondary_accession($1); $line = $self->_readtag(); } if ($line =~ /<DATE>([^>]*)<\/DATE>/o) { $tu->add_date($1) if $1 and $1 !~ /^\s*$/o; $line = $self->_readline(); } else { #$self->throw("Invalid Date: $line"); } if ($line =~ /<GENE_INFO>/o) { $self->_pushback($line); $self->_process_gene_info($tu); $line = $self->_readline(); } else { $self->throw("Invalid Gene_Info"); } my $source; my $end5; my $end3; if($line =~ /<COORDSET>/o) { $self->_pushback($line); my $cs = $self->_process_coordset(); $end5 = $cs->{end5}; $end3 = $cs->{end3}; my $length = $end3 - $end5; my $strand = $length <=> 0; $length = $length * $strand; $length++; # Correct for starting at 1, not 0 # Add X filler sequence $tu->seq('X' x $length); # Get the source tag: my($source) = grep { $_->primary_tag() eq 'source' } $tu->get_SeqFeatures(); # Set the start and end values $source->start(1); $source->end($length); $source->strand(1); # Add a bunch of tags to it $source->add_tag_value(clone => $self->{_assembly}->{clone}); $source->add_tag_value(clone_name => $self->{_assembly}->{clone_name}); $source->add_tag_value(end5 => $end5); $source->add_tag_value(end3 => $end3); $source->add_tag_value(chromosome => $self->{_assembly}->{chromosome}); $source->add_tag_value(strand => ( $strand == 1 ? 'positive' : 'negative' )); $line = $self->_readline(); } else { $self->throw("Invalid Coordset"); } if($line =~ /<MODEL[^>]*>/o) { do { $self->_pushback($line); $self->_process_model($tu, $end5, $end3); $line = $self->_readline(); } while($line =~ /<MODEL[^>]*>/o); $self->_pushback($line); $line = $self->_readtag(); } else { $self->throw("Expected <MODEL> not found"); } if($line =~ /<TRANSCRIPT_SEQUENCE>/o) { my @chunks; $line = $self->_readline(); while ($line =~ /^\s*([ACGT]+)\s*$/o) { push( @chunks, $1 ); $line = $self->_readline(); } # $line = $self->_readline(); } if($line =~ /<GENE_EVIDENCE>/o) { $line = $self->_readtag(); } while($line =~ /<URL[^>]*>[^<]*<\/URL>/o) { $line = $self->_readtag(); } if($line =~ /<\/TU>/o) { push(@{$self->{_sequences}}, $tu); return; } else { $self->throw("Expected </TU> not found: $line"); } } catch Bio::Root::OutOfRange with { my $E = shift; $self->warn(sprintf("One sub location of a sequence is invalid near line $.\: %s", $E->text())); $line = $self->_readline() until $line =~ /<\/TU>/o; return; }; } sub _process_gene_info { my($self, $tu) = @_; my $line = $self->_readline(); $self->throw("Invalid Gene Info: $line") if $line !~ /<GENE_INFO>/o; $line = $self->_readline(); if($line =~ /<LOCUS>\s*([\w\.]+)\s*<\/LOCUS>/o) { $tu->accession_number($1); $tu->add_secondary_accession($1); $line = $self->_readline(); } elsif( $line =~ /<LOCUS>.*<\/LOCUS>/o) { # We should throw an error, but TIGR doesn't alwasy play # nice with adhering to their dtd $line = $self->_readtag(); } else { #$self->throw("Invalid Locus: $line"); } if($line =~ /<ALT_LOCUS>\s*([\w\.]+)\s*<\/ALT_LOCUS>/o) { $tu->accession_number($1); $tu->add_secondary_accession($1); $line = $self->_readline(); } if($line =~ /<PUB_LOCUS>\s*([\w\.]+)\s*<\/PUB_LOCUS>/o) { $tu->accession_number($1); $tu->add_secondary_accession($1); $line = $self->_readtag(); } elsif( $line =~ /<PUB_LOCUS>.*<\/PUB_LOCUS>/o) { $line = $self->_readtag(); # $self->throw("Invalid Pub_Locus"); } if($line =~ /<GENE_NAME.*>.*<\/GENE_NAME>/o) { # Skip the GENE_NAME $line = $self->_readtag(); } if(my($attr, $value) = ($line =~ /<COM_NAME([^>]*)>([^>]+)<\/COM_NAME>/o)) { #%attribs = ($attr =~ /(\w+)\s*=\s+"(.*?)"/og); #$geneinfo->{'CURATED'} = $attribs{CURATED}; #$geneinfo->{IS_PRIMARY} = $attribs{IS_PRIMARY} # TODO: add a tag on sources for curated $tu->desc($value); $line = $self->_readtag(); } else { $self->throw("invalid com_name: $line"); } while($line =~ /<COMMENT>([^<]+)<\/COMMENT>/o) { my $comment = Bio::Annotation::Comment->new( -text => $1 ); $tu->annotation()->add_Annotation('comment', $comment); $line = $self->_readtag(); } while($line =~ /<PUB_COMMENT>([^<]+)<\/PUB_COMMENT>/o) { my $comment = Bio::Annotation::Comment->new( -text => $1 ); $tu->annotation()->add_Annotation('comment', $comment); $line = $self->_readtag(); } if($line =~ /<EC_NUM>([\w\-\\\.]+)<\/EC_NUM>/o) { #$geneinfo->{'EC_NUM'} = $1; $line = $self->_readtag(); } if($line =~ /<GENE_SYM>\s*([^<]+)\s*<\/GENE_SYM>/o) { #$tu->add_secondary_accession($1); $line = $self->_readtag(); } if($line =~ /<IS_PSEUDOGENE>([^>]+)<\/IS_PSEUDOGENE>/o) { #$geneinfo->{'IS_PSEUDOGENE'} = $1; $line = $self->_readtag(); } else { $self->throw("invalid is_pseudogene: $line"); } if($line =~ /<FUNCT_ANNOT_EVIDENCE/o) { $line = $self->_readtag(); } if($line =~ /<DATE>([^>]+)<\/DATE>/o) { #$geneinfo->{'DATE'} = $1; $line = $self->_readtag(); } while($line =~ /<GENE_ONTOLOGY>/o) { # Get the source tag my($source) = grep { $_->primary_tag() eq 'source' } $tu->get_SeqFeatures(); my @ids = ( $line =~ /(<GO_ID.*?<\/GO_ID>)/gso); foreach my $go (@ids) { my($assignment) = ($go =~ /<GO_ID\s+ASSIGNMENT\s+=\s+"GO:(\d+)">/os); my($term) = ($go =~ /<GO_TERM>([^<]+)<\/GO_TERM>/os); my($type) = ($go =~ /<GO_TYPE>([^<]+)<\/GO_TYPE>/os); # TODO: Add GO annotation if(defined $type and defined $assignment and defined $term) { # Add the GO Annotation $source->add_tag_value( GO => "ID: $assignment; Type: $type; $term" ); } } $line = $self->_readtag(); } if($line =~ /<\/GENE_INFO/o) { return; } $self->throw("unexpected end of gene_info"); } sub _build_location { my($self, $end5, $end3, $length, $cs) = @_; # Find the start and end of the location # relative to the sequence. my $start = abs( $end5 - $cs->{end5} ) + 1; my $end = abs( $end5 - $cs->{end3} ) + 1; # Do some bounds checking: if( $start < 1 ) { throw Bio::Root::OutOfRange( -text => "locations' start( $start) must be >= 1" ); } elsif( $end > $length ) { throw Bio::Root::OutOfRange( -text => "locations' end( $end ) must be <= length( $length )" ); } elsif( $start > $end ) { throw Bio::Root::OutOfRange( -text => "locations' start ( $start ) must be < end ( $end ) $end5, $end3, $cs->{end5}, $cs->{end3}" ); } return Bio::Location::Simple->new( -start => $start, -end => $end, -strand => 1 ); } sub _process_model { my($self, $tu, $end5, $end3) = @_; my $line; my( $source ) = grep { $_->primary_tag() eq 'source' } $tu->get_SeqFeatures(); my $model = Bio::SeqFeature::Generic->new( -source_tag => 'TIGR', -primary_tag => 'MODEL', ); $line = $self->_readline(); if($line !~ /<MODEL ([^>]+)>/o) { $self->throw("Invalid Model: $line") } my %attribs = ($1 =~ /(\w+)\s*=\s*"([^"]*)"/og); #$model->{'CURATED'} = $attribs{'CURATED'}; # TODO: Add tag to model $line = $self->_readline(); if($line =~ /<FEAT_NAME>\s*([\w\.]+)\s*<\/FEAT_NAME>/o) { $model->add_tag_value( feat_name => $1 ); $tu->add_secondary_accession($1); $line = $self->_readline(); } else { $self->throw("Invalid Feature Name: $line"); } if($line =~ /<PUB_LOCUS>\s*([\w\.]+)\s*<\/PUB_LOCUS>/o) { $model->add_tag_value( pub_locus => $1 ); $tu->add_secondary_accession($1); $line = $self->_readline(); } else { # $self->throw("Invalid Pub_Locus: $line"); } if($line =~ /<CDNA_SUPPORT>/o) { $self->_pushback($line); $self->_process_cdna_support( $model ); $line = $self->_readline(); } while($line =~ /<CHROMO_LINK>([^>]+)<\/CHROMO_LINK>/o) { $model->add_tag_value( chromo_link => $1 ); $line = $self->_readline(); } if($line =~ /<DATE>([^>]+)<\/DATE>/o) { $line = $self->_readline(); } else { $self->throw("Invalid Date: $line"); } if($line =~ /<COORDSET>/o) { $self->_pushback($line); my $cs = $self->_process_coordset(); my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs); $model->start( $loc->start() ); $model->end( $loc->end() ); $line = $self->_readline(); } else { $self->throw("Invalid Coordset: $line"); } my $exon = Bio::SeqFeature::Generic->new( -source_tag => 'TIGR', -primary_tag => 'EXON', -location => Bio::Location::Split->new(), -tags => [ locus => $tu->accession_number() ], ); $exon->add_tag_value( model => $model->get_tag_values('feat_name') ); my $cds = Bio::SeqFeature::Generic->new( -source_tag => 'TIGR', -primary_tag => 'CDS', -location => Bio::Location::Split->new(), -tags => [ locus => $tu->accession_number() ], ); $cds->add_tag_value( model => $model->get_tag_values('feat_name') ); my $utr = []; if($line =~ /<EXON>/o) { do { $self->_pushback($line); $self->_process_exon( $tu, $exon, $cds, $utr, $end5, $end3 ); $line = $self->_readline(); } while($line =~ /<EXON>/o); } else { $self->throw("Required <EXON> missing"); } until($line =~ /<\/MODEL>/o) { $line = $self->_readline(); } $_->add_tag_value( model => $model->get_tag_values('feat_name') ) foreach @$utr; # Add the model, EXONs, CDS, and UTRs $tu->add_SeqFeature($model) if $model and $model->start() >= 1; $tu->add_SeqFeature($exon) if $exon and scalar($exon->location()->each_Location()) >= 1; $tu->add_SeqFeature($cds) if $cds and scalar($cds->location()->each_Location()) >= 1; $tu->add_SeqFeature(@$utr); return; } sub _process_cdna_support { my($self, $model) = @_; my $line = $self->_readline(); if($line !~ /<CDNA_SUPPORT>/o) { $self->throw("Bio::SeqIO::tigr::_process_cdna_support called ", "but no <CDNA_SUPPORT> in the stream"); } $line = $self->_readline(); while( $line =~ /<ACCESSION([^>]+)>(.*)<\/ACCESSION>/o) { # Save the text my $desc = $2; # Get the element's attributes my %attribs = ($1 =~ /(\w+)\s*=\s*"([^"]*)"/og); # Add the tag to the model $model->add_tag_value( cdna_support => "DBXRef: $attribs{DBXREF}; $desc" ); $line = $self->_readline(); } if( $line =~ /<\/CDNA_SUPPORT>/o) { return; } $self->throw("reached end of _process_cdna_support"); } sub _process_exon { my($self, $tu, $exon, $cds, $utr, $end5, $end3 ) = @_; my $line = $self->_readline(); if($line !~ /<EXON>/o) { $self->throw("Bio::SeqIO::tigr::_process_exon called ", "but no <EXON> in the stream"); } $line = $self->_readtag(); if($line =~ /<FEAT_NAME>([^<]+)<\/FEAT_NAME>/o) { # Ignore $line = $self->_readtag(); } else { $self->throw("Required <FEAT_NAME> missing"); } if($line =~ /<DATE>([^<]+)<\/DATE>/o) { # Ignore $line = $self->_readtag(); } else { $self->throw("Required <DATE> missing"); } if($line =~ /<COORDSET>/o) { $self->_pushback($line); my $cs = $self->_process_coordset(); my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs); $exon->location()->add_sub_Location($loc); $line = $self->_readline(); } else { $self->throw("Required <COORDSET> missing"); } if($line =~ /<CDS>/o) { $self->_pushback($line); $self->_process_cds($tu, $end5, $end3, $cds); $line = $self->_readline(); } if($line =~ /<UTRS>/o) { $self->_pushback($line); $self->_process_utrs($tu, $end5, $end3, $utr); $line = $self->_readline(); } if($line =~ /<\/EXON>/o) { return; } $self->throw("Reached End of Bio::SeqIO::tigr::_process_exon"); } sub _process_cds { my($self, $tu, $end5, $end3, $cds) = @_; my $line = $self->_readline(); if($line !~ /<CDS>/o) { $self->throw("Bio::SeqIO::tigr::_process_cda_support called ", "but no <CDS> in the stream"); } $line = $self->_readtag(); if($line =~ /<FEAT_NAME>([^<]+)<\/FEAT_NAME>/o) { #$cds->{'FEAT_NAME'} = $1; $line = $self->_readtag(); } else { $self->throw("Required <FEAT_NAME> missing"); } if($line =~ /<DATE>([^<]+)<\/DATE>/o) { #$cds->{'DATE'} = $1; $line = $self->_readtag(); } else { $self->throw("Required <DATE> missing"); } if($line =~ /<COORDSET>/o) { $self->_pushback($line); my $cs = $self->_process_coordset(); my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs); $cds->location()->add_sub_Location($loc); $line = $self->_readline(); } else { $self->throw("Required <COORDSET> missing"); } if($line =~ /<\/CDS>/o) { return; } $self->throw("Reached onf of Bio::SeqIO::tigr::_process_cds"); } sub _process_utrs { my($self, $tu, $end5, $end3, $utrs) = @_; my $line = $self->_readline(); if($line !~ /<UTRS/o) { $self->throw("Bio::SeqIO::tigr::_process_utrs called but no ", "<UTRS> found in stream"); } $line = $self->_readline(); while($line !~ /<\/UTRS>/o) { $self->_pushback($line); if($line =~ /<LEFT_UTR>/o) { $self->_process_left_utr($tu, $end5, $end3, $utrs); } elsif ($line =~ /<RIGHT_UTR>/o) { $self->_process_right_utr($tu, $end5, $end3, $utrs); } elsif ($line =~ /<EXTENDED_UTR>/o) { $self->_process_ext_utr($tu, $end5, $end3, $utrs); } else { $self->throw("Unexpected tag"); } $line = $self->_readline(); } if($line =~ /<\/UTRS>/o) { return $utrs; } $self->throw("Reached end of Bio::SeqIO::tigr::_process_utrs"); } sub _process_left_utr { my($self, $tu, $end5, $end3, $utrs) = @_; my $line = $self->_readline(); my $coordset; if($line !~ /<LEFT_UTR>/o) { $self->throw("Bio::SeqIO::tigr::_process_left_utr called but ", "no <LEFT_UTR> found in stream"); } $line = $self->_readtag(); if($line =~ /<COORDSET>/o) { $self->_pushback($line); my $cs = $self->_process_coordset(); my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs); push(@$utrs, Bio::SeqFeature::Generic->new( -source_tag => 'TIGR', -primary_tag => 'LEFT_UTR', -strand => 1, -start => $loc->start(), -end => $loc->end() )); $line = $self->_readline(); } else { $self->throw("Required <COORDSET> missing"); } if($line =~ /<\/LEFT_UTR>/o) { return; } $self->throw("Reached end of Bio::SeqIO::tigr::_process_left_utr"); } sub _process_right_utr { my($self, $tu, $end5, $end3, $utrs) = @_; my $line = $self->_readline(); my $coordset; if($line !~ /<RIGHT_UTR>/o) { $self->throw("Bio::SeqIO::tigr::_process_right_utr called but ", "no <RIGHT_UTR> found in stream"); } $line = $self->_readtag(); if($line =~ /<COORDSET>/o) { $self->_pushback($line); $coordset = $self->_process_coordset(); $self->_pushback($line); my $cs = $self->_process_coordset(); my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs); push(@$utrs, Bio::SeqFeature::Generic->new( -source_tag => 'TIGR', -primary_tag => 'RIGHT_UTR', -strand => 1, -start => $loc->start(), -end => $loc->end() )); $line = $self->_readline(); } else { $self->throw("Required <COORDSET> missing"); } if($line =~ /<\/RIGHT_UTR>/o) { return $coordset; } $self->throw("Reached end of Bio::SeqIO::tigr::_process_right_utr"); } sub _process_ext_utr { my($self, $tu, $end5, $end3, $utrs) = @_; my $line = $self->_readline(); my $coordset; if($line !~ /<EXTENDED_UTR>/o) { $self->throw("Bio::SeqIO::tigr::_process_ext_utr called but ", "no <EXTENDED_UTR> found in stream"); } $line = $self->_readtag(); if($line =~ /<COORDSET>/o) { $self->_pushback($line); my $cs = $self->_process_coordset(); my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs); push(@$utrs, Bio::SeqFeature::Generic->new( -source_tag => 'TIGR', -primary_tag => 'EXTENDED_UTR', -strand => 1, -start => $loc->start(), -end => $loc->end() )); $line = $self->_readline(); } else { $self->throw("Required <COORDSET> missing"); } if($line =~ /<\/EXTENDED_UTR>/o) { return $coordset; } $self->throw("Reached end of Bio::SeqIO::tigr::_process_ext_utr"); } sub _readtag { my($self) = @_; my $line = $self->_readline(); chomp($line); my $tag; if(($tag) = ($line =~ /^[^<]*<\/(\w+)/o)) { $self->_pushback($1) if $line =~ /<\/$tag>(.+)$/; return "</$tag>"; } until(($tag) = ($line =~ /<(\w+)[^>]*>/o)) { $line = $self->_readline(); chomp $line; } until($line =~ /<\/$tag>/) { $line .= $self->_readline(); } if(my ($val) = ($line =~ /(<$tag.*>.*?<\/$tag>)/s)) { if($line =~ /<\/$tag>\s*(\w+[\s\w]*?)\s*$/s) { $self->_pushback($1) } return $val; } $self->throw("summerror"); } sub _readline { my($self) = @_; my $line; do { $line = $self->SUPER::_readline(); } while(defined($line) and $line =~ /^\s*$/o); return $line; } sub throw { my($self, @s) = @_; my $string = "[$.]" . join('', @s); $self->SUPER::throw($string); } 1; �������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/tigrxml.pm���������������������������������������������������������������000444��000766��000024�� 41537�13155576320� 17262� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::tigrxml # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl-dot-org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::tigrxml - Parse TIGR (new) XML =head1 SYNOPSIS use Bio::SeqIO; my $in = Bio::SeqIO->new(-format => 'tigrcoordset', -file => 'file.xml'); while( my $seq = $in->next_seq ) { # do something... } =head1 DESCRIPTION This is a parser for TIGR Coordset XML for their in-progress annotation dbs. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::tigrxml; use vars qw($Default_Source); use strict; use XML::SAX; use XML::SAX::Writer; use Data::Dumper; use Bio::Seq::SeqFactory; use Bio::Species; use Bio::SeqFeature::Generic; use Bio::Annotation::Reference; use Bio::Annotation::Comment; use Bio::Annotation::DBLink; use List::Util qw(min max); use base qw(Bio::SeqIO XML::SAX::Base); $Default_Source = 'TIGR'; sub _initialize { my ($self) = shift; $self->SUPER::_initialize(@_); $self->{'_parser'} = XML::SAX::ParserFactory->parser('Handler' => $self); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } return; } sub next_seq { my $self = shift; if( @{$self->{'_seendata'}->{'_seqs'} || []} || eof($self->_fh)) { return shift @{$self->{'_seendata'}->{'_seqs'}}; } $self->{'_parser'}->parse_file($self->_fh); return shift @{$self->{'_seendata'}->{'_seqs'}}; } # XML::SAX::Base methods sub start_document { my ($self,$doc) = @_; $self->{'_seendata'} = {'_seqs' => [], '_authors' => [], '_feats' => [] }; $self->SUPER::start_document($doc); } sub end_document { my ($self,$doc) = @_; $self->SUPER::end_document($doc); } sub start_element { my ($self,$ele) = @_; # attributes my $name = uc $ele->{'LocalName'}; my $attr = $ele->{'Attributes'}; my $seqid = defined $self->{'_seendata'}->{'_seqs'}->[-1] ? $self->{'_seendata'}->{'_seqs'}->[-1]->display_id : undef; # we're going to try and be SO-nice here if( $name eq 'ASSEMBLY' ) { # New sequence my ($len) = $attr->{'{}COORDS'}->{'Value'} =~ /\d+\-(\d+)/; push @{$self->{'_seendata'}->{'_seqs'}}, $self->sequence_factory->create ( -display_id => $attr->{'{}ASMBL_ID'}->{'Value'}, -length => $len, ); } elsif( $name eq 'HEADER' ) { } elsif( $name eq 'CLONE_NAME' ) { } elsif( $name eq 'ORGANISM' ) { } elsif( $name eq 'AUTHOR_LIST' ) { $self->{'_seendata'}->{'_authors'} = []; } elsif( $name eq 'TU' ) { # gene feature my ($s,$e) = ($attr->{'{}COORDS'}->{'Value'} =~ /(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $fname = $attr->{'{}FEAT_NAME'}->{'Value'}; my $f = Bio::SeqFeature::Generic->new (-seq_id => $seqid, -start => $s, -end => $e, -strand => $strand, -primary_tag => 'gene', # what does this really map to? -source_tag => $Default_Source, -tag => { 'Note' => $attr->{'{}COM_NAME'}->{'Value'}, 'ID' => $fname, 'locus' => $attr->{'{}LOCUS'}->{'Value'}, 'pub_locus' => $attr->{'{}PUB_LOCUS'}->{'Value'}, 'alt_locus' => $attr->{'{}ALT_LOCUS'}->{'Value'}, 'pub_comment' => $attr->{'{}PUB_COMMENT'}->{'Value'}, } ); push @{$self->{'_seendata'}->{'_feats'}}, $f; # add this feature to the current sequence $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); } elsif( $name eq 'MODEL' ) { # mRNA/transcript # reset the UTRs $self->{'_seendata'}->{"five_prime_UTR"}= undef; $self->{'_seendata'}->{"three_prime_UTR"} = undef; my ($s,$e) = ($attr->{'{}COORDS'}->{'Value'} =~ /(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $parent = $self->{'_seendata'}->{'_feats'}->[-1]; my ($parentid) = $parent->get_tag_values('ID'); my $f = Bio::SeqFeature::Generic->new (-primary_tag => 'transcript', -source_tag => $Default_Source, -start => $s, # we use parent start/stop because 'MODEL' means CDS start/stop -end => $e, # but we want to reflect -strand => $strand, -seq_id => $seqid, -tag => { 'ID' => $attr->{'{}FEAT_NAME'}->{'Value'}, 'Parent' => $parentid, 'Note' => $attr->{'{}COMMENT'}->{'Value'}, }); $parent->add_SeqFeature($f); push @{$self->{'_seendata'}->{'_feats'}}, $f; $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); } elsif( $name eq 'EXON' ) { # exon feature my ($s,$e) = ($attr->{'{}COORDS'}->{'Value'} =~ /(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $parent = $self->{'_seendata'}->{'_feats'}->[-1]; my ($parentid) = $parent->get_tag_values('ID'); my $f = Bio::SeqFeature::Generic->new (-primary_tag => 'exon', -source_tag => $Default_Source, -seq_id => $seqid, -start => $s, -end => $e, -strand => $strand, -tag => { 'ID' => $attr->{'{}FEAT_NAME'}->{'Value'}, 'Parent' => $parentid, }); $parent->add_SeqFeature($f,'EXPAND'); $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); # we'll still just add exons to the transcript } elsif( $name eq 'PROTEIN_SEQ' ) { } elsif( $name eq 'CDS' ) { # CDS will be the translation of the transcript my ($s,$e) = ($attr->{'{}COORDS'}->{'Value'} =~ /(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $parent = $self->{'_seendata'}->{'_feats'}->[-1]; my ($parentid) = $parent->get_tag_values('ID'); $self->assert($parent->primary_tag eq 'transcript', 'Testing for primary tag equivalent to mRNA'); $self->assert($parent->strand == $strand || abs($s-$e) == 0, 'Testing that parent feature and current feature strand are equal '. $parentid. ' '.$attr->{'{}FEAT_NAME'}->{'Value'}); my $f = Bio::SeqFeature::Generic->new (-primary_tag => 'CDS', -source_tag => $Default_Source, -seq_id => $seqid, -start => $s, -end => $e, -strand => $parent->strand, -tag => { 'ID' => $attr->{'{}FEAT_NAME'}->{'Value'}, 'Parent' => $parentid, # should be the mRNA }); $parent->add_SeqFeature($f); $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); } elsif( $name eq 'RNA-EXON' ) { my ($s,$e) = ($attr->{'{}COORDS'}->{'Value'} =~ /(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $parent = $self->{'_seendata'}->{'_feats'}->[-1]; my ($parentid) = $parent->get_tag_values('ID'); my $f = Bio::SeqFeature::Generic->new (-primary_tag => 'tRNA_exon', # tRNA_exon? -source_tag => $Default_Source, -seq_id => $seqid, -start => $s, -end => $e, -strand => $strand, -tag => { 'ID' => $attr->{'{}FEAT_NAME'}->{'Value'}, 'Parent' => $parentid, } ); $parent->add_SeqFeature($f); $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); } elsif( $name eq 'PRE-TRNA' ) { # tRNA gene my ($s,$e) = ( $attr->{'{}COORDS'}->{'Value'} =~/(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $f = Bio::SeqFeature::Generic->new ( -primary_tag => 'tRNA_coding_gene', -source_tag => $Default_Source, -seq_id => $seqid, -start => $s, -end => $e, -strand => $strand, -tag => {'ID' => $attr->{'{}FEAT_NAME'}->{'Value'}, } ); push @{$self->{'_seendata'}->{'_feats'}}, $f; $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); } elsif( $name eq 'TRNA' ) { # tRNA transcript my ($s,$e) = ($attr->{'{}COORDS'}->{'Value'} =~ /(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $parent = $self->{'_seendata'}->{'_feats'}->[-1]; my ($parentid) = $parent->get_tag_values('ID'); my $f = Bio::SeqFeature::Generic->new (-primary_tag => 'tRNA_primary_transcript', -source_tag => $Default_Source, -start => $s, -end => $e, -strand => $strand, -seq_id => $seqid, -tag => { 'ID' => $attr->{'{}FEAT_NAME'}->{'Value'}, 'Parent' => $parentid, 'Note' => $attr->{'{}COM_NAME'}->{'Value'}, 'anticodon' => $attr->{'{}ANTICODON'}->{'Value'}, 'pub_locus' => $attr->{'{}PUB_LOCUS'}->{'Value'}, }); $parent->add_SeqFeature($f); push @{$self->{'_seendata'}->{'_feats'}}, $f; $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); } elsif( $name eq 'REPEAT_LIST' ) { } elsif( $name eq 'REPEAT' ) { my ($s,$e) = ($attr->{'{}COORDS'}->{'Value'} =~ /(\d+)\-(\d+)/); my $strand = 1; if( $s > $e) { ($s,$e,$strand) = ( $e,$s,-1); } my $f = Bio::SeqFeature::Generic->new (-primary_tag => 'simple_repeat', -source_tag => $Default_Source, -seq_id => $seqid, -start => $s, -end => $e, -stand => $strand, -tag => { 'ID' => $attr->{'{}FEAT_NAME'}->{'Value'}, }); push @{$self->{'_seendata'}->{'_feats'}}, $f; $self->{'_seendata'}->{'_seqs'}->[-1]->add_SeqFeature($f); } elsif ( $name eq 'AUTHOR' ) { } elsif( $name eq 'GB_DESCRIPTION' ) { } elsif( $name eq 'GB_COMMENT' ) { } elsif( $name eq 'LINEAGE' ) { } else { $self->warn("Unknown element $name, ignored\n"); } push @{$self->{'_state'}}, $name; $self->SUPER::start_element($ele); } sub end_element { my ($self,$ele) = @_; pop @{$self->{'_state'}}; my $name = $ele->{'LocalName'}; my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1]; if( $name eq 'AUTHOR_LIST' ) { if( $curseq->can('annotation') ) { $curseq->annotation->add_Annotation ('reference',Bio::Annotation::Reference->new (-authors => join(',',@{$self->{'_seendata'}->{'_authors'}})) ); } $self->{'_seendata'}->{'_authors'} = []; } elsif( $name eq 'ASSEMBLY' ) { if( @{$self->{'_seendata'}->{'_feats'} || []} ) { $self->warn("Leftover features which were not finished!"); } $self->debug("end element for ASSEMBLY ". $curseq->display_id. "\n"); } elsif( $name eq 'TU' || $name eq 'TRNA' || $name eq 'PRE-TRNA' || $name eq 'REPEAT' ) { pop @{$self->{'_seendata'}->{'_feats'}}; } elsif( $name eq 'MODEL' ) { # This is all to for adding UTRs my $model = pop @{$self->{'_seendata'}->{'_feats'}}; my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1]; # sort smallest to largest, don't forget about # strandedness my ($parentid) = $model->get_tag_values('Parent'); my @features = $model->get_SeqFeatures(); my @exons = sort { $a->start <=> $b->start } grep { $_->primary_tag eq 'exon' } @features; my @cdsexons = sort { $a->start <=> $b->start } grep { $_->primary_tag eq 'CDS' } @features; # look at the exons, find those which come after the model start my $cdsexon = shift @cdsexons; my $exon = shift @exons; # first exon if( ! defined $cdsexon ) { $self->warn( "no CDS exons $parentid!"); return; } elsif( ! defined $exon ) { $self->warn("no exons $parentid!" ); return; } my $utrct = 1; while( defined $exon && $exon->start < $cdsexon->start ) { my ($pid) = $exon->get_tag_values('Parent'); $self->debug("LeftPhase: tu-id $parentid mrna-id $pid exon is ". $exon->location->to_FTstring. " CDSexon is ".$cdsexon->location->to_FTstring."\n"); my $utr = Bio::SeqFeature::Generic->new (-seq_id => $exon->seq_id, -strand => $exon->strand, -primary_tag => $exon->strand > 0 ? "five_prime_UTR" : "three_prime_UTR", -source_tag => $Default_Source, -tag => { 'ID' => "$pid.UTR".$utrct++, 'Parent' => $pid }, ); my ($ns,$ne); if( $utr->primary_tag eq 'five_prime_UTR' ) { $ns = $exon->start; $ne = min ( $exon->end, $cdsexon->start - 1); } else { $ne = min( $exon->end, $cdsexon->start - 1); $ns = $exon->start; } $utr->start($ns); $utr->end($ne); $model->add_SeqFeature($utr); $curseq->add_SeqFeature($utr); $exon = shift @exons; } @exons = sort { $a->start <=> $b->start } grep {$_->primary_tag eq 'exon' } @features; @cdsexons = sort { $a->start <=> $b->start } grep { $_->primary_tag eq 'CDS' } @features; $cdsexon = pop @cdsexons; $exon = pop @exons; if( ! defined $cdsexon ) { $self->warn( "no CDS exons $parentid!"); return; } elsif( ! defined $exon ) { $self->warn("no exons $parentid!" ); return; } $utrct = 1; while( defined $exon &&$exon->end > $cdsexon->end ) { my ($pid) = $exon->get_tag_values('Parent'); $self->debug("RightPhase: tu-id $parentid mrna-id $pid exon is ". $exon->location->to_FTstring. " CDSexon is ".$cdsexon->location->to_FTstring."\n"); my $utr = Bio::SeqFeature::Generic->new (-seq_id => $exon->seq_id, -strand => $exon->strand, -primary_tag => $exon->strand < 0 ? "five_prime_UTR" : "three_prime_UTR", -source_tag => $Default_Source, -tag => { 'Parent' => $pid, 'ID' => "$pid.UTR".$utrct++, } ); my ($ns,$ne); if( $utr->primary_tag eq 'three_prime_UTR' ) { $ns = max ( $exon->start, $cdsexon->end + 1); $ne = $exon->end; } else { $ns = $cdsexon->end+1; $ne = max ( $exon->end, $cdsexon->start + 1); } $utr->start($ns); $utr->end($ne); $model->add_SeqFeature($utr); $curseq->add_SeqFeature($utr); $exon = pop @exons; } } $self->SUPER::end_element($ele); } sub characters { my ($self,$data) = @_; if( ! @{$self->{'_state'}} ) { $self->warn("Calling characters with no previous start_element call. Ignoring data"); } else { my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1]; my $curfeat = $self->{'_seendata'}->{'_feats'}->[-1]; my $name = $self->{'_state'}->[-1]; if( defined $curseq ) { if( $name eq 'CLONE_NAME' ) { $self->debug("Clone name is ",$data->{'Data'}, "\n"); $curseq->display_id($data->{'Data'}); } elsif( $name eq 'ORGANISM' ) { my ($genus,$species,$subspec) = split(/\s+/,$data->{Data},3); $curseq->species(Bio::Species->new( -classification => [$species,$genus], -sub_species => $species)); } elsif( $name eq 'LINEAGE' ) { $curseq->species->classification( [ $curseq->species->species, $curseq->species->genus, reverse (map { s/^\s+//; s/\s+$//; $_; } split /[;\.]+/,$data->{'Data'} ), ] ); } elsif( $name eq 'AUTHOR' ) { push @{$self->{'_seendata'}->{'_authors'}}, $data->{'Data'}; } } if( defined $curfeat ) { if( $name eq 'EXON' ) { # exon feature } elsif( $name eq 'RNA-EXON' ) { } elsif( $name eq 'PROTEIN_SEQ' ) { $curfeat->add_tag_value('translation',$data->{'Data'}); } elsif( $name eq 'CDS' ) { } elsif( $name eq 'PRE-TRNA' ) { # tRNA gene } elsif( $name eq 'TRNA' ) { # tRNA transcript } elsif( $name eq 'REPEAT_LIST' ) { } elsif( $name eq 'REPEAT' ) { $curfeat->add_tag_value('Note',$data->{'Data'}); } elsif( $name eq 'GB_COMMENT' ) { $curseq->annotation->add_Annotation ('comment', Bio::Annotation::Comment->new(-text => $data->{'Data'})); } elsif( $name eq 'GB_DESCRIPTION' ) { $curseq->description($data->{'Data'}); } } } $self->SUPER::characters($data); } sub assert { my ($self,$test,$msg) = @_; $self->throw($msg) unless $test; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/tinyseq.pm���������������������������������������������������������������000444��000766��000024�� 26043�13155576320� 17263� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::tinyseq # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Donald Jackson, donald.jackson@bms.com # # Copyright Bristol-Myers Squibb # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::tinyseq - reading/writing sequences in NCBI TinySeq format =head1 SYNOPSIS Do not use this module directly; use the SeqIO handler system: $stream = Bio::SeqIO->new( -file => $filename, -format => 'tinyseq' ); while ( my $seq = $stream->next_seq ) { .... } =head1 DESCRIPTION This object reads and writes Bio::Seq objects to and from TinySeq XML format. A TinySeq is a lightweight XML file of sequence information, analgous to FASTA format. See L<https://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.mod.dtd> for the DTD. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 SEE ALSO L<Bio::SeqIO>, L<Bio::Seq>. =head1 AUTHOR Donald Jackson, E<lt>donald.jackson@bms.comE<gt> Parts of this module and the test script were patterned after Sheldon McKay's L<Bio::SeqIO::game>. If it breaks, however, it's my fault not his ;). =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqIO::tinyseq; use strict; use Bio::Seq::SeqFastaSpeedFactory; use Bio::Species; use Bio::SeqIO::tinyseq::tinyseqHandler; use XML::Parser::PerlSAX; use XML::Writer; use Bio::Root::Version; use base qw(Bio::SeqIO); sub _initialize { my ($self, @args) = @_; $self->SUPER::_initialize(@args); unless (defined $self->sequence_factory) { $self->sequence_factory(Bio::Seq::SeqFastaSpeedFactory->new); } $self->{'_species_objects'} = {}; $self->{_parsed} = 0; } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : NONE =cut sub next_seq { my ($self) = @_; $self->_get_seqs() unless ($self->{_parsed}); return shift @{$self->{_seqlist}}; } =head2 write_seq Title : write_seq Usage : $seq = $stream->write_seq(@sequence_objects); undef $stream Function: outputs one or more sequence objects as TinySeq XML Returns : 1 on success Args : one or more sequence objects as TinySeq XML Because the TSeq dtd includes closing tags after all sets are written, the output will not be complete until the program terminates or the object is forced out of scope (see close_writer()). May not perfectly reproduce TSeq_sid element for all sequences =cut sub write_seq { my ($self, @seqobjs) = @_; $self->throw('write_seq must be called with at least one Bio::SeqI or Bio::PrimarySeqI compliant object') unless (@seqobjs and ( $seqobjs[0]->isa('Bio::SeqI') || $seqobjs[0]->isa('Bio::PrimarySeqI'))); my $writer = $self->_get_writer; foreach my $seqobj (@seqobjs) { my ($id_element, $id_value) = $self->_get_idstring($seqobj); $writer->startTag('TSeq'); $writer->emptyTag('TSeq_seqtype', value => $self->_convert_seqtype($seqobj)); $writer->dataElement('TSeq_gi', $seqobj->primary_id || ''); $writer->dataElement($id_element, $id_value); #$writer->dataElement('TSeq_orgname', $seqobj->taxid) if ($seqobj->can('taxid')); # just a placeholder $writer->dataElement('TSeq_defline', $seqobj->desc); $writer->dataElement('TSeq_length', $seqobj->length); $writer->dataElement('TSeq_sequence', $seqobj->seq); if ($seqobj->can('species') && $seqobj->species) { $self->_write_species($writer, $seqobj->species); } $writer->endTag('TSeq'); } 1; } =head2 _get_seqs Title : _get_seqs Usage : Internal function - use next_seq() instead Function: parses the XML and creates Bio::Seq objects Returns : 1 on success Args : NONE Currently stores all sequence objects into memory. I will work on do more of a stream-based approach =cut sub _get_seqs { my ($self) = @_; my $fh = $self->_fh; my $handler = Bio::SeqIO::tinyseq::tinyseqHandler->new(); my $parser = XML::Parser::PerlSAX->new( Handler => $handler ); my @seqatts = $parser->parse( Source => { ByteStream => $fh }); my $factory = $self->sequence_factory; $self->{_seqlist} ||= []; foreach my $seqatt(@seqatts) { foreach my $subatt(@$seqatt) { # why are there two hashes? my $seqobj = $factory->create(%$subatt); $self->_assign_identifier($seqobj, $subatt); if ($seqobj->can('species')) { # my $class = [reverse(split(/ /, $subatt->{'-organism'}))]; # my $species = Bio::Species->new( -classification => $class, # -ncbi_taxid => $subatt->{'-taxid'} ); my $species = $self->_get_species($subatt->{'-organism'}, $subatt->{'-taxid'}); $seqobj->species($species) if ($species); } push(@{$self->{_seqlist}}, $seqobj); } } $self->{_parsed} = 1; } =head2 _get_species Title : _get_species Usage : Internal function Function: gets a Bio::Species object from cache or creates as needed Returns : a Bio::Species object on success, undef on failure Args : a classification string (eg 'Homo sapiens') and a NCBI taxon id (optional) Objects are cached for parsing multiple sequence files. =cut sub _get_species { my ($self, $orgname, $taxid) = @_; unless ($self->{'_species_objects'}->{$orgname}) { my $species = $self->_create_species($orgname, $taxid); $self->{'_species_objects'}->{$orgname} = $species; } return $self->{'_species_objects'}->{$orgname}; } =head2 _create_species Title : _create_species Usage : Internal function Function: creates a Bio::Species object Returns : a Bio::Species object on success, undef on failure Args : a classification string (eg 'Homo sapiens') and a NCBI taxon id (optional) =cut sub _create_species { my ($self, $orgname, $taxid) = @_; return unless ($orgname); # not required in TinySeq dtd so don't throw an error my %params; $params{'-classification'} = [reverse(split(/ /, $orgname))]; $params{'-ncbi_taxid'} = $taxid if ($taxid); my $species = Bio::Species->new(%params) or return; return $species; } =head2 _assign_identifier Title : _assign_identifier Usage : Internal function Function: looks for sequence accession Returns : 1 on success Args : NONE NCBI puts refseq accessions in TSeq_sid, others in TSeq_accver. =cut sub _assign_identifier { my ($self, $seqobj, $atts) = @_; my ($accession, $version); if ($atts->{'-accver'}) { ($accession, $version) = split(/\./, $atts->{'-accver'});; } elsif ($atts->{'-sid'}) { my $sidstring =$atts->{'-sid'}; $sidstring =~ s/^.+?\|//; $sidstring =~ s/\|[^\|]*//; ($accession, $version) = split(/\./, $sidstring);; } else { $self->throw('NO accession information found for this sequence'); } $seqobj->accession_number($accession) if ($seqobj->can('accession_number')); $seqobj->version($version) if ($seqobj->can('version')); } =head2 _convert_seqtype Title : _convert_seqtype Usage : Internal function Function: maps Bio::Seq::alphabet() values [dna/rna/protein] onto TSeq_seqtype values [protein/nucleotide] =cut sub _convert_seqtype { my ($self, $seqobj) = @_; return 'protein' if ($seqobj->alphabet eq 'protein'); return 'nucleotide' if ($seqobj->alphabet eq 'dna'); return 'nucleotide' if ($seqobj->alphabet eq 'rna'); # if we get here there's a problem! $self->throw("Alphabet not defined, can't assign type for $seqobj"); } =head2 _get_idstring Title : _get_idstring Usage : Internal function Function: parse accession and version info from TSeq_accver or TSeq_sid =cut sub _get_idstring { # NCBI puts refseq ids in TSeq_sid, others in TSeq_accver. No idea why. my ($self, $seqobj) = @_; my $accver = $seqobj->accession_number; $accver .= '.' . $seqobj->version if ($seqobj->can('version') and $seqobj->version); if ($accver =~ /^(NM_|NP_|XM_|XP_|NT_|NC_|NG_)/) { return ('TSeq_sid', join('|', 'ref', $accver, '')); } else { return ('TSeq_accver', $accver); } } =head2 _get_writer Title : _get_writer Usage : Internal function Function: instantiate XML::Writer object if needed, output initial XML =cut sub _get_writer { # initialize writer, start doc so write_seq can work one at a time my ($self) = @_; unless ($self->{_writer}) { my $fh = $self->_fh; my $writer = XML::Writer->new(OUTPUT => $fh, DATA_MODE => 1, DATA_INDENT => 2, NEWLINE => 1, ); $writer->doctype('TSeqSet', '-//NCBI//NCBI TSeq/EN', 'https://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd'); $writer->comment("Generated by Bio::SeqIO::tinyseq VERSION " . $Bio::Root::Version::VERSION); $writer->startTag('TSeqSet'); $self->{_writer} = $writer; } return $self->{_writer}; } =head2 close_writer Title : close_writer Usage : $self->close_writer() Function: terminate XML output Args : NONE Returns : 1 on success Called automatically by DESTROY when object goes out of scope =cut sub close_writer { # close out any dangling writer my ($self) = @_; if ($self->{_writer}) { my $writer = $self->{_writer}; $writer->endTag('TSeqSet'); $writer->end; undef $writer; } close($self->_fh) if ($self->_fh); 1; } sub _write_species { my ($self, $writer, $species) = @_; $writer->dataElement('TSeq_orgname', $species->binomial); $writer->dataElement('TSeq_taxid', $species->ncbi_taxid) if($species->ncbi_taxid); } sub DESTROY { # primarily to close out a writer! my ($self) = @_; $self->close_writer; undef $self; } 1; __END__ ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/ztr.pm�������������������������������������������������������������������000444��000766��000024�� 10225�13155576320� 16401� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::ztr # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Aaron Mackey <amackey@virginia.edu> # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::ztr - ztr trace sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from ztr trace files. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Aaron Mackey Email: amackey@virginia.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::ztr; use vars qw(@ISA $READ_AVAIL); use strict; use Bio::SeqIO; use Bio::Seq::SeqFactory; push @ISA, qw( Bio::SeqIO ); sub BEGIN { eval { require Bio::SeqIO::staden::read; }; if ($@) { $READ_AVAIL = 0; } else { push @ISA, "Bio::SeqIO::staden::read"; $READ_AVAIL = 1; } } sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::Quality')); } my ($compression) = $self->_rearrange([qw[COMPRESSION]], @args); $compression = 2 unless defined $compression; $self->compression($compression); unless ($READ_AVAIL) { Bio::Root::Root->throw( -class => 'Bio::Root::SystemException', -text => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!" ); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq::Quality object Args : NONE =cut sub next_seq { my ($self) = @_; my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'ztr'); # create the seq object $seq = $self->sequence_factory->create(-seq => $seq, -id => $id, -primary_id => $id, -desc => $desc, -alphabet => 'DNA', -qual => $qual ); return $seq; } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object =cut sub write_seq { my ($self,@seq) = @_; my $fh = $self->_fh; foreach my $seq (@seq) { $self->write_trace($fh, $seq, 'ztr' . $self->compression); } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } =head2 compression Title : compression Usage : $stream->compression(3); Function: determines the level of ZTR compression Returns : the current (or newly set) value. Args : 1, 2 or 3 - any other (defined) value will cause the compression to be reset to the default of 2. =cut sub compression { my ($self, $val) = @_; if (defined $val) { if ($val =~ m/^1|2|3$/o) { $self->{_compression} = $val; } else { $self->{_compression} = 2; } } return $self->{_compression}; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/Handler������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16424� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/Handler/GenericRichSeqHandler.pm�����������������������������������������000444��000766��000024�� 114117�13155576320� 23315� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::Handler::GenericRichSeqHandler # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::Handler::GenericRichSeqHandler - Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data =head1 SYNOPSIS # MyHandler is a GenericRichSeqHandler object. # inside a parser (driver) constructor.... $self->seq_handler($handler || MyHandler->new(-format => 'genbank')); # in next_seq() in driver... $hobj = $self->seqhandler(); # roll data up into hashref chunks, pass off into Handler for processing... $hobj->data_handler($data); # or retrieve Handler methods and pass data directly to Handler methods... my $hmeth = $hobj->handler_methods; if ($hmeth->{ $data->{NAME} }) { my $mth = $hmeth->{ $data->{NAME} }; $hobj->$mth($data); } =head1 DESCRIPTION This is an experimental implementation of a sequence-based HandlerBaseI parser and may change over time. It is possible (nay, likely) that the way handler methods are set up will change over development to allow more flexibility. Release pumpkins, please do not add this to a release until the API has settled. It is also likely that write_seq() will not work properly for some data. Standard Developer caveats: Do not use for production purposes. Not responsible for destroying (your data|computer|world). Do not stare directly at GenericRichSeqHandler. If GenericRichSeqHandler glows, back slowly away and call for help. Consider yourself warned! This class acts as a demonstration on how to handle similar data chunks derived from Bio::SeqIO::gbdriver, Bio::SeqIO::embldriver, and Bio::SeqIO::swissdriver using similar (or the same) handler methods. The modules currently pass all previous tests in t/genbank.t, t/embl.t, and t/swiss.t yet all use the same handler methods (the collected tests for handlers can be found in t/Handler.t). Some tweaking of the methods themselves is probably in order over the long run to ensure that data is consistently handled for each parser. Round-trip tests are probably in order here... Though a Bio::Seq::SeqBuilder is employed for building sequence objects no bypassing of data based on builder slots has been implemented (yet); this is planned in the near future. As a reminder: this is the current Annotation data chunk (via Data::Dumper): $VAR1 = { 'NAME' => 'REFERENCE', 'DATA' => '1 (bases 1 to 10001)' 'AUTHORS' => 'International Human Genome Sequencing Consortium.' 'TITLE' => 'The DNA sequence of Homo sapiens' 'JOURNAL' => 'Unpublished (2003)' }; ... This is the current SeqFeature data chunk (again via Data::Dumper): $VAR1 = { 'mol_type' => 'genomic DNA', 'LOCATION' => '<1..>10001', 'NAME' => 'FEATURES', 'FEATURE_KEY' => 'source', 'note' => 'Accession AL451081 sequenced by The Sanger Centre', 'db_xref' => 'taxon:9606', 'clone' => 'RP11-302I18', 'organism' => 'Homo sapiens' }; =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Fields Email cjfields at bioperl dot org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::Handler::GenericRichSeqHandler; use strict; use warnings; use Bio::SeqIO::FTHelper; use Bio::Annotation::Collection; use Bio::Annotation::DBLink; use Bio::Annotation::Comment; use Bio::Annotation::Reference; use Bio::Annotation::Collection; use Bio::Annotation::SimpleValue; use Bio::Annotation::TagTree; use Bio::SeqFeature::Generic; use Bio::Species; use Bio::Taxon; use Bio::DB::Taxonomy; use Bio::Factory::FTLocationFactory; use Data::Dumper; use base qw(Bio::Root::Root Bio::HandlerBaseI); my %HANDLERS = ( 'genbank' => { 'LOCUS' => \&_genbank_locus, 'DEFINITION' => \&_generic_description, 'ACCESSION' => \&_generic_accession, 'VERSION' => \&_generic_version, 'KEYWORDS' => \&_generic_keywords, 'DBSOURCE' => \&_genbank_dbsource, 'DBLINK' => \&_genbank_dbsource, 'SOURCE' => \&_generic_species, 'REFERENCE' => \&_generic_reference, 'COMMENT' => \&_generic_comment, 'FEATURES' => \&_generic_seqfeatures, 'BASE' => \&noop, # this is generated from scratch 'ORIGIN' => \&_generic_seq, # handles anything else (WGS, WGS_SCAFLD, CONTIG, PROJECT) '_DEFAULT_' => \&_generic_simplevalue, }, 'embl' => { 'ID' => \&_embl_id, 'DT' => \&_embl_date, 'DR' => \&_generic_dbsource, 'SV' => \&_generic_version, 'RN' => \&_generic_reference, 'KW' => \&_generic_keywords, 'DE' => \&_generic_description, 'AC' => \&_generic_accession, #'AH' => \&noop, # TPA data not dealt with yet... #'AS' => \&noop, 'SQ' => \&_generic_seq, 'OS' => \&_generic_species, 'CC' => \&_generic_comment, 'FT' => \&_generic_seqfeatures, # handles anything else (WGS, TPA, ANN...) '_DEFAULT_' => \&_generic_simplevalue, }, 'swiss' => { 'ID' => \&_swiss_id, 'DT' => \&_swiss_date, 'GN' => \&_swiss_genename, 'DR' => \&_generic_dbsource, 'RN' => \&_generic_reference, 'KW' => \&_generic_keywords, 'DE' => \&_generic_description, 'AC' => \&_generic_accession, 'SQ' => \&_generic_seq, 'OS' => \&_generic_species, 'CC' => \&_generic_comment, 'FT' => \&_generic_seqfeatures, # handles anything else, though I don't know what... '_DEFAULT_' => \&_generic_simplevalue, }, ); # can we do this generically? Seems like a lot of trouble... my %DBSOURCE = map {$_ => 1} qw( EchoBASE IntAct SWISS-2DPAGE ECO2DBASE ECOGENE TIGRFAMs TIGR GO InterPro Pfam PROSITE SGD GermOnline HSSP PhosSite Ensembl RGD AGD ArrayExpress KEGG H-InvDB HGNC LinkHub PANTHER PRINTS SMART SMR MGI MIM RZPD-ProtExp ProDom MEROPS TRANSFAC Reactome UniGene GlycoSuiteDB PIRSF HSC-2DPAGE PHCI-2DPAGE PMMA-2DPAGE Siena-2DPAGE Rat-heart-2DPAGE Aarhus/Ghent-2DPAGE Biocyc MetaCyc Biocyc:Metacyc GenomeReviews FlyBase TMHOBP COMPLUYEAST-2DPAGE OGP DictyBase HAMAP PhotoList Gramene WormBase WormPep Genew ZFIN PeroxiBase MaizeDB TAIR DrugBank REBASE HPA swissprot GenBank GenPept REFSEQ embl PDB UniProtKB); my %NOPROCESS = map {$_ => 1} qw(DBSOURCE ORGANISM FEATURES); our %VALID_ALPHABET = ( 'bp' => 'dna', 'aa' => 'protein', 'rc' => '' # rc = release candidate; file has no sequences ); =head2 new Title : new Usage : Function: Returns : Args : -format Sequence format to be mapped for handler methods -builder Bio::Seq::SeqBuilder object (normally defined in SequenceStreamI object implementation constructor) Throws : On undefined '-format' sequence format parameter Note : Still under heavy development =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self = {@args}; bless $self,$class; my ($format, $builder) = $self->_rearrange([qw(FORMAT BUILDER)], @args); $self->throw("Must define sequence record format") if !$format; $self->format($format); $self->handler_methods(); $builder && $self->seqbuilder($builder); $self->location_factory(); return $self; } =head1 L<Bio::HandlerBaseI> implementing methods =head2 handler_methods Title : handler_methods Usage : $handler->handler_methods('GenBank') %handlers = $handler->handler_methods(); Function: Retrieve the handler methods used for the current format() in the handler. This assumes the handler methods are already described in the HandlerI-implementing class. Returns : a hash reference with the data type handled and the code ref associated with it. Args : [optional] String representing the sequence format. If set here this will also set sequence_format() Throws : On unimplemented sequence format in %HANDLERS =cut sub handler_methods { my $self = shift; if (!($self->{'handlers'})) { $self->throw("No handlers defined for seqformat ",$self->format) unless exists $HANDLERS{$self->format}; $self->{'handlers'} = $HANDLERS{$self->format}; } return ($self->{'handlers'}); } =head2 data_handler Title : data_handler Usage : $handler->data_handler($data) Function: Centralized method which accepts all data chunks, then distributes to the appropriate methods for processing based on the chunk name from within the HandlerBaseI object. One can also use Returns : None Args : an hash ref containing a data chunk. =cut sub data_handler { my ($self, $data) = @_; my $nm = $data->{NAME} || $self->throw("No name tag defined!"); # this should handle data on the fly w/o caching; any caching should be # done in the driver! my $method = (exists $self->{'handlers'}->{$nm}) ? ($self->{'handlers'}->{$nm}) : (exists $self->{'handlers'}->{'_DEFAULT_'}) ? ($self->{'handlers'}->{'_DEFAULT_'}) : undef; if (!$method) { $self->debug("No handler defined for $nm\n"); return; }; $self->$method($data); } =head2 reset_parameters Title : reset_parameters Usage : $handler->reset_parameters() Function: Resets the internal cache of data (normally object parameters for a builder or factory) Returns : None Args : None =cut sub reset_parameters { my $self = shift; $self->{'_params'} = undef; } =head2 format Title : format Usage : $handler->format('GenBank') Function: Get/Set the format for the report/record being parsed. This can be used to set handlers in classes which are capable of processing similar data chunks from multiple driver modules. Returns : String with the sequence format Args : [optional] String with the sequence format Note : The format may be used to set the handlers (as in the current GenericRichSeqHandler implementation) =cut sub format { my $self = shift; return $self->{'_seqformat'} = lc shift if @_; return $self->{'_seqformat'}; } =head2 get_params Title : get_params Usage : $handler->get_params('-species') Function: Convenience method used to retrieve the specified parameters from the internal parameter cache Returns : Hash ref containing parameters requested and data as key-value pairs. Note that some parameter values may be objects, arrays, etc. Args : List (array) representing the parameters requested =cut sub get_params { my ($self, @ids) = @_; my %data; for my $id (@ids) { if (!index($id, '-')==0) { $id = '-'.$id ; } $data{$id} = $self->{'_params'}->{$id} if (exists $self->{'_params'}->{$id}); } return \%data; } =head2 set_params Title : set_params Usage : $handler->set_param({'-species') Function: Convenience method used to set specific parameters Returns : None Args : Hash ref containing the data to be passed as key-value pairs =cut sub set_params { shift->throw('Not implemented yet!'); } =head1 Methods unique to this implementation =head2 seqbuilder Title : seqbuilder Usage : Function: Returns : Args : Throws : Note : =cut sub seqbuilder { my $self = shift; return $self->{'_seqbuilder'} = shift if @_; return $self->{'_seqbuilder'}; } =head2 build_sequence Title : build_sequence Usage : Function: Returns : Args : Throws : Note : =cut sub build_sequence { my $self = shift; my $builder = $self->seqbuilder(); my $seq; if (defined($self->{'_params'})) { $builder->add_slot_value(%{ $self->{'_params'} }); $seq = $builder->make_object(); $self->reset_parameters; } return $seq if $seq; return 0; } =head2 location_factory Title : location_factory Usage : Function: Returns : Args : Throws : Note : =cut sub location_factory { my ($self, $factory) = @_; if ($factory) { $self->throw("Must have a Bio::Factory::LocationFactoryI when ". "explicitly setting factory()") unless (ref($factory) && $factory->isa('Bio::Factory::LocationFactoryI')); $self->{'_locfactory'} = $factory; } elsif (!defined($self->{'_locfactory'})) { $self->{'_locfactory'} = Bio::Factory::FTLocationFactory->new() } return $self->{'_locfactory'}; } =head2 annotation_collection Title : annotation_collection Usage : Function: Returns : Args : Throws : Note : =cut sub annotation_collection { my ($self, $coll) = @_; if ($coll) { $self->throw("Must have Bio::AnnotationCollectionI ". "when explicitly setting collection()") unless (ref($coll) && $coll->isa('Bio::AnnotationCollectionI')); $self->{'_params'}->{'-annotation'} = $coll; } elsif (!exists($self->{'_params'}->{'-annotation'})) { $self->{'_params'}->{'-annotation'} = Bio::Annotation::Collection->new() } return $self->{'_params'}->{'-annotation'}; } ####################### SEQUENCE HANDLERS ####################### # any sequence data sub _generic_seq { my ($self, $data) = @_; $self->{'_params'}->{'-seq'} = $data->{DATA}; } ####################### RAW DATA HANDLERS ####################### # GenBank LOCUS line sub _genbank_locus { my ($self, $data) = @_; my (@tokens) = split m{\s+}, $data->{DATA}; my $display_id = shift @tokens; $self->{'_params'}->{'-display_id'} = $display_id; my $seqlength = shift @tokens; if (exists $VALID_ALPHABET{$seqlength}) { # moved one token too far. No locus name? $self->warn("Bad LOCUS name? Changing [".$self->{'_params'}->{'-display_id'}. "] to 'unknown' and length to ".$self->{'_params'}->{'-display_id'}); $self->{'_params'}->{'-length'} = $self->{'_params'}->{'-display_id'}; $self->{'_params'}->{'-display_id'} = 'unknown'; # add token back... unshift @tokens, $seqlength; } else { $self->{'_params'}->{'-length'} = $seqlength; } my $alphabet = lc(shift @tokens); $self->{'_params'}->{'-alphabet'} = (exists $VALID_ALPHABET{$alphabet}) ? $VALID_ALPHABET{$alphabet} : $self->warn("Unknown alphabet: $alphabet"); if (($self->{'_params'}->{'-alphabet'} eq 'dna') || (@tokens > 2)) { $self->{'_params'}->{'-molecule'} = shift(@tokens); my $circ = shift(@tokens); if ($circ eq 'circular') { $self->{'_params'}->{'-is_circular'} = 1; $self->{'_params'}->{'-division'} = shift(@tokens); } else { # 'linear' or 'circular' may actually be omitted altogether $self->{'_params'}->{'-division'} = (CORE::length($circ) == 3 ) ? $circ : shift(@tokens); } } else { $self->{'_params'}->{'-molecule'} = 'PRT' if($self->{'_params'}->{'-alphabet'} eq 'aa'); $self->{'_params'}->{'-division'} = shift(@tokens); } my $date = join(' ', @tokens); # maybe use Date::Time for dates? if($date && $date =~ s{\s*((\d{1,2})-(\w{3})-(\d{2,4})).*}{$1}) { if( length($date) < 11 ) { # improperly formatted date # But we'll be nice and fix it for them my ($d,$m,$y) = ($2,$3,$4); if( length($d) == 1 ) { $d = "0$d"; } # guess the century here if( length($y) == 2 ) { if( $y > 60 ) { # arbitrarily guess that '60' means 1960 $y = "19$y"; } else { $y = "20$y"; } $self->warn("Date was malformed, guessing the century for $date to be $y\n"); } $self->{'_params'}->{'-dates'} = [join('-',$d,$m,$y)]; } else { $self->{'_params'}->{'-dates'} = [$date]; } } } # EMBL ID line sub _embl_id { my ($self, $data) = @_; my $alphabet; my ($name, $sv, $topology, $mol, $div); my $line = $data->{DATA}; #$self->debug("$line\n"); my ($idtype) = $line =~ tr/;/;/; if ( $idtype == 6) { # New style headers contain exactly six semicolons. # New style header (EMBL Release >= 87, after June 2006) my $topology; my $sv; # ID DQ299383; SV 1; linear; mRNA; STD; MAM; 431 BP. # This regexp comes from the new2old.pl conversion script, from EBI if ($line =~ m/^(\w+);\s+SV (\d+); (\w+); ([^;]+); (\w{3}); (\w{3}); (\d+) \w{2}\./) { ($name, $sv, $topology, $mol, $div) = ($1, $2, $3, $4, $6); } else { $self->throw("Unrecognized EMBL ID line:[$line]"); } if (defined($sv)) { $self->{'_params'}->{'-seq_version'} = $sv; $self->{'_params'}->{'-version'} = $sv; } if ($topology eq "circular") { $self->{'_params'}->{'-is_circular'} = 1; } if (defined $mol ) { if ($mol =~ /DNA/) { $alphabet='dna'; } elsif ($mol =~ /RNA/) { $alphabet='rna'; } elsif ($mol =~ /AA/) { $alphabet='protein'; } } } elsif ($idtype) { # has internal ';' # Old style header (EMBL Release < 87, before June 2006) if ($line =~ m{^(\S+)[^;]*;\s+(\S+)[^;]*;\s+(\S+)[^;]*;}) { ($name, $mol, $div) = ($1, $2, $3); #$self->debug("[$name][$mol][$div]"); } if($mol) { if ( $mol =~ m{circular} ) { $self->{'_params'}->{'-is_circular'} = 1; $mol =~ s{circular }{}; } if (defined $mol ) { if ($mol =~ /DNA/) { $alphabet='dna'; } elsif ($mol =~ /RNA/) { $alphabet='rna'; } elsif ($mol =~ /AA/) { $alphabet='protein'; } } } } else { $name = $data->{DATA}; } unless( defined $name && length($name) ) { $name = "unknown_id"; } $self->{'_params'}->{'-display_id'} = $name; $self->{'_params'}->{'-alphabet'} = $alphabet; $self->{'_params'}->{'-division'} = $div if $div; $self->{'_params'}->{'-molecule'} = $mol if $mol; } # UniProt/SwissProt ID line sub _swiss_id { my ($self, $data) = @_; my ($name, $seq_div); if($data->{DATA} =~ m{^ (\S+) \s+ # $1 entryname ([^\s;]+); \s+ # $2 DataClass (?:PRT;)? \s+ # Molecule Type (optional) [0-9]+[ ]AA \. # Sequencelength (capture?) $ }ox ) { ($name, $seq_div) = ($1, $2); $self->{'_params'}->{'-namespace'} = ($seq_div eq 'Reviewed' || $seq_div eq 'STANDARD') ? 'Swiss-Prot' : ($seq_div eq 'Unreviewed' || $seq_div eq 'PRELIMINARY') ? 'TrEMBL' : $seq_div; # we shouldn't be setting the division, but for now... my ($junk, $division) = split q(_), $name; $self->{'_params'}->{'-division'} = $division; $self->{'_params'}->{'-alphabet'} = 'protein'; # this is important to have the id for display in e.g. FTHelper, otherwise # you won't know which entry caused an error $self->{'_params'}->{'-display_id'} = $name; } else { $self->throw("Unrecognized UniProt/SwissProt ID line:[".$data->{DATA}."]"); } } # UniProt/SwissProt GN line sub _swiss_genename { my ($self, $data) = @_; #$self->debug(Dumper($data)); my $genename = $data->{DATA}; my $gn; if ($genename) { my @stags; if ($genename =~ /\w=\w/) { # new format (e.g., Name=RCHY1; Synonyms=ZNF363, CHIMP) for my $n (split(m{\s+and\s+},$genename)) { my @genenames; for my $section (split(m{\s*;\s*},$n)) { my ($tag, $rest) = split("=",$section); $rest ||= ''; for my $val (split(m{\s*,\s*},$rest)) { push @genenames, [$tag => $val]; } } push @stags, ['gene_name' => \@genenames]; } } else { # old format for my $section (split(/ AND /, $genename)) { my @genenames; $section =~ s/[\(\)\.]//g; my @names = split(m{\s+OR\s+}, $section); push @genenames, ['Name' => shift @names]; push @genenames, map {['Synonyms' => $_]} @names; push @stags, ['gene_name' => \@genenames] } } #use Data::Dumper; print Dumper $gn, $genename;# exit; my $gn = Bio::Annotation::TagTree->new(-tagname => 'gene_name', -value => ['gene_names' => \@stags]); $self->annotation_collection->add_Annotation('gene_name', $gn); } } # GenBank VERSION line # old EMBL SV line (now obsolete) # UniProt/SwissProt? sub _generic_version { my ($self, $data) = @_; my ($acc,$gi) = split(' ',$data->{DATA}); if($acc =~ m{^\w+\.(\d+)}xmso) { $self->{'_params'}->{'-version'} = $1; $self->{'_params'}->{'-seq_version'} = $1; } if($gi && (index($gi,"GI:") == 0)) { $self->{'_params'}->{'-primary_id'} = substr($gi,3); } } # EMBL DT lines sub _embl_date { my ($self, $data) = @_; while ($data->{DATA} =~ m{(\S+)\s\((.*?)\)}g) { my ($date, $version) = ($1, $2); $date =~ tr{,}{}d; # remove comma if new version if ($version =~ m{\(Rel\.\s(\d+),\sCreated\)}xmso ) { my $release = Bio::Annotation::SimpleValue->new( -tagname => 'creation_release', -value => $1 ); $self->annotation_collection->add_Annotation($release); } elsif ($version =~ m{\(Rel\.\s(\d+),\sLast\supdated,\sVersion\s(\d+)\)}xmso ) { my $release = Bio::Annotation::SimpleValue->new( -tagname => 'update_release', -value => $1 ); $self->annotation_collection->add_Annotation($release); my $update = Bio::Annotation::SimpleValue->new( -tagname => 'update_version', -value => $2 ); $self->annotation_collection->add_Annotation($update); } push @{ $self->{'_params'}->{'-dates'} }, $date; } } # UniProt/SwissProt DT lines sub _swiss_date { my ($self, $data) = @_; # swissprot my @dls = split m{\n}, $data->{DATA}; for my $dl (@dls) { my ($date, $version) = split(' ', $dl, 2); $date =~ tr{,}{}d; # remove comma if new version if ($version =~ m{\(Rel\. (\d+), Last sequence update\)} || # old $version =~ m{sequence version (\d+)\.}) { #new my $update = Bio::Annotation::SimpleValue->new( -tagname => 'seq_update', -value => $1 ); $self->annotation_collection->add_Annotation($update); } elsif ($version =~ m{\(Rel\. (\d+), Last annotation update\)} || #old $version =~ m{entry version (\d+)\.}) { #new $self->{'_params'}->{'-version'} = $1; $self->{'_params'}->{'-seq_version'} = $1; } push @{ $self->{'_params'}->{'-dates'} }, $date; } } # GenBank KEYWORDS line # EMBL KW line # UniProt/SwissProt KW line sub _generic_keywords { my ($self, $data) = @_; $data->{DATA} =~ s{\.$}{}; my @kw = split m{\s*\;\s*}xo ,$data->{DATA}; $self->{'_params'}->{'-keywords'} = \@kw; } # GenBank DEFINITION line # EMBL DE line # UniProt/SwissProt DE line sub _generic_description { my ($self, $data) = @_; $self->{'_params'}->{'-desc'} = $data->{DATA}; } # GenBank ACCESSION line # EMBL AC line # UniProt/SwissProt AC line sub _generic_accession { my ($self, $data) = @_; my @accs = split m{[\s;]+}, $data->{DATA}; $self->{'_params'}->{'-accession_number'} = shift @accs; $self->{'_params'}->{'-secondary_accessions'} = \@accs if @accs; } ####################### SPECIES HANDLERS ####################### # uses Bio::Species # GenBank SOURCE, ORGANISM lines # EMBL O* lines # UniProt/SwissProt O* lines sub _generic_species { my ($self, $data) = @_; my $seqformat = $self->format; # if data is coming in from GenBank parser... if ($seqformat eq 'genbank' && $data->{ORGANISM} =~ m{(.+?)\s(\S+;[^\n\.]+)}ox) { ($data->{ORGANISM}, $data->{CLASSIFICATION}) = ($1, $2); } # SwissProt stuff... # hybrid names in swissprot files are no longer valid per intergration into # UniProt. Files containing these have been split into separate entries, so # it is probably a good idea to update if one has these lingering around... my $taxid; if ($seqformat eq 'swiss') { if ($data->{DATA} =~ m{^([^,]+)}ox) { $data->{DATA} = $1; } if ($data->{CROSSREF} && $data->{CROSSREF} =~ m{NCBI_TaxID=(\d+)}) { $taxid = $1; } } my ($sl, $class, $sci_name) = ($data->{DATA}, $data->{CLASSIFICATION}, $data->{ORGANISM} || ''); my ($organelle,$abbr_name, $common); my @class = reverse split m{\s*;\s*}, $class; # have to treat swiss different from everything else... if ($sl =~ m{^(mitochondrion|chloroplast|plastid)? # GenBank format \s*(.*?) \s*(?: \( (.*?) \) )?\.?$ }xmso ){ ($organelle, $abbr_name, $common) = ($1, $2, $3); # optional } else { $abbr_name = $sl; # nothing caught; this is a backup! } # there is no 'abbreviated name' for EMBL $sci_name = $abbr_name if $seqformat ne 'genbank'; $organelle ||= ''; $common ||= ''; $sci_name || return; unshift @class, $sci_name; # no genus/species parsing here; moving to Bio::Taxon-based taxonomy my $make = Bio::Species->new(); $make->scientific_name($sci_name); $make->classification(@class) if @class > 0; $common && $make->common_name( $common ); $abbr_name && $make->name('abbreviated', $abbr_name); $organelle && $make->organelle($organelle); $taxid && $make->ncbi_taxid($taxid); $self->{'_params'}->{'-species'} = $make; } ####################### ANNOTATION HANDLERS ####################### # GenBank DBSOURCE line sub _genbank_dbsource { my ($self, $data) = @_; my $dbsource = $data->{DATA}; my $annotation = $self->annotation_collection; # deal with swissprot dbsources # we could possibly parcel these out to subhandlers... if( $dbsource =~ s/(UniProt(?:KB)|swissprot):\s+locus\s+(\S+)\,.+\n// ) { $annotation->add_Annotation ('dblink', Bio::Annotation::DBLink->new (-primary_id => $2, -database => $1, -tagname => 'dblink')); if( $dbsource =~ s/\s*created:\s+([^\.]+)\.\n// ) { $annotation->add_Annotation ('swissprot_dates', Bio::Annotation::SimpleValue->new (-tagname => 'date_created', -value => $1)); } while( $dbsource =~ s/\s*(sequence|annotation)\s+updated:\s+([^\.]+)\.\n//g ) { $annotation->add_Annotation ('swissprot_dates', Bio::Annotation::SimpleValue->new (-tagname => 'date_updated', -value => $1)); } $dbsource =~ s/\n/ /g; if( $dbsource =~ s/\s*xrefs:\s+((?:\S+,\s+)+\S+)\s+xrefs/xrefs/ ) { # will use $i to determine even or odd # for swissprot the accessions are paired my $i = 0; for my $dbsrc ( split(/,\s+/,$1) ) { if( $dbsrc =~ /(\S+)\.(\d+)/ || $dbsrc =~ /(\S+)/ ) { my ($id,$version) = ($1,$2); $version ='' unless defined $version; my $db; if( $id =~ /^\d\S{3}/) { $db = 'PDB'; } else { $db = ($i++ % 2 ) ? 'GenPept' : 'GenBank'; } $annotation->add_Annotation ('dblink', Bio::Annotation::DBLink->new (-primary_id => $id, -version => $version, -database => $db, -tagname => 'dblink')); } } } elsif( $dbsource =~ s/\s*xrefs:\s+(.+)\s+xrefs/xrefs/i ) { # download screwed up and ncbi didn't put acc in for gi numbers my $i = 0; for my $id ( split(/\,\s+/,$1) ) { my ($acc,$db); if( $id =~ /gi:\s+(\d+)/ ) { $acc= $1; $db = ($i++ % 2 ) ? 'GenPept' : 'GenBank'; } elsif( $id =~ /pdb\s+accession\s+(\S+)/ ) { $acc= $1; $db = 'PDB'; } else { $acc= $id; $db = ''; } $annotation->add_Annotation ('dblink', Bio::Annotation::DBLink->new (-primary_id => $acc, -database => $db, -tagname => 'dblink')); } } else { $self->warn("Cannot match $dbsource\n"); } if( $dbsource =~ s/xrefs\s+\(non\-sequence\s+databases\):\s+ ((?:\S+,\s+)+\S+)//x ) { for my $id ( split(/\,\s+/,$1) ) { my $db; # this is because GenBank dropped the spaces!!! # I'm sure we're not going to get this right ##if( $id =~ s/^://i ) { ## $db = $1; ##} $db = substr($id,0,index($id,':')); if (! exists $DBSOURCE{ $db }) { $db = ''; # do we want 'GenBank' here? } $id = substr($id,index($id,':')+1); $annotation->add_Annotation ('dblink',Bio::Annotation::DBLink->new (-primary_id => $id, -database => $db, -tagname => 'dblink')); } } } else { if( $dbsource =~ /^(\S*?):?\s*accession\s+(\S+)\.(\d+)/ ) { my ($db,$id,$version) = ($1,$2,$3); $annotation->add_Annotation ('dblink', Bio::Annotation::DBLink->new (-primary_id => $id, -version => $version, -database => $db || 'GenBank', -tagname => 'dblink')); } elsif ( $dbsource =~ /(\S+)([\.:])(\d+)/ ) { my ($id, $db, $version); if ($2 eq ':') { ($db, $id) = ($1, $3); } else { ($db, $id, $version) = ('GenBank', $1, $3); } $annotation->add_Annotation('dblink', Bio::Annotation::DBLink->new( -primary_id => $id, -version => $version, -database => $db, -tagname => 'dblink') ); } else { $self->warn("Unrecognized DBSOURCE data: $dbsource\n"); } } } # EMBL DR lines # UniProt/SwissProt DR lines sub _generic_dbsource { my ($self, $data) = @_; #$self->debug(Dumper($data)); while ($data->{DATA} =~ m{([^\n]+)}og) { my $dblink = $1; $dblink =~ s{\.$}{}; my $link; my @linkdata = split '; ',$dblink; if ( $dblink =~ m{([^\s;]+);\s*([^\s;]+);?\s*([^\s;]+)?}) { #if ( $dblink =~ m{([^\s;]+);\s*([^\s;]+);?\s*([^\s;]+)?}) { my ($databse, $prim_id, $sec_id) = ($1,$2,$3); $link = Bio::Annotation::DBLink->new(-database => $databse, -primary_id => $prim_id, -optional_id => $sec_id); } else { $self->warn("No match for $dblink"); } $self->annotation_collection->add_Annotation('dblink', $link); } } # GenBank REFERENCE and related lines # EMBL R* lines # UniProt/SwissProt R* lines sub _generic_reference { my ($self, $data) = @_; my $seqformat = $self->format; my ($start, $end); # get these in EMBL/Swiss if ($data->{CROSSREF}) { while ($data->{CROSSREF} =~ m{(pubmed|doi|medline)(?:=|;\s+)(\S+)}oig) { my ($db, $ref) = (uc $1, $2); $ref =~ s{[;.]+$}{}; $data->{$db} = $ref; } } # run some cleanup for swissprot if ($seqformat eq 'swiss') { for my $val (values %{ $data }) { $val =~ s{;$}{}; $val =~ s{(\w-)\s}{$1}; } } if ( $data->{POSITION} ) { if ($seqformat eq 'embl') { ($start, $end) = split '-', $data->{POSITION},2; } elsif ($data->{POSITION} =~ m{.+? OF (\d+)-(\d+).*}) { #swiss ($start, $end) = ($1, $2); } } if ($data->{DATA} =~ m{^\d+\s+\([a-z]+\s+(\d+)\s+to\s+(\d+)\)}xmso) { ($start, $end) = ($1, $2); } my $ref = Bio::Annotation::Reference->new( -comment => $data->{REMARK}, -location => $data->{JOURNAL}, -pubmed => $data->{PUBMED}, -consortium => $data->{CONSRTM}, -title => $data->{TITLE}, -authors => $data->{AUTHORS}, -medline => $data->{MEDLINE}, -doi => $data->{DOI}, -rp => $data->{POSITION}, # JIC... -start => $start, -end => $end, ); if ($data->{DATA} =~ m{^\d+\s+\((.*)\)}xmso) { $ref->gb_reference($1); } $self->annotation_collection->add_Annotation('reference', $ref); } # GenBank COMMENT lines # EMBL CC lines # UniProt/SwissProt CC lines sub _generic_comment { my ($self, $data) = @_; $self->annotation_collection->add_Annotation('comment', Bio::Annotation::Comment->new( -text => $data->{DATA} )); } ####################### SEQFEATURE HANDLER ####################### # GenBank Feature Table sub _generic_seqfeatures { my ($self, $data) = @_; return if $data->{FEATURE_KEY} eq 'FEATURES'; my $primary_tag = $data->{FEATURE_KEY}; # grab the NCBI taxon ID from the source SF if ($primary_tag eq 'source' && exists $data->{'db_xref'}) { if ( $self->{'_params'}->{'-species'} && $data->{'db_xref'} =~ m{taxon:(\d+)}xmso ) { $self->{'_params'}->{'-species'}->ncbi_taxid($1); } } my $source = $self->format; my $seqid = ${ $self->get_params('accession_number') }{'accession_number'}; my $loc; eval { $loc = $self->{'_locfactory'}->from_string($data->{'LOCATION'}); }; if(! $loc) { $self->warn("exception while parsing location line [" . $data->{'LOCATION'} . "] in reading $source, ignoring feature " . $data->{'primary_tag'}. " (seqid=" . $seqid . "): " . $@); return; } if($seqid && (! $loc->is_remote())) { $loc->seq_id($seqid); # propagates if it is a split location } my $sf = Bio::SeqFeature::Generic->direct_new(); $sf->location($loc); $sf->primary_tag($primary_tag); $sf->seq_id($seqid); $sf->source_tag($source); delete $data->{'FEATURE_KEY'}; delete $data->{'LOCATION'}; delete $data->{'NAME'}; delete $data->{'DATA'}; $sf->set_attributes(-tag => $data); push @{ $self->{'_params'}->{'-features'} }, $sf; } ####################### ODDS AND ENDS ####################### # Those things that don't fit anywhere else. If a specific name # maps to the below table, that class and method are used, otherwise # it goes into a SimpleValue (I think this is a good argument for why # we need a generic mechanism for storing annotation) sub _generic_simplevalue { my ($self, $data) = @_; $self->annotation_collection->add_Annotation( Bio::Annotation::SimpleValue->new(-tagname => lc($data->{NAME}), -value => $data->{DATA}) ); } sub noop {} sub _debug { my ($self, $data) = @_; $self->debug(Dumper($data)); } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/game���������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 15760� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/game/featHandler.pm������������������������������������������������������000444��000766��000024�� 53730�13155576320� 20720� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # # Helper module for Bio::SeqIO::game::featHandler # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Sheldon McKay <mckays@cshl.edu> # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::game::featHandler -- a class for handling feature elements =head1 SYNOPSIS This module is not used directly =head1 DESCRIPTION Bio::SeqIO::game::featHandler converts game XML E<lt>annotationE<gt> elements into flattened Bio::SeqFeature::Generic objects to be added to the sequence =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sheldon McKay Email mckays@cshl.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqIO::game::featHandler; use Bio::SeqFeature::Generic; use Bio::Location::Split; use Data::Dumper; use strict; use vars qw {}; use base qw(Bio::SeqIO::game::gameSubs); =head2 new Title : new Usage : my $featHandler = Bio::SeqIO::game::featHandler->new($seq, $seq_h, $ann_l) Function: creates an object to deal with sequence features Returns : a handler object Args : $seq -- a Bio::SeqI compliant object $seq_h -- ref. to a hash of other sequences associated with the main sequence (proteins, etc) $ann_l -- ref. to a list of annotations =cut sub new { my ($caller, $seq, $seq_h, $ann_l ) = @_; my $class = ref($caller) || $caller; my $self = bless ({ seq => $seq, curr_feats => [], curr_coords => [], seq_h => $seq_h, ann_l => $ann_l, }, $class); return $self; } =head2 add_source Title : add_source Usage : $featHandler->add_source($seq->length, \%tags); Function: creates a source feature Returns : a Bio::SeqFeature::Generic object Args : sequence length and a ref. to a hash of tag/value attributes =cut sub add_source { my ($self, $length, $tags) = @_; my $feat = Bio::SeqFeature::Generic->new( -primary => 'source', -start => 1, -end => $length, ); for ( keys %{$tags} ) { for my $val ( @{$tags->{$_}} ) { $feat->add_tag_value( $_ => $val ); } } return $feat; } =head2 has_gene Title : has_gene Usage : my $gene = $self->_has_gene($gene, $gname, $id) Function: method to get/set the current gene feature Returns : a Bio::SeqFeature::Generic object (if there is a gene) Args : (optional) $gene -- an XML element for the annotation $gname -- gene name $id -- gene ID (not always the same as the name) =cut sub has_gene { my ($self, $gene, $gname, $id) = @_; # use name preferentially over id. We can't edit IDs in Apollo # AFAIK, and this will create an orphan CDS for newly created # transcipts -- I think this needs more work #$id = $gname if $id && $gname; unless ( $gene ) { if ( defined $self->{curr_gene} ) { return $self->{curr_gene}; } else { return 0; } } else { if ( $id && !$self->{curr_ltag} ) { $self->{curr_ltag} = $id; } if ( $gname && !$self->{curr_gname} ) { $self->{curr_gname} = $gname; } my $tags = {}; for my $child ( @{$gene->{Children}} ) { my $name = $child->{Name}; if ( $name eq 'dbxref' ) { $tags->{dbxref} ||= []; push @{$tags->{dbxref}}, $self->dbxref( $child ); } elsif ( $name !~ /name/ ){ $self->complain("Unrecognized element '$name'. I don't " . "know what to do with $name elements"); } } my $feat = Bio::SeqFeature::Generic->new( -primary => 'gene', ); my %seen; for ( keys %{$tags} ) { for my $val ( @{$tags->{$_}} ) { $feat->add_tag_value( $_ => $val ) unless ++$seen{$_.$val} > 1; } } $self->{curr_gene} = $feat; return $feat; } } =head2 _has_CDS Title : _has_CDS Usage : my $cds = $self->_has_CDS Function: internal getter/setter for CDS features Returns : a Bio::SeqFeature::Generic transcript object (or nothing) Args : a Bio::SeqFeature::Generic transcript feature =cut sub _has_CDS { my ($self, $transcript) = @_; if ( !$transcript ) { if ( defined $self->{curr_cds} ) { return $self->{curr_cds}; } else { return 0; } } else { my $tags = $self->{curr_tags}; $self->{curr_cds} = $self->_add_CDS( $transcript, $tags ); } } =head2 add_annotation Title : add_annotation Usage : $featHandler->add_annotation($seq, $type, $id, $tags, $feats) Function: converts a containment hierarchy into an ordered list of flat features Returns : nothing Args : $seq -- a Bio::SeqI compliant object $type -- the annotation type $id -- the anotation ID $tags -- ref. to a hash of tag/value attributes $feats -- ref to an array of Bio::SeqFeature::Generic objects =cut sub add_annotation { my ($self, $seq, $type, $id, $tags, $feats) = @_; # is this a generic feature? unless ( $self->has_gene ) { shift; $self->_add_generic_annotation(@_); return 0; } my $feat; if ( $type eq 'gene' ) { $feat = $self->has_gene; $feat->add_tag_value( gene => ($self->{curr_gname} || $id) ) unless $feat->has_tag('gene'); } else { $feat = Bio::SeqFeature::Generic->new; $feat->primary_tag($type); my $gene = $self->has_gene; $gene->add_tag_value( gene => ($self->{curr_gname} || $id) ) unless $gene->has_tag('gene'); $feat->add_tag_value( gene => ($self->{curr_gname} || $id) ) unless $feat->has_tag('gene');; } for ( keys %{$tags} ) { # or else add simple tag/value pairs if ( $_ eq 'name' && $tags->{type}->[0] eq 'gene' ) { $feat->add_tag_value( gene => $tags->{name}->[0] ) unless $feat->has_tag( 'gene' ); delete $tags->{name}; } else { next if $_ eq 'type' && $tags->{$_}->[0] eq 'gene'; next if $_ eq 'gene' && $feat->has_tag( 'gene' ); for my $val ( @{$tags->{$_}} ) { $feat->add_tag_value( $_ => $val ); } } } $feat->strand( $self->{curr_strand} ); $feat->start( $self->{curr_coords}->[0] ); $feat->end( $self->{curr_coords}->[1] ); # create an array of features for the annotation (order matters) my @annotations = ( $feat ); # add the gene feature if the annotation is not a gene if ( $self->has_gene && $type ne 'gene') { my $gene = $self->has_gene; $gene->strand( $self->{curr_strand} ); $gene->start( $self->{curr_coords}->[0] ); $gene->end( $self->{curr_coords}->[-1] ); push @annotations, $gene; $self->{curr_gene} = ''; } # add the subfeatures for ( @{$feats} ) { $self->complain("bad feature $_") unless ref($_) =~ /Bio/; push @annotations, $_; } # add the annotation array to the list for this sequence my $seqid = $seq->id; my $list = $self->{ann_l}; # make sure the feature_sets appear in ascending order if ( $list->[0] && $annotations[0]->start < $list->[0]->start ) { unshift @{$list}, @annotations; } else { push @{$list}, @annotations; } # garbage collection $self->{curr_gene} = ''; $self->{curr_ltag} = ''; $self->{curr_gname} = ''; $self->{curr_coords} = []; $self->{curr_feats} = []; $self->{curr_strand} = 0; $self->{ann_seq} = $seq; $self->flush; } =head2 _add_generic_annotation Title : _add_generic_annotation Usage : $self->_add_generic_annotation($seq, $type, $id, $tags, $feats) Function: an internal method to handle non-gene annotations Returns : nothing Args : $seq -- a Bio::SeqI compliant object $type -- the annotation type $id -- the anotation ID $tags -- ref. to a hash of tag/value attributes $feats -- ref to an array of Bio::SeqFeature::Generic objects =cut sub _add_generic_annotation { my ($self, $seq, $type, $id, $tags, $feats) = @_; for ( @$feats ) { $_->primary_tag($type); } push @{$self->{ann_l}}, @$feats; $self->{curr_coords} = []; $self->{curr_feats} = []; $self->{curr_strand} = 0; $self->{ann_seq} = $seq; $self->flush; } =head2 feature_set Title : feature_set Usage : push @feats, $featHandler->feature_set($id, $gname, $set, $anntype); Function: handles <feature_span> hierarchies (usually a transcript) Returns : a list of Bio::SeqFeature::Generic objects Args : $id -- ID of the feature set $gname -- name of the gene $set -- the <feature_set> object $anntype -- type of the parent annotation =cut sub feature_set { my ($self, $id, $gname, $set, $anntype) = @_; my $stype = $set->{_type}->{Characters}; $self->{curr_loc} = []; $self->{curr_tags} = {}; $self->{curr_subfeats} = []; $self->{curr_strand} = 0; my @feats = (); my $tags = $self->{curr_tags}; my $sname = $set->{_name}->{Characters} || $set->{Attributes}->{id}; if ( $set->{Attributes}->{problem} ) { $tags->{problem} = [$set->{Attributes}->{problem}]; } my @fcount = grep { $_->{Name} eq 'feature_span' } @{$set->{Children}}; if ( @fcount == 1 ) { $self->_build_feature_set($set, 1); my ($feat) = @{$self->{curr_subfeats}}; $feat->primary_tag('transcript') if $feat->primary_tag eq 'exon'; if ( $feat->primary_tag eq 'transcript' ) { $feat->add_tag_value( gene => ($gname || $id) ) unless $feat->has_tag('gene'); } my %seen_tag; for my $tag ( keys %{$tags} ) { for my $val ( @{$tags->{$tag}} ) { $feat->add_tag_value( $tag => $val ) if $val && ++$seen_tag{$tag.$val} < 2; } } @feats = ($feat); } else { $self->{curr_ltag} = $id; $self->{curr_cds} = ''; $gname = $id if $gname eq 'gene'; $self->{curr_gname} = $gname; if ( $self->has_gene ) { unless ( $anntype =~/RNA/i ) { $stype =~ s/transcript/mRNA/; } } $self->{curr_feat} = Bio::SeqFeature::Generic->new( -primary => $stype, -id => $id, ); my $feat = $self->{curr_feat}; $self->_build_feature_set($set); my $gene = $gname || $self->{curr_ltag}; $feat->add_tag_value( gene => $gene ) unless $feat->has_tag('gene'); # if there is an annotated protein product my $cds = $self->_has_CDS( $feat ); if ( $cds ) { $feat->primary_tag('mRNA'); # we really just want one value here $cds->remove_tag('standard_name') if $cds->has_tag('standard_name'); $cds->add_tag_value( standard_name => $sname ); $cds->remove_tag('gene') if $cds->has_tag('gene'); $cds->add_tag_value( gene => $gene ); # catch empty protein ids if ( $cds->has_tag('protein_id' ) && !$cds->get_tag_values('protein_id') ) { my $pid = $self->protein_id($cds, $sname); $cds->remove_tag('protein_id'); $cds->add_tag_value( protein_id => $pid ); } # make sure other subfeats are tied to the transcript # via a 'standard_name' qualifier and the gene via a 'gene' qualifier my @subfeats = @{$self->{curr_subfeats}}; for my $sf ( @ subfeats ) { $sf->add_tag_value( standard_name => $sname ) unless $sf->has_tag('standard_name'); $sf->add_tag_value( gene => $gene ) unless $sf->has_tag('gene'); } $feat->add_tag_value( standard_name => $sname ) unless $feat->has_tag('standard_name'); $feat->add_tag_value( gene => $gene ) unless $feat->has_tag('gene'); # if the mRNA and CDS are the same length, the mRNA is redundant # lose the mRNA, steal its tags and give them to the CDS my %seen; if ( $feat->length == $cds->length ) { for my $t ( $feat->all_tags ) { next if $t =~ /gene|standard_name/; $cds->add_tag_value( $t => $feat->get_tag_values($t) ); } undef $feat; } @feats = sort { $a->start <=> $b->start } ($cds, @subfeats); unshift @feats, $feat if $feat; } else { if ( @{$self->{curr_loc}} > 1 ) { my $loc = Bio::Location::Split->new( -splittype => 'JOIN' ); # sort the exons in ascending start order my @loc = sort { $a->start <=> $b->start } @{$self->{curr_loc}}; # then add them to the transcript location for ( @loc ) { $loc->add_sub_Location( $_ ) } $feat->location( $loc ); } else { $feat->location( $self->{curr_loc}->[0] ); } for ( keys %$tags ) { # expunge duplicate gene attributes next if /gene/ && $feat->has_tag('gene'); for my $v ( @{$tags->{$_}} ) { $feat->add_tag_value( $_ => $v ); } } # make sure other subfeats are tied to the transcript my @subfeats = @{$self->{curr_subfeats}}; for my $sf ( @ subfeats ) { $sf->add_tag_value( standard_name => $sname ) unless $sf->has_tag('standard_name'); $sf->add_tag_value( gene => $gene ) unless $sf->has_tag('gene'); } @feats = ( $feat, @subfeats ); } } # adjust the maximum extent of the annotated feature # if req'd (ie the <annotation> element) $self->{curr_coords}->[0] ||= 1000000000000; $self->{curr_coords}->[1] ||= -1000000000000; for ( @feats ) { if ( $self->{curr_coords}->[0] > $_->start ) { $self->{curr_coords}->[0] = $_->start; } if ( $self->{curr_coords}->[1] < $_->end ) { $self->{curr_coords}->[1] = $_->end; } } $self->flush( $set ); return @feats; } =head2 _build_feature_set Title : _build_feature_set Usage : $self->_build_feature_set($set, 1) # 1 flag means retain the exon as a subfeat Function: an internal method to process attributes and subfeats of a feature set Returns : nothing Args : $set -- a <feature_set> element 1 -- optional flag to retain exons as subfeats. Otherwise, they will be converted to sublocations of a parent CDS feature =cut sub _build_feature_set { my ($self, $set, $keep_subfeat) = @_; for my $child ( @{$set->{Children}} ) { my $name = $child->{Name}; # these elements require special handling if ( $name eq 'date' ) { $self->date( $child ); } elsif ( $name eq 'comment' ) { $self->comment( $child ); } elsif ( $name eq 'evidence' ) { $self->evidence( $child ); } elsif ( $name eq 'feature_span' ) { $self->_add_feature_span( $child, $keep_subfeat ); } elsif ( $name eq 'property' ) { $self->property( $child ); } # need to add the db_xref tags to the gene? # otherwise, simple tag/value pairs elsif ( $name =~ /synonym|author|description/) { $self->{curr_tags}->{$name} = [$child->{Characters}]; } elsif ( $name !~ /name|type|seq/ ){ $self->complain("Unrecognized element '$name'. I don't " . "know what to do with $name elements"); } } } =head2 _add_feature_span Title : _add_feature_span Usage : $self->_add_feature_span($el, 1) Function: an internal method to process <feature_span> elements Returns : nothing Args : $el -- a <feature_span> element 1 -- an optional flag to retain exons as subfeatures =cut sub _add_feature_span { my ($self, $el, $keep_subfeat) = @_; my $tags = $self->{curr_tags}; my $feat = $self->{curr_feat}; my $type = $el->{_type}->{Characters} || $el->{Name}; my $id = $el->{Attributes}->{id} || $el->{_name}->{Characters}; my $seqr = $el->{_seq_relationship}; my $start = int $seqr->{_span}->{_start}->{Characters}; my $end = int $seqr->{_span}->{_end}->{Characters}; my $stype = $seqr->{Attributes}->{type}; my $seqid = $seqr->{Attributes}->{seq}; push @{$self->{seq_l}}, $self->{seq_h}->{$seqid}; if ( $start > $end ) { $self->{curr_strand} = -1; ($start, $end) = ($end, $start); } else { $self->{curr_strand} = 1; } # add exons to the transcript if ( $type eq 'exon' ) { my $sl = Bio::Location::Simple->new( -start => $start, -end => $end, -strand => $self->{curr_strand} ); push @{$self->{curr_loc}}, $sl; } # apollo and gadfly use different tags for the same thing if ( $type =~ /start_codon|translate offset/ ) { $self->{curr_tags}->{codon_start} = [$start]; } else { if ( $type eq 'exon' ) { return unless $keep_subfeat; } push @{$self->{curr_subfeats}}, Bio::SeqFeature::Generic->new( -start => $start, -end => $end, -strand => $self->{curr_strand}, -primary => $type ); } # identify the translation product my $tscript = $el->{Attributes}->{produces_seq}; if ( $tscript && $tscript ne 'null') { my $subseq = $self->{seq_h}->{$el->{Attributes}->{produces_seq}}; $self->{curr_tags}->{product} = [$el->{Attributes}->{produces_seq}]; $self->{curr_tags}->{translation} = [$subseq->seq] if $subseq; } $self->flush( $el ); } =head2 _add_CDS Title : _add_CDS Usage : my $cds = $self->_add_CDS($transcript, $tags) Function: an internal method to create a CDS feature from a transcript feature Returns : a Bio::SeqFeature::Generic object Args : $transcript -- a Bio::SeqFeature::Generic object for a transcript $tags -- ref. to a hash of tag/value attributes =cut sub _add_CDS { my ($self, $feat, $tags) = @_; my $loc = {}; my $single = 0; if ( @{$self->{curr_loc}} > 1 ) { $loc = Bio::Location::Split->new; # sort the exons in ascending start order my @loc = sort { $a->start <=> $b->start } @{$self->{curr_loc}}; # then add them to the location object for ( @loc ) { $loc->add_sub_Location( $_ ); } } else { $loc = $self->{curr_loc}->[0]; $single++; } # create a CDS my @exons = $single ? $loc : $loc->sub_Location(1); $feat->location($loc); # try to find a peptide my $seq = $self->{seq_h}->{ $tags->{protein_id}->[0] }; $seq ||= $self->{seq_h}->{ $tags->{product}->[0] } || $self->{seq_h}->{ $tags->{gene}->[0] } || $self->{seq_h}->{ $tags->{standard_name}->[0] }; # Can we count on the description format being consistent? # Why is CDS coordinate info saved as description text not # specified in the DTD? Anyone have a better idea? Aww, # who am I kidding, I'm the only one who will ever read this! my ($start, $stop, $peptide) = (); if ( $seq ) { $peptide = $seq->display_id; my $desc = $seq->description || ''; $desc =~ s/,|\n//g; $desc =~ s/\)(\w)/\) $1/g; if ( $desc =~ /cds_boundaries:.+?(\d+)\.\.(\d+)/ ) { ($start, $stop) = ($1 - $self->{offset}, $2 - $self->{offset}); } else { # OK, I guess the transcript must be the CDS then $start = $loc->start; $stop = $loc->end; } } else { $self->warn("I did not find a protein sequence for " . $feat->display_name); } delete $tags->{transcript}; # now chop off the UTRs to create a CDS my @exons_to_add = (); #warn scalar(@exons), " exons, $start, $stop\n"; for ( @exons ) { my $exon = Bio::Location::Simple->new; if ( $_->end < $start || $_->start > $stop ) { #warn "exon out of range\n"; next; } if ( $_->start < $start && $_->end > $start ) { #warn "chopping off left UTR\n"; $exon->start( $start ); } if ( $_->end > $stop && $_->start < $stop ) { #warn "chopping off right UTR\n"; $exon->end( $stop ); } unless ($exon->valid_Location) { $exon->start( $_->start ); $exon->end( $_->end ); } $exon->strand ( $self->{curr_strand} ); push @exons_to_add, $exon; } my $cds_loc; if ( @exons_to_add > 1 ) { $cds_loc = Bio::Location::Split->new( -splittype => 'JOIN' ); for ( @exons_to_add ) { $cds_loc->add_sub_Location( $_ ); } } else { $cds_loc = $exons_to_add[0]; } my $parent = $self->{curr_gname} || $self->{curr_ltag}; # try not to steal too many mRNA attributes for the CDS my $cds_tags = {}; for my $k ( keys %$tags ) { if ( $k =~ /product|protein|translation|codon_start/ ) { $cds_tags->{$k} = $tags->{$k}; delete $tags->{$k}; } } for ( keys %$tags ) { for my $v ( @{$tags->{$_}} ) { $feat->add_tag_value( $_ => $v ) unless $feat->has_tag($_); } } if ( $self->{curr_gname} ) { $cds_tags->{gene} = [$self->{curr_gname}]; } my $gene = $self->has_gene; my $cds = Bio::SeqFeature::Generic->new( -primary => 'CDS', -location => $cds_loc, ); $cds_tags->{translation} = [$seq->seq]; for ( keys %{$cds_tags} ) { my %seen; for my $val (@{$cds_tags->{$_}}) { next if ++$seen{$val} > 1; $cds->add_tag_value( $_ => $val ); } } $cds; } 1; ����������������������������������������BioPerl-1.007002/Bio/SeqIO/game/gameHandler.pm������������������������������������������������������000444��000766��000024�� 11604�13155576320� 20704� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# $Id: # # BioPerl module for Bio::SeqIO::game::gameHandler # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Sheldon McKay <mckays@cshl.edu> # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::game::gameHandler -- PerlSAX handler for game-XML =head1 SYNOPSIS This modules is not used directly =head1 DESCRIPTION Bio::SeqIO::game::gameHandler is the top-level XML handler invoked by PerlSAX =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sheldon McKay Email mckays@cshl.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqIO::game::gameHandler; use Bio::SeqIO::game::seqHandler; use strict; use vars qw {}; use base qw(Bio::SeqIO::game::gameSubs); =head2 start_document Title : start_document Function: begin parsing the document =cut sub start_document { my ($self, $document) = @_; $self->SUPER::start_document($document); $self->{sequences} = {}; $self->{annotations} = {}; $self->{computations} = {}; $self->{map_position} = {}; $self->{focus} = {}; } =head2 end_document Title : end_document Function: finish parsing the document =cut sub end_document { my ($self, $document) = @_; $self->SUPER::end_document($document); return $self; } =head2 load Title : load Usage : $seqs = $handler->load Function: start parsing Returns : a ref to a list of sequence objects Args : an optional flag to suppress <computation_analysis> elements (not used yet) =cut sub load { my $self = shift; my $suppress_comps = shift; my @seqs = (); for ( 1..$self->{game} ) { my $seq = $self->{sequences}->{$_} or $self->throw("No sequences defined"); my $ann = $self->{annotations}->{$_}; my $comp = $self->{computations}->{$_}; my $map = $self->{map_position}->{$_}; my $foc = $self->{focus}->{$_} or $self->throw("No main sequence defined"); my $src = $self->{has_source}; my $bio = Bio::SeqIO::game::seqHandler->new( $seq, $ann, $comp, $map, $src ); push @seqs, $bio->convert; } \@seqs; } =head2 s_game Title : s_game Function: begin parsing game element =cut sub s_game { my ($self, $e) = @_; my $el = $self->curr_element; $self->{game}++; my $version = $el->{Attributes}->{version}; unless ( defined $version ) { $self->complain("No GAME-xml version specified -- guessing v1.2\n"); $version = 1.2; } if ( defined($version) && $version == 1.2) { $self->{origin_offset} = 1; } else { $self->{origin_offset} = 0; } if (defined($version) && ($version != 1.2)) { $self->complain("GAME version $version is not supported\n", "I'll try anyway but I may fail!\n"); } } =head2 e_game Title : e_game Function: process the game element =cut sub e_game { my ($self, $el) = @_; $self->flush( $el ); } =head2 e_seq Title : e_seq Function: process the sequence element =cut sub e_seq { my ($self, $e) = @_; my $el = $self->curr_element(); $self->{sequences}->{$self->{game}} ||= []; my $seqs = $self->{sequences}->{$self->{game}}; if ( defined $el->{Attributes}->{focus} ) { $self->{focus}->{$self->{game}} = $el; } push @{$seqs}, $el; $self->flush; } =head2 e_map_position Title : e_map_position Function: process the map_position element =cut sub e_map_position { my ($self, $e) = @_; my $el = $self->curr_element; $self->{map_position}->{$self->{game}} = $el; } =head2 e_annotation Title : e_annotation Function: process the annotation =cut sub e_annotation { my ($self, $e) = shift; my $el = $self->curr_element; $self->{annotations}->{$self->{game}} ||= []; my $anns = $self->{annotations}->{$self->{game}}; push @{$anns}, $el; } 1; ����������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/game/gameSubs.pm���������������������������������������������������������000444��000766��000024�� 26422�13155576320� 20247� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# some of the following code was pillaged from the CPAN module # XML::Handler::Subs # # Copyright (C) 1999 Ken MacLeod # XML::Handler::XMLWriter is free software; you can redistribute it and/or # modify it under the same terms as Perl itself. # # BioPerl module for Bio::SeqIO::game::gameSubs # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Sheldon McKay <mckays@cshl.edu> # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::game::gameSubs -- a base class for game-XML parsing =head1 SYNOPSIS Not used directly =head1 DESCRIPTION A bag of tricks for game-XML parsing. The PerlSAX handler methods were stolen from Chris Mungall's XML base class, which he stole from Ken MacLeod's XML::Handler::Subs =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sheldon McKay Email mckays@cshl.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqIO::game::gameSubs; use XML::Parser::PerlSAX; use UNIVERSAL; use strict; use vars qw {}; use base qw(Bio::Root::Root); =head2 new Title : new Usage : not used directly Returns : a gameHandler object Args : an XML filename =cut sub new { my $type = shift; my $file = shift || ""; my $self = (@_ == 1) ? { %{ (shift) } } : { @_ }; if ($file) { $self->{file} = $file; } return bless $self, $type; } =head2 go Title : go Usage : not used directly Function: starts PerlSAX XML parsing =cut sub go { my $self = shift; XML::Parser::PerlSAX->new->parse(Source => { SystemId => "$self->{file}" }, Handler => $self); } =head2 start_document Title : start_document Usage : not used directly =cut sub start_document { my ($self, $document) = @_; $self->{Names} = []; $self->{Nodes} = []; } =head2 end_document Title : end_document Usage : not used directly =cut sub end_document { my ($self, $document) = @_; delete $self->{Names}; delete $self->{Nodes}; return(); } =head2 start_element Title : start_element Usage : not used directly =cut sub start_element { my ($self, $element) = @_; $element->{Children} = []; $element->{Name} =~ tr/A-Z/a-z/; push @{$self->{Names}}, $element->{Name}; push @{$self->{Nodes}}, $element; my $el_name = "s_" . $element->{Name}; $el_name =~ s/[^a-zA-Z0-9_]/_/g; if ($ENV{DEBUG_XML_SUBS}) { print STDERR "xml_subs:$el_name\n"; } if ($self->can($el_name)) { $self->$el_name($element); return 1; } return 0; } =head2 end_element Title : end_element Usage : not used directly =cut sub end_element { my ($self, $element) = @_; my $called_sub = 0; $element->{Name} =~ tr/A-Z/a-z/; my $el_name = "e_" . $element->{Name}; $el_name =~ s/[^a-zA-Z0-9_]/_/g; my $rval = 0; if ($ENV{DEBUG_XML_SUBS}) { print STDERR "xml_subs:$el_name\n"; } if ($self->can($ {el_name})) { $rval = $self->$el_name($element) || 0; $called_sub = 1; } my $curr_element = $self->{Nodes}->[$#{$self->{Nodes}}]; pop @{$self->{Names}}; pop @{$self->{Nodes}}; if ($rval eq -1 || !$called_sub) { if (@{$self->{Nodes}}) { my $parent = $self->{Nodes}->[$#{$self->{Nodes}}]; push(@{$parent->{Children}}, $curr_element); $parent->{"_".$curr_element->{Name}} = $curr_element; } } return $called_sub; } =head2 characters Title : characters Usage : not used directly =cut sub characters { my ($self, $characters) = @_; my $str = $self->strip_characters($characters->{Data}); my $curr_element = $self->curr_element(); $curr_element->{Characters} .= $str; 0; } =head2 strip_characters Title : strip_characters Usage : not used directly Function: cleans up XML element contents =cut sub strip_characters { my ($self, $str) = @_; $str =~ s/^[ \n\t]* *//g; $str =~ s/ *[\n\t]*$//g; $str; } =head2 curr_element Title : curr_element Usage : not used directly Function: returns the currently open element =cut sub curr_element { my $self = shift; return $self->{Nodes}->[-1]; } =head2 flush Title : flush Usage : $self->flush($element) # or $element->flush Function: prune a branch from the XML tree Returns : true if successful Args : an element object (optional) =cut sub flush { my $self = shift; my $victim = shift || $self->curr_element; $victim = {}; return 1; } # throw a non-fatal warning =head2 complain Title : complain Usage : $self->complain("This is terrible; I am not happy") Function: throw a non-fatal warning, formats message for pretty-printing Returns : nothing Args : a list of strings =cut sub complain { my $self = shift; return 0 unless $self->{verbose}; my $msg = join '', @_; $msg =~ s/\n/ /g; my @msg = split /\s+/, $msg; my $new_msg = ''; for ( @msg ) { my ($last_chunk) = $new_msg =~ /\n?(.+)$/; my $l = $last_chunk ? length $last_chunk : 0; if ( (length $_) + $l > 45 ) { $new_msg .= "\n$_ "; } else { $new_msg .= $_ . ' '; } } $self->warn($new_msg); } =head2 dbxref Title : dbxref Usage : $self->db_xref($el, $tags) Function: an internal method to flatten dbxref elements Returns : the db_xref (eg wormbase:C02D5.1) Args : an element object (reqd) and a hash ref of tag/values (optional) =cut sub dbxref { my ($self, $el, $tags) = @_; $tags ||= $self->{curr_tags}; my $db = $el->{_xref_db}->{Characters}; my $acc = $el->{_unique_id} || $el->{_db_xref_id} || $el->{_xref_db_id}; my $id = $acc->{Characters} or return 0; $self->flush( $el ); # capture both the database and accession number $id= $id =~ /^\w+$/ ? "$db:$id" : $id; $tags->{dbxref} ||= []; push @{$tags->{dbxref}}, $id; $id; } =head2 comment Title : comment Usage : $self->comment($comment_element) Function: a method to flatten comment elements Returns : a string Args : an comment element (reqd) and a hash ref of tag/values (optional) Note : The hope here is that we can unflatten structured comments in game-derived annotations happen to make a return trip =cut sub comment { my ($self, $el, $tags) = @_; $tags ||= $self->{curr_tags}; my $text = $el->{_text}->{Characters}; my $pers = $el->{_person}->{Characters}; my $date = $el->{_date}->{Characters}; my $int = $el->{_internal}->{Characters}; $self->flush( $el ); my $comment = "person=$pers; " if $pers; $comment .= "date=$date; " if $date; $comment .= "internal=$int; " if $int; $comment .= "text=$text" if $text; $tags->{comment} ||= []; push @{$tags->{comment}}, $comment; $comment; } =head2 property Title : property Usage : $self->property($property_element) Function: an internal method to flatten property elements Returns : a hash reference Args : an property/output element (reqd) and a hash ref of tag/values (optional) Note: This method is aliased to 'output' to handle structurally identical output elements =cut *output = \&property; sub property { my ($self, $el, $tags) = @_; $tags ||= $self->{curr_tags}; my $key = $el->{_type}->{Characters}; my $value = $el->{_value}->{Characters}; $self->flush( $el ); $tags->{$key} ||= []; push @{$tags->{$key}}, $value; $tags; } =head2 evidence Title : evidence Usage : $self->evidence($evidence_element) Function: a method to flatten evidence elements Returns : a string Args : an evidence element =cut sub evidence { my ($self, $el) = @_; my $tags = $self->{curr_tags}; my $text = $el->{Characters} or return 0; my $type = $el->{Attributes}->{type}; my $res = $el->{Attributes}->{result}; $self->flush( $el ); my $evidence = "type=$type; " if $type; $evidence .= "result=$res; " if $res; $evidence .= "evidence=$text"; $tags->{evidence}||= []; push @{$tags->{evidence}}, $evidence; $evidence; } =head2 date Title : date Usage : $self->date($date_element) Function: a method to flatten date elements Returns : true if successful Args : a date element =cut sub date { my ($self, $el) = @_; my $tags = $self->{curr_tags}; my $date = $el->{Characters} or return 0; my $stamp = $el->{Attributes}->{timestamp}; $self->flush( $el ); $tags->{date} ||= []; push @{$tags->{date}}, $date; $tags->{timestamp} ||= []; push @{$tags->{timestamp}}, $stamp; 1; } =head2 protein_id Title : protein_id Usage : $pid = $self->protein_id($cds, $standard_name) Function: a method to search for a protein name Returns : a string Args : the CDS object plus the transcript\'s 'standard_name' =cut sub protein_id { my ($self, $cds, $sn) = @_; my $psn; if ( $cds->has_tag('protein_id') ) { ($psn) = $cds->get_tag_values('protein_id'); } elsif ( $cds->has_tag('product') ) { ($psn) = $cds->get_tag_values('product'); $psn =~ s/.+?(\S+)$/$1/; } elsif ( $cds->has_tag('gene') ) { ($psn) = $cds->get_tag_values('gene'); } elsif ( $sn ) { $psn = $sn; } else { $self->complain("Could not find an ID for the protein"); return ''; } $psn =~ s/-R/-P/; return $psn; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/game/gameWriter.pm�������������������������������������������������������000444��000766��000024�� 104174�13155576320� 20630� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::game::gameWriter # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Sheldon McKay <mckays@cshl.edu> # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::game::gameWriter -- a class for writing game-XML =head1 SYNOPSIS use Bio::SeqIO; my $in = Bio::SeqIO->new( -format => 'genbank', -file => 'myfile.gbk' ); my $out = Bio::SeqIO->new( -format => 'game', -file => 'myfile.xml' ); # get a sequence object my $seq = $in->next_seq; #write it in GAME format $out->write_seq($seq); =head1 DESCRIPTION Bio::SeqIO::game::gameWriter writes GAME-XML (v. 1.2) that is readable by Apollo. It is best not used directly. It is accessed via Bio::SeqIO. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sheldon McKay Email mckays@cshl.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqIO::game::gameWriter; use strict; use IO::String; use XML::Writer; use Bio::SeqFeature::Generic; use Bio::SeqFeature::Tools::Unflattener; use base qw(Bio::SeqIO::game::gameSubs); =head2 new Title : new Usage : my $writer = Bio::SeqIO::game::gameWriter->new($seq); Function: constructor method for gameWriter Returns : a game writer object Args : a Bio::SeqI implementing object optionally, an argument to set map_position to on. ( map => 1 ). This will create a map_position elemant that will cause the feature coordinates to be remapped to a parent seqeunce. A sequence name in the format seq:xxx-xxx is expected to determine the offset for the map_position. The default behavior is to have features mapped relative to the sequence contained in the GAME-XML file =cut sub new { my ($caller, $seq, %arg) = @_; my $class = ref($caller) || $caller; my $self = bless ( { seq => $seq }, $class ); # make a <map_position> element only if requested $self->{map} = 1 if $arg{map}; $self->{anon_set_counters} = {}; #counters for numbering anonymous result and feature sets return $self; } =head2 write_to_game Title : write_to_game Usage : $writer->write_to_game Function: writes the sequence object to game-XML Returns : xml as a multiline string Args : none =cut sub write_to_game { my $self = shift; my $seq = $self->{seq}; my @feats = $seq->remove_SeqFeatures; # intercept nested features my @nested_feats = grep { $_->get_SeqFeatures } @feats; @feats = grep { !$_->get_SeqFeatures } @feats; map { $seq->add_SeqFeature($_) } @feats; # NB -- Maybe this belongs in Bio::SeqFeatute::Tools::Unflattener # # intercept non-coding RNAs and transposons with contained genes # # GAME-XML has these features as top level annotations which contain # # gene elements # my @gene_containers = (); # for ( @feats ) { # if ( $_->primary_tag =~ /[^m]RNA|repeat_region|transpos/ && # $_->has_tag('gene') ) { # my @genes = $_->get_tag_values('gene'); # my ($min, $max) = (10000000000000,-10000000000000); # for my $g ( @genes ) { # my $gene; # for my $item ( @feats ) { # next unless $item->primary_tag eq 'gene'; # my ($n) = $item->get_tag_values('gene'); # next unless $n =~ /$g/; # $gene = $item; # last; # } # next unless $gene && ref $gene; # $max = $gene->end if $gene->end > $max; # $min = $gene->start if $gene->start < $min; # } # # push @gene_containers, $_ if $_->length >= ($max - $min); # } # else { # $seq->add_SeqFeature($_); # } # } # unflatten my $uf = Bio::SeqFeature::Tools::Unflattener->new; $uf->unflatten_seq( -seq => $seq, use_magic => 1 ); # rearrange snRNA and transposon hierarchies # $self->_rearrange_hierarchies($seq, @gene_containers); # add back nested feats $seq->add_SeqFeature( $_ ) foreach @nested_feats; my $atts = {}; my $xml = ''; # write the XML to a string my $xml_handle = IO::String->new($xml); my $writer = XML::Writer->new(OUTPUT => $xml_handle, DATA_MODE => 1, DATA_INDENT => 2, NEWLINE => 1 ); $self->{writer} = $writer; # $writer->xmlDecl("UTF-8"); # $writer->doctype("game", 'game', "http://www.fruitfly.org/annot/gamexml.dtd.txt"); $writer->comment("GAME-XML generated by Bio::SeqIO::game::gameWriter"); $writer->comment("Created " . localtime); $writer->comment('Questions: mckays@cshl.edu'); $writer->startTag('game', version => 1.2); my @sources = grep { $_->primary_tag =~ /source|origin|region/i } $seq->get_SeqFeatures; for my $source ( @sources ) { next unless $source->length == $seq->length; for ( qw{ name description db_xref organism md5checksum } ) { if ( $source->has_tag($_) ) { $self->{has_organism} = 1 if /organism/; ($atts->{$_}) = $source->get_tag_values($_); } } } #set a name in the attributes if none was given $atts->{name} ||= $seq->accession_number ne 'unknown' ? $seq->accession_number : $seq->display_name; $self->_seq($seq, $atts); # make a map_position element if req'd if ( $self->{map} ) { my $seqtype; if ( $atts->{mol_type} || $seq->alphabet ) { $seqtype = $atts->{mol_type} || $seq->alphabet; } else { $seqtype = 'unknown'; } $writer->startTag( 'map_position', seq => $atts->{name}, type => $seqtype ); my ($arm, $start, undef, $end) = $atts->{name} =~ /(\S+):(-?\d+)(\.\.|-)(-?\d+)/; $self->_element('arm', $arm) if $arm; $self->_span($start, $end); $writer->endTag('map_position'); } for ( $seq->top_SeqFeatures ) { if($_->isa('Bio::SeqFeature::Computation')) { $self->_comp_analysis($_); } else { # if the feature has subfeatures, we will assume it is a gene # (hope this is safe!) if ( $_->get_SeqFeatures ) { $self->_write_gene($_); } else { # non-gene stuff only next if $_->primary_tag =~ /CDS|mRNA|exon|UTR/; $self->_write_feature($_); } } } $writer->endTag('game'); $writer->end; $xml; } =head2 _rearrange_hierarchies Title : _rearrange_hierarchies Usage : $self->_rearrange_hierarchies($seq) Function: internal method to rearrange gene containment hierarchies so that snRNA or transposon features contain their genes rather than the other way around Returns : nothing Args : a Bio::RichSeq object Note : Not currently used, may be removed =cut sub _rearrange_hierarchies { #renamed to not conflict with Bio::Root::_rearrange my ($self, $seq, @containers) = @_; my @feats = $seq->remove_SeqFeatures; my @genes = grep { $_->primary_tag eq 'gene' } @feats; my @addback = grep { $_->primary_tag ne 'gene' } @feats; for ( @containers ) { my @has_genes = $_->get_tag_values('gene'); for my $has_gene ( @has_genes ) { for my $gene ( @genes ) { next unless $gene; my ($gname) = $gene->get_tag_values('gene'); if ( $gname eq $has_gene ) { $_->add_SeqFeature($gene); undef $gene; } } } } push @addback, (@containers, grep { defined $_ } @genes ); $seq->add_SeqFeature($_) foreach @addback; } =head2 _write_feature Title : _write_feature Usage : $seld->_write_feature($feat, 1) Function: internal method for writing generic features as <annotation> elements Returns : nothing Args : a Bio::SeqFeature::Generic object and an optional flag to write a bare feature set with no annotation wrapper =cut sub _write_feature { my ($self, $feat, $bare) = @_; my $writer = $self->{writer}; my $id; for ( 'standard_name', $feat->primary_tag, 'ID' ) { $id = $self->_find_name($feat, $_ ); last if $id; } $id ||= $feat->primary_tag . '_' . ++$self->{$feat->primary_tag}->{id}; unless ( $bare ) { $writer->startTag('annotation', id => $id); $self->_element('name', $id); $self->_element('type', $feat->primary_tag); } $writer->startTag('feature_set', id => $id); $self->_element('name', $id); $self->_element('type', $feat->primary_tag); $self->_render_tags( $feat, \&_render_date_tags, \&_render_comment_tags, \&_render_tags_as_properties ); $self->_feature_span($id, $feat); $writer->endTag('feature_set'); $writer->endTag('annotation') unless $bare; } =head2 _write_gene Title : _write_gene Usage : $self->_write_gene($feature) Function: internal method for rendering gene containment hierarchies into a nested <annotation> element Returns : nothing Args : a nested Bio::SeqFeature::Generic gene feature Note : A nested gene hierarchy (gene->mRNA->CDS->exon) is expected. If other gene subfeatures occur as level one subfeatures (same level as mRNA subfeats) an attempt will be made to link them to transcripts via the 'standard_name' qualifier =cut sub _write_gene { my ($self, $feat) = @_; my $writer = $self->{writer}; my $str = $feat->strand; my $id = $self->_find_name($feat, 'standard_name') || $self->_find_name($feat, 'gene') || $self->_find_name($feat, $feat->primary_tag) || $self->_find_name($feat, 'locus_tag') || $self->_find_name($feat, 'symbol') || $self->throw(<<EOM."Feature name was: '".($feat->display_name || 'not set')."'"); Could not find a gene/feature ID, feature must have a primary tag or a tag with one of the names: 'standard_name', 'gene', 'locus_tag', or 'symbol'. EOM my $gid = $self->_find_name($feat, 'gene') || $id; $writer->startTag('annotation', id => $id); $self->_element('name', $gid); $self->_element('type', $feat->primary_tag); $self->_render_tags( $feat, \&_render_date_tags, \&_render_dbxref_tags, \&_render_comment_tags, \&_render_tags_as_properties, ); my @genes; if ( $feat->primary_tag eq 'gene' ) { @genes = ($feat); } else { # we are in a gene container; gene must then be one level down @genes = grep { $_->primary_tag eq 'gene' } $feat->get_SeqFeatures; } for my $g ( @genes ) { my $id ||= $self->_find_name($g, 'standard_name') || $self->_find_name($g, 'gene') || $self->_find_name($feat, 'locus_tag') || $self->_find_name($feat, 'symbol') || $self->throw("Could not find a gene ID"); my $gid ||= $self->_find_name($g, 'gene') || $self->_find_name($g); $writer->startTag('gene', association => 'IS'); $self->_element('name', $gid); $writer->endTag('gene'); my $proteins; my @mRNAs = grep { $_->primary_tag =~ /mRNA|transcript/ } $g->get_SeqFeatures; my @other_stuff = grep { $_->primary_tag !~ /mRNA|transcript/ } $g->get_SeqFeatures; my @variants = ('A' .. 'Z'); for my $mRNA (@mRNAs) { my ($sn, @units); # if the mRNA is a generic transcript, it must be a non-spliced RNA gene # Make a synthetic exon to help build a hierarchy. We have to assume that # the location is not segmented (otherwise it should be a mRNA) if ( $mRNA->primary_tag eq 'transcript') { my $exon = Bio::SeqFeature::Generic->new ( -primary => 'exon' ); $exon->location($mRNA->location); $mRNA->add_SeqFeature($exon); } # no subfeats? Huh? revert to generic feature unless ( $mRNA->get_SeqFeatures ) { $self->_write_feature($mRNA, 1); # 1 flag writes the bare feature # with no annotation wrapper next; } my $name = $self->_find_name($mRNA, $mRNA->primary_tag) || $self->_find_name($mRNA, 'standard_name'); my %attributes; my ($cds) = grep { $_->primary_tag eq 'CDS' } $mRNA->get_SeqFeatures; # make sure we have the right CDS for alternatively spliced genes # This is meant to deal with sequences from flattened game annotations, # where both the mRNA and CDS have split locations if ( $cds && @mRNAs > 1 && $name ) { $cds = $self->_check_cds($cds, $name); } elsif ( $cds && @mRNAs == 1 ) { # The mRNA/CDS pairing must be right. Get the transcript name from the CDS if ( $cds->has_tag('standard_name') ) { ($name) = $cds->get_tag_values('standard_name'); } } if ( !$name ) { # assign a name to the transcript if it has no 'standard_name' binder $name = $id . '-R' . (shift @variants); } my $pname; if ( $cds ) { ($sn) = $cds->get_tag_values('standard_name') if $cds->has_tag('standard_name'); ($sn) ||= $cds->get_tag_values('mRNA') if $cds->has_tag('mRNA'); # the protein needs a name my $psn = $self->protein_id($cds, $sn); $self->{curr_pname} = $psn; # the mRNA need to know the name of its protein unless ( $feat->has_tag('protein_id') ) { $feat->add_tag_value('protein_id', $psn); } # define the translation offset my ($c_start, $c_end); if ( $cds->has_tag('codon_start') ){ ($c_start) = $cds->get_tag_values('codon_start'); $cds->remove_tag('codon_start'); } else { $c_start = 1; } my $cs = Bio::SeqFeature::Generic->new; if ( $c_start == 1 ) { $c_start = $cds->strand > 0 ? $cds->start : $cds->end; } if ( $cds->strand < 1 ) { $c_end = $c_start; $c_start = $c_start - 2; } else { $c_end = $c_start + 2; } $cs->start($c_start); $cs->end($c_end); $cs->strand($cds->strand); $cs->primary_tag('start_codon'); $cs->add_tag_value( 'standard_name' => $name ); push @units, $cs; if ( $cds->has_tag('problem') ) { my ($val) = $cds->get_tag_values('problem'); $cds->remove_tag('problem'); $attributes{problem} = $val; } my ($aa) = $cds->get_tag_values('translation') if $cds->has_tag('translation'); if ( $aa && $psn ) { $cds->remove_tag('translation'); my %add_seq = (); $add_seq{residues} = $aa; $add_seq{header} = ['seq', id => $psn, length => length $aa, type => 'aa' ]; if ( $cds->has_tag('product_desc') ) { ($add_seq{desc}) = $cds->get_tag_values('product_desc'); $cds->remove_tag('product_desc'); } unless ( $add_seq{desc} && $add_seq{desc} =~ /cds_boundaries/ ) { my $start = $cds->start; my $end = $cds->end; my $str = $cds->strand; my $acc = $self->{seq}->accession || $self->{seq}->display_id; $str = $str < 0 ? '[-]' : ''; $add_seq{desc} = "translation from_gene[$gid] " . "cds_boundaries:(" . $acc . ":$start..$end$str) transcript_info:[$name]"; } $self->{add_seqs} ||= []; push @{$self->{add_seqs}}, \%add_seq; } } $writer->startTag('feature_set', id => $name); $self->_element('name', $name); $self->_element('type', 'transcript'); $self->_render_tags($_, \&_render_date_tags, \&_render_comment_tags, \&_render_tags_as_properties, ) for ( $mRNA, ($cds) || () ); # any UTR's, etc associated with this transcript? for my $thing ( @other_stuff ) { if ( $thing->has_tag('standard_name') ) { my ($v) = $thing->get_tag_values('standard_name'); if ( $v eq $sn ) { push @units, $thing; } } } # add the exons push @units, grep { $_->primary_tag eq 'exon' } $mRNA->get_SeqFeatures; @units = sort { $a->start <=> $b->start } @units; my $count = 0; if ( $str < 0 ) { @units = reverse @units; } for my $unit ( @units ) { if ( $unit->primary_tag eq 'exon' ) { my $ename = $id; $ename .= ':' . ++$count; $self->_feature_span($ename, $unit); } elsif ( $unit->primary_tag eq 'start_codon' ) { $self->_feature_span(($sn || $gid), $unit, $self->{curr_pname}); } else { my $uname = $unit->primary_tag . ":$id"; $self->_feature_span($uname, $unit); } } $self->{curr_pname} = ''; $writer->endTag('feature_set'); } $self->{other_stuff} = \@other_stuff; } $writer->endTag('annotation'); # add the protein sequences for ( @{$self->{add_seqs}} ) { my %h = %$_; $writer->startTag(@{$h{header}}); my @desc = split /\s+/, $h{desc}; my $desc = ''; for my $word (@desc) { my ($lastline) = $desc =~ /.*^(.+)$/sm; $lastline ||= ''; $desc .= length $lastline < 50 ? " $word " : "\n $word "; } $self->_element('description', "\n $desc\n "); my $aa = $h{residues}; $aa =~ s/(\w{60})/$1\n /g; $aa =~ s/\n\s+$//m; $aa = "\n " . $aa . "\n "; $self->_element('residues', $aa); $writer->endTag('seq'); $self->{add_seqs} = []; } # Is there anything else associated with the gene? We have to write other # features as stand-alone annotations or apollo will assume they are # transcripts for my $thing ( @{$self->{other_stuff}} ) { next if $thing->has_tag('standard_name'); $self->_write_feature($thing); } $self->{other_stuff} = []; } =head2 _check_cds Title : _check_cds Usage : $self->_check_cds($cds, $name) Function: internal method to check if the CDS associated with an mRNA is the correct alternative splice variant Returns : a Bio::SeqFeature::Generic CDS object Args : the CDS object plus the transcript\'s 'standard_name' Note : this method only works if alternatively spliced transcripts are bound together by a 'standard_name' or 'mRNA' qualifier. If none is present, we will hope that the exons were derived from a segmented RNA or a CDS with no associated mRNA feature. Neither of these two cases would be confounded by alternative splice variants. =cut sub _check_cds { my ($self, $cds, $name) = @_; my $cname = $self->_find_name( $cds, 'standard_name' ) || $self->_find_name( $cds, 'mRNA'); if ( $cname ) { if ( $cname eq $name ) { return $cds; } else { my @CDS = grep { $_->primary_tag eq 'CDS' } @{$self->{feats}}; for ( @CDS ) { my ($sname) = $_->_find_name( $_, 'standard_name' ) || $_->_find_name( $_, $_->primary_tag ); return $_ if $sname eq $name; } return ''; } } else { return $cds; } } =head2 _comp_analysis Usage: Desc : Ret : Args : Side Effects: Example: =cut sub _comp_analysis { my ($self, $feat) = @_; my $writer = $self->{writer}; $writer->startTag('computational_analysis'); $self->_element('program', $feat->program_name || 'unknown program'); $self->_element('database', $feat->database_name) if $feat->database_name; $self->_element('version', $feat->program_version) if $feat->program_version; $self->_element('type', $feat->primary_tag) if $feat->primary_tag; $self->_render_tags($feat, \&_render_date_tags, \&_render_tags_as_properties, ); $self->_comp_result($feat); $writer->endTag('computational_analysis'); } =head2 _comp_result Usage: Desc : recursively render a feature and its subfeatures as <result_set> and <result_span> elements Ret : nothing meaningful Args : a feature =cut sub _comp_result { my ($self,$feat) = @_; #check that all our subfeatures have the same strand #write result sets for things that have subfeatures, or things #that have some tags if( my @subfeats = $feat->get_SeqFeatures or $feat->get_all_tags ) { my $writer = $self->{writer}; $writer->startTag('result_set', ($feat->can('computation_id') && defined($feat->computation_id)) ? (id => $feat->computation_id) : () ); my $fakename = $feat->primary_tag || 'no_name'; $self->_element('name', $feat->display_name || ($fakename).'_'.++$self->{anon_result_set_counters}{$fakename} ); $self->_seq_relationship('query', $feat); $self->_render_tags($feat, \&_render_output_tags ); for (@subfeats) { #render the subfeats, if any $self->_comp_result($_); } $self->_comp_result_span($feat); #also have a span to hold this info $writer->endTag('result_set'); } else { #just write result spans for simple things $self->_comp_result_span($feat); } } =head2 _comp_result_span Usage: _comp_result_span('foo12',$feature); Desc : write GAME XML for a Bio::SeqFeature::Computation feature that has no subfeatures Ret : nothing meaningful Args : name for this span (some kind of identifier), SeqFeature object to put into this span Side Effects: Example: =cut sub _comp_result_span { my ($self, $feat) = @_; my $writer = $self->{writer}; $writer->startTag('result_span', ($feat->can('computation_id') && defined($feat->computation_id) ? (id => $feat->computation_id) : ()) ); $self->_element('name', $feat->display_name) if $feat->display_name; $self->_element('type', $feat->primary_tag) if $feat->primary_tag; my $has_score = $feat->can('has_score') ? $feat->has_score : defined($feat->score); $self->_element('score', $feat->score) if $has_score; $self->_render_tags($feat, \&_render_output_tags ); $self->_seq_relationship('query', $feat); $self->_render_tags($feat, \&_render_target_tags, ); $writer->endTag('result_span'); } =head2 _render_tags Usage: Desc : Ret : Args : Side Effects: Example: =cut sub _render_tags { my ($self,$feat,@render_funcs) = @_; my @tagnames = $feat->get_all_tags; #do a chain-of-responsibility down the allowed #tag handlers types for the context in which this is #called foreach my $func (@render_funcs) { @tagnames = $self->$func($feat,@tagnames); } } =head2 _render_output_tags Usage: Desc : print out <output> elements, with contents taken from the SeqFeature::Computation's 'output' tag Ret : array of tag names this did not render Args : feature object, list of tag names to maybe render In game xml, only <result_span> and <result_set> elements can have <output> elements. =cut sub _render_output_tags { my ($self, $feat, @tagnames) = @_; my $writer = $self->{writer}; my @passed_up; for my $tag (@tagnames) { if(lc($tag) eq 'output') { my @outputs = $feat->get_tag_values($tag); while(my($type,$val) = splice @outputs,0,2) { $writer->startTag('output'); $self->_element('type',$type); $self->_element('value',$val); $writer->endTag('output'); } } else { push @passed_up,$tag; } } return @passed_up; } =head2 _render_tags_as_properties Usage: Desc : Ret : empty array Args : feature object, array of tag names Side Effects: Example: In game xml, <annotation>, <computational_analysis>, and <feature_set> elements can have properties. =cut sub _render_tags_as_properties { my ($self,$feat,@tagnames) = @_; foreach my $tag (@tagnames) { if( $tag ne $feat->primary_tag ) { $self->_property($tag,$_) for $feat->get_tag_values($tag); } } return (); } =head2 _render_comment_tags Usage: Desc : Ret : names of tags that were not comment tags Args : feature object, tag names available for us to render Side Effects: writes XML Example: In game xml, <annotation> and <feature_set> elements can have comments. =cut sub _render_comment_tags { my ($self,$feat,@tagnames) = @_; my $writer = $self->{writer}; my @passed_up; for my $tag ( @tagnames ) { if( lc($tag) eq 'comment' ) { for my $val ($feat->get_tag_values($tag)) { if ( $val =~ /=.+?;.+=/ ) { $self->_unflatten_attribute('comment', $val); } else { $writer->startTag('comment'); $self->_element('text', $val); $writer->endTag('comment'); } } } else { push @passed_up,$tag; } } return @passed_up; } =head2 _render_date_tags Usage: Desc : Ret : names of tags that were not date tags Args : feature, list of tag names available for us to render Side Effects: writes XML for <date> elements Example: In game xml, <annotation>, <computational_analysis>, <transaction>, <comment>, and <feature_set> elements can have <date>s. =cut sub _render_date_tags { my ($self,$feat,@tagnames) = @_; my @passed_up; my $date; my %timestamp; foreach my $tag (@tagnames) { if ( lc($tag) eq 'date' ) { ($date) = $feat->get_tag_values($tag); } elsif ( lc($tag) eq 'timestamp' ) { ($timestamp{'timestamp'}) = $feat->get_tag_values($tag); #ignore timestamps, they are folded in with date elem above } else { push @passed_up,$tag; } } $self->_element('date', $date, \%timestamp) if defined($date); return @passed_up; } =head2 _render_dbxref_tags Desc : look for xref tags and render them if they are there Ret : tag names that we didn't render Args : feature object, list of tag names to render Side Effects: writes a <dbxref> element if a tag with name matching /xref$/i is present In game xml, <annotation> and <seq> elements can have dbxrefs. =cut #TODO: can't sequences also have database xrefs? how to find those? sub _render_dbxref_tags { my ($self, $feat, @tagnames) = @_; my @passed_up; for my $tag ( @tagnames ) { #look through all the tags if( $tag =~ /xref$/i ) { #if they are xref tags my $writer = $self->{writer}; for my $val ( $feat->get_all_tag_values($tag) ) { #get all their values if( my ($db,$dbid) = $val =~ /(\S+):(\S+)/ ) { #and render them as xrefs $writer->startTag('dbxref'); $self->_element('xref_db', $db); $dbid = $val if $db =~ /^[A-Z]O$/; # -> ontology, like GO $self->_element('db_xref_id', $dbid); $writer->endTag('dbxref'); } } } else { push @passed_up,$tag; } } return @passed_up; } =head2 _render_target_tags Usage: Desc : process any 'Target' tags that would indicate a sequence alignment subject Ret : array of tag names that we didn't render Args : feature object Side Effects: writes a <seq_relationship> of type 'subject' if it finds any properly formed tags named 'Target' Example: In game xml, <result_span>, <feature_span>, and <result_set> can have <seq_relationship>s. <result_set> can only have one, a 'query' relation. =cut sub _render_target_tags { my ($self,$feat,@tagnames) = @_; my @passed_up; foreach my $tag (@tagnames) { if($tag eq 'Target' && (my @alignment = $feat->get_tag_values('Target')) >= 3) { $self->_seq_relationship('subject', Bio::Location::Simple->new( -start => $alignment[1], -end => $alignment[2], ), $alignment[0], $alignment[3], ); } else { push @passed_up, $tag; } } return @passed_up; } =head2 _property Title : _property Usage : $self->_property($tag => $value); Function: an internal method to write property XML elements Returns : nothing Args : a tag/value pair =cut sub _property { my ($self, $tag, $val) = @_; my $writer = $self->{writer}; if ( length $val > 45 ) { my @val = split /\s+/, $val; $val = ''; for my $word (@val) { my ($lastline) = $val =~ /.*^(.+)$/sm; $lastline ||= ''; $val .= length $lastline < 45 ? " $word " : "\n $word"; } $val = "\n $val\n "; $val =~ s/(\S)\s{2}(\S)/$1 $2/g; } $writer->startTag('property'); $self->_element('type', $tag); $self->_element('value', $val); $writer->endTag('property'); } =head2 _unflatten_attribute Title : _unflatten_attribute Usage : $self->_unflatten_attribute($name, $value) Function: an internal method to unflatten and write comment or evidence elements Returns : nothing Args : a list of strings =cut sub _unflatten_attribute { my ($self, $name, $val) = @_; my $writer = $self->{writer}; my %pair; my @pairs = split ';', $val; for my $p ( @pairs ) { my @pair = split '=', $p; $pair[0] =~ s/^\s+|\s+$//g; $pair[1] =~ s/^\s+|\s+$//g; $pair{$pair[0]} = $pair[1]; } $writer->startTag($name); for ( keys %pair ) { $self->_element($_, $pair{$_}); } $writer->endTag($name); } =head2 _xref Title : _xref Usage : $self->_xref($value) Function: an internal method to write db_xref elements Returns : nothing Args : a list of strings =cut sub _xref { my ($self, @xrefs) = @_; my $writer = $self->{writer}; for my $xref ( @xrefs ) { my ($db, $acc) = $xref =~ /(\S+):(\S+)/; $writer->startTag('dbxref'); $self->_element('xref_db', $db); $acc = $xref if $db eq 'GO'; $self->_element('db_xref_id', $acc); $writer->endTag('dbxref'); } } =head2 _feature_span Title : _feature_span Usage : $self->_feature_span($name, $type, $loc) Function: an internal method to write a feature_span element (the actual feature with coordinates) Returns : nothing Args : a feature name and Bio::SeqFeatureI-compliant object =cut sub _feature_span { my ($self, $name, $feat, $pname) = @_; my $type = $feat->primary_tag; my $writer = $self->{writer}; my %atts = ( id => $name ); if ( $pname ) { $pname =~ s/-R/-P/; $atts{produces_seq} = $pname; } $writer->startTag('feature_span', %atts ); $self->_element('name', $name); $self->_element('type', $type); $self->_seq_relationship('query', $feat); $writer->endTag('feature_span'); } =head2 _seq_relationship Title : _seq_relationship Usage : $self->_seq_relationship($type, $loc) Function: an internal method to handle feature_span sequence relationships Returns : nothing Args : feature type, a Bio::LocationI-compliant object, (optional) sequence name (defaults to the query seq) and (optional) alignment string =cut sub _seq_relationship { my ($self, $type, $loc, $seqname, $alignment) = @_; my $writer = $self->{'writer'}; $seqname ||= #if no seqname passed in, use the name of our annotating seq $self->{seq}->accession_number ne 'unknown' && $self->{seq}->accession_number || $self->{seq}->display_id || 'unknown'; $writer->startTag( 'seq_relationship', type => $type, seq => $seqname, ); $self->_span($loc); $writer->_element('alignment',$alignment) if $alignment; $writer->endTag('seq_relationship'); } =head2 _element Title : _element Usage : $self->_element($name, $chars, $atts) Function: an internal method to generate 'generic' XML elements Example : my $name = 'foo'; my $content = 'bar'; my $attributes = { baz => 1 }; # print the element $self->_element($name, $content, $attributes); Returns : nothing Args : the element name and content plus a ref to an attribute hash =cut sub _element { my ($self, $name, $chars, $atts) = @_; my $writer = $self->{writer}; my %atts = $atts ? %$atts : (); $writer->startTag($name, %atts); $writer->characters($chars); $writer->endTag($name); } =head2 _span Title : _span Usage : $self->_span($loc) Function: an internal method to write the 'span' element Returns : nothing Args : a Bio::LocationI-compliant object =cut sub _span { my ($self, @loc) = @_; my ($loc, $start, $end); if ( @loc == 1 ) { $loc = $loc[0]; } elsif ( @loc == 2 ) { ($start, $end) = @loc; } if ( $loc ) { ($start, $end) = ($loc->start, $loc->end); ($start, $end) = ($end, $start) if $loc->strand < 0; } elsif ( !$start ) { ($start, $end) = (1, $self->{seq}->length); } my $writer = $self->{writer}; $writer->startTag('span'); $self->_element('start', $start); $self->_element('end', $end); $writer->endTag('span'); } =head2 _seq Title : _seq Usage : $self->_seq($seq, $dna) Function: an internal method to print the 'sequence' element Returns : nothing Args : and Bio::SeqI-compliant object and a reference to an attribute hash =cut sub _seq { my ($self, $seq, $atts) = @_; my $writer = $self->{'writer'}; # game moltypes my $alphabet = $seq->alphabet; $alphabet ||= $seq->mol_type if $seq->can('mol_type'); $alphabet =~ s/protein/aa/; $alphabet =~ s/rna/cdna/; my @seq = ( 'seq', id => $atts->{name}, length => $seq->length, type => $alphabet, focus => "true" ); if ( $atts->{md5checksum} ) { push @seq, (md5checksum => $atts->{md5checksum}); delete $atts->{md5checksum}; } $writer->startTag(@seq); for my $k ( keys %{$atts} ) { if ( $k =~ /xref/ ) { $self->_xref($atts->{$k}); } else { $self->_element($k, $atts->{$k}); } } # add leading spaces and line breaks for # nicer xml formatting/indentation my $sp = (' ' x 6); my $dna = $seq->seq; $dna =~ s/(\w{60})/$1\n$sp/g; $dna = "\n$sp" . $dna . "\n "; if ( $seq->species && !$self->{has_organism}) { my $species = $seq->species->binomial; $self->_element('organism', $species); } $self->_element('residues', $dna); $writer->endTag('seq'); } =head2 _find_name Title : _find_name Usage : my $name = $self->_find_name($feature) Function: an internal method to look for a gene name Returns : a string Args : a Bio::SeqFeatureI-compliant object =cut sub _find_name { my ($self, $feat, $key) = @_; my $name; if ( $key && $feat->has_tag($key) ) { ($name) = $feat->get_tag_values($key); return $name; } else { # warn "Could not find name '$key'\n"; return ''; } } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/game/seqHandler.pm�������������������������������������������������������000444��000766��000024�� 33760�13155576320� 20572� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::SeqIO::game::seqHandler # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Sheldon McKay <mckays@cshl.edu> # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::game::seqHandler -- a class for handling game-XML sequences =head1 SYNOPSIS This modules is not used directly =head1 DESCRIPTION Bio::SeqIO::game::seqHandler processes all of the sequences associated with a game record and, via feature handlers, processes the associated annotations =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sheldon McKay Email mckays@cshl.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqIO::game::seqHandler; use Data::Dumper; use Bio::SeqIO::game::featHandler; use Bio::SeqFeature::Generic; use Bio::Seq::RichSeq; use Bio::Species; use strict; use vars qw {}; use base qw(Bio::SeqIO::game::gameSubs); =head2 new Title : new Usage : my $seqHandler = Bio::SeqIO::game::seqHandler->new($seq, $ann, $comp, $map, $src ) Function: constructor method to create a sequence handler Returns : a sequence handler object Args : $seq -- an XML sequence element $ann -- a ref. to a list of <annotation> elements $comp -- a ref. to a list of <computational_analysis> elements (not used yet) $map -- a <map_position> element $src -- a flag to indicate that the sequence already has a source feature =cut sub new { my ($caller, $seq, $ann, $comp, $map, $src ) = @_; my $class = ref($caller) || $caller; my $self = bless ( { seqs => $seq, anns => $ann, comps => $comp, map_pos => $map, has_source => $src, seq_h => {}, ann_l => [] }, $class ); return $self; } =head2 convert Title : convert Usage : @seqs = $seqHandler->convert Function: converts the main XML sequence element and associated annotations to Bio:: Returns : a ref. to a an array containing the sequence object and a ref. to a list of features Args : none Note : The features and sequence are kept apart to facilitate downstream filtering of features =cut sub convert { my $self = shift; my @ann = @{$self->{anns}} if defined $self->{anns};; my @seq = @{$self->{seqs}}; # not used yet my @comp; if ( $self->{comps} ) { @comp = @{$self->{comps}} } # process the sequence elements for ( @seq ) { $self->_add_seq( $_ ); } # process the annotation elements for ( @ann ) { $self->_annotation( $_ ); } return $self->_order_feats( $self->{seq_h} ); } =head2 _order_feats Title : _order_feats Usage : $self->_order_feats( $self->{seq_h} ) Function: an internal method to ensure the source feature comes first and keep gene, mRNA and CDS features together Returns : a ref. to an array containing the sequence object and a ref. to a list of features Args : a ref. to a hash of sequences =cut sub _order_feats { my ($self, $seqs) = @_; my $seq = $self->{main_seq}; my $id = $seq->id; my $ann = $self->{ann_l}; # make sure source(s) come first my @src = grep { $_->primary_tag =~ /source|origin|\bregion\b/ } @$ann; # preserve gene->mRNA->CDS or ncRNA->gene->transcript order my @genes = grep { $_->primary_tag =~ /gene|CDS|[a-z]+RNA|transcript/ } @$ann; my @other = sort { $a->start <=> $b->start || $b->end <=> $a->end } grep { $_->primary_tag !~ /source|origin|\bregion\b/ } grep { $_->primary_tag !~ /gene|mRNA|CDS/ } @$ann; return [$seq, [@src, @genes, @other]]; } =head2 _add_seq Title : _add_seq Usage : $self->_add_seq($seq_element) Function: an internal method to process the sequence elements Returns : nothing Args : a sequence element =cut sub _add_seq { my ($self, $el) = @_; my $residues = ''; if ($el->{_residues}) { $residues = $el->{_residues}->{Characters}; $residues =~ s/[ \n\r]//g; $residues =~ s/\!//g; $residues =~ tr/a-z/A-Z/; } else { return 0; } my $id = $el->{Attributes}->{id}; my $ver = $el->{Attributes}->{version}; my $name = $el->{_name}->{Characters}; if ($name && $name ne $id) { $self->complain("The sequence name and unique ID do not match. Using ID"); } # get/set the sequence object my $seq = $self->_seq($id); # get/set the feature handler my $featHandler = $self->_feat_handler; # populate the sequence object $seq->seq($residues); $seq->seq_version($ver) if $ver; # assume the id is the accession number if ( $id =~ /^\w+$/ ) { $seq->accession($id); } # If the focus attribute is set to "true", this is the main # sequence my $focus = 0; if ( defined $el->{Attributes}->{focus} ) { $self->{main_seq} = $seq; $focus++; } # make sure real and annotated lengths match my $length = $el->{Attributes}->{'length'}; $length && $seq->length(int($length)); if ( $seq->seq && defined($length) && $seq->length != int($length) ) { $self->complain("The specified sequence has length ", $seq->length(), " but the length attribute= ", $length); $seq->seq( undef ); $seq->length( int($length) ); } # deal with top-level annotations my $tags = {}; if ( $el->{Attributes}->{md5checksum} ) { $tags->{md5checksum} = [$el->{Attributes}->{md5checksum}]; } if ($el->{_dbxref}) { $tags->{dbxref} ||= []; push @{$tags->{dbxref}}, $self->dbxref( $el->{_dbxref} ); } if ($el->{_description}) { my $desc = $el->{_description}->{Characters}; $seq->description( $desc ); } if ($el->{_organism}) { my @organism = split /\s+/, $el->{_organism}->{Characters}; if (@organism < 2) { $self->complain("Species name should have at least two words"); } else { my $species = Bio::Species->new( -classification => [reverse @organism] ); $seq->species($species); } } if ( defined($seq->species) ) { $tags->{organism} = [$seq->species->binomial]; } # elsif ($seq eq $self->{main_seq}) { # $self->warn("The source organism for this sequence was\n" . # "not specified. I will guess Drosophila melanogaster.\n" . # "Otherwise, add <organism>Genus species</organism>\n" . # "to the main sequence element"); # my @class = qw/ Eukaryota Metazoa Arthropoda Insecta Pterygota # Neoptera Endopterygota Diptera Brachycera # Muscomorpha Ephydroidea Drosophilidae Drosophila melanogaster/; # my $species = Bio::Species->new( -classification => [ reverse @class ], # -common_name => 'fruit fly' ); # $seq->species( $species ); # } # convert GAME to bioperl molecule types my $alphabet = $el->{Attributes}->{type}; if ( $alphabet ) { $alphabet =~ s/aa/protein/; $alphabet =~ s/cdna/rna/; $seq->alphabet($alphabet); } # add a source feature if req'd if ( !$self->{has_source} && $focus ) { #$self->{source} = $featHandler->add_source($seq->length, $tags); } if ( $focus ) { # add the map position $self->_map_position( $self->{map_pos}, $seq ); $featHandler->{offset} = $self->{offset}; } # prune the sequence from the parse tree $self->flush; } =head2 _map_position Title : _map_position Usage : $self->_map_position($map_posn_element) Function: an internal method to process the <map_position> element Returns : nothing Args : a map_position element =cut sub _map_position { my ($self, $el) = @_; # we can live without it if ( !$el ) { $self->{offset}= 0; return 0; } # chromosome and coordinates my $arm = $el->{_arm}->{Characters}; my $type = $el->{Attributes}->{type}; my $loc = $el->{_span}; my $start = $loc->{_start}->{Characters}; my $end = $loc->{_end}->{Characters}; # define the offset (may be a partial sequence) # The coordinates will be relative but the CDS description # coordinates may be absolute if the game-XML comes from apollo # or gadfly $self->{offset} = $start - 1; my $seq_id = $el->{Attributes}->{seq}; my $seq = $self->{seq_h}->{$seq_id}; unless ( $seq ) { $self->throw("Map position with no corresponding sequence object"); } unless ($seq eq $self->{main_seq}){ $self->throw("Map position does not correspond to the main sequence"); } my $species = ''; # create/update the top-level sequence feature if req'd if ( $self->{source} ) { my $feat = $self->{source}; unless ($feat->has_tag('organism')) { $species = eval {$seq->species->binomial} || 'unknown species'; $feat->add_tag_value( organism => $species ); } my %tags = ( mol_type => "genomic dna", chromosome => $arm, location => "$start..$end", type => $type ); for (keys %tags) { $feat->add_tag_value( $_ => $tags{$_} ); } $seq->add_SeqFeature($feat); } # come up with a description if there is none my $desc = $seq->description; if ( $species && $arm && $start && $end && !$desc) { $seq->description("$species chromosome $arm $start..$end " . "segment of complete sequence"); } $self->flush; } =head2 _annotation Title : _annotation Usage : $self->_annotation($annotation_element) Function: an internal method to process <annotation> elements Returns : nothing Args : an annotation element =cut sub _annotation { my ($self, $el) = @_; my $id = $el->{Attributes}->{id}; my $type = $el->{_type}->{Characters}; my $tags = {}; my $gname = $el->{_name}->{Characters} eq $id ? '' : $el->{_name}->{Characters}; # 'transposable element' is too long (breaks Bio::SeqIO::GenBank) # $type =~ s/transposable_element/repeat_region/; # annotations must be on the main sequence my $seqid = $self->{main_seq}->id; my $featHandler = $self->_feat_handler; my @feats = (); for my $child ( @{$el->{Children}} ) { my $name = $child->{Name}; # these elements require special handling if ( $name eq 'dbxref' ) { $tags->{dbxref} ||= []; push @{$tags->{dbxref}}, $self->dbxref( $child ); } elsif ( $name eq 'aspect' ) { $tags->{dbxref} ||= []; push @{$tags->{dbxref}}, $self->dbxref( $child->{_dbxref} ); } elsif ( $name eq 'feature_set' ) { push @feats, $featHandler->feature_set( $id, $gname, $child, $type ); } elsif ( $name eq 'comment' ) { $tags->{comment} = [$self->comment( $child )]; } elsif ( $name eq 'property' ) { $self->property( $child, $tags ); } elsif ( $name eq 'gene' ) { # we may be dealing with an annotation that is not # a gene, so we have to nest the gene inside it $featHandler->has_gene( $child, $gname, $id ) } # otherwise, tag/value pairs # -- mild dtd enforcement # synonym is not in the dtd but shows up in gadfly # annotations elsif ( $name =~ /type|synonym/ ) { $tags->{$name} = [$child->{Characters}]; } elsif ( $name ne 'name' ) { $self->complain("Unrecognized element '$name'. I don't " . "know what to do with $name elements in " . "top-level sequence annotations." ); } } # add a gene annotation if required unless ( $featHandler->has_gene || $type ne 'gene' ) { $featHandler->has_gene( $el, $gname, $id ) } if ( $tags->{symbol} ) { if ( !$tags->{gene} ) { $tags->{gene} = $tags->{symbol}; } delete $tags->{symbol}; } $featHandler->add_annotation( $self->{main_seq}, $type, $id, $tags, \@feats ); $self->flush; } # get/set the sequence object =head2 _seq Title : _seq Usage : my $seq = $self->_seq Function: an internal sequence getter/setter Returns : a Bio::RichSeq object Args : a sequence ID =cut sub _seq { my ($self, $id) = @_; $id || $self->throw("A unique id must be provided for the sequence"); my $seq = {}; if ( defined $self->{seq_h}->{$id}) { $seq = $self->{seq_h}->{$id}; } else { $seq = Bio::Seq::RichSeq->new( -id => $id ); $self->{seq_h}->{$id} = $seq; # store it } return $seq; } #get/set the feature handler =head2 _feat_handler Title : _feat_handler Usage : my $featHandler = $self->_featHandler Function: an internal getter/setter for feature handling objects Returns : a Bio::SeqIO::game::featHandler object Args : none =cut sub _feat_handler { my $self = shift; my $handler = {}; my $seq = $self->{main_seq}; if ( defined $self->{feat_handler} ) { $handler = $self->{feat_handler}; } else { my @args = ( $seq, $self->{seq_h}, $self->{ann_l} ); $handler = Bio::SeqIO::game::featHandler->new( @args ); $self->{feat_handler} = $handler; } return $handler; } 1; ����������������BioPerl-1.007002/Bio/SeqIO/tinyseq������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16543� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/SeqIO/tinyseq/tinyseqHandler.pm������������������������������������������������000444��000766��000024�� 14215�13155576320� 22253� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::SeqIO::tinyseqHandler # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Donald Jackson, donald.jackson@bms.com # # Copyright Bristol-Myers Squibb # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::tinyseq::tinyseqHandler - XML event handlers to support NCBI TinySeq XML parsing =head1 SYNOPSIS Do not use this module directly; use the SeqIO handler system: $stream = Bio::SeqIO->new( -file => $filename, -format => 'tinyseq' ); while ( my $seq = $stream->next_seq ) { .... } =head1 DESCRIPTION This object provides event handler methods for parsing sequence files in the NCBI TinySeq XML format. A TinySeq is a lightweight XML file of sequence information on one or more sequences, analgous to FASTA format. See L<https://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.mod.dtd> for the DTD. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 SEE ALSO L<Bio::SeqIO>, L<Bio::Seq>. =head1 AUTHOR Donald Jackson, E<lt>donald.jackson@bms.comE<gt> =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SeqIO::tinyseq::tinyseqHandler; use strict; use warnings; use vars qw(%ATTMAP); use base qw(Bio::Root::Root); # %ATTMAP defines correspondence between TSeq elements, PrimarySeq attributes # Format: element_name => { xml_attname => pseq_attname } %ATTMAP = ( TSeq_sequence => { Data => '-seq'}, TSeq_gi => { Data => '-primary_id' }, TSeq_defline => { Data => '-desc' }, TSeq_sid => { Data => '-sid' }, TSeq_accver => { Data => '-accver' }, TSeq_taxid => { Data => '-taxid' }, TSeq_orgname => { Data => '-organism' } ); =head2 new Title : new Usage : $handler = Bio::SeqIO::tinyseq::tinyseqHandler->new() Function : instantiates a tinyseqHandler for use by XML::Parser::PerlSAX Returns : Bio::SeqIO::tinyseq::tinyseqHandler object Args : NONE =cut sub new { my ($proto, @args) = @_; my $class = ref($proto) || $proto; my $self = bless({}, $class); return $self; } ####################################### # Event handling methods for PerlSax # ####################################### sub doctype_decl { my ($self, $doctype) = @_; # make sure we have a tinyseq unless ($doctype->{'SystemId'} eq 'https://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd') { $self->throw("This document doesn't use the NCBI TinySeq dtd; it's a ", $doctype->{'SystemId'} ); } } =head2 start_document Title : start_document Usage : NONE Function : start_document handler for use by XML::Parser::PerlSAX Returns : NONE Args : NONE =cut sub start_document { my ($self) = @_; $self->{'_seqatts'} = []; $self->{'_elements'} = []; } =head2 end_document Title : end_document Usage : NONE Function : end_document handler for use by XML::Parser::PerlSAX Returns : NONE Args : NONE =cut sub end_document { my ($self) = @_; return $self->{'_seqatts'}; } =head2 start_element Title : start_element Usage : NONE Function : start_element handler for use by XML::Parser::PerlSAX Returns : NONE Args : NONE =cut sub start_element { my ($self, $starting) = @_; push(@{$self->{'_elements'}}, $starting); } =head2 end_element Title : end_element Usage : NONE Function : end_element handler for use by XML::Parser::PerlSAX Returns : NONE Args : NONE =cut sub end_element { my ($self, $ending) = @_; # do I have a handler for this element? my $ename = $ending->{'Name'}; $self->$ename if ($self->can($ename)); } =head2 characters Title : characters Usage : NONE Function : characters handler for use by XML::Parser::PerlSAX Returns : NONE Args : NONE =cut sub characters { my ($self, $characters) = @_; my $data = $characters->{'Data'}; return unless (defined($data) and $data =~ /\S/); my $current = $self->_current_element; $current->{'Data'} = $data; } ########################################### # Element-specific handlers # called at END of element name ########################################## =head2 TSeq Title : TSeq Usage : NONE Function : event handler for END of a TSeq element Returns : loh of parsed sequence atts for Bio::SeqIO::tinyseq Args : NONE =cut sub TSeq { my ($self) = @_; my %seqatts; # map elements onto PrimarySeq keys while (my $element = pop @{ $self->{'_elements'} }) { my $element_name = $element->{'Name'}; last if ($element_name eq 'TSeq'); my $conversion = $ATTMAP{$element_name} or next; while(my($element_att, $pseq_att) = each %$conversion) { $seqatts{$pseq_att} = $element->{$element_att}; } } push(@{ $self->{'_seqatts'} }, \%seqatts); } ############################################# # Utility method to return current element info ############################################## =head2 _current_element Title : _current_element Usage : Internal method Function : Utility method to return current element info Returns : XML::Parser::PerlSAX hash for current element Args : NONE =cut sub _current_element { my ($self) = @_; return $self->{'_elements'}->[-1]; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Structure����������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16067� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Structure/Atom.pm��������������������������������������������������������������000444��000766��000024�� 25707�13155576320� 17515� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # bioperl module for Bio::Structure::Atom # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Kris Boulez <kris.boulez@algonomics.com> # # Copyright Kris Boulez # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Structure::Atom - Bioperl structure Object, describes an Atom =head1 SYNOPSIS #add synopsis here =head1 DESCRIPTION This object stores a Bio::Structure::Atom =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Kris Boulez Email kris.boulez@algonomics.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Structure::Atom; use strict; use Bio::Structure::Residue; use base qw(Bio::Root::Root); =head2 new() Title : new() Usage : $struc = Bio::Structure::Atom->new( -id => 'human_id', ); Function: Returns a new Bio::Structure::Atom object from basic constructors. Probably most called from Bio::Structure::IO. Returns : a new Bio::Structure::Atom object =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my($id, $x, $y, $z) = $self->_rearrange([qw( ID X Y Z )], @args); $id && $self->id($id); $x && $self->x($x); $y && $self->y($y); $z && $self->z($z); return $self; } =head2 x() Title : x Usage : $x = $atom->x($x); Function: Set/gets the X coordinate for an Atom Returns : The value for the X coordinate of the Atom (This is just a number, it is expected to be in Angstrom, but no garantees) Args : The X coordinate as a number =cut sub x { my ($self,$value) = @_; if( defined $value) { # do we want to check if $value contains really a number ? $self->{'x'} = $value; } return $self->{'x'}; } =head2 y() Title : y Usage : $y = $atom->y($y); Function: Set/gets the Y coordinate for an Atom Returns : The value for the Y coordinate of the Atom (This is just a number, it is eypected to be in Angstrom, but no garantees) Args : The Y coordinate as a number =cut sub y { my ($self,$value) = @_; if( defined $value) { # do we want to check if $value contains really a number ? $self->{'y'} = $value; } return $self->{'y'}; } =head2 z() Title : z Usage : $z = $atom->z($z); Function: Set/gets the Z coordinate for an Atom Returns : The value for the Z coordinate of the Atom (This is just a number, it is ezpected to be in Angstrom, but no garantees) Args : The Z coordinate as a number =cut sub z { my ($self,$value) = @_; if( defined $value) { # do we want to check if $value contains really a number ? $self->{'z'} = $value; } return $self->{'z'}; } =head2 xyz() Title : xyz Usage : ($x,$y,$z) = $atom->xyz; Function: Gets the XYZ coordinates for an Atom Returns : A list with the value for the XYZ coordinate of the Atom Args : =cut sub xyz { my ($self) = @_; return ($self->x, $self->y, $self->z); } =head2 residue() Title : residue Usage : Function: No code here, all parent/child stuff via Entry Returns : Args : =cut sub residue { my($self, $value) = @_; $self->throw("all parent/child stuff via Entry\n"); } =head2 icode() Title : icode Usage : $icode = $atom->icode($icode) Function: Sets/gets the icode Returns : Returns the icode for this atom Args : reference to an Atom =cut sub icode { my($self, $value) = @_; if (defined $value) { $self->{'icode'} = $value; } return $self->{'icode'}; } =head2 serial() Title : serial Usage : $serial = $atom->serial($serial) Function: Sets/gets the serial number Returns : Returns the serial number for this atom Args : reference to an Atom =cut sub serial { my($self, $value) = @_; if (defined $value) { $self->{'serial'} = $value; } return $self->{'serial'}; } =head2 occupancy() Title : occupancy Usage : $occupancy = $atom->occupancy($occupancy) Function: Sets/gets the occupancy Returns : Returns the occupancy for this atom Args : reference to an Atom =cut sub occupancy { my($self, $value) = @_; if (defined $value) { $self->{'occupancy'} = $value; } return $self->{'occupancy'}; } =head2 tempfactor() Title : tempfactor Usage : $tempfactor = $atom->tempfactor($tempfactor) Function: Sets/gets the tempfactor Returns : Returns the tempfactor for this atom Args : reference to an Atom =cut sub tempfactor { my($self, $value) = @_; if (defined $value) { $self->{'tempfactor'} = $value; } return $self->{'tempfactor'}; } =head2 segID() Title : segID Usage : $segID = $atom->segID($segID) Function: Sets/gets the segID Returns : Returns the segID for this atom Args : reference to an Atom =cut sub segID { my($self, $value) = @_; if (defined $value) { $self->{'segID'} = $value; } return $self->{'segID'}; } =head2 pdb_atomname() Title : pdb_atomname Usage : $pdb_atomname = $atom->pdb_atomname($pdb_atomname) Function: Sets/gets the pdb_atomname (atomname used in the PDB file) Returns : Returns the pdb_atomname for this atom Args : reference to an Atom =cut sub pdb_atomname { my($self, $value) = @_; if (defined $value) { $self->{'pdb_atomname'} = $value; } return $self->{'pdb_atomname'}; } =head2 element() Title : element Usage : $element = $atom->element($element) Function: Sets/gets the element Returns : Returns the element for this atom Args : reference to an Atom =cut sub element { my($self, $value) = @_; if (defined $value) { $self->{'element'} = $value; } return $self->{'element'}; } =head2 charge() Title : charge Usage : $charge = $atom->charge($charge) Function: Sets/gets the charge Returns : Returns the charge for this atom Args : reference to an Atom =cut sub charge { my($self, $value) = @_; if (defined $value) { $self->{'charge'} = $value; } return $self->{'charge'}; } =head2 sigx() Title : sigx Usage : $sigx = $atom->sigx($sigx) Function: Sets/gets the sigx Returns : Returns the sigx for this atom Args : reference to an Atom =cut sub sigx { my($self, $value) = @_; if (defined $value) { $self->{'sigx'} = $value; } return $self->{'sigx'}; } =head2 sigy() Title : sigy Usage : $sigy = $atom->sigy($sigy) Function: Sets/gets the sigy Returns : Returns the sigy for this atom Args : reference to an Atom =cut sub sigy { my($self, $value) = @_; if (defined $value) { $self->{'sigy'} = $value; } return $self->{'sigy'}; } =head2 sigz() Title : sigz Usage : $sigz = $atom->sigz($sigz) Function: Sets/gets the sigz Returns : Returns the sigz for this atom Args : reference to an Atom =cut sub sigz { my($self, $value) = @_; if (defined $value) { $self->{'sigz'} = $value; } return $self->{'sigz'}; } =head2 sigocc() Title : sigocc Usage : $sigocc = $atom->sigocc($sigocc) Function: Sets/gets the sigocc Returns : Returns the sigocc for this atom Args : reference to an Atom =cut sub sigocc { my($self, $value) = @_; if (defined $value) { $self->{'sigocc'} = $value; } return $self->{'sigocc'}; } =head2 sigtemp() Title : sigtemp Usage : $sigtemp = $atom->sigtemp($sigtemp) Function: Sets/gets the sigtemp Returns : Returns the sigtemp for this atom Args : reference to an Atom =cut sub sigtemp { my($self, $value) = @_; if (defined $value) { $self->{'sigtemp'} = $value; } return $self->{'sigtemp'}; } =head2 aniso() Title : aniso Usage : $u12 = $atom->aniso("u12", $u12) Function: Sets/gets the anisotropic temperature factors Returns : Returns the requested factor for this atom Args : reference to an Atom, name of the factor, value for the factor =cut sub aniso { my($self, $name, $value) = @_; if ( !defined $name) { $self->throw("You need to supply a name of the anisotropic temp factor you want to get"); } if (defined $value) { $self->{$name} = $value; } return $self->{$name}; } # placeholders sub u11 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub u22 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub u33 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub u12 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub u13 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub u23 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub sigu11 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub sigu22 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub sigu33 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub sigu12 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub sigu13 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub sigu23 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } =head2 id() Title : id Usage : $atom->id("CZ2") Function: Gets/sets the ID for this atom Returns : the ID Args : the ID =cut sub id { my ($self, $value) = @_;; if (defined $value) { $self->{'id'} = $value; } return $self->{'id'}; } sub DESTROY { my $self = shift; # dummy, nothing needs to be done here } # # from here on only private methods # =head2 _remove_residue() Title : _remove_residue Usage : Function: Removes the Residue this Atom is atttached to. Returns : Args : =cut sub _remove_residue { my ($self) = shift; $self->throw("no code here at the moment\n"); } =head2 _grandparent() Title : _grandparent Usage : Function: get/set a symbolic reference to our grandparent Returns : Args : =cut sub _grandparent { my($self,$symref) = @_; if (ref($symref)) { $self->throw("Thou shall only pass strings in here, no references $symref\n"); } if (defined $symref) { $self->{'grandparent'} = $symref; } return $self->{'grandparent'}; } 1; ���������������������������������������������������������BioPerl-1.007002/Bio/Structure/Chain.pm�������������������������������������������������������������000444��000766��000024�� 11253�13155576320� 17626� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # bioperl module for Bio::Structure::Chain # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Kris Boulez <kris.boulez@algonomics.com> # # Copyright Kris Boulez # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Structure::Chain - Bioperl structure Object, describes a chain =head1 SYNOPSIS #add synopsis here =head1 DESCRIPTION This object stores a Bio::Structure::Chain =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Kris Boulez Email kris.boulez@algonomics.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Structure::Chain; use strict; use Bio::Structure::Entry; use Bio::Structure::Model; use base qw(Bio::Root::Root); =head2 new() Title : new() Usage : $struc = Bio::Structure::Chain->new( -id => 'human_id', -accession_number => 'AL000012', ); Function: Returns a new Bio::Structure::Chain object from basic constructors. Usually called from Bio::Structure::IO. Returns : a new Bio::Structure::Chain object =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my($id, $residue ) = $self->_rearrange([qw( ID RESIDUE )], @args); $id && $self->id($id); $self->{'residue'} = []; # the 'smallest' item that can be added to a chain is a residue. $residue && $self->throw("use a method based on an Entry object for now"); return $self; } =head2 residue() Title : residue Usage : Function: nothing useful until I get symbolic references to do what I want Returns : Args : =cut sub residue { my ($self,$value) = @_; $self->throw("use a method on an Entry object to do what you want"); } =head2 add_residue() Title : add_residue Usage : Function: nothing useful until I get symbolic references to do what I want Returns : Args : =cut sub add_residue { my($self,$value) = @_; $self->throw("you want entry->add_residue(chain, residue)\n"); } =head2 model() Title : model Usage : Function: nothing useful until I get symbolic references to do what I want Returns : Args : =cut sub model { my($self, $value) = @_; $self->throw("go via a Entry object please\n"); } =head2 id() Title : id Usage : $chain->id("chain B") Function: Gets/sets the ID for this chain Returns : the ID Args : the ID =cut sub id { my ($self, $value) = @_;; if (defined $value) { $self->{'id'} = $value; } return $self->{'id'}; } sub DESTROY { my $self = shift; # no specific destruction for now } # # from here on only private methods # =head2 _remove_residues() Title : _remove_residues Usage : Function: Returns : Args : =cut sub _remove_residues { my ($self) = shift; $self->throw("nothing usefull in here, go see Entry\n"); } =head2 _remove_model() Title : _remove_model Usage : Function: Removes the Model this Chain is atttached to. Returns : Args : =cut sub _remove_model { my ($self) = shift; $self->throw("go see an Entry object, nothing here\n"); } =head2 _grandparent() Title : _grandparent Usage : Function: get/set a symbolic reference to our grandparent Returns : Args : =cut sub _grandparent { my($self,$symref) = @_; if (ref($symref)) { $self->throw("Thou shall only pass strings in here, no references $symref\n"); } if (defined $symref) { $self->{'grandparent'} = $symref; } return $self->{'grandparent'}; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Structure/Entry.pm�������������������������������������������������������������000444��000766��000024�� 63131�13155576320� 17707� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # bioperl module for Bio::Structure::Entry # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Kris Boulez <kris.boulez@algonomics.com> # # Copyright Kris Boulez # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Structure::Entry - Bioperl structure Object, describes the whole entry =head1 SYNOPSIS #add synopsis here =head1 DESCRIPTION This object stores a whole Bio::Structure entry. It can consist of one or more models (L<Bio::Structure::Model>), which in turn consist of one or more chains (L<Bio::Structure::Chain>). A chain is composed of residues (L<Bio::Structure::Residue>) and a residue consists of atoms (L<Bio::Structure::Atom>). If no specific model or chain is chosen, the first one is chosen. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Kris Boulez Email kris.boulez@algonomics.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Structure::Entry; use strict; use Bio::Structure::Model; use Bio::Structure::Chain; use Bio::Annotation::Collection; use Tie::RefHash; use base qw(Bio::Root::Root Bio::Structure::StructureI); =head2 new() Title : new() Usage : $struc = Bio::Structure::Entry->new( -id => 'structure_id', ); Function: Returns a new Bio::Structure::Entry object from basic constructors. Probably most called from Bio::Structure::IO. Returns : a new Bio::Structure::Model object =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my($id, $model, $chain, $residue ) = $self->_rearrange([qw( ID MODEL CHAIN RESIDUE )], @args); # where to store parent->child relations (1 -> 1..n) # value to this hash will be an array ref # by using Tie::RefHash we can store references in this hash $self->{'p_c'} = (); tie %{ $self->{'p_c'} } , "Tie::RefHash"; # where to store child->parent relations (1 -> 1) $self->{'c_p'} = (); tie %{ $self->{'c_p'} } , "Tie::RefHash"; $id && $self->id($id); $self->{'model'} = []; $model && $self->model($model); if($chain) { if ( ! defined($self->model) ) { # no model yet, create default one $self->_create_default_model; } for my $m ($self->model) { # add this chain on all models $m->chain($chain); } } $residue && $self->residue($residue); # taken from Bio::Seq (or should we just inherit Bio::Seq and override some methods) my $ann = Bio::Annotation::Collection->new; $self->annotation($ann); return $self; } =head2 model() Title : model Function: Connects a (or a list of) Model objects to a Bio::Structure::Entry. To add a Model (and keep the existing ones) use add_model() It returns a list of Model objects. Returns : List of Bio::Structure::Model objects Args : One Model or a reference to an array of Model objects =cut sub model { my ($self, $model) = @_; if( defined $model) { if( (ref($model) eq "ARRAY") || ($model->isa('Bio::Structure::Model')) ) { # remove existing ones, tell they've become orphan my @obj = $self->model; if (@obj) { for my $m (@obj) { $self->_remove_from_graph($m); $self->{'model'} = []; } } # add the new ones $self->add_model($self,$model); } else { $self->throw("Supplied a $model to model, we want a Bio::Structure::Model or a list of these\n"); } } # give back list of models via general get method $self->get_models($self); } =head2 add_model() Title : add_model Usage : $structure->add_model($model); Function: Adds a (or a list of) Model objects to a Bio::Structure::Entry. Returns : Args : One Model or a reference to an array of Model objects =cut sub add_model { my($self,$entry,$model) = @_; # if only one argument and it's a model, change evrything one place # this is for people calling $entry->add_model($model); if ( !defined $model && ref($entry) =~ /^Bio::Structure::Model/) { $model = $entry; $entry = $self; } # $self and $entry are the same here, but it's used for uniformicity if ( !defined($entry) || ref($entry) !~ /^Bio::Structure::Entry/) { $self->throw("first argument to add_model needs to be a Bio::Structure::Entry object\n"); } if (defined $model) { if (ref($model) eq "ARRAY") { # if the user passed in a reference to an array for my $m ( @{$model} ) { if( ! $m->isa('Bio::Structure::Model') ) { $self->throw("$m is not a Model\n"); } if ( $self->_parent($m) ) { $self->throw("$m already assigned to a parent\n"); } push @{$self->{'model'}}, $m; # create a stringified version of our ref # not used until we get symbolic ref working #my $str_ref = "$self"; #$m->_grandparent($str_ref); } } elsif ( $model->isa('Bio::Structure::Model') ) { if ( $self->_parent($model) ) { # already assigned to a parent $self->throw("$model already assigned\n"); } push @{$self->{'model'}}, $model; # create a stringified version of our ref #my $str_ref = "$self"; #$model->_grandparent($str_ref); } else { $self->throw("Supplied a $model to add_model, we want a Model or list of Models\n"); } } my $array_ref = $self->{'model'}; return $array_ref ? @{$array_ref} : (); } =head2 get_models() Title : get_models Usage : $structure->get_models($structure); Function: general get method for models attached to an Entry Returns : a list of models attached to this entry Args : an Entry =cut sub get_models { my ($self, $entry) = @_; # self and entry can be the same if ( !defined $entry) { $entry = $self; } # pass through to add_model $self->add_model($entry); } =head2 id() Title : id Usage : $entry->id("identity"); Function: Gets/sets the ID Returns : The ID Args : =cut sub id { my ($self, $value) = @_; if (defined $value) { $self->{'id'} = $value; } return $self->{'id'}; } =head2 chain() Title : chain Usage : @chains = $structure->chain($chain); Function: Connects a Chain or a list of Chain objects to a Bio::Structure::Entry. Returns : List of Bio::Structure::Chain objects Args : A Chain or a reference to an array of Chain objects =cut sub chain { my ($self, $chain) = @_; if ( ! $self->model ) { $self->_create_default_model; } my @models = $self->model; my $first_model = $models[0]; if ( defined $chain) { if( (ref($chain) eq "ARRAY") || ($chain->isa('Bio::Structure::Chain')) ) { # remove existing ones, tell they've become orphan my @obj = $self->get_chains($first_model); if (@obj) { for my $c (@obj) { $self->_remove_from_graph($c); } } # add the new ones $self->add_chain($first_model,$chain); } else { $self->throw("Supplied a $chain to chain, we want a Bio::Structure::Chain or a list of these\n"); } } $self->get_chains($first_model); } =head2 add_chain() Title : add_chain Usage : @chains = $structure->add_chain($model,$chain); Function: Adds one or more Chain objects to a Bio::Structure::Entry. Returns : List of Chain objects associated with the Model Args : A Model object and a Chain object or a reference to an array of of Chain objects =cut sub add_chain { my($self, $model, $chain) = @_; if (ref($model) !~ /^Bio::Structure::Model/) { $self->throw("add_chain: first argument needs to be a Model object ($model)\n"); } if (defined $chain) { if (ref($chain) eq "ARRAY") { # if the user passed in a reference to an array for my $c ( @{$chain} ) { if( ! $c->isa('Bio::Structure::Chain') ) { $self->throw("$c is not a Chain\n"); } if ( $self->_parent($c) ) { $self->throw("$c already assigned to a parent\n"); } $self->_parent($c, $model); $self->_child($model, $c); # stringify $self ref #my $str_ref = "$self"; #$c->_grandparent($str_ref); } } elsif ( $chain->isa('Bio::Structure::Chain') ) { if ( $self->_parent($chain) ) { # already assigned to parent $self->throw("$chain already assigned to a parent\n"); } $self->_parent($chain,$model); $self->_child($model, $chain); # stringify $self ref #my $str_ref = "$self"; #$chain->_grandparent($str_ref); } else { $self->throw("Supplied a $chain to add_chain, we want a Chain or list of Chains\n"); } } my $array_ref = $self->_child($model); return $array_ref ? @{$array_ref} : (); } =head2 get_chains() Title : get_chains Usage : $entry->get_chains($model); Function: General get method for Chains attached to a Model Returns : A list of Chains attached to this model Args : A Model =cut sub get_chains { my ($self, $model) = @_; if (! defined $model) { $model = ($self->get_models)[0]; } # pass through to add_chain $self->add_chain($model); } =head2 residue() Title : residue Usage : @residues = $structure->residue($residue); Function: Connects a (or a list of) Residue objects to a Bio::Structure::Entry. Returns : List of Bio::Structure::Residue objects Args : One Residue or a reference to an array of Residue objects =cut sub residue { my ($self, $residue) = @_; if ( ! $self->model ) { my $m = $self->_create_default_model; $self->add_model($self,$m); } my @models = $self->model; my $first_model = $models[0]; if ( ! $self->get_chains($first_model) ) { my $c = $self->_create_default_chain; $self->add_chain($first_model, $c); } my @chains = $self->get_chains($first_model); my $first_chain = $chains[0]; if( defined $residue) { if( (ref($residue) eq "ARRAY") || ($residue->isa('Bio::Structure::Residue')) ) { # remove existing ones, tell they've become orphan my @obj = $self->get_residues($first_chain); if (@obj) { for my $r (@obj) { $self->_remove_from_graph($r); } } # add the new ones $self->add_residue($first_chain,$residue); } else { $self->throw("Supplied a $residue to residue, we want a Bio::Structure::Residue or a list of these\n"); } } $self->get_residues($first_chain); } =head2 add_residue() Title : add_residue Usage : @residues = $structure->add_residue($chain,$residue); Function: Adds one or more Residue objects to a Bio::Structure::Entry. Returns : List of Bio::Structure::Residue objects Args : A Chain object and a Residue object or a reference to an array of Residue objects =cut sub add_residue { my($self,$chain,$residue) = @_; if (ref($chain) !~ /^Bio::Structure::Chain/) { $self->throw("add_residue: first argument needs to be a Chain object\n"); } if (defined $residue) { if (ref($residue) eq "ARRAY") { # if the user passed in a reference to an array for my $r ( @{$residue} ) { if( ! $r->isa('Bio::Structure::Residue') ) { $self->throw("$r is not a Residue\n"); } if ( $self->_parent($r) ) { $self->throw("$r already belongs to a parent\n"); } $self->_parent($r, $chain); $self->_child($chain, $r); # stringify my $str_ref = "$self"; $r->_grandparent($str_ref); } } elsif ( $residue->isa('Bio::Structure::Residue') ) { if ( $self->_parent($residue) ) { $self->throw("$residue already belongs to a parent\n"); } $self->_parent($residue, $chain); $self->_child($chain, $residue); # stringify my $str_ref = "$self"; $residue->_grandparent($str_ref); } else { $self->throw("Supplied a $residue to add_residue, we want a Residue or list of Residues\n"); } } my $array_ref = $self->_child($chain); return $array_ref ? @{$array_ref} : (); } =head2 get_residues() Title : get_residues Usage : $structure->get_residues($chain); Function: General get method for Residues attached to a Chain Returns : A list of residues attached to this Chain Args : A Chain =cut sub get_residues { my ($self, $chain) = @_; if ( !defined $chain) { $self->throw("get_residues needs a Chain as argument"); } # pass through to add_residue $self->add_residue($chain); } =head2 add_atom() Title : add_atom Usage : @atoms = $structure->add_atom($residue,$atom); Function: Adds a (or a list of) Atom objects to a Bio::Structure::Residue. Returns : List of Bio::Structure::Atom objects Args : A Residue and an Atom =cut sub add_atom { my($self,$residue,$atom) = @_; if (ref($residue) !~ /^Bio::Structure::Residue/) { $self->throw("add_atom: first argument needs to be a Residue object\n"); } if (defined $atom) { if (ref($atom) eq "ARRAY") { # if the user passed in a reference to an array for my $a ( @{$atom} ) { if( ! $a->isa('Bio::Structure::Atom') ) { $self->throw("$a is not an Atom\n"); } if ( $self->_parent($a) ) { $self->throw("$a already belongs to a parent\n"); } $self->_parent($a, $residue); $self->_child($residue, $a); # stringify #my $str_ref = "$self"; #$r->_grandparent($str_ref); } } #elsif ( $atom->isa('Bio::Structure::Atom') ) { elsif ( ref($atom) =~ /^Bio::Structure::Atom/ ) { if ( $self->_parent($atom) ) { $self->throw("$atom already belongs to a parent\n"); } $self->_parent($atom, $residue); $self->_child($residue, $atom); # stringify #my $str_ref = "$self"; #$atom->_grandparent($str_ref); } } my $array_ref = $self->_child($residue); return $array_ref ? @{$array_ref} : (); } =head2 get_atoms() Title : get_atoms Usage : $structure->get_atoms($residue); Function: General get method for Atoms attached to a Residue Returns : A list of Atoms attached to this Residue Args : A Residue =cut sub get_atoms { my ($self, $residue) = @_; if ( !defined $residue) { $self->throw("get_atoms needs a Residue as argument"); } # pass through to add_atom $self->add_atom($residue); } =head2 parent() Title : parent Usage : $structure->parent($residue); Function: Returns the parent of the argument Returns : The parent of the argument Args : A Bio::Structure object =cut =head2 connect Title : connect Usage : Function: Alias to conect() Returns : Args : =cut sub connect { my $self = shift; return $self->conect(@_); } =head2 conect() Title : conect Usage : $structure->conect($source); Function: Get/set method for conect Returns : A list of serial numbers for Atoms connected to source (together with $entry->get_atom_by_serial($model, $serial), this should be OK for now) Args : The source, the serial number for the source Atom, and the type =cut sub conect { my ($self, $source, $serial, $type) = @_; if ( !defined $source ) { $self->throw("You need to supply at least a source to connect"); } if ( defined $serial && defined $type ) { if ( !exists(${$self->{'conect'}}{$source}) || ref(${$self->{'conect'}}{$source} !~ /^ARRAY/ ) ) { ${$self->{'conect'}}{$source} = []; } # we also need to store type, a conect object might be better my $c = $serial . "_" . $type; push @{ ${$self->{'conect'}}{$source} }, $c; } # Bug 1894 return () if ( !exists $self->{'conect'}{$source} || !defined $self->{'conect'}{$source} ); return @{ ${$self->{'conect'}}{$source} }; } =head2 get_all_connect_source Title : get_all_connect_source Usage : Function: Alias to get_all_conect_source() Returns : Args : =cut sub get_all_connect_source { my $self = shift; return get_all_conect_source(@_); } =head2 get_all_conect_source() Title : get_all_conect_source Usage : @sources = $structure->get_all_conect_source; Function: Get all the sources for the conect records Returns : A list of serial numbers for atoms connected to source (together with $entry->get_atom_by_serial($model, $serial), this should be OK for now) Args : Notes : This is a bit of a kludge, but it is the best for now. Conect info might need to go in a separate object =cut sub get_all_conect_source { my ($self) = shift; my (@sources); for my $source (sort {$a<=>$b} keys %{$self->{'conect'}}) { push @sources, $source; } return @sources; } =head2 master() Title : master Usage : $structure->master($source); Function: Get/set method for master Returns : The master line Args : The master line for this entry =cut sub master { my ($self, $value) = @_; if (defined $value) { $self->{'master'} = $value; } return $self->{'master'}; } =head2 seqres() Title : seqres Usage : $seqobj = $structure->seqres("A"); Function: Gets a sequence object containing the sequence from the SEQRES record. if a chain-ID is given, the sequence for this chain is given, if none is provided the first chain is chosen Returns : A Bio::PrimarySeq Args : The chain-ID of the chain you want the sequence from =cut sub seqres { my ($self, $chainid) = @_; my $s_u = "x3 A1 x7 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3"; my (%seq_ch); if ( !defined $chainid) { my $m = ($self->get_models($self))[0]; my $c = ($self->get_chains($m))[0]; $chainid = $c->id; } my $seqres = ($self->annotation->get_Annotations("seqres"))[0]; my $seqres_string = $seqres->as_text; $self->debug("seqres : $seqres_string\n"); $seqres_string =~ s/^Value: //; # split into lines of 62 long my @l = unpack("A62" x (length($seqres_string)/62), $seqres_string); for my $line (@l) { # get out chain_id and sequence # we use a1, as A1 strips all spaces :( my ($chid, $seq) = unpack("x3 a1 x7 A51", $line); if ($chid eq " ") { $chid = "default"; } $seq =~ s/(\w+)/\u\L$1/g; # ALA -> Ala (for SeqUtils) $seq =~ s/\s//g; # strip all spaces $seq_ch{$chid} .= $seq; $self->debug("seqres : $chid $seq_ch{$chid}\n"); } # do we have a seqres for this chainid if(! exists $seq_ch{$chainid} ) { $self->warn("There is no SEQRES known for chainid \"$chainid\""); return; } # this will break for non-protein structures (about 10% for now) XXX KB my $pseq = Bio::PrimarySeq->new(-alphabet => 'protein'); $pseq = Bio::SeqUtils->seq3in($pseq,$seq_ch{$chainid}); my $id = $self->id . "_" . $chainid; $pseq->id($id); return $pseq; } =head2 get_atom_by_serial() Title : get_atom_by_serial Usage : $structure->get_atom_by_serial($model,$serial); Function: Get the Atom by serial Returns : The Atom object with this serial number in the model Args : Model on which to work, serial number for atom (if only a number is supplied, the first model is chosen) =cut sub get_atom_by_serial { my ($self, $model, $serial) = @_; if ($model =~ /^\d+$/ && !defined $serial) { # only serial given $serial = $model; my @m = $self->get_models($self); $model = $m[0]; } if ( !defined $model || ref($model) !~ /^Bio::Structure::Model/ ) { $self->throw("Could not find (first) model\n"); } if ( !defined $serial || ($serial !~ /^\d+$/) ) { $self->throw("The serial number you provided looks fishy ($serial)\n"); } for my $chain ($self->get_chains($model) ) { for my $residue ($self->get_residues($chain) ) { for my $atom ($self->get_atoms($residue) ) { # this could get expensive, do we cache ??? next unless ($atom->serial == $serial); return $atom; } } } } sub parent { my ($self, $obj) = @_; if ( !defined $obj) { $self->throw("parent: you need to supply an argument to get the parent from\n"); } # for now we pass on to _parent, until we get the symbolic ref thing working. $self->_parent($obj); } sub DESTROY { my $self = shift; %{ $self->{'p_c'} } = (); %{ $self->{'c_p'} } = (); } =head2 annotation Title : annotation Usage : $obj->annotation($seq_obj) Function: Example : Returns : value of annotation Args : newvalue (optional) =cut sub annotation { my ($obj,$value) = @_; if( defined $value) { $obj->{'annotation'} = $value; } return $obj->{'annotation'}; } # # from here on only private methods # =head2 _remove_models() Title : _remove_models Usage : Function: Removes the models attached to an Entry. Tells the models they do not belong to this Entry any more Returns : Args : =cut # sub _remove_models { my ($self) = shift; ; } =head2 _create_default_model() Title : _create_default_model Usage : Function: Creates a default Model for this Entry. Typical situation in an X-ray structure where there is only one model Returns : Args : =cut sub _create_default_model { my ($self) = shift; my $model = Bio::Structure::Model->new(-id => "default"); return $model; } =head2 _create_default_chain() Title : _create_default_chain Usage : Function: Creates a default Chain for this Model. Typical situation in an X-ray structure where there is only one chain Returns : Args : =cut sub _create_default_chain { my ($self) = shift; my $chain = Bio::Structure::Chain->new(-id => "default"); return $chain; } =head2 _parent() Title : _parent Usage : This is an internal function only. It is used to have one place that keeps track of which object has which other object as parent. Thus allowing the underlying modules (Atom, Residue,...) to have no knowledge about all this (and thus removing the possibility of reference cycles). This method hides the details of manipulating references to an anonymous hash. Function: To get/set an objects parent Returns : A reference to the parent if it exist, undef otherwise. In the current implementation each node should have a parent (except Entry). Args : =cut # manipulating the c_p hash sub _parent { no strict "refs"; my ($self, $key, $value) = @_; if ( (!defined $key) || (ref($key) !~ /^Bio::/) ) { $self->throw("First argument to _parent needs to be a reference to a Bio:: object ($key)\n"); } if ( (defined $value) && (ref($value) !~ /^Bio::/) ) { $self->throw("Second argument to _parent needs to be a reference to a Bio:: object\n"); } # no checking here for consistency of key and value, needs to happen in caller if (defined $value) { # is this value already in, shout if (defined ( $self->{'c_p'}->{$key}) && exists ( $self->{'c_p'}->{$key}) ) { $self->throw("_parent: $key already has a parent ${$self->{'c_p'}}{$key}\n"); } ${$self->{'c_p'}}{$key} = $value; } return ${$self->{'c_p'}}{$key}; } =head2 _child() Title : _child Usage : This is an internal function only. It is used to have one place that keeps track of which object has which other object as child. Thus allowing the underlying modules (Atom, Residue,...) to have no knowledge about all this (and thus removing the possibility to have no knowledge about all this (and thus removing the possibility of reference cycles). This method hides the details of manipulating references to an anonymous hash. Function: To get/set an the children of an object Returns : A reference to an array of child(ren) if they exist, undef otherwise. Args : =cut # manipulating the p_c hash sub _child { my ($self, $key, $value) = @_; if ( (!defined $key) || (ref($key) !~ /^Bio::/) ) { $self->throw("First argument to _child needs to be a reference to a Bio:: object\n"); } if ( (defined $value) && (ref($value) !~ /^Bio::/) ) { $self->throw("Second argument to _child needs to be a reference to a Bio:: object\n"); } # no checking here for consistency of key and value, needs to happen in caller if (defined $value) { if ( !exists(${$self->{'p_c'}}{$key}) || ref(${$self->{'p_c'}}{$key}) !~ /^ARRAY/ ) { ${$self->{'p_c'}}{$key} = []; } push @{ ${$self->{'p_c'}}{$key} }, $value; } return ${$self->{'p_c'}}{$key}; } =head2 _remove_from_graph() Title : _remove_from_graph Usage : This is an internal function only. It is used to remove from the parent/child graph. We only remove the links from object to his parent. Not the ones from object to its children. Function: To remove an object from the parent/child graph Returns : Args : The object to be orphaned =cut sub _remove_from_graph { my ($self, $object) = @_; if ( !defined($object) && ref($object) !~ /^Bio::/) { $self->throw("_remove_from_graph needs a Bio object as argument"); } if ( $self->_parent($object) ) { my $dad = $self->_parent($object); # if we have a parent, remove me as being a child for my $k (0 .. $#{$self->_child($dad)}) { if ($object eq ${$self->{'p_c'}{$dad}}[$k]) { splice(@{$self->{'p_c'}{$dad}}, $k,1); } } delete( $self->{'c_p'}{$object}); } } sub _print_stats_pc { # print stats about the parent/child hashes my ($self) =@_; my $pc = scalar keys %{$self->{'p_c'}}; my $cp = scalar keys %{$self->{'c_p'}}; my $now_time = Time::HiRes::time(); $self->debug("pc stats: P_C $pc C_P $cp $now_time\n"); } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Structure/IO.pm����������������������������������������������������������������000444��000766��000024�� 34471�13155576320� 17122� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Structure::IO # # Copyright 2001, 2002 Kris Boulez # # You may distribute this module under the same terms as perl itself # # _history # October 18, 1999 Largely rewritten by Lincoln Stein # November 16, 2001 Copied Bio::SeqIO to Bio::Structure::IO and modified # where needed. Factoring out common methods # (to Bio::Root::IO) might be a good idea. # POD documentation - main docs before the code =head1 NAME Bio::Structure::IO - Handler for Structure Formats =head1 SYNOPSIS use Bio::Structure::IO; $in = Bio::Structure::IO->new(-file => "inputfilename", -format => 'pdb'); while ( my $struc = $in->next_structure() ) { print "Structure ", $struc->id, " number of models: ", scalar $struc->model,"\n"; } =head1 DESCRIPTION Bio::Structure::IO is a handler module for the formats in the Structure::IO set (e.g. L<Bio::Structure::IO::pdb>). It is the officially sanctioned way of getting at the format objects, which most people should use. The Bio::Structure::IO system can be thought of like biological file handles. They are attached to filehandles with smart formatting rules (e.g. PDB format) and can either read or write structure objects (Bio::Structure objects, or more correctly, Bio::Structure::StructureI implementing objects, of which Bio::Structure is one such object). If you want to know what to do with a Bio::Structure object, read L<Bio::Structure>. The idea is that you request a stream object for a particular format. All the stream objects have a notion of an internal file that is read from or written to. A particular Structure::IO object instance is configured for either input or output. A specific example of a stream object is the Bio::Structure::IO::pdb object. Each stream object has functions $stream->next_structure(); and $stream->write_structure($struc); also $stream->type() # returns 'INPUT' or 'OUTPUT' As an added bonus, you can recover a filehandle that is tied to the Structure::IOIO object, allowing you to use the standard E<lt>E<gt> and print operations to read and write structure::IOuence objects: use Bio::Structure::IO; $stream = Bio::Structure::IO->newFh(-format => 'pdb'); # read from standard input while ( $structure = <$stream> ) { # do something with $structure } and print $stream $structure; # when stream is in output mode =head1 CONSTRUCTORS =head2 Bio::Structure::IO-E<gt>new() $stream = Bio::Structure::IO->new(-file => 'filename', -format=>$format); $stream = Bio::Structure::IO->new(-fh => \*FILEHANDLE, -format=>$format); $stream = Bio::Structure::IO->new(-format => $format); The new() class method constructs a new Bio::Structure::IO object. The returned object can be used to retrieve or print Bio::Structure objects. new() accepts the following parameters: =over 4 =item -file A file path to be opened for reading or writing. The usual Perl conventions apply: 'file' # open file for reading '>file' # open file for writing '>>file' # open file for appending '+<file' # open file read/write 'command |' # open a pipe from the command '| command' # open a pipe to the command =item -fh You may provide new() with a previously-opened filehandle. For example, to read from STDIN: $strucIO = Bio::Structure::IO->new(-fh => \*STDIN); Note that you must pass filehandles as references to globs. If neither a filehandle nor a filename is specified, then the module will read from the @ARGV array or STDIN, using the familiar E<lt>E<gt> semantics. =item -format Specify the format of the file. Supported formats include: pdb Protein Data Bank format If no format is specified and a filename is given, then the module will attempt to deduce it from the filename. If this is unsuccessful, PDB format is assumed. The format name is case insensitive. 'PDB', 'Pdb' and 'pdb' are all supported. =back =head2 Bio::Structure::IO-E<gt>newFh() $fh = Bio::Structure::IO->newFh(-fh => \*FILEHANDLE, -format=>$format); $fh = Bio::Structure::IO->newFh(-format => $format); # etc. This constructor behaves like new(), but returns a tied filehandle rather than a Bio::Structure::IO object. You can read structures from this object using the familiar E<lt>E<gt> operator, and write to it using print(). The usual array and $_ semantics work. For example, you can read all structure objects into an array like this: @structures = <$fh>; Other operations, such as read(), sysread(), write(), close(), and printf() are not supported. =head1 OBJECT METHODS See below for more detailed summaries. The main methods are: =head2 $structure = $structIO-E<gt>next_structure() Fetch the next structure from the stream. =head2 $structIO-E<gt>write_structure($struc [,$another_struc,...]) Write the specified structure(s) to the stream. =head2 TIEHANDLE(), READLINE(), PRINT() These provide the tie interface. See L<perltie> for more details. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Ewan Birney, Lincoln Stein, Kris Boulez Email birney@ebi.ac.uk, lstein@cshl.org, kris.boulez@algonomics.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Structure::IO; use strict; use Bio::PrimarySeq; use Symbol; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : $stream = Bio::Structure::IO->new(-file => $filename, -format => 'Format') Function: Returns a new structIOstream Returns : A Bio::Structure::IO handler initialised with the appropriate format Args : -file => $filename -format => format -fh => filehandle to attach to =cut my $entry = 0; sub new { my ($caller,@args) = @_; my $class = ref($caller) || $caller; # or do we want to call SUPER on an object if $caller is an # object? if( $class =~ /Bio::Structure::IO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys my $format = $param{'-format'} || $class->_guess_format( $param{-file} || $ARGV[0] ) || 'pdb'; $format = "\L$format"; # normalize capitalization to lower case # normalize capitalization return unless( &_load_format_module($format) ); return "Bio::Structure::IO::$format"->new(@args); } } =head2 newFh Title : newFh Usage : $fh = Bio::Structure::IO->newFh(-file=>$filename,-format=>'Format') Function: does a new() followed by an fh() Example : $fh = Bio::Structure::IO->newFh(-file=>$filename,-format=>'Format') $structure = <$fh>; # read a structure object print $fh $structure; # write a structure object Returns : filehandle tied to the Bio::Structure::IO::Fh class Args : =cut sub newFh { my $class = shift; return unless my $self = $class->new(@_); return $self->fh; } =head2 fh Title : fh Usage : $obj->fh Function: Example : $fh = $obj->fh; # make a tied filehandle $structure = <$fh>; # read a structure object print $fh $structure; # write a structure object Returns : filehandle tied to the Bio::Structure::IO::Fh class Args : =cut sub fh { my $self = shift; my $class = ref($self) || $self; my $s = Symbol::gensym; tie $$s,$class,$self; return $s; } =head2 format Title : format Usage : $format = $obj->format() Function: Get the structure format Returns : structure format Args : none =cut # format() method inherited from Bio::Root::IO # _initialize is chained for all SeqIO classes sub _initialize { my($self, @args) = @_; # not really necessary unless we put more in RootI $self->SUPER::_initialize(@args); # initialize the IO part $self->_initialize_io(@args); } =head2 next_structure Title : next_structure Usage : $structure = stream->next_structure Function: Reads the next structure object from the stream and returns a Bio::Structure::Entry object. Certain driver modules may encounter entries in the stream that are either misformatted or that use syntax not yet understood by the driver. If such an incident is recoverable, e.g., by dismissing a feature of a feature table or some other non-mandatory part of an entry, the driver will issue a warning. In the case of a non-recoverable situation an exception will be thrown. Do not assume that you can resume parsing the same stream after catching the exception. Note that you can always turn recoverable errors into exceptions by calling $stream->verbose(2) (see Bio::RootI POD page). Returns : a Bio::Structure::Entry object Args : none =cut sub next_structure { my ($self, $struc) = @_; $self->throw("Sorry, you cannot read from a generic Bio::Structure::IO object."); } # Do we want people to read out the sequence directly from a $structIO stream # ##=head2 next_primary_seq ## ## Title : next_primary_seq ## Usage : $seq = $stream->next_primary_seq ## Function: Provides a primaryseq type of sequence object ## Returns : A Bio::PrimarySeqI object ## Args : none ## ## ##=cut ## ##sub next_primary_seq { ## my ($self) = @_; ## ## # in this case, we default to next_seq. This is because ## # Bio::Seq's are Bio::PrimarySeqI objects. However we ## # expect certain sub classes to override this method to provide ## # less parsing heavy methods to retrieving the objects ## ## return $self->next_seq(); ##} =head2 write_structure Title : write_structure Usage : $stream->write_structure($structure) Function: writes the $structure object into the stream Returns : 1 for success and 0 for error Args : Bio::Structure object =cut sub write_seq { my ($self, $struc) = @_; $self->throw("Sorry, you cannot write to a generic Bio::Structure::IO object."); } # De we need this here # ##=head2 alphabet ## ## Title : alphabet ## Usage : $self->alphabet($newval) ## Function: Set/get the molecule type for the Seq objects to be created. ## Example : $seqio->alphabet('protein') ## Returns : value of alphabet: 'dna', 'rna', or 'protein' ## Args : newvalue (optional) ## Throws : Exception if the argument is not one of 'dna', 'rna', or 'protein' ## ##=cut ## ##sub alphabet { ## my ($self, $value) = @_; ## ## if ( defined $value) { ## # instead of hard-coding the allowed values once more, we check by ## # creating a dummy sequence object ## eval { ## my $seq = Bio::PrimarySeq->new('-alphabet' => $value); ## }; ## if($@) { ## $self->throw("Invalid alphabet: $value\n. See Bio::PrimarySeq for allowed values."); ## } ## $self->{'alphabet'} = "\L$value"; ## } ## return $self->{'alphabet'}; ##} =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL Structure::IO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($format) = @_; my ($module, $load, $m); $module = "_<Bio/Structure/IO/$format.pm"; $load = "Bio/Structure/IO/$format.pm"; return 1 if $main::{$module}; eval { require $load; }; if ( $@ ) { print STDERR <<END; $load: $format cannot be found Exception $@ For more information about the Structure::IO system please see the Bio::Structure::IO docs. This includes ways of checking for formats at compile time, not run time END ; return; } return 1; } =head2 _concatenate_lines Title : _concatenate_lines Usage : $s = _concatenate_lines($line, $continuation_line) Function: Private. Concatenates two strings assuming that the second stems from a continuation line of the first. Adds a space between both unless the first ends with a dash. Takes care of either arg being empty. Example : Returns : A string. Args : =cut sub _concatenate_lines { my ($self, $s1, $s2) = @_; $s1 .= " " if($s1 && ($s1 !~ /-$/) && $s2); return ($s1 ? $s1 : "") . ($s2 ? $s2 : ""); } =head2 _filehandle Title : _filehandle Usage : $obj->_filehandle($newval) Function: This method is deprecated. Call _fh() instead. Example : Returns : value of _filehandle Args : newvalue (optional) =cut sub _filehandle { my ($self,@args) = @_; return $self->_fh(@args); } =head2 _guess_format Title : _guess_format Usage : $obj->_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args : =cut sub _guess_format { my $class = shift; return unless $_ = shift; return 'fasta' if /\.(fasta|fast|seq|fa|fsa|nt|aa)$/i; return 'genbank' if /\.(gb|gbank|genbank)$/i; return 'scf' if /\.scf$/i; return 'pir' if /\.pir$/i; return 'embl' if /\.(embl|ebl|emb|dat)$/i; return 'raw' if /\.(txt)$/i; return 'gcg' if /\.gcg$/i; return 'ace' if /\.ace$/i; return 'bsml' if /\.(bsm|bsml)$/i; return 'pdb' if /\.(ent|pdb)$/i; } sub DESTROY { my $self = shift; $self->close(); } sub TIEHANDLE { my ($class,$val) = @_; return bless {'structio' => $val}, $class; } sub READLINE { my $self = shift; return $self->{'structio'}->next_seq() || undef unless wantarray; my (@list, $obj); push @list, $obj while $obj = $self->{'structio'}->next_seq(); return @list; } sub PRINT { my $self = shift; $self->{'structio'}->write_seq(@_); } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Structure/Model.pm�������������������������������������������������������������000444��000766��000024�� 13017�13155576320� 17644� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # bioperl module for Bio::Structure::Model # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Kris Boulez <kris.boulez@algonomics.com> # # Copyright Kris Boulez # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Structure::Model - Bioperl structure Object, describes a Model =head1 SYNOPSIS #add synopsis here =head1 DESCRIPTION This object stores a Bio::Structure::Chain =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Kris Boulez Email kris.boulez@algonomics.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Structure::Model; use strict; use Bio::Structure::Entry; use Bio::Structure::Chain; use base qw(Bio::Root::Root); =head2 new() Title : new() Usage : $struc = Bio::Structure::Model->new( -id => 'human_id', ); Function: Returns a new Bio::Structure::Model object from basic constructors. Probably most called from Bio::Structure::IO. Returns : a new Bio::Structure::Model object =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my($id, $chain, $residue ) = $self->_rearrange([qw( ID CHAIN RESIDUE )], @args); $id && $self->id($id); $chain && $self->throw("you have to add chain via an Entry object\n"); $residue && $self->throw("you have to add residues via an Entry object\n"); return $self; } =head2 chain() Title : chain Usage : Function: will eventually allow parent/child navigation not via an Entry object Returns : Args : =cut sub chain { my ($self,$value) = @_; $self->throw("go via an Entry object\n"); } =head2 add_chain() Title : add_chain Usage : Function: will eventually allow parent/child navigation not via an Entry object Returns : Args : =cut sub add_chain { my ($self,$value) = @_; $self->throw("go via an Entry object for now\n"); } =head2 entry() Title : entry Usage : Function: will eventually allow parent/child navigation not via an Entry object Returns : Args : =cut sub entry { my($self) = @_; $self->throw("Model::entry go via an Entry object please\n"); } =head2 id() Title : id Usage : $model->id("model 5") Function: Gets/sets the ID for this model Returns : the ID Args : the ID =cut sub id { my ($self, $value) = @_;; if (defined $value) { $self->{'id'} = $value; } return $self->{'id'}; } =head2 residue() Title : residue Usage : Function: will eventually allow parent/child navigation not via an Entry object Returns : Args : =cut sub residue { my ($self, @args) = @_; $self->throw("need to go via Entry object or learn symbolic refs\n"); } =head2 add_residue() Title : add_residue Usage : Function: will eventually allow parent/child navigation not via an Entry object Returns : Args : =cut sub add_residue { my ($self, @args) = @_; $self->throw("go via entry->add_residue(chain, residue)\n"); } sub DESTROY { my $self = shift; # no specific DESTROY for now } # # from here on only private methods # =head2 _remove_chains() Title : _remove_chains Usage : Function: Removes the chains attached to a Model. Tells the chains they don't belong to this Model any more Returns : Args : =cut sub _remove_chains { my ($self) = shift; $self->throw("use Entry methods pleae\n"); } =head2 _remove_entry() Title : _remove_entry Usage : Function: Removes the Entry this Model is atttached to. Returns : Args : =cut sub _remove_entry { my ($self) = shift; $self->throw("use a method based on an Entry object\n"); } =head2 _create_default_chain() Title : _create_default_chain Usage : Function: Creates a default Chain for this Model. Typical situation in an X-ray structure where there is only one chain Returns : Args : =cut sub _create_default_chain { my ($self) = shift; my $chain = Bio::Structure::Chain->new(-id => "default"); } =head2 _grandparent() Title : _grandparent Usage : Function: get/set a symbolic reference to our grandparent Returns : Args : =cut sub _grandparent { my($self,$symref) = @_; if (ref($symref)) { $self->throw("Thou shall only pass strings in here, no references $symref\n"); } if (defined $symref) { $self->{'grandparent'} = $symref; } return $self->{'grandparent'}; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Structure/Residue.pm�����������������������������������������������������������000444��000766��000024�� 11613�13155576320� 20204� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # bioperl module for Bio::Structure::Residue # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Kris Boulez <kris.boulez@algonomics.com> # # Copyright Kris Boulez # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Structure::Residue - Bioperl structure Object, describes a Residue =head1 SYNOPSIS #add synopsis here =head1 DESCRIPTION This object stores a Bio::Structure::Residue =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Kris Boulez Email kris.boulez@algonomics.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Structure::Residue; use strict; use Bio::Structure::Chain; use Bio::Structure::Atom; use base qw(Bio::Root::Root); =head2 new() Title : new() Usage : $residue = Bio::Structure::Residue->new( -id => 'human_id', ); Function: Returns a new Bio::Structure::Residue object from basic constructors. Probably most called from Bio::Structure::IO. Returns : a new Bio::Structure::Residue object =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my($id, $atom ) = $self->_rearrange([qw( ID ATOM )], @args); $id && $self->id($id); $self->{'atom'} = []; # the 'smallest' (and only) item that can be added to a residue is an atom $atom && $self->throw("add atoms via an Entry object entry->add_atom(residue,atom)\n"); return $self; } =head2 atom() Title : atom Usage : Function: nothing useful until I get symbolic references to do what I want Returns : Args : =cut sub atom { my ($self,$value) = @_; $self->throw("no code down here, go see an Entry object nearby\n"); } =head2 add_atom() Title : add_atom Usage : Function: nothing useful until I get symbolic references to do what I want Returns : Args : =cut sub add_atom { my($self,$value) = @_; $self->throw("nothing here, use a method on an Entry object\n"); } =head2 chain() Title : chain Usage : $chain = $residue->chain($chain) Function: Sets the Chain this Residue belongs to Returns : Returns the Chain this Residue belongs to Args : reference to a Chain =cut sub chain { my($self, $value) = @_; $self->throw("use an Entry based method please\n"); } =head2 id() Title : id Usage : $residue->id("TRP-35") Function: Gets/sets the ID for this residue Returns : the ID Args : the ID =cut sub id { my ($self, $value) = @_;; if (defined $value) { $self->{'id'} = $value; } return $self->{'id'}; } =head2 DESTROY() Title : DESTROY Usage : Function: destructor ( get rid of circular references ) Returns : Args : =cut sub DESTROY { my $self = shift; # no specific destruction for now } # # from here on only private methods # =head2 _remove_atoms() Title : _remove_atoms Usage : Function: Removes the atoms attached to a Residue. Tells the atoms they don't belong to this Residue any more Returns : Args : =cut sub _remove_atoms { my ($self) = shift; $self->throw("no code here\n"); } =head2 _remove_chain() Title : _remove_chain Usage : Function: Removes the Chain this Residue is atttached to. Returns : Args : =cut sub _remove_chain { my ($self) = shift; $self->{'chain'} = undef; } =head2 _grandparent() Title : _grandparent Usage : Function: get/set a symbolic reference to our grandparent Returns : Args : =cut sub _grandparent { my($self,$symref) = @_; if (ref($symref)) { $self->throw("Thou shall only pass strings in here, no references $symref\n"); } if (defined $symref) { $self->{'grandparent'} = $symref; } return $self->{'grandparent'}; } 1; ���������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Structure/StructureI.pm��������������������������������������������������������000444��000766��000024�� 3346�13155576320� 20701� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Structure::StructureI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Kris Boulez <kris.boulez@algonomics.com> # # Copyright Kris Boulez # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Structure::StructureI - Abstract Interface for a Structure objects =head1 SYNOPSIS Give standard usage here =head1 DESCRIPTION Describe the interface here =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Kris Boulez Email kris.boulez@algonomics.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Structure::StructureI; use strict; use base qw(Bio::Root::RootI); 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Structure/IO�������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16376� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Structure/IO/pdb.pm������������������������������������������������������������000444��000766��000024�� 131277�13155576320� 17711� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Structure::IO::pdb # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Kris Boulez <kris.boulez@algonomics.com> # # Copyright 2001, 2002 Kris Boulez # # Framework is a copy of Bio::SeqIO::embl.pm # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Structure::IO::pdb - PDB input/output stream =head1 SYNOPSIS It is probably best not to use this object directly, but rather go through the Bio::Structure::IO handler system. Go: $stream = Bio::Structure::IO->new(-file => $filename, -format => 'PDB'); while (my $structure = $stream->next_structure) { # do something with $structure } =head1 DESCRIPTION This object can transform Bio::Structure objects to and from PDB flat file databases. The working is similar to that of the Bio::SeqIO handlers. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Kris Boulez Email kris.boulez@algonomics.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Structure::IO::pdb; use strict; use Bio::Structure::Entry; #use Bio::Structure::Model; #use Bio::Structure::Chain; #use Bio::Structure::Residue; use Bio::Structure::Atom; use Bio::SeqFeature::Generic; use Bio::Annotation::Reference; use base qw(Bio::Structure::IO); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); my ($noheader, $noatom) = $self->_rearrange([qw( NOHEADER NOATOM )], @args); $noheader && $self->_noheader($noheader); $noatom && $self->_noatom($noatom); } =head2 next_structure; Title : next_structure Usage : $struc = $stream->next_structure() Function: returns the next structure in the stream Returns : Bio::Structure object Args : =cut sub next_structure { my ($self,@args) = @_; my ($line); my ($obslte, $title, $caveat, $compnd, $source, $keywds, $expdta, $author, %revdat, $revdat, $sprsde, $jrnl, %remark, $dbref, $turn, $ssbond, $link, $hydbnd, $sltbrg, $cispep, $site, $cryst1, $tvect,); my $struc = Bio::Structure::Entry->new(-id => 'created from pdb.pm'); my $all_headers = ( !$self->_noheader ); # we'll parse all headers and store as annotation my %header; # stores all header RECORDs an is stored as annotations when ATOM is reached $line = $self->_readline; # This needs to be before the first eof() test if( !defined $line ) { return; # no throws - end of file } if( $line =~ /^\s+$/ ) { while( defined ($line = $self->_readline) ) { $line =~/\S/ && last; } } if( !defined $line ) { return; # end of file } $line =~ /^HEADER\s+\S+/ || $self->throw("PDB stream with no HEADER. Not pdb in my book"); my($header_line) = unpack "x10 a56", $line; $header{'header'} = $header_line; my($class, $depdate, $idcode) = unpack "x10 a40 a9 x3 a4", $line; $idcode =~ s/^\s*(\S+)\s*$/$1/; $struc->id($idcode); $self->debug("PBD c $class d $depdate id $idcode\n"); # XXX KB my $buffer = $line; BEFORE_COORDINATES : until( !defined $buffer ) { $_ = $buffer; # Exit at start of coordinate section last if /^(MODEL|ATOM|HETATM)/; # OBSLTE line(s) if (/^OBSLTE / && $all_headers) { $obslte = $self->_read_PDB_singlecontline("OBSLTE","12-70",\$buffer); $header{'obslte'} = $obslte; } # TITLE line(s) if (/^TITLE / && $all_headers) { $title = $self->_read_PDB_singlecontline("TITLE","11-70",\$buffer); $header{'title'} = $title; } # CAVEAT line(s) if (/^CAVEAT / && $all_headers) { $caveat = $self->_read_PDB_singlecontline("CAVEAT","12-70",\$buffer); $header{'caveat'} = $caveat; } # COMPND line(s) if (/^COMPND / && $all_headers) { $compnd = $self->_read_PDB_singlecontline("COMPND","11-70",\$buffer); $header{'compnd'} = $compnd; $self->debug("get COMPND $compnd\n"); } # SOURCE line(s) if (/^SOURCE / && $all_headers) { $source = $self->_read_PDB_singlecontline("SOURCE","11-70",\$buffer); $header{'source'} = $source; } # KEYWDS line(s) if (/^KEYWDS / && $all_headers) { $keywds = $self->_read_PDB_singlecontline("KEYWDS","11-70",\$buffer); $header{'keywds'} = $keywds; } # EXPDTA line(s) if (/^EXPDTA / && $all_headers) { $expdta = $self->_read_PDB_singlecontline("EXPDTA","11-70",\$buffer); $header{'expdta'} = $expdta; } # AUTHOR line(s) if (/^AUTHOR / && $all_headers) { $author = $self->_read_PDB_singlecontline("AUTHOR","11-70",\$buffer); $header{'author'} = $author; } # REVDAT line(s) # a bit more elaborate as we also store the modification number if (/^REVDAT / && $all_headers) { ##my($modnum,$rol) = unpack "x7 A3 x3 A53", $_; ##$modnum =~ s/\s+//; # remove spaces ##$revdat{$modnum} .= $rol; my ($rol) = unpack "x7 a59", $_; $revdat .= $rol; $header{'revdat'} = $revdat; } # SPRSDE line(s) if (/^SPRSDE / && $all_headers) { $sprsde = $self->_read_PDB_singlecontline("SPRSDE","12-70",\$buffer); $header{'sprsde'} = $sprsde; } # jRNL line(s) if (/^JRNL / && $all_headers) { $jrnl = $self->_read_PDB_jrnl(\$buffer); $struc->annotation->add_Annotation('reference',$jrnl); $header{'jrnl'} = 1; # when writing out, we need a way to check there was a JRNL record (not mandatory) } # REMARK line(s) # we only parse the "REMARK 1" lines (additional references) # thre rest is stored in %remark (indexed on remarkNum) (pack does space-padding) if (/^REMARK\s+(\d+)\s*/ && $all_headers) { my $remark_num = $1; if ($remark_num == 1) { my @refs = $self->_read_PDB_remark_1(\$buffer); # How can we find the primary reference when writing (JRNL record) XXX KB foreach my $ref (@refs) { $struc->annotation->add_Annotation('reference', $ref); } # $_ still holds the REMARK_1 line, $buffer now contains the first non # REMARK_1 line. We need to parse it in this pass (so no else block) $_ = $buffer; } # for the moment I don't see a better solution (other then using goto) if (/^REMARK\s+(\d+)\s*/) { my $r_num = $1; if ($r_num != 1) { # other remarks, we store literlly at the moment my ($rol) = unpack "x11 a59", $_; $remark{$r_num} .= $rol; } } } # REMARK # DBREF line(s) # references to sequences in other databases # we store as 'dblink' annotations and whole line as simple annotation (round-trip) if (/^DBREF / && $all_headers) { my ($rol) = unpack "x7 a61", $_; $dbref .= $rol; $header{'dbref'} = $dbref; my ($db, $acc) = unpack "x26 a6 x1 a8", $_; $db =~ s/\s*$//; $acc =~ s/\s*$//; my $link = Bio::Annotation::DBLink->new; $link->database($db); $link->primary_id($acc); $struc->annotation->add_Annotation('dblink', $link); } # DBREF # SEQADV line(s) if (/^SEQADV / && $all_headers) { my ($rol) = unpack "x7 a63", $_; $header{'seqadv'} .= $rol; } # SEQADV # SEQRES line(s) # this is (I think) the sequence of macromolecule that was analysed # this will be returned when doing $struc->seq if (/^SEQRES / && $all_headers) { my ($rol) = unpack "x8 a62", $_; $header{'seqres'} .= $rol; } # SEQRES # MODRES line(s) if (/^MODRES / && $all_headers) { my ($rol) = unpack "x7 a63", $_; $header{'modres'} .= $rol; } # MODRES # HET line(s) if (/^HET / && $all_headers) { my ($rol) = unpack "x7 a63", $_; $header{'het'} .= $rol; } # HET # HETNAM line(s) if (/^HETNAM / && $all_headers) { my ($rol) = unpack "x8 a62", $_; $header{'hetnam'} .= $rol; } # HETNAM # HETSYN line(s) if (/^HETSYN / && $all_headers) { my ($rol) = unpack "x8 a62", $_; $header{'hetsyn'} .= $rol; } # HETSYN # FORMUL line(s) if (/^FORMUL / && $all_headers) { my ($rol) = unpack "x8 a62", $_; $header{'formul'} .= $rol; } # FORMUL # HELIX line(s) # store as specific object ?? if (/^HELIX / && $all_headers) { my ($rol) = unpack "x7 a69", $_; $header{'helix'} .= $rol; } # HELIX # SHEET line(s) # store as specific object ?? if (/^SHEET / && $all_headers) { my ($rol) = unpack "x7 a63", $_; $header{'sheet'} .= $rol; } # SHEET # TURN line(s) # store as specific object ?? if (/^TURN / && $all_headers) { my ($rol) = unpack "x7 a63", $_; $turn .= $rol; $header{'turn'} = $turn; } # TURN # SSBOND line(s) # store in connection-like object (see parsing of CONECT record) if (/^SSBOND / && $all_headers) { my ($rol) = unpack "x7 a65", $_; $ssbond .= $rol; $header{'ssbond'} = $ssbond; } # SSBOND # LINK # store like SSBOND ? if (/^LINK / && $all_headers) { my ($rol) = unpack "x12 a60", $_; $link .= $rol; $header{'link'} = $link; } # LINK # HYDBND # store like SSBOND if (/^HYDBND / && $all_headers) { my ($rol) = unpack "x12 a60", $_; $hydbnd .= $rol; $header{'hydbnd'} = $hydbnd; } # HYDBND # SLTBRG # store like SSBOND ? if (/^SLTBRG / && $all_headers) { my ($rol) = unpack "x12 a60",$_; $sltbrg .= $rol; $header{'sltbrg'} = $sltbrg; } # SLTBRG # CISPEP # store like SSBOND ? if (/^CISPEP / && $all_headers) { my ($rol) = unpack "x7 a52", $_; $cispep .= $rol; $header{'cispep'} = $cispep; } # SITE line(s) if (/^SITE / && $all_headers) { my ($rol) = unpack "x7 a54", $_; $site .= $rol; $header{'site'} = $site; } # SITE # CRYST1 line # store in some crystallographic subobject ? if (/^CRYST1/ && $all_headers) { my ($rol) = unpack "x6 a64", $_; $cryst1 .= $rol; $header{'cryst1'} = $cryst1; } # CRYST1 # ORIGXn line(s) (n=1,2,3) if (/^(ORIGX\d) / && $all_headers) { my $origxn = lc($1); my ($rol) = unpack "x10 a45", $_; $header{$origxn} .= $rol; } # ORIGXn # SCALEn line(s) (n=1,2,3) if (/^(SCALE\d) / && $all_headers) { my $scalen = lc($1); my ($rol) = unpack "x10 a45", $_; $header{$scalen} .= $rol; } # SCALEn # MTRIXn line(s) (n=1,2,3) if (/^(MTRIX\d) / && $all_headers) { my $mtrixn = lc($1); my ($rol) = unpack "x7 a53", $_; $header{$mtrixn} .= $rol; } # MTRIXn # TVECT line(s) if (/^TVECT / && $all_headers) { my ($rol) = unpack "x7 a63", $_; $tvect .= $rol; $header{'tvect'} = $tvect; } # Get next line. $buffer = $self->_readline; } # store %header entries a annotations if (%header) { for my $record (keys %header) { my $sim = Bio::Annotation::SimpleValue->new(); $sim->value($header{$record}); $struc->annotation->add_Annotation($record, $sim); } } # store %remark entries as annotations if (%remark) { for my $remark_num (keys %remark) { my $sim = Bio::Annotation::SimpleValue->new(); $sim->value($remark{$remark_num}); $struc->annotation->add_Annotation("remark_$remark_num", $sim); } } # Coordinate section, the real meat # # $_ contains a line beginning with (ATOM|MODEL) $buffer = $_; if (defined($buffer) && $buffer =~ /^(ATOM |MODEL |HETATM)/ ) { # can you have an entry without ATOM ? while( defined ($buffer) ) { # (yes : 1a7z ) # read in one model at a time my $model = $self->_read_PDB_coordinate_section(\$buffer, $struc); # add this to $struc $struc->add_model($struc, $model); if ($buffer && $buffer !~ /^MODEL /) { # if we get here we have multiple MODELs last; } } } else { $self->throw("Could not find a coordinate section in this record\n"); } until( !defined $buffer ) { $_ = $buffer; # CONNECT records if (/^CONECT/) { # do not differentiate between different type of connect (column dependant) my $conect_unpack = "x6 a5 a5 a5 a5 a5 a5 a5 a5 a5 a5 a5"; my (@conect) = unpack $conect_unpack, $_; for my $k (0 .. $#conect) { $conect[$k] =~ s/\s//g; } my $source = shift @conect; my $type; for my $k (0 .. 9) { next unless ($conect[$k] =~ /^\d+$/); # 0..3 bond if( $k <= 3 ) { $type = "bond"; } # 4..5,7..8 hydrogen bonded elsif( ($k >= 4 && $k <= 5) || ($k >= 7 && $k <= 8) ) { $type = "hydrogen"; } # 6, 9 salt bridged elsif( $k == 6 || $k == 9 ) { $type = "saltbridged"; } else { $self->throw("k has impossible value ($k), check brain"); } $struc->conect($source, $conect[$k], $type); } } # MASTER record if (/^MASTER /) { # the numbers in here a checksums, we should use them :) my ($rol) = unpack "x10 a60", $_; $struc->master($rol); } if (/^END/) { # this it the end ... } $buffer = $self->_readline; } return $struc; } =head2 write_structure Title : write_structure Usage : $stream->write_structure($struc) Function: writes the $struc object (must be a Bio::Structure) to the stream Returns : 1 for success and 0 for error Args : Bio::Structure object =cut sub write_structure { my ($self, $struc) = @_; if( !defined $struc ) { $self->throw("Attempting to write with no structure!"); } if( ! ref $struc || ! $struc->isa('Bio::Structure::StructureI') ) { $self->throw(" $struc is not a StructureI compliant module."); } my ($ann, $string, $output_string, $key); # HEADER ($ann) = $struc->annotation->get_Annotations("header"); if (defined $ann) { $string = $ann->as_text; $string =~ s/^Value: //; $output_string = pack ("A10 A56", "HEADER", $string); } else { # not read in via read_structure, create HEADER line my $id = $struc->id; if (!$id) { $id = "UNK1"; } if (length($id) > 4) { $id = substr($id,0,4); } my $classification = "DEFAULT CLASSIFICATION"; my $dep_date = "24-JAN-70"; $output_string = pack ("A10 A40 A12 A4", "HEADER", $classification, $dep_date, $id); } $output_string .= " " x (80 - length($output_string) ); $self->_print("$output_string\n"); my (%header); for $key ($struc->annotation->get_all_annotation_keys) { $header{$key} = 1;; } exists $header{'obslte'} && $self->_write_PDB_simple_record(-name => "OBSLTE ", -cont => "9-10", -annotation => $struc->annotation->get_Annotations("obslte"), -rol => "11-70"); exists $header{'title'} && $self->_write_PDB_simple_record(-name => "TITLE ", -cont => "9-10", -annotation => $struc->annotation->get_Annotations("title"), -rol => "11-70"); exists $header{'caveat'} && $self->_write_PDB_simple_record(-name => "CAVEAT ", -cont => "9-10", -annotation => $struc->annotation->get_Annotations("caveat"), -rol => "12-70"); exists $header{'compnd'} && $self->_write_PDB_simple_record(-name => "COMPND ", -cont => "9-10", -annotation => $struc->annotation->get_Annotations("compnd"), -rol => "11-70"); exists $header{'source'} && $self->_write_PDB_simple_record(-name => "SOURCE ", -cont => "9-10", -annotation => $struc->annotation->get_Annotations("source"), -rol => "11-70"); exists $header{'keywds'} && $self->_write_PDB_simple_record(-name => "KEYWDS ", -cont => "9-10", -annotation => $struc->annotation->get_Annotations("keywds"), -rol => "11-70"); exists $header{'expdta'} && $self->_write_PDB_simple_record(-name => "EXPDTA ", -cont => "9-10", -annotation => $struc->annotation->get_Annotations("expdta"), -rol => "11-70"); exists $header{'author'} && $self->_write_PDB_simple_record(-name => "AUTHOR ", -cont => "9-10", -annotation => $struc->annotation->get_Annotations("author"), -rol => "11-70"); exists $header{'revdat'} && $self->_write_PDB_simple_record(-name => "REVDAT ", -annotation => $struc->annotation->get_Annotations("revdat"), -rol => "8-66"); exists $header{'sprsde'} && $self->_write_PDB_simple_record(-name => "SPRSDE ", -cont => "9-10", -annotation => $struc->annotation->get_Annotations("sprsde"), -rol => "12-70"); # JRNL en REMARK 1 my ($jrnl_done, $remark_1_counter); if ( !exists $header{'jrnl'} ) { $jrnl_done = 1; } foreach my $ref ($struc->annotation->get_Annotations('reference') ) { if( !$jrnl_done ) { # JRNL record $ref->authors && $self->_write_PDB_simple_record(-name => "JRNL AUTH", -cont => "17-18", -rol => "20-70", -string => $ref->authors ); $ref->title && $self->_write_PDB_simple_record(-name => "JRNL TITL", -cont => "17-18", -rol => "20-70", -string => $ref->title ); $ref->editors && $self->_write_PDB_simple_record(-name => "JRNL EDIT", -cont => "17-18", -rol => "20-70", -string => $ref->editors ); $ref->location && $self->_write_PDB_simple_record(-name => "JRNL REF ", -cont => "17-18", -rol => "20-70", -string => $ref->location ); $ref->editors && $self->_write_PDB_simple_record(-name => "JRNL EDIT", -cont => "17-18", -rol => "20-70", -string => $ref->editors ); $ref->encoded_ref && $self->_write_PDB_simple_record(-name => "JRNL REFN", -cont => "17-18", -rol => "20-70", -string => $ref->encoded_ref ); $jrnl_done = 1; } else { # REMARK 1 if (!$remark_1_counter) { # header line my $remark_1_header_line = "REMARK 1" . " " x 70; $self->_print("$remark_1_header_line\n"); $remark_1_counter = 1; } # per reference header my $rem_line = "REMARK 1 REFERENCE " . $remark_1_counter; $rem_line .= " " x (80 - length($rem_line) ); $self->_print($rem_line,"\n"); $ref->authors && $self->_write_PDB_simple_record(-name => "REMARK 1 AUTH", -cont => "17-18", -rol => "20-70", -string => $ref->authors ); $ref->title && $self->_write_PDB_simple_record(-name => "REMARK 1 TITL", -cont => "17-18", -rol => "20-70", -string => $ref->title ); $ref->editors && $self->_write_PDB_simple_record(-name => "REMARK 1 EDIT", -cont => "17-18", -rol => "20-70", -string => $ref->editors ); $ref->location && $self->_write_PDB_simple_record(-name => "REMARK 1 REF ", -cont => "17-18", -rol => "20-70", -string => $ref->location ); $ref->editors && $self->_write_PDB_simple_record(-name => "REMARK 1 EDIT", -cont => "17-18", -rol => "20-70", -string => $ref->editors ); $ref->encoded_ref && $self->_write_PDB_simple_record(-name => "REMARK 1 REFN", -cont => "17-18", -rol => "20-70", -string => $ref->encoded_ref ); $remark_1_counter++; } } if (! defined $remark_1_counter ) { # no remark 1 record written yet my $remark_1_header_line = "REMARK 1" . " " x 70; $self->_print("$remark_1_header_line\n"); # write dummy (we need this line) } # REMARK's (not 1 at the moment, references) my (%remarks, $remark_num); for $key (keys %header) { next unless ($key =~ /^remark_(\d+)$/); next if ($1 == 1); $remarks{$1} = 1; } for $remark_num (sort {$a <=> $b} keys %remarks) { $self->_write_PDB_remark_record($struc, $remark_num); } exists $header{'dbref'} && $self->_write_PDB_simple_record(-name => "DBREF ", -annotation => $struc->annotation->get_Annotations("dbref"), -rol => "8-68"); exists $header{'seqadv'} && $self->_write_PDB_simple_record(-name => "SEQADV ", -annotation => $struc->annotation->get_Annotations("seqadv"), -rol => "8-70"); exists $header{'seqres'} && $self->_write_PDB_simple_record(-name => "SEQRES ", -annotation => $struc->annotation->get_Annotations("seqres"), -rol => "9-70"); exists $header{'modres'} && $self->_write_PDB_simple_record(-name => "MODRES ", -annotation => $struc->annotation->get_Annotations("modres"), -rol => "8-70"); exists $header{'het'} && $self->_write_PDB_simple_record(-name => "HET ", -annotation => $struc->annotation->get_Annotations("het"), -rol => "8-70"); exists $header{'hetnam'} && $self->_write_PDB_simple_record(-name => "HETNAM ", -annotation => $struc->annotation->get_Annotations("hetnam"), -rol => "9-70"); exists $header{'hetsyn'} && $self->_write_PDB_simple_record(-name => "HETSYN ", -annotation => $struc->annotation->get_Annotations("hetsyn"), -rol => "9-70"); exists $header{'formul'} && $self->_write_PDB_simple_record(-name => "FORMUL ", -annotation => $struc->annotation->get_Annotations("formul"), -rol => "9-70"); exists $header{'helix'} && $self->_write_PDB_simple_record(-name => "HELIX ", -annotation => $struc->annotation->get_Annotations("helix"), -rol => "8-76"); exists $header{'sheet'} && $self->_write_PDB_simple_record(-name => "SHEET ", -annotation => $struc->annotation->get_Annotations("sheet"), -rol => "8-70"); exists $header{'turn'} && $self->_write_PDB_simple_record(-name => "TURN ", -annotation => $struc->annotation->get_Annotations("turn"), -rol => "8-70"); exists $header{'ssbond'} && $self->_write_PDB_simple_record(-name => "SSBOND ", -annotation => $struc->annotation->get_Annotations("ssbond"), -rol => "8-72"); exists $header{'link'} && $self->_write_PDB_simple_record(-name => "LINK ", -annotation => $struc->annotation->get_Annotations("link"), -rol => "13-72"); exists $header{'hydbnd'} && $self->_write_PDB_simple_record(-name => "HYDBND ", -annotation => $struc->annotation->get_Annotations("hydbnd"), -rol => "13-72"); exists $header{'sltbrg'} && $self->_write_PDB_simple_record(-name => "SLTBRG ", -annotation => $struc->annotation->get_Annotations("sltbrg"), -rol => "13-72"); exists $header{'cispep'} && $self->_write_PDB_simple_record(-name => "CISPEP ", -annotation => $struc->annotation->get_Annotations("cispep"), -rol => "8-59"); exists $header{'site'} && $self->_write_PDB_simple_record(-name => "SITE ", -annotation => $struc->annotation->get_Annotations("site"), -rol => "8-61"); exists $header{'cryst1'} && $self->_write_PDB_simple_record(-name => "CRYST1", -annotation => $struc->annotation->get_Annotations("cryst1"), -rol => "7-70"); for my $k (1..3) { my $origxn = "origx".$k; my $ORIGXN = uc($origxn)." "; exists $header{$origxn} && $self->_write_PDB_simple_record(-name => $ORIGXN, -annotation => $struc->annotation->get_Annotations($origxn), -rol => "11-55"); } for my $k (1..3) { my $scalen = "scale".$k; my $SCALEN = uc($scalen)." "; exists $header{$scalen} && $self->_write_PDB_simple_record(-name => $SCALEN, -annotation => $struc->annotation->get_Annotations($scalen), -rol => "11-55"); } for my $k (1..3) { my $mtrixn = "mtrix".$k; my $MTRIXN = uc($mtrixn)." "; exists $header{$mtrixn} && $self->_write_PDB_simple_record(-name => $MTRIXN, -annotation => $struc->annotation->get_Annotations($mtrixn), -rol => "8-60"); } exists $header{'tvect'} && $self->_write_PDB_simple_record(-name => "TVECT ", -annotation => $struc->annotation->get_Annotations("tvect"), -rol => "8-70"); # write out coordinate section # my %het_res; # hetero residues $het_res{'HOH'} = 1; # water is default if (exists $header{'het'}) { my ($het_line) = ($struc->annotation->get_Annotations("het"))[0]->as_text; $het_line =~ s/^Value: //; for ( my $k = 0; $k <= length $het_line ; $k += 63) { my $l = substr $het_line, $k, 63; $l =~ s/^\s*(\S+)\s+.*$/$1/; $het_res{$l} = 1; } } for my $model ($struc->get_models) { # more then one model ? if ($struc->get_models > 1) { my $model_line = sprintf("MODEL %4d", $model->id); $model_line .= " " x (80 - length($model_line) ); $self->_print($model_line, "\n"); } for my $chain ($struc->get_chains($model)) { my ($residue, $atom, $resname, $resnum, $atom_line, $atom_serial, $atom_icode, $chain_id); my ($prev_resname, $prev_resnum, $prev_atomicode); # need these for TER record my $last_record = ""; # Used to spot an ATOM -> HETATM change within a chain $chain_id = $chain->id; if ( $chain_id eq "default" ) { $chain_id = " "; } $self->debug("model_id: $model->id chain_id: $chain_id\n"); for $residue ($struc->get_residues($chain)) { ($resname, $resnum) = split /-/, $residue->id; for $atom ($struc->get_atoms($residue)) { if ($het_res{$resname}) { # HETATM if ( $resname ne "HOH" && $last_record eq "ATOM " ) { # going from ATOM -> HETATM, we have to write TER my $ter_line = "TER "; $ter_line .= sprintf("%5d", $atom_serial + 1); $ter_line .= " "; $ter_line .= sprintf("%3s ", $prev_resname); $ter_line .= $chain_id; $ter_line .= sprintf("%4d", $prev_resnum); $ter_line .= $atom_icode ? $prev_atomicode : " "; # 27 $ter_line .= " " x (80 - length $ter_line); # extend to 80 chars $self->_print($ter_line,"\n"); } $atom_line = "HETATM"; } else { $atom_line = "ATOM "; } $last_record = $atom_line; $atom_line .= sprintf("%5d ", $atom->serial); $atom_serial = $atom->serial; # we need it for TER record $atom_icode = $atom->icode; # remember some stuff if next iteration needs writing TER $prev_resname = $resname; $prev_resnum = $resnum; $prev_atomicode = $atom_icode; # getting the name of the atom correct is subtrivial my $atom_id = $atom->id; # is pdb_atomname set, then use this (most probably set when # reading in the PDB record) my $pdb_atomname = $atom->pdb_atomname; if( defined $pdb_atomname ) { $atom_line .= sprintf("%-4s", $pdb_atomname); } else { # start (educated) guessing my $element = $atom->element; if( defined $element && $element ne "H") { # element should be at first two positions (right justified) # ie. Calcium should be "CA " # C alpha should be " CA " if( length($element) == 2 ) { $atom_line .= sprintf("%-4s", $atom->id); } else { $atom_line .= sprintf(" %-3s", $atom->id); } } else { # old behaviour do a best guess if ($atom->id =~ /^\dH/) { # H: four positions, left justified $atom_line .= sprintf("%-4s", $atom->id); } elsif (length($atom_id) == 4) { if ($atom_id =~ /^(H\d\d)(\d)$/) { # turn H123 into 3H12 $atom_line .= $2.$1; } else { # no more guesses, no more alternatives $atom_line .= $atom_id; } } else { # if we get here and it is not correct let me know $atom_line .= sprintf(" %-3s", $atom->id); } } } # we don't do alternate location at this moment $atom_line .= " "; # 17 $atom_line .= sprintf("%3s",$resname); # 18-20 $atom_line .= " ".$chain_id; # 21, 22 $atom_line .= sprintf("%4d", $resnum); # 23-26 $atom_line .= $atom->icode ? $atom->icode : " "; # 27 $atom_line .= " "; # 28-30 $atom_line .= sprintf("%8.3f", $atom->x); # 31-38 $atom_line .= sprintf("%8.3f", $atom->y); # 39-46 $atom_line .= sprintf("%8.3f", $atom->z); # 47-54 $atom_line .= sprintf("%6.2f", $atom->occupancy); # 55-60 $atom_line .= sprintf("%6.2f", $atom->tempfactor); # 61-66 $atom_line .= " "; # 67-72 $atom_line .= $atom->segID ? # segID 73-76 sprintf("%-4s", $atom->segID) : " "; $atom_line .= $atom->element ? sprintf("%2s", $atom->element) : " "; $atom_line .= $atom->charge ? sprintf("%2s", $atom->charge) : " "; $self->_print($atom_line,"\n"); } } # write out TER record if ( $resname ne "HOH" ) { my $ter_line = "TER "; $ter_line .= sprintf("%5d", $atom_serial + 1); $ter_line .= " "; $ter_line .= sprintf("%3s ", $resname); $ter_line .= $chain_id; $ter_line .= sprintf("%4d", $resnum); $ter_line .= $atom_icode ? $atom_icode : " "; # 27 $ter_line .= " " x (80 - length $ter_line); # extend to 80 chars $self->_print($ter_line,"\n"); } } if ($struc->get_models > 1) { # we need ENDMDL my $endmdl_line = "ENDMDL" . " " x 74; $self->_print($endmdl_line, "\n"); } } # for my $model # CONECT my @sources = $struc->get_all_conect_source; my ($conect_line,@conect, @bond, @hydbond, @saltbridge, $to, $type); for my $source (@sources) { # get all conect's my @conect = $struc->conect($source); # classify for my $con (@conect) { ($to, $type) = split /_/, $con; if($type eq "bond") { push @bond, $to; } elsif($type eq "hydrogenbonded") { push @hydbond, $to; } elsif($type eq "saltbridged") { push @saltbridge, $to; } else { $self->throw("type $type is unknown for conect"); } } # and write out CONECT lines as long as there is something # in one of the arrays while ( @bond || @hydbond || @saltbridge) { my ($b, $hb, $sb); $conect_line = "CONECT". sprintf("%5d", $source); for my $k (0..3) { $b = shift @bond; $conect_line .= $b ? sprintf("%5d", $b) : " "; } for my $k (4..5) { $hb = shift @hydbond; $conect_line .= $hb ? sprintf("%5d", $hb) : " "; } $sb = shift @saltbridge; $conect_line .= $sb ? sprintf("%5d", $sb) : " "; for my $k (7..8) { $hb = shift @hydbond; $conect_line .= $hb ? sprintf("%5d", $hb) : " "; } $sb = shift @saltbridge; $conect_line .= $sb ? sprintf("%5d", $sb) : " "; $conect_line .= " " x (80 - length($conect_line) ); $self->_print($conect_line, "\n"); } } # MASTER line contains checksums, we should calculate them of course :) my $master_line = "MASTER " . $struc->master; $master_line .= " " x (80 - length($master_line) ); $self->_print($master_line, "\n"); my $end_line = "END" . " " x 77; $self->_print($end_line,"\n"); } =head2 _filehandle Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional) =cut sub _filehandle{ my ($obj,$value) = @_; if( defined $value) { $obj->{'_filehandle'} = $value; } return $obj->{'_filehandle'}; } =head2 _noatom Title : _noatom Usage : $obj->_noatom($newval) Function: Example : Returns : value of _noatom Args : newvalue (optional) =cut sub _noatom{ my ($obj,$value) = @_; if( defined $value) { $obj->{'_noatom'} = $value; } return $obj->{'_noatom'}; } =head2 _noheader Title : _noheader Usage : $obj->_noheader($newval) Function: Example : Returns : value of _noheader Args : newvalue (optional) =cut sub _noheader{ my ($obj,$value) = @_; if( defined $value) { $obj->{'_noheader'} = $value; } return $obj->{'_noheader'}; } =head2 _read_PDB_singlecontline Title : _read_PDB_singlecontline Usage : $obj->_read_PDB_singlecontline($record, $fromto, $buffer)) Function: read single continued record from PDB Returns : concatenated record entry (between $fromto columns) Args : record, colunm delimiters, buffer =cut sub _read_PDB_singlecontline { my ($self, $record, $fromto, $buffer) = @_; my $concat_line; my ($begin, $end) = (split (/-/, $fromto)); my $unpack_string = "x8 a2 "; if($begin == 12) { # one additional space $unpack_string .= "x1 a59"; } else { $unpack_string .= "a60"; } $_ = $$buffer; while (defined( $_ ||= $self->_readline ) ) { if ( /^$record/ ) { my($cont, $rol) = unpack $unpack_string, $_; if($cont =~ /\d$/ && $begin == 11) { # continuation line # and text normally at pos 11 $rol =~ s/^\s//; # strip leading space } ## no space (store litteraly) $concat_line .= $rol . " "; $concat_line .= $rol; } else { last; } $_ = undef; } $concat_line =~ s/\s$//; # remove trailing space $$buffer = $_; return $concat_line; } =head2 _read_PDB_jrnl Title : _read_PDB_jrnl Usage : $obj->_read_PDB_jrnl($\buffer)) Function: read jrnl record from PDB Returns : Bio::Annotation::Reference object Args : =cut sub _read_PDB_jrnl { my ($self, $buffer) = @_; $_ = $$buffer; my ($auth, $titl,$edit,$ref,$publ,$refn, $pmid, $doi); while (defined( $_ ||= $self->_readline )) { if (/^JRNL /) { # this code belgons in a seperate method (shared with # remark 1 parsing) my ($rec, $subr, $cont, $rol) = unpack "A6 x6 A4 A2 x1 A51", $_; $auth = $self->_concatenate_lines($auth,$rol) if ($subr eq "AUTH"); $titl = $self->_concatenate_lines($titl,$rol) if ($subr eq "TITL"); $edit = $self->_concatenate_lines($edit,$rol) if ($subr eq "EDIT"); $ref = $self->_concatenate_lines($ref ,$rol) if ($subr eq "REF"); $publ = $self->_concatenate_lines($publ,$rol) if ($subr eq "PUBL"); $refn = $self->_concatenate_lines($refn,$rol) if ($subr eq "REFN"); $pmid = $self->_concatenate_lines($pmid,$rol) if ($subr eq "PMID"); $doi = $self->_concatenate_lines($doi,$rol) if ($subr eq "DOI"); } else { last; } $_ = undef; # trigger reading of next line } # while $$buffer = $_; my $jrnl_ref = Bio::Annotation::Reference->new; $jrnl_ref->authors($auth); $jrnl_ref->title($titl); $jrnl_ref->location($ref); $jrnl_ref->publisher($publ); $jrnl_ref->editors($edit); $jrnl_ref->encoded_ref($refn); $jrnl_ref->pubmed($pmid); $jrnl_ref->doi($doi); return $jrnl_ref; } # sub _read_PDB_jrnl =head2 _read_PDB_remark_1 Title : _read_PDB_remark_1 Usage : $obj->_read_PDB_remark_1($\buffer)) Function: read "remark 1" record from PDB Returns : array of Bio::Annotation::Reference objects Args : =cut sub _read_PDB_remark_1 { my ($self, $buffer) = @_; $_ = $$buffer; my ($auth, $titl,$edit,$ref,$publ,$refn,$refnum,$pmid, $doi); my @refs; while (defined( $_ ||= $self->_readline )) { if (/^REMARK 1 /) { if (/^REMARK 1\s+REFERENCE\s+(\d+)\s*/) { $refnum = $1; if ($refnum != 1) { # this is first line of a reference my $rref = Bio::Annotation::Reference->new; $rref->authors($auth); $rref->title($titl); $rref->location($ref); $rref->publisher($publ); $rref->editors($edit); $rref->encoded_ref($refn); $rref->pubmed($pmid); $rref->doi($doi); $auth = $titl = $edit = $ref = $publ = $refn = undef; push @refs, $rref; } } else { # this code belgons in a seperate method (shared with # remark 1 parsing) my ($rec, $subr, $cont, $rol) = unpack "A6 x6 A4 A2 x1 A51", $_; $auth = $self->_concatenate_lines($auth,$rol) if ($subr eq "AUTH"); $titl = $self->_concatenate_lines($titl,$rol) if ($subr eq "TITL"); $edit = $self->_concatenate_lines($edit,$rol) if ($subr eq "EDIT"); $ref = $self->_concatenate_lines($ref ,$rol) if ($subr eq "REF"); $publ = $self->_concatenate_lines($publ,$rol) if ($subr eq "PUBL"); $refn = $self->_concatenate_lines($refn,$rol) if ($subr eq "REFN"); $pmid = $self->_concatenate_lines($pmid,$rol) if ($subr eq "PMID"); $doi = $self->_concatenate_lines($doi,$rol) if ($subr eq "DOI"); } } else { # have we seen any reference at all (could be single REMARK 1 line if ( ! defined ($refnum) ) { last; # get out of while() } # create last reference my $rref = Bio::Annotation::Reference->new; $rref->authors($auth); $rref->title($titl); $rref->location($ref); $rref->publisher($publ); $rref->editors($edit); $rref->encoded_ref($refn); $rref->pubmed($pmid); $rref->doi($doi); push @refs, $rref; last; } $_ = undef; # trigger reading of next line } # while $$buffer = $_; return @refs; } # sub _read_PDB_jrnl =head2 _read_PDB_coordinate_section Title : _read_PDB_coordinate_section Usage : $obj->_read_PDB_coordinate_section($\buffer)) Function: read one model from a PDB Returns : Bio::Structure::Model object Args : =cut sub _read_PDB_coordinate_section { my ($self, $buffer, $struc) = @_; my ($model_num, $chain_name, $residue_name, $atom_name); # to keep track of state $model_num = ""; $chain_name = ""; $residue_name = ""; $atom_name = ""; my $atom_unpack = "x6 a5 x1 a4 a1 a3 x1 a1 a4 a1 x3 a8 a8 a8 a6 a6 x6 a4 a2 a2"; my $anisou_unpack = "x6 a5 x1 a4 a1 a3 x1 a1 a4 a1 x1 a7 a7 a7 a7 a7 a7 a4 a2 a2"; my $model = Bio::Structure::Model->new; $model->id('default'); my $noatom = $self->_noatom; my ($chain, $residue, $atom, $old); my (%_ch_in_model); # which chains are already in this model $_ = $$buffer; while (defined( $_ ||= $self->_readline )) { # start of a new model if (/^MODEL\s+(\d+)/) { $model_num = $1; $self->debug("_read_PDB_coor: parsing model $model_num\n"); $model->id($model_num); if (/^MODEL\s+\d+\s+\S+/) { # old format (pre 2.1) $old = 1; } } # old hier ook setten XXX # ATOM lines, if first set chain if (/^(ATOM |HETATM|SIGATM)/) { my @line_elements = unpack $atom_unpack, $_; my $pdb_atomname = $line_elements[1]; # need to get this before removing spaces for my $k (0 .. $#line_elements) { $line_elements[$k] =~ s/^\s+//; # remove leading space $line_elements[$k] =~ s/\s+$//; # remove trailing space $line_elements[$k] = undef if ($line_elements[$k] =~ /^\s*$/); } my ($serial, $atomname, $altloc, $resname, $chainID, $resseq, $icode, $x, $y, $z, $occupancy, $tempfactor, $segID, $element, $charge) = @line_elements; $chainID = 'default' if ( !defined $chainID ); if ($chainID ne $chain_name) { # possibly a new chain # fix for bug #1187 # we can have ATOM/HETATM of an already defined chain (A B A B) # e.g. 1abm if (exists $_ch_in_model{$chainID} ) { # we have already seen this chain in this model $chain = $_ch_in_model{$chainID}; } else { # we create a new chain $chain = Bio::Structure::Chain->new; $struc->add_chain($model,$chain); $chain->id($chainID); $_ch_in_model{$chainID} = $chain; } $chain_name = $chain->id; } #my $res_name_num = $resname."-".$resseq; my $res_name_num = $resname."-".$resseq; $res_name_num .= '.'.$icode if $icode; if ($res_name_num ne $residue_name) { # new residue $residue = Bio::Structure::Residue->new; $struc->add_residue($chain,$residue); $residue->id($res_name_num); $residue_name = $res_name_num; $atom_name = ""; # only needed inside a residue } # get out of here if we don't want the atom objects if ($noatom) { $_ = undef; next; } # alternative location: only take first one if ( $altloc && ($altloc =~ /\S+/) && ($atomname eq $atom_name) ) { $_ = undef; # trigger reading next line next; } if (/^(ATOM |HETATM)/) { # ATOM / HETATM $atom_name = $atomname; $atom = Bio::Structure::Atom->new; $struc->add_atom($residue,$atom); $atom->id($atomname); $atom->pdb_atomname($pdb_atomname); # store away PDB atomname for writing out $atom->serial($serial); $atom->icode($icode); $atom->x($x); $atom->y($y); $atom->z($z); $atom->occupancy($occupancy); $atom->tempfactor($tempfactor); $atom->segID($segID); # deprecated but used by people if (! $old ) { $atom->element($element); $atom->charge($charge); } } else { # SIGATM my $sigx = $x; my $sigy = $y; my $sigz = $z; my $sigocc = $occupancy; my $sigtemp = $tempfactor; if ($atom_name ne $atomname) { # something wrong with PDB file $self->throw("A SIGATM record should have the same $atomname as the previous record $atom_name\n"); } $atom->sigx($sigx); $atom->sigy($sigy); $atom->sigz($sigz); $atom->sigocc($sigocc); $atom->sigtemp($sigtemp); } } # ATOM|HETARM|SIGATM # ANISOU | SIGUIJ lines if (/^(ANISOU|SIGUIJ)/) { if ($noatom) { $_ = undef; next; } my @line_elements = unpack $anisou_unpack, $_; for my $k (0 .. $#line_elements) { $line_elements[$k] =~ s/^\s+//; # remove leading space $line_elements[$k] =~ s/\s+$//; # remove trailing space $line_elements[$k] = undef if ($line_elements[$k] =~ /^\s*$/); } my ($serial, $atomname, $altloc, $resname, $chainID, $resseq, $icode, $u11,$u22, $u33, $u12, $u13, $u23, $segID, $element, $charge) = @line_elements; $self->debug("read_PDB_coor: parsing ANISOU record: $serial $atomname\n"); if ( $altloc && ($altloc =~ /\S+/) && ($atomname eq $atom_name) ) { $_ = undef; next; } if (/^ANISOU/) { if ($atom_name ne $atomname) { # something wrong with PDB file $self->throw("A ANISOU record should have the same $atomname as the previous record $atom_name\n"); } $atom->aniso("u11",$u11); $atom->aniso("u22",$u22); $atom->aniso("u33",$u33); $atom->aniso("u12",$u12); $atom->aniso("u13",$u13); $atom->aniso("u23",$u23); } else { # SIGUIJ if ($atom_name ne $atomname) { # something wrong with PDB file $self->throw("A SIGUIJ record should have the same $atomname as the previous record $atom_name\n"); } # could use different variable names, but hey ... $atom->aniso("sigu11",$u11); $atom->aniso("sigu22",$u22); $atom->aniso("sigu33",$u33); $atom->aniso("sigu12",$u12); $atom->aniso("sigu13",$u13); $atom->aniso("sigu23",$u23); } } # ANISOU | SIGUIJ if (/^TER /) { $_ = undef; next; } if (/^ENDMDL/) { $_ = $self->_readline; last; } if (/^(CONECT|MASTER)/) { # get out of here # current line is OK last; } $_ = undef; } # while $$buffer = $_; return $model; } # _read_PDB_coordinate_section sub _write_PDB_simple_record { my ($self, @args) = @_; my ($name, $cont , $annotation, $rol, $string) = $self->_rearrange([qw( NAME CONT ANNOTATION ROL STRING )], @args); if (defined $string && defined $annotation) { $self->throw("you can only supply one of -annoation or -string"); } my ($output_string, $ann_string, $t_string); my ($rol_begin, $rol_end) = $rol =~ /^(\d+)-(\d+)$/; my $rol_length = $rol_end - $rol_begin +1; if ($string) { if (length $string > $rol_length) { # we might need to split $string in multiple lines while (length $string > $rol_length) { # other option might be to go for a bunch of substr's my @c = split//,$string; my $t = $rol_length; # index into @c while ($c[$t] ne " ") { # find first space, going backwards $self->debug("c[t]: $c[$t] $t\n"); $t--; if ($t == 0) { $self->throw("Found no space for $string\n"); } } $self->debug("t: $t rol_length: $rol_length\n"); $ann_string .= substr($string, 0, $t); $self->debug("ann_string: $ann_string\n"); $ann_string .= " " x ($rol_length - $t ); $string = substr($string, $t+1); $string =~ s/^\s+//; $self->debug("ann_string: $ann_string~~\nstring: $string~~\n"); } $ann_string .= $string; } else { $ann_string = $string; } } else { $ann_string = $annotation->as_text; $ann_string =~ s/^Value: //; } # ann_string contains the thing to write out, writing out happens below my $ann_length = length $ann_string; $self->debug("ann_string: $ann_string\n"); if ($cont) { my ($c_begin, $c_end) = $cont =~ /^(\d+)-(\d+)$/; if ( $ann_length > $rol_length ) { # we need to continuation lines my $first_line = 1; my $cont_number = 2; my $out_line; my $num_pos = $rol_length; my $i = 0; while( $i < $ann_length ) { $t_string = substr($ann_string, $i, $num_pos); $self->debug("t_string: $t_string~~$i $num_pos\n"); if ($first_line) { $out_line = $name . " " x ($rol_begin - $c_begin) . $t_string; $out_line .= " " x (80 - length($out_line) ) . "\n"; $first_line = 0; $output_string = $out_line; $i += $num_pos; # first do counter if ($rol_begin - $c_end == 1) { # next line one character less $num_pos--; } } else { $out_line = $name . sprintf("%2d",$cont_number); # a space after continuation number if ($rol_begin - $c_end == 1) { # one space after cont number $out_line .= " "; $out_line .= $t_string; } else { $out_line .= " " x ($rol_begin - $c_end - 1) . $t_string; } $out_line .= " " x (80 -length($out_line) ) . "\n"; $cont_number++; $output_string .= $out_line; $i += $num_pos; } } } else { # no continuation my $spaces = $rol_begin - $c_begin; # number of spaces need to insert $output_string = $name . " " x $spaces . $ann_string; $output_string .= " " x (80 - length($output_string) ); } } else { # no contintuation lines if ($ann_length < $rol_length) { $output_string = $name . $ann_string; $output_string .= " " x (80 - length($output_string) ); } else { for (my $i = 0; $i < $ann_length; $i += $rol_length) { my $out_line; $t_string = substr($ann_string, $i, $rol_length); $out_line = $name . $t_string; $out_line .= " " x (80 -length($out_line) ) . "\n"; $output_string .= $out_line; } } } $output_string =~ s/\n$//; # remove trailing newline $self->_print("$output_string\n"); } sub _write_PDB_remark_record { my ($self, $struc, $remark_num) = @_; my ($ann) = $struc->annotation->get_Annotations("remark_$remark_num"); my $name = sprintf("REMARK %3d ",$remark_num); $self->_write_PDB_simple_record(-name => $name, -annotation => $ann, -rol => "12-70"); } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Structure/SecStr���������������������������������������������������������������000755��000766��000024�� 0�13155576320� 17272� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Structure/SecStr/DSSP����������������������������������������������������������000755��000766��000024�� 0�13155576320� 20043� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Structure/SecStr/DSSP/Res.pm���������������������������������������������������000444��000766��000024�� 106466�13155576320� 21344� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# $Header$ # # bioperl module for Bio::Structure::SecStr::DSSP::Res.pm # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ed Green <ed@compbio.berkeley.edu> # # Copyright Univ. of California # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Structure::SecStr::DSSP::Res - Module for parsing/accessing dssp output =head1 SYNOPSIS my $dssp_obj = Bio::Structure::SecStr::DSSP::Res->new('-file'=>'filename.dssp'); # or my $dssp_obj = Bio::Structure::SecStr::DSSP::Res->new('-fh'=>\*STDOUT); # get DSSP defined Secondary Structure for residue 20 $sec_str = $dssp_obj->resSecStr( 20 ); # get dssp defined sec. structure summary for PDB residue # 10 of chain A $sec_str = $dssp_obj->resSecStrSum( '10:A' ); =head1 DESCRIPTION DSSP::Res is a module for objectifying DSSP output. Methods are then available for extracting all the information within the output file and convenient subsets of it. The principal purpose of DSSP is to determine secondary structural elements of a given structure. ( Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577-637. ) The DSSP program is available from: http://www.cmbi.kun.nl/swift/dssp This information is available on a per residue basis ( see resSecStr and resSecStrSum methods ) or on a per chain basis ( see secBounds method ). resSecStr() & secBounds() return one of the following: 'H' = alpha helix 'B' = residue in isolated beta-bridge 'E' = extended strand, participates in beta ladder 'G' = 3-helix (3/10 helix) 'I' = 5 helix (pi helix) 'T' = hydrogen bonded turn 'S' = bend '' = no assignment A more general classification is returned using the resSecStrSum() method. The purpose of this is to have a method for DSSP and STRIDE derived output whose range is the same. Its output is one of the following: 'H' = helix ( => 'H', 'G', or 'I' from above ) 'B' = beta ( => 'B' or 'E' from above ) 'T' = turn ( => 'T' or 'S' from above ) ' ' = no assignment ( => ' ' from above ) The methods are roughly divided into 3 sections: 1. Global features of this structure (PDB ID, total surface area, etc.). These methods do not require an argument. 2. Residue specific features ( amino acid, secondary structure, solvent exposed surface area, etc. ). These methods do require an argument. The argument is supposed to uniquely identify a residue described within the structure. It can be of any of the following forms: ('#A:B') or ( #, 'A', 'B' ) || | || - Chain ID (blank for single chain) |--- Insertion code for this residue. Blank for most residues. |--- Numeric portion of residue ID. (#) | --- Numeric portion of residue ID. If there is only one chain and it has no ID AND there is no residue with an insertion code at this number, then this can uniquely specify a residue. ('#:C') or ( #, 'C' ) | | | -Chain ID ---Numeric portion of residue ID. If a residue is incompletely specified then the first residue that fits the arguments is returned. For example, if 19 is the argument and there are three chains, A, B, and C with a residue whose number is 19, then 19:A will be returned (assuming its listed first). Since neither DSSP nor STRIDE correctly handle alt-loc codes, they are not supported by these modules. 3. Value-added methods. Return values are not verbatem strings parsed from DSSP or STRIDE output. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ed Green Email ed@compbio.berkeley.edu =head1 APPENDIX The rest of the documentation details each method. Internal methods are preceded with a _ =cut package Bio::Structure::SecStr::DSSP::Res; use strict; use Bio::Root::IO; use Bio::PrimarySeq; use base qw(Bio::Root::Root); # Would be a class variable if Perl had them #attribute begin col # columns our %lookUp = ( 'pdb_resnum' => [ 5, 5 ], 'insertionco' => [ 10, 1 ], 'pdb_chain' => [ 11, 1 ], 'amino_acid' => [ 13, 1 ], 'term_sig' => [ 14, 1 ], 'ss_summary' => [ 16, 1 ], '3tph' => [ 18, 1 ], '4tph' => [ 19, 1 ], '5tph' => [ 20, 1 ], 'geo_bend' => [ 21, 1 ], 'chirality' => [ 22, 1 ], 'beta_br1la' => [ 23, 1 ], 'beta_br2la' => [ 24, 1 ], 'bb_part1nu' => [ 25, 4 ], 'bb_part2nu' => [ 29, 4 ], 'betash_lab' => [ 33, 1 ], 'solv_acces' => [ 34, 4 ], 'hb1_nh_o_p' => [ 39, 6 ], 'hb1_nh_o_e' => [ 46, 4 ], 'hb1_o_hn_p' => [ 50, 6 ], 'hb1_o_hn_e' => [ 57, 4 ], 'hb2_nh_o_p' => [ 61, 6 ], 'hb2_nh_o_e' => [ 68, 4 ], 'hb2_o_hn_p' => [ 72, 6 ], 'hb2_o_hn_e' => [ 79, 4 ], 'tco' => [ 85, 6 ], 'kappa' => [ 91, 6 ], 'alpha' => [ 97, 6 ], 'phi' => [ 103, 6 ], 'psi' => [ 109, 6 ], 'x_ca' => [ 115, 7 ], 'y_ca' => [ 122, 7 ], 'z_ca' => [ 129, 7 ] ); =head1 CONSTRUCTOR =cut =head2 new Title : new Usage : makes new object of this class Function : Constructor Example : $dssp_obj = Bio::DSSP:Res->new( filename or FILEHANDLE ) Returns : object (ref) Args : filename ( must be proper DSSP output file ) =cut sub new { my ( $class, @args ) = @_; my $self = $class->SUPER::new( @args ); my $io = Bio::Root::IO->new( @args ); $self->_parse( $io->_fh() ); $io->close(); return $self; } =head1 ACCESSORS =cut # GLOBAL FEATURES / INFO / STATS =head2 totSurfArea Title : totSurfArea Usage : returns total accessible surface area in square And. Function : Example : $surArea = $dssp_obj->totSurfArea(); Returns : scalar Args : none =cut sub totSurfArea { my $self = shift; return $self->{ 'Head' }->{ 'ProAccSurf' }; } =head2 numResidues Title : numResidues Usage : returns the total number of residues in all chains or just the specified chain if a chain is specified Function : Example : $num_res = $dssp_obj->numResidues(); Returns : scalar int Args : none =cut sub numResidues { my $self = shift; my $chain = shift; if ( !( $chain ) ) { return $self->{'Head'}->{'TotNumRes'}; } else { my ( $num_res, $cont_seg ); my $cont_seg_pnt = $self->_contSegs(); foreach $cont_seg ( @{ $cont_seg_pnt } ) { if ( $chain eq $cont_seg->[ 2 ] ) { # this segment is part of the chain we want $num_res += ( $self->_toDsspKey( $cont_seg->[ 1 ] ) - $self->_toDsspKey( $cont_seg->[ 0 ] ) + 1 ); # this works because we know the # the region between the start # and end of a dssp key is # continuous } } return $num_res; } } # STRAIGHT FROM PDB ENTRY =head2 pdbID Title : pdbID Usage : returns pdb identifier ( 1FJM, e.g.) Function : Example : $pdb_id = $dssp_obj->pdbID(); Returns : scalar string Args : none =cut sub pdbID { my $self = shift; return $self->{'Head'}->{'PDB'}; } =head2 pdbAuthor Title : pdbAuthor Usage : returns author field Function : Example : $auth = $dssp_obj->pdbAuthor() Returns : scalar string Args : none =cut sub pdbAuthor { my $self = shift; return $self->{'Head'}->{'AUTHOR'}; } =head2 pdbCompound Title : pdbCompound Usage : returns pdbCompound given in PDB file Function : Example : $cmpd = $dssp_obj->pdbCompound(); Returns : scalar string Args : none =cut sub pdbCompound { my $self = shift; return $self->{'Head'}->{'COMPND'}; } =head2 pdbDate Title : pdbDate Usage : returns date given in PDB file Function : Example : $pdb_date = $dssp_obj->pdbDate(); Returns : scalar Args : none =cut sub pdbDate { my $self = shift; return $self->{'Head'}->{'DATE'}; } =head2 pdbHeader Title : pdbHeader Usage : returns header info from PDB file Function : Example : $header = $dssp_obj->pdbHeader(); Returns : scalar Args : none =cut sub pdbHeader { my $self = shift; return $self->{'Head'}->{'HEADER'}; } =head2 pdbSource Title : pdbSource Usage : returns pdbSource information from PDBSOURCE line Function : Example : $pdbSource = $dssp_obj->pdbSource(); Returns : scalar Args : none =cut sub pdbSource { my $self = shift; return $self->{'Head'}->{'SOURCE'}; } # RESIDUE SPECIFIC ACCESSORS =head2 resAA Title : resAA Usage : fetches the 1 char amino acid code, given an id Function : Example : $aa = $dssp_obj->resAA( '20:A' ); # pdb id as arg Returns : 1 character scalar string Args : RESIDUE_ID =cut sub resAA { my $self = shift; my @args = @_; my $dssp_key = $self->_toDsspKey( @args ); return $self->{ 'Res' }->[ $dssp_key ]->{ 'amino_acid' }; } =head2 resPhi Title : resPhi Usage : returns phi angle of a single residue Function : accessor Example : $phi = $dssp_obj->resPhi( RESIDUE_ID ) Returns : scalar Args : RESIDUE_ID =cut sub resPhi { my $self = shift; my @args = @_; my $dssp_key = $self->_toDsspKey( @args ); return $self->{ 'Res' }->[ $dssp_key ]->{ 'phi' }; } =head2 resPsi Title : resPsi Usage : returns psi angle of a single residue Function : accessor Example : $psi = $dssp_obj->resPsi( RESIDUE_ID ) Returns : scalar Args : RESIDUE_ID =cut sub resPsi { my $self = shift; my @args = @_; my $dssp_key = $self->_toDsspKey( @args ); return $self->{ 'Res' }->[ $dssp_key ]->{ 'psi' }; } =head2 resSolvAcc Title : resSolvAcc Usage : returns solvent exposed area of this residue in square Andstroms Function : Example : $solv_acc = $dssp_obj->resSolvAcc( RESIDUE_ID ); Returns : scalar Args : RESIDUE_ID =cut sub resSolvAcc { my $self = shift; my @args = @_; my $dssp_key = $self->_toDsspKey( @args ); return $self->{ 'Res' }->[ $dssp_key ]->{ 'solv_acces' }; } =head2 resSurfArea Title : resSurfArea Usage : returns solvent exposed area of this residue in square Andstroms Function : Example : $solv_acc = $dssp_obj->resSurfArea( RESIDUE_ID ); Returns : scalar Args : RESIDUE_ID =cut sub resSurfArea { my $self = shift; my @args = @_; my $dssp_key = $self->_toDsspKey( @args ); return $self->{ 'Res' }->[ $dssp_key ]->{ 'solv_acces' }; } =head2 resSecStr Title : resSecStr Usage : $ss = $dssp_obj->resSecStr( RESIDUE_ID ); Function : returns the DSSP secondary structural designation of this residue Example : Returns : a character ( 'B', 'E', 'G', 'H', 'I', 'S', 'T', or ' ' ) Args : RESIDUE_ID NOTE : The range of this method differs from that of the resSecStr method in the STRIDE SecStr parser. That is because of the slightly different format for STRIDE and DSSP output. The resSecStrSum method exists to map these different ranges onto an identical range. =cut sub resSecStr { my $self = shift; my @args = @_; my $dssp_key = $self->_toDsspKey( @args ); my $ss_char = $self->{ 'Res' }->[ $dssp_key ]->{ 'ss_summary' }; return $ss_char if $ss_char; return ' '; } =head2 resSecStrSum Title : resSecStrSum Usage : $ss = $dssp_obj->resSecStrSum( $id ); Function : returns what secondary structure group this residue belongs to. One of: 'H': helix ( H, G, or I ) 'B': beta ( B or E ) 'T': turn ( T or S ) ' ': none ( ' ' ) This method is similar to resSecStr, but the information it returns is less specific. Example : Returns : a character ( 'H', 'B', 'T', or ' ' ) Args : dssp residue number of pdb residue identifier =cut sub resSecStrSum { my $self = shift; my @args = @_; my $dssp_key = $self->_toDsspKey( @args ); my $ss_char = $self->{ 'Res' }->[ $dssp_key ]->{ 'ss_summary' }; if ( $ss_char eq 'H' || $ss_char eq 'G' || $ss_char eq 'I' ) { return 'H'; } if ( $ss_char eq ' ' || !( $ss_char ) ) { return ' '; } if ( $ss_char eq 'B' || $ss_char eq 'E' ) { return 'B'; } else { return 'T'; } } # DSSP SPECIFIC =head2 hBonds Title : hBonds Usage : returns number of 14 different types of H Bonds Function : Example : $hb = $dssp_obj->hBonds Returns : pointer to 14 element array of ints Args : none NOTE : The different type of H-Bonds reported are, in order: TYPE O(I)-->H-N(J) IN PARALLEL BRIDGES IN ANTIPARALLEL BRIDGES TYPE O(I)-->H-N(I-5) TYPE O(I)-->H-N(I-4) TYPE O(I)-->H-N(I-3) TYPE O(I)-->H-N(I-2) TYPE O(I)-->H-N(I-1) TYPE O(I)-->H-N(I+0) TYPE O(I)-->H-N(I+1) TYPE O(I)-->H-N(I+2) TYPE O(I)-->H-N(I+3) TYPE O(I)-->H-N(I+4) TYPE O(I)-->H-N(I+5) =cut sub hBonds { my $self = shift; return $self->{ 'HBond'}; } =head2 numSSBr Title : numSSBr Usage : returns info about number of SS-bridges Function : Example : @SS_br = $dssp_obj->numSSbr(); Returns : 3 element scalar int array Args : none =cut sub numSSBr { my $self = shift; return ( $self->{'Head'}->{'TotSSBr'}, $self->{'Head'}->{'TotIaSSBr'}, $self->{'Head'}->{'TotIeSSBr'} ); } =head2 resHB_O_HN Title : resHB_O_HN Usage : returns pointer to a 4 element array consisting of: relative position of binding partner #1, energy of that bond (kcal/mol), relative positionof binding partner #2, energy of that bond (kcal/mol). If the bond is not bifurcated, the second bond is reported as 0, 0.0 Function : accessor Example : $oBonds_ptr = $dssp_obj->resHB_O_HN( RESIDUE_ID ) Returns : pointer to 4 element array Args : RESIDUE_ID =cut sub resHB_O_HN { my $self = shift; my @args = @_; my $dssp_key = $self->_toDsspKey( @args ); return ( $self->{ 'Res' }->[ $dssp_key ]->{ 'hb1_o_hn_p' }, $self->{ 'Res' }->[ $dssp_key ]->{ 'hb1_o_hn_e' }, $self->{ 'Res' }->[ $dssp_key ]->{ 'hb2_o_hn_p' }, $self->{ 'Res' }->[ $dssp_key ]->{ 'hb2_o_hn_e' } ); } =head2 resHB_NH_O Title : resHB_NH_O Usage : returns pointer to a 4 element array consisting of: relative position of binding partner #1, energy of that bond (kcal/mol), relative positionof binding partner #2, energy of that bond (kcal/mol). If the bond is not bifurcated, the second bond is reported as 0, 0.0 Function : accessor Example : $nhBonds_ptr = $dssp_obj->resHB_NH_O( RESIDUE_ID ) Returns : pointer to 4 element array Args : RESIDUE_ID =cut sub resHB_NH_O { my $self = shift; my @args = @_; my $dssp_key = $self->_toDsspKey( @args ); return ( $self->{ 'Res' }->[ $dssp_key ]->{ 'hb1_nh_o_p' }, $self->{ 'Res' }->[ $dssp_key ]->{ 'hb1_nh_o_e' }, $self->{ 'Res' }->[ $dssp_key ]->{ 'hb2_nh_o_p' }, $self->{ 'Res' }->[ $dssp_key ]->{ 'hb2_nh_o_e' } ); } =head2 resTco Title : resTco Usage : returns tco angle around this residue Function : accessor Example : resTco = $dssp_obj->resTco( RESIDUE_ID ) Returns : scalar Args : RESIDUE_ID =cut sub resTco { my $self = shift; my @args = @_; my $dssp_key = $self->_toDsspKey( @args ); return $self->{ 'Res' }->[ $dssp_key ]->{ 'tco' }; } =head2 resKappa Title : resKappa Usage : returns kappa angle around this residue Function : accessor Example : $kappa = $dssp_obj->resKappa( RESIDUE_ID ) Returns : scalar Args : RESIDUE_ID ( dssp or PDB ) =cut sub resKappa { my $self = shift; my @args = @_; my $dssp_key = $self->_toDsspKey( @args ); return $self->{ 'Res' }->[ $dssp_key ]->{ 'kappa' }; } =head2 resAlpha Title : resAlpha Usage : returns alpha angle around this residue Function : accessor Example : $alpha = $dssp_obj->resAlpha( RESIDUE_ID ) Returns : scalar Args : RESIDUE_ID ( dssp or PDB ) =cut sub resAlpha { my $self = shift; my @args = @_; my $dssp_key = $self->_toDsspKey( @args ); return $self->{ 'Res' }->[ $dssp_key ]->{ 'alpha' }; } # VALUE ADDED METHODS (NOT JUST PARSE/REPORT) =head2 secBounds Title : secBounds Usage : gets residue ids of boundary residues in each contiguous secondary structural element of specified chain Function : returns pointer to array of 3 element arrays. First two elements are the PDB IDs of the start and end points, respectively and inclusively. The last element is the DSSP secondary structural assignment code, i.e. one of : ('B', 'E', 'G', 'H', 'I', 'S', 'T', or ' ') Example : $ss_elements_pts = $dssp_obj->secBounds( 'A' ); Returns : pointer to array of arrays Args : chain id ( 'A', for example ). No arg => no chain id =cut sub secBounds { my $self = shift; my $chain = shift; my %sec_bounds; $chain = '-' if ( !( $chain ) || $chain eq ' ' || $chain eq '-' ); # if we've memoized this chain, use that if ( $self->{ 'SecBounds' } ) { # check to make sure chain is valid if ( !( $self->{ 'SecBounds' }->{ $chain } ) ) { $self->throw( "No such chain: $chain\n" ); } return $self->{ 'SecBounds' }->{ $chain }; } my ( $cur_element, $i, $cur_chain, $beg, ); #initialize $cur_element = $self->{ 'Res' }->[ 1 ]->{ 'ss_summary' }; $beg = 1; for ( $i = 2; $i <= $self->_numResLines() - 1; $i++ ) { if ( $self->{ 'Res' }->[ $i ]->{ 'amino_acid' } eq '!' ) { # element is terminated by a chain discontinuity push( @{ $sec_bounds{ $self->_pdbChain( $beg ) } }, [ $self->_toPdbId( $beg ), $self->_toPdbId( $i - 1 ), $cur_element ] ); $i++; $beg = $i; $cur_element = $self->{ 'Res' }->[ $i ]->{ 'ss_summary' }; } elsif ( $self->{ 'Res' }->[ $i ]->{ 'ss_summary' } ne $cur_element ) { # element is terminated by beginning of a new element push( @{ $sec_bounds{ $self->_pdbChain( $beg ) } }, [ $self->_toPdbId( $beg ), $self->_toPdbId( $i - 1 ), $cur_element ] ); $beg = $i; $cur_element = $self->{ 'Res' }->[ $i ]->{ 'ss_summary' }; } } #last residue if ( $self->{ 'Res' }->[ $i ]->{ 'ss_summary' } eq $cur_element ) { push( @{ $sec_bounds{ $self->_pdbChain( $beg ) } }, [ $self->_toPdbId( $beg ), $self->_toPdbId( $i ), $cur_element ] ); } else { push( @{ $sec_bounds{ $self->_pdbChain( $beg ) } }, [ $self->_toPdbId( $beg ), $self->_toPdbId( $i - 1 ), $cur_element ] ); push( @{ $sec_bounds{ $self->_pdbChain( $i ) } }, [ $self->_toPdbId( $i ), $self->_toPdbId( $i ), $self->{ 'Res' }->[ $i ]->{ 'ss_summary' } ] ); } $self->{ 'SecBounds' } = \%sec_bounds; # check to make sure chain is valid if ( !( $self->{ 'SecBounds' }->{ $chain } ) ) { $self->throw( "No such chain: $chain\n" ); } return $self->{ 'SecBounds' }->{ $chain }; } =head2 chains Title : chains Usage : returns pointer to array of chain I.D.s (characters) Function : Example : $chains_pnt = $dssp_obj->chains(); Returns : array of characters, one of which may be ' ' Args : none =cut sub chains { my $self = shift; my $cont_segs = $self->_contSegs(); my %chains; my $seg; foreach $seg ( @{ $cont_segs } ) { $chains{ $seg->[ 2 ] } = 1; } my @chains = keys( %chains ); return \@chains; } =head2 residues Title : residues Usage : returns array of residue identifiers for all residues in the output file, or in a specific chain Function : Example : @residues_ids = $dssp_obj->residues() Returns : array of residue identifiers Args : if none => returns residue ids of all residues of all chains (in order); if chain id is given, returns just the residue ids of residues in that chain =cut # Can't use the standard interface for getting the amino acid, # pdb_resnum, etc. in this method because we don't *know* the residue # indentifiers - we are building a list of them. sub residues { my $self = shift; my $chain = shift; my @residues; my $num_res = $self->_numResLines(); my $aa; for ( my $i = 1; $i <= $num_res; $i++ ) { # find what character was in the slot for tha amino acid code, # if it's a '!' we know this is not a *real* amino acid, it's # a chain discontinuity marker $aa = $self->{ 'Res' }->[ $i ]->{ 'amino_acid' }; if ( $aa ne '!' ) { if ( !$chain || $chain eq $self->{ 'Res' }->[ $i ]->{ 'pdb_chain' } ) { push( @residues, $self->{ 'Res' }->[ $i ]->{ 'pdb_resnum' }. $self->{ 'Res' }->[ $i ]->{ 'insertionco' }. ":". $self->{ 'Res' }->[ $i ]->{ 'pdb_chain' } ); } } } return @residues; } =head2 getSeq Title : getSeq Usage : returns a Bio::PrimarySeq object which represents a good guess at the sequence of the given chain Function : For most chains of most entries, the sequence returned by this method will be very good. However, it is inherently unsafe to rely on DSSP to extract sequence information about a PDB entry. More reliable information can be obtained from the PDB entry itself. Example : $pso = $dssp_obj->getSeq( 'A' ); Returns : (pointer to) a PrimarySeq object Args : Chain identifier. If none given, ' ' is assumed. If no ' ' chain, the first chain is used. =cut sub getSeq { my $self = shift; my $chain = shift; my ( $pot_chain, $seq, $frag_num, $frag, $curPdbNum, $lastPdbNum, $gap_len, $i, $id, ); my @frags; if ( !( $chain ) ) { $chain = ' '; } if ( $self->{ 'Seq' }->{ $chain } ) { return $self->{ 'Seq' }->{ $chain }; } my $contSegs_pnt = $self->_contSegs(); # load up specified chain foreach $pot_chain ( @{ $contSegs_pnt } ) { if ( $pot_chain->[ 2 ] eq $chain ) { push( @frags, $pot_chain ); } } # if that didn't work, just get the first one if ( !( @frags ) ) { $chain = $contSegs_pnt->[ 0 ]->[ 2 ]; foreach $pot_chain ( @{ $contSegs_pnt } ) { if ( $pot_chain->[ 2 ] eq $chain ) { push( @frags, $pot_chain ); } } } # now build the sequence string $seq = ""; $frag_num = 0; foreach $frag ( @frags ) { $frag_num++; if ( $frag_num > 1 ) { # we need to put in some gap seq $curPdbNum = $self->_pdbNum( $frag->[ 0 ] ); $gap_len = $curPdbNum - $lastPdbNum - 1; if ( $gap_len > 0 ) { $seq .= 'u' x $gap_len; } else { $seq .= 'u'; } } for ( $i = $frag->[ 0 ]; $i <= $frag->[ 1 ]; $i++ ) { $seq .= $self->_resAA( $i ); } $lastPdbNum = $self->_pdbNum( $i - 1 ); } $id = $self->pdbID(); $id .= ":$chain"; $self->{ 'Seq' }->{ $chain } = Bio::PrimarySeq->new ( -seq => $seq, -id => $id, -moltype => 'protein' ); return $self->{ 'Seq' }->{ $chain }; } =head1 INTERNAL METHODS =cut =head2 _pdbChain Title : _pdbChain Usage : returns the pdb chain id of given residue Function : Example : $chain_id = $dssp_obj->pdbChain( DSSP_KEY ); Returns : scalar Args : DSSP_KEY ( dssp or pdb ) =cut sub _pdbChain { my $self = shift; my $dssp_key = shift; return $self->{ 'Res' }->[ $dssp_key ]->{ 'pdb_chain' }; } =head2 _resAA Title : _resAA Usage : fetches the 1 char amino acid code, given a dssp id Function : Example : $aa = $dssp_obj->_resAA( dssp_id ); Returns : 1 character scalar string Args : dssp_id =cut sub _resAA { my $self = shift; my $dssp_key = shift; return $self->{ 'Res' }->[ $dssp_key ]->{ 'amino_acid' }; } =head2 _pdbNum Title : _pdbNum Usage : fetches the numeric portion of the identifier for a given residue as reported by the pdb entry. Note, this DOES NOT uniquely specify a residue. There may be an insertion code and/or chain identifier differences. Function : Example : $pdbNum = $self->_pdbNum( DSSP_ID ); Returns : a scalar Args : DSSP_ID =cut sub _pdbNum { my $self = shift; my $dssp_key = shift; return $self->{ 'Res' }->[ $dssp_key ]->{ 'pdb_resnum' }; } =head2 _pdbInsCo Title : _pdbInsCo Usage : fetches the Insertion Code for this residue, if it has one. Function : Example : $pdbNum = $self->_pdbInsCo( DSSP_ID ); Returns : a scalar Args : DSSP_ID =cut sub _pdbInsCo { my $self = shift; my $dssp_key = shift; return $self->{ 'Res' }->[ $dssp_key ]->{ 'insertionco' }; } =head2 _toPdbId Title : _toPdbId Usage : Takes a dssp key and builds the corresponding PDB identifier string Function : Example : $pdbId = $self->_toPdbId( DSSP_ID ); Returns : scalar Args : DSSP_ID =cut sub _toPdbId { my $self = shift; my $dssp_key = shift; my $pdbId = ( $self->_pdbNum( $dssp_key ). $self->_pdbInsCo( $dssp_key ) ); my $chain = $self->_pdbChain( $dssp_key ); $pdbId = "$pdbId:$chain" if $chain; return $pdbId; } =head2 _contSegs Title : _contSegs Usage : find the endpoints of continuous regions of this structure Function : returns pointer to array of 3 element array. Elements are the dssp keys of the start and end points of each continuous element and its PDB chain id (may be blank). Note that it is common to have several continuous elements with the same chain id. This occurs when an internal region is disordered and no structural information is available. Example : $cont_seg_ptr = $dssp_obj->_contSegs(); Returns : pointer to array of arrays Args : none =cut sub _contSegs { my $self = shift; if ( $self->{ 'contSegs' } ) { return $self->{ 'contSegs' }; } else { # first time, so make contSegs my ( $cur_chain, $i, $beg ); my @contSegs; #initialize $cur_chain = $self->_pdbChain( 1 ); $beg = 1; #internal residues for ( $i = 2; $i <= $self->_numResLines() - 1; $i++ ) { if ( $self->{ 'Res' }->[ $i ]->{ 'amino_acid' } eq '!' ) { push( @contSegs, [ $beg, $i - 1, $cur_chain ] ); $beg = $i + 1; $cur_chain = $self->_pdbChain( $i + 1 ); } } # last residue must be the end of a chain push( @contSegs, [ $beg, $i, $cur_chain ] ); $self->{ 'contSegs' } = \@contSegs; return $self->{ 'contSegs' }; } } =head2 _numResLines Title : _numResLines Usage : returns the total number of residue lines in this dssp file. This number is DIFFERENT than the number of residues in the pdb file because dssp has chain termination and chain discontinuity 'residues'. Function : Example : $num_res = $dssp_obj->_numResLines(); Returns : scalar int Args : none =cut sub _numResLines { my $self = shift; return ( $#{$self->{ 'Res' }} ); } =head2 _toDsspKey Title : _toDsspKey Usage : returns the unique dssp integer key given a pdb residue id. All accessor methods require (internally) the dssp key. This method is very useful in converting pdb keys to dssp keys so the accessors can accept pdb keys as argument. PDB Residue IDs are inherently problematic since they have multiple parts of overlapping function and ill-defined or observed convention in form. Input can be in any of the formats described in the DESCRIPTION section above. Function : Example : $dssp_id = $dssp_obj->_pdbKeyToDsspKey( '10B:A' ) Returns : scalar int Args : pdb residue identifier: num[insertion code]:[chain] =cut sub _toDsspKey { # Consider adding lookup table for 'common' name (like 20:A) for # fast access. Could be built during parse of input. my $self = shift; my ( $key_num, $chain_id, $ins_code ) = @_; if ( ! $chain_id) { # parse the lone argument ( $key_num, $chain_id, $ins_code ) = $key_num =~ m/^(\-?[0-9]+) # PDB coords can be negative ([a-zA-Z]?) (?::([a-zA-Z\-]))?$/x # missing chains are '-' ? ( $1, $3, $2 ) : $self->throw("Could not derive PDB key $key_num"); } # Now find the residue which fits this description. Linear search is # probably not the best way to do this, but oh well... for ( my $i = 1; $i <= $self->_numResLines(); $i++ ) { unless ( ($self->{'Res'}->[$i]->{'term_sig'} eq '*') || ($self->{'Res'}->[$i]->{'amino_acid'} eq '!') ) { # chain break 'residue', doesn't match anything if ( $key_num == $self->{'Res'}->[$i]->{'pdb_resnum'} ) { if ( $chain_id ) { # if a chain was specified if ( $chain_id eq $self->{'Res'}->[$i]->{'pdb_chain'} ) { # and it's the right one if ( $ins_code ) { # if insertion code was specified if ( $ins_code eq $self->{'Res'}->[$i]->{'insertionco'} ) { # and it's the right one return $i; } } elsif ( $self->{'Res'}->[$i]->{'insertionco'} eq '' ) { # no isertion code specified, but need to check that the located residue doesn't have an insertion code E.g. pdb1aye fails on this return $i; } } } else { # no chain was specified return $i; } } } } $self->throw( "PDB key not found." ); } =head2 _parse Title : _parse Usage : parses dssp output Function : Example : used by the constructor Returns : Args : input source ( handled by Bio::Root:IO ) =cut sub _parse { my $self = shift; my $file = shift; my $cur; my $current_chain; my ( @elements, @hbond ); my ( %head, %his, ); my $element; my $res_num; $cur = <$file>; unless ( $cur =~ /^==== Secondary Structure Definition/ ) { $self->throw( "Not dssp output" ); return; } # REFERENCE line (always there) $cur = <$file>; ( $element ) = ( $cur =~ /^REFERENCE\s+(.+?)\s+\./ ); $head{ 'REFERENCE' } = $element; $cur = <$file>; # Check for HEADER line (not always there) if ( $cur =~ /^HEADER\s/ ) { @elements = split( /\s+/, $cur ); pop( @elements ); # take off that annoying period $head{ 'PDB' } = pop( @elements ); $head{ 'DATE' } = pop( @elements ); # now, everything else is "header" except for the word # HEADER shift( @elements ); $element = shift( @elements ); while ( @elements ) { $element = $element." ".shift( @elements ); } $head{ 'HEADER' } = $element; $cur = <$file>; } # Check for COMPND line (not always there) if ( $cur =~ /^COMPND\s/ ) { ($element) = ( $cur =~ /^COMPND\s+(.+?)\s+\./ ); $head{ 'COMPND' } = $element; $cur = <$file>; } # Check for SOURCE or PDBSOURCE line (not always there) if ( $cur =~ /^PDBSOURCE\s/ ) { ($element) = ( $cur =~ /^PDBSOURCE\s+(.+?)\s+\./ ); $head{ 'SOURCE' } = $element; $cur = <$file>; } elsif ( $cur =~ /^SOURCE\s/ ) { ($element) = ( $cur =~ /^SOURCE\s+(.+?)\s+\./ ); $head{ 'SOURCE' } = $element; $cur = <$file>; } # Check for AUTHOR line (not always there) if ( $cur =~ /^AUTHOR/ ) { ($element) = ( $cur =~ /^AUTHOR\s+(.+?)\s+/ ); $head{ 'AUTHOR' } = $element; $cur = <$file>; } # A B C D E TOTAL NUMBER OF RESIDUES, NUMBER ... line @elements = split( /\s+/, $cur ); shift( @elements ); $head{ 'TotNumRes' } = shift( @elements ); $head{ 'NumChain' } = shift( @elements ); $head{ 'TotSSBr' } = shift( @elements ); $head{ 'TotIaSSBr' } = shift( @elements ); $head{ 'TotIeSSBr' } = shift( @elements ); $cur = <$file>; ( $element ) = ( $cur =~ /\s*(\d+\.\d*)\s+ACCESSIBLE SURFACE OF PROTEIN/ ); $head{ 'ProAccSurf' } = $element; $self->{ 'Head' } = \%head; for ( my $i = 1; $i <= 14; $i++ ) { $cur = <$file>; ( $element ) = $cur =~ /\s*(\d+)\s+\d+\.\d+\s+TOTAL NUMBER OF HYDROGEN/; push( @hbond, $element ); # $hbond{ $hBondType } = $element; } $self->{ 'HBond' } = \@hbond; my $histogram_finished = 0; while ( !($histogram_finished) && chomp( $cur = <$file> ) ) { if ( $cur =~ /RESIDUE AA STRUCTURE/ ) { $histogram_finished = 1; } } while ( $cur = <$file> ) { if ( $cur =~ m/^\s*$/ ) { next; } $res_num = substr( $cur, 0, 5 ); $res_num =~ s/\s//g; $self->{ 'Res' }->[ $res_num ] = &_parseResLine( $cur ); } } =head2 _parseResLine Title : _parseResLine Usage : parses a single residue line Function : Example : used internally Returns : Args : residue line ( string ) =cut sub _parseResLine() { my $cur = shift; my ( $feat, $value ); my %elements; foreach $feat ( keys %lookUp ) { $value = substr( $cur, $lookUp{ $feat }->[0], $lookUp{ $feat }->[1] ); $value =~ s/\s//g; $elements{$feat} = $value ; } # if no chain id, make it '-' (like STRIDE...very convenient) if ( !( $elements{ 'pdb_chain' } ) || $elements{ 'pdb_chain'} eq ' ' ) { $elements{ 'pdb_chain' } = '-'; } return \%elements; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Structure/SecStr/STRIDE��������������������������������������������������������000755��000766��000024�� 0�13155576320� 20264� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Structure/SecStr/STRIDE/Res.pm�������������������������������������������������000444��000766��000024�� 67725�13155576320� 21551� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# $id $ # # bioperl module for Bio::Structure::SecStr::STRIDE::Res.pm # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ed Green <ed@compbio.berkeley.edu> # # Copyright Univ. of California # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Structure::SecStr::STRIDE::Res - Module for parsing/accessing stride output =head1 SYNOPSIS my $stride_obj = Bio::Structure::SecStr::STRIDE::Res->new( '-file' => 'filename.stride' ); # or my $stride_obj = Bio::Structure::SecStr::STRIDE::Res->new( '-fh' => \*STDOUT ); # Get secondary structure assignment for PDB residue 20 of chain A $sec_str = $stride_obj->resSecStr( '20:A' ); # same $sec_str = $stride_obj->resSecStr( 20, 'A' ) =head1 DESCRIPTION STRIDE::Res is a module for objectifying STRIDE output. STRIDE is a program (similar to DSSP) for assigning secondary structure to individual residues of a pdb structure file. ( Knowledge-Based Protein Secondary Structure Assignment, PROTEINS: Structure, Function, and Genetics 23:566-579 (1995) ) STRIDE is available here: http://webclu.bio.wzw.tum.de/stride/ Methods are then available for extracting all of the information present within the output or convenient subsets of it. Although they are very similar in function, DSSP and STRIDE differ somewhat in output format. Thes differences are reflected in the return value of some methods of these modules. For example, both the STRIDE and DSSP parsers have resSecStr() methods for returning the secondary structure of a given residue. However, the range of return values for DSSP is ( H, B, E, G, I, T, and S ) whereas the range of values for STRIDE is ( H, G, I, E, B, b, T, and C ). See individual methods for details. The methods are roughly divided into 3 sections: 1. Global features of this structure (PDB ID, total surface area, etc.). These methods do not require an argument. 2. Residue specific features ( amino acid, secondary structure, solvent exposed surface area, etc. ). These methods do require an argument. The argument is supposed to uniquely identify a residue described within the structure. It can be of any of the following forms: ('#A:B') or ( #, 'A', 'B' ) || | || - Chain ID (blank for single chain) |--- Insertion code for this residue. Blank for most residues. |--- Numeric portion of residue ID. (#) | --- Numeric portion of residue ID. If there is only one chain and it has no ID AND there is no residue with an insertion code at this number, then this can uniquely specify a residue. ('#:C') or ( #, 'C' ) | | | -Chain ID ---Numeric portion of residue ID. If a residue is incompletely specified then the first residue that fits the arguments is returned. For example, if 19 is the argument and there are three chains, A, B, and C with a residue whose number is 19, then 19:A will be returned (assuming its listed first). Since neither DSSP nor STRIDE correctly handle alt-loc codes, they are not supported by these modules. 3. Value-added methods. Return values are not verbatem strings parsed from DSSP or STRIDE output. =head1 FEEDBACK =head2 MailingLists UsUser feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ed Green Email ed@compbio.berkeley.edu =head1 APPENDIX The Rest of the documentation details each method. Internal methods are preceded with a _. =cut package Bio::Structure::SecStr::STRIDE::Res; use strict; use Bio::Root::IO; use Bio::PrimarySeq; use base qw(Bio::Root::Root); our %ASGTable = ( 'aa' => 0, 'resNum' => 1, 'ssAbbr' => 2, 'ssName' => 3, 'phi' => 4, 'psi' => 5, 'surfArea' => 6 ); our %AATable = ( 'ALA' => 'A', 'ARG' => 'R', 'ASN' => 'N', 'ASP' => 'D', 'CYS' => 'C', 'GLN' => 'Q', 'GLU' => 'E', 'GLY' => 'G', 'HIS' => 'H', 'ILE' => 'I', 'LEU' => 'L', 'LYS' => 'K', 'MET' => 'M', 'PHE' => 'F', 'PRO' => 'P', 'SER' => 'S', 'THR' => 'T', 'TRP' => 'W', 'TYR' => 'Y', 'VAL' => 'V' ); =head2 new Title : new Usage : makes new object of this class Function : Constructor Example : $stride_obj = Bio::Structure::SecStr::STRIDE:Res->new( '-file' => filename # or '-fh' => FILEHANDLE ) Returns : object (ref) Args : filename or filehandle( must be proper STRIDE output ) =cut sub new { my ( $class, @args ) = @_; my $self = $class->SUPER::new( @args ); my $io = Bio::Root::IO->new( @args ); $self->_parse( $io ); # not passing filehandle ! $io->close(); return $self; } # GLOBAL FEATURES / INFO / STATS =head2 totSurfArea Title : totSurfArea Usage : returns sum of surface areas of all residues of all chains considered. Result is memoized. Function : Example : $tot_SA = $stride_obj->totSurfArea(); Returns : scalar Args : none =cut sub totSurfArea { my $self = shift; my $total = 0; my ( $chain, $res ); if ( $self->{ 'SurfArea' } ) { return $self->{ 'SurfArea' }; } else { foreach $chain ( keys %{$self->{ 'ASG' }} ) { for ( my $i = 1; $i <= $#{$self->{'ASG'}->{$chain}}; $i++ ) { $total += $self->{'ASG'}->{$chain}->[$i]->[$ASGTable{'surfArea'}]; } } } $self->{ 'SurfArea' } = $total; return $self->{ 'SurfArea' }; } =head2 numResidues Title : numResidues Usage : returns total number of residues in all chains or just the specified chain Function : Example : $tot_res = $stride_obj->numResidues(); Returns : scalar int Args : none or chain id =cut sub numResidues { my $self = shift; my $chain = shift; my $total = 0; my $key; foreach $key ( keys %{$self->{ 'ASG' }} ) { if ( $chain ) { if ( $key eq $chain ) { $total += $#{$self->{ 'ASG' }{ $key }}; } } else { $total += $#{$self->{ 'ASG' }{ $key }}; } } return $total; } # STRAIGHT FROM THE PDB ENTRY =head2 pdbID Title : pdbID Usage : returns pdb identifier ( 1FJM, e.g. ) Function : Example : $pdb_id = $stride_obj->pdbID(); Returns : scalar string Args : none =cut sub pdbID { my $self = shift; return $self->{ 'PDB' }; } =head2 pdbAuthor Title : pdbAuthor Usage : returns author of this PDB entry Function : Example : $auth = $stride_obj->pdbAuthor() Returns : scalar string Args : none =cut sub pdbAuthor { my $self = shift; return join( ' ', @{ $self->{ 'HEAD' }->{ 'AUT' } } ); } =head2 pdbCompound Title : pdbCompound Usage : returns string of what was found on the CMP lines Function : Example : $cmp = $stride_obj->pdbCompound(); Returns : string Args : none =cut sub pdbCompound { my $self = shift; return join( ' ', @{ $self->{ 'HEAD' }->{ 'CMP' } } ); } =head2 pdbDate Title : pdbDate Usage : returns date given in PDB file Function : Example : $pdb_date = $stride_obj->pdbDate(); Returns : scalar Args : none =cut sub pdbDate { my $self = shift; return $self->{ 'DATE' }; } =head2 pdbHeader Title : pdbHeader Usage : returns string of characters found on the PDB header line Function : Example : $head = $stride_obj->pdbHeader(); Returns : scalar Args : none =cut sub pdbHeader { my $self = shift; return $self->{ 'HEAD' }->{ 'HEADER' }; } =head2 pdbSource Title : pdbSource Usage : returns string of what was found on SRC lines Function : Example : $src = $stride_obj->pdbSource(); Returns : scalar Args : none =cut sub pdbSource { my $self = shift; return join( ' ', @{ $self->{ 'HEAD' }->{ 'SRC' } } ); } # RESIDUE SPECIFIC ACCESSORS =head2 resAA Title : resAA Usage : returns 1 letter abbr. of the amino acid specified by the arguments Function : Examples : $aa = $stride_obj->resAA( RESIDUE_ID ); Returns : scalar character Args : RESIDUE_ID =cut sub resAA { my $self = shift; my @args = @_; my ( $ord, $chain ) = $self->_toOrdChain( @args ); return ( $AATable{$self->{'ASG'}->{$chain}->[$ord]->[$ASGTable{'aa'}]} ); } =head2 resPhi Title : resPhi Usage : returns phi angle of specified residue Function : Example : $phi = $stride_obj->resPhi( RESIDUE_ID ); Returns : scaler Args : RESIDUE_ID =cut sub resPhi { my $self = shift; my @args = @_; my ( $ord, $chain ) = $self->_toOrdChain( @args ); return $self->{ 'ASG' }->{ $chain }->[ $ord ]->[ $ASGTable{ 'phi' } ]; } =head2 resPsi Title : resPsi Usage : returns psi angle of specified residue Function : Example : $psi = $stride_obj->resPsi( RESIDUE_ID ); Returns : scalar Args : RESIDUE_ID =cut sub resPsi { my $self = shift; my @args = @_; my ( $ord, $chain ) = $self->_toOrdChain( @args ); return $self->{ 'ASG' }->{ $chain }->[ $ord ]->[ $ASGTable{ 'psi' } ]; } =head2 resSolvAcc Title : resSolvAcc Usage : returns stride calculated surface area of specified residue Function : Example : $sa = $stride_obj->resSolvAcc( RESIDUE_ID ); Returns : scalar Args : RESIDUE_ID =cut sub resSolvAcc { my $self = shift; my @args = @_; my ( $ord, $chain ) = $self->_toOrdChain( @args ); return $self->{ 'ASG' }->{ $chain }->[ $ord ]->[ $ASGTable{ 'surfArea' } ]; } =head2 resSurfArea Title : resSurfArea Usage : returns stride calculated surface area of specified residue Function : Example : $sa = $stride_obj->resSurfArea( RESIDUE_ID ); Returns : scalar Args : RESIDUE_ID =cut sub resSurfArea { my $self = shift; my @args = @_; my ( $ord, $chain ) = $self->_toOrdChain( @args ); return $self->{ 'ASG' }->{ $chain }->[ $ord ]->[ $ASGTable{ 'surfArea' } ]; } =head2 resSecStr Title : resSecStr Usage : gives one letter abbr. of stride determined secondary structure of specified residue Function : Example : $ss = $stride_obj->resSecStr( RESIDUE_ID ); Returns : one of: 'H' => Alpha Helix 'G' => 3-10 helix 'I' => PI-helix 'E' => Extended conformation 'B' or 'b' => Isolated bridge 'T' => Turn 'C' => Coil ' ' => None # NOTE: This range is slightly DIFFERENT from the # DSSP method of the same name Args : RESIDUE_ID =cut sub resSecStr { my $self = shift; my @args = @_; my ( $ord, $chain ) = $self->_toOrdChain( @args ); return $self->{ 'ASG' }->{ $chain }->[ $ord ]->[ $ASGTable{ 'ssAbbr' } ]; } =head2 resSecStrSum Title : resSecStrSum Usage : gives one letter summary of secondary structure of specified residue. More general than secStruc() Function : Example : $ss_sum = $stride_obj->resSecStrSum( RESIDUE_ID ); Returns : one of: 'H' (helix), 'B' (beta), 'T' (turn), or 'C' (coil) Args : residue identifier(s) ( SEE INTRO NOTE ) =cut sub resSecStrSum { my $self = shift; my @args = @_; my $ss_char = $self->resSecStr( @args ); if ( $ss_char eq 'H' || $ss_char eq 'G' || $ss_char eq 'I' ) { return 'H'; } if ( $ss_char eq 'E' || $ss_char eq 'B' || $ss_char eq 'b' ) { return 'B'; } if ( $ss_char eq 'T' ) { return 'T'; } else { return 'C'; } } # STRIDE SPECIFIC =head2 resSecStrName Title : resSecStrName Usage : gives full name of the secondary structural element classification of the specified residue Function : Example : $ss_name = $stride_obj->resSecStrName( RESIDUE_ID ); Returns : scalar string Args : RESIDUE_ID =cut sub resSecStrName { my $self = shift; my @args = @_; my ( $ord, $chain ) = $self->_toOrdChain( @args ); return $self->{ 'ASG' }->{ $chain }->[ $ord ]->[ $ASGTable{ 'ssName' } ]; } =head2 strideLocs Title : strideLocs Usage : returns stride determined contiguous secondary structural elements as specified on the LOC lines Function : Example : $loc_pnt = $stride_obj->strideLocs(); Returns : pointer to array of 5 element arrays. 0 => stride name of structural element 1 => first residue pdb key (including insertion code, if app.) 2 => first residue chain id 3 => last residue pdb key (including insertion code, if app.) 4 => last residue chain id NOTE the differences between this range and the range of SecBounds() Args : none =cut sub strideLocs { my $self = shift; return $self->{ 'LOC' }; } # VALUE ADDED METHODS (NOT JUST PARSE/REPORT) =head2 secBounds Title : secBounds Usage : gets residue ids of boundary residues in each contiguous secondary structural element of specified chain Function : Example : $ss_bound_pnt = $stride_obj->secBounds( 'A' ); Returns : pointer to array of 3 element arrays. First two elements are the PDB IDs of the start and end points, respectively and inclusively. The last element is the STRIDE secondary structural element code (same range as resSecStr). Args : chain identifier ( one character ). If none, '-' is assumed =cut sub secBounds { # Requires a chain name. If left blank, we assume ' ' which equals '-' my $self = shift; my $chain = shift; my @SecBounds; $chain = '-' if ( !( $chain ) || $chain eq ' ' || $chain eq '-' ); # if we've memoized this one, use that if ( $self->{ 'SecBounds' }->{ $chain } ) { return $self->{ 'SecBounds' }->{ $chain }; } #check to make sure chain is valid if ( !( $self->{ 'ASG' }->{ $chain } ) ) { $self->throw( "No such chain: $chain\n" ); } my $cur_element = $self->{ 'ASG' }->{ $chain }->[ 1 ]-> [ $ASGTable{ 'ssAbbr' } ]; my $beg = 1; my $i; for ( $i = 2; $i <= $#{$self->{'ASG'}->{$chain}}; $i++ ) { if ( $self->{ 'ASG' }->{ $chain }->[ $i ]->[ $ASGTable{ 'ssAbbr' } ] ne $cur_element ) { push( @SecBounds, [ $beg, $i -1 , $cur_element ] ); $beg = $i; $cur_element = $self->{ 'ASG' }->{ $chain }->[ $i ]-> [ $ASGTable{ 'ssAbbr' } ]; } } if ( $self->{ 'ASG' }->{ $chain }->[ $i ]->[ $ASGTable{ 'ssAbbr' } ] eq $cur_element ) { push( @SecBounds, [ $beg, $i, $cur_element ] ); } else { push( @SecBounds, [ $beg, $i - 1, $cur_element ], [ $i, $i, $self->{ 'ASG' }->{ $chain }->[ $i ]-> [ $ASGTable{ 'ssAbbr' } ] ] ); } $self->{ 'SecBounds' }->{ $chain } = \@SecBounds; return $self->{ 'SecBounds' }->{ $chain }; } =head2 chains Title : chains Usage : gives array chain I.D.s (characters) Function : Example : @chains = $stride_obj->chains(); Returns : array of characters Args : none =cut sub chains { my $self = shift; my @chains = keys ( %{ $self->{ 'ASG' } } ); return \@chains; } =head2 getSeq Title : getSeq Usage : returns a Bio::PrimarySeq object which represents an approximation at the sequence of the specified chain. Function : For most chain of most entries, the sequence returned by this method will be very good. However, it it inherently unsafe to rely on STRIDE to extract sequence information about a PDB entry. More reliable information can be obtained from the PDB entry itself. If a second option is given (and evaluates to true), the sequence generated will have 'X' in spaces where the pdb residue numbers are discontinuous. In some cases this results in a better sequence object (when the discontinuity is due to regions which were present, but could not be resolved). In other cases, it will result in a WORSE sequence object (when the discontinuity is due to historical sequence numbering and all sequence is actually resolved). Example : $pso = $dssp_obj->getSeq( 'A' ); Returns : (pointer to) a PrimarySeq object Args : Chain identifier. If none given, '-' is assumed. =cut sub getSeq { my $self = shift; my $chain = shift; my $fill_in = shift; if ( !( $chain ) ) { $chain = '-'; } if ( $self->{ 'Seq' }->{ $chain } ) { return $self->{ 'Seq' }->{ $chain }; } my ( $seq, $num_res, $last_res_num, $cur_res_num, $i, $step, $id ); $seq = ""; $num_res = $self->numResidues( $chain ); $last_res_num = $self->_pdbNum( 1, $chain ); for ( $i = 1; $i <= $num_res; $i++ ) { if ( $fill_in ) { $cur_res_num = $self->_pdbNum( $i, $chain ); $step = $cur_res_num - $last_res_num; if ( $step > 1 ) { $seq .= 'X' x ( $step - 1 ); } } $seq .= $self->_resAA( $i, $chain ); $last_res_num = $cur_res_num; } $id = $self->pdbID(); $id .= "$chain"; $self->{ 'Seq' }->{ $chain } = Bio::PrimarySeq->new( -seq => $seq, -id => $id, -moltype => 'protein' ); return $self->{ 'Seq' }->{ $chain }; } =head1 INTERNAL METHODS =head2 _pdbNum Title : _pdbNum Usage : fetches the numeric portion of the identifier for a given residue as reported by the pdb entry. Note, this DOES NOT uniquely specify a residue. There may be an insertion code and/or chain identifier differences. Function : Example : $pdbNum = $self->pdbNum( 3, 'A' ); Returns : a scalar Args : valid ordinal num / chain combination =cut sub _pdbNum { my $self = shift; my $ord = shift; my $chain = shift; if ( !( $self->{ 'ASG' }->{ $chain }->[ $ord ] ) ) { $self->throw( "No such ordinal $ord in chain $chain.\n" ); } my $pdb_junk = $self->{ 'ASG' }->{ $chain }->[ $ord ]->[ $ASGTable{ 'resNum' } ]; my $num_part; ( $num_part ) = ( $pdb_junk =~ /(-*\d+).*/ ); return $num_part; } =head2 _resAA Title : _resAA Usage : returns 1 letter abbr. of the amino acid specified by the arguments Function : Examples : $aa = $stride_obj->_resAA( 3, '-' ); Returns : scalar character Args : ( ord. num, chain ) =cut sub _resAA { my $self = shift; my $ord = shift; my $chain = shift; if ( !( $self->{ 'ASG' }->{ $chain }->[ $ord ] ) ) { $self->throw( "No such ordinal $ord in chain $chain.\n" ); } return ( $AATable{$self->{'ASG'}->{$chain}->[$ord]->[$ASGTable{'aa'}]} ); } =head2 _pdbInsCo Title : _pdbInsCo Usage : fetches the Insertion code for this residue. Function : Example : $pdb_ins_co = $self->_pdb_ins_co( 15, 'B' ); Returns : a scalar Args : ordinal number and chain =cut sub _pdbInsCo { my $self = shift; my $ord = shift; my $chain = shift; if ( !( $self->{ 'ASG' }->{ $chain }->[ $ord ] ) ) { $self->throw( "No such ordinal $ord in chain $chain.\n" ); } my $pdb_junk = $self->{ 'ASG' }->{ $chain }->[ $ord ]->[ $ASGTable{ 'resNum' } ]; my $letter_part; ( $letter_part ) = ( $pdb_junk =~ /\d+(\D+)/ ); # insertion code can be any # non-word character(s) return $letter_part; } =head2 _toOrdChain Title : _toOrdChain Usage : takes any set of residue identifying parameters and wrestles them into a two element array: the chain and the ordinal number of this residue. This two element array can then be efficiently used as keys in many of the above accessor methods ('#A:B') or ( #, 'A', 'B' ) || | || - Chain ID (blank for single chain) |--- Insertion code for this residue. Blank for most residues. |--- Numeric portion of residue ID. (#) | --- Numeric portion of residue ID. If there is only one chain and it has no ID AND there is no residue with an insertion code at this number, then this can uniquely specify a residue. # ('#:C) or ( #, 'C' ) | | | -Chain ID ---Numeric portion of residue ID. If a residue is incompletely specified then the first residue that fits the arguments is returned. For example, if 19 is the argument and there are three chains, A, B, and C with a residue whose number is 19, then 19:A will be returned (assuming its listed first). Function : Example : my ( $ord, $chain ) = $self->_toOrdChain( @args ); Returns : two element array Args : valid set of residue identifier(s) ( SEE NOTE ABOVE ) =cut sub _toOrdChain { my $self = shift; my $arg_str; my ( $key_num, $chain_id, $ins_code, $key, $i ); # check to see how many args are given if ( $#_ >= 1 ) { # multiple args $key_num = shift; if ( $#_ >= 1 ) { # still multiple args => ins. code, too $ins_code = shift; $chain_id = shift; } else { # just one more arg. => chain_id $chain_id = shift; } } else { # only single arg. Might be number or string $arg_str = shift; if ( $arg_str =~ /:/ ) { # a chain is specified ( $chain_id ) = ( $arg_str =~ /:(.)/); $arg_str =~ s/:.//; } if ( $arg_str =~ /[A-Z]|[a-z]/ ) { # an insertion code is specified ( $ins_code ) = ( $arg_str =~ /([A-Z]|[a-z])/ ); $arg_str =~ s/[A-Z]|[a-z]//g; } #now, get the number bit-> everything still around $key_num = $arg_str; } $key = "$key_num$ins_code"; if ( !( $chain_id ) || $chain_id eq ' ' ) { $chain_id = '-'; } if ( !( $self->{ 'ASG' }->{ $chain_id } ) ) { $self->throw( "No such chain: $chain_id" ); } for ( $i = 1; $i <= $#{$self->{ 'ASG' }->{ $chain_id }}; $i++ ) { if ( $self->{ 'ASG' }->{ $chain_id }->[ $i ]->[ $ASGTable{ 'resNum' } ] eq $key ) { return ( $i, $chain_id ); } } $self->throw( "No such key: $key" ); } =head2 _parse Title : _parse Usage : as name suggests, parses stride output, creating object Function : Example : $self->_parse( $io ); Returns : Args : valid Bio::Root::IO object =cut sub _parse { my $self = shift; my $io = shift; my $file = $io->_fh(); # Parse top lines if ( $self->_parseTop( $io ) ) { $self->throw( "Not stride output" ); } # Parse the HDR, CMP, SCR, and AUT lines $self->_parseHead( $io ); # Parse the CHN, SEQ, STR, and LOC lines $self->_parseSummary( $io ); # we're ignoring this # Parse the ASG lines $self->_parseASG( $io ); } =head2 _parseTop Title : _parseTop Usage : makes sure this looks like stride output Function : Example : Returns : Args : =cut sub _parseTop { my $self = shift; my $io = shift; my $file = $io->_fh(); my $cur = <$file>; if ( $cur =~ /^REM ---/ ) { return 0; } return 1; } =head2 _parseHead Title : _parseHead Usage : parses Function : HDR, CMP, SRC, and AUT lines Example : Returns : Args : =cut sub _parseHead { my $self = shift; my $io = shift; my $file = $io->_fh(); my $cur; my $element; my ( @elements, @cmp, @src, @aut ); my %head = {}; my $still_head = 1; $cur = <$file>; while ( $cur =~ /^REM / ) { $cur = <$file>; } if ( $cur =~ /^HDR / ) { @elements = split( /\s+/, $cur ); shift( @elements ); pop( @elements ); $self->{ 'PDB' } = pop( @elements ); $self->{ 'DATE' } = pop( @elements ); # now, everything else is "header" except for the word # HDR $element = join( ' ', @elements ); $head{ 'HEADER' } = $element; } $cur = <$file>; while ( $cur =~ /^CMP / ) { ( $cur ) = ( $cur =~ /^CMP\s+(.+?)\s*\w{4}$/ ); push( @cmp, $cur ); $cur = <$file>; } while ( $cur =~ /^SRC / ) { ( $cur ) = ( $cur =~ /^SRC\s+(.+?)\s*\w{4}$/ ); push( @src, $cur ); $cur = <$file>; } while ( $cur =~ /^AUT / ) { ( $cur ) = ( $cur =~ /^AUT\s+(.+?)\s*\w{4}$/ ); push( @aut, $cur ); $cur = <$file>; } $head{ 'CMP' } = \@cmp; $head{ 'SRC' } = \@src; $head{ 'AUT' } = \@aut; $self->{ 'HEAD' } = \%head; } =head2 _parseSummary Title : _parseSummary Usage : parses LOC lines Function : Example : Returns : Args : =cut sub _parseSummary { my $self = shift; my $io = shift; my $file = $io->_fh(); my $cur = <$file>; my $bound_set; my $element; my ( @elements, @cur ); my @LOC_lookup = ( [ 5, 12 ], # Element name # reduntdant [ 18, 3 ], # First residue name [ 22, 5 ], # First residue PDB number [ 28, 1 ], # First residue Chain ID # redundant [ 35, 3 ], # Last residue name [ 40, 5 ], # Last residue PDB number [ 46, 1 ] ); # Last residue Chain ID #ignore these lines while ( $cur =~ /^REM |^STR |^SEQ |^CHN / ) { $cur = <$file>; } while ( $cur =~ /^LOC / ) { foreach $bound_set ( @LOC_lookup ) { $element = substr( $cur, $bound_set->[ 0 ], $bound_set->[ 1 ] ); $element =~ s/\s//g; push( @cur, $element ); } push( @elements, [ @cur ] ); $cur = <$file>; @cur = (); } $self->{ 'LOC' } = \@elements; } =head2 _parseASG Title : _parseASG Usage : parses ASG lines Function : Example : Returns : Args : =cut sub _parseASG { my $self = shift; my $io = shift; my $file = $io->_fh(); my $cur = <$file>; my $bound_set; my $ord_num; my ( $chain, $last_chain ); my $element; my %ASG; my ( @cur, @elements ); my @ASG_lookup = ( [ 5, 3 ], # Residue name # [ 9, 1 ], # Chain ID [ 10, 5 ], # PDB residue number (w/ins.code) # [ 16, 4 ], # ordinal stride number [ 24, 1 ], # one letter sec. stru. abbr. [ 26, 13], # full sec. stru. name [ 42, 7 ], # phi angle [ 52, 7 ], # psi angle [ 64, 5 ] );# residue solv. acc. while ( $cur =~ /^REM / ) { $cur = <$file>; } while ( $cur =~ /^ASG / ) { # get ordinal number for array key $ord_num = substr( $cur, 16, 4 ); $ord_num =~ s/\s//g; # get the chain id $chain = substr( $cur, 9, 1 ); if ( $last_chain && ( $chain ne $last_chain ) ) { $ASG{ $last_chain } = [ @elements ]; @elements = (); } # now get the rest of the info on this line foreach $bound_set ( @ASG_lookup ) { $element = substr( $cur, $bound_set->[ 0 ], $bound_set->[ 1 ] ); $element =~ s/\s//g; push( @cur, $element ); } $elements[ $ord_num ] = [ @cur ]; $cur = <$file>; @cur = (); $last_chain = $chain; } $ASG{ $chain } = [ @elements ]; $self->{ 'ASG' } = \%ASG; } 1; �������������������������������������������BioPerl-1.007002/Bio/Symbol�������������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 15334� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Symbol/Alphabet.pm�������������������������������������������������������������000444��000766��000024�� 11561�13155576320� 17573� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Symbol::Alphabet # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Symbol::Alphabet - BSANE/BioCORBA compliant symbol list alphabet =head1 SYNOPSIS { my $alphabet = Bio::Symbols::Alphabet->new(-symbols => [ @s ], -subalphabets => [ @alphas ] ); my @symbols = $alphabet->symbols; my @subalphas = $alphabet->alphabets; if( $alphabet->contains($symbol) ) { # do something } } =head1 DESCRIPTION Alphabet contains set of symbols, which can be concatenated to form symbol lists. Sequence string, for example, is stringified representation of the symbol list (tokens of symbols). This module was implemented for the purposes of meeting the BSANE/BioCORBA spec 0.3 only. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Symbol::Alphabet; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root Bio::Symbol::AlphabetI); =head2 new Title : new Usage : my $obj = Bio::Symbol::Alphabet->new(); Function: Builds a new Bio::Symbol::Alphabet object Returns : Bio::Symbol::Alphabet Args : -symbols => Array ref of Bio::Symbol::SymbolI objects -subalphas=> Array ref of Bio::Symbol::AlphabetI objects representing sub alphabets =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_symbols'} = []; $self->{'_alphabets'} = []; my ($symbols, $subalphas) = $self->_rearrange([qw(SYMBOLS SUBALPHAS)], @args); defined $symbols && ref($symbols) =~ /array/i && $self->symbols(@$symbols); defined $subalphas && ref($subalphas) =~ /array/i && $self->alphabets(@$subalphas); return $self; } =head2 AlphabetI Interface methods =cut =head2 symbols Title : symbols Usage : my @symbols = $alphabet->symbols(); Function: Get/Set Symbol list for an alphabet List of symbols, which make up this alphabet. Returns : Array of Bio::Symbol::SymbolI objects Args : (optionalalphabets) Array of Bio::Symbol::SymbolI objects =cut sub symbols { my ($self,@args) = @_; if( @args ) { $self->{'_symbols'} = []; foreach my $symbol ( @args ) { if( ! defined $symbol || ! ref($symbol) || ! $symbol->isa('Bio::Symbol::SymbolI') ) { $self->warn("Did not provide a proper Bio::Symbol::SymbolI to method 'symbols' (got $symbol)"); } else { push @{$self->{'_symbols'}}, $symbol; } } } return @{$self->{'_symbols'}}; } =head2 alphabets Title : alphabets Usage : my @alphabets = $alphabet->alphabets(); Function: Get/Set Sub Alphabet list for an alphabet Sub-alphabets. E.g. codons made from DNAxDNAxDNA alphabets Returns : Array of Bio::Symbol::AlphabetI objects Args : (optional) Array of Bio::Symbol::AlphabetI objects =cut sub alphabets { my ($self,@args) = @_; if( @args ) { $self->{'_alphabets'} = []; foreach my $alpha ( @args ) { if( ! $alpha->isa('Bio::Symbol::AlphabetI') ) { $self->warn("Did not provide a proper Bio::Symbol::AlphabetI to method 'alphabets' (got $alpha)"); } else { push @{$self->{'_alphabets'}}, $alpha; } } } return @{$self->{'_alphabets'}}; } =head2 contains Title : contains Usage : if($alphabet->contains($symbol)) { } Function: Tests of Symbol is contained in this alphabet Returns : Boolean Args : Bio::Symbol::SymbolI =cut sub contains{ my ($self,$testsymbol) = @_; foreach my $symbol ( $self->symbols ) { return 1 if( $symbol->equals($testsymbol) ); } return 0; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Symbol/AlphabetI.pm������������������������������������������������������������000444��000766��000024�� 10636�13155576320� 17706� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Symbol::AlphabetI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Symbol::AlphabetI - A Symbol Alphabet =head1 SYNOPSIS # get a Bio::Symbol::AlphabetI object somehow my @symbols = $alphabet->symbols; my @subalphas = $alphabet->alphabets; if( $alphabet->contains($symbol) ) { # do something } =head1 DESCRIPTION Alphabet contains set of symbols, which can be concatenated to form symbol lists. Sequence string, for example, is stringified representation of the symbol list (tokens of symbols). This module was implemented for the purposes of meeting the BSANE/BioCORBA spec 0.3 only. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Symbol::AlphabetI; use strict; use Bio::Root::RootI; =head2 AlphabetI Interface methods =cut =head2 symbols Title : symbols Usage : my @symbols = $alphabet->symbols(); Function: Get/Set Symbol list for an alphabet List of symbols, which make up this alphabet. Returns : Array of L<Bio::Symbol::SymbolI> objects Args : (optional) Array of L<Bio::Symbol::SymbolI> objects =cut sub symbols{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 alphabets Title : alphabets Usage : my @alphabets = $alphabet->alphabets(); Function: Get/Set Sub Alphabet list for an alphabet Sub-alphabets. E.g. codons made from DNAxDNAxDNA alphabets Returns : Array of L<Bio::Symbol::AlphabetI> objects Args : (optional) Array of L<Bio::Symbol::AlphabetI> objects =cut sub alphabets{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 contains Title : contains Usage : if($alphabet->contains($symbol)) { } Function: Tests of Symbol is contained in this alphabet Returns : Boolean Args : L<Bio::Symbol::SymbolI> =cut sub contains{ my ($self,@args) = @_; $self->throw_not_implemented(); } # Other methods from BSANE - not sure if we will implement here or only in # BioCORBA implementation # Resolve symbols from the token string. # SymbolList to_symbol(in string tokens) raises ( IllegalSymbolException) ; # Convinience method, which returns gap symbol that do not # match with any other symbols in the alphabet. # Symbol get_gap_symbol() raises ( DoesNotExist) ; # Returns a ambiguity symbol, which represent list of # symbols. All symbols in a list must be members of # this alphabet otherwise IllegalSymbolException is # thrown. # Symbol get_ambiguity( in SymbolList symbols) raises( IllegalSymbolException); # Returns a Symbol, which represents ordered list of symbols # given as a parameter. Each symbol in the list must be member of # different sub-alphabet in the order defined by the alphabets # attribute. For example, codons can be represented by a compound # Alphabet of three DNA Alphabets, in which case the get_symbol( # SymbolList[ a,g,t]) method of the Alphabet returns Symbol for # the codon agt.<p> # IllegalSymbolException is raised if members of symbols # are not Symbols over the alphabet defined by # get_alphabets()-method # Symbol get_symbol(in SymbolList symbols) raises(IllegalSymbolException) ; 1; ��������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Symbol/DNAAlphabet.pm����������������������������������������������������������000444��000766��000024�� 5674�13155576320� 20106� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Symbol::DNAAlphabet # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Symbol::DNAAlphabet - A ready made DNA alphabet =head1 SYNOPSIS use Bio::Symbol::DNAAlphabet; my $alpha = Bio::Symbol::DNAAlphabet->new(); foreach my $symbol ( $alpha->symbols ) { print "symbol is $symbol\n"; } =head1 DESCRIPTION This object builds an Alphabet with DNA symbols. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Symbol::DNAAlphabet; use strict; use Bio::Symbol::Symbol; use Bio::Tools::IUPAC; use base qw(Bio::Symbol::Alphabet); =head2 new Title : new Usage : my $obj = Bio::Symbol::DNAAlphabet->new(); Function: Builds a new Bio::Symbol::DNAAlphabet object Returns : Bio::Symbol::DNAAlphabet Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my %alphabet = Bio::Tools::IUPAC::iupac_iub(); my %symbols; foreach my $let ( keys %alphabet ) { next unless @{$alphabet{$let}} == 1 || $let eq 'U'; $symbols{$let} = Bio::Symbol::Symbol->new(-name => $let, -token => $let); } foreach my $let ( keys %alphabet ) { next if( $symbols{$let} || $let eq 'U'); my @subsymbols; foreach my $sublet ( @{$alphabet{$let}} ) { push @subsymbols, $symbols{$sublet}; } my $alpha = Bio::Symbol::Alphabet->new(-symbols => \@subsymbols); $symbols{$let} = Bio::Symbol::Symbol->new(-name => $let, -token => $let, -matches => $alpha, -symbols => \@subsymbols); } $self->symbols(values %symbols); return $self; } 1; ��������������������������������������������������������������������BioPerl-1.007002/Bio/Symbol/ProteinAlphabet.pm������������������������������������������������������000444��000766��000024�� 5720�13155576320� 21114� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Symbol::ProteinAlphabet # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Symbol::ProteinAlphabet - A ready made Protein alphabet =head1 SYNOPSIS use Bio::Symbol::ProteinAlphabet; my $alpha = Bio::Symbol::ProteinAlphabet->new(); foreach my $symbol ( $alpha->symbols ) { print "symbol is $symbol\n"; } =head1 DESCRIPTION This object builds an Alphabet with Protein symbols. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Symbol::ProteinAlphabet; use strict; use Bio::Symbol::Symbol; use Bio::Tools::IUPAC; use Bio::SeqUtils; use base qw(Bio::Symbol::Alphabet); =head2 new Title : new Usage : my $obj = Bio::Symbol::ProteinAlphabet->new(); Function: Builds a new Bio::Symbol::ProteinAlphabet object Returns : Bio::Symbol::ProteinAlphabet Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my %aa = Bio::SeqUtils->valid_aa(2); my %codes = Bio::Tools::IUPAC->iupac_iup(); my %symbols; my @left; foreach my $let ( keys %codes ) { if( scalar @{$codes{$let}} != 1) { push @left, $let; next; } $symbols{$let} = Bio::Symbol::Symbol->new(-name => $aa{$let}, -token => $let); } foreach my $l ( @left ) { my @subsym; foreach my $sym ( @{$codes{$l}} ) { push @subsym, $symbols{$sym}; } my $alpha = Bio::Symbol::Alphabet->new(-symbols => \@subsym); $symbols{$l} = Bio::Symbol::Symbol->new(-name => $aa{$l}, -token => $l, -matches => $alpha, -symbols => \@subsym); } $self->symbols(values %symbols); return $self; } 1; ������������������������������������������������BioPerl-1.007002/Bio/Symbol/README.Symbol�����������������������������������������������������������000444��000766��000024�� 430�13155576320� 17572� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������This is unused code written simply for the benefit of impelementing the BioCORBA / OMG BSANE spec. We've pretty much given up on this in 2002 as anything useful. So unless someone finds a need for this code we'll probably remove it in future releases. -Jason Stajich August 2003 ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Symbol/Symbol.pm���������������������������������������������������������������000444��000766��000024�� 13257�13155576320� 17324� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Symbol::Symbol # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Symbol::Symbol - A biological symbol =head1 SYNOPSIS use Bio::Symbol::Symbol; my $thymine = Bio::Symbol::Symbol->new(-name => 'Thy', -token=> 'T'); my $a = Bio::Symbol::Symbol->new(-token => 'A' ); my $u = Bio::Symbol::Symbol->new(-token => 'U' ); my $g = Bio::Symbol::Symbol->new(-token => 'G' ); my $M = Bio::Symbol::Symbol->new(-name => 'Met', -token => 'M', -symbols => [ $a, $u, $g ]); my ($name,$token) = ($a->name, $a->token); my @symbols = $a->symbols; my $matches = $a->matches; =head1 DESCRIPTION Symbol represents a single token in the sequence. Symbol can have multiple synonyms or matches within the same Alphabet, which makes possible to represent ambiguity codes and gaps. Symbols can be also composed from ordered list other symbols. For example, codons can be represented by single Symbol using a compound Alphabet made from three DNA Alphabets. This module was implemented for the purposes of meeting the BSANE/BioCORBA spec 0.3 only. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Symbol::Symbol; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Symbol::Alphabet; use base qw(Bio::Root::Root Bio::Symbol::SymbolI); =head2 new Title : new Usage : my $obj = Bio::Symbol::Symbol->new(); Function: Builds a new Bio::Symbol::Symbol object Returns : Bio::Symbol::Symbol Args : -name => descriptive name (string) [e.g. Met] -token => Shorthand token (string) [e.g. M] -symbols => Symbols that make up this symbol (array) [e.g. AUG] -matches => Alphabet in the event symbol is an ambiguity code. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_symbols'} = []; my ($name, $token, $symbols, $matches) = $self->_rearrange([qw(NAME TOKEN SYMBOLS MATCHES)], @args); $token && $self->token($token); $name && $self->name($name); $symbols && ref($symbols) =~ /array/i && $self->symbols(@$symbols); $matches && $self->matches($matches); return $self; } =head2 name Title : name Usage : my $name = $symbol->name(); Function: Get/Set Descriptive name for Symbol Returns : string Args : (optional) string =cut sub name { my ($self,$value) = @_; if( $value ) { $self->{'_name'} = $value; } return $self->{'_name'} || ''; } =head2 token Title : token Usage : my $token = $self->token(); Function: Get/Set token for this symbol Example : Letter A,C,G,or T for a DNA alphabet Symbol Returns : string Args : (optional) string =cut sub token{ my ($self,$value) = @_; if( $value ) { $self->{'_token'} = $value; } return $self->{'_token'} || ''; } =head2 symbols Title : symbols Usage : my @symbols = $self->symbols(); Function: Get/Set Symbols this Symbol is composed from Example : Ambiguity symbols are made up > 1 base symbol Returns : Array of Bio::Symbol::SymbolI objects Args : (optional) Array of Bio::Symbol::SymbolI objects =cut sub symbols{ my ($self,@args) = @_; if( @args ) { $self->{'_symbols'} = [@args]; } return @{$self->{'_symbols'}}; } =head2 matches Title : matches Usage : my $matchalphabet = $symbol->matches(); Function: Get/Set (Sub) alphabet of symbols matched by this symbol including the symbol itself (i.e. if symbol is DNA ambiguity code W then the matches contains symbols for W and T) Returns : Bio::Symbol::AlphabetI Args : (optional) Bio::Symbol::AlphabetI =cut sub matches{ my ($self,$matches) = @_; if( $matches ) { if( ! $matches->isa('Bio::Symbol::AlphabetI') ) { $self->warn("Must pass in a Bio::Symbol::AlphabetI object to matches function"); # stick with previous value } else { $self->{'_matches'} = $matches; } } return $self->{'_matches'}; } =head2 equals Title : equals Usage : if( $symbol->equals($symbol2) ) { } Function: Tests if a symbol is equal to another Returns : Boolean Args : Bio::Symbol::SymbolI =cut sub equals{ my ($self,$symbol2) = @_; # Let's just test based on Tokens for now # Doesn't handle DNA vs PROTEIN accidential comparisons return $self->token eq $symbol2->token; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Symbol/SymbolI.pm��������������������������������������������������������������000444��000766��000024�� 7644�13155576320� 17420� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Symbol::SymbolI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Symbol::SymbolI - Interface for a Symbol =head1 SYNOPSIS # get a Bio::Symbol::SymbolI object somehow my ($name,$token) = ($symbol->name, $symbol->token); my @symbols = $symbol->symbols; my $matches = $symbol->matches; =head1 DESCRIPTION Symbol represents a single token in the sequence. Symbol can have multiple synonyms or matches within the same Alphabet, which makes possible to represent ambiguity codes and gaps. Symbols can be also composed from ordered list other symbols. For example, codons can be represented by single Symbol using a compound Alphabet made from three DNA Alphabets. This module was implemented for the purposes of meeting the BSANE/BioCORBA spec 0.3 only. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Symbol::SymbolI; use strict; use base qw(Bio::Root::RootI); =head2 Bio::Symbol::SymbolI interface methods =cut =head2 name Title : name Usage : my $name = $symbol->name(); Function: Get/Set Descriptive name for Symbol Returns : string Args : (optional) string =cut sub name{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 token Title : token Usage : my $token = $self->token(); Function: Get/Set token for this symbol Example : Letter A,C,G,or T for a DNA alphabet Symbol Returns : string Args : (optional) string =cut sub token{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 symbols Title : symbols Usage : my @symbols = $self->symbols(); Function: Get/Set Symbols this Symbol is composed from Example : A codon is composed of 3 DNA symbols Returns : Array of Bio::Symbol::SymbolI objects Args : (optional) Array of Bio::Symbol::SymbolI objects =cut sub symbols{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 matches Title : matches Usage : my $matchalphabet = $symbol->matches(); Function: Get/Set (Sub) alphabet of symbols matched by this symbol including the symbol itself (i.e. if symbol is DNA ambiguity code W then the matches contains symbols for W and T) Returns : Bio::Symbol::AlphabetI Args : (optional) Bio::Symbol::AlphabetI =cut sub matches{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 equals Title : equals Usage : if( $symbol->equals($symbol2) ) { } Function: Tests if a symbol is equal to another Returns : Boolean Args : Bio::Symbol::SymbolI =cut sub equals{ my ($self,@args) = @_; $self->throw_not_implemented(); } 1; ��������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Taxonomy�����������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 15705� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Taxonomy/FactoryI.pm�����������������������������������������������������������000444��000766��000024�� 5370�13155576320� 20125� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # # BioPerl interface of Bio::Taxnomoy::FactoryI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Juguang Xiao # # You may distribute this module under the same terms as Perl itself # # POD documentation - main does before the code =head1 NAME Bio::Taxonomy::FactoryI - interface to define how to access NCBI Taxonoy =head1 DESCRIPTION NB: This module has been deprecated. $factory-E<gt>fetch is a general method to fetch Taxonomy by either NCBI taxid or any types of names. $factory-E<gt>fetch_parent($taxonomy), returns a Taxonomy that is one-step higher rank of the taxonomy specified as argument. $factory-E<gt>fetch_children($taxonomy), reports an array of Taxonomy those are one-step lower rank of the taxonomy specified as the argument. =head1 AUTHOR - Juguang Xiao juguang@tll.org.sg =head1 CONTRIBUTORS Additional contributors' names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Taxonomy::FactoryI; use strict; use base qw(Bio::Root::Root); =head2 fetch Title: fetch Usage: my $taxonomy = $factory->fetch(-taxon_id => 9605); my $taxonomy = $factory->fetch(-common_name => 'mammals'); Fuctnion: Fetch taxonomy by taxon_id, common name or scientific name. Returns: an instance of Bio::Taxonomy Args: -taxon_id => NCBI taxonomy ID -common_name => comon name, such as 'human', 'mammals' -scientifc_name => specitic name, such as 'sapiens', 'Mammalia' =cut sub fetch { shift->throw_not_implemented; } =head2 fuzzy_fetch Title: fuzzy_fetch Usage: my @taxonomy = $factory->fuzzy_fetch(-name => 'mouse'); Function: Fuzzy fetch by name, or any text information found in DB Returns: an array reference of Bio::Taxonomy objects Args: -name => any name, such as common name, variant, scientific name -description, or -desc => any text information =cut sub fuzzy_fetch { shift->throw_not_implemented; } =head2 fetch_parent Title: fetch_parent Usage: my $parent_taxonomy = $factory->fetch_parent($taxonomy); Function: Fetch the parent that is one-rank higher than the argument. Returns: an instance of Bio::Taxonomy, or undef if the arg is the top one. Args: a Bio::Taxonomy object. =cut sub fetch_parent { shift->throw_not_implemented; } =head2 fetch_children Title: fetch_children Usage: my @children_taxonomy = $factory->fetch_children($taxonomy); Function: Fetch all children those are one-rank lower than the argument. Returns: an array reference of Bio::Taxonomy objects Args: a Bio::Taxonomy object. =cut sub fetch_children { shift->throw_not_implemented; } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Taxonomy/Node.pm���������������������������������������������������������������000444��000766��000024�� 4076�13155576320� 17274� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Taxonomy::Node # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl-dot-org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Taxonomy::Node - A node in a represented taxonomy =head1 SYNOPSIS use Bio::Taxon; # This module has been renamed Bio::Taxon - use that instead =head1 DESCRIPTION This module has been renamed Bio::Taxon - use that instead. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 CONTRIBUTORS Juguang Xiao, juguang@tll.org.sg Gabriel Valiente, valiente@lsi.upc.edu Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Taxonomy::Node; use strict; use base qw(Bio::Taxon); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->warn("This module has been renamed Bio::Taxon - use that instead"); return $self; } 1;������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Taxonomy/Taxon.pm��������������������������������������������������������������000444��000766��000024�� 36140�13155576320� 17515� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Taxonomy::Taxon # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Dan Kortschak but pilfered extensively from # the Bio::Tree::Node code of Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Taxonomy::Taxon - Generic Taxonomic Entity object =head1 SYNOPSIS # NB: This module is deprecated. Use Bio::Taxon instead. use Bio::Taxonomy::Taxon; my $taxonA = Bio::Taxonomy::Taxon->new(); my $taxonL = Bio::Taxonomy::Taxon->new(); my $taxonR = Bio::Taxonomy::Taxon->new(); my $taxon = Bio::Taxonomy::Taxon->new(); $taxon->add_Descendents($taxonL); $taxon->add_Descendents($taxonR); my $species = $taxon->species; =head1 DESCRIPTION Makes a taxonomic unit suitable for use in a taxonomic tree =head1 AUTHOR Dan Kortschak email B<kortschak@rsbs.anu.edu.au> =head1 CONTRIBUTORS Sendu Bala: bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # code begins... package Bio::Taxonomy::Taxon; use vars qw($CREATIONORDER); use strict; use Bio::Species; use base qw(Bio::Root::Root Bio::Tree::NodeI); BEGIN { $CREATIONORDER = 0; } =head2 new Title : new Usage : my $obj = Bio::Taxonomy::Taxon->new(); Function: Builds a new Bio::Taxonomy::Taxon object Returns : Bio::Taxonomy::Taxon Args : -descendents => array pointer to descendents (optional) -branch_length => branch length [integer] (optional) -taxon => taxon -id => unique taxon id for node (from NCBI's list preferably) -rank => the taxonomic level of the node (also from NCBI) =cut #' for emacs sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->warn("Bio::Taxonomy::Taxon is deprecated. Use Bio::Taxon instead."); my ($children,$branchlen,$id,$taxon,$rank,$desc) = $self->_rearrange([qw(DESCENDENTS BRANCH_LENGTH ID TAXON RANK DESC)], @args); $self->{'_desc'} = {}; defined $desc && $self->description($desc); defined $taxon && $self->taxon($taxon); defined $id && $self->id($id); defined $branchlen && $self->branch_length($branchlen); defined $rank && $self->rank($rank); if( defined $children ) { if( ref($children) !~ /ARRAY/i ) { $self->warn("Must specify a valid ARRAY reference to initialize a Taxon's Descendents"); } foreach my $c ( @$children ) { $self->add_Descendent($c); } } $self->_creation_id($CREATIONORDER++); return $self; } =head2 add_Descendent Title : add_Descendent Usage : $taxon->add_Descendent($taxon); Function: Adds a descendent to a taxon Returns : number of current descendents for this taxon Args : Bio::Taxonomy::Taxon boolean flag, true if you want to ignore the fact that you are adding a second node with the same unique id (typically memory location reference in this implementation). default is false and will throw an error if you try and overwrite an existing node. =cut sub add_Descendent{ my ($self,$node,$ignoreoverwrite) = @_; return -1 if( ! defined $node ) ; if( ! $node->isa('Bio::Taxonomy::Taxon') ) { $self->warn("Trying to add a Descendent who is not a Bio::Taxonomy::Taxon"); return -1; } # do we care about order? $node->{'_ancestor'} = $self; if( $self->{'_desc'}->{$node->internal_id} && ! $ignoreoverwrite ) { $self->throw("Going to overwrite a taxon which is $node that is already stored here, set the ignore overwrite flag (parameter 2) to true to ignore this in the future"); } $self->{'_desc'}->{$node->internal_id} = $node; # is this safely unique - we've tested before at any rate?? $self->invalidate_height(); return scalar keys %{$self->{'_desc'}}; } =head2 each_Descendent Title : each_Descendent($sortby) Usage : my @taxa = $taxon->each_Descendent; Function: all the descendents for this taxon (but not their descendents i.e. not a recursive fetchall) Returns : Array of Bio::Taxonomy::Taxon objects Args : $sortby [optional] "height", "creation" or coderef to be used to sort the order of children taxa. =cut sub each_Descendent{ my ($self, $sortby) = @_; # order can be based on branch length (and sub branchlength) $sortby ||= 'height'; if (ref $sortby eq 'CODE') { my @values = sort $sortby values %{$self->{'_desc'}}; return @values; } else { if ($sortby eq 'height') { return map { $_->[0] } sort { $a->[1] <=> $b->[1] || $a->[2] <=> $b->[2] } map { [$_, $_->height, $_->internal_id ] } values %{$self->{'_desc'}}; } else { return map { $_->[0] } sort { $a->[1] <=> $b->[1] } map { [$_, $_->height ] } values %{$self->{'_desc'}}; } } } =head2 remove_Descendent Title : remove_Descendent Usage : $taxon->remove_Descedent($taxon_foo); Function: Removes a specific taxon from being a Descendent of this taxon Returns : nothing Args : An array of Bio::taxonomy::Taxon objects which have be previously passed to the add_Descendent call of this object. =cut sub remove_Descendent{ my ($self,@nodes) = @_; foreach my $n ( @nodes ) { if( $self->{'_desc'}->{$n->internal_id} ) { $n->{'_ancestor'} = undef; $self->{'_desc'}->{$n->internal_id}->{'_ancestor'} = undef; delete $self->{'_desc'}->{$n->internal_id}; } else { $self->debug(sprintf("no taxon %s (%s) listed as a descendent in this taxon %s (%s)\n",$n->id, $n,$self->id,$self)); $self->debug("Descendents are " . join(',', keys %{$self->{'_desc'}})."\n"); } } 1; } =head2 remove_all_Descendents Title : remove_all_Descendents Usage : $taxon->remove_All_Descendents() Function: Cleanup the taxon's reference to descendents and reset their ancestor pointers to undef, if you don't have a reference to these objects after this call they will be cleanedup - so a get_nodes from the Tree object would be a safe thing to do first Returns : nothing Args : none =cut sub remove_all_Descendents{ my ($self) = @_; # this won't cleanup the taxa themselves if you also have # a copy/pointer of them (I think)... while( my ($node,$val) = each %{ $self->{'_desc'} } ) { $val->{'_ancestor'} = undef; } $self->{'_desc'} = {}; 1; } =head2 get_Descendents Title : get_Descendents Usage : my @taxa = $taxon->get_Descendents; Function: Recursively fetch all the taxa and their descendents *NOTE* This is different from each_Descendent Returns : Array or Bio::Taxonomy::Taxon objects Args : none =cut # implemented in the interface =head2 ancestor Title : ancestor Usage : $taxon->ancestor($newval) Function: Set the Ancestor Returns : value of ancestor Args : newvalue (optional) =cut sub ancestor { my ($self, $value) = @_; if (defined $value) { $self->{'_ancestor'} = $value; } return $self->{'_ancestor'}; } =head2 branch_length Title : branch_length Usage : $obj->branch_length($newval) Function: Example : Returns : value of branch_length Args : newvalue (optional) =cut sub branch_length { my ($self,$value) = @_; if( defined $value) { $self->{'branch_length'} = $value; } return $self->{'branch_length'}; } =head2 description Title : description Usage : $obj->description($newval) Function: Returns : value of description Args : newvalue (optional) =cut sub description { my ($self,$value) = @_; if( defined $value ) { $self->{'_description'} = $value; } return $self->{'_description'}; } =head2 rank Title : rank Usage : $obj->rank($newval) Function: Set the taxonomic rank Returns : taxonomic rank of taxon Args : newvalue (optional) =cut sub rank { my ($self,$value) = @_; if (defined $value) { $self->{'_rank'} = $value; } return $self->{'_rank'}; } =head2 taxon Title : taxon Usage : $obj->taxon($newtaxon) Function: Set the name of the taxon Example : Returns : name of taxon Args : newtaxon (optional) =cut # because internal taxa have names too... sub taxon { my ($self,$value) = @_; if( defined $value ) { $self->{'_taxon'} = $value; } return $self->{'_taxon'}; } =head2 id Title : id Usage : $obj->id($newval) Function: Example : Returns : value of id Args : newvalue (optional) =cut sub id { my ($self,$value) = @_; if( defined $value ) { $self->{'_id'} = $value; } return $self->{'_id'}; } sub DESTROY { my ($self) = @_; # try to insure that everything is cleaned up $self->SUPER::DESTROY(); if( defined $self->{'_desc'} && ref($self->{'_desc'}) =~ /ARRAY/i ) { while( my ($nodeid,$node) = each %{ $self->{'_desc'} } ) { $node->{'_ancestor'} = undef; # ensure no circular references $node->DESTROY(); $node = undef; } $self->{'_desc'} = {}; } } =head2 internal_id Title : internal_id Usage : my $internalid = $taxon->internal_id Function: Returns the internal unique id for this taxon (a monotonically increasing number for this in-memory implementation but could be a database determined unique id in other implementations) Returns : unique id Args : none =cut sub internal_id { return $_[0]->_creation_id; } =head2 _creation_id Title : _creation_id Usage : $obj->_creation_id($newval) Function: a private method signifying the internal creation order Returns : value of _creation_id Args : newvalue (optional) =cut sub _creation_id { my ($self,$value) = @_; if( defined $value) { $self->{'_creation_id'} = $value; } return $self->{'_creation_id'} || 0; } # The following methods are implemented by NodeI decorated interface =head2 is_Leaf Title : is_Leaf Usage : if( $node->is_Leaf ) Function: Get Leaf status Returns : boolean Args : none =cut sub is_Leaf { my ($self) = @_; my $rc = 0; $rc = 1 if( ! defined $self->{'_desc'} || keys %{$self->{'_desc'}} == 0); return $rc; } =head2 to_string Title : to_string Usage : my $str = $taxon->to_string() Function: For debugging, provide a taxon as a string Returns : string Args : none =cut =head2 height Title : height Usage : my $len = $taxon->height Function: Returns the height of the tree starting at this taxon. Height is the maximum branchlength. Returns : The longest length (weighting branches with branch_length) to a leaf Args : none =cut sub height { my ($self) = @_; return $self->{'_height'} if( defined $self->{'_height'} ); if( $self->is_Leaf ) { if( !defined $self->branch_length ) { $self->debug(sprintf("Trying to calculate height of a taxon when a taxon (%s) has an undefined branch_length",$self->id || '?' )); return 0; } return $self->branch_length; } my $max = 0; foreach my $subnode ( $self->each_Descendent ) { my $s = $subnode->height; if( $s > $max ) { $max = $s; } } return ($self->{'_height'} = $max + ($self->branch_length || 1)); } =head2 invalidate_height Title : invalidate_height Usage : private helper method Function: Invalidate our cached value of the taxon's height in the tree Returns : nothing Args : none =cut sub invalidate_height { my ($self) = @_; $self->{'_height'} = undef; if( $self->ancestor ) { $self->ancestor->invalidate_height; } } =head2 classify Title : classify Usage : @obj->classify() Function: a method to return the classification of a species Returns : name of taxon and ancestor's taxon recursively Args : boolean to specify whether we want all taxa not just ranked levels =cut sub classify { my ($self,$allnodes) = @_; my @classification=($self->taxon); my $node=$self; while (defined $node->ancestor) { push @classification, $node->ancestor->taxon if $allnodes==1; $node=$node->ancestor; } return (@classification); } =head2 has_rank Title : has_rank Usage : $obj->has_rank($rank) Function: a method to query ancestors' rank Returns : boolean Args : $rank =cut sub has_rank { my ($self,$rank) = @_; return $self if $self->rank eq $rank; while (defined $self->ancestor) { return $self if $self->ancestor->rank eq $rank; $self=$self->ancestor; } return; } =head2 has_taxon Title : has_taxon Usage : $obj->has_taxon($taxon) Function: a method to query ancestors' taxa Returns : boolean Args : Bio::Taxonomy::Taxon object =cut sub has_taxon { my ($self,$taxon) = @_; return $self if ((defined $self->id && $self->id == $taxon->id) || ($self->taxon eq $taxon->taxon && $self->rank eq $taxon->rank)); while (defined $self->ancestor) { return $self if ((defined $self->id && $self->id == $taxon->id) || ($self->taxon eq $taxon->taxon && $self->rank eq $taxon->rank) && ($self->taxon ne 'no rank')); $self=$self->ancestor; } return; } =head2 distance_to_root Title : distance_to_root Usage : $obj->distance_to_root Function: a method to query ancestors' taxa Returns : number of links to root Args : =cut sub distance_to_root { my ($self,$taxon) = @_; my $count=0; while (defined $self->ancestor) { $count++; $self=$self->ancestor; } return $count; } =head2 recent_common_ancestor Title : recent_common_ancestor Usage : $obj->recent_common_ancestor($taxon) Function: a method to query find common ancestors Returns : Bio::Taxonomy::Taxon of query or undef if no ancestor of rank Args : Bio::Taxonomy::Taxon =cut sub recent_common_ancestor { my ($self,$node) = @_; while (defined $node->ancestor) { my $common=$self->has_taxon($node); return $common if defined $common; $node=$node->ancestor; } return; } =head2 species Title : species Usage : $obj=$taxon->species; Function: Returns a Bio::Species object reflecting the taxon's tree position Returns : a Bio::Species object Args : none =cut sub species { my ($self) = @_; my $species; if ($self->has_rank('subspecies') && $self->ancestor->rank eq 'species') { $species = Bio::Species->new(-classification => $self->ancestor->classify); $species->genus($self->ancestor->ancestor->taxon); $species->species($self->ancestor->taxon); $species->sub_species($self->taxon); } elsif ($self->has_rank('species')) { $species = Bio::Species->new(-classification => $self->classify); $species->genus($self->ancestor->taxon); $species->species($self->taxon); } else { $self->throw("Trying to create a species from a taxonomic entity without species rank. Use classify instead of species.\n"); } return $species; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Taxonomy/Tree.pm���������������������������������������������������������������000444��000766��000024�� 26205�13155576320� 17324� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Taxonomy::Tree # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Dan Kortschak but pilfered extensively from Bio::Tree::Tree by Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Taxonomy::Tree - An Organism Level Implementation of TreeI interface. =head1 SYNOPSIS # NB: This module is deprecated. Use Bio::Taxon in combination with # Bio::Tree::Tree instead # like from a TreeIO my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'treefile.dnd'); my $tree = $treeio->next_tree; my @nodes = $tree->get_nodes; my $root = $tree->get_root_node; my @leaves = $tree->get_leaves; =head1 DESCRIPTION This object holds handles to Taxonomic Nodes which make up a tree. =head1 EXAMPLES use Bio::Species; use Bio::Taxonomy::Tree; my $human=Bio::Species->new(); my $chimp=Bio::Species->new(); my $bonobo=Bio::Species->new(); $human->classification(qw( sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota )); $chimp->classification(qw( troglodytes Pan Hominidae Catarrhini Primates Eutheria Mammalia Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota )); $bonobo->classification(qw( paniscus Pan Hominidae Catarrhini Primates Eutheria Mammalia Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota )); # ranks passed to $taxonomy match ranks of species my @ranks = ('superkingdom','kingdom','phylum','subphylum', 'no rank 1','no rank 2','class','no rank 3','order', 'suborder','family','genus','species'); my $taxonomy=Bio::Taxonomy->new(-ranks => \@ranks, -method => 'trust', -order => -1); my $tree1=Bio::Taxonomy::Tree->new(); my $tree2=Bio::Taxonomy::Tree->new(); $tree1->make_species_branch($human,$taxonomy); $tree2->make_species_branch($chimp,$taxonomy); my ($homo_sapiens)=$tree1->get_leaves; $tree1->splice($tree2); $tree1->add_species($bonobo,$taxonomy); my @taxa; foreach my $leaf ($tree1->get_leaves) { push @taxa,$leaf->taxon; } print join(", ",@taxa)."\n"; @taxa=(); $tree1->remove_branch($homo_sapiens); foreach my $leaf ($tree1->get_leaves) { push @taxa,$leaf->taxon; } print join(", ",@taxa)."\n"; =head1 FEEDBACK See AUTHOR =head1 AUTHOR - Dan Kortschak Email kortschak@rsbs.anu.edu.au =head1 CONTRIBUTORS Mainly Jason Stajich =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Code begins... package Bio::Taxonomy::Tree; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Taxonomy::Taxon; # Import rank information from Bio::Taxonomy.pm use vars qw(@RANK %RANK); use base qw(Bio::Root::Root Bio::Tree::TreeI Bio::Tree::TreeFunctionsI); =head2 new Title : new Usage : my $obj = Bio::Taxonomy::Tree->new(); Function: Builds a new Bio::Taxonomy::Tree object Returns : Bio::Taxonomy::Tree Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->warn("Bio::Taxonomy::Tree is deprecated. Use Bio::Taxon in combination with Bio::Tree::Tree instead."); $self->{'_rootnode'} = undef; $self->{'_maxbranchlen'} = 0; my ($root)= $self->_rearrange([qw(ROOT)], @args); if( $root ) { $self->set_root_node($root); } return $self; } =head2 get_nodes Title : get_nodes Usage : my @nodes = $tree->get_nodes() Function: Return list of Bio::Taxonomy::Taxon objects Returns : array of Bio::Taxonomy::Taxon objects Args : (named values) hash with one value order => 'b|breadth' first order or 'd|depth' first order =cut sub get_nodes{ my ($self, @args) = @_; my ($order, $sortby) = $self->_rearrange([qw(ORDER SORTBY)],@args); $order ||= 'depth'; $sortby ||= 'height'; if ($order =~ m/^b|(breadth)$/oi) { my $node = $self->get_root_node; my @children = ($node); for (@children) { push @children, $_->each_Descendent($sortby); } return @children; } if ($order =~ m/^d|(depth)$/oi) { # this is depth-first search I believe my $node = $self->get_root_node; my @children = ($node,$node->get_Descendents($sortby)); return @children; } } =head2 get_root_node Title : get_root_node Usage : my $node = $tree->get_root_node(); Function: Get the Top Node in the tree, in this implementation Trees only have one top node. Returns : Bio::Taxonomy::Taxon object Args : none =cut sub get_root_node{ my ($self) = @_; return $self->{'_rootnode'}; } =head2 set_root_node Title : set_root_node Usage : $tree->set_root_node($node) Function: Set the Root Node for the Tree Returns : Bio::Taxonomy::Taxon Args : Bio::Taxonomy::Taxon =cut sub set_root_node{ my ($self,$value) = @_; if( defined $value ) { if( ! $value->isa('Bio::Taxonomy::Taxon') ) { $self->warn("Trying to set the root node to $value which is not a Bio::Taxonomy::Taxon"); return $self->get_root_node; } $self->{'_rootnode'} = $value; } return $self->get_root_node; } =head2 get_leaves Title : get_leaves Usage : my @nodes = $tree->get_leaves() Function: Return list of Bio::Taxonomy::Taxon objects Returns : array of Bio::Taxonomy::Taxon objects Args : =cut sub get_leaves{ my ($self) = @_; my $node = $self->get_root_node; my @leaves; my @children = ($node); for (@children) { push @children, $_->each_Descendent(); } for (@children) { push @leaves, $_ if $_->is_Leaf; } return @leaves; } =head2 make_species_branch Title : make_species_branch Usage : @nodes = $tree->make_species_branch($species,$taxonomy) Function: Return list of Bio::Taxonomy::Taxon objects based on a Bio::Species object Returns : array of Bio::Taxonomy::Taxon objects Args : Bio::Species and Bio::Taxonomy objects =cut # I'm not happy that make_species_branch and make_branch are seperate routines # should be able to just make_branch and have it sort things out sub make_species_branch{ my ($self,$species,$taxonomy) = @_; if (! $species->isa('Bio::Species') ) { $self->throw("Trying to classify $species which is not a Bio::Species object"); } if (! $taxonomy->isa('Bio::Taxonomy') ) { $self->throw("Trying to classify with $taxonomy which is not a Bio::Taxonomy object"); } # this is done to make sure we aren't duplicating a path (let God sort them out) if (defined $self->get_root_node) { $self->get_root_node->remove_all_Descendents; } my @nodes; # nb taxa in [i][0] and ranks in [i][1] my @taxa=$taxonomy->classify($species); for (my $i = 0; $i < @taxa; $i++) { $nodes[$i]=Bio::Taxonomy::Taxon->new(-taxon => $taxa[$i][0], -rank => $taxa[$i][1]); } for (my $i = 0; $i < @taxa-1; $i++) { $nodes[$i]->add_Descendent($nodes[$i+1]); } $self->set_root_node($nodes[0]); return @nodes; } =head2 make_branch Title : make_branch Usage : $tree->make_branch($node) Function: Make a linear Bio::Taxonomy::Tree object from a leafish node Returns : Args : Bio::Taxonomy::Taxon object =cut sub make_branch{ my ($self,$node) = @_; # this is done to make sure we aren't duplicating a path (let God sort them out) # note that if you are using a linked set of node which include node # already in the tree, this will break $self->get_root_node->remove_all_Descendents; while (defined $node->ancestor) { $self->set_root_node($node); $node=$node->ancestor; } } =head2 splice Title : splice Usage : @nodes = $tree->splice($tree) Function: Return a of Bio::Taxonomy::Tree object that is a fusion of two Returns : array of Bio::Taxonomy::Taxon added to tree Args : Bio::Taxonomy::Tree object =cut sub splice{ my ($self,$tree) = @_; my @nodes; my @newleaves = $tree->get_leaves; foreach my $leaf (@newleaves) { push @nodes,$self->add_branch($leaf); } return @nodes; } =head2 add_species Title : add_species Usage : @nodes = $tree->add_species($species,$taxonomy) Function: Return a of Bio::Taxonomy::Tree object with a new species added Returns : array of Bio::Taxonomy::Taxon added to tree Args : Bio::Species object =cut sub add_species{ my ($self,$species,$taxonomy) = @_; my $branch=Bio::Taxonomy::Tree->new; my @nodes=$branch->make_species_branch($species,$taxonomy); my ($newleaf)=$branch->get_leaves; return $self->add_branch($newleaf); } =head2 add_branch Title : add_branch Usage : $tree->add_branch($node,boolean) Function: Return a of Bio::Taxonomy::Tree object with a new branch added Returns : array of Bio::Taxonomy::Taxon objects of the resulting tree Args : Bio::Taxonomy::Taxon object boolean flag to force overwrite of descendent (see Bio::Node->add_Descendent) =cut sub add_branch { my ($self,$node,$force) = @_; my $best_node_level=0; my ($best_node,@nodes,$common); my @leaves=$self->get_leaves; foreach my $leaf (@leaves) { $common=$node->recent_common_ancestor($leaf); # the root of the part to add if (defined $common && ($common->distance_to_root > $best_node_level)) { $best_node_level = $common->distance_to_root; $best_node = $common; } } return unless defined $best_node; push @nodes,($self->get_root_node,$self->get_root_node->get_Descendents); foreach my $node (@nodes) { if ((defined $best_node->id && $best_node->id == $node->id) || ($best_node->rank eq $node->rank && $best_node->taxon eq $node->taxon) && ($best_node->rank ne 'no rank')) { foreach my $descendent ($common->each_Descendent) { $node->add_Descendent($descendent,$force); } } $self->set_root_node($node) if $node->distance_to_root==0; } return ($common->get_Descendents); } =head2 remove_branch Title : remove_branch Usage : $tree->remove_branch($node) Function: remove a branch up to the next multifurcation Returns : Args : Bio::Taxonomy::Taxon object =cut sub remove_branch{ my ($self,$node) = @_; # we can define a branch at any point along it while (defined $node->ancestor) { last if $node->ancestor->each_Descendent > 1; $node=$node->ancestor; } $node->remove_all_Descendents; # I'm not sure if this is necessary, # but I don't see that remove_Descendent # has the side effect of deleting # descendent nodes of the deletee $node->ancestor->remove_Descendent($node); } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools��������������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 15167� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/AlignFactory.pm����������������������������������������������������������000444��000766��000024�� 5156�13155576320� 20253� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::AlignFactory # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@sanger.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::AlignFactory - Base object for alignment factories =head1 SYNOPSIS You won't be using this as an object, but using a dervied class like Bio::Tools::pSW =head1 DESCRIPTION Holds common Alignment Factory attributes in place =head1 CONTACT http://bio.perl.org/ or birney@sanger.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::AlignFactory; use strict; use base qw(Bio::Root::Root); BEGIN { eval { require Bio::Ext::Align; }; if ( $@ ) { print STDERR ("\nThe C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed.\n Please install the bioperl-ext package\n\n"); exit(1); } } sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize(@args); # set up defaults $self->{'kbyte'} = 20000; $self->{'report'} = 0; return $self; } =head2 kbyte Title : kbyte() Usage : set/gets the amount of memory able to be used Function : : $factory->kbyte(200); : Returns : Argument : memory in kilobytes =cut sub kbyte { my ($self,$value) = @_; if( defined $value ) { $self->{'kbyte'} = $value; } return $self->{'kbyte'}; } =head2 report Title : report() Usage : set/gets the report boolean to issue reports or not Function : : $factory->report(1); # reporting goes on : Returns : n/a Argument : 1 or 0 =cut sub report { my ($self,$value) = @_; if( defined $value ) { if( $value != 1 && $value != 0 ) { $self->throw("Attempting to modify AlignFactory Report with no boolean value!"); } $self->{'report'} = $value; } return $self->{'report'}; } =head2 set_memory_and_report Title : set_memory_and_report Usage : Only used by subclasses. Function: Example : Returns : Args : =cut sub set_memory_and_report{ my ($self) = @_; if( $self->{'kbyte'} < 5 ) { $self->throw("You can suggest aligning things with less than 5kb"); } &Bio::Ext::Align::change_max_BaseMatrix_kbytes($self->{'kbyte'}); if( $self->{'report'} == 0 ) { &Bio::Ext::Align::error_off(16); } else { &Bio::Ext::Align::error_on(16); } } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/AmpliconSearch.pm��������������������������������������������������������000444��000766��000024�� 37367�13155576320� 20612� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Tools::AmpliconSearch # # Copyright Florent Angly # # You may distribute this module under the same terms as perl itself package Bio::Tools::AmpliconSearch; use strict; use warnings; use Bio::Tools::IUPAC; use Bio::SeqFeature::Amplicon; use Bio::Tools::SeqPattern; # we require Bio::SeqIO # and Bio::SeqFeature::Primer use base qw(Bio::Root::Root); my $template_str; =head1 NAME Bio::Tools::AmpliconSearch - Find amplicons in a template using degenerate PCR primers =head1 SYNOPSIS use Bio::PrimarySeq; use Bio::Tools::AmpliconSearch; my $template = Bio::PrimarySeq->new( -seq => 'aaaaaCCCCaaaaaaaaaaTTTTTTaaaaaCCACaaaaaTTTTTTaaaaaaaaaa', ); my $fwd_primer = Bio::PrimarySeq->new( -seq => 'CCNC', ); my $rev_primer = Bio::PrimarySeq->new( -seq => 'AAAAA', ); my $search = Bio::Tools::AmpliconSearch->new( -template => $template, -fwd_primer => $fwd_primer, -rev_primer => $rev_primer, ); while (my $amplicon = $search->next_amplicon) { print "Found amplicon at position ".$amplicon->start.'..'.$amplicon->end.":\n"; print $amplicon->seq->seq."\n\n"; } # Now change the template (but you could change the primers instead) and look # for amplicons again $template = Bio::PrimarySeq->new( -seq => 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa', ); $search->template($template); while (my $amplicon = $search->next_amplicon) { print "Found amplicon at position ".$amplicon->start.'..'.$amplicon->end.":\n"; print $amplicon->seq->seq."\n\n"; } =head1 DESCRIPTION Perform an in silico PCR reaction, i.e. search for amplicons in a given template sequence using the specified degenerate primer. The template sequence is a sequence object, e.g. L<Bio::Seq>, and the primers can be a sequence or a L<Bio::SeqFeature::Primer> object and contain ambiguous residues as defined in the IUPAC conventions. The primer sequences are converted into regular expressions using L<Bio::Tools::IUPAC> and the matching regions of the template sequence, i.e. the amplicons, are returned as L<Bio::Seq::PrimedSeq> objects. AmpliconSearch will look for amplicons on both strands (forward and reverse- complement) of the specified template sequence. If the reverse primer is not provided, an amplicon will be returned and span a match of the forward primer to the end of the template. Similarly, when no forward primer is given, match from the beginning of the template sequence. When several amplicons overlap, only the shortest one to more accurately represent the biases of PCR. Future improvements may include modelling the effects of the number of PCR cycles or temperature on the PCR products. =head1 TODO Future improvements may include: =over =item * Allowing a small number of primer mismatches =item * Reporting all amplicons, including overlapping ones =item * Putting a limit on the length of amplicons, in accordance with the processivity of the polymerase used =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Florent Angly <florent.angly@gmail.com> =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =head2 new Title : new Usage : my $search = Bio::Tools::AmpliconSearch->new( ); Function : Initialize an amplicon search Args : -template Sequence object for the template sequence. This object will be converted to Bio::Seq if needed in since features (amplicons and primers) will be added to this object. -fwd_primer A sequence object representing the forward primer -rev_primer A sequence object representing the reverse primer -primer_file Read primers from a sequence file. It replaces -fwd_primer and -rev_primer (optional) -attach_primers Whether or not to attach primers to Amplicon objects. Default: 0 (off) Returns : A Bio::Tools::AmpliconSearch object =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($template, $primer_file, $fwd_primer, $rev_primer, $attach_primers) = $self->_rearrange([qw(TEMPLATE PRIMER_FILE FWD_PRIMER REV_PRIMER ATTACH_PRIMERS)], @args); # Get primers if (defined $primer_file) { $self->primer_file($primer_file); } else { $self->fwd_primer($fwd_primer || ''); $self->rev_primer($rev_primer || ''); } # Get template sequence $self->template($template) if defined $template; $self->attach_primers($attach_primers) if defined $attach_primers; return $self; } =head2 template Title : template Usage : my $template = $search->template; Function : Get/set the template sequence. Setting a new template resets any search in progress. Args : Optional Bio::Seq object Returns : A Bio::Seq object =cut sub template { my ($self, $template) = @_; if (defined $template) { if ( not(ref $template) || not $template->isa('Bio::PrimarySeqI') ) { # Not a Bio::Seq or Bio::PrimarySeq $self->throw("Expected a sequence object as input but got a '".ref($template)."'\n"); } if (not $template->isa('Bio::SeqI')) { # Convert sequence object to Bio::Seq Seq so that features can be added my $primary_seq = $template; $template = Bio::Seq->new(); $template->primary_seq($primary_seq); } $self->{template} = $template; # Reset search in progress $template_str = undef; } return $self->{template}; } =head2 fwd_primer Title : fwd_primer Usage : my $primer = $search->fwd_primer; Function : Get/set the forward primer. Setting a new forward primer resets any search in progress. Args : Optional sequence object or primer object or '' to match beginning of sequence. Returns : A sequence object or primer object or undef =cut sub fwd_primer { my ($self, $primer) = @_; if (defined $primer) { $self->_set_primer('fwd', $primer); } return $self->{fwd_primer}; } =head2 rev_primer Title : rev_primer Usage : my $primer = $search->rev_primer; Function : Get/set the reverse primer. Setting a new reverse primer resets any search in progress. Args : Optional sequence object or primer object or '' to match end of sequence. Returns : A sequence object or primer object or undef =cut sub rev_primer { my ($self, $primer) = @_; if (defined $primer) { $self->_set_primer('rev', $primer); } return $self->{rev_primer}; } sub _set_primer { # Save a primer (sequence object) and convert it to regexp. Type is 'fwd' for # the forward primer or 'rev' for the reverse primer. my ($self, $type, $primer) = @_; my $re; my $match_rna = 1; if ($primer eq '') { $re = $type eq 'fwd' ? '^' : '$'; } else { if ( not(ref $primer) || ( not($primer->isa('Bio::PrimarySeqI')) && not($primer->isa('Bio::SeqFeature::Primer')) ) ) { $self->throw('Expected a sequence or primer object as input but got a '.ref($primer)."\n"); } $self->{$type.'_primer'} = $primer; my $seq = $primer->isa('Bio::SeqFeature::Primer') ? $primer->seq : $primer; $re = Bio::Tools::IUPAC->new( -seq => $type eq 'fwd' ? $seq : $seq->revcom, )->regexp($match_rna); } $self->{$type.'_regexp'} = $re; # Reset search in progress $template_str = undef; $self->{regexp} = undef; return $self->{$type.'_primer'}; } =head2 primer_file Title : primer_file Usage : my ($fwd, $rev) = $search->primer_file; Function : Get/set a sequence file to read the primer from. The first sequence must be the forward primer, and the second is the optional reverse primer. After reading the file, the primers are set using fwd_primer() and rev_primer() and returned. Args : Sequence file Returns : Array containing forward and reverse primers as sequence objects. =cut sub primer_file { my ($self, $primer_file) = @_; # Read primer file and convert primers into regular expressions to catch # amplicons present in the database if (not defined $primer_file) { $self->throw("Need to provide an input file\n"); } # Mandatory first primer require Bio::SeqIO; my $in = Bio::SeqIO->new( -file => $primer_file ); my $fwd_primer = $in->next_seq; if (not defined $fwd_primer) { $self->throw("The file '$primer_file' contains no primers\n"); } $fwd_primer->alphabet('dna'); # Force the alphabet since degenerate primers can look like protein sequences # Optional reverse primers my $rev_primer = $in->next_seq; if (defined $rev_primer) { $rev_primer->alphabet('dna'); } else { $rev_primer = ''; } $in->close; $self->fwd_primer($fwd_primer); $self->rev_primer($rev_primer); return ($fwd_primer, $rev_primer); } =head2 attach_primers Title : attach_primers Usage : my $attached = $search->attach_primers; Function : Get/set whether or not to attach primer objects to the amplicon objects. Args : Optional integer (1 for yes, 0 for no) Returns : Integer (1 for yes, 0 for no) =cut sub attach_primers { my ($self, $attach) = @_; if (defined $attach) { $self->{attach_primers} = $attach; require Bio::SeqFeature::Primer; } return $self->{attach_primers} || 0; } =head2 next_amplicon Title : next_amplicon Usage : my $amplicon = $search->next_amplicon; Function : Get the next amplicon Args : None Returns : A Bio::SeqFeature::Amplicon object =cut sub next_amplicon { my ($self) = @_; # Initialize search if (not defined $template_str) { $self->_init; } my $re = $self->_regexp; my $amplicon; if ($template_str =~ m/$re/g) { my ($match, $rev_match) = ($1, $2); my $strand = $rev_match ? -1 : 1; $match = $match || $rev_match; my $end = pos($template_str); my $start = $end - length($match) + 1; $amplicon = $self->_attach_amplicon($start, $end, $strand); } # If no more matches. Make sure calls to next_amplicon() will return undef. if (not $amplicon) { $template_str = ''; } return $amplicon; } sub _init { my ($self) = @_; # Sanity checks if ( not $self->template ) { $self->throw('Need to provide a template sequence'); } if ( not($self->fwd_primer) && not($self->rev_primer) ) { $self->throw('Need to provide at least a primer'); } # Set the template sequence string $template_str = $self->template->seq; # Set the regular expression to match amplicons $self->_regexp; return 1; } sub _regexp { # Get the regexp to match amplicon. If the regexp is not set, initialize it. my ($self, $regexp) = @_; if ( not defined $self->{regexp} ) { # Build regexp that matches amplicons on both strands and reports shortest # amplicon when there are several overlapping amplicons my $fwd_regexp = $self->_fwd_regexp; my $rev_regexp = $self->_rev_regexp; my ($fwd_regexp_rc, $basic_fwd_match, $rev_regexp_rc, $basic_rev_match); if ($fwd_regexp eq '^') { $fwd_regexp_rc = ''; $basic_fwd_match = "(?:.*?$rev_regexp)"; } else { $fwd_regexp_rc = Bio::Tools::SeqPattern->new( -seq => $fwd_regexp, -type => 'dna', )->revcom->str; $basic_fwd_match = "(?:$fwd_regexp.*?$rev_regexp)"; } if ($rev_regexp eq '$') { $rev_regexp_rc = ''; $basic_rev_match = "(?:.*?$fwd_regexp_rc)"; } else { $rev_regexp_rc = Bio::Tools::SeqPattern->new( -seq => $rev_regexp, -type => 'dna', )->revcom->str; $basic_rev_match = "(?:$rev_regexp_rc.*?$fwd_regexp_rc)"; } my $fwd_exclude = "(?!$basic_rev_match". ($fwd_regexp eq '^' ? '' : "|$fwd_regexp"). ")"; my $rev_exclude = "(?!$basic_fwd_match". ($rev_regexp eq '$' ? '' : "|$rev_regexp_rc"). ')'; $self->{regexp} = qr/ ( $fwd_regexp (?:$fwd_exclude.)*? $rev_regexp ) | ( $rev_regexp_rc (?:$rev_exclude.)*? $fwd_regexp_rc ) /xi; } return $self->{regexp}; } =head2 annotate_template Title : annotate_template Usage : my $template = $search->annotate_template; Function : Search for all amplicons and attach them to the template. This is equivalent to running: while (my $amplicon = $self->next_amplicon) { # do something } my $annotated = $self->template; Args : None Returns : A Bio::Seq object with attached Bio::SeqFeature::Amplicons (and Bio::SeqFeature::Primers if you set -attach_primers to 1). =cut sub annotate_template { my ($self) = @_; # Search all amplicons and attach them to template 1 while $self->next_amplicon; # Return annotated template return $self->template; } sub _fwd_regexp { my ($self) = @_; return $self->{fwd_regexp}; } sub _rev_regexp { my ($self) = @_; return $self->{rev_regexp}; } sub _attach_amplicon { # Create an amplicon object and attach it to template my ($self, $start, $end, $strand) = @_; # Create Bio::SeqFeature::Amplicon feature and attach it to the template my $amplicon = Bio::SeqFeature::Amplicon->new( -start => $start, -end => $end, -strand => $strand, -template => $self->template, ); # Create Bio::SeqFeature::Primer feature and attach them to the amplicon if ($self->attach_primers) { for my $type ('fwd', 'rev') { my ($pstart, $pend, $pstrand, $primer_seq); # Coordinates relative to amplicon if ($type eq 'fwd') { # Forward primer $primer_seq = $self->fwd_primer; next if not defined $primer_seq; $pstart = 1; $pend = $primer_seq->length; $pstrand = $amplicon->strand; } else { # Optional reverse primer $primer_seq = $self->rev_primer; next if not defined $primer_seq; $pstart = $end - $primer_seq->length + 1; $pend = $end; $pstrand = -1 * $amplicon->strand; } # Absolute coordinates needed $pstart += $start - 1; $pend += $start - 1; my $primer = Bio::SeqFeature::Primer->new( -start => $pstart, -end => $pend, -strand => $pstrand, -template => $amplicon, ); # Attach primer to amplicon if ($type eq 'fwd') { $amplicon->fwd_primer($primer); } else { $amplicon->rev_primer($primer); } } } return $amplicon; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/AnalysisResult.pm��������������������������������������������������������000444��000766��000024�� 22556�13155576320� 20676� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::AnalysisResult # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp-at-gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::AnalysisResult - Base class for analysis result objects and parsers =head1 SYNOPSIS # obtain a AnalysisResult derived object somehow print "Method ", $result->analysis_method(), ", version ", $result->analysis_method_version(), ", performed on ", $result->analysis_date(), "\n"; # annotate a sequence utilizing SeqAnalysisParserI methods while($feat = $result->next_feature()) { $seq->add_SeqFeature($feat); } $result->close(); # query object, e.g. a Bio::SeqI implementing object $queryseq = $result->analysis_query(); # Subject of the analysis -- may be undefined. Refer to derived module # to find out what is returned. $subject = $result->analysis_subject(); =head1 DESCRIPTION The AnalysisResult module is supposed to be the base class for modules encapsulating parsers and interpreters for the result of a analysis that was carried out with a query sequence. The notion of an analysis represented by this base class is that of a unary or binary operator, taking either one query or a query and a subject and producing a result. The query is e.g. a sequence, and a subject is either a sequence, too, or a database of sequences. This module also implements the Bio::SeqAnalysisParserI interface, and thus can be used wherever such an object fits. See L<Bio::SeqAnalysisParserI>. Developers will find a ready-to-use B<parse()> method, but need to implement B<next_feature()> in an inheriting class. Support for initialization with input file names and reading from streams is also ready to use. Note that this module does not provide support for B<running> an analysis. Rather, it is positioned in the subsequent parsing step (concerned with turning raw results into BioPerl objects). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp-at-gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::AnalysisResult; use strict; use base qw(Bio::Root::Root Bio::SeqAnalysisParserI Bio::AnalysisResultI Bio::Root::IO); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } sub _initialize { my($self,@args) = @_; my $make = $self->SUPER::_initialize(@args); $self->_initialize_state(@args); return $make; # success - we hope! } =head2 _initialize_state Title : _initialize_state Usage : n/a; usually called by _initialize() Function: This method is for BioPerl B<developers> only, as indicated by the leading underscore in its name. Performs initialization or reset of the state of this object. The difference to _initialize() is that it may be called at any time, and repeatedly within the lifetime of this object. B<Note>, however, that this is potentially dangerous in a multi-threading environment. In general, calling this method twice is discouraged for this reason. This method is supposed to reset the state such that any 'history' is lost. State information that does not change during object lifetime is not considered as history, e.g. parent, name, etc shall not be reset. An inheriting object should only be concerned with state information it introduces itself, and for everything else call SUPER::_initialize_state(@args). An example is parsing an input file: a state reset implies discarding any unread input, and the actual input itself, followed by setting the new input. The argument syntax is the same as for L<new()|new> and L<_initialize()|_initialize>, i.e., named parameters following the -name=>$value convention. The following parameters are dealt with by the implementation provided here: -INPUT, -FH, -FILE (tags are case-insensitive). Example : Returns : Args : =cut sub _initialize_state { my ($self,@args) = @_; $self->close(); $self->_initialize_io(@args); $self->{'_analysis_sbjct'} = undef; $self->{'_analysis_query'} = undef; $self->{'_analysis_prog'} = undef; $self->{'_analysis_progVersion'} = undef; $self->{'_analysis_date'} = undef; return 1; } # =head2 parse # # Title : parse # Usage : $obj->parse(-input=>$inputobj, [ -params=>[@params] ], # [ -method => $method ] ) # Function: Sets up parsing for feature retrieval from an analysis file, # or object. # # This method was originally required by SeqAnalysisParserI, but # is now discouraged due to potential problems in a multi- # threading environment (CORBA!). If called only once, it doesn't # add any functionality to calling new() with the same # parameters. # # The implementation provided here calls automatically # _initialize_state() and passes on -input=>$inputobj and # @params as final arguments. # Example : # Returns : void # Args : B<input> - object/file where analysis are coming from # B<params> - parameter to use when parsing/running analysis # B<method> - method of analysis # # =cut sub parse { my ($self, @args) = @_; my ($input, $params, $method) = $self->_rearrange([qw(INPUT PARAMS METHOD )], @args); # initialize with new input if($params) { $self->_initialize_state('-input' => $input, @$params); } else { $self->_initialize_state('-input' => $input); } $self->analysis_method($method) if $method; } =head2 analysis_query Usage : $query_obj = $result->analysis_query(); Purpose : Set/Get the name of the query used to generate the result, that is, the entity on which the analysis was performed. Will mostly be a sequence object (Bio::PrimarySeq compatible). Argument : Returns : The object set before. Mostly a Bio::PrimarySeq compatible object. =cut #-------- sub analysis_query { my ($self, $obj) = @_; if($obj) { $self->{'_analysis_query'} = $obj; } return $self->{'_analysis_query'}; } #-------- =head2 analysis_subject Usage : $result->analyis_subject(); Purpose : Set/Get the subject of the analysis against which it was performed. For similarity searches it will probably be a database, and for sequence feature predictions (exons, promoters, etc) it may be a collection of models or homologous sequences that were used, or undefined. Returns : The object that was set before, or undef. Argument : =cut #--------------- sub analysis_subject { #--------------- my ($self, $sbjct_obj) = @_; if($sbjct_obj) { $self->{'_analysis_sbjct'} = $sbjct_obj; } return $self->{'_analysis_sbjct'}; } =head2 analysis_date Usage : $result->analysis_date(); Purpose : Set/Get the date on which the analysis was performed. Returns : String Argument : Comments : =cut #---------- sub analysis_date { my ($self, $date) = @_; if($date) { $self->{'_analysis_date'} = $date; } return $self->{'_analysis_date'}; } #---------- =head2 analysis_method Usage : $result->analysis_method(); Purpose : Set/Get the name of the sequence analysis method that was used to produce this result (BLASTP, FASTA, etc.). May also be the actual name of a program. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method) { $self->{'_analysis_prog'} = $method; } return $self->{'_analysis_prog'}; } =head2 analysis_method_version Usage : $result->analysis_method_version(); Purpose : Set/Get the version string of the analysis program. : (e.g., 1.4.9MP, 2.0a19MP-WashU). Returns : String Argument : n/a =cut #--------------------- sub analysis_method_version { #--------------------- my ($self, $version) = @_; if($version) { $self->{'_analysis_progVersion'} = $version; } return $self->{'_analysis_progVersion'}; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Blat.pm������������������������������������������������������������������000555��000766��000024�� 15442�13155576320� 16575� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Blat # # Written by Balamurugan Kumarasamy # # You may distribute this module under the same terms as perl itself # =head1 NAME Bio::Tools::Blat - parser for Blat program =head1 SYNOPSIS use Bio::Tools::Blat; my $blat_parser = Bio::Tools::Blat->new(-fh =>$filehandle ); while( my $blat_feat = $blat_parser->next_result ) { push @blat_feat, $blat_feat; } =head1 DESCRIPTION Parser for Blat program =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Balamurugan Kumarasamy Email: bala@tll.org.sg =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Blat; use strict; use Bio::SeqFeature::Generic; use Bio::SeqFeature::FeaturePair; use Bio::SeqFeature::Generic; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::Blat->new(-fh=>$filehandle); Function: Builds a new Bio::Tools::Blat object Returns : Bio::Tools::Blat Args : -filename -fh (filehandle) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_result Title : next_result Usage : my $feat = $blat_parser->next_result Function: Get the next result set from parser data Returns : L<Bio::SeqFeature::Generic> Args : none =cut sub next_result { my ($self) = @_; my $filehandle; my $line; my $id; while ($_=$self->_readline()){ # first split on spaces: $line = $_; chomp $line; my ($matches, $mismatches, $rep_matches, $n_count, $q_num_insert, $q_base_insert, $t_num_insert, $t_base_insert, $strand, $q_name, $q_length, $q_start, $q_end, $t_name, $t_length, $t_start, $t_end, $block_count, $block_sizes, $q_starts, $t_starts ) = split; my $superfeature = Bio::SeqFeature::Generic->new(); # ignore any preceeding text next unless ( $matches =~/^\d+$/ ); # create as many features as blocks there are in each output line my (%feat1, %feat2); $feat1{name} = $t_name; $feat2{name} = $q_name; $strand = $1 if ($strand =~/([+-])[+-]/); $feat2{strand} = 1; $feat1{strand} = $strand; my $percent_id = sprintf "%.2f", (100 * ($matches + $rep_matches)/( $matches + $mismatches + $rep_matches)); unless ( $q_length ){ $self->warn("length of query is zero, something is wrong!"); next; } my $score = sprintf "%.2f", (100 * ( $matches + $mismatches + $rep_matches ) / $q_length); # size of each block of alignment (inclusive) my @block_sizes = split ",",$block_sizes; # start position of each block (you must add 1 as psl output # is off by one in the start coordinate) my @q_start_positions = split ",",$q_starts; my @t_start_positions = split ",",$t_starts; $superfeature->seq_id($q_name); $superfeature->score( $score ); $superfeature->add_tag_value('percent_id',$percent_id); # each line of output represents one possible entire aligment # of the query (feat1) and the target(feat2) for (my $i=0; $i<$block_count; $i++ ){ my ($query_start,$query_end); if ( $strand eq '+' ){ $query_start = $q_start_positions[$i] + 1; $query_end = $query_start + $block_sizes[$i] - 1; }else{ $query_end = $q_length - $q_start_positions[$i]; $query_start = $query_end - $block_sizes[$i] + 1; } #$feat2 {start} = $q_start_positions[$i] + 1; #$feat2 {end} = $feat2{start} + $block_sizes[$i] - 1; $feat2 {start} = $query_start; $feat2 {end} = $query_end; if ( $query_end < $query_start ){ $self->warn("dodgy feature coordinates: end = $query_end, start = $query_start. Reversing..."); $feat2 {end} = $query_start; $feat2 {start} = $query_end; } $feat1 {start} = $t_start_positions[$i] + 1; $feat1 {end} = $feat1{start} + $block_sizes[$i] - 1; # we put all the features with the same score and percent_id $feat2 {score} = $score; $feat1 {score} = $feat2 {score}; $feat2 {percent} = $percent_id; $feat1 {percent} = $feat2 {percent}; # other stuff: $feat1 {db} = undef; $feat1 {db_version} = undef; $feat1 {program} = 'blat'; $feat1 {p_version} = '1'; $feat1 {source} = 'blat'; $feat1 {primary} = 'similarity'; $feat2 {source} = 'blat'; $feat2 {primary} = 'similarity'; my $feature_pair = $self->create_feature(\%feat1, \%feat2); $superfeature->add_sub_SeqFeature( $feature_pair,'EXPAND'); } return $superfeature; } } =head2 create_feature Title : create_feature Usage : my $feat=$blat_parser->create_feature($feature,$seqname) Function: creates a SeqFeature Generic object Returns : L<Bio::SeqFeature::Generic> Args : =cut sub create_feature { my ($self, $feat1,$feat2) = @_; my $feature1= Bio::SeqFeature::Generic->new( -seq_id =>$feat1->{name}, -start =>$feat1->{start}, -end =>$feat1->{end}, -strand =>$feat1->{strand}, -score =>$feat1->{score}, -source =>$feat1->{source}, -primary =>$feat1->{primary} ); my $feature2= Bio::SeqFeature::Generic->new( -seq_id =>$feat2->{name}, -start =>$feat2->{start}, -end =>$feat2->{end}, -strand =>$feat2->{strand}, -score =>$feat2->{score}, -source =>$feat2->{source}, -primary =>$feat2->{primary} ); my $featurepair = Bio::SeqFeature::FeaturePair->new; $featurepair->feature1 ($feature1); $featurepair->feature2 ($feature2); $featurepair->add_tag_value('evalue',$feat2->{p}); $featurepair->add_tag_value('percent_id',$feat2->{percent}); $featurepair->add_tag_value("hid",$feat2->{primary}); return $featurepair; } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/CodonTable.pm������������������������������������������������������������000444��000766��000024�� 66463�13155576320� 17733� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # bioperl module for Bio::Tools::CodonTable # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::CodonTable - Codon table object =head1 SYNOPSIS # This is a read-only class for all known codon tables. The IDs are # the ones used by nucleotide sequence databases. All common IUPAC # ambiguity codes for DNA, RNA and amino acids are recognized. use Bio::Tools::CodonTable; # defaults to ID 1 "Standard" $myCodonTable = Bio::Tools::CodonTable->new(); $myCodonTable2 = Bio::Tools::CodonTable->new( -id => 3 ); # change codon table $myCodonTable->id(5); # examine codon table print join (' ', "The name of the codon table no.", $myCodonTable->id(4), "is:", $myCodonTable->name(), "\n"); # print possible codon tables $tables = Bio::Tools::CodonTable->tables; while ( ($id,$name) = each %{$tables} ) { print "$id = $name\n"; } # translate a codon $aa = $myCodonTable->translate('ACU'); $aa = $myCodonTable->translate('act'); $aa = $myCodonTable->translate('ytr'); # reverse translate an amino acid @codons = $myCodonTable->revtranslate('A'); @codons = $myCodonTable->revtranslate('Ser'); @codons = $myCodonTable->revtranslate('Glx'); @codons = $myCodonTable->revtranslate('cYS', 'rna'); # reverse translate an entire amino acid sequence into a IUPAC # nucleotide string my $seqobj = Bio::PrimarySeq->new(-seq => 'FHGERHEL'); my $iupac_str = $myCodonTable->reverse_translate_all($seqobj); # boolean tests print "Is a start\n" if $myCodonTable->is_start_codon('ATG'); print "Is a terminator\n" if $myCodonTable->is_ter_codon('tar'); print "Is a unknown\n" if $myCodonTable->is_unknown_codon('JTG'); =head1 DESCRIPTION Codon tables are also called translation tables or genetic codes since that is what they represent. A bit more complete picture of the full complexity of codon usage in various taxonomic groups is presented at the NCBI Genetic Codes Home page. CodonTable is a BioPerl class that knows all current translation tables that are used by primary nucleotide sequence databases (GenBank, EMBL and DDBJ). It provides methods to output information about tables and relationships between codons and amino acids. This class and its methods recognized all common IUPAC ambiguity codes for DNA, RNA and animo acids. The translation method follows the conventions in EMBL and TREMBL databases. It is a nuisance to separate RNA and cDNA representations of nucleic acid transcripts. The CodonTable object accepts codons of both type as input and allows the user to set the mode for output when reverse translating. Its default for output is DNA. Note: This class deals primarily with individual codons and amino acids. However in the interest of speed you can L<translate> longer sequence, too. The full complexity of protein translation is tackled by L<Bio::PrimarySeqI::translate>. The amino acid codes are IUPAC recommendations for common amino acids: A Ala Alanine R Arg Arginine N Asn Asparagine D Asp Aspartic acid C Cys Cysteine Q Gln Glutamine E Glu Glutamic acid G Gly Glycine H His Histidine I Ile Isoleucine L Leu Leucine K Lys Lysine M Met Methionine F Phe Phenylalanine P Pro Proline O Pyl Pyrrolysine (22nd amino acid) U Sec Selenocysteine (21st amino acid) S Ser Serine T Thr Threonine W Trp Tryptophan Y Tyr Tyrosine V Val Valine B Asx Aspartic acid or Asparagine Z Glx Glutamine or Glutamic acid J Xle Isoleucine or Valine (mass spec ambiguity) X Xaa Any or unknown amino acid It is worth noting that, "Bacterial" codon table no. 11 produces an polypeptide that is, confusingly, identical to the standard one. The only differences are in available initiator codons. NCBI Genetic Codes home page: (Last update of the Genetic Codes: April 30, 2013) https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c ASN.1 version with ids 1 to 25 is at: ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt Thanks to Matteo diTomasso for the original Perl implementation of these tables. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::CodonTable; use vars qw(@NAMES @TABLES @STARTS $TRCOL $CODONS %IUPAC_DNA $CODONGAP $GAP %IUPAC_AA %THREELETTERSYMBOLS $VALID_PROTEIN $TERMINATOR); use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Tools::IUPAC; use Bio::SeqUtils; use base qw(Bio::Root::Root); # first set internal values for all translation tables BEGIN { use constant CODONSIZE => 3; $GAP = '-'; $CODONGAP = $GAP x CODONSIZE; @NAMES = #id ( 'Strict', #0, special option for ATG-only start 'Standard', #1 'Vertebrate Mitochondrial',#2 'Yeast Mitochondrial',# 3 'Mold, Protozoan, and Coelenterate Mitochondrial and Mycoplasma/Spiroplasma',#4 'Invertebrate Mitochondrial',#5 'Ciliate, Dasycladacean and Hexamita Nuclear',# 6 '', '', 'Echinoderm and Flatworm Mitochondrial',#9 'Euplotid Nuclear',#10 'Bacterial, Archaeal and Plant Plastid',# 11 'Alternative Yeast Nuclear',# 12 'Ascidian Mitochondrial',# 13 'Alternative Flatworm Mitochondrial',# 14 'Blepharisma Nuclear',# 15 'Chlorophycean Mitochondrial',# 16 '', '', '', '', 'Trematode Mitochondrial',# 21 'Scenedesmus obliquus Mitochondrial', #22 'Thraustochytrium Mitochondrial', #23 'Pterobranchia Mitochondrial', #24 'Candidate Division SR1 and Gracilibacteria', #25 ); @TABLES = qw( FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG '' '' FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG '' '' '' '' FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG ); # (bases used for these tables, for reference) # 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG # 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG # 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG @STARTS = qw( -----------------------------------M---------------------------- ---M---------------M---------------M---------------------------- --------------------------------MMMM---------------M------------ ----------------------------------MM---------------------------- --MM---------------M------------MMMM---------------M------------ ---M----------------------------MMMM---------------M------------ -----------------------------------M---------------------------- '' '' -----------------------------------M---------------M------------ -----------------------------------M---------------------------- ---M---------------M------------MMMM---------------M------------ -------------------M---------------M---------------------------- ---M------------------------------MM---------------M------------ -----------------------------------M---------------------------- -----------------------------------M---------------------------- -----------------------------------M---------------------------- '' '' '' '' -----------------------------------M---------------M------------ -----------------------------------M---------------------------- --------------------------------M--M---------------M------------ ---M---------------M---------------M---------------M------------ ---M-------------------------------M---------------M------------ ); my @nucs = qw(t c a g); my $x = 0; ($CODONS, $TRCOL) = ({}, {}); for my $i (@nucs) { for my $j (@nucs) { for my $k (@nucs) { my $codon = "$i$j$k"; $CODONS->{$codon} = $x; $TRCOL->{$x} = $codon; $x++; } } } %IUPAC_DNA = Bio::Tools::IUPAC->iupac_iub(); %IUPAC_AA = Bio::Tools::IUPAC->iupac_iup(); %THREELETTERSYMBOLS = Bio::SeqUtils->valid_aa(2); $VALID_PROTEIN = '['.join('',Bio::SeqUtils->valid_aa(0)).']'; $TERMINATOR = '*'; } sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my($id) = $self->_rearrange([qw(ID )], @args); $id = 1 if ( ! $id ); $id && $self->id($id); return $self; # success - we hope! } =head2 id Title : id Usage : $obj->id(3); $id_integer = $obj->id(); Function: Sets or returns the id of the translation table. IDs are integers from 0 (special ATG-only start) to 25, excluding 7-8 and 17-20 which have been removed. If an invalid ID is given the method returns 1, the standard table. Example : Returns : value of id, a scalar, warn and fall back to 1 (standard table) if specified id is not valid Args : newvalue (optional) =cut sub id{ my ($self,$value) = @_; if( defined $value) { if ( not defined $TABLES[$value] or $TABLES[$value] eq '') { $self->warn("Not a valid codon table ID [$value], using [1] instead "); $value = 1; } $self->{'id'} = $value; } return $self->{'id'}; } =head2 name Title : name Usage : $obj->name() Function: returns the descriptive name of the translation table Example : Returns : A string Args : None =cut sub name{ my ($self) = @_; my ($id) = $self->{'id'}; return $NAMES[$id]; } =head2 tables Title : tables Usage : $obj->tables() or Bio::Tools::CodonTable->tables() Function: returns a hash reference where each key is a valid codon table id() number, and each value is the corresponding codon table name() string Example : Returns : A hashref Args : None =cut sub tables{ my %tables; for my $id (0 .. $#NAMES) { my $name = $NAMES[$id]; $tables{$id} = $name if $name; } return \%tables; } =head2 translate Title : translate Usage : $obj->translate('YTR') Function: Returns a string of one letter amino acid codes from nucleotide sequence input. The imput can be of any length. Returns 'X' for unknown codons and codons that code for more than one amino acid. Returns an empty string if input is not three characters long. Exceptions for these are: - IUPAC amino acid code B for Aspartic Acid and Asparagine, is used. - IUPAC amino acid code Z for Glutamic Acid, Glutamine is used. - if the codon is two nucleotides long and if by adding an a third character 'N', it codes for a single amino acid (with exceptions above), return that, otherwise return empty string. Returns empty string for other input strings that are not three characters long. Example : Returns : a string of one letter ambiguous IUPAC amino acid codes Args : ambiguous IUPAC nucleotide string =cut sub translate { my ($self, $seq, $complete_codon) = @_; $self->throw("Calling translate without a seq argument!") unless defined $seq; return '' unless $seq; my $id = $self->id; my ($partial) = 0; $partial = 2 if length($seq) % CODONSIZE == 2; $seq = lc $seq; $seq =~ tr/u/t/; my $protein = ""; if ($seq =~ /[^actg]/ ) { #ambiguous chars for (my $i = 0; $i < (length($seq) - (CODONSIZE-1)); $i+= CODONSIZE) { my $triplet = substr($seq, $i, CODONSIZE); if( $triplet eq $CODONGAP ) { $protein .= $GAP; } elsif (exists $CODONS->{$triplet}) { $protein .= substr($TABLES[$id], $CODONS->{$triplet},1); } else { $protein .= $self->_translate_ambiguous_codon($triplet); } } } else { # simple, strict translation for (my $i = 0; $i < (length($seq) - (CODONSIZE -1)); $i+=CODONSIZE) { my $triplet = substr($seq, $i, CODONSIZE); if( $triplet eq $CODONGAP ) { $protein .= $GAP; } if (exists $CODONS->{$triplet}) { $protein .= substr($TABLES[$id], $CODONS->{$triplet}, 1); } else { $protein .= 'X'; } } } if ($partial == 2 && $complete_codon) { # 2 overhanging nucleotides my $triplet = substr($seq, ($partial -4)). "n"; if( $triplet eq $CODONGAP ) { $protein .= $GAP; } elsif (exists $CODONS->{$triplet}) { my $aa = substr($TABLES[$id], $CODONS->{$triplet},1); $protein .= $aa; } else { $protein .= $self->_translate_ambiguous_codon($triplet, $partial); } } return $protein; } sub _translate_ambiguous_codon { my ($self, $triplet, $partial) = @_; $partial ||= 0; my $id = $self->id; my $aa; my @codons = $self->unambiguous_codons($triplet); my %aas =(); foreach my $codon (@codons) { $aas{substr($TABLES[$id],$CODONS->{$codon},1)} = 1; } my $count = scalar keys %aas; if ( $count == 1 ) { $aa = (keys %aas)[0]; } elsif ( $count == 2 ) { if ($aas{'D'} and $aas{'N'}) { $aa = 'B'; } elsif ($aas{'E'} and $aas{'Q'}) { $aa = 'Z'; } else { $partial ? ($aa = '') : ($aa = 'X'); } } else { $partial ? ($aa = '') : ($aa = 'X'); } return $aa; } =head2 translate_strict Title : translate_strict Usage : $obj->translate_strict('ACT') Function: returns one letter amino acid code for a codon input Fast and simple translation. User is responsible to resolve ambiguous nucleotide codes before calling this method. Returns 'X' for unknown codons and an empty string for input strings that are not three characters long. It is not recommended to use this method in a production environment. Use method translate, instead. Example : Returns : A string Args : a codon = a three nucleotide character string =cut sub translate_strict{ my ($self, $value) = @_; my $id = $self->{'id'}; $value = lc $value; $value =~ tr/u/t/; return '' unless length $value == 3; return 'X' unless defined $CODONS->{$value}; return substr( $TABLES[$id], $CODONS->{$value}, 1 ); } =head2 revtranslate Title : revtranslate Usage : $obj->revtranslate('G') Function: returns codons for an amino acid Returns an empty string for unknown amino acid codes. Ambiguous IUPAC codes Asx,B, (Asp,D; Asn,N) and Glx,Z (Glu,E; Gln,Q) are resolved. Both single and three letter amino acid codes are accepted. '*' and 'Ter' are used for terminator. By default, the output codons are shown in DNA. If the output is needed in RNA (tr/t/u/), add a second argument 'RNA'. Example : $obj->revtranslate('Gly', 'RNA') Returns : An array of three lower case letter strings i.e. codons Args : amino acid, 'RNA' =cut sub revtranslate { my ($self, $value, $coding) = @_; my @codons; if (length($value) == 3 ) { $value = lc $value; $value = ucfirst $value; $value = $THREELETTERSYMBOLS{$value}; } if ( defined $value and $value =~ /$VALID_PROTEIN/ and length($value) == 1 ) { my $id = $self->{'id'}; $value = uc $value; my @aas = @{$IUPAC_AA{$value}}; foreach my $aa (@aas) { #print $aa, " -2\n"; $aa = '\*' if $aa eq '*'; while ($TABLES[$id] =~ m/$aa/g) { my $p = pos $TABLES[$id]; push (@codons, $TRCOL->{--$p}); } } } if ($coding and uc ($coding) eq 'RNA') { for my $i (0..$#codons) { $codons[$i] =~ tr/t/u/; } } return @codons; } =head2 reverse_translate_all Title : reverse_translate_all Usage : my $iup_str = $cttable->reverse_translate_all($seq_object) my $iup_str = $cttable->reverse_translate_all($seq_object, $cutable, 15); Function: reverse translates a protein sequence into IUPAC nucleotide sequence. An 'X' in the protein sequence is converted to 'NNN' in the nucleotide sequence. Returns : a string Args : a Bio::PrimarySeqI compatible object (mandatory) a Bio::CodonUsage::Table object and a threshold if only codons with a relative frequency above the threshold are to be considered. =cut sub reverse_translate_all { my ($self, $obj, $cut, $threshold) = @_; ## check args are OK if (!$obj || !$obj->isa('Bio::PrimarySeqI')){ $self->throw(" I need a Bio::PrimarySeqI object, not a [". ref($obj) . "]"); } if($obj->alphabet ne 'protein') { $self->throw("Cannot reverse translate, need an amino acid sequence .". "This sequence is of type [" . $obj->alphabet ."]"); } my @data; my @seq = split '', $obj->seq; ## if we're not supplying a codon usage table... if( !$cut && !$threshold) { ## get lists of possible codons for each aa. for my $aa (@seq) { if ($aa =~ /x/i) { push @data, (['NNN']); }else { my @cods = $self->revtranslate($aa); push @data, \@cods; } } }else{ #else we are supplying a codon usage table, we just want common codons #check args first. if(!$cut->isa('Bio::CodonUsage::Table')) { $self->throw("I need a Bio::CodonUsage::Table object, not a [". ref($cut). "]."); } my $cod_ref = $cut->probable_codons($threshold); for my $aa (@seq) { if ($aa =~ /x/i) { push @data, (['NNN']); next; } push @data, $cod_ref->{$aa}; } } return $self->_make_iupac_string(\@data); } =head2 reverse_translate_best Title : reverse_translate_best Usage : my $str = $cttable->reverse_translate_best($seq_object,$cutable); Function: Reverse translates a protein sequence into plain nucleotide sequence (GATC), uses the most common codon for each amino acid Returns : A string Args : A Bio::PrimarySeqI compatible object and a Bio::CodonUsage::Table object =cut sub reverse_translate_best { my ($self, $obj, $cut) = @_; if (!$obj || !$obj->isa('Bio::PrimarySeqI')){ $self->throw(" I need a Bio::PrimarySeqI object, not a [". ref($obj) . "]"); } if ($obj->alphabet ne 'protein') { $self->throw("Cannot reverse translate, need an amino acid sequence .". "This sequence is of type [" . $obj->alphabet ."]"); } if ( !$cut | !$cut->isa('Bio::CodonUsage::Table')) { $self->throw("I need a Bio::CodonUsage::Table object, not a [". ref($cut). "]."); } my $str = ''; my @seq = split '', $obj->seq; my $cod_ref = $cut->most_common_codons(); for my $aa ( @seq ) { if ($aa =~ /x/i) { $str .= 'NNN'; next; } if ( defined $cod_ref->{$aa} ) { $str .= $cod_ref->{$aa}; } else { $self->throw("Input sequence contains invalid character: $aa"); } } return $str; } =head2 is_start_codon Title : is_start_codon Usage : $obj->is_start_codon('ATG') Function: returns true (1) for all codons that can be used as a translation start, false (0) for others. Example : $myCodonTable->is_start_codon('ATG') Returns : boolean Args : codon =cut sub is_start_codon{ shift->_codon_is( shift, \@STARTS, 'M' ); } =head2 is_ter_codon Title : is_ter_codon Usage : $obj->is_ter_codon('GAA') Function: returns true (1) for all codons that can be used as a translation tarminator, false (0) for others. Example : $myCodonTable->is_ter_codon('ATG') Returns : boolean Args : codon =cut sub is_ter_codon{ my ($self, $value) = @_; my $id = $self->{'id'}; # We need to ensure U is mapped to T (ie. UAG) $value = uc $value; $value =~ tr/U/T/; if (length $value != 3 ) { # Incomplete codons are not stop codons return 0; } else { my $result = 0; # For all the possible codons, if any are not a stop # codon, fail immediately for my $c ( $self->unambiguous_codons($value) ) { my $m = substr( $TABLES[$id], $CODONS->{$c}, 1 ); if($m eq $TERMINATOR) { $result = 1; } else { return 0; } } return $result; } } # desc: compares the passed value with a single entry in the given # codon table # args: a value (typically a three-char string like 'atg'), # a reference to the appropriate set of codon tables, # a single-character value to check for at the position in the # given codon table # ret: boolean, true if the given codon table contains the $key at the # position corresponding to $value sub _codon_is { my ($self, $value, $table, $key ) = @_; return 0 unless length $value == 3; $value = lc $value; $value =~ tr/u/t/; my $id = $self->{'id'}; for my $c ( $self->unambiguous_codons($value) ) { my $m = substr( $table->[$id], $CODONS->{$c}, 1 ); if ($m eq $key) { return 1; } } return 0; } =head2 is_unknown_codon Title : is_unknown_codon Usage : $obj->is_unknown_codon('GAJ') Function: returns false (0) for all codons that are valid, true (1) for others. Example : $myCodonTable->is_unknown_codon('NTG') Returns : boolean Args : codon =cut sub is_unknown_codon{ my ($self, $value) = @_; $value = lc $value; $value =~ tr/u/t/; return 1 unless $self->unambiguous_codons($value); return 0; } =head2 unambiguous_codons Title : unambiguous_codons Usage : @codons = $self->unambiguous_codons('ACN') Returns : array of strings (one-letter unambiguous amino acid codes) Args : a codon = a three IUPAC nucleotide character string =cut sub unambiguous_codons{ my ($self,$value) = @_; my @nts = map { $IUPAC_DNA{uc $_} } split(//, $value); my @codons; for my $i ( @{$nts[0]} ) { for my $j ( @{$nts[1]} ) { for my $k ( @{$nts[2]} ) { push @codons, lc "$i$j$k"; }}} return @codons; } =head2 _unambiquous_codons deprecated, now an alias for unambiguous_codons =cut sub _unambiquous_codons { unambiguous_codons( undef, @_ ); } =head2 add_table Title : add_table Usage : $newid = $ct->add_table($name, $table, $starts) Function: Add a custom Codon Table into the object. Know what you are doing, only the length of the argument strings is checked! Returns : the id of the new codon table Args : name, a string, optional (can be empty) table, a string of 64 characters startcodons, a string of 64 characters, defaults to standard =cut sub add_table { my ($self, $name, $table, $starts) = @_; $name ||= 'Custom' . $#NAMES + 1; $starts ||= $STARTS[1]; $self->throw('Suspect input!') unless length($table) == 64 and length($starts) == 64; push @NAMES, $name; push @TABLES, $table; push @STARTS, $starts; return $#NAMES; } sub _make_iupac_string { my ($self, $cod_ref) = @_; if(ref($cod_ref) ne 'ARRAY') { $self->throw(" I need a reference to a list of references to codons, ". " not a [". ref($cod_ref) . "]."); } my %iupac_hash = Bio::Tools::IUPAC->iupac_rev_iub(); my $iupac_string = ''; ## the string to be returned for my $aa (@$cod_ref) { ## scan through codon positions, record the differing values, # then look up in the iub hash for my $index(0..2) { my %h; map { my $k = substr($_,$index,1); $h{$k} = undef;} @$aa; my $lookup_key = join '', sort{$a cmp $b}keys %h; ## extend string $iupac_string .= $iupac_hash{uc$lookup_key}; } } return $iupac_string; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Coil.pm������������������������������������������������������������������000555��000766��000024�� 14347�13155576320� 16604� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# Parser module for Coil Bio::Tools::Coil # # Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil # originally written by Marc Sohrmann (ms2@sanger.ac.uk) # Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org> # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org) # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Tools::Coil - parser for Coil output =head1 SYNOPSIS use Bio::Tools::Coil my $parser = Bio::Tools::Coil->new(); while( my $sp_feat = $parser->next_result($file) ) { #do something #eg push @sp_feat, $sp_feat; } =head1 DESCRIPTION Parser for Coil output =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil originally written by Marc Sohrmann (ms2@sanger.ac.uk) Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org> # Please direct questions and support issues to <bioperl-l@bioperl.org> # Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org) =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Coil; use strict; use Bio::SeqFeature::FeaturePair; use Bio::SeqFeature::Generic; use base qw(Bio::Root::Root Bio::Root::IO); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 parse_results Title : parse_results Usage : obj->parse_results Function: Parses the coil output. Automatically called by next_result() if not yet done. Example : Returns : =cut sub parse_results { my ($self,$resfile) = @_; my $filehandle = $resfile; my %result_hash =_read_fasta($filehandle);#bala no file handle my @ids = keys %result_hash; my @feats; foreach my $id (keys %result_hash){ my $pep = reverse ($result_hash{$id}); my $count = my $switch = 0; my ($start, $end); while (my $aa = chop $pep) { $count++; if (!$switch && $aa eq "x") { $start = $count; $switch = 1; } elsif ($switch && $aa ne "x") { $end = $count-1; my (%feature); $feature{name} = $id; $feature{start} = $start; $feature{end} = $end; $feature{source} = "Coils"; $feature{primary} = 'ncoils'; ($feature{program}) = 'ncoils'; $feature{logic_name} = 'Coils'; my $new_feat = $self->create_feature (\%feature); $self->_add_prediction($new_feat); $switch = 0; } } } $self->_predictions_parsed(1); } =head2 next_result Title : next_result Usage : while($feat = $coil->next_result($file)) { # do something } Function: Returns the next protein feature of the coil output file Returns : Args : =cut sub next_result { my ($self,$resfile) = @_; my $gene; $self->parse_results($resfile) unless $self->_predictions_parsed(); $gene = $self->_result(); return $gene; } =head2 _result Title : _result Usage : $feat = $obj->_result() Function: internal Example : Returns : =cut sub _result { my ($self) = @_; return unless(exists($self->{'_feats'}) && @{$self->{'_feats'}}); return shift(@{$self->{'_feats'}}); } =head2 _add_prediction Title : _add_prediction() Usage : $obj->_add_prediction($feat) Function: internal Example : Returns : =cut sub _add_prediction { my ($self, $gene) = @_; if(! exists($self->{'_feats'})) { $self->{'_feats'} = []; } push(@{$self->{'_feats'}}, $gene); } =head2 _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE =cut sub _predictions_parsed { my ($self, $val) = @_; $self->{'_preds_parsed'} = $val if $val; if(! exists($self->{'_preds_parsed'})) { $self->{'_preds_parsed'} = 0; } return $self->{'_preds_parsed'}; } =head2 create_feature Title : create_feature Usage : obj->create_feature(\%feature) Function: Internal(not to be used directly) Returns : Args : =cut sub create_feature { my ($self, $feat) = @_; # create feature object my $feature = Bio::SeqFeature::Generic->new (-seq_id => $feat->{name}, -start => $feat->{start}, -end => $feat->{end}, -score => $feat->{score}, -source => $feat->{source}, -primary => $feat->{primary}, -logic_name => $feat->{logic_name}, ); $feature->add_tag_value('evalue',0); $feature->add_tag_value('percent_id','NULL'); $feature->add_tag_value("hid",$feat->{primary}); return $feature; } =head2 _read_fasta Title : _read_fasta Usage : obj->_read_fasta($file) Function: Internal(not to be used directly) Returns : Args : =cut sub _read_fasta { local (*FILE) = @_; my( $id , $seq , %name2seq);#bala while (<FILE>) { chomp; #bala if (/^>(\S+)/) { my $new_id = $1; if ($id) { $name2seq{$id} = $seq; } $id = $new_id ; $seq = "" ; } elsif (eof) { if ($id) { $seq .= $_ ;#bala line instead of $_ $name2seq{$id} = $seq; } } else { $seq .= $_; } } return %name2seq; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/ECnumber.pm��������������������������������������������������������������000444��000766��000024�� 33757�13155576320� 17421� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::ECnumber # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Christian M. Zmasek <czmasek-at-burnham.org> or <cmzmasek@yahoo.com> # # (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::Tools::ECnumber - representation of EC numbers (Enzyme Classification) =head1 SYNOPSIS use Bio::Tools::ECnumber; # Creation of ECnumber objects my $EC1 = Bio::Tools::ECnumber->new( -ec_string => "4.3.2.1" ); my $EC2 = Bio::Tools::ECnumber->new( -ec_string => "EC 1.1.1.1" ); my $EC3 = Bio::Tools::ECnumber->new(); # Copying my $EC4 = $EC1->copy(); # Modification/canonicalization of ECnumber objects print $EC3->EC_string( "1.01.01.001" ); # Prints "1.1.1.1". # Stringify print $EC3->EC_string(); # or print $EC3->to_string(); # Test for equality # -- Against ECnumber object: if ( $EC3->is_equal( $EC2 ) ) { # Prints "equal". print "equal"; } # -- Against string representation of EC number: if ( ! $EC3->is_equal( "1.1.1.-" ) ) { # Prints "not equal". print "not equal"; } # Test for membership my $EC5 = Bio::Tools::ECnumber->new( -ec_string => "4.3.2.-" ); # -- Against ECnumber object. if ( $EC1->is_member( $EC5 ) ) { # Prints "member". print "member"; } # -- Against string representation of EC number. if ( ! $EC1->is_member( "4.3.1.-" ) ) { # Prints "not member". print "not member"; } =head1 DESCRIPTION L<Bio::Tools::ECnumber> is a representation of EC numbers, the numerical hierarchy for Enzyme Classification. See L<http://www.chem.qmul.ac.uk/iubmb/enzyme/> for more details. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Christian M. Zmasek Email: czmasek-at-burnham.org or cmzmasek@yahoo.com WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::ECnumber; use strict; use constant DEFAULT => "-"; use constant TRUE => 1; use constant FALSE => 0; use base qw(Bio::Root::Root); =head2 new Title : new Usage : $EC1 = Bio::Tools::ECnumber->new( -ec_string => "4.3.2.1" ); or $EC2 = Bio::Tools::ECnumber->new( -ec_string => "4.3.2.2", -comment => "Is EC 4.3.2.2" ); or $EC3 = Bio::Tools::ECnumber->new(); # EC3 is now "-.-.-.-" Function: Creates a new ECnumber object. Parses a EC number from "x.x.x.x", "EC x.x.x.x", "ECx.x.x.x", or "EC:x.x.x.x"; x being either a positive integer or a "-". Returns : A new ECnumber object. Args : A string representing a EC number, e.g. "4.3.2.1" or "EC 4.3.2.1" or "1.-.-.-". =cut sub new { my( $class, @args ) = @_; my $self = $class->SUPER::new( @args ); my ( $EC_string, $comment ) = $self->_rearrange( [ qw( EC_STRING COMMENT ) ], @args ); $self->init(); $EC_string && $self->EC_string( $EC_string ); $comment && $self->comment( $comment ); return $self; } # new =head2 init Title : init() Usage : $EC1->init(); # EC1 is now "-.-.-.-" Function: Initializes this ECnumber to default values. Returns : Args : =cut sub init { my( $self ) = @_; $self->enzyme_class( DEFAULT ); $self->sub_class( DEFAULT ); $self->sub_sub_class( DEFAULT ); $self->serial_number( DEFAULT ); $self->comment( "" ); } # init =head2 copy Title : copy() Usage : $EC2 = $EC1->copy(); Function: Creates a new ECnumber object which is an exact copy of this ECnumber. Returns : A copy of this ECnumber. Args : =cut sub copy { my( $self ) = @_; my $new_ec = $self->new(); $new_ec->enzyme_class( $self->enzyme_class() ); $new_ec->sub_class( $self->sub_class() ); $new_ec->sub_sub_class( $self->sub_sub_class() ); $new_ec->serial_number( $self->serial_number() ); $new_ec->comment( $self->comment() ); return $new_ec; } # copy =head2 EC_string Title : EC_string Usage : $EC3->EC_string( "1.1.1.-" ); or print $EC3->EC_string(); Function: Set/get for string representations of EC numbers. Parses a EC number from "x.x.x.x", "EC x.x.x.x", "ECx.x.x.x", or "EC:x.x.x.x"; x being either a positive integer or a "-". Returns : A string representations of a EC number. Args : A string representations of a EC number. =cut sub EC_string { my ( $self, $value ) = @_; if ( defined $value) { $value =~ s/\s+//g; # Removes white space. $value =~ s/^EC//i; # Removes "EC". $value =~ s/^://; # Removes ":". if ( $value =~ /^([\d-]*)\.([\d-]*)\.([\d-]*)\.([\d-]*)$/ ) { $self->enzyme_class( $1 ); $self->sub_class( $2 ); $self->sub_sub_class( $3 ); $self->serial_number( $4 ); } else { $self->throw( "Illegal format error [$value]" ); } } return $self->to_string(); } # EC_string =head2 to_string Title : to_string() Usage : print $EC3->to_string(); Function: To string method for EC numbers (equals the "get" functionality of "EC_string"). Returns : A string representations of a EC number. Args : =cut sub to_string { my ( $self ) = @_; my $s = $self->enzyme_class() . "."; $s .= $self->sub_class() . "."; $s .= $self->sub_sub_class() . "."; $s .= $self->serial_number(); return $s; } # to_string =head2 is_equal Title : is_equal Usage : if ( $EC3->is_equal( $EC2 ) ) or if ( $EC3->is_equal( "1.1.1.-" ) ) Function: Checks whether this ECnumber is equal to the argument EC number (please note: "1.1.1.1" != "1.1.1.-"). Returns : True (1) or false (0). Args : A ECnumber object or a string representation of a EC number. =cut sub is_equal { my ( $self, $value ) = @_; if ( $self->_is_not_reference( $value ) ) { $value = $self->new( -ec_string => $value ); } else { $self->_is_ECnumber_object( $value ); } unless ( $self->enzyme_class() eq $value->enzyme_class() ) { return FALSE; } unless ( $self->sub_class() eq $value->sub_class() ) { return FALSE; } unless ( $self->sub_sub_class() eq $value->sub_sub_class() ) { return FALSE; } unless ( $self->serial_number() eq $value->serial_number() ) { return FALSE; } return TRUE; } # is_equal =head2 is_member Title : is_member Usage : if ( $EC1->is_member( $EC5 ) ) or if ( $EC1->is_member( "4.3.-.-" ) ) Function: Checks whether this ECnumber is a member of the (incomplete) argument EC number (e.g. "1.1.1.1" is a member of "1.1.1.-" but not of "1.1.1.2"). Returns : True (1) or false (0). Args : A ECnumber object or a string representation of a EC number. =cut sub is_member { my ( $self, $value ) = @_; if ( $self->_is_not_reference( $value ) ) { $value = $self->new( -ec_string => $value ); } else { $self->_is_ECnumber_object( $value ); } $self->_check_for_illegal_defaults(); $value->_check_for_illegal_defaults(); unless ( $value->enzyme_class() eq DEFAULT || $self->enzyme_class() eq $value->enzyme_class() ) { return FALSE; } unless ( $value->sub_class() eq DEFAULT || $self->sub_class() eq $value->sub_class() ) { return FALSE; } unless ( $value->sub_sub_class() eq DEFAULT || $self->sub_sub_class() eq $value->sub_sub_class() ) { return FALSE; } unless ( $value->serial_number() eq DEFAULT || $self->serial_number() eq $value->serial_number() ) { return FALSE; } return TRUE; } # is_member =head2 enzyme_class Title : enzyme_class Usage : $EC1->enzyme_class( 1 ); or print $EC1->enzyme_class(); Function: Set/get for the enzyme class number of ECnumbers. Returns : The enzyme class number of this ECnumber. Args : A positive integer or "-". =cut sub enzyme_class { my ( $self, $value ) = @_; if ( defined $value) { $self->{ "_enzyme_class" } = $self->_check_number( $value ); } return $self->{ "_enzyme_class" }; } # enzyme_class =head2 sub_class Title : sub_class Usage : $EC1->sub_class( 4 ); or print $EC1->sub_class(); Function: Set/get for the enzyme sub class number of ECnumbers. Returns : The enzyme sub class number of this ECnumber. Args : A positive integer or "-". =cut sub sub_class { my ( $self, $value ) = @_; if ( defined $value) { $self->{ "_sub_class" } = $self->_check_number( $value ); } return $self->{ "_sub_class" }; } # sub_class =head2 sub_sub_class Title : sub_sub_class Usage : $EC1->sub_sub_class( 12 ); or print $EC1->sub_sub_class(); Function: Set/get for the enzyme sub sub class number of ECnumbers. Returns : The enzyme sub sub class number of this ECnumber. Args : A positive integer or "-". =cut sub sub_sub_class { my ( $self, $value ) = @_; if ( defined $value) { $self->{ "_sub_sub_class" } = $self->_check_number( $value ); } return $self->{ "_sub_sub_class" }; } # sub_sub_class =head2 serial_number Title : serial_number Usage : $EC1->serial_number( 482 ); or print $EC1->serial_number(); Function: Set/get for the serial number of ECnumbers. Returns : The serial number of this ECnumber. Args : A positive integer or "-". =cut sub serial_number { my ( $self, $value ) = @_; if ( defined $value) { $self->{ "_serial_number" } = $self->_check_number( $value ); } return $self->{ "_serial_number" }; } # serial_number =head2 comment Title : comment Usage : $EC1->comment( "deprecated" ); or print $EC1->comment(); Function: Set/get for a arbitrary comment. Returns : A comment [scalar]. Args : A comment [scalar]. =cut sub comment { my ( $self, $value ) = @_; if ( defined $value) { $self->{ "_comment" } = $value; } return $self->{ "_comment" }; } # comment # Title : _check_number # Function: Checks and standardizes the individual numbers of a EC number # (removes leading zeros, removes white spaces). # Returns : A standardized number. # Args : A string representing a number in a EC number. sub _check_number { my ( $self, $value ) = @_; my $original_value = $value; $value =~ s/\s+//g; # Removes white space. if ( $value eq "" ) { $value = DEFAULT; } $value =~ s/^0+//; # Removes leading zeros. if ( $value eq "" ) { # If it was "0" (or "00"), it would be "" now. $value = "0"; } elsif ( $value ne DEFAULT && $value =~ /\D/ ) { $self->throw( "Illegal format error [$original_value]" ); } return $value; } # _check_number # Title : _check_for_illegal_defaults() # Function: Checks for situations like "1.-.1.1", which # are illegal in membership tests. # Returns : # Args : sub _check_for_illegal_defaults { my ( $self ) = @_; if ( ( $self->sub_sub_class() eq DEFAULT && $self->serial_number() ne DEFAULT ) || ( $self->sub_class() eq DEFAULT && $self->sub_sub_class() ne DEFAULT ) || ( $self->enzyme_class() eq DEFAULT && $self->sub_class() ne DEFAULT ) ) { $self->throw( "Illegal format error for comparison [" . $self->to_string() . "]" ); } } # _check_for_illegal_defaults # Title : _is_not_reference # Function: Checks whether the argument is not a reference. # Returns : True or false. # Args : A scalar. sub _is_not_reference { my ( $self, $value ) = @_; return ( ! ref( $value ) ); } # _is_not_reference # Title : _is_ECnumber_object # Function: Checks whether the arument is a ECnumber. # Returns : # Args : A reference. sub _is_ECnumber_object { my ( $self, $value ) = @_; unless( $value->isa( "Bio::Tools::ECnumber" ) ) { $self->throw( "Found [". ref( $value ) ."] where [Bio::Tools::ECnumber] expected" ); } } # _is_ECnumber_object 1; �����������������BioPerl-1.007002/Bio/Tools/EPCR.pm������������������������������������������������������������������000444��000766��000024�� 14373�13155576320� 16443� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::EPCR # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::EPCR - Parse ePCR output and make features =head1 SYNOPSIS # A simple annotation pipeline wrapper for ePCR data # assuming ePCR data is already generated in file seq1.epcr # and sequence data is in fasta format in file called seq1.fa use Bio::Tools::EPCR; use Bio::SeqIO; my $parser = Bio::Tools::EPCR->new(-file => 'seq1.epcr'); my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => 'seq1.fa'); my $seq = $seqio->next_seq || die("cannot get a seq object from SeqIO"); while( my $feat = $parser->next_feature ) { # add EPCR annotation to a sequence $seq->add_SeqFeature($feat); } my $seqout = Bio::SeqIO->new(-format => 'embl'); $seqout->write_seq($seq); =head1 DESCRIPTION This object serves as a parser for ePCR data, creating a Bio::SeqFeatureI for each ePCR hit. These can be processed or added as annotation to an existing Bio::SeqI object for the purposes of automated annotation. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::EPCR; use strict; use Bio::SeqFeature::FeaturePair; use Bio::SeqFeature::Generic; use base qw(Bio::Root::Root Bio::SeqAnalysisParserI Bio::Root::IO); =head2 new Title : new Usage : my $epcr = Bio::Tools::EPCR->new(-file => $file, -primary => $fprimary, -source => $fsource, -groupclass => $fgroupclass); Function: Initializes a new EPCR parser Returns : Bio::Tools::EPCR Args : -fh => filehandle OR -file => filename -primary => a string to be used as the common value for each features '-primary' tag. Defaults to 'sts'. (This in turn maps to the GFF 'type' tag (aka 'method')). -source => a string to be used as the common value for each features '-source' tag. Defaults to 'e-PCR'. (This in turn maps to the GFF 'source' tag) -groupclass => a string to be used as the name of the tag which will hold the sts marker namefirst attribute. Defaults to 'name'. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($primary, $source, $groupclass) = $self->_rearrange([qw(PRIMARY SOURCE GROUPCLASS)],@args); $self->primary(defined $primary ? $primary : 'sts'); $self->source(defined $source ? $source : 'e-PCR'); $self->groupclass(defined $groupclass ? $groupclass : 'name'); $self->_initialize_io(@args); return $self; } =head2 next_feature Title : next_feature Usage : $seqfeature = $obj->next_feature(); Function: Returns the next feature available in the analysis result, or undef if there are no more features. Example : Returns : A Bio::SeqFeatureI implementing object, or undef if there are no more features. Args : none =cut sub next_feature { my ($self) = @_; my $line = $self->_readline; return unless defined($line); chomp($line); my($seqname,$location,$mkrname, $rest) = split(/\s+/,$line,4); my ($start,$end) = ($location =~ /(\S+)\.\.(\S+)/); # `e-PCR -direct` results code match strand in $rest as (+) and (-). Decode it if present. my $strandsign; if ($rest =~ m/^\(([+-])\)(.*)$/) { ($strandsign,$rest) = ($1, $2); } else { $strandsign = "?"; } my $strand = $strandsign eq "+" ? 1 : $strandsign eq "-" ? -1 : 0; my $markerfeature = Bio::SeqFeature::Generic->new ( '-start' => $start, '-end' => $end, '-strand' => $strand, '-source' => $self->source, '-primary' => $self->primary, '-seq_id' => $seqname, '-tag' => { $self->groupclass => $mkrname, ($rest ? ('Note' => $rest ) : ()), }); #$markerfeature->add_tag_value('Note', $rest) if defined $rest; return $markerfeature; } =head2 source Title : source Usage : $obj->source($newval) Function: Example : Returns : value of source (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub source{ my $self = shift; return $self->{'_source'} = shift if @_; return $self->{'_source'}; } =head2 primary Title : primary Usage : $obj->primary($newval) Function: Example : Returns : value of primary (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub primary{ my $self = shift; return $self->{'_primary'} = shift if @_; return $self->{'_primary'}; } =head2 groupclass Title : groupclass Usage : $obj->groupclass($newval) Function: Example : Returns : value of groupclass (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub groupclass{ my $self = shift; return $self->{'_groupclass'} = shift if @_; return $self->{'_groupclass'}; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/ESTScan.pm���������������������������������������������������������������000444��000766��000024�� 25626�13155576320� 17155� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::ESTScan # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp@gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::ESTScan - Results of one ESTScan run =head1 SYNOPSIS $estscan = Bio::Tools::ESTScan->new(-file => 'result.estscan'); # filehandle: $estscan = Bio::Tools::ESTScan->new( -fh => \*INPUT ); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same while($gene = $estscan->next_prediction()) { # $gene is an instance of Bio::Tools::Prediction::Gene foreach my $orf ($gene->exons()) { # $orf is an instance of Bio::Tools::Prediction::Exon $cds_str = $orf->predicted_cds(); } } # essential if you gave a filename at initialization (otherwise the file # will stay open) $estscan->close(); =head1 DESCRIPTION The ESTScan module provides a parser for ESTScan coding region prediction output. This module inherits off L<Bio::Tools::AnalysisResult> and therefore implements the L<Bio::SeqAnalysisParserI> interface. See L<Bio::SeqAnalysisParserI>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp@gmx.net (or hilmar.lapp@pharma.novartis.com) =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::ESTScan; use strict; use Symbol; use Bio::Root::Root; use Bio::Tools::Prediction::Exon; use base qw(Bio::Tools::AnalysisResult); sub _initialize_state { my ($self,@args) = @_; # first call the inherited method! my $make = $self->SUPER::_initialize_state(@args); if(! $self->analysis_method()) { $self->analysis_method('ESTScan'); } } =head2 analysis_method Usage : $estscan->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /estscan/i. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method && ($method !~ /estscan/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head2 next_feature Title : next_feature Usage : while($orf = $estscan->next_feature()) { # do something } Function: Returns the next gene structure prediction of the ESTScan result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_feature { my ($self,@args) = @_; # even though next_prediction doesn't expect any args (and this method # does neither), we pass on args in order to be prepared if this changes # ever return $self->next_prediction(@args); } =head2 next_prediction Title : next_prediction Usage : while($gene = $estscan->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the ESTScan result file. Call this method repeatedly until FALSE is returned. So far, this method DOES NOT work for reverse strand predictions, even though the code looks like. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_prediction { my ($self) = @_; my ($gene, $seq, $cds, $predobj); my $numins = 0; # predictions are in the format of FASTA sequences and can be parsed one # at a time $seq = $self->_fasta_stream()->next_seq(); return unless $seq; # there is a new prediction $gene = Bio::Tools::Prediction::Gene->new('-primary' => "ORFprediction", '-source' => "ESTScan"); # score starts the description $seq->desc() =~ /^([\d.]+)\s*(.*)/ or $self->throw("unexpected format of description: no score in " . $seq->desc()); $gene->score($1); $seq->desc($2); # strand may end the description if($seq->desc() =~ /(.*)minus strand$/) { my $desc = $1; $desc =~ s/;\s+$//; $seq->desc($desc); $gene->strand(-1); } else { $gene->strand(1); } # check for the format: default or 'all-in-one' (option -a) if($seq->desc() =~ /^(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s*(.*)/) { # default format $seq->desc($5); $predobj = Bio::Tools::Prediction::Exon->new('-source' => "ESTScan", '-start' => $3, '-end' => $4); $predobj->strand($gene->strand()); $predobj->score($gene->score()); # FIXME or $1, or $2 ? $predobj->primary_tag("InternalExon"); $predobj->seq_id($seq->display_id()); # add to gene structure object $gene->add_exon($predobj); # add predicted CDS $cds = $seq->seq(); $cds =~ s/[a-z]//g; # remove the deletions, but keep the insertions $cds = Bio::PrimarySeq->new('-seq' => $cds, '-display_id' => $seq->display_id(), '-desc' => $seq->desc(), '-alphabet' => "dna"); $gene->predicted_cds($cds); $predobj->predicted_cds($cds); if($gene->strand() == -1) { $self->warn("reverse strand ORF, but unable to reverse coordinates!"); } } else { # # All-in-one format (hopefully). This encodes the following information # into the sequence: # 1) untranslated regions: stretches of lower-case letters # 2) translated regions: stretches of upper-case letters # 3) insertions in the translated regions: capital X # 4) deletions in the translated regions: a single lower-case letter # # if reverse strand ORF, save a lot of hassle by reversing the sequence if($gene->strand() == -1) { $seq = $seq->revcom(); } my $seqstr = $seq->seq(); while($seqstr =~ /^([a-z]*)([A-Z].*)$/) { # leading 5'UTR my $utr5 = $1; # exon + 3'UTR my $exonseq = $2; # strip 3'UTR and following exons if($exonseq =~ s/([a-z]{2,}.*)$//) { $seqstr = $1; } else { $seqstr = ""; } # start: take care of yielding the absolute coordinate my $start = CORE::length($utr5) + 1; if($predobj) { $start += $predobj->end() + $numins; } # for the end coordinate, we need to subtract the insertions $cds = $exonseq; $cds =~ s/[X]//g; my $end = $start + CORE::length($cds) - 1; # construct next exon object $predobj = Bio::Tools::Prediction::Exon->new('-start' => $start, '-end' => $end); $predobj->source_tag("ESTScan"); $predobj->primary_tag("InternalExon"); $predobj->seq_id($seq->display_id()); $predobj->strand($gene->strand()); $predobj->score($gene->score()); # add the exon to the gene structure object $gene->add_exon($predobj); # add the predicted CDS $cds = $exonseq; $cds =~ s/[a-z]//g; # remove the deletions, but keep the insertions $cds = Bio::PrimarySeq->new('-seq' => $cds, '-display_id' => $seq->display_id(), '-desc' => $seq->desc(), '-alphabet' => "dna"); # only store the first one in the overall prediction $gene->predicted_cds($cds) unless $gene->predicted_cds(); $predobj->predicted_cds($cds); # add the predicted insertions and deletions as subfeatures # of the exon my $fea = undef; while($exonseq =~ /([a-zX])/g) { my $indel = $1; # start and end: start looking at the position after the # previous feature if($fea) { $start = $fea->start()+$numins; $start -= 1 if($fea->primary_tag() eq 'insertion'); } else { $start = $predobj->start()+$numins-1; } #print "# numins = $numins, indel = $indel, start = $start\n"; $start = index($seq->seq(), $indel, $start) + 1 - $numins; $fea = Bio::SeqFeature::Generic->new('-start' => $start, '-end' => $start); $fea->source_tag("ESTScan"); $fea->seq_id($seq->display_id()); $fea->strand($predobj->strand()); if($indel eq 'X') { # an insertion (depends on viewpoint: to get the 'real' # CDS, a base has to be inserted, i.e., the HMMER model # inserted a base; however, the sequencing process deleted # a base that was there). $fea->primary_tag("insertion"); # we need to count insertions because these are left out # of any coordinates saved in the objects (which is correct # because insertions change the original sequence, so # coordinates wouldn't match) $numins++; } else { # a deletion (depends on viewpoint: to get the 'real' # CDS, a base has to be deleted, i.e., the HMMER model # deleted a base; however, the sequencing process inserted # a base that wasn't there). $fea->primary_tag("deletion"); $fea->add_tag_value('base', $indel); } $predobj->add_sub_SeqFeature($fea); } } } return $gene; } =head2 close Title : close Usage : $result->close() Function: Closes the file handle associated with this result file. Inherited method, overridden. Example : Returns : Args : =cut sub close { my ($self, @args) = @_; delete($self->{'_fastastream'}); $self->SUPER::close(@args); } =head2 _fasta_stream Title : _fasta_stream Usage : $result->_fasta_stream() Function: Gets/Sets the FASTA sequence IO stream for reading the contents of the file associated with this MZEF result object. If called for the first time, creates the stream from the filehandle if necessary. Example : Returns : Args : =cut sub _fasta_stream { my ($self, $stream) = @_; if($stream || (! exists($self->{'_fastastream'}))) { if(! $stream) { $stream = Bio::SeqIO->new('-fh' => $self->_fh(), '-format' => "fasta"); } $self->{'_fastastream'} = $stream; } return $self->{'_fastastream'}; } 1; ����������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Eponine.pm���������������������������������������������������������������000444��000766��000024�� 17133�13155576320� 17304� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Eponine # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Tania Oh <gisoht@nus.edu.sg> # # Copyright Tania Oh # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Eponine - Results of one Eponine run =head1 SYNOPSIS use Bio::Tools::Eponine; use strict; my $seq = "/data/seq.fa"; my $threshold = "0.999"; my @params = ( -seq => $seq, -threshold => $threshold); my $factory = Bio::Tools::Run::Eponine->new(@params); # run eponine against fasta my $r = $factory->run_eponine($seq); my $parser = Bio::Tools::Eponine->new($r); while (my $feat = $parser->next_prediction){ #$feat contains array of SeqFeature foreach my $orf($feat) { print $orf->seq_id. "\n"; } } =head1 DESCRIPTION Parser for Eponine, a probabilistic transcription start site detector optimized for mammalian genomic sequence. This module inherits off Bio::Tools::AnalysisResult and therefore implements Bio::SeqAnalysisParserI (see L<Bio::Tools::AnalysisResult> and L<Bio::SeqAnalysisParserI>). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Tania Oh E<lt>gisoht-at-nus.edu.sgE<gt> =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Eponine; use strict; use Bio::Tools::Prediction::Gene; use Bio::Tools::Prediction::Exon; use base qw(Bio::Tools::AnalysisResult); sub _initialize_state { my($self,@args) = @_; # first call the inherited method! my $make = $self->SUPER::_initialize_state(@args); # handle our own parameters # our private state variables $self->{'_preds_parsed'} = 0; #array of Bio::SeqFeatures $self->{'_flist'} =[]; } =head2 analysis_method Usage : $mzef->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /mzef/i. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method && ($method !~ /epo/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head2 next_feature Title : next_feature Usage : while($gene = $mzef->next_feature()) { # do something } Function: Returns the next gene structure prediction of the MZEF result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes but just potential internal exons. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_feature { my ($self,@args) = @_; # even though next_prediction doesn't expect any args (and this method # does neither), we pass on args in order to be prepared if this changes # ever return $self->next_prediction(@args); } =head2 next_prediction Title : next_prediction Usage : while($gene = $mzef->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the MZEF result file. Call this method repeatedly until FALSE is returned. Note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes but just potential internal exons. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_prediction { my ($self) = @_; my $gene; # if the prediction section hasn't been parsed yet, we do this now $self->_parse_predictions() unless $self->_predictions_parsed(); # return the next gene structure (transcript) return $self->_prediction(); } =head2 _parse_predictions Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : =cut sub _parse_predictions { my ($self) = @_; while(defined($_ = $self->_readline())) { if (! /^\#/){ #ignore introductory lines my @element = split; my (%feature); $feature {name} = $element[0]; $feature {score} = $element[5]; $feature {start} = $element[3]; $feature {end} = $element[4]; $feature {strand} = $element[6]; $feature {source}= 'Eponine'; $feature {primary}= 'TSS'; $feature {program} = 'eponine-scan'; $feature {program_version} = '2'; $self->create_feature(\%feature); next; } } $self->_predictions_parsed(1); } =head2 create_feature Title : create_feature Usage : obj->create_feature($feature) Function: Returns an array of features Returns : Returns an array of features Args : none =cut sub create_feature { my ($self, $feat) = @_; #create and fill Bio::EnsEMBL::Seqfeature object my $tss = Bio::SeqFeature::Generic->new ( -seq_id => $feat->{'name'}, -start => $feat->{'start'}, -end => $feat->{'end'}, -strand => $feat->{'strand'}, -score => $feat->{'score'}, -source_tag => $feat->{'source'}, -primary_tag => $feat->{'primary'}); if ($tss) { # add to _flist push(@{$self->{'_flist'}}, $tss); } #print $tss->gff_string; } =head2 _prediction Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns : =cut sub _prediction { my ($self) = @_; return unless(exists($self->{'_flist'}) && @{$self->{'_flist'}}); return shift(@{$self->{'_flist'}}); } =head2 _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE =cut sub _predictions_parsed { my ($self, $val) = @_; $self->{'_preds_parsed'} = $val if $val; # array of pre-parsed predictions if(! exists($self->{'_preds_parsed'})) { $self->{'_preds_parsed'} = 0; } return $self->{'_preds_parsed'}; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Est2Genome.pm������������������������������������������������������������000444��000766��000024�� 27373�13155576320� 17666� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Est2Genome # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Est2Genome - Parse est2genome output, makes simple Bio::SeqFeature::Generic objects =head1 SYNOPSIS use Bio::Tools::Est2Genome; my $featureiter = Bio::Tools::Est2Genome->new(-file => 'output.est2genome'); # This is going to be fixed to use the SeqAnalysisI next_feature # Method eventually when we have the objects to put the data in # properly while( my $f = $featureiter->parse_next_gene ) { # process Bio::SeqFeature::Generic objects here } =head1 DESCRIPTION This module is a parser for C<est2genome> [EMBOSS] alignments of est/cdna sequence to genomic DNA. This is generally accepted as the best program for predicting splice sites based on est/dnas (as far as I know). This module currently does not try pull out the ungapped alignments (Segment) but may in the future. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Est2Genome; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Root::Root; use Bio::SeqFeature::Gene::Exon; use Bio::SeqFeature::Gene::Transcript; use Bio::SeqFeature::Gene::Intron; use Bio::SeqFeature::Gene::GeneStructure; use Bio::SeqFeature::SimilarityPair; use base qw(Bio::Tools::AnalysisResult); =head2 new Title : new Usage : my $obj = Bio::Tools::Est2Genome->new(); Function: Builds a new Bio::Tools::Est2Genome object Returns : an instance of Bio::Tools::Est2Genome Args : -file => 'output.est2genome' or -fh => \*EST2GENOMEOUTPUT -genomefirst => 1 # genome was the first input (not standard) =cut sub _initialize_state { my($self,@args) = @_; # call the inherited method first my $make = $self->SUPER::_initialize_state(@args); my ($genome_is_first) = $self->_rearrange([qw(GENOMEFIRST)], @args); delete($self->{'_genome_is_first'}); $self->{'_genome_is_first'} = $genome_is_first if(defined($genome_is_first)); $self->analysis_method("est2genome"); } =head2 analysis_method Usage : $sim4->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /est2genome/i. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method && ($method !~ /est2genome/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head2 parse_next_gene Title : parse_next_gene Usage : @gene = $est2genome_result->parse_next_gene; foreach $exon (@exons) { # do something } Function: Parses the next alignments of the est2genome result file and returns the found exons as an array of Bio::SeqFeature::SimilarityPair objects. Call this method repeatedly until an empty array is returned to get the results for all alignments. The $exon->seq_id() attribute will be set to the identifier of the respective sequence for both sequences. The length is accessible via the seqlength() attribute of $exon->query() and $exon->est_hit(). Returns : An array (or array reference) of Bio::SeqFeature::SimilarityPair and Bio::SeqFeature::Generic objects or Bio::SeqFeature::Gene::GeneStructure Args : flag(1/0) indicating to return Bio::SeqFeature::Gene::GeneStructure or Bio::SeqFeature::SimilarityPair defaults to 0 =cut sub parse_next_gene { my ($self,$return_gene) = @_; return $self->_parse_gene_struct if $return_gene; my $seensegment = 0; my @features; my ($qstrand,$hstrand) = (1,1); my $lasthseqname; while( defined($_ = $self->_readline) ) { if( /Note Best alignment is between (reversed|forward) est and (reversed|forward) genome, (but|and) splice\s+sites imply\s+(forward gene|REVERSED GENE)/) { if( $seensegment ) { $self->_pushback($_); return wantarray ? @features : \@features; } $hstrand = -1 if $1 eq 'reversed'; $qstrand = -1 if $4 eq 'REVERSED GENE'; #$self->debug( "1=$1, 2=$2, 4=$4\n"); } elsif( /^Exon/ ) { my ($name,$score,$perc_ident,$qstart,$qend,$qseqname, $hstart,$hend, $hseqname) = split; $lasthseqname = $hseqname; my $query = Bio::SeqFeature::Similarity->new(-primary => $name, -source => $self->analysis_method, -seq_id => $qseqname, # FIXME WHEN WE REDO THE GENERIC NAME CHANGE -start => $qstart, -end => $qend, -strand => $qstrand, -score => $score, -tag => { # 'Location' => "$hstart..$hend", 'Sequence' => "$hseqname", 'identity' => $perc_ident, } ); my $hit = Bio::SeqFeature::Similarity->new(-primary => 'exon_hit', -source => $self->analysis_method, -seq_id => $hseqname, -start => $hstart, -end => $hend, -strand => $hstrand, -score => $score, -tag => { # 'Location' => "$qstart..$qend", 'Sequence' => "$qseqname", 'identity' => $perc_ident, } ); push @features, Bio::SeqFeature::SimilarityPair->new (-query => $query, -hit => $hit, -source => $self->analysis_method); } elsif( /^([\-\+\?])(Intron)/) { my ($name,$score,$perc_ident,$qstart,$qend,$qseqname) = split; push @features, Bio::SeqFeature::Generic->new(-primary => $2, -source => $self->analysis_method, -start => $qstart, -end => $qend, -strand => $qstrand, -score => $score, -seq_id => $qseqname, -tag => { 'identity' => $perc_ident, 'Sequence' => $lasthseqname}); } elsif( /^Span/ ) { } elsif( /^Segment/ ) { $seensegment = 1; } elsif( /^\s+$/ ) { # do nothing } else { $self->warn( "unknown line $_\n"); } } return unless( @features ); return wantarray ? @features : \@features; } sub _parse_gene_struct { my ($self) = @_; my $seensegment = 0; my @features; my ($qstrand,$hstrand) = (1,1); my $lasthseqname; my $gene = Bio::SeqFeature::Gene::GeneStructure->new(-source => $self->analysis_method); my $transcript = Bio::SeqFeature::Gene::Transcript->new(-source => $self->analysis_method); my @suppf; my @exon; while( defined($_ = $self->_readline) ) { if( /Note Best alignment is between (reversed|forward) est and (reversed|forward) genome, (but|and) splice\s+sites imply\s+(forward gene|REVERSED GENE)/) { if( $seensegment ) { $self->_pushback($_); return $gene; } $hstrand = -1 if $1 eq 'reversed'; $qstrand = -1 if $4 eq 'REVERSED GENE'; } elsif( /^Exon/ ) { my ($name,$score,$perc_ident,$qstart,$qend,$qseqname,$hstart,$hend, $hseqname) = split; $lasthseqname = $hseqname; my $exon = Bio::SeqFeature::Gene::Exon->new(-primary => $name, -source => $self->analysis_method, -seq_id => $qseqname, # FIXME WHEN WE REDO THE GENERIC NAME CHANGE -start => $qstart, -end => $qend, -strand => $qstrand, -score => $score, -tag => { #'Location' => "$hstart..$hend", 'identity' => $perc_ident, 'Sequence' => "$hseqname", } ); $transcript->seq_id($qseqname) unless $transcript->seq_id; $exon->add_tag_value('phase',0); push @exon, $exon; } elsif( /^([\-\+\?])(Intron)/) { next; #intron auto matically built from exons..hope thats ok.. } elsif( /^Span/ ) { } elsif( /^Segment/ ) { my ($name,$score,$perc_ident,$qstart,$qend,$qseqname,$hstart,$hend, $hseqname) = split; my $query = Bio::SeqFeature::Similarity->new(-primary => $name, -source => $self->analysis_method, -seq_id => $qseqname, # FIXME WHEN WE REDO THE GENERIC NAME CHANGE -start => $qstart, -end => $qend, -strand => $qstrand, -score => $score, -tag => { # 'Location' => "$hstart..$hend", 'Sequence' => "$hseqname", 'identity' => $perc_ident, } ); my $hit = Bio::SeqFeature::Similarity->new(-primary => 'exon_hit', -source => $self->analysis_method, -seq_id => $hseqname, -start => $hstart, -end => $hend, -strand => $hstrand, -score => $score, -tag => { # 'Location' => "$qstart..$qend", 'Sequence' => "$qseqname", 'identity' => $perc_ident, } ); my $support = Bio::SeqFeature::SimilarityPair->new(-query => $query, -hit => $hit, -source => $self->analysis_method); push @suppf, $support; } elsif( /^\s+$/ ) { # do nothing } else { $self->warn( "unknown line $_\n"); } } return unless $#exon >=0; foreach my $e(@exon){ my @add; foreach my $sf(@suppf){ if($sf->overlaps($e)){ push @add,$sf; } } $e->add_tag_value('supporting_feature',@add); $transcript->add_exon($e); } $gene->add_transcript($transcript); $gene->seq_id($transcript->seq_id); return $gene; } =head2 next_feature Title : next_feature Usage : $seqfeature = $obj->next_feature(); Function: Returns the next feature available in the analysis result, or undef if there are no more features. Example : Returns : A Bio::SeqFeatureI implementing object, or undef if there are no more features. Args : none =cut sub next_feature { my ($self) = shift; $self->throw("We haven't really done this right, yet, use parse_next_gene"); } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Fgenesh.pm���������������������������������������������������������������000555��000766��000024�� 36275�13155576320� 17301� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Fgenesh # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Christopher Dwan (chris@dwan.org) # # Copied, lock stock & barrel from Genscan.pm # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Fgenesh - parse results of one Fgenesh run =head1 SYNOPSIS use Bio::Tools::Fgenesh; $fgenesh = Bio::Tools::Fgenesh->new(-file => 'result.fgenesh'); # filehandle: $fgenesh = Bio::Tools::Fgenesh->new( -fh => \*INPUT ); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $fgensh->next_feature() is the same while($gene = $fgenesh->next_prediction()) { # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits # off Bio::SeqFeature::Gene::Transcript. # # $gene->exons() returns an array of # Bio::Tools::Prediction::Exon objects # all exons: @exon_arr = $gene->exons(); # initial exons only @init_exons = $gene->exons('Initial'); # internal exons only @intrl_exons = $gene->exons('Internal'); # terminal exons only @term_exons = $gene->exons('Terminal'); # singleton exons: ($single_exon) = $gene->exons(); } # essential if you gave a filename at initialization (otherwise the file # will stay open) $fgenesh->close(); =head1 DESCRIPTION The Fgenesh module provides a parser for Fgenesh (version 2) gene structure prediction output. It parses one gene prediction into a Bio::SeqFeature::Gene::Transcript- derived object. This module also implements the L<Bio::SeqAnalysisParserI> interface, and thus can be used wherever such an object fits. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Dwan Email chris-at-dwan.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Fgenesh; use strict; use Symbol; use Bio::Root::Root; use Bio::Tools::Prediction::Gene; use Bio::Tools::Prediction::Exon; use base qw(Bio::Tools::AnalysisResult); my %ExonTags = ('CDSf' => 'Initial', 'CDSi' => 'Internal', 'CDSl' => 'Terminal', 'CDSo' => 'Singleton'); sub _initialize_state { my ($self,@args) = @_; # first call the inherited method! $self->SUPER::_initialize_state(@args); # our private state variables $self->{'_preds_parsed'} = 0; $self->{'_has_cds'} = 0; # array of pre-parsed predictions $self->{'_preds'} = []; # seq stack $self->{'_seqstack'} = []; } =head2 analysis_method Usage : $genscan->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /genscan/i. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method && ($method !~ /fgenesh/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head2 next_feature Title : next_feature Usage : while($gene = $fgenesh->next_feature()) { # do something } Function: Returns the next gene structure prediction of the Fgenesh result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_feature { my ($self,@args) = @_; # even though next_prediction doesn't expect any args (and this method # does neither), we pass on args in order to be prepared if this changes # ever return $self->next_prediction(@args); } =head2 next_prediction Title : next_prediction Usage : while($gene = $fgenesh->next_prediction()) { ... } Function: Returns the next gene structure prediction of the Genscan result file. Call this method repeatedly until FALSE is returned. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_prediction { my ($self) = @_; my $gene; # if the prediction section hasn't been parsed yet, we do this now $self->_parse_predictions() unless $self->_predictions_parsed(); # get next gene structure $gene = $self->_prediction(); if($gene) { # fill in predicted protein, and if available the predicted CDS # # use the seq stack if there's a seq on it my $seqobj = pop(@{$self->{'_seqstack'}}); my ($id, $seq); unless ($seqobj) { ($id, $seq) = $self->_read_fasta_seq(); my $alphabet; if (($id =~ /mrna/) || ($id =~ /cds/)) { $alphabet = 'dna'; } else { $alphabet = 'protein'; } $seqobj = Bio::PrimarySeq->new('-seq' => $seq, '-display_id' => $id, '-alphabet' => $alphabet); } if ($seqobj) { # check that prediction number matches the prediction number # indicated in the sequence id (there may be incomplete gene # predictions that contain only signals with no associated protein # prediction. $gene->primary_tag() =~ /[^0-9]([0-9]+)$/; my $prednr = $1; if ($id !~ /_predicted_(\w+)_$prednr/) { # this is not our sequence, so push back for next prediction push(@{$self->{'_seqstack'}}, $seqobj); } else { if ($1 eq "protein") { $gene->predicted_protein($seqobj); } elsif (($1 eq "mrna") || ($1 eq "cds")) { $self->_has_cds(1); $gene->predicted_cds($seqobj); # Have to go back in and get the protein... ($id, $seq) = $self->_read_fasta_seq(); if ($id =~ /_cds_/) { ($id, $seq) = $self->_read_fasta_seq(); } $seqobj = Bio::PrimarySeq->new('-seq' => $seq, '-display_id' => $id, '-alphabet' => "protein"); $gene->predicted_protein($seqobj); } } } } return $gene; } =head2 _parse_predictions Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : =cut sub _parse_predictions { my ($self) = @_; my $gene; my $seqname; while(defined($_ = $self->_readline())) { if(/^\s*(\d+)\s+([+\-])/) { my $line = $_; # exon or signal my $prednr = $1; my $strand = ($2 eq '+') ? 1 : -1; if(! defined($gene)) { $gene = Bio::Tools::Prediction::Gene->new( '-primary' => "GenePrediction$prednr", '-source' => 'Fgenesh'); } # split into fields chomp(); my @flds = split(/\s+/, ' ' . $line); ## NB - the above adds leading whitespace before the gene ## number in case there was none (as quick patch to code ## below which expects it but it is not present after 999 ## predictions!) This allows >999 predictions to be parsed. # create the feature object depending on the type of signal my $predobj; my $is_exon = grep {$line =~ $_} keys(%ExonTags); my ($start, $end); if($is_exon) { $predobj = Bio::Tools::Prediction::Exon->new(); $predobj->score($flds[8]); $start = $flds[5]; $end = $flds[7]; } else { # PolyA site, or TSS $predobj = Bio::SeqFeature::Generic->new(); $predobj->score($flds[5]); $start = $flds[4]; $end = $flds[4]; } # set common fields $predobj->source_tag('Fgenesh'); $predobj->strand($strand); # Following tactical commenting-out made by # malcolm.cook@stowers-institute.org since coordinate reversal is # apparently vestigial copy/paste detritus from Genscan.pm origins of # this module and this is NOT needed for fgenesh (at least in v # 2.1.4). # if($predobj->strand() == 1) { $predobj->start($start); $predobj->end($end); # } else { # $predobj->end($start); # $predobj->start($end); # } # print STDERR "start $start end $end\n"; # add to gene structure (should be done only when start and end # are set, in order to allow for proper expansion of the range) if($is_exon) { # first, set fields unique to exons $predobj->primary_tag($ExonTags{$flds[4]} . 'Exon'); $predobj->is_coding(1); my $cod_offset; if($predobj->strand() == 1) { $cod_offset = ($flds[9] - $predobj->start()) % 3; # Possible values are -2, -1, 0, 1, 2. -1 and -2 correspond # to offsets 2 and 1, resp. Offset 3 is the same as 0. $cod_offset += 3 if($cod_offset < 1); } else { # On the reverse strand the Genscan frame also refers to # the first base of the first complete codon, but viewed # from forward, which is the third base viewed from # reverse. $cod_offset = ($flds[11] - $predobj->end()) % 3; # Possible values are -2, -1, 0, 1, 2. Due to the reverse # situation, {2,-1} and {1,-2} correspond to offsets # 1 and 2, resp. Offset 3 is the same as 0. $cod_offset -= 3 if($cod_offset >= 0); $cod_offset = -$cod_offset; } # Offsets 2 and 1 correspond to frame 1 and 2 (frame of exon # is the frame of the first base relative to the exon, or the # number of bases the first codon is missing). $predobj->frame(3 - $cod_offset); # print STDERR " frame is " . $predobj->frame() . "\n"; # then add to gene structure object $gene->add_exon($predobj, $ExonTags{$flds[1]}); } elsif($flds[3] eq 'PolA') { $predobj->primary_tag("PolyAsite"); $gene->poly_A_site($predobj); } elsif($flds[3] eq 'TSS') { $predobj->primary_tag("Promoter"); # (hey! a TSS is NOT a promoter... what's going on here?... $gene->add_promoter($predobj); #I'd like to do this (for now): #$predobj->primary_tag("TSS"); #this is not the right model, but, it IS a feature at least. #but the followg errs out #$gene->add_SeqFeature($predobj); #err: MSG: start is undefined when bounds at Bio::SeqFeature::Generic::add_SeqFeature 671 check since gene has no start yet } else { $self->throw("unrecognized prediction line: " . $line); } next; } if(/^\s*$/ && defined($gene)) { # current gene is completed $gene->seq_id($seqname); $self->_add_prediction($gene); $gene = undef; next; } if(/^(FGENESH)\s+([\d\.]+)/) { $self->analysis_method($1); $self->analysis_method_version($2); if (/\s(\S+)\sgenomic DNA/) { $self->analysis_subject($1); } next; } if(/^\s*Seq name:\s+(\S+)/) { $seqname = $1; next; } /^Predicted protein/ && do { # section of predicted sequences $self->_pushback($_); last; }; } $self->_predictions_parsed(1); } =head2 _prediction Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns : =cut sub _prediction { my ($self) = @_; return unless(exists($self->{'_preds'}) && @{$self->{'_preds'}}); return shift(@{$self->{'_preds'}}); } =head2 _add_prediction Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns : =cut sub _add_prediction { my ($self, $gene) = @_; if(! exists($self->{'_preds'})) { $self->{'_preds'} = []; } push(@{$self->{'_preds'}}, $gene); } =head2 _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE =cut sub _predictions_parsed { my ($self, $val) = @_; $self->{'_preds_parsed'} = $val if $val; if(! exists($self->{'_preds_parsed'})) { $self->{'_preds_parsed'} = 0; } return $self->{'_preds_parsed'}; } =head2 _has_cds Title : _has_cds() Usage : $obj->_has_cds() Function: Whether or not the result contains the predicted CDSs, too. Example : Returns : TRUE or FALSE =cut sub _has_cds { my ($self, $val) = @_; $self->{'_has_cds'} = $val if $val; if(! exists($self->{'_has_cds'})) { $self->{'_has_cds'} = 0; } return $self->{'_has_cds'}; } =head2 _read_fasta_seq Title : _read_fasta_seq() Usage : ($id,$seqstr) = $obj->_read_fasta_seq(); Function: Simple but specialised FASTA format sequence reader. Uses $self->_readline() to retrieve input, and is able to strip off the traling description lines. Example : Returns : An array of two elements: fasta_id & sequence =cut sub _read_fasta_seq { my ($self) = @_; my ($id, $seq); #local $/ = ">"; my $entry = $self->_readline(); # print " ^^ $entry\n"; return unless ($entry); $entry = $self->_readline() if ($entry =~ /^Predicted protein/); # print " ^^ $entry\n"; # Pick up the header / id. if ($entry =~ /^>FGENESH:/) { if ($entry =~ /^>FGENESH:\s+(\d+)/) { # print STDERR " this is a predicted gene\n"; $id = "_predicted_protein_" . $1; } elsif ($entry =~ /^>FGENESH:\[mRNA\]\s*(\d+)/) { # print STDERR " this is an mRNA\n"; $id = "_predicted_mrna_" . $1; } elsif ($entry =~ /^>FGENESH:\[exon\]\s+Gene:\s*(\d+)/) { $id = "_predicted_cds_" . $1; } $seq = ""; $entry = $self->_readline(); } my $done = 0; while (!$done) { # print "*** $entry\n"; if (($entry =~ /^>FGENESH:\[exon\]/) && ($id =~ /^_predicted_cds_/)) { # print STDERR " -- informed about an exon header...\n"; $entry = $self->_readline(); } else { $seq .= $entry; # print STDERR " Added $entry\n"; } last unless $entry = $self->_readline(); if (($entry =~ /^>/) && (!(($entry =~ /^>FGENESH:\[exon\]/) && ($id =~ /^_predicted_cds_/)))) { $self->_pushback($entry); last; } } # id and sequence $seq =~ s/\s//g; # Remove whitespace return ($id, $seq); } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/FootPrinter.pm�����������������������������������������������������������000444��000766��000024�� 14712�13155576320� 20162� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Tools::FootPrinter # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Shawn Hoon <shawnh@fugu-sg.org> # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::FootPrinter - write sequence features in FootPrinter format =head1 SYNOPSIS use Bio::Tools::FootPrinter; my $tool = Bio::Tools::FootPrinter->new(-file=>"footprinter.out"); while (my $result = $tool->next_feature){ foreach my $feat($result->sub_SeqFeature){ print $result->seq_id."\t".$feat->start."\t".$feat->end."\t".$feat->seq->seq."\n"; } } =head1 DESCRIPTION This module writes sequence features in FootPrinter format. See L<http://bio.cs.washington.edu/software.html> for more details. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::FootPrinter; use strict; use Bio::SeqFeature::Generic; use Bio::PrimarySeq; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::FootPrinter->new(); Function: Builds a new Bio::Tools::FootPrinter object Returns : Bio::Tools::FootPrinter Args : -fh/-file => $val, # for initing input, see Bio::Root::IO =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_feature Title : next_feature Usage : my $r = $footprint->next_feature Function: Get the next feature from parser data Returns : L<Bio::SeqFeature::Generic> Args : none =cut sub next_feature{ my ($self) = @_; $self->_parse_predictions() unless $self->_predictions_parsed(); return shift @{$self->{'_feature'}}; } =head2 _add_feature Title : _add_feature Usage : $footprint->_add_feature($feat) Function: Add feature to array Returns : none Args : none =cut sub _add_feature { my ($self,$feat) = @_; if($feat){ push @{$self->{'_feature'}},$feat; } } =head2 _parse_predictions Title : _parse_predictions Usage : my $r = $footprint->_parse_predictions Function: do the parsing Returns : none Args : none =cut sub _parse_predictions { my ($self) = @_; $/=""; my ($seq,$second,$third,$name); while ($_ = $self->_readline) { chomp; my @array = split("\n",$_); if ($#array == 5) { # get rid of header shift(@array); shift(@array); } if($#array == 3){ if($name){ $name=~s/>//; my $feat = $self->_parse($name,$seq,$second,$third); $self->_add_feature($feat); } $name = shift @array; $seq = $array[0]; $second = $array[1]; $third = $array[2]; next; } $seq .= $array[0]; $third .= $array[2]; } $seq || return; $name=~s/>//; my $feat = $self->_parse($name,$seq,$second,$third); $self->_add_feature($feat); $self->_predictions_parsed(1); } =head2 _predictions_parsed Title : _predictions_parsed Usage : $footprint->_predictions_parsed(1) Function: Get/Set for whether predictions parsed Returns : 1/0 Args : none =cut sub _predictions_parsed { my ($self,$val) = @_; if($val){ $self->{'_predictions_parsed'} = $val; } return $self->{'_predictions_parsed'}; } =head2 _parse Title : _parse Usage : $footprint->_parse($name,$seq,$pattern) Function: do the actual parsing Returns : L<Bio::SeqFeature::Generic> Args : none =cut sub _parse { my ($self,$name,$seq,$score,$pattern) = @_; my @char = split('',$pattern); my @score = split('',$score); my ($prev,$word,@words,@word_scores,$word_score); my $i = 0; for my $c ( @char ) { if( ! $word) { $word .= $c; $prev = $c; defined $score[$i] && ($score[$i] =~ /\d/) && ($word_score += $score[$i]); } elsif ($c eq $prev){ $word .=$c; $prev = $c; defined $score[$i] && ($score[$i] =~ /\d/) && ($word_score += $score[$i]); } else { # remove words with only \s $word=~s/\s+//g; if ($word ne ''){ push @words, $word; push @word_scores, ($word_score/length($word)); } $word =$c; $prev = $c; $word_score = 0; defined $score[$i] && ($score[$i] =~ /\d/) && ($word_score += $score[$i]); } $i++; } $word =~s/\s+//g; if( length($word) ){ push @words, $word; } my $last; my $feat = Bio::SeqFeature::Generic->new(-seq_id=>$name); my $offset = $i = 0; my $count = 1; for my $w (@words){ if(length($w) ) { my $index = index($pattern,$w,$offset); $offset = $index + length($w); my $subfeat = Bio::SeqFeature::Generic->new ( -seq_id =>"$name-motif".$count++, -start => $index+1, -end => $index+length($w), -source =>"FootPrinter", -score => $word_scores[$i] ); # ugh - not sure the sub_SeqFeature situation will # be around forever- things should probably be # grouped by a 'group' tag instead ala GFF3 # perhaps when Lincoln's API changes are # made to SeqFeatures this will get changed $feat->add_sub_SeqFeature($subfeat,'EXPAND'); } $i++; } my $priseq = Bio::PrimarySeq->new(-id=>$name,-seq=>$seq); $feat->attach_seq($priseq); return $feat; } 1; ������������������������������������������������������BioPerl-1.007002/Bio/Tools/GFF.pm�������������������������������������������������������������������000444��000766��000024�� 112442�13155576320� 16330� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::GFF # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by the Bioperl core team # # Copyright Matthew Pocock # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser =head1 SYNOPSIS use Bio::Tools::GFF; # specify input via -fh or -file my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version => 2); my $feature; # loop over the input stream while($feature = $gffio->next_feature()) { # do something with feature } $gffio->close(); # you can also obtain a GFF parser as a SeqAnalasisParserI in # HT analysis pipelines (see Bio::SeqAnalysisParserI and # Bio::Factory::SeqAnalysisParserFactory) my $factory = Bio::Factory::SeqAnalysisParserFactory->new(); my $parser = $factory->get_parser(-input => \*STDIN, -method => "gff"); while($feature = $parser->next_feature()) { # do something with feature } =head1 DESCRIPTION This class provides a simple GFF parser and writer. In the sense of a SeqAnalysisParser, it parses an input file or stream into SeqFeatureI objects, but is not in any way specific to a particular analysis program and the output that program produces. That is, if you can get your analysis program spit out GFF, here is your result parser. =head1 GFF3 AND SEQUENCE DATA GFF3 supports sequence data; see http://www.sequenceontology.org/gff3.shtml There are a number of ways to deal with this - If you call $gffio->ignore_sequence(1) prior to parsing the sequence data is ignored; this is useful if you just want the features. It avoids the memory overhead in building and caching sequences Alternatively, you can call either $gffio->get_seqs() Or $gffio->seq_id_by_h() At the B<end> of parsing to get either a list or hashref of Bio::Seq objects (see the documentation for each of these methods) Note that these objects will not have the features attached - you have to do this yourself, OR call $gffio->features_attached_to_seqs(1) PRIOR to parsing; this will ensure that the Seqs have the features attached; ie you will then be able to call $seq->get_SeqFeatures(); And use Bio::SeqIO methods Note that auto-attaching the features to seqs will incur a higher memory overhead as the features must be cached until the sequence data is found =head1 TODO Make a Bio::SeqIO class specifically for GFF3 with sequence data =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Matthew Pocock Email mrp-at-sanger.ac.uk =head1 CONTRIBUTORS Jason Stajich, jason-at-biperl-dot-org Chris Mungall, cjm-at-fruitfly-dot-org Steffen Grossmann [SG], grossman at molgen.mpg.de Malcolm Cook, mec-at-stowers-institute.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::GFF; use vars qw($HAS_HTML_ENTITIES); use strict; use Bio::Seq::SeqFactory; use Bio::LocatableSeq; use Bio::SeqFeature::Generic; use base qw(Bio::Root::Root Bio::SeqAnalysisParserI Bio::Root::IO); my $i = 0; my %GFF3_ID_Tags = map { $_ => $i++ } qw(ID Parent Target); # for skipping data that may be represented elsewhere; currently, this is # only the score my %SKIPPED_TAGS = map { $_ => 1 } qw(score); =head2 new Title : new Usage : my $parser = Bio::Tools::GFF->new(-gff_version => 2, -file => "filename.gff"); or my $writer = Bio::Tools::GFF->new(-gff_version => 3, -file => ">filename.gff3"); Function: Creates a new instance. Recognized named parameters are -file, -fh, and -gff_version. Returns : a new object Args : named parameters -gff_version => [1,2,3] =cut { # make a class variable such that we can generate unique ID's over # a session, no matter how many instances of GFF.pm we make # since these have to be unique within the scope of a GFF file. my $gff3_featureID = 0; sub _incrementGFF3ID { my ($self) = @_; return ++ $gff3_featureID; } } sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($gff_version, $noparse) = $self->_rearrange([qw(GFF_VERSION NOPARSE)],@args); # initialize IO $self->_initialize_io(@args); $self->_parse_header() unless $noparse; $gff_version ||= 2; if( ! $self->gff_version($gff_version) ) { $self->throw("Can't build a GFF object with the unknown version ". $gff_version); } $self->{'_first'} = 1; return $self; } =head2 _parse_header Title : _parse_header Usage : $gffio->_parse_header() Function: used to turn parse GFF header lines. currently produces Bio::LocatableSeq objects from ##sequence-region lines Returns : 1 on success Args : none =cut sub _parse_header{ my ($self) = @_; my @unhandled; local $^W = 0; # hide warnings when we try and parse from a file opened # for writing - there isn't really a better way to do # AFAIK - cannot detech if a FH is read or write. while(my $line = $self->_readline()){ my $handled = 0; next if /^\s+$/; if($line =~ /^\#\#sequence-region\s+(\S+)\s+(\S+)\s+(\S+)\s*/){ my($seqid,$start,$end) = ($1,$2,$3); push @{ $self->{'segments'} }, Bio::LocatableSeq->new( -id => unescape($seqid), -start => $start, -end => $end, -length => ($end - $start + 1), ## make the length explicit ); $handled = 1; } elsif($line =~ /^(\#\#feature-ontology)/) { #to be implemented $self->warn("$1 header tag parsing unimplemented"); } elsif($line =~ /^(\#\#attribute-ontology)/) { #to be implemented $self->warn("$1 header tag parsing unimplemented"); } elsif($line =~ /^(\#\#source-ontology)/) { #to be implemented $self->warn("$1 header tag parsing unimplemented"); } elsif($line =~ /^(\#\#\#)/) { #to be implemented $self->warn("$1 header tag parsing unimplemented"); } elsif($line =~ /^(\#\#FASTA)/) { # initial ##FASTA is optional - artemis does not use it $line = $self->_readline(); if ($line !~ /^\>(\S+)/) { $self->throw("##FASTA directive must be followed by fasta header, not: $line"); } } if ($line =~ /^\>(.*)/) { # seq data can be at header or footer my $seq = $self->_parse_sequence($line); if ($seq) { $self->_seq_by_id_h->{$seq->primary_id} = $seq; } } if(!$handled){ push @unhandled, $line; } #looks like the header is over! last unless $line =~ /^\#/; } foreach my $line (@unhandled){ $self->_pushback($line); } return 1; } sub _parse_sequence { my ($self, $line) = @_; if ($line =~ /^\>(.*)/) { my $seqid = $1; $seqid =~ s/\s+$//; my $desc = ''; if ($seqid =~ /(\S+)\s+(.*)/) { ($seqid, $desc) = ($1,$2); } my $res = ''; while (my $line = $self->_readline) { if ($line =~ /^\#/) { last; } if ($line =~ /^\>/) { $self->_pushback($line); last; } $line =~ s/\s//g; $res .= $line; } return if $self->ignore_sequence; my $seqfactory = Bio::Seq::SeqFactory->new('Bio::Seq'); my $seq = $seqfactory->create(-seq=>$res, -id=>$seqid, -desc=>$desc); $seq->accession_number($seqid); if ($self->features_attached_to_seqs) { my @feats = @{$self->_feature_idx_by_seq_id->{$seqid}}; $seq->add_SeqFeature($_) foreach @feats; @{$self->_feature_idx_by_seq_id->{$seqid}} = (); } return $seq; } else { $self->throw("expected fasta header, not: $line"); } } =head2 next_segment Title : next_segment Usage : my $seq = $gffio->next_segment; Function: Returns a Bio::LocatableSeq object corresponding to a GFF "##sequence-region" header line. Example : Returns : A Bio::LocatableSeq object, or undef if there are no more sequences. Args : none =cut sub next_segment{ my ($self,@args) = @_; return shift @{ $self->{'segments'} } if defined $self->{'segments'}; return; } =head2 next_feature Title : next_feature Usage : $seqfeature = $gffio->next_feature(); Function: Returns the next feature available in the input file or stream, or undef if there are no more features. Example : Returns : A Bio::SeqFeatureI implementing object, or undef if there are no more features. Args : none =cut sub next_feature { my ($self) = @_; my $gff_string; # be graceful about empty lines or comments, and make sure we return undef # if the input's consumed while(($gff_string = $self->_readline()) && defined($gff_string)) { if ($gff_string =~ /^\#\#\#/) { # all forward refs have been seen; TODO } next if($gff_string =~ /^\#/ || $gff_string =~ /^\s*$/ || $gff_string =~ m{^//}); while ($gff_string =~ /^\>(.+)/) { # fasta can be in header or footer my $seq = $self->_parse_sequence($gff_string); if ($seq) { $self->_seq_by_id_h->{$seq->primary_id} = $seq; $gff_string = $self->_readline; last unless $gff_string; } } last; } return unless $gff_string; my $feat = Bio::SeqFeature::Generic->new(); $self->from_gff_string($feat, $gff_string); if ($self->features_attached_to_seqs) { push(@{$self->_feature_idx_by_seq_id->{$feat->seq_id}}, $feat); } return $feat; } sub _feature_idx_by_seq_id { my $self = shift; $self->{__feature_idx_by_seq_id} = shift if @_; $self->{__feature_idx_by_seq_id} = {} unless $self->{__feature_idx_by_seq_id}; return $self->{__feature_idx_by_seq_id}; } =head2 from_gff_string Title : from_gff_string Usage : $gff->from_gff_string($feature, $gff_string); Function: Sets properties of a SeqFeatureI object from a GFF-formatted string. Interpretation of the string depends on the version that has been specified at initialization. This method is used by next_feature(). It actually dispatches to one of the version-specific (private) methods. Example : Returns : void Args : A Bio::SeqFeatureI implementing object to be initialized The GFF-formatted string to initialize it from =cut sub from_gff_string { my ($self, $feat, $gff_string) = @_; if($self->gff_version() == 1) { return $self->_from_gff1_string($feat, $gff_string); } elsif( $self->gff_version() == 3 ) { return $self->_from_gff3_string($feat, $gff_string); } else { return $self->_from_gff2_string($feat, $gff_string); } } =head2 _from_gff1_string Title : _from_gff1_string Usage : Function: Example : Returns : void Args : A Bio::SeqFeatureI implementing object to be initialized The GFF-formatted string to initialize it from =cut sub _from_gff1_string { my ($gff, $feat, $string) = @_; chomp $string; my ($seqname, $source, $primary, $start, $end, $score, $strand, $frame, @group) = split(/\t/, $string); if ( !defined $frame ) { $feat->throw("[$string] does not look like GFF to me"); } $frame = 0 unless( $frame =~ /^\d+$/); $feat->seq_id($seqname); $feat->source_tag($source); $feat->primary_tag($primary); $feat->start($start); $feat->end($end); $feat->frame($frame); if ( $score eq '.' ) { #$feat->score(undef); } else { $feat->score($score); } if ( $strand eq '-' ) { $feat->strand(-1); } if ( $strand eq '+' ) { $feat->strand(1); } if ( $strand eq '.' ) { $feat->strand(0); } foreach my $g ( @group ) { if ( $g =~ /(\S+)=(\S+)/ ) { my $tag = $1; my $value = $2; $feat->add_tag_value($1, $2); } else { $feat->add_tag_value('group', $g); } } } =head2 _from_gff2_string Title : _from_gff2_string Usage : Function: Example : Returns : void Args : A Bio::SeqFeatureI implementing object to be initialized The GFF2-formatted string to initialize it from =cut sub _from_gff2_string { my ($gff, $feat, $string) = @_; chomp($string); # according to the Sanger website, GFF2 should be single-tab # separated elements, and the free-text at the end should contain # text-translated tab symbols but no "real" tabs, so splitting on # \t is safe, and $attribs gets the entire attributes field to be # parsed later # sendu: but the tag value pair can (should?) be separated by a tab. The # 'no tabs' thing seems to apply only to the free text that is allowed for # the value my ($seqname, $source, $primary, $start, $end, $score, $strand, $frame, @attribs) = split(/\t+/, $string); my $attribs = join ' ', @attribs; if ( !defined $frame ) { $feat->throw("[$string] does not look like GFF2 to me"); } $feat->seq_id($seqname); $feat->source_tag($source); $feat->primary_tag($primary); $feat->start($start); $feat->end($end); $feat->frame($frame); if ( $score eq '.' ) { # $feat->score(undef); } else { $feat->score($score); } if ( $strand eq '-' ) { $feat->strand(-1); } if ( $strand eq '+' ) { $feat->strand(1); } if ( $strand eq '.' ) { $feat->strand(0); } # <Begin Inefficient Code from Mark Wilkinson> # this routine is necessay to allow the presence of semicolons in # quoted text Semicolons are the delimiting character for new # tag/value attributes. it is more or less a "state" machine, with # the "quoted" flag going up and down as we pass thorugh quotes to # distinguish free-text semicolon and hash symbols from GFF control # characters my $flag = 0; # this could be changed to a bit and just be twiddled my @parsed; # run through each character one at a time and check it # NOTE: changed to foreach loop which is more efficient in perl # --jasons for my $a ( split //, $attribs ) { # flag up on entering quoted text, down on leaving it if( $a eq '"') { $flag = ( $flag == 0 ) ? 1:0 } elsif( $a eq ';' && $flag ) { $a = "INSERT_SEMICOLON_HERE"} elsif( $a eq '#' && ! $flag ) { last } push @parsed, $a; } $attribs = join "", @parsed; # rejoin into a single string # <End Inefficient Code> # Please feel free to fix this and make it more "perlish" my @key_vals = split /;/, $attribs; # attributes are semicolon-delimited foreach my $pair ( @key_vals ) { # replace semicolons that were removed from free-text above. $pair =~ s/INSERT_SEMICOLON_HERE/;/g; # separate the key from the value my ($blank, $key, $values) = split /^\s*([\w\d]+)\s/, $pair; if( defined $values ) { my @values; # free text is quoted, so match each free-text block # and remove it from the $values string while ($values =~ s/"(.*?)"//){ # and push it on to the list of values (tags may have # more than one value... and the value may be undef) push @values, $1; } # and what is left over should be space-separated # non-free-text values my @othervals = split /\s+/, $values; foreach my $othervalue(@othervals){ # get rid of any empty strings which might # result from the split if (CORE::length($othervalue) > 0) {push @values, $othervalue} } foreach my $value(@values){ $feat->add_tag_value($key, $value); } } } } sub _from_gff3_string { my ($gff, $feat, $string) = @_; chomp($string); # according to the now nearly final GFF3 spec, columns should # be tab separated, allowing unescaped spaces to occur in # column 9 my ($seqname, $source, $primary, $start, $end, $score, $strand, $frame, $groups) = split(/\t/, $string); if ( ! defined $frame ) { $feat->throw("[$string] does not look like GFF3 to me"); } $feat->seq_id($seqname); $feat->source_tag($source); $feat->primary_tag($primary); $feat->start($start); $feat->end($end); $feat->frame($frame); if ( $score eq '.' ) { #$feat->score(undef); } else { $feat->score($score); } if ( $strand eq '-' ) { $feat->strand(-1); } if ( $strand eq '+' ) { $feat->strand(1); } if ( $strand eq '.' ) { $feat->strand(0); } my @groups = split(/\s*;\s*/, $groups); for my $group (@groups) { my ($tag,$value) = split /=/,$group; $tag = unescape($tag); my @values = map {unescape($_)} split /,/,$value; for my $v ( @values ) { $feat->add_tag_value($tag,$v); } } } # taken from Bio::DB::GFF sub unescape { my $v = shift; $v =~ s/%([0-9a-fA-F]{2})/chr hex($1)/ge; return $v; } =head2 write_feature Title : write_feature Usage : $gffio->write_feature($feature); Function: Writes the specified SeqFeatureI object in GFF format to the stream associated with this instance. Returns : none Args : An array of Bio::SeqFeatureI implementing objects to be serialized =cut sub write_feature { my ($self, @features) = @_; return unless @features; if( $self->{'_first'} && $self->gff_version() == 3 ) { $self->_print("##gff-version 3\n"); } $self->{'_first'} = 0; foreach my $feature ( @features ) { $self->_print($self->gff_string($feature)."\n"); } } =head2 gff_string Title : gff_string Usage : $gffstr = $gffio->gff_string($feature); Function: Obtain the GFF-formatted representation of a SeqFeatureI object. The formatting depends on the version specified at initialization. This method is used by write_feature(). It actually dispatches to one of the version-specific (private) methods. Example : Returns : A GFF-formatted string representation of the SeqFeature Args : A Bio::SeqFeatureI implementing object to be GFF-stringified =cut sub gff_string{ my ($self, $feature) = @_; if($self->gff_version() == 1) { return $self->_gff1_string($feature); } elsif( $self->gff_version() == 3 ) { return $self->_gff3_string($feature); } elsif( $self->gff_version() == 2.5 ) { return $self->_gff25_string($feature); } else { return $self->_gff2_string($feature); } } =head2 _gff1_string Title : _gff1_string Usage : $gffstr = $gffio->_gff1_string Function: Example : Returns : A GFF1-formatted string representation of the SeqFeature Args : A Bio::SeqFeatureI implementing object to be GFF-stringified =cut sub _gff1_string{ my ($gff, $feat) = @_; my ($str,$score,$frame,$name,$strand); if( $feat->can('score') ) { $score = $feat->score(); } $score = '.' unless defined $score; if( $feat->can('frame') ) { $frame = $feat->frame(); } $frame = '.' unless defined $frame; $strand = $feat->strand(); if(! $strand) { $strand = "."; } elsif( $strand == 1 ) { $strand = '+'; } elsif ( $feat->strand == -1 ) { $strand = '-'; } if( $feat->can('seqname') ) { $name = $feat->seq_id(); $name ||= 'SEQ'; } else { $name = 'SEQ'; } $str = join("\t", $name, $feat->source_tag, $feat->primary_tag, $feat->start, $feat->end, $score, $strand, $frame); foreach my $tag ( $feat->get_all_tags ) { next if exists $SKIPPED_TAGS{$tag}; foreach my $value ( $feat->get_tag_values($tag) ) { $str .= " $tag=$value" if $value; } } return $str; } =head2 _gff2_string Title : _gff2_string Usage : $gffstr = $gffio->_gff2_string Function: Example : Returns : A GFF2-formatted string representation of the SeqFeature Args : A Bio::SeqFeatureI implementing object to be GFF2-stringified =cut sub _gff2_string{ my ($gff, $origfeat) = @_; my $feat; if ($origfeat->isa('Bio::SeqFeature::FeaturePair')){ $feat = $origfeat->feature2; } else { $feat = $origfeat; } my ($str1, $str2,$score,$frame,$name,$strand); if( $feat->can('score') ) { $score = $feat->score(); } $score = '.' unless defined $score; if( $feat->can('frame') ) { $frame = $feat->frame(); } $frame = '.' unless defined $frame; $strand = $feat->strand(); if(! $strand) { $strand = "."; } elsif( $strand == 1 ) { $strand = '+'; } elsif ( $feat->strand == -1 ) { $strand = '-'; } if( $feat->can('seqname') ) { $name = $feat->seq_id(); } $name ||= 'SEQ'; $str1 = join("\t", $name, $feat->source_tag(), $feat->primary_tag(), $feat->start(), $feat->end(), $score, $strand, $frame); # the routine below is the only modification I made to the original # ->gff_string routine (above) as on November 17th, 2000, the # Sanger webpage describing GFF2 format reads: "From version 2 # onwards, the attribute field must have a tag value structure # following the syntax used within objects in a .ace file, # flattened onto one line by semicolon separators. Tags must be # standard identifiers ([A-Za-z][A-Za-z0-9_]*). Free text values # must be quoted with double quotes". # MW my @group; foreach my $tag ( $feat->get_all_tags ) { next if exists $SKIPPED_TAGS{$tag}; my @v; foreach my $value ( $feat->get_tag_values($tag) ) { unless( defined $value && length($value) ) { # quote anything other than valid tag/value characters $value = '""'; } elsif ($value =~ /[^A-Za-z0-9_]/){ # substitute tab and newline chars by their UNIX equivalent $value =~ s/\t/\\t/g; $value =~ s/\n/\\n/g; $value = '"' . $value . '" '; } push @v, $value; # for this tag (allowed in GFF2 and .ace format) } push @group, "$tag ".join(" ", @v); } $str2 .= join(' ; ', @group); # Add Target information for Feature Pairs if( ! $feat->has_tag('Target') && # This is a bad hack IMHO ! $feat->has_tag('Group') && $origfeat->isa('Bio::SeqFeature::FeaturePair') ) { $str2 = sprintf("Target %s %d %d", $origfeat->feature1->seq_id, ( $origfeat->feature1->strand < 0 ? ( $origfeat->feature1->end, $origfeat->feature1->start) : ( $origfeat->feature1->start, $origfeat->feature1->end) )) . ($str2?" ; ".$str2:""); # need to put Target information before other tag/value pairs - mw } return $str1."\t".$str2; } =head2 _gff25_string Title : _gff25_string Usage : $gffstr = $gffio->_gff2_string Function: To get a format of GFF that is peculiar to Gbrowse/Bio::DB::GFF Example : Returns : A GFF2.5-formatted string representation of the SeqFeature Args : A Bio::SeqFeatureI implementing object to be GFF2.5-stringified =cut sub _gff25_string { my ($gff, $origfeat) = @_; my $feat; if ($origfeat->isa('Bio::SeqFeature::FeaturePair')){ $feat = $origfeat->feature2; } else { $feat = $origfeat; } my ($str1, $str2,$score,$frame,$name,$strand); if( $feat->can('score') ) { $score = $feat->score(); } $score = '.' unless defined $score; if( $feat->can('frame') ) { $frame = $feat->frame(); } $frame = '.' unless defined $frame; $strand = $feat->strand(); if(! $strand) { $strand = "."; } elsif( $strand == 1 ) { $strand = '+'; } elsif ( $feat->strand == -1 ) { $strand = '-'; } if( $feat->can('seqname') ) { $name = $feat->seq_id(); $name ||= 'SEQ'; } else { $name = 'SEQ'; } $str1 = join("\t", $name, $feat->source_tag(), $feat->primary_tag(), $feat->start(), $feat->end(), $score, $strand, $frame); my @all_tags = $feat->all_tags; my @group; my @firstgroup; if (@all_tags) { # only play this game if it is worth playing... foreach my $tag ( @all_tags ) { my @v; foreach my $value ( $feat->get_tag_values($tag) ) { next if exists $SKIPPED_TAGS{$tag}; unless( defined $value && length($value) ) { $value = '""'; } elsif ($value =~ /[^A-Za-z0-9_]/){ $value =~ s/\t/\\t/g; # substitute tab and newline # characters $value =~ s/\n/\\n/g; # to their UNIX equivalents $value = '"' . $value . '" '; } # if the value contains # anything other than valid # tag/value characters, then # quote it push @v, $value; # for this tag (allowed in GFF2 and .ace format) } if (($tag eq 'Group') || ($tag eq 'Target')){ # hopefully we won't get both... push @firstgroup, "$tag ".join(" ", @v); } else { push @group, "$tag ".join(" ", @v); } } } $str2 = join(' ; ', (@firstgroup, @group)); # Add Target information for Feature Pairs if( ! $feat->has_tag('Target') && # This is a bad hack IMHO ! $feat->has_tag('Group') && $origfeat->isa('Bio::SeqFeature::FeaturePair') ) { $str2 = sprintf("Target %s ; tstart %d ; tend %d", $origfeat->feature1->seq_id, ( $origfeat->feature1->strand < 0 ? ( $origfeat->feature1->end, $origfeat->feature1->start) : ( $origfeat->feature1->start, $origfeat->feature1->end) )) . ($str2?" ; ".$str2:""); # need to put the target info before other tag/value pairs - mw } return $str1 . "\t". $str2; } =head2 _gff3_string Title : _gff3_string Usage : $gffstr = $gffio->_gff3_string Function: Example : Returns : A GFF3-formatted string representation of the SeqFeature Args : A Bio::SeqFeatureI implementing object to be GFF3-stringified =cut sub _gff3_string { my ($gff, $origfeat) = @_; my $feat; if ($origfeat->isa('Bio::SeqFeature::FeaturePair')){ $feat = $origfeat->feature2; } else { $feat = $origfeat; } my $ID = $gff->_incrementGFF3ID(); my ($score,$frame,$name,$strand); if( $feat->can('score') ) { $score = $feat->score(); } $score = '.' unless defined $score; if( $feat->can('frame') ) { $frame = $feat->frame(); } $frame = '1' unless defined $frame; $strand = $feat->strand(); if(! $strand) { $strand = "."; } elsif( $strand == 1 ) { $strand = '+'; } elsif ( $feat->strand == -1 ) { $strand = '-'; } if( $feat->can('seqname') ) { $name = $feat->seq_id(); $name ||= 'SEQ'; } else { $name = 'SEQ'; } my @groups; # force leading ID and Parent tags my @all_tags = grep { ! exists $GFF3_ID_Tags{$_} } $feat->all_tags; for my $t ( sort { $GFF3_ID_Tags{$b} <=> $GFF3_ID_Tags{$a} } keys %GFF3_ID_Tags ) { unshift @all_tags, $t if $feat->has_tag($t); } for my $tag ( @all_tags ) { next if exists $SKIPPED_TAGS{$tag}; # next if $tag eq 'Target'; if ($tag eq 'Target' && ! $origfeat->isa('Bio::SeqFeature::FeaturePair')){ my @values = $feat->get_tag_values($tag); if(scalar(@values) > 1){ # How is it possible that Target is has a value list ?? # simple Target,start,stop my ($target_id, $b,$e,$strand) = $feat->get_tag_values($tag); next unless(defined($e) && defined($b) && $target_id); ($b,$e)= ($e,$b) if(defined $strand && $strand<0); #if we have the strand we will print it if($strand){ push @groups, sprintf("Target=%s %d %d %s", $target_id,$b,$e,$strand); } else{ push @groups, sprintf("Target=%s %d %d", $target_id,$b,$e); } next; } } my $valuestr; # a string which will hold one or more values # for this tag, with quoted free text and # space-separated individual values. my @v; for my $value ( $feat->get_tag_values($tag) ) { if( defined $value && length($value) ) { #$value =~ tr/ /+/; #spaces are allowed now if ( ref $value eq 'Bio::Annotation::Comment') { $value = $value->text; } if ($value =~ /[^a-zA-Z0-9\,\;\=\.:\%\^\*\$\@\!\+\_\?\-]/) { $value =~ s/\t/\\t/g; # substitute tab and newline # characters $value =~ s/\n/\\n/g; # to their UNIX equivalents # Unescaped quotes are not allowed in GFF3 # $value = '"' . $value . '"'; } $value =~ s/([\t\n\r%&\=;,])/sprintf("%%%X",ord($1))/ge; } else { # if it is completely empty, then just make empty double quotes $value = '""'; } push @v, $value; } # can we figure out how to improve this? $tag = lcfirst($tag) unless ( $tag =~ /^(ID|Name|Alias|Parent|Gap|Target|Derives_from|Note|Dbxref|Ontology_term)$/); push @groups, "$tag=".join(",",@v); } # Add Target information for Feature Pairs if( $feat->has_tag('Target') && ! $feat->has_tag('Group') && $origfeat->isa('Bio::SeqFeature::FeaturePair') ) { my $target_id = $origfeat->feature1->seq_id; $target_id =~ s/([\t\n\r%&\=;,])/sprintf("%%%X",ord($1))/ge; push @groups, sprintf("Target=%s %d %d", $target_id, ( $origfeat->feature1->strand < 0 ? ( $origfeat->feature1->end, $origfeat->feature1->start) : ( $origfeat->feature1->start, $origfeat->feature1->end) )); } # unshift @groups, "ID=autogenerated$ID" unless ($feat->has_tag('ID')); if ( $feat->can('name') && defined($feat->name) ) { # such as might be for Bio::DB::SeqFeature unshift @groups, 'Name=' . $feat->name; } my $gff_string = ""; if ($feat->location->isa("Bio::Location::SplitLocationI")) { my @locs = $feat->location->each_Location; foreach my $loc (@locs) { $gff_string .= join("\t", $name, $feat->source_tag() || '.', $feat->primary_tag(), $loc->start(), $loc->end(), $score, $strand, $frame, join(';', @groups)) . "\n"; } chop $gff_string; return $gff_string; } else { $gff_string = join("\t", $name, $feat->source_tag() || '.', $feat->primary_tag(), $feat->start(), $feat->end(), $score, $strand, $frame, join(';', @groups)); } return $gff_string; } =head2 gff_version Title : _gff_version Usage : $gffversion = $gffio->gff_version Function: Example : Returns : The GFF version this parser will accept and emit. Args : none =cut sub gff_version { my ($self, $value) = @_; if(defined $value && grep {$value == $_ } ( 1, 2, 2.5, 3)) { $self->{'GFF_VERSION'} = $value; } return $self->{'GFF_VERSION'}; } # Make filehandles =head2 newFh Title : newFh Usage : $fh = Bio::Tools::GFF->newFh(-file=>$filename,-format=>'Format') Function: does a new() followed by an fh() Example : $fh = Bio::Tools::GFF->newFh(-file=>$filename,-format=>'Format') $feature = <$fh>; # read a feature object print $fh $feature; # write a feature object Returns : filehandle tied to the Bio::Tools::GFF class Args : =cut sub newFh { my $class = shift; return unless my $self = $class->new(@_); return $self->fh; } =head2 fh Title : fh Usage : $obj->fh Function: Example : $fh = $obj->fh; # make a tied filehandle $feature = <$fh>; # read a feature object print $fh $feature; # write a feature object Returns : filehandle tied to Bio::Tools::GFF class Args : none =cut sub fh { my $self = shift; my $class = ref($self) || $self; my $s = Symbol::gensym; tie $$s,$class,$self; return $s; } # This accessor is used for accessing the Bio::Seq objects from a GFF3 # file; if the file you are using has no sequence data you can ignore # this accessor # This accessor returns a hash reference containing Bio::Seq objects, # indexed by Bio::Seq->primary_id sub _seq_by_id_h { my $self = shift; return $self->{'_seq_by_id_h'} = shift if @_; $self->{'_seq_by_id_h'} = {} unless $self->{'_seq_by_id_h'}; return $self->{'_seq_by_id_h'}; } =head2 get_seqs Title : get_seqs Usage : Function: Returns all Bio::Seq objects populated by GFF3 file Example : Returns : Args : =cut sub get_seqs { my ($self,@args) = @_; return values %{$self->_seq_by_id_h}; } =head2 features_attached_to_seqs Title : features_attached_to_seqs Usage : $obj->features_attached_to_seqs(1); Function: For use with GFF3 containing sequence only Setting this B<before> parsing ensures that all Bio::Seq object created will have the appropriate features added to them defaults to false (off) Note that this mode will incur higher memory usage because features will have to be cached until the relevant feature comes along Example : Returns : value of features_attached_to_seqs (a boolean) Args : on set, new value (a boolean, optional) =cut sub features_attached_to_seqs{ my $self = shift; return $self->{'_features_attached_to_seqs'} = shift if @_; return $self->{'_features_attached_to_seqs'}; } =head2 ignore_sequence Title : ignore_sequence Usage : $obj->ignore_sequence(1); Function: For use with GFF3 containing sequence only Setting this B<before> parsing means that all sequence data will be ignored Example : Returns : value of ignore_sequence (a boolean) Args : on set, new value (a boolean, optional) =cut sub ignore_sequence{ my $self = shift; return $self->{'_ignore_sequence'} = shift if @_; return $self->{'_ignore_sequence'}; } sub DESTROY { my $self = shift; $self->close(); } sub TIEHANDLE { my ($class,$val) = @_; return bless {'gffio' => $val}, $class; } sub READLINE { my $self = shift; return $self->{'gffio'}->next_feature() || undef unless wantarray; my (@list, $obj); push @list, $obj while $obj = $self->{'gffio'}->next_feature(); return @list; } sub PRINT { my $self = shift; $self->{'gffio'}->write_feature(@_); } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Gel.pm�������������������������������������������������������������������000444��000766��000024�� 13344�13155576320� 16416� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Gel # Copyright Allen Day <allenday@ucla.edu> # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Gel - Calculates relative electrophoretic migration distances =head1 SYNOPSIS use Bio::PrimarySeq; use Bio::Restriction::Analysis; use Bio::Tools::Gel; # get a sequence my $d = 'AAAAAAAAAGAATTCTTTTTTTTTTTTTTGAATTCGGGGGGGGGGGGGGGGGGGG'; my $seq1 = Bio::Seq->new(-id=>'groundhog day',-seq=>$d); # cut it with an enzyme my $ra=Bio::Restriction::Analysis->new(-seq=>$seq1); @cuts = $ra->fragments('EcoRI'), 3; # analyse the fragments in a gel my $gel = Bio::Tools::Gel->new(-seq=>\@cuts,-dilate=>10); my %bands = $gel->bands; foreach my $band (sort {$b <=> $a} keys %bands){ print $band,"\t", sprintf("%.1f", $bands{$band}),"\n"; } #prints: #20 27.0 #25 26.0 #10 30.0 =head1 DESCRIPTION This takes a set of sequences or Bio::Seq objects, and calculates their respective migration distances using: distance = dilation * (4 - log10(length(dna)); Source: Molecular Cloning, a Laboratory Manual. Sambrook, Fritsch, Maniatis. CSHL Press, 1989. Bio::Tools::Gel currently calculates migration distances based solely on the length of the nucleotide sequence. Secondary or tertiary structure, curvature, and other biophysical attributes of a sequence are currently not considered. Polypeptide migration is currently not supported. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Allen Day Email allenday@ucla.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Gel; use strict; use Bio::PrimarySeq; use base qw(Bio::Root::Root); =head2 new Title : new Usage : my $gel = Bio::Tools::Gel->new(-seq => $sequence,-dilate => 3); Function: Initializes a new Gel Returns : Bio::Tools::Gel Args : -seq => Bio::Seq(s), scalar(s) or list of either/both (default: none) -dilate => Expand band migration distances (default: 1) =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($seqs, $dilate) = $self->_rearrange([qw(SEQ DILATE)], @args); if( ! ref($seqs) ) { $self->add_band([$seqs]); } elsif( ref($seqs) =~ /array/i || $seqs->isa('Bio::PrimarySeqI') ) { $self->add_band($seqs); } $self->dilate($dilate || 1); return $self; } =head2 add_band Title : add_band Usage : $gel->add_band($seq); Function: Calls _add_band with a (possibly created) Bio::Seq object. Returns : Args : Bio::Seq, scalar sequence, or list of either/both. =cut sub add_band { my ($self, $args) = @_; foreach my $arg (@$args){ my $seq; if( ! ref $arg ) { if( $arg =~ /^\d+/ ) { # $arg is a number $seq = Bio::PrimarySeq->new(-seq=>'N'x$arg, -id => $arg); } else { # $arg is a sequence string $seq = Bio::PrimarySeq->new(-seq=>$arg, -id=>length $arg); } } elsif( $arg->isa('Bio::PrimarySeqI') ) { # $arg is a sequence object $seq = $arg; } $self->_add_band($seq); } return 1; } =head2 _add_band Title : _add_band Usage : $gel->_add_band($seq); Function: Adds a new band to the gel. Returns : Args : Bio::Seq object =cut sub _add_band { my ($self, $arg) = @_; if ( defined $arg) { push (@{$self->{'bands'}},$arg); } return 1; } =head2 dilate Title : dilate Usage : $gel->dilate(1); Function: Sets/retrieves the dilation factor. Returns : dilation factor Args : Float or none =cut sub dilate { my ($self, $arg) = @_; return $self->{dilate} unless $arg; $self->throw("-dilate should be numeric") if defined $arg and $arg =~ /[^e\d\.]/; $self->{dilate} = $arg; return $self->{dilate}; } sub migrate { my ($self, $arg) = @_; $arg = $self unless $arg; if ( $arg ) { return 4 - log10($arg); } else { return 0; } } =head2 bands Title : bands Usage : $gel->bands; Function: Calculates migration distances of sequences. Returns : hash of (seq_id => distance) Args : =cut sub bands { my $self = shift; $self->throw("bands() is read-only") if @_; my %bands = (); foreach my $band (@{$self->{bands}}){ my $distance = $self->dilate * migrate($band->length); $bands{$band->id} = $distance; } return %bands; } =head2 log10 Title : log10 Usage : log10($n); Function: returns base 10 log of $n. Returns : float Args : float =cut # from "Programming Perl" sub log10 { my $n = shift; return log($n)/log(10); } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Geneid.pm����������������������������������������������������������������000444��000766��000024�� 22231�13155576320� 17075� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Keith James # # Copyright Genome Research Ltd. # # You may distribute this module under the same terms as Perl itself # POD documentation - main docs before the code =encoding utf-8 =head1 NAME Bio::Tools::Geneid - Results of one geneid run =head1 SYNOPSIS use Bio::Tools::Geneid; my $gid = Bio::Tools::Geneid(-file => "geneid.out"); while (my $gene = $gid->next_prediction) { my @transcripts = $gene->transcripts; foreach my $t (@transcripts) { my @exons = $t->exons; foreach my $e (@exons) { printf("Exon %d..%d\n", $e->start, $e->end); } } } =head1 DESCRIPTION This is the parser for the output of geneid by Enrique Blanco and Roderic GuigE<243> (IMIM-UPF). See http://www1.imim.es/software/geneid. It relies on native geneid output format internally and will work with geneid versions 1.0 and 1.1. Currently this module supports only the default mode of operation which is to predict exons and assemble an optimal gene prediction. It takes either a file handle or a file name and returns a Bio::SeqFeature::Gene::GeneStructure object. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Keith James Email: kdj@sanger.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Geneid; use vars qw($SOURCE_TAG); use strict; use Bio::Tools::AnalysisResult; use Bio::SeqFeature::Generic; use Bio::SeqFeature::Gene::Exon; use Bio::SeqFeature::Gene::Transcript; use Bio::SeqFeature::Gene::GeneStructure; use base qw(Bio::Root::Root Bio::Root::IO); $SOURCE_TAG = 'geneid'; =head2 new Title : new Usage : $obj->new(-file = "<geneid.out"); $obj->new(-fh => \*GI); Function: Constructor for geneid wrapper. Takes either a file : or filehandle Returns : L<Bio::Tools::Geneid> =cut sub new { my($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_prediction Title : next_prediction Usage : while($gene = $geneid->next_prediction) { # do something } Function: Returns the gene structure prediction of the geneid result file. Call this method repeatedly until FALSE is returned. Returns : A Bio::SeqFeature::Gene::GeneStructure object Args : None =cut sub next_prediction { my ($self) = @_; my ($gene, $transcript, $current_gene_id); my $transcript_score = 0; my ($gene_id, $exon_type, $exon_start, $exon_end, $exon_score, $exon_strand, $start_phase, $end_phase, $start_sig_score, $end_sig_score, $coding_pot_score, $homol_score); while (defined($_ = $self->_readline)) { $self->debug($_); s/^\s+//; s/\s+$//; # We have a choice of geneid, gff or XML formats. The native # geneid format has more information than gff. However, we # then need to perform the hack of extracting the sequence ID # from the header of the embedded Fasta file which comes after # the exon data, as it is not stored elsewhere. Ack. # the new version of geneID includes the sequence ID in a slightly # different format and a new "or" statement was added below # also removed "unless defined $self->_target_id;" inorder to continue # generating new sequence IDs. if (/^>(\S+)\|GeneId/ or /^# Sequence (\S+)/) { my $target_id = $1; $self->_target_id($target_id); next; } next unless (/(Single|First|Internal|Terminal)/); my @fields = split(/\s+/, $_); # Grab gene_id from eol first as there are issues with # inconsistent whitespace in the AA coords field $gene_id = pop @fields; ($exon_type, $exon_start, $exon_end, $exon_score, $exon_strand, $start_phase, $end_phase, $start_sig_score, $end_sig_score, $coding_pot_score, $homol_score) = @fields[0..10]; if (! defined $current_gene_id) { # Starting the requested prediction $current_gene_id = $gene_id; $transcript_score = $exon_score; $gene = Bio::SeqFeature::Gene::GeneStructure->new(-source => $SOURCE_TAG); $transcript = Bio::SeqFeature::Gene::Transcript->new(-source => $SOURCE_TAG); $self->_add_exon($gene, $transcript, $exon_type, $exon_start, $exon_end, $exon_score, $exon_strand, $start_phase, $end_phase, $start_sig_score, $end_sig_score, $coding_pot_score, $homol_score); } elsif ($gene_id eq $current_gene_id) { # Still in requested prediction $transcript_score += $exon_score; $self->_add_exon($gene, $transcript, $exon_type, $exon_start, $exon_end, $exon_score, $exon_strand, $start_phase, $end_phase, $start_sig_score, $end_sig_score, $coding_pot_score, $homol_score); } else { # Found following prediction $self->_pushback($_); last; } } if (defined $gene) { $transcript->seq_id($self->_target_id); $transcript->score($transcript_score); $gene->add_transcript($transcript); $gene->seq_id($self->_target_id); foreach my $exon ($gene->exons) { $exon->seq_id($self->_target_id); } $self->_set_strand($gene); } return $gene; } =head2 _add_exon Title : _add_exon Usage : $obj->_add_exon($gene, $transcript, ... exon data ...) Function: Adds a new exon to both gene and transcript from the data : supplied as args Example : Returns : Nothing =cut sub _add_exon { my ($self, $gene, $transcript, $exon_type, $exon_start, $exon_end, $exon_score, $exon_strand, $start_phase, $end_phase, $start_sig_score, $end_sig_score, $coding_pot_score, $homol_score) = @_; $exon_type =~ s/First/Initial/; my $strand = $exon_strand eq '+' ? 1 : -1; my $exon = Bio::SeqFeature::Gene::Exon->new(-source => $SOURCE_TAG, -start => $exon_start, -end => $exon_end, -strand => $strand, -score => $exon_score); $exon->is_coding(1); $exon->add_tag_value("Type", $exon_type); $exon->add_tag_value('phase', $start_phase); $exon->add_tag_value('end_phase', $end_phase); $exon->add_tag_value('start_signal_score', $start_sig_score); $exon->add_tag_value('end_signal_score', $end_sig_score); $exon->add_tag_value('coding_potential_score', $coding_pot_score); $exon->add_tag_value('homology_score', $homol_score); $transcript->strand($strand) unless $transcript->strand != 0; $transcript->add_exon($exon, $exon_type); } =head2 _set_strand Title : _set_strand Usage : $obj->_set_strand($gene) Function: Sets the overall gene strand to the same strand as all : the exons if they are all on the same strand, or to strand 0 : if the exons are on different strands. Example : Returns : Nothing =cut sub _set_strand { my ($self, $gene) = @_; my $fwd = 0; my $rev = 0; my @exons = $gene->exons; foreach my $exon (@exons) { my $strand = $exon->strand; if ($strand == 1) { $fwd++; } elsif ($strand == -1) { $rev++; } } if ($#exons == $fwd) { $gene->strand(1); } elsif ($#exons == $rev) { $gene->strand(-1); } else { $gene->strand(0); } return $gene; } =head2 _target_id Title : _target_id Usage : $obj->_target_id Function: get/set for genomic sequence id Example : Returns : A target ID =cut sub _target_id { my ($self,$val) = @_; if ($val) { $self->{'_target_id'} = $val; } return $self->{'_target_id'}; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Genemark.pm��������������������������������������������������������������000444��000766��000024�� 35234�13155576320� 17442� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Genemark # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Mark Fiers <hlapp@gmx.net> # # Copyright Hilmar Lapp, Mark Fiers # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Genemark - Results of one Genemark run =head1 SYNOPSIS $Genemark = Bio::Tools::Genemark->new(-file => 'result.Genemark'); # filehandle: $Genemark = Bio::Tools::Genemark->new( -fh => \*INPUT ); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $Genemark->next_feature() is the same while($gene = $Genemark->next_prediction()) { # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits # off Bio::SeqFeature::Gene::Transcript. # # $gene->exons() returns an array of # Bio::Tools::Prediction::Exon objects # all exons: @exon_arr = $gene->exons(); # initial exons only @init_exons = $gene->exons('Initial'); # internal exons only @intrl_exons = $gene->exons('Internal'); # terminal exons only @term_exons = $gene->exons('Terminal'); # singleton exons: ($single_exon) = $gene->exons(); } # essential if you gave a filename at initialization (otherwise the file # will stay open) $Genemark->close(); =head1 DESCRIPTION The Genemark module provides a parser for Genemark gene structure prediction output. It parses one gene prediction into a Bio::SeqFeature::Gene::Transcript- derived object. This module has been developed around genemark.hmm for eukaryots v2.2a and will probably not work with other versions. This module also implements the Bio::SeqAnalysisParserI interface, and thus can be used wherever such an object fits. See L<Bio::SeqAnalysisParserI>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp, Mark Fiers Email hlapp@gmx.net m.w.e.j.fiers@plant.wag-ur.nl =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Genemark; use strict; use Symbol; use Bio::Root::Root; use Bio::Tools::Prediction::Gene; use Bio::Tools::Prediction::Exon; use Bio::Seq; use Bio::Factory::FTLocationFactory; use base qw(Bio::Tools::AnalysisResult); =head2 new Title : new Usage : my $obj = Bio::Tools::Genemark->new(); Function: Builds a new Bio::Tools::Genemark object Returns : an instance of Bio::Tools::Genemark Args : seqname =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($seqname) = $self->_rearrange([qw(SEQNAME)], @args); # hardwire seq_id when creating gene and exon objects $self->_seqname($seqname) if defined($seqname); return $self; } sub _initialize_state { my ($self,@args) = @_; # first call the inherited method! $self->SUPER::_initialize_state(@args); # our private state variables $self->{'_preds_parsed'} = 0; $self->{'_has_cds'} = 0; # array of pre-parsed predictions $self->{'_preds'} = []; # seq stack $self->{'_seqstack'} = []; } =head2 analysis_method Usage : $Genemark->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /GeneMark.hmm/i. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method && ($method !~ /Genemark\.hmm/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head2 next_feature Title : next_feature Usage : while($gene = $Genemark->next_feature()) { # do something } Function: Returns the next gene structure prediction of the Genemark result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_feature { my ($self,@args) = @_; # even though next_prediction doesn't expect any args (and this method # does neither), we pass on args in order to be prepared if this changes # ever return $self->next_prediction(@args); } =head2 next_prediction Title : next_prediction Usage : while($gene = $Genemark->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the Genemark result file. Call this method repeatedly until FALSE is returned. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_prediction { my ($self) = @_; my $gene; # if the prediction section hasn't been parsed yet, we do this now $self->_parse_predictions() unless $self->_predictions_parsed(); # get next gene structure $gene = $self->_prediction(); return $gene; } =head2 _parse_predictions Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : =cut sub _parse_predictions { my ($self) = @_; my %exontags = ('Initial' => 'Initial', 'Internal' => 'Internal', 'Terminal' => 'Terminal', 'Single' => '', '_na_' => ''); my $exontag; my $gene; my $exontype; my $current_gene_no = -1; # The prediction report does not contain a sequence identifier # (at least the prokaryotic version doesn't) my $seqname = $self->_seqname(); while(defined($_ = $self->_readline())) { if( (/^\s*(\d+)\s+(\d+)/) || (/^\s*(\d+)\s+[\+\-]/)) { # this is an exon, Genemark doesn't predict anything else # $prednr corresponds to geneno. my $prednr = $1; #exon no: my $signalnr = 0; if ($2) { my $signalnr = $2; } # used in tag: exon_no # split into fields chomp(); my @flds = split(' ', $_); # create the feature (an exon) object my $predobj = Bio::Tools::Prediction::Exon->new(); # define info depending on it being eu- or prokaryot my ($start, $end, $orientation, $prediction_source); if ($self->analysis_method() =~ /PROKARYOTIC/i) { $prediction_source = "Genemark.hmm.pro"; $orientation = ($flds[1] eq '+') ? 1 : -1; ($start, $end) = @flds[(2,3)]; $exontag = "_na_"; } else { $prediction_source = "Genemark.hmm.eu"; $orientation = ($flds[2] eq '+') ? 1 : -1; ($start, $end) = @flds[(4,5)]; $exontag = $flds[3]; } # instatiate a location object via # Bio::Factory::FTLocationFactory (to handle # inexact coordinates) my $location_string = join('..', $start, $end); my $location_factory = Bio::Factory::FTLocationFactory->new(); my $location_obj = $location_factory->from_string($location_string); $predobj->location($location_obj); #store the data in the exon object $predobj->source_tag($prediction_source); $predobj->strand($orientation); $predobj->primary_tag($exontags{$exontag} . "Exon"); $predobj->add_tag_value('exon_no',"$signalnr") if ($signalnr); $predobj->is_coding(1); $predobj->seq_id($seqname) if (defined($seqname) && ($seqname ne 'unknown')); # frame calculation as in the genscan module # is to be implemented... #If the $prednr is not equal to the current gene, we #need to make a new gene and close the old one if($prednr != $current_gene_no) { # a new gene, store the old one if it exists if (defined ($gene)) { $gene->seq_id($seqname); $gene = undef ; } #and make a new one $gene = Bio::Tools::Prediction::Gene->new ( '-primary' => "GenePrediction$prednr", '-source' => $prediction_source); $self->_add_prediction($gene); $current_gene_no = $prednr; $gene->seq_id($seqname) if (defined($seqname) && ($seqname ne 'unknown')); } # Add the exon to the gene $gene->add_exon($predobj, ($exontag eq "_na_" ? undef : $exontags{$exontag})); } if(/^(Genemark\.hmm\s*[PROKARYOTIC]*)\s+\(Version (.*)\)$/i) { $self->analysis_method($1); my $gm_version = $2; $self->analysis_method_version($gm_version); next; } #Matrix file for eukaryot version if (/^Matrices file:\s+(\S+)?/i) { $self->analysis_subject($1); # since the line after the matrix file is always the date # (in the output file's I have seen!) extract and store this # here if (defined(my $_date = $self->_readline())) { chomp ($_date); $self->analysis_date($_date); } } #Matrix file for prokaryot version if (/^Model file name:\s+(\S+)/) { $self->analysis_subject($1); # since the line after the matrix file is always the date # (in the output file's I have seen!) extract and store this # here my $_date = $self->_readline() ; if (defined($_date = $self->_readline())) { chomp ($_date); $self->analysis_date($_date); } } if(/^Sequence[ file]? name:\s+(.+)\s*$/i) { $seqname = $1; # $self->analysis_subject($seqname); next; } /^>/ && do { $self->_pushback($_); # section of predicted aa sequences on recognition # of a fasta start, read all sequences and find the # appropriate gene while (1) { my ($aa_id, $seq) = $self->_read_fasta_seq(); last unless ($aa_id); #now parse through the predictions to add the pred. protein FINDPRED: foreach my $gene (@{$self->{'_preds'}}) { $gene->primary_tag() =~ /[^0-9]([0-9]+)$/; my $geneno = $1; if ($aa_id =~ /\|gene.$geneno\|/) { #print "x SEQ : \n $seq \nXXXX\n"; my $seqobj = Bio::Seq->new('-seq' => $seq, '-display_id' => $aa_id, '-alphabet' => "protein"); $gene->predicted_protein($seqobj); last FINDPRED; } } } last; }; } # if the analysis query object contains a ref to a Seq of PrimarySeq # object, then extract the predicted sequences and add it to the gene # object. if (defined $self->analysis_query()) { my $orig_seq = $self->analysis_query(); FINDPREDSEQ: foreach my $gene (@{$self->{'_preds'}}) { my $predseq = ""; foreach my $exon ($gene->exons()) { #print $exon->start() . " " . $exon->end () . "\n"; $predseq .= $orig_seq->subseq($exon->start(), $exon->end()); } my $seqobj = Bio::PrimarySeq->new('-seq' => $predseq, '-display_id' => "transl"); $gene->predicted_cds($seqobj); } } $self->_predictions_parsed(1); } =head2 _prediction Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns : =cut sub _prediction { my ($self) = @_; return unless(exists($self->{'_preds'}) && @{$self->{'_preds'}}); return shift(@{$self->{'_preds'}}); } =head2 _add_prediction Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns : =cut sub _add_prediction { my ($self, $gene) = @_; if(! exists($self->{'_preds'})) { $self->{'_preds'} = []; } push(@{$self->{'_preds'}}, $gene); } =head2 _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE =cut sub _predictions_parsed { my ($self, $val) = @_; $self->{'_preds_parsed'} = $val if $val; if(! exists($self->{'_preds_parsed'})) { $self->{'_preds_parsed'} = 0; } return $self->{'_preds_parsed'}; } =head2 _has_cds Title : _has_cds() Usage : $obj->_has_cds() Function: Whether or not the result contains the predicted CDSs, too. Example : Returns : TRUE or FALSE =cut sub _has_cds { my ($self, $val) = @_; $self->{'_has_cds'} = $val if $val; if(! exists($self->{'_has_cds'})) { $self->{'_has_cds'} = 0; } return $self->{'_has_cds'}; } =head2 _read_fasta_seq Title : _read_fasta_seq() Usage : ($id,$seqstr) = $obj->_read_fasta_seq(); Function: Simple but specialised FASTA format sequence reader. Uses $self->_readline() to retrieve input, and is able to strip off the traling description lines. Example : Returns : An array of two elements. =cut sub _read_fasta_seq { my ($self) = @_; my ($id, $seq); local $/ = ">"; return 0 unless (my $entry = $self->_readline()); $entry =~ s/^>//; # complete the entry if the first line came from a pushback buffer while(! ($entry =~ />$/)) { last unless ($_ = $self->_readline()); $entry .= $_; } # delete everything onwards from an new fasta start (>) $entry =~ s/\n>.*$//s; # id and sequence if($entry =~ s/^(.+)\n//) { $id = $1; $id =~ s/ /_/g; $seq = $entry; $seq =~ s/\s//g; #print "\n@@ $id \n@@ $seq \n##\n"; } else { $self->throw("Can't parse Genemark predicted sequence entry"); } $seq =~ s/\s//g; # Remove whitespace return ($id, $seq); } =head2 _seqname Title : _seqname Usage : $obj->_seqname($seqname) Function: internal Example : Returns : String =cut sub _seqname { my ($self, $val) = @_; $self->{'_seqname'} = $val if $val; if(! exists($self->{'_seqname'})) { $self->{'_seqname'} = 'unknown'; } return $self->{'_seqname'}; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Genewise.pm��������������������������������������������������������������000444��000766��000024�� 21366�13155576320� 17460� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Genewise # # Copyright Fugu Team # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Genewise - Results of one Genewise run =head1 SYNOPSIS use Bio::Tools::Genewise; my $gw = Bio::Tools::Genewise(-file=>"genewise.out"); while (my $gene = $gw->next_prediction){ my @transcripts = $gene->transcripts; foreach my $t(@transcripts){ my @exons = $t->exons; foreach my $e(@exons){ print $e->start." ".$e->end."\n"; } } } =head1 DESCRIPTION This is the parser for the output of Genewise. It takes either a file handle or a file name and returns a Bio::SeqFeature::Gene::GeneStructure object. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Fugu Team, Jason Stajich Email: fugui@worf.fugu-sg.org Email: jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Genewise; use vars qw($Srctag); use strict; use Symbol; use Bio::Tools::AnalysisResult; use Bio::SeqFeature::Generic; use Bio::SeqFeature::Gene::Exon; use Bio::SeqFeature::FeaturePair; use Bio::SeqFeature::Gene::Transcript; use Bio::SeqFeature::Gene::GeneStructure; use base qw(Bio::Root::Root Bio::Root::IO); $Srctag = 'genewise'; =head2 new Title : new Usage : $obj->new(-file=>"genewise.out"); $obj->new(-fh=>\*GW); Function: Constructor for genewise wrapper. Takes either a file or filehandle Example : Returns : Bio::Tools::Genewise object See L<Bio::Tools::Genewise> =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 _get_strand Title : _get_strand Usage : $obj->_get_strand Function: takes start and end values, swap them if start>end and returns end Example : Returns :$start,$end,$strand =cut sub _get_strand { my ($self,$start,$end) = @_; defined($start) || $self->throw("Need a start"); defined($end) || $self->throw("Need an end"); my $strand; if ($start > $end) { my $tmp = $start; $start = $end; $end = $tmp; $strand = -1; } else { $strand = 1; } return ($start,$end,$strand); } =head2 _score Title : _score Usage : $obj->_score Function: get/set for score info Returns : a score value =cut sub _score { my $self = shift; return $self->{'_score'} = shift if @_; return $self->{'_score'}; } =head2 _prot_id Title : _prot_id Usage : $obj->_prot_id Function: get/set for protein id Returns :a protein id =cut sub _prot_id { my $self = shift; return $self->{'_prot_id'} = shift if @_; return $self->{'_prot_id'}; } =head2 _target_id Title : _target_id Usage : $obj->_target_id Function: get/set for genomic sequence id Example : Returns :a target id =cut sub _target_id { my $self = shift; return $self->{'_target_id'} = shift if @_; return $self->{'_target_id'}; } =head2 next_prediction Title : next_prediction Usage : while($gene = $genewise->next_prediction()) { # do something } Function: Returns the gene structure prediction of the Genewise result file. Call this method repeatedly until FALSE is returned. Example : Returns : a Bio::SeqFeature::Gene::GeneStructure object Args : See L<Bio::SeqFeature::Gene::GeneStructure> =cut sub next_prediction { my ($self) = @_; unless ( $self->parsed ){ $self->_parse_genes; $self->parsed(1); } return shift @{$self->{'_genes'}}; } sub parsed { my $self = shift; return $self->{'_parsed'} = 1 if @_ && $_[0]; return $self->{'_parsed'}; } sub _parse_genes { my ($self) = @_; my (@alignments,@genes); local ($/) = "//"; while ( defined($_ = $self->_readline) ) { $self->debug( $_ ); while( /Alignment\s+(\d+)\s+Score\s+(\S+)\s+\(Bits\)/g ) { $alignments[$1] = $2; } if( /Score\s+(\-?\d+(\.\d+)?)/ ) { $self->_score($1);# unless defined $self->_score; } if( /Query\s+(?:protein|model)\:\s+(\S+)/ ) { $self->_prot_id($1); #unless defined $self->_prot_id; } if( /Target Sequence\s+(\S+)/ ) { $self->_target_id($1);# unless defined $self->_target_id; } next unless /Gene\s+\d+\n/; my @genes_txt = split(/Gene\s+\d+\n/,$_); shift @genes_txt; #remove first empty entry my $gene_num = 1; foreach my $gene_txt (@genes_txt) { my $score = $alignments[$gene_num]; # If genewise has assigned a strand to the gene as a whole # overall gene start and end my ($g_start, $g_end, $type) = $gene_txt =~ m/Gene\s+ (\d+)[\s-]+ # start (1-based) (\d+)\s+ # end (?:\[(\w+)\])? # /x; my $g_strand; my $source_tag = $type ? "$Srctag". "_$type" : $Srctag; my $genes = Bio::SeqFeature::Gene::GeneStructure->new (-source => $source_tag, -score => $self->_score, ); $genes->add_tag_value('ID', $self->_prot_id.".gene"); my $transcript = Bio::SeqFeature::Gene::Transcript->new (-source => $source_tag, -score => $score); ($g_start, $g_end, $g_strand) = $self->_get_strand($g_start,$g_end); $genes->strand($g_strand); # grab exon + supporting feature info my @exons; unless ( @exons = $gene_txt =~ m/(Exon .+\s+Supporting .+)/g ) { @exons = $gene_txt =~ m/(Exon .+\s+)/g; } my $nbr = 1; # loop through each exon-supporting feature pair foreach my $e (@exons){ my ($e_start,$e_end,$phase) = $e =~ m/Exon\s+ (\d+)[\s-]+ # start (1 based) (\d+)\s+ # end phase\s+(\d+) # phase /x; my $e_strand; ($e_start,$e_end,$e_strand) = $self->_get_strand($e_start, $e_end); $transcript->strand($e_strand) unless $transcript->strand != 0; my $exon = Bio::SeqFeature::Gene::Exon->new (-seq_id =>$self->_target_id, -source => $source_tag, -start =>$e_start, -end =>$e_end, -score => $score, #-frame => $phase, -strand =>$e_strand); $exon->add_tag_value('phase',$phase); $exon->is_coding(1); if( $self->_prot_id ) { $exon->add_tag_value('Parent',$self->_prot_id); } $exon->add_tag_value("Exon",$nbr++); if( $e =~ m/Supporting\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)/) { my ($geno_start,$geno_end, $prot_start, $prot_end) = ($1,$2,$3,$4); my $prot_strand; ($prot_start,$prot_end, $prot_strand) = $self->_get_strand($prot_start,$prot_end); my $pf = Bio::SeqFeature::Generic->new ( -start => $prot_start, -end => $prot_end, -seq_id => $self->_prot_id, -score => $score, -strand => $prot_strand, -source => $source_tag, -primary_tag => 'supporting_protein_feature',); my $geno_strand; ($geno_start,$geno_end, $geno_strand) = $self->_get_strand($geno_start,$geno_end); my $gf = Bio::SeqFeature::Generic->new ( -start => $geno_start, -end => $geno_end, -seq_id => $self->_target_id, -score => $score, -strand => $geno_strand, -source => $source_tag, -primary_tag => 'supporting_genomic_feature',); my $fp = Bio::SeqFeature::FeaturePair->new (-feature1 =>$gf, -feature2 =>$pf); $exon->add_tag_value( 'supporting_feature',$fp ); if( $self->_prot_id ) { $exon->add_tag_value('Target','Protein:'.$self->_prot_id); $exon->add_tag_value('Target',$prot_start); $exon->add_tag_value('Target',$prot_end); } } $transcript->add_exon($exon); } $transcript->seq_id($self->_target_id); $transcript->add_tag_value('ID', $self->_prot_id); $transcript->add_tag_value('Parent', $self->_prot_id.".gene"); $genes->add_transcript($transcript); $genes->seq_id($self->_target_id); push @genes, $genes; $gene_num++; } } $self->{'_genes'} = \@genes; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Genomewise.pm������������������������������������������������������������000444��000766��000024�� 12343�13155576320� 20007� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Genomewise # # Copyright Jason Stajich <jason-at-bioperl.org> # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Tools::Genomewise - Results of one Genomewise run =head1 SYNOPSIS use Bio::Tools::Genomewise; my $gw = Bio::Tools::Genomewise(-file=>"genomewise.out"); while (my $gene = $gw->next_prediction){ my @transcripts = $gene->transcripts; foreach my $t(@transcripts){ my @exons = $t->exons; foreach my $e(@exons){ print $e->start." ".$e->end."\n"; } } } =head1 DESCRIPTION This is the parser for the output of Genewise. It takes either a file handle or a file name and returns a Bio::SeqFeature::Gene::GeneStructure object. You will need to specify the proper target sequence id on the object with the $feature-E<gt>seq_id($seqid). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Fugu Team, Jason Stajich Email: fugui-at-worf.fugu-sg.org jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Genomewise; use vars qw($Srctag); use strict; use Bio::Tools::AnalysisResult; use Bio::SeqFeature::Generic; use Bio::SeqFeature::Gene::Exon; use Bio::SeqFeature::FeaturePair; use Bio::SeqFeature::Gene::Transcript; use Bio::SeqFeature::Gene::GeneStructure; use base qw(Bio::Tools::Genewise); $Srctag = 'genomewise'; =head2 new Title : new Usage : $obj->new(-file=>"genewise.out"); $obj->new(-fh=>\*GW); Function: Constructor for genomewise wrapper. Takes either a file or filehandle Example : Returns : L<Bio::Tools::Genomewise> =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); return $self; } =head2 _get_strand Title : _get_strand Usage : $obj->_get_strand Function: takes start and end values, swap them if start>end and returns end Example : Returns :$start,$end,$strand =cut =head2 score Title : score Usage : $obj->score Function: get/set for score info Example : Returns : a score value =cut =head2 _prot_id Title : _prot_id Usage : $obj->_prot_id Function: get/set for protein id Example : Returns :a protein id =cut =head2 _target_id Title : _target_id Usage : $obj->_target_id Function: get/set for genomic sequence id Example : Returns :a target id =cut =head2 next_prediction Title : next_prediction Usage : while($gene = $genewise->next_prediction()) { # do something } Function: Returns the gene structure prediction of the Genomewise result file. Call this method repeatedly until FALSE is returned. Example : Returns : a Bio::SeqFeature::Gene::GeneStructure object Args : =cut sub next_prediction { my ($self) = @_; my $genes; while ($_ = $self->_readline) { $self->debug( $_ ); last if m{^//}; if( /^Gene\s+\d+\s*$/ ) { $genes = Bio::SeqFeature::Gene::GeneStructure->new (-source => $Srctag, -seq_id => $self->_target_id, # if this had been specified ); $_ = $self->_readline; $self->debug( $_ ); unless ( /^Gene\s+(\d+)\s+(\d+)\s*$/ ) { $self->warn("Unparseable genomewise output"); last; } my $transcript = Bio::SeqFeature::Gene::Transcript->new (-source => $Srctag, -seq_id => $self->_target_id, # if this had been specified -start => $1, -end => $2, ); my $nbr = 1; while( $_ = $self->_readline ) { $self->debug( $_ ); unless( m/^\s+Exon\s+(\d+)\s+(\d+)\s+phase\s+(\d+)/ ){ $self->_pushback($_); last; } my ($e_start,$e_end,$phase,$e_strand) = ($1,$2,$3); ($e_start,$e_end,$e_strand) = $self->_get_strand($e_start, $e_end); $transcript->strand($e_strand) unless $transcript->strand != 0; my $exon = Bio::SeqFeature::Gene::Exon->new (-seq_id=>$self->_target_id, -source => $Srctag, -start=>$e_start, -end=>$e_end, -frame => $phase, -strand=>$e_strand); $exon->add_tag_value("Exon",$nbr++); $exon->add_tag_value('phase',$phase); $transcript->add_exon($exon); } $genes->add_transcript($transcript); last; # only process a single gene at a time } } return $genes; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Genscan.pm���������������������������������������������������������������000444��000766��000024�� 32354�13155576320� 17267� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Genscan # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp@gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Genscan - Results of one Genscan run =head1 SYNOPSIS use Bio::Tools::Genscan; $genscan = Bio::Tools::Genscan->new(-file => 'result.genscan'); # filehandle: $genscan = Bio::Tools::Genscan->new( -fh => \*INPUT ); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same while($gene = $genscan->next_prediction()) { # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits # off Bio::SeqFeature::Gene::Transcript. # # $gene->exons() returns an array of # Bio::Tools::Prediction::Exon objects # all exons: @exon_arr = $gene->exons(); # initial exons only @init_exons = $gene->exons('Initial'); # internal exons only @intrl_exons = $gene->exons('Internal'); # terminal exons only @term_exons = $gene->exons('Terminal'); # singleton exons: ($single_exon) = $gene->exons(); } # essential if you gave a filename at initialization (otherwise the file # will stay open) $genscan->close(); =head1 DESCRIPTION The Genscan module provides a parser for Genscan gene structure prediction output. It parses one gene prediction into a Bio::SeqFeature::Gene::Transcript- derived object. This module also implements the Bio::SeqAnalysisParserI interface, and thus can be used wherever such an object fits. See L<Bio::SeqAnalysisParserI>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp@gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Genscan; use strict; use Symbol; use Bio::Root::Root; use Bio::Tools::Prediction::Gene; use Bio::Tools::Prediction::Exon; use base qw(Bio::Tools::AnalysisResult); my %ExonTags = ('Init' => 'Initial', 'Intr' => 'Internal', 'Term' => 'Terminal', 'Sngl' => ''); sub _initialize_state { my ($self,@args) = @_; # first call the inherited method! $self->SUPER::_initialize_state(@args); # our private state variables $self->{'_preds_parsed'} = 0; $self->{'_has_cds'} = 0; # array of pre-parsed predictions $self->{'_preds'} = []; # seq stack $self->{'_seqstack'} = []; } =head2 analysis_method Usage : $genscan->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /genscan/i. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method && ($method !~ /genscan/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head2 next_feature Title : next_feature Usage : while($gene = $genscan->next_feature()) { # do something } Function: Returns the next gene structure prediction of the Genscan result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_feature { my ($self,@args) = @_; # even though next_prediction doesn't expect any args (and this method # does neither), we pass on args in order to be prepared if this changes # ever return $self->next_prediction(@args); } =head2 next_prediction Title : next_prediction Usage : while($gene = $genscan->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the Genscan result file. Call this method repeatedly until FALSE is returned. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_prediction { my ($self) = @_; my $gene; # if the prediction section hasn't been parsed yet, we do this now $self->_parse_predictions() unless $self->_predictions_parsed(); # get next gene structure $gene = $self->_prediction(); if($gene) { # fill in predicted protein, and if available the predicted CDS # my ($id, $seq); # use the seq stack if there's a seq on it my $seqobj = pop(@{$self->{'_seqstack'}}); if(! $seqobj) { # otherwise read from input stream ($id, $seq) = $self->_read_fasta_seq(); # there may be no sequence at all, or none any more if($id && $seq) { $seqobj = Bio::PrimarySeq->new('-seq' => $seq, '-display_id' => $id, '-alphabet' => "protein"); } } if($seqobj) { # check that prediction number matches the prediction number # indicated in the sequence id (there may be incomplete gene # predictions that contain only signals with no associated protein # and CDS, like promoters, poly-A sites etc) $gene->primary_tag() =~ /[^0-9]([0-9]+)$/; my $prednr = $1; if($seqobj->display_id() !~ /_predicted_\w+_$prednr\|/) { # this is not our sequence, so push back for next prediction push(@{$self->{'_seqstack'}}, $seqobj); } else { $gene->predicted_protein($seqobj); # CDS prediction, too? if($self->_has_cds()) { ($id, $seq) = $self->_read_fasta_seq(); $seqobj = Bio::PrimarySeq->new('-seq' => $seq, '-display_id' => $id, '-alphabet' => "dna"); $gene->predicted_cds($seqobj); } } } } return $gene; } =head2 _parse_predictions Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : =cut sub _parse_predictions { my ($self) = @_; my $gene; my $seqname; while(defined($_ = $self->_readline())) { if(/^\s*(\d+)\.(\d+)/) { # exon or signal my $prednr = $1; my $signalnr = $2; # not used presently if(! defined($gene)) { $gene = Bio::Tools::Prediction::Gene->new( '-primary' => "GenePrediction$prednr", '-source' => 'Genscan'); } # split into fields chomp(); my @flds = split(' ', $_); # create the feature object depending on the type of signal my $predobj; my $is_exon = grep {$_ eq $flds[1];} (keys(%ExonTags)); if($is_exon) { $predobj = Bio::Tools::Prediction::Exon->new(); } else { # PolyA site, or Promoter $predobj = Bio::SeqFeature::Generic->new(); } # set common fields $predobj->source_tag('Genscan'); $predobj->score($flds[$#flds]); $predobj->strand((($flds[2] eq '+') ? 1 : -1)); my ($start, $end) = @flds[(3,4)]; if($predobj->strand() == 1) { $predobj->start($start); $predobj->end($end); } else { $predobj->end($start); $predobj->start($end); } # add to gene structure (should be done only when start and end # are set, in order to allow for proper expansion of the range) if($is_exon) { # first, set fields unique to exons $predobj->start_signal_score($flds[8]); $predobj->end_signal_score($flds[9]); $predobj->coding_signal_score($flds[10]); $predobj->significance($flds[11]); $predobj->primary_tag($ExonTags{$flds[1]} . 'Exon'); $predobj->is_coding(1); # Figure out the frame of this exon. This is NOT the frame # given by Genscan, which is the absolute frame of the base # starting the first predicted complete codon. By comparing # to the absolute frame of the first base we can compute the # offset of the first complete codon to the first base of the # exon, which determines the frame of the exon. my $cod_offset; if($predobj->strand() == 1) { $cod_offset = $flds[6] - (($predobj->start()-1) % 3); # Possible values are -2, -1, 0, 1, 2. -1 and -2 correspond # to offsets 2 and 1, resp. Offset 3 is the same as 0. $cod_offset += 3 if($cod_offset < 1); } else { # On the reverse strand the Genscan frame also refers to # the first base of the first complete codon, but viewed # from forward, which is the third base viewed from # reverse. $cod_offset = $flds[6] - (($predobj->end()-3) % 3); # Possible values are -2, -1, 0, 1, 2. Due to the reverse # situation, {2,-1} and {1,-2} correspond to offsets # 1 and 2, resp. Offset 3 is the same as 0. $cod_offset -= 3 if($cod_offset >= 0); $cod_offset = -$cod_offset; } # Offsets 2 and 1 correspond to frame 1 and 2 (frame of exon # is the frame of the first base relative to the exon, or the # number of bases the first codon is missing). $predobj->frame(3 - $cod_offset); # then add to gene structure object $gene->add_exon($predobj, $ExonTags{$flds[1]}); } elsif($flds[1] eq 'PlyA') { $predobj->primary_tag("PolyAsite"); $gene->poly_A_site($predobj); } elsif($flds[1] eq 'Prom') { $predobj->primary_tag("Promoter"); $gene->add_promoter($predobj); } next; } if(/^\s*$/ && defined($gene)) { # current gene is completed $gene->seq_id($seqname); $self->_add_prediction($gene); $gene = undef; next; } if(/^(GENSCAN)\s+(\S+)/) { $self->analysis_method($1); $self->analysis_method_version($2); next; } if(/^Sequence\s+(\S+)\s*:/) { $seqname = $1; next; } if(/^Parameter matrix:\s+(\S+)/i) { $self->analysis_subject($1); next; } if(/^Predicted coding/) { $self->_has_cds(1); next; } /^>/ && do { # section of predicted sequences $self->_pushback($_); last; }; } $self->_predictions_parsed(1); } =head2 _prediction Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns : =cut sub _prediction { my ($self) = @_; return unless(exists($self->{'_preds'}) && @{$self->{'_preds'}}); return shift(@{$self->{'_preds'}}); } =head2 _add_prediction Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns : =cut sub _add_prediction { my ($self, $gene) = @_; if(! exists($self->{'_preds'})) { $self->{'_preds'} = []; } push(@{$self->{'_preds'}}, $gene); } =head2 _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE =cut sub _predictions_parsed { my ($self, $val) = @_; $self->{'_preds_parsed'} = $val if $val; if(! exists($self->{'_preds_parsed'})) { $self->{'_preds_parsed'} = 0; } return $self->{'_preds_parsed'}; } =head2 _has_cds Title : _has_cds() Usage : $obj->_has_cds() Function: Whether or not the result contains the predicted CDSs, too. Example : Returns : TRUE or FALSE =cut sub _has_cds { my ($self, $val) = @_; $self->{'_has_cds'} = $val if $val; if(! exists($self->{'_has_cds'})) { $self->{'_has_cds'} = 0; } return $self->{'_has_cds'}; } =head2 _read_fasta_seq Title : _read_fasta_seq() Usage : ($id,$seqstr) = $obj->_read_fasta_seq(); Function: Simple but specialised FASTA format sequence reader. Uses $self->_readline() to retrieve input, and is able to strip off the traling description lines. Example : Returns : An array of two elements. =cut sub _read_fasta_seq { my ($self) = @_; my ($id, $seq); local $/ = ">"; my $entry = $self->_readline(); if($entry) { $entry =~ s/^>//; # complete the entry if the first line came from a pushback buffer while($entry !~ />$/) { last unless $_ = $self->_readline(); $entry .= $_; } # delete everything onwards from an intervening empty line (at the # end there might be statistics stuff) $entry =~ s/\n\n.*$//s; # id and sequence if($entry =~ /^(\S+)\n([^>]+)/) { $id = $1; $seq = $2; } else { $self->throw("Can't parse Genscan predicted sequence entry"); } $seq =~ s/\s//g; # Remove whitespace } return ($id, $seq); } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Glimmer.pm���������������������������������������������������������������000444��000766��000024�� 45042�13155576320� 17303� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Glimmer # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl-dot-org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Glimmer - parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions =head1 SYNOPSIS use Bio::Tools::Glimmer; # file my $parser = Bio::Tools::Glimmer->new(-file => $file); # filehandle: $parser = Bio::Tools::Glimmer->new( -fh => \*INPUT ); # provide a sequence identifier (Glimmer 2.X) my $parser = Bio::Tools::Glimmer->new(-file => $file, -seqname => seqname); # force format (override automatic detection) my $parser = Bio::Tools::Glimmer->new(-file => $file, -format => 'GlimmerM'); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $glimmer->next_feature() is the same while(my $gene = $parser->next_prediction()) { # For eukaryotic input (GlimmerM/GlimmerHMM), $gene will be an instance # of Bio::Tools::Prediction::Gene, which inherits off # Bio::SeqFeature::Gene::Transcript, and $gene->exons() will return an # array of Bio::Tools::Prediction::Exon objects. # For prokaryotic input (Glimmer2.X/Glimmer3.X), $gene will be an # instance of Bio::SeqFeature::Generic # all exons (eukaryotic only): @exon_arr = $gene->exons(); # initial exons only @init_exons = $gene->exons('Initial'); # internal exons only @intrl_exons = $gene->exons('Internal'); # terminal exons only @term_exons = $gene->exons('Terminal'); } =head1 DESCRIPTION This is a module for parsing Glimmer, GlimmerM and GlimmerHMM predictions. It will create gene objects from the prediction report which can be attached to a sequence using Bioperl objects, or output as GFF suitable for loading into Bio::DB::GFF for use with Gbrowse. Glimmer is open source and available at L<http://www.cbcb.umd.edu/software/glimmer/>. GlimmerM is open source and available at L<http://www.tigr.org/software/glimmerm/>. GlimmerHMM is open source and available at L<http://www.cbcb.umd.edu/software/GlimmerHMM/>. Note that Glimmer 2.X will only process the first sequence in a fasta file, and the prediction report does not contain any sort of sequence identifier Note that Glimmer 3.X produces two output files. This module only parses the .predict file. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 CONTRIBUTORS Torsten Seemann Mark Johnson =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Glimmer; use strict; use Bio::Factory::FTLocationFactory; use Bio::Tools::Prediction::Gene; use Bio::Tools::Prediction::Exon; use base qw(Bio::Tools::AnalysisResult); sub _initialize_state { my($self,@args) = @_; # first call the inherited method! my $make = $self->SUPER::_initialize_state(@args); $self->{'_preds_parsed'} = 0; # array of pre-parsed predictions $self->{'_preds'} = []; } =head2 new Title : new Usage : my $obj = Bio::Tools::Glimmer->new(); Function: Builds a new Bio::Tools::Glimmer object Returns : an instance of Bio::Tools::Glimmer Args : format ('Glimmer', 'GlimmerM', 'GlimmerHMM'), seqname =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($format, $seqname, $seqlength, $detail) = $self->_rearrange([qw(FORMAT SEQNAME SEQLENGTH DETAIL)], @args); # override automagic format detection if (defined($format) && (($format eq 'Glimmer') || ($format eq 'GlimmerM') || ($format eq 'GlimmerHMM')) ) { $self->_format($format); } if (defined($detail)) { $self->_format('Glimmer'); $self->_detail_file($detail); } # hardwire seq_id when creating gene and exon objects (Glimmer 2.X) $self->_seqname($seqname) if defined($seqname); # store the length of the input sequence (Glimmer 2.X) $self->_seqlength($seqlength) if defined($seqlength); return $self; } =head2 analysis_method Usage : $glimmer->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /glimmer/i. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method && ($method !~ /glimmer/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head2 next_feature Title : next_feature Usage : while($gene = $glimmer->next_feature()) { # do something } Function: Returns the next gene structure prediction of the Glimmer result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_feature { my ($self,@args) = @_; # even though next_prediction doesn't expect any args (and this method # does neither), we pass on args in order to be prepared if this changes # ever return $self->next_prediction(@args); } =head2 next_prediction Title : next_prediction Usage : while($gene = $glimmer->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the Glimmer result file. Call this method repeatedly until FALSE is returned. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_prediction { my ($self) = @_; my $gene; # if the prediction section hasn't been parsed yet, we do this now $self->_parse_predictions() unless $self->_predictions_parsed(); # get next gene structure $gene = $self->_prediction(); return $gene; } =head2 _parse_predictions Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : =cut sub _parse_predictions { my ($self) = @_; my %method = ( 'Glimmer' => '_parse_prokaryotic', 'GlimmerM' => '_parse_eukaryotic', 'GlimmerHMM' => '_parse_eukaryotic', '_DEFAULT_' => '_parse_eukaryotic', ); my $format = $self->_format(); if (!$format) { while (my $line = $self->_readline()) { if ( $line =~ /^Glimmer\S*\s+\(Version\s*\S+\)/ ) { $format = 'GlimmerM'; $self->_pushback($line); last; } elsif ( $line =~ /^Glimmer\S*$/ ) { $format = 'GlimmerHMM'; $self->_pushback($line); last; } elsif ($line =~ /^Putative Genes:$/) { $format = 'Glimmer'; $self->_pushback($line); last; } elsif ($line =~ /^>(\S+)/) { $format = 'Glimmer'; $self->_pushback($line); last; } } } my $method = (exists($method{$format})) ? $method{$format} : $method{'_DEFAULT_'}; return $self->$method(); } =head2 _parse_eukaryotic Title : _parse_eukaryotic() Usage : $obj->_parse_eukaryotic() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : =cut sub _parse_eukaryotic { my ($self) = @_; my ($gene,$seqname,$seqlen,$source,$lastgenenum); while(defined($_ = $self->_readline())) { if( /^(Glimmer\S*)\s+\(Version\s*(\S+)\)/ ) { $source = "$1_$2"; next; } elsif( /^(GlimmerHMM\S*)$/ ) { # GlimmerHMM has no version $source = $1; next; } elsif(/^Sequence name:\s+(.+)$/ ) { $seqname = $1; next; } elsif( /^Sequence length:\s+(\S+)/ ) { $seqlen = $1; next; } elsif( m/^(Predicted genes)|(Gene)|\s+\#/ || /^\s+$/ ) { next; } elsif( # GlimmerM/HMM gene-exon prediction line /^\s+(\d+)\s+ # gene num (\d+)\s+ # exon num ([\+\-])\s+ # strand (\S+)\s+ # exon type (\d+)\s+(\d+) # exon start, end \s+(\d+) # exon length /ox ) { my ($genenum,$exonnum,$strand,$type,$start,$end,$len) = ( $1,$2,$3,$4,$5,$6,$7); if( ! $lastgenenum || $lastgenenum != $genenum) { $self->_add_prediction($gene) if ( $gene ); $gene = Bio::Tools::Prediction::Gene->new ( '-seq_id' => $seqname, '-primary_tag' => "gene", '-source_tag' => $source, '-tag' => { 'Group' => "GenePrediction$genenum"}, ); } my $exon = Bio::Tools::Prediction::Exon->new ('-seq_id' => $seqname, '-start' => $start, '-end' => $end, '-strand' => $strand eq '-' ? '-1' : '1', '-source_tag' => $source, '-primary_tag'=> 'exon', '-tag' => { 'Group' => "GenePrediction$genenum"}, ); $gene->add_exon($exon,lc($type)); $lastgenenum = $genenum; } } $self->_add_prediction($gene) if( $gene ); $self->_predictions_parsed(1); } =head2 _parse_prokaryotic Title : _parse_prokaryotic() Usage : $obj->_parse_prokaryotic() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : =cut sub _parse_prokaryotic { my ($self) = @_; # default value, possibly overriden later my $source = 'Glimmer'; # Store the sequence length(s) here, either from the # seqlength arg to the constructor, or from the # Glimmer 3.X detail file my %seqlength = ( ); # Glimmer 2.X does not provide a sequence identifer # in the prediction report (will default to unknown # if not specified in the seqname arg to the # constructor # # Glimmer 2.X does not report the length of the # input sequence, either (will default to undef # if not specified in the seqlength arg to the # constructor my $seqname = $self->_seqname(); my $seqlength = $self->_seqlength(); if (defined($seqlength)) { $seqlength{$seqname} = $seqlength } # Parse the detail file, if we have one (Glimmer 3.X) my $detail_file = $self->_detail_file(); if (defined($detail_file)) { my $io = Bio::Root::IO->new(-file => $detail_file); my $seqname; while (defined($_ = $io->_readline())) { if ($_ =~ /^>(\S+)/) { $seqname = $1; next; } if (defined($seqname) && ($_ =~ /^Sequence length = (\d+)$/)) { $seqlength{$seqname} = $1; next; } } } my $location_factory = Bio::Factory::FTLocationFactory->new(); while(defined($_ = $self->_readline())) { # Glimmer 3.X does provide a sequence identifier - # beware whitespace at the end (comes through from # the fasta file) if ($_ =~ /^Putative Genes:$/) { $source = 'Glimmer_2.X'; next; } # Glimmer 3.X sequence identifier elsif ($_ =~ /^>(\S+)/) { $seqname = $1; $seqlength = $seqlength{$seqname}; $source = 'Glimmer_3.X'; next; } elsif ( # Glimmer 2.X prediction (/^\s+(\d+)\s+ # gene num (\d+)\s+(\d+)\s+ # start, end \[([\+\-])(\d{1})\s+ # strand, frame /ox ) || # Glimmer 3.X prediction (/^[^\d]+(\d+)\s+ # orf (numeric portion) (\d+)\s+(\d+)\s+ # start, end ([\+\-])(\d{1})\s+ # strand, frame ([\d\.]+) # score /ox)) { my ($genenum,$start,$end,$strand,$frame,$score) = ( $1,$2,$3,$4,$5,$6 ); my $circular_prediction = 0; # Check for a circular prediction before we # start fiddling with the coordinates if ($strand eq '+') { if ($start > $end) { $circular_prediction = 1; } } else { if ($start < $end) { $circular_prediction = 1; } } if ($circular_prediction) { unless (defined($seqlength)) { $self->throw("need to know the sequence length to handle wraparound genes"); } } # Glimmer 2.X predictions do not include # the stop codon - this might extend the # prediction off either end of the sequence. # This works fine even on circular/wraparound # predictions. if ($source eq 'Glimmer_2.X') { if ($strand eq '+') { $end += 3; } else { $end -= 3; } } # We might have extended a Glimmer 2.X prediction # beyond the boundaries of the input sequence. # Also, Glimmer 3.X (with -X) will output predictions # with coordinates less than 1 or greater than the # length of the sequence. my ($fst, $fend); foreach my $coord ($start, $end) { if ($coord < 1) { $coord = '<1'; $fst++; } elsif (defined($seqlength) && ($coord > $seqlength)) { $coord = ">$seqlength"; $fend++; } } my $location_string; if ($circular_prediction) { if ($strand eq '+') { $location_string = "join($start..$seqlength,1..$end)"; } else { $location_string = "join($start..1,$seqlength..$end)"; } } else { # start must always be less than end for gene locations if ($strand eq '-' && !$fst && !$fend && $start > $end) { ($start, $end) = ($end, $start); } $location_string = "$start..$end"; } my $location_object = $location_factory->from_string($location_string); # convert glimmer's frame range from 1-3 to SeqFeature's 0-2. $frame--; my $gene = Bio::SeqFeature::Generic->new ( '-seq_id' => $seqname, '-location' => $location_object, '-strand' => $strand eq '-' ? '-1' : '1', '-frame' => $frame, '-source_tag' => $source, '-display_name' => "orf$genenum", '-primary_tag'=> 'gene', '-tag' => { 'Group' => "GenePrediction_$genenum"}, '-score' => $score || undef ); $self->_add_prediction($gene) } } $self->_predictions_parsed(1); } =head2 _prediction Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns : =cut sub _prediction { my ($self) = @_; return unless(exists($self->{'_preds'}) && @{$self->{'_preds'}}); return shift(@{$self->{'_preds'}}); } =head2 _add_prediction Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns : =cut sub _add_prediction { my ($self, $gene) = @_; if(! exists($self->{'_preds'})) { $self->{'_preds'} = []; } push(@{$self->{'_preds'}}, $gene); } =head2 _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE =cut sub _predictions_parsed { my ($self, $val) = @_; $self->{'_preds_parsed'} = $val if $val; if(! exists($self->{'_preds_parsed'})) { $self->{'_preds_parsed'} = 0; } return $self->{'_preds_parsed'}; } =head2 _seqname Title : _seqname Usage : $obj->_seqname($seqname) Function: internal (for Glimmer 2.X) Example : Returns : String =cut sub _seqname { my ($self, $val) = @_; $self->{'_seqname'} = $val if $val; if(! exists($self->{'_seqname'})) { $self->{'_seqname'} = 'unknown'; } return $self->{'_seqname'}; } =head2 _seqlength Title : _seqlength Usage : $obj->_seqlength($seqlength) Function: internal (for Glimmer 2.X) Example : Returns : String =cut sub _seqlength { my ($self, $val) = @_; $self->{'_seqlength'} = $val if $val; return $self->{'_seqlength'}; } =head2 _format Title : _format Usage : $obj->_format($format) Function: internal Example : Returns : String =cut sub _format { my ($self, $val) = @_; $self->{'_format'} = $val if $val; return $self->{'_format'}; } =head2 _detail_file Title : _detail_file Usage : $obj->_detail_file($filename) Function: internal (for Glimmer 3.X) Example : Returns : String =cut sub _detail_file { my ($self, $val) = @_; $self->{'_detail_file'} = $val if $val; return $self->{'_detail_file'}; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Grail.pm�����������������������������������������������������������������000444��000766��000024�� 14306�13155576320� 16744� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Grail # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Grail - Results of one Grail run =head1 SYNOPSIS $grail = Bio::Tools::Grail->new(-file => 'result.grail'); # filehandle: $grail = Bio::Tools::Grail->new( -fh => \*INPUT ); # parse the results while($gene = $grail->next_prediction()) { # $gene is an instance of Bio::Tools::Prediction::Gene # $gene->exons() returns an array of # Bio::Tools::Prediction::Exon objects # all exons: @exon_arr = $gene->exons(); # initial exons only @init_exons = $gene->exons('Initial'); # internal exons only @intrl_exons = $gene->exons('Internal'); # terminal exons only @term_exons = $gene->exons('Terminal'); # singleton exons only -- should be same as $gene->exons() because # there are no other exons supposed to exist in this structure @single_exons = $gene->exons('Single'); } # essential if you gave a filename at initialization (otherwise the file # will stay open) $genscan->close(); =head1 DESCRIPTION The Grail module provides a parser for Grail gene structure prediction output. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Grail; use strict; use Bio::Tools::Prediction::Gene; use Bio::Tools::Prediction::Exon; use Symbol; use base qw(Bio::Root::IO Bio::Root::Root); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_prediction Title : next_prediction Usage : while($gene = $grail->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the Grail result file. Call this method repeatedly until FALSE is returned. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_prediction { my ($self) = @_; # get next gene structure my $gene = $self->_prediction(); if($gene) { # fill in predicted protein, and if available the predicted CDS # my ($id, $seq); # use the seq stack if there's a seq on it my $seqobj = pop(@{$self->{'_seqstack'}}); if(! $seqobj) { # otherwise read from input stream ($id, $seq) = $self->_read_fasta_seq(); $seqobj = Bio::PrimarySeq->new('-seq' => $seq, '-display_id' => $id, '-alphabet' => "protein"); } # check that prediction number matches the prediction number # indicated in the sequence id (there may be incomplete gene # predictions that contain only signals with no associated protein # and CDS, like promoters, poly-A sites etc) $gene->primary_tag() =~ /[^0-9]([0-9]+)$/; my $prednr = $1; if($seqobj->display_id() !~ /_predicted_\w+_$prednr\|/) { # this is not our sequence, so push back for the next prediction push(@{$self->{'_seqstack'}}, $seqobj); } else { $gene->predicted_protein($seqobj); # CDS prediction, too? if($self->_has_cds()) { ($id, $seq) = $self->_read_fasta_seq(); $seqobj = Bio::PrimarySeq->new('-seq' => $seq, '-display_id' => $id, '-alphabet' => "dna"); $gene->predicted_cds($seqobj); } } } return $gene; } =head2 _parse_predictions Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : =cut sub _parse_predictions { my ($self) = @_; # code needs to go here $self->_predictions_parsed(1); } =head2 _prediction Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns : =cut sub _prediction { my ($self) = @_; return unless(exists($self->{'_preds'}) && @{$self->{'_preds'}}); return shift(@{$self->{'_preds'}}); } =head2 _add_prediction Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns : =cut sub _add_prediction { my ($self, $gene) = @_; if(! exists($self->{'_preds'})) { $self->{'_preds'} = []; } push(@{$self->{'_preds'}}, $gene); } =head2 _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE =cut sub _predictions_parsed { my ($self, $val) = @_; $self->{'_preds_parsed'} = $val if $val; if(! exists($self->{'_preds_parsed'})) { $self->{'_preds_parsed'} = 0; } return $self->{'_preds_parsed'}; } =head2 _has_cds Title : _has_cds() Usage : $obj->_has_cds() Function: Whether or not the result contains the predicted CDSs, too. Example : Returns : TRUE or FALSE =cut sub _has_cds { my ($self, $val) = @_; $self->{'_has_cds'} = $val if $val; if(! exists($self->{'_has_cds'})) { $self->{'_has_cds'} = 0; } return $self->{'_has_cds'}; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/GuessSeqFormat.pm��������������������������������������������������������000444��000766��000024�� 54076�13155576320� 20626� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������#------------------------------------------------------------------ # # BioPerl module Bio::Tools::GuessSeqFormat # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Andreas Kähäri, andreas.kahari@ebi.ac.uk # # You may distribute this module under the same terms as perl itself #------------------------------------------------------------------ =encoding utf-8 =head1 NAME Bio::Tools::GuessSeqFormat - Module for determining the sequence format of the contents of a file, a string, or through a filehandle. =head1 SYNOPSIS # To guess the format of a flat file, given a filename: my $guesser = Bio::Tools::GuessSeqFormat->new( -file => $filename ); my $format = $guesser->guess; # To guess the format from an already open filehandle: my $guesser = Bio::Tools::GuessSeqFormat->new( -fh => $filehandle ); my $format = $guesser->guess; # The filehandle will be returned to its original position. Note that this # filehandle can be STDIN. # To guess the format of one or several lines of text (with # embedded newlines): my $guesser = Bio::Tools::GuessSeqFormat->new( -text => $linesoftext ); my $format = $guesser->guess; # To create a Bio::Tools::GuessSeqFormat object and set the # filename, filehandle, or line to parse afterwards: my $guesser = Bio::Tools::GuessSeqFormat->new(); $guesser->file($filename); $guesser->fh($filehandle); $guesser->text($linesoftext); # To guess in one go, given e.g. a filename: my $format = Bio::Tools::GuessSeqFormat->new( -file => $filename )->guess; =head1 DESCRIPTION Bio::Tools::GuessSeqFormat tries to guess the format ("swiss", "pir", "fasta" etc.) of the sequence or MSA in a file, in a scalar, or through a filehandle. The guess() method of a Bio::Tools::GuessSeqFormat object will examine the data, line by line, until it finds a line to which only one format can be assigned. If no conclusive guess can be made, undef is returned. If the Bio::Tools::GuessSeqFormat object is given a filehandle, e.g. STDIN, it will be restored to its original position on return from the guess() method. =head2 Formats Tests are currently implemented for the following formats: =over =item * ACeDB ("ace") =item * Blast ("blast") =item * ClustalW ("clustalw") =item * Codata ("codata") =item * EMBL ("embl") =item * FastA sequence ("fasta") =item * FastQ sequence ("fastq") =item * FastXY/FastA alignment ("fastxy") =item * Game XML ("game") =item * GCG ("gcg") =item * GCG Blast ("gcgblast") =item * GCG FastA ("gcgfasta") =item * GDE ("gde") =item * Genbank ("genbank") =item * Genscan ("genscan") =item * GFF ("gff") =item * HMMER ("hmmer") =item * PAUP/NEXUS ("nexus") =item * Phrap assembly file ("phrap") =item * NBRF/PIR ("pir") =item * Mase ("mase") =item * Mega ("mega") =item * GCG/MSF ("msf") =item * Pfam ("pfam") =item * Phylip ("phylip") =item * Prodom ("prodom") =item * Raw ("raw") =item * RSF ("rsf") =item * Selex ("selex") =item * Stockholm ("stockholm") =item * Swissprot ("swiss") =item * Tab ("tab") =item * Variant Call Format ("vcf") =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Andreas KE<228>hE<228>ri, andreas.kahari@ebi.ac.uk =head1 CONTRIBUTORS Heikki LehvE<228>slaiho, heikki-at-bioperl-dot-org Mark A. Jensen, maj-at-fortinbras-dot-us =cut package Bio::Tools::GuessSeqFormat; use strict; use warnings; use base qw(Bio::Root::Root); =head1 METHODS Methods available to Bio::Tools::GuessSeqFormat objects are described below. Methods with names beginning with an underscore are considered to be internal. =cut =head2 new Title : new Usage : $guesser = Bio::Tools::GuessSeqFormat->new( ... ); Function : Creates a new object. Example : See SYNOPSIS. Returns : A new object. Arguments : -file The filename of the file whose format is to be guessed, e.g. STDIN, or -fh An already opened filehandle from which a text stream may be read, or -text A scalar containing one or several lines of text with embedded newlines. If more than one of the above arguments are given, they are tested in the order -text, -file, -fh, and the first available argument will be used. =cut sub new { my $class = shift; my @args = @_; my $self = $class->SUPER::new(@args); my $attr; my $value; while (@args) { $attr = shift @args; $attr = lc $attr; $value = shift @args; $self->{$attr} = $value; } return $self; } =head2 file Title : file Usage : $guesser->file($filename); $filename = $guesser->file; Function : Gets or sets the current filename associated with an object. Returns : The new filename. Arguments : The filename of the file whose format is to be guessed. A call to this method will clear the current filehandle and the current lines of text associated with the object. =cut sub file { # Sets and/or returns the filename to use. my $self = shift; my $file = shift; if (defined $file) { # Set the active filename, and clear the filehandle and # text line, if present. $self->{-file} = $file; $self->{-fh} = $self->{-text} = undef; } return $self->{-file}; } =head2 fh Title : fh Usage : $guesser->fh($filehandle); $filehandle = $guesser->fh; Function : Gets or sets the current filehandle associated with an object. Returns : The new filehandle. Arguments : An already opened filehandle from which a text stream may be read. A call to this method will clear the current filename and the current lines of text associated with the object. =cut sub fh { # Sets and/or returns the filehandle to use. my $self = shift; my $fh = shift; if (defined $fh) { # Set the active filehandle, and clear the filename and # text line, if present. $self->{-fh} = $fh; $self->{-file} = $self->{-text} = undef; } return $self->{-fh}; } =head2 text Title : text Usage : $guesser->text($linesoftext); $linesofext = $guesser->text; Function : Gets or sets the current text associated with an object. Returns : The new lines of texts. Arguments : A scalar containing one or several lines of text, including embedded newlines. A call to this method will clear the current filename and the current filehandle associated with the object. =cut sub text { # Sets and/or returns the text lines to use. my $self = shift; my $text = shift; if (defined $text) { # Set the active text lines, and clear the filehandle # and filename, if present. $self->{-text} = $text; $self->{-fh} = $self->{-file} = undef; } return $self->{-text}; } =head2 guess Title : guess Usage : $format = $guesser->guess; @format = $guesser->guess; # if given a line of text Function : Guesses the format of the data accociated with the object. Returns : A format string such as "swiss" or "pir". If a format can not be found, undef is returned. Arguments : None. If the object is associated with a filehandle, the position of the filehandle will be returned to its original position before the method returns. =cut our %formats = ( ace => { test => \&_possibly_ace }, blast => { test => \&_possibly_blast }, bowtie => { test => \&_possibly_bowtie }, clustalw => { test => \&_possibly_clustalw }, codata => { test => \&_possibly_codata }, embl => { test => \&_possibly_embl }, fasta => { test => \&_possibly_fasta }, fastq => { test => \&_possibly_fastq }, fastxy => { test => \&_possibly_fastxy }, game => { test => \&_possibly_game }, gcg => { test => \&_possibly_gcg }, gcgblast => { test => \&_possibly_gcgblast }, gcgfasta => { test => \&_possibly_gcgfasta }, gde => { test => \&_possibly_gde }, genbank => { test => \&_possibly_genbank }, genscan => { test => \&_possibly_genscan }, gff => { test => \&_possibly_gff }, hmmer => { test => \&_possibly_hmmer }, nexus => { test => \&_possibly_nexus }, mase => { test => \&_possibly_mase }, mega => { test => \&_possibly_mega }, msf => { test => \&_possibly_msf }, pfam => { test => \&_possibly_pfam }, phrap => { test => \&_possibly_phrap }, phylip => { test => \&_possibly_phylip }, pir => { test => \&_possibly_pir }, prodom => { test => \&_possibly_prodom }, raw => { test => \&_possibly_raw }, rsf => { test => \&_possibly_rsf }, selex => { test => \&_possibly_selex }, stockholm => { test => \&_possibly_stockholm }, swiss => { test => \&_possibly_swiss }, tab => { test => \&_possibly_tab }, vcf => { test => \&_possibly_vcf }, ); sub guess { my $self = shift; while (my ($fmt_key) = each (%formats)) { $formats{$fmt_key}{fmt_string} = $fmt_key; } my $fh; my $start_pos; if (defined $self->{-text}) { # Break the text into separate lines. my $text = $self->{-text}; open $fh, '<', \$text or $self->throw("Could not read from string: $!"); } elsif (defined $self->{-file}) { # If given a filename, open the file. my $file = $self->{-file}; open $fh, '<', $file or $self->throw("Could not read file '$file': $!"); } elsif (defined $self->{-fh}) { # If given a filehandle, get the current position in the stream. $fh = $self->{-fh}; if (not seek $fh, 0, 1) { # seek to current position to determine seekability # Work around non-seekable filehandles if IO::Scalar is available # (adapted from http://www.perlmonks.org/?node_id=33587) # IO::Mark may be an option for very large streams? $self->throw("Need IO::Scalar to guess from unseekable filehandles") if not eval { require IO::Scalar }; my $data; { local $/; $data = <$fh>; $.-- }; # copy raw data from fh tie *$fh, 'IO::Scalar', my $s; # replace fh by scalar-tied fh print $fh $data; # write raw data to tied fh seek $fh, 0, 0; # return to start of tied fh } $start_pos = tell $fh; } my $done = 0; my $lineno = 0; my $guess; while (!$done) { my $line; # The next line of the file. my $match = 0; # Number of possible formats of this line. last if (!defined($line = <$fh>)); next if ($line =~ /^\s*$/); # Skip white and empty lines. chomp $line; $line =~ s/\r$//; # Fix for DOS files on Unix. ++$lineno; while (my ($fmt_key, $fmt) = each (%formats)) { if ($fmt->{test}($line, $lineno)) { ++$match; $guess = $fmt->{fmt_string}; } } # We're done if there was only one match. $done = ($match == 1); } if (defined $self->{-fh}) { # Go back to original position in filehandle seek $fh, $start_pos, 0 or $self->throw("Could not reset filehandle $fh: $!"); } else { # Close the filehandle we opened close $fh; } return ($done ? $guess : undef); } =head1 HELPER SUBROUTINES All helper subroutines will, given a line of text and the line number of the same line, return 1 if the line possibly is from a file of the type that they perform a test of. A zero return value does not mean that the line is not part of a certain type of file, just that the test did not find any characteristics of that type of file in the line. =head2 _possibly_ace From bioperl test data, and from "http://www.isrec.isb-sib.ch/DEA/module8/B_Stevenson/Practicals/transcriptome_recon/transcriptome_recon.html". =cut sub _possibly_ace { my ($line, $lineno) = (shift, shift); return ($line =~ /^(?:Sequence|Peptide|DNA|Protein) [":]/); } =head2 _possibly_blast From various blast results. =cut sub _possibly_blast { my ($line, $lineno) = (shift, shift); return ($lineno == 1 && $line =~ /^[[:upper:]]*BLAST[[:upper:]]*.*\[.*\]$/); } =head2 _possibly_bowtie Contributed by kortsch. =cut sub _possibly_bowtie { my ($line, $lineno) = (shift, shift); return ($line =~ /^[[:graph:]]+\t[-+]\t[[:graph:]]+\t\d+\t([[:alpha:]]+)\t([[:graph:]]+)\t\d+\t[[:graph:]]?/) && length($1)==length($2); } =head2 _possibly_clustalw From "http://www.ebi.ac.uk/help/formats.html". =cut sub _possibly_clustalw { my ($line, $lineno) = (shift, shift); return ($lineno == 1 && $line =~ /CLUSTAL/); } =head2 _possibly_codata From "http://www.ebi.ac.uk/help/formats.html". =cut sub _possibly_codata { my ($line, $lineno) = (shift, shift); return (($lineno == 1 && $line =~ /^ENTRY/) || ($lineno == 2 && $line =~ /^SEQUENCE/) || $line =~ m{^(?:ENTRY|SEQUENCE|///)}); } =head2 _possibly_embl From "http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3.3". =cut sub _possibly_embl { my ($line, $lineno) = (shift, shift); return ($lineno == 1 && $line =~ /^ID / && $line =~ /BP\.$/); } =head2 _possibly_fasta From "http://www.ebi.ac.uk/help/formats.html". =cut sub _possibly_fasta { my ($line, $lineno) = (shift, shift); return (($lineno != 1 && $line =~ /^[A-IK-NP-Z]+$/i) || $line =~ /^>\s*\w/); } =head2 _possibly_fastq From bioperl test data. =cut sub _possibly_fastq { my ($line, $lineno) = (shift, shift); return ( ($lineno == 1 && $line =~ /^@/) || ($lineno == 3 && $line =~ /^\+/) ); } =head2 _possibly_fastxy From bioperl test data. =cut sub _possibly_fastxy { my ($line, $lineno) = (shift, shift); return (($lineno == 1 && $line =~ /^ FAST(?:XY|A)/) || ($lineno == 2 && $line =~ /^ version \d/)); } =head2 _possibly_game From bioperl testdata. =cut sub _possibly_game { my ($line, $lineno) = (shift, shift); return ($line =~ /^<!DOCTYPE game/); } =head2 _possibly_gcg From bioperl, Bio::SeqIO::gcg. =cut sub _possibly_gcg { my ($line, $lineno) = (shift, shift); return ($line =~ /Length: .*Type: .*Check: .*\.\.$/); } =head2 _possibly_gcgblast From bioperl testdata. =cut sub _possibly_gcgblast { my ($line, $lineno) = (shift, shift); return (($lineno == 1 && $line =~ /^!!SEQUENCE_LIST/) || ($lineno == 2 && $line =~ /^[[:upper:]]*BLAST[[:upper:]]*.*\[.*\]$/)); } =head2 _possibly_gcgfasta From bioperl testdata. =cut sub _possibly_gcgfasta { my ($line, $lineno) = (shift, shift); return (($lineno == 1 && $line =~ /^!!SEQUENCE_LIST/) || ($lineno == 2 && $line =~ /FASTA/)); } =head2 _possibly_gde From "http://www.ebi.ac.uk/help/formats.html". =cut sub _possibly_gde { my ($line, $lineno) = (shift, shift); return ($line =~ /^[{}]$/ || $line =~ /^(?:name|longname|sequence-ID| creation-date|direction|strandedness| type|offset|group-ID|creator|descrip| comment|sequence)/x); } =head2 _possibly_genbank From "http://www.ebi.ac.uk/help/formats.html". Format of [apparantly optional] file header from "http://www.umdnj.edu/rcompweb/PA/Notes/GenbankFF.htm". (TODO: dead link) =cut sub _possibly_genbank { my ($line, $lineno) = (shift, shift); return (($lineno == 1 && $line =~ /GENETIC SEQUENCE DATA BANK/) || ($lineno == 1 && $line =~ /^LOCUS /) || ($lineno == 2 && $line =~ /^DEFINITION /) || ($lineno == 3 && $line =~ /^ACCESSION /)); } =head2 _possibly_genscan From bioperl test data. =cut sub _possibly_genscan { my ($line, $lineno) = (shift, shift); return (($lineno == 1 && $line =~ /^GENSCAN.*Date.*Time/) || ($line =~ /^(?:Sequence\s+\w+|Parameter matrix|Predicted genes)/)); } =head2 _possibly_gff From bioperl test data. =cut sub _possibly_gff { my ($line, $lineno) = (shift, shift); return (($lineno == 1 && $line =~ /^##gff-version/) || ($lineno == 2 && $line =~ /^##date/)); } =head2 _possibly_hmmer From bioperl test data. =cut sub _possibly_hmmer { my ($line, $lineno) = (shift, shift); return (($lineno == 2 && $line =~ /^HMMER/) || ($lineno == 3 && $line =~ /Washington University School of Medicine/)); } =head2 _possibly_nexus From "http://paup.csit.fsu.edu/nfiles.html". =cut sub _possibly_nexus { my ($line, $lineno) = (shift, shift); return ($lineno == 1 && $line =~ /^#NEXUS/); } =head2 _possibly_mase From bioperl test data. More detail from "http://www.umdnj.edu/rcompweb/PA/Notes/GenbankFF.htm" (TODO: dead link) =cut sub _possibly_mase { my ($line, $lineno) = (shift, shift); return (($lineno == 1 && $line =~ /^;;/) || ($lineno > 1 && $line =~ /^;[^;]?/)); } =head2 _possibly_mega From the ensembl broswer (AlignView data export). =cut sub _possibly_mega { my ($line, $lineno) = (shift, shift); return ($lineno == 1 && $line =~ /^#mega$/); } =head2 _possibly_msf From "http://www.ebi.ac.uk/help/formats.html". =cut sub _possibly_msf { my ($line, $lineno) = (shift, shift); return ($line =~ m{^//} || $line =~ /MSF:.*Type:.*Check:|Name:.*Len:/); } =head2 _possibly_phrap From "http://biodata.ccgb.umn.edu/docs/contigimage.html". (TODO: dead link) From "http://genetics.gene.cwru.edu/gene508/Lec6.htm". (TODO: dead link) From bioperl test data ("*.ace.1" files). =cut sub _possibly_phrap { my ($line, $lineno) = (shift, shift); return ($line =~ /^(?:AS\ |CO\ Contig|BQ|AF\ |BS\ |RD\ | QA\ |DS\ |RT\{)/x); } =head2 _possibly_pir From "http://www.ebi.ac.uk/help/formats.html". The ".,()" spotted in bioperl test data. =cut sub _possibly_pir # "NBRF/PIR" (?) { my ($line, $lineno) = (shift, shift); return (($lineno != 1 && $line =~ /^[\sA-IK-NP-Z.,()]+\*?$/i) || $line =~ /^>(?:P1|F1|DL|DC|RL|RC|N3|N1);/); } =head2 _possibly_pfam From bioperl test data. =cut sub _possibly_pfam { my ($line, $lineno) = (shift, shift); return ($line =~ m{^\w+/\d+-\d+\s+[A-IK-NP-Z.]+}i); } =head2 _possibly_phylip From "http://www.ebi.ac.uk/help/formats.html". Initial space allowed on first line (spotted in ensembl AlignView exported data). =cut sub _possibly_phylip { my ($line, $lineno) = (shift, shift); return (($lineno == 1 && $line =~ /^\s*\d+\s\d+/) || ($lineno == 2 && $line =~ /^\w\s+[A-IK-NP-Z\s]+/) || ($lineno == 3 && $line =~ /(?:^\w\s+[A-IK-NP-Z\s]+|\s+[A-IK-NP-Z\s]+)/) ); } =head2 _possibly_prodom From "http://prodom.prabi.fr/prodom/current/documentation/data.php". =cut sub _possibly_prodom { my ($line, $lineno) = (shift, shift); return ($lineno == 1 && $line =~ /^ID / && $line =~ /\d+ seq\.$/); } =head2 _possibly_raw From "http://www.ebi.ac.uk/help/formats.html". =cut sub _possibly_raw { my ($line, $lineno) = (shift, shift); return ($line =~ /^[A-Za-z\s]+$/); } =head2 _possibly_rsf From "http://www.ebi.ac.uk/help/formats.html". =cut sub _possibly_rsf { my ($line, $lineno) = (shift, shift); return (($lineno == 1 && $line =~ /^!!RICH_SEQUENCE/) || $line =~ /^[{}]$/ || $line =~ /^(?:name|type|longname| checksum|creation-date|strand|sequence)/x); } =head2 _possibly_selex From "http://www.ebc.ee/WWW/hmmer2-html/node27.html". Assuming presence of Selex file header. Data exported by Bioperl on Pfam and Selex formats are identical, but Pfam file only holds one alignment. =cut sub _possibly_selex { my ($line, $lineno) = (shift, shift); return (($lineno == 1 && $line =~ /^#=ID /) || ($lineno == 2 && $line =~ /^#=AC /) || ($line =~ /^#=SQ /)); } =head2 _possibly_stockholm From bioperl test data. =cut sub _possibly_stockholm { my ($line, $lineno) = (shift, shift); return (($lineno == 1 && $line =~ /^# STOCKHOLM/) || $line =~ /^#=(?:GF|GS) /); } =head2 _possibly_swiss From "http://ca.expasy.org/sprot/userman.html#entrystruc". =cut sub _possibly_swiss { my ($line, $lineno) = (shift, shift); return ($lineno == 1 && $line =~ /^ID / && $line =~ /AA\.$/); } =head2 _possibly_tab Contributed by Heikki. =cut sub _possibly_tab { my ($line, $lineno) = (shift, shift); return ($lineno == 1 && $line =~ /^[^\t]+\t[^\t]+/) ; } =head2 _possibly_vcf From "http://www.1000genomes.org/wiki/analysis/vcf4.0". Assumptions made about sanity - format and date lines are line 1 and 2 respectively. This is not specified in the format document. =cut sub _possibly_vcf { my ($line, $lineno) = (shift, shift); return (($lineno == 1 && $line =~ /##fileformat=VCFv/) || ($lineno == 2 && $line =~ /##fileDate=/)); } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Hmmpfam.pm���������������������������������������������������������������000555��000766��000024�� 13147�13155576320� 17300� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Tools::Hmmpfam # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Balamurugan Kumarasamy # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code # =head1 NAME Bio::Tools::Hmmpfam - Parser for Hmmpfam program =head1 SYNOPSIS use Bio::Tools::Hmmpfam; my @hmmpfam_feat; my $hmmpfam_parser = Bio::Tools::Hmmpfam->new(-fh =>$filehandle ); while( my $hmmpfam_feat = $hmmpfam_parser->next_result ) { push @hmmpfam_feat, $hmmpfam_feat; } =head1 DESCRIPTION Parser for Hmmpfam program. See also L<Bio::SearchIO::hmmer>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Balamurugan Kumarasamy Email: fugui@worf.fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Hmmpfam; use strict; use Bio::SeqFeature::FeaturePair; use Bio::SeqFeature::Generic; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::Hmmpfam->new(-fh=>$filehandle); Function: Builds a new Bio::Tools::Hmmpfam object Returns : Bio::Tools::Hmmpfam Args : -filename -fh (filehandle) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_result Title : next_result Usage : my $feat = $hmmpfam_parser->next_result Function: Get the next result set from parser data Returns : L<Bio::SeqFeature::Generic> Args : none =cut sub next_result { my ($self) = @_; my $filehandle; my $line; my $id; while ($_=$self->_readline()) { $line = $_; chomp $line; if ( $line=~m/^Alignments of top-scoring domains/ ) { while( my $rest = $self->_readline() ) { last if $rest =~ m!^//! } } next if ($line=~m/^Model/ || /^\-/ || /^$/); if ($line=~m/^Query sequence:\s+(\S+)/) { $id = $1; $self->seqname($id); } if (my ($hid, $start, $end, $hstart, $hend, $score, $evalue) = $line=~m/^(\S+)\s+\S+\s+(\d+)\s+(\d+)\s+\S+\s+(\d+)\s+(\d+)\s+\S+\s+(\S+)\s+(\S+)/) { my %feature; ($feature{name}) = $self->seqname; $feature{raw_score} = $score; $feature{p_value} = sprintf ("%.3e", $evalue); $feature{score} = $feature{p_value}; $feature{start} = $start; $feature{end} = $end; $feature{hname} = $hid; $feature{hstart} = $hstart; $feature{hend} = $hend; ($feature{source}) = 'pfam'; $feature{primary} = $hid; ($feature{program}) = 'pfam'; ($feature{db}) = 'db1'; ($feature{logic_name}) = 'hmmpfam'; my $new_feat = $self->create_feature (\%feature); return $new_feat } next; } return; } =head2 create_feature Title : create_feature Usage : my $feat=$hmmpfam_parser->create_feature($feature,$seqname) Function: creates a SeqFeature Generic object Returns : L<Bio::SeqFeature::Generic> Args : =cut sub create_feature { my ($self, $feat) = @_; my $feature1= Bio::SeqFeature::Generic->new( -seq_id =>$feat->{name}, -start =>$feat->{start}, -end =>$feat->{end}, -score =>$feat->{score}, -source =>$feat->{source}, -primary =>$feat->{primary}, ); my $feature2= Bio::SeqFeature::Generic->new( -start =>$feat->{hstart}, -end =>$feat->{hend}, ); my $featurepair = Bio::SeqFeature::FeaturePair->new; $featurepair->feature1 ($feature1); $featurepair->feature2 ($feature2); $featurepair->add_tag_value('evalue',$feat->{p_value}); $featurepair->add_tag_value('percent_id','NULL'); $featurepair->add_tag_value("hid",$feat->{primary}); return $featurepair; } =head2 seqname Title : seqname Usage : obj->seqname($seqname) Function: Internal(not to be used directly) Returns : Args : seqname =cut sub seqname{ my($self,$seqname)=@_; if(defined($seqname)) { $self->{'seqname'}=$seqname; } return $self->{'seqname'}; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/IUPAC.pm�����������������������������������������������������������������000444��000766��000024�� 33665�13155576320� 16560� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for IUPAC # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Aaron Mackey <amackey@virginia.edu> # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::IUPAC - Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence =head1 SYNOPSIS use Bio::PrimarySeq; use Bio::Tools::IUPAC; # Get the IUPAC code for proteins my %iupac_prot = Bio::Tools::IUPAC->new->iupac_iup; # Create a sequence with degenerate residues my $ambiseq = Bio::PrimarySeq->new(-seq => 'ARTCGUTGN', -alphabet => 'dna'); # Create all possible non-degenerate sequences my $iupac = Bio::Tools::IUPAC->new(-seq => $ambiseq); while ($uniqueseq = $iupac->next_seq()) { # process the unique Bio::Seq object. } # Get a regular expression that matches all possible sequences my $regexp = $iupac->regexp(); =head1 DESCRIPTION Bio::Tools::IUPAC is a tool that manipulates sequences with ambiguous residues following the IUPAC conventions. Non-standard characters have the meaning described below: IUPAC-IUB SYMBOLS FOR NUCLEOTIDE (DNA OR RNA) NOMENCLATURE: Cornish-Bowden (1985) Nucl. Acids Res. 13: 3021-3030 --------------------------------------------------------------- Symbol Meaning Nucleic Acid --------------------------------------------------------------- A A Adenine C C Cytosine G G Guanine T T Thymine U U Uracil M A or C aMino R A or G puRine W A or T Weak S C or G Strong Y C or T pYrimidine K G or T Keto V A or C or G not T (closest unused char after T) H A or C or T not G (closest unused char after G) D A or G or T not C (closest unused char after C) B C or G or T not A (closest unused char after A) X G or A or T or C Unknown (very rarely used) N G or A or T or C Unknown (commonly used) IUPAC-IUP AMINO ACID SYMBOLS: Biochem J. 1984 Apr 15; 219(2): 345-373 Eur J Biochem. 1993 Apr 1; 213(1): 2 ------------------------------------------ Symbol Meaning ------------------------------------------ A Alanine B Aspartic Acid, Asparagine C Cysteine D Aspartic Acid E Glutamic Acid F Phenylalanine G Glycine H Histidine I Isoleucine J Isoleucine/Leucine K Lysine L Leucine M Methionine N Asparagine O Pyrrolysine P Proline Q Glutamine R Arginine S Serine T Threonine U Selenocysteine V Valine W Tryptophan X Unknown Y Tyrosine Z Glutamic Acid, Glutamine * Terminator There are a few things Bio::Tools::IUPAC can do for you: =over =item * report the IUPAC mapping between ambiguous and non-ambiguous residues =item * produce a stream of all possible corresponding unambiguous Bio::Seq objects given an ambiguous sequence object =item * convert an ambiguous sequence object to a corresponding regular expression =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Aaron Mackey Email amackey-at-virginia.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::IUPAC; use strict; use base qw(Bio::Root::Root); use vars qw(%IUB %IUB_AMB %REV_IUB %IUP %IUP_AMB $AUTOLOAD); BEGIN { # Ambiguous nucleic residues are matched to unambiguous residues %IUB = ( A => [qw(A)], C => [qw(C)], G => [qw(G)], T => [qw(T)], U => [qw(U)], M => [qw(A C)], R => [qw(A G)], S => [qw(C G)], W => [qw(A T)], Y => [qw(C T)], K => [qw(G T)], V => [qw(A C G)], H => [qw(A C T)], D => [qw(A G T)], B => [qw(C G T)], N => [qw(A C G T)], X => [qw(A C G T)], ); # Same as %IUB but ambiguous residues are matched to ambiguous residues only %IUB_AMB = ( M => [qw(M)], R => [qw(R)], W => [qw(W)], S => [qw(S)], Y => [qw(Y)], K => [qw(K)], V => [qw(M R S V)], H => [qw(H M W Y)], D => [qw(D K R W)], B => [qw(B K S Y)], N => [qw(B D H K M N R S V W Y)], ); # The inverse of %IUB %REV_IUB = ( A => 'A', T => 'T', U => 'U', C => 'C', G => 'G', AC => 'M', AG => 'R', AT => 'W', CG => 'S', CT => 'Y', GT => 'K', ACG => 'V', ACT => 'H', AGT => 'D', CGT => 'B', ACGT => 'N', N => 'N' ); # Same thing with proteins now %IUP = ( A => [qw(A)], B => [qw(D N)], C => [qw(C)], D => [qw(D)], E => [qw(E)], F => [qw(F)], G => [qw(G)], H => [qw(H)], I => [qw(I)], J => [qw(I L)], K => [qw(K)], L => [qw(L)], M => [qw(M)], N => [qw(N)], O => [qw(O)], P => [qw(P)], Q => [qw(Q)], R => [qw(R)], S => [qw(S)], T => [qw(T)], U => [qw(U)], V => [qw(V)], W => [qw(W)], X => [qw(X)], Y => [qw(Y)], Z => [qw(E Q)], '*' => [qw(*)], ); %IUP_AMB = ( B => [qw(B)], J => [qw(J)], Z => [qw(Z)], ); } =head2 new Title : new Usage : Bio::Tools::IUPAC->new($seq); Function: Create a new IUPAC object, which acts as a sequence stream (akin to SeqIO) Args : an ambiguously coded sequence object that has a specified 'alphabet' Returns : a Bio::Tools::IUPAC object. =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($seq) = $self->_rearrange([qw(SEQ)],@args); if ( (not defined $seq) && @args && ref($args[0]) ) { # parameter not passed as named parameter? $seq = $args[0]; } if (defined $seq) { if (not $seq->isa('Bio::PrimarySeqI')) { $self->throw('Must supply a sequence object'); } if (length $seq->seq == 0) { $self->throw('Sequence had zero-length'); } $self->{'_seq'} = $seq; } return $self; } sub _initialize { my ($self) = @_; my %iupac = $self->iupac; $self->{'_alpha'} = [ map { $iupac{uc $_} } split('', $self->{'_seq'}->seq) ]; $self->{'_string'} = [(0) x length($self->{'_seq'}->seq())]; $self->{'_string'}->[0] = -1; } =head2 next_seq Title : next_seq Usage : $iupac->next_seq(); Function: returns the next unique sequence object Args : none. Returns : a Bio::Seq object =cut sub next_seq { my ($self) = @_; if (not exists $self->{'_string'}) { $self->_initialize(); } for my $i ( 0 .. $#{$self->{'_string'}} ) { next unless $self->{'_string'}->[$i] || @{$self->{'_alpha'}->[$i]} > 1; if ( $self->{'_string'}->[$i] == $#{$self->{'_alpha'}->[$i]} ) { # rollover if ( $i == $#{$self->{'_string'}} ) { # end of possibilities return; } else { $self->{'_string'}->[$i] = 0; next; } } else { $self->{'_string'}->[$i]++; my $j = -1; my $seqstr = join('', map { $j++; $self->{'_alpha'}->[$j]->[$_]; } @{$self->{'_string'}}); my $desc = $self->{'_seq'}->desc() || ''; $self->{'_num'}++; 1 while $self->{'_num'} =~ s/(\d)(\d\d\d)(?!\d)/$1,$2/; $desc =~ s/( \[Bio::Tools::IUPAC-generated\sunique sequence # [^\]]*\])|$/ \[Bio::Tools::IUPAC-generated unique sequence # $self->{'_num'}\]/; $self->{'_num'} =~ s/,//g; # Return a fresh sequence object return Bio::PrimarySeq->new(-seq => $seqstr, -desc => $desc); } } } =head2 iupac Title : iupac Usage : my %symbols = $iupac->iupac; Function: Returns a hash of symbols -> symbol components of the right type for the given sequence, i.e. it is the same as iupac_iup() if Bio::Tools::IUPAC was given a proteic sequence, or iupac_iub() if the sequence was nucleic. For example, the key 'M' has the value ['A', 'C']. Args : none Returns : Hash =cut sub iupac { my ($self) = @_; my $alphabet = lc( $self->{'_seq'}->alphabet() ); if ( ($alphabet eq 'dna') or ($alphabet eq 'rna') ) { return %IUB; # nucleic } elsif ( $alphabet eq 'protein' ) { return %IUP; # proteic } else { $self->throw("The input sequence had the unknown alphabet '$alphabet'\n"); } } =head2 iupac_amb Title : iupac_amb Usage : my %symbols = $iupac->iupac_amb; Function: Same as iupac() but only contains a mapping between ambiguous residues and the ambiguous residues they map to. For example, the key 'N' has the value ['R', 'Y', 'K', 'M', 'S', 'W', 'B', 'D', 'H', 'V', 'N'], i.e. it matches all other ambiguous residues. Args : none Returns : Hash =cut sub iupac_amb { my ($self) = @_; my $alphabet = lc( $self->{'_seq'}->alphabet() ); if ( ($alphabet eq 'dna') or ($alphabet eq 'rna') ) { return %IUB_AMB; # nucleic } elsif ( $alphabet eq 'protein' ) { return %IUP_AMB; # proteic } else { $self->throw("The input sequence had the unknown alphabet '$alphabet'\n"); } } =head2 iupac_iup Title : iupac_iup Usage : my %aasymbols = $iupac->iupac_iup; Function: Returns a hash of PROTEIN symbols -> non-ambiguous symbol components Args : none Returns : Hash =cut sub iupac_iup { return %IUP; } =head2 iupac_iup_amb Title : iupac_iup_amb Usage : my %aasymbols = $iupac->iupac_iup_amb; Function: Returns a hash of PROTEIN symbols -> ambiguous symbol components Args : none Returns : Hash =cut sub iupac_iup_amb { return %IUP_AMB; } =head2 iupac_iub Title : iupac_iub Usage : my %dnasymbols = $iupac->iupac_iub; Function: Returns a hash of DNA symbols -> non-ambiguous symbol components Args : none Returns : Hash =cut sub iupac_iub { return %IUB; } =head2 iupac_iub_amb Title : iupac_iub_amb Usage : my %dnasymbols = $iupac->iupac_iub; Function: Returns a hash of DNA symbols -> ambiguous symbol components Args : none Returns : Hash =cut sub iupac_iub_amb { return %IUB_AMB; } =head2 iupac_rev_iub Title : iupac_rev_iub Usage : my %dnasymbols = $iupac->iupac_rev_iub; Function: Returns a hash of nucleotide combinations -> IUPAC code (a reverse of the iupac_iub hash). Args : none Returns : Hash =cut sub iupac_rev_iub { return %REV_IUB; } =head2 count Title : count Usage : my $total = $iupac->count(); Function: Calculates the number of unique, unambiguous sequences that this ambiguous sequence could generate Args : none Return : int =cut sub count { my ($self) = @_; if (not exists $self->{'_string'}) { $self->_initialize(); } my $count = 1; $count *= scalar(@$_) for (@{$self->{'_alpha'}}); return $count; } =head2 regexp Title : regexp Usage : my $re = $iupac->regexp(); Function: Converts the ambiguous sequence into a regular expression that matches all of the corresponding ambiguous and non-ambiguous sequences. You can further manipulate the resulting regular expression with the Bio::Tools::SeqPattern module. After you are done building your regular expression, you might want to compile it and make it case- insensitive: $re = qr/$re/i; Args : 1 to match RNA: T and U characters will match interchangeably Return : regular expression =cut sub regexp { my ($self, $match_rna) = @_; my $re; my $seq = $self->{'_seq'}->seq; my %iupac = $self->iupac; my %iupac_amb = $self->iupac_amb; for my $pos (0 .. length($seq)-1) { my $res = substr $seq, $pos, 1; my $iupacs = $iupac{$res}; my $iupacs_amb = $iupac_amb{$res} || []; if (not defined $iupacs) { $self->throw("Primer sequence '$seq' is not a valid IUPAC sequence.". " Offending character was '$res'.\n"); } my $part = join '', (@$iupacs, @$iupacs_amb); if ($match_rna) { $part =~ s/T/TU/i || $part =~ s/U/TU/i; } if (length $part > 1) { $part = '['.$part.']'; } $re .= $part; } return $re; } sub AUTOLOAD { my $self = shift @_; my $method = $AUTOLOAD; $method =~ s/.*:://; return $self->{'_seq'}->$method(@_) unless $method eq 'DESTROY'; } 1; ���������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Lucy.pm������������������������������������������������������������������000444��000766��000024�� 52216�13155576320� 16624� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Lucy # # Copyright Her Majesty the Queen of England # written by Andrew Walsh (paeruginosa@hotmail.com) during employment with # Agriculture and Agri-food Canada, Cereal Research Centre, Winnipeg, MB # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Lucy - Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR =head1 SYNOPSIS # Create the Lucy object from an existing Lucy output file @params = ('seqfile' => 'lucy.seq', 'lucy_verbose' => 1); $lucyObj = Bio::Tools::Lucy->new(@params); # Get names of all sequences $names = $lucyObj->get_sequence_names(); # Print seq and qual values for sequences >400 bp in order to run CAP3 foreach $name (@$names) { next unless $lucyObj->length_clear($name) > 400; print SEQ ">$name\n", $lucyObj->sequence($name), "\n"; print QUAL ">$name\n", $lucyObj->quality($name), "\n"; } # Get an array of Bio::PrimarySeq objects @seqObjs = $lucyObj->get_Seq_Objs(); =head1 DESCRIPTION Bio::Tools::Lucy.pm provides methods for analyzing the sequence and quality values generated by Lucy program from TIGR. Lucy will identify vector, poly-A/T tails, and poor quality regions in a sequence. (www.genomics.purdue.edu/gcg/other/lucy.pdf) The input to Lucy can be the Phred sequence and quality files generated from running Phred on a set of chromatograms. Lucy can be obtained (free of charge to academic users) from www.tigr.org/softlab There are a few methods that will only be available if you make some minor changes to the source for Lucy and then recompile. The changes are in the 'lucy.c' file and there is a diff between the original and the modified file in the Appendix Please contact the author of this module if you have any problems making these modifications. You do not have to make these modifications to use this module. =head2 Creating a Lucy object @params = ('seqfile' => 'lucy.seq', 'adv_stderr' => 1, 'fwd_desig' => '_F', 'rev_desig' => '_R'); $lucyObj = Bio::Tools::Lucy->new(@params); =head2 Using a Lucy object You should get an array with the sequence names in order to use accessor methods. Note: The Lucy binary program will fail unless the sequence names provided as input are unique. $names_ref = $lucyObj->get_sequence_names(); This code snippet will produce a Fasta format file with sequence lengths and %GC in the description line. foreach $name (@$names) { print FILE ">$name\t", $lucyObj->length_clear($name), "\t", $lucyObj->per_GC($name), "\n", $lucyObj->sequence($name), "\n"; } Print seq and qual values for sequences >400 bp in order to assemble them with CAP3 (or other assembler). foreach $name (@$names) { next unless $lucyObj->length_clear($name) > 400; print SEQ ">$name\n", $lucyObj->sequence($name), "\n"; print QUAL ">$name\n", $lucyObj->quality($name), "\n"; } Get all the sequences as Bio::PrimarySeq objects (eg., for use with Bio::Tools::Run::StandaloneBlast to perform BLAST). @seqObjs = $lucyObj->get_Seq_Objs(); Or use only those sequences that are full length and have a Poly-A tail. foreach $name (@$names) { next unless ($lucyObj->full_length($name) and $lucy->polyA($name)); push @seqObjs, $lucyObj->get_Seq_Obj($name); } Get the names of those sequences that were rejected by Lucy. $rejects_ref = $lucyObj->get_rejects(); Print the names of the rejects and 1 letter code for reason they were rejected. foreach $key (sort keys %$rejects_ref) { print "$key: ", $rejects_ref->{$key}; } There is a lot of other information available about the sequences analyzed by Lucy (see APPENDIX). This module can be used with the DBI module to store this sequence information in a database. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Andrew G. Walsh paeruginosa@hotmail.com =head1 APPENDIX Methods available to Lucy objects are described below. Please note that any method beginning with an underscore is considered internal and should not be called directly. =cut package Bio::Tools::Lucy; use vars qw($AUTOLOAD @ATTR %OK_FIELD); use strict; use Bio::PrimarySeq; use base qw(Bio::Root::Root Bio::Root::IO); @ATTR = qw(seqfile qualfile stderrfile infofile lucy_verbose fwd_desig rev_desig adv_stderr); foreach my $attr (@ATTR) { $OK_FIELD{$attr}++ } sub AUTOLOAD { my $self = shift; my $attr = $AUTOLOAD; $attr =~ s/.*:://; $attr = lc $attr; $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr}; $self->{$attr} = shift if @_; return $self->{$attr}; } =head2 new Title : new Usage : $lucyObj = Bio::Tools::Lucy->new(seqfile => lucy.seq, rev_desig => '_R', fwd_desig => '_F') Function: creates a Lucy object from Lucy analysis files Returns : reference to Bio::Tools::Lucy object Args : seqfile Fasta sequence file generated by Lucy qualfile Quality values file generated by Lucy infofile Info file created when Lucy is run with -debug 'infofile' option stderrfile Standard error captured from Lucy when Lucy is run with -info option and STDERR is directed to stderrfile (ie. lucy ... 2> stderrfile). Info in this file will include sequences dropped for low quality. If you've modified Lucy source (see adv_stderr below), it will also include info on which sequences were dropped because they were vector, too short, had no insert, and whether a poly-A tail was found (if Lucy was run with -cdna option). lucy_verbose verbosity level (0-1). fwd_desig The string used to determine whether sequence is a forward read. The parser will assume that this match will occus at the end of the sequence name string. rev_desig As above, for reverse reads. adv_stderr Can be set to a true value (1). Will only work if you have modified the Lucy source code as outlined in DESCRIPTION and capture the standard error from Lucy. If you don't provide filenames for qualfile, infofile or stderrfile, the module will assume that .qual, .info, and .stderr are the file extensions and search in the same directory as the .seq file for these files. For example, if you create a Lucy object with $lucyObj = Bio::Tools::Lucy-E<gt>new(seqfile =E<gt>lucy.seq), the module will find lucy.qual, lucy.info and lucy.stderr. You can omit any or all of the quality, info or stderr files, but you will not be able to use all of the object methods (see method documentation below). =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($attr, $value); while (@args) { $attr = shift @args; $attr = lc $attr; $value = shift @args; $self->{$attr} = $value; } &_parse($self); return $self; } =head2 _parse Title : _parse Usage : n/a (internal function) Function: called by new() to parse Lucy output files Returns : nothing Args : none =cut sub _parse { my $self = shift; $self->{seqfile} =~ /^(\S+)\.\S+$/; my $file = $1; $self->warn("Opening $self->{seqfile} for parsing...\n") if $self->{lucy_verbose}; open my $SEQ, '<', $self->{seqfile} or $self->throw("Could not read sequence file '$self->{seqfile}': $!"); my ($name, $line); my $seq = ""; my @lines = <$SEQ>; while ($line = pop @lines) { chomp $line; if ($line =~ /^>(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)/) { $name = $1; if ($self->{fwd_desig}) { $self->{sequences}{$name}{direction} = "F" if $name =~ /^(\S+)($self->{fwd_desig})$/; } if ($self->{rev_desig}) { $self->{sequences}{$name}{direction} = "R" if $name =~ /^(\S+)($self->{rev_desig})$/; } $self->{sequences}{$name}{min_clone_len} = $2; # this is used for TIGR Assembler, as are $3 and $4 $self->{sequences}{$name}{max_clone_len} = $3; $self->{sequences}{$name}{med_clone_len} = $4; $self->{sequences}{$name}{beg_clear} = $5; $self->{sequences}{$name}{end_clear} = $6; $self->{sequences}{$name}{length_raw} = $seq =~ tr/[AGCTN]//; # from what I've seen, these are the bases Phred calls. Please let me know if I'm wrong. my $beg = $5-1; # substr function begins with index 0 $seq = $self->{sequences}{$name}{sequence} = substr ($seq, $beg, $6-$beg); my $count = $self->{sequences}{$name}{length_clear} = $seq =~ tr/[AGCTN]//; my $countGC = $seq =~ tr/[GC]//; $self->{sequences}{$name}{per_GC} = $countGC/$count * 100; $seq = ""; } else { $seq = $line.$seq; } } # now parse quality values (check for presence of quality file first) if ($self->{qualfile}) { open my $QUAL, '<', $self->{qualfile} or $self->throw("Could not read quality file '$self->{qualfile}': $!"); @lines = <$QUAL>; } elsif (-e "$file.qual") { $self->warn("You did not set qualfile, but I'm opening $file.qual\n") if $self->{lucy_verbose}; $self->qualfile("$file.qual"); open my $QUAL, '<', "$file.qual" or $self->throw("Could not read quality file '$file.qual': $!"); @lines = <$QUAL>; } else { $self->warn("I did not find a quality file. You will not be able to use all of the accessor methods.\n") if $self->{lucy_verbose}; @lines = (); } my (@vals, @slice, $num, $tot, $vals); my $qual = ""; while ($line = pop @lines) { chomp $line; if ($line =~ /^>(\S+)/) { $name = $1; @vals = split /\s/ , $qual; @slice = @vals[$self->{sequences}{$name}{beg_clear} - 1 .. $self->{sequences}{$name}{end_clear} - 1]; $vals = join "\t", @slice; $self->{sequences}{$name}{quality} = $vals; $qual = ""; foreach $num (@slice) { $tot += $num; } $num = @slice; $self->{sequences}{$name}{avg_quality} = $tot/$num; $tot = 0; } else { $qual = $line.$qual; } } # determine whether reads are full length if ($self->{infofile}) { open my $INFO, '<', $self->{infofile} or $self->throw("Could not read info file '$self->{infofile}': $!"); @lines = <$INFO>; } elsif (-e "$file.info") { $self->warn("You did not set infofile, but I'm opening $file.info\n") if $self->{lucy_verbose}; $self->infofile("$file.info"); open my $INFO, '<', "$file.info" or $self->throw("Could not read info file '$file.info': $!"); @lines = <$INFO>; } else { $self->warn("I did not find an info file. You will not be able to use all of the accessor methods.\n") if $self->{lucy_verbose}; @lines = (); } foreach (@lines) { /^(\S+).+CLV\s+(\d+)\s+(\d+)$/; if ($2>0 && $3>0) { $self->{sequences}{$1}{full_length} = 1 if $self->{sequences}{$1}; # will show cleavage info for rejected sequences too } } # parse rejects (and presence of poly-A if Lucy has been modified) if ($self->{stderrfile}) { open my $STDERR_LUCY, '<', $self->{stderrfile} or $self->throw("Could not read quality file '$self->{stderrfile}': $!"); @lines = <$STDERR_LUCY>; } elsif (-e "$file.stderr") { $self->warn("You did not set stderrfile, but I'm opening $file.stderr\n") if $self->{lucy_verbose}; $self->stderrfile("$file.stderr"); open my $STDERR_LUCY, '<', "$file.stderr" or $self->throw("Could not read quality file '$file.stderr': $!"); @lines = <$STDERR_LUCY>; } else { $self->warn("I did not find a standard error file. You will not be able to use all of the accessor methods.\n") if $self->{lucy_verbose}; @lines = (); } if ($self->{adv_stderr}) { foreach (@lines) { $self->{reject}{$1} = "Q" if /dropping\s+(\S+)/; $self->{reject}{$1} = "V" if /Vector: (\S+)/; $self->{reject}{$1} = "E" if /Empty: (\S+)/; $self->{reject}{$1} = "S" if m{Short/ no insert: (\S+)}; $self->{sequences}{$1}{polyA} = 1 if /(\S+) has PolyA/; if (/Dropped PolyA: (\S+)/) { $self->{reject}{$1} = "P"; delete $self->{sequences}{$1}; } } } else { foreach (@lines) { $self->{reject}{$1} = "R" if /dropping\s+(\S+)/; } } } =head2 get_Seq_Objs Title : get_Seq_Objs Usage : $lucyObj->get_Seq_Objs() Function: returns an array of references to Bio::PrimarySeq objects where -id = 'sequence name' and -seq = 'sequence' Returns : array of Bio::PrimarySeq objects Args : none =cut sub get_Seq_Objs { my $self = shift; my($seqobj, @seqobjs); foreach my $key (sort keys %{$self->{sequences}}) { $seqobj = Bio::PrimarySeq->new( -seq => "$self->{sequences}{$key}{sequence}", -id => "$key"); push @seqobjs, $seqobj; } return \@seqobjs; } =head2 get_Seq_Obj Title : get_Seq_Obj Usage : $lucyObj->get_Seq_Obj($seqname) Function: returns reference to a Bio::PrimarySeq object where -id = 'sequence name' and -seq = 'sequence' Returns : reference to Bio::PrimarySeq object Args : name of a sequence =cut sub get_Seq_Obj { my ($self, $key) = @_; my $seqobj = Bio::PrimarySeq->new( -seq => "$self->{sequences}{$key}{sequence}", -id => "$key"); return $seqobj; } =head2 get_sequence_names Title : get_sequence_names Usage : $lucyObj->get_sequence_names Function: returns reference to an array of names of the sequences analyzed by Lucy. These names are required for most of the accessor methods. Note: The Lucy binary will fail unless sequence names are unique. Returns : array reference Args : none =cut sub get_sequence_names { my $self = shift; my @keys = sort keys %{$self->{sequences}}; return \@keys; } =head2 sequence Title : sequence Usage : $lucyObj->sequence($seqname) Function: returns the DNA sequence of one of the sequences analyzed by Lucy. Returns : string Args : name of a sequence =cut sub sequence { my ($self, $key) = @_; return $self->{sequences}{$key}{sequence}; } =head2 quality Title : quality Usage : $lucyObj->quality($seqname) Function: returns the quality values of one of the sequences analyzed by Lucy. This method depends on the user having provided a quality file. Returns : string Args : name of a sequence =cut sub quality { my($self, $key) = @_; return $self->{sequences}{$key}{quality}; } =head2 avg_quality Title : avg_quality Usage : $lucyObj->avg_quality($seqname) Function: returns the average quality value for one of the sequences analyzed by Lucy. Returns : float Args : name of a sequence =cut sub avg_quality { my($self, $key) = @_; return $self->{sequences}{$key}{avg_quality}; } =head2 direction Title : direction Usage : $lucyObj->direction($seqname) Function: returns the direction for one of the sequences analyzed by Lucy providing that 'fwd_desig' or 'rev_desig' were set when the Lucy object was created. Strings returned are: 'F' for forward, 'R' for reverse. Returns : string Args : name of a sequence =cut sub direction { my($self, $key) = @_; return $self->{sequences}{$key}{direction} if $self->{sequences}{$key}{direction}; return ""; } =head2 length_raw Title : length_raw Usage : $lucyObj->length_raw($seqname) Function: returns the length of a DNA sequence prior to quality/ vector trimming by Lucy. Returns : integer Args : name of a sequence =cut sub length_raw { my($self, $key) = @_; return $self->{sequences}{$key}{length_raw}; } =head2 length_clear Title : length_clear Usage : $lucyObj->length_clear($seqname) Function: returns the length of a DNA sequence following quality/ vector trimming by Lucy. Returns : integer Args : name of a sequence =cut sub length_clear { my($self, $key) = @_; return $self->{sequences}{$key}{length_clear}; } =head2 start_clear Title : start_clear Usage : $lucyObj->start_clear($seqname) Function: returns the beginning position of good quality, vector free DNA sequence determined by Lucy. Returns : integer Args : name of a sequence =cut sub start_clear { my($self, $key) = @_; return $self->{sequences}{$key}{beg_clear}; } =head2 end_clear Title : end_clear Usage : $lucyObj->end_clear($seqname) Function: returns the ending position of good quality, vector free DNA sequence determined by Lucy. Returns : integer Args : name of a sequence =cut sub end_clear { my($self, $key) = @_; return $self->{sequences}{$key}{end_clear}; } =head2 per_GC Title : per_GC Usage : $lucyObj->per_GC($seqname) Function: returns the percente of the good quality, vector free DNA sequence determined by Lucy. Returns : float Args : name of a sequence =cut sub per_GC { my($self, $key) = @_; return $self->{sequences}{$key}{per_GC}; } =head2 full_length Title : full_length Usage : $lucyObj->full_length($seqname) Function: returns the truth value for whether or not the sequence read was full length (ie. vector present on both ends of read). This method depends on the user having provided the 'info' file (Lucy must be run with the -debug 'info_filename' option to get this file). Returns : boolean Args : name of a sequence =cut sub full_length { my($self, $key) = @_; return 1 if $self->{sequences}{$key}{full_length}; return 0; } =head2 polyA Title : polyA Usage : $lucyObj->polyA($seqname) Function: returns the truth value for whether or not a poly-A tail was detected and clipped by Lucy. This method depends on the user having modified the source for Lucy as outlined in DESCRIPTION and invoking Lucy with the -cdna option and saving the standard error. Note, the final sequence will not show the poly-A/T region. Returns : boolean Args : name of a sequence =cut sub polyA { my($self, $key) = @_; return 1 if $self->{sequences}{$key}{polyA}; return 0; } =head2 get_rejects Title : get_rejects Usage : $lucyObj->get_rejects() Function: returns a hash containing names of rejects and a 1 letter code for the reason Lucy rejected the sequence. Q- rejected because of low quality values S- sequence was short V- sequence was vector E- sequence was empty P- poly-A/T trimming caused sequence to be too short In order to get the rejects, you must provide a file with the standard error from Lucy. You will only get the quality category rejects unless you have modified the source and recompiled Lucy as outlined in DESCRIPTION. Returns : hash reference Args : none =cut sub get_rejects { my $self = shift; return $self->{reject}; } =head2 Diff for Lucy source code 352a353,354 > /* AGW added next line */ > fprintf(stderr, "Empty: %s\n", seqs[i].name); 639a642,643 > /* AGW added next line */ > fprintf(stderr, "Short/ no insert: %s\n", seqs[i].name); 678c682,686 < if (left) seqs[i].left+=left; --- > if (left) { > seqs[i].left+=left; > /* AGW added next line */ > fprintf(stderr, "%s has PolyA (left).\n", seqs[i].name); > } 681c689,693 < if (right) seqs[i].right-=right; --- > if (right) { > seqs[i].right-=right; > /* AGW added next line */ > fprintf(stderr, "%s has PolyA (right).\n", seqs[i].name); > } 682a695,696 > /* AGW added next line */ > fprintf(stderr, "Dropped PolyA: %s\n", seqs[i].name); 734a749,750 > /* AGW added next line */ > fprintf(stderr, "Vector: %s\n", seqs[i].name); =cut =head2 This patch is to be applied to lucy.c from the lucy-1.19p release 277a278,279 > /* AGW added next line */ > fprintf(stderr, "Short/ no insert: %s\n", seqs[i].name); 588c590,592 < if ((seqs[i].len=bases)<=0) --- > if ((seqs[i].len=bases)<=0) { > /* AGW added next line */ > fprintf(stderr, "Empty: %s\n", seqs[i].name); 589a594 > } 893c898,902 < if (left) seqs[i].left+=left; --- > if (left) { > seqs[i].left+=left; > /* AGW added next line */ > fprintf(stderr, "%s has PolyA (left).\n", seqs[i].name); > } 896c905,909 < if (right) seqs[i].right-=right; --- > if (right) { > seqs[i].right-=right; > /* AGW added next line */ > fprintf(stderr, "%s has PolyA (right).\n", seqs[i].name); > } 898a912,913 > /* AGW added next line */ > fprintf(stderr, "Dropped PolyA: %s\n", seqs[i].name); 949a965,966 > /* AGW added next line */ > fprintf(stderr, "Vector: %s\n", seqs[i].name); =cut 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/MZEF.pm������������������������������������������������������������������000444��000766��000024�� 23044�13155576320� 16446� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::MZEF # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp-at-gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::MZEF - Results of one MZEF run =head1 SYNOPSIS $mzef = Bio::Tools::MZEF->new(-file => 'result.mzef'); # filehandle: $mzef = Bio::Tools::MZEF->new( -fh => \*INPUT ); # to indicate that the sequence was reversed prior to feeding it to MZEF # and that you want to have this reflected in the strand() attribute of # the exons, as well have the coordinates translated to the non-reversed # sequence $mzef = Bio::Tools::MZEF->new( -file => 'result.mzef', -strand => -1 ); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same while($gene = $mzef->next_prediction()) { # $gene is an instance of Bio::Tools::Prediction::Gene # $gene->exons() returns an array of # Bio::Tools::Prediction::Exon objects # all exons: @exon_arr = $gene->exons(); # internal exons only @intrl_exons = $gene->exons('Internal'); # note that presently MZEF predicts only internal exons! } # essential if you gave a filename at initialization (otherwise the file # will stay open) $mzef->close(); =head1 DESCRIPTION The MZEF module provides a parser for MZEF gene structure prediction output. This module inherits off L<Bio::Tools::AnalysisResult> and therefore implements L<Bio::SeqAnalysisParserI>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp-at-gmx.net (or hilmar.lapp-at-pharma.novartis.com) =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::MZEF; use strict; use Bio::Tools::Prediction::Gene; use Bio::Tools::Prediction::Exon; use base qw(Bio::Tools::AnalysisResult); sub _initialize_state { my($self,@args) = @_; # first call the inherited method! my $make = $self->SUPER::_initialize_state(@args); # handle our own parameters my ($strand, $params) = $self->_rearrange([qw(STRAND )], @args); # our private state variables $strand = 1 unless defined($strand); $self->{'_strand'} = $strand; $self->{'_preds_parsed'} = 0; $self->{'_has_cds'} = 0; # array of pre-parsed predictions $self->{'_preds'} = []; } =head2 analysis_method Usage : $mzef->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /mzef/i. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method && ($method !~ /mzef/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head2 next_feature Title : next_feature Usage : while($gene = $mzef->next_feature()) { # do something } Function: Returns the next gene structure prediction of the MZEF result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes but just potential internal exons. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_feature { my ($self,@args) = @_; # even though next_prediction doesn't expect any args (and this method # does neither), we pass on args in order to be prepared if this changes # ever return $self->next_prediction(@args); } =head2 next_prediction Title : next_prediction Usage : while($gene = $mzef->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the MZEF result file. Call this method repeatedly until FALSE is returned. Note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes but just potential internal exons. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_prediction { my ($self) = @_; my $gene; # if the prediction section hasn't been parsed yet, we do this now $self->_parse_predictions() unless $self->_predictions_parsed(); # return the next gene structure (transcript) return $self->_prediction(); } =head2 _parse_predictions Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : =cut sub _parse_predictions { my ($self) = @_; my ($method); # set but not used presently my $exon_tag = "InternalExon"; my $gene; # my $seqname; # name given in output is poorly formatted my $seqlen; my $prednr = 1; while(defined($_ = $self->_readline())) { if(/^\s*(\d+)\s*-\s*(\d+)\s+/) { # exon or signal if(! defined($gene)) { $gene = Bio::Tools::Prediction::Gene->new( '-primary' => "GenePrediction$prednr", '-source' => 'MZEF'); } # we handle start-end first because may not be space delimited # for large numbers my ($start,$end) = ($1,$2); s/^\s*(\d+)\s*-\s*(\d+)\s+//; # split the rest into fields chomp(); # format: Coordinates P Fr1 Fr2 Fr3 Orf 3ss Cds 5ss # index: 0 1 2 3 4 5 6 7 my @flds = split(' ', $_); # create the feature object depending on the type of signal -- # which is always an (internal) exon for MZEF my $predobj = Bio::Tools::Prediction::Exon->new(); # set common fields $predobj->source_tag('MZEF'); $predobj->significance($flds[0]); $predobj->score($flds[0]); # what shall we set as overall score? $predobj->strand($self->{'_strand'}); # MZEF searches only one if($predobj->strand() == 1) { $predobj->start($start); $predobj->end($end); } else { $predobj->start($seqlen-$end+1); $predobj->end($seqlen-$start+1); } # set scores $predobj->start_signal_score($flds[5]); $predobj->end_signal_score($flds[7]); $predobj->coding_signal_score($flds[6]); # frame -- we simply extract the one with highest score from the # orf field, and store the individual scores for now my $frm = index($flds[4], "1"); $predobj->frame(($frm < 0) ? undef : $frm); $predobj->primary_tag($exon_tag); $predobj->is_coding(1); # add to gene structure (should be done only when start and end # are set, in order to allow for proper expansion of the range) $gene->add_exon($predobj); next; } if(/^\s*Internal .*(MZEF)/) { $self->analysis_method($1); next; } if(/^\s*File_Name:\s+(\S+)\s+Sequence_length:\s+(\d+)/) { # $seqname = $1; # this is too poor currently (file name truncated # to 10 chars) in order to be sensible enough $seqlen = $2; next; } } # $gene->seq_id($seqname); $self->_add_prediction($gene) if defined($gene); $self->_predictions_parsed(1); } =head2 _prediction Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns : =cut sub _prediction { my ($self) = @_; return unless(exists($self->{'_preds'}) && @{$self->{'_preds'}}); return shift(@{$self->{'_preds'}}); } =head2 _add_prediction Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns : =cut sub _add_prediction { my ($self, $gene) = @_; if(! exists($self->{'_preds'})) { $self->{'_preds'} = []; } push(@{$self->{'_preds'}}, $gene); } =head2 _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE =cut sub _predictions_parsed { my ($self, $val) = @_; $self->{'_preds_parsed'} = $val if $val; if(! exists($self->{'_preds_parsed'})) { $self->{'_preds_parsed'} = 0; } return $self->{'_preds_parsed'}; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Match.pm�����������������������������������������������������������������000555��000766��000024�� 12666�13155576320� 16754� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# $Id: Match.pm,v 1.2 2007/06/14 18:01:52 nathan Exp $ # # BioPerl module for Bio::Tools::Match # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Sendu Bala <bix@sendu.me.uk> # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Match - Parses output from Transfac's match(TM) =head1 SYNOPSIS use strict; use Bio::Tools::Match; my $parser = Bio::Tools::Match->new(-file => "match.out"); while (my $feat = $parser->next_result) { my $start = $feat->start; my $end = $feat->end; my $core_score = $feat->score; my $matrix_score = ($feat->annotation->get_Annotations('matrix_score'))[0]->value; my $matrix_id = ($feat->annotation->get_Annotations('matrix_id'))[0]->value; } =head1 DESCRIPTION This module is used to parse the output from Transfac's match(TM) program. It doesn't support the histogram output of match. Each result is a Bio::SeqFeature::Annotated representing a single matrix match. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Match; use strict; use Bio::SeqFeature::Generic; use Bio::Annotation::SimpleValue; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::Match->new(); Function: Builds a new Bio::Tools::Match object Returns : Bio::Tools::Match Args : -file (or -fh) should contain the contents of a standard match output =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_result Title : next_result Usage : $result = $obj->next_result(); Function: Returns the next result available from the input, or undef if there are no more results. Returns : Bio::SeqFeature::Annotated object. Features are annotated with tags for 'matrix_score', 'matrix_id' and a 'predicted' tag. Args : none =cut sub next_result { my ($self) = @_; my $line = $self->_readline || return; if (! $self->{found_seq_id} && $line =~ /^Inspecting sequence ID\s+(.+)/) { $self->{found_seq_id} = $1; } while ($line !~ /^\s\S+\s+\|\s+\d+/) { $line = $self->_readline || return; } # The first column gives the TRANSFAC(r) identifier of the matching matrix, # then comes the position and the strand where the respective match has been # found. The core similarity score is given in column three, the matrix # similarity score in column four. The last column gives the matching # sequence. # # #Search for sites by WeightMatrix library: /home/sendu/files/programs/transfac/cgi-bin/data/matrix.dat #Sequence file: sequence.fa #Site selection profile: mxprf Profile generated from /home/sendu/files/programs/transfac/cgi-bin/data/matrix.dat with default values. # # #Inspecting sequence ID Homo_sapiens # # V$MYOD_01 | 5 (+) | 0.751 | 0.784 | ttaGAGGTggcg # V$MYOD_01 | 5 (-) | 0.778 | 0.580 | ttagAGGTGgcg # V$MYOD_01 | 30 (+) | 0.751 | 0.581 | gctCAGGCaccc #[...] # V$RORA_Q4 | 53610 (+) | 0.775 | 0.668 | tgtgggGGCCA # V$RORA_Q4 | 53639 (+) | 0.775 | 0.636 | gtcgggGGACA # # Total sequences length=53654 # # Total number of found sites=1735559 # # Frequency of sites per nucleotide=32.347243 my ($matrix_id, $start, $strand, $core_score, $matrix_score, $seq) = $line =~ /^\s(\S+)\s+\|\s+(\d+)\s+\(([+-])\)\s+\|\s+(\S+)\s+\|\s+(\S+)\s+\|\s+(\S+)/; my $feat = Bio::SeqFeature::Generic->new( -seq_id => $self->{found_seq_id}, -start => $start, -end => $start + length($seq) - 1, -strand => 1, -score => $core_score, -source => 'transfac_match'); my $sv = Bio::Annotation::SimpleValue->new(-tagname => 'predicted', -value => 1); $feat->annotation->add_Annotation($sv); $sv = Bio::Annotation::SimpleValue->new(-tagname => 'matrix_score', -value => $matrix_score); $feat->annotation->add_Annotation($sv); $sv = Bio::Annotation::SimpleValue->new(-tagname => 'matrix_id', -value => $matrix_id); $feat->annotation->add_Annotation($sv); return $feat; } 1; ��������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/OddCodes.pm��������������������������������������������������������������000444��000766��000024�� 26646�13155576320� 17404� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������#$Id$ #----------------------------------------------------------------------------- # PACKAGE : OddCodes.pm # PURPOSE : To write amino acid sequences in alternative alphabets # AUTHOR : Derek Gatherer (D.Gatherer@organon.nhe.akzonobel.nl) # SOURCE : # CREATED : 8th July 2000 # MODIFIED : # DISCLAIMER : I am employed in the pharmaceutical industry but my # : employers do not endorse or sponsor this module # : in any way whatsoever. The above email address is # : given purely for the purpose of easy communication # : with the author, and does not imply any connection # : between my employers and anything written below. # LICENCE : You may distribute this module under the same terms # : as the rest of BioPerl. #---------------------------------------------------------------------------- =head1 NAME Bio::Tools::OddCodes - Object holding alternative alphabet coding for one protein sequence =head1 SYNOPSIS # Take a sequence object from eg, an inputstream, and creates an # object for the purposes of rewriting that sequence in another # alphabet. These are abbreviated amino acid sequence alphabets, # designed to simplify the statistical aspects of analysing protein # sequences, by reducing the combinatorial explosion of the # 20-letter alphabet. These abbreviated alphabets range in size # from 2 to 8. # Creating the OddCodes object, eg: my $inputstream = Bio::SeqIO->new( '-file' => "seqfile", '-format' => 'Fasta'); my $seqobj = $inputstream->next_seq(); my $oddcode_obj = Bio::Tools::Oddcodes->new(-seq => $seqobj); # or: my $seqobj = Bio::PrimarySeq->new (-seq=>'[cut and paste a sequence here]', -alphabet => 'protein', -id => 'test'); my $oddcode_obj = Bio::Tools::OddCodes->new(-seq => $seqobj); # do the alternative coding, returning the answer as a reference to # a string my $output = $oddcode_obj->structural(); my $output = $oddcode_obj->chemical(); my $output = $oddcode_obj->functional(); my $output = $oddcode_obj->charge(); my $output = $oddcode_obj->hydrophobic(); my $output = $oddcode_obj->Dayhoff(); my $output = $oddcode_obj->Sneath(); my $output = $oddcode_obj->Stanfel(); # display sequence in new form, eg: my $new_coding = $$output; print "\n$new_coding"; =head1 DESCRIPTION Bio::Tools::Oddcodes is a welterweight object for rewriting a protein sequence in an alternative alphabet. Eight of these are provided, ranging from the the 2-letter hydrophobic alphabet, to the 8-letter chemical alphabet. These are useful for the statistical analysis of protein sequences since they can partially avoid the combinatorial explosion produced by the full 20-letter alphabet (eg. 400 dimers, 8000 trimers etc.) The objects will print out a warning if the input sequence is not a protein. If you know what you are doing, you can silence the warning by setting verbose() to a negative value. See SYNOPSIS above for object creation code. =head1 REFERENCES Stanfel LE (1996) A new approach to clustering the amino acids. J. theor. Biol. 183, 195-205. Karlin S, Ost F and Blaisdell BE (1989) Patterns in DNA and amino acid sequences and their statistical significance. Chapter 6 of: Mathematical Methods for DNA Sequences. Waterman MS (ed.) CRC Press, Boca Raton , FL. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Derek Gatherer =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::OddCodes; use strict; use base qw(Bio::Root::Root); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($seqobj) = $self->_rearrange([qw(SEQ)],@args); if((! defined($seqobj)) && @args && ref($args[0])) { # parameter not passed as named parameter? $seqobj = $args[0]; } unless ($seqobj->isa("Bio::PrimarySeqI")) { $self->throw("Bio::Tools::OddCodes only works on PrimarySeqI objects"); } $self->{'_seqref'} = $seqobj; return $self; } =head2 structural Title : structural Usage : $output = $oddcode_obj->structural(); Function: turns amino acid sequence into 3-letter structural alphabet : A (ambivalent), E (external), I (internal) Example : a sequence ACDEFGH will become AAEEIAE Returns : Reference to the new sequence string Args : none =cut sub structural() { my $self = $_[0]; my $seqstring = &_pullseq($self); # see _pullseq() below # now the real business $seqstring =~ tr/[ACGPSTWY]/1/; $seqstring =~ tr/[RNDQEHK]/2/; $seqstring =~ tr/[ILMFV]/3/; $seqstring =~ tr/1/A/; $seqstring =~ tr/2/E/; $seqstring =~ tr/3/I/; return \$seqstring; # and that's that one } =head2 functional Title : functional Usage : $output = $oddcode_obj->functional(); Function: turns amino acid sequence into 4-letter functional alphabet : A (acidic), C (basic), H (hydrophobic), P (polar) Example : a sequence ACDEFGH will become HPAAHHC Returns : Reference to the new sequence string Args : none =cut sub functional() { my $self = $_[0]; my $seqstring = &_pullseq($self); # now the real business $seqstring =~ tr/[DE]/1/; $seqstring =~ tr/[HKR]/2/; $seqstring =~ tr/[AFILMPVW]/3/; $seqstring =~ tr/[CGNQSTY]/4/; $seqstring =~ tr/1/A/; $seqstring =~ tr/2/C/; $seqstring =~ tr/3/H/; $seqstring =~ tr/4/P/; return \$seqstring; # and that's that one } =head2 hydrophobic Title : hydrophobic Usage : $output = $oddcode_obj->hydrophobic(); Function: turns amino acid sequence into 2-letter hydrophobicity alphabet : O (hydrophobic), I (hydrophilic) Example : a sequence ACDEFGH will become OIIIOII Returns : Reference to the new sequence string Args : none =cut sub hydrophobic() { my $self = $_[0]; my $seqstring = &_pullseq($self); # now the real business $seqstring =~ tr/[AFILMPVW]/1/; $seqstring =~ tr/[CDEGHKNQRSTY]/2/; $seqstring =~ tr/1/I/; $seqstring =~ tr/2/O/; return \$seqstring; # and that's that one } =head2 Dayhoff Title : Dayhoff Usage : $output = $oddcode_obj->Dayhoff(); Function: turns amino acid sequence into 6-letter Dayhoff alphabet Example : a sequence ACDEFGH will become CADDGCE : A (=C), C (=AGPST), D (=DENQ), : E (=HKR), F (=ILMV), G (=FWY) Returns : Reference to the new sequence string Args : none =cut sub Dayhoff() { my $self = $_[0]; my $seqstring = &_pullseq($self); # now the real business $seqstring =~ tr/[C]/1/; $seqstring =~ tr/[AGPST]/2/; $seqstring =~ tr/[DENQ]/3/; $seqstring =~ tr/[HKR]/4/; $seqstring =~ tr/[ILMV]/5/; $seqstring =~ tr/[FWY]/6/; $seqstring =~ tr/1/A/; $seqstring =~ tr/2/C/; $seqstring =~ tr/3/D/; $seqstring =~ tr/4/E/; $seqstring =~ tr/5/F/; $seqstring =~ tr/6/G/; return \$seqstring; # and that's that one } =head2 Sneath Title : Sneath Usage : $output = $oddcode_obj->Sneath(); Function: turns amino acid sequence into 7-letter Sneath alphabet Example : a sequence ACDEFGH will become CEFFHCF : A (=ILV), C (=AGP), D (=MNQ), E (=CST), : F (=DE), G (=KR), H (=FHWY) Returns : Reference to the new sequence string Args : none =cut sub Sneath() { my $self = $_[0]; my $seqstring = &_pullseq($self); # now the real business $seqstring =~ tr/[ILV]/1/; $seqstring =~ tr/[AGP]/2/; $seqstring =~ tr/[MNQ]/3/; $seqstring =~ tr/[CST]/4/; $seqstring =~ tr/[DE]/5/; $seqstring =~ tr/[KR]/6/; $seqstring =~ tr/[FHWY]/7/; $seqstring =~ tr/1/A/; $seqstring =~ tr/2/C/; $seqstring =~ tr/3/D/; $seqstring =~ tr/4/E/; $seqstring =~ tr/5/F/; $seqstring =~ tr/6/G/; $seqstring =~ tr/7/H/; return \$seqstring; # and that's that one } =head2 Stanfel Title : Stanfel Usage : $output = $oddcode_obj->Stanfel(); Function: turns amino acid sequence into 4-letter Stanfel alphabet Example : a sequence ACDEFGH will become AACCDAE : A (=ACGILMPSTV), C (=DENQ), D (=FWY), E (=HKR) Returns : Reference to the new sequence string Args : none =cut sub Stanfel() { my $self = $_[0]; my $seqstring = &_pullseq($self); # now the real business $seqstring =~ tr/[ACGILMPSTV]/1/; $seqstring =~ tr/[DENQ]/2/; $seqstring =~ tr/[FWY]/3/; $seqstring =~ tr/[HKR]/4/; $seqstring =~ tr/1/A/; $seqstring =~ tr/2/C/; $seqstring =~ tr/3/D/; $seqstring =~ tr/4/E/; return \$seqstring; # and that's that one } =head2 chemical Title : chemical Usage : $output = $oddcode_obj->chemical(); Function: turns amino acid sequence into 8-letter chemical alphabet : A (acidic), L (aliphatic), M (amide), R (aromatic) : C (basic), H (hydroxyl), I (imino), S (sulphur) Example : a sequence ACDEFGH will become LSAARAC Returns : Reference to the new sequence string Args : none =cut sub chemical() { my $self = $_[0]; my $seqstring = &_pullseq($self); # now the real business $seqstring =~ tr/[DE]/1/; $seqstring =~ tr/[AGILV]/2/; $seqstring =~ tr/[NQ]/3/; $seqstring =~ tr/[FWY]/4/; $seqstring =~ tr/[RHK]/5/; $seqstring =~ tr/[ST]/6/; $seqstring =~ tr/P/7/; $seqstring =~ tr/[CM]/8/; $seqstring =~ tr/1/A/; $seqstring =~ tr/2/L/; $seqstring =~ tr/3/M/; $seqstring =~ tr/4/R/; $seqstring =~ tr/5/C/; $seqstring =~ tr/6/H/; $seqstring =~ tr/7/I/; $seqstring =~ tr/8/S/; return \$seqstring; # and that's that one } =head2 charge Title : charge Usage : $output = $oddcode_obj->charge(); Function: turns amino acid sequence into 3-letter charge alphabet Example : a sequence ACDEFGH will become NNAANNC : A (negative; NOT anode), C (positive; NOT cathode), N (neutral) Returns : Reference to the new sequence string Args : none =cut sub charge() { my $self = $_[0]; my $seqstring = &_pullseq($self); # now the real business $seqstring =~ tr/[DE]/1/; $seqstring =~ tr/[HKR]/2/; $seqstring =~ tr/[ACFGILMNPQSTVWY]/3/; $seqstring =~ tr/1/A/; $seqstring =~ tr/2/C/; $seqstring =~ tr/3/N/; return \$seqstring; # and that's that one } # _pullseq is called within each of the subroutines # it just checks a few things and returns the sequence sub _pullseq { my $self = $_[0]; my $seqobj = $self->{'_seqref'}; unless ($seqobj->isa("Bio::PrimarySeqI")) { $self->throw("die, OddCodes works only on PrimarySeqI objects\n"); } $self->warn("\tAll OddCode alphabets need a protein sequence,\n". "\tbut BioPerl thinks this is not: [". $seqobj->id. "]") unless $seqobj->alphabet eq 'protein' or $self->verbose < 0;; my $seqstring = uc $seqobj->seq(); if(length($seqstring)<1) { $self->throw("$seqstring: die, sequence has zero length\n"); } return $seqstring; } 1; ������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Primer3.pm���������������������������������������������������������������000555��000766��000024�� 30517�13155576320� 17234� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Primer3 # # Copyright (c) 2003 bioperl, Rob Edwards. All Rights Reserved. # This module is free software; you can redistribute it and/or # modify it under the same terms as Perl itself. # # Copyright Rob Edwards # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Primer3 - Create input for and work with the output from the program primer3 =head1 SYNOPSIS # parse primer3 output to get some data # this is also called from Bio::Tools::Run::Primer3 use Bio::Tools::Primer3; # read a primer3 output file my $p3 = Bio::Tools::Primer3->new(-file=>"data/primer3_output.txt"); # how many results were there? my $num = $p3->number_of_results; print "There were $num results\n"; # get all the results my $all_results = $p3->all_results; print "ALL the results\n"; foreach my $key (keys %{$all_results}) { print "$key\t${$all_results}{$key}\n"; } # get specific results my $result1 = $p3->primer_results(1); print "The first primer is\n"; foreach my $key (keys %{$result1}) { print "$key\t${$result1}{$key}\n"; } # get the results as a Bio::Seq::PrimedSeq stream my $primer = $p3->next_primer; print "The left primer in the stream is ", $primer->get_primer('-left_primer')->seq->seq, "\n"; =head1 DESCRIPTION Bio::Tools::Primer3 creates the input files needed to design primers using primer3 and provides mechanisms to access data in the primer3 output files. This module provides a bioperl interface to the program primer3. See http://www-genome.wi.mit.edu/genome_software/other/primer3.html for details and to download the software. This module is based on one written by Chad Matsalla (bioinformatics1@dieselwurks.com) I have ripped some of his code, and added a lot of my own. I hope he is not mad at me! This is probably best run in one of the two following ways: i. To parse the output from Bio::Tools::Run::Primer3. You will most likely just use next_primer to get the results from Bio::Tools::Run::Primer3. ii. To parse the output of primer3 handed to it as a file name. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Rob Edwards redwards@utmem.edu Based heavily on work of Chad Matsalla bioinformatics1@dieselwurks.com =head1 CONTRIBUTORS Brian Osborne bosborne at alum.mit.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Primer3; use strict; use Bio::Seq; use Bio::Seq::PrimedSeq; use Bio::SeqFeature::Primer; use vars qw($AUTOLOAD @PRIMER3_PARAMS %OK_FIELD $ID); BEGIN { @PRIMER3_PARAMS = qw(results seqobject); foreach my $attr (@PRIMER3_PARAMS) {$OK_FIELD{$attr}++} } use base qw(Bio::Root::Root Bio::Root::IO); sub AUTOLOAD { my $self = shift; my $attr = $AUTOLOAD; $attr =~ s/.*:://; $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr}; $self->{$attr} = shift if @_; return $self->{$attr}; } =head2 new Title : new() Usage : my $primer3 = Bio::Tools::Primer3->new(-file=>$file); Function: Parse primer3 output Returns : Does not return anything. If called with a filename will allow you to retrieve the results Args : -file (optional) file of primer3 results to parse -verbose (optional) set verbose output Notes : =cut sub new { my($class,%args) = @_; my $self = $class->SUPER::new(%args); if ($args{'-file'}) { $self->_readfile($args{'-file'}); } if ($args{'-verbose'}) { $self->{'verbose'} = 1; } return $self; } =head2 number_of_results Title : number_of_results() Usage : my $count = $primer3->number_of_results(); Function: Retrieve the number of primers returned from Primer3. Returns : A scalar Args : None Notes : This returns the count of the primers returned by Primer3 (aka how many of them there are). This is one more than the maximum offset into the zero based list of primers that is accessed by primer_results(). =cut sub number_of_results { my $self = shift; return $self->{'maximum_primers_returned'} + 1; } =head2 all_results Title : all_results() Usage : my $results = $primer3->all_results(); or my $results = $primer3->all_results('primer3 result name', 'other results'); Function: Retrieve the results returned from Primer3. Returns : A reference to a hash Args : Optional array of specific results to retrieve =cut sub all_results { my ($self, @results) = @_; my %hash; if (@results) { # we only want a few things foreach my $result (@results) { $hash{$result} = $self->{'results'}->$result; } } else { foreach my $result (keys %{$self->{'results'}}) { $hash{$result}=$self->{'results'}->{$result}; } } return \%hash; } =head2 primer_results Title : primer_results() Usage : my $results = $primer3->primer_results(2); # results for third primer Function: Retrieve the results returned from Primer3 for specific primer pairs. Returns : A reference to a hash Args : A number between 0 and the maximum number of primers to retrieve =cut sub primer_results { my ($self, $toget) = @_; if ($toget > $self->{'maximum_primers_returned'}) { $self->warn("Didn't get any results for $toget"); return 0; } else { return \%{$self->{'results_by_number'}->{$toget}}; } } =head2 _readfile Title : _readfile() Usage : $self->_readfile(); Function: An internal function that reads a file and sets up the results Returns : Nothing. Args : None Notes : =cut sub _readfile { my ($self, $file) = @_; $self->_initialize_io(-file=>$file); my $line; my $id='primer 3 parsed results'; # hopefully we'll get this, but we can set a temp id in case not. while (defined($line = $self->_readline()) ) { chomp $line; next unless ($line); my ($return, $value) = split /=/, $line; if (uc($return) eq "SEQUENCE") { $self->{seqobject} = Bio::Seq->new(-seq=>$value, $id=>$id); next; } if (uc($return) eq "PRIMER_SEQUENCE_ID") { if ($self->{seqobject}) {$self->{seqobject}->id($value)} else {$id=$value} } $self->{'results'}->{$return} = $value; } # convert the results to individual results $self->_separate(); } =head2 next_primer Title : next_primer() Usage : while (my $primed_seq = $primer3->next_primer()) { Function: Retrieve the primed sequence and a primer pair, one at a time Returns : Returns a Bio::Seq::PrimedSeq object, one at a time Args : None Notes : Use $primed_seq->annotated_seq to get an annotated sequence object you can write out. =cut sub next_primer { my $self = shift; # here we are going to convert the primers to Bio::SeqFeature::Primer objects # and the primer/sequence to Bio::Seq::PrimedSeq objects # the problem at the moment is that PrimedSeq can only take one sequence/primer pair, and # yet for each sequence we can have lots of primer pairs. We need a way to overcome this. # at the moment we can do this as a stream, I guess. $self->warn("No primers were found for: ".$self->{'seqobject'}->{'primary_id'}) if (! $self->number_of_results); $self->{'next_to_return'} = 0 unless ($self->{'next_to_return'}); return if ($self->{'next_to_return'} >= $self->number_of_results); my $results = $self->primer_results($self->{'next_to_return'}); $self->throw("No left primer sequence") unless (${$results}{'PRIMER_LEFT_SEQUENCE'}); $self->throw("No right primer sequence") unless (${$results}{'PRIMER_RIGHT_SEQUENCE'}); $self->throw("No target sequence") unless ($self->{'seqobject'}); my $left_seq = Bio::SeqFeature::Primer->new( -id => 'left_primer', -seq => ${$results}{'PRIMER_LEFT_SEQUENCE'}, -display_id => ($self->{'next_to_return'} + 1), ); my $right_seq = Bio::SeqFeature::Primer->new( -id => "right_primer", -seq => ${$results}{'PRIMER_RIGHT_SEQUENCE'}, -display_id => ($self->{'next_to_return'} + 1) ); # add data to the Primer objects for my $key (%$results) { # skip the primer sequence data, already added above next if ($key =~ /PRIMER_(LEFT|RIGHT)_SEQUENCE/i ); if ($key =~ /PRIMER_LEFT/i) { $left_seq->add_tag_value($key, $$results{$key}); } elsif ($key =~ /PRIMER_RIGHT/i) { $right_seq->add_tag_value($key, $$results{$key}); } } my $primed_seq = Bio::Seq::PrimedSeq->new( -target_sequence => $self->{'seqobject'}->clone, -left_primer => $left_seq, -right_primer => $right_seq, ); # add data to the the PrimedSeq object that's not specific to the Primers for my $key (%$results) { next if ($key =~ /PRIMER_(LEFT|RIGHT)/i ); $primed_seq->add_tag_value($key, $$results{$key}); } $self->{'next_to_return'}++; return $primed_seq; } =head2 primer_stream Title : primer_stream() Usage : while (my $primed_seq = $primer3->primer_stream()) { Function: Retrieve the primer/sequences one at a time Returns : Returns a Bio::Seq::PrimedSeq object, one at a time Args : None Notes : Deprecated, just a link to next_primer =cut sub primer_stream { my $self = shift; my $primedseq = $self->next_primer; return $primedseq; } =head2 _separate Title : _separate() Usage : $self->_separate(); Function: An internal function that groups the results by number (e.g. primer pair 1, etc) Returns : Nothing. Args : None Notes : =cut sub _separate { my $self = shift; my %results; # the results that we find my $maxlocation = -1; # the maximum number of primers returned foreach my $key (keys %{$self->{'results'}}) { next if (${$self->{'input_options'}}{$key}); # don't process it if it is an input key my $location; # the number of the primer pair # names will have values like # PRIMER_RIGHT_SEQUENCE, PRIMER_RIGHT_2_SEQUENCE, PRIMER_PRODUCT_SIZE, and # PRIMER_PRODUCT_SIZE_3 hence we need to find and remove the number my $tempkey = $key; if ($tempkey =~ s/_(\d+)//) { $location = $1; if ($location > $maxlocation) {$maxlocation = $location} } elsif ( $tempkey =~ /PRIMER_(RIGHT|LEFT)_SEQUENCE/ ) { # first primers reported without a number, therefore set $location to 0 $location = 0; if ($location > $maxlocation) {$maxlocation = $location} } else { $location = 0; } # we will hash the results by number, and then by name ${$results{$location}}{$tempkey}=${$self->{'results'}}{$key}; } $self->{'results_by_number'} = \%results; $self->{'maximum_primers_returned'} = $maxlocation; } =head2 _set_variable Title : _set_variable() Usage : $self->_set_variable('variable name', 'value'); Function: An internal function that sets a variable Returns : Nothing. Args : None Notes : Used to set $self->{results} and $self->seqobject =cut sub _set_variable { my ($self, $name, $value) = @_; next unless ($name); $self->{$name} = $value; } 1; __END__ ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Prints.pm����������������������������������������������������������������000555��000766��000024�� 13650�13155576320� 17171� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Prints # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Balamurugan Kumarasamy # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code # =head1 NAME Bio::Tools::Prints - Parser for FingerPRINTScanII program =head1 SYNOPSIS use Bio::Tools::Prints; my $prints_parser = Bio::Tools::Prints->new(-fh =>$filehandle ); while( my $prints_feat = $prints_parser->next_result ) { push @prints_feat, $prints_feat; } =head1 DESCRIPTION PRINTScan II is a PRINTS fingerprint identification algorithm. Copyright (C) 1998,1999 Phil Scordis =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Balamurugan Kumarasamy bala@tll.org.sg juguang@tll.org.sg =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Prints; use strict; use Bio::SeqFeature::FeaturePair; use Bio::SeqFeature::Generic; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::Prints->new(-fh=>$filehandle); Function: Builds a new Bio::Tools::Prints object Returns : Bio::Tools::Prints Args : -filename -fh (filehandle) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_result Title : next_result Usage : my $feat = $prints_parser->next_result Function: Get the next result set from parser data Returns : L<Bio::SeqFeature::Generic> Args : none =cut sub next_result { my ($self) = @_; my %printsac; my @features; my $line; my $sequenceId; while ($_=$self->_readline()) { $line = $_; chomp $line; if ($line =~ s/^Sn;//) { # We have identified a Sn; line so there should be the following: ($sequenceId) = $line =~ /^\s*(\w+)/; $self->seqname($sequenceId); next; } if ($line =~ s/^1TBH//) { my ($id) = $line =~ /^\s*(\w+)/; my ($ac) = $line =~ /(PR\w+)\s*$/; $printsac{$id} = $ac; $self->print_sac(\%printsac); next; } if ($line =~ s/^3TB//) { if ($line =~ s/^[HN]//) { my($num)=""; $line =~ s/^\s+//; my @elements = split /\s+/, $line; my ($fingerprintName,$motifNumber,$temp,$tot,$percentageIdentity,$profileScore,$pvalue,$subsequence,$motifLength,$lowestMotifPosition,$matchPosition,$highestMotifPosition) = @elements; my $start = $matchPosition; my $end = $matchPosition + $motifLength - 1; my $print_sac = $self->print_sac; my %printsac = %{$print_sac}; my $print = $printsac{$fingerprintName}; my $seqname=$self->seqname; my $feat = "$print,$start,$end,$percentageIdentity,$profileScore,$pvalue"; my $new_feat = $self->create_feature($feat,$seqname); return $new_feat; } if ($line =~ s/^F//) { return; } next; } next; } } =head2 create_feature Title : create_feature Usage : my $feat=$prints_parser->create_feature($feature,$seqname) Function: creates a SeqFeature Generic object Returns : L<Bio::SeqFeature::FeaturePair> Args : =cut sub create_feature { my ($self, $feat,$sequenceId) = @_; my @f = split (/,/,$feat); # create feature object my $feature= Bio::SeqFeature::Generic->new( -seq_id =>$sequenceId, -start=>$f[1], -end => $f[2], -score => $f[4], -source => "PRINTS", -primary =>$f[0], -logic_name => "PRINTS", ); $feature->add_tag_value('evalue',$f[5]); $feature->add_tag_value('percent_id',$f[3]); my $feature2 = Bio::SeqFeature::Generic->new( -seq_id => $f[0], -start => 0, -end => 0, ); my $fp = Bio::SeqFeature::FeaturePair->new( -feature1 => $feature, -feature2 => $feature2 ); return $fp; } =head2 print_sac Title : print_sac Usage : $prints_parser->print_sac($print_sac) Function: get/set for print_sac Returns : Args : =cut sub print_sac { my $self = shift; return $self->{'print_sac'} = shift if @_; return $self->{'print_sac'}; } =head2 seqname Title : seqname Usage : $prints_parser->seqname($seqname) Function: get/set for seqname Returns : Args : =cut sub seqname { my($self,$seqname)=@_; return $self->{'seqname'}=$seqname if(defined($seqname)); return $self->{'seqname'}; } 1; ����������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Profile.pm���������������������������������������������������������������000444��000766��000024�� 10727�13155576320� 17311� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Tools::Profile # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Balamurugan Kumarasamy # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Profile - parse Profile output =head1 SYNOPSIS use Bio::Tools::Profile; my $profile_parser = Bio::Tools::Profile->new(-fh =>$filehandle ); while( my $profile_feat = $profile_parser->next_result ) { push @profile_feat, $profile_feat; } =head1 DESCRIPTION Parser for Profile output =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Balamurugan Kumarasamy Email: fugui@worf.fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Profile; use strict; use Bio::SeqFeature::FeaturePair; use Bio::SeqFeature::Generic; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::Profile->new(); Function: Builds a new Bio::Tools::Profile object Returns : Bio::Tools::Profile Args : -filename -fh ($filehandle) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_result Title : next_result Usage : my $feat = $profile_parser->next_result Function: Get the next result set from parser data Returns : L<Bio::SeqFeature::FeaturePair> Args : none =cut sub next_result { my ($self) = @_; my %printsac; my $line; my @features; while ($_=$self->_readline()) { $line = $_; chomp $line; my ($nscore,$rawscore,$from,$to,$hfrom,$hto,$ac) = $line =~ /(\S+)\s+(\d+)\s*pos.\s+(\d*)\s*-\s+(\d*)\s*\[\s+(\d*),\s+(\S*)\]\s*(\w+)/; #for example in this output line #38.435 2559 pos. 19958 - 20212 [ 1, -1] PS50011|PROTEIN_KINASE_DOM Protein kinase domain profile. #$nscore = 38.435 #$rawscore = 2559 #$from = 19958 #$end = 20212 #$hfrom = 1 #$hto =-1 #$ac = PS50011 my $feat = "$ac,$from,$to,$hfrom,$hto,$nscore"; my $new_feat= $self->create_feature($feat); return $new_feat } } =head2 create_feature Title : create_feature Usage : my $feat= $profile_parser->create_feature($feature) Function: creates a Bio::SeqFeature::FeaturePair object Returns : L<Bio::SeqFeature::FeaturePair> Args : =cut sub create_feature { my ($self, $feat) = @_; my @f = split (/,/,$feat); my $hto = $f[4]; if ($f[4] =~ /-1/) { $hto = $f[2] - $f[1] + 1; } my $feat1 = Bio::SeqFeature::Generic->new( -start => $f[1], -end => $f[2], -score => $f[5], -source=>'pfscan', -primary=>$f[0]); my $feat2 = Bio::SeqFeature::Generic->new(-start => $f[3], -end => $hto, ); my $feature = Bio::SeqFeature::FeaturePair->new(-feature1 => $feat1, -feature2 => $feat2); return $feature; } 1; �����������������������������������������BioPerl-1.007002/Bio/Tools/Promoterwise.pm����������������������������������������������������������000444��000766��000024�� 16103�13155576320� 20402� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Tools::Promoterwise # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Shawn Hoon <shawnh@fugu-sg.org> # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Promoterwise - parser for Promoterwise tab format output =head1 SYNOPSIS use Bio::Tools::Promoterwise; my $pw = Bio::Tools::Promoterwise->new(-file=>"out", -query1_seq=>$seq1, -query2_seq=>$seq2); while (my $fp = $pw->next_result){ print "Hit Length: ".$fp->feature1->length."\n"; print "Hit Start: ".$fp->feature1->start."\n"; print "Hit End: ".$fp->feature1->end."\n"; print "Hsps: \n"; my @first_hsp = $fp->feature1->sub_SeqFeature; my @second_hsp = $fp->feature2->sub_SeqFeature; foreach my $i (0..$#first_hsp){ print $first_hsp[$i]->start. " ".$first_hsp[$i]->end." ". $second_hsp[$i]->start. " ".$second_hsp[$i]->end."\n"; } } =head1 DESCRIPTION Promoteriwise is an alignment algorithm that relaxes the constraint that local alignments have to be co-linear. Otherwise it provides a similar model to DBA, which is designed for promoter sequence alignments. Promoterwise is written by Ewan Birney. It is part of the wise2 package available at L<ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/> This module is the parser for the Promoterwise output in tab format. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Promoterwise; use strict; use Bio::SeqFeature::FeaturePair; use Bio::SeqFeature::Generic; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::Promoterwise->new(); Function: Builds a new Bio::Tools::Promoterwise object Returns : L<Bio::Tools::Promoterwise> Args : -fh/-file => $val, # for initing input, see Bio::Root::IO =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); my ($query1,$query2) = $self->_rearrange([qw(QUERY1_SEQ QUERY2_SEQ)],@args); $self->query1_seq($query1) if ($query1); $self->query2_seq($query2) if ($query2); return $self; } =head2 next_result Title : next_result Usage : my $r = $rpt_masker->next_result Function: Get the next result set from parser data Returns : an L<Bio::SeqFeature::FeaturePair> Args : none =cut sub next_result { my ($self) = @_; $self->_parse unless $self->_parsed; return $self->_next_result; } sub _parse{ my ($self) = @_; my (%hash,@fp); while (defined($_ = $self->_readline()) ) { chomp; my @array = split; push @{$hash{$array[-1]}}, \@array; } foreach my $key(keys %hash){ my $sf1 = Bio::SeqFeature::Generic->new(-primary=>"conserved_element", -source_tag=>"promoterwise"); $sf1->attach_seq($self->query1_seq) if $self->query1_seq; my $sf2 = Bio::SeqFeature::Generic->new(-primary=>"conserved_element", -source_tag=>"promoterwise"); $sf2->attach_seq($self->query2_seq) if $self->query2_seq; foreach my $info(@{$hash{$key}}){ my ($score,$id1,$start_1,$end_1, $strand_1,$s1_len, $id2,$start_2,$end_2,$strand_2,$s2_len, $group); if( @{$info} == 12 ) { ($score,$id1,$start_1,$end_1, $strand_1,$s1_len, $id2,$start_2,$end_2,$strand_2,$s2_len, $group) = @{$info}; } elsif( @{$info} == 10 ) { ($score,$id1,$start_1,$end_1, $strand_1, $id2,$start_2,$end_2,$s2_len, $group) = @{$info}; } else { $self->throw("unknown promoterwise output, ", scalar @{$info}, " columns, expected 10 or 12\n"); } if(!$sf1->strand && !$sf2->strand){ $sf1->strand($strand_1); $sf2->strand($strand_2); $sf1->seq_id($id1); $sf2->seq_id($id2); $sf1->score($score); $sf2->score($score); } my $sub1 = Bio::SeqFeature::Generic->new(-start=>$start_1, -seq_id=>$id1, -end =>$end_1, -strand=>$strand_1, -primary=>"conserved_element", -source_tag=>"promoterwise", -score=>$score); $sub1->attach_seq($self->query1_seq) if $self->query1_seq; my $sub2 = Bio::SeqFeature::Generic->new(-start=>$start_2, -seq_id=>$id2, -end =>$end_2, -strand=>$strand_2, -primary=>"conserved_element", -source_tag=>"promoterwise", -score=>$score); $sub2->attach_seq($self->query2_seq) if $self->query2_seq; $sf1->add_SeqFeature($sub1,'EXPAND'); $sf2->add_SeqFeature($sub2,'EXPAND'); } my $fp = Bio::SeqFeature::FeaturePair->new(-feature1=>$sf1, -feature2=>$sf2); push @fp, $fp; } $self->_feature_pairs(\@fp); $self->_parsed(1); return; } sub _feature_pairs { my ($self,$fp) = @_; if($fp){ $self->{'_feature_pairs'} = $fp; } return $self->{'_feature_pairs'}; } sub _next_result { my ($self) = @_; return unless (exists($self->{'_feature_pairs'}) && @{$self->{'_feature_pairs'}}); return shift(@{$self->{'_feature_pairs'}}); } sub _parsed { my ($self,$flag) = @_; if($flag){ $self->{'_flag'} = 1; } return $self->{'_flag'}; } sub query1_seq { my ($self,$val) = @_; if($val){ $self->{'query1_seq'} = $val; } return $self->{'query1_seq'}; } sub query2_seq { my ($self,$val) = @_; if($val){ $self->{'query2_seq'} = $val; } return $self->{'query2_seq'}; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/PrositeScan.pm�����������������������������������������������������������000444��000766��000024�� 11330�13155576320� 20132� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������� =head1 NAME Bio::Tools::PrositeScan - Parser for ps_scan result =head1 SYNOPSIS use Bio::Tools::PrositeScan; my $factory = Bio::Tools::PrositeScan->new( -file => 'out.PrositeScan', -format => 'fasta' ); while(my $match = $factory->next_prediction){ # $match is a Bio::SeqFeature::FeaturePair # Sequence ID my $seq_id = $match->seq_id; # PROSITE accession number my $psac = $match->hseq_id; # Coordinates my @coords = ( $match->start, $match->end ); # Subsequence my $seq = $match->feature1->seq; } =head1 DESCRIPTION This is a parser of the output of the ps_scan program. It takes either a file handle or a file name, and returns a L<Bio::SeqFeature::FeaturePair> object. Note that the current implementation parses the entire file at once. =head1 AUTHOR Juguang Xiao, juguang@tll.org.sg =head1 SEE ALSO =over =item * L<ps_scan software|ftp://ftp.expasy.org/databases/prosite/ps_scan> =item * L<PROSITE User Manual|http://prosite.expasy.org/prosuser.html> =back =cut # Let the code begin... package Bio::Tools::PrositeScan; use vars qw(@FORMATS); use strict; use Bio::Seq; use Bio::SeqFeature::Generic; use Bio::SeqFeature::FeaturePair; use base qw(Bio::Root::Root Bio::Root::IO); @FORMATS = qw(SCAN FASTA PSA MSA PFF MATCHLIST); =head2 new Title : new Usage : Bio::Tools::PrositeScan->new(-file => 'out.PrositeScan'); Bio::Tools::PrositeScan->new(-fh => \*FH); Returns : L<Bio::Tools::PrositeScan> Args : -format => string representing the format type for the ps_scan output, REQUIRED The C<-format> argument must currently be set to C<fasta> since this is the only parser implemented. This corresponds with using the ps_scan arguments C<-o fasta>. =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); my ($format) = $self->_rearrange([qw(FORMAT)], @args); $format || $self->throw("format needed"); if(grep /^$format$/i, @FORMATS){ $self->format($format); }else{ $self->throw("Invalid format, [$format]"); } return $self; } sub format { my $self = shift; return $self->{_format} = shift if(@_); return $self->{_format}; } =head2 next_prediction Title : new Usage : while($result = $factory->next_prediction){ ; } Returns : a Bio::SeqFeature::FeaturePair object where feature1 is the matched subsequence and feature2 is the PROSITE accession number. See <http://prosite.expasy.org/prosuser.html#conv_ac>. =cut sub next_prediction { my ($self) = @_; unless($self->_parsed){ $self->_parse; $self->_parsed(1); } return shift @{$self->{_matches}}; } sub next_result { return shift->next_prediction; } sub _parsed { my $self = shift; return $self->{_parsed} = 1 if @_ && $_[0]; return $self->{_parsed}; } sub _parse { my $self = shift; my $format = $self->format; if($self->format =~ /^fasta$/){ $self->_parse_fasta; }else{ $self->throw("the [$format] parser has not been written"); } } sub _parse_fasta { my ($self) = @_; my @matches; my $fp; my $seq; while(defined($_ = $self->_readline)){ chop; if(/^\>([^>]+)/){ my $fasta_head = $1; if($fasta_head =~ /([^\/]+)\/(\d+)\-(\d+)(\s+)\:(\s+)(\S+)/){ my $q_id = $1; my $q_start = $2; my $q_end = $3; my $h_id = $6; if(defined $fp){ $self->_attach_seq($seq, $fp); push @matches, $fp; } $fp = Bio::SeqFeature::FeaturePair->new( -feature1 => Bio::SeqFeature::Generic->new( -seq_id => $q_id, -start => $q_start, -end => $q_end ), -feature2 => Bio::SeqFeature::Generic->new( -seq_id => $h_id, -start => 0, -end => 0 ) ); $seq = ''; }else{ $self->throw("ERR:\t\[$_\]"); } }else{ # sequence lines, ignored $seq .= $_; } } if(defined $fp){ $self->_attach_seq($seq, $fp); push @matches, $fp; } push @{$self->{_matches}}, @matches; } sub _attach_seq { my ($self, $seq, $fp) = @_; if(defined $fp){ my $whole_seq = 'X' x ($fp->start-1); $whole_seq .= $seq; $fp->feature1->attach_seq( Bio::Seq->new(-seq => $whole_seq) ); } } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Protparam.pm�������������������������������������������������������������000444��000766��000024�� 25354�13155576320� 17660� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Protparam # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Richard Dobson, r.j.dobson at qmul dot ac dot uk # # Copyright Richard Dobson # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Protparam - submit to and parse output from protparam ; =head1 SYNOPSIS use Bio::DB::GenBank; use Bio::Tools::Protparam; my $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile' , -format => 'Fasta'); my @ids=qw(O14521 O43709 O43826); my $seqio = $gb->get_Stream_by_acc(\@ids ); while( my $seq = $seqio->next_seq ) { my $pp = Bio::Tools::Protparam->new(seq=>$seq->seq); print "ID : ", $seq->display_id,"\n", "Amino acid number : ",$pp->amino_acid_number(),"\n", "Number of negative amino acids : ",$pp->num_neg(),"\n", "Number of positive amino acids : ",$pp->num_pos(),"\n", "Molecular weight : ",$pp->molecular_weight(),"\n", "Theoretical pI : ",$pp->theoretical_pI(),"\n", "Total number of atoms : ", $pp->total_atoms(),"\n", "Number of carbon atoms : ",$pp->num_carbon(),"\n", "Number of hydrogen atoms : ",$pp->num_hydrogen(),"\n", "Number of nitrogen atoms : ",$pp->num_nitro(),"\n", "Number of oxygen atoms : ",$pp->num_oxygen(),"\n", "Number of sulphur atoms : ",$pp->num_sulphur(),"\n", "Half life : ", $pp->half_life(),"\n", "Instability Index : ", $pp->instability_index(),"\n", "Stability class : ", $pp->stability(),"\n", "Aliphatic_index : ",$pp->aliphatic_index(),"\n", "Gravy : ", $pp->gravy(),"\n", "Composition of A : ", $pp->AA_comp('A'),"\n", "Composition of R : ", $pp->AA_comp('R'),"\n", "Composition of N : ", $pp->AA_comp('N'),"\n", "Composition of D : ", $pp->AA_comp('D'),"\n", "Composition of C : ", $pp->AA_comp('C'),"\n", "Composition of Q : ", $pp->AA_comp('Q'),"\n", "Composition of E : ", $pp->AA_comp('E'),"\n", "Composition of G : ", $pp->AA_comp('G'),"\n", "Composition of H : ", $pp->AA_comp('H'),"\n", "Composition of I : ", $pp->AA_comp('I'),"\n", "Composition of L : ", $pp->AA_comp('L'),"\n", "Composition of K : ", $pp->AA_comp('K'),"\n", "Composition of M : ", $pp->AA_comp('M'),"\n", "Composition of F : ", $pp->AA_comp('F'),"\n", "Composition of P : ", $pp->AA_comp('P'),"\n", "Composition of S : ", $pp->AA_comp('S'),"\n", "Composition of T : ", $pp->AA_comp('T'),"\n", "Composition of W : ", $pp->AA_comp('W'),"\n", "Composition of Y : ", $pp->AA_comp('Y'),"\n", "Composition of V : ", $pp->AA_comp('V'),"\n", "Composition of B : ", $pp->AA_comp('B'),"\n", "Composition of Z : ", $pp->AA_comp('Z'),"\n", "Composition of X : ", $pp->AA_comp('X'),"\n"; } =head1 DESCRIPTION This module takes an amino acid sequence and submits it to the Protparam program at www.expasy.org/cgi-bin/protparam. Many properties of the submitted sequence are returned. =head1 AUTHOR Richard Dobson, r.j.dobson at qmul dot ac dot uk =cut # Let the code begin... package Bio::Tools::Protparam; use strict; use base qw(Bio::Root::Root); use LWP 5.64; =head2 new Title : new Usage : $pp = Protparam->new(seq=>$seq->seq); Function : Creates a new Protparam object Returns : A Protparam object Args : A sequence =cut sub new { my ($class,@args) = @_; @args=('-url'=>'http://web.expasy.org/cgi-bin/protparam/protparam','-form'=>'sequence',@args); my $self=$class->SUPER::new(@args); my ($url,$seq,$form)=$self->_rearrange([qw(URL SEQ FORM)],@args); my $browser = LWP::UserAgent->new; my $response; #send request to PROTPARAM @ Expasy $response = $browser->post($url, [ $form => $seq ], 'User-Agent' => 'Mozilla/4.76 [en] (Win2000; U)', ); #Check if successful $self->throw("$url error: ".$response->status_line) unless $response->is_success; $self->throw("Bad content type at $url ".$response->content_type) unless $response->content_type eq 'text/html'; my $protParamOutput=$response->decoded_content; $self->{'output'}=$protParamOutput; return bless $self,$class; } =head2 num_neg Title : num_neg Usage : $pp->num_neg() Function : Retrieves the number of negative amino acids in a sequence Returns : Returns the number of negative amino acids in a sequence Args : none =cut sub num_neg{ my $self=shift; ($self->{'negAA'})=$self->{'output'}=~/<B>Total number of negatively charged residues.*?<\/B>\s*(\d*)/; return $self->{'negAA'}; } =head2 num_pos Title : num_pos Usage : $pp->num_pos() Function : Retrieves the number of positive amino acids in a sequence Returns : Returns the number of positive amino acids in a sequence Args : none =cut sub num_pos{ my $self=shift; ($self->{'posAA'})=$self->{'output'}=~/<B>Total number of positively charged residues.*?<\/B>\s*(\d*)/; return $self->{'posAA'}; } =head2 amino_acid_number Title : amino_acid_number Usage : $pp->amino_acid_number() Function : Retrieves the number of amino acids within a sequence Returns : Returns the number of amino acids within a sequence Args : none =cut sub amino_acid_number{ my $self=shift; ($self->{'numAA'})=$self->{'output'}=~/<B>Number of amino acids:<\/B> (\d+)/; return $self->{'numAA'}; } =head2 total_atoms Title : total_atoms Usage : $pp->total_atoms() Function : Retrieves the total number of atoms within a sequence Returns : Returns the total number of atoms within a sequence Args : none =cut sub total_atoms{ my $self=shift; $self->{'total_atoms'}=$self->{'output'}=~/<B>Total number of atoms:<\/B>\s*(\d*)/; return $self->{'total_atoms'}; } =head2 molecular_weight Title : molecular_weight Usage : $pp->molecular_weight() Function : Retrieves the molecular weight of a sequence Returns : Returns the molecular weight of a sequence Args : none =cut sub molecular_weight{ my $self=shift; ($self->{'MolWt'})=$self->{'output'}=~/<B>Molecular weight:<\/B> (\d*\.{0,1}\d*)/; return $self->{'MolWt'}; } =head2 theoretical_pI Title : theoretical_pI Usage : $pp->theoretical_pI() Function : Retrieve the theoretical pI for a sequence Returns : Return the theoretical pI for a sequence Args : none =cut sub theoretical_pI{ my $self=shift; ($self->{'TpI'})=$self->{'output'}=~/<B>Theoretical pI:<\/B> (-{0,1}\d*\.{0,1}\d*)/; return $self->{'TpI'}; } =head2 num_carbon Title : num_carbon Usage : $pp->num_carbon() Function : Retrieves the number of carbon atoms in a sequence Returns : Returns the number of carbon atoms in a sequence Args : none =cut sub num_carbon{ my $self=shift; ($self->{'car'}) = $self->{'output'}=~/Carbon\s+C\s+(\d+)/; return $self->{'car'}; } =head2 num_hydrogen Title : num_hydrogen Usage : $pp->num_hydrogen Function : Retrieves the number of hydrogen atoms in a sequence Returns : Returns the number of hydrogen atoms in a sequence Args : none =cut sub num_hydrogen{ my $self=shift; ($self->{'hyd'}) = $self->{'output'}=~/Hydrogen\s+H\s+(\d+)/; return $self->{'hyd'} } =head2 num_nitro Title : num_nitro Usage : $pp->num_nitro Function : Retrieves the number of nitrogen atoms in a sequence Returns : Returns the number of nitrogen atoms in a sequence Args : none =cut sub num_nitro{ my $self=shift; ($self->{'nitro'}) = $self->{'output'}=~/Nitrogen\s+N\s+(\d+)/; return $self->{'nitro'}; } =head2 num_oxygen Title : num_oxygen Usage : $pp->num_oxygen() Function : Retrieves the number of oxygen atoms in a sequence Returns : Returns the number of oxygen atoms in a sequence Args : none =cut sub num_oxygen{ my $self=shift; ($self->{'oxy'}) = $self->{'output'}=~/Oxygen\s+O\s+(\d+)/; return $self->{'oxy'}; } =head2 num_sulphur Title : num_sulphur Usage : $pp->num_sulphur() Function : Retrieves the number of sulphur atoms in a sequence Returns : Returns the number of sulphur atoms in a sequence Args : none =cut sub num_sulphur{ my $self=shift; ($self->{'sul'}) = $self->{'output'}=~/Sulfur\s+S\s+(\d+)/; return $self->{'sul'}; } =head2 half_life Title : half_life Usage : $pp->half_life() Function : Retrieves the half life of a sequence Returns : Returns the half life of a sequence Args : none =cut sub half_life{ my $self=shift; ($self->{'half_life'}) = $self->{'output'}=~/The estimated half-life is.*?(-{0,1}\d*\.{0,1}\d*)\s*hours \(mammalian reticulocytes, in vitro\)/; return $self->{'half_life'}; } =head2 instability_index Title : instability_index Usage : $pp->instability_index() Function : Retrieves the instability index of a sequence Returns : Returns the instability index of a sequence Args : none =cut sub instability_index{ my $self=shift; ($self->{'InstabilityIndex'})=$self->{'output'}=~/The instability index \(II\) is computed to be (-{0,1}\d*\.{0,1}\d*)/; return $self->{'InstabilityIndex'}; } =head2 stability Title : stability Usage : $pp->stability() Function : Calculates whether the sequence is stable or unstable Returns : 'stable' or 'unstable' Args : none =cut sub stability{ my $self=shift; ($self->{'Stability'})=$self->{'output'}=~/This classifies the protein as\s(\w+)\./; return $self->{'Stability'}; } =head2 aliphatic_index Title : aliphatic_index Usage : $pp->aliphatic_index() Function : Retrieves the aliphatic index of the sequence Returns : Returns the aliphatic index of the sequence Args : none =cut sub aliphatic_index{ my $self=shift; ($self->{'AliphaticIndex'})=$self->{'output'}=~/<B>Aliphatic index:<\/B>\s*(-{0,1}\d*\.{0,1}\d*)/; return $self->{'AliphaticIndex'}; } =head2 gravy Title : gravy Usage : $pp->gravy() Function : Retrieves the grand average of hydropathicity (GRAVY) of a sequence Returns : Returns the grand average of hydropathicity (GRAVY) of a sequence Args : none =cut sub gravy{ my $self=shift; ($self->{'GRAVY'})=$self->{'output'}=~/<B>Grand average of hydropathicity \(GRAVY\):<\/B>\s*(-{0,1}\d*\.{0,1}\d*)/; return $self->{'GRAVY'}; } =head2 AA_comp Title : AA_comp Usage : $pp->AA_comp('P') Function : Retrieves the percentage composition of a given amino acid for a sequence Returns : Returns the percentage composition of a given amino acid for a sequence Args : A single letter amino acid code eg A, R, G, P etc =cut sub AA_comp{ my $self=shift; my $aa=shift; $aa=uc($aa); my $AA={qw(A Ala R Arg N Asn D Asp C Cys Q Gln E Glu G Gly H His I Ile L Leu K Lys M Met F Phe P Pro S Ser T Thr W Trp Y Tyr V Val B Asx Z Glx X Xaa)}; ($self->{$aa})= $self->{'output'}=~/$AA->{$aa} \($aa\)\s+\d+\s+(\d+\.\d+)%/; return $self->{$aa}; } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Pseudowise.pm������������������������������������������������������������000444��000766��000024�� 14510�13155576320� 20032� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Tools::Pseudowise # # # Copyright Jason Stajich, Fugu Team # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Pseudowise - Results of one Pseudowise run =head1 SYNOPSIS use Bio::Tools::Pseudowise; my $parser = Bio::Tools::Pseudowise->new(-file=>"pw.out"); while(my $feat = $parser->next_result){ push @feat, $feat; } =head1 DESCRIPTION Pseudowise is a pseudogene prediction program written by Ewan Birney as part of the Wise Package. This module is the parser for the output of the program. http://www.sanger.ac.uk/software/wise2 =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Previous committed by the Fugu Team Re-written by Jason Stajich jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Pseudowise; use strict; use Symbol; use Bio::Root::Root; use Bio::SeqFeature::Generic; use Bio::SeqFeature::Gene::Exon; use Bio::SeqFeature::FeaturePair; use Bio::SeqFeature::Gene::Transcript; use Bio::SeqFeature::Gene::GeneStructure; use base qw(Bio::Tools::AnalysisResult); sub _initialize_state { my ($self,@args) = @_; # first call the inherited method! $self->SUPER::_initialize_state(@args); # our private state variables $self->{'_preds_parsed'} = 0; $self->{'_has_cds'} = 0; # array of pre-parsed predictions $self->{'_preds'} = []; # seq stack $self->{'_seqstack'} = []; } =head2 analysis_method Usage : $pseudowise->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /pseudowise/i. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method && ($method !~ /pseudowise/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head2 next_feature Title : next_feature Usage : $seqfeature = $obj->next_feature(); Function: Returns the next feature available in the analysis result, or undef if there are no more features. Example : Returns : A Bio::SeqFeatureI implementing object, or undef if there are no more features. Args : none See Also L<Bio::SeqFeatureI> =cut sub next_feature { return shift->next_prediction(@_); } =head2 next_prediction Title : next_prediction Usage : while($gene = $pseudowise->next_prediction()) { # do something } Function: Returns the gene of the Pseudowise result file. Call this method repeatedly until FALSE is returned. Example : Returns : a Bio::SeqFeature::Generic Args : none See Also L<Bio::SeqFeature::Generic> =cut sub next_prediction { my ($self) = @_; # if the prediction section hasn't been parsed yet, we do this now $self->_parse_predictions unless $self->_predictions_parsed; # get next gene structure return $self->_prediction(); } =head2 _parse_predictions Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : =cut sub _parse_predictions { my ($self) = @_; my $gene; my @genes; local $/= "\n"; local($_); my %tags; while (defined( $_ = $self->_readline)){ if( /^(Total codons|\S+)\s+:\s+(\S+)/ ) { $tags{$1} = $2; } elsif(m!^//! ) { if( $gene ) { $gene = undef; %tags = (); } } elsif (/Gene\s+(\d+)\s*$/i) { $gene = Bio::SeqFeature::Generic->new ( -primary => 'pseudogene', -source => 'pseudowise', -tag => \%tags); push @genes, $gene; } elsif( /Gene\s+(\d+)\s+(\d+)/i ) { if( $1 < $2 ) { $gene->start($1); $gene->end($2); $gene->strand(1); } else { $gene->start($2); $gene->end($1); $gene->strand(-1); } } elsif (/Exon\s+(\d+)\s+(\d+)\s+phase\s+(\S+)/i) { my ($s,$e,$st) = ($1,$2,1); if( $s > $e) { ($s,$e,$st)=($e,$s,-1); } my $exon = Bio::SeqFeature::Generic->new ( -start => $s, -end => $e, -strand => $st, -primary => 'exon', -source => 'pseudowise', -tag => {'frame' => $3}); $gene->add_sub_SeqFeature($exon); } } $self->_add_prediction(\@genes); $self->_predictions_parsed(1); } =head1 _prediction Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns : =cut sub _prediction { my ($self) = @_; return shift(@{$self->{'_preds'} || []}); } =head2 _add_prediction Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns : =cut sub _add_prediction { my ($self, $gene) = @_; $self->{'_preds'} ||= []; if( ref($gene) =~ /ARRAY/ ) { push(@{$self->{'_preds'}}, @$gene); } else { push(@{$self->{'_preds'}}, $gene); } } =head2 _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE =cut sub _predictions_parsed { my ($self, $val) = @_; $self->{'_preds_parsed'} = $val if $val; if(! exists($self->{'_preds_parsed'})) { $self->{'_preds_parsed'} = 0; } return $self->{'_preds_parsed'}; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/QRNA.pm������������������������������������������������������������������000444��000766��000024�� 27355�13155576320� 16457� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::QRNA # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl-dot-org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::QRNA - A Parser for qrna output =head1 SYNOPSIS use Bio::Tools::QRNA; my $parser = Bio::Tools::QRNA->new(-file => $qrnaoutput); while( my $feature = $parser->next_feature ) { # do something here } =head1 DESCRIPTION Parses QRNA output (E.Rivas: http://selab.janelia.org/software.html ftp://selab.janelia.org/pub/software/qrna/). This module is not complete, but currently it packs information from each QRNA alignment into a single Bio::SeqFeature::Generic object. Not all options for QRNA output have been tested or tried. It has been tested on sliding window output (-w -x) and shuffled output (-b or -B). See t/QRNA.t for example usage. At some point we may have more complicated feature object which will support this data rather than forcing most of the information into tag/value pairs in a SeqFeature::Generic. Running with -verbose =E<gt> 1 will store extra data in the feature. The entire unparsed entry for a particular feature will be stored as a string in the tag 'entry' it is accessible via: my ($entry) = $f->each_tag_value('entry'); The winning model for any given alignment test will be the name stored in the primary_tag field of feature. The bit score will stored in the score field. The logoddpost is available via the a tag/value pair. This example code will show how to print out the score and log odds post for each model. # assuming you got a feature already print "model score logoddspost\n"; foreach my $model ( qw(OTH COD RNA) ) { my ($score) = $f->get_tag_values("$model\_score"); my ($logoddspost) = $f->get_tag_values("$model\_logoddspost"); print "$model $score $logoddspost\n"; } The start and end of the alignment for both the query and hit sequence are available through the L<Bio::SeqFeature::FeaturePair> interface, specifically L<Bio::SeqFeature::FeaturePair::feature1> and L<Bio::SeqFeature::FeaturePair::feature2>. Additionally if you have run QRNA with an input file which has the location of the alignment stored in the FASTA filename as in (ID/START-END) which is the default output format from L<Bio::AlignIO::fasta> produced alignment output, this module will re-number start/end for the two sequences so they are in the actual coordinates of the sequence rather than the relative coordinates of the alignment. You may find the bioperl utillity script search2alnblocks useful in creating your input files for QRNA. Some other words of warning, QRNA uses a 0 based numbering system for sequence locations, Bioperl uses a 1 based system. You'll notice that locations will be +1 they are reported in the raw QRNA output. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::QRNA; use vars qw(@Models); use strict; use Bio::SeqFeature::Generic; use Bio::SeqFeature::FeaturePair; use base qw(Bio::Root::IO Bio::SeqAnalysisParserI); @Models = qw(OTH COD RNA); =head2 new Title : new Usage : my $obj = Bio::Tools::QRNA->new(); Function: Builds a new Bio::Tools::QRNA object Returns : an instance of Bio::Tools::QRNA Args : -fh/-file filehandle/filename standard input for Bio::Root:IO objects =cut =head2 next_feature Title : next_feature Usage : my $feature = $parser->next_feature Function: Get the next QRNA feature Returns : Args : =cut sub next_feature { my ($self) = @_; my $f = shift @{$self->{'_parsed_features'} || []}; if( ! defined $f && $self->_parse_pair ) { $f = shift @{$self->{'_parsed_features'} || []}; } return $f; } sub _parse_pair { my ($self,@args) = @_; my (@features,%data); my $seenstart = 0; while( defined( $_ = $self->_readline) ) { next if( /^\#\-\-/o ); if( /^\#\s+(qrna)\s+(\S+)\s+\(([^\)]+)\)/o ) { $self->program_name($1); $self->program_version($2); $self->program_date($3); } elsif( /^\#\s+(PAM model)\s+\=\s+(.+)\s+$/o ) { $self->PAM_model($2); } elsif( /^\#\s+(RNA model)\s+\=\s+(\S+)/o ) { $self->RNA_model($2); } elsif( /^\#\s+(seq file)\s+\=\s+(.+)\s+$/o ) { $self->seq_file($2); } elsif( /^\#\s+(\d+)\s+\[([\-+])\s+strand\]/o ) { if( $seenstart ) { if( $data{'alignment_len'} ) { push @features, $self->_make_feature(\%data); } $self->_pushback($_); last; } $seenstart = 1; } elsif( /^\#/ ) { next; } elsif( />(\S+)\s+\((\d+)\)/ ) { if( @{$data{'seqs'} || []} == 2 ) { $self->warn( "already seen seqs ".join(' ', ,map { $_->[0] } @{$data{'seqs'}}). "\n"); } else { push @{$data{'seqs'}}, [$1,$2]; } } elsif( /^length alignment:\s+(\d+)\s+\(id\=(\d+(\.\d+)?)\)/o ) { if( $data{'alignment_len'} ) { push @features, $self->_make_feature(\%data); # reset all the data but the 'seqs' field %data = ( 'seqs' => $data{'seqs'} ); } if( /\(((sre_)?shuffled)\)/ ) { $data{'shuffled'} = $1; } $data{'alignment_len'} = $1; $data{'alignment_pid'} = $2; } elsif ( /^pos([XY]):\s+(\d+)\-(\d+)\s+\[(\d+)\-(\d+)\]\((\d+)\)\s+ \-\-\s+\((\S+\s+\S+\s+\S+\s+\S+)\)/ox ) { $data{"seq\_$1"}->{'aln'} = [ $2,$3, $4,$5, $6]; @{$data{"seq\_$1"}->{'base_comp'}} = split(/\s+/,$7); } elsif( /^winner\s+\=\s+(\S{3})/ ) { $data{'winning_model'} = $1; } elsif( /^(\S{3})\s+ends\s+\=\s+(\-?\d+)\s+(\-?\d+)/ ) { # QRNA is 0-based # Bioperl is 1 based $data{'model_location'}->{$1} = [ $2,$3 ]; } elsif( /^\s+(logoddspost)?OTH\s+\=\s+/ox ) { while( /(\S+)\s+\=\s+(\-?\d+(\.\d+))/g ) { my ($model,$score)= ($1,$2); if( $model =~ s/^logoddspost// ) { $data{'model_scores'}->{'logoddspost'}->{$model} = $score; } else { $data{'model_scores'}->{'bits'}->{$model} = $score; } } } $data{'entry'} .= $_; } if( @features ) { push @{$self->{'_parsed_features'}}, @features; return scalar @features; } return 0; } =head2 PAM_model Title : PAM_model Usage : $obj->PAM_model($newval) Function: Example : Returns : value of PAM_model (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub PAM_model{ my $self = shift; return $self->{'PAM_model'} = shift if @_; return $self->{'PAM_model'}; } =head2 RNA_model Title : RNA_model Usage : $obj->RNA_model($newval) Function: Example : Returns : value of RNA_model (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub RNA_model{ my $self = shift; return $self->{'RNA_model'} = shift if @_; return $self->{'RNA_model'}; } =head2 seq_file Title : seq_file Usage : $obj->seq_file($newval) Function: Example : Returns : value of seq_file (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub seq_file{ my $self = shift; return $self->{'seq_file'} = shift if @_; return $self->{'seq_file'}; } =head2 program_name Title : program_name Usage : $obj->program_name($newval) Function: Example : Returns : value of program_name (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub program_name{ my $self = shift; return $self->{'program_name'} = shift if @_; return $self->{'program_name'} || 'qrna'; } =head2 program_version Title : program_version Usage : $obj->program_version($newval) Function: Example : Returns : value of program_version (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub program_version{ my $self = shift; return $self->{'program_version'} = shift if @_; return $self->{'program_version'}; } =head2 program_date Title : program_date Usage : $obj->program_date($newval) Function: Example : Returns : value of program_date (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub program_date{ my $self = shift; return $self->{'program_date'} = shift if @_; return $self->{'program_date'}; } sub _make_feature { my ($self,$data) = @_; my ($qoffset,$hoffset) = (1,1); # when you run qrna and have produced ID/START-END # formatted input strings we can remap the location # to the original # name is stored as the first entry in the seq array ref my ($qid,$hid) = ( $data->{'seqs'}->[0]->[0], $data->{'seqs'}->[1]->[0]); if( $qid =~ /(\S+)\/(\d+)\-(\d+)/ ) { ($qid,$qoffset) = ($1,$2); } if( $hid =~ /(\S+)\/(\d+)\-(\d+)/ ) { ($hid,$hoffset) = ($1,$2); } my $f = Bio::SeqFeature::FeaturePair->new(); my ($s,$e) = @{$data->{'model_location'}->{$data->{'winning_model'}}}; my $qf = Bio::SeqFeature::Generic->new ( -primary_tag => $data->{'winning_model'}, -source_tag => $self->program_name, -score => $data->{'model_scores'}->{'bits'}->{$data->{'winning_model'}}, -start => $s+$qoffset, -end => $e+$qoffset, -seq_id => $qid, -strand => ($s < $e ) ? 1 : -1, ); my $hf = Bio::SeqFeature::Generic->new ( -primary_tag => $qf->primary_tag, -source_tag => $qf->source_tag, -score => $qf->score, -seq_id => $hid, -start => $s + $hoffset, -end => $e + $hoffset, -strand => $qf->strand, ); $f->feature1($qf); $f->feature2($hf); $f->add_tag_value('alignment_len', $data->{'alignment_len'}); $f->add_tag_value('alignment_pid', $data->{'alignment_pid'}); # store the other model scores and data foreach my $model ( @Models ) { $f->add_tag_value("$model\_score", $data->{'model_scores'}->{'bits'}->{$model}); $f->add_tag_value("$model\_logoddspost", $data->{'model_scores'}->{'logoddspost'}->{$model}); if( ! $data->{'model_location'}->{$model} ) { if( $self->verbose > 0 ) { $self->debug( $data->{'entry'} ); } $self->throw("no location parsed for $model in ", (map { @$_ } @{$data->{'seqs'}}), " ", $f->start, " ", $f->end); } else { $f->add_tag_value("$model\_positions", join("..",@{$data->{'model_location'}->{$model} })); } } # probably a better way to store this - as # a seq object perhaps $f->add_tag_value('seq1', @{$data->{'seqs'}->[0]}); $f->add_tag_value('seq2', @{$data->{'seqs'}->[1]}); $f->add_tag_value('entry', $data->{'entry'}) if $self->verbose > 0; if( $data->{'shuffled'} ) { $f->add_tag_value('shuffled', $data->{'shuffled'}); } return $f; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/RandomDistFunctions.pm���������������������������������������������������000444��000766��000024�� 13261�13155576320� 21642� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::RandomDistFunctions # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::RandomDistFunctions - A set of routines useful for generating random data in different distributions =head1 SYNOPSIS use Bio::Tools::RandomDistFunctions; my $dist = Bio::Tools::RandomDistFunctions->new(); for my $v ( 1..1000 ) { my $birth_dist = $dist->rand_birth_distribution($lambda); # ... do something with the variable } =head1 DESCRIPTION Most of the code is based on the C implementation of these routines in Mike Sanderson's r8s's package. See http://loco.biosci.arizona.edu/r8s/ for information on his software. =for comment This code tries to be fast and use available faster BigInt and GMP library methods when those modules are available. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Thanks to Mike Sanderson for assistance in the getting this implementation together. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::RandomDistFunctions; require Exporter; use vars qw(%LOADED @EXPORT_OK); use strict; #use Math::BigFloat lib => 'GMP,Bit::Vector'; #use Math::BigInt lib => 'GMP,Bit::Vector'; use POSIX; use base qw(Bio::Root::Root); =head2 birth_distribution Title : rand_birth_distribution Usage : my $randvar = $dist-> rand_birth_distribution($lambda); Function: Returns a random number from a birth process waiting time with a fixed interval 1.0. Times are measured from 0=present,1=root; Returns : floating point number Args : $lambda ( > 0 ) References : This is based on code by Mike Sanders in r8s. Ross, Stochastic Processes, p. 145 for the density =cut sub rand_birth_distribution{ my ($self,$lambda) = @_; if( ! ref($self) && $self !~ /RandomDistFunctions/ ) { $lambda = $self; } unless( $lambda ) { $self->throw("Cannot call birth_distribution without a valid lambda value (>0)"); } return 1 - (log(rand(1) * (exp($lambda) - 1)+1)/ $lambda); } =head2 rand_geometric_distribution Title : rand_geometric_distribution Usage : my $randvar = $dist->rand_geometric_distribution($param); Function: Returns a random geometric variate distributed with parameter $param, according to c.d.f. 1 - ( 1- param) ^ n Returns : integer Args : $param ( 0 > $param < 1 ) =cut sub rand_geometric_distribution{ my ($self,$param) = @_; if( ! ref($self) && $self !~ /RandomDistFunctions/ ) { $param = $self; } unless( $param ) { $self->throw("Cannot call rand_geometric_distribution without a valid param value (>0)"); } my $den; if( $param < 1e-8) { $den = (-1 * $param) - ( $param * $param ) / 2; } else { $den = log(1 - $param); } my $z = log(1 - rand(1)) / $den; return POSIX::floor($z) + 1; # MSanderson comments from r8s code # Is this the right truncation of the real-valued expression above? # YES # Checked by reference to the expected mean of the distribution in # 100,000 replicates # EX = 1/param Var = (1-param)/param^2 See Olkin, Gleser, and # Derman, p. 193ff. Probability Models and Applications, 1980. } =head2 rand_exponentional_distribution Title : rand_exponentional_distribution Usage : my $var = $dist->rand_exponentional_distribution($param); Function: Returns a random exponential variate distributed with parameter $param, according to c.d.f 1 - e^(-param * x) Returns : floating point number Args : $param ( > 0 ) =cut sub rand_exponentional_distribution { my ($self,$param) = @_; if( ! ref($self) && $self !~ /RandomDistFunctions/ ) { $param = $self; } unless( $param ) { $self->throw("Cannot call rand_exponentional_distribution without a valid param value (>0)"); } return log( 1- rand(1)) / $param; } =head2 rand_normal_distribution Title : rand_normal_distribution Usage : my $var = $dist->rand_normal_distribution() Function: Returns a random normal (gaussian) variate distributed Returns : floating point number Args : none =cut sub rand_normal_distribution{ my $gset; my ($rsq,$v1,$v2) = ( 0,0,0); do { $v1 = 2 * rand(1) - 1; $v2 = 2 * rand(1) - 1; $rsq= $v1**2 + $v2 ** 2; } while( $rsq >= 1 || $rsq == 0); my $fac = sqrt(-2.0 * log($rsq) / $rsq ); $gset = $v1 * $fac; return $v2 * $fac; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/RepeatMasker.pm����������������������������������������������������������000444��000766��000024�� 10121�13155576320� 20260� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::RepeatMasker # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Shawn Hoon <shawnh@fugu-sg.org> # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::RepeatMasker - a parser for RepeatMasker output =head1 SYNOPSIS use Bio::Tools::RepeatMasker; my $parser = Bio::Tools::RepeatMasker->new(-file => 'seq.fa.out'); while( my $result = $parser->next_result ) { # get some value } =head1 DESCRIPTION A parser for RepeatMasker output =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::RepeatMasker; use strict; use Bio::SeqFeature::FeaturePair; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::RepeatMasker->new(); Function: Builds a new Bio::Tools::RepeatMasker object Returns : Bio::Tools::RepeatMasker Args : -fh/-file => $val, for initing input, see Bio::Root::IO =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_result Title : next_result Usage : my $r = $rpt_masker->next_result Function: Get the next result set from parser data Returns : Bio::SeqFeature::FeaturePair Feature1 is the Query coordinates and Feature2 is the Hit Args : none =cut sub next_result { my ($self) = @_; local $_; while (defined($_=$self->_readline()) ) { if (/no repetitive sequences detected/) { $self->warn( "RepeatMasker didn't find any repetitive sequences\n"); return ; } #ignore introductory lines if (/\d+/) { my @element = split; # ignore features with negatives next if ($element[11-13] =~ /-/); my (%feat1, %feat2); my @line = split; my ($score, $query_name, $query_start, $query_end, $strand, $repeat_name, $repeat_class ) = @line[0, 4, 5, 6, 8, 9, 10]; my ($hit_start,$hit_end); if ($strand eq '+') { ($hit_start, $hit_end) = @line[11, 12]; $strand = 1; } elsif ($strand eq 'C') { ($hit_end, $hit_start) = @line[12, 13]; $strand = -1; } my $rf = Bio::SeqFeature::Generic->new (-seq_id => $query_name, -score => $score, -start => $query_start, -end => $query_end, -strand => $strand, -source_tag => 'RepeatMasker', -primary_tag => $repeat_class, -tag => { 'Target'=> [$repeat_name, $hit_start, $hit_end]}, ); my $rf2 = Bio::SeqFeature::Generic->new (-seq_id => $repeat_name, -score => $score, -start => $hit_start, -end => $hit_end, -strand => $strand, -source_tag => "RepeatMasker", -primary_tag => $repeat_class, -tag => { 'Target'=> [$query_name,$query_start,$query_end] }, ); my $fp = Bio::SeqFeature::FeaturePair->new(-feature1 => $rf, -feature2 => $rf2); return $fp; } } } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Seg.pm�������������������������������������������������������������������000555��000766��000024�� 6660�13155576320� 16413� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Seg # # Copyright Balamurugan Kumarasamy # Totally re-written, added docs and tests -- Torsten Seemann, Sep 2006 # # Copyright # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Tools::Seg - parse C<seg> output =head1 SYNOPSIS use Bio::Tools::Seg; my $parser = Bio::Tools::Seg->(-file => 'seg.fasta'); while ( my $f = $parser->next_result ) { if ($f->score < 1.5) { print $f->location->to_FTstring, " is low complexity\n"; } } =head1 DESCRIPTION C<seg> identifies low-complexity regions on a protein sequence. It is usually part of the C<WU-BLAST> and C<InterProScan> packages. The L<Bio::Tools::Seg> module will only parse the "fasta" output modes of C<seg>, i.e. C<seg -l> (low complexity regions only), C<seg -h> (high complexity regions only), or C<seg -a> (both low and high). It creates a L<Bio::SeqFeature::Generic> for each FASTA-like entry found in the input file. It is up to the user to appropriately filter these using the feature's score. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Torsten Seemann Email - torsten.seemann AT infotech.monash.edu.au =head1 CONTRIBUTOR - Bala Email - savikalpa@fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Seg; use strict; use Bio::SeqFeature::Generic; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::Seg->new(); Function: Builds a new Bio::Tools::Seg object Returns : Bio::Tools::Seg Args : -fh/-file => $val, # for initing input, see Bio::Root::IO =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_result Title : next_result Usage : my $feat = $seg->next_result Function: Get the next result set from parser data Returns : Bio::SeqFeature::Generic Args : none =cut sub next_result { my ($self) = @_; # For example in this line # test_prot(214-226) complexity=2.26 (12/2.20/2.50) # $1 is test_prot # $2 is 214 # $3 is 226 # $4 is 2.26 while (my $line = $self->_readline) { if ($line =~ /^\>\s*?(\S+)?\s*?\((\d+)\-(\d+)\)\s*complexity=(\S+)/) { return Bio::SeqFeature::Generic->new( -seq_id => $1, -start => $2, -end => $3, -score => $4, -source_tag => 'Seg', -primary => 'low_complexity' ); } } } 1; ��������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/SeqPattern.pm������������������������������������������������������������000444��000766��000024�� 62777�13155576320� 20013� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # bioperl module for Bio::Tools::SeqPattern # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Steve Chervitz (sac-at-bioperl.org) # # Copyright Steve Chervitz # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::SeqPattern - represent a sequence pattern or motif =head1 SYNOPSIS use Bio::Tools::SeqPattern; my $pat1 = 'T[GA]AA...TAAT'; my $pattern1 = Bio::Tools::SeqPattern->new(-SEQ =>$pat1, -TYPE =>'Dna'); my $pat2 = '[VILM]R(GXX){3,2}...[^PG]'; my $pattern2 = Bio::Tools::SeqPattern->new(-SEQ =>$pat2, -TYPE =>'Amino'); =head1 DESCRIPTION L<Bio::Tools::SeqPattern> module encapsulates generic data and methods for manipulating regular expressions describing nucleic or amino acid sequence patterns (a.k.a, "motifs"), such as the ones produced by L<Bio::Tools::IUPAC>. L<Bio::Tools::SeqPattern> is a concrete class that inherits from L<Bio::Seq>. This class grew out of a need to have a standard module for doing routine tasks with sequence patterns such as: -- Forming a reverse-complement version of a nucleotide sequence pattern -- Expanding patterns containing ambiguity codes -- Checking for invalid regexp characters -- Untainting yet preserving special characters in the pattern Other features to look for in the future: -- Full pattern syntax checking -- Conversion between expanded and condensed forms of the pattern =head1 MOTIVATIONS A key motivation for L<Bio::Tools::SeqPattern> is to have a way to generate a reverse complement of a nucleotide sequence pattern. This makes possible simultaneous pattern matching on both sense and anti-sense strands of a query sequence. In principle, one could do such a search more inefficiently by testing against both sense and anti-sense versions of a sequence. It is entirely equivalent to test a regexp containing both sense and anti-sense versions of the *pattern* against one copy of the sequence. The latter approach is much more efficient since: 1) You need only one copy of the sequence. 2) Only one regexp is executed. 3) Regexp patterns are typically much smaller than sequences. Patterns can be quite complex and it is often difficult to generate the reverse complement pattern. The Bioperl SeqPattern.pm addresses this problem, providing a convenient set of tools for working with biological sequence regular expressions. Not all patterns have been tested. If you discover a pattern that is not handled properly by Bio::Tools::SeqPattern.pm, please send me some email (sac@bioperl.org). Thanks. =head1 OTHER FEATURES =head2 Extended Alphabet Support This module supports the same set of ambiguity codes for nucleotide sequences as supported by L<Bio::Seq>. These ambiguity codes define the behavior or the L<expand> method. ------------------------------------------ Symbol Meaning Nucleic Acid ------------------------------------------ A A (A)denine C C (C)ytosine G G (G)uanine T T (T)hymine U U (U)racil M A or C a(M)ino group R A or G pu(R)ine W A or T (W)eak bond S C or G (S)trong bond Y C or T p(Y)rimidine K G or T (K)eto group V A or C or G H A or C or T D A or G or T B C or G or T X G or A or T or C N G or A or T or C . G or A or T or C ------------------------------------------ Symbol Meaning ------------------------------------------ A Alanine C Cysteine D Aspartic Acid E Glutamic Acid F Phenylalanine G Glycine H Histidine I Isoleucine K Lysine L Leucine M Methionine N Asparagine P Proline Q Glutamine R Arginine S Serine T Threonine V Valine W Tryptophan Y Tyrosine B Aspartic Acid, Asparagine Z Glutamic Acid, Glutamine X Any amino acid . Any amino acid =head2 Multiple Format Support Ultimately, this module should be able to build SeqPattern.pm objects using a variety of pattern formats such as ProSite, Blocks, Prints, GCG, etc. Currently, this module only supports patterns using a grep-like syntax. =head1 USAGE A simple demo script called seq_pattern.pl is included in the examples/ directory of the central Bioperl distribution. =head1 SEE ALSO L<Bio::Seq> - Lightweight sequence object. L<Bio::Tools::IUPAC> - The IUPAC code for degenerate residues and their conversion to a regular expression. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Steve Chervitz, sac-at-bioperl.org =head1 COPYRIGHT Copyright (c) 1997-8 Steve Chervitz. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut # ## ### #### END of main POD documentation. ### ## #' # CREATED : 28 Aug 1997 package Bio::Tools::SeqPattern; use base qw(Bio::Root::Root); use strict; use vars qw ($ID); $ID = 'Bio::Tools::SeqPattern'; ## These constants may be more appropriate in a Bio::Dictionary.pm ## type of class. my $PURINES = 'AG'; my $PYRIMIDINES = 'CT'; my $BEE = 'DN'; my $ZED = 'EQ'; my $Regexp_chars = '\w,.\*()\[\]<>\{\}^\$'; # quoted for use in regexps ## Package variables used in reverse complementing. my (%Processed_braces, %Processed_asterics); ##################################################################################### ## CONSTRUCTOR ## ##################################################################################### =head1 new Title : new Usage : my $seqpat = Bio::Tools::SeqPattern->new(); Purpose : Verifies that the type is correct for superclass (Bio::Seq.pm) : and calls superclass constructor last. Returns : n/a Argument : Parameters passed to new() Throws : Exception if the pattern string (seq) is empty. Comments : The process of creating a new SeqPattern.pm object : ensures that the pattern string is untained. See Also : L<Bio::Root::Root::new>, L<Bio::Seq::_initialize> =cut #---------------- sub new { #---------------- my($class, %param) = @_; my $self = $class->SUPER::new(%param); my ($seq,$type) = $self->_rearrange([qw(SEQ TYPE)], %param); $seq || $self->throw("Empty pattern."); my $t; # Get the type ready for Bio::Seq.pm if ($type =~ /nuc|[dr]na/i) { $t = 'Dna'; } elsif ($type =~ /amino|pep|prot/i) { $t = 'Amino'; } $seq =~ tr/a-z/A-Z/; #ps 8/8/00 Canonicalize to upper case $self->str($seq); $self->type($t); return $self; } =head1 alphabet_ok Title : alphabet_ok Usage : $mypat->alphabet_ok; Purpose : Checks for invalid regexp characters. : Overrides Bio::Seq::alphabet_ok() to allow : additional regexp characters ,.*()[]<>{}^$ : in addition to the standard genetic alphabet. : Also untaints the pattern and sets the sequence : object's sequence to the untained string. Returns : Boolean (1 | 0) Argument : n/a Throws : Exception if the pattern contains invalid characters. Comments : Does not call the superclass method. : Actually permits any alphanumeric, not just the : standard genetic alphabet. =cut #----------------' sub alphabet_ok { #---------------- my( $self) = @_; return 1 if $self->{'_alphabet_checked'}; $self->{'_alphabet_checked'} = 1; my $pat = $self->seq(); if($pat =~ /[^$Regexp_chars]/io) { $self->throw("Pattern contains invalid characters: $pat", 'Legal characters: a-z,A-Z,0-9,,.*()[]<>{}^$ '); } # Untaint pattern (makes code taint-safe). $pat =~ /([$Regexp_chars]+)/io; $self->setseq(uc($1)); # print STDERR "\npattern ok: $pat\n"; 1; } =head1 expand Title : expand Usage : $seqpat_object->expand(); Purpose : Expands the sequence pattern using special ambiguity codes. Example : $pat = $seq_pat->expand(); Returns : String containing fully expanded sequence pattern Argument : n/a Throws : Exception if sequence type is not recognized : (i.e., is not one of [DR]NA, Amino) See Also : L<Extended Alphabet Support>, L<_expand_pep>(), L<_expand_nuc>() =cut #---------- sub expand { #---------- my $self = shift; if($self->type =~ /[DR]na/i) { $self->_expand_nuc(); } elsif($self->type =~ /Amino/i) { $self->_expand_pep(); } else{ $self->throw("Don't know how to expand ${\$self->type} patterns.\n"); } } =head1 _expand_pep Title : _expand_pep Usage : n/a; automatically called by expand() Purpose : Expands peptide patterns Returns : String (the expanded pattern) Argument : String (the unexpanded pattern) Throws : n/a See Also : L<expand>(), L<_expand_nuc>() =cut #---------------- sub _expand_pep { #---------------- my ($self,$pat) = @_; $pat ||= $self->str; $pat =~ s/X/./g; $pat =~ s/^</\^/; $pat =~ s/>$/\$/; ## Avoid nested situations: [bmnq] --/--> [[$ZED]mnq] ## Yet correctly deal with: fze[bmnq] ---> f[$BEE]e[$ZEDmnq] if($pat =~ /\[\w*[BZ]\w*\]/) { $pat =~ s/\[(\w*)B(\w*)\]/\[$1$ZED$2\]/g; $pat =~ s/\[(\w*)Z(\w*)\]/\[$1$BEE$2\]/g; $pat =~ s/B/\[$ZED\]/g; $pat =~ s/Z/\[$BEE\]/g; } else { $pat =~ s/B/\[$ZED\]/g; $pat =~ s/Z/\[$BEE\]/g; } $pat =~ s/\((.)\)/$1/g; ## Doing these last since: $pat =~ s/\[(.)\]/$1/g; ## Pattern could contain [B] (for example) return $pat; } =head1 _expand_nuc Title : _expand_nuc Purpose : Expands nucleotide patterns Returns : String (the expanded pattern) Argument : String (the unexpanded pattern) Throws : n/a See Also : L<expand>(), L<_expand_pep>() =cut #--------------- sub _expand_nuc { #--------------- my ($self,$pat) = @_; $pat ||= $self->str; $pat =~ s/N|X/./g; $pat =~ s/pu/R/ig; $pat =~ s/py/Y/ig; $pat =~ s/U/T/g; $pat =~ s/^</\^/; $pat =~ s/>$/\$/; ## Avoid nested situations: [ya] --/--> [[ct]a] ## Yet correctly deal with: sg[ya] ---> [gc]g[cta] if($pat =~ /\[\w*[RYSWMK]\w*\]/) { $pat =~ s/\[(\w*)R(\w*)\]/\[$1$PURINES$2\]/g; $pat =~ s/\[(\w*)Y(\w*)\]/\[$1$PYRIMIDINES$2\]/g; $pat =~ s/\[(\w*)S(\w*)\]/\[$1GC$2\]/g; $pat =~ s/\[(\w*)W(\w*)\]/\[$1AT$2\]/g; $pat =~ s/\[(\w*)M(\w*)\]/\[$1AC$2\]/g; $pat =~ s/\[(\w*)K(\w*)\]/\[$1GT$2\]/g; $pat =~ s/\[(\w*)V(\w*)\]/\[$1ACG$2\]/g; $pat =~ s/\[(\w*)H(\w*)\]/\[$1ACT$2\]/g; $pat =~ s/\[(\w*)D(\w*)\]/\[$1AGT$2\]/g; $pat =~ s/\[(\w*)B(\w*)\]/\[$1CGT$2\]/g; $pat =~ s/R/\[$PURINES\]/g; $pat =~ s/Y/\[$PYRIMIDINES\]/g; $pat =~ s/S/\[GC\]/g; $pat =~ s/W/\[AT\]/g; $pat =~ s/M/\[AC\]/g; $pat =~ s/K/\[GT\]/g; $pat =~ s/V/\[ACG\]/g; $pat =~ s/H/\[ACT\]/g; $pat =~ s/D/\[AGT\]/g; $pat =~ s/B/\[CGT\]/g; } else { $pat =~ s/R/\[$PURINES\]/g; $pat =~ s/Y/\[$PYRIMIDINES\]/g; $pat =~ s/S/\[GC\]/g; $pat =~ s/W/\[AT\]/g; $pat =~ s/M/\[AC\]/g; $pat =~ s/K/\[GT\]/g; $pat =~ s/V/\[ACG\]/g; $pat =~ s/H/\[ACT\]/g; $pat =~ s/D/\[AGT\]/g; $pat =~ s/B/\[CGT\]/g; } $pat =~ s/\((.)\)/$1/g; ## Doing thses last since: $pat =~ s/\[(.)\]/$1/g; ## Pattern could contain [y] (for example) return $pat; } =head1 revcom Title : revcom Usage : revcom([1]); Purpose : Forms a pattern capable of recognizing the reverse complement : version of a nucleotide sequence pattern. Example : $pattern_object->revcom(); : $pattern_object->revcom(1); ## returns expanded rev complement pattern. Returns : Object reference for a new Bio::Tools::SeqPattern containing : the revcom of the current pattern as its sequence. Argument : (1) boolean (optional) (default= false) : true : expand the pattern before rev-complementing. : false: don't expand pattern before or after rev-complementing. Throws : Exception if called for amino acid sequence pattern. Comments : This method permits the simultaneous searching of both : sense and anti-sense versions of a nucleotide pattern : by means of a grep-type of functionality in which any : number of patterns may be or-ed into the recognition : pattern. : Overrides Bio::Seq::revcom() and calls it first thing. : The order of _fixpat() calls is critical. See Also : L<Bio::Seq::revcom>, L</_fixpat_1>, L</_fixpat_2>, L</_fixpat_3>, L</_fixpat_4>, L</_fixpat_5> =cut #-----------' sub revcom { #----------- my($self,$expand) = @_; if ($self->type !~ /Dna|Rna/i) { $self->throw("Can't get revcom for ${\$self->type} sequence types.\n"); } # return $self->{'_rev'} if defined $self->{'_rev'}; $expand ||= 0; my $str = $self->str; $str =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; my $rev = CORE::reverse $str; $rev =~ tr/[](){}<>/][)(}{></; if($expand) { $rev = $self->_expand_nuc($rev); # print "\nExpanded: $rev\n"; } %Processed_braces = (); %Processed_asterics = (); my $fixrev = _fixpat_1($rev); # print "FIX 1: $fixrev";<STDIN>; $fixrev = _fixpat_2($fixrev); # print "FIX 2: $fixrev";<STDIN>; $fixrev = _fixpat_3($fixrev); # print "FIX 3: $fixrev";<STDIN>; $fixrev = _fixpat_4($fixrev); # print "FIX 4: $fixrev";<STDIN>; $fixrev = _fixpat_5($fixrev); # print "FIX 5: $fixrev";<STDIN>; ##### Added by ps 8/7/00 to allow non-greedy matching $fixrev = _fixpat_6($fixrev); # print "FIX 6: $fixrev";<STDIN>; # $self->{'_rev'} = $fixrev; return Bio::Tools::SeqPattern->new(-seq =>$fixrev, -type =>$self->type); } =head1 backtranslate Title : backtranslate Usage : backtranslate(); Purpose : Produce a degenerate oligonucleotide whose translation would produce : the original protein motif. Example : $pattern_object->backtranslate(); Returns : Object reference for a new Bio::Tools::SeqPattern containing : the reverse translation of the current pattern as its sequence. Throws : Exception if called for nucleotide sequence pattern. =cut sub backtranslate { my $self = shift; # _load_module loads dynamically, caches call if successful $self->_load_module('Bio::Tools::SeqPattern::Backtranslate'); Bio::Tools::SeqPattern::Backtranslate->import("_reverse_translate_motif"); if ($self->type ne 'Amino') { $self->throw( "Can't get backtranslate for ${\$self->type} sequence types.\n" ); } return __PACKAGE__->new( -SEQ => _reverse_translate_motif($self->str), -TYPE => 'Dna', ); } =head1 _fixpat_1 Title : _fixpat_1 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all {7,5} --> {5,7} (Part I) : and [T^] --> [^T] (Part II) : and *N --> N* (Part III) Returns : String (the new, partially reversed pattern) Argument : String (the expanded pattern) Throws : n/a See Also : L<revcom>() =cut #-------------- sub _fixpat_1 { #-------------- my $pat = shift; ## Part I: my (@done,@parts); while(1) { $pat =~ /(.*)\{(\S+?)\}(.*)/ or do{ push @done, $pat; last; }; $pat = $1.'#{'.reverse($2).'}'.$3; # print "1: $1\n2: $2\n3: $3\n"; # print "modified pat: $pat";<STDIN>; @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>; last if not $pat; } $pat = join('', reverse @done); ## Part II: @done = (); while(1) { $pat =~ /(.*)\[(\S+?)\](.*)/ or do{ push @done, $pat; last; }; $pat = $1.'#['.reverse($2).']'.$3; # print "1: $1\n2: $2\n3: $3\n"; # print "modified pat: $pat";<STDIN>; @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>; last if not $pat; } $pat = join('', reverse @done); ## Part III: @done = (); while(1) { $pat =~ /(.*)\*([\w.])(.*)/ or do{ push @done, $pat; last; }; $pat = $1.'#'.$2.'*'.$3; $Processed_asterics{$2}++; # print "1: $1\n2: $2\n3: $3\n"; # print "modified pat: $pat";<STDIN>; @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>; last if not $pat; } return join('', reverse @done); } =head1 _fixpat_2 Title : _fixpat_2 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all {5,7}Y ---> Y{5,7} : and {10,}. ---> .{10,} Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : L<revcom>() =cut #-------------- sub _fixpat_2 { #-------------- my $pat = shift; local($^W) = 0; my (@done,@parts,$braces); while(1) { # $pat =~ s/(.*)([^])])(\{\S+?\})([\w.])(.*)/$1$2#$4$3$5/ or do{ push @done, $pat; last; }; $pat =~ s/(.*)(\{\S+?\})([\w.])(.*)/$1#$3$2$4/ or do{ push @done, $pat; last; }; $braces = $2; $braces =~ s/[{}]//g; $Processed_braces{"$3$braces"}++; # print "modified pat: $pat";<STDIN>; @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>; last if not $pat; } return join('', reverse @done); } =head1 _fixpat_3 Title : _fixpat_3 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all {5,7}(XXX) ---> (XXX){5,7} Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : L<revcom>() =cut #------------- sub _fixpat_3 { #------------- my $pat = shift; my (@done,@parts,$braces,$newpat,$oldpat); while(1) { # $pat =~ s/(.+)(\{\S+\})(\(\w+\))(.*)/$1#$3$2$4/ or do{ push @done, $pat; last; }; if( $pat =~ /(.*)(.)(\{\S+\})(\(\w+\))(.*)/) { $newpat = "$1#$2$4$3$5"; ##ps $oldpat = "$1#$2$3$4$5"; # print "1: $1\n2: $2\n3: $3\n4: $4\n5: $5\n"; ##ps $braces = $3; ##ps $braces =~ s/[{}]//g; ##ps if( exists $Processed_braces{"$2$braces"} || exists $Processed_asterics{$2}) { ##ps $pat = $oldpat; # Don't change it. Already processed. # print "saved pat: $pat";<STDIN>; ##ps } else { # print "new pat: $newpat";<STDIN>; $pat = $newpat; # Change it. ##ps } } elsif( $pat =~ /^(\{\S+\})(\(\w+\))(.*)/) { $pat = "#$2$1$3"; } else { push @done, $pat; last; } @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>; last if not $pat; } return join('', reverse @done); } =head1 _fixpat_4 Title : _fixpat_4 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all {5,7}[XXX] ---> [XXX]{5,7} Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : L<revcom>() =cut #--------------- sub _fixpat_4 { #--------------- my $pat = shift; my (@done,@parts,$braces,$newpat,$oldpat); while(1) { # $pat =~ s/(.*)(\{\S+\})(\[\w+\])(.*)/$1#$3$2$4/ or do{ push @done, $pat; last; }; # $pat =~ s/(.*)([^\w.])(\{\S+\})(\[\w+\])(.*)/$1$2#$4$3$5/ or do{ push @done, $pat; last; }; if( $pat =~ /(.*)(.)(\{\S+\})(\[\w+\])(.*)/) { $newpat = "$1#$2$4$3$5"; $oldpat = "$1#$2$3$4$5"; # print "1: $1\n2: $2\n3: $3\n4: $4\n5: $5\n"; $braces = $3; $braces =~ s/[{}]//g; if( (defined $braces and defined $2) and exists $Processed_braces{"$2$braces"} || exists $Processed_asterics{$2}) { $pat = $oldpat; # Don't change it. Already processed. # print "saved pat: $pat";<STDIN>; } else { $pat = $newpat; # Change it. # print "new pat: $pat";<STDIN>; } } elsif( $pat =~ /^(\{\S+\})(\[\w+\])(.*)/) { $pat = "#$2$1$3"; } else { push @done, $pat; last; } @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>; last if not $pat; } return join('', reverse @done); } =head1 _fixpat_5 Title : _fixpat_5 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all *[XXX] ---> [XXX]* : and *(XXX) ---> (XXX)* Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : L<revcom>() =cut #-------------- sub _fixpat_5 { #-------------- my $pat = shift; my (@done,@parts,$newpat,$oldpat); while(1) { # $pat =~ s/(.*)(\{\S+\})(\[\w+\])(.*)/$1#$3$2$4/ or do{ push @done, $pat; last; }; # $pat =~ s/(.*)([^\w.])(\{\S+\})(\[\w+\])(.*)/$1$2#$4$3$5/ or do{ push @done, $pat; last; }; if( $pat =~ /(.*)(.)\*(\[\w+\]|\(\w+\))(.*)/) { $newpat = "$1#$2$3*$4"; $oldpat = "$1#$2*$3$4"; # print "1: $1\n2: $2\n3: $3\n4: $4\n"; if( exists $Processed_asterics{$2}) { $pat = $oldpat; # Don't change it. Already processed. # print "saved pat: $pat";<STDIN>; } else { $pat = $newpat; # Change it. # print "new pat: $pat";<STDIN>; } } elsif( $pat =~ /^\*(\[\w+\]|\(\w+\))(.*)/) { $pat = "#$1*$3"; } else { push @done, $pat; last; } @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>; last if not $pat; } return join('', reverse @done); } ############################ # # PS: Added 8/7/00 to allow non-greedy matching patterns # ###################################### =head1 _fixpat_6 Title : _fixpat_6 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all ?Y{5,7} ---> Y{5,7}? : and ?(XXX){5,7} ---> (XXX){5,7}? : and ?[XYZ]{5,7} ---> [XYZ]{5,7}? Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : L<revcom>() =cut #-------------- sub _fixpat_6 { #-------------- my $pat = shift; my (@done,@parts); @done = (); while(1) { $pat =~ /(.*)\?(\[\w+\]|\(\w+\)|\w)(\{\S+?\})?(.*)/ or do{ push @done, $pat; last; }; my $quantifier = $3 ? $3 : ""; # Shut up warning if no explicit quantifier $pat = $1.'#'.$2.$quantifier.'?'.$4; # $pat = $1.'#'.$2.$3.'?'.$4; # print "1: $1\n2: $2\n3: $3\n"; # print "modified pat: $pat";<STDIN>; @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>; last if not $pat; } return join('', reverse @done); } =head2 str Title : str Usage : $obj->str($newval) Function: Returns : value of str Args : newvalue (optional) =cut sub str{ my $obj = shift; if( @_ ) { my $value = shift; $obj->{'str'} = $value; } return $obj->{'str'}; } =head2 type Title : type Usage : $obj->type($newval) Function: Returns : value of type Args : newvalue (optional) =cut sub type{ my $obj = shift; if( @_ ) { my $value = shift; $obj->{'type'} = $value; } return $obj->{'type'}; } 1; __END__ ######################################################################### # End of class ######################################################################### =head1 FOR DEVELOPERS ONLY =head2 Data Members Information about the various data members of this module is provided for those wishing to modify or understand the code. Two things to bear in mind: =over 2 =item 1 Do NOT rely on these in any code outside of this module. All data members are prefixed with an underscore to signify that they are private. Always use accessor methods. If the accessor doesn't exist or is inadequate, create or modify an accessor (and let me know, too!). =item 2 This documentation may be incomplete and out of date. It is easy for this documentation to become obsolete as this module is still evolving. Always double check this info and search for members not described here. =back An instance of Bio::Tools::RestrictionEnzyme.pm is a blessed reference to a hash containing all or some of the following fields: FIELD VALUE ------------------------------------------------------------------------ _rev : The corrected reverse complement of the fully expanded pattern. INHERITED DATA MEMBERS: _seq : (From Bio::Seq.pm) The original, unexpanded input sequence after untainting. _type : (From Bio::Seq.pm) 'Dna' or 'Amino' =cut �BioPerl-1.007002/Bio/Tools/SeqStats.pm��������������������������������������������������������������000444��000766��000024�� 67136�13155576320� 17466� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::SeqStats # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by # # Copyright Peter Schattner # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::SeqStats - Object holding statistics for one particular sequence =head1 SYNOPSIS # build a primary nucleic acid or protein sequence object somehow # then build a statistics object from the sequence object $seqobj = Bio::PrimarySeq->new(-seq => 'ACTGTGGCGTCAACTG', -alphabet => 'dna', -id => 'test'); $seq_stats = Bio::Tools::SeqStats->new(-seq => $seqobj); # obtain a hash of counts of each type of monomer # (i.e. amino or nucleic acid) print "\nMonomer counts using statistics object\n"; $seq_stats = Bio::Tools::SeqStats->new(-seq=>$seqobj); $hash_ref = $seq_stats->count_monomers(); # e.g. for DNA sequence foreach $base (sort keys %$hash_ref) { print "Number of bases of type ", $base, "= ", %$hash_ref->{$base},"\n"; } # obtain the count directly without creating a new statistics object print "\nMonomer counts without statistics object\n"; $hash_ref = Bio::Tools::SeqStats->count_monomers($seqobj); foreach $base (sort keys %$hash_ref) { print "Number of bases of type ", $base, "= ", %$hash_ref->{$base},"\n"; } # obtain hash of counts of each type of codon in a nucleic acid sequence print "\nCodon counts using statistics object\n"; $hash_ref = $seq_stats-> count_codons(); # for nucleic acid sequence foreach $base (sort keys %$hash_ref) { print "Number of codons of type ", $base, "= ", %$hash_ref->{$base},"\n"; } # or print "\nCodon counts without statistics object\n"; $hash_ref = Bio::Tools::SeqStats->count_codons($seqobj); foreach $base (sort keys %$hash_ref) { print "Number of codons of type ", $base, "= ", %$hash_ref->{$base},"\n"; } # Obtain the molecular weight of a sequence. Since the sequence # may contain ambiguous monomers, the molecular weight is returned # as a (reference to) a two element array containing greatest lower # bound (GLB) and least upper bound (LUB) of the molecular weight $weight = $seq_stats->get_mol_wt(); print "\nMolecular weight (using statistics object) of sequence ", $seqobj->id(), " is between ", $$weight[0], " and " , $$weight[1], "\n"; # or $weight = Bio::Tools::SeqStats->get_mol_wt($seqobj); print "\nMolecular weight (without statistics object) of sequence ", $seqobj->id(), " is between ", $$weight[0], " and " , $$weight[1], "\n"; # Calculate mean Kyte-Doolittle hydropathicity (aka "gravy" score) my $prot = Bio::PrimarySeq->new(-seq=>'MSFVLVAPDMLATAAADVVQIGSAVSAGS', -alphabet=>'protein'); my $gravy = Bio::Tools::SeqStats->hydropathicity($seqobj); print "might be hydropathic" if $gravy > 1; =head1 DESCRIPTION Bio::Tools::SeqStats is a lightweight object for the calculation of simple statistical and numerical properties of a sequence. By "lightweight" I mean that only "primary" sequences are handled by the object. The calling script needs to create the appropriate primary sequence to be passed to SeqStats if statistics on a sequence feature are required. Similarly if a codon count is desired for a frame-shifted sequence and/or a negative strand sequence, the calling script needs to create that sequence and pass it to the SeqStats object. Nota that nucleotide sequences in bioperl do not strictly separate RNA and DNA sequences. By convention, sequences from RNA molecules are shown as is they were DNA. Objects are supposed to make the distinction when needed. This class is one of the few where this distinctions needs to be made. Internally, it changes all Ts into Us before weight and monomer count. SeqStats can be called in two distinct manners. If only a single computation is required on a given sequence object, the method can be called easily using the SeqStats object directly: $weight = Bio::Tools::SeqStats->get_mol_wt($seqobj); Alternately, if several computations will be required on a given sequence object, an "instance" statistics object can be constructed and used for the method calls: $seq_stats = Bio::Tools::SeqStats->new($seqobj); $monomers = $seq_stats->count_monomers(); $codons = $seq_stats->count_codons(); $weight = $seq_stats->get_mol_wt(); $gravy = $seq_stats->hydropathicity(); As currently implemented the object can return the following values from a sequence: =over =item * The molecular weight of the sequence: get_mol_wt() =item * The number of each type of monomer present: count_monomers() =item * The number of each codon present in a nucleic acid sequence: count_codons() =item * The mean hydropathicity ("gravy" score) of a protein: hydropathicity() =back For DNA and RNA sequences single-stranded weights are returned. The molecular weights are calculated for neutral, or not ionized, nucleic acids. The returned weight is the sum of the base-sugar-phosphate residues of the chain plus one weight of water to to account for the additional OH on the phosphate of the 5' residue and the additional H on the sugar ring of the 3' residue. Note that this leads to a difference of 18 in calculated molecular weights compared to some other available programs (e.g. Informax VectorNTI). Note that since sequences may contain ambiguous monomers (e.g. "M", meaning "A" or "C" in a nucleic acid sequence), the method get_mol_wt returns a two-element array containing the greatest lower bound and least upper bound of the molecule. For a sequence with no ambiguous monomers, the two elements of the returned array will be equal. The method count_codons() handles ambiguous bases by simply counting all ambiguous codons together and issuing a warning to that effect. =head1 DEVELOPERS NOTES Ewan moved it from Bio::SeqStats to Bio::Tools::SeqStats Heikki made tiny adjustments (+/- 0.01 daltons) to amino acid molecular weights to have the output match values in SWISS-PROT. Torsten added hydropathicity calculation. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Peter Schattner Email schattner AT alum.mit.edu =head1 CONTRIBUTOR - Torsten Seemann Email torsten.seemann AT infotech.monash.edu.au =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::SeqStats; use strict; use vars qw(%Alphabets %Alphabets_strict $amino_weights $rna_weights $dna_weights %Weights $amino_hydropathicity); use Bio::Seq; use base qw(Bio::Root::Root); BEGIN { %Alphabets = ( 'dna' => [ qw(A C G T R Y M K S W H B V D X N) ], 'rna' => [ qw(A C G U R Y M K S W H B V D X N) ], 'protein' => [ qw(A R N D C Q E G H I L K M F U P S T W X Y V B Z J O *) ], # sac: added B, Z ); # SAC: new strict alphabet: doesn't allow any ambiguity characters. %Alphabets_strict = ( 'dna' => [ qw( A C G T ) ], 'rna' => [ qw( A C G U ) ], 'protein' => [ qw(A R N D C Q E G H I L K M F U P S T W Y V O) ], ); # IUPAC-IUB SYMBOLS FOR NUCLEOTIDE NOMENCLATURE: # Cornish-Bowden (1985) Nucl. Acids Res. 13: 3021-3030. # Amino Acid alphabet # ------------------------------------------ # Symbol Meaning # ------------------------------------------ my $amino_A_wt = 89.09; my $amino_C_wt = 121.15; my $amino_D_wt = 133.1; my $amino_E_wt = 147.13; my $amino_F_wt = 165.19; my $amino_G_wt = 75.07; my $amino_H_wt = 155.16; my $amino_I_wt = 131.17; my $amino_K_wt = 146.19; my $amino_L_wt = 131.17; my $amino_M_wt = 149.21; my $amino_N_wt = 132.12; my $amino_O_wt = 255.31; my $amino_P_wt = 115.13; my $amino_Q_wt = 146.15; my $amino_R_wt = 174.20; my $amino_S_wt = 105.09; my $amino_T_wt = 119.12; my $amino_U_wt = 168.06; my $amino_V_wt = 117.15; my $amino_W_wt = 204.23; my $amino_Y_wt = 181.19; $amino_weights = { 'A' => [$amino_A_wt, $amino_A_wt], # Alanine 'B' => [$amino_N_wt, $amino_D_wt], # Aspartic Acid, Asparagine 'C' => [$amino_C_wt, $amino_C_wt], # Cysteine 'D' => [$amino_D_wt, $amino_D_wt], # Aspartic Acid 'E' => [$amino_E_wt, $amino_E_wt], # Glutamic Acid 'F' => [$amino_F_wt, $amino_F_wt], # Phenylalanine 'G' => [$amino_G_wt, $amino_G_wt], # Glycine 'H' => [$amino_H_wt, $amino_H_wt], # Histidine 'I' => [$amino_I_wt, $amino_I_wt], # Isoleucine 'J' => [$amino_L_wt, $amino_I_wt], # Leucine, Isoleucine 'K' => [$amino_K_wt, $amino_K_wt], # Lysine 'L' => [$amino_L_wt, $amino_L_wt], # Leucine 'M' => [$amino_M_wt, $amino_M_wt], # Methionine 'N' => [$amino_N_wt, $amino_N_wt], # Asparagine 'O' => [$amino_O_wt, $amino_O_wt], # Pyrrolysine 'P' => [$amino_P_wt, $amino_P_wt], # Proline 'Q' => [$amino_Q_wt, $amino_Q_wt], # Glutamine 'R' => [$amino_R_wt, $amino_R_wt], # Arginine 'S' => [$amino_S_wt, $amino_S_wt], # Serine 'T' => [$amino_T_wt, $amino_T_wt], # Threonine 'U' => [$amino_U_wt, $amino_U_wt], # SelenoCysteine 'V' => [$amino_V_wt, $amino_V_wt], # Valine 'W' => [$amino_W_wt, $amino_W_wt], # Tryptophan 'X' => [$amino_G_wt, $amino_W_wt], # Unknown 'Y' => [$amino_Y_wt, $amino_Y_wt], # Tyrosine 'Z' => [$amino_Q_wt, $amino_E_wt], # Glutamic Acid, Glutamine }; # Extended Dna / Rna alphabet use vars ( qw($C $O $N $H $P $water) ); use vars ( qw($adenine $guanine $cytosine $thymine $uracil)); use vars ( qw($ribose_phosphate $deoxyribose_phosphate $ppi)); use vars ( qw($dna_A_wt $dna_C_wt $dna_G_wt $dna_T_wt $rna_A_wt $rna_C_wt $rna_G_wt $rna_U_wt)); use vars ( qw($dna_weights $rna_weights %Weights)); $C = 12.01; $O = 16.00; $N = 14.01; $H = 1.01; $P = 30.97; $water = 18.015; $adenine = 5 * $C + 5 * $N + 5 * $H; $guanine = 5 * $C + 5 * $N + 1 * $O + 5 * $H; $cytosine = 4 * $C + 3 * $N + 1 * $O + 5 * $H; $thymine = 5 * $C + 2 * $N + 2 * $O + 6 * $H; $uracil = 4 * $C + 2 * $N + 2 * $O + 4 * $H; $ribose_phosphate = 5 * $C + 7 * $O + 9 * $H + 1 * $P; # neutral (unionized) form $deoxyribose_phosphate = 5 * $C + 6 * $O + 9 * $H + 1 * $P; # the following are single strand molecular weights / base $dna_A_wt = $adenine + $deoxyribose_phosphate - $water; $dna_C_wt = $cytosine + $deoxyribose_phosphate - $water; $dna_G_wt = $guanine + $deoxyribose_phosphate - $water; $dna_T_wt = $thymine + $deoxyribose_phosphate - $water; $rna_A_wt = $adenine + $ribose_phosphate - $water; $rna_C_wt = $cytosine + $ribose_phosphate - $water; $rna_G_wt = $guanine + $ribose_phosphate - $water; $rna_U_wt = $uracil + $ribose_phosphate - $water; $dna_weights = { 'A' => [$dna_A_wt,$dna_A_wt], # Adenine 'C' => [$dna_C_wt,$dna_C_wt], # Cytosine 'G' => [$dna_G_wt,$dna_G_wt], # Guanine 'T' => [$dna_T_wt,$dna_T_wt], # Thymine 'M' => [$dna_C_wt,$dna_A_wt], # A or C 'R' => [$dna_A_wt,$dna_G_wt], # A or G 'W' => [$dna_T_wt,$dna_A_wt], # A or T 'S' => [$dna_C_wt,$dna_G_wt], # C or G 'Y' => [$dna_C_wt,$dna_T_wt], # C or T 'K' => [$dna_T_wt,$dna_G_wt], # G or T 'V' => [$dna_C_wt,$dna_G_wt], # A or C or G 'H' => [$dna_C_wt,$dna_A_wt], # A or C or T 'D' => [$dna_T_wt,$dna_G_wt], # A or G or T 'B' => [$dna_C_wt,$dna_G_wt], # C or G or T 'X' => [$dna_C_wt,$dna_G_wt], # G or A or T or C 'N' => [$dna_C_wt,$dna_G_wt], # G or A or T or C }; $rna_weights = { 'A' => [$rna_A_wt,$rna_A_wt], # Adenine 'C' => [$rna_C_wt,$rna_C_wt], # Cytosine 'G' => [$rna_G_wt,$rna_G_wt], # Guanine 'U' => [$rna_U_wt,$rna_U_wt], # Uracil 'M' => [$rna_C_wt,$rna_A_wt], # A or C 'R' => [$rna_A_wt,$rna_G_wt], # A or G 'W' => [$rna_U_wt,$rna_A_wt], # A or U 'S' => [$rna_C_wt,$rna_G_wt], # C or G 'Y' => [$rna_C_wt,$rna_U_wt], # C or U 'K' => [$rna_U_wt,$rna_G_wt], # G or U 'V' => [$rna_C_wt,$rna_G_wt], # A or C or G 'H' => [$rna_C_wt,$rna_A_wt], # A or C or U 'D' => [$rna_U_wt,$rna_G_wt], # A or G or U 'B' => [$rna_C_wt,$rna_G_wt], # C or G or U 'X' => [$rna_C_wt,$rna_G_wt], # G or A or U or C 'N' => [$rna_C_wt,$rna_G_wt], # G or A or U or C }; %Weights = ( 'dna' => $dna_weights, 'rna' => $rna_weights, 'protein' => $amino_weights, ); # Amino acid scale: Hydropathicity. # Ref: Kyte J., Doolittle R.F. J. Mol. Biol. 157:105-132(1982). # http://au.expasy.org/tools/pscale/Hphob.Doolittle.html $amino_hydropathicity = { A => 1.800, R => -4.500, N => -3.500, D => -3.500, C => 2.500, Q => -3.500, E => -3.500, G => -0.400, H => -3.200, I => 4.500, L => 3.800, K => -3.900, M => 1.900, F => 2.800, P => -1.600, S => -0.800, T => -0.700, W => -0.900, Y => -1.300, V => 4.200, }; } sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($seqobj) = $self->_rearrange([qw(SEQ)],@args); unless ($seqobj->isa("Bio::PrimarySeqI")) { $self->throw("SeqStats works only on PrimarySeqI objects"); } if ( !defined $seqobj->alphabet || !defined $Alphabets{$seqobj->alphabet}) { $self->throw("Must have a valid alphabet defined for seq (". join(",",keys %Alphabets)); } $self->{'_seqref'} = $seqobj; # check the letters in the sequence $self->{'_is_strict'} = _is_alphabet_strict($seqobj); return $self; } =head2 count_monomers Title : count_monomers Usage : $rcount = $seq_stats->count_monomers(); or $rcount = $seq_stats->Bio::Tools::SeqStats->($seqobj); Function: Counts the number of each type of monomer (amino acid or base) in the sequence. Ts are counted as Us in RNA sequences. Example : Returns : Reference to a hash in which keys are letters of the genetic alphabet used and values are number of occurrences of the letter in the sequence. Args : None or reference to sequence object Throws : Throws an exception if type of sequence is unknown (ie amino or nucleic)or if unknown letter in alphabet. Ambiguous elements are allowed. =cut sub count_monomers{ my %count = (); my $seqobj; my $_is_strict; my $element = ''; my $_is_instance = 1 ; my $self = shift @_; my $object_argument = shift @_; # First we need to determine if the present object is an instance # object or if the sequence object has been passed as an argument if (defined $object_argument) { $_is_instance = 0; } # If we are using an instance object... if ($_is_instance) { if ($self->{'_monomer_count'}) { return $self->{'_monomer_count'}; # return count if previously calculated } $_is_strict = $self->{'_is_strict'}; # retrieve "strictness" $seqobj = $self->{'_seqref'}; } else { # otherwise... $seqobj = $object_argument; # Following two lines lead to error in "throw" routine $seqobj->isa("Bio::PrimarySeqI") || $self->throw("SeqStats works only on PrimarySeqI objects"); # is alphabet OK? Is it strict? $_is_strict = _is_alphabet_strict($seqobj); } my $alphabet = $_is_strict ? $Alphabets_strict{$seqobj->alphabet} : $Alphabets{$seqobj->alphabet} ; # get array of allowed letters # convert everything to upper case to be safe my $seqstring = uc $seqobj->seq(); # Since T is used in RichSeq RNA sequences, do conversion locally $seqstring =~ s/T/U/g if $seqobj->alphabet eq 'rna'; # For each letter, count the number of times it appears in # the sequence LETTER: foreach $element (@$alphabet) { # skip terminator symbol which may confuse regex next LETTER if $element eq '*'; $count{$element} = ( $seqstring =~ s/$element/$element/g); } if ($_is_instance) { $self->{'_monomer_count'} = \%count; # Save in case called again later } return \%count; } =head2 get_mol_wt Title : get_mol_wt Usage : $wt = $seqobj->get_mol_wt() or $wt = Bio::Tools::SeqStats ->get_mol_wt($seqobj); Function: Calculate molecular weight of sequence Ts are counted as Us in RNA sequences. Example : Returns : Reference to two element array containing lower and upper bounds of molecule molecular weight. For DNA and RNA sequences single-stranded weights are returned. If sequence contains no ambiguous elements, both entries in array are equal to molecular weight of molecule. Args : None or reference to sequence object Throws : Exception if type of sequence is unknown (ie not amino or nucleic) or if unknown letter in alphabet. Ambiguous elements are allowed. =cut sub get_mol_wt { my $seqobj; my $_is_strict; my $element = ''; my $_is_instance = 1 ; my $self = shift @_; my $object_argument = shift @_; my ($weight_array, $rcount); if (defined $object_argument) { $_is_instance = 0; } if ($_is_instance) { if ($weight_array = $self->{'_mol_wt'}) { # return mol. weight if previously calculated return $weight_array; } $seqobj = $self->{'_seqref'}; $rcount = $self->count_monomers(); } else { $seqobj = $object_argument; $seqobj->isa("Bio::PrimarySeqI") || $self->throw("Error: SeqStats works only on PrimarySeqI objects"); $_is_strict = _is_alphabet_strict($seqobj); # is alphabet OK? $rcount = $self->count_monomers($seqobj); } # We will also need to know what type of monomer we are dealing with my $moltype = $seqobj->alphabet(); # In general,the molecular weight is bounded below by the sum of the # weights of lower bounds of each alphabet symbol times the number of # occurrences of the symbol in the sequence. A similar upper bound on # the weight is also calculated. # Note that for "strict" (i.e. unambiguous) sequences there is an # inefficiency since the upper bound = the lower bound and there are # two calculations. However, this decrease in performance will be # minor and leads to significantly more readable code. my $weight_lower_bound = 0; my $weight_upper_bound = 0; my $weight_table = $Weights{$moltype}; my $total_res; # compute weight of all the residues foreach $element (keys %$rcount) { $weight_lower_bound += $$rcount{$element} * $$weight_table{$element}->[0]; $weight_upper_bound += $$rcount{$element} * $$weight_table{$element}->[1]; # this tracks only the residues used for counting MW $total_res += $$rcount{$element}; } if ($moltype =~ /protein/) { # remove H2O during peptide bond formation. $weight_lower_bound -= $water * ($total_res - 1); $weight_upper_bound -= $water * ($total_res - 1); } else { # Correction because phosphate of 5' residue has additional OH and # sugar ring of 3' residue has additional H $weight_lower_bound += $water; $weight_upper_bound += $water; } $weight_lower_bound = sprintf("%.1f", $weight_lower_bound); $weight_upper_bound = sprintf("%.1f", $weight_upper_bound); $weight_array = [$weight_lower_bound, $weight_upper_bound]; if ($_is_instance) { $self->{'_mol_wt'} = $weight_array; # Save in case called again later } return $weight_array; } =head2 count_codons Title : count_codons Usage : $rcount = $seqstats->count_codons() or $rcount = Bio::Tools::SeqStats->count_codons($seqobj) Function: Counts the number of each type of codons for a dna or rna sequence, starting at the 1st triple of the input sequence. Example : Returns : Reference to a hash in which keys are codons of the genetic alphabet used and values are number of occurrences of the codons in the sequence. All codons with "ambiguous" bases are counted together. Args : None or sequence object Throws : an exception if type of sequence is unknown or protein. =cut sub count_codons { my $rcount = {}; my $codon ; my $seqobj; my $_is_strict; my $element = ''; my $_is_instance = 1 ; my $self = shift @_; my $object_argument = shift @_; if (defined $object_argument) { $_is_instance = 0; } if ($_is_instance) { if ($rcount = $self->{'_codon_count'}) { return $rcount; # return count if previously calculated } $_is_strict = $self->{'_is_strict'}; # retrieve "strictness" $seqobj = $self->{'_seqref'}; } else { $seqobj = $object_argument; $seqobj->isa("Bio::PrimarySeqI") || $self->throw("Error: SeqStats works only on PrimarySeqI objects"); $_is_strict = _is_alphabet_strict($seqobj); } # Codon counts only make sense for nucleic acid sequences my $alphabet = $seqobj->alphabet(); unless ($alphabet =~ /[dr]na/i) { $seqobj->throw("Codon counts only meaningful for dna or rna, ". "not for $alphabet sequences."); } # If sequence contains ambiguous bases, warn that codons # containing them will all be lumped together in the count. if (!$_is_strict ) { $seqobj->warn("Sequence $seqobj contains ambiguous bases.". " All codons with ambiguous bases will be added together in count.") if $self->verbose >= 0 ; } my $seq = $seqobj->seq(); # Now step through the string by threes and count the codons CODON: while (length($seq) > 2) { $codon = uc substr($seq,0,3); $seq = substr($seq,3); if ($codon =~ /[^ACTGU]/i) { $$rcount{'ambiguous'}++; #lump together ambiguous codons next CODON; } if (!defined $$rcount{$codon}) { $$rcount{$codon}= 1 ; next CODON; } $$rcount{$codon}++; # default } if ($_is_instance) { $self->{'_codon_count'} = $rcount; # Save in case called again later } return $rcount; } =head2 hydropathicity Title : hydropathicity Usage : $gravy = $seqstats->hydropathicity(); or $gravy = Bio::Tools::SeqStats->hydropathicity($seqobj); Function: Calculates the mean Kyte-Doolittle hydropathicity for a protein sequence. Also known as the "gravy" score. Refer to Kyte J., Doolittle R.F., J. Mol. Biol. 157:105-132(1982). Example : Returns : float Args : None or reference to sequence object Throws : an exception if type of sequence is not protein. =cut sub hydropathicity { my $seqobj; my $_is_strict; my $element = ''; my $_is_instance = 1 ; my $self = shift @_; my $object_argument = shift @_; if (defined $object_argument) { $_is_instance = 0; } if ($_is_instance) { if (my $gravy = $self->{'_hydropathicity'}) { return $gravy; # return value if previously calculated } $_is_strict = $self->{'_is_strict'}; # retrieve "strictness" $seqobj = $self->{'_seqref'}; } else { $seqobj = $object_argument; $seqobj->isa("Bio::PrimarySeqI") || $self->throw("Error: SeqStats works only on PrimarySeqI objects"); $_is_strict = _is_alphabet_strict($seqobj); } # hydropathicity not menaingful for empty sequences unless ($seqobj->length() > 0) { $seqobj->throw("hydropathicity not defined for zero-length sequences"); } # hydropathicity only make sense for protein sequences my $alphabet = $seqobj->alphabet(); unless ($alphabet =~ /protein/i) { $seqobj->throw("hydropathicity only meaningful for protein, ". "not for $alphabet sequences."); } # If sequence contains ambiguous bases, warn that codons # containing them will all be lumped together in the count. unless ($_is_strict ) { $seqobj->throw("Sequence $seqobj contains ambiguous amino acids. ". "Hydropathicity can not be caculated.") } my $seq = $seqobj->seq(); # Now step through the string and add up the hydropathicity values my $gravy = 0; for my $i ( 0 .. length($seq) ) { my $codon = uc(substr($seq,$i,1)); $gravy += $amino_hydropathicity->{$codon}||0; # table look-up } $gravy /= length($seq); if ($_is_instance) { $self->{'_hydropathicity'} = $gravy; # Save in case called again later } return $gravy; } =head2 _is_alphabet_strict Title : _is_alphabet_strict Usage : Function: internal function to determine whether there are any ambiguous elements in the current sequence Example : Returns : 1 if strict alphabet is being used, 0 if ambiguous elements are present Args : Throws : an exception if type of sequence is unknown (ie amino or nucleic) or if unknown letter in alphabet. Ambiguous monomers are allowed. =cut sub _is_alphabet_strict { my ($seqobj) = @_; my $moltype = $seqobj->alphabet(); # convert everything to upper case to be safe my $seqstring = uc $seqobj->seq(); # Since T is used in RichSeq RNA sequences, do conversion locally $seqstring =~ s/T/U/g if $seqobj->alphabet eq 'rna'; # First we check if only the 'strict' letters are present in the # sequence string If not, we check whether the remaining letters # are ambiguous monomers or whether there are illegal letters in # the string # $alpha_array is a ref to an array of the 'strictly' allowed letters my $alpha_array = $Alphabets_strict{$moltype} ; # $alphabet contains the allowed letters in string form my $alphabet = join ('', @$alpha_array) ; unless ($seqstring =~ /[^$alphabet]/) { return 1 ; } # Next try to match with the alphabet's ambiguous letters $alpha_array = $Alphabets{$moltype} ; $alphabet = join ('', @$alpha_array) ; unless ($seqstring =~ /[^$alphabet]/) { return 0 ; } # If we got here there is an illegal letter in the sequence $seqobj->throw("Alphabet not OK for $seqobj"); } =head2 _print_data Title : _print_data Usage : $seqobj->_print_data() or Bio::Tools::SeqStats->_print_data(); Function: Displays dna / rna parameters (used for debugging) Returns : 1 Args : None Used for debugging. =cut sub _print_data { print "\n adenine = : $adenine \n"; print "\n guanine = : $guanine \n"; print "\n cytosine = : $cytosine \n"; print "\n thymine = : $thymine \n"; print "\n uracil = : $uracil \n"; print "\n dna_A_wt = : $dna_A_wt \n"; print "\n dna_C_wt = : $dna_C_wt \n"; print "\n dna_G_wt = : $dna_G_wt \n"; print "\n dna_T_wt = : $dna_T_wt \n"; print "\n rna_A_wt = : $rna_A_wt \n"; print "\n rna_C_wt = : $rna_C_wt \n"; print "\n rna_G_wt = : $rna_G_wt \n"; print "\n rna_U_wt = : $rna_U_wt \n"; return 1; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/SeqWords.pm��������������������������������������������������������������000444��000766��000024�� 22401�13155576320� 17450� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������#--------------------------------------------------------------------------- # PACKAGE : Bio::Tools::SeqWords # PURPOSE : To count n-mers in any sequence of characters # AUTHOR : Derek Gatherer (d.gatherer@vir.gla.ac.uk) # SOURCE : # CREATED : 21st March 2000 # MODIFIED : 11th November 2003 (DG - new method, count_overlap_words) # LICENCE : You may distribute this module under the same terms # : as the rest of BioPerl. #--------------------------------------------------------------------------- =head1 NAME Bio::Tools::SeqWords - Object holding n-mer statistics for a sequence =head1 SYNOPSIS # Create the SeqWords object, e.g.: my $inputstream = Bio::SeqIO->new(-file => "seqfile", -format => 'Fasta'); my $seqobj = $inputstream->next_seq(); my $seq_word = Bio::Tools::SeqWords->new(-seq => $seqobj); # Or: my $seqobj = Bio::PrimarySeq->new(-seq => "agggtttccc", -alphabet => 'dna', -id => 'test'); my $seq_word = Bio::Tools::SeqWords->new(-seq => $seqobj); # obtain a hash of word counts, eg: my $hash_ref = $seq_stats->count_words($word_length); # display hash table, eg: my %hash = %$hash_ref; foreach my $key(sort keys %hash) { print "\n$key\t$hash{$key}"; } # Or: my $hash_ref = Bio::Tools::SeqWords->count_words($seqobj,$word_length); =head1 DESCRIPTION L<Bio::Tools::SeqWords> is a featherweight object for the calculation of n-mer word occurrences in a single sequence. It is envisaged that the object will be useful for construction of scripts which use n-mer word tables as the raw material for statistical calculations; for instance, hexamer frequency for the calculation of coding protential, or the calculation of periodicity in repetitive DNA. Triplet frequency is already handled by L<Bio::Tools::SeqStats> (author: Peter Schattner). There are a few possible applications for protein, e.g. hypothesised amino acid 7-mers in heat shock proteins, or proteins with multiple simple motifs. Sometimes these protein periodicities are best seen when the amino acid alphabet is truncated, e.g. Shulman alphabet. Since there are quite a few of these shortened alphabets, this module does not specify any particular alphabet. See Synopsis above for object creation code. =head2 Rationale Take a sequence object and create an object for the purposes of holding n-mer word statistics about that sequence. The sequence can be nucleic acid or protein. In count_words() the words are counted in a non-overlapping manner, ie. in the style of a codon table, but with any word length. In count_overlap_words() the words are counted in an overlapping manner. For counts on opposite strand (DNA/RNA), a reverse complement method should be performed, and then the count repeated. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Derek Gatherer, in the loosest sense of the word 'author'. The general shape of the module is lifted directly from the SeqStat module of Peter Schattner. The central subroutine to count the words is adapted from original code provided by Dave Shivak, in response to a query on the bioperl mailing list. At least 2 other people provided alternative means (equally good but not used in the end) of performing the same calculation. Thanks to all for your assistance. =head1 CONTRIBUTORS Jason Stajich, jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::SeqWords; use strict; use base qw(Bio::Root::Root); sub new { my($class,@args) = @_; # our new standard way of instantiation my $self = $class->SUPER::new(@args); my ($seqobj) = $self->_rearrange([qw(SEQ)],@args); if((! defined($seqobj)) && @args && ref($args[0])) { # parameter not passed as named parameter? $seqobj = $args[0]; } if(! $seqobj->isa("Bio::PrimarySeqI")) { $self->throw(ref($self) . " works only on PrimarySeqI objects\n"); } $self->{'_seqref'} = $seqobj; return $self; } =head2 count_words Title : count_words Usage : $word_count = $seq_stats->count_words($word_length) or $word_count = $seq_stats->Bio::Tools::SeqWords->($seqobj,$word_length); Function: Counts non-overlapping words within a string, any alphabet is used Example : a sequence ACCGTCCGT, counted at word length 4, will give the hash {ACCG => 1, TCCG => 1} Returns : Reference to a hash in which keys are words (any length) of the alphabet used and values are number of occurrences of the word in the sequence. Args : Word length as scalar and, reference to sequence object if required Throws an exception word length is not a positive integer or if word length is longer than the sequence. =cut sub count_words { my ($self,$seqobj,$word_length) = @_; # check how we were called, and if necessary rearrange arguments if(ref($seqobj)) { # call as SeqWords->count_words($seq, $wordlen) if(! $seqobj->isa("Bio::PrimarySeqI")) { $self->throw("SeqWords works only on PrimarySeqI objects\n"); } } else { # call as $obj->count_words($wordlen) $word_length = $seqobj; $seqobj = undef; } if(! defined($seqobj)){ $seqobj = $self->{'_seqref'}; } if($word_length eq "" || $word_length =~ /[a-z]/i){ $self->throw("SeqWords cannot accept non-numeric characters". " or a null value in the \$word_length variable\n"); }elsif ($word_length <1 || ($word_length - int($word_length)) >0){ $self->throw("SeqWords requires the word length to be a ". "positive integer\n"); } my $seqstring = uc $seqobj->seq(); if($word_length > length($seqstring)){ $self->throw("die in _count, \$word_length is bigger ". "than sequence length\n"); } my $type = "non-overlap"; my $words = _count($seqobj, $word_length, $type); return $words; # ref. to a hash } =head2 count_overlap_words Title : count_overlap_words Usage : $word_count = $word_obj->count_overlap_words($word_length); Function: Counts overlapping words within a string, any alphabet is used Example : A sequence ACCAACCA, counted at word length 4, will give the hash {ACCA=>2, CCAA=>1, CAAC=>1, AACC=>1} Returns : Reference to a hash in which keys are words (any length) of the alphabet used and values are number of occurrences of the word in the sequence. Args : Word length as scalar Throws an exception if word length is not a positive integer or if word length is longer than the sequence. =cut sub count_overlap_words { my ($self,$seqobj,$word_length) = @_; # check how we were called, and if necessary rearrange arguments if(ref($seqobj)){ # call as SeqWords->count_words($seq, $wordlen) if(! $seqobj->isa("Bio::PrimarySeqI")){ $self->throw("SeqWords works only on PrimarySeqI objects\n"); } }else{ # call as $obj->count_words($wordlen) $word_length = $seqobj; $seqobj = undef; } if(! defined($seqobj)) { $seqobj = $self->{'_seqref'}; } my $seqstring = uc $seqobj->seq(); if($word_length > length($seqstring)){ $self->throw("die in _count, \$word_length is bigger ". "than sequence length\n"); } my $type = "overlap"; my $words = _count($seqobj, $word_length, $type); return $words; # ref. to a hash } # the actual counting routine # used by both count_words and count_overlap_words sub _count { my ($seqobj, $word_length, $type) = @_; my %codon = (); # now the real business # JS - remove DNA assumption my $seqstring = uc $seqobj->seq(); if($type eq "non-overlap") { while($seqstring =~ /((\w){$word_length})/gim){ $codon{uc($1)}++; } } elsif($type eq "overlap"){ my $seqlen = $seqobj->length(); # measure length for (my $frame = 1; $frame <= $word_length; $frame++) { # run through frames my $seqstring = uc($seqobj->subseq($frame,$seqlen)); # take the relevant substring while($seqstring =~ /((\w){$word_length})/gim){ $codon{uc($1)}++; # keep adding to hash } } } else { Bio::Root::Root->throw("\nSomething badly wrong here. \$type: $type can only be overlap or non-overlap"); } return \%codon; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/SiRNA.pm�����������������������������������������������������������������000444��000766��000024�� 37766�13155576320� 16641� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::SiRNA # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Donald Jackson, donald.jackson@bms.com # # Copyright Bristol-Myers Squibb # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME SiRNA - Perl object for designing small inhibitory RNAs. =head1 SYNOPSIS use Bio::Tools::SiRNA; my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq, -rules => 'saigo' ); my @pairs = $sirna_designer->design; foreach $pair (@pairs) { my $sense_oligo_sequence = $pair->sense->seq; my $antisense_oligo_sequence = $pair->antisense->seq; # print out results print join ("\t", $pair->start, $pair->end, $pair->rank, $sense_oligo_sequence, $antisense_oligo_sequence), "\n"; } =head1 DESCRIPTION Package for designing siRNA reagents. Input is a L<Bio::SeqI>-compliant object (the target). Output is a list of Bio::SeqFeature::SiRNA::Pair objects, which are added to the feature table of the target sequence. Each Bio::SeqFeature::SiRNA::Pair contains two subfeatures (Bio::SeqFeature::Oligo objects) which correspond to the individual oligos. These objects provide accessors for the information on the individual reagent pairs. This version of Bio::Tools::SiRNA represents a major change in architecture. Specific 'rulesets' for siRNA selection as developed by various groups are implemented as Bio::Tools::SiRNA::Ruleset objects, which inherit from Bio::Tools::SiRNA. This will make it easier to add new rule sets or modify existing approaches. Currently the Tuschl and Ui-Tei (2004) rules are implemented. For consistency, the Tuschl rules are implemented by default. In addition, this module provides three 'extra' rules which can be added above and beyond any ruleset. =over 3 =item 1. SiRNAs that overlap known SNPs (identified as SeqFeatures with primary tag = variation) can be avoided. =item 2. Other regions (with primary tag = 'Excluded') can also be skipped. I use this with Bio::Tools::Run::Mdust to avoid low-complexity regions (must be run separately), but other programs could also be used. =item 3. SiRNAs may also be selected in the 3 prime UTR of a gene by setting $sirna_designer-E<gt>include_3pr() to true. =back =head2 EXPORT None. =head1 SEE ALSO L<Bio::Tools::Run::Mdust>, L<Bio::SeqFeature::SiRNA::Pair>, L<Bio::SeqFeature::SiRNA::Oligo>.. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Donald Jackson (donald.jackson@bms.com) =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::SiRNA; use strict; use warnings; use vars qw($AUTOLOAD); use Bio::Seq::RichSeq; use Bio::SeqFeature::Generic; use Bio::SeqFeature::SiRNA::Oligo; use Bio::SeqFeature::SiRNA::Pair; use base qw(Bio::Root::Root); our %COMP = ( A => 'T', T => 'A', C => 'G', G => 'C', N => 'N', ); our @ARGNAMES = qw(RULES START_PAD END_PAD MIN_GC CUTOFF OLIGOS AVOID_SNPS GSTRING TMPDIR TARGET DEBUG); =head2 new Title : new Usage : my $sirna_designer = Bio::Tools::SiRNA->new(); Function : Constructor for designer object Returns : Bio::Tools::SiRNA object Args : target - the target sequence for the SiRNAs as a Bio::Seq::RichSeq start_pad - distance from the CDS start to skip (default 75) end_pad - distance from the CDS end to skip (default 50) include_3pr - set to true to include SiRNAs in the 3prime UTR (default false) rules - rules for selecting siRNAs, currently supporting saigo and tuschl min_gc - minimum GC fraction (NOT percent) (default 0.4) max_gc - maximum GC fraction (NOT percent) (default 0.6) cutoff - worst 'rank' accepted(default 3) avoid_snps - boolean - reject oligos that overlap a variation SeqFeature in the target (default true) gstring - maximum allowed consecutive Gs. Too many can cause problems in synthesis (default 4) Note : All arguments can also be changed/accessed using autoloaded methods such as: my $start_pad = $sirna_designer->start_pad(). =cut sub new { my ($proto, @args) = @_; my $pkg = ref($proto) || $proto; my $self = {}; bless ($self, $pkg); my %args; @args{@ARGNAMES} = $self->_rearrange(\@ARGNAMES, @args); if ($args{'RULES'}) { $self->rules($args{'RULES'}); } $self->{'start_pad'} = $args{'START_PAD'} || 75; # nt from start to mask $self->{'end_pad'} = $args{'END_PAD'} || 50; # nt from end to mask $self->{'include_3pr'} = $args{'INCLUDE_3PR'} || 0; # look for oligos in 3prime UTR $self->{'min_gc'} = $args{'MIN_GC'} || 0.40; $self->{'max_gc'} = $args{'MAX_GC'} || 0.60; $self->{'cutoff'} = $args{'CUTOFF'} || 3; # highest (worst) rank wanted $self->{'oligos'} = []; defined($args{'AVOID_SNPS'}) ? $self->{'avoid_snps'} = $args{'AVOID_SNPS'} : $self->{'avoid_snps'} = 1; # (t/f to avoid or include reagents that cover SNPs) $self->{'gstring'} = $args{'GSTRING'} || 4; # maximum allowed consecutive Gs - too many can cause problems in oligo synthesis $self->{'tmpdir'} = $args{'TMPDIR'} || $ENV{'TMPDIR'} || $ENV{'TMP'} || ''; $self->{'debug'} = $args{'DEBUG'} || 0; $self->target($args{'TARGET'}) if ($args{'TARGET'}); return $self; } =head2 target Title : target Usage : my $target_seq = $sirna_designer->target(); # get the current target OR $sirna_designer->target($new_target_seq); # set a new target Function : Set/get the target as a Bio::SeqI-compliant object Returns : a Bio::SeqI-compliant object Args : a Bio::SeqI-compliant object (optional) =cut sub target { my ($self, $target) = @_; if ($target) { unless ($target->isa('Bio::SeqI')) { $self->throw( -class => 'Bio::Root::BadParameter', -text => "Target must be passed as a Bio::Seq object" ); } if ($target->can('molecule')) { ( grep { uc($target->molecule) eq $_ } qw(DNA MRNA CDNA)) or $self->throw( -class => 'Bio::Root::BadParameter', -text => "Sequences of type ". $target->molecule. " are not supported" ); } else { ($target->alphabet eq 'dna') or $self->throw( -class => 'Bio::Root::BadParameter', -text => "Sequences of alphabet ". $target->alphabet. " are not supported" ); } $self->{'target'} = $target; return 1; } elsif ($self->{'target'}) { return $self->{'target'}; } else { $self->throw("Target sequence not defined"); } } =head2 rules Title : rules Usage : $sirna->rules('ruleset') Purpose : set/get ruleset to use for selecting SiRNA oligo pairs. Returns : not sure yet Args : a ruleset name (currently supported: Tuschl, Saigo) or a Bio::Tools::SiRNA::RulesetI compliant object =cut sub rules { my ($self, $rules) = @_; if ($rules) { $self->_load_ruleset($rules); } # default: use tuschl rules unless ($self->{_rules}) { $self->_load_ruleset('tuschl'); } return $self->{_rules}; } sub _load_ruleset { my ($self, $ruleset) = @_; my $rule_module = join('::', ref($self), 'Ruleset', lc($ruleset)); eval "require $rule_module"; if ($@) { #warn join("\n", '@INC contains:', @INC, undef); $self->throw("Unable to load $rule_module: $@"); return; } else { $self->{_rules} = $rule_module; bless($self, $rule_module); # recast as subclass } return 1; } =head2 design Title : design Usage : my @pairs = $sirna_designer->design(); Purpose : Design SiRNA oligo pairs. Returns : A list of SiRNA pairs as Bio::SeqFeature::SiRNA::Pair objects Args : none =cut sub design { my ($self) = @_; ($self->rules) or $self->throw('Unable to design siRNAs: no rule set specified'); # unless ( grep { $_->primary_tag eq 'Target' } $self->target->top_SeqFeatures ) { # $self->_define_target(); # } my @oligos = $self->_get_oligos(); return ( grep { $_->isa('Bio::SeqFeature::SiRNA::Pair') } $self->target->top_SeqFeatures ); } sub _define_target { my ($self) = @_; my ($feat, $cds, $left, $right); my $target = $self->target or $self->throw("Unable to design oligos - no target provided"); ($cds) = grep { $_->primary_tag eq 'CDS' } $target->top_SeqFeatures if ($target->can('top_SeqFeatures')); if ($cds) { $left = $cds->start + $self->start_pad; if (!$self->include_3pr) { $right = $cds->end - $self->end_pad; } else { $right = $target->length - $self->end_pad; } } else { $left = 0 + $self->start_pad; $right = $target->length - $self->end_pad; } # is there anything left? if (($right - $left) < 20) { $self->throw("There isn't enough sequence to design oligos. Please reduce start_pad and end_pad or supply more sequence"); } # define target region my $targregion = Bio::SeqFeature::Generic->new( -start => $left, -end => $right, -primary => 'Target' ); $self->target->add_SeqFeature($targregion); # locate excluded regions my @excluded = grep { $_->primary_tag eq 'Excluded' } $self->target->top_SeqFeatures; if ($self->avoid_snps) { my @snps = grep { $_->primary_tag eq 'variation' } $self->target->top_SeqFeatures; push(@excluded, @snps); } $self->excluded(\@excluded); return $targregion; } sub _get_targetregion { my ($self) = @_; my ($targregion) = grep { $_->primary_tag eq 'Target' } $self->target->top_SeqFeatures; $targregion ||= $self->_define_target; $self->throw("Target region for SiRNA design not defined") unless ($targregion); my $seq = $targregion->seq->seq; # but this way I loose start info my $targstart = $targregion->start; return ($seq, $targstart); } # MOVE to SiRNA::Ruleset::tuschl # sub _regex { # my ($self, $rank) = @_; # return $PATTERNS{$rank}; # } # sub _get_oligos { # # use regular expressions to pull out oligos # my ($self, $rank) = @_; # my $regex = $self->_regex($rank); # my @exclude; # my ($targregion) = grep { $_->primary_tag eq 'Target' } $self->target->top_SeqFeatures; # my $seq = $targregion->seq->seq; # # but this way I loose start info # my $targstart = $targregion->start; # # exclude masked region # push(@exclude, grep { $_->primary_tag eq 'Excluded' } $self->target->top_SeqFeatures); # # add SNP checking # if ($self->avoid_snps) { # my @snps = grep { $_->primary_tag eq 'variation' } $self->target->top_SeqFeatures; # push(@exclude, @snps); # } # while ( $seq =~ /$regex/gi ) { # my $target = $1; # # check for too many Gs (or Cs on the other strand) # next if ( $target =~ /G{ $self->gstring,}/io ); # next if ( $target =~ /C{ $self->gstring,}/io ); # # skip Ns (for filtering) # next if ( $target =~ /N/i); # my $start = length($`) + $targstart; # my $stop = $start + length($target) -1; # my @gc = ( $target =~ /G|C/gi); # my $fxGC = sprintf("%2.2f", (scalar(@gc) / length($target))); # next if ($fxGC < $self->min_gc); # next if ($fxGC > $self->max_gc); # my $sense = Bio::SeqFeature::SiRNA::Oligo->new( -start => $start, # -end => $stop, # -strand => 1, # -seq => _get_sense($target), # -source_tag => ref($self), # ); # my $asense = Bio::SeqFeature::SiRNA::Oligo->new( -start => $start, # -end => $stop, # -strand => -1, # -seq => _get_anti($target), # -source_tag => ref($self), # ); # my $sirna = Bio::SeqFeature::SiRNA::Pair->new( -rank => $rank, # -fxGC => $fxGC, # -sense => $sense, # -antisense => $asense, # -source_tag => ref($self), # ); # unless ($self->_has_overlap($sirna, \@exclude)) { # $self->target->add_SeqFeature($sirna); # } # } # } =head2 add_oligos Title : add_oligos Usage : $sirna_designer->add_oligos($sequence, $start, $rank); Purpose : Add SiRNA olgos to target Bio::Seq as Bio::SeqFeature::SiRNA::Pair objects Args : Oligo sequence and start position (required), rank/score (optional) =cut sub add_oligos { my ($self, $seq, $start, $rank) = @_; ($seq) or throw ('No sequence supplied for add_oligos'); (defined $start) or throw ('No start position specified for add_oligos'); my ($end) = $start + length($seq); my ($sseq) = $self->_get_sense($seq); my $sense = Bio::SeqFeature::SiRNA::Oligo->new( -start => $start, -end => ($start + length($sseq)), -strand => 1, -seq => $sseq, -source_tag => ref($self), ); my $aseq = $self->_get_anti($seq); my $asense = Bio::SeqFeature::SiRNA::Oligo->new( -start => $end, -end => ($end - length($aseq)), -strand => -1, -seq => $aseq, -source_tag => ref($self), ); my $sirna = Bio::SeqFeature::SiRNA::Pair->new( -rank => $rank, # -fxGC => $fxGC, -sense => $sense, -antisense => $asense, -source_tag => ref($self), ); unless ($self->_has_overlap($sirna, $self->excluded)) { $self->target->add_SeqFeature($sirna); } } sub _has_overlap { # flag any pairs that overlap an UNDESIRED feature (eg SNP) # return true if there is overlap, false if not my ($self, $test, $flist) = @_; print STDERR "Checking oligo at ", $test->start, " to ",$test->end, "\n" if ($self->debug); foreach my $feat (@$flist) { if (($test->start <= $feat->end) and ($test->end >= $feat->start)) { print STDERR "Overlaps ", $feat->primary_tag, " at ", $feat->start, " to ", $feat->end, "\n" if ($self->debug); return 1; } } return 0; # default - no overlap } # MOVE to SiRNA::Ruleset::tuschl # sub _get_sense { # my ($target) = @_; # # trim off 1st 2 nt to get overhang # $target =~ s/^..//; # # convert T's to U's (transcribe) # $target =~ s/T/U/gi; # # force last 2 nt to be T's # $target =~ s/..$/TT/; # return $target; # } # sub _get_anti { # my ($target) = @_; # my @target = split(//, $target); # my ($nt,@antitarget); # while ($nt = pop @target) { # push(@antitarget, $COMP{$nt}); # } # my $anti = join('', @antitarget); # # trim off 1st 2 nt to get overhang # $anti =~ s/^..//; # # convert T's to U's # $anti =~ s/T/U/gi; # # convert last 2 NT's to T # $anti =~ s/..$/TT/; # return $anti; # } sub AUTOLOAD { my ($self, $value) = @_; my $name = $AUTOLOAD; $name =~ s/.+:://; return if ($name eq 'DESTROY'); if (defined $value) { $self->{$name} = $value; } unless (exists $self->{$name}) { $self->throw("Attribute $name not defined for ". ref($self)); } return $self->{$name}; } sub _comp { my ($self, $char) = @_; return unless ($char); $char = uc($char); return $COMP{ $char }; } 1; ����������BioPerl-1.007002/Bio/Tools/Sigcleave.pm�������������������������������������������������������������000444��000766��000024�� 43672�13155576320� 17620� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������#----------------------------------------------------------------------------- # PACKAGE : Bio::Tools::Sigcleave # AUTHOR : Chris Dagdigian, dag@sonsorol.org # CREATED : Jan 28 1999 # # Copyright (c) 1997-9 bioperl, Chris Dagdigian and others. All Rights Reserved. # This module is free software; you can redistribute it and/or # modify it under the same terms as Perl itself. # # _History_ # # Object framework ripped from Steve Chervits's SeqPattern.pm # # Core EGCG Sigcleave emulation from perl code developed by # Danh Nguyen & Kamalakar Gulukota which itself was based # loosely on Colgrove's signal.c program. # # The overall idea is to replicate the output of the sigcleave # program which was distributed with the EGCG extension to the GCG sequence # analysis package. There is also an accessor method for just getting at # the raw results. # #----------------------------------------------------------------------------- =head1 NAME Bio::Tools::Sigcleave - Bioperl object for sigcleave analysis =head1 SYNOPSIS =head2 Object Creation use Bio::Tools::Sigcleave (); # to keep the module backwar compatible, you can pass it a sequence string, but # there recommended say is to pass it a Seq object # this works $seq = "MVLLLILSVLLLKEDVRGSAQSSERRVVAHMPGDIIIGALFSVHHQPTVDKVHERKCGAVREQYGI"; $sig = Bio::Tools::Sigcleave->new(-seq => $seq, -type => 'protein', -threshold=>'3.5', ); # but you do: $seqobj = Bio::PrimarySeq->new(-seq => $seq); $sig = Bio::Tools::Sigcleave->new(-seq => $seqobj, -threshold=>'3.5', ); # now you can detect procaryotic signal sequences as well as eucaryotic $sig->matrix('eucaryotic'); # or 'procaryotic' =head2 Object Methods & Accessors # you can use this method to fine tune the threshod before printing out the results $sig->result_count: %raw_results = $sig->signals; $formatted_output = $sig->pretty_print; =head1 DESCRIPTION "Sigcleave" was a program distributed as part of the free EGCG add-on to earlier versions of the GCG Sequence Analysis package. A new implementation of the algorithm is now part of EMBOSS package. From the EGCG documentation: SigCleave uses the von Heijne method to locate signal sequences, and to identify the cleavage site. The method is 95% accurate in resolving signal sequences from non-signal sequences with a cutoff score of 3.5, and 75-80% accurate in identifying the cleavage site. The program reports all hits above a minimum value. The EGCG Sigcleave program was written by Peter Rice (E-mail: pmr@sanger.ac.uk Post: Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs, CB10 1SA, UK). Since EGCG is no longer distributed for the latest versions of GCG, this code was developed to emulate the output of the original program as much as possible for those who lost access to sigcleave when upgrading to newer versions of GCG. There are 2 accessor methods for this object. "signals" will return a perl associative array containing the sigcleave scores keyed by amino acid position. "pretty_print" returns a formatted string similar to the output of the original sigcleave utility. In both cases, the "threshold" setting controls the score reporting level. If no value for threshold is passed in by the user, the code defaults to a reporting value of 3.5. In this implementation the accessor will never return any score/position pair which does not meet the threshold limit. This is the slightly different from the behaviour of the 8.1 EGCG sigcleave program which will report the highest of the under-threshold results if nothing else is found. Example of pretty_print output: SIGCLEAVE of sigtest from: 1 to 146 Report scores over 3.5 Maximum score 4.9 at residue 131 Sequence: FVILAAMSIQGSA-NLQTQWKSTASLALET | (signal) | (mature peptide) 118 131 Other entries above 3.5 Maximum score 3.7 at residue 112 Sequence: CSRQLFGWLFCKV-HPGAIVFVILAAMSIQGSANLQTQWKSTASLALET | (signal) | (mature peptide) 99 112 =head1 FEEDBACK When updating and maintaining a module, it helps to know that people are actually using it. Let us know if you find a bug, think this code is useful or have any improvements/features to suggest. =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Chris Dagdigian, dag-at-sonsorol.org & others =head1 CONTRIBUTORS Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 VERSION Bio::Tools::Sigcleave, $Id$ =head1 COPYRIGHT Copyright (c) 1999 Chris Dagdigian & others. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 REFERENCES / SEE ALSO von Heijne G. (1986) "A new method for predicting signal sequences cleavage sites." Nucleic Acids Res. 14, 4683-4690. von Heijne G. (1987) in "Sequence Analysis in Molecular Biology: Treasure Trove or Trivial Pursuit" (Acad. Press, (1987), 113-117). =head1 APPENDIX The following documentation describes the various functions contained in this module. Some functions are for internal use and are not meant to be called by the user; they are preceded by an underscore ("_"). =cut # ## ### #### END of main POD documentation. ### ## # package Bio::Tools::Sigcleave; use Bio::PrimarySeq; use base qw(Bio::Root::Root); use strict; use vars qw ($ID %WeightTable_euc %WeightTable_pro ); $ID = 'Bio::Tools::Sigcleave'; %WeightTable_euc = ( #Sample: 161 aligned sequences # R -13 -12 -11 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 +1 +2 Expect 'A' => [16, 13, 14, 15, 20, 18, 18, 17, 25, 15, 47, 6, 80, 18, 6, 14.5], 'C' => [ 3, 6, 9, 7, 9, 14, 6, 8, 5, 6, 19, 3, 9, 8, 3, 4.5], 'D' => [ 0, 0, 0, 0, 0, 0, 0, 0, 5, 3, 0, 5, 0, 10, 11, 8.9], 'E' => [ 0, 0, 0, 1, 0, 0, 0, 0, 3, 7, 0, 7, 0, 13, 14, 10.0], 'F' => [13, 9, 11, 11, 6, 7, 18, 13, 4, 5, 0, 13, 0, 6, 4, 5.6], 'G' => [ 4, 4, 3, 6, 3, 13, 3, 2, 19, 34, 5, 7, 39, 10, 7, 12.1], 'H' => [ 0, 0, 0, 0, 0, 1, 1, 0, 5, 0, 0, 6, 0, 4, 2, 3.4], 'I' => [15, 15, 8, 6, 11, 5, 4, 8, 5, 1, 10, 5, 0, 8, 7, 7.4], 'K' => [ 0, 0, 0, 1, 0, 0, 1, 0, 0, 4, 0, 2, 0, 11, 9, 11.3], 'L' => [71, 68, 72, 79, 78, 45, 64, 49, 10, 23, 8, 20, 1, 8, 4, 12.1], 'M' => [ 0, 3, 7, 4, 1, 6, 2, 2, 0, 0, 0, 1, 0, 1, 2, 2.7], 'N' => [ 0, 1, 0, 1, 1, 0, 0, 0, 3, 3, 0, 10, 0, 4, 7, 7.1], 'P' => [ 2, 0, 2, 0, 0, 4, 1, 8, 20, 14, 0, 1, 3, 0, 22, 7.4], 'Q' => [ 0, 0, 0, 1, 0, 6, 1, 0, 10, 8, 0, 18, 3, 19, 10, 6.3], 'R' => [ 2, 0, 0, 0, 0, 1, 0, 0, 7, 4, 0, 15, 0, 12, 9, 7.6], 'S' => [ 9, 3, 8, 6, 13, 10, 15, 16, 26, 11, 23, 17, 20, 15, 10, 11.4], 'T' => [ 2, 10, 5, 4, 5, 13, 7, 7, 12, 6, 17, 8, 6, 3, 10, 9.7], 'V' => [20, 25, 15, 18, 13, 15, 11, 27, 0, 12, 32, 3, 0, 8, 17, 11.1], 'W' => [ 4, 3, 3, 1, 1, 2, 6, 3, 1, 3, 0, 9, 0, 2, 0, 1.8], 'Y' => [ 0, 1, 4, 0, 0, 1, 3, 1, 1, 2, 0, 5, 0, 1, 7, 5.6] ); %WeightTable_pro = ( #Sample: 36 aligned sequences # R -13 -12 -11 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 +1 +2 Expect 'A' => [0, 8, 8, 9, 6, 7, 5, 6, 7, 7, 24, 2, 31, 18, 4, 3.2], 'C' => [1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1.0], 'D' => [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 8, 2.0], 'E' => [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 4, 8, 2.2], 'F' => [2, 4, 3, 4, 1, 1, 8, 0, 4, 1, 0, 7, 0, 1, 0, 1.3], 'G' => [4, 2, 2, 2, 3, 5, 2, 4, 2, 2, 0, 2, 2, 1, 0, 2.7], 'H' => [0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 7, 0, 1, 0, 0.8], 'I' => [3, 1, 5, 1, 5, 0, 1, 3, 0, 0, 0, 0, 0, 0, 2, 1.7], 'K' => [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 0, 3, 0, 2.5], 'L' => [8, 11, 9, 8, 9, 13, 1, 0, 2, 2, 1, 2, 0, 0, 1, 2.7], 'M' => [0, 2, 1, 1, 3, 2, 3, 0, 1, 2, 0, 4, 0, 0, 1, 0.6], 'N' => [0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 3, 0, 1, 4, 1.6], 'P' => [0, 1, 1, 1, 1, 1, 2, 3, 5, 2, 0, 0, 0, 0, 5, 1.7], 'Q' => [0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 0, 3, 0, 0, 1, 1.4], 'R' => [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1.7], 'S' => [1, 0, 1, 4, 4, 1, 5, 15, 5, 8, 5, 2, 2, 0, 0, 2.6], 'T' => [2, 0, 4, 2, 2, 2, 2, 2, 5, 1, 3, 0, 1, 1, 2, 2.2], 'V' => [5, 7, 1, 3, 1, 4, 7, 0, 0, 4, 3, 0, 0, 2, 0, 2.5], 'W' => [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0.4], 'Y' => [0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 1, 0, 0, 0, 1.3] ); ## ## Now we calculate the _real_ values for the weight tables ## ## ## yeah yeah yeah there is lots of math here that gets repeated ## every single time a sigcleave object gets created. This is ## a quick hack to make sure that we get the scores as accurate as ## possible. Need all those significant digits.... ## ## suggestions for speedup aproaches welcome ## foreach my $i (keys %WeightTable_euc) { my $expected = $WeightTable_euc{$i}[15]; if ($expected > 0) { for (my $j=0; $j<16; $j++) { if ($WeightTable_euc{$i}[$j] == 0) { $WeightTable_euc{$i}[$j] = 1; if ($j == 10 || $j == 12) { $WeightTable_euc{$i}[$j] = 1.e-10; } } $WeightTable_euc{$i}[$j] = log($WeightTable_euc{$i}[$j]/$expected); } } } foreach my $i (keys %WeightTable_pro) { my $expected = $WeightTable_pro{$i}[15]; if ($expected > 0) { for (my $j=0; $j<16; $j++) { if ($WeightTable_pro{$i}[$j] == 0) { $WeightTable_pro{$i}[$j] = 1; if ($j == 10 || $j == 12) { $WeightTable_pro{$i}[$j] = 1.e-10; } } $WeightTable_pro{$i}[$j] = log($WeightTable_pro{$i}[$j]/$expected); } } } ##################################################################################### ## CONSTRUCTOR ## ##################################################################################### sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); #my $self = Bio::Seq->new(@args); my ($seq, $threshold, $matrix) = $self->_rearrange([qw(SEQ THRESHOLD MATRIX)],@args); defined $threshold && $self->threshold($threshold); $matrix && $self->matrix($matrix); $seq && $self->seq($seq); return $self; } =head1 threshold Title : threshold Usage : $value = $self->threshold Purpose : Read/write method sigcleave score reporting threshold. Returns : float. Argument : new value, float Throws : on non-number argument Comments : defaults to 3.5 See Also : n/a =cut #---------------- sub threshold { #---------------- my ($self, $value) = @_; if( defined $value) { $self->throw("I need a number, not [$value]") if $value !~ /^[+-]?[\d\.]+$/; $self->{'_threshold'} = $value; } return $self->{'_threshold'} || 3.5 ; } =head1 matrix Title : matrix Usage : $value = $self->matrix('procaryotic') Purpose : Read/write method sigcleave matrix. Returns : float. Argument : new value: 'eucaryotic' or 'procaryotic' Throws : on non-number argument Comments : defaults to 3.5 See Also : n/a =cut #---------------- sub matrix { #---------------- my ($self, $value) = @_; if( defined $value) { $self->throw("I need 'eucaryotic' or 'procaryotic', not [$value]") unless $value eq 'eucaryotic' or $value eq 'procaryotic'; $self->{'_matrix'} = $value; } return $self->{'_matrix'} || 'eucaryotic' ; } =head1 seq Title : seq Usage : $value = $self->seq($seq_object) Purpose : set the Seq object to be used Returns : Seq object Argument : protein sequence or Seq object See Also : n/a =cut #---------------- sub seq { #---------------- my ($self, $value) = @_; if( defined $value) { if ($value->isa('Bio::PrimarySeqI')) { $self->{'_seq'} = $value; } else { $self->{'_seq'} = Bio::PrimarySeq->new(-seq => $value, -alphabet => 'protein'); } } return $self->{'_seq'}; } =head1 _Analyze Title : _Analyze Usage : N/A This is an internal method. Not meant to be called from outside : the package : Purpose : calculates sigcleave score and amino acid position for the : given protein sequence. The score reporting threshold can : be adjusted by passing in the "threshold" parameter during : object construction. If no threshold is passed in, the code : defaults to reporting any scores equal to or above 3.5 : Returns : nothing. results are added to the object Argument : none. Throws : nothing. Comments : nothing. See Also : n/a =cut #---------------- sub _Analyze { #---------------- my($self) = @_; my %signals; my @hitWeight = (); my @hitsort = (); my @hitpos = (); my $maxSite = ""; my $seqPos = ""; my $istart = ""; my $iend = ""; my $icol = ""; my $i = ""; my $weight = ""; my $k = 0; my $c = 0; my $seqBegin = 0; my $pVal = -13; my $nVal = 2; my $nHits = 0; my $seqEnd = $self->seq->length; my $pep = $self->seq->seq; my $minWeight = $self->threshold; my $matrix = $self->matrix; ## The weight table is keyed by UPPERCASE letters so we uppercase ## the pep string because we don't want to alter the actual object ## sequence. $pep =~ tr/a-z/A-Z/; for ($seqPos = $seqBegin; $seqPos < $seqEnd; $seqPos++) { $istart = (0 > $seqPos + $pVal)? 0 : $seqPos + $pVal; $iend = ($seqPos + $nVal - 1 < $seqEnd)? $seqPos + $nVal - 1 : $seqEnd; $icol= $iend - $istart + 1; $weight = 0.00; for ($k=0; $k<$icol; $k++) { $c = substr($pep, $istart + $k, 1); ## CD: The if(defined) stuff was put in here because Sigcleave.pm ## CD: kept getting warnings about undefined vals during 'make test' ... if ($matrix eq 'eucaryotic') { $weight += $WeightTable_euc{$c}[$k] if defined $WeightTable_euc{$c}[$k]; } else { $weight += $WeightTable_pro{$c}[$k] if defined $WeightTable_pro{$c}[$k]; } } $signals{$seqPos+1} = sprintf ("%.1f", $weight) if $weight >= $minWeight; } $self->{"_signal_scores"} = { %signals }; } =head1 signals Title : signals Usage : %sigcleave_results = $sig->signals; : Purpose : Accessor method for sigcleave results : Returns : Associative array. The key value represents the amino acid position : and the value represents the score. Only scores that : are greater than or equal to the THRESHOLD value are reported. : Argument : none. Throws : none. Comments : none. See Also : THRESHOLD =cut #---------------- sub signals { #---------------- my $self = shift; my %results; my $position; # do the calculations $self->_Analyze; foreach $position ( sort keys %{ $self->{'_signal_scores'} } ) { $results{$position} = $self->{'_signal_scores'}{$position}; } return %results; } =head1 result_count Title : result_count Usage : $count = $sig->result_count; : Purpose : Accessor method for sigcleave results : Returns : Integer, number of results above the threshold : Argument : none. Throws : none. Comments : none. See Also : THRESHOLD =cut #---------------- sub result_count { #---------------- my $self = shift; $self->_Analyze; return keys %{ $self->{'_signal_scores'} }; } =head1 pretty_print Title : pretty_print Usage : $output = $sig->pretty_print; : print $sig->pretty_print; : Purpose : Emulates the output of the EGCG Sigcleave : utility. : Returns : A formatted string. Argument : none. Throws : none. Comments : none. See Also : n/a =cut #---------------- sub pretty_print { #---------------- my $self = shift; my $pos; my $output; my $cnt = 1; my %results = $self->signals; my @hits = keys %results; my $hitcount = $#hits; $hitcount++; my $thresh = $self->threshold; my $seqlen = $self->seq->length || 0; my $name = $self->seq->id || 'NONAME'; my $pep = $self->seq->seq; $pep =~ tr/a-z/A-Z/; $output = "SIGCLEAVE of $name from: 1 to $seqlen\n\n"; if ($hitcount > 0) { $output .= "Report scores over $thresh\n"; foreach $pos ((sort { $results{$b} cmp $results{$a} } keys %results)) { my $start = $pos - 15; $start = 1 if $start < 1; my $sig = substr($pep,$start -1,$pos-$start ); $output .= sprintf ("Maximum score %1.1f at residue %3d\n",$results{$pos},$pos); $output .= "\n"; $output .= " Sequence: "; $output .= $sig; $output .= "-" x (15- length($sig)); $output .= "-"; $output .= substr($pep,$pos-1,50); $output .= "\n"; $output .= " " x 12; $output .= "| \(signal\) | \(mature peptide\)\n"; $output .= sprintf(" %3d %3d\n\n",$start,$pos); if (($hitcount > 1) && ($cnt == 1)) { $output .= " Other entries above $thresh\n\n"; } $cnt++; } } $output; } 1; __END__ ######################################################################### # End of class ######################################################################### ����������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Signalp.pm���������������������������������������������������������������000555��000766��000024�� 17042�13155576320� 17306� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# Parser module for Signalp Bio::Tools::Signalp # # # Based on the EnsEMBL module # Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp originally # written by Marc Sohrmann (ms2@sanger.ac.uk) Written in BioPipe by # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Balamurugan Kumarasamy <savikalpa@fugu-sg.org> Cared for by the Fugu # Informatics team (fuguteam@fugu-sg.org) # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Tools::Signalp - parser for Signalp output =head1 SYNOPSIS use Bio::Tools::Signalp; my $parser = Bio::Tools::Signalp->new(-fh =>$filehandle ); while( my $sp_feat = $parser->next_result ) { if ($sp_feat->score > 0.9) { push @likely_sigpep, $sp_feat; } } =head1 DESCRIPTION C<SignalP> predicts the presence and location of signal peptide cleavage sites in amino acid sequences. L<Bio::Tools::Signalp> parses the output of C<SignalP> to provide a L<Bio::SeqFeature::Generic> object describing the signal peptide found, if any. It returns a variety of tags extracted from the NN and HMM analysis. Most importantly, the C<score()> attribute contains the NN probability of this being a true signal peptide. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted va the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR # Please direct questions and support issues to I<bioperl-l@bioperl.org> Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp originally written by Marc Sohrmann (ms2_AT_sanger.ac.uk). Written in BioPipe by Balamurugan Kumarasamy savikalpa_AT_fugu-sg.org. Cared for by the Fugu Informatics team (fuguteam_AT_fugu-sg.org) =head1 CONTRIBUTORS Torsten Seemann - torsten.seemann AT infotech.monash.edu.au =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Signalp; use strict; use Bio::SeqFeature::Generic; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::Signalp->new(); Function: Builds a new Bio::Tools::Signalp object Returns : Bio::Tools::Signalp Args : -fh/-file => $val, # for initing input, see Bio::Root::IO =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_result Title : next_result Usage : my $feat = $signalp->next_result Function: Get the next result set from parser data Returns : Bio::SeqFeature::Generic Args : none =cut sub next_result { my ($self) = @_; while (my $line=$self->_readline()) { chomp $line; if ($line=~/^\>(\S+)/) { $self->_seqname($1); } elsif ($line=~/max\.\s+Y\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) { $self->_fact1($2); } elsif ($line=~/mean\s+S\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) { my $fact2 = $2; if ($fact2 eq 'YES' and $self->_fact1 eq 'YES') { my $line = $self->_readline(); ########################################### # modification to suit new SignalP output ########################################### chomp $line; #print STDERR "********** <$line>\n"; if ($line =~ /\s+D\s+.*/) { $line = $self->_readline(); } #print STDERR "********** <$line>\n"; my $end; ########################################### if ($line =~ /Most likely cleavage site between pos\.\s+(\d+)/) { my $end = $1; my (%feature); $feature{seq_id} = $self->_seqname; $feature{start} = 1; $feature{end} = $end; $feature{source_tag} = 'Signalp'; $feature{primary}= 'signal_peptide'; $self->_parse_hmm_result(\%feature); my $new_feat = $self->_create_feature (\%feature); return $new_feat; } else { $self->throw ("parsing problem in signalp"); } } } } } =head2 _parse_hmm_result Title : _parse_hmm_result Usage : $self->_parse_hmm_result(\%feature) Function: Internal (not to be used directly) Returns : hash of feature values Args : hash of more feature values =cut sub _parse_hmm_result { my ($self, $feature_hash) = @_; while(my $line = $self->_readline){ chomp $line; if($line =~ /Prediction: (.+)$/){ $feature_hash->{hmmProdiction} = $1; }elsif($line =~ /Signal peptide probability: ([0-9\.]+)/){ $feature_hash->{peptideProb} = $1; }elsif($line =~ /Signal anchor probability: ([0-9\.]+)/){ $feature_hash->{anchorProb} = $1; last; } } } =head2 _create_feature Title : _create_feature Usage : $self->create_feature(\%feature) Function: Internal (not to be used directly) Returns : hash of feature values Args : hash of more feature values =cut sub _create_feature { my ($self, $feat) = @_; # create feature object my $feature = Bio::SeqFeature::Generic->new( -seq_id => $feat->{name}, -start => $feat->{start}, -end => $feat->{end}, -score => $feat->{score}, -source => $feat->{source}, -primary => $feat->{primary}, -logic_name => $feat->{logic_name}, ); $feature->score($feat->{peptideProb}); $feature->add_tag_value('peptideProb', $feat->{peptideProb}); $feature->add_tag_value('anchorProb', $feat->{anchorProb}); $feature->add_tag_value('evalue',$feat->{anchorProb}); $feature->add_tag_value('percent_id','NULL'); $feature->add_tag_value("hid",$feat->{primary}); $feature->add_tag_value('SignalpPrediction', $feat->{hmmProdiction}); return $feature; } =head2 _seqname Title : _seqname Usage : $self->_seqname($name) Function: Internal (not to be used directly) Returns : Args : =cut sub _seqname{ my ($self,$seqname)=@_; if (defined$seqname){ $self->{'seqname'}=$seqname; } return $self->{'seqname'}; } =head2 _fact1 Title : _fact1 Usage : $self->fact1($fact1) Function: Internal (not to be used directly) Returns : Args : =cut sub _fact1{ my ($self, $fact1)=@_; if (defined $fact1){ $self->{'fact1'}=$fact1; } return $self->{'fact1'}; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/TandemRepeatsFinder.pm���������������������������������������������������000444��000766��000024�� 21775�13155576320� 21602� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������� =head1 NAME Bio::Tools::TandemRepeatsFinder - a parser for Tandem Repeats Finder output =head1 SYNOPSIS use Bio::Tools::TandemRepeatsFinder; # create parser my $parser = Bio::Tools::Bio::Tools::TandemRepeatsFinder->new(-file => 'tandem_repeats.out'); # loop through results while( my $feature = $parser->next_result ) { # print the source sequence id, start, end, percent matches, and the consensus sequence my ($percent_matches) = $feat->get_tag_values('percent_matches'); my ($consensus_sequence) = $feat->get_tag_values('consensus_sequence'); print $feat->seq_id()."\t".$feat->start()."\t".$feat->end()."\t$percent_matches\t$consensus_sequence\n"; } =head1 DESCRIPTION A parser for Tandem Repeats Finder output. Written and tested for version 4.00 Location, seq_id, and score are stored in Bio::SeqFeature::Generic feature. All other data is stored in tags. The availabale tags are period_size copy_number consensus_size percent_matches percent_indels percent_a percent_c percent_g percent_t entropy consensus_sequence repeat_sequence run_parameters sequence_description The run_parameters are stored in a hashref with the following key: match_weight mismatch_weight indel_weight match_prob indel_prob min_score max_period_size =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Eric Just Email e-just@northwestern.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::TandemRepeatsFinder; use strict; use constant DEBUG => 0; use Bio::SeqFeature::Generic; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::TandemRepeatsFinder->new(); Function: Builds a new Bio::Tools::TandemRepeatsFinder object Returns : Bio::Tools::TandemRepeatsFinder Args : -fh/-file => $val, for initing input, see Bio::Root::IO =cut sub new { my ( $class, @args ) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 version Title : version Usage : $self->version( $version ) Function: get/set the version of Tandem Repeats finder that was used in analysis Returns : value of version of Args : new value (optional) =cut sub version { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'version'} = $value; } return $self->{'version'}; } =head2 _current_seq_id Title : _current_seq_id Usage : $self->_current_seq_id( $current_seq_id ) Function: get/set the _current_seq_id Returns : value of _current_seq_id Args : new value (optional) =cut sub _current_seq_id { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_current_seq_id'} = $value; } return $self->{'_current_seq_id'}; } =head2 _current_seq_description Title : _current_seq_description Usage : $self->_current_seq_description( $current_seq_id ) Function: get/set the _current_seq_description Returns : value of _current_seq_description Args : new value (optional) =cut sub _current_seq_description { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_current_seq_description'} = $value; } return $self->{'_current_seq_description'}; } =head2 _current_parameters Title : _current_parameters Usage : $self->_current_parameters( $parameters_hashref ) Function: get/set the _current_parameters Returns : hashref representing current parameters parsed from results file : keys are match_weight mismatch_weight indel_weight match_prob indel_prob min_score max_period_size Args : parameters hashref (optional) =cut sub _current_parameters { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_current_parameters'} = $value; } return $self->{'_current_parameters'}; } =head2 next_result Title : next_result Usage : my $r = $trf->next_result() Function: Get the next result set from parser data Returns : Bio::SeqFeature::Generic Args : none =cut sub next_result { my ($self) = @_; while ( defined( $_ = $self->_readline() ) ) { # Parse Version line if (/^Version (.+)/) { my $version = $1; $self->warn("parsed version: $version\n") if DEBUG; $self->warn( qq{ Bio::Tools::TandemRepeatsFinder was written and tested for Tandem Repeats Masker Version 4.00 output You appear to be using Verion $version. Use at your own risk.}) if ($version != 4); $self->version($version); } # Parse Sequence identifier # i.e. Sequence: DDB0215018 |Masked Chromosomal Sequence| Chr 2f elsif ( /^Sequence: ([^\s]+)\s(.+)?/ ) { my $seq_id = $1; my $seq_description = $2; $self->warn("parsed sequence_id: $seq_id\n") if DEBUG; $self->_current_seq_id($seq_id); $self->_current_seq_description($seq_description); } # Parse Parameters # i.e. Parameters: 2 7 7 80 10 50 12 elsif (/^Parameters: (.+)/) { my $params = $1; $self->warn("parsed parameters: $params\n") if DEBUG; my @param_array = split /\s/, $params; my $param_hash = { match_weight => $param_array[0], mismatch_weight => $param_array[1], indel_weight => $param_array[2], match_prob => $param_array[3], indel_prob => $param_array[4], min_score => $param_array[5], max_period_size => $param_array[6] }; $self->_current_parameters($param_hash); } # Parse Data # i.e. 13936 13960 12 2.1 12 100 0 50 16 8 52 24 1.70 T TTTTTTTTTT elsif (/^\d+\s\d+\s\d+/) { # call internal method to create Bio::SeqFeature::Generic # to represent tandem repeat return $self->_create_feature($_); } elsif (DEBUG) { $self->warn( "UNPARSED LINE:\n" . $_ ); } } return; } =head2 _create_feature Title : _create_feature Usage : internal method used by 'next_feature' Function: Takes a line from the results file and creates a bioperl object Returns : Bio::SeqFeature::Generic Args : none =cut sub _create_feature { my ( $self, $line ) = @_; # split the line and store into named variables my @element = split /\s/, $line; my ( $start, $end, $period_size, $copy_number, $consensus_size, $percent_matches, $percent_indels, $score, $percent_a, $percent_c, $percent_g, $percent_t, $entropy, $consensus_sequence, $repeat_sequence ) = @element; # create tag hash from data in line my $tags = { period_size => $period_size, copy_number => $copy_number, consensus_size => $consensus_size, percent_matches => $percent_matches, percent_indels => $percent_indels, percent_a => $percent_a, percent_c => $percent_c, percent_g => $percent_g, percent_t => $percent_t, entropy => $entropy, consensus_sequence => $consensus_sequence, repeat_sequence => $repeat_sequence, run_parameters => $self->_current_parameters(), sequence_description => $self->_current_seq_description() }; # create feature from start/end etc my $feat = Bio::SeqFeature::Generic->new( -seq_id => $self->_current_seq_id(), -score => $score, -start => $start, -end => $end, -source_tag => 'Tandem Repeats Finder', -primary_tag => 'tandem repeat', -tag => $tags ); return $feat; } 1; ���BioPerl-1.007002/Bio/Tools/TargetP.pm���������������������������������������������������������������000444��000766��000024�� 27630�13155576320� 17260� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # Bioperl module for TargetP # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Emmanuel Quevillon <emmanuel.quevillon@versailles.inra.fr> # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Tools::TargetP - Results of one TargetP run =head1 SYNOPSIS use Bio::Tools::TargetP; #filename for TargetP result : $targetp = Bio::Tools::TargetP->new(-file => 'targetp.out'); # filehandle for TargetP : $targetp = Bio::Tools::TargetP->new( -fh => \*INPUT ); ### targetp v1.1 prediction results ################################## #Number of query sequences: 11 #Cleavage site predictions included. #Using NON-PLANT networks. # #Name Len mTP SP other Loc RC TPlen #---------------------------------------------------------------------- #swall|Q9LIP3|C72Y_AR 500 0.245 0.935 0.009 S 2 22 #swall|Q52813|AAPQ_RH 400 0.170 0.462 0.577 _ 5 - #swall|O86459|AAT_RHI 400 0.346 0.046 0.660 _ 4 - # parse the results while($feature = $targetp->next_prediction()) { #$feature is a Bio::SeqFeature::Generic object my $method = $targetp->analysis_method(); my $vesion = $targetp->analysis_method_version() || $feature->source(); my $seqid = $feature->seq_id(); # ... } # essential if you gave a filename at initialization (otherwise the file # will stay open) $targetp->close(); =head1 DESCRIPTION TargetP modules will provides parsed information about protein localization. It reads in a targetp output file. It parses the results, and returns a Bio::SeqFeature::Generic object for each seqeunces found to have a subcellular localization =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Emmanuel Quevillon Email emmanuel.quevillon@versailles.inra.fr Describe contact details here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::TargetP; use strict; use Bio::Tools::AnalysisResult; use Bio::SeqFeature::Generic; use Data::Dumper; use base qw(Bio::Tools::AnalysisResult); #Definition of 'Loc' field according to http://www.cbs.dtu.dk/services/TargetP/output.php my $MAPLOC = { 'S' => 'Secretory pathway', 'M' => 'Mitochondrion', 'C' => 'Chloroplast', '_' => 'Any other', '*' => 'Unknown', '?' => 'Unknown', }; =head1 analysis_method Usage : $self->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches Returns : String Argument : n/a =cut sub analysis_method { my ($self, $method) = @_; if($method && ($method !~ /TargetP/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head1 network Title : network Usage : $self->network($network) Function: This method Get/Set the network used for the analysis (PLANT or NON-PLANT) Example : Returns : string Arguments: On set, the network used =cut sub network { my($self, $net) = @_; if(defined($net)){ $self->{'_network'} = $net; } return $self->{'_network'}; } =head1 cleavage Title : cleavage Usage : $self->cleavage($cleavage) Function : This method Get/Set if SignalP program was used to run TargetP Example : Returns : 1 or 0 Arguments: On set, the cleavage used or not =cut sub cleavage { my($self, $cleavage) = @_; if(defined($cleavage)){ $self->{'_cleavage'} = $cleavage =~ /not included/ ? '0' : '1'; } return $self->{'_cleavage'}; } =head1 next_prediction Usage : $targetp->next_prediction() Purpose : Returns the next TargetP prediction Returns : A Bio::SeqFeature::Generic object Arguments: n/a =cut sub next_prediction { my($self) = @_; unless($self->_parsed()){ $self->_parse_results(); $self->_parsed(1); } return shift @{$self->{'_features'}} || undef; } =head1 create_feature Title : create_feature Usage : $self->create_feature(\%hash); Function : This method creates a new Bio::SeqFeature::Generic object Example : Returns : Bio::SeqFeature::Generic Arguments : hash reference =cut sub create_feature { my($self, $feat) = @_; $self->throw("Need a reference to hash table") unless($feat && ref($feat) eq 'HASH'); my $feature = Bio::SeqFeature::Generic->new( -seq_id => $feat->{seqid}, -source_tag => $self->analysis_method(), -primary_tag => 'signal_peptide', #Sequence Ontology compliant -strand => '+', ); if(defined($feat->{seqlen})){ $feature->start(1); $feature->end($feat->{seqlen}); } $feature->add_tag_value('location', $MAPLOC->{$feat->{loc}}) if(exists($MAPLOC->{$feat->{loc}})); $feature->add_tag_value('chloroplastCutOff', $feat->{cTP}) if(defined($feat->{cTP})); $feature->add_tag_value('mitochondrionCutOff', $feat->{mTP}) if(defined($feat->{mTP})); $feature->add_tag_value('signalPeptideCutOff', $feat->{SP}) if(defined($feat->{SP})); $feature->add_tag_value('otherCutOff', $feat->{other}) if(defined($feat->{other})); $feature->add_tag_value('reliabilityClass', $feat->{RC}) if(defined($feat->{RC})); $feature->add_tag_value('signalPeptideLength', $feat->{TPLen}) if(defined($feat->{TPLen})); $feature->add_tag_value('network', $self->network()); return $feature; } =head2 PRIVATE METHODS =cut =head2 _initialize_state Title : _initialize_state Usage : n/a; usually called by _initialize() itself called by new() Function: This method is supposed to reset the state such that any 'history' is lost. State information that does not change during object lifetime is not considered as history, e.g. parent, name, etc shall not be reset. An inheriting object should only be concerned with state information it introduces itself, and for everything else call SUPER::_initialize_state(@args). The argument syntax is the same as for new() and _initialize(), i.e., named parameters following the -name=>$value convention. The following parameters are dealt with by the implementation provided here: -INPUT, -FH, -FILE (tags are case-insensitive). Example : Returns : Args : =cut sub _initialize_state { my ($self,@args,) = @_; # first call the inherited method! $self->SUPER::_initialize_state(@args); # our private state variables $self->{'_features'} = [ ]; $self->{'_parameters'} = undef; $self->{'_format'} = undef; $self->{'_network'} = undef; $self->{'_cleavage'} = undef; $self->{'_parsed'} = 0; $self->analysis_method('TargetP'); return 1; } =head2 _predictions Usage : $targetp->_prediction() Purpose : Returns the number of TargetP predictions Returns : A scalar (number) Arguments: n/a =cut sub _predictions { my($self) = @_; return scalar(@{$self->{'_features'}}) || 0; } =head2 _parsed Title : _parsed Usage : $targetp->_parsed(1) Function : This method is used to know if the output result is parsed or not For internal use only Example : Returns : 1/0 Arguments : 1/0 for setting =cut sub _parsed { my($self, $value) = @_; if(defined($value)){ $self->{'_parsed'} = $value; } return $self->{'_parsed'}; } =head2 _parse_results Title : _parse_results Usage : $self->_parse_results() Function : This method parses a TargetP output For internal use only Example : Returns : n/a Arguments: none =cut sub _parse_results { my($self) = @_; ### targetp v1.1 prediction results ################################## #Number of query sequences: 11 #Cleavage site predictions included. #Using NON-PLANT networks. # #Name Len mTP SP other Loc RC TPlen #---------------------------------------------------------------------- #swall|Q9LIP3|C72Y_AR 500 0.245 0.935 0.009 S 2 22 #swall|Q52813|AAPQ_RH 400 0.170 0.462 0.577 _ 5 - #swall|O86459|AAT_RHI 400 0.346 0.046 0.660 _ 4 - while(defined(my $line = $self->_readline())){ if($line =~ /targetp (v[\d\.]+)/){ $self->analysis_method_version($1); }elsif($line =~ /Cleavage site predictions (.*)/){ $self->cleavage($1); }elsif($line =~ /Using (\S+) networks/){ $self->network($1); }elsif($line =~ /^Name/){ #We skip the next line which is '------------------' $self->_readline(); my $hash = { }; while(defined(my $line = $self->_readline())){ last if($line =~ /^----/); my $hash = $self->_parse_line($line); my $new_feature = $self->create_feature($hash); $self->_add_feature($new_feature); } } } return; } =head2 _parse_line Title : _parse_line Usage : $self->_parse_line($line) Function : This method parses the line result For internal use only Example : Returns : Hash reference Arguemnts: line to parse =cut sub _parse_line { my($self, $line) = @_; $self->throw("No line to parse given") unless($line); my $hash = { }; my ($seqid, $seqlen, $cTP, $mTP, $SP, $other, $loc, $RC, $TPlen); if($self->network() eq 'NON-PLANT'){ ($seqid, $seqlen, $mTP, $SP, $other, $loc, $RC, $TPlen) = split(/\s+/, $line); }else{ ($seqid, $seqlen, $cTP, $mTP, $SP, $other, $loc, $RC, $TPlen) = split(/\s+/, $line); } $hash->{seqid} = $seqid; $hash->{seqlen} = $seqlen; $hash->{cTP} = $cTP || undef; $hash->{mTP} = $mTP; $hash->{SP} = $SP; $hash->{other} = $other; $hash->{loc} = $loc; $hash->{RC} = $RC; $hash->{TPLen} = ($TPlen && $TPlen =~ /\d+/) ? $TPlen : undef; return $hash; } =head2 _add_feature Title : _add_feature Usage : $self->_add_feature($feature) Function : This method stores a feature object For internal use only Example : Returns : n/a Arguments: Bio::SeqFeature::Generic =cut sub _add_feature { my($self, $feature) = @_; $self->throw("Need a Bio::SeqFeature::Generic object") unless $feature->isa("Bio::SeqFeature::Generic"); push(@{$self->{'_features'}}, $feature); return; } =head2 _toString_location Title : _toString_location Usage : $self->_toString_location($key) Function : This method convert the 'one letter code' location to the corresponding definition For internal use only Example : Returns : Location or undef Arguments: String =cut sub _toString_location { my($self, $key) = @_; if($key && exists($MAPLOC->{$key})){ return $MAPLOC->{$key}; } return; } 1; ��������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Tmhmm.pm�����������������������������������������������������������������000555��000766��000024�� 6615�13155576320� 16757� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Tmhmm # # Original copyright Balamurugan Kumarasamy # Re-written cleanly by Torsten Seemann, Sep 2006 # # Copyright: # You may distribute this module under the same terms as Perl itself =head1 NAME Bio::Tools::Tmhmm - parse TMHMM output (TransMembrane HMM) =head1 SYNOPSIS use Bio::Tools::Tmhmm; my $parser = Bio::Tools::Tmhmm->new(-fh => $filehandle ); while ( my $tmhmm_feat = $parser->next_result ) { # do something, e.g. push @tmhmm_feat, $tmhmm_feat; } =head1 DESCRIPTION TMHMM is software for the prediction of transmembrane helices in proteins. See L<http://www.cbs.dtu.dk/services/TMHMM/> for more details. This module parses the "long output" format of TMHMM 2.0 and creates a Bio:SeqFeature::Generic object for each C<TMHelix> feature found from lines like this: my_sequence_id TMHMM2.0 TMhelix 54 76 =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Torsten Seemann Email torsten.seemann AT infotech.monash.edu.au =head1 CONTRIBUTOR - Bala Email savikalpa@fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Tmhmm; use strict; use Bio::Tools::AnalysisResult; use Bio::Root::Root; use Bio::Root::IO; use base qw(Bio::Root::Root Bio::Root::IO Bio::Tools::AnalysisResult); use Bio::SeqFeature::Generic; =head2 new Title : new Usage : my $obj = Bio::Tools::Tmhmm->new(); Function: Builds a new Bio::Tools::Tmhmm object Returns : Bio::Tools::Tmhmm Args : Either of the following as per L<Bio::Root::IO> interface -fh => $filehandle -file => $filename =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_result Title : next_result Usage : my $feat = $Tmhmm->next_result Function: Get the next result set from parser data Returns : Bio::SeqFeature::Generic Args : none =cut sub next_result { my $self = shift; # # my_sequence_id Length: 178 # my_sequence_id TMHMM2.0 outside 1 53 # my_sequence_id TMHMM2.0 TMhelix 54 76 # my_sequence_id TMHMM2.0 inside 77 115 while (my $line = $self->_readline) { if ( $line =~ m/^(\S+)\s+(\S+)\s+(TMhelix)\s+(\d+)\s+(\d+)$/i ) { return Bio::SeqFeature::Generic->new( -primary => 'transmembrane', -seq_id => $1, -source => $2, -start => $4, -end => $5, ); } } } 1; �������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/dpAlign.pm���������������������������������������������������������������000444��000766��000024�� 56640�13155576320� 17273� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������� # BioPerl module for Bio::Tools::dpAlign # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Yee Man Chan <ymc@yahoo.com> # # Copyright Yee Man Chan # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::dpAlign - Perl extension to do pairwise dynamic programming sequence alignment =head1 SYNOPSIS use Bio::Tools::dpAlign; use Bio::SeqIO; use Bio::SimpleAlign; use Bio::AlignIO; use Bio::Matrix::IO; $seq1 = Bio::SeqIO->new(-file => $ARGV[0], -format => 'fasta'); $seq2 = Bio::SeqIO->new(-file => $ARGV[1], -format => 'fasta'); # create a dpAlign object # to do global alignment, specify DPALIGN_GLOBAL_MILLER_MYERS # to do ends-free alignment, specify DPALIGN_ENDSFREE_MILLER_MYERS $factory = new dpAlign(-match => 3, -mismatch => -1, -gap => 3, -ext => 1, -alg => Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS); # actually do the alignment $out = $factory->pairwise_alignment($seq1->next_seq, $seq2->next_seq); $alnout = Bio::AlignIO->new(-format => 'pfam', -fh => \*STDOUT); $alnout->write_aln($out); # To do protein alignment, set the sequence type to protein # By default all protein alignments are using BLOSUM62 matrix # the gap opening cost is 7 and gap extension is 1. These # values are from ssearch. To use your own custom substitution # matrix, you can create a Bio::Matrix::MatrixI object. $parser = Bio::Matrix::IO->new(-format => 'scoring', -file => 'blosum50.mat'); $matrix = $parser->next_matrix; $factory = Bio::Tools::dpAlign->new(-matrix => $matrix, -alg => Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLERMYERS); $seq1->alphabet('protein'); $seq2->alphabet('protein'); $out = $factory->pairwise_alignment($seq1->next_seq, $seq2->next_seq); $alnout->write_aln($out); # use the factory to make some output $factory->align_and_show($seq1, $seq2, STDOUT); # use Phil Green's algorithm to calculate the optimal local # alignment score between two sequences quickly. It is very # useful when you are searching a query sequence in a database # of sequences. Since finding a alignment is more costly # than just calculating scores, you can save time if you only # align sequences that have a high alignment score. # To use this feature, first you call the sequence_profile function # to obtain the profile of the query sequence. $profile = $factory->sequence_profile($query); %scores = (); # Then use a loop to run a database of sequences against the # profile to obtain a table of alignment scores $dbseq = Bio::SeqIO(-file => 'dbseq.fa', -format => 'fasta'); while (defined($seq = $dbseq->next_seq)) { $scores{$seq->id} = $factory->pairwise_alignment_score($profile, $seq); } =head1 DESCRIPTION Dynamic Programming approach is considered to be the most sensitive way to align two biological sequences. There are currently three major types of dynamic programming algorithms: Global Alignment, Local Alignment and Ends-free Alignment. Global Alignment compares two sequences in their entirety. By inserting gaps in the two sequences, it aligns two sequences to minimize the edit distance as defined by the gap cost function and the substitution matrix. Global Alignment is generally applied to two sequences that are very similar in length and content. Local Alignment instead attempts to find out the subsequences that has the minimal edit distance among all possible subsequences. It is good for sequences that has a stretch of subsequences that are similar to each other. Ends-free Alignment is a special case of Global Alignment. There are no gap penalty imposed for the gaps that extended from the end points of two sequences. Therefore it will be a good application when you think one sequence is contained by the other or when you think two sequences overlap each other. Dynamic Programming was first introduced by Needleman-Wunsch (1970) to globally align two sequences. The idea of local alignment was later introduced by Smith-Waterman (1981). Gotoh (1982) improved both algorithms by introducing auxiliary arrays that reduced the time complexity of the algorithms to O(m*n). Miller-Myers (1988) exploits the divide-and-conquer idea introduced by Hirschberg (1975) to solve the affine gap cost dynamic programming using only linear space. At the time of this writing, it is accepted that Miller-Myers is the fastest single CPU implementation and using the least memory that is truly equivalent to original algorithm introduced by Needleman-Wunsch. According to Aaron Mackey, Phil Green's SWAT implementation introduced a heuristic that does not consider paths through the matrix where the score would be less than the gap opening penalty, yielding a 1.5-2X speedup on most comparisons. to skip the calculation of some cells. However, his approach is only good for calculating the minimum edit distance and find out the corresponding subsequences (aka search phase). Bill Pearson's popular dynamic programming alignment program SSEARCH uses Phil Green's algorithm to find the subsequences and then Miller-Myers's algorithm to find the actual alignment. (aka alignment phase) The current implementation supports local alignment of either DNA sequences or protein sequences. It allows you to specify either the Miller-Myers Global Alignment (DPALIGN_GLOBAL_MILLER_MYERS) or Miller-Myers Local Alignment (DPALIGN_LOCAL_MILLER_MYERS). For DNA alignment, you can specify the scores for match, mismatch, gap opening cost and gap extension cost. For protein alignment, it is using BLOSUM62 by default. Currently the substitution matrix is not configurable. Note: If you supply LocatableSeq objects to pairwise_alignment, pairwise_alignment_score, align_and_show or sequence_profile and the sequence supplied contains gaps, these functions will treat these sequences as if they are without gaps. =head1 DEPENDENCIES This package comes with the main bioperl distribution. You also need to install the lastest bioperl-ext package which contains the XS code that implements the algorithms. This package won't work if you haven't compiled the bioperl-ext package. =head1 TO-DO =over 3 =item 1. Basic support for IUPAC code for DNA sequence is now implemented. X will mismatch any character. T will match U. For others, whenever there is a possibility for match, it is considered a full match, for example, W will match B. =item 2. Allow custom substitution matrix for DNA. Note that for proteins, you can now use your own subsitution matirx. =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR This implementation was written by Yee Man Chan (ymc@yahoo.com). Copyright (c) 2003 Yee Man Chan. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. Special thanks to Aaron Mackey and WIlliam Pearson for the helpful discussions. [The portion of code inside pgreen subdirectory was borrowed from ssearch. It should be distributed in the same terms as ssearch.] =cut package Bio::Tools::dpAlign; use Bio::SimpleAlign; use base qw(Bio::Tools::AlignFactory); # Gotoh algorithm as defined in J. Mol. Biol. (1982) 162, 705-708 # use constant DSW_GOTOH => 1; # Hirschberg's algorithm as defined in Myers & Miller in # CABIOS, Vol 4, No. 1, 1988, p 11-17 # This algorithm is used in both the search phase and the # alignment phase. use constant DPALIGN_LOCAL_MILLER_MYERS => 1; use constant DPALIGN_GLOBAL_MILLER_MYERS => 2; use constant DPALIGN_ENDSFREE_MILLER_MYERS => 3; # my toy algorithm that tries to do SW as fast as possible # use constant DSW_FSW => 3; # Phil Green's approximation to Smith-Waterman. It avoid calculations # that might result in a score less than the opening gap penalty. # This is the algorithm used by ssearch. Phil Green's algorithm is # used in the search phase while Miller-Myers algorithm is used in # the alignment phase #use constant DPALIGN_LOCAL_GREEN => 2; BEGIN { eval { require Bio::Ext::Align; }; if ( $@ ) { die("\nThe C-compiled engine for Smith Waterman alignments (Align) has not been installed.\n Please read the install the bioperl-ext package\n\n"); exit(1); } } sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($match, $mismatch, $gap, $ext, $alg, $matrix) = $self->_rearrange([qw(MATCH MISMATCH GAP EXT ALG MATRIX )], @args); $self->match(3) unless defined $match; $self->mismatch(-1) unless defined $mismatch; $self->gap(3) unless defined $gap; $self->ext(1) unless defined $ext; $self->alg(DPALIGN_LOCAL_MILLER_MYERS) unless defined $alg; if (defined $match) { if ($match =~ /^\d+$/) { $self->match($match); } else { $self->throw("Match score must be a number, not [$match]"); } } if (defined $mismatch) { if ($match =~ /^\d+$/) { $self->mismatch($mismatch); } else { $self->throw("Mismatch penalty must be a number, not [$mismatch]"); } } if (defined $gap) { if ($gap =~ /^\d+$/) { $self->gap($gap); } else { $self->throw("Gap penalty must be a number, not [$gap]"); } } if (defined $ext) { if ($ext =~ /^\d+$/) { $self->ext($ext); } else { $self->throw("Extension penalty must be a number, not [$ext]"); } } if (defined $alg) { if ($alg == DPALIGN_LOCAL_MILLER_MYERS or $alg == DPALIGN_GLOBAL_MILLER_MYERS or $alg == DPALIGN_ENDSFREE_MILLER_MYERS) { $self->alg($alg); } else { $self->throw("Algorithm must be either 1, 2 or 3"); } } if (defined $matrix and $matrix->isa('Bio::Matrix::MatrixI')) { $self->{'matrix'} = Bio::Ext::Align::ScoringMatrix->new(join("", $matrix->row_names), $self->gap, $self->ext); foreach $rowname ($matrix->row_names) { foreach $colname ($matrix->column_names) { Bio::Ext::Align::ScoringMatrix->set_entry($self->{'matrix'}, $rowname, $colname, $matrix->entry($rowname, $colname)); } } } else { $self->{'matrix'} = 0; } return $self; } =head2 sequence_profile Title : sequence_profile Usage : $prof = $factory->sequence_profile($seq1) Function: Makes a dpAlign_SequenceProfile object from one sequence Returns : A dpAlign_SequenceProfile object Args : The lone argument is a Bio::PrimarySeqI that we want to build a profile for. Usually, this would be the Query sequence =cut sub sequence_profile { my ($self, $seq1) = @_; if( ! defined $seq1 || ! $seq1->isa('Bio::PrimarySeqI')) { $self->warn("Cannot call sequence_profilewithout specifing one sequence (Bio::PrimarySeqI object)"); return; } # fix Jitterbug #1044 if( $seq1->length() < 2) { $self->warn("cannot create sequence profile with length less than 2"); return; } if ($seq1->isa('Bio::LocatableSeq')) { my $seqstr = $seq1->seq; $seqstr =~ s/\-//g; $seq1 = Bio::Seq->new(-id => $seq1->id, -seq => $seqstr, -alphabet => $seq1->alphabet); } # create engine objects $seq1->display_id('seq1') unless ( defined $seq1->id() ); if ($seq1->alphabet eq 'dna') { return Bio::Ext::Align::SequenceProfile->dna_new($seq1->seq, $self->{'match'}, $self->{'mismatch'}, $self->{'gap'}, $self->{'ext'}); } elsif ($seq1->alphabet eq 'protein') { return Bio::Ext::Align::SequenceProfile->protein_new($seq1->seq, $self->{'matrix'}); } else { croak("There is currently no support for the types of sequences you want to align!\n"); return; } } =head2 pairwise_alignment_score Title : pairwise_alignment_score Usage : $score = $factory->pairwise_alignment_score($prof,$seq2) Function: Makes a SimpleAlign object from two sequences Returns : An integer that is the score of the optimal alignment. Args : The first argument is the sequence profile obtained from a call to the sequence_profile function. The second argument is a Bio::PrimarySeqI object to be aligned. The second argument is usually a sequence in the database sequence. Note that this function only uses Phil Green's algorithm and therefore theoretically may not always give you the optimal score. =cut sub pairwise_alignment_score { my ($self, $prof, $seq2) = @_; if( ! defined $prof || ! $prof->isa('Bio::Ext::Align::SequenceProfile') || ! defined $seq2 || ! $seq2->isa('Bio::PrimarySeqI') ) { $self->warn("Cannot call pairwise_alignment_score without specifing 2 sequences (Bio::PrimarySeqI objects)"); return; } # fix Jitterbug #1044 if( $seq2->length() < 2) { $self->warn("cannot align sequences with length less than 2"); return; } if ($seq2->isa('Bio::LocatableSeq')) { my $seqstr = $seq2->seq; $seqstr =~ s/\-//g; $seq2 = Bio::Seq->new(-id => $seq2->id, -seq => $seqstr, -alphabet => $seq2->alphabet); } $self->set_memory_and_report(); # create engine objects $seq2->display_id('seq2') unless ( defined $seq2->id() ); if ($prof->alphabet eq 'dna' and $seq2->alphabet eq 'dna') { return Bio::Ext::Align::Score_DNA_Sequences($prof, $seq2->seq); } elsif ($prof->alphabet eq 'protein' and $seq2->alphabet eq 'protein') { return Bio::Ext::Align::Score_Protein_Sequences($prof, $seq2->seq); } else { $self->throw("There is currently no support for the types of sequences you want to align!\n"); return; } } =head2 pairwise_alignment Title : pairwise_alignment Usage : $aln = $factory->pairwise_alignment($seq1,$seq2) Function: Makes a SimpleAlign object from two sequences Returns : A SimpleAlign object if there is an alignment with positive score. Otherwise, return undef. Args : The first and second arguments are both Bio::PrimarySeqI objects that are to be aligned. =cut sub pairwise_alignment { my ($self, $seq1, $seq2) = @_; my ($aln, $out); if( ! defined $seq1 || ! $seq1->isa('Bio::PrimarySeqI') || ! defined $seq2 || ! $seq2->isa('Bio::PrimarySeqI') ) { $self->warn("Cannot call pairwise_alignment without specifing 2 sequences (Bio::PrimarySeqI objects)"); return; } # fix Jitterbug #1044 if( $seq1->length() < 2 || $seq2->length() < 2 ) { $self->warn("cannot align sequences with length less than 2"); return; } if ($seq1->isa('Bio::LocatableSeq')) { my $seqstr = $seq1->seq; $seqstr =~ s/\-//g; $seq1 = Bio::Seq->new(-id => $seq1->id, -seq => $seqstr, -alphabet => $seq1->alphabet); } if ($seq2->isa('Bio::LocatableSeq')) { my $seqstr = $seq2->seq; $seqstr =~ s/\-//g; $seq2 = Bio::Seq->new(-id => $seq2->id, -seq => $seqstr, -alphabet => $seq2->alphabet); } $self->set_memory_and_report(); # create engine objects $seq1->display_id('seq1') unless ( defined $seq1->id() ); $seq2->display_id('seq2') unless ( defined $seq2->id() ); if ($seq1->alphabet eq 'dna' and $seq2->alphabet eq 'dna') { $aln = Bio::Ext::Align::Align_DNA_Sequences($seq1->seq, $seq2->seq, $self->{'match'}, $self->{'mismatch'}, $self->{'gap'}, $self->{'ext'}, $self->{'alg'}); } elsif ($seq1->alphabet eq 'protein' and $seq2->alphabet eq 'protein') { $aln = Bio::Ext::Align::Align_Protein_Sequences($seq1->seq, $seq2->seq, $self->{'matrix'}, $self->{'alg'}); } else { croak("There is currently no support for the types of sequences you want to align!\n"); return; } if (not defined $aln or $aln == 0) { return; } $out = Bio::SimpleAlign->new(); $out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln1, -start => $aln->start1, -end => $aln->end1, -id => $seq1->id)); $out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln2, -start => $aln->start2, -end => $aln->end2, -id => $seq2->id)); $out->score($aln->score); return $out; } =head2 align_and_show Title : align_and_show Usage : $factory->align_and_show($seq1,$seq2,STDOUT) =cut sub align_and_show { my ($self, $seq1, $seq2, $fh) = @_; my ($aln, $out); if (! defined $fh) { $fh = \*STDOUT; } if( ! defined $seq1 || ! $seq1->isa('Bio::PrimarySeqI') || ! defined $seq2 || ! $seq2->isa('Bio::PrimarySeqI') ) { $self->warn("Cannot call pairwise_alignment without specifing 2 sequences (Bio::PrimarySeqI objects)"); return; } # fix Jitterbug #1044 if( $seq1->length() < 2 || $seq2->length() < 2 ) { $self->warn("cannot align sequences with length less than 2"); return; } if ($seq1->isa('Bio::LocatableSeq')) { my $seqstr = $seq1->seq; $seqstr =~ s/\-//g; $seq1 = Bio::Seq->new(-id => $seq1->id, -seq => $seqstr, -alphabet => $seq1->alphabet); } if ($seq2->isa('Bio::LocatableSeq')) { my $seqstr = $seq2->seq; $seqstr =~ s/\-//g; $seq2 = Bio::Seq->new(-id => $seq2->id, -seq => $seqstr, -alphabet => $seq2->alphabet); } $self->set_memory_and_report(); # create engine objects $seq1->display_id('seq1') unless ( defined $seq1->id() ); $seq2->display_id('seq2') unless ( defined $seq2->id() ); if ($seq1->alphabet eq 'dna' and $seq2->alphabet eq 'dna') { $aln = Bio::Ext::Align::Align_DNA_Sequences($seq1->seq, $seq2->seq, $self->{'match'}, $self->{'mismatch'}, $self->{'gap'}, $self->{'ext'}, $self->{'alg'}); } elsif ($seq1->alphabet eq 'protein' and $seq2->alphabet eq 'protein') { $aln = Bio::Ext::Align::Align_Protein_Sequences($seq1->seq, $seq2->seq, $self->{'matrix'}, $self->{'alg'}); } else { croak("There is currently no support for the types of sequences you want to align!\n"); } $out = Bio::Ext::Align::AlnBlock->new(); my $s1 = Bio::Ext::Align::AlnSequence->new(); my $s2 = Bio::Ext::Align::AlnSequence->new(); my $a1 = $aln->aln1; my $a2 = $aln->aln2; my $first_col = undef; my $last_col = undef; my $col; my $alu1; my $alu2; my $g1 = 0; my $g2 = 0; # construct AlnBlock for (my $i = 0; $i < length($a1); ++$i) { $col = Bio::Ext::Align::AlnColumn->new(); $alu1 = Bio::Ext::Align::AlnUnit->new(); $alu2 = Bio::Ext::Align::AlnUnit->new(); $first_col = $col unless defined $first_col; Bio::Ext::Align::AlnColumn::set_next($last_col, $col) if defined $last_col; if (substr($a1, $i, 1) eq "-") { Bio::Ext::Align::AlnUnit::set_text_label($alu1, "INSERT"); Bio::Ext::Align::AlnUnit::set_text_label($alu2, "SEQUENCE"); ++$g1; } elsif (substr($a2, $i, 1) eq "-") { Bio::Ext::Align::AlnUnit::set_text_label($alu1, "SEQUENCE"); Bio::Ext::Align::AlnUnit::set_text_label($alu2, "INSERT"); ++$g2; } else { Bio::Ext::Align::AlnUnit::set_text_label($alu1, "SEQUENCE"); Bio::Ext::Align::AlnUnit::set_text_label($alu2, "SEQUENCE"); } Bio::Ext::Align::AlnUnit::set_start($alu1, $aln->start1+$i-$g1-2); Bio::Ext::Align::AlnUnit::set_end($alu1, $aln->start1+$i-$g1-2); Bio::Ext::Align::AlnUnit::set_start($alu2, $aln->start2+$i-$g2-2); Bio::Ext::Align::AlnUnit::set_end($alu2, $aln->start2+$i-$g2-2); Bio::Ext::Align::AlnColumn::add_alu($col, $alu1); Bio::Ext::Align::AlnColumn::add_alu($col, $alu2); $last_col = $col; } Bio::Ext::Align::AlnBlock::set_start($out, $first_col); $col = Bio::Ext::Align::AlnColumn->new(); $alu1 = Bio::Ext::Align::AlnUnit->new(); $alu2 = Bio::Ext::Align::AlnUnit->new(); Bio::Ext::Align::AlnUnit::set_start($alu1, $aln->end1); Bio::Ext::Align::AlnUnit::set_end($alu1, $aln->end1); Bio::Ext::Align::AlnUnit::set_text_label($alu1, "END"); Bio::Ext::Align::AlnUnit::set_start($alu2, $aln->end2); Bio::Ext::Align::AlnUnit::set_end($alu2, $aln->end2); Bio::Ext::Align::AlnUnit::set_text_label($alu2, "END"); Bio::Ext::Align::AlnColumn::add_alu($col, $alu1); Bio::Ext::Align::AlnColumn::add_alu($col, $alu2); Bio::Ext::Align::AlnColumn::set_next($last_col, $col); &Bio::Ext::Align::write_pretty_str_align($out,$seq1->id,$seq1->seq,$seq2->id,$seq2->seq,12,50,$fh); } =head2 match Title : match Usage : $match = $factory->match() #get : $factory->match($value) #set Function : the set get for the match score Example : Returns : match value Arguments : new value =cut sub match { my ($self,$val) = @_; if( defined $val ) { if( $val < 0 ) { # Fixed so that match==0 is allowed /AE $self->throw("Can't have a match score less than 0"); } $self->{'match'} = $val; } return $self->{'match'}; } =head2 mismatch Title : mismatch Usage : $mismatch = $factory->mismatch() #get : $factory->mismatch($value) #set Function : the set get for the mismatch penalty Example : Returns : mismatch value Arguments : new value =cut sub mismatch { my ($self,$val) = @_; if( defined $val ) { if( $val > 0 ) { # Fixed so that mismatch==0 is allowed /AE $self->throw("Can't have a mismatch penalty greater than 0"); } $self->{'mismatch'} = $val; } return $self->{'mismatch'}; } =head2 gap Title : gap Usage : $gap = $factory->gap() #get : $factory->gap($value) #set Function : the set get for the gap penalty Example : Returns : gap value Arguments : new value =cut sub gap { my ($self,$val) = @_; if( defined $val ) { if( $val < 0 ) { # Fixed so that gap==0 is allowed /AE $self->throw("Can't have a gap penalty less than 0"); } $self->{'gap'} = $val; } return $self->{'gap'}; } =head2 ext Title : ext Usage : $ext = $factory->ext() #get : $factory->ext($value) #set Function : the set get for the ext penalty Example : Returns : ext value Arguments : new value =cut sub ext { my ($self,$val) = @_; if( defined $val ) { if( $val < 0 ) { # Fixed so that ext==0 is allowed /AE $self->throw("Can't have a extension penalty less than 0"); } $self->{'ext'} = $val; } return $self->{'ext'}; } =head2 alg Title : alg Usage : $alg = $factory->alg() #get : $factory->alg($value) #set Function : the set get for the algorithm Example : Returns : alg value Arguments : new value =cut sub alg { my ($self,$val) = @_; if( defined $val ) { if( $val != DPALIGN_LOCAL_MILLER_MYERS and $val != DPALIGN_GLOBAL_MILLER_MYERS and $val != DPALIGN_ENDSFREE_MILLER_MYERS) { $self->throw("Can't have an algorithm that is not 1, 2 or 3"); } $self->{'alg'} = $val; } return $self->{'alg'}; } 1; ������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/ipcress.pm���������������������������������������������������������������000444��000766��000024�� 16604�13155576320� 17361� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::ipcress # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Sheldon McKay <mckays@cshl.edu> # # Copyright Sheldon McKay # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::ipcress - Parse ipcress output and make features =head1 SYNOPSIS # A simple annotation pipeline wrapper for ipcress data # assuming ipcress data is already generated in file seq1.ipcress # and sequence data is in fasta format in file called seq1.fa use Bio::Tools::ipcress; use Bio::SeqIO; my $parser = Bio::Tools::ipcress->new(-file => 'seq1.ipcress'); my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => 'seq1.fa'); my $seq = $seqio->next_seq || die("cannot get a seq object from SeqIO"); while( my $feat = $parser->next_feature ) { # add ipcress annotation to a sequence $seq->add_SeqFeature($feat); } my $seqout = Bio::SeqIO->new(-format => 'embl'); $seqout->write_seq($seq); =head1 DESCRIPTION This object serves as a parser for ipcress data, creating a Bio::SeqFeatureI for each ipcress hit. These can be processed or added as annotation to an existing Bio::SeqI object for the purposes of automated annotation. This module is adapted from the Bio::Tools::EPCR module written by Jason Stajich (jason-at-bioperl.org). Ipcress is available through Guy Slater's Exonerate package http://www.ebi.ac.uk/~guy/exonerate/ =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sheldon McKay Email mckays@cshl.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::ipcress; use strict; use Bio::SeqFeature::Generic; use base qw(Bio::Root::Root); =head2 new Title : new Usage : my $ipcress = Bio::Tools::ipcress->new(-file => $file, -primary => $fprimary, -source => $fsource, -groupclass => $fgroupclass); Function: Initializes a new ipcress parser Returns : Bio::Tools::ipcress Args : -fh => filehandle OR -file => filename -primary => a string to be used as the common value for each features '-primary' tag. Defaults to the sequence ontology term 'PCR_product'. (This in turn maps to the GFF 'type' tag (aka 'method')). -source => a string to be used as the common value for each features '-source' tag. Defaults to 'ipcress'. (This in turn maps to the GFF 'source' tag) -groupclass => a string to be used as the name of the tag which will hold the sts marker namefirst attribute. Defaults to 'name'. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($primary, $source, $groupclass, $file, $fh) = $self->_rearrange([qw(PRIMARY SOURCE GROUPCLASS FILE FH)],@args); $self->primary(defined $primary ? $primary : 'PCR_product'); $self->source(defined $source ? $source : 'ipcress'); $self->groupclass(defined $groupclass ? $groupclass : 'name'); local $/ = 'Ipcress result'; my @result; if ($file) { open my $FH, '<', $file or $self->throw("Could not read file '$file': $!"); @result = (<$FH>); close $FH; } elsif ($fh) { @result = (<$fh>); } else { $self->throw("Bio::Tools::ipcress: no input file"); } shift @result; $self->{result} = \@result; return $self; } =head2 next_feature Title : next_feature Usage : $seqfeature = $obj->next_feature(); Function: Returns the next feature available in the analysis result, or undef if there are no more features. Example : Returns : A Bio::SeqFeatureI implementing object, or undef if there are no more features. Args : none =cut sub next_feature { my ($self) = @_; my $result = shift @{$self->{result}}; return unless defined($result); chomp $result; my @lines = split "\n", $result; my ($ipcress) = grep /ipcress: /, @lines; my (undef,$seqname,$mkrname,$length,undef,$start,$mismatchL, undef,undef,$mismatchR,$desc) = split /\s+/, $ipcress; my $end = $start + $length; $start += 1; my $strand = $desc eq 'forward' ? '+' : $desc eq 'revcomp' ? '-' : 0; my ($left) = grep /\# forward/, @lines; $left =~ s/[^A-Z]+//g; my ($right) = grep /\# revcomp/, @lines; $right =~ s/[^A-Z]+//g; $right = reverse $right; # if there are multiple hits, increment the name for # the groupclass if (++$self->{seen}->{$mkrname} > 1) { $mkrname .= "\.$self->{seen}->{$mkrname}"; } my $markerfeature = Bio::SeqFeature::Generic->new ( '-start' => $start, '-end' => $end, '-strand' => $strand, '-source' => $self->source, '-primary' => $self->primary, '-seq_id' => $seqname, '-tag' => { $self->groupclass => $mkrname, }); if (!$strand) { $markerfeature->add_tag_value('Note' => "bad product: single primer amplification"); } $markerfeature->add_tag_value('left_primer' => $left); $markerfeature->add_tag_value('right_primer' => $right); $markerfeature->add_tag_value('left_mismatches' => $mismatchL) if $mismatchL; $markerfeature->add_tag_value('right_mismatches' => $mismatchR) if $mismatchR; return $markerfeature; } =head2 source Title : source Usage : $obj->source($newval) Function: Example : Returns : value of source (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub source{ my $self = shift; return $self->{'_source'} = shift if @_; return $self->{'_source'}; } =head2 primary Title : primary Usage : $obj->primary($newval) Function: Example : Returns : value of primary (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub primary{ my $self = shift; return $self->{'_primary'} = shift if @_; return $self->{'_primary'}; } =head2 groupclass Title : groupclass Usage : $obj->groupclass($newval) Function: Example : Returns : value of groupclass (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub groupclass{ my $self = shift; return $self->{'_groupclass'} = shift if @_; return $self->{'_groupclass'}; } 1; ����������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/isPcr.pm�����������������������������������������������������������������000555��000766��000024�� 15164�13155576320� 16774� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::isPcr # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Sheldon McKay <mckays@cshl.edu> # # Copyright Sheldon McKay # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::isPcr - Parse isPcr output and make features =head1 SYNOPSIS # A simple annotation pipeline wrapper for isPcr data # assuming isPcr data is already generated in file seq1.isPcr # and sequence data is in fasta format in file called seq1.fa # Note: this parser is meant for the default fasta output from # isPcr. bed and psl output formats are not supported. use Bio::Tools::IsPcr; use Bio::SeqIO; my $parser = Bio::Tools::isPcr->new(-file => 'seq1.isPcr'); my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => 'seq1.fa'); my $seq = $seqio->next_seq || die("cannot get a seq object from SeqIO"); while( my $feat = $parser->next_feature ) { # add isPcr annotation to a sequence $seq->add_SeqFeature($feat); } my $seqout = Bio::SeqIO->new(-format => 'embl'); $seqout->write_seq($seq); =head1 DESCRIPTION This object serves as a parser for isPcr data (in the default fasta format), creating a Bio::SeqFeatureI for each isPcr hit. These can be processed or added as annotation to an existing Bio::SeqI object for the purposes of automated annotation. This module is adapted from the Bio::Tools::EPCR module written by Jason Stajich (jason-at-bioperl.org). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sheldon McKay Email mckays@cshl.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::isPcr; use strict; use Bio::SeqIO; use Bio::SeqFeature::Generic; use base qw(Bio::Root::Root); =head2 new Title : new Usage : my $ispcr = Bio::Tools::isPcr->new( -file => $file, -primary => $fprimary, -source => $fsource, -groupclass => $fgroupclass); Function: Initializes a new isPcr parser Returns : Bio::Tools::isPcr Args : -fh => filehandle OR -file => filename -primary => a string to be used as the common value for each features '-primary' tag. Defaults to the sequence ontology term 'PCR_product'. (This in turn maps to the GFF 'type' tag (aka 'method')). -source => a string to be used as the common value for each features '-source' tag. Defaults to 'isPcr'. (This in turn maps to the GFF 'source' tag) -groupclass => a string to be used as the name of the tag which will hold the sts marker namefirst attribute. Defaults to 'name'. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($primary,$source,$groupclass) = $self->_rearrange([qw/PRIMARY SOURCE GROUPCLASS/],@args); $self->primary(defined $primary ? $primary : 'PCR_product'); $self->source(defined $source ? $source : 'isPcr'); $self->groupclass(defined $groupclass ? $groupclass : 'name'); # default output for isPcr is fasta format $self->{io} = Bio::SeqIO->new(-format => 'fasta', @args); return $self; } =head2 next_feature Title : next_feature Usage : $seqfeature = $obj->next_feature(); Function: Returns the next feature available in the analysis result, or undef if there are no more features. Example : Returns : A Bio::SeqFeatureI implementing object, or undef if there are no more features. Args : none =cut sub next_feature { my ($self) = @_; my $result = $self->{io}->next_seq; return unless defined $result; my ($seqname,$location) = split ':', $result->primary_id; my ($pcrname,$left,$right) = split /\s+/, $result->desc; my ($start,$strand,$end) = $location =~ /^(\d+)([-+])(\d+)$/; my $amplicon = $result->seq; # if there are multiple hits, increment the name for # the groupclass if (++$self->{seen}->{$pcrname} > 1) { $pcrname .= "\.$self->{seen}->{$pcrname}"; } my $tags = { $self->groupclass => $pcrname, amplicon => $amplicon, left_primer => $left, right_primer => $right }; my $markerfeature = Bio::SeqFeature::Generic->new( '-start' => $start, '-end' => $end, '-strand' => $strand, '-source' => $self->source, '-primary' => $self->primary, '-seq_id' => $seqname, '-tag' => $tags ); return $markerfeature; } =head2 source Title : source Usage : $obj->source($newval) Function: Example : Returns : value of source (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub source{ my $self = shift; return $self->{'_source'} = shift if @_; return $self->{'_source'}; } =head2 primary Title : primary Usage : $obj->primary($newval) Function: Example : Returns : value of primary (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub primary{ my $self = shift; return $self->{'_primary'} = shift if @_; return $self->{'_primary'}; } =head2 groupclass Title : groupclass Usage : $obj->groupclass($newval) Function: Example : Returns : value of groupclass (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub groupclass{ my $self = shift; return $self->{'_groupclass'} = shift if @_; return $self->{'_groupclass'}; } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/pICalculator.pm����������������������������������������������������������000555��000766��000024�� 24260�13155576320� 20273� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::pICalculator # # Copyright (c) 2002, Merck & Co. Inc. All Rights Reserved. # # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::pICalculator - calculate the isoelectric point of a protein =head1 DESCRIPTION Calculates the isoelectric point of a protein, the pH at which there is no overall charge on the protein. Calculates the charge on a protein at a given pH. Can use built-in sets of pK values or custom pK sets. =head1 SYNOPSIS use Bio::Tools::pICalculator; use Bio::SeqIO; my $in = Bio::SeqIO->new( -fh => \*STDIN , -format => 'Fasta' ); my $calc = Bio::Tools::pICalculator->new(-places => 2, -pKset => 'EMBOSS'); while ( my $seq = $in->next_seq ) { $calc->seq($seq); my $iep = $calc->iep; print sprintf( "%s\t%s\t%.2f\n", $seq->id, $iep, $calc->charge_at_pH($iep) ); for( my $i = 0; $i <= 14; $i += 0.5 ){ print sprintf( "pH = %.2f\tCharge = %.2f\n", $i, $calc->charge_at_pH($i) ); } } =head1 SEE ALSO http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf http://emboss.sourceforge.net/apps/cvs/emboss/apps/iep.html http://us.expasy.org/tools/pi_tool.html =head1 LIMITATIONS There are various sources for the pK values of the amino acids. The set of pK values chosen will affect the pI reported. The charge state of each residue is assumed to be independent of the others. Protein modifications (such as a phosphate group) that have a charge are ignored. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Mark Southern (mark_southern@merck.com). From an algorithm by David Tabb found at http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf. Modification for Bioperl, additional documentation by Brian Osborne. =head1 COPYRIGHT Copyright (c) 2002, Merck & Co. Inc. All Rights Reserved. This module is free software. It may be used, redistributed and/or modified under the terms of the Perl Artistic License (see http://www.perl.com/perl/misc/Artistic.html) =head1 APPENDIX The rest of the documentation details each of the object methods. Private methods are usually preceded by a _. =cut # Let the code begin... package Bio::Tools::pICalculator; use strict; use base qw(Bio::Root::Root); # pK values from the DTASelect program from Scripps # http://fields.scripps.edu/DTASelect my $DTASelect_pK = { N_term => 8.0, K => 10.0, # Lys R => 12.0, # Arg H => 6.5, # His D => 4.4, # Asp E => 4.4, # Glu C => 8.5, # Cys Y => 10.0, # Tyr C_term => 3.1 }; # pK values from the iep program from EMBOSS # http://emboss.sourceforge.net/apps/cvs/emboss/apps/iep.html my $Emboss_pK = { N_term => 8.6, K => 10.8, # Lys R => 12.5, # Arg H => 6.5, # His D => 3.9, # Asp E => 4.1, # Glu C => 8.5, # Cys Y => 10.1, # Tyr C_term => 3.6 }; =head2 desc Title : new Usage : Bio::Tools::pICalculator->new Function: Instantiates the Bio::Tools::pICalculator object Example : $calc = Bio::Tools::pICalculator->new( -pKset => \%pKvalues, # a Bio::Seq object -seq => $seq, -places => 2 ); or: $calc = Bio::Tools::pICalculator->new( -pKset => 'string', # a Bio::Seq object -seq => $seq, -places => 1 ); Constructs a new pICalculator. Arguments are a flattened hash. Valid, optional keys are: pKset - A reference to a hash with key value pairs for the pK values of the charged amino acids. Required keys are: N_term C_term K R H D E C Y pKset - A string ( 'DTASelect' or 'EMBOSS' ) that will specify an internal set of pK values to be used. The default is 'EMBOSS' seq - A Bio::Seq sequence object to analyze places - The number of decimal places to use in the isoelectric point calculation. The default is 2. Returns : The description Args : The description or none =cut sub new { my( $class, %opts ) = @_; my $self = $class->SUPER::new(%opts); $self = bless {}, ref $self || $self; $self->seq( $opts{-seq} ) if exists $opts{-seq}; $self->pKset( $opts{-pKset} || 'EMBOSS' ); exists $opts{-places} ? $self->places( $opts{-places} ) : $self->places(2); return $self; } =head2 seq Title : seq Usage : $calc->seq($seqobj) Function: Sets or returns the Bio::Seq used in the calculation Example : $seqobj = Bio::Seq->new(-seq=>"gghhhmmm",-id=>"GHM"); $calc = Bio::Tools::pICalculator->new; $calc->seq($seqobj); Returns : Bio::Seq object Args : Bio::Seq object or none =cut sub seq { my( $this, $seq ) = @_; unless( defined $seq && UNIVERSAL::isa($seq,'Bio::Seq') ){ $this->throw("$seq is not a valid Bio::Seq object"); } $this->{-seq} = $seq; $this->{-count} = count_charged_residues( $seq ); return $this->{-seq}; } =head2 pKset Title : pKset Usage : $pkSet = $calc->pKSet(\%pKSet) Function: Sets or returns the hash of pK values used in the calculation Example : $calc->pKset('emboss') Returns : reference to pKset hash Args : The reference to a pKset hash, a string, or none. Examples: pKset - A reference to a hash with key value pairs for the pK values of the charged amino acids. Required keys are: N_term C_term K R H D E C Y pKset - A valid string ( 'DTASelect' or 'EMBOSS' ) that will specify an internal set of pK values to be used. The default is 'EMBOSS' =cut sub pKset { my ( $this, $pKset ) = @_; if( ref $pKset eq 'HASH' ){ # user defined pK values $this->{-pKset} = $pKset; }elsif( $pKset =~ /^emboss$/i ){ # from EMBOSS's iep program $this->{-pKset} = $Emboss_pK; }elsif( $pKset =~ /^dtaselect$/i ){ # from DTASelect (scripps) $this->{-pKset} = $DTASelect_pK; }else{ # default to EMBOSS $this->{-pKset} = $Emboss_pK; } return $this->{-pKset}; } sub places { my $this = shift; $this->{-places} = shift if @_; return $this->{-places}; } =head2 iep Title : iep Usage : $calc->iep Function: Returns the isoelectric point Example : $calc = Bio::Tools::pICalculator->new(-places => 2); $calc->seq($seqobj); $iep = $calc->iep; Returns : The isoelectric point of the sequence in the Bio::Seq object Args : None =cut sub iep { my $this = shift; return _calculate_iep($this->{-pKset}, $this->{-places}, $this->{-seq}, $this->{-count} ); } =head2 charge_at_pH Title : charge_at_pH Usage : $charge = $calc->charge_at_pH($pH) Function: Sets or gets the description of the sequence Example : $calc = Bio::Tools::pICalculator->new(-places => 2); $calc->seq($seqobj); $charge = $calc->charge_at_ph("7"); Returns : The predicted charge at the given pH Args : pH =cut sub charge_at_pH { my $this = shift; return _calculate_charge_at_pH( shift, $this->{-pKset}, $this->{-count} ); } sub count_charged_residues { my $seq = shift; my $sequence = $seq->seq; my $count; for ( qw( K R H D E C Y ) ){ # charged AA's $count->{$_}++ while $sequence =~ /$_/ig; } return $count; } sub _calculate_iep { my( $pK, $places, $seq, $count ) = @_; my $pH = 7.0; my $step = 3.5; my $last_charge = 0.0; my $format = "%.${places}f"; unless( defined $count ){ $count = count_charged_residues($seq); } while(1){ my $charge = _calculate_charge_at_pH( $pH, $pK, $count ); last if sprintf($format,$charge) == sprintf($format,$last_charge); $charge > 0 ? ( $pH += $step ) : ( $pH -= $step ); $step /= 2.0; $last_charge = $charge; } return sprintf( $format, $pH ); } # it's the sum of all the partial charges for the # termini and all of the charged aa's! sub _calculate_charge_at_pH { no warnings; # don't complain if a given key doesn't exist my( $pH, $pK, $count ) = @_; my $charge = _partial_charge( $pK->{N_term}, $pH ) + $count->{K} * _partial_charge( $pK->{K}, $pH ) + $count->{R} * _partial_charge( $pK->{R}, $pH ) + $count->{H} * _partial_charge( $pK->{H}, $pH ) - $count->{D} * _partial_charge( $pH, $pK->{D} ) - $count->{E} * _partial_charge( $pH, $pK->{E} ) - $count->{C} * _partial_charge( $pH, $pK->{C} ) - $count->{Y} * _partial_charge( $pH, $pK->{Y} ) - _partial_charge( $pH, $pK->{C_term} ); return $charge; } # Concentration Ratio is 10**(pK - pH) for positive groups # and 10**(pH - pK) for negative groups sub _partial_charge { my $cr = 10 ** ( $_[0] - $_[1] ); return $cr / ( $cr + 1 ); } 1; __END__ ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/pSW.pm�������������������������������������������������������������������000444��000766��000024�� 25440�13155576320� 16420� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������� # # BioPerl module for Bio::Tools::pSW # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@sanger.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::pSW - pairwise Smith Waterman object =head1 SYNOPSIS use Bio::Tools::pSW; use Bio::AlignIO; my $factory = Bio::Tools::pSW->new( '-matrix' => 'blosum62.bla', '-gap' => 12, '-ext' => 2, ); #use the factory to make some output $factory->align_and_show($seq1,$seq2,STDOUT); # make a Bio::SimpleAlign and do something with it my $aln = $factory->pairwise_alignment($seq1,$seq2); my $alnout = Bio::AlignIO->new(-format => 'msf', -fh => \*STDOUT); $alnout->write_aln($aln); =head1 INSTALLATION This module is included with the central Bioperl distribution: http://bio.perl.org/Core/Latest ftp://bio.perl.org/pub/DIST Follow the installation instructions included in the INSTALL file. =head1 DESCRIPTION pSW is an Alignment Factory for protein sequences. It builds pairwise alignments using the Smith-Waterman algorithm. The alignment algorithm is implemented in C and added in using an XS extension. The XS extension basically comes from the Wise2 package, but has been slimmed down to only be the alignment part of that (this is a good thing!). The XS extension comes from the bioperl-ext package which is distributed along with bioperl. I<Warning:> This package will not work if you have not compiled the bioperl-ext package. The mixture of C and Perl is ideal for this sort of problem. Here are some plus points for this strategy: =over 2 =item Speed and Memory The algorithm is actually implemented in C, which means it is faster than a pure perl implementation (I have never done one, so I have no idea how faster) and will use considerably less memory, as it efficiently assigns memory for the calculation. =item Algorithm efficiency The algorithm was written using Dynamite, and so contains an automatic switch to the linear space divide-and-conquer method. This means you could effectively align very large sequences without killing your machine (it could take a while though!). =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Ewan Birney, birney-at-sanger.ac.uk or birney-at-ebi.ac.uk =head1 CONTRIBUTORS Jason Stajich, jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with an underscore "_". =cut # Let the code begin... package Bio::Tools::pSW; use strict; no strict ( 'refs'); BEGIN { eval { require Bio::Ext::Align; }; if ( $@ ) { die("\nThe C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed.\n Please read the install the bioperl-ext package\n\n"); exit(1); } } use Bio::SimpleAlign; use base qw(Bio::Tools::AlignFactory); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my($matrix,$gap,$ext) = $self->_rearrange([qw(MATRIX GAP EXT )],@args); #default values - we have to load matrix into memory, so # we need to check it out now if( ! defined $matrix || !($matrix =~ /\w/) ) { $matrix = 'blosum62.bla'; } $self->matrix($matrix); # will throw exception if it can't load it $self->gap(12) unless defined $gap; $self->ext(2) unless defined $ext; # I'm pretty sure I am not doing this right... ho hum... # This was not roght ($gap and $ext could not be 0) It is fixed now /AE if( defined $gap ) { if( $gap =~ /^\d+$/ ) { $self->gap($gap); } else { $self->throw("Gap penalty must be a number, not [$gap]"); } } if( defined $ext ) { if( $ext =~ /^\d+$/ ) { $self->ext($ext); } else { $self->throw("Extension penalty must be a number, not [$ext]"); } } return $self; } =head2 pairwise_alignment Title : pairwise_alignment Usage : $aln = $factory->pairwise_alignment($seq1,$seq2) Function: Makes a SimpleAlign object from two sequences Returns : A SimpleAlign object Args : =cut sub pairwise_alignment{ my ($self,$seq1,$seq2) = @_; my($t1,$t2,$aln,$out,@str1,@str2,@ostr1,@ostr2,$alc,$tstr,$tid,$start1,$end1,$start2,$end2,$alctemp); if( ! defined $seq1 || ! $seq1->isa('Bio::PrimarySeqI') || ! defined $seq2 || ! $seq2->isa('Bio::PrimarySeqI') ) { $self->warn("Cannot call pairwise_alignment without specifing 2 sequences (Bio::PrimarySeqI objects)"); return; } # fix Jitterbug #1044 if( $seq1->length() < 2 || $seq2->length() < 2 ) { $self->warn("cannot align sequences with length less than 2"); return; } $self->set_memory_and_report(); # create engine objects $seq1->display_id('seq1') unless ( defined $seq1->id() ); $seq2->display_id('seq2') unless ( defined $seq2->id() ); $t1 = &Bio::Ext::Align::new_Sequence_from_strings($seq1->id(), $seq1->seq()); $t2 = &Bio::Ext::Align::new_Sequence_from_strings($seq2->id(), $seq2->seq()); $aln = &Bio::Ext::Align::Align_Sequences_ProteinSmithWaterman($t1,$t2,$self->{'matrix'},-$self->gap,-$self->ext); if( ! defined $aln || $aln == 0 ) { $self->throw("Unable to build an alignment"); } # free sequence engine objects $t1 = $t2 = 0; # now we have to get into the AlnBlock structure and # figure out what is aligned to what... # we are going to need the sequences as arrays for convience @str1 = split(//, $seq1->seq()); @str2 = split(//, $seq2->seq()); # get out start points # The alignment is in alignment coordinates - ie the first # residues starts at -1 and ends at 0. (weird I know). # bio-coordinates are +2 from this... $start1 = $aln->start()->alu(0)->start +2; $start2 = $aln->start()->alu(1)->start +2; # step along the linked list of alc units... for($alc = $aln->start();$alc->at_end() != 1;$alc = $alc->next()) { if( $alc->alu(0)->text_label eq 'SEQUENCE' ) { push(@ostr1,$str1[$alc->alu(0)->start+1]); } else { # assume it is in insert! push(@ostr1,'-'); } if( $alc->alu(1)->text_label eq 'SEQUENCE' ) { push(@ostr2,$str2[$alc->alu(1)->start+1]); } else { # assume it is in insert! push(@ostr2,'-'); } $alctemp = $alc; } # # get out end points # # end points = real residue end in 'C' coordinates = residue # end in biocoordinates. Oh... the wonder of coordinate systems! $end1 = $alctemp->alu(0)->end+1; $end2 = $alctemp->alu(1)->end+1; # get rid of the alnblock $alc = 0; $aln = 0; # new SimpleAlignment $out = Bio::SimpleAlign->new(); # new SimpleAlignment $tstr = join('',@ostr1); $tid = $seq1->id(); $out->add_seq(Bio::LocatableSeq->new( -seq=> $tstr, -start => $start1, -end => $end1, -id=>$tid )); $tstr = join('',@ostr2); $tid = $seq2->id(); $out->add_seq(Bio::LocatableSeq->new( -seq=> $tstr, -start => $start2, -end => $end2, -id=> $tid )); # give'm back the alignment return $out; } =head2 align_and_show Title : align_and_show Usage : $factory->align_and_show($seq1,$seq2,STDOUT) =cut sub align_and_show { my($self,$seq1,$seq2,$fh) = @_; my($t1,$t2,$aln,$id,$str); if( ! defined $seq1 || ! $seq1->isa('Bio::PrimarySeqI') || ! defined $seq2 || ! $seq2->isa('Bio::PrimarySeqI') ) { $self->warn("Cannot call align_and_show without specifing 2 sequences (Bio::PrimarySeqI objects)"); return; } # fix Jitterbug #1044 if( $seq1->length() < 2 || $seq2->length() < 2 ) { $self->warn("cannot align sequences with length less than 2"); return; } if( ! defined $fh ) { $fh = \*STDOUT; } $self->set_memory_and_report(); $seq1->display_id('seq1') unless ( defined $seq1->id() ); $seq2->display_id('seq2') unless ( defined $seq2->id() ); $t1 = &Bio::Ext::Align::new_Sequence_from_strings($seq1->id(),$seq1->seq()); $t2 = &Bio::Ext::Align::new_Sequence_from_strings($seq2->id(),$seq2->seq()); $aln = &Bio::Ext::Align::Align_Sequences_ProteinSmithWaterman($t1,$t2,$self->{'matrix'},-$self->gap,-$self->ext); if( ! defined $aln || $aln == 0 ) { $self->throw("Unable to build an alignment"); } &Bio::Ext::Align::write_pretty_seq_align($aln,$t1,$t2,12,50,$fh); } =head2 matrix Title : matrix() Usage : $factory->matrix('blosum62.bla'); Function : Reads in comparison matrix based on name : Returns : Argument : comparison matrix =cut sub matrix { my($self,$comp) = @_; my $temp; if( !defined $comp ) { $self->throw("You must have a comparison matrix to set!"); } # talking to the engine here... $temp = &Bio::Ext::Align::CompMat::read_Blast_file_CompMat($comp); if( !(defined $temp) || $temp == 0 ) { $self->throw("$comp cannot be read as a BLAST comparison matrix file"); } $self->{'matrix'} = $temp; } =head2 gap Title : gap Usage : $gap = $factory->gap() #get : $factory->gap($value) #set Function : the set get for the gap penalty Example : Returns : gap value Arguments : new value =cut sub gap { my ($self,$val) = @_; if( defined $val ) { if( $val < 0 ) { # Fixed so that gap==0 is allowed /AE $self->throw("Can't have a gap penalty less than 0"); } $self->{'gap'} = $val; } return $self->{'gap'}; } =head2 ext Title : ext Usage : $ext = $factory->ext() #get : $factory->ext($value) #set Function : the set get for the ext penalty Example : Returns : ext value Arguments : new value =cut sub ext { my ($self,$val) = @_; if( defined $val ) { if( $val < 0 ) { # Fixed so that gap==0 is allowed /AE $self->throw("Can't have a gap penalty less than 0"); } $self->{'ext'} = $val; } return $self->{'ext'}; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/tRNAscanSE.pm������������������������������������������������������������000444��000766��000024�� 20251�13155576320� 17603� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::tRNAscanSE # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::tRNAscanSE - A parser for tRNAscan-SE output =head1 SYNOPSIS use Bio::Tools::tRNAscanSE; my $parser = Bio::Tools::tRNAscanSE->new(-file => 'result.tRNAscanSE'); # parse the results while( my $gene = $parser->next_prediction ) { @exon_arr = $gene->get_SeqFeatures(); } =head1 DESCRIPTION This script will parse tRNAscan-SE output. Just the tabular output of the tRNA locations in the genome for now. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::tRNAscanSE; use strict; use Bio::SeqFeature::Generic; use base qw(Bio::Tools::AnalysisResult); use vars qw($GeneTag $SrcTag $ExonTag); ($GeneTag,$SrcTag,$ExonTag) = qw(gene tRNAscan-SE exon); =head2 new Title : new Usage : my $obj = Bio::Tools::tRNAscanSE->new(); Function: Builds a new Bio::Tools::tRNAscanSE object Returns : an instance of Bio::Tools::tRNAscanSE Args : -fh/-file for input filename -genetag => primary tag used in gene features (default 'tRNA_gene') -exontag => primary tag used in exon features (default 'tRNA_exon') -srctag => source tag used in all features (default 'tRNAscan-SE') =cut sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); my ($genetag,$exontag,$srctag) = $self->SUPER::_rearrange([qw(GENETAG SRCTAG EXONTAG)], @args); $self->gene_tag(defined $genetag ? $genetag : $GeneTag); $self->source_tag(defined $srctag ? $srctag : $SrcTag); $self->exon_tag(defined $exontag ? $exontag : $ExonTag); $self->{'_seen'} = {}; } =head2 gene_tag Title : gene_tag Usage : $obj->gene_tag($newval) Function: Get/Set the value used for the 'gene_tag' of genes Default is 'tRNA_gene' as set by the global $GeneTag Returns : value of gene_tag (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub gene_tag{ my $self = shift; return $self->{'gene_tag'} = shift if @_; return $self->{'gene_tag'}; } =head2 source_tag Title : source_tag Usage : $obj->source_tag($newval) Function: Get/Set the value used for the 'source_tag' of exons and genes Default is 'tRNAscan-SE' as set by the global $SrcTag Returns : value of source_tag (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub source_tag{ my $self = shift; return $self->{'_source_tag'} = shift if @_; return $self->{'_source_tag'}; } =head2 exon_tag Title : exon_tag Usage : $obj->exon_tag($newval) Function: Get/Set the value used for the 'primary_tag' of exons Default is 'tRNA_exon' as set by the global $ExonTag Returns : value of exon_tag (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub exon_tag{ my $self = shift; return $self->{'_exon_tag'} = shift if @_; return $self->{'_exon_tag'}; } =head2 analysis_method Usage : $genscan->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /tRNAscan-SE/i. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method && ($method !~ /tRNAscan-SE/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head2 next_feature Title : next_feature Usage : while($gene = $genscan->next_feature()) { # do something } Function: Returns the next gene structure prediction of the Genscan result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Example : Returns : A Bio::SeqFeature::Generic object. Args : See also : L<Bio::SeqFeature::Generic> =cut sub next_feature { my ($self,@args) = @_; # even though next_prediction doesn't expect any args (and this method # does neither), we pass on args in order to be prepared if this changes # ever return $self->next_prediction(@args); } =head2 next_prediction Title : next_prediction Usage : while($gene = $genscan->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the Genscan result file. Call this method repeatedly until FALSE is returned. Example : Returns : A Bio::SeqFeature::Generic object. Args : See also : L<Bio::SeqFeature::Generic> =cut sub next_prediction { my ($self) = @_; my ($genetag,$srctag,$exontag) = ( $self->gene_tag, $self->source_tag, $self->exon_tag); while( defined($_ = $self->_readline) ) { if( m/^(\S+)\s+ # sequence name (\d+)\s+ # tRNA # (\d+)\s+(\d+)\s+ # tRNA start,end (\w{3})\s+ # tRNA type ([CAGT]{3})\s+ # Codon (\d+)\s+(\d+)\s+ # Intron Begin End (\d+\.\d+)/ox # Cove Score ) { my ($seqid,$tRNAnum,$start,$end,$type, $codon,$intron_start,$intron_end, $score) = ($1,$2,$3,$4,$5,$6,$7,$8,$9); my $strand = 1; if( $start > $end ) { ($start,$end,$strand) = ($end,$start,-1); } if( $self->{'_seen'}->{$type}++ ) { $type .= "-".$self->{'_seen'}->{$type}; } my $gene = Bio::SeqFeature::Generic->new ( -seq_id => $seqid, -start => $start, -end => $end, -strand => $strand, -score => $score, -primary_tag => $genetag, -source_tag => $srctag, -tag => { 'ID' => "tRNA:$type", 'Name' => "tRNA:$type", 'AminoAcid' => $type, 'Codon' => $codon, }); if( $intron_start ) { if( $intron_start > $intron_end ) { ($intron_start,$intron_end) = ($intron_end,$intron_start); } $gene->add_SeqFeature(Bio::SeqFeature::Generic->new ( -seq_id=> $seqid, -start => $start, -end => $intron_start-1, -strand=> $strand, -primary_tag => $exontag, -source_tag => $srctag, -tag => { 'Parent' => "tRNA:$type", })); $gene->add_SeqFeature(Bio::SeqFeature::Generic->new ( -seq_id=> $seqid, -start => $intron_end+1, -end => $end, -strand=> $strand, -primary_tag => $exontag, -source_tag => $srctag, -tag => { 'Parent' => "tRNA:$type" })); } else { $gene->add_SeqFeature(Bio::SeqFeature::Generic->new ( -seq_id=> $seqid, -start => $start, -end => $end, -strand=> $strand, -primary_tag => $exontag, -source_tag => $srctag, -tag => { 'Parent' => "tRNA:$type" })); } return $gene; } } } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Alignment����������������������������������������������������������������000755��000766��000024�� 0�13155576320� 17105� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Alignment/Consed.pm������������������������������������������������������000444��000766��000024�� 176310�13155576320� 21063� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# Bio::Tools::Alignment::Consed # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chad Matsalla # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Alignment::Consed - A module to work with objects from consed .ace files =head1 SYNOPSIS # a report for sequencing stuff my $o_consed = Bio::Tools::Alignment::Consed->new( -acefile => "/path/to/an/acefile.ace.1", -verbose => 1); my $foo = $o_consed->set_reverse_designator("r"); my $bar = $o_consed->set_forward_designator("f"); # get the contig numbers my @keys = $o_consed->get_contigs(); # construct the doublets my $setter_doublets = $o_consed->choose_doublets(); # get the doublets my @doublets = $o_consed->get_doublets(); =head1 DESCRIPTION L<Bio::Tools::Alignment::Consed> provides methods and objects to deal with the output from the Consed software suite. Specifically, takes an C<.ace> file and provides objects for the results. A word about doublets: This module was written to accommodate a large EST sequencing operation. In this case, EST's were sequenced from the 3' and from the 5' end of the EST. The objective was to find a consensus sequence for these two reads. Thus, a contig of two is what we wanted, and this contig should consist of the forward and reverse reads of a getn clone. For example, for a forward designator of "F" and a reverse designator of "R", if the two reads chad1F and chad1R were in a single contig (for example Contig 5) it will be determined that the consensus sequence for Contig 5 will be the sequence for clone chad1. Doublets are good! This module parses C<.ace> and related files. A detailed list of methods can be found at the end of this document. I wrote a detailed rationale for design that may explain the reasons why some things were done the way they were done. That document is beyond the scope of this pod and can probably be found in the directory from which this module was 'made' or at L<http://www.dieselwurks.com/bioinformatics/consedpm_documentation.pdf>. Note that the POD in that document might be old but the original rationale still stands. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email chad-at-dieselwurks.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' package Bio::Tools::Alignment::Consed; use strict; use FileHandle; use Dumpvalue qw(dumpValue); use Bio::Tools::Alignment::Trim; use File::Spec; use base qw(Bio::Root::Root Bio::Root::IO); our %DEFAULTS = ( 'f_designator' => 'f', 'r_designator' => 'r'); =head2 new() Title : new(-acefile => $path_to_some_acefile, -verbose => "1") Usage : $o_consed = Bio::Tools::Alignment::Consed-> new(-acefile => $path_to_some_acefile, -verbose => "1"); Function: Construct the Bio::Tools::Alignment::Consed object. Sets verbosity for the following procedures, if necessary: 1. Construct a new Bio::Tools::Alignment::Trim object, to handle quality trimming 2. Read in the acefile and parse it Returns : A reference to a Bio::Tools::Alignment::Consed object. Args : A hash. (-acefile) is the filename of an acefile. If a full path is not specified "./" is prepended to the filename and used from instantiation until destruction. If you want Bio::Tools::Alignment::Consed to be noisy during parsing of the acefile, specify some value for (-verbose). =cut sub new { my ($class,%args) = @_; my $self = $class->SUPER::new(%args); $self->{'filename'} = $args{'-acefile'}; # this is special to UNIX and should probably use catfile : DONE! # if (!($self->{'filename'} =~ m{/})) { # $self->{'filename'} = "./".$self->{'filename'}; # } # $self->{'filename'} =~ s#\\#\/#g if $^O =~ m/mswin/i; # $self->{'filename'} =~ m/(.*\/)(.*)ace.*$/; # $self->{'path'} = $1; # this is more generic and should work on most systems (undef, $self->{'path'}, undef) = File::Spec->splitpath($self->{'filename'}); $self->_initialize_io('-file'=>$self->{'filename'}); $self->{'o_trim'} = Bio::Tools::Alignment::Trim->new(-verbose => $self->verbose()); $self->set_forward_designator($DEFAULTS{'f_designator'}); $self->set_reverse_designator($DEFAULTS{'r_designator'}); $self->_read_file(); return $self; } =head2 set_verbose() Title : set_verbose() Usage : $o_consed->set_verbose(1); Function: Set the verbosity level for debugging messages. On instantiation of the Bio::Tools::Alignment::Consed object the verbosity level is set to 0 (quiet). Returns : 1 or 0. Args : The verbosity levels are: 0 - quiet 1 - noisy 2 - noisier 3 - annoyingly noisy This method for setting verbosity has largely been superseded by a sub-by-sub way, where for every sub you can provide a (-verbose) switch. I am doing converting this bit-by-bit so do not be surprised if some subs do not honour this. =cut # from RootI # backwards compat sub set_verbose { (shift)->verbose(@_) } =head2 get_filename() Title : get_filename() Usage : $o_consed->get_filename(); Function: Returns the name of the acefile being used by the Bio::Tools::Alignment::Consed object. Returns : A scalar containing the name of a file. Args : None. =cut sub get_filename { my $self = shift; return $self->{'filename'}; } =head2 count_sequences_with_grep() Title : count_sequences_with_grep() Usage : $o_consed->count_sequences_with_grep(); Function: Use /bin/grep to scan through the files in the ace project dir and count sequences in those files. I used this method in the development of this module to verify that I was getting all of the sequences. It works, but it is (I think) unix-like platform dependent. Returns : A scalar containing the number of sequences in the ace project directory. Args : None. If you are on a non-UNIX platform, you really do not have to use this. It is more of a debugging routine designed to address very specific problems. This method was reimplemented to be platform independent with a pure perl implementation. The above note can be ignored. =cut sub count_sequences_with_grep { my $self = shift; my ($working_dir,$grep_cli,@total_grep_sequences); # this should be migrated to a pure perl implementation ala # Tom Christiansen's 'tcgrep' # http://www.cpan.org/modules/by-authors/id/TOMC/scripts/tcgrep.gz open my $FILE, '<', $self->{'filename'} or do { $self->warn("Could not read file '$self->{'filename'}' for grepping: $!"); return }; my $counter =0; while(<$FILE>) { $counter++ if(/^AF/); } close $FILE; opendir my $SINGLETS, $self->{'path'}; foreach my $f ( readdir($SINGLETS) ) { next unless ($f =~ /\.singlets$/); my $singlet_file = File::Spec->catfile($self->{'path'}, $f); open my $S_FILE, '<', $singlet_file or do { $self->warn("Could not read file '$singlet_file': $!"); next }; while(<$S_FILE>) { $counter++ if(/^>/) } close $S_FILE; } closedir $SINGLETS; return $counter; } =head2 get_path() Title : get_path() Usage : $o_consed->get_path(); Function: Returns the path to the acefile this object is working with. Returns : Scalar. The path to the working acefile. Args : None. =cut sub get_path { my $self = shift; return $self->{'path'}; } =head2 get_contigs() Title : get_contigs() Usage : $o_consed->get_contigs(); Function: Return the keys to the Bio::Tools::Alignment::Consed object. Returns : An array containing the keynames in the Bio::Tools::Alignment::Consed object. Args : None. This would normally be used to get the keynames for some sort of iterator. These keys are worthless in general day-to-day use because in the Consed acefile they are simply Contig1, Contig2, ... =cut sub get_contigs { my ($self,$contig) = @_; my @contigs = sort keys %{$self->{'contigs'}}; return @contigs; } =head2 get_class($contig_keyname) Title : get_class($contig_keyname) Usage : $o_consed->get_class($contig_keyname); Function: Return the class name for this contig Returns : A scalar representing the class of this contig. Args : None. Notes : =cut sub get_class { my ($self,$contig) = @_; return $self->{contigs}->{$contig}->{class}; } =head2 get_quality_array($contig_keyname) Title : get_quality_array($contig_keyname) Usage : $o_consed->get_quality_array($contig_keyname); Function: Returns the quality for the consensus sequence for the given contig as an array. See get_quality_scalar to get this as a scalar. Returns : An array containing the quality for the consensus sequence with the given keyname. Args : The keyname of a contig. Note: This is a keyname. The key would normally come from get_contigs. Returns an array, not a reference. Is this a bug? I<thinking> No. Well, maybe. Why was this developed like this? I was using FreezeThaw for object persistence, and when it froze out these arrays it took a long time to thaw it. Much better as a scalar. See L<get_quality_scalar()|get_quality_scalar> =cut sub get_quality_array { my ($self,$contig) = @_; return split ' ', $self->{contigs}->{$contig}->{quality}; } =head2 get_quality_scalar($contig_keyname) Title : get_quality_scalar($contig_keyname) Usage : $o_consed->get_quality_scalar($contig_keyname); Function: Returns the quality for the consensus sequence for the given contig as a scalar. See get_quality_array to get this as an array. Returns : An scalar containing the quality for the consensus sequence with the given keyname. Args : The keyname of a contig. Note this is a _keyname_. The key would normally come from get_contigs. Why was this developed like this? I was using FreezeThaw for object persistence, and when it froze out these arrays it took a coon's age to thaw it. Much better as a scalar. See L<get_quality_array()|get_quality_array> =cut #' sub get_quality_scalar { my ($self,$contig) = @_; return $self->{'contigs'}->{$contig}->{'quality'}; } =head2 freeze_hash() Title : freeze_hash() Usage : $o_consed->freeze_hash(); Function: Use Ilya's FreezeThaw module to create a persistent data object for this Bio::Tools::Alignment::Consed data structure. In the case of AAFC, we use Bio::Tools::Alignment::Consed to pre-process bunches of sequences, freeze the structures, and send in a harvesting robot later to do database stuff. Returns : 0 or 1; Args : None. This procedure was removed so Consed.pm won't require FreezeThaw. =cut #' sub freeze_hash { my $self = shift; $self->warn("This method (freeze_hash) was removed ". "from the bioperl consed.pm. Sorry.\n"); if (1==2) { $self->debug("Bio::Tools::Alignment::Consed::freeze_hash:". " \$self->{path} is $self->{path}\n"); my $filename = $self->{'path'}."frozen"; my %contigs = %{$self->{'contigs'}}; my $frozen = freeze(%contigs); umask 0001; open my $FREEZE, '>', $filename or do { $self->warn( "Bio::Tools::Alignment::Consed could not ". "freeze the contig hash because the file ". "($filename) could not be opened: $!"); return 1; }; print $FREEZE $frozen; return 0; } } =head2 get_members($contig_keyname) Title : get_members($contig_keyname) Usage : $o_consed->get_members($contig_keyname); Function: Return the _names_ of the reads in this contig. Returns : An array containing the names of the reads in this contig. Args : The keyname of a contig. Note this is a keyname. The keyname would normally come from get_contigs. See L<get_contigs()|get_contigs> =cut sub get_members { my ($self,$contig) = @_; if (!$contig) { $self->warn("You need to provide the name of a contig to ". "use Bio::Tools::Alignment::Consed::get_members!\n"); return; } return @{$self->{'contigs'}->{$contig}->{'member_array'}}; } =head2 get_members_by_name($some_arbitrary_name) Title : get_members_by_name($some_arbitrary_name) Usage : $o_consed->get_members_by_name($some_arbitrary_name); Function: Return the names of the reads in a contig. This is the name given to $contig{key} based on what is in the contig. This is different from the keys retrieved through get_contigs(). Returns : An array containing the names of the reads in the contig with this name. Args : The name of a contig. Not a key, but a name. Highly inefficient. use some other method if possible. See L<get_contigs()|get_contigs> =cut sub get_members_by_name { my ($self,$name) = @_; # build a list to try to screen for redundancy my @contigs_with_that_name; foreach my $currkey ( sort keys %{$self->{'contigs'}} ) { next if (!$self->{'contigs'}->{$currkey}->{'name'}); if ($self->{'contigs'}->{$currkey}->{'name'} eq "$name") { push @contigs_with_that_name,$currkey; } } my $count = @contigs_with_that_name; if ($count == 1) { my $contig_num = $contigs_with_that_name[0]; return @{$self->{'contigs'}->{$contig_num}->{'member_array'}}; } } =head2 get_contig_number_by_name($some_arbitrary_name) Title : get_contig_number_by_name($some_arbitrary_name) Usage : $o_consed->get_contig_number_by_name($some_arbitrary_name); Function: Return the names of the reads in a contig. This is the name given to $contig{key} based on what is in the contig. This is different from the keys retrieved through get_contigs(). Returns : An array containing the names of the reads in the contig with this name. Args : The name of a contig. Not a key, but a name. See L<get_contigs()|get_contigs> =cut sub get_contig_number_by_name { my ($self,$name) = @_; foreach my $currkey (sort keys %{$self->{'contigs'}}) { if ($self->{'contigs'}->{$currkey}->{'name'} && $self->{'contigs'}->{$currkey}->{'name'} eq "$name") { return $currkey; } } } =head2 get_sequence($contig_keyname) Title : get_sequence($contig_keyname) Usage : $o_consed->get_sequence($contig_keyname); Function: Returns the consensus sequence for a given contig. Returns : A scalar containing a sequence. Args : The keyname of a contig. Note this is a key. The key would normally come from get_contigs. See L<get_contigs()|get_contigs> =cut sub get_sequence { my ($self,$contig) = @_; return $self->{'contigs'}->{$contig}->{'consensus'}; } =head2 set_final_sequence($some_sequence) Title : set_final_sequence($name,$some_sequence) Usage : $o_consed->set_final_sequence($name,$some_sequence); Function: Provides a manual way to set the sequence for a given key in the contig hash. Rarely used. Returns : 0 or 1; Args : The name (not the keyname) of a contig and an arbitrary string. A method with a questionable and somewhat mysterious origin. May raise the dead or something like that. =cut sub set_final_sequence { my ($self,$name,$sequence) = @_; if (!$self->{'contigs'}->{$name}) { $self->warn("You cannot set the final sequence for ". "$name because it doesn't exist!\n"); return 1; } else { $self->{'contigs'}->{$name}->{'final_sequence'} = $sequence; } return 0; } =head2 _read_file() Title : _read_file(); Usage : _read_file(); Function: An internal subroutine used to read in an acefile and parse it into a Bio::Tools::Alignment::Consed object. Returns : 0 or 1. Args : Nothing. This routine creates and saves the filhandle for reading the files in {fh} =cut sub _read_file { my ($self) = @_; my ($line,$in_contig,$in_quality,$contig_number,$top); # make it easier to type $fhl while (defined($line=$self->_readline()) ) { chomp $line; # check if there is anything on this line # if not, you can stop gathering consensus sequence if (!$line) { # if the line is blank you are no longer to gather consensus # sequence or quality values $in_contig = 0; $in_quality = 0; } # you are currently gathering consensus sequence elsif ($in_contig) { if ($in_contig == 1) { $self->debug("Adding $line to consensus of contig number $contig_number.\n"); $self->{'contigs'}->{$contig_number}->{'consensus'} .= $line; } } elsif ($in_quality) { if (!$line) { $in_quality = undef; } else { # I wrote this in here because acefiles produced by # cap3 do not have a leading space like the acefiles # produced by phrap and there is the potential to have # concatenated quality values like this: 2020 rather # then 20 20 whre lines collide. Thanks Andrew for # noticing. if ($self->{'contigs'}->{$contig_number}->{'quality'} && !($self->{'contigs'}->{$contig_number}->{'quality'} =~ m/\ $/)) { $self->{'contigs'}->{$contig_number}->{'quality'} .= " "; } $self->{'contigs'}->{$contig_number}->{'quality'} .= $line; } } elsif ($line =~ /^BQ/) { $in_quality = 1; } # the line /^CO/ like this: # CO Contig1 796 1 1 U # can be broken down as follows: # CO - Contig! # Contig1 - the name of this contig # 796 - Number of bases in this contig # 1 - Number of reads in this contig # 1 - number of base segments in this contig # U - Uncomplemented elsif ($line =~ /^CO/) { $line =~ m/^CO\ Contig(\d+)\ \d+\ \d+\ \d+\ (\w)/; $contig_number = $1; if ($2 eq "C") { $self->debug("Contig $contig_number is complemented!\n"); } $self->{'contigs'}->{$contig_number}->{'member_array'} = []; $self->{'contigs'}->{$contig_number}->{'contig_direction'} = "$2"; $in_contig = 1; } # 000713 # this BS is deprecated, I think. # haha, I am really witty. <ew> elsif ($line =~ /^BSDEPRECATED/) { $line =~ m/^BS\s+\d+\s+\d+\s+(.+)/; my $member = $1; $self->{'contigs'}->{$contig_number}->{$member}++; } # the members of the contigs are determined by the AF line in the ace file elsif ($line =~ /^AF/) { $self->debug("I see an AF line here.\n"); $line =~ /^AF\ (\S+)\ (\w)\ (\S+)/; # push the name of the current read onto the member array for this contig push @{$self->{'contigs'}->{$contig_number}->{'member_array'}},$1; # the first read in the contig will be named the "top" read if (!$top) { $self->debug("\$top is not set.\n"); if ($self->{'contigs'}->{$contig_number}->{'contig_direction'} eq "C") { $self->debug("Reversing the order of the reads. The bottom will be $1\n"); # if the contig sequence is marked as the # complement, the top becomes the bottom and$ $self->{'contigs'}->{$contig_number}->{'bottom_name'} = $1; $self->{'contigs'}->{$contig_number}->{'bottom_complement'} = $2; $self->{'contigs'}->{$contig_number}->{'bottom_start'} = $3; } else { $self->debug("NOT reversing the order of the reads. ". "The top_name will be $1\n"); # if the contig sequence is marked as the # complement, the top becomes the bottom and$ $self->{'contigs'}->{$contig_number}->{'top_name'} = $1; $self->{'contigs'}->{$contig_number}->{'top_complement'} = $2; $self->{'contigs'}->{$contig_number}->{'top_start'} = $3; } $top = 1; } else { # if the contig sequence is marked as the complement, # the top becomes the bottom and the bottom becomes # the top if ($self->{'contigs'}->{$contig_number}->{'contig_direction'} eq "C") { $self->debug("Reversing the order of the reads. The top will be $1\n"); $self->{'contigs'}->{$contig_number}->{'top_name'} = $1; $self->{'contigs'}->{$contig_number}->{'top_complement'} = $2; $self->{'contigs'}->{$contig_number}->{'top_start'} = $3; } else { $self->debug("NOT reversing the order of the reads. The bottom will be $1\n"); $self->{'contigs'}->{$contig_number}->{'bottom_name'} = $1; $self->{'contigs'}->{$contig_number}->{'bottom_complement'} = $2; $self->{'contigs'}->{$contig_number}->{'bottom_start'} = $3; } $top = undef; } } } return 0; } =head2 set_reverse_designator($some_string) Title : set_reverse_designator($some_string) Usage : $o_consed->set_reverse_designator($some_string); Function: Set the designator for the reverse read of contigs in this Bio::Tools::Alignment::Consed object. Used to determine if contigs containing two reads can be named. Returns : The value of $o_consed->{reverse_designator} so you can check to see that it was set properly. Args : An arbitrary string. May be useful only to me. I<shrug> =cut sub set_reverse_designator { my ($self,$reverse_designator) = @_; $self->{'reverse_designator'} = $reverse_designator; $self->{'o_trim'}->set_reverse_designator($reverse_designator); return $self->{'reverse_designator'}; } # end set_reverse_designator =head2 set_forward_designator($some_string) Title : set_forward_designator($some_string) Usage : $o_consed->set_forward_designator($some_string); Function: Set the designator for the forward read of contigs in this Bio::Tools::Alignment::Consed object. Used to determine if contigs containing two reads can be named. Returns : The value of $o_consed->{forward_designator} so you can check to see that it was set properly. Args : An arbitrary string. May be useful only to me. I<shrug> =cut sub set_forward_designator { my ($self,$forward_designator) = @_; $self->{'forward_designator'} = $forward_designator; $self->{'o_trim'}->set_forward_designator($forward_designator); return $self->{'forward_designator'}; } # end set_forward_designator =head2 set_designator_ignore_case("yes") Title : set_designator_ignore_case("yes") Usage : $o_consed->set_designator_ignore_case("yes"); Function: Deprecated. Returns : Deprecated. Args : Deprecated. Deprecated. Really. Trust me. =cut sub set_designator_ignore_case { my ($self,$ignore_case) = @_; if ($ignore_case eq "yes") { $self->{'designator_ignore_case'} = 1; } return $self->{'designator_ignore_case'}; } # end set_designator_ignore_case =head2 set_trim_points_singlets_and_singletons() Title : set_trim_points_singlets_and_singletons() Usage : $o_consed->set_trim_points_singlets_and_singletons(); Function: Set the trim points for singlets and singletons based on quality. Uses the Bio::Tools::Alignment::Trim object. Use at your own risk because the Bio::Tools::Alignment::Trim object was designed specifically for me and is mysterious in its ways. Every time somebody other then me uses it a swarm of locusts decends on a small Central American village so do not say you weren't warned. Returns : Nothing. Args : None. Working on exceptions and warnings here. See L<Bio::Tools::Alignment::Trim> for more information =cut #' to make my emacs happy sub set_trim_points_singlets_and_singletons { my ($self) = @_; $self->debug("Consed.pm : \$self is $self\n"); my (@points,$trimmed_sequence); if (!$self->{'doublets_set'}) { $self->debug("You need to set the doublets before you use ". "set_trim_points_singlets_and_doublets. Doing that now."); $self->set_doublets(); } foreach (sort keys %{$self->{'contigs'}}) { if ($self->{'contigs'}->{$_}->{'class'} eq "singlet") { $self->debug("Singlet $_\n"); # this is what Warehouse wants # my ($self,$sequence,$quality,$name) = @_; # this is what Bio::Tools::Alignment::Trim::trim_singlet wants: # my ($self,$sequence,$quality,$name,$class) = @_; # the following several lines are to make the parameter passing legible. my ($sequence,$quality,$name,$class); $sequence = $self->{'contigs'}->{$_}->{'consensus'}; if (!$self->{'contigs'}->{$_}->{'quality'}) { $quality = "unset"; } else { $quality = $self->{'contigs'}->{$_}->{'quality'}; } $name = $self->{'contigs'}->{$_}->{'name'}; $class = $self->{'contigs'}->{$_}->{'class'}; @points = @{$self->{'o_trim'}->trim_singlet($sequence,$quality,$name,$class)}; $self->{'contigs'}->{$_}->{'start_point'} = $points[0]; $self->{'contigs'}->{$_}->{'end_point'} = $points[1]; $self->{'contigs'}->{$_}->{'sequence_trimmed'} = substr($self->{contigs}->{$_}->{'consensus'},$points[0],$points[1]-$points[0]); } } $self->debug("Bio::Tools::Alignment::Consed::set_trim_points_singlets". "_and_singletons: Done setting the quality trimpoints.\n"); return; } # end set_trim_points_singlet =head2 set_trim_points_doublets() Title : set_trim_points_doublets() Usage : $o_consed->set_trim_points_doublets(); Function: Set the trim points for doublets based on quality. Uses the Bio::Tools::Alignment::Trim object. Use at your own risk because the Bio::Tools::Alignment::Trim object was designed specifically for me and is mysterious in its ways. Every time somebody other then me uses it you risk a biblical plague being loosed on your city. Returns : Nothing. Args : None. Notes : Working on exceptions here. See L<Bio::Tools::Alignment::Trim> for more information =cut sub set_trim_points_doublets { my $self = shift; my @points; $self->debug("Bio::Tools::Alignment::Consed::set_trim_points_doublets:". " Restoring zeros for doublets.\n"); # &show_missing_sequence($self); $self->debug("Bio::Tools::Alignment::Consed::set_trim_points_doublets:". " Setting doublet trim points.\n"); foreach (sort keys %{$self->{'contigs'}}) { if ($self->{'contigs'}->{$_}->{'class'} eq "doublet") { # my ($self,$sequence,$quality,$name,$class) = @_; my @quals = split(' ',$self->{'contigs'}->{$_}->{'quality'}); @points = $self->{o_trim}->trim_doublet ($self->{'contigs'}->{$_}->{'consensus'}, $self->{'contigs'}->{$_}->{'quality'}, $self->{'contigs'}->{$_}->{name}, $self->{'contigs'}->{$_}->{'class'}); $self->{'contigs'}->{$_}->{'start_point'} = $points[0]; $self->{'contigs'}->{$_}->{'end_point'} = $points[1]; # now set this $self->{'contigs'}->{$_}->{'sequence_trimmed'} = substr($self->{contigs}->{$_}->{'consensus'}, $points[0],$points[1]-$points[0]); # 010102 the deprecated way to do things: } } $self->debug("Bio::Tools::Alignment::Consed::set_trim_points_doublets:". " Done setting doublet trim points.\n"); return; } # end set_trim_points_doublets =head2 get_trimmed_sequence_by_name($name) Title : get_trimmed_sequence_by_name($name) Usage : $o_consed->get_trimmed_sequence_by_name($name); Function: Returns the trimmed_sequence of a contig with {name} eq $name. Returns : A scalar- the trimmed sequence. Args : The {name} of a contig. Notes : =cut sub get_trimmed_sequence_by_name { my ($self,$name) = @_; my $trimmed_sequence; my $contigname = &get_contig_number_by_name($self,$name); my $class = $self->{'contigs'}->{$contigname}->{'class'}; # what is this business and who was smoking crack while writing this? # if ($class eq "singlet") { # send the sequence, the quality, and the name # $trimmed_sequence = $self->{o_trim}->trim_singlet # ($self->{'contigs'}->{$contigname}->{consensus}, # $self->{'contigs'}->{$contigname}->{'quality'},$name); # } return $self->{'contigs'}->{$contigname}->{'sequence_trimmed'}; } =head2 set_dash_present_in_sequence_name("yes") Title : set_dash_present_in_sequence_name("yes") Usage : $o_consed->set_dash_present_in_sequence_name("yes"); Function: Deprecated. Part of an uncompleted thought. ("Oooh! Shiny!") Returns : Nothing. Args : "yes" to set {dash_present_in_sequence_name} to 1 Notes : =cut sub set_dash_present_in_sequence_name { my ($self,$dash_present) = @_; if ($dash_present eq "yes") { $self->{'dash_present_in_sequence_name'} = 1; } else { $self->{'dash_present_in_sequence_name'} = 0; } return $self->{'dash_present_in_sequence_name'}; } # end set_dash_present_in_sequence_name =head2 set_doublets() Title : set_doublets() Usage : $o_consed->set_doublets(); Function: Find pairs that have similar names and mark them as doublets and set the {name}. Returns : 0 or 1. Args : None. A complicated subroutine that iterates over the Bio::Tools::Alignment::Consed looking for contigs of 2. If the forward and reverse designator are removed from each of the reads in {'member_array'} and the remaining reads are the same, {name} is set to that name and the contig's class is set as "doublet". If any of those cases fail the contig is marked as a "pair". =cut #' make my emacs happy sub set_doublets { my ($self) = @_; # set the designators in the Bio::Tools::Alignment::Trim object $self->{'o_trim'}->set_designators($self->{'reverse_designator'}, $self->{'forward_designator'}); foreach my $key_contig (sort keys %{$self->{'contigs'}}) { # if there is a member array (why would there not be? This should be a die()able offence # but for now I will leave it if ($self->{'contigs'}->{$key_contig}->{'member_array'}) { # if there are two reads in this contig # i am pretty sure that this is wrong but i am keeping it for reference # if (@{$self->{'contigs'}->{$key_contig}->{'member_array'}} == 2 || !$self->{'contigs'}->{$key_contig}->{'class'}) { # <seconds later> # <nod> WRONG. Was I on crack? if (@{$self->{'contigs'}->{$key_contig}->{'member_array'}} == 2) { $self->{'contigs'}->{$key_contig}->{'num_members'} = 2; $self->debug("\tThere are 2 members! Looking for the contig name...\n"); my $name = _get_contig_name($self,$self->{'contigs'}->{$key_contig}->{'member_array'}); $self->debug("The name is $name\n") if defined $name; if ($name) { $self->{'contigs'}->{$key_contig}->{'name'} = $name; $self->{'contigs'}->{$key_contig}->{'class'} = "doublet"; } else { $self->debug("$key_contig is a pair.\n"); $self->{'contigs'}->{$key_contig}->{'class'} = "pair"; } } # this is all fair and good but what about singlets? # they have one reads in the member_array but certainly are not singletons elsif (@{$self->{'contigs'}->{$key_contig}->{'member_array'}} == 1) { # set the name to be the name of the read $self->{'contigs'}->{$key_contig}->{name} = @{$self->{'contigs'}->{$key_contig}->{'member_array'}}[0]; # set the number of members to be one $self->{'contigs'}->{$key_contig}->{num_members} = 1; # if this was a singlet, it would already belong to the class "singlet" # so leave it alone # if it is not a singlet, it is a singleton! lablel it appropriately unless ($self->{'contigs'}->{$key_contig}->{'class'}) { $self->{'contigs'}->{$key_contig}->{'class'} = "singleton"; } } # set the multiplet characteristics elsif (@{$self->{'contigs'}->{$key_contig}->{'member_array'}} >= 3) { $self->{'contigs'}->{$key_contig}->{'num_members'} = @{$self->{'contigs'}->{$key_contig}->{'member_array'}}; $self->{'contigs'}->{$key_contig}->{'class'} = "multiplet"; } $self->{'contigs'}->{$key_contig}->{'num_members'} = @{$self->{'contigs'}->{$key_contig}->{'member_array'}}; } } $self->{'doublets_set'} = "done"; return 0; } # end set_doublets =head2 set_singlets Title : set_singlets Usage : $o_consed->set_singlets(); Function: Read in a singlets file and place them into the Bio::Tools::Alignment::Consed object. Returns : Nothing. Args : A scalar to turn on verbose parsing of the singlets file. Notes : =cut sub set_singlets { # parse out the contents of the singlets file my ($self) = @_; $self->debug("Bio::Tools::Alignment::Consed Adding singlets to the contig hash...\n"); my $full_filename = $self->{'filename'}; $self->debug("Bio::Tools::Alignment::Consed::set_singlets: \$full_filename is $full_filename\n"); $full_filename =~ s#\\#\/#g if $^O =~ m/mswin/i; $full_filename =~ m/(.*\/)(.*ace.*)$/; my ($base_path,$filename) = ($1,$2); $self->debug("Bio::Tools::Alignment::Consed::set_singlets: singlets filename is $filename and \$base_path is $base_path\n"); $filename =~ m/(.*)ace.*$/; my $singletsfile = $base_path.$1."singlets"; $self->debug("\$singletsfile is $singletsfile\n"); if (!-f $singletsfile) { # there is no singlets file. $self->{'singlets_set'} = "done"; return; } $self->debug("$singletsfile is indeed a file. Trying to open it...\n"); my $singlets_fh = Bio::Root::IO->new(-file => $singletsfile); my ($sequence,$name,$count); while ($_ = $singlets_fh->_readline()) { chomp $_; if (/\>/) { if ($name && $sequence) { $self->debug("Adding $name with sequence $sequence to hash...\n"); push @{$self->{'contigs'}->{$name}->{'member_array'}},$name; $self->{'contigs'}->{$name}->{'consensus'} = $sequence; $self->{'contigs'}->{$name}->{'name'} = $name; $self->{'contigs'}->{$name}->{"singlet"} = 1; $self->{'contigs'}->{$name}->{'class'} = "singlet"; } $sequence = $name = undef; $count++; m/^\>(.*)\s\sCHROMAT/; $name = $1; if (!$name) { m/\>(\S+)\s/; $name = $1; } } else { $sequence .= $_; } } if ($name && $sequence) { $self->debug("Pushing the last of the singlets ($name)\n"); @{$self->{'contigs'}->{$name}->{'member_array'}} = $name; $self->{'contigs'}->{$name}->{'consensus'} = $sequence; $self->{'contigs'}->{$name}->{'name'} = $name; $self->{'contigs'}->{$name}->{"singlet"} = 1; $self->{'contigs'}->{$name}->{'class'} = "singlet"; } $self->debug("Bio::Tools::Alignment::Consed::set_singlets: Done adding singlets to the singlets hash.\n"); $self->{'singlets_set'} = "done"; return 0; } # end sub set_singlets =head2 get_singlets() Title : get_singlets() Usage : $o_consed->get_singlets(); Function: Return the keynames of the singlets. Returns : An array containing the keynames of all Bio::Tools::Alignment::Consed sequences in the class "singlet". Args : None. Notes : =cut sub get_singlets { # returns an array of singlet names # singlets have "singlet"=1 in the hash my $self = shift; if (!$self->{singlets_set}) { $self->debug("You need to set the singlets before you get them. Doing that now."); $self->set_singlets(); } my (@singlets,@array); foreach my $key (sort keys %{$self->{'contigs'}}) { # @array = @{$Consed::contigs{$key}->{'member_array'}}; # somethimes a user will try to get a list of singlets before the classes for the rest of the # contigs has been set (see t/test.t for how I figured this out. <bah> # so either way, just return class=singlets if (!$self->{'contigs'}->{$key}->{'class'}) { # print("$key has no class. why?\n"); } elsif ($self->{'contigs'}->{$key}->{'class'} eq "singlet") { push @singlets,$key; } } return @singlets; } =head2 set_quality_by_name($name,$quality) Title : set_quality_by_name($name,$quality) Usage : $o_consed->set_quality_by_name($name,$quality); Function: Deprecated. Make the contig with {name} have {'quality'} $quality. Probably used for testing. Returns : Nothing. Args : The name of a contig and a scalar for its quality. Notes : Deprecated. =cut sub set_quality_by_name { # this is likely deprecated my ($self,$name,$quality) = shift; my $return; foreach (sort keys %{$self->{'contigs'}}) { if ($self->{'contigs'} eq "$name" || $self->{'contigs'}->{'name'} eq "$name") { $self->{'contigs'}->{'quality'} = $quality; $return=1; } } if ($return) { return "0"; } else { return "1"; } } # end set quality by name =head2 set_singlet_quality() Title : set_singlet_quality() Usage : $o_consed->set_singlet_quality(); Function: For each singlet, go to the appropriate file in phd_dir and read in the phred quality for that read and place it into {'quality'} Returns : 0 or 1. Args : None. Notes : This is the next subroutine that will receive substantial revision in the next little while. It really should eval the creation of Bio::Tools::Alignment::Phred objects and go from there. =cut sub set_singlet_quality { my $self = shift; my $full_filename = $self->{'filename'}; $full_filename =~ s#\\#\/#g if $^O =~ m/mswin/i; $full_filename =~ m/(.*\/)(.*)ace.*$/; my ($base_path,$filename) = ($1,"$2"."qual"); my $singletsfile = $base_path.$filename; if (-f $singletsfile) { # print("$singletsfile is indeed a file. Trying to open it...\n"); } else { $self->warn("$singletsfile is not a file. Sorry.\n"); return; } my $singlets_fh = Bio::Root::IO->new(-file => $singletsfile); my ($sequence,$name,$count); my ($identity,$line,$quality,@qline); while ($line = $singlets_fh->_readline()) { chomp $line; if ($line =~ /^\>/) { $quality = undef; $line =~ m/\>(\S*)\s/; $identity = $1; } else { if ($self->{'contigs'}->{$identity}) { $self->{'contigs'}->{$identity}->{'quality'} .= "$line "; } } } return 0; } =head2 set_contig_quality() Title : set_contig_quality() Usage : $o_consed->set_contig_quality(); Function: Deprecated. Returns : Deprecated. Args : Deprecated. Notes : Deprecated. Really. Trust me. =cut sub set_contig_quality { # note: contigs _include_ singletons but _not_ singlets my ($self) = shift; # the unexpected results I am referring to here are a doubling of quality values. # the profanity I uttered on discovering this reminded me of the simpsons: # Ned Flanders: "That is the loudest profanity I have ever heard!" $self->warn("set_contig_quality is deprecated and will likely produce unexpected results"); my $full_filename = $self->{'filename'}; # Run_SRC3700_2000-08-01_73+74.fasta.screen.contigs.qual # from Consed.pm $full_filename =~ s#\\#\/#g if $^O =~ m/mswin/i; $full_filename =~ m/(.*\/)(.*)ace.*$/; my ($base_path,$filename) = ($1,"$2"."contigs.qual"); my $singletsfile = $base_path.$filename; if (-f $singletsfile) { # print("$singletsfile is indeed a file. Trying to open it...\n"); } else { $self->warn("Bio::Tools::Alignment::Consed::set_contig_quality $singletsfile is not a file. Sorry.\n"); return; } my $contig_quality_fh = Bio::Root::IO->new(-file => $singletsfile); my ($sequence,$name,$count,$identity,$line,$quality); while ($line = $contig_quality_fh->_readline()) { chomp $line; if ($line =~ /^\>/) { $quality = undef; $line =~ m/\>.*Contig(\d+)\s/; $identity = $1; } else { if ($self->{'contigs'}->{$identity} ) { $self->{'contigs'}->{$identity}->{'quality'} .= " $line"; } } } } # end set_contig_quality =head2 get_multiplets() Title : get_multiplets() Usage : $o_consed->get_multiplets(); Function: Return the keynames of the multiplets. Returns : Returns an array containing the keynames of all Bio::Tools::Alignment::Consed sequences in the class "multiplet". Args : None. Notes : =cut sub get_multiplets { # returns an array of multiplet names # multiplets have # members > 2 my $self = shift; my (@multiplets,@array); foreach my $key (sort keys %{$self->{'contigs'}}) { if ($self->{'contigs'}->{$key}->{'class'}) { if ($self->{'contigs'}->{$key}->{'class'} eq "multiplet") { push @multiplets,$key; } } } return @multiplets; } =head2 get_all_members() Title : get_all_members() Usage : @all_members = $o_consed->get_all_members(); Function: Return a list of all of the read names in the Bio::Tools::Alignment::Consed object. Returns : An array containing all of the elements in all of the {'member_array'}s. Args : None. Notes : =cut sub get_all_members { my $self = shift; my @members; foreach my $key (sort keys %{$self->{'contigs'}}) { if ($key =~ /^singlet/) { push @members,$self->{'contigs'}->{$key}->{'member_array'}[0]; } elsif ($self->{'contigs'}->{$key}->{'member_array'}) { push @members,@{$self->{'contigs'}->{$key}->{'member_array'}}; } # else { # print("Bio::Tools::Alignment::Consed: $key is _not_ an array. Pushing $self->{'contigs'}->{$key}->{'member_array'} onto \@members\n"); # push @members,$self->{'contigs'}->{$key}->{'member_array'}; # } } return @members; } =head2 sum_lets($total_only) Title : sum_lets($total_only) Usage : $statistics = $o_consed->sum_lets($total_only); Function: Provide numbers for how many sequences were accounted for in the Bio::Tools::Alignment::Consed object. Returns : If a scalar is present, returns the total number of sequences accounted for in all classes. If no scalar passed then returns a string that looks like this: Singt/singn/doub/pair/mult/total : 2,0,1(2),0(0),0(0),4 This example means the following: There were 1 singlets. There were 0 singletons. There were 1 doublets for a total of 2 sequences in this class. There were 0 pairs for a total of 0 sequences in this class. There were 0 multiplets for a total of 0 sequences in this class. There were a total of 4 sequences accounted for in the Bio::Tools::Alignment::Consed object. Args : A scalar is optional to change the way the numbers are returned. Notes: =cut sub sum_lets { my ($self,$total_only) = @_; my ($count,$count_multiplets,$multiplet_count); my $singlets = &get_singlets($self); $count += $singlets; my $doublets = &get_doublets($self); $count += ($doublets * 2); my $pairs = &get_pairs($self); $count += ($pairs * 2); my $singletons = &get_singletons($self); $count += $singletons; my @multiplets = &get_multiplets($self); $count_multiplets = @multiplets; my $return_string; foreach (@multiplets) { my $number_members = $self->{'contigs'}->{$_}->{num_members}; $multiplet_count += $number_members; } if ($multiplet_count) { $count += $multiplet_count; } foreach (qw(multiplet_count singlets doublets pairs singletons multiplets count_multiplets)) { no strict 'refs'; # renege for the block if (!${$_}) { ${$_} = 0; } } if (!$multiplet_count) { $multiplet_count = 0; } if ($total_only) { return $count; } $return_string = "Singt/singn/doub/pair/mult/total : ". "$singlets,$singletons,$doublets(". ($doublets*2)."),$pairs(".($pairs*2). "),$count_multiplets($multiplet_count),$count"; return $return_string; } =head2 write_stats() Title : write_stats() Usage : $o_consed->write_stats(); Function: Write a file called "statistics" containing numbers similar to those provided in sum_lets(). Returns : Nothing. Write a file in $o_consed->{path} containing something like this: 0,0,50(100),0(0),0(0),100 Where the numbers provided are in the format described in the documentation for sum_lets(). Args : None. Notes : This might break platform independence, I do not know. See L<sum_lets()|sum_lets> =cut sub write_stats { # worry about platform dependence here? # oh shucksdarn. my $self = shift; my $stats_filename = $self->{'path'}."statistics"; my $statistics_raw = $self->sum_lets; my ($statsfilecontents) = $statistics_raw =~ s/.*\ \:\ //g; umask 0001; my $fh = Bio::Root::IO->new(-file=>"$stats_filename"); # open my $STATSFILE, '>', $stats_filename or print "Could not write the statsfile: $!\n"); $fh->_print("$statsfilecontents"); # close $STATSFILE; $fh->close(); } =head2 get_singletons() Title : get_singletons() Usage : @singletons = $o_consed->get_singletons(); Function: Return the keynames of the singletons. Returns : Returns an array containing the keynames of all Bio::Tools::Alignment::Consed sequences in the class "singleton". Args : None. Notes : =cut sub get_singletons { # returns an array of singleton names # singletons are contigs with one member (see consed documentation) my $self = shift; my (@singletons,@array); foreach my $key (sort keys %{$self->{'contigs'}}) { if ($self->{'contigs'}->{$key}->{'class'}) { # print ("$key class: $self->{'contigs'}->{$key}->{'class'}\n"); } else { # print("$key belongs to no class. why?\n"); } if ($self->{'contigs'}->{$key}->{'member_array'}) { @array = @{$self->{'contigs'}->{$key}->{'member_array'}}; } my $num_array_elem = @array; if ($num_array_elem == 1 && $self->{'contigs'}->{$key}->{'class'} && $self->{'contigs'}->{$key}->{'class'} eq "singleton") { push @singletons,$key; } } return @singletons; } =head2 get_pairs() Title : get_pairs() Usage : @pairs = $o_consed->get_pairs(); Function: Return the keynames of the pairs. Returns : Returns an array containing the keynames of all Bio::Tools::Alignment::Consed sequences in the class "pair". Args : None. Notes : =cut sub get_pairs { # returns an array of pair contig names # a pair is a contig of two where the names do not match my $self = shift; my (@pairs,@array); foreach my $key (sort keys %{$self->{'contigs'}}) { if ($self->{'contigs'}->{$key}->{'member_array'}) { if (@{$self->{'contigs'}->{$key}->{'member_array'}} == 2 && $self->{'contigs'}->{$key}->{'class'} eq "pair") { push @pairs,$key; } } } return @pairs; } =head2 get_name($contig_keyname) Title : get_name($contig_keyname) Usage : $name = $o_consed->get_name($contig_keyname); Function: Return the {name} for $contig_keyname. Returns : A string. ({name}) Args : A contig keyname. Notes : =cut sub get_name { my ($self,$contig) = @_; return $self->{'contigs'}->{$contig}->{'name'}; } =head2 _get_contig_name(\@array_containing_reads) Title : _get_contig_name(\@array_containing_reads) Usage : $o_consed->_get_contig_name(\@array_containing_reads); Function: The logic for the set_doublets subroutine. Returns : The name for this contig. Args : A reference to an array containing read names. Notes : Depends on reverse_designator. Be sure this is set the way you intend. =cut sub _get_contig_name { my ($self,$r_array) = @_; my @contig_members = @$r_array; my @name_nodir; foreach (@contig_members) { # how can I distinguish the clone name from the direction label? # look for $Consed::reverse_designator and $Consed::forward_designator # what if you do not find _any_ of those? my $forward_designator = $self->{'forward_designator'} || "f"; my $reverse_designator = $self->{'reverse_designator'} || "r"; my $any_hits = /(.+)($forward_designator.*)/ || /(.+)($reverse_designator.*)/||/(.+)(_.+)/; my $name = $1; my $suffix = $2; if ($name) { # print("\t\$name is $name "); } if ($suffix) { # print("and \$suffix is $suffix.\n"); } # Jee, I hope we get a naming convention soon if ($suffix) { if ($suffix =~ /^$forward_designator/ || $suffix =~ /^$reverse_designator/) { push @name_nodir,$name; } # bugwatch here! should this be unnested? else { push @name_nodir,"$name$suffix"; } } } # print("\@name_nodir: @name_nodir\n"); my $mismatch = 0; for (my $counter=0; $counter<@name_nodir;$counter++) { next if ($name_nodir[0] eq $name_nodir[$counter]); $mismatch = 1; } if ($mismatch == 0) { # print("\tYou have a cohesive contig named $name_nodir[0].\n\n"); return $name_nodir[0]; } else { # print("\tYou have mixed names in this contig.\n\n"); } } # end _get_contig_name =head2 get_doublets() Title : get_doublets() Usage : @doublets = $o_consed->get_doublets(); Function: Return the keynames of the doublets. Returns : Returns an array containing the keynames of all Bio::Tools::Alignment::Consed sequences in the class "doublet". Args : None. Notes : =cut sub get_doublets { my $self = shift; if (!$self->{doublets_set}) { $self->warn("You need to set the doublets before you can get them. Doing that now."); $self->set_doublets(); } my @doublets; foreach (sort keys %{$self->{'contigs'}}) { if ($self->{'contigs'}->{$_}->{name} && $self->{'contigs'}->{$_}->{'class'} eq "doublet") { push @doublets,$_; } } return @doublets; } # end get_doublets =head2 dump_hash() Title : dump_hash() Usage : $o_consed->dump_hash(); Function: Use dumpvar.pl to dump out the Bio::Tools::Alignment::Consed object to STDOUT. Returns : Nothing. Args : None. Notes : I used this a lot in debugging. =cut sub dump_hash { my $self = shift; my $dumper = Dumpvalue->new(); $self->debug( "Bio::Tools::Alignment::Consed::dump_hash - ". "The following is the contents of the contig hash...\n"); $dumper->dumpValue($self->{'contigs'}); } =head2 dump_hash_compact() Title : dump_hash_compact() Usage : $o_consed->dump_hash_compact(); Function: Dump out the Bio::Tools::Alignment::Consed object in a compact way. Returns : Nothing. Args : Nothing. Notes : Cleaner then dumpValue(), dumpHash(). I used this a lot in debugging. =cut sub dump_hash_compact { no strict 'refs'; # renege for the block my ($self,$sequence) = @_; # get the classes my @singlets = $self->get_singlets(); my @singletons = $self->get_singletons(); my @doublets = $self->get_doublets(); my @pairs = $self->get_pairs(); my @multiplets = $self->get_multiplets(); print("Name\tClass\tMembers\tQuality?\n"); foreach (@singlets) { my @members = $self->get_members($_); print($self->get_name($_)."\tsinglets\t".(join',',@members)."\t"); if ($self->{'contigs'}->{$_}->{'quality'}) { print("qualities found here\n"); } else { print("no qualities found here\n"); } } foreach (@singletons) { my @members = $self->get_members($_); print($self->get_name($_)."\tsingletons\t".(join',',@members)."\t"); if ($self->{'contigs'}->{$_}->{'quality'}) { print("qualities found here\n"); } else { print("no qualities found here\n"); } } foreach my $pair (@pairs) { my @members = $self->get_members($pair); my $name; if (!$self->get_name($pair)) { $name = "BLANK"; } else { $name = $self->get_name($pair); } print("$name\tpairs\t".(join',',@members)."\n"); } foreach (@doublets) { my @members = $self->get_members_by_name($_); print("$_\tdoublets\t".(join',',@members)."\t"); my $contig_number = &get_contig_number_by_name($self,$_); if ($self->{'contigs'}->{$contig_number}->{'quality'}) { print("qualities found here\n"); } else { print("no qualities found here\n"); } # print($_."\tdoublets\t".(join',',@members)."\n"); } foreach (@multiplets) { my @members = $self->get_members($_); print("Contig $_"."\tmultiplets\t".(join',',@members)."\n"); } } # end dump_hash_compact =head2 get_phreds() Title : get_phreds() Usage : @phreds = $o_consed->get_phreds(); Function: For each doublet in the Bio::Tools::Alignment::Consed hash, go and get the phreds for the top and bottom reads. Place them into {top_phreds} and {bottom_phreds}. Returns : Nothing. Args : Nothing. Requires parse_phd() and reverse_and_complement(). I realize that it would be much more elegant to pull qualities as required but there were certain "features" in the acefile that required a bit more detailed work be done to get the qualities for certain parts of the consensus sequence. In order to make _sure_ that this was done properly I wrote things to do all steps and then I used dump_hash() and checked each one to ensure expected behavior. I have never changed this, so there you are. =cut sub get_phreds { # this subroutine is the target of a rewrite to use the Bio::Tools::Alignment::Phred object. my $self = shift; my $current_contig; foreach $current_contig (sort keys %{$self->{'contigs'}}) { if ($self->{'contigs'}->{$current_contig}->{'class'} eq "doublet") { $self->debug("$current_contig is a doublet. Going to parse_phd for top($self->{'contigs'}->{$current_contig}->{'top_name'}) and bottom($self->{'contigs'}->{$current_contig}->{'bottom_name'})\n"); my $r_phreds_top = &parse_phd($self,$self->{'contigs'}->{$current_contig}->{'top_name'}); my $r_phreds_bottom = &parse_phd($self,$self->{'contigs'}->{$current_contig}->{'bottom_name'}); if ($self->{'contigs'}->{$current_contig}->{'top_complement'} eq "C") { # print("Reversing and complementing...\n"); $r_phreds_top = &reverse_and_complement($r_phreds_top); } if ($self->{'contigs'}->{$current_contig}->{'bottom_complement'} eq "C") { $r_phreds_bottom = &reverse_and_complement($r_phreds_bottom); } $self->{'contigs'}->{$current_contig}->{'top_phreds'} = $r_phreds_top; $self->{'contigs'}->{$current_contig}->{'bottom_phreds'} = $r_phreds_bottom; } } } =head2 parse_phd($read_name) Title : parse_phd($read_name) Usage : $o_consed->parse_phd($read_name); Function: Suck in the contents of a .phd file. Returns : A reference to an array containing the quality values for the read. Args : The name of a read. Notes : This is a significantly weak subroutine because it was always intended that these functions, along with the functions provided by get_phreds() be put into the Bio::SeqIO:phd module. This is done now but the Bio::Tools::Alignment::Consed module has not be rewritten to reflect this change. See L<Bio::SeqIO::phd> for more information. =cut sub parse_phd { my ($self,$sequence_name) = @_; $self->debug("Parsing phd for $sequence_name\n"); my $in_dna = 0; my $base_number = 0; my (@bases,@current_line); # print("parse_phd: $sequence_name\n"); my $fh = Bio::Root::IO->new (-file=>"$self->{path}/../phd_dir/$sequence_name.phd.1"); while ($fh->_readline()) { # print("Reading a line from a phredfile!\n"); chomp; if (/^BEGIN_DNA/) { $in_dna = 1; next} if (/^END_DNA/) { last; } if (!$in_dna) { next; } push(@bases,$_); } return \@bases; } =head2 reverse_and_complement(\@source) Title : reverse_and_complement(\@source) Usage : $reference_to_array = $o_consed->reverse_and_complement(\@source); Function: A stub for the recursive routine reverse_recurse(). Returns : A reference to a reversed and complemented array of phred data. Args : A reference to an array of phred data. Notes : =cut sub reverse_and_complement { my $r_source = shift; my $r_destination; $r_destination = &reverse_recurse($r_source,$r_destination); return $r_destination; } =head2 reverse_recurse($r_source,$r_destination) Title : reverse_recurse(\@source,\@destination) Usage : $o_consed->reverse_recurse(\@source,\@destination); Function: A recursive routine to reverse and complement an array of phred data. Returns : A reference to an array containing reversed phred data. Args : A reference to a source array and a reverence to a destination array. Recursion is kewl, but this sub should likely be _reverse_recurse. =cut sub reverse_recurse($$) { my ($r_source,$r_destination) = @_; if (!@$r_source) { return $r_destination; } $_=pop(@$r_source); s/c/g/ || s/g/c/ || s/a/t/ || s/t/a/; push(@$r_destination,$_); &reverse_recurse($r_source,$r_destination); } =head2 show_missing_sequence() Title : show_missing_sequence(); Usage : $o_consed->show_missing_sequence(); Function: Used by set_trim_points_doublets() to fill in quality values where consed (phrap?) set them to 0 at the beginning and/or end of the consensus sequences. Returns : Nothing. Args : None. Acts on doublets only. Really very somewhat quite ugly. A disgusting kludge. I<insert pride here> It was written stepwise with no real plan because it was not really evident why consed (phrap?) was doing this. =cut sub show_missing_sequence() { # decide which sequence should not have been clipped at consensus # position = 0 my $self = shift; &get_phreds($self); my ($current_contig,@qualities); foreach $current_contig (sort keys %{$self->{'contigs'}}) { if ($self->{'contigs'}->{$current_contig}->{'class'} eq "doublet") { my $number_leading_xs = 0; my $number_trailing_xs = 0; my $measurer = $self->{'contigs'}->{$current_contig}->{'quality'}; while ($measurer =~ s/^\ 0\ /\ /) { $number_leading_xs++; } while ($measurer =~ s/\ 0(\s*)$/$1/) { $number_trailing_xs++; } @qualities = split(' ',$self->{'contigs'}->{$current_contig}->{'quality'}); my $in_initial_zeros = 0; for (my $count=0;$count<scalar(@qualities); $count++) { if ($qualities[$count] == 0) { my ($quality,$top_phred_position,$bottom_phred_position,$top_phred_data,$bottom_phred_data); # print("The quality of the consensus at ".($count+1)." is zero. Retrieving the real quality value.\n"); # how do I know which strand to get these quality values from???? # boggle my $top_quality_here = $self->{'contigs'}->{$current_contig}->{'top_phreds'}->[0-$self->{'contigs'}->{$current_contig}->{'top_start'}+$count+1]; my $bottom_quality_here = $self->{'contigs'}->{$current_contig}->{'bottom_phreds'}->[1-$self->{'contigs'}->{$current_contig}->{'bottom_start'}+$count]; if (!$bottom_quality_here || (1-$self->{'contigs'}->{$current_contig}->{'bottom_start'}+$count)<0) { $bottom_quality_here = "not found"; } if (!$top_quality_here) { $top_quality_here = "not found"; } # print("Looking for quals at position $count of $current_contig: top position ".(0-$self->{'contigs'}->{$current_contig}->{top_start}+$count)." ($self->{'contigs'}->{$current_contig}->{top_name}) $top_quality_here , bottom position ".(1-$self->{'contigs'}->{$current_contig}->{bottom_start}+$count)." ($self->{'contigs'}->{$current_contig}->{bottom_name}) $bottom_quality_here\n"); if ($count<$number_leading_xs) { # print("$count is less then $number_leading_xs so I will get the quality from the top strand\n"); # print("retrieved quality is ".$self->{'contigs'}->{$current_contig}->{top_phreds}[0-$self->{'contigs'}->{$current_contig}->{top_start}+$count+1]."\n"); my $quality = $top_quality_here; $quality =~ /\S+\s(\d+)\s+/; $quality = $1; # print("retrieved quality for leading zero $count is $quality\n"); # t 9 9226 $qualities[$count] = $quality; } else { # this part is tricky # if the contig is like this # cccccccccccccccc # ffffffffffffffffff # rrrrrrrrrrrrrrrrr # then take the quality value for the trailing zeros in the cons. seq from the r # # but if the contig is like this # cccccccccccccccccc # ffffffffffffffffffffffffffffffff # rrrrrrrrrrrrrrrrrrrrrrrxxxxxxxxr # ^^^ # then any zeros that fall in the positions (^) must be decided whether the quality # is the qual from the f or r strand. I will use the greater number # does a similar situation exist for the leading zeros? i dunno # # print("$count is greater then $number_leading_xs so I will get the quality from the bottom strand\n"); # print("retrieved quality is ".$contigs->{$current_contig}->{top_phreds}[0-$contigs->{$current_contig}->{top_start}+$count+1]."\n"); # my ($quality,$top_phred_position,$bottom_phred_position,$top_phred_data,$bottom_phred_data); if ($bottom_quality_here eq "not found") { # $top_phred_position = 1-$contigs->{$current_contig}->{bottom_start}+$count; # print("Going to get quality from here: $top_phred_position of the top.\n"); # my $temp_quality - $contigs->{$current_contig}->{top_phreds} # $quality = $contigs->{$current_contig}->{top_phreds}[$top_phred_position]; $top_quality_here =~ /\w+\s(\d+)\s/; $quality = $1; } elsif ($top_quality_here eq "not found") { # $bottom_phred_position = 1+$contigs->{$current_contig}->{bottom_start}+$count; # print("Going to get quality from here: $bottom_phred_position of the bottom.\n"); # $quality = $contigs->{$current_contig}->{bottom_phreds}[$bottom_phred_position]; # print("Additional: no top quality but bottom is $quality\n"); $bottom_quality_here =~ /\w+\s(\d+)\s/; $quality = $1; } else { # print("Oh jeepers, there are 2 qualities to choose from at this position.\n"); # print("Going to compare these phred qualities: top: #$top_quality_here# bottom: #$bottom_quality_here#\n"); # now you have to compare them # my $top_quality_phred = $contigs->{$current_contig}->{top_phreds}[$top_phred_position]; # #t 40 875# # print("regexing #$top_quality_here#... "); $top_quality_here =~ /\w\ (\d+)\s/; my $top_quality = $1; # print("$top_quality\nregexing #$bottom_quality_here#... "); $bottom_quality_here =~ /\w\ (\d+)\s/; my $bottom_quality = $1; # print("$bottom_quality\n"); # print("top_quality: $top_quality bottom quality: $bottom_quality\n"); if ($bottom_quality > $top_quality) { # print("Chose to take the bottom quality: $bottom_quality\n"); $quality = $bottom_quality; } else { # print("Chose to take the top quality: $top_quality\n"); $quality = $top_quality; } } if (!$quality) { # print("Warning: no quality value for $current_contig, position $count!\n"); # print("Additional data: top quality phred: $top_quality_here\n"); # print("Additional data: bottom quality phred: $bottom_quality_here\n"); } else { $qualities[$count] = $quality; } } } } unless (!@qualities) { $self->{'contigs'}->{$current_contig}->{'quality'} = join(" ",@qualities); } $self->{'contigs'}->{$current_contig}->{'bottom_phreds'} = undef; $self->{'contigs'}->{$current_contig}->{'top_phreds'} = undef; my $count = 1; } # end foreach key } } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Alignment/Trim.pm��������������������������������������������������������000555��000766��000024�� 53375�13155576320� 20553� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# Bio::Tools::Alignment::Trim.pm # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chad Matsalla # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Alignment::Trim - A kludge to do specialized trimming of sequence based on quality. =head1 SYNOPSIS use Bio::Tools::Alignment::Trim; $o_trim = Bio::Tools::Alignment::Trim->new(); $o_trim->set_reverse_designator("R"); $o_trim->set_forward_designator("F"); =head1 DESCRIPTION This is a specialized module designed by Chad for Chad to trim sequences based on a highly specialized list of requirements. In other words, write something that will trim sequences 'just like the people in the lab would do manually'. I settled on a sliding-window-average style of search which is ugly and slow but does _exactly_ what I want it to do. Mental note: rewrite this. It is very important to keep in mind the context in which this module was written: strictly to support the projects for which Consed.pm was designed. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics-at-dieselwurks.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Alignment::Trim; use strict; use Dumpvalue; use vars qw(%DEFAULTS); use base qw(Bio::Root::Root); BEGIN { %DEFAULTS = ( 'f_designator' => 'f', 'r_designator' => 'r', 'windowsize' => '10', 'phreds' => '20'); } =head2 new() Title : new() Usage : $o_trim = Bio::Tools::Alignment::Trim->new(); Function: Construct the Bio::Tools::Alignment::Trim object. No parameters are required to create this object. It is strictly a bundle of functions, as far as I am concerned. Returns : A reference to a Bio::Tools::Alignment::Trim object. Args : (optional) -windowsize (default 10) -phreds (default 20) =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my($windowsize,$phreds) = $self->_rearrange([qw( WINDOWSIZE PHREDS )], @args); $self->{windowsize} = $windowsize || $DEFAULTS{'windowsize'}; $self->{phreds} = $phreds || $DEFAULTS{'phreds'}; # print("Constructor set phreds to ".$self->{phreds}."\n") if $self->verbose > 0; $self->set_designators($DEFAULTS{'f_designator'}, $DEFAULTS{'r_designator'}); return $self; } =head2 set_designators($forward_designator,$reverse_designator) Title : set_designators(<forward>,<reverse>) Usage : $o_trim->set_designators("F","R") Function: Set the string by which the system determines whether a given sequence represents a forward or a reverse read. Returns : Nothing. Args : two scalars: one representing the forward designator and one representing the reverse designator =cut sub set_designators { my $self = shift; ($self->{'f_designator'},$self->{'r_designator'}) = @_; } =head2 set_forward_designator($designator) Title : set_forward_designator($designator) Usage : $o_trim->set_forward_designator("F") Function: Set the string by which the system determines if a given sequence is a forward read. Returns : Nothing. Args : A string representing the forward designator of this project. =cut sub set_forward_designator { my ($self,$desig) = @_; $self->{'f_designator'} = $desig; } =head2 set_reverse_designator($reverse_designator) Title : set_reverse_designator($reverse_designator) Function: Set the string by which the system determines if a given sequence is a reverse read. Usage : $o_trim->set_reverse_designator("R") Returns : Nothing. Args : A string representing the forward designator of this project. =cut sub set_reverse_designator { my ($self,$desig) = @_; $self->{'r_designator'} = $desig; } =head2 get_designators() Title : get_designators() Usage : $o_trim->get_designators() Returns : A string describing the current designators. Args : None Notes : Really for informational purposes only. Duh. =cut sub get_designators { my $self = shift; return("forward: ".$self->{'f_designator'}." reverse: ".$self->{'r_designator'}); } =head2 trim_leading_polys() Title : trim_leading_polys() Usage : $o_trim->trim_leading_polys() Function: Not implemented. Does nothing. Returns : Nothing. Args : None. Notes : This function is not implemented. Part of something I wanted to do but never got around to doing. =cut sub trim_leading_polys { my ($self, $sequence) = @_; } =head2 dump_hash() Title : dump_hash() Usage : $o_trim->dump_hash() Function: Unimplemented. Returns : Nothing. Args : None. Notes : Does nothing. =cut sub dump_hash { my $self = shift; my %hash = %{$self->{'qualities'}}; } # end dump_hash =head2 trim_singlet($sequence,$quality,$name,$class) Title : trim_singlet($sequence,$quality,$name,$class) Usage : ($r_trim_points,$trimmed_sequence) = @{$o_trim->trim_singlet($sequence,$quality,$name,$class)}; Function: Trim a singlet based on its quality. Returns : a reference to an array containing the forward and reverse trim points and the trimmed sequence. Args : $sequence : A sequence (SCALAR, please) $quality : A _scalar_ of space-delimited quality values. $name : the name of the sequence $class : The class of the sequence. One of qw(singlet singleton doublet pair multiplet) Notes : At the time this was written the bioperl objects SeqWithQuality and PrimaryQual did not exist. This is what is with the clumsy passing of references and so on. I will rewrite this next time I have to work with it. I also wasn't sure whether this function should return just the trim points or the points and the sequence. I decided that I always wanted both so that's how I implemented it. - Note that the size of the sliding windows is set during construction of the Bio::Tools::Alignment::Trim object. =cut sub trim_singlet { my ($self,$sequence,$quality,$name,$class) = @_; # this split is done because I normally store quality values in a # space-delimited scalar rather then in an array. # I do this because serialization of the arrays is tough. my @qual = split(' ',$quality); my @points; my $sequence_length = length($sequence); my ($returnstring,$processed_sequence); # smooth out the qualities my $r_windows = &_sliding_window(\@qual,$self->{windowsize}); # find out the leading and trailing trimpoints my $start_base = $self->_get_start($r_windows,$self->{windowsize},$self->{phreds}); my (@new_points,$trimmed_sequence); # do you think that any sequence shorter then 100 should be # discarded? I don't think that this should be the decision of this # module. # removed, 020926 $points[0] = $start_base; # whew! now for the end base # required parameters: reference_to_windows,windowsize,$phredvalue,start_base my $end_base = &_get_end($r_windows,$self->{windowsize}, $self->{phreds},$start_base); $points[1] = $end_base; # now do the actual trimming # CHAD : I don't think that it is a good idea to call chop_sequence here # because chop_sequence also removes X's and N's and things # and that is not always what is wanted return \@points; } =head2 trim_doublet($sequence,$quality,$name,$class) Title : trim_doublet($sequence,$quality,$name,$class) Usage : ($r_trim_points,$trimmed_sequence) = @{$o_trim->trim_singlet($sequence,$quality,$name,$class)}; Function: Trim a singlet based on its quality. Returns : a reference to an array containing the forward and reverse Args : $sequence : A sequence $quality : A _scalar_ of space-delimited quality values. $name : the name of the sequence $class : The class of the sequence. One of qw(singlet singleton doublet pair multiplet) Notes : At the time this was written the bioperl objects SeqWithQuality and PrimaryQual did not exist. This is what is with the clumsy passing of references and so on. I will rewrite this next time I have to work with it. I also wasn't sure whether this function should return just the trim points or the points and the sequence. I decided that I always wanted both so that's how I implemented it. =cut #' sub trim_doublet { my ($self,$sequence,$quality,$name,$class) = @_; my @qual = split(' ',$quality); my @points; my $sequence_length = length($sequence); my ($returnstring,$processed_sequence); # smooth out the qualities my $r_windows = &_sliding_window(\@qual,$self->{windowsize}); # determine where the consensus sequence starts my $offset = 0; for (my $current = 0; $current<$sequence_length;$current++) { if ($qual[$current] != 0) { $offset = $current; last; } } # start_base required: r_quality,$windowsize,$phredvalue my $start_base = $self->_get_start($r_windows,$self->{windowsize},$self->{phreds},$offset); if ($start_base > ($sequence_length - 100)) { $points[0] = ("FAILED"); $points[1] = ("FAILED"); return @points; } $points[0] = $start_base; # # whew! now for the end base # # required parameters: reference_to_windows,windowsize,$phredvalue,start_base # | # 010420 NOTE: We will no longer get the end base to avoid the Q/--\___/-- syndrome my $end_base = $sequence_length; my $start_of_trailing_zeros = &count_doublet_trailing_zeros(\@qual); $points[1] = $end_base; # CHAD : I don't think that it is a good idea to call chop_sequence here # because chop_sequence also removes X's and N's and things # and that is not always what is wanted return @points; } # end trim_doublet =head2 chop_sequence($name,$class,$sequence,@points) Title : chop_sequence($name,$class,$sequence,@points) Usage : ($start_point,$end_point,$chopped_sequence) = $o_trim->chop_sequence($name,$class,$sequence,@points); Function: Chop a sequence based on its name, class, and sequence. Returns : an array containing three scalars: 1- the start trim point 2- the end trim point 3- the chopped sequence Args : $name : the name of the sequence $class : The class of the sequence. One of qw(singlet singleton doublet pair multiplet) $sequence : A sequence @points : An array containing two elements- the first contains the start trim point and the second conatines the end trim point. =cut sub chop_sequence { my ($self,$name,$class,$sequence,@points) = @_; print("Coming into chop_sequence, \@points are @points\n"); my $fdesig = $self->{'f_designator'}; my $rdesig = $self->{'r_designator'}; if (!$points[0] && !$points[1]) { $sequence = "junk"; return $sequence; } if ($class eq "singlet" && $name =~ /$fdesig$/) { $sequence = substr($sequence,$points[0],$points[1]-$points[0]); } elsif ($class eq "singlet" && $name =~ /$rdesig$/) { $sequence = substr($sequence,$points[0],$points[1]-$points[0]); } elsif ($class eq "singleton" && $name =~ /$fdesig$/) { $sequence = substr($sequence,$points[0],$points[1]-$points[0]); } elsif ($class eq "singleton" && $name =~ /$rdesig$/) { $sequence = substr($sequence,$points[0],$points[1]-$points[0]); } elsif ($class eq "doublet") { $sequence = substr($sequence,$points[0],$points[1]-$points[0]); } # this is a _terrible_ to do this! i couldn't seem to find a better way # i thought something like s/(^.*[Xx]{5,})//g; might work, but no go # no time to find a fix! my $length_before_trimming = length($sequence); my $subs_Xs = $sequence =~ s/^.*[Xx]{5,}//g; if ($subs_Xs) { my $length_after_trimming = length($sequence); my $number_Xs_trimmed = $length_before_trimming - $length_after_trimming; $points[0] += $number_Xs_trimmed; } $length_before_trimming = length($sequence); my $subs_Ns = $sequence =~ s/[Nn]{1,}$//g; if ($subs_Ns) { my $length_after_trimming = length($sequence); my $number_Ns_trimmed = $length_before_trimming - $length_after_trimming; $points[1] -= $number_Ns_trimmed; $points[1] -= 1; } push @points,$sequence; print("chop_sequence \@points are @points\n"); return @points; } =head2 _get_start($r_quals,$windowsize,$phreds,$offset) Title : _get_start($r_quals,$windowsize,$phreds,$offset) Usage : $start_base = $self->_get_start($r_windows,5,20); Function: Provide the start trim point for this sequence. Returns : a scalar representing the start of the sequence Args : $r_quals : A reference to an array containing quality values. In context, this array of values has been smoothed by then sliding window-look ahead algorithm. $windowsize : The size of the window used when the sliding window look-ahead average was calculated. $phreds : <fill in what this does here> $offset : <fill in what this does here> =cut sub _get_start { my ($self,$r_quals,$windowsize,$phreds,$offset) = @_; print("Using $phreds phreds\n") if $self->verbose > 0; # this is to help determine whether the sequence is good at all my @quals = @$r_quals; my ($count,$count2,$qualsum); if ($offset) { $count = $offset; } else { $count = 0; } # search along the length of the sequence for (; ($count+$windowsize) <= scalar(@quals); $count++) { # sum all of the quality values in this window. my $cumulative=0; for($count2 = $count; $count2 < $count+$windowsize; $count2++) { if (!$quals[$count2]) { # print("Quals don't exist here!\n"); } else { $qualsum += $quals[$count2]; # print("Incremented qualsum to ($qualsum)\n"); } $cumulative++; } # print("The sum of this window (starting at $count) is $qualsum. I counted $cumulative bases.\n"); # if the total of windowsize * phreds is if ($qualsum && $qualsum >= $windowsize*$phreds) { return $count; } $qualsum = 0; } # if ($count > scalar(@quals)-$windowsize) { return; } return $count; } =head2 _get_end($r_qual,$windowsize,$phreds,$count) Title : _get_end($r_qual,$windowsize,$phreds,$count) Usage : my $end_base = &_get_end($r_windows,20,20,$start_base); Function: Get the end trim point for this sequence. Returns : A scalar representing the end trim point for this sequence. Args : $r_qual : A reference to an array containing quality values. In context, this array of values has been smoothed by then sliding window-look ahead algorithm. $windowsize : The size of the window used when the sliding window look-ahead average was calculated. $phreds : <fill in what this does here> $count : Start looking for the end of the sequence here. =cut sub _get_end { my ($r_qual,$windowsize,$phreds,$count) = @_; my @quals = @$r_qual; my $total_bases = scalar(@quals); my ($count2,$qualsum,$end_of_quals,$bases_counted); if (!$count) { $count=0; } BASE: for (; $count < $total_bases; $count++) { $bases_counted = 0; $qualsum = 0; POSITION: for($count2 = $count; $count2 < $total_bases; $count2++) { $bases_counted++; if ($count2 == $total_bases-1) { $qualsum += $quals[$count2]; $bases_counted++; last BASE; } elsif ($bases_counted == $windowsize) { $qualsum += $quals[$count2]; if ($qualsum < $bases_counted*$phreds) { return $count+$bases_counted+$windowsize; } next BASE; } else { $qualsum += $quals[$count2]; } } if ($qualsum < $bases_counted*$phreds) { return $count+$bases_counted+$windowsize; } else { } $qualsum = 0; } # end for if ($end_of_quals) { my $bases_for_average = $total_bases-$count2; return $count2; } else { } if ($qualsum) { } # print ("$qualsum\n"); return $total_bases; } # end get_end =head2 count_doublet_trailing_zeros($r_qual) Title : count_doublet_trailing_zeros($r_qual) Usage : my $start_of_trailing_zeros = &count_doublet_trailing_zeros(\@qual); Function: Find out when the trailing zero qualities start. Returns : A scalar representing where the zeros start. Args : A reference to an array of quality values. Notes : Again, this should be rewritten to use PrimaryQual objects. A more detailed explanation of why phrap puts these zeros here should be written and placed here. Please email and hassle the author. =cut sub count_doublet_trailing_zeros { my ($r_qual) = shift; my $number_of_trailing_zeros = 0; my @qualities = @$r_qual; for (my $current=scalar(@qualities);$current>0;$current--) { if ($qualities[$current] && $qualities[$current] != 0) { $number_of_trailing_zeros = scalar(@qualities)-$current; return $current+1; } } return scalar(@qualities); } # end count_doublet_trailing_zeros =head2 _sliding_window($r_quals,$windowsize) Title : _sliding_window($r_quals,$windowsize) Usage : my $r_windows = &_sliding_window(\@qual,$windowsize); Function: Create a sliding window, look-forward-average on an array of quality values. Used to smooth out differences in qualities. Returns : A reference to an array containing the smoothed values. Args : $r_quals: A reference to an array containing quality values. $windowsize : The size of the sliding window. Notes : This was written before PrimaryQual objects existed. They should use that object but I haven't rewritten this yet. =cut #' sub _sliding_window { my ($r_quals,$windowsize) = @_; my (@window,@quals,$qualsum,$count,$count2,$average,@averages,$bases_counted); @quals = @$r_quals; my $size_of_quality = scalar(@quals); # do this loop for all of the qualities for ($count=0; $count <= $size_of_quality; $count++) { $bases_counted = 0; BASE: for($count2 = $count; $count2 < $size_of_quality; $count2++) { $bases_counted++; # if the search hits the end of the averages, stop # this is for the case near the end where bases remaining < windowsize if ($count2 == $size_of_quality) { $qualsum += $quals[$count2]; last BASE; } # if the search hits the size of the window elsif ($bases_counted == $windowsize) { $qualsum += $quals[$count2]; last BASE; } # otherwise add the quality value unless (!$quals[$count2]) { $qualsum += $quals[$count2]; } } unless (!$qualsum || !$windowsize) { $average = $qualsum / $bases_counted; if (!$average) { $average = "0"; } push @averages,$average; } $qualsum = 0; } # 02101 Yes, I repaired the mismatching numbers between averages and windows. # print("There are ".scalar(@$r_quals)." quality values. They are @$r_quals\n"); # print("There are ".scalar(@averages)." average values. They are @averages\n"); return \@averages; } =head2 _print_formatted_qualities Title : _print_formatted_qualities(\@quals) Usage : &_print_formatted_qualities(\@quals); Returns : Nothing. Prints. Args : A reference to an array containing quality values. Notes : An internal procedure used in debugging. Prints out an array nicely. =cut sub _print_formatted_qualities { my $rquals = shift; my @qual = @$rquals; for (my $count=0; $count<scalar(@qual) ; $count++) { if (($count%10)==0) { print("\n$count\t"); } if ($qual[$count]) { print ("$qual[$count]\t");} else { print("0\t"); } } print("\n"); } =head2 _get_end_old($r_qual,$windowsize,$phreds,$count) Title : _get_end_old($r_qual,$windowsize,$phreds,$count) Usage : Deprecated. Don't use this! Returns : Deprecated. Don't use this! Args : Deprecated. Don't use this! =cut #' sub _get_end_old { my ($r_qual,$windowsize,$phreds,$count) = @_; warn("Do Not Use this function (_get_end_old)"); my $target = $windowsize*$phreds; my @quals = @$r_qual; my $total_bases = scalar(@quals); my ($count2,$qualsum,$end_of_quals); if (!$count) { $count=0; } BASE: for (; $count < $total_bases; $count++) { for($count2 = $count; $count2 < $count+$windowsize; $count2++) { if ($count2 == scalar(@quals)-1) { $qualsum += $quals[$count2]; $end_of_quals = 1; last BASE; } $qualsum += $quals[$count2]; } if ($qualsum < $windowsize*$phreds) { return $count+$windowsize; } $qualsum = 0; } # end for } # end get_end_old # Autoload methods go after =cut, and are processed by the autosplit program. 1; __END__ �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Analysis�����������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16752� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Analysis/SimpleAnalysisBase.pm�������������������������������������������000444��000766��000024�� 15434�13155576320� 23224� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Analysis::SimpleAnalysisBase # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> # # Copyright Richard Adams # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Analysis::SimpleAnalysisBase - abstract superclass for SimpleAnalysis implementations =head1 SYNOPSIS # not to be run directly =head1 DESCRIPTION This class is a generic implementation of SimpleAnalysisI and should be used as a base class for specific implementations. Modules implementing SimpleAnalysisBase only need to provide specific _init(), _run() and result() methods, plus any get/set methods for parameters to the analysis program. =head1 SEE ALSO L<Bio::SimpleAnalysisI>, L<Bio::WebAgent> =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Analysis::SimpleAnalysisBase; use strict; use Data::Dumper; my $FLOAT = '[+-]?\d*\.\d*'; my %STATUS = map { $_ => 1 } qw(CREATED COMPLETED TERMINATED_BY_ERROR); use base qw(Bio::WebAgent Bio::SimpleAnalysisI); =head2 new Usage : $job->new(...) Returns : a new analysis object, Args : none (but an implementation may choose to add arguments representing parameters for the analysis program. Each key value of must have a method implemented for it in a subclass. A seq () method is provided here as this will probably be needed by all sequence analysis programs =cut sub new { my $class = shift; my $self = $class->SUPER::new(); #WebAgent new $self->_init; #this line has to be before the attributes are filled in while ( @_ ) { my $key = lc shift; $key =~ s/^-//; $self->$key(shift); } return $self; } =head2 seq Usage : $job->seq() Returns : a Bio::PrimarySeqI implementing sequence object, or void Args : None, or a Bio::PrimarySeqI implementing object =cut sub seq { my ($self,$value) = @_; if ( defined $value) { $self->throw("I need a Bio::PrimarySeqI, not [". $value. "]") unless $value->isa('Bio::PrimarySeqI'); $self->throw(" I need a PrimarySeq object, not a BioSeq object ") if $value->isa('Bio::SeqI'); my $mol_type = $self->analysis_spec->{'type'}; $self->throw("I need a [" . $mol_type . "] seq, not a [". $value->alphabet. "]") unless $value->alphabet =~/$mol_type/i; $self->{'_seq'} = $value; return $self; } return $self->{'_seq'} ; } =head2 analysis_name Usage : $analysis->analysis_name(); Returns : The analysis name Arguments : none =cut sub analysis_name { my $self = shift; return $self->{'_ANALYSIS_NAME'}; } =head2 analysis_spec Usage : $analysis->analysis_spec(); Returns : a hash reference to a hash of analysis parameters. See Bio::SimpleAnalysisI for a list of recommended key values. Arguments: none =cut sub analysis_spec { my $self = shift; return $self->{'_ANALYSIS_SPEC'}; } =head2 clear Usage : $analysis->clear(); Returns : true value on success Arguments : none Purpose : to remove raw results from a previous analysis so that an analysis can be repeated with different parameters. =cut sub clear { my $self= shift; if (defined($self->{'_result'})) { delete $self->{'_result'}; } if (defined ($self->{'_parsed'})) { delete $self->{'_parsed'}; } return 1; } =head2 input_spec Usage : $analysis->input_spec(); Returns : a reference to an array of hashes of analysis parameters. See Bio::SimpleAnalysisI for a list of recommended key values. Arguments : none =cut sub input_spec { my $self = shift; return $self->{'_INPUT_SPEC'}; } =head2 result_spec Usage : $analysis->result_spec(); Returns : a reference to a hashes of resultformats. See Bio::SimpleAnalysisI for a list of recommended key values. The key values can be used as parameters to the result() method, the values provide descriptions. Arguments : none =cut sub result_spec { my $self = shift; return $self->{'_RESULT_SPEC'}; } sub run { my ($self, $args) = @_; $self->_process_arguments ($args) if $args; # check input $self->throw("Need a sequence object as an input") unless $self->seq; $self->debug(Data::Dumper->Dump([$self],[$self])); # internal run() $self->_run; return $self; } sub wait_for { my ($self, $args) = @_; $self->run($args); } sub status { my ($self,$value) = @_; if( defined $value) { no strict 'refs'; my $class = ref($self); $self->throw("Not a valid status value [$value]\n". "Valid values are ". join(", ", keys %STATUS )) unless defined $STATUS{$value}; $self->{'_status'} = $value; use strict; } return $self->{'_status'} || 'CREATED' ; } sub _process_arguments { my ($self, $args) = @_; my %spec; map {$spec{ $_->{'name'} } = $_ } @{$self->input_spec}; $self->debug(Data::Dumper->Dump([\%spec, $args],[\%spec, $args])); foreach my $key (keys %$args) { my $value = $args->{$key}; $self->throw("Unknown argument [$key]") unless $spec{$key}; $self->$key($value); } foreach my $key (keys %spec) { $self->throw("Mandatory argument [$key] is not set") if $spec{$key}{'mandatory'} eq 'true' and not defined $self->$key; } } sub _run { shift->throw_not_implemented();} 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Analysis/DNA�������������������������������������������������������������000755��000766��000024�� 0�13155576320� 17354� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Analysis/DNA/ESEfinder.pm������������������������������������������������000444��000766��000024�� 23330�13155576320� 21674� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Analysis::DNA::ESEfinder # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> # # Copyright Richard Adams # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Analysis::DNA::ESEfinder - a wrapper around ESEfinder server =head1 SYNOPSIS use Bio::Tools::Analysis::DNA::ESEfinder; use strict; my $seq; # a Bio::PrimarySeqI or Bio::SeqI object $seq = Bio::Seq->new( -primary_id => 'test', -seq=>'atgcatgctaggtgtgtgttttgtgggttgtactagctagtgat'. -alphabet=>'dna'); my $ese_finder = Bio::Tools::Analysis::DNA::ESEfinder-> new(-seq => $seq); # run ESEfinder prediction on a DNA sequence $ese_finder->run(); die "Could not get a result" unless $ese_finder->status =~ /^COMPLETED/; print $ese_finder->result; # print raw prediction to STDOUT foreach my $feat ( $ese_finder->result('Bio::SeqFeatureI') ) { # do something to SeqFeature # e.g. print as GFF print $feat->gff_string, "\n"; # or store within the sequence - if it is a Bio::SeqI $seq->add_SeqFeature($feat) } =head1 DESCRIPTION This class is a wrapper around the ESEfinder web server which uses experimentally defined scoring matrices to identify possible exonic splicing enhancers in human transcripts. The results can be retrieved in 4 ways. =over 4 =item 1. C<$ese_finder-E<gt>result('')> retrieves the raw text output of the program =item 2. C<$ese_finder-E<gt>result('all')> returns a Bio::Seq::Meta::Array object with prediction scores for all residues in the sequence =item 3. C<$ese_finder-E<gt>result('Bio::SeqFeatureI')> returns an array of Bio::SeqFeature objects for sequences with significant scores. Feature tags are score, motif, SR_protein and method =item 4. C<$ese_finder-E<gt>result('raw')> returns an array of significant matches with each element being a reference to [SR_protein, position, motif, score] =back See L<http://rulai.cshl.edu/tools/ESE2/> This the second implementation of Bio::SimpleAnalysisI which hopefully will make it easier to write wrappers on various services. This class uses a web resource and therefore inherits from L<Bio::WebAgent>. =head1 SEE ALSO L<Bio::SimpleAnalysisI>, L<Bio::WebAgent> =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... #should have own package Bio::Tools::Analysis::DNA::ESEfinder; use Data::Dumper; use IO::String; use Bio::SeqIO; use HTTP::Request::Common qw (POST); use HTML::HeadParser; use Bio::SeqFeature::Generic; use Bio::Seq::Meta::Array; use Bio::WebAgent; use strict; #inherits directly from SimpleAnalysisBase use base qw(Bio::Tools::Analysis::SimpleAnalysisBase); #global vars are now file-scoped lexicals my $URL = 'http://rulai.cshl.org/cgi-bin/tools/ESE/esefinder.cgi'; my $ANALYSIS_NAME = 'ESEfinder'; my $ANALYSIS_SPEC = { 'name' => 'ESEfinder', 'type' => 'DNA', #compulsory entry as is used for seq checking 'version' => '2.0', 'supplier' => 'Krainer lab, Cold Spring Harbor Laboratory, POBOX100, Bungtown Rd, COld Spring Harbor, NY, USA', 'description' => 'to identify exonic splicing elements in human transcripts', }; my $INPUT_SPEC = [{ 'mandatory' => 'true', 'type' => 'Bio::PrimarySeqI', 'name' => 'sequence', }]; my $RESULT_SPEC = { '' => 'bulk', # same as undef 'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeature::Generic', 'raw' => 'Array of [ SR_protein, position, motif, score]', 'all' => 'Bio::Seq::Meta::Array object' }; ### unique to this module ## sub _init { ## fills in fixed data for class ## my $self = shift; $self->url($URL); $self->{'_ANALYSIS_SPEC'} =$ANALYSIS_SPEC; $self->{'_INPUT_SPEC'} =$INPUT_SPEC; $self->{'_RESULT_SPEC'} =$RESULT_SPEC; $self->{'_ANALYSIS_NAME'} =$ANALYSIS_NAME; return $self; } sub _run { my $self = shift; my $seq_fasta; my $stringfh = IO::String->new($seq_fasta); my $seqout = Bio::SeqIO->new(-fh => $stringfh, -format => 'fasta'); $seqout->write_seq($self->seq); $self->debug($seq_fasta); $self->delay(1); # delay repeated calls by default by 3 sec, set delay() to change $self->sleep; $self->status('TERMINATED_BY_ERROR'); my $request = POST $self->url, #Content_Type => 'x-www-form-urlencoded', Content => [ protein1 => 1, protein2 => 1, protein3 => 1, protein4 => 1, radio_sf2 => 0, radio_sc35 => 0, radio_srp40 => 0, radio_srp55 => 0, sequence =>$seq_fasta, ]; my $content = $self->request($request); if( $content->is_error ) { $self->throw(ref($self)." Request Error:\n".$content->as_string); } my $text = $content->content; #1st reponse my ($tmpfile) = $text =~ /value="(tmp\/.+txt)"/; # now get data for all residues # my $rq2 = POST 'http://rulai.cshl.org/cgi-bin/tools/ESE/resultfile.txt', #Content_Type => 'x-www-form-urlencoded', Content => [ fname => $tmpfile, ]; my $ua2 = Bio::WebAgent->new(); my $content2 = $ua2->request($rq2); if( $content2->is_error ) { $self->throw(ref($self)." Request Error:\n".$content2->as_string); } my $text2 = $content2->content; $self->{'_result'} = $text2; $self->status('COMPLETED') if $text2 ne ''; #print Dumper $response; } sub result { #make sec feat of above threshold scores # my ($self,$value) = @_; my @sig_pdctns; my @fts; if ($value ) { my $result = IO::String->new($self->{'_result'}); my $current_SR; my $all_st_flag = 0; my %all; while (my $line = <$result>) { #make array of all scores or threshold depending on $value last if $line =~ /^All scores/ && $value ne 'all' or $line =~ /2001,/; $all_st_flag++ if $line =~ /All scores/; next if $value eq 'all' && $all_st_flag == 0; #parse line if ($line =~ /^Protein/) { ($current_SR) = $line =~/:\s+(\S+)/; $current_SR =~ s{/}{_}; # remove unallowed charcters from hash } if ( $line =~/^\d+/ && $value ne 'all') { push @sig_pdctns, [$current_SR, split /\s+/, $line] ; } elsif ($line =~ /^\d+/) { push @{$all{$current_SR}}, [split /\s+/, $line]; } } if ($value eq 'Bio::SeqFeatureI') { foreach (@sig_pdctns) { #make new ese object for each row of results push @fts, Bio::SeqFeature::Generic->new ( -start => $_->[1], -end => $_->[1] + length($_->[2]) -1, -source => 'ESEfinder', -primary => 'ESE', -tag =>{ score =>$_->[3], motif=> $_->[2], SR_protein=> $_->[0], method=> 'ESEfinder', }, ); } return @fts; } ## convert parsed data into a meta array format elsif ($value eq 'all') { bless ($self->seq, "Bio::Seq::Meta::Array"); $self->seq->isa("Bio::Seq::MetaI") || $self->throw("$self is not a Bio::Seq::MetaI"); for my $prot (keys %all) { my @meta; my $len = scalar @{$all{$prot}} ; for (my $i = 0; $i < $len; $i++ ) { $meta[$i] = $all{$prot}[$i][2]; } # assign default name here so that the # Bio::Seq::Meta::Array can work for all classes # implementing it and we can avoid having to make # asubclass for each implementation $Bio::Seq::Meta::Array::DEFAULT_NAME = "ESEfinder_SRp55"; my $meta_name = $self->analysis_spec->{'name'} . "_" . "$prot"; $self->seq->named_meta($meta_name,\@meta ); } # return seq array object implementing meta sequence # return $self->seq; } #return ref to array of arrays return \@sig_pdctns; } return $self->{'_result'}; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Analysis/Protein���������������������������������������������������������000755��000766��000024�� 0�13155576320� 20372� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Analysis/Protein/Domcut.pm�����������������������������������������������000444��000766��000024�� 25165�13155576320� 22351� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# $Id: Domcut.pm,v 1.0 2003/07/ 11 # # BioPerl module for Bio::Tools::Analysis::Protein::Domcut # # Copyright Richard Adams # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Analysis::Protein::Domcut - a wrapper around Domcut server =head1 SYNOPSIS use Bio::Tools::Analysis::Protein::Domcut; #get a Bio::PrimarySeq use Bio::PrimarySeq; my $seq = Bio::PrimarySeq->new (-seq=>'IKLCVNLAILAKAHLIELALAL', -primary_id=>'test'); # a Bio::PrimarySeqI object my $domcut = Bio::Tools::Analysis::Protein::Domcut->new (-seq=>$seq); $domcut->run; print $domcut->result;# #raw text to standard out =head1 DESCRIPTION A module to remotely retrieve predictions of protein domain boundaries. Each residue in the protein receives a score, those better than the significance threshold and at a local minimum receive a rank - i.e., the best minimum is rank 1, the second best minimum is rank2 etc. These correspond to domain boundaries. e.g., my $analysis_object = Bio::Tools::Analysis::Protein::Domcut->new (-seq => $seq); creates a new object. The sequence supplied must be a Bio::PrimarySeq and not a Bio::Seq object. $analysis_object->run; submits the query to the server and obtains raw text output Given an amino acid sequence the results can be obtained in 4 formats, determined by the argument to the result method =over 4 =item 1 The raw text of the program output my $rawdata = $analysis_object->result; =item 2 A reference to an array of hashes of scores for each state and the assigned state. Each element in the array is a residue (indexed from 0). my $data_ref = $analysis_object->result('parsed'); print "score for helix at residue 2 is $data_ref->[1]{'helix'}\n"; print "predicted struc at residue 2 is $data_ref->[1]{'struc}\n"; =item 3 An array of Bio::SeqFeature::Generic objects where each feature is a predicted unit of secondary structure. Only stretches of helix/sheet predictions for longer than 4 residues are defined as helices. So, in order to add features to an existing Bio::Seq object; # get a Bio::Seq object my $seqobj; my $tool = Bio::Tools::Analysis::Protein::Domcut->new ( -seq => $seqobj->primary_seq); $tool->run; my @fts = $tool->result(Bio::SeqFeatureI); $seqobj->add_SeqFeature(@fts); # if you want meta sequences as well : my $meta = $tool->result('meta'); $seqobj->primary_seq($meta); # can access meta data in a Bio::Seq object via a # call to primary_seq: print $seq4->primary_seq->named_submeta_text('Domcut', 1,2), "\n"; =item 4 A Bio::Seq::Meta::Array implementing sequence. This is a Bio::Seq object that can also hold data about each residue in the sequence. In this case, the sequence can be associated with a single array of Domcut prediction scores. e.g., my $meta_sequence = $analysis_object->result('meta'); print "scores from residues 10 -20 are ", $meta_sequence->submeta_text(10,20), "\n"; Many methods common to all analyses are inherited from Bio::Tools::Analysis::SimpleAnalysisBase. =back =head1 SEE ALSO L<Bio::SimpleAnalysisI>, L<Bio::Tools::Analysis::SimpleAnalysisBase>, L<Bio::Seq::Meta::Array>, L<Bio::WebAgent> =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Richard Adams, Richard.Adams@ed.ac.uk, =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut use strict; package Bio::Tools::Analysis::Protein::Domcut; use IO::String; use Bio::SeqIO; use HTTP::Request::Common qw(GET); use Bio::SeqFeature::Generic; use Bio::Seq::Meta::Array; use base qw(Bio::Tools::Analysis::SimpleAnalysisBase); my $URL = 'http://www.Bork.EMBL-Heidelberg.DE/Docu/mikita/domplot.cgi?'; my $ANALYSIS_NAME = 'Domcut'; my $ANALYSIS_SPEC = { 'name' => 'Domcut', 'type' => 'protein', #compulsory entry as is used for seq checking 'version' => 'n/a', 'supplier' => 'Ohara lab, Laboratory of DNA technology, Kazusa DNA Research Institute, 1532-3 Yana, Kisarazu, Japan', 'description' => 'to predict domain boundaries in proteins', 'reference' => 'Bioinformatics 19, 673-674 (2003)', }; my $INPUT_SPEC = [ { 'mandatory' => 'true', 'type' => 'Bio::PrimarySeqI', 'name' => 'seq', }, ]; my $RESULT_SPEC = { '' => 'bulk', # same as undef 'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeature::Generic', 'parsed' => "Array of {'score' =>, 'rank'=> ]", 'meta' => 'Bio::Seq::Meta::Array object' }; =head2 result Name : result Purpose : To retrieve results of analysis in one of several formats. Usage : $job->result (...) Returns : a result created by running an analysis Args : various - see keysin $RESULT_SPEC. The method returns a result of an executed job. If the job was terminated by an error the result may contain an error message instead of the real data. This implementation returns differently processed data depending on argument: =over 3 =item undef Returns the raw ASCII data stream but without HTML tags =item 'Bio::SeqFeatureI' The argument string defines the type of bioperl objects returned in an array. The objects are L<Bio::SeqFeature::Generic>. Tagnames are 'score' and 'rank'. =item 'parsed' Array of array references of [score, rank]. =item 'all' A Bio::Seq::Meta::Array object. Scores can be accessed using methods from this class. Meta sequence name is Domcut. =back =cut sub result { my ($self,$value) = @_; my @scores; my @fts; if ($value ) { # parse raw text if not already done so if (!exists($self->{'_parsed'})) { my $result = IO::String->new($self->{'_result'}); while (my $line = <$result>) { next if $line =~/#/; $line =~/(\-?\d\.\d+)\s+(\d+)?/; push @scores, {score => $1, rank => ($2)?$2:'' , }; } #hold parsed results in object, saves having to reparse each time $self->{'_parsed'} = \@scores; } #make aarray of Bio::SeqFeature::Generic objects if ($value eq 'Bio::SeqFeatureI') { my $i = 0; #array index (= aa num -1) my $in_trough = 0; my ($st, $end, $rank, $min_score, $min_locus) = (0,0,0,0,0); my $seqlen = $self->seq->length(); for my $score (@{$self->{'_parsed'}}) { ##start a potential trough if ($in_trough == 0 && $score->{'score'} < -0.09) { $in_trough = 1; $st = $i+1; } ## in a trough, is it ranked? elsif ( $in_trough == 1 && $score->{'score'} < -0.09 && $i +1 < $seqlen){ if ($score->{'rank'} ) { $rank = $score->{'rank'}; $min_score = $score->{'score'}; $min_locus = $i + 1; } } ## end of trough or end of sequence, make into feature ## if possible elsif ($in_trough == 1 && ($score->{'score'} > -0.09 || $i +1 == $seqlen) ){ if ($rank != 0) { push @fts, Bio::SeqFeature::Generic->new ( -start => $st, -end => $i +1, #current position -primary => 'Linker', -source => 'Domcut', -tag => { score => $min_score, rank => $rank, residue => $min_locus, }, ); } ##and reset parameters ## ($st, $in_trough, $min_locus, $min_score, $rank) = (0,0,0,0,0); } $i++; } return @fts; } ## convert parsed data into a meta array format elsif ($value eq 'meta') { ## only need to bless once if (! $self->seq->isa("Bio::Seq::MetaI")){ bless ($self->seq, "Bio::Seq::Meta::Array"); } $self->seq->isa("Bio::Seq::MetaI") || $self->throw("$self is not a Bio::Seq::MetaI"); my $meta_name = "Domcut"; #test that sequence does not have already a meta seq with same name if (grep{$_ eq $meta_name}$self->seq->meta_names ) { $self->warn ("$meta_name already exists , not overwriting!"); next; } ### or should be an instance variable?? ## $Bio::Seq::Meta::Array::DEFAULT_NAME = 'Domcut'; my @meta = map{$_->{'score'}} @{$self->{'_parsed'}}; $self->seq->named_meta($meta_name,\@meta ); # return seq array object implementing meta sequence # return $self->seq; } # return ref to array of predictions; elsif ($value eq 'parsed') { return $self->{'_parsed'}; } } #else if no arguments return raw text return $self->{'_result'}; } sub _init { my $self = shift; $self->url($URL); $self->{'_ANALYSIS_SPEC'} = $ANALYSIS_SPEC; $self->{'_INPUT_SPEC'} = $INPUT_SPEC; $self->{'_RESULT_SPEC'} = $RESULT_SPEC; $self->{'_ANALYSIS_NAME'} = $ANALYSIS_NAME; return $self; } sub _run { my $self = shift; my $seq_fasta = $self->seq->seq; $self->delay(1); # delay repeated calls by default by 3 sec, set delay() to change $self->sleep; $self->status('TERMINATED_BY_ERROR'); my $rqst = GET $self->url . "&seqnam=". "&sequence=". $seq_fasta. "&outform=dat"; my $content = $self->request($rqst); my $text = $content->content; #1st reponse $self->{'_result'} = $text; $self->status('COMPLETED') if $text ne ''; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Analysis/Protein/ELM.pm��������������������������������������������������000555��000766��000024�� 27226�13155576320� 21536� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Analysis::Protein::ELM # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Richard Adams <richard.adams@ed.ac.uk> # # Copyright Richard Adams # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Analysis::Protein::ELM - a wrapper around the ELM server which predicts short functional motifs on amino acid sequences =head1 SYNOPSIS # get a Bio::Seq object to start with, or a Bio::PrimaryI object. my $tool = Bio::Tools::Analysis::Protein::ELM-> new(seq => $seqobj->primary_seq() ); $tool->compartment(['ER', 'Golgi']); $tool->species(9606); $tool->run; my @fts = $tool->Result('Bio::SeqFeatureI'); $seqobj->addSeqFeature(@fts); =head1 DESCRIPTION This module is a wrapper around the ELM server L<http://elm.eu.org/> which predicts short functional motifs on amino acid sequences. False positives can be limited by providing values for the species and cellular compartment of the protein. To set the species attribute, use either a L<Bio::Species> object or an NCBI taxon ID number. To set the cell compartment attribute (any number of compartments can be chosen) use an array reference to a list of compartment names. Results can be obtained either as raw text output, parsed into a data structure, or as Bio::SeqFeature::Generic objects. =head1 SEE ALSO L<Bio::SimpleAnalysisI>, L<Bio::WebAgent> =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Richard Adams, Richard.Adams@ed.ac.uk, =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut use strict; package Bio::Tools::Analysis::Protein::ELM; use vars qw(%cc); use HTML::HeadParser; use Bio::SeqFeature::Generic; use HTTP::Request::Common qw(POST); use IO::String; use base qw(Bio::Tools::Analysis::SimpleAnalysisBase); ## valid cell compartments ## %cc = ( all => 1, nucleus => 'GO:0005634', extracellular => 'GO:0005576', cytoplasm => 'GO:0005737', peroxisome => 'GO:0005777', glycosome => 'GO:0020015', glyoxisome => 'GO:0009514', golgi => 'GO:0005794', er => 'GO:0005783', lysosome => 'GO:0005764', endosome => 'GO:0005768', plasma_membrane=> 'GO:0005886', ); my $URL = 'http://elm.eu.org/cgimodel.py'; my $ANALYSIS_NAME = 'ELM'; my $INPUT_SPEC = [ { 'mandatory' => 'true', 'type' => 'Bio::PrimarySeqI', 'name' => 'seq', }, { 'mandatory' => 'false', 'type' => 'taxon_id or Bio::Species object', 'name' => 'species', 'default' => '9606', }, { 'mandatory' => 'false', 'type' => 'string', 'name' => 'compartment', 'default' => [1], }, ]; my $RESULT_SPEC = { '' => 'bulk', # same as undef 'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeature::Generic', 'parsed' => '{motif1_name=>{locus=>[], peptide=>[], regexp=>[] }, }', }; my $ANALYSIS_SPEC= {name => 'ELM', type => 'Protein', version => 'n/a', supplier =>'BioComputing Unit, EMBL', description =>'Prediction of linear functional motifs in proteins', reference => 'NAR, 31:3625-3630'}; sub _init { my $self = shift; $self->url($URL); $self->{'_ANALYSIS_SPEC'} = $ANALYSIS_SPEC; $self->{'_INPUT_SPEC'} = $INPUT_SPEC; $self->{'_RESULT_SPEC'} = $RESULT_SPEC; $self->{'_ANALYSIS_NAME'} = $ANALYSIS_NAME; return $self; } =head2 compartment name : compartment usage : $elm->compartment(['golgi', 'er']); purpose : get/setter for cell compartment specifications arguments : None, single compartment string or ref to array of compartment names. returns : Array of compartment names (default if not previously set). =cut sub compartment { my ($self, $arg) = @_; if ($arg) { # convert to array ref if not one already if (ref ($arg) ne 'ARRAY') { $arg = [$arg]; } ## now add params if valid for my $param (@$arg) { if (exists($cc{lc($param)})) { push @{$self->{'_compartment'}} , $cc{$param}; } else { $self->warn("invalid argument ! Must be one of " . join "\n", keys %cc ); } } #end of for loop } #endif $arg return defined($self->{'_compartment'})? $self->{'_compartment'} : $self->input_spec()->[2]{'default'}; } =head1 species name : species usage : $tool->species('9606'); purpose : get/setter for species selection for ELM server arguments : none, taxon_id or Bio::Species object returns : a string of the ncbi taxon_id =cut sub species { my ($self, $arg) = @_; if ($arg) { if (ref($arg) && $arg->isa('Bio::Species')) { $self->{'_species'} = $arg->ncbi_taxid(); } elsif ($arg =~ /^\d+$/) { $self->{'_species'} = $arg; } else { $self->warn("Argument must be a Bio::Species object or ". " an integer NCBI taxon id. "); } } #end if $arg return defined($self->{'_species'})?$self->{'_species'} :$self->input_spec()->[1]{'default'}; } sub _run { my $self = shift; $self->delay(1); # delay repeated calls by default by 3 sec, set delay() to change #$self->sleep; $self->status('TERMINATED_BY_ERROR'); #### this deals with being able to submit multiple checkboxed #### slections #1st of all make param array my @cc_str; my @cmpts = @{$self->compartment()}; for (my $i = 0; $i <= $#cmpts ; $i++) { splice @cc_str, @cc_str, 0, 'userCC',$cmpts[$i]; } my %h = (swissprotId => "", sequence => $self->seq->seq, userSpecies => $self->species, typedUserSpecies => '', fun => "Submit"); splice (@cc_str, @cc_str,0, ( map{$_, $h{$_}} keys %h)); my $request = POST $self->url(), Content_Type => 'form-data', Content => \@cc_str; $self->debug( $request->as_string); my $r1 = $self->request($request); if ( $r1->is_error ) { $self->warn(ref($self)." Request Error:\n".$r1->as_string); return; } my $text = $r1->content; my ($url) = $text =~ /URL=\S+(fun=\S+r=\d)/s; #$url =~ s/amp;//g ; my ($resp2); $url = $URL . "?" .$url; while (1) { my $req2 = HTTP::Request->new(GET=>$url); my $r2 = $self->request ($req2); if ( $r2->is_error ) { $self->warn(ref($self)." Request Error:\n".$r2->as_string); return; } $resp2 = $r2->content(); if ($resp2 !~ /patient/s) { $self->status('COMPLETED'); $resp2=~ s/<[^>]+>/ /sg; $self->{'_result'} = $resp2; return; } else { print "." if $self->verbose > 0; $self->sleep(1); } } } =head1 result name : result usage : $tool->result('Bio::SeqFeatureI'); purpose : parse results into sequence features or basic data format arguments : 1. none (retrieves raw text without html) 2. a value (retrieves data structure) 3. 'Bio::SeqFeatureI' (returns array of sequence features) tag names are : {method => 'ELM', motif => motifname, peptide => seqeunce of match, concensus => regexp of match}. returns : see arguments. =cut sub result { my ($self, $val) = @_; if ($val) { if (!exists($self->{'_parsed'}) ) { $self->_parse_raw(); } if ($val eq 'Bio::SeqFeatureI') { my @fts; for my $motif (keys %{$self->{'_parsed'}}) { for (my $i = 0; $i< scalar @{$self->{'_parsed'}{$motif}{'locus'}};$i++) { my ($st, $end) = split /\-/, $self->{'_parsed'}{$motif}{'locus'}[$i]; push @fts, Bio::SeqFeature::Generic->new ( -start => $st, -end => $end, -primary_tag => 'Domain', -source => 'ELM', -tag => { method => 'ELM', motif => $motif, peptide => $self->{'_parsed'}{$motif}{'peptide'}[$i], concensus => $self->{'_parsed'}{$motif}{'regexp'}[0], }); } } return @fts; } #end if BioSeqFeature return $self->{'_parsed'}; } #endif ($val) return $self->{'_result'}; } ## internal sub to parse raw data into internal data structure which is cached. sub _parse_raw { my $self = shift; my $result = IO::String->new($self->{'_result'}); my $in_results = 0; my $name; my %results; my $last; while (my $l = <$result>) { next unless $in_results > 0 ||$l =~ /^\s+Elm\s+Name\s+Instances/; $in_results++; #will be set whnstart of results reached. last if $l =~ /List of excluded/; next unless $in_results >1; my @line_parts = split /\s+/, $l; shift @line_parts; ## if result has motif name on 1 line if (scalar @line_parts == 1 && $line_parts[0]=~ /^\s*(\w+_\w+)/) { $name = $1; next; } ## else if is line with loci /seq matches elsif (@line_parts > 1) { my $index = 0; ## array index my $read_loci = 0; ## flag to know that loci are being read while ($index <= $#line_parts) { my $word = $line_parts[$index++]; if ($read_loci ==0 && $word =~/_/) { $name = $word; } elsif ($read_loci == 0 && $word =~ /^\w+$/ ) { push @{$results{$name}{'peptide'}}, $word; } elsif ($word =~ /\d+\-\d+/) { $read_loci = 1; push @{$results{$name}{'locus'}}, $word; } else { ## only get here if there are elements last; } } #end of while push @{$results{$name}{'regexp'}}, $line_parts[$#line_parts]; } #end of elsif } #end of while $self->{'_parsed'} = \%results; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Analysis/Protein/GOR4.pm�������������������������������������������������000444��000766��000024�� 26610�13155576320� 21625� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# $Id: GOR4.pm,v 1.0 2003/07/ 11 # # BioPerl module for Bio::Tools::Analysis::Protein::GOR4 # # Copyright Richard Adams # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Analysis::Protein::GOR4 - a wrapper around GOR4 protein secondary structure prediction server =head1 SYNOPSIS use Bio::Tools::Analysis::Protein::GOR4; #get a Bio::Seq or Bio::PrimarySeq use Bio::PrimarySeq; $seq = Bio::PrimarySeq->new (-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL', -primary_id=>'test'); # a Bio::PrimarySeqI object my $gor4 = Bio::Tools::Analysis::Protein::GOR4->new (-seq=>$seq); $gor4->run; print $gor4->result;# #raw text to standard error =head1 DESCRIPTION A module to remotely retrieve predictions of protein secondary structure. Each residue in the protein receives a score representing the likelihood of existing in each of three different states (helix, coil or sheet), e.g., my $analysis_object = Bio::Tools::SimpleAnalysis::Protein::GOR4-> new(-seq => $seq); creates a new object $analysis_object->run; submits the query to the server and obtains raw text output Given an amino acid sequence the results can be obtained in 4 formats, determined by the argument to the result method =over 4 =item 1 The raw text of the program output my $rawdata = $analysis_object->result; =item 2 An reference to an array of hashes of scores for each state and the assigned state. my $data_ref = $analysis_object->result('parsed'); print "score for helix at residue 2 is $data_ref->[1]{'helix'}\n"; print "predicted struc at residue 2 is $data_ref->[1]{'struc}\n"; =item 3 An array of Bio::SeqFeature::Generic objects where each feature is a predicted unit of secondary structure. Only stretches of helix/sheet predictions for longer than 4 residues are defined as helices. See Bio::Tools::Analysis::Domcut.pm for examples of how to add sequence features. my @fts = $analysis_object->result(Bio::SeqFeatureI); for my $ft (@fts) { print " From ", $ft->start, " to ",$ft->end, " struc: " , ($ft->each_tag_value('type'))[0] ,"\n"; } =item 4 A Bio::Seq::Meta::Array implementing sequence. This is a Bio::Seq object that can also hold data about each residue in the sequence In this case, the sequence can be associated with a single array of GOR4 prediction scores. e.g., my $meta_sequence = $analysis_object->result('all'); print "helix scores from residues 10-20 are ", $meta_sequence->named_submeta_text("GOR4_helix",10,20), "\n"; Meta sequence names are : GOR4_helix, GOR4_sheet, GOR4_coil, GOR4_struc, representing the scores for each residue. Many methods common to all analyses are inherited from Bio::Tools::Analysis::SimpleAnalysisBase. =back =head1 SEE ALSO L<Bio::SimpleAnalysisI>, L<Bio::Tools::Analysis::SimpleAnalysisBase>, L<Bio::Seq::Meta::Array>, L<Bio::WebAgent> =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Richard Adams, Richard.Adams@ed.ac.uk, =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut use strict; package Bio::Tools::Analysis::Protein::GOR4; use IO::String; use Bio::SeqIO; use HTTP::Request::Common qw(POST); use Bio::SeqFeature::Generic; use Bio::Seq::Meta::Array; $ENV{PERL_LWP_SSL_VERIFY_HOSTNAME} = 0; use base qw(Bio::Tools::Analysis::SimpleAnalysisBase); use constant MIN_STRUC_LEN => 3; my $URL = 'https://npsa-prabi.ibcp.fr/cgi-bin/secpred_sopma.pl'; my $ANALYSIS_NAME = 'GOR4'; my $ANALYSIS_SPEC = {name => 'Gor4', type => 'Protein'}; my $INPUT_SPEC = [ {mandatory =>'true', type => 'Bio::PrimarySeqI', 'name' => 'seq', }, ]; my $RESULT_SPEC = { '' => 'bulk', # same as undef 'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeature::Generic', raw => '[ {struc =>, helix=> ,sheet=>, coil=>}]', meta => 'Bio::Seq::Meta::Array object', }; =head2 result Name : result Usage : $job->result (...) Returns : a result created by running an analysis Args : see keys of $RESULT_SPEC The method returns a result of an executed job. If the job was terminated by an error the result may contain an error message instead of the real data. This implementation returns differently processed data depending on argument: =over 3 =item undef Returns the raw ASCII data stream but without HTML tags =item 'Bio::SeqFeatureI' The argument string defines the type of bioperl objects returned in an array. The objects are L<Bio::SeqFeature::Generic>. Feature primary tag is "2ary". Feature tags are "type" (which can be helix, sheet or coil) "method" (GOR4). =item 'parsed' Array of hash references of { helix =E<gt>, sheet =E<gt> , coil =E<gt> , struc=E<gt>}. =item 'meta' A Bio::Seq::Meta::Array object. Scores can be accessed using methods from this class. Meta sequence names are GOR4_helix, GOR4_sheet, GOR4_coil, GOR4_struc. =back =cut sub result { my ($self,$value) = @_; my @scores; my @fts; if ($value ) { #parse into basic raw form, store this as well as '_result' if (!exists($self->{'_parsed'}) ) { my $result = IO::String->new($self->{'_result'}); while (my $line = <$result>) { next unless $line =~ /^\w\s/; # or for sopma/hnn /^[A-Z]\s/ $line =~/(\w)\s+(\d+)\s+(\d+)\s+(\d+)/; # or for so push @scores, { struc => $1, helix => $2, sheet => $3, coil => $4, }; } $self->{'_parsed'} = \@scores; } if ($value eq 'Bio::SeqFeatureI') { $self->_get_2ary_coords(); for my $type (keys %{$self->{'_parsed_coords'}} ) { next if $type =~ /\w{2,}/; #if not H,C,E or T for my $loc (@{$self->{'_parsed_coords'}{$type}} ) { push @fts, Bio::SeqFeature::Generic->new (-start => $loc->{'start'}, -end => $loc->{'end'}, -source => 'GOR4', -primary => 'Region', -tag => { type => $type, method => $self->analysis_name, }); } #end of array of strucs of type } # end of all 2nd struc elements delete $self->{'_parsed_coords'}; #remove temp data return @fts; } #endif BioSeqFeature elsif ($value eq 'meta') { #1st of all make 3 or 4 arrays of scores for each type from column data my %type_scores; for my $aa (@{$self->{'_parsed'}}) { push @{$type_scores{'struc'}}, $aa->{'struc'}; push @{$type_scores{'helix'}}, $aa->{'helix'}; push @{$type_scores{'sheet'}}, $aa->{'sheet'}; push @{$type_scores{'coil'}}, $aa->{'coil'}; } ## bless if necessary ## if (!$self->seq->isa("Bio::Seq::Meta::Array")){ bless ($self->seq, "Bio::Seq::Meta::Array"); } $self->seq->isa("Bio::Seq::MetaI") || $self->throw("$self is not a Bio::Seq::MetaI"); $Bio::Seq::Meta::Array::DEFAULT_NAME = 'GOR4_struc'; ## now make meta_Sequence for my $struc_type (keys %type_scores) { my $meta_name = "GOR4". "_" . "$struc_type"; my @meta = map{$_->{$struc_type}} @{$self->{'_parsed'}}; if (grep{$_ eq $meta_name}$self->seq->meta_names ) { $self->warn ("$meta_name already exists , not overwriting!"); next; } $self->seq->named_meta($meta_name,\@meta ); } # return seq array object implementing meta sequence # return $self->seq; } else { return $self->{'_parsed'}; } } #endif ($value) #return raw result if no return fomrt stated return $self->{'_result'}; } sub _get_2ary_coords { #helper sub for result; ##extracts runs of structure > MIN_STRUC_LENresidues or less if Turn: #i.e., helical prediction for 1 residue isn't very meaningful... ## and poulates array of hashes with start/end values. ##keys of $Result are 'H' 'T' 'C' 'E'. #could be put into a secondary base class if need be my ($self) = @_; my @prot = @{$self->{'_parsed'}}; my %Result; for (my $index = 0; $index <= $#prot; $index++) { my $type = $prot[$index]{'struc'}; next unless $type =~ /[HTCE]/; my $length = 1; for (my $j = $index + 1; $j <= $#prot; $j++) { my $test = $prot[$j]; if ($test->{'struc'} eq $type) { $length++; } elsif ( $length > MIN_STRUC_LEN || ($length <= MIN_STRUC_LEN && $type eq 'T') ) { push @{$Result{$type}}, {start => $index + 1 , end => $j}; $index += $length -1; last; } else { $index += $length - 1; last; } } } $self->{'_parsed_coords'} = \%Result; #temp assignment } sub _init { my $self = shift; $self->url($URL); $self->{'_ANALYSIS_SPEC'} =$ANALYSIS_SPEC; $self->{'_INPUT_SPEC'} =$INPUT_SPEC; $self->{'_RESULT_SPEC'} =$RESULT_SPEC; $self->{'_ANALYSIS_NAME'} =$ANALYSIS_NAME; return $self; } sub _run { my $self = shift; $self->delay(1); # delay repeated calls by default by 3 sec, set delay() to change $self->sleep; $self->status('TERMINATED_BY_ERROR'); my $request = POST $self->url, Content_Type => 'form-data', Content => [title => "", notice => $self->seq->seq, ali_width => 70, ]; my $content = $self->request($request); my $text = $content->content; return unless $text; my ($next) = $text =~ /Prediction.*?=(.*?)>/; return unless $next; my $out = 'http://npsa-pbil.ibcp.fr/'.$next; my $req2 = HTTP::Request->new(GET=>$out); my $resp2 = $self->request($req2); $self->status('COMPLETED') if $resp2 ne ''; $self->{'_result'} = $resp2->content; } 1; ������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Analysis/Protein/HNN.pm��������������������������������������������������000444��000766��000024�� 26653�13155576320� 21544� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# $Id: HNN.pm,v 1.0 2003/07/ 11 # # BioPerl module for Bio::Tools::Analysis::Protein::HNN # # Copyright Richard Adams # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Analysis::Protein::HNN - a wrapper around the HNN protein secondary structure prediction server =head1 SYNOPSIS use Bio::Tools::Analysis::Protein::HNN; #get a Bio::Seq or Bio::PrimarySeq use Bio::PrimarySeq; my $seq = Bio::PrimarySeq->new (-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL', -primary_id=>'test'); # a Bio::PrimarySeqI object my $hnn = Bio::Tools::Analysis::Protein::HNN->new (-seq=>$seq); $hnn->run; print $hnn->result;# #raw text to standard error =head1 DESCRIPTION A module to remotely retrieve predictions of protein secondary structure. Each residue in the protein receives a score representing the likelihood of existing in each of three different states (helix, coil or sheet), e.g.: my $analysis_object = Bio::Tools::SimpleAnalysis::Protein::HNN->new (-seq => $seq); creates a new object $analysis_object->run; submits the query to the server and obtains raw text output. Given an amino acid sequence the results can be obtained in 4 formats, determined by the argument to the result method: =over 4 =item 1 The raw text of the program output. my $rawdata = $analysis_object->result; =item 2 A reference to an array of hashes of scores for each state and the assigned state. my $data_ref = $analysis_object->result('parsed'); print "score for helix at residue 2 is $data_ref->[1]{'helix'}\n"; print "predicted struc at residue 2 is $data_ref->[1]{'struc}\n"; =item 3 An array of Bio::SeqFeature::Generic objects where each feature is a predicted unit of secondary structure. Only stretches of helix/sheet predictions for longer than 4 residues are defined as helices. my @fts = $analysis_object->result(Bio::SeqFeatureI); for my $ft (@fts) { print " From ", $ft->start, " to ",$ft->end, " struc: " , ($ft->each_tag_value('type'))[0] ,"\n"; } =item 4 A Bio::Seq::Meta::Array implementing sequence. This is a Bio::Seq object that can also hold data about each residue in the sequence In this case, the sequence can be associated with a single array of HNN prediction scores. e.g., my $meta_sequence = $analysis_object->result('meta'); print "helix scores from residues 10-20 are ", $meta_sequence->named_submeta_text("HNN_helix",10,20), "\n"; Meta sequence default names are : HNN_helix, HNN_sheet, HNN_coil, HNN_struc, representing the scores for each residue. Many methods common to all analyses are inherited from L<Bio::Tools::Analysis::SimpleAnalysisBase>. =back =head1 SEE ALSO L<Bio::SimpleAnalysisI>, L<Bio::Tools::Analysis::SimpleAnalysisBase>, L<Bio::Seq::Meta::Array>, L<Bio::WebAgent> =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Richard Adams, Richard.Adams@ed.ac.uk, =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut use strict; package Bio::Tools::Analysis::Protein::HNN; use IO::String; use Bio::SeqIO; use HTTP::Request::Common qw (POST); use Bio::SeqFeature::Generic; use Bio::Seq::Meta::Array; $ENV{PERL_LWP_SSL_VERIFY_HOSTNAME} = 0; use base qw(Bio::Tools::Analysis::SimpleAnalysisBase); #extends array for 2struc. my $URL = 'http://npsa-pbil.ibcp.fr/cgi-bin/secpred_hnn.pl'; my $ANALYSIS_NAME= 'HNN'; my $ANALYSIS_SPEC= {name => 'HNN', type => 'Protein'}; my $INPUT_SPEC = [ { mandatory => 'true', type => 'Bio::PrimarySeqI', 'name' => 'seq', }, ]; my $RESULT_SPEC = { '' => 'bulk', # same as undef 'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeature::Generic', raw => '[ {helix=>, sheet=>, struc=>, coil=>}]', meta => 'Bio::Seq::Meta::Array object', }; use constant MIN_STRUC_LEN => 3; sub _init { my $self = shift; $self->url($URL); $self->{'_ANALYSIS_SPEC'} = $ANALYSIS_SPEC; $self->{'_INPUT_SPEC'} = $INPUT_SPEC; $self->{'_RESULT_SPEC'} = $RESULT_SPEC; $self->{'_ANALYSIS_NAME'} = $ANALYSIS_NAME; return $self; } sub _run { my $self = shift; $self->delay(1); # delay repeated calls by default by 3 sec, set delay() to change $self->sleep; $self->status('TERMINATED_BY_ERROR'); my $request = POST 'https://npsa-prabi.ibcp.fr/cgi-bin/secpred_hnn.pl', Content_Type => 'form-data', Content => [ title => "", notice => $self->seq->seq, ali_width => 70, ]; my $text = $self->request($request)->content; return unless $text; my ($next) = $text =~ /Prediction.*?=(.*?)>/; return unless $next; my $out = "http://npsa-pbil.ibcp.fr/".$next; my $req2 = HTTP::Request->new(GET=>$out); my $resp2 = $self->request ($req2); $self->status('COMPLETED') if $resp2 ne ''; $self->{'_result'} = $resp2->content; return $self; } =head2 result NAme : result Usage : $job->result (...) Returns : a result created by running an analysis Args : see keys of $INPUT_SPEC The method returns a result of an executed job. If the job was terminated by an error the result may contain an error message instead of the real data. This implementation returns differently processed data depending on argument: =over 3 =item undef Returns the raw ASCII data stream but without HTML tags. =item 'Bio::SeqFeatureI' The argument string defines the type of bioperl objects returned in an array. The objects are L<Bio::SeqFeature::Generic>. Feature primary tag is "2ary". Feature tags are "type" (which can be helix, sheet or coil) "method" (HNN). =item 'parsed' Array of hash references of scores/structure assignations { helix =E<gt>, sheet =E<gt> , coil =E<gt> , struc=E<gt>}. =item 'all' A Bio::Seq::Meta::Array object. Scores can be accessed using methods from this class. Meta sequence names are HNN_helix, HNN_sheet, HNN_coil, HNN_struc. =back =cut sub result { my ($self,$value) = @_; my @scores; my @fts; if ($value ) { #parse into basic raw form, store this as well as '_result' if (!exists($self->{'_parsed'}) ) { my $result = IO::String->new($self->{'_result'}); while (my $line = <$result>) { next unless $line =~ /^[HEC]\s/; # or for sopma/hnn /^[A-Z]\s/ $line =~/^([A-Z])\s+(\d+)\s+(\d+)\s+(\d+)/; # or for so push @scores, { struc => $1, helix => $2, sheet => $3, coil => $4, }; } $self->{'_parsed'} = \@scores; } if ($value eq 'Bio::SeqFeatureI') { $self->_get_2ary_coords(); for my $type (keys %{$self->{'_parsed_coords'}} ) { next if $type =~ /\w{2,}/; #if not H,C,E or T for my $loc (@{$self->{'_parsed_coords'}{$type}} ) { push @fts, Bio::SeqFeature::Generic->new (-start => $loc->{'start'}, -end => $loc->{'end'}, -source => 'HNN', -primary => 'Domain', -tag => { type => $type, method => $self->analysis_name, }); } #end of array of strucs of type } # end of all 2nd struc elements delete $self->{'_parsed_coords'}; #remove temp data return @fts; } #endif BioSeqFeature elsif ($value eq 'meta') { #1st of all make 3 or 4 arrays of scores for each type from column data my %type_scores; for my $aa (@{$self->{'_parsed'}}) { push @{$type_scores{'struc'}}, $aa->{'struc'}; push @{$type_scores{'helix'}}, $aa->{'helix'}; push @{$type_scores{'sheet'}}, $aa->{'sheet'}; push @{$type_scores{'coil'}}, $aa->{'coil'}; } ## bless as metasequence if necessary if (!$self->seq->isa("Bio::Seq::MetaI")) { bless ($self->seq, "Bio::Seq::Meta::Array"); } $self->seq->isa("Bio::Seq::MetaI") || $self->throw("$self is not a Bio::Seq::MetaI"); ## now make meta sequence $Bio::Seq::Meta::Array::DEFAULT_NAME = 'HNN_struc'; for my $struc_type (keys %type_scores) { my $meta_name = "HNN". "_" . "$struc_type"; my @meta = map{$_->{$struc_type}} @{$self->{'_parsed'}}; if (grep{$_ eq $meta_name}$self->seq->meta_names ) { $self->warn ("$meta_name already exists , not overwriting!"); next; } $self->seq->named_meta($meta_name,\@meta ); } # return seq array object implementing meta sequence # return $self->seq; } ## else for aa true value get data structure back ## else { return $self->{'_parsed'}; } } #endif ($value) #return raw result if no return fomrt stated return $self->{'_result'}; } sub _get_2ary_coords { #helper sub for result; ##extracts runs of structure > MIN_STRUC_LENresidues or less if Turn: #i.e., helical prediction for 1 residue isn't very meaningful... ## and poulates array of hashes with start/end values. #could be put into a secondary base class if need be my ($self) = @_; my @prot = @{$self->{'_parsed'}}; my %Result; for (my $index = 0; $index <= $#prot; $index++) { my $type = $prot[$index]{'struc'}; next unless $type =~ /[HTCE]/; my $length = 1; for (my $j = $index + 1; $j <= $#prot; $j++) { my $test = $prot[$j]; if ($test->{'struc'} eq $type) { $length++; } elsif ( $length > MIN_STRUC_LEN || ($length <= MIN_STRUC_LEN && $type eq 'T') ) { push @{$Result{$type}}, {start => $index + 1 , end => $j}; $index += $length -1; last; } else { $index += $length - 1; last; } } } $self->{'_parsed_coords'} = \%Result; #temp assignment } 1; �������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Analysis/Protein/NetPhos.pm����������������������������������������������000444��000766��000024�� 20240�13155576320� 22463� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Analysis::Protein::NetPhos # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> # # Copyright Richard Adams # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Analysis::Protein::NetPhos - a wrapper around NetPhos server =head1 SYNOPSIS use Bio::Tools::Analysis::Protein::NetPhos; my $seq; # a Bio::PrimarySeqI object my $threshold = "0.90"; my $netphos = Bio::Tools::Analysis::Protein::NetPhos->new ( -seq => $seq, -threshold => $threshold ); # run NetPhos prediction on a sequence my $netphos->run(); # alternatively you can say $netphos->seq($seq)->threshold($threshold)->run; die "Could not get a result" unless $netphos->status =~ /^COMPLETED/; print $netphos->result; # print raw prediction to STDOUT foreach my $feat ( $netphos->result('Bio::SeqFeatureI') ) { # do something to SeqFeature # e.g. print as GFF print $feat->gff_string, "\n"; # or store within the sequence - if it is a Bio::RichSeqI $seq->add_SeqFeature($feat) } =head1 DESCRIPTION This class is wrapper around the NetPhos 2.0 server which produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins. See L<http://www.cbs.dtu.dk/services/NetPhos/>. This the first implementation of Bio::SimpleAnalysisI which hopefully will make it easier to write wrappers on various services. This class uses a web resource and therefore inherits from Bio::WebAgent. =head1 SEE ALSO L<Bio::SimpleAnalysisI>, L<Bio::WebAgent> =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Analysis::Protein::NetPhos; use vars qw($FLOAT); use strict; use IO::String; use Bio::SeqIO; use HTTP::Request::Common qw (POST); use Bio::SeqFeature::Generic; use base qw(Bio::Tools::Analysis::SimpleAnalysisBase); $FLOAT = '[+-]?\d*\.\d*'; my $URL = 'http://www.cbs.dtu.dk/cgi-bin/nph-webface'; my $ANALYSIS_SPEC = { 'name' => 'NetPhos', 'type' => 'Protein', 'version' => '2.0', 'supplier' => 'Center for Biological Sequence Analysis, Technical University of Denmark', 'description' => 'Prediction of serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins', }; my $INPUT_SPEC = [ { 'mandatory' => 'true', 'type' => 'Bio::PrimarySeqI', 'name' => 'seq', }, { 'mandatory' => 'false', 'type' => 'float', 'name' => 'threshold', 'default' => 0.8, } ]; my $RESULT_SPEC = { '' => 'bulk', # same as undef 'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeeature::Generic', 'raw' => 'Array of [ position, score, residue ]' }; =head2 result Name : result Usage : $job->result (...) Returns : a result created by running an analysis Args : none (but an implementation may choose to add arguments for instructions how to process the raw result) The method returns a scalar representing a result of an executed job. If the job was terminated by an error the result may contain an error message instead of the real data (or both, depending on the implementation). This implementation returns differently processed data depending on argument: =over 3 =item undef Returns the raw ASCII data stream but without HTML tags =item 'Bio::SeqFeatureI' The argument string defined the type of bioperl objects returned in an array. The objects are L<Bio::SeqFeature::Generic>. =item anything else Array of array references of [ position, score, residue]. =back =cut sub result { my ($self,$value) = @_; my @predictions; my @fts; if ($value ) { my $result = IO::String->new($self->{'_result'}); while (<$result>) { next if /^____/; /^\S+ +(\d+) +\w+ +(0\.\d+) +.([STY])/; next unless $3 and $2 > $self->threshold; push @predictions, [$1, $2, $3]; } if ($value eq 'Bio::SeqFeatureI') { foreach (@predictions) { push @fts, Bio::SeqFeature::Generic->new (-start => $_->[0], -end => $_->[0] , -source => 'NetPhos', -primary => 'Site', -tag => { score => $_->[1], residue => $_->[2] }); } return @fts; } return \@predictions; } return $self->{'_result'}; } =head2 threshold Usage : $job->threshold(...) Returns : The significance threshold of a prediction Args : None (retrieves value) or a value between 0 and 1. Purpose : Get/setter of the threshold to be sumitted for analysis. =cut sub threshold { my ($self,$value) = @_; if( defined $value) { if ( $value !~ /$FLOAT/ or $value < 0 or $value > 1 ) { $self->throw("I need a value between 0 and 1 , not [". $value. "]") } $self->{'_threshold'} = $value; return $self; } return $self->{'_threshold'} || $self->input_spec->[1]{'default'} ; } sub _init { my $self = shift; $self->url($URL); $self->{'_ANALYSIS_SPEC'} =$ANALYSIS_SPEC; $self->{'_INPUT_SPEC'} =$INPUT_SPEC; $self->{'_RESULT_SPEC'} =$RESULT_SPEC; $self->{'_ANALYSIS_NAME'} =$ANALYSIS_SPEC->{name}; return $self; } sub _run { my $self = shift; # format the sequence into fasta my $seq_fasta; my $stringfh = IO::String->new($seq_fasta); my $seqout = Bio::SeqIO->new(-fh => $stringfh, -format => 'fasta'); $seqout->write_seq($self->seq); $self->debug($seq_fasta); # delay repeated calls by default by 3 sec, set delay() to change $self->sleep; $self->status('TERMINATED_BY_ERROR'); my $request = POST $self->url, Content_Type => 'form-data', Content => [configfile => '/usr/opt/www/pub/CBS/services/NetPhos-2.0/NetPhos.cf', SEQPASTE => $seq_fasta]; my $content = $self->request($request); my $text = $content->content; my ($result_url) = $text =~ /follow <a href="(.*?)"/; return 0 unless $result_url; $self->debug("url is $result_url\n\n"); my $ua2 = $self->clone; my $content2 = $ua2->request(POST $result_url); my $ua3 = $self->clone; $result_url =~ s/&.*//; $self->debug("final result url is $result_url\n"); my $content3 = $ua3->request(POST $result_url); #print Dumper $content3; my $response = $content3->content; $response =~ s/.*<pre>(.*)<\/pre>.*/$1/s; $response =~ s/<.*?>//gs; $self->{'_result'} = $response; $self->status('COMPLETED') if $response ne ''; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Analysis/Protein/Scansite.pm���������������������������������������������000444��000766��000024�� 27134�13155576320� 22665� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Analysis::Protein::Scansite # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Richard Adams <richard.adams@ed.ac.uk> # # Copyright Richard Adams # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Analysis::Protein::Scansite - a wrapper around the Scansite server =head1 SYNOPSIS use Bio::Tools::Analysis::Protein::Scansite; my $seq; # a Bio::PrimarySeqI object my $tool = Bio::Tools::Analysis::Protein::Scansite->new ( -seq => $seq->primary_seq ); # run Scansite prediction on a sequence $tool->run(); # alternatively you can say $tool->seq($seq->primary_seq)->run; die "Could not get a result" unless $tool->status =~ /^COMPLETED/; print $tool->result; # print raw prediction to STDOUT foreach my $feat ( $tool->result('Bio::SeqFeatureI') ) { # do something to SeqFeature # e.g. print as GFF print $feat->gff_string, "\n"; # or store within the sequence - if it is a Bio::RichSeqI $seq->add_SeqFeature($feat); } =head1 DESCRIPTION This class is a wrapper around the Scansite 2.0 server which produces predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins. At present this is a basic wrapper for the "Scan protein by input sequence" functionality, which takes a sequence and searches for motifs, with the option to select the search stringency. At present, searches for specific phosphorylation sites are not supported; all predicted sites are returned. =head2 Return formats The Scansite results can be obtained in several formats: =over 3 =item 1. By calling my $res = $tool->result(''); $res holds a string of the predicted sites in tabular format. =item 2. By calling my $data_ref = $tool->result('value') $data_ref is a reference to an array of hashes. Each element in the array represents a predicted phosphorylation site. The hash keys are the names of the data fields,i.e., 'motif' => 'Casn_Kin1' # name of kinase 'percentile' => 0.155 # see Scansite docs 'position' => 9 # position in protein 'protein' => 'A1' # protein id 'score' => 0.3696 # see Scansite docs 'sequence' => 'ASYFDTASYFSADAT' # sequence surrounding site 'site' => 'S9' # phosphorylated residue 'zscore' => '-3.110' # see Scansite docs =item 3. By calling my @fts = $tool->Result('Bio::SeqFeatureI'); which returns an array of L<Bio::SeqFeatureI> compliant objects with primary tag value 'Site' and tag names of 'motif', 'score', 'sequence', 'zscore' as above. =back See L<http://scansite.mit.edu/>. This inherits Bio::SimpleAnalysisI which hopefully makes it easier to write wrappers on various services. This class uses a web resource and therefore inherits from L<Bio::WebAgent>. =head1 SEE ALSO L<Bio::SimpleAnalysisI>, L<Bio::WebAgent> =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Richard Adams, Richard.Adams@ed.ac.uk, =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Analysis::Protein::Scansite; use vars qw($FLOAT @STRINGENCY); use strict; use IO::String; use Bio::SeqIO; use HTTP::Request::Common qw(POST); use Bio::SeqFeature::Generic; use base qw(Bio::Tools::Analysis::SimpleAnalysisBase); $FLOAT = '[+-]?\d*\.\d*'; @STRINGENCY = qw(High Medium Low); my $URL = 'http://scansite.mit.edu/cgi-bin/motifscan_seq'; my $ANALYSIS_SPEC = { 'name' => 'Scansite', 'type' => 'Protein', 'version' => '2.0', 'supplier' => 'Massachusetts Institute of Technology', 'description' => 'Prediction of serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins', }; my $INPUT_SPEC = [ { 'mandatory' => 'true', 'type' => 'Bio::PrimarySeqI', 'name' => 'seq', }, { 'mandatory' => 'false', 'type' => 'text', 'name' => 'protein_id', 'default' => 'unnamed', }, { 'mandatory' => 'false', 'type' => 'text', 'name' => 'stringency', 'default' => 'High', }, ]; my $RESULT_SPEC = { '' => 'bulk', # same as undef 'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeature::Generic', 'raw' => 'Array of {motif=>, percentile=>, position=>, protein=>, score=>, site=>, zscore=> sequence=> }', }; =head2 result Name : result Usage : $job->result (...) Returns : a result created by running an analysis Args : none (but an implementation may choose to add arguments for instructions how to process the raw result) The method returns a scalar representing a result of an executed job. If the job was terminated by an error, the result may contain an error message instead of the real data. This implementation returns differently processed data depending on argument: =over 3 =item undef Returns the raw ASCII data stream but without HTML tags =item 'Bio::SeqFeatureI' The argument string defined the type of bioperl objects returned in an array. The objects are L<Bio::SeqFeature::Generic>. =item 'parsed' Returns a reference to an array of hashes containing the data of one phosphorylation site prediction. Key values are: motif, percentile, position, protein, score, site, zscore, sequence. =back =cut sub result { my ($self,$value) = @_; if( !exists($self->{'_result'}) || $self->status ne 'COMPLETED'){ $self->throw("Cannot get results, analysis not run!"); } my @fts; if ($value ) { if ($value eq 'Bio::SeqFeatureI') { for my $hit (@{$self->{'_parsed'}}) { push @fts, Bio::SeqFeature::Generic->new( -start => $hit->{'position'}, -end => $hit->{'position'}, -primary_tag => 'Site', -source => 'Scansite', -tag => { score => $hit->{'score'}, zscore => $hit->{'zscore'}, motif => $hit->{'motif'}, site => $hit->{'site'}, sequence => $hit->{'sequence'}, }, ); } return @fts; } elsif ($value eq 'meta') { $self->throw("No meta sequences available in this analysis!"); } ## else get here return $self->{'_parsed'}; } return $self->{'_result'}; } =head2 stringency Usage : $job->stringency(...) Returns : The significance stringency of a prediction Args : None (retrieves value) or 'High', 'Medium' or 'Low'. Purpose : Get/setter of the stringency to be sumitted for analysis. =cut sub stringency { my ($self,$value) = @_; if( $value) { if (! grep{$_=~ /$value/i}@STRINGENCY ) { $self->throw("I need a stringency of [". join " ", @STRINGENCY . "], not [$value]"); } $self->{'_stringency'} = $value; return $self; } return $self->{'_stringency'} || $self->input_spec->[2]{'default'} ; } =head2 protein_id Usage : $job->protein_id(...) Returns : The sequence id of the protein or 'unnamed' if not set. Args : None Purpose : Getter of the seq_id. Returns the display_id of the sequence object. =cut sub protein_id { my $self = shift; return defined ($self->seq())? $self->seq->display_id() : $self->input_spec->[1]{'default'}; } sub _init { my $self = shift; $self->url($URL); $self->{'_ANALYSIS_SPEC'} = $ANALYSIS_SPEC; $self->{'_INPUT_SPEC'} = $INPUT_SPEC; $self->{'_RESULT_SPEC'} = $RESULT_SPEC; $self->{'_ANALYSIS_NAME'} = $ANALYSIS_SPEC->{'name'}; return $self; } sub _run { my $self = shift; # format the sequence into fasta $self->delay(1); # delay repeated calls by default by 3 sec, set delay() to change $self->sleep; $self->status('TERMINATED_BY_ERROR'); my $request = POST $self->url, Content => [sequence => $self->seq->seq(), protein_id => $self->protein_id(), motif_option => 'all', motifs => '', motif_groups => '', stringency => $self->stringency(), #domain_flag => '', submit => "Submit Request", ]; ## raw html report, my $content = $self->request($request); my $text = $content->content; ##access result data from tag in html my @parsed_Results = (); my @unwantedParams = qw(db source class); my @results = split /sitestats\.phtml\?/, $text; shift @results; ##this module generates 'parsed' output directly from html, ## avoids having toparse twice. for my $hit (@results) { ## get results string my ($res) = $hit =~ /^(.+?)"/; #get key value pairs my %params = $res =~/(\w+)=([^&]+)/g; ##remove unwanted data from hash map{delete $params{$_}} @unwantedParams; push @parsed_Results, \%params; } ## now generate text output in table format my $out_Str = ''; $out_Str .= $self->_make_header(\@parsed_Results); $out_Str .= $self->_add_data(\@parsed_Results); $self->{'_result'} = $out_Str; $self->{'_parsed'} = \@parsed_Results; ## is successsful if there are results or if there are no results and ## this beacuse there are no matches, not because of parsing errors etc. $self->status('COMPLETED') if $text ne '' && (scalar @results > 0 || (scalar @results == 0 && $text =~/No sites found/)); if ($text =~ /server\s+error/i) { $self->throw("Internal server error:\n\n $text"); return; } } sub _process_arguments { # extra checking for sequence length # mitoprot specific argument testing my ($self, $args) = @_; #use base checking for existence of mandatory fields $self->SUPER::_process_arguments($args); # specific requirements $self->throw("Sequence must be > 15 amino acids long!") if $self->seq->length < 15; $self->throw("Sequence must be protein") unless $self->seq->alphabet() eq 'protein'; } sub _make_header { my ($self, $res) = @_; my $header = ''; for my $k (sort keys %{$res->[0]} ){ next if $k eq 'sequence'; $header .= $k; $header .= ' 'x(12 -length($k)); } $header .= "sequence\n\n"; return $header; } sub _add_data { my ($self, $res) = @_; my $outstr = ''; for my $hit (@$res) { for my $k (sort keys %$hit ){ next if $k eq 'sequence'; $outstr .= $hit->{$k}; $outstr .= ' 'x(12 - length($hit->{$k})); } $outstr .= $hit->{'sequence'}. "\n" if $hit->{'sequence'}; } return $outstr; } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Analysis/Protein/Sopma.pm������������������������������������������������000444��000766��000024�� 36214�13155576320� 22172� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# $Id: Sopma.pm,v 1.0 2003/07/ 11 # # BioPerl module for Bio::Tools::Analysis::Protein::Sopma # # Copyright Richard Adams # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Analysis::Protein::Sopma - a wrapper around the Sopma protein secondary structure prediction server =head1 SYNOPSIS use Bio::Tools::Analysis::Protein::Sopma; #get a Bio::Seq or Bio::PrimarySeq my $seq; my $sopma = Bio::Tools::Analysis::Protein::Sopma->new (-seq=>$seq, states=>4); $sopma->run; print $sopma->result;# #raw text to standard error =head1 DESCRIPTION A module to remotely retrieve predictions of protein secondary structure. Each residue in the protein receives a score representing the likelihood of existing in each of four different states (helix, coil, turn or sheet), e.g., my $analysis_object = Bio::Tools::SimpleAnalysis::Protein::Sopma->new ( -seq => $seq, -states => 4, -window_width => 15, ); creates a new object. Compulsory argument -seq. Optional arguments -states, -window_width,-similarity_threshold. These arguments can also be set by direct methods , e.g., $analysis_object->states(4); $analysis_object->run; submits the query to the server and obtains raw text output. Given an amino acid sequence the results can be obtained in 4 formats, determined by the argument to the result method: =over 4 =item 1 The raw text of the program output. my $rawdata = $analysis_object->result; =item 2 A reference to an array of hashes of scores for each state and the assigned state. my $data_ref = $analysis_object->result('parsed'); print "score for helix at residue 2 is $data_ref->[1]{'helix'}\n"; print "predicted struc at residue 2 is $data_ref->[1]{'struc}\n"; Hash keys are 'helix', 'struc', 'sheet', 'coil', 'turn'. =item 3 An array of Bio::SeqFeature::Generic objects where each feature is a predicted unit of secondary structure. Only stretches of helix/sheet predictions for longer than 4 residues are defined as helices/sheets. my @fts = $analysis_object->result(Bio::SeqFeatureI); for my $ft (@fts) { print " From ", $ft->start, " to ",$ft->end, " struc: " , ($ft->each_tag_value('type'))[0] ,"\n"; } =item 4 A Bio::Seq::Meta::Array implementing sequence. This is a Bio::Seq object that can also hold data about each residue in the sequence. In this case, the sequence can be associated with a arrays of Sopma prediction scores. e.g., my $meta_sequence = $analysis_object->result('meta'); print "scores from residues 10 -20 are ", $meta_sequence->named_submeta_text("Sopma_helix",10,20), "\n"; Meta sequence names are : Sopma_helix, Sopma_sheet, Sopma_turn, Sopma_coil, Sopma_struc, representing the scores for each residue. Many methods common to all analyses are inherited from Bio::Tools::Analysis::SimpleAnalysisBase. =back =head1 SEE ALSO L<Bio::SimpleAnalysisI>, L<Bio::Tools::Analysis::SimpleAnalysisBase> L<Bio::Seq::Meta::Array>, L<Bio::WebAgent> =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS Richard Adams, Richard.Adams@ed.ac.uk, =head1 APPENDIX =cut use strict; package Bio::Tools::Analysis::Protein::Sopma; use IO::String; use Bio::SeqIO; use HTTP::Request::Common qw (POST); use Bio::SeqFeature::Generic; use Bio::Seq::Meta::Array; $ENV{PERL_LWP_SSL_VERIFY_HOSTNAME} = 0; use base qw(Bio::Tools::Analysis::SimpleAnalysisBase); #extends array for 2struc. my $URL = 'https://npsa-prabi.ibcp.fr/cgi-bin/secpred_sopma.pl'; my $ANALYSIS_NAME= 'Sopma'; my $ANALYSIS_SPEC= {name => 'Sopma', type => 'Protein'}; my $INPUT_SPEC = [ {mandatory=>'true', type => 'Bio::PrimarySeqI', 'name' => 'seq', }, {mandatory =>'false', type => 'integer', name => 'similarity_threshold', default => 8, }, {mandatory =>'false', type => 'integer', name => 'window_width', default => 17, }, {mandatory =>'false', type => 'integer', name => 'states', default => 4, }, ]; my $RESULT_SPEC = { '' => 'bulk', # same as undef raw => '[{struc=>, helix=>, turn=>, coil=>, sheet=>}]', meta => 'Bio::Seq::Meta::Array object', 'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeature::Generic', }; use constant MIN_STRUC_LEN => 3; =head2 similarity_threshold Useage : $job->similarity_threshold(...) Returns : The similarity threshold used in the analysis Args : None (retrieves value) or an integer (default = 8) that sets the similarity threshold . This method gets/sets the similarity threshold for the prediction. =cut sub similarity_threshold { my ($self, $value) = @_; if ($value) { $self->throw ("similarity_threshold must be integer") unless $value =~ /^\d+$/; $self->{'_similarity_threshold'} = $value; } $self->{'_similarity_threshold'} ||= $self->input_spec->[1]{'default'}; return $self->{'_similarity_threshold'}; } =head2 window_width Usage : $job->window_width(...) Returns : The window width used in the analysis Args : None (retrieves value) or an integer (default = 17) that sets the window width. This method gets/sets the window width for the prediction, . If attempted to set longer than the sequence, warns of error. =cut sub window_width { my ($self, $value) = @_; if ($value) { $self->throw ("window_width must be integer") unless $value =~ /^\d+$/; $self->{'_window_width'} = $value; } $self->{'_window_width'} ||= $self->input_spec->[2]{'default'}; $self->warn ("window width longer than sequence!") unless $self->{'_window_width'} < $self->seq->length; return $self->{'_window_width'}; } =head2 states Usage : $job->states(...) Returns : The number of secondary structure prediction states Args : None (retrieves value) or either '3' or '4' to set prior to running analysis. This method gets/sets the number of states for the prediction, either 3 or 4 (includes turns). =cut sub states { my ($self, $value) = @_; if ($value) { $self->throw ("number of states must be 3 or 4") unless $value == 3 or $value ==4; $self->{'_states'} = $value; } $self->{'_states'} ||= $self->input_spec->[3]{'default'}; return $self->{'_states'}; } =head2 result Usage : $job->result (...) Returns : a result created by running an analysis Args : various The method returns a result of an executed job. If the job was terminated by an error the result may contain an error message instead of the real data. This implementation returns differently processed data depending on argument: =over 3 =item undef Returns the raw ASCII data stream but without HTML tags =item 'Bio::SeqFeatureI' The argument string defines the type of bioperl objects returned in an array. The objects are L<Bio::SeqFeature::Generic>. Feature primary tag is "2ary". Feature tags are "type" (which can be helix, sheet coil, or turn if 4 state prediction requested) "method" (Sopma) =item 'parsed' Array of hash references of scores/structure assignations { helix =E<gt> , sheet =E<gt> , coil =E<gt> , struc=E<gt>}. =item 'all' A Bio::Seq::Meta::Array object. Scores can be accessed using methods from this class. Meta sequence names are Sopma_helix, Sopma_sheet, Sopma_coil, Sopma_turn (if defined), and Sopma_struc. =back =cut sub result { my ($self,$value, $run_id) = @_; my @score; my @fts; if ($value ) { if (!exists($self->{'_parsed'} )) { my $result = IO::String->new($self->{'_result'}); while (my $line = <$result>) { next unless $line =~ /^[HCET]\s/; # or for sopma/hnn /^[A-Z]\s/ $line =~/^([A-Z])\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)/; # or for so push @score, { struc => $1, helix => $2, sheet => $3, coil => $5, }; #include turn if 4states are requested $score[$#score]{'turn'} = $4 if $self->states == 4; #can optimize by duplicating code here } $self->{'_parsed'} = \@score; } if ($value eq 'Bio::SeqFeatureI') { $self->_get_2ary_coords(); for my $type (keys %{$self->{'_parsed_coords'}} ) { next if $type =~ /\w{2,}/; #if not H,C,E or T ## these 2 are added to distinguish features on same ## sequence run with different params my $tag_hash = { type => $type, method => $self->analysis_name, }; $self->_add_params_to_result($tag_hash); ## now make feature object for my $loc (@{$self->{'_parsed_coords'}{$type}} ) { push @fts, Bio::SeqFeature::Generic->new (-start => $loc->{'start'}, -end => $loc->{'end'}, -source => 'Sopma', -primary => 'Domain', -tag => $tag_hash, ); } #end of array of strucs of type } # end of all 2nd struc elements delete $self->{'_parsed_coords'}; #remove temp data return @fts; } #endif BioSeqFeature elsif ($value eq 'meta') { #1st of all make 3 or 4 arrays of scores for each type from column data my %type_scores; for my $aa (@{$self->{'_parsed'}}) { for my $type (qw(struc helix sheet coil)) { push @{$type_scores{$type}}, $aa->{$type}; } push @{$type_scores{'turn'}}, $aa->{'turn'} if exists $aa->{'turn'}; } ## convert to meta sequence array ## if (!$self->seq->isa("Bio::Seq::Meta::Array")) { bless ($self->seq, "Bio::Seq::Meta::Array"); } $self->seq->isa("Bio::Seq::MetaI") || $self->throw("$self is not a Bio::Seq::MetaI"); $Bio::Seq::Meta::Array::DEFAULT_NAME = 'Sopma_struc'; for my $struc_type (keys %type_scores) { my $meta_name = "Sopma". "_" . "$struc_type"; if ($run_id) { $meta_name .= "|$run_id"; } my @meta = map{$_->{$struc_type}} @{$self->{'_parsed'}}; if (grep{$_ eq $meta_name}$self->seq->meta_names >0) { $self->warn ("$meta_name already exists , not overwriting!"); next; } $self->seq->named_meta($meta_name,\@meta ); } # return seq array object implementing meta sequence # return $self->seq; } ## else return parsed data if $value is defined else { return $self->{'_parsed'}; } } #endif ($value) #return raw result if no return format stated return $self->{'_result'}; } sub _init { my $self = shift; $self->url($URL); $self->{'_ANALYSIS_SPEC'} = $ANALYSIS_SPEC; $self->{'_INPUT_SPEC'} = $INPUT_SPEC; $self->{'_RESULT_SPEC'} = $RESULT_SPEC; $self->{'_ANALYSIS_NAME'} = $ANALYSIS_NAME; return $self; } sub _get_2ary_coords { #helper sub for result; ##extracts runs of structure > MIN_STRUC_LENresidues or less if Turn: #i.e., helical prediction for 1 residue isn't very meaningful... ## and poulates array of hashes with start/end values. ##keys of $Result are 'H' 'T' 'C' 'E'. my ($self) = @_; my @prot = @{$self->{'_parsed'}}; my %Result; for (my $index = 0; $index <= $#prot; $index++) { my $type = $prot[$index]{'struc'}; next unless $type && $type =~ /[HTCE]/; my $length = 1; for (my $j = $index + 1; $j <= $#prot; $j++) { my $test = $prot[$j]; if ($test->{'struc'} eq $type) { $length++; } elsif ( $length > MIN_STRUC_LEN || ($length <= MIN_STRUC_LEN && $type eq 'T') ) { push @{$Result{$type}}, {start => $index + 1 , end => $j}; $index += $length -1; last; } else { $index += $length - 1; last; } } } $self->{'_parsed_coords'} = \%Result; #temp assignment } sub _run { my $self = shift; $self->delay(1); # delay repeated calls by default by 3 sec, set delay() to change $self->sleep; $self->status('TERMINATED_BY_ERROR'); my $request = POST 'https://npsa-prabi.ibcp.fr/cgi-bin/secpred_sopma.pl', Content_Type => 'form-data', Content => [title => "", notice => $self->seq->seq, ali_width => 70, states => $self->states, threshold => $self->similarity_threshold , width => $self->window_width, ]; my $text = $self->request($request)->content; return $self unless $text; #### get text only version of results ## my ($next) = $text =~ /Prediction.*?=(.*?)>/; return $self unless $next; my $out = "http://npsa-pbil.ibcp.fr/". "$next"; my $req2 = HTTP::Request->new(GET=>$out); my $resp2 = $self->request ($req2); $self->{'_result'} = $resp2->content; $self->status('COMPLETED') if $resp2 ne ''; return $self; } sub _add_params_to_result{ ## called when making Seqfeature objects my ($self, $tag_hash) = @_; my $hash; ## adds input parameter values to SeqFeatureI results where multiple ## parameter values are possible. Only adds value if not default. map{$hash->{$_->{'name'}} = $_}@{$self->input_spec()}; for my $p (keys %$hash) { if (!ref($self->$p) && $self->$p ne $hash->{$p}{'default'}) { $tag_hash->{$p} = $self->$p; } } } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/EMBOSS�������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16157� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/EMBOSS/Palindrome.pm�����������������������������������������������������000444��000766��000024�� 12606�13155576320� 20771� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::EMBOSS::Palindrome # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl-dot-org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::EMBOSS::Palindrome - parse EMBOSS palindrome output =head1 SYNOPSIS # a simple script to turn palindrome output into GFF3 use Bio::Tools::EMBOSS::Palindrome; use Bio::Tools::GFF; my $parser = Bio::Tools::EMBOSS::Palindrome->new(-file => $filename); my $out = Bio::Tools::GFF->new(-gff_version => 3, -file => ">$filename.gff"); while( my $seq = $parser->next_seq ) { for my $feat ( $seq->get_SeqFeatures ) { $out->write_feature($feat); } } =head1 DESCRIPTION This is a parser for the EMBOSS tool 'palindrome'. It will produce a L<Bio::Seq> object for each sequence analyzed. The sequence will be empty (but will be of the correct length) and will have attached to it L<Bio::SeqFeature::FeaturePair> objects which wil =head2 FUTURE WORK It may be consolidated into another framework at a later time, but for the time being it will stay a separate modules. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::EMBOSS::Palindrome; use vars qw($DEFAULT_SOURCETAG); use strict; use Bio::SeqFeature::FeaturePair; use Bio::SeqFeature::Generic; use base qw(Bio::Root::IO); $DEFAULT_SOURCETAG = 'palindrome'; =head2 new Title : new Usage : my $obj = Bio::Tools::EMBOSS::Palindrome->new(); Function: Builds a new Bio::Tools::EMBOSS::Palindrome object Returns : an instance of Bio::Tools::EMBOSS::Palindrome Args : -file/-fh => a filename or filehandle for initializing the parser =cut =head2 next_seq Title : next_seq Usage : my $seq = $parser->next_seq; Function: Get the next feature set from the Returns : L<Bio::SeqI> object Args : none =cut sub next_seq { my ($self) = @_; my (%searching, $seq,$state); my $source = $self->source_tag; $state = 0; while(defined($_ = $self->_readline)) { if( /^\s+$/ ) { next; } elsif( /^Palindromes\s+of\s*:\s+(\S+)/o ) { $state = 0; if( $seq ) { $self->_pushback($_); return $seq; } $seq = Bio::Seq->new(-display_id => $1); # now get ready to store for the next record $searching{'-seq_id'} = $1; } elsif( /^Sequence\s+length\s+is\s*:\s+(\d+)/o ) { $seq->length($1); $searching{'-tag'}->{'seqlength'} = $1; } elsif( /^(Start|End)\s+at\s+position\s*:\s+(\d+)/ ) { $searching{'-tag'}->{lc($1)} = $2; } elsif( m/^(Maximum|Minimum)\s+length\s+of\s+Palindromes\s+ is\s*:\s+(\d+)/ox) { $searching{'-tag'}->{lc($1).'_length'} = $2; } elsif( /^(Maximum\s+gap)\s+between\s+elements\s+is\s*:\s+(\d+)/o ) { $searching{'-tag'}->{lc($1)} = $2; } elsif( m/^Number\s+of\s+mismatches\s+allowed\s+ in\s+Palindrome\s*:\s+(\d+)/ox ) { $searching{'-tag'}->{'allowed_mismatches'} = $1; } elsif( /^Palindromes:/o ) { $state = 1; } elsif( $state == 1 ) { my $feature = Bio::SeqFeature::FeaturePair->new (-primary_tag => 'similarity', -source_tag => $source); for(my $i = 0; $i < 3; $i++ ) { if ($i != 1) { if( /^(\d+)\s+(\S+)\s+(\d+)/o ) { my ($start,$match,$end) = ($1,$2,$3); my $type = $i == 0 ? 'feature1' : 'feature2'; ($start,$end) = sort { $a <=> $b } ($start,$end); $feature->$type( Bio::SeqFeature::Generic->new (%searching, -start => $start, -end => $end, -strand => $i == 0 ? 1 : -1, -primary_tag => 'similarity', -source_tag => $source) ); } else { chomp; warn("Out of sync, line did not match:'$_'\n"); } } $_ = $self->_readline; } $seq->add_SeqFeature($feature); } } return $seq; } =head2 source_tag Title : source_tag Usage : $obj->source_tag($newval) Function: Get/Set Source Tag ('palindrome') by default Returns : value of source_tag (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub source_tag{ my $self = shift; return $self->{'source_tag'} = shift if @_; return $self->{'source_tag'} || $DEFAULT_SOURCETAG; } 1; ��������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/HMMER��������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16037� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/HMMER/Domain.pm����������������������������������������������������������000444��000766��000024�� 14435�13155576320� 17770� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::HMMER::Domain # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@sanger.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::HMMER::Domain - One particular domain hit from HMMER =head1 SYNOPSIS Read the Bio::Tools::HMMER::Results docs =head1 DESCRIPTION A particular domain score. We reuse the Homol SeqFeature system here, so this inherits off Homol SeqFeature. As this code originally came from a separate project, there are some backward compatibility stuff provided to keep this working with old code. Don't forget this inherits off Bio::SeqFeature, so all your usual nice start/end/score stuff is ready for use. =head1 CONTACT Ewan Birney, birney@ebi.ac.uk =head1 CONTRIBUTORS Jason Stajich, jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' package Bio::Tools::HMMER::Domain; use Bio::SeqFeature::Generic; use strict; use base qw(Bio::SeqFeature::FeaturePair); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'alignlines'} = []; my $hmmf1 = Bio::SeqFeature::Generic->new(@args); my $hmmf2 = Bio::SeqFeature::Generic->new(@args); $self->feature1($hmmf1); $self->feature2($hmmf2); return $self; } =head2 add_alignment_line Title : add_alignment_line Usage : $domain->add_alignment_line($line_from_hmmer_output); Function: add an alignment line to this Domain object Returns : Nothing Args : scalar Adds an alignment line, mainly for storing the HMMER alignments as flat text which can be reguritated. You're right. This is *not nice* and not the right way to do it. C'est la vie. =cut sub add_alignment_line { my $self = shift; my $line = shift; push(@{$self->{'alignlines'}},$line); } =head2 each_alignment_line Title : each_alignment_line Usage : foreach $line ( $domain->each_alignment_line ) Function: reguritates the alignment lines as they were fed in. only useful realistically for printing. Example : Returns : Args : None =cut sub each_alignment_line { my $self = shift; return @{$self->{'alignlines'}}; } =head2 get_nse Title : get_nse Usage : $domain->get_nse() Function: Provides a seqname/start-end format, useful for unique keys. nse stands for name-start-end It is used a lot in Pfam Example : Returns : A string Args : Optional separator 1 and separator 2 (default / and -) =cut sub get_nse { my $self = shift; my $sep1 = shift; my $sep2 = shift; if( !defined $sep2 ) { $sep2 = "-"; } if( !defined $sep1 ) { $sep1 = "/"; } return sprintf("%s%s%d%s%d",$self->seq_id,$sep1,$self->start,$sep2,$self->end); } # =head2 start_seq # Title : start_seq # Usage : Backward compatibility with old HMMER modules. # should use $domain->start # Function: # Example : # Returns : # Args : # =cut sub start_seq { my $self = shift; my $start = shift; $self->warn("Using old domain->start_seq. Should use domain->start"); return $self->start($start); } # =head2 end_seq # Title : end_seq # Usage : Backward compatibility with old HMMER modules. # should use $domain->end # Function: # Example : # Returns : # Args : # =cut sub end_seq { my $self = shift; my $end = shift; $self->warn("Using old domain->end_seq. Should use domain->end"); return $self->end($end); } # =head2 start_hmm # Title : start_hmm # Usage : Backward compatibility with old HMMER modules, and # for convience. Equivalent to $self->homol_SeqFeature->start # Function: # Example : # Returns : # Args : # =cut sub start_hmm { my $self = shift; my $start = shift; $self->warn("Using old domain->start_hmm. Should use domain->hstart"); return $self->hstart($start); } # =head2 end_hmm # Title : end_hmm # Usage : Backward compatibility with old HMMER modules, and # for convience. Equivalent to $self->homol_SeqFeature->start # Function: # Example : # Returns : # Args : # =cut sub end_hmm { my $self = shift; my $end = shift; $self->warn("Using old domain->end_hmm. Should use domain->hend"); return $self->hend($end); } =head2 hmmacc Title : hmmacc Usage : $domain->hmmacc($newacc) Function: set get for HMM accession number. This is placed in the homol feature of the HMM Example : Returns : Args : =cut sub hmmacc{ my ($self,$acc) = @_; if( defined $acc ) { $self->feature2->add_tag_value('accession',$acc); } my @vals = $self->feature2->each_tag_value('accession'); return shift @vals; } =head2 hmmname Title : hmmname Usage : $domain->hmmname($newname) Function: set get for HMM accession number. This is placed in the homol feature of the HMM Example : Returns : Args : =cut sub hmmname { return shift->hseq_id(@_); } =head2 bits Title : bits Usage : Function: backward compatibility. Same as score Example : Returns : Args : =cut sub bits{ return shift->score(@_); } =head2 evalue Title : evalue Usage : Function: $domain->evalue($value); Example : Returns : Args : =cut sub evalue{ return shift->_tag_value('evalue',@_); } =head2 seqbits Title : seqbits Usage : Function: $domain->seqbits($value); Example : Returns : Args : =cut sub seqbits { return shift->_tag_value('seqbits',@_); } =head2 seq_range Title : seq_range Usage : Function: Throws an exception to catch scripts which need to upgrade Example : Returns : Args : =cut sub seq_range{ my ($self,@args) = @_; $self->throw("You have accessed an old method. Please recode your script to the new bioperl HMMER module"); } =head2 hmm_range Title : hmm_range Usage : Function: Throws an exception to catch scripts which need to upgrade Example : Returns : Args : =cut sub hmm_range{ my ($self,@args) = @_; $self->throw("You have accessed an old method. Please recode your script to the new bioperl HMMER module"); } 1; # says use was ok __END__ �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/HMMER/Results.pm���������������������������������������������������������000444��000766��000024�� 52003�13155576320� 20213� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # Perl Module for HMMResults # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@sanger.ac.uk> # #Copyright Genome Research Limited (1997). =head1 NAME Bio::Tools::HMMER::Results - Object representing HMMER output results =head1 SYNOPSIS # parse a hmmsearch file (can also parse a hmmpfam file) $res = Bio::Tools::HMMER::Results->new( -file => 'output.hmm' , -type => 'hmmsearch'); # print out the results for each sequence foreach $seq ( $res->each_Set ) { print "Sequence bit score is",$seq->bits,"\n"; foreach $domain ( $seq->each_Domain ) { print " Domain start ",$domain->start," end ",$domain->end, " score ",$domain->bits,"\n"; } } # new result object on a sequence/domain cutoff of # 25 bits sequence, 15 bits domain $newresult = $res->filter_on_cutoff(25,15); # alternative way of getting out all domains directly foreach $domain ( $res->each_Domain ) { print "Domain on ",$domain->seq_id," with score ", $domain->bits," evalue ",$domain->evalue,"\n"; } =head1 DESCRIPTION This object represents HMMER output, either from hmmsearch or hmmpfam. For hmmsearch, a series of HMMER::Set objects are made, one for each sequence, which have the the bits score for the object. For hmmpfam searches, only one Set object is made. These objects come from the original HMMResults modules used internally in Pfam, written by Ewan Birney. Ewan then converted them to BioPerl objects in 1999. That conversion is meant to be backwardly compatible, but may not be (caveat emptor). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 CONTRIBUTORS Jason Stajich, jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::HMMER::Results; use strict; use Bio::Tools::HMMER::Domain; use Bio::Tools::HMMER::Set; use Symbol; use base qw(Bio::Root::Root Bio::Root::IO Bio::SeqAnalysisParserI); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'domain'} = []; # array of HMMUnits $self->{'seq'} = {}; my ($parsetype) = $self->_rearrange([qw(TYPE)],@args); $self->_initialize_io(@args); if( !defined $parsetype ) { $self->throw("No parse type provided. should be hmmsearch or hmmpfam"); } $self->parsetype($parsetype); if( defined $self->_fh() ) { if( $parsetype eq 'hmmsearch' ) { $self->_parse_hmmsearch($self->_fh()); } elsif ( $parsetype eq 'hmmpfam' ) { $self->_parse_hmmpfam($self->_fh()); } else { $self->throw("Did not recoginise type $parsetype"); } } return $self; # success - we hope! } =head2 next_feature Title : next_feature Usage : while( my $feat = $res->next_feature ) { # do something } Function: SeqAnalysisParserI implementing function Example : Returns : A Bio::SeqFeatureI compliant object, in this case, each DomainUnit object, ie, flattening the Sequence aspect of this. Args : None =cut sub next_feature{ my ($self) = @_; if( $self->{'_started_next_feature'} == 1 ) { return shift @{$self->{'_next_feature_array'}}; } else { $self->{'_started_next_feature'} = 1; my @array; foreach my $seq ( $self->each_Set() ) { foreach my $unit ( $seq->each_Domain() ) { push(@array,$unit); } } my $res = shift @array; $self->{'_next_feature_array'} = \@array; return $res; } $self->throw("Should not reach here! Error!"); } =head2 number Title : number Usage : print "There are ",$res->number," domains hit\n"; Function: provides the number of domains in the HMMER report =cut sub number { my $self = shift; my @val; my $ref; $ref = $self->{'domain'}; @val = @{$self->{'domain'}}; return scalar @val; } =head2 seqfile Title : seqfile Usage : $obj->seqfile($newval) Function: Example : Returns : value of seqfile Args : newvalue (optional) =cut sub seqfile{ my ($self,$value) = @_; if( defined $value) { $self->{'seqfile'} = $value; } return $self->{'seqfile'}; } =head2 hmmfile Title : hmmfile Usage : $obj->hmmfile($newval) Function: Example : Returns : value of hmmfile Args : newvalue (optional) =cut sub hmmfile{ my ($self,$value) = @_; if( defined $value) { $self->{'hmmfile'} = $value; } return $self->{'hmmfile'}; } =head2 add_Domain Title : add_Domain Usage : $res->add_Domain($unit) Function: adds a domain to the results array. Mainly used internally. Args : A Bio::Tools::HMMER::Domain =cut sub add_Domain { my $self = shift; my $unit = shift; my $name; $name = $unit->seq_id(); if( ! exists $self->{'seq'}->{$name} ) { $self->warn("Adding a domain of $name but with no HMMSequence. Will be kept in domain array but not added to a HMMSequence"); } else { $self->{'seq'}->{$name}->add_Domain($unit); } push(@{$self->{'domain'}},$unit); } =head2 each_Domain Title : each_Domain Usage : foreach $domain ( $res->each_Domain() ) Function: array of Domain units which are held in this report Returns : array Args : none =cut sub each_Domain { my $self = shift; my (@arr,$u); foreach $u ( @{$self->{'domain'}} ) { push(@arr,$u); } return @arr; } =head2 domain_bits_cutoff_from_evalue Title : domain_bits_cutoff_from_evalue Usage : $cutoff = domain_bits_cutoff_from_evalue(0.01); Function: return a bits cutoff from an evalue using the scores here. Somewhat interesting logic: Find the two bit score which straddle the evalue if( 25 is between these two points) return 25 else return the midpoint. This logic tries to ensure that with large signal to noise separation one still has sensible 25 bit cutoff Returns : Args : =cut sub domain_bits_cutoff_from_evalue { my $self = shift; my $eval = shift; my ($dom,$prev,@doms,$cutoff,$sep,$seen); @doms = $self->each_Domain; @doms = map { $_->[0] } sort { $b->[1] <=> $a->[1] } map { [ $_, $_->bits] } @doms; $seen = 0; foreach $_ ( @doms ) { if( $_->evalue > $eval ) { $seen = 1; $dom = $_; last; } $prev = $_; } if( ! defined $prev || $seen == 0) { $self->throw("Evalue is either above or below the list..."); return; } $sep = $prev->bits - $dom->bits ; if( $sep < 1 ) { return $prev->bits(); } if( $dom->bits < 25 && $prev->bits > 25 ) { return 25; } return int( $dom->bits + $sep/2 ) ; } sub dictate_hmm_acc { my $self = shift; my $acc = shift; my ($unit); foreach $unit ( $self->eachHMMUnit() ) { $unit->hmmacc($acc); } } =head2 write_FT_output Title : write_FT_output Usage : $res->write_FT_output(\*STDOUT,'DOMAIN') Function: writes feature table output ala swissprot Returns : Args : =cut sub write_FT_output { my $self = shift; my $file = shift; my $idt = shift; my ($seq,$unit); if( !defined $idt ) { $idt = "DOMAIN"; } foreach $seq ( $self->each_Set() ) { print $file sprintf("ID %s\n",$seq->name()); foreach $unit ( $seq->each_Domain() ) { print $file sprintf("FT %s %d %d %s\n",$idt, $unit->start,$unit->end,$unit->hmmname); } print $file "//\n"; } } =head2 filter_on_cutoff Title : filter_on_cutoff Usage : $newresults = $results->filter_on_cutoff(25,15); Function: Produces a new HMMER::Results module which has been trimmed at the cutoff. Returns : a Bio::Tools::HMMER::Results module Args : sequence cutoff and domain cutoff. in bits score if you want one cutoff, simply use same number both places =cut sub filter_on_cutoff { my $self = shift; my $seqthr = shift; my $domthr = shift; my ($new,$seq,$unit,@array,@narray); if( !defined $domthr ) { $self->throw("hmmresults filter on cutoff needs two arguments"); } $new = Bio::Tools::HMMER::Results->new(-type => $self->parsetype); foreach $seq ( $self->each_Set()) { next if( $seq->bits() < $seqthr ); $new->add_Set($seq); foreach $unit ( $seq->each_Domain() ) { next if( $unit->bits() < $domthr ); $new->add_Domain($unit); } } $new; } =head2 write_ascii_out Title : write_ascii_out Usage : $res->write_ascii_out(\*STDOUT) Function: writes as seq seq_start seq_end model-acc model_start model_end model_name Returns : Args : FIXME: Now that we have no modelacc, this is probably a bad thing. =cut # writes as seq sstart send modelacc hstart hend modelname sub write_ascii_out { my $self = shift; my $fh = shift; my ($unit,$seq); if( !defined $fh) { $fh = \*STDOUT; } foreach $seq ( $self->each_Set()) { foreach $unit ( $seq->each_Domain()) { print $fh sprintf("%s %4d %4d %s %4d %4d %4.2f %4.2g %s\n", $unit->seq_id(),$unit->start(),$unit->end(), $unit->hmmacc,$unit->hstart,$unit->hend, $unit->bits,$unit->evalue,$unit->hmmname); } } } =head2 write_GDF_bits Title : write_GDF_bits Usage : $res->write_GDF_bits(25,15,\*STDOUT) Function: writes GDF format with a sequence,domain threshold Returns : Args : =cut sub write_GDF_bits { my $self = shift; my $seqt = shift; my $domt = shift; my $file = shift; my $seq; my $unit; my (@array,@narray); if( !defined $file ) { $self->throw("Attempting to use write_GDF_bits without passing in correct arguments!"); return; } foreach $seq ( $self->each_Set()) { if( $seq->bits() < $seqt ) { next; } foreach $unit ( $seq->each_Domain() ) { if( $unit->bits() < $domt ) { next; } push(@array,$unit); } } @narray = sort { my ($aa,$bb,$st_a,$st_b); $aa = $a->seq_id(); $bb = $b->seq_id(); if ( $aa eq $bb) { $st_a = $a->start(); $st_b = $b->start(); return $st_a <=> $st_b; } else { return $aa cmp $bb; } } @array; foreach $unit ( @narray ) { print $file sprintf("%-24s\t%6d\t%6d\t%15s\t%.1f\t%g\n",$unit->get_nse(),$unit->start(),$unit->end(),$unit->seq_id(),$unit->bits(),$unit->evalue); } } sub write_scores_bits { my $self = shift; my $seqt = shift; my $domt = shift; my $file = shift; my $seq; my $unit; my (@array,@narray); if( !defined $file ) { $self->warn("Attempting to use write_scores_bits without passing in correct arguments!"); return; } foreach $seq ( $self->eachHMMSequence()) { if( $seq->bits() < $seqt ) { next; } foreach $unit ( $seq->eachHMMUnit() ) { if( $unit->bits() < $domt ) { next; } push(@array,$unit); } } @narray = sort { my ($aa,$bb,$st_a,$st_b); $aa = $a->bits(); $bb = $b->bits(); return $aa <=> $bb; } @array; foreach $unit ( @narray ) { print $file sprintf("%4.2f %s\n",$unit->bits(),$unit->get_nse()); } } sub write_GDF { my $self = shift; my $file = shift; my $unit; if( !defined $file ) { $file = \*STDOUT; } foreach $unit ( $self->eachHMMUnit() ) { print $file sprintf("%-24s\t%6d\t%6d\t%15s\t%.1f\t%g\n",$unit->get_nse(),$unit->start(),$unit->end(),$unit->seq_id(),$unit->bits(),$unit->evalue); } } sub highest_noise { my $self = shift; my $seqt = shift; my $domt = shift; my ($seq,$unit,$hseq,$hdom,$noiseseq,$noisedom); $hseq = $hdom = -100000; foreach $seq ( $self->eachHMMSequence()) { if( $seq->bits() < $seqt && $seq->bits() > $hseq ) { $hseq = $seq->bits(); $noiseseq = $seq; } foreach $unit ( $seq->eachHMMUnit() ) { if( (($seq->bits() < $seqt) || ($seq->bits() > $seqt && $unit->bits < $domt)) && $unit->bits() > $hdom ) { $hdom = $unit->bits(); $noisedom = $unit; } } } return ($noiseseq,$noisedom); } sub lowest_true { my $self = shift; my $seqt = shift; my $domt = shift; my ($seq,$unit,$lowseq,$lowdom,$trueseq,$truedom); if( ! defined $domt ) { $self->warn("lowest true needs at least a domain threshold cut-off"); return (0,0); } $lowseq = $lowdom = 100000; foreach $seq ( $self->eachHMMSequence()) { if( $seq->bits() >= $seqt && $seq->bits() < $lowseq ) { $lowseq = $seq->bits(); $trueseq = $seq; } if( $seq->bits() < $seqt ) { next; } foreach $unit ( $seq->eachHMMUnit() ) { if( $unit->bits() >= $domt && $unit->bits() < $lowdom ) { $lowdom = $unit->bits(); $truedom = $unit; } } } return ($trueseq,$truedom); } =head2 add_Set Title : add_Set Usage : Mainly internal function Function: Returns : Args : =cut sub add_Set { my $self = shift; my $seq = shift; my $name; $name = $seq->name(); if( exists $self->{'seq'}->{$name} ) { $self->throw("You alredy have $name in HMMResults!"); } $self->{'seq'}->{$name} = $seq; } =head2 each_Set Title : each_Set Usage : Function: Returns : Args : =cut sub each_Set { my $self = shift; my (@array,$name); foreach $name ( keys %{$self->{'seq'}} ) { push(@array,$self->{'seq'}->{$name}); } return @array; } =head2 get_Set Title : get_Set Usage : $set = $res->get_Set('sequence-name'); Function: returns the Set for a particular sequence Returns : a HMMER::Set object Args : name of the sequence =cut sub get_Set { my $self = shift; my $name = shift; return $self->{'seq'}->{$name}; } =head2 _parse_hmmpfam Title : _parse_hmmpfam Usage : $res->_parse_hmmpfam($filehandle) Function: Returns : Args : =cut sub _parse_hmmpfam { my $self = shift; my $file = shift; my ($id,$sqfrom,$sqto,$hmmf,$hmmt,$sc,$ev, $unit,$nd,$seq,$name,$seqname,$from, $to,%hash,%acc,$acc); my $count = 0; while(<$file>) { if( /^HMM file:\s+(\S+)/ ) { $self->hmmfile($1); next; } elsif( /^Sequence file:\s+(\S+)/ ) { $self->seqfile($1); next } elsif( /^Query(\s+sequence)?:\s+(\S+)/ ) { $seqname = $2; $seq = Bio::Tools::HMMER::Set->new(); $seq ->name($seqname); $self->add_Set($seq); %hash = (); while(<$file>){ if( /Accession:\s+(\S+)/ ) { $seq->accession($1); next } elsif( s/^Description:\s+// ) { chomp; $seq->desc($_); next } /^Parsed for domains/ && last; # This is to parse out the accession numbers in old Pfam format. # now not support due to changes in HMMER. if( (($id,$acc, $sc, $ev, $nd) = /^\s*(\S+)\s+(\S+).+?\s(\S+)\s+(\S+)\s+(\d+)\s*$/)) { $hash{$id} = $sc; # we need this for the sequence # core of the domains below! $acc {$id} = $acc; # this is the more common parsing routine } elsif ( (($id,$sc, $ev, $nd) = /^\s*(\S+).+?\s(\S+)\s+(\S+)\s+(\d+)\s*$/) ) { $hash{$id} = $sc; # we need this for the # sequence score of hte domains below! } } while(<$file>) { /^Align/ && last; m{^//} && last; # this is meant to match #Sequence Domain seq-f seq-t hmm-f hmm-t score E-value #-------- ------- ----- ----- ----- ----- ----- ------- #PF00621 1/1 198 372 .. 1 207 [] 281.6 1e-80 if( (($id, $sqfrom, $sqto, $hmmf,$hmmt,$sc, $ev) = /(\S+)\s+\S+\s+(\d+)\s+(\d+).+?(\d+)\s+(\d+)\s+\S+\s+(\S+)\s+(\S+)\s*$/)) { $unit = Bio::Tools::HMMER::Domain->new(); $unit->seq_id ($seqname); $unit->hmmname ($id); $unit->start ($sqfrom); $unit->end ($sqto); $unit->hstart($hmmf); $unit->hend ($hmmt); $unit->bits ($sc); $unit->evalue ($ev); if( !exists($hash{$id}) ) { $self->throw("HMMResults parsing error in hmmpfam for $id - can't find sequecne score"); } $unit->seqbits($hash{$id}); if( defined $acc{$id} ) { $unit->hmmacc($acc{$id}); } # this should find it's own sequence! $self->add_Domain($unit); } } if( m{^//} ) { next; } $_ = <$file>; # parses alignment lines. Icky as we have to break on the same line # that we need to read to place the alignment lines with the unit. while(1) { (!defined $_ || m{^//}) && last; # matches: # PF00621: domain 1 of 1, from 198 to 372 if( /^\s*(\S+):.*from\s+(\d+)\s+to\s+(\d+)/ ) { $name = $1; $from = $2; $to = $3; # find the HMMUnit which this alignment is from $unit = $self->get_unit_nse($seqname,$name,$from,$to); if( !defined $unit ) { $self->warn("Could not find $name $from $to unit even though I am reading it in. ugh!"); $_ = <$file>; next; } while(<$file>) { m{^//} && last; /^\s*\S+:.*from\s+\d+\s+to\s+\d+/ && last; $unit->add_alignment_line($_); } } else { $_ = <$file>; } } # back to main 'Query:' loop } } } # mainly internal function sub get_unit_nse { my $self = shift; my $seqname = shift; my $domname = shift; my $start = shift; my $end = shift; my($seq,$unit); $seq = $self->get_Set($seqname); if( !defined $seq ) { $self->throw("Could not get sequence name $seqname - so can't get its unit"); } foreach $unit ( $seq->each_Domain() ) { if( $unit->hmmname() eq $domname && $unit->start() == $start && $unit->end() == $end ) { return $unit; } } return; } =head2 _parse_hmmsearch Title : _parse_hmmsearch Usage : $res->_parse_hmmsearch($filehandle) Function: Returns : Args : =cut sub _parse_hmmsearch { my $self = shift; my $file = shift; my ($id,$sqfrom,$sqto,$sc,$ev,$unit,$nd,$seq,$hmmf,$hmmt, $hmmfname,$hmmacc, $hmmid, %seqh); my $count = 0; while(<$file>) { /^HMM file:\s+(\S+)/ and do { $self->hmmfile($1); $hmmfname = $1 }; /^Accession:\s+(\S+)/ and do { $hmmacc = $1 }; /^Query HMM:\s+(\S+)/ and do { $hmmid = $1 }; /^Sequence database:\s+(\S+)/ and do { $self->seqfile($1) }; /^Scores for complete sequences/ && last; } $hmmfname = "given" if not $hmmfname; while(<$file>) { /^Parsed for domains/ && last; if( (($id, $sc, $ev, $nd) = /(\S+).+?\s(\S+)\s+(\S+)\s+(\d+)\s*$/)) { $seq = Bio::Tools::HMMER::Set->new(); $seq->name($id); $seq->bits($sc); $seqh{$id} = $sc; $seq->evalue($ev); $self->add_Set($seq); $seq->accession($hmmacc); } } while(<$file>) { /^Alignments of top-scoring domains/ && last; if( (($id, $sqfrom, $sqto, $hmmf, $hmmt, $sc, $ev) = /(\S+)\s+\S+\s+(\d+)\s+(\d+).+?(\d+)\s+(\d+)\s+\S+\s+(\S+)\s+(\S+)\s*$/)) { $unit = Bio::Tools::HMMER::Domain->new(); $unit->seq_id($id); $unit->hmmname($hmmfname); $unit->start($sqfrom); $unit->end($sqto); $unit->bits($sc); $unit->hstart($hmmf); $unit->hend($hmmt); $unit->evalue($ev); $unit->seqbits($seqh{$id}); $self->add_Domain($unit); $count++; } } $_ = <$file>; ## Recognize and store domain alignments while(1) { if( !defined $_ ) { last; } /^Histogram of all scores/ && last; # matches: # PF00621: domain 1 of 1, from 198 to 372 if( /^\s*(\S+):.*from\s+(\d+)\s+to\s+(\d+)/ ) { my $name = $1; my $from = $2; my $to = $3; # find the HMMUnit which this alignment is from $unit = $self->get_unit_nse($name,$hmmfname,$from,$to); if( !defined $unit ) { $self->warn("Could not find $name $from $to unit even though I am reading it in. ugh!"); next; } while(<$file>) { /^Histogram of all scores/ && last; /^\s*\S+:.*from\s+\d+\s+to\s+\d+/ && last; $unit->add_alignment_line($_); } } else { $_ = <$file>; } } return $count; } =head2 parsetype Title : parsetype Usage : $obj->parsetype($newval) Function: Returns : value of parsetype Args : newvalue (optional) =cut sub parsetype{ my ($self,$value) = @_; if( defined $value) { $self->{'_parsetype'} = $value; } return $self->{'_parsetype'}; } 1; # says use was ok __END__ �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/HMMER/Set.pm�������������������������������������������������������������000444��000766��000024�� 12255�13155576320� 17312� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::HMMER::Set # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@sanger.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches =head1 SYNOPSIS # get a Set object probably from the results object print "Bits score over set ",$set->bits," evalue ",$set->evalue,"\n"; foreach $domain ( $set->each_Domain ) { print "Domain start ",$domain->start," end ",$domain->end,"\n"; } =head1 DESCRIPTION Represents a set of HMMER domains hitting one sequence. HMMER reports two different scores, a per sequence total score (and evalue) and a per domain score and evalue. This object represents a collection of the same domain with the sequence bits score and evalue. (these attributes are also on the per domain scores, which you can get there). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney-at-ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::HMMER::Set; use strict; use Bio::Tools::HMMER::Domain; use base qw(Bio::Root::Root); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($name,$acc,$desc) = $self->_rearrange([qw(NAME ACCESSION DESC)], @args); $name && $self->name($name); $acc && $self->accession($acc); $desc && $self->desc($desc); $self->{'domains'} = []; $self->{'domainnames'} = {}; return $self; } =head2 add_Domain Title : add_Domain Usage : $set->add_Domain($domain) Function: adds the domain to the list Returns : nothing Args : A Bio::Tools::HMMER::Domain object =cut sub add_Domain{ my ($self,$domain) = @_; if( ! defined $domain || ! $domain->isa("Bio::Tools::HMMER::Domain") ) { $self->throw("[$domain] is not a Bio::Tools::HMMER::Domain. aborting"); } return if $self->{'domainnames'}->{$domain->get_nse}++; push(@{$self->{'domains'}},$domain); } =head2 each_Domain Title : each_Domain Usage : foreach $domain ( $set->each_Domain() ) Function: returns an array of domain objects in this set Returns : array Args : none =cut sub each_Domain{ my ($self,@args) = @_; return @{$self->{'domains'}}; } =head2 name Title : name Usage : $obj->name($newval) Function: Example : Returns : value of name Args : newvalue (optional) =cut sub name{ my ($obj,$value) = @_; if( defined $value) { $obj->{'name'} = $value; } return $obj->{'name'}; } =head2 desc Title : desc Usage : $obj->desc($newval) Function: Example : Returns : value of desc Args : newvalue (optional) =cut sub desc{ my ($self,$value) = @_; if( defined $value) { $self->{'desc'} = $value; } return $self->{'desc'}; } =head2 accession Title : accession Usage : $obj->accession($newval) Function: Example : Returns : value of accession Args : newvalue (optional) =cut sub accession{ my ($self,$value) = @_; if( defined $value) { $self->{'accession'} = $value; } return $self->{'accession'}; } =head2 bits Title : bits Usage : $obj->bits($newval) Function: Example : Returns : value of bits Args : newvalue (optional) =cut sub bits{ my ($obj,$value) = @_; if( defined $value) { $obj->{'bits'} = $value; } return $obj->{'bits'}; } =head2 evalue Title : evalue Usage : $obj->evalue($newval) Function: Example : Returns : value of evalue Args : newvalue (optional) =cut sub evalue{ my ($obj,$value) = @_; if( defined $value) { $obj->{'evalue'} = $value; } return $obj->{'evalue'}; } sub addHMMUnit { my $self = shift; my $unit = shift; $self->warn("Using old addHMMUnit call on Bio::Tools::HMMER::Set. Should replace with add_Domain"); return $self->add_Domain($unit); } sub eachHMMUnit { my $self = shift; $self->warn("Using old eachHMMUnit call on Bio::Tools::HMMER::Set. Should replace with each_Domain"); return $self->each_Domain(); } 1; # says use was ok __END__ ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Phylo��������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16262� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Phylo/Gerp.pm������������������������������������������������������������000555��000766��000024�� 10707�13155576320� 17702� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# $Id: Gumby.pm,v 1.2 2007/06/14 18:01:52 nathan Exp $ # # BioPerl module for Bio::Tools::Phylo::Gerp # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Sendu Bala <bix@sendu.me.uk> # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Phylo::Gerp - Parses output from GERP =head1 SYNOPSIS use strict; use Bio::Tools::Phylo::Gerp; my $parser = Bio::Tools::Phylo::Gerp->new(-file => "alignment.rates.elems"); while (my $feat = $parser->next_result) { my $start = $feat->start; my $end = $feat->end; my $rs_score = $feat->score; my $p_value = ($feat->annotation->get_Annotations('p-value'))[0]->value; } =head1 DESCRIPTION This module is used to parse the output from 'GERP' (v2) by Eugene Davydov (originally Gregory M. Cooper et al.). You can get details here: http://mendel.stanford.edu/sidowlab/ It works on the .elems files produced by gerpelem. Each result is a Bio::SeqFeature::Annotated representing a single constrained element. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Phylo::Gerp; use strict; use Bio::SeqFeature::Generic; use Bio::Annotation::SimpleValue; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::Phylo::Gerp->new(); Function: Builds a new Bio::Tools::Phylo::Gerp object Returns : Bio::Tools::Phylo::Gerp Args : -file (or -fh) should contain the contents of a gerpelem .elems file =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_result Title : next_result Usage : $result = $obj->next_result(); Function: Returns the next result available from the input, or undef if there are no more results. Returns : Bio::SeqFeature::Annotated object. Features are annotated with a tag for 'pvalue', and a 'predicted' tag. They have no sequence id unless the input GERP file is non-standard, with the seq id as the 6th column. NB: feature coordinates are alignment columns of the alignment used to create the result file. Args : none =cut sub next_result { my ($self) = @_; my $line = $self->_readline || return; while ($line !~ /^\d+\s+\d+\s+\d+\s+\S+\s+\S+\s*(?:\S+\s*)?$/) { $line = $self->_readline || return; } #start end length RS-score p-value # code elsewhere adds seq_id on the end (not valid GERP), so we capture that # if present my ($start, $end, undef, $rs_score, $p_value, $seq_id) = split(/\s+/, $line); my $feat = Bio::SeqFeature::Generic->new( $seq_id ? (-seq_id => $seq_id) : (), -start => $start, -end => $end, -strand => 1, -score => $rs_score, #-type => 'conserved_region', ***causes 740x increase in SeqFeatureDB storage requirements! -source => 'GERP'); my $sv = Bio::Annotation::SimpleValue->new(-tagname => 'predicted', -value => 1); $feat->annotation->add_Annotation($sv); $sv = Bio::Annotation::SimpleValue->new(-tagname => 'pvalue', -value => $p_value); $feat->annotation->add_Annotation($sv); return $feat; } 1; ���������������������������������������������������������BioPerl-1.007002/Bio/Tools/Phylo/Gumby.pm�����������������������������������������������������������000444��000766��000024�� 11232�13155576320� 20057� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Phylo::Gumby # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Sendu Bala <bix@sendu.me.uk> # # Copyright Sendu Bala # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Phylo::Gumby - Parses output from gumby =head1 SYNOPSIS #!/usr/bin/perl -Tw use strict; use Bio::Tools::Phylo::Gumby; my $parser = Bio::Tools::Phylo::Gumby->new(-file => "out.align"); my @features = $parser->next_result(); =head1 DESCRIPTION This module is used to parse the output from 'gumby' by Shyam Prabhakar. You can get details here: http://pga.lbl.gov/gumby/ It works on the .align files produced. The result is a list of feature objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Sendu Bala Email bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Phylo::Gumby; use strict; use Bio::SeqFeature::Annotated; use Bio::Annotation::SimpleValue; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::Phylo::Gumby->new(); Function: Builds a new Bio::Tools::Phylo::Gumby object Returns : Bio::Tools::Phylo::Gumby Args : -file (or -fh) should contain the contents of a gumby .align output file =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_result Title : next_result Usage : $result = $obj->next_result(); Function: Returns the next set of results available from the input, or undef if there are no more results. Returns : list of Bio::SeqFeature::Annotated (one per sequence). Features are annotated with tags for pvalue and 'kind' (holding 'all', 'exon', or 'nonexon'). NB: Gumby ignores sequence coordinates in input alignments, treating each sequence as if it started at position 1. If you're running this manually (ie. not via the Bio::Tools::Run::Phylo::Gumby) you will have to adjust the coordinates to match up with your input alignment and sequences. Args : none =cut sub next_result { my ($self) = @_; my $line = $self->_readline || return; while ($line !~ /^start/) { $line = $self->_readline || return; if ($line =~ /^(all|exon|nonexon):/) { $self->{_kind} = $1; } } my ($score, $pvalue) = $line =~ /score (\d+), pvalue (\S+)/; my @feats; while ($line = $self->_readline) { $line =~ /^$/ && last; $line || last; my ($seq_id, $start, $end) = split(/\s+/, $line); my $feature = Bio::SeqFeature::Annotated->new(-seq_id => $seq_id, -start => $start, -end => $end, -score => $score, -strand => 1, -source => 'gumby'); my $sv = Bio::Annotation::SimpleValue->new(-tagname => 'pvalue', -value => $pvalue); $feature->annotation->add_Annotation($sv); $sv = Bio::Annotation::SimpleValue->new(-tagname => 'kind', -value => $self->{_kind}); $feature->annotation->add_Annotation($sv); $sv = Bio::Annotation::SimpleValue->new(-tagname => 'predicted', -value => 1); $feature->annotation->add_Annotation($sv); push(@feats, $feature); } return @feats; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Phylo/Molphy.pm����������������������������������������������������������000444��000766��000024�� 20350�13155576320� 20245� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Phylo::Molphy # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Phylo::Molphy - parser for Molphy output =head1 SYNOPSIS use Bio::Tools::Phylo::Molphy; my $parser = Bio::Tools::Phylo::Molphy->new(-file => 'output.protml'); while( my $r = $parser->next_result ) { # r is a Bio::Tools::Phylo::Molphy::Result object # print the model name print $r->model, "\n"; # get the substitution matrix # this is a hash of 3letter aa codes -> 3letter aa codes representing # substitution rate my $smat = $r->substitution_matrix; print "Arg -> Gln substitution rate is %d\n", $smat->{'Arg'}->{'Gln'}, "\n"; # get the transition probablity matrix # this is a hash of 3letter aa codes -> 3letter aa codes representing # transition probabilty my $tmat = $r->transition_probability_matrix; print "Arg -> Gln transition probablity is %.2f\n", $tmat->{'Arg'}->{'Gln'}, "\n"; # get the frequency for each of the residues my $rfreqs = $r->residue_frequencies; foreach my $residue ( keys %{$rfreqs} ) { printf "residue %s expected freq: %.2f observed freq: %.2f\n", $residue,$rfreqs->{$residue}->[0], $rfreqs->{$residue}->[1]; } my @trees; while( my $t = $r->next_tree ) { push @trees, $t; } print "search space is ", $r->search_space, "\n", "1st tree score is ", $trees[0]->score, "\n"; # writing to STDOUT, use -file => '>filename' to specify a file my $out = Bio::TreeIO->new(-format => "newick"); $out->write_tree($trees[0]); # writing only the 1st tree } =head1 DESCRIPTION A parser for Molphy output (protml,dnaml) =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Phylo::Molphy; use strict; use Bio::Tools::Phylo::Molphy::Result; use Bio::TreeIO; use IO::String; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::Phylo::Molphy->new(); Function: Builds a new Bio::Tools::Phylo::Molphy object Returns : Bio::Tools::Phylo::Molphy Args : -fh/-file => $val, # for initing input, see Bio::Root::IO =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_result Title : next_result Usage : my $r = $molphy->next_result Function: Get the next result set from parser data Returns : Bio::Tools::Phylo::Molphy::Result object Args : none =cut sub next_result{ my ($self) = @_; # A little statemachine for the parser here my ($state,$transition_ct, @transition_matrix, %transition_mat, @resloc,) = ( 0,0); my ( %subst_matrix, @treelines, @treedata, %frequencies); my ( $treenum,$possible_trees, $model); my ($trans_type,$trans_amount); my $parsed = 0; while( defined ( $_ = $self->_readline()) ) { $parsed = 1; if( /^Relative Substitution Rate Matrix/ ) { if( %subst_matrix ) { $self->_pushback($_); last; } $state = 0; my ( @tempdata); @resloc = (); while( defined ($_ = $self->_readline) ) { last if (/^\s+$/); # remove leading/trailing spaces s/^\s+//; s/\s+$//; my @data = split; my $i = 0; for my $l ( @data ) { if( $l =~ /\D+/ ) { push @resloc, $l; } $i++; } push @tempdata, \@data; } my $i = 0; for my $row ( @tempdata ) { my $j = 0; for my $col ( @$row ) { if( $i == $j ) { # empty string for diagonals $subst_matrix{$resloc[$i]}->{$resloc[$j]} = ''; } else { $subst_matrix{$resloc[$i]}->{$resloc[$j]} = $col; } $j++; } $i++; } } elsif( /^Transition Probability Matrix/ ) { if( /(1\.0e(5|7))\)\s+(\S+)/ ) { $state = 1; my $newtrans_type = "$3-$1"; $trans_amount = $1; if( defined $trans_type ) { # finish processing the transition_matrix my $i =0; foreach my $row ( @transition_matrix ) { my $j = 0; foreach my $col ( @$row ) { $transition_mat{$trans_type}->{$resloc[$i]}->{$resloc[$j]} = $col; $j++; } $i++; } } $trans_type = $newtrans_type; $transition_ct = 0; @transition_matrix = (); } } elsif ( /Acid Frequencies/ ) { $state = 0; $self->_readline(); # skip the next line while( defined( $_ = $self->_readline) ) { unless( /^\s+/) { $self->_pushback($_); last; } s/^\s+//; s/\s+$//; my ($index,$res,$model,$data) = split; $frequencies{$res} = [ $model,$data]; } } elsif( /^(\d+)\s*\/\s*(\d+)\s+(.+)\s+model/ ) { my @save = ($1,$2,$3); # finish processing the transition_matrix my $i =0; foreach my $row ( @transition_matrix ) { my $j = 0; foreach my $col ( @$row ) { $transition_mat{$trans_type}->{$resloc[$i]}->{$resloc[$j]} = $col; $j++; } $i++; } if( defined $treenum ) { $self->_pushback($_); last; } $state = 2; ($treenum,$possible_trees, $model) = @save; $model =~ s/\s+/ /g; } elsif( $state == 1 ) { next if( /^\s+$/ || /^\s+Ala/); s/^\s+//; s/\s+$//; if( $trans_type eq '1PAM-1.0e7' ) { # because the matrix is split up into 2-10 column sets push @{$transition_matrix[$transition_ct++]}, split ; $transition_ct = 0 if $transition_ct % 20 == 0; } elsif( $trans_type eq '1PAM-1.0e5' ) { # because the matrix is split up into 2-10 column sets my ($res,@row) = split; next if $transition_ct >= 20; # skip last push @{$transition_matrix[$transition_ct++]}, @row; } } elsif( $state == 2 ) { if( s/^(\d+)\s+(\-?\d+(\.\d+)?)\s+// ) { push @treedata, [ $1,$2]; } # save this for the end so that we can # be efficient and only open one tree parser push @treelines, $_; } } # waiting till the end to do this, is it better my @trees; if( @treelines ) { my $strdat = IO::String->new(join('',@treelines)); my $treeio = Bio::TreeIO->new(-fh => $strdat, -format => 'newick'); while( my $tree = $treeio->next_tree ) { if( @treedata ) { my $dat = shift @treedata; # set the associated information $tree->id($dat->[0]); $tree->score($dat->[1]); } push @trees, $tree; } } return unless( $parsed ); my $result = Bio::Tools::Phylo::Molphy::Result->new (-trees => \@trees, -substitution_matrix => \%subst_matrix, -frequencies => \%frequencies, -model => $model, -search_space => $possible_trees, ); while( my ($type,$mat) = each %transition_mat ) { $result->transition_probability_matrix( $type,$mat); } $result; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Phylo/Molphy�������������������������������������������������������������000755��000766��000024�� 0�13155576320� 17532� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Phylo/Molphy/Result.pm���������������������������������������������������000444��000766��000024�� 21135�13155576320� 21525� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Phylo::Molphy::Result # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Phylo::Molphy::Result - container for data parsed from a ProtML run =head1 SYNOPSIS # do not use this object directly, you will get it back as part of a # Molphy parser use Bio::Tools::Phylo::Molphy; my $parser = Bio::Tools::Phylo::Molphy->new(-file => 'output.protml'); while( my $r = $parser->next_result ) { # r is a Bio::Tools::Phylo::Molphy::Result object # print the model name print $r->model, "\n"; # get the substitution matrix # this is a hash of 3letter aa codes -> 3letter aa codes representing # substitution rate my $smat = $r->substitution_matrix; print "Arg -> Gln substitution rate is %d\n", $smat->{'Arg'}->{'Gln'}, "\n"; # get the transition probablity matrix # this is a hash of 3letter aa codes -> 3letter aa codes representing # transition probabilty my $tmat = $r->transition_probability_matrix; print "Arg -> Gln transition probablity is %.2f\n", $tmat->{'Arg'}->{'Gln'}, "\n"; # get the frequency for each of the residues my $rfreqs = $r->residue_frequencies; foreach my $residue ( keys %{$rfreqs} ) { printf "residue %s expected freq: %.2f observed freq: %.2f\n", $residue,$rfreqs->{$residue}->[0], $rfreqs->{$residue}->[1]; } my @trees; while( my $t = $r->next_tree ) { push @trees, $t; } print "search space is ", $r->search_space, "\n", "1st tree score is ", $trees[0]->score, "\n"; # writing to STDOUT, use -file => '>filename' to specify a file my $out = Bio::TreeIO->new(-format => "newick"); $out->write_tree($trees[0]); # writing only the 1st tree } =head1 DESCRIPTION A container for data parsed from a ProtML run. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Phylo::Molphy::Result; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root); =head2 new Title : new Usage : my $obj = Bio::Tools::Phylo::Molphy::Result->new(); Function: Builds a new Bio::Tools::Phylo::Molphy::Result object Returns : Bio::Tools::Phylo::Molphy::Result Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($trees,$smat,$freq, $model, $sspace, ) = $self->_rearrange([qw(TREES SUBSTITUTION_MATRIX FREQUENCIES MODEL SEARCH_SPACE)], @args); if( $trees ) { if(ref($trees) !~ /ARRAY/i ) { $self->warn("Must provide a valid array reference to initialize trees"); } else { foreach my $t ( @$trees ) { $self->add_tree($t); } } } # initialize things through object methods to be a good # little OO programmer if( ref($smat) =~ /HASH/i ) { $self->substitution_matrix($smat); } if( ref($freq) =~ /HASH/i ) { $self->residue_frequencies($freq); } $model && $self->model($model); $sspace && $self->search_space($sspace); $self->{'_treeiterator'} = 0; return $self; } =head2 model Title : model Usage : $obj->model($newval) Function: Returns : value of model Args : newvalue (optional) =cut sub model{ my ($self,$value) = @_; if( defined $value) { $self->{'model'} = $value; } return $self->{'model'}; } =head2 substitution_matrix Title : substitution_matrix Usage : my $smat = $result->subsitution_matrix; Function: Get the relative substitution matrix calculated in the ML procedure Returns : reference to hash of hashes where key is the aa/nt name and value is another hash ref which contains keys for all the aa/nt possibilities Args : none =cut sub substitution_matrix{ my ($self,$val) = @_; if(defined $val ) { if( ref($val) =~ /HASH/ ) { foreach my $v (values %{$val} ) { if( ref($v) !~ /HASH/i ) { $self->warn("Must be a valid hashref of hashrefs for substition_matrix"); return; } } $self->{'_substitution_matrix'} = $val; } else { $self->warn("Must be a valid hashref of hashrefs for substition_matrix"); return; } } return $self->{'_substitution_matrix'}; } =head2 transition_probability_matrix Title : transition_probability_matrix Usage : my $matrixref = $molphy->transition_probablity_matrix(); Function: Gets the observed transition probability matrix Returns : hash of hashes of aa/nt transition to each other aa/nt Args : Transition matrix type, typically '1PAM-1.0e05' or '1PAM-1.0e07' =cut sub transition_probability_matrix { my ($self,$type,$val) = @_; $type = '1PAM-1.0e7' unless defined $type; if(defined $val ) { if( ref($val) =~ /HASH/ ) { foreach my $v (values %{$val} ) { if( ref($v) !~ /HASH/i ) { $self->warn("Must be a valid hashref of hashrefs for transition_probability_matrix"); return; } } $self->{'_TPM'}->{$type} = $val; } else { $self->warn("Must be a valid hashref of hashrefs for transition_probablity_matrix"); return; } } # fix this for nucml where there are 2 values (one is just a transformation # of the either, but how to represent?) return $self->{'_TPM'}->{$type}; } =head2 residue_frequencies Title : residue_frequencies Usage : my %data = $molphy->residue_frequencies() Function: Get the modeled and expected frequencies for each of the residues in the sequence Returns : hash of either aa (protml) or nt (nucml) frequencies each key will point to an array reference where 1st slot is model's expected frequency 2nd slot is observed frequency in the data $hash{'A'}->[0] = Args : none =cut #' sub residue_frequencies { my ($self,$val) = @_; if(defined $val ) { if( ref($val) =~ /HASH/ ) { $self->{'_residue_frequencies'} = $val; } else { $self->warn("Must be a valid hashref of hashrefs for residue_frequencies"); } } return %{$self->{'_residue_frequencies'}}; } =head2 next_tree Title : next_tree Usage : my $tree = $factory->next_tree; Function: Get the next tree from the factory Returns : L<Bio::Tree::TreeI> Args : none =cut sub next_tree{ my ($self,@args) = @_; return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef; } =head2 rewind_tree Title : rewind_tree_iterator Usage : $result->rewind_tree() Function: Rewinds the tree iterator so that next_tree can be called again from the beginning Returns : none Args : none =cut sub rewind_tree_iterator { shift->{'_treeiterator'} = 0; } =head2 add_tree Title : add_tree Usage : $result->add_tree($tree); Function: Adds a tree Returns : integer which is the number of trees stored Args : L<Bio::Tree::TreeI> =cut sub add_tree{ my ($self,$tree) = @_; if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) { push @{$self->{'_trees'}},$tree; } return scalar @{$self->{'_trees'}}; } =head2 search_space Title : search_space Usage : $obj->search_space($newval) Function: Returns : value of search_space Args : newvalue (optional) =cut sub search_space{ my ($self,$value) = @_; if( defined $value) { $self->{'search_space'} = $value; } return $self->{'search_space'}; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Phylo/Phylip�������������������������������������������������������������000755��000766��000024�� 0�13155576320� 17527� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Phylo/Phylip/ProtDist.pm�������������������������������������������������000444��000766��000024�� 7444�13155576320� 22003� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Tools::Phylo::Phylip::ProtDist # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Shawn Hoon <shawnh@fugu-sg.org> # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Phylo::Phylip::ProtDist - parser for ProtDist output =head1 SYNOPSIS use Bio::Tools::Phylo::Phylip::ProtDist; my $parser = Bio::Tools::Phylo::Phylip::ProtDist->new(-file => 'outfile'); while( my $result = $parser->next_matrix) { # do something with it } =head1 DESCRIPTION A parser for ProtDist output into a L<Bio::Matrix::PhylipDist> object. See also L<Bio::Matrix::IO::phylip> this module may go away. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Phylo::Phylip::ProtDist; use strict; use Bio::Matrix::PhylipDist; use base qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : my $obj = Bio::Tools::Phylo::Phylip::ProtDist->new(); Function: Builds a new Bio::Tools::Phylo::Phylip::ProtDist object Returns : Bio::Tools::ProtDist Args : -fh/-file => $val, # for initing input, see Bio::Root::IO -program => 'programname' # name of the program =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); my ($prog) = $self->_rearrange([qw(PROGRAM)], @args); $self->{'_program'} = $prog; return $self; } =head2 next_matrix Title : next_matrix Usage : my $matrix = $parser->next_matrix Function: Get the next result set from parser data Returns : L<Bio::Matrix::PhylipDist> Args : none =cut sub next_matrix{ my ($self) = @_; my @names; my @values; my $entry; my $size = 0; while ($entry=$self->_readline) { if($#names >=0 && $entry =~/^\s+\d+\n$/){ $self->_pushback($entry); last; } elsif($entry=~/^\s+(\d+)\n$/){ $size = $1; next; } elsif( $entry =~ s/^\s+(\-?\d+\.\d+)/$1/ ) { my (@line) = split( /\s+/,$entry); push @{$values[-1]}, @line; next; } my ($n,@line) = split( /\s+/,$entry); push @names, $n; push @values, [@line]; } if( scalar @names != $size ) { $self->warn("The number of entries ".(scalar @names). " is not the same $size"); } $#names>=0 || return; my %dist; my $i=0; for my $name (@names){ my $j=0; for my $n (@names) { $dist{$name}{$n} = [$i,$j]; $j++; } $i++; } return Bio::Matrix::PhylipDist->new(-program => $self->{'_program'}, -matrix => \%dist, -names => \@names, -values => \@values); } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Prediction���������������������������������������������������������������000755��000766��000024�� 0�13155576320� 17267� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Prediction/Exon.pm�������������������������������������������������������000444��000766��000024�� 12673�13155576320� 20724� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Prediction::Exon # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp@gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Prediction::Exon - A predicted exon feature =head1 SYNOPSIS # See documentation of methods. =head1 DESCRIPTION A feature representing a predicted exon. This class actually inherits off Bio::SeqFeature::Gene::Exon and therefore has all that functionality (also implements Bio::SeqFeatureI), plus a few methods supporting predicted features, like various scores and a significance. Even though these were inspired by GenScan results, at least a subset should be generally useable for exon prediction results. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp-at-gmx.net =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Prediction::Exon; use strict; use base qw(Bio::SeqFeature::Gene::Exon); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); return $self; } =head2 predicted_cds Title : predicted_cds Usage : $predicted_cds_dna = $exon->predicted_cds(); $exon->predicted_cds($predicted_cds_dna); Function: Get/Set the CDS (coding sequence) as predicted by a program. This method is independent of an attached_seq. There is no guarantee whatsoever that the returned CDS has anything to do (e.g., matches) with the sequence covered by the exons as annotated through this object. Example : Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program. Args : On set, a Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program. =cut sub predicted_cds { my ($self, $cds) = @_; if(defined($cds)) { $self->{'_predicted_cds'} = $cds; } return $self->{'_predicted_cds'}; } =head2 predicted_protein Title : predicted_protein Usage : $predicted_protein_seq = $exon->predicted_protein(); $exon->predicted_protein($predicted_protein_seq); Function: Get/Set the protein translation as predicted by a program. This method is independent of an attached_seq. There is no guarantee whatsoever that the returned translation has anything to do with the sequence covered by the exons as annotated through this object, or the sequence returned by predicted_cds(), although it should usually be just the standard translation. Example : Returns : A Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program. Args : On set, a Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program. =cut sub predicted_protein { my ($self, $aa) = @_; if(defined($aa)) { $self->{'_predicted_aa'} = $aa; } return $self->{'_predicted_aa'}; } =head2 significance Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Returns : Args : =cut sub significance { return shift->_tag_value('signif', @_); } =head2 start_signal_score Title : start_signal_score Usage : $sc = $obj->start_signal_score(); $obj->start_signal_score($evalue); Function: Get/Set a score for the exon start signal (acceptor splice site or initiation signal). Returns : Args : =cut sub start_signal_score { return shift->_tag_value('AccScore', @_); } =head2 end_signal_score Title : end_signal_score Usage : $sc = $obj->end_signal_score(); $obj->end_signal_score($evalue); Function: Get/Set a score for the exon end signal (donor splice site or termination signal). Returns : Args : =cut sub end_signal_score { return shift->_tag_value('DonScore', @_); } =head2 coding_signal_score Title : coding_signal_score Usage : $sc = $obj->coding_signal_score(); $obj->coding_signal_score($evalue); Function: Get/Set a score for the exon coding signal (e.g., coding potential). Returns : Args : =cut sub coding_signal_score { return shift->_tag_value('CodScore', @_); } # # Everything else is just inherited from SeqFeature::Generic. # 1; ���������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Prediction/Gene.pm�������������������������������������������������������000444��000766��000024�� 11164�13155576320� 20663� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Prediction::Gene # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Hilmar Lapp <hlapp@gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Prediction::Gene - a predicted gene structure feature =head1 SYNOPSIS #See documentation of methods. =head1 DESCRIPTION A feature representing a predicted gene structure. This class actually inherits off Bio::SeqFeature::Gene::Transcript and therefore has all that functionality, plus a few methods supporting predicted sequence features, like a predicted CDS and a predicted translation. Exons held by an instance of this class will usually be instances of Bio::Tools::Prediction::Exon, although they do not have to be. Refer to the documentation of the class that produced the instance. Normally, you will not want to create an instance of this class yourself. Instead, classes representing the results of gene structure prediction programs will do that. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Hilmar Lapp Email hlapp-at-gmx.net or hilmar.lapp-at-pharma.novartis.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Prediction::Gene; use strict; use base qw(Bio::SeqFeature::Gene::Transcript); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($primary,$ptag) = $self->_rearrange([qw(PRIMARY PRIMARY_TAG)],@args); $self->primary_tag('predicted_gene') unless $primary || $ptag; return $self; } =head2 predicted_cds Title : predicted_cds Usage : $predicted_cds_dna = $gene->predicted_cds(); $gene->predicted_cds($predicted_cds_dna); Function: Get/Set the CDS (coding sequence) as predicted by a program. This method is independent of an attached_seq. There is no guarantee whatsoever that the returned CDS has anything to do (e.g., matches) with the sequence covered by the exons as annotated through this object. Example : Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program. Args : On set, a Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program. =cut sub predicted_cds { my ($self, $cds) = @_; if(defined($cds)) { $self->{'_predicted_cds'} = $cds; } return $self->{'_predicted_cds'}; } =head2 predicted_protein Title : predicted_protein Usage : $predicted_protein_seq = $gene->predicted_protein(); $gene->predicted_protein($predicted_protein_seq); Function: Get/Set the protein translation as predicted by a program. This method is independent of an attached_seq. There is no guarantee whatsoever that the returned translation has anything to do with the sequence covered by the exons as annotated through this object, or the sequence returned by predicted_cds(), although it should usually be just the standard translation. Example : Returns : A Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program. Args : On set, a Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program. =cut sub predicted_protein { my ($self, $aa) = @_; if(defined($aa)) { $self->{'_predicted_aa'} = $aa; } return $self->{'_predicted_aa'}; } # # Everything else is just inherited from SeqFeature::GeneStructure. # 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Primer�������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16425� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Primer/AssessorI.pm������������������������������������������������������000444��000766��000024�� 4017�13155576320� 21035� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Tools::Primer::AssessorI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Primer::AssessorI - interface for assessing primer pairs =head1 SYNOPSIS use Bio::Tools::Primer::AssessorI; if( $obj->isa('Bio::Tools::Primer::AssessorI') ) { my $score = $obj->assess($primer_pair); } =head1 DESCRIPTION The Primer Assessor interface provides a interface for scoring functions of primer pairs to comply to. It is mainly used by Bio::Tools::Primer::Design module =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney-at-ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Primer::AssessorI; use base qw(Bio::Root::RootI); sub assess { my ($self) = shift; $self->throw_not_implemented(); } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Primer/Feature.pm��������������������������������������������������������000444��000766��000024�� 6344�13155576320� 20522� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Primer::Feature # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Primer::Feature - position of a single primer =head1 SYNOPSIS use Bio::Tools::Primer::Feature; my $pf = Bio::Tools::Primer::Feature->new( -start => $start, -end => $end, -strand => $strand); $pf->attach_seq($seq); # is a SeqFeatureI print "primer starts at ",$pf->start," with sequence ",$pf->seq->seq(),"\n"; # helper functions print "GC percentage ",$pf->gc(),"\n"; print "has inversion of size 4 at ",$pf->inversion(4),"\n"; =head1 DESCRIPTION Primer Features represents one primer in a primer pair. This object is mainly for designing primers, and probably principly used in the primer design system =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney-at-ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Primer::Feature; use base qw(Bio::SeqFeature::Generic); sub new { my ( $caller, @args) = @_; my ($self) = $caller->SUPER::new(@args); # done - we hope return $self; } sub gc_percent { my $self = shift; my $seq = $self->seq(); if( !defined $seq ) { $self->throw("Primer feature has no attached sequence, can't calculate GC"); } my $str = $seq->seq(); my $count = $str =~ tr/GCgc/GCgc/; return $count*100.0 / $seq->length; } sub inversion { my $self = shift; my $size = shift; if( !defined $size ) { $self->throw("Must have size paramter in inversion"); } my $seq = $self->seq(); if( !defined $seq ) { $self->throw("Primer feature has no attached sequence, can't calculate inversion"); } my $len = $seq->length - $size; my $str = $seq->seq(); foreach my $i ( 0 .. $len ) { my $revstr = substr($str,$i,$size); my $orig = $revstr; $revstr = reverse $revstr; $revstr = s/[^ATGCNatgcn]/N/g; $revstr =~ tr/ATGCNatgcn/TACGNtacgn/; if( $str =~ /$revstr/ ) { return $orig; } } return; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Primer/Pair.pm�����������������������������������������������������������000444��000766��000024�� 6337�13155576320� 20024� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Tools::Primer::Pair # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Primer::Pair - two primers on left and right side =head1 SYNOPSIS use Bio::Tools::Primer::Pair; my $pair = Bio::Tools::Primer::Pair->new( -left => $leftp , -right => $rightp); # helper functions print "GC percentage different",$pf->gc_difference(),"\n"; print "product length is ",$pf->product_length,"\n"; =head1 DESCRIPTION Primer Pairs represents one primer in a primer pair. This object is mainly for designing primers, and probably principly used in the primer design system =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney-at-ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Primer::Pair; use base qw(Bio::Root::Root); sub new { my ( $caller, @args) = @_; my ($self) = $caller->SUPER::new(@args); my ($left,$right) = $self->_rearrange([qw(LEFT RIGHT)],@args); if( !defined $left || !defined $right ) { $self->throw("Pair must be initialised with left and right primers"); } $self->left($left); $self->right($right); # done - we hope return $self; } sub left { my $self = shift; my $left = shift; if( defined $left ) { if( !ref $left || !$left->isa("Bio::Tools::Primer::Feature") ) { $self->throw("left primer must be a Bio::Tools::Primer::Feature, not $left"); } $self->{'left'} = $left; } return $self->{'left'}; } sub right { my $self = shift; my $right = shift; if( defined $right ) { if( !ref $right || !$right->isa("Bio::Tools::Primer::Feature") ) { $self->throw("right primer must be a Bio::Tools::Primer::Feature, not $right"); } $self->{'right'} = $right; } return $self->{'right'}; } sub gc_difference { my $self = shift; return abs ( $self->left->gc_percent - $self->right->gc_percent ); } sub product_length { my $self = shift; return $self->right->end - $self->left->start +1; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Primer/Assessor����������������������������������������������������������000755��000766��000024�� 0�13155576320� 20227� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Primer/Assessor/Base.pm��������������������������������������������������000444��000766��000024�� 4345�13155576320� 21602� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Primer::Assessor::Base # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Primer::Assessor::Base - base class for common assessor things =head1 SYNOPSIS use Bio::Tools::Primer::Assessor::Base $base->weight(10); =head1 DESCRIPTION Base class for assessors, probably only defining the weight function =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney Email birney-at-ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Primer::Assessor::Base; use base qw(Bio::Root::Root); sub new { my ( $caller, @args) = @_; my ($self) = $caller->SUPER::new(@args); my ($weight) = $self->_rearrange([qw(WEIGHT)],@args); if( !defined $weight ) { $weight = 10; } $self->weight($weight); # done - we hope return $self; } sub weight { my $self = shift; my $weight = shift; if( defined $weight ) { $self->{'weight'} = $weight; } return $self->{'weight'}; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Run����������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 15733� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Run/GenericParameters.pm�������������������������������������������������000555��000766��000024�� 6352�13155576320� 22037� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for wrapping runtime parameters # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chad Matsalla (bioinformatics1 at dieselwurks dot com) # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Run::GenericParameters - An object for the parameters used to run programs =head1 SYNOPSIS my $void = $obj->set_parameter("parameter_name","parameter_value"); my $value = $obj->get_parameter("parameter_name"); =head1 DESCRIPTION This is a basic container to hold the parameters used to run a program. This module may get incorporated into the more generic Bio::Tools::Run framework in bioperl-run distribution. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics1 at dieselwurks dot com =head1 CONTRIBUTORS Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Run::GenericParameters; use strict; use base qw(Bio::Root::Root Bio::Tools::Run::ParametersI); sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); return $self; } =head2 get_parameter Title : get_parameter Usage : $parameter_object->get_parameter($param_name); Function: Get the value of a parameter named $param_name Returns : A scalar that should be a string Args : A scalar that should be a string =cut sub get_parameter { my ($self,$arg) = @_; return $self->{params}->{$arg}; } =head2 set_parameter Title : set_parameter Usage : $parameter_object->set_parameter($param_name => $param_value); Function: Set the value of a parameter named $param_name to $param_value Returns : Void Args : A hash containing name=>value pairs =cut sub set_parameter { my ($self,$name,$value) = @_; $self->{params}->{$name} = $value; } =head2 available_parameters Title : available_parameters Usage : my @paramnames = $parameter_object->available_parameters Function: Returns the names of the available parameters Returns : list of available parameter names Args : none =cut sub available_parameters { my $self = shift; return keys %{$self->{params}}; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Run/ParametersI.pm�������������������������������������������������������000555��000766��000024�� 5372�13155576320� 20654� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for wrapping runtime parameters # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chad Matsalla (bioinformatics1 at dieselwurks dot com) # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Run::ParametersI - A Base object for the parameters used to run programs =head1 SYNOPSIS # do not use this object directly, it provides the following methods # for its subclasses my $void = $obj->set_parameter("parameter_name","parameter_value"); my $value = $obj->get_parameter("parameter_name"); =head1 DESCRIPTION This is a basic container to hold the parameters used to run a program. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chad Matsalla Email bioinformatics1 at dieselwurks dot com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Run::ParametersI; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::RootI); =head2 get_parameter Title : get_parameter Usage : $parameter_object->get_parameter($param_name); Function: Get the value of a parameter named $param_name Returns : A scalar that should be a string Args : A scalar that should be a string =cut sub get_parameter { my ($self,$arg) = @_; $self->throw_not_implemented; } =head2 set_parameter Title : set_parameter Usage : $parameter_object->set_parameter($param_name => $param_value); Function: Set the value of a parameter named $param_name to $param_value Returns : Void Args : A hash containing name=>value pairs =cut sub set_parameter { my ($self,$name,$value) = @_; $self->throw_not_implemented; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Run/README���������������������������������������������������������������000444��000766��000024�� 561�13155576320� 16732� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������� This directory is now mainly in bioperl-run package which you should install alongside Bioperl to get over 50 different runnable options. We might decide to merge the two packages again, but the feeling is that bioperl "core" is getting a little too big. Bioperl-run follows the same release tagging schedule as Bioperl. Pick it up from www.bioperl.org and/or CPAN �����������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Run/RemoteBlast.pm�������������������������������������������������������000444��000766��000024�� 60126�13155576320� 20674� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Run::RemoteBlast # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # FORMERLY Cared for by Jason Stajich, Mat Wiepert # # Somewhat cared for by Roger Hall, Chris Fields (when they have time) # # Copyright Jason Stajich, Bioperl # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Run::RemoteBlast - Object for remote execution of the NCBI Blast via HTTP =head1 SYNOPSIS #Remote-blast "factory object" creation and blast-parameter initialization use Bio::Tools::Run::RemoteBlast; use strict; my $prog = 'blastp'; my $db = 'swissprot'; my $e_val= '1e-10'; my @params = ( '-prog' => $prog, '-data' => $db, '-expect' => $e_val, '-readmethod' => 'SearchIO' ); my $factory = Bio::Tools::Run::RemoteBlast->new(@params); #change a query parameter $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]'; #change a retrieval parameter $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'DESCRIPTIONS'} = 1000; #remove a parameter delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'}; #$v is just to turn on and off the messages my $v = 1; my $str = Bio::SeqIO->new(-file=>'amino.fa' , -format => 'fasta' ); #optional: send BLAST request to a cloud service provider instead of NCBI #$factory->set_url_base("http://host.my.cloud.service.provider.com/cgi-bin/blast.cgi"); while (my $input = $str->next_seq()){ #Blast a sequence against a database: #Alternatively, you could pass in a file with many #sequences rather than loop through sequence one at a time #Remove the loop starting 'while (my $input = $str->next_seq())' #and swap the two lines below for an example of that. my $r = $factory->submit_blast($input); #my $r = $factory->submit_blast('amino.fa'); print STDERR "waiting..." if( $v > 0 ); while ( my @rids = $factory->each_rid ) { foreach my $rid ( @rids ) { my $rc = $factory->retrieve_blast($rid); if( !ref($rc) ) { if( $rc < 0 ) { $factory->remove_rid($rid); } print STDERR "." if ( $v > 0 ); sleep 5; } else { my $result = $rc->next_result(); #save the output my $filename = $result->query_name()."\.out"; $factory->save_output($filename); $factory->remove_rid($rid); print "\nQuery Name: ", $result->query_name(), "\n"; while ( my $hit = $result->next_hit ) { next unless ( $v > 0); print "\thit name is ", $hit->name, "\n"; while( my $hsp = $hit->next_hsp ) { print "\t\tscore is ", $hsp->score, "\n"; } } } } } } # This example shows how to change a CGI parameter: $Bio::Tools::Run::RemoteBlast::HEADER{'MATRIX_NAME'} = 'BLOSUM45'; $Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '15 2'; # And this is how to delete a CGI parameter: delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'}; =head1 DESCRIPTION Class for remote execution of the NCBI Blast via HTTP. For a description of the many CGI parameters see: https://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html Various additional options and input formats are available. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Please do NOT contact Jason directly about this module. Please post to the bioperl mailing list (L<FEEDBACK>). If you would like to be the official maintainer of this module, please volunteer on the list and we will make it official in this POD. First written by Jason Stajich, many others have helped keep it running. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Run::RemoteBlast; use strict; use warnings; use Bio::SeqIO; use IO::String; use Bio::SearchIO; use LWP; use HTTP::Request::Common; use Bio::Root::Version; use constant { NOT_FINISHED => 0, ERR_QBSTATUS => 1, ERR_NOCONTENT => 2, ERR_HTTPFAIL => 4, ERR_QBNONSPEC => 8 }; # Bio::Root::IO is-a Bio::Root::Roo use base qw(Bio::Root::IO Exporter); our @EXPORT = qw( NOT_FINISHED ERR_QBSTATUS ERR_NOCONTENT ERR_HTTPFAIL ERR_QBNONSPEC ); our $MODVERSION = $Bio::Root::Version::VERSION; our $URLBASE = 'https://blast.ncbi.nlm.nih.gov/Blast.cgi'; # In GET/PUTPARAMS the values are regexes which validate the input. our %PUTPARAMS = ( 'AUTO_FORMAT' => '(Off|(Semi|Full)auto)', # Off, Semiauto, Fullauto 'COMPOSITION_BASED_STATISTICS' => '(0|1)', # yes, no on NCBI's site, but actually binary 0/1 'DATABASE' => '.*', 'DB_GENETIC_CODE' => '([1-9]|1[1-6]|2(1|2))', # 1..16,21,22 'DISPLAY_SORT' => '\d', 'ENDPOINTS' => '(yes|no)', # yes,no 'ENTREZ_QUERY' => '.*', 'EXPECT' => '\d+(\.\d+)?([eE]-\d+)?', # Positive double 'FILTER' => '[LRm]', # L or R or m 'GAPCOSTS' => '-?\d+(\.\d+)\s+-?\d+(\.\d+)', # Two space separated float values 'GENETIC_CODE' => '([1-9]|1[1-6]|2(1|2))', # 1..16,21,22 'HITLIST_SIZE' => '\d+', # Positive integer 'I_THRESH' => '-?\d+(\.\d+)([eE]-\d+)?', # float 'LAYOUT' => '(One|Two)Windows?', # onewindow, twowindows 'LCASE_MASK' => '(yes|no)', # yes, no 'MATRIX_NAME' => '.*', 'NUCL_PENALTY' => '-\d+', # Negative integer 'NUCL_REWARD' => '-?\d+', # Integer 'OTHER_ADVANCED' => '.*', 'PERC_IDENT' => '\d\d+', # Integer, 0-99 inclusive 'PHI_PATTERN' => '.*', 'PROGRAM' => 't?blast[pnx]', # tblastp, tblastn, tblastx, blastp, blastn, blastx 'QUERY' => '.*', 'QUERY_FILE' => '.*', 'QUERY_BELIEVE_DEFLINE' => '(yes|no)', # yes, no 'QUERY_FROM' => '\d+', # Positive integer 'QUERY_TO' => '\d+', # Positive integer 'SEARCHSP_EFF' => '\d+', # Positive integer 'SERVICE' => '(plain|p[sh]i|(rps|mega)blast)', # plain,psi,phi,rpsblast,megablast 'SHORT_QUERY_ADJUST' => '(true|false)', 'THRESHOLD' => '-?\d+', # Integer 'UNGAPPED_ALIGNMENT' => '(yes|no)', # yes, no 'WORD_SIZE' => '\d+' # Positive integer ); our %GETPARAMS = ( 'ALIGNMENTS' => '\d+', # Positive integer 'ALIGNMENT_VIEW' => '(Pairwise|(Flat)?QueryAnchored(NoIdentities)?|Tabular)', # Pairwise, QueryAnchored, QueryAnchoredNoIdentities, # FlatQueryAnchored, FlatQueryAnchoredNoIdentities, Tabular 'DATABASE_SORT' => '\d', 'DESCRIPTIONS' => '\d+', # Positive integer 'ENTREZ_LINKS_NEW_WINDOW' => '(yes|no)', # yes, no 'EXPECT_LOW' => '\d+(\.\d+)?([eE]-\d+)?', # Positive double 'EXPECT_HIGH' => '\d+(\.\d+)?([eE]-\d+)?', # Positive double 'FORMAT_ENTREZ_QUERY' => '', 'FORMAT_OBJECT' => '(Alignment|Neighbors|PSSM|SearchInfo|TaxBlast(Parent|MultiFrame)?)', # Alignment, Neighbors, PSSM, SearchInfo # TaxBlast, TaxblastParent, TaxBlastMultiFrame 'FORMAT_TYPE' => '((HT|X)ML|ASN\.1|Text)', # HTML, Text, ASN.1, XML 'NCBI_GI' => '(yes|no)', # yes, no 'NEW_VIEW' => '(true|false)', 'RID' => '.*', 'RESULTS_FILE' => '(yes|no)', # yes, no 'SERVICE' => '(plain|p[sh]i|(rps|mega)blast)', # plain,psi,phi,rpsblast,megablast 'SHOW_OVERVIEW' => '(yes|no)' # yes, no ); # Default values go in here for PUT our %HEADER = ( 'CMD' => 'Put', 'FORMAT_OBJECT' => 'Alignment', 'COMPOSITION_BASED_STATISTICS' => 'off', 'DATABASE' => 'nr', 'EXPECT' => '1e-3', 'FILTER' => 'L', 'PROGRAM' => 'blastp', 'SERVICE' => 'plain' ); # Default values go in here for GET our %RETRIEVALHEADER = ( 'CMD' => 'Get', 'ALIGNMENTS' => '50', 'ALIGNMENT_VIEW' => 'Pairwise', 'DESCRIPTIONS' => '100', 'FORMAT_TYPE' => 'Text', ); sub new { my ($caller, @args) = @_; # chained new my $self = $caller->SUPER::new(@args); # so that tempfiles are cleaned up $self->_initialize_io(); my ($prog, $data, $readmethod, $url_base) = $self->_rearrange([qw(PROG DATA READMETHOD URL_BASE)], @args); # Use these two parameters for backward-compatibility. # Overridden by PROGRAM and DATABASE if supplied. $self->submit_parameter('PROGRAM',$prog) if $prog; $self->submit_parameter('DATABASE',$data) if $data; $readmethod = 'SearchIO' unless defined $readmethod; $self->readmethod($readmethod); # Now read the rest of the parameters and set them all # PUT parameters first my @putValues = $self->_rearrange([keys %PUTPARAMS],@args); my %putNames; @putNames{keys %PUTPARAMS} = @putValues; foreach my $putName (keys %putNames) { $self->submit_parameter($putName,$putNames{$putName}); } # GET parameters second my @getValues = $self->_rearrange([keys %GETPARAMS],@args); my %getNames; @getNames{keys %GETPARAMS} = @getValues; foreach my $getName (keys %getNames) { $self->retrieve_parameter($getName,$getNames{$getName}); } # private variable to keep track of total rids $self->{'_total_rids'} = 0; $url_base ||= $URLBASE; # default to regular NCBI BLAST URL $self->set_url_base($url_base); return $self; } =head2 retrieve_parameter Title : retrieve_parameter Usage : my $db = $self->retrieve_parameter Function: Get/Set the named parameter for the retrieve_blast operation. Returns : string Args : $name : name of GET parameter $val : optional value to set the parameter to =cut sub retrieve_parameter { my ($self, $name, $val) = @_; $name = uc($name); $self->throw($name." is not a valid GET parameter.") unless exists $GETPARAMS{$name}; if (defined $val) { my $regex = $GETPARAMS{$name}; $val =~ m/^$regex$/i or $self->throw("Value ".$val." for GET parameter ".$name." does not match expression ".$regex.". Rejecting."); $RETRIEVALHEADER{$name} = $val; } return $RETRIEVALHEADER{$name}; } =head2 submit_parameter Title : submit_parameter Usage : my $db = $self->submit_parameter Function: Get/Set the named parameter for the submit_blast operation. Returns : string Args : $name : name of PUT parameter $val : optional value to set the parameter to =cut sub submit_parameter { my ($self, $name, $val) = @_; $name = uc($name); $self->throw($name." is not a valid PUT parameter.") unless exists $PUTPARAMS{$name}; if (defined $val) { my $regex = $PUTPARAMS{$name}; $val =~ m/^$regex$/i or $self->throw("Value ".$val." for PUT parameter ".$name." does not match expression ".$regex.". Rejecting."); $HEADER{$name} = $val; } return $HEADER{$name}; } =head2 header Title : header Usage : my $header = $self->header Function: Get HTTP header for blast query Returns : string Args : none =cut sub header { my ($self) = @_; return %HEADER; } =head2 readmethod Title : readmethod Usage : my $readmethod = $self->readmethod Function: Get/Set the method to read the blast report Returns : string Args : string [ blast, blasttable, xml ] =cut sub readmethod { my ($self, $val) = @_; if( defined $val ) { if ($val =~ /bplite/i) { $self->throw("Use of Bio::Tools::BPlite is deprecated; use Bio::SearchIO modules instead"); } $self->{'_readmethod'} = $val; } return $self->{'_readmethod'}; } =head2 program Title : program Usage : my $prog = $self->program Function: Get/Set the program to run. Retained for backwards-compatibility. Returns : string Args : string [ blastp, blastn, blastx, tblastn, tblastx ] =cut sub program { my ($self, $val) = @_; return $self->submit_parameter('PROGRAM',$val); } =head2 database Title : database Usage : my $db = $self->database Function: Get/Set the database to search. Retained for backwards-compatibility. Returns : string Args : string [ swissprot, nr, nt, etc... ] =cut sub database { my ($self, $val) = @_; return $self->submit_parameter('DATABASE',$val); } =head2 expect Title : expect Usage : my $expect = $self->expect Function: Get/Set the E value cutoff. Retained for backwards-compatibility. Returns : string Args : string [ '1e-4' ] =cut sub expect { my ($self, $val) = @_; return $self->submit_parameter('EXPECT',$val); } =head2 ua Title : ua Usage : my $ua = $self->ua or $self->ua($ua) Function: Get/Set a LWP::UserAgent for use Returns : reference to LWP::UserAgent Object Args : none Comments: Will create a UserAgent if none has been requested before. =cut sub ua { my ($self, $value) = @_; if( ! defined $self->{'_ua'} ) { $self->{'_ua'} = LWP::UserAgent->new(env_proxy => 1, parse_head => 0); my $nm = ref($self); $nm =~ s/::/_/g; $self->{'_ua'}->agent("bioperl-$nm/$MODVERSION"); } return $self->{'_ua'}; } =head2 proxy Title : proxy Usage : $httpproxy = $db->proxy('http') or $db->proxy(['http','ftp'], 'http://myproxy' ) Function: Get/Set a proxy for use of proxy Returns : a string indicating the proxy Args : $protocol : an array ref of the protocol(s) to set/get $proxyurl : url of the proxy to use for the specified protocol =cut sub proxy { my ($self,$protocol,$proxy) = @_; return if ( !defined $self->ua || !defined $protocol || !defined $proxy ); return $self->ua->proxy($protocol,$proxy); } sub add_rid { my ($self, @vals) = @_; foreach ( @vals ) { $self->{'_rids'}->{$_} = $self->{'_total_rids'}; $self->{'_total_rids'}++; } return scalar keys %{$self->{'_rids'}}; } sub remove_rid { my ($self, @vals) = @_; foreach ( @vals ) { delete $self->{'_rids'}->{$_}; } return scalar keys %{$self->{'_rids'}}; } sub each_rid { my ($self) = @_; # sort on key value, a little tricky... my @sort_rids = sort {$self->{'_rids'}->{$a} <=> $self->{'_rids'}->{$b}} keys %{$self->{'_rids'}}; return @sort_rids; } =head2 submit_blast Title : submit_blast Usage : $self->submit_blast([$seq1,$seq2]); Function: Submit blast jobs to ncbi blast queue on sequence(s) Returns : Blast report object as defined by $self->readmethod Args : input can be: * sequence object * array ref of sequence objects * filename of file containing fasta formatted sequences =cut sub submit_blast { my ($self, $input) = @_; my @seqs = $self->_load_input($input); my $url_base = $self->get_url_base; return 0 unless ( @seqs ); my $tcount = 0; my %header = $self->header; $header{$_} ||= $RETRIEVALHEADER{$_} foreach (keys %RETRIEVALHEADER); foreach my $seq ( @seqs ) { #If query has a fasta header, the output has the query line. $header{'QUERY'} = ">".(defined $seq->display_id() ? $seq->display_id() : ""). " ".(defined $seq->desc() ? $seq->desc() : "")."\n".$seq->seq(); my $request = POST $url_base, [%header]; $self->debug($request->as_string) if ( $self->verbose > 1); my $response = $self->ua->request( $request); if( $response->is_success ) { my @subdata = split(/\n/, $response->content ); my $count = 0; foreach ( @subdata ) { if( /^\s+RID\s+=\s+(\S+)/ ) { $count++; #$self->debug("RID: $1\n"); $self->add_rid($1); } elsif (/^\s+RTOE\s+=\s+(.*$)/) { $self->{rtoe} = $1; $count++; } last if $count >= 2; } if( $count == 0 ) { $self->warn("req was ". $request->as_string() . "\n"); $self->warn(join('', @subdata)); } $tcount += $count; } else { # should try and be a little more verbose here $self->warn("req was ". $request->as_string() . "\n" . $response->error_as_HTML); $tcount = -1; } } return $tcount; } =head2 retrieve_blast Title : retrieve_blast Usage : my $blastreport = $blastfactory->retrieve_blast($rid); Function: Attempts to retrieve a blast report from remote blast queue Returns : scalar int (constant) or Bio::SearchIO object Constants: NOT_FINISHED (= 0) : 'job not finished' code on error: ERR_QBSTATUS (= 1) : return line matches 'Status=ERROR' ERR_NOCONTENT (= 2): HTTP request successful, but no content returned ERR_HTTPFAIL (= 4) : HTTP request failed ERR_QBNONSPEC (= 8): return line matches 'ERROR' (not status line) Args : Remote Blast ID (RID) =cut sub retrieve_blast { my($self, $rid) = @_; my $url_base = $self->get_url_base; my %hdr = %RETRIEVALHEADER; $hdr{'RID'} = $rid; my $req = HTTP::Request->new( GET => $url_base."?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=$rid", ); #$self->debug("SearchInfo request is " . $req->as_string()); my $response = $self->ua->request($req); if( $response->is_success ) { my $status; if($response->content =~ /Status=(WAITING|ERROR|FAILED|UNKNOWN|READY)/i ) { $status = $1; if( $status eq 'ERROR' ) { $self->warn("Server Error"); return ERR_QBSTATUS; } elsif( $status eq 'FAILED' ) { $self->warn("Request Failed"); return ERR_QBSTATUS; } } else { $self->warn("Error: No status reported\n"); } if ( $status ne 'READY' ) { return 0; } else { my ($fh,$tempfile) = $self->tempfile(); close $fh; my $req = POST $url_base, [%hdr]; $self->debug("retrieve request is " . $req->as_string()); my $response = $self->ua->request($req, $tempfile); my $blastobj; my $mthd = $self->readmethod; $mthd = ($mthd =~ /blasttable/i) ? 'blasttable' : ($mthd =~ /xml/i) ? 'blastxml' : ($mthd =~ /pull/i) ? 'blast_pull' : 'blast'; $blastobj = Bio::SearchIO->new( -file => $tempfile, -format => $mthd); ## store filename in object ## $self->file($tempfile); return $blastobj; } } else { $self->warn($response->error_as_HTML); return ERR_HTTPFAIL; } } =head2 save_output Title : saveoutput Usage : my $saveoutput = $self->save_output($filename) Function: Method to save the blast report Returns : 1 (throws error otherwise) Args : string [rid, filename] =cut sub save_output { my ($self, $filename) = @_; if( not defined $filename ) { $self->throw("Can't save blast output. You must specify a filename to save to."); } my $blastfile = $self->file; #open temp file and output file, have to filter out some HTML open my $TMP, '<', $blastfile or $self->throw("Could not read file '$blastfile': $!"); open my $SAVEOUT, '>', $filename or $self->throw("Could not write file '$filename': $!"); my $seentop = 0; while (my $line = <$TMP>) { next if ($line =~ /<pre>/); if ( $line =~ /^(?:[T]?BLAST[NPX])\s*.+$/i or $line =~ /^RPS-BLAST\s*.+$/i or $line =~ /<\?xml\sversion=/ or $line =~ /^#\s+(?:[T]?BLAST[NPX])\s*.+$/ ) { $seentop = 1; } next if !$seentop; if ( $seentop ) { print $SAVEOUT $line; } } return 1; } sub _load_input { my ($self, $input) = @_; if( ! defined $input ) { $self->throw("Calling remote blast with no input"); } my @seqs; if( ! ref $input ) { if( -e $input ) { my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => $input); while( my $seq = $seqio->next_seq ) { push @seqs, $seq; } } else { $self->throw("Input $input was not a valid filename"); } } elsif( ref($input) =~ /ARRAY/i ) { foreach ( @$input ) { if( ref($_) && $_->isa('Bio::PrimarySeqI') ) { push @seqs, $_; } else { $self->warn("Trying to add a " . ref($_) . " but expected a Bio::PrimarySeqI"); } } if( ! @seqs) { $self->throw("Did not pass in valid input -- no sequence objects found"); } } elsif( $input->isa('Bio::PrimarySeqI') ) { push @seqs, $input; } return @seqs; } =head2 set_url_base Title : set_url_base Usage : $self->set_url_base($url) Function: Method to override the default URL to access the NCBI BLAST web service Returns : None Args : string (URL used for remote BLAST searches) NOTE : This is highly experimental; we cannot maintain support on web services other than the default NCBI BLAST web service at this time. Only some URL parameters may be supported by other BLAST web services. =cut sub set_url_base { my $self = shift; $self->{'_urlbase'} = shift if @_; } =head2 get_url_base Title : get_url_base Usage : my $url = $self->set_url_base Function: Get the current URL for BLAST searching Returns : string (URL used for remote blast searches) Args : None =cut sub get_url_base { my $self = shift; return $self->{'_urlbase'}; } =head2 get_rtoe Title : get_rtoe Usage : my $url = $self->rtoe Function: Retrieve the retrieval time (defined after submit_blast()) Returns : number Args : None =cut sub get_rtoe { my $self = shift; return $self->{rtoe}; } 1; __END__ ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/SeqPattern���������������������������������������������������������������000755��000766��000024�� 0�13155576320� 17255� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/SeqPattern/Backtranslate.pm����������������������������������������������000444��000766��000024�� 53566�13155576320� 22565� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������package Bio::Tools::SeqPattern::Backtranslate; use strict; use warnings; use base qw(Bio::Root::Root); use base qw(Exporter); =head1 NAME Bio::Tools::SeqPattern::Backtranslate =head1 DESCRIPTION This module should not be used directly. It provides helper methods to Bio::Tools::SeqPattern to reverse translate protein patterns. =cut use Bio::Seq; use Bio::Tools::CodonTable; use List::MoreUtils qw(uniq); use Carp qw(croak); our @EXPORT_OK = qw(_reverse_translate_motif); our @EXPORT = @EXPORT_OK; sub _reverse_translate_motif { # Main subroutine. It takes a Profam-like motif and returns its # reverse translation using degenerate codons. # Steps: # 1. Tokenize, then parse tokens. # 2. Reverse translate each token type. # 3. Join tokens in original order. Return the resulting string. my $motif = shift; $motif =~ s/\./X/g; $motif = uc $motif; ### 1. Tokenize, parse the motif. my ( $ordered, $classified ) = _parse_motif($motif); ### 2. Reverse translate each token type. # Reverse translate the plain (unambiguous) tokens. my $ct = Bio::Tools::CodonTable->new; foreach my $seq ( @{ $classified->{plain} } ) { my $seqO = Bio::Seq->new( -seq => $$seq, -alphabet => 'protein' ); $$seq = $ct->reverse_translate_all($seqO); } # Reverse translate the ambiguous tokens. foreach my $token ( @{ $classified->{ambiguous} } ) { my ($aas) = $$token =~ m(([A-Za-z\.]+)); my @codons_to_contract; foreach my $residue ( split '', $aas ) { push @codons_to_contract, $ct->revtranslate($residue); } my $ambiguous_codon = _contract_codons(@codons_to_contract); $$token = $ambiguous_codon; } # Reverse translate the negated residues. foreach my $token ( @{ $classified->{negated} } ) { my ($aas) = $$token =~ m(([A-Za-z\.]+)); my $ambiguous_codon = _negated_aas_to_codon($aas); $$token = $ambiguous_codon; } ### 3. Join the profile back from its tokens. return join '', map {$$_} @{$ordered}; } sub _parse_motif { # Profam-like motif parser. It takes the pattern as a string, and # returns two data structures that contain the tokens, organized # by order of appearance in the pattern (first return value) and by # category (second return value). my $motif = shift; my $parser = _tokenize_motif($motif); my ( %tokens, @tokens ); while ( my $token = $parser->() ) { croak ("Unknown syntax token: <", $token->[1], ">") if ( $token->[0] eq 'UNKNOWN' ); push @{ $tokens{ $token->[0] } }, \$token->[1]; push @tokens, \$token->[1]; } return ( \@tokens, \%tokens ); } sub _tokenize_motif { # Return a tokenizer iterator that sequentially recognizes and # returns each token in the input pattern. # Examples of each token type: # ambiguous: a position with more than one possible residue. # eg. [ALEP] # negated: a position in which some residues are excluded. # eg. [^WY] # plain: a common sequence of residues. One position, one residue. # eg. MAAEIK # open_par, close_par: tags surrounding a motif that is repeated # a certain number of times. # eg. (...){3} my $target = shift; return sub { return [ 'ambiguous', $1 ] if $target =~ /\G (\[[A-Za-z\.]+\]) /gcx; return [ 'negated', $1 ] if $target =~ /\G (\[\^[A-Za-z\.]+\]) /gcx; return [ 'plain', $1 ] if $target =~ /\G ([A-Za-z\.]+) /gcx; return [ 'open_par', $1 ] if $target =~ /\G (\() /gcx; return [ 'close_par', $1 ] if $target =~ /\G (\)[\{\d+[,\d+]*\}]*) /gcx; return [ 'UNKNOWN', $1 ] if $target =~ /\G (.) /gcx; return; }; } sub _contract_codons { # Take a list of codons, return an ambiguous codon. my @codons = map { uc $_ } @_; my @by_letter = ( [], [], [], ); my $ambiguous_codon; foreach my $codon (@codons) { my @letters = split '', $codon; for my $i ( 0 .. 2 ) { push @{ $by_letter[$i] }, $letters[$i]; } } for my $i ( 0 .. 2 ) { $ambiguous_codon .= _convert( 'dna', _uniq_string( @{ $by_letter[$i] } ) ); } return $ambiguous_codon; } sub _expand_codon { # Given a degenerate codon, return a list with all its # constituents. Takes a three-letter string (codon) as # input, returns a list with three-letter scalars. my $codon = shift; die "Wrong codon length!\n" if length $codon != 3; my ( @codons, @return_bases ); my @orig_bases = split '', $codon; for my $i ( 0 .. 2 ) { # from each redundant base, create a list with all their # components (e.g., N -> (A, C, G, T) ); my @components = split '', _convert('dna', $orig_bases[$i] ); $orig_bases[$i] = [@components]; } # Combine all the bases of each of the three positions of the # codons, and build the return list. for my $i ( @{ $orig_bases[0] } ) { for my $j ( @{ $orig_bases[1] } ) { for my $k ( @{ $orig_bases[2] } ) { push @return_bases, $i . $j . $k; } } } return @return_bases; } { my %convert; sub _convert { # Interconvert between redundant and non-redundant protein and # dna alphabets. Takes an alphabet (protein or dna) and a string # with the letter, and returns its equivalent in # redundant/non-redundant alphabet. Example ACTG -> N. my ($alphabet, $letter) = @_; unless ( $alphabet and $alphabet =~ /^dna$|^protein$/i and $letter and length $letter <= 4 ) { croak "Wrong arguments!\n"; } unless (%convert) { %convert = ( 'dna' => { qw(N ACGT B CGT D AGT H ACT V ACG K GT M AC R AG S CG W AT Y CT A A C C T T G G) }, 'protein' => { '.' => 'ACDEFGHIJKLMNOPQRSTUVWY', X => 'ACDEFGHIJKLMNOPQRSTUVWY', Z => 'QE', B => 'ND', }, ); # Make %convert hash key/value agnostic. foreach my $alphabet ( keys %convert ) { map { $convert{$alphabet}->{ $convert{$alphabet}{$_} } = $_ } keys %{ $convert{$alphabet} }; } } return $convert{$alphabet}{$letter}; } } sub _uniq_string { # Takes a list of letters and returns an alphabetically sorted # list with unique elements. my @letters = @_; return join '', sort { $a cmp $b } uniq @letters; } { my ( @codon_library, $ct ); sub _negated_aas_to_codon { # Given a string of residues, returns a degenerate codon that will # not be translated into any of them, while maximizing degeneracy # (ie, it tries to also translate into as many residues as possible). # This functionality is required for reverse translating profiles # that contain negative patterns: [^X]. This means that the current # position should not contain aminoacid X, but can have any of the # others. The reverse translated nucleotide sequence should # reflect this. # Approach: construct a list of all possible codons, incluiding all # degenerate bases. This is an array of 15x15x15 = 3375 elements. # Order them by descendent "degeneracy". # Return the first one whose expansion in 4-lettered codons # doesn't contain a codon that translates into any of the # non-wanted residues. # * Since this takes some time, I presorted them and saved them. # Reading them from a file takes a fraction of the time that it taes # to re-sort them every time the application is launched. my $aas_to_avoid = shift; # Initialize reusable variables if it's the first time the sub # is called. unless (@codon_library) { while (<DATA>) { chomp; push @codon_library, split ' ', $_ } } unless ($ct) { $ct = Bio::Tools::CodonTable->new; } # Reverse translate the unwanted aminoacids to unwanted codons. my @unwanted_codons; foreach my $aa ( split '', $aas_to_avoid ) { push @unwanted_codons, $ct->revtranslate($aa); } foreach my $degenerate_codon (@codon_library) { my @codons = _expand_codon($degenerate_codon); my $success = 1; foreach my $unwanted (@unwanted_codons) { if ( grep { uc $unwanted eq $_ } @codons ) { $success = 0; } } if ($success) { return $degenerate_codon } } } } 1; =head1 COPYRIGHT & LICENSE Copyright 2009 Bruno Vecchi, all rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut __DATA__ NNN NNB NND NNH NNV NBN NDN NHN NVN BNN DNN HNN VNN NBB NBD NBH NBV NDB NDD NDH NDV NHB NHD NHH NHV NVB NVD NVH NVV BNB BND BNH BNV BBN BDN BHN BVN DNB DND DNH DNV DBN DDN DHN DVN HNB HND HNH HNV HBN HDN HHN HVN VNB VND VNH VNV VBN VDN VHN VVN NNK NNM NNR NNS NNW NNY NKN NMN NRN NSN NWN NYN KNN MNN RNN SNN WNN YNN BBB BBD BBH BBV BDB BDD BDH BDV BHB BHD BHH BHV BVB BVD BVH BVV DBB DBD DBH DBV DDB DDD DDH DDV DHB DHD DHH DHV DVB DVD DVH DVV HBB HBD HBH HBV HDB HDD HDH HDV HHB HHD HHH HHV HVB HVD HVH HVV VBB VBD VBH VBV VDB VDD VDH VDV VHB VHD VHH VHV VVB VVD VVH VVV NBK NBM NBR NBS NBW NBY NDK NDM NDR NDS NDW NDY NHK NHM NHR NHS NHW NHY NVK NVM NVR NVS NVW NVY NKB NKD NKH NKV NMB NMD NMH NMV NRB NRD NRH NRV NSB NSD NSH NSV NWB NWD NWH NWV NYB NYD NYH NYV BNK BNM BNR BNS BNW BNY BKN BMN BRN BSN BWN BYN DNK DNM DNR DNS DNW DNY DKN DMN DRN DSN DWN DYN HNK HNM HNR HNS HNW HNY HKN HMN HRN HSN HWN HYN VNK VNM VNR VNS VNW VNY VKN VMN VRN VSN VWN VYN KNB KND KNH KNV KBN KDN KHN KVN MNB MND MNH MNV MBN MDN MHN MVN RNB RND RNH RNV RBN RDN RHN RVN SNB SND SNH SNV SBN SDN SHN SVN WNB WND WNH WNV WBN WDN WHN WVN YNB YND YNH YNV YBN YDN YHN YVN BBK BBM BBR BBS BBW BBY BDK BDM BDR BDS BDW BDY BHK BHM BHR BHS BHW BHY BVK BVM BVR BVS BVW BVY BKB BKD BKH BKV BMB BMD BMH BMV BRB BRD BRH BRV BSB BSD BSH BSV BWB BWD BWH BWV BYB BYD BYH BYV DBK DBM DBR DBS DBW DBY DDK DDM DDR DDS DDW DDY DHK DHM DHR DHS DHW DHY DVK DVM DVR DVS DVW DVY DKB DKD DKH DKV DMB DMD DMH DMV DRB DRD DRH DRV DSB DSD DSH DSV DWB DWD DWH DWV DYB DYD DYH DYV HBK HBM HBR HBS HBW HBY HDK HDM HDR HDS HDW HDY HHK HHM HHR HHS HHW HHY HVK HVM HVR HVS HVW HVY HKB HKD HKH HKV HMB HMD HMH HMV HRB HRD HRH HRV HSB HSD HSH HSV HWB HWD HWH HWV HYB HYD HYH HYV VBK VBM VBR VBS VBW VBY VDK VDM VDR VDS VDW VDY VHK VHM VHR VHS VHW VHY VVK VVM VVR VVS VVW VVY VKB VKD VKH VKV VMB VMD VMH VMV VRB VRD VRH VRV VSB VSD VSH VSV VWB VWD VWH VWV VYB VYD VYH VYV KBB KBD KBH KBV KDB KDD KDH KDV KHB KHD KHH KHV KVB KVD KVH KVV MBB MBD MBH MBV MDB MDD MDH MDV MHB MHD MHH MHV MVB MVD MVH MVV RBB RBD RBH RBV RDB RDD RDH RDV RHB RHD RHH RHV RVB RVD RVH RVV SBB SBD SBH SBV SDB SDD SDH SDV SHB SHD SHH SHV SVB SVD SVH SVV WBB WBD WBH WBV WDB WDD WDH WDV WHB WHD WHH WHV WVB WVD WVH WVV YBB YBD YBH YBV YDB YDD YDH YDV YHB YHD YHH YHV YVB YVD YVH YVV NNA NNC NNT NNG NKK NKM NKR NKS NKW NKY NMK NMM NMR NMS NMW NMY NRK NRM NRR NRS NRW NRY NSK NSM NSR NSS NSW NSY NWK NWM NWR NWS NWW NWY NYK NYM NYR NYS NYW NYY NAN NCN NTN NGN KNK KNM KNR KNS KNW KNY KKN KMN KRN KSN KWN KYN MNK MNM MNR MNS MNW MNY MKN MMN MRN MSN MWN MYN RNK RNM RNR RNS RNW RNY RKN RMN RRN RSN RWN RYN SNK SNM SNR SNS SNW SNY SKN SMN SRN SSN SWN SYN WNK WNM WNR WNS WNW WNY WKN WMN WRN WSN WWN WYN YNK YNM YNR YNS YNW YNY YKN YMN YRN YSN YWN YYN ANN CNN TNN GNN NBA NBC NBT NBG NDA NDC NDT NDG NHA NHC NHT NHG NVA NVC NVT NVG NAB NAD NAH NAV NCB NCD NCH NCV NTB NTD NTH NTV NGB NGD NGH NGV BNA BNC BNT BNG BKK BKM BKR BKS BKW BKY BMK BMM BMR BMS BMW BMY BRK BRM BRR BRS BRW BRY BSK BSM BSR BSS BSW BSY BWK BWM BWR BWS BWW BWY BYK BYM BYR BYS BYW BYY BAN BCN BTN BGN DNA DNC DNT DNG DKK DKM DKR DKS DKW DKY DMK DMM DMR DMS DMW DMY DRK DRM DRR DRS DRW DRY DSK DSM DSR DSS DSW DSY DWK DWM DWR DWS DWW DWY DYK DYM DYR DYS DYW DYY DAN DCN DTN DGN HNA HNC HNT HNG HKK HKM HKR HKS HKW HKY HMK HMM HMR HMS HMW HMY HRK HRM HRR HRS HRW HRY HSK HSM HSR HSS HSW HSY HWK HWM HWR HWS HWW HWY HYK HYM HYR HYS HYW HYY HAN HCN HTN HGN VNA VNC VNT VNG VKK VKM VKR VKS VKW VKY VMK VMM VMR VMS VMW VMY VRK VRM VRR VRS VRW VRY VSK VSM VSR VSS VSW VSY VWK VWM VWR VWS VWW VWY VYK VYM VYR VYS VYW VYY VAN VCN VTN VGN KBK KBM KBR KBS KBW KBY KDK KDM KDR KDS KDW KDY KHK KHM KHR KHS KHW KHY KVK KVM KVR KVS KVW KVY KKB KKD KKH KKV KMB KMD KMH KMV KRB KRD KRH KRV KSB KSD KSH KSV KWB KWD KWH KWV KYB KYD KYH KYV MBK MBM MBR MBS MBW MBY MDK MDM MDR MDS MDW MDY MHK MHM MHR MHS MHW MHY MVK MVM MVR MVS MVW MVY MKB MKD MKH MKV MMB MMD MMH MMV MRB MRD MRH MRV MSB MSD MSH MSV MWB MWD MWH MWV MYB MYD MYH MYV RBK RBM RBR RBS RBW RBY RDK RDM RDR RDS RDW RDY RHK RHM RHR RHS RHW RHY RVK RVM RVR RVS RVW RVY RKB RKD RKH RKV RMB RMD RMH RMV RRB RRD RRH RRV RSB RSD RSH RSV RWB RWD RWH RWV RYB RYD RYH RYV SBK SBM SBR SBS SBW SBY SDK SDM SDR SDS SDW SDY SHK SHM SHR SHS SHW SHY SVK SVM SVR SVS SVW SVY SKB SKD SKH SKV SMB SMD SMH SMV SRB SRD SRH SRV SSB SSD SSH SSV SWB SWD SWH SWV SYB SYD SYH SYV WBK WBM WBR WBS WBW WBY WDK WDM WDR WDS WDW WDY WHK WHM WHR WHS WHW WHY WVK WVM WVR WVS WVW WVY WKB WKD WKH WKV WMB WMD WMH WMV WRB WRD WRH WRV WSB WSD WSH WSV WWB WWD WWH WWV WYB WYD WYH WYV YBK YBM YBR YBS YBW YBY YDK YDM YDR YDS YDW YDY YHK YHM YHR YHS YHW YHY YVK YVM YVR YVS YVW YVY YKB YKD YKH YKV YMB YMD YMH YMV YRB YRD YRH YRV YSB YSD YSH YSV YWB YWD YWH YWV YYB YYD YYH YYV ANB AND ANH ANV ABN ADN AHN AVN CNB CND CNH CNV CBN CDN CHN CVN TNB TND TNH TNV TBN TDN THN TVN GNB GND GNH GNV GBN GDN GHN GVN BBA BBC BBT BBG BDA BDC BDT BDG BHA BHC BHT BHG BVA BVC BVT BVG BAB BAD BAH BAV BCB BCD BCH BCV BTB BTD BTH BTV BGB BGD BGH BGV DBA DBC DBT DBG DDA DDC DDT DDG DHA DHC DHT DHG DVA DVC DVT DVG DAB DAD DAH DAV DCB DCD DCH DCV DTB DTD DTH DTV DGB DGD DGH DGV HBA HBC HBT HBG HDA HDC HDT HDG HHA HHC HHT HHG HVA HVC HVT HVG HAB HAD HAH HAV HCB HCD HCH HCV HTB HTD HTH HTV HGB HGD HGH HGV VBA VBC VBT VBG VDA VDC VDT VDG VHA VHC VHT VHG VVA VVC VVT VVG VAB VAD VAH VAV VCB VCD VCH VCV VTB VTD VTH VTV VGB VGD VGH VGV ABB ABD ABH ABV ADB ADD ADH ADV AHB AHD AHH AHV AVB AVD AVH AVV CBB CBD CBH CBV CDB CDD CDH CDV CHB CHD CHH CHV CVB CVD CVH CVV TBB TBD TBH TBV TDB TDD TDH TDV THB THD THH THV TVB TVD TVH TVV GBB GBD GBH GBV GDB GDD GDH GDV GHB GHD GHH GHV GVB GVD GVH GVV NKA NKC NKT NKG NMA NMC NMT NMG NRA NRC NRT NRG NSA NSC NST NSG NWA NWC NWT NWG NYA NYC NYT NYG NAK NAM NAR NAS NAW NAY NCK NCM NCR NCS NCW NCY NTK NTM NTR NTS NTW NTY NGK NGM NGR NGS NGW NGY KNA KNC KNT KNG KKK KKM KKR KKS KKW KKY KMK KMM KMR KMS KMW KMY KRK KRM KRR KRS KRW KRY KSK KSM KSR KSS KSW KSY KWK KWM KWR KWS KWW KWY KYK KYM KYR KYS KYW KYY KAN KCN KTN KGN MNA MNC MNT MNG MKK MKM MKR MKS MKW MKY MMK MMM MMR MMS MMW MMY MRK MRM MRR MRS MRW MRY MSK MSM MSR MSS MSW MSY MWK MWM MWR MWS MWW MWY MYK MYM MYR MYS MYW MYY MAN MCN MTN MGN RNA RNC RNT RNG RKK RKM RKR RKS RKW RKY RMK RMM RMR RMS RMW RMY RRK RRM RRR RRS RRW RRY RSK RSM RSR RSS RSW RSY RWK RWM RWR RWS RWW RWY RYK RYM RYR RYS RYW RYY RAN RCN RTN RGN SNA SNC SNT SNG SKK SKM SKR SKS SKW SKY SMK SMM SMR SMS SMW SMY SRK SRM SRR SRS SRW SRY SSK SSM SSR SSS SSW SSY SWK SWM SWR SWS SWW SWY SYK SYM SYR SYS SYW SYY SAN SCN STN SGN WNA WNC WNT WNG WKK WKM WKR WKS WKW WKY WMK WMM WMR WMS WMW WMY WRK WRM WRR WRS WRW WRY WSK WSM WSR WSS WSW WSY WWK WWM WWR WWS WWW WWY WYK WYM WYR WYS WYW WYY WAN WCN WTN WGN YNA YNC YNT YNG YKK YKM YKR YKS YKW YKY YMK YMM YMR YMS YMW YMY YRK YRM YRR YRS YRW YRY YSK YSM YSR YSS YSW YSY YWK YWM YWR YWS YWW YWY YYK YYM YYR YYS YYW YYY YAN YCN YTN YGN ANK ANM ANR ANS ANW ANY AKN AMN ARN ASN AWN AYN CNK CNM CNR CNS CNW CNY CKN CMN CRN CSN CWN CYN TNK TNM TNR TNS TNW TNY TKN TMN TRN TSN TWN TYN GNK GNM GNR GNS GNW GNY GKN GMN GRN GSN GWN GYN BKA BKC BKT BKG BMA BMC BMT BMG BRA BRC BRT BRG BSA BSC BST BSG BWA BWC BWT BWG BYA BYC BYT BYG BAK BAM BAR BAS BAW BAY BCK BCM BCR BCS BCW BCY BTK BTM BTR BTS BTW BTY BGK BGM BGR BGS BGW BGY DKA DKC DKT DKG DMA DMC DMT DMG DRA DRC DRT DRG DSA DSC DST DSG DWA DWC DWT DWG DYA DYC DYT DYG DAK DAM DAR DAS DAW DAY DCK DCM DCR DCS DCW DCY DTK DTM DTR DTS DTW DTY DGK DGM DGR DGS DGW DGY HKA HKC HKT HKG HMA HMC HMT HMG HRA HRC HRT HRG HSA HSC HST HSG HWA HWC HWT HWG HYA HYC HYT HYG HAK HAM HAR HAS HAW HAY HCK HCM HCR HCS HCW HCY HTK HTM HTR HTS HTW HTY HGK HGM HGR HGS HGW HGY VKA VKC VKT VKG VMA VMC VMT VMG VRA VRC VRT VRG VSA VSC VST VSG VWA VWC VWT VWG VYA VYC VYT VYG VAK VAM VAR VAS VAW VAY VCK VCM VCR VCS VCW VCY VTK VTM VTR VTS VTW VTY VGK VGM VGR VGS VGW VGY KBA KBC KBT KBG KDA KDC KDT KDG KHA KHC KHT KHG KVA KVC KVT KVG KAB KAD KAH KAV KCB KCD KCH KCV KTB KTD KTH KTV KGB KGD KGH KGV MBA MBC MBT MBG MDA MDC MDT MDG MHA MHC MHT MHG MVA MVC MVT MVG MAB MAD MAH MAV MCB MCD MCH MCV MTB MTD MTH MTV MGB MGD MGH MGV RBA RBC RBT RBG RDA RDC RDT RDG RHA RHC RHT RHG RVA RVC RVT RVG RAB RAD RAH RAV RCB RCD RCH RCV RTB RTD RTH RTV RGB RGD RGH RGV SBA SBC SBT SBG SDA SDC SDT SDG SHA SHC SHT SHG SVA SVC SVT SVG SAB SAD SAH SAV SCB SCD SCH SCV STB STD STH STV SGB SGD SGH SGV WBA WBC WBT WBG WDA WDC WDT WDG WHA WHC WHT WHG WVA WVC WVT WVG WAB WAD WAH WAV WCB WCD WCH WCV WTB WTD WTH WTV WGB WGD WGH WGV YBA YBC YBT YBG YDA YDC YDT YDG YHA YHC YHT YHG YVA YVC YVT YVG YAB YAD YAH YAV YCB YCD YCH YCV YTB YTD YTH YTV YGB YGD YGH YGV ABK ABM ABR ABS ABW ABY ADK ADM ADR ADS ADW ADY AHK AHM AHR AHS AHW AHY AVK AVM AVR AVS AVW AVY AKB AKD AKH AKV AMB AMD AMH AMV ARB ARD ARH ARV ASB ASD ASH ASV AWB AWD AWH AWV AYB AYD AYH AYV CBK CBM CBR CBS CBW CBY CDK CDM CDR CDS CDW CDY CHK CHM CHR CHS CHW CHY CVK CVM CVR CVS CVW CVY CKB CKD CKH CKV CMB CMD CMH CMV CRB CRD CRH CRV CSB CSD CSH CSV CWB CWD CWH CWV CYB CYD CYH CYV TBK TBM TBR TBS TBW TBY TDK TDM TDR TDS TDW TDY THK THM THR THS THW THY TVK TVM TVR TVS TVW TVY TKB TKD TKH TKV TMB TMD TMH TMV TRB TRD TRH TRV TSB TSD TSH TSV TWB TWD TWH TWV TYB TYD TYH TYV GBK GBM GBR GBS GBW GBY GDK GDM GDR GDS GDW GDY GHK GHM GHR GHS GHW GHY GVK GVM GVR GVS GVW GVY GKB GKD GKH GKV GMB GMD GMH GMV GRB GRD GRH GRV GSB GSD GSH GSV GWB GWD GWH GWV GYB GYD GYH GYV NAA NAC NAT NAG NCA NCC NCT NCG NTA NTC NTT NTG NGA NGC NGT NGG KKA KKC KKT KKG KMA KMC KMT KMG KRA KRC KRT KRG KSA KSC KST KSG KWA KWC KWT KWG KYA KYC KYT KYG KAK KAM KAR KAS KAW KAY KCK KCM KCR KCS KCW KCY KTK KTM KTR KTS KTW KTY KGK KGM KGR KGS KGW KGY MKA MKC MKT MKG MMA MMC MMT MMG MRA MRC MRT MRG MSA MSC MST MSG MWA MWC MWT MWG MYA MYC MYT MYG MAK MAM MAR MAS MAW MAY MCK MCM MCR MCS MCW MCY MTK MTM MTR MTS MTW MTY MGK MGM MGR MGS MGW MGY RKA RKC RKT RKG RMA RMC RMT RMG RRA RRC RRT RRG RSA RSC RST RSG RWA RWC RWT RWG RYA RYC RYT RYG RAK RAM RAR RAS RAW RAY RCK RCM RCR RCS RCW RCY RTK RTM RTR RTS RTW RTY RGK RGM RGR RGS RGW RGY SKA SKC SKT SKG SMA SMC SMT SMG SRA SRC SRT SRG SSA SSC SST SSG SWA SWC SWT SWG SYA SYC SYT SYG SAK SAM SAR SAS SAW SAY SCK SCM SCR SCS SCW SCY STK STM STR STS STW STY SGK SGM SGR SGS SGW SGY WKA WKC WKT WKG WMA WMC WMT WMG WRA WRC WRT WRG WSA WSC WST WSG WWA WWC WWT WWG WYA WYC WYT WYG WAK WAM WAR WAS WAW WAY WCK WCM WCR WCS WCW WCY WTK WTM WTR WTS WTW WTY WGK WGM WGR WGS WGW WGY YKA YKC YKT YKG YMA YMC YMT YMG YRA YRC YRT YRG YSA YSC YST YSG YWA YWC YWT YWG YYA YYC YYT YYG YAK YAM YAR YAS YAW YAY YCK YCM YCR YCS YCW YCY YTK YTM YTR YTS YTW YTY YGK YGM YGR YGS YGW YGY ANA ANC ANT ANG AKK AKM AKR AKS AKW AKY AMK AMM AMR AMS AMW AMY ARK ARM ARR ARS ARW ARY ASK ASM ASR ASS ASW ASY AWK AWM AWR AWS AWW AWY AYK AYM AYR AYS AYW AYY AAN ACN ATN AGN CNA CNC CNT CNG CKK CKM CKR CKS CKW CKY CMK CMM CMR CMS CMW CMY CRK CRM CRR CRS CRW CRY CSK CSM CSR CSS CSW CSY CWK CWM CWR CWS CWW CWY CYK CYM CYR CYS CYW CYY CAN CCN CTN CGN TNA TNC TNT TNG TKK TKM TKR TKS TKW TKY TMK TMM TMR TMS TMW TMY TRK TRM TRR TRS TRW TRY TSK TSM TSR TSS TSW TSY TWK TWM TWR TWS TWW TWY TYK TYM TYR TYS TYW TYY TAN TCN TTN TGN GNA GNC GNT GNG GKK GKM GKR GKS GKW GKY GMK GMM GMR GMS GMW GMY GRK GRM GRR GRS GRW GRY GSK GSM GSR GSS GSW GSY GWK GWM GWR GWS GWW GWY GYK GYM GYR GYS GYW GYY GAN GCN GTN GGN BAA BAC BAT BAG BCA BCC BCT BCG BTA BTC BTT BTG BGA BGC BGT BGG DAA DAC DAT DAG DCA DCC DCT DCG DTA DTC DTT DTG DGA DGC DGT DGG HAA HAC HAT HAG HCA HCC HCT HCG HTA HTC HTT HTG HGA HGC HGT HGG VAA VAC VAT VAG VCA VCC VCT VCG VTA VTC VTT VTG VGA VGC VGT VGG ABA ABC ABT ABG ADA ADC ADT ADG AHA AHC AHT AHG AVA AVC AVT AVG AAB AAD AAH AAV ACB ACD ACH ACV ATB ATD ATH ATV AGB AGD AGH AGV CBA CBC CBT CBG CDA CDC CDT CDG CHA CHC CHT CHG CVA CVC CVT CVG CAB CAD CAH CAV CCB CCD CCH CCV CTB CTD CTH CTV CGB CGD CGH CGV TBA TBC TBT TBG TDA TDC TDT TDG THA THC THT THG TVA TVC TVT TVG TAB TAD TAH TAV TCB TCD TCH TCV TTB TTD TTH TTV TGB TGD TGH TGV GBA GBC GBT GBG GDA GDC GDT GDG GHA GHC GHT GHG GVA GVC GVT GVG GAB GAD GAH GAV GCB GCD GCH GCV GTB GTD GTH GTV GGB GGD GGH GGV KAA KAC KAT KAG KCA KCC KCT KCG KTA KTC KTT KTG KGA KGC KGT KGG MAA MAC MAT MAG MCA MCC MCT MCG MTA MTC MTT MTG MGA MGC MGT MGG RAA RAC RAT RAG RCA RCC RCT RCG RTA RTC RTT RTG RGA RGC RGT RGG SAA SAC SAT SAG SCA SCC SCT SCG STA STC STT STG SGA SGC SGT SGG WAA WAC WAT WAG WCA WCC WCT WCG WTA WTC WTT WTG WGA WGC WGT WGG YAA YAC YAT YAG YCA YCC YCT YCG YTA YTC YTT YTG YGA YGC YGT YGG AKA AKC AKT AKG AMA AMC AMT AMG ARA ARC ART ARG ASA ASC AST ASG AWA AWC AWT AWG AYA AYC AYT AYG AAK AAM AAR AAS AAW AAY ACK ACM ACR ACS ACW ACY ATK ATM ATR ATS ATW ATY AGK AGM AGR AGS AGW AGY CKA CKC CKT CKG CMA CMC CMT CMG CRA CRC CRT CRG CSA CSC CST CSG CWA CWC CWT CWG CYA CYC CYT CYG CAK CAM CAR CAS CAW CAY CCK CCM CCR CCS CCW CCY CTK CTM CTR CTS CTW CTY CGK CGM CGR CGS CGW CGY TKA TKC TKT TKG TMA TMC TMT TMG TRA TRC TRT TRG TSA TSC TST TSG TWA TWC TWT TWG TYA TYC TYT TYG TAK TAM TAR TAS TAW TAY TCK TCM TCR TCS TCW TCY TTK TTM TTR TTS TTW TTY TGK TGM TGR TGS TGW TGY GKA GKC GKT GKG GMA GMC GMT GMG GRA GRC GRT GRG GSA GSC GST GSG GWA GWC GWT GWG GYA GYC GYT GYG GAK GAM GAR GAS GAW GAY GCK GCM GCR GCS GCW GCY GTK GTM GTR GTS GTW GTY GGK GGM GGR GGS GGW GGY AAA AAC AAT AAG ACA ACC ACT ACG ATA ATC ATT ATG AGA AGC AGT AGG CAA CAC CAT CAG CCA CCC CCT CCG CTA CTC CTT CTG CGA CGC CGT CGG TAA TAC TAT TAG TCA TCC TCT TCG TTA TTC TTT TTG TGA TGC TGT TGG GAA GAC GAT GAG GCA GCC GCT GCG GTA GTC GTT GTG GGA GGC GGT GGG ������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/SiRNA��������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16103� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/SiRNA/Ruleset������������������������������������������������������������000755��000766��000024�� 0�13155576320� 17526� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/SiRNA/Ruleset/saigo.pm���������������������������������������������������000444��000766��000024�� 12730�13155576320� 21346� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Tools::SiRNA::Ruleset::saigo # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Donald Jackson, donald.jackson@bms.com # # Copyright Bristol-Myers Squibb # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::SiRNA::Ruleset::saigo - Perl object implementing the Saigo group's rules for designing small inhibitory RNAs =head1 SYNOPSIS Do not use this module directly. Instead, use Bio::Tools::SiRNA and specify the saigo ruleset: use Bio::Tools::SiRNA; my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq, -rules => 'saigo' ); my @pairs = $sirna_designer->design; foreach $pair (@pairs) { my $sense_oligo_sequence = $pair->sense->seq; my $antisense_oligo_sequence = $pair->antisense->seq; # print out results print join ("\t", $pair->start, $pair->end, $pair->rank, $sense_oligo_sequence, $antisense_oligo_sequence), "\n"; } =head1 DESCRIPTION This package implements the rules for designing siRNA reagents published by Ui-Tei et al (2004). The rules are: =over 5 =item 1. The first base in the sense strand of the duplex must be a G or C =item 2. The first base in the antisense strand of the duplex must be an A or U =item 3. The first 7 nucleotides in the antisense strand of the duplex must be A or U =item 4. There cannot be more than 9 consecutive G or C nucleotides =item 5. The first 12 nucleotides in the sense strand of the duplex should have 33-66% GC =back The module inherits from Bio::Tools::SiRNA. See the documentation for that module for information on how to specify the target and recover the SiRNA duplex information. =head2 EXPORT None. =head1 SEE ALSO L<Bio::Tools::SiRNA>, L<Bio::SeqFeature::SiRNA::Pair>, L<Bio::SeqFeature::SiRNA::Oligo>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Donald Jackson (donald.jackson@bms.com) =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::SiRNA::Ruleset::saigo; use strict; use warnings; use base qw(Bio::Tools::SiRNA); =head2 new Title : new Usage : Do not call directly - use Bio::Tools::SiRNA->new instead. Returns : Bio::Tools::SiRNA::Ruleset::saigo object Args : none =cut sub new { my ($proto, %args) = @_; my $class = ref($proto) || $proto; $args{'RULES'} = 'saigo'; return $class->SUPER::new(%args); } sub _get_oligos { my ($self) = @_; my ($targseq, $targstart) = $self->_get_targetregion; foreach my $i (0 .. (length($targseq) - 23)) { my $testseq = substr($targseq, $i, 23); $self->add_oligos($testseq, $targstart + $i + 1) if ($self->_oligo_ok($testseq)); } } sub _get_sense { my ($self, $target) = @_; #trim off 1st 2 nt to get overhang $target =~ s/^..//; #convert T's to U's (transcribe) $target =~ s/T/U/gi; return $target; } sub _get_anti { my ($self, $target) = @_; my @target = split(//, $target); my ($nt,@antitarget); while ($nt = pop @target) { push(@antitarget, $self->_comp($nt)); } my $anti = join('', @antitarget); #trim off 1st 2 nt to get overhang $anti =~ s/^..//; #convert T's to U's $anti =~ s/T/U/gi; return $anti; } sub _oligo_ok { my ($self, $testseq) = @_; $self->debug("Testing $testseq...\n"); my @testseq = split(//, $testseq); # is 5p end of sense strand a G/C? unless ($testseq[2] =~ /[GC]/i) { $self->debug("No G/C at sense 5' end\n"); return 0; } # is 5p end of antisense strand an A/T? unless ($testseq[20] =~ /[AT]/i) { $self->debug("No A/T at antisense 5' end\n"); return 0; } # are 4 of the last 7 bases in the duplex A/T? my $atcount_3p = grep { /[AT]/i } @testseq[14 .. 20]; unless ($atcount_3p >= 4) { $self->debug("Found $atcount_3p A/T in last 7 bases of duplex\n"); return 0; } # what is gc fraction in rest of duplex? Target: 33 to 66 pct gc (4-8 of 12) my $gccount_5p = grep { /[GC]/i } @testseq[2 .. 13]; if ($gccount_5p < 4) { $self->debug("Found only $gccount_5p GCs in 5p end of duplex\n"); return 0; } if ($gccount_5p > 8) { $self->debug("Found only $gccount_5p GCs in 5p end of duplex\n"); return 0; } # no more than 9 consecutive GC if ($testseq =~ /[GC]{9,}?/i) { $self->debug("Found more than 9 consecutive GCs\n"); return 0; } $self->debug("Oligo passed \n"); return 1; } 1; ����������������������������������������BioPerl-1.007002/Bio/Tools/SiRNA/Ruleset/tuschl.pm��������������������������������������������������000444��000766��000024�� 12656�13155576320� 21555� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # # BioPerl module for Bio::Tools::SiRNA::Ruleset::tuschl # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Donald Jackson, donald.jackson@bms.com # # Copyright Bristol-Myers Squibb # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::SiRNA::Ruleset::tuschl - Perl object implementing the tuschl group's rules for designing small inhibitory RNAs =head1 SYNOPSIS Do not use this module directly. Instead, use Bio::Tools::SiRNA and specify the tuschl ruleset: use Bio::Tools::SiRNA; my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq, -rules => 'tuschl' ); my @pairs = $sirna_designer->design; foreach $pair (@pairs) { my $sense_oligo_sequence = $pair->sense->seq; my $antisense_oligo_sequence = $pair->antisense->seq; # print out results print join ("\t", $pair->start, $pair->end, $pair->rank, $sense_oligo_sequence, $antisense_oligo_sequence), "\n"; } =head1 DESCRIPTION This package implements the rules for designing siRNA reagents developed by Tuschl and colleagues (see http://www.rockefeller.edu/labheads/tuschl/sirna.html). It looks for oligos that match the following patterns in the target sequence: 1. AA(N19)TT (rank 1) 2. AA(N21) (rank 2) 3. NA(N21) (rank 3) The package also supports selection of siRNA seqences that can be transcribed by pol3: A[A,G]N17[C,T] =head1 SEE ALSO L<Bio::Tools::SiRNA>, L<Bio::SeqFeature::SiRNA::Pair>, L<Bio::SeqFeature::SiRNA::Oligo>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Donald Jackson (donald.jackson@bms.com) =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::SiRNA::Ruleset::tuschl; use strict; use warnings; use base qw(Bio::Tools::SiRNA); our %PATTERNS = ( 1 => '(AA.{19}TT)', 2 => '(AA.{19}[ACG][ACG])', 3 => '([CGT]A.{21})', Pol3 => '(.A[AG].{17}[CT]..)' ); our $DEFAULT_CUTOFF = 2; =head2 new Title : new Usage : Do not call directly - use Bio::Tools::SiRNA->new instead. Returns : Bio::Tools::SiRNA::Ruleset::saigo object Args : none =cut sub new { my ($proto, %args) = @_; my $class = ref($proto) || $proto; $args{'RULES'} = 'tuschl'; return $class->SUPER::new(%args); } sub _regex { my ($self, $rank) = @_; return $PATTERNS{$rank}; } sub cutoff { my ($self, $cutoff) = @_; if ($cutoff) { $self->{'cutoff'} = $cutoff; } elsif (!$self->{'cutoff'}) { $self->{'cutoff'} = $DEFAULT_CUTOFF; } return $self->{'cutoff'}; } sub _get_oligos { #use regular expressions to pull out oligos my ($self) = @_; my @ranks; if ($self->cutoff eq 'pol3') { @ranks = ('pol3'); } else { @ranks = (1 .. $self->cutoff); } foreach my $rank (@ranks) { my $regex = $self->_regex($rank); #my @exclude; # my ($targregion) = grep { $_->primary_tag eq 'Target' } $self->target->top_SeqFeatures; # my $seq = $targregion->seq->seq; # # but this way I loose start info # my $targstart = $targregion->start; my ($seq, $targstart) = $self->_get_targetregion(); while ( $seq =~ /(.*?)$regex/gi ) { my $target = $2; # check for too many Gs (or Cs on the other strand) my $max_g = $self->gstring; next if ( $target =~ /G{$max_g,}/io ); next if ( $target =~ /C{$max_g,}/io ); # skip Ns (for filtering) next if ( $target =~ /N/i); my $start = length($1) + $targstart; my $stop = $start + length($target) -1; my @gc = ( $target =~ /G|C/gi); my $fxGC = sprintf("%2.2f", (scalar(@gc) / length($target))); next if ($fxGC < $self->min_gc); next if ($fxGC > $self->max_gc); $self->add_oligos($target, $start, $rank); } } } sub _get_sense { my ($self, $target) = @_; # trim off 1st 2 nt to get overhang $target =~ s/^..//; # convert T's to U's (transcribe) $target =~ s/T/U/gi; # force last 2 nt to be T's $target =~ s/..$/TT/; return $target; } sub _get_anti { my ($self, $target) = @_; my @target = split(//, $target); my ($nt,@antitarget); while ($nt = pop @target) { push(@antitarget, $self->_comp($nt)); } my $anti = join('', @antitarget); # trim off 1st 2 nt to get overhang $anti =~ s/^..//; # convert T's to U's $anti =~ s/T/U/gi; # convert last 2 NT's to T $anti =~ s/..$/TT/; return $anti; } 1; ����������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Signalp������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16564� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Signalp/ExtendedSignalp.pm�����������������������������������������������000444��000766��000024�� 41644�13155576320� 22366� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Signalp::ExtendedSignalp # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Emmanuel Quevillon <emmanuel.quevillon@versailles.inra.fr> # # Copyright Emmanuel Quevillon # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Tools::Signalp::ExtendedSignalp - enhanced parser for Signalp output =head1 SYNOPSIS use Bio::Tools::Signalp::ExtendedSignalp; my $params = [qw(maxC maxY maxS meanS D)]; my $parser = new Bio::Tools::Signalp::ExtendedSignalp( -fh => $filehandle -factors => $params ); $parser->factors($params); while( my $sp_feat = $parser->next_feature ) { #do something #eg push @sp_feat, $sp_feat; } =head1 DESCRIPTION # Please direct questions and support issues to I<bioperl-l@bioperl.org> Parser module for Signalp. Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp originally written by Marc Sohrmann (ms2 a sanger.ac.uk) Written in BioPipe by Balamurugan Kumarasamy (savikalpa a fugu-sg.org) Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org) You may distribute this module under the same terms as perl itself Compared to the original SignalP, this method allow the user to filter results out based on maxC maxY maxS meanS and D factor cutoff for the Neural Network (NN) method only. The HMM method does not give any filters with 'YES' or 'NO' as result. The user must be aware that the filters can only by applied on NN method. Also, to ensure the compatibility with original Signalp parsing module, the user must know that by default, if filters are empty, max Y and mean S filters are automatically used to filter results. If the used gives a list, then the parser will only report protein having 'YES' for each factor. This module supports parsing for full, summary and short output form signalp. Actually, full and summary are equivalent in terms of filtering results. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Based on the Bio::Tools::Signalp module Emmanuel Quevillon <emmanuel.quevillon@versailles.inra.fr> =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Signalp::ExtendedSignalp; use strict; use Data::Dumper; use Bio::SeqFeature::Generic; # don't need Bio::Root::Root/IO (already in inheritance tree) use base qw(Bio::Tools::Signalp Bio::Tools::AnalysisResult); #Supported arguments my $FACTS = { 'maxC' => 1, 'maxS' => 1, 'maxY' => 1, 'meanS' => 1, 'D' => 1, }; =head2 new Title : new Usage : my $obj = new Bio::Tools::Signalp::ExtendedSignalp(); Function: Builds a new Bio::Tools::Signalp::ExtendedSignalp object Returns : Bio::Tools::Signalp::ExtendedSignalp Args : -fh/-file => $val, # for initing input, see Bio::Root::IO =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); my $factors = $self->_rearrange([qw(FACTORS)], @args); #To behave like the parent module (Bio::Tools::Signalp) we default factors to these two factors if($factors && scalar(@$factors)){ $factors = $factors; } else{ $factors = [qw(maxY meanS)]; } $factors && $self->factors($factors); return $self; } =head2 next_feature Title : next_feature Usage : my $feat = $signalp->next_feature Function: Get the next result feature from parser data Returns : Bio::SeqFeature::Generic Args : none =cut sub next_feature { my ($self) = @_; if(!$self->_parsed()){ $self->_parse(); } return shift @{$self->{_features}} || undef; } =head2 _filterok Title : _filterok Usage : my $feat = $signalp->_filterok Function: Check if the factors required by the user are all ok. Returns : 1/0 Args : hash reference =cut sub _filterok { my($self, $hash) = @_; #We hope everything will be fine ;) my $bool = 1; #If the user did not give any filter, we keep eveything return $bool unless keys %{$self->{_factors}}; #If only one of the factors parsed is equal to NO based on the user factors cutoff #Then the filter is not ok. foreach my $fact (keys %{$self->factors()}){ if(exists($hash->{$fact}) && $hash->{$fact} =~ /^N/){ $bool = 0; } } return $bool; } =head2 factors Title : factors Usage : my $feat = $signalp->factors Function: Get/Set the filters required from the user Returns : hash Args : array reference =cut sub factors { my($self, $array) = @_; if($array){ $self->{_factors} = { }; foreach my $f (@$array){ if(exists($FACTS->{$f})){ $self->{_factors}->{$f} = 1; } else{ $self->throw("[$f] incorrect factor. Supported:\n- ".join("\n- ", keys %$FACTS)."\n"); } } } return $self->{_factors}; } =head2 _parsed Title : _parsed Usage : obj->_parsed() Function: Get/Set if the result is parsed or not Returns : 1/0 scalar Args : On set 1 =cut sub _parsed { my($self, $parsed) = @_; if(defined($parsed)){ $self->{_parsed} = $parsed; } return $self->{_parsed}; } =head2 _parse Title : _parse Usage : obj->_parse Function: Parse the SignalP result Returns : Args : =cut sub _parse { my($self) = @_; #Let's read the file... while (my $line = $self->_readline()) { chomp $line; #We want to be sure to catch the first non empty line to be ablte to determine #which format we are working with... next unless ($line =~ /^>(\S+)|^# SignalP-[NHM]+ \S+ predictions/); if($line =~ /^>(\S+)/){ $self->_pushback($line); $self->_parse_summary_format(); last; } elsif($line =~ /^# SignalP-[NHM]+ \S+ predictions/){ $self->_pushback($line); $self->_parse_short_format(); last; } else{ $self->throw("Unable to determine the format type."); } } return; } =head2 _parse_summary_format Title : _parse_summary_format Usage : $self->_parse_summary_format Function: Method to parse summary/full format from signalp output It automatically fills filtered features. Returns : Args : =cut sub _parse_summary_format { my($self) = @_; my $feature = undef; my $ok = 0; while(my $line = $self->_readline()){ if($line =~ /^SignalP-NN result:/){ $self->_pushback($line); $feature = $self->_parse_nn_result($feature); } if($line =~ /^SignalP-HMM result:/){ $self->_pushback($line); $feature = $self->_parse_hmm_result($feature); } if($line =~ /^---------/ && $feature){ my $new_feature = $self->create_feature($feature); push @{$self->{_features}}, $new_feature if $new_feature; $feature = undef; } } return; } =head2 _parse_nn_result Title : _parse_nn_result Usage : obj->_parse_nn_result Function: Parses the Neuronal Network (NN) part of the result Returns : Hash reference Args : =cut sub _parse_nn_result { my($self, $feature) = @_; my $ok = 0; my %facts; #SignalP-NN result: #>MGG_11635.5 length = 100 ## Measure Position Value Cutoff signal peptide? # max. C 37 0.087 0.32 NO # max. Y 37 0.042 0.33 NO # max. S 3 0.062 0.87 NO # mean S 1-36 0.024 0.48 NO # D 1-36 0.033 0.43 NO while(my $line = $self->_readline()){ chomp $line; if($line =~ /^SignalP-NN result:/){ $ok = 1; next; } $self->throw("Wrong line for parsing NN results.") unless $ok; if ($line=~/^\>(\S+)\s+length/) { $self->seqname($1); %facts = (); next; } elsif($line =~ /max\.\s+C\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) { $feature->{maxCprob} = $1; $facts{maxC} = $2; next; } elsif ($line =~ /max\.\s+Y\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) { $feature->{maxYprob} = $1; $facts{maxY} = $2; next; } elsif($line =~ /max\.\s+S\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) { $feature->{maxSprob} = $1; $facts{maxS} = $2; next; } elsif ($line=~/mean\s+S\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) { $feature->{meanSprob} = $1; $facts{meanS} = $2; next; } elsif ($line=~/\s+D\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) { $feature->{Dprob} = $1; $facts{D} = $2; next; } #If we don't have this line it means that all the factors cutoff are equal to 'NO' elsif ($line =~ /Most likely cleavage site between pos\.\s+(\d+)/) { #if($self->_filterok(\%facts)){ #$feature->{name} = $self->seqname(); #$feature->{start} = 1; $feature->{end} = $1 + 1; #To be consistent with end given in short format #} #return $feature; } elsif($line =~ /^\s*$/){ last; } } if($self->_filterok(\%facts)){ $feature->{name} = $self->seqname(); $feature->{start} = 1; $feature->{nnPrediction} = 'signal-peptide'; } return $feature; } =head2 _parse_hmm_result Title : _parse_hmm_result Usage : obj->_parse_hmm_result Function: Parses the Hiden Markov Model (HMM) part of the result Returns : Hash reference Args : =cut sub _parse_hmm_result { my ($self, $feature_hash) = @_; my $ok = 0; #SignalP-HMM result: #>MGG_11635.5 #Prediction: Non-secretory protein #Signal peptide probability: 0.000 #Signal anchor probability: 0.000 #Max cleavage site probability: 0.000 between pos. -1 and 0 while(my $line = $self->_readline()){ chomp $line; next if $line =~ /^\s*$/o; if($line =~ /^SignalP-HMM result:/){ $ok = 1; next; } $self->throw("Wrong line for parsing HMM result.") unless $ok; if($line =~ /^>(\S+)/){ #In case we already seen a name with NN results $feature_hash->{name} = $1 unless $self->seqname(); } elsif($line =~ /Prediction: (.+)$/){ $feature_hash->{hmmPrediction} = $1; } elsif($line =~ /Signal peptide probability: ([0-9\.]+)/){ $feature_hash->{peptideProb} = $1; } elsif($line =~ /Signal anchor probability: ([0-9\.]+)/){ $feature_hash->{anchorProb} = $1; } elsif($line =~ /Max cleavage site probability: (\S+) between pos. \S+ and (\S+)/){ $feature_hash->{cleavageSiteProb} = $1; #Strange case, if we don't have an end value in NN result (no nn method launched) #We try anyway to get an end value, unless this value is lower than 1 which is #the start $feature_hash->{end} = $2 if($2 > 1 && !$feature_hash->{end}); $feature_hash->{start} = 1 unless $feature_hash->{start}; last; } } return $feature_hash; } =head2 _parse_short_format Title : _parse_short_format Usage : $self->_parse_short_format Function: Method to parse short format from signalp output It automatically fills filtered features. Returns : Args : =cut sub _parse_short_format { my($self) = @_; my $ok = 0; my $method = undef; $self->{_oformat} = 'short'; #Output example # SignalP-NN euk predictions # SignalP-HMM euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? D ? # name ! Cmax pos ? Sprob ? #Q5A8M1_CANAL 0.085 27 N 0.190 35 N 0.936 27 Y 0.418 N 0.304 N Q5A8M1_CANAL Q 0.001 35 N 0.002 N #O74127_YARLI 0.121 21 N 0.284 21 N 0.953 11 Y 0.826 Y 0.555 Y O74127_YARLI S 0.485 23 N 0.668 Y #Q5VJ86_9PEZI 0.355 24 Y 0.375 24 Y 0.798 12 N 0.447 N 0.411 N Q5VJ86_9PEZI Q 0.180 23 N 0.339 N #Q5A8U5_CANAL 0.085 27 N 0.190 35 N 0.936 27 Y 0.418 N 0.304 N Q5A8U5_CANAL Q 0.001 35 N 0.002 N while(my $line = $self->_readline()){ chomp $line; next if $line =~ /^\s*$|^# name/; if($line =~ /^#/){ $method = $line =~ /SignalP-NN .+ SignalP-HMM/ ? 'both' : $line =~ /SignalP-NN/ ? 'nn' : 'hmm'; next; } #$self->throw("It looks like the format is not 'short' format.") unless($ok); my @data = split(/\s+/, $line); $self->seqname($data[0]); my $factors = { }; my $feature = { }; #NN results gives more fields than HMM if($method eq 'both' || $method eq 'nn'){ $feature->{maxCprob} = $data[1]; $factors->{maxC} = $data[3]; $feature->{maxYprob} = $data[4]; $factors->{maxY} = $data[6]; $feature->{maxSprob} = $data[7]; $factors->{maxS} = $data[9]; $feature->{meanSprob}= $data[10]; $factors->{meanS} = $data[11]; $feature->{Dprob} = $data[12]; $factors->{D} = $data[13]; #It looks like the max Y position is reported as the most likely cleavage position $feature->{end} = $data[5]; $feature->{nnPrediction} = 'signal-peptide'; if($method eq 'both'){ $feature->{hmmPrediction} = $data[15] eq 'Q' ? 'Non-secretory protein' : 'Signal peptide'; $feature->{cleavageSiteProb} = $data[16]; $feature->{peptideProb} = $data[19]; } } elsif($method eq 'hmm'){ #In short output anchor probability is not given $feature->{hmmPrediction} = $data[1] eq 'Q' ? 'Non-secretory protein' : 'Signal peptide'; $feature->{cleavageSiteProb} = $data[2]; $feature->{peptideProb} = $data[5]; #It looks like the max cleavage probability position is given by the Cmax proability $feature->{end} = $data[3]; } #Unfortunately, we cannot parse the filters for hmm method. if($self->_filterok($factors)){ $feature->{name} = $self->seqname(); $feature->{start} = 1; $feature->{source} = 'Signalp'; $feature->{primary} = 'signal_peptide'; $feature->{program} = 'Signalp'; $feature->{logic_name} = 'signal_peptide'; my $new_feat = $self->create_feature($feature); push @{$self->{_features}}, $new_feat if $new_feat; } } return; } =head2 create_feature Title : create_feature Usage : obj->create_feature(\%feature) Function: Internal(not to be used directly) Returns : Args : =cut sub create_feature { my ($self, $feat) = @_; #If we don't have neither start nor end, we return. unless($feat->{name} && $feat->{start} && $feat->{end}){ return; } # create feature object my $feature = Bio::SeqFeature::Generic->new( -seq_id => $feat->{name}, -start => $feat->{start}, -end => $feat->{end}, -score => defined($feat->{peptideProb}) ? $feat->{peptideProb} : '', -source => 'Signalp', -primary => 'signal_peptide', -logic_name => 'signal_peptide', ); $feature->add_tag_value('peptideProb', $feat->{peptideProb}); $feature->add_tag_value('anchorProb', $feat->{anchorProb}); $feature->add_tag_value('evalue',$feat->{anchorProb}); $feature->add_tag_value('percent_id','NULL'); $feature->add_tag_value("hid",$feat->{primary}); $feature->add_tag_value('signalpPrediction', $feat->{hmmPrediction}); $feature->add_tag_value('cleavageSiteProb', $feat->{cleavageSiteProb}) if($feat->{cleavageSiteProb}); $feature->add_tag_value('nnPrediction', $feat->{nnPrediction}) if($feat->{nnPrediction}); $feature->add_tag_value('maxCprob', $feat->{maxCprob}) if(defined($feat->{maxCprob})); $feature->add_tag_value('maxSprob', $feat->{maxSprob}) if(defined($feat->{maxSprob})); $feature->add_tag_value('maxYprob', $feat->{maxYprob}) if(defined($feat->{maxYprob})); $feature->add_tag_value('meanSprob', $feat->{meanSprob}) if(defined($feat->{meanSprob})); $feature->add_tag_value('Dprob', $feat->{Dprob}) if(defined($feat->{Dprob})); return $feature; } =head2 seqname Title : seqname Usage : obj->seqname($name) Function: Internal(not to be used directly) Returns : Args : =cut sub seqname{ my ($self,$seqname)=@_; if (defined($seqname)){ $self->{'seqname'} = $seqname; } return $self->{'seqname'}; } 1; ��������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Sim4���������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16003� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Sim4/Exon.pm�������������������������������������������������������������000444��000766��000024�� 12462�13155576320� 17434� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Sim4::Exon # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney-at-sanger.ac.uk> # and Hilmar Lapp <hlapp-at-gmx.net> # # Copyright Ewan Birney, Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Sim4::Exon - A single exon determined by an alignment =head1 SYNOPSIS # See Bio::Tools::Sim4::Results for a description of the context. # an instance of this class is-a Bio::SeqFeature::SimilarityPair # coordinates of the exon (recommended way): print "exon from ", $exon->start(), " to ", $exon->end(), "\n"; # the same (feature1() inherited from Bio::SeqFeature::FeaturePair) print "exon from ", $exon->feature1()->start(), " to ", $exon->feature1()->end(), "\n"; # also the same (query() inherited from Bio::SeqFeature::SimilarityPair): print "exon from ", $exon->query()->start(), " to ", $exon->query()->end(), "\n"; # coordinates on the matching EST (recommended way): print "matches on EST from ", $exon->est_hit()->start(), " to ", $exon->est_hit()->end(), "\n"; # the same (feature2() inherited from Bio::SeqFeature::FeaturePair) print "matches on EST from ", $exon->feature2()->start(), " to ", $exon->feature2()->end(), "\n"; # also the same (subject() inherited from Bio::SeqFeature::SimilarityPair): print "exon from ", $exon->subject()->start(), " to ", $exon->subject()->end(), "\n"; =head1 DESCRIPTION This class inherits from Bio::SeqFeature::SimilarityPair and represents an exon on a genomic sequence determined by similarity, that is, by aligning an EST sequence (using Sim4 in this case). Consequently, the notion of query and subject is always from the perspective of the genomic sequence: query refers to the genomic seq, subject to the aligned EST hit. Because of this, $exon-E<gt>start(), $exon-E<gt>end() etc will always return what you expect. To get the coordinates on the matching EST, refer to the properties of the feature returned by L<est_hit>(). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney, Hilmar Lapp Ewan Birney E<lt>birney-at-sanger.ac.ukE<gt> Hilmar Lapp E<lt>hlapp-at-gmx.netE<gt> or E<lt>hilmar.lapp-at-pharma.novartis.comE<gt>. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Sim4::Exon; use strict; use base qw(Bio::SeqFeature::SimilarityPair); sub new { my ($class,@args) = @_; my %param = @args; my $self = $class->SUPER::new(@args); my ($prim, $prim_tag, $source, $source_tag) = $self->_rearrange([qw(PRIMARY PRIMARY_TAG SOURCE SOURCE_TAG)], @args); $self->primary_tag('exon') unless $prim || $prim_tag; $self->source_tag('Sim4') unless $source || $source_tag; $self->strand(0) unless defined($self->strand()); $self->query(); return $self; } =head2 percentage_id Title : percentage_id Usage : $obj->percentage_id($newval) Function: This is a synonym for 100 * $obj->est_hit()->frac_identical(). Returns : value of percentage_id Args : newvalue (optional) =cut sub percentage_id { my ($self, @args) = @_; my $frac; my $val; my $delegated = 0; if(@args) { $frac = $args[0]; $frac /= 100.0 if defined($frac); } if($self->query()->can('frac_identical')) { if(defined($frac)) { $self->query()->frac_identical($frac); } $val = 100.0 * $self->query()->frac_identical(); $delegated = 1; } if($self->est_hit()->can('frac_identical')) { if(defined($frac)) { $self->est_hit()->frac_identical($frac); } # this intentiously overwrites previous $val $val = 100.0 * $self->est_hit()->frac_identical(); $delegated = 1; } if(! $delegated) { if(@args) { $val = shift(@args); $self->{'percentage_id'} = $val; } else { $val = $self->{'percentage_id'}; } } return $val; } =head2 est_hit Title : est_hit Usage : $est_feature = $obj->est_hit(); Function: Returns the EST hit pointing to (i.e., aligned to by Sim4) this exon (i.e., genomic region). At present, merely a synonym for $obj->feature2(). Returns : An Bio::SeqFeatureI implementing object. Args : =cut sub est_hit { my $self = shift; return $self->feature2(@_); } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Sim4/Results.pm����������������������������������������������������������000444��000766��000024�� 35540�13155576320� 20166� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Sim4::Results # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ewan Birney <birney-at-sanger.ac.uk> # and Hilmar Lapp <hlapp-at-gmx.net> # # Copyright Ewan Birney and Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Sim4::Results - Results of one Sim4 run =head1 SYNOPSIS # to preset the order of EST and genomic file as given on the sim4 # command line: my $sim4 = Bio::Tools::Sim4::Results->new(-file => 'result.sim4', -estfirst => 1); # to let the order be determined automatically (by length comparison): $sim4 = Bio::Tools::Sim4::Results->new( -file => 'sim4.results' ); # filehandle: $sim4 = Bio::Tools::Sim4::Results->new( -fh => \*INPUT ); # parse the results while(my $exonset = $sim4->next_exonset()) { # $exonset is-a Bio::SeqFeature::Generic with Bio::Tools::Sim4::Exons # as sub features print "Delimited on sequence ", $exonset->seq_id(), "from ", $exonset->start(), " to ", $exonset->end(), "\n"; foreach my $exon ( $exonset->sub_SeqFeature() ) { # $exon is-a Bio::SeqFeature::FeaturePair print "Exon from ", $exon->start, " to ", $exon->end, " on strand ", $exon->strand(), "\n"; # you can get out what it matched using the est_hit attribute my $homol = $exon->est_hit(); print "Matched to sequence ", $homol->seq_id, " at ", $homol->start," to ", $homol->end, "\n"; } } # essential if you gave a filename at initialization (otherwise the file # stays open) $sim4->close(); =head1 DESCRIPTION The sim4 module provides a parser and results object for sim4 output. The sim4 results are specialised types of SeqFeatures, meaning you can add them to AnnSeq objects fine, and manipulate them in the "normal" seqfeature manner. The sim4 Exon objects are Bio::SeqFeature::FeaturePair inherited objects. The $esthit = $exon-E<gt>est_hit() is the alignment as a feature on the matching object (normally, an EST), in which the start/end points are where the hit lies. To make this module work sensibly you need to run sim4 genomic.fasta est.database.fasta or sim4 est.fasta genomic.database.fasta To get the sequence identifiers recorded for the first sequence, too, use A=4 as output option for sim4. One fiddle here is that there are only two real possibilities to the matching criteria: either one sequence needs reversing or not. Because of this, it is impossible to tell whether the match is in the forward or reverse strand of the genomic DNA. We solve this here by assuming that the genomic DNA is always forward. As a consequence, the strand attribute of the matching EST is unknown, and the strand attribute of the genomic DNA (i.e., the Exon object) will reflect the direction of the hit. See the documentation of parse_next_alignment() for abilities of the parser to deal with the different output format options of sim4. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ewan Birney, Hilmar Lapp Ewan Birney E<lt>birney-at-sanger.ac.ukE<gt> Hilmar Lapp E<lt>hlapp-at-gmx.netE<gt> or E<lt>hilmar.lapp-at-pharma.novartis.comE<gt>. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Sim4::Results; use strict; use File::Basename; use Bio::Root::Root; use Bio::Tools::Sim4::Exon; use base qw(Bio::Tools::AnalysisResult); sub _initialize_state { my($self,@args) = @_; # call the inherited method first my $make = $self->SUPER::_initialize_state(@args); my ($est_is_first) = $self->_rearrange([qw(ESTFIRST)], @args); delete($self->{'_est_is_first'}); $self->{'_est_is_first'} = $est_is_first if(defined($est_is_first)); $self->analysis_method("Sim4"); } =head2 analysis_method Usage : $sim4->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /sim4/i. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method && ($method !~ /sim4/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head2 parse_next_alignment Title : parse_next_alignment Usage : @exons = $sim4_result->parse_next_alignment; foreach $exon (@exons) { # do something } Function: Parses the next alignment of the Sim4 result file and returns the found exons as an array of Bio::Tools::Sim4::Exon objects. Call this method repeatedly until an empty array is returned to get the results for all alignments. The $exon->seq_id() attribute will be set to the identifier of the respective sequence for both sequences if A=4 was used in the sim4 run, and otherwise for the second sequence only. If the output does not contain the identifier, the filename stripped of path and extension is used instead. In addition, the full filename will be recorded for both features ($exon inherits off Bio::SeqFeature::SimilarityPair) as tag 'filename'. The length is accessible via the seqlength() attribute of $exon->query() and $exon->est_hit(). Note that this method is capable of dealing with outputs generated with format 0,1,3, and 4 (via the A=n option to sim4). It automatically determines which of the two sequences has been reversed, and adjusts the coordinates for that sequence. It will also detect whether the EST sequence(s) were given as first or as second file to sim4, unless this has been specified at creation time of the object. Example : Returns : An array of Bio::Tools::Sim4::Exon objects Args : =cut sub parse_next_alignment { my ($self) = @_; my @exons = (); my %seq1props = (); my %seq2props = (); # we refer to the properties of each seq by reference my ($estseq, $genomseq, $to_reverse); my $started = 0; my $hit_direction = 1; my $output_fmt = 3; # same as 0 and 1 (we cannot deal with A=2 produced # output yet) while(defined($_ = $self->_readline())) { #chomp(); # # bascially, each sim4 'hit' starts with seq1... # /^seq1/ && do { if($started) { $self->_pushback($_); last; } $started = 1; # filename and length of seq 1 /^seq1\s+=\s+(\S+)\,\s+(\d+)/ || $self->throw("Sim4 parsing error on seq1 [$_] line. Sorry!"); $seq1props{'filename'} = $1; $seq1props{'length'} = $2; next; }; /^seq2/ && do { # the second hit has also the database name in the >name syntax # (in brackets). /^seq2\s+=\s+(\S+)\s+\(>?(\S+)\s*\)\,\s+(\d+)/|| $self->throw("Sim4 parsing error on seq2 [$_] line. Sorry!"); $seq2props{'filename'} = $1; $seq2props{'seqname'} = $2; $seq2props{'length'} = $3; next; }; if(/^>(\S+)\s*(.*)$/) { # output option was A=4, which not only gives the complete # description lines, but also causes the longer sequence to be # reversed if the second file contained one (genomic) sequence $seq1props{'seqname'} = $1; $seq1props{'description'} = $2 if $2; $output_fmt = 4; # we handle seq1 and seq2 both here if(defined($_ = $self->_readline()) && (/^>(\S+)\s*(.*)$/)) { $seq2props{'seqname'} = $1; # redundant, since already set above $seq2props{'description'} = $2 if $2; } next; } /^\(complement\)/ && do { $hit_direction = -1; next; }; # this matches # start-end (start-end) pctid% if(/(\d+)-(\d+)\s+\((\d+)-(\d+)\)\s+(\d+)%/) { $seq1props{'start'} = $1; $seq1props{'end'} = $2; $seq2props{'start'} = $3; $seq2props{'end'} = $4; my $pctid = $5; if(! defined($estseq)) { # for the first time here: need to set the references referring # to seq1 and seq2 if(! exists($self->{'_est_is_first'})) { # detect which one is the EST by looking at the lengths, # and assume that this holds throughout the entire result # file (i.e., when this method is called for the next # alignment, this will not be checked again) if($seq1props{'length'} > $seq2props{'length'}) { $self->{'_est_is_first'} = 0; } else { $self->{'_est_is_first'} = 1; } } if($self->{'_est_is_first'}) { $estseq = \%seq1props; $genomseq = \%seq2props; # if the EST is given first, A=4 selects the genomic # seq for being reversed (reversing the EST is default) $to_reverse = ($output_fmt == 4) ? $genomseq : $estseq; } else { $estseq = \%seq2props; $genomseq = \%seq1props; # if the EST is the second, A=4 does not change the # seq being reversed (always the EST is reversed) $to_reverse = $estseq; } } if($hit_direction == -1) { # we have to reverse the coordinates of one of both seqs my $tmp = $to_reverse->{'start'}; $to_reverse->{'start'} = $to_reverse->{'length'} - $to_reverse->{'end'} + 1; $to_reverse->{'end'} = $to_reverse->{'length'} - $tmp + 1; } # create and initialize the exon object my $exon = Bio::Tools::Sim4::Exon->new( '-start' => $genomseq->{'start'}, '-end' => $genomseq->{'end'}, '-strand' => $hit_direction); if(exists($genomseq->{'seqname'})) { $exon->seq_id($genomseq->{'seqname'}); } else { # take filename stripped of path as fall back my ($basename) = &File::Basename::fileparse($genomseq->{'filename'}, '\..*'); $exon->seq_id($basename); } $exon->feature1()->add_tag_value('filename', $genomseq->{'filename'}); # feature1 is supposed to be initialized to a Similarity object, # but we provide a safety net if($exon->feature1()->can('seqlength')) { $exon->feature1()->seqlength($genomseq->{'length'}); } else { $exon->feature1()->add_tag_value('SeqLength', $genomseq->{'length'}); } # create and initialize the feature wrapping the 'hit' (the EST) my $fea2 = Bio::SeqFeature::Similarity->new( '-start' => $estseq->{'start'}, '-end' => $estseq->{'end'}, '-strand' => 0, '-primary' => "aligning_EST"); if(exists($estseq->{'seqname'})) { $fea2->seq_id($estseq->{'seqname'}); } else { # take filename stripped of path as fall back my ($basename) = &File::Basename::fileparse($estseq->{'filename'}, '\..*'); $fea2->seq_id($basename); } $fea2->add_tag_value('filename', $estseq->{'filename'}); $fea2->seqlength($estseq->{'length'}); # store $exon->est_hit($fea2); # general properties $exon->source_tag($self->analysis_method()); $exon->percentage_id($pctid); $exon->score($exon->percentage_id()); # push onto array push(@exons, $exon); next; # back to while loop } } return @exons; } =head2 next_exonset Title : next_exonset Usage : $exonset = $sim4_result->parse_next_exonset; print "Exons start at ", $exonset->start(), "and end at ", $exonset->end(), "\n"; foreach $exon ($exonset->sub_SeqFeature()) { # do something } Function: Parses the next alignment of the Sim4 result file and returns the set of exons as a container of features. The container is itself a Bio::SeqFeature::Generic object, with the Bio::Tools::Sim4::Exon objects as sub features. Start, end, and strand of the container will represent the total region covered by the exons of this set. See the documentation of parse_next_alignment() for further reference about parsing and how the information is stored. Example : Returns : An Bio::SeqFeature::Generic object holding Bio::Tools::Sim4::Exon objects as sub features. Args : =cut sub next_exonset { my $self = shift; my $exonset; # get the next array of exons my @exons = $self->parse_next_alignment(); unless( @exons ) { return if eof($self->_fh); return $self->next_exonset; } # create the container of exons as a feature object itself, with the # data of the first exon for initialization $exonset = Bio::SeqFeature::Generic->new('-start' => $exons[0]->start(), '-end' => $exons[0]->end(), '-strand' => $exons[0]->strand(), '-primary' => "ExonSet"); $exonset->source_tag($exons[0]->source_tag()); $exonset->seq_id($exons[0]->seq_id()); # now add all exons as sub features, with enabling EXPANsion of the region # covered in total foreach my $exon (@exons) { $exonset->add_sub_SeqFeature($exon, 'EXPAND'); } return $exonset; } =head2 next_feature Title : next_feature Usage : while($exonset = $sim4->next_feature()) { # do something } Function: Does the same as L<next_exonset()>. See there for documentation of the functionality. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_exonset() at present. Example : Returns : A Bio::SeqFeature::Generic object. Args : =cut sub next_feature { my ($self,@args) = @_; # even though next_exonset doesn't expect any args (and this method # does neither), we pass on args in order to be prepared if this changes # ever return $self->next_exonset(@args); } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Spidey�������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16424� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Spidey/Exon.pm�����������������������������������������������������������000555��000766��000024�� 14226�13155576320� 20060� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Spidey::Exon # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ryan Golhar <golharam@umdnj.edu> # # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Spidey::Exon - A single exon determined by an alignment =head1 SYNOPSIS # See Bio::Tools::Spidey::Results for a description of the context. # an instance of this class is-a Bio::SeqFeature::SimilarityPair # coordinates of the exon (recommended way): print "exon from ", $exon->start(), " to ", $exon->end(), "\n"; # the same (feature1() inherited from Bio::SeqFeature::FeaturePair) print "exon from ", $exon->feature1()->start(), " to ", $exon->feature1()->end(), "\n"; # also the same (query() inherited from Bio::SeqFeature::SimilarityPair): print "exon from ", $exon->query()->start(), " to ", $exon->query()->end(), "\n"; # coordinates on the matching EST (recommended way): print "matches on EST from ", $exon->est_hit()->start(), " to ", $exon->est_hit()->end(), "\n"; # the same (feature2() inherited from Bio::SeqFeature::FeaturePair) print "matches on EST from ", $exon->feature2()->start(), " to ", $exon->feature2()->end(), "\n"; # also the same (subject() inherited from Bio::SeqFeature::SimilarityPair): print "exon from ", $exon->subject()->start(), " to ", $exon->subject()->end(), "\n"; =head1 DESCRIPTION This class inherits from Bio::SeqFeature::SimilarityPair and represents an exon on a genomic sequence determined by similarity, that is, by aligning an EST sequence (using Spidey in this case). Consequently, the notion of query and subject is always from the perspective of the genomic sequence: query refers to the genomic seq, subject to the aligned EST hit. Because of this, $exon-E<gt>start(), $exon-E<gt>end() etc will always return what you expect. To get the coordinates on the matching EST, refer to the properties of the feature returned by L<est_hit>(). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ryan Golhar Email golharam@umdnj.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Spidey::Exon; use strict; use base qw(Bio::SeqFeature::SimilarityPair); sub new { my ($class,@args) = @_; my %param = @args; my $self = $class->SUPER::new(@args); my ($prim, $prim_tag, $source, $source_tag) = $self->_rearrange([qw(PRIMARY PRIMARY_TAG SOURCE SOURCE_TAG)], @args); $self->primary_tag('exon') unless $prim || $prim_tag; $self->source_tag('Spidey') unless $source || $source_tag; $self->strand(0) unless defined($self->strand()); $self->query(); return $self; } =head2 percentage_id Title : percentage_id Usage : $obj->percentage_id Function: This is the percent id as reported by Spidey Returns : value of percentage_id Args : =cut sub percentage_id { my ($self, @args) = @_; my $val; if(@args) { $val = shift(@args); $self->{'percentage_id'} = $val; } else { $val = $self->{'percentage_id'}; } return $val; } =head2 est_hit Title : est_hit Usage : $est_feature = $obj->est_hit(); Function: Returns the EST hit pointing to (i.e., aligned to by Spidey) this exon (i.e., genomic region). At present, merely a synonym for $obj->feature2(). Returns : An Bio::SeqFeatureI implementing object. Args : =cut sub est_hit { my $self = shift; return $self->feature2(@_); } =head2 mismatches Title : mismatches Usage : $obj->mismatches; Function: Returns the mismatches of the cDNA to (i.e., aligned to by Spidey) this exon (i.e., genomic region). Returns : value of mismatches. Args : =cut sub mismatches { my ($self, @args) = @_; my $val; if(@args) { $val = shift(@args); $self->{'mismatches'} = $val; } else { $val = $self->{'mismatches'}; } return $val; } =head2 gaps Title : gaps Usage : $obj->gaps; Function: Returns the gaps of the cDNA to (i.e., aligned to by Spidey) this exon (i.e., genomic region). Returns : value of gaps. Args : =cut sub gaps { my ($self, @args) = @_; my $val; if(@args) { $val = shift(@args); $self->{'gaps'} = $val; } else { $val = $self->{'gaps'}; } return $val; } =head2 donor Title : donor Usage : $obj->donor; Function: Returns 0 if a splice donor site does not exist, or 1 if a splice donor site exists Returns : value of existence of donor splice site (0 or 1) Args : =cut sub donor { my ($self, @args) = @_; my $val; if (@args) { $val = shift @args; $self->{'donor'} = $val; } else { $val = $self->{'donor'}; } return $val; } =head2 acceptor Title : acceptor Usage : $obj->acceptor; Function: Returns 0 if a splice acceptor site does not exist, or 1 if a splice acceptor site exists Returns : value of existence of acceptor splice site (0 or 1) Args : =cut sub acceptor { my ($self, @args) = @_; my $val; if (@args) { $val = shift @args; $self->{'acceptor'} = $val; } else { $val = $self->{'acceptor'}; } return $val; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tools/Spidey/Results.pm��������������������������������������������������������000555��000766��000024�� 34377�13155576320� 20621� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tools::Spidey::Results # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Ryan Golhar <golharam@umdnj.edu> # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Spidey::Results - Results of a Spidey run =head1 SYNOPSIS use Bio::Tools::Spidey::Results; my $spidey = Bio::Tools::Spidey::Results->new(-file => 'result.spidey' ); # or my $spidey = Bio::Tools::Spidey::Results->new( -fh => \*INPUT ); # get the exons before doing anything else my $exonset = $spidey->next_exonset(); # parse the results my @exons = $exonset->sub_SeqFeature(); print "Total no of Exons: ", scalar(@exons), "\n"; print "Genomic sequence length: ", $spidey->genomic_dna_length(), "\n"; # $exonset is-a Bio::SeqFeature::Generic with Bio::Tools::Spidey::Exons # as sub features print "Delimited on sequence ", $exonset->seq_id(), " from ", $exonset->start(), " to ", $exonset->end(), "\n"; foreach my $exon ( $exonset->sub_SeqFeature() ) { # $exon is-a Bio::SeqFeature::FeaturePair print "Exon from ", $exon->start, " to ", $exon->end, " on strand ", $exon->strand(), "\n"; # you can get out what it matched using the est_hit attribute my $homol = $exon->est_hit(); print "Matched to sequence ", $homol->seq_id, " at ", $homol->start," to ", $homol->end, "\n"; } # essential if you gave a filename at initialization (otherwise # the file stays open) $spidey->close(); =head1 DESCRIPTION The spidey module provides a parser and results object for spidey output. The spidey results are specialised types of SeqFeatures, meaning you can add them to AnnSeq objects fine, and manipulate them in the "normal" seqfeature manner. The spidey Exon objects are Bio::SeqFeature::FeaturePair inherited objects. The $esthit = $exon-E<gt>est_hit() is the alignment as a feature on the matching object (normally, a cDNA), in which the start/end points are where the hit lies. To make this module work sensibly you need to run spidey -i genomic.fasta -m cDNA.fasta =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Ryan Golhar Email golharam@umdnj.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Spidey::Results; use strict; use File::Basename; use Bio::Root::Root; use Bio::Tools::Spidey::Exon; use base qw(Bio::Tools::AnalysisResult); sub _initialize_state { my($self,@args) = @_; # call the inherited method first my $make = $self->SUPER::_initialize_state(@args); # my ($est_is_first) = $self->_rearrange([qw(ESTFIRST)], @args); # delete($self->{'_est_is_first'}); # $self->{'_est_is_first'} = $est_is_first if(defined($est_is_first)); $self->analysis_method("Spidey"); } =head2 analysis_method Usage : $spidey->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /Spidey/i. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method && ($method !~ /Spidey/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head2 parse_next_alignment Title : parse_next_alignment Usage : @exons = $spidey_result->parse_next_alignment; foreach $exon (@exons) { # do something } Function: Parses the next alignment of the Spidey result file and returns the found exons as an array of Bio::Tools::Spidey::Exon objects. Call this method repeatedly until an empty array is returned to get the results for all alignments. Example : Returns : An array of Bio::Tools::Spidey::Exon objects Args : =cut sub parse_next_alignment { my ($self) = @_; # for strand 1 = plus, -1 = minus my ($started,$version,$strand, $exoncount) = (0,0,0,-1); my (%seq1props,%seq2props,@exons); # we refer to the properties of each seq by reference while(defined($_ = $self->_readline())) { chomp; # # bascially, parse a Spidey result... # # matches: --SPIDEY version 1.40-- if( /^--SPIDEY\s+version\s+(\d+\.\d+)--/) { if($started) { $self->_pushback($_); return \@exons; } $version = $1; if ($version != 1.40) { $self->throw("Spidey parser only designed to work with Spidey v1.40\n"); } $started = 1; } elsif (/^Genomic:\s+(\S+)\s.*,\s+(\d+)\sbp$/ ) { # matches: Genomic: lcl|some_name other information, 1234 bp # $seq1props{'filename'} = $1; $seq1props{'seqname'} = $1; $seq1props{'length'} = $2; $self->genomic_dna_length($seq1props{'length'}); } elsif( /^mRNA:\s+(\S+)\s.*,(?:\s+mRNA\s+sequence,)?\s(\d+)\sbp$/ ) { # matches: mRNA: # $seq2props{'filename'} = $1; $seq2props{'seqname'} = $1; $seq2props{'length'} = $2; } elsif( /^Strand:/ ) { if (/plus/) { $strand = 1; } else { $strand = -1; } } elsif( /^Number of exons: (\d+)/ ) { $exoncount = $1; my ($genomic_start, $genomic_stop, $cdna_start, $cdna_stop, $id, $mismatches, $gaps, $splice_donor, $splice_acceptor, $uncertain); # the next $exoncount lines contains information # about the matches of each exon. we should parse # this information here for (my $ec = 1; $ec <= $exoncount; $ec++) { if (defined($_ = $self->_readline())) { chomp; if (/^Exon\s$ec[\(\)-]*:\s(\d+)-(\d+)\s\(gen\)\s+(\d+)-(\d+)\s\(mRNA\)\s+id\s([\d\.inf-]+)%\s+mismatches\s(\d+)\s+gaps\s(\d+)\s+splice\ssite\s\(d\s+a\):\s(\d+)\s+(\d+)\s*(\w*)/) { $genomic_start = $1; $genomic_stop = $2; $cdna_start = $3; $cdna_stop = $4; $id = $5; $mismatches = $6; $gaps = $7; $splice_donor = $8; $splice_acceptor = $9; $uncertain = $10; } else { $self->throw( "Failed to match anything:\n$_\n"); } my $exon = Bio::Tools::Spidey::Exon->new (-start => $genomic_start, -end => $genomic_stop, -strand => $strand); $exon->seq_id($seq1props{'seqname'}); # feature1 is supposed to be initialized to a Similarity object, but we provide a safety net if ($exon->feature1->can('seqlength')) { $exon->feature1->seqlength($seq1props{'length'}); } else { $exon->feature1->add_tag_value('seqlength', $seq1props{'length'}); } # create and initialize the feature wrapping the 'hit' (the cDNA) my $fea2 = Bio::SeqFeature::Similarity->new (-start => $cdna_start, -end => $cdna_stop, -strand => $strand, -seq_id => $seq2props{'seqname'}, -primary => "aligning_cDNA"); $fea2->seqlength($seq2props{'length'}); # store $exon->est_hit($fea2); # general properties $exon->source_tag($self->analysis_method()); $exon->percentage_id($5); $exon->mismatches($6); $exon->gaps($7); $exon->donor($8); $exon->acceptor($9); # push onto array push(@exons, $exon); } else { $self->throw("Unexpected end of file reached\n"); } } } elsif( /^Number of splice sites:\s+(\d+)/ ) { $self->splicesites($1); } elsif( /^mRNA coverage:\s+(\d+)%/ ) { $self->est_coverage($1); } elsif(/^overall percent identity:\s+([\d\.]+)%/ ) { $self->overall_percentage_id($1); } elsif(/^Missing mRNA ends:\s+(\w+)/ ) { $self->missing_mrna_ends($1); } elsif( /^Exon (\d+): (\d+)-(\d+) \(gen\)\s+(\d+)-(\d+) \(mRNA\)/ ) { my ($exon_num, $gen_start, $gen_stop, $cdna_start, $cdna_stop); $exon_num = $1; $gen_start = $2; $gen_stop = $3; $cdna_start = $4; $cdna_stop = $5; } elsif( /No alignment found/ ) { return []; } else { #$self->debug("unmatched $_\n"); } } # Typical format: # Exon 1: 36375798-36375691 (gen) 1-108 (mRNA) # # # CCTCTTTTTCTTTGCAGGGTATATACCCAGTTACTTAGACAAGGATGAGCTATGTGTAGT # | |||||||||||||||||||||||||||||||||||||||||||||| # ATGTCAGGGTATATACCCAGTTACTTAGACAAGGATGAGCTATGTGTAGT # M S G Y I P S Y L D K D E L C V V # # # ATGTGGGGACAAAGCCACCGGATATCATTATCGCTGCATCACTTGTGAAGGTTGCAAGGT # |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| # ATGTGGGGACAAAGCCACCGGATATCATTATCGCTGCATCACTTGTGAAGGTTGCAAG # C G D K A T G Y H Y R C I T C E G C K # # # AAATGGCA # @exons ? return \@exons : return ; } =head2 next_exonset Title : next_exonset Usage : $exonset = $spidey_result->parse_next_exonset; print "Exons start at ", $exonset->start(), "and end at ", $exonset->end(), "\n"; for $exon ($exonset->sub_SeqFeature()) { # do something } Function: Parses the next alignment of the Spidey result file and returns the set of exons as a container of features. The container is itself a Bio::SeqFeature::Generic object, with the Bio::Tools::Spidey::Exon objects as sub features. Start, end, and strand of the container will represent the total region covered by the exons of this set. See the documentation of parse_next_alignment() for further reference about parsing and how the information is stored. Example : Returns : An Bio::SeqFeature::Generic object holding Bio::Tools::Spidey::Exon objects as sub features. Args : =cut sub next_exonset { my $self = shift; my $exonset; # get the next array of exons my $exons = $self->parse_next_alignment(); if( ! defined $exons ) { $self->warn("No exons returned"); return; } if( @$exons == 0 ) { return Bio::SeqFeature::Generic->new(); } # create the container of exons as a feature object itself, with the # data of the first exon for initialization $exonset = Bio::SeqFeature::Generic->new('-start' => $exons->[0]->start(), '-end' => $exons->[-1]->end(), '-strand' => $exons->[0]->strand(), '-primary' => "ExonSet"); $exonset->source_tag($exons->[0]->source_tag()); $exonset->seq_id($exons->[0]->seq_id()); # now add all exons as sub features, with enabling EXPANsion of the region # covered in total foreach my $exon (@$exons) { $exonset->add_sub_SeqFeature($exon, 'EXPAND'); } return $exonset; } =head2 next_feature Title : next_feature Usage : while($exonset = $spidey->next_feature()) { # do something } Function: Does the same as L<next_exonset()>. See there for documentation of the functionality. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_exonset() at present. Example : Returns : A Bio::SeqFeature::Generic object. Args : =cut sub next_feature { my ($self,@args) = @_; # even though next_exonset doesn't expect any args (and this method # does neither), we pass on args in order to be prepared if this changes # ever return $self->next_exonset(@args); } =head2 genomic_dna_length Title : genomic_dna_length Usage : $spidey->genomic_dna_length(); Function: Returns the length of the genomic DNA used in this Spidey result Example : Returns : An integer value. Args : =cut sub genomic_dna_length { my ($self, @args) = @_; my $val; if(@args) { $val = shift(@args); $self->{'genomic_dna_length'} = $val; } else { $val = $self->{'genomic_dna_length'}; } return $val; } =head2 splicesites Title : splicesites Usage : $spidey->splicesites(); Function: Returns the number of splice sites found in this Spidey result Example : Returns : An integer value. Args : =cut sub splicesites { my ($self, @args) = @_; my $val; if(@args) { $val = shift(@args); $self->{'splicesites'} = $val; } else { $val = $self->{'splicesites'}; } return $val; } =head2 est_coverage Title : est_coverage Usage : $spidey->est_coverage(); Function: Returns the percent of est coverage in this Spidey result Example : Returns : An integer value. Args : =cut sub est_coverage { my ($self, @args) = @_; my $val; if(@args) { $val = shift(@args); $self->{'est_coverage'} = $val; } else { $val = $self->{'est_coverage'}; } return $val; } =head2 overall_percentage_id Title : overall_percentage_id Usage : $spidey->overall_percentage_id(); Function: Returns the overall percent id in this Spidey result Example : Returns : An float value. Args : =cut sub overall_percentage_id { my ($self, @args) = @_; my $val; if(@args) { $val = shift(@args); $self->{'overall_percentage_id'} = $val; } else { $val = $self->{'overall_percentage_id'}; } return $val; } =head2 missing_mrna_ends Title : missing_mrna_ends Usage : $spidey->missing_mrna_ends(); Function: Returns left/right/neither from Spidey Example : Returns : A string value. Args : =cut sub missing_mrna_ends { my ($self, @args) = @_; my $val; if(@args) { $val = shift(@args); $self->{'missing_mrna_ends'} = $val; } else { $val = $self->{'missing_mrna_ends'}; } return $val; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tree���������������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 14766� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tree/AlleleNode.pm�������������������������������������������������������������000444��000766��000024�� 30577�13155576320� 17521� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tree::AlleleNode # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tree::AlleleNode - A Node with Alleles attached =head1 SYNOPSIS use Bio::Tree::AlleleNode; =head1 DESCRIPTION AlleleNodes are basic L<Bio::Tree::Node>s with the added ability to add Genotypes alleles as defined by the L<Bio::PopGen::IndividualI> interface. Genotypes are defined by the L<Bio::PopGen::GenotypeI> interface, you will probably want to use the L<Bio::PopGen::Genotype> implementation. This is implemented via containment to avoid multiple inheritance problems. Their is a L<Bio::PopGen::Individual> object which handles the L<Bio::PopGen::IndividualI> interface, and is accessible via the L<Bio::Tree::AlleleNode::individual> method. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =head1 HISTORY This module was re-written to be a combination of L<Bio::PopGen::Individual> and L<Bio::Tree::Node> primarily for use in L<Bio::PopGen::Simulation::Coalescent> simulations. =cut # Let the code begin... package Bio::Tree::AlleleNode; use vars qw($UIDCOUNTER); use strict; BEGIN { $UIDCOUNTER = 1 } use Bio::PopGen::Individual; use Bio::PopGen::Genotype; use base qw(Bio::Tree::Node Bio::PopGen::IndividualI); =head2 new Title : new Usage : my $obj = Bio::Tree::AlleleNode->new(); Function: Builds a new Bio::Tree::AlleleNode() object Returns : an instance of Bio::Tree::AlleleNode Args : -unique_id => $id, -genotypes => \@genotypes -left => pointer to Left descendent (optional) -right => pointer to Right descenent (optional) -branch_length => branch length [integer] (optional) -bootstrap => value bootstrap value (string) -description => description of node -id => human readable (unique) id for node Should NOT contain the characters '();:' =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->individual( Bio::PopGen::Individual->new(@args)); return $self; } =head2 individual Title : individual Usage : $obj->individual($newval) Function: Get/Set Access to the underlying individual object Returns : L<Bio::PopGen::Individual> object Args : on set, new value (L<Bio::PopGen::Individual>) =cut sub individual { my ($self,$newval) = @_; if( defined $newval || ! defined $self->{'individual'} ) { $newval = Bio::PopGen::Individual->new() unless defined $newval; $self->{'individual'} = $newval; } return $self->{'individual'}; } =head2 Bio::PopGen::Individual methods Methods required by L<Bio::PopGen::IndividualI>. =head2 unique_id Title : unique_id Usage : my $id = $individual->unique_id Function: Unique Identifier Returns : string representing unique identifier Args : string =cut sub unique_id{ my $self = shift; $self->individual->unique_id(@_); } =head2 num_of_results Title : num_of_results Usage : my $count = $person->num_results; Function: returns the count of the number of Results for a person Returns : integer Args : none =cut sub num_of_results { my $self = shift; $self->individual->num_of_results(@_); } =head2 add_Genotype Title : add_Genotype Usage : $individual->add_Genotype Function: add a genotype value, only a single genotype may be associated Returns : count of the number of genotypes associated with this individual Args : @genotypes - Bio::PopGen::GenotypeI object(s) containing alleles plus a marker name =cut sub add_Genotype { my $self = shift; $self->individual->add_Genotype(@_); } =head2 reset_Genotypes Title : reset_Genotypes Usage : $individual->reset_Genotypes; Function: Reset the genotypes stored for this individual Returns : none Args : none =cut sub reset_Genotypes{ my $self = shift; $self->individual->reset_Genotypes(@_); } =head2 remove_Genotype Title : remove_Genotype Usage : $individual->remove_Genotype(@names) Function: Removes the genotypes for the requested markers Returns : none Args : Names of markers =cut sub remove_Genotype{ my $self = shift; $self->individual->remove_Genotype(@_); } =head2 get_Genotypes Title : get_Genotypes Usage : my @genotypes = $ind->get_Genotypes(-marker => $markername); Function: Get the genotypes for an individual, based on a criteria Returns : Array of genotypes Args : either none (return all genotypes) or -marker => name of marker to return (exact match, case matters) =cut sub get_Genotypes{ my $self = shift; $self->individual->get_Genotypes(@_); } =head2 has_Marker Title : has_Marker Usage : if( $ind->has_Marker($name) ) {} Function: Boolean test to see if an Individual has a genotype for a specific marker Returns : Boolean (true or false) Args : String representing a marker name =cut sub has_Marker{ my $self = shift; $self->individual->has_Marker(@_); } =head2 get_marker_names Title : get_marker_names Usage : my @names = $individual->get_marker_names; Function: Returns the list of known marker names Returns : List of strings Args : none =cut sub get_marker_names{ my $self = shift; $self->individual->get_marker_names(@_); } =head2 Bio::Tree::Node methods Methods inherited from L<Bio::Tree::Node>. =head2 add_Descendent Title : add_Descendent Usage : $node->add_Descendent($node); Function: Adds a descendent to a node Returns : number of current descendents for this node Args : Bio::Node::NodeI boolean flag, true if you want to ignore the fact that you are adding a second node with the same unique id (typically memory location reference in this implementation). default is false and will throw an error if you try and overwrite an existing node. =head2 each_Descendent Title : each_Descendent($sortby) Usage : my @nodes = $node->each_Descendent; Function: all the descendents for this Node (but not their descendents i.e. not a recursive fetchall) Returns : Array of Bio::Tree::NodeI objects Args : $sortby [optional] "height", "creation" or coderef to be used to sort the order of children nodes. =head2 remove_Descendent Title : remove_Descendent Usage : $node->remove_Descedent($node_foo); Function: Removes a specific node from being a Descendent of this node Returns : nothing Args : An array of Bio::Node::NodeI objects which have be previously passed to the add_Descendent call of this object. =head2 remove_all_Descendents Title : remove_all_Descendents Usage : $node->remove_All_Descendents() Function: Cleanup the node's reference to descendents and reset their ancestor pointers to undef, if you don't have a reference to these objects after this call they will be cleaned up - so a get_nodes from the Tree object would be a safe thing to do first Returns : nothing Args : none =head2 get_all_Descendents Title : get_all_Descendents Usage : my @nodes = $node->get_all_Descendents; Function: Recursively fetch all the nodes and their descendents *NOTE* This is different from each_Descendent Returns : Array or Bio::Tree::NodeI objects Args : none =cut # implemented in the interface =head2 ancestor Title : ancestor Usage : $obj->ancestor($newval) Function: Set the Ancestor Returns : value of ancestor Args : newvalue (optional) =head2 branch_length Title : branch_length Usage : $obj->branch_length() Function: Get/Set the branch length Returns : value of branch_length Args : newvalue (optional) =head2 bootstrap Title : bootstrap Usage : $obj->bootstrap($newval) Function: Get/Set the bootstrap value Returns : value of bootstrap Args : newvalue (optional) =head2 description Title : description Usage : $obj->description($newval) Function: Get/Set the description string Returns : value of description Args : newvalue (optional) =head2 id Title : id Usage : $obj->id($newval) Function: The human readable identifier for the node Returns : value of human readable id Args : newvalue (optional) Note : id cannot contain the characters '();:' "A name can be any string of printable characters except blanks, colons, semicolons, parentheses, and square brackets. Because you may want to include a blank in a name, it is assumed that an underscore character ("_") stands for a blank; any of these in a name will be converted to a blank when it is read in." from L<http://evolution.genetics.washington.edu/phylip/newicktree.html> =cut =head2 internal_id Title : internal_id Usage : my $internalid = $node->internal_id Function: Returns the internal unique id for this Node (a monotonically increasing number for this in-memory implementation but could be a database determined unique id in other implementations) Returns : unique id Args : none =head2 Bio::Node::NodeI decorated interface implemented The following methods are implemented by L<Bio::Node::NodeI> decorated interface. =head2 is_Leaf Title : is_Leaf Usage : if( $node->is_Leaf ) Function: Get Leaf status Returns : boolean Args : none =cut =head2 to_string Title : to_string Usage : my $str = $node->to_string() Function: For debugging, provide a node as a string Returns : string Args : none =head2 height Title : height Usage : my $len = $node->height Function: Returns the height of the tree starting at this node. Height is the maximum branchlength. Returns : The longest length (weighting branches with branch_length) to a leaf Args : none =head2 invalidate_height Title : invalidate_height Usage : private helper method Function: Invalidate our cached value of the node's height in the tree Returns : nothing Args : none =cut #' =head2 add_tag_value Title : add_tag_value Usage : $node->add_tag_value($tag,$value) Function: Adds a tag value to a node Returns : number of values stored for this tag Args : $tag - tag name $value - value to store for the tag =head2 remove_tag Title : remove_tag Usage : $node->remove_tag($tag) Function: Remove the tag and all values for this tag Returns : boolean representing success (0 if tag does not exist) Args : $tag - tagname to remove =head2 remove_all_tags Title : remove_all_tags Usage : $node->remove_all_tags() Function: Removes all tags Returns : None Args : None =head2 get_all_tags Title : get_all_tags Usage : my @tags = $node->get_all_tags() Function: Gets all the tag names for this Node Returns : Array of tagnames Args : None =head2 get_tag_values Title : get_tag_values Usage : my @values = $node->get_tag_value($tag) Function: Gets the values for given tag ($tag) Returns : Array of values or empty list if tag does not exist Args : $tag - tag name =head2 has_tag Title : has_tag Usage : $node->has_tag($tag) Function: Boolean test if tag exists in the Node Returns : Boolean Args : $tag - tagname =cut 1; ���������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tree/AnnotatableNode.pm��������������������������������������������������������000444��000766��000024�� 20212�13155576320� 20534� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Tree::AnnotatableNode # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Mira Han <mirhan@indiana.edu> # # Copyright Mira Han # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tree::AnnotatableNode - A Tree Node with support for annotation =head1 SYNOPSIS use Bio::Tree::AnnotatableNode; my $nodeA = Bio::Tree::AnnotatableNode->new(); my $nodeL = Bio::Tree::AnnotatableNode->new(); my $nodeR = Bio::Tree::AnnotatableNode->new(); my $node = Bio::Tree::AnnotatableNode->new(); $node->add_Descendents($nodeL); $node->add_Descendents($nodeR); print "node is not a leaf \n" if( $node->is_leaf); # $node is-a Bio::AnnotatableI, hence: my $ann_coll = $node->annotation(); # $ann_coll is-a Bio::AnnotationCollectionI, hence: my @all_anns = $ann_coll->get_Annotations(); # do something with the annotation objects =head1 DESCRIPTION Makes a Tree Node with Annotations, suitable for building a Tree. See L<Bio::Tree::Node> for a full list of functionality. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Mira Han Email mirhan@indiana.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tree::AnnotatableNode; use strict; use Bio::Annotation::Collection; use Bio::Seq; use base qw(Bio::Tree::Node Bio::AnnotatableI); =head2 new Title : new Usage : my $obj = Bio::Tree::AnnotatableNode->new(); Function: Builds a new Bio::Tree::AnnotatableNode object Returns : Bio::Tree::AnnotatableNode Args : -tostring => code reference to the tostring callback function (optional) =cut sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); my $to_string_cb = $self->_rearrange([qw(TOSTRING)], @args); if ($to_string_cb) { $self->to_string_callback($to_string_cb); } return $self; } sub DESTROY { my ($self) = @_; # try to insure that everything is cleaned up $self->SUPER::DESTROY(); } =head1 Methods for implementing Bio::AnnotatableI =cut =head2 annotation Title : annotation Usage : $ann = $node->annotation or $node->annotation($ann) Function: Gets or sets the annotation Returns : Bio::AnnotationCollectionI object Args : None or Bio::AnnotationCollectionI object See L<Bio::AnnotationCollectionI> and L<Bio::Annotation::Collection> for more information =cut sub annotation { my ($self,$value) = @_; if( defined $value ) { $self->throw("object of class ".ref($value)." does not implement ". "Bio::AnnotationCollectionI. Too bad.") unless $value->isa("Bio::AnnotationCollectionI"); $self->{'_annotation'} = $value; } elsif( ! defined $self->{'_annotation'}) { $self->{'_annotation'} = Bio::Annotation::Collection->new(); } return $self->{'_annotation'}; } =head1 Methods for implementing tag access through Annotation::SimpleValue =cut =head2 add_tag_value Title : add_tag_value Usage : $node->add_tag_value($tag,$value) Function: Adds a tag value to a node Returns : number of values stored for this tag Args : $tag - tag name $value - value to store for the tag =cut sub add_tag_value { my ($self,$tag,$value) = @_; if( ! defined $tag || ! defined $value ) { $self->warn("cannot call add_tag_value with an undefined value"); } my $ac = $self->annotation(); my $sv = Bio::Annotation::SimpleValue->new(-value => $value); $ac->add_Annotation($tag, $sv); return scalar $ac->get_Annotations($tag); } =head2 remove_tag Title : remove_tag Usage : $node->remove_tag($tag) Function: Remove the tag and all values for this tag Returns : boolean representing success (0 if tag does not exist) Args : $tag - tagname to remove =cut sub remove_tag { my ($self,$tag) = @_; my $ac = $self->annotation(); if( @{$ac->get_Annotations($tag)} ) { $ac->remove_Annotations($tag); return 1; } return 0; } =head2 remove_all_tags Title : remove_all_tags Usage : $node->remove_all_tags() Function: Removes all tags Returns : None Args : None =cut sub remove_all_tags { my ($self) = @_; my $ac = $self->annotation(); $ac->remove_Annotations(); return; } =head2 get_all_tags Title : get_all_tags Usage : my @tags = $node->get_all_tags() Function: Gets all the tag names for this Node Returns : Array of tagnames Args : None =cut sub get_all_tags{ my ($self) = @_; my $ac = $self->annotation(); my @tags = sort $ac->get_all_annotation_keys(); # how to restrict it to SimpleValues? return @tags; } =head2 get_tag_values Title : get_tag_values Usage : my @values = $node->get_tag_value($tag) Function: Gets the values for given tag ($tag) Returns : Array of values or empty list if tag does not exist Args : $tag - tag name =cut sub get_tag_values{ my ($self,$tag) = @_; my $ac = $self->annotation(); my @values = map {$_->value()} $ac->get_Annotations($tag); return @values; } =head2 has_tag Title : has_tag Usage : $node->has_tag($tag) Function: Boolean test if tag exists in the Node Returns : Boolean Args : $tag - tagname =cut sub has_tag { my ($self,$tag) = @_; my $ac = $self->annotation(); return ( scalar $ac->get_Annotations($tag) > 0); } =head1 Methods for implementing to_string =cut =head2 to_string_callback Title : to_string_callback Usage : $node->to_string_callback(\&func) Function: get/set callback for to_string Returns : code reference for the to_string callback function Args : \&func - code reference to be set as the callback function =cut sub to_string_callback { # get/set callback, using $DEFAULT_CB if nothing is set my ($self, $foo) = @_; if ($foo) { # $foo is callback code ref, self as first arg (so you have access to object data) $self->{'_to_string_cb'} = $foo; } else { if (! defined $self->{'_to_string_cb'}) { $self->{'_to_string_cb'} = \&Bio::Tree::NodeI::to_string; } } return $self->{'_to_string_cb'}; } sub to_string { my ($self) = @_; my $cb = $self->to_string_callback(); return $cb->($self); } =head1 Methods for accessing Bio::Seq =cut =head2 sequence Title : sequence Usage : $ann = $node->sequence or $node->sequence($seq) Function: Gets or sets the sequence Returns : array reference of Bio::SeqI objects Args : None or Bio::SeqI object See L<Bio::SeqI> and L<Bio::Seq> for more information =cut sub sequence { my ($self,$value) = @_; if( defined $value ) { $self->throw("object of class ".ref($value)." does not implement ". "Bio::SeqI. Too bad.") unless $value->isa("Bio::SeqI"); push (@{$self->{'_sequence'}}, $value); } #elsif( ! defined $self->{'_sequence'}) #{ # $self->{'_sequence'} = Bio::Seq->new(); #} return $self->{'_sequence'}; } =head2 has_sequence Title : has_sequence Usage : if( $node->has_sequence) { # do something } Function: tells if node has sequence attached Returns : Boolean for whether or not node has Bio::SeqI attached. Args : None =cut sub has_sequence { my ($self) = @_; return $self->{'_sequence'} && @{$self->{'_sequence'}}; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tree/Compatible.pm�������������������������������������������������������������000444��000766��000024�� 31001�13155576320� 17553� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tree::Compatible # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Gabriel Valiente <valiente@lsi.upc.edu> # # Copyright Gabriel Valiente # # You may distribute this module under the same terms as Perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tree::Compatible - Testing compatibility of phylogenetic trees with nested taxa. =head1 SYNOPSIS use Bio::Tree::Compatible; use Bio::TreeIO; my $input = Bio::TreeIO->new('-format' => 'newick', '-file' => 'input.tre'); my $t1 = $input->next_tree; my $t2 = $input->next_tree; my ($incompat, $ilabels, $inodes) = Bio::Tree::Compatible::is_compatible($t1,$t2); if ($incompat) { my %cluster1 = %{ Bio::Tree::Compatible::cluster_representation($t1) }; my %cluster2 = %{ Bio::Tree::Compatible::cluster_representation($t2) }; print "incompatible trees\n"; if (scalar(@$ilabels)) { foreach my $label (@$ilabels) { my $node1 = $t1->find_node(-id => $label); my $node2 = $t2->find_node(-id => $label); my @c1 = sort @{ $cluster1{$node1} }; my @c2 = sort @{ $cluster2{$node2} }; print "label $label"; print " cluster"; map { print " ",$_ } @c1; print " cluster"; map { print " ",$_ } @c2; print "\n"; } } if (scalar(@$inodes)) { while (@$inodes) { my $node1 = shift @$inodes; my $node2 = shift @$inodes; my @c1 = sort @{ $cluster1{$node1} }; my @c2 = sort @{ $cluster2{$node2} }; print "cluster"; map { print " ",$_ } @c1; print " properly intersects cluster"; map { print " ",$_ } @c2; print "\n"; } } } else { print "compatible trees\n"; } =head1 DESCRIPTION NB: This module has exclusively class methods that work on Bio::Tree::TreeI objects. An instance of Bio::Tree::Compatible cannot itself represent a tree, and so typically there is no need to create one. Bio::Tree::Compatible is a Perl tool for testing compatibility of phylogenetic trees with nested taxa represented as Bio::Tree::Tree objects. It is based on a recent characterization of ancestral compatibility of semi-labeled trees in terms of their cluster representations. A semi-labeled tree is a phylogenetic tree with some of its internal nodes labeled, and it can represent a classification tree as well as a phylogenetic tree with nested taxa, with labeled internal nodes corresponding to taxa at a higher level of aggregation or nesting than that of their descendents. Two semi-labeled trees are compatible if their topological restrictions to the common labels are such that for each node label, the smallest clusters containing it in each of the trees coincide and, furthermore, no cluster in one of the trees properly intersects a cluster of the other tree. Future extensions of Bio::Tree::Compatible include a Bio::Tree::Supertree module for combining compatible phylogenetic trees with nested taxa into a common supertree. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 SEE ALSO =over =item * Philip Daniel and Charles Semple. Supertree Algorithms for Nested Taxa. In: Olaf R. P. Bininda-Emonds (ed.) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, I<Computational Biology>, vol. 4, chap. 7, pp. 151-171. Kluwer (2004). =item * Charles Semple, Philip Daniel, Wim Hordijk, Roderic D. M. Page, and Mike Steel: Supertree Algorithms for Ancestral Divergence Dates and Nested Taxa. Bioinformatics B<20>(15), 2355-2360 (2004). =item * Merce Llabres, Jairo Rocha, Francesc Rossello, and Gabriel Valiente: On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa. J. Math. Biol. B<53>(3), 340-364 (2006). =back =head1 AUTHOR - Gabriel Valiente Email valiente@lsi.upc.edu =head1 APPENDIX The rest of the documentation details each of the object methods. =cut package Bio::Tree::Compatible; use strict; # Object preamble - inherits from Bio::Root::Root use Set::Scalar; use base qw(Bio::Root::Root); =head2 postorder_traversal Title : postorder_traversal Usage : my @nodes = @{ $tree->postorder_traversal } Function: Return list of nodes in postorder Returns : reference to array of Bio::Tree::Node Args : none For example, the postorder traversal of the tree C<(((A,B)C,D),(E,F,G));> is a reference to an array of nodes with internal_id 0 through 9, because the Newick standard representation for phylogenetic trees is based on a postorder traversal. +---A +---0 | | +---+---C +---4---2 | | | | | | | | +---B | | +---1 | | | | + +-------D 9 +-------3 | | | +-----E | +-----5 | | | | +-----+-----F +-----8-----6 | | +-----G +-----7 =cut sub postorder_traversal { my($self) = @_; my @stack; my @queue; push @stack, $self->get_root_node; while (@stack) { my $node = pop @stack; push @queue, $node; foreach my $child ($node->each_Descendent(-sortby => 'internal_id')) { push @stack, $child; } } my @postorder = reverse @queue; return \@postorder; } =head2 cluster_representation Title : cluster_representation Usage : my %cluster = %{ $tree->cluster_representation } Function: Compute the cluster representation of a tree Returns : reference to hash of array of string indexed by Bio::Tree::Node Args : none For example, the cluster representation of the tree C<(((A,B)C,D),(E,F,G));> is a reference to a hash associating an array of string (descendent labels) to each node, as follows: 0 --> [A] 1 --> [B] 2 --> [A,B,C] 3 --> [D] 4 --> [A,B,C,D] 5 --> [E] 6 --> [F] 7 --> [G] 8 --> [E,F,G] 9 --> [A,B,C,D,E,F,G] =cut sub cluster_representation { my ($tree) = @_; my %cluster; my @postorder = @{ postorder_traversal($tree) }; foreach my $node ( @postorder ) { my @labeled = map { $_->id } grep { $_->id } $node->get_Descendents; push @labeled, $node->id if $node->id; $cluster{$node} = \@labeled; } return \%cluster; } =head2 common_labels Title : common_labels Usage : my $labels = $tree1->common_labels($tree2); Function: Return set of common node labels Returns : Set::Scalar Args : Bio::Tree::Tree For example, the common labels of the tree C<(((A,B)C,D),(E,F,G));> and the tree C<((A,B)H,E,(J,(K)G)I);> are: C<[A,B,E,G]>. +---A +---A | | +---+---C +-------H | | | | | | | +---B | +---B | | | + +-------D +-----------E | | | +-----E | +-------J | | | | +-----+-----F +---I | | +-----G +---G---K =cut sub common_labels { my($self,$arg) = @_; my @labels1 = map { $_->id } grep { $_->id } $self->get_nodes; my $common = Set::Scalar->new( @labels1 ); my @labels2 = map { $_->id } grep { $_->id } $arg->get_nodes; my $temp = Set::Scalar->new( @labels2 ); return $common->intersection($temp); } =head2 topological_restriction Title : topological_restriction Usage : $tree->topological_restriction($labels) Function: Compute the topological restriction of a tree to a subset of node labels Returns : Bio::Tree::Tree Args : Set::Scalar For example, the topological restrictions of each of the trees C<(((A,B)C,D),(E,F,G));> and C<((A,B)H,E,(J,(K)G)I);> to the labels C<[A,B,E,G]> are as follows: +---A +---A | | +---+---+ +---+ | | | | | +---B | +---B + | | +---E +-------E | | | +-------+ +---+---G | +---G =cut sub topological_restriction { my ($tree, $labels) = @_; for my $node ( @{ postorder_traversal($tree) } ) { unless (ref($node)) { # skip $node if already removed my @cluster = map { $_->id } grep { $_->id } $node->get_Descendents; push @cluster, $node->id if $node->id; my $cluster = Set::Scalar->new(@cluster); if ($cluster->is_disjoint($labels)) { $tree->remove_Node($node); } else { if ($node->id and not $labels->has($node->id)) { $node->{'_id'} = undef; } } } } } =head2 is_compatible Title : is_compatible Usage : $tree1->is_compatible($tree2) Function: Test compatibility of two trees Returns : boolean Args : Bio::Tree::Tree For example, the topological restrictions of the trees C<(((A,B)C,D),(E,F,G));> and C<((A,B)H,E,(J,(K)G)I);> to their common labels, C<[A,B,E,G]>, are compatible. The respective cluster representations are as follows: [A] [A] [B] [B] [E] [E] [G] [G] [A,B] [A,B] [E,G] [A,B,E,G] [A,B,E,G] As a second example, the trees C<(A,B);> and C<((B)A);> are incompatible. Their respective cluster representations are as follows: [A] [B] [B] [A,B] [A,B] The reason is, the smallest cluster containing label C<A> is C<[A]> in the first tree but C<[A,B]> in the second tree. +---A A---B | + | +---B As a second example, the trees C<(((B,A),C),D);> and C<((A,(D,B)),C);> are also incompatible. Their respective cluster representations are as follows: [A] [A] [B] [B] [C] [C] [D] [D] [A,B] [B,D] [A,B,C] [A,B,D] [A,B,C,D] [A,B,C,D] The reason is, cluster C<[A,B]> properly intersects cluster C<[B,D]>. There are further incompatibilities between these trees: C<[A,B,C]> properly intersects both C<[B,D]> and C<[A,B,D]>. +---B +-------A | | +---+ +---+ +---D | | | | | +---+ +---A | +---+ | | + | + +-------C | +---B | | +-----------D +-----------C =cut sub is_compatible { my ($tree1, $tree2) = @_; my $common = $tree1->Bio::Tree::Compatible::common_labels($tree2); $tree1->Bio::Tree::Compatible::topological_restriction($common); $tree2->Bio::Tree::Compatible::topological_restriction($common); my @postorder1 = @{ postorder_traversal($tree1) }; my @postorder2 = @{ postorder_traversal($tree2) }; my %cluster1 = %{ cluster_representation($tree1) }; my %cluster2 = %{ cluster_representation($tree2) }; my $incompat = 0; # false my @labels; foreach my $label ( $common->elements ) { my $node1 = $tree1->find_node(-id => $label); my @labels1 = @{ $cluster1{$node1} }; my $cluster1 = Set::Scalar->new(@labels1); my $node2 = $tree2->find_node(-id => $label); my @labels2 = @{ $cluster2{$node2} }; my $cluster2 = Set::Scalar->new(@labels2); unless ( $cluster1->is_equal($cluster2) ) { $incompat = 1; # true push @labels, $label; } } my @nodes; foreach my $node1 ( @postorder1 ) { my @labels1 = @{ $cluster1{$node1} }; my $cluster1 = Set::Scalar->new(@labels1); foreach my $node2 ( @postorder2 ) { my @labels2 = @{$cluster2{$node2} }; my $cluster2 = Set::Scalar->new(@labels2); if ($cluster1->is_properly_intersecting($cluster2)) { $incompat = 1; # true push @nodes, $node1, $node2; } } } return ($incompat, \@labels, \@nodes); } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tree/DistanceFactory.pm��������������������������������������������������������000444��000766��000024�� 41233�13155576320� 20566� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tree::DistanceFactory # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tree::DistanceFactory - Construct a tree using distance based methods =head1 SYNOPSIS use Bio::Tree::DistanceFactory; use Bio::AlignIO; use Bio::Align::DNAStatistics; my $tfactory = Bio::Tree::DistanceFactory->new(-method => "NJ"); my $stats = Bio::Align::DNAStatistics->new(); my $alnin = Bio::AlignIO->new(-format => 'clustalw', -file => 'file.aln'); my $aln = $alnin->next_aln; # Of course matrix can come from a different place # like PHYLIP if you prefer, Bio::Matrix::IO should be able # to parse many things my $jcmatrix = $stats->distance(-align => $aln, -method => 'Jukes-Cantor'); my $tree = $tfactory->make_tree($jcmatrix); =head1 DESCRIPTION This is a factory which will construct a phylogenetic tree based on the pairwise sequence distances for a set of sequences. Currently UPGMA (Sokal and Michener 1958) and NJ (Saitou and Nei 1987) tree construction methods are implemented. =head1 REFERENCES Eddy SR, Durbin R, Krogh A, Mitchison G, (1998) "Biological Sequence Analysis", Cambridge Univ Press, Cambridge, UK. Howe K, Bateman A, Durbin R, (2002) "QuickTree: building huge Neighbour-Joining trees of protein sequences." Bioinformatics 18(11):1546-1547. Saitou N and Nei M, (1987) "The neighbor-joining method: a new method for reconstructing phylogenetic trees." Mol Biol Evol 4(4):406-25. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tree::DistanceFactory; use vars qw($DefaultMethod $Precision); use strict; # some defaults $DefaultMethod = 'UPGMA'; $Precision = 5; use Bio::Tree::Node; use Bio::Tree::Tree; use base qw(Bio::Root::Root); =head2 new Title : new Usage : my $obj = Bio::Tree::DistanceFactory->new(); Function: Builds a new Bio::Tree::DistanceFactory object Returns : an instance of Bio::Tree::DistanceFactory Args : -method => 'NJ' or 'UPGMA' =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($method) = $self->_rearrange([qw(METHOD)], @args); $self->method($method || $DefaultMethod); return $self; } =head2 make_tree Title : make_tree Usage : my $tree = $disttreefact->make_tree($matrix); Function: Build a Tree based on a distance matrix Returns : L<Bio::Tree::TreeI> Args : L<Bio::Matrix::MatrixI> object =cut sub make_tree{ my ($self,$matrix) = @_; if( ! defined $matrix || !ref($matrix) || ! $matrix->isa('Bio::Matrix::MatrixI') ) { $self->warn("Need to provide a valid Bio::Matrix::MatrixI object to make_tree"); return; } my $method = uc ($self->method); if( $method =~ /NJ/i ) { return $self->_nj($matrix); } elsif( $method =~ /UPGMA/i ) { return $self->_upgma($matrix); } else { $self->warn("Unknown tree construction method '$method'. Cannot run."); return; } } =head2 _nj Title : _nj Usage : my $tree = $disttreefact->_nj($matrix); Function: Construct a tree based on distance matrix using the Neighbor Joining algorithm (Saitou and Nei, 1987) Implementation based on Kevin Howe's Quicktree implementation and uses his tricks (some based on Bill Bruno's work) to eliminate negative branch lengths Returns : L<Bio::Tree::TreeI> Args : L<Bio::Matrix::MatrixI> object =cut sub _nj { my ($self,$distmat) = @_; # we assume type checking of $aln has already been done # client shouldn't be calling this directly anyways, using the # make_tree method is preferred # so that we can trim the number of digits shown as the branch length my $precisionstr = "%.$Precision"."f"; my @names = $distmat->column_names; my $N = scalar @names; my ($i,$j,$m,@nodes,$mat,@r); my $L = $N; if( $N < 2 ) { $self->warn("Can only perform NJ treebuilding on sets of 2 or more species\n"); return; } elsif( $N == 2 ) { $i = 0; my $d = sprintf($precisionstr, $distmat->get_entry($names[0],$names[1]) / 2); my $root = Bio::Tree::Node->new(); for my $nm ( @names ) { $root->add_Descendents( Bio::Tree::Node->new(-id => $nm, -branch_length => $d)); } return Bio::Tree::Tree(-root => $root); } my $c = 0; for ( $i = 0; $i < $N; $i++ ) { push @nodes, Bio::Tree::Node->new(-id => $names[$i]); my $ri = 0; for( $j = 0; $j < $N; $j++ ) { $mat->[$i][$j] = $distmat->get_entry($names[$i],$names[$j]); $ri += $mat->[$i][$j]; } $r[$i] = $ri / ($L -2); } for( my $nodecount = 0; $nodecount < $N-3; $nodecount++) { my ($mini,$minj,$min); for($i = 0; $i < $N; $i++ ) { next unless defined $nodes[$i]; for( $j = 0; $j < $i; $j++ ) { next unless defined $nodes[$j]; my $dist = $mat->[$i][$j] - ($r[$i] + $r[$j]); if( ! defined $min || $dist <= $min) { ($mini,$minj,$min) = ($i,$j,$dist); } } } my $dij = $mat->[$mini][$minj]; my $dist_i = ($dij + $r[$mini] - $r[$minj]) / 2; my $dist_j = $dij - $dist_i; # deal with negative branch lengths # per code in K.Howe's quicktree if( $dist_i < 0 ) { $dist_i = 0; $dist_j = $dij; $dist_j = 0 if( $dist_j < 0 ); } elsif( $dist_j < 0 ) { $dist_j = 0; $dist_i = $dij; $dist_i = 0 if( $dist_i < 0 ); } $nodes[$mini]->branch_length(sprintf($precisionstr,$dist_i)); $nodes[$minj]->branch_length(sprintf($precisionstr,$dist_j)); my $newnode = Bio::Tree::Node->new(-descendents => [ $nodes[$mini], $nodes[$minj] ]); $nodes[$mini] = $newnode; delete $nodes[$minj]; # update the distance matrix $r[$mini] = 0; my ($dmi,$dmj); for( $m = 0; $m < $N; $m++ ) { next unless defined $nodes[$m]; if( $m != $mini ) { $dmj = $mat->[$m][$minj]; my ($row,$col); ($row,$col) = ($m,$mini); $dmi = $mat->[$row][$col]; # from K.Howe's notes in quicktree # we can actually adjust r[m] here, by using the form: # rm = ((rm * numseqs) - dmi - dmj + dmk) / (numseqs-1) # Note: in Bill Bruno's method for negative branch # elimination, then if either dist_i is positive and # dist_j is 0, or dist_i is zero and dist_j is positive # (after adjustment) then the matrix entry is formed # from the distance to the node in question (m) to the # node with the zero branch length (whichever it was). # I think my code already has the same effect; this is # certainly true if dij is equal to dist_i + dist_j, # which it should have been fixed to my $dmk = $mat->[$row][$col] = $mat->[$col][$row] = ($dmi + $dmj - $dij) / 2; # If we don't want to try and correct negative brlens # this is essentially what is in Edddy et al, BSA book. # $r[$m] = (($r[$m] * $L) - $dmi - $dmj + $dmk) / ($L-1); # $r[$m] = (($r[$m] * ($L - 2)) - $dmi - $dmj + $mat->[$row][$col]) / ( $L - 3); $r[$mini] += $dmk; } } $L--; $r[$mini] /= $L - 2; } # should be 3 nodes left my (@leftovernodes,@leftovers); for( my $k = 0; $k < $N; $k++ ) { if( defined $nodes[$k] ) { push @leftovers, $k; push @leftovernodes, $nodes[$k]; } } my ($l_0,$l_1,$l_2) = @leftovers; my $dist_i = ( $mat->[$l_1][$l_0] + $mat->[$l_2][$l_0] - $mat->[$l_2][$l_1] ) / 2; my $dist_j = ( $mat->[$l_1][$l_0] - $dist_i); my $dist_k = ( $mat->[$l_2][$l_0] - $dist_i); # This is Kev's code to get rid of negative branch lengths if( $dist_i < 0 ) { $dist_i = 0; $dist_j = $mat->[$l_1][$l_0]; $dist_k = $mat->[$l_2][$l_0]; if( $dist_j < 0 ) { $dist_j = 0; $dist_k = ( $mat->[$l_2][$l_0] + $mat->[$l_2][$l_1] ) / 2; $dist_k = 0 if( $dist_k < 0 ); } elsif( $dist_k < 0 ) { $dist_k = 0; $dist_j = ($mat->[$l_1][$l_0] + $mat->[$l_2][$l_1]) / 2; $dist_j = 0 if( $dist_j < 0 ); } } elsif( $dist_j < 0 ) { $dist_j = 0; $dist_i = $mat->[$l_1][$l_0]; $dist_k = $mat->[$l_2][$l_1]; if( $dist_i < 0 ) { $dist_i = 0; $dist_k = ( $mat->[$l_2][$l_0] + $mat->[$l_2][$l_1]) / 2; $dist_k = 0 if( $dist_k < 0 ); } elsif( $dist_k < 0 ) { $dist_k = 0; $dist_i = ( $mat->[$l_1][$l_0] + $mat->[$l_2][$l_0]) / 2; $dist_i = 0 if( $dist_i < 0 ); } } elsif( $dist_k < 0 ) { $dist_k = 0; $dist_i = $mat->[$l_2][$l_0]; $dist_j = $mat->[$l_2][$l_1]; if( $dist_i < 0 ) { $dist_i = 0; $dist_j = ( $mat->[$l_1][$l_0] + $mat->[$l_2][$l_1] ) / 2; $dist_j = 0 if $dist_j < 0; } elsif( $dist_j < 0 ) { $dist_j = 0; $dist_i = ($mat->[$l_1][$l_0] + $mat->[$l_2][$l_0]) / 2; $dist_i = 0 if $dist_i < 0; } } $leftovernodes[0]->branch_length(sprintf($precisionstr,$dist_i)); $leftovernodes[1]->branch_length(sprintf($precisionstr,$dist_j)); $leftovernodes[2]->branch_length(sprintf($precisionstr,$dist_k)); Bio::Tree::Tree->new(-root => Bio::Tree::Node->new (-descendents => \@leftovernodes)); } =head2 _upgma Title : _upgma Usage : my $tree = $disttreefact->_upgma($matrix); Function: Construct a tree based on alignment using UPGMA Returns : L<Bio::Tree::TreeI> Args : L<Bio::Matrix::MatrixI> object =cut sub _upgma{ my ($self,$distmat) = @_; # we assume type checking of $matrix has already been done # client shouldn't be calling this directly anyways, using the # make_tree method is preferred # algorithm, from Eddy, Durbin, Krogh, Mitchison, 1998 # originally by Sokal and Michener 1956 my $precisionstr = "%.$Precision"."f"; my ($i,$j,$x,$y,@dmat,@orig,@nodes); my @names = $distmat->column_names; my $c = 0; my @clusters = map { my $r = { 'id' => $c, 'height' => 0, 'contains' => [$c], }; $c++; $r; } @names; my $K = scalar @clusters; my (@mins,$min); for ( $i = 0; $i < $K; $i++ ) { for( $j = $i+1; $j < $K; $j++ ) { my $d = $distmat->get_entry($names[$i],$names[$j]); # get Min here on first time around, save 1 cycle $dmat[$j][$i] = $dmat[$i][$j] = $d; $orig[$i][$j] = $orig[$j][$i] = $d; if ( ! defined $min || $d <= $min ) { if( defined $min && $min == $d ) { push @mins, [$i,$j]; } else { @mins = [$i,$j]; $min = $d; } } } } # distance between each cluster is avg distance # between pairs of sequences from each cluster while( $K > 1 ) { # fencepost - we already have found the $min # so very first time loop is executed we can skip checking unless( defined $min ) { for($i = 0; $i < $K; $i++ ) { for( $j = $i+1; $j < $K; $j++ ) { my $dij = $dmat[$i][$j]; if( ! defined $min || $dij <= $min) { if( defined $min && $min == $dij ) { push @mins, [$i,$j]; } else { @mins = [ $i,$j ]; $min = $dij; } } } } } # randomly break ties ($x,$y) = @{ $mins[int(rand(scalar @mins))] }; # now we are going to join clusters x and y, make a new cluster my $node = Bio::Tree::Node->new(); my @subids; for my $cid ( $x,$y ) { my $nid = $clusters[$cid]->{'id'}; if( ! defined $nodes[$nid] ) { $nodes[$nid] = Bio::Tree::Node->new(-id => $names[$nid]); } $nodes[$nid]->branch_length (sprintf($precisionstr,$min/2 - $clusters[$cid]->{'height'})); $node->add_Descendent($nodes[$nid]); push @subids, @{ $clusters[$cid]->{'contains'} }; } my $cluster = { 'id' => $c++, 'height' => $min / 2, 'contains' => [@subids], }; $K--; # we are going to drop the last node so go ahead and decrement K $nodes[$cluster->{'id'}] = $node; if ( $y != $K ) { $clusters[$y] = $clusters[$K]; $dmat[$y] = $dmat[$K]; for ( $i = 0; $i < $K; $i++ ) { $dmat[$i][$y] = $dmat[$y][$i]; } } delete $clusters[$K]; $clusters[$x] = $cluster; # now recalculate @dmat for( $i = 0; $i < $K; $i++ ) { if( $i != $x) { $dmat[$i][$x] = $dmat[$x][$i] = &_upgma_distance($clusters[$i],$clusters[$x],\@orig); } else { $dmat[$i][$i] = 0; } } # reset so next loop iteration # we will find minimum distance @mins = (); $min = undef; } Bio::Tree::Tree->new(-root => $nodes[-1]); } # calculate avg distance between clusters - be they # single sequences or the combination of multiple seqences # $cluster_i and $cluster_j are the clusters to operate on # and $distances is a matrix (arrayref of arrayrefs) of pairwise # differences indexed on the sequence ids - # so $distances->[0][1] is the distance between sequences 0 and 1 sub _upgma_distance { my ($cluster_i, $cluster_j, $distances) = @_; my $ilen = scalar @{ $cluster_i->{'contains'} }; my $jlen = scalar @{ $cluster_j->{'contains'} }; my ($d,$count); for( my $i = 0; $i < $ilen; $i++ ) { my $i_id = $cluster_i->{'contains'}->[$i]; for( my $j = 0; $j < $jlen; $j++) { my $j_id = $cluster_j->{'contains'}->[$j]; if( ! defined $distances->[$i_id][$j_id] ) { warn("no value for $i_id $j_id\n"); } else { $d += $distances->[$i_id][$j_id]; } $count++; } } return $d / $count; } =head2 method Title : method Usage : $obj->method($newval) Function: Example : Returns : value of method (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub method{ my $self = shift; return $self->{'_method'} = shift if @_; return $self->{'_method'}; } =head2 check_additivity Title : check_additivity Usage : if( $distance->check_additivity($matrix) ) { } Function : See if matrix obeys additivity principal Returns : boolean Args : Bio::Matrix::MatrixI References: Based on a Java implementation by Peter Sestoft, sestoft@dina.kvl.dk 1999-12-07 version 0.3 http://www.dina.kvl.dk/~sestoft/bsa.html which in turn is based on algorithms described in R. Durbin, S. Eddy, A. Krogh, G. Mitchison. Biological Sequence Analysis CUP 1998, Chapter 7. =cut sub check_additivity{ my ($self,$matrix) = @_; my @names = $matrix->column_names; my $len = scalar @names; return unless $len >= 4; # look at all sets of 4 for( my $i = 0; $i < $len; $i++ ) { for( my $j = $i+1; $j< $len; $j++) { for( my $k = $j+1; $k < $len; $k ++ ) { for( my $m = $k +1; $m < $len; $m++ ) { my $DijDkm = $matrix->get_entry($names[$i],$names[$j]) + $matrix->get_entry($names[$k],$names[$m]); my $DikDjm = $matrix->get_entry($names[$i],$names[$k]) + $matrix->get_entry($names[$j],$names[$m]); my $DimDjk = $matrix->get_entry($names[$i],$names[$m]) + $matrix->get_entry($names[$j],$names[$k]); if( !( ( $DijDkm == $DikDjm && $DijDkm >= $DimDjk) || ( $DijDkm == $DimDjk && $DijDkm >= $DikDjm) || ( $DikDjm == $DimDjk && $DikDjm >= $DijDkm) )) { return 0; } } } } } return 1; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tree/Node.pm�������������������������������������������������������������������000444��000766��000024�� 52641�13155576320� 16376� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tree::Node # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tree::Node - A Simple Tree Node =head1 SYNOPSIS use Bio::Tree::Node; my $nodeA = Bio::Tree::Node->new(); my $nodeL = Bio::Tree::Node->new(); my $nodeR = Bio::Tree::Node->new(); my $node = Bio::Tree::Node->new(); $node->add_Descendent($nodeL); $node->add_Descendent($nodeR); print "node is not a leaf \n" if( $node->is_leaf); =head1 DESCRIPTION Makes a Tree Node suitable for building a Tree. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 CONTRIBUTORS Aaron Mackey, amackey-at-virginia-dot-edu Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tree::Node; use vars qw($CREATIONORDER); use strict; use base qw(Bio::Root::Root Bio::Tree::NodeI); BEGIN { $CREATIONORDER = 1; } =head2 new Title : new Usage : my $obj = Bio::Tree::Node->new(); Function: Builds a new Bio::Tree::Node object Returns : Bio::Tree::Node Args : -descendents => arrayref of descendents (they will be updated s.t. their ancestor point is this node) -branch_length => branch length [integer] (optional) -bootstrap => value bootstrap value (string) -description => description of node -id => human readable id for node =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($children, $branchlen,$id, $bootstrap, $desc,$d) = $self->_rearrange([qw( DESCENDENTS BRANCH_LENGTH ID BOOTSTRAP DESC DESCRIPTION )], @args); $self->_register_for_cleanup(\&node_cleanup); $self->{'_desc'} = {}; # for descendents if( defined $d && defined $desc ) { $self->warn("can only accept -desc or -description, not both, accepting -description"); $desc = $d; } elsif( defined $d && ! defined $desc ) { $desc = $d; } defined $desc && $self->description($desc); defined $bootstrap && $self->bootstrap($bootstrap); defined $id && $self->id($id); defined $branchlen && $self->branch_length($branchlen); if( defined $children ) { if( ref($children) !~ /ARRAY/i ) { $self->throw("Must specify a valid ARRAY reference to initialize a Node's Descendents"); } foreach my $c ( @$children ) { $self->add_Descendent($c); } } $self->_creation_id($CREATIONORDER++); return $self; } =head2 create_node_on_branch Title : create_node_on_branch Usage : $node->create_node_on_branch($at_length) Function: Create a node on the ancestral branch of the calling object. Example : Returns : the created node Args : -POSITION=>$absolute_branch_length_from_caller (default) -FRACTION=>$fraction_of_branch_length_from_caller -ANNOT=>{ -id => "the id", -desc => "the description" } -FORCE, set to allow nodes with zero branch lengths =cut sub create_node_on_branch{ my ($self,@args) = @_; my ($pos, $frac, $annot, $force) = $self->_rearrange([qw(POSITION FRACTION ANNOT FORCE)], @args); my ($newpos); my $blen = $self->branch_length; # arg checks $force||=0; $annot||={}; unless ($self->ancestor) { $self->throw("Refusing to create nodes above the root--exiting"); } unless ($blen) { $self->throw("Calling node's branch length is zero") unless $force; } unless ((defined $pos && !defined $frac)||(defined $frac && !defined $pos)) { $self->throw("Either position or fraction must be specified, but not both"); } if (defined $frac) { $self->throw("FRACTION arg must be in the range [0,1]") unless ( (0 <= $frac) && ($frac <= 1) ); $newpos = $frac*$blen; } elsif (defined $pos) { $self->throw("POSITION arg must be in the range [0,$blen]") unless ( (0 <= $pos) && ($pos <= $blen) ); $newpos = $pos; } else { $self->throw("How did I get here?"); } $self->throw("Calling node's branch length will be zero (set -FORCE to force)--exiting") unless ($newpos > 0) || $force; $self->throw("Created nodes branch length would be zero (set -FORCE to force)--exiting") unless ($newpos < $blen) || $force; #guts $annot->{'-branch_length'} = $blen-$newpos; my $node = Bio::Tree::Node->new(%$annot); my $anc = $self->ancestor; # null anc check is above $node->add_Descendent($self); $anc->add_Descendent($node); $anc->remove_Descendent($self); $self->branch_length($newpos); return $node; } =head2 add_Descendent Title : add_Descendent Usage : $node->add_Descendent($node); Function: Adds a descendent to a node Returns : number of current descendents for this node Args : Bio::Node::NodeI boolean flag, true if you want to ignore the fact that you are adding a second node with the same unique id (typically memory location reference in this implementation). default is false and will throw an error if you try and overwrite an existing node. =cut sub add_Descendent{ my ($self,$node,$ignoreoverwrite) = @_; return -1 if( ! defined $node ); if( ! ref($node) || ref($node) =~ /HASH/ || ! $node->isa('Bio::Tree::NodeI') ) { $self->throw("Trying to add a Descendent who is not a Bio::Tree::NodeI"); return -1; } $self->{_adding_descendent} = 1; # avoid infinite recurse $node->ancestor($self) unless $node->{_setting_ancestor}; $self->{_adding_descendent} = 0; if( $self->{'_desc'}->{$node->internal_id} && ! $ignoreoverwrite ) { $self->throw("Going to overwrite a node which is $node that is already stored here, set the ignore overwrite flag (parameter 2) to true to ignore this in the future"); } $self->{'_desc'}->{$node->internal_id} = $node; # is this safely unique - we've tested before at any rate?? $self->invalidate_height(); return scalar keys %{$self->{'_desc'}}; } =head2 each_Descendent Title : each_Descendent($sortby) Usage : my @nodes = $node->each_Descendent; Function: all the descendents for this Node (but not their descendents i.e. not a recursive fetchall) Returns : Array of Bio::Tree::NodeI objects Args : $sortby [optional] "height", "creation", "alpha", "revalpha", or coderef to be used to sort the order of children nodes. =cut sub each_Descendent{ my ($self, $sortby) = @_; # order can be based on branch length (and sub branchlength) $sortby ||= 'none'; if (ref $sortby eq 'CODE') { my @values = sort { $sortby->($a,$b) } values %{$self->{'_desc'}}; return @values; } elsif ($sortby eq 'height') { return map { $_->[0] } sort { $a->[1] <=> $b->[1] || $a->[2] <=> $b->[2] } map { [$_, $_->height, $_->internal_id ] } values %{$self->{'_desc'}}; } elsif( $sortby eq 'alpha' ) { my @set; for my $v ( values %{$self->{'_desc'}} ) { unless( $v->is_Leaf ) { my @lst = ( sort { $a cmp $b } map { $_->id } grep { $_->is_Leaf } $v->get_all_Descendents($sortby)); push @set, [$v, $lst[0], $v->internal_id]; } else { push @set, [$v, $v->id, $v->internal_id]; } } return map { $_->[0] } sort {$a->[1] cmp $b->[1] || $a->[2] <=> $b->[2] } @set; } elsif( $sortby eq 'revalpha' ) { my @set; for my $v ( values %{$self->{'_desc'}} ) { if( ! defined $v->id && ! $v->is_Leaf ) { my ($l) = ( sort { $b cmp $a } map { $_->id } grep { $_->is_Leaf } $v->get_all_Descendents($sortby)); push @set, [$v, $l, $v->internal_id]; } else { push @set, [$v, $v->id, $v->internal_id]; } } return map { $_->[0] } sort {$b->[1] cmp $a->[1] || $b->[2] <=> $a->[2] } @set; } else { # creation return map { $_->[0] } sort { $a->[1] <=> $b->[1] } map { [$_, $_->internal_id ] } grep {defined $_} values %{$self->{'_desc'}}; } } =head2 remove_Descendent Title : remove_Descendent Usage : $node->remove_Descendent($node_foo); Function: Removes a specific node from being a Descendent of this node Returns : nothing Args : An array of Bio::Node::NodeI objects which have been previously passed to the add_Descendent call of this object. =cut sub remove_Descendent{ my ($self,@nodes) = @_; my $c= 0; foreach my $n ( @nodes ) { if( $self->{'_desc'}->{$n->internal_id} ) { $self->{_removing_descendent} = 1; $n->ancestor(undef); $self->{_removing_descendent} = 0; # should be redundant $self->{'_desc'}->{$n->internal_id}->ancestor(undef); delete $self->{'_desc'}->{$n->internal_id}; $c++; } else { if( $self->verbose ) { $self->debug(sprintf("no node %s (%s) listed as a descendent in this node %s (%s)\n",$n->id, $n,$self->id,$self)); $self->debug("Descendents are " . join(',', keys %{$self->{'_desc'}})."\n"); } } } $c; } =head2 remove_all_Descendents Title : remove_all_Descendents Usage : $node->remove_All_Descendents() Function: Cleanup the node's reference to descendents and reset their ancestor pointers to undef, if you don't have a reference to these objects after this call they will be cleaned up - so a get_nodes from the Tree object would be a safe thing to do first Returns : nothing Args : none =cut sub remove_all_Descendents{ my ($self) = @_; # This won't cleanup the nodes themselves if you also have # a copy/pointer of them (I think)... # That's true. But that's not a bug; if we retain a reference to them it's # very possible we want to keep them. The only way to truly destroy them is # to call DESTROY on the instance. while( my ($node,$val) = each %{ $self->{'_desc'} } ) { delete $self->{'_desc'}->{$node} } $self->{'_desc'} = {}; 1; } =head2 get_all_Descendents Title : get_all_Descendents Usage : my @nodes = $node->get_all_Descendents; Function: Recursively fetch all the nodes and their descendents *NOTE* This is different from each_Descendent Returns : Array or Bio::Tree::NodeI objects Args : none =cut # get_all_Descendents implemented in the interface =head2 ancestor Title : ancestor Usage : $obj->ancestor($newval) Function: Set the Ancestor Returns : ancestral node Args : newvalue (optional) =cut sub ancestor { my $self = shift; if (@_) { my $new_ancestor = shift; # we can set ancestor to undef if ($new_ancestor) { $self->throw("This is [$new_ancestor], not a Bio::Tree::NodeI") unless $new_ancestor->isa('Bio::Tree::NodeI'); } my $old_ancestor = $self->{'_ancestor'} || ''; if (!$old_ancestor || ($old_ancestor && ( !$new_ancestor || $new_ancestor ne $old_ancestor)) ) { if( $old_ancestor && ! $old_ancestor->{_removing_descendent}) { $old_ancestor->remove_Descendent($self); } if ($new_ancestor && ! $new_ancestor->{_adding_descendent} ) { # avoid infinite recurse $self->{_setting_ancestor} = 1; $new_ancestor->add_Descendent($self, 1); $self->{_setting_ancestor} = 0; } } $self->{'_ancestor'} = $new_ancestor; } return $self->{'_ancestor'}; } =head2 branch_length Title : branch_length Usage : $obj->branch_length() Function: Get/Set the branch length Returns : value of branch_length Args : newvalue (optional) =cut sub branch_length{ my $self = shift; if( @_ ) { my $bl = shift; if( defined $bl && $bl =~ s/\[(\d+)\]// ) { $self->bootstrap($1); } $self->{'_branch_length'} = $bl; $self->invalidate_height(); } return $self->{'_branch_length'}; } =head2 bootstrap Title : bootstrap Usage : $obj->bootstrap($newval) Function: Get/Set the bootstrap value Returns : value of bootstrap Args : newvalue (optional) =cut sub bootstrap { my $self = shift; if( @_ ) { if( $self->has_tag('B') ) { $self->remove_tag('B'); } $self->add_tag_value('B',shift); } return ($self->get_tag_values('B'))[0]; } =head2 description Title : description Usage : $obj->description($newval) Function: Get/Set the description string Returns : value of description Args : newvalue (optional) =cut sub description { my $self = shift; $self->{'_description'} = shift @_ if @_; return $self->{'_description'}; } =head2 id Title : id Usage : $obj->id($newval) Function: The human readable identifier for the node Returns : value of human readable id Args : newvalue (optional) "A name can be any string of printable characters except blanks, colons, semicolons, parentheses, and square brackets. Because you may want to include a blank in a name, it is assumed that an underscore character ("_") stands for a blank; any of these in a name will be converted to a blank when it is read in." from L<http://evolution.genetics.washington.edu/phylip/newicktree.html> Also note that these objects now support spaces, ();: because we can automatically quote the strings if they contain these characters. The L<id_output> method does this for you so use the id() method to get the raw string while L<id_output> to get the pre-escaped string. =cut sub id { my ($self, $value) = @_; if (defined $value) { #$self->warn("Illegal characters ();: and space in the id [$value], converting to _ ") # if $value =~ /\(\);:/ and $self->verbose >= 0; #$value =~ s/[\(\);:\s]/_/g; $self->{'_id'} = $value; } return $self->{'_id'}; } =head2 Helper Functions =cut =head2 id_output Title : id_output Usage : my $id = $node->id_output; Function: Return an id suitable for output in format like newick so that if it contains spaces or ():; characters it is properly quoted Returns : $id string if $node->id has a value Args : none =cut # implemented in NodeI interface =head2 internal_id Title : internal_id Usage : my $internalid = $node->internal_id Function: Returns the internal unique id for this Node (a monotonically increasing number for this in-memory implementation but could be a database determined unique id in other implementations) Returns : unique id Args : none =cut sub internal_id { return $_[0]->_creation_id; } =head2 _creation_id Title : _creation_id Usage : $obj->_creation_id($newval) Function: a private method signifying the internal creation order Returns : value of _creation_id Args : newvalue (optional) =cut sub _creation_id { my $self = shift @_; $self->{'_creation_id'} = shift @_ if( @_); return $self->{'_creation_id'} || 0; } =head2 Bio::Node::NodeI decorated interface implemented The following methods are implemented by L<Bio::Node::NodeI> decorated interface. =head2 is_Leaf Title : is_Leaf Usage : if( $node->is_Leaf ) Function: Get Leaf status Returns : boolean Args : none =cut sub is_Leaf { my ($self) = @_; my $isleaf = ! (defined $self->{'_desc'} && (keys %{$self->{'_desc'}} > 0) ); return $isleaf; } =head2 height Title : height Usage : my $len = $node->height Function: Returns the height of the tree starting at this node. Height is the maximum branchlength to get to the tip. Returns : The longest length (weighting branches with branch_length) to a leaf Args : none =cut sub height { my ($self) = @_; return $self->{'_height'} if( defined $self->{'_height'} ); return 0 if( $self->is_Leaf ); my $max = 0; foreach my $subnode ( $self->each_Descendent ) { my $bl = $subnode->branch_length; $bl = 1 unless (defined $bl && $bl =~ /^\-?\d+(\.\d+)?$/); my $s = $subnode->height + $bl; if( $s > $max ) { $max = $s; } } return ($self->{'_height'} = $max); } =head2 invalidate_height Title : invalidate_height Usage : private helper method Function: Invalidate our cached value of the node height in the tree Returns : nothing Args : none =cut sub invalidate_height { my ($self) = @_; $self->{'_height'} = undef; if( defined $self->ancestor ) { $self->ancestor->invalidate_height; } } =head2 set_tag_value Title : set_tag_value Usage : $node->set_tag_value($tag,$value) $node->set_tag_value($tag,@values) Function: Sets a tag value(s) to a node. Replaces old values. Returns : number of values stored for this tag Args : $tag - tag name $value - value to store for the tag =cut sub set_tag_value{ my ($self,$tag,@values) = @_; if( ! defined $tag || ! scalar @values ) { $self->warn("cannot call set_tag_value with an undefined value"); } $self->remove_tag ($tag); map { push @{$self->{'_tags'}->{$tag}}, $_ } @values; return scalar @{$self->{'_tags'}->{$tag}}; } =head2 add_tag_value Title : add_tag_value Usage : $node->add_tag_value($tag,$value) Function: Adds a tag value to a node Returns : number of values stored for this tag Args : $tag - tag name $value - value to store for the tag =cut sub add_tag_value{ my ($self,$tag,$value) = @_; if( ! defined $tag || ! defined $value ) { $self->warn("cannot call add_tag_value with an undefined value".($tag ? " ($tag)" : '')); $self->warn($self->stack_trace_dump,"\n"); } push @{$self->{'_tags'}->{$tag}}, $value; return scalar @{$self->{'_tags'}->{$tag}}; } =head2 remove_tag Title : remove_tag Usage : $node->remove_tag($tag) Function: Remove the tag and all values for this tag Returns : boolean representing success (0 if tag does not exist) Args : $tag - tagname to remove =cut sub remove_tag { my ($self,$tag) = @_; if( exists $self->{'_tags'}->{$tag} ) { $self->{'_tags'}->{$tag} = undef; delete $self->{'_tags'}->{$tag}; return 1; } return 0; } =head2 remove_all_tags Title : remove_all_tags Usage : $node->remove_all_tags() Function: Removes all tags Returns : None Args : None =cut sub remove_all_tags{ my ($self) = @_; $self->{'_tags'} = {}; return; } =head2 get_all_tags Title : get_all_tags Usage : my @tags = $node->get_all_tags() Function: Gets all the tag names for this Node Returns : Array of tagnames Args : None =cut sub get_all_tags{ my ($self) = @_; my @tags = sort keys %{$self->{'_tags'} || {}}; return @tags; } =head2 get_tag_values Title : get_tag_values Usage : my @values = $node->get_tag_values($tag) Function: Gets the values for given tag ($tag) Returns : In array context returns an array of values or an empty list if tag does not exist. In scalar context returns the first value or undef. Args : $tag - tag name =cut sub get_tag_values{ my ($self,$tag) = @_; return wantarray ? @{$self->{'_tags'}->{$tag} || []} : (@{$self->{'_tags'}->{$tag} || []})[0]; } =head2 has_tag Title : has_tag Usage : $node->has_tag($tag) Function: Boolean test if tag exists in the Node Returns : Boolean Args : $tag - tagname =cut sub has_tag { my ($self,$tag) = @_; return exists $self->{'_tags'}->{$tag}; } sub node_cleanup { my $self = shift; return unless defined $self; #*** below is wrong, cleanup doesn't actually occur. Will replace with: # $self->remove_all_Descendents; once further fixes in place.. #if( defined $self->{'_desc'} && # ref($self->{'_desc'}) =~ /HASH/i ) { # while( my ($nodeid,$node) = each %{ $self->{'_desc'} } ) { # $node->ancestor(undef); # insure no circular references # $node = undef; # } #} $self->remove_all_Descendents; #$self->{'_desc'} = {}; 1; } =head2 reverse_edge Title : reverse_edge Usage : $node->reverse_edge(child); Function: makes child be a parent of node Requires: child must be a direct descendent of node Returns : 1 on success, 0 on failure Args : Bio::Tree::NodeI that is in the tree =cut sub reverse_edge { my ($self,$node) = @_; if( $self->delete_edge($node) ) { $node->add_Descendent($self); return 1; } return 0; } 1; �����������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tree/NodeI.pm������������������������������������������������������������������000444��000766��000024�� 27071�13155576320� 16506� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tree::NodeI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tree::NodeI - Interface describing a Tree Node =head1 SYNOPSIS # get a Tree::NodeI somehow # like from a TreeIO use Bio::TreeIO; # read in a clustalw NJ in phylip/newick format my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'file.dnd'); my $tree = $treeio->next_tree; # we'll assume it worked for demo purposes # you might want to test that it was defined my $rootnode = $tree->get_root_node; # process just the next generation foreach my $node ( $rootnode->each_Descendent() ) { print "branch len is ", $node->branch_length, "\n"; } # process all the children my $example_leaf_node; foreach my $node ( $rootnode->get_all_Descendents() ) { if( $node->is_Leaf ) { print "node is a leaf ... "; # for example use below $example_leaf_node = $node unless defined $example_leaf_node; } print "branch len is ", $node->branch_length, "\n"; } # The ancestor() method points to the parent of a node # A node can only have one parent my $parent = $example_leaf_node->ancestor; # parent won't likely have an description because it is an internal node # but child will because it is a leaf print "Parent id: ", $parent->id," child id: ", $example_leaf_node->id, "\n"; =head1 DESCRIPTION A NodeI is capable of the basic structure of building a tree and storing the branch length between nodes. The branch length is the length of the branch between the node and its ancestor, thus a root node in a Tree will not typically have a valid branch length. Various implementations of NodeI may extend the basic functions and allow storing of other information (like attaching a species object or full sequences used to build a tree or alternative sequences). If you don't know how to extend a Bioperl object please ask, happy to help, we would also greatly appreciate contributions with improvements or extensions of the objects back to the Bioperl code base so that others don't have to reinvent your ideas. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 CONTRIBUTORS Aaron Mackey amackey@virginia.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tree::NodeI; use strict; no warnings 'recursion'; use base qw(Bio::Root::RootI); =head2 add_Descendent Title : add_Descendent Usage : $node->add_Descendent($node); Function: Adds a descendent to a node Returns : number of current descendents for this node Args : Bio::Node::NodeI =cut sub add_Descendent{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 each_Descendent Title : each_Descendent Usage : my @nodes = $node->each_Descendent; Function: all the descendents for this Node (but not their descendents i.e. not a recursive fetchall) Returns : Array of Bio::Tree::NodeI objects Args : none =cut sub each_Descendent{ my ($self) = @_; $self->throw_not_implemented(); } =head2 Decorated Interface methods =cut =head2 get_all_Descendents Title : get_all_Descendents($sortby) Usage : my @nodes = $node->get_all_Descendents; Function: Recursively fetch all the nodes and their descendents *NOTE* This is different from each_Descendent Returns : Array or Bio::Tree::NodeI objects Args : $sortby [optional] "height", "creation", "alpha", "revalpha", or a coderef to be used to sort the order of children nodes. =cut sub get_all_Descendents{ my ($self, $sortby) = @_; $sortby ||= 'none'; my @nodes; foreach my $node ( $self->each_Descendent($sortby) ) { push @nodes, ($node,$node->get_all_Descendents($sortby)); } return @nodes; } *get_Descendents = \&get_all_Descendents; =head2 is_Leaf Title : is_Leaf Usage : if( $node->is_Leaf ) Function: Get Leaf status Returns : boolean Args : none =cut sub is_Leaf{ my ($self) = @_; $self->throw_not_implemented(); } =head2 descendent_count Title : descendent_count Usage : my $count = $node->descendent_count; Function: Counts the number of descendents a node has (and all of their subnodes) Returns : integer Args : none =cut sub descendent_count{ my ($self) = @_; my $count = 0; foreach my $node ( $self->each_Descendent ) { $count += 1; $node->can('descendent_count') ? $count += $node->descendent_count : next; } return $count; } =head2 to_string Title : to_string Usage : my $str = $node->to_string() Function: For debugging, provide a node as a string Returns : string Args : none =cut sub to_string{ my ($self) = @_; return join('',defined $self->id_output ? $self->id_output : '', defined $self->branch_length ? ':' . $self->branch_length : ' ') } =head2 height Title : height Usage : my $len = $node->height Function: Returns the height of the tree starting at this node. Height is the maximum branchlength to get to the tip. Returns : The longest length (weighting branches with branch_length) to a leaf Args : none =cut sub height{ my ($self) = @_; return 0 if( $self->is_Leaf ); my $max = 0; foreach my $subnode ( $self->each_Descendent ) { my $s = $subnode->height + $subnode->branch_length;; if( $s > $max ) { $max = $s; } } return $max; } =head2 depth Title : depth Usage : my $len = $node->depth Function: Returns the depth of the tree starting at this node. Depth is the distance from this node to the root. Returns : The branch length to the root. Args : none =cut sub depth{ my ($self) = @_; my $depth = 0; my $node = $self; while( defined $node->ancestor ) { $depth += $node->branch_length; $node = $node->ancestor; } return $depth; } =head2 Get/Set methods =cut =head2 branch_length Title : branch_length Usage : $obj->branch_length() Function: Get/Set the branch length Returns : value of branch_length Args : newvalue (optional) =cut sub branch_length{ my ($self)= @_; $self->throw_not_implemented(); } =head2 id Title : id Usage : $obj->id($newval) Function: The human readable identifier for the node Returns : value of human readable id Args : newvalue (optional) =cut sub id{ my ($self)= @_; $self->throw_not_implemented(); } =head2 internal_id Title : internal_id Usage : my $internalid = $node->internal_id Function: Returns the internal unique id for this Node Returns : unique id Args : none =cut sub internal_id{ my ($self) = @_; $self->throw_not_implemented(); } =head2 description Title : description Usage : $obj->description($newval) Function: Get/Set the description string Returns : value of description Args : newvalue (optional) =cut sub description{ my ($self) = @_; $self->throw_not_implemented(); } =head2 bootstrap Title : bootstrap Usage : $obj->bootstrap($newval) Function: Get/Set the bootstrap value Returns : value of bootstrap Args : newvalue (optional) =cut sub bootstrap{ my ($self) = @_; $self->throw_not_implemented(); } =head2 ancestor Title : ancestor Usage : my $node = $node->ancestor; Function: Get/Set the ancestor node pointer for a Node Returns : Null if this is top level node Args : none =cut sub ancestor{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 invalidate_height Title : invalidate_height Usage : private helper method Function: Invalidate our cached value of the node height in the tree Returns : nothing Args : none =cut sub invalidate_height { shift->throw_not_implemented(); } =head2 Methods for associating Tag/Values with a Node These methods associate tag/value pairs with a Node =head2 set_tag_value Title : set_tag_value Usage : $node->set_tag_value($tag,$value) $node->set_tag_value($tag,@values) Function: Sets a tag value(s) to a node. Replaces old values. Returns : number of values stored for this tag Args : $tag - tag name $value - value to store for the tag =cut sub set_tag_value{ shift->throw_not_implemented(); } =head2 add_tag_value Title : add_tag_value Usage : $node->add_tag_value($tag,$value) Function: Adds a tag value to a node Returns : number of values stored for this tag Args : $tag - tag name $value - value to store for the tag =cut sub add_tag_value{ shift->throw_not_implemented(); } =head2 remove_tag Title : remove_tag Usage : $node->remove_tag($tag) Function: Remove the tag and all values for this tag Returns : boolean representing success (0 if tag does not exist) Args : $tag - tagname to remove =cut sub remove_tag { shift->throw_not_implemented(); } =head2 remove_all_tags Title : remove_all_tags Usage : $node->remove_all_tags() Function: Removes all tags Returns : None Args : None =cut sub remove_all_tags{ shift->throw_not_implemented(); } =head2 get_all_tags Title : get_all_tags Usage : my @tags = $node->get_all_tags() Function: Gets all the tag names for this Node Returns : Array of tagnames Args : None =cut sub get_all_tags { shift->throw_not_implemented(); } =head2 get_tag_values Title : get_tag_values Usage : my @values = $node->get_tag_values($tag) Function: Gets the values for given tag ($tag) Returns : Array of values or empty list if tag does not exist Args : $tag - tag name =cut sub get_tag_values{ shift->throw_not_implemented(); } =head2 has_tag Title : has_tag Usage : $node->has_tag($tag) Function: Boolean test if tag exists in the Node Returns : Boolean Args : $tag - tagname =cut sub has_tag{ shift->throw_not_implemented(); } =head2 Helper Functions =cut =head2 id_output Title : id_output Usage : my $id = $node->id_output; Function: Return an id suitable for output in format like newick so that if it contains spaces or ():; characters it is properly quoted Returns : $id string if $node->id has a value Args : none =cut sub id_output{ my $node = shift; my $id = $node->id; return unless( defined $id && length($id ) ); # single quotes must become double quotes # $id =~ s/'/''/g; if( $id =~ /[\(\);:,\s]/ ) { $id = '"'.$id.'"'; } return $id; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tree/NodeNHX.pm����������������������������������������������������������������000444��000766��000024�� 11040�13155576320� 16740� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tree::NodeNHX # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Aaron Mackey <amackey@virginia.edu> # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags =head1 SYNOPSIS use Bio::Tree::NodeNHX; my $nodeA = Bio::Tree::NodeNHX->new(); my $nodeL = Bio::Tree::NodeNHX->new(); my $nodeR = Bio::Tree::NodeNHX->new(); my $node = Bio::Tree::NodeNHX->new(); $node->add_Descendents($nodeL); $node->add_Descendents($nodeR); print "node is not a leaf \n" if( $node->is_leaf); =head1 DESCRIPTION Makes a Tree Node with NHX tags, suitable for building a Tree. See L<Bio::Tree::Node> for a full list of functionality. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Aaron Mackey Email amackey@virginia.edu =head1 CONTRIBUTORS The NHX (New Hampshire eXtended) format was created by Chris Zmasek, and is described at: http://sourceforge.net/projects/forester-atv/ =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tree::NodeNHX; use strict; use base qw(Bio::Tree::Node); =head2 new Title : new Usage : my $obj = Bio::Tree::NodeNHX->new(); Function: Builds a new Bio::Tree::NodeNHX object Returns : Bio::Tree::NodeNHX Args : -left => pointer to Left descendent (optional) -right => pointer to Right descenent (optional) -branch_length => branch length [integer] (optional) -bootstrap => bootstrap value (string) -description => description of node -id => unique id for node -nhx => hashref of NHX tags and values =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($nhx) = $self->_rearrange([qw(NHX)], @args); $self->nhx_tag($nhx); return $self; } sub DESTROY { my ($self) = @_; # try to insure that everything is cleaned up $self->SUPER::DESTROY(); if( defined $self->{'_desc'} && ref($self->{'_desc'}) =~ /ARRAY/i ) { while( my ($nodeid,$node) = each %{ $self->{'_desc'} } ) { $node->{'_ancestor'} = undef; # insure no circular references $node->DESTROY(); $node = undef; } $self->{'_desc'} = {}; } } sub to_string{ my ($self) = @_; my @tags = $self->get_all_tags; my $tagstr = ''; if( scalar(@tags) > 0 ) { $tagstr = '[' . join(":", "&&NHX", map { "$_=" .join(',', $self->get_tag_values($_))} @tags ) . ']'; } return sprintf("%s%s%s", defined $self->id ? $self->id : '', defined $self->branch_length ? ':' . $self->branch_length : ' ', $tagstr); } =head2 nhx_tag Title : nhx_tag Usage : my $tag = $nodenhx->nhx_tag(%tags); Function: Set tag-value pairs for NHX nodes Returns : none Args : hashref to update the tags/value pairs OR with a scalar value update the bootstrap value by default =cut sub nhx_tag { my ($self, $tags) = @_; if (defined $tags && (ref($tags) =~ /HASH/i)) { while( my ($tag,$val) = each %$tags ) { if( ref($val) =~ /ARRAY/i ) { for my $v ( @$val ) { $self->add_tag_value($tag,$v); } } else { $self->add_tag_value($tag,$val); } } if (exists $tags->{'B'}) { $self->bootstrap($tags->{'B'}); } } elsif (defined $tags and ! ref ($tags)) { $self->debug( "here with $tags\n"); # bootstrap by default $self->bootstrap($tags); } } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tree/RandomFactory.pm����������������������������������������������������������000444��000766��000024�� 33504�13155576320� 20256� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tree::RandomFactory # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tree::RandomFactory - TreeFactory for generating Random Trees =head1 SYNOPSIS use Bio::Tree::RandomFactory my @taxonnames; my $factory = Bio::Tree::RandomFactory->new( -taxa => \@taxonnames, -maxcount => 10); # or for anonymous samples my $factory = Bio::Tree::RandomFactory->new( -num_taxa => 6, -maxcount => 50); my $tree = $factory->next_tree; =head1 DESCRIPTION Builds a random tree every time next_tree is called or up to -maxcount times. This module was originally written for Coalescent simulations see L<Bio::PopGen::Simulation::Coalescent>. I've left the next_tree method intact although it is not generating random trees in the phylogenetic sense. I would be happy for someone to provide alternative implementations which can be used here. As written it will generate random topologies but the branch lengths are built from assumptions in the coalescent and are not appropriate for phylogenetic analyses. This algorithm is based on the make_tree algorithm from Richard Hudson 1990. Hudson, R. R. 1990. Gene genealogies and the coalescent process. Pp. 1-44 in D. Futuyma and J. Antonovics, eds. Oxford surveys in evolutionary biology. Vol. 7. Oxford University Press, New York Sanderson, M ... =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-AT-bioperl.org =head1 CONTRIBUTORS Matthew Hahn, E<lt>matthew.hahn@duke.eduE<gt> Mike Sanderson =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tree::RandomFactory; use vars qw($PRECISION_DIGITS $DefaultNodeType %Defaults); use strict; $PRECISION_DIGITS = 3; # Precision for the branchlength $DefaultNodeType = 'Bio::Tree::Node'; %Defaults = ('YuleRate' => 1.0, # as set by Sanderson in Rates 'Speciation' => 1.0, # 'DefaultTreeMethod' => 'yule', ); use Bio::Tools::RandomDistFunctions; use Bio::Tree::Tree; use base qw(Bio::Root::Root Bio::Factory::TreeFactoryI); =head2 new Title : new Usage : my $factory = Bio::Tree::RandomFactory->new(-samples => \@samples, -maxcount=> $N); Function: Initializes a Bio::Tree::RandomFactory object Returns : Bio::Tree::RandomFactory Args : -nodetype => Type of Nodes to create [default Bio::Tree::Node] -maxcount => [optional] Maximum num trees to create -randtype => Type of random trees so far support - yule/backward_yule/BY [default] - forward_yule/FY - birthdeath_forward/BDF - birthdeath_backwards/BDB ONE of the following must be specified -taxa => $arrayref of taxa names -num_taxa => integer indicating number of taxa in the tree =cut sub new{ my ($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->{'_treecounter'} = 0; $self->{'_maxcount'} = 0; my ($nodetype,$randtype, $maxcount, $samps,$samplesize, $taxa, $num_taxa) = $self->_rearrange([qw(NODETYPE RANDTYPE MAXCOUNT SAMPLES SAMPLE_SIZE TAXA NUM_TAXA)], @args); my @taxa; $nodetype ||= $DefaultNodeType; $self->nodetype($nodetype); $taxa = $samps if defined $samps && ! defined $taxa; $num_taxa = $samplesize if $samplesize && ! $num_taxa; if( ! defined $taxa ) { if( ! defined $num_taxa || $num_taxa <= 0 ) { $self->throw("Must specify a valid num_taxa if parameter -TAXA is not specified"); } foreach ( 1..$num_taxa ) { push @taxa, "Taxon$_"; } } else { if( ref($taxa) !~ /ARRAY/i ) { $self->throw("Must specify a valid ARRAY reference to the parameter -TAXA, did you forget a leading '\\'? for $taxa"); } @taxa = @$taxa; } $self->taxa(\@taxa); defined $maxcount && $self->maxcount($maxcount); $self->{'_count'} = 0; return $self; } =head2 next_tree Title : next_tree Usage : my $tree = $factory->next_tree Function: Returns a random tree based on the initialized number of nodes NOTE: if maxcount is not specified on initialization or set to a valid integer, subsequent calls to next_tree will continue to return random trees and never return undef Returns : Bio::Tree::TreeI object Args : none =cut sub next_tree{ my ($self,%options) = @_; return if $self->maxcount && $self->{'_count'}++ >= $self->maxcount; my $rand_type = $options{'randtype'} || $self->random_tree_method; my $nodetype = $self->nodetype; my $treearray; if( $rand_type =~ /(birthdeath_forward|birth|BDF)/i ) { } elsif ( $rand_type =~ /(birthdeath_backward|BDB)/i ) { $treearray = $self->rand_birthdeath_backwards_tree; } elsif( $rand_type =~ /(BY|backwards_yule)/i || $rand_type =~ /^yule/i ) { my $speciation = $options{'speciation'}; # can be undef $treearray = $self->rand_yule_c_tree($speciation); } else { $self->warn("unrecognized random type $rand_type"); } my @nodes = (); foreach my $n ( @$treearray ) { for my $k ( qw(desc1 desc2) ) { next unless defined $n->{$k}; push @{$n->{'descendents'}}, $nodes[$n->{$k}]; } push @nodes, $nodetype->new(-id => $n->{'nodenum'}, -branch_length => $n->{'time'}, -descendents => $n->{'descendents'}, ); } my $T = Bio::Tree::Tree->new(-root => pop @nodes ); return $T; } =head2 maxcount Title : maxcount Usage : $obj->maxcount($newval) Function: Returns : Maxcount value Args : newvalue (optional) =cut sub maxcount{ my ($self,$value) = @_; if( defined $value) { if( $value =~ /^(\d+)/ ) { $self->{'_maxcount'} = $1; } else { $self->warn("Must specify a valid Positive integer to maxcount"); $self->{'_maxcount'} = 0; } } return $self->{'_maxcount'}; } =head2 reset_tree_count Title : reset_tree_count Usage : $factory->reset_tree_count; Function: Reset the tree counter Returns : none Args : none =cut sub reset_count{ shift->{'_count'} = 0; } =head2 taxa Title : taxa Usage : $obj->taxa($newval) Function: Set the leaf node names Returns : value of taxa Args : Arrayref of Taxon names =cut sub taxa { my ($self,$value) = @_; if( defined $value) { if( ref($value) !~ /ARRAY/i ) { $self->warn("Must specify a valid array ref to the method 'taxa'"); $value = []; } $self->{'_taxa'} = $value; $self->{'_num_taxa'} = scalar @$value; } return $self->{'_taxa'}; } =head2 num_taxa Title : num_taxa Usage : $obj->num_taxa($newval) Function: Get the number of Taxa Returns : value of num_taxa Args : none =cut sub num_taxa { my ($self) = @_; return $self->{'_num_taxa'}; } # alias old methods *num_samples = \&num_taxa; *samples = \&taxa; =head2 random Title : random Usage : my $rfloat = $node->random($size) Function: Generates a random number between 0 and $size This is abstracted so that someone can override and provide their own special RNG. This is expected to be a uniform RNG. Returns : Floating point random Args : $maximum size for random number (defaults to 1) =cut sub random{ my ($self,$max) = @_; return rand($max); } =head2 random_tree_method Title : random_tree_method Usage : $obj->random_tree_method($newval) Function: Example : Returns : value of random_tree_method (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub random_tree_method{ my $self = shift; return $self->{'random_tree_method'} = shift if @_; return $self->{'random_tree_method'} || $Defaults{'DefaultTreeMethod'}; } =head2 nodetype Title : nodetype Usage : $obj->nodetype($newval) Function: Example : Returns : value of nodetype (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub nodetype{ my ($self,$value) = @_; if( defined $value) { eval "require $value"; if( $@ ) { $self->throw("$@: Unrecognized Node type for ".ref($self). "'$value'");} my $a = bless {},$value; unless( $a->isa('Bio::Tree::NodeI') ) { $self->throw("Must provide a valid Bio::Tree::NodeI or child class to SeqFactory Not $value"); } $self->{'nodetype'} = $value; } return $self->{'nodetype'}; } # The assignment of times are based on Mike Sanderson's r8s code # The topology assignment code is based on Richard Hudson's # make_trees sub rand_yule_c_tree { my ($self,$speciation) = @_; $speciation ||= $Defaults{'Speciation'}; my $n_taxa = $self->num_taxa; my $taxa = $self->taxa || []; my $nodetype = $self->nodetype; my $randfuncs = Bio::Tools::RandomDistFunctions->new(); my $rate = $Defaults{'YuleRate'}; my (@tree,@list,@times,$i,$in); my $max = 2 * $n_taxa - 1; for($in=0;$in < $max; $in++ ) { push @tree, { 'nodenum' => "Node$in" }; } # setup leaf nodes for($in=0;$in < $n_taxa;$in++) { $tree[$in]->{'time'} = 0; $tree[$in]->{'desc1'} = undef; $tree[$in]->{'desc2'} = undef; if( my $r = $taxa->[$in] ) { $tree[$in]->{'nodenum'} = $r; } push @list, $in; } for( $i = 0; $i < $n_taxa - 1; $i++ ) { # draw random interval times push @times, $randfuncs->rand_birth_distribution($speciation); } # sort smallest to largest @times = sort {$a <=> $b} @times; # topology generation for ($in = $n_taxa; $in > 1; $in-- ) { my $time = shift @times; my $pick = int $self->random($in); my $nodeindex = $list[$pick]; $tree[$list[$pick]]->{'time'} = $time; my $swap = 2 * $n_taxa - $in; $tree[$swap]->{'desc1'} = $nodeindex; $list[$pick] = $list[$in-1]; $pick = int rand($in - 1); $nodeindex = $list[$pick]; $tree[$list[$pick]]->{'time'} = $time; $tree[$swap]->{'desc2'} = $nodeindex; $list[$pick] = $swap; } $tree[-1]->{'time'} = shift @times; return \@tree; } sub rand_birthdeath_backwards_tree { my ($self) = @_; my $n_taxa = $self->num_taxa; my $taxa = $self->taxa || []; my $randfuncs = Bio::Tools::RandomDistFunctions->new(); my $rate = $Defaults{'YuleRate'}; my (@tree,@list,@times,$i,$in); my $max = 2 * $n_taxa - 1; for($in=0;$in < $max; $in++ ) { push @tree, { 'nodenum' => "Node$in" }; } # setup leaf nodes for($in=0;$in < $n_taxa;$in++) { $tree[$in]->{'time'} = 0; $tree[$in]->{'desc1'} = undef; $tree[$in]->{'desc2'} = undef; if( my $r = $taxa->[$in] ) { # deal with pre-labeled nodes $tree[$in]->{'nodenum'} = $r; } push @list, $in; } my ($time) = (0); # topology generation for ($in = $n_taxa; $in > 1; $in-- ) { my $pick = int $self->random($in); my $nodeindex = $list[$pick]; my $swap = 2 * $n_taxa - $in; $time += $randfuncs->rand_geometric_distribution($n_taxa * $rate);; $tree[$list[$pick]]->{'time'} = $time; $tree[$swap]->{'desc1'} = $nodeindex; $list[$pick] = $list[$in-1]; $pick = int rand($in - 1); $nodeindex = $list[$pick]; $tree[$list[$pick]]->{'time'} = $time; $tree[$swap]->{'desc2'} = $nodeindex; $list[$pick] = $swap; } my $root = $tree[-1]; $time += $randfuncs->rand_geometric_distribution($n_taxa * $rate);; $root->{'time'} = $time; # Normalize times by the root node... for my $node ( @tree ) { $node->{'time'} /= $root->{'time'}; } return \@tree; } # The assignment of times are based on Mike Sanderson's r8s code # The topology assignment code is based on Richard Hudson's # make_trees sub rand_birth_death_tree { # Still need to finish # my ($self,$spec_rate,$extinct_rate,$char_rate) = @_; # my $n_taxa = $self->num_taxa; # my $dt = 0.1 / $n_taxa; # my @tree; # my $max = 3 * $n_taxa - 1; # # setup leaf nodes # for($in=0;$in < $size;$in++) { # push @tree, { 'nodenum' => $taxa->[$in] || "Node$in", # 'time' => 0, # 'desc1' => undef, # 'desc2' => undef, # }; # } # my $time = $dt; # my $idx = 0; # while( $n_taxa > 1 ) { # if ( event($dt * $spec_rate, $n_taxa) ) { # my $pick = int $self->random($n_taxa); # my $pick2 = int $self->random($n_taxa); # while( $pick2 == $pick ) { # $pick2 = int $self->random($n_taxa); # } # to finish.... # $tree[$swap]->{'desc1'} = $nodeindex; # } # } # $list[$pick] = $list[$in-1]; # $pick = int rand($in - 1); # $nodeindex = $list[$pick]; # $tree[$swap]->{'desc2'} = $nodeindex; # $list[$pick] = $swap; # $tree[$swap]->{'time'} = $times[$ix++]; # } } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tree/Statistics.pm�������������������������������������������������������������000444��000766��000024�� 60060�13155576320� 17635� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tree::Statistics # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tree::Statistics - Calculate certain statistics for a Tree =head1 SYNOPSIS use Bio::Tree::Statistics; =head1 DESCRIPTION This should be where Tree statistics are calculated. It was previously where statistics from a Coalescent simulation. It now contains several methods for calculating L<Tree-Trait statistics>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason AT bioperl.org =head1 CONTRIBUTORS Heikki Lehvaslaiho, heikki at bioperl dot org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tree::Statistics; use strict; use base qw(Bio::Root::Root); =head2 new Title : new Usage : my $obj = Bio::Tree::Statistics->new(); Function: Builds a new Bio::Tree::Statistics object Returns : Bio::Tree::Statistics Args : =head2 assess_bootstrap Title : assess_bootstrap Usage : my $tree_with_bs = $stats->assess_bootstrap(\@bs_trees,$guide_tree); Function: Calculates the bootstrap for internal nodes based on the percentage of times \@bs_trees agree with each internal node Returns : L<Bio::Tree::TreeI> Args : Arrayref of L<Bio::Tree::TreeI>s Guide tree, L<Bio::Tree::TreeI>s =cut sub assess_bootstrap{ my ($self,$bs_trees,$guide_tree) = @_; my @consensus; # internal nodes are defined by their children my (%lookup,%internal); my $i = 0; for my $tree ( $guide_tree, @$bs_trees ) { # Do this as a top down approach, can probably be # improved by caching internal node states, but not going # to worry about it right now. my @allnodes = $tree->get_nodes; my @internalnodes = grep { ! $_->is_Leaf } @allnodes; for my $node ( @internalnodes ) { my @tips = sort map { $_->id } grep { $_->is_Leaf() } $node->get_all_Descendents; my $id = "(".join(",", @tips).")"; if( $i == 0 ) { $internal{$id} = $node->internal_id; } else { $lookup{$id}++; } } $i++; } my @save; for my $l ( keys %lookup ) { if( defined $internal{$l} ) {#&& $lookup{$l} > $min_seen ) { my $intnode = $guide_tree->find_node(-internal_id => $internal{$l}); $intnode->bootstrap(sprintf("%d",100 * $lookup{$l} / $i)); } } return $guide_tree; } =head2 cherries Example : cherries($tree, $node); Description: Count number of paired leaf nodes in a binary tree Returns : integer Exceptions : Args : 1. Bio::Tree::TreeI object 2. Bio::Tree::NodeI object within the tree, optional Commonly used statistics assume a binary tree, but this methods returns a value even for trees with polytomies. =cut sub cherries ($;$) { my $self = shift; my $tree = shift; my $node = shift || $tree->get_root_node; my $cherries = 0; my @descs = $node->each_Descendent; if ($descs[0]->is_Leaf and $descs[1]->is_Leaf) { if ($descs[3]) { #polytomy at leaf level $cherries = 0; } else { $cherries = 1; } } else { # recurse foreach my $desc (@descs) { $cherries += $self->cherries($tree, $desc); } } return $cherries; } =head2 Tree-Trait statistics The following methods produce descriptors of trait distribution among leaf nodes within the trees. They require that a trait has been set for each leaf node. The tag methods of Bio::Tree::Node are used to store them as key/value pairs. In this way, one tree can store more than one trait. Trees have method add_traits() to set trait values from a file. See the add_trait() method in L<Bio::Tree::TreeFunctionsI>. =head2 fitch Example : fitch($tree, $key, $node); Description: Calculates Parsimony Score (PS) and internal trait values using the Fitch 1971 parsimony algorithm for the subtree a defined by the (internal) node. Node defaults to the root. Returns : true on success Exceptions : leaf nodes have to have the trait defined Args : 1. Bio::Tree::TreeI object 2. trait name string 3. Bio::Tree::NodeI object within the tree, optional Runs first L<fitch_up> that calculates parsimony scores and then L<fitch_down> that should resolve most of the trait/character state ambiguities. Fitch, W.M., 1971. Toward defining the course of evolution: minimal change for a specific tree topology. Syst. Zool. 20, 406-416. You can access calculated parsimony values using: $score = $node->->get_tag_values('ps_score'); and the trait value with: $traitvalue = $node->->get_tag_values('ps_trait'); # only the first @traitvalues = $node->->get_tag_values('ps_trait'); Note that there can be more that one trait value, especially for the root node. =cut sub fitch { my $self = shift; my $tree = shift; my $key = shift || $self->throw("Trait name is needed"); my $node = shift || $tree->get_root_node; $self->fitch_up($tree, $key, $node); $self->fitch_down($tree, $node); } =head2 ps Example : ps($tree, $key, $node); Description: Calculates Parsimony Score (PS) from Fitch 1971 parsimony algorithm for the subtree as defined by the (internal) node. Node defaults to the root. Returns : integer, 1 < PS < n, where n is number of branches Exceptions : leaf nodes have to have the trait defined Args : 1. Bio::Tree::TreeI object 2. trait name string 3. Bio::Tree::NodeI object within the tree, optional This is the first half of the Fitch algorithm that is enough for calculating the resolved parsimony values. The trait/chararacter states are commonly left in ambiguous state. To resolve them, run L<fitch_down>. =cut sub ps { shift->fitch_up(@_) } =head2 fitch_up Example : fitch_up($tree, $key, $node); Description: Calculates Parsimony Score (PS) from the Fitch 1971 parsimony algorithm for the subtree as defined by the (internal) node. Node defaults to the root. Returns : integer, 1< PS < n, where n is number of branches Exceptions : leaf nodes have to have the trait defined Args : 1. Bio::Tree::TreeI object 2. trait name string 3. Bio::Tree::NodeI object within the tree, optional This is a more generic name for L<ps> and indicates that it performs the first bottom-up tree traversal that calculates the parsimony score but usually leaves trait/character states ambiguous. If you are interested in internal trait states, running L<fitch_down> should resolve most of the ambiguities. =cut sub fitch_up { my $self = shift; my $tree = shift; my $key = shift || $self->throw("Trait name is needed"); my $node = shift || $tree->get_root_node; if ($node->is_Leaf) { $self->throw ("ERROR: ". $node->internal_id. " needs a value for trait $key") unless $node->has_tag($key); $node->set_tag_value('ps_trait', $node->get_tag_values($key) ); $node->set_tag_value('ps_score', 0 ); return; # end of recursion } foreach my $child ($node->each_Descendent) { $self->fitch_up($tree, $key, $child); } my %intersection; my %union; my $score; foreach my $child ($node->each_Descendent) { foreach my $trait ($child->get_tag_values('ps_trait') ) { $intersection{$trait}++ if $union{$trait}; $union{$trait}++; } $score += $child->get_tag_values('ps_score'); } if (keys %intersection) { $node->set_tag_value('ps_trait', keys %intersection); $node->set_tag_value('ps_score', $score); } else { $node->set_tag_value('ps_trait', keys %union); $node->set_tag_value('ps_score', $score+1); } if ($self->verbose) { print "-- node --------------------------\n"; print "iID: ", $node->internal_id, " (", $node->id, ")\n"; print "Trait: ", join (', ', $node->get_tag_values('ps_trait') ), "\n"; print "length :", scalar($node->get_tag_values('ps_score')) , "\n"; } return scalar $node->get_tag_values('ps_score'); } =head2 fitch_down Example : fitch_down($tree, $node); Description: Runs the second pass from Fitch 1971 parsimony algorithm to resolve ambiguous trait states left by first pass. by the (internal) node. Node defaults to the root. Returns : true Exceptions : dies unless the trait is defined in all nodes Args : 1. Bio::Tree::TreeI object 2. Bio::Tree::NodeI object within the tree, optional Before running this method you should have ran L<fitch_up> (alias to L<ps> ). Note that it is not guaranteed that all states are completely resolved. =cut sub fitch_down { my $self = shift; my $tree = shift; my $node = shift || $tree->get_root_node; my $key = 'ps_trait'; $self->throw ("ERROR: ". $node->internal_id. " needs a value for $key") unless $node->has_tag($key); my $nodev; foreach my $trait ($node->get_tag_values($key) ) { $nodev->{$trait}++; } foreach my $child ($node->each_Descendent) { next if $child->is_Leaf; # end of recursion my $intersection; foreach my $trait ($child->get_tag_values($key) ) { $intersection->{$trait}++ if $nodev->{$trait}; } $self->fitch_down($tree, $child); $child->set_tag_value($key, keys %$intersection); } return 1; # success } =head2 persistence Example : persistence($tree, $node); Description: Calculates the persistence for node in the subtree defined by the (internal) node. Node defaults to the root. Returns : int, number of generations trait value has to remain same Exceptions : all the nodes need to have the trait defined Args : 1. Bio::Tree::TreeI object 2. Bio::Tree::NodeI object within the tree, optional Persistence measures the stability that the trait value has in a tree. It expresses the number of generations the trait value remains the same. All the decendants of the root in the same generation have to share the same value. Depends on Fitch's parsimony score (PS). =cut sub _persistence { my $self = shift; my $tree = shift; my $node = shift; my $value = shift || $self->throw("Value is needed"); my $key = 'ps_trait'; $self->throw("Node is needed") unless $node->isa('Bio::Tree::NodeI'); return 0 unless $node->get_tag_values($key) eq $value; # wrong value return 1 if $node->is_Leaf; # end of recursion my $persistence = 10000000; # an arbitrarily large number foreach my $child ($node->each_Descendent) { my $pers = $self->_persistence($tree, $child, $value); $persistence = $pers if $pers < $persistence; } return $persistence + 1; } sub persistence { my $self = shift; my $tree = shift; my $node = shift || $tree->get_root_node; $self->throw("Node is needed") unless $node->isa('Bio::Tree::NodeI'); my $key = 'ps_trait'; my $value = $node->get_tag_values($key); #calculate my $persistence = $self->_persistence($tree, $node, $value); $node->set_tag_value('persistance', $persistence); return $persistence; } =head2 count_subclusters Example : count_clusters($tree, $node); Description: Calculates the number of sub-clusters in the subtree defined by the (internal) node. Node defaults to the root. Returns : int, count Exceptions : all the nodes need to have the trait defined Args : 1. Bio::Tree::TreeI object 2. Bio::Tree::NodeI object within the tree, optional Depends on Fitch's parsimony score (PS). =cut sub _count_subclusters { my $self = shift; my $tree = shift; my $node = shift; my $value = shift || $self->throw("Value is needed"); my $key = 'ps_trait'; $self->throw ("ERROR: ". $node->internal_id. " needs a value for trait $key") unless $node->has_tag($key); if ($node->get_tag_values($key) eq $value) { if ($node->get_tag_values('ps_score') == 0) { return 0; } else { my $count = 0; foreach my $child ($node->each_Descendent) { $count += $self->_count_subclusters($tree, $child, $value); } return $count; } } return 1; } sub count_subclusters { my $self = shift; my $tree = shift; my $node = shift || $tree->get_root_node; $self->throw("Node is needed") unless $node->isa('Bio::Tree::NodeI'); my $key = 'ps_trait'; my $value = $node->get_tag_values($key); return $self->_count_subclusters($tree, $node, $value); } =head2 count_leaves Example : count_leaves($tree, $node); Description: Calculates the number of leaves with same trait value as root in the subtree defined by the (internal) node. Requires an unbroken line of identical trait values. Node defaults to the root. Returns : int, number of leaves with this trait value Exceptions : all the nodes need to have the trait defined Args : 1. Bio::Tree::TreeI object 2. Bio::Tree::NodeI object within the tree, optional Depends on Fitch's parsimony score (PS). =cut sub _count_leaves { my $self = shift; my $tree = shift; my $node = shift || $tree->get_root_node; my $value = shift; my $key = 'ps_trait'; $self->throw ("ERROR: ". $node->internal_id. " needs a value for trait $key") unless $node->has_tag($key); if ($node->get_tag_values($key) eq $value) { #print $node->id, ": ", $node->get_tag_values($key), "\n"; return 1 if $node->is_Leaf; # end of recursion my $count = 0; foreach my $child ($node->each_Descendent) { $count += $self->_count_leaves($tree, $child, $value); } return $count; } return 0; } sub count_leaves { my $self = shift; my $tree = shift; my $node = shift || $tree->get_root_node; $self->throw("Node is needed") unless $node->isa('Bio::Tree::NodeI'); my $key = 'ps_trait'; my $value = $node->get_tag_values($key); return $self->_count_leaves($tree, $node, $value); } =head2 phylotype_length Example : phylotype_length($tree, $node); Description: Sums up the branch lengths within phylotype exluding the subclusters where the trait values are different Returns : float, length Exceptions : all the nodes need to have the trait defined Args : 1. Bio::Tree::TreeI object 2. Bio::Tree::NodeI object within the tree, optional Depends on Fitch's parsimony score (PS). =cut sub _phylotype_length { my $self = shift; my $tree = shift; my $node = shift; my $value = shift; my $key = 'ps_trait'; $self->throw ("ERROR: ". $node->internal_id. " needs a value for trait $key") unless $node->has_tag($key); return 0 if $node->get_tag_values($key) ne $value; return $node->branch_length if $node->is_Leaf; # end of recursion my $length = 0; foreach my $child ($node->each_Descendent) { my $sub_len = $self->_phylotype_length($tree, $child, $value); $length += $sub_len; $length += $child->branch_length if not $child->is_Leaf and $sub_len; } return $length; } sub phylotype_length { my $self = shift; my $tree = shift; my $node = shift || $tree->get_root_node; my $key = 'ps_trait'; my $value = $node->get_tag_values($key); return $self->_phylotype_length($tree, $node, $value); } =head2 sum_of_leaf_distances Example : sum_of_leaf_distances($tree, $node); Description: Sums up the branch lengths from root to leaf exluding the subclusters where the trait values are different Returns : float, length Exceptions : all the nodes need to have the trait defined Args : 1. Bio::Tree::TreeI object 2. Bio::Tree::NodeI object within the tree, optional Depends on Fitch's parsimony score (PS). =cut sub _sum_of_leaf_distances { my $self = shift; my $tree = shift; my $node = shift; my $value = shift; my $key = 'ps_trait'; $self->throw ("ERROR: ". $node->internal_id. " needs a value for trait $key") unless $node->has_tag($key); return 0 if $node->get_tag_values($key) ne $value; #return $node->branch_length if $node->is_Leaf; # end of recursion return 0 if $node->is_Leaf; # end of recursion my $length = 0; foreach my $child ($node->each_Descendent) { $length += $self->_count_leaves($tree, $child, $value) * $child->branch_length + $self->_sum_of_leaf_distances($tree, $child, $value); } return $length; } sub sum_of_leaf_distances { my $self = shift; my $tree = shift; my $node = shift || $tree->get_root_node; my $key = 'ps_trait'; my $value = $node->get_tag_values($key); return $self->_sum_of_leaf_distances($tree, $node, $value); } =head2 genetic_diversity Example : genetic_diversity($tree, $node); Description: Diversity is the sum of root to leaf distances within the phylotype normalised by number of leaf nodes Returns : float, value of genetic diversity Exceptions : all the nodes need to have the trait defined Args : 1. Bio::Tree::TreeI object 2. Bio::Tree::NodeI object within the tree, optional Depends on Fitch's parsimony score (PS). =cut sub genetic_diversity { my $self = shift; my $tree = shift; my $node = shift || $tree->get_root_node; return $self->sum_of_leaf_distances($tree, $node) / $self->count_leaves($tree, $node); } =head2 statratio Example : statratio($tree, $node); Description: Ratio of the stem length and the genetic diversity of the phylotype L<genetic_diversity> Returns : float, separation score Exceptions : all the nodes need to have the trait defined Args : 1. Bio::Tree::TreeI object 2. Bio::Tree::NodeI object within the tree, optional Statratio gives a measure of separation and variability within the phylotype. Larger values identify more rapidly evolving and recent phylotypes. Depends on Fitch's parsimony score (PS). =cut sub statratio { my $self = shift; my $tree = shift; my $node = shift || $tree->get_root_node; my $div = $self->genetic_diversity($tree, $node); return 0 if $div == 0; return $node->branch_length / $div; } =head2 ai Example : ai($tree, $key, $node); Description: Calculates the Association Index (AI) of Whang et al. 2001 for the subtree defined by the (internal) node. Node defaults to the root. Returns : real Exceptions : leaf nodes have to have the trait defined Args : 1. Bio::Tree::TreeI object 2. trait name string 3. Bio::Tree::NodeI object within the tree, optional Association index (AI) gives a more fine grained results than PS since the result is a real number. ~0 E<lt>= AI. Wang, T.H., Donaldson, Y.K., Brettle, R.P., Bell, J.E., Simmonds, P., 2001. Identification of shared populations of human immunodeficiency Virus Type 1 infecting microglia and tissue macrophages outside the central nervous system. J. Virol. 75 (23), 11686-11699. =cut sub _node_ai { my $self = shift; my $node = shift; my $key = shift; my $traits; my $leaf_count = 0; for my $desc ( $node->get_all_Descendents ) { next unless $desc->is_Leaf; $leaf_count++; $self->throw ("Node ". $desc->id. " needs a value for trait [$key]") unless $desc->has_tag($key); my $trait = $desc->get_tag_values($key); $traits->{$trait}++; } my $most_common = 0; foreach ( keys %$traits) { $most_common = $traits->{$_} if $traits->{$_} > $most_common; } return sprintf "%1.6f", (1 - ($most_common/$leaf_count) ) / (2**($leaf_count-1) ); } sub ai { my $self = shift; my $tree = shift; my $key = shift || $self->throw("Trait name is needed"); my $start_node = shift || $tree->get_root_node; return unless $start_node; my $sum = 0; for my $node ( $start_node->get_all_Descendents ) { next if $node->is_Leaf; $sum += $self->_node_ai($node, $key); } return $sum; } =head2 mc Example : mc($tree, $key, $node); Description: Calculates the Monophyletic Clade (MC) size statistics for the subtree a defined by the (internal) node. Node defaults to the root; Returns : hashref with trait values as keys Exceptions : leaf nodes have to have the trait defined Args : 1. Bio::Tree::TreeI object 2. trait name string 3. Bio::Tree::NodeI object within the tree, optional Monophyletic Clade (MC) size statistics by Salemi at al 2005. It is calculated for each trait value. 1 E<lt>= MC E<lt>= nx, where nx is the number of tips with value x: pick the internal node with maximim value for number of of tips with only trait x MC was defined by Parker et al 2008. Salemi, M., Lamers, S.L., Yu, S., de Oliveira, T., Fitch, W.M., McGrath, M.S., 2005. Phylodynamic analysis of Human Immunodeficiency Virus Type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS. J. Virol. 79 (17), 11343-11352. Parker, J., Rambaut A., Pybus O., 2008. Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty Infection, Genetics and Evolution 8 (2008), 239-246. =cut sub _node_mc { my $self = shift; my $node = shift; my $key = shift; my $traits; my $leaf_count = 0; for my $node2 ( $node->get_all_Descendents ) { next unless $node2->is_Leaf; $leaf_count++; my $trait = $node2->get_tag_values($key); $traits->{$trait}++; } return $traits; } sub mc { my $self = shift; my $tree = shift; my $key = shift || die "Trait name is needed"; my $start_node = shift || $tree->get_root_node; return unless $start_node; my $sum; # hashref, keys are trait values my $keys; # hashref, keys are trait values foreach my $node ( $start_node->get_all_Descendents ) { next if $node->is_Leaf; my $traits = $self->_node_mc($node, $key); if (scalar keys %$traits == 1) { my ($value) = keys %$traits; no warnings; $sum->{$value} = $traits->{$value} if $sum->{$value} < $traits->{$value}; } else { map { $keys->{$_} = 1 } keys %$traits; } } # check for cases where there are no clusters foreach my $value (keys %$keys) { $sum->{$value} = 1 unless defined $sum->{$value}; } return $sum; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tree/Tree.pm�������������������������������������������������������������������000444��000766��000024�� 35262�13155576320� 16410� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tree::Tree # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tree::Tree - An implementation of the TreeI interface. =head1 SYNOPSIS use Bio::TreeIO; # like from a TreeIO my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'treefile.dnd'); my $tree = $treeio->next_tree; my @nodes = $tree->get_nodes; my $root = $tree->get_root_node; =head1 DESCRIPTION This object holds handles to Nodes which make up a tree. =head1 IMPLEMENTATION NOTE This implementation of Bio::Tree::Tree contains Bio::Tree:::NodeI; mainly linked via the root node. As NodeI can potentially contain circular references (as nodes will need to refer to both parent and child nodes), Bio::Tree::Tree will remove those circular references when the object is garbage-collected. This has some side effects; primarily, one must keep the Tree in scope or have at least one reference to it if working with nodes. The fix is to count the references to the nodes and if it is greater than expected retain all of them, but it requires an additional prereq and thus may not be worth the effort. This only shows up in minor edge cases, though (see Bug #2869). Example of issue: # tree is not assigned to a variable, so passes from memory after # root node is passed my $root = Bio::TreeIO->new(-format => 'newick', -file => 'foo.txt')->next_tree ->get_root_node; # gets nothing, as all Node links are broken when Tree is garbage-collected above my @descendents = $root->get_all_Descendents; =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 CONTRIBUTORS Aaron Mackey amackey@virginia.edu Sendu Bala bix@sendu.me.uk Mark A. Jensen maj@fortinbras.us =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tree::Tree; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root Bio::Tree::TreeI Bio::Tree::TreeFunctionsI); =head2 new Title : new Usage : my $obj = Bio::Tree::Tree->new(); Function: Builds a new Bio::Tree::Tree object Returns : Bio::Tree::Tree Args : -root => L<Bio::Tree::NodeI> object which is the root OR -node => L<Bio::Tree::NodeI> object from which the root will be determined -nodelete => boolean, whether or not to try and cleanup all the nodes when this this tree goes out of scope. -id => optional tree ID -score => optional tree score value =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); $self->{'_rootnode'} = undef; $self->{'_maxbranchlen'} = 0; $self->_register_for_cleanup(\&cleanup_tree); my ($root, $node, $nodel, $id, $score) = $self->_rearrange([qw(ROOT NODE NODELETE ID SCORE)], @args); if ($node && ! $root) { $self->throw("Must supply a Bio::Tree::NodeI") unless ref($node) && $node->isa('Bio::Tree::NodeI'); my @lineage = $self->get_lineage_nodes($node); $root = shift(@lineage) || $node; # to stop us pulling in entire database of a Bio::Taxon when we later do # get_nodes() or similar, specifically set ancestor() for each node if ($node->isa('Bio::Taxon')) { push(@lineage, $node) unless $node eq $root; my $ancestor = $root; foreach my $lineage_node (@lineage) { $lineage_node->ancestor($ancestor); } continue { $ancestor = $lineage_node; } } } if ($root) { $self->set_root_node($root); } $self->nodelete($nodel || 0); $self->id($id) if defined $id; $self->score($score) if defined $score; return $self; } =head2 nodelete Title : nodelete Usage : $obj->nodelete($newval) Function: Get/Set Boolean whether or not to delete the underlying nodes when it goes out of scope. By default this is false meaning trees are cleaned up. Returns : boolean Args : on set, new boolean value =cut sub nodelete { my $self = shift; return $self->{'nodelete'} = shift if @_; return $self->{'nodelete'}; } =head2 get_nodes Title : get_nodes Usage : my @nodes = $tree->get_nodes() Function: Return list of Bio::Tree::NodeI objects Returns : array of Bio::Tree::NodeI objects Args : (named values) hash with one value order => 'b|breadth' first order or 'd|depth' first order sortby => [optional] "height", "creation", "alpha", "revalpha", or coderef to be used to sort the order of children nodes. See L<Bio::Tree::Node> for details =cut sub get_nodes { my ($self, @args) = @_; my ($order, $sortby) = $self->_rearrange([qw(ORDER SORTBY)], @args); $order ||= 'depth'; $sortby ||= 'none'; my @children; my $node = $self->get_root_node; if ($node) { if ($order =~ m/^b/oi) { # breadth-first @children = ($node); my @to_process = ($node); while( @to_process ) { my $n = shift @to_process; my @c = $n->each_Descendent($sortby); push @children, @c; push @to_process, @c; } } elsif ($order =~ m/^d/oi) { # depth-first @children = ($node, $node->get_all_Descendents($sortby)); } else { $self->verbose(1); $self->warn("specified an order '$order' which I don't understan\n"); } } return @children; } =head2 get_root_node Title : get_root_node Usage : my $node = $tree->get_root_node(); Function: Get the Top Node in the tree, in this implementation Trees only have one top node. Returns : Bio::Tree::NodeI object Args : none =cut sub get_root_node { my ($self) = @_; return $self->{'_rootnode'}; } =head2 set_root_node Title : set_root_node Usage : $tree->set_root_node($node) Function: Set the Root Node for the Tree Returns : Bio::Tree::NodeI Args : Bio::Tree::NodeI =cut sub set_root_node { my $self = shift; if ( @_ ) { my $value = shift; if ( defined $value && ! $value->isa('Bio::Tree::NodeI') ) { $self->warn("Trying to set the root node to $value which is not a Bio::Tree::NodeI"); return $self->get_root_node; } $self->{'_rootnode'} = $value; } return $self->get_root_node; } =head2 total_branch_length Title : total_branch_length Usage : my $size = $tree->total_branch_length Function: Returns the sum of the length of all branches Returns : real Args : none =cut sub total_branch_length { shift->subtree_length } =head2 subtree_length Title : subtree_length Usage : my $subtree_size = $tree->subtree_length($internal_node) Function: Returns the sum of the length of all branches in a subtree under the node. Calculates the size of the whole tree without an argument (but only if root node is defined) Returns : real or undef Args : Bio::Tree::NodeI object, defaults to the root node =cut sub subtree_length { my $tree = shift; my $node = shift || $tree->get_root_node; return unless $node; my $sum = 0; for ( $node->get_all_Descendents ) { $sum += $_->branch_length || 0; } return $sum; } =head2 id Title : id Usage : my $id = $tree->id(); Function: An id value for the tree Returns : scalar Args : [optional] new value to set =cut sub id { my ($self, $val) = @_; if ( defined $val ) { $self->{'_treeid'} = $val; } return $self->{'_treeid'}; } =head2 score Title : score Usage : $obj->score($newval) Function: Sets the associated score with this tree This is a generic slot which is probably best used for log likelihood or other overall tree score Returns : value of score Args : newvalue (optional) =cut sub score { my ($self, $val) = @_; if ( defined $val ) { $self->{'_score'} = $val; } return $self->{'_score'}; } # decorated interface TreeI Implements this =head2 height Title : height Usage : my $height = $tree->height Function: Gets the height of tree - this LOG_2($number_nodes) WARNING: this is only true for strict binary trees. The TreeIO system is capable of building non-binary trees, for which this method will currently return an incorrect value!! Returns : integer Args : none =head2 number_nodes Title : number_nodes Usage : my $size = $tree->number_nodes Function: Returns the number of nodes in the tree Returns : integer Args : none =head2 as_text Title : as_text Usage : my $tree_as_string = $tree->as_text($format) Function: Returns the tree as a string representation in the desired format, e.g.: 'newick', 'nhx' or 'tabtree' (the default) Returns : scalar string Args : format type as specified by Bio::TreeIO Note : This method loads the Bio::TreeIO::$format module on the fly, and commandeers the _write_tree_Helper routine therein to create the tree string. =cut sub as_text { my $self = shift; my $format = shift || 'tabtree'; my $params_input = shift || {}; my $iomod = "Bio::TreeIO::$format"; $self->_load_module($iomod); my $string = ''; open my $fh, '>', \$string or $self->throw("Could not write '$string' as file: $!"); my $test = $iomod->new( -format => $format, -fh => $fh ); # Get the default params for the given IO module. $test->set_params($params_input); $test->write_tree($self); close $fh; return $string; } =head2 Methods for associating Tag/Values with a Tree These methods associate tag/value pairs with a Tree =head2 set_tag_value Title : set_tag_value Usage : $tree->set_tag_value($tag,$value) $tree->set_tag_value($tag,@values) Function: Sets a tag value(s) to a tree. Replaces old values. Returns : number of values stored for this tag Args : $tag - tag name $value - value to store for the tag =cut sub set_tag_value { my ($self, $tag, @values) = @_; if ( ! defined $tag || ! scalar @values ) { $self->warn("cannot call set_tag_value with an undefined value"); } $self->remove_tag ($tag); map { push @{$self->{'_tags'}->{$tag}}, $_ } @values; return scalar @{$self->{'_tags'}->{$tag}}; } =head2 add_tag_value Title : add_tag_value Usage : $tree->add_tag_value($tag,$value) Function: Adds a tag value to a tree Returns : number of values stored for this tag Args : $tag - tag name $value - value to store for the tag =cut sub add_tag_value { my ($self, $tag, $value) = @_; if ( ! defined $tag || ! defined $value ) { $self->warn("cannot call add_tag_value with an undefined value"); } push @{$self->{'_tags'}->{$tag}}, $value; return scalar @{$self->{'_tags'}->{$tag}}; } =head2 remove_tag Title : remove_tag Usage : $tree->remove_tag($tag) Function: Remove the tag and all values for this tag Returns : boolean representing success (0 if tag does not exist) Args : $tag - tagname to remove =cut sub remove_tag { my ($self, $tag) = @_; if ( exists $self->{'_tags'}->{$tag} ) { $self->{'_tags'}->{$tag} = undef; delete $self->{'_tags'}->{$tag}; return 1; } return 0; } =head2 remove_all_tags Title : remove_all_tags Usage : $tree->remove_all_tags() Function: Removes all tags Returns : None Args : None =cut sub remove_all_tags { my ($self) = @_; $self->{'_tags'} = {}; return; } =head2 get_all_tags Title : get_all_tags Usage : my @tags = $tree->get_all_tags() Function: Gets all the tag names for this Tree Returns : Array of tagnames Args : None =cut sub get_all_tags { my ($self) = @_; my @tags = sort keys %{$self->{'_tags'} || {}}; return @tags; } =head2 get_tag_values Title : get_tag_values Usage : my @values = $tree->get_tag_values($tag) Function: Gets the values for given tag ($tag) Returns : Array of values or empty list if tag does not exist Args : $tag - tag name =cut sub get_tag_values { my ($self, $tag) = @_; return wantarray ? @{$self->{'_tags'}->{$tag} || []} : (@{$self->{'_tags'}->{$tag} || []})[0]; } =head2 has_tag Title : has_tag Usage : $tree->has_tag($tag) Function: Boolean test if tag exists in the Tree Returns : Boolean Args : $tag - tagname =cut sub has_tag { my ($self, $tag) = @_; return exists $self->{'_tags'}->{$tag}; } # safe tree clone that doesn't seg fault =head2 clone Title : clone Alias : _clone Usage : $tree_copy = $tree->clone(); $subtree_copy = $tree->clone($internal_node); Function: Safe tree clone that doesn't segfault Returns : Bio::Tree::Tree object Args : [optional] $start_node, Bio::Tree::Node object =cut sub clone { my ($self, $parent, $parent_clone) = @_; $parent ||= $self->get_root_node; $parent_clone ||= $self->_clone_node($parent); foreach my $node ($parent->each_Descendent()) { my $child = $self->_clone_node($node); $child->ancestor($parent_clone); $self->_clone($node, $child); } $parent->ancestor && return; my $tree = $self->new(-root => $parent_clone); return $tree; } # -- private internal methods -- sub cleanup_tree { my $self = shift; unless( $self->nodelete ) { for my $node ($self->get_nodes(-order => 'b', -sortby => 'none')) { $node->node_cleanup; } } $self->{'_rootnode'} = undef; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tree/TreeFunctionsI.pm���������������������������������������������������������000444��000766��000024�� 104660�13155576320� 20431� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tree::TreeFunctionsI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl-dot-org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods =head1 SYNOPSIS use Bio::TreeIO; my $in = Bio::TreeIO->new(-format => 'newick', -file => 'tree.tre'); my $tree = $in->next_tree; my @nodes = $tree->find_node('id1'); if( $tree->is_monophyletic(-nodes => \@nodes, -outgroup => $outnode) ){ #... } =head1 DESCRIPTION This interface provides a set of implemented Tree functions which only use the defined methods in the TreeI or NodeI interface. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich, Aaron Mackey, Justin Reese Email jason-at-bioperl-dot-org Email amackey-at-virginia.edu Email jtr4v-at-virginia.edu =head1 CONTRIBUTORS Sendu Bala, bix@sendu.me.uk Rerooting code was worked on by Daniel Barker d.barker-at-reading.ac.uk Ramiro Barrantes Ramiro.Barrantes-at-uvm.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tree::TreeFunctionsI; use strict; use base qw(Bio::Tree::TreeI); =head2 find_node Title : find_node Usage : my @nodes = $self->find_node(-id => 'node1'); Function: returns all nodes that match a specific field, by default this is id, but different branch_length, Returns : List of nodes which matched search Args : text string to search for OR -fieldname => $textstring =cut sub find_node { my ($self, $type, $field) = @_; if( ! defined $type ) { $self->warn("Must request a either a string or field and string when searching"); } # all this work for a '-' named field # is so that we could potentially # expand to other constraints in # different implementations # like 'find all nodes with boostrap < XX' if( ! defined $field ) { # only 1 argument, default to searching by id $field = $type; $type = 'id'; } else { $type =~ s/^-//; } # could actually do this by testing $rootnode->can($type) but # it is possible that a tree is implemented with different node types # - although it is unlikely that the root node would be richer than the # leaf nodes. Can't handle NHX tags right now my @nodes = grep { $_->can($type) && defined $_->$type() && $_->$type() eq $field } $self->get_nodes(); if ( wantarray) { return @nodes; } else { if( @nodes > 1 ) { $self->warn("More than 1 node found but caller requested scalar, only returning first node"); } return shift @nodes; } } =head2 remove_Node Title : remove_Node Usage : $tree->remove_Node($node) Function: Removes a node from the tree Returns : boolean represent status of success Args : either Bio::Tree::NodeI or string of the node id =cut sub remove_Node { my ($self,$input) = @_; my $node = undef; unless( ref($input) ) { $node = $self->find_node($input); } elsif( ! $input->isa('Bio::Tree::NodeI') ) { $self->warn("Did not provide either a valid Bio::Tree::NodeI object or id to remove_node"); return 0; } else { $node = $input; } if( ! $node->ancestor && $self->get_root_node->internal_id != $node->internal_id) { $self->warn("Node (".$node->to_string . ") has no ancestor, can't remove!"); } else { $node->ancestor->remove_Descendent($node); } } =head2 get_lineage_nodes Title : get_lineage_nodes Usage : my @nodes = $tree->get_lineage_nodes($node); Function: Given a node or its ID, get its full lineage, i.e. all its ancestors, from the root to the most recent ancestor. Only use the node ID as input if the nodes have been added to the tree. Returns : list of nodes Args : either Bio::Tree::NodeI (or string of the node id) =cut sub get_lineage_nodes { my ($self, $input) = @_; my $node; # Sanity checks if (ref $input) { if (not $input->isa('Bio::Tree::NodeI')) { $self->throw("Did not provide a valid Bio::Tree::NodeI object or ID string to get_lineage_nodes"); } $node = $input; } else { $node = $self->find_node($input); } # When dealing with Bio::Taxon objects with databases, the root will always # be the database's root, ignoring this Tree's set root node; prefer the # Tree's idea of root. my $root = $self->get_root_node || ''; my @lineage; while ($node) { $node = $node->ancestor || last; unshift(@lineage, $node); $node eq $root && last; } return @lineage; } =head2 get_lineage_string Title : get_lineage_string Usage : my $lineage = $tree->get_lineage_string($node); Function: Get the string representation of the full lineage of a node, e.g. for the Enterobacteriales node, return Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales. This method uses get_lineage_nodes internally and therefore inherits of all of its caveats. Returns : string Args : * either Bio::Tree::NodeI (or string of the node id) * an optional separator (default: ';') =cut sub get_lineage_string { my ($self, $input, $sep) = @_; $sep ||= ';'; my $node; unless (ref $input) { $node = $self->find_node($input); } elsif (! $input->isa('Bio::Tree::NodeI')) { $self->warn("Did not provide either a valid Bio::Tree::NodeI object or id to get_lineage_nodes"); return; } else { $node = $input; } my @nodes = ($self->get_lineage_nodes($node), $node); for my $i (0 .. scalar @nodes - 1) { my $node_name = $nodes[$i]->node_name || ''; if ($node_name =~ m/$sep/) { $self->warn("Separator '$sep' is not safe to use because the node ". "called '$node_name' contains it. Consider using another separator". " or sanitizing the node name."); } $nodes[$i] = $node_name; } return join $sep, @nodes; } =head2 splice Title : splice Usage : $tree->splice(-remove_id => \@ids); Function: Remove all the nodes from a tree that correspond to the supplied args, making all the descendents of a removed node the descendents of the removed node's ancestor. You can ask to explicitly remove certain nodes by using -remove_*, remove them conditionally by using -remove_* in combination with -keep_*, or remove everything except certain nodes by using only -keep_*. Returns : n/a Args : just a list of Bio::Tree::NodeI objects to remove, OR -key => value pairs, where -key has the prefix 'remove' or 'keep', followed by an underscore, followed by a fieldname (like for the method find_node). Value should be a scalar or an array ref of scalars (again, like you might supply to find_node). So (-remove_id => [1, 2]) will remove all nodes from the tree that have an id() of '1' or '2', while (-remove_id => [1, 2], -keep_id => [2]) will remove all nodes with an id() of '1'. (-keep_id => [2]) will remove all nodes unless they have an id() of '2' (note, no -remove_*). -preserve_lengths => 1 : setting this argument will splice out intermediate nodes, preserving the original total length between the ancestor and the descendants of the spliced node. Undef by default. =cut sub splice { my ($self, @args) = @_; $self->throw("Must supply some arguments") unless @args > 0; my $preserve_lengths = 0; my @nodes_to_remove; if (ref($args[0])) { $self->throw("When supplying just a list of Nodes, they must be Bio::Tree::NodeI objects") unless $args[0]->isa('Bio::Tree::NodeI'); @nodes_to_remove = @args; } else { $self->throw("When supplying -key => value pairs, must be an even number of args") unless @args % 2 == 0; my %args = @args; my @keep_nodes; my @remove_nodes; my $remove_all = 1; while (my ($key, $value) = each %args) { my @values = ref($value) ? @{$value} : ($value); if ($key =~ s/remove_//) { $remove_all = 0; foreach my $value (@values) { push(@remove_nodes, $self->find_node($key => $value)); } } elsif ($key =~ s/keep_//) { foreach my $value (@values) { push(@keep_nodes, $self->find_node($key => $value)); } } elsif ($key =~ /preserve/) { $preserve_lengths = $value; } } if ($remove_all) { if (@keep_nodes == 0) { $self->warn("Requested to remove everything except certain nodes, but those nodes were not found; doing nothing instead"); return; } @remove_nodes = $self->get_nodes; } if (@keep_nodes > 0) { my %keep_iids = map { $_->internal_id => 1 } @keep_nodes; foreach my $node (@remove_nodes) { push(@nodes_to_remove, $node) unless exists $keep_iids{$node->internal_id}; } } else { @nodes_to_remove = @remove_nodes; } } # do the splicing #*** the algorithm here hasn't really been thought through and tested much, # will probably need revising my %root_descs; my $reroot = 0; foreach my $node (@nodes_to_remove) { my @descs = $node->each_Descendent; my $ancestor = $node->ancestor; if (! $ancestor && ! $reroot) { # we're going to remove the tree root, so will have to re-root the # tree later $reroot = 1; %root_descs = map { $_->internal_id => $_ } @descs; $node->remove_all_Descendents; next; } if (exists $root_descs{$node->internal_id}) { # well, this one can't be the future root anymore delete $root_descs{$node->internal_id}; # but maybe one of this one's descs will become the root foreach my $desc (@descs) { $root_descs{$desc->internal_id} = $desc; } } # make the ancestor of our descendents our own ancestor, and give us # no ancestor of our own to remove us from the tree foreach my $desc (@descs) { $desc->ancestor($ancestor); $desc->branch_length($desc->branch_length + $node->branch_length) if $preserve_lengths; } $node->ancestor(undef); } if ($reroot) { my @candidates = values %root_descs; $self->throw("After splicing, there was no tree root!") unless @candidates > 0; $self->throw("After splicing, the original root was removed but there are multiple candidates for the new root!") unless @candidates == 1; $self->set_root_node($candidates[0]); # not sure its valid to use the reroot() method } } =head2 get_lca Title : get_lca Usage : get_lca(-nodes => \@nodes ); OR get_lca(@nodes); Function: given two or more nodes, returns the lowest common ancestor (aka most recent common ancestor) Returns : node object or undef if there is no common ancestor Args : -nodes => arrayref of nodes to test, OR just a list of nodes =cut sub get_lca { my ($self, @args) = @_; my ($nodes) = $self->_rearrange([qw(NODES)],@args); my @nodes; if (ref($nodes) eq 'ARRAY') { @nodes = @{$nodes}; } else { @nodes = @args; } @nodes >= 2 or $self->throw("At least 2 nodes are required"); # We must go root->leaf to get the correct answer to lca (in a world where # internal_id might not be uniquely assigned), but leaf->root is more # forgiving (eg. lineages may not all have the same root, or they may have # different numbers of 'minor' taxa inbeteen 'major' ones). # # I use root->leaf so that we can easily do multiple nodes at once - no # matter what taxa are below the lca, the lca and all its ancestors ought to # be identical. my @paths; foreach my $node (@nodes) { unless(ref($node) && $node->isa('Bio::Tree::NodeI')) { $self->throw("Cannot process get_lca() with a non-NodeI object ($node)\n"); } my @path = ($self->get_lineage_nodes($node), $node); push(@paths, \@path); } return unless @paths >= 2; my $lca; LEVEL: while ($paths[0] > 0) { my %node_ids; my $node; foreach my $path (@paths) { $node = shift(@{$path}) || last LEVEL; my $node_id = $node->internal_id; unless (defined $node_id) { $self->warn("One of the lineages had a node with no internal_id, can't calculate the common ancestor"); return; } $node_ids{$node_id}++; } if (keys %node_ids == 1) { $lca = $node; } else { # at this point in the lineage the nodes are different; the previous # loop had the lca last LEVEL; } } # If the tree that we are contains the lca (get_lca could have been called # on an empty tree, since it works with plain Nodes), prefer to return the # node object that belongs to us if ($lca && $self->number_nodes > 0) { my $own_lca = $self->find_node(-internal_id => $lca->internal_id); $lca = $own_lca if $own_lca; } return $lca; } =head2 merge_lineage Title : merge_lineage Usage : merge_lineage($node) Function: Merge a lineage of nodes with this tree. Returns : true for success, false (and a warning) otherwise Args : Bio::Tree::TreeI with only one leaf, OR Bio::Tree::NodeI which has an ancestor For example, if we are the tree $tree: +---B | A | +---C and we want to merge the lineage $other_tree: A---C---D After calling $tree->merge_lineage($other_tree), $tree looks like: +---B | A | +---C---D =cut sub merge_lineage { my ($self, $thing) = @_; $self->throw("Must supply an object reference") unless ref($thing); my $lineage_leaf; if ($thing->isa('Bio::Tree::TreeI')) { my @leaves = $thing->get_leaf_nodes; $self->throw("The supplied Tree can only have one leaf") unless @leaves == 1; $lineage_leaf = shift(@leaves); } elsif ($thing->isa('Bio::Tree::NodeI')) { $self->throw("The supplied Node must have an ancestor") unless $thing->ancestor; $lineage_leaf = $thing; } # Find the lowest node in the supplied lineage that is in the tree # That will be our lca and we can merge at the node below my @lineage = ($lineage_leaf, reverse($self->get_lineage_nodes($lineage_leaf))); my $merged = 0; my $node; my $i = 0; while ($i <= $#lineage) { $node = $self->find_node(-internal_id => $lineage[$i]->internal_id); if (defined $node) { $merged = 1; last; } $i++; } if (not $merged) { $self->warn("Could not merge the lineage of ".$lineage_leaf->id." with the rest of the tree"); } # Merge descendents, recursively while ($i > 0) { $node->add_Descendent($lineage[$i-1]); $node = $self->find_node(-internal_id => $lineage[$i-1]->internal_id); $i--; } return $merged; } =head2 contract_linear_paths Title : contract_linear_paths Usage : contract_linear_paths() Function: Splices out all nodes in the tree that have an ancestor and only one descendent. Returns : n/a Args : none for normal behaviour, true to dis-regard the ancestor requirement and re-root the tree as necessary For example, if we are the tree $tree: +---E | A---B---C---D | +---F After calling $tree->contract_linear_paths(), $tree looks like: +---E | A---D | +---F Instead, $tree->contract_linear_paths(1) would have given: +---E | D | +---F =cut sub contract_linear_paths { my $self = shift; my $reroot = shift; my @remove; foreach my $node ($self->get_nodes) { if ($node->ancestor && $node->each_Descendent == 1) { push(@remove, $node); } } $self->splice(@remove) if @remove; if ($reroot) { my $root = $self->get_root_node; my @descs = $root->each_Descendent; if (@descs == 1) { my $new_root = shift(@descs); $self->set_root_node($new_root); $new_root->ancestor(undef); } } } =head2 is_binary Example : is_binary(); is_binary($node); Description: Finds if the tree or subtree defined by the internal node is a true binary tree without polytomies Returns : boolean Exceptions : Args : Internal node Bio::Tree::NodeI, optional =cut sub is_binary { my $self = shift; my $node = shift || $self->get_root_node; my $binary = 1; my @descs = $node->each_Descendent; $binary = 0 unless @descs == 2 or @descs == 0; #print "$binary, ", scalar @descs, "\n"; # recurse foreach my $desc (@descs) { $binary += $self->is_binary($desc) -1; } $binary = 0 if $binary < 0; return $binary; } =head2 force_binary Title : force_binary Usage : force_binary() Function: Forces the tree into a binary tree, splitting branches arbitrarily and creating extra nodes as necessary, such that all nodes have exactly two or zero descendants. Returns : n/a Args : none For example, if we are the tree $tree: +---G | +---F | +---E | A | +---D | +---C | +---B (A has 6 descendants B-G) After calling $tree->force_binary(), $tree looks like: +---X | +---X | | | +---X | +---X | | | | +---G | | | | +---X | | | +---F A | +---E | | | +---X | | | | | +---D | | +---X | | +---C | | +---X | +---B (Where X are artificially created nodes with ids 'artificial_n', where n is an integer making the id unique within the tree) =cut sub force_binary { my $self = shift; my $node = shift || $self->get_root_node; my @descs = $node->each_Descendent; if (@descs > 2) { # Removed overly verbose warning - cjfields 3-12-11 # Many nodes have no identifying names, a simple warning is probably # enough. $self->warn("Node has more than two descendants\nWill do an arbitrary balanced split"); my @working = @descs; # create an even set of artifical nodes on which to later hang the descs my $half = @working / 2; $half++ if $half > int($half); $half = int($half); my @artificials; while ($half > 1) { my @this_level; foreach my $top_node (@artificials || $node) { for (1..2) { my $art = $top_node->new(-id => "artificial_".++$self->{_art_num}); $top_node->add_Descendent($art); push(@this_level, $art); } } @artificials = @this_level; $half--; } # attach two descs to each artifical leaf foreach my $art (@artificials) { for (1..2) { my $desc = shift(@working) || $node->new(-id => "artificial_".++$self->{_art_num}); $desc->ancestor($art); } } } elsif (@descs == 1) { # ensure that all nodes have 2 descs $node->add_Descendent($node->new(-id => "artificial_".++$self->{_art_num})); } # recurse foreach my $desc (@descs) { $self->force_binary($desc); } } =head2 simplify_to_leaves_string Title : simplify_to_leaves_string Usage : my $leaves_string = $tree->simplify_to_leaves_string() Function: Creates a simple textual representation of the relationship between leaves in self. It forces the tree to be binary, so the result may not strictly correspond to the tree (if the tree wasn't binary), but will be as close as possible. The tree object is not altered. Only leaf node ids are output, in a newick-like format. Returns : string Args : none =cut sub simplify_to_leaves_string { my $self = shift; # Before contracting and forcing binary we need to clone self, but Clone.pm # clone() seg faults and fails to make the clone, whilst Storable dclone # needs $self->{_root_cleanup_methods} deleted (code ref) and seg faults at # end of script. Let's make our own clone... my $tree = $self->_clone; $tree->contract_linear_paths(1); $tree->force_binary; foreach my $node ($tree->get_nodes) { my $id = $node->id; $id = ($node->is_Leaf && $id !~ /^artificial/) ? $id : ''; $node->id($id); } my %paired; my @data = $self->_simplify_helper($tree->get_root_node, \%paired); return join(',', @data); } # alias sub _clone { shift->clone(@_) } # safe node clone that doesn't seg fault, but deliberately loses ancestors and # descendents sub _clone_node { my ($self, $node) = @_; my $clone = $node->new; while (my ($key, $val) = each %{$node}) { if ($key eq '_desc' || $key eq '_ancestor') { next; } ${$clone}{$key} = $val; } return $clone; } # tree string generator for simplify_to_leaves_string, based on # Bio::TreeIO::newick::_write_tree_Helper sub _simplify_helper { my ($self, $node, $paired) = @_; return () if (!defined $node); my @data = (); foreach my $node ($node->each_Descendent()) { push(@data, $self->_simplify_helper($node, $paired)); } my $id = $node->id_output || ''; if (@data) { unless (exists ${$paired}{"@data"} || @data == 1) { $data[0] = "(" . $data[0]; $data[-1] .= ")"; ${$paired}{"@data"} = 1; } } elsif ($id) { push(@data, $id); } return @data; } =head2 distance Title : distance Usage : distance(-nodes => \@nodes ) Function: returns the distance between two given nodes Returns : numerical distance Args : -nodes => arrayref of nodes to test or ($node1, $node2) =cut sub distance { my ($self,@args) = @_; my ($nodes) = $self->_rearrange([qw(NODES)],@args); if( ! defined $nodes ) { $self->warn("Must supply two nodes or -nodes parameter to distance() method"); return; } elsif (ref($nodes) eq 'ARRAY') { 1; } elsif ( @args == 2) { # assume these are nodes... $nodes = \@args; } else { $self->warn("Must supply two nodes or -nodes parameter to distance() method"); return; } $self->throw("Must provide 2 nodes") unless @{$nodes} == 2; my $lca = $self->get_lca(@{$nodes}); unless($lca) { $self->warn("could not find the lca of supplied nodes; can't find distance either"); return; } my $cumul_dist = 0; my $warned = 0; foreach my $current_node (@{$nodes}) { while (1) { last if $current_node eq $lca; if ($current_node->branch_length) { $cumul_dist += $current_node->branch_length; } elsif (! $warned) { $self->warn("At least some nodes do not have a branch length, the distance returned could be wrong"); $warned = 1; } $current_node = $current_node->ancestor || last; } } return $cumul_dist; } =head2 is_monophyletic Title : is_monophyletic Usage : if( $tree->is_monophyletic(-nodes => \@nodes, -outgroup => $outgroup) Function: Will do a test of monophyly for the nodes specified in comparison to a chosen outgroup Returns : boolean Args : -nodes => arrayref of nodes to test -outgroup => outgroup to serve as a reference =cut sub is_monophyletic{ my ($self,@args) = @_; my ($nodes,$outgroup) = $self->_rearrange([qw(NODES OUTGROUP)],@args); if( ! defined $nodes || ! defined $outgroup ) { $self->warn("Must supply -nodes and -outgroup parameters to the method is_monophyletic"); return; } if( ref($nodes) !~ /ARRAY/i ) { $self->warn("Must provide a valid array reference for -nodes"); } my $clade_root = $self->get_lca(@{$nodes}); unless( defined $clade_root ) { $self->warn("could not find clade root via lca"); return; } my $og_ancestor = $outgroup->ancestor; while( defined ($og_ancestor ) ) { if( $og_ancestor->internal_id == $clade_root->internal_id ) { # monophyly is violated return 0; } $og_ancestor = $og_ancestor->ancestor; } return 1; } =head2 is_paraphyletic Title : is_paraphyletic Usage : if( $tree->is_paraphyletic(-nodes =>\@nodes, -outgroup => $node) ){ } Function: Tests whether or not a given set of nodes are paraphyletic (representing the full clade) given an outgroup Returns : [-1,0,1] , -1 if the group is not monophyletic 0 if the group is not paraphyletic 1 if the group is paraphyletic Args : -nodes => Array of Bio::Tree::NodeI objects which are in the tree -outgroup => a Bio::Tree::NodeI to compare the nodes to =cut sub is_paraphyletic{ my ($self,@args) = @_; my ($nodes,$outgroup) = $self->_rearrange([qw(NODES OUTGROUP)],@args); if( ! defined $nodes || ! defined $outgroup ) { $self->warn("Must suply -nodes and -outgroup parameters to the method is_paraphyletic"); return; } if( ref($nodes) !~ /ARRAY/i ) { $self->warn("Must provide a valid array reference for -nodes"); return; } # Algorithm # Find the lca # Find all the nodes beneath the lca # Test to see that none are missing from the nodes list my %nodehash; foreach my $n ( @$nodes ) { $nodehash{$n->internal_id} = $n; } my $clade_root = $self->get_lca(-nodes => $nodes ); unless( defined $clade_root ) { $self->warn("could not find clade root via lca"); return; } my $og_ancestor = $outgroup->ancestor; # Is this necessary/correct for paraphyly test? while( defined ($og_ancestor ) ) { if( $og_ancestor->internal_id == $clade_root->internal_id ) { # monophyly is violated, could be paraphyletic return -1; } $og_ancestor = $og_ancestor->ancestor; } my $tree = Bio::Tree::Tree->new(-root => $clade_root, -nodelete => 1); foreach my $n ( $tree->get_nodes() ) { next unless $n->is_Leaf(); # if any leaf node is not in the list # then it is part of the clade and so the list # must be paraphyletic return 1 unless ( $nodehash{$n->internal_id} ); } return 0; } =head2 reroot Title : reroot Usage : $tree->reroot($node); Function: Reroots a tree making a new node the root Returns : 1 on success, 0 on failure Args : Bio::Tree::NodeI that is in the tree, but is not the current root =cut sub reroot { my ($self,$new_root) = @_; unless (defined $new_root && $new_root->isa("Bio::Tree::NodeI")) { $self->warn("Must provide a valid Bio::Tree::NodeI when rerooting"); return 0; } my $old_root = $self->get_root_node; if( $new_root == $old_root ) { $self->warn("Node requested for reroot is already the root node!"); return 0; } my $anc = $new_root->ancestor; unless( $anc ) { # this is already the root $self->warn("Node requested for reroot is already the root node!"); return 0; } my $tmp_node = $new_root->create_node_on_branch(-position=>0,-force=>1); # reverse the ancestor & children pointers my $former_anc = $tmp_node->ancestor; my @path_from_oldroot = ($self->get_lineage_nodes($tmp_node), $tmp_node); for (my $i = 0; $i < $#path_from_oldroot; $i++) { my $current = $path_from_oldroot[$i]; my $next = $path_from_oldroot[$i + 1]; $current->remove_Descendent($next); $current->branch_length($next->branch_length); $current->bootstrap($next->bootstrap) if defined $next->bootstrap; $next->remove_tag('B'); $next->add_Descendent($current); } $new_root->add_Descendent($former_anc); $tmp_node->remove_Descendent($former_anc); $tmp_node = undef; $new_root->branch_length(undef); $old_root = undef; $self->set_root_node($new_root); return 1; } =head2 reroot_at_midpoint Title : reroot_at_midpoint Usage : $tree->reroot_at_midpoint($node, $new_root_id); Function: Reroots a tree on a new node created halfway between the argument and its ancestor Returns : the new midpoint Bio::Tree::NodeIon success, 0 on failure Args : non-root Bio::Tree::NodeI currently in $tree scalar string, id for new node (optional) =cut sub reroot_at_midpoint { my $self = shift; my $node = shift; my $id = shift; unless (defined $node && $node->isa("Bio::Tree::NodeI")) { $self->warn("Must provide a valid Bio::Tree::NodeI when rerooting"); return 0; } my $midpt = $node->create_node_on_branch(-FRACTION=>0.5); if (defined $id) { $self->warn("ID argument is not a scalar") if (ref $id); $midpt->id($id) if defined($id) && !ref($id); } $self->reroot($midpt); return $midpt; } =head2 findnode_by_id Title : findnode_by_id Usage : my $node = $tree->findnode_by_id($id); Function: Get a node by its id (which should be unique for the tree) Returns : L<Bio::Tree::NodeI> Args : node id =cut sub findnode_by_id { my $tree = shift; $tree->deprecated("use of findnode_by_id() is deprecated; ". "use find_node() instead"); my $id = shift; my $rootnode = $tree->get_root_node; if ( ($rootnode->id) and ($rootnode->id eq $id) ) { return $rootnode; } # process all the children foreach my $node ( $rootnode->get_Descendents ) { if ( ($node->id) and ($node->id eq $id ) ) { return $node; } } } =head2 move_id_to_bootstrap Title : move_id_to_bootstrap Usage : $tree->move_id_to_bootstrap Function: Move internal IDs to bootstrap slot Returns : undef Args : undef =cut sub move_id_to_bootstrap{ my ($tree) = shift; for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) { $node->bootstrap(defined $node->id ? $node->id : ''); $node->id(''); } } =head2 add_trait Title : add_trait Usage : my $key = $tree->add_trait($trait_file, 3); Function: Add traits to the leaf nodes of a Bio::Tree:Tree from a file. The trait file is a tab-delimited text file and needs to have a header line giving names to traits. The first column contains the leaf node ids. Subsequent columns contain different trait value sets. Single or double quotes are removed from the trait values. Traits are added to leaf nodes as a tag named $key using the add_tag_value() method. This means that you can retrieve the trait values using the get_tag_values() method (see the documentation for Bio::Tree::Node). Returns : Trait name (a scalar) on success, undef on failure (for example, if the column index requested was too large). Args : * Name of trait file (scalar string). * Index of trait file column (scalar int). Note that numbering starts at 0. Default: 1 (second column). * Ignore missing values. Typically, if a leaf node has no value in the trait file, an exception is thrown. If you set this option to 1, then no trait will be given to the node (no exception thrown). =cut sub _read_trait_file { my ($self, $file, $column) = @_; $column ||= 1; my $trait_name; my $trait_values; open my $TRAIT, '<', $file or $self->throw("Could not read file '$file': $!"); my $first_line = 1; while (<$TRAIT>) { chomp; s/['"]//g; my @line = split /\t/; if ($first_line) { $first_line = 0; $trait_name = $line[$column]; next; } my $id = $line[0]; last if (not defined $id) or ($id eq ''); # Skip empty trait values my $value = $line[$column]; next if (not defined $value) or ($value eq ''); $trait_values->{$id} = $value; } close $TRAIT; return $trait_name, $trait_values; } sub add_trait { my ($self, $file, $column, $ignore) = @_; $ignore = 0 if not defined $ignore; my ($trait_name, $trait_values) = $self->_read_trait_file($file, $column); if (defined $trait_name) { for my $node ($self->get_leaf_nodes) { # strip quotes from the node id $node->id($1) if $node->id =~ /^['"]+(.*)['"]+$/; if ( not exists $trait_values->{$node->id} ) { if ($ignore) { next; } else { $self->throw("No trait for node [".$node->id."/".$node->internal_id."]"); } } $node->add_tag_value($trait_name, $trait_values->{ $node->id } ); } } return $trait_name; } 1; ��������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tree/TreeI.pm������������������������������������������������������������������000444��000766��000024�� 15673�13155576320� 16525� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Tree::TreeI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tree::TreeI - A Tree object suitable for lots of things, designed originally for Phylogenetic Trees. =head1 SYNOPSIS # get a Bio::Tree::TreeI somehow # like from a TreeIO my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'treefile.dnd'); my $tree = $treeio->next_tree; my @nodes = $tree->get_nodes; my @leaves = $tree->get_leaf_nodes; my $root = $tree->get_root_node; =head1 DESCRIPTION This object holds a pointer to the Root of a Tree which is a Bio::Tree::NodeI. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 CONTRIBUTORS Aaron Mackey, amackey@virginia.edu Elia Stupka, elia@fugu-sg.org Sendu Bala, bix@sendu.me.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tree::TreeI; use strict; use base qw(Bio::Root::RootI); =head2 get_nodes Title : get_nodes Usage : my @nodes = $tree->get_nodes() Function: Return list of Tree::NodeI objects Returns : array of Tree::NodeI objects Args : (named values) hash with one value order => 'b|breadth' first order or 'd|depth' first order =cut sub get_nodes{ my ($self) = @_; $self->throw_not_implemented(); } =head2 get_root_node Title : get_root_node Usage : my $node = $tree->get_root_node(); Function: Get the Top Node in the tree, in this implementation Trees only have one top node. Returns : Bio::Tree::NodeI object Args : none =cut sub get_root_node{ my ($self) = @_; $self->throw_not_implemented(); } =head2 number_nodes Title : number_nodes Usage : my $size = $tree->number_nodes Function: Find the number of nodes in the tree. Returns : int Args : none =cut sub number_nodes{ my ($self) = @_; my $root = $self->get_root_node; if( defined $root && $root->isa('Bio::Tree::NodeI')) { return ($root->descendent_count + 1); } return 0; } =head2 total_branch_length Title : total_branch_length Usage : my $size = $tree->total_branch_length Function: Returns the sum of the length of all branches Returns : integer Args : none =cut sub total_branch_length { my ($self) = @_; $self->throw_not_implemented(); } =head2 height Title : height Usage : my $height = $tree->height Function: Gets the height of tree - this LOG_2($number_nodes) WARNING: this is only true for strict binary trees. The TreeIO system is capable of building non-binary trees, for which this method will currently return an incorrect value!! Returns : integer Args : none =cut sub height{ my ($self) = @_; my $nodect = $self->number_nodes; return 0 if( ! $nodect ); return log($nodect) / log(2); } =head2 id Title : id Usage : my $id = $tree->id(); Function: An id value for the tree Returns : scalar Args : =cut sub id{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 score Title : score Usage : $obj->score($newval) Function: Sets the associated score with this tree This is a generic slot which is probably best used for log likelihood or other overall tree score Returns : value of score Args : newvalue (optional) =cut sub score{ my ($self,$value) = @_; $self->throw_not_implemented(); } =head2 get_leaf_nodes Title : get_leaf_nodes Usage : my @leaves = $tree->get_leaf_nodes() Function: Returns the leaves (tips) of the tree Returns : Array of Bio::Tree::NodeI objects Args : none =cut sub get_leaf_nodes{ my ($self) = @_; return grep { $_->is_Leaf() } $self->get_nodes(-sortby => 'none'); } =head2 Methods for associating Tag/Values with a Tree These methods associate tag/value pairs with a Tree =head2 set_tag_value Title : set_tag_value Usage : $tree->set_tag_value($tag,$value) $tree->set_tag_value($tag,@values) Function: Sets a tag value(s) to a tree. Replaces old values. Returns : number of values stored for this tag Args : $tag - tag name $value - value to store for the tag =cut sub set_tag_value{ shift->throw_not_implemented(); } =head2 add_tag_value Title : add_tag_value Usage : $tree->add_tag_value($tag,$value) Function: Adds a tag value to a tree Returns : number of values stored for this tag Args : $tag - tag name $value - value to store for the tag =cut sub add_tag_value{ shift->throw_not_implemented(); } =head2 remove_tag Title : remove_tag Usage : $tree->remove_tag($tag) Function: Remove the tag and all values for this tag Returns : boolean representing success (0 if tag does not exist) Args : $tag - tagname to remove =cut sub remove_tag { shift->throw_not_implemented(); } =head2 remove_all_tags Title : remove_all_tags Usage : $tree->remove_all_tags() Function: Removes all tags Returns : None Args : None =cut sub remove_all_tags{ shift->throw_not_implemented(); } =head2 get_all_tags Title : get_all_tags Usage : my @tags = $tree->get_all_tags() Function: Gets all the tag names for this Tree Returns : Array of tagnames Args : None =cut sub get_all_tags { shift->throw_not_implemented(); } =head2 get_tag_values Title : get_tag_values Usage : my @values = $tree->get_tag_values($tag) Function: Gets the values for given tag ($tag) Returns : Array of values or empty list if tag does not exist Args : $tag - tag name =cut sub get_tag_values{ shift->throw_not_implemented(); } =head2 has_tag Title : has_tag Usage : $tree->has_tag($tag) Function: Boolean test if tag exists in the Tree Returns : Boolean Args : $tag - tagname =cut sub has_tag{ shift->throw_not_implemented(); } 1; ���������������������������������������������������������������������BioPerl-1.007002/Bio/Tree/Draw����������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 15663� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Tree/Draw/Cladogram.pm���������������������������������������������������������000444��000766��000024�� 44172�13155576320� 20277� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Cladogram # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Gabriel Valiente <valiente@lsi.upc.edu> # # Copyright Gabriel Valiente # # You may distribute this module under the same terms as Perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tree::Draw::Cladogram - Drawing phylogenetic trees in Encapsulated PostScript (EPS) format. =head1 SYNOPSIS use Bio::Tree::Draw::Cladogram; use Bio::TreeIO; my $treeio = Bio::TreeIO->new('-format' => 'newick', '-file' => 'input.nwk'); my $t1 = $treeio->next_tree; my $t2 = $treeio->next_tree; my $obj1 = Bio::Tree::Draw::Cladogram->new(-tree => $t1); $obj1->print(-file => 'cladogram.eps'); if ($t2) { my $obj2 = Bio::Tree::Draw::Cladogram->new(-tree => $t1, -second => $t2); $obj2->print(-file => 'tanglegram.eps'); } =head1 DESCRIPTION Bio::Tree::Draw::Cladogram is a Perl tool for drawing Bio::Tree::Tree objects in Encapsulated PostScript (EPS) format. It can be utilized both for displaying a single phylogenetic tree (a cladogram) and for the comparative display of two phylogenetic trees (a tanglegram) such as a gene tree and a species tree, a host tree and a parasite tree, two alternative trees for the same set of taxa, or two alternative trees for overlapping sets of taxa. Phylogenetic trees are drawn as rectangular cladograms, with horizontal orientation and ancestral nodes centered over their descendents. The font used for taxa is Courier at 10 pt. A single Bio::Tree::Tree object is drawn with ancestors to the left and taxa flushed to the right. Two Bio::Tree::Tree objects are drawn with the first tree oriented left-to-right and the second tree oriented right-to-left, and with corresponding taxa connected by straight lines in a shade of gray. Each correspondence between a $taxon1 of the first tree and a $taxon2 of the second tree is established by setting $taxon1-E<gt>add_tag_value('connection',$taxon2). Thus, a taxon of the first tree can be connected to more than one taxon of the second tree, and vice versa. The branch from the parent to a child $node, as well as the child label, can be colored by setting $node-E<gt>add_tag_value('Rcolor',$r), $node-E<gt>add_tag_value('Gcolor',$g), and $node-E<gt>add_tag_value('Bcolor',$b), where $r, $g, and $b are the desired values for red, green, and blue (zero for lowest, one for highest intensity). This is a preliminary release of Bio::Tree::Draw::Cladogram. Future improvements include an option to output phylograms instead of cladograms. Beware that cladograms are automatically scaled according to branch lengths, but the current release has only been tested with trees having unit branch lengths. The print method could be extended to output graphic formats other than EPS, although there are many graphics conversion programs around that accept EPS input. For instance, most Linux distributions include epstopdf, a Perl script that together with Ghostscript, converts EPS to PDF. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Gabriel Valiente Email valiente@lsi.upc.edu Code for coloring branches contributed by Georgii A Bazykin (gbazykin@princeton.edu). =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tree::Draw::Cladogram; use strict; use PostScript::TextBlock; use base qw(Bio::Root::Root); # The following private package variables are set by the new method # and used by the print method. my %xx; # horizontal coordinate for each node my %yy; # vertical coordinate for each node my $t1; # first Bio::Tree::Tree object my $t2; # second Bio::Tree::Tree object my $font; # font name my $size; # font size my $width; # total drawing width my $height; # total drawing height my $xstep; # branch length in drawing my $tip; # extra space between tip and label my $tipwidth1; # width of longest label among $t1 taxa my $tipwidth2; # width of longest label among $t2 taxa my $compact; # whether or not to ignore branch lengths my $ratio; # horizontal to vertical ratio my $colors; # use colors to color edges my %Rcolor; # red color for each node my %Gcolor; # green color for each node my %Bcolor; # blue color for each node my $bootstrap; # Draw Bootstrap boolean =head2 new Title : new Usage : my $obj = Bio::Tree::Draw::Cladogram->new(); Function: Builds a new Bio::Tree::Draw::Cladogram object Returns : Bio::Tree::Draw::Cladogram Args : -tree => Bio::Tree::Tree object -second => Bio::Tree::Tree object (optional) -font => font name [string] (optional) -size => font size [integer] (optional) -top => top margin [integer] (optional) -bottom => bottom margin [integer] (optional) -left => left margin [integer] (optional) -right => right margin [integer] (optional) -tip => extra tip space [integer] (optional) -column => extra space between cladograms [integer] (optional) -compact => ignore branch lengths [boolean] (optional) -ratio => horizontal to vertical ratio [integer] (optional) -colors => use colors to color edges [boolean] (optional) -bootstrap => draw bootstrap or internal ids [boolean] =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); ($t1, $t2, $font, $size, my $top, my $bottom, my $left, my $right, $tip, my $column, $compact, $ratio, $colors,$bootstrap) = $self->_rearrange([qw(TREE SECOND FONT SIZE TOP BOTTOM LEFT RIGHT TIP COLUMN COMPACT RATIO COLORS BOOTSTRAP)], @args); $font ||= "Helvetica-Narrow"; $size ||= 12; $top ||= 10; $bottom ||= 10; $left ||= 10; $right ||= 10; $tip ||= 5; $column ||= 60; $compact ||= 0; $ratio ||= 1 / 1.6180339887; $colors ||= 0; $bootstrap ||= 0; # Roughly, a cladogram is set according to the following parameters. ################################# # # T # $top (T, top margin) # +---------+ XXX # # $bottom (B, bottom margin) # | # # $left (L, left margin) # | # # $right (R, right margin) # +----+ # # $tip (X, extra tip space) # | +----+ XXXX # # $width (total drawing width) # | | # # $height (total drawing height) # +----+ # Y # $xstep (S, stem length) # | # # $ystep (Y, space between taxa) # +----+ XX # # $tiplen (string length of longest name) # # B # $tipwidth (N, size of longest name) ################################# # L S X N R # ############################# # A tanglegram is roughly set as follows. The only additional # parameter is $column (C, length of connection lines between taxa # of the two trees), but $tip occurs four times, and $tiplen and # $tipwidth differ for the first and the second tree. ########################################################### # # # +---------+ XXX ----- XXXXXX +----+ # # | | # # | +----+ # # +----+ | | # # | +----+ XXXX ----- XXX +----+ | # # | | +----+ # # +----+ | # # | | # # +----+ XX ----- XXXX +---------+ # # # ########################################################### # L X X C X X R # ########################################################### # An alternative would be to let the user set $width and $height in # points and to scale down everything to fit the desired # dimensions. However, the final EPS can later be scaled down to any # desired size anyway. my @taxa1 = $t1->get_leaf_nodes; my $root1 = $t1->get_root_node; $tipwidth1 = 0; foreach my $taxon (@taxa1) { my $w = PostScript::Metrics::stringwidth($taxon->id,$font,$size); if ($w > $tipwidth1) { $tipwidth1 = $w; } } my @taxa2; my $root2; my $ystep = 20; if ($t2) { @taxa2 = $t2->get_leaf_nodes; $root2 = $t2->get_root_node; $tipwidth2 = 0; foreach my $taxon (@taxa2) { my $w = PostScript::Metrics::stringwidth($taxon->id,$font,$size); if ($w > $tipwidth2) { $tipwidth2 = $w; } } } my $stems = $root1->height + 1; if ($t2) { $stems += $root2->height + 1; } my $labels = $tipwidth1; if ($t2) { $labels += $tipwidth2; } $xstep = 20; $width = $left + $stems * $xstep + $tip + $labels + $right; if ($t2) { $width += $tip + $column + $tip + $tip; } $height = $bottom + $ystep * (@taxa1 - 1) + $top; if ($t2) { if ( scalar(@taxa2) > scalar(@taxa1) ) { $height = $bottom + $ystep * (@taxa2 - 1) + $top; } } my $ystep1 = $height / scalar(@taxa1); my $ystep2; if ($t2) { $ystep2 = $height / scalar(@taxa2); } my $x = $left + $xstep * ($root1->height + 1) + $tip; my $y = $bottom; for my $taxon (reverse @taxa1) { $xx{$taxon} = $x - $tip; $yy{$taxon} = $y; $y += $ystep1; } $x -= $xstep; my @stack; my @queue; # postorder traversal push @stack, $t1->get_root_node; while (@stack) { my $node = pop @stack; push @queue, $node; foreach my $child ($node->each_Descendent(-sortby => 'internal_id')) { push @stack, $child; } } @queue = reverse @queue; for my $node (@queue) { if (!$node->is_Leaf) { my @children = $node->each_Descendent; my $child = shift @children; my $xmin = $xx{$child}; my $ymin = my $ymax = $yy{$child}; foreach $child (@children) { $xmin = $xx{$child} if $xx{$child} < $xmin; $ymax = $yy{$child} if $yy{$child} > $ymax; $ymin = $yy{$child} if $yy{$child} < $ymin; } $xx{$node} = $xmin - $xstep; $yy{$node} = ($ymin + $ymax)/2; } } $xx{$t1->get_root_node} = $left + $xstep; my @preorder = $t1->get_nodes(-order => 'depth'); for my $node (@preorder) { #print "\n$node"; if ($colors) { if ($node->has_tag('Rcolor')) { $Rcolor{$node} = $node->get_tag_values('Rcolor') } else { $Rcolor{$node} = 0 } if ($node->has_tag('Gcolor')) { $Gcolor{$node} = $node->get_tag_values('Gcolor') } else { $Gcolor{$node} = 0 } if ($node->has_tag('Bcolor')) { $Bcolor{$node} = $node->get_tag_values('Bcolor') } else { $Bcolor{$node} = 0 } #print "\t$Rcolor{$node}\t$Gcolor{$node}\t$Bcolor{$node}"; } } if ($compact) { # ragged right, ignoring branch lengths $width = 0; shift @preorder; # skip root for my $node (@preorder) { $xx{$node} = $xx{$node->ancestor} + $xstep; $width = $xx{$node} if $xx{$node} > $width; } $width += $tip + $tipwidth1 + $right; } else { # set to aspect ratio and use branch lengths if available my $total_height = (scalar($t1->get_leaf_nodes) - 1) * $ystep; my $scale_factor = $total_height * $ratio / $t1->get_root_node->height; $width = $t1->get_root_node->height * $scale_factor; $width += $left + $xstep; $width += $tip + $tipwidth1 + $right; shift @preorder; # skip root for my $node (@preorder) { my $bl = $node->branch_length; $bl = 1 unless (defined $bl && $bl =~ /^\-?\d+(\.\d+)?$/); $xx{$node} = $xx{$node->ancestor} + $bl * $scale_factor; } } if ($t2) { $x = $left + $xstep * ($root1->height + 1) + $tip; $x += $tipwidth1 + $tip + $column + $tip; my $y = $bottom; for my $taxon (reverse @taxa2) { $xx{$taxon} = $x + $tipwidth2 + $tip; $yy{$taxon} = $y; $y += $ystep2; } $x += $xstep; my @stack; my @queue; # postorder traversal push @stack, $t2->get_root_node; while (@stack) { my $node = pop @stack; push @queue, $node; foreach my $child ($node->each_Descendent(-sortby => 'internal_id')) { push @stack, $child; } } @queue = reverse @queue; for my $node (@queue) { if (!$node->is_Leaf) { my @children = $node->each_Descendent; my $child = shift @children; my $xmax = $xx{$child}; my $ymin = my $ymax = $yy{$child}; foreach $child (@children) { $xmax = $xx{$child} if $xx{$child} > $xmax; $ymax = $yy{$child} if $yy{$child} > $ymax; $ymin = $yy{$child} if $yy{$child} < $ymin; } $xx{$node} = $xmax + $xstep; $yy{$node} = ($ymin + $ymax)/2; } } } return $self; } =head2 print Title : print Usage : $obj->print(); Function: Outputs $obj in Encapsulated PostScript (EPS) format Returns : Args : -file => filename (optional) =cut sub print { my($self,@args) = @_; my ($file) = $self->_rearrange([qw(FILE)], @args); $file ||= "output.eps"; # stdout open my $INFO, '>', $file or $self->throw("Could not write file '$file': $!"); print $INFO "%!PS-Adobe-\n"; print $INFO "%%BoundingBox: 0 0 ", $width, " ", $height, "\n"; print $INFO "1 setlinewidth\n"; print $INFO "/$font findfont\n"; print $INFO "$size scalefont\n"; print $INFO "setfont\n"; # taxa labels are centered to 1/3 the font size for my $taxon (reverse $t1->get_leaf_nodes) { if ($colors) { print $INFO $Rcolor{$taxon}, " ", $Gcolor{$taxon}, " ", $Bcolor{$taxon}, " setrgbcolor\n"; } print $INFO $xx{$taxon} + $tip, " ", $yy{$taxon} - $size / 3, " moveto\n"; print $INFO "(", $taxon->id, ") show\n"; } my $root1 = $t1->get_root_node; for my $node ($t1->get_nodes) { if ($node->ancestor) { # print $xx{$node->ancestor}, " ", $yy{$node->ancestor}, " moveto\n"; # print $xx{$node}, " ", $yy{$node}, " lineto\n"; if ($colors) { print $INFO "stroke\n"; print $INFO $Rcolor{$node}, " ", $Gcolor{$node}, " ", $Bcolor{$node}, " setrgbcolor\n"; } print $INFO $xx{$node}, " ", $yy{$node}, " moveto\n"; print $INFO $xx{$node->ancestor}, " ", $yy{$node}, " lineto\n"; if( $bootstrap ) { print $INFO $xx{$node->ancestor}+ $size/10, " ", $yy{$node->ancestor} - ($size / 3), " moveto\n"; print $INFO "(", $node->ancestor->id, ") show\n"; print $INFO $xx{$node->ancestor}, " ", $yy{$node}, " moveto\n"; } print $INFO $xx{$node->ancestor}, " ", $yy{$node->ancestor}, " lineto\n"; } } my $ymin = $yy{$root1}; my $ymax = $yy{$root1}; foreach my $child ($root1->each_Descendent) { $ymax = $yy{$child} if $yy{$child} > $ymax; $ymin = $yy{$child} if $yy{$child} < $ymin; } my $zz = ($ymin + $ymax)/2; if ($colors) { print $INFO "stroke\n"; print $INFO $Rcolor{$root1}, " ", $Gcolor{$root1}, " ", $Bcolor{$root1}, " setrgbcolor\n"; } print $INFO $xx{$root1}, " ", $zz, " moveto\n"; print $INFO $xx{$root1} - $xstep, " ", $zz, " lineto\n"; if ($t2) { for my $taxon (reverse $t2->get_leaf_nodes) { my $tiplen2 = PostScript::Metrics::stringwidth($taxon->id,$font,$size); print $INFO $xx{$taxon} - $tiplen2 - $tip, " ", $yy{$taxon} - $size / 3, " moveto\n"; printf $INFO "(%s) show\n", $taxon->id; } for my $node ($t2->get_nodes) { if ($node->ancestor) { print $INFO $xx{$node}, " ", $yy{$node}, " moveto\n"; print $INFO $xx{$node->ancestor}, " ", $yy{$node}, " lineto\n"; print $INFO $xx{$node->ancestor}, " ", $yy{$node->ancestor}, " lineto\n"; } } my $root2 = $t2->get_root_node; my $ymin = $yy{$root2}; my $ymax = $yy{$root2}; foreach my $child2 ($root2->each_Descendent) { $ymax = $yy{$child2} if $yy{$child2} > $ymax; $ymin = $yy{$child2} if $yy{$child2} < $ymin; } my $zz = ($ymin + $ymax)/2; print $INFO $xx{$root2}, " ", $zz, " moveto\n"; print $INFO $xx{$root2} + $xstep, " ", $zz, " lineto\n"; my @taxa1 = $t1->get_leaf_nodes; my @taxa2 = $t2->get_leaf_nodes; # set default connection between $t1 and $t2 taxa, unless # overridden by the user (the latter not implemented yet) foreach my $taxon1 (@taxa1) { foreach my $taxon2 (@taxa2) { if ($taxon1->id eq $taxon2->id) { $taxon1->add_tag_value('connection',$taxon2); last; } } } # draw connection lines between $t1 and $t2 taxa print $INFO "stroke\n"; print $INFO "0.5 setgray\n"; foreach my $taxon1 (@taxa1) { my @match = $taxon1->get_tag_values('connection'); foreach my $taxon2 (@match) { my $x0 = $xx{$taxon1} + $tip + PostScript::Metrics::stringwidth($taxon1->id,$font,$size) + $tip; my $x1 = $xx{$taxon1} + $tip + $tipwidth1 + $tip; my $y1 = $yy{$taxon1}; my $x2 = $xx{$taxon2} - $tip - $tipwidth2 - $tip; my $x3 = $xx{$taxon2} - $tip - PostScript::Metrics::stringwidth($taxon2->id,$font,$size) - $tip; my $y2 = $yy{$taxon2}; print $INFO $x0, " ", $y1, " moveto\n"; print $INFO $x1, " ", $y1, " lineto\n"; print $INFO $x2, " ", $y2, " lineto\n"; print $INFO $x3, " ", $y2, " lineto\n"; } } } print $INFO "stroke\n"; print $INFO "showpage\n"; } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/TreeIO�������������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 15216� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/TreeIO/NewickParser.pm���������������������������������������������������������000444��000766��000024�� 17156�13155576320� 20340� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# POD documentation - main docs before the code =head1 NAME Module which implements a newick string parser as a finite state machine which enables it to parse the full Newick specification. Taken largely from the Ensembl Compara file with the same name (Bio::EnsEMBL::Compara::Graph::NewickParser), this module adapts the parser to work with BioPerl's event handler-based parsing scheme. This module is used by nhx.pm and newick.pm, and is NOT called directly. Instead, both of those parsing modules extend this module in order to gain access to the main parsing method. =head1 SYNOPSIS # From newick.pm use base qw(Bio::TreeIO Bio::TreeIO::NewickParser); # in the next_tree method... $self->parse_newick($_); =head1 DESCRIPTION This module correctly parses the Newick and NHX formats, sending calls to the BioPerl TreeEventHandler when appropriate in order to build and populate the node objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jessica Severin (EnsEMBL implementation), Greg Jordan (BioPerl adaptation) =cut package Bio::TreeIO::NewickParser; use strict; use base qw(Bio::Root::Root); sub parse_newick { my $self = shift; my $newick = shift; $newick = $newick . ";" unless ($newick =~ m/;/); my $count=1; my $debug = $self->verbose; my $token = next_token(\$newick, "(;"); my $state=1; my $bracket_level = 0; $self->_start('tree'); my $leaf_flag = 0; while(defined($token)) { # backwards-compat. with 5.8.1, no Switch (but we hate if-elsif-ad-infinitum if ($state == 1) { #new node $self->_start('node'); $self->debug(" -> [$token]\n"); if($token eq '(') { #create new set $self->debug(" create set\n") if($debug); $token = next_token(\$newick, "[(:,)"); $state = 1; $bracket_level++; } else { $state = 2; $leaf_flag = 1; } } elsif ($state == 2) { #naming a node if(!($token =~ /[\[\:\,\)\;]/)) { if (!$leaf_flag && $self->param('internal_node_id') eq 'bootstrap') { $self->_start('bootstrap'); $self->_chars($token); $self->_end('bootstrap'); $token = ''; } $self->_start('id'); $self->_chars($token); $self->_end('id'); $self->debug(" naming leaf\n") if ($debug); $token = next_token(\$newick, "[:,);"); } $state = 3; } elsif ($state == 3) { # optional : and distance if($token eq ':') { $token = next_token(\$newick, "[,);"); $self->_start('branch_length'); $self->_chars($token); $self->_end('branch_length'); $token = next_token(\$newick, ",);"); #move to , or ) } elsif ($token eq '[') { # NHX tag without previous blength $token .= next_token(\$newick, ",);"); } $state = 4; } elsif ($state == 4) { # optional NHX tags if($token =~ /\[\&\&NHX/) { # careful: this regexp gets rid of all NHX wrapping in one step $self->_start('nhx_tag'); $token =~ /\[\&\&NHX\:(\S+)\]/; if ($1) { # NHX may be empty, presumably at end of file, just before ";" my @attributes = split ':', $1; foreach my $attribute (@attributes) { $attribute =~ s/\s+//; my($key,$value) = split '=', $attribute; $self->_start('tag_name'); $self->_chars($key); $self->_end('tag_name'); $self->_start('tag_value'); $self->_chars($value); $self->_end('tag_value'); } } $self->_end('nhx_tag'); $token = next_token(\$newick, ",);"); #move to , or ) } elsif ($token =~ /\[/) { # This is a hack to make AMPHORA2 work if ($token =~ /\[(\S+)\]/) { $self->_start('bootstrap'); $self->_chars($1); $self->_end('bootstrap'); } $token = next_token(\$newick, ",);"); } $state = 5; } elsif ($state == 5) { # end node if($token eq ')') { $self->_end('node'); $token = next_token(\$newick, "[:,);"); if (defined $token && $token eq '[') { # It is possible to have anonymous internal nodes w/ no name # and no blength but with NHX tags # # We use leaf_flag=0 to let the parser know that it's labeling an internal # node. This affects how potential bootstrap values are handled in state 2. $leaf_flag = 0; $state = 2; } else { $leaf_flag = 0; $state = 2; } $bracket_level--; } elsif($token eq ',') { $self->_end('node'); $token = next_token(\$newick, "[(:,)"); #can be un_blengthed nhx nodes $state=1; } elsif($token eq ';') { #done with tree $self->throw("parse error: unbalanced ()\n") if($bracket_level ne 0); $self->_end('node'); $self->_end('tree'); $token = next_token(\$newick, "("); $state=13; } else { $self->debug("[$token]]\n"); $self->throw("parse error: expected ; or ) or ,\n"); } } elsif ($state == 13) { $self->throw("parse error: nothing expected after ;"); } } if ($self->_eventHandler->within_element('tree')) { $self->_end('node'); $self->_end('tree'); } } sub _chars { my $self = shift; my $chars = shift; $self->_eventHandler->characters($chars); } sub _start { my $self = shift; my $name = shift; $self->_eventHandler->start_element({Name=>$name}); } sub _end { my $self = shift; my $name = shift; $self->_eventHandler->end_element({Name=>$name}); } sub next_token { my $string = shift; my $delim = shift; $$string =~ s/^(\s)+//; return undef unless(length($$string)); #print("input =>$$string\n"); #print("delim =>$delim\n"); my $index=undef; my @delims = split(/ */, $delim); foreach my $dl (@delims) { my $pos = index($$string, $dl); if($pos>=0) { $index = $pos unless(defined($index)); $index = $pos if($pos<$index); } } unless(defined($index)) { # have to call as class here (this is not an instance method) Bio::Root::Root->throw("couldn't find delimiter $delim\n $$string"); } my $token =''; if($index==0) { $token = substr($$string,0,1); $$string = substr($$string, 1); } else { $token = substr($$string, 0, $index); $$string = substr($$string, $index); } #print(" token =>$token\n"); #print(" outstring =>$$string\n\n"); return $token; } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/TreeIO/TreeEventBuilder.pm�����������������������������������������������������000444��000766��000024�� 20131�13155576320� 21136� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::TreeIO::TreeEventBuilder # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::TreeIO::TreeEventBuilder - Build Bio::Tree::Tree's and Bio::Tree::Node's from Events =head1 SYNOPSIS # internal use only =head1 DESCRIPTION This object will take events and build a Bio::Tree::TreeI compliant object makde up of Bio::Tree::NodeI objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::TreeIO::TreeEventBuilder; use strict; use Bio::Tree::Tree; use Bio::Tree::Node; use base qw(Bio::Root::Root Bio::Event::EventHandlerI); =head2 new Title : new Usage : my $obj = Bio::TreeIO::TreeEventBuilder->new(); Function: Builds a new Bio::TreeIO::TreeEventBuilder object Returns : Bio::TreeIO::TreeEventBuilder Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($treetype, $nodetype) = $self->_rearrange([qw(TREETYPE NODETYPE)], @args); $treetype ||= 'Bio::Tree::Tree'; $nodetype ||= 'Bio::Tree::Node'; eval { $self->_load_module($treetype); $self->_load_module($nodetype); }; if( $@ ) { $self->throw("Could not load module $treetype or $nodetype. \n$@\n") } $self->treetype($treetype); $self->nodetype($nodetype); $self->{'_treelevel'} = 0; return $self; } =head2 treetype Title : treetype Usage : $obj->treetype($newval) Function: Returns : value of treetype Args : newvalue (optional) =cut sub treetype{ my ($self,$value) = @_; if( defined $value) { $self->{'treetype'} = $value; } return $self->{'treetype'}; } =head2 nodetype Title : nodetype Usage : $obj->nodetype($newval) Function: Returns : value of nodetype Args : newvalue (optional) =cut sub nodetype{ my ($self,$value) = @_; if( defined $value) { $self->{'nodetype'} = $value; } return $self->{'nodetype'}; } =head2 SAX methods =cut =head2 start_document Title : start_document Usage : $handler->start_document Function: Begins a Tree event cycle Returns : none Args : none =cut sub start_document { my ($self) = @_; $self->{'_lastitem'} = {}; $self->{'_currentitems'} = []; $self->{'_currentnodes'} = []; return; } =head2 end_document Title : end_document Usage : my @trees = $parser->end_document Function: Finishes a Phylogeny cycle Returns : An array Bio::Tree::TreeI Args : none =cut sub end_document { my ($self,$label) = @_; my ($root) = @{$self->{'_currentnodes'}}; $self->debug("Root node is " . $root->to_string()."\n"); if( $self->verbose > 0 ) { foreach my $node ( $root->get_Descendents ) { $self->debug("node is ". $node->to_string(). "\n"); } } my $tree = $self->treetype->new(-verbose => $self->verbose, -root => $root); return $tree; } =head2 start_element Title : start_element Usage : Function: Example : Returns : Args : $data => hashref with key 'Name' =cut sub start_element{ my ($self,$data) =@_; $self->{'_lastitem'}->{$data->{'Name'}}++; $self->debug("starting element: $data->{Name}\n"); push @{$self->{'_lastitem'}->{'current'}},$data->{'Name'}; my %data; if( $data->{'Name'} eq 'node' ) { push @{$self->{'_currentitems'}}, \%data; $self->{'_treelevel'}++; } elsif ( $data->{Name} eq 'tree' ) { } } =head2 end_element Title : end_element Usage : Function: Returns : none Args : $data => hashref with key 'Name' =cut sub end_element{ my ($self,$data) = @_; $self->debug("end of element: $data->{Name}\n"); # this is the stack where we push/pop items from it my $curcount = scalar @{$self->{'_currentnodes'}}; my $level = $self->{'_treelevel'}; my $levelct = $self->{'_nodect'}->[$self->{'_treelevel'}+1] || 0; if( $data->{'Name'} eq 'node' ) { my $tnode; my $node = pop @{$self->{'_currentitems'}}; $tnode = $self->nodetype->new( -verbose => $self->verbose, %{$node}); $self->debug( "new node will be ".$tnode->to_string."\n"); if ( !$node->{'-leaf'} && $levelct > 0) { $self->debug(join(',', map { $_->to_string } @{$self->{'_currentnodes'}}). "\n"); $self->throw("something wrong with event construction treelevel ". "$level is recorded as having $levelct nodes ". "but current nodes at this level is $curcount\n") if( $levelct > $curcount); for ( splice( @{$self->{'_currentnodes'}}, - $levelct)) { $self->debug("adding desc: " . $_->to_string . "\n"); $tnode->add_Descendent($_); } $self->{'_nodect'}->[$self->{'_treelevel'}+1] = 0; } push @{$self->{'_currentnodes'}}, $tnode; $self->{'_nodect'}->[$self->{'_treelevel'}]++; $curcount = scalar @{$self->{'_currentnodes'}}; $self->debug ("added node: count is now $curcount, treelevel: $level, nodect: $levelct\n"); $self->{'_treelevel'}--; } elsif( $data->{'Name'} eq 'tree' ) { $self->debug("end of tree: nodes in stack is $curcount\n"); } $self->{'_lastitem'}->{ $data->{'Name'} }--; pop @{$self->{'_lastitem'}->{'current'}}; } =head2 in_element Title : in_element Usage : Function: Example : Returns : Args : =cut sub in_element{ my ($self,$e) = @_; return 0 if ! defined $self->{'_lastitem'} || ! defined $self->{'_lastitem'}->{'current'}->[-1]; return ($e eq $self->{'_lastitem'}->{'current'}->[-1]); } =head2 within_element Title : within_element Usage : Function: Example : Returns : Args : =cut sub within_element{ my ($self,$e) = @_; return $self->{'_lastitem'}->{$e}; } =head2 characters Title : characters Usage : $handler->characters($text); Function: Processes characters Returns : none Args : text string =cut sub characters{ my ($self,$ch) = @_; if( $self->within_element('node') ) { my $hash = pop @{$self->{'_currentitems'}}; if( $self->in_element('bootstrap') ) { # leading/trailing Whitespace-B-Gone $ch =~ s/^\s+//; $ch =~ s/\s+$//; $hash->{'-bootstrap'} = $ch; } elsif( $self->in_element('branch_length') ) { # leading/trailing Whitespace-B-Gone $ch =~ s/^\s+//; $ch =~ s/\s+$//; $hash->{'-branch_length'} = $ch; } elsif( $self->in_element('id') ) { $hash->{'-id'} = $ch; } elsif( $self->in_element('description') ) { $hash->{'-desc'} = $ch; } elsif ( $self->in_element('tag_name') ) { $hash->{'-NHXtagname'} = $ch; } elsif ( $self->in_element('tag_value') ) { $hash->{'-nhx'}->{$hash->{'-NHXtagname'}} = $ch; delete $hash->{'-NHXtagname'}; } elsif( $self->in_element('leaf') ) { $hash->{'-leaf'} = $ch; } push @{$self->{'_currentitems'}}, $hash; } $self->debug("chars: $ch\n"); } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/TreeIO/cluster.pm��������������������������������������������������������������000444��000766��000024�� 12364�13155576320� 17420� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::TreeIO::cluster # # Contributed by Guillaume Rousse <Guillaume-dot-Rousse-at-inria-dot-fr> # # Copyright INRIA # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::TreeIO::cluster - A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output =head1 SYNOPSIS # do not use this module directly use Bio::TreeIO; use Algorithm::Cluster; my ($result, $linkdist) = Algorithm::Cluster::treecluster( distances => $matrix ); my $treeio = Bio::TreeIO->new( -format => 'cluster', -result => $result, -linkdist => $linkdist, -labels => $labels ); my $tree = $treeio->next_tree; =head1 DESCRIPTION This is a driver module for parsing Algorithm::Cluster::treecluster() output. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Guillaume Rousse Email Guillaume-dot-Rousse-at-inria-dot-fr =head1 CONTRIBUTORS Jason Stajich - jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::TreeIO::cluster; use strict; use Bio::Event::EventGeneratorI; use IO::String; use base qw(Bio::TreeIO); =head2 new Title : new Usage : my $obj = Bio::TreeIO::cluster->new(); Function: Builds a new Bio::TreeIO::cluster object for reading Algorithm::Cluster::treecluster output Returns : Bio::TreeIO::cluster Args :-result => Algorithm::Cluster result -linkdist => distance between links -labels => node labels =cut sub _initialize { my $self = shift; ($self->{_result},$self->{_linkdist}, $self->{_labels}) = $self->_rearrange([qw (RESULT LINKDIST LABELS)], @_); $self->SUPER::_initialize(@_); } =head2 next_tree Title : next_tree Usage : my $tree = $treeio->next_tree Function: Gets the next tree in the stream Returns : Bio::Tree::TreeI Args : none =cut sub next_tree { my ($self) = @_; if( ! $self->{_result} ){ $self->warn("Must provide value 'result' and 'linkdist' and 'labels' when initializing a TreeIO::cluster object"); return; } $self->_eventHandler->start_document(); # build tree from the root $self->_eventHandler->start_element({Name => 'tree'}); $self->_recurse(-1, 0); $self->_recurse(-1, 1); $self->_eventHandler->end_element({Name => 'tree'}); return $self->_eventHandler->end_document; } sub _recurse { my ($self, $line, $column) = @_; my $id = $self->{_result}->[$line]->[$column]; if ($id >= 0) { # leaf $self->debug("leaf $id\n"); $self->debug("distance $self->{_linkdist}->[$line]\n"); $self->debug("label $self->{_labels}->[$id]\n"); $self->_eventHandler->start_element({Name => 'node'}); $self->_eventHandler->start_element({Name => 'branch_length'}); $self->_eventHandler->characters($self->{_linkdist}->[$line]); $self->_eventHandler->end_element({Name => 'branch_length'}); $self->_eventHandler->start_element({Name => 'id'}); $self->_eventHandler->characters($self->{_labels}->[$id]); $self->_eventHandler->end_element({Name => 'id'}); $self->_eventHandler->start_element({Name => 'leaf'}); $self->_eventHandler->characters(1); $self->_eventHandler->end_element({Name => 'leaf'}); $self->_eventHandler->end_element({Name => 'node'}); } else { # internal node $self->debug("internal node $id\n"); $self->debug("distance $self->{_linkdist}->[$line]\n"); $self->_eventHandler->start_element({Name => 'node'}); $self->_eventHandler->start_element({Name => 'branch_length'}); $self->_eventHandler->characters($self->{_linkdist}->[$line]); $self->_eventHandler->end_element({Name => 'branch_length'}); $self->_eventHandler->start_element({Name => 'leaf'}); $self->_eventHandler->characters(0); $self->_eventHandler->end_element({Name => 'leaf'}); $self->_eventHandler->start_element({Name => 'tree'}); my $child_id = - ($id + 1); $self->_recurse($child_id, 0); $self->_recurse($child_id, 1); $self->_eventHandler->end_element({Name => 'tree'}); $self->_eventHandler->end_element({Name => 'node'}); } } =head2 write_tree Title : write_tree Usage : Function: Sorry not possible with this format Returns : none Args : none =cut sub write_tree{ $_[0]->throw("Sorry the format 'cluster' can only be used as an input format"); } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/TreeIO/lintree.pm��������������������������������������������������������������000444��000766��000024�� 14602�13155576320� 17376� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::TreeIO::lintree # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl-dot-org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::TreeIO::lintree - Parser for lintree output trees =head1 SYNOPSIS # do not use directly, use through Bio::TreeIO use Bio::TreeIO; my $treeio = Bio::TreeIO->new(-format => 'lintree', -file => 't/data/crab.nj'); my $tree = $treeio->next_tree; =head1 DESCRIPTION Parser for the lintree output which looks like this 13 sequences 1000 bootstraping 1 A-salina 2 C-vittat 3 C-sp. 4 L-aequit 5 P-camtsc 6 E-tenuim 7 L-splend 8 P-bernha 9 P-acadia 10 P-p(NE) 11 P-p(GU) 12 P-l(NE) 13 P-l(GU) 14 and 2 0.098857 1000 14 and 3 0.127932 1000 15 and 1 0.197471 1000 15 and 14 0.029273 874 16 and 10 0.011732 1000 16 and 11 0.004529 1000 17 and 12 0.002258 1000 17 and 13 0.000428 1000 18 and 16 0.017512 1000 18 and 17 0.010824 998 19 and 4 0.006534 1000 19 and 5 0.006992 1000 20 and 15 0.070461 1000 20 and 18 0.030579 998 21 and 8 0.003339 1000 21 and 9 0.002042 1000 22 and 6 0.011142 1000 22 and 21 0.010693 983 23 and 20 0.020714 996 23 and 19 0.020350 1000 24 and 23 0.008665 826 24 and 22 0.013457 972 24 and 7 0.025598 1000 See http://www.bio.psu.edu/People/Faculty/Nei/Lab/software.htm for access to the program and N Takezaki, A Rzhetsky, and M Nei, "Phylogenetic test of the molecular clock and linearized trees." Mol Biol Evol 12(5):823-33. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 CONTRIBUTORS Ideas and discussion from: Alan Christoffels Avril Coghlan =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::TreeIO::lintree; use vars qw(%Defaults); use strict; use base qw(Bio::TreeIO); $Defaults{'NodeType'} = "Bio::Tree::Node"; =head2 new Title : new Usage : my $obj = Bio::TreeIO::lintree->new(); Function: Builds a new Bio::TreeIO::lintree object Returns : an instance of Bio::TreeIO::lintree Args : -nodetype => Node type to create [default Bio::Tree::Node] =cut sub _initialize { my ($self,@args) = @_; $self->SUPER::_initialize(@args); my ($nodetype) = $self->_rearrange([qw(NODETYPE)],@args); $nodetype ||= $Defaults{'NodeType'}; $self->nodetype($nodetype); } =head2 next_tree Title : next_tree Usage : my $tree = $treeio->next_tree Function: Gets the next tree in the stream Returns : Bio::Tree::TreeI Args : none =cut sub next_tree { my ($self) = @_; my $seentop = 0; my ($tipcount,%data,@nodes) = (0); my $nodetype = $self->nodetype; while( defined( $_ = $self->_readline) ) { if( /^\s*(\d+)\s+sequences/ox ) { if( $seentop ) { $self->_pushback($_); last; } $tipcount = $1; $seentop = 1; } elsif( /^(\d+)\s+(\S+)\s*$/ox ) { # deal with setting an outgroup unless( defined $data{'outgroup'} ) { $data{'outgroup'} = [$1,$2]; } $nodes[$1 - 1] = { '-id' => $2 }; } elsif( m/^\s*(\d+)\s+and\s+(\d+)\s+(\-?\d+\.\d+)(?:\s+(\d+))?/ox ) { my ($node,$descend,$blength,$bootstrap) = ( $1, $2, $3, $4 ); # need to -- descend and node because # array is 0 based $node--;$descend--; $nodes[$descend]->{'-branch_length'} = $blength; $nodes[$descend]->{'-bootstrap'} = $bootstrap; #? here $nodes[$node]->{'-id'} = $node+1; push @{$nodes[$node]->{'-d'}}, $descend; } elsif( /\s+(\S+)\-distance was used\./ox ) { $data{'method'} = $1; } elsif( /\s*seed=(\d+)/ox ) { $data{'seed'} = $1; } elsif( m/^outgroup:\s+(\d+)\s+(\S+)/ox ) { $data{'outgroup'} = [$1,$2]; } } if( @nodes ) { my @treenodes; foreach my $n ( @nodes ) { push @treenodes, $nodetype->new(%{$n}); } foreach my $tn ( @treenodes ) { my $n = shift @nodes; for my $ptr ( @{ $n->{'-d'} || [] } ) { $tn->add_Descendent($treenodes[$ptr]); } } my $T = Bio::Tree::Tree->new(-root => (pop @treenodes) ); if( $data{'outgroup'} ) { my ($outgroup) = $treenodes[$data{'outgroup'}->[0]]; if( ! defined $outgroup) { $self->warn("cannot find '". $data{'outgroup'}->[1]. "'\n"); } else { $T->reroot($outgroup->ancestor); } } return $T; } return; # if there are no more trees, return undef } =head2 nodetype Title : nodetype Usage : $obj->nodetype($newval) Function: Example : Returns : value of nodetype (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub nodetype{ my ($self,$value) = @_; if( defined $value) { eval "require $value"; if( $@ ) { $self->throw("$@: Unrecognized Node type for ".ref($self). "'$value'");} my $a = bless {},$value; unless( $a->isa('Bio::Tree::NodeI') ) { $self->throw("Must provide a valid Bio::Tree::NodeI or child class to SeqFactory Not $value"); } $self->{'nodetype'} = $value; } return $self->{'nodetype'}; } 1; ������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/TreeIO/newick.pm���������������������������������������������������������������000444��000766��000024�� 21474�13155576320� 17221� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::TreeIO::newick # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::TreeIO::newick =head1 SYNOPSIS # do not use this module directly use Bio::TreeIO; my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 't/data/LOAD_Ccd1.dnd'); my $tree = $treeio->next_tree; =head1 DESCRIPTION This module handles parsing and writing of Newick/PHYLIP/New Hampshire format. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::TreeIO::newick; use strict; use Bio::Event::EventGeneratorI; use base qw(Bio::TreeIO Bio::TreeIO::NewickParser); =head2 new Title : new Args : -print_count => boolean default is false -bootstrap_style => set the bootstrap style (one of nobranchlength, molphy, traditional) -order_by => set the order by sort method See L<Bio::Node::Node::each_Descendent()> =cut sub _initialize { my $self = shift; $self->SUPER::_initialize(@_); my ( $print_count ) = $self->_rearrange( [ qw(PRINT_COUNT) ], @_ ); $self->print_tree_count( $print_count || 0 ); return; } =head2 next_tree Title : next_tree Usage : my $tree = $treeio->next_tree Function: Gets the next tree in the stream Returns : L<Bio::Tree::TreeI> Args : none =cut sub next_tree { my ($self) = @_; local $/ = ";\n"; return unless $_ = $self->_readline; s/[\r\n]//gs; my $score; my $despace = sub { my $dirty = shift; $dirty =~ s/\s+//gs; return $dirty }; my $dequote = sub { my $dirty = shift; $dirty =~ s/^"?\s*(.+?)\s*"?$/$1/; return $dirty; }; s/([^"]*)(".+?")([^"]*)/$despace->($1) . $dequote->($2) . $despace->($3)/egsx; if (s/^\s*\[([^\]]+)\]//) { my $match = $1; $match =~ s/\s//g; $match =~ s/lh\=//; if ( $match =~ /([-\d\.+]+)/ ) { $score = $1; } } $self->_eventHandler->start_document; # Call the parse_newick method as defined in NewickParser.pm $self->parse_newick($_); my $tree = $self->_eventHandler->end_document; # Add the tree score afterwards if it exists. if (defined $tree) { $tree->score($score); return $tree; } } # Returns the default set of parsing & writing parameters for the Newick format. sub get_default_params { my $self = shift; return { newline_each_node => 0, order_by => '', # ??? bootstrap_style => 'traditional', # Can be 'traditional', 'molphy', 'nobranchlength' internal_node_id => 'id', # Can be 'id' or 'bootstrap' no_branch_lengths => 0, no_bootstrap_values => 0, no_internal_node_labels => 0 }; } =head2 write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Write a tree out to data stream in newick/phylip format Returns : none Args : L<Bio::Tree::TreeI> object =cut sub write_tree { my ( $self, @trees ) = @_; if ( $self->print_tree_count ) { $self->_print( sprintf( " %d\n", scalar @trees ) ); } my $params = $self->get_params; foreach my $tree (@trees) { if ( !defined $tree || ref($tree) =~ /ARRAY/i || !$tree->isa('Bio::Tree::TreeI') ) { $self->throw( "Calling write_tree with non Bio::Tree::TreeI object\n"); } my @data = $self->_write_tree_Helper( $tree->get_root_node, $params); $self->_print( join( ',', @data ).";" ); } $self->flush if $self->_flush_on_write && defined $self->_fh; return; } sub _write_tree_Helper { my $self = shift; my ( $node, $params ) = @_; my @data; foreach my $n ( $node->each_Descendent($params->{order_by}) ) { push @data, $self->_write_tree_Helper( $n, $params ); } my $label = $self->_node_as_string($node,$params); if ( scalar(@data) >= 1) { $data[0] = "(" . $data[0]; $data[-1] .= ")"; $data[-1] .= $label; } else { push @data, $label; } return @data; } sub _node_as_string { my $self = shift; my $node = shift; my $params = shift; my $label_stringbuffer = ''; if ($params->{no_bootstrap_values} != 1 && !$node->is_Leaf && defined $node->bootstrap && $params->{bootstrap_style} eq 'traditional' && $params->{internal_node_id} eq 'bootstrap') { # If we're an internal node and we're using 'traditional' bootstrap style, # we output the bootstrap instead of any label. my $bootstrap = $node->bootstrap; $label_stringbuffer .= $bootstrap if (defined $bootstrap); } elsif ($params->{no_internal_node_labels} != 1) { my $id = $node->id; $label_stringbuffer .= $id if( defined $id ); } if ($params->{no_branch_lengths} != 1) { my $blen = $node->branch_length; $label_stringbuffer .= ":". $blen if (defined $blen); } if ($params->{bootstrap_style} eq 'molphy') { my $bootstrap = $node->bootstrap; $label_stringbuffer .= "[$bootstrap]" if (defined $bootstrap); } if ($params->{newline_each_node} == 1) { $label_stringbuffer .= "\n"; } return $label_stringbuffer; } =head2 print_tree_count Title : print_tree_count Usage : $obj->print_tree_count($newval) Function: Get/Set flag for printing out the tree count (paml,protml way) Returns : value of print_tree_count (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub print_tree_count { my $self = shift; return $self->{'_print_tree_count'} = shift if @_; return $self->{'_print_tree_count'} || 0; } =head2 bootstrap_style Title : bootstrap_style Usage : $obj->bootstrap_style($newval) Function: A description of how bootstraps and branch lengths are written, as the ID part of the internal node or else in [] in the branch length (Molphy-like; I am sure there is a better name for this but am not sure where to go for some sort of format documentation) If no branch lengths are requested then no bootstraps are usually written (unless someone REALLY wants this functionality...) Can take on strings which contain the possible values of 'nobranchlength' --> don't draw any branch lengths - this is helpful if you don't want to have to go through and delete branch len on all nodes 'molphy' --> draw bootstraps (100) like (A:0.11,B:0.22):0.33[100]; 'traditional' --> draw bootstraps (100) like (A:0.11,B:0.22)100:0.33; Returns : value of bootstrap_style (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub bootstrap_style { my $self = shift; my $val = shift; if ( defined $val ) { if ( $val !~ /^nobranchlength|molphy|traditional/i ) { $self->warn( "requested an unknown bootstrap style $val, expect one of nobranchlength,molphy,traditional, not updating value.\n" ); } else { $self->{'_bootstrap_style'} = $val; } } return $self->{'_bootstrap_style'} || 'traditional'; } =head2 order_by Title : order_by Usage : $obj->order_by($newval) Function: Allow node order to be specified (typically "alpha") See L<Bio::Node::Node::each_Descendent()> Returns : value of order_by (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub order_by { my $self = shift; return $self->{'order_by'} = shift if @_; return $self->{'order_by'}; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/TreeIO/nexml.pm����������������������������������������������������������������000444��000766��000024�� 11017�13155576320� 17054� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::TreeIO::nexml # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Chase Miller <chmille4@gmail.com> # # Copyright Chase Miller # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::TreeIO::nexml - A TreeIO driver module for parsing NeXML tree files =head1 SYNOPSIS use Bio::TreeIO; my $in = Bio::TreeIO->new(-file => 'data.nexml' -format => 'Nexml'); while( my $tree = $in->next_tree ) { } =head1 DESCRIPTION This is a driver module for parsing tree data in a NeXML format. For more information on NeXML, visit L<http://www.nexml.org>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chase Miller Email chmille4@gmail.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::TreeIO::nexml; use strict; use lib '../..'; use Bio::Event::EventGeneratorI; use IO::String; use Bio::Nexml::Factory; use Bio::Phylo::IO qw (parse unparse); use base qw(Bio::TreeIO); sub _initialize { my $self = shift; $self->SUPER::_initialize(@_); $self->{_doc} = undef; } =head2 next_tree Title : next_tree Usage : my $tree = $treeio->next_tree Function: Gets the next tree in the stream Returns : L<Bio::Tree::TreeI> Args : none =cut sub next_tree { my ($self) = @_; unless ( $self->{'_parsed'} ) { $self->_parse; } return $self->{'_trees'}->[ $self->{'_treeiter'}++ ]; } =head2 doc Title : doc Usage : $treeio->doc Function: Returns the biophylo nexml document object Returns : Bio::Phylo::Project Args : none or Bio::Phylo::Project object =cut sub doc { my ($obj,$value) = @_; if( defined $value) { $obj->{'_doc'} = $value; } return $obj->{'_doc'}; } =head2 rewind Title : rewind Usage : $treeio->rewind Function: Resets the stream Returns : none Args : none =cut sub rewind { my $self = shift; $self->{'_treeiter'} = 0; } sub _parse { my ($self) = @_; $self->{'_parsed'} = 1; $self->{'_treeiter'} = 0; my $fac = Bio::Nexml::Factory->new(); # Only pass filename if filehandle is not available, # or "Bio::Phylo" will create a new filehandle that ends # out of scope and can't be closed directly, leaving 2 open # filehandles for the same file (so file can't be deleted) my $file_arg; my $file_value; if ( exists $self->{'_filehandle'} and defined $self->{'_filehandle'} ) { $file_arg = '-handle'; $file_value = $self->{'_filehandle'}; } else { $file_arg = '-file'; $file_value = $self->{'_file'}; } $self->doc(parse( $file_arg => $file_value, '-format' => 'nexml', '-as_project' => '1' ) ); $self->{'_trees'} = $fac->create_bperl_tree($self); } =head2 write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Writes a tree onto the stream Returns : none Args : L<Bio::Tree::TreeI> =cut sub write_tree { my ($self, $bp_tree) = @_; my $fac = Bio::Nexml::Factory->new(); my $taxa = $fac->create_bphylo_taxa($bp_tree); my ($tree) = $fac->create_bphylo_tree($bp_tree, $taxa); my $forest = Bio::Phylo::Factory->create_forest(); $self->doc(Bio::Phylo::Factory->create_project()); $forest->set_taxa($taxa); $forest->insert($tree); $self->doc->insert($forest); my $ret = $self->_print($self->doc->to_xml()); $self->flush; return $ret; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/TreeIO/nexus.pm����������������������������������������������������������������000444��000766��000024�� 24677�13155576320� 17113� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::TreeIO::nexus # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-open-bio-dot-org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP =head1 SYNOPSIS use Bio::TreeIO; my $in = Bio::TreeIO->new(-file => 't/data/cat_tre.tre'); while( my $tree = $in->next_tree ) { } =head1 DESCRIPTION This is a driver module for parsing PAUP Nexus tree format which basically is just a remapping of trees. =head2 Comments The nexus format allows node comments that are placed inside square brackets. Usually the comments (implemented as tags for nodes) are used to give a name for an internal node or record the bootstrap value, but other uses are possible. The FigTree program by Andrew Rambaut adds various rendering parameters inside comments and flags these comments by starting them with '&!'. The parameters implemented here are 'label' and 'color'. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-open-bio-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::TreeIO::nexus; use strict; use Bio::Event::EventGeneratorI; use IO::String; use base qw(Bio::TreeIO); =head2 new Title : new Args : -header => boolean default is true print/do not print #NEXUS header -translate => boolean default is true print/do not print Node Id translation to a number =cut sub _initialize { my $self = shift; $self->SUPER::_initialize(@_); my ( $hdr, $trans ) = $self->_rearrange( [ qw(HEADER TRANSLATE) ], @_ ); $self->header( defined $hdr ? $hdr : 1 ); $self->translate_node( defined $trans ? $trans : 1 ); } =head2 next_tree Title : next_tree Usage : my $tree = $treeio->next_tree Function: Gets the next tree in the stream Returns : Bio::Tree::TreeI Args : none =cut sub next_tree { my ($self) = @_; unless ( $self->{'_parsed'} ) { $self->_parse; } return $self->{'_trees'}->[ $self->{'_treeiter'}++ ]; } sub rewind { shift->{'_treeiter'} = 0; } sub _parse { my ($self) = @_; $self->{'_parsed'} = 1; $self->{'_treeiter'} = 0; while ( defined( $_ = $self->_readline ) ) { next if /^\s+$/; last; } return unless ( defined $_ ); unless (/^\#NEXUS/i) { $self->warn("File does not start with #NEXUS"); #' return; } my $line; while ( defined( $_ = $self->_readline ) ) { $line .= $_; } my @sections = split( /#NEXUS/i, $line ); for my $s (@sections) { my %translate; if ( $self->verbose > 0 ) { while ( $s =~ s/(\[[^\]]+\])// ) { $self->debug("removing comment $1\n"); } } else { $s =~ s/(\[[^\]]+\])//g; } if ( $s =~ /begin trees;(.+)(end;)?/si ) { my $trees = $1; if ( $trees =~ s/\s+translate\s+([^;]+);//i ) { my @trans; my $tr = $1; while ($tr =~ m{\s*([^,\s]+?\s+(?:'[^']+'|[^'\s]+)),?}gc) { push @trans, $1; } for my $n ( @trans ) { if ($n =~ /^\s*(\S+)\s+(.+)$/) { my ($id,$tag) = ($1,$2); $tag =~ s/[\s,]+$//; # remove the extra spaces of the last taxon $translate{$id} = $tag; } } } else { $self->debug("no translate in: $trees\n"); } while ($trees =~ /\s+tree\s+\*?\s*(\S+)\s*\= \s*(?:\[\S+\])?\s*([^\;]+;)/igx) { my ( $tree_name, $tree_str ) = ( $1, $2 ); # MrBayes does not print colons for node label # $tree_str =~ s/\)(\d*\.\d+)\)/:$1/g; my $buf = IO::String->new($tree_str); my $treeio = Bio::TreeIO->new( -format => 'newick', -fh => $buf ); my $tree = $treeio->next_tree; foreach my $node ( grep { $_->is_Leaf } $tree->get_nodes ) { my $id = $node->id; my $lookup = $translate{$id}; $node->id( $lookup || $id ); } $tree->id($tree_name) if defined $tree_name; push @{ $self->{'_trees'} }, $tree; } } else { $self->debug("begin_trees failed: $s\n"); } } if ( !@sections ) { $self->debug("warn no sections: $line\n"); } } =head2 write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Writes a tree onto the stream Returns : none Args : Bio::Tree::TreeI =cut sub write_tree { my ( $self, @trees ) = @_; if ( $self->header ) { $self->_print("#NEXUS\n\n"); } my $translate = $self->translate_node; my $time = localtime(); $self->_print( sprintf( "Begin trees; [Treefile created %s]\n", $time ) ); my ( $first, $nodecter, %node2num ) = ( 0, 1 ); foreach my $tree (@trees) { if ( $first == 0 && $translate ) { $self->_print("\tTranslate\n"); $self->_print( join( ",\n", map { $node2num{ $_->id } = $nodecter; sprintf( "\t\t%d %s", $nodecter++, $_->id ) } grep { $_->is_Leaf } $tree->get_nodes ), "\n;\n" ); } my @data = _write_tree_Helper( $tree->get_root_node, \%node2num ); if ( $data[-1] !~ /\)$/ ) { $data[0] = "(" . $data[0]; $data[-1] .= ")"; } # by default all trees in bioperl are currently rooted # something we'll try and fix one day.... $self->_print( sprintf( "\t tree %s = [&%s] %s;\n", ( $tree->id || sprintf( "Bioperl_%d", $first + 1 ) ), ( $tree->get_root_node ) ? 'R' : 'U', join( ',', @data ) ) ); $first++; } $self->_print("End;\n"); $self->flush if $self->_flush_on_write && defined $self->_fh; return; } sub _write_tree_Helper { my ( $node, $node2num ) = @_; return () if ( !defined $node ); my @data; foreach my $n ( $node->each_Descendent() ) { push @data, _write_tree_Helper( $n, $node2num ); } if ( @data > 1 ) { # internal node $data[0] = "(" . $data[0]; $data[-1] .= ")"; # FigTree comments start my $comment_flag; $comment_flag = 0 if ( $node->has_tag('color') or $node->has_tag('label') ); $data[-1] .= '[&!' if defined $comment_flag; if ( $node->has_tag('color')) { my $color = $node->get_tag_values('color'); $data[-1] .= "color=$color"; $comment_flag++; } if ( $node->has_tag('label')) { my $label = $node->get_tag_values('label'); $data[-1] .= ',' if $comment_flag; $data[-1] .= 'label="'. $label. '"'; } $data[-1] .= ']' if defined $comment_flag; # FigTree comments end # let's explicitly write out the bootstrap if we've got it my $b; my $bl = $node->branch_length; if ( !defined $bl ) { } elsif ( $bl =~ /\#/ ) { $data[-1] .= $bl; } else { $data[-1] .= ":$bl"; } if ( defined( $b = $node->bootstrap ) ) { $data[-1] .= sprintf( "[%s]", $b ); } elsif ( defined( $b = $node->id ) ) { $b = $node2num->{$b} if ( $node2num->{$b} ); # translate node2num $data[-1] .= sprintf( "[%s]", $b ) if defined $b; } } else { # leaf node if ( defined $node->id || defined $node->branch_length ) { my $id = defined $node->id ? $node->id : ''; if ( length($id) && $node2num->{$id} ) { $id = $node2num->{$id}; } if ( $node->has_tag('color')) { my ($color) = $node->get_tag_values('color'); $id .= "[&!color=$color\]"; } push @data, sprintf( "%s%s", $id, defined $node->branch_length ? ":" . $node->branch_length : '' ); } } return @data; } =head2 header Title : header Usage : $obj->header($newval) Function: Example : Returns : value of header (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub header { my $self = shift; return $self->{'header'} = shift if @_; return $self->{'header'}; } =head2 translate_node Title : translate_node Usage : $obj->translate_node($newval) Function: Example : Returns : value of translate_node (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub translate_node { my $self = shift; return $self->{'translate_node'} = shift if @_; return $self->{'translate_node'}; } 1; �����������������������������������������������������������������BioPerl-1.007002/Bio/TreeIO/nhx.pm������������������������������������������������������������������000444��000766��000024�� 5240�13155576320� 16507� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::TreeIO::nhx # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Aaron Mackey <amackey@virginia.edu> # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::TreeIO::nhx - TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. =head1 SYNOPSIS # do not use this module directly use Bio::TreeIO; my $treeio = Bio::TreeIO->new(-format => 'nhx', -file => 'tree.dnd'); my $tree = $treeio->next_tree; =head1 DESCRIPTION This module handles parsing and writing of Newick/New Hampshire eXtended (NHX) format. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted viax the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Aaron Mackey Email amackey-at-virginia.edu =head1 CONTRIBUTORS Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::TreeIO::nhx; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Tree::NodeNHX; use Bio::Event::EventGeneratorI; #use XML::Handler::Subs; use base qw(Bio::TreeIO::newick); sub _initialize { my($self, %args) = @_; $args{-nodetype} ||= 'Bio::Tree::NodeNHX'; $self->SUPER::_initialize(%args); } sub _node_as_string { my $self = shift; my $node = shift; my $params = shift; my $label_stringbuffer = $self->SUPER::_node_as_string($node,$params); my @tags = $node->get_all_tags; if( scalar(@tags) > 0 ) { @tags = sort @tags; $label_stringbuffer .= '[' . join(":", "&&NHX", map { "$_=" .join(',',$node->get_tag_values($_)) } @tags ) . ']'; } return $label_stringbuffer; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/TreeIO/pag.pm������������������������������������������������������������������000444��000766��000024�� 15563�13155576320� 16512� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::TreeIO::pag # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason-at-bioperl-dot-org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::TreeIO::pag - Bio::TreeIO driver for Pagel format =head1 SYNOPSIS use Bio::TreeIO; my $in = Bio::TreeIO->new(-format => 'nexus', -file => 't/data/adh.mb_tree.nexus'); my $out = Bio::TreeIO->new(-format => 'pag'); while( my $tree = $in->next_tree ) { $out->write_tree($tree); } =head1 DESCRIPTION Convert a Bio::TreeIO to Pagel format. More information here http://www.evolution.reading.ac.uk/index.html =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::TreeIO::pag; use strict; our $TaxonNameLen = 10; use base qw(Bio::TreeIO); =head2 new Title : new Usage : my $obj = Bio::TreeIO::pag->new(); Function: Builds a new Bio::TreeIO::pag object Returns : an instance of Bio::TreeIO::pag Args : -file/-fh for filename or filehandles -name_length for minimum name length (default = 10) =cut sub _initialize { my $self = shift; $self->SUPER::_initialize(@_); my ( $name_length ) = $self->_rearrange( [ qw(NAME_LENGTH) ], @_ ); $self->name_length( defined $name_length ? $name_length : $TaxonNameLen ); } =head2 write_tree Title : write_tree Usage : Function: Write a tree out in Pagel format Some options are only appropriate for bayesianmultistate and the simpler output is only proper for discrete Returns : none Args : -no_outgroups => (number) -print_header => 0/1 (leave 0 for discrete, 1 for bayesianms) -special_node => special node - not sure what they wanted to do here -keep_outgroup => 0/1 (keep the outgroup node in the output) -outgroup_ancestor => Bio::Tree::Node (if we want to exclude or include the outgroup this is what we operate on) -tree_no => a tree number label - only useful for BayesianMultistate =cut sub write_tree { my ($self,$tree,@args) = @_; my ($keep_outgroup, $print_header, $no_outgroups, $special_node, $outgroup_ancestor, $tree_no) = (0,0,1); my $name_len = $self->name_length; if( @args ) { ($no_outgroups, $print_header, $special_node, $outgroup_ancestor, $tree_no, $keep_outgroup) = $self->_rearrange([qw( NO_OUTGROUPS PRINT_HEADER SPECIAL_NODE OUTGROUP_ANCESTOR TREE_NO KEEP_OUTGROUP NAME_LENGTH)],@args); } my $newname_base = 1; my $root = $tree->get_root_node; my $eps = 0.0001; my (%chars,%names); my @nodes = $tree->get_nodes; my $species_ct; my $traitct; for my $node ( @nodes ) { if ((defined $special_node) && ($node eq $special_node)) { my $no_of_tree_nodes = scalar(@nodes); my $node_name = sprintf("N%d",$no_of_tree_nodes+1); $names{$node->internal_id} = $node_name; } elsif ($node->is_Leaf) { $species_ct++; my $node_name = $node->id; if( length($node_name)> $name_len ) { $self->warn( "Found a taxon name longer than $name_len letters, \n", "name will be abbreviated.\n"); $node_name = substr($node_name, 0,$name_len); } else { # $node_name = sprintf("%-".$TaxonNameLen."s",$node_name); } $names{$node->internal_id} = $node_name; my @tags = sort $node->get_all_tags; my @charstates = map { ($node->get_tag_values($_))[0] } @tags; $traitct = scalar @charstates unless defined $traitct; $chars{$node->internal_id} = [@charstates]; } else { $names{$node->internal_id} = sprintf("N%d", $newname_base++); } } # generate PAG representation if( $print_header ) { if ($keep_outgroup) { $self->_print(sprintf("%d %d\n",$species_ct,$traitct)); } else { $self->_print( sprintf("%d %d\n",$species_ct-$no_outgroups,$traitct)); } } my @ancestors = (); if ($keep_outgroup) { push @ancestors, $root; } else { push @ancestors, ( $root, $outgroup_ancestor); } my @rest; foreach my $node (@nodes) { my $i = 0; foreach my $anc (@ancestors) { if ($anc && $node eq $anc) { $i = 1; last } } unless ($i > 0) { # root not given in PAG my $current_name = $names{$node->internal_id}; my $branch_length_to_output; if ($node->branch_length < $eps) { my $msg_nodename = $current_name; $msg_nodename =~ s/\s+$//; warn( "TREE $tree_no, node \"$msg_nodename\": branch too ", "short (", $node->branch_length, "): increasing length to ", "$eps\n"); $branch_length_to_output = $eps; } else { $branch_length_to_output = $node->branch_length; } my @line = ( $current_name, $names{$node->ancestor->internal_id}, $branch_length_to_output); if ($node->is_Leaf) { push @line, @{$chars{$node->internal_id}}; $self->_print(join(',', @line),"\n"); } else { push @rest, \@line; } } } for ( @rest ) { $self->_print(join(',', @$_),"\n"); } } =head2 next_tree Title : next_tree Usage : Function: Example : Returns : Args : =cut sub next_tree{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 name_length Title : name_length Usage : $self->name_length(20); Function: set minimum taxon name length Returns : integer (length of name) Args : integer =cut sub name_length { my ($self, $val) = @_; return $self->{'name_len'} = $val if $val; return $self->{'name_len'}; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/TreeIO/phyloxml.pm�������������������������������������������������������������000444��000766��000024�� 123511�13155576320� 17630� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# $Id: phyloxml.pm 11507 2007-06-23 01:37:45Z jason $ # # BioPerl module for Bio::TreeIO::phyloxml # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Mira Han <mirhan@indiana.edu> # # Copyright Mira Han # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::TreeIO::phyloxml - TreeIO implementation for parsing PhyloXML format. =head1 SYNOPSIS # do not use this module directly use Bio::TreeIO; my $treeio = Bio::TreeIO->new(-format => 'phyloxml', -file => 'tree.dnd'); my $tree = $treeio->next_tree; =head1 DESCRIPTION This module handles parsing and writing of phyloXML format. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted viax the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Mira Han Email mirhan@indiana.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::TreeIO::phyloxml; use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Tree::Tree; use Bio::Tree::AnnotatableNode; use Bio::Annotation::SimpleValue; use Bio::Annotation::Relation; use XML::LibXML; use XML::LibXML::Reader; use base qw(Bio::TreeIO); sub _initialize { my($self, %args) = @_; $args{-treetype} ||= 'Bio::Tree::Tree'; $args{-nodetype} ||= 'Bio::Tree::AnnotatableNode'; $self->SUPER::_initialize(%args); # phyloxml TreeIO does not use SAX, # therefore no need to attach EventHandler # instead we will define a reader that is a pull-parser of libXML if ($self->mode eq 'r') { if ($self->_fh) { $self->{'_reader'} = XML::LibXML::Reader->new( IO => $self->_fh, no_blanks => 1 ); } if (!$self->{'_reader'}) { $self->throw("XML::LibXML::Reader not initialized"); } } elsif ($self->mode eq 'w') { # print default lines $self->_print('<?xml version="1.0" encoding="UTF-8"?>',"\n"); $self->_print('<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.phyloxml.org" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd">'); } $self->treetype($args{-treetype}); $self->nodetype($args{-nodetype}); $self->{'_lastitem'} = {}; # holds open items and the attribute hash $self->_init_func(); } sub _init_func { my ($self) = @_; my %start_elements = ( 'phylogeny' => \&element_phylogeny, 'clade' => \&element_clade, 'sequence_relation' => \&element_relation, 'clade_relation' => \&element_relation, ); $self->{'_start_elements'} = \%start_elements; my %end_elements = ( 'phylogeny' => \&end_element_phylogeny, 'clade' => \&end_element_clade, 'sequence_relation' => \&end_element_relation, 'clade_relation' => \&end_element_relation, ); $self->{'_end_elements'} = \%end_elements; } sub DESTROY { my $self = shift; if ($self->mode eq 'w') { $self->_print('</phyloxml>'); $self->flush if $self->_flush_on_write && defined $self->_fh; } $self->SUPER::DESTROY; } =head2 next_tree Title : next_tree Usage : my $tree = $treeio->next_tree Function: Gets the next tree in the stream Returns : Bio::Tree::TreeI Args : none =cut sub next_tree { my ($self) = @_; my $reader = $self->{'_reader'}; my $tree; while ($reader->read) { if ($reader->nodeType == XML_READER_TYPE_END_ELEMENT) { if ($reader->name eq 'phylogeny') { $tree = $self->end_element_phylogeny(); last; } } $self->processXMLNode; } return $tree; } =head2 add_attribute Title : add_phyloXML_annotation Usage : my $node = $treeio->add_phyloXML_annotation(-obj=>$node, -attr=>"id_source = \"A\"") Function: add attributes to an object Returns : the node that we added annotations to Args : -obj => object that will have the Annotation. (Bio::Tree::AnnotatableNode) -attr => string in the form "A = B", where A is the attribute name and B is the attribute value =cut sub add_attribute { my ($self, @args) = @_; my ($obj, $attr) = $self->_rearrange([qw(OBJ ATTR)], @args); if ($attr) { $attr = '<dummy '.$attr.'/>'; } my $oldreader = $self->{'_reader'}; # save reader $self->{'_reader'} = XML::LibXML::Reader->new( string => $attr, no_blanks => 1 ); my $reader = $self->{'_reader'}; $self->{'_currentannotation'} = []; # holds annotationcollection $self->{'_currenttext'} = ''; #$self->{'_id_link'} = {}; # pretend we saw a <clade> element $self->{'_lastitem'}->{'dummy'}++; push @{$self->{'_lastitem'}->{'current'}}, { 'dummy'=>{}}; # current holds current element and empty hash for its attributes # push object to annotate push @{$self->{'_currentitems'}}, $obj; # read attributes of element while ($reader->read) { #$self->processXMLNode; $self->processAttribute($self->current_attr); } # if there is id_source add sequence to _id_link if (exists $self->current_attr->{'id_source'}) { my $idsrc = $self->current_attr->{'id_source'}; $self->{'_id_link'}->{$idsrc} = $obj; } # check idref my $idref = ''; if (exists $self->current_attr->{'id_ref'}) { $idref = $self->current_attr->{'id_ref'}; } my $srcbyidref = ''; $srcbyidref = $self->{'_id_link'}->{$idref}; # exception when id_ref is defined but id_src is not, or vice versa. if ($idref xor $srcbyidref) { $self->throw("id_ref and id_src incompatible: $idref, $srcbyidref"); } # if attribute exists then add Annotation::Collection with tag '_attr' my $newac = $obj->annotation; if ( scalar keys %{$self->current_attr} ) { my $newattr = Bio::Annotation::Collection->new(); foreach my $tag (keys %{$self->current_attr}) { my $sv = Bio::Annotation::SimpleValue->new( -value => $self->current_attr->{$tag} ); $newattr->add_Annotation($tag, $sv); } $newac->add_Annotation('_attr', $newattr); } # pop from temporary list pop @{$self->{'_currentitems'}}; $self->{'_lastitem'}->{ $reader->name }-- if $reader->name; pop @{$self->{'_lastitem'}->{'current'}}; $self->{'_reader'} = $oldreader; # restore reader return $obj; } =head2 add_phyloXML_annotation Title : add_phyloXML_annotation Usage : my $node = $treeio->add_phyloXML_annotation(-obj=>$node, -xml=>$xmlstring) my $tree = $treeio->add_phyloXML_annotation('-obj'=>$tree, '-xml'=>'<sequence_relation id_ref_0="A" id_ref_1="B" type="orthology"/>') Function: add annotations to a node in the phyloXML format string Returns : the node that we added annotations to Args : -obj => object that will have the Annotation. (Bio::Tree::AnnotatableNode) -xml => string in phyloXML format that describes the annotation for the node =cut sub add_phyloXML_annotation { my ($self, @args) = @_; my ($obj, $xml_string) = $self->_rearrange([qw(OBJ XML)], @args); $xml_string = '<phyloxml>'.$xml_string.'</phyloxml>'; $self->debug( $xml_string ); my $oldreader = $self->{'_reader'}; # save reader $self->{'_reader'} = XML::LibXML::Reader->new( string => $xml_string, no_blanks => 1 ); my $reader = $self->{'_reader'}; #$self->{'_currentannotation'} = []; # holds annotationcollection #$self->{'_currenttext'} = ''; #$self->{'_id_link'} = {}; # pretend we saw a <clade> element $self->{'_lastitem'}->{'clade'}++; push @{$self->{'_lastitem'}->{'current'}}, { 'clade'=>{}}; # current holds current element and empty hash for its attributes # our object to annotate (nodeI) # push into temporary list push @{$self->{'_currentitems'}}, $obj; $reader->read; #read away the first element 'phyloxml' while ($reader->read) { $self->processXMLNode; } # pop from temporary list pop @{$self->{'_currentitems'}}; $self->{'_lastitem'}->{ $reader->name }-- if $reader->name; pop @{$self->{'_lastitem'}->{'current'}}; $self->{'_reader'} = $oldreader; # restore reader return $obj; } =head2 write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Write a tree out to data stream in phyloxml format Returns : none Args : Bio::Tree::TreeI object =cut sub write_tree { my ($self, @trees) = @_; foreach my $tree (@trees) { my $root = $tree->get_root_node; $self->_print("<phylogeny"); my @tags = $tree->get_all_tags(); my $attr_str = ''; foreach my $tag (@tags) { my @values = $tree->get_tag_values($tag); foreach (@values) { $attr_str .= " ".$tag."=\"".$_."\""; } } # check if rooted my ($b_rooted) = $tree->get_tag_values('rooted'); if ($b_rooted) { $attr_str .= " rooted=\"true\""; } else { if($tree->is_binary($tree->get_root_node)) { $attr_str .= " rooted=\"true\""; } else { $attr_str .= " rooted=\"false\""; } } $self->_print($attr_str); $self->_print(">"); if ($root->isa('Bio::Tree::AnnotatableNode')) { $self->_print($self->_write_tree_Helper_annotatableNode($root)); } else { $self->_print($self->_write_tree_Helper_generic($root)); } # print clade relations while (my $str = pop (@{$self->{'_tree_attr'}->{'clade_relation'}})) { $self->_print($str); } # print sequence relations while (my $str = pop (@{$self->{'_tree_attr'}->{'sequence_relation'}})) { $self->_print($str); } $self->_print("</phylogeny>"); } $self->flush if $self->_flush_on_write && defined $self->_fh; return; } =head2 _write_tree_Helper_annotatableNode Title : _write_tree_Helper_annotatableNode Usage : internal method used by write_tree, not to be used directly Function: recursive helper function of write_tree for the annotatableNodes. translates annotations into xml elements. Returns : string describing the node Args : Bio::Node::AnnotatableNode object, string =cut sub _write_tree_Helper_annotatableNode { my ($self, $node, $str) = @_; # this self is a Bio::Tree::phyloxml my $ac = $node->annotation; # if clade_relation exists my @relations = $ac->get_Annotations('clade_relation'); foreach (@relations) { my $clade_rel = $self->_relation_to_string($node, $_, ''); # set as tree attr push (@{$self->{'_tree_attr'}->{'clade_relation'}}, $clade_rel); } # start <clade> $str .= '<clade'; my ($attr) = $ac->get_Annotations('_attr'); # check id_source if ($attr) { my ($id_source) = $attr->get_Annotations('id_source'); if ($id_source) { $str .= " id_source=\"".$id_source->value."\""; } } $str .= ">"; # print all descendent nodes foreach my $child ( $node->each_Descendent() ) { $str = $self->_write_tree_Helper_annotatableNode($child, $str); } # print all annotations $str = print_annotation( $node, $str, $ac ); # print all sequences if ($node->has_sequence) { foreach my $seq (@{$node->sequence}) { # if sequence_relation exists my @relations = $seq->annotation->get_Annotations('sequence_relation'); foreach (@relations) { my $sequence_rel = $self->_relation_to_string($seq, $_, ''); # set as tree attr push (@{$self->{'_tree_attr'}->{'sequence_relation'}}, $sequence_rel); } $str = print_seq_annotation( $node, $str, $seq ); } } $str .= "</clade>"; return $str; } =head2 _write_tree_Helper_generic Title : _write_tree_Helper_generic Usage : internal method used by write_tree, not to be used directly Function: recursive helper function of write_tree for generic NodesI. all tags are translated into property elements. Returns : string describing the node Args : Bio::Node::NodeI object, string =cut sub _write_tree_Helper_generic { my ($self, $node, $str) = @_; # this self is a Bio::Tree::phyloxml # start <clade> $str .= '<clade>'; # print all descendent nodes foreach my $child ( $node->each_Descendent() ) { $str = $self->_write_tree_Helper_generic($child, $str); } # print all tags my @tags = $node->get_all_tags(); foreach my $tag (@tags) { my @values = $node->get_tag_values($tag); foreach my $val (@values) { $str .= "<property datatype=\"xsd:string\" ref=\"tag:$tag\" applies_to=\"clade\">"; $str .=$val; $str .= "</property>"; } } # print NodeI features if ($node->id) { $str .= "<name>"; $str .= $node->id; $str .= "</name>"; } if ($node->branch_length) { $str .= "<branch_length>"; $str .= $node->branch_length; $str .= "</branch_length>"; } if ($node->bootstrap) { $str .= "<confidence type = \"bootstrap\">"; $str .= $node->bootstrap; $str .= "</confidence>"; } $str .= "</clade>"; return $str; } =head2 _relation_to_string Title : _relation_to_string Usage : internal method used by write_tree, not to be used directly Function: internal function used by write_tree to translate Annotation::Relation objects into xml elements. Returns : string describing the node Args : Bio::Node::AnnotatableNode (or Bio::SeqI) object that contains the Annotation::Relation, the Annotation::Relation object, the string =cut # It may be more appropriate to make Annotation::Relation have # a to_string callback function, # and have this subroutine set as the callback when we are in # phyloXML context. # I've put it here for now, since write_tree is the only place it is used. sub _relation_to_string { my ($self, $obj, $rel, $str) = @_; my @attr = $obj->annotation->get_Annotations('_attr'); # check id_source if (@attr) { my @id_source = $attr[0]->get_Annotations('id_source'); } my ($id_ref_0) = $obj->annotation->get_nested_Annotations( '-keys' => ['id_source'], '-recursive' => 1); my ($id_ref_1) = $rel->to->annotation->get_nested_Annotations( '-keys' => ['id_source'], '-recursive' => 1); my $confidence = $rel->confidence(); my $confidence_type = $rel->confidence_type(); $str .= "<"; $str .= $rel->tagname; $str .= " id_ref_0=\"".$id_ref_0->value."\""; $str .= " id_ref_1=\"".$id_ref_1->value."\""; $str .= " type=\"".$rel->type."\""; if ($confidence) { $str .= " ><confidence"; if ($confidence_type) { $str .= " type=\"".$confidence_type."\""; } $str .= ">"; $str .= $confidence; $str .= "</confidence>"; $str .= "</"; $str .= $rel->tagname; $str .= ">"; } else { $str .= "/>"; } return $str; } =head2 read_annotation Title : read_annotation Usage : $treeio->read_annotation(-obj=>$node, -path=>$path, -attr=>1); Function: read text value (or attribute value) of the annotations corresponding to the element path Returns : list of text values of the annotations matching the path Args : -obj => object that contains the Annotation. (Bio::Tree::AnnotatableNode or Bio::SeqI) -path => path of the nested elements -attr => Boolean value to indicate whether to get the attribute of the element or the text value. (default is 0, meaning text value is returned) =cut # It may be more appropriate to make a separate Annotation::phyloXML object # and have this subroutine within that object so it can handle the # reading and writing of the values and attributes. # but since tagTree is a temporary stub and I didn't want to make # a redundant object I've put it here for now. sub read_annotation { my ($self, @args) = @_; my ($obj, $path, $attr) = $self->_rearrange([qw(OBJ PATH ATTR)], @args); my $ac = $obj->annotation; if ($attr) { my @elements = split ('/', $path); my $final = pop @elements; push (@elements, '_attr'); push (@elements, $final); $path = join ('/', @elements); return $self->_read_annotation_attr_Helper( [$ac], $path); } else { return $self->_read_annotation_text_Helper( [$ac], $path); } } sub _read_annotation_text_Helper { my ($self, $acs, $path) = @_; my @elements = split ('/', $path); my $key = shift @elements; my @nextacs = (); foreach my $ac (@$acs) { foreach my $ann ($ac->get_Annotations($key)) { if ($ann->isa('Bio::AnnotationCollectionI')) {push (@nextacs, $ann)} } } if (@elements == 0) { my @values = (); my @texts = map {$_->get_Annotations('_text')} @nextacs; foreach (@texts) { $_ && push (@values, $_->value); } return @values; } else { $path = join ('/', @elements); return $self->_read_annotation_text_Helper( \@nextacs, $path); } } sub _read_annotation_attr_Helper { my ($self, $acs, $path) = @_; my @elements = split ('/', $path); my $key = shift @elements; my @nextacs = (); foreach my $ac (@$acs) { foreach my $ann ($ac->get_Annotations($key)) { if ($ann->isa('Bio::AnnotationCollectionI')) {push (@nextacs, $ann)} } } if (@elements == 1) { my $attrname = $elements[0]; my @sv = map {$_->get_Annotations($attrname)} @nextacs; return map {$_->value} @sv; } else { $path = join ('/', @elements); return $self->_read_annotation_attr_Helper( \@nextacs, $path); } } =head1 Methods for parsing the XML document =cut =head2 processXMLNode Title : processXMLNode Usage : $treeio->processXMLNode Function: read the XML node and process according to the node type Returns : none Args : none =cut sub processXMLNode { my ($self) = @_; my $reader = $self->{'_reader'}; my $nodetype = $reader->nodeType; if ( $nodetype == XML_READER_TYPE_ELEMENT) { $self->{'_lastitem'}->{$reader->name}++; push @{$self->{'_lastitem'}->{'current'}}, { $reader->name=>{}}; # current holds current element and empty hash for its attributes if (exists $self->{'_start_elements'}->{$reader->name}) { my $method = $self->{'_start_elements'}->{$reader->name}; $self->$method(); } else { $self->element_default(); } if ($reader->isEmptyElement) { # element is complete # set nodetype so it can jump and # do procedures for XML_READER_TYPE_END_ELEMENT $nodetype = XML_READER_TYPE_END_ELEMENT; } } if ($nodetype == XML_READER_TYPE_TEXT) { $self->{'_currenttext'} = $reader->value; } if ($nodetype == XML_READER_TYPE_END_ELEMENT) { if (exists $self->{'_end_elements'}->{$reader->name}) { my $method = $self->{'_end_elements'}->{$reader->name}; $self->$method(); } else { $self->end_element_default(); } $self->{'_lastitem'}->{ $reader->name }--; pop @{$self->{'_lastitem'}->{'current'}}; $self->{'_currenttext'} = ''; } } =head2 processAttribute Title : processAttribute Usage : $treeio->processAttribute(\%hash_for_attribute); Function: reads the attributes of the current element into a hash Returns : none Args : hash reference where the attributes will be stored. =cut sub processAttribute { my ($self, $data) = @_; my $reader = $self->{'_reader'}; # several ways of reading attributes: # read all attributes: if ($reader-> moveToFirstAttribute) { do { $data->{$reader->name()} = $reader->value; } while ($reader-> moveToNextAttribute); $reader-> moveToElement; } } =head2 element_phylogeny Title : element_phylogeny Usage : $treeio->element_phylogeny Function: initialize the parsing of a tree Returns : none Args : none =cut sub element_phylogeny { my ($self) = @_; $self->{'_currentitems'} = []; # holds nodes while parsing current level $self->{'_currentnodes'} = []; # holds nodes while constructing tree $self->{'_currentannotation'} = []; # holds annotationcollection $self->{'_currenttext'} = ''; $self->{'_levelcnt'} = []; $self->{'_id_link'} = {}; $self->{'_tree_attr'} = $self->current_attr; $self->processAttribute($self->current_attr); return; } =head2 end_element_phylogeny Title : end_element_phylogeny Usage : $treeio->end_element_phylogeny Function: ends the parsing of a tree building a Tree::TreeI object. Returns : Tree::TreeI Args : none =cut sub end_element_phylogeny { my ($self) = @_; my $root; # if there is more than one node in _currentnodes # aggregate the nodes into trees basically ad-hoc. if ( @{$self->{'_currentnodes'}} > 1) { $root = $self->nodetype->new( -id => '', tostring => \&node_to_string, ); while ( @{$self->{'_currentnodes'}} ) { my ($node) = ( shift @{$self->{'_currentnodes'}}); $root->add_Descendent($node); } } # if there is only one node in _currentnodes # that node is root. elsif ( @{$self->{'_currentnodes'}} == 1) { $root = shift @{$self->{'_currentnodes'}}; } my $tree = $self->treetype->new( -root => $root, -id => $self->current_attr->{'name'}, %{$self->current_attr} ); foreach my $tag ( keys %{$self->current_attr} ) { $tree->add_tag_value( $tag, $self->current_attr->{$tag} ); } return $tree; } =head2 element_clade Title : element_clade Usage : $treeio->element_clade Function: initialize the parsing of a node creates a new AnnotatableNode with annotations Returns : none Args : none =cut sub element_clade { my ($self) = @_; my $reader = $self->{'_reader'}; my %clade_attr = (); # doesn't use current attribute in order to save memory $self->processAttribute(\%clade_attr); # create a node (Annotatable Node) my $tnode = $self->nodetype->new( -id => '', tostring => \&node_to_string, %clade_attr, ); # add all attributes as annotation collection with tag '_attr' my $ac = $tnode->annotation; my $newattr = Bio::Annotation::Collection->new(); foreach my $tag (keys %clade_attr) { my $sv = Bio::Annotation::SimpleValue->new( -value => $clade_attr{$tag} ); $newattr->add_Annotation($tag, $sv); } $ac->add_Annotation('_attr', $newattr); # if there is id_source add clade to _id_link if (exists $clade_attr{'id_source'}) { $self->{'_id_link'}->{$clade_attr{'id_source'}} = $tnode; } # push into temporary list push @{$self->{'_currentitems'}}, $tnode; } =head2 end_element_clade Title : end_element_clade Usage : $treeio->end_element_clade Function: ends the parsing of a node Returns : none Args : none =cut sub end_element_clade { my ($self) = @_; my $reader = $self->{'_reader'}; my $curcount = scalar @{$self->{'_currentnodes'}}; my $level = $reader->depth() - 2; my $childcnt = $self->{'_levelcnt'}->[$level+1] || 0; # pop from temporary list my $tnode = pop @{$self->{'_currentitems'}}; if ( $childcnt > 0) { if( $childcnt > $curcount) { $self->throw("something wrong with event construction treelevel ". "$level is recorded as having $childcnt nodes ". "but current nodes at this level is $curcount\n"); } my @childnodes = splice( @{$self->{'_currentnodes'}}, - $childcnt); for ( @childnodes ) { $tnode->add_Descendent($_); } $self->{'_levelcnt'}->[$level+1] = 0; } push @{$self->{'_currentnodes'}}, $tnode; $self->{'_levelcnt'}->[$level]++; } =head2 element_relation Title : element_relation Usage : $treeio->element_relation Function: starts the parsing of clade relation & sequence relation Returns : none Args : none =cut sub element_relation { my ($self) = @_; $self->processAttribute($self->current_attr); my $relationtype = $self->current_attr->{'type'}; my $id_ref_0 = $self->current_attr->{'id_ref_0'}; my $id_ref_1 = $self->current_attr->{'id_ref_1'}; my @srcbyidref = (); $srcbyidref[0] = $self->{'_id_link'}->{$id_ref_0}; $srcbyidref[1] = $self->{'_id_link'}->{$id_ref_1}; # exception when id_ref is defined but id_src is not, or vice versa. if ( ($id_ref_0 xor $srcbyidref[0])||($id_ref_1 xor $srcbyidref[1]) ) { $self->throw("id_ref and id_src incompatible: $id_ref_0, $id_ref_1, ", $srcbyidref[0], $srcbyidref[1]); } # set id_ref_0 my $ac0 = $srcbyidref[0]->annotation; my $newann = Bio::Annotation::Relation->new( '-type' => $relationtype, '-to' => $srcbyidref[1], '-tagname' => $self->current_element ); $ac0->add_Annotation($self->current_element, $newann); # set id_ref_1 my $ac1 = $srcbyidref[1]->annotation; $newann = Bio::Annotation::Relation->new( '-type' => $relationtype, '-to' => $srcbyidref[0], '-tagname' => $self->current_element ); $ac1->add_Annotation($self->current_element, $newann); push (@{$self->{'_currentannotation'}}, $newann); } =head2 end_element_relation Title : end_element_relation Usage : $treeio->end_element_relation Function: ends the parsing of clade relation & sequence relation Returns : none Args : none =cut sub end_element_relation { my ($self) = @_; my $ac = pop (@{$self->{'_currentannotation'}}); } =head2 element_default Title : element_default Usage : $treeio->element_default Function: starts the parsing of all other elements Returns : none Args : none =cut sub element_default { my ($self) = @_; my $reader = $self->{'_reader'}; my $current = $self->current_element(); my $prev = $self->prev_element(); # read attributes of element $self->processAttribute($self->current_attr); # check idref my $idref = ''; if (exists $self->current_attr->{'id_ref'}) { $idref = $self->current_attr->{'id_ref'}; } my $srcbyidref = ''; $srcbyidref = $self->{'_id_link'}->{$idref}; # exception when id_ref is defined but id_src is not, or vice versa. if ($idref xor $srcbyidref) { $self->throw("id_ref and id_src incompatible: $idref, $srcbyidref"); } # we are annotating a Node # set _currentannotation if ( ($srcbyidref && $srcbyidref->isa($self->nodetype)) || ((!$srcbyidref) && $prev eq 'clade') ) { # find node to annotate my $tnode; if ($srcbyidref) { $tnode = $srcbyidref; } else { $tnode = $self->{'_currentitems'}->[-1]; } my $ac = $tnode->annotation(); # add the new anncollection with the current element as key my $newann = Bio::Annotation::Collection->new(); $ac->add_Annotation($current, $newann); # push to current annotation push (@{$self->{'_currentannotation'}}, $newann); } # we are within sequence_relation or clade_relation elsif ($prev eq 'clade_relation' || $prev eq 'sequence_relation') { # do nothing? } # we are already within an annotation else { my $ac = $self->{'_currentannotation'}->[-1]; if ($ac) { # add the new anncollection with the current element as key my $newann = Bio::Annotation::Collection->new(); $ac->add_Annotation($current, $newann); push (@{$self->{'_currentannotation'}}, $newann); } } } =head2 end_element_default Title : end_element_default Usage : $treeio->end_element_default Function: ends the parsing of all other elements Returns : none Args : none =cut sub end_element_default { my ($self) = @_; my $reader = $self->{'_reader'}; my $current = $self->current_element(); my $prev = $self->prev_element(); # check idsrc my $idsrc = $self->current_attr->{'id_source'}; # check idref my $idref = ''; if (exists $self->current_attr->{'id_ref'}) { $idref = $self->current_attr->{'id_ref'}; delete $self->current_attr->{'id_ref'}; } my $srcbyidref = ''; $srcbyidref = $self->{'_id_link'}->{$idref}; # exception when id_ref is defined but id_src is not, or vice versa. if ($idref xor $srcbyidref) { $self->throw("id_ref and id_src incompatible: $idref, $srcbyidref"); } # we are annotating a Tree if ((!$srcbyidref) && $prev eq 'phylogeny') { # annotate Tree via tree attribute $self->prev_attr->{$current} = $self->{'_currenttext'}; } # we are within sequence_relation or clade_relation elsif ($prev eq 'clade_relation' || $prev eq 'sequence_relation') { my $ann_relation = $self->{'_currentannotation'}->[-1]; # we are here only with <confidence> if ($current eq 'confidence') { if (exists $self->current_attr->{'type'}) { $ann_relation->confidence_type($self->current_attr->{'type'}); } $ann_relation->confidence($self->{'_currenttext'}); } else { $self->throw($current, " is not allowed within <*_relation>"); } } # we are annotating a Node elsif (( $srcbyidref && $srcbyidref->isa($self->nodetype)) || ((!$srcbyidref) && $prev eq 'clade')) { # pop from current annotation my $ac = pop (@{$self->{'_currentannotation'}}); $self->annotateNode( $current, $ac); # additional setups for compatibility with NodeI my $tnode; if ($srcbyidref) { $tnode = $srcbyidref; } else { $tnode = $self->{'_currentitems'}->[-1]; } if ($current eq 'name') { $tnode->id($self->{'_currenttext'}); } elsif ($current eq 'branch_length') { $tnode->branch_length($self->{'_currenttext'}); } elsif ($current eq 'confidence') { if ((exists $self->current_attr->{'type'}) && ($self->current_attr->{'type'} eq 'bootstrap')) { $tnode->bootstrap($self->{'_currenttext'}); # this needs to change (adds 'B' annotation) } } elsif ($current eq 'sequence') { # if annotation is <sequence> # transform the Bio::Annotation object into a Bio::Seq object my $str = ''; # retrieve the sequence if (my ($molseq) = $ac->get_Annotations('mol_seq')) { my ($strac) = $molseq->get_Annotations('_text'); $str = $strac->value(); } # create Seq object with sequence my $newseq = Bio::Seq->new( -seq => $str, -annotation=>$ac, -nowarnonempty=>1); $tnode->sequence($newseq); $ac->remove_Annotations('mol_seq'); $tnode->annotation->remove_Annotations($current); # if there is id_source add sequence to _id_link if ($idsrc) { $self->{'_id_link'}->{$idsrc} = $newseq; } } elsif ($idsrc && $current eq 'taxonomy') { # if there is id_source add sequence to _id_link $self->{'_id_link'}->{$idsrc} = $ac; } } # we are within a default Annotation else { my $ac = pop (@{$self->{'_currentannotation'}}); if ($ac) { $self->annotateNode( $current, $ac); } } } =head2 annotateNode Title : annotateNode Usage : $treeio->annotateNode($element, $ac) Function: adds text value and attributes to the AnnotationCollection that has element name as key. If there are nested elements, optional AnnotationCollections are added recursively, with the nested element name as key. The structure of each AnnotationCollection is 'element' => AnnotationCollection { '_text' => SimpleValue (text value) '_attr' => AnnotationCollection { attribute1 => SimpleValue (attribute value 1) attribute2 => SimpleValue (attribute value 2) ... } ['nested element' => AnnotationCollection ] } Returns : none Args : none =cut sub annotateNode { my ($self, $element, $newac) = @_; # if attribute exists then add Annotation::Collection with tag '_attr' if ( scalar keys %{$self->current_attr} ) { my $newattr = Bio::Annotation::Collection->new(); foreach my $tag (keys %{$self->current_attr}) { my $sv = Bio::Annotation::SimpleValue->new( -value => $self->current_attr->{$tag} ); $newattr->add_Annotation($tag, $sv); } $newac->add_Annotation('_attr', $newattr); } # if text exists add text as SimpleValue with tag '_text' if ( $self->{'_currenttext'} ) { my $newvalue = Bio::Annotation::SimpleValue->new( -value => $self->{'_currenttext'} ); $newac->add_Annotation('_text', $newvalue); } } =head1 Methods for exploring the document =cut =head2 current_attr Title : current_attr Usage : $attr_hash = $treeio->current_attr; Function: returns the attribute hash for current item Returns : reference of the attribute hash Args : none =cut sub current_attr { my ($self) = @_; return 0 if ! defined $self->{'_lastitem'} || ! defined $self->{'_lastitem'}->{'current'}->[-1]; my @keys = keys %{$self->{'_lastitem'}->{'current'}->[-1]}; (@keys == 1) || die "there should be only one key for each hash"; return $self->{'_lastitem'}->{'current'}->[-1]->{$keys[0]}; } =head2 prev_attr Title : prev_attr Usage : $hash_ref = $treeio->prev_attr Function: returns the attribute hash for previous item Returns : reference of the attribute hash Args : none =cut sub prev_attr { my ($self) = @_; return 0 if ! defined $self->{'_lastitem'} || ! defined $self->{'_lastitem'}->{'current'}->[-2]; my @keys = keys %{$self->{'_lastitem'}->{'current'}->[-2]}; (@keys == 1) || die "there should be only one key for each hash"; return $self->{'_lastitem'}->{'current'}->[-2]->{$keys[0]}; } =head2 current_element Title : current_element Usage : $element = $treeio->current_element Function: returns the name of the current element Returns : string (element name) Args : none =cut sub current_element { my ($self) = @_; return 0 if ! defined $self->{'_lastitem'} || ! defined $self->{'_lastitem'}->{'current'}->[-1]; my @keys = keys %{$self->{'_lastitem'}->{'current'}->[-1]}; (@keys == 1) || die "there should be only one key for each hash"; return $keys[0]; } =head2 prev_element Title : prev_element Usage : $element = $treeio->current_element Function: returns the name of the previous element Returns : string (element name) Args : none =cut sub prev_element { my ($self) = @_; return 0 if ! defined $self->{'_lastitem'} || ! defined $self->{'_lastitem'}->{'current'}->[-2]; my @keys = keys %{$self->{'_lastitem'}->{'current'}->[-2]}; (@keys == 1) || die "there should be only one key for each hash"; return $keys[0]; } =head2 treetype Title : treetype Usage : $obj->treetype($newval) Function: returns the tree type (default is Bio::Tree::Tree) Returns : value of treetype Args : newvalue (optional) =cut sub treetype{ my ($self,$value) = @_; if( defined $value) { $self->{'treetype'} = $value; } return $self->{'treetype'}; } =head2 nodetype Title : nodetype Usage : $obj->nodetype($newval) Function: returns the node type (default is Bio::Node::AnnotatableNode) Returns : value of nodetype Args : newvalue (optional) =cut sub nodetype{ my ($self,$value) = @_; if( defined $value) { $self->{'nodetype'} = $value; } return $self->{'nodetype'}; } =head1 Methods for implementing to_string callback for AnnotatableNode =cut =head2 node_to_string Title : node_to_string Usage : $annotatablenode->to_string_callback(\&node_to_string) Function: set as callback in AnnotatableNode, prints the node information in string Returns : string of node information Args : none =cut # this function is similar to _write_tree_Helper_annotatableNode, # but it is not recursive sub node_to_string { my ($self) = @_; # this self is a Bio::Tree::AnnotatableNode # not a Bio::TreeIO::phyloxml my $str = ''; my $ac = $self->annotation; # start <clade> $str .= '<clade'; my @attr = $ac->get_Annotations('_attr'); # check id_source if (@attr) { my @id_source = $attr[0]->get_Annotations('id_source'); if (@id_source) { $str .= " id_source=\"".$id_source[0]->value."\""; } } $str .= '>'; # print all annotations $str = print_annotation( $self, $str, $ac ); # print all sequences if ($self->has_sequence) { foreach my $seq (@{$self->sequence}) { $str = print_seq_annotation( $self, $str, $seq ); } } $str .= '</clade>'; return $str; } =head2 print_annotation Title : print_annotation Usage : $str = $annotatablenode->print_annotation($str, $annotationcollection) Function: prints the annotationCollection in a phyloXML format. Returns : string of annotation information Args : string to which the Annotation should be concatenated to, annotationCollection that holds the Annotations =cut # Again, it may be more appropriate to make a separate Annotation::phyloXML object # and have this subroutine within that object so it can handle the # reading and writing of the values and attributes. # especially since this function is used both by # Bio::TreeIO::phyloxml (through write_tree) and # Bio::Node::AnnotatableNode (through node_to_string). # but since tagTree is a temporary stub and I didn't want to make # a redundant object I've put it here for now. sub print_annotation { my ($self, $str, $ac) = @_; my @all_anns = $ac->get_Annotations(); foreach my $ann (@all_anns) { my $key = $ann->tagname; if ($key eq '_attr') { next; } # attributes are already printed in the previous level if ($ann->isa('Bio::Annotation::SimpleValue')) { if ($key eq '_text') { $str .= $ann->value; } else { $str .= "<$key>"; $str .= $ann->value; $str .= "</$key>"; } } elsif ($ann->isa('Bio::Annotation::Collection')) { my @attrs = $ann->get_Annotations('_attr'); if (@attrs) { # if there is a attribute collection $str .= "<$key"; $str = print_attr($self, $str, $attrs[0]); $str .= ">"; } else { $str .= "<$key>"; } $str = print_annotation($self, $str, $ann); $str .= "</$key>"; } } return $str; } =head2 print_attr Title : print_attr Usage : $str = $annotatablenode->print_attr($str, $annotationcollection) Function: prints the annotationCollection in a phyloXML format. Returns : string of attributes Args : string to which the Annotation should be concatenated to, AnnotationCollection that holds the attributes =cut # Again, it may be more appropriate to make a separate Annotation::phyloXML object # and have this subroutine within that object so it can handle the # reading and writing of the values and attributes. # especially since this function is used both by # Bio::TreeIO::phyloxml and Bio::Node::AnnotatableNode # (through print_annotation). # but since tagTree is a temporary stub and I didn't want to make # a redundant object I've put it here for now. sub print_attr { my ($self, $str, $ac) = @_; my @all_attrs = $ac->get_Annotations(); foreach my $attr (@all_attrs) { if (!$attr->isa('Bio::Annotation::SimpleValue')) { $self->throw("attribute should be a SimpleValue"); } $str .= ' '; $str .= $attr->tagname; $str .= '='; $str .= '"'.$attr->value.'"'; } return $str; } =head2 print_sequence_annotation Title : print_sequence_annotation Usage : $str = $node->print_seq_annotation( $str, $seq ); Function: prints the Bio::Seq object associated with the node in a phyloXML format. Returns : string that describes the sequence Args : string to which the Annotation should be concatenated to, Seq object to print in phyloXML =cut # Again, it may be more appropriate to make a separate Annotation::phyloXML object # and have this subroutine within that object so it can handle the # reading and writing of the values and attributes. # especially since this function is used both by # Bio::TreeIO::phyloxml (through write_tree) and # Bio::Node::AnnotatableNode (through node_to_string). # but since tagTree is a temporary stub and I didn't want to make # a redundant object I've put it here for now. sub print_seq_annotation { my ($self, $str, $seq) = @_; $str .= "<sequence"; my ($attr) = $seq->annotation->get_Annotations('_attr'); # check id_source if ($attr) { my ($id_source) = $attr->get_Annotations('id_source'); if ($id_source) { $str .= " id_source=\"".$id_source->value."\""; } } $str .= ">"; my @all_anns = $seq->annotation->get_Annotations(); foreach my $ann (@all_anns) { my $key = $ann->tagname; if ($key eq '_attr') { next; } # attributes are already printed in the previous level if ($ann->isa('Bio::Annotation::SimpleValue')) { if ($key eq '_text') { $str .= $ann->value; } else { $str .= "<$key>"; $str .= $ann->value; $str .= "</$key>"; } } elsif ($ann->isa('Bio::Annotation::Collection')) { my @attrs = $ann->get_Annotations('_attr'); if (@attrs) { # if there is a attribute collection $str .= "<$key"; $str = print_attr($self, $str, $attrs[0]); $str .= ">"; } else { $str .= "<$key>"; } $str = print_annotation($self, $str, $ann); $str .= "</$key>"; } } # print mol_seq if ($seq->seq()) { $str .= "<mol_seq>"; $str .= $seq->seq(); $str .= "</mol_seq>"; } $str .= "</sequence>"; return $str; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/TreeIO/svggraph.pm�������������������������������������������������������������000444��000766��000024�� 12675�13155576320� 17565� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::TreeIO::svg-graph # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Allen Day <allenday@ucla.edu> # # Copyright Brian O'Connor # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::TreeIO::svggraph - A simple output format that converts a Tree object to an SVG output =head1 SYNOPSIS use Bio::TreeIO; my $in = Bio::TreeIO->new(-file => 'input', -format => 'newick'); my $out = Bio::TreeIO->new(-file => '>output', -format => 'svggraph'); while( my $tree = $in->next_tree ) { my $svg_xml = $out->write_tree($tree); } =head1 DESCRIPTION This outputs a tree as an SVG graphic using the SVG::Graph API =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Brian OConnor Email brian.oconnor-at-excite.com =head1 CONTRIBUTORS Allen Day Guillaume Rousse, Guillaume-dot-Rousse-at-inria-dot-fr =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::TreeIO::svggraph; use strict; # Object preamble - inherits from Bio::Root::Root use SVG::Graph; use SVG::Graph::Data; use SVG::Graph::Data::Tree; use SVG::Graph::Data::Node; use Bio::Tree::TreeI; use Bio::Tree::Node; use Tree::DAG_Node; use base qw(Bio::TreeIO); =head2 new Title : new Usage : my $obj = Bio::TreeIO::svggraph->new(); Function: Builds a new Bio::TreeIO::svggraph object Returns : Bio::TreeIO::svggraph Args :-width => image width (default 1600) -height => image height (default 1000) -margin => margin (default 30) -stroke => stroke color (default 'black') -stroke_width=> stroke width (default 2) -font_size=> font size (default '10px') -nomalize => undef or 'log' (default is undef) =cut sub _initialize { my $self = shift; my ($width,$height,$margin,$stroke, $stroke_width,$font_size, $normalize) = $self->_rearrange([qw (WIDTH HEIGHT MARGIN STROKE STROKE_WIDTH FONT_SIZE NORMALIZE)], @_); $self->{_width} = $width || 1600; $self->{_height} = $height || 1000; $self->{_margin} = defined $margin ? $margin : 30; $self->{_stroke} = $stroke || 'black'; $self->{_stroke_width} = $stroke_width || 2; $self->{_font_size} = $font_size || '10px'; $self->{_normalize} = $normalize || ''; $self->SUPER::_initialize(@_); } =head2 write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Write a tree out to data stream in newick/phylip format Returns : none Args : Bio::Tree::TreeI object =cut sub write_tree{ my ($self,$tree) = @_; my $line = $self->_write_tree_Helper($tree->get_root_node); $self->_print($line. "\n"); $self->flush if $self->_flush_on_write && defined $self->_fh; return; } sub _write_tree_Helper { my ($self,$node) = @_; my $graph = SVG::Graph->new ('width' => $self->{'_width'}, 'height' => $self->{'_height'}, 'margin' => $self->{'_margin'}); my $group0 = $graph->add_frame; my $tree = SVG::Graph::Data::Tree->new; my $root = SVG::Graph::Data::Node->new; $root->name($node->id); $self->_decorateRoot($root, $node->each_Descendent()); $tree->root($root); $group0->add_data($tree); $group0->add_glyph('tree', 'stroke' =>$self->{'_stroke'}, 'stroke-width'=>$self->{'_stroke_width'}, 'font-size' =>$self->{'_font_size'}); return($graph->draw); } =head2 decorateRoot Title : _decorateRoot Usage : internal methods Function: Example : Returns : Args : =cut sub _decorateRoot { my ($self,$previousNode,@children) = @_; for my $child (@children) { my $currNode = SVG::Graph::Data::Node->new; # if no ID is set, the branch label is intentionally set blank (bug in SVG::Graph) my $id = $child->id || ''; $currNode->branch_label($id); my $length = $child->branch_length; if ($self->{_normalize} eq 'log') { $length = log($length + 1); } $currNode->branch_length($length); $previousNode->add_daughter($currNode); $self->_decorateRoot($currNode, $child->each_Descendent()); } } =head2 next_tree Title : next_tree Usage : Function: Sorry not possible with this format Returns : none Args : none =cut sub next_tree{ $_[0]->throw("Sorry the format 'svggraph' can only be used as an output format"); } 1; �������������������������������������������������������������������BioPerl-1.007002/Bio/TreeIO/tabtree.pm��������������������������������������������������������������000444��000766��000024�� 7060�13155576320� 17342� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::TreeIO::tabtree # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::TreeIO::tabtree - A simple output format which displays a tree as an ASCII drawing =head1 SYNOPSIS use Bio::TreeIO; my $in = Bio::TreeIO->new(-file => 'input', -format => 'newick'); my $out = Bio::TreeIO->new(-file => '>output', -format => 'tabtree'); while( my $tree = $in->next_tree ) { $out->write_tree($tree); } =head1 DESCRIPTION This is a made up format just for outputting trees as an ASCII drawing. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::TreeIO::tabtree; use strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::TreeIO); =head2 new Title : new Usage : my $obj = Bio::TreeIO::tabtree->new(); Function: Builds a new Bio::TreeIO::tabtree object Returns : Bio::TreeIO::tabtree Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); } =head2 write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Write a tree out to data stream in newick/phylip format Returns : none Args : Bio::Tree::TreeI object =cut sub write_tree{ my ($self,$tree) = @_; my $line = _write_tree_Helper($tree->get_root_node,""); $self->_print($line. "\n"); $self->flush if $self->_flush_on_write && defined $self->_fh; return; } sub _write_tree_Helper { my ($node,$indent) = @_; return unless defined $node; my @d = $node->each_Descendent(); my $line = ""; my ($i,$lastchild) = (0,scalar @d - 1); for my $n ( @d ) { if( $n->is_Leaf ) { $line .= sprintf("%s| \n%s\\-%s\n", $indent,$indent,$n->id || ''); } else { $line .= sprintf("$indent| %s\n",( $n->id ? sprintf("(%s)",$n->id) : '')); } my $new_indent = $indent . (($i == $lastchild) ? "| " : " "); if( $n != $node ) { # avoid the unlikely case of cycles $line .= _write_tree_Helper($n,$new_indent); } } return $line; } =head2 next_tree Title : next_tree Usage : Function: Sorry not possible with this format Returns : none Args : none =cut sub next_tree{ $_[0]->throw("Sorry the format 'tabtree' can only be used as an output format at this time"); } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Variation����������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16023� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Variation/AAChange.pm����������������������������������������������������������000444��000766��000024�� 33030�13155576320� 20124� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Variation::AAChange # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Variation::AAChange - Sequence change class for polypeptides =head1 SYNOPSIS $aamut = Bio::Variation::AAChange->new ('-start' => $start, '-end' => $end, '-length' => $len, '-proof' => $proof, '-isMutation' => 1, '-mut_number' => $mut_number ); my $a1 = Bio::Variation::Allele->new; $a1->seq($ori) if $ori; $aamut->allele_ori($a1); my $a2 = Bio::Variation::Allele->new; $a2->seq($mut) if $mut; $aachange->add_Allele($a2); $aachange->allele_mut($a2); print "\n"; # add it to a SeqDiff container object $seqdiff->add_Variant($rnachange); # and create links to and from RNA level variant objects $aamut->RNAChange($rnachange); $rnachange->AAChange($rnachange); =head1 DESCRIPTION The instantiable class Bio::Variation::RNAChange describes basic sequence changes at polypeptide level. It uses methods defined in superclass Bio::Variation::VariantI, see L<Bio::Variation::VariantI> for details. If the variation described by a AAChange object has a known Bio::Variation::RNAAChange object, create the link with method AAChange(). See L<Bio::Variation::AAChange> for more information. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Variation::AAChange; use vars qw($MATRIX); use strict; # Object preamble - inheritance use base qw(Bio::Variation::VariantI); BEGIN { my $matrix = << "__MATRIX__"; # Matrix made by matblas from blosum62.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/2 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 62 # Entropy = 0.6979, Expected = -0.5209 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4 N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4 D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4 C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4 E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4 H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4 I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4 L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4 K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4 M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4 F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4 P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4 S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4 W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4 Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4 V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4 B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4 Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4 * -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1 __MATRIX__ my %blosum = (); $matrix =~ /^ +(.+)$/m; my @aas = split / +/, $1; foreach my $aa (@aas) { my $tmp = $aa; $tmp = "\\$aa" if $aa eq '*'; $matrix =~ /^($tmp) +([-+]?\d.*)$/m; my @scores = split / +/, $2 if defined $2; my $count = 0; foreach my $ak (@aas) { $blosum{$aa}->{$aas[$count]} = $scores[$count]; $count++; } } sub _matrix; $MATRIX = \%blosum; } sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($start, $end, $length, $strand, $primary, $source, $frame, $score, $gff_string, $allele_ori, $allele_mut, $upstreamseq, $dnstreamseq, $label, $status, $proof, $re_changes, $region, $region_value, $region_dist, $numbering, $mut_number, $ismutation) = $self->_rearrange([qw(START END LENGTH STRAND PRIMARY SOURCE FRAME SCORE GFF_STRING ALLELE_ORI ALLELE_MUT UPSTREAMSEQ DNSTREAMSEQ LABEL STATUS PROOF RE_CHANGES REGION REGION_VALUE REGION_DIST NUMBERING MUT_NUMBER ISMUTATION )],@args); $self->primary_tag("Variation"); $self->{ 'alleles' } = []; $start && $self->start($start); $end && $self->end($end); $length && $self->length($length); $strand && $self->strand($strand); $primary && $self->primary_tag($primary); $source && $self->source_tag($source); $frame && $self->frame($frame); $score && $self->score($score); $gff_string && $self->_from_gff_string($gff_string); $allele_ori && $self->allele_ori($allele_ori); $allele_mut && $self->allele_mut($allele_mut); $upstreamseq && $self->upstreamseq($upstreamseq); $dnstreamseq && $self->dnstreamseq($dnstreamseq); $label && $self->label($label); $status && $self->status($status); $proof && $self->proof($proof); $region && $self->region($region); $region_value && $self->region_value($region_value); $region_dist && $self->region_dist($region_dist); $numbering && $self->numbering($numbering); $mut_number && $self->mut_number($mut_number); $ismutation && $self->isMutation($ismutation); return $self; # success - we hope! } =head2 RNAChange Title : RNAChange Usage : $mutobj = $self->RNAChange; : $mutobj = $self->RNAChange($objref); Function: Returns or sets the link-reference to a mutation/change object. If there is no link, it will return undef Returns : an obj_ref or undef =cut sub RNAChange { my ($self,$value) = @_; if (defined $value) { if( ! $value->isa('Bio::Variation::RNAChange') ) { $self->throw("Is not a Bio::Variation::RNAChange object but a [$self]"); return; } else { $self->{'RNAChange'} = $value; } } unless (exists $self->{'RNAChange'}) { return; } else { return $self->{'RNAChange'}; } } =head2 label Title : label Usage : $obj->label(); Function: Sets and returns mutation event label(s). If value is not set, or no argument is given returns false. Each instantiable subclass of L<Bio::Variation::VariantI> needs to implement this method. Valid values are listed in 'Mutation event controlled vocabulary' in http://www.ebi.ac.uk/mutations/recommendations/mutevent.html. Example : Returns : string Args : string =cut sub label { my ($self) = @_; my ($o, $m, $type); $o = $self->allele_ori->seq if $self->allele_ori and $self->allele_ori->seq; $m = $self->allele_mut->seq if $self->allele_mut and $self->allele_mut->seq; if ($self->start == 1 ) { if ($o and substr($o, 0, 1) ne substr($m, 0, 1)) { $type = 'no translation'; } elsif ($o and $m and $o eq $m ) { $type = 'silent'; } # more ... } elsif ($o and substr($o, 0, 1) eq '*' ) { if ($m and substr($o, 0, 1) ne substr($m, 0, 1)) { $type = 'post-elongation'; } elsif ($m and $o eq $m ) { $type = 'silent, conservative'; } } elsif ($o and $m and $o eq $m) { $type = 'silent, conservative'; } elsif ($m and $m eq '*') { $type = 'truncation'; } elsif ($o and $m and $o eq $m) { $type = 'silent, conservative'; } elsif (not $m or ($o and $m and length($o) > length($m) and substr($m, -1, 1) ne '*')) { $type = 'deletion'; if ($o and $m and $o !~ $m and $o !~ $m) { $type .= ', complex'; } } elsif (not $o or ($o and $m and length($o) < length($m) and substr($m, -1, 1) ne '*' ) ) { $type = 'insertion'; if ($o and $m and $o !~ $m and $o !~ $m) { $type .= ', complex'; } } elsif ($o and $m and $o ne $m and length $o == 1 and length $m == 1 ) { $type = 'substitution'; my $value = $self->similarity_score; if (defined $value) { my $cons = ($value < 0) ? 'nonconservative' : 'conservative'; $type .= ", ". $cons; } } else { $type = 'out-of-frame translation, truncation'; } $self->{'label'} = $type; return $self->{'label'}; } =head2 similarity_score Title : similarity_score Usage : $self->similarity_score Function: Measure for evolutionary conservativeness of single amino substitutions. Uses BLOSUM62. Negative numbers are noncoservative changes. Returns : integer, undef if not single amino acid change =cut sub similarity_score { my ($self) = @_; my ($o, $m, $type); $o = $self->allele_ori->seq if $self->allele_ori and $self->allele_ori->seq; $m = $self->allele_mut->seq if $self->allele_mut and $self->allele_mut->seq; return unless $o and $m and length $o == 1 and length $m == 1; return unless $o =~ /[ARNDCQEGHILKMFPSTWYVBZX*]/i and $m =~ /[ARNDCQEGHILKMFPSTWYVBZX*]/i; return $MATRIX->{"\U$o"}->{"\U$m"}; } =head2 trivname Title : trivname Usage : $self->trivname Function: Given a Bio::Variation::AAChange object with linked Bio::Variation::RNAChange and Bio::Variation::DNAMutation objects, this subroutine creates a string corresponding to the 'trivial name' of the mutation. Trivial name is specified in Antonorakis & MDI Nomenclature Working Group: Human Mutation 11:1-3, 1998. Returns : string =cut sub trivname { my ($self,$value) = @_; if( defined $value) { $self->{'trivname'} = $value; } else { my ( $aaori, $aamut,$aamutsymbol, $aatermnumber, $aamutterm) = ('', '', '', '', ''); my $o = $self->allele_ori->seq if $self->allele_ori and $self->allele_ori->seq; #my $m = $self->allele_mut->seq if $self->allele_mut and $self->allele_mut->seq; $aaori = substr ($o, 0, 1) if $o; $aaori =~ tr/\*/X/; my $sep; if ($self->isMutation) { $sep = '>'; } else { $sep = '|'; } my $trivname = $aaori. $self->start; $trivname .= $sep if $sep eq '|'; my @alleles = $self->each_Allele; foreach my $allele (@alleles) { my $m = $allele->seq if $allele->seq; $self->allele_mut($allele); #$trivname .= $sep. uc $m if $m; $aamutterm = substr ($m, -1, 1) if $m; if ($self->RNAChange->label =~ /initiation codon/ and ( $o and $m and $o ne $m)) { $aamut = 'X'; } elsif (CORE::length($o) == 1 and CORE::length($m) == 1 ) { $aamutsymbol = ''; $aamut = $aamutterm; } elsif ($self->RNAChange->label =~ /deletion/) { $aamutsymbol = 'del'; if ($aamutterm eq '*') { $aatermnumber = $self->start + length($m) -1; $aamut = 'X'. $aatermnumber; } if ($self->RNAChange && $self->RNAChange->label =~ /inframe/){ $aamut = '-'. length($self->RNAChange->allele_ori->seq)/3 ; } } elsif ($self->RNAChange->label =~ /insertion/) { $aamutsymbol = 'ins'; if (($aamutterm eq '*') && (length($m)-1 != 0)) { $aatermnumber = $self->start + length($m)-1; $aamut = $aatermnumber. 'X'; } if ($self->RNAChange->label =~ /inframe/){ $aamut = '+'. int length($self->RNAChange->allele_mut->seq)/3 ; } } elsif ($self->RNAChange->label =~ /complex/ ) { my $diff = length($m) - length($o); if ($diff >= 0 ) { $aamutsymbol = 'ins'; } else { $aamutsymbol = 'del' ; } if (($aamutterm eq '*') && (length($m)-1 != 0)) { $aatermnumber = $self->start + length($m)-1; $aamut = $aatermnumber. 'X'; } if ($self->RNAChange->label =~ /inframe/){ if ($diff >= 0 ) { $aamut = '+'. $diff ; } else { $aamut = $diff ; } } } elsif ($self->label =~ /truncation/) { $aamut = $m; } else { $aamutsymbol = ''; $aamut = $aamutterm; } $aamut =~ tr/\*/X/; $trivname .= $aamutsymbol. $aamut. $sep; } chop $trivname; $self->{'trivname'} = $trivname; } return $self->{'trivname'}; } 1; ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Variation/AAReverseMutate.pm���������������������������������������������������000444��000766��000024�� 16451�13155576320� 21542� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Variation::AAReverseMutate # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Variation::AAReverseMutate - point mutation and codon information from single amino acid changes =head1 SYNOPSIS $aamut = Bio::Variation::AAReverseMutate->new (-aa_ori => 'F', -aa_mut => 'S', -codon_ori => 'ttc', # optional -codon_table => '3' # defaults to 1 ); @points = $aamut->each_Variant; if (scalar @points > 0 ) { foreach $rnachange ( @points ) { # $rnachange is a Bio::Variation::RNAChange object print " ", $rnachange->allele_ori->seq, ">", $rnachange->allele_mut->seq, " in ", $rnachange->codon_ori, ">", $rnachange->codon_mut, " at position ", $rnachange->codon_pos, "\n"; } } else { print "No point mutations possible\n", } =head1 DESCRIPTION Bio::Variation::AAReverseMutate objects take in reference and mutated amino acid information and deduces potential point mutations at RNA level leading to this change. The choice can be further limited by letting the object know what is the the codon in the reference sequence. The results are returned as L<Bio::Variation::RNAChange> objects. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Variation::AAReverseMutate; use strict; # Object preamble - inheritance use Bio::Tools::CodonTable; use Bio::Variation::RNAChange; use Bio::Variation::Allele; use base qw(Bio::Root::Root); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($aa_ori, $aa_mut, $codon_ori, $codon_table) = $self->_rearrange([qw(AA_ORI AA_MUT CODON CODON_TABLE )],@args); $aa_ori && $self->aa_ori($aa_ori); $aa_mut && $self->aa_mut($aa_mut); $codon_ori && $self->codon_ori($codon_ori); $codon_table && $self->codon_table($codon_table); return $self; # success - we hope! } =head2 aa_ori Title : aa_ori Usage : $obj->aa_ori(); Function: Sets and returns original aa sequence. If value is not set, returns false. Amino acid sequences are stored in upper case characters, others in lower case. Example : Returns : string Args : single character amino acid code =cut sub aa_ori { my ($self,$value) = @_; if( defined $value) { if ( uc($value) !~ /^[ARNDCQEGHILKMFPSTWYVBZX*]$/ ) { $self->throw("'$value' is not a valid one letter amino acid symbol\n"); } else { $self->{'aa_ori'} = uc $value; } } return $self->{'aa_ori'}; } =head2 aa_mut Title : aa_mut Usage : $obj->aa_mut(); Function: Sets and returns the mutated allele sequence. If value is not set, returns false. Example : Returns : string Args : single character amino acid code =cut sub aa_mut { my ($self,$value) = @_; if( defined $value) { if ( uc($value) !~ /^[ARNDCQEGHILKMFPSTWYVBZX*]$/ ) { $self->throw("'$value' is not a valid one letter amino acid symbol\n"); } else { $self->{'aa_mut'} = uc $value; } } return $self->{'aa_mut'}; } =head2 codon_ori Title : codon_ori Usage : $obj->codon_ori(); Function: Sets and returns codon_ori triplet. If value is not set, returns false. The string has to be three characters long. The character content is not checked. Example : Returns : string Args : string =cut sub codon_ori { my ($self,$value) = @_; if( defined $value) { if (length $value != 3 or lc $value =~ /[^atgc]/) { $self->warn("Codon string \"$value\" is not valid unique codon"); } $self->{'codon_ori'} = lc $value; } return $self->{'codon_ori'}; } =head2 codon_table Title : codon_table Usage : $obj->codon_table(); Function: Sets and returns the codon table id of the RNA If value is not set, returns 1, 'universal' code, as the default. Example : Returns : integer Args : none if get, the new value if set =cut sub codon_table { my ($self,$value) = @_; if( defined $value) { if ( not $value =~ /^\d+$/ ) { $self->throw("'$value' is not a valid codon table ID\n". "Has to be a positive integer. Defaulting to 1\n"); } else { $self->{'codon_table'} = $value; } } if( ! exists $self->{'codon_table'} ) { return 1; } else { return $self->{'codon_table'}; } } =head2 each_Variant Title : each_Variant Usage : $obj->each_Variant(); Function: Returns a list of Variants. Example : Returns : list of Variants Args : none =cut sub each_Variant{ my ($self,@args) = @_; $self->throw("aa_ori is not defined\n") if not defined $self->aa_ori; $self->throw("aa_mut is not defined\n") if not defined $self->aa_mut; my (@points, $codon_pos, $allele_ori, $allele_mut); my $ct = Bio::Tools::CodonTable->new( '-id' => $self->codon_table ); foreach my $codon_ori ($ct->revtranslate($self->aa_ori)) { next if $self->codon_ori and $self->codon_ori ne $codon_ori; foreach my $codon_mut ($ct->revtranslate($self->aa_mut)) { my $k = 0; my $length = 0; $codon_pos = $allele_ori = $allele_mut = undef; while ($k<3) { my $nt_ori = substr ($codon_ori, $k, 1); my $nt_mut = substr ($codon_mut, $k, 1); if ($nt_ori ne $nt_mut) { $length++; $codon_pos = $k+1; $allele_ori = $nt_ori; $allele_mut = $nt_mut; } $k++; } if ($length == 1) { my $rna = Bio::Variation::RNAChange->new ('-length' => '1', '-codon_ori' => $codon_ori, '-codon_mut' => $codon_mut, '-codon_pos' => $codon_pos, '-isMutation' => 1 ); my $all_ori = Bio::Variation::Allele->new('-seq'=>$allele_ori); $rna->allele_ori($all_ori); my $all_mut = Bio::Variation::Allele->new('-seq'=>$allele_mut); $rna->allele_mut($all_mut); push @points, $rna; } } } return @points; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Variation/Allele.pm������������������������������������������������������������000444��000766��000024�� 14707�13155576320� 17745� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Variation::Allele # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Variation::Allele - Sequence object with allele-specific attributes =head1 SYNOPSIS $allele1 = Bio::Variation::Allele->new ( -seq => 'A', -id => 'AC00001.1', -alphabet => 'dna', -is_reference => 1 ); =head1 DESCRIPTION List of alleles describe known sequence alternatives in a variable region. Alleles are contained in Bio::Variation::VariantI complying objects. See L<Bio::Variation::VariantI> for details. Bio::Varation::Alleles are PrimarySeqI complying objects which can contain database cross references as specified in Bio::DBLinkContainerI interface, too. A lot of the complexity with dealing with Allele objects are caused by null alleles; Allele objects that have zero length sequence string. In addition describing the allele by its sequence , it possible to give describe repeat structure within the sequence. This done using methods repeat_unit (e.g. 'ca') and repeat_count (e.g. 7). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Variation::Allele; use strict; # Object preamble - inheritance use base qw(Bio::PrimarySeq Bio::DBLinkContainerI); sub new { my($class, @args) = @_; my $self = $class->SUPER::new(@args); my($is_reference, $repeat_unit, $repeat_count) = $self->_rearrange([qw(IS_REFERENCE REPEAT_UNIT REPEAT_COUNT )], @args); $is_reference && $self->is_reference($is_reference); $repeat_unit && $self->repeat_unit($repeat_unit); $repeat_count && $self->repeat_count($repeat_count); return $self; # success - we hope! } =head2 is_reference Title : is_reference Usage : $obj->is_reference() Function: sets and returns boolean values. Unset values return false. Example : $obj->is_reference() Returns : boolean Args : optional true of false value =cut sub is_reference { my ($self,$value) = @_; if( defined $value) { $value ? ($value = 1) : ($value = 0); $self->{'is_reference'} = $value; } if( ! exists $self->{'is_reference'} ) { return 0; } else { return $self->{'is_reference'}; } } =head2 add_DBLink Title : add_DBLink Usage : $self->add_DBLink($ref) Function: adds a link object Example : Returns : Args : =cut sub add_DBLink{ my ($self,$com) = @_; if( ! $com->isa('Bio::Annotation::DBLink') ) { $self->throw("Is not a link object but a [$com]"); } push(@{$self->{'link'}},$com); } =head2 each_DBLink Title : each_DBLink Usage : foreach $ref ( $self->each_DBlink() ) Function: gets an array of DBlink of objects Example : Returns : Args : =cut sub each_DBLink{ my ($self) = @_; return @{$self->{'link'}}; } =head2 repeat_unit Title : repeat_unit Usage : $obj->repeat_unit('ca'); Function: Sets and returns the sequence of the repeat_unit the allele is composed of. Example : Returns : string Args : string =cut sub repeat_unit { my ($self,$value) = @_; if( defined $value) { $self->{'repeat_unit'} = $value; } if ($self->{'seq'} && $self->{'repeat_unit'} && $self->{'repeat_count'} ) { $self->warn("Repeats do not add up!") if ( $self->{'repeat_unit'} x $self->{'repeat_count'}) ne $self->{'seq'}; } return $self->{'repeat_unit'}; } =head2 repeat_count Title : repeat_count Usage : $obj->repeat_count(); Function: Sets and returns the number of repeat units in the allele. Example : Returns : string Args : string =cut sub repeat_count { my ($self,$value) = @_; if( defined $value) { if ( not $value =~ /^\d+$/ ) { $self->throw("[$value] for repeat_count has to be a positive integer\n"); } else { $self->{'repeat_count'} = $value; } } if ($self->{'seq'} && $self->{'repeat_unit'} && $self->{'repeat_count'} ) { $self->warn("Repeats do not add up!") if ( $self->{'repeat_unit'} x $self->{'repeat_count'}) ne $self->{'seq'}; } return $self->{'repeat_count'}; } =head2 count Title : count Usage : $obj->count(); Function: Sets and returns the number of times this allele was observed. Example : Returns : string Args : string =cut sub count { my ($self,$value) = @_; if( defined $value) { if ( not $value =~ /^\d+$/ ) { $self->throw("[$value] for count has to be a positive integer\n"); } else { $self->{'count'} = $value; } } return $self->{'count'}; } =head2 frequency Title : frequency Usage : $obj->frequency(); Function: Sets and returns the frequency of the allele in the observed population. Example : Returns : string Args : string =cut sub frequency { my ($self,$value) = @_; if( defined $value) { if ( not $value =~ /^\d+$/ ) { $self->throw("[$value] for frequency has to be a positive integer\n"); } else { $self->{'frequency'} = $value; } } return $self->{'frequency'}; } 1; ���������������������������������������������������������BioPerl-1.007002/Bio/Variation/DNAMutation.pm�������������������������������������������������������000444��000766��000024�� 23350�13155576320� 20664� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Variation::DNAMutation # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Variation::DNAMutation - DNA level mutation class =head1 SYNOPSIS $dnamut = Bio::Variation::DNAMutation->new ('-start' => $start, '-end' => $end, '-length' => $len, '-upStreamSeq' => $upflank, '-dnStreamSeq' => $dnflank, '-proof' => $proof, '-isMutation' => 1, '-mut_number' => $mut_number ); $a1 = Bio::Variation::Allele->new; $a1->seq('a'); $dnamut->allele_ori($a1); my $a2 = Bio::Variation::Allele->new; $a2->seq('t'); $dnamut->add_Allele($a2); print "Restriction changes are ", $dnamut->restriction_changes, "\n"; # add it to a SeqDiff container object $seqdiff->add_Variant($dnamut); =head1 DESCRIPTION The instantiable class Bio::Variation::DNAMutation describes basic sequence changes in genomic DNA level. It uses methods defined in superclass Bio::Variation::VariantI. See L<Bio::Variation::VariantI> for details. If the variation described by a DNAMutation object is transcibed, link the corresponding Bio::Variation::RNAChange object to it using method RNAChange(). See L<Bio::Variation::RNAChange> for more information. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Variation::DNAMutation; use strict; # Object preamble - inheritance use base qw(Bio::Variation::VariantI); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($start, $end, $length, $strand, $primary, $source, $frame, $score, $gff_string, $allele_ori, $allele_mut, $upstreamseq, $dnstreamseq, $label, $status, $proof, $region, $region_value, $region_dist, $numbering, $cpg, $mut_number, $ismutation) = $self->_rearrange([qw(START END LENGTH STRAND PRIMARY SOURCE FRAME SCORE GFF_STRING ALLELE_ORI ALLELE_MUT UPSTREAMSEQ DNSTREAMSEQ LABEL STATUS PROOF REGION REGION_VALUE REGION_DIST NUMBERING CPG MUT_NUMBER ISMUTATION )], @args); $self->primary_tag("Variation"); $self->{ 'alleles' } = []; $start && $self->start($start); $end && $self->end($end); $length && $self->length($length); $strand && $self->strand($strand); $primary && $self->primary_tag($primary); $source && $self->source_tag($source); $frame && $self->frame($frame); $score && $self->score($score); $gff_string && $self->_from_gff_string($gff_string); $allele_ori && $self->allele_ori($allele_ori); $allele_mut && $self->allele_mut($allele_mut); $upstreamseq && $self->upStreamSeq($upstreamseq); $dnstreamseq && $self->dnStreamSeq($dnstreamseq); $label && $self->label($label); $status && $self->status($status); $proof && $self->proof($proof); $region && $self->region($region); $region_value && $self->region_value($region_value); $region_dist && $self->region_dist($region_dist); $numbering && $self->numbering($numbering); $mut_number && $self->mut_number($mut_number); $ismutation && $self->isMutation($ismutation); $cpg && $self->CpG($cpg); return $self; # success - we hope! } =head2 CpG Title : CpG Usage : $obj->CpG() Function: sets and returns boolean values for variation hitting a CpG site. Unset value return -1. Example : $obj->CpG() Returns : boolean Args : optional true of false value =cut sub CpG { my ($obj,$value) = @_; if( defined $value) { $value ? ($value = 1) : ($value = 0); $obj->{'cpg'} = $value; } elsif (not defined $obj->{'label'}) { $obj->{'cpg'} = $obj->_CpG_value; } else { return $obj->{'cpg'}; } } sub _CpG_value { my ($self) = @_; if ($self->allele_ori eq $self->allele_mut and length ($self->allele_ori) == 1 ) { # valid only for point mutations # CpG methylation-mediated deamination: # CG -> TG | CG -> CA substitutions # implementation here is less strict: if CpG dinucleotide was hit if ( ( ($self->allele_ori eq 'c') && (substr($self->upStreamSeq, 0, 1) eq 'g') ) || ( ($self->allele_ori eq 'g') && (substr($self->dnStreamSeq, -1, 1) eq 'c') ) ) { return 1; } else { return 0; } } else { $self->warn('CpG makes sense only in the context of point mutation'); return; } } =head2 RNAChange Title : RNAChange Usage : $mutobj = $obj->RNAChange; : $mutobj = $obj->RNAChange($objref); Function: Returns or sets the link-reference to a mutation/change object. If there is no link, it will return undef Returns : an obj_ref or undef =cut sub RNAChange { my ($self,$value) = @_; if (defined $value) { if( ! $value->isa('Bio::Variation::RNAChange') ) { $self->throw("Is not a Bio::Variation::RNAChange object but a [$self]"); return; } else { $self->{'RNAChange'} = $value; } } unless (exists $self->{'RNAChange'}) { return; } else { return $self->{'RNAChange'}; } } =head2 label Title : label Usage : $obj->label(); Function: Sets and returns mutation event label(s). If value is not set, or no argument is given returns false. Each instantiable subclass of L<Bio::Variation::VariantI> needs to implement this method. Valid values are listed in 'Mutation event controlled vocabulary' in http://www.ebi.ac.uk/mutations/recommendations/mutevent.html. Example : Returns : string Args : string =cut sub label { my ($self, $value) = @_; my ($o, $m, $type); $o = $self->allele_ori->seq if $self->allele_ori and $self->allele_ori->seq; $m = $self->allele_mut->seq if $self->allele_mut and $self->allele_mut->seq; if (not $o and not $m ) { $self->warn("[DNAMutation, label] Both alleles should not be empty!\n"); $type = 'no change'; # is this enough? } elsif ($o && $m && length($o) == length($m) && length($o) == 1) { $type = 'point'; $type .= ", ". _point_type_label($o, $m); } elsif (not $o ) { $type = 'insertion'; } elsif (not $m ) { $type = 'deletion'; } else { $type = 'complex'; } $self->{'label'} = $type; return $self->{'label'}; } sub _point_type_label { my ($o, $m) = @_; my ($type); my %transition = ('a' => 'g', 'g' => 'a', 'c' => 't', 't' => 'c'); $o = lc $o; $m = lc $m; if ($o eq $m) { $type = 'no change'; } elsif ($transition{$o} eq $m ) { $type = 'transition'; } else { $type = 'transversion'; } } =head2 sysname Title : sysname Usage : $self->sysname Function: This subroutine creates a string corresponding to the 'systematic name' of the mutation. Systematic name is specified in Antonorakis & MDI Nomenclature Working Group: Human Mutation 11:1-3, 1998. Returns : string =cut sub sysname { my ($self,$value) = @_; if( defined $value) { $self->{'sysname'} = $value; } else { $self->warn('Mutation start position is not defined') if not defined $self->start; my $sysname = ''; # show the alphabet only if $self->SeqDiff->alphabet is set; my $mol = ''; if ($self->SeqDiff ) { if ($self->SeqDiff && $self->SeqDiff->alphabet && $self->SeqDiff->alphabet eq 'dna') { $mol = 'g.'; } elsif ($self->SeqDiff->alphabet && $self->SeqDiff->alphabet eq 'rna') { $mol = 'c.'; } } my $sep; if ($self->isMutation) { $sep = '>'; } else { $sep = '|'; } my $sign = '+'; $sign = '' if $self->start < 1; $sysname .= $mol ;#if $mol; $sysname .= $sign. $self->start; my @alleles = $self->each_Allele; $self->allele_mut($alleles[0]); $sysname .= 'del' if $self->label =~ /deletion/; $sysname .= 'ins' if $self->label =~ /insertion/; $sysname .= uc $self->allele_ori->seq if $self->allele_ori->seq; #push @alleles, $self->allele_mut if $self->allele_mut; foreach my $allele (@alleles) { $self->allele_mut($allele); $sysname .= $sep if $self->label =~ /point/ or $self->label =~ /complex/; $sysname .= uc $self->allele_mut->seq if $self->allele_mut->seq; } $self->{'sysname'} = $sysname; #$self->{'sysname'} = $sign. $self->start. # uc $self->allele_ori->seq. $sep. uc $self->allele_mut->seq; } return $self->{'sysname'}; } 1; ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Variation/IO.pm����������������������������������������������������������������000444��000766��000024�� 22231�13155576320� 17045� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Variation::IO # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Variation::IO - Handler for sequence variation IO Formats =head1 SYNOPSIS use Bio::Variation::IO; $in = Bio::Variation::IO->new(-file => "inputfilename" , -format => 'flat'); $out = Bio::Variation::IO->new(-file => ">outputfilename" , -format => 'xml'); while ( my $seq = $in->next() ) { $out->write($seq); } # or use Bio::Variation::IO; #input file format can be read from the file extension (dat|xml) $in = Bio::Variation::IO->newFh(-file => "inputfilename"); $out = Bio::Variation::IO->newFh(-format => 'xml'); # World's shortest flat<->xml format converter: print $out $_ while <$in>; =head1 DESCRIPTION Bio::Variation::IO is a handler module for the formats in the Variation IO set (eg, Bio::Variation::IO::flat). It is the officially sanctioned way of getting at the format objects, which most people should use. The structure, conventions and most of the code is inherited from L<Bio::SeqIO> module. The main difference is that instead of using methods next_seq and write_seq, you drop '_seq' from the method names. The idea is that you request a stream object for a particular format. All the stream objects have a notion of an internal file that is read from or written to. A particular SeqIO object instance is configured for either input or output. A specific example of a stream object is the Bio::Variation::IO::flat object. Each stream object has functions $stream->next(); and $stream->write($seqDiff); also $stream->type() # returns 'INPUT' or 'OUTPUT' As an added bonus, you can recover a filehandle that is tied to the SeqIO object, allowing you to use the standard E<lt>E<gt> and print operations to read and write sequence objects: use Bio::Variation::IO; $stream = Bio::Variation::IO->newFh(-format => 'flat'); # read from standard input while ( $seq = <$stream> ) { # do something with $seq } and print $stream $seq; # when stream is in output mode This makes the simplest ever reformatter #!/usr/local/bin/perl $format1 = shift; $format2 = shift; use Bio::Variation::IO; $in = Bio::Variation::IO->newFh(-format => $format1 ); $out = Bio::Variation::IO->newFh(-format => $format2 ); print $out $_ while <$in>; =head1 CONSTRUCTORS =head2 Bio::Variation::IO-E<gt>new() $seqIO = Bio::Variation::IO->new(-file => 'filename', -format=>$format); $seqIO = Bio::Variation::IO->new(-fh => \*FILEHANDLE, -format=>$format); $seqIO = Bio::Variation::IO->new(-format => $format); The new() class method constructs a new Bio::Variation::IO object. The returned object can be used to retrieve or print BioSeq objects. new() accepts the following parameters: =over 4 =item -file A file path to be opened for reading or writing. The usual Perl conventions apply: 'file' # open file for reading '>file' # open file for writing '>>file' # open file for appending '+<file' # open file read/write 'command |' # open a pipe from the command '| command' # open a pipe to the command =item -fh You may provide new() with a previously-opened filehandle. For example, to read from STDIN: $seqIO = Bio::Variation::IO->new(-fh => \*STDIN); Note that you must pass filehandles as references to globs. If neither a filehandle nor a filename is specified, then the module will read from the @ARGV array or STDIN, using the familiar E<lt>E<gt> semantics. =item -format Specify the format of the file. Supported formats include: flat pseudo EMBL format xml seqvar xml format If no format is specified and a filename is given, then the module will attempt to deduce it from the filename. If this is unsuccessful, Fasta format is assumed. The format name is case insensitive. 'FLAT', 'Flat' and 'flat' are all supported. =back =head2 Bio::Variation::IO-E<gt>newFh() $fh = Bio::Variation::IO->newFh(-fh => \*FILEHANDLE, -format=>$format); $fh = Bio::Variation::IO->newFh(-format => $format); # etc. #e.g. $out = Bio::Variation::IO->newFh( '-FORMAT' => 'flat'); print $out $seqDiff; This constructor behaves like new(), but returns a tied filehandle rather than a Bio::Variation::IO object. You can read sequences from this object using the familiar E<lt>E<gt> operator, and write to it using print(). The usual array and $_ semantics work. For example, you can read all sequence objects into an array like this: @mutations = <$fh>; Other operations, such as read(), sysread(), write(), close(), and printf() are not supported. =head1 OBJECT METHODS See below for more detailed summaries. The main methods are: =head2 $sequence = $seqIO-E<gt>next() Fetch the next sequence from the stream. =head2 $seqIO-E<gt>write($sequence [,$another_sequence,...]) Write the specified sequence(s) to the stream. =head2 TIEHANDLE(), READLINE(), PRINT() These provide the tie interface. See L<perltie> for more details. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Variation::IO; use strict; use base qw(Bio::SeqIO Bio::Root::IO); =head2 new Title : new Usage : $stream = Bio::Variation::IO->new(-file => $filename, -format => 'Format') Function: Returns a new seqstream Returns : A Bio::Variation::IO::Handler initialised with the appropriate format Args : -file => $filename -format => format -fh => filehandle to attach to =cut sub new { my ($class, %param) = @_; my ($format); @param{ map { lc $_ } keys %param } = values %param; # lowercase keys $format = $param{'-format'} || $class->_guess_format( $param{-file} || $ARGV[0] ) || 'flat'; $format = "\L$format"; # normalize capitalization to lower case return unless $class->_load_format_module($format); return "Bio::Variation::IO::$format"->new(%param); } =head2 format Title : format Usage : $format = $stream->format() Function: Get the variation format Returns : variation format Args : none =cut # format() method inherited from Bio::Root::IO sub _load_format_module { my ($class, $format) = @_; my $module = "Bio::Variation::IO::" . $format; my $ok; eval { $ok = $class->_load_module($module); }; if ( $@ ) { print STDERR <<END; $class: $format cannot be found Exception $@ For more information about the IO system please see the IO docs. This includes ways of checking for formats at compile time, not run time END ; } return $ok; } =head2 next Title : next Usage : $seqDiff = $stream->next Function: reads the next $seqDiff object from the stream Returns : a Bio::Variation::SeqDiff object Args : =cut sub next { my ($self, $seq) = @_; $self->throw("Sorry, you cannot read from a generic Bio::Variation::IO object."); } sub next_seq { my ($self, $seq) = @_; $self->throw("These are not sequence objects. Use method 'next' instead of 'next_seq'."); $self->next($seq); } =head2 write Title : write Usage : $stream->write($seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Variation::SeqDiff object =cut sub write { my ($self, $seq) = @_; $self->throw("Sorry, you cannot write to a generic Bio::Variation::IO object."); } sub write_seq { my ($self, $seq) = @_; $self->warn("These are not sequence objects. Use method 'write' instead of 'write_seq'."); $self->write($seq); } =head2 _guess_format Title : _guess_format Usage : $obj->_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args : =cut sub _guess_format { my $class = shift; return unless $_ = shift; return 'flat' if /\.dat$/i; return 'xml' if /\.xml$/i; } 1; �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Variation/README���������������������������������������������������������������000444��000766��000024�� 1736�13155576320� 17047� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������� README for Bio::Variation classes These classes are part of "Computational Mutation Expression Toolkit" project at European Bioinformatics Institute <http://www.ebi.ac.uk/mutations/toolkit/>, but they are written to be as general as possinble. Bio::Variation name space contains modules to store sequence variation information as differences between the reference sequence and changes sequences. Also included are classes to write out and recrete objects from EMBL-like flat files and XML. Lastly, there are simple classes to calculate values for sequence change objects. See "Computational Mutation Expression Toolkit" web pages for more information: http://www.ebi.ac.uk/mutations/toolkit/ Send bug reports using the bioperl bug-tracking system at https://github.com/bioperl/bioperl-live/issues. Send general comments, questions, and feature requests to the bioperl mailing list: bioperl-l@bioperl.org Heikki Lehväslaiho <heikki-at-bioperl-dot-org> ����������������������������������BioPerl-1.007002/Bio/Variation/RNAChange.pm���������������������������������������������������������000444��000766��000024�� 37335�13155576320� 20277� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Variation::RNAChange # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Variation::RNAChange - Sequence change class for RNA level =head1 SYNOPSIS $rnachange = Bio::Variation::RNAChange->new ('-start' => $start, '-end' => $end, '-length' => $len, '-codon_pos' => $cp, '-upStreamSeq' => $upflank, '-dnStreamSeq' => $dnflank, '-proof' => $proof, '-isMutation' => 1, '-mut_number' => $mut_number ); $a1 = Bio::Variation::Allele->new; $a1->seq('a'); $rnachange->allele_ori($a1); my $a2 = Bio::Variation::Allele->new; $a2->seq('t'); $rnachange->add_Allele($a2); $rnachange->allele_mut($a2); print "The codon change is ", $rnachange->codon_ori, ">", $rnachange->codon_mut, "\n"; # add it to a SeqDiff container object $seqdiff->add_Variant($rnachange); # and create links to and from DNA level mutation objects $rnachange->DNAMutation($dnamut); $dnamut->RNAChange($rnachange); =head1 DESCRIPTION The instantiable class Bio::Variation::DNAMutation describes basic sequence changes at RNA molecule level. It uses methods defined in superclass Bio::Variation::VariantI. See L<Bio::Variation::VariantI> for details. You are normally expected to create a corresponding Bio::Variation::DNAMutation object even if mutation is defined at RNA level. The numbering follows then cDNA numbering. Link the DNAMutation object to the RNAChange object using the method DNAMutation(). If the variation described by a RNAChange object is translated, link the corresponding Bio::Variation::AAChange object to it using method AAChange(). See L<Bio::Variation::DNAMutation> and L<Bio::Variation::AAChange> for more information. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Variation::RNAChange; use strict; # Object preamble - inheritance use Bio::Tools::CodonTable; use base qw(Bio::Variation::VariantI); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($start, $end, $length, $strand, $primary, $source, $frame, $score, $gff_string, $allele_ori, $allele_mut, $upstreamseq, $dnstreamseq, $label, $status, $proof, $region, $region_value, $region_dist, $numbering, $mut_number, $isMutation, $codon_ori, $codon_mut, $codon_pos, $codon_table, $cds_end) = $self->_rearrange([qw(START END LENGTH STRAND PRIMARY SOURCE FRAME SCORE GFF_STRING ALLELE_ORI ALLELE_MUT UPSTREAMSEQ DNSTREAMSEQ LABEL STATUS PROOF REGION REGION_VALUE REGION_DIST NUMBERING MUT_NUMBER ISMUTATION CODON_ORI CODON_MUT CODON_POS TRANSLATION_TABLE CDS_END )],@args); $self->primary_tag("Variation"); $self->{ 'alleles' } = []; $start && $self->start($start); $end && $self->end($end); $length && $self->length($length); $strand && $self->strand($strand); $primary && $self->primary_tag($primary); $source && $self->source_tag($source); $frame && $self->frame($frame); $score && $self->score($score); $gff_string && $self->_from_gff_string($gff_string); $allele_ori && $self->allele_ori($allele_ori); $allele_mut && $self->allele_mut($allele_mut); $upstreamseq && $self->upStreamSeq($upstreamseq); $dnstreamseq && $self->dnStreamSeq($dnstreamseq); $label && $self->label($label); $status && $self->status($status); $proof && $self->proof($proof); $region && $self->region($region); $region_value && $self->region_value($region_value); $region_dist && $self->region_dist($region_dist); $numbering && $self->numbering($numbering); $mut_number && $self->mut_number($mut_number); $isMutation && $self->isMutation($isMutation); $codon_ori && $self->codon_ori($codon_ori); $codon_mut && $self->codon_mut($codon_mut); $codon_pos && $self->codon_pos($codon_pos); $codon_table && $self->codon_table($codon_table); $cds_end && $self->cds_end($cds_end); return $self; # success - we hope! } =head2 codon_ori Title : codon_ori Usage : $obj->codon_ori(); Function: Sets and returns codon_ori triplet. If value is not set, creates the codon triplet from the codon position and flanking sequences. The string has to be three characters long. The character content is not checked. Example : Returns : string Args : string =cut sub codon_ori { my ($self,$value) = @_; if (defined $value) { if (length $value != 3) { $self->warn("Codon string \"$value\" is not three characters long"); } $self->{'codon_ori'} = $value; } elsif (! $self->{'codon_ori'}) { my $codon_ori = ''; if ($self->region eq 'coding' && $self->start && $self->start >= 1) { $self->warn('Codon position is not defined') if not defined $self->codon_pos; $self->warn('Upstream flanking sequence is not defined') if not defined $self->upStreamSeq; $self->warn('Downstream flanking sequence is not defined') if not defined $self->dnStreamSeq; my $cpos = $self->codon_pos; $codon_ori = substr($self->upStreamSeq, -$cpos +1 , $cpos-1); $codon_ori .= substr($self->allele_ori->seq, 0, 4-$cpos) if $self->allele_ori and $self->allele_ori->seq; $codon_ori .= substr($self->dnStreamSeq, 0, 3-length($codon_ori)); } $self->{'codon_ori'} = lc $codon_ori; } return $self->{'codon_ori'}; } =head2 codon_mut Title : codon_mut Usage : $obj->codon_mut(); Function: Sets and returns codon_mut triplet. If value is not set, creates the codon triplet from the codon position and flanking sequences. Return undef for other than point mutations. Example : Returns : string Args : string =cut sub codon_mut { my ($self,$value) = @_; if (defined $value) { if (length $value != 3 ) { $self->warn("Codon string \"$value\" is not three characters long"); } $self->{'codon_mut'} = $value; } else { my $codon_mut = ''; if ($self->allele_ori->seq and $self->allele_mut->seq and CORE::length($self->allele_ori->seq) == 1 and CORE::length($self->allele_mut->seq) == 1 and $self->region eq 'coding' and $self->start >= 1) { $self->warn('Codon position is not defined') if not defined $self->codon_pos; $self->warn('Upstream flanking sequnce is not defined') if not defined $self->upStreamSeq; $self->warn('Downstream flanking sequnce is not defined') if not defined $self->dnStreamSeq; $self->throw('Mutated allele is not defined') if not defined $self->allele_mut; my $cpos = $self->codon_pos; $codon_mut = substr($self->upStreamSeq, -$cpos +1 , $cpos-1); $codon_mut .= substr($self->allele_mut->seq, 0, 4-$cpos) if $self->allele_mut and $self->allele_mut->seq; $codon_mut .= substr($self->dnStreamSeq, 0, 3-length($codon_mut)); $self->{'codon_mut'} = lc $codon_mut; } } return $self->{'codon_mut'}; } =head2 codon_pos Title : codon_pos Usage : $obj->codon_pos(); Function: Sets and returns the position of the mutation start in the codon. If value is not set, returns false. Example : Returns : 1,2,3 Args : none if get, the new value if set =cut sub codon_pos { my ($self,$value) = @_; if( defined $value) { if ( $value !~ /[123]/ ) { $self->throw("'$value' is not a valid codon position"); } $self->{'codon_pos'} = $value; } return $self->{'codon_pos'}; } =head2 codon_table Title : codon_table Usage : $obj->codon_table(); Function: Sets and returns the codon table id of the RNA If value is not set, returns 1, 'universal' code, as the default. Example : Returns : integer Args : none if get, the new value if set =cut sub codon_table { my ($self,$value) = @_; if( defined $value) { if ( not $value =~ /^\d$/ ) { $self->throw("'$value' is not a valid codon table ID\n". "Has to be a positive integer. Defaulting to 1\n"); } else { $self->{'codon_table'} = $value; } } if( ! exists $self->{'codon_table'} ) { return 1; } else { return $self->{'codon_table'}; } } =head2 DNAMutation Title : DNAMutation Usage : $mutobj = $obj->DNAMutation; : $mutobj = $obj->DNAMutation($objref); Function: Returns or sets the link-reference to a mutation/change object. If there is no link, it will return undef Returns : an obj_ref or undef =cut sub DNAMutation { my ($self,$value) = @_; if (defined $value) { if( ! $value->isa('Bio::Variation::DNAMutation') ) { $self->throw("Is not a Bio::Variation::DNAMutation object but a [$self]"); return; } else { $self->{'DNAMutation'} = $value; } } unless (exists $self->{'DNAMutation'}) { return; } else { return $self->{'DNAMutation'}; } } =head2 AAChange Title : AAChange Usage : $mutobj = $obj->AAChange; : $mutobj = $obj->AAChange($objref); Function: Returns or sets the link-reference to a mutation/change object. If there is no link, it will return undef Returns : an obj_ref or undef =cut sub AAChange { my ($self,$value) = @_; if (defined $value) { if( ! $value->isa('Bio::Variation::AAChange') ) { $self->throw("Is not a Bio::Variation::AAChange object but a [$self]"); return; } else { $self->{'AAChange'} = $value; } } unless (exists $self->{'AAChange'}) { return; } else { return $self->{'AAChange'}; } } =head2 exons_modified Title : exons_modified Usage : $modified = $obj->exons_modified; : $modified = $obj->exons_modified(1); Function: Returns or sets information (example: a simple boolean flag) about the modification of exons as a result of a mutation. =cut sub exons_modified { my ($self,$value)=@_; if (defined($value)) { $self->{'exons_modified'}=$value; } return ($self->{'exons_modified'}); } =head2 region Title : region Usage : $obj->region(); Function: Sets and returns the name of the sequence region type or protein domain at this location. If value is not set, returns false. Example : Returns : string Args : string =cut sub region { my ($self,$value) = @_; if( defined $value) { $self->{'region'} = $value; } elsif (not defined $self->{'region'}) { $self->warn('Mutation start position is not defined') if not defined $self->start and $self->verbose; $self->warn('Mutation end position is not defined') if not defined $self->end and $self->verbose; $self->warn('Length of the CDS is not defined, the mutation can be beyond coding region!') if not defined $self->cds_end and $self->verbose; $self->region('coding'); if ($self->end && $self->end < 0 ){ $self->region('5\'UTR'); } elsif ($self->start && $self->cds_end && $self->start > $self->cds_end ) { $self->region('3\'UTR'); } } return $self->{'region'}; } =head2 cds_end Title : cds_end Usage : $cds_end = $obj->get_cds_end(); Function: Sets or returns the cds_end from the beginning of the DNA sequence to the coordinate start used to describe variants. Should be the location of the last nucleotide of the terminator codon of the gene. Example : Returns : value of cds_end, a scalar Args : =cut sub cds_end { my ($self, $value) = @_; if (defined $value) { $self->warn("[$value] is not a good value for sequence position") if not $value =~ /^\d+$/ ; $self->{'cds_end'} = $value; } else { $self->{'cds_end'} = $self->SeqDiff->cds_end if $self->SeqDiff; } return $self->{'cds_end'}; } =head2 label Title : label Usage : $obj->label(); Function: Sets and returns mutation event label(s). If value is not set, or no argument is given returns false. Each instantiable subclass of L<Bio::Variation::VariantI> needs to implement this method. Valid values are listed in 'Mutation event controlled vocabulary' in http://www.ebi.ac.uk/mutations/recommendations/mutevent.html. Example : Returns : string Args : string =cut sub label { my ($self) = @_; my ($o, $m, $type); $o = $self->allele_ori->seq if $self->allele_ori and $self->allele_ori->seq; $m = $self->allele_mut->seq if $self->allele_mut and $self->allele_mut->seq; my $ct = Bio::Tools::CodonTable -> new ( -id => $self->codon_table ); if ($o and $m and CORE::length($o) == 1 and CORE::length($m) == 1) { if (defined $self->AAChange) { if ($self->start > 0 and $self->start < 4 ) { $type = 'initiation codon'; } elsif ($self->codon_ori && $ct->is_ter_codon($self->codon_ori) ) { #AAChange->allele_ori and $self->AAChange->allele_ori->seq eq '*' ) { $type = 'termination codon'; } elsif ($self->codon_mut && $ct->is_ter_codon($self->codon_mut) ) { #elsif ($self->AAChange->allele_mut and $self->AAChange->allele_mut->seq eq "*") { $type = 'nonsense'; } elsif ($o and $m and ($o eq $m or $self->AAChange->allele_ori->seq eq $self->AAChange->allele_mut->seq)) { $type = 'silent'; } else { $type = 'missense'; } } else { $type = 'unknown'; } } else { my $len = 0; $len = CORE::length($o) if $o; $len -= CORE::length($m) if $m; if ($len%3 == 0 ) { $type = 'inframe'; } else { $type = 'frameshift'; } if (not $m ) { $type .= ', '. 'deletion'; } elsif (not $o ) { $type .= ', '. 'insertion'; } else { $type .= ', '. 'complex'; } if ($self->codon_ori && $ct->is_ter_codon($self->codon_ori) ) { $type .= ', '. 'termination codon'; } } $self->{'label'} = $type; return $self->{'label'}; } =head2 _change_codon_pos Title : _change_codon_pos Usage : $newCodonPos = _change_codon_pos($myCodonPos, 5) Function: Keeps track of the codon position in a changeing sequence Returns : codon_pos = integer 1, 2 or 3 Args : valid codon position signed integer offset to a new location in sequence =cut sub _change_codon_pos ($$) { my ($cpos, $i) = @_; $cpos = ($cpos + $i%3)%3; if ($cpos > 3 ) { $cpos = $cpos - 3; } elsif ($cpos < 1 ) { $cpos = $cpos + 3; } return $cpos; } 1; ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Variation/SNP.pm���������������������������������������������������������������000444��000766��000024�� 11417�13155576320� 17202� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# bioperl module for Bio::Variation::SNP # # Copyright Allen Day <allenday@ucla.edu>, Stan Nelson <snelson@ucla.edu> # Human Genetics, UCLA Medical School, University of California, Los Angeles =head1 NAME Bio::Variation::SNP - submitted SNP =head1 SYNOPSIS $SNP = Bio::Variation::SNP->new (); =head1 DESCRIPTION Inherits from Bio::Variation::SeqDiff and Bio::Variation::Allele, with additional methods that are (db)SNP specific (ie, refSNP/subSNP IDs, batch IDs, validation methods). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR Allen Day E<lt>allenday@ucla.eduE<gt> =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Variation::SNP; use strict; use vars qw($AUTOLOAD); use Bio::Root::Root; use base qw(Bio::Variation::SeqDiff Bio::Variation::Allele); =head2 get/set-able methods Usage : $is = $snp->method() Function: for getting/setting attributes Returns : a value. probably a scalar. Args : if you're trying to set an attribute, pass in the new value. Methods: -------- id type observed seq_5 seq_3 ncbi_build ncbi_chr_hits ncbi_ctg_hits ncbi_seq_loc ucsc_build ucsc_chr_hits ucsc_ctg_hits heterozygous heterozygous_SE validated genotype handle batch_id method locus_id symbol mrna protein functional_class =cut #' my %OK_AUTOLOAD = ( id => '', type => '', observed => [], seq_5 => '', seq_3 => '', ncbi_build => '', ncbi_chr_hits => '', ncbi_ctg_hits => '', ncbi_seq_loc => '', ucsc_build => '', ucsc_chr_hits => '', ucsc_ctg_hits => '', heterozygous => '', heterozygous_SE => '', validated => '', genotype => '', handle => '', batch_id => '', method => '', locus_id => '', symbol => '', mrna => '', protein => '', functional_class => '', ); sub AUTOLOAD { my $self = shift; my $param = $AUTOLOAD; $param =~ s/.*:://; $self->throw(__PACKAGE__." doesn't implement $param") unless defined $OK_AUTOLOAD{$param}; if( ref $OK_AUTOLOAD{$param} eq 'ARRAY' ) { push @{$self->{$param}}, shift if @_; return $self->{$param}->[scalar(@{$self->{$param}}) - 1]; } else { $self->{$param} = shift if @_; return $self->{$param}; } } #foreach my $slot (keys %RWSLOT){ # no strict "refs"; #add class methods to package # *$slot = sub { # shift; # $RWSLOT{$slot} = shift if @_; # return $RWSLOT{$slot}; # }; #} =head2 is_subsnp Title : is_subsnp Usage : $is = $snp->is_subsnp() Function: returns 1 if $snp is a subSNP Returns : 1 or undef Args : NONE =cut sub is_subsnp { return shift->{is_subsnp}; } =head2 subsnp Title : subsnp Usage : $subsnp = $snp->subsnp() Function: returns the currently active subSNP of $snp Returns : Bio::Variation::SNP Args : NONE =cut sub subsnp { my $self = shift; return $self->{subsnps}->[ scalar($self->each_subsnp) - 1 ]; } =head2 add_subsnp Title : add_subsnp Usage : $subsnp = $snp->add_subsnp() Function: pushes the previous value returned by subsnp() onto a stack, accessible with each_subsnp(). Sets return value of subsnp() to a new Bio::Variation::SNP object, and returns that object. Returns : Bio::Varitiation::SNP Args : NONE =cut sub add_subsnp { my $self = shift; $self->throw("add_subsnp(): cannot add subSNP to subSNP, only to refSNP") if $self->is_subsnp; my $subsnp = Bio::Variation::SNP->new; push @{$self->{subsnps}}, $subsnp; $self->subsnp->{is_subsnp} = 1; return $self->subsnp; } =head2 each_subsnp Title : each_subsnp Usage : @subsnps = $snp->each_subsnp() Function: returns a list of the subSNPs of a refSNP Returns : list Args : NONE =cut sub each_subsnp { my $self = shift; $self->throw("each_subsnp(): cannot be called on a subSNP") if $self->is_subsnp; return @{$self->{subsnps}}; } 1; �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Variation/SeqDiff.pm�����������������������������������������������������������000444��000766��000024�� 60637�13155576320� 20073� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# bioperl module for Bio::Variation::SeqDiff # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code # cds_end definition? =head1 NAME Bio::Variation::SeqDiff - Container class for mutation/variant descriptions =head1 SYNOPSIS $seqDiff = Bio::Variation::SeqDiff->new ( -id => $M20132, -alphabet => 'rna', -gene_symbol => 'AR' -chromosome => 'X', -numbering => 'coding' ); # get a DNAMutation object somehow $seqDiff->add_Variant($dnamut); print $seqDiff->sys_name(), "\n"; =head1 DESCRIPTION SeqDiff stores Bio::Variation::VariantI object references and descriptive information common to all changes in a sequence. Mutations are understood to be any kind of sequence markers and are expected to occur in the same chromosome. See L<Bio::Variation::VariantI> for details. The methods of SeqDiff are geared towards describing mutations in human genes using gene-based coordinate system where 'A' of the initiator codon has number 1 and the one before it -1. This is according to conventions of human genetics. There will be class Bio::Variation::Genotype to describe markers in different chromosomes and diploid genototypes. Classes implementing Bio::Variation::VariantI interface are Bio::Variation::DNAMutation, Bio::Variation::RNAChange, and Bio::Variation::AAChange. See L<Bio::Variation::VariantI>, L<Bio::Variation::DNAMutation>, L<Bio::Variation::RNAChange>, and L<Bio::Variation::AAChange> for more information. Variant objects can be added using two ways: an array passed to the constructor or as individual Variant objects with add_Variant method. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 CONTRIBUTORS Eckhard Lehmann, ecky@e-lehmann.de =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Variation::SeqDiff; use strict; use Bio::Tools::CodonTable; use Bio::PrimarySeq; use base qw(Bio::Root::Root); =head2 new Title : new Usage : $seqDiff = Bio::Variation::SeqDiff->new; Function: generates a new Bio::Variation::SeqDiff Returns : reference to a new object of class SeqDiff Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my($id, $sysname, $trivname, $chr, $gene_symbol, $desc, $alphabet, $numbering, $offset, $rna_offset, $rna_id, $cds_end, $dna_ori, $dna_mut, $rna_ori, $rna_mut, $aa_ori, $aa_mut #@variants, @genes ) = $self->_rearrange([qw(ID SYSNAME TRIVNAME CHR GENE_SYMBOL DESC ALPHABET NUMBERING OFFSET RNA_OFFSET RNA_ID CDS_END DNA_ORI DNA_MUT RNA_ORI AA_ORI AA_MUT )], @args); #my $make = $self->SUPER::_initialize(@args); $id && $self->id($id); $sysname && $self->sysname($sysname); $trivname && $self->trivname($trivname); $chr && $self->chromosome($chr); $gene_symbol && $self->gene_symbol($chr); $desc && $self->description($desc); $alphabet && $self->alphabet($alphabet); $numbering && $self->numbering($numbering); $offset && $self->offset($offset); $rna_offset && $self->rna_offset($rna_offset); $rna_id && $self->rna_id($rna_id); $cds_end && $self->cds_end($cds_end); $dna_ori && $self->dna_ori($dna_ori); $dna_mut && $self->dna_mut($dna_mut); $rna_ori && $self->rna_ori($rna_ori); $rna_mut && $self->rna_mut($rna_mut); $aa_ori && $self->aa_ori ($aa_ori); $aa_mut && $self->aa_mut ($aa_mut); $self->{ 'variants' } = []; #@variants && push(@{$self->{'variants'}},@variants); $self->{ 'genes' } = []; #@genes && push(@{$self->{'genes'}},@genes); return $self; # success - we hope! } =head2 id Title : id Usage : $obj->id(H0001); $id = $obj->id(); Function: Sets or returns the id of the seqDiff. Should be used to give the collection of variants a UID without semantic associations. Example : Returns : value of id, a scalar Args : newvalue (optional) =cut sub id { my ($self,$value) = @_; if (defined $value) { $self->{'id'} = $value; } else { return $self->{'id'}; } } =head2 sysname Title : sysname Usage : $obj->sysname('5C>G'); $sysname = $obj->sysname(); Function: Sets or returns the systematic name of the seqDiff. The name should follow the HUGO Mutation Database Initiative approved nomenclature. If called without first setting the value, will generate it from L<Bio::Variation::DNAMutation> objects attached. Example : Returns : value of sysname, a scalar Args : newvalue (optional) =cut sub sysname { my ($self,$value) = @_; if (defined $value) { $self->{'sysname'} = $value; } elsif (not defined $self->{'sysname'}) { my $sysname = ''; my $c = 0; foreach my $mut ($self->each_Variant) { if( $mut->isa('Bio::Variation::DNAMutation') ) { $c++; if ($c == 1 ) { $sysname = $mut->sysname ; } else { $sysname .= ";". $mut->sysname; } } } $sysname = "[". $sysname. "]" if $c > 1; $self->{'sysname'} = $sysname; } return $self->{'sysname'}; } =head2 trivname Title : trivname Usage : $obj->trivname('[A2G;T56G]'); $trivname = $obj->trivname(); Function: Sets or returns the trivial name of the seqDiff. The name should follow the HUGO Mutation Database Initiative approved nomenclature. If called without first setting the value, will generate it from L<Bio::Variation::AAChange> objects attached. Example : Returns : value of trivname, a scalar Args : newvalue (optional) =cut sub trivname { my ($self,$value) = @_; if (defined $value) { $self->{'trivname'} = $value; } elsif (not defined $self->{'trivname'}) { my $trivname = ''; my $c = 0; foreach my $mut ($self->each_Variant) { if( $mut->isa('Bio::Variation::AAChange') ) { $c++; if ($c == 1 ) { $trivname = $mut->trivname ; } else { $trivname .= ";". $mut->trivname; } } } $trivname = "[". $trivname. "]" if $c > 1; $self->{'trivname'} = $trivname; } else { return $self->{'trivname'}; } } =head2 chromosome Title : chromosome Usage : $obj->chromosome('X'); $chromosome = $obj->chromosome(); Function: Sets or returns the chromosome ("linkage group") of the seqDiff. Example : Returns : value of chromosome, a scalar Args : newvalue (optional) =cut sub chromosome { my ($self,$value) = @_; if (defined $value) { $self->{'chromosome'} = $value; } else { return $self->{'chromosome'}; } } =head2 gene_symbol Title : gene_symbol Usage : $obj->gene_symbol('FOS'); $gene_symbol = $obj->gene_symbol; Function: Sets or returns the gene symbol for the studied CDS. Example : Returns : value of gene_symbol, a scalar Args : newvalue (optional) =cut sub gene_symbol { my ($self,$value) = @_; if (defined $value) { $self->{'gene_symbol'} = $value; } else { return $self->{'gene_symbol'}; } } =head2 description Title : description Usage : $obj->description('short description'); $descr = $obj->description(); Function: Sets or returns the short description of the seqDiff. Example : Returns : value of description, a scalar Args : newvalue (optional) =cut sub description { my ($self,$value) = @_; if (defined $value) { $self->{'description'} = $value; } else { return $self->{'description'}; } } =head2 alphabet Title : alphabet Usage : if( $obj->alphabet eq 'dna' ) { /Do Something/ } Function: Returns the type of primary reference sequence being one of 'dna', 'rna' or 'protein'. This is case sensitive. Returns : a string either 'dna','rna','protein'. Args : none =cut sub alphabet { my ($self,$value) = @_; my %type = (dna => 1, rna => 1, protein => 1); if( defined $value ) { if ($type{$value}) { $self->{'alphabet'} = $value; } else { $self->throw("$value is not valid alphabet value!"); } } return $self->{'alphabet'}; } =head2 numbering Title : numbering Usage : $obj->numbering('coding'); $numbering = $obj->numbering(); Function: Sets or returns the string giving the numbering schema used to describe the variants. Example : Returns : value of numbering, a scalar Args : newvalue (optional) =cut sub numbering { my ($self,$value) = @_; if (defined $value) { $self->{'numbering'} = $value; } else { return $self->{'numbering'}; } } =head2 offset Title : offset Usage : $obj->offset(124); $offset = $obj->offset(); Function: Sets or returns the offset from the beginning of the DNA sequence to the coordinate start used to describe variants. Typically the beginning of the coding region of the gene. The cds_start should be 1 + offset. Example : Returns : value of offset, a scalar Args : newvalue (optional) =cut sub offset { my ($self,$value) = @_; if (defined $value) { $self->{'offset'} = $value; } elsif (not defined $self->{'offset'} ) { return $self->{'offset'} = 0; } else { return $self->{'offset'}; } } =head2 cds_start Title : cds_start Usage : $obj->cds_start(123); $cds_start = $obj->cds_start(); Function: Sets or returns the cds_start from the beginning of the DNA sequence to the coordinate start used to describe variants. Typically the beginning of the coding region of the gene. Needs to be and is implemented as 1 + offset. Example : Returns : value of cds_start, a scalar Args : newvalue (optional) =cut sub cds_start { my ($self,$value) = @_; if (defined $value) { $self->{'offset'} = $value - 1; } else { return $self->{'offset'} + 1; } } =head2 cds_end Title : cds_end Usage : $obj->cds_end(321); $cds_end = $obj->cds_end(); Function: Sets or returns the position of the last nucleotitide of the termination codon. The coordinate system starts from cds_start. Example : Returns : value of cds_end, a scalar Args : newvalue (optional) =cut sub cds_end { my ($self,$value) = @_; if (defined $value) { $self->{'cds_end'} = $value; } else { return $self->{'cds_end'}; #$self->{'cds_end'} = CORE::length($self->SeqDiff->rna_ori)/3; } } =head2 rna_offset Title : rna_offset Usage : $obj->rna_offset(124); $rna_offset = $obj->rna_offset(); Function: Sets or returns the rna_offset from the beginning of the RNA sequence to the coordinate start used to describe variants. Typically the beginning of the coding region of the gene. Example : Returns : value of rna_offset, a scalar Args : newvalue (optional) =cut sub rna_offset { my ($self,$value) = @_; if (defined $value) { $self->{'rna_offset'} = $value; } elsif (not defined $self->{'rna_offset'} ) { return $self->{'rna_offset'} = 0; } else { return $self->{'rna_offset'}; } } =head2 rna_id Title : rna_id Usage : $obj->rna_id('transcript#3'); $rna_id = $obj->rna_id(); Function: Sets or returns the ID for original RNA sequence of the seqDiff. Example : Returns : value of rna_id, a scalar Args : newvalue (optional) =cut sub rna_id { my ($self,$value) = @_; if (defined $value) { $self->{'rna_id'} = $value; } else { return $self->{'rna_id'}; } } =head2 add_Variant Title : add_Variant Usage : $obj->add_Variant($variant) Function: Pushes one Bio::Variation::Variant into the list of variants. At the same time, creates a link from the Variant to SeqDiff using its SeqDiff method. Example : Returns : 1 when succeeds, 0 for failure. Args : Variant object =cut sub add_Variant { my ($self,$value) = @_; if (defined $value) { if( ! $value->isa('Bio::Variation::VariantI') ) { $self->throw("Is not a VariantI complying object but a [$self]"); return 0; } else { push(@{$self->{'variants'}},$value); $value->SeqDiff($self); return 1; } } else { return 0; } } =head2 each_Variant Title : each_Variant Usage : $obj->each_Variant(); Function: Returns a list of Variants. Example : Returns : list of Variants Args : none =cut sub each_Variant{ my ($self,@args) = @_; return @{$self->{'variants'}}; } =head2 add_Gene Title : add_Gene Usage : $obj->add_Gene($gene) Function: Pushes one L<Bio::LiveSeq::Gene> into the list of genes. Example : Returns : 1 when succeeds, 0 for failure. Args : Bio::LiveSeq::Gene object See L<Bio::LiveSeq::Gene> for more information. =cut sub add_Gene { my ($self,$value) = @_; if (defined $value) { if( ! $value->isa('Bio::LiveSeq::Gene') ) { $value->throw("Is not a Bio::LiveSeq::Gene object but a [$value]"); return 0; } else { push(@{$self->{'genes'}},$value); return 1; } } else { return 0; } } =head2 each_Gene Title : each_Gene Usage : $obj->each_Gene(); Function: Returns a list of L<Bio::LiveSeq::Gene>s. Example : Returns : list of Genes Args : none =cut sub each_Gene{ my ($self,@args) = @_; return @{$self->{'genes'}}; } =head2 dna_ori Title : dna_ori Usage : $obj->dna_ori('atgctgctgctgct'); $dna_ori = $obj->dna_ori(); Function: Sets or returns the original DNA sequence string of the seqDiff. Example : Returns : value of dna_ori, a scalar Args : newvalue (optional) =cut sub dna_ori { my ($self,$value) = @_; if (defined $value) { $self->{'dna_ori'} = $value; } else { return $self->{'dna_ori'}; } } =head2 dna_mut Title : dna_mut Usage : $obj->dna_mut('atgctggtgctgct'); $dna_mut = $obj->dna_mut(); Function: Sets or returns the mutated DNA sequence of the seqDiff. If sequence has not been set generates it from the original sequence and DNA mutations. Example : Returns : value of dna_mut, a scalar Args : newvalue (optional) =cut sub dna_mut { my ($self,$value) = @_; if (defined $value) { $self->{'dna_mut'} = $value; } else { $self->_set_dnamut() unless $self->{'dna_mut'}; return $self->{'dna_mut'}; } } sub _set_dnamut { my $self = shift; return unless $self->{'dna_ori'} && $self->each_Variant; $self->{'dna_mut'} = $self->{'dna_ori'}; foreach ($self->each_Variant) { next unless $_->isa('Bio::Variation::DNAMutation'); next unless $_->isMutation; my ($s, $la, $le); #lies the mutation less than 25 bases after the start of sequence? if ($_->start < 25) { $s = 0; $la = $_->start - 1; } else { $s = $_->start - 25; $la = 25; } #is the mutation an insertion? $_->end($_->start) unless $_->allele_ori->seq; #does the mutation end greater than 25 bases before the end of #sequence? if (($_->end + 25) > length($self->{'dna_mut'})) { $le = length($self->{'dna_mut'}) - $_->end; } else { $le = 25; } $_->dnStreamSeq(substr($self->{'dna_mut'}, $s, $la)); $_->upStreamSeq(substr($self->{'dna_mut'}, $_->end, $le)); my $s_ori = $_->dnStreamSeq . $_->allele_ori->seq . $_->upStreamSeq; my $s_mut = $_->dnStreamSeq . $_->allele_mut->seq . $_->upStreamSeq; (my $str = $self->{'dna_mut'}) =~ s/$s_ori/$s_mut/; $self->{'dna_mut'} = $str; } } =head2 rna_ori Title : rna_ori Usage : $obj->rna_ori('atgctgctgctgct'); $rna_ori = $obj->rna_ori(); Function: Sets or returns the original RNA sequence of the seqDiff. Example : Returns : value of rna_ori, a scalar Args : newvalue (optional) =cut sub rna_ori { my ($self,$value) = @_; if (defined $value) { $self->{'rna_ori'} = $value; } else { return $self->{'rna_ori'}; } } =head2 rna_mut Title : rna_mut Usage : $obj->rna_mut('atgctggtgctgct'); $rna_mut = $obj->rna_mut(); Function: Sets or returns the mutated RNA sequence of the seqDiff. Example : Returns : value of rna_mut, a scalar Args : newvalue (optional) =cut sub rna_mut { my ($self,$value) = @_; if (defined $value) { $self->{'rna_mut'} = $value; } else { return $self->{'rna_mut'}; } } =head2 aa_ori Title : aa_ori Usage : $obj->aa_ori('MAGVLL*'); $aa_ori = $obj->aa_ori(); Function: Sets or returns the original protein sequence of the seqDiff. Example : Returns : value of aa_ori, a scalar Args : newvalue (optional) =cut sub aa_ori { my ($self,$value) = @_; if (defined $value) { $self->{'aa_ori'} = $value; } else { return $self->{'aa_ori'}; } } =head2 aa_mut Title : aa_mut Usage : $obj->aa_mut('MA*'); $aa_mut = $obj->aa_mut(); Function: Sets or returns the mutated protein sequence of the seqDiff. Example : Returns : value of aa_mut, a scalar Args : newvalue (optional) =cut sub aa_mut { my ($self,$value) = @_; if (defined $value) { $self->{'aa_mut'} = $value; } else { return $self->{'aa_mut'}; } } =head2 seqobj Title : seqobj Usage : $dnaobj = $obj->seqobj('dna_mut'); Function: Returns the any original or mutated sequences as a Bio::PrimarySeq object. Example : Returns : Bio::PrimarySeq object for the requested sequence Args : string, method name for the sequence requested See L<Bio::PrimarySeq> for more information. =cut sub seqobj { my ($self,$value) = @_; my $out; my %valid_obj = map {$_, 1} qw(dna_ori rna_ori aa_ori dna_mut rna_mut aa_mut); $valid_obj{$value} || $self->throw("Sequence type '$value' is not a valid type (". join(',', map "'$_'", sort keys %valid_obj) .") lowercase"); my ($alphabet) = $value =~ /([^_]+)/; my $id = $self->id; $id = $self->rna_id if $self->rna_id; $alphabet = 'protein' if $alphabet eq 'aa'; $out = Bio::PrimarySeq->new ( '-seq' => $self->{$value}, '-display_id' => $id, '-accession_number' => $self->id, '-alphabet' => $alphabet ) if $self->{$value} ; return $out; } =head2 alignment Title : alignment Usage : $obj->alignment Function: Returns a pretty RNA/AA sequence alignment from linked objects. Under construction: Only simple coding region point mutations work. Example : Returns : Args : none =cut sub alignment { my $self = shift; my (@entry, $text); my $maxflanklen = 12; foreach my $mut ($self->each_Variant) { if( $mut->isa('Bio::Variation::RNAChange') ) { my $upflank = $mut->upStreamSeq; my $dnflank = $mut->dnStreamSeq; my $cposd = $mut->codon_pos; my $rori = $mut->allele_ori->seq; my $rmut = $mut->allele_mut->seq; my $rseqoriu = ''; my $rseqmutu = ''; my $rseqorid = ''; my $rseqmutd = ''; my $aaseqmutu = ''; my (@rseqori, @rseqmut ); # point if ($mut->DNAMutation->label =~ /point/) { if ($cposd == 1 ) { my $nt2d = substr($dnflank, 0, 2); push @rseqori, $rori. $nt2d; push @rseqmut, uc ($rmut). $nt2d; $dnflank = substr($dnflank, 2); } elsif ($cposd == 2) { my $ntu = chop $upflank; my $ntd = substr($dnflank, 0, 1); push @rseqori, $ntu. $rori. $ntd; push @rseqmut, $ntu. uc ($rmut). $ntd; $dnflank = substr($dnflank, 1); } elsif ($cposd == 3) { my $ntu1 = chop $upflank; my $ntu2 = chop $upflank; push (@rseqori, $ntu2. $ntu1. $rori); push (@rseqmut, $ntu2. $ntu1. uc $rmut); } } #deletion elsif ($mut->DNAMutation->label =~ /deletion/) { if ($cposd == 2 ) { $rseqorid = chop $upflank; $rseqmutd = $rseqorid; } for (my $i=1; $i<=$mut->length; $i++) { my $ntd .= substr($mut->allele_ori, $i-1, 1); $rseqorid .= $ntd; if (length($rseqorid) == 3 ) { push (@rseqori, $rseqorid); push (@rseqmut, " "); $rseqorid = ''; } } if ($rseqorid) { $rseqorid .= substr($dnflank, 0, 3-$rseqorid); push (@rseqori, $rseqorid); push (@rseqmut, " "); $dnflank = substr($dnflank,3-$rseqorid); } } $upflank = reverse $upflank; # loop throught the flanks for (my $i=1; $i<=length($dnflank); $i++) { last if $i > $maxflanklen; my $ntd .= substr($dnflank, $i-1, 1); my $ntu .= substr($upflank, $i-1, 1); $rseqmutd .= $ntd; $rseqorid .= $ntd; $rseqmutu = $ntu. $rseqmutu; $rseqoriu = $ntu. $rseqoriu; if (length($rseqorid) == 3 and length($rseqorid) == 3) { push (@rseqori, $rseqorid); push (@rseqmut, $rseqmutd); $rseqorid = $rseqmutd =''; } if (length($rseqoriu) == 3 and length($rseqoriu) == 3) { unshift (@rseqori, $rseqoriu); unshift (@rseqmut, $rseqmutu); $rseqoriu = $rseqmutu =''; } #print "|i=$i, $cposd, $rseqmutd, $rseqorid\n"; #print "|i=$i, $cposu, $rseqmutu, $rseqoriu\n\n"; } push (@rseqori, $rseqorid); unshift (@rseqori, $rseqoriu); push (@rseqmut, $rseqmutd); unshift (@rseqmut, $rseqmutu); return unless $mut->AAChange; #translate my $tr = Bio::Tools::CodonTable->new('-id' => $mut->codon_table); my $apos = $mut->AAChange->start; my $aposmax = CORE::length($self->aa_ori); #terminator codon no my $rseqori; my $rseqmut; my $aaseqori; my $aaseqmut = ""; for (my $i = 0; $i <= $#rseqori; $i++) { my $a = ''; $a = $tr->translate($rseqori[$i]) if length($rseqori[$i]) == 3; if (length($a) != 1 or $apos - ( $maxflanklen/2 -1) + $i < 1 or $apos - ( $maxflanklen/2 -1) + $i > $aposmax ) { $aaseqori .= " "; } else { $aaseqori .= " ". $a. " "; } my $b = ''; if (length($rseqmut[$i]) == 3) { if ($rseqmut[$i] eq ' ') { $b = "_"; } else { $b = $tr->translate($rseqmut[$i]); } } if (( $b ne $a and length($b) == 1 and $apos - ( $maxflanklen/2 -1) + $i >= 1 ) or ( $apos - ( $maxflanklen/2 -1) + $i >= $aposmax and $mut->label =~ 'termination') ) { $aaseqmut .= " ". $b. " "; } else { $aaseqmut .= " "; } if ($i == 0 and length($rseqori[$i]) != 3) { my $l = 3 - length($rseqori[$i]); $rseqori[$i] = (" " x $l). $rseqori[$i]; $rseqmut[$i] = (" " x $l). $rseqmut[$i]; } $rseqori .= $rseqori[$i]. " " if $rseqori[$i] ne ''; $rseqmut .= $rseqmut[$i]. " " if $rseqmut[$i] ne ''; } # collect the results push (@entry, "\n" ); $text = " ". $aaseqmut; push (@entry, $text ); $text = "Variant : ". $rseqmut; push (@entry, $text ); $text = "Reference: ". $rseqori; push (@entry, $text ); $text = " ". $aaseqori; push (@entry, $text ); push (@entry, "\n" ); } } my $res; foreach my $line (@entry) { $res .= "$line\n"; } return $res; } 1; �������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Variation/VariantI.pm����������������������������������������������������������000444��000766��000024�� 65346�13155576320� 20271� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# # BioPerl module for Bio::Variation::VariantI # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Variation::VariantI - Sequence Change SeqFeature abstract class =head1 SYNOPSIS #get Bio::Variant::VariantI somehow print $var->restriction_changes, "\n"; foreach $allele ($var->each_Allele) { #work on Bio::Variation::Allele objects } =head1 DESCRIPTION This superclass defines common methods to basic sequence changes. The instantiable classes Bio::Variation::DNAMutation, Bio::Variation::RNAChange and Bio::Variation::AAChange use them. See L<Bio::Variation::DNAMutation>, L<Bio::Variation::RNAChange>, and L<Bio::Variation::AAChange> for more information. These classes store information, heavy computation to determine allele sequences is done elsewhere. The database cross-references are implemented as Bio::Annotation::DBLink objects. The methods to access them are defined in Bio::DBLinkContainerI. See L<Bio::Annotation::DBLink> and L<Bio::DBLinkContainerI> for details. Bio::Variation::VariantI redifines and extends Bio::SeqFeature::Generic for sequence variations. This class describes specific sequence change events. These events are always from a specific reference sequence to something different. See L<Bio::SeqFeature::Generic> for more information. IMPORTANT: The notion of reference sequence permeates all Bio::Variation classes. This is especially important to remember when dealing with Alleles. In a polymorphic site, there can be a large number of alleles. One of then has to be selected to be the reference allele (allele_ori). ALL the rest has to be passed to the Variant using the method add_Allele, including the mutated allele in a canonical mutation. The IO modules and generated attributes depend on it. They ignore the allele linked to using allele_mut and circulate each Allele returned by each_Allele into allele_mut and calculate the changes between that and allele_ori. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Variation::VariantI; use strict; # Object preamble - inheritance use base qw(Bio::Root::Root Bio::SeqFeature::Generic Bio::DBLinkContainerI); =head2 id Title : id Usage : $obj->id Function: Read only method. Returns the id of the variation object. The id is the id of the first DBLink object attached to this object. Example : Returns : scalar Args : none =cut sub id { my ($self) = @_; my @ids = $self->each_DBLink; my $id = $ids[0] if scalar @ids > 0; return $id->database. "::". $id->primary_id if $id; } =head2 add_Allele Title : add_Allele Usage : $self->add_Allele($allele) Function: Adds one Bio::Variation::Allele into the list of alleles. Note that the method forces the convention that nucleotide sequence is in lower case and amino acds are in upper case. Example : Returns : 1 when succeeds, 0 for failure. Args : Allele object =cut sub add_Allele { my ($self,$value) = @_; if (defined $value) { if( ! $value->isa('Bio::Variation::Allele') ) { my $com = ref $value; $self->throw("Is not a Allele object but a [$com]"); return 0; } else { if ( $self->isa('Bio::Variation::AAChange') ) { $value->seq( uc $value->seq) if $value->seq; } else { $value->seq( lc $value->seq) if $value->seq; } push(@{$self->{'alleles'}},$value); $self->allele_mut($value); #???? return 1; } } else { return 0; } } =head2 each_Allele Title : alleles Usage : $obj->each_Allele(); Function: Returns a list of Bio::Variation::Allele objects Example : Returns : list of Alleles Args : none =cut sub each_Allele{ my ($self,@args) = @_; return @{$self->{'alleles'}}; } =head2 isMutation Title : isMutation Usage : print join('/', $obj->each_Allele) if not $obj->isMutation; Function: Returns or sets the boolean value indicating that the variant described is a canonical mutation with two alleles assinged to be the original (wild type) allele and mutated allele, respectively. If this value is not set, it is assumed that the Variant describes polymorphisms. Returns : a boolean =cut sub isMutation { my ($self,$value) = @_; if (defined $value) { if ($value ) { $self->{'isMutation'} = 1; } else { $self->{'isMutation'} = 0; } } return $self->{'isMutation'}; } =head2 allele_ori Title : allele_ori Usage : $obj->allele_ori(); Function: Links to and returns the Bio::Variation::Allele object. If value is not set, returns false. All other Alleles are compared to this. Amino acid sequences are stored in upper case characters, others in lower case. Example : Returns : string Args : string See L<Bio::Variation::Allele> for more. =cut sub allele_ori { my ($self,$value) = @_; if( defined $value) { if ( ! ref $value || ! $value->isa('Bio::Variation::Allele')) { $self->throw("Value is not Bio::Variation::Allele but [$value]"); } else { if ( $self->isa('Bio::Variation::AAChange') ) { $value->seq( uc $value->seq) if $value->seq; } else { $value->seq( lc $value->seq) if $value->seq; } $self->{'allele_ori'} = $value; } } return $self->{'allele_ori'}; } =head2 allele_mut Title : allele_mut Usage : $obj->allele_mut(); Function: Links to and returns the Bio::Variation::Allele object. Sets and returns the mutated allele sequence. If value is not set, returns false. Amino acid sequences are stored in upper case characters, others in lower case. Example : Returns : string Args : string See L<Bio::Variation::Allele> for more. =cut sub allele_mut { my ($self,$value) = @_; if( defined $value) { if ( ! ref $value || ! $value->isa('Bio::Variation::Allele')) { $self->throw("Value is not Bio::Variation::Allele but [$value]"); } else { if ( $self->isa('Bio::Variation::AAChange') ) { $value->seq( uc $value->seq) if $value->seq; } else { $value->seq( lc $value->seq) if $value->seq; } $self->{'allele_mut'} = $value; } } return $self->{'allele_mut'}; } =head2 length Title : length Usage : $obj->length(); Function: Sets and returns the length of the affected original allele sequence. If value is not set, returns false == 0. Value 0 means that the variant position is before the start=end sequence position. (Value 1 would denote a point mutation). This follows the convension to report an insertion (2insT) in equivalent way to a corresponding deletion (2delT) (Think about indel polymorpism ATC <=> AC where the origianal state is not known ). Example : Returns : string Args : string =cut sub length { my ($self,$value) = @_; if ( defined $value) { $self->{'length'} = $value; } if ( ! exists $self->{'length'} ) { return 0; } return $self->{'length'}; } =head2 upStreamSeq Title : upStreamSeq Usage : $obj->upStreamSeq(); Function: Sets and returns upstream flanking sequence string. If value is not set, returns false. The sequence should be >=25 characters long, if possible. Example : Returns : string or false Args : string =cut sub upStreamSeq { my ($self,$value) = @_; if( defined $value) { $self->{'upstreamseq'} = $value; } return $self->{'upstreamseq'}; } =head2 dnStreamSeq Title : dnStreamSeq Usage : $obj->dnStreamSeq(); Function: Sets and returns dnstream flanking sequence string. If value is not set, returns false. The sequence should be >=25 characters long, if possible. Example : Returns : string or false Args : string =cut sub dnStreamSeq { my ($self,$value) = @_; if( defined $value) { $self->{'dnstreamseq'} = $value; } return $self->{'dnstreamseq'}; } =head2 label Title : label Usage : $obj->label(); Function: Sets and returns mutation event label(s). If value is not set, or no argument is given returns false. Each instantiable class needs to implement this method. Valid values are listed in 'Mutation event controlled vocabulary' in http://www.ebi.ac.uk/mutations/recommendations/mutevent.html. Example : Returns : string Args : string =cut sub label { my ($self,$value) = @_; $self->throw_not_implemented(); } =head2 status Title : status Usage : $obj->status() Function: Returns the status of the sequence change object. Valid values are: 'suspected' and 'proven' Example : $obj->status('proven'); Returns : scalar Args : valid string (optional, for setting) =cut sub status { my ($self,$value) = @_; my %status = (suspected => 1, proven => 1 ); if( defined $value) { $value = lc $value; if ($status{$value}) { $self->{'status'} = $value; } else { $self->throw("$value is not valid status value!"); } } if( ! exists $self->{'status'} ) { return "$self"; } return $self->{'status'}; } =head2 proof Title : proof Usage : $obj->proof() Function: Returns the proof of the sequence change object. Valid values are: 'computed' and 'experimental'. Example : $obj->proof('computed'); Returns : scalar Args : valid string (optional, for setting) =cut sub proof { my ($self,$value) = @_; my %proof = (computed => 1, experimental => 1 ); if( defined $value) { $value = lc $value; if ($proof{$value}) { $self->{'proof'} = $value; } else { $self->throw("$value is not valid proof value!"); } } return $self->{'proof'}; } =head2 region Title : region Usage : $obj->region(); Function: Sets and returns the name of the sequence region type or protein domain at this location. If value is not set, returns false. Example : Returns : string Args : string =cut sub region { my ($self,$value) = @_; if( defined $value) { $self->{'region'} = $value; } return $self->{'region'}; } =head2 region_value Title : region_value Usage : $obj->region_value(); Function: Sets and returns the name of the sequence region_value or protein domain at this location. If value is not set, returns false. Example : Returns : string Args : string =cut sub region_value { my ($self,$value) = @_; if( defined $value) { $self->{'region_value'} = $value; } return $self->{'region_value'}; } =head2 region_dist Title : region_dist Usage : $obj->region_dist(); Function: Sets and returns the distance tot the closest region (i.e. intro/exon or domain) boundary. If distance is not set, returns false. Example : Returns : integer Args : integer =cut sub region_dist { my ($self,$value) = @_; if( defined $value) { if ( not $value =~ /^[+-]?\d+$/ ) { $self->throw("[$value] for region_dist has to be an integer\n"); } else { $self->{'region_dist'} = $value; } } return $self->{'region_dist'}; } =head2 numbering Title : numbering Usage : $obj->numbering() Function: Returns the numbering chema used locating sequnce features. Valid values are: 'entry' and 'coding' Example : $obj->numbering('coding'); Returns : scalar Args : valid string (optional, for setting) =cut sub numbering { my ($self,$value) = @_; my %numbering = (entry => 1, coding => 1 ); if( defined $value) { $value = lc $value; if ($numbering{$value}) { $self->{'numbering'} = $value; } else { $self->throw("'$value' is not a valid for numbering!"); } } if( ! exists $self->{'numbering'} ) { return "$self"; } return $self->{'numbering'}; } =head2 mut_number Title : mut_number Usage : $num = $obj->mut_number; : $num = $obj->mut_number($number); Function: Returns or sets the number identifying the order in which the mutation has been issued. Numbers shouldstart from 1. If the number has never been set, the method will return '' If you want the output from IO modules look nice and, for multivariant/allele variations, make sense you better set this attribute. Returns : an integer =cut sub mut_number { my ($self,$value) = @_; if (defined $value) { $self->{'mut_number'} = $value; } unless (exists $self->{'mut_number'}) { return (''); } else { return $self->{'mut_number'}; } } =head2 SeqDiff Title : SeqDiff Usage : $mutobj = $obj->SeqDiff; : $mutobj = $obj->SeqDiff($objref); Function: Returns or sets the link-reference to the umbrella Bio::Variation::SeqDiff object. If there is no link, it will return undef Note: Adding a variant into a SeqDiff object will automatically set this value. Returns : an obj_ref or undef See L<Bio::Variation::SeqDiff> for more information. =cut sub SeqDiff { my ($self,$value) = @_; if (defined $value) { if( ! $value->isa('Bio::Variation::SeqDiff') ) { $self->throw("Is not a Bio::Variation::SeqDiff object but a [$value]"); return; } else { $self->{'seqDiff'} = $value; } } unless (exists $self->{'seqDiff'}) { return; } else { return $self->{'seqDiff'}; } } =head2 add_DBLink Title : add_DBLink Usage : $self->add_DBLink($ref) Function: adds a link object Example : Returns : Args : =cut sub add_DBLink{ my ($self,$com) = @_; if( $com && ! $com->isa('Bio::Annotation::DBLink') ) { $self->throw("Is not a link object but a [$com]"); } $com && push(@{$self->{'link'}},$com); } =head2 each_DBLink Title : each_DBLink Usage : foreach $ref ( $self->each_DBlink() ) Function: gets an array of DBlink of objects Example : Returns : Args : =cut sub each_DBLink{ my ($self) = @_; return @{$self->{'link'}}; } =head2 restriction_changes Title : restriction_changes Usage : $obj->restriction_changes(); Function: Returns a string containing a list of restriction enzyme changes of form +EcoRI, separated by commas. Strings need to be valid restriction enzyme names as stored in REBASE. allele_ori and allele_mut need to be assigned. Example : Returns : string Args : string =cut sub restriction_changes { my ($self) = @_; if (not $self->{'re_changes'}) { my %re = &_enzymes; # complain if used on AA data if ($self->isa('Bio::Variation::AAChange')) { $self->throw('Restriction enzymes do not bite polypeptides!'); } #sanity checks $self->warn('Upstream sequence is empty!') if $self->upStreamSeq eq ''; $self->warn('Downstream sequence is empty!') if $self->dnStreamSeq eq ''; # $self->warn('Original allele sequence is empty!') # if $self->allele_ori eq ''; # $self->warn('Mutated allele sequence is empty!') # if $self->allele_mut eq ''; #reuse the non empty DNA level list at RNA level if the flanks are identical #Hint: Check DNAMutation object first if ($self->isa('Bio::Variation::RNAChange') and $self->DNAMutation and $self->upStreamSeq eq $self->DNAMutation->upStreamSeq and $self->dnStreamSeq eq $self->DNAMutation->dnStreamSeq and $self->DNAMutation->restriction_changes ne '' ) { $self->{'re_changes'} = $self->DNAMutation->restriction_changes; } else { #maximum length of a type II restriction site in the current REBASE my ($le_dn) = 15; my ($le_up) = $le_dn; #reduce the flank lengths if the desired length is not available $le_dn = CORE::length ($self->dnStreamSeq) if $le_dn > CORE::length ($self->dnStreamSeq); $le_up = CORE::length ($self->upStreamSeq) if $le_up > CORE::length ($self->upStreamSeq); #Build sequence strings to compare my ($oriseq, $mutseq); $oriseq = $mutseq = substr($self->upStreamSeq, -$le_up, $le_up); $oriseq .= $self->allele_ori->seq if $self->allele_ori->seq; $mutseq .= $self->allele_mut->seq if $self->allele_mut->seq; $oriseq .= substr($self->dnStreamSeq, 0, $le_dn); $mutseq .= substr($self->dnStreamSeq, 0, $le_dn); # ... and their reverse complements my $oriseq_rev = _revcompl ($oriseq); my $mutseq_rev = _revcompl ($mutseq); # collect results into a string my $rec = ''; foreach my $enz (sort keys (%re)) { my $site = $re{$enz}; my @ori = ($oriseq=~ /$site/g); my @mut = ($mutseq=~ /$site/g); my @ori_r = ($oriseq_rev =~ /$site/g); my @mut_r = ($mutseq_rev =~ /$site/g); $rec .= '+'. $enz. ", " if (scalar @ori < scalar @mut) or (scalar @ori_r < scalar @mut_r); $rec .= '-'. $enz. ", " if (scalar @ori > scalar @mut) or (scalar @ori_r > scalar @mut_r); } $rec = substr($rec, 0, CORE::length($rec) - 2) if $rec ne ''; $self->{'re_changes'} = $rec; } } return $self->{'re_changes'} } sub _revcompl { # side effect: lower case letters my ($seq) = shift; $seq = lc $seq; $seq =~ tr/acgtrymkswhbvdnx/tgcayrkmswdvbhnx/; return CORE::reverse $seq; } sub _enzymes { #REBASE version 005 type2.005 my %enzymes = ( 'AarI' => 'cacctgc', 'AatII' => 'gacgtc', 'AccI' => 'gt[ac][gt]ac', 'AceIII' => 'cagctc', 'AciI' => 'ccgc', 'AclI' => 'aacgtt', 'AcyI' => 'g[ag]cg[ct]c', 'AflII' => 'cttaag', 'AflIII' => 'ac[ag][ct]gt', 'AgeI' => 'accggt', 'AhaIII' => 'tttaaa', 'AloI' => 'gaac[acgt][acgt][acgt][acgt][acgt][acgt]tcc', 'AluI' => 'agct', 'AlwNI' => 'cag[acgt][acgt][acgt]ctg', 'ApaBI' => 'gca[acgt][acgt][acgt][acgt][acgt]tgc', 'ApaI' => 'gggccc', 'ApaLI' => 'gtgcac', 'ApoI' => '[ag]aatt[ct]', 'AscI' => 'ggcgcgcc', 'AsuI' => 'gg[acgt]cc', 'AsuII' => 'ttcgaa', 'AvaI' => 'c[ct]cg[ag]g', 'AvaII' => 'gg[at]cc', 'AvaIII' => 'atgcat', 'AvrII' => 'cctagg', 'BaeI' => 'ac[acgt][acgt][acgt][acgt]gta[ct]c', 'BalI' => 'tggcca', 'BamHI' => 'ggatcc', 'BbvCI' => 'cctcagc', 'BbvI' => 'gcagc', 'BbvII' => 'gaagac', 'BccI' => 'ccatc', 'Bce83I' => 'cttgag', 'BcefI' => 'acggc', 'BcgI' => 'cga[acgt][acgt][acgt][acgt][acgt][acgt]tgc', 'BciVI' => 'gtatcc', 'BclI' => 'tgatca', 'BetI' => '[at]ccgg[at]', 'BfiI' => 'actggg', 'BglI' => 'gcc[acgt][acgt][acgt][acgt][acgt]ggc', 'BglII' => 'agatct', 'BinI' => 'ggatc', 'BmgI' => 'g[gt]gccc', 'BplI' => 'gag[acgt][acgt][acgt][acgt][acgt]ctc', 'Bpu10I' => 'cct[acgt]agc', 'BsaAI' => '[ct]acgt[ag]', 'BsaBI' => 'gat[acgt][acgt][acgt][acgt]atc', 'BsaXI' => 'ac[acgt][acgt][acgt][acgt][acgt]ctcc', 'BsbI' => 'caacac', 'BscGI' => 'cccgt', 'BseMII' => 'ctcag', 'BsePI' => 'gcgcgc', 'BseRI' => 'gaggag', 'BseSI' => 'g[gt]gc[ac]c', 'BsgI' => 'gtgcag', 'BsiI' => 'cacgag', 'BsiYI' => 'cc[acgt][acgt][acgt][acgt][acgt][acgt][acgt]gg', 'BsmAI' => 'gtctc', 'BsmI' => 'gaatgc', 'Bsp1407I' => 'tgtaca', 'Bsp24I' => 'gac[acgt][acgt][acgt][acgt][acgt][acgt]tgg', 'BspGI' => 'ctggac', 'BspHI' => 'tcatga', 'BspLU11I' => 'acatgt', 'BspMI' => 'acctgc', 'BspMII' => 'tccgga', 'BsrBI' => 'ccgctc', 'BsrDI' => 'gcaatg', 'BsrI' => 'actgg', 'BstEII' => 'ggt[acgt]acc', 'BstXI' => 'cca[acgt][acgt][acgt][acgt][acgt][acgt]tgg', 'BtrI' => 'cacgtc', 'BtsI' => 'gcagtg', 'Cac8I' => 'gc[acgt][acgt]gc', 'CauII' => 'cc[cg]gg', 'Cfr10I' => '[ag]ccgg[ct]', 'CfrI' => '[ct]ggcc[ag]', 'CjeI' => 'cca[acgt][acgt][acgt][acgt][acgt][acgt]gt', 'CjePI' => 'cca[acgt][acgt][acgt][acgt][acgt][acgt][acgt]tc', 'ClaI' => 'atcgat', 'CviJI' => '[ag]gc[ct]', 'CviRI' => 'tgca', 'DdeI' => 'ct[acgt]ag', 'DpnI' => 'gatc', 'DraII' => '[ag]gg[acgt]cc[ct]', 'DraIII' => 'cac[acgt][acgt][acgt]gtg', 'DrdI' => 'gac[acgt][acgt][acgt][acgt][acgt][acgt]gtc', 'DrdII' => 'gaacca', 'DsaI' => 'cc[ag][ct]gg', 'Eam1105I' => 'gac[acgt][acgt][acgt][acgt][acgt]gtc', 'EciI' => 'ggcgga', 'Eco31I' => 'ggtctc', 'Eco47III' => 'agcgct', 'Eco57I' => 'ctgaag', 'EcoNI' => 'cct[acgt][acgt][acgt][acgt][acgt]agg', 'EcoRI' => 'gaattc', 'EcoRII' => 'cc[at]gg', 'EcoRV' => 'gatatc', 'Esp3I' => 'cgtctc', 'EspI' => 'gct[acgt]agc', 'FauI' => 'cccgc', 'FinI' => 'gggac', 'Fnu4HI' => 'gc[acgt]gc', 'FnuDII' => 'cgcg', 'FokI' => 'ggatg', 'FseI' => 'ggccggcc', 'GdiII' => 'cggcc[ag]', 'GsuI' => 'ctggag', 'HaeI' => '[at]ggcc[at]', 'HaeII' => '[ag]gcgc[ct]', 'HaeIII' => 'ggcc', 'HaeIV' => 'ga[ct][acgt][acgt][acgt][acgt][acgt][ag]tc', 'HgaI' => 'gacgc', 'HgiAI' => 'g[at]gc[at]c', 'HgiCI' => 'gg[ct][ag]cc', 'HgiEII' => 'acc[acgt][acgt][acgt][acgt][acgt][acgt]ggt', 'HgiJII' => 'g[ag]gc[ct]c', 'HhaI' => 'gcgc', 'Hin4I' => 'ga[cgt][acgt][acgt][acgt][acgt][acgt][acg]tc', 'HindII' => 'gt[ct][ag]ac', 'HindIII' => 'aagctt', 'HinfI' => 'ga[acgt]tc', 'HpaI' => 'gttaac', 'HpaII' => 'ccgg', 'HphI' => 'ggtga', 'Hpy178III' => 'tc[acgt][acgt]ga', 'Hpy188I' => 'tc[acgt]ga', 'Hpy99I' => 'cg[at]cg', 'KpnI' => 'ggtacc', 'Ksp632I' => 'ctcttc', 'MaeI' => 'ctag', 'MaeII' => 'acgt', 'MaeIII' => 'gt[acgt]ac', 'MboI' => 'gatc', 'MboII' => 'gaaga', 'McrI' => 'cg[ag][ct]cg', 'MfeI' => 'caattg', 'MjaIV' => 'gt[acgt][acgt]ac', 'MluI' => 'acgcgt', 'MmeI' => 'tcc[ag]ac', 'MnlI' => 'cctc', 'MseI' => 'ttaa', 'MslI' => 'ca[ct][acgt][acgt][acgt][acgt][ag]tg', 'MstI' => 'tgcgca', 'MwoI' => 'gc[acgt][acgt][acgt][acgt][acgt][acgt][acgt]gc', 'NaeI' => 'gccggc', 'NarI' => 'ggcgcc', 'NcoI' => 'ccatgg', 'NdeI' => 'catatg', 'NheI' => 'gctagc', 'NlaIII' => 'catg', 'NlaIV' => 'gg[acgt][acgt]cc', 'NotI' => 'gcggccgc', 'NruI' => 'tcgcga', 'NspBII' => 'c[ac]gc[gt]g', 'NspI' => '[ag]catg[ct]', 'PacI' => 'ttaattaa', 'Pfl1108I' => 'tcgtag', 'PflMI' => 'cca[acgt][acgt][acgt][acgt][acgt]tgg', 'PleI' => 'gagtc', 'PmaCI' => 'cacgtg', 'PmeI' => 'gtttaaac', 'PpiI' => 'gaac[acgt][acgt][acgt][acgt][acgt]ctc', 'PpuMI' => '[ag]gg[at]cc[ct]', 'PshAI' => 'gac[acgt][acgt][acgt][acgt]gtc', 'PsiI' => 'ttataa', 'PstI' => 'ctgcag', 'PvuI' => 'cgatcg', 'PvuII' => 'cagctg', 'RleAI' => 'cccaca', 'RsaI' => 'gtac', 'RsrII' => 'cgg[at]ccg', 'SacI' => 'gagctc', 'SacII' => 'ccgcgg', 'SalI' => 'gtcgac', 'SanDI' => 'ggg[at]ccc', 'SapI' => 'gctcttc', 'SauI' => 'cct[acgt]agg', 'ScaI' => 'agtact', 'ScrFI' => 'cc[acgt]gg', 'SduI' => 'g[agt]gc[act]c', 'SecI' => 'cc[acgt][acgt]gg', 'SexAI' => 'acc[at]ggt', 'SfaNI' => 'gcatc', 'SfeI' => 'ct[ag][ct]ag', 'SfiI' => 'ggcc[acgt][acgt][acgt][acgt][acgt]ggcc', 'SgfI' => 'gcgatcgc', 'SgrAI' => 'c[ag]ccgg[ct]g', 'SimI' => 'gggtc', 'SmaI' => 'cccggg', 'SmlI' => 'ct[ct][ag]ag', 'SnaBI' => 'tacgta', 'SnaI' => 'gtatac', 'SpeI' => 'actagt', 'SphI' => 'gcatgc', 'SplI' => 'cgtacg', 'SrfI' => 'gcccgggc', 'Sse232I' => 'cgccggcg', 'Sse8387I' => 'cctgcagg', 'Sse8647I' => 'agg[at]cct', 'SspI' => 'aatatt', 'Sth132I' => 'cccg', 'StuI' => 'aggcct', 'StyI' => 'cc[at][at]gg', 'SwaI' => 'atttaaat', 'TaqI' => 'tcga', 'TaqII' => 'gaccga', 'TatI' => '[at]gtac[at]', 'TauI' => 'gc[cg]gc', 'TfiI' => 'ga[at]tc', 'TseI' => 'gc[at]gc', 'Tsp45I' => 'gt[cg]ac', 'Tsp4CI' => 'ac[acgt]gt', 'TspEI' => 'aatt', 'TspRI' => 'ca[cg]tg[acgt][acgt]', 'Tth111I' => 'gac[acgt][acgt][acgt]gtc', 'Tth111II' => 'caa[ag]ca', 'UbaGI' => 'cac[acgt][acgt][acgt][acgt]gtg', 'UbaPI' => 'cgaacg', 'VspI' => 'attaat', 'XbaI' => 'tctaga', 'XcmI' => 'cca[acgt][acgt][acgt][acgt][acgt][acgt][acgt][acgt][acgt]tgg', 'XhoI' => 'ctcgag', 'XhoII' => '[ag]gatc[ct]', 'XmaIII' => 'cggccg', 'XmnI' => 'gaa[acgt][acgt][acgt][acgt]ttc' ); return %enzymes; } 1; ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Variation/IO�������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16332� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/Bio/Variation/IO/flat.pm�����������������������������������������������������������000444��000766��000024�� 50757�13155576320� 20011� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Variation::IO::flat # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Variation::IO::flat - flat file sequence variation input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::Variation::IO class. =head1 DESCRIPTION This object can transform Bio::Variation::SeqDiff objects to and from flat file databases. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Variation::IO::flat; use strict; use Text::Wrap; use Bio::Variation::SeqDiff; use Bio::Variation::DNAMutation; use Bio::Variation::RNAChange; use Bio::Variation::AAChange; use Bio::Variation::Allele; use base qw(Bio::Variation::IO); sub new { my($class, @args) = @_; my $self = bless {}, $class; $self->_initialize(@args); return $self; } sub _initialize { my($self,@args) = @_; return unless $self->SUPER::_initialize(@args); } =head2 next Title : next Usage : $haplo = $stream->next() Function: returns the next seqDiff in the stream Returns : Bio::Variation::SeqDiff object Args : NONE =cut sub next { my( $self ) = @_; local $/ = '//'; return unless my $entry = $self->_readline; return if $entry =~ /^\s+$/; $entry =~ /\s*ID\s+\S+/ || $self->throw("We do need an ID!"); my ($id, $offset, $alphabet) = $entry =~ /\s*ID +([^:]+)..(\d+)[^\)]*.\[?([cg])?/ or $self->throw("Can't parse ID line"); # $self->throw("$1|$2|$3"); my $h =Bio::Variation::SeqDiff->new(-id => $id, -offset => $offset, ); if ($alphabet) { if ($alphabet eq 'g') { $alphabet = 'dna'; } elsif ($alphabet eq 'c') { $alphabet = 'rna'; } $h->alphabet($alphabet); } # # DNA # my @dna = split ( / DNA;/, $entry ); shift @dna; my $prevdnaobj; foreach my $dna (@dna) { $dna =~ s/Feature[ \t]+//g; ($dna) = split "RNA; ", $dna; #$self->warn("|$dna|") ; #exit; my ($mut_number, $proof, $location, $upflank, $change, $dnflank) = $dna =~ m|\W+([\d\.]+).+/proof: (\w+).+/location: ([^ \n]+).+/upflank: ([ \n\w]+).+/change: ([^ /]+).+/dnflank: ([ \n\w]+)|s; $change =~ s/[ \n]//g; my ($ori, $mut) = split /[>\|]/, $change; my ($variation_number, $change_number) = split /\./, $mut_number; #$self->warn("|$mut_number|>|$variation_number|$change_number|"); my $dnamut; if ($change_number and $change_number > 1 ) { my $a3 = Bio::Variation::Allele->new; $a3->seq($mut) if $mut; #$dnamut->add_Allele($a3); $prevdnaobj->add_Allele($a3); } else { $upflank =~ s/[ \n]//g; $dnflank =~ s/[ \n]//g; my ($region, $junk, $region_value, $junk2, $region_dist) = $dna =~ m|.+/region: ([\w\']+)(; )?(\w+)?( ?\(\+?)?(-?\d+)?|s; #my $s = join ("|", $mut_number, $proof, $location, $upflank, # $change, $dnflank, $region, $region_value, $region_dist, $1,$2,$3,$4,$5); #$self->warn($s); #exit; my ($start, $sep, $end) = $location =~ /(-?\d+)(.)?\D?(-?\d+)?/; $end = $start if not defined $end ; my ($len) = $end - $start +1; $len = 0, $start = $end if defined $sep and $sep eq '^'; my $ismut = 0; $ismut = 1 if $change =~ m/>/; $dnamut = Bio::Variation::DNAMutation->new ('-start' => $start, '-end' => $end, '-length' => $len, '-upStreamSeq' => $upflank, '-dnStreamSeq' => $dnflank, '-proof' => $proof, '-mut_number' => $mut_number ); $prevdnaobj = $dnamut; my $a1 = Bio::Variation::Allele->new; $a1->seq($ori) if $ori; $dnamut->allele_ori($a1); my $a2 = Bio::Variation::Allele->new; $a2->seq($mut) if $mut; $dnamut->add_Allele($a2); if ($ismut) { $dnamut->isMutation(1); $dnamut->allele_mut($a2); } $dnamut->region($region) if defined $region; $dnamut->region_value($region_value) if defined $region_value; $dnamut->region_dist($region_dist) if defined $region_dist; $h->add_Variant($dnamut); $dnamut->SeqDiff($h); } } # # RNA # my @rna = split ( / RNA;/, $entry ); shift @rna; my $prevrnaobj; foreach my $rna (@rna) { $rna = substr ($rna, 0, index($rna, 'Feature AA')); $rna =~ s/Feature[ \t]+//g; ($rna) = split "DNA; ", $rna; #$self->warn("|$rna|") ; my ($mut_number, $proof, $location, $upflank, $change, $dnflank) = $rna =~ m|\W+([\d\.]+).+/proof: (\w+).+/location: ([^ \n]+).+/upflank: (\w+).+/change: ([^/]+).+/dnflank: (\w+)|s ;#' my ($region, $junk, $region_value, $junk2, $region_dist) = $rna =~ m|.+/region: ([\w\']+)(; )?(\w+)?( ?\(\+?)?(-?\d+)?|s; #my $s = join ("|", $mut_number, $proof, $location, $upflank, # $change, $dnflank, $region, $region_value, $region_dist, $1,$2,$3,$4,$5); #$self->warn($s); #exit; $change =~ s/[ \n]//g; my ($ori, $mut) = split /[>\|]/, $change; my $rnamut; my ($variation_number, $change_number) = split /\./, $mut_number; if ($change_number and $change_number > 1 ) { my $a3 = Bio::Variation::Allele->new; $a3->seq($mut) if $mut; #$rnamut->add_Allele($a3); $prevrnaobj->add_Allele($a3); } else { my ($start, $sep, $end) = $location =~ /(-?\d+)(.)?\D?(-?\d+)?/; $end = $start if not defined $end ; my ($len) = $end - $start + 1; $len = 0, $start = $end if defined $sep and $sep eq '^'; my $ismut; $ismut = 1 if $change =~ m/>/; my ($codon_table) = $rna =~ m|.+/codon_table: (\d+)|s; my ($codon_pos) = $rna =~ m|.+/codon:[^;]+; ([123])|s; $rnamut = Bio::Variation::RNAChange->new ('-start' => $start, '-end' => $end, '-length' => $len, '-upStreamSeq' => $upflank, '-dnStreamSeq' => $dnflank, '-proof' => $proof, '-mut_number' => $mut_number ); $prevrnaobj = $rnamut; my $a1 = Bio::Variation::Allele->new; $a1->seq($ori) if $ori; $rnamut->allele_ori($a1); my $a2 = Bio::Variation::Allele->new; $a2->seq($mut) if $mut; $rnamut->add_Allele($a2); if ($ismut) { $rnamut->isMutation(1); $rnamut->allele_mut($a2); } $rnamut->region($region) if defined $region; $rnamut->region_value($region_value) if defined $region_value; $rnamut->region_dist($region_dist) if defined $region_dist; $rnamut->codon_table($codon_table) if $codon_table; $rnamut->codon_pos($codon_pos) if $codon_pos; $h->add_Variant($rnamut); foreach my $mut ($h->each_Variant) { if ($mut->isa('Bio::Variation::DNAMutation') ) { if ($mut->mut_number == $rnamut->mut_number) { $rnamut->DNAMutation($mut); $mut->RNAChange($rnamut); } } } } } # # AA # my @aa = split ( / AA;/, $entry ); shift @aa; my $prevaaobj; foreach my $aa (@aa) { $aa = substr ($aa, 0, index($aa, 'Feature AA')); $aa =~ s/Feature[ \t]+//g; ($aa) = split "DNA; ", $aa; #$self->warn("|$aa|") ; my ($mut_number, $proof, $location, $change) = $aa =~ m|\W+([\d\.]+).+/proof: (\w+).+/location: ([^ \n]+)./change: ([^/;]+)|s; $change =~ s/[ \n]//g; #my $s = join ("|", $mut_number, $proof, $location, $change); #$self->warn($s); #exit; $change =~ s/[ \n]//g; $change =~ s/DNA$//; my ($ori, $mut) = split /[>\|]/, $change; #print "------$location----$ori-$mut-------------\n"; my ($variation_number, $change_number) = split /\./, $mut_number; my $aamut; if ($change_number and $change_number > 1 ) { my $a3 = Bio::Variation::Allele->new; $a3->seq($mut) if $mut; $prevaaobj->add_Allele($a3); } else { my ($start, $sep, $end) = $location =~ /(-?\d+)(.)?\D?(-?\d+)?/; $end = $start if not defined $end ; my ($len) = $end - $start + 1; $len = 0, $start = $end if defined $sep and $sep eq '^'; my $ismut; $ismut = 1 if $change =~ m/>/; my ($region) = $aa =~ m|.+/region: (\w+)|s ; $aamut = Bio::Variation::AAChange->new ('-start' => $start, '-end' => $end, '-length' => $len, '-proof' => $proof, '-mut_number' => $mut_number ); $prevaaobj = $aamut; my $a1 = Bio::Variation::Allele->new; $a1->seq($ori) if $ori; $aamut->allele_ori($a1); my $a2 = Bio::Variation::Allele->new; $a2->seq($mut) if $mut; $aamut->add_Allele($a2); if ($ismut) { $aamut->isMutation(1); $aamut->allele_mut($a2); } $region && $aamut->region($region); $h->add_Variant($aamut); foreach my $mut ($h->each_Variant) { if ($mut->isa('Bio::Variation::RNAChange') ) { if ($mut->mut_number == $aamut->mut_number) { $aamut->RNAChange($mut); $mut->AAChange($aamut); } } } } } return $h; } =head2 write Title : write Usage : $stream->write(@seqDiffs) Function: writes the $seqDiff object into the stream Returns : 1 for success and 0 for error Args : Bio::Variation::SeqDiff object =cut sub write { my ($self,@h) = @_; #$columns = 75; #default for Text::Wrap my %tag = ( 'ID' => 'ID ', 'Description' => 'Description ', 'FeatureKey' => 'Feature ', 'FeatureQual' => "Feature ", 'FeatureWrap' => "Feature ", 'ErrorComment' => 'Comment ' #'Comment' => 'Comment -!-', #'CommentLine' => 'Comment ', ); if( !defined $h[0] ) { $self->throw("Attempting to write with no information!"); } foreach my $h (@h) { my @entry =(); my ($text, $tmp, $tmp2, $sep); my ($count) = 0; $text = $tag{ID}; $text .= $h->id; $text .= ":(". $h->offset; $text .= "+1" if $h->sysname =~ /-/; $text .= ")". $h->sysname; $text .= "; ". $h->trivname if $h->trivname; push (@entry, $text); #Variants need to be ordered accoding to mutation_number attribute #put them into a hash of arrays holding the Variant objects #This is necessary for cases like several distict mutations present # in the same sequence. my @allvariants = $h->each_Variant; my %variants = (); foreach my $mut ($h->each_Variant) { push @{$variants{$mut->mut_number} }, $mut; } #my ($variation_number, $change_number) = split /\./, $mut_number; foreach my $var (sort keys %variants) { #print $var, ": ", join (" ", @{$variants{$var}}), "\n"; foreach my $mut (@{$variants{$var}}) { # # DNA # if ( $mut->isa('Bio::Variation::DNAMutation') ) { #collect all non-reference alleles $self->throw("allele_ori needs to be defined in [$mut]") if not $mut->allele_ori; if ($mut->isMutation) { $sep = '>'; } else { $sep = '|'; } my @alleles = $mut->each_Allele; #push @alleles, $mut->allele_mut if $mut->allele_mut; my $count = 0; # two alleles foreach my $allele (@alleles) { $count++; my ($variation_number, $change_number) = split /\./, $mut->mut_number; if ($change_number and $change_number != $count){ $mut->mut_number("$change_number.$count"); } $mut->allele_mut($allele); push (@entry, $tag{FeatureKey}. 'DNA'. "; ". $mut->mut_number ); #label $text=$tag{FeatureQual}. '/label: '. $mut->label; push (@entry, $text); #proof if ($mut->proof) { $text = $tag{FeatureQual}. '/proof: '. $mut->proof; push (@entry, $text) ; } #location $text = $tag{FeatureQual}. '/location: '; #$mut->id. '; '. $mut->start; if ($mut->length > 1 ) {# if ($mut->end - $mut->start ) { my $l = $mut->start + $mut->length -1; $text .= $mut->start. '..'. $l; } elsif ($mut->length == 0) { my $tmp_start = $mut->start - 1; $tmp_start-- if $tmp_start == 0; $text .= $tmp_start. '^'. $mut->end; } else { $text .= $mut->start; } if ($h->alphabet && $h->alphabet eq 'dna') { $tmp = $mut->start + $h->offset; $tmp-- if $tmp <= 0; $mut->start < 1 && $tmp++; #$text.= ' ('. $h->id. '::'. $tmp; $tmp2 = $mut->end + $h->offset; if ( $mut->length > 1 ) { $mut->end < 1 && $tmp2++; $text.= ' ('. $h->id. '::'. $tmp. "..". $tmp2; } elsif ($mut->length == 0) { $tmp--; $tmp-- if $tmp == 0; $text .= ' ('. $h->id. '::'. $tmp. '^'. $tmp2; } else { $text.= ' ('. $h->id. '::'. $tmp; } $text .= ')'; } push (@entry, $text); #sequence push (@entry, $tag{FeatureQual}. '/upflank: '. $mut->upStreamSeq ); $text = ''; $text = $mut->allele_ori->seq if $mut->allele_ori->seq; $text .= $sep; $text .= $mut->allele_mut->seq if $mut->allele_mut->seq; push (@entry, wrap($tag{FeatureQual}. '/change: ', $tag{FeatureWrap}, $text) ); push (@entry, $tag{FeatureQual}. '/dnflank: '. $mut->dnStreamSeq ); #restriction enzyme if ($mut->restriction_changes ne '') { $text = $mut->restriction_changes; $text = wrap($tag{FeatureQual}. '/re_site: ', $tag{FeatureWrap}, $text); push (@entry, $text ); } #region if ($mut->region ) { $text = $tag{FeatureQual}. '/region: '. $mut->region; $text .= ';' if $mut->region_value or $mut->region_dist; $text .= ' '. $mut->region_value if $mut->region_value; if ($mut->region_dist ) { $tmp = ''; $tmp = '+' if $mut->region_dist > 1; $text .= " (". $tmp. $mut->region_dist. ')'; } push (@entry, $text); } #CpG if ($mut->CpG) { push (@entry, $tag{FeatureQual}. "/CpG" ); } } } # # RNA # elsif ($mut->isa('Bio::Variation::RNAChange') ) { #collect all non-reference alleles $self->throw("allele_ori needs to be defined in [$mut]") if not $mut->allele_ori; my @alleles = $mut->each_Allele; #push @alleles, $mut->allele_mut if $mut->allele_mut; if ($mut->isMutation) { $sep = '>'; } else { $sep = '|'; } my $count = 0; # two alleles foreach my $allele (@alleles) { $count++; my ($variation_number, $change_number) = split /\./, $mut->mut_number; if ($change_number and $change_number != $count){ $mut->mut_number("$change_number.$count"); } $mut->allele_mut($allele); push (@entry, $tag{FeatureKey}. 'RNA'. "; ". $mut->mut_number ); #label $text=$tag{FeatureQual}. '/label: '. $mut->label; push (@entry, $text); #proof if ($mut->proof) { $text = $tag{FeatureQual}. '/proof: '. $mut->proof; push (@entry, $text) ; } #location $text = $tag{FeatureQual}. '/location: ' ; if ($mut->length > 1 ) { $text .= $mut->start. '..'. $mut->end; $tmp2 = $mut->end + $h->offset; } elsif ($mut->length == 0) { my $tmp_start = $mut->start; $tmp_start--; $tmp_start-- if $tmp_start == 0; $text .= $tmp_start. '^'. $mut->end; } else { $text .= $mut->start; } if ($h->alphabet && $h->alphabet eq 'rna') { $tmp = $mut->start + $h->offset; $tmp-- if $tmp <= 0; #$mut->start < 1 && $tmp++; #$text.= ' ('. $h->id. '::'. $tmp; $tmp2 = $mut->end + $h->offset; #$mut->end < 1 && $tmp2++; if ( $mut->length > 1 ) { $text.= ' ('. $h->id. '::'. $tmp. "..". $tmp2; } elsif ($mut->length == 0) { $tmp--; $text .= ' ('. $h->id. '::'. $tmp. '^'. $tmp2; } else { $text.= ' ('. $h->id. '::'. $tmp; } $text .= ')'; } push (@entry, $text); #sequence push (@entry, $tag{FeatureQual}. '/upflank: '. $mut->upStreamSeq ); $text = ''; $text = $mut->allele_ori->seq if $mut->allele_ori->seq; $text .= $sep; $text .= $mut->allele_mut->seq if $mut->allele_mut->seq; push (@entry, wrap($tag{FeatureQual}. '/change: ', $tag{FeatureWrap}, $text) ); push (@entry, $tag{FeatureQual}. '/dnflank: '. $mut->dnStreamSeq ); #restriction if ($mut->restriction_changes ne '') { $text = $mut->restriction_changes; $text = wrap($tag{FeatureQual}. '/re_site: ', $tag{FeatureWrap}, $text); push (@entry, $text ); } #coding if ($mut->region eq 'coding') { #codon table $text = $tag{FeatureQual}. '/codon_table: '; $text .= $mut->codon_table; push (@entry, $text); #codon $text = $tag{FeatureQual}. '/codon: '. $mut->codon_ori. $sep; if ($mut->DNAMutation->label =~ /.*point/) { $text .= $mut->codon_mut; } else { $text .= '-'; } $text .= "; ". $mut->codon_pos; push (@entry, $text); } #region if ($mut->region ) { $text = $tag{FeatureQual}. '/region: '. $mut->region; $text .= ';' if $mut->region_value or $mut->region_dist; $text .= ' '. $mut->region_value if $mut->region_value; if ($mut->region_dist ) { $tmp = ''; $tmp = '+' if $mut->region_dist > 1; $text .= " (". $tmp. $mut->region_dist. ')'; } push (@entry, $text); } } } # # AA # elsif ($mut->isa('Bio::Variation::AAChange')) { #collect all non-reference alleles $self->throw("allele_ori needs to be defined in [$mut]") if not $mut->allele_ori; if ($mut->isMutation) { $sep = '>'; } else { $sep = '|'; } my @alleles = $mut->each_Allele; #push @alleles, $mut->allele_mut if $mut->allele_mut; my $count = 0; # two alleles foreach my $allele (@alleles) { $count++; my ($variation_number, $change_number) = split /\./, $mut->mut_number; if ($change_number and $change_number != $count){ $mut->mut_number("$change_number.$count"); } $mut->allele_mut($allele); push (@entry, $tag{FeatureKey}. 'AA'. "; ". $mut->mut_number ); #label $text=$tag{FeatureQual}. '/label: '. $mut->label; push (@entry, $text) ; #proof if ($mut->proof) { $text = $tag{FeatureQual}. '/proof: '. $mut->proof; push (@entry, $text) ; } #location $text = $tag{FeatureQual}. '/location: '. #$mut->id. '; '. $mut->start; $mut->start; if ($mut->length > 1 ) { $tmp = $mut->start + $mut->length -1; $text .= '..'. $tmp; } push (@entry, $text); #sequence $text = ''; $text = $mut->allele_ori->seq if $mut->allele_ori->seq; $text .= $sep; $text .= $mut->allele_mut->seq if $mut->allele_mut->seq; push (@entry, wrap($tag{FeatureQual}. '/change: ', $tag{FeatureWrap}, $text) ); #region if ($mut->region ) { $text = $tag{FeatureQual}. '/region: '. $mut->region; $text .= ';' if $mut->region_value or $mut->region_dist; $text .= ' '. $mut->region_value if $mut->region_value; if ($mut->region_dist ) { $tmp = ''; $tmp = '+' if $mut->region_dist > 1; $text .= " (". $tmp. $mut->region_dist. ')'; } push (@entry, $text); } } } } } push (@entry, "//" ); my $str = join ("\n", @entry). "\n"; $str =~ s/\t/ /g; $self->_print($str); } return 1; } 1; �����������������BioPerl-1.007002/Bio/Variation/IO/xml.pm������������������������������������������������������������000444��000766��000024�� 34660�13155576320� 17656� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# BioPerl module for Bio::Variation::IO::xml # # Please direct questions and support issues to <bioperl-l@bioperl.org> # # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Variation::IO::xml - XML sequence variation input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::Variation::IO class. =head1 DESCRIPTION This object can transform L<Bio::Variation::SeqDiff> objects to and from XML file databases. The XML format, although consistent, is still evolving. The current DTD for it is at L<http://www.ebi.ac.uk/mutations/DTDE/seqDiff.dtd>. =head1 REQUIREMENTS To use this code you need the module L<XML::Twig> which creates an interface to L<XML::Parser> to read XML and modules L<XML::Writer> and L<IO::String> to write XML out. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I<bioperl-l@bioperl.org> rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Variation::IO::xml; use vars qw($seqdiff $var $prevdnaobj $prevrnaobj $prevaaobj); use strict; use XML::Twig; use XML::Writer 0.4; use IO::String; use Bio::Variation::SeqDiff; use Bio::Variation::DNAMutation; use Bio::Variation::RNAChange; use Bio::Variation::AAChange; use Bio::Variation::Allele; use base qw(Bio::Variation::IO); # _initialize is where the heavy stuff will happen when new is called sub new { my ($class,@args) = @_; my $self = bless {}, $class; $self->_initialize(@args); return $self; } sub _initialize { my($self,@args) = @_; return unless $self->SUPER::_initialize(@args); } =head2 next Title : next Usage : $haplo = $stream->next() Function: returns the next seqDiff in the stream Returns : Bio::Variation::SeqDiff object Args : NONE =cut sub _seqDiff { my ($t, $term)= @_; $seqdiff->id( $term->att('id') ); $seqdiff->alphabet( $term->att('moltype') ); $seqdiff->offset( $term->att('offset') ); foreach my $child ($term->children) { _variant($t, $child); } } sub _variant { my ($t, $term)= @_; my $var; my $att = $term->atts(); my ($variation_number, $change_number) = split /\./, $att->{number}; # if more than two alleles if ($variation_number and $change_number and $change_number > 1 ) { my $a3 = Bio::Variation::Allele->new; $a3->seq( $term->first_child_text('allele_mut') ) if $term->first_child_text('allele_mut'); if ($term->gi eq 'DNA') { $prevdnaobj->add_Allele($a3); } elsif ($term->gi eq 'RNA') { $prevrnaobj->add_Allele($a3); } else { # AA $prevaaobj->add_Allele($a3); } } else { # create new variants if ($term->gi eq 'DNA') { $var = Bio::Variation::DNAMutation->new(); } elsif ($term->gi eq 'RNA') { $var = Bio::Variation::RNAChange->new(); } else { # AA $var = Bio::Variation::AAChange->new(); } # these are always present $var->start( $att->{start} ); $var->end( $att->{end}); $var->length($att->{len}); $var->mut_number( $att->{number}); $var->upStreamSeq($term->first_child_text('upFlank')); $var->dnStreamSeq($term->first_child_text('dnFlank')); $var->proof($term->first_child_text('proof')); # region my $region = $term->first_child('region'); if ($region) { $var->region($region->text); my $region_atts = $region->atts; $var->region_value( $region_atts->{value} ) if $region_atts->{value}; $var->region_dist( $region_atts->{dist} ) if $region_atts->{dist}; } # alleles my $a1 = Bio::Variation::Allele->new; $a1->seq($term->first_child_text('allele_ori') ) if $term->first_child_text('allele_ori'); $var->allele_ori($a1); my $a2 = Bio::Variation::Allele->new; $a2->seq($term->first_child_text('allele_mut') ) if $term->first_child_text('allele_mut'); $var->isMutation(1) if $term->att('isMutation'); $var->allele_mut($a2); $var->add_Allele($a2); $var->length( $term->att('length') ); $seqdiff->add_Variant($var); # variant specific code if ($term->gi eq 'DNA') { $prevdnaobj = $var; } elsif ($term->gi eq 'RNA') { my $codon = $term->first_child('codon'); if ($codon) { my $codon_atts = $codon->atts; $var->codon_table( $codon->att('codon_table') ) if $codon_atts->{codon_table} and $codon_atts->{codon_table} != 1; $var->codon_pos( $codon->att('codon_pos') ) if $codon_atts->{codon_pos}; } $prevdnaobj->RNAChange($var); $var->DNAMutation($prevdnaobj); $prevrnaobj = $var; } else { $prevrnaobj->AAChange($var); $var->RNAChange($prevrnaobj); $prevaaobj = $var; } } } sub next { my( $self ) = @_; local $/ = "</seqDiff>\n"; return unless my $entry = $self->_readline; # print STDERR "|$entry|"; return unless $entry =~ /^\W*<seqDiff/; $seqdiff = Bio::Variation::SeqDiff->new; # create new parser object my $twig_handlers = {'seqDiff' => \&_seqDiff }; my $t = XML::Twig->new ( TwigHandlers => $twig_handlers, KeepEncoding => 1 ); $t->parse($entry); return $seqdiff; } =head2 write Title : write Usage : $stream->write(@haplos) Function: writes the $seqDiff objects into the stream Returns : 1 for success and 0 for error Args : Bio::Variation::SeqDiff object =cut sub write { my ($self,@h) = @_; if( !defined $h[0] ) { $self->throw("Attempting to write with no information!"); } my $str; my $output = IO::String->new($str); my $w = XML::Writer->new(OUTPUT => $output, DATA_MODE => 1, DATA_INDENT => 4 ); foreach my $h (@h) { # # seqDiff # $h->alphabet || $self->throw("Moltype of the reference sequence is not set!"); my $hasAA = 0; foreach my $mut ($h->each_Variant) { $hasAA = 1 if $mut->isa('Bio::Variation::AAChange'); } if ($hasAA) { $w->startTag("seqDiff", "id" => $h->id, "moltype" => $h->alphabet, "offset" => $h->offset, "sysname" => $h->sysname, "trivname" => $h->trivname ); } else { $w->startTag("seqDiff", "id" => $h->id, "moltype" => $h->alphabet, "offset" => $h->offset, "sysname" => $h->sysname ); } my @allvariants = $h->each_Variant; #print "allvars:", scalar @allvariants, "\n"; my %variants = (); foreach my $mut ($h->each_Variant) { #print STDERR $mut->mut_number, "\t", $mut, "\t", #$mut->proof, "\t", scalar $mut->each_Allele, "\n"; push @{$variants{$mut->mut_number} }, $mut; } foreach my $var (sort keys %variants) { foreach my $mut (@{$variants{$var}}) { # # DNA # if( $mut->isa('Bio::Variation::DNAMutation') ) { $mut->isMutation(0) if not $mut->isMutation; my @alleles = $mut->each_Allele; my $count = 0; foreach my $allele (@alleles) { $count++; my ($variation_number, $change_number) = split /\./, $mut->mut_number; if ($change_number and $change_number != $count){ $mut->mut_number("$change_number.$count"); } $mut->allele_mut($allele); $w->startTag("DNA", "number" => $mut->mut_number, "start" => $mut->start, "end" => $mut->end, "length" => $mut->length, "isMutation" => $mut->isMutation ); if ($mut->label) { foreach my $label (split ', ', $mut->label) { $w->startTag("label"); $w->characters($label); $w->endTag; } } if ($mut->proof) { $w->startTag("proof"); $w->characters($mut->proof ); $w->endTag; } if ($mut->upStreamSeq) { $w->startTag("upFlank"); $w->characters($mut->upStreamSeq ); $w->endTag; } #if ( $mut->isMutation) { #if ($mut->allele_ori) { $w->startTag("allele_ori"); $w->characters($mut->allele_ori->seq) if $mut->allele_ori->seq ; $w->endTag; #} #if ($mut->allele_mut) { $w->startTag("allele_mut"); $w->characters($mut->allele_mut->seq) if $mut->allele_mut->seq; $w->endTag; #} #} if ($mut->dnStreamSeq) { $w->startTag("dnFlank"); $w->characters($mut->dnStreamSeq ); $w->endTag; } if ($mut->restriction_changes) { $w->startTag("restriction_changes"); $w->characters($mut->restriction_changes); $w->endTag; } if ($mut->region) { if($mut->region_value and $mut->region_dist) { $w->startTag("region", "value" => $mut->region_value, "dist" => $mut->region_dist ); } elsif($mut->region_value) { $w->startTag("region", "value" => $mut->region_value ); } elsif($mut->region_dist) { $w->startTag("region", "dist" => $mut->region_dist ); } else { $w->startTag("region"); } $w->characters($mut->region ); $w->endTag; } $w->endTag; #DNA } } # # RNA # elsif( $mut->isa('Bio::Variation::RNAChange') ) { $mut->isMutation(0) if not $mut->isMutation; my @alleles = $mut->each_Allele; my $count = 0; foreach my $allele (@alleles) { $count++; my ($variation_number, $change_number) = split /\./, $mut->mut_number; if ($change_number and $change_number != $count){ $mut->mut_number("$change_number.$count"); } $mut->allele_mut($allele); $w->startTag("RNA", "number" => $mut->mut_number, "start" => $mut->start, "end" => $mut->end, "length" => $mut->length, "isMutation" => $mut->isMutation ); if ($mut->label) { foreach my $label (split ', ', $mut->label) { $w->startTag("label"); $w->characters($label ); $w->endTag; } } if ($mut->proof) { $w->startTag("proof"); $w->characters($mut->proof ); $w->endTag; } if ($mut->upStreamSeq) { $w->startTag("upFlank"); $w->characters($mut->upStreamSeq ); $w->endTag; } #if ( $mut->isMutation) { if ($mut->allele_ori) { $w->startTag("allele_ori"); $w->characters($mut->allele_ori->seq) if $mut->allele_ori->seq ; $w->endTag; } if ($mut->allele_mut) { $w->startTag("allele_mut"); $w->characters($mut->allele_mut->seq) if $mut->allele_mut->seq ; $w->endTag; } #} if ($mut->dnStreamSeq) { $w->startTag("dnFlank"); $w->characters($mut->dnStreamSeq ); $w->endTag; } if ($mut->region eq 'coding') { if (! $mut->codon_mut) { $w->startTag("codon", "codon_ori" => $mut->codon_ori, "codon_pos" => $mut->codon_pos ); } else { $w->startTag("codon", "codon_ori" => $mut->codon_ori, "codon_mut" => $mut->codon_mut, "codon_pos" => $mut->codon_pos ); } $w->endTag; } if ($mut->codon_table != 1) { $w->startTag("codon_table"); $w->characters($mut->codon_table); $w->endTag; } if ($mut->restriction_changes) { $w->startTag("restriction_changes"); $w->characters($mut->restriction_changes); $w->endTag; } if ($mut->region) { if($mut->region_value and $mut->region_dist) { $w->startTag("region", "value" => $mut->region_value, "dist" => $mut->region_dist ); } elsif($mut->region_value) { $w->startTag("region", "value" => $mut->region_value ); } elsif($mut->region_dist) { $w->startTag("region", "dist" => $mut->region_dist ); } else { $w->startTag("region"); } $w->characters($mut->region ); $w->endTag; } $w->endTag; #RNA } } # # AA # elsif( $mut->isa('Bio::Variation::AAChange') ) { $mut->isMutation(0) if not $mut->isMutation; my @alleles = $mut->each_Allele; my $count = 0; foreach my $allele (@alleles) { $count++; my ($variation_number, $change_number) = split /\./, $mut->mut_number; if ($change_number and $change_number != $count){ $mut->mut_number("$change_number.$count"); } $mut->allele_mut($allele); $w->startTag("AA", "number" => $mut->mut_number, "start" => $mut->start, "end" => $mut->end, "length" => $mut->length, "isMutation" => $mut->isMutation ); if ($mut->label) { foreach my $label (split ', ', $mut->label) { $w->startTag("label"); $w->characters($label ); $w->endTag; } } if ($mut->proof) { $w->startTag("proof"); $w->characters($mut->proof ); $w->endTag; } #if ( $mut->isMutation) { if ($mut->allele_ori) { $w->startTag("allele_ori"); $w->characters($mut->allele_ori->seq) if $mut->allele_ori->seq; $w->endTag; } if ($mut->allele_mut) { $w->startTag("allele_mut"); $w->characters($mut->allele_mut->seq) if $mut->allele_mut->seq; $w->endTag; } #} if ($mut->region) { if($mut->region_value and $mut->region_dist) { $w->startTag("region", "value" => $mut->region_value, "dist" => $mut->region_dist ); } elsif($mut->region_value) { $w->startTag("region", "value" => $mut->region_value ); } elsif($mut->region_dist) { $w->startTag("region", "dist" => $mut->region_dist ); } else { $w->startTag("region"); } $w->characters($mut->region ); $w->endTag; } $w->endTag; #AA } } } } } $w->endTag; $w->end; $self->_print($str); $output = undef; return 1; } 1; ��������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator�����������������������������������������������������������������������000755��000766��000024�� 0�13155576320� 16036� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/makedoc.PL������������������������������������������������������������000555��000766��000024�� 273�13155576320� 20020� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������#!/usr/bin/perl use lib "."; use strict; require Bio::Root::Version; foreach ( @ARGV ) { `perl -pi -e 's/\\\@\\\@VERSION\\\@\\\@/$Bio::Root::Version::VERSION/g;' "$_"`; } __END__ �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator����������������������������������������������������������000755��000766��000024�� 0�13155576320� 20456� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator/Build.PL�������������������������������������������������000555��000766��000024�� 1123�13155576320� 22107� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������use strict; use warnings; use Module::Build; my $builder = Module::Build->new( module_name => 'Deobfuscator', license => 'perl', dist_author => 'Dave Messina <dave-pause@davemessina.net>', dist_version_from => 'lib/Deobfuscator.pm', script_files => ['bin/deob_index.pl',], requires => { 'Test::More' => 0, 'version' => 0, 'Class::Inspector' => 0, 'DB_File' => 0, 'CGI' => 0, }, add_to_cleanup => [ 'Deobfuscator-*' ], ); $builder->create_build_script(); ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator/Changes��������������������������������������������������000444��000766��000024�� 6751�13155576320� 22117� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������Revision history for Deobfuscator 0.0.1 Fri Apr 7 14:34:50 2006 Initial release. 0.0.2 Mon Apr 24 13:27:52 CDT 2006 NEW: Laura's cool flowchart added, which shows how the Deobfuscator works. Updated README and deob_help.html to reflect that. FIX: Cryptic "Can't close MODS file" error message rewritten. NEW: Indulged my POD formatting obsession. Again. (Lots of minor updates to the POD) NEW: Added Feedback section to deob_help.html. NEW: Added DOCUMENTATION section to README. FIX: "About the mailing lists" URL changed throughout. 0.0.3 Mon Oct 2 20:01:45 CDT 2006 FIX: change default $deob_detail_path to be a relative URL instead of having localhost hardcoded. Thanks to Jason Stajich for pointing this out. FIX: Bio::Ontology modules are no longer missing their prefix in the class list, and their methods are now shown in the lower pane as expected. Thanks to Hilmar Lapp for reporting this bug. FIX: can now handle (and ignore) VERSION POD section. FIX: missing SYNOPSIS section now handled properly. In fact, the SYNOPSIS and DESCRIPTION sections can be in reverse order now, although for consistency this is not recommended. FIX: Bug #2114: "Obfuscator doesn't show "Bio:Matrix:Generic" has been fixed. This bug turned out to afflict multiple modules, which weren't getting parsed correctly by deob_index.pl. NEW: Table cells have been padded out to get rid of that "scrunched" look. Thanks to Sendu Bala for this great suggestion. NEW: If the 'Returns' subsection of a method's documentation contains a POD L<> link, the Deobfuscator assumes this to be a package name, and wraps it in an href for display. This feature is not robust, but seems to work well enough for now. NEW: the list of classes is now sorted alphabetically depth-first, so that subclasses appear just after their parent class. Thanks to Amir Karger for noticing the strange sorting behavior. NEW: HTML page title now 'BioPerl Deobfuscator' to distinguish it from other Deobfuscators out there. Thanks to Amir Karger for suggesting this. NEW: 'No match' search string now more prominent. Yep, kudos to Amir Karger again -- another great idea! NEW: Search box caption now explicitly states that only package names can be searched. Big ups to Amir Karger for this suggestion. The ability to search method names is planned for a future version. NEW: added -x option to deob_index.pl. This allows the use of an 'excluded modules' file. This feature was added to resolve an issue with four modules which rely on external modules to compile. Class::Inspector, used by the Deobfuscator needs to load a module to traverse its inheritance tree, and modules must compile before they can be loaded. CHANGE: using short name now when traversing with File::Find to help identify excluded modules (deob_index.pl). Added since 0.0.3: NEW: deob_index.pl can now accept relative paths for BioPerl lib dir and output dir NEW: -s <version_string> option now can be passed to deob_index.pl to store a version string in packages.db which deob_interface.cgi can read and show. �����������������������BioPerl-1.007002/deobfuscator/Deobfuscator/LICENSE��������������������������������������������������000444��000766��000024�� 50101�13155576320� 21635� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������Terms of Perl itself a) the GNU General Public License as published by the Free Software Foundation; either version 1, or (at your option) any later version, or b) the "Artistic License" --------------------------------------------------------------------------- The General Public License (GPL) Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 675 Mass Ave, Cambridge, MA 02139, USA. 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Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. 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The End ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator/MANIFEST�������������������������������������������������000444��000766��000024�� 424�13155576320� 21724� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������Build.PL Changes excluded_modules.txt LICENSE MANIFEST META.yml # Will be created by "make dist" Makefile.PL README bin/deob_index.pl cgi-bin/deob_detail.cgi cgi-bin/deob_flowchart.png cgi-bin/deob_interface.cgi cgi-bin/deob_help.html lib/Deobfuscator.pm t/00.load.t t/pod.t ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator/META.yml�������������������������������������������������000444��000766��000024�� 757�13155576320� 22055� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# http://module-build.sourceforge.net/META-spec.html #XXXXXXX This is a prototype!!! It will change in the future!!! XXXXX# name: Deobfuscator version: v0.0.3 version_from: lib/Deobfuscator.pm installdirs: site requires: CGI: 0 Class::Inspector: 0 DB_File: 0 Test::More: 0 version: 0 distribution_type: module generated_by: ExtUtils::MakeMaker version 6.30 �����������������BioPerl-1.007002/deobfuscator/Deobfuscator/Makefile.PL����������������������������������������������000555��000766��000024�� 1244�13155576320� 22571� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������use strict; use warnings; use ExtUtils::MakeMaker; WriteMakefile( NAME => 'Deobfuscator', AUTHOR => 'Dave Messina <dave-pause@davemessina.net>', VERSION_FROM => 'lib/Deobfuscator.pm', ABSTRACT_FROM => 'lib/Deobfuscator.pm', EXE_FILES => ['bin/deob_index.pl',], PL_FILES => {}, PREREQ_PM => { 'Test::More' => 0, 'version' => 0, 'Class::Inspector' => 0, 'DB_File' => 0, 'CGI' => 0, }, dist => { COMPRESS => 'gzip -9f', SUFFIX => 'gz', }, clean => { FILES => 'Deobfuscator-*' }, ); ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator/README���������������������������������������������������000444��000766��000024�� 10526�13155576320� 21517� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������Deobfuscator version 0.0.3 The Deobfuscator was written to make it easier to determine the methods that are available from a given BioPerl module. BioPerl is a highly object-oriented software package, with often multiple levels of inheritance. Although each individual module is usually well documented for the methods specific to it, identifying the inherited methods is less straightforward. The Deobfuscator indexes all of the BioPerl POD documentation, taking account of the inheritance tree, and then presents all of the methods available to each module through a searchable web interface. DOCUMENTATION All of the code in this distribution have POD documentation, which can be read using the perldoc command. For example, perldoc lib/Deobfuscator.pm will show the POD documentation for the Deobfuscator module. Also, there are two files in the cgi-bin directory which may be helpful: cgi-bin/deob_help.html cgi-bin/deob_flowchart.png INSTALLATION Installation of the Deobfuscator package requires a little bit more than a typical CPAN module because there are some cgi scripts, and these need to be placed in a directory accessible to a webserver. Follow these steps to install the Deobfuscator on your system: 1) Follow the standard CPAN installation procedure to install the Deobfuscator.pm module and the deob_index.pl program. Run the following commands: perl Makefile.PL make make test make install Alternatively, to install with Module::Build, you can use the following commands: perl Build.PL ./Build ./Build test ./Build install 2) Copy the contents of the cgi-bin directory to your cgi-bin directory, or any directory from which the webserver allows scripts to be executed over the web. 3) Make sure deob_interface.cgi and deob_detail.cgi are world-executable. On a UNIX system, the command chmod o+x deob_interface.cgi deob_detail.cgi should do it. 4) Run deob_index.pl. For a default installation, run it from your webserver's cgi-bin directory. On UNIX systems, it should be something like: cd /Library/WebServer/CGI-Executables deob_index.pl /Library/Perl/5.8.6/Bio . When the command finishes, it should show you some stats on the indexing. On my system it looked like this for BioPerl 1.5.1: This indexing run found: 803 files 798 pkg_name 772 desc 788 synopsis 5660 methods If the number of files is much lower than this (like 0), then deob_index.pl may have been pointed to the wrong directory. There should also be some new files in the directory you ran it from: packages.db methods.db package_list.txt deob_index.log You can move or delete deob_index.log and the Deobfuscator should still work, but the other three files need to be in the same directory as deob_interface.cgi and deob_index.cgi unless you change the hardcoded variables in those scripts. See their documentation if you want to do that. 5) Test your installation by pointing your browser to the deob_interface.cgi script. On my system, the URL is: http://localhost/cgi-bin/deob_interface.cgi If you get an error, check the permissions on the cgi-scripts and the files that deob_index.pl created in the last step. Your webserver error log may also be helpful. If you moved any of the files outside of your webserver's cgi-bin directory, make sure that the hardcoded variables in deob_interface.cgi point to their new location. The BioPerl code itself (the modules) need to be in the @INC (PERL5LIB) of the user running the Deobfuscator itself. (Class::Inspector, used under the hood by the Deobfuscator, must be able to 'use' a module in order to find its methods.) You may need to add a 'use lib' directive at the beginning of deob_interface.cgi. 6) That should be it! As always, check the POD documentation in the individual files for more information. And if you have comments, suggesions, or problems, send an email to the BioPerl mailing list <bioperl-l@bioperl.org>. DEPENDENCIES - version Available from CPAN. - Class::Inspector Available from CPAN. - Test::Pod Available from CPAN. - BioPerl Tested with v1.5.1, but other versions should work too. Get the latest from http://www.bioperl.org. COPYRIGHT AND LICENSE Copyright (C) 2006, Dave Messina and Laura Kavanaugh This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator/excluded_modules.txt�������������������������������������000444��000766��000024�� 1175�13155576320� 24705� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������# Excluded Modules file for the BioPerl Deobfuscator # # Module to be excluded from indexing should be listed here as a path, # each on its own line. # # Blank lines and lines starting with '#' are ignored. # Module names are matched by a right-end-anchored regular expression # (i.e. /Module.pm$/ ), so the shortest unique path is probably best. # Example: Bio/Tools/pSW.pm # # $Id$ # # The modules below are excluded because they require external dependencies # to compile (e.g. bioperl-ext), and Class::Inspector can't load modules it # can't compile. Bio/SearchDist.pm Bio/Tools/AlignFactory.pm Bio/Tools/dpAlign.pm Bio/Tools/pSW.pm���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator/bin������������������������������������������������������000755��000766��000024�� 0�13155576320� 21226� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator/bin/deob_index.pl����������������������������������������000555��000766��000024�� 57216�13155576320� 24056� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������#!/usr/bin/perl # deob_index.pl # part of the Deobfuscator package # by Laura Kavanaugh and Dave Messina # # cared for by Dave Messina <dave-pause@davemessina.net> # # POD documentation - main docs before the code =head1 NAME deob_index.pl - extracts BioPerl documentation and indexes it in a database for easy retrieval =head1 VERSION This document describes deob_index.pl version 0.0.3 =head1 SYNOPSIS deob_index.pl <path to BioPerl lib> <output path> =over =item <path to BioPerl lib> a directory path pointing to the root of the BioPerl lib tree. e.g. /export/share/lib/perl5/site_perl/5.8.7/Bio/ =item <output path> where you would like deob_index.pl to put its output files. =back =head1 DESCRIPTION deob_index.pl goes through the entire BioPerl library tree looking for .pm and .pl files. For each one it finds, it tries to extract module-level POD documentation (e.g. SYNOPSIS, DESCRIPTION) and store it in a BerkeleyDB. It also tries to extract documentation for each method in the module and store that in a separate BerkeleyDB. Specific parts of the documentation for a module or method may be retrieved individually using the functions available in Deobfuscator.pm. See that module for details. While going through and trying to parse each module, deob_index.pl also reports what pieces of the documentation it can't find. For example, if a method's documentation doesn't describe the data type it returns, this script logs that information to a file. This type of automated documentation- checking could be used to standardize and improve the documentation in BioPerl. deob_index.pl creates four files: =over =item C<< package_list.txt >> A plaintext file listing each package found in the BioPerl directory that was searched. Packages are listed by their module names, such as 'Bio::SeqIO'. This file is used by L<deob_interface.cgi>. =item C<< packages.db >> A Berkeley DB, which stores package-level documentation, such as the synopsis and the description. Each key is a package name, e.g. "Bio::SeqIO", and each value string is composed of the individual pieces of the documentation kept separate by unique string record separators. The individual pieces of documentation are pulled out of the string using the get_pkg_docs function in Deobfuscator.pm. See that package for details. =item C<< methods.db >> Like packages.db, methods.db is also a Berkeley DB, except it stores various pieces of information about individual methods available to a class. Each method might have documentation about its usage, its arguments, its return values, an example, and a description of its function. Each key is the fully-qualified method name, e.g. "Bio::SeqIO::next_seq". Each value is a string containing all of the pieces of documentation concatenated together and separated by unique strings serving as record separators. The extraction of the actual documentation in these strings is handled by the get_method_docs subroutine in the Deobfuscator.pm module. See that package for details. Not all methods will have all of these types of documentation, and some methods will not have the different pieces of information clearly labeled and separated. For the latter type, deob_index.pl will try to store whatever free-form documentation that does exist, and the get_method_docs function in Deobfuscator.pm, if called without arguments, will return that documentation. =item C<< deob_index.log >> This file contains detailed information about errors encountered while trying to extract documentation during the indexing process. Each line in deob_index.log is a key-value pair describing a single parsing error. =back =head1 DIAGNOSTICS These are the parsing error codes reported in 'deob_index.log'. =head2 Package errors =over =item C<< PKG_NAME >> couldn't find the name of the package =item C<< SYNOPSIS >> couldn't find the synopsis =item C<< DESC >> couldn't find the description =item C<< METHODS >> couldn't find any methods =item C<< PKG_DUP >> This package name occurs more than once =back =head2 Method errors =over =item C<< FUNCTION >> couldn't find the function description =item C<< EXAMPLE >> couldn't find the example =item C<< ARGS >> couldn't find the method's arguments =item C<< USAGE >> couldn't find the usage statement =item C<< RETURNS >> couldn't find the return values =item C<< FREEFORM >> This method's documentation doesn't conform to the BioPerl standard of having clearly-labeled fields for title, function, example, args, usage, and returns. =item C<< METH_DUP >> This method name occurs more than once =back =head1 CONFIGURATION AND ENVIRONMENT This software requires: =over =item A working installation of the Berkeley DB The Berkeley DB comes standard with most UNIX distributions, so you may already have it installed. See L<http://www.sleepycat.com> for more information. =item BioPerl deob_index.pl recursively navigates a directory of BioPerl modules. Note that the BioPerl module directory need not be "installed"; any old location will do. See L<http://www.bioperl.org> for the latest version. =back =head1 DEPENDENCIES L<version>, L<File::Find>, L<DB_File> =head1 INCOMPATIBILITIES None reported. =head1 BUGS AND LIMITATIONS No bugs have been reported. deob_index.pl currently expects the sections of POD in a BioPerl module to be in a particular order, namely: NAME, SYNOPSIS, DESCRIPTION, CONSTRUCTORS, ... , APPENDIX. Those sections are expected to be marked with =head1 POD tags, and the documentation for each method is expected to be in =head2 sections in the APPENDIX. The order of SYNOPSIS and DESCRIPTION can be flipped, but this behavior should not be taken as encouragement to do so. Most, but not all BioPerl modules conform to this standard. Those that do not will cause deob_index.pl to report them as errors. Although the consistency of this standard is desirable for end-users of the documentation, this code probably needs to be a little bit more flexible (patches welcome!). This software has only been tested in a UNIX environment. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 SEE ALSO L<Deobfuscator>, L<deob_interface.cgi>, L<deob_detail.cgi> =head1 AUTHOR Dave Messina C<< <dave-pause@davemessina.net> >> =head1 CONTRIBUTORS =over =item Laura Kavanaugh =item David Curiel =back =head1 ACKNOWLEDGMENTS This software was developed originally at the Cold Spring Harbor Laboratory's Advanced Bioinformatics Course between Oct 12-25, 2005. Many thanks to David Curiel, who provided much-needed guidance and assistance on this project. =head1 LICENSE AND COPYRIGHT Copyright (C) 2005-6 Laura Kavanaugh and Dave Messina. All Rights Reserved. This module is free software; you may redistribute it and/or modify it under the same terms as Perl itself. See L<perlartistic>. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =cut use version; $VERSION = qv('0.0.2'); use warnings; use strict; use File::Find; use DB_File; use IO::File; use Getopt::Std; use File::Spec; # GetOpt::Std-related settings $Getopt::Std::STANDARD_HELP_VERSION = 1; getopts('s:x:'); my $DEBUG = 0; my $usage = " deob_index.pl - extracts and parses BioPerl POD and stores the info in a database. USAGE: deob_index.pl [-s bioperl-version] [-x exclude_file] <BioPerl lib dir> <output dir> where <BioPerl lib dir> is the BioPerl distribution you'd like to index e.g. /export/share/lib/perl5/site_perl/5.8.7/Bio/ and <output dir> is where the output files should be placed OPTIONS: -s user-supplied string to declare BioPerl's version (which will be displayed by deob_interface.cgi) -x excluded modules file (a module paths to skip; see POD for details) "; unless ( @ARGV == 2 ) { die $usage; } my ( $source_dir, $dest_dir ) = @ARGV; # check source_dir for full path and repair if it's a relative path unless ( File::Spec->file_name_is_absolute( $source_dir ) ) { $source_dir = File::Spec->rel2abs( $source_dir ) ; } # check dest_dir for full path and repair if it's a relative path unless ( File::Spec->file_name_is_absolute( $dest_dir ) ) { $dest_dir = File::Spec->rel2abs( $dest_dir ) ; } # NOTE: we're allowing only one source directory, but File::Find supports # passing an array of dirs. # read in an optional list of modules to exclude from indexing # - this is aimed at modules with external dependencies that are often not # - present and thus will prevent deob_interface.cgi from loading them our ($opt_s, $opt_x); my %exclude; if (defined $opt_x) { my $exclude_fh = IO::File->new($opt_x, "r") or die "couldn't open $opt_x\n"; while (<$exclude_fh>) { chomp; next if ( /^\#/ || /^\s*$/ ); # ignore comments and blank lines $exclude{$_} = 1; } print STDERR "Found ", scalar keys %exclude, " modules to be excluded.\n"; } # save a list of the BioPerl modules to a file my $list; # filehandle my $list_file = $dest_dir . "/package_list.txt"; if ( -e $list_file) { unlink($list_file); } open $list, ">$list_file" or die "deob_index.pl: couldn't open $list_file:$!\n"; my @list_holder; # hold all package names so we can sort them before writing. # record misbehaving BioPerl docs to a file my $log; # filehandle my $logfile = $dest_dir . "/deob_index.log"; open $log, ">$logfile" or die "deob_index.pl: couldn't open $logfile:$!\n"; # create databases my $meth_file = $dest_dir . '/methods.db'; if ( -e $meth_file ) { unlink($meth_file); } # remove for production? my $meth_db = create_db($meth_file) or die "deob_index.pl: couldn't create $meth_file: $!\n"; my $pkg_file = $dest_dir . '/packages.db'; if ( -e $pkg_file ) { unlink($pkg_file); } # remove for production? my $pkg_db = create_db($pkg_file) or die "deob_index.pl: couldn't create $pkg_file: $!\n"; # used to make sure we're parsing in the right order my %FLAG; # store version string in packages.db $pkg_db->{'__BioPerl_Version'} = $opt_s ? $opt_s : 'unknown'; # keep stats on our indexing my %stats = ( 'files' => 0, 'pkg_name' => 0, 'desc' => 0, 'synopsis' => 0, 'methods' => 0, ); # wanted points to the subroutine which is run on each found file # ( in this program, that subroutine is &extract_pod ) # no_chdir prevents find from chdir'ing into each subsequent directory my %FIND_OPTIONS = ( wanted => \&extract_pod);#, no_chdir => 1 ); # This is the important line - Find::File actually doing the # traversal of the directory tree. find( \%FIND_OPTIONS, $source_dir ); # sort and write out package list foreach my $sorted_pkg (sort @list_holder) { print $list $sorted_pkg, "\n"; } # store user-supplied BioPerl version number # output stats print STDOUT "\nThis indexing run found:\n"; print $log "\nThis indexing run found:\n"; foreach my $stat ( 'files', 'pkg_name', 'desc', 'synopsis', 'methods' ) { printf STDOUT "%5d %s\n", $stats{$stat}, $stat; printf $log "%5d %s\n", $stats{$stat}, $stat; } # close files and DBs untie $meth_db or die "deob_index.pl: couldn't close $meth_file: $!\n"; untie $pkg_db or die "deob_index.pl: couldn't close $pkg_file: $!\n"; close $list or die "deob_index.pl: couldn't close $list: $!\n"; close $log or die "deob_index.pl: couldn't close $log: $!\n"; my $mode = 0666; chmod($mode, $pkg_file, $meth_file, $list_file); ### Parsing subroutines ### sub extract_pod { my ($file) = $_; my $long_file = $File::Find::name; # skip if it's on our exclude list foreach my $one (keys %exclude) { if ($File::Find::name =~ /$one$/) { print STDERR "Excluding $file\n"; print $log "Excluding $file\n"; return; } } # skip unless it's a perl file that exists return unless ( $file =~ /\.PLS$/ ) or ( $file =~ /\.p[ml]$/ ); return unless -e $file; $stats{'files'}++; open my $fh, '<', $File::Find::name or die "deob_index.pl: could not read file '$file': $!\n"; # these have to be done in order my ( $pkg_name, $short_desc ) = get_pkg_name($fh); my ($synopsis, $desc); LOOP: while (my ($type, $section) = get_generic($fh) ) { if ($type eq 'synopsis') { $synopsis = $section; } elsif ($type eq 'description') { $desc = $section; } else { last LOOP; } } my $constructors = get_constructors($fh); my $methods = get_methods($fh); # record package name to our package list file if ($pkg_name) { push @list_holder, $pkg_name; } # store valid package data here my @pkg_data; # error reporting if ($pkg_name) { $stats{'pkg_name'}++; print $pkg_name, "\n" if $DEBUG == 1; } else { print $log " PKG_NAME: $long_file\n"; } if ($short_desc) { $stats{'short_desc'}++; push @pkg_data, $short_desc; print $short_desc, "\n" if $DEBUG == 1; } else { push @pkg_data, 'no short description available'; # store something print $log "SHORT_DESC: $long_file\n"; } if ($synopsis) { $stats{'synopsis'}++; print $synopsis, "\n" if $DEBUG == 1; push @pkg_data, $synopsis; } else { push @pkg_data, 'no synopsis available'; # store something print $log " SYNOPSIS: $long_file\n"; } if ($desc) { $stats{'desc'}++; print $desc, "\n" if $DEBUG == 1; push @pkg_data, $desc; } else { push @pkg_data, 'no description available'; # store something print $log " DESC: $long_file\n"; } if ($methods) { my $method_count = scalar keys %$methods; print "**** Found $method_count methods in $pkg_name\n" if $DEBUG == 2; foreach my $method ( keys %$methods ) { $stats{'methods'}++; print $method, "\n//\n" if $DEBUG == 2; } } else { print $log " METHODS: $long_file\n"; } # prepare data for databases my $pkg_record = pkg_prep(@pkg_data); my $meth_records = meth_prep( $pkg_name, $methods ); # load data in databases if ($pkg_name) { pkg_load( $pkg_db, $pkg_name, $pkg_record ); meth_load( $meth_db, $meth_records ); } } sub slurp_until_next { my ($fh) = @_; my @lines; my $prev_line = $_; LINE: while (<$fh>) { next LINE if $_ eq $prev_line; # if it's a POD directive if (/^\=/) { # reset our position to the beginning of the line # so it is seen as part of the next POD section seek $fh, -length($_), 1; last LINE; } else { push @lines, $_; } } return join q{}, @lines; } sub get_pkg_name { my ($fh) = @_; my $pkg_name; my $short_desc; LINE: while (<$fh>) { chomp; print "**", $_, "\n" if $DEBUG == 2; # grab package name # - "short desc" is the one-line description of the package if ( $_ =~ /^\=head1\s+NAME/ ) { <$fh>; my $next_line = <$fh>; ( $pkg_name, $short_desc ) = split /\s+/, $next_line, 2; $short_desc .= slurp_until_next($fh); # strip off leading dash $short_desc =~ s/^(\-)+\s+//; # strip off trailing spaces $short_desc =~ s/\s+$//; # strip any newlines $short_desc =~ s/\n/ /; print $pkg_name, "\n" if $DEBUG == 1; last LINE; } # we've hit a =head1, but it's the wrong one elsif ( $_ =~ /^\=head1\s+/ ) { last LINE; } } if ($pkg_name) { $FLAG{'pkg_name'} = 1; return $pkg_name, $short_desc; } } sub get_generic { my ($fh) = @_; my $section; LINE: while (<$fh>) { chomp; print "**", $_, "\n" if $DEBUG == 2; if ( $_ =~ /^\=head1\s+SYNOPSIS/ ) { $section = slurp_until_next($fh); if ($section) { $FLAG{'synopsis'} = 1; return ('synopsis', $section); } else { last LINE; } } elsif ( $_ =~ /^\=head1\s+DESCRIPTION/ ) { $section = slurp_until_next($fh); if ($section) { $FLAG{'description'} = 1; return ('description', $section); } else { last LINE; } } # if we hit the APPENDIX, time to stop elsif (/^\=head1\s+APPENDIX/) { # reset our position to the beginning of the line # so it is seen by the next parser seek $fh, -length($_)*2, 1; last LINE; } } } sub get_synopsis { my ($fh) = @_; my $synopsis; LINE: while (<$fh>) { chomp; print "**", $_, "\n" if $DEBUG == 2; if ( $_ =~ /^\=head1\s+SYNOPSIS/ ) { $synopsis = slurp_until_next($fh); last LINE; } # we've hit a =head1, but it's the wrong one elsif ( $_ =~ /^\=head1\s+/ ) { last LINE; } } if ($synopsis) { $FLAG{'synopsis'} = 1; return $synopsis; } } sub get_desc { my ($fh) = @_; my $desc; LINE: while (<$fh>) { chomp; print "**", $_, "\n" if $DEBUG == 2; if ($_ =~ /^=head1\s+VERSION/ ) { slurp_until_next($fh); } if ( $_ =~ /^\=head1\s+DESCRIPTION/ ) { $desc = slurp_until_next($fh); last LINE; } # we've hit a =head1, but it's the wrong one elsif ( $_ =~ /^\=head1\s+/ ) { last LINE; } } if ($desc) { $FLAG{'description'} = 1; return $desc; } } sub get_constructors { # not implemented # should return a hashref } sub get_methods { my ($fh) = @_; my %methods; # we shouldn't see any methods until after the APPENDIX my $seen_appendix = 0; # there's an '=cut' after we enter the APPENDIX # we know the method '=head2' tags will come after it my $seen_first_cut = 0; LINE: while (<$fh>) { if ( $_ =~ /^\=head1\s+APPENDIX/ ) { $seen_appendix = 1; } # this should be the first tag after the APPENDIX if ( $seen_appendix && $_ =~ /^\=cut/ ) { $seen_first_cut = 1; } # this should be a method if ( $seen_first_cut && $_ =~ /^\=head2\s+(\S+)/ ) { $methods{$1} = slurp_until_next($fh); } } # returns a hashref return \%methods; } ### Database subroutines ### sub create_db { my ($filename) = @_; my %hash; my $hashref = \%hash; tie %hash, "DB_File", $filename or die "ERROR: couldn't open $filename:$!\n"; return $hashref; } sub pkg_prep { # unique string on which to split our sub-records my $rec_sep = 'DaVe-ReC-sEp'; my $record = join $rec_sep, @_; return $record; } sub meth_prep { my ( $pkg_name, $methods ) = @_; my %records; foreach my $entry ( keys %$methods ) { my $key = $pkg_name . '::' . $entry; my $record; # what will be stored in the db my $rec_sep = 'DaVe-ReC-sEp'; # if the method conforms to the BioPerl doc spec, # we will split it into constituent pieces before storing # it in the db. If not, we store the whole thing as one lump. my $last; # for grabbing multi-line entries my %fields = ( 'title' => '', 'usage' => '', 'function' => '', 'example' => '', 'returns' => '', 'args' => '', ); my @lines = split "\n", $methods->{$entry}; foreach my $line (@lines) { if ( $line =~ /^\s+Title\s+:(.*)/ ) { next if $1 =~ /^\s+$/; $fields{'title'} = $1; $last = \$fields{'title'}; } elsif ( $line =~ /^\s+Usage\s+:(.*)/ ) { next if $1 =~ /^\s+$/; $fields{'usage'} = $1; $last = \$fields{'usage'}; } elsif ( $line =~ /^\s+Function\s?:(.*)/ ) { next if $1 =~ /^\s+$/; $fields{'function'} = $1; $last = \$fields{'function'}; } elsif ( $line =~ /^\s+Example\s+:(.*)/ ) { next if $1 =~ /^\s+$/; $fields{'example'} = $1; $last = \$fields{'example'}; } elsif ( $line =~ /^\s+Returns\s+:(.*)/ ) { next if $1 =~ /^\s+$/; $fields{'returns'} = $1; $last = \$fields{'returns'}; } elsif ( $line =~ /^\s+Args\s+:(.*)/ ) { next if $1 =~ /^\s+$/; $fields{'args'} = $1; $last = \$fields{'args'}; } # grab multi-line entries elsif ( $line =~ /^\s{8,}(\s.*)/ ) { $$last .= $1; } } # debugging if ( $DEBUG == 2 ) { print "** $entry **\n"; foreach my $field ( keys %fields ) { print STDOUT $field, "\t", $fields{$field}, "\n"; } print "\n"; } # if any of our fields have a value, store subrecords my $filled_fields = grep /\w+/, values %fields; print STDERR $key, "\t", $filled_fields, "\n" if $DEBUG == 3; if ( $filled_fields > 0 ) { if ( !$fields{'title'} ) { print $log ' TITLE: ', $key, "\n"; } if ( !$fields{'usage'} ) { print $log ' USAGE: ', $key, "\n"; } if ( !$fields{'function'} ) { print $log ' FUNCTION: ', $key, "\n"; } if ( !$fields{'example'} ) { print $log ' EXAMPLE: ', $key, "\n"; } if ( !$fields{'returns'} ) { print $log ' RETURNS: ', $key, "\n"; } if ( !$fields{'args'} ) { print $log ' ARGS: ', $key, "\n"; } # create the records to be stored in the db foreach my $field ( keys %fields ) { my $subrecord = $rec_sep . '-' . $field . '|' . $fields{$field}; $record .= $subrecord; } # store the records $records{$key} = $record; } # if no subfields, store whatever docs we do have for the method else { $record = $methods->{$entry}; print $log ' FREEFORM: ', $key, "\n"; } } return \%records; } sub pkg_load { my ( $pkg_db, $pkg_name, $record ) = @_; if ( exists $pkg_db->{$pkg_name} ) { print $log ' PKG_DUP: ', $pkg_name, "\n"; warn( "$pkg_name already exists in package db!\n", "existing record:\n$pkg_db->{$pkg_name}\n", "attempted to add:\n$record\n", ) if $DEBUG == 2; } else { $pkg_db->{$pkg_name} = $record; } } sub meth_load { my ( $meth_db, $records ) = @_; foreach my $method ( keys %$records ) { if ( exists( $meth_db->{$method} ) ) { print $log ' METH_DUP: ', $method, "\n"; warn( "$method already exists in method db!\n", "existing record:\n$meth_db->{$method}\n", "attempted to add:\n$records->{$method}\n", ) if $DEBUG == 2; } else { $meth_db->{$method} = $records->{$method}; } } } __END__ ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator/bin/run-deobfuscator-update.pl���������������������������000444��000766��000024�� 1112�13155576320� 26455� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������#!/usr/bin/perl -w use strict; my $base = '/home/websites/bioperl.org'; my $srcdir = "$base/src/git"; my $deob_index = "$base/src/Deobfuscator/bin/deob_index.pl"; my @modules = qw( bioperl-corba-client bioperl-corba-server bioperl-db bioperl-dev bioperl-ext bioperl-gui bioperl-live bioperl-microarray bioperl-network bioperl-pedigree bioperl-pipeline bioperl-pise bioperl-run ); chdir $srcdir; for my $module (@modules) { system("/usr/bin/perl $deob_index -s $module $srcdir/$module/Bio $srcdir/$module"); } exit(); ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator/cgi-bin��������������������������������������������������000755��000766��000024�� 0�13155576320� 21766� 5����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi����������������������������������000444��000766��000024�� 12354�13155576320� 25067� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������#!/usr/bin/perl -w # Deob_detail.cgi # part of the Deobfuscator package # by Laura Kavanaugh and Dave Messina # # cared for by Dave Messina <dave-pause@davemessina.net> # # POD documentation - main docs before the code =head1 NAME deob_detail.cgi - displays a web page of detailed information about a BioPerl method =head1 VERSION This document describes deob_detail.cgi version 0.0.3 =head1 SYNOPSIS This program is designed to be called by deob_interface.cgi. See L</"DESCRIPTION"> for details. To install deob_detail.cgi and the rest of the Deobfuscator package, see the README. =head1 DESCRIPTION Deob_detail.cgi is called by deob_interface.cgi when a user clicks on a method name. This program extracts the documentation about that method from the Deobfuscator Berkeley DBs and returns it in some simple HTML formatting. =head1 DIAGNOSTICS None. =head1 CONFIGURATION AND ENVIRONMENT This program expects to have the 'methods.db' and 'packages.db' files in the same directory as itself. These two files are automatically generated when L<deob_index.pl> is run. If your installation requires that they be in a different location, change the $BerkeleyDB_packages and $BerkeleyDB_methods variables below to be fully qualified paths to the db files. =head1 DEPENDENCIES L<version>, L<CGI>, L<Deobfuscator> =head1 INCOMPATIBILITIES None reported. =head1 BUGS AND LIMITATIONS No bugs have been reported. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.bioperl.org/ =head1 SEE ALSO L<Deobfuscator>, L<deob_interface.cgi>, L<deob_index.pl> =head1 AUTHOR Laura Kavanaugh =head1 CONTRIBUTORS =over =item Dave Messina C<< <dave-pause@davemessina.net> >> =item David Curiel =back =head1 ACKNOWLEDGMENTS This software was developed originally at the Cold Spring Harbor Laboratory's Advanced Bioinformatics Course between Oct 12-25, 2005. Many thanks to David Curiel, who provided much-needed guidance and assistance on this project. =head1 LICENSE AND COPYRIGHT Copyright (C) 2005-6 Laura Kavanaugh and Dave Messina. All Rights Reserved. This module is free software; you may redistribute it and/or modify it under the same terms as Perl itself. See L<perlartistic>. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =cut # Let the code begin... ## HARDCODED VALUES ## # Change these to fit your installation. use lib './lib'; my $BerkeleyDB_packages = './packages.db'; my $BerkeleyDB_methods = './methods.db'; ## You shouldn't need to change anything below here ## use version; $VERSION = qv('0.0.2'); use warnings; use strict; use CGI ':standard'; use Deobfuscator; # Open BerkeleyDBs my $packages_ref = Deobfuscator::open_db($BerkeleyDB_packages); my $methods_ref = Deobfuscator::open_db($BerkeleyDB_methods); # 'method' is the name of the method passed in from deob_interface.cgi my $class_method = param('method'); # Get all of the documentation fields out of the db my $title = Deobfuscator::get_method_docs( $methods_ref, $class_method, "title" ); if ( $title eq "0" ) { $title = "not documented"; } my $usage = Deobfuscator::get_method_docs( $methods_ref, $class_method, "usage" ); if ( $usage eq "0" ) { $usage = "not documented"; } my $function = Deobfuscator::get_method_docs( $methods_ref, $class_method, "function" ); if ( $function eq "0" ) { $function = "not documented"; } my $returns = Deobfuscator::get_method_docs( $methods_ref, $class_method, "returns" ); if ( $returns eq "0" ) { $returns = "not documented"; } my $args = Deobfuscator::get_method_docs( $methods_ref, $class_method, "args" ); if ( $args eq "0" ) { $args = "not documented"; } ### Make the output page # Start the page print header; print start_html($class_method); # Define some styles my $style1 = qq{style="border-collapse:collapse;border:solid black 1px;font-family:verdana;font-size:10px;background-color:lightgrey"}; my $style2 = qq{style="border-collapse:collapse;border:solid black 1px;font-family:verdana;font-size:10px"}; my $style3 = qq{style="border-collapse:collapse;border:solid black 1px;font-family:verdana;font-size:14px"}; # open the table print '<div style="border:solid black 1px; width:100%; height:200; overflow:auto">'; print '<table width="100%" $style3>'; print "<tr><td colspan=4><center>$class_method</center></td></tr>"; my @sections = ('Usage', 'Function', 'Returns', 'Args'); my $sec_ndx = 0; foreach my $section ($usage, $function, $returns, $args) { my $section_html = Deobfuscator::htmlify($section); print "<tr><td $style1>$sections[$sec_ndx++]</td><td $style2>$section_html</td></tr>\n"; } # close the table print "</table></div>"; # finish the page print end_html; # close BerkeleyDB Deobfuscator::close_db($BerkeleyDB_packages); Deobfuscator::close_db($BerkeleyDB_methods); __END__ ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator/cgi-bin/deob_flowchart.png�������������������������������000444��000766��000024�� 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���€(—š���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���%H���õ:sP,¤-> ����IEND®B`‚���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator/cgi-bin/deob_help.html�����������������������������������000444��000766��000024�� 4317�13155576320� 24737� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������<html> <head> <body style="font-family:verdana;font-size:14px"> <h2>What is the BioPerl Deobfuscator?</h2> <p>The Deobfuscator was written to make it easier to determine the methods that are available from a given BioPerl module.</p> <p>BioPerl is a highly object-oriented software package, with often multiple levels of inheritance. Although each individual module is usually well documented for the methods specific to it, identifying the inherited methods is less straightforward.</p> <p>The Deobfuscator indexes all of the BioPerl POD documentation, taking account of the inheritance tree, and then presents all of the methods available to each module through a searchable web interface.</p> <p>The following diagram lays out what each part of the Deobfuscator does, and how the pieces interact. For more details, see the POD documentation for Deobfuscator.pm, deob_interface.cgi, and deob_index.pl. <img src="deob_flowchart.png" ALT="a diagram showing how the Deobfuscator works" width=640 height=480 border=0> <h2>Feedback</h2> <p>Find a bug? Have a suggestion for improving the Deobfuscator or other BioPerl modules? Or better yet, have a patch you want to submit?</p> <h3>Mailing Lists</h3> <p>User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.</p> <ul> <li><a href="mailto:bioperl-l@bioperl.org">General discussion</a> <li><a href="http://bioperl.org/Support.html">About the mailing lists</a> </ul> <h3>Reporting Bugs</h3> <p>Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:</p> <ul> <li><a href="https://github.com/bioperl/bioperl-live/issues">GitHub issue tracker</a> </ul> <h2>Credits</h2> <p>This software was developed originally at the Cold Spring Harbor Laboratory's <a href="http://meetings.cshl.edu/courses/c-info05.shtml">Advanced Bioinformatics Course</a> between Oct 12-25, 2005. Many thanks to David Curiel, who provided much-needed guidance and assistance on this project.</p> <p>The BioPerl Deobfuscator was developed by Laura Kavanaugh and Dave Messina.</p> </body> </html> �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������BioPerl-1.007002/deobfuscator/Deobfuscator/cgi-bin/deob_interface.cgi�������������������������������000555��000766��000024�� 42220�13155576320� 25563� 0����������������������������������������������������������������������������������������������������ustar�00cjfields������������������������staff���������������������������000000��000000�������������������������������������������������������������������������������������������������������������������������������������������������������������������������#!/usr/bin/perl # Deob_interface.cgi # part of the Deobfuscator package # by Laura Kavanaugh and Dave Messina # # cared for by Dave Messina <dave-pause@davemessina.net> # # POD documentation - main docs before the code =head1 NAME deob_interface.cgi - a WWW user interface to the BioPerl Deobfuscator =head1 VERSION This document describes deob_interface.cgi version 0.0.3 =head1 SYNOPSIS This program is designed to be used through a web browser. To install deob_interface.cgi and the rest of the Deobfuscator package, see the README. =head1 DESCRIPTION Deob_interface.cgi provides a web-based front-end to the BioPerl Deobfuscator. It uses the Deobfuscator package to open the Berkeley databases storing the BioPerl documentation and then display a list of the available modules. A search box is also provided if the user wants to pare down the list. When a user clicks on the name of a class, deob_interface.cgi looks up the stored documentation on the methods in that class, and all of the classes that class inherits from, and displays a list of those methods. The list shows the class, return values, and usage statement for each method. A user can see more extensive documentation for a method by clicking on its name or its class's name. =head1 DIAGNOSTICS =over =item C<< Can't open list of Perl module names >> deob_interface.cgi can't locate the textfile F<package_list.txt> containing the full list of BioPerl packages. By default this file should be in the same directory as F<deob_interface.cgi>. See L</"CONFIGURATION AND ENVIRONMENT"> for more information. =item C<< Can't close list of Perl module names >> deob_interface.cgi was unsuccessful in closing the F<package_list.txt> file after reading it. This is most likely a transient filesystem error. =item C<< Unknown sort option selected in deob_interface.cgi >> In the event a sort parameter other than I<sort by class> or I<sort by method> was sent to the sorting subroutine, deob_interface.cgi will exit with a fatal error. =back =head1 CONFIGURATION AND ENVIRONMENT See the F<README> for installation instructions. There are four hardcoded variables you may need to set. Look in deob_interface.cgi for a section labeled 'SET HARDCODED VALUES HERE'. =over =item C<< $deob_detail_path >> The URL of the F<deob_detail.cgi> program. Set to L<< http://localhost/cgi-bin/deob_detail.cgi >> by default. F<deob_detail.cgi> needs to be in your webserver's F<cgi-bin> directory or some location where you are allowed to serve executable code to the web. If you are setting up the Deobfuscator package on your own machine, the default URL will probably work. Otherwise, you will need to change the URL, replacing the C<< localhost portion >> with the hostname of your webserver, and replacing C<< cgi-bin >> with the path to F<deob_detail.cgi> (starting at your webserver's root directory). =item C<< $PERLMODULES >> The textfile containing a list of the BioPerl modules. Set to F<package_list.txt> by default. F<package_list.txt> is automatically generated by the L<< deob_index.pl >> script and its name is a hardcoded value. If your copy of F<package_list.txt> has a different name or is not in the same directory as F<deob_detail.cgi>, set $PERLMODULES to the full path of F<package_list.txt>'s location. =item C<< $BerkeleyDB_packages >> The Berkeley DB file storing documentation on BioPerl packages. Set to F<packages.db> by default. F<packages.db> is automatically generated by the L<< deob_index.pl >> script and its name is a hardcoded value. If your copy of F<packages.db> has a different name or is not in the same directory as F<deob_detail.cgi>, set C<< $BerkeleyDB_packages >> to the full path of F<packages.db>'s location. =item C<< $BerkeleyDB_methods >> The Berkeley DB file storing documentation on BioPerl methods. Set to F<methods.db> by default. F<methods.db> is automatically generated by the F<deob_index.pl> script and its name is a hardcoded value. If your copy of F<methods.db> has a different name or is not in the same directory as F<deob_detail.cgi>, set C<< $BerkeleyDB_methods >> to the full path of F<methods.db>'s location. =back =head1 DEPENDENCIES L<version>, L<CGI>, L<Deobfuscator> =head1 INCOMPATIBILITIES None reported. =head1 BUGS AND LIMITATIONS =over =item C<< Selecting a class name returns no methods >> Clicking on C<< Bio::Tools::dpAlign >> or C<< Bio::Tools::AlignFactory >> in the upper class selection pane produces an empty lower methods pane. There are undoubtedly other modules that will display this behavior. Reported by Laura Kavanaugh 2006-04-18. =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 SEE ALSO L<Deobfuscator>, L<deob_detail.cgi>, L<deob_index.pl> =head1 AUTHOR Laura Kavanaugh =head1 CONTRIBUTORS =over =item Dave Messina C<< <dave-pause@davemessina.net> >> =item David Curiel =back =head1 ACKNOWLEDGMENTS This software was developed originally at the Cold Spring Harbor Laboratory's Advanced Bioinformatics Course between Oct 12-25, 2005. Many thanks to David Curiel, who provided much-needed guidance and assistance on this project. Also, special thanks to Todd Wylie for his help with CGI. =head1 LICENSE AND COPYRIGHT Copyright (C) 2005-6 Laura Kavanaugh and Dave Messina. All Rights Reserved. You may use modify or redistribute this software under the same terms as Perl itself. =head1 DISCLAIMER This module is free software; you may redistribute it and/or modify it under the same terms as Perl itself. See L<perlartistic>. =cut # Let the code begin... ## SET HARDCODED VALUES HERE ## use lib './lib'; my $PERLMODULES = 'package_list.txt'; my $BerkeleyDB_packages = 'packages.db'; my $BerkeleyDB_methods = 'methods.db'; my $help_path = 'deob_help.html'; my $deob_detail_path = 'deob_detail.cgi'; ## You shouldn't need to change anything below here ## use version; $VERSION = qv('0.0.2'); use warnings; use strict; use CGI ':standard'; use Deobfuscator; my @available_modules; my $sort_method; my $ref_Class_hash; my $filter; my $search; my $sort_order; my $pattern_found = 0; my @all_modules; my $ref_BerkeleyDB_packages; my $ref_BerkeleyDB_methods; my $ref_sorted_keys; # if user previously set the sort order, we can send it with the first form $sort_order = param('sort_order') ? param('sort_order') : 'by method'; # define some styles my $style1 = qq{style="border-collapse:collapse;border:solid black 1px;font-family:verdana;font-size:10px;background-color:lightgrey;padding:3"}; my $style2 = qq{style="border-collapse:collapse;border:solid black 1px;font-family:verdana;font-size:10px;padding:3"}; my $style3 = qq{style="border-collapse:collapse;border:solid black 1px;font-family:verdana;font-size:14px;padding:3"}; my $style4 = qq{style="border-collapse:collapse;border:0px;font-family:verdana;font-size:18px;font-weight:bold;padding:3"}; my $style5 = qq{style="font-family:verdana;font-size:14px;padding:3"}; # Open file containing all Bioperl package names open my $MODS, '<', $PERLMODULES or die "Could not read list of Perl module names '$PERLMODULES': $!\n"; # Open BerkeleyDB by getting hash references $ref_BerkeleyDB_packages = Deobfuscator::open_db($BerkeleyDB_packages); $ref_BerkeleyDB_methods = Deobfuscator::open_db($BerkeleyDB_methods); # Grab input and remove whitespace my $pattern = param('search_string') ? param('search_string') : ' '; $pattern =~ s/\s//g; # Filter file names with user search string if one has been entered while (<$MODS>) { if (/\S+/) { # capture list of all module names in case there are no # matches found to user input string push @all_modules, $_; } if ($pattern) { if (/$pattern/i) { push @available_modules, $_; $pattern_found = 1; } } else { if (/\S+/) { push @available_modules, $_; } } } if ( scalar @available_modules < 1 ) { @available_modules = @all_modules; } close $MODS or die "Could not close list of Perl module names $PERLMODULES: $!\n"; # grab BioPerl version string my $version_string = '__BioPerl_Version'; # specified in deob_index.pl my $BioPerl_version = $ref_BerkeleyDB_packages->{$version_string}; print header; print <<CSHL; <html> <head> <title>BioPerl Deobfuscator

Welcome to the BioPerl Deobfuscator

[ $BioPerl_version ]

what is it?


Search class names by string or Perl regex (examples: Bio::SeqIO, seq, fasta\$)

OR select a class from the list:
CSHL print < CSHL2 foreach my $package (@available_modules) { chomp $package; my $packageDesc = Deobfuscator::get_pkg_docs( $ref_BerkeleyDB_packages, $package, 'short_desc' ); my $link = qq{$package}; print "\n"; } print <
EOP # keep track of all our form values my $input_module = param('module'); $filter = param('Filter') ? param('Filter') : ' '; $search = param('Search'); $sort_order = param('sort_order'); # set position of sort button based on current sort order my $is_method; my $is_class; if ($sort_order) { if ($sort_order eq 'by method') { $is_method = 'selected'; $is_class = ''; } elsif ($sort_order eq 'by class') { $is_method = ''; $is_class = 'selected'; } else { $is_method = 'selected'; $is_class = ''; } } # Process user input and return result if ( param() ) { #1 # show button allowing user to set sort order print < SORT_CODE # grab sort order from form or sort by method as a default $sort_method = param('sort_order') ? param('sort_order') : 'by method'; # filter not yet implemented, so this 'if' should never be true if ( ( $filter eq "" ) && ( $input_module eq "" ) ) { print "filter = $filter
search=$search
"; print "Please select a class from the menu or enter a search \n"; print "string and press \"Filter\" button\n"; } elsif ($search) { # Determine methods available to user's input class and the class # where the methods reside. Store results in a hash. $ref_Class_hash = get_methods($input_module); # Sort the method/class data according to user input and display $ref_sorted_keys = sorting( $input_module, $sort_method, $ref_Class_hash ); # Display results display( $input_module, $ref_sorted_keys, $ref_Class_hash, $ref_BerkeleyDB_methods, $deob_detail_path ); } # filter not yet implemented, so this 'if' should never be true elsif ($filter) { if ( !($pattern_found) ) { print qq{

No match to string found, please try again

}; h1('Welcome to the BioPerl Deobfuscator!'),; } } else { print "Not sure about that input. Please submit error report\n"; } } #1 # footer print "\n"; # Close BerkeleyDB Deobfuscator::close_db($BerkeleyDB_packages); Deobfuscator::close_db($BerkeleyDB_methods); ######################## SUBROUTINES ################################# sub get_methods { #1 # Get all available methods for user input class. Deobfuscator package # returns hash with key as user input class and value as ref to array. The # array contains references to an array for each Class, method pair. This # subroutine unpacks this data structure and, for each user input class # creates a hash where the keys are a concatinated class--method pair and the # values are the method (There is method to the maddness, its just obscure). my ($user_class) = shift; my $hashref = Deobfuscator::return_methods($user_class); # Put data from Deobfuscaotr into hash so it can be sorted later according # to user specification my %Package_hash = (); foreach my $array_ref ( @{ $hashref->{$user_class} } ) { #3 my $key = $array_ref->[1] . "::" . $array_ref->[0]; $Package_hash{$key} = $array_ref->[0]; } #3 return \%Package_hash; } #1 End sub get_methods sub sorting { #1 my ( $package, $sort, $ref_hash ) = @_; my @sorted_keys; # Sort by Class or method, depending on user request if ( $sort =~ 'by class' ) { #3 # Sort by Class name (use "lc" to ensure names containing capital # letters are not sorted separately from lower case names foreach my $first ( sort { lc $a cmp lc $b } keys %$ref_hash ) { #4 $first =~ /^(.+)::/; my $package_name = $1; push @sorted_keys, $first; } #4 } elsif ( $sort =~ 'by method' ) { #3 # Sort alphabetically by method name (use "lc" in sort because some # method names are capitalized and will appear first in # an alphabetized list unless lower cased.) foreach my $first ( sort { lc $ref_hash->{$a} cmp lc $ref_hash->{$b} } keys %$ref_hash ) { #5 $first =~ /^(.+)::/; my $package_name = $1; push @sorted_keys, $first; } #5 } else { #3 die "Unknown sort option >$sort< in deob_interface.cgi::sorting()\n"; } #3 return \@sorted_keys; } #1 End sorting subroutine sub display { #1 my ( $package, $ref_sorted_array, $ref_hash, $db_hashref, $detail_path ) = @_; my $search_word; print <
$link$packageDesc
methods for $package
CSHL foreach my $first (@$ref_sorted_array) { #4 $first =~ /^(.+)::/; my $package_name = Deobfuscator::urlify_pkg($1); # Get the return values part of the documentation my $return_methods_raw = Deobfuscator::get_method_docs( $db_hashref, $first, "returns" ); if ( $return_methods_raw eq "0" ) { $return_methods_raw = "not documented"; } # Get the usage part of the documentation my $return_usage_raw = Deobfuscator::get_method_docs( $db_hashref, $first, "usage" ); if ( $return_usage_raw eq "0" ) { $return_usage_raw = "not documented"; } # clean up formatting a little my $return_methods = Deobfuscator::htmlify($return_methods_raw); my $return_usage = Deobfuscator::htmlify($return_usage_raw); # Display output my $href = $detail_path . "?method=$first"; my $link = qq{$ref_hash->{$first}}; my @columns = ( $link, $package_name, $return_methods, $return_usage ); print "\n"; } #4 print < EOP } #1 End display subroutine __END__ BioPerl-1.007002/deobfuscator/Deobfuscator/lib000755000766000024 013155576320 21224 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/deobfuscator/Deobfuscator/lib/Deobfuscator.pm000444000766000024 3421513155576320 24364 0ustar00cjfieldsstaff000000000000package Deobfuscator; # module for retrieving method-specific documentation from a # Berkeley database # # first version by Dave Messina (dmessina@watson.wustl.edu) at the # Cold Spring Harbor Laboratory Advanced Bioinformatics Course # Oct 12-25, 2005 # part of the Deobfuscator package # by Laura Kavanaugh and Dave Messina # # cared for by Dave Messina # # POD documentation - main docs before the code =head1 NAME Deobfuscator - get BioPerl method and package information from a Berkeley DB =head1 VERSION This document describes Deobfuscator version 0.0.3 =head1 SYNOPSIS use Deobfuscator; # get all the methods available to objects belonging to a class # (including those inherited from parent classes) my $hashref = Deobfuscator::return_methods('Bio::SeqIO', 'Bio::AlignIO'); # retrieve the return values for a method my $method_db_ref = Deobfuscator::open_db('methods.db'); my $ret_vals = Deobfuscator::get_method_docs( $method_db_ref, 'Bio::SeqIO::next_seq', 'returns' ); close_db($method_db_ref); # retrieve the synopsis documentation for a class my $pkg_db_ref = Deobfuscator::open_db('packages.db'); my $synopsis = Deobfuscator::get_pkg_docs( $pkg_db_ref, 'Bio::SeqIO', 'synopsis' ); close_db($pkg_db_ref); =head1 DESCRIPTION The Deobfuscator module contains functions which relate to retrieving specific types of documentation about BioPerl packages and methods. The deob_index.pl script reads through all of the BioPerl files, extracts the documentation, and stores it in two BerkeleyDB databases. This module is then used to query those databases for information about a given method or package. (see the deob_index.pl documentation for more info.) The types of information available for individual methods include: the usage statement, the return values, the arguments to give to the method, the description of the function, and an example of how to use the method. The Deobfuscator module can be used also to retrieve the synopsis and description documentation for a given class. =head1 DIAGNOSTICS =over =item C<< error: couldn't eval $module >> A package couldn't be loaded (eval'd), which would prevent us from determining what its methods are. =item C<< error: couldn't open $filename >> One of the Berkeley databases couldn't be opened. Possible causes are: deob_index.pl wasn't run and so the databases weren't created, or the database files aren't in the correct place. =item C<< error: couldn't close database >> One of the Berkeley databases couldn't be closed. This might just be a transient filesystem error. =back =item C<< error: couldn't load [module] >> The BioPerl modules aren't in the Perl lib (PERL5LIB) and so can't be searched (the Deobfuscator uses I for this. Check that the value of your PERL5LIB includes BioPerl's modules. If need be, you can set a use lub directive at the beginning of deob_interface.cgi. =back =head1 CONFIGURATION AND ENVIRONMENT This software requires: =over =item A working installation of the Berkeley DB The Berkeley DB comes standard with most UNIX distributions, so you may already have it installed. See L for more information. =item BioPerl Deobfuscator.pm recursively navigates a directory of BioPerl modules. Note that the BioPerl module directory need not be "installed"; any old location will do. See L for the latest version. =back =head1 DEPENDENCIES L, L, L =head1 INCOMPATIBILITIES None reported. =head1 BUGS AND LIMITATIONS In the current implementation, Deobfuscator does not show internal or private methods (i.e. those whose name begins with an underscore). This is simply an option in the Class::Inspector->methods call, and so could be presented as an option to the user (patches welcome). No bugs have been reported. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/Support.html - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.bioperl.org/ =head1 SEE ALSO L =head1 AUTHOR Dave Messina C<< >> =head1 CONTRIBUTORS =over =item Laura Kavanaugh =item David Curiel =back =head1 ACKNOWLEDGMENTS This software was developed originally at the Cold Spring Harbor Laboratory's Advanced Bioinformatics Course between Oct 12-25, 2005. Many thanks to David Curiel, who provided much-needed guidance and assistance on this project. =head1 LICENSE AND COPYRIGHT Copyright (C) 2005-6 Laura Kavanaugh and Dave Messina. All Rights Reserved. This module is free software; you may redistribute it and/or modify it under the same terms as Perl itself. See L. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 APPENDIX The rest of the documentation details each of the functions. Internal methods are preceded with a "_". =cut use version; $VERSION = qv('0.0.3'); use warnings; use strict; use Class::Inspector; use DB_File; use lib './lib'; =head2 return_methods Title : return_methods Usage : $methods_hashref = Deobfuscator::return_methods('Bio::AlignIO', 'Bio::SeqIO'); Function: traverses the inheritance tree for a given class to determine the methods available to objects belonging to that class Returns : a reference to a hash. The hash keys are fully-qualified class names, such as 'Bio::SeqIO'. The hash values are references to an array of hashes, where each array element is a reference to a hash containing two key-value pairs, 'method' and 'class'; Args : a list of fully-qualified class names =cut sub return_methods { my @input = @_; # key: full class name # value: a reference to an array of hashes # where each array element is a pointer to a hash # which contains two key: 'method' and 'class' my %methods_of; foreach my $class (@input) { # fancy eval so that we can loop through different modules my $retval = _load_module($class); if ($retval) { die "error: couldn't load $class: $retval\n"; } # methods returned from Class::Inspector as: # [ # [ 'Class::method1', 'Class', 'method1', \&Class::method1 ], # [ 'Another::method2', 'Another', 'method2', \&Another::method2 ], # [ 'Foo::bar', 'Foo', 'bar', \&Foo::bar ], # ] my $methods_aryref3 = Class::Inspector->methods( $class, 'expanded', 'public' ); for ( my $i = 0; $i < scalar @{$methods_aryref3}; $i++ ) { foreach my $meth ( $methods_aryref3->[$i] ) { my $method_name = $meth->[2]; my $inherited_from = $meth->[1]; push @{$methods_of{$class}}, [$method_name, $inherited_from]; } } } return \%methods_of; } =head2 print_methods Title : print_methods Usage : print_methods('Bio::AlignIO','Bio::SeqIO'); Function: traverses the inheritance tree for a given class to determine the methods available to objects belonging to that class, then pretty-prints the resulting information. Returns : nothing. But it does print to the current filehandle (usually STDOUT). Args : a list of fully-qualified class names =cut sub print_methods { my @input = @_; foreach my $class (@input) { # fancy eval so that we can loop through different modules my $retval = _load_module($class); if ($retval) { die "error: couldn't load $class: $retval\n"; } # methods returned as # [ # [ 'Class::method1', 'Class', 'method1', \&Class::method1 ], # [ 'Another::method2', 'Another', 'method2', \&Another::method2 ], # [ 'Foo::bar', 'Foo', 'bar', \&Foo::bar ], # ] my $methods_aryref3 = Class::Inspector->methods( $class, 'expanded', 'public' ); print "methods for $class\n"; print "=========================================\n"; for ( my $i = 0; $i < scalar @{$methods_aryref3}; $i++ ) { print "method $i\n"; foreach my $meth ( $methods_aryref3->[$i] ) { print "\t class: $meth->[1]\n"; print "\t method: $meth->[2]\n"; } print "--------------------------------------\n"; } } } =head2 _load_module Title : _load_module Usage : * INTERNAL USE ONLY * Function: attempts to load a module Returns : nothing. But it does die upon failure to load. Args : a module name =cut sub _load_module { my $module = shift; eval "require $module"; my $err = $@ || 'eval returned undef'; if ($@) { return $@ } else { return } } =head2 open_db Title : open_db Usage : open_db($filename) Function: opens a Berkeley DB Returns : a hashref tied to the DB Args : a filename as a scalar =cut sub open_db { my ($filename) = @_; my %hash; my $hashref = \%hash; tie %hash, "DB_File", $filename or die "error: couldn't open $filename: $!\n"; return $hashref; } =head2 close_db Title : close_db Usage : closes a Berkeley DB Function: closes a database Returns : nothing. Args : a hashref to a tied Berkeley DB =cut sub close_db { my ($hashref) = @_; untie $hashref or die "error: couldn't close database: $!\n"; } =head2 get_pkg_docs Title : get_pkg_docs Usage : get_pkg_docs($db_hashref, 'Class name', 'documentation type'); Function: returns a specified part of the documentation for a class Returns : a string containing the desired documentation or ' ' if the documentation doesn't exist Args : - $db_hashref is the ref to the hash tied to the DB - Class name is of the form 'Bio::SeqIO' - documentation type is the subfield of the method's POD. The possible values of documentation type are: short_desc, synopsis, desc =cut sub get_pkg_docs { my ($db_hashref, $pkg_name, $info_type) = @_; # hash to store our hash value, now split out into its constituent parts my %record; my $rec_sep = 'DaVe-ReC-sEp'; # if the method isn't in our db if ( ! exists($db_hashref->{$pkg_name}) ) { return 0; } # grab the constituent parts of the pkg record ( $record{'short_desc'}, $record{'synopsis'}, $record{'desc'} ) = ( split $rec_sep, $db_hashref->{$pkg_name} ); # return just the part that was asked for if ( exists($record{$info_type}) ) { return $record{$info_type}; } else { return ' '; } } =head2 get_method_docs Title : get_method_docs Usage : get_method_docs($db_hashref, 'Class+method name', 'documentation type'); Example : get_method_docs($db_hashref, 'Bio::SeqIO::next_aln', 'args'); Function: returns a specified part of the documentation for a class's method Returns : a string containing the desired documentation, or 0 if the desired documentation doesn't exist Args : - $db_hashref is the ref to the hash tied to the DB - Class+method name is of the form 'Bio::SeqIO::next_aln', where Bio::SeqIO is the class and next_aln is the method. - documentation type is the subfield of the method's POD. The possible values of documentation type are: title, usage, function, returns, args =cut sub get_method_docs { my ($db_hashref, $meth_name, $info_type) = @_; my %record; my $whole_record; my $rec_sep = 'DaVe-ReC-sEp'; # if the method isn't in our db if ( !exists( $db_hashref->{$meth_name} ) ) { return 0; } # separate the sub-records using the record separator and field tag my @parts = split $rec_sep, $db_hashref->{$meth_name}; # put individual info types into separate hash entries... foreach my $part (@parts) { if ($part =~ /^-(\w+)\|(.*)/) { $record{$1} = $2; } # ... and put the whole thing into one big string $whole_record .= "$part\n"; } # return a specific part if that was asked for if ($info_type) { # return just the part that was asked for if ( exists( $record{$info_type} ) ) { # if there's really nothing in there, say so. if ( ( $record{$info_type} =~ /^[\s\n]*$/) || ( $record{$info_type} eq '') ) { return 0; } else { return $record{$info_type}; } } # or return everything else { return $whole_record; } } # otherwise return whole record else { return $whole_record; } } =head2 htmlify Title : htmlify Usage : htmlify($string); Example : htmlify('this is a : doc); Function: does some crude reformatting of POD method documentation by swapping isolated colons (':') into HTML
tags Returns : a string Args : a string =cut sub htmlify { my ($string) = @_; # change isolated colons into
tags $string =~ s/\s:\s/
/g; # change L<> POD link into HTML link if ( $string =~ /L<(.+)>/ ) { $string = urlify_pkg($1); } return $string; } =head2 urlify_pkg Title : urlify_pkg Usage : urlify_pkg($string); Example : urlify('this is a : doc); Function: wraps a package name in an HTML href pointing to the bioperl.org pdoc docs for that package Returns : a string (an href in HTML) Args : a string =cut sub urlify_pkg { my ($pkg_name) = @_; my $bioperl_doc_url = q{http://doc.bioperl.org/bioperl-live/}; my $pkg_as_path = $pkg_name; # convert Bio::DB::RefSeq to Bio/DB/RefSeq $pkg_as_path =~ s/::/\//g; my $url = $bioperl_doc_url . $pkg_as_path . '.html'; my $href = qq{$pkg_name}; return $href; } 1; __END__ BioPerl-1.007002/deobfuscator/Deobfuscator/t000755000766000024 013155576320 20721 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/deobfuscator/Deobfuscator/t/00.load.t000444000766000024 17013155576320 22356 0ustar00cjfieldsstaff000000000000use Test::More tests => 1; BEGIN { use_ok( 'Deobfuscator' ); } diag( "Testing Deobfuscator $Deobfuscator::VERSION" ); BioPerl-1.007002/deobfuscator/Deobfuscator/t/pod.t000444000766000024 21413155576320 22002 0ustar00cjfieldsstaff000000000000#!perl -T use Test::More; eval "use Test::Pod 1.14"; plan skip_all => "Test::Pod 1.14 required for testing POD" if $@; all_pod_files_ok(); BioPerl-1.007002/examples000755000766000024 013155576320 15174 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/bioperl.pl000555000766000024 4051713155576320 17354 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl # bioperl.pl # cjm@fruitfly.org use strict; use lib '.'; no strict "vars"; use Data::Dumper; use Bio::Perl; use Bio::SeqIO; use Getopt::Long; my $h = {}; GetOptions($h, "file|f=s", ); my @cmds = get_default_cmds(); shell($h, \@cmds, @ARGV); # prepare for some seriously hacky code.... sub shell { my $h = shift; my @cmds = @{shift || []}; my @args = @_; my $prompt = $ENV{BIOPERL_PROMPT} || "BioPerl> "; my $quit = 0; my @lines = (); my $r; my $rv; my $seq; my @pseqs = (); my $seqio; my $wseqio; my $fastadb; my $options = {echo=>0, chatty=>10}; my $loadfn = $h->{'file'}; if ($loadfn) { @lines = ("load '$loadfn'"); } sub hr { print "\n===============================\n"; } sub nl { print "\n"; } sub demo { if (! -d 't/data') { print "To run the demo, you must be in the bioperl directory\n"; } @lines = split(/\n/, q[ %keep = %$options; +format '' +outformat '' +echo 1 # BioPerl shell utility - Demo # # We're now going to take a tour # through some of the features of # this tool. # # # This demo will go through some of # the major commands, feeding you # the commands as you go. all you have # to do is hit every time # you see the prompt $prompt # you will then see the output of # the command on your terminal window. # type 'q' to end the tour # at any time. # waitenter # PARSING GENBANK RECORDS # ----------------------- # to parse genbank files, use # the read_seq() method, or # simply use the '<' command. # # First of all we're going to # take a look at the file # 't/data/test.genbank' # Let's examine the file itself # using the unix command "cat" # (you can use any unix command # using the ! at the beginning # of a line) ^!cat t/data/test.genbank waitenter # Ok, you can see this is a # typical file of genbank records. # Let's get the first sequence # from the file ^seq() waitenter # # we can cycle through all the # sequences in the file using # the ',' command. ^, waitenter # this fetched the second sequence # and placed it in the $seq variable # # we can change the output format # by setting the 'outformat' parameter # like this: ^+outformat fasta ^, waitenter # now the sequences are output in # fasta format # to change to embl format: ^+outformat embl ^, waitenter # we can also fetch _all_ seqs from # a file; for this example we will # use t/data/swiss.dat, which is in # swiss format. usually bioperl can guess # the file format from the file extension # but this isn't possible here, so we # must help by setting the input format: ^+format swiss # now lets get all the sequences, like this: ^<*t/data/swiss.dat waitenter # typing <* is equivalent to # using the read_seqs() function, # like this: ^read_seqs('t/data/swiss.dat') waitenter # we now have all the sequences in # the array @seqs # we can write these all out as fasta ^+outformat fasta ^>* # we can also write these out to a file: ^>*myfile.tmp ^!cat myfile.tmp # # RANDOM ACCESS OF FASTA FILES # END +echo 0 %$options = %keep ]); @lines = map { s/^ *//; $_; } @lines; } sub error { if ($error) { print "Error:\n$error"; } else { print "No errors have been reported\n"; } } sub fmt { $options->{format} = shift if @_; print "format=$options->{format}\n"; } # should this move to Bio::Perl ? sub seqio { my $filename = shift; $options->{format} = shift if @_; if( !defined $filename ) { warn "read_sequence($filename) - usage incorrect"; } if( defined $options->{format} ) { $seqio = Bio::SeqIO->new( '-file' => $filename, '-format' => $options->{format}); } else { $seqio = Bio::SeqIO->new( '-file' => $filename); } $seqio; } sub wseqio { my $filename = shift; $options->{format} = shift if @_; my @args = (); if ($filename && $filename !~ /^\>/) { $filename = ">$filename"; } push(@args, -file => "$filename") if $filename; push(@args, -fh => \*STDOUT) unless $filename; push(@args, -format => $options->{outformat}) if $options->{outformat}; $wseqio = Bio::SeqIO->new( @args ); $wseqio; } sub show_seq { return unless $seq; if ($wseqio) { $wseqio->write_seq($seq); } else { printf "seq display id: %s\n", $seq->display_id; } } sub addseq { push(@pseqs, @_); while (scalar(@pseqs) > 50) { # todo - history variable shift @pseqs; } } sub next_seq { if ($seqio) { eval { $seq = $seqio->next_seq; }; if ($@) { $error = $@; print "There was an error getting the seq. Type 'error'\n"; print "for full details\n"; print "(Maybe you have to explicitly set the format?)"; } addseq($seq); } else { print STDERR "use read_seq first\n"; } show_seq; $seq; } sub next_seqs { @seqs = (); if ($seqio) { while ($seq = $seqio->next_seq) { printf "%s\n", $seq->display_id; push(@seqs, $seq); } } $seq = $seqs[$#seqs] if @seqs; @seqs } sub read_seq { seqio(@_); next_seq(); } sub read_seqs { seqio(@_); next_seqs(); } sub write_seq { wseqio(@_); $wseqio->write_seq($seq) if $seq; } sub write_seqs { wseqio(@_); map { $wseqio->write_seq($_) } @seqs; } sub pod { if (!-d "Bio") { print "You need to be in the bioperl directory!\n"; } else { my $mod = shift; unix("pod2text", "Bio/$mod.pm"); } } sub fastadb { require "Bio/DB/Fasta.pm"; my $f = shift; $fastadb = Bio::DB::Fasta->new($f); print "Set \$fastadb object\n"; $fastadb; } sub subseq { if (!$fastadb) { fastadb(shift); } $seq = $fastadb->get_Seq_by_id(shift); if (@_) { printf "%s\n", $seq->subseq(@_); } $seq; } sub load { open(F, shift); @lines = map {chomp;$_} ; close(F); } sub waitenter { print ""; ; } sub showintro { hr; print "This is a text-based commandline interface to BioPerl;\n"; print "\n"; } sub checkoptions { } sub showoptions { my $k = shift; my @k = defined $k ? ($k) : keys %$options; foreach my $ok ($k) { my $v = sprintf("%s", $options->{$k}); if ($v =~ /HASH/) { # hide perl internal details # from user; if they are experienced # perlhackers they can just # type "x $options" to see the # gory details $v = "undisplayable"; } printf("%20s:%s\n", $ok, $b); } } sub set { my ($k,$v) = @_; if (defined($v)) { $options->{$k} = $v; checkoptions; } else { showoptions($k); } # if ($k eq "format") { # seqio; # } if ($k eq "outformat") { wseqio; } } sub echo { my $e = shift; if (defined($e)) { set("echo", $e); } else { set("echo", !$options->{echo}); } } sub options { map {print "$_ = $options->{$_}\n"} keys%$options; } sub showcommands { hr; print "BioPerl Shell Commands:\n"; my $layout = "%5s : %-20s - %s\n"; printf $layout, "cmd", "function", "summary"; printf "%s\n", ("-" x 40); foreach my $c (@cmds) { my $sc = $c->{shortcut}; $sc =~ s/\\//g; printf($layout, $sc, $c->{'func'} . "()", $c->{'summary'} ); } } sub showexamples { print "\nExamples:\n-------\n"; } sub showvariables { hr; print "Shell variables:\n"; print q[ $seq : Bio::SeqI object $seqio : Bio::SeqIO object @pseqs : array of previous Bio::SeqI objects ]; nl; } sub welcome { print "Welcome to the BioPerl shell interface!\n\n"; print "\n\nType 'help' for instructions\n"; print "\n\nType 'demo' for demonstration\n"; print "\n\nThis is ALPHA software - commands may change\n"; print "-lots more commands need to be added to take full\n"; print "advantage of the bioperl functionality\n\n"; } sub help { my $topic = shift; my $c; if ($topic) { ($c) = grep {$_->{func} eq $topic} @cmds; } if ($c) { print "Function: $c->{func}\n"; print "Shortcut: $c->{shortcut}\n" if $c->{shortcut}; print "Summary: $c->{summary}\n" if $c->{summary}; print "=======\n"; print "$c->{docs}\n" if $c->{docs}; } elsif ($topic eq "advanced") { hr; nl; } else { hr; print "\nBioPerl Shell Help\n\n"; showintro; waitenter; showcommands; waitenter; showvariables; waitenter; showexamples; nl; nl; nl; print "Type \"demo\" for an interactive demo of commands\n\n"; print "Type \"help advanced\" for advanced options\n\n"; hr; nl; } } sub p { print shift; print "\n"; } sub x { print Dumper shift; print "\n"; } # trick to allow barewords as keywords... sub advanced {"advanced"} sub unix { my @cmds = @_; my $c = join(" ", @cmds); print `$c`; } welcome; require Term::ReadLine; require Shell; checkoptions; print "\n"; my $termline = shift || Term::ReadLine->new($prompt); my $rcfile = "$ENV{HOME}/.goshellrc"; if (-f $rcfile) { open(F, $rcfile); @lines = ; close(F); } my $end_signal = ""; while (!$quit) { if ($end_signal) { @lines = ($lines); while ($end_signal && ($line = $termline->readline("? "))) { if($line !~ /$end_signal/) { $lines[0].= "\n$line"; } else { $end_signal = ""; } } next; } my $line = @lines ? shift @lines : $termline->readline($prompt); if ($line =~ /^\^/) { $line =~ s/^\^//; print "$prompt$line"; my $e = ; if ($e =~ /^q/) { $line = ""; @lines = (); } } if ($options->{echo} && $line !~ /\+?wait/) { if ($line =~ /^\#/) { print "$line\n"; } else { print "$prompt$line\n"; } if ($options->{sleep}) { sleep $options->{sleep}; } if ($options->{wait}) { sleep $options->{wait}; } } my ($cmd, @w) = split(' ',$line); $_ = $cmd; if (/^\<\<(.*)/) { $end_signal = $1; } # check for shortcuts my $selected; foreach my $c (@cmds) { my $shortcut = $c->{'shortcut'}; next unless $shortcut; if ($line =~ /^$shortcut(.*)/) { if (!defined($selected) || length($shortcut) > length($selected->{shortcut} || "")) { # get the most specific match $selected = $c; } } } if ($selected) { my $shortcut = $selected->{'shortcut'}; if ($line =~ /^$shortcut(.*)/) { my @w = map {"'".$_."'" } split(' ', $1); $line = $selected->{'func'}." ".join(", ", @w); } } $rv = eval $line; # print "\n"; # print "RV=$rv;;;\n"; if ($@) { print STDERR $@; } if ($options->{sleep}) { sleep $options->{sleep}; } if ($options->{wait}) { sleep $options->{wait}; $options->{wait} = 0; } } } sub get_default_cmds { my @cmds = ( { func => 'read_seq', shortcut => '\<', summary => 'read a Seq from a file', }, { func => 'next_seq', shortcut => ',', summary => 'get the next Seq', }, { func => 'read_seqs', shortcut => '\<\*', summary => 'read all Seqs from a file', }, { func => 'write_seq', shortcut => '\>', summary => 'write a Seq to screen/file', }, { func => 'write_seqs', shortcut => '\>\*', summary => 'write a Seq to screen/file', }, { func => 'fastadb', shortcut => 'fa', summary => 'fast fasta access', }, { func => 'subseq', summary => 'get a subseq from a fastadb', }, { func => 'set', shortcut => '\+', summary => 'set a shell parameter', }, { func => 'unix', shortcut => '\!', summary => 'run a unix command', }, { func => 'x', summary => 'display variable (and internals) using dumper', }, ); return @cmds; } BioPerl-1.007002/examples/generate_random_seq.pl000555000766000024 467013155576320 21702 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl use strict; use vars qw($USAGE); # random sequence generator # # -c=1 option will cause prot sequences to be built # using vertebrate aa frequencies, # with option -a putting a 1st methionine residues on. Frequencies are # calculated from the NCBI human RefSeq protein sequences # -c and -a only affect protein sequences # -a only works in conjunction with -c # -n number of random sequences, default = 1 use Bio::PrimarySeq; use Bio::SeqIO; use Getopt::Long; my ($length,$type,$filename,$comp,$met); $USAGE = 'usage: generate_random_seq.pl --length=1000 --type=dna --filename=/tmp/test.seq --number=50'; my %alphabets = ( 'dna' => [qw(C A G T)], 'rna' => [qw(C A G U)], 'prot'=> [qw( A C D E F G H I K L M N P Q R S T V W Y)], ); # make random num from 1-10000. numbers in this array reflect the frequency, # e.g., a random number from 1.744 = A, 745-991 = C etc; my @aa_frequencies = qw(744 991 1398 2017 2378 3104 3349 3726 4239 5273 5443 5749 6410 6848 7455 8263 8760 9340 9488 9713 10000); my $number = 1; &GetOptions ( 'l|length:s' => \$length, 't|type|m|alphabet:s' => \$type, 'f|file|filename:s' => \$filename, 'c|composition:s' => \$comp, 'a|methionine:s' => \$met, 'n|number:s' => \$number ); assert ( $type && defined ($alphabets{lc $type}), $USAGE); assert ( $length && $length =~ /^\d+$/, $USAGE ); foreach my $num (1..$number) { my $sequence = ""; my $alphabet = $alphabets{lc $type}; my $sspace = scalar @$alphabet; if (!$comp || $type ne 'prot') { foreach ( 1..$length ) { $sequence .= $alphabet->[ int rand($sspace) ]; } }elsif ($type eq 'prot') { $sequence = build_seq($length, \@aa_frequencies); } my $seq = Bio::PrimarySeq->new(-seq => $sequence, -display_id => 'randomseq'.$num); my %args = (-format => 'fasta'); if( $filename ) { $args{-file} = ">>$filename" } my $seqio = Bio::SeqIO->new(%args); $seqio->write_seq($seq); } sub assert { die $_[1] unless( $_[0] ); } sub build_seq { #takes seqlen and ref to frequency data as parameters my ($len, $pf) = @_; my $str = ($met)?'M':''; my $i = ($met)?1:0; for ($i..$len-1) { my $aa = int(rand (10000)) ; my $j = 0; while ($pf->[$j] < $aa && $j <19) { $j++; } $str .= $alphabets{'prot'}[$j]; } print "str is $str\n"; return $str; } BioPerl-1.007002/examples/longorf.pl000555000766000024 1027113155576320 17360 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl # longorf.pl v0208020920 # (c) Dan Kortschak 2002 use vars qw($USAGE); use strict; use Getopt::Long; use Bio::SeqIO; $USAGE = "longorf [--help] [--notstrict] [--verbose] [--graph] [--width printwidth] [--format seqformat] --input seqfile\n"; my ($sequencefile,$sequenceformat,$notstrict,$graph,$verb,$printwidth,$help) = (undef, 'fasta', undef, undef,undef,50, undef); &GetOptions('input|i=s' => \$sequencefile, 'format|f=s' => \$sequenceformat, 'notstrict|n' => \$notstrict, 'width|w=s' => \$printwidth, 'graph|g' => \$graph, 'verbose|v' => \$verb, 'help|h' => \$help, ); if ($help) { exec('perldoc', $0); die; } if (!defined $sequencefile) { die($USAGE . "\nPlease specify an input filename.\n"); } sub longestORF { my $best=0; my ($bests,$beste,$beststrand)=(-1,-1,0); my $bestorf=""; my $relaxed=$_[1]; my $dna=Bio::Seq->new(-seq => $_[0]); my %strand=('+'=>$dna->seq, '-'=>$dna->revcom->seq); foreach my $direction (keys %strand) { my @starts=(); my @ends=(); if ($relaxed) { for (my $frame=0;$frame<3;$frame++) { unless ($strand{$direction}=~m/^.{$frame}(taa|tga|tag)/i) { push @starts,$frame+1; } } } while ($strand{$direction}=~m/(atg)/gi) { push @starts,pos($strand{$direction})-2; } while ($strand{$direction}=~m/(taa|tga|tag)/gi) { push @ends,pos($strand{$direction})-2; } push @ends,($dna->length-2,$dna->length-1,$dna->length); for my $s (@starts) { for my $e (@ends) { if ($e%3==$s%3 and $e>$s) { if ($e-$s>$best) { $best=$e-$s; ($bests,$beste,$beststrand)=($s,$e,$direction); $bestorf=Bio::Seq->new(-seq=>$strand{$direction})->subseq($s,$e); } last } else { next } } } } return ($best,$bests,$beste,$beststrand,$bestorf); } my $seqio = new Bio::SeqIO('-format' => $sequenceformat, '-file' => $sequencefile ); my ($length,$start,$end,$direction,$sequence); my $count=0; my @lengths; my $totallength=0; while (my $dna = $seqio->next_seq) { $count++; ($length,$start,$end,$direction,$sequence)=longestORF($dna->seq,$notstrict); if ($verb) { print $dna->display_id," ",$dna->desc,": "; print "$length, $start, $end ($direction)\n$sequence\n\n",Bio::Seq->new(-seq=>$sequence)->translate->seq,"\n\n--\n\n"; } $totallength+=$length; $lengths[$length/3]++; } print "Average ORF length: ", $totallength/$count,"\n\n"; print "Length distribution is:\n"; if ($graph) { my $length; my $maxlength=0; for ($length=0;$length<@lengths;$length++) { $lengths[$length]=0 unless $lengths[$length]; $maxlength=$lengths[$length] if ($lengths[$length]>$maxlength); } for ($length=0;$length<@lengths;$length++) { print $length*3,"\t",$lengths[$length],"\t|"; print "#"x(($lengths[$length])*$printwidth/$maxlength); print "\n"; } } else { for ($length=0;$length<@lengths;$length++) { print $length*3,"\t",($lengths[$length]or"0"),"\n"; } } __END__ =head1 NAME longorf.pl - perl script to find the longest ORF of a sequence =head1 SYNOPSIS % longorf.pl [-h] [-n] [-v] [-g] [-w printwidth] [-f seqformat] -i seqfile =head1 DESCRIPTION This script will examine a set of nucleotide sequences and determine the longest ORF in each sequence. ORFs may start at the canonical ATG or at the beginning of the sequence if the notstrict option is chosen. The script will output a list of the longest ORF lengths, starts, ends and strands with the ORF and amino acid sequence if the verbose option is chosen. A histogram of the longest ORFs in the input set may be printed by choosing the graph option. =head1 FEEDBACK This script is not supported by anyone, but requests can be made to the author. =head1 AUTHOR - Dan Kortschak =cut BioPerl-1.007002/examples/make_primers.pl000444000766000024 1226613155576320 20373 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl # Author: cckim@stanford.edu # Description: This program designs primers for constructing knockouts # of genes by transformation of PCR products (ref: Datsenko & Wanner, # PNAS 2000). A tab-delimited file containing ORF START STOP is read, # and primers flanking the start & stop coordinates are designed based # on the user-designated sequence file. In addition, primers flanking # the knockout regions are chosen for PCR screening purposes once the # knockout is generated. The script uses Bioperl in order to # determine the primer sequences, which requires getting subsequences # and reverse complementing some of the objects. # make_primers.pl # Purpose: Design primers for the Wanner method of PCR product-based knockouts # Input: FASTA sequence file, tab-delimited coordinates file # Output: Primer output file # July 4, 2001 # Charles C. Kim ########### # MODULES # ########### use Bio::Seq; use Getopt::Std; ############# # VARIABLES # ############# $upgap = 0; # the number of nt upstream of the 5' end to include in the deletion $downgap = 0; # the number of nucleotides downstream of the 3' end to include # in the deletion $oligolength = 40; # the length of the homologous region on each primer $seqfile = ''; # don't specify these filenames unless you want to run $coordfile = ''; # the program on these filenames exclusively $outfile = ''; # %fiveprime_primers = ( "P1" => "GTGTAGGCTGGAGCTGCTTC", ); %threeprime_primers = ( "P2" => "CATATGAATATCCTCCTTAG", "P4" => "ATTCCGGGGATCCGTCGACC", ); ######### # FILES # ######### getopts('s:c:o:'); # sequence file, coordinates file, output file $seqfile = $opt_s if $opt_s; $coordfile = $opt_c if $opt_c; $outfile = $opt_o if $opt_o; &open_readfile(*SEQFILE, 'sequence', $seqfile); &open_readfile(*COORDFILE, 'coordinate', $coordfile); &open_writefile(*PRIMERFILE, 'output', $outfile); ######## # MAIN # ######## $seq = ''; $count = 0; while () { if (/>/) { $count++; if ($count > 1) { die "More than one sequence present in the input file\n"; } next; } chomp($_); $_ =~ tr/gatc/GATC/; $seq .= $_; } close SEQFILE; $seq = Bio::Seq-> new('-seq'=>$seq ); while () { chomp($_); next if !$_; (my $name, my $start, my $stop) = split(/\t/, $_); if ($start < $stop) { $upprimer = $seq->subseq($start-$oligolength-$upgap, $start-1-$upgap); $downprimer = $seq->subseq($stop+1+$downgap,$stop+$oligolength+$downgap); $downprimer = Bio::Seq->new('-seq'=>$downprimer); $downprimer = $downprimer->revcom(); $downprimer = $downprimer->seq(); $uppcr = $seq->subseq($start-$oligolength-$upgap-20,$start-1-$upgap-$oligolength); $downpcr = $seq->subseq($stop+1+$downgap+$oligolength,$stop+$oligolength+$downgap+20); $downpcr = Bio::Seq->new('-seq'=>$downpcr); $downpcr = $downpcr->revcom(); $downpcr = $downpcr->seq(); } elsif ($start > $stop) { $upprimer = $seq->subseq($start+$upgap+1,$start+$oligolength+$upgap); $downprimer = $seq->subseq($stop-$oligolength-$downgap, $stop-1-$downgap); $upprimer = Bio::Seq->new('-seq'=>$upprimer); $upprimer = $upprimer->revcom(); $upprimer = $upprimer->seq(); $uppcr = $seq->subseq($start+$oligolength+$upgap+1,$start+$oligolength+$upgap+20); $downpcr = $seq->subseq($stop-$oligolength-$downgap-20,$stop-1-$downgap-$oligolength); $uppcr = Bio::Seq->new('-seq'=>$uppcr); $uppcr = $uppcr->revcom(); $uppcr = $uppcr->seq(); } else { die "Problem with start and stop coordinates\n"; } print PRIMERFILE "$name\n"; print PRIMERFILE "5'pcr\t$uppcr\n"; print PRIMERFILE "3'pcr\t$downpcr\n"; print PRIMERFILE "\tExpected wildtype product size: ",abs($start-$stop)+121," bp\n"; foreach $entry (sort keys %fiveprime_primers) { print PRIMERFILE "5'+$entry\t$upprimer$fiveprime_primers{$entry}\n"; } foreach $entry (sort keys %threeprime_primers) { print PRIMERFILE "3'+$entry\t$downprimer$threeprime_primers{$entry}\n"; } print PRIMERFILE "\n"; $upprimer = ''; $downprimer = ''; $uppcr = ''; $downpcr = ''; } ############### # SUBROUTINES # ############### sub open_readfile { my $filehandle = $_[0]; my $filetype = $_[1] if $_[1]; my $filename = $_[2] if $_[2]; unless ($filename) { print "Enter $filetype filename: "; chomp ($filename=); } unless (-e $filename) { die "$filename not found\n"; } open $filehandle,'<', $filename or die "Could not read file '$filename': $!\n"; $filehandle = ''; $filetype = ''; $filename = ''; } sub open_writefile { my $filehandle = $_[0]; my $filetype = $_[1] if $_[1]; my $filename = $_[2] if $_[2]; unless ($filename) { print "Enter $filetype filename: "; chomp ($filename=); } if (-e $filename) { print "$filename already exists! Overwrite (Y/N)? "; chomp ($_ = ); while (/[^yn]/i) { print 'Y or N, please: '; chomp ($_ = ); } if (/n/i) { die "$filename not overwritten.\n"; } else { open $filehandle, '>', $filename or die "Could nott write file '$filename':·$!\n"; } } else { open $filehandle, '>', $filename or die "Could not write file '$filename': $!\n"; } $filehandle = ''; $filetype = ''; $filename = ''; } BioPerl-1.007002/examples/rev_and_trans.pl000555000766000024 221313155576320 20514 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl # PROGRAM : rev_and_trans.pl # PURPOSE : Simple driver for Bio::Seq revcom and translate # AUTHOR : Ewan Birney birney@sanger.ac.uk # CREATED : Tue Oct 27 1998 # # INSTALLATION # If you have installed bioperl using the standard # makefile system everything should be fine and # dandy. # # if not edit the use lib "...." line to point the directory # containing your Bioperl modules. # use Bio::Seq; use Bio::SeqIO; # new sequence from raw memory... # it is *very* important to get the type right so it # is translated correctly. $seq = Bio::Seq->new ( -id => "myseq", -seq => "CGCCGAAGAAGCATCGTTAAAGTCTCTCTTCACCCTGCCGTCATGTCTAAGTCAGAGTCTCCT", -type => 'Dna'); $seqout = Bio::SeqIO->new('-format' => 'fasta', -fh => \*STDOUT); # make a reverse complement sequence $rev = $seq->revcom(); # the actual sequence is here $actual_bases = $rev->seq(); print "Reversed sequence as a string is [$actual_bases]\n"; # we could also write it as fasta formatted output $seqout->write_seq($rev); # make a translation $trans = $seq->translate(); print "Translated sequence!\n"; $seqout->write_seq($trans); BioPerl-1.007002/examples/revcom_dir.pl000555000766000024 436613155576320 20033 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl # ################################################################################ #11-17-2001 #Jianwen Fang (jwfang1999@yahoo.com) # #THis program returns reverse complement sequences of all sequences in the current directory #and save them in the same directory, using the same name with extension ".rev" ############################################################################### use strict; use Bio::Seq; use Bio::SeqIO; my @files = (); my $folder = '.'; my $inputFormat; my $outputFormat; my $numSeq; #Fasta FASTA format #EMBL EMBL format #GenBank GenBank format #GCG GCG format #raw Raw format (one sequence per line, no ID) my @format = ('Fasta', 'EMBL', 'GenBank', 'GCG', 'Raw'); print("\nWhat is the format of the original sequence files?\n"); print("type 0 for Fasta; 1 for EMBL; 2 for GenBank; 3 for GCG; 4 for Raw\n"); $inputFormat = ; chomp ($inputFormat); print("\nWhat is the format of the reverse complement sequence files you want?\n"); print("type 0 for Fasta; 1 for EMBL; 2 for GenBank; 3 for GCG; 4 for Raw\n"); $outputFormat = ; chomp ($outputFormat); unless(opendir(FOLDER, $folder)) { print "cannot open folder $folder!\n"; exit; } @files = grep(!/^\.\.?$/, readdir(FOLDER)); foreach my $file (@files) { if($file =~ /seq/i) { getRevcom($file); $numSeq++; } } print "$numSeq reverse complement sequences have been saved in current directory\n"; exit; ############################################################################ #subroutine getRevcom take an backward sequence file name(should with .seq extension) as parameter #return its revcom sequence using the same name with the extension replaced with rev ############################################################################ sub getRevcom { my $seqFile = $_[0]; my $in = Bio::SeqIO->new('-file'=>$seqFile, '-format'=>$format[$inputFormat]); my $seq = $in->next_seq(); my $revcomSeq = $seq->revcom(); my @outSeqFile = split (/\./, $seqFile); pop @outSeqFile; push(@outSeqFile, 'rev'); my $outSeqFile = join('.', @outSeqFile); print "$outSeqFile\n"; my $out = Bio::SeqIO->new('-file'=>">$outSeqFile", '-format'=>$format[$outputFormat]); $out->write_seq($revcomSeq); } BioPerl-1.007002/examples/subsequence.cgi000444000766000024 1002613155576320 20356 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl # see http://zfish.nichd.nih.gov/tools/subsequence.cgi # uncomment and modify the next two lines # if your perl is in a nonstandard directory #use lib '/disk3/local/lib/perl5/site_perl'; #use lib '/disk3/local/lib/perl5/'; use CGI qw/:standard :html3/; use Bio::DB::GenBank; use File::Temp; use FileHandle; print header, start_html(-title => 'find subsequence of large GenBank entries',-author => 'Jonathan_Epstein\@nih.gov'); print_form() unless param; print_results() if param; sub print_results { $gb = new Bio::DB::GenBank; $accession = param('accession'); eval { $seq = $gb->get_Seq_by_acc($accession); # Accession Number }; if ($@) { print "***ERROR: accession $accession not found***\n"; return; } $segment_start = param('start'); $segment_end = param('length_or_end_value'); $segment_end = $segment_start+$segment_end-1 if param('length_or_end_choice') eq 'Length'; if ($segment_end<$segment_start || $segment_start<0) { print "***ERROR: invalid segment start and end values:$segment_start,$segment_end***\n"; return; } $len = $seq->length(); if ($segment_end>$len) { print "***ERROR: maximum length $len exceeded***\n"; return; } $subseq = $seq->subseq ($segment_start,$segment_end); $name = "subsequence of $accession"; $strand = "+"; $strand = "-" if (param('reverse')); # For some reason, there seems to be a problem if you use the file # handle provided by File::Temp. Similarly, there's a problem if you # pass a filename to BioPerl below rather than a file handle. However, # constructing our own file handle and then passing it to BioPerl works # fine. (undef, $filename) = File::Temp::tempfile(); $fh = new FileHandle "> $filename"; $seqoutlong = Bio::SeqIO->new( '-format' => 'Fasta',-fh => $fh); $seqobj = Bio::PrimarySeq->new ( -seq => $subseq, -id => $name . "[length:$len]:" . $segment_start . "-" . $segment_end . "(" . $strand . "strand)", -moltype => 'dna' ); $seqobj = $seqobj->revcom if ($strand ne "+"); $seqoutlong->write_seq($seqobj); $fh->close; undef $fh; # Now we parse the FASTA file which was just generated, and perform # some simple conversions to HTML. open my $TEMPORARY, '<', $filename or die "Could not read temporary file '$filename': $!\n"; print "\n"; while (<$TEMPORARY>) { print $_; print "
\n"; } close $TEMPORARY; print "\n"; unlink $filename; } sub print_form { print p("This web page permits you to extract a short subsequence of DNA from a large GenBank entry. This is especially useful in an era of huge \"contigs\" of genomic DNA, where you only want to extract a few hundred base pairs for subsequent analysis.\n"); print p,"This program also illustrates the power of ",a({-href => 'http://www.BioPerl.org/'}, "BioPerl"), ", a powerful set of tools for molecular biology analysis. The ", a({-href => 'subsequence.pl.txt'}, "source code"), " for this program is less than 90 lines long.\n"; print p,"You must specify the GenBank accession number along with a start position. You may specify either the length of the subsequence you wish to extract or, equivalently, the endpoint.\n"; print "The sequence may be reverse-complemented if you wish, e.g., the reverse complement of ATCGC is GCGAT.\n"; print p,"To test this web page, try accession NT_004002, start 50000, length 400.\n"; print start_form,table( Tr(td("Enter your GenBank accession"),td(textfield(-name => 'accession',-size => 20))), Tr(td("Start position"),td(textfield(-name => 'start',-size => 10))), Tr(td("Specify length or end position"), td(radio_group (-name => 'length_or_end_choice',-values => [Length, End], default => Length))), Tr(td("Length or end position"), td(textfield (-name => length_or_end_value,-size => 20))), Tr(td("Reverse complement?"), td(checkbox (-name => 'reverse')))), submit ("Find my subsequence"); print hr(),"Credits: Jonathan Epstein (Jonathan_Epstein\@nih.gov)"; } BioPerl-1.007002/examples/Bio-DB-GFF000755000766000024 013155576320 16570 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/Bio-DB-GFF/load_ucsc.pl000555000766000024 3566013155576320 21253 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl use strict; use enum qw(:u_ refmethod refsource refgroup refseq refstart refstop refscore refstrand refphase qrystart qrystop sizes starts); use enum qw(:v_ refmethod refsource refgroup refseq refstrand refscore refphase txstart txstop cdsstart cdsstop exonstarts exonstops); use enum qw(:all_bacends__ x matches misMatches repMatches nCount qNumInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts); use enum qw(:all_est__ bin matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts); use enum qw(:all_mrna__ bin matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts); use enum qw(:all_sts_primer__ matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts); use enum qw(:all_sts_seq__ matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts); use enum qw(:bacEndPairs__ bin chrom chromStart chromEnd name score strand pslTable lfCount lfStarts lfSizes lfNames); use enum qw(:blatFish__ bin matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts); use enum qw(:gap__ bin chrom chromStart chromEnd ix n size type bridge); use enum qw(:gl__ bin frag start end strand); use enum qw(:gold__ bin chrom chromStart chromEnd ix type frag fragStart fragEnd strand); use enum qw(:intronEst__ bin matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts); use enum qw(:mrna__ bin matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts); use enum qw(:rmsk__ bin swScore milliDiv milliDel milliIns genoName genoStart genoEnd genoLeft strand repName repClass repFamily repStart repEnd repLeft id); use enum qw(:clonePos__ name seqSize phase chrom chromStart chromEnd stage faFile); use enum qw(:ctgPos__ contig size chrom chromStart chromEnd); use enum qw(:cytoBand__ chrom chromStart chromEnd name gieStain); use enum qw(:fishClones__ chrom chromStart chromEnd name score placeCount bandStarts bandEnds labs placeType accCount accNames stsCount stsNames beCount beNames); use enum qw(:gcPercent__ chrom chromStart chromEnd name gcPpt); use enum qw(:genscan__ name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds); use enum qw(:genscanSubopt__ bin chrom chromStart chromEnd name score strand); use enum qw(:jaxOrtholog__ humanSymbol humanBand mgiId mouseSymbol mouseChr mouseCm mouseBand); use enum qw(:refGene__ name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds); use enum qw(:refLink__ name product mrnaAcc protAcc geneName prodName locusLinkID omimId); use enum qw(:refSeqAli__ bin matches misMatches repMatches nCount qNumInsert qBaseInsert tNumInsert tBaseInsert strand qName qSize qStart qEnd tName tSize tStart tEnd blockCount blockSizes qStarts tStarts); use enum qw(:simpleRepeat__ bin chrom chromStart chromEnd name period copyNum consensusSize perMatch perIndel score A C G T entropy sequence); use enum qw(:stsAlias__ alias identNo trueName); use enum qw(:stsInfo__ identNo name gbCount genbank gdbCount gdb nameCount otherNames dbSTSid otherDbstsCount otherDbSTS leftPrimer rightPrimer distance organism sequence otherUCSCcount otherUCSC mergeUCSCcount mergeUCSC genethonName genethonChr genethonPos genethonLOD marshfieldName marshfieldChr marshfieldPos marshfieldLOD wiyacName wiyacChr wiyacPos wiyacLOD wirhName wirhChr wirhPos wirhLOD gm99gb4Name gm99gb4Chr gm99gb4Pos gm99gb4LOD gm99g3Name gm99g3Chr gm99g3Pos gm99g3LOD tngName tngChr tngPos tngLOD); use enum qw(:stsMap__ chrom chromStart chromEnd name score identNo ctgAcc otherAcc genethonChrom genethonPos marshfieldChrom marshfieldPos gm99Gb4Chrom gm99Gb4Pos shgcTngChrom shgcTngPos shgcG3Chrom shgcG3Pos wiYacChrom wiYacPos wiRhChrom wiRhPos fishChrom beginBand endBand lab); use enum qw(:uniGene_2__ bin chrom chromStart chromEnd name score strand txStart txEnd reserved exonCount exonStarts exonEnds); ############################################### # end enum ############################################### my %parentpos; my %nolandmark = map {$_=>1} qw(gap cpgIsland recombRate_decode recombRate_marshfield recombRate_genethon humMusL zoom1_humMusL zoom50_humMusL zoom2500_humMusL genscanSubopt simpleRepeat snpNih snpTsc ); foreach my $filename (@ARGV){ my $newfilename = $filename; $newfilename =~ s/txt\.gz/gff/; open(my $fhi, "zcat $filename |"); open(my $fho, ">$newfilename"); while(my $line = <$fhi>){ #these three should work the same way as unigene, but the fields are different order # $filename =~ /affyRatio/ ? toGFF($line,$fho,['affyRatio', '', 3, 0, 1, 2, 4, 5,-1,-1,-1,10,11]) : # $filename =~ /nci60/ ? toGFF($line,$fho,['nci60', '', 3, 0, 1, 2, 4, 5,-1,-1,-1,10,11]) : # $filename =~ /rnaCluster/ ? toGFF($line,$fho,['rnaCluster', '', 4, 1, 2, 3, 5, 6,-1, 7, 8,11,12]) : #these two are not yet handled # $filename =~ /cpgIsland/ ? toGFF($line,$fho,['cpgIsland', '', 3, 0, 1, 2,-1,-1,-1]) : # $filename =~ /estOrientInfo/ ? toGFF($line,$fho,['estOrientInfo', '',]) : $filename =~ /uniGene_2/ ? toGFF($line,$fho,['uniGene_2', '', 4, 1, 2, 3, 5, 6,-1,-1,-1,11,12]) : $filename =~ /all_bacends/ ? toGFF($line,$fho,['bacends', '', 9,13,15,16,-1, 8,-1,11,12,18,20]) : $filename =~ /all_est/ ? toGFF($line,$fho,['est', '',10,14,16,17,-1, 9,-1,12,13,19,21]) : $filename =~ /all_mrna/ ? toGFF($line,$fho,['mrna', '',10,14,16,17,-1, 9,-1,12,13,19,21]) : $filename =~ /all_sts_primer/ ? toGFF($line,$fho,['sts_primer', '', 9,13,15,16,-1, 8,-1,11,12,18,20]) : $filename =~ /all_sts_seq/ ? toGFF($line,$fho,['sts_seq', '', 9,13,15,16,-1, 8,-1,11,12,18,20]) : $filename =~ /blastzBestMouse/ ? toGFF($line,$fho,['blastzBestMouse', '',10,14,16,17,-1, 9,-1,12,13,19,21]) : $filename =~ /blastzMm2/ ? toGFF($line,$fho,['blastzMm2', '',10,14,16,17,-1, 9,-1,12,13,19,21]) : $filename =~ /blastzTightMouse/ ? toGFF($line,$fho,['blastzTightMouse', '',10,14,16,17,-1, 9,-1,12,13,19,21]) : $filename =~ /blatFish/ ? toGFF($line,$fho,['blatFish', '',10,14,16,17,-1, 9,-1,12,13,19,21]) : $filename =~ /chimpBac/ ? toGFF($line,$fho,['chimpBac', '',10,14,16,17,-1, 9,-1,12,13,19,21]) : $filename =~ /chimpBlat/ ? toGFF($line,$fho,['chimpBlat', '',10,14,16,17,-1, 9,-1,12,13,19,21]) : $filename =~ /clonePos/ ? toGFF($line,$fho,['clonePos', '', 0, 3, 4, 5,-1,-1, 2]) : $filename =~ /ctgPos/ ? toGFF($line,$fho,['ctgPos', '', 0, 2, 3, 4,-1,-1,-1]) : $filename =~ /cytoBand/ ? toGFF($line,$fho,['cytoBand', '', 3, 0, 1, 2,-1,-1,-1]) : $filename =~ /est/ ? toGFF($line,$fho,['est', '',10,14,16,17,-1,9,-1,12,13,19,21]) : $filename =~ /fishClones/ ? toGFF($line,$fho,['fishClones', '', 3, 0, 1, 2, 4,-1,-1]) : $filename =~ /gap/ ? toGFF($line,$fho,['gap', '', 7, 1, 2, 3,-1,-1,-1]) : $filename =~ /gcPercent/ ? toGFF($line,$fho,['gcPercent', '', 3, 0, 1, 2, 4,-1,-1]) : $filename =~ /genMapDb/ ? toGFF($line,$fho,['genMapDb', '', 3, 0, 1, 2, 4, 5,-1]) : $filename =~ /genscanSubopt/ ? toGFF($line,$fho,['genscanSubopt', '', 4, 1, 2, 3, 5, 6,-1]) : $filename =~ /gold/ ? toGFF($line,$fho,['gold', '', 6, 1, 2, 3,-1, 9,-1, 7, 8]) : $filename =~ /intronEst/ ? toGFF($line,$fho,['intron_est', '',10,14,16,17,-1, 9,-1,12,13,19,21]) : $filename =~ /recombRate/ ? eval { toGFF($line,$fho,['recombRate_decode', '', 3, 0, 1, 2, 4,-1,-1]); toGFF($line,$fho,['recombRate_marshfield', '', 3, 0, 1, 2, 7,-1,-1]); toGFF($line,$fho,['recombRate_genethon', '', 3, 0, 1, 2,10,-1,-1]); } : $filename =~ /refSeqAli/ ? toGFF($line,$fho,['refSeqAli', '',10,14,16,17,-1, 9,-1,12,13,19,21]) : $filename =~ /rmsk/ ? toGFF($line,$fho,['rmsk', '',10, 5, 6, 7,-1, 9,-1,13,14]) : $filename =~ /simpleRepeat/ ? toGFF($line,$fho,['simpleRepeat', '', 4, 1, 2, 3,10,-1,-1]) : $filename =~ /snpNih/ ? toGFF($line,$fho,['snpNih', '', 4, 1, 2, 3]) : $filename =~ /snpTsc/ ? toGFF($line,$fho,['snpTsc', '', 4, 1, 2, 3]) : $filename =~ /stsMap/ ? toGFF($line,$fho,['stsMap', '', 3, 0, 1, 2, 4,-1,-1]) : $filename =~ /xenoEst/ ? toGFF($line,$fho,['xenoEst', '',10,14,16,17,-1, 9,-1,12,13,19,21]) : $filename =~ /xenoMrna/ ? toGFF($line,$fho,['xenoMrna', '',10,14,16,17,-1, 9,-1,12,13,19,21]) : $filename =~ /zoom1_humMusL/ ? toGFF($line,$fho,['zoom1_humMusL', '', 4, 1, 2, 3, 5, 6,-1]) : $filename =~ /zoom2500_humMusL/ ? toGFF($line,$fho,['zoom2500_humMusL', '', 4, 1, 2, 3, 5, 6,-1]) : $filename =~ /zoom50_humMusL/ ? toGFF($line,$fho,['zoom50_humMusL', '', 4, 1, 2, 3, 5, 6,-1]) : $filename =~ /humMusL/ ? toGFF($line,$fho,['humMusL', '', 4, 1, 2, 3, 5, 6,-1]) : $filename =~ /(refGene|genscan|acembly|ensGene|refFlat|sanger22pseudo|sanger22|softberryGene|twinscan)/ ? toGFF2($line,$fho, [$1, -1, 0, 2, 3, -1, -1, 4, 5, 6, 7, 9, 10]) : 0; } close($fhi); close($fho); } ############################################### # begin filetype-specific subroutines ############################################### sub toGFF2 { my($line,$fho, $maps) = @_; chomp $line; my @fields = split /\t/, $line; if(!$nolandmark{render($maps->[v_refmethod],\@fields)}){ print $fho join "\t", map {render($maps->[$_],\@fields)} (v_refseq, v_refsource, v_refmethod, v_txstart, v_txstop, v_refscore, v_refstrand, v_refphase,); print $fho "\t"; print $fho "Sequence " . render($maps->[v_refgroup],\@fields); print $fho "\n"; } if(!$nolandmark{render($maps->[v_refmethod],\@fields)}){ print $fho join "\t", map {render($maps->[$_],\@fields)} (v_refseq, v_refsource, v_refmethod, v_cdsstart, v_cdsstop, v_refscore, v_refstrand, v_refphase,); print $fho "\t"; print $fho "CDS " . render($maps->[v_refgroup],\@fields); print $fho "\n"; } if(defined($maps->[v_exonstarts]) and defined($maps->[v_exonstops])){ my @starts = split /,/, render($maps->[v_exonstarts],\@fields); my @stops = split /,/, render($maps->[v_exonstops],\@fields); while(my $start = shift @starts){ my $stop = shift @stops; print $fho join "\t", (render($maps->[v_refseq],\@fields), render($maps->[v_refsource],\@fields), render($maps->[v_refmethod],\@fields), $start, $stop, render($maps->[v_refscore],\@fields), render($maps->[v_refstrand],\@fields), render($maps->[v_refphase],\@fields), render($maps->[v_refmethod],\@fields) . " " . render($maps->[v_refgroup],\@fields) ), "\n"; } } } sub toGFF { my($line,$fho, $maps) = @_; chomp $line; my @fields = split /\t/, $line; if(!$maps->[u_qrystart] and !$nolandmark{render($maps->[u_refmethod],\@fields)}){ print $fho join "\t", map {render($maps->[$_],\@fields)} (u_refseq, u_refsource, u_refmethod, u_refstart, u_refstop, u_refscore, u_refstrand, u_refphase); print $fho "\t"; print $fho "Sequence " . render($maps->[u_refgroup],\@fields); print $fho "\n"; } print $fho join "\t", map {render($maps->[$_],\@fields)} (u_refseq, u_refsource, u_refmethod, u_refstart, u_refstop, u_refscore, u_refstrand, u_refphase); print $fho "\t"; if($maps->[u_qrystart] >= 0){ print $fho "Target:" . render($maps->[u_refmethod],\@fields) . " "; print $fho render($maps->[u_refgroup],\@fields) . " " . render($maps->[u_qrystart],\@fields) . " " . render($maps->[u_qrystop], \@fields); } else { print $fho "Sequence " . render($maps->[u_refgroup],\@fields) . " "; } print $fho "\n"; if(defined($maps->[u_starts]) and defined($maps->[u_sizes])){ my @starts = split /,/, render($maps->[u_starts],\@fields); my @sizes = split /,/, render($maps->[u_sizes],\@fields); my $start; while(defined($start = shift @starts)){ my $size = shift @sizes; if($maps->[u_qrystart] < 1 and $maps->[u_qrystop] < 1){ print $fho join "\t", (render($maps->[u_refseq],\@fields), render($maps->[u_refsource],\@fields), render($maps->[u_refmethod],\@fields), render($maps->[u_refstart],\@fields) + $start, render($maps->[u_refstart],\@fields) + $start + $size, render($maps->[u_refscore],\@fields), render($maps->[u_refstrand],\@fields), render($maps->[u_refphase],\@fields), render($maps->[u_refmethod],\@fields) . " " . render($maps->[u_refgroup],\@fields) ), "\n"; } else { print $fho join "\t", (render($maps->[u_refseq],\@fields), render($maps->[u_refsource],\@fields), render($maps->[u_refmethod],\@fields), $start, $start + $size, render($maps->[u_refscore],\@fields), render($maps->[u_refstrand],\@fields), render($maps->[u_refphase],\@fields), render($maps->[u_refmethod],\@fields) . " " . render($maps->[u_refgroup],\@fields) ), "\n"; } } } } sub render { my($index,$fields) = @_; return '.' if $index == -1; return $index unless $index =~ /^\d+$/; return $fields->[$index]; } BioPerl-1.007002/examples/align000755000766000024 013155576320 16266 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/align/FastAlign.pl000444000766000024 1524613155576320 20660 0ustar00cjfieldsstaff000000000000#! /usr/bin/perl ##################################################### # Fasta # | # Align # # By # Antony Vincent # (a.vincent.0312@gmail.com) # # FastAlign is a perl script which uses the heuristic method # of tfasty36 for find similarity between a query sequence # in amino acids and a sequence in nucleotides. It provides # a more intuitive output to find exon-intron junctions. # The query string is in amino acids and the hit string is # in nucleotides. There are extra nucleotides at the end of # the hit string (option -diff and by default = 10), that # allow to verify if the intron start with common rules # (5'-GTGCGA-... for group II intron and after an exonic T # for group I intron). # # The FASTA version can be changed by the user by changing # the line with tfasty36 for tfastyXX. # # If you have Emboss, you can genarate a graphic with option # -graph 1. # # For complete help: type perl fastalign.pl -help # Last Update: 01/06/13 ####################################################### =head1 Copyright (C) 2013 Antony Vincent Licence: This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . =cut use strict; use Bio::SearchIO; use Bio::SeqIO; use Getopt::Long; use Bio::SeqUtils; ## Set the default variables my $identity = 75; my $length = 50; my $diff = 10; my $out = 'output'; my $graphic = 10; my $query; my $library; my $help; GetOptions( 'seq=s' => \$query, 'db=s' => \$library, 'graph=s' => \$graphic, 'i=i' => \$identity, 'l=i' => \$length, 'diff=s' => \$diff, 'out=s' => \$out, 'help!' => \$help, ) or die "Incorrect usage! Try perl fastalign.pl -help for an exhaustif help.\n"; ### if( $help ) { # if start print "\n"; print "Two options are required:\n"; print " -seq: Your sequence in amino acids\n"; print " -db: The sequence in nucleotides (Could be a whole genome or a partial sequence...)\n"; print "\n"; print "There are few miscellaneous options:\n"; print " -i: Minimum identity percentage (default = 75)\n"; print " -l: Minimum match length (default = 50)\n"; print " -diff: Difference between the hit string and the alignement (default = 10)\n"; print " -out: Name of the output file (default = output.txt)\n"; print " -graph: If this option = 1, a graph will be generated (default = no)\n"; } # if help else { # else start my $date = `date`; open (WRITE, ">>$out.txt"); ## Open the output file print WRITE " Fasta\n"; print WRITE " |\n"; print WRITE " Align\n\n"; print WRITE "Date:", $date, "\n"; print WRITE "PARAMETERS\n"; print WRITE "Minimum identity =", $identity, "\n"; print WRITE "Minimum length =", $length, "\n"; print WRITE "Diff =", $diff, "\n\n"; if ( $graphic == 1 ) { open (WRITE, ">>$out.txt"); ## Open the output file open (WRITE2, ">>lindna.lnp"); ## Open the lindna config file ## start the lindna header print WRITE2 "start"; print WRITE2 "\t"; print WRITE2 "1"; print WRITE2 "\n"; print WRITE2 "End"; print WRITE2 "\t"; my $seqio_obj = Bio::SeqIO->new(-file => "$library", -format => "fasta" ); my $seq_obj = $seqio_obj->next_seq; my $count_obj = $seq_obj->length; print WRITE2 "$count_obj"; print WRITE2 "\n\n"; print WRITE2 "group"; print WRITE2 "\n"; } else { print "No graphic generated \n"; } ## run tfasty36 my $fh; my $fasta = "tfasty36"; # <------ You can change this line for newest fasta algorithm my $command = "$fasta $query $library"; open $fh,"$command |" || die("cannot run fasta cmd of $command: $!\n"); my $searchio = Bio::SearchIO->new(-format => 'fasta', -fh => $fh); print WRITE "Fasta algorithm:", $fasta, "\n\n"; ## start the parsing part of the script while( my $result = $searchio->next_result ) { ## $result is a Bio::Search::Result::ResultI compliant object while( my $hit = $result->next_hit ) { ## $hit is a Bio::Search::Hit::HitI compliant object while( my $hsp = $hit->next_hsp ) { ## $hsp is a Bio::Search::HSP::HSPI compliant object if( $hsp->length('total') > $length ) { if ( $hsp->percent_identity >= $identity ) { ## Generals informations print WRITE "Rank=", $hsp->rank, "\n", "Query=", $result->query_name, "\n", "Hit=", $hit->name, "\n" , "Length=", $hsp->length('total'), "\n", "Percent_id=", $hsp->percent_identity, "\n", "Strand=", $hsp->strand('hit'), "\n"; print WRITE "\n"; ## Search for nucleotide sequences print WRITE "\n"; my $start_hit = $hsp->start('hit'), "\n"; my $end_hit = $hsp->end('hit') , "\n"; my $in = Bio::SeqIO->new(-file => "$library" , '-format' => 'fasta'); while ( my $seq = $in->next_seq() ) {#1 ## looking for query position my $start_query = $hsp->start('query'), "\n"; my $end_query = $hsp->end('query') , "\n"; ## aa_to_3aa my $seqobj = Bio::PrimarySeq->new ( -seq => $hsp->query_string); my $polypeptide_3char = Bio::SeqUtils->seq3($seqobj); ## modify the homology string my $homo = $hsp->homology_string; $homo =~ s/:/|||/g; $homo =~ s/\./***/g; $homo =~ s/ /XXX/g; ## HSP print WRITE "Query($start_query,$end_query)\n"; print WRITE "Hit($start_hit,$end_hit)\n\n"; print WRITE $polypeptide_3char, "\n"; print WRITE $homo, "\n"; print WRITE $seq->subseq($start_hit,$end_hit+$diff), "\n"; if ( $graphic == 1) { ## if start ## write in lindna file print WRITE2 "label", "\n", "Block", "\t", "$start_hit", "\t", "$end_hit", "\t", "3", "\t", "H", "\n"; print WRITE2 "Exon", $hsp->rank, "\n"; print WRITE2 "endlabel"; print WRITE2 "\n\n"; } ## if end else {print "No lindna file generated\n";} } #1 print WRITE "\n"; } } } } } if ( $graphic == 1) { ## if start print WRITE2 "endgroup"; system ("lindna -infile lindna.lnp -ruler y -blocktype filled -graphout svg"); system ("rm *.lnp"); } ## if end } # else end BioPerl-1.007002/examples/align/align_on_codons.pl000555000766000024 1113413155576320 22136 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl use strict; use vars qw($USAGE %VALIDALIGN $CODONSIZE); use Bio::SeqIO; use Bio::AlignIO; use Bio::LocatableSeq; use Bio::SimpleAlign; use Getopt::Long; use Bio::Tools::CodonTable; use Carp; BEGIN { $CODONSIZE = 3; # parametrize everything like a good little programmer if( ! defined $ENV{'CLUSTALDIR'} ) { $ENV{'CLUSTALDIR'} = '/usr/local/bin'; } if( ! defined $ENV{'TCOFFEEDIR'} ) { $ENV{'TCOFFEEDIR'} = '/usr/local/bin'; } $USAGE = qq{align_on_codons.pl < file.fa -h/--help See this information -f/--frame Translation Frame (0,1,2) are valid (defaults to '0') -ct/--codontable Codon table to use (defaults to '1') see perldoc Bio::PrimarySeq for more information -i/--input Input Filename (defaults to STDIN) -o/--output Output Filename (defaults to STDOUT) -sf/--seqformat Input format (defaults to FASTA/Pearson) -af/--alignformat Alignment output format (clustal,fasta,nexus,phylip, msf,pfam,mase,meme,prodom,selex,stockholm) -ap/--alignprog ClustalW, TCoffee (currently only support local execution) -v/--verbose Run in verbose mode }; %VALIDALIGN = ('clustalw' => 'Bio::Tools::Run::Alignment::Clustalw', 'tcoffee' => 'Bio::Tools::Run::Alignment::TCoffee'); } my ($help, $input, $output); my ($alignprog, $sformat, $aformat, $frame, $codontable, $verbose) = ('clustalw', 'fasta', 'clustalw', 0, 1, 0); GetOptions( 'h|help' => \$help, 'i|input:s' => \$input, 'o|output:s' => \$output, 'sf|seqformat:s' => \$sformat, 'af|alignformat:s' => \$aformat, 'ap|alignprog:s' => \$alignprog, # for translate 'f|frame:s' => \$frame, 'ct|codontable:s' => \$codontable, 'v|verbose' => \$verbose, ); if( $help ) { die($USAGE); } if( ! $alignprog || !defined $VALIDALIGN{$alignprog} ) { die("Cannot use $alignprog as 'alignprog' parameter"); } else { my $modname = $VALIDALIGN{$alignprog} .".pm"; $modname =~ s/::/\//g; require $modname; } my $alignout; if( $output ) { $alignout = new Bio::AlignIO('-format' => $aformat, '-file' => ">$output"); } else { $alignout = new Bio::AlignIO('-format' => $aformat); } my (@nucseqs,@protseqs); my $seqio; if( $input ) { $seqio = new Bio::SeqIO('-format' => $sformat, '-file' => $input); } else { $seqio = new Bio::SeqIO('-format' => $sformat, '-fh' => \*STDIN); } my $table = new Bio::Tools::CodonTable(); while( my $seq = $seqio->next_seq ) { # if( $frame == 0 && $alignprog eq 'tcoffee' ) { # print "last codon is ",$seq->subseq($seq->length() -2, # $seq->length()), "\n"; # if( $table->is_ter_codon($seq->subseq($seq->length() -2, # $seq->length())) ) { # $seq->seq($seq->subseq(1,$seq->length() - 3)); # } # } push @nucseqs, $seq; push @protseqs, $seq->translate(-frame => $frame, -codontable_id => $codontable ); } if( @nucseqs <= 1 ) { die("Must specify > 1 sequence for alignment on codons"); } # allow these to be tweaked by cmdline parameters at some point my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM'); my $alignengine = $VALIDALIGN{$alignprog}->new('-verbose' => $verbose, @params); my $aln = $alignengine->align(\@protseqs); my $dnaalign = new Bio::SimpleAlign; my $seqorder = 0; my $alnlen = $aln->length; foreach my $seq ( $aln->each_seq ) { my $newseq; foreach my $pos ( 1..$alnlen ) { my $loc = $seq->location_from_column($pos); my $dna = ''; if( !defined $loc || $loc->location_type ne 'EXACT' ) { $dna = '---'; } else { # to readjust to codon boundaries # end needs to be +1 so we can just multiply by CODONSIZE # to get this my ($start,$end) = ((($loc->start - 1)*$CODONSIZE) +1, ($loc->end)*$CODONSIZE); if( $start <=0 || $end > $nucseqs[$seqorder]->length() ) { print "start is ", $loc->start, " end is ", $loc->end, "\n"; warn("codons don't seem to be matching up for $start,$end"); $dna = '---'; } else { $dna = $nucseqs[$seqorder]->subseq($start,$end); } } $newseq .= $dna; } $seqorder++; # funky looking math is to readjust to codon boundaries and deal # with fact that sequence start with 1 my $newdna = new Bio::LocatableSeq(-display_id => $seq->id(), -start => (($seq->start - 1) * $CODONSIZE) + 1, -end => ($seq->end * $CODONSIZE), -strand => $seq->strand, -seq => $newseq); $dnaalign->add_seq($newdna); } $alignout->write_aln($dnaalign); BioPerl-1.007002/examples/align/aligntutorial.pl000555000766000024 664113155576320 21650 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl # An example of how to use the different alignment tools in bioperl # to align some sequences # All these methods except Bio::Tools::pSW will work for DNA sequence # (need to use a different matrix however) use Bio::Factory::EMBOSS; use Bio::SeqIO; use Bio::AlignIO; use Bio::Tools::pSW; use Bio::PrimarySeq; use Bio::Tools::Run::Alignment::Clustalw; use Bio::Tools::Run::Alignment::TCoffee; use Bio::Tools::Run::StandAloneBlast; use strict; # build the sequences since EMBOSS expects seqs to be in files my $seq = new Bio::PrimarySeq(-seq => 'MAVNPELAPFTLSRGIPSFDDQALSTIIQLQDCIQQAIQQLNYSTAEFLAELLYAECSILDKSSVYWSDAVYLYALSLFLNKSYHTAFQISKEFKEYHLGIAYIFGRCALQLSQGVNEAILTLLSIINVFSSNSSNTRINMVLNSNLVHIPDLATLNCLLGNLYMKLDHSKEGAFYHSEALAINPYLWESYEAICKMRATVDLKRVFFDIAGKKSNSHNNNAASSFPSTSLSHFEPRSQPSLYSKTNKNGNNNINNNVNTLFQSSNSPPSTSASSFSSIQHFSRSQQQQANTSIRTCQNKNTQTPKNPAINSKTSSALPNNISMNLVSPSSKQPTISSLAKVYNRNKLLTTPPSKLLNNDRNHQNNNNNNNNNNNNNNNNNNNNNNNNIINKTTFKTPRNLYSSTGRLTTSKKNPRSLIISNSILTSDYQITLPEIMYNFALILRSSSQYNSFKAIRLFESQIPSHIKDTMPWCLVQLGKLHFEIINYDMSLKYFNRLKDLQPARVKDMEIFSTLLWHLHDKVKSSNLANGLMDTMPNKPETWCCIGNLLSLQKDHDAAIKAFEKATQLDPNFAYAYTLQGHEHSSNDSSDSAKTCYRKALACDPQHYNAYYGLGTSAMKLGQYEEALLYFEKARSINPVNVVLICCCGGSLEKLGYKEKALQYYELACHLQPTSSLSKYKMGQLLYSMTRYNVALQTFEELVKLVPDDATAHYLLGQTYRIVGRKKDAIKELTVAMNLDPKGNQVIIDELQKCHMQE', -id => 'seq1' ); my $seq2 = new Bio::PrimarySeq( -seq => 'CLIFXRLLLIQMIHPQARRAFTFLQQQEPYRIQSMEQLSTLLWHLADLPALSHLSQSLISISRSSPQAWIAVGNCFSLQKDHDEAMRCFRRATQVDEGCAYAWTLCGYEAVEMEEYERAMAFYRTAIRTDARHYNAWYVLFFFFFFFFVPGDIDSXPKKGMEWGXFISKRIDRGMRSIILKEPSKSIQLIPFFYVALVWXVGVSSYPLETMTNIDFPKKKKALEKSNDVVQALHFYERASKYAPTSAMVQFKRIRALVALQRYDEAISALVPLTHSAPDEANVFFLLGKCLLKKERRQEATMAFTNARELEPK', -id => 'seq2'); my $out = new Bio::SeqIO(-format => 'fasta', -file => ">seq1.fa"); $out->write_seq($seq); $out->close(); $out = new Bio::SeqIO(-format => 'fasta', -file => ">seq2.fa"); $out->write_seq($seq2); $out->close(); my $embossfactory = Bio::Factory::EMBOSS->new(); my @alignprogs = qw(water needle stretcher matcher); my $alignout = new Bio::AlignIO(-format => 'msf'); foreach my $prog ( @alignprogs ) { my $alignfactory = $embossfactory->program('water'); $alignfactory->run({ '-sequencea' => 'seq1.fa', '-seqall' => 'seq2.fa', '-gapext' => 2.0, '-datafile' => 'EBLOSUM62', '-gapopen' => 14.0, '-outfile' => "seq1_vs_seq2.$prog"}); my $alnin = new Bio::AlignIO(-format => 'emboss', -file => "seq1_vs_seq2.$prog"); my $aln = $alnin->next_aln(); $alignout->write_aln($aln); } # this should produce the same alignment as 'water' my $factory = new Bio::Tools::pSW(-matrix=> 'blosum62.bla', -gap => 14, -ext => 2); my $aln = $factory->pairwise_alignment($seq,$seq2); $alignout->write_aln($aln); $factory = new Bio::Tools::Run::Alignment::Clustalw('ktuple' => 2, 'matrix' => 'BLOSUM'); $aln = $factory->align([$seq,$seq2]); $alignout->write_aln($aln); $factory = new Bio::Tools::Run::Alignment::TCoffee('ktuple' => 2, 'matrix' => 'BLOSUM'); $aln = $factory->align([$seq,$seq2]); $alignout->write_aln($aln); $factory = new Bio::Tools::Run::StandAloneBlast(); $aln = $factory->bl2seq($seq,$seq2); # this actually returns a Bio::Tools::BPbl2seq object # it can be transformed to a SimpleAlign object see # the code in Bio::AlignIO::bl2seq # A transformer object will be written at some point BioPerl-1.007002/examples/align/clustalw.pl000555000766000024 2176413155576320 20653 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl # PROGRAM : clustalw.pl # PURPOSE : Demonstrate possible uses of Bio::Tools::Run::Alignment::Clustalw.pm # AUTHOR : Peter Schattner schattner@alum.mit.edu # CREATED : Oct 06 2000 # # INSTALLATION # # You will need to have installed clustalw and to ensure that Clustalw.pm can find it. # This can be done in different ways (bash syntax): # export PATH=$PATH:/home/peter/clustalw1.8 # or # define an environmental variable CLUSTALDIR: # export CLUSTALDIR=/home/peter/clustalw1.8 # or # include a definition of an environmental variable CLUSTALDIR in every # script that will use Clustal.pm. # BEGIN {$ENV{CLUSTALDIR} = '/home/peter/clustalw1.8/'; } # # We are going to demonstrate 3 possible applications of Clustalw.pm: # 1. Test effect of varying clustalw alignment parameter(s) on resulting alignment # 2. Test effect of changing the order that sequences are added to the alignment # on the resulting alignment # 3. Test effect of incorporating an "anchor point" in the alignment process # # Before we can do any tests, we need to set up the environment, create the factory # and read in the unaligned sequences. # #BEGIN { # $ENV{CLUSTALDIR} = '/home/peter/clustalw1.8/'; #} use Getopt::Long; use Bio::Tools::Run::Alignment::Clustalw; use Bio::SimpleAlign; use Bio::AlignIO; use Bio::SeqIO; use strict; # set some default values my $infile = 't/data/cysprot1a.fa'; my @params = ('quiet' => 1 ); my $do_only = '123'; # string listing examples to be executed. Default is to # execute all tests (ie 1,2 and 3) my $param = 'ktuple'; # parameter to be varied in example 1 my $startvalue = 1; # initial value for parameter $param my $stopvalue = 3; # final value for parameter $param my $regex = 'W[AT]F'; # regular expression for 'anchoring' alignment in example 3 my $extension = 30; # distance regexp anchor should be extended in each direction # for local alignment in example 3 my $helpflag = 0; # Flag to show usage info. # get user options my @argv = @ARGV; # copy ARGV before GetOptions() massacres it. &GetOptions("h!" => \$helpflag, "help!" => \$helpflag, "in=s" => \$infile, "param=s" => \$param, "do=s" => \$do_only, "start=i" => \$startvalue, "stop=i" => \$stopvalue, "ext=i" => \$extension, "regex=s" => \$regex,) ; if ($helpflag) { &clustalw_usage(); exit 0;} # create factory & set user-specified global clustalw parameters foreach my $argv (@argv) { unless ($argv =~ /^(.*)=>(.*)$/) { next;} push (@params, $1 => $2); } my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params); # put unaligned sequences in a Bio::Seq array my $str = Bio::SeqIO->new(-file=> $infile, '-format' => 'Fasta'); my ($paramvalue, $aln, $subaln, @consensus, $seq_num, $string, $strout, $id); my @seq_array =(); while ( my $seq = $str->next_seq() ) { push (@seq_array, $seq) ;} # Do each example that has digit present in variable $do_only $_= $do_only; /1/ && &vary_params(); /2/ && &vary_align_order(); /3/ && &anchored_align(); ## End of "main" ################################################# # vary_params(): Example demonstrating varying of clustalw parameter # sub vary_params { print "Beginning parameter-varying example... \n"; # Now we'll create several alignments, 1 for each value of the selected # parameter. We also compute a simple consensus string for each alignment. # (In the default case, we vary the "ktuple" parameter, creating 3 # alignments using ktuple values from 1 to 3.) my $index =0; for ($paramvalue = $startvalue; $paramvalue < ($stopvalue + 1); $paramvalue++) { $factory->$param($paramvalue); # set parameter value print "Performing alignment with $param = $paramvalue \n"; $aln = $factory->align(\@seq_array); $string = $aln->consensus_string(); # Get consensus of alignment # convert '?' to 'X' at non-consensus positions $string =~ s/\?/X/g; $consensus[$index] = Bio::Seq->new(-id=>"$param=$paramvalue",-seq=>$string); $index++; } # Compare consensus strings for alignments with different $param values by # making an alignment of the different consensus strings # $factory->ktuple(1); # set ktuple parameter print "Performing alignment of $param consensus sequences \n"; $aln = $factory->align(\@consensus); $strout = Bio::AlignIO->newFh('-format' => 'msf'); print $strout $aln; return 1; } ################################################# # vary_align_order(): # # For our second example, we'll test the effect of changing the order # that sequences are added to the alignment sub vary_align_order { print "\nBeginning alignment-order-changing example... \n"; @consensus = (); # clear array for ($seq_num = 0; $seq_num < scalar(@seq_array); $seq_num++) { my $obj_out = shift @seq_array; # remove one Seq object from array and save $id = $obj_out->display_id; # align remaining sequences print "Performing alignment with sequence $id left out \n"; $subaln = $factory->align(\@seq_array); # add left-out sequence to subalignment $aln = $factory->profile_align($subaln,$obj_out); $string = $aln->consensus_string(); # Get consensus of alignment # convert '?' to 'X' for non-consensus positions $string =~ s/\?/X/g; $consensus[$seq_num] = Bio::Seq->new(-id=>"$id left out",-seq=>$string); push @seq_array, $obj_out; # return Seq object for next (sub) alignment } # Compare consensus strings for alignments created in different orders # $factory->ktuple(1); # set ktuple parameter print "\nPerforming alignment of consensus sequences for different reorderings \n"; print "Each consensus is labeled by the sequence which was omitted in the initial alignment\n"; $aln = $factory->align(\@consensus); $strout = Bio::AlignIO->newFh('-format' => 'msf'); print $strout $aln; return 1; } ################################################# # anchored_align() # # For our last example, we'll test a way to perform a local alignment by # "anchoring" the alignment to a regular expression. This is similar # to the approach taken in the recent dbclustal program. # In principle, we could write a script to search for a good regular expression # to use. Instead, here we'll simply choose one manually after looking at the # previous alignments. sub anchored_align { my @local_array = (); my @seqs_not_matched = (); print "\n Beginning anchored-alignment example... \n"; for ($seq_num = 0; $seq_num < scalar(@seq_array); $seq_num++) { my $seqobj = $seq_array[$seq_num]; my $seq = $seqobj->seq(); my $id = $seqobj->id(); # if $regex is not found in the sequence, save sequence id name and set # array value =0 for later unless ($seq =~/$regex/) { $local_array[$seq_num] = 0; push (@seqs_not_matched, $id) ; next; } # find positions of start and of subsequence to be aligned my $match_start_pos = length($`); my $match_stop_pos = length($`) + length($&); my $start = ($match_start_pos - $extension) > 1 ? ($match_start_pos - $extension) +1 : 1; my $stop = ($match_stop_pos + $extension) < length($seq) ? ($match_stop_pos + $extension) : length($seq); my $string = $seqobj->subseq($start, $stop); $local_array[$seq_num] = Bio::Seq->new(-id=>$id, -seq=>$string); } @local_array = grep $_ , @local_array; # remove array entries with no match # Perform alignment on the local segments of the sequences which match "anchor" $aln = $factory->align(\@local_array); my $consensus = $aln->consensus_string(); # Get consensus of local alignment if (scalar(@seqs_not_matched) ) { print " Sequences not matching $regex : @seqs_not_matched \n" } else { print " All sequences match $regex : @seqs_not_matched \n" } print "Consensus sequence of local alignment: $consensus \n"; return 1; } #---------------- sub clustalw_usage { #---------------- #----------------------- # Prints usage information for general parameters. print STDERR <<"QQ_PARAMS_QQ"; Command-line accessible script variables and commands: ------------------------------- -h : Display this usage info and exit. -in : File containing input sequences in fasta format (default = $infile) . -do : String listing examples to be executed. Default is to execute all tests (ie default = '123') -param : Parameter to be varied in example 1. Any clustalw parameter which takes inteer values can be varied (default = 'ktuple') -start : Initial value for varying parameter in example 1 (default = 1) -stop : Final value for varying parameter (default = 3) -regex : Regular expression for 'anchoring' alignment in example 3 (default = $regex) -ext : Distance regexp anchor should be extended in each direction for local alignment in example 3 (default = 30) In addition, any valid Clustalw parameter can be set using the syntax "parameter=>value" as in "ktuple=>3" So a typical command lines might be: > clustalw.pl -param=pairgap -start=2 -stop=3 -do=1 "ktuple=>3" or > clustalw.pl -ext=10 -regex='W[AST]F' -do=23 -in='t/cysprot1a.fa' QQ_PARAMS_QQ } BioPerl-1.007002/examples/align/simplealign.pl000555000766000024 3232613155576320 21315 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl # PROGRAM : simplealign.pl # PURPOSE : Simple driver for Bio::SimpleAlign # AUTHOR : Ewan Birney birney@sanger.ac.uk # CREATED : Tue Oct 27 1998 # # INSTALLATION # If you have installed bioperl using the standard # makefile system everything should be fine and # dandy. # # if not edit the use lib "...." line to point the directory # containing your Bioperl modules. # #use lib "/nfs/disk21/birney/prog/bioperl/"; # Modified 3/5/01 to use AlignIO by Peter Schattner schattner@alum.mit.edu # # This uses the internal DATA stream (past the end of this # file, on the __END__ tag) to load in the data. We then # do some reformats, sort in a different way and a quick # getting into the alignment. All pretty simple ;) # # # The simplealign module does not do the following things # a) give you sensible ways of asking if residues are a # column of gaps or conservation # b) provide ways of editing the alignment # c) making alignments # # # a) and b) are probably best done by UnivAlign from Georg Fuellen # c) is done for pairwise alignments in Bio::Tools::pSW; and # also you can read in stuff from programs like clustal and hmmer # into this. # use strict; use Bio::SimpleAlign; use Bio::AlignIO; # read from a stream my $str = Bio::AlignIO->newFh('-fh'=> \*DATA, '-format' => 'pfam' ); my $al = <$str>; # write out a MSF file my $out = Bio::AlignIO->newFh('-fh'=> \*STDOUT, '-format' => 'msf'); my $status = print $out $al; # order by alphabetically then start end $al->sort_alphabetically(); # write in Pfam format now... my $out2=Bio::AlignIO->newFh( '-fh'=> \*STDOUT, '-format' => 'pfam'); $status = print $out2 $al; # now set the display name to be # name_# like roa1_human_1, roa1_human_2 etc # This **doesn't** change the underlying names of the # sequences you'll be glad to hear. $al->set_displayname_count(); # dump again... bored of this yet? $status = print $out2 $al; # get into the alignment and get things out # we just want to see how many unique names # there are in this alignment my ($seq, $id, %hash) ; # loop over the alignment foreach $seq ( $al->eachSeq() ) { # increment a hash on the name by one each time $hash{$seq->id()}++; } # disgorge the hash foreach $id ( keys %hash ) { print "$id has $hash{$id} subsequences in this alignment\n"; } __END__ GR10_BRANA/8-79 CFVGGL......AWATGDAELERTFS.....Q.FGEV..IDSKIIND.............RETGRSRGFGFVTFKDEKSMKDAIDEMNG.K...ELDGRTITV HUD_HUMAN/48-119 LIVNYL......PQNMTQEEFRSLFG.....S.IGEI..ESCKLVRD.............KITGQSLGYGFVNYIDPKDAEKAINTLNG.L...RLQTKTIKV IF32_SCHPO/41-124 VVIEGAP....VVEEAKQQDFFRFLSSKVLAK.IGKVKENGFYMPFE.........EKNGK..KMSLGLVFADFENVDGADLCVQELDGKQ...ILKNHTFVV IF32_YEAST/79-157 IVVNGAPVIPSAKVPVLKKALTSLFS.....K.AGKV..VNMEFPID.............EATGKTKGFLFVECGSMNDAKKIIKSFHGKR...LDLKHRLFL IF4B_HUMAN/98-168 AFLGNL......PYDVTEESIKEFFR.....G.LNIS...AVRLPR............EPSNPERLKGFGYAEFEDLDSLLSALS.LNE.E...SLGNRRIRV LA_DROME/151-225 AYAKGF......PLDSQISELLDFTA.....N.YDKV..VNLTMRNS.........YDKPTKSYKFKGSIFLTFETKDQAKAFLE.QEK.I...VYKERELLR LA_HUMAN/113-182 VYIKGF......PTDATLDDIKEWLE.....D.KGQV..LNIQMRR..............TLHKAFKGSIFVVFDSIESAKKFVE.TPG.Q...KYKETDLLI MEI2_SCHPO/197-265 LFVTNL......PRIVPYATLLELFS.....K.LGDV..KGIDTSSL.................STDGICIVAFFDIRQAIQAAKSLRSQR...FFNDRLLYF MODU_DROME/177-246 VFVTNL......PNEYLHKDLVALFA.....K.FGRL..SALQRFTN................LNGNKSVLIAFDTSTGAEAVLQAKPKAL...TLGDNVLSV MODU_DROME/260-326 VVVGLI......GPNITKDDLKTFFE.....K.VAPV..EAVTISSN.................RLMPRAFVRLASVDDIPKALK.LHS.T...ELFSRFITV MODU_DROME/342-410 LVVENVG....KHESYSSDALEKIFK.....K.FGDV..EEIDVVC..................SKAVLAFVTFKQSDAATKALAQLDG.K...TVNKFEWKL MODU_DROME/422-484 ILVTNL......TSDATEADLRKVFN.....D.SGEI..ESIIMLG.....................QKAVVKFKDDEGFCKSFL.ANE.S...IVNNAPIFI MSSP_HUMAN/31-102 LYIRGL......PPHTTDQDLVKLCQ.....P.YGKI..VSTKAILD.............KTTNKCKGYGFVDFDSPAAAQKAVSALKA.S...GVQAQKAKQ NAM8_YEAST/165-237 IFVGDL......APNVTESQLFELFI.....NRYAST..SHAKIVHD.............QVTGMSKGYGFVKFTNSDEQQLALSEMQG.V...FLNGRAIKV NONA_DROME/304-369 LYVGNL......TNDITDDELREMFK.....P.YGEI..SEIFSNLD...................KNFTFLKVDYHPNAEKAKRALDG.S...MRKGRQLRV NONA_DROME/378-448 LRVSNL......TPFVSNELLYKSFE.....I.FGPI..ERASITVD..............DRGKHMGEGIVEFAKKSSASACLRMCNE.K...CFFLTASLR NOP3_YEAST/127-190 LFVRPF......PLDVQESELNEIFG.....P.FGPM..KEVKILN.....................GFAFVEFEEAESAAKAIEEVHG.K...SFANQPLEV NOP3_YEAST/202-270 ITMKNL......PEGCSWQDLKDLAR.....E.NSLE..TTFSSVN................TRDFDGTGALEFPSEEILVEALERLNN.I...EFRGSVITV NOP4_YEAST/28-98 LFVRSI......PQDVTDEQLADFFS.....N.FAPI..KHAVVVKD..............TNKRSRGFGFVSFAVEDDTKEALAKARK.T...KFNGHILRV NOP4_YEAST/292-363 VFVRNV......PYDATEESLAPHFS.....K.FGSV..KYALPVID.............KSTGLAKGTAFVAFKDQYTYNECIKNAPA.A...GSTSLLIGD NSR1_YEAST/170-241 IFVGRL......SWSIDDEWLKKEFE.....H.IGGV..IGARVIYE.............RGTDRSRGYGYVDFENKSYAEKAIQEMQG.K...EIDGRPINC NSR1_YEAST/269-340 LFLGNL......SFNADRDAIFELFA.....K.HGEV..VSVRIPTH.............PETEQPKGFGYVQFSNMEDAKKALDALQG.E...YIDNRPVRL NUCL_CHICK/283-352 LFVKNL......TPTKDYEELRTAIK.....EFFGKK...NLQVSEV..............RIGSSKRFGYVDFLSAEDMDKALQ.LNG.K...KLMGLEIKL PABP_DROME/4-75 LYVGDL......PQDVNESGLFDKFS.....S.AGPV..LSIRVCRD.............VITRRSLGYAYVNFQQPADAERALDTMNF.D...LVRNKPIRI PABP_DROME/92-162 VFIKNL......DRAIDNKAIYDTFS.....A.FGNI..LSCKVATD..............EKGNSKGYGFVHFETEEAANTSIDKVNG.M...LLNGKKVYV PABP_DROME/183-254 VYVKNF......TEDFDDEKLKEFFE.....P.YGKI..TSYKVMS..............KEDGKSKGFGFVAFETTEAAEAAVQALNGKD...MGEGKSLYV PABP_SCHPO/249-319 VYIKNL......DTEITEQEFSDLFG.....Q.FGEI..TSLSLVKD..............QNDKPRGFGFVNYANHECAQKAVDELND.K...EYKGKKLYV PES4_YEAST/93-164 LFIGDL......HETVTEETLKGIFK.....K.YPSF..VSAKVCLD.............SVTKKSLGHGYLNFEDKEEAEKAMEELNY.T...KVNGKEIRI PES4_YEAST/305-374 IFIKNL......PTITTRDDILNFFS.....E.VGPI..KSIYLSN...............ATKVKYLWAFVTYKNSSDSEKAIKRYNN.F...YFRGKKLLV PR24_YEAST/43-111 VLVKNL......PKSYNQNKVYKYFK.....H.CGPI..IHVDVAD...............SLKKNFRFARIEFARYDGALAAIT.KTH.K...VVGQNEIIV PR24_YEAST/119-190 LWMTNF......PPSYTQRNIRDLLQ.....D.INVV.ALSIRLPSL..............RFNTSRRFAYIDVTSKEDARYCVEKLNG.L...KIEGYTLVT PR24_YEAST/212-284 IMIRNL.....STELLDENLLRESFE.....G.FGSI..EKINIPAG............QKEHSFNNCCAFMVFENKDSAERALQ.MNR.S...LLGNREISV PSF_HUMAN/373-443 LSVRNL......SPYVSNELLEEAFS.....Q.FGPI..ERAVVIVD..............DRGRSTGKGIVEFASKPAARKAFERCSE.G...VFLLTTTPR PTB_HUMAN/61-128 IHIRKL......PIDVTEGEVISLGL.....P.FGKV..TNLLMLKG...................KNQAFIEMNTEEAANTMVN.YYT.SVTPVLRGQPIYI PTB_HUMAN/186-253 IIVENL......FYPVTLDVLHQIFS.....K.FGTV....LKIIT...............FTKNNQFQALLQYADPVSAQHAKLSLDG.Q...NIYNACCTL PUB1_YEAST/76-146 LYVGNL......DKAITEDILKQYFQ.....V.GGPI..ANIKIMID..............KNNKNVNYAFVEYHQSHDANIALQTLNG.K...QIENNIVKI PUB1_YEAST/163-234 LFVGDL......NVNVDDETLRNAFK.....D.FPSY..LSGHVMWD.............MQTGSSRGYGFVSFTSQDDAQNAMDSMQG.Q...DLNGRPLRI PUB1_YEAST/342-407 AYIGNI......PHFATEADLIPLFQ.....N.FGFI..LDFKHYPE...................KGCCFIKYDTHEQAAVCIVALAN.F...PFQGRNLRT RB97_DROME/34-104 LFIGGL......APYTTEENLKLFYG.....Q.WGKV..VDVVVMRD.............AATKRSRGFGFITYTKSLMVDRAQE..NRPH...IIDGKTVEA RN12_YEAST/200-267 IVIKFQ......GPALTEEEIYSLFR.....R.YGTI....IDIFP...............PTAANNNVAKVRYRSFRGAISAKNCVSG.I...EIHNTVLHI RN15_YEAST/20-91 VYLGSI......PYDQTEEQILDLCS.....N.VGPV..INLKMMFD.............PQTGRSKGYAFIEFRDLESSASAVRNLNG.Y...QLGSRFLKC RNP1_YEAST/37-109 LYVGNL......PKNCRKQDLRDLFE.....PNYGKI..TINMLKKK.............PLKKPLKRFAFIEFQEGVNLKKVKEKMNG.K...IFMNEKIVI RO28_NICSY/99-170 LFVGNL......PYDIDSEGLAQLFQ.....Q.AGVV..EIAEVIYN.............RETDRSRGFGFVTMSTVEEADKAVELYSQ.Y...DLNGRLLTV RO33_NICSY/116-187 LYVGNL......PFSMTSSQLSEIFA.....E.AGTV..ANVEIVYD.............RVTDRSRGFAFVTMGSVEEAKEAIRLFDG.S...QVGGRTVKV RO33_NICSY/219-290 LYVANL......SWALTSQGLRDAFA.....D.QPGF..MSAKVIYD.............RSSGRSRGFGFITFSSAEAMNSALDTMNE.V...ELEGRPLRL ROA1_BOVIN/106-176 IFVGGI......KEDTEEHHLRDYFE.....Q.YGKI..EVIEIMTD.............RGSGKKRGFAFVTFDDHDSVDKIVI.QKY.H...TVNGHNCEV ROC_HUMAN/18-82 VFIGNL.....NTLVVKKSDVEAIFS.....K.YGKI..VGCSVHK.....................GFAFVQYVNERNARAAVAGEDG.R...MIAGQVLDI ROF_HUMAN/113-183 VRLRGL......PFGCTKEEIVQFFS.....G.LEIV.PNGITLPVD..............PEGKITGEAFVQFASQELAEKALG.KHK.E...RIGHRYIEV ROG_HUMAN/10-81 LFIGGL......NTETNEKALEAVFG.....K.YGRI..VEVLLMKD.............RETNKSRGFAFVTFESPADAKDAARDMNG.K...SLDGKAIKV RT19_ARATH/33-104 LYIGGL......SPGTDEHSLKDAFS.....S.FNGV..TEARVMTN.............KVTGRSRGYGFVNFISEDSANSAISAMNG.Q...ELNGFNISV RU17_DROME/104-175 LFIARI......NYDTSESKLRREFE.....F.YGPI..KKIVLIHD.............QESGKPKGYAFIEYEHERDMHAAYKHADG.K...KIDSKRVLV RU1A_HUMAN/12-84 IYINNLNE..KIKKDELKKSLYAIFS.....Q.FGQI..LDILVSR................SLKMRGQAFVIFKEVSSATNALRSMQG.F...PFYDKPMRI RU1A_HUMAN/210-276 LFLTNL......PEETNELMLSMLFN.....Q.FPGF..KEVRLVPG..................RHDIAFVEFDNEVQAGAARDALQG.F...KITQNNAMK RU1A_YEAST/229-293 LLIQNL......PSGTTEQLLSQILG.....N.EALV...EIRLVSV...................RNLAFVEYETVADATKIKNQLGS.T...YKLQNNDVT RU2B_HUMAN/9-81 IYINNMND..KIKKEELKRSLYALFS.....Q.FGHV..VDIVALK................TMKMRGQAFVIFKELGSSTNALRQLQG.F...PFYGKPMRI RU2B_HUMAN/153-220 LFLNNL......PEETNEMMLSMLFN.....Q.FPGF..KEVRLVPG..................RHDIAFVEFENDGQAGAARDALQGFK...ITPSHAMKI SC35_CHICK/16-87 LKVDNL......TYRTSPDTLRRVFE.....K.YGRV..GDVYIPRD.............RYTKESRGFAFVRFHDKRDAEDAMDAMDG.A...VLDGRELRV SP33_HUMAN/17-85 IYVGNL......PPDIRTKDIEDVFY.....K.YGAI..RDIDLKNR................RGGPPFAFVEFEDPRDAEDAVYGRDG.Y...DYDGYRLRV SP33_HUMAN/122-186 VVVSGL......PPSGSWQDLKDHMR.....E.AGDV..CYADVYRD....................GTGVVEFVRKEDMTYAVRKLDN.T...KFRSHEGET SQD_DROME/58-128 LFVGGL......SWETTEKELRDHFG.....K.YGEI..ESINVKTD.............PQTGRSRGFAFIVFTNTEAIDKVSA.ADE.H...IINSKKVDP SQD_DROME/138-208 IFVGGL......TTEISDEEIKTYFG.....Q.FGNI..VEVEMPLD.............KQKSQRKGFCFITFDSEQVVTDLLK.TPK.Q...KIAGKEVDV SR55_DROME/5-68 VYVGGL......PYGVRERDLERFFK.....G.YGRT..RDILIKN.....................GYGFVEFEDYRDADDAVYELNG.K...ELLGERVVV SSB1_YEAST/39-114 IFIGNV......AHECTEDDLKQLFV.....EEFGDE..VSVEIPIK..........EHTDGHIPASKHALVKFPTKIDFDNIKENYDT.K...VVKDREIHI SXLF_DROME/127-198 LIVNYL......PQDMTDRELYALFR.....A.IGPI..NTCRIMRD.............YKTGYSFGYAFVDFTSEMDSQRAIKVLNG.I...TVRNKRLKV SXLF_DROME/213-285 LYVTNL......PRTITDDQLDTIFG.....K.YGSI..VQKNILRD.............KLTGRPRGVAFVRYNKREEAQEAISALNNVI...PEGGSQPLS TIA1_HUMAN/9-78 LYVGNL......SRDVTEALILQLFS.....Q.IGPC..KNCKMIMD...............TAGNDPYCFVEFHEHRHAAAALAAMNG.R...KIMGKEVKV TIA1_HUMAN/97-168 VFVGDL......SPQITTEDIKAAFA.....P.FGRI..SDARVVKD.............MATGKSKGYGFVSFFNKWDAENAIQQMGG.Q...WLGGRQIRT TIA1_HUMAN/205-270 VYCGGV......TSGLTEQLMRQTFS.....P.FGQI..MEIRVFPD...................KGYSFVRFNSHESAAHAIVSVNG.T...TIEGHVVKC TRA2_DROME/99-170 IGVFGL......NTNTSQHKVRELFN.....K.YGPI..ERIQMVID.............AQTQRSRGFCFIYFEKLSDARAAKDSCSG.I...EVDGRRIRV U2AF_HUMAN/261-332 LFIGGL......PNYLNDDQVKELLT.....S.FGPL..KAFNLVKD.............SATGLSKGYAFCEYVDINVTDQAIAGLNG.M...QLGDKKLLV U2AF_SCHPO/312-383 IYISNL......PLNLGEDQVVELLK.....P.FGDL..LSFQLIKN.............IADGSSKGFCFCEFKNPSDAEVAISGLDG.K...DTYGNKLHA U2AG_HUMAN/67-142 CAVSDVEM..QEHYDEFFEEVFTEME.....EKYGEV..EEMNVCDN..............LGDHLVGNVYVKFRREEDAEKAVIDLNN.R...WFNGQPIHA WHI3_YEAST/540-614 LYVGNL......PSDATEQELRQLFS.....G.QEGF..RRLSFRNK..........NTTSNGHSHGPMCFVEFDDVSFATRALAELYG.R...QLPRSTVSS X16_HUMAN/12-78 VYVGNL......GNNGNKTELERAFG.....Y.YGPL..RSVWVARN..................PPGFAFVEFEDPRDAADAVRELDG.R...TLCGCRVRV YHC4_YEAST/348-415 IFVGQL......DKETTREELNRRFS.....T.HGKI..QDINLIFK.................PTNIFAFIKYETEEAAAAALESENH.A...IFLNKTMHV YHH5_YEAST/315-384 ILVKNL......PSDTTQEEVLDYFS.....T.IGPI..KSVFISEK...............QANTPHKAFVTYKNEEESKKAQKCLNK.T...IFKNHTIWV YIS1_YEAST/66-136 IFVGNI......TPDVTPEQIEDHFK.....D.CGQI..KRITLLYD.............RNTGTPKGYGYIEFESPAYREKALQ.LNG.G...ELKGKKIAV YIS5_YEAST/33-104 IYIGNL......NRELTEGDILTVFS.....E.YGVP..VDVILSRD.............ENTGESQGFAYLKYEDQRSTILAVDNLNG.F...KIGGRALKI ARP2_PLAFA/364-438 VEVTYLF....STYLVNGQTL..IYS.....N.ISVV....LVILY........HQKFKETVLGRNSGFGFVSYDNVISAQHAIQFMNG.Y...FVNNKYLKV CABA_MOUSE/77-147 MFVGGL......SWDTSKKDLKDYFT.....K.FGEV..VDCTIKMD.............PNTGRSRGFGFILFKDSSSVEKVLD.QKE.H...RLDGRVIDP CABA_MOUSE/161-231 IFVGGL......NPEATEEKIREYFG.....Q.FGEI..EAIELPID.............PKLNKRRGFVFITFKEEDPVKKVLE.KKF.H...TVSGSKCEI CPO_DROME/453-526 LFVSGL......PMDAKPRELYLLFR.....A.YEGY..EGSLLKV............TSKNGKTASPVGFVTFHTRAGAEAAKQDLQGVR...FDPDMPQTI CST2_HUMAN/18-89 VFVGNI......PYEATEEQLKDIFS.....E.VGPV..VSFRLVYD.............RETGKPKGYGFCEYQDQETALSAMRNLNG.R...EFSGRALRV D111_ARATH/281-360 LLLRNMVG.PGQVDDELEDEVGGECA.....K.YGTV..TRVLIFE..........ITEPNFPVHEAVRIFVQFSRPEETTKALVDLDG.R...YFGGRTVRA ELAV_DROME/250-322 LYVSGL......PKTMTQQELEAIFA.....P.FGAI..ITSRILQN............AGNDTQTKGVGFIRFDKREEATRAIIALNG.T...TPSSCTDPI ELAV_DROME/404-475 IFIYNL......APETEEAALWQLFG.....P.FGAV..QSVKIVKD.............PTTNQCKGYGFVSMTNYDEAAMAIRALNG.Y...TMGNRVLQV EWS_HUMAN/363-442 IYVQGL......NDSVTLDDLADFFK.....Q.CGVV..K.MNKRTG....QPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDG.K...DFQGSKLKV GBP2_YEAST/124-193 IFVRNL......TFDCTPEDLKELFG.....T.VGEV..VEADIIT...............SKGHHRGMGTVEFTKNESVQDAISKFDG.A...LFMDRKLMV GBP2_YEAST/221-291 VFIINL......PYSMNWQSLKDMFK.....E.CGHV..LRADVELD..............FNGFSRGFGSVIYPTEDEMIRAIDTFNG.M...EVEGRVLEV GBP2_YEAST/351-421 IYCSNL......PFSTARSDLFDLFG.....P.IGKI..NNAELKP..............QENGQPTGVAVVEYENLVDADFCIQKLNN.Y...NYGGCSLQI BioPerl-1.007002/examples/cluster000755000766000024 013155576320 16655 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/cluster/dbsnp.pl000555000766000024 105613155576320 20462 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl # allenday@ucla.edu # parses a dbsnp xml file, prints some info for each refsnp and subsnp use strict; use Bio::ClusterIO; use Bio::Root::IO; use IO::File; my $file = shift @ARGV; my $io = Bio::ClusterIO->new ( -tempfile => 0, -format => 'dbsnp', -fh => IO::File->new("zcat $file |"), ); while(my $cluster = $io->next_cluster){ print $cluster->id,"\t", $cluster->observed, "\n"; foreach my $subsnp ($cluster->each_subsnp){ print "\t\t\t", $subsnp->id, "\t", $subsnp->handle, "\t", $subsnp->method, "\n"; } } BioPerl-1.007002/examples/contributed000755000766000024 013155576320 17516 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/contributed/nmrpdb_parse.pl000555000766000024 1105213155576320 22706 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl use strict; # This program will read in an NMR derived PDB file containing # multiple conformers, and will allow the user to extract either # one or all of the models to separate files. # # Although the program will run interactively, the command line # usage is "nmrsplit [input.file] [number of model to extract]" # # # # Written 13/12/00 by Simon Andrews (simon.andrews@bbsrc.ac.uk) # Submitted to bioperl script project 2001/08/06 # Description: Script which reads an NMR-derived multiple structure # PDB file, and will either extract a single structure from it, or # will extract all of the structures into single files. This is # useful when you want to work with a single representative structure # from an NMR ensemble - especially in conjunction with the OLDERADO # database (http://neon.chem.le.ac.uk/olderado/) which finds the # most representative structure from an ensemble. my $Input = $ARGV[0]; # File to be read my $Pullout = $ARGV[1]; # Specific model to extract my @Pdbfile; # Array for whole PDB file my $Header = ""; # String to hold the PDB header my $Model = ""; # String to hold individual models my $Output; # Prefix for output files my $Modno = 1; # Number of the model being processed while () { if ($Input) { if (-r $Input) { last; }else{ print "\"$Input\" does not exist, or could not be read\n"; } } print "\nEnter name of multiple PDB file: "; $Input = ; chomp $Input; $Input =~ s/^\s*//; $Input =~ s/\s*$//; next; } while () { if ($Pullout) { if ($Pullout =~ /^\d+$/){ if ($Pullout == int $Pullout) { last; }else { print "\"$Pullout\" should be an integer\n"; } }else { print "\"$Pullout\" should be a number\n"; } } print "\nEnter number of specific model to extract (Return for none): "; $Pullout = ; chomp $Pullout; $Pullout =~ s/^\s*//; $Pullout =~ s/\s*$//; last unless ($Pullout); next; } ($Output = $Input) =~ s/\.\w*$//; # Take off everything after the last . to use as prefix open (PDB,$Input) || die "Can't open $Input because $!"; ########## Read the header information #################### while () { if (/^MODEL\b/){last;} $Header = $Header . $_; } ######### Read the separate models ####################### while () { model(); if ($Model) { # Check if we're past the last model if ($Pullout) { # Check if we're writing one or all last if ($Modno > $Pullout);# No point continuing if we've got the one we want readout(); }else { writeout(); } $Model = ""; ++$Modno; }else { last; } } --$Modno; # Correct last increment which didn't find a model if (($Pullout) & ($Modno < $Pullout)) { print "\nCannot find model $Pullout : Only $Modno models in this file\n"; } #################### subroutines start here ########################## sub model { while () { if (/^(MODEL\b|END\b|MASTER\b)/){next;} # Stops you getting MODEL... at the top of the output # and makes sure there isn't a file containing just END or MASTER if (/^ENDMDL\b/){last;} # Check for the end of the model $Model = $Model . $_; # Append the line to $Model } } sub writeout { # Used when all files are being written out if (-e "$Output\_$Modno.pdb"){ # Check whether we're overwriting anything print "\n$Output\_$Modno.pdb already exists. Overwrite (y/n)? "; my $Question = ; unless ($Question =~ /^y/i) { print "\nSkipping $Output\_$Modno.pdb"; return; } } open (OUT,">$Output\_$Modno.pdb") || die "Can't open $Output\_$Modno.pdb because $!"; print "\nWriting $Output\_$Modno.pdb ..."; print OUT $Header; print OUT $Model; print OUT "END\n"; # Adds and END statement to the PDB file close OUT || die "Couldn't close $Output\_$Modno.pdb because $!"; } sub readout { if ($Modno == $Pullout) { if (-e "$Output\_$Modno.pdb") { # Check whether we're overwriting anything print "\n$Output\_$Modno.pdb already exists. Overwrite (y/n)? "; my $Question = ; unless ($Question =~ /^y/i) { print "\nModel not extracted\n"; $Model = ""; return; } } open (OUT,">$Output\_$Modno.pdb") || die "Can't open $Output\_$Modno.pdb because $!"; print "\nWriting $Output\_$Modno.pdb ...\n"; print OUT $Header; print OUT $Model; print OUT "END\n"; # Adds and END statement to the PDB file close OUT || die "Couldn't close $Output\_$Modno.pdb because $!"; $Model = ""; # Stops the reading after this model }else { print "\nReading Model $Modno ..."; } } BioPerl-1.007002/examples/contributed/prosite2perl.pl000555000766000024 120413155576320 22642 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl # prosite2perl -- convert Prosite patterns to Perl regular expressions # # Jordan Dimov (jdimov@cis.clarion.edu) # # Submitted to bioperl scripts project 2001/08/03 # # Description: # Prosite patterns to Perl regular expressions. # The prositeRegEx($) sub accepts a string # containing a Prosite pattern and returns a # string containing a valid Perl regex. The code # is self-explanatory. sub prositeRegEx($); while (<>) { chomp ($_); print prositeRegEx ($_), "\n"; } sub prositeRegEx ($) { my $regex = shift; $regex =~ s/[\-\.]//g; $regex =~ s/\{/[^/g; $regex =~ tr/x()<>}/.{}^$]/; return ($regex); } BioPerl-1.007002/examples/contributed/rebase2list.pl000555000766000024 104513155576320 22432 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl # Generate an enzyme list for RestrictionEnzyme.pm from rebase # From Ryan Brinkman my $strider = $ARGV[0]; #commercial_version_rebase_strider_format open my $FILEIN, '<', $strider or die "Could not read file '$strider': $!\n"; while (<$FILEIN>){ chomp; if ( /^[A-Z]\S+,\S+/ ){ ($enzyme,$cutsite)=split(','); if ($cutsite =~ m#/#){ $match=$-[0]; } ($seqfixed=$cutsite) =~ s/\///g; $seqfixed=uc $seqfixed; print " \'$enzyme\'\t=> \'".$seqfixed." ".$match."\'\,\n"; } } close $FILEIN; BioPerl-1.007002/examples/db000755000766000024 013155576320 15561 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/db/dbfetch000555000766000024 4437413155576320 17277 0ustar00cjfieldsstaff000000000000#!/usr/local/bin/perl -- # -*-Perl-*- =head1 NAME dbfetch - generic CGI program to retrieve biological database entries in various formats and styles (using SRS) =head1 SYNOPSIS # URL examples: # prints the interactive page with the HTML form http://www.ebi.ac.uk/Tools/dbfetch/dbfetch # for backward compatibility, implements # single entry queries defaulting to EMBL sequence database http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?J00231 # retrieves one or more entries in default format # and default style (html) # returns nothing for IDs which are not valid http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?id=J00231.1,hsfos,bum # retrieve entries in fasta format without html tags http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?format=fasta&style=raw&id=J00231,hsfos,bum # retrieve a raw Ensembl entry http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ensembl&style=raw&id=AL122059 =head1 DESCRIPTION This program generates a page allowing a web user to retrieve database entries from a local SRS in two styles: html and raw. Other database engines can be used to implement te same interfase. At this stage, on unique identifier queries are supported. Free text searches returning more than one entry per query term are not in these specs. In its default setup, type one or more EMBL accession numbers (e.g. J00231), entry name (e.g. HSFOS) or sequence version into the seach dialog to retieve hypertext linked enties. Note that for practical reasons only the first 50 identifiers submitted are processed. Additional input is needed to change the sequence format or suppress the HTML tags. The styles are html and raw. In future there might be additional styles (e.g. xml). Currently XML is a 'raw' format used by Medline. Each style is implemented as a separate subroutine. =head1 MAINTANENCE A new database can be added simply by adding a new entry in the global hash %IDS. Additionally, if the database defines new formats add an entry for each of them into the hash %IDMATCH. After modifying the hash, run this script from command line for some sanity checks with parameter debug set to true (e.g. dbfetch debug=1 ). Finally, the user interface needs to be updated in the L subroutine. =head1 VERSIONS Version 3 uses EBI SRS server 6.1.3. That server is able to merge release and update libraries automatically which makes this script simpler. The other significant change is the way sequence versions are indexed. They used to be indexed together with the string accession (e.g. 'J00231.1'). Now they are indexed as integers (e.g. '1'). Version 3.1 changes the command line interface. To get the debug information use attribute 'debug' set to true. Also, it uses File::Temp module to create temporary files securely. Version 3.2 fixes fasta format parsing to get the entry id. Version 3.3. Adds RefSeq to the database list. Version 3.4. Make this compliant to BioFetch specs. =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki-at-bioperl-dot-org =cut # Let the code begin... $VERSION = '3.4'; $DATE = '28 Jan 2002'; use CGI "standard"; #use POSIX; use CGI::Carp qw/ fatalsToBrowser /; use File::Temp qw/ tempfile tempdir /; use strict; no strict "refs"; use constant MAXIDS => 50; use constant TMPDIR => '/usr/tmp'; use vars qw( $VERSION $DATE %DBS %STYLES $RWGETZ $RGETZ %IDMATCH %IDLIST $XEMBL $FH ); BEGIN { # paths to SRS binaries $RWGETZ = '/ebi/srs/srs/bin/osf_5/wgetz -e'; $RGETZ = '/ebi/srs/srs/bin/osf_5/getz -e'; $XEMBL = "cd /ebi/www/pages/cgi-bin/xembl/; ./XEMBL.pl"; #$EMBOSSDIR = '/ebi/services/pkgs/emboss/bin'; # RE matching the unique ID in the db entry # - key is the # - put the id string in parenthesis %IDMATCH = ( # 123 embl => 'ID (\w+)', fasta => '>\w+.(\w+)', medlinefull => '[\n><]MedlineID. ?(\w+)', swissprot => 'ID (\w+)', pdb => '.{62}(\w+)', bsml => 'DUMMY', agave => 'DUMMY', refseq => 'LOCUS ([\w_]+)' ); %DBS = ( embl => { fields => ['id', 'acc'], version => 'sv', # name of the SRS field format => { default => 'embl', embl => 1, fasta => 'FastaSeqs', bsml => 1, agave => 1 } }, medline => { fields => ['id'], format => { default => 'medlinefull', # medlineref => 'MedlineRef', medlinefull => 'MedlineFull' } }, ensembl => { fields => ['id'], format => { default => 'embl', embl => 1, fasta => 'FastaSeqs' } }, swall => { fields => ['id', 'acc'], format => { default => 'swissprot', swissprot => 1, fasta => 'FastaSeqs' } }, pdb => { fields => ['id'], format => { default => 'pdb', pdb => '1' } }, refseq => { fields => ['id', 'acc'], format => { default => 'refseq', refseq => 1, fasta => 'FastaSeqs' } } #add more databases here... ); %STYLES = ( html => 1, raw => 1 ); %IDLIST = (); #redundancy check list built during the execution } my $q = new CGI; # sanity checks if the script is running from command line # and debug parameter is set. my $debug = protect($q->param('debug')) if $q->param('debug'); &debugging if not $q->user_agent and $debug; if ( $q->param('id') or $q->param('keywords') ) { # pacify input strings my $value; $value = protect($q->param('id')) if $q->param('id'); $value = protect($q->param('keywords')) if $q->param('keywords'); my $db = lc protect($q->param('db')); # let's keep the case lower my $format = lc protect($q->param('format')); my $style = lc protect($q->param('style')); # check input and set defaults $style ||= 'html'; # default style input_error($q, $style, "2 Unknown style [$style].") unless $STYLES{$style}; $db ||= 'embl'; # default db input_error($q, $style, "1 Unknown database [$db].") unless $DBS{$db}; $format ||= $DBS{$db}{format}{default}; # default format input_error($q, $style, "3 Format [$format] not known for database [$db]") unless $DBS{$db}{format}{$format}; $format = $DBS{$db}{format}{default} if $format eq 'default'; # If people choose Bsml or AGAVE, DB can only be 'embl' input_error($q, $style, "1 Unknown database [$db].") if ($format eq 'bsml' or $format eq 'agave') and $db ne 'embl'; # If people choose Bsml or AGAVE, internal style has to be xml . Make it so. $style = ($format =~ /(bsml|agave)/i) ? 'xml' : $style; if ($style eq 'html') { print $q->header(-type => 'text/html', -charset => 'UTF-8'); } elsif ($style eq 'raw') { print "Content-Type: text/plain; charset=UTF-8\n\n"; } $FH = tempfile('dbfetchXXXXXX', DIR => TMPDIR, UNLINK => 1 ); #automatic unlinking # Check the number of IDs my @ids = split (/ /, $value); input_error($q, $style, "6 Too many IDs [". scalar @ids. "]. Max [". MAXIDS. "] allowed.") if scalar @ids > MAXIDS; # XEMBL cannot 'glue' single entries due to XML setup #- we need to send things in one go. if ($style eq 'xml') { &xml($format, @ids); } else { my $counter; foreach my $id (@ids) { &$style($db, $id, $format); } no_entries($q, $value) if $style eq 'html' and tell($FH) == 0; } seek $FH, 0, 0; print '
' if $style eq 'html';
    print $_ while <$FH>;
} else {
    print_prompt($q);
}


=head2 print_prompt

 Title   : print_prompt
 Usage   :
 Function: Prints the default page with the query form
           to STDOUT (Web page)
 Args    :
 Returns :

=cut

sub print_prompt {
    print $q->header(),
         $q->start_html(-title => 'DB Entry Retrieval',
                        -bgcolor => 'white',
			-author => 'heikki-at-bioperl-dot-org'
			),
	 '',
	  $q->h1('Generic DB Entry Retrieval'),
	  $q->p("This page allows you to retrieve up to ". MAXIDS .
		 " entries at the time from various up-to-date biological databases."),
	  $q->p("For EMBL, enter an  accession number (e.g. J00231) or entry name (e.g.
		 HSFOS) or a sequence version (e.g. J00231.1), or any combination of them
		 separated by a non-word character into your browser's search dialog.
		 SWALL examples are: fos_human, p53_human.
		 For short Ensembl entries, try : AL122059, AL031002, AL031030 .
		 'Random' Medline entry examples are: 20063307, 98276153.
		 PDB entry examples are: 100D, 1FOS. Try NM_006732 for RefSeq.
		 Only one copy of the latest version of the entry is returned."),
	  $q->hr,
	  $q->startform,
	  $q->popup_menu(-name => 'db',
			 -values => ['EMBL',
				     'SWALL',
				     'PDB',
				     'Medline',
				     'Ensembl',
				     'RefSeq'
				     ]),
	  $q->textfield(-name => 'id',
			 -size => 40,
			 -maxlength => 1000),
	  $q->popup_menu(-name => 'format',
			 -values => ['default','Fasta','bsml','agave']),
	  $q->popup_menu(-name => 'style',
			 -values => ['html','raw']),
	  $q->submit('Retrieve'),
	  $q->endform,
	  $q->hr,
	  $q->h2('Direct access'),
	  $q->p('For backward compatibility, the script defaults to EMBL:'),
	  $q->code('
		     http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?J00231'),
	  $q->p('but the preferred way of calling it is:'),
	  $q->code('
		     http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?id=J00231.1,hsfos,bum'),
	  $q->p('which can be extended to retrieve entries in alternative sequence formats
		      and other databases:'),
	  $q->code('
		     http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=swall&format=fasta&id=fos_human'),
	  $q->p('Set style to raw to retrieve plain text entries for computational purposes
                 and saving to disk:'),
	  $q->code('
                    http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline&style=raw&id=21131735'),
 	  $q->p('There is now the possibility to retrieve EMBL sequences formatterd into two XML standards:
                Bsml (Bioinformatic Sequence Markup Language - from 
                Labbook, Inc.) or as AGAVE (Architecture for Genomic Annotation, 
                Visualisation, and Exchange - from Labbook, Inc.). To do this, use the 
                formats \'bsml\' or \'agave\', as follows:'),
	  $q->code('
                   http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?format=bsml&id=J00231
'),
	  $q->code('
                   http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?format=agave&id=J00231'),
          $q->p("Version numbers are not supported with the XML retrieval."),
	  $q->hr,
          $q->address("Version $VERSION, $DATE, support\@ebi.ac.uk"),
	  $q->end_html, "\n" ;
}

=head2 protect

 Title   : protect
 Usage   : $value = protect($q->param('id'));
 Function:

           Removes potentially dangerous characters from the input
	   string.  At the same time, converts word separators into a
	   single space character.

 Args    : scalar, string with one or more IDs or accession numbers
 Returns : scalar

=cut

sub protect {
    my ($s) = @_;
    $s =~ s![^\w\.\_]+! !g; # allow version numbers with '.' & RefSeq IDs with '_'
    $s =~ s|^\W+||;
    $s =~ s|\W+$||;
    return $s;
}

=head2 input_error

 Title   : input_error
 Usage   : input_error($q, 'html', "Error message");
 Function: Standard error message behaviour
 Args    : reference to the CGI object
           scalar, string to display on input error.
 Returns : scalar

=cut

sub input_error {
    my ($q, $style, $s) = @_;

    if ($style eq 'html' ) {
	print $q->header,
	$q->start_html(-title => 'DB Entry Retrieval: Input error', 
		       -bgcolor => 'white'
		       ),
	"
ERROR in input:
$s\n",
	$q->end_html, "\n";
    } else {
	print "Content-type: text/plain\n\n", "ERROR $s\n";
    }
    exit 0;
}

=head2 no_entries

 Title   : no_entries
 Usage   : no_entries($q, "Message");
 Function: Standard behaviour when no entries found
 Args    : reference to the CGI object
           scalar, string to display on input error.
 Returns : scalar

=cut

sub no_entries {
    my ($q, $value) = @_;

    print $q->start_html(-title => 'DB Entry Retrieval: Input warning',
			 -bgcolor => 'white'
			 ),
	  "
Sorry, your query retrieved no entries.
",
	  "Entries with [$value] where not found.",
	  "Please go back or press here to try again",
	   $q->end_html, "\n";
    exit 0;
}


=head2 raw

 Title   : raw
 Usage   :
 Function: Retrieves a single database entry in plain text
 Args    : scalar, an ID
           scaler, format
 Returns : scalar

=cut

sub raw {
    my ($db, $value, $format) = @_;
    my ($srsq, $qdb, $entry, $id);
    my ($seqformat) = '';
    $seqformat = '-view '. $DBS{$db}{format}{$format}
       if $format ne $DBS{$db}{format}{default};

    my $version = '';
    $value =~ /(.+)\.(.+)/;
    $version = $2 if $2;
    $value = $1 if $1;

    # main db
    $qdb = $db;
    $srsq = '';
    foreach my $field (@{$DBS{$db}{fields}}) {
	$srsq .= " [$qdb-$field:$value] |";
    }
    chop $srsq;

    # if database supports versions (EMBL, GenBank, RefSeq...)
    if ($version) {
	my $vfname = $DBS{$db}{version};
	$srsq = "[$qdb-$vfname:$version] & (". $srsq. ")"
    }

#    print "rsh srs $RGETZ $seqformat $srsq\n";
    $entry = `rsh srs "$RGETZ $seqformat '$srsq'"`;

    $entry =~ s|EMBL[^\n]+\n||;
    $entry =~ s|^\s+||g;
    $entry =~ s|\s+$|\n|g;

    my $idmatch = $IDMATCH{$format};
    ($id) = $entry =~ /$idmatch/;
    # die if ID not found
    input_error(' ', 'raw', "5 ID [$value] not found in database [$db].")
	     unless $id;

#    my $tmp = substr($entry, 0, 20);
#    print "Entry:$tmp\n";
#    print  "-----id=$id---\$1=$1----idmatch=$idmatch=format=$format=\n";
#
    print $FH $entry unless $IDLIST{$id};
    $IDLIST{$id} = 1;
}

=head2 html

 Title   : html
 Usage   :
 Function: Retrieves a single database entry with HTML
           hypertext links in place. Limits retieved enties to 
           ones with correct version if the string has '.' in it.
 Args    : scalar, a UID
           scalar, format
 Returns : scalar

=cut

sub html {
    my ($db, $value, $format) = @_;
    my ($srsq, $qdb, $entry, $id, $idmatch);
    my ($seqformat) = '';
    $seqformat = '-view '. $DBS{$db}{format}{$format}
       if $format ne $DBS{$db}{format}{default};

    my $version = '';
    $value =~ /(.+)\.(.+)/;
    $version = $2 if $2;
    $value = $1 if $1;

    # SWALL plain format at EBI
    $seqformat .= ' -vn 2 ' if $db eq 'swall' or $db eq 'refseq';
    
    $qdb = $db;
    $srsq = '';
    foreach my $field (@{$DBS{$db}{fields}}) {
	$srsq .= " [$qdb-$field:$value] |";
    }
    chop $srsq;

    # if database supports versions (EMBL...)
    if ($version) {
	my $vfname = $DBS{$db}{version};
	$srsq = "[$qdb-$vfname:$version] & (". $srsq. ")"
    }

#    print "rsh srs $RWGETZ $seqformat $srsq\n";
    ### '-id EBISRS' is (hopefully) a temporary addtion until SRS HTML output is fixed 
    $entry = `rsh srs "$RWGETZ $seqformat '$srsq'"`;
  
    return if $entry =~ /SRS error/;

    $entry =~ s|^Content-type:[^\n]+\n||;
    $entry =~ s|\n||g;
    $entry =~ s|||g;
    $entry =~ s|\n+|\n|g;
    $entry =~ s|^\n+||g;

    $idmatch = $IDMATCH{$format};
    ($id) = $entry =~ /$idmatch/;

#    my $tmp = substr($entry, 0, 20);
#    print "Entry:$tmp\n";
#    print  "-----id=$id---\$1=$1----idmatch=$idmatch=format=$format=\n";
    print $FH $entry unless $IDLIST{$id};
    $IDLIST{$id} = 1;
}

=head2 xml

 Title   : xml
 Usage   : 
 Function: Retrieves an entry formatted as XML
 Args    : array, UID
           scalar, format 
 Returns : scalar

=cut

sub xml {
    my ($format, @ids) = @_;
    my ($entry, $id, $content, $counter, $reg);

    $content = ($ENV{'HTTP_USER_AGENT'} =~ /MSIE/) ? "Content-type: text/xml\n\n" : 
      "Content-type: text/plain\n\n";

    $entry = "--format ".(($format eq "bsml") ? "Bsml" : "sciobj") .
	     " " . join (" ", @ids);

    $entry = `rsh mercury "$XEMBL $entry"`;

    $reg = (($format eq "bsml") ? 'tissue
my $VERBOSE = 0;# verbosity option
my $blastfile;  # blastfile to parse
my $pvalue;     # Max P-Value allowed when parsing blastfile
my $remote;     # flag for remote database 
my $db;         # generic database handle
my %accessions; # cache results
my $format = 'blast';

&GetOptions( 'd|dir:s'   => \$dir,
	     'i|index:s' => \$index,
	     'v|verbose' => \$VERBOSE,
	     'b|blast:s' => \$blastfile,
	     'f|format:s' => \$format,
	     'c|cache:s' => \$cache,
	     'p|pvalue:s'       => \$pvalue,
	     'r|remote:s'=> \$remote);

if( $cache && -w $cache ) {
    print "creating cache file\n";
    tie %accessions, "DB_File", $cache,  O_RDWR|O_CREAT,0660, $DB_HASH;
}

if( ! $remote ) {
    opendir(GBEST, $dir) or die("cannot open $dir");
    
    my $indexfile = new Bio::Index::GenBank(-filename   => $index,
					    -write_flag => 'WRITE');
    foreach my $file  ( readdir(GBEST) ) {
#	print "file is $file\n";
	    next unless ( $file =~ /(gbest\d+\.seq)(.gz)?$/ );
	    if( $2 ) {		
		`$GUNZIP $dir/$file`;
	    }
	    $indexfile->make_index("$dir/$1");
    }

    $indexfile = undef;
    $db = new Bio::Index::GenBank(-filename => $index);
    
} else { 
    if( $remote =~ /(ncbi)|(genbank)/i ) {

	$db = new Bio::DB::GenBank;
    } elsif( $remote =~ /embl/i ) {
	$db = new Bio::DB::EMBL;
    } else { 
	die("remote must be either 'NCBI' or 'EMBL'");
    }
    # would need to add code to set proxy info for those who need it
}

if(! $blastfile || ! -r $blastfile ) {
    die("Must specify a valid blastfile");
}

my $parser = new Bio::SearchIO(-format => $format,
			       -file => $blastfile);

my %tissues_seen = ();
my ($result,$hit,$hsp);
while( my $result = $parser->next_result )  {
  HIT: while( my $hit = $result->next_hit ) {
      if( defined $pvalue ) {
	  while( my $hsp = $hit->next_hsp ) {
	      if( $hsp->evalue > $pvalue ) {
		  print "skipping ", $hit->name, " because of low evalue \n";
		  # skip this Subject if it contains a pvalue of > $pvalue
		  next HIT;
	      }
	  }
      }
      my  ($id) = split(/\s+/, $hit->name);
      # get the last value
      my @ids = split(/\|/, $id);
      $id = pop @ids;
      my ($tissuetype) = get_tissue($id);
      if( defined $tissuetype ) {
	  push @{$tissues_seen{$tissuetype}}, $hit->name;
      } else { 
	  print STDERR "could not find tissue for $id\n" if( $VERBOSE);
      }
  }
  print "tissues seen for: ", $result->query_name, "\n";

  foreach my $tissue ( sort keys %tissues_seen ) {
      print "* $tissue\n-----------\n\t", 
      join("\n\t",@{$tissues_seen{$tissue}}), "\n\n";
  }
}

# cleanup -- avoid segfault here
$db = undef;

# subroutines

sub get_tissue {
    my ($id) = @_;
    my $tissue;
    if( $tissue = $accessions{$id} ) {
	return $tissue;
    }

    my $seq = $db->get_Seq_by_acc($id);
    return  unless(  $seq );

    foreach my $feature ( $seq->all_SeqFeatures ) {
	if( $feature->primary_tag eq 'source' ) {
	    foreach my $tag ( sort { $b cmp $a }
			      $feature->all_tags ) {
		if( $tag =~ /tissue/i  || 
		    ( ! $tissue && 
		      $tag =~ /clone_lib/i ) ){
		    ($tissue) = $feature->each_tag_value($tag);
		    $accessions{$seq->display_id} = $tissue;
		    return $tissue;
		}
	    }
	}
    }	    
    return;
}
BioPerl-1.007002/examples/db/gb2features.pl000555000766000024      1231613155576320 20512 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
# Author: Damien Mattei C.N.R.S / U.N.S.A - UMR 6549
# example: ./idfetch.pl AP001266

use Bio::DB::GenBank;

$gb = new Bio::DB::GenBank();

# this returns a Seq object :
$seq1 = $gb->get_Seq_by_acc($ARGV[0]);
print $seq1->display_id() . "\n" ;


foreach $feat ($seq1->all_SeqFeatures()) {

  #print $feat->primary_tag . " " . $feat->source_tag() . "\n" ;

  print "Feature from ", $feat->start, " to ",
   $feat->end, " Primary tag  ", $feat->primary_tag,
   ", produced by ", $feat->source_tag(), "\n";

  if( $feat->strand == 0 ) {
    print "Feature applicable to either strand\n";
  } else {
    print "Feature on strand ", $feat->strand,"\n"; # -1,1
  }

  foreach $tag ( $feat->all_tags() ) {
    print "Feature has tag ", $tag, " with values, ",
    join(' ',$feat->each_tag_value($tag)), "\n";
  }

  print "new feature\n" if $feat->has_tag('new');

}


exit;

__END__

It will display something like that:

[dmattei@pclgmch2 gmap]$ ./idfetch.pl AP001266
AP001266
Feature from 1 to 168978 Primary tag  source, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag chromosome with values, 11
Feature has tag map with values, 11q13
Feature has tag clone with values, RP11-770G2
Feature has tag organism with values, Homo sapiens
Feature has tag db_xref with values, taxon:9606
Feature from 1 to 31550 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 31651 to 48510 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 48611 to 64044 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 64145 to 78208 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 78309 to 89008 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 89109 to 99704 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 99805 to 107965 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 108066 to 116032 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 116133 to 124010 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 124111 to 130494 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 130595 to 136072 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 136173 to 139649 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 139750 to 144590 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 144691 to 148482 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 148583 to 152279 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 152380 to 153632 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment clone_end:T7 
vector_side:left
Feature from 153733 to 155746 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 155847 to 156405 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment clone_end:SP6 
vector_side:right
Feature from 156506 to 158398 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 158499 to 161333 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 161434 to 163304 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 163405 to 164604 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 164705 to 166693 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 166794 to 168978 Primary tag  misc_feature, produced by 
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment

BioPerl-1.007002/examples/db/getGenBank.pl000555000766000024       142113155576320 20261 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
#
# How to retrieve GenBank entries over the Web
#
# by Jason Stajich
#
use Bio::DB::GenBank;
use Bio::SeqIO;
my $gb = new Bio::DB::GenBank;

# the output stream for your seqs, this can be a file
# instead or STDOUT, see the Bio::SeqIO module for info

my $seqout = new Bio::SeqIO(-fh => \*STDOUT, -format => 'fasta');

# if you want a single seq
my $seq = $gb->get_Seq_by_id('J00522');
$seqout->write_seq($seq);
# or by accession
$seq = $gb->get_Seq_by_acc('AF303112');

$seqout->write_seq($seq);

# feel free to pull multiple sequences...
# if you want to get a bunch of sequences use the get_Stream_by_id/acc methods
my $seqio = $gb->get_Stream_by_id([ qw(J00522 AF303112 2981014)]);

while( defined ($seq = $seqio->next_seq )) {
        $seqout->write_seq($seq);
}
BioPerl-1.007002/examples/db/get_seqs.pl000555000766000024       321313155576320 20067 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
use strict;
use vars qw($USAGE);
use Carp;
use Getopt::Long;
use Bio::SeqIO;

$USAGE = "get_seqs.pl\t[--db=DBNAME] [--format=FORMAT] \n\t\t[--output=FILENAME] [--proxy=PROXY] accession1, accession2, ...\n Defaults: db=GenBank format=fasta output=STDOUT proxy=none\n See LWP::UserAgent for more information on proxy syntax";
my %dbs = (
  'genbank'   => 'Bio::DB::GenBank',
  'embl'      => 'Bio::DB::EMBL',
  'swissprot' => 'Bio::DB::SwissProt', 
);

my ($db,$format,$file,$proxy,$help) = ( 'genbank', 'fasta' );

&GetOptions
    (
     'db:s'       => \$db,
     'f|format:s' => \$format,
     "file|out|output:s" => \$file,
     'proxy:s'           => \$proxy,
     "h|\?|help"  => \$help ,     
     );

if( $help ) { print $USAGE, "\n";exit; }

if( $db =~ /gb|gen|genbank/i ) {
    $db = 'genbank';
} elsif( $db =~ /embl|em|e/i ) {
    $db = 'embl';
} elsif( $db =~ /swiss|sp/i ) {
    $db = 'swissprot';
} else { 
    croak("Unknown db parameter '$db' valid parameters are (" . join(',', keys %dbs) . ")");
}

my %params = ( '-format' => $format );

if( defined $file ) {
    $params{'-file'} = ">$file";
} else { 
    $params{'-fh'} = \*STDOUT;
}

my $seqio = new Bio::SeqIO(%params);

my $remotedb;

eval {
    my $filename = "$dbs{$db}.pm";
    $filename =~ s!::!/!g;
    require $filename;
    $remotedb = "$dbs{$db}"->new();
};

die($@) unless ! $@;

if( defined $proxy ) { $remotedb->proxy($proxy); }

my $stream;

if( $remotedb->can('get_Stream_by_batch') ) {
    $stream = $remotedb->get_Stream_by_batch(@ARGV);
} else {
    $stream = $remotedb->get_Stream_by_acc(\@ARGV);
}

while( my $seq = $stream->next_seq ) {
    $seqio->write_seq($seq);
}
BioPerl-1.007002/examples/db/rfetch.pl000555000766000024       241213155576320 17530 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

#
# Fetch sequence data via OBDA registry system
#
# usage: rfetch -i  -a -v -d embl -s start -e end
#

use Bio::DB::Registry;
use Bio::SeqIO;
use Getopt::Long;
use strict;

my $database = 'embl_biosql';
my $start    = undef;
my $end      = undef;
my $format   = 'fasta';
my $file     = undef;
my $acc      = undef;
my $verbose  = undef;

&GetOptions(
	    'd|database:s' => \$database,
	    's|start:i' => \$start,
	    'e|end:i'   => \$end,
	    'f|format:s' => \$format,
	    'i|input:s' => \$file,
	    'a|acc'     => \$acc,
	    'v|verbose' => \$verbose,
	   );


my $registry = Bio::DB::Registry->new();

my $db = $registry->get_database($database);

my $seqout = Bio::SeqIO->new( '-format' => $format, '-fh' => \*STDOUT);

my @ids;

if( defined $file ) {
  open my $F, '<', $file or die "Could not read file '$file': $!\n";
  while( <$F> ) {
    my ($id) = split;
    push(@ids,$id);
  }
  close $F;
} else {
  @ids = @ARGV;
}

foreach my $id ( @ids ) {
  my $seq;
  if( $verbose ){
    print STDERR "fetching $id\n";
  }

  if( $acc ) {
    $seq = $db->get_Seq_by_acc($id);
  } else {
    $seq = $db->get_Seq_by_id($id);
  }

  if( defined $start && defined $end ) {
    $seq = $seq->trunc($start,$end);
  }

  $seqout->write_seq($seq);
}
BioPerl-1.007002/examples/db/use_registry.pl000555000766000024        47213155576320 20765 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
use strict;

use Bio::DB::Registry;
use Bio::SeqIO;
use strict;

my $registry = new Bio::DB::Registry();

print "services are ", join(',', $registry->services), "\n";
my $db = $registry->get_database("embl");
my $seq = $db->get_Seq_by_id("J02231");
my $out = new Bio::SeqIO;
$out->write_seq($seq);
BioPerl-1.007002/examples/liveseq000755000766000024          013155576320 16644 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/liveseq/change_gene.pl000555000766000024       345413155576320 21572 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

use strict;
use Bio::LiveSeq::IO::BioPerl;
use Bio::LiveSeq::Mutator;
use Bio::LiveSeq::Mutation;
use Bio::Variation::IO;

if ($#ARGV < 1) { # one argument input
    print <load(-file => "$filename");

    my $gene_name=$ARGV[1];
    my $gene=$loader->gene2liveseq(-gene_name => $gene_name,
				   -getswissprotinfo => 0);

    print STDERR "Gene: ",$gene->name,"\n";
    print STDERR "    Moltype: ", $gene->get_DNA->alphabet,  "\n";
    print STDERR "    Features:\n";
    print STDERR $gene->printfeaturesnum();
    print STDERR "    Gene has boundaries ",$gene->upbound," - ",$gene->downbound,"\n";
    print STDERR "    Gene has maxtranscript with start ",$gene->maxtranscript->start,
          " end ",$gene->maxtranscript->end," strand ",$gene->maxtranscript->strand,"\n";
    print STDERR "    DNA  has boundaries ",$gene->get_DNA->start," - ",$gene->get_DNA->end,"\n";
    print STDERR "\n";

    print STDERR "Now issuing mutations to the gene....\n";

    my $mutation = new Bio::LiveSeq::Mutation (-seq =>'A',
				       -pos => 64
				       );
    my $mutate = Bio::LiveSeq::Mutator->new(-gene => $gene,
					 -numbering => "coding"
					 );
    $mutate->add_Mutation($mutation);
    my $results=$mutate->change_gene();
    print "\n";
    if ($results) {
	my $out = Bio::Variation::IO->new( '-format' => 'flat');
	$out->write($results);
    }
}
BioPerl-1.007002/examples/popgen000755000766000024          013155576320 16464 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/popgen/parse_calc_stats.pl000555000766000024       632513155576320 22501 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
# Author: Jason Stajich, jason@bioperl.org
# $Revision: 6576 $

use strict;

use Bio::PopGen::IO;
use Bio::PopGen::Statistics;
use Bio::PopGen::Population;

my $io = new Bio::PopGen::IO(-format => 'prettybase',
			     # the Bio::Root::IO->catfile is only
			     # to make file access platform independent
			     -file   => Bio::Root::IO->catfile
			     (qw( t data popstats.prettybase)));

# This is an example of how to read in data from Bio::PopGen::IO
# We're going to make 2 lists, @outgroup, @ingroup
# @outgroup is a single individual which is named 'out'
# @ingroup is the set of individuals we are testing
my (@ingroup,@outgroup);
while( my $ind = $io->next_individual ) {
    if($ind->unique_id =~ /out/) {
	push @outgroup, $ind;
    } else { 
	push @ingroup, $ind;	
    }
}

# We'll get the names of all the markers (or sites)
# that this individual has genotypes for
my @marker_names = $ingroup[0]->get_marker_names();

# the number of sites is the same as the number of markers
# we assume that all the individuals have the same number of sites
# or that this data is 'aligned' if these were derived from a 
# multiple sequence alignment
my $sitecount = scalar @marker_names;

foreach my $ind ( @ingroup ) {
    # here let's print out the individual name and all their alleles
    # for all the markers
    # like this
    # Name: INDIVIDUALNAME
    #      A1,A2 B1,B2,...
    print "Name: ", $ind->unique_id,"\n";
    print "\t";
    foreach my $marker ( @marker_names ) {
	for my $genotype ( $ind->get_Genotypes($marker) ) {
	    my @alleles = $genotype->get_Alleles();
	    # In this example these are actually single alleles anyways...
	    print join(",", @alleles), " ";
	}
    }
    print "\n";
    
    # There is a more compact way to write that
    print "Name: ", $ind->unique_id,
          "\n\t", join(" ", map { join(",",$_->get_Alleles) } 
		          map { $ind->get_Genotypes($_) } @marker_names),"\n";
    print "--\n";
}

# We can compute some statistics about these individuals
# (underlying assumption is that they are unrelated...)

print "Pi: ",Bio::PopGen::Statistics->pi(\@ingroup), "\n";
print "Theta: ",Bio::PopGen::Statistics->theta(\@ingroup), "\n";

# we can also treat them like a population
my $ingroup_pop = new Bio::PopGen::Population(-individuals => \@ingroup);

print "Pi: ",Bio::PopGen::Statistics->pi($ingroup_pop), "\n";
print "Theta: ",Bio::PopGen::Statistics->theta($ingroup_pop), "\n";





# You can also simulate individuals from a coalescent 
use Bio::PopGen::Simulation::Coalescent;

my $ssize = 5;
my $sim = new Bio::PopGen::Simulation::Coalescent(-sample_size => $ssize);
my $tree = $sim->next_tree;
my $mutcount = 100;
$sim->add_Mutations($tree, $mutcount);

# The leaves are the simulated individuals
my @leaves = $tree->get_leaf_nodes;

# We can use the Stats module either like Bio::PopGen::Statistics->XXX
# or like this:
my $stats = new Bio::PopGen::Statistics;
# $stats->verbose(1);
print "Coalescent pi: ", $stats->pi(\@leaves), "\n";
print "Coalescent theta: ", $stats->theta(\@leaves), "\n";
my $coalescent_pop = new Bio::PopGen::Population(-individuals => \@leaves);

print "Coalescent pi: ", $stats->pi($coalescent_pop), "\n";
print "Coalescent theta: ", $stats->theta($coalescent_pop), "\n";
BioPerl-1.007002/examples/quality000755000766000024          013155576320 16664 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/quality/svgtrace.pl000555000766000024       305113155576320 21176 0ustar00cjfieldsstaff000000000000#! /usr/bin/perl

use warnings;
use strict;
use Bio::SeqIO;
use SVG;

my $USAGE = <

This simple example script reads the ABI data and uses the trace data to
generate a SVG-formatted chromatogram. Requires the CPAN SVG module and
Bio::SeqIO::staden::read (from bioperl-ext), which itself requires io_lib from
the Staden package.

END_USAGE

my $file = shift || die $USAGE;

my $img_width = 6000;
my $img_height = 200;

my $svg = SVG->new(width => $img_width, height => $img_height, xmlns => "http://www.w3.org/2000/svg");

my $seq_io = Bio::SeqIO->new( -file => $file, -format => 'abi', -get_trace_data => 1);

my $seq = $seq_io->next_seq;

my $points = scalar($seq->get_trace_graph( -trace => 'a' ));

my @xdata = map { $_ / $points * $img_width } (0..$points-1);

my %colours = ( 'a' => 'green', 'c' => 'blue', 'g' => 'black', 't' => 'red' );
foreach my $element ('a', 'c', 'g', 't')
{
	my @trace = $seq->get_trace_graph( -trace => $element, -scale => $img_height); 
	@trace = map { $img_height - $_ } @trace;
	my $points = $svg->get_path(-type => 'polyline', -closed => 0, x => \@xdata, y => \@trace);
	$svg->polyline(%$points, id=> $element, 'stroke-width' => 0.5, stroke => $colours{$element}, 'fill-opacity' => 0, 'fill' => 'white');
}

my $count = 0;
my $text_group = $svg->group( id => 'text_layer');
foreach my $base_loc (@{$seq->trace})
{
	$text_group->text(x => ($base_loc / $points * $img_width), y => 50, 'text-anchor' => 'middle', fill => 'black', 'font-size' => '5pt')->cdata(substr($seq->seq,$count,1));
	++$count;
}

print $svg->xmlify();
BioPerl-1.007002/examples/root000755000766000024          013155576320 16157 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/root/README000555000766000024      1714313155576320 17225 0ustar00cjfieldsstaff000000000000README for Bioperl examples/root 

This directory contains some sample scripts and modules that
illustrate the use of the Bio::Root::* modules. Currently, these
example scripts focus on how exception handling. 

Here are some short descriptions of the examples/root scripts:

Script            Description
--------------    ----------------------------------------
exceptions1.pl    How to throw and catch Error.pm objects
exceptions2.pl    How to throw Error.pm objects via Bio::Root::Root
exceptions3.pl    Illustrates inheritance between Error.pm types
exceptions4.pl    Shows what happens when Error.pm isn't installed

These demo scripts should be executed within the
examples/root directory of the Bioperl distribution.


Using Error.pm for Exception Handling
--------------------------------------

The Bio::Root::Root module interfaces with Graham Barr's Error.pm.
Error.pm provides a handy way to create, throw, and catch exceptions
as objects. Error.pm is quite convenient and easy to use and adds a
level of control for managing errors within your Perl code using
familiar object-oriented, try-catch-finally semantics. You can define
subclasses of Error.pm representing particular types of exceptions,
and you can define catch blocks to handle these types of exceptions.

This has distinct advantages over simply catching any and all errors
with an eval{} block, as is currently done in Bioperl. Strongly typed
exception objects make it easy to write appropriate handlers. It also
makes you code easier to understand because it's clear what type of
things can/did go wrong.

Throwing exceptions that are Error.pm-compliant is a little more work
than throwing them the usual Bioperl way. Here's an example:

Using Error.pm-compliant syntax:

  if( !$feat->isa("Bio::SeqFeatureI") ) {
      $self->throw(-class => 'Bio::Root::BadParameter',
                   -text  =>"$feat is not a SeqFeatureI and that's what we expect.",
                   -value => $feat);
  }

Not using Error.pm-compliant syntax:

  if( !$feat->isa("Bio::SeqFeatureI") ) {
      $self->throw("$feat is not a SeqFeatureI and that's what we expect.");
  }

The advantage of using the Error.pm-compliant syntax is that, even if
Error.pm isn't installed, the exception message that gets thrown will
contain the name of the class of the exception. This provides a more
informative description of what went wrong.

In the Error.pm-compliant case above, the exception string starts with:

    ------------- EXCEPTION: Bio::Root::BadParameter -------------

Compare this to the non-Error.pm-compliant exception string:

    -------------------- EXCEPTION --------------------

There are a variety of exception classes that are declared in
Bio::Root::Exception for common types of error conditions:

    Bio::Root::Exception
    Bio::Root::NotImplemented
    Bio::Root::IOException
    Bio::Root::FileOpenException
    Bio::Root::SystemException
    Bio::Root::BadParameter
    Bio::Root::OutOfRange
    Bio::Root::NoSuchThing

Feel free to use these, or subclass from them to derive more specific
classes of exceptions. For more information about these types of
exceptions, see perldoc Bio::Root::Exception.

Error.pm is available through CPAN and I encourage Bioperl users and
developers to install it and experiment with it.


Bio::Root::Exception.pm
-----------------------

The Bio::Root::Exception.pm module contains a number of Error.pm
subclasses representing common types of errors. If you want to throw
an exception within your Bioperl module that doesn't correspond to any
of the ones defined in Bio::Root::Exception, feel free to define a new
one, but be sure it inherits from Bio::Root::Exception or one of its
subclasses. This will allow anyone to write a handler for any type of
Bioperl exception.

Defining a new type of exception can be done quite simply. All you
need to do is to specify the @ISA array for your new type, as in:

    @Bio::Root::Exception::MyBad::ISA = qw( Bio::Root::Exception );

If you want to override any of the available methods or add new ones,
you'll have to provide a package statement and the appropriate
method definitions.

Programming tip: Be careful not to use exceptions as your primary
means of flow control within your code. Throwing and handling
exceptions come with some execution overhead. Also, such excessive use
of exceptions can make your logic hard to follow.


Bio::Root::RootI.pm and Bio::Root::Root.pm 
-------------------------------------------

The modules in the lib directory also demonstrate the use of the Bioperl
modules Bio::Root::RootI and Bio::Root::Root. RootI.pm should be used
as the base class for any Bioperl module that specifies an
interface. It simplifies the process of writing virtual
methods. Root.pm implements RootI.pm should be used as a base class
for any Bioperl module that specifies a concrete object.

The module TestInterface.pm demonstrates how to use
Bio::Root::RootI.pm. The module TestObject.pm demonstrates how to use
Bio::Root::Root.pm.

Bio::Root::RootI defines a method called "throw_not_implemented()"
that will throw a Bio::Root::NotImplemented exception. This is useful
for ensuring that an implementing class has implemented all
methods. Any method within a Bio::Root::RootI subclass can call
throw_not_implemented() to indicate that a method has not been
implemented. Implementations of the interface must implement the
method or an exception will result when someone tries to use it.

Note that Bio::Root::Root can make use of Error.pm if available, but
Error.pm is not required. 


Bio::Root::Root::throw() with Error.pm
---------------------------------------

Bio::Root::Root can determine if Error.pm is available and if so, can
make use of it when Bio::Root::Root::throw() is called. For a demo,
see test2.pl.


Real-Life Examples
------------------

For additional examples of how to make use of the Error.pm-related capabilities
of Bio::Root::Root.pm, I created new versions of Bio::SeqI.pm,
Bio::Seq.pm, Bio::PrimarySeqI.pm, and Bio::PrimarySeq.pm within the
lib/Bio subdirectory. This conversion is pretty straightforward and could
be done on the other Bioperl modules without too much effort.

TODO: Update the lib/Bio modules based on the latest versions in bioperl-live.


Using Error.pm's try{} and catch{} within Bioperl Modules
----------------------------------------------------------

For developers, using Error.pm's try{} and catch{} blocks within
Bioperl modules themselves could come in handy. But doing so would add
an external dependency for Error.pm, which is not part of the standard
Perl distribution. So at this stage, it's best to stick with just
using Error.pm's throw() method (via Bio::Root::Root) and leave the
try{} and catch{} blocks for use only within your scripts.

If you really want to use try{} and catch{} within your module and
still want to be capable of running when Error.pm isn't available, you
can check $Bio::Root::Root::ERRORLOADED variable.

If we really want to incorporate it within Bioperl, a reasonable
solution would be to distribute Error.pm with Bioperl. 

So why use Error.pm instead of some other utility? Well, Perl 6 will
most likely include some form of structured exception handling akin to
that provided by Error.pm (see these RFC's:
http://dev.perl.org/rfc/63.pod and http://dev.perl.org/rfc/88.pod).
So it will probably be easy to convert Error.pm-based exception handling
to whatever is adopted for Perl 6.

(Side note for any CORBA folks out there: Error.pm is used in some
other CPAN modules, notably CORBA::MICO. Thus, using Error.pm within
Bioperl allows consistent exception handling methodology when working
with such modules and Bioperl together.)

--
Steve Chervitz 
21 April 2001
Updated 6 March 2003

BioPerl-1.007002/examples/root/exceptions1.pl000555000766000024      1076013155576320 21142 0ustar00cjfieldsstaff000000000000#!/usr/bin/env perl

# A simple tester script for demonstrating how to throw and catch
# Error.pm objects. It also shows how to define new types of
# Error.pm-based objects. 
#
# It relies on the tester modules TestObject.pm and TestInterface.pm
# which you should also look at.
#
# Note that Bio::Root::NotImplemented is a subclass of Error.pm 
# and is defined in Bio::Root::Exception.pm
#
# This code requires Graham Barr's Error.pm module available from CPAN.
#
# Author: Steve Chervitz 
#

use strict;
use lib qw(lib/ ../../);
use Error qw(:try);
use TestObject;
use Getopt::Long;

# Command-line options:
my $eg = 0;        # which example to run (a number 1-4)
my $help = 0;      # print usage info

# $Error::Debug is set to true by default in Bio::Root::Interface.
$Error::Debug = 1; # enables verbose stack trace 

GetOptions( "debug!" => \$Error::Debug,
	    "eg=s"   => \$eg,    
	    "h"      => \$help   
	  ); 

my $options = << "OPTS";
      -eg  1|2|3|4   Run a particular example
      -nodebug       Deactivate verbose stacktrace
      -h             Print this usage
OPTS

(!$eg || $help) and die "Usage: $0 -eg 1|2|3|4 [-nodebug] [-h]\nOptions:\n$options";

print $Error::Debug ? "Try a -nodebug option to supress stack trace." : "Verbose stacktrace off.";
print "\n\n";

# Set up a tester object.
my $test = TestObject->new();
$test->data('Eeny meeny miney moe.');

try {

    test_notimplemented( $test ) if $eg == 1;

    test_custom_error( $test ) if $eg == 2;

    test_simple_error() if $eg == 3;

    # This subroutine doesn't even exist. But because it occurs within a try block,
    # the Error module will create a Error::Simple to capture it. Handy eh?
    if(  $eg == 4 ) {
	print "Test #4: Calling an undefined subroutine.\n";
	test_foobar();
    }

    # We shouldn't see this stuff.
    print "----\n";
    print "----\n";
    print "Some other code within the try block after the last throw...\n";
    print "----\n";
    print "----\n";
}

# Multiple catch blocks to handle different types of errors:

catch Bio::Root::NotImplemented with {
    my $error = shift;
    print "\nCaught a Bio::Root::NotImplemented.\n",
      "  file  : ", $error->file, "\n",
      "  line  : ", $error->line, "\n",
      "  text  : ", $error->text, "\n",
      "  value : ", $error->value, "\n",
      "  object: ", ref($error->object), "\n";

    print "\nstacktrace:\n", $error->stacktrace, "\n";

    print "\nstringify:\n$error\n";
    # The above line is equivalent to this:
    #print "\nstringify:\n", $error->stringify, "\n";
}

catch Bio::TestException with {
    # Since we know what type of error we're getting,
    # we can extract more information about the offending object
    # which is retrievable from the error object.
    my $error = shift;
    print "\nCaught a Bio::TestException.\n",
      "  file  : ", $error->file, "\n",
      "  line  : ", $error->line, "\n",
      "  text  : ", $error->text, "\n",
      "  value : ", $error->value, "\n",
      "  object: ", ref($error->object), "\n",
      "  data  : ", $error->object->data, "\n";

    print "\nstacktrace:\n", $error->stacktrace, "\n";
    print "\nstringify:\n", $error->stringify, "\n";

}

otherwise {
    # This is a catch-all handler for any type of error not handled above.
    my $error = shift;
    print "\nCaught an other type of error: ", ref($error), "\n",
      "  file  : ", $error->file, "\n",
      "  line  : ", $error->line, "\n",
      "  text  : ", $error->text, "\n",
      "  value : ", $error->value, "\n",
      "  object: ", ref($error->object), "\n";

#    print "\nstack_trace_dump:\n", $error->stack_trace_dump(), "\n";

    print "\nstacktrace:\n", $error->stacktrace, "\n";

    print "\nstringify:\n$error\n";

};  # This semicolon is essential.

print "\nDone $0\n";

sub test_notimplemented {

    my $test = shift;
    # This demonstrates what will happen if a method defined in an interface 
    # that is not implemented in the implementating object.

    print "Test #1: Inducing a Bio::Root::NotImplemented exception from TestObject\n";

    $test->foo();
}


sub test_custom_error {

    my $test = shift;

    # TestObject::bar() deliberately throws a Bio::TestException, 
    # which is defined in TestObject.pm

    print "Test #2: Throwing a Bio::TestException exception from TestObject\n";

    $test->bar;

}


sub test_simple_error {

    # Error::Simple comes with Error.pm and can have only a string and a value.

    print "Test #3: Throwing a Error::Simple object\n";

    throw Error::Simple( "A simple error", 42 );
}


BioPerl-1.007002/examples/root/exceptions2.pl000555000766000024      1066713155576320 21151 0ustar00cjfieldsstaff000000000000#!/usr/bin/env perl

# This shows how Error.pm-based objects can be thrown 
# by Bio::Root::Root::throw() when Error.pm is available.
# When Error.pm isn't available, Bio::Root::Root::throw() 
# works as usual.
#
# It also demonstrates what happens when you use an outer eval{}
# instead of a try{} to trap thrown Error.pm-based exceptions. 
# The behavior is the same as when Error.pm is not used.
# This is important for backward compatibility.
#
# Author: Steve Chervitz 
#

use strict;

use lib qw(lib/ ../../);

# Uncomment this line to force Bio::Root::Root::throw() to 
# not use Error.pm even if it's available.
# Some of the tests in this script will be skipped .
#BEGIN { $main::DONT_USE_ERROR = 1; }

use Bio::Root::Root;
#use Bio::Root::Exception;  # Not necessary since Bio::Root::Root uses it.
use Error qw(:try);

my $foo = Bio::Root::Root->new();

if (!$main::DONT_USE_ERROR) {
    try {
        # This is the new, fancier way to handle exceptions. 
        # You must have Error.pm to do this (tarball included in this dir).
        
        print "[1] Throwing Error within try block via call to Bio::Root::Root::throw()\n";
        $foo->throw( -class => 'Bio::Root::Exception',
                     -text  => "Oopsie!",
                     -value => "123" 
                   );
    }
    
    catch Bio::Root::Exception with {
        my $err = shift;
        print "[1] Caught Bio::Root::Exception:\n$err";

    }

    otherwise {
        my $err = shift;
        print "[1] Caught other Error: ", ref($err), "\n$err";
    };

    
    print "\n\n";
}

eval {

    # This example demonstrates the traditional method for throwing
    # an exception using Bio::Root::Root->throw('string').
    # Notice how an exception of type Bio::Root::Exception is created.

    print "[2] Calling Bio::Root::Root->throw('string') within an eval{}\n";
    $foo->throw("Error message string.");

};

if($@) {
    print "[2] Caught eval{}-based exception: ", ref($@), "\n$@";
}
else {
    print "[2] Nothing to catch.\n";
}



print "\n\n";

eval {

    # This example shows that calling Error::throw directly within
    # an eval{} doesn't lead to a true value in $@ if
    # the error lacks a value. 

    print "[3] Attempting to throw a valueless Error within an eval{} block\n    (this should fail to be caught by Error.pm v0.13 but is caught by v0.14 and greater).\n";

    if( $ENV{OSTYPE} =~ /cygwin/ ) {
        die "[3] This causes a segmentation fault with cygwin perl! Skipping.\n";
    }

    throw Error::Simple ("A simple error.");

};

if($@) {
    print "[3] Caught eval{}-based exception: ", ref($@), "\n$@\n";
}
else {
    print "[3] Nothing to catch.\n";
}


print "\n\n";

eval {

    # This example shows that calling Error::throw directly within
    # an eval{} *does* lead to a true value in $@ if the error 
    # contains a non-zero value. 

    print "[4] Attempting to throw a valued Error within an eval{} block.\n";

    throw Error::Simple ("A simple error.", 42);

};

if($@) {
    print "[4] Caught eval{}-based exception: ", ref($@), "\n$@\n";
}
else {
    print "[4] Nothing to catch.\n";
}

print "\n\n";

if (!$main::DONT_USE_ERROR) {
    eval {

        # This example shows what happens if we try to create a
        # Bio::Root::IOException (a subclass of Bio::Root::Exception)
        # with a zero value. Bio::Root::Exception::new() catches this
        # faux pas and substitutes a value that will register as true in if($@).

        print "[5] Attempting to throw a zero-valued Bio::Root::IOException\n    within an eval{} block.\n";

        throw Bio::Root::IOException ( -text =>"An error with zero value.",
                                   -value => 0);

    };

    if($@) {
        print "[5] Caught eval{}-based zero-valued exception: ", ref($@), "\n$@\n";
    }
    else {
        print "[5] Nothing to catch.\n";
    }
    print "\n\n";
}


eval {

    # If Error::throw is called *indirectly* within an eval{}
    # (i.e., by calling a method which then calls Error::throw),
    # $@ is defined and it consists of a reference to the Error.pm object.

    print "[6] Attempting to throw Error indirectly within an eval{} block \n    via Bio::Root::Root::throw()\n";

    $foo->throw( -class => 'Bio::Root::Exception',
                 -text  => "Oopsie!",
                 -value => "456"
                );

};

if($@) {
    print "[6] Caught eval{}-based exception: ", ref($@), "\n$@";
}
else {
    print "[6] Nothing to catch.\n";
}

print "Done.\n";


BioPerl-1.007002/examples/root/exceptions3.pl000555000766000024       243213155576320 21121 0ustar00cjfieldsstaff000000000000#!/usr/bin/env perl

# This shows that Error objects can be subclassed into more specialized types.
# Bio::Root::FileOpenException is a subclass of  Bio::Root::IOException. 
#
# We can write a generic handler to trap any type of IOException
# or we could handle FileOpenExceptions explicitly.
#
# To demo, run this script without any arguments, then try it with an argument
# that doesn't correspond to any file on your system (e.g., foobar). 
# Then try running with a valid file name.
#
# This requires Graham Barr's Error.pm module available from CPAN.
#
# Author: Steve Chervitz 
#

use strict;
use lib qw(lib/ ../../);
use Error qw(:try);
use Bio::Root::Exception;

try {
   print "Starting try block.\n";
   my $file = shift @ARGV || throw Bio::Root::IOException(-text=>"No file supplied.");

   open ( IN, $file) || throw Bio::Root::FileOpenException(-text=>"Can't open file \"$file\"", -value=> $!); 

   print "Opened file $file\n";

}
catch Bio::Root::IOException with {
    # This handler deals with IOException or any of its subclasses.
    # We could also write a handler with a `catch Bio::Root::FileOpenException'.
    # Such a handler would appear before this one.
    my $e = shift;
    print "Caught IOException:\n\n$e";
}
finally {
     close IN;
};

print "\nDone.\n";
BioPerl-1.007002/examples/root/exceptions4.pl000555000766000024       644713155576320 21134 0ustar00cjfieldsstaff000000000000#!/usr/bin/env perl

# This shows how the examples work when Error.pm isn't installed.
# It also shows how to supress using Error.pm if it is installed
# and you don't want to use it for some reason.
#
# Here we use the eval{} style exception handling that's currently
# in vogue trapping Bioperl exceptions.
#
# Author: Steve Chervitz 
#


# Setting this variable simulates not having Error.pm installed.
BEGIN { $DONT_USE_ERROR = 1; }

use strict;
use lib qw(lib/ ../../);
use TestObject;
use Getopt::Long;

# Command-line options:
my $eg = 0;        # which example to run (a number 1-4)
my $help = 0;      # print usage info
$Error::Debug = 1; # enables verbose stack trace 

GetOptions( "debug!" => \$Error::Debug,
	    "eg=s"   => \$eg,    
	    "h"      => \$help   
	  ); 

my $options = << "OPTS";
      -eg  1|2|3|4   Run a particular example
      -nodebug       Deactivate verbose stacktrace
      -h             Print this usage
OPTS

(!$eg || $help) and die "Usage: $0 -eg 1|2|3|4|5 [-nodebug] [-h]\nOptions:\n$options";

# Set up a tester object.
my $test = TestObject->new();
$test->data('Eeny meeny miney moe.');

eval {

    test_notimplemented( $test ) if $eg == 1;

    test_custom_error( $test ) if $eg == 2;

    test_simple_error() if $eg == 3;

    # This subroutine doesn't even exist. But because it occurs within a try block,
    # the Error module will create a Error::Simple to capture it. Handy eh?
    if(  $eg == 4 ) {
	print "Test #4: Calling an undefined subroutine.\n";
	test_foobar();
    }

    # Throwing an exception the traditional bioperl way.
    if(  $eg == 5 ) {
	print "Test #5: Creating a Bio::Root::Root object and calling throw('string').\n";
        my $obj = Bio::Root::Root->new();
        $obj->throw("Throwing string from Bio::Root::Root object.");
    }

    # We shouldn't see this stuff.
    print "----\n";
    print "----\n";
    print "Some other code within the try block after the last throw...\n";
    print "----\n";
    print "----\n";
};

if($@) {
    my $error = shift;
    print "\nAn exception occurred:\n$@\n";
}
else {
    print "\nNo exception occurred\n";
}

print "\nDone $0\n";

sub test_notimplemented {

    my $test = shift;
    # This demonstrates what will happen if a method defined in an interface 
    # that is not implemented in the implementation.

    print "Test #1: Inducing a Bio::Root::NotImplemented exception from TestObject\n";

    $test->foo();
}    


sub test_custom_error {

    my $test = shift;

    # TestObject::bar() deliberately throws a Bio::Root::TestError, 
    # which is defined in TestObject.pm

    print "Test #2: Throwing a Bio::TestException exception from TestObject\n";

    $test->bar;  

}


sub test_simple_error {

    # This example won't work without Error.pm installed.
    # It shows how setting $DONT_USE_ERROR = 1 
    # really does simulate the absence of Error.pm.
    # The exception should report something like:
    # "Can't locate object method "throw" via package "Error::Simple"

    # Error::Simple comes with Error.pm and can have only a string and a value.

    print "Test #3: Throwing a Error::Simple object\n\n";

    print "This should fail to find object method 'throw' via package 'Error::Simple'\n";
    print "because Error.pm is not available.\n\n";

    throw Error::Simple( "A simple error", 42 );
}


BioPerl-1.007002/examples/searchio000755000766000024          013155576320 16771 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/searchio/blast_example.pl000555000766000024      1527613155576320 22341 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
# Example that shows values returned by Bio::SearchIO::Blast.
# Note that some methods will return objects or arrays, not text.
# For example, $hsp->get_aln will return a Bio::SimpleAlign object,
# not the alignment in a printable form.
# This script was used to create the table in the SearchIO HOWTO,
# found at http://bioperl.org/howtos/SearchIO_HOWTO.html
# Brian Osborne

use strict;
use Bio::SearchIO;
use Bio::SimpleAlign;
use Bio::AlignIO;

my $file = shift or die "Usage: $0 \n";
my $in = new Bio::SearchIO(-format => 'blast',
			   # comment out the next line to read STDIN
			   -file   => $file );

while ( my $result = $in->next_result ) {
   my @stats =  $result->available_statistics;
   my @params = $result->available_parameters;
   print "Result\tavailable_statistics\t@stats\n";
   print "Result\tavailable_parameters\t@params\n";
   print "Result\talgorithm\t" .         $result->algorithm . "\n";
   print "Result\talgorithm_version\t" . $result->algorithm_version . "\n";
   print "Result\tquery_name\t" .        $result->query_name . "\n";
   print "Result\tquery_accession\t" .   $result->query_accession . "\n";
   print "Result\tquery_length\t" .      $result->query_length . "\n";
   print "Result\tquery_description\t" . $result->query_description . "\n";
   print "Result\tdatabase_name\t" .     $result->database_name . "\n";
   print "Result\tdatabase_letters\t" .  $result->database_letters . "\n";
   print "Result\tdatabase_entries\t" .  $result->database_entries . "\n";
   print "Result\tnum_hits\t" .          $result->num_hits . "\n";
   print "Result\thits\t" .              $result->hits . "\n";
   while ( my $hit = $result->next_hit ) {
      my $id =         $hit->matches('id');
      my $cons =       $hit->matches('cons');
      my @accs =       $hit->each_accession_number;
      my @qidentical = $hit->seq_inds('query','identical');
      my @qconserved = $hit->seq_inds('query','conserved');
      my @hidentical = $hit->seq_inds('hit','identical');
      my @hconserved = $hit->seq_inds('hit','conserved');
      print "Hit\tseq_inds('query','identical')\t@qidentical\n";
      print "Hit\tseq_inds('query','conserved')\t@qconserved\n";
      print "Hit\tseq_inds('hit','identical')\t@hidentical\n";
      print "Hit\tseq_inds('hit','conserved')\t@hconserved\n";
      print "Hit\teach_accession_number\t@accs\n";
      print "Hit\tmatches('id')\t" . $id . "\n";
      print "Hit\tmatches('cons')\t" . $cons . "\n";
      print "Hit\tname\t" .                $hit->name . "\n";
      print "Hit\taccession\t" .           $hit->accession . "\n";
      print "Hit\tdescription\t" .         $hit->description . "\n";
      print "Hit\tlength\t" .              $hit->length . "\n";
      print "Hit\talgorithm\t" .           $hit->algorithm . "\n";
      print "Hit\traw_score\t" .           $hit->raw_score . "\n";
      print "Hit\tsignificance\t" .        $hit->significance . "\n";
      print "Hit\tbits\t" .                $hit->bits . "\n";
      print "Hit\thsps\t" .                $hit->hsps . "\n";
      print "Hit\tnum_hsps\t" .            $hit->num_hsps . "\n";
      print "Hit\tambiguous_aln\t" .       $hit->ambiguous_aln . "\n";
      print "Hit\toverlap\t" .             $hit->overlap . "\n";
      print "Hit\tn\t" .                   $hit->n . "\n";
      print "Hit\tlogical_length\t" .      $hit->logical_length . "\n";
      print "Hit\tlength_aln\t" .          $hit->length_aln . "\n";
      print "Hit\tgaps\t" .                $hit->gaps . "\n";
      print "Hit\tfrac_identical\t" .      $hit->frac_identical . "\n";
      print "Hit\tfrac_conserved\t" .      $hit->frac_conserved . "\n";
      print "Hit\tfrac_aligned_query\t" .  $hit->frac_aligned_query . "\n";
      print "Hit\tfrac_aligned_hit\t" .    $hit->frac_aligned_hit . "\n";
      print "Hit\tnum_unaligned_sbjct\t" . $hit->num_unaligned_sbjct . "\n";
      print "Hit\tnum_unaligned_hit\t" .   $hit->num_unaligned_hit . "\n";
      print "Hit\tnum_unaligned_query\t" . $hit->num_unaligned_query . "\n";
      print "Hit\tstrand\t" .              $hit->strand . "\n";
      print "Hit\tframe\t" .               $hit->frame . "\n";
      print "Hit\trank\t" .                $hit->rank . "\n";
      print "Hit\tlocus\t" .               $hit->locus . "\n";
      while ( my $hsp = $hit->next_hsp ) {
	 my ($qid,$qcons) = $hsp->matches('hit');
	 my ($id,$cons) = $hsp->matches('query');
	 @qidentical = $hsp->seq_inds('query','identical');
	 @qconserved = $hsp->seq_inds('query','conserved');
	 @hidentical = $hsp->seq_inds('hit','identical');
	 @hconserved = $hsp->seq_inds('hit','conserved');
	 my @hrange =  $hsp->range('hit');
	 my @qrange =  $hsp->range('query');
	 my $aln =     $hsp->get_aln;
	 my $alnIO = Bio::AlignIO->new(-format=>"clustalw");
	 print "HSP\trange('hit')\t@hrange\n";
	 print "HSP\trange('query')\t@qrange\n";
	 print "HSP\tseq_inds('hit','identical')\t@hidentical\n";
	 print "HSP\tseq_inds('query','conserved')\t@qconserved\n";
	 print "HSP\tseq_inds('query','identical')\t@qidentical\n";
	 print "HSP\tseq_inds('hit','conserved')\t@hconserved\n";
	 print "HSP\tmatches('hit')\t" .   $qid . " " . $qcons . "\n";
	 print "HSP\tmatches('query')\t" . $id . " " . $cons . "\n";
	 print "HSP\talgorithm\t" .        $hsp->algorithm . "\n";
	 print "HSP\tevalue\t" .           $hsp->evalue . "\n";
	 print "HSP\tfrac_identical\t" .   $hsp->frac_identical . "\n";
	 print "HSP\tfrac_conserved\t" .   $hsp->frac_conserved . "\n";
	 print "HSP\tgaps\t" .             $hsp->gaps     . "\n";
	 print "HSP\tquery_string\t" .     $hsp->query_string . "\n";
	 print "HSP\thit_string\t" .       $hsp->hit_string . "\n";
	 print "HSP\thomology_string\t" .  $hsp->homology_string . "\n";
	 print "HSP\tlength('total')\t" .  $hsp->length('total') . "\n";
	 print "HSP\tlength('hit')\t" .    $hsp->length('hit') . "\n";
	 print "HSP\tlength('query')\t" .  $hsp->length('query') . "\n";
	 print "HSP\thsp_length\t" .       $hsp->hsp_length . "\n";
	 print "HSP\tframe\t" .            $hsp->frame . "\n";
	 print "HSP\tnum_conserved\t" .    $hsp->num_conserved . "\n";
	 print "HSP\tnum_identical\t" .    $hsp->num_identical . "\n";
	 print "HSP\trank\t" .             $hsp->rank . "\n";
	 print "HSP\tscore\t" .            $hsp->score . "\n";
	 print "HSP\tbits\t" .             $hsp->bits . "\n";
	 print "HSP\tpercent_identity\t" . $hsp->percent_identity . "\n";
	 print "HSP\tstrand()\t" .         $hsp->strand() . "\n";
	 print "HSP\tstart('hit')\t" .     $hsp->start('hit') . "\n";
	 print "HSP\tstart('query')\t" .   $hsp->start('query') . "\n";
	 print "HSP\tend('hit')\t" .       $hsp->end('hit') . "\n";
	 print "HSP\tend('query')\t" .     $hsp->end('query') . "\n";
	 print "HSP\talignment\n";
	 print $alnIO->write_aln($aln),"\n\n";
      }
   }
}

__END__
BioPerl-1.007002/examples/searchio/custom_writer.pl000555000766000024       621713155576320 22402 0ustar00cjfieldsstaff000000000000#!/usr/bin/env perl 

# Demonstrates the use of a SearchIO Blast parser and a SearchWriterI object
# for producing custom output of Blast hit data from a Blast report 
# input stream.
#
# Here we define a custom SearchWriterI object that ouputs just the data we want
# from each BLAST report.
# 
# NOTE: If you just want pick and choose which columns you want 
# in the output table, you don't need to create your own custom
# SearchWriterI implementation as we do here. HitTableWriter and HSPTableWriter
# are configurable as to what columns and order you want. 
# The hitwriter*.pl and hspwriter.pl examples in this directory
# illustrate this.
#
# For a complete list of columns, see the docs for these modules:
#   Bio::SearchIO::Writer::HitTableWriter
#   Bio::SearchIO::Writer::HSPTableWriter
#
# This example serves as an illustration of how to use the 
# SearchWriterI api and plug it in to a SearchIO parser,
# which you may want to do if you want to generate data column(s)
# not provided by the available writers.
#
# Usage:
#   STDIN:  stream containing one or more BLAST or PSI-BLAST reports.
#   STDOUT: none, but generates an output file "custom_writer.out"
#           containing tab-delimited data on a per-hit basis.
#   STDERR: Progress info.
#
# Author: Steve Chervitz 

package MyBlastWriter;

use strict;
use lib '../../';
use Bio::Root::Root;
use Bio::SearchIO::SearchWriterI;

use base qw( Bio::Root::Root Bio::SearchIO::SearchWriterI );

sub to_string {
    my ($self, $result, @args) = @_;
    my $str = '';

    my $hits_reported = 0;

    foreach my $hit($result->hits) {

      # If this is a PSI-BLAST report, only report novel hits
      if( $result->psiblast ) {
	# Note that we could have supplied this has a -HIT_FILTER function
	# when we defined our input SearchIO object. Then we wouldn't need 
	# to define a custom writer.
	next unless $hit->iteration > 1 and not $hit->found_again;
      }

      $hits_reported++;
      printf STDERR "$hit\n";

      $str .= sprintf "%s\t%d\t%s\t%d\t%.2f\t%d\t%.1e\t%d\t%d\t%d\t%d\t%s\n", 
	               $result->query_name, $result->query_length, $hit->name,
	               $hit->length, $hit->frac_identical('query'), $hit->length_aln,
	               $hit->expect, $hit->score, $hit->bits,
	               $hit->gaps('total'), $hit->num_hsps, $hit->iteration || '-';
    }

    printf STDERR "\n%d hits written\n", $hits_reported;

    $str;

}

package main;

#===================================================
# Start of script 
#===================================================

use strict;

use lib '../../../';
use Bio::SearchIO;

select STDOUT; $|=1; 

my $in     = Bio::SearchIO->new( -format => 'blast', 
				 -fh => \*ARGV,
                                 -signif => 0.1 );
my $writer = MyBlastWriter->new();
my $out    = Bio::SearchIO->new( -format => 'blast',
				 -writer => $writer,
				 -file   => ">custom_writer.out" );

while ( my $result = $in->next_result() ) {
    printf STDERR "Report %d: $result\n", $in->result_count;
    $out->write_result($result);
}

printf STDERR "\n%d Results processed.\n", $in->result_count;
printf STDERR "Output sent to file: %s\n",  $out->file if $out->file;

BioPerl-1.007002/examples/searchio/hitwriter.pl000555000766000024       772613155576320 21523 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl 

# Demonstrates the use of a SearchIO Blast parser and a SearchWriterI object
# for producing tab-delimited output of hit data from a Blast report 
# input stream.
#
# Each row in the output represents data for a single hit.
# For hits containing multiple HSPs, the output information represents a
# summary across all HSPs.
#
# This parser represents a new and improved version of Bio::Tools::Blast.
#
# Usage:
#   STDIN:  stream containing one or more BLAST or PSI-BLAST reports.
#   STDOUT: none, but generates an output file "hitwriter.out"
#           containing tab-delimited data on a per-hit basis.
#   STDERR: Progress info and any errors.
# 
# In this example, we create a SearchIO parser that screens out hits 
# based on expect (or P) scores and a default HitTableWriter. This writer
# provides the same functionality as the original Bio::Tools::Blast::table()
# function (i.e., a tab-delimited summary of each hit per row).
# HitTableWriter, however, is customizable so you can specify just the columns
# you want to have in the output table.
#
# For more documentation about the writer, including
# a complete list of columns, execute:
#   perldoc Bio::SearchIO::Writer::HitTableWriter.
#
# For more documentation about working with Blast result objects,
# see docs for these modules:
#   Bio::Search::Result::BlastResult
#   Bio::Search::Iteration::IterationI
#   Bio::Search::Hit::BlastHit
#   Bio::Search::HSP::BlastHSP
#
# For more documentation about the Blast parser, see docs for
#   Bio::SearchIO
#
# Author: Steve Chervitz 

use strict;
use lib '../../';

use Bio::SearchIO;
use Bio::SearchIO::Writer::HitTableWriter;

# These are the columns that will be in the output table of BLAST results.
my @columns = qw(
		 query_name
		 query_length
                 hit_name
                 hit_length
		 num_hsps
                 expect
                 frac_aligned_query
                 frac_identical_query
                 length_aln_query
                 gaps_total
                 strand_query
                 strand_hit
		);

# The following columns require HSP alignment data:
# 		  num_hsps
#                 frac_identical_query
#                 length_aln_query
#                 gaps_total
#                 strand_query
#                 strand_hit

print STDERR "\nUsing SearchIO->new()\n";

# Note that all parameters for the $in, $out, and $writer objects are optional.
# Default in = STDIN; Default out = STDOUT; Default writer = all columns 
# In this example, we're reading from STDIN and  writing to a file 
# called "hitwriter.out"
# TODO: write hitless reports to STDERR and note if filtered.
my $in     = Bio::SearchIO->new( -format => 'blast', 
				 -fh => \*ARGV,
				 -signif => 0.1, 
				# -verbose=> 2
                               );
my $writer = Bio::SearchIO::Writer::HitTableWriter->new( -columns => \@columns
						       );
my $out    = Bio::SearchIO->new( -format => 'blast',
				 -writer => $writer,
				 -file   => ">hitwriter.out" );
# Need to keep a separate count of reports with hits
# to know when to include labels. The first report may be hitless, 
# so we can't use $in->result_count
my $hit_count = 0;
while ( my $blast = $in->next_result() ) {
  printf STDERR "\nReport %d: $blast\n", $in->result_count;
  
  printf STDERR "query=%s, length=%d\n", $blast->query_name, $blast->query_length;

  if( $blast->hits ) {
      print STDERR "# hits= ", $blast->num_hits, "\n";
      $hit_count++;
      my @hits= $blast->hits;
      print STDERR "frac_aligned_query= ", $hits[0]->frac_aligned_query, "\n";

      $out->write_result($blast, $hit_count==1 );
  }
  else {
    print STDERR "Hitless Blast Report ";
    print STDERR ($blast->no_hits_found ? "\n" : "(filtered)\n");
  }
  
  ## For a simple progress monitor, uncomment this line:
  #print STDERR "."; print STDERR "\n" if $in->result_count % 50 == 0;
}

printf STDERR "\n%d Blast report(s) processed.\n", $in->result_count;
printf STDERR "Output sent to file: %s\n",  $out->file if $out->file;

BioPerl-1.007002/examples/searchio/hspwriter.pl000555000766000024       607513155576320 21525 0ustar00cjfieldsstaff000000000000#!/usr/bin/env perl 

# Demonstrates the use of a SearchIO Blast parser and a SearchWriterI object
# for producing tab-delimited output of HSP data from a Blast report 
# input stream.
#
# Each row in the output represents data for a single HSP.
#
# This parser represents a new and improved version of Bio::Tools::Blast.
#
# Usage:
#   STDIN:  stream containing one or more BLAST or PSI-BLAST reports.
#   STDOUT: none, but generates an output file "hspwriter.out"
#           containing tab-delimited data on a per-HSP basis.
#   STDERR: Progress info and any errors.
#
# In this example, we create a SearchIO parser that screens out hits 
# based on expect (or P) scores and a default HSPTableWriter. This writer
# provides the same functionality as the original Bio::Tools::Blast::table2()
# function (i.e., a tab-delimited summary of each hit per row).
# HSPTableWriter, however, is customizable so you can specify just the columns
# you want to have in the output table.
#
# For more documentation about the writer, including
# a complete list of columns, execute:
#   perldoc Bio::SearchIO::Writer::HSPTableWriter.
#
# For more documentation about working with Blast result objects,
# see docs for these modules:
#   Bio::Search::Result::BlastResult
#   Bio::Search::Iteration::IterationI
#   Bio::Search::Hit::BlastHit
#   Bio::Search::HSP::BlastHSP
#
# For more documentation about the Blast parser, see docs for
#   Bio::SearchIO
#
# Author: Steve Chervitz 

use strict;
use lib '../../';

use Bio::SearchIO;
use Bio::SearchIO::Writer::HSPTableWriter;

# These are the columns that will be in the output table of BLAST results.
my @columns = qw(
		 query_name
		 query_length
                 hit_name
                 hit_length
		 rank
                 expect
                 frac_identical_query
                 length_aln_query
                 gaps_total
                 strand_query
                 strand_hit
		);


print STDERR "\nUsing SearchIO->new()\n";

# Note that all parameters for the $in, $out, and $writer objects are optional.
# Default in = STDIN; Default out = STDOUT; Default writer = all columns 
# In this example, we're reading from STDIN and  writing to a STDOUT
my $in     = Bio::SearchIO->new( -format => 'blast',
				 -fh => \*ARGV
                               );
my $writer = Bio::SearchIO::Writer::HSPTableWriter->new( -columns => \@columns );
my $out    = Bio::SearchIO->new( -format => 'blast', 
				 -writer => $writer,
				 -file   => ">hspwriter.out" );

while ( my $result = $in->next_result() ) {
  printf STDERR "\nReport %d: $result\n", $in->result_count;
  
  if( $result->hits ) {
    $out->write_result($result, ($in->result_count - 1 ? 0 : 1) );
  }
  else {
    print STDERR "Hitless Blast Report: $result ";
    print STDERR ($result->no_hits_found ? "\n" : "(filtered)\n");
  }
  
  ## For a simple progress monitor, uncomment this line:
  #print STDERR "."; print STDERR "\n" if $in->result_count % 50 == 0;
}

printf STDERR "\n%d Blast report(s) processed.\n", $in->result_count;
printf STDERR "Output sent to file: %s\n",  $out->file if $out->file;

BioPerl-1.007002/examples/searchio/htmlwriter.pl000555000766000024       365513155576320 21700 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl 

# Demonstrates the use of a SearchIO Blast parser and a SearchWriterI object
# for producing HTML Blast output from a Blast report input stream.
#
# Usage:
#   STDIN:  none; supply filename of BLAST report on command-line
#   STDOUT: none; generates an output file "searchio.html"
#           containing HTML-formatted Blast Report
#   STDERR: Any errors that occurred.
#
# For more documentation about the writer, including
# a complete list of columns, see the docs for 
#   Bio::SearchIO::Writer::HTMLResultWriter.
#
# For more documentation about working with Blast result objects,
# see docs for these modules:
#   Bio::Search::Result::BlastResult
#   Bio::Search::Iteration::IterationI
#   Bio::Search::Hit::BlastHit
#   Bio::Search::HSP::BlastHSP
#
# For more documentation about the Blast parser, see docs for
#   Bio::SearchIO
#
# Author: Steve Chervitz 


use strict;
use lib '../../';

use Bio::SearchIO;
use Bio::SearchIO::Writer::HTMLResultWriter;

my $outfile = "searchio.html";
my $file = shift or die "Usage: $0 \n       HTML output is saved to $outfile\n";

my $in = Bio::SearchIO->new( -format => 'blast', 
                             -file => $file,  #comment this out to read STDIN
                             #-fh => \*ARGV,  #uncomment this to read from STDIN
                             -verbose => 0 );

my $writer = new Bio::SearchIO::Writer::HTMLResultWriter();
my $out = new Bio::SearchIO(-writer => $writer,
                            -file   => ">$outfile");


while ( my $result = $in->next_result() ) {
    eval {
        # printf STDERR "Report %d: $result\n", $in->result_count;
        $out->write_result($result, 1);
    };
    if($@) {
        warn "Warning: Blast parsing or writing exception caught for $result:\n$@\n";
    }
}

printf STDERR "\n%d Blast report(s) processed.\n", $in->result_count;
printf STDERR "Output sent to file: %s\n",  $out->file if $out->file;
BioPerl-1.007002/examples/searchio/psiblast_features.pl000555000766000024       315613155576320 23212 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

# Example usage of a SearchIO::psiblast parser of traditional format Blast 
# and PSI-Blast reports.
# Illustrates how to grab a set of SeqFeatures from a Blast report.
# This parser represents a new and improved version of Bio/Tools/Blast.pm.
#
# Usage:
#   STDIN:  stream containing one or more BLAST or PSI-BLAST reports.
#   STDOUT: feature start, end data
#   STDERR: Processing info, such as the number of reports processed
#           and the number of hitless reports.
# 
# For more documentation about working with Blast result objects,
# see to documentation for these modules:
#   Bio::Search::Result::BlastResult
#   Bio::Search::Hit::BlastHit
#   Bio::Search::HSP::BlastHSP
#
# For more documentation about the PSI-Blast parser, see docs for
#   Bio::SearchIO::psiblast
#
# Author: Steve Chervitz 

use strict;
use lib '../../';
use Bio::SearchIO;

my $in = Bio::SearchIO->new( -format => 'psiblast',
                             -fh => \*ARGV,
			     -signif => 0.1, 
			     -verbose => 0 );
my @hitless_reports = ();

while ( my $blast = $in->next_result() ) {

    if( $blast->hits ) {
      while( my $feature = $blast->next_feature() ) {
	print "Feature from ", $feature->start, " to ", $feature->end, "\n";
      }
    }
    else {
      push @hitless_reports, $blast;
    }
}

printf STDERR "\n%d Blast report(s) processed.\n", $in->result_count;
printf STDERR "\n%d reports had no hits:\n", scalar(@hitless_reports);

foreach my $blast (@hitless_reports) {
    print STDERR "No hits for query ", $blast->query_name;
    print STDERR ($blast->no_hits_found ? "\n" : "(filtered)\n")
;
}
  

BioPerl-1.007002/examples/searchio/psiblast_iterations.pl000555000766000024       426713155576320 23561 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl 

# Demonstrates the use of a SearchIO parser for processing
# the iterations within a PSI-BLAST report.
#
# Usage:
#   STDIN:  none; supply filename of PSI-BLAST report on command-line
#   STDOUT: information parsed from the input data.
#   STDERR: errors.
#
# For more documentation about working with Iteration objects,
# see docs for:
#   Bio::Search::Iteration::IterationI
#
# Author: Steve Chervitz 

use strict;
use lib '../../';

use Bio::SearchIO;

my $file = shift or die "Usage: $0 \n";
my $in = new Bio::SearchIO(-format => 'blast',
                           -file => $file, #comment this out to read STDIN
                           #-fh => \*ARGV,  #uncomment this to read STDIN
                          );

# Iterate over all results in the input stream
while (my $result = $in->next_result) {

    printf "Result #%d: %s\n", $in->result_count, $result->to_string;
    printf "Total Iterations: %d\n", $result->num_iterations();

    # Iterate over all iterations and process old and new hits
    # separately.

    while( my $it = $result->next_iteration) { 
        printf "\nIteration %d\n", $it->number;
        printf "Converged: %d\n", $it->converged;

        # Print out the hits not found in previous iteration
        printf "New hits: %d\n", $it->num_hits_new;
        while( my $hit = $it->next_hit_new ) {
            printf "  %s, Expect=%g\n", $hit->name, $hit->expect; 
        }

        # Print out the hits found in previous iteration
        printf "Old hits: %d\n", $it->num_hits_old; 
        while( my $hit = $it->next_hit_old ) {
            printf "  %s, Expect=%g\n", $hit->name, $hit->expect; 
        }
    }
    printf "%s\n\n", '-' x 50;
}

printf "Total Reports processed: %d: %s\n", $in->result_count;

__END__

# NOTE: The following functionality is just proposed
# (does not yet exist but might, given sufficient hew and cry):

# Zero-in on the new hits found in last iteration.
# By default, iteration() returns the last one.

my $last_iteration = $result->iteration();
while( my $hit = $last_iteration->next_hit) {
    # Do something with new hit...
}

# Get the first iteration

my $first_iteration = $result->iteration(1);

BioPerl-1.007002/examples/searchio/rawwriter.pl000555000766000024       365213155576320 21522 0ustar00cjfieldsstaff000000000000#!/usr/bin/env perl 

# Demonstrates the use of a SearchIO Blast parser for producing
# output of raw HSP data from a Blast report input stream.
#
# Shows how to print out raw BLAST alignment data for each HSP.
#
# Usage:
#   STDIN:  stream containing one or more BLAST or PSI-BLAST reports.
#   STDOUT: Raw alignment data for each HSP of each hit (BLAST format)
#   STDERR: Progress info and any errors.
#
# For more documentation about working with Blast result objects,
# see docs for these modules:
#   Bio::Search::Result::BlastResult
#   Bio::Search::Hit::BlastHit
#   Bio::Search::HSP::BlastHSP
#
# For more documentation about the PSI-Blast parser, see docs for
#   Bio::SearchIO::psiblast
#
# Author: Steve Chervitz 
#
# TODO: 
#   * Implement a Bio::SearchIO::Writer::HSPTextWriter object
#     that can do this. Then this example can fit into the standard
#     model used by the other writer examples in which a writer
#     object is created and hooked up with a SearchIO output object.

use strict;

use lib '../../';

use Bio::SearchIO;

# In this case, we only want raw alignments, and we only need to screen
# on significance info (E- or P-value) so we don't need
# to do a full parse of the alignments. Thus, we're using a -shalow_parse
# flag to indicate that we don't need to parse alignments. This should
# result in faster processing.
# TODO: Convert this to use -format='blast'. Shallow-parse option not supported there.
my $in = Bio::SearchIO->new(-format => 'psiblast', 
                            -fh => \*ARGV,
			    -signif => 0.1,
			    -shallow_parse => 1,
			    -hold_raw_data => 1 );

while ( my $result = $in->next_result() ) {
  print STDERR "\nBLAST Results for $result\n\n";
  my $count = 0;
  foreach( $result->hits ) {
    print "Alignment for hit #", ++$count, "\n\n";
    print $_->raw_hit_data();
  }
  print "=" x 50 , "\n";
}

printf STDERR "\n%d Blast report(s) processed.\n", $in->result_count;

BioPerl-1.007002/examples/searchio/resultwriter.pl000555000766000024       735413155576320 22252 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl 

# Demonstrates the use of a SearchIO Blast parser and a SearchWriterI object
# for producing tab-delimited output of result data from a Blast report 
# input stream.
#
# This writer only outputs information at the level of the result object.
# This shows that you can work with a writer that only knows about 
# Bio::Search::Result objects and doesn't care about hit or HSP data. 
# Therefore, the output from this example doesn't contain any information 
# about hits or HSPs. 
# See the hitwriter.pl and hspwriter.pl examples for that.
#
# This parser represents a new and improved version of Bio::Tools::Blast.
#
# Usage:
#   STDIN:  stream containing one or more BLAST or PSI-BLAST reports.
#   STDOUT: none, but generates an output file "resultwriter.out"
#           containing tab-delimited data on a per-report basis.
#   STDERR: Any errors that occurred.
#
# For more documentation about the writer, including
# a complete list of columns, see the docs for 
#   Bio::SearchIO::Writer::ResultTableWriter.
#
# For more documentation about working with Blast result objects,
# see docs for these modules:
#   Bio::Search::Result::BlastResult
#   Bio::Search::Iteration::IterationI
#   Bio::Search::Hit::BlastHit
#   Bio::Search::HSP::BlastHSP
#
# For more documentation about the Blast parser, see docs for
#   Bio::SearchIO
#
# Author: Steve Chervitz 


use strict;
use lib '../../';

use Bio::SearchIO;
use Bio::SearchIO::Writer::ResultTableWriter;
use Bio::SearchIO::Writer::HTMLResultWriter;

print "\nUsing SearchIO->new()\n";


# Note that all parameters for the $in, $out, and $writer objects are optional.
# Default in = STDIN; Default out = STDOUT; Default writer = all columns
# In this example, we're reading from STDIN and  writing to STDOUT
# and using the default columns for the writer.
# We're also telling the script to timeout if input isn't received
# within 10 sec. (Note the clock is still ticking when you background the job.)
# Setting verbose to 1 is useful for debugging.
my $in = Bio::SearchIO->new( -format => 'blast', 
                             -fh => \*ARGV,
                             -signif => 0.1, 
                             -verbose => 0, 
                             -timeout_sec => 10 );
# not specifying any columns to get the default.
my $writer = Bio::SearchIO::Writer::ResultTableWriter->new();
my $out    = Bio::SearchIO->new( -format => 'blast', 
                                 -writer => $writer,
                                 -file => ">resultwriter.out");

my $writerhtml = new Bio::SearchIO::Writer::HTMLResultWriter();
my $outhtml = new Bio::SearchIO(-writer => $writerhtml,
                                -file   => ">searchio.html");


while ( my $result = $in->next_result() ) {
    eval {
        # printf STDERR "Report %d: $result\n", $in->result_count;
        $out->write_result($result, ($in->result_count - 1 ? 0 : 1) );
        
        $outhtml->write_result($result, 1);

        # To get at the statistical parameters:
        # Calling raw_statistics() returns a list containing the
        # unparsed lines of the parameters section of the report.
        # Here we're only interested in parameters beginning with "effective".
        #         print "Report Stats, effective data:\n";
        #         foreach( $result->raw_statistics) {
        #             print "$_" if /^effective/i;
        #         }
        
	## For a simple progress monitor, uncomment this line:
	#print STDERR "."; print STDERR "\n" if $in->result_count % 50 == 0;
    };
    if($@) {
        warn "Warning: Blast parsing or writing exception caught for $result:\n$@\n";
    }
}

printf STDERR "\n%d Blast report(s) processed.\n", $in->result_count;
printf STDERR "Output sent to file: %s\n",  $out->file if $out->file;
BioPerl-1.007002/examples/searchio/waba2gff.pl000555000766000024       141313155576320 21144 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
use strict;
use Bio::SearchIO;
use Getopt::Long;
use Benchmark;

my ($infile,$outfile,$verbose);

GetOptions( 
	    'i|input:s'  => \$infile,
	    'o|output:s' => \$outfile,
	    'v|verbose'  => \$verbose,
	    );
$infile = shift unless $infile;

my $in = new Bio::SearchIO(-format => 'waba',
			   -file   => $infile, #comment out to read from STDIN
                           #-fh => \*ARGV,  # uncomment to read from STDIN
			   -verbose => $verbose);

my $out;
if( defined $outfile) {
    $out = new Bio::Tools::GFF(-file => ">$outfile");
} else {
    $out = new Bio::Tools::GFF(-verbose => $verbose);
}

while( my $r = $in->next_result ) {
    while( my $hit = $r->next_hit ) {
	while( my $hsp = $hit->next_hsp ) {
	    $out->write_feature($hsp);
	}
    }
}
BioPerl-1.007002/examples/searchio/waba2gff3.pl000555000766000024      1066513155576320 21260 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=head1 NAME

waba2gff3.pl - convert waba output into GFF3 suitable for Gbrowse

=head1 DESCRIPTION

This script turns WABA output into GFF3 output for the query sequence.
If you need to get this where the Hit sequence is the reference
sequence you'll want to flip-flop the code to use hit instead of
query.  I didn't try and make it that general yet.

I don't (yet) know how the 'score' field is calculate by Wormbase
folks for WABA data in their GFF dumps.  I'm checking on that but it
shouldn't make a difference for Gbrowse.

=head1 AUTHOR

Jason Stajich, jason-at-bioperl-dot-org
Duke University, 

=head1 LICENSE

This script is available under the Perl Artistic License meaning you
can do with it what you wish.  

Please do tell me about bugs or improvements so I can roll those back
in for other people to use.


=cut

 

use strict;
use Bio::SearchIO;
use Bio::SeqFeature::Generic;
use Bio::Tools::GFF;
use Getopt::Long;

my %States = ('1' => 'coding',
	      '2' => 'coding',
	      '3' => 'coding',
	      'L'  => 'weak',
	      'H'  => 'strong',
	     );
my ($infile,$outfile,$verbose,$version);
$version = 3;
my $ptag = 'nucleotide_match';
GetOptions( 
    'i|input:s'  => \$infile,
    'o|output:s' => \$outfile,
    'v|verbose'  => \$verbose,
    'version'    => \$version,
    'p|primary|primary_tag:s' => \$ptag,
);
$infile = shift unless $infile;

my $in;

if( $infile ) {
    $in = new Bio::SearchIO(-verbose => $verbose,
			    -format  => 'waba',
			    -file    => $infile);
} else {
    $in = new Bio::SearchIO(-verbose => $verbose,
			    -format  => 'waba',
			    -fh      => \*ARGV);
}

my $out;
if( defined $outfile) {
    $out = new Bio::Tools::GFF(-gff_version => $version,
			       -file => ">$outfile",
			       -verbose => $verbose);
} else {
    $out = new Bio::Tools::GFF(-gff_version => $version,
			       -verbose     => $verbose);
}

while( my $r = $in->next_result ) {
    while( my $hit = $r->next_hit ) {
	while( my $hsp = $hit->next_hsp ) {
	    # now split this HSP up into pieces
	    my ($qs,$qe,$hs,$he)= ($hsp->query->start,
				   $hsp->query->end,
				   $hsp->hit->start,
				   $hsp->hit->end);
	    my $i = 0;
	    # grab the HMM states from Jim's WABA output
	    my $stateseq = $hsp->hmmstate_string;
	    my $state_len = length($stateseq);
	    my ($piece,$gap,@pieces);
	    $piece = {'length'   => 0,
		      'str'      => '',
		      'start'    => $i};
	    $gap = 0;
	    
	    # parse the state string, finding the gaps (Q and T states)
	    # runs of Non Q or T letters indicate a 'piece'
	    while($i <  $state_len ) {
		my $char = substr($stateseq,$i,1);
		if($char =~ /[QT]/ ) {
		    $gap++;
		} elsif( $gap ) {
		    # just finished a gap
		    $piece->{'length'} = length($piece->{'str'});
		    push @pieces, $piece;
		    $piece = {'length' => 0,
			      'str'    => '',
			      'start'  => $i };
		    $gap = 0;
		} else {
		    $piece->{'str'} .= $char;
		}
		$i++;
	    }
	    # for each piece, this could be made up of things either 
	    # as H,L, or 123 state. 
	    # In retrospect this could all probably be contained in a 
	    # single loop, but now I'm feeling lazy. I had just converted this
	    # from using 'split' in the first place if you want to know
	    # why it is structured this way....
	    for my $piece ( @pieces ) {
		
		my $len = $piece->{length};
		my $start = $piece->{start};
		my $end = $start + $len;
		my ($j) = 0;
		my $state = substr($piece->{str},$j++,1);
		warn("start is $start end is $end len is $len\n") if $verbose;
		my ($set,@sets) = ($state);
		while( $j < $len ) {
		    my $char = substr($piece->{str},$j++,1);
		    next unless( $char);
		    if( ($char =~ /\d/ && $state =~ /\d/) ||
			($char =~ /\w/ && $char eq $state) ) {
			$set .= $char;
		    } else {
			push @sets, $set;
			$set = $state = $char;
		    }		    
		}
		push @sets, $set;
		for my $set (@sets ) {
		    my $c = substr($set,0,1);
		    if( ! $c ) {
			warn("no char for '$set'\n") if $verbose;
			next;
		    }
		    my $type ='waba_'.$States{$c};
		    my $f = Bio::SeqFeature::Generic->new(
			-start => $qs + $start,
			-end   => $qs + $start + length($set),
			-strand=> $hsp->query->strand,
			-seq_id=> $hsp->query->seq_id,
			-score => $hsp->query->score,
			-primary_tag => $ptag,
			-source_tag  => $type,
			-tag    => {
			    'ID' => $hsp->hit->seq_id
			    });
		    $f->add_tag_value('ID',$hs+$start,$hs+$start+$f->length);
		    $out->write_feature($f);
		    $start += $f->length+1;
		}
	    }
	}
    }
}
BioPerl-1.007002/examples/sirna000755000766000024          013155576320 16310 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/sirna/TAG000444000766000024        11113155576320 16754 0ustar00cjfieldsstaff000000000000These are scripts for designing SiRNA reagents using Bio::Tools::SiRNA.pmBioPerl-1.007002/examples/sirna/rnai_finder.cgi000555000766000024      3545413155576320 21447 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=pod

=head1 NAME

rnai_finder.cgi

=head1 DESCRIPTION

A CGI script using the Bio::Tools::SiRNA package to design RNAi reagents.  
Retrieves sequences from NCBI and generates output in graphic and tabular form.

=head1 INSTALLATION

To use this script, place it in an appropriate cgi-bin directory on a web server.  
The script needs to write its graphic maps to a temporary directory.  Please update
$TMPDIR and $TMPURL to suit your local configuation.

=head1 AUTHOR

Donald Jackson (donald.jackson@bms.com)

=head1 SEE ALSO

L, L, L, L

=cut

use Bio::Tools::SiRNA;

use Bio::Graphics::Panel;
use Bio::DB::NCBIHelper;
use Bio::Seq::RichSeq; # for hand-entry
use Bio::SeqFeature::Generic; 

use GD::Text::Align;
use Clone qw(clone);

use CGI;
use CGI::Carp qw (fatalsToBrowser carpout);

my $q = CGI->new;



# define a bunch of constants
my %COLORRANKS = ( 1 => 'red',
		   2 => 'orchid',
		   3 => 'blue' );
my $TMPDIR = '/var/www/htdocs/tmp/';
my $TMPURL = '/tmp/';
my $ATGPAD = 75; # how far from start do we wait?
my $NOLIGOS = 3;

my $log = $TMPDIR . 'RNAiFinder.log';
open (LOG, ">>$log") or die $!;
carpout(LOG);

print $q->header,
    $q->start_html;
    
print $q->h1('RNAi Finder');


if ($q->param('Design')) {
    if ($q->param('accession') and !$q->param('seq')) {
	$target = get_target();
    }
    else { 
	$target = make_target();
    }
    get_rnai($target);
}
else {
    get_settings();
}


sub get_settings {
    print <Oligos are designed as described on the Tuschl lab web page and are ranked as follows: 

    

  • New: Selecting 'Pol3-compatible targets' looks for oligos with the 
pattern NAR(N17)YNN which can be synthesized or expressed from a Pol3 promoter.

    This selection overrides the 'Cutoff' rank.

  • Oligos with Rank = 1 (best) match the AAN(19)TT rule.

  • Oligos with Rank = 2 match the AAN(21) rule 

  • Oligos with Rank = 3 match the NAN(21) rule.



If percent GC and specificity are similar, Rank 1 oligos are better. All 3 prime overhangs are converted to TT; the rest of the sequence is transcribed into RNA



Modifications to published rules:


    

  • 
Runs of 3 or more consecutive Gs on either strand are skipped - these can cause problems in synthesis. 

  • Users may choose to exclude oligos that overlap single nucleotide polymorphisms (ON by default).  SNP data comes from the NCBI dbSNP database.  

  • 'Low-complexity' regions (such as runs of a single nucleotide) are also excluded.



EOM1
    
    print $q->start_form;
    print $q->h2('Enter your sequence and other parameters:'), "\n";
    print $q->p('The values already here are DEFAULTS - you should change them to suit YOUR sequence');
    print $q->start_table();
    print $q->TR( $q->td({-align=> 'left'}, 
		       [
			$q->textfield(-name 	=> 'mingc', -default => '0.40'),
			$q->textfield(-name 	=> 'maxgc', -default => '0.60'),
			]
		       ),
		      $q->td({-align=> 'left'},
			     $q->popup_menu(-name	 => 'worstrank', 
				      -values 	=> [1,2,3], 
				      -default 	=> 2,
				      ),
			     $q->b('OR'),
			     $q->checkbox(-name 		=> 'pol3',
				    -label		=> 'Pol3 compatible',
				    -default	=> 0,
				    ),
			     ),
		      );	
    print    $q->TR( $q->th({-align=> 'left'}, 'Exclude oligos with SNPs?'),
		     $q->td($q->radio_group(-name => 'avoid_snps', 
					    -values => [1,0],
					    -default => 1,
					    -labels => {1 => 'Yes', 0 => 'No'}
					    )),
		     );

    print $q->TR( $q->th({-align=> 'left'}, 'Sequence Name:'),
		  $q->td({-align=> 'left'},$q->textfield('accession')),
		  $q->td({-align=> 'left'}, 
			 $q->em( q(Enter an accession and you won't have to enter the 
sequence or start/stop. Use accessions beginning with NM_ if possible.))),
		  );

    print $q->TR( $q->th({-align=> 'left'}, ['Position of initiator ATG:', 
					     'NT after start to exclude:',
					     'Position of Stop codon:' ]));
    print $q->TR( $q->td({-align=> 'left'}, 
					   [$q->textfield(-name => 'cdstart', -default => 1),
					    $q->textfield(-name => 'atgpad', -default => $ATGPAD),
					    $q->textfield('cdend'), ]));
    print $q->TR( $q->th({-align=> 'left'}, ['Minimum Fraction GC:', 
					     'Maximum Fraction GC:', 
					     'Rank cutoff',
					     ]));
    print $q->TR($q->th({-align=> 'left', -colspan=>2},'cDNA Sequence in plain text or FASTA format'),
		 $q->td( $q->a({-href =>'Fasta_format.html', -target => 'Fasta_desc'}, 'What is FASTA format?')),
		 );
    print $q->TR($q->td({-align => 'left', -colspan=>3},
		  $q->textarea( -name =>'seq',
				-rows => 4,
				-columns => 80, 
				-wrap => 'virtual',
				)));
    print $q->TR( $q->th({-align => 'left', -colspan=>3},
			 'Output options: '));
    print $q->TR( $q->td({-align=> 'left'},
		   [ $q->checkbox(-name => 'Graphic', -checked => 'checked'), 
		     $q->checkbox(-name =>  'Table',  -checked => 'checked'), 
						 ]));			       		   		
    print $q->TR($q->td({-align=> 'left', -colspan=>3}, $q->submit('Design')));
    print $q->end_table();		
    print $q->end_form;

}

sub get_rnai {
    # design and output RNAi reagents
    my ($gene) = @_;

    my $factory = Bio::Tools::SiRNA->new( -target 	=> $gene, 
					  -tmpdir	=> $TMPDIR,
					  -cutoff 	=> $q->param('worstrank') || 2,
					  -avoid_snps	=> $q->param('avoid_snps') || 1, 
					  -min_gc	=> $q->param('min_gc') || 0.40,
					  -max_gc	=> $q->param('max_gc') || 0.60,
					  -pol3		=> $q->param('pol3') || 0,
					  );

    print $q->p('Designing Pol3-compatible oligos') if ($q->param('pol3'));

    my @pairs = $factory->design;

    draw_gene($gene) if ($q->param('Graphic'));
    print_table($gene->accession, \@pairs) if ($q->param('Table'));
    print_text($gene->accession, \@pairs) if ($q->param('Text'));
}

sub get_target {
    my ($acc) = $q->param('accession');
    my $gb = Bio::DB::NCBIHelper->new();
    my $seq = $gb->get_Seq_by_acc($acc);

    if ($seq) { 
	return $seq;
    }
    else {
	print_error("Unable to retrieve sequence from GenBank using accession $acc");
	return;
    }

}

sub make_target {
      # sanity chex - do we have the necessary info?
      $q->param('seq') or print_error("Please supply a sequence", 1);
      my $seq = $q->param('seq');
      my $name;

      # is sequence in fasta format?
      if ($seq =~ /^>/) {
	  my ($head, $realseq) = split (/\n/, $seq, 2);
	  $head =~ /^>(.+?) /;
	  $name = $1;
	  $realseq =~ s/[\n|\r|\s]//g;
	  $seq = $realseq;
      }
      elsif ($q->param('accession')) {
  	$name = $q->param('accession');
	$seq =~ s/[\n|\r|\s]//g;
      }
      else {
  	print_error('Please supply a sequence name!');
  	return;
      }

      $cds_start = $q->param('cds_start') || 1;
      $cds_end = $q->param('cds_end') || length($seq);

      # create a new Bio::Seq::RichSeq object from parameters 
      my $seqobj = Bio::Seq::RichSeq->new( -seq 		=> $seq,
					   -accession_number	=> $name,
					   -molecule		=> 'DNA',
					   
  				     );
      my $cds = Bio::SeqFeature::Generic->new( -start 	=> $cds_start,
					       -end	=> $cds_end,
  					     );
      $cds->primary_tag('CDS');
      $seqobj->add_SeqFeature($cds);
      return $seqobj;
     
}
sub draw_gene {
# now draw a pretty picture
    my ($gene) = @_;

    my $panel = Bio::Graphics::Panel->new( -segment 	=> $gene,
					   -width 	=> 600,
					   -pad_top	=> 100,
					   -pad_bottom  => 20,
					   -pad_left	=> 50,
					   -pad_right	=> 50,
					   -fontcolor	=> 'black',
					   -fontcolor2  => 'black',
					   -key_color	=> 'white',
					   -grid	=> 1,
					   -key_style	=> 'between',
					   #-gridcolor	=> 'lightgray',
					   );

    my $genefeat = Bio::SeqFeature::Generic->new( -start	=> 1,
						  -end 	       	=> $gene->length);

    $panel->add_track( arrow	=> $genefeat,
		       -bump	=> 0,
		       -tick	=> 2,
		       -label 	=> 1,
		       );

    my %feature_classes;

    foreach $feat($gene->top_SeqFeatures) {
	$feature_classes{ $feat->primary_tag } ||= [];

	push(@{ $feature_classes{ $feat->primary_tag } }, $feat);
    }

# for some reason, Bio::Graphics insists on drawing subfeatures for SiRNA::Pair objects...
    $cleanpairs = cleanup_feature($feature_classes{'SiRNA::Pair'});

# draw
    $panel->add_track( transcript	=> $feature_classes{'gene'},
		       -bgcolor	=> 'green',
		       -fgcolor	=> 'black',
		       -fontcolor2  => 'black',
		       -key		=> 'Gene',
		       -bump	=> +1,
		       -height	=> 8,
		       -label	=> \&feature_label,
		       -description	=> 1,
		       );

    $panel->add_track( transcript2	=> $feature_classes{'CDS'},
		       -bgcolor		=> 'blue',
		       -fontcolor2  => 'black',
		       -fgcolor		=> 'black',
		       -key		=> 'CDS',
		       -bump		=> +1,
		       -height		=> 8,
		       -label		=> \&feature_label,
		       -description		=> \&feature_desc,
		       );

    $panel->add_track( $feature_classes{'variation'},
		       -bgcolor	=> 'black',
		       -fgcolor	=> 'black',
		       -fontcolor2  => 'black',
		       -key	=> 'SNPs',
		       -bump	=> +1,
		       -height	=> 8,
		       -label	=> \&snp_label,
		       #-glyph	=> 'triangle',
		       -glyph	=> 'diamond',
		       -description		=> \&feature_desc,
		       );

    $panel->add_track( generic	=> $feature_classes{'Excluded'},
		       -bgcolor	=> 'silver',
		       -fgcolor	=> 'black',
		       -fontcolor  => 'black',
		       -fontcolor2  => 'black',
		       -key	=> 'Excluded Regions',
		       -bump	=> +1,
		       -height	=> 6,
		       -label	=> \&feature_label,
		       -description		=> \&feature_desc,
		       );

    $panel->add_track( 
		       generic => $cleanpairs,
		       -bgcolor	=> \&feature_color,
		       -fgcolor	=> \&feature_color,
		       -fontcolor  => 'black',
		       -fontcolor2  => 'black',
		       -key	=> 'SiRNA Reagents',
		       -bump	=> +1,
		       -height	=> 8,
		       -label	=> \&feature_label,
		       -glyph	=> 'generic',
		       -description		=> \&feature_desc,
		       );

    my $gd = $panel->gd;
    my $black = $gd->colorAllocate(0,0,0);
    my $txt = GD::Text::Align->new($gd);    
    $txt->set( valign => 'center', align => 'center', color => $black);
    #$txt->set_font(['/usr/share/fonts/truetype/VERDANA.TTF',gdGiantFont ], 10);
    $txt->set_font(gdGiantFont);
    $txt->set_text("RNAi Reagents for ".$gene->accession );
    $txt->draw(200, 50, 0);

    my $pngfile = $TMPDIR . $gene->accession . '.png';
    my $pngurl = $TMPURL . $gene->accession . '.png';
    open (IMG, ">$pngfile") or die $!;
    binmode IMG;
    print IMG $gd->png;
    close IMG;

    # also get the imagemap boxes
    my @pairboxes = extract_pairs($panel->boxes);

    print $q->img({-src => $pngurl, -usemap=>"#MAP"});
    print $q->p('Oligos are color coded: rank 1 in ', 
		$q->font({-color => $COLORRANKS{1}}, $COLORRANKS{1}),
		', rank 2 in ',
		$q->font({-color => $COLORRANKS{2}}, $COLORRANKS{2}),
		' and rank 3 in ',
		$q->font({-color => $COLORRANKS{3}}, $COLORRANKS{3}),
		'. Click on an oligo to bring it up in the table below');

    print_imagemap(@pairboxes);

}

sub feature_label {
    my ($feature) = @_;
    my (@notes, @label);
    #$label = ucfirst($feature->primary_tag);
    foreach (qw(note name product gene)) {
	if ($feature->has_tag($_)) {
	    @notes = $feature->each_tag_value($_);
	    #$label .= ': ' . $notes[0];
	    push(@label, $notes[0]);
	    last;
	}
    }
    return join(': ', @label);
    #return $label;
}

sub feature_color {
    my ($feature) = @_;
    my ($rank) = $feature->each_tag_value('rank');
    #print STDERR "Feature rank: $rank COLOR $COLORRANKS{$rank}\n";
    return $COLORRANKS{$rank};
    #return 'red';
}


sub print_table {
    my ($accession, $pairs) = @_;

    print $q->h2("RNAi Reagents for $accession");
    print $q->start_table({-border => 1, -cellpadding => 2});
    print $q->TR( $q->th(['Reagent #', 'Start', 'Stop', 'Rank', 'Fxn GC', 'Sense Oligo', 'Antisense Oligo', 'Target' ]) ), "\n";


    my $i = 1;

    foreach $pair ( sort { $a->start <=> $b->start } @$pairs ) {
	my $sense = $pair->sense;
	my $anti = $pair->antisense;
	my $color = feature_color($pair);

#  	my $blasturl = "http://nunu.hpw.pri.bms.com/biocgi/versablast.pl?p=blastn&sequence=";
#  	$blasturl .= $pair->seq->seq;
#  	$blasturl .= "&action=Nucleotide Databases";

	print 
	    $q->TR( $q->td( [ $q->a({-name => 'RNAi' . $pair->start}) . $i,
			      $pair->start, 
			      $pair->end,
			      $q->font({-color => $color},$pair->rank), 
			      $pair->fxGC,
			      $q->tt($sense->seq), 	
			      $q->tt($anti->seq),
			      $q->tt($pair->seq->seq),
#  			      $q->a({-href=>$blasturl,
#  				     -target=>"blastn"},
#  				    "BLAST this target"),
			      ] ) ),
	"\n";
	$i++;
    }
    print $q->end_table;
}





sub print_text {
    my ($accession,  $pairs ) = @_;
    my ($pair);

    print "RNAi reagents for $accession \n";

    print join("\t", qw(Start Stop Rank Sense Antisense)), "\n";
    foreach $pair (@$pairs ) {
	my $sense = $pair->sense;
	my $anti = $pair->antisense;

	print join("\t", $pair->start, $pair->end, $pair->rank, $sense->seq, $anti->seq), "\n";


    }


}

sub cleanup_feature {
    my ($flist) = @_;

    my ($feat, @clean, $cfeat);

    foreach $feat(@$flist) {
	$cfeat = clone($feat);
#	$cfeat = $feat->clone;
	$cfeat->flush_sub_SeqFeature;
	push (@clean, $cfeat); # will they 
    }
    return \@clean;
}


sub extract_pairs {
    # get SiRNA::Pair features ONLY for imagemap
    return ( grep {ref($_->[0]) eq "Bio::SeqFeature::SiRNA::Pair"} @_ );
}

sub print_imagemap {
    my @items = @_;

    print q(), "\n";

    my $i = 1;
    
    foreach $item (@items) {
	my ($feature, $x1, $y1, $x2, $y2) = @$item;
	my $fstart = $feature->start; # should be unique
	my $text = 'RNAi #' . $i. ' Start=' . $feature->start . ' Rank='.$feature->rank;
	print qq(), "\n";
	warn "Mouseover text: $text\n";

	$i++;
    }
    print "\n";
}


sub print_error {
    # print error messages in big red type. Provide more graceful die/warn to end user
    my ($msg, $fatal) = @_;
    print $q->h3($q->font({-color=>'RED'}, $msg));
    
    if ($fatal) {
	print $q->end_html;
	die "$msg \n";
    }
    else {
	warn $msg;
    }
}

sub dump {
    print $q->start_ul;

    foreach ($q->param) {
	print $q->li($_),
	$q->ul($q->li([ $q->param($_) ]));
    }
}
    
sub snp_label {
    # special format for SNPs
    my ($feature) = @_;
    my $label;

    if ( $feature->has_tag('db_xref') ) {
	my @notes = $feature->each_tag_value('db_xref');
	$label .= $notes[0];
	$label .= ' ';
    }
    if ( $feature->has_tag('allele') ) {
	my ($nt1, $nt2) = $feature->each_tag_value('allele');
	$label .=  $nt1 . '->' . $nt2;
    }
    return $label;
}

sub feature_desc {
    my ($feature) = @_;
    my $desc = $feature->start;
    $desc .= '-' . $feature->end unless ($feature->start == $feature->end);
    return $desc;
}
BioPerl-1.007002/examples/structure000755000766000024          013155576320 17234 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/structure/structure-io.pl000555000766000024       126713155576320 22404 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
# Getting  Entry, Chain, Residue, and Atom objects given a PDB file

use Bio::Structure::IO;
use strict;

my $file = shift or die "No PDB file\n";
my $structio = Bio::Structure::IO->new(-file => $file);
my $struc = $structio->next_structure;

for my $chain ($struc->get_chains) {
   my $chainid = $chain->id;
   # one-letter chaincode if present, 'default' otherwise
   for my $res ($struc->get_residues($chain)) {
      my $resid = $res->id;
      # format is 3-lettercode - dash - residue number, e.g. PHE-20
      my $atoms = $struc->get_atoms($res);
      # actually a list of atom objects, used here to get a count
      print join "\t", $chainid,$resid,$atoms,"\n";
   }
}
BioPerl-1.007002/examples/tk000755000766000024          013155576320 15612 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/tk/gsequence.pl000555000766000024     14717413155576320 20344 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
# gSequence - Protein Sequence Control Panel
# by Lorenz Pollsk
#
# this is work in progress! use this only for testing

use Gtk;
use strict;
use Bio::Seq;
use Bio::SeqIO;
use Bio::Tools::SeqStats;
use Bio::SeqFeature::Generic;
use Bio::Index::Abstract;
use Bio::DB::GenBank;
use Bio::DB::GenPept;

init Gtk;

# constant
my $false = 0;
my $true = 1;

# global widgets
my ($main_notebook,@main_label,@seq_edit);
my $about_dialog;
my ($import_dialog,$import_entry,@import_buttons,$import_from);
my ($description_window,$description_edit);
my ($comment_window,$comment_edit,$current_comment,$comment_frame);
my ($seqstats_window,$seqstats_edit);
my ($dblink_window,@dblink_entry,$current_dblink,$dblink_clist,$dblink_handler_id);
my ($ref_window,@ref_entry,$current_ref,$ref_clist,$ref_handler_id);
my ($feature_window,@feature_entry,$current_feature_item,@feature_spinner,
    $feature_handler_id,$feature_tree);
my ($pref_window,@pref_entry);

# global file data
my @seq;
my @filename;
my @modified;
my @locked; # locked sequence for editing ?
my $current;

# menu
my @menu_items = ( { path        => '/_File',
		     type        => '' },
		   { path        => '/File/_New',
		     accelerator => 'N',
		     callback    => \&new },
		   { path        => '/File/_Open SwissProt',
		     accelerator => 'O',
		     callback    => \&open_dialog },
		   { path        => '/File/_Save SwissProt',
		     accelerator => 'S',
		     callback    => \&save },
		   { path        => '/File/Save _As...',
		     callback    => \&saveas_dialog },
		   { path        => '/File/Close',
		     callback    => \&close },
		   { path        => '/File/sep1',
		     type        => '' },
		   { path        => '/File/_Import from...',
		     type        => '' },
                   { path        => '/File/Import from.../Remote DB',
		     type        => '' },
                   { path        => '/File/Import from.../Remote DB/AceDB',
		     callback    => sub { &seq_import("ace"); } },
                   { path        => '/File/Import from.../Remote DB/GenPept',
		     callback    => sub { &seq_import("genpept"); } },
                   { path        => '/File/Import from.../Flat File Index',
		     type        => '' },
                   { path        => '/File/Import from.../Flat File Index/Fasta',
		     callback    => sub { &seq_import("fasta"); } },
                   { path        => '/File/Import from.../Flat File Index/SwissProt',
		     callback    => sub { &seq_import("swissprot"); } },
                   { path        => '/File/Import from.../Flat File Index/SwissPfam',
		     callback    => sub { &seq_import("swisspfam"); } },
		   { path        => '/File/_Export to...' },
		   { path        => '/File/sep2',
		     type        => '' },
		   { path        => '/File/_Quit',
		     callback    => sub { Gtk->exit( 0 ); } },

		   { path        => '/_Edit',
		     type        => '' },
		   { path        => '/Edit/C_ut',
		     callback    => sub { $seq_edit[$current]->cut_clipboard(); },
		     accelerator => 'X' },
		   { path        => '/Edit/_Copy',
		     callback    => sub { $seq_edit[$current]->copy_clipboard(); },
		     accelerator => 'C' },
		   { path        => '/Edit/_Paste',
		     callback    => sub { $seq_edit[$current]->paste_clipboard(); },
		     accelerator => 'V' },
		   { path        => '/Edit/Select All',
		     callback    => sub { $seq_edit[$current]->select_region(0,-1); } },

		   { path        => '/_Specs',
		     type        => '' },
		   { path        => '/Specs/_Sequence Stats',
		     callback    => sub {&update_seqstats_window(1);} },
		   { path        => '/Specs/sep1',
		     type        => '' },
		   { path        => '/Specs/_Description',
		     callback    => sub {&update_description_window(1);} },
		   { path        => '/Specs/_Comments',
		     callback    => sub {&update_comment_window(1);} },
		   { path        => '/Specs/_DB Links',
		     callback    => sub {&update_dblink_window(1);} },
		   { path        => '/Specs/_References',
		     callback    => sub {&update_reference_window(1);} },
		   { path        => '/Specs/sep2',
		     type        => '' },
		   { path        => '/Specs/_Features',
		     callback    => sub {&update_feature_window(1);} },

		   { path        => '/_Tools',
		     type        => '' },
		   { path        => '/Tools/Code Table' },
		   { path        => '/Tools/sep1',
		     type        => '' },
		   { path        => '/Tools/local Blast' },
		   { path        => '/Tools/local HMMER' },
		   { path        => '/Tools/hmmpfam' },
		   { path        => '/Tools/web Blast' },

		   { path        => '/_Options',
		     type        => '' },
		   { path        => '/Options/_Preferences',
		     callback    => sub {&update_pref_window(1);} },

		   { path        => '/_Help',
		     type        => '' },
		   { path        => '/Help/Help' },
		   { path        => '/Help/_About...',
		     callback    => sub { $about_dialog->show_all();} } );

### main

$current = 0;
&init_windows();
main Gtk;
exit( 0 );


### Subroutines

sub init_windows
{
    &init_main_window();
    &init_about_dialog();
    &init_import_dialog();
    &init_seqstats_window();
    &init_description_window();
    &init_comment_window();
    &init_dblink_window();
    &init_reference_window();
    &init_feature_window();
    &init_pref_window();
}

sub init_main_window
{
    # toplevel window
    my $window;
    $window = new Gtk::Window( 'toplevel' );
    $window->signal_connect( 'destroy', sub { Gtk->exit( 0 ); } );
    $window->set_title( "gSequence" );
    $window->set_usize( 600, 400 );

    # vertical box containing menu and text editor widget
    my $main_vbox;
    $main_vbox = new Gtk::VBox( $false, 1 );
    $main_vbox->border_width( 1 );
    $window->add( $main_vbox );

    # handlebox for menubar
    my $handlebox;
    $handlebox = new Gtk::HandleBox();
    $main_vbox->pack_start( $handlebox, $false, $true, 0 );

    # menubar
    my $menubar;
    $menubar = get_menu( $window );
    $handlebox->add( $menubar );

    # text widget
    $seq_edit[$current] = new Gtk::Text( undef, undef );
    $seq_edit[$current]->set_editable( $true );

    # vertical scrollbar for text widget
    my $scrollbar;
    $scrollbar = new Gtk::VScrollbar( $seq_edit[$current]->vadj );

    # horizontal box containing text widget and scrollbar
    my $seq_edit_hbox;
    $seq_edit_hbox = new Gtk::HBox( $false, 1 );
    $seq_edit_hbox->border_width( 1 );
    $seq_edit_hbox->pack_start( $seq_edit[$current], $true, $true, 0);
    $seq_edit_hbox->pack_end( $scrollbar, $false, $true, 0);

    $main_notebook = new Gtk::Notebook();
    $main_notebook->set_tab_pos( 'top' );

    $main_vbox->pack_end( $main_notebook, $true, $true, 0);

    # show everything
    $window->show_all();

    $main_notebook->signal_connect_after("switch-page",
       sub{ #$seq[$current]->seq($seq_edit[$current]->get_chars(0,-1)) 
	    #   if (defined($seq[$current]));
	    $current = $main_notebook->get_current_page(); 
	    &update_seq_data(); } );
}

sub get_menu
{
    my ( $window ) = @_;
    
    my $menubar;
    my $item_factory;
    my $accel_group;

    $accel_group = new Gtk::AccelGroup();

    # This function initializes the item factory.
    # Param 1: The type of menu - can be 'Gtk::MenuBar', 'Gtk::Menu',
    #          or 'Gtk::OptionMenu'.
    # Param 2: The path of the menu.
    # Param 3: The accelerator group.  The item factory sets up
    #          the accelerator table while generating menus.
    $item_factory = new Gtk::ItemFactory( 'Gtk::MenuBar',
					  '
',
					  $accel_group );

    # This function generates the menu items. Pass the item factory,
    # the number of items in the array, the array itself, and any
    # callback data for the the menu items.
    $item_factory->create_items( @menu_items );

    # Attach the new accelerator group to the window.
    $window->add_accel_group( $accel_group );

    # Finally, return the actual menu bar created by the item factory.
    #*menubar = gtk_item_factory_get_widget (item_factory, "<main>");
    return ( $item_factory->get_widget( '
' ) );
}

sub new_seq_page
{
    my ($seq) = shift;
    my $curr;

    push @seq,$seq;
    $curr = @seq - 1;
    $main_label[$curr] = new Gtk::Label($seq[$curr]->id())
	if (defined($seq[$curr]));
    $main_label[$curr] = new Gtk::Label("")
	if (!defined($seq[$curr]));

    # text widget
    $seq_edit[$curr] = new Gtk::Text( undef, undef );
    $seq_edit[$curr]->set_editable( $true );

    # vertical scrollbar for text widget
    my $scrollbar;
    $scrollbar = new Gtk::VScrollbar( $seq_edit[$curr]->vadj );

    # horizontal box containing text widget and scrollbar
    my $seq_edit_hbox;
    $seq_edit_hbox = new Gtk::HBox( $false, 1 );
    $seq_edit_hbox->border_width( 1 );
    $seq_edit_hbox->pack_start( $seq_edit[$curr], $true, $true, 0);
    $seq_edit_hbox->pack_end( $scrollbar, $false, $true, 0);

    $main_notebook->append_page( $seq_edit_hbox, $main_label[$curr] );
    $main_notebook->show_all();
    $main_notebook->set_page(-1);
}

sub seq_fetch
{
    my ($server,$port,$dir,$db); # read from preferences
    my ($dbobj);

    return if (!defined($import_from) || !($import_from));

    $dbobj = Bio::DB::GenPept->new() if ($import_from eq "genpept");
    $dbobj = Bio::DB::Ace->new(-host=>$server,-port=>$port)
	if ($import_from eq "ace");
    $dbobj = Bio::Index::Abstract->new("$dir/$db") 
	if ($import_from eq "fasta") ||
	   ($import_from eq "swissprot") ||
	   ($import_from eq "swisspfam");

    if( $import_buttons[0]->get_active() ) {
	&new_seq_page($dbobj->get_Seq_by_id($import_entry->get_text()));
    } else {
	&new_seq_page($dbobj->get_Seq_by_acc($import_entry->get_text()));
    }
}

sub seq_import
{
    ($import_from) = @_;
    my %names = ( "ace" => "AceDB",
			 "genpept" => "GenPept DB",
			 "fasta" => "Fasta Flat File",
			 "swissprot" => "SwissProt Flat File",
			 "swisspfam" => "SwissPfam Flat File"
		     );
    $import_dialog->set_title("Import from ".$names{$import_from});
    $import_entry->set_text("");
    $import_dialog->show_all();
}

sub init_import_dialog
{
    $import_dialog = new Gtk::Dialog();
    $import_dialog->border_width(5);

    # create the first button and add it to a box
    my $button = new Gtk::RadioButton( "Fetch by ID" );
    $import_dialog->vbox->pack_start($button,$false,$false,2);
         
    # create the second button and add it to a box
    $button = new Gtk::RadioButton( "Fetch by ACCESSION", $button );
    $import_dialog->vbox->pack_start($button,$false,$false,2);
    @import_buttons = $button->group();

    $import_entry = new Gtk::Entry();
    my $frame = new Gtk::Frame("Enter here:");
    $frame->add($import_entry);
    $import_dialog->vbox->pack_start( $frame, $true, $true, 5);
    
    my $bbox = new Gtk::HButtonBox();
    $bbox->set_layout("end");
    
    $button = new Gtk::Button( "OK" );
    $bbox->add( $button );
    $button->signal_connect("clicked",
           # OK button handler
           sub{ $import_dialog->hide();
		&seq_fetch();
	      });

    $button = new Gtk::Button( "Cancel" );
    $bbox->add( $button );
    $button->signal_connect("clicked",
           # close button handler
           sub{ $import_dialog->hide();
	      });

    $import_dialog->action_area->pack_start( $bbox, $true, $true, 0 );

    $import_dialog->signal_connect_after( "delete_event",
           # window delete handler
           sub{ $import_dialog->hide();
                return &Gtk::true;
	      });
}

sub open_dialog
{
    # Create a new file selection widget
    my $open_dialog = new Gtk::FileSelection( "Open File..." );
    # Connect the ok_button to open_ok_sel function
    $open_dialog->ok_button->signal_connect( "clicked",
					     \&ok_open_dialog,
					     $open_dialog );
    # Connect the cancel_button to destroy the widget
    $open_dialog->cancel_button->signal_connect( "clicked",
						 sub { $open_dialog->destroy(); } );
    $open_dialog->show();
}

# Get the selected filename
sub ok_open_dialog
  {
    my ( $widget, $file_selection ) = @_;
    push @filename, $file_selection->get_filename();

    $widget->parent->parent->parent->destroy();

    my $in = Bio::SeqIO->new(-file => $filename[-1] , '-format' => 'swiss');

    &new_seq_page($in->next_seq());
}

sub update_seq_data
{    
    $main_label[$current]->set_text($seq[$current]->id) if (defined($seq[$current]));
    $main_label[$current]->set_text("") if (!defined($seq[$current]));

    $seq_edit[$current]->freeze();
    $seq_edit[$current]->delete_text(0,-1);
    $seq_edit[$current]->insert(undef,undef,undef,$seq[$current]->seq()) if (defined($seq[$current]));
    $seq_edit[$current]->thaw();

    &update_comment_window();
    &update_description_window();
    &update_seqstats_window();
    &update_dblink_window();
    &update_reference_window();
    &update_feature_window();
}

sub new
{
    &new_seq_page(undef);
}

sub close
{
}

sub save
{
    if (!defined($filename[$current])||!$filename[$current])
    {
	&saveas_dialog;
	return;
    }
    my $out = Bio::SeqIO->new(-file => ">$filename[$current]" , '-format' => 'swiss');
    $out->write_seq($seq[$current]);
}

sub saveas_dialog
{
    # Create a new file selection widget
    my $saveas_dialog = new Gtk::FileSelection( "Save As..." );
    # Connect the ok_button to saveas_ok_sel function
    $saveas_dialog->ok_button->signal_connect( "clicked",
					       \&ok_saveas_dialog,
					       $saveas_dialog );
    # Connect the cancel_button to destroy the widget
    $saveas_dialog->cancel_button->signal_connect( "clicked",
						   sub { $saveas_dialog->destroy(); } );
    $saveas_dialog->show();
}

# Get the selected filename and print it to the console
sub ok_saveas_dialog
  {
    my ( $widget, $file_selection ) = @_;
    my $filename = $file_selection->get_filename();
    $widget->parent->parent->parent->destroy();
    $filename[$current] = $filename;
    my $out = Bio::SeqIO->new(-file => ">$filename[$current]" , '-format' => 'swiss');
    $out->write_seq($seq[$current]);
  }

sub init_comment_window
{
    $current_comment = 0;
    
    $comment_window = new Gtk::Dialog();
    $comment_window->set_default_size(650,300);
    $comment_window->set_policy($false,$true,$false);
    $comment_window->set_title("Comments");
    $comment_window->border_width(5);
    
    # frame
    $comment_frame = new Gtk::Frame( "Comment[".$current_comment."]" );
    
    # text widget
    $comment_edit = new Gtk::Text( undef, undef );
    $comment_edit->set_editable( $true );
    $comment_edit->set_word_wrap( $true );
	
    # vertical scrollbar for text widget
    my $scrollbar;
    $scrollbar = new Gtk::VScrollbar( $comment_edit->vadj );
	
    # horizontal box containing text widget and scrollbar
    my $hbox;
    $hbox = new Gtk::HBox( $false, 1 );
    $hbox->border_width( 1 );
    $hbox->pack_start( $comment_edit, $true, $true, 0);
    $hbox->pack_end( $scrollbar, $false, $true, 0);
    $comment_frame->add($hbox);
    $comment_window->vbox->pack_start( $comment_frame, $true, $true, 5);

    my $bbox = new Gtk::HBox( $false, 5 );
    $bbox->border_width(10);
    my $arrow = new Gtk::Arrow('right','out');
    my $button = new Gtk::Button();
    $button->add($arrow);
    $bbox->pack_end( $button, $false, $false, 0);
    $button->signal_connect
	( "clicked", 
	  # next comment button handler
	  sub { return if !defined($seq[$current]);
		 &store_current_comment;
		$current_comment++ 
		    if ($current_comment <((scalar $seq[$current]->annotation->each_Comment)-1));
		&update_comment_window;
	    } );

    $arrow = new Gtk::Arrow('left','out');
    $button = new Gtk::Button();
    $button->add($arrow);
    $bbox->pack_end( $button, $false, $false, 0);
    $button->signal_connect( "clicked", 
           # prev comment button handler
	   sub { return if !defined($seq[$current]);
		 &store_current_comment;
		 $current_comment-- 
		     if ($current_comment > 0);
		 &update_comment_window;
	       } );

    $button = new Gtk::Button("Add");
    $bbox->pack_start( $button, $false, $false, 0);
    $button->signal_connect( "clicked",
           # add comment button handler 
           sub { return if !defined($seq[$current]);
		 &store_current_comment;
		 my $comment = new Bio::Annotation::Comment;
		 $comment->text("");
		 $seq[$current]->annotation->add_Comment( $comment );
		 $current_comment = $seq[$current]->annotation->each_Comment - 1;
		 &update_comment_window;
	       } );

     $button = new Gtk::Button("Delete");
     $bbox->pack_start( $button, $false, $false, 0);
     $button->signal_connect( "clicked", 
           # delete comment button handler
           sub { return if !defined($seq[$current]); 
		 $seq[$current]->annotation->remove_Comment( $current_comment );
		 $current_comment = $current_comment - 1 
		     if ($current_comment > 0);
		 &update_comment_window;		 
	       } );

     $comment_window->vbox->pack_end( $bbox, $false, $false, 0);

     $bbox = new Gtk::HButtonBox();
     $bbox->set_layout("end");
	
     $button = new Gtk::Button( "Close" );
     $bbox->add( $button );
     $button->signal_connect("clicked",
           # close button handler
           sub{ $comment_window->hide();
		&store_current_comment;
	      });

     $comment_window->action_area->pack_start( $bbox, $true, $true, 0 );
     $comment_window->signal_connect_after( "delete_event",
           # window delete handler
           sub{ $comment_window->hide();
		&store_current_comment;
                return &Gtk::true;
	      });
}

sub store_current_comment
{
    (($seq[$current]->annotation->each_Comment)[$current_comment])->
	text($comment_edit->get_chars(0,-1) )
	    if ((defined($seq[$current])) && ($seq[$current]->annotation->each_Comment));
}

sub update_comment_window
{
    my ($show_me) = @_;
    $comment_frame->set_label("Comment[".$current_comment."]");
    # insert comment text
    $comment_edit->freeze();
    $comment_edit->delete_text(0,-1);
    if (defined($seq[$current]))
    {
	my @comment = $seq[$current]->annotation->each_Comment;
	$comment_edit->insert(undef,undef,undef, $comment[$current_comment]->text)
	    if (@comment);
    }
    $comment_edit->thaw();
    
    $comment_window->show_all() if (defined($show_me));
}

sub init_description_window
{
    $description_window = new Gtk::Dialog();
    $description_window->set_default_size(620,250);
    $description_window->border_width(5);
    $description_window->set_title("Description");
    
    # frame
    my $description_frame = new Gtk::Frame( "Description" );
    
    # text widget
    $description_edit = new Gtk::Text( undef, undef );
    $description_edit->set_editable( $true );
    $description_edit->set_word_wrap( $true );	
    
    # vertical scrollbar for text widget
    my $scrollbar;
    $scrollbar = new Gtk::VScrollbar( $description_edit->vadj );
    
    # horizontal box containing text widget and scrollbar
    my $hbox;
    $hbox = new Gtk::HBox( $false, 1 );
    $hbox->border_width( 1 );
    $hbox->pack_start( $description_edit, $true, $true, 0);
    $hbox->pack_end( $scrollbar, $false, $true, 0);
    $description_frame->add($hbox);
    $description_window->vbox->pack_start( $description_frame, $true, $true, 5);
    
    my $bbox = new Gtk::HButtonBox();
    $bbox->set_layout("end");
    
    my $button = new Gtk::Button( "Close" );
    $bbox->add( $button );
    $button->signal_connect("clicked",
           # close button handler
           sub{ $description_window->hide();
		$seq[$current]->desc($description_edit->get_chars(0,-1))
		    if $description_edit->get_chars(0,-1);
	      });

    $description_window->action_area->pack_start( $bbox, $true, $true, 0 );
    $description_window->signal_connect_after( "delete_event",
           # window delete handler
           sub{ $description_window->hide();
		$seq[$current]->desc($description_edit->get_chars(0,-1))
		    if $description_edit->get_chars(0,-1);
                return &Gtk::true;
	      });
}

sub update_description_window
{
    my ($show_me) = @_;
    $description_edit->freeze();
    $description_edit->delete_text(0,-1);
    $description_edit->insert(undef,undef,undef,$seq[$current]->desc)
	if defined($seq[$current]) && defined($seq[$current]->desc);
    $description_edit->thaw();
    
    $description_window->show_all() if (defined($show_me));
}

sub init_seqstats_window
{
    $seqstats_window = new Gtk::Dialog();
    $seqstats_window->border_width(5);
    $seqstats_window->set_default_size(100,250);
    $seqstats_window->set_title("Sequence Statistics");

    # frame
    my $seqstats_frame = new Gtk::Frame( "Sequence Statistics" );
    
    # text widget
    $seqstats_edit = new Gtk::Text( undef, undef );
    $seqstats_edit->set_editable( $false );
    $seqstats_edit->set_word_wrap( $true );
    
    # vertical scrollbar for text widget
    my $scrollbar;
    $scrollbar = new Gtk::VScrollbar( $seqstats_edit->vadj );
    
    # horizontal box containing text widget and scrollbar
    my $hbox;
    $hbox = new Gtk::HBox( $false, 1 );
    $hbox->border_width( 1 );
    $hbox->pack_start( $seqstats_edit, $true, $true, 0);
    $hbox->pack_end( $scrollbar, $false, $true, 0);
    $seqstats_frame->add($hbox);
    $seqstats_window->vbox->pack_start( $seqstats_frame, $true, $true, 5);
    
    my $bbox = new Gtk::HButtonBox();
    $bbox->set_layout("end");
    
    my $button = new Gtk::Button( "Close" );
    $bbox->add( $button );
    $button->signal_connect("clicked",
       # close button handler
       sub{ $seqstats_window->hide();
	  });
    
    $seqstats_window->action_area->pack_start( $bbox, $true, $true, 0 );
    $seqstats_window->signal_connect_after( "delete_event",
       # window delete handler
       sub{ $seqstats_window->hide();
	    return &Gtk::true;
	  });
}

sub update_seqstats_window
{
    my ($show_me) = @_;
    my ($data,$weight,$count_hash,$percent);

    $seqstats_edit->freeze();
    $seqstats_edit->delete_text(0,-1);
    if (defined($seq[$current]))
    {
	$data = $seq[$current]->id."\n\n";
	$weight = Bio::Tools::SeqStats->get_mol_wt($seq[$current]->primary_seq);
	if ($$weight[0] == $$weight[1]) {
	    $data .= "Molecular weight of sequence equals to ".$$weight[0]."\n\n";
	} else {
	    $data .= "Molecular weight of sequence is greater than ";
	    $data .= $$weight[0]." and less than ".$$weight[1]."\n\n";
	}
	$count_hash = Bio::Tools::SeqStats->count_monomers($seq[$current]->primary_seq);
	$data .= "Amino Acids:\n";
	foreach (sort keys %$count_hash)
	{
	    $percent = sprintf "%.1f",
	    (($$count_hash{$_} / $seq[$current]->length)*100);
	    $data .= "${_}: ".$$count_hash{$_}." (${percent}%) \n"
	    }
	$seqstats_edit->insert(undef,undef,undef,$data)
	}
    $seqstats_edit->thaw();
    
    $seqstats_window->show_all() if (defined($show_me));
}

sub init_dblink_window
{
    $current_dblink = 0;
    
    $dblink_window = new Gtk::Dialog();
    $dblink_window->set_default_size(500,400);
    $dblink_window->set_policy($true,$true,$false);
    $dblink_window->set_title("Database Links");
    $dblink_window->border_width(5);
    
    # Create a scrolled window to pack the CList widget into
    my $scrolled_window = new Gtk::ScrolledWindow( undef, undef );
    $dblink_window->vbox->pack_start( $scrolled_window, $true, $true, 0 );
    $scrolled_window->set_policy( 'automatic', 'always' );

    # Create the CList. For this example we use 2 columns
    $dblink_clist = new_with_titles Gtk::CList( "Primary Id","Database" );

    # When a selection is made, we want to know about it. The callback
    # used is selection_made, and its code can be found further down
    $dblink_handler_id = $dblink_clist->signal_connect( "select_row", 
       sub{ return if (!defined($seq[$current]));
	    my ( $clist, $row ) = @_;
	    &store_current_dblink;
	    $current_dblink = $row;
	    &update_dblink_window;
          } );

    # It isn't necessary to shadow the border, but it looks nice :)
    $dblink_clist->set_shadow_type( 'out' );

    # What however is important, is that we set the column widths as
    # they will never be right otherwise. Note that the columns are
    # numbered from 0 and up (to 1 in this case).
    $dblink_clist->set_column_width( 0, 150 );

    # Add the CList widget to the vertical box
    $scrolled_window->add( $dblink_clist );

    my $bbox = new Gtk::HBox( $false, 5 );
    $bbox->border_width(10);
    my $arrow = new Gtk::Arrow('down','out');
    my $button = new Gtk::Button();
    $button->add($arrow);
    $bbox->pack_end( $button, $false, $false, 0);
    $button->signal_connect
	( "clicked", 
	  # next dblink button handler
	  sub { return if (!defined($seq[$current]));
		&store_current_dblink;
		$current_dblink++
		    if ($current_dblink <((scalar $seq[$current]->annotation->each_DBLink)-1));
		&update_dblink_window;
	      } );

    $arrow = new Gtk::Arrow('up','out');
    $button = new Gtk::Button();
    $button->add($arrow);
    $bbox->pack_end( $button, $false, $false, 0);
    $button->signal_connect( "clicked", 
           # prev comment button handler
	   sub { return if (!defined($seq[$current]));
		 &store_current_dblink;
		 $current_dblink--
		     if ($current_dblink > 0);
		 &update_dblink_window;
	       } );

    $button = new Gtk::Button("Add");
    $bbox->pack_start( $button, $false, $false, 0);
    $button->signal_connect( "clicked",
           # add comment button handler 
           sub { return if (!defined($seq[$current]));
		 &store_current_dblink;
		 my $dblink = new Bio::Annotation::DBLink;
		 $dblink->primary_id("");
		 $seq[$current]->annotation->add_DBLink( $dblink );
		 $current_dblink = $seq[$current]->annotation->each_DBLink - 1;
		 $dblink_clist->append("","");
		 &update_dblink_window;
	       } );

     $button = new Gtk::Button("Delete");
     $bbox->pack_start( $button, $false, $false, 0);
     $button->signal_connect( "clicked", 
           # delete comment button handler
           sub { return if !defined($seq[$current]); 
		 $seq[$current]->annotation->remove_DBLink( $current_dblink );
		 $dblink_clist->remove($current_dblink);
		 $current_dblink-- if ($current_dblink > 0);
		 &update_dblink_window;
	       } );

     $dblink_window->vbox->pack_start( $bbox, $false, $false, 0);

    # horizontal box containing primary_id & optional_id entries
    my $hbox;
    $hbox = new Gtk::HBox( $true, 10 );
    $hbox->border_width( 1 );

    # text entries
    $dblink_entry[0] = new Gtk::Entry();
    my $frame = new Gtk::Frame("primary id");
    $frame->add($dblink_entry[0]);
    $hbox->pack_start( $frame, $true, $true, 0);

    $dblink_entry[1] = new Gtk::Entry();
    $frame = new Gtk::Frame("optional id");
    $frame->add($dblink_entry[1]);
    $hbox->pack_end( $frame, $true, $true, 0);

    $dblink_window->vbox->pack_start( $hbox, $false, $false, 5);

    $dblink_entry[2] = new Gtk::Entry();
    $frame = new Gtk::Frame("Database");
    $frame->add($dblink_entry[2]);
    $dblink_window->vbox->pack_start( $frame, $false, $false, 5);

    $dblink_entry[3] = new Gtk::Entry();
    $frame = new Gtk::Frame("Comment");
    $frame->add($dblink_entry[3]);
    $dblink_window->vbox->pack_end( $frame, $false, $false, 5);

     $bbox = new Gtk::HButtonBox();
     $bbox->set_layout("end");
	
     $button = new Gtk::Button( "Close" );
     $bbox->add( $button );
     $button->signal_connect("clicked",
           # close button handler
           sub{ $dblink_window->hide();
		&store_current_dblink;
	      });

     $dblink_window->action_area->pack_start( $bbox, $true, $true, 0 );
     $dblink_window->signal_connect_after( "delete_event",
           # window delete handler
           sub{ $dblink_window->hide();
		&store_current_dblink;
                return &Gtk::true;
	      });
}

sub store_current_dblink
{
    if ((defined($seq[$current])) && ($seq[$current]->annotation->each_DBLink))
    {
	(($seq[$current]->annotation->each_DBLink)[$current_dblink])->
	    primary_id($dblink_entry[0]->get_chars(0,-1) );		
	(($seq[$current]->annotation->each_DBLink)[$current_dblink])->
	    optional_id($dblink_entry[1]->get_chars(0,-1) );		
	(($seq[$current]->annotation->each_DBLink)[$current_dblink])->
	    database($dblink_entry[2]->get_chars(0,-1) );		
	(($seq[$current]->annotation->each_DBLink)[$current_dblink])->
	    comment($dblink_entry[3]->get_chars(0,-1) );		
    }
}

sub update_dblink_window
{
    my ($show_me) = @_;
    $dblink_window->show_all() if (defined($show_me));

    $dblink_clist->freeze();
    if (!defined($seq[$current]))
    {
	$dblink_clist->clear();
	$dblink_clist->thaw();
	foreach (@dblink_entry) { $_->set_text(""); }
	return;
    }
    my @dblinks = $seq[$current]->annotation->each_DBLink;
    # reset clist if rows are different to links
    if ($dblink_clist->rows != @dblinks) {
	$dblink_clist->clear();
	foreach (@dblinks) { $dblink_clist->append("",""); }
    }
    # redraw references
    for(my $i=0;$i<@dblinks;$i++)
    {
	$dblink_clist->set_text($i,0,$dblinks[$i]->primary_id);
	$dblink_clist->set_text($i,1,$dblinks[$i]->database);
    }
    # redraw text widgets
    foreach (@dblink_entry) { $_->set_text(""); }
    if (@dblinks)
    {
	$dblink_entry[0]->set_text($dblinks[$current_dblink]->primary_id);
	$dblink_entry[1]->set_text($dblinks[$current_dblink]->optional_id);
	$dblink_entry[2]->set_text($dblinks[$current_dblink]->database);
	$dblink_entry[3]->set_text($dblinks[$current_dblink]->comment);
    }

    $dblink_clist->moveto($current_dblink,0,0.3,0.0)
	if ($dblink_clist->row_is_visible($current_dblink) ne 'full');
    $dblink_clist->signal_handler_block($dblink_handler_id);
    $dblink_clist->select_row($current_dblink,0);
    $dblink_clist->signal_handler_unblock($dblink_handler_id);
    Gtk::CList::set_focus_row($dblink_clist,$current_dblink);
    $dblink_clist->thaw();
}

sub init_reference_window
{
    $current_ref = 0;
    
    $ref_window = new Gtk::Dialog();
    $ref_window->set_default_size(620,500);
    $ref_window->set_policy($true,$true,$false);
    $ref_window->set_title("References");
    $ref_window->border_width(5);
    
    # Create a scrolled window to pack the CList widget into
    my $scrolled_window = new Gtk::ScrolledWindow( undef, undef );
    $ref_window->vbox->pack_start( $scrolled_window, $true, $true, 0 );
    $scrolled_window->set_policy( 'automatic', 'always' );

    # Create the CList. For this example we use 2 columns
    $ref_clist = new_with_titles Gtk::CList( "Medline","Title","Authors" );

    # When a selection is made, we want to know about it. The callback
    # used is selection_made, and its code can be found further down
    $ref_handler_id = $ref_clist->signal_connect( "select_row", 
       sub{ return if (!defined($seq[$current]));
	    my ( $clist, $row ) = @_;
	    &store_current_reference;
	    $current_ref = $row;
	    &update_reference_window;
          } );

    # It isn't necessary to shadow the border, but it looks nice :)
    $ref_clist->set_shadow_type( 'out' );

    # What however is important, is that we set the column widths as
    # they will never be right otherwise. Note that the columns are
    # numbered from 0 and up (to 1 in this case).
    $ref_clist->set_column_width( 0, 70 );
    $ref_clist->set_column_width( 1, 350 );
    $ref_clist->set_column_width( 2, 300 );

    # Add the CList widget to the vertical box
    $scrolled_window->add( $ref_clist );

    my $bbox = new Gtk::HBox( $false, 5 );
    $bbox->border_width(10);
    my $arrow = new Gtk::Arrow('down','out');
    my $button = new Gtk::Button();
    $button->add($arrow);
    $bbox->pack_end( $button, $false, $false, 0);
    $button->signal_connect
	( "clicked", 
	  # next ref button handler
	  sub { return if (!defined($seq[$current]));
		&store_current_reference;
		$current_ref++
		    if ($current_ref <((scalar $seq[$current]->annotation->each_Reference)-1));
		&update_reference_window;
	    } );

    $arrow = new Gtk::Arrow('up','out');
    $button = new Gtk::Button();
    $button->add($arrow);
    $bbox->pack_end( $button, $false, $false, 0);
    $button->signal_connect( "clicked", 
           # prev comment button handler
	   sub { return if (!defined($seq[$current]));
		 &store_current_reference;
		 $current_ref--
		     if ($current_ref > 0);
		 &update_reference_window;
	       } );

    $button = new Gtk::Button("Add");
    $bbox->pack_start( $button, $false, $false, 0);
    $button->signal_connect( "clicked",
           # add comment button handler 
           sub { return if (!defined($seq[$current]));
		 &store_current_reference;
		 my $ref = new Bio::Annotation::Reference;
		 $ref->medline("");
		 $seq[$current]->annotation->add_Reference( $ref );
		 $ref_clist->append("","","");
		 $current_ref = ($seq[$current]->annotation->each_Reference)-1;
		 &update_reference_window;
	       } );

     $button = new Gtk::Button("Delete");
     $bbox->pack_start( $button, $false, $false, 0);
     $button->signal_connect( "clicked", 
           # delete comment button handler
           sub { return if !defined($seq[$current]); 
		 $seq[$current]->annotation->remove_Reference( $current_ref );
		 $ref_clist->remove($current_ref);
		 $current_ref-- if ($current_ref > 0);
		 &update_reference_window;
	       } );

     $ref_window->vbox->pack_start( $bbox, $false, $false, 0);

    # horizontal box containing primary_id & optional_id entries
    my $hbox;
    $hbox = new Gtk::HBox( $true, 10 );
    $hbox->border_width( 1 );

    # text entries
    $ref_entry[0] = new Gtk::Entry();
    my $frame = new Gtk::Frame("Title");
    $frame->add($ref_entry[0]);
    $ref_window->vbox->pack_start( $frame, $false, $false, 5);

    $ref_entry[1] = new Gtk::Entry();
    $frame = new Gtk::Frame("Authors");
    $frame->add($ref_entry[1]);
    $ref_window->vbox->pack_start( $frame, $false, $false, 5);

    # horizontal box
    $hbox = new Gtk::HBox( $true, 10 );
    $hbox->border_width( 1 );

    # text entries
    $ref_entry[2] = new Gtk::Entry();
    $frame = new Gtk::Frame("Comment");
    $frame->add($ref_entry[2]);
    $hbox->pack_start( $frame, $true, $true, 0);

    $ref_entry[3] = new Gtk::Entry();
    $frame = new Gtk::Frame("Location");
    $frame->add($ref_entry[3]);
    $hbox->pack_end( $frame, $true, $true, 0);

    $ref_window->vbox->pack_start( $hbox, $false, $false, 5);

    # horizontal box
    $hbox = new Gtk::HBox( $false, 10 );
    $hbox->border_width( 1 );

    # text entries
    $ref_entry[4] = new Gtk::Entry();
    $frame = new Gtk::Frame("Medline");
    $frame->add($ref_entry[4]);
    $hbox->pack_start( $frame, $false, $false, 0);

#    $ref_entry[5] = new Gtk::Entry();
#    $frame = new Gtk::Frame("Start");
#    $frame->add($ref_entry[5]);
#    $hbox->pack_start( $frame, $false, $false, 0);

    $ref_entry[5] = new Gtk::Entry();
    $frame = new Gtk::Frame("Reference Position");
    $frame->add($ref_entry[5]);
    $hbox->pack_end( $frame, $true, $true, 0);

    $ref_window->vbox->pack_start( $hbox, $false, $false, 5);


     $bbox = new Gtk::HButtonBox();
     $bbox->set_layout("end");
	
     $button = new Gtk::Button( "Close" );
     $bbox->add( $button );
     $button->signal_connect("clicked",
           # close button handler
           sub{ $ref_window->hide();
		&store_current_reference;
	      });

     $ref_window->action_area->pack_start( $bbox, $true, $true, 0 );
     $ref_window->signal_connect_after( "delete_event",
           # window delete handler
           sub{ $ref_window->hide();
		&store_current_reference;
                return &Gtk::true;
	      });
}

sub store_current_reference
{
    if ((defined($seq[$current])) && ($seq[$current]->annotation->each_Reference))
    {
	(($seq[$current]->annotation->each_Reference)[$current_ref])->
	    title($ref_entry[0]->get_chars(0,-1) );		
	(($seq[$current]->annotation->each_Reference)[$current_ref])->
	    authors($ref_entry[1]->get_chars(0,-1) );		
	(($seq[$current]->annotation->each_Reference)[$current_ref])->
	    comment($ref_entry[2]->get_chars(0,-1) );		
	(($seq[$current]->annotation->each_Reference)[$current_ref])->
	    location($ref_entry[3]->get_chars(0,-1) );		
	(($seq[$current]->annotation->each_Reference)[$current_ref])->
	    medline($ref_entry[4]->get_chars(0,-1) );		
#	(($seq[$current]->annotation->each_Reference)[$current_ref])->
#	    start($ref_entry[5]->get_chars(0,-1) );		
	(($seq[$current]->annotation->each_Reference)[$current_ref])->
	    rp($ref_entry[5]->get_chars(0,-1) );		
    }
}

sub update_reference_window
{
    my ($show_me) = @_;
    $ref_window->show_all() if (defined($show_me));

    $ref_clist->freeze();
    if (!defined($seq[$current]))
    {
	$ref_clist->clear();
	$ref_clist->thaw();
	foreach (@ref_entry) { $_->set_text(""); }
	return;
    }
    my @refs = $seq[$current]->annotation->each_Reference;
    # reset clist if rows are different to references
    if ($ref_clist->rows != @refs) {
	$ref_clist->clear();
	foreach (@refs) { $ref_clist->append("","",""); }
    }
    # redraw references
    for(my $i=0;$i<@refs;$i++)
    {
	$ref_clist->set_text($i,0,$refs[$i]->medline)
	  if ($refs[$i]->medline);
	$ref_clist->set_text($i,1,$refs[$i]->title)
	  if ($refs[$i]->title);
	$ref_clist->set_text($i,2,$refs[$i]->authors)
	  if ($refs[$i]->authors);
    }
    # redraw text widgets
    foreach (@ref_entry) { $_->set_text(""); }
    if (@refs) {
	$ref_entry[0]->set_text($refs[$current_ref]->title);
	$ref_entry[1]->set_text($refs[$current_ref]->authors);
	$ref_entry[2]->set_text($refs[$current_ref]->comment);
	$ref_entry[3]->set_text($refs[$current_ref]->location);
	$ref_entry[4]->set_text($refs[$current_ref]->medline);
#	$ref_entry[5]->set_text($refs[$current_ref]->start);
	$ref_entry[5]->set_text($refs[$current_ref]->rp);
    }

    $ref_clist->moveto($current_ref,0,0.3,0.0)
	if ($ref_clist->row_is_visible($current_ref) ne 'full');
    $ref_clist->signal_handler_block($ref_handler_id);
    $ref_clist->select_row($current_ref,0);
    $ref_clist->signal_handler_unblock($ref_handler_id);
    Gtk::CList::set_focus_row($ref_clist,$current_ref);
    $ref_clist->thaw();
}


sub init_about_dialog {
 	my ($window,$bg,$tbox,$vbox,$hbox,$sep,$butbox,$button,$pixmap);
 	$about_dialog = new Gtk::Window("dialog");
 	$about_dialog->set_title("About gSequence");
 	$about_dialog->signal_connect_after("destroy" => 
					    sub { $about_dialog->hide; 
					          return &Gtk::true; });
 	$about_dialog->set_default_size('350','350');
 	$about_dialog->set_policy(1,1,0);
 	$window = $about_dialog->window;
 	$bg = $about_dialog->style->bg('normal');
 	$vbox= new Gtk::VBox(0,0);
 	$about_dialog->add($vbox);
    	$tbox = new Gtk::Label("\ngSequence\nAuthor: Lorenz Pollak\n\n
gSequence is cool! :-)\n(this text is to be written...)
\n");
 	$vbox->pack_start($tbox,1,1,1);
   
    	$hbox = new Gtk::HBox(0,0);   
    	$vbox->pack_start($hbox,0,0,0);
 	$sep = new Gtk::HSeparator;
   	$sep->set_usize(-1,5);
    	$vbox->pack_start($sep,0,1,0);
    
     	$butbox = new Gtk::HButtonBox;
     	$butbox->set_usize(-1,32);
     	$vbox->pack_start($butbox, 0,1,0); 
 	$button = new_with_label Gtk::Button("OK");
     	$button->set_usize(50,-1);
     	$button->signal_connect('clicked', sub { $about_dialog->hide; });
	$button->can_default(1);
	$button->grab_default;
	$butbox->add($button);
     
  return 1;
}    

sub init_feature_window
{
    $current_feature_item = 0;
    
    $feature_window = new Gtk::Dialog();
    $feature_window->set_default_size(500,400);
    $feature_window->set_policy($true,$true,$false);
    $feature_window->set_title("Sequence Features");
    $feature_window->border_width(5);

    my $pane = new Gtk::HPaned();
    $feature_window->vbox->pack_start( $pane, $true, $true, 0);
    $pane->set_handle_size( 10 );
    $pane->set_gutter_size( 8 );

    # Create a VBox for the Entry and Tree Scrolled Window
    my $vbox = new Gtk::VBox( $false, 0 );
    $pane->add1( $vbox );

    # Create a ScrolledWindow for the tree
    my $tree_scrolled_win = new Gtk::ScrolledWindow( undef, undef );
    $tree_scrolled_win->set_usize( 150, 400 );
    $vbox->pack_start( $tree_scrolled_win, $true, $true, 0 );
    $tree_scrolled_win->set_policy( 'automatic', 'automatic' );

    #my $list_scrolled_win = new Gtk::ScrolledWindow( undef, undef );
    #$list_scrolled_win->set_policy( 'automatic', 'automatic' );
    $vbox = new Gtk::VBox( $false, 0 );
    $pane->add2( $vbox );

    # add stuff to the vbox
    # text entries
    my $hbox = new Gtk::HBox( $true, 10 );

    $feature_entry[0] = new Gtk::Entry();
    my $frame = new Gtk::Frame("Primary Tag");
    $frame->add($feature_entry[0]);
    $hbox->pack_start( $frame, $true, $true, 0);

    $feature_entry[1] = new Gtk::Entry();
    $frame = new Gtk::Frame("Source Tag");
    $frame->add($feature_entry[1]);
    $hbox->pack_end( $frame, $true, $true, 0);

    $vbox->pack_start( $hbox, $false, $false, 5);

    $hbox = new Gtk::HBox( $true, 10 );

    my $adj = new Gtk::Adjustment( 0, 0, 0, 0, 0, 0 );
    $feature_spinner[0] = new Gtk::SpinButton( $adj, 0.0, 0 );
    $feature_spinner[0]->signal_connect( "changed", \&select_feature_region);
    $frame = new Gtk::Frame("Start");
    $frame->add($feature_spinner[0]);
    $hbox->pack_start( $frame, $true, $true, 0);

    $adj = new Gtk::Adjustment( 0, 0, 0, 0, 0, 0 );
    $feature_spinner[1] = new Gtk::SpinButton( $adj, 0.0, 0 );
    $feature_spinner[1]->signal_connect( "changed", \&select_feature_region);
    $frame = new Gtk::Frame("End");
    $frame->add($feature_spinner[1]);
    $hbox->pack_start( $frame, $true, $true, 0);

    $frame = new Gtk::Frame("Strand");
    $hbox->pack_start( $frame, $true, $true, 0);
    $frame = new Gtk::Frame("Score");
    $hbox->pack_start( $frame, $true, $true, 0);

    $vbox->pack_start( $hbox, $false, $false, 5);

    $feature_entry[2] = new Gtk::Entry();
    $frame = new Gtk::Frame("Description");
    $frame->add($feature_entry[2]);

    $vbox->pack_start( $frame, $false, $false, 5);

    my $bbox = new Gtk::HBox( $false, 5 );
    $bbox->border_width(10);
    my $button = new Gtk::Button("Add");
    $bbox->pack_start( $button, $false, $false, 0);
    $button->signal_connect( "clicked",
           # add comment button handler 
           sub { return if (!defined($seq[$current]));
		 &store_current_feature if ($current_feature_item);
		 my $feature = new Bio::SeqFeature::Generic;
		 $feature->primary_tag("");
		 $seq[$current]->add_SeqFeature( $feature );
		 my $item_new = new_with_label Gtk::TreeItem( "" );
		 $item_new->set_user_data( $feature );
		 $item_new->signal_connect( 'select', \&select_feature_item );
		 $current_feature_item->parent->append( $item_new )
		     if ($current_feature_item);
		 $feature_tree->append( $item_new ) if (!$current_feature_item);
		 $item_new->show();
		 $current_feature_item->deselect()
		     if ($current_feature_item);
		 $item_new->select();
	       } );
    $button = new Gtk::Button("Add Subfeature");
    $bbox->pack_start( $button, $false, $false, 0);
    $button->signal_connect( "clicked",
           # add comment button handler 
           sub { return if (!defined($seq[$current])||!$current_feature_item);
		 &store_current_feature;
		 my $feature = new Bio::SeqFeature::Generic;
		 $feature->primary_tag("");
		 $feature->start($current_feature_item->get_user_data->start);
		 $feature->end($current_feature_item->get_user_data->end);
		 $current_feature_item->get_user_data->add_sub_SeqFeature( $feature );
		 my $new_subtree = new Gtk::Tree();
		 $current_feature_item->set_subtree( $new_subtree );
		 my $item_new = new_with_label Gtk::TreeItem( "" );
		 $item_new->set_user_data( $feature );
		 $item_new->signal_connect( 'select', \&select_feature_item );
		 $new_subtree->append( $item_new );
		 $item_new->show();
		 $current_feature_item->deselect();
		 $current_feature_item->expand();
		 $item_new->select();
	       } );
     $button = new Gtk::Button("Delete");
     $bbox->pack_start( $button, $false, $false, 0);
     $button->signal_connect( "clicked", 
           # delete comment button handler
           sub { return if (!$current_feature_item); 
		 &store_current_feature;
		 my $flist = $seq[$current]->{_as_feat};
		 my $pos;
		 for(my $i=0;$i<@$flist;$i++) {
		   $pos=$i if $$flist[$i]==$current_feature_item->get_user_data();
		 }
		 splice @$flist, $pos, 1;
		 $seq[$current]->{_as_feat} = $flist;
		 $current_feature_item->parent->remove_item($current_feature_item);
		 $current_feature_item=0;
	       } );

     $vbox->pack_end( $bbox, $false, $false, 0);

    # Create root tree
    $feature_tree = new Gtk::Tree();
    $tree_scrolled_win->add_with_viewport( $feature_tree );
    $feature_tree->set_selection_mode( 'single' );
    $feature_tree->set_view_mode( 'item' );

    $bbox = new Gtk::HButtonBox();
    $bbox->set_layout("end");
    
    $button = new Gtk::Button( "Close" );
    $bbox->add( $button );
    $button->signal_connect("clicked",
			    # close button handler
			    sub{ $feature_window->hide();
				 &store_current_feature;
			     });
    
    $feature_window->action_area->pack_start( $bbox, $true, $true, 0 );
    $feature_window->signal_connect_after( "delete_event",
					   # window delete handler
					   sub{ $feature_window->hide();
						&store_current_feature;
						return &Gtk::true;
					    });
}

# Callback for expanding tree
sub expand_feature_tree
  {
    my ( $item, $subtree ) = @_;
    my ($feature,$subfeature,$item_new,$new_subtree);
    $feature = $item->get_user_data();

    foreach $subfeature ($feature->sub_SeqFeature)
      {
	  $item_new = new_with_label Gtk::TreeItem( $subfeature->primary_tag );
	  $item_new->set_user_data( $subfeature );
	  $item_new->signal_connect( 'select', \&select_feature_item );
	  $subtree->append( $item_new );
	  $item_new->show();
	  
	  if ( $subfeature->sub_SeqFeature )
	  {
	      $new_subtree = new Gtk::Tree();
	      $item_new->set_subtree( $new_subtree );
	      $item_new->signal_connect( 'expand',
					 \&expand_feature_tree,
					 $new_subtree );
	      $item_new->signal_connect( 'collapse', \&collapse_feature_tree );
	  }
	  $item_new->expand();
      }
  }


# Callback for collapsing tree
sub collapse_feature_tree
  {
    my ( $item ) = @_;

    my $subtree = new Gtk::Tree();

    $item->remove_subtree();
    $item->set_subtree( $subtree );
    $item->signal_connect( 'expand', \&expand_feature_tree, $subtree );
  }


sub store_current_feature
{
  if ((defined($seq[$current])) && ($seq[$current]->top_SeqFeatures) && ($current_feature_item))
  {
    my $current_feature = $current_feature_item->get_user_data();
    $current_feature->primary_tag( $feature_entry[0]->get_chars(0,-1) );		
    $current_feature->source_tag( $feature_entry[1]->get_chars(0,-1) );		
    if ($current_feature->has_tag("description"))
    {
      $current_feature->remove_tag("description");
      $current_feature->add_tag_value("description",
				      $feature_entry[2]->get_chars(0,-1));
    }
    $current_feature->start($feature_spinner[0]->get_value_as_int());
    $current_feature->end($feature_spinner[1]->get_value_as_int());
    # set tree item
    ($current_feature_item->children)[0]->set($current_feature->primary_tag);
  }
}

sub select_feature_item
{
    my ($widget) = @_;
    &store_current_feature;
    $current_feature_item->deselect()
      if $current_feature_item;
    $current_feature_item = $widget;
    &update_feature_paned2;
}

sub update_feature_paned2
{
  $feature_entry[0]->set_text("");
  $feature_entry[1]->set_text("");
  $feature_entry[2]->set_text("");

  return if (!defined($seq[$current])||(!$current_feature_item));
  my $current_feature = $current_feature_item->get_user_data();
  $feature_entry[0]->set_text($current_feature->primary_tag);
  $feature_entry[1]->set_text($current_feature->source_tag)
    if (defined($current_feature->source_tag));
  $feature_entry[2]->set_text(($current_feature->each_tag_value("description"))[0])
    if ($current_feature->has_tag("description"));
  my $adj = new Gtk::Adjustment($current_feature->start,
				0,
				$seq[$current]->length-1,
				1,
				1,
				0
			       );
  $feature_spinner[0]->set_adjustment($adj);
  $feature_spinner[0]->set_value($current_feature->start);
  $feature_spinner[0]->show_all();
  $adj = new Gtk::Adjustment($current_feature->end,
			     0,
			     $seq[$current]->length-1,
			     1,
			     1,
			     0
			    );
  $feature_spinner[1]->set_adjustment($adj);
  $feature_spinner[1]->set_value($current_feature->end);
  $feature_spinner[1]->show_all();
}

sub select_feature_region
{
  $seq_edit[$current]->freeze;
  $seq_edit[$current]->select_region($feature_spinner[0]->get_value_as_int(),
			   $feature_spinner[1]->get_value_as_int()+1);
  $seq_edit[$current]->thaw;
}

sub update_feature_window
{
    my ($show_me) = @_;
    $feature_window->show_all() if (defined($show_me));

    $feature_tree->clear_items(0,-1);
    if (!defined($seq[$current]))
    {
	&update_feature_paned2;
	return;
    }

    my ($item_new,$new_subtree);
    foreach ($seq[$current]->top_SeqFeatures)
      {
	  $item_new = new_with_label Gtk::TreeItem( $_->primary_tag );
	  $item_new->set_user_data( $_ );
	  $item_new->signal_connect( 'select', \&select_feature_item );
	  $feature_tree->append( $item_new );
	  if ( $_->sub_SeqFeature )
	  {
	      $new_subtree = new Gtk::Tree();
	      $item_new->set_subtree( $new_subtree );
	      $item_new->signal_connect( 'expand',
					 \&expand_feature_tree,
					 $new_subtree );
	      $item_new->signal_connect( 'collapse', \&collapse_feature_tree );
	  }
	  $item_new->expand();
      }
    $feature_tree->select_item($current_feature_item) 
      if $current_feature_item;
    $feature_tree->show_all();

    &update_feature_paned2;
}

sub store_prefs
{
}

sub update_pref_window
{
  $pref_window->show_all();
}

sub init_pref_window
{
  $pref_window = new Gtk::Dialog();
  $pref_window->set_default_size(500,400);
  $pref_window->set_policy($true,$true,$false);
  $pref_window->border_width( 5 );

  # Create a new notebook, place the position of the tabs
  my $notebook = new Gtk::Notebook();
  $pref_window->vbox->pack_start( $notebook, $true, $true, 0);
  $notebook->set_tab_pos( 'top' );

  my $main_vbox = new Gtk::VBox($false,10);

  my $label = new Gtk::Label( "Import Options" );
  my $frame = new Gtk::Frame("Flat File Indexes");
  my $vbox = new Gtk::VBox($false,10);
  $frame->add($vbox);
  $main_vbox->pack_start($frame,$false,$false,10);

  $notebook->append_page( $main_vbox, $label );

  my $hbox = new Gtk::HBox($false,0);

  $pref_entry[0] = new Gtk::Entry();
  $frame = new Gtk::Frame("Indexes Directory");
  $frame->add($pref_entry[0]);
  $hbox->pack_start( $frame, $true, $false, 0);

  $pref_entry[1] = new Gtk::Entry();
  $frame = new Gtk::Frame("Index Type");
  $frame->add($pref_entry[1]);
  $hbox->pack_start( $frame, $false, $false, 0);

  $vbox->pack_start( $hbox, $false, $false, 0);

  $pref_entry[2] = new Gtk::Entry();
  $frame = new Gtk::Frame("Fasta Index Name");
  $frame->add($pref_entry[2]);
  $vbox->pack_start( $frame, $false, $false, 0);

  $pref_entry[3] = new Gtk::Entry();
  $frame = new Gtk::Frame("SwissProt Index Name");
  $frame->add($pref_entry[3]);
  $vbox->pack_start( $frame, $false, $false, 0);

  $pref_entry[4] = new Gtk::Entry();
  $frame = new Gtk::Frame("SwissPfam Index Name");
  $frame->add($pref_entry[4]);
  $vbox->pack_start( $frame, $false, $false, 0);

  $frame = new Gtk::Frame("Remote DBs");
  $hbox = new Gtk::HBox($false,10);
  $frame->add($hbox);
  $main_vbox->pack_start($frame,$false,$false,10);

  $pref_entry[5] = new Gtk::Entry();
  $frame = new Gtk::Frame("AceDB host");
  $frame->add($pref_entry[5]);
  $hbox->pack_start( $frame, $true, $false, 0);

  $pref_entry[6] = new Gtk::Entry();
  $frame = new Gtk::Frame("AceDB port");
  $frame->add($pref_entry[6]);
  $hbox->pack_start( $frame, $false, $false, 0);

  $notebook->set_page( 0 );

  my $bbox = new Gtk::HButtonBox();
  $bbox->set_layout("end");

  my $button = new Gtk::Button( "Save" );
  $bbox->add( $button );
  $button->signal_connect("clicked",
			  # close button handler
			  sub{ $pref_window->hide();
			       &store_prefs();
			     });
  
  $button = new Gtk::Button( "Close" );
  $bbox->add( $button );
  $button->signal_connect("clicked",
			  # close button handler
			  sub{ $pref_window->hide();
			     });
  
  $pref_window->action_area->pack_start( $bbox, $true, $true, 0 );
  $pref_window->signal_connect_after( "delete_event",
					 # window delete handler
					 sub{ $pref_window->hide();
					      return &Gtk::true;
					    });
}
BioPerl-1.007002/examples/tk/hitdisplay.pl000555000766000024       645713155576320 20475 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
#
# PROGRAM  : hitdisplay.pl
# PURPOSE  : Demonstrate Bio::Tk::HitDisplay
# AUTHOR   : Keith James kdj@sanger.ac.uk
# CREATED  : Nov 1 2000
#
# Requires Bio::Tk::HitDisplay
#
# To use, just pipe Blast output into this script. Try clicking on
# the blue Subject ids with the left button to activate a callback
# or with the right button to show text describing the hit.
# 

use strict;
use Text::Wrap qw(wrap $columns);
use Bio::Tools::BPlite;
BEGIN { 
	print STDERR "This example uses deprecated BioPerl code; feel free to refactor as needed\n";
	exit;
    eval { 
	require 'Tk.pm';
	require 'Bio/Tk/HitDisplay.pm'; 
    };
    if( $@ ) {
	print STDERR "Must have bioperl-gui and Tk installed to run this test, see bioperl website www.bioperl.org for instructions on how to installed bioperl-gui modules\n";    
	exit;
    }

}
use Tk;
    $columns = 80;

my $report = Bio::Tools::BPlite->new(-fh => \*STDIN);

# Normally the code ref below is in a separate package and I do 
# something like:
#
# my $adapter = Bio::PSU::IO::Blast::HitAdapter->new;
#
# while (my $hit = $result->next_hit)
# {
#     my $text     = " ... ";
#     my $callback = sub { ... };
#     push(@hits, $adapter->($sbjct, $text, $callback));
# }
#
# It's easy to roll your own for Fasta, or whatever.

my $adapter = sub
{
    my ($sbjct, $text, $callback) = @_;

    my (@data, $expect, $percent, $length);
    my ($q_id, $s_id, $q_len, $s_len);

    while (my $hsp = $sbjct->nextHSP)
    {
	$q_id ||= $hsp->query->seqname;
	$s_id ||= $hsp->subject->seqname;

	$q_len ||= $hsp->query->seqlength;
	$s_len ||= $hsp->subject->seqlength;

	my $q_x1 = $hsp->query->start;
	my $q_x2 = $hsp->query->end;

	my $s_x1 = $hsp->subject->start;
	my $s_x2 = $hsp->subject->end;

	push(@data, [$q_x1, $q_x2,
		     $s_x1, $s_x2]);

	if (defined $expect)
	{
	    if ($hsp->P < $expect)
	    {
		$expect  = $hsp->P;
		$percent = $hsp->percent;
		$length  = $hsp->length;
	    }
	}
	else
	{
	    $expect  = $hsp->P;
	    $percent = $hsp->percent;
	    $length  = $hsp->length;
	}
    }

    return { q_id     => $q_id,
	     s_id     => $s_id,
	     expect   => $expect,
	     score    => $percent,
	     overlap  => $length,
	     q_len    => $q_len,
	     s_len    => $s_len,
	     data     => \@data,
	     text     => $text,
	     callback => $callback }

};

my @hits;

while (my $sbjct = $report->nextSbjct)
{
    # Make some text to show when the left button is clicked
    my $text = wrap("", "", "Blast hit to: ", $sbjct->name, "\n");

    # Make a callback to actiavte when the right button is clicked
    my $callback = sub { print "Blast hit to ", $sbjct->name, "\n" };

    # Convert Subjct, text and callback into hash
    push(@hits, $adapter->($sbjct, $text, $callback));
}

# Create the main window and HitDisplay
my $mw = MainWindow->new;
my $hds = $mw->Scrolled('HitDisplay',
			-borderwidth => 5,
			-scrollbars  => 'ose',
			-width       => 600,
			-height      => 300,
			-background  => 'white',
			-hitcolours  => {
					 10 => 'pink',
					 20 => 'purple',
					 40 => 'yellow',
					 60 => 'gold',
					 70 => 'orange',
					 90 => 'red'
					},
			-interval    => 15,
			-hitdata     => \@hits);

$hds->pack(-side => 'top', -fill => 'both', -expand => 1);
$hds->waitVisibility;
$hds->configure(-height => 900);
$hds->configure(-scrollregion => [$hds->bbox("all")]);

MainLoop;
BioPerl-1.007002/examples/tools000755000766000024          013155576320 16334 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/tools/extract_genes.pl000555000766000024       655513155576320 21677 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
=pod

=head1 NAME

extract_genes.pl - extract genomic sequences from NCBI files
using BioPerl

=head1 DESCRIPTION

This script is a simple solution to the problem of
extracting genomic regions corresponding to genes. There are other 
solutions, this particular approach uses genomic sequence 
files from NCBI and gene coordinates from Entrez Gene.

The first time this script is run it will be slow as it will
extract species-specific data from the gene2accession file and create
a storable hash (retrieving the positional data from this hash is
significantly faster than reading gene2accession each time the script
runs). The subsequent runs should be fast.

=head1 INSTALLATION

=head2

Install BioPerl, full instructions at http://bioperl.org.

=head2 Download gene2accession.gz

Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into 
your working directory and gunzip it.

=head2 Download sequence files

Create one or more species directories in the working directory, the
directory names do not have to match those at NCBI (e.g. "Sc", "Hs").

Download the nucleotide fasta files for a given species from its CHR*
directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a 
species directory. The sequence files will have the suffix ".fna" or 
"fa.gz", gunzip if necessary.

=head2 Determine Taxon id

Determine the taxon id for the given species. This id is the first column
in the gene2accession file. Modify the %species hash in this script
such that name of your species directory is a key and the taxon id is the 
value.

=head2 Command-line options

  -i   Gene id
  -s   Name of species directory
  -h   Help

Example:

  extract_genes.pl -i 850302 -s Sc

=cut

use strict;
use Bio::DB::Fasta;
use Getopt::Long;
use Storable;

my %species = ( "Sc" => 4932,  # Saccharomyces cerevisiae
				     "Ec" => 83333, # Escherichia coli K12
					  "Hs" => 9606   # H. sapiens
				   );

my ($help,$id,$name);

GetOptions( "s=s"  =>  \$name,
            "i=i"  =>  \$id,
				"h"    =>  \$help );

usage() if ($help || !$id || !$name);

my $storedHash = $name . ".dump";

# create index for a directory of fasta files
my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id);

# extract species-specific data from gene2accession
unless (-e $storedHash) {
	my $ref;
	# extract species-specific information from gene2accession
	my $file = 'gene2accession';
	open my $MYIN, '<', $file or die "Could not read file '$file': $!\n";
	while (my $line = <$MYIN>) {
		my @arr = split "\t", $line;
		if ($arr[0] == $species{$name} && $arr[9] =~ /\d+/ && $arr[10] =~ /\d+/) {
			($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, 
			 $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) =	
				($arr[9], $arr[10], $arr[11], $arr[7]);
		}
	}
	close $MYIN;
	# save species-specific information using Storable
	store $ref, $storedHash;
} 

# retrieve the species-specific data from a stored hash
my $ref = retrieve($storedHash);

# retrieve sequence and sub-sequence
if (defined $ref->{$id}) {
	my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"});
	my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"});
	$seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-");

	# Insert SeqIO options here...
	print $seq->seq,"\n";
} else {
	print "Cannot find id: $id\n";
}

sub make_my_id {
	my $line = shift;
	$line =~ /ref\|([^|]+)/;
	$1;
}

sub usage {
	system "perldoc $0";
	exit;
}

__END__
BioPerl-1.007002/examples/tools/gb_to_gff.pl000555000766000024       114013155576320 20741 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
use strict;

use Bio::Tools::GFF;
use Bio::SeqIO;

my ($seqfile) = @ARGV;
die("must define a valid seqfile to read") unless ( defined $seqfile && -r $seqfile);

my $seqio = new Bio::SeqIO(-format => 'genbank',
			   -file   => $seqfile);
my $count = 0;
while( my $seq = $seqio->next_seq ) {
    $count++;
    # defined a default name
    my $fname = sprintf("%s.gff", $seq->display_id || "seq-$count");
    my $gffout = new Bio::Tools::GFF(-file => ">$fname" ,
				     -gff_version => 1);
    
    foreach my $feature ( $seq->top_SeqFeatures() ) {
	$gffout->write_feature($feature);
    }
}
BioPerl-1.007002/examples/tools/gff2ps.pl000555000766000024      1320413155576320 20240 0ustar00cjfieldsstaff000000000000#!/usr/local/bin/perl


=head1 NAME

gff2ps - you will want to change this script

=head2 SYNOPSIS

   perl gff2ps < file.gff > file.ps

=head2 DESCRIPTION

This script provides GFF to postscript handling. Due to the ... ummm
... potential for flexible reinterpretation that is GFF, this script
will almost certainly need modifying for anyone elses use (basically,
you need to know what you want to get out of the GFF file and how to
draw it). But it does include code to draw the most challenging thing
out there - genes - and should give you a good example of where to
start

=head2 AUTHOR

Ewan Birney

=cut


use Bio::Tools::GFF;

my $font      = 8;
my $scale     = 200;
my $rotate    = 1;
my $feature_off = 0;

use Getopt::Long;

&GetOptions(
	    "scale=i"   => \$scale,
	    "font=i"    => \$font,
	    "rotate=i"  => \$rotate,
	    "start=i"   => \$feature_off
	    );


my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version => 1);
my $feature;

use Data::Dumper;

my %set;

# loop over the input stream
while( my $f = $gffio->next_feature()) {
    $f->start($f->start - $feature_off);
    $f->end  ($f->end   - $feature_off);

    if( $f->start < 0 ) {
	next;
    }

    if( $f->start > $scale*1000 ) {
      next;
    }
    
    
    if( $f->primary_tag =~ /coding_exon/ ) {
	#print STDERR "Seen ",$f->start," ",$f->end,"\n";
	($group) = $f->each_tag_value('group');
	$group =~ s/\s+//g;

	

	if( !defined $set{$group} ) {
	    $set{$group} = Bio::SeqFeature::Generic->new();
	    $set{$group}->seqname($f->seqname);
	    $set{$group}->primary_tag('transcript');
	    $set{$group}->source_tag($f->source_tag);
	    $set{$group}->add_tag_value('id',$group);
	}
	$set{$group}->add_sub_SeqFeature($f,'EXPAND');
	$set{$group}->strand($f->strand);
    }
}
$gffio->close();


#foreach my $set ( values %set ) {
#    print $set->gff_string,"\n";
#    foreach $sub ( $set->sub_SeqFeature ) {
#	print $sub->gff_string,"\n";
#    }
#}


# sort into forward and reverse strands

my @forward;
my @reverse;

$max = 0;

foreach my $set ( values %set ) {
    if( $set->end > $max ) {
	$max = $set->end;
    }

    if( $set->strand == -1 ) {
	push(@reverse,$set);
    } else {
	push(@forward,$set);
    }
}

@forward = sort { $a->start <=> $b->start } @forward;
@reverse = sort { $a->start <=> $b->start } @reverse;

&print_header(\*STDOUT);

if( $rotate ) {
   print "0 700 translate\n";
   print "-90 rotate\n";
}

print "0 200 moveto 900 200 lineto stroke\n";

my $bp_max = $scale*900;

for(my $bp = 0;$bp < $bp_max ;$bp = $bp + 5000) {
    print STDOUT $bp/$scale," 200 moveto ",$bp/$scale," 197 lineto\n";
    $text = int( $feature_off + ($bp/1000));
    print STDOUT $bp/$scale," 195 moveto ($text) show\n";
}


&draw_gene(\@forward,1,$scale,220,\*STDOUT);
&draw_gene(\@reverse,-1,$scale,180,\*STDOUT);

print "showpage\n";




sub draw_gene {
    my ($gene_array,$strand,$scale,$offset,$fh) = @_;


    my @bump_array;
    my $bump_row_max = 1;
    my $bump_end = int $max/$scale;

    $bump_array[0] = '0' x $bump_end;


    foreach my $f ( @$gene_array ) {

	#
	# Bump it baby!
	#

	# We keep an array of strings for currently draw areas. Do this in pixel
	# coordinates to save on space. If the region has all 0's then we know we
	# can draw here. If so, we set it to 1's. If not, we go up a row and see if
	# we can fit it in there. If we exhausted the rows we make a new row. 

	$bump_start = (int $f->start/$scale)-1;
	$bump_len   = int(($f->end - $f->start)/$scale) +1;

	# text might be longer than gene. Mystic number 5 looks good for 8 point helvetica
	# you will have to change this otherwise.

	my ($gene_id) = $f->each_tag_value('id');
	if( (length $gene_id)*5 > $bump_len ) {
	    $bump_len = (length $gene_id)*5; 
	}

	# figure out the first place to fit in this gene;
	for($i=0;$i<$bump_row_max;$i++) {
	    #print STDERR "Seeing $bump_start $bump_len $i ",substr($bump_array[$i],$bump_start,$bump_len),"\n";
	    
	    if( substr($bump_array[$i],$bump_start,$bump_len) !~ /1/ ) {
		#print STDERR "Going to break with $i\n";
		last;
	    }
	}
	#print STDERR "i is $i\n";
	# if $i == bump_row_max then we need a new bump row
	if( $i == $bump_row_max ) {
	    $bump_array[$bump_row_max] = '0' x $bump_end;
	    $bump_row_max++;
	}
	
	# now blank out this bump row to 1's
	
	substr($bump_array[$i],$bump_start,$bump_len) = '1' x $bump_len;
	
	# now print it out ;)

	
	#
	# Need to be portable between strands. Gene hats go the
	# other way up on reverse strand, but not the text. 
	#

	if( $strand == 1 ) {
	    $text   = $offset+($i*20)+1;
	    $bottom = $offset+($i*20)+10;
	    $top    = $offset+($i*20)+20;
	    $mid    = $offset+($i*20)+15;
	} else {
	    $text   = $offset-($i*20)-19;
	    $bottom = $offset-($i*20);
	    $top    = $offset-($i*20)-10;
	    $mid    = $offset-($i*20)-5;
	}

	print $fh $f->start/$scale," ",$text," moveto\n";
	print $fh "($gene_id) show\n";

	my $prev = undef;
	    
	foreach $exon ( $f->sub_SeqFeature ) {
	    print $fh $exon->start/$scale," ",$bottom," moveto\n";
	    print $fh $exon->end/$scale," ",$bottom," lineto\n";
	    print $fh $exon->end/$scale," ",$top, " lineto\n";
	    print $fh $exon->start/$scale," ",$top," lineto\n";
	    print $fh "closepath stroke\n";

	    # draw the intron hat
	    if( defined $prev ) {
		print $prev->end/$scale," ",$mid," moveto\n";
		my $intron_len = $exon->start - $prev->end;
		
		print $fh ($prev->end+($intron_len/2))/$scale," ",$top," lineto\n";
		print $fh $exon->start/$scale," ",$mid," lineto stroke\n";
	    }
		
	    $prev = $exon;
	}
	
    }
}


sub print_header {
    my $fh = shift;

    print $fh <
0.5 setlinewidth
/Helvetica findfont $font scalefont setfont
EOF

}
BioPerl-1.007002/examples/tools/parse_codeml.pl000555000766000024       230113155576320 21462 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

use strict;
use Bio::Tools::Phylo::PAML;
use Bio::Root::IO;

my $parser = new Bio::Tools::Phylo::PAML(-file    => shift,
					 -verbose => shift);

my $result = $parser->next_result;
my @otus = $result->get_seqs();
my $MLmatrix = $result->get_MLmatrix();
my $NGmatrix = $result->get_NGmatrix();

# These matrices are length(@otu) x length(@otu) "strict lower
# triangle" 2D-matrices, which means that the diagonal and
# everything above it is undefined.  Each of the defined cells is a
# hashref of estimates for "dN", "dS", "omega" (dN/dS ratio), "t",
# "S" and "N".  If a ML matrix, "lnL" will also be defined.

@otus = $result->get_seqs();
$MLmatrix = $result->get_MLmatrix();
$NGmatrix = $result->get_NGmatrix();
for( my $i=0;$i[$i]}; $j++ ) { 
		printf "The ML omega ratio for sequences %s vs %s was: %g\n",
		  $otus[$i]->id, $otus[$j]->id, $MLmatrix->[$i]->[$j]->{omega};
	}
}

for( my $i=0;$i[$i]}; $j++ ) { 
	
		printf "The NG omega ratio for sequences %s vs %s was: %g\n",
		  $otus[$i]->id, $otus[$j]->id, $NGmatrix->[$i]->[$j]->{'omega'};
	}
}
BioPerl-1.007002/examples/tools/psw.pl000555000766000024       635313155576320 17651 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

# PROGRAM  : psw.pl
# PURPOSE  : Simple driver for Bio::Tools::pSW
# AUTHOR   : Ewan Birney birney@sanger.ac.uk 
# CREATED  : Tue Oct 27 1998
#
# INSTALLATION
#  
# you almost certainly have to have installed bioperl 
# from the makefile system for this to work. This is
# because this module use XS extensions (C source code
# 'compiled into' perl)
#
# The lib system below is just so that I (ewan) can test it
# on site... 
#

use lib "/nfs/disk100/pubseq/wise/PerlMod/";

# 
# This is a simple example script. We are going
# to make 3 sequences directly from memory and
# then align them once using blosum matrix and once
# using a gonnet matrix. These matrices should
# in the examples directory.
#

use Bio::Tools::pSW;

# redundant, as Bio::Tools::pSW uses them, but useful to say
# precisely what we are using ;)

use Bio::Seq; 
use Bio::SimpleAlign;
use Bio::AlignIO;

# for legibility - write with newlines and then strip them!

$tseq = 'SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT
YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL
RDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL
SKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSG
DGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGRGFGGG
SGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSS
SSSSYGSGRRF';

$tseq =~ s/[^A-Z]//g;

$seq1 = Bio::Seq->new(-id=>'roa1_human',-seq=>$tseq);

$tseq = 'MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHFEKWGNIVDV
VVMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVVEPKRAVPRQDIDSPNAGAT
VKKLFVGALKDDHDEQSIRDYFQHFGNIVDINIVIDKETGKKRGFAFVEFDDYDPVDKVV
LQKQHQLNGKMVDVKKALPKQNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWN
NGGNNWGNNRGGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNW
NNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGGNNQGFNNGG
NNRRY';

$tseq =~ s/[^A-Z]//g;

$seq2 = Bio::Seq->new(-id=>'roa1_drome',-seq=>$tseq);

$tseq = 'MHKSEAPNEPEQLRKLFIGGLSFETTDESLREHFEQWGTLTDCVVMRDPNSKRSRGFGFV
TYLSTDEVDAAMTARPHKVDGRVVEPKRAVSREDSSRPGAHLTVKKIFVGGIKEDTEEDH
LREYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFEDHDSVDKIVIQKYHTVNNHNSQVRKA
LSKQEMASVSGSQRERGGSGNYGSRGGFGNDNFGGRGGNFGGNRGGGGGFGNRGYGGDGY
NGDGQLWWQPSLLGWNRGYGAGQGGGYGAGQGGGYGGGGQGGGYGGNGGYDGYNGGGSGF
SGSGGNFGSSGGYNDFGNYNSQSSSNFGPMKGGNYGGGRNSGPYGGGYGGGSASSSSGYG
GGRRF';

$tseq =~ s/[^A-Z]//g;
$seq3 = Bio::Seq->new(-id=>'roa1_xenla',-seq=>$tseq);


#
# Now make an Alignment Factory with blosum62 as a matrix
# gap -12 and ext -2
#

$fac = Bio::Tools::pSW->new(-matrix => 'blosum62.bla',-gap => 12, -ext => 2);


#
# run seq1 vs seq2 and seq1 vs seq3 and write the output direct 
# to stdout using the 'pretty' method
#

$fac->align_and_show($seq1,$seq2,STDOUT);
print "Next alignment\n";
$fac->align_and_show($seq1,$seq3,STDOUT);


#
# a different factory, using gonnet, and now make a simple align and 
# provide MSF format
#

$fac = Bio::Tools::pSW->new(-matrix => 'gon250.bla',-gap => 12, -ext => 2);


# switch on reporting this time and change the amount of memory it is allowed

print STDOUT "Doing the next calculation in limited memory, with a progress report\n";

$fac->report(1);
$fac->kbyte(100);

$al = $fac->pairwise_alignment($seq1,$seq2);


# write out a MSF file
my $out = Bio::AlignIO->newFh('-fh'=> \*STDOUT,  '-format' => 'msf');
my $status = print $out $al;
#$al->write_MSF(\*STDOUT);



BioPerl-1.007002/examples/tools/reverse-translate.pl000555000766000024       254113155576320 22501 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=head1 NAME

reverse-translate.pl

=head1 DESCRIPTION

Reverse-translates a nucleotide sequence using the most frequent codons.
Requires an input sequence file and a nucleotide sequence file containing 
one sequence comprised of one or more ORFs. This file supplies the codon
frequency data and will be parsed starting at the first triplet in the sequence.

=head1 OPTIONS

  -i   Input sequence, amino acid
  -c   Input sequence, nucleotide ORFs

Example:

 reverse-translate.pl -i ~/bioperl-live/t/data/cysprot.fa -c ~/bioperl-live/t/data/HUMBETGLOA.fa 

=cut

use strict;
use Bio::SeqIO;
use Bio::Tools::CodonTable;
use Bio::Tools::SeqStats;
use Bio::CodonUsage::Table;
use Getopt::Long;

my ($codonFile,$seqFile);

GetOptions( "c=s" => \$codonFile,
            "i=s" => \$seqFile );

die "Need input sequence and file containing coding regions"
  if ( !$codonFile || !$seqFile );

my $codonIn = Bio::SeqIO->new(-file => $codonFile,
										-format => 'fasta');

my $codonSeq = $codonIn->next_seq;

my $codonStats = Bio::Tools::SeqStats->count_codons($codonSeq);

my $codonUsage = Bio::CodonUsage::Table->new(-data => $codonStats );

my $codonTable = Bio::Tools::CodonTable->new;

my $seqIn = Bio::SeqIO->new(-file => $seqFile);

my $seq = $seqIn->next_seq;

my $rvSeq = $codonTable->reverse_translate_best($seq,$codonUsage);

print $rvSeq,"\n";

__END__
BioPerl-1.007002/examples/tools/run_genscan.pl000555000766000024       452213155576320 21336 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
# Brian Osborne
# script to run genscan on all nucleotide sequences in a fasta file
# and save results as the fasta files .gs.pept and .gs.cds,
# and .gs.exons

use Bio::SeqIO;
use Bio::Seq;
use Getopt::Long;
use Bio::Tools::Genscan;
use strict;

# GENSCAN matrix
my $matrix = "/home/bosborne/src/genscan/HumanIso.smat";

my ($file,$i);

GetOptions( "f|file=s" => \$file );
usage() if ( !$file );

my $pept_out = Bio::SeqIO->new(-file   => ">$file.gs.pept",
			       -format => "fasta");
my $cds_out = Bio::SeqIO->new(-file   => ">$file.gs.cds",
			      -format => "fasta");
my $exons_out = Bio::SeqIO->new(-file   => ">$file.gs.exons",
				-format => "fasta");

my $in = Bio::SeqIO->new(-file => $file , -format => 'Fasta');

while ( my $seq = $in->next_seq() ) {
   die "Input sequence is protein\n" if ( $seq->alphabet eq 'protein' );

   # create temp file, input to GENSCAN
   my $temp_out = Bio::SeqIO->new(-file   => ">temp.fa",
				   -format => "fasta");
   $temp_out->write_seq($seq);

   my $file_id = $seq->display_id;
   $file_id =~ s/\|/-/g;

   system "genscan $matrix temp.fa -cds > $file_id.gs.raw";
   unlink "temp.fa";

   my $genscan = Bio::Tools::Genscan->new( -file => "$file_id.gs.raw");
   while ( my $gene = $genscan->next_prediction() ) {
      $i++;
      my $pept = $gene->predicted_protein;
      my $cds = $gene->predicted_cds;
      my @exon_arr = $gene->exons;

      if ( defined $cds  ) {
	 my $cds_seq = Bio::Seq->new(-seq => $cds->seq,
				     -display_id => $cds->display_id);
	 $cds_out->write_seq($cds_seq);
      }

      if ( defined $pept ) {
	 my $pept_seq = Bio::Seq->new(-seq => $pept->seq,
				      -display_id => $pept->display_id);
	 $pept_out->write_seq($pept_seq);
      }

      for my $exon (@exon_arr) {
	 my $desc = $exon->strand . " " . $exon->start . "-" . $exon->end .
	   " " . $exon->primary_tag . " " . "GENSCAN_predicted_$i";
	 my $exon_seq = Bio::Seq->new(-seq => $seq->subseq($exon->start,
							   $exon->end),
				      -display_id => $seq->display_id,
				      -desc => $desc );
	 $exons_out->write_seq($exon_seq);
      }
   }
   $genscan->close();
   unlink "$file_id.gs.raw";
}

sub usage {
    print "
Usage    : $0 -f 
Function : run genscan on all nucleotide sequences in a multiple fasta file
Output   : .gs.pept, .gs.cds, .gs.exons

";
    exit;
}
BioPerl-1.007002/examples/tools/run_primer3.pl000555000766000024       451313155576320 21301 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=head1 NAME

run_primer3.pl - run primer3 and parse its output

=head1 SYNOPSIS

  ./run_primer3.pl -i test.fa

  #or

  ./run_primer3.pl --input=test.fa

=head1 DESCRIPTION

Example of how to run primer3 and parse its output, essentially taken from an
email written by Paul Wiersma to bioperl-l.

=head1 FEEDBACK

User feedback is an integral part of the evolution of this and other
Bioperl scripts. Send your comments and suggestions to the Bioperl 
mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

Brian Osborne, bosborne at alum.mit.edu

=cut

use strict;
use Getopt::Long;
use Bio::Tools::Run::Primer3;
use Bio::SeqIO;

my $in_file;

GetOptions("i|input:s" => \$in_file );

usage() unless $in_file;

my $seqio = Bio::SeqIO->new(-file => $in_file);

while (my $seq = $seqio->next_seq) {
	my $primer3 = Bio::Tools::Run::Primer3->new(-seq => $seq);
	$primer3->program_name('primer3_core') unless $primer3->executable;

	$primer3->add_targets('PRIMER_MIN_TM' => 56, 'PRIMER_MAX_TM' => 90);

	my $results = $primer3->run;

	unless ($results->number_of_results) {
		print "No results for ",$seq->display_id;
		next;
	}

	my @out_keys_part = qw(START
								    LENGTH
								    TM
									 GC_PERCENT
									 SELF_ANY
									 SELF_END
									 SEQUENCE );

	print "\n", $seq->display_id, "\n";

	for (my $i = 0 ; $i < $results->number_of_results ; $i++){
		my $result = $results->primer_results($i);
 
		print "\n", $i + 1;	
		for my $key qw(PRIMER_LEFT PRIMER_RIGHT){	
			my ($start, $length) = split /,/, $result->{$key};
			$result->{$key . "_START"} = $start;
			$result->{$key . "_LENGTH"} = $length;
			foreach my $partkey (@out_keys_part) {
				print "\t", $result->{$key . "_" . $partkey};
			} 
			print "\n";
		}
		print "\tPRODUCT SIZE: ", $result->{'PRIMER_PRODUCT_SIZE'}, ", PAIR ANY COMPL: ",
		  $result->{'PRIMER_PAIR_COMPL_ANY'};
		print ", PAIR 3\' COMPL: ", $result->{'PRIMER_PAIR_COMPL_END'}, "\n";
	}
}

sub usage {
   exec('perldoc',$0);
   exit(0);
}

__END__
BioPerl-1.007002/examples/tools/seq_pattern.pl000555000766000024       765113155576320 21367 0ustar00cjfieldsstaff000000000000#!/usr/bin/env perl

#-----------------------------------------------------------------------------
# PROGRAM : seq_pattern.pl 
# PURPOSE : This is a simple driver used to test the Bio::Tools::SeqPattern.pm
#           module for working with sequence patterns (regexps that recognize
#           nucleotide or peptide sequences).
# AUTHOR  : Steve Chervitz (sac@bioperl.org)
# CREATED : 28 Aug 1997
# USAGE   : seq_pattern.pl -h
# COMMENTS: 
#    This is a driver script for the Bio::Tools::SeqPattern.pm Bioperl module
#    that can be used for working with both nucleotide and peptide sequence and 
#    offers features such as:
#    
#      -- generate reverse complement of sequence pattern
#      -- ensuring pattern has no invalid characters
#      -- untainting pattern
#      -- expanding ambiguity codes. 
#    
#     Functionality is not yet complete but it may be of use as-is. 
# 
# INSTALLATION
#    Edit the use lib "...." line to point the directory
#    containing your Bioperl modules.
#
# DOCUMENTATION:
#  http://genome-www.stanford.edu/perlOOP/bioperl/lib/Bio/Tools/SeqPattern.pm.html
#
#-----------------------------------------------------------------------------

use lib "/Users/steve/lib/perl";
use Bio::Tools::SeqPattern ();
use Getopt::Std;

$opt_h = 0;
$opt_n = 0;
$opt_p = 0;
$opt_r = 0;

getopts('hnprv:');
$pat = $ARGV[0] || '';

$opt_h and die <<"QQ_USAGE_QQ";

Usage: seq_pattern.pl [-n|p|r|h] 'REGEXP' 

 regexp : full-regular expression for a nucleotide or peptide sequence.
          Must be listed *after* one of the following options:
 -n     : interpret regexp as a nucleotide pattern.
 -p     : interpret regexp as a peptide pattern.
 -r     : output only the reverse complement of the nucleotide pattern.
 -h     : print usage.
 
QQ_USAGE_QQ


## Nucleotide test patterns (most are based on actual patterns submitted by users):

%nucpat = (1 =>'YR...CG(CCG){5,7}CG[^G]TN{10,}[SA]{4}NN(ACA){2,}GCGTTT.{20,40}GT>',
	   2 =>'cggnnn[ta][ta][ta]n{3,5}[ta][ta][ta]nnnccg',
	   3 =>''cggnnnwwwn{3,5}wwwnnnccg',
	   5 =>'(CCCCT)N{1,200}(agggg)N{1,200}(agggg)', 
	   6 =>'cccct{2,}', 
	   7 =>'(a){10,40}', 
	   8 =>'(cag){36,}', 
	   9 =>'rgaatgx{2,}ygtttca(cag){5,}',
	   10 =>'yattgtt(n){20,80}yattgtt', 
	   11 =>'yattgtt(aca){20,80}yattgtt', 
	   12 =>'TATAAAN{30,100}[AT][CAT][AT]YCAAR[CAT][AT][CAT]', 
	   13 =>'TGACTC[N]{1,300}TGACTC',
	   14 =>'TGACTCN*GAGTCAN*GAGTCAN*TGACTC',
	   15 =>'TGACTC(TCA)*GAGTCA',
	   16 =>'TGACTCN*GAG(TCA)*GAGTCA',
	   17 =>'[at][at]ttcacatgy',
	   );

%peppat = (1 =>'',
	   2 =>'', 
	   );

#----------------------
# Main

if($opt_r) {
    print Bio::Tools::SeqPattern->new(-SEQ =>$pat, -TYPE =>'Dna')->revcom->str,"\n";
    
} else {
    test_nuc($pat) if ($opt_n and !$opt_p);
    test_pep($pat) if ($opt_p and !$opt_n);
    (test_nuc($pat), test_pep($pat)) if !($opt_p or $opt_n);
}
    
exit 0;

#----------------------

sub test_nuc {
# Create nucleotide pattern object:
    my $pat = shift;
    $pat ||= $nucpat{9};

    $npat = new Bio::Tools::SeqPattern(-seq =>$pat, -type =>'Dna');

    print "\nNucleotide Pattern:\n";
    print "-----------------------\n";
    printf "%18s: %s\n", 'Type',    $npat->type;
    printf "%18s: %s\n", 'Original',$npat->str;
    printf "%18s: %s\n", 'Expanded', $npat->expand;
    printf "%18s: %s\n", 'Reverse-Comp', $npat->revcom->str;
    printf "%18s: %s\n", 'Rev-Comp+Expanded', $npat->revcom(1)->str; # Hate this syntax. May change.
    print "\n";
}


sub test_pep {
# Create peptide pattern object:
    my $pat = shift;
    $pat ||= $peppat{1};

    $ppat = new Bio::Tools::SeqPattern(-seq =>$pat, -type =>'Amino');

    print "\nPeptide Pattern:\n";
    print "-----------------------\n";
    printf "%18s: %s\n", 'Type',    $ppat->type;
    printf "%18s: %s\n", 'Original',$ppat->str;
    printf "%18s: %s\n", 'Expanded', $ppat->expand;
    print "\n";
}    






BioPerl-1.007002/examples/tools/standaloneblast.pl000555000766000024      3524013155576320 22233 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

# PROGRAM  : standaloneblast.pl
# PURPOSE  : Demonstrate possible uses of Bio::Tools::StandAloneBlast.pm
# AUTHOR   : Peter Schattner schattner@alum.mit.edu
# CREATED  : Nov 01 2000
#
# INSTALLATION
#

# You will need to enable Blast to find the Blast program. This can be done
# in (at least) two ways:
#  1. define an environmental variable blastDIR:
#	export BLASTDIR=/home/peter/blast   or
#  2. include a definition of an environmental variable BLASTDIR in every script that will
#     use StandAloneBlast.pm.
#	BEGIN {$ENV{BLASTDIR} = '/home/peter/blast/'; }
#
#  We also need to select the database to be used
my $amino_database = 'swissprot';


# 
#  We are going to demonstrate 3 possible applications of StandAloneBlast.pm:
#	1. Test effect of varying choice of substitution matrices	
#	2. Test effect of varying choice of gap penalty 
#	3. Comparison of results of psiblast depending on whether psiblast itself is used
#	to identify an alignment to use for blasting or whether an external alignment is given to 
#	psiblast
#
use strict;
use Getopt::Long;
use Bio::SimpleAlign;
use Bio::Tools::Run::StandAloneBlast;
use Bio::SearchIO;
use Bio::AlignIO;
use Bio::SeqIO;
use Bio::Root::IO;

# set some default values
my $queryseq = Bio::Root::IO->catfile(qw(t data cysprot1.fa) );
my $executable = 'blastpgp';
my $queryaln = Bio::Root::IO->catfile(qw(t data cysprot.msf) );
my @params = ('database' => $amino_database);
# string listing examples to be executed. Default is to execute
# all tests (ie 1,2 and 3)
my $do_only = ''; 	
my $example1param = 'MATRIX';  # parameter to be varied in example 1
my $example2param = 'GAP';  # parameter to be varied in example 1
my $example1values = [ 'BLOSUM62', 'BLOSUM80', 'PAM70']; # MATRIX values to try
my $example2values = [ 7, 9, 25]; # GAP values to be tried
my $queryalnformat = 'msf';
my $jiter = 2;
# only use pos. specific scoring matrix if > 50% of residues have
# consensus letter (and compare with 25% or 75% cut off)
my  $maskvalues = [50, 25, 75] ; my $helpflag = 0;   # Flag to show usage info.

# get user options
my @argv       = @ARGV;  # copy ARGV before GetOptions() massacres it.
my $paramvalstring;
my $maskvalstring;

&GetOptions("h!"          => \$helpflag, 
				"help!"       => \$helpflag,
				"in=s"        => \$queryseq,
				"inaln=s"     => \$queryaln,
				"alnfmt=s"    => \$queryalnformat,
				"param=s"     => \$example1param,
				"exec=s"      => \$executable,
				"paramvals=s" => \$paramvalstring,
				"do=i"        =>  \$do_only,
				"maskvals=s"  => \$maskvalstring,
				"iter=i"      =>  \$jiter,
	) ;

if ($paramvalstring) { @$example1values = split (":", $paramvalstring); }
if ($maskvalstring)  { @$maskvalues     = split (":", $maskvalstring);  }

if ($helpflag) { &example_usage(); exit 0;}

# create factory & set user-specified global blast parameters
foreach my $argv (@argv) {
	next unless ($argv =~ /^(.*)=>(.*)$/);
	push (@params, $1 => $2);
}
my  $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
	
# If "do" variable not set, do all four examples
if ( ! $do_only)  {
    &vary_params($queryseq, $example1param, $example1values); # ex. 1

    # To compare gap penalties of 7, 9 and 25 we need to set the
    # scoring matrix to BLOSUM62 and extension penalty to 2 (these are
    # limitations of BLAST)

    $factory->MATRIX('BLOSUM62');  

    $factory->EXTENSION(2);  
    &vary_params($queryseq, $example2param, $example2values); # ex. 2
 
    # For the psiblast tests we want to restore gap opening and
    # extension values to their defaults

    $factory->GAP(11);
    $factory->EXTENSION(1);
    # now do the mask comparison example and ..
    &vary_masks($queryseq, $maskvalues); # ex. 3
    # do the jumpstart-align vs multiple iteration examples with the 
    # mask value set to 50%
    &aligned_blast($queryseq, $queryaln, $queryalnformat, 
		   $jiter, $maskvalues->[0]); # ex. 4
} elsif ($do_only  == 1) {
    &vary_params($queryseq,$example1param, $example1values);
} elsif ($do_only  == 3) {
    &vary_masks($queryseq, $maskvalues);
} elsif ($do_only  == 4 ) {
    &aligned_blast($queryseq, $queryaln, $queryalnformat, $jiter, $maskvalues->[0]);
}  else {
    &example_usage();
}

exit 0;

##########
## End of "main"


#################################################
#   compare_runs(): Prints out display of which hits were found by different methods
#	Various methods are labeled by "tags" found in array @runtags
#
#  args: 
#	$typetag  -  label describing type of "tags"
#	$runtags  -  reference to array @runtags
#	$hashhits  - reference to hash of all the hits found by all runs (%hashhits) 
#		value for each hit is string which is the concatenation of all the "tags" of
#		runs that found that hit
#  returns: nothing  

sub compare_runs {
    my $typetag = shift;
    my $runtags = shift;

    my $hashhits = shift;   

    my ($tag, @taghits);

    print "Comparing BLAST results... \n";

# Get total number of hits found by any method
    my $numhits = keys %$hashhits ; # scalar context to get total number of hits by all methods
    print  "Total number of hits found: $numhits \n";

# Get total number of hits found by every method
    my $alltags =  join ( "" ,  @$runtags );
    my  @alltaghits = grep  $$hashhits{$_} =~ /$alltags/  ,  keys %$hashhits;
    print  " Number of hits found by every method / parameter-value: " ,   
    scalar(@alltaghits), "\n";

# If one desires to see the hits found by all methods, uncomment next 2 lines
#print  " Hits were found all methods / parameters: \n";
#print   join ( "\n", @alltaghits ) ,  "\n";

# For each method/parameter-value (labeled by type) display  hits found 
# exclusively by that method
    foreach $tag (@$runtags)  {
		 @taghits = grep  $$hashhits{$_} =~ /^$tag$/  ,  keys %$hashhits;
		 print  " Hits found only when $typetag was $tag: \n";
		 print   join ( "\n", @taghits ) ,  "\n";
    }
    return 1;
}


#################################################
#   vary_params(): Example demonstrating varying of parameter
#
#  args: 
#	$queryseq  - query sequence (can be filename (fasta),  or Bio:Seq object) 
#	$param  - name of parameter to be varied 
#	$values  - reference to array of values to be used for the parameter 
#  returns: nothing  



sub vary_params {

    my $queryseq = shift;   
    my $param = shift;   
    my $values = shift;  


    print "Beginning $param parameter-varying example... \n";

    # Now we'll perform several blasts, 1 for each value of the
    # selected parameter.  In the first default case, we vary the
    # MATRIX substitution parameter, creating 3 BLAST reports, using
    # MATRIX values of BLOSUM62, BLOSUM80 or PAM70.

    # In the second default case, we vary the GAP penalty parameter,
    # creating 3 BLAST reports, using GAP penalties of 7, 9 and 25. In
    # either case we then automatically parse the resulting report to
    # identify which hits are found with any of the parameter values
    # and which with only one of them.

 
    # To test the BLAST results to some other parameter it is only
    # necessary to change the parameters passed to the script on the
    # commandline.  The only tricky part is that the BLAST program
    # itself only supports a limited range of parameters.  See the
    # BLAST documentation.

    my ($report, $sbjct, $paramvalue);

    my $hashhits = { };	# key is hit id, value is string of param values for which hit was found
    
    foreach $paramvalue (@$values)  {
	
	$factory->$param($paramvalue); # set parameter value

	print "Performing BLAST with $param = $paramvalue \n";

	$report = $factory->$executable($queryseq);
	my $r = $report->next_result;
	while( my $hit = $r->next_hit ) {
	    $hashhits->{$hit->name} .= "$paramvalue";
	}
    }

    &compare_runs( $param , $values , $hashhits);  

    return 1;

}

#################################################

#   vary_masks(): Example demonstrating varying of parameter
#
#  args:
#	$queryseq  - query sequence (can be filename (fasta),  or Bio:Seq object)
#	$maskvalues  - reference to array of values to be used for the mask threshold
#  returns: nothing

# Now we'll perform several blasts, 1 for each value of the mask threshold.
# In the default case, we use thresholds of 25%, 50% and 75%. (Recall the threshold is
# % of resudues which must match the consensus residue before deciding to use the
# position specific scoring matrix rather than the default - BLOSUM or PAM - matrix)
# We then automatically parse the resulting reports to identify which hits
# are found with any of the mask threshold values and which with only one of them.
#

sub vary_masks {

my $queryseq = shift;
my $values = shift;


print "Beginning mask-varying example... \n";

my ($report, $sbjct, $maskvalue);

my $hashhits = { };     # key is hit id, value is string of param values for which hit was found

# Get the alignment file
my $str = Bio::AlignIO->new(-file=> "$queryaln", '-format' => "$queryalnformat", );
my $aln = $str->next_aln();

foreach $maskvalue (@$values)  {

    print "Performing BLAST with mask threshold = $maskvalue % \n";

    # Create the proper mask for 'jumpstarting'
    my $mask = &create_mask($aln, $maskvalue);
    my $report2 = $factory->blastpgp($queryseq, $aln, $mask);
    my $r = $report2->next_result;
    while($sbjct = $r->next_hit) {
	$hashhits->{$sbjct->name} .= "$maskvalue";			
    }
}

&compare_runs( 'mask threshold' , $values , $hashhits);

return 1;

}

#################################################
#  aligned_blast ():
#
#
#  args: 
#	$queryseq  - query sequence (can be filename (fasta),  or Bio:Seq object) 
#	$queryaln  - file containing alignment to be used to "jumpstart" psiblast in "-B mode"
#			$queryaln *must contain $queryseq with the same name and length
#				(psiblast is very picky)
#	$queryalnformat  - format of alignment (can = "fasta", "msf", etc)
#	$jiter  - number of iterations in psiblast run
#	$maskvalue  - threshold indicating how similar residues must be at a sequence location
#		before position-specific-scoring matrix is used
#		: "0" => use position specific matrix at all residues,  or
#			"100" => use default (eg BLOSUM) at all residues
#  returns: nothing  


# For this example, we'll compare the results of psiblast depending on whether psiblast itself is 

#  used to identify an alignment to use for blasting or whether an external alignment is given to 
#  psiblast

sub aligned_blast {


my     $queryseq  =  shift; 
my	$queryaln  =  shift; 
my	$queryalnformat  =  shift;
my	$jiter  =  shift;
my	$maskvalue  =  shift;

my $hashhits = { };
my ($sbjct, $id);

print "\nBeginning aligned blast example... \n";


# First we do a  single-iteration psiblast search but with a specified alignment to
#  "jump start" psiblast


print "\nBeginning jump-start psiblast ... \n";


my $tag1 = 'jumpstart';

# $factory->j('1');    # perform single iteration

# Get the alignment file
my $str = Bio::AlignIO->new(-file=> "$queryaln", '-format' => "$queryalnformat", );
my $aln = $str->next_aln();


# Create the proper mask for 'jumpstarting'
my $mask = &create_mask($aln, $maskvalue);


my $report2 = $factory->blastpgp($queryseq, $aln, $mask);
while($sbjct = $report2->next_result) {
		$hashhits->{$sbjct->name} .= "$tag1";			
}

# Then we do a "plain" psiblast multiple-iteration search

print "\nBeginning multiple-iteration psiblast ... \n";

my $undefineB ;
  $factory->B($undefineB);

my $tag2 = 'iterated';
$factory->j($jiter);    # 'j' is blast parameter for # of iterations
my $report1 = $factory->blastpgp($queryseq);
my $total_iterations = $report1->number_of_iterations;
my $last_iteration = $report1->round($total_iterations);


 while($sbjct = $last_iteration->next_result) {
		$hashhits->{$sbjct->name} .= "$tag2";			
	}

# Now we compare the results of the searches

my $tagtype = 'iterated_or_jumpstart'; 
my $values = [ $tag1, $tag2];

&compare_runs( $tagtype , $values , $hashhits);  
 
return 1;

}


#################################################


# create_mask(): creates a mask for the psiblast jumpstart alignment
#                that determines at what residues position-specific
#                scoring matrices (PSSMs) are used and at what
#                residues default scoring matrices (eg BLOSUM) are
#                used. See psiblast documentation for more details,

#  args: 
#	$aln  -  SimpleAlign object with alignment
#	$maskvalue  -  label describing type of "tags"
#  returns: actual mask, ie a string of 0's and 1's which is the 
#           same length as each sequence in the alignment and has 
#           a "1" at locations where (PSSMs) are to be used
#           and a "0" at all other locations.


sub create_mask {
	my $aln = shift;
	my $maskvalue = shift;
	my $mask = "";

	die "psiblast jumpstart requires all sequences to be same length \n"
	  unless $aln->is_flush();
	my $len = $aln->length();

	if ($maskvalue =~ /^(\d){1,3}$/  ) {
		$mask = $aln->consensus_string($maskvalue) ;
		$mask =~ s/[^\?]/1/g ;
		$mask =~ s/\?/0/g ;
	}
	else { die "maskvalue must be an integer between 0 and 100 \n"; }
	return $mask ;
}

#----------------
sub example_usage {
#----------------

#-----------------------
# Prints usage information for general parameters.

    print STDERR <<"QQ_PARAMS_QQ";

 Command-line accessible script variables and commands:
 -------------------------------
 -h 		:  Display this usage info and exit.
 -in 	:  File containing input sequences in fasta format (default = $queryseq) .
 -inaln 	:  File containing input alignment for example 3 (default = $queryaln) .
 -alnfmt 	:  Format of input alignment for example 3, eg "msf", "fasta", "pfam".
		   (default = $queryalnformat) .
 -do 	:  Number of test to be executed ("1" => vary parameters,
		   "3" => compare iterated & jumpstart psiblast.) If omitted,
		   three default tests performed.
 -exec   	:  Blast executable to be used in example 1.  Can be "blastall" or
		   "blastpgp" (default is "blastpgp").
 -param   	:  Parameter to be varied in example 1. Any blast parameter
		   can be varied (default = 'MATRIX')
 -paramvals :  String containing parameter values in example 1, separated
		   by ":"'s. (default = 'BLOSUM62:BLOSUM80:PAM70')
 -iter     :  Maximum number of iterations in psiblast in example 3 (default = 2)
 -maskvals :  String containing mask threshold values (in per-cents) for example 3,
		   separated by ":"'s. (default = '50:75:25')

In addition, any valid Blast parameter can be set using the syntax "parameter=>value" as in "database=>swissprot"

So some typical command lines might be:
 >standaloneblast.pl -do 1 -param expectation -paramvals '1e-10:1e-5'
or
 >standaloneblast.pl -do 1 -exec blastall -param q -paramvals '-1:-7' -in='t/dna1.fa' "pr=>blastn" "d=>ecoli.nt"
or
 >standaloneblast.pl -do 4 -maskvals 0 -iter 3
or
 >standaloneblast.pl -do 3 -maskvals '10:50:90'  -in 't/data/cysprot1.fa' -alnfmt msf -inaln 't/cysprot.msf'



QQ_PARAMS_QQ
}
BioPerl-1.007002/examples/tree000755000766000024          013155576320 16133 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/examples/tree/paup2phylip.pl000555000766000024       101613155576320 21103 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
# Author: Jason Stajich 
# Convert a PAUP tree block to Phylip format

use strict;

my @data;
while(<>) {     
    last if( /Translate/ );
}
while(<>) { 
    last if (/;/);
    my ($num, $taxon) = (/\s+(\d+)\s([A-Za-z\.\_]+),/);
    $data[$num] = substr($taxon,0,10);
}
while(<>) {    
    next unless (s/^\s*tree (\S+) = \[\S+\] //i);
    my $tree = $_;    
    for( my $i=scalar @data; $i > 0; $i-- ) {
	my $taxon = $data[$i];
	$tree =~ s/$i/$taxon/;
    }    
    print $tree;    
}
BioPerl-1.007002/ide000755000766000024          013155576320 14117 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/ide/bioperl.komodo000444000766000024       326313155576320 17126 0ustar00cjfieldsstaff000000000000# $Id: [[%f]],v 0.01 2007-03-27 12:43:27 heikki Exp $
#
# BioPerl module for [[%ask1:Perl class name]]
#
# Cared for by [[%ask2:Caretaker name]] [[%ask3:Caretaker email]]
#
# Copyright [[%ask2]]
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code

=head1 NAME

[[%ask1]] - DESCRIPTION of Object

=head1 SYNOPSIS

Give standard usage here

=head1 DESCRIPTION

Describe the object here

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  
=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:

  https://github.com/bioperl/bioperl-live/issues
  
=head1 AUTHOR - [[%ask2]]

  Email [[%ask3]]

Describe contact details here

=head1 CONTRIBUTORS

Additional contributors names and emails here

=head1 APPENDIX

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _

=cut

# Let the code begin...

package [[%ask1]];

use strict;

# Object preamble - inherits from Bio::Root::Root

use base qw(Bio::Root::Root);

=head2 new

 Title   : new
 Usage   : my $obj = new
 Function: Builds a new [[%ask1]] object 
 Returns : an instance of [[%ask1]]
 Args    : 
 
=cut

sub new {
	my($class,@args) = @_;
	my $self = $class->SUPER::new(@args);
	return $self;
}

1;
BioPerl-1.007002/ide/bioperl-mode000755000766000024          013155576320 16475 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/ide/bioperl-mode/README000555000766000024       172213155576320 17517 0ustar00cjfieldsstaff000000000000$Id$

bioperl-mode : a minor mode for BioPerl documentation and template insertion

Release 0.1

== Description ==

bioperl-mode is an Emacs minor mode that allows rapid browsing of
BioPerl pod and source code. It contains facilities for inserting
coding and documentation templates that save typing and ensure BioPerl
best practice compliance.

See http://www.bioperl.org/wiki/Emacs_bioperl-mode for a full
description and list of features.

== Installation ==

Copy the file dist/bioperl-mode.tar into your Emacs root directory,
often 

 /usr/share/emacs/[version]/ 

in Linux, or 

 C:\Program Files\emacs-[version]\ 

in Windows.

Untar in situ with

 $ tar -xf bioperl-mode.tar

In your .emacs file, add the line

 (require 'bioperl-mode)

and restart.

Source files are available in site-lisp and etc directories.

For more details, see http://www.bioperl.org/wiki/Emacs_bioperl-mode.

== Support == 

Please direct questions to bioperl-l@lists.open-bio.org

Happy coding!BioPerl-1.007002/ide/bioperl-mode/dist000755000766000024          013155576320 17440 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/ide/bioperl-mode/dist/Changes000555000766000024       147713155576320 21104 0ustar00cjfieldsstaff000000000000$Id$
07 Dec 2009 03:57:00 UTC
   - add parent/base class browse functionality to 
     source view too
06 Dec 2009 22:38:00 UTC
   - new feature : browse the pod of parent/base classes
     (press [B] or [P] in pod view)
04 Dec 2009 22:15:00 UTC
   - fixed a bug that led to borks when 'view-mode' not
     present in minor-mode-alist
   - little template tweak
15 Nov 2009 00:32:00 UTC
   - added bioperl-source-mode for source viewing
     'i' mapped to imenu in bioperl-source-mode
     'q' now quits and closes source viewer
   - when running 'bioperl-view-pod' (RETURN key) in pod
     view mode, the default completion namespace is the 
     namespace of the module that is currently being 
     viewed (rather than plain 'Bio::')
   - added a generic method pod template inserter, accessed 
     with C-c C-k or C-c C-g
   
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ƒr£ºLÜ–TYzšÿeß_>_>_>_>ÿŸÿüªÇ¸BioPerl-1.007002/ide/bioperl-mode/dist/bioperl-mode.tar.md5000444000766000024         6313155576320 23306 0ustar00cjfieldsstaff00000000000082f272a7b044182e218753a0ccaa31ae *bioperl-mode.tar
BioPerl-1.007002/ide/bioperl-mode/dist/package-me000555000766000024        74213155576320 21500 0ustar00cjfieldsstaff000000000000#!/bin/bash
#$Id$
tar -czvf bioperl-mode.tar  --directory=.. --exclude-tag-all=SKIP --exclude=#*.* --exclude=*.*~ --exclude=.svn --exclude=dist .
find -L ../xemacs -type f > ../xemacs/xemacs-packages/pkginfo/MANIFEST.bioperl-mode
tar -chzvf bioperl-mode-xemacs.tar  --directory=../xemacs --exclude-tag-all=SKIP --exclude=#*.* --exclude=*.*~ --exclude=.svn --exclude=dist .
md5sum bioperl-mode.tar > bioperl-mode.tar.md5
md5sum bioperl-mode-xemacs.tar > bioperl-mode-xemacs.tar.md5

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BioPerl-1.007002/ide/bioperl-mode/etc/images/bpmode-tool.xpm000555000766000024      1371613155576320 23654 0ustar00cjfieldsstaff000000000000/* XPM */
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BioPerl-1.007002/ide/bioperl-mode/site-lisp000755000766000024          013155576320 20406 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/ide/bioperl-mode/site-lisp/bioperl-init.el000555000766000024      3536413155576320 23520 0ustar00cjfieldsstaff000000000000;; $Id$

;;
;; Init functions for Bioperl minor mode
;; 
;; Author: Mark A. Jensen
;; Email : maj -at- fortinbras -dot- us
;;
;; Part of The Documentation Project
;; http://www.bioperl.org/wiki/The_Documentation_Project
;;
;;

;; Copyright (C) 2009 Mark A. Jensen

;; This program is free software; you can redistribute it and/or
;; modify it under the terms of the GNU General Public License as
;; published by the Free Software Foundation; either version 3 of
;; the License, or (at your option) any later version.

;; This program is distributed in the hope that it will be
;; useful, but WITHOUT ANY WARRANTY; without even the implied
;; warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
;; PURPOSE.  See the GNU General Public License for more details.

;; You should have received a copy of the GNU General Public
;; License along with this program; if not, write to the Free
;; Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
;; Boston, MA 02110-1301 USA


(defconst bioperl-init-revision "$Id$"
  "The revision string of bioperl-init.el")


;;
;; menu bar keymaps
;;

(defvar menu-bar-bioperl-doc-menu
  (let (
	(map (make-sparse-keymap "BioPerl Docs"))
	)
    (define-key map [bp-pod-apx]
      '(menu-item "View appendix" bioperl-view-pod-appendix
		  :help "View pod APPENDIX of a module (where most methods are described)"
		  :keys "\\[bioperl-view-pod-appendix]"))
    (define-key map [bp-pod-dsc]
      '(menu-item "View description" bioperl-view-pod-description
		  :help "View pod DESCRIPTION of a module"
		  :keys "\\[bioperl-view-pod-description]"))
    (define-key map [bp-pod-syn]
      '(menu-item "View synopsis" bioperl-view-pod-synopsis
		  :help "View pod SYNOPSIS of a module"
		  :keys "\\[bioperl-view-pod-synopsis]"))
    (define-key map [bp-pod]
      '(menu-item "View pod" bioperl-view-pod
		  :help "Examine entire pod of a module"
		  :keys "\\[bioperl-view-pod]"))
    (define-key map [bp-pod-mth]
      '(menu-item "View method pod" bioperl-view-pod-method
		  :help "View pod (Title:, Usage:, etc) for a single method"
		  :keys "\\[bioperl-view-pod-method]"))
    map)
  "Menu-bar map for doc functions in bioperl-mode.")


(defvar menu-bar-bioperl-ins-menu
  (let (
	(map (make-sparse-keymap "BioPerl Ins"))
	)
    (define-key map [bp-ins-arr]
      '(menu-item "Insert container template" bioperl-insert-array-accessor
		  :help "Insert template functions for an object array"
		  :keys "\\[bioperl-insert-array-accessor]"))
    (define-key map [bp-ins-obj]
      '(menu-item "Insert class/object template" bioperl-insert-class
		  :help "Insert full object template plus std pod"
		  :keys "\\[bioperl-insert-class]"))
    (define-key map [bp-ins-mthpod]
      '(menu-item "Insert method pod template" bioperl-insert-method-pod
		  :help "Insert Bioperl standard method pod template"
		  :keys "\\[bioperl-insert-method-pod]"))
    (define-key map [bp-ins-genpod]
      '(menu-item "Insert generic class pod template" bioperl-insert-generic-class
		  :help "Insert package declaration plus std pod"
		  :keys "\\[bioperl-insert-generic-class]"))
    (define-key map [bp-ins-acc]
      '(menu-item "Insert accessor template" bioperl-insert-accessor
		  :help "Insert accessor (getter/setter) with std pod"
		  :keys "\\[bioperl-insert-accessor]"))
    (define-key map [bp-ins-mod]
      '(menu-item "Insert module identifier" bioperl-insert-module
		  :help "Insert module identifier, with completion"
		  :keys "\\[bioperl-insert-module]"))
    map)
  "Menu-bar map for insertion functions in bioperl-mode")

;;
;; keymap
;;
;; principles: 
;; C-c accesses mode functions
;; meta key commands - documentation reading (pod display, etc.)
;; control key command - documentation writing (template insertions, etc.)
;;


(defvar bioperl-mode-map
  (let ((map (make-sparse-keymap)))
    (define-key map "\C-c\M-p" 'bioperl-view-pod)
    (define-key map "\C-c\M-d" 'bioperl-view-pod-description)
    (define-key map "\C-c\M-s" 'bioperl-view-pod-synopsis)
    (define-key map "\C-c\M-a" 'bioperl-view-pod-appendix)
    (define-key map "\C-c\M-f" 'bioperl-view-pod-method)
    (define-key map "\C-c\M-m" 'bioperl-view-pod-method)
    (define-key map "\C-cm"   'bioperl-insert-module)
    (define-key map "\C-c\C-a" 'bioperl-insert-accessor)
    (define-key map "\C-c\C-v" 'bioperl-insert-accessor)
    (define-key map "\C-c\C-A" 'bioperl-insert-array-accessor)
    (define-key map "\C-c\C-b" 'bioperl-insert-class)
    (define-key map "\C-c\C-M" 'bioperl-insert-class)
    (define-key map "\C-c\C-k" 'bioperl-insert-generic-class)
    (define-key map "\C-c\C-g" 'bioperl-insert-generic-class)
    (define-key map "\C-c\C-p" 'bioperl-insert-method-pod)
    (define-key map [menu-bar] nil)
    (define-key map [menu-bar bp-ins]
      (list 'menu-item "BP Templs" menu-bar-bioperl-ins-menu))
    (define-key map [menu-bar bp-doc] 
      (list 'menu-item "BP Docs" menu-bar-bioperl-doc-menu))
    map)
  "Keymap for Bioperl minor mode")

;;
;; finders
;;


(defun bioperl-find-module-path (&optional symb val)
  "Find path to Bioperl modules and set `bioperl-module-path'.
This path points to the directory containing Bio; same principle
as 'use lib'. SYMB and VAL are dummies allowing `defcustom' to do
initializaton."
  (let (
	(old-exec-path exec-path) 
	(pth) )
    ;; ask BPMODE_PATH first...
    (setq pth (getenv "BPMODE_PATH"))
    ;; try the environment
    (unless pth
      (let (
	    ( plib (concat (getenv "PERL5LIB") path-separator (getenv "PATH")))
	    ( pths )
	    )
	(if plib
	  (progn
	    (setq pths (split-string plib path-separator))
	    (while (and (not pth) pths)
	    ;; unixize
;;	    (setq pth (replace-regexp-in-string "\\\\" "/" pth))
	      (setq pth (pop pths))
	      (setq pth (if (file-exists-p (concat pth "/" "Bio")) pth nil)))
	    ))))
    ;; then ask Perl...
    (unless pth 
      ;; safe path
      (if (or (not (boundp 'bioperl-mode-safe-flag))
	      bioperl-mode-safe-flag)
	  (setq exec-path bioperl-safe-PATH))
      
      (setq pth
	    (with-temp-buffer
	      (call-process 
	       "perl" nil t t
	       "-MConfig" "-e" "print $Config{sitelib}")
	      (goto-char (point-min))
	      (thing-at-point 'line)
	      ))
      ;; reset exec-path
      (setq exec-path old-exec-path)
      ;; file name port issue - unixize
      (setq pth (replace-regexp-in-string "\\\\" "/" pth))
      (setq pth (if (file-exists-p (concat pth "/" "Bio")) pth nil)))
    ;; fall back to pwd
    (unless pth
      (setq pth (nth 1 (split-string (pwd))))
      ;; unixize
      (setq pth (replace-regexp-in-string "\\\\" "/" pth))
      (setq pth (if (file-exists-p (concat pth "/" "Bio")) pth nil))
      )
    (if pth
	(setq bioperl-module-path pth)
      (message "Can't find Bio modules; defaulting to pwd -- try setting bioperl-module-path manually")
      (setq bioperl-module-path "."))
  pth))

(defun bioperl-set-safe-PATH (&optional symb val)
  "Portably sets the safe-PATH, used when bioperl-mode calls the system.
SYMB and VAL are dummies allowing defcustom to do
initialization."
  (cond
   ( (string-match "windows\\|mingw\\|nt" system-configuration)
     (setq bioperl-safe-PATH '("c:/Perl/bin" "c:/Windows/system32")) )
   ( (string-match "unix\\|linux" system-configuration)
     (setq bioperl-safe-PATH '("/bin" "/usr/bin" "/usr/local/bin")) )
   ( (string-match "cygwin" system-configuration)
     (setq bioperl-safe-PATH '("/bin" "/usr/local/bin" 
			       "/cygdrive/c/Windows/system32") ) )
   ( t
     (setq bioperl-safe-PATH '()))))

(defvar bioperl-enabled-buffer-flag nil
  "Buffer-local flag for enabling/disabling the bioperl-mode toolbar icon.")

(make-local-variable 'bioperl-enabled-buffer-flag)

;;
;; minor mode definition functions
;;

(define-minor-mode bioperl-mode
  "Toggles Bioperl minor mode.
Bioperl mode provides Bioperl-flavored template insertion and
convenient access to POD documentation. More documentation to
come."
  :init-value nil
  :lighter "[bio]"
  :keymap bioperl-mode-map
  :group 'bioperl
  ;; version check
  (if (string-match "\\(2[0-9]\\)\.[0-9]+\\(?:\.[0-9]+\\)?" (emacs-version))
      (if (or (string-match "^XEmacs" (emacs-version))
              (>= (string-to-number (match-string 1 (emacs-version))) 22))
	  t
	(error "Must upgrade to XEmacs 22 to use bioperl-mode"))
    (error "Must upgrade to Emacs 22 to use bioperl-mode"))
  ;; set up mode
  (bioperl-skel-elements))

(define-minor-mode bioperl-view-mode 
  "A derived view mode for bioperl pod."
  :init-value nil
  :lighter "[bio]"
  :keymap ( let* (
		  (vmap (cdr (assoc 'view-mode minor-mode-map-alist)))
		  (map (if vmap (copy-keymap vmap) (make-sparse-keymap)  ))
		  )
	    (if map
		(progn
		  (define-key map [menu-bar] nil)
		  (define-key map [menu-bar bp-doc] (list 'menu-item "BP Docs" menu-bar-bioperl-doc-menu))
		  (define-key map "q" 'View-kill-and-leave)
		  (define-key map "f" 'bioperl-view-source)
		  (define-key map "P" 'bioperl-view-parents)
		  (define-key map "B" 'bioperl-view-parents)
		  (define-key map "\C-m" 'bioperl-view-pod)
		  (define-key map "\C-\M-m" 'bioperl-view-pod-method)))
	    map )
  ;; and now, a total kludge.
    (view-mode))

(define-minor-mode bioperl-source-mode 
  "A derived view mode for bioperl source code."
  :init-value nil
  :lighter "[bio]"
  :keymap ( let ( (map (copy-keymap (cdr (assoc 'view-mode minor-mode-map-alist)))) )
	    (if map
		(progn
		  (define-key map [menu-bar] nil)
		  (define-key map [menu-bar bp-doc] (list 'menu-item "BP Docs" menu-bar-bioperl-doc-menu))
		  (define-key map "q" 'View-kill-and-leave)
		  (define-key map "g" 'goto-line)
		  (define-key map "i" 'imenu)
		  (define-key map "P" 'bioperl-view-parents-this-buffer)
		  (define-key map "B" 'bioperl-view-parents-this-buffer)
		  (define-key map "\C-m" 'bioperl-view-pod)
		  (define-key map "\C-\M-m" 'bioperl-view-pod-method)))
	    map )
  ;; and now, a total kludge.
    (view-mode))

(defface pod-section-face
  '( (t (:weight bold :foreground "maroon3") ) )
  "Highlight for pod section names.")
(defvar pod-section-face 'pod-section-face)

(defface pod-bioperl-identifier-face
  '( (t (:foreground "blue3" :weight bold)))
  "Highlight for bioperl identifiers")
(defvar pod-bioperl-identifier-face 'pod-bioperl-identifier-face)

(defface pod-method-pod-tag-face
  '( (t (:foreground "blue4")) )
  "Highlight for method pod tags (Title, Usage, etc.)")
(defvar pod-method-pod-tag-face 'pod-method-pod-tag-face)

(defface pod-blue-man-face
  '( (t (:background "blue" :foreground "dark blue")))
  "My world is blue.")
(defvar pod-blue-man-face 'pod-blue-man-face)

(defface pod-subsec-header-face
  '( (t (:weight bold :slant italic :foreground "blue4")))
  "Highlight pod subsection headers")
(defvar pod-subsec-header-face 'pod-subsec-header-face)

(defface pod-method-subsec-face
  '( (t (:slant italic :foreground "maroon4")))
  "Highlight for APPENDIX subsections")
(defvar pod-method-subsec-face 'pod-method-subsec-face)

(defface pod-method-name-face
  '( (t (:weight bold) ) )
  "Highlight pod method names")
(defvar pod-method-name-face 'pod-method-name-face)

(defface pod-key-value-arg-face
  '( (t (:slant italic :foreground "green3")) )
  "Highlight for key-value keys (-something)" )
(defvar pod-key-value-arg-face 'pod-key-value-arg-face)

(defface pod-deref-symb-face
  '( (t (:weight bold :foreground "blue4")))
  "Highlight '->' ")
(defvar pod-deref-symb-face 'pod-deref-symb-face)

(defface pod-assoc-symb-face
  '( (t (:weight bold :foreground "green3")))
  "Highlight '=>' ")
(defvar pod-assoc-symb-face 'pod-assoc-symb-face)

(defvar bioperl-pod-font-lock-keywords
  '( 
    ;; rudimentary perl syntax highlighting
    ("[%$][{]?\\([a-zA-Z0-9_]+\\)[}]?" 1 font-lock-variable-name-face)
    ("[^a-zA-Z0-9]@[{]?\\([a-zA-Z0-9_]+\\)[}]?" 1 font-lock-variable-name-face)
    ("\\>->\\<" . pod-deref-symb-face)
    ("\\(?:\\s \\|\\>\\)\\(=>\\)\\(?:\\s \\|\\<\\|[\'\"]\\)" 1 pod-assoc-symb-face)
    ("\\(?:\\W\\|\\s \\)\\(-[a-zA-Z0-9_]+\\)\\>" 1 pod-key-value-arg-face)
;    ("'[^']+'" . 'font-lock-string-face)
    (pod-find-syntactic-string 1 font-lock-string-face)
    ("\#\\s +.*"  0 font-lock-comment-face t)
    ;; headers
    ("^\\(?:[A-Z]+\\s \\)+" . pod-section-face )
    ("^\\s \\{2\\}\\([A-Z][a-z]+\\s \\)+" . (0 pod-subsec-header-face))
    ("^\\s \\{2\\}[a-z_][a-zA-Z0-9_()]+\\s " . pod-method-name-face)
    ("^\\s +[a-zA-Z]+\\s *:\\s " . pod-method-pod-tag-face)
    ("^[A-Z].*" . pod-method-subsec-face)
    ("Bio::\\(?:[a-zA-Z0-9_:]+\\)+" . pod-bioperl-identifier-face) 
    ;; post-header syntax highlights
    ("\\(\\<[a-zA-Z0-9_]+\\>\\)()" 0 font-lock-function-name-face )
    ("\\(\\<[a-zA-Z0-9_]+\\>\\)[\(]" 1 font-lock-function-name-face )
    ("\\>->\\(\\<[a-zA-Z0-9_]+\\>\\)" 1 font-lock-function-name-face)

     )
  "Font lock keywords for highlighting Perl pod."
)

(defconst bioperl-pod-font-lock-defaults
  '(bioperl-pod-font-lock-keywords t nil nil ))

(define-derived-mode pod-mode fundamental-mode "Pod Fundamental"
  "Derived fundamental mode for highlighting BioPerl pod."
  :group 'bioperl
  :syntax-table nil
  :abbrev-table nil
  (set (make-local-variable 'font-lock-defaults)
       bioperl-pod-font-lock-defaults))

(defun pod-find-syntactic-string (bound)
  "String searcher for bioperl-mode font-lock."
  ;; try to infer from symbol context
  (re-search-forward "\\(?:[$@%(),]\\|->\\|=>\\|print\\).*?\\(['][^']+[']\\|[\"][^\"]+[\"]\\)" bound t))

(defun bioperl-pod-synopsis-region (buffer)
  "Return beginning & end of SYNOPSIS region (excluding the header)."
  (unless (bufferp buffer)
    (error "Buffer required at arg BUFFER"))
  (save-excursion
    (goto-char (point-min))
    (let ( (beg) (end) )
      (setq beg 
	    (if (re-search-forward "^SYNOPSIS" (point-max) t)
		(progn (forward-line 1) (if (bolp) (point) nil))
	      nil))
      (setq end
	    (if (re-search-forward "^[A-Z]" (point-max) t)
		(progn (beginning-of-line) (if (bolp) (point) nil))
	    nil))
      (if (not (and beg end))
	  nil
	`(,beg ,end)))))
	  

(defun bioperl-perl-mode-infect ()
  "Add this function to `perl-mode-hook' to associate bioperl-mode with perl-mode."
  (unless (or (key-binding [tool-bar bpmode]) bioperl-this-is-xemacs (not (display-graphic-p)) )
    (define-key (current-local-map) [tool-bar bpmode]
      `(menu-item "bpmode" bioperl-mode 
		  :image [,(find-image (list 
					'(:type xpm :file "bpmode-tool.xpm")))
			  ,(find-image (list 
					'(:type xpm :file "bpmode-tool.xpm")))
			  ,(find-image (list 
					'(:type xpm :file "bpmode-tool-dis.xpm")))
			  ,(find-image (list 
					'(:type xpm :file "bpmode-tool-dis.xpm")))]
		  :enable bioperl-enabled-buffer-flag
		  )))
  ;; do something else in XEmacs...
  (if bioperl-this-is-xemacs 1 0)
  (setq bioperl-enabled-buffer-flag t)
  (if bioperl-mode-active-on-perl-mode-flag (bioperl-mode) nil))

;; where are you, subr.el?

(unless (boundp 'booleanp)
  (defun booleanp (x)
    "Is it boolean? Let's find out."
    (if (or (equal x t) (equal x nil))
	t
      nil)))

(provide 'bioperl-init)

;;; end bioperl-init.elBioPerl-1.007002/ide/bioperl-mode/site-lisp/bioperl-mode.el000555000766000024     14625413155576320 23522 0ustar00cjfieldsstaff000000000000;; $Id$

;; use multiple paths in bioperl-module-path

;;
;; Bioperl minor (haha!) mode
;; 
;; Author: Mark A. Jensen
;; Email : maj -at- fortinbras -dot- us
;;
;; Part of The Documentation Project
;; http://www.bioperl.org/wiki/The_Documentation_Project

;; Copyright (C) 2009 Mark A. Jensen

;; This program is free software; you can redistribute it and/or
;; modify it under the terms of the GNU General Public License as
;; published by the Free Software Foundation; either version 3 of
;; the License, or (at your option) any later version.

;; This program is distributed in the hope that it will be
;; useful, but WITHOUT ANY WARRANTY; without even the implied
;; warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
;; PURPOSE.  See the GNU General Public License for more details.

;; You should have received a copy of the GNU General Public
;; License along with this program; if not, write to the Free
;; Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
;; Boston, MA 02110-1301 USA

;;
;;
;; TODOs
;;
;;  - compile to byte code
;;
;; issues
;; - missing tool in tool-bar??
;; - xemacs support?
;;
;; Installation
;;
;;  The files bioperl-mode.el, bioperl-skel.el, and bioperl-init.el
;;  should be placed in $EMACS_ROOT/site-lisp, and the .xpm image
;;  files in $EMACS_ROOT/etc/images, then add
;;  (require 'bioperl-mode)
;;  to your .emacs file.
;;
;;  See http://www.bioperl.org/wiki/Emacs_bioperl-mode
;;  for more information.
;;
;; Design Notes
;; 
;; POD content is obtained exclusively by accessing the user's installed
;; Bioperl modules -- so it's as up-to-date as the user's installation.
;;
;; Pod is parsed with a homebrew parser found in pod.el.
;;
;; Much of the parsing in this package depends on the standard form of
;; Bioperl pod; particularly on the typical division into NAME,
;; SYNOPSIS, DESCRIPTION, and APPENDIX sections, and on the fact that
;; pod for individual methods is found in the APPENDIX. There is some
;; dependence on the usual head levels for the headers, but this can
;; be hacked out if necessary.
;;
;; Some attempts at efficiency were made. Parsing pod for methods
;; and associated data can take a while, so parse results are cached
;; for the last module so parsed, and the cache is checked when 
;; method information is requested before parsing again.
;;
;; The Bio/ path is parsed to provide a namespace completion facility
;; The relevant path names and structure is stored in an alist tree
;; called bioperl-module-names-cache. The cache is loaded lazily,
;; so that the directory structure is accessed on a desire-to-know 
;; basis.
;;
;; Lazy loading of the name cache necessitated "programmed completion"
;; of namespace names in prompts. See Programmed Completion in the 
;; info (elisp) node, and the function 
;; bioperl-namespace-completion-function.
;;
;; Skeletons (implemented in the emacs standard package skeleton.el)
;; have been used for template insertions. These are very powerful, if
;; cumbersome, offer plug-in interactor functions, and I think allow
;; more modularity and scope for new additions than (insert)ing text
;; 'by hand'. Skeletons and (define-skeleton) declarations are
;; distributed in a separate file 'bioperl-skel.el', which is loaded
;; when the mode is initialized.
;;                                                                        

(require 'skeleton)
(require 'bioperl-skel)
(require 'bioperl-init)
(require 'pod)

(defconst bioperl-mode-revision "$Id$"
  "The revision string of bioperl-mode.el")

;;
;; User customizations
;;

(defgroup bioperl nil
  "BioPerl templates and documentation access")

(defcustom bioperl-mode-active-on-perl-mode-flag t
  "If set, perl-mode will begin with bioperl-mode active.
Boolean."
  :type 'boolean
  :group 'bioperl)

(defcustom bioperl-mode-safe-flag t
  "If set, bioperl-mode with substitute `exec-path' with `bioperl-safe-PATH'.
Nil means use your current `exec-path'."
  :type 'boolean
  :group 'bioperl)

(defcustom bioperl-safe-PATH '()
  "Safe exec-path for bioperl-mode."
  :type 'sexp
  :initialize 'bioperl-set-safe-PATH
  :group 'bioperl)

(defcustom bioperl-module-path nil
  "Local path to Bioperl modules.
On init, set is attempted by `bioperl-find-module-path' Can indicate multiple search paths; define as PATH in your OS. The environment variable BPMODE_PATH will override everything."
;; better type 'choice; do later
  :type 'string
  :initialize 'bioperl-find-module-path
  :group 'bioperl)

;;
;; Hooks
;;

;;
;; bioperl- namespace variables
;;

(defvar bioperl-method-pod-cache nil
  "Stores the alist returned by the last successful `bioperl-slurp-methods-from-pod' call.
The module filepath represented by the cached info is contained
in `bioperl-cached-module'.")

(defvar bioperl-cached-module nil
  "Contains the module name whose method pod information is
  currently stored in `bioperl-method-pod-cache'.
The value is in double colon format.")

(defvar bioperl-cached-pmfile nil
  "Contains the filepath whose method pod information is
  currently stored in `bioperl-method-pod-cache'.")

(defvar bioperl-module-names-cache '( ("Bio" . nil) )
  "Storage for an alist tree structure of available module names.
Structure follows the Bio library tree:
 ( (\"Bio\" \"Seq\" ( \"SeqIO\" \"fasta\" \"msf\" ...) \"PrimarySeqI\" ...  ) )
Use `bioperl-add-module-names-to-cache' to, well, do it.")

(defvar bioperl-source-file nil
  "Contains the source file of pod being viewed. Buffer-local.
Set in `bioperl-view-full-pod'")

(make-variable-buffer-local 'bioperl-source-file)

(defvar bioperl-source-file-path-component nil
  "Contains the path index (from `bioperl-module-path') for the source file of pod being viewed. Buffer-local.
Set in `bioperl-view-full-pod'")

(make-variable-buffer-local 'bioperl-source-file-path-component)

(defvar bioperl-this-is-xemacs (or (string-match "^XEmacs" (emacs-version)))
  "Flag indicating whether we're in XEmacs.")
       
;;
;; User-interface functions
;;

(defun bioperl-insert-module (namespace module &optional dummy beg pt end)
  "Insert BioPerl module declaration interactively, using completion."
  (interactive
   (let* (
	 (mod-at-pt (bioperl-module-at-point))
	 (beg (if mod-at-pt (match-beginning 0) nil))
	 (pt (point))
	 (end (if mod-at-pt (match-end 0) nil))
	 (cr (bioperl-completing-read mod-at-pt nil nil "[insert] " t) )
	 )
     (if (not (member nil (mapcar 'not cr))) (signal 'quit t))
     (append cr (list beg pt end))
     ))
  (if namespace
      (progn
	(setq namespace (replace-regexp-in-string "::$" "" namespace))
	(let ( 
	      ( mod (apply 'concat 
			   namespace 
			   (if module (list "::" module) '(nil))) )
	      )
	  (if (not beg)
	      (insert mod)
	    (string-match (concat 
			   (buffer-substring beg pt)
			   "\\(.*\\)")
			  mod)
	    (delete-region pt end)
	    (insert (substring mod (match-beginning 1) (match-end 1))))))
    nil))

;;
;; pod viewers
;;

;; TODO: refactor bioperl-view-pod to take separate nmspc mod parms...

(defun bioperl-view-pod (module &optional n)
  "View the full pod for a BioPerl module. Use completion facilities to browse interactively.
MODULE is in double-colon format. N is an index associated with a
component of `bioperl-module-path'."
  (interactive
   (let* (
	 (mod-at-pt (bioperl-module-at-point))
	 (mod (bioperl-completing-read 
	       (if mod-at-pt
		   mod-at-pt
		 (if (and (boundp 'bioperl-source-file) bioperl-source-file)
		     ;; in pod view --
		     (elt (bioperl-perl-from-path bioperl-source-file) 0)
		   nil)) nil t "[pod] "))
	 )
     (if (not (member nil (mapcar 'not mod))) (signal 'quit t))     
     (list (apply 'concat 
		  (elt mod 0) 
		  (if (elt mod 1) (list "::" (elt mod 1)) 
		    (signal 'quit t))) (car (last mod)))))
  (bioperl-view-full-pod module n))

(defun bioperl-view-pod-method (namespace module method &optional n)
  "View desired method pod interactively. Use completion facilities to browse interactively.
N is an index associated with a component of `bioperl-module-path'."
  (interactive 
   (let (
	 (cr (bioperl-completing-read (bioperl-module-at-point) t nil "[pod mth] ") )
	 )
     (if (not (member nil (mapcar 'not cr))) (signal 'quit t))
     cr))
  (if (not method) (signal 'quit t))
  (let (
	( cache-pos (if method (bioperl-assoc-string method bioperl-method-pod-cache t) nil) )
	)
    (if (not cache-pos)
	(message "No such method")
      (bioperl-render-method-pod-from-cons cache-pos))
    ))

(defun bioperl-view-pod-synopsis (module &optional n)
  "View the pod synopsis for a Bioperl module.
N is an index associated with a component of `bioperl-module-path'."
  (interactive
   (let (
	 (mod (bioperl-completing-read (bioperl-module-at-point) nil t "[pod syn] "))
	 )
     (if (not (member nil (mapcar 'not mod))) (signal 'quit t))     
     (list (apply 'concat 
		  (elt mod 0) 
		  (if (elt mod 1) (list "::" (elt mod 1)) 
		    (signal 'quit t) )) (car (last mod)))))
  (bioperl-view-pod-section module "SYNOPSIS" n))

(defun bioperl-view-pod-description (module &optional n)
  "View the pod synopsis for a BioPerl module.
N is an index associated with a component of `bioperl-module-path'."
  (interactive
   (let (
	 (mod (bioperl-completing-read (bioperl-module-at-point) nil t "[pod dsc] " ))
	 )
     (if (not (member nil (mapcar 'not mod))) (signal 'quit t))     
     (list (apply 'concat 
		  (elt mod 0) 
		  (if (elt mod 1) (list "::" (elt mod 1)) 
		    (signal 'quit t))) (car (last mod)))))
  (bioperl-view-pod-section module "DESCRIPTION" n))

(defun bioperl-view-pod-appendix (module &optional n)
  "View the pod appendix (containing individual method information) for a Bioperl module.
N is an index associated with a component of `bioperl-module-path'."
  (interactive
   (let (
	 (mod (bioperl-completing-read (bioperl-module-at-point) nil t "[pod apx] "))
	 )
     (if (not (member nil (mapcar 'not mod))) (signal 'quit t)) 
     (list (apply 'concat 
		  (elt mod 0) 
		  (if (elt mod 1) (list "::" (elt mod 1)) 
		    (signal 'quit t))) (car (last mod)))))
  (bioperl-view-pod-section module "APPENDIX" n))


(defun bioperl-view-pod-parents (module)
  "Browse the pod for BioPerl modules from which MODULE inherits.
MODULE is in double-colon format. Most useful when called from a pod view."
  (unless (and module (stringp module))
    (error "String required at arg MODULE"))
  (if (not module)
      nil
    (let* (
	   (pth-comp (if (boundp 'bioperl-source-file-path-component)
			 bioperl-source-file-path-component nil))
	  (pmfile (bioperl-path-from-perl module nil pth-comp))
	  (parents)
	  (mod)
	  )
      (unless pmfile
	(error "Module specified by MODULE not found in installation"))
      (with-temp-buffer
	(insert-file-contents pmfile)
	(setq parents (bioperl-find-class-parents (current-buffer))))
      (if (not parents)
	  (error "Unable to identify module parents")
	;; create a (degenerate) alist
	(setq parents (mapcar 'list parents))
	(setq mod (completing-read "[pod]: " parents nil t 
				   (if (= (length parents) 1) 
				       (elt parents 0)
				     "Bio::")))
	(if mod
	    (bioperl-view-pod mod pth-comp)
	  nil))
      )))


(defun bioperl-view-source ()
  "Display the file in the variable `bioperl-source-file' in view mode in a new buffer.  
When in bioperl-view-mode, `bioperl-source-file' will contain the
path to the source of the module whose pod is being viewed."
  (interactive)
  (if (not (file-exists-p bioperl-source-file))
      nil
    (let ( (fname bioperl-source-file) 
	   (pth-comp bioperl-source-file-path-component) )
      (set-buffer (generate-new-buffer "*BioPerl Src*"))
      (insert-file fname)
      (perl-mode)
      (bioperl-source-mode)
      (pop-to-buffer (current-buffer))
      (setq bioperl-source-file fname)
      (setq bioperl-source-file-path-component pth-comp))))

(defun bioperl-view-parents ()
  "Browse pod of base classes for the file in `bioperl-source-file' by completion menu.  
When in bioperl-view-mode, `bioperl-source-file' will contain the
path to the source of the module whose pod is being viewed."
  (interactive)
  (if (not (file-exists-p bioperl-source-file))
      nil
    (let (
	  (mod)
	  )
      (mapcar (lambda (x) (setq mod (if mod (concat mod "::" x) x)))
	      (bioperl-perl-from-path bioperl-source-file))
      (bioperl-view-pod-parents mod))))

(defun bioperl-view-parents-this-buffer ()
  "Browse the pod for BioPerl modules from which the current source inherits.
Callable from bioperl-source-mode only."
  (interactive)
  (unless bioperl-source-file
    (error "This function current works in bioperl-source-mode only."))
  (let* (
	 (pth-comp (if (boundp 'bioperl-source-file-path-component)
		       bioperl-source-file-path-component nil))
	 (parents)
	 (mod)
	 )
    (setq parents (bioperl-find-class-parents (current-buffer)))
    (if (not parents)
	(error "Unable to identify module parents")
      ;; create a degenerate alist
      (setq parents (mapcar 'list parents))
      (setq mod (completing-read "[pod]: " parents nil t 
				 (if (= (length parents) 1) 
				     (elt parents 0)
				   "Bio::")))
      (if mod
	  (bioperl-view-pod mod pth-comp)
	nil))))


;; "uninstall..."

(defun bioperl-mode-unload-hook &optional local
  "Remove the perl-mode hook.
If LOCAL is set, remove hook from the buffer-local value of perl-mode-hook."
  (remove-hook 'perl-mode-hook 'bioperl-perl-mode-infect local)
  (if bioperl-this-is-xemacs
        (remove-hook 'cperl-mode-hook 'bioperl-perl-mode-infect local)))


;;
;; Internal functions
;;

;;
;; pod slurpers
;;

(defun bioperl-view-full-pod (module &optional n) 
  "Open the Bioperl POD for the MODULE for viewing in another buffer.
MODULE is in double-colon format."
  (unless (and module (stringp module))
    (error "String required at arg MODULE"))
  (unless (or (not n) (numberp n))
    (error "Number required at arg N"))
  (unless n
    (setq n 0))
  (if (not module)
      nil
    (let (
	  (pod-buf (generate-new-buffer "*BioPerl POD*"))
	  (pmfile (bioperl-path-from-perl module nil n))
	  )
      (unless pmfile
	(error "Module specified by MODULE not found in installation"))
      (save-excursion
	(set-buffer pod-buf)
	(pod-mode)
	(setq header-line-format (concat "POD - BioPerl module " module " @ " 
					 (file-name-squish
					  (elt (split-string bioperl-module-path path-separator) n)) ))
	(insert-file-contents pmfile)
	(pod-parse-buffer (current-buffer))
	(goto-char (point-min))
	(bioperl-view-mode)
	(set (make-local-variable 'bioperl-source-file) pmfile)
	(set (make-local-variable 'bioperl-source-file-path-component) nil)
	;; set the path component
	(let (
	      (i 0) (done 0) (pth-comp (parse-colon-path bioperl-module-path))
	      )
	  (while (and (= done 0) (elt pth-comp i))
	    (if (string-match 
		 (regexp-quote (elt pth-comp i)) bioperl-source-file)
		(setq done 1)
	      (setq i (1+ i))))
	  (if (elt pth-comp i)
	      (setq bioperl-source-file-path-component i)))
	(pop-to-buffer pod-buf))
      )
    ;;return val
    t ))

(defun bioperl-view-pod-section (module section &optional n)
  "Open the Bioperl POD for the module PMFILE for viewing in another buffer.
MODULE is in double-colon format. SECTION is a string; one of
SYNOPSIS, DESCRIPTION, or APPENDIX. N is the index of the desired
component of bioperl-module-path."
  (unless (stringp module)
    (error "String required at arg MODULE"))
  (unless (stringp section) 
    (error "String required at arg SECTION"))
  (unless (member (upcase section) '("SYNOPSIS" "DESCRIPTION" "METHODS" "APPENDIX"))
    (error "SECTION not recognized or handled yet"))
  (unless (or (not n) (numberp n))
    (error "Number required at arg N"))
  (unless n
    (setq n 0))
  (let (
	(pod-buf (generate-new-buffer "*BioPerl POD*"))
	(ret nil)
	(pmfile (bioperl-path-from-perl module nil n))
	)
    (unless pmfile
      (error "Module specified by MODULE not found in installation"))
    (save-excursion
      (set-buffer pod-buf)
      (pod-mode)
      (setq header-line-format (concat section " - BioPerl module " module 
				       " @ " (file-name-squish
					      (elt (split-string bioperl-module-path path-separator) n)) ))
      (insert-file-contents pmfile)
      (pod-parse-buffer (current-buffer) t)
      (goto-char (point-min))
      ;; clip to desired section
      (if (search-forward (concat "== " section) (point-max) t)
	  (progn
	    (beginning-of-line)
	    (delete-region (point-min) (point))
	    (forward-line 1)
	    (search-forward "====" (point-max) 1)
	    (beginning-of-line)
	    (delete-region (point) (point-max))
	    (goto-char (point-min))
	    (while (re-search-forward "^====\\s +\\([a-zA-Z0-9_:()]+\\)\\s +==+" (point-max) t)
	      (replace-match "\\1" nil nil))
	    (goto-char (point-min))
	    (while (re-search-forward "^==\\s +\\([a-zA-Z0-9_:()]+\\)\\s +==+" (point-max) t)
	      (replace-match "  \\1" nil nil))
	    (bioperl-view-mode)
	    (set (make-local-variable 'bioperl-source-file) pmfile)
	    (pop-to-buffer pod-buf)
	    (setq ret t))
	(kill-buffer pod-buf)
	)
    )
    ret ))


(defun bioperl-slurp-methods-from-pod (module &optional n) 
  "Parse pod for individual methods for module MODULE.
MODULE is in double-colon format. N is an index corresponding 
to a component of `bioperl-module-path'.

Returns an associative array of the following form:

 ( METHOD_NAME . ( (PODKEY . CONTENT) (PODKEY . CONTENT) ... )
   METHOD_NAME . ( (PODKEY . CONTENT) (PODKEY . CONTENT) ... )
   ... )

where all elements are strings. The alist is sorted by
METHOD_NAME. METHOD_NAME is the name of the method (without
trailing parens), PODKEY is 'Title', 'Usage', 'Function',
'Returns', 'Args' (these keys are read directly from pod and not
standardized), CONTENT is the text that follows the colon
separating the PODKEY heading from the information (including all
text up until the next 'PODKEY :' line. Newlines are converted to
';' in the content, and whitespace is squished to single
spaces/semicolons.

This function, when successful, also sets the cache vars
`bioperl-method-pod-cache' and `bioperl-cached-module'."
  (unless (stringp module) 
    (error "String required at arg MODULE"))
  (let (
	(pmfile (bioperl-path-from-perl module nil n))
	)
    (unless pmfile
      (error (concat "Module specified by MODULE not found in installation at path component " (number-to-string (if n n 0)) ".\nCheck contents of `bioperl-module-path' and call `bioperl-clear-module-cache'.") ))
    (let (
	(method nil)
	(pod-key nil)
	(content nil)
	(bound nil)
	(data '())
	(data-elt '())
	(data-elt-cdr '())
	(old-exec-path exec-path)
	)
      (with-temp-buffer
	(insert-file-contents pmfile)
	(pod-parse-buffer (current-buffer) t)
	;; clip to desired section
	(goto-char (point-min))
	(if (search-forward "= APPENDIX" (point-max) t)
	    (progn
	      (beginning-of-line)
	      (delete-region (point-min) (point))
	      ;; looking down into appendix
	      ;; 
	      (while (re-search-forward "^==\\s +\\([a-zA-Z0-9_]+\\)" 
					(point-max) t)
		(setq method (match-string 1))
		(setq data-elt (cons method '()))
		;; now we have the current method...
		;; find the boundary of this method's pod
		(save-excursion
		  (setq bound (progn (re-search-forward "^=" 
							(point-max) 1)
				     (beginning-of-line)
				     (point))))
		;; now parse out the guts of this method's pod
		;; getting pod-keys and their content...
		(while (re-search-forward 
			"^\\s +\\([A-Za-z]+\\)\\s *:\\s *\\(.*\\)$"
			bound t)
		  (setq pod-key (match-string 1))
		  (setq content (match-string 2))
		  (save-excursion 
		    (setq content 
			  (concat content 
				  (buffer-substring 
				   (point) (if (re-search-forward "^\\s +[A-Za-z]+\\s *:" bound 1)
					       (progn (beginning-of-line) (point))
					     (point)))))
		    )
		  ;; squeeze whitespace from content
		  (setq content (replace-regexp-in-string "\n+" "!!" content))
		  (setq content (replace-regexp-in-string ";$" "" content))
		  (setq content (replace-regexp-in-string "\\s +" " " content))
		;; here we have, for the current method,
		  ;; the current pod-key and its content...
		  (setq data-elt-cdr (cdr data-elt))
		  (setcdr data-elt (push (cons pod-key content) data-elt-cdr )))
		;; copy the data-elt into the data alist...
		(setq data-elt-cdr (cdr data-elt))
		(push (cons (car data-elt) data-elt-cdr) data))
	      ;; set cache vars
	      (setq bioperl-method-pod-cache 
		    (sort data (lambda (a b) (string-lessp (car a) (car b)))))
	      (setq bioperl-cached-module module)
	      (setq bioperl-cached-pmfile pmfile)
	      ;; return the data alist for this module...
	      bioperl-method-pod-cache )
	  ;; the APPENDIX was not found...return nil
	  nil ) ))))

;;
;; list getters
;;

(defun bioperl-method-names (module &optional as-alist n) 

  "Returns a list of method names as given in the pod of MODULE. 
MODULE is in double-colon format. If AS-ALIST is t, return an
alist with elts as (NAME . nil). N is an index associated with a 
component of `bioperl-module-path'.

This function looks first to see if methods for MODULE are
already loaded in `bioperl-method-pod-cache'; if not, calls
`bioperl-slurp-methods-from-pod'."
  (unless (stringp module) 
    (error "String required at arg MODULE"))
  (unless (bioperl-path-from-perl module nil n)
    (error "Module specified by MODULE not found in installation"))
  ;; check the cache; might get lucky...
  (let ( (ret) ) 
    (setq ret 
	  (if (string-equal module bioperl-cached-module)
	      (progn
		(mapcar 'car bioperl-method-pod-cache)
		;; path handling...
		)
	    (mapcar 'car (bioperl-slurp-methods-from-pod module n)))) 
    ;; fix alist for path handling??
    (if as-alist
	(mapcar (lambda (x) (list x nil)) ret)
      ret)))


(defun bioperl-module-names (module-dir &optional retopt as-alist)
  "Returns a list of modules contained in the directory indicated by MODULE-DIR.
MODULE-DIR is in double-colon format.  Optional RETOPT: nil,
return module names only (default); t, return directory names
only; other, return all names as a flat list. Optional AS-ALIST:
if t, return an alist with elts (NAME . PATH_STRING) (when used in 
completing functions). This function checks all paths specified
in `bioperl-module-path'.


 This function is responsible for the lazy loading of the module
names cache: it will look first in `bioperl-module-names-cache';
if the MODULE-DIR is not available,
`bioperl-add-module-names-to-cache' will be called."
  (let* (
	(module-components (split-string module-dir "::" t))
	(unlist (lambda (x) (if (listp x) (car x) x)) )
	(choose-dirs (lambda (x) (if (listp (cdr x)) x nil)) )
	(choose-mods  (lambda (x) (if (listp (cdr x)) nil x)) )
	(ret) (i)
	(pths (split-string bioperl-module-path path-separator))
	(alists) (alist)
	)
    ;; add to cache
    (setq i 0)
    (while (< i (length pths))
      (bioperl-add-module-names-to-cache module-dir i)
      (setq i (1+ i)))
    ;; search
    (setq alists (deep-assoc-all module-components bioperl-module-names-cache))
    ;; here pick the directory alist
    (setq alist (if (stringp (cdr (elt alists 0)))
		    (elt alists 1) (elt alists 0)))
    (if (and alist (cdr alist))
	(cond 
	 ( (not (booleanp retopt))
	   (if (stringp (cdr alist))
	       (setq ret alist)
	     (setq ret (cdr alist))))
	 ((not retopt)
	   (if (stringp (cdr alist))
	       (setq ret alist)
	     (setq ret (delete nil (mapcar choose-mods (cdr alist))))
	     ))
	 ( retopt
	   (if (stringp (cdr alist))
	       (setq ret nil)
	     (setq ret (delete nil (mapcar choose-dirs (cdr alist))))
	     ))))
    (if (not ret)
	nil
      (if (not as-alist) 
	  (if (stringp (cdr ret))
	      (car ret)
	    (mapcar 'car ret))
	ret))))


;;
;; directory slurpers
;;

(defun bioperl-add-module-names-to-cache (module-dir &optional n)
  "Add alists to `bioperl-module-names-cache'.
MODULE-DIR is in double colon format. Allows for lazy build of
the cache.  Returns t if we added anything, nil if not. N is the index
of the desired bioperl-module-path component.

Cache alist format:
 ( \"Bio\" . 
   ( (MODULE_NAME PATH_INDEX_STRING) ...        ; .pm file base names
     (DIRNAME . nil) ...           ; dirname read but not yet followed
     (DIRNAME . ( ... ) ) ... )    ; dirname assoc with >=1 level structure
 )	      
"				     
 
  (unless (and module-dir (stringp module-dir))
    (error "String required at arg MODULE-DIR"))
  (unless (or (not n) (numberp n))
    (error "Number required at arg N"))
  (unless n
    (setq n 0))
  (if (and (> n 0) (> n (1- (length (split-string bioperl-module-path path-separator)))))
      (error "Path index out of bounds at arg N"))
  (let* (
	(pth (bioperl-path-from-perl module-dir 1 n))
	(module-components (split-string module-dir "::" t))
	(module-string)
	(modules)
	(alist)
	(cache (deep-assoc-all module-components bioperl-module-names-cache))
	(cache-pos)
	(keys)
	(this-key)
	(good-keys)
	(ret)
       )
    (if (not pth)
	;; no path returned for module-dir...
	nil
      (setq cache-pos 
	    (cond
	     ((not cache)
	      nil)
	     ((stringp (cdr (car cache)))
	      (elt cache 1))
	     ( t
	       (elt cache 0))))
      (if cache-pos ;; something there
	  ;; easy - a stub
	  (if (null (cdr cache-pos))
	      (progn 
		(setcdr cache-pos (bioperl-slurp-module-names module-dir n))
		(setq ret t))
	      ;; less hard - branch exists
	    (let* ( 
		   (mod-alist (bioperl-slurp-module-names module-dir n))
		   (mod-alist-keys (mapcar 'car mod-alist))
		   (cache-item) (key)
		   )
	      (while (setq key (pop mod-alist-keys))
		(setq alist (assoc-all key cache-pos))
		(setq cache-item (if (stringp (cdr (elt alist 0))) 
				     (elt alist 0) (elt alist 1)))
		(if (null cache-item)
		    (if alist
			nil
		    ;; create a new list member(s)
		      (setcdr cache-pos (append (cdr cache-pos) 
						(assoc-all key mod-alist))))
		  ;; 
		  (if (member n (mapcar 'string-to-number (split-string (cdr cache-item) path-separator)))
		      ;; deja vu
		      (setq mod-alist-keys nil) ;; fall-through
		    (setcdr cache-item (concat (cdr (bioperl-assoc-string key mod-alist t)) path-separator (cdr cache-item)))
		    (setq ret t))))
	      ))

	;; hard - branch dne
	(setq keys module-components)
	(while (
		let ( (da (deep-assoc-all 
			   (append (reverse good-keys) (list (car keys))) 
			   bioperl-module-names-cache) ) )
		 (setq da (if (stringp (elt da 0)) (elt da 1) (elt da 0)))
		 (car da) );; has a member whose cdr is a list 
	  (setq good-keys (push (car keys) good-keys))
	  (setq keys (cdr keys)))
	(push (pop good-keys) keys)
	(setq good-keys (nreverse good-keys))
	;; keys contains the directories we need to add, in order
	;; address for doing additions: cache-pos
	(setq alist (deep-assoc-all good-keys bioperl-module-names-cache))
	(setq cache-pos 
	      (if (stringp (cdr (elt alist 0))) (elt alist 1) (elt alist 0)))
	(setq module-string (pop good-keys))
	;; prep for bioperl-anastomose
	(while good-keys
	  (setq module-string (concat module-string "::" (pop good-keys))))
	;; module-string is suitable for passing to bioperl-slurp-module-names
	(setq ret (bioperl-anastomose keys module-string cache-pos n)))
      )
    ret ))

(defun bioperl-anastomose (keys module-string cache-pos n)
  "Extends `bioperl-module-names-cache' recursively. No user-serviceable parts inside.
Call first CACHE-POS set to node to be extended.
MODULE-STRING must indicate directory corresponding to CACHE-POS."
  (unless cache-pos
    (setq cache-pos bioperl-module-names-cache))
  (if (not keys)
      t ; success
    (let (
	  (this-key (pop keys))
	  (modules)
	  (cache-ins-pos)
	  (alist)
	  )
      (setq alist (assoc-all this-key cache-pos))
      (setq cache-ins-pos (if (stringp (cdr (elt alist 0))) (elt alist 1) (elt alist 0)))
      (setq module-string (if module-string 
			      (concat module-string "::" this-key) 
			    this-key))
      (setq modules (bioperl-slurp-module-names module-string n))
      (if (not modules)
	  nil ; fail
	(let ( (cache-item) (uniq-modules) )
	  (while (setq cache-item (pop modules))
	    (if (or (null (cdr cache-ins-pos)) (not (member cache-item (cdr cache-ins-pos))))
		(push cache-item uniq-modules)))
	  (setcdr cache-ins-pos (append (cdr cache-ins-pos) uniq-modules )))
	(bioperl-anastomose keys module-string (cdr cache-ins-pos) n)
	t))))
	

(defun bioperl-slurp-module-names (module-dir &optional n)
  "Return list of the  basenames for .pm files contained in MODULE-DIR.
MODULE-DIR is in double-colon format. N is the index of the desired 
bioperl-module-path component.

Return is a list of the form

 ( (MODULE_NAME . PATH_INDEX_STRING) ... 
   (DIR_NAME . nil) ... )
"
  (unless (and module-dir (stringp module-dir))
    (error "String required at arg MODULE-DIR"))
  (unless (or (not n) (numberp n))
    (error "Number required at arg N"))
  (unless n
    (setq n 0))
  (let (
	(module-path (split-string bioperl-module-path path-separator))
	(pth (bioperl-path-from-perl module-dir 1 n))
	(modules)
	(fnames)
	(choose-dirs (lambda (x) (if (listp (cdr x)) x nil)) )
	(nmspc-only t)
       )
    (if (and (> n 0) (> n (1- (length module-path))))
	(error "Path index out of bounds at arg N"))
    ;; following (elt ... 0) checks if pth is dir or symlink:
    ;;  possible bug...
    (if (and pth (elt (file-attributes pth) 0))
	(progn
	  (setq fnames (directory-files pth))
	  (while fnames 
 	    (let ( (str (pop fnames)))
	      ;; files - conses with path-index cdr
	      (if (string-match "\\([a-zA-Z0-9_]+\\)\.pm$" str)
		  (progn
		    (push (cons (match-string 1 str) 
				(number-to-string n))  modules)
		    (setq nmspc-only nil)))
	      ;; directories - conses with nil cdr
	      (if (string-match "^\\([a-zA-Z0-9_]+\\)$" str)
		  (if (not (string-equal (match-string 1 str) "README")) (push (cons (match-string 1 str) nil) modules)))
	      ))
;; 	  (if nmspc-only
;; 	      (let ( (dirs (delete nil (mapcar choose-dirs modules)))
;; 		     (module-dir-next) )
;; 		(while dirs
;; 		  (setq module-dir-next (concat module-dir "::" (car (pop dirs))))
;; 		  (append modules (bioperl-slurp-module-names module-dir-next n)))))
	  (if (not modules)
	      nil
	    modules))
      nil)))

;;
;; string converters and finders
;;

(defun bioperl-find-class-parents (buf)
  "Look in the current buffer for parent classes to the displayed module.
Searches for 'use base' and @ISA statements in buffer
BUF. Returns a list of BioPerl modules in double colon
format. Will probably fail (not dismally) if multiple packages
are present in a single module file."
  ;; how? by searching for 
  ;; use base STUFF
  ;; @ISA = STUFF
  ;; push @ISA, STUFF
  (unless (or (bufferp buf) (stringp buf))
    (error "Require buffer or buffer name at BUF"))
  (let (
	(retmods)
	)
    (save-excursion
      (set-buffer buf)
      (goto-char (point-min))
      ;; search for 'use base'...
      (let* (
	     (beg (re-search-forward "use base " (point-max) t))
	     (end (if beg (re-search-forward ";" (point-max) t) nil))
	     (txt (if beg (buffer-substring-no-properties beg (1- end)) nil))
	     (toks)
	     )
	(if (not txt)
	    nil
	  (setq txt (replace-regexp-in-string "\n" " " txt))
	  (setq txt (replace-regexp-in-string "\\(?:qw[\[\(\{\|][ \f\t\n\r\v]?\\)" "" txt))
	  (setq txt (replace-regexp-in-string "[](){}'\"]" "" txt))
	  (setq toks (split-string txt "[ \f\t\n\r\v]+" t))
	  (mapcar (lambda (x) (push x retmods)) toks) ))
      ;; search for @ISA
      ;; ISA set needs to search over multi lines
      ;; look at Bio::
      (goto-char (point-min))
      (let* (
	     (beg (re-search-forward "@ISA\s?[,=]\s?" (point-max) t))
	     (end (if beg (re-search-forward ";" (point-max) t) nil))
	     (txt (if beg (buffer-substring-no-properties beg (1- end)) nil))
	     (toks)
	     (pass 1)
	     )
	(while (<= pass 2)
	  (if (not txt)
	      (setq pass (1+ pass))
	    (setq txt (replace-regexp-in-string "\n" " " txt))
	    (setq txt (replace-regexp-in-string "\\(?:qw[\[\(\{\|][ \f\t\n\r\v]?\\)" "" txt))
	    (setq txt (replace-regexp-in-string "[](){}'\"]" "" txt))
	    (setq toks (split-string txt "[ \f\t\n\r\v]+" t))
	    (mapcar (lambda (x) (push x retmods)) toks) 
	    (setq pass (1+ pass)))
	  (setq beg (re-search-forward "@ISA\s?[,=]\s?" (point-max) t))
	  (setq end (if beg (re-search-forward ";" (point-max) t) nil))
	  (setq txt (if beg (buffer-substring-no-properties beg (1- end)) nil))
	  )))
      ;; filter for fully-qualified Bio:: modules...
      (setq retmods 
	    (delete nil (mapcar 
			 (lambda (x) (if (string-match "^Bio::" x) x nil)) 
		       retmods)))
    (nreverse retmods) ))

(defun bioperl-module-at-point ()
  "Look for something like a module identifier at point, and return it."
  (interactive)
  (let (
	(found (thing-at-point-looking-at "Bio::[a-zA-Z0-9_:]+"))
	(module nil)
	(pth nil)
	)
    (if (not found) 
	nil
      (setq module (apply 'buffer-substring (match-data)))
      module)))

(defun bioperl-find-module-at-point (&optional n)
  "Look for something like a module declaration at point, and return a filepath corresponding to it.
N is the index of the desired bioperl-module-path component."
  (interactive)
  (unless (or (not n) (numberp n))
    (error "Number required at arg N"))
  (unless n
    (setq n 0))
  (unless bioperl-module-path
      (error "bioperl-module-path not yet set; you can set it with bioperl-find-module-path"))
  (let ( 
	(module-path (elt (split-string bioperl-module-path path-separator) n))
	(found) (module) (pth)
	)
    (if (and (> n 0) (> n (1- (length module-path))))
	(error "Path index out of bounds at arg N"))
    (unless (file-exists-p (concat module-path "/Bio"))
      (error (concat "Bio modules not present in path component" module-path )))
    (setq found (thing-at-point-looking-at "Bio::[a-zA-Z0-9_:]+"))
    (if (not found) 
	nil
      (setq module (apply 'buffer-substring (match-data)))
      (setq pth (bioperl-path-from-perl module n)))
    pth))

(defun bioperl-perl-from-path (pth)
  "Return a list (namespace module) represented by the path in PTH.
Returns nil if the path can't be parsed reasonably. namespace is returned
in double colon format."
  (unless pth
    nil)
  (let (
	(pth-components) (nmspc "Bio") (mod) (pc)
	)
    (setq pth (replace-regexp-in-string "\\\\" "/" pth))
    (setq pth-components (split-string pth "/"))
    (while (and pth-components (not (string-equal "Bio" (pop pth-components))))
      nil)
    (if (not pth-components) 
	nil
      (while pth-components
	(setq pc (pop pth-components))
	(if (string-match "\\([a-zA-Z0-9_]+\\)\.pm" pc)
	    (setq mod (match-string 1 pc))
	  (setq nmspc (concat nmspc "::" pc))))
      (list nmspc mod))
    ))

(defun bioperl-path-from-perl (module &optional dir-first n) 
  "Return a path to the module file represented by the perl string MODULE.
Returns nil if no path found. If DIR-FIRST is t, return a
directory over a .pm file if there is a choice. If DIR-FIRST is
not t or nil, return a directory only. N is an integer, indicating the
desired member of bioperl-module-path to search."
  (unless bioperl-module-path
    (error "bioperl-module-path not yet set; you can set it with bioperl-find-module-path"))
  (unless (stringp module)
    (error "string arg required at MODULE"))
  (unless (or (not n) (numberp n))
    (error "number arg required at N"))
  ; default
  (unless n
    (setq n 0))
  (let (
	(module-path (elt (split-string bioperl-module-path path-separator) n))
	(module-components (split-string module "::" t))
	(pth)
	(dir (if (not (boundp 'dir-first)) nil dir-first))
	)
    (if (and (> n 0) (> n (1- (length module-path))))
	(error "Path index out of bounds at arg N"))
    (unless (file-exists-p (concat module-path "/Bio"))
      (error (concat "Bio modules not present in path component " module-path)))
    (setq module-components (split-string module "::" t))
    ;; unixize...
    (setq pth (replace-regexp-in-string "\\\\" "/" module-path))
    
    (while (not (null module-components))
      (setq pth (concat pth "/" (car module-components)))
      (setq module-components (cdr module-components)))
    (if (not (booleanp dir))
	(if (file-exists-p pth)
	    t
	  (setq pth nil))
      (if (and dir (file-exists-p pth))
	  t
	(if (file-exists-p (concat pth ".pm"))
	    (setq pth (concat pth ".pm"))
	  (if (file-exists-p pth)
	      t
	    (setq pth nil)))))
    pth))

(defun bioperl-split-name (module &optional dir-first n)
  "Examine MODULE and return a list splitting the argument into an existing namespace and module name.
MODULE is in double-colon format. This checks existence as well,
and returns nil if no split corresponds to an existing file. The
algorithm uses `bioperl-path-from-perl' to do its tests.  Default
behavior is to return (namespace module) if there is a choice.
If DIR-FIRST is t, return (namespace nil) over (namespace module)
if there is a choice. If DIR-FIRST is not t or nil, return only
\(namespace nil) or nil.

Finally, if the namespace portion of MODULE exists, but the module
 specified by MODULE does not, (namespace nil) is returned.
N specifies the index of the desired bioperl-module-path component. "

  (unless (or (not module) (stringp module))
    (error "String arg required at MODULE"))
  (unless (or (not n) (numberp n))
    (error "Number required at arg N"))
  (unless n
    (setq n 0))
  (if (not module)
      (list nil nil)
    (if (not (string-match "^Bio" module))
	nil
      ( let (
	     (module-path (elt 
			   (split-string bioperl-module-path path-separator) n))
	     (nmspc) (mod) (pmfile) 
	     )
	(if (and (> n 0) (> n (1- (length module-path))))
	    (error "Path index out of bounds at arg N"))
	(if (not (string-match "::\\([a-zA-Z0-9_]+\\)$" module))
	    (setq nmspc module)
	  (setq mod (match-string 1 module))
	  (setq nmspc (substring module 0 (- (match-beginning 1) 2))))
	(cond
	 ( (not (booleanp dir-first))
	   (if (bioperl-path-from-perl module dir-first n)
	       (list module nil)
	     (list (concat "*" module) nil)) )
	 ( t 
	   (setq pmfile (bioperl-path-from-perl module dir-first n))
	   (if pmfile
	       (if (string-match "\.pm$" pmfile)
		   (list nmspc mod)
		 (list module nil))
	     (if dir-first
		 (progn (setq nmspc (concat nmspc "::" mod))
			(setq mod nil)))
	     (if (bioperl-path-from-perl nmspc 1 n)
		 (list nmspc (concat "*" mod))
	       (list (concat "*" nmspc) nil))
	     ))) 
	))))

(defun bioperl-render-method-pod-from-cons (cons)
  "Create a view buffer containing method pod using a member of the `bioperl-method-pod-cache' alist.

CONS has the form 

 ( METHOD_NAME . ( ( POD_TAG . CONTENT) (POD_TAG . CONTENT) ... ) ). 

The module name for this method is assumed to be present in
`bioperl-cached-module'"
  (unless (listp cons)
    (error "List required at arg CONS"))
  (if (not cons) 
      nil
    (let* ( 
	  (module bioperl-cached-module)
	  (method (car cons))
	  (content (cdr cons))
	  ;; reverse below is a sort-of kludge
	  (tags (if content (reverse (mapcar 'car content)) nil))
	  (cur-tag nil)
	  (cur-content nil)
	  (pod-buf (generate-new-buffer "*BioPerl POD*"))
	  )
      (if (not content)
	  (message "No pod available")
	(save-excursion
	  (set-buffer pod-buf)
	  (pod-mode)
	  (setq header-line-format (concat "Method " method 
					   "() - BioPerl module " module
					   " @ " 
					   (file-name-squish
					    (elt (split-string bioperl-module-path path-separator) n))))
	  (insert "  " method)
	  (insert "\n")
	  (while (setq cur-tag (pop tags))
	    (setq cur-content (cdr (bioperl-assoc-string cur-tag content t)))
	    (setq cur-content (replace-regexp-in-string "!!$" "\n" cur-content))
	    (setq cur-content (replace-regexp-in-string "!!" 
							"\n             " cur-content))
	    (insert "    " cur-tag)
	    (insert-char ?  (- 8 (length cur-tag)))
	    (insert ": " cur-content))
	  (goto-char (point-min))
	  (bioperl-view-mode)
	  (set (make-local-variable 'bioperl-source-file) bioperl-cached-pmfile)
	  (pop-to-buffer pod-buf)))
      )))

;; 
;; completion tricks
;;

;; TODO: modularize...
(defun bioperl-completing-read (initial-input &optional get-method dir-first prompt-prefix no-retry)
  "Specialized completing read for bioperl-mode.
INITIAL-INPUT is a namespace/module name in double-colon format,
or nil. Returns a list: (namespace module path-string) if GET-METHOD is nil,
\(namespace module method path-string) if GET-METHOD is t. DIR-FIRST is
passed along to `bioperl-split-name'; controls what is returned
when a namespace name is also a module name (e.g., Bio::SeqIO).
If NO-RETRY is nil, the reader works hard to return a valid entity;
if t, the reader barfs out whatever was finally entered."
  (let ( (parsed (bioperl-split-name initial-input dir-first)) 
	 (nmspc) (mod) (mth) (pthn) (name-list)
	 (done nil))
    (if (not parsed)
	nil
      (setq nmspc (elt parsed 0))
      (setq mod (elt parsed 1)))
    (while (not done)
      ;; namespace completion
      (unless (and nmspc (not (string-match "^\*" nmspc)))
	(cond 
	 ( (not nmspc) nil )
	 ( (string-match "^\*" nmspc)
	   (setq initial-input (replace-regexp-in-string "^\*" "" nmspc))))
	(setq nmspc (completing-read 
		     (concat prompt-prefix "Namespace: ")
		     'bioperl-namespace-completion-function
		     nil (not no-retry) (or initial-input "Bio::")) )
	(if (or (string-equal nmspc "Bio") (not (string-equal nmspc "")))
	    t
	  ;; back up
	  (setq nmspc 
		(if (string-match ":" nmspc)
		    (car (split-string nmspc "::[^:]+$"))
		  nil))
	  (setq done nil)))
      ;; module completion
      (if (or (not nmspc)
		  (and mod (not (string-match "^\*" mod))))
	  (setq done t)
	(let (
	      ;; local vars here
	      )
	  (setq name-list (bioperl-module-names nmspc nil t))
	  (setq mod (completing-read 
		     (concat prompt-prefix nmspc " Module: ")
		     name-list nil (not no-retry)
		     (if mod (replace-regexp-in-string "^\*" "" mod) nil)))
	  ;; allow a backup into namespace completion
	  (if (or no-retry (not (string-equal mod "")))
	      (setq done t)
	    ;; retry setup
	    ;; try again, backing up
	    (setq done nil)
	    (let ( (splt (bioperl-split-name nmspc nil)) )
	      (if (elt splt 1)
		  (progn
		    (setq nmspc (elt splt 0))
		    ;; kludge : "pretend" mod is not found using the "*"
		    (setq mod (concat "*" (elt splt 1))))
		(setq nmspc (concat "*" nmspc))
		(setq mod nil)))
	    (setq initial-input nmspc))))
      ;; path completion
      (unless (or (not (and nmspc mod)) (not done) no-retry)
	(if (not name-list)
	  (setq name-list (bioperl-module-names 
			   nmspc nil t)))
	(setq pthn (cdr (bioperl-assoc-string mod name-list t)))
	(if (not pthn) 
	    (error "Shouldn't be here(1). Check `bioperl-module-path' and try running `bioperl-clear-module-cache'."))
	(if (not (string-match path-separator pthn))
	    ;; single path 
	    (setq pthn (string-to-number pthn))
	  ;; multiple paths (e.g., "0;1") - do completion
	  (let* (
		 (module-path 
		  (split-string bioperl-module-path path-separator))
		 (pthns (mapcar 'string-to-number
				(split-string pthn path-separator)))
		 (i -1)
		 (module-path-list 
		  (mapcar 
		   (lambda (x) (setq i (1+ i)) (list x i) )
		   module-path))
		 )
	    ;; filter list by pthns
	    (setq module-path-list
		  (delete nil (mapcar 
			       (lambda (x) (if (member (elt x 1) pthns) x nil))
			       module-path-list)))
	    (if (not module-path-list)
		(error "Shouldn't be here(2). Run `bioperl-clear-module-cache' and try again"))
	    (setq pthn (completing-read 
			(concat prompt-prefix nmspc "::" mod " Lib: ")
			module-path-list
			nil t (car (car module-path-list))))
	    (if (string-equal pthn "")
		(setq pthn (car (car module-path-list))))
	    (setq pthn (elt (bioperl-assoc-string pthn module-path-list t) 1))
	    )))
      ;; method completion
      (setq nmspc (replace-regexp-in-string "::$" "" nmspc))
      (unless (or (not done) (not (and nmspc mod)) (not get-method))
	;; path completion if necessary
	(if pthn
	    t
	  (setq pthn (cdr (bioperl-module-names nmspc nil t)))
	  (if (not (string-match path-separator pthn))
	      ;; single path
	      (setq pthn (string-to-number pthn))
	    ;; multiple paths (e.g., "0;1") - do completion
	    (let* (
		   (module-path 
		    (split-string bioperl-module-path path-separator))
		   (pthns (mapcar 'string-to-number
				  (split-string pthn path-separator)))
		   (i -1)
		   (module-path-list 
		    (mapcar 
		     (lambda (x) (setq i (1+ i)) (list x i) )
		     module-path))
		   )
	      ;; filter list by pthns
	      (setq module-path-list
		    (delete nil (mapcar 
				 (lambda (x) (if (member (elt x 1) pthns) x nil))
				 module-path-list)))
	      (if (not module-path-list)
		  (error "Shouldn't be here(3). Run `bioperl-clear-module-cache' and try again"))
	      (setq pthn (completing-read 
			  (concat prompt-prefix "Lib: ")
			  module-path-list
			nil t (car (car module-path-list))))
	      (if (string-equal pthn "")
		  (setq pthn (car (car module-path-list))))
	      (setq pthn (elt (bioperl-assoc-string pthn module-path-list t) 1))
	      )
	    ))
	(setq name-list (bioperl-method-names (concat nmspc "::" mod) t pthn))
	(let (
	      ;; local vars here...
	      )
	  (setq mth (completing-read
		     (concat prompt-prefix "Method in " nmspc "::" mod ": ")
		     name-list nil (not no-retry)))
	  (if (or no-retry (not (string-equal mth "")))
	      (setq done t)
	    ;; retry setup
	    ;; allow a backup into module completion
	    (setq done nil)
	    (let ( 
		  (splt (bioperl-split-name (concat nmspc "::" mod) nil pthn))
		  )
	      (setq nmspc (elt splt 0))
	      ;; kludge : "pretend" mod is not found using the "*"
	      (setq mod (concat "*" (elt splt 1))))))
	))
    ;; return values
    (if get-method
	(list nmspc mod mth pthn)
      (list nmspc mod pthn)) ))

(defun bioperl-namespace-completion-function (str pred flag)
  "A custom completion function for bioperl-mode.
Allows the lazy build of the `bioperl-module-names-cache' via `bioperl-make-collection' and `bioperl-module-names'."
  (if (not pred) 
      (setq pred 
	    (lambda (x) (setq x (if (listp x) (car x) x) ) (if (string-match "[a-zA-Z0-9_:]+" x) t nil))
	    ))
  (let (
	( collection (if (string-equal str "") '(("Bio" . nil )) (bioperl-make-collection str t)) )
	)
    ;; offer the right collection:
    ;; if collection was set, the str was complete and valid
    ;; if not, back up to the last :: in str (see str-trunc in above
    ;; let) and try again
   
    (if (not collection) 
	nil
      (setq collection (sort collection (lambda (x y) (string< (car x) (car y)))))
      (cond
       ((not (booleanp flag)) ;; 'lambda' or test-completion option
	;; this is a back-compat issue: emacs 21 will send 'lambda', 
	;; but doesn't have 'test-completion
	;;
	;; Note without test-completion, weird completion bugs can crop
        ;; up -- best upgrade to 22--
	(if (condition-case nil
		(symbol-function 'test-completion)
	      ('error nil))
	    (test-completion str collection pred)
	  collection
	  (try-completion str collection pred))
	)
       ( (not flag) ;; try-completion option
	   (try-completion str collection pred)
	   )
       ( flag ;; all-completion option
	   (all-completions str collection pred)
	   )
       ))))

(defun bioperl-make-collection (module-dir &optional retopt)
  "Create a completion collection for MODULE-DIR.
MODULE-DIR is in double-colon format, possibly with two trailing
colons.  RETOPT is as for `bioperl-module-names'.

This function searches all paths specified in
`bioperl-module-path'."

  ;; handle the boundary
  (if (or (not module-dir) (not (string-match ":" module-dir)))
      '(("Bio") ("Bio::"))
    (setq module-dir (progn (string-match "^\\([a-zA-Z0-9_:]+[^:]\\):*$" module-dir)
			    (match-string 1 module-dir)))
    (let* (
	   ( dirs (bioperl-module-names module-dir retopt t) )
	   ( modules (split-string module-dir "::" t) )
	   ( complet ) 
	   )

      ;; check once and recalc
      (if (not dirs)
	  (progn 
	    ;; trim back to last ::
	    (setq module-dir
		  (progn 
		    (string-match  "^\\(\\(?:[a-zA-Z0-9_]+::\\)+\\)\\(?::*\\|[a-zA-Z0-9_]*\\)$" module-dir) 
		    (match-string 1 module-dir)))
	    (setq dirs (bioperl-module-names module-dir retopt t))
	    (setq modules (split-string module-dir "::" t))
	    ))
      (if (not dirs)
	  ;; fail
	  nil
	(setq complet (let* ( (l modules)
			      (m (list (pop l))) )
			(while l (push (concat (car m) "::" (pop l)) m))
			(mapcar (lambda (x) (cons x nil)) m ) ))
	;; make sure module-dir is trimmed
	(setq module-dir (replace-regexp-in-string "::$" "" module-dir))
	complet
	(append complet (mapcar (lambda (x) 
				  (list
				   (concat module-dir "::" (car x)) 
				   (cdr x))) dirs))
	))
      ))

;;
;; utilities
;;

(defun bioperl-clear-module-cache ()
  (interactive)
  "Clears the variable `bioperl-module-names-cache'. Run if you change `bioperl-module-path'."
  (setq bioperl-module-names-cache nil)
  (setq bioperl-module-names-cache '(("Bio"))))

; XEmacs compability for assoc-string (from http://web.mit.edu/shutkin/MacData_1124b/afs/athena/contrib/xemacs/share/xemacs-packages/lisp/calendar/cal-compat.el):
; thanks Adam
(if (fboundp 'assoc-string)
    (defalias 'bioperl-assoc-string 'assoc-string)
  (defun bioperl-assoc-string (key list case-fold)
    (if case-fold
        (bioperl-assoc-ignore-case key list)
      (assoc key list)))  
  )


;;
;; utilities (out of bioperl- namespace)
;;

    
(defun assoc-all (key alist &optional ret)
  "Return list of *pointers* (like assoc) to all matching conses in the alist.
Uses `bioperl-assoc-string' for case control."
  (let ( (c (bioperl-assoc-string key alist t)) ) 
    (if c 
	(assoc-all key (cdr alist) (if ret (add-to-list 'ret c t) (list c)))
      ret)))

(defun deep-assoc (keys alist)
  "Return the associations of a set of keys in an alist tree.
Uses `bioperl-assoc-string' for case control."
  (cond
   ((not keys) 
    nil)
   ((not (listp alist))
    nil)
   ((= (length keys) 1)
    (bioperl-assoc-string (pop keys) alist t))
   (t
    (let* ( (key (pop keys))
	    (newlist (bioperl-assoc-string key alist t)) ) 
      (if newlist
	  (deep-assoc keys (cdr newlist))
	(deep-assoc nil nil)))
    )))

(defun deep-assoc-all (keys alist)
  "Return all associations AT THE TIP described by the set of KEYS in an alist tree.
So this is not completely general, but is specialized to the structure of `bioperl-module-names-cache'."
  (cond
   ((not keys) 
    nil)
   ((not (listp alist))
    nil)
   ((= (length keys) 1)
    (assoc-all (pop keys) alist))
   (t
    (let* ( (key (pop keys))
	    (newlist (assoc-all key alist)) ) 
      (if newlist
	  (let ( ( i 0 ) (r)  )
	    (while (< i (length newlist))
	      (if (listp (cdr (elt newlist i)))
		  (setq r (deep-assoc-all keys (cdr (elt newlist i)))))
	      (setq i (1+ i)))
	    r)
	(deep-assoc-all nil nil)))
    )))


(defun pm-p (x)
  (not (null (string-match "[.]pm\$" x))))

(defun split-string-compat (str &optional sep omit-nulls)
  "`split-string' for 21"
  (if omit-nulls
      (delete nil (mapcar (lambda (x) (if (string-equal x "") nil x)) (split-st\
ring str sep)))
    (split-string str sep)))

(defun file-name-squish (fname)
  "Squish long file names with central elipses.
FNAME is the file name as string. Doesn't work very hard."
  (let* (
	 (fname-list (split-string fname "/"))
	 (squished)
	 )
    (if (> (length fname-list) 3)
	(concat (elt fname-list 0) "/" 
		(elt fname-list 1) "/"
		(if (= (length fname-list) 4) (elt fname-list 2)  "...")
		"/"
		(car (last fname-list)))
      fname)))

;; XEmacs compatibility

(defun bioperl-assoc-ignore-case (key alist)
  "Like `assoc', but assume KEY is a string and ignores case when comparing.
This version allows alist cars to be strings and not necessarily lists."
  (setq key (downcase key))
  (let (element)
    (while (and alist (not element))
      (if (equal key (downcase
		      (if (listp (car alist)) (car (car alist)) (car alist))))
	  (setq element (car alist)))
      (setq alist (cdr alist)))
    element))

;; hook into perl-mode

(add-hook 'perl-mode-hook 'bioperl-perl-mode-infect)
(if bioperl-this-is-xemacs
    (add-hook 'cperl-mode-hook 'bioperl-perl-mode-infect))

(provide 'bioperl-mode)




;;; end bioperl-mode.el
  
  
;;
;; scratch area
;;
(unless nil






)
BioPerl-1.007002/ide/bioperl-mode/site-lisp/bioperl-skel.el000555000766000024      2607413155576320 23511 0ustar00cjfieldsstaff000000000000;; $Id$

;;
;; Template insertion skeletons for Bioperl minor mode
;;
;; Author: Mark A. Jensen
;; Email : maj -at- fortinbras -dot- us
;;
;; Part of The Documentation Project
;; http://www.bioperl.org/wiki/The_Documentation_Project
;;
;; This file is loaded upon bioperl-mode initialization
;; 
;; templates based on bioperl.lisp by Heikki Lehvaslaiho
;;

;; Copyright (C) 2009 Mark A. Jensen

;; This program is free software; you can redistribute it and/or
;; modify it under the terms of the GNU General Public License as
;; published by the Free Software Foundation; either version 3 of
;; the License, or (at your option) any later version.

;; This program is distributed in the hope that it will be
;; useful, but WITHOUT ANY WARRANTY; without even the implied
;; warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
;; PURPOSE.  See the GNU General Public License for more details.

;; You should have received a copy of the GNU General Public
;; License along with this program; if not, write to the Free
;; Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
;; Boston, MA 02110-1301 USA

;; For these to work properly, `bioperl-skel-elements' must be called
;; from within the buffer. This is done automatically when
;; bioperl-mode is enabled.

;; A gotcha:
;;
;; There is a funky requirement for `prompt-once', that seems to 
;; have to do with the `skeleton-insert' internals.
;;
;; You appear to need to do a print of str before leaving
;; a skeleton or subskeleton, or you get an infinite loop
;;
;; e.g., in `bioperl-array-accessor-skel', we do
;;
;;    ( (prompt-once "Class name of base object: ")
;;      " Returns : An array of " str " objects"
;;      '(setq v1 str) )
;; 
;; which completes and makes v1 available in the top-level
;; skeleton, rather than, say,
;;
;;    ( (prompt-once "Class name of base object: ")
;;      '(setq v1 str) )
;;    " Returns : An array of " v1 " objects"
;;
;; which hangs.

(defconst bioperl-skel-revision "$Id$"
  "The revision string of bioperl-skel.el")

(make-variable-buffer-local 'prompt-once-alist)
(defvar prompt-once-alist '()
  "An internal var for the skeleton prompt-once facility.")


(define-skeleton bioperl-insert-class
  "Insert a template for a new BioPerl class/method."
  nil
  bioperl-class-pod-skel)

(define-skeleton bioperl-insert-method-pod
  "Insert a standard pod template for BioPerl methods."
  nil
  bioperl-method-pod-skel)

(define-skeleton bioperl-insert-accessor
  "Insert a standard accessor (getter/setter)."
  nil
  bioperl-accessor-skel)

(define-skeleton bioperl-insert-array-accessor
  "Insert a set of standard object array methods."
  nil
  bioperl-array-accessor-skel)

(define-skeleton bioperl-insert-abstract-method
  "Insert an abstract (\"throw_not_implemented\") method."
  nil
  bioperl-abstract-method-skel)

(define-skeleton bioperl-insert-generic-class
  "Insert a generic package pod template."
  nil
  bioperl-generic-class-pod-skel)

(defvar bioperl-method-pod-skel 
      '((prompt-once "Method name:")
	\N 
	\N "=head2 " str "()" 
	\N 
	\N " Title   : " str 
	\N " Usage   : " 
	\N " Function: " - 
	\N " Returns : " 
	\N " Args    : " 
	\N 
	\N "=cut" \N)
"Skeleton for a basic method pod header."
 )

(defvar bioperl-generic-class-pod-skel
  '(
    (prompt-once "Class name: ")
    "package " str ";" \N
    "use strict;" \N
    "use warnings;" \N
    \N
    "=head1 NAME" \N 
    \N 
    str " - " - "DESCRIPTION of Object" \N 
    \N
    "=head1 SYNOPSIS" \N 
    \N
    "Give standard usage here" \N
    \N
    "=head1 DESCRIPTION" \N
    \N
    _ "Describe the object here" \N
    \N
    ( (prompt-once "Author: ")
      "=head1 AUTHOR - " str \N )
    \N
    "=head1 METHODS" \N
    \N
    "=cut" \N
    \N
    "# Let the code begin..." \N
    \N \N \N
    "1;")
  "Skeleton for a generic package template")

(defvar bioperl-class-pod-skel
  '(
    (prompt-once "Class name: ")
    "# $Id" "$" \N
    "#" \N
    "# BioPerl module for " str \N
    "#" \N
    "# Please direct questions and support issues to " \N
    "#" \N
    ( (prompt-once "Caretaker: ")
      "# Cared for by " str '(setq v1 str) )
    ( (prompt-once "Email: ")
      " <" str ">" \N '(setq v2 str))
    "#" \N
    "# Copyright " v1 \N
    "#" \N
    "# You may distribute this module under the same terms as perl itself" \N \N
    "# POD documentation - main docs before the code" \N 
    \N
    "=head1 NAME" \N 
    \N 
    str " - " - "DESCRIPTION of Object" \N 
    \N
    "=head1 SYNOPSIS" \N 
    \N
    "Give standard usage here" \N
    \N
    "=head1 DESCRIPTION" \N
    \N
    "Describe the object here" \N
    \N
    "=head1 FEEDBACK" \N
    \N
    "=head2 Mailing Lists" \N
    \N
    "User feedback is an integral part of the evolution of this and other" \N
    "Bioperl modules. Send your comments and suggestions preferably to" \N
    "the Bioperl mailing list.  Your participation is much appreciated." \N
    \N
    "  bioperl-l@bioperl.org                  - General discussion" \N  
    "http://bioperl.org/wiki/Mailing_lists  - About the mailing lists" \N
    \N
    "=head2 Support" \N
    \N
    "Please direct usage questions or support issues to the mailing list:" \N
    \N
    "L" \N
    \N
    "rather than to the module maintainer directly. Many experienced and" \N
    "reponsive experts will be able look at the problem and quickly" \N
    "address it. Please include a thorough description of the problem" \N
    "with code and data examples if at all possible." \N 
    \N
    "=head2 Reporting Bugs" \N
    \N
    "Report bugs to the Bioperl bug tracking system to help us keep track" \N
    "of the bugs and their resolution. Bug reports can be submitted via" \N
    "the web:" \N
    \N
    "  https://github.com/bioperl/bioperl-live/issues" \N 
    \N
    "=head1 AUTHOR - " v1 \N
    \N
    "Email " v2 \N
    \N
    "Describe contact details here" \N
    \N
    "=head1 CONTRIBUTORS" \N
    \N
    "Additional contributors names and emails here" \N
    \N
    "=head1 APPENDIX" \N
    \N
    "The rest of the documentation details each of the object methods." \N
    "Internal methods are usually preceded with a _" \N
    \N
    "=cut" \N
    \N
    "# Let the code begin..." \N
    \N \N
    "package " str ";" \n
    "use strict;" \n
    \n
    "# Object preamble - inherits from Bio::Root::Root" \n
    \n
    "use Bio::Root::Root;" \n \n
    \n
    "use base qw(Bio::Root::Root );" \n
    \n
    "=head2 new" \N
    \N 
    " Title   : new" \N 
    " Usage   : my $obj = new " str "();" \N 
    " Function: Builds a new " str " object" \N 
    " Returns : an instance of " str \N 
    " Args    :" \N
    \N
    "=cut" \N
    \N
    "sub new {" \n  
    "my ($class,@args) = @_;" \n
    \n  
    "my $self = $class->SUPER::new(@args);" \n
    "return $self;" \n
    "}" > \n
    \N
    "1;")
  "Skeleton for a BioPerl module template." )

(defvar bioperl-accessor-skel
  '(
    (prompt-once "Field name: ")
    "=head2 " str "()" \N
    \N
    " Title   : " str \N 
    " Usage   : $obj->" str "($newval)" \N 
    " Function: " _ \N 
    " Example : " \N 
    " Returns : value of " str " (a scalar)" \N 
    " Args    : on set, new value (a scalar or undef, optional)" \N
    \N
    "=cut" \N
    \N
    "sub " str " {" \n
    "my $self = shift;" > \n
    \n
    "return $self->{'" str "'} = shift if @_;"
    \n
    "return $self->{'" str "'};" \n
    "}" > \n
    \N)
  "Skeleton for a BioPerl accessor (getter/setter).")

(defvar bioperl-array-accessor-skel
  '(
    (prompt-once "Array base object: ")
    "=head2 get_" str "s" \N
    \N 
    " Title   : get_" str "s" \N
    " Usage   : @arr = get_" str "s()" \N 
    " Function: Get the list of " str "(s) for this object." \N 
    " Example : " \N 
    ( (prompt-once "Class name of base object: ")
      " Returns : An array of " str " objects" \N
      '(setq v1 str) )
    " Args    : " \N
    \N
    "=cut" \N
    \N
    "sub get_" str "s{" > \n
    "my $self = shift;" \n
    \n
    "return @{$self->{'_" str "s'}} if exists($self->{'_" str "s'});" \n 
    "return ();" \n
    "}" \n
    \n
    "=head2 add_" str \N
    \N
    " Title   : add_" str \N 
    " Usage   : " \N 
    " Function: Add one or more " str "(s) to this object." \N 
    " Example : " \N 
    " Returns : " \N
    " Args    : One or more " v1 " objects." \N
    \N
    "=cut" \N
    \N
    "sub add_" str "{" > \n 
    "my $self = shift;" \n
    \n 
    "$self->{'_" str "s'} = [] unless exists($self->{'_" str "s'});" \n 
    "push(@{$self->{'_" str "s'}}, @_);" \n
    "}" \n
    \n
    "=head2 remove_" str "s" \N
    \N
    " Title   : remove_" str "s" \N
    " Usage   : "
    \N
    " Function: Remove all " str "s for this class." \N 
    " Example : " \N
    " Returns : The list of previous " str "s as an array of" \N           
    "          " v1 " objects." \N
    " Args    : " \N
    \N
    "=cut" \N 
    \N
    "sub remove_" str "s{" > \n 
    "my $self = shift;" \n
    \n 
    "my @arr = $self->get_" str "s();" \n
    "$self->{'_" str "s'} = [];" \n 
    "return @arr;" \n
    "}" > \n
    \N)
  "Skeleton for object array get/add/remove methods.")

(defvar bioperl-abstract-method-skel
  '(
    (prompt-once "Method name: ")
    "=head2 " str \N
    \N
    " Title   : " str \N
    " Usage   : " \N
    " Function: " _ \N
    " Example : " \N
    " Returns : " \N
    " Args    : " \N
    \N
    "=cut" \N
    \N
    "sub " str "{" \n
    "my ($self) = @_;" \n
    \n    
    "$self->throw_not_implemented();" \n
    "}" > \n
    \N
    )
  "Skeleton for an abstract BioPerl method (for interface classes).")

;;; skeleton helpers

(defun bioperl-skel-elements ()
  "Set some `skeleton-further-elements' for bioperl-skel in the buffer."
  (interactive)
  (setq skeleton-further-elements '( (\N "\n") )))
  
(defun prompt-once (prom)
  "Use in place of plain interactor string to prompt only once in a skeleton.
Entering a blank value quits the skeleton completely.

The skeleton system default behavior is to recursively insert a
skeleton as long as the user continues to provide input to a
prompt. The recursion ends when an empty string is entered as a
prompt. This is rather irritating when the user expects to make a
single entry and then move on. Using prompt-once as the
INTERACTOR for the skeleton or subskeleton will inhibit the
recursion.

Example:
 (define-skeleton myskel 
  \"Insert a pretend skeleton, with prompts\"
  nil ;; important
  '(
    (prompt-once \"Enter froob:\") ;; NO quote
    \"Froob is \" str \\n
    \"Now do a sub-skeleton with prompts...\" \\n
    ( (prompt-once \"Sklarb:\")
      \"Sklarb is \" str \\n )
    \"You've been a wonderful audience. Good night.\" \\n) )"

  (condition-case nil
      (let ( (flag (assoc prom prompt-once-alist) )
	     (inp) )
	(cond
	 ( (not flag)
	  (setq inp (read-string prom))
	  (if (> (length inp) 0)
	      (add-to-list 'prompt-once-alist (cons prom "1"))
	    (if (> (length prompt-once-alist) 0) 
		(signal 'quit t)))
	  inp)
	 ( flag
	   (setq prompt-once-alist (delq flag prompt-once-alist))
	   nil)))
    ('quit
     (if (= (length prompt-once-alist) 0) 
	 (signal 'quit t)
       (setq prompt-once-alist nil) 
       (signal 'quit 'recursive))
)))

(provide 'bioperl-skel)

;;; end bioperl-skel.elBioPerl-1.007002/ide/bioperl-mode/site-lisp/pod.el000555000766000024      1465013155576320 21700 0ustar00cjfieldsstaff000000000000;; $Id$
;;

;;
;; Emacs functions for simple Perl pod parsing
;;  parse result format based on pod2text
;;
;; required in bioperl-mode.el
;; 
;; Author: Mark A. Jensen
;; Email : maj -at- fortinbras -dot- us
;;
;; Part of The Documentation Project
;; http://www.bioperl.org/wiki/The_Documentation_Project
;;
;;

;; Copyright (C) 2009 Mark A. Jensen

;; This program is free software; you can redistribute it and/or
;; modify it under the terms of the GNU General Public License as
;; published by the Free Software Foundation; either version 3 of
;; the License, or (at your option) any later version.

;; This program is distributed in the hope that it will be
;; useful, but WITHOUT ANY WARRANTY; without even the implied
;; warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
;; PURPOSE.  See the GNU General Public License for more details.

;; You should have received a copy of the GNU General Public
;; License along with this program; if not, write to the Free
;; Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
;; Boston, MA 02110-1301 USA

(defvar pod-keywords 
  '( "pod" "head1" "head2" "head3" "head4" "over" "item" "back" "begin" "end" "for" "encoding" "cut" )
  "Perl pod keywords (sans '=') ")

(defvar pod-format-codes 
  '( "I" "B" "C" "L" "E" "F" "S" "X" "Z" )
  "Perl pod format codes (sans <>)" )

(defun pod-parse-buffer (buf &optional alt-format)
  "Parse the pod in the BUF.
Removes code and leaves pod. Does some simple formatting a la
pod2text as setup for pod-mode. If ALT-FORMAT is true, headers 
are flanked by '='s as in pod2text -a. "
  (save-excursion
    (set-buffer buf)
    (let (
	  (cur-state)
	  (cur-content)
	  (tmp-state)
	  (tmp-content)
	  (encoding-type)
	  (parse-tree '(("Root")))
	  (line)
	  (header-level)
	  (beg (goto-char (point-min)))
	  (end)
	  (tbeg) (tend) ;; text region
	  )
      (goto-char (point-min))
      ;; get encoding if present
      (if (re-search-forward "^=encoding\\s +\\(.*?\\)\\s " (point-max) t)
	  (setq encoding-type (match-string 1)))
      (goto-char (point-min))
      (while (not (eobp))
	(setq end (re-search-forward "^=\\([a-z0-9]+\\)\\(?:$\\|\\s *\\(.*?\\)\\)$" (point-max) 1))
	(if (not end)
	    t ;; done
	  (setq tmp-state (match-string 1))
	  (setq tmp-content (match-string 2))
	  (if (not cur-state)
	      (progn
		(beginning-of-line)
		(pod-do-format "ignore" beg (point))
		(setq end beg)))
	  (setq cur-state tmp-state)
	  (setq cur-content tmp-content)
	  (if (not cur-state)
	      t ;; done
	    ;; otherwise, in a pod region
	    (if (not (member cur-state pod-keywords))
		(error (concat "'" cur-state "' not a pod keyword")))
	    (cond 
	     ( (not cur-state) 
	       nil ;; ????
	       )
	     ( (string-equal cur-state "cut")
	       (forward-line 0)
	       (kill-line 2)
	       (pod-do-format "text" beg (point))
	       (setq cur-state nil) )
	     ( (string-equal cur-state "pod")
	       (forward-line 0)
	       (kill-line 2)
	       (pod-do-format "text" beg (point))
	       )
	     ( (string-match "head\\([1-4]\\)" cur-state)
	       (setq head-level (string-to-number (match-string 1 cur-state)))
	       (forward-line 0)
	       (kill-line 2)
	       (pod-do-format "text" beg (point))
	       (if (not cur-content)
		   nil
		 (if (not alt-format)
		     (progn 
		       (insert-char ?  (* 2 (1- head-level)))
		       (insert cur-content "\n"))
		   (cond 
		    ((= head-level 1)
		     (insert "==== " cur-content " ====\n"))
		    ((= head-level 2)
		     (insert "==   " cur-content "   ==\n"))
		    ((= head-level 3)
		     (insert "=    " cur-content "    =\n"))
		    ((= head-level 4)
		     (insert "-    " cur-content "    -\n"))))
		 ))
	     ( (string-equal cur-state "over") 
	       (let (
		     (indent-level cur-content)
		     (back (save-excursion
			     (re-search-forward "^=back" (point-max) t)))
		     )
		 (unless back
		   (error "=over has no matching =back"))
		 (forward-line 0)
		 (kill-line 2)
		 (pod-do-format "text" beg (point))
		 (setq beg (point))
		 (while (re-search-forward "^=item\\s +\\(.*?\\)$" back t)
		   (let ( (item (match-string 1) ) )
		     (forward-line 0)
		     (kill-line 2)
		     (pod-do-format "text" beg (point))
		     (if (not alt-format)
			 (insert "    * " item "\n")
		       (insert ":   " item "\n")))
		   (setq beg (point)))
		 (re-search-forward "^=back" (point-max))
		 (forward-line 0)
		 (kill-line 2) 
		 (pod-do-format "text" beg (point))
		 ))
	     ( (string-equal cur-state "begin")
	       (let (
		     (format cur-content)
		     (end (save-excursion
			    (re-search-forward (concat "^=end\\s +" format)
					       (point-max) t)))
		     (content-beg) (content-end)
		     )
		 (unless end
		   (error (concat "=begin " format " has no matching end.")))
		 (forward-line 0)
		 (kill-line 2)
		 (setq content-beg (point))
		 (re-search-forward  (concat "^=end\\s +" format))
		 (forward-line 0)
		 (kill-line 2)
		 (setq content-end (point))
		 (pod-do-format format content-beg content-end)
		 ))
	     ( (string-equal cur-state "for")
	       (string-match "\\([a-z]+\\)\\s +\\(.*?\\)$" cur-content)
	       (let (
		     (format (match-string 1 cur-content))
		     (content (match-string 2 cur-content))
		     )
		 (forward-line 0)
		 (kill-line 2)
		 (pod-do-format "text" beg (point))
		 ))
	     ( (string-equal cur-state "encoding")
	       (let (
		     (type cur-content)
		     )
		 (forward-line 0)
		 (kill-line 2)
		 (pod-do-format "text" beg (point))		 
		 t))
	     ))	   
	  ;; movement here?
	  (setq beg (point))
	  (setq cur-content nil) ;; clear means 'moved off pod descr line'
	))
      (pod-do-format (if cur-state "text" "ignore") beg (point-max))
      t)
    ))

(defun pod-do-format (format beg end)
  "Handle pod =begin format ... =end format blocks.
FORMAT is a format identifier (a string); BEG and END define the
text region."
  ;; ignore for now
  (if (= beg end)
      nil
    (cond
     ((string-equal format "ignore")
      (delete-region beg end))
     ((string-equal format "text")
      ;; format ordinary and verbatim lines
      (save-excursion
	(goto-char beg)
	(forward-line 0)
	(while (and (< (point) end) (not (eobp)))
	  (cond
	   ((string-match "[[:blank:]]" (char-to-string (char-after)))
	    (insert-char ?  4)
	    (setq end (+ end 4)))
	   ((string-match "[[:space:]]" (char-to-string (char-after)))
	    t)
	   (t
	    (insert-char ?  4)
	    (setq end (+ end 4))))
	  (forward-line 1)
	  )))
     (t 
      ;; otherwise, remove (ignore)
      (delete-region beg end)) )))

(provide 'pod)BioPerl-1.007002/maintenance000755000766000024          013155576320 15640 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/maintenance/README000444000766000024       111313155576320 16651 0ustar00cjfieldsstaff000000000000
The scripts in this directory are meant for bioperl maintainers.  They
count and test modules that make up the bioperl core library.

The scripts are not expected to run under any other than UNIXy
operating systems.

Run them from this directory.

Dependencies (not required for bioperl):
========================================

Module                         Script
------------------------------------------------
Data::Dumper                   authors.pl
                               modules.pl
Regexp::Common                 check_URLs.pl
Pod::Checker                   pod.pl

BioPerl-1.007002/maintenance/authors.pl000555000766000024      1336013155576320 20045 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
#
=head1 NAME

authors.pl - check modules and scripts for authors not in AUTHORS file

=head1 SYNOPSIS

B [B<-d|--dir> path ] [B<-v|--verbose>] B<-a|--authorsfile>
    [B<-?|-h|--help>]

=head1 DESCRIPTION

Checks Plain Old Documentation (POD) of all bioperl live modules for
AUTHORS and CONTRIBUTORS tags and prints out any emails missing from
the AUTHORS file

=cut

use Data::Dumper;
use File::Find;
use Getopt::Long;
use strict;

sub findauthors;

#
# command line options
#

my ($verbose, $dir, $authorsfile, $help) = (0, undef, "../AUTHORS", undef);
GetOptions(
           'v|verbose' => \$verbose,
           'dir:s' => \$dir,
           'authorsfile:s' => \$authorsfile,
	   'h|help|?' => sub{ exec('perldoc',$0); exit(0) }
	   );

#
# global variables
#

# known authors from the AUTHORS file are read into
# the hash which is initialized with known synonymes
our %AUTHORS = map {$_=>1} qw{
                              birney@sanger.ac.uk
                              jinsana@gmx.net
                              Insana@ebi.ac.uk
                              fugui@worf.fugu-sg.org
                              cjm@fruitfly.bdgp.berkeley.edu
                              elia@tll.org.sg
                              heikki-at-bioperl-dot-org
                              bioinformatics@dieselwurks.com
                              bioinformatics1@dieselwurks.com
                              bioperl-l@bio.perl.org
                              paul@systemsbiology.org
                              gattiker@isb-sib.ch
                              elia@fugu-sg.org
                              jason@cgt.mc.duke.edu
                              jason@chg.mc.duke.edu
                              jason@open-bio.org
                              hilmar.lapp@pharma.novartis.com
                              richard.adams@ed.ac.uk
                              dblock@gene.pbi.nrc.ca
                              ak@ebi.ac.uk
                              day@cshl.org
                              bala@tll.org.sg
                              mrp@sanger.ac.uk
                              m.w.e.j.fiers@plant.wag-ur.nl
                              cmzmasek@yahoo.com
                              fuguteam@fugu-sg.org
                              shawnh@gmx.net
                          };
our %NEWAUTHORS;     # new authors
our %FIND_OPTIONS = ( wanted => \&findauthors, no_chdir => 1 );


# Directories to check
my @dirs = qw( ../Bio/ ../scripts . );

#print Dumper \%AUTHORS;

#
# Read the AUTHORS file
#


open my $F, '<', $authorsfile or die "Could not read file '$authorsfile': $!\n";


while (my $line = <$F>) {
    my ($email) = ($line =~/([\.\w_-]+ at [\.\w_-]+)/);
    next unless $email;
    #print $email, "\n";
    $email =~ s/ at /@/;
    $AUTHORS{$email} = 1;
}
close $F;


#
# run
#

if ($dir) {
    find \%FIND_OPTIONS, $dir;
} else {
    find \%FIND_OPTIONS, @dirs;
}

#
# results
#
print Dumper \%NEWAUTHORS;


#
##
### end main
##
#

#
# this is where the action is
#
sub findauthors {
    my ($filename) = $_;
    return unless ($filename =~ /\.PLS$/ or $filename =~ /\.p[ml]$/);
    return unless -e $filename;

    print "$filename\n" if $verbose;
    #local $/=undef;
    open my $F, '<', $filename or die "Could not read file '$filename': $!\n";
    while (my $line = <$F>) {
        #print $line;
        last if $line =~ /=head1 +AUTHOR/;
    }
    my $authorblock;
    while (my $line = <$F>) {
        last if $line =~ /=head/ and $line !~ /CONTRIBUTORS/;
        $authorblock .= $line;
    }
    close $F;
    return unless $authorblock;

    while ( $authorblock =~ /([\.\w_-]+@[\.a-z_-]+)/g) {
        #my $email = $1;
        #$email =~ //
        next if $AUTHORS{$1};
        #print "$filename\t$1\n";

        push @{$NEWAUTHORS{$1}}, $filename;
    }
}



=head1 OPTIONS

=over 3

=item B<-d | --dir> path

Overides the default directories to check by one directory 'path' and
all its subdirectories.

=item B<-a | --authorsfile>

path from working directory the AUTHORS file.

Redundant as this information could be had from --dir option butI am
feeling too lazy to change the code.

=cut

sub blankline {
    my ($file) = @_;
    return unless ($file =~ /\.PLS$/ or $file =~ /\.p[ml]$/);
    return unless -e $file;

    open my $F, '<', $file or warn "Could not read file '$file': $!\n" && return;
    local $/ = "";
    while (my $line = <$F>) {
        print "$file: +|$1|\n"  if $line =~ /[ \t]\n(=[a-z][^\n]+$)/m and $verbose;
        print "$file: ++|$1|\n" if $line =~ /\w\n(=[a-z][^\n]+$)/m    and $verbose;
        print "$file:|$1|+\n"   if $line =~ /(^=[a-z][^\n]+)\n[\t ]/m;
        #print "$file:|$1|++\n" if /(^=[^\n]+)\n\w/m;
    }
    close $F;
}

__END__

=item B<-v | --verbose>

Show the progress through files during the POD checking.

=item B<-? | -h  | --help>

This help text.

=back

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org

=cut


# find . -name '*.pm' -print | xargs  perl -e '$/=""; while (<>) {$n = $1 if /^package\s+([\w:]+)/; print "$n:|$1|"  if  /(\s\s^=[^\n]+$)/m ; }'  ;

# find . -name '*.pm' -print | xargs  perl -e '$/=""; while (<>) {$n = $1 if /^package\s+([\w:]+)/; print "$n:|$1|\n"  if /(^=[^\n]+\n[\t ])/m ; }'  ;
BioPerl-1.007002/maintenance/check_NAME.pl000555000766000024       503713155576320 20217 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=head1 NAME

check_NAMEs.pl - check NAME in module POD has fully qualified object name

=head1 SYNOPSIS

B [B<-d|--dir> path] [B<-v|--verbose>] [B<-?|-h|--help>]

=head1 DESCRIPTION

This script is designed to find all Bioperl modules which don't
have the fully qualified object name with correct capitalization
in the "NAME" section of the POD. 

The full name is required for the PDOC POD to HTML script to
correctly render the module documentation.

=cut

use strict;
use File::Find;
use Getopt::Long;

#
# command line options
#

my ($verbose, $dir, $help) = (0, '../Bio/', undef);
GetOptions(
    'v|verbose' => \$verbose,
    'd|dir:s' => \$dir,
    'h|help|?' => sub{ exec('perldoc',$0); exit(0) }
);

#
# globals
#

my $num_found = 0;

#
# find all modules
#

print STDERR "Searching for incorrect NAME POD section of all modules in: $dir\n";
find( \&find_modules, $dir );
print STDERR "$num_found found.\n";

# this is where the action is

sub find_modules {
    # only want files with .pm
    return unless m/\.pm$/;
    return unless -f $_;
    
    my $fname = $_;
    my $pm = $File::Find::name;
    $pm =~ s{.*?/(?=Bio/)}{};  # remove up to first slash before Bio/
    $pm =~ s{\.pm$}{};         # remove .pm suffix
    $pm =~ s{/}{::}g;          # convert / to ::
    
    print STDERR "# $File::Find::name\n" if $verbose;
    
    # slurp in the file
    my $text = do { local( @ARGV, $/ ) = $fname ; <> } ;

    # check if the NAME section has the _full_ module name in it
    if ($text !~ m/^=head1\s+NAME.*?^$pm/xms) {
      print "$pm\n";
      $num_found++;
    }
}


=head1 OPTIONS

=over 3

=item B<-d | --dir> path

Overides the default directory to recursively look for .pm file 
(Default is '../Bio')

=item B<-v | --verbose>

Show the progress through files during the POD checking.

=item B<-? | -h  | --help>

This help text.

=back

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Torsten Seemann

Email: torsten-dot-seemann-at-infotech-dot-monash-dot-edu-dot-au

=cut
BioPerl-1.007002/maintenance/check_URLs.pl000555000766000024       710613155576320 20323 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=head1 NAME

check_URLs.pl - validate URLs located in module code and POD

=head1 SYNOPSIS

B [B<-d|--dir> path] [B<-v|--verbose>] [B<-?|-h|--help>]
    [B<-o|--outfile> filename]

=head1 DESCRIPTION

Checks code and POD of all bioperl-live modules for URLs, and validates them.

Output is a series of lines containing two fields, tab separated.
The first field is the file with the bad URL, the second is the URL itself.

The whole URL is not retrieved, only a HTTP "HEAD" request is done
to see if the URL exists on the server. The request is done using 
B so the B environmental variable will be
honoured.

The URL parsing may not be perfect - although I use the B
module, I have to manually clean up some URLs which are embedded in Perl
strings to convert the matched URL to a more probable real world URL,
e.g. most URLs don\'t end in "'," or ")" :-)

=cut

use strict;
use Data::Dumper;
use File::Find;
use Getopt::Long;
use Regexp::Common qw(URI);
use LWP::Simple qw($ua head);

$ua->timeout(15);

#
# command line options
#

my ($verbose, $dir, $help) = (0, '../Bio/', undef);
my $file;
GetOptions(
    'v|verbose' => \$verbose,
    'd|dir:s' => \$dir,
    'o|outfile:s' => \$file,
    'h|help|?' => sub{ exec('perldoc',$0); exit(0) }
);

my $fh;

if (defined $file) {
    open $fh, '>', $file or die "Could not write file '$file': $!\n";
} else {
    $fh = \*STDOUT;
}

#
# find all modules
#

find( \&find_modules, $dir );

#
# validate unique URLs and print fail cases to stdout
#

my %cached_urls;

sub check_url {
    my ($url, $file) = @_;
    if (exists $cached_urls{$url}) {
        print STDERR "$url checked in ".$cached_urls{$url}[0].":".$cached_urls{$url}[1]."\n" if $verbose;
        print $fh "$file\t$url\n" if $cached_urls{$url}[1] ne 'ok';
        return;
    }
    print STDERR "Checking $url in $file... " if $verbose;
    my $ok = head($url);
    my $status = $ok ? 'ok' : 'FAIL!';
    print STDERR "$status!\n" if $verbose;
    print $fh "$file\t$url\n" if !$ok;
    $cached_urls{$url} = [$file, $status];
}

close $fh if $file; # don't close STDOUT

#
# this is where the action is
#

sub find_modules {
    # only want files with .pm
    return unless m/\.pm$/;
    return unless -f $_;
    
    my $fname = $_;
    
    # slurp in the file
    my $text = do { local( @ARGV, $/ ) = $fname ; <> } ;
    
    # keep track of URLs
    while ($text =~ m/$RE{URI}{HTTP}{-keep}/g) {
        my $url = $1 or next;
        # remove Perl code if URL was embedded in string and other stuff
        $url =~ s/\s*[.,;'")]*\s*$//;
        check_url($url, $File::Find::name);
    }    
}


=head1 OPTIONS

=over 3

=item B<-d | --dir> path

Overides the default directory to recursively look for .pm file 
(Default is '../Bio')

=item B<-v | --verbose>

Show the progress through files during the POD checking.

=item B<-? | -h  | --help>

This help text.

=back

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Torsten Seemann

Email: torsten-dot-seemann-at-infotech-dot-monash-dot-edu-dot-au

=cut
BioPerl-1.007002/maintenance/cvs2cl_by_file.pl000555000766000024     26710313155576320 21273 0ustar00cjfieldsstaff000000000000#!/bin/sh
exec perl -w -x $0 ${1+"$@"} # -*- mode: perl; perl-indent-level: 2; -*-
#!perl -w

###########################################################################
# This is a quick hack version of cvs2cl.pl (see below)
# that simply outputs in a file-centric mannor.
# only CVS::Utils::ChangeLog::EntrySet::Output::output_changelog
# was altered
# 
# Usage:
# cvs2cl_by_file.pl --delta bioperl-release-1-5-1:bioperl-release-1-5-2
# Generates a file called ChangeLog showing, per file, all the commit
# messages since tag bioperl-release-1-5-1 up to tag bioperl-release-1-5-2
# It generates in wikipedia format suitable for immediate pasting into the
# a wiki page for the delta
#
# Sendu Bala 
###########################################################################


##############################################################
###                                                        ###
### cvs2cl.pl: produce ChangeLog(s) from `cvs log` output. ###
###                                                        ###
##############################################################

##

use strict;

use File::Basename qw( fileparse );
use Getopt::Long   qw( GetOptions );
use Text::Wrap     qw( );
use Time::Local    qw( timegm );
use User::pwent    qw( getpwnam );
use File::Spec;

# The Plan:
#
# Read in the logs for multiple files, spit out a nice ChangeLog that
# mirrors the information entered during `cvs commit'.
#
# The problem presents some challenges. In an ideal world, we could
# detect files with the same author, log message, and checkin time --
# each  would be a changelog entry.
# We'd sort them; and spit them out.  Unfortunately, CVS is *not atomic*
# so checkins can span a range of times.  Also, the directory structure
# could be hierarchical.
#
# Another question is whether we really want to have the ChangeLog
# exactly reflect commits. An author could issue two related commits,
# with different log entries, reflecting a single logical change to the
# source. GNU style ChangeLogs group these under a single author/date.
# We try to do the same.
#
# So, we parse the output of `cvs log', storing log messages in a
# multilevel hash that stores the mapping:
#   directory => author => time => message => filelist
# As we go, we notice "nearby" commit times and store them together
# (i.e., under the same timestamp), so they appear in the same log
# entry.
#
# When we've read all the logs, we twist this mapping into
# a time => author => message => filelist mapping for each directory.
#
# If we're not using the `--distributed' flag, the directory is always
# considered to be `./', even as descend into subdirectories.

# Call Tree

# name                         number of lines (10.xii.03)
# parse_options                         192
# derive_changelog                       13
# +-maybe_grab_accumulation_date         38
# +-read_changelog                      277
#   +-maybe_read_user_map_file           94
#     +-run_ext                           9
#   +-read_file_path                     29
#   +-read_symbolic_name                 43
#   +-read_revision                      49
#   +-read_date_author_and_state         25
#     +-parse_date_author_and_state      20
#   +-read_branches                      36
# +-output_changelog                    424
#   +-pretty_file_list                  290
#     +-common_path_prefix               35
#   +-preprocess_msg_text                30
#     +-min                               1
#   +-mywrap                             16
#   +-last_line_len                       5
#   +-wrap_log_entry                    177
#
# Utilities
#
# xml_escape                              6
# slurp_file                             11
# debug                                   5
# version                                 2
# usage                                 142

# -*- -*- -*- -*- -*- -*- -*- -*- -*- -*- -*- -*- -*- -*- -*- -*- -*- -*-
#
# Note about a bug-slash-opportunity:
# -----------------------------------
#
# There's a bug in Text::Wrap, which affects cvs2cl.  This script
# reveals it:
#
#   #!/usr/bin/perl -w
#
#   use Text::Wrap;
#
#   my $test_text =
#   "This script demonstrates a bug in Text::Wrap.  The very long line
#   following this paragraph will be relocated relative to the surrounding
#   text:
#
#   ====================================================================
#
#   See?  When the bug happens, we'll get the line of equal signs below
#   this paragraph, even though it should be above.";
#
#
#   # Print out the test text with no wrapping:
#   print "$test_text";
#   print "\n";
#   print "\n";
#
#   # Now print it out wrapped, and see the bug:
#   print wrap ("\t", "        ", "$test_text");
#   print "\n";
#   print "\n";
#
# If the line of equal signs were one shorter, then the bug doesn't
# happen.  Interesting.
#
# Anyway, rather than fix this in Text::Wrap, we might as well write a
# new wrap() which has the following much-needed features:
#
# * initial indentation, like current Text::Wrap()
# * subsequent line indentation, like current Text::Wrap()
# * user chooses among: force-break long words, leave them alone, or die()?
# * preserve existing indentation: chopped chunks from an indented line
#   are indented by same (like this line, not counting the asterisk!)
# * optional list of things to preserve on line starts, default ">"
#
# Note that the last two are essentially the same concept, so unify in
# implementation and give a good interface to controlling them.
#
# And how about:
#
# Optionally, when encounter a line pre-indented by same as previous
# line, then strip the newline and refill, but indent by the same.
# Yeah...

# Globals --------------------------------------------------------------------

# In case we have to print it out:
my $VERSION = '$Revision$';
$VERSION =~ s/\S+\s+(\S+)\s+\S+/$1/;

## Vars set by options:

# Print debugging messages?
my $Debug = 0;

# Just show version and exit?
my $Print_Version = 0;

# Just print usage message and exit?
my $Print_Usage = 0;

# What file should we generate (defaults to "ChangeLog")?
my $Log_File_Name = "ChangeLog";

# Grab most recent entry date from existing ChangeLog file, just add
# to that ChangeLog.
my $Cumulative = 0;

# `cvs log -d`, this will repeat the last entry in the old log.  This is OK,
# as it guarantees at least one entry in the update changelog, which means
# that there will always be a date to extract for the next update.  The repeat
# entry can be removed in postprocessing, if necessary.

# MJP 2003-08-02
# I don't think this actually does anything useful
my $Update = 0;

# Expand usernames to email addresses based on a map file?
my $User_Map_File = '';
my $User_Passwd_File;
my $Mail_Domain;

# Output log in chronological order? [default is reverse chronological order]
my $Chronological_Order = 0;

# Grab user details via gecos
my $Gecos = 0;

# User domain for gecos email addresses
my $Domain;

# Output to a file or to stdout?
my $Output_To_Stdout = 0;

# Eliminate empty log messages?
my $Prune_Empty_Msgs = 0;

# Tags of which not to output
my %ignore_tags;

# Show only revisions with Tags
my %show_tags;

# Don't call Text::Wrap on the body of the message
my $No_Wrap = 0;

# Indentation of log messages
my $Indent = "\t";

# Don't do any pretty print processing
my $Summary = 0;

# Separates header from log message.  Code assumes it is either " " or
# "\n\n", so if there's ever an option to set it to something else,
# make sure to go through all conditionals that use this var.
my $After_Header = " ";

# XML Encoding
my $XML_Encoding = '';

# Format more for programs than for humans.
my $XML_Output = 0;
my $No_XML_Namespace = 0;
my $No_XML_ISO_Date = 0;

# Do some special tweaks for log data that was written in FSF
# ChangeLog style.
my $FSF_Style = 0;

# Show times in UTC instead of local time
my $UTC_Times = 0;

# Show times in output?
my $Show_Times = 1;

# Show day of week in output?
my $Show_Day_Of_Week = 0;

# Show revision numbers in output?
my $Show_Revisions = 0;

# Show dead files in output?
my $Show_Dead = 0;

# Hide dead trunk files which were created as a result of additions on a
# branch?
my $Hide_Branch_Additions = 1;

# Show tags (symbolic names) in output?
my $Show_Tags = 0;

# Show tags separately in output?
my $Show_Tag_Dates = 0;

# Show branches by symbolic name in output?
my $Show_Branches = 0;

# Show only revisions on these branches or their ancestors.
my @Follow_Branches;
# Show only revisions on these branches or their ancestors; ignore descendent
# branches.
my @Follow_Only;

# Don't bother with files matching this regexp.
my @Ignore_Files;

# How exactly we match entries.  We definitely want "o",
# and user might add "i" by using --case-insensitive option.
my $Case_Insensitive = 0;

# Maybe only show log messages matching a certain regular expression.
my $Regexp_Gate = '';

# Pass this global option string along to cvs, to the left of `log':
my $Global_Opts = '';

# Pass this option string along to the cvs log subcommand:
my $Command_Opts = '';

# Read log output from stdin instead of invoking cvs log?
my $Input_From_Stdin = 0;

# Don't show filenames in output.
my $Hide_Filenames = 0;

# Don't shorten directory names from filenames.
my $Common_Dir = 1;

# Max checkin duration. CVS checkin is not atomic, so we may have checkin
# times that span a range of time. We assume that checkins will last no
# longer than $Max_Checkin_Duration seconds, and that similarly, no
# checkins will happen from the same users with the same message less
# than $Max_Checkin_Duration seconds apart.
my $Max_Checkin_Duration = 180;

# What to put at the front of [each] ChangeLog.
my $ChangeLog_Header = '';

# Whether to enable 'delta' mode, and for what start/end tags.
my $Delta_Mode = 0;
my $Delta_From = '';
my $Delta_To = '';

my $TestCode;

# Whether to parse filenames from the RCS filename, and if so what
# prefix to strip.
my $RCS_Root;

# Whether to output information on the # of lines added and removed
# by each file modification.
my $Show_Lines_Modified = 0;

## end vars set by options.

# latest observed times for the start/end tags in delta mode
my $Delta_StartTime = 0;
my $Delta_EndTime = 0;

my $No_Ancestors = 0;

my $No_Extra_Indent = 0;

my $GroupWithinDate = 0;

# ----------------------------------------------------------------------------

package CVS::Utils::ChangeLog::EntrySet;

sub new {
  my $class = shift;
  my %self;
  bless \%self, $class;
}

# -------------------------------------

sub output_changelog {
  my $output_type = $XML_Output ? 'XML' : 'Text';
  my $output_class = "CVS::Utils::ChangeLog::EntrySet::Output::${output_type}";
  my $output = $output_class->new(follow_branches => \@Follow_Branches,
                                  follow_only     => \@Follow_Only,
                                  ignore_tags     => \%ignore_tags,
                                  show_tags       => \%show_tags,
                                 );
  $output->output_changelog(@_);
}

# -------------------------------------

sub add_fileentry {
  my ($self, $file_full_path, $time, $revision, $state, $lines,
      $branch_names, $branch_roots, $branch_numbers,
      $symbolic_names, $author, $msg_txt) = @_;

      my $qunk =
        CVS::Utils::ChangeLog::FileEntry->new($file_full_path, $time, $revision,
                                              $state, $lines,
                                              $branch_names, $branch_roots,
                                              $branch_numbers,
                                              $symbolic_names);

      # We might be including revision numbers and/or tags and/or
      # branch names in the output.  Most of the code from here to
      # loop-end deals with organizing these in qunk.

      unless ( $Hide_Branch_Additions
               and
               $msg_txt =~ /file .+ was initially added on branch \S+./ ) {
        # Add this file to the list
        # (We use many spoonfuls of autovivication magic. Hashes and arrays
        # will spring into existence if they aren't there already.)

        &main::debug ("(pushing log msg for ". $qunk->dir_key . $qunk->filename . ")\n");

        # Store with the files in this commit.  Later we'll loop through
        # again, making sure that revisions with the same log message
        # and nearby commit times are grouped together as one commit.
        $self->{$qunk->dir_key}{$author}{$time}{$msg_txt} =
          CVS::Utils::ChangeLog::Message->new($msg_txt)
              unless exists $self->{$qunk->dir_key}{$author}{$time}{$msg_txt};
        $self->{$qunk->dir_key}{$author}{$time}{$msg_txt}->add_fileentry($qunk);
      }

}

# ----------------------------------------------------------------------------

package CVS::Utils::ChangeLog::EntrySet::Output::Text;

use base qw( CVS::Utils::ChangeLog::EntrySet::Output );

use File::Basename qw( fileparse );

sub new {
  my $class = shift;
  my $self = $class->SUPER::new(@_);
}

# -------------------------------------

sub wday {
  my $self = shift; my $class = ref $self;
  my ($wday) = @_;

  return $Show_Day_Of_Week ? ' ' . $class->weekday_en($wday) : '';
}

# -------------------------------------

sub header_line {
  my $self = shift;
  my ($time, $author, $lastdate) = @_;

  my $header_line = '';

  my (undef,$min,$hour,$mday,$mon,$year,$wday)
    = $UTC_Times ? gmtime($time) : localtime($time);

  my $date = $self->fdatetime($time);

  if ($Show_Times) {
    $header_line =
      sprintf "%s  %s\n\n", $date, $author;
  } else {
    if ( ! defined $lastdate or $date ne $lastdate or ! $GroupWithinDate ) {
      if ( $GroupWithinDate ) {
        $header_line = "$date\n\n";
      } else {
        $header_line = "$date  $author\n\n";
      }
    } else {
      $header_line = '';
    }
  }
}

# -------------------------------------

sub preprocess_msg_text {
  my $self = shift;
  my ($text) = @_;

  $text = $self->SUPER::preprocess_msg_text($text);

  unless ( $No_Wrap ) {
    # Strip off lone newlines, but only for lines that don't begin with
    # whitespace or a mail-quoting character, since we want to preserve
    # that kind of formatting.  Also don't strip newlines that follow a
    # period; we handle those specially next.  And don't strip
    # newlines that precede an open paren.
    1 while $text =~ s/(^|\n)([^>\s].*[^.\n])\n([^>\n])/$1$2 $3/g;

    # If a newline follows a period, make sure that when we bring up the
    # bottom sentence, it begins with two spaces.
    1 while $text =~ s/(^|\n)([^>\s].*)\n([^>\n])/$1$2  $3/g;
  }

  return $text;
}

# -------------------------------------

# Here we take a bunch of qunks and convert them into printed
# summary that will include all the information the user asked for.
sub pretty_file_list {
  my $self = shift;

  return ''
    if $Hide_Filenames;

  my $qunksref = shift;

  my @filenames;
  my $beauty = '';          # The accumulating header string for this entry.
  my %non_unanimous_tags;   # Tags found in a proper subset of qunks
  my %unanimous_tags;       # Tags found in all qunks
  my %all_branches;         # Branches found in any qunk
  my $fbegun = 0;           # Did we begin printing filenames yet?

  my ($common_dir, $qunkrefs) =
    $self->_pretty_file_list(\(%unanimous_tags, %non_unanimous_tags, %all_branches), $qunksref);

  my @qunkrefs = @$qunkrefs;

  # Not XML output, so complexly compactify for chordate consumption.  At this
  # point we have enough global information about all the qunks to organize
  # them non-redundantly for output.

  if ($common_dir) {
    # Note that $common_dir still has its trailing slash
    $beauty .= "$common_dir: ";
  }

  if ($Show_Branches)
  {
    # For trailing revision numbers.
    my @brevisions;

    foreach my $branch (keys (%all_branches))
    {
      foreach my $qunkref (@qunkrefs)
      {
        if ((defined ($qunkref->branch))
            and ($qunkref->branch eq $branch))
        {
          if ($fbegun) {
            # kff todo: comma-delimited in XML too?  Sure.
            $beauty .= ", ";
          }
          else {
            $fbegun = 1;
          }
          my $fname = substr ($qunkref->filename, length ($common_dir));
          $beauty .= $fname;
          $qunkref->{'printed'} = 1;  # Just setting a mark bit, basically

          if ( $Show_Tags and defined $qunkref->tags ) {
            my @tags = grep ($non_unanimous_tags{$_}, @{$qunkref->tags});

            if (@tags) {
              $beauty .= " (tags: ";
              $beauty .= join (', ', @tags);
              $beauty .= ")";
            }
          }

          if ($Show_Revisions) {
            # Collect the revision numbers' last components, but don't
            # print them -- they'll get printed with the branch name
            # later.
            $qunkref->revision =~ /.+\.([\d]+)$/;
            push (@brevisions, $1);

            # todo: we're still collecting branch roots, but we're not
            # showing them anywhere.  If we do show them, it would be
            # nifty to just call them revision "0" on a the branch.
            # Yeah, that's the ticket.
          }
        }
      }
      $beauty .= " ($branch";
      if (@brevisions) {
        if ((scalar (@brevisions)) > 1) {
          $beauty .= ".[";
          $beauty .= (join (',', @brevisions));
          $beauty .= "]";
        }
        else {
          # Square brackets are spurious here, since there's no range to
          # encapsulate
          $beauty .= ".$brevisions[0]";
        }
      }
      $beauty .= ")";
    }
  }

  # Okay; any qunks that were done according to branch are taken care
  # of, and marked as printed.  Now print everyone else.

  my %fileinfo_printed;
  foreach my $qunkref (@qunkrefs)
  {
    next if (defined ($qunkref->{'printed'}));   # skip if already printed

    my $b = substr ($qunkref->filename, length ($common_dir));
    # todo: Shlomo's change was this:
    # $beauty .= substr ($qunkref->filename,
    #              (($common_dir eq "./") ? '' : length ($common_dir)));
    $qunkref->{'printed'} = 1;  # Set a mark bit.

    if ($Show_Revisions || $Show_Tags || $Show_Dead)
    {
      my $started_addendum = 0;

      if ($Show_Revisions) {
        $started_addendum = 1;
        $b .= " (";
        $b .= $qunkref->revision;
      }
      if ($Show_Dead && $qunkref->state =~ /dead/)
      {
        # Deliberately not using $started_addendum. Keeping it simple.
        $b .= "[DEAD]";
      }
      if ($Show_Tags && (defined $qunkref->tags)) {
        my @tags = grep ($non_unanimous_tags{$_}, @{$qunkref->tags});
        if ((scalar (@tags)) > 0) {
          if ($started_addendum) {
            $b .= ", ";
          }
          else {
            $b .= " (tags: ";
          }
          $b .= join (', ', @tags);
          $started_addendum = 1;
        }
      }
      if ($started_addendum) {
        $b .= ")";
      }
    }

    unless ( exists $fileinfo_printed{$b} ) {
      if ($fbegun) {
        $beauty .= ", ";
      } else {
        $fbegun = 1;
      }
      $beauty .= $b, $fileinfo_printed{$b} = 1;
    }
  }

  # Unanimous tags always come last.
  if ($Show_Tags && %unanimous_tags)
  {
    $beauty .= " (utags: ";
    $beauty .= join (', ', sort keys (%unanimous_tags));
    $beauty .= ")";
  }

  # todo: still have to take care of branch_roots?

  $beauty = "$beauty:";

  return $beauty;
}

# -------------------------------------

sub output_tagdate {
  my $self = shift;
  my ($fh, $time, $tag) = @_;

  my $fdatetime = $self->fdatetime($time);
  print $fh "$fdatetime  tag $tag\n\n";
  return;
}

# -------------------------------------

sub format_body {
  my $self = shift;
  my ($msg, $files, $qunklist) = @_;

  my $body;

  if ( $No_Wrap and ! $Summary ) {
    $msg = $self->preprocess_msg_text($msg);
    $files = $self->mywrap("\t", "\t  ", "* $files");
    $msg =~ s/\n(.+)/\n$Indent$1/g;
    unless ($After_Header eq " ") {
      $msg =~ s/^(.+)/$Indent$1/g;
    }
    if ( $Hide_Filenames ) {
      $body = $After_Header . $msg;
    } else {
      $body = $files . $After_Header . $msg;
    }
  } elsif ( $Summary ) {
    my ($filelist, $qunk);
    my (@DeletedQunks, @AddedQunks, @ChangedQunks);

    $msg = $self->preprocess_msg_text($msg);
    #
    #     Sort the files (qunks) according to the operation that was
    # performed.  Files which were added have no line change
    # indicator, whereas deleted files have state dead.
    #
    foreach $qunk ( @$qunklist ) {
      if ( "dead" eq $qunk->state) {
        push @DeletedQunks, $qunk;
      } elsif ( ! defined $qunk->lines ) {
        push @AddedQunks, $qunk;
      } else {
        push @ChangedQunks, $qunk;
      }
    }
    #
    #     The qunks list was  originally in tree search order.  Let's
    # get that back.  The lists, if they exist, will be reversed upon
    # processing.
    #

    #
    #     Now write the three sections onto $filelist
    #
    if ( @DeletedQunks ) {
      $filelist .= "\tDeleted:\n";
      foreach $qunk ( @DeletedQunks ) {
        $filelist .= "\t\t" . $qunk->filename;
        $filelist .= " (" . $qunk->revision . ")";
        $filelist .= "\n";
      }
      undef @DeletedQunks;
    }

    if ( @AddedQunks ) {
      $filelist .= "\tAdded:\n";
      foreach $qunk (@AddedQunks) {
        $filelist .= "\t\t" . $qunk->filename;
        $filelist .= " (" . $qunk->revision . ")";
        $filelist .= "\n";
      }
      undef @AddedQunks ;
    }

    if ( @ChangedQunks ) {
      $filelist .= "\tChanged:\n";
      foreach $qunk (@ChangedQunks) {
        $filelist .= "\t\t" . $qunk->filename;
        $filelist .= " (" . $qunk->revision . ")";
        $filelist .= ", \"" . $qunk->state . "\"";
        $filelist .= ", lines: " . $qunk->lines;
        $filelist .= "\n";
      }
      undef @ChangedQunks;
    }

    chomp $filelist;

    if ( $Hide_Filenames ) {
      $filelist = '';
    }

    $msg =~ s/\n(.*)/\n$Indent$1/g;
    unless ( $After_Header eq " " or $FSF_Style ) {
      $msg =~ s/^(.*)/$Indent$1/g;
    }

    unless ( $No_Wrap ) {
      if ( $FSF_Style ) {
        $msg = $self->wrap_log_entry($msg, '', 69, 69);
        chomp($msg);
        chomp($msg);
      } else {
        $msg = $self->mywrap('', $Indent, "$msg");
        $msg =~ s/[ \t]+\n/\n/g;
      }
    }

    $body = $filelist . $After_Header . $msg;
  } else {  # do wrapping, either FSF-style or regular
    my $latter_wrap = $No_Extra_Indent ? $Indent : "$Indent  ";

    if ( $FSF_Style ) {
      $files = $self->mywrap($Indent, $latter_wrap, "* $files");

      my $files_last_line_len = 0;
      if ( $After_Header eq " " ) {
        $files_last_line_len = $self->last_line_len($files);
        $files_last_line_len += 1;  # for $After_Header
      }

      $msg = $self->wrap_log_entry($msg, $latter_wrap, 69-$files_last_line_len, 69);
      $body = $files . $After_Header . $msg;
    } else {  # not FSF-style
      $msg = $self->preprocess_msg_text($msg);
      $body = $files . $After_Header . $msg;
      $body = $self->mywrap($Indent, $latter_wrap, "* $body");
      $body =~ s/[ \t]+\n/\n/g;
    }
  }

  return $body;
}

# ----------------------------------------------------------------------------

package CVS::Utils::ChangeLog::EntrySet::Output::XML;

use base qw( CVS::Utils::ChangeLog::EntrySet::Output );

use File::Basename qw( fileparse );

sub new {
  my $class = shift;
  my $self = $class->SUPER::new(@_);
}

# -------------------------------------

sub header_line {
  my $self = shift;
  my ($time, $author, $lastdate) = @_;

  my $header_line = '';

  my $isoDate;

  my ($y, $m, $d, $H, $M, $S) = (gmtime($time))[5,4,3,2,1,0];

  # Ideally, this would honor $UTC_Times and use +HH:MM syntax
  $isoDate = sprintf("%04d-%02d-%02dT%02d:%02d:%02dZ",
                     $y + 1900, $m + 1, $d, $H, $M, $S);

  my (undef,$min,$hour,$mday,$mon,$year,$wday)
    = $UTC_Times ? gmtime($time) : localtime($time);

  my $date = $self->fdatetime($time);
  $wday = $self->wday($wday);

  $header_line =
    sprintf ("%4u-%02u-%02u\n${wday}\n",
             $year+1900, $mon+1, $mday, $hour, $min);
  $header_line .= "$isoDate\n"
    unless $No_XML_ISO_Date;
  $header_line .= sprintf("%s\n" , $author);
}

# -------------------------------------

sub wday {
  my $self = shift; my $class = ref $self;
  my ($wday) = @_;

  return '' . $class->weekday_en($wday) . "\n";
}

# -------------------------------------

sub escape {
  my $self = shift;

  my $txt = shift;
  $txt =~ s/&/&/g;
  $txt =~ s//>/g;
  return $txt;
}

# -------------------------------------

sub output_header {
  my $self = shift;
  my ($fh) = @_;

  my $encoding    =
    length $XML_Encoding ? qq'encoding="$XML_Encoding"' : '';
  my $version     = 'version="1.0"';
  my $declaration =
    sprintf '', join ' ', grep length, $version, $encoding;
  my $root        =
    $No_XML_Namespace ?
      ''     :
        '';
  print $fh "$declaration\n\n$root\n\n";
}

# -------------------------------------

sub output_footer {
  my $self = shift;
  my ($fh) = @_;

  print $fh "\n";
}

# -------------------------------------

sub preprocess_msg_text {
  my $self = shift;
  my ($text) = @_;

  $text = $self->SUPER::preprocess_msg_text($text);

  $text = $self->escape($text);
  chomp $text;
  $text = "${text}\n";

  return $text;
}

# -------------------------------------

# Here we take a bunch of qunks and convert them into a printed
# summary that will include all the information the user asked for.
sub pretty_file_list {
  my $self = shift;
  my ($qunksref) = @_;

  my $beauty = '';          # The accumulating header string for this entry.
  my %non_unanimous_tags;   # Tags found in a proper subset of qunks
  my %unanimous_tags;       # Tags found in all qunks
  my %all_branches;         # Branches found in any qunk
  my $fbegun = 0;           # Did we begin printing filenames yet?

  my ($common_dir, $qunkrefs) =
    $self->_pretty_file_list(\(%unanimous_tags, %non_unanimous_tags, %all_branches),
      $qunksref);

  my @qunkrefs = @$qunkrefs;

  # If outputting XML, then our task is pretty simple, because we
  # don't have to detect common dir, common tags, branch prefixing,
  # etc.  We just output exactly what we have, and don't worry about
  # redundancy or readability.

  foreach my $qunkref (@qunkrefs)
  {
    my $filename    = $qunkref->filename;
    my $state       = $qunkref->state;
    my $revision    = $qunkref->revision;
    my $tags        = $qunkref->tags;
    my $branch      = $qunkref->branch;
    my $branchroots = $qunkref->roots;
    my $lines       = $qunkref->lines;

    $filename = $self->escape($filename);   # probably paranoia
    $revision = $self->escape($revision);   # definitely paranoia

    $beauty .= "\n";
    $beauty .= "${filename}\n";
    $beauty .= "${state}\n";
    $beauty .= "${revision}\n";

    if ($Show_Lines_Modified
        && $lines && $lines =~ m/\+(\d+)\s+-(\d+)/) {
        $beauty .= "$1\n";
        $beauty .= "$2\n";
    }

    if ($branch) {
      $branch   = $self->escape($branch);     # more paranoia
      $beauty .= "${branch}\n";
    }
    foreach my $tag (@$tags) {
      $tag = $self->escape($tag);  # by now you're used to the paranoia
      $beauty .= "${tag}\n";
    }
    foreach my $root (@$branchroots) {
      $root = $self->escape($root);  # which is good, because it will continue
      $beauty .= "${root}\n";
    }
    $beauty .= "\n";
  }

  # Theoretically, we could go home now.  But as long as we're here,
  # let's print out the common_dir and utags, as a convenience to
  # the receiver (after all, earlier code calculated that stuff
  # anyway, so we might as well take advantage of it).

  if ((scalar (keys (%unanimous_tags))) > 1) {
    foreach my $utag ((keys (%unanimous_tags))) {
      $utag = $self->escape($utag);   # the usual paranoia
      $beauty .= "${utag}\n";
    }
  }
  if ($common_dir) {
    $common_dir = $self->escape($common_dir);
    $beauty .= "${common_dir}\n";
  }

  # That's enough for XML, time to go home:
  return $beauty;
}

# -------------------------------------

sub output_tagdate {
  my $self = shift;
  my ($fh, $time, $tag) = @_;

  my ($y, $m, $d, $H, $M, $S) = (gmtime($time))[5,4,3,2,1,0];

  # Ideally, this would honor $UTC_Times and use +HH:MM syntax
  my $isoDate = sprintf("%04d-%02d-%02dT%02d:%02d:%02dZ",
                       $y + 1900, $m + 1, $d, $H, $M, $S);

  print $fh "\n";
  print $fh "$isoDate\n";
  print $fh "$tag\n";
  print $fh "\n\n";
  return;
}

# -------------------------------------

sub output_entry {
  my $self = shift;
  my ($fh, $entry) = @_;
  print $fh "\n$entry\n\n";
}

# -------------------------------------

sub format_body {
  my $self = shift;
  my ($msg, $files, $qunklist) = @_;

  $msg = $self->preprocess_msg_text($msg);
  return $files . $msg;
}

# ----------------------------------------------------------------------------

package CVS::Utils::ChangeLog::EntrySet::Output;

use Carp           qw( croak );
use File::Basename qw( fileparse );

# Class Utility Functions -------------

{ # form closure

my @weekdays = (qw(Sunday Monday Tuesday Wednesday Thursday Friday Saturday));
sub weekday_en {
  my $class = shift;
  return $weekdays[$_[0]];
}

}

# -------------------------------------

sub new {
  my ($proto, %args) = @_;
  my $class = ref $proto || $proto;

  my $follow_branches = delete $args{follow_branches};
  my $follow_only     = delete $args{follow_only};
  my $ignore_tags     = delete $args{ignore_tags};
  my $show_tags       = delete $args{show_tags};
  die "Unrecognized arg to EntrySet::Output::new: '$_'\n"
    for keys %args;

  bless +{follow_branches => $follow_branches,
          follow_only     => $follow_only,
          show_tags       => $show_tags,
          ignore_tags     => $ignore_tags,
         }, $class;
}

# Abstract Subrs ----------------------

sub wday               { croak "Whoops.  Abtract method call (wday).\n" }
sub pretty_file_list   { croak "Whoops.  Abtract method call (pretty_file_list).\n" }
sub output_tagdate     { croak "Whoops.  Abtract method call (output_tagdate).\n" }
sub header_line        { croak "Whoops.  Abtract method call (header_line).\n" }

# Instance Subrs ----------------------

sub output_header { }

# -------------------------------------

sub output_entry {
  my $self = shift;
  my ($fh, $entry) = @_;
  print $fh "$entry\n";
}

# -------------------------------------

sub output_footer { }

# -------------------------------------

sub escape { return $_[1] }

# -------------------------------------

sub _revision_is_wanted {
  my ($self, $qunk) = @_;

  my ($revision, $branch_numbers) = @{$qunk}{qw( revision branch_numbers )};
  my $follow_branches = $self->{follow_branches};
  my $follow_only     = $self->{follow_only};

  for my $ignore_tag (keys %{$self->{ignore_tags}}) {
    return
      if defined $qunk->{tags} and grep $_ eq $ignore_tag, @{$qunk->{tags}};
  }

  if ( keys %{$self->{show_tags}} ) {
    for my $show_tag (keys %{$self->{show_tags}}) {
      return
        if ! defined $qunk->{tags} or ! grep $_ eq $show_tag, @{$qunk->{tags}};
    }
  }

  return 1
    unless @$follow_branches + @$follow_only; # no follow is follow all

  for my $x (map([$_, 1], @$follow_branches),
             map([$_, 0], @$follow_only    )) {
    my ($branch, $followsub) = @$x;

    # Special case for following trunk revisions
    return 1
      if $branch =~ /^trunk$/i and $revision =~ /^[0-9]+\.[0-9]+$/;

    if ( my $branch_number = $branch_numbers->{$branch} ) {
      # Are we on one of the follow branches or an ancestor of same?

      # If this revision is a prefix of the branch number, or possibly is less
      # in the minormost number, OR if this branch number is a prefix of the
      # revision, then yes.  Otherwise, no.

      # So below, we determine if any of those conditions are met.

      # Trivial case: is this revision on the branch?  (Compare this way to
      # avoid regexps that screw up Emacs indentation, argh.)
      if ( substr($revision, 0, (length($branch_number) + 1))
           eq
           ($branch_number . ".") ) {
        if ( $followsub ) {
          return 1;
#        } elsif ( length($revision) == length($branch_number)+2 ) {
        } elsif ( substr($revision, length($branch_number)+1) =~ /^\d+$/ ) {
          return 1;
        }
      } elsif ( length($branch_number) > length($revision)
                and
                ! $No_Ancestors ) {
        # Non-trivial case: check if rev is ancestral to branch

        # r_left still has the trailing "."
        my ($r_left, $r_end) = ($revision =~ /^((?:\d+\.)+)(\d+)$/);

        # b_left still has trailing "."
        # b_mid has no trailing "."
        my ($b_left, $b_mid) = ($branch_number =~ /^((?:\d+\.)+)(\d+)\.\d+$/);
        return 1
          if $r_left eq $b_left and $r_end <= $b_mid;
      }
    }
  }

  return;
}

# -------------------------------------

sub output_changelog {
my $self = shift; my $class = ref $self;
    my ($grand_poobah) = @_;
    ### Process each ChangeLog
    
    while (my ($dir,$authorhash) = each %$grand_poobah) {
        &main::debug ("DOING DIR: $dir\n");
        
        # Here we twist our hash around, from being
        #   author => time => message => filelist
        # in %$authorhash to
        #   time => author => message => filelist
        # in %changelog.
        #
        # This is also where we merge entries.  The algorithm proceeds
        # through the timeline of the changelog with a sliding window of
        # $Max_Checkin_Duration seconds; within that window, entries that
        # have the same log message are merged.
        #
        # (To save space, we zap %$authorhash after we've copied
        # everything out of it.)
        
        # commit messages matching these will be ignored
        # should probably read these in from a file since they
        # will mostly change each release, but this is a quick hack!
        my @skip = ("Updating mailing lists URL",
                    "Updated bug reporting",
                    "use base, return true",
                    "Removed spurious ",
                    "cleaning unnecessary ",
                    "Updating emails",
                    "Improved POD markup",
                    "Fixed spaces",
                    "I'll be using bioperl.org mail address",
                    "Switched vanilla throw",
                    "regexp madness",
                    "minor edit",
                    "pod",
                    "pdoc",
                    "email address",
                    "typo",
                    "be explicit",
                    "using 'our'",
                    "silly email",
                    "regex clarity",
                    "polishing",
                    "Removed unused \"use vars",
                    "return, not return undef",
                    "lexically scoped file handles",
                    "No setting of own \$VERSION",
                    "do not return directly from sort",
                    "have NAME match module",
                    "Updating URLs",
                    "Changing emails",
                    "Updated doc",
                    "No setting own version",
                    "no log message");
        
        # not interested in these files
        my %files_to_skip = ( AUTHORS => 1,
                              Changes => 1,
                              'INSTALL.PROGRAMS' => 1,
                              README => 1,
                              BUGS => 1,
                              INSTALL => 1,
                              LICENSE => 1,
                              DEPENDENCIES => 1,
                              DEPRECATED => 1,
                              'INSTALL.WIN' => 1,
                              MANIFEST => 1,
                              'MANIFEST.SKIP' => 1,
                              PLATFORMS => 1);
        
        my %changelog;
        while (my ($author,$timehash) = each %$authorhash) {
            foreach my $time (sort {$a <=> $b} (keys %$timehash)) {
                next if ($Delta_Mode && (($time <= $Delta_StartTime) || ($time > $Delta_EndTime && $Delta_EndTime)));
                
                my $msghash = $timehash->{$time};
                MSG: while (my ($msg, $qunklist) = each %$msghash) {
                    foreach my $skip (@skip) {
                        if ($msg =~ /$skip/i) {
                            next MSG;
                        }
                    }
                    if ($msg =~ /merge/i && $msg =~ /head/i) {
                        next MSG;
                    }
                    
                    $msg =~ s/\n/ /g;
                    
                    foreach my $file (@{$qunklist->files}) {
                        $changelog{$file->filename}{$time} = $msg;
                    }
                }
            }
        }
        undef (%$authorhash);
        
        ### Now we can write out the ChangeLog!
        
        my ($logfile_here, $logfile_bak, $tmpfile);
        my $lastdate;
        
        if (! $Output_To_Stdout) {
            $logfile_here =  $dir . $Log_File_Name;
            $logfile_here =~ s/^\.\/\//\//;   # fix any leading ".//" problem
            $tmpfile      = "${logfile_here}.cvs2cl$$.tmp";
            $logfile_bak  = "${logfile_here}.bak";
            
            open (LOG_OUT, ">$tmpfile") or die "Unable to open \"$tmpfile\"";
        }
        else {
            open (LOG_OUT, ">-") or die "Unable to open stdout for writing";
        }
        
        print LOG_OUT $ChangeLog_Header;
        
        print LOG_OUT "These are detailed notes on changes made between $Delta_From and $Delta_To.\n\n";
        
        my %tag_date_printed;
        
        $self->output_header(\*LOG_OUT);
        
        my @file_list = sort {$a cmp $b} (keys %changelog);
        foreach my $file (@file_list) {
            # skip files we don't need to see changes for
            next if exists $files_to_skip{$file};
            next if $file =~ /^t\//;
            
            # convert module filenames to module name
            my $module = $file;
            if ($module =~ /^Bio/) {
                $module = ''.join("::", File::Spec->splitdir($file)).'';
                $module =~ s/\.pm//;
            }
            print LOG_OUT "; $module\n";
            foreach my $time (sort {$a <=> $b} keys %{$changelog{$file}}) {
                my $msg = $changelog{$file}{$time};
                
                # uppercase first letter
                $msg =~ s/^(\w)/\U$1/;
                
                # link bugs to bugzilla
                $msg =~ s/bug.*(\d{4})/{{Bugzilla|$1}}/i;
                
                print LOG_OUT ": $msg\n";
            }
            print LOG_OUT "\n";
        }
        
        $self->output_footer(\*LOG_OUT);
        
        close (LOG_OUT);
        
        if ( ! $Output_To_Stdout ) {
            # If accumulating, append old data to new before renaming.  But
            # don't append the most recent entry, since it's already in the
            # new log due to CVS's idiosyncratic interpretation of "log -d".
            if ($Cumulative && -f $logfile_here) {
                open $NEW_LOG, '>>', $tmpfile
                  or die "Could not append to file '$tmpfile': $!\n";
              
                open $OLD_LOG, '<', $logfile_here
                  or die "Could not read file '$logfile_here': $!";
                  
                my $started_first_entry = 0;
                my $passed_first_entry = 0;
                while (<$OLD_LOG>) {
                    if ( ! $passed_first_entry ) {
                        if (   ( ! $started_first_entry )
                            and /^(\d\d\d\d-\d\d-\d\d\s+(\w+\s+)?\d\d:\d\d)/
                            ) {
                            $started_first_entry = 1;
                        }
                        elsif ( /^(\d\d\d\d-\d\d-\d\d\s+(\w+\s+)?\d\d:\d\d)/ ) {
                            $passed_first_entry = 1;
                            print $NEW_LOG $_;
                        }
                    }
                    else {
                        print $NEW_LOG $_;
                    }
                }
                close $NEW_LOG;
                close $OLD_LOG;
            }
            
            if ( -f $logfile_here ) {
                rename $logfile_here, $logfile_bak;
            }
            rename $tmpfile, $logfile_here;
        }
    }
}

# -------------------------------------

# Don't call this wrap, because with 5.5.3, that clashes with the
# (unconditional :-( ) export of wrap() from Text::Wrap
sub mywrap {
  my $self = shift;
  my ($indent1, $indent2, @text) = @_;
  # If incoming text looks preformatted, don't get clever
  my $text = Text::Wrap::wrap($indent1, $indent2, @text);
  if ( grep /^\s+/m, @text ) {
    return $text;
  }
  my @lines = split /\n/, $text;
  $indent2 =~ s!^((?: {8})+)!"\t" x (length($1)/8)!e;
  $lines[0] =~ s/^$indent1\s+/$indent1/;
  s/^$indent2\s+/$indent2/
    for @lines[1..$#lines];
  my $newtext = join "\n", @lines;
  $newtext .= "\n"
    if substr($text, -1) eq "\n";
  return $newtext;
}

# -------------------------------------

sub preprocess_msg_text {
  my $self = shift;
  my ($text) = @_;

  # Strip out carriage returns (as they probably result from DOSsy editors).
  $text =~ s/\r\n/\n/g;
  # If it *looks* like two newlines, make it *be* two newlines:
  $text =~ s/\n\s*\n/\n\n/g;

  return $text;
}

# -------------------------------------

sub last_line_len {
  my $self = shift;

  my $files_list = shift;
  my @lines = split (/\n/, $files_list);
  my $last_line = pop (@lines);
  return length ($last_line);
}

# -------------------------------------

# A custom wrap function, sensitive to some common constructs used in
# log entries.
sub wrap_log_entry {
  my $self = shift;

  my $text = shift;                  # The text to wrap.
  my $left_pad_str = shift;          # String to pad with on the left.

  # These do NOT take left_pad_str into account:
  my $length_remaining = shift;      # Amount left on current line.
  my $max_line_length  = shift;      # Amount left for a blank line.

  my $wrapped_text = '';             # The accumulating wrapped entry.
  my $user_indent = '';              # Inherited user_indent from prev line.

  my $first_time = 1;                # First iteration of the loop?
  my $suppress_line_start_match = 0; # Set to disable line start checks.

  my @lines = split (/\n/, $text);
  while (@lines)   # Don't use `foreach' here, it won't work.
  {
    my $this_line = shift (@lines);
    chomp $this_line;

    if ($this_line =~ /^(\s+)/) {
      $user_indent = $1;
    }
    else {
      $user_indent = '';
    }

    # If it matches any of the line-start regexps, print a newline now...
    if ($suppress_line_start_match)
    {
      $suppress_line_start_match = 0;
    }
    elsif (($this_line =~ /^(\s*)\*\s+[a-zA-Z0-9]/)
           || ($this_line =~ /^(\s*)\* [a-zA-Z0-9_\.\/\+-]+/)
           || ($this_line =~ /^(\s*)\([a-zA-Z0-9_\.\/\+-]+(\)|,\s*)/)
           || ($this_line =~ /^(\s+)(\S+)/)
           || ($this_line =~ /^(\s*)- +/)
           || ($this_line =~ /^()\s*$/)
           || ($this_line =~ /^(\s*)\*\) +/)
           || ($this_line =~ /^(\s*)[a-zA-Z0-9](\)|\.|\:) +/))
    {
      # Make a line break immediately, unless header separator is set
      # and this line is the first line in the entry, in which case
      # we're getting the blank line for free already and shouldn't
      # add an extra one.
      unless (($After_Header ne " ") and ($first_time))
      {
        if ($this_line =~ /^()\s*$/) {
          $suppress_line_start_match = 1;
          $wrapped_text .= "\n${left_pad_str}";
        }

        $wrapped_text .= "\n${left_pad_str}";
      }

      $length_remaining = $max_line_length - (length ($user_indent));
    }

    # Now that any user_indent has been preserved, strip off leading
    # whitespace, so up-folding has no ugly side-effects.
    $this_line =~ s/^\s*//;

    # Accumulate the line, and adjust parameters for next line.
    my $this_len = length ($this_line);
    if ($this_len == 0)
    {
      # Blank lines should cancel any user_indent level.
      $user_indent = '';
      $length_remaining = $max_line_length;
    }
    elsif ($this_len >= $length_remaining) # Line too long, try breaking it.
    {
      # Walk backwards from the end.  At first acceptable spot, break
      # a new line.
      my $idx = $length_remaining - 1;
      if ($idx < 0) { $idx = 0 };
      while ($idx > 0)
      {
        if (substr ($this_line, $idx, 1) =~ /\s/)
        {
          my $line_now = substr ($this_line, 0, $idx);
          my $next_line = substr ($this_line, $idx);
          $this_line = $line_now;

          # Clean whitespace off the end.
          chomp $this_line;

          # The current line is ready to be printed.
          $this_line .= "\n${left_pad_str}";

          # Make sure the next line is allowed full room.
          $length_remaining = $max_line_length - (length ($user_indent));

          # Strip next_line, but then preserve any user_indent.
          $next_line =~ s/^\s*//;

          # Sneak a peek at the user_indent of the upcoming line, so
          # $next_line (which will now precede it) can inherit that
          # indent level.  Otherwise, use whatever user_indent level
          # we currently have, which might be none.
          my $next_next_line = shift (@lines);
          if ((defined ($next_next_line)) && ($next_next_line =~ /^(\s+)/)) {
            $next_line = $1 . $next_line if (defined ($1));
            # $length_remaining = $max_line_length - (length ($1));
            $next_next_line =~ s/^\s*//;
          }
          else {
            $next_line = $user_indent . $next_line;
          }
          if (defined ($next_next_line)) {
            unshift (@lines, $next_next_line);
          }
          unshift (@lines, $next_line);

          # Our new next line might, coincidentally, begin with one of
          # the line-start regexps, so we temporarily turn off
          # sensitivity to that until we're past the line.
          $suppress_line_start_match = 1;

          last;
        }
        else
        {
          $idx--;
        }
      }

      if ($idx == 0)
      {
        # We bottomed out because the line is longer than the
        # available space.  But that could be because the space is
        # small, or because the line is longer than even the maximum
        # possible space.  Handle both cases below.

        if ($length_remaining == ($max_line_length - (length ($user_indent))))
        {
          # The line is simply too long -- there is no hope of ever
          # breaking it nicely, so just insert it verbatim, with
          # appropriate padding.
          $this_line = "\n${left_pad_str}${this_line}";
        }
        else
        {
          # Can't break it here, but may be able to on the next round...
          unshift (@lines, $this_line);
          $length_remaining = $max_line_length - (length ($user_indent));
          $this_line = "\n${left_pad_str}";
        }
      }
    }
    else  # $this_len < $length_remaining, so tack on what we can.
    {
      # Leave a note for the next iteration.
      $length_remaining = $length_remaining - $this_len;

      if ($this_line =~ /\.$/)
      {
        $this_line .= "  ";
        $length_remaining -= 2;
      }
      else  # not a sentence end
      {
        $this_line .= " ";
        $length_remaining -= 1;
      }
    }

    # Unconditionally indicate that loop has run at least once.
    $first_time = 0;

    $wrapped_text .= "${user_indent}${this_line}";
  }

  # One last bit of padding.
  $wrapped_text .= "\n";

  return $wrapped_text;
}

# -------------------------------------

sub _pretty_file_list {
  my $self = shift;

  my ($unanimous_tags, $non_unanimous_tags, $all_branches, $qunksref) = @_;

  my @qunkrefs =
    grep +( ( ! $_->tags_exists
              or
              ! grep exists $ignore_tags{$_}, @{$_->tags})
            and
            ( ! keys %show_tags
              or
              ( $_->tags_exists
                and
                grep exists $show_tags{$_}, @{$_->tags} )
            )
          ),
    @$qunksref;

  my $common_dir;           # Dir prefix common to all files ('' if none)

  # First, loop over the qunks gathering all the tag/branch names.
  # We'll put them all in non_unanimous_tags, and take out the
  # unanimous ones later.
 QUNKREF:
  foreach my $qunkref (@qunkrefs)
  {
    # Keep track of whether all the files in this commit were in the
    # same directory, and memorize it if so.  We can make the output a
    # little more compact by mentioning the directory only once.
    if ($Common_Dir && (scalar (@qunkrefs)) > 1)
    {
      if (! (defined ($common_dir)))
      {
        my ($base, $dir);
        ($base, $dir, undef) = fileparse ($qunkref->filename);

        if ((! (defined ($dir)))  # this first case is sheer paranoia
            or ($dir eq '')
            or ($dir eq "./")
            or ($dir eq ".\\"))
        {
          $common_dir = '';
        }
        else
        {
          $common_dir = $dir;
        }
      }
      elsif ($common_dir ne '')
      {
        # Already have a common dir prefix, so how much of it can we preserve?
        $common_dir = &main::common_path_prefix ($qunkref->filename, $common_dir);
      }
    }
    else  # only one file in this entry anyway, so common dir not an issue
    {
      $common_dir = '';
    }

    if (defined ($qunkref->branch)) {
      $all_branches->{$qunkref->branch} = 1;
    }
    if (defined ($qunkref->tags)) {
      foreach my $tag (@{$qunkref->tags}) {
        $non_unanimous_tags->{$tag} = 1;
      }
    }
  }

  # Any tag held by all qunks will be printed specially... but only if
  # there are multiple qunks in the first place!
  if ((scalar (@qunkrefs)) > 1) {
    foreach my $tag (keys (%$non_unanimous_tags)) {
      my $everyone_has_this_tag = 1;
      foreach my $qunkref (@qunkrefs) {
        if ((! (defined ($qunkref->tags)))
            or (! (grep ($_ eq $tag, @{$qunkref->tags})))) {
          $everyone_has_this_tag = 0;
        }
      }
      if ($everyone_has_this_tag) {
        $unanimous_tags->{$tag} = 1;
        delete $non_unanimous_tags->{$tag};
      }
    }
  }

  return $common_dir, \@qunkrefs;
}

# -------------------------------------

sub fdatetime {
  my $self = shift;

  my ($year, $mday, $mon, $wday, $hour, $min);

  if ( @_ > 1 ) {
    ($year, $mday, $mon, $wday, $hour, $min) = @_;
  } else {
    my ($time) = @_;
    (undef, $min, $hour, $mday, $mon, $year, $wday) =
      $UTC_Times ? gmtime($time) : localtime($time);

    $year += 1900;
    $mon  += 1;
    $wday  = $self->wday($wday);
  }

  my $fdate = $self->fdate($year, $mon, $mday, $wday);

  if ($Show_Times) {
    my $ftime = $self->ftime($hour, $min);
    return "$fdate $ftime";
  } else {
    return $fdate;
  }
}

# -------------------------------------

sub fdate {
  my $self = shift;

  my ($year, $mday, $mon, $wday);

  if ( @_ > 1 ) {
    ($year, $mon, $mday, $wday) = @_;
  } else {
    my ($time) = @_;
    (undef, undef, undef, $mday, $mon, $year, $wday) =
      $UTC_Times ? gmtime($time) : localtime($time);

    $year += 1900;
    $mon  += 1;
    $wday  = $self->wday($wday);
  }

  return sprintf '%4u-%02u-%02u%s', $year, $mon, $mday, $wday;
}

# -------------------------------------

sub ftime {
  my $self = shift;

  my ($hour, $min);

  if ( @_ > 1 ) {
    ($hour, $min) = @_;
  } else {
    my ($time) = @_;
    (undef, $min, $hour) = $UTC_Times ? gmtime($time) : localtime($time);
  }

  return sprintf '%02u:%02u', $hour, $min;
}

# ----------------------------------------------------------------------------

package CVS::Utils::ChangeLog::Message;

sub new {
  my $class = shift;
  my ($msg) = @_;

  my %self = (msg => $msg, files => []);

  bless \%self, $class;
}

sub add_fileentry {
  my $self = shift;
  my ($fileentry) = @_;

  die "Not a fileentry: $fileentry"
    unless $fileentry->isa('CVS::Utils::ChangeLog::FileEntry');

  push @{$self->{files}}, $fileentry;
}

sub files { wantarray ? @{$_[0]->{files}} : $_[0]->{files} }

# ----------------------------------------------------------------------------

package CVS::Utils::ChangeLog::FileEntry;

use File::Basename qw( fileparse );

# Each revision of a file has a little data structure (a `qunk')
# associated with it.  That data structure holds not only the
# file's name, but any additional information about the file
# that might be needed in the output, such as the revision
# number, tags, branches, etc.  The reason to have these things
# arranged in a data structure, instead of just appending them
# textually to the file's name, is that we may want to do a
# little rearranging later as we write the output.  For example,
# all the files on a given tag/branch will go together, followed
# by the tag in parentheses (so trunk or otherwise non-tagged
# files would go at the end of the file list for a given log
# message).  This rearrangement is a lot easier to do if we
# don't have to reparse the text.
#
# A qunk looks like this:
#
#   {
#     filename    =>    "hello.c",
#     revision    =>    "1.4.3.2",
#     time        =>    a timegm() return value (moment of commit)
#     tags        =>    [ "tag1", "tag2", ... ],
#     branch      =>    "branchname" # There should be only one, right?
#     roots       =>    [ "branchtag1", "branchtag2", ... ]
#     lines       =>    "+x -y" # or undefined; x and y are integers
#   }

# Single top-level ChangeLog, or one per subdirectory?
my $distributed;
sub distributed { $#_ ? ($distributed = $_[1]) : $distributed; }

sub new {
  my $class = shift;
  my ($path, $time, $revision, $state, $lines,
      $branch_names, $branch_roots, $branch_numbers, $symbolic_names) = @_;

  my %self = (time     => $time,
              revision => $revision,
              state    => $state,
              lines    => $lines,
              branch_numbers => $branch_numbers,
             );

  if ( $distributed ) {
    @self{qw(filename dir_key)} = fileparse($path);
  } else {
    @self{qw(filename dir_key)} = ($path, './');
  }

  { # Scope for $branch_prefix
    (my ($branch_prefix) = ($revision =~ /((?:\d+\.)+)\d+/));
    $branch_prefix =~ s/\.$//;
    if ( $branch_names->{$branch_prefix} ) {
      my $branch_name = $branch_names->{$branch_prefix};
      $self{branch}   = $branch_name;
      $self{branches} = [$branch_name];
    }
    while ( $branch_prefix =~ s/^(\d+(?:\.\d+\.\d+)+)\.\d+\.\d+$/$1/ ) {
      push @{$self{branches}}, $branch_names->{$branch_prefix}
        if exists $branch_names->{$branch_prefix};
    }
  }

  # If there's anything in the @branch_roots array, then this
  # revision is the root of at least one branch.  We'll display
  # them as branch names instead of revision numbers, the
  # substitution for which is done directly in the array:
  $self{'roots'} = [ map { $branch_names->{$_} } @$branch_roots ]
    if @$branch_roots;

  if ( exists $symbolic_names->{$revision} ) {
    $self{tags} = delete $symbolic_names->{$revision};
    &main::delta_check($time, $self{tags});
  }

  bless \%self, $class;
}

sub filename       { $_[0]->{filename}       }
sub dir_key        { $_[0]->{dir_key}        }
sub revision       { $_[0]->{revision}       }
sub branch         { $_[0]->{branch}         }
sub state          { $_[0]->{state}          }
sub lines          { $_[0]->{lines}          }
sub roots          { $_[0]->{roots}          }
sub branch_numbers { $_[0]->{branch_numbers} }

sub tags        { $_[0]->{tags}     }
sub tags_exists {
  exists $_[0]->{tags};
}

# This may someday be used in a more sophisticated calculation of what other
# files are involved in this commit.  For now, we don't use it much except for
# delta mode, because the common-commit-detection algorithm is hypothesized to
# be "good enough" as it stands.
sub time     { $_[0]->{time}     }

# ----------------------------------------------------------------------------

package CVS::Utils::ChangeLog::EntrySetBuilder;

use File::Basename qw( fileparse );
use Time::Local    qw( timegm );

use constant MAILNAME => "/etc/mailname";

# In 'cvs log' output, one long unbroken line of equal signs separates files:
use constant FILE_SEPARATOR => '=' x 77;# . "\n";
# In 'cvs log' output, a shorter line of dashes separates log messages within
# a file:
use constant REV_SEPARATOR  => '-' x 28;# . "\n";

use constant EMPTY_LOG_MESSAGE => '*** empty log message ***';

# -------------------------------------

sub new {
  my ($proto) = @_;
  my $class = ref $proto || $proto;

  my $poobah  = CVS::Utils::ChangeLog::EntrySet->new;
  my $self = bless +{ grand_poobah => $poobah }, $class;

  $self->clear_file;
  $self->maybe_read_user_map_file;
  return $self;
}

# -------------------------------------

sub clear_msg {
  my ($self) = @_;

  # Make way for the next message
  undef $self->{rev_msg};
  undef $self->{rev_time};
  undef $self->{rev_revision};
  undef $self->{rev_author};
  undef $self->{rev_state};
  undef $self->{lines};
  $self->{rev_branch_roots} = [];       # For showing which files are branch
                                        # ancestors.
  $self->{collecting_symbolic_names} = 0;
}

# -------------------------------------

sub clear_file {
  my ($self) = @_;
  $self->clear_msg;

  undef $self->{filename};
  $self->{branch_names}   = +{};        # We'll grab branch names while we're
                                        # at it.
  $self->{branch_numbers} = +{};        # Save some revisions for
                                        # @Follow_Branches
  $self->{symbolic_names} = +{};        # Where tag names get stored.
}

# -------------------------------------

sub grand_poobah { $_[0]->{grand_poobah} }

# -------------------------------------

sub read_changelog {
  my ($self, $command) = @_;

  local (*READER, *WRITER);
  my $pid;
  if (! $Input_From_Stdin) {
    pipe(READER, WRITER)
      or die "Couldn't form pipe: $!\n";
    $pid = fork;
    die "Couldn't fork: $!\n"
      if ! defined $pid;
    if ( ! $pid ) { # child
      open STDOUT, '>&=' . fileno WRITER
        or die "Couldn't dup stderr to ", fileno WRITER, "\n";
      # strangely, some perls give spurious warnings about STDIN being opened
      # for output only these close calls precede the STDOUT reopen above.
      # I think they must be reusing fd 1.
      close READER;
      close STDIN;

      exec @$command;
    }

    close WRITER;

    &main::debug ("(run \"@$command\")\n");
  }
  else {
    open READER, '-' or die "Unable to open stdin for reading";
  }

  binmode READER;

 XX_Log_Source:
  while () {
    chomp;
    s!\r$!!;

    # If on a new file and don't see filename, skip until we find it, and
    # when we find it, grab it.
    if ( ! defined $self->{filename} ) {
      $self->read_file_path($_);
    } elsif ( /^symbolic names:$/ ) {
      $self->{collecting_symbolic_names} = 1;
    } elsif ( $self->{collecting_symbolic_names} ) {
      $self->read_symbolic_name($_);
    } elsif ( $_ eq FILE_SEPARATOR and ! defined $self->{rev_revision} ) {
      $self->clear_file;
    } elsif ( ! defined $self->{rev_revision} ) {
        # If have file name, but not revision, and see revision, then grab
        # it.  (We collect unconditionally, even though we may or may not
        # ever use it.)
      $self->read_revision($_);
    } elsif ( ! defined $self->{rev_time} ) { # and /^date: /) {
      $self->read_date_author_and_state($_);
    } elsif ( /^branches:\s+(.*);$/ ) {
      $self->read_branches($1);
    } elsif ( ! ( $_ eq FILE_SEPARATOR or $_ eq REV_SEPARATOR ) ) {
      # If have file name, time, and author, then we're just grabbing
      # log message texts:
      $self->{rev_msg} .= $_ . "\n";   # Normally, just accumulate the message...
    } else {
      my $noadd = 0;
      if ( ! $self->{rev_msg}
           or $self->{rev_msg} =~ /^\s*(\.\s*)?$/
           or index($self->{rev_msg}, EMPTY_LOG_MESSAGE) > -1 ) {
        # ... until a msg separator is encountered:
        # Ensure the message contains something:
        $self->clear_msg, $noadd = 1
          if $Prune_Empty_Msgs;
        $self->{rev_msg} = "[no log message]\n";
      }

      $self->add_file_entry
        unless $noadd;

      if ( $_ eq FILE_SEPARATOR ) {
        $self->clear_file;
      } else {
        $self->clear_msg;
      }
    }
  }

  close READER
    or die "Couldn't close pipe reader: $!\n";
  if ( defined $pid ) {
    my $rv;
    waitpid $pid, 0;
    0 == $?
      or $!=1, die sprintf("Problem reading log input (pid/exit/signal/core: %d/%d/%d/%d)\n",
                           $pid, $? >> 8, $? & 127, $? & 128);
  }
  return;
}

# -------------------------------------

sub add_file_entry {
  $_[0]->grand_poobah->add_fileentry(@{$_[0]}{qw(filename rev_time rev_revision
                                                 rev_state lines branch_names
                                                 rev_branch_roots
                                                 branch_numbers
                                                 symbolic_names
                                                 rev_author rev_msg)});
}

# -------------------------------------

sub maybe_read_user_map_file {
  my ($self) = @_;

  my %expansions;
  my $User_Map_Input;

  if ($User_Map_File)
  {
    if ( $User_Map_File =~ m{^([-\w\@+=.,\/]+):([-\w\@+=.,\/:]+)} and
         !-f $User_Map_File )
    {
      my $rsh = (exists $ENV{'CVS_RSH'} ? $ENV{'CVS_RSH'} : 'ssh');
      $User_Map_Input = "$rsh $1 'cat $2' |";
      &main::debug ("(run \"${User_Map_Input}\")\n");
    }
    else
    {
      $User_Map_Input = "<$User_Map_File";
    }

    open (MAPFILE, $User_Map_Input)
        or die ("Unable to open $User_Map_File ($!)");

    while ()
    {
      next if /^\s*#/;  # Skip comment lines.
      next if not /:/;  # Skip lines without colons.

      # It is now safe to split on ':'.
      my ($username, $expansion) = split ':';
      chomp $expansion;
      $expansion =~ s/^'(.*)'$/$1/;
      $expansion =~ s/^"(.*)"$/$1/;

      # If it looks like the expansion has a real name already, then
      # we toss the username we got from CVS log.  Otherwise, keep
      # it to use in combination with the email address.

      if ($expansion =~ /^\s*<{0,1}\S+@.*/) {
        # Also, add angle brackets if none present
        if (! ($expansion =~ /<\S+@\S+>/)) {
          $expansions{$username} = "$username <$expansion>";
        }
        else {
          $expansions{$username} = "$username $expansion";
        }
      }
      else {
        $expansions{$username} = $expansion;
      }
    } # fi ($User_Map_File)

    close (MAPFILE);
  }

  if (defined $User_Passwd_File)
  {
    if ( ! defined $Domain ) {
      if ( -e MAILNAME ) {
        chomp($Domain = slurp_file(MAILNAME));
      } else {
      MAILDOMAIN_CMD:
        for ([qw(hostname -d)], 'dnsdomainname', 'domainname') {
          my ($text, $exit, $sig, $core) = run_ext($_);
          if ( $exit == 0 && $sig == 0 && $core == 0 ) {
            chomp $text;
            if ( length $text ) {
              $Domain = $text;
              last MAILDOMAIN_CMD;
            }
          }
        }
      }
    }

    die "No mail domain found\n"
      unless defined $Domain;

    open (MAPFILE, "<$User_Passwd_File")
        or die ("Unable to open $User_Passwd_File ($!)");
    while ()
    {
      # all lines are valid
      my ($username, $pw, $uid, $gid, $gecos, $homedir, $shell) = split ':';
      my $expansion = '';
      ($expansion) = split (',', $gecos)
        if defined $gecos && length $gecos;

      my $mailname = $Domain eq '' ? $username : "$username\@$Domain";
      $expansions{$username} = "$expansion <$mailname>";
    }
    close (MAPFILE);
  }

 $self->{usermap} = \%expansions;
}

# -------------------------------------

sub read_file_path {
  my ($self, $line) = @_;

  my $path;

  if ( $line =~ /^Working file: (.*)/ ) {
    $path = $1;
  } elsif ( defined $RCS_Root
            and
            $line =~ m|^RCS file: $RCS_Root[/\\](.*),v$| ) {
    $path = $1;
    $path =~ s!Attic/!!;
  } else {
    return;
  }

  if ( @Ignore_Files ) {
    my $base;
    ($base, undef, undef) = fileparse($path);

    my $xpath = $Case_Insensitive ? lc($path) : $path;
    return
      if grep $path =~ /$_/, @Ignore_Files;
  }

  $self->{filename} = $path;
  return;
}

# -------------------------------------

sub read_symbolic_name {
  my ($self, $line) = @_;
  
  # All tag names are listed with whitespace in front in cvs log
  # output; so if see non-whitespace, then we're done collecting.
  if ( /^\S/ ) {
    $self->{collecting_symbolic_names} = 0;
    return;
  } else {
    # we're looking at a tag name, so parse & store it

    # According to the Cederqvist manual, in node "Tags", tag names must start
    # with an uppercase or lowercase letter and can contain uppercase and
    # lowercase letters, digits, `-', and `_'.  However, it's not our place to
    # enforce that, so we'll allow anything CVS hands us to be a tag:
    my ($tag_name, $tag_rev) = ($line =~ /^\s+([^:]+): ([\d.]+)$/);

    # A branch number either has an odd number of digit sections
    # (and hence an even number of dots), or has ".0." as the
    # second-to-last digit section.  Test for these conditions.
    my $real_branch_rev = '';
    if ( $tag_rev =~ /^(\d+\.\d+\.)+\d+$/             # Even number of dots...
         and
         $tag_rev !~ /^(1\.)+1$/ ) {                  # ...but not "1.[1.]1"
      $real_branch_rev = $tag_rev;
    } elsif ($tag_rev =~ /(\d+\.(\d+\.)+)0.(\d+)/) {  # Has ".0."
      $real_branch_rev = $1 . $3;
    }

    # If we got a branch, record its number.
    if ( $real_branch_rev ) {
      $self->{branch_names}->{$real_branch_rev} = $tag_name;
      $self->{branch_numbers}->{$tag_name} = $real_branch_rev;
      $tag_rev =~ s/^(\d+\.\d+).+/$1/;
    }
    
    # regardless if it is a name on a branch, store it as symbolic name so that tag deltas always work
    push @{$self->{symbolic_names}->{$tag_rev}}, $tag_name;
  }

  $self->{collecting_symbolic_names} = 1;
  return;
}

# -------------------------------------

sub read_revision {
  my ($self, $line) = @_;

  my ($revision) = ( $line =~ /^revision (\d+\.[\d.]+)/ );

  return
    unless $revision;

  $self->{rev_revision} = $revision;
  return;
}

# -------------------------------------

{ # Closure over %gecos_warned
my %gecos_warned;
sub read_date_author_and_state {
  my ($self, $line) = @_;

  my ($time, $author, $state) = $self->parse_date_author_and_state($line);

  if ( defined($self->{usermap}->{$author}) and $self->{usermap}->{$author} ) {
    $author = $self->{usermap}->{$author};
  } elsif ( defined $Domain or $Gecos == 1 ) {
    my $email = $author;
    $email = $author."@".$Domain
      if defined $Domain && $Domain ne '';

    my $pw = getpwnam($author);
    my ($fullname, $office, $workphone, $homephone, $gcos);
    if ( defined $pw ) {
      $gcos = (getpwnam($author))[6];
      ($fullname, $office, $workphone, $homephone) =
        split /\s*,\s*/, $gcos;
    } else {
      warn "Couldn't find gecos info for author '$author'\n"
        unless $gecos_warned{$author}++;
      $fullname = '';
    }
    for (grep defined, $fullname, $office, $workphone, $homephone) {
      s/&/ucfirst(lc($pw->name))/ge;
    }
    $author = $fullname . "  <" . $email . ">"
      if $fullname ne '';
  }

  $self->{rev_state}  = $state;
  $self->{rev_time}   = $time;
  $self->{rev_author} = $author;
  return;
}
}

# -------------------------------------

sub read_branches {
  # A "branches: ..." line here indicates that one or more branches
  # are rooted at this revision.  If we're showing branches, then we
  # want to show that fact as well, so we collect all the branches
  # that this is the latest ancestor of and store them in
  # $self->[rev_branch_roots}.  Just for reference, the format of the
  # line we're seeing at this point is:
  #
  #    branches:  1.5.2;  1.5.4;  ...;
  #
  # Okay, here goes:
  my ($self, $line) = @_;

  # Ugh.  This really bothers me.  Suppose we see a log entry
  # like this:
  #
  #    ----------------------------
  #    revision 1.1
  #    date: 1999/10/17 03:07:38;  author: jrandom;  state: Exp;
  #    branches:  1.1.2;
  #    Intended first line of log message begins here.
  #    ----------------------------
  #
  # The question is, how we can tell the difference between that
  # log message and a *two*-line log message whose first line is
  #
  #    "branches:  1.1.2;"
  #
  # See the problem?  The output of "cvs log" is inherently
  # ambiguous.
  #
  # For now, we punt: we liberally assume that people don't
  # write log messages like that, and just toss a "branches:"
  # line if we see it but are not showing branches.  I hope no
  # one ever loses real log data because of this.
  if ( $Show_Branches ) {
    $line =~ s/(1\.)+1;|(1\.)+1$//;  # ignore the trivial branch 1.1.1
    $self->{rev_branch_roots} = [split /;\s+/, $line]
      if length $line;
  }
}

# -------------------------------------

sub parse_date_author_and_state {
  my ($self, $line) = @_;
  # Parses the date/time and author out of a line like:
  #
  # date: 1999/02/19 23:29:05;  author: apharris;  state: Exp;
  #
  # or, in CVS 1.12.9:
  #
  # date: 2004-06-05 16:10:32 +0000; author: somebody; state: Exp;

  my ($year, $mon, $mday, $hours, $min, $secs, $utcOffset, $author, $state, $rest) =
    $line =~
      m!(\d+)[-/](\d+)[-/](\d+)\s+(\d+):(\d+):(\d+)(\s+[+-]\d{4})?;\s+
        author:\s+([^;]+);\s+state:\s+([^;]+);(.*)!x
    or  die "Couldn't parse date ``$line''";
  die "Bad date or Y2K issues"
    unless $year > 1969 and $year < 2258;
  # Kinda arbitrary, but useful as a sanity check
  my $time = timegm($secs, $min, $hours, $mday, $mon-1, $year-1900);
  if ( defined $utcOffset ) {
    my ($plusminus, $hour, $minute) = ($utcOffset =~ m/([+-])(\d\d)(\d\d)/);
    my $offset = (($hour * 60) + $minute) * 60 * ($plusminus eq '+' ? -1 : 1);
    $time += $offset;
  }
  if ( $rest =~ m!\s+lines:\s+(.*)! ) {
    $self->{lines} = $1;
  }

  return $time, $author, $state;
}

# Subrs ----------------------------------------------------------------------

package main;

sub delta_check {
  my ($time, $tags) = @_;

  # If we're in 'delta' mode, update the latest observed times for the
  # beginning and ending tags, and when we get around to printing output, we
  # will simply restrict ourselves to that timeframe...
  return
    unless $Delta_Mode;

  $Delta_StartTime = $time
    if $time > $Delta_StartTime and grep { $_ eq $Delta_From } @$tags;

  $Delta_EndTime = $time
    if $time > $Delta_EndTime and grep { $_ eq $Delta_To } @$tags;
}

sub run_ext {
  my ($cmd) = @_;
  $cmd = [$cmd]
    unless ref $cmd;
  local $" = ' ';
  my $out = qx"@$cmd 2>&1";
  my $rv  = $?;
  my ($sig, $core, $exit) = ($? & 127, $? & 128, $? >> 8);
  return $out, $exit, $sig, $core;
}

# -------------------------------------

# If accumulating, grab the boundary date from pre-existing ChangeLog.
sub maybe_grab_accumulation_date {
  if (! $Cumulative || $Update) {
    return '';
  }

  # else

  open (LOG, "$Log_File_Name")
      or die ("trouble opening $Log_File_Name for reading ($!)");

  my $boundary_date;
  while ()
  {
    if (/^(\d\d\d\d-\d\d-\d\d\s+(\w+\s+)?\d\d:\d\d)/)
    {
      $boundary_date = "$1";
      last;
    }
  }

  close (LOG);

  # convert time from utc to local timezone if the ChangeLog has
  # dates/times in utc
  if ($UTC_Times && $boundary_date)
  {
    # convert the utc time to a time value
    my ($year,$mon,$mday,$hour,$min) = $boundary_date =~
      m#(\d+)-(\d+)-(\d+)\s+(\d+):(\d+)#;
    my $time = timegm(0,$min,$hour,$mday,$mon-1,$year-1900);
    # print the timevalue in the local timezone
    my ($ignore,$wday);
    ($ignore,$min,$hour,$mday,$mon,$year,$wday) = localtime($time);
    $boundary_date=sprintf ("%4u-%02u-%02u %02u:%02u",
                            $year+1900,$mon+1,$mday,$hour,$min);
  }

  return $boundary_date;
}

# -------------------------------------

# Fills up a ChangeLog structure in the current directory.
sub derive_changelog {
  my ($command) = @_;

  # See "The Plan" above for a full explanation.

  # Might be adding to an existing ChangeLog
  my $accumulation_date = maybe_grab_accumulation_date;
  if ($accumulation_date) {
    # Insert -d immediately after 'cvs log'
    my $Log_Date_Command = "-d>${accumulation_date}";

    my ($log_index) = grep $command->[$_] eq 'log', 0..$#$command;
    splice @$command, $log_index+1, 0, $Log_Date_Command;
    &debug ("(adding log msg starting from $accumulation_date)\n");
  }

#  output_changelog(read_changelog($command));
  my $builder = CVS::Utils::ChangeLog::EntrySetBuilder->new;
  $builder->read_changelog($command);
  $builder->grand_poobah->output_changelog;
}

# -------------------------------------

sub min { $_[0] < $_[1] ? $_[0] : $_[1] }

# -------------------------------------

sub common_path_prefix {
  my ($path1, $path2) = @_;

  # For compatibility (with older versions of cvs2cl.pl), we think in UN*X
  # terms, and mould windoze filenames to match.  Is this really appropriate?
  # If a file is checked in under UN*X, and cvs log run on windoze, which way
  # do the path separators slope?  Can we use fileparse as per the local
  # conventions?  If so, we should probably have a user option to specify an
  # OS to emulate to handle stdin-fed logs.  If we did this, we could avoid
  # the nasty \-/ transmogrification below.

  my ($dir1, $dir2) = map +(fileparse($_))[1], $path1, $path2;

  # Transmogrify Windows filenames to look like Unix.
  # (It is far more likely that someone is running cvs2cl.pl under
  # Windows than that they would genuinely have backslashes in their
  # filenames.)
  tr!\\!/!
    for $dir1, $dir2;

  my ($accum1, $accum2, $last_common_prefix) = ('') x 3;

  my @path1 = grep length($_), split qr!/!, $dir1;
  my @path2 = grep length($_), split qr!/!, $dir2;

  my @common_path;
  for (0..min($#path1,$#path2)) {
    if ( $path1[$_] eq $path2[$_]) {
      push @common_path, $path1[$_];
    } else {
      last;
    }
  }

  return join '', map "$_/", @common_path;
}

# -------------------------------------

sub parse_options {
  # Check this internally before setting the global variable.
  my $output_file;

  # If this gets set, we encountered unknown options and will exit at
  # the end of this subroutine.
  my $exit_with_admonishment = 0;

  # command to generate the log
  my @log_source_command = qw( cvs log );

  my (@Global_Opts, @Local_Opts);

  Getopt::Long::Configure(qw( bundling permute no_getopt_compat
                              pass_through no_ignore_case ));
  GetOptions('help|usage|h'   => \$Print_Usage,
             'debug'          => \$Debug,        # unadvertised option, heh
             'version'        => \$Print_Version,

             'file|f=s'       => \$output_file,
             'accum'          => \$Cumulative,
             'update'         => \$Update,
             'fsf'            => \$FSF_Style,
             'rcs=s'          => \$RCS_Root,
             'usermap|U=s'    => \$User_Map_File,
             'gecos'          => \$Gecos,
             'domain=s'       => \$Domain,
             'passwd=s'       => \$User_Passwd_File,
             'window|W=i'     => \$Max_Checkin_Duration,
             'chrono'         => \$Chronological_Order,
             'ignore|I=s'     => \@Ignore_Files,
             'case-insensitive|C' => \$Case_Insensitive,
             'regexp|R=s'     => \$Regexp_Gate,
             'stdin'          => \$Input_From_Stdin,
             'stdout'         => \$Output_To_Stdout,
             'distributed|d'  => sub { CVS::Utils::ChangeLog::FileEntry->distributed(1) },
             'prune|P'        => \$Prune_Empty_Msgs,
             'no-wrap'        => \$No_Wrap,
             'gmt|utc'        => \$UTC_Times,
             'day-of-week|w'  => \$Show_Day_Of_Week,
             'revisions|r'    => \$Show_Revisions,
             'show-dead'      => \$Show_Dead,
             'tags|t'         => \$Show_Tags,
             'tagdates|T'     => \$Show_Tag_Dates,
             'branches|b'     => \$Show_Branches,
             'follow|F=s'     => \@Follow_Branches,
             'follow-only=s'  => \@Follow_Only,
             'xml-encoding=s' => \$XML_Encoding,
             'xml'            => \$XML_Output,
             'noxmlns'        => \$No_XML_Namespace,
             'no-xml-iso-date' => \$No_XML_ISO_Date,
             'no-ancestors'   => \$No_Ancestors,
             'lines-modified' => \$Show_Lines_Modified,

             'no-indent'    => sub {
               $Indent = '';
             },

             'summary'      => sub {
               $Summary = 1;
               $After_Header = "\n\n"; # Summary implies --separate-header
             },

             'no-times'     => sub {
               $Show_Times = 0;
             },

             'no-hide-branch-additions' => sub {
               $Hide_Branch_Additions = 0;
             },

             'no-common-dir'  => sub {
               $Common_Dir = 0;
             },

             'ignore-tag=s'   => sub {
               $ignore_tags{$_[1]} = 1;
             },

             'show-tag=s'     => sub {
               $show_tags{$_[1]} = 1;
             },

             # Deliberately undocumented.  This is not a public interface, and
             # may change/disappear at any time.
             'test-code=s'    => \$TestCode,

             'delta=s'        => sub {
               my $arg = $_[1];
               if ( $arg =~
                    /^([A-Za-z][A-Za-z0-9_\-\]\[]*):([A-Za-z][A-Za-z0-9_\-\]\[]*)$/ ) {
                 $Delta_From = $1;
                 $Delta_To = $2;
                 $Delta_Mode = 1;
               } else {
                 die "--delta FROM_TAG:TO_TAG is what you meant to say.\n";
               }
             },

             'FSF'             => sub {
               $Show_Times = 0;
               $Common_Dir = 0;
               $No_Extra_Indent = 1;
               $Indent = "\t";
             },

             'header=s'        => sub {
               my $narg = $_[1];
               $ChangeLog_Header = &slurp_file ($narg);
               if (! defined ($ChangeLog_Header)) {
                 $ChangeLog_Header = '';
               }
             },

             'global-opts|g=s' => sub {
               my $narg = $_[1];
               push @Global_Opts, $narg;
               splice @log_source_command, 1, 0, $narg;
             },

             'log-opts|l=s' => sub {
               my $narg = $_[1];
               push @Local_Opts, $narg;
               push @log_source_command, $narg;
             },

             'mailname=s'   => sub {
               my $narg = $_[1];
               warn "--mailname is deprecated; please use --domain instead\n";
               $Domain = $narg;
             },

             'separate-header|S' => sub {
               $After_Header = "\n\n";
               $No_Extra_Indent = 1;
             },

             'group-within-date' => sub {
               $GroupWithinDate = 1;
               $Show_Times = 0;
             },

             'hide-filenames' => sub {
               $Hide_Filenames = 1;
               $After_Header = '';
             },
            )
    or die "options parsing failed\n";

  push @log_source_command, map "$_", @ARGV;

  ## Check for contradictions...

  if ($Output_To_Stdout && CVS::Utils::ChangeLog::FileEntry->distributed) {
    print STDERR "cannot pass both --stdout and --distributed\n";
    $exit_with_admonishment = 1;
  }

  if ($Output_To_Stdout && $output_file) {
    print STDERR "cannot pass both --stdout and --file\n";
    $exit_with_admonishment = 1;
  }

  if ($Input_From_Stdin && @Global_Opts) {
    print STDERR "cannot pass both --stdin and -g\n";
    $exit_with_admonishment = 1;
  }

  if ($Input_From_Stdin && @Local_Opts) {
    print STDERR "cannot pass both --stdin and -l\n";
    $exit_with_admonishment = 1;
  }

  if ($XML_Output && $Cumulative) {
    print STDERR "cannot pass both --xml and --accum\n";
    $exit_with_admonishment = 1;
  }

  # Other consistency checks and option-driven logic

  # Bleargh.  Compensate for a deficiency of custom wrapping.
  if ( ($After_Header ne " ") and $FSF_Style ) {
    $After_Header .= "\t";
  }

  @Ignore_Files = map lc, @Ignore_Files
    if $Case_Insensitive;

  # Or if any other error message has already been printed out, we
  # just leave now:
  if ($exit_with_admonishment) {
    &usage ();
    exit (1);
  }
  elsif ($Print_Usage) {
    &usage ();
    exit (0);
  }
  elsif ($Print_Version) {
    &version ();
    exit (0);
  }

  ## Else no problems, so proceed.

  if ($output_file) {
    $Log_File_Name = $output_file;
  }

  return \@log_source_command;
}

# -------------------------------------

sub slurp_file {
  my $filename = shift || die ("no filename passed to slurp_file()");
  my $retstr;

  open (SLURPEE, "<${filename}") or die ("unable to open $filename ($!)");
  local $/ = undef;
  $retstr = ;
  close (SLURPEE);
  return $retstr;
}

# -------------------------------------

sub debug {
  if ($Debug) {
    my $msg = shift;
    print STDERR $msg;
  }
}

# -------------------------------------

sub version {
  print "cvs2cl.pl version ${VERSION}; distributed under the GNU GPL.\n";
}

# -------------------------------------

sub usage {
  &version ();

  eval "use Pod::Usage qw( pod2usage )";

   if ( $@ ) {
    print <<'END';

* Pod::Usage was not found.  The formatting may be suboptimal.  Consider
  upgrading your Perl --- Pod::Usage is standard from 5.6 onwards, and
  versions of perl prior to 5.6 are getting rather rusty, now.  Alternatively,
  install Pod::Usage direct from CPAN.
END

    local $/ = undef;
    my $message = ;
    $message =~ s/^=(head1|item) //gm;
    $message =~ s/^=(over|back).*\n//gm;
    $message =~ s/\n{3,}/\n\n/g;
    print $message;
  } else {
    print "\n";
    pod2usage( -exitval => 'NOEXIT',
               -verbose => 1,
               -output  => \*STDOUT,
             );
  }

  return;
}

# Main -----------------------------------------------------------------------

my $log_source_command = parse_options;
if ( defined $TestCode ) {
  eval $TestCode;
  die "Eval failed: '$@'\n"
    if $@;
} else {
  derive_changelog($log_source_command);
}

__DATA__

=head1 NAME

cvs2cl_by_file.pl - convert cvs log messages to changelogs

=head1 SYNOPSIS

B [I] [I [I ...]]
cvs2cl_by_file.pl --delta bioperl-release-1-5-1:bioperl-release-1-5-2

=head1 DESCRIPTION

This is a quick hack version of cvs2cl.pl that simply outputs in a
file-centric way.
Only CVS::Utils::ChangeLog::EntrySet::Output::output_changelog
was altered

Usage:
cvs2cl_by_file.pl --delta bioperl-release-1-5-1:bioperl-release-1-5-2
Generates a file called ChangeLog showing, per file, all the commit
messages since tag bioperl-release-1-5-1 up to tag bioperl-release-1-5-2

Original cvs2cl docs now follow, but some things may not work because of
the hack!


cvs2cl produces a GNU-style ChangeLog for CVS-controlled sources by
running "cvs log" and parsing the output. Duplicate log messages get
unified in the Right Way.

The default output of cvs2cl is designed to be compact, formally unambiguous,
but still easy for humans to read.  It should be largely self-explanatory; the
one abbreviation that might not be obvious is "utags".  That stands for
"universal tags" -- a universal tag is one held by all the files in a given
change entry.

If you need output that's easy for a program to parse, use the B<--xml> option.
Note that with XML output, just about all available information is included
with each change entry, whether you asked for it or not, on the theory that
your parser can ignore anything it's not looking for.

If filenames are given as arguments cvs2cl only shows log information for the
named files.

=head1 OPTIONS

=over 4

=item B<-h>, B<-help>, B<--help>, B<-?>

Show a short help and exit.

=item B<--version>

Show version and exit.

=item B<-r>, B<--revisions>

Show revision numbers in output.

=item B<-b>, B<--branches>

Show branch names in revisions when possible.

=item B<-t>, B<--tags>

Show tags (symbolic names) in output.

=item B<-T>, B<--tagdates>

Show tags in output on their first occurance.

=item B<--show-dead>

Show dead files.

=item B<--stdin>

Read from stdin, don't run cvs log.

=item B<--stdout>

Output to stdout not to ChangeLog.

=item B<-d>, B<--distributed>

Put ChangeLogs in subdirs.

=item B<-f> I, B<--file> I

Write to I instead of ChangeLog.

=item B<--fsf>

Use this if log data is in FSF ChangeLog style.

=item B<--FSF>

Attempt strict FSF-standard compatible output.

=item B<-W> I, B<--window> I

Window of time within which log entries unify.

=item -B I, B<--usermap> I

Expand usernames to email addresses from I.

=item B<--passwd> I

Use system passwd file for user name expansion.  If no mail domain is provided
(via B<--domain>), it tries to read one from B, output of B, B, or B.  cvs2cl exits with an error if none of
those options is successful. Use a domain of '' to prevent the addition of a
mail domain.

=item B<--domain> I

Domain to build email addresses from.

=item B<--gecos>

Get user information from GECOS data.

=item B<-R> I, B<--regexp> I

Include only entries that match I.  This option may be used multiple
times.

=item B<-I> I, B<--ignore> I

Ignore files whose names match I.  This option may be used multiple
times.  The regexp is a perl regular expression.  It is matched as is; you may
want to prefix with a ^ or suffix with a $ to anchor the match.

=item B<-C>, B<--case-insensitive>

Any regexp matching is done case-insensitively.

=item B<-F> I, B<--follow> I

Show only revisions on or ancestral to I.

=item B<--follow-only> I

Like --follow, but sub-branches are not followed.

=item B<--no-ancestors>

When using B<-F>, only track changes since the I started.

=item B<--no-hide-branch-additions>

By default, entries generated by cvs for a file added on a branch (a dead 1.1
entry) are not shown.  This flag reverses that action.

=item B<-S>, B<--separate-header>

Blank line between each header and log message.

=item B<--summary>

Add CVS change summary information.

=item B<--no-wrap>

Don't auto-wrap log message (recommend B<-S> also).

=item B<--no-indent>

Don't indent log message

=item B<--gmt>, B<--utc>

Show times in GMT/UTC instead of local time.

=item B<--accum>

Add to an existing ChangeLog (incompatible with B<--xml>).

=item B<-w>, B<--day-of-week>

Show day of week.

=item B<--no-times>

Don't show times in output.

=item B<--chrono>

Output log in chronological order (default is reverse chronological order).

=item B<--header> I

Get ChangeLog header from I ("B<->" means stdin).

=item B<--xml>

Output XML instead of ChangeLog format.

=item B<--xml-encoding> I

Insert encoding clause in XML header.

=item B<--noxmlns>

Don't include xmlns= attribute in root element.

=item B<--hide-filenames>

Don't show filenames (ignored for XML output).

=item B<--no-common-dir>

Don't shorten directory names from filenames.

=item B<--rcs> I

Handle filenames from raw RCS, for instance those produced by "cvs rlog"
output, stripping the prefix I.

=item B<-P>, B<--prune>

Don't show empty log messages.

=item B<--lines-modified>

Output the number of lines added and the number of lines removed for
each checkin (if applicable). At the moment, this only affects the
XML output mode.

=item B<--ignore-tag> I

Ignore individual changes that are associated with a given tag.
May be repeated, if so, changes that are associated with any of
the given tags are ignored.

=item B<--show-tag> I

Log only individual changes that are associated with a given
tag.  May be repeated, if so, changes that are associated with
any of the given tags are logged.

=item B<--delta> IB<:>I

Attempt a delta between two tags (since I up to and
including I).  The algorithm is a simple date-based one
(this is a hard problem) so results are imperfect.

=item B<-g> I, B<--global-opts> I

Pass I to cvs like in "cvs I log ...".

=item B<-l> I, B<--log-opts> I

Pass I to cvs log like in "cvs ... log I".

=back

Notes about the options and arguments:

=over 4

=item *

The B<-I> and B<-F> options may appear multiple times.

=item *

To follow trunk revisions, use "B<-F trunk>" ("B<-F TRUNK>" also works).  This is
okay because no would ever, ever be crazy enough to name a branch "trunk",
right?  Right.

=item *

For the B<-U> option, the I should be formatted like CVSROOT/users. That is,
each line of I looks like this:

       jrandom:jrandom@red-bean.com

or maybe even like this

       jrandom:'Jesse Q. Random '

Don't forget to quote the portion after the colon if necessary.

=item *

Many people want to filter by date.  To do so, invoke cvs2cl.pl like this:

       cvs2cl.pl -l "-d'DATESPEC'"

where DATESPEC is any date specification valid for "cvs log -d".  (Note that
CVS 1.10.7 and below requires there be no space between -d and its argument).

=item *

Dates/times are interpreted in the local time zone.

=item *

Remember to quote the argument to `B<-l>' so that your shell doesn't interpret
spaces as argument separators.

=item *

See the 'Common Options' section of the cvs manual ('info cvs' on UNIX-like
systems) for more information.

=item *

Note that the rules for quoting under windows shells are different.

=item *

To run in an automated environment such as CGI or PHP, suidperl may be needed
in order to execute as the correct user to enable /cvsroot read lock files to
be written for the 'cvs log' command.  This is likely just a case of changing
the /usr/bin/perl command to /usr/bin/suidperl, and explicitly declaring the
PATH variable.

=back

=head1 EXAMPLES

Some examples (working on UNIX shells):

      # logs after 6th March, 2003 (inclusive)
      cvs2cl.pl -l "-d'>2003-03-06'"
      # logs after 4:34PM 6th March, 2003 (inclusive)
      cvs2cl.pl -l "-d'>2003-03-06 16:34'"
      # logs between 4:46PM 6th March, 2003 (exclusive) and
      # 4:34PM 6th March, 2003 (inclusive)
      cvs2cl.pl -l "-d'2003-03-06 16:46>2003-03-06 16:34'"

Some examples (on non-UNIX shells):

      # Reported to work on windows xp/2000
      cvs2cl.pl -l  "-d"">2003-10-18;today<"""

=head1 AUTHORS

=over 4

=item Karl Fogel

=item Melissa O'Neill

=item Martyn J. Pearce

=back

Contributions from

=over 4

=item Mike Ayers

=item Tim Bradshaw

=item Richard Broberg

=item Nathan Bryant

=item Oswald Buddenhagen

=item Neil Conway

=item Arthur de Jong

=item Mark W. Eichin

=item Dave Elcock

=item Reid Ellis

=item Simon Josefsson

=item Robin Hugh Johnson

=item Terry Kane

=item Pete Kempf

=item Akos Kiss

=item Claus Klein

=item Eddie Kohler

=item Richard Laager

=item Kevin Lilly

=item Karl-Heinz Marbaise

=item Mitsuaki Masuhara

=item Henrik Nordstrom

=item Joe Orton

=item Peter Palfrader

=item Thomas Parmelan

=item Jordan Russell

=item Jacek Sliwerski

=item Johannes Stezenbach

=item Joseph Walton

=item Ernie Zapata

=back

=head1 BUGS

Please report bugs to C.

=head1 PREREQUISITES

This script requires C, C, and C.  It
also seems to require C or higher.

=head1 OPERATING SYSTEM COMPATIBILITY

Should work on any OS.

=head1 SCRIPT CATEGORIES

Version_Control/CVS

=head1 COPYRIGHT

(C) 2001,2002,2003,2004 Martyn J. Pearce Efluffy@cpan.orgE, under the GNU GPL.

(C) 1999 Karl Fogel Ekfogel@red-bean.comE, under the GNU GPL.

cvs2cl.pl is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2, or (at your option)
any later version.

cvs2cl.pl is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You may have received a copy of the GNU General Public License
along with cvs2cl.pl; see the file COPYING.  If not, write to the
Free Software Foundation, Inc., 59 Temple Place - Suite 330,
Boston, MA 02111-1307, USA.

=head1 SEE ALSO

cvs(1)
BioPerl-1.007002/maintenance/dependencies.pl000444000766000024      1703713155576320 21010 0ustar00cjfieldsstaff000000000000# $Id: dependencies.pl 10084 2006-07-04 22:23:29Z cjfields $
#
#!/usr/bin/perl

use strict;
use warnings;
use File::Find;
use Perl6::Form;
use Getopt::Long;
use Module::CoreList;
use CPANPLUS::Backend;

my $dep_header = < \$verbose,
        'dir:s' => \$dir,
        'depfile:s' => \$depfile,
        'p|perl:s' => \$version,
        's|skipbio' => \$skipbio,
        'h|help|?' => sub{ exec('perldoc',$0); exit(0) }
	   );

# Directories to check
my @dirs = qw(../Bio/ );

#
# run
#

my %dependencies;
my %bp_packages;
my %core = %{$Module::CoreList::version{$version}};

# pragmas and BioPerl modules not in core (not required)
my %SKIP = map {$_ => 1} qw(base
vars
warnings
strict
constant
overload
Bio::Tools::Run::Ensembl
Bio::Ext::HMM
);

if ($dir) {
    find {wanted => \&parse_core, no_chdir => 1}, $dir;
} else {
    find {wanted => \&parse_core, no_chdir => 1}, @dirs;    
}

#
# process results
#

for my $k (keys %dependencies) {
    if (exists $bp_packages{$k} || exists $core{$k}) {
        delete $dependencies{$k};
    }
}

my $b = CPANPLUS::Backend->new();

# sort by distribution into a hash, keep track of modules

my %distrib;

for my $key (sort keys %dependencies) {
    MODULE:
    for my $m ($b->module_tree($key)) {
        if (!$m) {
            warn "$key not found, skipping";
            next MODULE;
        }
        push @{$distrib{$m->package_name}}, [$m, @{$dependencies{$m->module}}]
    }
}

open my $dfile, '>', $depfile or die "Could not write dependency file '$depfile': $!\n";

print $dfile $dep_header;

for my $d (sort keys %distrib) {
    my $min_ver = 0;
    for my $moddata (@{$distrib{$d}}) {
        my ($mod, @bp) = @$moddata;
        for my $bp (@bp) {
            $min_ver = $bp->{ver} if $bp->{ver} >  $min_ver;
        }
    }
    print $dfile
            form
    {bullet => "* "},
    " ============================================================================== ",
    "| Distribution              | Module used - Description            | Min. ver. |",
    "|---------------------------+--------------------------------------+-----------|",
    "| {<<<<<<<<<<<<<<<<<<<<<<<} | * {[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[} | {|||||||} |",
    $d,
    [
        map {
            $_->[0]->module.' - '.$_->[1]
        } map {
            [$_->[0], $_->[0]->description || 'NA']
        } @{$distrib{$d}}
    ],
    $min_ver eq 0 ? 'None' : $min_ver,
    "|==============================================================================|",
    "| Used by:                                                                     |",
    "|------------------------------------------------------------------------------|",
    "| * {[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[} |",
    [
     map {
        my $md = $_->[0]->module;
        map {join(' - ',( $_->{file}.' - '. $md ))} @{$_}[1..$#{$_}] # obfuscated ain't it!!!
     } @{$distrib{$d}}
    ],
    " ============================================================================== ";
}

close $dfile;

exit;
#
##
### end main
##
#

#
# this is where the action is
#

sub parse_core {
    my $file = $_;
    return unless $file =~ /\.PLS$/ || $file =~ /\.p[ml]$/ ;
    return unless -e $file;
    open my $F, '<', $file or die "Could not read file '$file': $!\n";
    my $pod = '';
    MODULE_LOOP:
    while (my $line = <$F>) {
        # skip POD, starting comments
        next if $line =~ /^\s*\#/xms;
        if ($line =~ /^=(\w+)/) {
            $pod = $1;
        }
        if ($pod) {
            if ($pod eq 'cut') {
                $pod = '';
            } else {
                next MODULE_LOOP;
            }
        }
        # strip off end comments
        $line =~ s/\#[^\n]+//;
        if ($line =~ /^\bpackage\s+(\S+)\s*;/) {
            $bp_packages{$1}++;
        } elsif ($line =~ /(?:['"])?\b(use|require)\s+([A-Za-z0-9:_\.\(\)]+)\s*([^;'"]+)?(?:['"])?\s*;/) {
            my ($use, $mod, $ver) = ($1, $2, $3);
            if ($mod eq 'one') {
                print "$File::Find::name: $. $line";
            }
            if (exists $SKIP{$mod}) {
                next MODULE_LOOP;
            }            
            if ($ver && $ver !~ /^v?[\d\.]+$/) {
                next MODULE_LOOP;
            }
            my $nm = $File::Find::name;
            $nm =~ s{.*(Bio.*)\.pm}{$1};
            $nm =~ s{[\\\/]}{::}g;
            if (!exists $dependencies{$mod} ||
                !(grep {$_->{file} eq $nm} @{$dependencies{$mod}})) {
                push @{ $dependencies{$mod} }, {
                    ver => $ver || 0,
                    file => $nm};
                }
        }
    }
    close $F;
}

__END__

=head1 NAME

dependencies.pl - check modules and scripts for dependencies not in core

=head1 SYNOPSIS

B [B<--dir> path ] [B<-v|--verbose>] [B<--depfile> file]
    [B<-?|-h|--help>] [B<-p|--perl> version]

=head1 DESCRIPTION

Recursively parses directory tree given (defaults to '../Bio') and checks files
for possible dependencies and versions (use/require statements).  Checks that
modules aren't part of perl core (--version, defaults to 5.006001).  Module
information is returned using CPANPLUS and data is output to a table using
Perl6::Form (yes I managed to get perl6 in here somehow).

Requires:

File::Find        - core
Getopt::Long      - core
CPANPLUS::Backend
Perl6::Form
Module::CoreList  

=head1 OPTIONS

=over 3

=item B<--dir> path

Overides the default directories to check by one directory 'path' and
all its subdirectories.

=item B<--depfile> file

The name of the output file for the dependencies table.  Default is
'../DEPENDENCIES.NEW'

=item B<-v | --verbose>

Show the progress through files during the checking.  Not used currently.

=item B<-p | --perl> version

Perl version (in long form, i.e. 5.010, 5.006001).  Used to weed out the
core modules that should be already present (ActiveState, we're staring at
you sternly).

=item B<-s | --skipbio> 

Skips BioPerl-related modules in DEPENDENCIES.

We may add something in the future to allow other forms.

=item B<-? | -h  | --help>

This help text.

=back

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Chris Fields

Email cjfields-at-bioperl-dot-org

=cut
BioPerl-1.007002/maintenance/deprecated.pl000444000766000024      1341713155576320 20460 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

use strict;
use warnings;

use version;
use Bio::Root::Version;
use File::Find;
use Getopt::Long;
use Perl6::Form;
use Carp;

#
# command line options
#

my ($verbose, $dir, $depfile, $help, $new, $outfile, $write, $version) =
(0, undef, "../DEPRECATED", undef, [], '../DEPRECATED.NEW', 0, $Bio::Root::Version::VERSION);
GetOptions(
        'v|verbose' => \$verbose,
		'b|bp_version:s' => \$version,
        'dir:s' => \$dir,
        'depfile:s' => \$depfile,
        'n|new=s@' => \$new,
        'o|outfile:s' => \$outfile,
        'w|write' => \$write,
        'h|help|?' => sub{ exec('perldoc',$0); exit(0) }
	   );

# Default directories to check
my @dirs = qw(../Bio/ );

# use version to consolidate old vs new versioning schemes
my $base_version = version->new( $version );

print "Version: $base_version\n";

my %deprecated;
my %removed;
my @dep_data;

# parse DEPRECATED file

open my $DFILE, '<', $depfile or die "Could not read file '$depfile': $!\n";
my $seen_top;
while (my $data = <$DFILE>) {
    if ($data =~ /^-+$/) {
        $seen_top = 1;
        next;
    }
    next unless $seen_top;
    chomp $data;
    my ($module, $dep, $rem, $note) = split(/\s+/,$data,4);
    next unless $module;
    my $d = version->new($dep);
    my $r = version->new($rem);
	print "$module Dep: $d Rem: $r\n" if $verbose;
    if ($rem <= $base_version) {
        $removed{$module}++;
    } elsif ($dep <= $base_version) {
        $deprecated{$module}++;
    }
    push @dep_data, {module => $module,
                     dep => $dep,
                     remove => $rem,
                     note => $note}
}
close $DFILE;

for my $new (@$new) {
    my ($module, $dep, $rem, $note) = split(',',$new,4);
    last if !$module || !$dep || !$rem;
    if ($module !~ /Bio/) {
        croak "Can only deprecate BioPerl modules, not $module"
    }
    push @dep_data, {module => $module,
                 dep => $dep,
                 remove => $rem,
                 note => $note}
}

# run through all files in core (checks to see if anything is still present)

if ($dir) {
    find {wanted => \&parse_core, no_chdir => 1}, $dir;
} else {
    find {wanted => \&parse_core, no_chdir => 1}, @dirs;
}

#
# results
#

# uses Perl6::Form

if ($write || @$new) {

open my $NEWDEP, '>', $outfile or croak "Could not write file '$outfile': $!\n";

print $NEWDEP <{$_}} qw (module dep remove note);
    
print $NEWDEP form
"{[[[[[[[[[[[[[[[[[[[[[[[[[[[[[} {|||||}  {|||||}   {[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[}",
    $mod,     $dep,        $rem,       $note;
}

}

#
##
### end main
##
#

#
# this is where the action is
#

sub parse_core {
    my $file = $_;
    return unless $file =~ /\.PLS$/ || $file =~ /\.p[ml]$/ ;
    return unless -e $file;
    open my $F, '<', $file or die "Could not read file '$file': $!\n";
    while (my $line = <$F>) {
        if ($line =~ /(?:['"])?\b(use|require)\s+([A-Za-z0-9:_\.\(\)]+)\s*([^;'"]+)?(?:['"])?\s*;/) {
            my ($use, $mod) = ($1, $2);
			if (exists $removed{$mod}) {
                print "$File::Find::name: Line $.: $mod is removed\n";
            } elsif (exists $deprecated{$mod}) {
                print "$File::Find::name: Line $.: $mod is deprecated\n";
            } 
        }
    }
    close $F;
}

# $Id: deprecated.pl 10084 2006-07-04 22:23:29Z mauricio $
#
=head1 NAME

deprecated.pl - Check modules and scripts for use of deprecated modules and
methods, indicates presence in a file to STDERR. Optionally accepts new modules
and adds them to a newly formatted deprecation file.

=head1 SYNOPSIS

B [B<-d|--dir> path ] [B<-v|--verbose>] [B<-a|--depfile>]
    [B<-n|--new>] [B<-w|--write>] [B<-o|--outfile>]
    [B<-?|-h|--help>]

=head1 OPTIONS

=over 3

=item B<-d | --dir> path

Overides the default directories to check by one directory 'path' and
all its subdirectories.

=item B<-a | --depfile>

path from working directory that contains the DEPRECATED file.

=item B<-n | --new>

New addition to the deprecation list; this should be in the form of
'Module,dep_release,remove_release,notes'. Notes should only be 40 chars long.

=item B<-b | --bp_version>

BioPerl version.  This only appears to work correctly when using numerical
versions (1.5.2 instead of 1.005002)

=item B<-w | --write>

Write out new deprecation file to $outfile.  If --new is used this is assumed.

=item B<-o | --outfile>

Name of output file to write deprecation table to. DEPRECATED.NEW is the default
name

=item B<-v | --verbose>

Show the progress through files during the checking.

=item B<-? | -h  | --help>

This help text.

=back

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Chris Fields

Email cjfields-at-bioperl-dot-org

=cut
BioPerl-1.007002/maintenance/find_mod_deps.pl000555000766000024      1324213155576320 21151 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=head1 NAME

find_mod_deps.pl - inspect B dependencies of sets of perl files

=head1 DESCRIPTION

Inspects the hard-coded dependencies of a set of perl files and prints
a summary of which modules they use (by default not including
inter-dependencies between the modules being inspected).

=head1 USAGE

find_mod_deps.pl [options]  [ path ... ]

If given any paths, inspects only the files in those paths.  Defaults
to inspecting all perl files in the current directory.

=head2 Options

=over 4

=item -i

If set, also print internal dependencies, i.e. the inter-dependencies
between the files we are inspecting.

=item -B

If set, print the dependencies in a format suitable for cutting and
pasting directly into a Build.PL (i.e. Module::Build)

=item -M

If set, print the dependencies in a format suitable for cutting and
pasting directly into a Makefile.PL (i.e. Module::Install)

=item -Z

If set, print the dependencies in a format suitable for cutting and
pasting directly into a dist.ini (i.e. Dist::Zilla).  Although, if
you're using Dist::Zilla, you probably have it configured to be
auto-discovering deps, and it will find the same deps as this script.

=back

=head1 AUTHOR

Robert Buels, rbuels@cpan.org

=cut

use strict;
use warnings;

use File::Find;
use Getopt::Std;
use IO::String;
use List::MoreUtils qw/ first_value all /;
use Module::CoreList;
use Pod::Strip;
use Pod::Usage;

use Data::Dump 'dump';
use Hash::Merge;

my %opt;
getopts('iBMZ', \%opt) or pod2usage();

-d './lib' or -d './bin' or -d './scripts' or die "run this script from the root dir of a distribution\n";

my @paths = @ARGV;

@paths = qw( t lib scripts bin cgi-bin Bio )
   unless @paths;

# expand any dirs into the perl files they contain
my @perl_files = map {
    if( -d ) {
        my @f;
        find( sub { push @f, $File::Find::name if is_perl_file($_) },
              $_,
            );
        @f
    } elsif( -e ) {
        if( is_perl_file($_) ) {
            $_
        } else {
            warn "WARNING: skipping user-specified file $_, since it is not a perl file.\n";
            ()
        }
    } else {
        ()
    }
} @paths;

my %perl_files = map { $_ => 1 } @perl_files;

my %deps;
my $merger = Hash::Merge->new('RETAINMENT_PRECEDENT');
for my $file ( @perl_files ) {
    my $deps = find_deps( $file );
    %deps = %{ $merger->merge( \%deps, $deps ) };
}

# classify the deps
my %classified;
for my $modname ( keys %deps ) {
    if( all { m|^(./)?t/| } @{$deps{$modname}} ) {
        $classified{build_requires}{$modname} = $deps{$modname};
    }
    else {
        $classified{requires}{$modname} = $deps{$modname};
    }
}

# decide which format to print in
if( $opt{B} ) {
    for ( values %classified ) {
        $_ = 0 for values %$_;
    }
    print dump \%classified;
} elsif( $opt{M} ) {
    print "requires      '$_' => 0;\n"
      for sort { lc $a cmp lc $b } keys %{$classified{requires}};
    print "test_requires '$_' => 0;\n"
      for sort { lc $a cmp lc $b } keys %{$classified{build_requires}};
} elsif( $opt{Z} ) {
    print "[Prereqs]\n";
    print "$_  =  0\n"
      for sort { lc $a cmp lc $b } keys %{$classified{requires}};

    print "\n[Prereqs / TestRequires]\n";
    print "$_  =  0\n"
      for sort { lc $a cmp lc $b } keys %{$classified{build_requires}};

} else {
    print dump \%classified;
}

exit;

################## helpers #####################

sub modfile {
    my $modname = shift;
    my $modfile = "$modname.pm";
    $modfile =~ s|::|/|g;
    return first_value {
        $_ =~ /$modfile$/;
    } @perl_files;
}

sub namespace_parent {
    my $modname = shift;
    $modname =~ s/(?:::)?[^:]+$//;
    return $modname;
}

sub find_deps {
    my ( $file ) = @_;

    my $nopod;
    { open my $p, '<', $file or die "Could not read file '$file': $!\n";
      local $/;
      my $code = <$p>;
      my $strip = Pod::Strip->new;
      $strip->output_string(\$nopod);
      $strip->parse_string_document( $code );
    }
    my $f = IO::String->new( \$nopod );

    my %deps;
    while( my $depline = <$f> ) {
        $depline =~ s/#.+//; #remove comments
        next unless $depline =~ /^\s*(use|require|extends|with)\s+.+;/;
        next unless $depline && $depline =~ /\S/;

        my @toks = $depline =~ /([\w:]{3,})/ig
            or die 'cannot parse: '.$depline;

        #warn "    adding to $k->{name}\n";
        shift @toks;
        if( @toks ) {
            if ( $toks[0] eq 'base' ) {
                shift @toks;
                shift @toks if $toks[0] eq 'qw';
            } else {
                @toks = ($toks[0]);
            }
        }

      MODNAME:
        foreach my $modname (@toks) {

            chomp $depline;
            #warn "'$depline' goes to $modname\n";

            #skip if the module is in the distribution
            my $modfile = modfile($modname);
            next if !$opt{i} && $modfile && -f $modfile;

            #skip if the module is in core before 5.6
            my $rl = Module::CoreList->first_release($modname);
            next if $rl && $rl <= 5.006;

            #skip if the module is actually defined in a parent file
            my $p = $modname;
            while( $p = namespace_parent($p) ) {
                my $p_modfile = modfile($p);
                #warn  "checking $p / $p_modfile\n";

                next unless $p_modfile && -f $p_modfile;

                open my $p, '<', $p_modfile or die "Could not read file '$p_modfile': $!\n";
                while( <$p> ) {
                    next MODNAME if /^\s*package\s+$p\b/;
                }
            }

            push @{$deps{$modname} ||= []}, $file;
        }
    }

    return \%deps;
}

sub is_perl_file {
    local $_ = shift;
    return -f && ( -x || /\.(pm|t|pl)$/ );
}
BioPerl-1.007002/maintenance/module_usage.pl000444000766000024      2477113155576320 21036 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
# 
# Counts up all the used and inherited modules in a directory of modules to
# help indicate which the most important modules are, graphs it also
#
# Written by Sendu Bala, using much code directly from
# http://www.perlmonks.org/?displaytype=displaycode;node_id=87329
# and also
# http://search.cpan.org/src/NEILB/pmusage-1.2/pmusage

use strict;
use warnings;

use IO::File;
use File::Find;
use Getopt::Std;
use GraphViz;

sub usage
{
	print <new($opts{l}) or die "can't open -l file $opts{l} : $!\n";
	my @largs = <$lFile>;
	chomp(@largs);
	splice(@ARGV, 0, 0, @largs);
	delete($opts{l});
	getopts($opts, \%opts) || usage(1);
	$lFile->close();
}

my $outfile = defined($opts{f}) ? $opts{f} : "module_usage";
my $format = defined($opts{i}) ? $opts{i} : 'jpeg';

# now filenames are in @ARGV
push(@ARGV, '.') if !@ARGV;

my @files;
my %sections;

sub findPerlFiles {
	-f $_ && /^.*\.p[ml]\z/si && push(@files, $File::Find::name);
}

# process directories
foreach my $top (@ARGV) {
	File::Find::find({wanted => \&findPerlFiles}, $top);
}

my %usage;
my %users;
my %inheritance;
my %packages;

sub store_package_usage {
    my ($package, $used) = @_;
    my %used = %{$used};
    
    STDERR->print("package $package used (".join(' ', keys %used).")\n") if $opts{v};
    
    $packages{$package} = \%used;
    
    foreach my $module (keys %used) {
        $usage{$module}++;
        push (@{$users{$module}}, $package);
    }
}

foreach my $file (@files) {
	$file =~ s#^./##;
	STDERR->print("processing $file\n") if $opts{v};
	my $f = IO::File->new($file) or warn "can't open $file: $!\n", next;
    
	my ($package, %used);
    
	my $pod = 0;
	while (<$f>) {
		if (/^=cut/) {
			$pod=0;
			next;
		}
		if (/^=[a-zA-Z]+/) {
			$pod=1;
			next;
		}
		next if $pod;
        
		if (/^\s*package\s+([[:word:]:]+)\s*;/) {
            if ($package) {
                store_package_usage($package, \%used);
                %used = ();
            }
            
			$package = $1;
			next;
		}
		if (/use base\s*(.*)/) {
			my $tmp = $1;
			while (!/;/)	# accumulate ISA value for multiple lines
			{
				$_ = <$f>;
				$tmp .= $_;
			}
			my @use_base = eval $tmp;
			if ($@) { warn "Unparseable 'use base' line for $package: $tmp"; next }
			
            foreach my $module (@use_base) {
                $used{$module} = 1;
				$inheritance{$package}->{$module} = 1;
            }
		}
		elsif (/^\s*use\s+([^\s;()]+)/ || /^\s*require\s+([^\s;()'"]+)/) {
            $used{$1} = 1;
		}
	}
	$f->close();
    
    if ($package) {
        store_package_usage($package, \%used);
    }
}

# simplify so we can view a graph of usage: we group all packages that have
# identical usage. NB: this doesn't look at external modules at all
my %groups;
while (my ($package, $used_hash) = each %packages) {
    my @used_packages;
    foreach my $used_module (sort keys %{$used_hash}) {
        next unless defined $packages{$used_module};
        push(@used_packages, $used_module);
    }
    @used_packages || next;
    
    push(@{$groups{join('|', @used_packages)}}, $package);
}

# we're going to shade boxes based on usage later, figure out an appropriate
# shade range by ranking
my %counts;
while (my ($group, $pack_list) = each %groups) {
    my @children = @{$pack_list};
    
    @children > 1 || next;
    
    my @parents = split(/\|/, $group);
    foreach my $parent (@parents) {
        my $count = $usage{$parent};
        $counts{$parent} = $count;
    }
}
my %ranks;
my $rank = 0;
my $prev_count;
foreach my $parent (sort { $counts{$a} <=> $counts{$b} } keys %counts) {
    my $this_count = $counts{$parent};
    $ranks{$parent} = $prev_count && $prev_count != $this_count ? ++$rank : $rank;
    $prev_count = $this_count;
}

sub class_to_subdir {
    my $class = shift;
    $class =~ s/::[^:]+$//;
    return $class;
}

my $g = GraphViz->new(concentrate => 1,
                      node => {shape => 'box'},
                      $format eq 'ps' ? (pagewidth => 46.81, pageheight => 33.11) : ()); # A0 for ps output
my $inherited_edge_colour = 'green';
my $used_edge_colour = 'blue';
my $cluster_colour = 'black'; #*** darkgray, 0,0,0.31 don't work, why?!
my $child_id = 0;
my $group_definitions = '';
my %parents;
while (my ($group, $pack_list) = each %groups) {
    my @children = @{$pack_list};
    
    # ignore single child groups (required or graph gets too wide to jpeg)
    @children > 1 || next;
    
    # we'll cluster if all children belong to the same subdirectory
    my %subdirs;
    foreach my $child (@children) {
        $subdirs{class_to_subdir($child)} = 1;
    }
    my $subdir;
    if (keys %subdirs == 1) {
        ($subdir) = keys %subdirs;
        undef $subdir if $subdir eq 'Bio';
    }
    
    my $this_child = 'group'.++$child_id;
    $g->add_node($this_child,
                 style => 'dashed',
                 label => "$this_child:\n".join("\n", @children),
                 $subdir ? (cluster => {name => $subdir, style => 'dotted', color => $cluster_colour}) : ());
    
    my @parents = split(/\|/, $group);
    
    $group_definitions .= "  $this_child consists of ".scalar(@children)." packages: ".join(', ', @children)."\n  $this_child members use ".scalar(@parents)." other packages: ".join(', ', @parents)."\n\n";
    
    foreach my $parent (@parents) {
        # we'll shade the parent box based on how many packages use it
        my $this_rank = $ranks{$parent};
        my $shade = (1 / $rank) * $this_rank;
        
		# we'll colour the edge based on if we inherited this parent or just
		# used it, going by the most common for the group
		my ($inherited, $used) = (0, 0);
		foreach my $child (@children) {
			if (defined $inheritance{$child}->{$parent}) {
				$inherited++;
			}
			else {
				$used++;
			}
		}
		my $edge_colour = $inherited > $used ? $inherited_edge_colour : $used_edge_colour;
		
        # we'll cluster if this isn't a base Bio::x class
        my $subdir = class_to_subdir($parent);
        undef $subdir if $subdir eq 'Bio';
        
        $g->add_node($parent,
                     style => 'filled',
                     fillcolor => "0,$shade,1",
                     $subdir ? (cluster => {name => $subdir, style => 'dotted', color => $cluster_colour}) : ());
        $parents{$parent} = 1;
        $g->add_edge($this_child => $parent, color => $edge_colour);
    }
}

# show links between parents
foreach my $parent (keys %parents) {
    my %used = %{$packages{$parent}};
    
    foreach my $used (keys %used) {
        next unless defined $parents{$used};
        $g->add_edge($parent => $used, color => defined $inheritance{$parent}->{$used} ? $inherited_edge_colour : $used_edge_colour);
    }
}

# write out graph
my $output = IO::File->new($outfile.".$format", 'w') or die "can't open $outfile.$format: $!\n";
$output->print(eval "\$g->as_$format()");
$output->close();


my $package_count = keys %packages;
my $total_used = keys %usage;

my $results_str = "Packages investigated: $package_count\nTotal modules used: $total_used\n\n";


# descriptive text output
# list by popularity
my @internal;
my @external;
foreach my $module (sort { $usage{$b} <=> $usage{$a} || $a cmp $b } keys %usage) {
    my $count = $usage{$module};
    
    if (defined $packages{$module}) {
        push(@internal, "  $module => used $count times");
    }
    else {
        my $by = '';
        if ($count <= 5) {
            $by = " by ".join(", ", @{$users{$module}});
        }
        push(@external, "  $module => used $count times$by");
    }
}

$results_str .= "External module usage:\n".join("\n", @external);
$results_str .= "\n\nPackage usage:\n".join("\n", @internal);

# list the packages that aren't used by any other package
$results_str .= "\n\nPackages not used by any other:\n";
foreach my $package (sort keys %packages) {
    next if $usage{$package};
    $results_str .= "  $package\n";
}

# define the groups referenced in the graph
$results_str .= "\nGroup definitions:\n$group_definitions";

# write out descriptive text file
$output = IO::File->new($outfile.'.txt', 'w') or die "can't open $outfile.txt: $!\n";
$output->print($results_str);
$output->close();

exit;
BioPerl-1.007002/maintenance/modules.pl000555000766000024      3404013155576320 20026 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
#
=head1 NAME

modules.pl - information about modules in BioPerl core

=head1 SYNOPSIS

B [B<-V|--verbose>] [B<-c|--count>] | [B<-l|--list>] |
  [B<-u|--untested>] | [B<-i|--info> class] | [B<-i|--inherit> |
  [B<-d|--dir> path ] | [B<-v|--version> | [B<-?|-h|--help>]

=head1 DESCRIPTION

This script counts, lists and provides other information about bioperl
modules. It is mainly meant to be run by bioperl maintainers.

The default action is to count modules in the bioperl core
distribution. Based on the class name it tries to classify them into
categories. The following is a tentative glossary of terms used.


=over 4

=item Base

Synonyms: Generic class, parameterized class, generic module.

A class that you don't instantiate in your scripts, but that it's a
template for other classes.

Examples: Bio::Tools::Run::WrapperBase - a base object for wrappers
around executables. Bio::Tools::Analysis::SimpleAnalysisBase - an
abstract superclass for SimpleAnalysis implementations

This are counted with C; They have "Base" in the
beginning or end of the name.

=item Interface

Synonyms: protocol, feature set.

Class that defines a set of features that are common to a group of
classes.

Example: Bio::Tree::NodeI - interface describing a Tree Node.

This are counted with C; They have "I" at the end of the
name.

=item Component

A class that implements a small subset of their superclass. They are in
a directory with an identical name of the superclass. There are plenty
of them. You need only a small number of methods to be overridden.

Example: Bio::SeqIO::fasta.

This is counted with C; Classes are inside their base directory
and all in lowercase.

=item Instance

The rest of them. It is sometimes helpful to divide them into two
types:

=over 2

=item Algorithmic classes

Example: Bio::AlignIO - Handler for AlignIO formats

=item Storage classes

Example: Bio::SimpleAlign - Multiple alignments held as a set of
sequences

=back

=back

=cut

#
# The helper class to store class status;
#
package BioClass;

sub new {
    my $class = shift;
    my $name = shift;
    die unless $name;

    my $self = {};
    $self->{'name'} = $name;
    $self->{'tested'} = 0;
    $self->{'type'} = '';
    $self->{'path'} = '';

    bless $self, $class;
}


sub name {
    my $self = shift;
    return $self->{'name'};
}

sub tested {
    my $self = shift;
    my $value = shift;
    $self->{'tested'} = 1 if defined $value && $value;
    return $self->{'tested'} || 0;
}

sub type {
    my $self = shift;
    my $value = shift;
    $self->{'type'} = $value if defined $value;
    return $self->{'type'};
}

sub path {
    my $self = shift;
    my $value = shift;
    $self->{'path'} = $value if defined $value;
    return $self->{'path'};
}

sub add_superclass {
    my $self = shift;
    my $superclass = shift;
    return unless $superclass;
    $self->{'superclasses'}->{$superclass} = 1 ;
}

sub each_superclass {
    my $self = shift;
    return  keys %{$self->{'superclasses'}};
}

sub add_used_class {
    my $self = shift;
    my $used_class = shift;
    return unless $used_class;
    $self->{'used_classes'}->{$used_class} = 1 ;
}

sub each_used_class {
    my $self = shift;
    return  keys %{$self->{'used_classes'}};
}

package main;

use File::Find;
use Getopt::Long;
use Data::Dumper;
use strict;


# declare subroutines
sub dir;
sub modules;
sub count;
sub list_all;
sub untested;
sub info;
sub inherit;
sub synopsis;
sub version;

# command line options
my ($dir, $count,$list, $verbose,$info,$untested, $inherit, $synopsis,
    $version);
GetOptions(
	   'dir:s'      => \$dir,
	   'count'    => \$count,
	   'list'     => \$list,
           'test_BioClass' => \&_test_BioClass,
           'V|verbose'  => \$verbose,
           'untested' => \$untested,
           'info:s' =>  \$info,
           'inherit' => \$inherit,
           'synopsis' => \$synopsis,
           'version' => \$version,
	   'h|help|?' => sub{ exec('perldoc',$0); exit(0) }
	   );


our %MODULES; # storage structure

# find modules
my $pwd = $ENV{PWD};
my $seachdir = "$pwd/../Bio"; #default
my %FIND_OPTIONS = ( wanted => \&modules );

$seachdir = "$pwd/$dir" if $dir;
find \%FIND_OPTIONS, $seachdir;


# call subroutines
if    ($list)     { list_all }
elsif ($untested) { untested }
elsif ($info)     { info($info) }
elsif ($inherit)  { inherit }
elsif ($synopsis) { synopsis }
elsif ($version)   { version }
else              { count }


################# end main ####################


#
# subroutines;
#

sub _test_BioClass {
    $a = new BioClass('Bio::Test');
    print "Class name: ", $a->name(), "\n";
    $a->add_superclass('Bio::Super');
    $a->add_superclass('Bio::Super2');
    $a->tested(1);
    $a->type('instance');
    print Dumper [$a->each_superclass] if $a->tested;
    print Dumper $a;
    exit;
}

sub modules {
    return unless /\.pm$/ ;
    #return unless -e $_;
    #print "file: $_\n" if $verbose;
    open my $F, '<', $_ or warn "Could not read file '$_': $!\n" && return;
    my $class;
    while (<$F>) {
        if (/^package\s+([\w:]+)\s*;/) {
            #print $1, "\n" if $verbose;
            $_ = $1;
            $class = new BioClass($_);
            $MODULES{$_} = $class;
            if (/.*:[a-z]/) {
                $class->type('component');
            } elsif (/:Base/ | /Base$/) {
                $class->type('base');
            } elsif (/[^A-Z]I$/) {
                $class->type('interface');
            } else {
                $class->type('instance');
            }
            $class->path($File::Find::name);
        }
        if (/^\w*use/ && /(Bio[\w:]+)\W*;/ && not /base/) {
	    next unless $class;
            #print "\t$1\n" if $verbose;
            $class->add_used_class($1);
        }
        if ((/\@ISA/ || /use base/) && /Bio/) {
            next unless $class;
            my $line = $_;
            while ( $line =~ /(Bio[\w:]+)/g) {
                #print "\t$1\n" if $verbose;
                $class->add_superclass($1);
            }
        }
        if (/\@ISA/ && /Bio/) {
            next unless $class;
            my $line = $_;
            while ( $line =~ /(Bio[\w:]+)/g) {
                #print "\t$1\n" if $verbose;
                $class->add_superclass($1);
            }
        }
    }
    close $F;
}

=head1 OPTIONS

Only one option is processed on each run of the script. The --verbose
is an exception, it modifies the amount of output.

=over 4

=item B<-V | --verbose>

B

Set this option if you want to see more verbose output. Often that
will mean seeing warnings normally going into STDERR.

=cut

=item B<-d | --dir> path

Overides the default directories to check by one directory 'path' and
all its subdirectories.

=item B<-c | --count>

The default action if no other option is given. Gives the count of
modules broken to B ("usable"), B ( (abstract)?
superclass) , B (the "I" files) and B (used from
instantiable parent) modules, in addition to total number of modules.

Note that abstract superclass in bioperl is not an enforced concept and
they are not clearly indicateded in the class name.

=cut

sub count {
    printf "Instance : %3d\n",
        scalar (grep $MODULES{$_}->type =~ /instance/ , keys %MODULES);
    printf "Base     : %3d\n",
        scalar (grep $MODULES{$_}->type =~ /base/ , keys %MODULES);
    printf "Interface: %3d\n",
        scalar (grep $MODULES{$_}->type =~ /interface/ , keys %MODULES);
    printf "Component: %3d\n",
        scalar (grep $MODULES{$_}->type =~ /component/ , keys %MODULES);
    print  "--------------\n";
    printf "Total    : %3d\n", scalar (keys %MODULES);

}

=item B<-l | --list>

Prints all the module names in alphabetical order. The output is a tab
separated list of category (see above) and module name per line. The
output can be processed with standard UNIX command line tools.

=cut

sub list_all {
    foreach ( sort keys %MODULES) {
        print $MODULES{$_}->type. "\t$_\n";
    }
}

=item B<-u | --untested>

Prints a list of instance modules which are I explicitly used by
test files in the directory. Superclasess or any classes used by others
are not reported, either, since their methods are assumed to be tested
by subclass tests.


=cut

sub _used_and_super {
    my $name = shift;
#    print "-:$name\n" if /Locati/; 
    foreach ($MODULES{$name}->each_superclass) {
        next unless defined $MODULES{$_};
#        print "-^$_\n" if /Locati/; 
#        unless (defined $MODULES{$_} or $MODULES{$_}->tested) {
        if (not  $MODULES{$_}->tested) {
            $MODULES{$_}->tested(1);
            _used_and_super($_);
        }
    }
    foreach ($MODULES{$name}->each_used_class) {
        next unless defined $MODULES{$_};
#        print "--$_\n" if /Locati/; 
#        unless (defined $MODULES{$_} or $MODULES{$_}->tested) {
        if (not  $MODULES{$_}->tested) {
            $MODULES{$_}->tested(1);
            _used_and_super($_);
        }
#        $MODULES{$_}->tested(1) && _used_and_super($_)
#            unless defined $MODULES{$_} or $MODULES{$_}->tested;
    }
    return 1;
}

sub untested {
    foreach (`find ../t -name "*.t" -print | xargs grep -hs "[ur][se][eq]"`) {
        s/.*use +//;
        s/.*require +//;
        next unless /^Bio/;

        s/[\W;]+$//;
        s/([\w:]+).*/$1/;
        my $name = $_;

        next unless $MODULES{$_};
        $MODULES{$_}->tested(1) 
            unless defined $MODULES{$_} and $MODULES{$_}->tested;

        next if $MODULES{$name}->name eq "Bio::SeqIO::abi"; # exception: requires bioperl ext package
        next if $MODULES{$name}->name eq "Bio::SeqIO::ctf"; # exception: requires bioperl ext package
        next if $MODULES{$name}->name eq "Bio::SeqIO::exp"; # exception: requires bioperl ext package
        next if $MODULES{$name}->name eq "Bio::SeqIO::pln"; # exception: requires bioperl ext package
        next if $MODULES{$name}->name eq "Bio::SeqIO::ztr"; # exception: requires bioperl ext package
#        print $MODULES{$name}->name, "\n";
#        print Dumper $MODULES{$name};

        _used_and_super($name);

    }

    foreach ( sort keys %MODULES) {

        # skip some name spaces 
        next  if /^Bio::Search/; # Bio::Search and Bio::SearchIO are extensively tested 
                                 # but classes are used by attribute naming 

        print "$_\n" if
            $MODULES{$_}->type eq 'instance' and ($MODULES{$_}->tested == 0) ;
    }

}

=item B<-i | --info> class

Dumps information about a class given as an argument.

=cut

sub info {
    my $class = shift;
    die "" unless $class;
    #print Dumper $MODULES{$class};
    my $c = $MODULES{$class};
    print $c->name, "\n";
    printf "  Type:\n\t%s\n", $c->type;
    print "  Superclasses:\n";
    foreach (sort $c->each_superclass) {
        print "\t$_\n";
    }
    print "  Used classes:\n";
    foreach (sort $c->each_used_class) {
        print "\t$_\n";
    }
}


=item B<-i | --inherit>

Finds interface modules which inherit from an instantiable class.

Could be extended to check other bad inheritance patterns.

=cut

sub inherit {
    foreach ( sort keys %MODULES) {
        my $c=$MODULES{$_};
        next unless $c->type =~ /interface/;
        foreach my $super ($c->each_superclass) {
            next if $super =~ /I$/;
            print "Check this inheritance: ", $c->name, " <-- $super\n";
        }
    }
}

=item B<-s | --synopsis>

Test SYNOPSIS section of bioperl modules for runnability

=cut

sub synopsis {
    foreach ( sort keys %MODULES) {
        my $c=$MODULES{$_};

        next unless $c->type eq "instance";
        next if $c->name eq 'Bio::Root::Version';
        next if $c->name eq 'Bio::Tools::HMM';

        my $synopsis = '';
        open my $F, '<', $c->path or warn "Could not read file '".$c->name."': $!\n" && return;

        my $flag = 0;
        while (<$F>) {
            last if $flag && /^=/;
            $synopsis .= $_ if $flag;
            $flag = 1 if /^=head1 +SYNOPSIS/;
        }

        # remove comments
        $synopsis =~ s/[^\$]#[^\n]*//g;
        # allow linking to an other Bio module, e.g.: See L.
        $synopsis =~ s/[^\n]*L&1 `;
        next if $res =~ /syntax OK/;
        print $c->path, "\n";
        print $synopsis;
        print $res;
        print "-" x 70, "\n"; 
        # print "SYNOPSIS not runnable\n";
        close $F;
    }
}

=item B<-v | --version>

Test the VERSION of the module against the global one set in
Bio::Root::Variation. Print out the different ones.

=cut

sub version {

    use Bio::Root::Version;
    my $version =  $Bio::Root::Version::VERSION;

    my %skip = ( # these are defined together with an other module
                 # and can not be use independently
                'Bio::AnalysisI::JobI' => 1,
                'Bio::PrimarySeq::Fasta' => 1,
                'Bio::DB::Fasta::Stream' => 1,
                'Bio::DB::GFF::ID_Iterator' => 1,
                'Bio::DB::GFF::Adaptor::dbi::faux_dbh' =>1,
                'Bio::LiveSeq::IO::SRS' =>1 # tries to call an external module
               );

    foreach ( sort keys %MODULES) {
        my $n=$MODULES{$_}->name;
        next if $skip{$n};
        my $vv= "\$${n}::VERSION";
        my $v = `perl -we 'use $n; print $vv;'`;
        printf "%50s %-3s\n", $n, $v unless $version eq $v;
    }
}

__END__

=item B<-? | -h  | --help>

This help text.

=back

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

=head1 Contributors

Albert Vilella, avilella-AT-gmail-DOT-com

=cut
BioPerl-1.007002/maintenance/ncbi_blast_switches.pl000555000766000024       100313155576320 22340 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

# This script determines all the valid command line switches
# from the four main NCBI BLAST tools, and produces Perl code
# to put into Bio/Tools/Run/StandAloneBlast.pm
#
# Torsten Seemann
# 27 June 2006


my @exe = qw(blastall blastpgp rpsblast bl2seq);

for my $exe (@exe) {
  open(HELP, "$exe - |") or die $!;
  my @switch;
  while () {
    next unless m/^\s*-(\w)\s/;
    push @switch, $1;
  }
  close(HELP);
  print "\t\@",uc($exe),"_PARAMS = qw(", join(q{ }, sort @switch), ");\n";
}

BioPerl-1.007002/maintenance/perltidy.conf000444000766000024        62113155576320 20457 0ustar00cjfieldsstaff000000000000# A declarative version of PDD07 for perl.

# Must apply...

-l=100 # Source line width is limited to 100 characters.
-i=4   # must be indented four columns (no tabs)
-ola   # Labels (including case labels) must be outdented two columns
-ci=4  # Long lines, when split, must use at least one extra level of indentation on the continued line.
-ce   # Cuddled elses are forbidden: i.e. avoid } else { .
BioPerl-1.007002/maintenance/pod.pl000555000766000024      1066413155576320 17146 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
#
=head1 NAME

pod.pl - check the POD documentation syntax in modules and scripts

=head1 SYNOPSIS

B [B<-d|--dir> path ] [B<-v|--verbose>] B<-b|--blankline>
    [B<-?|-h|--help>]

=head1 DESCRIPTION

Checks Plain Old Documentation (POD) with highest possible stringency
in every bioperl module and script in CVS modules 'core' and 'run'.

Amounts to same as running

  podchecker -warnings -warnings

on every file.

=head2 Results

The results are written into file '/tmp/bioperl_pod_check' and
displayed after the run. The output is filtered not to show
confirmations of correct syntax. The result file is not removed.

The aim is to have as few warnings, and no errors, as possible.  Links
to web URLs give a warning but that seems to be spurious, so they are
filtered out.  Currently there are a few cases of "multiple occurrence
of link target" in several modules which are harmless.

=head1 SEE ALSO

L, L

=cut

use File::Find;
use Pod::Checker;
use Getopt::Long;
use strict;

sub podcheck;
sub blankline;

#
## Directories to check
#
my @dirs = qw( ../Bio/ ../scripts . );

# command line options
my ($verbose, $blankline, $dir, $help) = (0, undef, undef, undef);
GetOptions(
           'v|verbose' => \$verbose,
           'dir:s' => \$dir,
           'blankline' => \$blankline,
	   'h|help|?' => sub{ exec('perldoc',$0); exit(0) }
	   );

# setup
my $tmpfile = '/tmp/bioperl_pod_check';
our %POD_CHECKER_OPTIONS = ( '-warnings' => 2 );
our %FIND_OPTIONS = ( wanted => \&podcheck, no_chdir => 1 );

# run
open (F, ">$tmpfile") || die "can't open file $tmpfile: $!";
$FIND_OPTIONS{wanted} = \&blankline if $blankline;

if ($dir) {
    find \%FIND_OPTIONS, $dir;
} else {
    find \%FIND_OPTIONS, @dirs;
}
close F;
open (F, "grep -v OK $tmpfile|") || die "can't open file $tmpfile: $!";
while () { print unless /http/ and /non-escaped/ }


# this is where the action is
sub podcheck {
    return unless /\.PLS$/ or /\.p[ml]$/ ;
    return unless -e $_;
    print "$_\n" if $verbose;
    my $checker = Pod::Checker->new( %POD_CHECKER_OPTIONS );
    $checker->parse_from_file($_, \*F);
    print "$_\tno POD\n" if $checker->num_errors() < 0;
}

=head1 OPTIONS

=over 3

=item B<-d | --dir> path

Overides the default directories to check by one directory 'path' and
all its subdirectories.

=item B<-b | --blankline>

Checks POD command paragraphs (lines starting with '=' character) for
preceding nonblank lines. These lines are printed out with '++'.

Also, if verbose is turned on, it will report on lines whitespace
characters which prevent paragrafs to be recognised by older POD
parsers (marked with '+'). Modern perlpod parsers (5.6.0 and later, I
suppose) allow for whitespace lines surrounding command lines, but
since bioperl still supports older versions, these lines should be
cleaned to contain only '\n' and no space or tab characters.


See: L


=cut

sub blankline {
    return unless /\.PLS$/ or /\.p[ml]$/ ;
    return unless -e $_;
    my $file = $_;
    open (F, $_) or warn "can't open file $_: $!" && return;
    local $/="";
    while () {
        print "$file: +|$1|\n" if /[ \t]\n(=[a-z][^\n]+$)/m and $verbose;
        print "$file: ++|$1|\n" if /\w\n(=[a-z][^\n]+$)/m and $verbose;
        print "$file:|$1|+\n" if /(^=[a-z][^\n]+)\n[\t ]/m;
        #print "$file:|$1|++\n" if /(^=[^\n]+)\n\w/m;
    }
    close F;
}

__END__

=item B<-v | --verbose>

Show the progress through files during the POD checking.

=item B<-? | -h  | --help>

This help text.

=back

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org

=cut


# find . -name '*.pm' -print | xargs  perl -e '$/=""; while (<>) {$n = $1 if /^package\s+([\w:]+)/; print "$n:|$1|"  if  /(\s\s^=[^\n]+$)/m ; }'  ;

# find . -name '*.pm' -print | xargs  perl -e '$/=""; while (<>) {$n = $1 if /^package\s+([\w:]+)/; print "$n:|$1|\n"  if /(^=[^\n]+\n[\t ])/m ; }'  ;
BioPerl-1.007002/maintenance/symlink_script.pl000555000766000024       520113155576320 21405 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
use Module::Build;
use strict;
use warnings;

my $build = Module::Build->current;

my %symlink_scripts = ('bp_bulk_load_gff.pl' => 'bp_pg_bulk_load_gff.pl');

#my $blib_dir = File::Spec->catdir($build->blib, 'script');
# using blib prior to installation, post build, always 'works', but the
# installation process installs the symlink as the actual file, so we may as
# well have just done a copy

my $install_dir = $build->install_destination('script');
$build->log_info("Will try to install symlinks to $install_dir\n");
my $orig_dir = $build->cwd;
chdir($install_dir);

while (my ($source, $destination) = each %symlink_scripts) {
	if ($^O !~ /Win32/) {
		eval { symlink($source, $destination) };
		$build->log_warn("Cannot create symbolic link named $destination on your system for $source in $install_dir\n") if $@;
	} else {
		# Win32 perl does not implement symlink(), as it would not work on all filesystems.
		require File::Copy;
		eval { File::Copy::copy($source, $destination) };
		$build->log_warn("Cannot create copy of script named $destination on your system for $source in $install_dir\n") if $@;
	}
}

chdir($orig_dir);

exit;

__END__

=head1 NAME

symlink_script.pl - install script to create symbolic links

=head1 SYNOPSIS

  perl Build.pl
  ./Build install

=head1 DESCRIPTION

Used during "./Build install". Only works if the script installation directory
used during "perl Build.pl" matches that used for the actual installation during
"./Build install". So if you install to a special place, do

  perl Build.pl --install_base /home/me
  ./Build install

not

  perl Build.pl
  ./Build install --install_base /home/me

This script will create a symlink to a script in that same directory. It was
written to create a symlink with the name 'bp_pg_bulk_load_gff.pl' that targeted
'bp_bulk_load_gff.pl' but can be extended by adding files to the
%symlink_scripts hash.

Perl function 'symlink' is used to keep the script from crashing on systems
that don't allow symbolic linking.

=head1 SEE ALSO

=cut

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Sendu Bala

Email bix@sendu.me.uk

=cut
BioPerl-1.007002/maintenance/version.pl000555000766000024       223313155576320 20022 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
#
=head1 version

This script is to add or modify version declaration for each bioperl pm.

[Currently, it just add version. Later I will update it to modify version.]

=head1 USAGE

  perl version.pl  

=cut

use strict;

if(@ARGV < 2) {
    die "USAGE: perl version.pl  \n";
}
my $dir=shift || "$ENV{HOME}/src/bioperl-live/";
my $version=shift || '1.4';

sub traveral_dir {
    my ($dir, )=@_;
    opendir DIR, $dir;
    my @allfiles= grep{$_ ne '.' and $_ ne '..'}readdir DIR;
    closedir DIR;
    my @full_path = map{"$dir/$_"} @allfiles;
    my @out = grep -f, @full_path;
    foreach(grep -d, @full_path){
        push @out, traveral_dir($_);
    }
    return @out;
}

my @pm=sort grep /\.pm$/, traveral_dir($dir);

use ExtUtils::MakeMaker;

map {
    my $f=$_; 
    my $v = MM->parse_version($f);
    print "$v\t$f\n";
    my $ep ='s/^(package\s+[\w:]+;\r?)$/$1\nour \$VERSION="'. $version.'";/';

    if((not defined $v) or $v eq 'undef'){ # This is strange on parse_version. 
    # It return scalar 'undef', not the undef can be detected by defined.
        `perl -p -i -e '$ep' $f`;
    }

} @pm;

BioPerl-1.007002/maintenance/big_split000755000766000024          013155576320 17614 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/maintenance/big_split/file_classification.csv000444000766000024     21111113155576320 24515 0ustar00cjfieldsstaff000000000000,"AUTHORS"
"Bio-Analysis","Bio/AnalysisI.pm"
,"Bio/Draw/Pictogram.pm"
"Bio-Taxonomy","Bio/Taxonomy/Tree.pm"
"Bio-Taxonomy","Bio/Taxonomy/FactoryI.pm"
"Bio-Taxonomy","Bio/Taxonomy/Node.pm"
"Bio-Taxonomy","Bio/Taxonomy/Taxon.pm"
,"Bio/HandlerBaseI.pm"
,"Bio/DescribableI.pm"
,"Bio/Nexml/Factory.pm"
,"Bio/MapIO/mapmaker.pm"
,"Bio/MapIO/fpc.pm"
"Bio-SeqEvolution","Bio/SeqEvolution/DNAPoint.pm"
"Bio-SeqEvolution","Bio/SeqEvolution/EvolutionI.pm"
"Bio-SeqEvolution","Bio/SeqEvolution/Factory.pm"
"Bio-SeqIO","Bio/SeqIO.pm"
,"Bio/OntologyIO.pm"
,"Bio/PhyloNetwork.pm"
,"Bio/DBLinkContainerI.pm"
"Bio-Map","Bio/Map/Contig.pm"
"Bio-Map","Bio/Map/CytoMap.pm"
"Bio-Map","Bio/Map/MapI.pm"
"Bio-Map","Bio/Map/Gene.pm"
"Bio-Map","Bio/Map/SimpleMap.pm"
"Bio-Map","Bio/Map/LinkagePosition.pm"
"Bio-Map","Bio/Map/CytoMarker.pm"
"Bio-Map","Bio/Map/PositionI.pm"
"Bio-Map","Bio/Map/Microsatellite.pm"
"Bio-Map","Bio/Map/OrderedPositionWithDistance.pm"
"Bio-Map","Bio/Map/Prediction.pm"
"Bio-Map","Bio/Map/Physical.pm"
"Bio-Map","Bio/Map/PositionHandler.pm"
"Bio-Map","Bio/Map/Position.pm"
"Bio-Map","Bio/Map/PositionWithSequence.pm"
"Bio-Map","Bio/Map/GenePosition.pm"
"Bio-Map","Bio/Map/MarkerI.pm"
"Bio-Map","Bio/Map/RelativeI.pm"
"Bio-Map","Bio/Map/MappableI.pm"
"Bio-Map","Bio/Map/GeneMap.pm"
"Bio-Map","Bio/Map/TranscriptionFactor.pm"
"Bio-Map","Bio/Map/Clone.pm"
"Bio-Map","Bio/Map/Mappable.pm"
"Bio-Map","Bio/Map/OrderedPosition.pm"
"Bio-Map","Bio/Map/Marker.pm"
"Bio-Map","Bio/Map/LinkageMap.pm"
"Bio-Map","Bio/Map/GeneRelative.pm"
"Bio-Map","Bio/Map/Relative.pm"
"Bio-Map","Bio/Map/CytoPosition.pm"
"Bio-Map","Bio/Map/FPCMarker.pm"
"Bio-Map","Bio/Map/PositionHandlerI.pm"
"Bio-Map","Bio/Map/EntityI.pm"
"Bio-Restriction","Bio/Restriction/EnzymeCollection.pm"
"Bio-Restriction","Bio/Restriction/IO/withrefm.pm"
"Bio-Restriction","Bio/Restriction/IO/itype2.pm"
"Bio-Restriction","Bio/Restriction/IO/prototype.pm"
"Bio-Restriction","Bio/Restriction/IO/bairoch.pm"
"Bio-Restriction","Bio/Restriction/IO/base.pm"
"Bio-Restriction","Bio/Restriction/Enzyme/MultiSite.pm"
"Bio-Restriction","Bio/Restriction/Enzyme/MultiCut.pm"
"Bio-Restriction","Bio/Restriction/IO.pm"
"Bio-Restriction","Bio/Restriction/Analysis.pm"
"Bio-Restriction","Bio/Restriction/Enzyme.pm"
"Bio-Restriction","Bio/Restriction/EnzymeI.pm"
,"Bio/LocationI.pm"
"Bio-Tree","Bio/TreeIO/phyloxml.pm"
"Bio-Tree","Bio/TreeIO/pag.pm"
"Bio-Tree","Bio/TreeIO/lintree.pm"
"Bio-Tree","Bio/TreeIO/svggraph.pm"
"Bio-Tree","Bio/TreeIO/nexml.pm"
"Bio-Tree","Bio/TreeIO/nhx.pm"
"Bio-Tree","Bio/TreeIO/nexus.pm"
"Bio-Tree","Bio/TreeIO/tabtree.pm"
"Bio-Tree","Bio/TreeIO/newick.pm"
"Bio-Tree","Bio/TreeIO/cluster.pm"
"Bio-Tree","Bio/TreeIO/TreeEventBuilder.pm"
"Bio-Analysis","Bio/AnalysisResultI.pm"
,"Bio/Range.pm"
"Bio-Tree","Bio/TreeIO.pm"
,"Bio/IdentifiableI.pm"
"Bio-Das","Bio/Das/SegmentI.pm"
"Bio-Das","Bio/Das/FeatureTypeI.pm"
,"Bio/PullParserI.pm"
"Bio-Analysis","Bio/Factory/AnalysisI.pm"
,"Bio/Factory/SequenceProcessorI.pm"
,"Bio/Factory/SequenceStreamI.pm"
,"Bio/Factory/ObjectFactoryI.pm"
,"Bio/Factory/TreeFactoryI.pm"
,"Bio/Factory/SeqAnalysisParserFactoryI.pm"
,"Bio/Factory/MapFactoryI.pm"
,"Bio/Factory/SequenceFactoryI.pm"
,"Bio/Factory/SeqAnalysisParserFactory.pm"
,"Bio/Factory/ObjectBuilderI.pm"
,"Bio/Factory/ApplicationFactoryI.pm"
,"Bio/Factory/FTLocationFactory.pm"
,"Bio/Factory/ObjectFactory.pm"
,"Bio/Factory/DriverFactory.pm"
,"Bio/Factory/LocationFactoryI.pm"
,"Bio/Species.pm"
,"Bio/NexmlIO.pm"
"Bio-Cluster","Bio/Cluster/UniGene.pm"
"Bio-Cluster","Bio/Cluster/UniGeneI.pm"
"Bio-Cluster","Bio/Cluster/FamilyI.pm"
"Bio-Cluster","Bio/Cluster/SequenceFamily.pm"
"Bio-Cluster","Bio/Cluster/ClusterFactory.pm"
,"Bio/SimpleAlign.pm"
"Bio-Cluster","Bio/ClusterI.pm"
"Bio-Coordinate","Bio/Coordinate/Graph.pm"
"Bio-Coordinate","Bio/Coordinate/GeneMapper.pm"
"Bio-Coordinate","Bio/Coordinate/Chain.pm"
"Bio-Coordinate","Bio/Coordinate/Collection.pm"
"Bio-Coordinate","Bio/Coordinate/Result.pm"
"Bio-Coordinate","Bio/Coordinate/ResultI.pm"
"Bio-Coordinate","Bio/Coordinate/Pair.pm"
"Bio-Coordinate","Bio/Coordinate/MapperI.pm"
"Bio-Coordinate","Bio/Coordinate/ExtrapolatingPair.pm"
"Bio-Coordinate","Bio/Coordinate/Utils.pm"
"Bio-Coordinate","Bio/Coordinate/Result/Gap.pm"
"Bio-Coordinate","Bio/Coordinate/Result/Match.pm"
,"Bio/Seq.pm"
"Bio-Tree","Bio/Tree/Draw/Cladogram.pm"
"Bio-Tree","Bio/Tree/DistanceFactory.pm"
"Bio-Tree","Bio/Tree/Compatible.pm"
"Bio-Tree","Bio/Tree/TreeI.pm"
"Bio-Tree","Bio/Tree/Tree.pm"
"Bio-Tree","Bio/Tree/AnnotatableNode.pm"
"Bio-Tree","Bio/Tree/NodeI.pm"
"Bio-Tree","Bio/Tree/AlleleNode.pm"
"Bio-Tree","Bio/Tree/Statistics.pm"
"Bio-Tree","Bio/Tree/RandomFactory.pm"
"Bio-Tree","Bio/Tree/Node.pm"
"Bio-Tree","Bio/Tree/TreeFunctionsI.pm"
"Bio-Tree","Bio/Tree/NodeNHX.pm"
,"Bio/Structure/IO/pdb.pm"
"Bio-Structure","Bio/Structure/Atom.pm"
"Bio-Structure","Bio/Structure/Residue.pm"
"Bio-Structure","Bio/Structure/StructureI.pm"
"Bio-Structure","Bio/Structure/Chain.pm"
"Bio-Structure","Bio/Structure/IO.pm"
"Bio-Structure","Bio/Structure/Model.pm"
"Bio-Structure","Bio/Structure/Entry.pm"
"Bio-Structure","Bio/Structure/SecStr/DSSP/Res.pm"
"Bio-Structure","Bio/Structure/SecStr/STRIDE/Res.pm"
"Bio-SeqFeature-Annotated","Bio/SeqFeature/Annotated.pm"
"Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/ExonI.pm"
"Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/UTR.pm"
"Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/Exon.pm"
"Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/Transcript.pm"
"Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/GeneStructure.pm"
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"Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/NC_Feature.pm"
"Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/Promoter.pm"
"Bio-SeqFeature-Gene","Bio/SeqFeature/Gene/Intron.pm"
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"Bio-Variation","Bio/Variation/IO/flat.pm"
"Bio-Variation","Bio/Variation/IO/xml.pm"
"Bio-Variation","Bio/Variation/AAChange.pm"
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"Bio-Variation","Bio/Variation/README"
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"Bio-Variation","Bio/Variation/RNAChange.pm"
"Bio-Variation","Bio/Variation/DNAMutation.pm"
"Bio-Variation","Bio/Variation/Allele.pm"
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"Bio-Align","Bio/AlignIO/clustalw.pm"
"Bio-Align","Bio/AlignIO/xmfa.pm"
"Bio-Align","Bio/AlignIO/selex.pm"
"Bio-Align","Bio/AlignIO/fasta.pm"
"Bio-Align","Bio/AlignIO/bl2seq.pm"
"Bio-Align","Bio/AlignIO/emboss.pm"
"Bio-Align","Bio/AlignIO/arp.pm"
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"Bio-Align","Bio/AlignIO/meme.pm"
"Bio-Align","Bio/AlignIO/mega.pm"
"Bio-Align","Bio/AlignIO/pfam.pm"
"Bio-Align","Bio/AlignIO/largemultifasta.pm"
"Bio-Align","Bio/AlignIO/maf.pm"
"Bio-Align","Bio/AlignIO/nexus.pm"
"Bio-Align","Bio/AlignIO/msf.pm"
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"Bio-Seq","Bio/Seq/Quality.pm"
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"Bio-Seq","Bio/Seq/SequenceTrace.pm"
"Bio-Seq-Meta","Bio/Seq/Meta.pm"
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"Bio-Seq","Bio/Seq/RichSeqI.pm"
"Bio-Seq","Bio/Seq/BaseSeqProcessor.pm"
"Bio-Seq","Bio/Seq/PrimaryQual.pm"
"Bio-Seq-Meta","Bio/Seq/Meta/Array.pm"
"Bio-Seq","Bio/Seq/LargePrimarySeq.pm"
"Bio-Seq","Bio/Seq/SeqFactory.pm"
"Bio-Seq","Bio/Seq/RichSeq.pm"
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"Bio-Analysis","Bio/AnalysisParserI.pm"
"Bio-Ontology","Bio/Ontology/GOterm.pm"
"Bio-Ontology","Bio/Ontology/DocumentRegistry.pm"
"Bio-Ontology","Bio/Ontology/RelationshipFactory.pm"
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"Bio-Ontology","Bio/Ontology/InterProTerm.pm"
"Bio-Ontology","Bio/Ontology/TermI.pm"
"Bio-Ontology","Bio/Ontology/Path.pm"
"Bio-Ontology","Bio/Ontology/TermFactory.pm"
"Bio-Ontology","Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm"
"Bio-Ontology","Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm"
"Bio-Ontology","Bio/Ontology/Relationship.pm"
"Bio-Ontology","Bio/Ontology/RelationshipI.pm"
"Bio-Ontology","Bio/Ontology/Term.pm"
"Bio-Ontology","Bio/Ontology/OBOEngine.pm"
"Bio-Ontology","Bio/Ontology/OntologyEngineI.pm"
"Bio-Ontology","Bio/Ontology/OntologyI.pm"
"Bio-Ontology","Bio/Ontology/PathI.pm"
"Bio-Ontology","Bio/Ontology/SimpleOntologyEngine.pm"
"Bio-Ontology","Bio/Ontology/OBOterm.pm"
"Bio-Ontology","Bio/Ontology/RelationshipType.pm"
"Bio-Ontology","Bio/Ontology/OntologyStore.pm"
,"Bio/AnnotatableI.pm"
"Bio-Assembly","Bio/Assembly/Contig.pm"
"Bio-Assembly","Bio/Assembly/IO/maq.pm"
"Bio-Assembly","Bio/Assembly/IO/ace.pm"
"Bio-Assembly","Bio/Assembly/IO/phrap.pm"
"Bio-Assembly","Bio/Assembly/IO/sam.pm"
"Bio-Assembly","Bio/Assembly/IO/tigr.pm"
"Bio-Assembly","Bio/Assembly/IO/bowtie.pm"
"Bio-Assembly","Bio/Assembly/ScaffoldI.pm"
"Bio-Assembly","Bio/Assembly/IO.pm"
"Bio-Assembly","Bio/Assembly/Singlet.pm"
"Bio-Assembly","Bio/Assembly/ContigAnalysis.pm"
"Bio-Assembly","Bio/Assembly/Scaffold.pm"
"Bio-Assembly","Bio/Assembly/Tools/ContigSpectrum.pm"
,"Bio/Symbol/DNAAlphabet.pm"
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"Bio-Annotation","Bio/Annotation/SimpleValue.pm"
"Bio-Annotation","Bio/Annotation/Relation.pm"
"Bio-Annotation","Bio/Annotation/OntologyTerm.pm"
"Bio-Annotation","Bio/Annotation/TypeManager.pm"
"Bio-Annotation","Bio/Annotation/Tree.pm"
"Bio-Annotation","Bio/Annotation/AnnotationFactory.pm"
"Bio-Annotation","Bio/Annotation/Collection.pm"
"Bio-Annotation","Bio/Annotation/StructuredValue.pm"
"Bio-Annotation","Bio/Annotation/Reference.pm"
"Bio-Annotation","Bio/Annotation/TagTree.pm"
"Bio-Annotation","Bio/Annotation/DBLink.pm"
"Bio-Annotation","Bio/Annotation/Target.pm"
"Bio-Annotation","Bio/Annotation/Comment.pm"
"Bio-Phenotype","Bio/Phenotype/PhenotypeI.pm"
"Bio-Phenotype","Bio/Phenotype/MeSH/Twig.pm"
"Bio-Phenotype","Bio/Phenotype/MeSH/Term.pm"
"Bio-Phenotype","Bio/Phenotype/Phenotype.pm"
"Bio-Phenotype","Bio/Phenotype/Measure.pm"
"Bio-Phenotype","Bio/Phenotype/Correlate.pm"
"Bio-Phenotype","Bio/Phenotype/OMIM/MiniMIMentry.pm"
"Bio-Phenotype","Bio/Phenotype/OMIM/OMIMentry.pm"
"Bio-Phenotype","Bio/Phenotype/OMIM/OMIMparser.pm"
"Bio-Phenotype","Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm"
"Bio-Index","Bio/Index/BlastTable.pm"
"Bio-Index","Bio/Index/Qual.pm"
"Bio-HMMER","Bio/Index/Hmmer.pm"
"Bio-Index","Bio/Index/Swissprot.pm"
"Bio-Index","Bio/Index/Fasta.pm"
"Bio-Index","Bio/Index/SwissPfam.pm"
"Bio-Index","Bio/Index/AbstractSeq.pm"
"Bio-Index","Bio/Index/Stockholm.pm"
"Bio-Index","Bio/Index/EMBL.pm"
"Bio-Index","Bio/Index/Blast.pm"
"Bio-Index","Bio/Index/Abstract.pm"
"Bio-Index","Bio/Index/GenBank.pm"
"Bio-Index","Bio/Index/Fastq.pm"
"Bio-PhyloNetwork","Bio/PhyloNetwork/TreeFactoryMulti.pm"
"Bio-PhyloNetwork","Bio/PhyloNetwork/TreeFactoryX.pm"
"Bio-PhyloNetwork","Bio/PhyloNetwork/TreeFactory.pm"
"Bio-PhyloNetwork","Bio/PhyloNetwork/FactoryX.pm"
"Bio-PhyloNetwork","Bio/PhyloNetwork/RandomFactory.pm"
"Bio-PhyloNetwork","Bio/PhyloNetwork/GraphViz.pm"
"Bio-PhyloNetwork","Bio/PhyloNetwork/muVector.pm"
"Bio-PhyloNetwork","Bio/PhyloNetwork/Factory.pm"
"Bio-Matrix","Bio/Matrix/IO/mlagan.pm"
"Bio-Matrix","Bio/Matrix/IO/phylip.pm"
"Bio-Matrix","Bio/Matrix/IO/scoring.pm"
"Bio-Matrix","Bio/Matrix/Generic.pm"
"Bio-Matrix","Bio/Matrix/Scoring.pm"
"Bio-Matrix","Bio/Matrix/IO.pm"
"Bio-Matrix","Bio/Matrix/PhylipDist.pm"
"Bio-Matrix","Bio/Matrix/Mlagan.pm"
"Bio-Matrix","Bio/Matrix/MatrixI.pm"
"Bio-Matrix","Bio/Matrix/PSM/IO/mast.pm"
"Bio-Matrix","Bio/Matrix/PSM/IO/psiblast.pm"
"Bio-Matrix","Bio/Matrix/PSM/IO/masta.pm"
"Bio-Matrix","Bio/Matrix/PSM/IO/meme.pm"
"Bio-Matrix","Bio/Matrix/PSM/IO/transfac.pm"
"Bio-Matrix","Bio/Matrix/PSM/SiteMatrixI.pm"
"Bio-Matrix","Bio/Matrix/PSM/SiteMatrix.pm"
"Bio-Matrix","Bio/Matrix/PSM/ProtMatrix.pm"
"Bio-Matrix","Bio/Matrix/PSM/IO.pm"
"Bio-Matrix","Bio/Matrix/PSM/ProtPsm.pm"
"Bio-Matrix","Bio/Matrix/PSM/InstanceSiteI.pm"
"Bio-Matrix","Bio/Matrix/PSM/Psm.pm"
"Bio-Matrix","Bio/Matrix/PSM/PsmHeaderI.pm"
"Bio-Matrix","Bio/Matrix/PSM/InstanceSite.pm"
"Bio-Matrix","Bio/Matrix/PSM/PsmHeader.pm"
"Bio-Matrix","Bio/Matrix/PSM/PsmI.pm"
,"Bio/RangeI.pm"
"Bio-Search","Bio/SearchIO/axt.pm"
"Bio-Search","Bio/SearchIO/rnamotif.pm"
"Bio-Search","Bio/SearchIO/SearchResultEventBuilder.pm"
"Bio-HMMER","Bio/SearchIO/hmmer_pull.pm"
"Bio-Search","Bio/SearchIO/fasta.pm"
"Bio-Search","Bio/SearchIO/SearchWriterI.pm"
"Bio-Search","Bio/SearchIO/psl.pm"
"Bio-Search","Bio/SearchIO/erpin.pm"
"Bio-Search","Bio/SearchIO/IteratedSearchResultEventBuilder.pm"
"Bio-Search","Bio/SearchIO/cross_match.pm"
"Bio-Search","Bio/SearchIO/EventHandlerI.pm"
"Bio-Search","Bio/SearchIO/exonerate.pm"
"Bio-Search","Bio/SearchIO/gmap_f9.pm"
"Bio-HMMER","Bio/SearchIO/hmmer3.pm"
"Bio-Search","Bio/SearchIO/infernal.pm"
"Bio-Search","Bio/SearchIO/Writer/GbrowseGFF.pm"
"Bio-Search","Bio/SearchIO/Writer/HSPTableWriter.pm"
"Bio-Search","Bio/SearchIO/Writer/BSMLResultWriter.pm"
"Bio-Search","Bio/SearchIO/Writer/HitTableWriter.pm"
"Bio-Search","Bio/SearchIO/Writer/HTMLResultWriter.pm"
"Bio-Search","Bio/SearchIO/Writer/TextResultWriter.pm"
"Bio-Search","Bio/SearchIO/Writer/ResultTableWriter.pm"
"Bio-Search","Bio/SearchIO/megablast.pm"
"Bio-Search","Bio/SearchIO/blastxml.pm"
"Bio-Search","Bio/SearchIO/FastHitEventBuilder.pm"
"Bio-Search","Bio/SearchIO/wise.pm"
"Bio-Search","Bio/SearchIO/blast_pull.pm"
"Bio-Search","Bio/SearchIO/waba.pm"
"Bio-HMMER","Bio/SearchIO/hmmer.pm"
"Bio-Search","Bio/SearchIO/blasttable.pm"
"Bio-Search","Bio/SearchIO/blast.pm"
"Bio-Search","Bio/SearchIO/sim4.pm"
"Bio-Search","Bio/SearchIO/XML/BlastHandler.pm"
"Bio-Search","Bio/SearchIO/XML/PsiBlastHandler.pm"
"Bio-FeatureIO","Bio/FeatureIO/gtf.pm"
"Bio-FeatureIO","Bio/FeatureIO/interpro.pm"
"Bio-FeatureIO","Bio/FeatureIO/bed.pm"
"Bio-FeatureIO","Bio/FeatureIO/gff.pm"
"Bio-FeatureIO","Bio/FeatureIO/vecscreen_simple.pm"
"Bio-FeatureIO","Bio/FeatureIO/ptt.pm"
,"Bio/ParameterBaseI.pm"
"Bio-Search","Bio/Search/Tiling/MapTiling.pm"
"Bio-Search","Bio/Search/Tiling/MapTileUtils.pm"
"Bio-Search","Bio/Search/Tiling/TilingI.pm"
"Bio-Search","Bio/Search/SearchUtils.pm"
"Bio-Search","Bio/Search/GenericDatabase.pm"
"Bio-Search","Bio/Search/Iteration/GenericIteration.pm"
"Bio-Search","Bio/Search/Iteration/IterationI.pm"
"Bio-Search","Bio/Search/BlastStatistics.pm"
"Bio-Search","Bio/Search/Processor.pm"
"Bio-Search","Bio/Search/Hit/BlastHit.pm"
"Bio-Search","Bio/Search/Hit/GenericHit.pm"
"Bio-Search","Bio/Search/Hit/Fasta.pm"
"Bio-Search","Bio/Search/Hit/ModelHit.pm"
"Bio-Search","Bio/Search/Hit/HitI.pm"
"Bio-HMMER","Bio/Search/Hit/hmmer3Hit.pm"
"Bio-HMMER","Bio/Search/Hit/HMMERHit.pm"
"Bio-Search","Bio/Search/Hit/PsiBlastHit.pm"
"Bio-Search","Bio/Search/Hit/BlastPullHit.pm"
"Bio-Search","Bio/Search/Hit/HitFactory.pm"
"Bio-Search","Bio/Search/Hit/PullHitI.pm"
"Bio-Search","Bio/Search/Hit/HmmpfamHit.pm"
"Bio-Search","Bio/Search/BlastUtils.pm"
"Bio-Search","Bio/Search/GenericStatistics.pm"
"Bio-Search","Bio/Search/StatisticsI.pm"
"Bio-Search","Bio/Search/HSP/GenericHSP.pm"
"Bio-Search","Bio/Search/HSP/HSPI.pm"
"Bio-Search","Bio/Search/HSP/FastaHSP.pm"
"Bio-Search","Bio/Search/HSP/BlastHSP.pm"
"Bio-Search","Bio/Search/HSP/WABAHSP.pm"
"Bio-Search","Bio/Search/HSP/HmmpfamHSP.pm"
"Bio-Search","Bio/Search/HSP/BlastPullHSP.pm"
"Bio-Search","Bio/Search/HSP/ModelHSP.pm"
"Bio-Search","Bio/Search/HSP/HSPFactory.pm"
"Bio-HMMER","Bio/Search/HSP/HMMERHSP.pm"
"Bio-HMMER","Bio/Search/HSP/hmmer3HSP.pm"
"Bio-Search","Bio/Search/HSP/PSLHSP.pm"
"Bio-Search","Bio/Search/HSP/PsiBlastHSP.pm"
"Bio-Search","Bio/Search/HSP/PullHSPI.pm"
"Bio-HMMER","Bio/Search/Result/hmmer3Result.pm"
"Bio-Search","Bio/Search/Result/BlastResult.pm"
"Bio-Search","Bio/Search/Result/ResultFactory.pm"
"Bio-Search","Bio/Search/Result/CrossMatchResult.pm"
"Bio-Search","Bio/Search/Result/WABAResult.pm"
"Bio-Search","Bio/Search/Result/ResultI.pm"
"Bio-Search","Bio/Search/Result/BlastPullResult.pm"
"Bio-Search","Bio/Search/Result/HmmpfamResult.pm"
"Bio-HMMER","Bio/Search/Result/HMMERResult.pm"
"Bio-Search","Bio/Search/Result/GenericResult.pm"
"Bio-Search","Bio/Search/Result/PullResultI.pm"
"Bio-Search","Bio/Search/DatabaseI.pm"
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"Bio-Biblio","Bio/Biblio/Organisation.pm"
"Bio-Biblio","Bio/Biblio/Ref.pm"
"Bio-Biblio","Bio/Biblio/PubmedArticle.pm"
"Bio-Biblio","Bio/Biblio/IO/pubmed2ref.pm"
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"Bio-Biblio","Bio/Biblio/IO/medline2ref.pm"
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"Bio-Biblio","Bio/Biblio/Service.pm"
"Bio-Biblio","Bio/Biblio/Journal.pm"
"Bio-Biblio","Bio/Biblio/MedlineArticle.pm"
"Bio-Biblio","Bio/Biblio/Patent.pm"
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"Bio-Biblio","Bio/Biblio/JournalArticle.pm"
"Bio-Biblio","Bio/Biblio/BookArticle.pm"
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"Bio-Biblio","Bio/Biblio/MedlineJournalArticle.pm"
"Bio-Biblio","Bio/Biblio/Article.pm"
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"Bio-Biblio","Bio/Biblio/MedlineBookArticle.pm"
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"Bio-Biblio","Bio/Biblio/PubmedBookArticle.pm"
"Bio-Biblio","Bio/Biblio/MedlineBook.pm"
"Bio-Biblio","Bio/Biblio/MedlineJournal.pm"
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"Bio-DB-SeqFeature","Bio/DB/SeqFeature/NormalizedFeature.pm"
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/Segment.pm"
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/NormalizedFeatureI.pm"
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/berkeleydb.pm"
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/LoadHelper.pm"
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/GFF2Loader.pm"
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/Loader.pm"
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/DBI/Iterator.pm"
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/DBI/mysql.pm"
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/DBI/SQLite.pm"
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/DBI/Pg.pm"
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"Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/FeatureFileLoader.pm"
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/bdb.pm"
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store/memory.pm"
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/Store.pm"
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/NormalizedTableFeatureI.pm"
"AcePerl","Bio/DB/Ace.pm"
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"Bio-DB-GFF","Bio/DB/GFF/Homol.pm"
"Bio-DB-GFF","Bio/DB/GFF/Feature.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/berkeleydb.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/memory/feature_serializer.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/memory/iterator.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/ace.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/caching_handle.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/mysql.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/pg.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/oracleace.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/pg_fts.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/oracle.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/mysqlace.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/dbi/iterator.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/biofetch_oracle.pm"
"Bio-DB-GFF","Bio/DB/GFF/Adaptor/memory.pm"
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"Bio-DB-GFF","Bio/DB/GFF/Segment.pm"
"Bio-DB-GFF","Bio/DB/GFF/Util/Binning.pm"
"Bio-DB-GFF","Bio/DB/GFF/Util/Rearrange.pm"
"Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm"
"Bio-DB-GFF","Bio/DB/GFF/Aggregator/coding.pm"
"Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_twinscan.pm"
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"Bio-DB-GFF","Bio/DB/GFF/Aggregator/transcript.pm"
"Bio-DB-GFF","Bio/DB/GFF/Aggregator/processed_transcript.pm"
"Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_acembly.pm"
"Bio-DB-GFF","Bio/DB/GFF/Aggregator/orf.pm"
"Bio-DB-GFF","Bio/DB/GFF/Aggregator/alignment.pm"
"Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_ensgene.pm"
"Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_refgene.pm"
"Bio-DB-GFF","Bio/DB/GFF/Aggregator/ucsc_genscan.pm"
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,"t/Tools/EUtilities/epost.t"
,"t/Tools/EUtilities/elink_ncheck.t"
,"t/Tools/EUtilities/egquery.t"
,"t/Tools/Analysis/DNA/ESEfinder.t"
,"t/Tools/Analysis/Protein/Sopma.t"
,"t/Tools/Analysis/Protein/GOR4.t"
,"t/Tools/Analysis/Protein/Scansite.t"
,"t/Tools/Analysis/Protein/ELM.t"
,"t/Tools/Analysis/Protein/HNN.t"
,"t/Tools/Analysis/Protein/NetPhos.t"
,"t/Tools/Analysis/Protein/Domcut.t"
,"t/Tools/TargetP.t"
,"t/Tools/ePCR.t"
,"t/Tools/rnamotif.t"
,"t/Tools/Pseudowise.t"
,"t/Tools/RepeatMasker.t"
,"t/Tools/Geneid.t"
,"t/Tools/Est2Genome.t"
,"t/Tools/Genewise.t"
,"t/Tools/Genpred.t"
,"t/Tools/TandemRepeatsFinder.t"
,"t/Tools/Tmhmm.t"
,"t/Tools/IUPAC.t"
,"t/Tools/tRNAscanSE.t"
,"t/Tools/Signalp.t"
,"t/Tools/Spidey/Spidey.t"
,"t/Tools/Genomewise.t"
,"t/Tools/EMBOSS/Palindrome.t"
,"t/Tools/Seg.t"
BioPerl-1.007002/maintenance/big_split/rbuels_notes.txt000444000766000024        20213155576320 23170 0ustar00cjfieldsstaff000000000000


make a dist skel
fill in its build conf, with dependencies







group modules according to function (tags) and dependencies

BioPerl-1.007002/models000755000766000024          013155576320 14641 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/models/README000444000766000024       130013155576320 15650 0ustar00cjfieldsstaff000000000000# $Id$

This is the README file for the BioPerl models directory.

o What the models/ directory is about.

This directory is for files about schemas and plans in BioPerl.


o Are any of these files important?

It is definitely worth having a look at file bioperl.dia - if you can
open it. It gives you an overview of most important BioPerl modules.


o How do I open these files?

Most files in this directory are XML files for a program dia (with
extension .dia) which is a free GTK-library based diagram editor. It
is part of the GNOME desktop and is included in most GNU/LINUX
distributions (or see http://www.lysator.liu.se/~alla/dia).


o Are these up-to-date?

These are Bioperl version 1.0 models.BioPerl-1.007002/models/biblio.dia000444000766000024       672313155576320 16725 0ustar00cjfieldsstaff000000000000‹íKoÛHÇïù†s•Êý~˜“&{XÌbdg±Ç€¶[;²hPtsØϾÝ$Ù–dQj¶(: 	$—YúS¬ú±»‹Õ?ýüõvzò9+æ“|öæ”9ýùí«Ÿ®&é¹û{]¤·'Î`6÷¯ÞœÞ”åÝùÙÙ—/_`úmž–yÓÉ=̳³ÿ¥ÓizæŒÎNß¾:9yx€«´Lý{Í»iY“‹û2;™¥·Ù›Ó‹ôòÏë"¿Ÿ]ÖVÝe>Í‹“ÏéôÍéëOÕŸÓ³æ0gŽó̱ïÒ»¬xzØÛ»|>q&å·»“
Çñÿ>°i¬æÎhvýöõ/âuý‘š7–ÇZ÷A7:)oÓâz2[õSdé´>[œ…Ý\Äv0í ˆí`2ÿx—e‘NÊU'y>ÍÒYí§,î³ýýÌ/Ó©»TžB÷?ú§IYæ[>ÿ§t:o# ~û{Ôì×Åäêù|d±á(_&WåÍǯ‘NW}ôo‘Žþy2Ÿ\L³uŸ~2+;;ü·ÀÇ~Ï÷“«l¾å›~l³áH7ÙÙ6áOíÚ*¨ßz§ÊÅ4ý–Íáß-±tÒœã&蜅üâ¿ÙeÙÈû÷oÿ<ŸümšÎç§K¢’Ó“ÉÕ›Ó÷äñ¹yªÆÉež•“s—ÿ-¡	1PZhúT÷êºÉÍÅÅS/…‘ή§Ù“¶'æ<%L€‘z$À²½gÓìöãe^ÌVaÛµÆÊUÓ«:¿Ç³£“M®oÊÍÇgÀö;ú“;G÷ïÜE8ÉÏÏ}~~wq›]±"û´öÞc—ó2+²Ü_Ãëï¥#½p¿œ^®œ¢ç´Ó‡¾¿»+²ùüã÷Ì£»ÊÝbZº¨Žæj‘Ì[Šz|²£–’öwô)/²:~¬n蟺yx—Oª?ûùYŽ"¶ûy<šØñº^~3gÏgÚå™}Þ°Ìnï¦i™Åº¦ÇŸ?>ÕèÚe4”ec)=[Ĉ ÜŠˆ0«\içŠZ°ÆŠd,(ÿsIÚìë»ϺÑÙ
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#A4####Bio::Coordinate##MapperI######map########swap########test########Pair##########Collection####################ExtrapolatingPair##########Result######Result::Match######Result::Gap######Bio::Location::Simple################################2##create##########Chain##########GeneMapper##########Bio::Location::Split####################Utils######from_align########ResultI##########Bio::Location::Simple##############Graph######shortest path#########
BioPerl-1.007002/models/map_proposal.txt000444000766000024      1313713155576320 20260 0ustar00cjfieldsstaff000000000000
Map data is a critical component in many aspects of genetics and
biological research.   Well defined toolkits for manipulating map data
do not exist at this point, we propose to build a system for
manipulating most types of map data (Genetic, RH, RFLP, Sequence, and
LD).  

Map Proposal

This document proposes an object heirarchy for maps, markers, and
their manipulation. 

Key Points
* A Map is an object which contains mapable elements.
* A Map can be defined for a given organism or population of individuals.
* A Mappable element is an element with a position within a map.

Background information
 Maps are made up of elements which are mappable.  This includes
 genetic and physical markers.  

 A genetic map consists of markers which have a given recombination
 distance between them.  This distance is usually given as
 centi-morgans or 1% recombination between them.  Other distances
 include ... Examples of these are the publicly available
 Marshfield and Genethon maps.  

 Radiation hybrid maps consist of markers which have been mapped to
 radiation hybrid panels.  Typically these markers are STSes which
 have been processed on RH panels.  The distance between markers is
 calculated in centi-Rads which represent .  Examples of these include
 Whitehead STS, GeneMap '99.

 Restriction Enzyme (RE) maps are used to describe RE cut points in a
 given sequence and can be used to "fingerprint" sections of DNA
 (typically BAC clones).  Clones which share a statitistically (based
 on known frequency of RE cutting) signifigant collection fingerprints
 are likely to overlap.  Additionally 

 Physical maps or BAC/PAC/YAC maps represent clone fragment overlap.
 These maps are used to to represent how clones overlap and form a
 consensus sequence of a genomic or cDNA region.
 
 Sequence maps represent the known consensus sequence for a given
 region of typically genomic DNA.

 LD and Haplotype maps ...
 
 Comparisions between maps from different organisms can yield useful
 observations about trends in evolution.  Additionally comparisons of
 maps for the same species can provide insight into information such
 as recombination hot spots and DNA stability.

Object proposal
 Maps are objects which are made up of mappable elements.  A mappable
 element has a position on a map and can be tested for equality and
 relative position to other mappable element positions. 
 
 These are some baseline interface and object definitions.  Other work
 has been done by Philip Lijnzaad, Emmanuel Barillot and OMG folks to
 create definitions for maps.

 Interfaces
  Bio::IdentifiableI 
    string    getID // unique identifier -- this goes with Juha's
                    // identifiable property?
   
  Bio::NameableI
    string    getName
    
  Bio::AliasableI isa Bio::NameableI
    string    getAliases


  Bio::Map::MapI isa Bio::NameableI isa Bio::Identifiable
    MapIterator	       getAllElements // for in-order iterator access)
    ?Bio::ChromosomeI? chromosome     // Should maps be build one per
                                      // chromosome aggregated for
				      // a whole report set.
    Bio::SpeciesI      species        // use existing BP species object
				      // which may need to be more robust
    numeric	       length         // not sure what to return for
                                      // relative or RFLP maps
    string	       units          // Map units
    string	       name	      // Map Name


  Bio::Map::MappableI 
   // Where to handle the fact that RFLP 
   // Markers have multiple Map positions
    PositionI position(MapI) 
    boolean   equals(MappableI)
    boolean   less_than(MappableI)
    boolean   greater_than(MappableI)

    Bio::Map::PositionI 
     // may be undef to handle relative maps [RE].  
     // This is where a known position for a marker can be retrieved  
     // Multiple positions are possible for RE on a sequence map
     Array  positionValues  
  
  Bio::MarkerI isa Bio::MappableI isa Bio::AliasableI

  // heikki to help fill in Variant and Allele information
  Bio::LiveSeq::AlleleI

  Bio::LiveSeq::VariantI isa Bio::MarkerI
    Bio::PrimarySeqI getFwdPrimer()
    Bio::PrimarySeqI getRevPrimer()
    // I assume there should always be a primary set of 
    // of markers which defined start/end points 
    // should this be hidden inside more methods to 
    // handle RFLP, etc?
    Bio::LiveSeq::AlleleI getAlleles()
     
 Implementations
   Bio::Marker::RestrictionEnzyme isa Bio::MarkerI
   Bio::Marker::STS isa Bio::MarkerI
   Bio::Marker::Microsat isa Bio::LiveSeq::VariantI
   Bio::Marker::CytogeneticBand isa Bio::MarkerI
   Bio::Marker::VLTR isa Bio::MarkerI
   Bio::Marker::SNP
   Bio::Bin 
   
   Bio::Map::Cytogenetic isa Bio::Map::MapI 
     
   Bio::Map::RadiationHybrid
   Bio::Map::Genetic
   Bio::Map::GeneticMap 
     string	       getSex         // code as a string? - only 
   Bio::Map::RFLP
   Bio::Map::Sequence // Should probably be Bio::Assembly or these two
                      // need to work together Sequence Map could be 
		      // be built with Bio::Assemblies
   Bio::Map::Haplotype // what would this entail -- SNP components?
   

Caveats, questions, etc
-----------------------
Namespace is very flexible here.  

An important useful result of this toolkit will be the ability to
programatically go from one map to another.  So Querying Maps for a
marker - perhaps based on that marker's unique id will allow on to
compare distances on different maps or go from genetic to sequence
maps very easily.  

Not sure if we should be doing a Bio::ChromosomeI or can just code
with a string/numeric?  Does Polyploidy cause any problems in maps or
just in population/allele issues?
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`³¯i ª·³Ù˜Üg³ÉPÔÂOÁ«àÛz«ÏfË|7)Ù&*yd<ÝIÔPèMÔMÔMÔMãÆú¢nÞ8à³sè­(ÝRéÇ"ôÎk•Ø;–H›J¸ªñA»pA:Ìz¤j?zÆÔn…“:­vëÛéÔƒSåUnQåUn
^¹¥zè›7ÀyݹÆr·Ëz( ê"§ŠÆ¬<ИÎ=J§QÏvYõD5VÐÁ© C7YF£t(¥†"PŠ@û‰@•H8Ÿb»K~¸ó)T/”
®y2×n,©î`gp^W_gÏ ·hÚ&ìUP-Hdâobâoâïù['lþº|ôݘAƦآЊÑý°Ìg¬ÐþË@k‰nˆößž=ÖþßÊY•ú¥,2e‘)‹LYäYäFÓ}lƒ²°=l»ÈLbËl°l•AG‡+\nëGÓ83æÐXìÅõ”hŒhŒhŒhlO›¡&ÌÀ29PDÆX•Jåj½*À`…nAgî¥iÑ´UX†¦]ŒË»vNò(¥J)UJÊÑ·Gý4÷RªÍ3ŸN©nçclˆµ½5Uã”òǤJð¥k7 ³Ãx£šm²ø$+X©ÐIV‡“†i®*888í‰æØíDàÛÝ´ƒlŠ¦ŸöíÀ­7*`nîþœÑõXU>YÇÝTæ¬	å~T=Ö„òßåï7åìü%”)¡L	eJ(žPÆôë
0.µ|$”êŸÍ<–å"Љõ,ØLƒÓ5º†™ƒÑfU[…=ÏFËZ±ŽÂ4¡‰R
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®ŸÛdBzT꺥Ô
Ñêú¨¢-²*0k„lh‹í$œ6ƒh˜h˜9}{´±Û–î4èx»Qv¸]ýhå?§ `á]¬a{]›5m®JÉÚ…ït±v‘¥ŽWbqbqbq
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Ï;ñŒZ#	Žc	B3RèW<Ï;ì§õí×O48žœdr’ÉI~Îæ=zÉlf/™{îRRo Æ¸A­äHZ0Œë¼ämE[…ý”°Q»
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‚&Ð`¸6b€$—­×HUÑ7à”öD¦C‡bÖ¢ƒ^”|5
T¾zYª9 p”ÂÑCG›Ü—5gÜ\M?Ÿ>ÉÕ[¦áy˜•¬5	»8[F¡Oç¦z'Óï©»Ëo‡²¹Qçöß,Ïçh}Ã]ÿo¼—÷üž8×9˳÷¶Ëž>zúöñô]L–Þ=§çž¿.¡ç±ÔPèô±7˜Ó|€à’3@{[?0dýD£’-¢¡ BbtíDœ(ÕN|±µZZíDòLnª!Ï#ÅüSo³ŽÔÒàì‰Y7ŒVþµÍlÞ‘Z}(•¸b Î˜¹’ ûÏ\ý\\SÒŠ’V”´¢¤Õ–ex7«%n¸í#qà¦w“V•o¼’7”@ çðHþ}òЦp´·U<±Î)2w dÄë±ð¯1¼v ‘ë¬þ}JÆø÷a.ÕÁƒzó矟Ž¡“pw¿‘ü{òï©Fz_¦Óû{ ³¡÷Eäîï Uú{ªÓ@mèïÁìý==èCa^~hö—ßoæ«ñëkïV×¥4ÑÑÑØ4–<šL…ýnFÊÚ¬4æ‘äIzã¬
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Tæ@	4&P™ÉLeý¨y¬aÙ?«b³îlÖC*“ȌȌîºÇjÉSñœ\œ3aÛÊäÝ0³`ðRØ0ó¯Sè¾ÇF%›E‘Ó¦½™Ñ+ ‚D“u¥c¼2µ%¦ÌÓÒ.ß1^OÛqÀ6€JÝäÈfB:É>!)¸Ô]$“5¥õÿ׿Ýçú—‡³þ9Hg®úŒJÙŽ¢IɲÏÔ–Ï´Æ6ª·åŸ½fÎsRºªÖÛ„åÏs©Âªä»#w3ÛJ¶ˆj°ZËvQt:ýu­uÿÀ«¯ßË“"9?1[Ð|lšMßÞÁ~{ÙÙ¼Ó˜!ƒÃ2ÉmÈaÖÐb€#š<ß …..€yè!ÎhêEɸ3šd2mGQqíGÑ~ÔÐ38î¡TPI>qÌ¢¬Æf0®ÃYÜZ`êᆱ#8Õ±Y’ƒVBµJz®2!`]kN8{áÝêhÄ+ÿq,Ÿùîä1o;½¢S|³éãH¸>Ž(‹=8Yl°ªá=Á
	ÔCïéIÑÈñœˆ‡w¸iø¢h€yÐäA“½7:¹m”TÒ±!r@„« 6N´g„PC8ÑÍj¶Ér@‡­Þ±•
ñ¢äH¹Æ,%Ålò9ÌíFÆ¥
c`„TƒÌ
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–ÃDÛC&†LL›‰Ñ‡hb,K/IYKdwc$0sg‘h•ŽY’Ò d‹(ù0d`r&ýžiJúÙ䎗3®Á‘ÐÀ‘‰œî‚à(ÆÄXeB`8ÿJ1&²¦üzQóXvWsN)ßGù>Ê÷Q¾o_ù>+ÒCñ°q­1œè¨4ãYCqoæ‘WÜ%=ŸŒýV]HÃŽŒÅ›ôl‘Þk¶R>!«L¥TÙú wùËq—7¯÷>‡÷xÓ϶U€šáˆû‡\ÝmTì¿°Æ#ñI9´cFýûׂƒq»"GŽàêCÉwד‡æî~7™¿|ù«ÿ¢Ê©<”œ]rvÉÙÜÙM?FY‚æV…„†Ùýðð(“žK’§-Ï%cnË:•bÒŽ-º>´IÉQ	Ι֭$n@Û @ÑZwòr¿¼¤ðö)ë*A½»šÍE~r‚ÅjЙÔ6y.³‘aÀí-Rð•™K=$>¶ýq›Ee(÷q®M4¼¥:H¦kJ£†1݆¡¨|£cäôóïÂf¨g=@fPæÌ£y @¯ üÿäXúÕ‚#åÉ~gØÈý Œ	½ßrpS=.®¯ßPpLÁ1Ç›ª”@fGº"•·ªA™¥@K:>óž¬a‚©D𸭠FE[d0¼ÓVÙПU)ÑIØ3w‚Ã@aò{É<¥8Óê=ì$ÙôýæÐ?,ýÚ“]Þíæ0‡> 	ã‘Æg>RŽlðžÏ{LtJƸÊœ;¼¤9Éä$““LNòàNrK˜ÆAèKçø¨‹œ‚Y-Õ f³(9Èä ÷î [ûLäö‰ºŽõeglH¹bgÖHã3
Æ	ñr
afhÙ,ö¼$kÙ
 Zk-kA'æŽ{+)b‚.£	º4A—¾½ý}{ü™Mе)›ÀÛ¹1 ½åÒ[¹ÎiáÎûí"ïd¥k(´!Bå\Ê_¬˜7ÃÕ‡ž1).¯ÓÁõþû§ß~¥å¸(ÇE9®“=êèDñ§±ÊŒB!³Ê»fç"Ó(ÏcœØI>®g›,‚pâ‰V?¯Ju‘MÖ—Ê3mÔb‚'ëxj9cýzZ|*¯¾ª_ø?—‹âêÕWÿôSoï0BioPerl-1.007002/models/popgen.dia000444000766000024     50403113155576320 17010 0ustar00cjfieldsstaff000000000000

  
    
      
    
    
      
    
    
      
        
          #A4#
        
        
          
        
        
          
        
        
          
        
        
          
        
        
          
        
        
          
        
        
          
        
        
          
        
        
          
        
      
    
    
      
        
          
        
        
          
        
        
          
        
        
          
        
        
      
    
    
      
    
    
      
        
        
      
    
  
  
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        ##
      
      
        #Bio::PopGen#
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        #Bio::PopGen::Population#
      
      
        ##
      
      
        ##
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
          
            #self#
          
          
            ##
          
          
            ##
          
          
            ##
          
          
            
          
          
            
          
          
            
          
        
      
      
        
          
            #new#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #name#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #description#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #source#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #set_Allele_Frequency#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #add_Individual#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #remove_Individuals#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Individuals#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Genotypes#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_marker_names#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Marker#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_number_individuals#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #set_number_individuals#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Frequency_Homozygotes#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Frequency_Heterozygotes#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
      
      
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        #Bio::PopGen::Statistics#
      
      
        ##
      
      
        ##
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
      
        
          
            #fu_and_li_D#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #fu_and_li_D_star#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #fu_and_li_F#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #fu_and_li_F_star#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #tajima_D#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #pi#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #theta#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #singleton_count#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #segregating_sites_count#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #heterozygosity#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #derived_mutations#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #composite_LD#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
      
      
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        #Bio::PopGen::Marker#
      
      
        ##
      
      
        ##
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
          
            #self#
          
          
            ##
          
          
            ##
          
          
            ##
          
          
            
          
          
            
          
          
            
          
        
      
      
        
          
            #new#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #name#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #description#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #type#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #unique_id#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Alleles#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Allele_Frequencies#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #add_Allele_Frequency#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #reset_alleles#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
      
      
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        #Bio::PopGen::Individual#
      
      
        ##
      
      
        ##
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
          
            #self#
          
          
            ##
          
          
            ##
          
          
            ##
          
          
            
          
          
            
          
          
            
          
        
      
      
        
          
            #new#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #unique_id#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #num_of_results#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #add_Genotype#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #reset_Genotypes#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #remove_Genotype#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Genotypes#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #has_Marker#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_marker_names#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
      
      
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        #Bio::PopGen::PopStats#
      
      
        ##
      
      
        ##
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
          
            #self#
          
          
            ##
          
          
            ##
          
          
            ##
          
          
            
          
          
            
          
          
            
          
        
      
      
        
          
            #new#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #haploid_status#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #Fst#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
      
      
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        #Bio::PopGen::GenotypeI#
      
      
        ##
      
      
        ##
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
      
        
          
            #marker_name#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #individual_id#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Alleles#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
      
      
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        #Bio::PopGen::MarkerI#
      
      
        ##
      
      
        ##
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
      
        
          
            #name#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #description#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #type#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #unique_id#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #annotation#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Alleles#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Allele_Frequencies#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
      
      
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        #Bio::PopGen::IO#
      
      
        ##
      
      
        ##
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
          
            #self#
          
          
            ##
          
          
            ##
          
          
            ##
          
          
            
          
          
            
          
          
            
          
        
      
      
        
          
            #new#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #_initialize#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #next_individual#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #next_population#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #write_individual#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #write_population#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #newFh#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #fh#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #_load_format_module#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #_guess_format#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #close#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #DESTROY#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #TIEHANDLE#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #READLINE#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #PRINT#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
      
      
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        #Bio::PopGen::PopulationI#
      
      
        ##
      
      
        ##
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
      
        
          
            #name#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #description#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #source#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Individuals#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Genotypes#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Marker#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_marker_names#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Markers#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_number_individuals#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
      
      
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        #Bio::PopGen::IndividualI#
      
      
        ##
      
      
        ##
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
      
        
          
            #unique_id#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #num_genotypes#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #num_of_results#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Genotypes#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #has_Marker#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_marker_names#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
      
      
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        #Bio::PopGen::Genotype#
      
      
        ##
      
      
        ##
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
          
            #self#
          
          
            ##
          
          
            ##
          
          
            ##
          
          
            
          
          
            
          
          
            
          
        
      
      
        
          
            #new#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #marker_name#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #individual_id#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #get_Alleles#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #add_Allele#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
        
          
            #reset_Alleles#
          
          
            ##
          
          
            ##
          
          
            
          
          
            ##
          
          
            
          
          
            
          
          
            
          
          
            
          
          
        
      
      
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        #Bio::AnnotatableI#
      
      
        ##
      
      
        ##
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
      
      
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        #Bio::Root::IO#
      
      
        ##
      
      
        ##
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
      
      
        
      
      
    
    
      
        
      
      
        
      
      
        
        
        
        
      
      
        
        
        
      
      
        
      
      
        ##
      
      
        ##
      
      
        
        
      
    
    
      
        
      
      
        
      
      
        
        
        
        
      
      
        
        
        
      
      
        
      
      
        ##
      
      
        ##
      
      
        
        
      
    
    
      
        
      
      
        
      
      
        
        
        
        
      
      
        
        
        
      
      
        ##
      
      
        
      
      
        
          
            ##
          
          
            ##
          
          
            
          
          
            
          
        
        
          
            ##
          
          
            ##
          
          
            
          
          
            
          
        
      
      
        
        
      
    
    
      
        
      
      
        
      
      
        
          
            #Bio::PopGen#
          
          
            
          
          
            
          
          
            
          
          
            
          
          
            
          
        
      
    
    
      
        
      
      
        
      
      
        
        
        
        
      
      
        
        
        
      
      
        
      
      
        ##
      
      
        ##
      
      
        
        
      
    
    
      
        
      
      
        
      
      
        
        
        
        
      
      
        
        
        
      
      
        
      
      
        ##
      
      
        ##
      
      
        
        
      
    
    
      
        
      
      
        
      
      
        
        
        
        
      
      
        
        
        
      
      
        
      
      
        ##
      
      
        ##
      
      
        
        
      
    
    
      
        
      
      
        
      
      
        
        
        
        
      
      
        
        
        
      
      
        
      
      
        ##
      
      
        ##
      
      
        
        
      
    
  

BioPerl-1.007002/models/population_proposal.txt000444000766000024       215013155576320 21646 0ustar00cjfieldsstaff000000000000A toolkit for manipulating population data is critical for population
geneticists, epidemiologists, evo-devo and others.


This proposal will outline basic set of objects which are useful for
manipulating population data.  Our primary driving force will be to
process the data generated from the SNP haplotype project.


Population Objects

Bio::Population namespace

Bio::Population::HaplotypeCohortI  a collection (likely) co-inherited
			             markers
Bio::Population::HaplotypeI  -- a score for a particular haplotype
			        cohort or an individual
Bio::Population::GenotypeI   -- a score value for a marker for an individual 
Bio::Population::FrequencyI  -- an allele frequency in a Population
Bio::Population::PopulationI -- group of unrelated individuals
Bio::Population::PedigreeI   -- group of related individuals w/ relationships
Bio::Population::IndividualI -- a single identifiable entity with distinct
				genotypes for markers
Bio::Population::PhenotypeI  -- a trait associated with an individual 

Relationships
--------------- 
A PedigreeI isa PopulationI
A PopulationI can contain other PopulationIs
BioPerl-1.007002/scripts000755000766000024          013155576320 15045 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/scripts/README000555000766000024       134613155576320 16071 0ustar00cjfieldsstaff000000000000These scripts have been contributed by the developers and users of
Bioperl. The scripts in scripts/ are production quality scripts that 
have POD documentation and accept command-line arguments, and all of 
these scripts have the PLS suffix.

You can install the scripts in the scripts/ directory if you'd like,
simply follow the instructions on 'make install'. The installation
directory is specified by the INSTALLSCRIPT variable in the Makefile,
the default directory is /usr/bin. Installation will copy the scripts
to the specified directory, change the 'PLS' suffix to 'pl' and
prepend 'bp_' to the script name if it isn't so named already.

Please contact bioperl-l at bioperl.org if you are interested in
contributing your own script.
BioPerl-1.007002/scripts/Bio-DB-GFF000755000766000024          013155576320 16441 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/scripts/Bio-DB-GFF/README000444000766000024        30613155576320 17435 0ustar00cjfieldsstaff000000000000These are scripts that go with the Bio::DB::GFF module, a basic
seqfeature database.  Install these scripts if you wish to use the
LDAS distributed annotation server or the Generic Genome Browser.

BioPerl-1.007002/scripts/Bio-DB-GFF/bp_bulk_load_gff.pl000444000766000024      5064713155576320 22426 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

use strict;
use warnings;
# use lib './blib/lib';
use DBI;
use IO::File;
use File::Spec;
use Getopt::Long;
use Bio::DB::GFF;
use Bio::DB::GFF::Util::Binning 'bin';

use constant MYSQL => 'mysql';
use constant FDATA      => 'fdata';
use constant FTYPE      => 'ftype';
use constant FGROUP     => 'fgroup';
use constant FDNA       => 'fdna';
use constant FATTRIBUTE => 'fattribute';
use constant FATTRIBUTE_TO_FEATURE => 'fattribute_to_feature';

=head1 NAME

bp_bulk_load_gff.pl - Bulk-load a Bio::DB::GFF database from GFF files.

=head1 SYNOPSIS

  % bp_bulk_load_gff.pl -d testdb dna1.fa dna2.fa features1.gff features2.gff ...

=head1 DESCRIPTION

This script loads a Bio::DB::GFF database with the features contained
in a list of GFF files and/or FASTA sequence files.  You must use the
exact variant of GFF described in L.  Various
command-line options allow you to control which database to load and
whether to allow an existing database to be overwritten.

This script differs from bp_load_gff.pl in that it is hard-coded to use
MySQL and cannot perform incremental loads.  See L for an
incremental loader that works with all databases supported by
Bio::DB::GFF, and L for a MySQL loader that supports
fast incremental loads.

=head2 NOTES

If the filename is given as "-" then the input is taken from standard
input. Compressed files (.gz, .Z, .bz2) are automatically
uncompressed.

FASTA format files are distinguished from GFF files by their filename
extensions.  Files ending in .fa, .fasta, .fast, .seq, .dna and their
uppercase variants are treated as FASTA files.  Everything else is
treated as a GFF file.  If you wish to load -fasta files from STDIN,
then use the -f command-line swith with an argument of '-', as in 

    gunzip my_data.fa.gz | bp_fast_load_gff.pl -d test -f -

The nature of the bulk load requires that the database be on the local
machine and that the indicated user have the "file" privilege to load
the tables and have enough room in /usr/tmp (or whatever is specified
by the \$TMPDIR environment variable), to hold the tables transiently.

Local data may now be uploaded to a remote server via the --local option
with the database host specified in the dsn, e.g. dbi:mysql:test:db_host

The adaptor used is dbi::mysqlopt.  There is currently no way to
change this.

About maxfeature: the default value is 100,000,000 bases.  If you have
features that are close to or greater that 100Mb in length, then the
value of maxfeature should be increased to 1,000,000,000. This value
must be a power of 10.

Note that Windows users must use the --create option.

If the list of GFF or fasta files exceeds the kernel limit for the 
maximum number of command-line arguments, use the 
--long_list /path/to/files option. 


=head1 COMMAND-LINE OPTIONS

Command-line options can be abbreviated to single-letter options.
e.g. -d instead of --database.

   --database       Database name (default dbi:mysql:test)
   --adaptor             Adaptor name (default mysql)
   --create              Reinitialize/create data tables without asking
   --user                Username to log in as
   --fasta               File or directory containing fasta files to load
   --long_list           Directory containing a very large number of 
                         GFF and/or FASTA files
   --password            Password to use for authentication
                           (Does not work with Postgres, password must be
                           supplied interactively or be left empty for
                           ident authentication)
   --maxbin              Set the value of the maximum bin size
   --local               Flag to indicate that the data source is local
   --maxfeature          Set the value of the maximum feature size (power of 10)
   --group               A list of one or more tag names (comma or space separated)
                         to be used for grouping in the 9th column.
   --gff3_munge          Activate GFF3 name munging (see Bio::DB::GFF)
   --summary             Generate summary statistics for drawing coverage histograms.
                           This can be run on a previously loaded database or during
                           the load.
   --Temporary           Location of a writable scratch directory

=head1 SEE ALSO

L, L, L

=head1 AUTHOR

Lincoln Stein, lstein@cshl.org

Copyright (c) 2002 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut

package Bio::DB::GFF::Adaptor::fauxmysql;

use Bio::DB::GFF::Adaptor::dbi::mysqlopt;
use vars '@ISA';
@ISA = 'Bio::DB::GFF::Adaptor::dbi::mysqlopt';

sub insert_sequence {
  my $self = shift;
  my ($id,$offset,$seq) = @_;
  print join("\t",$id,$offset,$seq),"\n";
};

package Bio::DB::GFF::Adaptor::fauxmysqlcmap;

use Bio::DB::GFF::Adaptor::dbi::mysqlcmap;
use vars '@ISA';
@ISA = 'Bio::DB::GFF::Adaptor::dbi::mysqlcmap';

sub insert_sequence {
  my $self = shift;
  my ($id,$offset,$seq) = @_;
  print join("\t",$id,$offset,$seq),"\n";
};

package Bio::DB::GFF::Adaptor::fauxpg;

use Bio::DB::GFF::Adaptor::dbi::pg;
use vars '@ISA';
@ISA = 'Bio::DB::GFF::Adaptor::dbi::pg';

#these two subs are to separate the table creation from the
#index creation
sub do_initialize {
  my $self = shift;
  my $erase = shift;
  $self->drop_all if $erase;
                                                                                
  my $dbh = $self->features_db;
  my $schema = $self->schema;
  foreach my $table_name ($self->tables) {
    my $create_table_stmt = $schema->{$table_name}{table} ;
    $dbh->do($create_table_stmt) ||  warn $dbh->errstr;
  #  $self->create_other_schema_objects(\%{$schema->{$table_name}});
  }
  1;
}

sub _create_indexes_etc {
  my $self = shift;

  my $dbh = $self->features_db;
  my $schema = $self->schema;
  foreach my $table_name ($self->tables) {
    $self->create_other_schema_objects(\%{$schema->{$table_name}});
  }
}

sub insert_sequence {
  my $self = shift;
  my ($id,$offset,$seq) = @_;
  print "$id\t$offset\t$seq\n";
}

package main;

eval "use Time::HiRes"; undef $@;
my $timer = defined &Time::HiRes::time;

my $bWINDOWS = 0;    # Boolean: is this a MSWindows operating system?
if ($^O =~ /MSWin32/i) {
    $bWINDOWS = 1;
}

my ($DSN,$ADAPTOR,$FORCE,$USER,$PASSWORD,$FASTA,$LOCAL,$MAX_BIN,$GROUP_TAG,$LONG_LIST,$MUNGE,$TMPDIR);

GetOptions ('database:s'    => \$DSN,
	    'adaptor:s'     => \$ADAPTOR,
	    'create'        => \$FORCE,
	    'user:s'        => \$USER,
	    'password:s'    => \$PASSWORD,
	    'fasta:s'       => \$FASTA,
	    'local'         => \$LOCAL,
	    'maxbin|maxfeature:s'    => \$MAX_BIN,
	    'group:s'       => \$GROUP_TAG,
	    'long_list:s'   => \$LONG_LIST,
	    'gff3_munge'    => \$MUNGE,
	    'Temporary:s'   => \$TMPDIR,
	   ) or (system('pod2text', $0), exit -1);

# If called as pg_bulk_load_gff.pl behave as that did.
if ($0 =~/pg_bulk_load_gff.pl/){
    $ADAPTOR ||= 'Pg';
    $DSN     ||= 'test';
}
$DSN     ||= 'dbi:mysql:test';
$MAX_BIN ||= 1_000_000_000; # to accomodate human-sized chromosomes


if ($bWINDOWS && not $FORCE) {
  die "Note that Windows users must use the --create option.\n";
}

unless ($FORCE) {
  die "This will delete all existing data in database $DSN.  If you want to do this, rerun with the --create option.\n"
    if $bWINDOWS;
  open (TTY,"/dev/tty") or die "/dev/tty: $!\n";  #TTY use removed for win compatability
  print STDERR "This operation will delete all existing data in database $DSN.  Continue? ";
  my $f = ;
  die "Aborted\n" unless $f =~ /^[yY]/;
  close TTY;
}

# postgres DBD::Pg allows 'database', but also 'dbname', and 'db':
# and it must be Pg (not pg)
$DSN=~s/pg:database=/Pg:/i;
$DSN=~s/pg:dbname=/Pg:/i;
$DSN=~s/pg:db=/Pg:/i;

# leave these lines for mysql
$DSN=~s/database=//i;
$DSN=~s/;host=/:/i; #cater for dsn in the form of "dbi:mysql:database=$dbname;host=$host"


my($DBI,$DBD,$DBNAME,$HOST)=split /:/,$DSN;
$DBNAME=$DSN unless $DSN=~/:/;
$ADAPTOR ||= $DBD; 
$ADAPTOR ||= 'mysql';

if ($DBD eq 'Pg') {
        # rebuild DSN, DBD::Pg requires full dbname= format
        $DSN = "dbi:Pg:dbname=$DBNAME";
        if ($HOST) { $DSN .= ";host=$HOST"; }
}

my ($use_mysql,$use_mysqlcmap,$use_pg) = (0,0,0);
if ( $ADAPTOR eq 'mysqlcmap' ) {
  $use_mysqlcmap = 1;
}
elsif ( $ADAPTOR =~ /^mysql/ ) {
  $use_mysql = 1;
}
elsif ( $ADAPTOR eq "Pg" ) {
  $use_pg = 1;
}
else{
    die "$ADAPTOR is not an acceptable database adaptor.";
}


my (@auth,$AUTH);
if (defined $USER) {
  push @auth,(-user=>$USER);
  if ( $use_mysql or $use_mysqlcmap ) {
    $AUTH .= " -u$USER";
  }
  elsif ( $use_pg ) {
    $AUTH .= " -U $USER ";
  }
}
if (defined $PASSWORD) {
  push @auth,(-pass=>$PASSWORD);
  if ( $use_mysql or $use_mysqlcmap ) {
    $AUTH .= " -p$PASSWORD";
  }
#  elsif ( $use_pg ) {
#    $AUTH .= " -W $PASSWORD ";
#  }
}

if (defined $HOST) {
  $AUTH .= " -h$HOST";  
}
if (defined $DBNAME) {
  if ( $use_mysql or $use_mysqlcmap ) {
    $AUTH .= " -D$DBNAME ";
  }
}
if (defined $LOCAL) {
  $LOCAL='local';
  $AUTH.=' --local-infile=1';
}else {
  $LOCAL='';
}

my $faux_adaptor;
if ( $use_mysqlcmap ) {
  $faux_adaptor = "fauxmysqlcmap";
}
elsif ( $use_mysql ) {
  $faux_adaptor = "fauxmysql";
}
elsif ( $use_pg ) {
  $faux_adaptor = "fauxpg";
}

my $db = Bio::DB::GFF->new(-adaptor=>$faux_adaptor,-dsn => $DSN,@auth)
  or die "Can't open database: ",Bio::DB::GFF->error,"\n";

$db->gff3_name_munging(1) if $MUNGE;

$MAX_BIN ? $db->initialize(-erase=>1,-MAX_BIN=>$MAX_BIN) : $db->initialize(1);
$MAX_BIN ||= $db->meta('max_bin') || 100_000_000;

# deal with really long lists of files
if ($LONG_LIST) {
  -d $LONG_LIST or die "The --long_list argument must be a directory\n";
  opendir GFFDIR,$LONG_LIST or die "Could not open $LONG_LIST for reading: $!";
  @ARGV = map { "$LONG_LIST\/$_" } readdir GFFDIR;
  closedir GFFDIR;

  if (defined $FASTA && -d $FASTA) {
    opendir FASTA,$FASTA or die "Could not open $FASTA for reading: $!";
    push @ARGV, map { "$FASTA\/$_" } readdir FASTA;
    closedir FASTA;
  }
  elsif (defined $FASTA && -f $FASTA) {
    push @ARGV, $FASTA;
  }
}

foreach (@ARGV) {
  $_ = "gunzip -c $_ |" if /\.gz$/;
  $_ = "uncompress -c $_ |" if /\.Z$/;
  $_ = "bunzip2 -c $_ |" if /\.bz2$/;
}

my (@gff,@fasta);
foreach (@ARGV) {
  if (/\.(fa|fasta|dna|seq|fast)(?:$|\.)/i) {
    push @fasta,$_;
  } else {
    push @gff,$_;
  }
}
@ARGV = @gff;
push @fasta,$FASTA if defined $FASTA;

# drop everything that was there before
my %FH;
my $tmpdir = File::Spec->tmpdir() || '/tmp';
$tmpdir =~ s!\\!\\\\!g if $bWINDOWS; #eliminates backslash mis-interpretation
-d $tmpdir or die <new(">$tmpdir/$_.$$") or die $_,": $!";
  $FH{$_}->autoflush;
}

if ( $use_pg ) {
  $FH{FDATA()                }->print("COPY fdata (fid, fref, fstart, fstop, fbin, ftypeid, fscore, fstrand, fphase, gid, ftarget_start, ftarget_stop) FROM stdin;\n");
  $FH{FTYPE()                }->print("COPY ftype (ftypeid, fmethod, fsource) FROM stdin;\n");
  $FH{FGROUP()               }->print("COPY fgroup (gid, gclass, gname) FROM stdin;\n");
  $FH{FATTRIBUTE()           }->print("COPY fattribute (fattribute_id, fattribute_name) FROM stdin;\n");
  $FH{FATTRIBUTE_TO_FEATURE()}->print("COPY fattribute_to_feature (fid, fattribute_id, fattribute_value) FROM stdin;\n");
}
my $FID     = 1;
my $GID     = 1;
my $FTYPEID = 1;
my $ATTRIBUTEID = 1;
my %GROUPID     = ();
my %FTYPEID     = ();
my %ATTRIBUTEID = ();
my %DONE        = ();
my $FEATURES    = 0;

my %tmpfiles; # keep track of temporary fasta files
my $count;
my $fasta_sequence_id;
my $gff3;
my $current_file; #used to reset GFF3 flag in mix of GFF and GFF3 files

$db->preferred_groups(split (/[,\s]+/,$GROUP_TAG)) if defined $GROUP_TAG;

my $last  = Time::HiRes::time() if $timer;
my $start = $last;

  # avoid hanging on standalone --fasta load
if (!@ARGV) {
    $FH{NULL} = IO::File->new(">$tmpdir/null");
    push @ARGV, "$tmpdir/null";
}

my ($cmap_db);
if ($use_mysqlcmap){
  my $options = {
		 AutoCommit       => 1,
		 FetchHashKeyName => 'NAME_lc',
		 LongReadLen      => 3000,
		 LongTruncOk      => 1,
		 RaiseError       => 1,
		};

  $cmap_db = DBI->connect( $DSN, $USER, $PASSWORD, $options );
}
# Only load CMap::Utils if using cmap
unless (!$use_mysqlcmap or
	eval {
	  require Bio::GMOD::CMap::Utils;
	  Bio::GMOD::CMap::Utils->import('next_number');
	  1;
	} 
       ) {
  print STDERR "Error loading Bio::GMOD::CMap::Utils\n";
}


while (<>) {

  $current_file ||= $ARGV;

  # reset GFF3 flag if new filehandle
  unless($current_file eq $ARGV){
    undef $gff3;
    $current_file = $ARGV;
  }

  chomp;
  my ($ref,$source,$method,$start,$stop,$score,$strand,$phase,$group);

  # close sequence filehandle if required
  if ( /^\#|\s+|^$|^>|\t/ && defined $FH{FASTA}) {
    $FH{FASTA}->close;
    delete $FH{FASTA};
  }

  # print to fasta file if the handle is open
  if ( defined $FH{FASTA} ) {
    $FH{FASTA}->print("$_\n");
    next;
  }

  elsif (/^>(\S+)/) {  # uh oh, sequence coming
    $FH{FASTA} = IO::File->new(">$tmpdir/$1\.fa") or die "FASTA: $!\n";
    $FH{FASTA}->print("$_\n");
    print STDERR "Preparing embedded sequence $1\n";
    push @fasta, "$tmpdir/$1\.fa";
    push @fasta_files_to_be_unlinked,"$tmpdir/$1\.fa";
    $tmpfiles{"$tmpdir/$1\.fa"}++;
    next;
  }

  elsif (/^\#\#\s*gff-version\s+(\d+)/) {
    $gff3 = ($1 >= 3);
    $db->print_gff3_warning() if $gff3;
    next;
  }

  elsif (/^\#\#\s*group-tags\s+(.+)/) {
    $db->preferred_groups(split(/\s+/,$1));
    next;
  }

  elsif (/^\#\#\s*sequence-region\s+(\S+)\s+(\d+)\s+(\d+)/i) { # header line
    ($ref,$source,$method,$start,$stop,$score,$strand,$phase,$group) =
	($1,'reference','Component',$2,$3,'.','.','.',$gff3 ? "ID=Sequence:$1": qq(Sequence "$1"));
  }

  elsif (/^\#/) {
    next;
  }

  else {
    ($ref,$source,$method,$start,$stop,$score,$strand,$phase,$group) = split "\t";
  }
  if ( not defined( $ref ) or length ($ref) == 0) {
    warn "\$ref is null.  source = $source, method = $method, group = $group\n";
    next;
  }
  $FEATURES++;
  my $size = $stop-$start+1;
  warn "Feature $group ($size) is larger than $MAX_BIN. You will have trouble retrieving this feature.\nRerun script with --maxfeature set to a higher power of 10.\n" if $size > $MAX_BIN;

  $source = '\N' unless defined $source;
  $score  = '\N' if $score  eq '.';
  $strand = '\N' if $strand eq '.';
  $phase  = '\N' if $phase  eq '.';

  my ($group_class,$group_name,$target_start,$target_stop,$attributes) = $db->split_group($group,$gff3);

  # GFF2/3 transition
  $group_class = [$group_class] unless ref $group_class;
  $group_name  = [$group_name]  unless ref $group_name;

  for (my $i=0; $i < @$group_name; $i++) {
    $group_class->[$i]  ||= '\N';
    $group_name->[$i]   ||= '\N';
    $target_start ||= '\N';
    $target_stop  ||= '\N';
    $method       ||= '\N';
    $source       ||= '\N';

    my $fid     = $FID++;
    my $gid     = $GROUPID{lc join('',$group_class->[$i],$group_name->[$i])}  ||= $GID++;
    my $ftypeid = $FTYPEID{lc join('',$source,$method)}                       ||= $FTYPEID++;

    my $bin = bin($start,$stop,$db->min_bin);
    $FH{ FDATA()  }->print(    join("\t",$fid,$ref,$start,$stop,$bin,$ftypeid,$score,$strand,$phase,$gid,$target_start,$target_stop),"\n"   );
    if ($use_mysqlcmap){
      my $feature_id    = next_number(
				      db         => $cmap_db,
				      table_name => 'cmap_feature',
				      id_field   => 'feature_id',
				     )
	or die 'No feature id';
      my $direction = $strand eq '-' ? -1:1;
      $FH{ FGROUP() }->print(    
			     join("\t",$feature_id,$feature_id,'NULL',0, $group_name->[$i],0,0,'NULL',1,$direction, $group_class->[$i],)
			     ,"\n"
			    ) unless $DONE{"G$gid"}++;
    }
    else {
      $FH{ FGROUP() }->print(    join("\t",$gid,$group_class->[$i],$group_name->[$i]),"\n") unless $DONE{"G$gid"}++;
    }
    $FH{ FTYPE()  }->print(    join("\t",$ftypeid,$method,$source),"\n"                   ) unless $DONE{"T$ftypeid"}++;

    foreach (@$attributes) {
      my ($key,$value) = @$_;
      my $attributeid = $ATTRIBUTEID{$key}   ||= $ATTRIBUTEID++;
      $FH{ FATTRIBUTE() }->print( join("\t",$attributeid,$key),"\n"                       ) unless $DONE{"A$attributeid"}++;
      $FH{ FATTRIBUTE_TO_FEATURE() }->print( join("\t",$fid,$attributeid,$value),"\n");
    }

    if ( $fid % 1000 == 0) {
      my $now    = Time::HiRes::time() if $timer;
      my $elapsed = $timer ? sprintf(" in %5.2fs",$now - $last) : '';
      $last = $now;
      print STDERR "$fid features parsed$elapsed...";
      print STDERR -t STDOUT && !$ENV{EMACS} ? "\r" : "\n";
    }
  }
}

$FH{FASTA}->close if exists $FH{FASTA};

for my $file (@fasta) {
  warn "Preparing DNA file $file....\n";
  if ($use_pg){
    $FH{FDNA() }->print("COPY fdna (fref, foffset, fdna) FROM stdin;\n");
  }
  my $old = select($FH{FDNA()});
  $db->load_fasta($file) or warn "Couldn't load fasta file $file: $!";
  if ($use_pg){
    $FH{FDNA() }->print("\\.\n\n");
  }
  warn "done...\n";
  select $old;
  unlink $file if $tmpfiles{$file};
}

if ($use_pg) { 
  $FH{FDATA()                }->print("\\.\n\n");
  $FH{FTYPE()                }->print("\\.\n\n");
  $FH{FGROUP()               }->print("\\.\n\n");
  $FH{FATTRIBUTE()           }->print("\\.\n\n");
  $FH{FATTRIBUTE_TO_FEATURE()}->print("\\.\n\n");
}


$_->close foreach values %FH;
printf STDERR "Total parse time %5.2fs\n",(Time::HiRes::time() - $start) if $timer;
warn "Loading feature data and analyzing tables.  You may see RDBMS messages here...\n";

if ($use_pg){
  warn "Loading feature data.  You may see Postgres comments...\n";

  foreach (@files) {
    my $file = "$tmpdir/$_.$$";

    $AUTH ? system("psql $AUTH -f $file $DBNAME")
          : system('psql','-f', $file, $DBNAME);

    unlink $file;
  }

  warn "Updating sequences ...\n";
  $db->update_sequences();

  warn "Creating indexes ...\n";
  $db->_create_indexes_etc();

  warn "done...\n";

}

elsif( $use_mysql or $use_mysqlcmap ) {
  $start = time();

  my $success = 1;
  my $TERMINATEDBY = $bWINDOWS ? q( LINES TERMINATED BY '\r\n') : ''; 
  for my $f (@files) {
    my $table = function_to_table($f,$ADAPTOR);
    my $sql = join ('; ',
		    "lock tables $table write",
		    "delete from $table",
		    "load data $LOCAL infile '$tmpdir/$f.$$' replace into table $table $TERMINATEDBY",
		    "unlock tables");
    my $command = MYSQL . qq[$AUTH -s -e "$sql"];
    $command =~ s/\n/ /g;
    $success &&= system($command) == 0;
    unlink "$tmpdir/$f.$$";
  }
  printf STDERR "Total load time %5.2fs\n",(time() - $start) if $timer;
  print STDERR "done...\n";

  print STDERR "Analyzing/optimizing tables. You will see database messages...\n";
  $start = time();
  my $sql = '';
  for my $f (@files) {
    my $table = function_to_table($f,$ADAPTOR);
    $sql       .= "analyze table $table;";
  }
  my $command = MYSQL . qq[$AUTH -N -s -e "$sql"];
  $success &&= system($command) == 0;
  printf STDERR "Optimization time time %5.2fs\n",(time() - $start);

  if ($success) {
    print "$FEATURES features successfully loaded\n";
  } else {
    print "FAILURE: Please see standard error for details\n";
    exit -1;
  }
}

foreach (@fasta_files_to_be_unlinked) {
  unlink "$tmpdir/$_.$$";
}

warn "Building summary statistics for coverage histograms...\n";
my (@args,$AUTH);
if (defined $USER) {
  push @args,(-user=>$USER);
  $AUTH .= " -u$USER";
}
if (defined $PASSWORD) {
  push @args,(-pass=>$PASSWORD);
  $AUTH .= " -p$PASSWORD";
}
push @args,(-preferred_groups=>[split(/[,\s+]+/,$GROUP_TAG)]) if defined $GROUP_TAG;
my $db = Bio::DB::GFF->new(-adaptor=>"dbi::$ADAPTOR",-dsn => $DSN,@args)
  or die "Can't open database: ",Bio::DB::GFF->error,"\n";
$db->build_summary_statistics;

exit 0;

sub function_to_table {
    my $function = shift;
    my $adaptor  = shift;

    if ($function eq 'fdata'){
        return 'fdata';
    }
    elsif ($function eq 'ftype'){
        return 'ftype';
    }
    elsif ($function eq 'fgroup'){
        return 'cmap_feature' if ($adaptor eq 'mysqlcmap');
        return 'fgroup';
    }
    elsif ($function eq 'fdna'){
        return 'fdna';
    }
    elsif ($function eq 'fattribute'){
        return 'fattribute';
    }
    elsif ($function eq 'fattribute_to_feature'){
        return 'fattribute_to_feature';
    }
    return '';
}

__END__
BioPerl-1.007002/scripts/Bio-DB-GFF/bp_fast_load_gff.pl000444000766000024      3641513155576320 22423 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

use strict;
use warnings;
# use lib './blib/lib';
use DBI;
use IO::File;
use Getopt::Long;
use Bio::DB::GFF::Util::Binning 'bin';
use Bio::DB::GFF::Adaptor::dbi::mysqlopt;

use constant MYSQL => 'mysql';

use constant FDATA      => 'fdata';
use constant FTYPE      => 'ftype';
use constant FGROUP     => 'fgroup';
use constant FDNA       => 'fdna';
use constant FATTRIBUTE => 'fattribute';
use constant FATTRIBUTE_TO_FEATURE => 'fattribute_to_feature';

my $DO_FAST = eval "use POSIX 'WNOHANG'; 1;";

=head1 NAME

bp_fast_load_gff.pl - Fast-load a Bio::DB::GFF database from GFF files.

=head1 SYNOPSIS

  % bp_fast_load_gff.pl -d testdb dna1.fa dna2.fa features1.gff features2.gff ...

=head1 DESCRIPTION

This script loads a Bio::DB::GFF database with the features contained
in a list of GFF files and/or FASTA sequence files.  You must use the
exact variant of GFF described in L.  Various
command-line options allow you to control which database to load and
whether to allow an existing database to be overwritten.

This script is similar to load_gff.pl, but is much faster.  However,
it is hard-coded to use MySQL and probably only works on Unix
platforms due to its reliance on pipes.  See L for an
incremental loader that works with all databases supported by
Bio::DB::GFF, and L for a fast MySQL loader that
supports all platforms.

=head2 NOTES

If the filename is given as "-" then the input is taken from
standard input. Compressed files (.gz, .Z, .bz2) are automatically
uncompressed.

FASTA format files are distinguished from GFF files by their filename
extensions.  Files ending in .fa, .fasta, .fast, .seq, .dna and their
uppercase variants are treated as FASTA files.  Everything else is
treated as a GFF file.  If you wish to load -fasta files from STDIN,
then use the -f command-line swith with an argument of '-', as in 

    gunzip my_data.fa.gz | bp_fast_load_gff.pl -d test -f -

The nature of the load requires that the database be on the local
machine and that the indicated user have the "file" privilege to load
the tables and have enough room in /usr/tmp (or whatever is specified
by the \$TMPDIR environment variable), to hold the tables transiently.
If your MySQL is version 3.22.6 and was compiled using the "load local
file" option, then you may be able to load remote databases with local
data using the --local option.

About maxfeature: the default value is 100,000,000 bases.  If you have
features that are close to or greater that 100Mb in length, then the
value of maxfeature should be increased to 1,000,000,000. This value
must be a power of 10.

If the list of GFF or fasta files exceeds the kernel limit for the
maximum number of command-line arguments, use the
--long_list /path/to/files option.

The adaptor used is dbi::mysqlopt.  There is currently no way to
change this.

=head1 COMMAND-LINE OPTIONS

Command-line options can be abbreviated to single-letter options.
e.g. -d instead of --database.

   --database       Mysql database name
   --create              Reinitialize/create data tables without asking
   --local               Try to load a remote database using local data.
   --user                Username to log in as
   --fasta               File or directory containing fasta files to load
   --password            Password to use for authentication
   --long_list           Directory containing a very large number of
                         GFF and/or FASTA files
   --maxfeature          Set the value of the maximum feature size (default 100Mb; must be a power of 10)
   --group               A list of one or more tag names (comma or space separated)
                         to be used for grouping in the 9th column.
   --gff3_munge          Activate GFF3 name munging (see Bio::DB::GFF)
   --summary             Generate summary statistics for drawing coverage histograms.
                           This can be run on a previously loaded database or during
                           the load.
   --Temporary           Location of a writable scratch directory

=head1 SEE ALSO

L, L, L

=head1 AUTHOR

Lincoln Stein, lstein@cshl.org

Copyright (c) 2002 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut

package Bio::DB::GFF::Adaptor::faux;

use Bio::DB::GFF::Adaptor::dbi::mysqlopt;
use vars '@ISA';
@ISA = 'Bio::DB::GFF::Adaptor::dbi::mysqlopt';

sub insert_sequence {
  my $self = shift;
  my ($id,$offset,$seq) = @_;
  print join "\t",$id,$offset,$seq,"\n";
}

package main;

eval "use Time::HiRes"; undef $@;
my $timer = defined &Time::HiRes::time;

my ($DSN,$CREATE,$USER,$PASSWORD,$FASTA,$FAILED,$LOCAL,%PID,$MAX_BIN,$GROUP_TAG,$LONG_LIST,$MUNGE,$TMPDIR,$SUMMARY_STATS);

if ($DO_FAST) {
  $SIG{CHLD} = sub {
    while ((my $child = waitpid(-1,&WNOHANG)) > 0) {
      delete $PID{$child} or next;
      $FAILED++ if $? != 0;
    }
  }
};

$SIG{INT} = $SIG{TERM} = sub {cleanup(); exit -1};

GetOptions ('database:s'    => \$DSN,
	    'create'        => \$CREATE,
	    'user:s'        => \$USER,
            'local'         => \$LOCAL,
	    'password:s'    => \$PASSWORD,
	    'fasta:s'       => \$FASTA,
	    'group:s'       => \$GROUP_TAG,
	    'long_list:s'   => \$LONG_LIST,
            'maxbin|maxfeature:s'    => \$MAX_BIN,
	    'gff3_munge'    => \$MUNGE,
	    'summary'       => \$SUMMARY_STATS,
	    'Temporary:s'   => \$TMPDIR,
	   ) or (system('pod2text',$0), exit -1);

$DSN ||= 'test';
$MAX_BIN ||= 1_000_000_000; # to accomodate human-sized chromosomes

my (@args,$AUTH);
if (defined $USER) {
  push @args,(-user=>$USER);
  $AUTH .= " -u$USER";
}
if (defined $PASSWORD) {
  push @args,(-pass=>$PASSWORD);
  $AUTH .= " -p$PASSWORD";
}
push @args,(-preferred_groups=>[split(/[,\s+]+/,$GROUP_TAG)]) if defined $GROUP_TAG;

my $db = Bio::DB::GFF->new(-adaptor=>'faux',-dsn => $DSN,@args)
  or die "Can't open database: ",Bio::DB::GFF->error,"\n";

$db->gff3_name_munging(1) if $MUNGE;

if ($CREATE) {
  $SUMMARY_STATS++;
  $MAX_BIN ? $db->initialize(-erase=>1,-MAX_BIN=>$MAX_BIN) : $db->initialize(1);
}

$MAX_BIN ||= $db->meta('max_bin') || 100_000_000;

# deal with really long lists of files
if ($LONG_LIST) {
  -d $LONG_LIST or die "The --long_list argument must be a directory\n";
  opendir GFFDIR,$LONG_LIST or die "Could not open $LONG_LIST for reading: $!";
  @ARGV = map { "$LONG_LIST\/$_" } readdir GFFDIR;
  closedir GFFDIR;
  
  if (defined $FASTA && -d $FASTA) {
    opendir FASTA,$FASTA or die "Could not open $FASTA for reading: $!";
    push @ARGV, map { "$FASTA\/$_" } readdir FASTA;
    closedir FASTA;
  }
}

foreach (@ARGV) {
  $_ = "gunzip -c $_ |" if /\.gz$/;
  $_ = "uncompress -c $_ |" if /\.Z$/;
  $_ = "bunzip2 -c $_ |" if /\.bz2$/;
}
my(@fasta,@gff);
foreach (@ARGV) {
  if (/\.(fa|fasta|dna|seq|fast)(?:\.|$)/i) {
    push @fasta,$_;
  } else {
    push @gff,$_;
  }
}
@ARGV = @gff;
push @fasta,$FASTA if defined $FASTA;

# initialize state variables
my $FID     = 1;
my $GID     = 1;
my $FTYPEID = 1;
my $ATTRIBUTEID = 1;
my %GROUPID     = ();
my %FTYPEID     = ();
my %ATTRIBUTEID = ();
my %DONE        = ();
my $FEATURES    = 0;

load_tables($db->dbh) unless $CREATE;
my ($major,$minor,$sub) = split /\./,$db->dbh->get_info(18); # SQL_DBMS_VER
my $can_disable_indexes = ($major >= 4 and $minor >= 0);

# open up pipes to the database
my (%FH,%COMMAND);
my $MYSQL  = MYSQL;
my $tmpdir = $TMPDIR || $ENV{TMPDIR} || $ENV{TMP} || File::Spec->tmpdir();
-d $tmpdir or die <new($file,'>') or die $_,": $!";
  print STDERR "ok\n";
  $FH{$_}->autoflush;
}

print STDERR "Fast loading enabled\n"    if $DO_FAST;

my ($count,$gff3,$last,$start,$beginning,$current_file);

$last  = Time::HiRes::time() if $timer;
$beginning = $start = $last;

# avoid hanging on standalone --fasta load
if (!@ARGV) {
    $FH{NULL} = IO::File->new(">$tmpdir/null");
    push @ARGV, "$tmpdir/null";
}

while (<>) {

  # reset GFF3 flag if new filehandle
  $current_file ||= $ARGV;
  unless ($current_file eq $ARGV) {
    undef $gff3;
    $current_file = $ARGV;
  }

  chomp;
  my ($ref,$source,$method,$start,$stop,$score,$strand,$phase,$group);

  # close sequence filehandle if required
  if ( /^\#|\s+|^$|^>|\t/ && defined $FH{FASTA}) {
      $FH{FASTA}->close;
      delete $FH{FASTA};
  }

  # print to fasta file if the handle is open
  if ( defined $FH{FASTA} ) {
      $FH{FASTA}->print("$_\n");
      next;
  }

  elsif (/^>(\S+)/) {  # uh oh, sequence coming
      $FH{FASTA} = IO::File->new(">$tmpdir/$1\.fa") or die "FASTA: $!\n";
      $FH{FASTA}->print("$_\n");
      push @fasta, "$tmpdir/$1\.fa";
      push @fasta_files_to_be_unlinked,"$tmpdir/$1\.fa";
      print STDERR "Processing embedded sequence $1\n";
      next;
  }

  elsif (/^\#\#\s*group-tags\s+(.+)/) {
    $db->preferred_groups(split(/\s+/,$1));
    next;
  }

  elsif (/^\#\#\s*gff-version\s+(\d+)/) {
    $gff3 = ($1 >= 3);
    $db->print_gff3_warning() if $gff3;
    next;
  }

  elsif (/^\#\#\s*sequence-region\s+(\S+)\s+(\d+)\s+(\d+)/i) { # header line
    ($ref,$source,$method,$start,$stop,$score,$strand,$phase,$group) = 
      ($1,'reference','Component',$2,$3,'.','.','.',$gff3 ? "ID=Sequence:$1": qq(Sequence "$1"));
  }

  elsif (/^\#/) {
    next;
  }

  else {
    ($ref,$source,$method,$start,$stop,$score,$strand,$phase,$group) = split "\t";
  }
  next unless defined $ref;
  $FEATURES++;

  warn "Feature $group is larger than $MAX_BIN. You will have trouble retrieving this feature.\nRerun script with --maxfeature set to a higher power of 10.\n" if $stop-$start+1 > $MAX_BIN;

  $source = '\N' unless defined $source;
  $score  = '\N' if $score  eq '.';
  $strand = '\N' if $strand eq '.';
  $phase  = '\N' if $phase  eq '.';

  my ($gclass,$gname,$target_start,$target_stop,$attributes) = $db->split_group($group,$gff3);
  # GFF2/3 transition
  $gclass = [$gclass] unless ref $gclass;
  $gname  = [$gname]  unless ref $gname;

  for (my $i=0; $i < @$gname; $i++) {
    my $group_class = $gclass->[$i];
    my $group_name  = $gname->[$i];
    $group_class  ||= '\N';
    $group_name   ||= '\N';
    $target_start ||= '\N';
    $target_stop  ||= '\N';
    $method       ||= '\N';
    $source       ||= '\N';

    my $fid     = $FID++;
    my $gid     = $GROUPID{lc join($;,$group_class,$group_name)} ||= $GID++;
    my $ftypeid = $FTYPEID{lc join($;,$source,$method)}          ||= $FTYPEID++;

    my $bin = bin($start,$stop,$db->min_bin);
    $FH{ FDATA()  }->print(    join("\t",$fid,$ref,$start,$stop,$bin,$ftypeid,$score,$strand,$phase,$gid,$target_start,$target_stop),"\n"   );
    $FH{ FGROUP() }->print(    join("\t",$gid,$group_class,$group_name),"\n"              ) unless $DONE{"fgroup$;$gid"}++;
    $FH{ FTYPE()  }->print(    join("\t",$ftypeid,$method,$source),"\n"                   ) unless $DONE{"ftype$;$ftypeid"}++;

    foreach (@$attributes) {
      my ($key,$value) = @$_;
      my $attributeid = $ATTRIBUTEID{lc $key}   ||= $ATTRIBUTEID++;
      $FH{ FATTRIBUTE() }->print( join("\t",$attributeid,$key),"\n"                       ) unless $DONE{"fattribute$;$attributeid"}++;
      $FH{ FATTRIBUTE_TO_FEATURE() }->print( join("\t",$fid,$attributeid,$value),"\n");
    }

    if ( $FEATURES % 1000 == 0) {
      my $now    = Time::HiRes::time() if $timer;
      my $elapsed = $timer ? sprintf(" in %5.2fs",$now - $last) : '';
      $last = $now;
      print STDERR "$fid features parsed$elapsed...";
      print STDERR -t STDOUT && !$ENV{EMACS} ? "\r" : "\n";
    }
  }
}

$FH{FASTA}->close if exists $FH{FASTA};

printf STDERR "Feature load time %5.2fs\n",(Time::HiRes::time() - $start) if $timer;
$start = time();

for my $fasta (@fasta) {
  warn "Loading fasta ",(-d $fasta?"directory":"file"), " $fasta\n";
  my $old = select($FH{FDNA()});
  my $loaded = $db->load_fasta($fasta);
  warn "$fasta: $loaded records loaded\n";
  select $old;
}

printf STDERR "Fasta load time %5.2fs\n",(Time::HiRes::time() - $start) if $timer;
$start = time();

my $success = 1;
if ($DO_FAST) {
  warn "Indexing and analyzing tables.  This may take some time (you may see database messages during the process)...\n";
}

$_->close foreach values %FH;

if (!$DO_FAST) {
  warn "Loading feature data and analyzing tables.  You may see database messages here...\n";
  $success &&= system($COMMAND{$_}) == 0 foreach @files;
}

# wait for children
while (%PID) {
  sleep;
}
$success &&= !$FAILED;

cleanup();

printf STDERR "Total parse & load time %5.2fs\n",(Time::HiRes::time() - $beginning) if $timer;

if ($success) {
  print "SUCCESS: $FEATURES features successfully loaded\n";
  exit 0;
} else {
  print "FAILURE: Please see standard error for details\n";
  exit -1;
}

if ($SUMMARY_STATS) {
    warn "Building summary statistics for coverage histograms...\n";
    $db->build_summary_statistics;
}

exit 0;

sub cleanup {
  foreach (@files,@fasta_files_to_be_unlinked) {
    unlink "$tmpdir/$_.$$";
  }
}

# load copies of some of the tables into memory
sub load_tables {
  my $dbh = shift;
  print STDERR "loading normalized group, type and attribute information...";
  $FID         = 1 + get_max_id($dbh,'fdata','fid');
  $GID         = 1 + get_max_id($dbh,'fgroup','gid');
  $FTYPEID     = 1 + get_max_id($dbh,'ftype','ftypeid');
  $ATTRIBUTEID = 1 + get_max_id($dbh,'fattribute','fattribute_id');
  get_ids($dbh,\%DONE,\%GROUPID,'fgroup','gid','gclass','gname');
  get_ids($dbh,\%DONE,\%FTYPEID,'ftype','ftypeid','fsource','fmethod');
  get_ids($dbh,\%DONE,\%ATTRIBUTEID,'fattribute','fattribute_id','fattribute_name');
  print STDERR "ok\n";
}

sub get_max_id {
  my $dbh = shift;
  my ($table,$id) = @_;
  my $sql = "select max($id) from $table";
  my $result = $dbh->selectcol_arrayref($sql) or die $dbh->errstr;
  $result->[0];
}

sub get_ids {
  my $dbh = shift;
  my ($done,$idhash,$table,$id,@columns) = @_;
  my $columns = join ',',$id,@columns;
  my $sql = "select $columns from $table";
  my $sth = $dbh->prepare($sql) or die $dbh->errstr;
  $sth->execute or die $dbh->errstr;
  while (my($id,@cols) = $sth->fetchrow_array) {
    my $key = lc join $;,@cols;
    $idhash->{$key} = $id;
    $done->{$table,$id}++;
  }
}

__END__
BioPerl-1.007002/scripts/Bio-DB-GFF/bp_genbank2gff.pl000444000766000024      2415213155576320 22012 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

use lib '.';

use strict;
use warnings;
use Bio::DB::GFF;
use Getopt::Long;

=head1 NAME

bp_genbank2gff.pl - Load a Bio::DB::GFF database from GENBANK files.

=head1 SYNOPSIS

  % bp_genbank2gff.pl -d genbank -f localfile.gb
  % bp_genbank2gff.pl -d genbank --accession AP003256
  % bp_genbank2gff.pl --accession AP003256 --stdout

=head1 DESCRIPTION

This script loads a Bio::DB::GFF database with the features contained
in a either a local genbank file or an accession that is fetched from
genbank.  Various command-line options allow you to control which
database to load and whether to allow an existing database to be
overwritten.

The database must already have been created and the current user must
have appropriate INSERT and UPDATE privileges.  The --create option
will initialize a new database with the appropriate schema, deleting
any tables that were already there.

=head1 COMMAND-LINE OPTIONS

Command-line options can be abbreviated to single-letter options.
e.g. -d instead of --database.

   --create                 Force creation and initialization of database
   --dsn               Data source (default dbi:mysql:test)
   --user             Username for mysql authentication
   --pass         Password for mysql authentication
   --proxy           Proxy server to use for remote access
   --stdout                 direct output to STDOUT
   --adaptor       adaptor to use (eg dbi::mysql, dbi::pg, dbi::oracle)   --viral                  the genome you are loading is viral (changes tag
                                 choices)
   --source         source field for features ['genbank']
    EITHER --file           Arguments that follow are Genbank/EMBL file names
    OR --gb_folder          What follows is a folder full of gb files to process    OR --accession          Arguments that follow are genbank accession numbers
                                 (not gi!)
    OR --acc_file           Accession numbers (not gi!) in a file (one per line,                                 no punc.)
    OR --acc_pipe           Accession numbers (not gi!) from a STDIN pipe (one
                                 per line)


=head1 SEE ALSO

L, L, L

=head1 AUTHOR

Scott Cain, cain@cshl.org

Copyright (c) 2003 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut

package Bio::DB::GFF::Adaptor::biofetch_to_stdout;
use CGI 'escape';
use Bio::DB::GFF::Util::Rearrange;
use Bio::DB::GFF::Adaptor::biofetch;
use vars '@ISA';
@ISA = 'Bio::DB::GFF::Adaptor::biofetch';

sub load_gff_line {
  my ($self,$options) = @_;
  # synthesize GFF3-compatible line
  my @attributes;
  if (my $id = $options->{gname}) {
    my $parent = $id;
    $parent    =~ s/\..\d+$//                  if     $options->{method} =~ /^(mRNA|transcript|exon|gene)$/;
    push @attributes,"Parent=".escape($parent) if     $options->{method} =~ /^(variation|exon|CDS|transcript|mRNA|coding)$/;
    push @attributes,"ID=".escape($id)         unless $options->{method} =~ /^(exon|CDS)$/;
  }
  if (my $tstart = $options->{tstart}) {
    my $tstop    = $options->{tstop};
    my $target   = escape($options->{gname});
    push @attributes,"Target=$target+$tstart+$tstop";
  }
  my %a;
  if (my $attributes = $options->{attributes}) {
    for my $a (@$attributes) {
      my ($tag,$value) = @$a;
      push @{$a{escape($tag)}},escape($value);
    }
    for my $a (keys %a) {
       push @attributes,"$a=".join(',',@{$a{$a}});
    }
  }
  ${$options}{'score'} = "." unless ${$options}{'score'};
  ${$options}{'strand'} = "." unless ${$options}{'strand'};
  ${$options}{'phase'} = "." unless ${$options}{'phase'};
  my $last_column = join ';',@attributes;
  if ($options->{method} eq 'origin') {
     print "##sequence-region $options->{gname} $options->{start} $options->{stop}\n";
  }
  print join("\t",@{$options}{qw(ref source method start stop score strand phase)},$last_column),"\n";
}

sub load_sequence_string {
  my $self = shift;
  my ($acc,$seq)  = @_;
  return unless $seq;
  $seq =~ s/(.{1,60})/$1\n/g;
  print ">$acc\n\L$seq\U\n";
}

sub setup_load {
   my $self = shift;
   print "##gff-version 3\n";
}

sub finish_load { }

1;

package main;

my $USAGE = < ] ...
Load a Bio::DB::GFF database from GFF files.

 Options:
   --create                 Force creation and initialization of database
   --dsn               Data source (default dbi:mysql:test)
   --user             Username for mysql authentication
   --pass         Password for mysql authentication
   --proxy           Proxy server to use for remote access
   --stdout                 direct output to STDOUT
   --adaptor       adaptor to use (eg dbi::mysql, dbi::pg, dbi::oracle)
   --viral                  the genome you are loading is viral (changes tag
                                 choices)
   --source         source field for features ['genbank']
    EITHER --file           Arguments that follow are Genbank/EMBL file names
    OR --gb_folder          What follows is a folder full of gb files to process
    OR --accession          Arguments that follow are genbank accession numbers
                                 (not gi!)
    OR --acc_file           Accession numbers (not gi!) in a file (one per line,
                                 no punc.) 
    OR --acc_pipe           Accession numbers (not gi!) from a STDIN pipe (one
                                 per line)   


This script loads a Bio::DB::GFF database with the features contained
in a either a local genbank file or an accession that is fetched from
genbank.  Various command-line options allow you to control which
database to load and whether to allow an existing database to be
overwritten.

USAGE
;

my ($DSN,$ADAPTOR,$CREATE,$USER,$VIRAL,$PASSWORD,$gbFOLDER,
    $FASTA,$ACC,$accFILE, $accPIPE, $FILE,$PROXY,$STDOUT,$SOURCE);


GetOptions (
            'dsn:s'       => \$DSN,
            'user:s'      => \$USER,
            'password:s'  => \$PASSWORD,
            'adaptor:s'   => \$ADAPTOR,
            'accession'   => \$ACC,
            'file'        => \$FILE,
            'viral'       => \$VIRAL,
            'acc_file'    => \$accFILE,
            'acc_pipe'    => \$accPIPE,
	    'source:s'    => \$SOURCE,
            'gb_folder=s' => \$gbFOLDER,
            'proxy:s'     => \$PROXY,
            'stdout'      => \$STDOUT,
            'create'      => \$CREATE) or die $USAGE;


die $USAGE unless ($DSN || $STDOUT);  # at a minimum we need to have a place to write to!

# some local defaults
$DSN     ||= 'dbi:mysql:test';
$ADAPTOR ||= $STDOUT ? 'memory' : 'dbi::mysql';

# Ensure that biofetch inherits from the "right" adaptor.
# This is a horrible hack and should be fixed.
eval "use Bio::DB::GFF::Adaptor::${ADAPTOR}";
local @Bio::DB::GFF::Adaptor::biofetch::ISA = "Bio::DB::GFF::Adaptor::${ADAPTOR}";

my $biofetch = $STDOUT ? 'biofetch_to_stdout' : 'biofetch';
my @dsn      = $STDOUT ? () : (-dsn => $DSN);

my @auth;
push @auth,(-user=>$USER)     if defined $USER;
push @auth,(-pass=>$PASSWORD) if defined $PASSWORD;
push @auth,(-proxy=>$PROXY)   if defined $PROXY;

my %preferred_tags = (
		      strain        => 10,
		      organism      => 20,
		      protein_id    => 40,
		      locus_tag     => 50,
		      locus         => 60,
		      gene          => 70,
		      standard_name => 80,
                     );
$preferred_tags{'product'} = 90 if $VIRAL; # added this to the default list for viral genomes
       # since most functions come from post-translational processing, so the default labels are c**p!

my $db = Bio::DB::GFF->new(-adaptor=>$biofetch,
			   @dsn,
			   @auth,
			   -preferred_tags => \%preferred_tags,
			   -source=> $SOURCE || 'Genbank')
  or die "Can't open database: ",Bio::DB::GFF->error,"\n";

if ($CREATE) {
  $db->initialize(1);
}

die "you must specify either an accession to retrieve from\nembl or a local file containing data in embl format\n" if (($FILE || $ACC) && !scalar(@ARGV));

if ($ACC) {
  while ($_ = shift) {
    status(loading => $_);
    my $result = $db->load_from_embl(/^NC_/?'refseq':'embl' => $_);
    status(done    => $result);
  }
  exit 1;
}

elsif ($FILE) {
  while ($_ = shift) {
    status('loading' => $_);
    my $result = $db->load_from_file($_);
    status (done => $result);
  }
  exit 1;
}

elsif ($accFILE){
    my $filename = shift;
    die "you must supply a filename after the --accFILE command line flag\n" unless $filename;
    die "file $filename does not exist\n" unless (-e $filename && !(-d $filename));
    open my $IN, '<', $filename or die "Could not read file '$filename' for reading accession numbers: $!\n";
    while (my $line = <$IN>){
        chomp $line;
	status(loading => $line);
        my $result = $db->load_from_embl(/^NC_/?'refseq':'embl' => $line);
	status(done => $result);
    }
    close $IN;
    exit 1;
}

elsif ($gbFOLDER){
    my $dir = $gbFOLDER;
    die "folder $dir does not exist\n" unless (-e $dir && -d $dir);
    opendir DIR, "$dir" || die "can't open directory $dir for reading: $!\n";
    my @files = readdir DIR;
    foreach my $file(@files){
        if (!(-e "$gbFOLDER/$file") || (-d "$gbFOLDER/$file")){
            print STDERR " $gbFOLDER/$file is not a filename!  Skipping...\n";
            next
        }
        my $result = $db->load_from_file("$gbFOLDER/$file");
        print STDERR $result ? "ok\n" : "failed\n";        
    }
} elsif ($accPIPE){
    my @accessions = ;
    chomp @accessions;
    foreach (@accessions){
      status(loading => $_);
      my $result = $db->load_from_embl(/^NC_/?'refseq':'embl' => $_);
      status(done => $result);
    }
    exit 1;
}

else {
  my $done;
  while ($_ = shift) {
    $done = 1;
    status(loading => $_);
    my $result = $db->load_from_file($_);
    status(done => $result);
  }

  $done || die "\n\nno source of data provided\n\n";
  exit 1;
}

sub status {
  my ($state,$msg) = @_;
  return if $STDOUT;
  if ($state eq 'loading') {
    print STDERR "Loading $msg...";
  } elsif ($state eq 'done') {
    print STDERR $msg ? "ok\n" : "failed\n";
  }
}
BioPerl-1.007002/scripts/Bio-DB-GFF/bp_genbank2gff3.pl000444000766000024     23377613155576320 22133 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl



=pod

=head1 NAME 

bp_genbank2gff3.pl -- Genbank-Egbrowse-friendly GFF3

=head1 SYNOPSIS

  bp_genbank2gff3.pl [options] filename(s)

  # process a directory containing GenBank flatfiles
  perl bp_genbank2gff3.pl --dir path_to_files --zip

  # process a single file, ignore explicit exons and introns
  perl bp_genbank2gff3.pl --filter exon --filter intron file.gbk.gz

  # process a list of files 
  perl bp_genbank2gff3.pl *gbk.gz

  # process data from URL, with Chado GFF model (-noCDS), and pipe to database loader
  curl ftp://ftp.ncbi.nih.gov/genomes/Saccharomyces_cerevisiae/CHR_X/NC_001142.gbk \
  | perl bp_genbank2gff3.pl -noCDS -in stdin -out stdout \
  | perl gmod_bulk_load_gff3.pl -dbname mychado -organism fromdata

    Options:
        --noinfer  -r  don't infer exon/mRNA subfeatures
        --conf     -i  path to the curation configuration file that contains user preferences
                       for Genbank entries (must be YAML format)
                       (if --manual is passed without --ini, user will be prompted to 
                        create the file if any manual input is saved)
        --sofile  -l  path to to the so.obo file to use for feature type mapping
                       (--sofile live will download the latest online revision)
        --manual   -m  when trying to guess the proper SO term, if more than
                       one option matches the primary tag, the converter will 
                       wait for user input to choose the correct one
                       (only works with --sofile)
        --dir      -d  path to a list of genbank flatfiles
        --outdir   -o  location to write GFF files (can be 'stdout' or '-' for pipe)
        --zip      -z  compress GFF3 output files with gzip
        --summary  -s  print a summary of the features in each contig
        --filter   -x  genbank feature type(s) to ignore
        --split    -y  split output to separate GFF and fasta files for
                       each genbank record
        --nolump   -n  separate file for each reference sequence
                       (default is to lump all records together into one 
                       output file for each input file)
        --ethresh  -e  error threshold for unflattener
                       set this high (>2) to ignore all unflattener errors
        --[no]CDS  -c  Keep CDS-exons, or convert to alternate gene-RNA-protein-exon 
                       model. --CDS is default. Use --CDS to keep default GFF gene model, 
                       use --noCDS to convert to g-r-p-e.
        --format   -f  Input format (SeqIO types): GenBank, Swiss or Uniprot, EMBL work
                       (GenBank is default)
        --GFF_VERSION  3 is default, 2 and 2.5 and other Bio::Tools::GFF versions available
        --quiet        don't talk about what is being processed 
        --typesource   SO sequence type for source (e.g. chromosome; region; contig)
        --help     -h  display this message


=head1 DESCRIPTION

This script uses Bio::SeqFeature::Tools::Unflattener and
Bio::Tools::GFF to convert GenBank flatfiles to GFF3 with gene
containment hierarchies mapped for optimal display in gbrowse.

The input files are assumed to be gzipped GenBank flatfiles for refseq
contigs.  The files may contain multiple GenBank records.  Either a
single file or an entire directory can be processed.  By default, the
DNA sequence is embedded in the GFF but it can be saved into separate
fasta file with the --split(-y) option.

If an input file contains multiple records, the default behaviour is
to dump all GFF and sequence to a file of the same name (with .gff
appended).  Using the 'nolump' option will create a separate file for
each genbank record.  Using the 'split' option will create separate
GFF and Fasta files for each genbank record.


=head2 Notes

=head3 'split' and 'nolump' produce many files

In cases where the input files contain many GenBank records (for
example, the chromosome files for the mouse genome build), a very
large number of output files will be produced if the 'split' or
'nolump' options are selected.  If you do have lists of files E 6000,
use the --long_list option in bp_bulk_load_gff.pl or
bp_fast_load_gff.pl to load the gff and/ or fasta files.

=head3 Designed for RefSeq

This script is designed for RefSeq genomic sequence entries.  It may
work for third party annotations but this has not been tested.
But see below, Uniprot/Swissprot works, EMBL and possibly EMBL/Ensembl
if you don't mind some gene model unflattener errors (dgg).

=head3 G-R-P-E Gene Model

Don Gilbert worked this over with needs to produce GFF3 suited to
loading to GMOD Chado databases.  Most of the changes I believe are
suited for general use.  One main chado-specific addition is the
  --[no]cds2protein  flag

My favorite GFF is to set the above as ON by default (disable with --nocds2prot)
For general use it probably should be OFF, enabled with --cds2prot.

This writes GFF with an alternate, but useful Gene model,
instead of the consensus model for GFF3 

  [ gene > mRNA> (exon,CDS,UTR) ]

This alternate is

  gene > mRNA > polypeptide > exon 

means the only feature with dna bases is the exon.  The others
specify only location ranges on a genome.  Exon of course is a child
of mRNA and protein/peptide.   

The protein/polypeptide feature is an important one, having all the
annotations of the GenBank CDS feature, protein ID, translation, GO
terms, Dbxrefs to other proteins.

UTRs, introns, CDS-exons are all inferred from the primary exon bases
inside/outside appropriate higher feature ranges.   Other special gene
model features remain the same.

Several other improvements and bugfixes, minor but useful are included

  * IO pipes now work:
    curl ftp://ncbigenomes/... | bp_genbank2gff3 --in stdin --out stdout | gff2chado ...

  * GenBank main record fields are added to source feature, e.g. organism, date,
    and the sourcetype, commonly chromosome for  genomes, is used.

  * Gene Model handling for ncRNA, pseudogenes are added.

  * GFF header is cleaner, more informative.
    --GFF_VERSION flag allows choice of v2 as well as default v3

  * GFF ##FASTA inclusion is improved, and
    CDS translation sequence is moved to FASTA records.

  * FT -> GFF attribute mapping is improved.

  * --format choice of SeqIO input formats (GenBank default). 
    Uniprot/Swissprot and EMBL work and produce useful GFF.

  * SeqFeature::Tools::TypeMapper has a few FT -> SOFA additions
      and more flexible usage.

=head1 TODO

=head2 Are these additions desired?

 * filter input records by taxon (e.g. keep only organism=xxx or taxa level = classYYY
 * handle Entrezgene, other non-sequence SeqIO structures (really should change
    those parsers to produce consistent annotation tags).

=head2 Related bugfixes/tests

These items from Bioperl mail were tested (sample data generating
errors), and found corrected:

 From: Ed Green  eva.mpg.de>
 Subject: genbank2gff3.pl on new human RefSeq
 Date: 2006-03-13 21:22:26 GMT 
   -- unspecified errors (sample data works now).

 From: Eric Just  northwestern.edu>
 Subject: genbank2gff3.pl
 Date: 2007-01-26 17:08:49 GMT
   -- bug fixed in genbank2gff3 for multi-record handling

This error is for a /trans_splice gene that is hard to handle, and
unflattner/genbank2 doesn't

 From: Chad Matsalla  dieselwurks.com> 
 Subject: genbank2gff3.PLS and the unflatenner - Inconsistent order?
 Date: 2005-07-15 19:51:48 GMT 

=head1 AUTHOR 

Sheldon McKay (mckays@cshl.edu)

Copyright (c) 2004 Cold Spring Harbor Laboratory.

=head2 AUTHOR of hacks for GFF2Chado loading

Don Gilbert (gilbertd@indiana.edu)


=cut

use strict;
use warnings;

use lib "$ENV{HOME}/bioperl-live";
# chad put this here to enable situations when this script is tested
# against bioperl compiled into blib along with other programs using blib
BEGIN {
        unshift(@INC,'blib/lib');
};
use Pod::Usage;
use Bio::Root::RootI;
use Bio::SeqIO;
use File::Spec;
use Bio::SeqFeature::Tools::Unflattener;
use Bio::SeqFeature::Tools::TypeMapper;
use Bio::SeqFeature::Tools::IDHandler;
use Bio::Location::SplitLocationI;
use Bio::Location::Simple;
use Bio::Tools::GFF;
use Getopt::Long;
use List::Util qw(first);
use Bio::OntologyIO;
use YAML qw(Dump LoadFile DumpFile);
use File::Basename; 

use vars qw/$split @filter $zip $outdir $help $ethresh
            $ONTOLOGY %FEATURES %DESCENDANTS @RETURN $MANUAL @GFF_LINE_FEAT
            $CONF $YAML $TYPE_MAP $SYN_MAP $noinfer $SO_FILE 
            $file @files $dir $summary $nolump 
            $source_type %proteinfa %exonpar $didheader $verbose $DEBUG $GFF_VERSION 
            $gene_id $rna_id $tnum $ncrna_id $rnum %method %id %seen/;

use constant SO_URL => 
    'http://song.cvs.sourceforge.net/viewvc/*checkout*/song/ontology/so.obo';
use constant ALPHABET => [qw(a b c d e f g h i j k l m n o p q r s t u v w x y z)];
use constant ALPHABET_TO_NUMBER => {
    a => 0, b => 1, c => 2, d => 3, e => 4, f => 5, g => 6, h => 7, i => 8, 
    j => 9, k => 10, l => 11, m => 12, n => 13, o => 14, p => 15, q => 16,
    r => 17, s => 18, t => 19, u => 20, v => 21, w => 22, x => 23, y => 24,
    z => 25,
    };
use constant ALPHABET_DIVISOR => 26;
use constant GM_NEW_TOPLEVEL => 2;
use constant GM_NEW_PART => 1;
use constant GM_DUP_PART => 0;
use constant GM_NOT_PART => -1;

# Options cycle in multiples of 2 because of left side/right side pairing. 
# You can make this number odd, but displayed matches will still round up
use constant OPTION_CYCLE => 6; 

$GFF_VERSION = 3; # allow v2 ...
$verbose = 1; # right default? -nov to turn off

# dgg: change the gene model to  Gene/mRNA/Polypeptide/exons...
my $CDSkeep= 1; # default should be ON (prior behavior), see gene_features()
my $PROTEIN_TYPE = 'polypeptide'; # for noCDSkeep; 
  # protein = flybase chado usage; GMOD Perls use 'polypeptide' with software support

my $FORMAT="GenBank"; # swiss ; embl; genbank ; ** guess from SOURCEID **
my $SOURCEID= $FORMAT; # "UniProt" "GenBank"  "EMBL" should work  
   # other Bio::SeqIO formats may work.  TEST: EntrezGene < problematic tags; InterPro  KEGG 


my %TAG_MAP = (
  db_xref => 'Dbxref',
  name => 'Name',
  note => 'Note', # also pull GO: ids into Ontology_term
  synonym => 'Alias',
  symbol => 'Alias',  # is symbol still used?
  # protein_id => 'Dbxref', also seen Dbxref tags: EC_number 
  # translation: handled in gene_features
);


$| = 1;
my $quiet= !$verbose;
my $ok= GetOptions( 'd|dir|input:s'   => \$dir,
            'z|zip'     => \$zip, 
            'h|help'    => \$help,
            's|summary' => \$summary,
            'r|noinfer' => \$noinfer,
            'i|conf=s' => \$CONF,
            'sofile=s' => \$SO_FILE,
            'm|manual' => \$MANUAL,
            'o|outdir|output:s'=> \$outdir,
            'x|filter:s'=> \@filter,
            'y|split'   => \$split,
            "ethresh|e=s"=>\$ethresh,
            'c|CDS!'    => \$CDSkeep,
            'f|format=s' => \$FORMAT,
            'typesource=s' => \$source_type,
            'GFF_VERSION=s' => \$GFF_VERSION,
            'quiet!'    => \$quiet, # swap quiet to verbose
            'DEBUG!'    => \$DEBUG,
            'n|nolump'  => \$nolump);

my $lump = 1 unless $nolump || $split;
$verbose= !$quiet;

# look for help request
pod2usage(2) if $help || !$ok;

# keep SOURCEID as-is and change FORMAT for SeqIO types; 
# note SeqIO uses file.suffix to guess type; not useful here
$SOURCEID= $FORMAT; 
$FORMAT  = "swiss" if $FORMAT =~/UniProt|trembl/;
$verbose =1 if($DEBUG);

# initialize handlers
my $unflattener = Bio::SeqFeature::Tools::Unflattener->new; # for ensembl genomes (-trust_grouptag=>1);
$unflattener->error_threshold($ethresh) if $ethresh;
$unflattener->verbose(1) if($DEBUG);
# $unflattener->group_tag('gene') if($FORMAT =~ /embl/i) ; #? ensembl only? 
# ensembl parsing is still problematic, forget this

my $tm  = Bio::SeqFeature::Tools::TypeMapper->new;
my $idh = Bio::SeqFeature::Tools::IDHandler->new;

# dgg
$source_type ||= "region"; # should really parse from FT.source contents below

#my $FTSOmap = $tm->FT_SO_map();
my $FTSOmap;
my $FTSOsynonyms;

if (defined($SO_FILE) && $SO_FILE eq 'live') {
    print "\nDownloading the latest SO file from ".SO_URL."\n\n";
    use LWP::UserAgent;
    my $ua = LWP::UserAgent->new(timeout => 30);
    my $request = HTTP::Request->new(GET => SO_URL);
    my $response = $ua->request($request);


    if ($response->status_line =~ /200/) {
        use File::Temp qw/ tempfile /;
        my ($fh, $fn) = tempfile();
        print $fh $response->content;
        $SO_FILE = $fn;
    } else {
        print "Couldn't download SO file online...skipping validation.\n" 
            . "HTTP Status was " . $response->status_line . "\n" 
            and undef $SO_FILE
    }
}

if ($SO_FILE) {


    my (%terms, %syn);

    my $parser = Bio::OntologyIO->new( -format => "obo", -file => $SO_FILE );
    $ONTOLOGY = $parser->next_ontology();

    for ($ONTOLOGY->get_all_terms) { 
        my $feat = $_;

        $terms{$feat->name} = $feat->name;
        #$terms{$feat->name} = $feat;

        my @syn = $_->each_synonym;

        push @{$syn{$_}}, $feat->name for @syn;
        #push @{$syn{$_}}, $feat for @syn;
    }

    $FTSOmap = \%terms;
    $FTSOsynonyms = \%syn;

    my %hardTerms = %{ $tm->FT_SO_map() };
    map { $FTSOmap->{$_} ||= $hardTerms{$_} } keys %hardTerms;

} else { 
    my %terms = %{ $tm->FT_SO_map() };
    while (my ($k,$v) = each %terms) {
        $FTSOmap->{$k} = ref($v) ? shift @$v : $v;
    }
}

$TYPE_MAP = $FTSOmap;
$SYN_MAP = $FTSOsynonyms;


# #convert $FTSOmap undefined to valid SO : moved to TypeMapper->map_types( -undefined => "region")

# stringify filter list if applicable
my $filter = join ' ', @filter  if @filter;

# determine input files
my $stdin=0; # dgg: let dir == stdin == '-' for pipe use
if ($dir && ($dir eq '-' || $dir eq 'stdin')) {
  $stdin=1;  $dir=''; @files=('stdin');
  
} elsif ( $dir ) {
    if ( -d $dir ) {
        opendir DIR, $dir or die "could not open $dir for reading: $!";
        @files = map { "$dir/$_";} grep { /\.gb.*/ } readdir DIR;  
        closedir DIR;
    }
    else {
        die "$dir is not a directory\n";
    }
}
else {
    @files = @ARGV;
    $dir = '';
}

# we should have some files by now
pod2usage(2) unless @files;


my $stdout=0; # dgg: let outdir == stdout == '-' for pipe use
if($outdir && ($outdir eq '-' || $outdir eq 'stdout')) {
  warn("std. output chosen: cannot split\n") if($split);
  warn("std. output chosen: cannot zip\n") if($zip);
  warn("std. output chosen: cannot nolump\n") if($nolump);
  $stdout=1; $lump=1; $split= 0; $zip= 0; # unless we pipe stdout thru gzip
  
} elsif ( $outdir && !-e $outdir ) {
    mkdir($outdir) or die "could not create directory $outdir: $!\n";        
}
elsif ( !$outdir ) {
    $outdir = $dir || '.';
}

for my $file ( @files ) {
    # dgg ; allow 'stdin' / '-' input ?
    chomp $file;
    die "$! $file" unless($stdin || -e $file);
    print "# Input: $file\n" if($verbose);

    my ($lump_fh, $lumpfa_fh, $outfile, $outfa);
    if ($stdout) {
      $lump_fh= *STDOUT; $lump="stdout$$";
      $outfa= "stdout$$.fa";  # this is a temp file ... see below
      open $lumpfa_fh, ">$outfa" or die "Could not create a lump outfile called ($outfa) because ($!)\n";

    } elsif ( $lump ) {
        my ($vol,$dirs,$fileonly) = File::Spec->splitpath($file); 
        $lump = File::Spec->catfile($outdir, $fileonly.'.gff');
        ($outfa = $lump) =~ s/\.gff/\.fa/;
        open $lump_fh, ">$lump" or die "Could not create a lump outfile called ($lump) because ($!)\n";
        open $lumpfa_fh, ">$outfa" or die "Could not create a lump outfile called ($outfa) because ($!)\n";

    }
    
    # open input file, unzip if req'd
    if ($stdin) {
       *FH = *STDIN;
    } elsif ( $file =~ /\.gz/ ) {
        open FH, "gunzip -c $file |";
    }
    else {
        open FH, '<', $file;
    }

    my $in = Bio::SeqIO->new(-fh => \*FH, -format => $FORMAT, -debug=>$DEBUG);
    my $gffio = Bio::Tools::GFF->new( -noparse => 1, -gff_version => $GFF_VERSION );

    while ( my $seq = $in->next_seq() ) {
        my $seq_name = $seq->accession_number;
        my $end = $seq->length;
        my @to_print;

        # arrange disposition of GFF output
        $outfile = $lump || File::Spec->catfile($outdir, $seq_name.'.gff');
        my $out;

        if ( $lump ) {
            $outfile = $lump;
            $out = $lump_fh;
        }
        else {
            $outfile = File::Spec->catfile($outdir, $seq_name.'.gff');
            open $out, ">$outfile";
        }

        # filter out unwanted features
        my $source_feat= undef;
        my @source= filter($seq); $source_feat= $source[0];

        ($source_type,$source_feat)= 
          getSourceInfo( $seq, $source_type, $source_feat ) ;
          # always; here we build main prot $source_feat; # if @source;
          
        # abort if there are no features
        warn "$seq_name has no features, skipping\n" and next
            if !$seq->all_SeqFeatures;


        $FTSOmap->{'source'} = $source_type;
        ## $FTSOmap->{'CDS'}= $PROTEIN_TYPE; # handle this in gene_features

        # construct a GFF header
        # add: get source_type from attributes of source feature? chromosome=X tag
        # also combine 1st ft line here with source ft from $seq ..
        my($header,$info)= gff_header($seq_name, $end, $source_type, $source_feat);
        print $out $header;
        print "# working on $info\n" if($verbose);
        
        # unflatten gene graphs, apply SO types, etc; this also does TypeMapper ..
        unflatten_seq($seq);

        # Note that we use our own get_all_SeqFeatures function 
        # to rescue cloned exons

        @GFF_LINE_FEAT = ();
        for my $feature ( get_all_SeqFeatures($seq) ) {
            
            my $method = $feature->primary_tag;
            next if($SOURCEID =~/UniProt|swiss|trembl/i && $method ne $source_type);
            
            $feature->seq_id($seq->id) unless($feature->seq_id);
            $feature->source_tag($SOURCEID);
            
            # dgg; need to convert some Genbank to GFF tags: note->Note; db_xref->Dbxref;
            ## also, pull any GO:000 ids from /note tag and put into Ontology_term
            maptags2gff($feature);
            
            # current gene name.  The unflattened gene features should be in order so any
            # exons, CDSs, etc that follow will belong to this gene
            my $gene_name;
            if ( $method eq 'gene' || $method eq 'pseudogene' ) {
              @to_print= print_held($out, $gffio, \@to_print);
              $gene_id = $gene_name= gene_name($feature); 
            } else {
              $gene_name= gene_name($feature);
            }
        
            #?? should gene_name from /locus_tag,/gene,/product,/transposon=xxx
            # be converted to or added as  Name=xxx (if not ID= or as well)
            ## problematic: convert_to_name ($feature); # drops /locus_tag,/gene, tags
            convert_to_name($feature); 
            
            ## dgg: extended to protein|polypeptide
            ## this test ($feature->has_tag('gene') ||) is not good: repeat_regions over genes
            ## in yeast have that genbank tag; why?
            ## these include pseudogene ...
            
            ## Note we also have mapped types to SO, so these RNA's are now transcripts:
            # pseudomRNA => "pseudogenic_transcript", 
            # pseudotranscript" => "pseudogenic_transcript", 
            # misc_RNA=>'processed_transcript',

            warn "#at: $method $gene_id/$gene_name\n" if $DEBUG;

            if ( $method =~ /(gene|RNA|CDS|exon|UTR|protein|polypeptide|transcript)/ 
               || ( $gene_id && $gene_name eq $gene_id ) ) {
               
                my $action = gene_features($feature, $gene_id, $gene_name);  # -1, 0, 1, 2 result
                if ($action == GM_DUP_PART) {
                  # ignore, this is dupl. exon with new parent ...
                  
                } elsif ($action == GM_NOT_PART) {
                  add_generic_id( $feature, $gene_name, "nocount");
                  my $gff = $gffio->gff_string($feature);
                  push @GFF_LINE_FEAT, $feature;
                  #print $out "$gff\n" if $gff;

                } elsif ($action > 0) {
                 # hold off print because exon etc. may get 2nd, 3rd parents
                  @to_print= print_held($out, $gffio, \@to_print) if ($action == GM_NEW_TOPLEVEL);
                  push(@to_print, $feature);
                }

            }
            
            # otherwise handle as generic feats with IDHandler labels 
            else {
                add_generic_id( $feature, $gene_name, "");
                my $gff= $gffio->gff_string($feature);
                push @GFF_LINE_FEAT, $feature;
                #print $out "$gff\n" if $gff;
            }
        }

        # don't like doing this after others; do after each new gene id?
        @to_print= print_held($out, $gffio, \@to_print);

        gff_validate(@GFF_LINE_FEAT);

        for my $feature (@GFF_LINE_FEAT) {
            my $gff= $gffio->gff_string($feature);
            print $out "$gff\n" if $gff;
        }

        # deal with the corresponding DNA
        my ($fa_out,$fa_outfile);
        my $dna = $seq->seq;
        if($dna || %proteinfa) {
          $method{'RESIDUES'} += length($dna);
          $dna    =~ s/(\S{60})/$1\n/g;
          $dna   .= "\n";
          
          if ($split) {
              $fa_outfile = $outfile;
              $fa_outfile =~ s/gff$/fa/;
              open $fa_out, ">$fa_outfile" or die $!; 
              print $fa_out ">$seq_name\n$dna" if $dna;
              foreach my $aid (sort keys %proteinfa) { 
                my $aa= delete $proteinfa{$aid}; 
                $method{'RESIDUES(tr)'} += length($aa);
                $aa =~ s/(\S{60})/$1\n/g; 
                print $fa_out ">$aid\n$aa\n"; 
                }
               
          }
          else {
          ## problem here when multiple GB Seqs in one file; all FASTA needs to go at end of $out
          ## see e.g. Mouse: mm_ref_chr19.gbk has NT_082868 and NT_039687 parts in one .gbk
          ## maybe write this to temp .fa then cat to end of lumped gff $out
              print $lumpfa_fh ">$seq_name\n$dna" if $dna;
              foreach my $aid (sort keys %proteinfa) { 
                my $aa= delete $proteinfa{$aid}; 
                $method{'RESIDUES(tr)'} += length($aa);
                $aa =~ s/(\S{60})/$1\n/g; 
                print $lumpfa_fh ">$aid\n$aa\n"; 
                }
          }
          
        %proteinfa=();
        }
     
        if ( $zip && !$lump ) {
            system "gzip -f $outfile";
            system "gzip -f $fa_outfile" if($fa_outfile);
            $outfile .= '.gz';
            $fa_outfile .= '.gz' if $split;
        }

        # print "\n>EOF\n" if($stdout); #?? need this if summary goes to stdout after FASTA
        print "# GFF3 saved to $outfile" unless( !$verbose || $stdout || $lump);
        print ($split ? "; DNA saved to $fa_outfile\n" : "\n") unless($stdout|| $lump);
        
        # dgg: moved to after all inputs; here it prints cumulative sum for each record
        #if ( $summary ) {
        #      print "# Summary:\n# Feature\tCount\n# -------\t-----\n";
        #  
        #      for ( keys %method ) {
        #          print "# $_  $method{$_}\n";
        #      }
        #      print "# \n";
        #  }       
    
    }

    print "# GFF3 saved to $outfile\n" if( $verbose && $lump);
    if ( $summary ) {
        print "# Summary:\n# Feature\tCount\n# -------\t-----\n";
        for ( keys %method ) {
            print "# $_  $method{$_}\n";
        }
        print "# \n";
    }
    
    ## FIXME for piped output w/ split FA files ...
    close($lumpfa_fh) if $lumpfa_fh;
    if (!$split && $outfa && $lump_fh) {     
        print $lump_fh "##FASTA\n"; # GFF3 spec
        open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!";
        while( <$lumpfa_fh>) {
            print $lump_fh $_;
        } # is $lump_fh still open?
        close($lumpfa_fh);
        unlink($outfa);
    }
        

    if ( $zip && $lump ) {
        system "gzip -f $lump";
    }
    
    close FH;
}





sub typeorder {
  return 1 if ($_[0] =~ /gene/);
  return 2 if ($_[0] =~ /RNA|transcript/);
  return 3 if ($_[0] =~ /protein|peptide/);
  return 4 if ($_[0] =~ /exon|CDS/);
  return 3; # default before exon (smallest part)
}

sub sort_by_feattype {
  my($at,$bt)= ($a->primary_tag, $b->primary_tag);
  return (typeorder($at) <=> typeorder($bt))  
    or ($at cmp $bt);
    ## or ($a->name() cmp $b->name());
}

sub print_held {  
  my($out,$gffio,$to_print)= @_;
  return unless(@$to_print);
  @$to_print = sort sort_by_feattype  @$to_print; # put exons after mRNA, otherwise chado loader chokes
  while ( my $feature = shift @$to_print) {
    my $gff= $gffio->gff_string($feature); # $gff =~ s/\'/./g; # dang bug in encode
    push @GFF_LINE_FEAT, $feature;
    #print $out "$gff\n";
    }
  return (); # @to_print
}

sub maptags2gff {
  my $f = shift;
  ## should copy/move locus_tag to Alias, if not ID/Name/Alias already
  # but see below /gene /locus_tag usage
  foreach my $tag (keys %TAG_MAP) {
    if ($f->has_tag($tag)) {
      my $newtag= $TAG_MAP{$tag};
      my @v= $f->get_tag_values($tag);
      $f->remove_tag($tag);
      $f->add_tag_value($newtag,@v);
      
      ## also, pull any GO:000 ids from /note tag and put into Ontology_term
      ## ncbi syntax in CDS /note is now '[goid GO:0005886]' OR '[goid 0005624]'
      if ($tag eq 'note') {  
        map { s/\[goid (\d+)/\[goid GO:$1/g; } @v; 
        my @go= map { m/(GO:\d+)/g } @v; 
        $f->add_tag_value('Ontology_term',@go) if(@go);
        }
      
      }
    }    
}


sub getSourceInfo {
  my ($seq, $source_type, $sf) = @_;  
  
  my $is_swiss= ($SOURCEID =~/UniProt|swiss|trembl/i);
  my $is_gene = ($SOURCEID =~/entrezgene/i);
  my $is_rich = (ref($seq) =~ /RichSeq/);
  my $seq_name= $seq->accession_number();
  
  unless($sf) { # make one
    $source_type=  $is_swiss ? $PROTEIN_TYPE 
        : $is_gene ? "eneg" # "gene"  # "region" # 
        : $is_rich ? $seq->molecule : $source_type;
    $sf = Bio::SeqFeature::Generic->direct_new();
    
    my $len = $seq->length(); $len=1 if($len<1); my $start = 1; ##$start= $len if ($len<1);
    my $loc= $seq->can('location') ? $seq->location() 
            :  new Bio::Location::Simple( -start => $start, -end => $len);
    $sf->location( $loc ); 
    $sf->primary_tag($source_type);
    $sf->source_tag($SOURCEID);
    $sf->seq_id( $seq_name);
    #? $sf->display_name($seq->id()); ## Name or Alias ?
    $sf->add_tag_value( Alias => $seq->id()); # unless id == accession
    $seq->add_SeqFeature($sf);
    ## $source_feat= $sf;
  }
  
  if ($sf->has_tag("chromosome")) {
    $source_type= "chromosome"; 
    my ($chrname) = $sf->get_tag_values("chromosome");
    ## PROBLEM with Name <> ID, RefName for Gbrowse; use Alias instead
    ## e.g. Mouse chr 19 has two IDs in NCBI genbank now
    $sf->add_tag_value( Alias => $chrname );
  }

  # pull GB Comment, Description for source ft ...
  # add reference - can be long, not plain string...             
  warn "# $SOURCEID:$seq_name fields = ", join(",", $seq->annotation->get_all_annotation_keys()),"\n" if $DEBUG;
  # GenBank   fields: keyword,comment,reference,date_changed
  # Entrezgene fields 850293 =ALIAS_SYMBOL,RefSeq status,chromosome,SGD,dblink,Entrez Gene Status,OntologyTerm,LOCUS_SYNONYM

  # is this just for main $seq object or for all seqfeatures ?
  my %AnnotTagMap= ( 
      'gene_name' => 'Alias',   
      'ALIAS_SYMBOL' => 'Alias',  # Entrezgene
      'LOCUS_SYNONYM' => 'Alias', #?
      'symbol' => 'Alias',   
      'synonym' => 'Alias',   
      'dblink' => 'Dbxref',   
      'product' => 'product',
      'Reference' => 'reference',
      'OntologyTerm' => 'Ontology_term',
      'comment'  => 'Note',
      'comment1' => 'Note',
      # various map-type locations
      # gene accession tag is named per source db !??
      # 'Index terms' => keywords ??
      );
  
  
  my ($desc)= $seq->annotation->get_Annotations("desc") || ( $seq->desc() );
  my ($date)= $seq->annotation->get_Annotations("dates") 
      || $seq->annotation->get_Annotations("update-date")
      || $is_rich ? $seq->get_dates() : ();
  my ($comment)= $seq->annotation->get_Annotations("comment");
  my ($species)= $seq->annotation->get_Annotations("species");
  if (!$species 
       && $seq->can('species') 
       && defined $seq->species() 
       && $seq->species()->can('binomial') ) {
    $species= $seq->species()->binomial();
  }

  # update source feature with main GB fields
  $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID');
  $sf->add_tag_value( Note => $desc ) if($desc && ! $sf->has_tag('Note'));
  $sf->add_tag_value( organism => $species ) if($species && ! $sf->has_tag('organism'));
  $sf->add_tag_value( comment1 => $comment ) if(!$is_swiss && $comment && ! $sf->has_tag('comment1'));
  $sf->add_tag_value( date => $date ) if($date && ! $sf->has_tag('date'));

  $sf->add_tag_value( Dbxref => $SOURCEID.':'.$seq_name ) if $is_swiss || $is_gene;

  foreach my $atag (sort keys %AnnotTagMap) {
      my $gtag= $AnnotTagMap{$atag}; next unless($gtag);
      my @anno = map{ 
          if (ref $_ && $_->can('get_all_values')) { 
              split( /[,;] */, join ";", $_->get_all_values) 
          }
          elsif (ref $_ && $_->can('display_text')) { 
              split( /[,;] */, $_->display_text) 
          }
          elsif (ref $_ && $_->can('value')) { 
              split( /[,;] */, $_->value) 
          } 
          else {
             ();
          }
      } $seq->annotation->get_Annotations($atag);  
      foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); }
  }
    
  #my @genes = map{ split( /[,;] */, "$_"); } $seq->annotation->get_Annotations('gene_name');  
  #$sf->add_tag_value( Alias => $_ ) foreach(@genes);
  # 
  #my @dblink= map { "$_"; } $seq->annotation->get_Annotations("dblink"); # add @all 
  #$sf->add_tag_value( Dbxref => $_ ) foreach(@dblink);
  
  return (wantarray)? ($source_type,$sf) : $source_type; #?
}


sub gene_features {
    my ($f, $gene_id, $genelinkID) = @_;
    local $_ = $f->primary_tag;
    $method{$_}++;
    
    if ( /gene/ ) {
        $f->add_tag_value( ID => $gene_id ) unless($f->has_tag('ID')); # check is same value!? 
        $tnum = $rnum= 0; $ncrna_id= $rna_id  = '';
        return GM_NEW_TOPLEVEL;
        
    } elsif ( /mRNA/ ) {  
        return GM_NOT_PART unless $gene_id;
        return GM_NOT_PART if($genelinkID && $genelinkID ne $gene_id);
        ($rna_id  = $gene_id ) =~ s/gene/mRNA/;
        $rna_id   .= '.t0' . ++$tnum;
        $f->add_tag_value( ID => $rna_id );
        $f->add_tag_value( Parent => $gene_id );
        
    } elsif ( /RNA|transcript/) { 
        ## misc_RNA here; missing exons ... flattener problem?
        #  all of {t,nc,sn}RNA can have gene models now
        ## but problem in Worm chr: mRNA > misc_RNA > CDS with same locus tag
        ## CDS needs to use mRNA, not misc_RNA, rna_id ...
        ## also need to fix cases where tRNA,... lack a 'gene' parent: make this one top-level

        if($gene_id) {
          return GM_NOT_PART if($genelinkID && $genelinkID ne $gene_id);
          ($ncrna_id = $gene_id) =~ s/gene/ncRNA/;
          $ncrna_id .= '.r0' . ++$rnum;
          $f->add_tag_value( Parent => $gene_id );
          $f->add_tag_value( ID => $ncrna_id );
        } else {
          unless ($f->has_tag('ID')) {
            if($genelinkID) {
              $f->add_tag_value( ID => $genelinkID  ) ;
            } else {
              $idh->generate_unique_persistent_id($f);
            }
          }
         ($ncrna_id)= $f->get_tag_values('ID'); 
         return GM_NEW_TOPLEVEL;
          # this feat now acts as gene-top-level; need to print @to_print to flush prior exons?
        }
        
    } elsif ( /exon/ ) { # can belong to any kind of RNA
        return GM_NOT_PART unless ($rna_id||$ncrna_id);
        return GM_NOT_PART if($genelinkID && $genelinkID ne $gene_id);
        ## we are getting duplicate Parents here, which chokes chado loader, with reason...
        ## problem is when mRNA and ncRNA have same exons, both ids are active, called twice
        ## check all Parents
        for my $expar ($rna_id, $ncrna_id) { 
          next unless($expar);
          if ( $exonpar{$expar} and $f->has_tag('Parent') ) {
            my @vals = $f->get_tag_values('Parent');
            next if (grep {$expar eq $_} @vals);
            }
          $exonpar{$expar}++;
          $f->add_tag_value( Parent => $expar); 
          # last; #? could be both
        }
        # now we can skip cloned exons
        # dgg note: multiple parents get added and printed for each unique exon
        return GM_DUP_PART if ++$seen{$f} > 1;
        
    } elsif ( /CDS|protein|polypeptide/ ) {
        return GM_NOT_PART unless $rna_id; ## ignore $ncrna_id ??
        return GM_NOT_PART if($genelinkID && $genelinkID ne $gene_id); #??
        (my $pro_id = $rna_id) =~ s/\.t/\.p/;
        
        if( ! $CDSkeep && /CDS/) {  
          $f->primary_tag($PROTEIN_TYPE); 
        
          ## duplicate problem is Location ..
          if ($f->location->isa("Bio::Location::SplitLocationI")) {
            # my($b,$e)=($f->start, $f->end); # is this all we need?
            my($b,$e)=(-1,0);
            foreach my $l ($f->location->each_Location) {
               $b = $l->start if($b<0 || $b > $l->start);
               $e = $l->end if($e < $l->end);
               }
            $f->location( Bio::Location::Simple->new(
                -start => $b, -end => $e, -strand => $f->strand) );
            }

            $f->add_tag_value( Derives_from => $rna_id ); 
          }
          else {
            $f->add_tag_value( Parent => $rna_id );
          }

        $f->add_tag_value( ID => $pro_id );
        
        move_translation_fasta($f, $pro_id);
        #if( $f->has_tag('translation')) {
        #   my ($aa) = $f->get_tag_values("translation");
        #    $proteinfa{$pro_id}= $aa;
        #    $f->remove_tag("translation");
        #    $f->add_tag_value("translation","length.".length($aa)); # hack for odd chado gbl problem
        #}
    } elsif ( /region/ ) {       
        $f->primary_tag('gene_component_region');
        $f->add_tag_value( Parent => $gene_id ); 
    } else {
        return GM_NOT_PART unless $gene_id;
        $f->add_tag_value( Parent => $gene_id );  
    }
    
    ## return GM_DUP_PART if /exon/ && ++$seen{$f} > 1;
    
    return GM_NEW_PART;
}

## was generic_features >  add_generic_id
sub add_generic_id {
    my ($f, $ft_name, $flags) = @_;
    my $method = $f->primary_tag;
    $method{$method}++ unless($flags =~ /nocount/); ## double counts GM_NOT_PART from above
     
    if ($f->has_tag('ID')) {
    
    }
    elsif ( $f->has_tag($method) ) {
        my ($name) = $f->get_tag_values($method);
        $f->add_tag_value( ID => "$method:$name" );
    }
    elsif($ft_name) { # is this unique ?
        $f->add_tag_value( ID => $ft_name ); 
    }
    else {
        $idh->generate_unique_persistent_id($f);
    }

    move_translation_fasta( $f, ($f->get_tag_values("ID"))[0] )
      if($method =~ /CDS/);

    # return $io->gff_string($f);
}

sub move_translation_fasta {
    my ($f, $ft_id) = @_;
    if( $ft_id && $f->has_tag('translation') ) {
      my ($aa) = $f->get_tag_values("translation");
      if($aa && $aa !~ /^length/) {
        $proteinfa{$ft_id}= $aa;
        $f->remove_tag("translation");
        $f->add_tag_value("translation","length.".length($aa)); # hack for odd chado gbl problem
        }
    }
}

sub gff_header {
    my ($name, $end, $source_type, $source_feat) = @_;
    $source_type ||= "region";

    my $info = "$source_type:$name";
    my $head = "##gff-version $GFF_VERSION\n".
               "##sequence-region $name 1 $end\n".
               "# conversion-by bp_genbank2gff3.pl\n";
    if ($source_feat) {
        ## dgg: these header comment fields are not useful when have multi-records, diff organisms
        for my $key (qw(organism Note date)) {
            my $value;
            if ($source_feat->has_tag($key)) { 
                ($value) = $source_feat->get_tag_values($key);
            }
            if ($value) {
                $head .= "# $key $value\n";
                $info .= ", $value";
            }
        }
        $head = "" if $didheader;
    } else {
        $head .= "$name\t$SOURCEID\t$source_type\t1\t$end\t.\t.\t.\tID=$name\n";
    }
    $didheader++;
    return (wantarray) ? ($head,$info) : $head;
}

sub unflatten_seq {
    my $seq = shift;

    ## print "# working on $source_type:", $seq->accession, "\n"; 
    my $uh_oh = "Possible gene unflattening error with" .  $seq->accession_number .
                ": consult STDERR\n";
    
    eval {
        $unflattener->unflatten_seq( -seq => $seq, 
                                     -noinfer => $noinfer,
                                     -use_magic => 1 );
    };
    
    # deal with unflattening errors
    if ( $@ ) {
        warn $seq->accession_number . " Unflattening error:\n";
        warn "Details: $@\n";
        print "# ".$uh_oh;
    }

    return 0 if !$seq || !$seq->all_SeqFeatures;

    # map feature types to the sequence ontology
    ## $tm->map_types_to_SO( -seq => $seq );
    #$tm->map_types( -seq => $seq, -type_map => $FTSOmap, -undefined => "region" ); #dgg

    map_types( 
        $tm, 
        -seq => $seq, 
        -type_map  => $FTSOmap, 
        -syn_map  => $FTSOsynonyms, 
        -undefined => "region" 
    ); #nml

}

sub filter {
    my $seq = shift;
    ## return unless $filter;
    my @feats;
    my @sources; # dgg; pick source features here; only 1 always?
    if ($filter) {
      for my $f ( $seq->remove_SeqFeatures ) {
        my $m = $f->primary_tag;
        push @sources, $f if ($m eq 'source'); # dgg? but leave in @feats ?
        push @feats, $f unless $filter =~ /$m/i;
      }
      $seq->add_SeqFeature($_) foreach @feats;
    } else {
      for my $f ( $seq->get_SeqFeatures ){
        my $m = $f->primary_tag;
        push @sources, $f if ($m eq 'source'); # dgg? but leave in @feats ?
        }
    }

    return @sources;
}


# The default behaviour of Bio::FeatureHolderI:get_all_SeqFeatures
# changed to filter out cloned features.  We have to implement the old
# method.  These two subroutines were adapted from the v1.4 Bio::FeatureHolderI
sub get_all_SeqFeatures  {
    my $seq = shift;
    my @flatarr;

    foreach my $feat ( $seq->get_SeqFeatures ){
        push(@flatarr,$feat);
        _add_flattened_SeqFeatures(\@flatarr,$feat);
    }
    return @flatarr;
}

sub gene_name {
    my $g = shift;
    my $gene_id = ''; # zero it;

    if ($g->has_tag('locus_tag')) {
        ($gene_id) = $g->get_tag_values('locus_tag');
    }

    elsif ($g->has_tag('gene')) {
        ($gene_id) = $g->get_tag_values('gene'); 
    }
    elsif ($g->has_tag('ID')) { # for non-Genbank > Entrezgene
        ($gene_id) = $g->get_tag_values('ID');
    }

    ## See Unflattener comment:
    # on rare occasions, records will have no /gene or /locus_tag
    # but it WILL have /product tags. These serve the same purpose
    # for grouping. For an example, see AY763288 (also in t/data)
    # eg. product=tRNA-Asp ;  product=similar to crooked neck protein
    elsif ($g->has_tag('product')) {
        my ($name)= $g->get_tag_values('product');
        ($gene_id) = $name unless($name =~ / /); # a description not name
    }

    ## dgg; also handle transposon=xxxx ID/name
    # ID=GenBank:repeat_region:NC_004353:1278337:1281302;transposon=HeT-A{}1685;Dbxref=FLYBASE:FBti0059746
    elsif ($g->has_tag('transposon')) {
        my ($name)= $g->get_tag_values('transposon');
        ($gene_id) = $name unless($name =~ / /); # a description not name
    }
  
    return $gene_id;
}

# same list as gene_name .. change tag to generic Name
sub convert_to_name {
    my $g = shift;
    my $gene_id = ''; # zero it;
    
    if ($g->has_tag('gene')) {
        ($gene_id) = $g->get_tag_values('gene'); 
        $g->remove_tag('gene');
        $g->add_tag_value('Name', $gene_id);
    }
    elsif ($g->has_tag('locus_tag')) {
        ($gene_id) = $g->get_tag_values('locus_tag');
        $g->remove_tag('locus_tag');
        $g->add_tag_value('Name', $gene_id);
    }

    elsif ($g->has_tag('product')) {
        my ($name)= $g->get_tag_values('product');
        ($gene_id) = $name unless($name =~ / /); # a description not name
        ## $g->remove_tag('product');
        $g->add_tag_value('Name', $gene_id);
    }

    elsif ($g->has_tag('transposon')) {
        my ($name)= $g->get_tag_values('transposon');
        ($gene_id) = $name unless($name =~ / /); # a description not name
        ## $g->remove_tag('transposon');
        $g->add_tag_value('Name', $gene_id);
    }
    elsif ($g->has_tag('ID')) { 
        my ($name)= $g->get_tag_values('ID');
        $g->add_tag_value('Name', $name);
    }    
    return $gene_id;
}


sub _add_flattened_SeqFeatures  {
    my ($arrayref,$feat) = @_;
    my @subs = ();

    if ($feat->isa("Bio::FeatureHolderI")) {
        @subs = $feat->get_SeqFeatures;
    } 
    elsif ($feat->isa("Bio::SeqFeatureI")) {
        @subs = $feat->sub_SeqFeature;
    }
    else {
        warn ref($feat)." is neither a FeatureHolderI nor a SeqFeatureI. ".
            "Don't know how to flatten.";
    }

    for my $sub (@subs) {
        push(@$arrayref,$sub);
        _add_flattened_SeqFeatures($arrayref,$sub);
    }

}

sub map_types {

    my ($self, @args) = @_;

    my($sf, $seq, $type_map, $syn_map, $undefmap) =
        $self->_rearrange([qw(FEATURE
                    SEQ
                    TYPE_MAP
                    SYN_MAP
                    UNDEFINED
                    )],
                @args);

    if (!$sf && !$seq) {
        $self->throw("you need to pass in either -feature or -seq");
    }

    my @sfs = ($sf);
    if ($seq) {
        $seq->isa("Bio::SeqI") || $self->throw("$seq NOT A SeqI");
        @sfs = $seq->get_all_SeqFeatures;
    }
    $type_map = $type_map || $self->typemap; # dgg: was type_map;
    foreach my $feat (@sfs) {

        $feat->isa("Bio::SeqFeatureI") || $self->throw("$feat NOT A SeqFeatureI");
        $feat->isa("Bio::FeatureHolderI") || $self->throw("$feat NOT A FeatureHolderI");

        my $primary_tag = $feat->primary_tag;

        #if ($primary_tag =~ /^pseudo(.*)$/) {
        #    $primary_tag = $1;
        #    $feat->primary_tag($primary_tag);
        #}

        my $mtype = $type_map->{$primary_tag};
        if ($mtype) {
            if (ref($mtype)) {
                if (ref($mtype) eq 'ARRAY') {
                    my $soID;
                    ($mtype, $soID) = @$mtype;

                    if ($soID && ref($ONTOLOGY)) {
                        my ($term) = $ONTOLOGY->find_terms(-identifier => $soID);
                        $mtype = $term->name if $term;
                    } 
                    # if SO ID is undefined AND we have an ontology to search, we want to delete 
                    # the feature type hash entry in order to force a fuzzy search
                    elsif (! defined $soID && ref($ONTOLOGY)) {
                        undef $mtype;
                        delete $type_map->{$primary_tag};
                    } 
                    elsif ($undefmap && $mtype eq 'undefined') { # dgg
                        $mtype= $undefmap;
                    }

                    $type_map->{$primary_tag} = $mtype if $mtype;
                }
                elsif (ref($mtype) eq 'CODE') {
                    $mtype = $mtype->($feat);
                }
                else {
                    $self->throw('must be scalar or CODE ref');
                }
            }
            elsif ($undefmap && $mtype eq 'undefined') { # dgg
                $mtype= $undefmap;
            }
            $feat->primary_tag($mtype);
        }

        if ($CONF) {
            conf_read(); 
            my %perfect_matches;
            while (my ($p_tag,$rules) = each %$YAML) {
                RULE:
                for my $rule (@$rules) {
                    for my $tags (@$rule) {
                        while (my ($tag,$values) = each %$tags) {
                            for my $value (@$values) {
                                if ($feat->has_tag($tag)) {
                                    for ($feat->get_tag_values($tag)) {
                                        next RULE unless $_ =~ /\Q$value\E/;
                                    }
                                } elsif ($tag eq 'primary_tag') {
                                    next RULE unless $value eq
                                        $feat->primary_tag; 
                                } elsif ($tag eq 'location') {
                                    next RULE unless $value eq
                                        $feat->start.'..'.$feat->end;
                                } else { next RULE }
                            }
                        }
                    }
                    $perfect_matches{$p_tag}++;
                }
            }
            if (scalar(keys %perfect_matches) == 1) {
                $mtype = $_ for keys %perfect_matches;
            } elsif (scalar(keys %perfect_matches) > 1) {
                warn "There are conflicting rules in the config file for the" .
                     " following types: ";
                warn "\t$_\n" for keys %perfect_matches;
                warn "Until conflict resolution is built into the converter," .
                     " you will have to manually edit the config file to remove the" .
                     " conflict. Sorry :(. Skipping user preference for this entry";
                sleep(2);
            }
        } 

        if ( ! $mtype  && $syn_map) {
            if ($feat->has_tag('note')) {

                my @all_matches;

                my @note = $feat->each_tag_value('note');

                for my $k (keys %$syn_map) {

                    if ($k =~ /"(.+)"/) {

                        my $syn = $1;

                        for my $note (@note) {

                            # look through the notes to see if the description
                            # is an exact match for synonyms
                            if ( $syn eq $note ) { 

                                my @map = @{$syn_map->{$k}};

                                
                                my $best_guess = $map[0];

                                unshift @{$all_matches[-1]}, [$best_guess];

                                $mtype = $MANUAL
                                    ? manual_curation($feat, $best_guess, \@all_matches)
                                    : $best_guess;

                                print '#' x 78 . "\nGuessing the proper SO term for GenBank"
                                    . " entry:\n\n" . GenBank_entry($feat) . "\nis:\t$mtype\n" 
                                    . '#' x 78 . "\n\n";

                            } else {
                                # check both primary tag and and note against
                                # SO synonyms for best matching description

                                SO_fuzzy_match( $k, $primary_tag, $note, $syn, \@all_matches); 
                            }

                        }
                    } 
                }

                #unless ($mtype) {
                for my $note (@note) {
                    for my $name (values %$type_map) {
                    # check primary tag against SO names for best matching
                    # descriptions //NML also need to check against
                    # definition && camel case split terms

                        SO_fuzzy_match($name, $primary_tag, $note, $name, \@all_matches);
                    }
                }
                #}

                if (scalar(@all_matches) && !$mtype) {

                    my $top_matches = first { defined $_ } @{$all_matches[-1]}; 

                    my $best_guess = $top_matches->[0];



                    # if guess has quotes, it is a synonym term. we need to 
                    # look up the corresponding name term
                    # otherwise, guess is a name, so we can use it directly
                    if ($best_guess =~ /"(.+)"/) {

                        $best_guess = $syn_map->{$best_guess}->[0];

                    } 

                    @RETURN = @all_matches;
                    $mtype = $MANUAL
                        ? manual_curation($feat, $best_guess, \@all_matches)
                        : $best_guess;

                    print '#' x 78 . "\nGuessing the proper SO term for GenBank"
                        . " entry:\n\n" . GenBank_entry($feat) . "\nis:\t$mtype\n" 
                        . '#' x 78 . "\n\n";

                }
            }
            $mtype ||= $undefmap;
            $feat->primary_tag($mtype);
        } 
    }


}

sub SO_fuzzy_match {

    my $candidate = shift;
    my $primary_tag = shift;
    my $note = shift;
    my $SO_terms = shift;
    my $best_matches_ref = shift;
    my $modifier = shift; 

    $modifier ||= '';

        my @feat_terms;

    for ( split(" |_", $primary_tag) ) {
        #my @camelCase = /(?:[A-Z]|[a-z])(?:[A-Z]+|[a-z]*)(?=$|[A-Z])/g;
        my @camelCase = /(?:[A-Z]|[a-z])(?:[A-Z]+|[a-z]*)(?=$|[A-Z]|[;:.,])/g;
        push @feat_terms, @camelCase;
    }

    for ( split(" |_", $note) ) {
        #my @camelCase = /(?:[A-Z]|[a-z])(?:[A-Z]+|[a-z]*)(?=$|[A-Z])/g;
        #my @camelCase = /(?:[A-Z]|[a-z])(?:[A-Z]+|[a-z]*)(?=$|[A-Z]|[;:.,])/g;
        (my $word = $_) =~ s/[;:.,]//g;
        push @feat_terms, $word;
    }


    my @SO_terms = split(" |_", $SO_terms);

    # fuzzy match works on a simple point system. When 2 words match,
    # the $plus counter adds one. When they don't, the $minus counter adds
    # one. This is used to sort similar matches together. Better matches
    # are found at the end of the array, near the top.

    # NML: can we improve best match by using synonym tags
    # EXACT,RELATED,NARROW,BROAD?

    my ($plus, $minus) = (0, 0); 
    my %feat_terms;
    my %SO_terms;

    #unique terms
    map {$feat_terms{$_} = 1} @feat_terms;
    map {$SO_terms{$_} = 1} @SO_terms;

    for my $st (keys %SO_terms) {
        for my $ft (keys %feat_terms) {

            ($st =~ m/$modifier\Q$ft\E/) ? $plus++ : $minus++;

        }
    }

    push @{$$best_matches_ref[$plus][$minus]}, $candidate if $plus;

}

sub manual_curation {

    my ($feat, $default_opt,  $all_matches) = @_; 

    my @all_matches = @$all_matches;

    # convert all SO synonyms into names and filter
    # all matches into unique term list because
    # synonyms can map to multiple duplicate names

    my (@unique_SO_terms, %seen);
    for (reverse @all_matches) {
        for (@$_) {
            for (@$_) {
                #my @names;
                if ($_ =~ /"(.+)"/) {
                    for (@{$SYN_MAP->{$_}}) {
                        push @unique_SO_terms, $_ unless $seen{$_};
                        $seen{$_}++;
                    }
                } else { 
                    push @unique_SO_terms, $_ unless $seen{$_};
                    $seen{$_}++;
                }
            }
        }
    }

    my $s = scalar(@unique_SO_terms);

    my $choice = 0;

    my $more = 
        "[a]uto   : automatic input (selects best guess for remaining entries)\r" .
        "[f]ind   : search for other SO terms matching your query (e.g. f gene)\r" . 
        "[i]nput  : add a specific term\r" .
        "[r]eset  : reset to the beginning of matches\r" .
        "[s]kip   : skip this entry (selects best guess for this entry)\r"
    ;

    $more .= 
        "[n]ext   : view the next ".OPTION_CYCLE." terms\r" .
        "[p]rev   : view the previous ".OPTION_CYCLE." terms" if ($s > OPTION_CYCLE);

    my $msg = #"\n\n" . '-' x 156 . "\n"
         "The converter found $s possible matches for the following GenBank entry: ";

    my $directions = 
        "Type a number to select the SO term that best matches"
        . " the genbank entry, or use any of the following options:\r" . '_' x 76 . "\r$more"; 


    # lookup filtered list to pull out definitions
    my @options = map { 
        my $term = $_;
        my %term;
        for (['name', 'name'], ['def', 'definition'], ['synonym',
                'each_synonym']) {
            my ($label, $method) = @$_;
            $term{$label} = \@{[$term->$method]};
        }
        [++$choice, $_->name, ($_->definition || 'none'), \%term, $_->each_synonym ];
    }  map { $ONTOLOGY->find_terms(-name => $_) } @unique_SO_terms;


    my $option = options_cycle(0, OPTION_CYCLE, $msg, $feat, $directions,
            $default_opt, @options);

    if ($option eq 'skip') { return $default_opt 
    } elsif ($option eq 'auto') {
        $MANUAL = 0;
        return $default_opt;
    } else { return $option }

}

sub options_cycle {

    my ($start, $stop, $msg, $feat, $directions, $best_guess, @opt) = @_;

    #NML: really should only call GenBank_entry once. Will need to change
    #method to return array & shift off header
    my $entry = GenBank_entry($feat, "\r");

    my $total = scalar(@opt);

    ($start,$stop) = (0, OPTION_CYCLE) 
        if ( ($start < 0) && ($stop > 0) );

    ($start,$stop) = (0, OPTION_CYCLE) 
        if ( ( ($stop - $start) < OPTION_CYCLE ) && $stop < $total);

    ($start,$stop) = ($total - OPTION_CYCLE, $total) if $start < 0;
    ($start,$stop) = (0, OPTION_CYCLE) if $start >= $total;

    $stop = $total if $stop > $total;

    my $dir_copy = $directions;
    my $msg_copy = $msg;
    my $format = "format STDOUT = \n" .
        '-' x 156 . "\n" . 
        '^' . '<' x 77 .  '| Available Commands:' . "\n" .
        '$msg_copy' . "\n" .
        '-' x 156 . "\n" . 
        ' ' x 78 . "|\n" .
        '^' . '<' x 77 . '| ^' . '<' x 75 . '~' . "\n" .
        '$entry' . ' ' x 74 . '$dir_copy,' . "\n" .
        (' ' x 20 . '^' . '<' x 57 . '| ^' . '<' x 75 . '~' . "\n" .
        ' ' x 20 . '$entry,' . ' ' x 53 . '$dir_copy,' . "\n") x 1000  . ".\n";

    {
        # eval throws redefined warning that breaks formatting. 
        # Turning off warnings just for the eval to fix this.
        no warnings 'redefine';
        eval $format;
    }

    write;

    print '-' x 156 . "\n" .
        'Showing results ' . ( $stop ? ( $start + 1 ) : $start ) . 
        " - $stop of possible SO term matches: (best guess is \"$best_guess\")" .
        "\n" . '-' x 156 . "\n"; 

    for  (my $i = $start; $i < $stop; $i+=2) {

        my ($left, $right) = @opt[$i,$i+1];

        my ($nL, $nmL, $descL, $termL, @synL) = @$left;

        #odd numbered lists can cause fatal undefined errors, so check
        #to make sure we have data
        
        my ($nR, $nmR, $descR, $termR, @synR) = ref($right) ? @$right : (undef, undef, undef);


        my $format = "format STDOUT = \n";

        $format .=
            ' ' x 78 . "|\n" .

            '@>>: name: ^' . '<' x 64 . '~' . ' |' .
                ( ref($right) ? ('@>>: name: ^' . '<' x 64 . '~' ) : '' ) .  "\n" .
            '$nL,' . ' ' x 7 . '$nmL,' .
                ( ref($right) ? (' ' x 63 . '$nR,' .  ' ' x 7 .  "\$nmR,") : '' ) . "\n" .

            ' ' x 11 . '^' . '<' x 61 . '...~' . ' |' . 
                (ref($right) ? ('           ^' . '<' x 61 .  '...~') : '') . "\n" .
            ' ' x 11 . '$nmL,' . 
                (ref($right) ? (' ' x 74 . '$nmR,') : '') . "\n" .
            #' ' x 78 . '|' . "\n" .


            '     def:  ^' . '<' x 65 . ' |' . 
                (ref($right) ? ('     def:  ^' . '<' x 64 . '~') : '') . "\n" .
            ' ' x 11 . '$descL,' . 
                (ref($right) ? (' ' x 72 . '$descR,') : '') . "\n" .


            ('           ^' . '<' x 65 . ' |' . 
                (ref($right) ? ('           ^' . '<' x 64 . '~') : '') . "\n" .
            ' ' x 11 . '$descL,' . 
                (ref($right) ? (' ' x 72 . '$descR,') : '') . "\n") x 5 .


            '           ^' . '<' x 61 . '...~ |' . 
                (ref($right) ? ('           ^' . '<' x 61 . '...~') : '') . "\n" .
            ' ' x 11 . '$descL,' . 
                (ref($right) ? (' ' x 72 . '$descR,') : '') . "\n" .

            ".\n";

        {
            # eval throws redefined warning that breaks formatting. 
            # Turning off warnings just for the eval to fix this.
            no warnings 'redefine';
            eval $format;
        }
        write;

    }   
    print '-' x 156 . "\nenter a command:";

    while () {

        (my $input = $_) =~ s/\s+$//;

        if ($input =~ /^\d+$/) {
            if ( $input && defined $opt[$input-1] ) {
                return $opt[$input-1]->[1]
            } else {
                print "\nThat number is not an option. Please enter a valid number.\n:";
            }
        } elsif ($input =~ /^n/i | $input =~ /next/i ) {
            return options_cycle($start + OPTION_CYCLE, $stop + OPTION_CYCLE, $msg, 
                    $feat, $directions, $best_guess, @opt)
        } elsif ($input =~ /^p/i | $input =~ /prev/i ) {
            return options_cycle($start - OPTION_CYCLE, $stop - OPTION_CYCLE, $msg,
                    $feat, $directions, $best_guess, @opt)
        } elsif ( $input =~ /^s/i || $input =~ /skip/i ) { return 'skip' 
        } elsif ( $input =~ /^a/i || $input =~ /auto/i ) { return 'auto' 
        } elsif ( $input =~ /^r/i || $input =~ /reset/i ) { 
            return manual_curation($feat, $best_guess, \@RETURN );
        } elsif ( $input =~ /^f/i || $input =~ /find/i ) {

            my ($query, @query_results);

            if ($input =~ /(?:^f|find)\s+?(.*?)$/) { $query = $1;
            } else {

                #do a SO search
                print "Type your search query\n:";
                while () { chomp($query = $_); last }
            }

            for (keys(%$TYPE_MAP), keys(%$SYN_MAP)) {
                SO_fuzzy_match($_, $query, '', $_, \@query_results, '(?i)');
            }

            return manual_curation($feat, $best_guess, \@query_results);

        } elsif ( $input =~ /^i/i || $input =~ /input/i ) {

            #NML fast input for later
            #my $query;
            #if ($input =~ /(?:^i|input)\s+?(.*?)$/) { $query = $1 };

            #manual input
            print "Type the term you want to use\n:";
            while () {
                chomp(my $input = $_);

                if (! $TYPE_MAP->{$input}) {

                    print "\"$input\" doesn't appear to be a valid SO term. Are ".
                        "you sure you want to use it? (y or n)\n:";

                    while () {

                        chomp(my $choice = $_);

                        if ($choice eq 'y') {
                            print 
                                "\nWould you like to save your preference for " .
                                "future use (so you don't have to redo manual " .
                                "curation for this feature everytime you run " . 
                                "the converter)? (y or n)\n";

                            #NML: all these while loops are a mess. Really should condense it.
                            while () {

                                chomp(my $choice = $_);

                                if ($choice eq 'y') {
                                    curation_save($feat, $input);
                                    return $input;
                                } elsif ($choice eq 'n') {
                                    return $input
                                } else {
                                    print "\nDidn't recognize that command. Please " . 
                                        "type y or n.\n:" 
                                }
                            }

                                
                        } elsif ($choice eq 'n') {
                            return options_cycle($start, $stop, $msg, $feat,
                                    $directions, $best_guess, @opt)
                        } else {
                            print "\nDidn't recognize that command. Please " . 
                                "type y or n.\n:" 
                        }
                    }

                } else { 
                    print 
                        "\nWould you like to save your preference for " .
                        "future use (so you don't have to redo manual " .
                        "curation for this feature everytime you run  " . 
                        "the converter)? (y or n)\n";

                    #NML: all these while loops are a mess. Really should condense it.
                    while () {

                        chomp(my $choice = $_);

                        if ($choice eq 'y') {
                            curation_save($feat, $input);
                            return $input;
                        } elsif ($choice eq 'n') {
                            return $input
                        } else {
                            print "\nDidn't recognize that command. Please " . 
                                "type y or n.\n:" 
                        }
                    }

                } 

            }
        } else { 
            print "\nDidn't recognize that command. Please re-enter your choice.\n:" 
        }
    }

}

sub GenBank_entry {
    my ($f, $delimiter, $num) = @_;

    $delimiter ||= "\n";


    my $entry  = 

        ($num ? ' [1] ' : ' ' x 5) . $f->primary_tag 
        . ($num 
            ? ' ' x (12 - length $f->primary_tag ) . ' [2] '
            : ' ' x (15 - length $f->primary_tag) 
          )
        . $f->start.'..'.$f->end

        . "$delimiter";

    if ($num) {
        words_tag($f, \$entry);
    } else {
        for my $tag ($f->all_tags) {
            for my $val ( $f->each_tag_value($tag) ) {
                $entry .= ' ' x 20;
                #$entry .= "/$tag=\"$val\"$delimiter";
                $entry .= $val eq '_no_value'
                    ? "/$tag$delimiter"
                    : "/$tag=\"$val\"$delimiter";
            }
        }

    }

    return $entry;
}


sub gff_validate {
    warn "Validating GFF file\n" if $DEBUG;
    my @feat = @_;

    my (%parent2child, %all_ids, %descendants, %reserved);

    for my $f (@feat) {
        for my $aTags (['Parent', \%parent2child], ['ID', \%all_ids]) {
            map { push @{$$aTags[1]->{$_}}, $f } $f->get_tag_values($$aTags[0])
                if $f->has_tag($$aTags[0]); 
        }
    }

    if ($SO_FILE) {
        while (my ($parentID, $aChildren) = each %parent2child) {
            parent_validate($parentID, $aChildren, \%all_ids, \%descendants, \%reserved);
        }
    }

    id_validate(\%all_ids, \%reserved);        
}

sub parent_validate {
    my ($parentID, $aChildren, $hAll, $hDescendants, $hReserved) = @_;

    my $aParents = $hAll->{$parentID};

    map { 
        my $child = $_;
        $child->add_tag_value( validation_error => 
        "feature tried to add Parent tag, but no Parent found with ID $parentID"
        );
        my %parents;
        map { $parents{$_} = 1 } $child->get_tag_values('Parent');
        delete $parents{$parentID};
        my @parents = keys %parents;

        $child->remove_tag('Parent');

        unless ($child->has_tag('ID')) {
            my $id = gene_name($child);
            $child->add_tag_value('ID', $id);
            push @{$hAll->{$id}}, $child
        }

        $child->add_tag_value('Parent', @parents) if @parents;

    } @$aChildren and return unless scalar(@$aParents);

    my $par = join(',', map { $_->primary_tag } @$aParents);
    warn scalar(@$aParents)." POSSIBLE PARENT(S): $par" if $DEBUG;

    #NML manual curation needs to happen here


    my %parentsToRemove;

    CHILD:
    for my $child (@$aChildren) {
        my $childType  = $child->primary_tag;

        warn "WORKING ON $childType at ".$child->start.' to '.$child->end 
            if $DEBUG;

        for (my $i = 0; $i < scalar(@$aParents); $i++) {
            my $parent = $aParents->[$i];
            my $parentType = $parent->primary_tag;

            warn "CHECKING $childType against $parentType" if $DEBUG;

            #cache descendants so we don't have to do repeat searches
            unless ($hDescendants->{$parentType}) {

                for my $term ($ONTOLOGY->find_terms(
                        -name => $parentType
                    ) ) {
                    
                    map {
                        $hDescendants->{$parentType}{$_->name}++
                    } $ONTOLOGY->get_descendant_terms($term);

                }

                # NML: hopefully temporary fix.
                # SO doesn't consider exon/CDS to be a child of mRNA
                # even though common knowledge dictates that they are
                # This cheat fixes the false positives for now
                if ($parentType eq 'mRNA') {
                    $hDescendants->{$parentType}{'exon'} = 1;
                    $hDescendants->{$parentType}{'CDS'} = 1;
                }

            }

            warn "\tCAN $childType at " . $child->start . ' to ' . $child->end .
                " be a child of $parentType?" if $DEBUG;
            if ($hDescendants->{$parentType}{$childType}) {
                warn "\tYES, $childType can be a child of $parentType" if $DEBUG;

                #NML need to deal with multiple children matched to multiple different
                #parents. This model only assumes the first parent id that matches a child will
                #be the reserved feature. 

                $hReserved->{$parentID}{$parent}{'parent'} = $parent;
                push @{$hReserved->{$parentID}{$parent}{'children'}}, $child;

                #mark parent for later removal from all IDs 
                #so we don't accidentally change any parents

                $parentsToRemove{$i}++;

                next CHILD;
            } 
        }


        
        #NML shouldn't have to check this; somehow child can lose Parent
        #it's happening W3110
        #need to track this down
        if ( $child->has_tag('Parent') ) {

            warn "\tNO, @{[$child->primary_tag]} cannot be a child of $parentID"
                if $DEBUG;

            my %parents;

            map { $parents{$_} = 1 } $child->get_tag_values('Parent');

            delete $parents{$parentID};
            my @parents = keys %parents;

            warn 'VALIDATION ERROR '.$child->primary_tag." at ".$child->start .
                ' to ' . $child->end . " cannot be a child of ID $parentID"
                if $DEBUG;

            $child->add_tag_value( validation_error => 
                    "feature cannot be a child of $parentID");

            $child->remove_tag('Parent');

            unless ($child->has_tag('ID')) {
                my $id = gene_name($child);
                $child->add_tag_value('ID', $id);
                push @{$hAll->{$id}}, $child
            }

            $child->add_tag_value('Parent', @parents) if @parents;
        }

    }
    
    #delete $aParents->[$_] for keys %parentsToRemove;
    splice(@$aParents, $_, 1) for keys %parentsToRemove;
}

sub id_validate {
    my ($hAll, $hReserved) = @_;


    for my $id (keys %$hAll) {

        #since 1 feature can have this id, 
        #let's just shift it off and uniquify
        #the rest (unless it's reserved)

        shift @{$hAll->{$id}} unless $hReserved->{$id};
        for my $feat (@{$hAll->{$id}}) {
            id_uniquify(0, $id, $feat, $hAll);
        }
    }

    for my $parentID (keys %$hReserved) {

        my @keys = keys %{$hReserved->{$parentID}};

        shift @keys;

        for my $k (@keys) {
            my $parent = $hReserved->{$parentID}{$k}{'parent'};
            my $aChildren= $hReserved->{$parentID}{$k}{'children'};

            my $value = id_uniquify(0, $parentID, $parent, $hAll);
            for my $child (@$aChildren) {

                my %parents;
                map { $parents{$_}++ } $child->get_tag_values('Parent');
                $child->remove_tag('Parent');
                delete $parents{$parentID};
                $parents{$value}++;
                my @parents = keys %parents;
                $child->add_tag_value('Parent', @parents);
            }

        }
    }
}

sub id_uniquify {
    my ($count, $value, $feat, $hAll) = @_;

    warn "UNIQUIFYING $value" if $DEBUG;

    if (! $count) {
        $feat->add_tag_value(Alias => $value);
        $value .= ('.' . $feat->primary_tag) 
    } elsif ($count == 1) {
        $value .= ".$count" 
    } else { 
        chop $value;
        $value .= $count 
    }
    $count++;

    warn "ENDED UP WITH $value" if $DEBUG;
    if ( $hAll->{$value} ) { 
        warn "$value IS ALREADY TAKEN" if $DEBUG;
        id_uniquify($count, $value, $feat, $hAll);
    } else { 
        #warn "something's breaking ".$feat->primary_tag.' at '.$feat->start.' to '.$feat->end;
        $feat->remove_tag('ID');
        $feat->add_tag_value('ID', $value);
        push @{$hAll->{$value}}, $value;
    }

    $value;
}

sub conf_read {

    print "\nCannot read $CONF. Change file permissions and retry, " .
        "or enter another file\n" and conf_locate() unless -r $CONF;

    print "\nCannot write $CONF. Change file permissions and retry, " .
        "or enter another file\n" and conf_locate() unless -w $CONF;

    $YAML = LoadFile($CONF);

}

sub conf_create {

    my ($path, $input) = @_;

    print "Cannot write to $path. Change directory permissions and retry " .
        "or enter another save path\n" and conf_locate() unless -w $path;

    $CONF = $input;

    open(FH, '>', $CONF);
    close(FH);
    conf_read();


}

sub conf_write { DumpFile($CONF, $YAML) }

sub conf_locate {

    print "\nEnter the location of a previously saved config, or a new " .
        "path and file name to create a new config (this step is " .
        "necessary to save any preferences)";

    print "\n\nenter a command:";

    while () {
        chomp(my $input = $_);
        my ($fn, $path, $suffix) = fileparse($input, qr/\.[^.]*/);

        if (-e $input && (! -d $input)) {

            print "\nReading $input...\n";
            $CONF = $input;

            conf_read(); 
            last;

        } elsif (! -d $input && $fn.$suffix) {

            print "Creating $input...\n";
            conf_create($path, $input);
            last;

        } elsif (-e $input && -d $input) {
            print "You only entered a directory. " .
                "Please enter BOTH a directory and filename\n";
        } else { 
            print "$input does not appear to be a valid path. Please enter a " .
                "valid directory and filename\n";
        }
        print "\nenter a command:";
    }
}

sub curation_save {

    my ($feat, $input) = @_;

    #my $error = "Enter the location of a previously saved config, or a new " .
    #    "path and file name to create a new config (this step is " .
    #    "necessary to save any preferences)\n";

    if (!$CONF) {
        print "\n\n"; 
        conf_locate();
    } elsif (! -e $CONF) {
        print "\n\nThe config file you have chosen doesn't exist.\n";
        conf_locate();
    } else { conf_read() }

    my $entry = GenBank_entry($feat, "\r", 1);

    my $msg = "Term entered: $input";
    my $directions = "Please select any/all tags that provide evidence for the term you
have entered. You may enter multiple tags by separating them by commas/dashes
(e.g 1,3,5-7). For tags with more than one word value (i.e 'note'), you have
the option of either selecting the entire note as evidence, or specific
keywords. If a tag has multiple keywords, they will be tagged alphabetically
for selection. To select a specific keyword in a tag field, you must enter the
tag number followed by the keyword letter (e.g 3a). Multiple keywords may be
selected by entering each letter separated by commas/dashes (e.g 3b,f,4a-c). The more tags you select, the more specific the GenBank entry will have
to be to match your curation. To match the GenBank entry exactly as it
appears, type every number (start-end), or just type 'all'. Remember, once the converter saves your
preference, you will no longer be prompted to choose a feature type for any
matching entries until you edit the curation.ini file.";
    my $msg_copy = $msg;
    my $dir_copy = $directions;

    my $format = "format STDOUT = \n" .
        '-' x 156 . "\n" . 
        '^' . '<' x 77 .  '| Directions:' . "\n" .
        '$msg_copy' . "\n" .
        '-' x 156 . "\n" . 
        ' ' x 78 . "|\n" .
        '^' . '<' x 77 . '| ^' . '<' x 75 . '~' . "\n" .
        '$entry' . ' ' x 74 . '$dir_copy,' . "\n" .
        (' ' x 15 . '^' . '<' x 62 . '| ^' . '<' x 75 . '~' . "\n" .
        ' ' x 15 . '$entry,' . ' ' x 58 . '$dir_copy,' . "\n") x 20  . ".\n";

    {
        # eval throws redefined warning that breaks formatting. 
        # Turning off warnings just for the eval to fix this.
        no warnings 'redefine';
        eval $format;
    }

    write;
    print '-' x 156 . "\nenter a command:";

    my @tags = words_tag($feat); 

    my $final = {};
    my $choices;
    while () {

        chomp(my $choice = $_);

        if (scalar(keys %$final) && $choice =~ /^y/i) { last 

        } elsif (scalar(keys %$final) && $choice =~ /^n/i) { curation_save($feat, $input) 

        } elsif (scalar(keys %$final)) { print "\nInvalid selection. Please try again\n";

        } elsif ($choice eq 'all') {

            $choice = '';
            for (my $i=1; $i < scalar(@tags); $i++) {
                $choice .= "$i,";
            }
            chop $choice;
        } 
        #print "CHOICE [$choice]";

        my @selections;
        for (split(/(?<=\w)[^[:alnum:]\-]+(?=\d)/, $choice)) {
            if ($_ =~ /(\d+)(?:\D*)-(\d+)(.*)/) { 

                for ($1..$2) { push @selections, $_ }

                my $dangling_alphas = $3;
                alpha_expand($dangling_alphas, \@selections);

            } else { 
                alpha_expand($_, \@selections);
            }
        }

        foreach my $numbers (@selections) {

            my @c = split(/(?=[\w])/, $numbers);
            s/\W+//g foreach @c;
            my $num;
            
            {
                $^W = 0;
                $num = 0 + shift @c;
            }

            my $tag = $tags[$num];
            if (ref $tag && scalar(@c)) {
                my $no_value;
                foreach (@c) {
                    if (defined $tag->{$_}) {
                        $choices .= "${num}[$_] ";
                        my ($t,$v) = @{$tag->{$_}};
                        push @{${$final->{$input}}[0]{$t}}, $v;

                    } else { $no_value++ }
                    }

                if ($no_value) { 
                    _selection_add($tag,$final,$input,\$choices,$num);
                    #my ($t,$v) = @{$tag->{'all'}};
                    #unless (defined ${$final->{$input}}[0]{$t}) {
                        #$choices .= "$num, ";
                        #push @{${$final->{$input}}[0]{$t}}, $v
                    #}
                }

                $choices = substr($choices, 0, -2);
                $choices .= ', ';

            } elsif (ref $tag) { 
                _selection_add($tag,$final,$input,\$choices,$num);
                #my ($t,$v) = @{$tag->{'all'}};
                #unless (defined ${$final->{$input}}[0]{$t}) {
                    #$choices .= "$num, ";
                    #push @{${$final->{$input}}[0]{$t}}, $v
                #}
            } 
        }
        $choices = substr($choices, 0, -2) if $choices;
        if ($final) {
            print "\nYou have chosen the following tags:\n$choices\n";
            print "This will be written to the config file as:\n";
            print Dump $final;
            print "\nIs this correct? (y or n)\n";
        } else { print "\nInvalid selection. Please try again\n" }
    }
    push @{$YAML->{$input}}, $final->{$input};
    conf_write();
}

#  words_tag() splits each tag value string into multiple words so that the 
#  user can select the parts he/she wants to use for curation
#  it can tag 702 (a - zz) separate words; this should be enough

sub words_tag {

    my ($feat, $entry) = @_;

    my @tags;

    @tags[1,2] = ({'all' => ['primary_tag', $feat->primary_tag]}, {'all' => ['location', $feat->start.'..'.$feat->end]});
    my $i = 3;
    foreach my $tag ($feat->all_tags) {
        foreach my $value ($feat->each_tag_value($tag)) {

            my ($string, $tagged_string);

            my @words = split(/(?=\w+?)/, $value);

            my $pos = 0;


            foreach my $word (@words) {

                (my $sanitized_word = $word) =~ s/\W+?//g;
                $string .= $word;

                my $lead = int($pos/ALPHABET_DIVISOR);
                my $lag = $pos % ALPHABET_DIVISOR;

                my $a =  $lead ? ${(ALPHABET)}[$lead-1] : '';
                $a .= $lag ? ${(ALPHABET)}[$lag] : 'a';

                $tagged_string .= " ($a) $word";

                $tags[$i]{$a} = [$tag, $sanitized_word];
                $pos++;
            }

            $value = $tagged_string if scalar(@words) > 1;

            $$entry .= "[$i] /$tag=\"$value\"\r";

            $tags[$i]{'all'} = [$tag, $string];
        }
        $i++;
    }

    return @tags;
    
}

sub alpha_expand {

    my ($dangling_alphas, $selections) = @_;

    if (defined($dangling_alphas) && $dangling_alphas =~ /(\d)*([[:alpha:]]+)-([[:alpha:]]+)/) {

        my $digit = $1;
        push @$selections, $digit if $digit;

        my $start = $2;
        my $stop = $3;

        my @starts = split('', $start);
        my @stops = split('', $stop);

        my ($final_start, $final_stop);

        for ([\$final_start, \@starts], [\$final_stop, \@stops]) {

            my ($final, $splits) = @$_;

            my $int = ${(ALPHABET_TO_NUMBER)}{$$splits[0]};
            my $rem;


            if ($$splits[1]) {
                $rem = ${(ALPHABET_TO_NUMBER)}{$$splits[1]};
                $int++
            } else {
                $rem = $int;
                $int = 0;
            }


            $$final = $int * ALPHABET_DIVISOR;
            $$final += $rem;

        }

        my $last_number = pop @$selections;
        for my $pos ($final_start..$final_stop) {
            my $lead = int($pos/ALPHABET_DIVISOR);
            my $lag = $pos % ALPHABET_DIVISOR;
            my $alpha =  $lead ? ${(ALPHABET)}[$lead-1] : '';
            $alpha .= $lag ? ${(ALPHABET)}[$lag] : 'a';
            push @$selections, $last_number.$alpha;        
        }

    } elsif (defined($dangling_alphas)) { 
        if ($dangling_alphas =~ /^\d/) {
            push @$selections, $dangling_alphas;
        } elsif ($dangling_alphas =~ /^\D/) {
            #print "$dangling_alphas ".Dumper @$selections;
            my $last_number = pop @$selections;
            $last_number ||= '';
            push @$selections, $last_number.$dangling_alphas;
            #$$selections[-1] .= $dangling_alphas;
        }
    }

}

sub _selection_add {

    my ($tag, $final, $input, $choices, $num) = @_;
    my ($t,$v) = @{$tag->{'all'}};
    unless (defined ${$final->{$input}}[0]{$t}) {
        $$choices .= "$num, ";
        push @{${$final->{$input}}[0]{$t}}, $v
    }

}
BioPerl-1.007002/scripts/Bio-DB-GFF/bp_generate_histogram.pl000444000766000024       711313155576320 23465 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

use strict;
use warnings;
use lib '.','./blib','../../blib/lib';
use Bio::DB::GFF;
use Getopt::Long;

my $usage = <       Data source (default dbi:mysql:test)
   --adaptor       Schema adaptor (default dbi::mysqlopt)
   --user             Username for mysql authentication
   --pass         Password for mysql authentication
   --bin                Bin size in base pairs.
   --aggregator       Comma-separated list of aggregators
   --sort                   Sort the resulting list by type and bin
   --merge                  Merge features with same method but different sources
USAGE
;

my ($DSN,$ADAPTOR,$AGG,$USER,$PASSWORD,$BINSIZE,$SORT,$MERGE);
GetOptions ('dsn:s'         => \$DSN,
	    'adaptor:s'     => \$ADAPTOR,
	    'user:s'        => \$USER,
	    'password:s'    => \$PASSWORD,
            'aggregators:s' => \$AGG,
            'bin:i'         => \$BINSIZE,
	    'sort'          => \$SORT,
	    'merge'         => \$MERGE,
	   ) or die $usage;

my @types = @ARGV or die $usage;

# some local defaults
$DSN     ||= 'dbi:mysql:test';
$ADAPTOR ||= 'dbi::mysqlopt';
$BINSIZE ||= 1_000_000;   # 1 megabase bins

my @options;
push @options,(-user=>$USER)     if defined $USER;
push @options,(-pass=>$PASSWORD) if defined $PASSWORD;
push @options,(-aggregator=>[split /\s+/,$AGG]) if defined $AGG;

my $db = Bio::DB::GFF->new(-adaptor=>$ADAPTOR,-dsn => $DSN,@options)
  or die "Can't open database: ",Bio::DB::GFF->error,"\n";

my @features = $db->features(-binsize=>$BINSIZE,-types=>\@types);

if ($MERGE) {
  my %MERGE;
  for my $f (@features) {
    my $name  = $f->name;
    my $class = $name->class;
    $name =~ s/^(.+:.+):.+$/$1/;
    $f->group(Bio::DB::GFF::Featname->new($class,$name));
    my $source = $f->source;
    $source =~ s/:.+$//;
    $f->source($source);
    if (my $already_there = $MERGE{$f->source,$f->abs_ref,$f->abs_start}) {
      $already_there->score($already_there->score + $f->score);
    } else {
      $MERGE{$f->source,$f->abs_ref,$f->abs_start} = $f;
    }
  }
  @features = values %MERGE;
}

# sort features by type, ref and start if requested
if ($SORT) {
  @features = sort {
    $a->type cmp $b->type
      || $a->abs_ref cmp $b->abs_ref
	|| $a->start <=> $b->start
      }
    @features;
}

for my $f (@features) {
  print $f->gff_string,"\n";
}


__END__

=head1 NAME

bp_generate_histogram.pl -- Generate a histogram of Bio::DB::GFF features

=head1 SYNOPSIS

  bp_generate_histogram.pl -d gadfly variation gene:curated

=head1 DESCRIPTION

Use this utility to generate feature density histograms from
Bio::DB::GFF databases.  The result is a GFF data file that is
suitable for loading with load_gff.pl.

=head2 OPTIONS

The following options are recognized:

  Option        Description
  ------        -----------

   --dsn               Data source (default dbi:mysql:test)
   --adaptor       Schema adaptor (default dbi::mysqlopt)
   --user             Username for mysql authentication
   --pass         Password for mysql authentication
   --aggregator       Comma-separated list of aggregators

=head1 BUGS

Please report them.

=head1 SEE ALSO

L

=head1 AUTHOR

Lincoln Stein Elstein@cshl.orgE

Copyright (c) 2001 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut

BioPerl-1.007002/scripts/Bio-DB-GFF/bp_load_gff.pl000444000766000024      1403613155576320 21401 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

use strict;
use warnings;
use lib '../blib/lib';
use Bio::DB::GFF;
use Getopt::Long;

=head1 NAME

bp_load_gff.pl - Load a Bio::DB::GFF database from GFF files.

=head1 SYNOPSIS

  % bp_load_gff.pl -d testdb -u user -p pw
     --dsn 'dbi:mysql:database=dmel_r5_1;host=myhost;port=myport'
        dna1.fa dna2.fa features1.gff features2.gff ...

=head1 DESCRIPTION

This script loads a Bio::DB::GFF database with the features contained
in a list of GFF files and/or FASTA sequence files.  You must use the
exact variant of GFF described in L.  Various
command-line options allow you to control which database to load and
whether to allow an existing database to be overwritten.

This script uses the Bio::DB::GFF interface, and so works with all
database adaptors currently supported by that module (MySQL, Oracle,
PostgreSQL soon).  However, it is slow.  For faster loading, see the
MySQL-specific L and L scripts.

=head2 NOTES

If the filename is given as "-" then the input is taken from standard
input. Compressed files (.gz, .Z, .bz2) are automatically
uncompressed.

FASTA format files are distinguished from GFF files by their filename
extensions.  Files ending in .fa, .fasta, .fast, .seq, .dna and their
uppercase variants are treated as FASTA files.  Everything else is
treated as a GFF file.  If you wish to load -fasta files from STDIN,
then use the -f command-line swith with an argument of '-', as in 

    gunzip my_data.fa.gz | bp_fast_load_gff.pl -d test -f -

On the first load of a database, you will see a number of "unknown
table" errors.  This is normal.

About maxfeature: the default value is 100,000,000 bases.  If you have
features that are close to or greater that 100Mb in length, then the
value of maxfeature should be increased to 1,000,000,000, or another
power of 10.

=head1 COMMAND-LINE OPTIONS

Command-line options can be abbreviated to single-letter options.
e.g. -d instead of --database.

   --dsn            Data source (default dbi:mysql:test)
   --adaptor    Schema adaptor (default dbi::mysqlopt)
   --user          Username for mysql authentication
   --pass      Password for mysql authentication
   --fasta         Fasta file or directory containing fasta files for the DNA
   --create              Force creation and initialization of database
   --maxfeature          Set the value of the maximum feature size (default 100 Mb; must be a power of 10)
   --group               A list of one or more tag names (comma or space separated)
                          to be used for grouping in the 9th column.
   --upgrade             Upgrade existing database to current schema
   --gff3_munge          Activate GFF3 name munging (see Bio::DB::GFF)
   --quiet               No progress reports
   --summary             Generate summary statistics for drawing coverage histograms.
                           This can be run on a previously loaded database or during
                           the load.

=head1 SEE ALSO

L, L, L

=head1 AUTHOR

Lincoln Stein, lstein@cshl.org

Copyright (c) 2002 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut

my ($DSN,$ADAPTOR,$CREATE,$USER,$PASSWORD,$FASTA,$UPGRADE,$MAX_BIN,$GROUP_TAG,$MUNGE,$QUIET,$SUMMARY_STATS);

GetOptions ('dsn:s'                  => \$DSN,
	    'adaptor:s'              => \$ADAPTOR,
	    'u|user:s'               => \$USER,
	    'p|password:s'           => \$PASSWORD,
            'fasta:s'                => \$FASTA,
            'upgrade'                => \$UPGRADE,
            'maxbin|maxfeature:s'    => \$MAX_BIN,
	    'group:s'                => \$GROUP_TAG,
	    'gff3_munge'             => \$MUNGE,
	    'quiet'                  => \$QUIET,
	    'summary'                => \$SUMMARY_STATS,
	    'create'                 => \$CREATE) or (system('pod2text',$0), exit -1);

# some local defaults
$DSN     ||= 'dbi:mysql:test';
$ADAPTOR ||= 'dbi::mysqlopt';
$MAX_BIN ||= 1_000_000_000; # to accomodate human-sized chromosomes

my @args;
push @args,(-user=>$USER)     if defined $USER;
push @args,(-pass=>$PASSWORD) if defined $PASSWORD;
push @args,(-preferred_groups=>[split(/[,\s+]+/,$GROUP_TAG)]) if defined $GROUP_TAG;
push @args,(-create=>1)       if $CREATE;
push @args,(-write=>1);

my $db = Bio::DB::GFF->new(-adaptor=>$ADAPTOR,-dsn => $DSN,@args)
  or die "Can't open database: ",Bio::DB::GFF->error,"\n";

$db->gff3_name_munging(1) if $MUNGE;

if ($CREATE) {
    $SUMMARY_STATS++;
    $MAX_BIN ? $db->initialize(-erase=>1,-MAX_BIN=>$MAX_BIN) :
               $db->initialize(1);
} elsif ($UPGRADE) {
  warn qq(expect to see several "table already exists" messages\n);
  $db->initialize(0);
  my $dbi = $db->dbh;  # get the raw database handle
  my ($count) = $dbi->selectrow_array('SELECT COUNT(*) FROM fnote');
  if (defined($count) && $count > 0) {
    warn qq(fnote table detected.  Translating into fattribute table.  This may take a while.\n);
    $dbi->do("INSERT INTO fattribute VALUES (1,'Note')") or die "failed: ",$dbi->errstr;
    $dbi->do("INSERT INTO fattribute_to_feature (fid,fattribute_id,fattribute_value) SELECT fnote.fid,1,fnote FROM fnote") or die "failed: ",$dbi->errstr;
    warn qq(Schema successfully upgraded.  You might want to drop the fnote table when you're sure everything's working.\n);
  }
}

my (@gff,@fasta);
foreach (@ARGV) {
  if (/\.(fa|fasta|dna|seq|fast)$/i) {
    push @fasta,$_;
  } else {
    push @gff,$_;
  }
}

for my $file (@gff) {
  warn "$file: loading...\n";
  my $loaded = $db->load_gff($file,!$QUIET);
  warn "$file: $loaded records loaded\n";
}

unshift @fasta,$FASTA if defined $FASTA;

for my $file (@fasta) {
  warn "Loading fasta ",(-d $file?"directory":"file"), " $file\n";
  my $loaded = $db->load_fasta($file,!$QUIET);
  warn "$file: $loaded records loaded\n";
}

if ($SUMMARY_STATS) {
    warn "Building summary statistics for coverage histograms...\n";
    $db->build_summary_statistics;
}
BioPerl-1.007002/scripts/Bio-DB-GFF/bp_meta_gff.pl000444000766000024       426613155576320 21374 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

use strict;
use warnings;
use DBI;
use Getopt::Long;
use Bio::DB::GFF;

=head1 NAME

bp_meta_gff.pl - Get/set Bio::DB::GFF meta-data

=head1 SYNOPSIS

  # set the following meta data values
  % bp_meta_gff.pl -d testdb tag1=value1 tag2=value2

  # get the indicated meta data value
  % bp_meta_gff.pl -d testdb tag1 tag2

=head1 DESCRIPTION

This script gets or sets metadata in a Bio::DB::GFF database.  Not all
adaptors support this operation!  To set a series of tags, pass a set
of tag=value pairs to the script.  To get the contents of a series of
tags, pass the bare tag names.

The output from the get operation will be an easily parseable set of
tag=value pairs, one per line.

=head1 COMMAND-LINE OPTIONS

Command-line options can be abbreviated to single-letter options.
e.g. -d instead of --database.

   --database       Mysql database name (default dbi:mysql:test)
   --adaptor    Mysql adaptor (default dbi::mysqlopt)
   --user          Username for mysql authentication
   --pass      Password for mysql authentication

=head1 SEE ALSO

L

=head1 AUTHOR

Lincoln Stein, lstein@cshl.org

Copyright (c) 2002 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut

my ($DSN,$ADAPTOR,$USER,$PASSWORD);

GetOptions ('database:s'    => \$DSN,
	    'adaptor:s'     => \$ADAPTOR,
	    'user:s'      => \$USER,
	    'password:s'  => \$PASSWORD,
	   ) or (system('pod2text', $0), exit -1);

$DSN     ||= 'dbi:mysql:test';
$ADAPTOR ||= 'dbi::mysqlopt';

my @args;
push @args,(-user=>$USER)     if defined $USER;
push @args,(-pass=>$PASSWORD) if defined $PASSWORD;

my $db = Bio::DB::GFF->new(-adaptor=>$ADAPTOR,-dsn => $DSN,@args)
  or die "Can't open database: ",Bio::DB::GFF->error,"\n";

for my $pair (@ARGV) {
  my ($tag,$value) = split /=/,$pair;
  if ($value) {  # set operation
    $db->meta($tag,$value);
    unless ($db->meta($tag) eq $value) {
      print STDERR "value for '$tag' not set; perhaps this adaptor does not support meta data?\n";
    }
  } else {
    print "$tag=",$db->meta($tag),"\n";
  }
}

__END__
BioPerl-1.007002/scripts/Bio-DB-GFF/bp_process_gadfly.pl000444000766000024      1606413155576320 22647 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
if ($ARGV[0]=~/^-?-h/ || @ARGV < 1) {
die <<'USAGE';

This script massages the RELEASE 3 Flybase/Gadfly GFF files located at
http://www.fruitfly.org/sequence/release3download.shtml into the
"correct" version of the GFF format.

To use this script, download the whole genome FASTA file and save it
to disk.  (The downloaded file will be called something like
"na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the
HTML page doesn't give the filename.)  Do the same for the whole
genome GFF annotation file (the saved file will be called something
like "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".)  If
you wish you can download the ZIP compressed versions of these files.

Next run this script on the two files, indicating the name of the
downloaded FASTA file first, followed by the gff file:

 % process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff

The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database
using the following command:

  % bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff 

(Where "fly" is the name of the database.  Change it as appropriate.
The database must already exist and be writable by you!)

The resulting database will have the following feature types
(represented as "method:source"):

  Component:arm              A chromosome arm
  Component:scaffold	     A chromosome scaffold (accession #)
  Component:gap	             A gap in the assembly
  clone:clonelocator         A BAC clone
  gene:gadfly                A gene accession number
  transcript:gadfly          A transcript accession number
  translation:gadfly         A translation
  codon:gadfly               Significance unknown
  exon:gadfly                An exon
  symbol:gadfly              A classical gene symbol
  similarity:blastn          A BLASTN hit
  similarity:blastx          A BLASTX hit
  similarity:sim4            EST->genome using SIM4
  similarity:groupest        EST->genome using GROUPEST
  similarity:repeatmasker    A repeat

IMPORTANT NOTE: This script will *only* work with the RELEASE3 gadfly
files and will not work with earlier releases.

USAGE
;
}

use strict;
use warnings;

foreach (@ARGV) {
  $_ = "gunzip -c $_ |" if /\.gz$/;
}

if ($ARGV[0] =~ /fasta/i) {
  process_fasta();
} else {
  die "call as process_gadfly.pl \"release3_dna.FASTA\" \"release3_features.GFF\"";
}

while (<>) {
  next if /^\#/;
  chomp;
  my ($ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,$cgroup) = split "\t";
  next if $start > $stop;  # something wrong. Don't bother fixing it.

  my $fixed_group = fix_group($csource,$cmethod,$cgroup);
  print join("\t",$ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,$fixed_group),"\n";
  dump_symbol($ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,$cgroup) if $cgroup =~ /symbol/i;
}

sub fix_group {
  my ($source,$method,$group) = @_;
  my (@group,$gene);
  push @group,"Transcript $1" if $group =~ /transgrp=([^; ]+)/;
  push @group,"Gene $1"       if $method eq 'gene' && $group =~ /genegrp=([^; ]+)/;

  $gene ||= qq(Note "FlyBase $1")  if $group =~ /dbxref=FlyBase:(\w+)/;
  $gene ||= qq(Note "GadFly $1")   if $group =~ /genegrp=([^; ]+)/;
  push @group,qq(Note "Symbol $1") if $group =~ /symbol=([^; ]+)/ && "Gene $1" ne $group[0];
  push @group,$gene;
  return join ' ; ',@group;
}

# called when we encounter a gene symbol
sub dump_symbol {
  my ($ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,$cgroup) = @_;
  my ($symbol) = $cgroup=~/symbol=([^;]+)/;
  my ($gene)   = $cgroup=~/genegrp=([^;]+)/;
  return if $symbol eq $gene;
  $cmethod = 'symbol';
  print join("\t",$ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,qq(Symbol "$symbol")),"\n";
}

sub process_fasta {
  my $file = shift @ARGV;
  open my $F, '<', $file or die "Could not read file '$file': $!\n";
  print STDERR "Reading big FASTA file, please be patient...\n";
  my ($current_id,%lengths);
  while (my $line = <$F>) {
    if ($line =~ /^>(\S+)/) {
      $current_id = $1;
      next;
    }
    die "this doesn't look like a fasta file to me" unless $current_id;
    chomp $line;
    $lengths{$current_id} += length $line;
  }
  close $F;

  foreach my $id (sort keys %lengths) {
    print join("\t", $id, 'arm', 'Component', 1, $lengths{$id},
                     '.', '+', '.', qq(Sequence "$id")
               ), "\n";
  }
}

__END__

=head1 NAME

bp_process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser

=head1 SYNOPSIS

  % bp_process_gadfly.pl ./RELEASE2 > gadfly.gff

=head1 DESCRIPTION

This script massages the RELEASE 3 Flybase/Gadfly GFF files located at
http://www.fruitfly.org/sequence/release3download.shtml into the "correct"
version of the GFF format.

To use this script, download the whole genome FASTA file and save it
to disk.  (The downloaded file will be called something like
"na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the
HTML page doesn't give the filename.)  Do the same for the whole
genome GFF annotation file (the saved file will be called something
like "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".)  If
you wish you can download the ZIP compressed versions of these files.

Next run this script on the two files, indicating the name of the
downloaded FASTA file first, followed by the gff file:

 % bp_process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff

The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database
using the following command:

  % bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff 

(Where "fly" is the name of the database.  Change it as appropriate.
The database must already exist and be writable by you!)

The resulting database will have the following feature types
(represented as "method:source"):

  Component:arm              A chromosome arm
  Component:scaffold	     A chromosome scaffold (accession #)
  Component:gap	             A gap in the assembly
  clone:clonelocator         A BAC clone
  gene:gadfly                A gene accession number
  transcript:gadfly          A transcript accession number
  translation:gadfly         A translation
  codon:gadfly               Significance unknown
  exon:gadfly                An exon
  symbol:gadfly              A classical gene symbol
  similarity:blastn          A BLASTN hit
  similarity:blastx          A BLASTX hit
  similarity:sim4            EST->genome using SIM4
  similarity:groupest        EST->genome using GROUPEST
  similarity:repeatmasker    A repeat

IMPORTANT NOTE: This script will *only* work with the RELEASE3 gadfly
files and will not work with earlier releases.

=head1 SEE ALSO

L, L, L

=head1 AUTHOR

Lincoln Stein, lstein@cshl.org

Copyright (c) 2002 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut
BioPerl-1.007002/scripts/Bio-DB-GFF/bp_process_sgd.pl000444000766000024       710713155576320 22134 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

# This script will convert from SGD format to GFF format
# See http://db.yeastgenome.org/schema/Schema.html

use strict;
use warnings;

# hard-coded length data that I couldn't get directly
my %CHROMOSOMES = (I => 230_203,
		   II => 813_139,
		   III => 316_613,
		   IV  => 1_531_929,
		   V   => 576_869,
		   VI => 270_148,
		   VII => 1_090_937,
		   VIII => 562_639,
		   IX => 439_885,
		   X => 745_444,
		   XI => 666_445,
		   XII => 1_078_173,
		   XIII => 924_430,
		   XIV => 784_328,
		   XV  => 1_091_284,
		   XVI => 948_061,
		   Mit => 85_779);
my @ROMAN = qw(I II III IV V VI VII VIII IX X
	       XI XII XIII XIV XV XVI Mit);

if ($ARGV[0] =~ /^--?h/) {
  die <

This script massages the SGD sequence annotation flat files located at
ftp://genome-ftp.stanford.edu/pub/yeast/data_dump/feature/chromosomal_features.tab
into a version of the GFF format suitable for display by the generic
genome browser.

To use this script, get the SGD chromosomal_features.tab file from the
FTP site listed above, and run the following command:

  % process_sgd.pl chromosomal_features.tab > yeast.gff

The yeast.gff file can then be loaded into a Bio::DB::GFF database
using the following command:

  % bulk_load_gff.pl -d  yeast.gff

USAGE
;
}

# first print out chromosomes
# We hard coded the lengths because they are not available in the features table.
for my $chrom (sort keys %CHROMOSOMES) {
  print join("\t",$chrom,'chromosome','Component',1,$CHROMOSOMES{$chrom},'.','.','.',qq(Sequence "$chrom")),"\n";
}

# this is hard because the SGD idea of a feature doesn't really map onto the GFF idea.
while (<>) {
  chomp;
  my($id,$gene,$aliases,$type,$chromosome,$start,$stop,$strand,$sgdid,$sgdid2,$description,$date) = split "\t";
  my $ref = $ROMAN[$chromosome-1];
  $description =~ s/"/\\"/g;
  $description =~ s/;/\\;/g;

  $strand = $strand eq 'W' ? '+' : '-';
  ($start,$stop) = ($stop,$start) if $strand eq '-';
  die "Strand logic is messed up" if $stop < $start;

  if ($gene) {
     my @aliases = split(/\|/,$aliases);
     my $aliases = join " ; ",map {qq(Alias "$_")} @aliases;
     my $group = qq(Gene "$gene" ; Note "$description");
     $group .= " ; $aliases" if $aliases;
     print join("\t",$ref,'sgd','gene',$start,$stop,'.',$strand,'.',$group),"\n";
     $description .= "\\; AKA @aliases" if @aliases;
  }

  print join("\t",$ref,'sgd',$type,$start,$stop,'.',$strand,'.',qq($type "$id" ; Note "$description")),"\n";
}

__END__

=head1 NAME

bp_process_sgd.pl - Massage SGD annotation flat files into a version suitable for the Generic Genome Browser

=head1 SYNOPSIS

  % bp_process_sgd.pl chromosomal_features.tab > yeast.gff

=head1 DESCRIPTION

This script massages the SGD sequence annotation flat files located at
ftp://genome-ftp.stanford.edu/pub/yeast/data_dump/feature/chromosomal_features.tab
into a version of the GFF format suitable for display by the generic
genome browser.

To use this script, get the SGD chromosomal_features.tab file from the
FTP site listed above, and run the following command:

  % bp_process_sgd.pl chromosomal_features.tab > yeast.gff

The yeast.gff file can then be loaded into a Bio::DB::GFF database
using the following command:

  % bulk_load_gff.pl -d  yeast.gff

=head1 SEE ALSO

L, L, L

=head1 AUTHOR

Lincoln Stein, lstein@cshl.org

Copyright (c) 2002 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut


BioPerl-1.007002/scripts/Bio-DB-GFF/bp_process_wormbase.pl000444000766000024      1676513155576320 23230 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

use constant ACEDB => 'sace://aceserver.cshl.org:2005'; 
use strict;
use warnings;
use Ace;

my @framework = qw(mex-3 spe-15 lin-17 unc-11 dhc-1 unc-40 smg-5
		   unc-13 unc-29 eat-16 lin-11 spe-9 par-6 unc-59 unc-54 mab-9 lin-42
		   sri-71 smu-2 vab-1 bli-2 dpy-10 him-14 mig-5 unc-4 bli-1 sqt-1 rol-1
		   his-14 unc-52 unc-45 par-2 let-805 sel-8 mab-21 daf-4 sma-3 lin-39
		   unc-32 tax-4 ced-9 tra-1 nob-1 daf-1 ced-2 lin-1 unc-17 dpy-13 unc-5
		   smg-7 dif-1 lin-49 elt-1 daf-14 dpy-20 dpy-26 unc-30 tra-3 sup-24
		   rho-1 egl-8 unc-60 srh-36 apx-1 unc-62 let-418 dpy-11 let-413 sel-9
		   unc-42 egl-9 sma-1 sqt-3 odr-3 hda-1 unc-76 gcy-20 skr-5 par-4 unc-51
		   egl-17 lim-6 fox-1 fax-1 lon-2 unc-97 unc-6 unc-18 mec-10 sop-1 mab-18
		   sdc-2 odr-7 unc-9 unc-3 gas-1 ace-1);
my %framework = map {$_=>1} @framework;
my %framework_seen = ();

my $USAGE = < wormbase.gff

It may take a while before you see output from this script, since it
must first fetch gene and protein database from the remote AceDB
running at www.wormbase.org.
The wormbase.gff file can then be loaded into a Bio::DB::GFF database
using the following command:

  % bulk_load_gff.pl -d  wormbase.gff
USAGE
;
#'

die $USAGE if $ARGV[0]=~/^-?-h/i;

my $db = Ace->connect(-url=>ACEDB,
		      -query_timeout=>500) or die "Can't open ace database:",Ace->error;

if (-d $ARGV[0]) {
  @ARGV = <$ARGV[0]/*.gff.gz>;
}

@ARGV || die $USAGE;

foreach (@ARGV) { # GFF FILES
  $_ = "gunzip -c $_ |" if /\.gz$/;
}

my (%NOTES,%LOCUS,%GENBANK,%CONFIRMED,%ORFEOME);
get_confirmed($db,\%CONFIRMED);
get_genbank($db,\%GENBANK);
get_loci($db,\%LOCUS);
get_notes($db,\%NOTES);
get_orfeome($db,\%ORFEOME);

while (<>) {
  chomp;
  next if /^\#/;
  my ($ref,$source,$method,$start,$stop,$score,$strand,$phase,$group) = split /\t/;
  next if $source eq 'assembly_tag';  # don't want 'em, don't need 'em
  $ref    =~ s/^CHROMOSOME_//;
  $group  =~ s/CHROMOSOME_//;

  $source ='' if $source eq '*UNKNOWN*';

  if ($method eq 'Sequence' && ($source eq 'curated' || $source eq 'RNA') && $group =~ /Sequence "(\w+\.\d+[a-z]?)"/) {
    my @notes;
    push @notes,map { qq(Note "$_")        } @{$NOTES{$1}}     if $NOTES{$1};
    push @notes,map { qq(Note "$_")        } @{$LOCUS{$1}}     if $LOCUS{$1};
    push @notes,qq(Confirmed_by "$CONFIRMED{$1}")              if $CONFIRMED{$1};
    $group = join ' ; ',$group,@notes;
    if (my $loci = $LOCUS{$1}) {
      foreach (@$loci) {
        print join("\t",$ref,$source,'gene',$start,$stop,$score,$strand,$phase,"Locus $_"),"\n";
        print join("\t",$ref,'framework','gene',$start,$stop,$score,$strand,$phase,"Locus $_"),"\n" 
          if $framework{$_} && !$framework_seen{$_}++;
      }
    }
  }

  if ($method eq 'Sequence' && $source eq 'Genomic_canonical' && $group =~ /Sequence "(\w+)"/) {
    if (my $accession = $GENBANK{$1}) {
      $group .= qq( ; Note "Genbank $accession");
      print join("\t",$ref,'Genbank',$method,$start,$stop,$score,$strand,$phase,"Genbank \"$accession\""),"\n";
    }
  }

  if ($method eq 'reagent' && $source eq 'Orfeome_project' && $group =~ /PCR_product "([^\"]+)"/) {
    my $amp = $ORFEOME{$1};
    $group .= qq( ; Amplified $amp) if defined $amp;
  }

  # fix variant fields: Variant "T" => Note "T"
  $group =~ s/(?:Variant|Insert) "(\w+)"/Note "$1"/;

  # fix UTR fields
  if ($group =~ /UTR "([35])_UTR:(\S+)"/) {
    $method = 'UTR';
    $source = "$1_UTR";
    $group = qq(Sequence "$2");
  }

  print join("\t",$ref,$source,$method,$start,$stop,$score,$strand,$phase,$group),"\n";
}

sub get_loci {
  my ($db,$hash) = @_;  # hash keys are predicted gene names, values are one or more loci names
  my @genes = $db->fetch(-query=>'find Locus Genomic_sequence',-filltag=>'Genomic_sequence');
  foreach my $obj (@genes) {
    my @genomic = $obj->Genomic_sequence or next;
    foreach (@genomic) {
      push @{$hash->{$_}},$obj;
    }
  }
}

sub get_notes {
  my ($db,$hash) = @_;  # hash keys are predicted gene names, values are one or more brief identifications
  my @genes = $db->fetch(-query=>'find Sequence Brief_identification',-filltag=>'Brief_identification');
  foreach my $obj (@genes) {
    my @notes = $obj->Brief_identification or next;
    $hash->{$obj} = \@notes;
  }
}

sub get_genbank {
  my ($db,$hash) = @_;   # hash keys are cosmid names, values are genbank accessions (1 to 1)
  my @cosmids = $db->fetch(-query=>'find Genome_Sequence Database',-filltag=>'Database');
  for my $cosmid (@cosmids) {
    my ($database,undef,$accession) = $cosmid->Database(1)->row;
    next unless $accession;
    $hash->{$cosmid} = $accession;
  }
}

sub get_confirmed {
  my ($db,$hash) = @_;  # hash keys are predicted gene names, values are confirmation type
  my @confirmed = $db->fetch(-query=>'find Sequence Confirmed_by',-filltag=>'Confirmed_by');
  foreach my $obj (@confirmed) {
    my $confirmed_by = $obj->Confirmed_by || 'Unknown';
    $hash->{$obj} = $confirmed_by;
  }
}

sub get_orfeome {
  my ($db,$hash) = @_;
  my @mv_primers = $db->fetch(-query=>'find PCR_Product mv*',-filltag=>'Amplified');
  for my $obj (@mv_primers) {
    my $amplified = $obj->Amplified;
    $hash->{$obj} = $amplified;
  }
}

__END__

=head1 NAME

bp_process_wormbase.pl - Massage WormBase GFF files into a version suitable for the Generic Genome Browser

=head1 SYNOPSIS

  % bp_process_wormbase.pl ./WS61 > wormbase.gff

=head1 DESCRIPTION

This script massages the Wormbase GFF files located at
ftp://www.wormbase.org/pub/wormbase/GENE_DUMPS into a version of the
GFF format suitable for display by the generic genome browser.  It
mainly adds comments to the annotations and designates certain
well-spaced genetic loci as framework landmarks.

This script requires the AcePerl distribution, which is available on
CPAN (look for the "Ace" module).

To use this script, get the WormBase GFF files from the FTP site
listed above and place them in a directory.  It might be a good idea
to name the directory after the current release, such as WS61.  You do
not need to uncompress the files.

Then give that directory as the argument to this script and capture
the script's output to a file:

  % bp_process_wormbase.pl ./WS61 > wormbase.gff

It may take a while before you see output from this script, since it
must first fetch gene and protein database from the remote AceDB
running at www.wormbase.org.
The wormbase.gff file can then be loaded into a Bio::DB::GFF database
using the following command:

  % bulk_load_gff.pl -d  wormbase.gff

=head1 SEE ALSO

L, L, L

=head1 AUTHOR

Lincoln Stein Elstein@cshl.orgE

Copyright (c) 2002 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut

BioPerl-1.007002/scripts/Bio-DB-SeqFeature-Store000755000766000024          013155576320 21175 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl000444000766000024      1107113155576320 26056 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

use strict;
use warnings;

use Getopt::Long;
use File::Spec;
use Bio::DB::SeqFeature::Store;

my $DSN      = 'dbi:mysql:test';
my $USER     = '';
my $PASS     = '';
my $ADAPTOR  = 'DBI::mysql';
my $NAME     = 0;
my $TYPE     = 0;
my $ID       = 0;
my $VERBOSE  = 1;
my $TEST     = 0;
my $FAST     = 0;

GetOptions(
	   'dsn|d=s'       => \$DSN,
	   'adaptor=s'   => \$ADAPTOR,
	   'verbose!'    => \$VERBOSE,
           'dryrun|dry-run' => \$TEST,
           'name|n'      => \$NAME,
           'type|t'      => \$TYPE,
           'id'          => \$ID,
           'fast|f'          => \$FAST,
	   'user=s'      => \$USER,
	   'password=s'  => \$PASS,
	   ) || die <  
  Options:
          -d --dsn        The database name ($DSN)
          -a --adaptor    The storage adaptor to use ($ADAPTOR)
          -n --name       Delete features based on name or wildcard pattern (default)
          -t --type       Delete features based on type
          -i --id         Delete features based on primary id
          -v --verbose    Turn on verbose progress reporting (default)
             --noverbose  Turn off verbose progress reporting
          --dryrun        Dry run; report features to be deleted without actually deleting them
          -u --user       User to connect to database as
          -p --password   Password to use to connect to database
          -f --fast       Deletes each item instantly not atomic for full dataset (mainly for deleting massive datasets linked to a type)

Examples:
  
 Delete from mysql database volvox features named f08 f09 f10
     $0 -d volvox -n f08 f09 f10

 Delete features whose names start with f  
     $0 -d volvox -n 'f*'

 Delete all features of type remark, source example
     $0 -d volvox -t remark:example

 Delete all remark features, regardless of source
     $0 -d volvox -t 'remark:*'

 Delete the feature with ID 1234
     $0 -d volvox -i 1234

 Delete all features named f* from a berkeleydb database
     $0 -a berkeleydb -d /usr/local/share/db/volvox -n 'f*'

Remember to protect wildcards against shell interpretation by putting
single quotes around them!
END
    ;

if ($NAME+$TYPE+$ID > 1) {
    die "Please provide only one of the --name, --type or --id options.\nRun \"$0 --help\" for usage.\n";
}

unless (@ARGV) {
    die "Please provide a list of feature names, types or ids.\n Run \"$0 --help\" for usage.\n";
}

my $mode = $ID   ? 'id'
          :$TYPE ? 'type'
          :$NAME ? 'name'
          :'name';


my @options;
@options = ($USER,$PASS) if $USER || $PASS;

my $store = Bio::DB::SeqFeature::Store->new(
					    -dsn     => $DSN,
					    -adaptor => $ADAPTOR,
					    -user    => $USER,
					    -pass    => $PASS,
					    -write    => 1,
    )
  or die "Couldn't create connection to the database";

my @features = retrieve_features($store,$mode,\@ARGV);

if ($VERBOSE || $TEST) {
    print scalar (@features)," feature(s) match.\n\n";
    my $heading;
    foreach (@features) {
	printf "%-20s %-20s %-12s\n%-20s %-20s %-12s\n",
	       'Name','Type','Primary ID',
	       '----','----','----------'
		   unless $heading++;
	printf "%-20s %-20s %-12d\n",$_->display_name,$_->type,$_->primary_id;
    }
    print "\n";
}

if (@features && !$TEST) {
    if($FAST) {
      my $del = 0;
      foreach my $feat(@features) {
        my @tmp_feat = ($feat);
        my $deleted = $store->delete(@tmp_feat);
        $del++ if($deleted);
        if ($VERBOSE && $deleted) {
          print 'Feature ',$del," successfully deleted.\n";
        } elsif (!$deleted) {
          die "An error occurred. Some or all of the indicated features could not be deleted.";
        }
      }
    }
    else {
        my $deleted = $store->delete(@features);
        if ($VERBOSE && $deleted) {
	        print scalar(@features)," features successfully deleted.\n";
        } elsif (!$deleted) {
	        die "An error occurred. Some or all of the indicated features could not be deleted.";
        }
    }
}

exit 0;

sub retrieve_features {
    my($db,$mode,$list) = @_;
    my @features;
    if ($mode eq 'name') {
	@features = map {$db->get_features_by_alias($_)} @$list;
    }
    elsif ($mode eq 'type') {
	my $regexp = glob2regexp(@$list);
	my @types  = grep {/$regexp/} $db->types;
	@features  = $db->get_features_by_type(@types) if @types;
    }
    elsif ($mode eq 'id') {
	@features  = grep {defined $_} map {$db->get_feature_by_primary_id($_)} @$list;
    }
    return @features;
}

sub glob2regexp {
    my @globs = map {
	$_ = quotemeta($_);
	s/\\\*/.*/g;
	s/\?/./g;
	$_ } @_;
    return '^(?:'.join('|',@globs).')$';
 }
BioPerl-1.007002/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl000444000766000024       454013155576320 25424 0ustar00cjfieldsstaff000000000000#!/usr/bin/env perl
# AUTHOR: malcolm.cook@stowers-institute.org

use strict;
use warnings;

use Carp;
use Getopt::Long;
use File::Spec;
use Bio::DB::SeqFeature::Store;

#use Carp::Always;

my $DSN;
my $ADAPTOR;
my $VERBOSE  = 1;
my $USER     = '';
my $PASS     = '';
my @gff3opt;

GetOptions(
	   'dsn=s'       => \$DSN,
	   'adaptor=s'   => \$ADAPTOR,
	   'user=s'      => \$USER,
	   'password=s'  => \$PASS,
	   'gff3opt=i{,}'    => \@gff3opt,
	  ) || die <features().

END

$ADAPTOR     ||= 'DBI::mysql';
$DSN         ||= $ADAPTOR eq 'DBI::mysql' ? "mysql_read_default_file=$ENV{HOME}/.my.cnf" : '';

my $store = Bio::DB::SeqFeature::Store->new(
					    -dsn     => $DSN,
					    -adaptor => $ADAPTOR,
					    -user    => $USER,
					    -pass    => $PASS,
					   )
  or die "Couldn't create connection to the database";

# on signals, give objects a chance to call their DESTROY methods
$SIG{TERM} = $SIG{INT} = sub {   undef $store; die "Aborted..."; };

my $seq_stream = $store->get_seq_stream(@ARGV)  or die "failed to get_seq_stream(@ARGV)"; 
while (my $seq = $seq_stream->next_seq) {
  ### 20100725 // genehack
  # Try to call a gff3_string() method, but fall back to gff_string() if $seq
  # doesn't support that. Note that gff_string() is required per
  # Bio::SeqFeatureI, while gff3_string() is not. Currently, only
  # Bio::SeqFeature::Lite implements gff3_string().
  if ( $seq->can( 'gff3_string' )) {
    print $seq->gff3_string(@gff3opt) . "\n";
  }
  elsif ( $seq->can( 'gff_string' )) {
    # since we intend on getting a GFF3 string, make sure to pass the version
    $seq->gff_format->gff_version(3);
    print $seq->gff_string() . "\n";
  }
  else {
    confess "sequence object $seq does not support gff3_string() or gff_string() methods!"
  }
}

exit 0;
BioPerl-1.007002/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl000555000766000024      1614013155576320 25540 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

use strict;
use warnings;

## Used to output the 'usage' message
use Pod::Usage;

## Used to parse command line options
use Getopt::Long;

## Used to create temporary files, if necessary
use File::Spec;

## BioPerl!
use Bio::DB::SeqFeature::Store;
use Bio::DB::SeqFeature::Store::GFF3Loader;



## The available options. Note, these defaults are 'hard coded' into
## the USAGE POD, so if you change one of the defaults (you shouldn't),
## you should update the USAGE.

my $DSN			= 'dbi:mysql:test';
my $SFCLASS		= 'Bio::DB::SeqFeature';
my $ADAPTOR		= 'DBI::mysql';
my $NAMESPACE;
my $VERBOSE		= 1;
my $FAST		= 0;
my $TMP			= File::Spec->tmpdir();
my $IGNORE_SEQREGION	= 0;
my $CREATE		= 0;
my $USER 		= '';
my $PASS 		= '';
my $COMPRESS		= 0;
my $INDEX_SUB		= 1;
my $NOALIAS_TARGET	= 0;
my $SUMMARY_STATS	= 0;
my $NOSUMMARY_STATS  = 0;
my $FTS = 0;

## Two flags based on http://stackoverflow.com/questions/1232116
## how-to-create-pod-and-use-pod2usage-in-perl
my $opt_help;
my $opt_man;

GetOptions( 'd|dsn=s'			=> \$DSN,
	    's|seqfeature=s'		=> \$SFCLASS,
	    'n|namespace=s'		=> \$NAMESPACE,
	    'a|adaptor=s'		=> \$ADAPTOR,
	    'v|verbose!'		=> \$VERBOSE,
	    'f|fast'			=> \$FAST,
	    'T|temporary-directory=s'	=> \$TMP,
	    'i|ignore-seqregion'	=> \$IGNORE_SEQREGION,
	    'c|create'			=> \$CREATE,
	    'u|user=s'			=> \$USER,
	    'p|password=s'		=> \$PASS,
	    'z|zip'			=> \$COMPRESS,
	    'S|subfeatures!'		=> \$INDEX_SUB,

	    ## Any good single letter choices here?
	    'noalias-target'		=> \$NOALIAS_TARGET,
	    'summary'			=> \$SUMMARY_STATS,
        'N|nosummary'    => \$NOSUMMARY_STATS,
	    'fts'			=> \$FTS,

	    ## I miss '--help' when it isn't there!
	    'h|help!'			=> \$opt_help,
	    'm|man!'			=> \$opt_man,
	  )
  or pod2usage( -message =>
		"\nTry 'bp_seqfeature_load.pl --help' for more information\n",
		-verbose => 0,
		-exitval => 2,
	      );

## Should we output usage information?
pod2usage( -verbose => 1 ) if $opt_help;
pod2usage( -verbose => 2 ) if $opt_man;

## Did we get any files to process?
@ARGV
  or pod2usage( -message =>
		"\nYou need to pass some GFF or fasta files to load\n",
		-verbose => 0,
		-exitval => 2,
	      );

pod2usage( -message => "\n--fts requires --create\n",
           -verbose => 0,
           -exitval => 2,
) if ($FTS and not $CREATE);


## POD

=head1 NAME

bp_seqfeature_load.pl - Load GFF into a SeqFeature database

=head1 DESCRIPTION

Pass any number of GFF or fasta format files (or GFF with embedded
fasta) to load the features and sequences into a SeqFeature
database. The database (and adaptor) to use is specified on the
command line. Use the --create flag to create a new SeqFeature
database.

=head1 SYNOPSIS

 bp_seqfeature_load.pl [options] gff_or_fasta_file1 [gff_or_fasta_file2 [...]]

Try 'bp_seqfeature_load.pl --help' or '--man' for more information.

=head1 OPTIONS

=over 4

=item -d, --dsn

DBI data source (default dbi:mysql:test)

=item -n, --namespace

The table prefix to use (default undef) Allows several independent
sequence feature databases to be stored in a single database

=item -s, --seqfeature

The type of SeqFeature to create... RTSC (default Bio::DB::SeqFeature)

=item -a, --adaptor

The storage adaptor (class) to use (default DBI::mysql)

=item -v, --verbose

Turn on verbose progress reporting (default true) Use --noverbose to
switch this off.

=item -f, --fast

Activate fast loading. (default 0) Only available for some adaptors.

=item -T, --temporary-directory

Specify temporary directory for fast loading (default
File::Spec->tmpdir())

=item -i, --ignore-seqregion

If true, then ignore ##sequence-region directives in the GFF3 file
(default, create a feature for each region)

=item -c, --create

Create the database and reinitialize it (default false) Note, this
will erase previous database contents, if any.

=item -u, --user

User to connect to database as

=item -p, --password

Password to use to connect to database

=item -z, --zip

Compress database tables to save space (default false)

=item -S, --subfeatures

Turn on indexing of subfeatures (default true) Use --nosubfeatures to
switch this off.

=item --fts

Index the attribute table for full-text search (default false). Applicable
only when --create is specified. Currently applicable to the DBI::SQLite
storage adaptor only (using the most recent supported FTS indexing method,
which may not be portable to older DBI::SQLite versions). 

=item --summary

Generate summary statistics for coverage graphs (default false) This
can be run on a previously loaded database or during the load. It will
default to true if --create is used.

=item -N, --nosummary

Do not generate summary statistics to save some space and load time (default if
--create is not specified, use this option to explicitly turn off summary
statistics when --create is specified)

=item --noalias-target

Don't create an Alias attribute whose value is the target_id in a
Target attribute (if the feature contains a Target attribute, the
default is to create an Alias attribute whose value is the target_id
in the Target attribute)

=back

Please see http://www.sequenceontology.org/gff3.shtml for information
about the GFF3 format. BioPerl extends the format slightly by adding a
##index-subfeatures directive. Set this to a true value if you wish
the database to be able to retrieve a feature's individual parts (such
as the exons of a transcript) independently of the top level feature:

  ##index-subfeatures 1

It is also possible to control the indexing of subfeatures on a
case-by-case basis by adding "index=1" or "index=0" to the feature's
attribute list. This should only be used for subfeatures.

Subfeature indexing is true by default. Set to false (0) to save lots
of database space and speed performance. You may use --nosubfeatures
to force this.

=cut





if ($FAST) {
  -d $TMP && -w $TMP
    or die "Fast loading is requested, but I cannot write into the directory $TMP";
  $DSN .= ";mysql_local_infile=1" if $ADAPTOR =~ /mysql/i && $DSN !~ /mysql_local_infile/;
}

my @options;
@options = ($USER,$PASS) if $USER || $PASS;

my $store = Bio::DB::SeqFeature::Store->new
(
    -dsn        => $DSN,
    -namespace  => $NAMESPACE,
    -adaptor    => $ADAPTOR,
    -tmpdir     => $TMP,
    -user       => $USER,
    -pass       => $PASS,
    -write      => 1,
    -create     => $CREATE,
    -compress   => $COMPRESS,
    -fts        => $FTS,
)
or die "Couldn't create connection to the database";

$store->init_database('erase') if $CREATE;
$SUMMARY_STATS++               if $CREATE; # this is a good thing

my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new
(
    -store              => $store,
    -sf_class           => $SFCLASS,
    -verbose            => $VERBOSE,
    -tmpdir             => $TMP,
    -fast               => $FAST,
    -ignore_seqregion   => $IGNORE_SEQREGION,
    -index_subfeatures  => $INDEX_SUB,
    -noalias_target     => $NOALIAS_TARGET,
    -summary_stats      => $NOSUMMARY_STATS ? 0 : $SUMMARY_STATS,
)
or die "Couldn't create GFF3 loader";

# on signals, give objects a chance to call their DESTROY methods
$SIG{TERM} = $SIG{INT} = sub {  undef $loader; undef $store; die "Aborted..."; };

$loader->load(@ARGV);

exit 0;
BioPerl-1.007002/scripts/DB000755000766000024          013155576320 15332 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/scripts/DB/TAG000444000766000024        24613155576320 16007 0ustar00cjfieldsstaff000000000000These are scripts to fetch sequence data from local and remote
sequence repositories using the Open Bio Database Access registry
protocol (http://obda.open-bio.org).
BioPerl-1.007002/scripts/DB/bp_biofetch_genbank_proxy.pl000444000766000024      2005513155576320 23240 0ustar00cjfieldsstaff000000000000#!perl

# dbfetch style caching proxy for GenBank
use strict;
use warnings;
use CGI qw(:standard);
use HTTP::Request::Common;
use LWP::UserAgent;
use Cache::FileCache;

use vars qw(%GOT $BUFFER %MAPPING $CACHE);

use constant CACHE_LOCATION => '/usr/tmp/dbfetch_cache';
use constant MAX_SIZE   => 100_000_000;  # 100 megs, roughly
use constant CACHE_DEPTH => 4;
use constant EXPIRATION => "1 week";
use constant PURGE      => "1 hour";

%MAPPING = (genbank => {db=>'nucleotide',
			rettype => 'gb'},
	    genpep  => {db=>'protein',
			rettype => 'gp'});
# we're doing everything in callbacks, so initialize globals.
$BUFFER = '';
%GOT    = ();

print header('text/plain');

param() or print_usage();

my $db     = param('db');
my $style  = param('style');
my $format = param('format');
my $id     = param('id');
my @ids    = split /\s+/,$id;

$format = 'genbank' if $format eq 'default';  #h'mmmph

$MAPPING{$db}        or error(1=>"Unknown database [$db]");
$style  eq 'raw'     or error(2=>"Unknown style [$style]");
$format eq 'genbank' or error(3=>"Format [$format] not known for database [$db]");

$CACHE = Cache::FileCache->new({cache_root          => CACHE_LOCATION,
				default_expires_in  => EXPIRATION,
				cache_DEPTH         => CACHE_DEPTH,
				namespace           => 'dbfetch',
				auto_purge_interval => PURGE});

# handle cached entries
foreach (@ids) {
  if (my $obj = $CACHE->get($_)) {
    $GOT{$_}++;
    print $obj,"//\n";
  }
}

# handle the remainder
@ids = grep {!$GOT{$_}} @ids;
if (@ids) {
  my $request = POST('https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi',
		     [rettype    => $MAPPING{$db}{rettype},
		      db         => $MAPPING{$db}{db},
		      tool       => 'bioperl',
		      retmode    => 'text',
		      usehistory => 'n',
		      id         => join(',',@ids),
		     ]
		    );

  my $ua = LWP::UserAgent->new;
  my $response = $ua->request($request,\&callback);

  if ($response->is_error) {
    my $status = $response->status_line;
    error(6 => "HTTP error from GenBank [$status]");
  }
}

my @missing_ids = grep {!$GOT{$_}} @ids;
foreach (@missing_ids) {
  error(4=>"ID [$_] not found in database [$db]",1);
}

# my $response = $response->content;

sub process_record {
  my $record = shift;
  print "$record//\n";
  my ($locus)       = $record =~ /^LOCUS\s+(\S+)/m;
  my ($accession)   = $record =~ /^ACCESSION\s+(\S+)/m;
  my ($version,$gi) = $record =~ /^VERSION\s+(\S+)\s+GI:(\d+)/m;
  foreach ($locus,$accession,$version,$gi) {
    $GOT{$_}++;
    $CACHE->set($_,$record);
  }
}

sub callback {
  my $data = shift;
  $BUFFER .= $data;
  my $index = 0;
  while (($index = index($BUFFER,"//\n\n",$index))>=0) {
    my $record = substr($BUFFER,0,$index);
    $index += length("//\n\n");
    substr($BUFFER,0,$index) = '';
    process_record($record);
  }
}



sub print_usage {
  print <<'END';
This script is intended to be used non-interactively.

Brief summary of arguments:
URL

This interface does not specify what happens when biofetch is called
in interactive context. The implementations can return the entries
decorated with HTML tags and hypertext links.

A URL for biofetch consists of four sections:

			e.g.
1. protocol		http://
2. host			www.ebi.ac.uk
3. path to program	/Tools/dbfetch/dbfetch
4. query string		?style=raw;format=embl;db=embl;id=J00231


QUERY STRING

The query string options are separated from the base URL (protocol +
host + path) by a question mark (?) and from each other by a semicolon
';' (or by ampersand '&'). See CGI GET documents at
http://www.w3.org/CGI/). The order of options is not critical. It is
recommended to leave the ID to be the last item.

Input for options should be case insensitive.


option: db

  Option  : db
  Descr   : database name
  Type    : required
  Usage   : db=genpep | db=genbank
  Arg     : string 

Currently this server accepts "genbank" and "genpep"

option: style

  Option  : style
  Descr   : +/- HTML tags
  Type    : required
  Usage   : style=raw | db=html
  Arg     : enum (raw|html)

In non-interactive context, always give "style=raw". This uses
"Content-Type: text/plain". If other content types are needed (XML),
this part of the spesifications can be extended to accommodate them.

This server only accepts "raw".


option: format

  Option  : format
  Descr   : format of the database entries returned
  Type    : optional
  Usage   : format=genbank
  Arg     : enum

Format defaults to the distribution format of the database (embl for
EMBL database). If some other supported format is needed this option
is needed (E.g. formats for EMBL: fasta, bsml, agave).

This server only accepts "genbank" format.

option: id

  Option  : id
  Descr   : unique database identifier(s)
  Type    : required
  Usage   : db=J00231 | id=J00231+HSFOS
  Arg     : string 

The ID option should be able to process all UIDS in a database. It
should not be necessary to know if the UID is an ID, accession number
or accession.version.

The number of entry UIDs allowed is implementation specific. If the
limit is exceeded, the the program reports an error. The UIDs should
be separated by spaces (use '+' in a GET method string).


ERROR MESSAGES

The following standardized one line messages should be printed out in
case of an error.

ERROR 1 Unknown database [$db].
ERROR 2 Unknown style [$style].
ERROR 3 Format [$format] not known for database [$db].
ERROR 4 ID [$id] not found in database [$db].
ERROR 5 Too many IDs [$count]. Max [$MAXIDS] allowed.

END
;

exit 0;
}

sub error {
  my ($code,$message,$noexit) = @_;
  print "ERROR $code $message\n";
  exit 0 unless $noexit;
}

__END__

=head1 NAME

bp_biofetch_genbank_proxy.pl - Caching BioFetch-compatible web proxy for GenBank

=head1 SYNOPSIS

  Install in cgi-bin directory of a Web server.  Stand back.

=head1 DESCRIPTION

This CGI script acts as the server side of the BioFetch protocol as
described in http://obda.open-bio.org/Specs/.  It provides two
database access services, one for data source "genbank" (nucleotide
entries) and the other for data source "genpep" (protein entries).

This script works by forwarding its requests to NCBI's eutils script,
which lives at https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi.
It then reformats the output according to the BioFetch format so the
sequences can be processed and returned by the Bio::DB::BioFetch
module.  Returned entries are temporarily cached on the Web server's
file system, allowing frequently-accessed entries to be retrieved
without another round trip to NCBI.

=head2 INSTALLATION

You must have the following installed in order to run this script:

   1) perl
   2) the perl modules LWP and Cache::FileCache
   3) a web server (Apache recommended)

To install this script, copy it into the web server's cgi-bin
directory.  You might want to shorten its name; "dbfetch" is
recommended.

There are several constants located at the top of the script that you
may want to adjust.  These are:

CACHE_LOCATION

This is the location on the filesystem where the cached files will be
located.  The default is /usr/tmp/dbfetch_cache.

MAX_SIZE

This is the maximum size that the cache can grow to.  When the cache
exceeds this size older entries will be deleted automatically.  The
default setting is 100,000,000 bytes (100 MB).

EXPIRATION

Entries that haven't been accessed in this length of time will be
removed from the cache.  The default is 1 week.

PURGE

This constant specifies how often the cache will be purged for older
entries.  The default is 1 hour.

=head1 TESTING

To see if this script is performing as expected, you may test it with
this script:

 use Bio::DB::BioFetch;
 my $db = Bio::DB::BioFetch->new(-baseaddress=>'http://localhost/cgi-bin/dbfetch',
	 			 -format     =>'genbank',
				 -db         =>'genbank');
 my $seq = $db->get_Seq_by_id('DDU63596');
 print $seq->seq,"\n";

This should print out a DNA sequence.

=head1 SEE ALSO

L, L

=head1 AUTHOR

Lincoln Stein, Elstein-at-cshl.orgE

Copyright (c) 2003 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut

BioPerl-1.007002/scripts/DB/bp_bioflat_index.pl000444000766000024       701713155576320 21321 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl


=head1 NAME

bp_bioflat_index.pl - index sequence files using Bio::DB::Flat

=head1 DESCRIPTION

 Create or update a biological sequence database indexed with the
 Bio::DB::Flat indexing scheme.  The arguments are a list of flat files
 containing the sequence information to be indexed.

=head1 USAGE

 bp_bioflat_index.pl  file1 file2 file3...

 Options:

     --create              Create or reinitialize the index.  If not specified,
                           the index must already exist.

     --format      The format of the sequence files.  Must be one
                           of "genbank", "swissprot", "embl" or "fasta".

     --location      Path to the directory in which the index files
                           are stored.

     --dbname        The symbolic name of the database to be created.

     --indextype     Type of index to create.  Either "bdb" or "flat".
                           "binarysearch" is the same as "flat".

Options can be abbreviated.  For example, use -i for --indextype.

The following environment variables will be used as defaults if the 
corresponding options are not provided:

     OBDA_FORMAT      format of sequence file
     OBDA_LOCATION    path to directory in which index files are stored
     OBDA_DBNAME      name of database
     OBDA_INDEX       type of index to create

=cut

use strict;
use warnings;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::DB::Flat;
use Getopt::Long;
use File::Path qw(mkpath rmtree);

my ($CREATE,$FORMAT,$LOCATION,$DBNAME,$INDEXTYPE);

GetOptions( 'create'      => \$CREATE,
				'format:s'    => \$FORMAT,
				'location:s'  => \$LOCATION,
				'dbname:s'    => \$DBNAME,
				'indextype:s' => \$INDEXTYPE );

$FORMAT    = $ENV{OBDA_FORMAT}    unless defined $FORMAT;
$LOCATION  = $ENV{OBDA_LOCATION}  unless defined $LOCATION;
$DBNAME    = $ENV{OBDA_DBNAME}    unless defined $DBNAME;
$INDEXTYPE = $ENV{OBDA_INDEXTYPE} unless defined $INDEXTYPE;

my $root = 'Bio::Root::Root';
my $io   = 'Bio::Root::IO';

# confirm that database directory is there
defined $LOCATION or 
  $root->throw("please provide a base directory with the --location option");

-d $LOCATION or 
  $root->throw("$LOCATION is not a valid directory; use --create to create a new index");

defined $DBNAME or 
  $root->throw("please provide a database name with the --dbname option");

defined $FORMAT or 
  $root->throw("please specify the format for the input files with the --format option");

unless (defined $INDEXTYPE) {
	$INDEXTYPE = 'flat';
	$root->warn('setting index type to "flat", use the --indextype option to override');
}

# Confirm that database is there and that --create flag is sensible.
my $path = $io->catfile($LOCATION,$DBNAME,'config.dat');
if (-e $path) {
  if ($CREATE) {
    $root->warn("existing index detected; deleting.");
    rmtree($io->catfile($LOCATION,$DBNAME),1,1);
  } else {
    $root->warn("existing index detected; ignoring --indextype and --format options.");
    undef $INDEXTYPE;
  }
}
elsif (!$CREATE) {
  $root->throw("Cannot find database config file at location $path; use --create to create a new index");
}

# open for writing/updating
my $db = Bio::DB::Flat->new(-directory  => $LOCATION,
									 -dbname     => $DBNAME,
									 $INDEXTYPE ? (
														-index      => $INDEXTYPE
													  )
									 : (),
									 -write_flag => 1,
									 -format     => $FORMAT) or 
  $root->throw("can't create Bio::DB::Flat object");

my $entries = $db->build_index(@ARGV);

print STDERR "(Re)indexed $entries entries.\n ";

__END__
BioPerl-1.007002/scripts/DB/bp_biogetseq.pl000444000766000024       273313155576320 20474 0ustar00cjfieldsstaff000000000000#!perl
#
# OBDA Registry compliant sequence retrieval script
#
# Copyright Heikki Lehvaslaiho 
# You may distribute this program under the same terms as perl itself


use Bio::DB::Registry;
use Bio::SeqIO;
use Getopt::Long;
use strict;
use warnings;

my ($help, $format, $namespace, $dbname) = ('', 'embl', 'acc', 'embl');
GetOptions ("help" => \$help, "format=s" => \$format,
            "namespace=s" => \$namespace, "dbname=s" => \$dbname );
if ($help || !@ARGV) {
  system("perldoc $0");
  exit 0;
}

my $get_function = 'get_Seq_by_'. $namespace;

my $registry = new Bio::DB::Registry();
while (my $id = shift) {
    my $db = $registry->get_database($dbname);
    my $seq = $db->$get_function($id);

    if ($seq) {
        my $out = new Bio::SeqIO('-format' => $format);
        $out->write_seq($seq);
    } else {
        print STDERR "Could not find sequence with identifier [$id]\n";
    }
}

=head1 NAME

bp_biogetseq - sequence retrieval using OBDA registry

=head1 DESCRIPTION

This script retrieves sequences from the source defined by users
registry setup.  The current alternatives are from a local indexed
file, sql database or over the web.

=head1 USAGE

  Usage: bp_biogetseq --dbname embl --format embl
                   --namespace acc id [ ids... ]
         * dbname defaults to embl
         * format defaults to embl
         * namespace defaults to 'acc' ['id', 'acc', 'version']
         * unnamed arguments are ids in the given namespace

=cut

BioPerl-1.007002/scripts/DB/bp_flanks.pl000444000766000024      2216713155576320 20013 0ustar00cjfieldsstaff000000000000#!perl
# -*-Perl-*-
#
# Heikki Lehvaslaiho 
# Finding flanking sequences for a variant.
#
#
#   v. 1     16 Mar 2001
#   v. 1.1    9 Aug 2001 interface change, more info in fasta header
#   v. 2.0   23 Nov 2001 new code from the flanks CGI program
#                         support for EMBL-like positions
#   v. 3.0   21 Feb 2003 new command line interface


use Bio::PrimarySeq;
use Bio::SeqIO;
use Bio::DB::EMBL;
use Bio::DB::GenBank;
use Getopt::Long;
use strict;
use warnings;

use constant VERSION => '3.0';

my $help = '';
my $flank = 100;              # flank length on both sides of the region
my $in_format = 'EMBL';       # format of the file to read in
my @pos;                      # position(s) in the sequence


GetOptions ("help" => \$help, "flanklength=i" => \$flank,
            "position=s" => \@pos );

@pos = split(/,/,join(',',@pos));

system("perldoc $0") if $help;
system("perldoc $0") unless @ARGV;
print STDERR "\nYou need to provide --position option\n" and system("perldoc $0") 
    unless @pos;

my $file = shift;
$file || system("perldoc $0");

my $seq = get_seq($file);
exit 0 unless $seq;

&extract($seq, \@pos, $flank);

#
## end main
#

sub get_seq {
    my ($file) = @_;
    my $IN_FORMAT = 'EMBL';	# format of the local file on disk

    if (-e $file ) {		# local file
	my $in  = Bio::SeqIO->new('-file' => $file,
				  '-format' => $IN_FORMAT);
	$seq = $in->next_seq();
    }
    elsif ($file =~ /\./) {	# sequence version from GenBank
	eval {
	    my $gb = new Bio::DB::GenBank;
	    $seq = $gb->get_Seq_by_version($file);
	};
    } else {			# plain accession mumber from more reliable EMBL
	eval {
	    my $gb = new Bio::DB::EMBL;
	    $seq = $gb->get_Seq_by_acc($file);
	};
	
    }
    print STDERR "Could not find sequence [$file]" && return unless $seq;
    return $seq;
}

sub extract {
    my ($seq, $pos, $flank) = @_;
    my ($out_seq);
    my $OUT_FORMAT = 'FASTA';	# output format, going into STDOUT
    my $strand = 1;		# default for the forward strand

    my $out = Bio::SeqIO->new('-format' => $OUT_FORMAT);

    my $count = 1;
    foreach my $idpos (@$pos) {

	my ($id, $pos_range, $start, $end, $allele_len);
	my $inbetween = 0;	# handle 23^24 notation as well as plain integer (24)
                          	# but set flag and make corrections when needed

	if ($idpos =~ /:/ ) {	# id and position separator
	    ($id, $pos_range) = split /:/, $idpos;
	} else {		# no id
	    $id = $count;
	    $count++;
	    $pos_range = $idpos;
	}
	$strand = -1 if $pos_range =~ /-$/; # opposite strand
	$pos_range = $1 if $pos_range =~ /(.+)-/; # remove trailing '-'

	if ($pos_range =~ /\^/) { # notation 23^24 used
	    ($start, $end) = split /\^/, $pos_range;
	    print STDERR $id, ": Give adjacent nucleotides flanking '^' character, not [",
	        $start, "] and [", $end, "]\n" and next
		unless $end == $start + 1;
	    $end = $start;
	    $inbetween = 1;
	} else {		#  notation 23..24 used
	    ($start, $end) = split /\.\./, $pos_range;
	}
	$end ||= $start;	# notation 23 used
	print STDERR $id, ": Start can not be larger than end. Not [",
	        $start, "] and [", $end, "]\n" and next
		if $start > $end;
	$allele_len = $end - $start;

	# sanity checks
	next unless defined $start && $start =~ /\d+/ && $start != 0;
	print STDERR "Position '$start' not in sequence '$file'\n",  and next
	    if $start < 1 or $start > $seq->length;
	print STDERR "End position '$end' not in sequence '$file'\n",  and next
	    if $end < 1 or $end > $seq->length;
	
	# determine nucleotide positions
	# left edge
	my $five_start = $start - $flank;
	$five_start = 1 if $five_start < 1; # not outside the sequence
	# right edge
	my $three_end = $start + $allele_len + $flank;
	$three_end = $seq->length if $start + $allele_len + $flank > $seq->length;
	$three_end-- if $inbetween;

	# extract the sequences
	my $five_prime = lc $seq->subseq($five_start , $start - 1); # left flank
	my $snp = uc $seq->subseq($start, $end); # allele (always > 0 length)
	$snp = lc $snp if $inbetween;

	my $three_prime;	# right flank
	if ($end < $seq->length) { # make sure we are not beyond reference sequece
	    $three_prime = lc $seq->subseq($end + 1, $three_end);
	} else {
	    $three_prime = '';
	}

	# allele positions in local, extracted coordinates
	my $locpos = length($five_prime) + 1;
	my $loc_end;
	if ($allele_len) {
	    $loc_end = "..". ($locpos+$allele_len);
	} else {
	    $loc_end = '';
	    $loc_end = '^'. ($locpos+1) if $inbetween;
	}
	# build FASTA id and description line
	my $fastaid = uc($id). "_". uc($file).
	    " oripos=$pos_range strand=$strand allelepos=$locpos$loc_end";

	#build BioPerl sequence objects
	if ($strand == -1) {
	    my $five_prime_seq = new Bio::PrimarySeq(-alphabet=>'dna',-seq=>$five_prime);
	    my $snp_seq = new Bio::PrimarySeq(-alphabet=>'dna',-seq=>$snp);
	    my $three_prime_seq = new Bio::PrimarySeq(-alphabet=>'dna',-seq=>$three_prime);

	    my $str = $three_prime_seq->revcom->seq. " ".
		$snp_seq->revcom->seq. " ". $five_prime_seq->revcom->seq;
	    $str =~ s/ //g;
	    $out_seq = new Bio::PrimarySeq (-id => $fastaid,
					    -alphabet=>'dna',
					    -seq => $str );
	} else {
	    my $str = $five_prime. " ". $snp. " ". $three_prime;
	    $str =~ s/ //g;
	    $out_seq = new Bio::PrimarySeq (-id => $fastaid,
					    -alphabet=>'dna',
					    -seq => $str );
	}
	$out->write_seq($out_seq); # print sequence out
    }
}



=head1 NAME

bp_flanks - finding flanking sequences for a variant in a sequence position

=head1 SYNOPSIS

  bp_flanks --position POS [-p POS ...]  [--flanklen INT]
         accession | filename

=head1 DESCRIPTION

This script allows you to extract a subsequence around a region of
interest from an existing sequence. The output if fasta formatted
sequence entry where the header line contains additional information
about the location.

=head1 OPTIONS

The script takes one unnamed argument which be either a file name in
the local file system or a nucleotide sequence accession number.


  -p         Position uses simple nucleotide sequence feature table
  --position notation to define the region of interest, typically a
             SNP or microsatellite repeat around which the flanks are
             defined.

             There can be more than one position option or you can
             give a comma separated list to one position option.

             The format of a position is:

                 [id:] int | range | in-between [-]

             The optional id is the name you want to call the new
             sequence. If it not given in joins running number to the
             entry name with an underscore.

             The position is either a point (e.g. 234), a range (e.g
             250..300) or insertion point between nucleotides
             (e.g. 234^235)

             If the position is not completely within the source
             sequence the output sequence will be truncated and it
             will print a warning.

             The optional hyphen [-] at the end of the position
             indicates that that you want the retrieved sequence to be
             in the opposite strand.


  -f         Defaults to 100. This is the length of the nucleotides
  --flanklen sequence retrieved on both sides of the given position.

             If the source file does not contain 

=head1 OUTPUT FORMAT

The output is a fasta formatted entry where the description file
contains tag=value pairs for information about where in the original
sequence the subsequence was taken.

The ID of the fasta entry is the name given at the command line joined
by hyphen to the filename or accesion of the source sequence. If no id
is given a series of consecutive integers is used.

The tag=value pairs are:

=over 3

=item oripos=int

position in the source file

=item strand=1|-1

strand of the sequence compared to the source sequence

=item allelepos=int

position of the region of interest in the current entry.
The tag is the same as used by dbSNP@NCBI

=back

The sequence highlights the allele variant position by showing it in
upper case and rest of the sequence in lower case characters.

=head1 EXAMPLE

  % bp_flanks ~/seq/ar.embl

  >1_/HOME/HEIKKI/SEQ/AR.EMBL oripos=100 strand=1 allelepos=100
  taataactcagttcttatttgcacctacttcagtggacactgaatttggaaggtggagga
  ttttgtttttttcttttaagatctgggcatcttttgaatCtacccttcaagtattaagag
  acagactgtgagcctagcagggcagatcttgtccaccgtgtgtcttcttctgcacgagac
  tttgaggctgtcagagcgct


=head1 TODO

The input files are assumed to be in EMBL format and the sequences are
retrieved only from the EMB database. Make this more generic and use
the registry.


head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing lists  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Heikki Lehvaslaiho

Email:  Eheikki-at-bioperl-dot-orgE

=cut
BioPerl-1.007002/scripts/DB-HIV000755000766000024          013155576320 15756 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/scripts/DB-HIV/bp_hivq.pl000444000766000024      3551213155576320 20126 0ustar00cjfieldsstaff000000000000#!perl
# command-line script for HIV sequence queries
# using HIV.pm and HIVQuery.pm

=head1 NAME

bp_hivq.PL - an interactive command-line interface to L and L

=head1 SYNOPSIS

 $ perl bp_hivq.PL
 hivq> query C[subtype] SI[phenotype]
 hivq> prerun
 80 sequences returned
 Query: C[subtype] SI[phenotype]
 hivq> outfile csi.fas
 hivq> run
 Download complete.
 hivq> outfile dsi.fas
 hivq> run D[subtype] SI[phenotype]
 Download complete.
 hivq> count
 25 sequences returned
 Query: D[subtype] SI[phenotype]
 hivq> exit
 $

=head1 DESCRIPTION

The BioPerl modules L and L
together allow batch queries against the Los Alamos National
Laboratories' HIV Sequence Database using a simple query
language. C provides both an example of the use of these
modules, and a standalone interactive command-line interface to the
LANL HIV DB. Simple commands allow the user to retrieve HIV sequences
and annotations using the query language implemented in
L. Visit the man pages for those modules for
more details.

=head1 USAGE

Run the script using C or, in Unix, C<./bp_hivq.PL>. You will see
the

 hivq>

prompt. Type commands with queries to retrieve sequence and annotation
data.  See the SYNOPSIS for a sample session. Available commands
are described below.

=head2 TIPS

The LANL database is pretty complex and extensive. Use the C facility to
explore the available database tables and fields. To identify aliases for a particular field, use C. For example, to find a short alias to the
weirdly named field C, do

 hivq> find alias seq_sample.ssam_second_receptor

which returns

 coreceptor             second_receptor

Now, instead of the following query

 hivq> run C[subtype] CCR5[seq_sample.ssam_second_receptor]

you know you can do

 hivq> run C[subtype] CCR5[coreceptor]

Use the C command to set the file that receives the retrieved
sequences. You can change the current output file simply by issuing a
new C command during the session. The output file defaults to
standard output.

Use the C command to validate a query without hitting the
database. Use the C or C commands to get a count of
sequence hits for a query without retrieving the data. Use C or
C to perform a complete query, retrieving sequence data into the
currently set output files.

To process C commands in batch, create a text file
(C, for example) containing desired commands one per
line. Then execute the following from the shell:

 $ cat bp_hivq.cmd | perl bp_hivq.PL

=head1 COMMANDS

Here is a complete list of commands. Options in single brackets (C<[req_option]>) are
required; options in double brackets (C<[[opt_option]]>) are optional.

 confirm            : Toggle interactive confirmation before
                      executing queries
 exit               : Quit script
 find               : Explore database schema
  find tables                 Display all database tables
  find fields                 Display all database fields (columns)
  find fields [table]         Display all fields in [table]
  find alias [field]          Display valid aliases for [field]
 help [[command]]   : Show command help
                      if [[command]] not specified, list all
                      available commands
 id                 : Display current session id
 outfile [filename] : Set file for collecting retrieved data
 ping               : Check if LANL DB is available
 prerun [[query]]   : Execute query but retrieve hit count only
                      if [[query]] not specified, use current query
 query [query]      : Validate and set current query
 run [[query]]      : Execute query and retrieve data
                      if [[query]] not specified, use current query
 state              : Display current state of the script

 bye                : Alias for 'exit'
 config             : Alias for 'state'
 count              : Alias for 'prerun'
 do                 : Alias for 'run'
 out                : Alias for 'outfile'
 quit               : Alias for 'exit'

=head1 OPTIONS

 -v : verbose; turns on the internal debug() function

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Mark A. Jensen

Mark A. Jensen  Emaj@fortinbras.usE

=cut

$|=1;
use strict;
use warnings;
use Term::ReadLine;
use Bio::DB::HIV;
use Bio::DB::Query::HIVQuery;
use Bio::SeqIO;
use Error qw(:try);

use Getopt::Std;
our ($opt_v);
getopts('v');
my $db = new Bio::DB::HIV;

my $q = new Bio::DB::Query::HIVQuery();
my $schema = $q->_schema;
my $seqio;
my @cmds = qw(
bye
config
confirm
count
do
exit
find
help
id
out
outfile
ping
prerun
query
quit
run
state
);

my %state = (
    'confirm'    => 0,
    'outfile'    => {'text'=>'[stdout]','handle'=>\*STDOUT},
    'query'      => '',
    'session_id' => '',
    'timeout'    => '',
    'curct'      => 0
);

my %help = (
    'bye' => 'bye: End script',
    'config' => 'config: Print current configuration state of hivq',
    'confirm' => 'confirm: Toggle user confirmation of query execution',
    'count' => 'count [[query string]]: Get number of sequences available for query',
    'do' => 'do [[query string]]: Run query to completion',
    'exit' => 'exit: End script',
    'find' => join("\n","find tables: Print all LANL table names",
               "find fields: Print all field names",
               "find fields [tablename]: Print all fields in specified table",
               "find aliases [fieldname]: Print all valid aliases for specified field",
		   "find options [fieldname/alias]: Print valid match options for specified field"),
    'help' => 'help [[command]]: Get description of command',
    'id' => 'id: Print current session id',
    'out' => 'out [output filename]: Set filename to hold returned sequences',
    'outfile' => 'outfile [output filename]: Set filename to hold returned sequences',
    'ping' => 'ping: Ping LANL database',
    'prerun' => 'prerun [[query string]]: Get number of sequences available',
    'query' => 'query [[query string]]: Validate and set current query string',
    'quit' => 'quit: End script',
    'run' => 'run [[query string]]: Run query to completion',
    'state' => 'state: Print current configuration state of hivq',
    );
my $done = 0;
debug("We have arrived.");
#### main loop
my ($cmd, @tok);
my $prompt = "hivq> ";
my $term = new Term::ReadLine 'hivq';
CMD:
while ( !$done ) {
    @tok=();$cmd='';
    for ( $cmd = $term->readline($prompt) ) {
	chomp;
	s/^\s+//; #trim whsp
	$term->addhistory($_);
	@tok = split(/\s+/);
	$tok[0] = lc $tok[0]; # normalize
	for ($tok[0]) {
	    (!$_ || /^\#/) && do {
		next CMD;
	    };
	    !(grep(/^$tok[0]$/, @cmds)) && do {
		error("Unrecognized command \'$tok[0]\'");
		next CMD;
	    };
	    (m/^quit$/ || m/^bye$/ || m/^exit$/) && do {
		my $fh = $state{outfile}->{handle};
		unless ($fh == \*STDOUT) {
		    close $fh;
		}
		$done=1;
		next CMD;
	    };
	    m/^confirm$/ && do {
		$state{confirm} = !$state{confirm};
		print "User confirmation before running query: ". ($state{confirm} ? "yes" : "no")."\n";
		next CMD;
	    };
	    (m/^outfile$/ || m/^out$/) && do {
		unless ($tok[1]) {
		    error('Output filename not specified');
		    next CMD;
		}
		my $fh;
		eval {
		    open $fh, ">$tok[1]" or die $!;
		};
		if ($@) {
		    error($@);
		}
		else {
		    my $oldfh = $state{outfile}->{handle};
		    if ($state{outfile}->{text} ne '[stdout]') {
			close($oldfh);
		    }
		    $state{outfile}->{handle} = $fh;
		    $state{outfile}->{text} = $tok[1];
		}
		next CMD;
	    };
	    m/^query$/ && do {
		my $query = join(' ', @tok[1..$#tok]);
		if ($query) {
		    $q->_reset;
		    $q->query($query);
		}
		else {
		    if ($state{query}) {
			print "Current query: $state{query}\n";
		    }
		    else {
			print "No query set\n";
		    }
		    next CMD;
		}
		try { #catch errors
		    $q->_do_query(0);
		}
		catch Error with {
		    my $E = shift;
		    error($E->text);
		    next CMD;
		};
		$state{session_id} = $q->_session_id;
		$state{query} = $query;
		next CMD;
	    };
	    (m/^prerun$/ || m/^count$/) && do {
		my $query = join(' ', @tok[1..$#tok]);
		if (!$query) {
		    if (!$q->query()) {
			error('No query currently set');
			next CMD;
		    }
		    elsif ($q->{'_RUN_LEVEL'} >= 1 &&
			($q->query() eq $state{query})) {
			outputPrerun();
			next CMD;
		    }
		    # else, fallthrough to prerun current query
		}
		else { # new query
		    $q->_reset;
		    $q->query($query);
		    try {
			$q->_do_query(0);
		    }
		    catch Error with {
			my $E = shift;
			error($E->text);
			next CMD;
		    };
		}
		# on success:
		$state{confirm} && do { next CMD unless getConfirm(); };
		$state{session_id} = $q->_session_id;
		$state{query} = $query;
		try {
		    $q->_do_query(1);
		}
		catch Error with {
		    my $E = shift;
		    error($E->text);
		    next CMD;
		};
		# on success:
		$state{curct} = $q->count;
		$state{query} = $q->query;
		outputPrerun();
		next CMD;

	    };
	    (m/^run$/ || m/^do$/) && do {
		my $query = join(' ', @tok[1..$#tok]);
		if (!$query) {
		    unless (defined $q->{'_RUN_LEVEL'} && $q->{'_RUN_LEVEL'} < 2) {
			error('No query currently set');
			next CMD;
		    }
		}
		else { # new query
		    $q->_reset;
		    $q->query($query);
		    try {
			$q->_do_query(0);
		    }
		    catch Error with {
			my $E = shift;
			error($E->text);
			next CMD;
		    };
		    $state{query} = $query;
		    $state{curct} = 0;
		    $state{session_id} = $q->_session_id;
		}
		# on success:
		$state{confirm} && do { next CMD unless getConfirm(); };
		try {
		    $q->_do_query(2);
		    $seqio = $db->get_Stream_by_query($q);
		}
		catch Error with {
		    my $E = shift;
		    error($E->text);
		    next CMD;
		};
		# on success:
		$state{curct} = $q->count;
		# output the seqs
		if ($q->count) {
		    outputSeqs($seqio);
		}
		else {
		    error('No sequences returned');
		}
		next CMD;
	    };
	    m/^find$/ && do {
		outputFind(@tok);
		next CMD;
	    };
	    m/^help$/ && do {
		unless ($tok[1]) {
		    outputUsage();
		    next CMD;
		}
		if (grep(/$tok[1]/, @cmds)) {
		    print $help{$tok[1]}, "\n";
		}
		else {
		    error("Command \'$tok[1]\' unrecognized\n");
		}
		next CMD;
	    };
	    (m/^state$/ || m/^config$/) && do {
		foreach my $k (sort keys %state) {
		    if (ref($state{$k}) eq 'HASH') {
			print "$k: ".$state{$k}->{text}."\n";
		    }
		    else {
			print "$k: ";
			if ($k eq 'confirm') {
			    print $state{$k} ? "yes" : "no";
			    print "\n";
			}
			else {
			    print "$state{$k}\n";
			}
		    }
		}
		next CMD;
	    };
	    do {
		error("Command currently unimplemented\n");
		next CMD;
	    };
	}
    }
}

### end main

sub error {
    my $msg = shift;
    if ($msg =~ /MSG:/) {
	($msg) = grep (/^MSG:/, split(/\n|\r/,$msg));
	$msg =~ s/^MSG: *//;
	$msg =~ s/\sat\s.*$//;
    }
    print STDERR "hivq: $msg\n";
    return 1;
}

sub outputPrerun {
    print (($state{curct} ? $state{curct} : "No")
	. " sequence"
	. ($state{curct}>1 ? "s" : "")
	. " returned\n");
    print "Query: ".$state{query}."\n";
    return 1;
}

sub outputSeqs {
    my ($seqio) = @_;
    my @ret;
    while (my $seq = $seqio->next_seq) {
	my $nameline = ">";
	$nameline .= $seq->annotation->get_value('Special', 'accession').
	    '('.$seq->id.') ';
	# loop through categories:
	foreach my $cat ($seq->annotation->get_keys()) {
	    foreach my $an ($seq->annotation->get_keys($cat)) {
		next if ($an eq 'accession');
		my $value = $seq->annotation->get_value($cat, $an);
		# next line: kludge to skip if there's an annotation
		# object instead of a value (I believe this is a bug)
		next if ref($value);
		$nameline .= "\t".join('=', "'$an'", "'".$value."'");
	    }
	}
	push @ret, $nameline."\n";
	push @ret, $seq->seq()."\n";
    }
    doOutputSeqs(@ret);
}

sub doOutputSeqs {
    my @lines = @_;
    if (!@lines) {
	error("No sequences to output");
    }
    my $fh = $state{outfile}->{handle};
    print $fh @lines;
    print "Download complete\n";
    return 1;
}

sub getConfirm {
    print "Run query? [y/n]";
    my $ans = ;
    ($ans =~ /^[yY]/) && do {return 1;};
    return 0;
}

sub outputUsage {
    print "Available commands:\n";
    outputInColumns(\@cmds);
    return 1;
}

sub outputFind {
    my @tok = @_;
    for my $arg ($tok[1]) {
	!$arg && do {
	    print $help{find},"\n";
	    return;
	};
	($arg =~ m/^tables$/) && do {
	    outputInColumns([$schema->tables]);
	    return;
	};
	($arg =~ m/^fields$/) && do {
	    my $tbl = $tok[2];
	    if (!$tbl) {
		outputInColumns([$schema->fields]);
	    }
	    else {
		unless (grep /^$tbl$/, $schema->tables) {
		    error("Table \'$tbl\' not valid");
		    return;
		}
		outputInColumns([grep /^$tbl/, $schema->fields()]);
	    }
	    return;
	};
	($arg =~ /^options$/) && do {
	    my $fld = $tok[2];
	    my @aliases = $schema->aliases($fld);
	    if (!@aliases) {
		unless (grep /^$fld$/, $schema->aliases) {
		    error("Field \'$tok[2]\' not valid");
		    return;
		}
		foreach ($schema->fields) {
		    if ( grep /$fld/, $schema->aliases($_) ) {
			$fld = $_;
			last;
		    }
		}
		# on success: $fld is set to valid field
	    }
	    my @options = sort {$a cmp $b}  $schema->options($fld);
	    @options = (@options ? @options : ('Free text'));
	    outputInColumns(\@options);
	    return;
	};
	do {
	    ($arg =~ /^alias/) && ($arg = $tok[2]);
	    if (grep /$arg/, $schema->fields) {
		my @aliases = sort $schema->aliases($arg);
		if (@aliases) {
		    outputInColumns(\@aliases);
		}
		else {
		    error("No aliases to field \'$arg\'");
		}
	    }
	    else {
		error("Field \'$arg\' not valid");
	    }
	    return;
	};
    }
}




sub outputInColumns {
    my ($items, $n, $w) = @_;
    my $i = 0;
    my @items = @$items;
    my $maxl = length([sort {length($b)<=>length($a)} @items]->[0]);
    $n ||= int(60/($maxl+3)) || 1;
    $w ||= $maxl+3;
    my $coll = int(@items/$n);
    $coll == @items/$n ? $coll : ++$coll;
    my @t;
    for my $j (0..$n-1) {
	if ($j<$n-1) {
	    $t[$j] = [@items[$j*$coll..$j*$coll+$coll-1]];
	}
	else {
	    $t[$j] = [@items[$j*$coll..$#items]];
	}
    }
    @items = map { my $j = $_; map { $t[$_]->[$j] || () } (0..$#t) } (0..scalar(@{$t[0]})-1);
    foreach (@items) {
	$_ .= (' ' x ($w-length($_)));
    }
    while ($i < @items) {
	print join('', map { $_ || ()  } @items[$i..$i+$n-1] ),"\n";
	$i+=$n;
    }
    return 1;
}

sub debug {
    print STDERR shift()."\n" if $opt_v;
    return;
}
BioPerl-1.007002/scripts/das000755000766000024          013155576320 15614 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/scripts/das/README000444000766000024        14213155576320 16606 0ustar00cjfieldsstaff000000000000For a lightweight Distributed Annotation System (DAS) server, see
http://www.biodas.org/servers/

BioPerl-1.007002/scripts/das/TAG000444000766000024        21013155576320 16260 0ustar00cjfieldsstaff000000000000This directory is currently empty.  For the Lightweight Distributed
Annotation System (LDAS) server, see http://www.biodas.org/servers/
BioPerl-1.007002/scripts/das/bp_das_server.pl000444000766000024      3507013155576320 21151 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

# minimal annotation server

use strict;
use warnings;
use Apache::DBI;
use Bio::DB::GFF;
use CGI qw/header path_info param url request_method/;
use Digest::MD5 'md5_hex';
use Carp;

my $VERSION = 'DAS/1.00';
(my $BASENAME = url(-absolute=>1)) =~ s!http://[^/]+/!!;

use vars qw($DB %ERRCODES %CATEGORIES $HEADER
	    %DSN %TYPE2CATEGORY %TYPEOBJECTS
	    %EXCLUDE
	   );

#         dsn          description              db server    map master
%DSN = (
	'chr22_transcripts'     => [q(EST-predicted transcripts on chr22 from Jean Thierry-Mieg),
				    'dbi:mysql:database=tm_chr22;host=brie3.cshl.org',
				    'http://servlet.sanger.ac.uk:8080/das/ensembl110']
	);
########################################################################################

%ERRCODES = (
	     200 => 'OK',
	     400 => 'Bad command',
	     401 => 'Bad data source',
	     402 => 'Bad command arguments',
	     403 => 'Bad reference object',
	     404 => 'Bad stylesheet',
	     405 => 'Coordinate error',
	     500 => 'Internal server error (oops)',
	     501 => 'Unimplemented feature',
	     );

%CATEGORIES = (
	       component     => [qw(Sequence:Contig Sequence:Link Sequence:Genomic_canonical 
				    static_golden_path_contig:ensembl ensembl_contig:ensembl)],
	       transcription => [qw(Sequence:curated polyA_site stop CpG misc_signal intron exon transcript CDS)],
	       homology      => [qw(similarity)],
	       repeat        => [qw(Alu repeat repeat_region repeat_unit misc_feature)],
	       structural    => [qw(Clone cosmid OLIGO PCR_product structural compression Comment Conflict)],
	       experimental  => [qw(experimental RNAi)],
);

%EXCLUDE = (
	    'static_golden_path_contig:ensembl' => 1,
	    'ensembl_contig:ensembl' => 1,
	    'Sequence:Contig' => 1,
	    );

while (my($c,$v) = each %CATEGORIES) { # invert nicely
  for my $typename (@$v) {
    my $typeobj      = Bio::DB::GFF::Typename->new($typename);
    $TYPE2CATEGORY{$typeobj} = $c;
    $TYPEOBJECTS{$typeobj}   = $typeobj;
  }
}

$HEADER = 0;
my ($junk,$DSN,$OPERATION) = split '/',path_info();

do { error_header('invalid request',400); exit 0 } unless $DSN;
do { list_dsns();   exit 0 } if $DSN eq 'dsn' or $OPERATION eq 'dsn';
do { error_header('invalid data source, use the dsn command to get list',401); exit 0 } unless $DSN{$DSN};

do { error_header('Could not open database',500); exit 0 }
     unless $DB = openDB($DSN);

do { entry_points(); exit 0 } if $OPERATION eq 'entry_points';
do { types();        exit 0 } if $OPERATION eq 'types';
do { features();     exit 0 } if $OPERATION eq 'features';
do { stylesheet();   exit 0 } if $OPERATION eq 'stylesheet';

error_header('invalid request',400);
exit 0;

# -----------------------------------------------------------------
sub openDB {
  my $name = shift;
  my $db = Bio::DB::GFF->new(-adaptor=>'dbi::mysqlopt',-dsn=>$DSN{$name}[1]);
  $db->automerge(0);
  $db->debug(0);
  return $db;
}

# -----------------------------------------------------------------
sub list_dsns {
  my $j = ' 'x3;
  ok_header();
  print qq(\n\n);
  print "\n";

  for my $dsn (sort keys %DSN) {
    print "$j\n";
    print qq($j$j$DSN{$dsn}[0]\n);
    print qq($j$j$DSN{$dsn}[2]/\n);
    print qq($j$jThis is the $DSN{$dsn}[0] database\n);
    print "$j\n";
  }
  print "\n";
}

# -----------------------------------------------------------------
sub entry_points {
  my $segments = get_segments();

  my @parts;
  if ($segments) {
    @parts = map { get_segment_obj(@$_) } @$segments;
    @parts = map { $_->contained_features(-types=>['Sequence:Link','Sequence:Contig','Sequence:Genomic_canonical'],-merge=>0) } @parts;
  } else {
    @parts = grep {$_->name =~ /^CHR/i} $DB->features(-types=>['Sequence:Link','Sequence:Contig','Sequence:Genomic_canonical'],-merge=>0);
  }

  my $url = get_url();

  ok_header();
  print <



END
;

  for my $part (@parts) {
    $part->absolute(1);
    my $name  = $part->name;
    my $st    = $part->start;
    my $en    = $part->stop;
    my $class = $part->class;
    my $length = $part->length;
    my $orientation = $part->strand > 0 ? '+' : '-';
    my $subparts = $part->source =~ /Link|Chromosome|Contig/ ? 'yes' : 'no';
    print qq($name\n);
  }
  print "\n\n";
}

# -----------------------------------------------------------------
# get the features for the segment indicated
sub features {
  my @segments = get_segments() or return;

  my $summary = param('summary');
  my $url = get_url();
  my @filter = param('type');
  my @category = param('category');
  push @filter,make_categories(@category);


  ok_header();
  print <



END
;

  foreach (@segments) {
    my ($reference,$refclass,$start,$stop) = @$_;
    my $seq = get_segment_obj($reference,$refclass,$start,$stop);
    unless ($seq) {
      print qq(\n);
      next;
    }

    if (lc(param('category')) eq 'component') {
      dump_framework($seq);
      next;
    }

    my $r = $seq->refseq;
    my $s = $seq->start;
    my $e = $seq->stop;
    ($s,$e) = ($e,$s) if $s > $e;

    print qq(\n);

    my $iterator = $seq->features(-types=>\@filter,-merge=>0,-iterator=>1);

    while (my $f = $iterator->next_seq) {
      my $type        = $f->type;
      next if $EXCLUDE{$type};

      my $flabel      = $f->info || $f->type;
      my $source      = $f->source;
      my $method      = $f->method;
      my $start       = $f->start;
      my $end         = $f->stop;
      my $score       = $f->score;
      my $orientation = $f->strand;
      my $phase       = $f->phase;
      my $group       = $f->group;
      my $id          = $f->id;

      $phase       ||= 0;
      $orientation ||= 0;
      $score       ||= '-';
      $orientation = $orientation >= 0 ? '+' : '-';

      # hack hack hack
      my $category = transmute($type);
      ($start,$end) = ($end,$start) if $start > $end;

      # group stuff
      my $hash       = $group;
#      my @notes      = $f->notes;
      my @notes;
      my $info       = $f->info;
      my $group_info;

      if (ref($info)) {
	my $class = $info->class;
	$id = "$class:$info";
	if ($DSN eq 'elegans') {
	  $group_info = qq($info);
	}
      } else {
	$hash       = md5_hex($group);
	$group_info = join "\n",map {qq($_)} @notes;
      }

      my ($target,$target_info);
      if (($target = $f->target) && $target->can('start')) {
	my $start = $target->start;
	my $stop  = $target->stop;
	$target_info = qq();
      }

      if ($category eq 'component') {
	my $strt = 1;
	my $stp  = $stop - $start + 1;
	$target_info = qq();
      }

    my $map;
    if ($type =~ /Segment|Link|Genomic_canonical|Contig/i) { $map = qq( reference="yes") } else { $map = qq() }
    $map .= qq( subparts="yes") if $type =~ /Segment|Link/i;

    ## Need not print feature for map in annotation services
    ## The next 2 lines are ucommented at Wash U:
    # if (($DSN ne "welegans") && ($c eq "structural")) {
    # } else {

      print <
      $type
      $method
      $start
      $end
      $score
      $orientation
      $phase
END
;
      if ($hash) {
	print qq(      \n);
	print qq(        $group_info\n)  if $group_info;
	print qq(        $target_info\n) if $target_info;
	print qq(      \n);
      }
      print <
END
      ;
      # }  # End Wash U if statement
    }

    print qq(\n);
  }

print <

END
}

sub dump_framework {
  my $seq = shift;
  my $start = $seq->start;
  my $stop  = $seq->stop;

  my @parts = $seq->contained_features(-type=>['Sequence:Link','Sequence:Genomic_canonical','Sequence:Contig'],-merge=>0);

  print qq(\n);

  for my $part (@parts) {
    my ($st,$en)    = ($part->start,$part->stop);
    my $orientation = $part->strand >= 0 ? '+1' : '-1';
    my $length = $part->length;
    my $type   = $part->type;
    my $method = $type->method;
    my $description = qq(category="component" reference="yes");
    $description .= qq( subparts="yes") unless $part->source eq 'Genomic_canonical';

    print <
   $part
   $method
   $st
   $en
   -
   $orientation
   -
   
      $part
   

END
  ;
  }
  print qq(\n);
}

sub types {
  return all_types() unless param('ref') or param('segment');

  my $type    = param('entry_type') || 'Sequence';
  my $summary = param('summary');
  my $url     = get_url();
  my @filter  = param('type');

  my @segments = get_segments() or return;

  ok_header();

  print <



END
;

  foreach (@segments) {
    my ($reference,$class,$start,$stop) = @$_;
    next unless $reference;
    my $seq = get_segment_obj($reference,$class,$start,$stop) or next;
    unless ($seq) {  #empty section
      print qq(\n);
      print qq(\n);
      next;
    }

    my $s = $seq->start;
    my $e = $seq->stop;

    # use absolute coordinates -- people expect it
    my $name = $seq->refseq;

    print qq(\n);

    my @args = (-enumerate=>1);
    push @args,(-types=>\@filter) if @filter;
    my %histogram = $seq->types(@args);
    foreach (keys %histogram) {
      my ($method,$source) = split ':';
      my $count = $histogram{$_};
      my $category  = transmute($_);
      print qq(\t$count\n)
	unless $EXCLUDE{$_};
    }
    print qq(\n);
  }
print <

END
}

# list of all the types
sub all_types {
  my @methods = $DB->types;

  ok_header();
  my $url = get_url();
  print <




END
    ;

  for my $id (@methods) {
    next if $EXCLUDE{$id};
    my $category = transmute($id);
    my $method   = $id->method;
    my $source   = $id->source;
    print qq(\t\n);
  }

  print <


END
    ;

}

# Big time kludge -- just outputs the prebuilt stylesheet in this
# directory.  Used primarily for testing.
sub stylesheet {
  ok_header();
  open my $STYLE, '<', "style.xml" or die "Could not read file 'style.xml': $!\n";
  while(<$STYLE>) {
    print $_;
  }
  close $STYLE;
}

# really, really bad shit
# calculate type and category from acedb type and method
sub transmute {
    my $type = shift;

    # look in $TYPE2CATEGORY first to see if we have an exact match
    my $category = $TYPE2CATEGORY{$type};
    return $category if $category;

    # otherwise do a fuzzy match using the values of %TYPEOBJECTS
    for my $typeobj (values %TYPEOBJECTS) {
      warn "comparing $typeobj to $type";

      if ($typeobj->match($type)) {
	$category = $TYPE2CATEGORY{$typeobj};  # fetch category for this object
	$TYPE2CATEGORY{$type} = $category;     # remember this match for later
	return $category;
      }
    }
    return 'miscellaneous';  # no success
}

# -----------------------------------------------------------------
sub get_url {
  my $url = url(-path=>1, -query=>1);
  $url =~ tr/&/\;/;
  return $url;
}

# -----------------------------------------------------------------
sub error_header {
  my ($message,$code) = @_;
  $code ||= 500;
#  $code = "$code $ERRCODES{$code}";
  print header(-type          =>'text/plain',
	       -X_DAS_Version => $VERSION,
	       -X_DAS_Status  => $code,
	      ) unless $HEADER++;
  return if request_method() eq 'HEAD';
  print $message;
}

sub ok_header {
  print header(-type          =>'text/plain',
	       -X_DAS_Version => $VERSION,
	       -X_DAS_Status  => "200 OK", 
	      ) unless $HEADER++;
}

# phony dtd
sub dtd {
    ok_header();
    print <
DTD
}

# -----------------------------------------------------------------
sub get_segments {
  # extended segment argument
  my @segments;
  foreach (param('segment')) {
    my ($ref,$start,$stop) = /^(\S+?)(?::(\d+),(\d+))?$/;
    push @segments,[$ref,$start,$stop];
  }
  push @segments,[scalar param('ref'),scalar param('start'),scalar param('stop')] if param('ref');
  return unless @segments;

  foreach (@segments){
    my ($reference,$start,$stop) = @$_;
    my $class = param('entry_type') || 'Sequence';
    my $name  = $reference;

    if ($reference =~ /^(\w+):(\S+)$/) {
      $class = $1;
      $name  = $2;
    }
    my @values = ($name,$class,$start,$stop);
    $_ = \@values;
  }

  return wantarray ? @segments : \@segments;
}

# -----------------------------------------------------------------
sub get_segment_obj {
  my ($reference,$class,$start,$stop) = @_;
  my @args = (-name=>$reference);
  push @args,(-class=>$class) if defined $class;
  push @args,(-start=>$start) if defined $start;
  push @args,(-stop=>$stop)   if defined $stop;

  my $segment = $DB->segment(@args) or return;
  return $segment;
}


# -----------------------------------------------------------------
sub make_categories {
  my @filter;
  for my $category (@_) {
    my $c = lc $category;
    push @filter,@{$CATEGORIES{$c}} if $CATEGORIES{$c};
    push @filter,$category         unless  $CATEGORIES{$c};
  }
  return @filter;
}
BioPerl-1.007002/scripts/index000755000766000024          013155576320 16154 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/scripts/index/TAG000444000766000024        16313155576320 16627 0ustar00cjfieldsstaff000000000000These are scripts to create and maintain flatfile databases indexed
with the Bio::Index or Bio::DB::Fasta modules.
BioPerl-1.007002/scripts/index/bp_fetch.pl000444000766000024      2066413155576320 20450 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=head1 NAME

bp_fetch.pl - fetches sequences from bioperl indexed databases

=head1 SYNOPSIS

  bp_fetch.pl swiss:ROA1_HUMAN

  bp_fetch.pl net::genbank:JX295726

  bp_fetch.pl net::genpept:ROA1_HUMAN

  bp_fetch.pl ace::myserver.somewhere.edu,21000:X56676

  bp_fetch.pl -fmt GCG swiss:ROA1_HUMAN

=head1 DESCRIPTION

Fetches sequences using the DB access systems in Bioperl. The most
common use of this is to bp_fetch sequences from bioperl indices built
using bpindex.pl, or to fetch sequences from the NCBI website

The format for retrieving sequences is delibrately like the
GCG/EMBOSS format like the following:

  db:name

with the potential of putting in a 'meta' database type, being

  meta::db:name

The meta information can be one of three types

  local - local indexed flat file database
  net   - networked http: based database
  ace   - ACeDB database

This information defaults to 'local' for database names with no meta
db information

=head1 OPTIONS

  -fmt   - Output format
                   Fasta (default), EMBL, Raw, swiss or GCG
  -acc           - string is an accession number, not an
                   id.

options only for expert use

  -dir      - directory to find the index files
                  (overrides BIOPERL_INDEX environment variable)
  -type    - type of DBM file to open
                  (overrides BIOPERL_INDEX_TYPE environment variable)

=head1 ENVIRONMENT

bp_index and bp_fetch coordinate where the databases lie using the
environment variable BIOPERL_INDEX. This can be overridden using the
-dir option. The index type (SDBM or DB_File or another index file)
is controlled by the BIOPERL_INDEX_TYPE variable. This defaults to
SDBM_File

=head1 USING IT YOURSELF

bp_fetch is a wrapper around the bioperl modules which support
the Bio::DB::BioSeqI abstract interface. These include:

  Author          Code

  James Gilbert - Fasta indexer, Abstract indexer
  Aaron Mackay  - GenBank and GenPept DB access
  Ewan Birney   - EMBL .dat indexer
  Many people   - SeqIO code

These modules can be used directly, which is far better than using
this script as a system call or a pipe to read from. Read the
source code for bp_fetch to see how it is used.

=head1 EXTENDING IT

bp_fetch uses a number of different modules to provide access to
databases. Any module which subscribes to the Bio::DB::BioSeqI
interface can be used here. For flat file indexers, this is
best done by extending Bio::Index::Abstract, as is done in
Bio::Index::EMBL and Bio::Index::Fasta. For access to other
databases you will need to roll your own interface.

For new output formats, you need to add a new SeqIO module. The
easiest thing is to look at Bio::SeqIO::Fasta and figure out
how to hack it for your own format (call it something different
obviously).

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

Ewan Birney Ebirney@ebi.ac.ukE

=cut

use strict;
use warnings;
use Getopt::Long;

#
# Dofus catcher for people who are trying this script without
# installing bioperl. In your own script, you can just go
#
# use Bio::Index::Fasta etc, rather than this
#
use Bio::SeqIO;
BEGIN {
  eval {
    require Bio::Index::Fasta;
    require Bio::Index::EMBL;
    require Bio::Index::GenBank;
    require Bio::Index::Swissprot;
    require Bio::Index::SwissPfam;
  };
  if ( $@ ) {
    # one up from here is Bio directory - we hope!
    push(@INC,"..");
    eval {
      require Bio::Index::Fasta;
      require Bio::Index::EMBL;
      require Bio::Index::GenBank;
      require Bio::Index::Swissprot;
      require Bio::Index::SwissPfam;
    };
    if ( $@ ) {
      print STDERR ("\nbp_index cannot find Bio::Index::Fasta and Bio::Index::EMBL\nbp_index needs to have bioperl installed for it to run.\nBioperl is very easy to install\nSee http://bio.perl.org for more information\n\n");
      exit(1);
    } else {
      print STDERR ("\nYou are running bp_index.pl without installing bioperl.\nYou have done it from bioperl/scripts, and so we can find the necessary information\nbut it is much better to install bioperl\n\nPlease read the README in the bioperl distribution\n\n");
    }
  }

  eval {
    require Bio::DB::GenBank;
    require Bio::DB::GenPept;
    require Bio::DB::EMBL;
    require Bio::DB::SwissProt;
  };

  if ( $@ ) {
    if ( !exists $ENV{'BIOPERL_SAVVY'} ) {
      print STDERR ("\nbp_fetch cannot find Bio::DB::GenBank and Bio::DB::EMBL modules\nThis is most likely because LWP has not been installed\nThis does not effect local indexing\nset environment variable BIOPERL_SAVVY to suppress this message\n\n");
    }
  }
}

#
# Start processing the command line
#

my $dir = $ENV{'BIOPERL_INDEX'};
my $type = $ENV{'BIOPERL_INDEX_TYPE'};
my $fmt = 'Fasta';
my $useacc = 0;
my $ret = GetOptions('d|dir=s' => \$dir,
		     'f|fmt=s' => \$fmt ,
		     't|type=s' => \$type ,
		     'acc!' => \$useacc);

#
# print pod documentation if we have no arguments
#

exec('perldoc',$0) unless @ARGV;

my ($isnet,$db,$dbobj,$id,$seq,$seqio,$out,$meta);

#
# Reset the type if needed
#

if( $type ) {
   $Bio::Index::Abstract::USE_DBM_TYPE = $type;
}

#
# Build at run time the SeqIO output
#
if ( $fmt !~ /swisspfam|pfam/ ) {
  $out = Bio::SeqIO->new(-fh => \*STDOUT , -format => $fmt);
}

#
# Main loop over remaining arguments
#

for my $arg ( @ARGV ) {
  $_= $arg;
  # strip out meta:: if there
  if ( /^(\w+)::/ ) {
    $meta = $1;
    s/^(\w+):://;
  } else {
    $meta = 'local';
  }

  # parse to db:id

  /^(\S+)\:(\S+)$/ || do { warn "$_ is not parsed as db:name\n"; next; };
  ($db,$id) = split/:/,$_,2;
  #
  # the eval block catches exceptions if they occur
  # in the code in the block. The exception goes in $@
  #

  eval {
    SWITCH : {
      $_ = $meta;
      /^net$/ && do {
	if ( $db =~ /genbank/i ) {
	  $dbobj = Bio::DB::GenBank->new(-format => $fmt);
	} elsif ( $db =~ /genpept/i ) {
	  $dbobj = Bio::DB::GenPept->new();
	} elsif ( $db =~ /embl/i ) {
	  $dbobj = Bio::DB::EMBL->new();
	} else {
	  die "Net database $db not available";
	}
	last SWITCH;
      };
      /^ace$/ && do {
	# yank in Bio::DB::Ace at runtime
	eval {
	  require Bio::DB::Ace;
	};
	if ( $@ ) {
	  die "Unable to load Bio::DB::Ace for ace::$db\n\n$@\n";
	}

	# db is server,port
	my ($server,$port);

	$db =~ /(\S+)\,(\d+)/ || die "$db is not server.name,port for acedb database";
	$server = $1;
	$port = $2;
	# print STDERR "Connecting to $server,$port\n";

	$dbobj = Bio::DB::Ace->new(-host => $server, -port => $port);
	last SWITCH;
      };
      /^local$/ && do {
	if ( !$dir ) {
	  die "\nNo directory specified for index\nDirectory must be specified by the environment variable BIOPERL_INDEX or --dir option\ngo bp_index with no arguments for more help\n\n";
	}

	#
	# $db gets re-blessed to the correct index when
	# it is made from the abstract class. Cute eh?
	#

	$dbobj = Bio::Index::Abstract->new("$dir/$db");
	last SWITCH;
      };
      die "Meta database $meta is not valid";
    }
    };				# end of eval to get db
  if ( $@ ) {
    warn("Database $db in $arg is not loadable. Skipping\n\nError $@");
    next;
  }

  #
  # We expect the databases to adhere to the BioSeqI
  # the sequence index databases and the GenBank/GenPept do already
  #
  if ( $dbobj->isa("Bio::Index::SwissPfam") ) {
    my $seq = $dbobj->fetch($id);
    if ( $seq ) {
      my $started;
      while ( <$seq> ) {
	last if ( /^\s+$/ );
	print;
      }
    } else {
      warn("Cannot find $id\n");
    }
    next;
  }
  if ( ! $dbobj->isa('Bio::DB::RandomAccessI') ) {
    warn("$db in $arg does not inherit from Bio::DB::RandomAccessI, so is not expected to work under the DB guidlines. Going to try it anyway");
  }
  eval {
    if ( $useacc == 0 ) {
      $seq = $dbobj->get_Seq_by_id($id);
    } else {
      $seq = $dbobj->get_Seq_by_acc($id);
    }
  };
  if ( $@ ) {
    warn("Sequence $id in Database $db in $arg is not loadable. Skipping.\n\nError $@");
    next;
  } elsif ( !defined $seq ) {
    warn("Sequence $id in Database $db is not present\n");
    next;
  }
  $out->write_seq($seq);
}
BioPerl-1.007002/scripts/index/bp_index.pl000444000766000024      1222313155576320 20456 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=head1 NAME

bp_index.pl - indexes files for use by bp_fetch.pl

=head1 SYNOPSIS

bp_index.pl index_name file1 file2 etc.

=head1 DESCRIPTION

bp_index.pl builds a bioperl index for the sequence files given in the
argument list, under the index name. For example

   bp_index.pl nrdb /data/nrdb/nrdb.fasta

would build an index called 'nrdb' as the index name for the file
nrdb.fasta, and

   bp_index.pl -fmt EMBL swiss /data/swiss/*.dat

would build an index called swiss for all the files in /data/swiss
which end in .dat which are in EMBL format.

The indexes are built using the Bio/Index/* modules, in particular,
Bio::Index::EMBL and the Bio::Index::Fasta modules. Any script which
uses these modules can use the index. A good example script is bp_fetch
which fetches sequences and pipes them to STDOUT, for example

   bp_fetch swiss:ROA1_HUMAN

gets the ROA1_HUMAN sequence from the swiss index and writes it as
fasta format on STDOUT.

=head1 OPTIONS

  -fmt     - Fasta (default), swiss or EMBL
  -dir        - directory where the index files are found
                     (overrides BIOPERL_INDEX environment variable)

Options for expert use

  -type   - DBM_file type. 
                     (overrides BIOPERL_INDEX_TYPE environment variable)
  -v               - report every index addition (debugging)

=head1 ENVIRONMENT

bp_index and bp_fetch coordinate where the databases lie using the
environment variable BIOPERL_INDEX. This can be overridden using the
-dir option. There is no default value, so you must use the -dir option 
or set BIOPERL_INDEX.

The DB type is coordinated with BIOPERL_INDEX_TYPE which if it
is not there, defaults to whatever the bioperl modules have installed,
which itself defaults to SDBM_File.

=head1 USING IT YOURSELF

bp_index.pl is a script that drives the Index modules. If you want to 
use this script heavily in your work, if it is Perl based, it is 
almost certainly better to look at the code in this script and copy
it across (probably you will be more likely to want to use the bp_fetch
code).

=head1 EXTENDING IT

bp_index is just a wrapper around James Gilbert's excellent Index modules
found in bioperl

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Ewan Birney

Ewan Birney Ebirney@ebi.ac.ukE

=cut

#'
use strict;
use warnings;

#
# Doofus catcher for people who are trying this script without
# installing bioperl
#

BEGIN {
    eval {
	require Bio::Index::Fasta;
	require Bio::Index::EMBL;
	require Bio::Index::Swissprot;
	require Bio::Index::GenBank;
	require Bio::Index::SwissPfam;
    };
    if ( $@ ) {
	# one up from here is Bio directory - we hope!
	push(@INC,"..");
	eval {
	    require Bio::Index::Fasta;
	    require Bio::Index::EMBL;
	};
	if ( $@ ) {
	    print STDERR ("\nbp_index cannot find Bio::Index::Fasta and Bio::Index::EMBL\nbp_index needs to have bioperl installed for it to run.\nBioperl is very easy to install\nSee http://bio.perl.org for more information\n\n");
	    exit(1);
	} else {
	    print STDERR ("\nYou are running bp_index.pl without installing bioperl.\nYou have done it from bioperl/scripts, and so we can find the necessary information\nbut it is much better to install bioperl\n\nPlease read the README in the bioperl distribution\n\n");
	}
    }
}

my $dir = $ENV{'BIOPERL_INDEX'};
my $type = $ENV{'BIOPERL_INDEX_TYPE'};
my $fmt = 'Fasta';
my $verbose = 0;

use Getopt::Long;
&GetOptions("f|fmt=s" => \$fmt,
	    "d|dir=s" => \$dir,
	    "t|type=s" => \$type,
	    "v!" => \$verbose);

exec('perldoc',$0) unless @ARGV;

my $name = shift;

if( !$dir ) {
    print STDERR "\nNo directory specified for index\nDirectory must be specified by the environment variable BIOPERL_INDEX or -dir option\ngo bp_index with no arguments for more help\n\n";
    exit(1);
}

#
# Reset the type if needed
#

if( $type ) {
   $Bio::Index::Abstract::USE_DBM_TYPE = $type;
}
#
# Rock and roll...
# 
my $index;
$_ = $fmt;
SWITCH : {
    /Fasta/i && do {
	$index = Bio::Index::Fasta->new("$dir/$name", 'WRITE');
	last;
    };
    /EMBL/i && do {
	$index = Bio::Index::EMBL->new("$dir/$name", 'WRITE');
	last;
    };
    /swisspfam|pfam/i && do {
	$index = Bio::Index::SwissPfam->new("$dir/$name", 'WRITE');
	last;
    };
    /swiss/i && do {
	$index = Bio::Index::Swissprot->new("$dir/$name", 'WRITE');
	last;
    };
    /GenBank/i && do {
	$index = Bio::Index::GenBank->new("$dir/$name", 'WRITE');
	last;
    };
    die("No index format called $fmt");
}

if( $verbose != 0 ) {
  $index->verbose(1);
}

$index->make_index(@ARGV);

# finished. Neat eh.

#
# if you are using this in a script, to 
# to force deallocation + closing of the index, go
# $index = undef;
#

	





BioPerl-1.007002/scripts/index/bp_seqret.pl000444000766000024       430213155576320 20631 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
# -*-Perl-*- mode (for emacs)

=head1 NAME

bp_seqret - bioperl implementation of sequence fetch from local db (like EMBOSS seqret)

=head1 USAGE

bp_seqret [-f/--format outputformat] [-o/--out/--outfile outfile] [-d/--db dbname] [-i/--id/-s/--seqname seqname1]

Example usage:

   bp_seqret -f fasta -db db.fa -i seq1 -i seq2 > output.fas
   bp_seqret db.fa:seq1 output.fas
   bp_seqret db.fa:seq1 -o output.fas
   bp_seqret -db db.fa -o output.fas seq1 seq2 seq3
   bp_seqret -db db.fa seq1 seq2 seq3 output.fas
   bp_seqret -db db.fa seq1 seq2 seq3 - > output.fas  

The DB is expected to be a Fasta formatted sequence file with multiple
sequences.

Output format is Fasta by default.

If no output filename is provided then output is written to STDOUT.
Providing '-' as the output filename will accomplish the same thing.


=head1 AUTHOR

Jason Stajich jason_AT_bioperl-dot-org

=cut

use strict;
use warnings;
use Bio::DB::Fasta;
use Bio::SeqIO;
use Getopt::Long;

my $dbname;
my @names;
my $format = 'fasta';
my $outfile;
my ($start,$end);
GetOptions(
	   'f|format:s'   => \$format,
	   'o|out|outfile:s' => \$outfile,
	   's|sbegin|begin|start:s'  => \$start,
	   'e|send|end|stop:s'       => \$end,
	   'd|db|dbname:s'   => \$dbname,
	   'i|id|seqname:s' => \@names);


if( ! $dbname ) {
    die "need a dbname\n" unless @ARGV;
    $dbname = shift @ARGV;	
    if( $dbname =~ s/^([^:]+):// ) {
	push @names, $dbname;
	$dbname = $1;
    }				
}

my $db = Bio::DB::Fasta->new($dbname, -glob => "*.{fa,fas,fsa,fasta,pep,aa,seq,cds,peps}");
if( ! $outfile ) {
    $outfile = pop @ARGV;
}
my $out;
if( $outfile ) {
    $out = Bio::SeqIO->new(-format => $format,
			   -file   => ">$outfile");
} else {
    $out = Bio::SeqIO->new(-format => $format);
}
for my $nm ( @names ) {   
    my $seq;
    if( $start || $end ) {
	$seq = $db->seq($nm, $start => $end);
    } else { 
	$seq = $db->seq($nm);
    }
    if( $seq ) { 
	my ($id,$desc) = split(/\s+/,$db->header($nm),2);
	if( $start && $end ) { 
	    $id = sprintf("%s_%d-%d",$id,$start || 0,$end || 0);
	}
	
	$out->write_seq(Bio::PrimarySeq->new(-display_id => $id,
					     -description => $desc,
					     -seq => $seq));
    } else {
	warn("$nm not found\n");
    }
}

BioPerl-1.007002/scripts/popgen000755000766000024          013155576320 16335 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/scripts/popgen/bp_composite_LD.pl000444000766000024       505413155576320 22075 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
# -*-Perl-*- 

=head1 NAME 

bp_composite_LD -i filename.prettybase.txt --sortbyld E outfile

=head1 SYNOPSIS

  bp_composite_LD -i filename.prettybase [-o out.LD] [-f prettybase/csv] [--sortbyld] [--noconvertindels]

=head2 DESCRIPTION

This a script which allows an easy way to calculate composite LD.  

=head2 OPTIONS

-i or --in     filename

-f or --format genotype format (prettybase or CSV)

--sortbyld     To see data sorted by LD instead of just all the 
               site1/site2 pair LD values.

-o or --out    output filename, otherwise will print to STDOUT

--noconvert    (applicable for prettybase format file only)
               if specified will NOT attempt to convert indel
               states to 'I' and delete states ('-') to 'D'.

-h or --help   see this documentation

=head2 AUTHOR Jason Stajich, Matthew Hahn

For more information contact:

Matthew Hahn, Ematthew.hahn-at-duke.eduE
Jason Stajich Ejason-at-bioperl-dot-orgE


=cut

use strict;
use warnings;

use Bio::PopGen::IO;
use Bio::PopGen::Statistics;
use Bio::PopGen::Population;

use Getopt::Long;

my ($file,$outfile,$sortbyld,$format,$noconvert,$verbose);
$format = 'prettybase'; # default format is prettybase
GetOptions(
	   'i|in:s'       => \$file, # pass the filename as 
	   'o|out:s'      => \$outfile,
	   'f|format:s'   => \$format,
	   'sortbyld'     => \$sortbyld,
	   'noconvert'    => \$noconvert,
	   'v|verbose'    => \$verbose,
	   'h|help'       => sub { system('perldoc', $0);
				   exit; }, 
	   );

if( ! $file ) { 
    $file = shift @ARGV;  # if no -i specified
}

my $io = Bio::PopGen::IO->new(-format => $format,
			      -verbose=> $verbose,
			      -CONVERT_INDEL_STATES => ! $noconvert,
			      -file   => $file);

my $stats = Bio::PopGen::Statistics->new(-verbose => $verbose);
my $pop = $io->next_population;

my %LD_matrix = $stats->composite_LD($pop);

# sites can be ordered by sorting their names

my @sites;
my $out;
if( $outfile ) { 
    open $out, '>', $outfile or die "Could not write file '$outfile': $!\n";
} else { 
    $out = \*STDOUT;
}
foreach my $site1 ( sort keys %LD_matrix ) {
    foreach my $site2 ( sort keys %{ $LD_matrix{$site1} } ) {
	my $LD = $LD_matrix{$site1}->{$site2}; # LD for site1,site2 
	if( $sortbyld ) {
	    push @sites, [ $site1,$site2,@$LD];
	} else { 
	    printf $out "%s,%s - LD=%.4f chisq=%.4f\n",$site1,$site2,@$LD;
	}
    }
}

if( $sortbyld ) {
    foreach my $s ( sort { $b->[3] <=> $a->[3] } @sites ) {
	my ($site1,$site2,$ld,$chisq) = @$s;
	print $out "$site1,$site2 - LD=$ld, chisq=$chisq\n";
    }
}
BioPerl-1.007002/scripts/popgen/bp_heterogeneity_test.pl000444000766000024      1107613155576320 23447 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
# -*-Perl-*- (for my emacs)

use strict;
use warnings;

=head1 NAME 

bp_heterogeneity_test - a test for distinguishing between selection and population expansion.

=head1 SYNOPSIS

heterogenetity_test -mut_1/--mutsyn synonymous_mut_count -mut_2/--mutnon nonsyn_mut_count -s/--smaplesize sample_size [-i/--iterations iterations] [-o/--observed observed_D] [-v/--verbose] [--silent ] [-m/--method tajimaD or fuD] [--precision]

=head2 DESCRIPTION

This is an implementation of the Heterogenetity test as described in
Hahn MW, Rausher MD, and Cunningham CW. 2002. Genetics 161(1):11-20. 

=head2 OPTIONS

 Options in brackets above are optional

 -s or --samplesize samplesize 
 -mut_1 or --mutsyn synonymous mutation count 
 -mut_2 or --mutnon nonsynonmous mutation count 
 -i or --iterations number of iterations 
 -o or --observed   observed D 
 -m or --method     tajimaD or fuD  for Tajima's D or Fu and Li's D
 -v or --verbose    print out extra verbose messages
 --silent           Be extra quiet
 --precision        Level of precision - specify the number of digits 
                   (default 4)

=head2 AUTHOR Matthew Hahn Ematthew.hahn-at-duke.eduE

For more information contact:

Matthew Hahn, Ematthew.hahn-at-duke.eduE
Jason Stajich Ejason-at-bioperl-dot-orgE

=cut

use Getopt::Long;
use Bio::PopGen::Simulation::Coalescent;
use Bio::PopGen::Statistics;
use Bio::PopGen::Individual;
use Bio::PopGen::Genotype;

my $sample_size = 4;
my $mut_count_1 = 10; # synonymous
my $mut_count_2 = 20; # non-synonymous
my $iterations = 1;
my $verbose = 0;
my $observedD = undef;
my $method = 'fuD';
my $help = 0;
my $precision = '4'; # Let's make the random precision between
                     # 0->1 to 1000th digits

GetOptions( 
	    's|samplesize|samp_size:i' => \$sample_size,
	    'mut_1|mutsyn:i'           => \$mut_count_1,
	    'mut_2|mutnon:i'           => \$mut_count_2, 
	    'i|iterations:i'           => \$iterations,
	    'o|obsered|observedD:f'    => \$observedD, 
	    'v|verbose'                => \$verbose,
	    'm|method:s'               => \$method,
	    'h|help'                   => \$help,
	    'silent'                   => sub { $verbose = -1; },
	    'p|precision:i'            => \$precision,
	    );

if( $help ) {
    system("perldoc",$0);
    exit(0);
}

if( $method ne 'fuD' and $method ne 'tajimaD' ) {
    die("available methods are [fu and li's D] (fuD) and Tajima's D (tajimaD)");
}
my @D_distribution;  
printf("sample size is %d iteration count = %d\n", $sample_size, 
       $iterations);

my $sim = new Bio::PopGen::Simulation::Coalescent
    (-sample_size => $sample_size);

for(my $iter = 0; $iter < $iterations; $iter++ ) {
    my $tree = $sim->next_tree($sample_size);
    my $f1 = 0;
    if( $mut_count_1 > 0 ) {
	$sim->add_Mutations($tree,$mut_count_1,$precision);

	my @leaves = $tree->get_leaf_nodes;
	# the outgroup is just an individual with the ancestral state 
	# (no mutations)
	my $outgroup = new Bio::PopGen::Individual();
	foreach my $m ( $leaves[0]->get_marker_names ) {
	    $outgroup->add_Genotype(Bio::PopGen::Genotype->new
				    (-marker_name=> $m,
				     -alleles    => [ 0 ]));
	}
	if( $method eq 'fuD' ) {
	    $f1 = Bio::PopGen::Statistics->fu_and_li_D(\@leaves,[$outgroup]);
	} elsif( $method eq 'tajimaD' ) {
	    $f1 = Bio::PopGen::Statistics->tajima_D(\@leaves);
	}
	print "(mutation count = $mut_count_1) D=$f1\n" 
	    if( $verbose >= 0);
    }
    
    my $f2 = 0;
    if( $mut_count_2 > 0 ) {
	$sim->add_Mutations($tree,$mut_count_2,$precision);
	my @leaves = $tree->get_leaf_nodes;
        # the outgroup is just an individual with the ancestral state 
	# (no mutations)
	my $outgroup = new Bio::PopGen::Individual();
	foreach my $m ( $leaves[0]->get_marker_names ) {
	    $outgroup->add_Genotype(Bio::PopGen::Genotype->new
				    (-marker_name=> $m,
				     -alleles    => [ 0 ]));
	}
	if( $method eq 'fuD' ) {
	    $f2 = Bio::PopGen::Statistics->fu_and_li_D(\@leaves,[$outgroup]);
	} elsif( $method eq 'tajimaD' ) {
	    $f2 = Bio::PopGen::Statistics->tajima_D(\@leaves);
	}
	print "(mutation count = $mut_count_2) D=$f2\n" if( $verbose >= 0);

    }
    my $deltaD = ( $f1 - $f2 );
    push @D_distribution, $deltaD;
    if( $iter % 10 == 0 && $iter > 0 ) { 
	print STDERR "iter = $iter\n"; 
    }
}

if( defined $observedD && $iterations > 1 ) { 
    my @sortedD = sort { $a <=> $b } @D_distribution;
    my $i;
    for($i = 0; $i < scalar @sortedD; $i++ ) {
	if( $sortedD[$i] > $observedD ) { 
	    last;
	}
    }
    
    printf( "index %d value=%.4f out of %d total (obs=%.4f)\n", 
	    $i, $sortedD[$i], scalar @sortedD, $observedD);
}

BioPerl-1.007002/scripts/searchio000755000766000024          013155576320 16642 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/scripts/searchio/README000444000766000024       103213155576320 17653 0ustar00cjfieldsstaff000000000000These are scripts that run on top of Bio::SearchIO or generally fit
into the Database search result parsingframework.

fastam9_to_table.PLS -- script which doesn't use Bio::SearchIO but provides fast parsing of FASTA -m9 output to an NCBI m9-like table.
hmmer_to_table.PLS -- script which doesn't use Bio::SearchIO but provides fast parsing of HMMER output into a tabular format.

search2table.PLS -- Turn any Bio::SearchIO parseable report into NCBI m9-like tablular output

filter_search.PLS - produce tabular output, filtering first. 
BioPerl-1.007002/scripts/searchio/TAG000444000766000024        20213155576320 17307 0ustar00cjfieldsstaff000000000000These are scripts related to parsing Search Result output like HMMER, FASTA, BLAST.
Not all of these scripts use Bioperl objects.
BioPerl-1.007002/scripts/searchio/bp_fastam9_to_table.pl000444000766000024       750113155576320 23235 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=head1 NAME 

fastm9_to_table  - turn FASTA -m 9 output into NCBI -m 9 tabular output

=head1 SYNOPSIS

 fastm9_to_table [-e evaluefilter] [-b bitscorefilter] [--header] [-o outfile] inputfile1 inputfile2 ... 

=head1 DESCRIPTION

Command line options:
  -e/--evalue   evalue    -- filter by evalue
  -b/--bitscore bitscore  -- filter by bitscore
  --header                -- boolean flag to print column header 
  -o/--out                -- optional outputfile to write data, 
                             otherwise will write to STDOUT
  -h/--help               -- show this documentation

Not technically a SearchIO script as this doesn't use any Bioperl
components but is a useful and fast.  The output is tabular output
with the standard NCBI -m9 columns.

 queryname
 hit name
 percent identity
 alignment length
 number mismatches 
 number gaps
 query start  (if on rev-strand start > end)
 query end 
 hit start (if on rev-strand start > end)
 hit end 
 evalue
 bit score

Additionally 3 more columns are provided
 fasta score
 sw-score
 percent similar
 query length
 hit length
 query gaps
 hit gaps

=head1 AUTHOR - Jason Stajich

Jason Stajich jason_at_bioperl-dot-org

=cut

use strict;
use warnings;
use Getopt::Long;
my $hitsection = 0;
my %data;

my ($evalue,$bitscore,$header,$outfile) = ( 10, 0);
GetOptions(
	   'b|bitscore|bits:f'   => \$bitscore,
	   'e|evalue:f'          => \$evalue,
	   'header'              => \$header,
	   'o|out|outfile:s'     => \$outfile,
	   'h|help'              => sub { exec('perldoc',$0); exit; }
	   );

my $outfh;
if( $outfile ) { 
    open $outfh, '>', $outfile or die "Could not write file '$outfile': $!\n";
} else { 
    $outfh = \*STDOUT; 
}
	   
# query start -- an0
# query en    -- ax0
# hit start   -- an1
# hit end     -- ax1

my @fields = qw(qname hname percid alen mmcount gapcount 
		qstart qend hstart hend evalue score bits fs sw-score 
		percsim qlen hlen qgap hgap);
print $outfh "#",uc(join("", map{ sprintf("%-10s",$_) } @fields)), "\n" if $header;

while(<>) {
    my $linestr = $_;
    if( /^\s*\d+>>>(\S+).+/ ) {	
	$data{'qname'} = $1;
	if( /\-?\s+(\d+)\s+(aa|nt)\s+$/ ){
	    $data{'qlen'} = $1;
	}
    } elsif( $hitsection && (/^>>>\Q$data{'qname'}/ || /^>>>/) ) {	
	$hitsection = 0;
    } elsif( /^The best scores are:/ ) {	       
	$hitsection = 1;
    } elsif( /^\s+$/ ) {
    } elsif( $hitsection ) {
	if( s/^(\S+)\s+(.+)\(\s*(\d+)\)\s+// ) {
	    my ($hit, $desc,$hitlen) = ($1,$2,$3);
	    my ($dir) = ( s/^\[(r|f)\]\s+// );
	    my @line = split(/\s+/,$_);
	    $data{'hname'}    = $hit;
	    $data{'hlen'}     = $hitlen;
	    $data{'score'}    = shift @line;
	    $data{'bits'}     = shift @line;
	    $data{'evalue'}   = shift @line;
	    $data{'percid'}   = shift @line;
	    
	    $data{'percsim'}  = shift @line;
	    $data{'sw-score'} = shift @line;
	    $data{'alen'}     = shift @line;
	    $data{'qstart'}   = shift @line;
	    $data{'qend'}     = shift @line;
	    $data{'pn0'}      = shift @line; # pn0
	    $data{'px0'}      = shift @line; # px0
	    $data{'hstart'}   = shift @line; # an1 
	    $data{'hend'}     = shift @line; # ax1
	    $data{'pn1'}      = shift @line; # pn1
	    $data{'px1'}      = shift @line; # px1
	    # query + hit gaps
	    $data{'qgap'}     = shift @line;
	    $data{'hgap'}     = shift @line;
	    $data{'gapcount'} = $data{'qgap'} + $data{'hgap'};
	    $data{'fs'}       = shift @line;
	    
	    $data{'mmcount'} = $data{'alen'} - ( int($data{'percid'} * $data{'alen'}) + $data{'gapcount'});
	    #next if( $data{'evalue'} > $evalue || 
	#	     $data{'bits'} < $bitscore );
	    
	    for ( $data{'percid'}, $data{'percsim'} ) {
		$_ = sprintf("%.2f",$_*100);
	    }
	    print $outfh join( "\t",map { $data{$_} } @fields),"\n";
	} else { 
	    # print STDERR "unrecognized line \n$linestr";
	}
    } else { 
	# warn("skipping a line like this: $_");
    }
}
BioPerl-1.007002/scripts/searchio/bp_filter_search.pl000444000766000024       324713155576320 22635 0ustar00cjfieldsstaff000000000000#!perl
use strict;
use warnings;


=head1 NAME

bp_filter_search - filters searchio results, outputting a tab delimited summary

=head1 SYNOPSIS

  #bp_filter_search -format blast -score 200 < search.bl > search.tab

=head1 DESCRIPTION 

This script filters searchio results allowing a number of different
filters to be applied before outputting to stdout in a tab delimited
format.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

  Ewan Birney 

=cut

use Bio::SearchIO;
use Getopt::Long;

my ($format,$score);

$format  = 'blast';
$score   = 150;

GetOptions(
	   'format:s'  => \$format,
	   'score:s'  => \$score,
	);


my $searchin = Bio::SearchIO->new( -format => $format);


while( (my $result = $searchin->next_result()) ) { 
  while( (my $hit = $result->next_hit())) {

      if( $score ) {
        if( $hit->raw_score < $score ) {
           next;
        }
       }


      foreach my $hsp ( $hit->hsps() ) {
         print $result->query_name,"\t",$hit->score,"\t",$hsp->start,"\t",$hsp->end,"\t",$hsp->strand,"\t",$hsp->hseq_id,"\t",$hsp->hstart,"\t",$hsp->hend,"\t",$hsp->strand,"\n";
      }
    }
}


BioPerl-1.007002/scripts/searchio/bp_hmmer_to_table.pl000444000766000024       516313155576320 23003 0ustar00cjfieldsstaff000000000000#!perl
use strict;
use warnings;

=head1 NAME 

bp_hmmer_to_table  - turn HMMER output into tabular format

=head1 SYNOPSIS

 bp_hmmer_to_table [-e evaluefilter] [-b bitscorefilter] [--header] [-o outfile] inputfile1 inputfile2 ... 

=head1 DESCRIPTION

Command line options:
  -e/--evalue   evalue    -- filter by evalue
  -b/--bitscore bitscore  -- filter by bitscore
  --header                -- boolean flag to print column header 
  -o/--out                -- optional outputfile to write data, 
                             otherwise will write to STDOUT
  -h/--help               -- show this documentation

Not technically a SearchIO script as this doesn't use any Bioperl
components but is a useful and fast.  The output is tabular output.

  query sequence/domain (these are flip-flopped for hmmsearch / hmmpfam)  
  query start
  query end
  domain/sequence name or PFAM accession 
  hit start
  hit end
  score
  e-value
  domain/sequence name (these are flip-flopped for hmmsearch / hmmpfam)  

=head1 AUTHOR - Jason Stajich

Jason Stajich jason_at_bioperl-dot-org

=cut

use Getopt::Long;

my ($evalue,$bitscore,$header,$outfile);
GetOptions(
	   'b|bitscore|bits:f'   => \$bitscore,
	   'e|evalue:f'          => \$evalue,
	   'header'              => \$header,
	   'o|out|outfile:s'     => \$outfile,
	   'h|help'              => sub { exec('perldoc',$0); exit; }
	   );

my $outfh;
if( $outfile ) { 
    open $outfh, '>', $outfile or die "Could not write file '$outfile': $!\n";
} else { 
    $outfh = \*STDOUT; 
}

my @fields = qw(QNAME QSTART QEND HACCESSION HSTART HEND SCORE EVALUE HNAME);
if( $header ) {
    print $outfh join("\t", @fields), "\n";
}
my %dat;
while(<>) {
    if( s/^Query(\s+(sequence|HMM))?:\s+// ) {	
	s/\s+$//;
	$dat{'Query'} = $_;
    } elsif( /^Parsed for domains:/ ) {
	my $ready = 0;
	while(<>) {
	    if(/^Model|Sequence\s+Domain/ ) { $ready = 1; }
	    elsif( $ready && /^\-\-/) { $ready = 2; }
	    elsif( /^Alignments of/ ) { undef %dat; last; }
	    elsif( $ready == 2 ) {
		if( my ($n,$domainnum,$domainct, @vals) = 
		    (m!^(\S+)\s+      # domain name
		     (\d+)\/(\d+)\s+  # num/num (ie 1 of 2) 
		     (\d+)\s+(\d+).+? # sequence start and end
		     (\d+)\s+(\d+)\s+ # hmm start and end
		     \S+\s+           # []
		     (\S+)\s+         # score
		     (\S+)            # evalue
		     \s*$!ox)  ) {
		    next if( defined $bitscore && $vals[4] < $bitscore );
		    next if (defined $evalue && $vals[5] > $evalue);
		    print $outfh join("\t",
				      $dat{'Query'},
				      $vals[0], $vals[1],
				      $n,
				      $vals[2],$vals[3],
				      $vals[4],$vals[5],
				      $n),"\n";
		}
	    }
	}
    }
}
BioPerl-1.007002/scripts/searchio/bp_parse_hmmsearch.pl000444000766000024      1457413155576320 23211 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

use strict;
use warnings;

=head1 NAME

bp_parse_hmmsearch - parse single/multiple HMMSEARCH results file(s) with
                  different output options

=head1 SYNOPSIS

bp_parse_hmmsearch [--po] [--ps] -s hmmsearch_file

bp_parse_hmmsearch [--po] [--ps] -m index_file

=head1 DESCRIPTION

=head2 Mandatory Options:

  -s  HMMSEARCH file to parse.
  -m  INDEX file that contains a list of HMMSEARCH files for multiple
      parsing.

=head2 Special Options:

  --po    Print only the hits that have positive scores.
  --ps    Print the total of positive scores found.
  --help  Show this documentation.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

  Mauricio Herrera Cuadra 

=cut

# Modules, pragmas and variables to use
use Bio::SearchIO;
use Getopt::Long;
use vars qw($opt_s $opt_m $opt_po $opt_ps $opt_help);

# Gets options from the command line
GetOptions qw(-s:s -m:s --po --ps --help);

# Print documentation if help switch was given
exec('perldoc', $0) and exit() if $opt_help;

# If no mandatory options are given prints an error and exits
if (!$opt_s && !$opt_m) {
    print "ERROR: No HMMSEARCH or INDEX file has been specified.\n       Use
'--help' switch for documentation.\n" and exit();
} elsif ($opt_s && $opt_m) {
    print "ERROR: You must select only one option (-s or -m) for input.\n      
Use '--help' switch for documentation.\n" and exit();
}

# Initializes a counter for the domain positive scores if the option
# was given
my $pos_scores = 0 if $opt_ps;

# If single file mode was selected
if ($opt_s) {
    parse_hmmsearch($opt_s);

    # Prints the total domain positive scores if the option was given
    if ($opt_ps) {
        print "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - -\n";
        print "Total domain positive scores: $pos_scores\n";
    }

# If multiple files mode was selected
} elsif ($opt_m) {

    # Opens the INDEX file sent as input
    open my $FH, '<', $opt_m or die "Could not read INDEX file '$opt_m': $!\n";

    # Cycle that extracts one line for every loop until finding the
    # end of file
    while (my $line = <$FH>) {

        # Deletes the new line characters from the line
        chomp $line;

        # Parses the result file in turn
        parse_hmmsearch($line);
        print "= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
= = = =\n";
    }

    # Prints the total domain positive scores if the option was given
    print "Total domain positive scores: $pos_scores\n" if $opt_ps;

    # Closes INDEX files
    close $FH;
}

# Exits the program
exit();

# Subroutine that parses a HMMSEARCH results file
sub parse_hmmsearch {

    # Gets the parameters sent to the function
    my ($file) = @_;

    # Creates a new Bio::SearchIO object
    my $in = new Bio::SearchIO(
        -format => 'hmmer',
        -file   => $file,
    );

    # Loops through the results file
    while (my $result = $in->next_result()) {

        # Prints program name and version (these are values from
        # Bio::Search::Result::GenericResult methods)
        print $result->algorithm(), " ", $result->algorithm_version(), "\n";
        print "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - -\n";

        # Prints HMM file and sequence database (these are values from
        # Bio::Search::Result::HMMERResult methods)
        print "HMM file:\t\t\t", $result->hmm_name(), "\n";
        print "Sequence database:\t\t", $result->sequence_file(), "\n";
        print "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-\n";

        # Prints some values from Bio::Search::Result::GenericResult
        # methods
        print "Query HMM:\t\t\t", $result->query_name(), "\n";
        print "Accession:\t\t\t", $result->query_accession(), "\n";
        print "Description:\t\t\t", $result->query_description(), "\n";
        print "Total hits:\t\t\t", $result->num_hits(), "\n";

        # Loops through the sequence in turn
        while (my $hit = $result->next_hit()) {

            # If only positive scores option was given and the score
            # in turn is greater than zero
            if ($opt_po) {
                printHits($hit) if ($hit->score() >= 0);

            # Prints all hits otherwise
            } else {
                printHits($hit);
            }
        }
    }
}

# Subroutine that prints the values from a Bio::Search::Hit::HitI
# object
sub printHits {

    # Gets the parameters sent to the function
    my ($hit) = @_;

    # Prints some values from Bio::Search::Hit::HitI methods
    print "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n";
    print "Hit ", $hit->rank(), "\n";
    print "Sequence:\t\t\t", $hit->name(), "\n";
    print "Description:\t\t\t", $hit->description(), "\n";
    print "Score:\t\t\t\t", $hit->score(), "\n";
    print "E-value:\t\t\t", $hit->significance(), "\n";
    print "Number of domains:\t\t", $hit->num_hsps(), "\n";

    # Loops through the domain in turn
    while (my $hsp = $hit->next_hsp()) {

        # Prints some values from Bio::Search::HSP::HSPI methods
        print "   - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n";
        print "   Domain:\t\t\t", $hsp->rank(), " of ", $hit->num_hsps(), "\n";
        print "   seq-f:\t\t\t", $hsp->start('hit'), "\n";
        print "   seq-t:\t\t\t", $hsp->end('hit'), "\n";
        print "   hmm-f:\t\t\t", $hsp->start(), "\n";
        print "   hmm-t:\t\t\t", $hsp->end(), "\n";
        print "   score:\t\t\t", $hsp->score(), "\n";
        $pos_scores++ if ($hsp->score() >= 0) && $opt_ps;
        print "   E-value:\t\t\t", $hsp->evalue(), "\n";
        my $hmm_string = $hsp->query_string();
        $hmm_string =~ s/<-\*$//;
        print "   hmm string:\t\t\t", $hmm_string, "\n";
        print "   homology string:\t\t", $hsp->homology_string(), "\n";
        print "   hit string:\t\t\t", $hsp->hit_string(), "\n";
    }
}
BioPerl-1.007002/scripts/searchio/bp_search2table.pl000444000766000024       446613155576320 22366 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=head1 NAME

bp_search2table - turn SearchIO parseable reports into tab delimited format like NCBI's -m 9 

=head1 SYNOPSIS

  bp_search2table -f fasta -i file.FASTA -o output.table

=head1 DESCRIPTION 

Turn SearchIO reports into a tabular format like NCBI's -m 9 output.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

  Jason Stajich jason_at_bioperl-dot-org

=cut

use strict;
use warnings;
use Bio::SearchIO;
use Getopt::Long;

my ($format, $file,$output) = ('blast');

GetOptions(
	   'f|format:s'   => \$format,
	   'i|input:s'    => \$file,
	   'o|output:s'   => \$output);

if( @ARGV ) { 
    $file = shift;
}
    
my $in = Bio::SearchIO->new(-format => $format,
			    -file   => $file);
my $out;
if( $output ) { 
    open $out, '>', $output or die "Could not write file '$output': $!\n";
} else { 
    $out = \*STDOUT;
}

while( my $r = $in->next_result ) {
    while( my $hit = $r->next_hit ) {
	while( my $hsp = $hit->next_hsp ) {
	    my $mismatchcount = $hsp->length('total') - 
		($hsp->num_conserved + $hsp->gaps('total'));
	    print $out join("\t", ( $r->query_name,
				    $hit->name,
				    sprintf("%.2f",$hsp->percent_identity),
				    $hsp->length('total'),
				    $mismatchcount,
				    $hsp->gaps('total'),
				    # flip start/end on rev strand
				    $hsp->query->strand < 0 ?
				    ( $hsp->query->end,
				      $hsp->query->start ) :
				    ( $hsp->query->start,
				      $hsp->query->end ),
				    $hsp->hit->strand < 0 ?
				    ( $hsp->hit->end,
				      $hsp->hit->start ) :
				    ( $hsp->hit->start,
				      $hsp->hit->end ),

				    $hsp->evalue,
				    # chance this to $hsp->sw_score 
				    # if you would rather have that
				    # it will only work for FASTA parsing though!
				    $hsp->bits)),"\n";
	}
    }
}
BioPerl-1.007002/scripts/seq000755000766000024          013155576320 15635 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/scripts/seq/TAG000444000766000024        14713155576320 16312 0ustar00cjfieldsstaff000000000000These are scripts to interconvert sequence formats and to perform
other common sequence manipulations.
BioPerl-1.007002/scripts/seq/bp_extract_feature_seq.pl000444000766000024       531013155576320 23044 0ustar00cjfieldsstaff000000000000#!perl
use strict;
use warnings;
use Bio::SeqIO;
use Getopt::Long;
# Author Jason Stajich 

=head1 NAME

bp_extract_feature_seq - extract the corresponding sequence for a specified feature type

=head1 SYNOPSIS

bp_extract_feature_seq [--format FORMAT] [--feature CDS] [--output FILE] [--input] FILE

=head1 DESCRIPTION

This script will extract the sequence for all the features you specify.

=head1 OPTIONS

=over

=item B<-i>, B<--input>

Specifies the sequence file to be read.

=item B<--format>

Format of the file specified by B<--input>. If not given, it will try to guess the
correct format from the file extension.

=item B<--feature>

Feature to be extracted. By default, it extracts the CDS feature.

=item B<-o>, B<--output>

File where the extracted features will be saved. If not specified, STDOUT is used.

=back

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

  L                  - General discussion
  L  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:

  L

=head1 AUTHOR

 Jason Stajich 

=cut

my ($input,$format,$featuretype,$output);
$featuretype ='CDS';
GetOptions(
           'i|input:s' => \$input,
           'format:s'  => \$format,
           'feature:s' => \$featuretype,
           'o|output:s'=> \$output);

$input || shift if @ARGV;

my $in = new Bio::SeqIO(-file => $input,
                        -format => $format);
my $out;
if ($output ) {
    $out = new Bio::SeqIO(-file => ">$output", -format => 'fasta');
} else {
    $out = new Bio::SeqIO(-format => 'fasta'); # use STDOUT for output
}

my $count = 1;
while( my $seq = $in->next_seq ) {
    foreach my $f ( grep { $_->primary_tag =~ /$featuretype/i }
                    $seq->get_SeqFeatures ) {
        my $s = $f->spliced_seq;
        if( $featuretype =~ /gene|CDS/ ) {
            $s->display_id($f->has_tag('gene') ? join(',',sort $f->each_tag_value('gene')) :
                           $f->has_tag('label') ? join(',',$f->each_tag_value('label')):
                           $s->display_id);
        } else {
            $s->display_id(sprintf("%s_%s_%d",
                                   $seq->display_id,
                                   $f->primary_tag,
                                   $count++));
        }
        $out->write_seq($s);
    }
}
BioPerl-1.007002/scripts/seq/bp_make_mrna_protein.pl000444000766000024       607513155576320 22512 0ustar00cjfieldsstaff000000000000#!perl
#
=head1 NAME

bp_make_mrna_protein - Convert an input mRNA/cDNA sequence into protein

=head1 DESCRIPTION

Convert an input mRNA/cDNA sequence into protein using translate()

  -f/--frame           Specifies frame [0,1,2]

One can also specify:

  -t/--terminator      Stop Codon character (defaults to '*')
  -u/--unknown         Unknown Protein character (defaults to 'X')
  -cds/--fullcds       Expected Full CDS (with start and Stop codon)
  -throwOnError        Throw error if no Full CDS (defaults to 0)
  -if/--format         Input format (defaults to FASTA/Pearson)
  -of/--format         Output format (defaults to FASTA/Pearson)
  -o/--output          Output Filename (defaults to STDOUT)
  -i/--input           Input Filename (defaults to STDIN)
  -ct/--codontable     Codon table to use (defaults to '1')

See L for more information on codon tables
and the translate() method

=head1 AUTHOR - Jason Stajich

  Email jason-at-bioperl-dot-org

=cut

use strict;
use warnings;
use Bio::SeqIO;
use Getopt::Long;

use vars qw($USAGE);

BEGIN {
    $USAGE =
qq{make_mrna_protein.pl < file.fa > file.prots
-f/--frame            Translation Frame (0,1,2) are valid (defaults to '0')
-t/--terminator	    Stop Codon Character ('*' by default)
-u/--unknown          Unknown Protein character (defaults to 'X')
-ct/--codontable      Codon table to use (defaults to '1')
                      (see Bio::PrimarySeq for more information)
-cds/--fullcds        Expected Full CDS (with start and Stop codon)
-throwOnError         Throw an error if no Full CDS (defaults to 0)
-if/--iformat         Input format (defaults to FASTA/Pearson)
-of/--oformat         Output format (defaults to FASTA/Pearson)
-o/--output           Output Filename (defaults to STDOUT)
-i/--input            Input Filename (defaults to STDIN)
};

}
my ($iformat, $oformat, $frame, $termchar, $unknownProt, $codontable, $fullCDS,
    $throw_on_Incomp_CDS, $help) = ('fasta','fasta', 0, undef, undef, 1, 0, 0);
my ($input,$output);

GetOptions('f|frame:s'       => \$frame,
			  't|terminator:s'  => \$termchar,
			  'u|unknown:s'     => \$unknownProt,
			  'ct|codontable:s' => \$codontable,
			  'cds|fullcds'     => \$fullCDS,
			  'throwOnError'    => \$throw_on_Incomp_CDS,
			  'h|help'          => \$help,
			  'i|input:s'       => \$input,
			  'if|iformat:s'    => \$iformat,
			  'of|oformat:s'    => \$oformat,
			  'o|output:s'      => \$output,
			 );

die $USAGE if( $help );

my ($in,$out);
if( $input ) {
	$in = new Bio::SeqIO('-format' => $iformat, '-file' => $input);
} else {
	$in = new Bio::SeqIO('-format' => $iformat, '-fh' => \*STDIN);
}

if( $output ) { 
	$out = new Bio::SeqIO('-format' => $oformat, '-file' => ">$output" );
} else {
	$out = new Bio::SeqIO('-format' => $oformat );
}

while( my $seq = $in->next_seq ) {
    my $protseq = $seq->translate(-terminator => $termchar,
											 -unknown => $unknownProt,
											 -frame => $frame,
											 -codontable_id => $codontable,
											 -complete => $fullCDS,
											 -throw => $throw_on_Incomp_CDS );
    $out->write_seq($protseq);
}

__END__
BioPerl-1.007002/scripts/seq/bp_seqconvert.pl000444000766000024       420713155576320 21204 0ustar00cjfieldsstaff000000000000#!perl

use strict;
use warnings;
use Getopt::Long;
use Bio::SeqIO;

my $help;
my $from=undef;
my $to=undef;

### please add to this list (see the modules under Bio/SeqIO):
my @known_formats=
  qw(gcg fasta ace raw fastq phd pir scf swiss genbank locuslink
     embl game qual bsml tab raw abi chado alf ctf exp ztr pln
     chaosxml chadoxml yaml tigr tigrxml agave chaos kegg interpro
     lasergene strider gbdriver embldriver swissdriver);

my $script=substr($0, 1+rindex($0,'/'));
my $usage="Usage:

  $script --from in-format --to out-format < file.in-format > file.out-format

Known formats:\n  " . join(' ', @known_formats) . "\n\n";

die $usage unless
  &GetOptions( 'from:s'   => \$from,
               'to:s'     => \$to,
               'h|help'   => \$help
	     )
  && !$help &&  $from && $to
  && grep($from eq $_, @known_formats)
  && grep($to eq $_, @known_formats);

my $in  = Bio::SeqIO->newFh(-fh => \*STDIN , '-format' => $from);
my $out = Bio::SeqIO->newFh(-fh=> \*STDOUT, '-format' => $to);

print $out $_ while <$in>;


__END__

=head1 NAME

bp_seqconvert - generic BioPerl sequence format converter

=head1 SYNOPSIS

  bp_seqconvert --from in-format --to out-format < file.in-format > file.out-format
  # or
  bp_seqconvert -f in-format -t out-format < file.in-format > file.out-format

=head1 DESCRIPTION

This script gives command line interface to BioPerl Bio::SeqIO. 

=head1 SEE ALSO

L
L for similar functionality which also supports AlignIO.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Philip Lijnzaad

Email Ep.lijnzaad-at-med.uu.nlE

=cut

__END__
BioPerl-1.007002/scripts/seq/bp_seqcut.pl000444000766000024       723413155576320 20322 0ustar00cjfieldsstaff000000000000#!/usr/bin/env perl

=head1 NAME

bp_seqcut.pl - cut FASTA sequences with a given range

=head1 USAGE

 bp_seqcut.pl [options -h,-s,-e,-f,-w] ...
 bp_seqcut.pl [options -h,-f,-w] s-e ...

   -h this help message
   -s which residue to start cutting on
   -e which residue to finish cutting on
   -f format of the files, defaults to FASTA but you can specify anything supported by SeqIO from BioPerl
   -w hard wrap width, this might not be supported depending on which format you are using

=head1 Description

A script to cut FASTA sequences with a given range `fastacut -s 1 -e 10 *.fasta` or `fastacut 1-10 *.fasta`.
This is just a convenience wrapper around the Bio::SeqIO module. Useful if you wish to trim out a section of an
alignment to build a profile of a specific region of sequence.

=head1 AUTHOR

B - I

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:

  https://github.com/bioperl/bioperl-live/issues

=head1 EDIT HISTORY

2010-11-22 - Matt Oates
First features added.

=head1 DEPENDENCY

B Used to parse command line options.
B Used for usage and help output.
B Used to cut up sequences and parse FASTA.

=cut

use strict;
use warnings;
use Getopt::Long;                     #Deal with command line options
use Pod::Usage;                       #Print a usage man page from the POD comments after __END__
use Bio::SeqIO;

# Command Line Options
my $help;    #Same again but this time should we output the POD man page defined after __END__
my $format = "Fasta";
my $start;
my $end;
my $width = 72; #Default for Jalview output
my $outfile = '/dev/stdout';

#Set command line flags and parameters.
GetOptions("help|h!" => \$help,
           "start|s=s" => \$start,
           "format|f=s" => \$format,
           "end|e=s" => \$end,
           "width|w=s" => \$width,
           "outfile|o=s" => \$outfile,
        ) or die "Fatal Error: Problem parsing command-line ".$!;

#Get other command line arguments that weren't optional flags.
($start,$end) = split (/-/, shift) unless ($start and $end);
my @files = @ARGV;

#Print out some help if it was asked for or if no arguments were given.
pod2usage(-exitstatus => 0, -verbose => 2) if $help;

pod2usage(-exitstatus => 0, -verbose => 1, -msg => 'Please specify the sequence files you wish to cut.')
    unless scalar @files;

pod2usage(-exitstatus => 0, -verbose => 1, -msg => 'Please specify the region you wish to cut -s 1 -e 10 or 1-10.')
    unless defined $end;

my $out = Bio::SeqIO->newFh(-file => ">$outfile", -format => $format) or die "Couldn't open selected output sequence file.";

#Open and iterate over all sequence in all files
foreach my $file (@files) {
	my $in  = Bio::SeqIO->new(-file => $file, -format => $format);
	while ( my $seq = $in->next_seq() ) {
            #Alter the ID to be postfixed with '/s-e'
            $seq->display_id($seq->display_id."/$start-$end");
            #Edit the sequence we have cut out
	        my $sequence = $seq->subseq($start,$end);
	        $sequence =~ s/([^\n]{0,$width})/$1\n/gi;
	        chomp $sequence;
            $seq->seq($sequence);
            #Print the sequence back out
        	print $out $seq;
	}
}

1;
__END__

BioPerl-1.007002/scripts/seq/bp_seqpart.pl000555000766000024      1062313155576320 20514 0ustar00cjfieldsstaff000000000000#!/usr/bin/env perl
use strict;
use warnings;

=head1 NAME

I - Takes one or more sequence files and splits them into a number of load balanced files.

=head1 USAGE

 bp_seqpart.pl -n  [-h, -p , -f , -o ] 

   -n number of files to create through partitioning
   -h this help message
   -p prefix for all FASTA file names output, files are of the form /#.
   -f format of the files, defaults to FASTA but you can specify anything supported by SeqIO from BioPerl
   -o output directory where to dump the split sequence files

=head1 DESCRIPTION

Script wrapping SeqIO that allows partitioning of multiple sequence files into near equal sized parts for later parallel processing. Even if you have 10 input files outputting to 10 files will balance the files to contain similar total length of sequence. ID's are ignored when deciding on how to balance each sequence.

=head1 AUTHOR

B - I

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:

  https://github.com/bioperl/bioperl-live/issues

=head1 EDIT HISTORY

2012-04-03 - Matt Oates
	First features added.
=cut

=head1 DEPENDANCY
B Used to parse command line options.
B Used for usage and help output.
B Used to cut up sequences and parse FASTA.
=cut
use Getopt::Long;                     #Deal with command line options
use Pod::Usage;                       #Print a usage man page from the POD comments after __END__
use Bio::SeqIO;                       #Deal with sequence parsing, format and file IO

# Command Line Options
my $help;               #Same again but this time should we output the POD man page defined after __END__
my $prefix = 'part';    #Name each part
my $format = 'fasta';   #Sequence format we are using, default to fasta
my $outdir = '.';       #Use the current directory as default
my $num_splits;         #Number of files to split into
my @partitions;         #Details of each partition for the split

#Set command line flags and parameters.
GetOptions("help|h!" => \$help,
           "prefix|p=s" => \$prefix,
           "format|f=s" => \$format,
           "num-splits|n=i" => \$num_splits,
           "outdir|o=s" => \$outdir,
        ) or die "Fatal Error: Problem parsing command-line ".$!;

#Print out some help if it was asked for or if no arguments were given.
pod2usage(-exitstatus => 0, -verbose => 2) if $help;

pod2usage(-exitstatus => 0, -verbose => 1, -msg => 'Please specify the number of split parts with -n ') 
    unless defined $num_splits;

#Setup a bunch of empty partitions including some SeqIO file handles to write to
@partitions = map { 
    $_ = { length => 0, 
           size => 0,
           file => Bio::SeqIO->new(
                    -file   => ">$outdir/$prefix$_.$format",
                    -format => $format,
               )
         } 
    } 1..$num_splits;

#Get sequences from all the files specified.
foreach my $file (@ARGV) {
    #Open each input file in turn for reading
    my $in  = Bio::SeqIO->new(
        -file => "<$file",
        -format => $format
    );
    #While there are still sequences to consume
    while ( my $seq = $in->next_seq() ) {
        #Sort the partitions on how full they are
        @partitions = sort {$a->{size} <=> $b->{size}} @partitions;
        #Add the length of the current seq to the smallest partition size
        my $length = $seq->length;
        $partitions[0]{size} += $length;
        #Increase the length of the partition
        $partitions[0]{length}++;
        #Write this sequence to the partitions file
        $partitions[0]{file}->write_seq($seq);
    }
}

#Report some basic statistics after the job
my $part = 1;
foreach my $partition (@partitions) {
    print STDERR "$outdir/$prefix$part.$format\n";
    print STDERR "\tSequence count = $partition->{length}\n";
    print STDERR "\tSequence characters = $partition->{size}\n";
    $part++;
}

1;
__END__

BioPerl-1.007002/scripts/seq/bp_seqretsplit.pl000444000766000024       265413155576320 21376 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
#
=head1 NAME

bp_seqretsplit - split a sequence (or stream) into a single file per sequence

=head1 SYNOPSIS

  bp_seqretsplit file1 file2 .. 
  # or
  bp_seqretsplit < file1 

=head1 DESCRIPTION 

The script will split all sequences from fasta file(s) (or stdin) to
individual files. The filename is the sequence ID (everything before
the 1st whitespace in a FASTA header).  Currently it doesn't check to
see that it isn't overwriting an existing file so IDs should be unique

This is inspired by EMBOSS seqretsplit tool.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
    http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:

https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

Jason Stajich Ejason_AT_bioperl_DOT_orgE

=cut

use strict;
use warnings;
use Bio::SeqIO;
my $in = Bio::SeqIO->new(-format => 'fasta',
			 -fh   => \*ARGV);
while( my $s = $in->next_seq ) {
    Bio::SeqIO->new(-format => 'fasta',
		    -file   => ">".$s->id.".fa")->write_seq($s);
}
    
BioPerl-1.007002/scripts/seq/bp_split_seq.pl000444000766000024      1013113155576320 21027 0ustar00cjfieldsstaff000000000000#!perl
use strict;
use warnings;

=head1 NAME

bp_split_seq - splits a sequence into equal sized chunks with an optional
            overlapping range

=head1 SYNOPSIS

bp_split_seq -c 10000 [-o 1000] [-i] -f seq.in

=head1 DESCRIPTION 

The script will split sequences into chunks

Mandatory Options:

  -c  Desired length of the resulting sequences.
  -f  Input file (must be FASTA format).

Special Options:

  -o  Overlapping range between the resulting sequences.
  -i  Create an index file with the resulting sequence files. This is
      useful if you want to pass this list as input arguments into
      another programs (i.e. CLUSTAL, HMMER, etc.).

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHORS

  Ewan Birney Ebirney-at-ebi.ac.ukE
  Mauricio Herrera Cuadra Emauricio at open-bio.orgE
  (some enhancements)

=cut

# Modules, pragmas and variables to use
use Bio::Seq;
use Bio::SeqIO;
use Getopt::Long;
use vars qw($opt_c $opt_o $opt_i $opt_f $index_file);

# Gets options from the command line
GetOptions qw(-c=i -o:i -i -f=s);

# If no mandatory options are given prints an error and exits
if (!$opt_c) {
    print "ERROR: No chunk size has been specified.\n" and exit();
} elsif (!$opt_f) {
    print "ERROR: No FASTA file has been specified.\n" and exit();
}

# Declares offset size
my $offset = $opt_o ? $opt_o : "0";

# Opens the FASTA file
my $in = Bio::SeqIO->new(
    -file   => "$opt_f",
    -format => "Fasta",
);
print "==> Opening FASTA file:\t\t\t\t$opt_f\n";

# Reads the next sequence object
while (my $seq = $in->next_seq()) {

    # Reads the ID for the sequence and prints it
    my $id = $seq->id();
    print "--> The ID for this sequence is:\t\t$id\n";

    # Reads the description for the sequence and prints it
    my $desc = $seq->desc();
    print "--> The description for this sequence is:\t$desc\n";

    # Gets sequence length and prints it
    my $seq_length = $seq->length();
    print "--> The length of this sequence is:\t\t$seq_length\n";

    # If the chunk size is bigger than the sequence length prints the error and exits
    (print "ERROR: Specified chunk size is bigger than sequence length.\n" and exit()) if ($opt_c > $seq_length);

    # Creates a directory for writing the resulting files
    mkdir("split", 0755) unless -e "split" and -d "split";

    # Creates the INDEX file if the option was given
    my $FH;
    if ($opt_i) {
        $index_file = "$id.c$opt_c.o$offset.INDEX";
        open $FH, '>', $index_file or die "Could not write file '$index_file': $!\n";
    }

    # Loops through the sequence
    for (my $i = 1; $i < $seq_length; $i += $opt_c) {
        my $end = (($i + $opt_c) > $seq_length) ? ($seq_length + 1) : ($i + $opt_c);
        my $seq_range = (($i + $opt_c) > $seq_length) ? "$i-".($end - 1) : "$i-$end";
        my $id = $seq->id();
        $id .= "_$seq_range";

        # Stores chunk into its corresponding FASTA file
        my $out = Bio::SeqIO->new(
            -file   => ">split/$id.faa",
            -format => "Fasta",
        );
        my $trunc_seq = $seq->trunc($i, $end - 1);
        $trunc_seq->id($id);
        $out->write_seq($trunc_seq);
        print "==> Sequence chunk:\t$seq_range\tstored in file:\tsplit/$id.faa\n";

        # Prints the current file name into the INDEX file if the option was given
        print $FH "split/$id.faa\n" if $opt_i;

        # Decreases the $i value with the offset value
        $i -= $offset;
    }

    # Closes the INDEX file if the option was given
    if ($opt_i) {
        print "==> INDEX stored in file:\t\t\t$index_file\n";
        close $FH;
    }
}

__END__
BioPerl-1.007002/scripts/seq/bp_translate_seq.pl000444000766000024       275613155576320 21667 0ustar00cjfieldsstaff000000000000#!perl
use strict;
use warnings;

=head1 NAME

bp_translate_seq - translates a sequence

=head1 SYNOPSIS

bp_translate_seq E cdna_cds.fa E protein.fa

=head1 DESCRIPTION 

The script will translate one fasta file (on stdin) to protein on stdout

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

  Ewan Birney Ebirney@ebi.ac.ukE

=cut

use Bio::SeqIO;
use Getopt::Long;

my ($format,$outfile) = 'fasta';

GetOptions(
    'f|format:s'  => \$format,
    'o|out|outfile:s' => \$outfile,
    );

my $oformat = 'fasta';

# this implicity uses the <> file stream
my $seqin = Bio::SeqIO->new( -format => $format, -fh => \*ARGV); 
my $seqout;
if( $outfile ) {
    $seqout = Bio::SeqIO->new( -format => $oformat, -file => ">$outfile" );
} else {
# defaults to writing to STDOUT
    $seqout = Bio::SeqIO->new( -format => $oformat );
}
while( (my $seq = $seqin->next_seq()) ) {
	my $pseq = $seq->translate();
	$seqout->write_seq($pseq);
}

__END__
BioPerl-1.007002/scripts/seq/bp_unflatten_seq.pl000444000766000024      1634613155576320 21712 0ustar00cjfieldsstaff000000000000#!perl
use strict;
use warnings;
# Author Chris Mungall 

=head1 NAME

bp_unflatten_seq - unflatten a genbank or genbank-style feature file into
a nested SeqFeature hierarchy

=head1 SYNOPSIS

  bp_unflatten_seq.PLS -e 3 -gff ~/cvs/bioperl-live/t/data/AE003644_Adh-genomic.gb

  bp_unflatten_seq.PLS --detail ~/cvs/bioperl-live/t/data/AE003644_Adh-genomic.gb

  bp_unflatten_seq.PLS -i foo.embl --from embl --to chadoxml -o out.chado.xml

  bp_unflatten_seq.PLS --notypemap --detail --to asciitree -ethresh 2 AE003644_Adh-genomic.gb

=head1 DESCRIPTION 

This script will B a genbank or genbank-style file of
SeqFeatures into a nested hierarchy.

See L

In a GenBank/EMBL representation, features are 'flat' - for example,
there is no link between an mRNA and a CDS, other than implicit links
(eg via tags or via splice site coordinates) which may be hard to code
for.

This is most easily illustrated with the default output format,
B

An unflattened genbank feature set may look like this (AB077698)

  Seq: AB077698
    databank_entry                                   1..2701[+]
    gene                                             
      mRNA                                           
        CDS hCHCR-G                                  80..1144[+]
        exon                                         80..1144[+]
      five_prime_UTR                                 1..79[+]
      located_sequence_feature                       137..196[+]
      located_sequence_feature                       239..292[+]
      located_sequence_feature                       617..676[+]
      located_sequence_feature                       725..778[+]
      three_prime_UTR                                1145..2659[+]
      polyA_site                                     1606..1606[+]
      polyA_site                                     2660..2660[+]

Or like this (portion of AE003734)


  gene                                             
    mRNA CG3320-RA                                 
      CDS CG3320-PA                                53126..54971[-]
      exon                                         52204..53323[-]
      exon                                         53404..53631[-]
      exon                                         53688..53735[-]
      exon                                         53798..53918[-]
      exon                                         54949..55287[-]
    mRNA CG3320-RB                                 
      CDS CG3320-PB                                53383..54971[-]
      exon                                         52204..53631[-]
      exon                                         53688..53735[-]
      exon                                         53798..53918[-]
      exon                                         54949..55287[-]

The unflattening will also 'normalize' the containment hierarchy (in
the sense of standardising it - e.g. making sure there is always a
transcript record, even if genbank just specifies CDS and gene)

By default, the GenBank types will be mapped to SO types

See L

=head1 COMMAND LINE ARGUMENTS

=over

=item -i|input FILE

input file (can also be specified as last argument)

=item -from FORMAT

input format (defaults to genbank)

probably doesn't make so much sense to use this for non-flat formats;
ie other than embl/genbank

=item -to FORMAT

output format (defaults to asciitree)

should really be a format that is nested SeqFeature aware; I think
this is only asciitree, chadoxml and gff3

=item -gff

with export to GFF3 format (pre-3 GFFs make no sense with unflattened
sequences, as they have no set way of representing feature graphs)

=item -o|output FILE

outfile defaults to STDOUT

=item -detail

show extra detail on features (asciitree mode only)

=item -e|ethresh INT

sets the error threshold on unflattening

by default this script will throw a wobbly if it encounters weird
stuff in the genbank file - raise the error threshold to signal these
to be ignored (and reported on STDERR)

=item -nomagic

suppress use_magic in unflattening (see
L

=item -notypemap

suppress type mapping (see
L


=back

=head1 TODO

L allows fine-grained control
over the unflattening process - need to add more options to allow this
control at the command line


=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

 Chris Mungall Ecjm-at-bioperl.orgE

=cut

use Bio::SeqIO;
use Bio::SeqFeature::Tools::Unflattener;
use Bio::SeqFeature::Tools::TypeMapper;
use Bio::SeqFeature::Tools::IDHandler;
use Bio::Tools::GFF;

use Getopt::Long;

my ($input,$from,$to,$output,$verbosity,$ethresh,$nomagic,$group_tag,$detail,
    $notypemap);
$from = 'genbank';
$to = 'asciitree';
$ethresh = 3;
my $gff;
my @remove_types = ();

GetOptions(
	   'i|input:s' => \$input,
	   'from:s'  => \$from,
	   'to:s'  => \$to,
	   'o|output:s'=> \$output,
	   "verbosity|v=s"=>\$verbosity,
	   "ethresh|e=s"=>\$ethresh,
	   "remove_type=s@"=>\@remove_types,
	   "nomagic"=>\$nomagic,
	   "notypemap"=>\$notypemap,
	   "group_tag"=>\$group_tag,
	   "detail"=>\$detail,
           "gff"=>\$gff,
	   "h|help"=>sub {
	       system("perldoc $0");
	       exit 0;
	   },
	  );
                       
                       
if ($to =~ /^gff/i) {
    $gff = 1;
}

$input = $input || shift if @ARGV;

my $in = new Bio::SeqIO(-file => $input,
			-format => $from);
my $out;
my @out_opt = $output ? (-file => ">$output") : ();
unless ($gff) {
    $out = new Bio::SeqIO(-format=>$to, @out_opt);
    $out->show_detail($detail) if $out->can("show_detail") && $detail;
}

my $unflattener = Bio::SeqFeature::Tools::Unflattener->new;
$unflattener->verbose($verbosity);
$unflattener->error_threshold($ethresh);
my $tm = Bio::SeqFeature::Tools::TypeMapper->new;
my $idhandler = Bio::SeqFeature::Tools::IDHandler->new;

while( my $seq = $in->next_seq ) {    
    $unflattener->remove_types(-seq=>$seq,
                               -types=>\@remove_types)
      if @remove_types;

    $unflattener->unflatten_seq(-seq=>$seq,
				-use_magic=>!$nomagic,
				-group_tag=>$group_tag,
			       );
    $unflattener->report_problems(\*STDERR);
    $tm->map_types_to_SO(-seq=>$seq) unless $notypemap;

    my @seq_args = ($seq);
    if ($to eq 'chadoxml') {
	@seq_args = (-seq=>$seq, -nounflatten=>1)
    }
    if ($gff) {
        my $gffio = Bio::Tools::GFF->new(@out_opt, -noparse=>1, -gff_version => 3);
        $idhandler->set_ParentIDs_from_hierarchy($seq);
        foreach my $feature ($seq->get_all_SeqFeatures) {
            $gffio->write_feature($feature);
        }
        $gffio->close();
    }
    else {
        $out->write_seq(@seq_args);
    }

}

__END__
BioPerl-1.007002/scripts/seqstats000755000766000024          013155576320 16714 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/scripts/seqstats/TAG000444000766000024        12613155576320 17366 0ustar00cjfieldsstaff000000000000These are scripts to generate common statistics on protein and
nucleotide sequences.

BioPerl-1.007002/scripts/seqstats/bp_aacomp.pl000444000766000024       530313155576320 21330 0ustar00cjfieldsstaff000000000000#!perl
use strict;
use warnings;
use Carp;

use Bio::SeqIO;
use Getopt::Long;
use Bio::SeqUtils;
use Bio::Tools::IUPAC;

my $table = new Bio::SeqUtils;
my @BASES = $table->valid_aa(0);
my %all = $table->valid_aa(2);
my ($file,$format,$help) = ( undef, 'fasta');
GetOptions(
	   'i|in:s'  => \$file,
	   'f|format:s' => \$format,
	   'h|help|?'  => \$help,
	   );

my $USAGE = "usage: aacomp [-f format] filename\n\tdefault format is fasta\n";
$file = shift unless $file;

die $USAGE if $help;

my $seqin;
if( defined $file ) {
    print "Could not open file [$file]\n$USAGE" and exit unless -e $file;
    $seqin = new Bio::SeqIO(-format => $format,
			    -file   => $file);
} else {
    $seqin = new Bio::SeqIO(-format => $format,
			    -fh     => \*STDIN);
}

my %composition;
my $total;
foreach my $base ( @BASES ) {
    $composition{$base} = 0;
}
while ( my $seq = $seqin->next_seq ) {
    if( $seq->alphabet ne 'protein' ) {
	confess("Must only provide amino acid sequences to aacomp...skipping this seq");
	next;
    }
    foreach my $base ( split(//,$seq->seq()) ) {
	$composition{uc $base}++;
	$total++;
    }
}

printf("%d aa\n",$total); 
printf("%5s %4s\n", 'aa', '#' );
my $ct = 0;
foreach my $base ( @BASES ) {
    printf(" %s %s %3d\n", $base, $all{$base}, $composition{$base} );
    $ct += $composition{$base};
}
printf( "%6s %s\n", '','-'x5);
printf( "%6s %3d\n", '',$ct);


__END__


=head1 NAME

bp_aacomp - amino acid composition of protein sequences

=head1 SYNOPSIS

  bp_aacomp [-f/--format FORMAT] [-h/--help] filename
  or
  bp_aacomp [-f/--format FORMAT] < filename
  or
  bp_aacomp [-f/--format FORMAT] -i filename

=head1 DESCRIPTION

This scripts prints out the count of amino acids over all protein
sequences from the input file.

=head1 OPTIONS

The default sequence format is fasta.

The sequence input can be provided using any of the three methods:

=over 3

=item unnamed argument

  bp_aacomp filename

=item named argument

  bp_aacomp -i filename

=item standard input

  bp_aacomp < filename

=back

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Jason Stajich

Email jason@bioperl.org

=head1 HISTORY

Based on aacomp.c from an old version of EMBOSS

=cut
BioPerl-1.007002/scripts/seqstats/bp_chaos_plot.pl000444000766000024      1030713155576320 22243 0ustar00cjfieldsstaff000000000000#!perl

use strict;
use warnings;

use Bio::SeqIO;
use Getopt::Long;
use GD;

use vars qw( $USAGE %VALIDFORMATS);

%VALIDFORMATS = ( 'png'  => 1,
		  'jpeg' => 1,
		  'gd2'  => 1,
		  'gd'   => 1,
		  'gif'	 => 1,
		  'wbmp' => 1 );

$USAGE = "usage:\tchaos_plot -i/--input=INPUTFILE -f/--format=SEQFORMAT \n".
    "\t-o/--output=OUTPUTFILE -g/--graphics=GRAPHIC TYPE\n".
    "\t-w/--width=600 -h/--height=400\n";

$USAGE .= "\tValid graphics formats: (" . join(",", ( keys %VALIDFORMATS )) .")\n";
$USAGE .= "\tImage size defaults to 600x400, SEQFORMAT to fasta\n";
$USAGE .= "\tINPUTFILE can also be read from STDIN\n";

my ($format,$graph,$width,$height,$seqfile,$output) = ('fasta', 'png', 600, 400);
GetOptions( "i|input:s"           => \$seqfile,
	    "f|format:s"          => \$format,
	    "o|output:s"          => \$output,
	    "g|graph|graphics:s"  => \$graph,
            "width:i"             => \$width,
            "height:i"            => \$height
	    );

if( ! $output || ! $VALIDFORMATS{$graph} ) {
    die $USAGE ;
}
my $seqin;
$seqfile = shift unless $seqfile;
if( defined $seqfile ) {
    print "Could not open file [$seqfile]\n$USAGE" and exit unless -e $seqfile;
    $seqin = new Bio::SeqIO(-format => $format,
			    -file   => $seqfile);
} else {
    $seqin = new Bio::SeqIO(-format => $format,
			    -fh     => \*STDIN);
}

my $img = new GD::Image($width,$height);
my $white = $img->colorAllocate(255,255,255); 
my $black = $img->colorAllocate(0,0,0); 

my $seq = $seqin->next_seq;
die("Sequence type must be DNA not " . $seq->alphabet())
    unless $seq->alphabet ne 'dna' or $seq->alphabet ne 'rna';
my %nmerdata;
my $len = $seq->length();
my $max = 0;

my ($x,$y) = ( 0.5, 0.5);
$img->string(gdGiantFont, 1,1, 'A', $black);
$img->string(gdGiantFont, 0,$height - 15, 'C', $black);
$img->string(gdGiantFont, $width - 15,1, 'T', $black);
$img->string(gdGiantFont, $width - 15,$height -20, 'G', $black);

for( my $i = 1; $i <= $len; $i++ ) {

    my $base = lc $seq->subseq($i,$i);
    if( $base eq 'a' ) {
	$x *= 0.5;
	$y  *= 0.5;
    } elsif ( $base eq 'g' ) {
	$x = ( $x + 1.0 ) * 0.5;
	$y  = ( $y + 1.0  ) * 0.5; 
    } elsif ( $base eq 'c' ) {
	$x *= 0.5;
	$y  = ( $y + 1.0  ) * 0.5; 
    } elsif ( $base eq 't' or $base eq 'u' ) {
	$x = ( $x + 1.0 ) * 0.5;
	$y  *= 0.5;
    }

    $img->setPixel($x * $width,$y * $height, $black);
}
open my $OUT, '>', $output or die "Could not write file '$output': $!\n";
binmode $OUT;
$graph =~ s/jpg/jpeg/;

print $OUT $img->$graph();
close $OUT;


__END__

=head1 NAME

bp_chaos_plot - a chaos plot from DNA and RNA sequences

=head1 SYNOPSIS

  bp_chaos_plot.pl -i/--input=INPUTFILE -f/--format=SEQFORMAT
        -o/--output=OUTPUTFILE -g/--graphics=GRAPHIC FORMAT
        -w/--width=WIGHT -h/--height=HEIGHT

=head1 DESCRIPTION

This scripts generates image files using GD image library to visualize
nucleotide sequences using chaos plot.

=head1 OPTIONS

Valid graphics formats are currently gd, gd2, png, wbmp, jpeg and gif.

The default size of the image file is 600x400.

The sequence input can be provided using any of the three methods:

=over 3

=item unnamed argument

  bp_chaos_plot filename

=item named argument

  bp_chaos_plot -i filename

=item standard input

  bp_chaos_plot < filename

=back

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Jason Stajich

Email jason@bioperl.org

=head1 HISTORY

This code is based on EMBOSS C code for chaos.c by Ian Longden.
Included are documentation from EMBOSS code:

Chaos produces a chaos plot.  The original application is part of the
ACEDB genome database package, written by ** Richard Durbin (MRC LMB,
UK) rd@mrc-lmba.cam.ac.uk, and Jean Thierry-Mieg (CRBM du CNRS,
France) mieg@crbm1.cnusc.fr

=cut
BioPerl-1.007002/scripts/seqstats/bp_gccalc.pl000444000766000024       637113155576320 21312 0ustar00cjfieldsstaff000000000000#!perl

use strict;
use warnings;

use Bio::SeqIO;
use Bio::Tools::SeqStats;
use Getopt::Long;
my $format = 'fasta';
my $file;
my $help =0;
my $aggregate;
GetOptions(
	    'f|format:s' => \$format,
	    'i|in:s'     => \$file,
	    'h|help|?'    => \$help,
	    'a|aggregate!'=> \$aggregate,
	    );


my $USAGE = "usage: gccalc.pl -f format -i filename\n";
if( $help ) {
    die $USAGE;
}

$file = shift unless $file;
my $seqin;
if( defined $file ) {
    print "Could not open file [$file]\n$USAGE" and exit unless -e $file;
    $seqin = new Bio::SeqIO(-format => $format,
			    -file   => $file);
} else {
    $seqin = new Bio::SeqIO(-format => $format,
			    -fh     => \*STDIN);
}
my ($total_base, $total_gc);
while( my $seq = $seqin->next_seq ) {
    next if( $seq->length == 0 );
    if( $seq->alphabet eq 'protein' ) {
	warn("gccalc does not work on amino acid sequences ...skipping this seq");
	next;
    }

    my $seq_stats  =  Bio::Tools::SeqStats->new('-seq'=>$seq);
    my $hash_ref = $seq_stats->count_monomers();  # for DNA sequence
    print "Seq: ", $seq->display_id, " ";
    print $seq->desc if $seq->desc;
    print " Len:", $seq->length, "\n";
    $total_base += $seq->length;
    $total_gc   += $hash_ref->{'G'} + $hash_ref->{'C'};
    printf "GC content is %.4f\n", ($hash_ref->{'G'} + $hash_ref->{'C'}) /
	$seq->length();

    foreach my $base (sort keys %{$hash_ref}) {
	print "Number of bases of type ", $base, "= ", $hash_ref->{$base},"\n";
    }
    print "--\n";
}
if( $aggregate ) {
  printf "Total GC content is %.4f out of %d bases\n", $total_gc / $total_base, $total_base;
}
# alternatively one could use code submitted by
# cckim@stanford.edu

sub calcgc {
    my $seq = $_[0];
    my @seqarray = split('',$seq);
    my $count = 0;
    foreach my $base (@seqarray) {
	$count++ if $base =~ /[G|C]/i;
    }

    my $len = $#seqarray+1;
    return $count / $len;
}


__END__

=head1 NAME

bp_gccalc - GC content of nucleotide sequences

=head1 SYNOPSIS

  bp_gccalc [-f/--format FORMAT] [-h/--help] filename
  or
  bp_gccalc [-f/--format FORMAT] < filename
  or
  bp_gccalc [-f/--format FORMAT] -i filename

=head1 DESCRIPTION

This scripts prints out the GC content for every nucleotide sequence
from the input file.

=head1 OPTIONS

The default sequence format is fasta.

The sequence input can be provided using any of the three methods:

=over 3

=item unnamed argument

  bp_gccalc filename

=item named argument

  bp_gccalc -i filename

=item standard input

  bp_gccalc < filename

=back

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Jason Stajich

Email jason@bioperl.org

=head1 HISTORY

Based on script code (see bottom) submitted by cckim@stanford.edu

Submitted as part of bioperl script project 2001/08/06

=cut
BioPerl-1.007002/scripts/seqstats/bp_oligo_count.pl000444000766000024      1412113155576320 22427 0ustar00cjfieldsstaff000000000000#!perl
#
# oligomer_freq.pl
# We use this to determine what primers are useful for frequent priming of
# nucleic acid for random labeling
# Input: Sequence file, oligomer length
# Output: Tab-delimited text file of oligomer frequencies
# Written July 2, 2001
# Charles C. Kim

###########
# MODULES #
###########
use Bio::Seq;
use Bio::SeqIO;
use Getopt::Long;

#########################
# VARIABLES & FILENAMES #
#########################

use strict;
use warnings;

my ($format, $infile, $help, $outfile, $oligomerlength) = ('fasta');
GetOptions(
           'f|format:s'            => \$format,
           'i|in|s|sequence:s'     => \$infile,
           'h|help|?'              => \$help,
           'o|out:s'               => \$outfile,
           'length:i'              => \$oligomerlength
          );

my $USAGE = "Usage:\toligo_count [-h/--help] [-l/--length OLIGOLENGTH]\n".
    "\t[-f/--format SEQFORMAT] [-i/--in/-s/--sequence SEQFILE]\n".
    "\t[-o/--out OUTFILE]\n".
    "\tDefault SEQFORMAT is fasta\n";

print $USAGE and exit if $help;

unless ($infile ) {
    print 'Enter your concatenated FASTA sequence filename: ';
    chomp ($infile=);
}
unless (-e $infile) { die "$infile not found\n"; }

if ($outfile) {
    if (-e $outfile) {
	print "$outfile already exists!  Overwrite (Y/N)? ";
	chomp ($_ = );
	while (/[^yn]/i) {
	    print 'Y or N, please: ';
	    chomp ($_ = );
	}
	if (/n/i) { die "$outfile not overwritten.\n"; }
    }
#} else {
#    print 'Enter an output filename: ';
#    chomp ($outfile=);
#    if (-e $outfile) {
#	print "$outfile already exists!  Overwrite (Y/N)? ";
#	chomp ($_ = );
#	while (/[^yn]/i) {
#	    print 'Y or N, please: ';
#	    chomp ($_ = );
#	}
#	if (/n/i) { die "$outfile not overwritten.\n"; }
#    }
}

unless ($oligomerlength) {
    while () {
	print 'Enter an oligomer length to count: ';
	chomp($oligomerlength=);
	if ($oligomerlength !~ /\d/) {
	    print "Value is non-numeric!\n";
	}
	else {last;}
    }
}


########
# MAIN #
########

if ($oligomerlength >= 9) {
    print "An oligomer length of $oligomerlength will generate ";
    print 4 ** $oligomerlength, " combinations,\nwhich could cause ";
    print "an out of memory error.  Proceed? (y/n) ";
    chomp($_=);
    if (/y/i) { ; }
    else { die "Program terminated\n"; }
}
my @oligoseqs = &generate_all_oligos($oligomerlength);
my %oligos = ();
foreach  (@oligoseqs) {
    $oligos{$_} = 0;
}

my $in = Bio::SeqIO->new( -file => $infile,
		       -format => $format);
my $seqnumber = 0;
my $oligocounts = 0;
my $exception;
while (my $seq = $in->next_seq() ) {
    my $len = $seq->length();
    my $position = 1;
    if ($position+$oligomerlength > $len) {
	$exception = 2;
	next;
    }
    $seq = uc $seq->seq; #string
    $exception = 1 if $seq =~ /[^GATC]/;

    while ($position + $oligomerlength-1 <= $len) {
	$oligos{substr $seq, $position-1, $oligomerlength}++;
	$position++;
	if ($position%250000 == 0) {print "$position\n";}
    }
    $oligocounts += $position-1;
    $seqnumber++;
}

my $OUTFILE;
if ($outfile) {
    open $OUTFILE, '>', $outfile or die "Could not open file '$outfile': $!\n";
} else {
    open $OUTFILE, '>-'; # STDOUT
}
print $OUTFILE "$seqnumber sequences analyzed\n";
print $OUTFILE "$oligocounts total $oligomerlength-mers counted\n";
print $OUTFILE "$oligomerlength-mer\tNumber\tFrequency\n";
foreach my $key (sort keys %oligos) {
    print $OUTFILE "$key\t$oligos{$key}\t", $oligos{$key}/$oligocounts, "\n";
}
close $OUTFILE;

if ($exception) {
    if ($exception == 1) {
	print "Non-standard (non-GATC) bases were found in sequence\n";
    }
    if ($exception == 2) {
	print "Oligomer length greater than sequence length\n";
    }
}

#¬ify();

###############
# SUBROUTINES #
###############

sub generate_all_oligos {
    my $oligolength = $_[0];
    my $iter = 1;
    my @newarray = qw{A C G T};
    my @bases = qw{A C G T};

    while ($iter < $oligolength) {
	my @oldarray = @newarray;
	@newarray = ();
	foreach my $oligoseq (@oldarray) {
	    foreach my $newbase (@bases) {
		push @newarray, $oligoseq . $newbase;
	    }
	}
	$iter++;
    }
    return @newarray;
}

# if you wanted to be notified about status of running
#my $EMAILADDRESS = undef;
#die("Must change script to a valid email addres for notification") 
#    unless( defined $EMAILADDRESS );

#sub notify {
#    $address = $EMAILADDRESS;
#    $address = $_[0] if $_[0];
#    open(SENDMAIL, "|/usr/lib/sendmail -oi -t") or die "Can't fork for sendmail: $!\n";
#    print SENDMAIL <<"EOF";
#From: Computer
#To: $address
#Subject: Program Finished
#	
#EOF
#    close(SENDMAIL) or warn "sendmail didn't close nicely";
#}

__END__

=head1 NAME

bp_oligo_count - oligo count and frequency

=head1 SYNOPSIS

  Usage:  bp_oligo_count [-h/--help] [-l/--length OLIGOLENGTH]
          [-f/--format SEQFORMAT] [-i/--in/-s/--sequence SEQFILE]
          [-o/--out OUTFILE]

=head1 DESCRIPTION

This scripts counts occurrence and frequency for all oligonucleotides
of given length.

It can be used to determine what primers are useful for
frequent priming of nucleic acid for random labeling.

Note that this script could be run by utilizing the compseq
program which is part of EMBOSS.

=head1 OPTIONS

The default sequence format is fasta. If no outfile is given, the
results will be printed to standard out. All other options can entered
interactively.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Charles C. Kim

Email cckim@stanford.edu

=head1 HISTORY

Written July 2, 2001

Submitted to bioperl scripts project 2001/08/06

EE 100 x speed optimization by Heikki Lehvaslaiho

=cut
BioPerl-1.007002/scripts/taxa000755000766000024          013155576320 16002 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/scripts/taxa/TAG000444000766000024         6713155576320 16440 0ustar00cjfieldsstaff000000000000These are scripts to create and query taxonomic trees.
BioPerl-1.007002/scripts/taxa/bp_classify_hits_kingdom.pl000444000766000024      1720213155576320 23553 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=head1 NAME

bp_classify_hits_kingdom - classify BLAST hits by taxonomic kingdom

=head2 USAGE

bp_classify_hits_kingdom [-i tab_file] [-i second_BLAST_file] [-e evalue_cutoff]
                      [-t dir_where_TAXONOMY_files_are] [-g gi2taxid] 
                      [-z PATH_TO_zcat] [-v]

=head2 DESCRIPTION

Will print out the taxonomic distribution (at the kingdom level) for a
set of hits against the NR database.  By default, this script assumes you
did a search against the protein database (gi_taxid_nuc.dump file).

This expects BLAST files in tabbed -m9 or -m8 format.  Output with -m
8 or use blast2table.pl to convert (or fastam9_to_table.PLS if using
FASTA).

  Input values:
    -t/--taxonomy Directory where the taxonomy .dmp files are (from NCBI)
    -g/--gi       File path of the gi2taxid file (gi_taxid_prot.dmp for proteins
                  or gi_taxid_nucl.dmp if the search was against a nucleid database)
    -i/--in       The name of the tab delimited -m8/-m9 output files to process
    -e/--evalue   Provide an E-value cutoff for hits to be considered
    -z/--zcat     Path to the 'zcat' executable, can also be 'gunzip -c'
                  if no zcat on your system.
  Flags:
    -v/--verbose  To turn on verbose messages
    -h/--help     Display this helpful information

This is intended to be useful starting script, but users may want to
customize the output and parameters. Note that I am summarizing the
kingdoms here and Eukaryota not falling into Metazoa, Viridiplantae, or
Fungi gets grouped into the general superkingdom Eukaryota for simplicity.
There are comments in the code directing you to where changes can be made
if you wanted to display hits by phylum for example.  Note that you must
wipe out the cache file 'gi2class' that is created in your directory after
making these changes.

=head2 AUTHOR

Jason Stajich jason_at_bioperl_dot_org

=cut

use strict;
use warnings;
use Bio::DB::Taxonomy;
use DBI;
use Env;
use File::Spec;
use vars qw($SEP);
my $DEBUG = 0;
use Getopt::Long;
$SEP = '_';

my $evalue_filter = 1e-3;
my @files;
my $zcat = 'zcat'; # or gunzip -c 
my $prefix = File::Spec->catfile($HOME,'taxonomy');
my $gi2taxidfile = "$prefix/gi_taxid_prot.dmp.gz";
my $force = 0; # don't use the cached gi2taxid file
GetOptions(
       'v|verbose|debug' => \$DEBUG,
       'force!'          => \$force,
       'z|zcat:s'        => \$zcat,
       'i|in:s'          => \@files,
       'e|evalue:f'      => \$evalue_filter,
       't|taxonomy:s'    => \$prefix,
       'g|gi|gi2taxid:s' => \$gi2taxidfile,
       'h|help'          => sub { system('perldoc', $0); exit },
       );

# insure idx location is created
mkdir(File::Spec->catfile($prefix,'idx')) 
    unless -d File::Spec->catfile($prefix,'idx');

# these files came from ftp://ftp.ncbi.nih.gov/pub/taxonomy
my $taxdb = Bio::DB::Taxonomy->new
    (-source => 'flatfile',
     -directory => File::Spec->catfile
     ($prefix, 'idx'), 
     -nodesfile => File::Spec->catfile($prefix,'nodes.dmp'),
     -namesfile => File::Spec->catfile($prefix,'names.dmp')
     );
my %query;

my (%taxid4gi,%gi2node);
my $dbh = tie(%gi2node, 'DB_File', 'gi2class');
my $giidxfile = File::Spec->catfile($prefix,'idx','gi2taxid');
my $done = -f $giidxfile;
$done = 0 if $force;
my $dbh2 = $dbh = DBI->connect("dbi:SQLite:dbname=$giidxfile","","");
if( ! $done ) {
    $dbh2->do("CREATE TABLE gi2taxid ( gi integer PRIMARY KEY,
                      taxid integer NOT NULL)");
    $dbh2->{AutoCommit} = 0;
    my $fh;
    # this file came from ftp://ftp.ncbi.nih.gov/pub/taxonomy
    # I'm interested in protein hits therefor _prot file.
    if (not -f $gi2taxidfile) {
        die "Error: File $gi2taxidfile does not exist\n";
    }
    if( $gi2taxidfile =~ /\.gz$/ ) {
        open($fh, "$zcat $gi2taxidfile |" ) || die "$zcat $gi2taxidfile: $!";
    } else {
        open($fh, $gi2taxidfile ) || die "Error: could not read file $gi2taxidfile: $!";
    }
    my $i = 0;
    my $sth = $dbh2->prepare("INSERT INTO gi2taxid (gi,taxid) VALUES (?,?)");

    while(<$fh>) {
        my ($gi,$taxid) = split;
        $sth->execute($gi,$taxid);
        $i++;
        if( $i % 500000 == 0 ) {
            $dbh->commit;
            warn("$i\n") if $DEBUG;
        } 
    }
    $dbh->commit;
    $sth->finish;
}

for my $file ( @files ) {
    warn("$file\n");
    my $gz;
    if( $file =~ /\.gz$/) {
        $gz = 1;
    }
    my ($spname) = split(/\./,$file); 
    my ($fh,$i);
    if( $gz ) {
        open($fh, "$zcat $file |")  || die "$zcat $file: $!";
    } else {
        open($fh, $file) || die "$file: $!";
    }
    my $sth = $dbh->prepare("SELECT taxid from gi2taxid WHERE gi=?");
    while(<$fh>) {
        next if /^\#/;
        my ($qname,$hname,$pid,$qaln,$mismatch,$gaps,
            $qstart,$qend,$hstart,$hend,
            $evalue,$bits,$score) = split(/\t/,$_);        
        next if( $evalue > $evalue_filter );
        if( ! exists $query{$spname}->{$qname} ) {
            $query{$spname}->{$qname} = {};
        }
        
        if( $hname =~ /gi\|(\d+)/) {
            my $gi = $1;
            if( ! $gi2node{$gi} ){ # see if we cached the results from before
                $sth->execute($gi);
                my $taxid;
                $sth->bind_columns(\$taxid);
                if( ! $sth->fetch ) {
                    warn("no taxid for $gi\n");
                    next;
                }
                my $node = $taxdb->get_Taxonomy_Node($taxid);
                if( ! $node ) {
                    warn("cannot find node for gi=$gi ($hname) (taxid=$taxid)\n");
                    next;
                }
                my $parent = $taxdb->get_Taxonomy_Node($node->parent_id);

                # THIS IS WHERE THE KINGDOM DECISION IS MADE
                # DON'T FORGET TO WIPE OUT YOUR CACHE FILE
                # gi2class after you make changes here
                while( defined $parent && $parent->node_name ne 'root' ) { 
                    # this is walking up the taxonomy hierarchy
                    # can be a little slow, but works...
                    #warn( "\t",$parent->rank, " ", $parent->node_name, "\n");
                    # deal with Eubacteria, Archea separate from 
                    # Metazoa, Fungi, Viriplantae differently
                    # (everything else Eukaryotic goes in Eukaryota)
                    if( $parent->rank eq 'kingdom') {
                        # caching in ... 
                        ($gi2node{$gi}) = $parent->node_name;
                        last;
                    } elsif( $parent->rank eq 'superkingdom' ) {
                        # caching in ... 
                        ($gi2node{$gi}) = $parent->node_name;
                        $gi2node{$gi} =~ s/ \<(bacteria|archaea)\>//g;
                        last;
                    }
                    $parent = $taxdb->get_Taxonomy_Node($parent->parent_id);
                }
            } 
            my ($kingdom) = $gi2node{$gi};
            #warn("$gi2node{$gi}\n");
            unless( defined $kingdom && length($kingdom) ) {
                #warn("no kingdom for $hname\n");
            } else {
                $query{$spname}->{$qname}->{$kingdom}++;
            }
        } else {
            warn("no GI in $hname\n");
        }
    }
    last if ( $DEBUG && $i++ > 10000);
    $sth->finish;
}

# print out the taxonomic distribution
while( my ($sp,$d) = each %query ) {
    my $total = scalar keys %$d;
    print "$sp total=$total\n";
    my %seen;
    for my $v ( values %$d ) {
        my $tag = join(",",sort keys %$v );
        $seen{$tag}++;
    }
    for my $t ( sort { $seen{$a} <=> $seen{$b} } keys %seen ) {
        printf " %-20s\t%d\t%.2f%%\n",
        $t,$seen{$t}, 100 * $seen{$t} / $total;
    }
    print "\n\n";
}
BioPerl-1.007002/scripts/taxa/bp_local_taxonomydb_query.pl000444000766000024       336413155576320 23746 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
use strict;
use warnings;
use Bio::DB::Taxonomy;

use strict;
use Getopt::Long;
my $verbose = 0;
my $plain   = 0;
my ($nodesfile,$namesfile);
my $idx_dir = '/tmp/idx';
GetOptions('v|verbose' => \$verbose,
	   'nodes:s'   => \$nodesfile,
	   'names:s'   => \$namesfile,
	   'idx:s'     => \$idx_dir,
	   'h|help'    => sub{ exec('perldoc',$0);
				exit(0)
				} );

unless( @ARGV || $nodesfile || $namesfile ) {
    exec('perldoc',$0);
    exit(0);
}
mkdir($idx_dir) unless -d $idx_dir;

my $db = new Bio::DB::Taxonomy(-source    => 'flatfile',
			       -nodesfile => $nodesfile,
			       -namesfile => $namesfile,
			       -directory => $idx_dir);
foreach my $sp ( @ARGV ) {
    my $node = $db->get_Taxonomy_Node(-name => $sp);
    if( defined $node ) {
	print "id is ", $node->id, "\n"; # 9606
	print "rank is ", $node->rank, "\n"; # species
	print "scientific name is ", $node->scientific_name, "\n"; # Homo sapiens
	print "division is ", $node->division, "\n"; # Primates
    } else {
	warn("no node found for query $sp");
    }
}

=head1 NAME

bp_local_taxonomydb_query - query a local TaxonomyDB for species or taxonid

=head1 DESCRIPTION

This script provides an example implementation of access to a local
Taxonomy database implemented with Berkeley DB (DB_File module is needed).

Usage:

 bp_local_taxonomydb_query.PLS: [-v] --nodes nodes.dmp --names names.dmp "Genus1 species1" "Genus2 species2"

Providing the nodes.dmp and names.dmp files from the NCBI Taxonomy
dump (see Bio::DB::Taxonomy::flatfile for more info) is only necessary
on the first time running.  This will create the local indexes and may
take quite a long time.  However once created, these indexes will
allow fast access for species to taxon id OR taxon id to species name
lookups.
BioPerl-1.007002/scripts/taxa/bp_query_entrez_taxa.pl000444000766000024       521513155576320 22731 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
# This is a -*-Perl-* file (make my emacs happy)

=head1 NAME

bp_query_entrez_taxa - query Entrez taxonomy database and print out information 

=head1 USAGE

bp_query_entrez_taxa "Homo sapiens" "Saccharomyces cerevisiae" Rhizopus Metazoa
bp_query_entrez_taxa -gi 28800981 -gi 54301680 -db nucleotide
bp_query_entrez_taxa -gi 71836523 -db protein

 Provide the genus and species name in quotes, you can also query for
 a non-species node like Family or Order

Command-line options:
   -v or --verbose  : print verbose debugging info
   -gi              : one or many GI numbers to lookup taxon id for
   -db              : the sequence db (nucleotide or protein) the GI is for

   other arguments are assumed to be species names to lookup in taxonomy db


=head1 AUTHOR

Jason Stajich jason-at-bioperl-dot-org

=cut

use strict;
use warnings;
use Bio::DB::Taxonomy;
use Getopt::Long;

my $verbose = 0;
my (@gi, $dbname);
GetOptions('v|verbose' => \$verbose,
	   'gi:i'      => \@gi,
	   'db:s'      => \$dbname);

my $db = new Bio::DB::Taxonomy(-source => 'entrez', -verbose => $verbose);
if( @gi ) {
    my @nodes= $db->get_Taxonomy_Node(-gi => \@gi,
				      -db => $dbname);
    for my $node ( @nodes ) {
	my $gi = shift @gi;
	print " for gi $gi:\n";
	print " taxonid is ",$node->ncbi_taxid,"\n";    
	print " node is ", join(", ",$node->classification), "\n";
	print " species is ", $node->species,"\n";
	print " parent is ", $node->parent_id, "\n";
	print " rank is ", $node->rank, "\n";
	print " genetic_code  ", $node->genetic_code, "\n";
	print " mito_genetic_code  ", $node->mitochondrial_genetic_code, "\n";
	print " scientfic name is ", $node->binomial, "\n";
    }	
}

print "\n\n";
for my $name ( @ARGV ) {
    my $taxonid = $db->get_taxonid($name);
    my $node   = $db->get_Taxonomy_Node(-taxonid => $taxonid);
    print "taxonid is $taxonid\n";

    print " node is ", join(", ",$node->classification), "\n";
    print " species is ", $node->species,"\n";
    print " parent is ", $node->parent_id, "\n";
    print " rank is ", $node->rank, "\n";
    print " genetic_code  ", $node->genetic_code, "\n";
    print " mito_genetic_code  ", $node->mitochondrial_genetic_code, "\n";
    print " scientfic name is ", $node->binomial, "\n";
    print " common name is ", $node->common_name, "\n";
    print " create date is ", $node->create_date, "\n";
    print " update date is ", $node->update_date, "\n";
    print " pub date is ", ($node->pub_date || ''), "\n";
    print " variant is ", $node->variant, "\n";
    print " sub_species is ", $node->sub_species, "\n";
    print " organelle is ", $node->organelle, "\n";
    print " division is ", $node->division, "\n";
}
BioPerl-1.007002/scripts/taxa/bp_taxid4species.pl000444000766000024       610113155576320 21724 0ustar00cjfieldsstaff000000000000#!perl
# Author:  Jason Stajich 
# Purpose: Retrieve the NCBI Taxa ID for organism(s)

# TODO: add rest of POD
#

use LWP::UserAgent;
use XML::Twig;
use strict;
use warnings;
use Getopt::Long;
use Data::Dumper;
my $verbose = 0;
my $plain   = 0;
my $help    = 0;
my $USAGE = "taxid4species: [-v] [-p] \"Genus1 species1\" \"Genus2 species2\"";

GetOptions('v|verbose' => \$verbose,
	   'p|plain'   => \$plain,
	   'h|help'    => \$help);
die("$USAGE\n") if $help;

my $ua = new LWP::UserAgent();

my $urlbase = 'https://www.ncbi.nlm.nih.gov/entrez/eutils/';
my $esearch = 'esearch.fcgi?db=taxonomy&usehistory=y&term=';
my $esummary = 'esummary.fcgi?db=taxonomy&query_key=QUERYKEY&WebEnv=WEBENV';

my (@organisms) = @ARGV;
die("must provide valid organism") unless @organisms;
my $organismstr = join(" OR ", @organisms);
$organismstr =~ s/\s/\+/g;

# Esearch
my $response = $ua->get($urlbase . $esearch . $organismstr);
my $t = XML::Twig->new();
print $response->content,"\n"if($verbose);
$t->parse($response->content);
my $root = $t->root;
my $querykey = $root->first_child('QueryKey')->text;
my $webenv = $root->first_child('WebEnv')->text;

# Esummary
$esummary =~ s/QUERYKEY/$querykey/;
$esummary =~ s/WEBENV/$webenv/;
$response = $ua->get($urlbase . $esummary);
$t = XML::Twig->new();
print $response->content,"\n"if($verbose);
$t->parse($response->content);
$root = $t->root;

# Parse XML
my %taxinfo;
foreach my $docsum ($root->children) {
    foreach my $item ($docsum->children('Item')) {
        if ($item->{att}{Name} eq 'ScientificName') {
            my $sciname = $item->text;
            $taxinfo{lc $sciname}{sciname} = $sciname;
            $taxinfo{lc $sciname}{tid} = $docsum->first_child_text('Id');
            last;
        }
    }
}

# Output in same order as given on command line
foreach my $orgn (@organisms) {
    if (exists $taxinfo{lc $orgn}) {
        my $tid = $taxinfo{lc $orgn}{tid};
        
        if ($plain) { print $tid, "\n"; }
        else { print join(", ", "'$orgn'", $tid), "\n"; }
    }
    else { print "'$orgn' not found\n"; }
}



=head1 NAME

bp_taxid4species - simple script which returns the NCBI Taxonomic id for a requested species

=head1 SYNOPSIS

bp_taxid4species [-v] [-p] [-h] "Genus1 species1" "Genus2 species2"

Options:
  -v   verbose
  -p   plain
  -h   help

=head1 DESCRIPTION

This simple script shows how to get the taxa id from NCBI Entrez and
will return a list of taxa ids for requested organisms.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

 Jason Stajich jason-at-bioperl-dot-org

=cut

BioPerl-1.007002/scripts/taxa/bp_taxonomy2tree.pl000444000766000024       543313155576320 22002 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=head1 NAME

bp_taxonomy2tree - Building a taxonomic tree based on the full lineages of a set of species names

=head1 DESCRIPTION

This scripts looks up the provided species names in the NCBI Taxonomy database,
retrieves their full lineage and puts them in a Newick taxonomic tree displayed
on screen.

  bp_taxonomy2tree.pl -s Orangutan -s Gorilla -s Chimpanzee -s Human
  bp_taxonomy2tree.pl -s Orangutan -s Gorilla -s Chimpanzee -s "Homo Sapiens"

Can also provide -d to specify the directory to store index files in, -o to
specify the location of your NCBI nodes file, and -a for the NCBI names file.
Or the option -e to use the web-based Entrez taxonomy database if you do not
have the NCBI flatfiles installed.

This script requires that the bioperl-run pkg be also installed.

Providing the nodes.dmp and names.dmp files from the NCBI Taxonomy
dump (see Bio::DB::Taxonomy::flatfile for more info) is only necessary
on the first time running.  This will create the local indexes and may
take quite a long time.  However once created, these indexes will
allow fast access for species to taxon id OR taxon id to species name
lookups.

=head1 AUTHOR - Gabriel Valiente, reimplemented by Sendu Bala

Email valiente@lsi.upc.edu
Email bix@sendu.me.uk

=cut

use strict;
use warnings;
use Bio::DB::Taxonomy;
use Bio::TreeIO;
use Bio::Tree::Compatible;
use Getopt::Long;

my @species;
my $index_dir = "./db/";
my $nodesfile = "nodes.dmp";
my $namesfile = "names.dmp";
my $use_entrez = 0;

# the input to the script is an array of species names
GetOptions( 's|species=s'   => \@species,
            'd|dir:s'       => \$index_dir,
            'o|nodesfile:s' => \$nodesfile,
            'a|namesfile:s' => \$namesfile,
            'e|entrez'      => \$use_entrez,
            'h|help'        => sub { system('perldoc', $0); exit }, );

my $db = Bio::DB::Taxonomy->new( -source    => $use_entrez ? 'entrez' : 'flatfile',
                                 -directory => $index_dir,
                                 -nodesfile => $nodesfile,
                                 -namesfile => $namesfile );

# the full lineages of the species are merged into a single tree
my $tree;
for my $name (@species) {
  my $node = $db->get_taxon(-name => $name);
  if ($node) {
    if ($tree) {
      $tree->merge_lineage($node);
    }
    else {
      $tree = Bio::Tree::Tree->new(-node => $node);
    }
  }
  else {
    warn "no NCBI Taxonomy node for species ",$name,"\n";
  }
}

# simple paths are contracted by removing degree one nodes
$tree->contract_linear_paths;

# convert tree ids to their names for nice output with TreeIO
foreach my $node ($tree->get_nodes) {
  $node->id($node->node_name);
}

# the tree is output in Newick format
my $output = Bio::TreeIO->new(-format => 'newick');
$output->write_tree($tree);
$output->close;

1;
BioPerl-1.007002/scripts/tree000755000766000024          013155576320 16004 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/scripts/tree/TAG000444000766000024         6413155576320 16437 0ustar00cjfieldsstaff000000000000These are utilities to manipulate and create trees.
BioPerl-1.007002/scripts/tree/bp_blast2tree.pl000444000766000024      1106313155576320 21247 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
# Author:  Jason Stajich 
# Purpose: Blast Report -> MSA -> Tree 


# This needs lots more error checking, cmdline input of parameters
# and support for other treebuilding -- only Phylip Neighbor for 
# protein data is supported

# Also proper pulling in of the correct sequence data from the
# alignment - multiple hits on different parts of a protein aren't
# going to work properly right now.  So this is mostly and example
# starting point which needs a lot more work to be made robust.

use strict;
use warnings;
use Bio::AlignIO;
use Bio::Tools::Run::Alignment::Clustalw;
use Bio::Tools::Run::Phylo::Phylip::ProtDist;
use Bio::Tools::Run::Phylo::Phylip::Neighbor;
use Bio::Tools::Run::Phylo::Molphy::ProtML;
use Bio::Tools::Run::Phylo::Phylip::ProtPars;
use Bio::SearchIO;
use Bio::SimpleAlign;
use Bio::PrimarySeq;
use Bio::TreeIO;
use Getopt::Long;

my $IDLENGTH = 12;


# we could in fact pull the tree out of the guide tree calculated
# by Clustalw in the alignment, but I believe that is UPGMA 
# which would *NOT* be a good thing to be giving people.

my $aln_factory = Bio::Tools::Run::Alignment::Clustalw->new
    ('ktuple' => 2, "quiet" => 1,
     'matrix' => 'BLOSUM');
my ($report,$format,$tree_method,$cutoff,$keepall);

$format = 'blast';
$tree_method = 'neighbor';
$cutoff = '0.01';
GetOptions(
	   'h|help'       => sub { exec('perldoc', $0);
				   exit(0); },
	   'i|input:s'    => \$report,
	   'f|format:s'   => \$format,
	   'm|method:s'   => \$tree_method,
	   'e|evalue:s'   => \$cutoff,
	   'k|keepall:s'  => \$keepall, # keep all HSPs not just best
	   );


unless( $format =~ /blast|fasta|hmmer/i ) {
    die("Must request a valid search report format (fasta,blast,hmmer)");
}

unless ( $tree_method =~ /nj|neighbor/i || $tree_method =~ /protml|ml/i ) {
    die("Must request a valid tree building method (neighbor,protml)");
} 

my (@alns,@seqs);

my $in = new Bio::SearchIO(-file   => $report,
			   -format => $format);
while( my $r = $in->next_result ) {
    # Let's build the simplest system first
    die("Cannot process report that does not contain protein sequence") 
	unless ($r->algorithm =~ /HMMER|BLASTP|FASTP/i );
    my @seqs;
    while( my $hit = $r->next_hit ) {
	next if $hit->significance > $cutoff;
	while( my $hsp = $hit->next_hsp ) {
	    next if $hsp->evalue > $cutoff;
	    my $seq = $hsp->get_aln->get_seq_by_pos(2)->seq();
	    push @seqs, new Bio::PrimarySeq(-seq => $seq,
					    -id  => $hsp->hit->seq_id,
					    -desc => $r->algorithm . " best align to ". $hsp->query->seq_id );
	    last unless $keepall;
	}
    }
    push @alns, $aln_factory->align(\@seqs);    
}

my $out = new Bio::AlignIO(-format => 'phylip',
			   -interleaved => 1,
			   -idlength => $IDLENGTH,
			   -file => ">alignfile.phy");
$out->write_aln(@alns);
$out = undef;

# these need to be parameterized for cmdline arguments
my @params = ('idlength'=>$IDLENGTH,
	      'model'=>'cat',
	      'gencode'=>'U',
	      'category'=>'H',
	      'probchange'=>'0.4',
	      'trans'=>'5',
	      'freq'=>'0.25,0.5,0.125,0.125');
my $dist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
$dist_factory->quiet(1);
@params = ('type'=>'NJ',
	   'outgroup'=>1,
	   'upptri'=>1,
	   'jumble'=>17);

my $tree_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);
$tree_factory->quiet(1);
my $count = 1;
my $outtrees = new Bio::TreeIO(-file => ">trees.tre",
			       -format => 'newick');
foreach my $aln ( @alns ) {
# NOTE NOTE NOTE 
# This interface is probably going to change from create_tree to
# next_tree per some discussions I'm having with Shawn - we may need
# to tweak any scripts before you publish

# also may move the create_distance_matrix method around some
# and need to write in the switched support for Molphy's ProtML
    
    my $matrix = $dist_factory->create_distance_matrix($aln);
    my @seqnames = keys %$matrix; 
    open my $MATRIX, '>', "Group$count.dist" or die "Could not write file 'Group$count.dist': $!\n";
    printf $MATRIX "%4d\n",scalar @seqnames;
    for(my $i =0; $i< (scalar @seqnames  - 1); $i++ ) {
	printf $MATRIX "%-12s     ", $seqnames[$i];
	for( my $j = $i+1; $j < scalar @seqnames; $j++ ) {
	    print $MATRIX $matrix->{$seqnames[$i]}->{$seqnames[$j]},"  ";
	}
	print $MATRIX "\n";
    }
    close $MATRIX;

    my $tree = $tree_factory->create_tree("Group$count.dist");
    $outtrees->write_tree($tree);   
    $count++;
}

=head1 NAME

tree_from_seqsearch - builds a phylogenetic tree based on a sequence
search (FastA,BLAST,HMMER)

=head1 DESCRIPTION

This script requires that the bioperl-run pkg be also installed.

=cut
BioPerl-1.007002/scripts/tree/bp_nexus2nh.pl000444000766000024       146513155576320 20737 0ustar00cjfieldsstaff000000000000#!perl

=head1 NAME

bp_nexus2nh - convert nexus format trees (from PAUP* and MrBayes) to new hampshire

=head1 SYNOPSIS

 bp_nexus2nh file.nexus > file.nh

 # OR pipe in through STDIN

 cat file.nexus | bp_nexus2nh > file.nh

 # OR specify an output

 bp_nexus2nh -o file.nh file.nexus

=head1 DESCRIPTION

Convert Nexus Tree files into Newick/New Hampshire format tree files.


=cut

use strict;
use warnings;
use Bio::TreeIO;
use Getopt::Long;

my $outfile;

GetOptions('o|out|outfile:s' => \$outfile);

my $in = Bio::TreeIO->new(-format => 'nexus', -fh => \*ARGV);
my $out;
if( $outfile ) { 
    $out= Bio::TreeIO->new(-format => 'newick',
			   -file   => ">$outfile");
} else { 
    # write to STDOUT
    $out= Bio::TreeIO->new(-format => 'newick');
}

while( my $t = $in->next_tree ) {
    $out->write_tree($t);
}
BioPerl-1.007002/scripts/tree/bp_tree2pag.pl000444000766000024       254613155576320 20677 0ustar00cjfieldsstaff000000000000#!perl

=head1 NAME

bp_tree2pag - convert Bio::TreeIO parseable format trees to pagel format

=head1 SYNOPSIS

 bp_tree2pag -if nexus -i file.nexus > file.pag

 # OR pipe in through STDIN, and use newick format instead

 cat file.newick | bp_tree2pag -if newick > file.nh

 # OR specify an output and input

 bp_tree2pag -o file.pag -i file.newick

=head1 DESCRIPTION

Convert TreeIO parseable files into Pagel format tree files.  Be
warned that pagel format only really supports a single tree per file
so.  Also Pagel parsing is not yet available in bioperl.

=cut

use strict;
use warnings;
use Bio::TreeIO;
use Getopt::Long;
my ($iformat,$oformat) = ('newick', 'pag');
my ($outfile,$infile);
GetOptions(
	   'if|informat:s'    => \$iformat,
	   'of|outformat:s'   => \$oformat,
	   'i|in:s'           => \$infile,
	   'o|out:s'          => \$outfile,
	   'h|help'           => sub { exec('perldoc', $0);
				       exit(0); },
	   );
my $in;
if( ! $infile ) {
    $in = Bio::TreeIO->new(-format => $iformat,
			   -fh     => \*ARGV);
} else { 
    $in = Bio::TreeIO->new(-format => $iformat,
			   -file   => $infile);
}

my $out;
if( $outfile) {
    $out = Bio::TreeIO->new(-format => $oformat,
			    -file   => ">$outfile");
} else { 
    $out = Bio::TreeIO->new(-format => $oformat); #print to STDOUT instead
}

while( my $t = $in->next_tree ) {
    $out->write_tree($t);
}
BioPerl-1.007002/scripts/utilities000755000766000024          013155576320 17060 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/scripts/utilities/README000444000766000024        41213155576320 20052 0ustar00cjfieldsstaff000000000000This directory is for robust scripts which have documentation,
cmdline arguments, and can be used in a production environment.
Their extensions will be renamed .pl and will be installed in
the SCRIPT_INSTALL directory as defined in the Makefile.PL 
configuration.


BioPerl-1.007002/scripts/utilities/TAG000444000766000024        21313155576320 17527 0ustar00cjfieldsstaff000000000000These are various sequence-related scripts that were difficult to
classify more specifically but are considered general purpose
utilities.
BioPerl-1.007002/scripts/utilities/bp_dbsplit.pl000444000766000024       521113155576320 21673 0ustar00cjfieldsstaff000000000000#!perl
#-*-Perl-*-

=head1 NAME

bp_dbsplit - script to split an input set of database(s) into smaller pieces

=head1 SYNOPSIS

  bp_dbsplit.PLS --size 50 [-i inputfile] [-if inputformat] [-of outputformat]
              [--prefix outputprefix] [ < file1 file 2  OR file1 file2]

=head1 DESCRIPTION

This script will take as input a list of filenames or a single file or
from STDIN a sequence database and split the database into separate
files of X numbers of sequences.  You specify X with the C<--size/-s>
parameter.  The input and output sequence format is any that is
supported by bioperl (fasta,embl,genbank,gcg, swissprot, etc).

You can specify the input data either as a single file with -i
filename, or as a single file as an argument like

  % bp_dbsplit file1 file2

or as a list of sequence data with 

  % cat file1 file2 file3 | bp_dbsplit

You'll want to use the C<--prefix> to specify what the output prefix will
be.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

Jason Stajich, jason-at-bioperl-dot-org

=cut

use strict;
use warnings;
use Bio::SeqIO;
use Bio::SeqIO::MultiFile;

use Getopt::Long;
my $dbsize = 100;
my $prefix;
my ($informat,$outformat,$infile) = ( 'fasta', 'fasta');

GetOptions (
	    's|size:s'     => \$dbsize,
	    'if:s'         => \$informat,
	    'of:s'         => \$outformat,
	    'i:s'          => \$infile,
	    'p|prefix:s'   => \$prefix,
	    
);
if( @ARGV == 1 ) {
    $infile = shift @ARGV;
}
$prefix ||= $infile || $ARGV[0] || 'db';

my $in;
if( @ARGV ) {
    $in = new Bio::SeqIO::MultiFile(-files => [@ARGV],
				    -format => $informat || 'fasta');
} elsif( $infile ) {
    $in = new Bio::SeqIO(-file  => $infile,
			 -format=> $informat);
} else { 
    $in = new Bio::SeqIO(-format=> $informat);
}
my $count = 1;
my $out = new Bio::SeqIO(-format => $outformat,
			 -file   => ">$prefix.$count");
my $scount = 0;
while( my $seq = $in->next_seq ) {    
    if( ++$scount > $dbsize && $count ) { 
	$out->close();
	undef($out);
	$count++;
	$out = new Bio::SeqIO(-format => $outformat,
			      -file   => ">$prefix.$count");
	$scount = 1;
    }
    $out->write_seq($seq);
}


__END__
BioPerl-1.007002/scripts/utilities/bp_download_query_genbank.pl000444000766000024       636413155576320 24765 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl


=head1 NAME

bp_download_query_genbank - script to query Genbank and retrieve records

=head1 USAGE

 bp_download_query_genbank --query "Neurospora[ORGN]" --db nucest -o Ncrassa_ESTs.fa --format fasta

 bp_download_query_genbank --queryfile 'filewithquery' --db nucest -o Ncrassa_ESTs.fa --format fasta 

=head2 Other options

 Provide ONE of:

  -q --query query string OR
  --queryfile profile file with query OR
  --gi --gis --gifile file with list of GIs to download

 Database type:

 -d --db database (nucleotide [default], nucest, protein, )

 -o --out --outfile output file (results are displayed on screen otherwise)
 -f --format sequence file output format (fasta by default)
 -v --verbose debugging output

=head2 Query options

 --maxids maximum number of IDs to retrieve in a set (100 at a time by default)
 --reldate 
 --maxdate maxdate for a record
 --mindate minimum date for record
 --datetype edat or mdat (entered or modified)

=head1 AUTHOR Jason Stajich

Jason Stajich, jason-AT-bioperl.org

=cut

use strict;
use warnings;
use Bio::DB::GenBank;
use Bio::DB::GenPept;
use Bio::DB::Query::GenBank;
use Bio::SeqIO;
use Getopt::Long;

my ($queryfile,$outfile,$format,$debug,%options);

$format = 'fasta';

$options{'-maxids'} = '100';
$options{'-db'} = 'nucleotide'; # can be nucleotide, nucest, protein 
my $gifile;
GetOptions(
		   'h|help' => sub { exec('perldoc', $0); 
									exit(0);
								},
			  'v|verbose'       => \$debug,
			  'f|format:s'      => \$format,
			  'queryfile:s'     => \$queryfile,
			  'o|out|outfile:s' => \$outfile,
			  'gi|gifile|gis:s' => \$gifile,
			  # DB::Query options	   
			  'd|db:s'     => \$options{'-db'},
			  'mindate:s'  => \$options{'-mindate'},
			  'maxdate:s'  => \$options{'-maxdate'},
			  'reldate:s'  => \$options{'-reldate'}, 
			  'datetype:s' => \$options{'-datetype'}, # edat or mdat
			  'maxids:i'   => \$options{'-maxids'},
			  'q|query:s'  => \$options{'-query'},
			 );

my $out;

if( $outfile ) {
	$out = Bio::SeqIO->new(-format => $format,
								  -file   => ">$outfile");
} else {
	$out = Bio::SeqIO->new(-format => $format); # write to STDOUT
}

my $dbh;
if( $options{'-db'} eq 'protein' ) {
	$dbh = Bio::DB::GenPept->new(-verbose => $debug);
} else {
	$dbh = Bio::DB::GenBank->new(-verbose => $debug);
}
my $query;
if( $gifile ) {
	my @ids;
	open my $fh, '<', $gifile or die "Could not read file '$gifile': $!\n";
	while(<$fh>) {
		push @ids, split;
	}
	close $fh;
	while( @ids ) {
		my @mini_ids = splice(@ids, 0, $options{'-maxids'});
		$query = Bio::DB::Query::GenBank->new(%options, 
						      -verbose =>$debug,
					              -ids => \@mini_ids,
						     );
		my $stream = $dbh->get_Stream_by_query($query);
		while( my $seq = $stream->next_seq ) {
			$out->write_seq($seq);
		}
	}
	exit;
} elsif( $options{'-query'}) {
	$query = Bio::DB::Query::GenBank->new(%options,-verbose => $debug);
} elsif( $queryfile ) {
	open my $fh, '<', $queryfile or die "Could not read file '$queryfile': $!\n";
	while(<$fh>) {
		chomp;
		$options{'-query'} .= $_;
	}
	$query = Bio::DB::Query::GenBank->new(%options,-verbose => $debug);
	close $fh;
} else {
	die("no query string or gifile\n");
}
my $stream = $dbh->get_Stream_by_query($query);
while( my $seq = $stream->next_seq ) {
	$out->write_seq($seq);
}
BioPerl-1.007002/scripts/utilities/bp_find-blast-matches.pl000444000766000024      3531113155576320 23723 0ustar00cjfieldsstaff000000000000#!/usr/bin/env perl
use strict;
use warnings;

=head1 NAME

bp_find-blast-matches.pl - extract DNA sequences based on BLAST hits

=head1 SYNOPSIS

bp_find-blast-matches.pl [-h -e -p -5 -n -o -3 -header] -blast  -fasta 

=head1 OPTIONS

=head2 Mandatory:

=over

=item B<-blast>

BLAST output file to read from. The alignment should use the file specified by
'-fasta' option ideally

=item B<-fasta>

FASTA file to read from. This is where the sequence will be extracted from

=back

=head2 Optional:

=over

=item B<-h>

Displays this help message

=item B<-e>

Maximum e-value for matches (0.01 by default)

=item B<-p>

Number of base pairs of 5' region to be included with the sequence

=item B<-5>

Number of base pairs of 5' region only, excluding the regular sequence

=item B<-3>

Number of base pairs of 3' region only, excluding the regular sequence

=item B<-n>

Number of top hits to display, starting with the best hit

=item B<-o>

Exact match to display (this option can't be used in conjunction with '-n'

=item B<-header>

The FASTA header to display instead of the default

=back

=head1 DESCRIPTION

This script takes a BLAST output file and a FASTA file as arguments, 
given after the '-blast' and '-fasta' options respectively. The BLAST output 
file should have been generated with your sequence of interest and the 
FASTA file supplied as an argument.
Example: find-blast-matches.pl -blast BLAST_FILE -fasta FASTA_FILE

It parses through the BLAST file to check for high quality matches, 
which are then searched for in the FASTA file.  The sequence may vary 
from you candidate sequence, hence the BLAST search prior. 

The sequence from the FASTA file is then displayed to STDOUT.
Optional arguments can be used, such as to extract the 5' or 3' region.

=head1 AUTHOR

Gabriel Abud - Egabriel.jabud-at-gmail.comE

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules.  Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via 
email or the web:

  https://github.com/bioperl/bioperl-live/issues

=head1 EDIT HISTORY

2014-08-04 - Gabriel Abud
    First features added

=head1 DEPENDANCIES

Getopt::long, Pod::Usage, Bio::SearchIO, Bio::Seq, Bio::SeqIO, Bio::Perl,
File::Basename

=cut


# Modules
use Bio::SearchIO qw(new);
use Bio::Seq qw(new);
use Bio::SeqIO qw(new);
use Bio::Perl qw(revcom_as_string);
use File::Basename qw(basename);
use Getopt::Long qw(GetOptions);
use Pod::Usage;

# Variables
my $baseProg = basename($0);    # Program name
my $line;
my @scaffolds;
my $inputFile;
my $blastFile;
my $scaffoldFind;
my $baseList;
my @start;
my @end;
my @strand;
my @arrayBases;
my $query_name;
my @query_names;
my @accessions;
my $accession;
my $baseFile;
my $total_size;
my $title;
my $default_header;
my $in;
my $out;

# Command line options
my $exact_match;    # Undef by default
my $e_value = 0.01; # Default e-value
my $matches = 1;    # Default number of matches
my $promoter;       # Undef by default
my $three_prime;    # Undef by default
my $promoter_only;  # Undef by default
my $opt_help;       # Undef by default
my $header;         # Undef by default

# Functions for proper command line usage
sub syntax {
    print STDERR
      "Usage: $baseProg -blast 'BLAST_file' -fasta 'FASTA_file' [OPTIONS]\n";
    print STDERR "Try '$baseProg --help' for more information.\n";
    exit;
}

sub help {
    print STDERR
      "\nNAME:\n",
      "\t$baseProg - extract a DNA sequence based on BLAST hits\n\n",
      "SYNTAX:\n",
      "\t$baseProg -blast 'BLAST_file' -fasta 'FASTA__file'  [OPTIONS]\n\n",
      "OPTIONS:\n",
      "\t(All options require an additional number argument [ie: -e 0.01])\n\n",
      "\t-e, maximum e-value for matches (0.01 by default)\n\n",
      "\t-p, number of base pairs of 5' region to be included with the\n",
      "\t sequence of interest\n\n",
      "\t-5, number of base pairs of 5' region, excluding the sequence\n",
      "\t of interest (unlike '-p')\n\n",
      "\t-n, number of top hits to display, starting with the highest hit\n",
      "\t(1 by default)\n\n",
      "\t-o, exact match to display (this option can't be used in conjuction\n",
      "\t with '-n')\n\n",
      "\t-3, number of base pairs of 3' region to display\n\n",
      "\t-header, the fasta header to display instead of the default\n\n";
    exit;
}

# Get command line options
GetOptions(
    'e=f'      => \$e_value,
    'p=i'      => \$promoter,
    'n=i'      => \$matches,
    'o=i'      => \$exact_match,
    '5=i'      => \$promoter_only,
    '3=i'      => \$three_prime,
    'help|h'     => \$opt_help,
    'header|head=s' => \$header,
    'blast|b=s'  => \$blastFile,
    'fasta|f=s'  => \$inputFile
) or pod2usage(-exitstatus => 0, -verbose => 1);

# Help screen
pod2usage(-exitstatus => 0, -verbose => 2) if $opt_help;
#help() if defined $opt_help;

# Checks for required arguments
pod2usage(-exitstatus => 0, -verbose => 1, 
          -msg => "You must specify the FASTA and BLAST files to read from!\n")
    if (!defined $blastFile || !defined $inputFile);
#syntax() if ( !defined $blastFile || !defined $inputFile );

# Checks for any negative numbers
#syntax()
pod2usage(-exitstatus => 0, -verbose => 1,
          -msg => "You must use positive numbers as values to options!")
  if ( (defined $e_value && $e_value < 0)
    || (defined $promoter && $promoter < 0)
    || (defined $matches && $matches < 0)
    || (defined $exact_match && $exact_match < 0)
    || (defined $promoter_only && $promoter_only < 0)
    || (defined $three_prime && $three_prime < 0 ) );

if ( $matches > 1 && defined $exact_match ) {
    print STDERR "Cannot use both options '-n' and '-o' at the same time\n";
    print STDERR "(Type '$baseProg --help' for more information\n)";
    exit;
}

if ( defined $promoter && defined $promoter_only ) {
    print STDERR "Cannot use both options '-p' and '-5' at the same time\n";
    print STDERR "(Type '$baseProg --help' for more information)\n";
    exit;
}

if ( defined $three_prime && ( defined $promoter || defined $promoter_only ) ) {
    print STDERR "Cannot use both '-3' with '-p' or '-5' at the same time\n";
    print STDERR "(Type $baseProg --help' for more information)\n";
    exit;
}

# Class used to search through the blast file
eval { $in = Bio::SearchIO->new( -file => $blastFile, -format => "blast" ); };
if ($@) {
    die "'$blastFile' does not appear to be a BLAST output file! Exiting...\n";
}
$out = Bio::SeqIO->new( -fh => \*STDOUT, -format => "fasta" );

# Creates arrays of all the scaffold names and the coordinates of where those scaffolds are found
my $n = 0;
OUTERLOOP: while ( my $result = $in->next_result ) {
  LOOP: while ( my $hit = $result->next_hit ) {
        while ( my $hsp = $hit->next_hsp ) {

            # Finds all matches with an evalue <= $e_value (or 0.01 by default)
            if ( $hsp->evalue <= $e_value ) {
                ( $start[$n], $end[$n] ) = $hsp->range('hit');
                $scaffolds[$n] = $hit->name, $strand[$n] = $hsp->strand('hit');
                $n += 1;
            }

            # If an exact_match option is given
            if ( defined($exact_match) && $exact_match == $n ) {
                ( $start[0], $end[0] ) = $hsp->range('hit');
                $scaffolds[0] = $hit->name, $strand[0] = $hsp->strand('hit');
                last OUTERLOOP;
            }
            elsif ( !defined($exact_match) && $n >= $matches )
            { # Exits after the correct amount of matches have been found (1 by default)
                last LOOP;
            }
        }
    }
}

$baseFile = basename $inputFile;

open INFILE, "<$inputFile"
  or die "Couldn't open the input file '$inputFile'! Exiting...\n";

$scaffoldFind = 0;
my %scaffoldList;
my %baseList;

# Extracts only the scaffolds of interest, avoiding duplicates
if ( defined $exact_match ) {
    $scaffoldList{ $scaffolds[0] } = 1;
}
else {
    foreach my $num ( 0 .. $#scaffolds ) {
        if ( !defined $scaffoldList{ $scaffolds[$num] } ) {
            $scaffoldList{ $scaffolds[$num] } = 1;
        }
    }
}
my $remaining_scaffolds = my $unique_scaffolds = keys(%scaffoldList);

local $/ = "\n>";

# Reads the FASTA file here, storing FASTA headers where the sequence is found
while ( $line =  ) {
    chomp($line);
    next if ( $line =~ m/^\s*?$/ );

    foreach my $scaffold ( sort keys %scaffoldList ) {
        if ( $line =~ /^[ \t]{0,5}$scaffold/ )
        {    # True if FASTA segment contains the scaffold
            $line =~ s/^.*?\n//;
            $line =~ s/\s//g;
            $baseList{$scaffold} = $line;
            $scaffoldFind++;
            $remaining_scaffolds--;
        }
    }
    last unless ($remaining_scaffolds);
}

if ( $scaffoldFind != $unique_scaffolds ) {
    print STDERR "The scaffold specified in the BLAST file was not found.\n";
    print STDERR "Make sure you are using the correct FASTA file.\n";
    exit;
}

for my $m ( 0 .. $#scaffolds )
{    # Runs a loop as many times as there are scaffolds
    $baseList = $baseList{ $scaffolds[$m] };

    # Print title line for each scaffold
    $accession      = $baseFile;
    $default_header = "(BLAST hit:$scaffolds[$m]|";

    my $real_start = $start[$m];
    my $real_end   = $end[$m];

    # For "normal", positive strands (+/+)
    if ( $strand[$m] == 1 ) {

        # If the -p flag was used
        if ( defined $promoter ) {    # 5' region specified with -p flag
             # If 5' region is too large for sequence, don't include the 5' region
            if ( $promoter >= $start[$m] ) {
                print STDERR "ERROR: 5' region is too big!! (max promoter = ",
                  $start[$m] - 1, " )\n",
                  "Showing sequence without 5' region...\n";
                $baseList = substr $baseList, $start[$m], $end[$m] - $start[$m];
            }
            else {
                my $real_start = $start[$m] - $promoter;
                $baseList = substr $baseList, $start[$m] - $promoter - 1,
                  $promoter + $end[$m] - $start[$m] + 1;
            }
        }

        # If the -3 flag was used
        elsif ( defined $three_prime ) {
            $total_size = length($baseList);

            if ( ( $three_prime + $end[$m] ) > $total_size ) {
                die "ERROR: 3' region is too big!! ",
                  "(max 3' region = ", $total_size - $end[$m], ")\n",
                  ;
            }
            else {
                $real_start = $end[$m] + 1;
                $real_end   = $end[$m] + $three_prime;
                $baseList   = substr $baseList, $end[$m], $three_prime;
            }
        }

        # If the -5 flag was used
        elsif ( defined $promoter_only )
        {    # 5' region was specified with -5 flag
             # If 5' region is too large for sequence, don't include the 5' region
            if ( $promoter_only >= $start[$m] ) {
                die "ERROR: 5' region is too big!! (max promoter = ",
                  $start[$m] - 1, " )\n",
                  ;
            }
            else {
                $real_start = $start[$m] - $promoter_only;
                $real_end   = $start[$m] - 1;
                $baseList   = substr $baseList, $start[$m] - $promoter_only - 1,
                  $promoter_only;
            }
        }
        else {    # Default: just the BLAST hit (no 5' or 3')
            $baseList = substr $baseList, $start[$m] - 1,
              $end[$m] - $start[$m] + 1;
        }
    }

    # Checks to see if the hit sequence is the reverse compliment
    elsif ( $strand[$m] == -1 ) {

        # If -p flag was used:
        if ( defined $promoter ) {
            $total_size = length($baseList);

            if ( ( $promoter + $end[$m] ) > $total_size ) {
                print STDERR "ERROR: 5' region is too big!! ",
                  "(max 5' region = ", $total_size - $end[$m], ")\n",
                  "Showing sequence without 5' region...\n";
                $baseList = substr $baseList, $start[$m], $end[$m] - $start[$m];
            }
            else {
                $real_start = $start[$m] + 1;
                $real_end   = $end[$m] + $promoter;
                $baseList   = substr $baseList, $start[$m] - 1,
                  $end[$m] - $start[$m] + $promoter + 1;
            }

        }

        # If -3 flag was used
        elsif ( defined $three_prime ) {
            if ( $three_prime >= $start[$m] ) {
                die "ERROR: 3' region is too big!! (max = ", $start[$m] - 1,
                  " )\n";
            }
            else {
                $real_start = $start[$m] - $three_prime;
                $real_end   = $start[$m] - 1;
                $baseList   = substr $baseList, $start[$m] - $three_prime - 1,
                  $three_prime;
            }
        }

        # If -5 flag was used
        elsif ( defined $promoter_only ) {
            $total_size = length($baseList);

            if ( ( $promoter_only + $end[$m] ) > $total_size ) {
                die "ERROR: 5' region is too big!! ",
                  "(max promoter = ", $total_size - $end[$m], ")\n",
                  ;
            }
            else {
                $real_start = $end[$m] + 1;
                $real_end   = $end[$m] + $promoter_only;
                $baseList   = substr $baseList, $end[$m], $promoter_only;
            }

        }
        else {    # If 5' region wasn't specified at all
            $baseList = substr $baseList, $start[$m] - 1,
              $end[$m] - $start[$m] + 1;
        }
        $baseList = revcom_as_string($baseList);
    }
    $default_header .= "$real_start-$real_end)";
    $default_header .= " showing 5' region ($promoter_only bp) only"
      if defined($promoter_only);
    $default_header .= " showing 3' region ($three_prime bp)"
      if defined($three_prime);
    $default_header .= " with 5' region ($promoter bp)" if defined($promoter);
    my $seq_obj = Bio::Seq->new( -seq => "$baseList", -alphabet => 'dna' );

    if ( defined $header ) {
        $header =~ s/^\s*//;
        $header =~ s/\s*$//;
        $header =~ s/^>//;
        $header =~ s/^([^\s]+)//;
        my $default_name = $1;
        $seq_obj->display_id($default_name);
        $seq_obj->desc($header);
    }
    else {
        $seq_obj->desc($default_header);
        $seq_obj->display_id($accession);
    }

    # Prints the sequence to STDOUT
    $out->write_seq($seq_obj);
    print "\n";

   # If 'exact_match' option is specified, exit after first (and only) iteration
    if ( defined($exact_match) ) {
        close INFILE;
        exit;
    }

    close INFILE;
}    # End of major for loop

__END__
BioPerl-1.007002/scripts/utilities/bp_mask_by_search.pl000444000766000024      1127013155576320 23226 0ustar00cjfieldsstaff000000000000#!perl
# Author:  Jason Stajich 


=head1 NAME

bp_mask_by_search - mask sequence(s) based on its alignment results

=head1 SYNOPSIS 

  bp_mask_by_search.pl -f blast genomefile blastfile.bls > maskedgenome.fa

=head1 DESCRIPTION

Mask sequence based on significant alignments of another sequence.
You need to provide the report file and the entire sequence data which
you want to mask.  By default this will assume you have done a TBLASTN
(or TFASTY) and try and mask the hit sequence assuming you've provided
the sequence file for the hit database.  If you would like to do the
reverse and mask the query sequence specify the -t/--type query flag.

This is going to read in the whole sequence file into memory so for
large genomes this may fall over.  I'm using DB_File to prevent
keeping everything in memory, one solution is to split the genome into
pieces (BEFORE you run the DB search though, you want to use the exact
file you BLASTed with as input to this program).

Below the double dash (--) options are of the form
--format=fasta or --format fasta
or you can just say
-f fasta

By -f/--format I mean either are acceptable options.  The =s or =n
or =c specify these arguments expect a 'string'

Options:
    -f/--format=s    Search report format (fasta,blast,axt,hmmer,etc)
    -sf/--sformat=s  Sequence format (fasta,genbank,embl,swissprot)
    --hardmask       (booelean) Hard mask the sequence
                     with the maskchar [default is lowercase mask]
    --maskchar=c     Character to mask with [default is N], change 
                     to 'X' for protein sequences
    -e/--evalue=n    Evalue cutoff for HSPs and Hits, only 
                     mask sequence if alignment has specified evalue 
                     or better
    -o/--out/
    --outfile=file   Output file to save the masked sequence to.
    -t/--type=s      Alignment seq type you want to mask, the 
                     'hit' or the 'query' sequence. [default is 'hit']
    --minlen=n       Minimum length of an HSP for it to be used 
                     in masking [default 0]
    -h/--help        See this help information

=head1 AUTHOR - Jason Stajich

Jason Stajich, jason-at-bioperl-dot-org.

=cut 


use strict;
use warnings;
use Bio::SeqIO;
use Bio::SearchIO;
use Getopt::Long;
use Bio::Seq;
use DB_File;
# assuming tblastn or tfasty type alignment

my $format = 'blast';
my $sformat= undef;
my $evalue = undef;
my $type   = 'hit';
my $minlen = 50;
my $hardmask = 0; # mask with $maskchar instead of lowercase
my $maskchar = 'N'; # if we hard mask, mask with this cahr
my $outfile;
GetOptions(
	   'f|format:s'  => \$format,
	   'sf|sformat:s'=> \$sformat,
	   'hardmask'    => \$hardmask,
	   'maskchar:s'  => \$maskchar,
	   'e|evalue:s'  => \$evalue,
	   'o|out|outfile:s' => \$outfile,
	   't|type:s'    => \$type,
	   'minlen:s'    => \$minlen,
	   'h|help'      => sub { system('perldoc', $0);
				  exit; },
	   );
if( $type !~ /^(hit|query)/i ) {
    die("type must be query or hit[default] not $type") ;
}
$type = lc($type);

if(length($maskchar) > 1 ) {
    die("expected a mask character, not a string (you gave $maskchar)");
}
my $genomefile = shift || die('need a file containing the genome');
my $reportfile = shift;

# this could be problem for large genomes, figure out a 
# better way to do this later on
# or force people to split it up
my $genomeparser = new Bio::SeqIO(-file  => $genomefile,
				  -format=> $sformat);
my %seqs; 
unlink('/tmp/genome.idx');
tie(%seqs,'DB_File','/tmp/genome.idx');
while( my $seq = $genomeparser->next_seq ) {
    # should we pre-force to upper case?
    $seqs{$seq->display_id} = $seq->seq();
}

my $parser = new Bio::SearchIO(-file   => $reportfile,
			       -format => $format);

while( my $r = $parser->next_result ) {
    while( my $h = $r->next_hit ) {
	last if( defined $evalue && $h->significance > $evalue );
	my $hname = $h->name;
	if( ! $seqs{$hname} ) { 
	    die("Cannot find sequence $hname in genome seq");
	}
	while( my $hsp = $h->next_hsp ) {
	    last if( defined $evalue && $hsp->evalue > $evalue );
	    next if( $hsp->length('total') < $minlen);
	    my ($s,$len) = ( $hsp->$type()->start,
			     $hsp->$type()->length);
	    
	    if( $hardmask ) { 
		substr($seqs{$hname}, $s,$len, $maskchar x $len);
	    } else { 
		substr($seqs{$hname}, $s,$len, 
		       lc(substr($seqs{$hname}, $s,$len)));
	    }
	}
    }
}

my $out;
if( $outfile ) { 
    $out = new Bio::SeqIO(-file   => ">$outfile",
			  -format => $sformat);
} else { 
    $out = new Bio::SeqIO(-format => $sformat);
}

while( my ($seqname,$seq) = each %seqs ) {
    $out->write_seq(Bio::Seq->new(-seq        => $seq,
				  -display_id => $seqname,
				  -description=> 'MASKED'));
}
END { 
    unlink('/tmp/genome.idx');
}
BioPerl-1.007002/scripts/utilities/bp_mrtrans.pl000444000766000024       556713155576320 21736 0ustar00cjfieldsstaff000000000000#!perl
use strict;

# Author:      Jason Stajich 
# Description: Perl implementation of Bill Pearson's mrtrans
#              to project protein alignment back into cDNA coordinates
#

=head1 NAME

bp_mrtrans - implement a transformer of alignments from protein to mrna coordinates

=head1 SYNOPSIS

Usage:
  bp_mrtrans -i inputfile -o outputfile [-if input format] [-of output format] [-s cDNA sequence database]  [-sf cDNA sequence format] [-h]

=head1 DESCRIPTION

This script will convert a protein alignment back into a cDNA.  Loosely
based on Bill Pearson's mrtrans.

The options are:

   -o filename          - the output filename [default STDOUT]
   -of format           - output sequence format
                          (multiple sequence alignment)
                          [default phylip]
   -i filename          - the input filename [required]
   -if format           - input sequence format
                          (multiple sequence alignment)
                          [ default clustalw]
   -s --seqdb filename  - the cDNA sequence database file
   -sf --seqformat      - the cDNA seq db format (flatfile sequence format)
   -h                   - this help menu

=head1 AUTHOR

Jason Stajich, jason-at-bioperl-dot-org

=cut

use strict;
use warnings;
use Bio::Align::Utilities qw(aa_to_dna_aln);
use Bio::AlignIO;
use Bio::SeqIO;
use Getopt::Long;

# TODO - finish documentation,
#      - add support for extra options in output alignment formats
#        such as idnewline in phylip out to support Molphy input files

my ($iformat,$seqformat,$oformat,$seqdb,$input,$output) = ('clustalw','fasta',
							   'phylip');
my ($help,$usage);

$usage = "usage: bp_mrtrans.pl -i prot_alignment -if align_format -o out_dna_align -of output_format -s cDNA_seqdb -sf fasta\n".
"defaults: -if clustalw
          -of phylip
          -sf fasta\n";

GetOptions(
	   'if|iformat:s'  => \$iformat,
	   'i|input:s'     => \$input,
	   'o|output:s'    => \$output,
	   'of|outformat:s'=> \$oformat,
	   's|seqdb|db:s'  => \$seqdb,
	   'sf|seqformat:s'=> \$seqformat,
	   'h|help'        => sub{ exec('perldoc',$0);
				   exit(0)
				   },
	   );

$input ||= shift;
$seqdb ||= shift;
$output ||= shift;
if( ! defined $seqdb ) {
    die("cannot proceed without a valid seqdb\n$usage");
}
if( ! defined $input ) {
    die("cannot proceed without an input file\n$usage");
}
my $indb = new Bio::SeqIO(-file => $seqdb,
			  -format=>$seqformat);
my %seqs;
while( my $seq = $indb->next_seq ) {
    $seqs{$seq->id} = $seq;
}

my $in = new Bio::AlignIO(-format => $iformat,
			  -file   => $input);
my $out = new Bio::AlignIO(-format => $oformat,
			   -idlength => 22,
			   -interleaved => 0,
			   defined $output ? (-file   => ">$output") : () );

while( my $aln = $in->next_aln ) {
    my $dnaaln = aa_to_dna_aln($aln,\%seqs);
    $dnaaln->set_displayname_flat(1);
    $out->write_aln($dnaaln);
}

__END__
BioPerl-1.007002/scripts/utilities/bp_mutate.pl000444000766000024      1014313155576320 21551 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=head1 NAME

bp_mutate.pl - randomly mutagenize a single protein or DNA sequence

=head1 SYNOPSIS

  ./bp_mutate.pl -p 25 -i test.fa -n 5 -f swiss -o muts.swiss

  #or

  ./bp_mutate.pl --percent=25 --input=test.fa --number=5 -output=x.fa

=head1 DESCRIPTION

Randomly mutagenize a single protein or DNA sequence one or more times.
Specify percentage mutated and number of resulting mutant sequences.
Print mutagenized sequences to STDOUT or write to an output file.

  -h|--help    Help
  -p|--percent Percent mutagenized
  -n|--number  Number of mutant sequences created
  -o|--output  Output file (optional)
  -f|--format  Output format (default: fasta)
  -i|--input   Input file

=head1 FEEDBACK

User feedback is an integral part of the evolution of this and other
Bioperl scripts. Send your comments and suggestions to the Bioperl 
mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

Brian Osborne, bosborne at alum.mit.edu

=cut

use strict;
use warnings;
use Getopt::Long;
use Bio::SeqIO;

my ( $help, $in_file, $percent, $out_file, $number );
my $format = "fasta";
my @dna    = qw(a g c t);
my @amino  = qw(a c d e f g h i k l m n p q r s t v w y);

GetOptions(
    "h|help"      => \$help,
    "p|percent:i" => \$percent,
    "n|number:i"  => \$number,
    "o|output:s"  => \$out_file,
    "f|format:s"  => \$format,
    "i|input:s"   => \$in_file
);

usage() if ( $help || !$percent || !$in_file || !$number || $percent > 100 );

# Seed the random number generator. "time|$$" combines the
# current time with the current process id
srand( time | $$ );

my $seqio   = Bio::SeqIO->new( -file => $in_file );
my $seqobj  = $seqio->next_seq;
my $num_mut = percent_to_num($percent);
my @seq_arr = ();

# don't keep a mutant that's already been made
while ( $number > $#seq_arr + 1 ) {
    my $mut_seq = mutate_all( $seqobj, $num_mut );
    push @seq_arr, $mut_seq unless ( grep /$mut_seq/, @seq_arr );
}

foreach my $mut_seq (@seq_arr) {
    my $name   = $seqobj->display_id . "-${percent}_percent-$number";
    my $outseq = Bio::Seq->new(
        -seq        => $mut_seq,
        -display_id => $name,
        -desc       => $seqobj->desc
    );
    my %args = ( -format => $format );
    $args{-file} = ">>$out_file" if $out_file;
    my $seqio = Bio::SeqIO->new(%args);
    $seqio->write_seq($outseq);
    $number--;
}

# mutagenize the sequence, one-by-one
sub mutate_all {
    my ( $seq_obj, $num ) = @_;
    my $type = $seq_obj->alphabet;
    my $str  = $seq_obj->seq;

    # store the mutagenized positions in $positions
    my $positions = "";
    for ( my $i = 0 ; $i < $num_mut ; ++$i ) {
        ( $str, $positions ) = mutate_one( $str, $type, $positions );
    }
    $str;
}

# mutagenize one position
sub mutate_one {
    my ( $str, $type, $positions ) = @_;
    my ( $position, $new_char );

    # pick a random position in the sequence, checking
    # that the position isn't already mutagenized
    do {
        $position = random_position($str);
    } until ( $positions !~ /\b$position\b/ );
    $positions .= "$position ";
    my $current_char = substr( $str, $position, 1 );

    # pick a random char that's not the existing char
    do {
        $new_char = random_char($type);
    } until ( $new_char ne $current_char );
    substr( $str, $position, 1, $new_char );
    ( $str, $positions );
}

# randomly select a position in the sequence
sub random_position {
    my $string = shift;
    int( rand( length($string) ) );
}

# randomly select one of the chars depending on alphabet
sub random_char {
    my $type = shift;
    $type eq "protein"
      ? return $amino[ rand @amino ]
      : return $dna[ rand @dna ];
}

sub percent_to_num {
    my $percent = shift;
    int( $percent / 100 * length( $seqobj->seq ) );
}

sub usage {
    exec( 'perldoc', $0 );
    exit(0);
}

__END__
BioPerl-1.007002/scripts/utilities/bp_netinstall.pl000444000766000024      3273513155576320 22442 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl

=head1 NAME

bp_netinstall.pl - Net-based installer of BioPerl

=head1 SYNOPSIS

  bp_netinstall.pl -b|--build_param_str BUILD_STRING [options]

  options:

 -h|--help                Show this message
 -d|--dev                 Use the development version of bioperl from git
 --build_param_str= Parameters that are passed in at 'perl Build.PL'
 --install_param_str=
                          Use this string to predefine './Build install'
                            parameters such as 'install_base' for
                            bioperl installation
 --bioperl_path           Path to BioPerl tarball (will not download BioPerl)
 --skip_start             Don't wait for 'Enter' at program start

=head1 DESCRIPTION

Net-based installer of BioPerl; this is based on the GBrowse netinstaller
and hopefully all references to GBrowse have been removed.  Let me know if not.

Save this to disk as "bp_netinstall.pl" and run:

   [sudo] perl bp_netinstall.pl

=head1 AUTHOR

Scott Cain scain@cpan.org

=head1 COPYRIGHT

2010. This script may be distributed under the same license as perl.

=cut

# Universal Net-based installer
# Save this to disk as "bp_netinstall.pl" and run:
#   perl bp_netinstall.pl

use warnings;
use strict;
use CPAN '!get';
use Config;
use Getopt::Long;
use Pod::Usage;
use File::Copy qw( cp move );
use File::Temp qw(tempdir);
use LWP::Simple;
use Cwd;

use constant NMAKE => 'http://download.microsoft.com/download/vc15/patch/1.52/w95/en-us/nmake15.exe';

my ( $show_help, $get_from_cvs, $build_param_string, $working_dir,
     $get_bioperl_svn, $is_cygwin, $windows,
     $binaries, $make, $tmpdir, $bioperl_path,
     $skip_start, $install_param_string, $perl_path);

BEGIN {

  GetOptions(
        'h|help'              => \$show_help,             # Show help and exit
        'd|dev'               => \$get_from_cvs,          # Use the dev svn
        'build_param_str=s'   => \$build_param_string,    # Build parameters
        'bioperl_dev'         => \$get_bioperl_svn,
        'bioperl_path=s'      => \$bioperl_path,
        'install_param_str=s' => \$install_param_string,
        'skip_start'          => \$skip_start,
        )
        or pod2usage(2);
  pod2usage(2) if $show_help;

  $perl_path = $Config{perlpath};

  print STDERR "\nAbout to install BioPerl and all its prerequisites.\n";
  print STDERR "\nYou will be asked various questions during this process. You can almost always";
  print STDERR "\naccept the default answer.\n";
  print STDERR "The whole process will take several minutes and will generate lots of messages.\n";
  print STDERR "\nPress return when you are ready to start!\n";
  my $h = <> unless $skip_start;
  print STDERR "*** Installing Perl files needed for a net-based install ***\n";

  $windows = $Config{osname} =~ /mswin/i;


# MAY not be necessary--we'll have to see.
#  if ($windows and $] == 5.010) {
#     print STDERR "\n\nActiveState Perl 5.10 is not compatible with GBrowse due to problems\n";
#     print STDERR "with the AS implementation.  Please remove it and install Perl 5.8 instead.\n\n\n";
#     exit(0);
#  }

# Also MAY not be necessary
#  if ($windows) {
#     print STDERR "\n\nInstalling Win32 perl module\n\n";
#     system("ppm install Win32");
#  }

  eval "CPAN::Config->load";
  eval "CPAN::Config->commit";

  $working_dir = getcwd;

  $tmpdir = tempdir(CLEANUP=>1)
    or die "Could not create temporary directory: $!";

  $binaries = $Config{'binexp'};
  $make     = $Config{'make'};

  if ($windows) {
    system("ppm install YAML");
  }
  else {
    CPAN::Shell->install('YAML');
  }
  CPAN::Shell->install('Archive::Zip');
  CPAN::Shell->install('HTML::Tagset');
  CPAN::Shell->install('LWP::Simple');
  eval "use Archive::Zip ':ERROR_CODES',':CONSTANTS'";

  if ($windows && !-e "$binaries/${make}.exe") {

    print STDERR "Installing make utility...\n";
    -w $binaries or die "$binaries directory is not writeable. Please re-login as Admin.\n";
    chdir $tmpdir;

    my $rc = mirror(NMAKE,"nmake.zip");
    die "Could not download nmake executable from Microsoft web site."
      unless $rc == RC_OK() or $rc == RC_NOT_MODIFIED();

    my $zip = Archive::Zip->new('nmake.zip') or die "Couldn't open nmake zip file for decompression: $!";
    $zip->extractTree == AZ_OK() or die "Couldn't unzip file: $!";
    -e 'NMAKE.EXE' or die "Couldn't extract nmake.exe";

    cp('NMAKE.EXE',"$binaries/${make}.EXE") or die "Couldn't install nmake.exe: $!";
    cp('NMAKE.ERR',"$binaries/${make}.ERR"); # or die "Couldn't install nmake.err: $!"; # not fatal
  }

  CPAN::Shell->install('Archive::Tar');
  #print STDERR $@;
  #print STDERR "at end of BEGIN{}\n";
  1;
};

#print STDERR "here i am\n";
#print STDERR $@;

use Archive::Tar;
#use CPAN '!get';

$is_cygwin = 1 if ( $^O eq 'cygwin' );

if ($get_from_cvs) {
    $get_bioperl_svn = 1;
}

#if ($wincvs or ($windows and $get_from_cvs)) {
#    die "\n\nGBrowse is now in svn and fetching from svn on Windows\nis not currently supported\n ";
#}

#if ($windows and !$wincvs and $get_gbrowse_cvs ) {
#    die "\n\nThe development/cvs tags are not supported on Windows when\n"
#        ."WinCVS is not installed; exiting...\n";
#}

$build_param_string ||="";
$install_param_string ||="";

use constant BIOPERL_VERSION      => 'BioPerl-1.6.1';
use constant BIOPERL_REQUIRES     => '1.006001';  # sorry for the redundancy
use constant BIOPERL_LIVE_URL     => 'http://github.com/bioperl/bioperl-live/tarball/master';
use constant BIOPERL              => 'http://bioperl.org/DIST/'.BIOPERL_VERSION.'.tar.gz';

my %REPOSITORIES = (
                    #'BioPerl-Release-Candidates' => 'http://bioperl.org/DIST/RC',
		    'BioPerl-Regular-Releases'   => 'http://bioperl.org/DIST',
	            'Kobes'                      => 'http://theoryx5.uwinnipeg.ca/ppms',
                    'Bribes'                     => 'http://www.Bribes.org/perl/ppm',
                     'tcool'                     => 'http://ppm.tcool.org/archives/',
                    );


# this is so that ppm can be called in a pipe
$ENV{COLUMNS} = 80; # why do we have to do this?
$ENV{LINES}   = 24;

setup_ppm() if $windows;

unless ( eval "use GD 2.31; 1" ) {
   if ($windows) {
     print STDERR "Installing GD via ppm.\n";
     print STDERR "(This may take a while...\n";
     system("ppm install GD");
  }
  else {
     print STDERR "Installing GD via CPAN...\n";
     CPAN::Shell->install('GD') unless eval "use GD 2.31; 1";
  }
}

print STDERR "\n*** Installing prerequisites for BioPerl ***\n";

if ($windows and !eval "use DB_File; 1") {
  print STDERR "Installing DB_File for BioPerl.\n";

  # GBrowse doesn't like DB_File 1.820, so we explicitly get DB_File by url
  system("ppm install http://ppm.tcool.org/archives/DB_File.ppd");
}
#system("ppm install SVG") if $windows;
#CPAN::Shell->install('GD::SVG');

#needed?
CPAN::Shell->install('IO::String');
#CPAN::Shell->install('Text::Shellwords');
#if ($windows) {
#    #CGI::Session and Digest::MD5 both fail to install via cpan on windows
#    system("ppm install CGI-Session");
#    system("ppm install Digest-MD5");
#}
#else {
#    CPAN::Shell->install('CGI::Session');
#    CPAN::Shell->install('Digest::MD5');
#}
#CPAN::Shell->install('File::Temp');
#CPAN::Shell->install('Class::Base');
#CPAN::Shell->install('Statistics::Descriptive');
#CPAN::Shell->install('Data::Stag');

my $version = BIOPERL_REQUIRES;
if (!(eval "use Bio::Perl $version; 1") or $get_bioperl_svn or $bioperl_path) {
    print STDERR "\n*** Installing BioPerl ***\n";

    #would like to use ppm, but ppm won't install 1.6
    #if ($windows and !$get_bioperl_svn and !$bioperl_path) {
    #  my $bioperl_index = find_bioperl_ppm();
    #  system("ppm install --force $bioperl_index");
    #} else {
        # recent versions of Module::Build fail to install without force!
        CPAN::Shell->force('Module::Build') unless eval "require Module::Build; 1";
        do_install(BIOPERL,
                   'bioperl.tgz',
                   BIOPERL_VERSION,
                   'Build',
                   $get_bioperl_svn ? 'svn' : '',
                   $build_param_string,
                   $bioperl_path,
                   $install_param_string,
                   $perl_path);
    #}
}
else {
    print STDERR "BioPerl is up to date.\n";
}

print STDERR "\n *** Installing Bio::Graphics ***\n";


#install biographics?
CPAN::Shell->install('Bio::Graphics');

exit 0;

END {
  my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
  open STDERR,">$null"; # windows has an annoying message when cleaning up temp file
}

sub do_install {
  my ($download,$local_name,$distribution,$method,
         $from_cvs,$build_param_string,$file_path,$install_param_string,
         $perl_path) = @_;

  $install_param_string ||= '';
  chdir $tmpdir;

  do_get_distro($download,$local_name,$distribution,$from_cvs,$file_path);

  my $build_str = $windows ? "Build" : "./Build";

  if ($method eq 'make') {
      system("$perl_path Makefile.PL $build_param_string") == 0
            or die "Couldn't run perl Makefile.PL command\n";
      system("$make install UNINST=1 $install_param_string")    == 0 ;
  }
  elsif ($method eq 'Build') {
      system("$perl_path $build_str.PL --yes=1 $build_param_string")   == 0
            or die "Couldn't run perl Build.PL command\n";
      system("$build_str install --uninst 1 $install_param_string") == 0;
  }
}

sub do_get_distro {
    my ($download,$local_name,$distribution,$distribution_method,$file_path) = @_;

    if ($file_path) {
        chdir $working_dir;
        if (-e $file_path) { #must be an absolute path
            cp($file_path, "$tmpdir/$local_name");
        }
        elsif (-e "$working_dir/$file_path") { #assume it's a rel path from the original directory
            cp("$working_dir/$file_path", "$tmpdir/$local_name");
        }
        else {
            print "Couldn't find $file_path; nothing to do so quitting...\n";
            exit(-1);
        }
        $distribution = ($local_name =~ /gbrowse/)
                      ? "Generic-Genome-Browser" : "bioperl-live";
        chdir $tmpdir;
        extract_tarball($local_name,$distribution);
    }
    elsif ($distribution_method) {
        my $distribution_dir;
        print STDERR "Downloading bioperl-live...\n";
        $distribution_dir = 'bioperl-live';

        my $filename = 'bioperl-live.tar.gz'; # =determine_filename();
        my $url = BIOPERL_LIVE_URL."/$filename";

        my $rc = mirror($url, $filename);
        unless ($rc == RC_OK or $rc == RC_NOT_MODIFIED){
            print STDERR "Failed to get nightly bioperl-live file: $rc\n";
            return undef;
        }
        extract_tarball($filename,$distribution_dir);
        return 1;
        chdir $distribution_dir
            or die "Couldn't enter $distribution_dir directory: $@";
    }
    else {
        print STDERR "Downloading $download...\n";
        my $rc = mirror($download,$local_name);
        die "Could not download $distribution distribution from $download."
            unless $rc == RC_OK or $rc == RC_NOT_MODIFIED;

        extract_tarball($local_name,$distribution);
    }
    return 1;
}

#this is probably not going to be needed again, as the nightly
#bioperl build names have been simplified
sub determine_filename {
  my $listing = "dirlisting.html";
  my $rc = mirror(BIOPERL_LIVE_URL, $listing);
  die "Could not get directory listing of bioperl nightly build url: $rc\n"
      unless ($rc == RC_OK or $rc == RC_NOT_MODIFIED);

  my $filename;
  open my $LIST, '<', $listing or die "Could not read file '$listing': $!\n";
  while (my $line = <$LIST>) {
    if ($line =~ /href="(bioperl-live.*?\.tar\.gz)"/) {
      $filename = $1;
      last;
    }
  }
  close $LIST;
  unlink $listing;
  return $filename;
}

sub extract_tarball {
  my ($local_name,$distribution) = @_;

  print STDERR "Unpacking $local_name...\n";
  my $z = Archive::Tar->new($local_name,1)
        or die "Couldn't open $distribution archive: $@";
  my @extracted = $z->extract()
        or die "Couldn't extract $distribution archive: $@";

  if ($extracted[0]->{'name'} =~ /^(bioperl.*?)\//) {
    my $bioperl_dir = $1;
    move($bioperl_dir, $distribution) or die "couldn't move bioperl dir: $@";
  }

  chdir $distribution
        or die "Couldn't enter $distribution directory: $@";
  return;
}

# make sure ppm repositories are correct!
sub setup_ppm {
  open my $S, "ppm repo list --csv|" or die "Could not open ppm for listing: $!\n";
  my %repository;
  while (my $line = <$S>) {
     chomp $line;
     my ($index, $package_count, $name) = split /,/, $line;
     $repository{$name} = $index;
  }
  close $S;
  print STDERR "Adding needed PPM repositories. This may take a while....\n";
  for my $name (keys %REPOSITORIES) {
     next if $repository{$name};
     system("ppm rep add $name $REPOSITORIES{$name}");
  }
}

sub find_bioperl_ppm {
  print STDERR "Finding most recent bioperl...";
  open my $S,"ppm search bioperl |" or die "Could not open ppm for listing: $!\n";
  local $/ = ''; # paragraph mode
  my ($blessed_one, $blessed_version);
  my $best = 0;
  while (my $line = <$S>) {
    chomp $line;
    my ($number)     = ($line =~ /^(\d+): bioperl/m);
    my ($version)    = ($line =~ /^\s+Version: (.+)/m);
    my ($repository) = ($line =~ /^\s+Repo: (.+)/m);
    my $multiplier = 10000000;
    my $magnitude  = 0;
    # this dumb thing converts 1.5.1 into a real number
    foreach my $piece (split /[._]/, $version) {
      $magnitude += $piece * ($multiplier/=10);
    }
    ($blessed_one,$best,$blessed_version) = ($number,$magnitude,$version) if $best < $magnitude;
  }
  close $S;
  print STDERR $blessed_version ? "found $blessed_version\n" : "not found\n";
  return $blessed_one;
}
BioPerl-1.007002/scripts/utilities/bp_nrdb.pl000444000766000024       654313155576320 21170 0ustar00cjfieldsstaff000000000000#!perl

# Author Jason Stajich 
# 
# Make a non-redundant database based on sequence (not on ID!)
# This script is still in progress but is intended to mimic what 
# Warren Gish's nrdb does

# It requires that Digest::MD5 is installed (for now)

=head1 NAME

bp_nrdb.PLS - a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases

=head1 SYNOPSIS


Usage: 
  bp_nrdb.PLS [options] file1 file2 file3

Alternative usage
  bp_nrdb.PLS -p [options] file1 id1 file2 id2 file3 id3

=head1 DESCRIPTION

This script will create a unique database of sequences
(quasi-nonredundant).  The options are:

   -o filename          - the filename the db is written (STDOUT by default)
   -a filename          - the filename to append the db to
   -l#                  - minimum required sequence length
   -i                   - do not check for duplicates
   -n#                  - max number of descriptions to report per seq
   -d#                  - delimiter to use between consecutive descriptions
   -p                   - use database id prefixes from command line

=head1 AUTHOR

Jason Stajich, jason-at-bioperl-dot-org

=cut

use strict;
use warnings;
use Bio::SeqIO;
use Getopt::Long;

use Digest::MD5 qw(md5_hex);
my ($output,$append,$min_len, 
    $no_duplicate_check,$desc_count,
    $delimiter, $expect_prefixes,$help);
$delimiter = ';';

GetOptions(
	   'o|output:s'    => \$output,
	   'a|append:s'    => \$append,
	   'n:s'           => \$desc_count,
	   'l:s'           => \$min_len,
	   'd:s'           => \$delimiter,
	   'p'             => \$expect_prefixes,
	   'i'             => \$no_duplicate_check,
	   'h'             => \$help,
	   );

die("must supply a positive integer for -d") if ( defined $desc_count &&
						  ( $desc_count !~ /^\d+$/ ||
						    $desc_count < 1) );
die("must supply a positive integer for -l") if ( defined $min_len &&
						  ( $min_len !~ /^\d+$/ ||
						    $min_len < 1) );
my @files;

if( $help || ! @ARGV ) {
    exec('perldoc',$0);
    exit(0);
}
while( @ARGV ) {
    
    my ($file, $id) = (undef,'');
    if( $expect_prefixes ) {
	($file,$id) = (shift @ARGV, shift @ARGV);
	if( ! $id ) { 
	    die("Must provide 'name id' pairing of dbfile and id");
	}
    } else { 
	$file = shift @ARGV;
    }
    push @files, [ $file,$id];
}


my $out;
if( $append ) {
    $out = new Bio::SeqIO(-file => ">>$append");
} elsif( $output ) { 
    $out = new Bio::SeqIO(-file => ">$output");
} else {
    $out = new Bio::SeqIO(); # use STDOUT
}

my %unique;
my %seqcount;
my $counter = 0;
foreach my $pair ( @files ) {
    my ($file,$id) = @$pair;
    my $in = new Bio::SeqIO(-file => $file);
    while( my $seq = $in->next_seq ) {
	next if defined $min_len && $seq->length < $min_len;
	if( $id ) { 
	    $seq->display_id("$id:".$seq->display_id);
	}
	my $s = lc($seq->seq());
	my $md5sum = md5_hex($s);
	if( $no_duplicate_check ) {
	    $md5sum = $counter++;
	}
	    
	if( defined $unique{$md5sum} ) {
	    $seqcount{$md5sum}++;
	    next if defined $desc_count && $seqcount{$md5sum++} > $desc_count;
	    my $desc = $unique{$md5sum}->description;	    
	    my $id2 = sprintf("%s %s:%s %s",$delimiter,
			      $id,$seq->display_id,$seq->description);
	    $unique{$md5sum}->desc($desc . $id2);
	} else { 
	    $unique{$md5sum} = $seq;	
	}
    }
}

foreach my $seq ( values %unique ) {
    $out->write_seq($seq);
}

__END__
BioPerl-1.007002/scripts/utilities/bp_remote_blast.pl000444000766000024      1132313155576320 22733 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
#
# BioPerl module for bp_remote_blast.pl
#
# Revived by Evan Weaver for bioperl-1.5.1
# 3/14/2006
#
# Copyright Jason Stajich, Evan Weaver
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs after the code

use strict;
use warnings;
use vars qw($USAGE);

use Bio::Tools::Run::RemoteBlast;
use Bio::SeqIO;
use Getopt::Long;

$USAGE = "remote_blast.pl [-h] [-p prog] [-d db] [-e expect] [-mod
Blast] [-f seqformat] -z=\"entrez query\" -v 1 -t output_format -i
seqfile\n";

my ($prog, $db, $expect,$method) = ( 'blastp', 'nr', '10', 'Blast');

my ($sequencefile,$sequenceformat,$help, $entrez, $outputformat,
$verbose) = (undef, 'fasta',undef, undef, undef, 1);

&GetOptions('prog|p=s'               => \$prog,
				'db|d=s'                 => \$db,
				'expect|e=s'             => \$expect,
				'blsmod|module|method=s' => \$method,
				'input|i=s'              => \$sequencefile,  	
				'format|f=s'             => \$sequenceformat,
				'help|h'                 => \$help,
				'entrez|z=s'             => \$entrez,
				'output_format|t=s'      => \$outputformat,
				'verbose|v=s'            => \$verbose
			  );

if( $help ) {
    exec('perldoc', $0);
    die;
}

if( !defined $prog ) {
    die($USAGE . "\n\tMust specify a valid program name ([t]blast[pxn])\n");
}
if( !defined $db ) {
    die($USAGE . "\n\tMust specify a db to search\n");
}
if( !defined $sequencefile ) {
    die($USAGE . "\n\tMust specify an input file\n");
}

my $blastfactory = new Bio::Tools::Run::RemoteBlast ('-prog' => $prog,
																	  '-data'      => $db,
																	  '-expect'    => $expect,
																	  'readmethod' => $method,
																	 );

if ($entrez) {
  if ($verbose) {
    print "Entrez query (submission side): $entrez\n";
  }
  #$Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{ FORMAT_ENTREZ_QUERY} = $entrez;
  $Bio::Tools::Run::RemoteBlast::HEADER{ ENTREZ_QUERY } = $entrez;
}
if ($outputformat) {
  print "Don't use output format type; it doesn't work.\n";
  $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{ FORMAT_TYPE } = $outputformat;
}

# submit_blast can only currenly handle fasta format files so I'll
# preprocess outside of the module but I'd rather be sure here

my $input;
if( $sequenceformat !~ /fasta/ ) {
	my @seqs;
	my $seqio = new Bio::SeqIO('-format' => $sequenceformat,
										'-file'   => $sequencefile );
	while( my $seq = $seqio->next_seq() ) {
		push @seqs, $seq;
	}
	$input = \@seqs;
} else {
	$input = $sequencefile;
}

my $r = $blastfactory->submit_blast($input);
#my $r = $factory->submit_blast(?amino.fa?);

print STDERR "waiting...\n" if( $verbose > 0 );
while ( my @rids = $blastfactory->each_rid ) {
  foreach my $rid ( @rids ) {
    my $rc = $blastfactory->retrieve_blast($rid);
    if( !ref($rc) ) {
      if( $rc < 0 ) {
        $blastfactory->remove_rid($rid);
      }
      print STDERR "   checking $rid\n" if ( $verbose > 0 );
      sleep 5;
    } else {
      my $result = $rc->next_result();
      #save the output
      my $filename = $result->query_name()."\.out";
      $blastfactory->save_output($filename);
      $blastfactory->remove_rid($rid);
      print "\nQuery Name: ", $result->query_name(), "\n";
      while ( my $hit = $result->next_hit ) {
        next unless ( $verbose > 0);
        print "\thit name is ", $hit->name, "\n";
        while( my $hsp = $hit->next_hsp ) {
          print "\t\tscore is ", $hsp->score, "\n";
        }
      }
    }
  }
  print STDERR scalar(@rids) . " left\n";
}
	

__END__

#
# BioPerl module for bp_remote_blast.pl
#
# Cared for by Jason Stajich 
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

bp_remote_blast.pl - script for submitting jobs to a remote blast server
(ncbi blast queue at this time)

=head1 SYNOPSIS

% bp_remote_blast.pl -p blastp -d ecoli -e 1e-5 -i myseqs.fa

=head1 DESCRIPTION

This module will run a remote blast on a set of sequences by
submitting them to the NCBI blast queue and printing the output of the
request.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

=cut
BioPerl-1.007002/scripts/utilities/bp_revtrans-motif.pl000444000766000024      5737713155576320 23256 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
use warnings;
use strict;

use Bio::Seq;
use Bio::Tools::CodonTable;

use List::MoreUtils qw(uniq);
use Carp qw(croak);

use Getopt::Long;
use Pod::Usage;

=head1 NAME

bp_revtrans-motif - Reverse translate a Profam-like protein motif

=head1 VERSION

Version 0.01

=cut

our $VERSION = '0.01';

=head1 SYNOPSIS

From a file:

    bp_revtrans-motif.pl -i motifs.txt

Using pipes:

   bp_revtrans-motif.pl < motifs.txt > output.txt

Using interactively at the command prompt:

   $ bp_revtrans-motif.pl
   MAAEEL[VIKP]
   1.	ATGGCNGCNGARGARYTNVHN
   [^P]H(IW){2,3}
   2.	NDNCAY(ATHTGG){2,3}

=cut

# File IO, default to STDIN.
my ($help, $infile);
GetOptions( "h|help" => \$help, "i|infile:s" => \$infile );

# Parse command line arguments.
unless (defined $infile) { $infile = '-' };
open my $fh, '<', $infile or die "Could not read file '$infile': $!\n";

if ($help) { pod2usage(-verbose => 3) };

# Process each line, output to STDOUT.
while (my $motif = <$fh>) {
   if ($motif =~ /^\s*#/) { next }; # Ignore comments.
   chomp $motif;
   my $line = $.;

   my $result;
   eval { $result = reverse_translate_motif($motif) };
   if ($@) { warn $@; next }

   print $line, ".\t", $result, "\n";
}

sub reverse_translate_motif {
   # Main subroutine. It takes a Profam-like motif and returns its
   # reverse translation using degenerate codons.

   # Steps:
   # 1. Tokenize, then parse tokens.
   # 2. Reverse translate each token type.
   # 3. Join tokens in original order. Return the resulting string.

   my $motif = shift;

   $motif =~ s/\./X/g;
   $motif = uc $motif;

   ### 1. Tokenize, parse the motif.
   my ( $ordered, $classified ) = parse_motif($motif);

   ### 2. Reverse translate each token type.
   # Reverse translate the plain (unambiguous) tokens.
   my $ct = Bio::Tools::CodonTable->new;
   foreach my $seq ( @{ $classified->{plain} } ) {
      my $seqO
          = Bio::Seq->new( -seq => $$seq, -alphabet => 'protein' );
      $$seq = $ct->reverse_translate_all($seqO);
   }

   # Reverse translate the ambiguous tokens.
   foreach my $token ( @{ $classified->{ambiguous} } ) {
      my ($aas) = $$token =~ m(([A-Za-z\.]+));
      my @codons_to_contract;

      foreach my $residue ( split '', $aas ) {
         push @codons_to_contract, $ct->revtranslate($residue);
      }

      my $ambiguous_codon = contract_codons(@codons_to_contract);
      $$token             = $ambiguous_codon;
   }

   # Reverse translate the negated residues.
   foreach my $token ( @{ $classified->{negated} } ) {
      my ($aas) = $$token =~ m(([A-Za-z\.]+));
      my $ambiguous_codon = negated_aas_to_codon($aas);
      $$token = $ambiguous_codon;
   }

   ### 3. Join the profile back from its tokens.
   return join '', map {$$_} @{$ordered};

}

sub parse_motif {
   # Profam-like motif parser. It takes the pattern as a string, and
   # returns two data structures that contain the tokens, organized
   # by order of appearance in the pattern (first return value) and by
   # category (second return value).

   my $motif = shift;
   my $parser  = tokenize_motif($motif);
   my ( %tokens, @tokens );

   while ( my $token = $parser->() ) {
      croak "Unknown syntax token: <", $token->[1], ">"
          if ( $token->[0] eq 'UNKNOWN' );
      push @{ $tokens{ $token->[0] } }, \$token->[1];
      push @tokens, \$token->[1];
   }
   return ( \@tokens, \%tokens );
}

sub tokenize_motif {

   # Return a tokenizer iterator that sequentially recognizes and
   # returns each token in the input pattern.
   # Examples of each token type:

   # ambiguous: a position with more than one possible residue.
   #     eg. [ALEP]
   # negated: a position in which some residues are excluded.
   #     eg. [^WY]
   # plain: a common sequence of residues. One position, one residue.
   #     eg. MAAEIK
   # open_par, close_par: tags surrounding a motif that is repeated
   #     a certain number of times.
   #     eg. (...){3}

   my $target = shift;
   return sub {
      return [ 'ambiguous', $1 ]
          if $target =~ /\G (\[[A-Za-z\.]+\])     /gcx;
      return [ 'negated',   $1 ]
          if $target =~ /\G (\[\^[A-Za-z\.]+\])   /gcx;
      return [ 'plain',     $1 ]
          if $target =~ /\G ([A-Za-z\.]+)         /gcx;
      return [ 'open_par',  $1 ]
          if $target =~ /\G (\()                  /gcx;
      return [ 'close_par', $1 ]
          if $target =~ /\G (\)[\{\d+[,\d+]*\}]*) /gcx;
      return [ 'UNKNOWN',   $1 ]
          if $target =~ /\G (.)                   /gcx;
      return;
   };
}

sub contract_codons {

   # Take a list of codons, return an ambiguous codon.
   my @codons = map { uc $_ } @_;

   my @by_letter = ( [], [], [], );
   my $ambiguous_codon;
   foreach my $codon (@codons) {
      my @letters = split '', $codon;
      for my $i ( 0 .. 2 ) {
         push @{ $by_letter[$i] }, $letters[$i];
      }
   }
   for my $i ( 0 .. 2 ) {
      $ambiguous_codon
          .= convert( 'dna', uniq_string( @{ $by_letter[$i] } ) );
   }
   return $ambiguous_codon;
}

sub expand_codon {

   # Given a degenerate codon, return a list with all its
   # constituents. Takes a three-letter string (codon) as
   # input, returns a list with three-letter scalars.

   my $codon = shift;
   die "Wrong codon length!\n" if length $codon != 3;


   my ( @codons, @return_bases );
   my @orig_bases = split '', $codon;

   for my $i ( 0 .. 2 ) {

      # from each redundant base, create a list with all their
      # components (e.g., N -> (A, C, G, T) );
      my @components = split '', convert('dna', $orig_bases[$i] );
      $orig_bases[$i] = [@components];
   }

   # Combine all the bases of each of the three positions of the
   # codons, and build the return list.
   for my $i ( @{ $orig_bases[0] } ) {
      for my $j ( @{ $orig_bases[1] } ) {
         for my $k ( @{ $orig_bases[2] } ) {
            push @return_bases, $i . $j . $k;
         }
      }
   }
   return @return_bases;
}

{
   my %convert;

   sub convert {
      # Interconvert between redundant and non-redundant protein and
      # dna alphabets. Takes an alphabet (protein or dna) and a string
      # with the letter, and returns its equivalent in
      # redundant/non-redundant alphabet. Example ACTG -> N.

      my ($alphabet, $letter) = @_;
      unless (
         $alphabet and $alphabet =~ /^dna$|^protein$/i
         and $letter and length $letter <= 4
      ) { croak "Wrong arguments!\n"; }

      unless (%convert) {
         %convert = (
            'dna' => {
               qw(N ACGT B CGT D AGT H ACT V ACG K GT
                   M AC R AG S CG W AT Y CT A A C C T T G G)
            },
            'protein' => {
               '.' => 'ACDEFGHIJKLMNOPQRSTUVWY',
               X   => 'ACDEFGHIJKLMNOPQRSTUVWY',
               Z   => 'QE',
               B   => 'ND',
            },
         );

         # Make %convert hash key/value agnostic.
         foreach my $alphabet ( keys %convert ) {
            map { $convert{$alphabet}->{ $convert{$alphabet}{$_} } = $_ }
                keys %{ $convert{$alphabet} };
         }
      }

      return $convert{$alphabet}{$letter};
   }

}

sub uniq_string {
   # Takes a list of letters and returns an alphabetically sorted
   # list with unique elements.

   my @letters = @_;
   return join '', sort { $a cmp $b } uniq @letters;
}

{
   my ( @codon_library, $ct );

   sub negated_aas_to_codon {

      # Given a string of residues, returns a degenerate codon that will
      # not be translated into any of them, while maximizing degeneracy
      # (ie, it tries to also translate into as many residues as possible).

      # This functionality is required for reverse translating profiles
      # that contain negative patterns: [^X]. This means that the current
      # position should not contain aminoacid X, but can have any of the
      # others. The reverse translated nucleotide sequence should
      # reflect this.

      # Approach: construct a list of all possible codons, incluiding all
      # degenerate bases. This is an array of 15x15x15 = 3375 elements.
      # Order them by descendent "degeneracy".
      # Return the first one whose expansion in 4-lettered codons
      # doesn't contain a codon that translates into any of the
      # non-wanted residues.
      
      # * Since this takes some time, I presorted them and saved them.
      # Reading them from a file takes a fraction of the time that it taes
      # to re-sort them every time the application is launched.

      my $aas_to_avoid = shift;

      # Initialize reusable variables if it's the first time the sub
      # is called.
      unless (@codon_library) {
         while () { chomp; push @codon_library, split ' ', $_ }
      }
      unless ($ct) { $ct = Bio::Tools::CodonTable->new; }

      # Reverse translate the unwanted aminoacids to unwanted codons.
      my @unwanted_codons;
      foreach my $aa ( split '', $aas_to_avoid ) {
         push @unwanted_codons, $ct->revtranslate($aa);
      }

      foreach my $degenerate_codon (@codon_library) {
         my @codons  = expand_codon($degenerate_codon);
         my $success = 1;

         foreach my $unwanted (@unwanted_codons) {
            if ( grep { uc $unwanted eq $_ } @codons ) {
               $success = 0;
            }
         }

         if ($success) { return $degenerate_codon }
      }
   }

}

=head1 DESCRIPTION

This script takes a protein motif as input and returns a degenerate
oligonucleotide sequence corresponding to it. The main reason for doing this
is to design degenerate primers that amplify a given sequence pattern.

The input motif consists of a string of one-letter residues, with any of
the following syntactic elements:

=over 4

=item B<[...]> : Redundant position.

A position in which more than one residue is allowed. Example: 

    [TS]YW[RKSD]
     ^^    ^^^^

=item B<[^...]> : Negated position.

A position in which any residue is allowed, saved for those between
brackets. Example:

    [^PW]MK[LAE]
      ^^

=item B<(...){n,m,...}> : Repeated motif.

A motif that is repeated B or B times. It can have any of the previous
syntactic elements. Example:

    A[SN]C(TXX){2,4,8}
           ^^^

=back

The allowed letters are those that correspond to the 20 natural aminoacids,
plus:

    B = N + D
    Z = Q + E
    X = All

=head1 OPTIONS

=head2 B<-i input-file>:

A file with a list of motifs to reverse translate.

=head2 B<-h>

Display this help message.

=cut

=head1 AUTHOR

Bruno Vecchi, C

=head1 BUGS

Please report any bugs or feature requests to C

=head1 COPYRIGHT & LICENSE

Copyright 2009 Bruno Vecchi, all rights reserved.

This program is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.


=cut

__DATA__
NNN NNB NND NNH NNV NBN NDN NHN NVN BNN DNN HNN VNN NBB NBD NBH NBV NDB NDD
NDH NDV NHB NHD NHH NHV NVB NVD NVH NVV BNB BND BNH BNV BBN BDN BHN BVN DNB
DND DNH DNV DBN DDN DHN DVN HNB HND HNH HNV HBN HDN HHN HVN VNB VND VNH VNV
VBN VDN VHN VVN NNK NNM NNR NNS NNW NNY NKN NMN NRN NSN NWN NYN KNN MNN RNN
SNN WNN YNN BBB BBD BBH BBV BDB BDD BDH BDV BHB BHD BHH BHV BVB BVD BVH BVV
DBB DBD DBH DBV DDB DDD DDH DDV DHB DHD DHH DHV DVB DVD DVH DVV HBB HBD HBH
HBV HDB HDD HDH HDV HHB HHD HHH HHV HVB HVD HVH HVV VBB VBD VBH VBV VDB VDD
VDH VDV VHB VHD VHH VHV VVB VVD VVH VVV NBK NBM NBR NBS NBW NBY NDK NDM NDR
NDS NDW NDY NHK NHM NHR NHS NHW NHY NVK NVM NVR NVS NVW NVY NKB NKD NKH NKV
NMB NMD NMH NMV NRB NRD NRH NRV NSB NSD NSH NSV NWB NWD NWH NWV NYB NYD NYH
NYV BNK BNM BNR BNS BNW BNY BKN BMN BRN BSN BWN BYN DNK DNM DNR DNS DNW DNY
DKN DMN DRN DSN DWN DYN HNK HNM HNR HNS HNW HNY HKN HMN HRN HSN HWN HYN VNK
VNM VNR VNS VNW VNY VKN VMN VRN VSN VWN VYN KNB KND KNH KNV KBN KDN KHN KVN
MNB MND MNH MNV MBN MDN MHN MVN RNB RND RNH RNV RBN RDN RHN RVN SNB SND SNH
SNV SBN SDN SHN SVN WNB WND WNH WNV WBN WDN WHN WVN YNB YND YNH YNV YBN YDN
YHN YVN BBK BBM BBR BBS BBW BBY BDK BDM BDR BDS BDW BDY BHK BHM BHR BHS BHW
BHY BVK BVM BVR BVS BVW BVY BKB BKD BKH BKV BMB BMD BMH BMV BRB BRD BRH BRV
BSB BSD BSH BSV BWB BWD BWH BWV BYB BYD BYH BYV DBK DBM DBR DBS DBW DBY DDK
DDM DDR DDS DDW DDY DHK DHM DHR DHS DHW DHY DVK DVM DVR DVS DVW DVY DKB DKD
DKH DKV DMB DMD DMH DMV DRB DRD DRH DRV DSB DSD DSH DSV DWB DWD DWH DWV DYB
DYD DYH DYV HBK HBM HBR HBS HBW HBY HDK HDM HDR HDS HDW HDY HHK HHM HHR HHS
HHW HHY HVK HVM HVR HVS HVW HVY HKB HKD HKH HKV HMB HMD HMH HMV HRB HRD HRH
HRV HSB HSD HSH HSV HWB HWD HWH HWV HYB HYD HYH HYV VBK VBM VBR VBS VBW VBY
VDK VDM VDR VDS VDW VDY VHK VHM VHR VHS VHW VHY VVK VVM VVR VVS VVW VVY VKB
VKD VKH VKV VMB VMD VMH VMV VRB VRD VRH VRV VSB VSD VSH VSV VWB VWD VWH VWV
VYB VYD VYH VYV KBB KBD KBH KBV KDB KDD KDH KDV KHB KHD KHH KHV KVB KVD KVH
KVV MBB MBD MBH MBV MDB MDD MDH MDV MHB MHD MHH MHV MVB MVD MVH MVV RBB RBD
RBH RBV RDB RDD RDH RDV RHB RHD RHH RHV RVB RVD RVH RVV SBB SBD SBH SBV SDB
SDD SDH SDV SHB SHD SHH SHV SVB SVD SVH SVV WBB WBD WBH WBV WDB WDD WDH WDV
WHB WHD WHH WHV WVB WVD WVH WVV YBB YBD YBH YBV YDB YDD YDH YDV YHB YHD YHH
YHV YVB YVD YVH YVV NNA NNC NNT NNG NKK NKM NKR NKS NKW NKY NMK NMM NMR NMS
NMW NMY NRK NRM NRR NRS NRW NRY NSK NSM NSR NSS NSW NSY NWK NWM NWR NWS NWW
NWY NYK NYM NYR NYS NYW NYY NAN NCN NTN NGN KNK KNM KNR KNS KNW KNY KKN KMN
KRN KSN KWN KYN MNK MNM MNR MNS MNW MNY MKN MMN MRN MSN MWN MYN RNK RNM RNR
RNS RNW RNY RKN RMN RRN RSN RWN RYN SNK SNM SNR SNS SNW SNY SKN SMN SRN SSN
SWN SYN WNK WNM WNR WNS WNW WNY WKN WMN WRN WSN WWN WYN YNK YNM YNR YNS YNW
YNY YKN YMN YRN YSN YWN YYN ANN CNN TNN GNN NBA NBC NBT NBG NDA NDC NDT NDG
NHA NHC NHT NHG NVA NVC NVT NVG NAB NAD NAH NAV NCB NCD NCH NCV NTB NTD NTH
NTV NGB NGD NGH NGV BNA BNC BNT BNG BKK BKM BKR BKS BKW BKY BMK BMM BMR BMS
BMW BMY BRK BRM BRR BRS BRW BRY BSK BSM BSR BSS BSW BSY BWK BWM BWR BWS BWW
BWY BYK BYM BYR BYS BYW BYY BAN BCN BTN BGN DNA DNC DNT DNG DKK DKM DKR DKS
DKW DKY DMK DMM DMR DMS DMW DMY DRK DRM DRR DRS DRW DRY DSK DSM DSR DSS DSW
DSY DWK DWM DWR DWS DWW DWY DYK DYM DYR DYS DYW DYY DAN DCN DTN DGN HNA HNC
HNT HNG HKK HKM HKR HKS HKW HKY HMK HMM HMR HMS HMW HMY HRK HRM HRR HRS HRW
HRY HSK HSM HSR HSS HSW HSY HWK HWM HWR HWS HWW HWY HYK HYM HYR HYS HYW HYY
HAN HCN HTN HGN VNA VNC VNT VNG VKK VKM VKR VKS VKW VKY VMK VMM VMR VMS VMW
VMY VRK VRM VRR VRS VRW VRY VSK VSM VSR VSS VSW VSY VWK VWM VWR VWS VWW VWY
VYK VYM VYR VYS VYW VYY VAN VCN VTN VGN KBK KBM KBR KBS KBW KBY KDK KDM KDR
KDS KDW KDY KHK KHM KHR KHS KHW KHY KVK KVM KVR KVS KVW KVY KKB KKD KKH KKV
KMB KMD KMH KMV KRB KRD KRH KRV KSB KSD KSH KSV KWB KWD KWH KWV KYB KYD KYH
KYV MBK MBM MBR MBS MBW MBY MDK MDM MDR MDS MDW MDY MHK MHM MHR MHS MHW MHY
MVK MVM MVR MVS MVW MVY MKB MKD MKH MKV MMB MMD MMH MMV MRB MRD MRH MRV MSB
MSD MSH MSV MWB MWD MWH MWV MYB MYD MYH MYV RBK RBM RBR RBS RBW RBY RDK RDM
RDR RDS RDW RDY RHK RHM RHR RHS RHW RHY RVK RVM RVR RVS RVW RVY RKB RKD RKH
RKV RMB RMD RMH RMV RRB RRD RRH RRV RSB RSD RSH RSV RWB RWD RWH RWV RYB RYD
RYH RYV SBK SBM SBR SBS SBW SBY SDK SDM SDR SDS SDW SDY SHK SHM SHR SHS SHW
SHY SVK SVM SVR SVS SVW SVY SKB SKD SKH SKV SMB SMD SMH SMV SRB SRD SRH SRV
SSB SSD SSH SSV SWB SWD SWH SWV SYB SYD SYH SYV WBK WBM WBR WBS WBW WBY WDK
WDM WDR WDS WDW WDY WHK WHM WHR WHS WHW WHY WVK WVM WVR WVS WVW WVY WKB WKD
WKH WKV WMB WMD WMH WMV WRB WRD WRH WRV WSB WSD WSH WSV WWB WWD WWH WWV WYB
WYD WYH WYV YBK YBM YBR YBS YBW YBY YDK YDM YDR YDS YDW YDY YHK YHM YHR YHS
YHW YHY YVK YVM YVR YVS YVW YVY YKB YKD YKH YKV YMB YMD YMH YMV YRB YRD YRH
YRV YSB YSD YSH YSV YWB YWD YWH YWV YYB YYD YYH YYV ANB AND ANH ANV ABN ADN
AHN AVN CNB CND CNH CNV CBN CDN CHN CVN TNB TND TNH TNV TBN TDN THN TVN GNB
GND GNH GNV GBN GDN GHN GVN BBA BBC BBT BBG BDA BDC BDT BDG BHA BHC BHT BHG
BVA BVC BVT BVG BAB BAD BAH BAV BCB BCD BCH BCV BTB BTD BTH BTV BGB BGD BGH
BGV DBA DBC DBT DBG DDA DDC DDT DDG DHA DHC DHT DHG DVA DVC DVT DVG DAB DAD
DAH DAV DCB DCD DCH DCV DTB DTD DTH DTV DGB DGD DGH DGV HBA HBC HBT HBG HDA
HDC HDT HDG HHA HHC HHT HHG HVA HVC HVT HVG HAB HAD HAH HAV HCB HCD HCH HCV
HTB HTD HTH HTV HGB HGD HGH HGV VBA VBC VBT VBG VDA VDC VDT VDG VHA VHC VHT
VHG VVA VVC VVT VVG VAB VAD VAH VAV VCB VCD VCH VCV VTB VTD VTH VTV VGB VGD
VGH VGV ABB ABD ABH ABV ADB ADD ADH ADV AHB AHD AHH AHV AVB AVD AVH AVV CBB
CBD CBH CBV CDB CDD CDH CDV CHB CHD CHH CHV CVB CVD CVH CVV TBB TBD TBH TBV
TDB TDD TDH TDV THB THD THH THV TVB TVD TVH TVV GBB GBD GBH GBV GDB GDD GDH
GDV GHB GHD GHH GHV GVB GVD GVH GVV NKA NKC NKT NKG NMA NMC NMT NMG NRA NRC
NRT NRG NSA NSC NST NSG NWA NWC NWT NWG NYA NYC NYT NYG NAK NAM NAR NAS NAW
NAY NCK NCM NCR NCS NCW NCY NTK NTM NTR NTS NTW NTY NGK NGM NGR NGS NGW NGY
KNA KNC KNT KNG KKK KKM KKR KKS KKW KKY KMK KMM KMR KMS KMW KMY KRK KRM KRR
KRS KRW KRY KSK KSM KSR KSS KSW KSY KWK KWM KWR KWS KWW KWY KYK KYM KYR KYS
KYW KYY KAN KCN KTN KGN MNA MNC MNT MNG MKK MKM MKR MKS MKW MKY MMK MMM MMR
MMS MMW MMY MRK MRM MRR MRS MRW MRY MSK MSM MSR MSS MSW MSY MWK MWM MWR MWS
MWW MWY MYK MYM MYR MYS MYW MYY MAN MCN MTN MGN RNA RNC RNT RNG RKK RKM RKR
RKS RKW RKY RMK RMM RMR RMS RMW RMY RRK RRM RRR RRS RRW RRY RSK RSM RSR RSS
RSW RSY RWK RWM RWR RWS RWW RWY RYK RYM RYR RYS RYW RYY RAN RCN RTN RGN SNA
SNC SNT SNG SKK SKM SKR SKS SKW SKY SMK SMM SMR SMS SMW SMY SRK SRM SRR SRS
SRW SRY SSK SSM SSR SSS SSW SSY SWK SWM SWR SWS SWW SWY SYK SYM SYR SYS SYW
SYY SAN SCN STN SGN WNA WNC WNT WNG WKK WKM WKR WKS WKW WKY WMK WMM WMR WMS
WMW WMY WRK WRM WRR WRS WRW WRY WSK WSM WSR WSS WSW WSY WWK WWM WWR WWS WWW
WWY WYK WYM WYR WYS WYW WYY WAN WCN WTN WGN YNA YNC YNT YNG YKK YKM YKR YKS
YKW YKY YMK YMM YMR YMS YMW YMY YRK YRM YRR YRS YRW YRY YSK YSM YSR YSS YSW
YSY YWK YWM YWR YWS YWW YWY YYK YYM YYR YYS YYW YYY YAN YCN YTN YGN ANK ANM
ANR ANS ANW ANY AKN AMN ARN ASN AWN AYN CNK CNM CNR CNS CNW CNY CKN CMN CRN
CSN CWN CYN TNK TNM TNR TNS TNW TNY TKN TMN TRN TSN TWN TYN GNK GNM GNR GNS
GNW GNY GKN GMN GRN GSN GWN GYN BKA BKC BKT BKG BMA BMC BMT BMG BRA BRC BRT
BRG BSA BSC BST BSG BWA BWC BWT BWG BYA BYC BYT BYG BAK BAM BAR BAS BAW BAY
BCK BCM BCR BCS BCW BCY BTK BTM BTR BTS BTW BTY BGK BGM BGR BGS BGW BGY DKA
DKC DKT DKG DMA DMC DMT DMG DRA DRC DRT DRG DSA DSC DST DSG DWA DWC DWT DWG
DYA DYC DYT DYG DAK DAM DAR DAS DAW DAY DCK DCM DCR DCS DCW DCY DTK DTM DTR
DTS DTW DTY DGK DGM DGR DGS DGW DGY HKA HKC HKT HKG HMA HMC HMT HMG HRA HRC
HRT HRG HSA HSC HST HSG HWA HWC HWT HWG HYA HYC HYT HYG HAK HAM HAR HAS HAW
HAY HCK HCM HCR HCS HCW HCY HTK HTM HTR HTS HTW HTY HGK HGM HGR HGS HGW HGY
VKA VKC VKT VKG VMA VMC VMT VMG VRA VRC VRT VRG VSA VSC VST VSG VWA VWC VWT
VWG VYA VYC VYT VYG VAK VAM VAR VAS VAW VAY VCK VCM VCR VCS VCW VCY VTK VTM
VTR VTS VTW VTY VGK VGM VGR VGS VGW VGY KBA KBC KBT KBG KDA KDC KDT KDG KHA
KHC KHT KHG KVA KVC KVT KVG KAB KAD KAH KAV KCB KCD KCH KCV KTB KTD KTH KTV
KGB KGD KGH KGV MBA MBC MBT MBG MDA MDC MDT MDG MHA MHC MHT MHG MVA MVC MVT
MVG MAB MAD MAH MAV MCB MCD MCH MCV MTB MTD MTH MTV MGB MGD MGH MGV RBA RBC
RBT RBG RDA RDC RDT RDG RHA RHC RHT RHG RVA RVC RVT RVG RAB RAD RAH RAV RCB
RCD RCH RCV RTB RTD RTH RTV RGB RGD RGH RGV SBA SBC SBT SBG SDA SDC SDT SDG
SHA SHC SHT SHG SVA SVC SVT SVG SAB SAD SAH SAV SCB SCD SCH SCV STB STD STH
STV SGB SGD SGH SGV WBA WBC WBT WBG WDA WDC WDT WDG WHA WHC WHT WHG WVA WVC
WVT WVG WAB WAD WAH WAV WCB WCD WCH WCV WTB WTD WTH WTV WGB WGD WGH WGV YBA
YBC YBT YBG YDA YDC YDT YDG YHA YHC YHT YHG YVA YVC YVT YVG YAB YAD YAH YAV
YCB YCD YCH YCV YTB YTD YTH YTV YGB YGD YGH YGV ABK ABM ABR ABS ABW ABY ADK
ADM ADR ADS ADW ADY AHK AHM AHR AHS AHW AHY AVK AVM AVR AVS AVW AVY AKB AKD
AKH AKV AMB AMD AMH AMV ARB ARD ARH ARV ASB ASD ASH ASV AWB AWD AWH AWV AYB
AYD AYH AYV CBK CBM CBR CBS CBW CBY CDK CDM CDR CDS CDW CDY CHK CHM CHR CHS
CHW CHY CVK CVM CVR CVS CVW CVY CKB CKD CKH CKV CMB CMD CMH CMV CRB CRD CRH
CRV CSB CSD CSH CSV CWB CWD CWH CWV CYB CYD CYH CYV TBK TBM TBR TBS TBW TBY
TDK TDM TDR TDS TDW TDY THK THM THR THS THW THY TVK TVM TVR TVS TVW TVY TKB
TKD TKH TKV TMB TMD TMH TMV TRB TRD TRH TRV TSB TSD TSH TSV TWB TWD TWH TWV
TYB TYD TYH TYV GBK GBM GBR GBS GBW GBY GDK GDM GDR GDS GDW GDY GHK GHM GHR
GHS GHW GHY GVK GVM GVR GVS GVW GVY GKB GKD GKH GKV GMB GMD GMH GMV GRB GRD
GRH GRV GSB GSD GSH GSV GWB GWD GWH GWV GYB GYD GYH GYV NAA NAC NAT NAG NCA
NCC NCT NCG NTA NTC NTT NTG NGA NGC NGT NGG KKA KKC KKT KKG KMA KMC KMT KMG
KRA KRC KRT KRG KSA KSC KST KSG KWA KWC KWT KWG KYA KYC KYT KYG KAK KAM KAR
KAS KAW KAY KCK KCM KCR KCS KCW KCY KTK KTM KTR KTS KTW KTY KGK KGM KGR KGS
KGW KGY MKA MKC MKT MKG MMA MMC MMT MMG MRA MRC MRT MRG MSA MSC MST MSG MWA
MWC MWT MWG MYA MYC MYT MYG MAK MAM MAR MAS MAW MAY MCK MCM MCR MCS MCW MCY
MTK MTM MTR MTS MTW MTY MGK MGM MGR MGS MGW MGY RKA RKC RKT RKG RMA RMC RMT
RMG RRA RRC RRT RRG RSA RSC RST RSG RWA RWC RWT RWG RYA RYC RYT RYG RAK RAM
RAR RAS RAW RAY RCK RCM RCR RCS RCW RCY RTK RTM RTR RTS RTW RTY RGK RGM RGR
RGS RGW RGY SKA SKC SKT SKG SMA SMC SMT SMG SRA SRC SRT SRG SSA SSC SST SSG
SWA SWC SWT SWG SYA SYC SYT SYG SAK SAM SAR SAS SAW SAY SCK SCM SCR SCS SCW
SCY STK STM STR STS STW STY SGK SGM SGR SGS SGW SGY WKA WKC WKT WKG WMA WMC
WMT WMG WRA WRC WRT WRG WSA WSC WST WSG WWA WWC WWT WWG WYA WYC WYT WYG WAK
WAM WAR WAS WAW WAY WCK WCM WCR WCS WCW WCY WTK WTM WTR WTS WTW WTY WGK WGM
WGR WGS WGW WGY YKA YKC YKT YKG YMA YMC YMT YMG YRA YRC YRT YRG YSA YSC YST
YSG YWA YWC YWT YWG YYA YYC YYT YYG YAK YAM YAR YAS YAW YAY YCK YCM YCR YCS
YCW YCY YTK YTM YTR YTS YTW YTY YGK YGM YGR YGS YGW YGY ANA ANC ANT ANG AKK
AKM AKR AKS AKW AKY AMK AMM AMR AMS AMW AMY ARK ARM ARR ARS ARW ARY ASK ASM
ASR ASS ASW ASY AWK AWM AWR AWS AWW AWY AYK AYM AYR AYS AYW AYY AAN ACN ATN
AGN CNA CNC CNT CNG CKK CKM CKR CKS CKW CKY CMK CMM CMR CMS CMW CMY CRK CRM
CRR CRS CRW CRY CSK CSM CSR CSS CSW CSY CWK CWM CWR CWS CWW CWY CYK CYM CYR
CYS CYW CYY CAN CCN CTN CGN TNA TNC TNT TNG TKK TKM TKR TKS TKW TKY TMK TMM
TMR TMS TMW TMY TRK TRM TRR TRS TRW TRY TSK TSM TSR TSS TSW TSY TWK TWM TWR
TWS TWW TWY TYK TYM TYR TYS TYW TYY TAN TCN TTN TGN GNA GNC GNT GNG GKK GKM
GKR GKS GKW GKY GMK GMM GMR GMS GMW GMY GRK GRM GRR GRS GRW GRY GSK GSM GSR
GSS GSW GSY GWK GWM GWR GWS GWW GWY GYK GYM GYR GYS GYW GYY GAN GCN GTN GGN
BAA BAC BAT BAG BCA BCC BCT BCG BTA BTC BTT BTG BGA BGC BGT BGG DAA DAC DAT
DAG DCA DCC DCT DCG DTA DTC DTT DTG DGA DGC DGT DGG HAA HAC HAT HAG HCA HCC
HCT HCG HTA HTC HTT HTG HGA HGC HGT HGG VAA VAC VAT VAG VCA VCC VCT VCG VTA
VTC VTT VTG VGA VGC VGT VGG ABA ABC ABT ABG ADA ADC ADT ADG AHA AHC AHT AHG
AVA AVC AVT AVG AAB AAD AAH AAV ACB ACD ACH ACV ATB ATD ATH ATV AGB AGD AGH
AGV CBA CBC CBT CBG CDA CDC CDT CDG CHA CHC CHT CHG CVA CVC CVT CVG CAB CAD
CAH CAV CCB CCD CCH CCV CTB CTD CTH CTV CGB CGD CGH CGV TBA TBC TBT TBG TDA
TDC TDT TDG THA THC THT THG TVA TVC TVT TVG TAB TAD TAH TAV TCB TCD TCH TCV
TTB TTD TTH TTV TGB TGD TGH TGV GBA GBC GBT GBG GDA GDC GDT GDG GHA GHC GHT
GHG GVA GVC GVT GVG GAB GAD GAH GAV GCB GCD GCH GCV GTB GTD GTH GTV GGB GGD
GGH GGV KAA KAC KAT KAG KCA KCC KCT KCG KTA KTC KTT KTG KGA KGC KGT KGG MAA
MAC MAT MAG MCA MCC MCT MCG MTA MTC MTT MTG MGA MGC MGT MGG RAA RAC RAT RAG
RCA RCC RCT RCG RTA RTC RTT RTG RGA RGC RGT RGG SAA SAC SAT SAG SCA SCC SCT
SCG STA STC STT STG SGA SGC SGT SGG WAA WAC WAT WAG WCA WCC WCT WCG WTA WTC
WTT WTG WGA WGC WGT WGG YAA YAC YAT YAG YCA YCC YCT YCG YTA YTC YTT YTG YGA
YGC YGT YGG AKA AKC AKT AKG AMA AMC AMT AMG ARA ARC ART ARG ASA ASC AST ASG
AWA AWC AWT AWG AYA AYC AYT AYG AAK AAM AAR AAS AAW AAY ACK ACM ACR ACS ACW
ACY ATK ATM ATR ATS ATW ATY AGK AGM AGR AGS AGW AGY CKA CKC CKT CKG CMA CMC
CMT CMG CRA CRC CRT CRG CSA CSC CST CSG CWA CWC CWT CWG CYA CYC CYT CYG CAK
CAM CAR CAS CAW CAY CCK CCM CCR CCS CCW CCY CTK CTM CTR CTS CTW CTY CGK CGM
CGR CGS CGW CGY TKA TKC TKT TKG TMA TMC TMT TMG TRA TRC TRT TRG TSA TSC TST
TSG TWA TWC TWT TWG TYA TYC TYT TYG TAK TAM TAR TAS TAW TAY TCK TCM TCR TCS
TCW TCY TTK TTM TTR TTS TTW TTY TGK TGM TGR TGS TGW TGY GKA GKC GKT GKG GMA
GMC GMT GMG GRA GRC GRT GRG GSA GSC GST GSG GWA GWC GWT GWG GYA GYC GYT GYG
GAK GAM GAR GAS GAW GAY GCK GCM GCR GCS GCW GCY GTK GTM GTR GTS GTW GTY GGK
GGM GGR GGS GGW GGY AAA AAC AAT AAG ACA ACC ACT ACG ATA ATC ATT ATG AGA AGC
AGT AGG CAA CAC CAT CAG CCA CCC CCT CCG CTA CTC CTT CTG CGA CGC CGT CGG TAA
TAC TAT TAG TCA TCC TCT TCG TTA TTC TTT TTG TGA TGC TGT TGG GAA GAC GAT GAG
GCA GCC GCT GCG GTA GTC GTT GTG GGA GGC GGT GGG
BioPerl-1.007002/scripts/utilities/bp_search2alnblocks.pl000444000766000024       776413155576320 23471 0ustar00cjfieldsstaff000000000000#!perl
# Author:      Jason Stajich 
# Description: Turn SearchIO parseable report(s) into a set of Aligned blocks
#

=head1 NAME

bp_search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocks

=head1 SYNOPSIS

  bp_search2alnblocks --minid PERCENTID --minlen LEN --minevalue EVALUE file1.
  blast file2.blast ...> out.fas

=head1 DESCRIPTION

This script will parse and filter BLAST (or other formats
L can parse) output and format the alignment as blocks
of alignments based on the HSPs.  Note this can only work if the input
file parsed contains the necessary.

Typically this can be used to turn BLAST output into a FASTA alignment format for input into the QRNA comparative gene finder for RNA genes (E.Rivas).

=head1 OPTIONS

 --maxevalue   Maximum E-value for an HSP
 --minevalue   Minimum E-value for an HSP 
 --minlen      Minimum length of an HSP [default 0] 
 --maxid       Maximum Percent Id [default 100]
               (to help remove sequences which are really close)
 --minid       Minimum Percent Identity for an HSP [default 0]
 -i/--input    An optional input filename (expects input on STDIN by default)
 -o/--output   An optional output filename (exports to STDOUT by default)
 -f/--format   Specify a different Search Alignment format- 
               {fasta, axt, waba, blast, blastxml} are all permitted
               although the format must have actual alignment 
               sequence for this script to work
               See L for more information.
 -of/--outformat Output format for the alignment blocks, anything
               L supports.
 -v/--verbose  Turn on debugging

=head1 AUTHOR - Jason Stajich

Jason Stajich, jason-at-bioperl-dot-org.

=cut


use strict;
use warnings;

use Bio::SearchIO;
use Bio::AlignIO;
use Math::BigFloat;
use Getopt::Long;

my $Usage = 'search2alnblocks --minid PERCENTID --minlen LEN --maxevalue EVALUE file1.blast file2.blast ... > blocks.fas';

my ($min_id,$min_len,$max_id,$max_len,$max_evalue,$min_evalue,$format,
    $outformat,$verbose,$input,$output);
$min_id  = 0;
$max_evalue = 0;
$min_evalue = undef;
$min_len = 0;
$format = 'blast';
$outformat= 'fasta';
GetOptions(
	   'minid:s'      => \$min_id,
	   'maxid:s'      => \$max_id,
	   'minlen:s'     => \$min_len,
	   'maxlen:s'     => \$max_len,
	   'minevalue:s'  => \$min_evalue,
	   'maxevalue:s'  => \$max_evalue,
	   'f|format:s'   => \$format,
	   'i|input:s'    => \$input,
	   'o|output:s'   => \$output,
	   'of|oformat:s' => \$outformat,
	   'v|verbose'    => \$verbose,
	   'h|help'       => sub { system('perldoc', $0);
				   exit(0) },
	   );
$max_evalue =~ s/^e/1e/;

# if $input is undef then will read from STDIN
my $parser =  new Bio::SearchIO(-format => $format,
				-file   => $input,
				-verbose=> $verbose);
my $out;

if( $output ) {
    $out = new Bio::AlignIO(-format => $outformat,
			    -file   => ">$output");
} else { 
    $out = new Bio::AlignIO(-format => $outformat);
}

my $id = 1;
while( my $r = $parser->next_result ) {
    while( my $hit = $r->next_hit ) {
	while( my $hsp = $hit->next_hsp ) {
	    my $hsplen = $hsp->length('total');
	    next if( $min_len && $hsplen < $min_len);
	    my $pid = $hsp->percent_identity;
	    next if( ($min_id && $pid < $min_id) || 
		     ($max_id && $pid > $max_id ) );
	    next if( defined $min_evalue && 
		     $hsp->evalue > $min_evalue ); 
	    next if( $max_evalue && 
		     $hsp->evalue < $max_evalue);	    
	    $verbose && $hsp->verbose($verbose);	    
	    my $aln = $hsp->get_aln();
	    my @seqs;
	    foreach my $seq ( $aln->each_seq ) {
		if( $seq->display_id =~ /(\S+)[\/\_](\d+)\-(\d+)/ ) {
		    $seq->display_id($1);
		    $seq->start($seq->start + $2 - 1);
		    $seq->end($seq->end + $2 - 1);
		}
		$seq->description(sprintf("PID=%.2f LEN=%d HSP=%d",
					  $pid,$hsplen,$id));
		push @seqs, $seq;
	    }
	    $aln = new Bio::SimpleAlign();
	    $aln->add_seq(shift @seqs);
	    $aln->add_seq(shift @seqs);
	    
	    $id++;
	    $out->write_aln($aln);
	}
    }
}
BioPerl-1.007002/scripts/utilities/bp_search2gff.pl000444000766000024      3017513155576320 22273 0ustar00cjfieldsstaff000000000000#!perl

=head1 NAME

bp_search2gff - turn a SearchIO report into GFF

=head1 SYNOPSIS

Usage:

  bp_search2gff [-o outputfile] [-f reportformat] [-i inputfilename]  OR file1 file2 ..

=head1 DESCRIPTION

This script will turn a SearchIO report (BLAST, FASTP, SSEARCH,
AXT, WABA) into GFF.

The options are:

   -i infilename      - (optional) inputfilename, will read
                        either ARGV files or from STDIN
   -o filename        - the output filename [default STDOUT]
   -f format          - search result format (blast, fasta,waba,axt)
                        (ssearch is fasta format). default is blast.
   -t/--type seqtype  - if you want to see query or hit information
                        in the GFF report
   -s/--source        - specify the source (will be algorithm name
                        otherwise like BLASTN)
   --method           - the method tag (primary_tag) of the features
                        (default is similarity)
   --scorefunc        - a string or a file that when parsed evaluates
                        to a closure which will be passed a feature
                        object and that returns the score to be printed
   --locfunc          - a string or a file that when parsed evaluates
                        to a closure which will be passed two
                        features, query and hit, and returns the
                        location (Bio::LocationI compliant) for the
                        GFF3 feature created for each HSP; the closure
                        may use the clone_loc() and create_loc()
                        functions for convenience, see their PODs
   --onehsp           - only print the first HSP feature for each hit
   -p/--parent        - the parent to which HSP features should refer
                        if not the name of the hit or query (depending
                        on --type)
   --target/--notarget - whether to always add the Target tag or not
   -h                 - this help menu
   --version          - GFF version to use (put a 3 here to use gff 3)
   --component        - generate GFF component fields (chromosome)
   -m/--match         - generate a 'match' line which is a container
                        of all the similarity HSPs
   --addid            - add ID tag in the absence of --match
   -c/--cutoff        - specify an evalue cutoff

Additionally specify the filenames you want to process on the
command-line.  If no files are specified then STDIN input is assumed.
You specify this by doing: bp_search2gff E file1 file2 file3

=head1 AUTHOR

Jason Stajich, jason-at-bioperl-dot-org

=head1 Contributors

Hilmar Lapp, hlapp-at-gmx-dot-net

=cut

use strict;
use warnings;
use Bio::Tools::GFF;
use Getopt::Long;
use Bio::SearchIO;
use Bio::Location::Simple;    # pre-declare to simplify $locfunc implementations
use Bio::Location::Atomic;    # pre-declare to simplify $locfunc implementations
use Storable qw(dclone);      # for cloning location objects
use Bio::Factory::FTLocationFactory;

my (
    $output,       # output file (if not stdout)
    $input,        # name of the input file
    $format,       # format of the input file, defauly is blast
    $type,         # 'query' or 'hit'
    $cutoff,       # cut-off value for e-value filter
    $sourcetag,    # explicit source tag (will be taken from program
                   # otherwise
    $methodtag,    # primary tag (a.k.a. method), default 'similarity'
    $gffver,       # GFF version (dialect) to write
    $scorefunc,    # closure returning the score for a passed feature
    $locfunc,      # closure returning a location object for a passed
                   # query and hit feature
    $addid,        # flag: whether to always add the ID for $match == 0
    $parent,       # the name of the parent to use; if set and $match == 0
                   # will always add the target
    $comp,         # flag: whether to print a component feature
    $addtarget,    # flag: whether to always add the Target tag, default
                   # is true
    $match,        # flag: whether to print match lines as containers
    $onehsp,       # flag: whether to consider only the first HSP for a hit
    $quiet,        # flag: run quietly
    $help          # flag: show help screen
);

# set defaults:
$format    = 'blast';
$type      = 'query';
$gffver    = 2;
$methodtag = "similarity";
$addtarget = 1;

GetOptions(
    'i|input:s'   => \$input,
    'component'   => \$comp,
    'm|match'     => \$match,
    'o|output:s'  => \$output,
    'f|format:s'  => \$format,
    's|source:s'  => \$sourcetag,
    'method=s'    => \$methodtag,
    'addid'       => \$addid,
    'scorefunc=s' => \$scorefunc,
    'locfunc=s'   => \$locfunc,
    'p|parent=s'  => \$parent,
    'target!'     => \$addtarget,
    'onehsp'      => \$onehsp,
    't|type:s'    => \$type,
    'c|cutoff:s'  => \$cutoff,
    'v|version:i' => \$gffver,
    'q|quiet'     => \$quiet,
    'h|help'      => sub {
        exec( 'perldoc', $0 );
        exit(0);
    },
);
$type = lc($type);
if ( $type =~ /target/ ) { $type = 'hit' }
elsif ( $type ne 'query' && $type ne 'hit' ) {
    die("seqtype must be either 'query' or 'hit'");
}

# custom or default function returning the score
$scorefunc =
  defined($scorefunc) ? parse_code($scorefunc) : sub { shift->score };

# custom or default function returning the location
$locfunc = defined($locfunc) ? parse_code($locfunc) : sub { shift->location };

# if --match is given then $addid needs to be disabled
$addid = undef if $addid && $match;

# if no input is provided STDIN will be used
my $parser = new Bio::SearchIO(
    -format  => $format,
    -verbose => $quiet ? -1 : 0,
    -file    => $input
);

my $out;
if ( defined $output ) {
    $out = new Bio::Tools::GFF(
        -gff_version => $gffver,
        -file        => ">$output"
    );
}
else {
    $out = new Bio::Tools::GFF( -gff_version => $gffver );    # STDOUT
}
my ( %seen_hit, %seen );
my $other = $type eq 'query' ? 'hit' : 'query';

while ( my $result = $parser->next_result ) {
    my $qname = $result->query_name;
    if (   $comp
        && $type eq 'query'
        && $result->query_length )
    {
        $out->write_feature(
            Bio::SeqFeature::Generic->new(
                -start       => 1,
                -end         => $result->query_length,
                -seq_id      => $qname,
                -source_tag  => 'chromosome',
                -primary_tag => 'Component',
                -tag         => {
                    'Sequence' => $qname
                }
            )
        );
    }
    while ( my $hit = $result->next_hit ) {
        next if ( defined $cutoff && $hit->significance > $cutoff );
        my $acc = $qname;
        if ( $seen{ $qname . "-" . $hit->name }++ ) {
            $acc = $qname . "-" . $seen{ $qname . '-' . $hit->name };
        }

        if (   $comp
            && $type eq 'hit'
            && $hit->length
            && !$seen_hit{ $hit->name }++ )
        {
            $out->write_feature(
                Bio::SeqFeature::Generic->new(
                    -start       => 1,
                    -end         => $hit->length,
                    -seq_id      => $hit->name,
                    -source_tag  => 'chromosome',
                    -primary_tag => 'Component',
                    -tag         => {
                        'Sequence' => $hit->name
                    }
                )
            );
        }
        my ( %min, %max, $seqid, $name, $st );
        while ( my $hsp = $hit->next_hsp ) {
            my $feature = new Bio::SeqFeature::Generic;
            my ( $proxyfor, $otherf );
            if ( $type eq 'query' ) {
                ( $proxyfor, $otherf ) = ( $hsp->query, $hsp->hit );
                $name ||= $hit->name;
            }
            else {
                ( $otherf, $proxyfor ) = ( $hsp->query, $hsp->hit );
                $name ||= $acc;
            }
            $proxyfor->score( $hit->bits ) unless ( $proxyfor->score );
            if ( ( $gffver == 3 ) && ( $match || $parent ) ) {
                $feature->add_tag_value( 'Parent', $parent || $name );
            }

            $min{$type} = $proxyfor->start
              unless defined $min{$type} && $min{$type} < $proxyfor->start;
            $max{$type} = $proxyfor->end
              unless defined $max{$type} && $max{$type} > $proxyfor->end;
            $min{$other} = $otherf->start
              unless defined $min{$other} && $min{$other} < $otherf->start;
            $max{$other} = $otherf->end
              unless defined $max{$other} && $max{$other} > $otherf->end;
            if ( $addtarget || $match ) {
                $feature->add_tag_value( 'Target', 'Sequence:' . $name );
                $feature->add_tag_value( 'Target', $otherf->start );
                $feature->add_tag_value( 'Target', $otherf->end );
            }
            if ($addid) {
                $feature->add_tag_value( 'ID', $name );
            }

            $feature->location( &$locfunc( $proxyfor, $otherf ) );

            #  strand for feature is always going to be product of
            #  query & hit strands so that target can always be just
            #  '+'
            $feature->strand( $proxyfor->strand * $otherf->strand );
            if ($sourcetag) {
                $feature->source_tag($sourcetag);
            }
            else {
                $feature->source_tag( $proxyfor->source_tag );
            }
            $feature->score( &$scorefunc($proxyfor) );
            $feature->frame( $proxyfor->frame );
            $feature->seq_id( $proxyfor->seq_id );
            $feature->primary_tag($methodtag);

            # add annotation if encoded in the query description
            my $desc = $result->query_description;
            while ( $desc =~ /\/([^=]+)=(\S+)/g ) {
                $feature->add_tag_value( $1, $2 );
            }
            $seqid ||= $proxyfor->seq_id;
            $out->write_feature($feature);
            $st ||= $sourcetag || $proxyfor->source_tag;
            last if $onehsp;
        }
        if ($match) {

            my $matchf = Bio::SeqFeature::Generic->new(
                -start       => $min{$type},
                -end         => $max{$type},
                -strand      => $hit->strand($type) * $hit->strand($other),
                -primary_tag => 'match',
                -source_tag  => $st,
                -score       => $hit->bits,
                -seq_id      => $seqid
            );
            if ( $gffver == 3 ) {
                $matchf->add_tag_value( 'ID', $name );
            }
            $matchf->add_tag_value( 'Target', "Sequence:$name" );
            $out->write_feature($matchf);
        }
    }
}

sub parse_code {
    my $src = shift;
    my $code;

    # file or subroutine?
    if ( -r $src ) {
        if ( !( ( $code = do $src ) && ( ref($code) eq "CODE" ) ) ) {
            die "error in parsing code block $src: $@" if $@;
            die "unable to read file $src: $!"         if $!;
            die "failed to run $src, or it failed to return a closure";
        }
    }
    else {
        $code = eval $src;
        die "error in parsing code block \"$src\": $@" if $@;
        die "\"$src\" fails to return a closure"
          unless ref($code) eq "CODE";
    }
    return $code;
}

=head2 clone_loc

Title   : clone_loc
Usage   : my $l = clone_loc($feature->location);
Function: Helper function to simplify the task of cloning locations
           for --locfunc closures.

          Presently simply implemented using Storable::dclone().
Example :
Returns : A L object of the same type and with the
          same properties as the argument, but physically different.
          All structured properties will be cloned as well.
Args    : A L compliant object

=cut

sub clone_loc {
    return dclone(shift);
}

=head2 create_loc

Title   : create_loc
Usage   : my $l = create_loc("10..12");
Function: Helper function to simplify the task of creating locations
          for --locfunc closures. Creates a location from a feature-
          table formatted string.

Example :
Returns : A L object representing the location given
          as formatted string.
Args    : A GenBank feature-table formatted string.

=cut

sub create_loc {
    return Bio::Factory::FTLocationFactory->from_string(shift);
}
BioPerl-1.007002/scripts/utilities/bp_search2tribe.pl000444000766000024       511113155576320 22606 0ustar00cjfieldsstaff000000000000#!perl

# Author:      Jason Stajich 
# Description: Turn SearchIO parseable report(s) into a TRIBE matrix
#
=head1 NAME

bp_search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix

=head1 SYNOPSIS

Usage:
  bp_search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1 file2 ..

=head1 DESCRIPTION

This script is probably too slow for most people's uses.  It is better
to use something like scripts/searchio/fastam9_to_table, -m 9 output
from BLAST, or the blast2table from the BLAST O'Reilly book to get a
tabular output from these programs and then feed the table into MCL
with the mcxdeblast script and the --m9 option.

This script will turn a protein Search report (BLASTP, FASTP, SSEARCH)
into a Markov Matrix for TribeMCL clustering.

The options are:

   -o filename          - the output filename [default STDOUT]
   -f format            - search result format (blast, fasta)
                          (ssearch is fasta format). default is blast.
   -w or --weight VALUE - Change the default weight for E(0.0) hits
                          to VALUE (default=200 (i.e. 1e-200) )
   -h                   - this help menu

Additionally specify the filenames you want to process on the
command-line.  If no files are specified then STDIN input is assumed.
You specify this by doing: bp_search2tribe E file1 file2 file3

=head1 AUTHOR

Jason Stajich, jason-at-bioperl-dot-org

=cut

use strict;
use warnings;
use Bio::SearchIO;
use Bio::SearchIO::FastHitEventBuilder; # employ a speedup
use Getopt::Long;
use constant DEFAULT_WEIGHT => 200;
use constant DEFAULT_FORMAT => 'blast';

my ($format,@files,$output,$weight);
$weight = DEFAULT_WEIGHT; # default weight value
$format = DEFAULT_FORMAT;

my ($help);

GetOptions(
	   'f|format:s'    => \$format,
	   'o|output:s'    => \$output,
	   'w|weight:i'  => \$weight,
	   'h|help'        => sub{ exec('perldoc',$0);
				   exit(0)
				   },
	   );

my $outfh;
if( $output ) { 
    open $outfh, '>', $output or die "Could not write output file '$output': $!\n";
} else {
    $outfh = *STDOUT;
}

my $parser = new Bio::SearchIO(-format => $format, -fh => \*ARGV);

# Let's throw away HSP events
$parser->attach_EventHandler(new Bio::SearchIO::FastHitEventBuilder);
while( my $report = $parser->next_result ) {
    my $q = $report->query_name;
    while( my $hit = $report->next_hit ) {
	my $evalue = $hit->significance;
	$evalue =~ s/^e/1e/i;

	if( $evalue == 0 ) {	    
	    $evalue = "1e-$weight";
	} else { 
	    $evalue = sprintf("%e",$evalue);
	}

	print $outfh join("\t",$q,$hit->name, split('e-',$evalue)), "\n"; 
    }
}
BioPerl-1.007002/scripts/utilities/bp_seq_length.pl000444000766000024       321113155576320 22361 0ustar00cjfieldsstaff000000000000#!perl

=head1 NAME

bp_seq_length.pl - lists the number of bases and number of sequences in specified sequence database files

=head1 SYNOPSIS

bp_seq_length.pl *.fa

=head1 DESCRIPTION

bp_seq_length.pl will report the total number of residues and total number of individual sequences contained within a specified sequence database file.

=head1 OPTIONS

 -f/--format          - Specify the database format ('fasta' is default).
                        This script uses SeqIO and as such formats are 
                        limited to those which SeqIO system supports.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Jason Stajich

Jason Stajich Ejason@bioperl.orgE

=cut

use strict;
use warnings;
use Bio::SeqIO;
use Getopt::Long;

my $format = 'fasta';
GetOptions('f|format:s' => \$format);

exec('perldoc',$0) unless @ARGV;

foreach my $f ( @ARGV ) {
    my $in = new Bio::SeqIO(-file => $f,
			    -format => $format);
    my $len = 0;
    my $count = 0;
    while( my $seq = $in->next_seq ) {
	$len += $seq->length();
	$count++;
    }
    
    printf "%-10s %d bp $count sequences\n",$f,$len;
}
BioPerl-1.007002/scripts/utilities/bp_sreformat.pl000444000766000024      1325613155576320 22264 0ustar00cjfieldsstaff000000000000#!perl
# Author:  Jason Stajich 
# Purpose: Bioperl implementation of Sean Eddy's sreformat
#          We're not as clever as Sean's squid library though so
#          you have to specify the input format rather than letting
#          the application guess.

use strict;
use warnings;
use Bio::SeqIO;
use Bio::AlignIO;
use Getopt::Long;

my $USAGE = "bp_sreformat -if INFORMAT -of OUTFORMAT -i FILENAME -o output.FORMAT

-h/--help               Print this help
-if/--informat          Specify the input format
-of/--outformat         Specify the output format
-i/--input              Specify the input file name
                        (to pass in data on STDIN use minus sign as filename)
-o/--output             Specify the output file name
                        (to pass data out on STDOUT use minus sign as filename)
--msa                   Specify this is multiple sequence alignment data
--special=specialparams Specify special params supported by some formats
                        Comma or space separated please.
                        These include:
                        nointerleaved   -- for phylip,non-interleaved format
                        idlinebreak     -- for phylip, makes it molphy format
                        percentages     -- for clustalw, show % id per line
                        flat            -- don't show start-end in seqid
                        linelength      -- line length for clustalw
                        mrbayes         -- for MrBayes proper NEXUS output
";


my ($input,$output,$informat,$outformat,$msa,$special);

GetOptions(
	   'h|help'          => sub { print STDERR ($USAGE); exit(0) },
	   'i|input:s'         => \$input,
	   'o|output:s'        => \$output,
	   'if|informat:s'     => \$informat,
	   'of|outformat:s'    => \$outformat,
	   'msa'               => \$msa,
	   's|special:s'       => \$special,
	   );

unless( defined $informat && defined $outformat ) { 
    die(sprintf("Cannot proceed without a defined input and output you gave (%s,%s)\n",
		defined $informat ? $informat : "''" ,
		defined $outformat ? $outformat : "''"));
}

my ($in,$out);
my @extra;
if( $special ) {
    @extra = map { my @rc;
		   if( /nointerleaved/) {
		       @rc = ('-interleaved' => '0');
		   } elsif( /mrbayes/ ) {
		       @rc = ('-show_symbols' => 0,
			      '-show_endblock' => 0);
		   } elsif( /(\S+)\=(\S+)/ ) { @rc = ( "-$1" => $2) } 
	           else{ @rc = ("-$_" => 1) }
		   @rc;
	       } split(/[\s,]/,$special);
}
# guess we're talking about MSA if any of the standard MSA names are used
if( $informat =~ /nexus|phylip|clustal|maf|stockholm|bl2seq|msf/ ||
    $outformat =~ /nexus|phylip|clustal|maf|stockholm|bl2seq|msf/ ) {
    $msa = 1;
}

if( $msa ) {
    eval {
	if( defined $input ) {
	    $in = new Bio::AlignIO(-format => $informat, -file => $input);
	} else {
	    $in = new Bio::AlignIO(-format => $informat, -fh => \*ARGV);
	}
    };
    if( $@ ) {
	die("Unknown MSA format to bioperl $informat\n");
    }
    eval {
	if( $output ) {
	    $out = new Bio::AlignIO(-format => $outformat,
				    -file => ">$output", @extra);
	} else {
	    # default to STDOUT for output
	    $out = new Bio::AlignIO(-format => $outformat,@extra);
	}
    };
    if( $@ ) {
	die("Unknown MSA format to bioperl $outformat\n");
    }
    while( my $aln = $in->next_aln) { 
	 if( $special =~ /flat/ ) {$aln->set_displayname_flat(1); }
	 $out->write_aln($aln) }

} else {
    eval {
	if( defined $input ) {
	    $in = new Bio::SeqIO(-format => $informat, -file => $input);
	} else { 
	    $in = new Bio::SeqIO(-format => $informat, -fh => \*ARGV);
	}
    };
    if( $@ ) {
	if( $@ =~ /Could not open/ ) {
	    die("Could not open input file: $input\n");
	} else { 
	    die("Unknown sequence format to bioperl $informat\n");
	}	
    }
    eval {
	   if( $output ) {
	       $out = new Bio::SeqIO(-format => $outformat,
				     -file => ">$output");
	   } else {
	       # default to STDOUT for output
	       $out = new Bio::SeqIO(-format => $outformat);
	   }
       };
    if( $@ ) {
	if( $@ =~ /Could not open/ ) {
	    die("Could not open output file: $output\n");
	} else { 
	    die("Unknown sequence format to bioperl $outformat: $@\n");
	}
    }
    while( my $seq = $in->next_seq ) {
	$out->write_seq($seq);
    }
}

=head1 NAME

bpsreformat - convert sequence formats

=head1 DESCRIPTION

This script uses the SeqIO system that allows conversion of sequence
formats either sequence data or multiple sequence alignment data.  The
name comes from the fact that Sean Eddy's program sreformat (part of
the HMMER pkg) already does this.  Sean's program tries to guess the
input formats while in our code we currently require your to specify what
the input and output formats are and if the data is from a multiple
sequence alignment or from straight sequence files.

Usage:

bpsreformat -if INFORMAT -of OUTFORMAT -i FILENAME -o output.FORMAT

  -h/--help        Print this help

  -if/--informat   Specify the input format

  -of/--outformat  Specify the output format

  -i/--input       Specify the input file name
                   (to pass in data on STDIN use minus sign as filename)
  -o/--output      Specify the output file name
                   (to pass data out on STDOUT use minus sign as filename)

  --msa            Specify this is multiple sequence alignment data

  --special        Will pass on special parameters to the AlignIO/SeqIO
                   object -- most of these are for Bio::AlignIO objects
                   Comma separated list of the following
                   nointerleaved   -- for phylip,non-interleaved format
                   idlinebreak     -- for phylip, makes it molphy format
                   percentages     -- for clustalw, show % id per line

=cut
BioPerl-1.007002/t000755000766000024          013155576322 13623 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Alphabet.t000444000766000024       367313155576321 15675 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 100);
	
	use_ok('Bio::Symbol::Alphabet');
	use_ok('Bio::Symbol::Symbol');
	use_ok('Bio::Symbol::DNAAlphabet');
	use_ok('Bio::Symbol::ProteinAlphabet');
}

my $A = Bio::Symbol::Symbol->new(-token => 'A' );
my $U = Bio::Symbol::Symbol->new(-token => 'U' );
my $G = Bio::Symbol::Symbol->new(-token => 'G' );
my $T = Bio::Symbol::Symbol->new(-token => 'T' );

my $rna = Bio::Symbol::Alphabet->new( -symbols => [ $A, $U, $G, $T ] );
				     
isa_ok($rna, 'Bio::Symbol::Alphabet');
my @symbols = $rna->symbols;
is(scalar @symbols, 4);

ok($rna->contains($A));
ok($rna->contains($T));
ok($rna->contains($U));
ok($rna->contains($G));

my $dna = Bio::Symbol::DNAAlphabet->new();
isa_ok($dna, 'Bio::Symbol::AlphabetI');
my $count = 0;

my @dnasymbols = sort qw( A B C D G H K M N R S T U V W X Y );
foreach my $s ( sort { $a->name cmp $b->name } $dna->symbols ) {
    is($s->name, $dnasymbols[$count]);    
    is($s->token, $dnasymbols[$count++]);    
}

my $prot = Bio::Symbol::ProteinAlphabet->new();
isa_ok($prot, 'Bio::Symbol::AlphabetI');

my @protsymbols = sort qw( * A B C D E F G H I J K L M N O P Q R S T U V W X Y Z);
my %h = (
	 'Ala' => 'A',     'Asx' => 'B',     'Cys' => 'C',     'Asp' => 'D',
	 'Glu' => 'E',     'Phe' => 'F',     'Gly' => 'G',     'His' => 'H',
	 'Ile' => 'I',     'Lys' => 'K',     'Leu' => 'L',     'Met' => 'M',
	 'Asn' => 'N',     'Pro' => 'P',     'Gln' => 'Q',     'Arg' => 'R',
	 'Ser' => 'S',     'Thr' => 'T',     'Val' => 'V',     'Trp' => 'W',
	 'Xaa' => 'X',     'Tyr' => 'Y',     'Glx' => 'Z',     'Ter' => '*',     
	 'Sec' => 'U',     'Pyl' => 'O',     'Xle' => 'J',     
	 );
my @protnms = sort { $h{$a} cmp $h{$b} } keys %h;
$count = 0;
foreach my $s ( sort { $a->token cmp $b->token } $prot->symbols ) {
    is($s->name, $protnms[$count]);
    is($s->token, $protsymbols[$count++]);    
}
BioPerl-1.007002/t/Perl.t000444000766000024       603013155576321 15045 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 31,
			   -requires_module => 'IO::String');
	
	use_ok('Bio::Perl');
}

# Bio::Perl isn't OO so we don't see Bio::Perl->new() here

my ($seq_object,$filename,$blast_report,@seq_object_array);

# will guess file format from extension
$filename = test_input_file('cysprot1.fa');
ok ($seq_object = read_sequence($filename));
isa_ok $seq_object, 'Bio::SeqI';

# forces genbank format
$filename = test_input_file('AF165282.gb');
ok  ($seq_object = read_sequence($filename,'genbank'));
isa_ok $seq_object, 'Bio::SeqI';

# reads an array of sequences
$filename = test_input_file('amino.fa');
is (@seq_object_array = read_all_sequences($filename,'fasta'), 2);
isa_ok $seq_object_array[0], 'Bio::SeqI';
isa_ok $seq_object_array[1], 'Bio::SeqI';

$filename = test_output_file();
ok write_sequence(">$filename",'genbank',$seq_object);
ok ($seq_object = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA","myname","AL12232"));
isa_ok $seq_object, 'Bio::SeqI';

my $trans;

ok ($trans = translate($seq_object));

isa_ok $trans, 'Bio::SeqI';

ok ($trans = translate("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA"));

isa_ok $trans, 'Bio::PrimarySeqI';

ok ($trans = translate_as_string($seq_object));

is $trans, 'IGLGTQFVCYM';

$trans = '';

ok ($trans = translate_as_string("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA"));

is $trans, 'IGLGTQFVCYM';

# we need to keep tests that depend on net connection at the end
# these now run only with BIOPERLDEBUG set

SKIP: {
	test_skip(-tests => 12, -requires_networking => 1, -requires_module => 'LWP::UserAgent');
	
	# swissprot
	SKIP: {
		test_skip(-tests => 2, -requires_module => 'Data::Stag');
		eval {
			$seq_object = get_sequence('swissprot',"ROA1_HUMAN");
		};
		if ($@) {
			skip("problem connecting to SwissProt:$@",2);
		} else {
			ok $seq_object;
			isa_ok $seq_object, 'Bio::SeqI';
		}
	}
	
    # embl
	SKIP: {
		eval {
			$seq_object = get_sequence('embl',"HSFOS");
		};
		if ($@) {
			skip("problem connecting to EMBL:$@",2);
		} else {
			ok $seq_object;
			isa_ok $seq_object, 'Bio::SeqI';
		}
	}

	# genbank	
	SKIP: {
		eval {
			$seq_object = get_sequence('genbank',"AI129902");
		};
		if ($@) {
			skip("problem connecting to GenBank:$@",2);
		} else {
			ok $seq_object;
			isa_ok $seq_object, 'Bio::SeqI';
		}
	}

    # refseq
	SKIP: {
		eval {
			$seq_object = get_sequence('genbank',"NM_006732");
		};
		if( $@ ) {
			skip("problem connecting to RefSeq:$@",2);
		} else {
			ok $seq_object;
			isa_ok $seq_object, 'Bio::SeqI';
		}
	}
	
	# genpept
	SKIP: {
		eval {
			$seq_object = get_sequence('genpept',"AAC06201");
		};
		if ($@) {
			skip("problem connecting to RefSeq:$@",2);
		} else {
			ok $seq_object;
			isa_ok $seq_object, 'Bio::SeqI';
		}
	}
    
    # blast
    SKIP: {
		eval {
			$blast_report = blast_sequence($seq_object, 0);
		};
		if ($@) {
			skip("problem connecting to NCBI BLAST:$@",2);
		} else {
			ok $blast_report;
			isa_ok $blast_report, 'Bio::Search::Result::ResultI';
		}
    }
}
BioPerl-1.007002/t/PodSyntax.t000444000766000024        45513155576321 16061 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use Test::More;
	eval 'use Test::Pod 1.00';
	plan (skip_all => 'Test::Pod 1.00 required for testing POD' ) if $@;
}

# check pod is syntactically correct
all_pod_files_ok( all_pod_files(qw(Bio scripts examples maintenance)) )
BioPerl-1.007002/t/SearchDist.t000444000766000024       121713155576321 16176 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 3,
			   -requires_module => 'Bio::Ext::Align');
	
	use_ok('Bio::SearchDist');
}

my $dist = Bio::SearchDist->new();

isa_ok $dist, 'Bio::SearchDist';

my @scores;
foreach my $i ( 1..5000 ) {
    my $score = rand(1300);
    #print STDERR "Got $score\n";
    $dist->add_score($score);
    push(@scores,$score);
}

# this just checks that this routine runs ;)
# as the distribution is not gaussian, it gives
# non-sensical results    

is $dist->fit_Gaussian(1200), 1;

# TODO? there are no useful tests here!
BioPerl-1.007002/t/SeqEvolution.t000444000766000024      1413613155576321 16626 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 39);
	
    use_ok('Bio::SeqEvolution::Factory');
    use_ok('Bio::PrimarySeq');
}

#
# point mutations
#

ok my $evolve = Bio::SeqEvolution::Factory->new (-verbose => 1);
isa_ok $evolve, 'Bio::SeqEvolution::DNAPoint';

ok $evolve = Bio::SeqEvolution::DNAPoint->new (-verbose => 2);
isa_ok $evolve, 'Bio::SeqEvolution::DNAPoint';

ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 3,
                                             -type => 'Bio::SeqEvolution::DNAPoint');
isa_ok $evolve, 'Bio::SeqEvolution::DNAPoint';


my $seq = Bio::PrimarySeq->new(-id=>'test',
                              -seq=>'aaacccgggtta'
                             );

ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 0,
                                              -foo => 'bar',
                                              -rate => 5,
                                              -seq => $seq
                                             );

is $evolve->seq->id, 'test';
is $evolve->rate, 5,               'get rate()';
is $evolve->rate(2), 2,            'get and set rate()';


is $evolve->identity(80), 80, 'identity()';
is $evolve->identity(undef), undef, 'identity()';

is $evolve->pam, undef, 'pam()';
is $evolve->pam(80), 80, 'pam()';

is $evolve->mutation_count, undef, 'mutation_count()';
is $evolve->mutation_count(5), 5, , 'mutation_count()';



is $evolve->seq_type, 'Bio::PrimarySeq', 'seq_type()';
is $evolve->seq_type('Bio::Seq'), 'Bio::Seq', 'seq_type()';

ok my $newseq = $evolve->next_seq, 'next_seq()';

foreach ( $evolve->each_mutation('string')) {
    ok $_;
}
is $evolve->each_mutation, 5, 'each_mutation()';

ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 0,
                                              -rate => 5,
                                              -seq => $seq,
                                              -identity => 50     ###
                                             );
ok $newseq = $evolve->next_seq;
cmp_ok $evolve->get_alignment_identity, '<=', 50, "get_alignment_identity()";

ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 0,
                                              -rate => 5,
                                              -seq => $seq,
                                              -pam => 50     ###
                                             );
ok $newseq = $evolve->next_seq;
is $evolve->get_mutation_counter, 6, 'get_mutation_counter()';
$newseq = $evolve->next_seq;
is $evolve->get_sequence_counter, 2, 'get_sequence_counter()';
ok $evolve->reset_sequence_counter(), 'reset_sequence_counter()';
is $evolve->get_sequence_counter, 0, 'get_sequence_counter() == 0';

ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 0,
                                              -rate => 5,
                                              -seq => $seq,
                                              -pam => 50
                                             );

ok $newseq = $evolve->next_seq;
# ok $evolve->get_alignment_identity <= 50, "get_alignment_identity()";
isa_ok $evolve->get_alignmet, 'Bio::SimpleAlign';


#
#print "-----------------------------------------\n";
#print $evolve->{'_ori_locatableseq'}->seq, "\n";
#print $evolve->{'_mut_locatableseq'}->seq, "\n";
#print $evolve->{'_align'}->overall_percentage_identity, "\n";
#print $evolve->get_mutation_counter, "\n";
#print "-----------------------------------------\n";
#


#
# indels
#

#use Bio::SeqEvolution::DNAIndel;
#ok $evolve = Bio::SeqEvolution::DNAIndel->new (-verbose => 0,
#                                               -mutation_count => 3,
#                                               -rate => 1,
#                                               -seq => $seq
#                                             );
#
#
#
#ok $newseq = $evolve->next_seq;
#ok $evolve->get_mutation_counter, 3;
##print Dumper $evolve;
#
#foreach ( $evolve->each_mutation) {
##    print Dumper $_;
##    print $_->sysname, "\n";
#    ok $_->sysname;
#}
#
#
#ok $evolve = Bio::SeqEvolution::DNAIndel->new (-verbose => 0,
#                                               -duplication => 1,
##                                               -identity =>50,
#                                               -mutation_count => 3,
#                                               -rate => 1,
#                                               -seq => $seq
#                                             );
##$evolve->{'_mut_string'} = $evolve->{'_ori_string'};
#
##ok $newseq = $evolve->mutate(12);
#ok $newseq = $evolve->next_seq;
##print Dumper $evolve;
##print $evolve->{'_ori_locatableseq'}->seq, "\n";
##print $evolve->{'_mut_locatableseq'}->seq, "\n";
#
#print "-----------------------------------------\n";
#print $evolve->{'_ori_locatableseq'}->seq, "\n";
#print $evolve->{'_mut_locatableseq'}->seq, "\n";
#print $evolve->{'_align'}->overall_percentage_identity, "\n";
#print "-----------------------------------------\n";
#
#
##
## mixer, simulation
##
#
#
#ok my $evolve2 = Bio::SeqEvolution::Factory->new (-verbose => 0,
#                                                  -rate => 2,
#                                                  -seq => $seq,
#                                                  -set_mutated_seq => $newseq,
##                                                  -identity => 50
#                                                  -mutation_count => 1     ###
#                                             );
#ok $evolve2->seq_type('Bio::LocatableSeq');
#
#print "=-----------------------------------------\n";
#print $evolve2->{'_ori_locatableseq'}->seq, "\n";
#print $evolve2->{'_mut_locatableseq'}->seq, "\n";
#print $evolve2->{'_align'}->overall_percentage_identity, "\n";
#print "-----------------------------------------\n";
#
#ok $newseq = $evolve2->next_seq;
#
#
#print "-----------------------------------------\n";
#print $evolve2->{'_ori_locatableseq'}->seq, "\n";
#print $evolve2->{'_mut_locatableseq'}->seq, "\n";
#print $evolve2->{'_align'}->overall_percentage_identity, "\n";
#print "-----------------------------------------\n";
#
BioPerl-1.007002/t/Species.t000444000766000024       716513155576321 15550 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;
my $CYCLE;
my $WEAKEN;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    eval { require Test::Memory::Cycle; 1; };
    $CYCLE = $@ ? 0 : 1;
    eval { require Test::Weaken; 1; };
    $WEAKEN = $@ ? 0 : 1;
    test_begin(-tests => 27);
        
        use_ok('Bio::Species');
        use_ok('Bio::DB::Taxonomy');
}

ok my $sps = Bio::Species->new();
$sps->classification(qw( sapiens Homo Hominidae
             Catarrhini Primates Eutheria Mammalia Vertebrata
             Chordata Metazoa Eukaryota));

is $sps->binomial, 'Homo sapiens';

ok $sps->sub_species('sapiensis');
is $sps->binomial, 'Homo sapiens';
is $sps->binomial('FULL'), 'Homo sapiens sapiensis';
is $sps->sub_species, 'sapiensis';

$sps->classification(qw( sapiens Homo Hominidae
             Catarrhini Primates Eutheria Mammalia Vertebrata
             Chordata Metazoa Eukaryota));
is $sps->binomial, 'Homo sapiens';


# test cmd line initializtion
ok my $species = Bio::Species->new( -classification => 
                [ qw( sapiens Homo Hominidae
                      Catarrhini Primates Eutheria 
                      Mammalia Vertebrata
                      Chordata Metazoa Eukaryota) ],
                -common_name => 'human');
is $species->binomial, 'Homo sapiens';
is $species->species, 'sapiens';
is $species->genus, 'Homo';
# test -common_name parameter, bug 2549
is $species->common_name, 'human';

# A Bio::Species isa Bio::Taxon, so test some things from there briefly
is $species->scientific_name, 'sapiens';
is $species->rank, 'species';

# We can make a species object from just an id an db handle
SKIP: {
    test_skip(-tests => 5,
              -requires_module     => 'LWP::UserAgent',
              -requires_networking => 1);
    
    $species = Bio::Species->new(-id => 51351);
    my $taxdb = Bio::DB::Taxonomy->new(-source => 'entrez');
    eval {$species->db_handle($taxdb);};
    skip "Unable to connect to entrez database; no network or server busy?", 5 if $@;
    is $species->binomial, 'Brassica rapa subsp.';
    is $species->binomial('FULL'), 'Brassica rapa subsp. pekinensis';
    is $species->genus, 'Brassica';
    is $species->species, 'rapa subsp.';
    is $species->sub_species, 'pekinensis';
}

SKIP: {
    skip("Test::Memory::Cycle not installed, skipping", 3) if !$CYCLE;
    # this sub leaks, should return true
    my ($a, $b); $a = \$b; $b = \$a;
    Test::Memory::Cycle::memory_cycle_exists($a);
    # this sub shouldn't leak (no circ. refs)
    $species = Bio::Species->new( -classification => 
                [ qw( sapiens Homo Hominidae
                      Catarrhini Primates Eutheria 
                      Mammalia Vertebrata
                      Chordata Metazoa Eukaryota) ],
                -common_name => 'human');
    Test::Memory::Cycle::memory_cycle_exists($species);
    
    # Github issue #81
    Test::Memory::Cycle::memory_cycle_exists(Bio::Species->new(-classification => ['A']));
}

SKIP: {
    skip("Test::Weaken not installed, skipping", 3) if !$WEAKEN;
    
    # this sub leaks, should return true
    ok(Test::Weaken::leaks({
        constructor => sub { my ($a, $b); $a = \$b; $b = \$a}
    }));
    
    # this sub shouldn't leak (no circ. refs)
    ok(!Test::Weaken::leaks({
      constructor => sub{ Bio::Species->new( -classification => 
				[ qw( sapiens Homo Hominidae
				      Catarrhini Primates Eutheria 
				      Mammalia Vertebrata
				      Chordata Metazoa Eukaryota) ],
				-common_name => 'human') },
      }
    ));
    
    # Github issue #81    
    ok(!Test::Weaken::leaks({
      constructor => sub{ Bio::Species->new( -classification => ['A']) },
      }
    ));
}
BioPerl-1.007002/t/Symbol.t000444000766000024       133513155576321 15413 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 9);
	
	use_ok('Bio::Symbol::Symbol');
}

ok my $thymine = Bio::Symbol::Symbol->new(-name => 'Arg',
				      -token=> 'R');
my $a = Bio::Symbol::Symbol->new(-token => 'A' );
my $u = Bio::Symbol::Symbol->new(-token => 'U' );
my $g = Bio::Symbol::Symbol->new(-token => 'G' );

is($thymine->name, "Arg");
is($thymine->token, "R");
my $M = Bio::Symbol::Symbol->new(-name  => 'Met',
				-token => 'M',
				-symbols => [ $a, $u, $g ]);

is($M->name, "Met");
is($M->token, 'M');
my @symbols = $M->symbols;
my @expected = ($a, $u, $g);
foreach ( 0..2 ) {
    is($expected[$_], $symbols[$_]);
}
BioPerl-1.007002/t/TaxonTree.t000444000766000024      1077613155576321 16110 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

# These modules are now deprecated, don't bother testing them. --sendubala

## I am pretty sure this module is going the way of the dodo bird so 
## I am not sure how much work to put into fixing the tests/module
## --jasonstajich

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 0);
}

if (0) {
	use Bio::Taxonomy::Taxon;
	ok(1);
	
	
	ok my $taxonL = Bio::Taxonomy::Taxon->new;
	ok $taxonL->description('this could be anything');
	ok $taxonL->taxon('could this be called name?');
	ok $taxonL->id('could this be called taxid?');
	skip 1, $taxonL->branch_length('should accept only numerical values?');
	ok  $taxonL->branch_length(5);
	
	ok $taxonL->id('could this be called taxid?');
	ok $taxonL->rank('species');
	ok $taxonL->rank, 'species';
	# ok $taxonL->has_rank, 'species'; #why two methods that do mostly the same thing, but work differently?
	
	skip 1, $taxonL->rank('foo is not a rank, class variable @RANK not initialised'); 
	ok $taxonL->to_string, '"could this be called taxid?":5';
	
	my $taxonR = Bio::Taxonomy::Taxon->new();
	
	my $taxon = Bio::Taxonomy::Taxon->new(-id =>'ancient', -taxon => 'genus');
	ok $taxon->id(), 'ancient'; 
	ok $taxon->taxon(), 'genus'; 
	ok $taxon->internal_id, 2;
	ok $taxonL->internal_id, 0; # would not it be better to start numebering from 1?
	ok $taxon->add_Descendent($taxonL);
	$taxon->add_Descendent($taxonR);
	
	ok  scalar $taxon->each_Descendent, 2;  # dies
	ok $taxon->remove_Descendent($taxonR); # better to return number of Descendants removed
	
	ok $taxon->remove_all_Descendents();
	
	
	$taxon->add_Descendent($taxonL);
	ok $taxonL->ancestor->id, 'ancient';
	ok $taxonL->branch_length(5);
	
	
	ok $taxonL->is_Leaf, 1;
	ok $taxon->is_Leaf, 0;
	ok $taxon->height, 6;
	ok $taxonL->height, 5;
	ok $taxon->invalidate_height, undef;
	ok $taxonL->classify(1), 2;
	skip(1,"skip classify weirdness");
	# ok $taxonL->classify(0), 2, 'ancestor has rank, but implementation prevents showing anything more than one value';
	skip(1,"skip classify weirdness");
	#ok $taxonL->has_rank, 1, 'documentation claims this returns a boolean; and that it queries ancestors rank?, needs an agrument but does not test it';
	skip(1,"skip classify weirdness");
	#ok $taxonL->has_rank('species'), 1;
	
	#ok $taxon->has_taxon(); # why docs and code talk about ancestor?
	#ok $taxonL->has_taxon('genus');  returns undef or oan object, not boolean
	
	ok $taxon->distance_to_root, 0;
	ok $taxonL->distance_to_root, 1;
	#ok $taxonL->recent_common_ancestor($taxon)->id, 'ancient';
	
	
	
	#use Data::Dumper;
	#print Dumper  $taxonL->classify();
	skip(1, 'Skip this weird function');
	# ok $taxonL->has_rank('species'), 1;
	#ok my $species = $taxonL->species;
	
	
	
	
	
	##################################################################################################
	
	# tests for Bio::Taxonomy::Tree;
	# code from synopsis
	
	use Bio::Species;
	use Bio::Taxonomy::Tree;
	use Bio::Taxonomy;
	
	my $human=Bio::Species->new();
	my $chimp=Bio::Species->new();
	my $bonobo=Bio::Species->new();
	
	$human->classification(qw( sapiens Homo Hominidae
							   Catarrhini Primates Eutheria
							   Mammalia Euteleostomi Vertebrata 
							   Craniata Chordata
							   Metazoa Eukaryota ));
	$chimp->classification(qw( troglodytes Pan Hominidae
							   Catarrhini Primates Eutheria
							   Mammalia Euteleostomi Vertebrata 
							   Craniata Chordata
							   Metazoa Eukaryota ));
	$bonobo->classification(qw( paniscus Pan Hominidae
								Catarrhini Primates Eutheria
								Mammalia Euteleostomi Vertebrata 
								Craniata Chordata
								Metazoa Eukaryota ));
	
	# ranks passed to $taxonomy match ranks of species
	my @ranks = ('superkingdom','kingdom','phylum','subphylum',
				 'no rank 1','no rank 2','class','no rank 3','order',
				 'suborder','family','genus','species');
	
	my $taxonomy=Bio::Taxonomy->new(-ranks => \@ranks,
								   -method => 'trust',
								   -order => -1);
	
	
	ok my $tree1=Bio::Taxonomy::Tree->new();
	my $tree2=Bio::Taxonomy::Tree->new();
	
	$tree1->make_species_branch($human,$taxonomy);
	$tree2->make_species_branch($chimp,$taxonomy);
	
	my ($homo_sapiens) = $tree1->get_leaves;
	ok ref $homo_sapiens, 'Bio::Taxonomy::Taxon';
	
	ok $tree1->splice($tree2);
	
	ok $tree1->add_species($bonobo,$taxonomy);
	
	
	ok join (", ", map {$_->taxon} $tree1->get_leaves), 'Homo sapiens, Pan troglodytes, Pan paniscus';
	ok $tree1->remove_branch($homo_sapiens);
	ok join (", ", map {$_->taxon} $tree1->get_leaves), 'Pan troglodytes, Pan paniscus';
}
BioPerl-1.007002/t/nexml.t000444000766000024      1706013155576322 15314 0ustar00cjfieldsstaff000000000000#-*-perl-*-
# $Id$

use strict;

use Bio::Root::Test;
use Bio::Tree::Tree;
use Bio::TreeIO;
test_begin( -tests=>125,
	    -requires_modules => [qw(Bio::Phylo)]);

use_ok('Bio::NexmlIO');
diag("WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support");
SKIP: {
    skip("NeXML parsing for NeXML v0.9 is currently very experimental support", 124);
#Read in Data
my $in_nexmlIO = Bio::NexmlIO->new(-file => test_input_file('characters+trees.nexml.xml'));

	#Read in some alignments
	my $aln1 = $in_nexmlIO->next_aln();#, 'nexml matrix to aln' );
	isa_ok($aln1, 'Bio::SimpleAlign', 'obj ok');
	is ($aln1->id,	'DNA sequences', 'aln id');
	my $num =0;
	my @expected_seqs = ('ACGCTCGCATCGCATC', 'ACGCTCGCATCGCATT', 'ACGCTCGCATCGCATG');
	#checking sequence objects
	foreach my $seq_obj ($aln1->each_seq()) {
		$num++;
		
		is( $seq_obj->alphabet, 'dna', "alphabet" );
		is( $seq_obj->display_id, "dna_seq_$num", "display_id");
		is( $seq_obj->seq, $expected_seqs[$num-1], "sequence correct");
	}
	my $aln2 = $in_nexmlIO->next_aln();
	my @alns1;
	push @alns1, $aln1;
	push @alns1, $aln2;
	#checking taxa object
	my %expected_taxa = (dna_seq_1 => 'Homo sapiens', dna_seq_2 => 'Pan paniscus', dna_seq_3 => 'Pan troglodytes');
	my @feats = $aln1->get_all_SeqFeatures();
	foreach my $feat (@feats) {
		if ($feat->has_tag('taxa_id')){
			is ( ($feat->get_tag_values('taxa_id'))[0], 'taxa1', 'taxa id ok' );
			is ( ($feat->get_tag_values('taxa_label'))[0], 'Primary taxa block', 'taxa label ok');
			is ( $feat->get_tag_values('taxon'), 5, 'Number of taxa ok')
		}
		else{
			my $seq_num = ($feat->get_tag_values('id'))[0];
			is ( ($feat->get_tag_values('taxon'))[0], $expected_taxa{$seq_num}, "$seq_num taxon ok" )
		}
	}
	
	#Read in some sequences
	ok( my $seq1 = $in_nexmlIO->next_seq() );
	isa_ok($seq1, 'Bio::Seq');
	is( $seq1->alphabet,		'dna',					"alphabet" );
	is( $seq1->primary_id,	'dna_seq_1',	"primary_id");
	is( $seq1->display_id,	'dna_seq_1',			"display_id");
	is( $seq1->seq,			'ACGCTCGCATCGCATC',		"sequence");

	#checking second sequence object
	ok( my $seq2 = $in_nexmlIO->next_seq() );
	is( $seq2->alphabet,		'dna',					"alphabet" );
	is( $seq2->primary_id,	'dna_seq_2',	"primary_id");
	is( $seq2->display_id,	'dna_seq_2',			"display_id");
	is( $seq2->seq,			'ACGCTCGCATCGCATT',		"sequence");
	ok( my $seq3 = $in_nexmlIO->next_seq() );
	ok( my $seq4 = $in_nexmlIO->next_seq() );
	my @seqs1;
	push @seqs1, $seq1;
	push @seqs1, $seq2;
	push @seqs1, $seq3;
	push @seqs1, $seq4;
	
	#Read in some trees
	ok( my $tree1 = $in_nexmlIO->next_tree() );
	isa_ok($tree1, 'Bio::Tree::Tree');
	is( $tree1->get_root_node()->id(), 'n1', "root node");
	my @nodes = $tree1->get_nodes();
	is( @nodes, 9, "number of nodes");
	ok ( my $node7 = $tree1->find_node('n7') );
	is( $node7->branch_length, 0.3247, "branch length");
	is( $node7->ancestor->id, 'n3');
	is( $node7->ancestor->branch_length, '0.34534');
	#Check leaf nodes and taxa
	my %expected_leaves = (
							'n8'	=>	'bird',
							'n9'	=>	'worm',
							'n5'	=>	'dog',
							'n6'	=>	'mouse',
							'n2'	=>	'human'
	);
	ok( my @leaves = $tree1->get_leaf_nodes() );
	is( @leaves, 5, "number of leaf nodes");
	foreach my $leaf (@leaves) {
		my $leafID = $leaf->id();
		ok( exists $expected_leaves{$leaf->id()}, "$leafID exists"  );
		is( $leaf->get_tag_values('taxon'), $expected_leaves{$leaf->id()}, "$leafID taxon");
	}
	my $tree2 = $in_nexmlIO->next_tree();
	my @trees1;
	push @trees1, $tree1;
	push @trees1, $tree2;


#Write Data
diag('Begin tests for write/read roundtrip');
my $outdata = test_output_file();


my $nexml_out = Bio::NexmlIO->new(-file => ">$outdata", -format => 'Nexml');	

ok( $nexml_out->write(-seqs => \@seqs1, -alns =>\@alns1, -trees => \@trees1), "write to stream" );
close($outdata);

#Read in the out file to test roundtrip
my $in_nexmlIO_roundtrip = Bio::NexmlIO->new(-file => $outdata);

 
	#Read in some alignments
	my $aln3 = $in_nexmlIO_roundtrip->next_aln();#, 'nexml matrix to aln' );
	isa_ok($aln3, 'Bio::SimpleAlign', 'obj ok');
	is ($aln3->id,	'DNA sequences', 'aln id');
	$num =0;
	#checking sequence objects
	foreach my $seq_obj ($aln3->each_seq()) {
		$num++;
		
		is( $seq_obj->alphabet, 'dna', "alphabet" );
		is( $seq_obj->display_id, "dna_seq_$num", "display_id");
		is( $seq_obj->seq, $expected_seqs[$num-1], "sequence correct");
	}
	#checking taxa object
	my @feats_r = $aln3->get_all_SeqFeatures();
	foreach my $feat (@feats_r) {
		if ($feat->has_tag('taxa_id')){
			is ( ($feat->get_tag_values('taxa_id'))[0], 'taxa1', 'taxa id ok' );
			is ( ($feat->get_tag_values('taxa_label'))[0], 'Primary taxa block', 'taxa label ok');
			is ( $feat->get_tag_values('taxon'), 5, 'Number of taxa ok')
		}
		else{
			my $seq_num = ($feat->get_tag_values('id'))[0];
			is ( ($feat->get_tag_values('taxon'))[0], $expected_taxa{$seq_num}, "$seq_num taxon ok" )
		}
	}
	#check extract_alns method
	my $alns_outfile = test_output_file();
	ok ( $in_nexmlIO_roundtrip->extract_alns(-file => ">$alns_outfile", -format => "fasta"), 'extract_alns write' );
	close($alns_outfile);
	my $alnIO = Bio::SeqIO->new(-file => "$alns_outfile", -format => 'fasta');
	my $alns_array = $in_nexmlIO_roundtrip->{_seqs};
	my $alnNum = 1;
	while (my $aln = $alnIO->next_seq()) {
		is( $aln->seq, $alns_array->[$alnNum-1]->seq, "extract_alns roundtrip $alnNum" );
		$alnNum++;
	}
	
	#Read in some sequences
	ok( my $seq5 = $in_nexmlIO_roundtrip->next_seq() );
	isa_ok($seq5, 'Bio::Seq');
	is( $seq5->alphabet,		'dna',					"alphabet" );
	is( $seq5->primary_id,	'dna_seq_1',	"primary_id");
	is( $seq5->display_id,	'dna_seq_1',			"display_id");
	is( $seq5->seq,			'ACGCTCGCATCGCATC',		"sequence");

	#checking second sequence object
	ok( my $seq6 = $in_nexmlIO_roundtrip->next_seq() );
	is( $seq6->alphabet,		'dna',					"alphabet" );
 	is( $seq6->primary_id,	'dna_seq_2',	"primary_id");
	is( $seq6->display_id,	'dna_seq_2',			"display_id");
	is( $seq6->seq,			'ACGCTCGCATCGCATT',		"sequence");
	#check extract_seqs method
	my $seqs_outfile = test_output_file();
	ok ( $in_nexmlIO_roundtrip->extract_seqs(-file => ">$seqs_outfile", -format => "fasta"), 'extract_seqs write' );
	close($seqs_outfile);
	my $seqIO = Bio::SeqIO->new(-file => "$seqs_outfile", -format => 'fasta');
	my $seqs_array = $in_nexmlIO_roundtrip->{_seqs};
	my $seqNum = 1;
	while (my $seq = $seqIO->next_seq()) {
		is( $seq->seq, $seqs_array->[$seqNum-1]->seq, "extract_seqs roundtrip $seqNum" );
		$seqNum++;
	}
	
	#Read in some trees
	ok( my $tree3 = $in_nexmlIO_roundtrip->next_tree() );
	isa_ok($tree3, 'Bio::Tree::Tree');
	is( $tree3->get_root_node()->id(), 'n1', "root node");
	my @nodes3 = $tree3->get_nodes();
	is( @nodes3, 9, "number of nodes");
	ok ( my $node7_r = $tree3->find_node('n7') );
	is( $node7_r->branch_length, 0.3247, "branch length");
	is( $node7_r->ancestor->id, 'n3');
	is( $node7_r->ancestor->branch_length, '0.34534');
	#Check leaf nodes and taxa
	ok( my @leaves3 = $tree3->get_leaf_nodes() );
	is( @leaves3, 5, "number of leaf nodes");
	foreach my $leaf (@leaves3) {
		my $leafID = $leaf->id();
		ok( exists $expected_leaves{$leaf->id()}, "$leafID exists"  );
		is( $leaf->get_tag_values('taxon'), $expected_leaves{$leaf->id()}, "$leafID taxon");
	}
	#check extract_trees method
	my $trees_outfile = test_output_file();
	ok ( $in_nexmlIO_roundtrip->extract_trees(-file => ">$trees_outfile", -format => "nexus"), 'extract_trees write' );
	close($seqs_outfile);
	my $treeIO = Bio::TreeIO->new(-file => "$trees_outfile", -format => 'nexus');
	my $trees_array = $in_nexmlIO_roundtrip->{_trees};
	my $treeNum = 1;
	while (my $tree = $treeIO->next_tree()) {
		is( $tree->id, $trees_array->[$treeNum-1]->id, "extract_trees roundtrip $treeNum" );
		$treeNum++;
	}
}
BioPerl-1.007002/t/Align000755000766000024          013155576320 14653 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Align/AlignStats.t000444000766000024      1172313155576320 17272 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 45);
	
	use_ok('Bio::Align::DNAStatistics');
	use_ok('Bio::Align::ProteinStatistics');
	use_ok('Bio::AlignIO');
}

my $debug = test_debug();

my $in = Bio::AlignIO->new(-format => 'emboss',
			  -file   => test_input_file('insulin.water'));
my $aln = $in->next_aln();
isa_ok($aln, 'Bio::Align::AlignI');
my $stats = Bio::Align::DNAStatistics->new(-verbose => $debug);
is( $stats->transversions($aln),4);
is( $stats->transitions($aln),9);
is( $stats->pairwise_stats->number_of_gaps($aln),21);
is( $stats->pairwise_stats->number_of_comparable_bases($aln),173);
is( $stats->pairwise_stats->number_of_differences($aln),13);
is( $stats->pairwise_stats->score_nuc($aln), 224);
is( $stats->pairwise_stats->score_nuc( -aln => $aln, -match => 1,
  -mismatch => -1, -gap_open => -1, -gap_ext => -1), 126);

my $d = $stats->distance(-align => $aln,
			 -method=> 'f81');
is(  $d->get_entry('hs_insulin','seq2'), '0.07918');

$d = $stats->distance(-align=> $aln,
		      -method => 'JC');
is( $d->get_entry('hs_insulin','seq2'), '0.07918');

$d = $stats->distance(-align=> $aln,
		      -method => 'Kimura');
is( $d->get_entry('hs_insulin','seq2'), '0.07984');

$d = $stats->distance(-align=> $aln,
		      -method => 'TajimaNei');
is( $d->get_entry('seq2','hs_insulin'), '0.08106');

$d = $stats->distance(-align=> $aln,
		      -method => 'Tamura');
is( $d->get_entry('seq2','hs_insulin'), '0.08037');

#$d =  $stats->distance(-align => $aln,
#		       -method => 'JinNei');
#is( $d->get_entry('seq2','hs_insulin'), 0.0850);

$in = Bio::AlignIO->new(-format => 'clustalw',
		       -file   => test_input_file('hs_owlmonkey.aln'));

$aln = $in->next_aln();
isa_ok($aln,'Bio::Align::AlignI');

is( $stats->transversions($aln),10);
is( $stats->transitions($aln),17);
is( $stats->pairwise_stats->number_of_gaps($aln),19);
is( $stats->pairwise_stats->number_of_comparable_bases($aln),170);
is( $stats->pairwise_stats->number_of_differences($aln),27);
is( $stats->pairwise_stats->score_nuc($aln), 134);
is( $stats->pairwise_stats->score_nuc( -aln => $aln, -match => 1,
  -mismatch => -1, -gap_open => -1, -gap_ext => -1), 97);

# now test the distance calculations
$d = $stats->distance(-align => $aln, -method => 'jc');
is( $d->get_entry('human','owlmonkey'), 0.17847);

$d = $stats->distance(-align => $aln,
			  -method=> 'f81');
is(  $d->get_entry('human','owlmonkey'), '0.17847');

$d = $stats->distance(-align => $aln, -method => 'uncorrected');
is( $d->get_entry('human','owlmonkey'), 0.15882);

$d =  $stats->distance(-align => $aln, -method => 'Kimura');
is( $d->get_entry('human','owlmonkey'), 0.18105);

$d =  $stats->distance(-align => $aln, -method => 'TajimaNei');
is( $d->get_entry('human','owlmonkey'), 0.18489);

$d =  $stats->distance(-align => $aln,
			   -method => 'Tamura');

is( $d->get_entry('human','owlmonkey'), 0.18333);
#$d =  $stats->distance(-align => $aln,
#		       -method => 'JinNei');
#is( $d->get_entry('human','owlmonkey'), 0.2079);

### now test Nei_gojobori methods, hiding the expected warnings so we can
# avoid printing them ###
$stats->verbose($debug ? $debug : -1);
my ($alnobj, $result);
$in = Bio::AlignIO->new(-format => 'fasta',
			-file   => test_input_file('nei_gojobori_test.aln'));
$alnobj = $in->next_aln();
isa_ok($alnobj,'Bio::Align::AlignI');
$result = $stats->calc_KaKs_pair($alnobj, 'seq1', 'seq2');
is (sprintf ("%.1f", $result->[0]{'S'}), 40.5);
is (sprintf ("%.1f", $result->[0]{'z_score'}), '4.5');
$result = $stats->calc_all_KaKs_pairs($alnobj);
is (int( $result->[1]{'S'}), 41);
is (int( $result->[1]{'z_score'}), 4);
$result = $stats->calc_average_KaKs($alnobj, 100);
is (sprintf ("%.4f", $result->{'D_n'}), 0.1628);
$stats->verbose($debug);

# now test Protein Distances
my $pstats = Bio::Align::ProteinStatistics->new();
$in = Bio::AlignIO->new(-format => 'clustalw',
			-file   => test_input_file('testaln.clustalw'));
$alnobj = $in->next_aln();
isa_ok($alnobj,'Bio::Align::AlignI');
$result = $pstats->distance(-method => 'Kimura',
			    -align  => $alnobj);
isa_ok($result, 'Bio::Matrix::PhylipDist');

is ($result->get_entry('P84139','P814153'),   '0.01443');
is ($result->get_entry('P841414','P851414'),  '0.01686');
is ($result->get_entry('P84139','P851414'),   '3.58352');

my $seq = Bio::Seq->new(-id=>'NOT3MUL', -seq=>'gatac');
isa_ok($seq, 'Bio::PrimarySeqI');
eval { 
  Bio::Align::DNAStatistics->count_syn_sites($seq); 
};
like($@, qr/not integral number of codons/);

# bug 2901
$in = Bio::AlignIO->new(-file => test_input_file('bug2901.fa'),
                        -format => 'fasta');

$stats = Bio::Align::DNAStatistics->new(-verbose => 2);
$aln = $in->next_aln();
my $matrix;
throws_ok {
$matrix = $stats->distance(-align=>$aln,-method=>'Uncorrected');
} qr/No distance calculated between seq3 and seq4/, "Warn if seqs don't overlap";
$stats->verbose(-1);
$matrix = $stats->distance(-align=>$aln,-method=>'Uncorrected');
like($matrix->print_matrix, qr/-1/);

BioPerl-1.007002/t/Align/AlignUtil.t000444000766000024       315213155576320 17066 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin( -tests => 47 );

    use_ok( 'Bio::Align::Utilities',
        qw( aa_to_dna_aln bootstrap_replicates cat dna_to_aa_aln ) );
    use_ok('Bio::AlignIO');
    use_ok('Bio::SeqIO');
}

my $in = Bio::AlignIO->new(
    -format => 'clustalw',
    -file   => test_input_file('pep-266.aln')
);
my $pep_aln = $in->next_aln();
isa_ok( $pep_aln, 'Bio::Align::AlignI' );
$in->close();

# aa_to_dna_aln
my $seqin = Bio::SeqIO->new(
    -format => 'fasta',
    -file   => test_input_file('cds-266.fas')
);

my %dna_seq;
while ( my $seq = $seqin->next_seq ) {
    $dna_seq{ $seq->display_id } = $seq;
}

my $dna_aln = aa_to_dna_aln( $pep_aln, \%dna_seq );

my @aa_seqs = $pep_aln->each_seq;

for my $dna_seq ( $dna_aln->each_seq ) {
    my $peptrans = $dna_seq->translate();
    my $aaseq    = shift @aa_seqs;
    is( $peptrans->seq(), $aaseq->seq() );
}

# dna_to_aa_aln
my $aa_aln = dna_to_aa_aln($dna_aln);

my @pep_seqs = $aa_aln->each_seq;

for my $dna_seq ( $dna_aln->each_seq ) {
    my $peptrans = $dna_seq->translate();
    my $aaseq    = shift @pep_seqs;
    is( $peptrans->seq, $aaseq->seq );
}

# bootstrap_replicates
my $bootstraps = bootstrap_replicates( $pep_aln, 10 );
is( scalar @$bootstraps, 10 );

# cat
my $sub_aln1 = $pep_aln->slice( 1,   100 );
my $sub_aln2 = $pep_aln->slice( 101, 200 );
my $sub_aln3 = $pep_aln->slice( 1,   200 );
my $cat_aln = cat( $sub_aln1, $sub_aln2 );
my @seq = $sub_aln3->each_seq;
for my $seq ( $cat_aln->each_seq ) {
    my $refseq = shift @seq;
    is( $seq->seq, $refseq->seq );
}
BioPerl-1.007002/t/Align/Graphics.t000444000766000024      1007113155576320 16754 0ustar00cjfieldsstaff000000000000#!usr/bin/perl
use strict;

use Bio::Root::Test;
test_begin( -tests => 41,
            -requires_modules => [qw(GD)]); 

#Check if module and all its methods can be loaded
use_ok('Bio::Align::Graphics');
require_ok('Bio::Align::Graphics');
can_ok('Bio::Align::Graphics', qw(new draw height width aln_length aln_format no_sequences));
    
 
#Get an alignment file
my $file = Bio::Root::IO->catfile("t","data","pep-266.aln");
ok($file, 'input is defined');
	
#Create an AlignI object using AlignIO
my $in=new Bio::AlignIO(-file=>$file, -format=>'clustalw');
ok(defined $in, 'AlignIO object is defined');
isa_ok($in, 'Bio::AlignIO');

#Read the alignment
my $aln=$in->next_aln();
ok(defined $aln, 'alignment is there and defined');

#Create some domains for highlighting
my @domain_start = ( 25, 50, 80 );
my @domain_end = ( 40 , 65 , 100 );
my @domain_color = ( 'red' , 'cyan' , 'green' );
ok(exists $domain_start[2], 'all starts are present');
ok(exists $domain_end[2],'all ends are present');
ok(exists $domain_color[2], 'all colors are present');
cmp_ok($domain_start[0], '<=', $domain_end[0],'first end is further than first start');   #Some  
cmp_ok($domain_start[1], '<=', $domain_end[1],'second end is further than second start');	#logical
cmp_ok($domain_start[2], '<=', $domain_end[2],'third end is further than third start');   #tests 

#Create Labels for the domains
my @dml = ("CARD", "Proline Rich", "Transmembrane");
my @dml_start = (25, 50, 80);
my @dml_end = (40, 65, 100);
my @dml_color = ("lightpink", "lightblue", "lightgreen");
ok(exists $dml[2], 'domain labels are present');
ok(exists $dml_start[2], 'domain starts are present');
ok(exists $dml_end[2], 'domain ends are present');
ok(exists $dml_color[2], 'domain colors are present');

#Some logical tests 
cmp_ok($dml_start[0], '<=', $dml_end[0],'label - first end is further than first start');         
cmp_ok($dml_start[1], '<=', $dml_end[1],'label - second end is further than second start');	
cmp_ok($dml_start[2], '<=', $dml_end[2],'label - third end is further than third start');          
cmp_ok($domain_start[0], '>=', $dml_start[0],'first label start is within domain range');        
cmp_ok($domain_start[1], '>=',$dml_start[1],'second label start is within domain range');        
cmp_ok($domain_start[2], '>=',$dml_start[2],'third label start is within domain range');        
cmp_ok($domain_end[0], '>=',$dml_end[0],'first label end is within domain range');        
cmp_ok($domain_end[1], '>=',$dml_end[1],'second label end is within domain range');        
cmp_ok($domain_end[2], '>=',$dml_end[2],'third label end is within domain range');        
 
#Create individual labels
my %labels = ( 145 => "Hep-c target");
ok(exists $labels{145}, 'individual labels work');

#my $output_file = test_output_file();
 
my $print_align = Bio::Align::Graphics->new( align => $aln,
					pad_bottom => 5,
					dm_start => \@domain_start,
					dm_end => \@domain_end,
					dm_color => \@domain_color,
					dm_labels => \@dml,
					dml_start => \@dml_start,
					dml_end => \@dml_end,
					dml_color => \@dml_color,
				 	labels => \%labels,
					out_format => "png",
#					output=>$output_file,
					wrap=>80);

isa_ok($print_align, 'Bio::Align::Graphics');
ok( defined $print_align, 'new object is defined');
is($print_align->{pad_bottom}, 5, '  pad_bottom is right');
is($print_align->{pad_top}, 5, '  default pad_top is right');
is_deeply($print_align->{domain_start}, \@domain_start,'  start point loaded');
is_deeply($print_align->{domain_end}, \@domain_end,'  end point loaded');
is_deeply($print_align->{domain_color}, \@domain_color,'  color of domain loaded');
is_deeply($print_align->{dm_labels}, \@dml, '  domain labels loaded');
is_deeply($print_align->{dm_label_start}, \@dml_start, '  label starts loaded');
is_deeply($print_align->{dm_label_end}, \@dml_end, '  label ends loaded');
is_deeply($print_align->{dm_label_color}, \@dml_color, '  label colors loaded');
is_deeply($print_align->{labels}, \%labels, '  labels loaded');
is($print_align->{out_format}, 'png', '  output file is png');
isnt($print_align->{wrapping}, 0, '  wrapping length is not zero');

exit;
BioPerl-1.007002/t/Align/SimpleAlign.t000444000766000024      7161113155576320 17427 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin( -tests => 206 );

    use_ok('Bio::SimpleAlign');
    use_ok('Bio::AlignIO');
    use_ok('Bio::SeqFeature::Generic');
    use_ok('Bio::Location::Simple');
    use_ok('Bio::Location::Split');
}

my $DEBUG = test_debug();

my ( $str, $aln, @seqs, $seq );

$str = Bio::AlignIO->new( -file => test_input_file('testaln.pfam') );
isa_ok( $str, 'Bio::AlignIO' );
$aln = $str->next_aln();
is $aln->get_seq_by_pos(1)->get_nse, '1433_LYCES/9-246', "pfam input test";

my $aln1 = $aln->remove_columns( ['mismatch'] );
is(
    $aln1->match_line,
    '::*::::*:**:*:*:***:**.***::*.*::**::**:***..**:'
      . '*:*.::::*:.:*.*.**:***.**:*.:.**::**.*:***********:::*:.:*:**.*::*:'
      . '.*.:*:**:****************::',
    'match_line'
);

my $aln2 = $aln->select( 1, 3 );
isa_ok( $aln2, 'Bio::Align::AlignI' );
is( $aln2->num_sequences, 3, 'num_sequences' );

# test select non contiguous-sorted by default
$aln2 = $aln->select_noncont( 6, 7, 8, 9, 10, 1, 2, 3, 4, 5 );
is( $aln2->num_sequences, 10, 'num_sequences' );
is(
    $aln2->get_seq_by_pos(2)->id,
    $aln->get_seq_by_pos(2)->id,
    'select_noncont'
);
is(
    $aln2->get_seq_by_pos(8)->id,
    $aln->get_seq_by_pos(8)->id,
    'select_noncont'
);

# test select non contiguous-nosort option
$aln2 = $aln->select_noncont( 'nosort', 6, 7, 8, 9, 10, 1, 2, 3, 4, 5 );
is( $aln2->num_sequences, 10, 'num_sequences' );
is(
    $aln2->get_seq_by_pos(2)->id,
    $aln->get_seq_by_pos(7)->id,
    'select_noncont'
);
is(
    $aln2->get_seq_by_pos(8)->id,
    $aln->get_seq_by_pos(3)->id,
    'select_noncont'
);

# test select non contiguous by name
my $aln3 = $aln->select_noncont_by_name('1433_LYCES','BMH1_YEAST','143T_HUMAN');
is( $aln3->num_sequences, 3, 'select_noncont_by_name' );
my @seqs3 = $aln3->each_seq();
is $seqs3[0]->id, '1433_LYCES', 'select_noncont_by_name';
is $seqs3[1]->id, 'BMH1_YEAST', 'select_noncont_by_name';
is $seqs3[2]->id, '143T_HUMAN', 'select_noncont_by_name';


@seqs = $aln->each_seq();
is scalar @seqs, 16, 'each_seq';
is $seqs[0]->get_nse, '1433_LYCES/9-246', 'get_nse';
is $seqs[0]->id,      '1433_LYCES',       'id';
is $seqs[0]->num_gaps, 3,                  'num_gaps';
@seqs = $aln->each_alphabetically();
is scalar @seqs, 16, 'each_alphabetically';

is $aln->column_from_residue_number( '1433_LYCES', 10 ), 2,
  'column_from_residue_number';
is $aln->displayname( '1433_LYCES/9-246', 'my_seq' ), 'my_seq',
  'display_name get/set';
is $aln->displayname('1433_LYCES/9-246'), 'my_seq', 'display_name get';
is substr( $aln->consensus_string(50), 0, 60 ),
  "RE??VY?AKLAEQAERYEEMV??MK?VAE??????ELSVEERNLLSVAYKNVIGARRASW",
  'consensus_string';
is substr( $aln->consensus_string(100), 0, 60 ),
  "?????????L????E????M???M????????????L??E?RNL?SV?YKN??G??R??W",
  'consensus_string';
is substr( $aln->consensus_string(0), 0, 60 ),
  "REDLVYLAKLAEQAERYEEMVEFMKKVAELGAPAEELSVEERNLLSVAYKNVIGARRASW",
  'consensus_string';

ok( @seqs = $aln->each_seq_with_id('143T_HUMAN') );
is scalar @seqs, 1, 'each_seq_with_id';

is $aln->is_flush, 1, 'is_flush';
ok( $aln->id('x') && $aln->id eq 'x', 'id get/set' );

is $aln->length,        242,  'length';
is $aln->num_residues,  3769, 'num_residues';
is $aln->num_sequences, 16,   'num_sequences';
is( sprintf( "%.2f", $aln->overall_percentage_identity() ),
    33.06, 'overall_percentage_identity' );
is( sprintf( "%.2f", $aln->overall_percentage_identity('align') ),
    33.06, 'overall_percentage_identity (align)' );
is( sprintf( "%.2f", $aln->overall_percentage_identity('short') ),
    35.24, 'overall_percentage_identity (short)' );
is( sprintf( "%.2f", $aln->overall_percentage_identity('long') ),
    33.47, 'overall_percentage_identity (long)' );
is( sprintf( "%.2f", $aln->average_percentage_identity() ),
    66.91, 'average_percentage_identity' );

ok $aln->set_displayname_count;
is $aln->displayname('1433_LYCES/9-246'), '1433_LYCES_1',
  'set_displayname_count';
ok $aln->set_displayname_flat;
is $aln->displayname('1433_LYCES/9-246'), '1433_LYCES', 'set_displayname_flat';
ok $aln->set_displayname_normal;
is $aln->displayname('1433_LYCES/9-246'), '1433_LYCES/9-246',
  'set_displayname_normal';
ok $aln->uppercase;
ok $aln->map_chars( '\.', '-' );
@seqs = $aln->each_seq_with_id('143T_HUMAN');
is substr( $seqs[0]->seq, 0, 60 ),
  'KTELIQKAKLAEQAERYDDMATCMKAVTEQGA---ELSNEERNLLSVAYKNVVGGRRSAW',
  'uppercase, map_chars';

is(
    $aln->match_line,
    '       ::*::::*  : *   *:           *: *:***:**.***::*.'
      . ' *::**::**:***      .  .      **  :* :*   .  :: ::   *:  .     :* .*. **:'
      . '***.** :*.            :  .*  *   :   : **.*:***********:::* : .: *  :** .'
      . '*::*: .*. : *: **:****************::     ',
    'match_line'
);
ok $aln->remove_seq( $seqs[0] ), 'remove_seqs';
is $aln->num_sequences, 15, 'remove_seqs';
ok $aln->add_seq( $seqs[0] ), 'add_seq';
is $aln->num_sequences, 16, 'add_seq';
ok $seq = $aln->get_seq_by_pos(1), 'get_seq_by_pos';
is( $seq->id, '1433_LYCES', 'get_seq_by_pos' );
ok( ( $aln->missing_char(), 'P' ) and ( $aln->missing_char('X'), 'X' ) );
ok( ( $aln->match_char(),   '.' ) and ( $aln->match_char('-'),   '-' ) );
ok( ( $aln->gap_char(),     '-' ) and ( $aln->gap_char('.'),     '.' ) );

is $aln->purge(0.7), 12, 'purge';
is $aln->num_sequences, 4, 'purge';

SKIP: {
    test_skip( -tests => 24, -requires_module => 'IO::String' );

    my $string;
    my $out = IO::String->new($string);

    my $s1 = Bio::LocatableSeq->new(
        -id       => 'AAA',
        -seq      => 'aawtat-tn-',
        -start    => 1,
        -end      => 8,
        -alphabet => 'dna'
    );
    my $s2 = Bio::LocatableSeq->new(
        -id       => 'BBB',
        -seq      => '-aaaat-tt-',
        -start    => 1,
        -end      => 7,
        -alphabet => 'dna'
    );
    $a = Bio::SimpleAlign->new();
    $a->add_seq($s1);
    $a->add_seq($s2);

    is( $a->consensus_iupac, "aAWWAT-TN-", 'IO::String consensus_iupac' );
    $s1->seq('aaaaattttt');
    $s1->alphabet('dna');
    $s1->end(10);
    $s2->seq('-aaaatttt-');
    $s2->end(8);
    $a = Bio::SimpleAlign->new();
    $a->add_seq($s1);
    $a->add_seq($s2);

    my $strout = Bio::AlignIO->new( -fh => $out, -format => 'pfam' );
    $strout->write_aln($a);
    is(
        $string,
        "AAA/1-10    aaaaattttt\n" . "BBB/1-8     -aaaatttt-\n",
        'IO::String write_aln normal'
    );

    $out->setpos(0);
    $string = '';
    my $b = $a->slice( 2, 9 );
    $strout->write_aln($b);
    is $string,
      "AAA/2-9    aaaatttt\n" . "BBB/1-8    aaaatttt\n",
      'IO::String write_aln slice';

    $out->setpos(0);
    $string = '';
    $b = $a->slice( 9, 10 );
    $strout->write_aln($b);
    is $string,
      "AAA/9-10    tt\n" . "BBB/8-8     t-\n",
      'IO::String write_aln slice';

    $a->verbose(-1);
    $out->setpos(0);
    $string = '';
    $b = $a->slice( 1, 2 );
    $strout->write_aln($b);
    is $string,
      "AAA/1-2    aa\n" . "BBB/1-1    -a\n",
      'IO::String write_aln slice';

    # not sure what coordinates this should return...
    $a->verbose(-1);
    $out->setpos(0);
    $string = '';
    $b = $a->slice( 1, 1, 1 );
    $strout->write_aln($b);
    is $string,
      "AAA/1-1    a\n" . "BBB/1-0    -\n",
      'IO::String write_aln slice';

    $a->verbose(-1);
    $out->setpos(0);
    $string = '';
    $b = $a->slice( 2, 2 );
    $strout->write_aln($b);
    is $string,
      "AAA/2-2    a\n" . "BBB/1-1    a\n",
      'IO::String write_aln slice';

    eval { $b = $a->slice( 11, 13 ); };

    like( $@, qr/EX/ );

    # remove_columns by position
    $out->setpos(0);
    $string = '';
    $str    = Bio::AlignIO->new( -file => test_input_file('mini-align.aln') );
    $aln1   = $str->next_aln;
    $aln2   = $aln1->remove_columns( [ 0, 0 ] );
    $strout->write_aln($aln2);
    is $string,
        "P84139/2-33              NEGEHQIKLDELFEKLLRARLIFKNKDVLRRC\n"
      . "P814153/2-33             NEGMHQIKLDVLFEKLLRARLIFKNKDVLRRC\n"
      . "BAB68554/1-14            ------------------AMLIFKDKQLLQQC\n"
      . "gb|443893|124775/1-32    MRFRFQIKVPPAVEGARPALLIFKSRPELGGC\n",
      'remove_columns by position';

    # and when arguments are entered in "wrong order"?
    $out->setpos(0);
    $string = '';
    my $aln3 = $aln1->remove_columns( [ 1, 1 ], [ 30, 30 ], [ 5, 6 ] );
    $strout->write_aln($aln3);
    is $string,
        "P84139/1-33              MEGEIKLDELFEKLLRARLIFKNKDVLRC\n"
      . "P814153/1-33             MEGMIKLDVLFEKLLRARLIFKNKDVLRC\n"
      . "BAB68554/1-14            ----------------AMLIFKDKQLLQC\n"
      . "gb|443893|124775/2-32    -RFRIKVPPAVEGARPALLIFKSRPELGC\n",
      'remove_columns by position (wrong order)';

    my %cigars = $aln1->cigar_line;
    is $cigars{'gb|443893|124775/1-32'}, '19,19:21,24:29,29:32,32',
      'cigar_line';
    is $cigars{'P814153/1-33'},  '20,20:22,25:30,30:33,33', 'cigar_line';
    is $cigars{'BAB68554/1-14'}, '1,1:3,6:11,11:14,14',     'cigar_line';
    is $cigars{'P84139/1-33'},   '20,20:22,25:30,30:33,33', 'cigar_line';

    # sort_alphabetically
    my $s3 = Bio::LocatableSeq->new(
        -id       => 'ABB',
        -seq      => '-attat-tt-',
        -start    => 1,
        -end      => 7,
        -alphabet => 'dna'
    );
    $a->add_seq($s3);

    is $a->get_seq_by_pos(2)->id, "BBB", 'sort_alphabetically - before';
    ok $a->sort_alphabetically;
    is $a->get_seq_by_pos(2)->id, "ABB", 'sort_alphabetically - after';

    $b = $a->remove_gaps();
    is $b->consensus_string, "aaaattt", 'remove_gaps';

    $s1->seq('aaaaattt--');

    $b = $a->remove_gaps( undef, 'all_gaps_only' );
    is $b->consensus_string, "aaaaatttt", 'remove_gaps all_gaps_only';

    # test set_new_reference:
    $str = Bio::AlignIO->new( -file => test_input_file('testaln.clustalw') );
    $aln = $str->next_aln();
    my $new_aln = $aln->set_new_reference(3);
    $a       = $new_aln->get_seq_by_pos(1)->display_id;
    $new_aln = $aln->set_new_reference('P851414');
    $b       = $new_aln->get_seq_by_pos(1)->display_id;
    is $a, 'P851414', 'set_new_reference';
    is $b, 'P851414', 'set_new_reference';

    # test uniq_seq:
    $str = Bio::AlignIO->new(
        -verbose => $DEBUG,
        -file    => test_input_file('testaln2.fasta')
    );
    $aln     = $str->next_aln();
    $new_aln = $aln->uniq_seq();
    $a       = $new_aln->num_sequences;
    is $a, 11, 'uniq_seq';

    # check if slice works well with a LocateableSeq in its negative strand
    my $seq1 = Bio::LocatableSeq->new(
        -SEQ    => "ATGCTG-ATG",
        -START  => 1,
        -END    => 9,
        -ID     => "test1",
        -STRAND => -1
    );

    my $seq2 = Bio::LocatableSeq->new(
        -SEQ    => "A-GCTGCATG",
        -START  => 1,
        -END    => 9,
        -ID     => "test2",
        -STRAND => 1
    );

    $string = '';
    my $aln_negative = Bio::SimpleAlign->new();
    $aln_negative->add_seq($seq1);
    $aln_negative->add_seq($seq2);
    my $start_column =
      $aln_negative->column_from_residue_number(
        $aln_negative->get_seq_by_pos(1)->display_id, 2 );
    my $end_column =
      $aln_negative->column_from_residue_number(
        $aln_negative->get_seq_by_pos(1)->display_id, 5 );
    $aln_negative = $aln_negative->slice( $end_column, $start_column );
    my $seq_negative = $aln_negative->get_seq_by_pos(1);
    is( $seq_negative->start, 2, "bug 2099" );
    is( $seq_negative->end,   5, "bug 2099" );

    # bug 2793
    my $s11 = Bio::LocatableSeq->new( -id => 'testseq1', -seq => 'AAA' );
    my $s21 = Bio::LocatableSeq->new( -id => 'testseq2', -seq => 'CCC' );
    $a = Bio::SimpleAlign->new();
    ok( $a->add_seq( $s11, 1 ), "bug 2793" );
    is( $a->get_seq_by_pos(1)->seq, 'AAA', "bug 2793" );
    ok( $a->add_seq( $s21, 2 ), "bug 2793" );
    is( $a->get_seq_by_pos(2)->seq, 'CCC', "bug 2793" );
    throws_ok { $a->add_seq( $s21, 0 ) } qr/must be >= 1/, 'Bad sequence, bad!';
}

# test for Bio::SimpleAlign annotation method and
# Bio::FeatureHolder stuff

$aln = Bio::SimpleAlign->new;
isa_ok($aln,"Bio::AnnotatableI");

for my $seqset ( [qw(one AGAGGAT)], [qw(two AGACGAT)], [qw(three AGAGGTT)] ) {
    $aln->add_seq(
        Bio::LocatableSeq->new(
            -id  => $seqset->[0],
            -seq => $seqset->[1]
        )
    );
}

is $aln->num_sequences, 3, 'added 3 seqs';

$aln->add_SeqFeature(
    Bio::SeqFeature::Generic->new(
        -start       => 1,
        -end         => 1,
        -primary_tag => 'charLabel',
    )
);
$aln->add_SeqFeature(
    Bio::SeqFeature::Generic->new(
        -start       => 3,
        -end         => 3,
        -primary_tag => 'charLabel',

    )
);
is( $aln->feature_count, 2, 'first 2 features added' );

my $splitloc = Bio::Location::Split->new;
$splitloc->add_sub_Location(
    Bio::Location::Simple->new(
        -start => 2,
        -end   => 3
    )
);

$splitloc->add_sub_Location(
    Bio::Location::Simple->new(
        -start => 5,
        -end   => 6
    )
);

$aln->add_SeqFeature(
    Bio::SeqFeature::Generic->new(
        -location    => $splitloc,
        -primary_tag => 'charLabel',
    )
);

is( $aln->feature_count, 3, '3rd feature added' );

#do slices and masks as defined by the feature
my $i          = 0;
my @slice_lens = qw(1 1 2 2);
for my $feature ( $aln->get_SeqFeatures ) {
    for my $loc ( $feature->location->each_Location ) {
        my $masked = $aln->mask_columns( $loc->start, $loc->end, '?');
        $masked->verbose(2);
        lives_ok {my $fslice = $masked->slice( $loc->start, $loc->end )};

        $masked->verbose(-1);
        my $fslice = $masked->slice( $loc->start, $loc->end );
        is( $fslice->length, $slice_lens[ $i++ ], "slice $i len" );
        for my $s ( $fslice->each_seq ) {
            like( $s->seq, qr/^\?+$/, 'correct masked seq' );
        }
    }
}

# test set_displayname_safe & restore_displayname:
$str = Bio::AlignIO->new( -file => test_input_file('pep-266.aln') );
$aln = $str->next_aln();
is $aln->get_seq_by_pos(3)->display_id, 'Smik_Contig1103.1',
  'initial display id ok';
my ( $new_aln, $ref ) = $aln->set_displayname_safe();
is $new_aln->get_seq_by_pos(3)->display_id, 'S000000003', 'safe display id ok';
my $restored_aln = $new_aln->restore_displayname($ref);
is $restored_aln->get_seq_by_pos(3)->display_id, 'Smik_Contig1103.1',
  'restored display id ok';

# test sort_by_list:
$str = Bio::AlignIO->new( -file => test_input_file('testaln.clustalw') );
my $list_file = test_input_file('testaln.list');
$aln     = $str->next_aln();
$new_aln = $aln->sort_by_list($list_file);
$a       = $new_aln->get_seq_by_pos(1)->display_id;
is $a, 'BAB68554', 'sort by list ok';

# test for Binary/Morphological/Mixed data

# sort_by_start

# test sort_by_list:

my $s1 = Bio::LocatableSeq->new(
    -id       => 'AAA',
    -seq      => 'aawtat-tn-',
    -start    => 12,
    -end      => 19,
    -alphabet => 'dna'
);
my $s2 = Bio::LocatableSeq->new(
    -id       => 'BBB',
    -seq      => '-aaaat-tt-',
    -start    => 1,
    -end      => 7,
    -alphabet => 'dna'
);
my $s3 = Bio::LocatableSeq->new(
    -id       => 'BBB',
    -seq      => '-aaaat-tt-',
    -start    => 31,
    -end      => 37,
    -alphabet => 'dna'
);
$a = Bio::SimpleAlign->new();
$a->add_seq($s1);
$a->add_seq($s2);
$a->add_seq($s3);

@seqs = $a->each_seq;
is( $seqs[0]->start, 12 );
is( $seqs[1]->start, 1 );
is( $seqs[2]->start, 31 );

$a->sort_by_start;
@seqs = $a->each_seq;

is( $seqs[0]->start, 1 );
is( $seqs[1]->start, 12 );
is( $seqs[2]->start, 31 );

my %testdata = (
    'allele1' => 'GGATCCATT[C/C]CTACT',
    'allele2' => 'GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT',
    'allele3' => 'G[G/C]ATCCATT[C/G]CTACT',
    'allele4' => 'GGATCCATT[C/G]CTACT',
    'allele5' => 'GGATCCATT[C/G]CTAC[T/A]',
    'allele6' => 'GGATCCATT[C/G]CTA[C/G][T/A]',
    'testseq' => 'GGATCCATT[C/G]CTACT'
);

my $alnin = Bio::AlignIO->new(
    -format => 'fasta',
    -file   => test_input_file('alleles.fas')
);

$aln = $alnin->next_aln;

my $ct = 0;

# compare all to test seq

for my $ls ( sort keys %testdata ) {
    $ct++;
    my $str = $aln->bracket_string(
        -refseq  => 'testseq',
        -allele1 => 'allele1',
        -allele2 => $ls,
    );
    is( $str, $testdata{$ls}, "BIC:$str" );
}

%testdata = (
    'allele1' => 'GGATCCATT{C.C}CTACT',
    'allele2' => 'GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT',
    'allele3' => 'G{G.C}ATCCATT{C.G}CTACT',
    'allele4' => 'GGATCCATT{C.G}CTACT',
    'allele5' => 'GGATCCATT{C.G}CTAC{T.A}',
    'allele6' => 'GGATCCATT{C.G}CTA{C.G}{T.A}',
    'testseq' => 'GGATCCATT{C.G}CTACT'
);

for my $ls ( sort keys %testdata ) {
    $ct++;
    my $str = $aln->bracket_string(
        -refseq     => 'testseq',
        -allele1    => 'allele1',
        -allele2    => $ls,
        -delimiters => '{}',
        -separator  => '.'
    );
    is( $str, $testdata{$ls}, "BIC:$str" );
}

# is _remove_col really working correctly?
my $a = Bio::LocatableSeq->new(
    -id    => 'a',
    -strand => 1,
    -seq   => 'atcgatcgatcgatcg',
    -start => 5,
    -end   => 20
);
my $b = Bio::LocatableSeq->new(
    -id    => 'b',
    -strand => 1,
    -seq   => '-tcgatc-atcgatcg',
    -start => 30,
    -end   => 43
);
my $c = Bio::LocatableSeq->new(
    -id    => 'c',
    -strand => -1,
    -seq   => 'atcgatcgatc-atc-',
    -start => 50,
    -end   => 63
);
my $d = Bio::LocatableSeq->new(
    -id    => 'd',
    -strand => -1,
    -seq   => '--cgatcgatcgat--',
    -start => 80,
    -end   => 91
);
my $e = Bio::LocatableSeq->new(
    -id    => 'e',
    -strand => 1,
    -seq   => '-t-gatcgatcga-c-',
    -start => 100,
    -end   => 111
);
$aln = Bio::SimpleAlign->new();
$aln->add_seq($a);
$aln->add_seq($b);
$aln->add_seq($c);

my $gapless = $aln->remove_gaps();
foreach my $seq ( $gapless->each_seq ) {
    if ( $seq->id eq 'a' ) {
        is $seq->start, 6;
        is $seq->end,   19;
        is $seq->seq,   'tcgatcatcatc';
    }
    elsif ( $seq->id eq 'b' ) {
        is $seq->start, 30;
        is $seq->end,   42;
        is $seq->seq,   'tcgatcatcatc';
    }
    elsif ( $seq->id eq 'c' ) {
        is $seq->start, 51;
        is $seq->end,   63;
        is $seq->seq,   'tcgatcatcatc';
    }
}

$aln->add_seq($d);
$aln->add_seq($e);
$gapless = $aln->remove_gaps();
foreach my $seq ( $gapless->each_seq ) {
    if ( $seq->id eq 'a' ) {
        is $seq->start, 8;
        is $seq->end,   17;
        is $seq->seq,   'gatcatca';
    }
    elsif ( $seq->id eq 'b' ) {
        is $seq->start, 32;
        is $seq->end,   40;
        is $seq->seq,   'gatcatca';
    }
    elsif ( $seq->id eq 'c' ) {
        is $seq->start, 53;
        is $seq->end,   61;
        is $seq->seq,   'gatcatca';
    }
    elsif ( $seq->id eq 'd' ) {
        is $seq->start, 81;
        is $seq->end,   90;
        is $seq->seq,   'gatcatca';
    }
    elsif ( $seq->id eq 'e' ) {
        is $seq->start, 101;
        is $seq->end,   110;
        is $seq->seq,   'gatcatca';
    }
}

# bug 3077

my $slice = $aln->slice(1,4);

for my $seq ($slice->each_seq) {
    if ( $seq->id eq 'a' ) {
        is $seq->start, 5;
        is $seq->end,   8;
        is $seq->strand, 1;
        is $seq->seq,   'atcg';
    }
    elsif ( $seq->id eq 'b' ) {
        is $seq->start, 30;
        is $seq->end,   32;
        is $seq->strand, 1;
        is $seq->seq,   '-tcg';
    }
    elsif ( $seq->id eq 'c' ) {
        is $seq->start, 60;
        is $seq->end,   63;
        is $seq->strand, -1;
        is $seq->seq,   'atcg';
    }
    elsif ( $seq->id eq 'd' ) {
        is $seq->start, 90;
        is $seq->end,   91;
        is $seq->strand, -1;
        is $seq->seq,   '--cg';
    }
    elsif ( $seq->id eq 'e' ) {
        is $seq->start, 100;
        is $seq->end,   101;
        is $seq->strand, 1;
        is $seq->seq,   '-t-g';
    }
}

my $f = Bio::LocatableSeq->new(
    -id    => 'f',
    -seq   => 'a-cgatcgatcgat-g',
    -start => 30,
    -end   => 43
);
$aln = Bio::SimpleAlign->new();
$aln->add_seq($a);
$aln->add_seq($f);

$gapless = $aln->remove_gaps();
foreach my $seq ( $gapless->each_seq ) {
    if ( $seq->id eq 'a' ) {
        is $seq->start, 5;
        is $seq->end,   20;
        is $seq->seq,   'acgatcgatcgatg';
    }
    elsif ( $seq->id eq 'f' ) {
        is $seq->start, 30;
        is $seq->end,   43;
        is $seq->seq,   'acgatcgatcgatg';
    }
}

my $g =
  Bio::LocatableSeq->new( -id => 'g', -seq => 'atgc', -start => 5, -end => 8 );
my $h = Bio::LocatableSeq->new(
    -id    => 'h',
    -seq   => '-tcg',
    -start => 30,
    -end   => 32
);
$aln = Bio::SimpleAlign->new();
$aln->add_seq($g);
$aln->add_seq($h);

# test for new method in API get_seq_by_id
my $retrieved = $aln->get_seq_by_id('g');
is( defined $retrieved, 1 );
my $removed = $aln->remove_columns( [ 1, 3 ] );
foreach my $seq ( $removed->each_seq ) {
    if ( $seq->id eq 'g' ) {
        is $seq->start, 5;
        is $seq->end,   5;
        is $seq->seq,   'a';
    }
    elsif ( $seq->id eq 'h' ) {
        is $seq->start, 0;
        is $seq->end,   0;
        is $seq->seq,   '-';
    }
}

# work out mask_columns(), see bug 2842
SKIP: {
    test_skip(-tests => 6, -requires_module => 'IO::String');
    my $io = Bio::AlignIO->new( -file => test_input_file("testaln.clustalw") );
    my $aln = $io->next_aln();
    isa_ok( $aln, 'Bio::SimpleAlign' );
    my $consensus = <consensus_string, $consensus, 'consensus string looks ok' );


    my @cons_got = $aln->consensus_conservation;
    # 422 positions, mostly two of six sequences conserved, set as default
    my @cons_expect = (100 * 2/6) x 422;
    # Exceptionally columns as a mask, manually determined (1-based columns)
    $cons_expect[$_-1] = 100 * 1/6 for (5,12,41,70,82,310,390);
    $cons_expect[$_-1] = 100 * 3/6 for (27,30,32,36,47,49,61,66,69,71,77,79,
        81,91,96,97,105,114,115,117,118,121,122,129,140,146,156,159,160,162,
        183,197,217,221,229,242,247,248,261,266,282,287,295,316,323,329,335,337,344,);
    $cons_expect[$_-1] = 100 * 4/6 for (84,93,99,100,102,107,108,112,113,119,150,);
    $cons_expect[$_-1] = 100 * 5/6 for (81,110);
    # Format for string comparison
    @cons_expect = map { sprintf "%4.1f", $_ } @cons_expect;
    @cons_got = map { sprintf "%4.1f", $_ } @cons_got;
    is(length($aln->consensus_string), scalar(@cons_got),"conservation length");
    is_deeply(\@cons_got, \@cons_expect, "conservation scores");


    is( aln2str( $aln => 'pfam' ), <mask_columns(12,20,'?');
    is( aln2str( $newaln, 'pfam' ), <new( $phylip_str );

    my $in = Bio::AlignIO->new( -fh => $phy_fh, -format => 'phylip' );
    unified_diff;

    $aln = $in->next_aln();
    eq_or_diff( aln2str( $aln, 'phylip' ), $phylip_str );

    $newaln = $aln->mask_columns(15,20,'?');
    eq_or_diff( aln2str( $newaln,'phylip' ), $phylip_masked, 'align after looks ok' );
}

######## SUBROUTINES

sub aln2str {
    my ( $aln, $fmt ) = @_;
    my $out;
    my $out_fh = IO::String->new( $out );
    my $alignio_out = Bio::AlignIO->new(-fh => $out_fh, -format => $fmt);
    $alignio_out->write_aln( $aln );
    return $out;
}
BioPerl-1.007002/t/Align/TreeBuild.t000444000766000024       316013155576320 17054 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 13);
	
	for my $mod ( qw(Bio::Align::DNAStatistics
					 Bio::Align::ProteinStatistics
					 Bio::Align::Utilities
					 Bio::AlignIO
					 Bio::Tree::DistanceFactory
					 Bio::TreeIO) ) {
		use_ok($mod);
    }
}

my $debug = test_debug();

use Bio::Align::Utilities qw(:all);

my $in = Bio::AlignIO->new(-format => 'clustalw',
       			  -file   => test_input_file('pep-266.aln'));
my $aln = $in->next_aln();
isa_ok($aln, 'Bio::SimpleAlign','SimpleAlign object parsed out');
my $pstats = Bio::Align::ProteinStatistics->new(-verbose => $debug);
my $matrix = $pstats->distance(-method => 'Kimura',
			       -align  => $aln);
isa_ok($matrix,'Bio::Matrix::MatrixI','Protein distance matrix retrieved');

my $treebuilder = Bio::Tree::DistanceFactory->new(-method => 'NJ');
my $tree = $treebuilder->make_tree($matrix);
isa_ok($tree,'Bio::Tree::TreeI', 'Tree object gotten back');

my ($cn) = $tree->find_node('183.m01790');

# brlens checked against tree generated by PHYLIP NJ
is($tree->find_node('AN2438.1')->branch_length, '0.28221','NJ calculated Branch length');
is($tree->find_node('FG05298.1')->branch_length, '0.20593','NJ calculated Branch length');

# simple topology test - make sure these 2 are sister
is($tree->find_node('YOR262W')->ancestor->id, 
   $tree->find_node('Smik_Contig1103.1')->ancestor->id, 'Make sure two nodes are sister');

# TODO?
# UPGMA tests


# test the bootstrap
my $replicates = &bootstrap_replicates($aln,10);
is(scalar @$replicates, 10,'10 replicates formulated');
BioPerl-1.007002/t/Align/Utilities.t000444000766000024       326613155576320 17157 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 14);
	
	use_ok('Bio::Align::Utilities', qw(:all));
	use_ok('Bio::SimpleAlign');
	use_ok('Bio::PrimarySeq');
	use_ok('Bio::LocatableSeq');
	use_ok('Bio::AlignIO');
}

my $DEBUG = test_debug();

my $aa_align = Bio::SimpleAlign->new();
$aa_align->add_seq(Bio::LocatableSeq->new(-id => "n1", -seq => "MLIDVG-MLVLR"));
$aa_align->add_seq(Bio::LocatableSeq->new(-id => "n2", -seq => "MLIDVRTPLALR"));
$aa_align->add_seq(Bio::LocatableSeq->new(-id => "n3", -seq => "MLI-VR-SLALR"));

my %dnaseqs = ();
$dnaseqs{'n1'} = Bio::PrimarySeq->new(-id => "n1dna", -seq => 'atgctgatagacgtaggcatgctagtactgaga');
$dnaseqs{'n2'} = Bio::PrimarySeq->new(-id => "n2dna", -seq => 'atgctgatcgacgtacgcaccccgctagcactcaga');
$dnaseqs{'n3'} = Bio::PrimarySeq->new(-id => "n3dna", -seq => 'atgttgattgtacgctcgcttgcacttaga');
my $dna_aln;

ok( $dna_aln = &aa_to_dna_aln($aa_align, \%dnaseqs));
if( $DEBUG ) {
	Bio::AlignIO->new(-format=>'clustalw')->write_aln($dna_aln);
}

is $dna_aln->length, 36;
is $dna_aln->num_residues, 99;
is $dna_aln->num_sequences, 3;
is $dna_aln->consensus_string(50), "atgctgat?gacgtacgc????cgctagcact?aga";

my @dnaseqs = $dna_aln->each_seq;
is $dnaseqs[0]->display_id, 'n1dna';
$dna_aln->verbose(-1);
my $replicates;
ok $replicates = &bootstrap_replicates($dna_aln,3);

is scalar @$replicates, 3;
my $repl_aln = pop @$replicates;
is $repl_aln->num_sequences, 3;

##use IO::String;
##use Bio::AlignIO;
##my $string;
##my $out = IO::String->new($string);
##
##my $strout = Bio::AlignIO->new(-fh   => $out,'-format' => 'pfam');
##$strout->write_aln($repl_aln);
##is $string, "";
BioPerl-1.007002/t/AlignIO000755000766000024          013155576321 15104 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/AlignIO/AlignIO.t000444000766000024       467013155576320 16716 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests           => 29,
               -requires_module => 'Data::Stag');

    use_ok('Bio::AlignIO');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# general filehandle tests
# not all parsers support output (noted as 0)
my %files = (
    # file                   format       I  O
    'testaln.phylip'     => ['phylip',     1, 1],
    'testaln.psi'         => ['psi',        1, 1],
    'testaln.arp'       => ['arp',        1, 0],
    'rfam_tests.stk'    => ['stockholm',  1, 1],
    'testaln.pfam'      => ['pfam',       1, 1],
    'testaln.msf'       => ['msf',        1, 1],
    'testaln.fasta'     => ['fasta',      1, 1],
    'testaln.selex'     => ['selex',      1, 1],
    'testaln.mase'      => ['mase',       1, 0],
    'testaln.prodom'    => ['prodom',     1, 0],
    'testaln.clustalw'  => ['clustalw',   1, 1],
    'testaln.metafasta' => ['metafasta',  1, 1],
    'testaln.nexus'     => ['nexus',      1, 1],
    'testaln.po'        => ['po',         1, 1],
    'testaln.xmfa'      => ['xmfa',       1, 1],
 );

# input file handles

$aln = Bio::AlignIO->new(
    -file  => test_input_file('longnames.aln'),
    -format=>'clustalw',
)->next_aln();
isa_ok($aln, 'Bio::AnnotatableI');

while (my ($file, $fdata) = each %files) {
    my ($format, $in, $out) = @{$fdata};
    if ($in) {
        my $fhin = Bio::AlignIO->newFh(
           '-file'  => test_input_file($file),
                           '-format' => $format);
        my $fhout = Bio::AlignIO->newFh(
           '-file' => ">".test_output_file(),
                        '-format' => 'clustalw');
        while ( $aln = <$fhin>) {
            cmp_ok($aln->num_sequences, '>=', 2, "input filehandle method test : $format");
            last;
        }
    }
}

# output file handles

while (my ($file, $fdata) = each %files) {
    my ($format, $in, $out) = @{$fdata};
    if ($out) {
        my $status = 0;
        my $fhin = Bio::AlignIO->newFh(
           '-file' => test_input_file('testaln.clustalw'),
                        '-format' => 'clustalw');
        my $fhout = Bio::AlignIO->newFh(
           '-file'  => '>'.test_output_file(),
                           '-format' => $format);
        while ( $aln = <$fhin> ) {
            $status = print $fhout $aln;
            last;
        }
        is $status, 1, "filehandle output test : $format";
    }
}
BioPerl-1.007002/t/AlignIO/arp.t000444000766000024       623713155576320 16217 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: arp.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests           => 48,
               -requires_module => 'Data::Stag');
	
	use_ok('Bio::AlignIO::arp');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# ARP format
$str  = Bio::AlignIO ->new(
    '-file'	=> test_input_file("testaln.arp"),
    -verbose => 1,
    '-format'	=> 'arp');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, '01/1-399','ARP get_nse()');
is($aln->get_seq_by_pos(1)->length, '407');
is($aln->num_sequences, 60,'ARP num_sequences()');
is($aln->id, 'Mandenka', 'ARP id()');
is($aln->description, 'mtDNA sequences in the Senegalese Mandenka (hypervariable region 1)', 'ARP description()');
my $coll = $aln->annotation;
isa_ok($coll, 'Bio::AnnotationCollectionI');
my ($ann) = $coll->get_Annotations('Samples');
isa_ok($ann, 'Bio::AnnotationI');
my %nodes = $ann->pairs;
is(keys %nodes, 60);
is($nodes{'03'}, 10);
is(($coll->get_Annotations('DataType'))[0]->value,'DNA');
is(($coll->get_Annotations('MissingData'))[0]->value,'?');

$str  = Bio::AlignIO->new(
    '-file'	=> test_input_file("testaln2.arp"),
    '-format'	=> 'arp');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, '000/1-29','ARP get_nse()');
is($aln->num_sequences, 3,'ARP num_sequences()');
is($aln->id, 'Population 1', 'ARP id()');
is($aln->description, 'An example of DNA sequence data', 'ARP description()');
$coll = $aln->annotation;
isa_ok($coll, 'Bio::AnnotationCollectionI');
($ann) = $coll->get_Annotations('Samples');
isa_ok($ann, 'Bio::AnnotationI');
%nodes = $ann->pairs;
is(keys %nodes, 3);
is($nodes{'001'}, 1);
is(($coll->get_Annotations('DataType'))[0]->value, 'DNA');
is(($coll->get_Annotations('SampleSize'))[0]->value, 6);

$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(2)->get_nse, '001/1-29','ARP get_nse()');
is($aln->num_sequences, 8,'ARP num_sequences()');
is($aln->id, 'Population 2', 'ARP id()');
is($aln->description, 'An example of DNA sequence data', 'ARP description()');
$coll = $aln->annotation;
isa_ok($coll, 'Bio::AnnotationCollectionI');
($ann) = $coll->get_Annotations('Samples');
isa_ok($ann, 'Bio::AnnotationI');
%nodes = $ann->pairs;
is(keys %nodes, 8);
is($nodes{'001'}, 1);
is(($coll->get_Annotations('DataType'))[0]->value, 'DNA');
is(($coll->get_Annotations('SampleSize'))[0]->value, 8);

$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(2)->get_nse, '024/1-29','ARP get_nse()');
is($aln->num_sequences, 6,'ARP num_sequences()');
is($aln->id, 'Population 3', 'ARP id()');
is($aln->description, 'An example of DNA sequence data', 'ARP description()');
$coll = $aln->annotation;
isa_ok($coll, 'Bio::AnnotationCollectionI');
($ann) = $coll->get_Annotations('Samples');
isa_ok($ann, 'Bio::AnnotationI');
%nodes = $ann->pairs;
is(keys %nodes, 6);
is($nodes{'024'}, 1);
is(($coll->get_Annotations('DataType'))[0]->value, 'DNA');
is(($coll->get_Annotations('SampleSize'))[0]->value, 6);
BioPerl-1.007002/t/AlignIO/bl2seq.t000444000766000024       203313155576320 16613 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: bl2seq.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 7);
    
    use_ok('Bio::AlignIO::bl2seq');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# BL2SEQ
$str = Bio::AlignIO->new(-file        => test_input_file("bl2seq.out"),
                         -format      => 'bl2seq',
                         -report_type => 'blastp');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(2)->get_nse, 'ALEU_HORVU/60-360', "BLAST bl2seq format test";

# Bug 2978, test report_type guessing for TBLASTN and correct Frame assignment to HitFrame
$str = Bio::AlignIO->new(-file   => test_input_file("bl2seq.tblastn.out"),
                         -format => 'bl2seq');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
foreach my $seq ( $aln->each_seq_with_id('WAN03UHTX_1') ) {
    is $seq->start(),  946;
    is $seq->end(),    990;
    is $seq->strand(),  -1;
}
BioPerl-1.007002/t/AlignIO/clustalw.t000444000766000024       255613155576320 17273 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: clustalw.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 6);
	
	use_ok('Bio::AlignIO::clustalw');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# CLUSTAL
my $io = Bio::AlignIO->new(
   -file => test_input_file("testaln.clustalw") );
$aln = $io->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->consensus_string, "MNEGEHQIKLDELFEKLLRARKIFKNKDVLRHSWEPKDLPHRHEQIEA".
"LAQILVPVLRGETMKIIFCGHHACELGEDRGTKGFVIDELKDVDEDRNGKVDVIEINCEHMDTHYRVLPNIAKLF".
"DDCTGIGVPMHGGPTDEVTAKLKQVIDMKERFVIIVLDEIDKLVKKSGDEVLYSLTRINTELKRAKVSVIGISND".
"LKFKEYLDPRVLSSLSEEEVVFPPYDANQLRDILTQRAEEAFYPGVLDEGVIPLCAALAAREHGDARKALDLLRV".
"AGEIAEREGASKVTEKHVWKAQEKIEQDMMEEVIKTLPLQSKVLLYAIVLLDENGDLPANTGDVYAVYRELCEYI".
"DLEPLTQRRISDLINELDMLGIINAKVVSKGRYGRTKEIRLMVTSYKIRNVLRYDYSIQPLLTISLKSEQRRLI",
"clustalw consensus_string test";

my $outfile = test_output_file();
$strout = Bio::AlignIO->new(
   '-file' => ">$outfile", 
			      '-format' => 'clustalw');
$status = $strout->write_aln($aln);
is $status, 1, "clustalw output test";
undef $strout;
$str = Bio::AlignIO->new(
   '-file'=> $outfile, 
			   '-format' => 'clustalw');
$aln = $str->next_aln($aln);
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'P84139/1-420', "clustalw input test";
BioPerl-1.007002/t/AlignIO/emboss.t000444000766000024       745113155576320 16724 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: emboss.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 37);
	
	use_ok('Bio::AlignIO::emboss');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# EMBOSS water
$str = Bio::AlignIO->new('-format' => 'emboss',
		 '-file'   => test_input_file('cysprot.water'));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->score,'501.50');
is($aln->get_seq_by_pos(1)->get_nse,'PAPA_CARPA/3-342');
is($aln->get_seq_by_pos(2)->get_nse,'CATL_HUMAN/1-331');
is(sprintf("%.1f",$aln->overall_percentage_identity),33.8);
is(sprintf("%.1f",$aln->average_percentage_identity),40.1);

is($aln->get_seq_by_pos(1)->start, 3);
is($aln->length,364);


# EMBOSS needle
$str = Bio::AlignIO->new('-format' => 'emboss',
	  '-file'   => test_input_file('cysprot.needle'));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->score,'499.50');
is($aln->get_seq_by_pos(1)->get_nse,'PAPA_CARPA/1-345');
is($aln->get_seq_by_pos(2)->get_nse,'CATL_HUMAN/1-333');


# EMBOSS water 2.2.x
$str = Bio::AlignIO->new('-format' => 'emboss',
	 '-file'   => test_input_file('cys1_dicdi.water'));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse,'CYS1_DICDI/1-343');
is($aln->get_seq_by_pos(2)->get_nse,'CYS1_DICDI-1/1-343');
is($aln->score,'1841.0');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse,'CYS1_DICDI/29-343');
is($aln->get_seq_by_pos(2)->get_nse,'ALEU_HORVU/61-360');


# EMBOSS water 2.2.x sparse needle
$str = Bio::AlignIO->new(-verbose => $DEBUG,
	  '-format' => 'emboss',
   	'-file'   => test_input_file('sparsealn.needle'));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->score,'18.0');
is(sprintf("%.1f",$aln->overall_percentage_identity), 2.1);
is(sprintf("%.1f",$aln->average_percentage_identity), 38.5);
is($aln->get_seq_by_pos(1)->length, 238);
is($aln->length,238);
is($aln->get_seq_by_pos(1)->get_nse,'KV1K_HUMAN/1-108');
is($aln->get_seq_by_pos(2)->get_nse,'IF1Y_HUMAN/1-143');
is($aln->get_seq_by_pos(1)->seq(), 'DIQMTQSPSTLSVSVGDRVTITCEASQTVLSYLNWYQQK'.
   'PGKAPKLLIYAASSLETGVPSRFSGQGSGTBFTFTISSVZPZBFATYYCQZYLDLPRTFGQGTKVDLKR'.
   '-'x130);
is($aln->get_seq_by_pos(2)->seq(), ('-'x94).'PKNKGKGGK-NRRRGKNENESEKRELVFKE'.
   'DGQEYAQVIKMLGNGRLEALCFDGVKRLCHIRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEAR'.
   'SLKAYGGLPEHAKINETDTFGPGDDDEIQFDDIGDDDEDIDDI');
is($aln->is_flush, 1);

# EMBOSS needle
$str = Bio::AlignIO->new('-format' => 'emboss',
	  '-file'   => test_input_file('gf-s71.needle'));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(2)->seq(), 'MEDVTLFQFTWRKPI-RLQGEIVYKTSETQTIETNKKDVECVANFQENKEVQTDS-VDNGVGENVKKDITISKEVLNLLYDFVRDDSKVNYDRLLEFHKFDKVALETVQKYHVETRNENIILMISSSSRKTLILFGGISHETFCSHQARALLCSSSTSFSIPLPVCAISAVFYSSTQFILGDVSGNISMCSKDKIIFEKKITDGAVTCLEMCRHGLLSGSDDGNIILWQIGTSGLEKLGGTKLTVSDLSRKIRRSSTSNKPVAIVSMQVYVWPSGEEACVATETGGLYLLTLPTLDYKPLSHQTATSINKILFENQFVAVIYHTSNAAVFNSEGLVDEIPFVATLAVR----------PKLVLF--YTSVCVQDITLNCTSPFREFNNEYNPVIKFSKIRFSADLSVING-FRTSSPNSNN-----------------------------------------------');
is($aln->get_seq_by_pos(1)->seq(), 'MEDVTLHHFRWRKPVENKNGEIVYKTSETQTAEISRKDVECVANFQKSQESQTDDFMQNGVGDGIKKEIRISKEVLGHIYDFLRDDSKVNYDRLLEFHKFDKVSLETVQKYHVETRNENIILMISNSSRKTLILFGGLSHETFCSHQARAVLCSSSTTSSLPLPVCAISAVFYSSTQFLLGDISGNISMWTKEKMIFENKVTDGSVTSLELCRYGLLSGSDDGNVILWKVEESKIEKIEGIKLTVSDLSRKIRRSSTSNKPVAIVSMQV----SGDEVCVATETGGLYLLTLPTLESKPLT-QSATSIFKILYEHPYIAVVYHTSNSAIFNSEGLVDEIPFVATLAVRCGAYFIFSNQSRLIIWSMNTRSTVIDENLNCHS-ICSLSND--------------TLQVLDGDFNLNSQSENSATSESENLRISDLQNLRMLKLQNLRTSEFQNFRTSESQYFKKDNGEL');
is($aln->is_flush(), 1);
is($aln->get_seq_by_pos(1)->get_nse,'gf.s71.44/1-448');
is($aln->get_seq_by_pos(2)->get_nse,'Y50C1A.2/1-406');

BioPerl-1.007002/t/AlignIO/fasta.t000444000766000024       320413155576320 16522 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 12);
	
	use_ok('Bio::AlignIO::fasta');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# FASTA
$str = Bio::AlignIO->new(
		 -file => test_input_file("testaln.fasta"), 
		 -format => 'fasta');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->display_id, 'AK1H_ECOLI/114-431', 
  "fasta input test ";
is $aln->get_seq_by_pos(1)->get_nse, 'AK1H_ECOLI/114-431/1-318', 
  "fasta input test ";
is ($aln->get_seq_by_pos(1)->description, 'DESCRIPTION HERE', 
    "fasta input test for description");
is ($aln->get_seq_by_pos(11)->display_id, 'AK_YEAST/134-472',
    "fasta input test for id");
is $aln->get_seq_by_pos(11)->get_nse, 'AK_YEAST/134-472/134-472', 
  "fasta input test, captures formatted start/end";

is ($aln->get_seq_by_pos(2)->end, 318,
    "fasta input test for end");

is ($aln->get_seq_by_pos(11)->description, 'A COMMENT FOR YEAST', 
    "fasta input test for description");

$strout = Bio::AlignIO->new(
   '-file' => ">".test_output_file(), 
			      '-format' => 'fasta');
$status = $strout->write_aln($aln);
is $status, 1,"fasta output test";

my $in = Bio::AlignIO->newFh(
   '-file'  => test_input_file("testaln.fasta"), 
			       '-format' => 'fasta');
my $out = Bio::AlignIO->newFh(
   '-file' => ">".test_output_file(), 
				'-format' => 'pfam');
while ( $aln = <$in>) {
    is $aln->get_seq_by_pos(1)->get_nse, 'AK1H_ECOLI/114-431/1-318',
     "filehandle input test  ";
    $status = print $out $aln;
    last;
}
is $status, 1, "filehandle output test";
BioPerl-1.007002/t/AlignIO/largemultifasta.t000444000766000024       233113155576320 20610 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: largemultifasta.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 7);
	
	use_ok('Bio::AlignIO::largemultifasta');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# LARGEMULTIFASTA
$str = Bio::AlignIO->new(
   '-file' => test_input_file('little.largemultifasta'),
                         '-format' => 'largemultifasta');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'Human:/1-81', "fasta input test ";
is ($aln->get_seq_by_pos(1)->description,
    '72.0:1018606-3386002; 73.0:0-14850845; 74.0:0-83355922; SPECIAL_hsApr2003_3.0:0-414023;',
    "fasta input test for description");
is ($aln->get_seq_by_pos(3)->display_id, 'Rat:',
    "fasta input test for id");

is ($aln->get_seq_by_pos(3)->description,
    '72.0:1018606-3386002; 73.0:0-14850845; 74.0:0-83355922; SPECIAL_hsApr2003_3.0:0-414023;',
    "fasta input test for description");

$strout = Bio::AlignIO->new(
   '-file' => ">".test_output_file(),
                            '-format' => 'largemultifasta');
$status = $strout->write_aln($aln);
is $status, 1,"fasta output test";

BioPerl-1.007002/t/AlignIO/maf.t000444000766000024       213413155576321 16171 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: maf.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 11);
	
	use_ok('Bio::AlignIO::maf');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# MAF
$str = Bio::AlignIO->new(
	  '-file' => test_input_file("humor.maf"));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'NM_006987/5000-1', "maf input test";
is $aln->get_seq_by_pos(1)->strand, -1;

# MAF - bug 2453
$str = Bio::AlignIO->new(
	  '-file' => test_input_file("bug2453.maf"));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'hg16.chr7/27578829-27578866', "maf input test";
is $aln->get_seq_by_pos(1)->strand, 1;
$aln = $str->next_aln();
is $aln->get_seq_by_pos(1)->get_nse, 'hg16.chr7/27699740-27699745', "maf input test";
is $aln->get_seq_by_pos(1)->strand, 1;
$aln = $str->next_aln();
is $aln->get_seq_by_pos(1)->get_nse, 'hg16.chr7/27707222-27707234', "maf input test";
is $aln->get_seq_by_pos(1)->strand, 1;

BioPerl-1.007002/t/AlignIO/mase.t000444000766000024       102613155576321 16352 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: mase.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 3);
	
	use_ok('Bio::AlignIO::mase');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# MASE
$str = Bio::AlignIO->new(
   '-file' => test_input_file("testaln.mase"),
			   '-format' => 'mase');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'AK1H_ECOLI/1-318', "mase input test ";

BioPerl-1.007002/t/AlignIO/mega.t000444000766000024       143413155576321 16341 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: mega.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 6);
	
	use_ok('Bio::AlignIO::mega');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# MEGA
$str = Bio::AlignIO->new('-format' => 'mega',
  	'-file'   => test_input_file("testaln.mega"));

$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse,'Human/1-141');
is($aln->get_seq_by_pos(2)->get_nse,'Horse/1-144');
$aln->unmatch();
is($aln->get_seq_by_pos(3)->subseq(1,10), 'V-LSAADKGN');

$strout = Bio::AlignIO->new('-format' => 'mega',
	  '-file'   => ">" .test_output_file());

$status = $strout->write_aln($aln);
is $status, 1, "mega output test";


BioPerl-1.007002/t/AlignIO/meme.t000444000766000024       252513155576321 16355 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 20);
	
	use_ok('Bio::AlignIO::meme');
}

my $DEBUG = test_debug();

# MEME
# this file has no Strand column, and it's version 3.0
my $str = Bio::AlignIO->new(
		-file => test_input_file('test-3.0-1.meme'),
		-format => 'meme');
isa_ok($str,'Bio::AlignIO');
my $aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');is $aln->length,25;
is $aln->num_sequences,4;
is $aln->get_seq_by_pos(3)->seq(),"CCTTAAAATAAAATCCCCACCACCA";
is $aln->get_seq_by_pos(3)->strand,"1";

# this file has a Strand column, also version 3.0
$str = Bio::AlignIO->new(
		-file => test_input_file('test-3.0-2.meme'),
		-format => 'meme');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');is $aln->length,20;
is $aln->num_sequences,8;
is $aln->get_seq_by_pos(8)->seq(),"CCAGTCTCCCCTGAATACCC";
is $aln->get_seq_by_pos(7)->strand,"-1";
is $aln->get_seq_by_pos(6)->strand,"1";

# version 4.9
$str = Bio::AlignIO->new(
		-file => test_input_file('test-4.9.meme'),
		-format => 'meme');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');is $aln->length,21;
is $aln->num_sequences,47;
is $aln->get_seq_by_pos(3)->seq(),"AGAGAAACAAGAGGCCTCTTT";
is $aln->get_seq_by_pos(3)->strand,"1";
BioPerl-1.007002/t/AlignIO/metafasta.t000444000766000024       125713155576321 17400 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: megafasta.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 4);
	
	use_ok('Bio::AlignIO::metafasta');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# METAFASTA
#print STDERR "Better Metafasta tests needed\n" if $DEBUG;
my $io = Bio::AlignIO->new(-verbose => $DEBUG ? $DEBUG : -1, 
   -file => test_input_file('testaln.metafasta'));
$aln = $io->next_aln;
isa_ok($aln,'Bio::Align::AlignI');
is $aln->consensus_string,'CDEFHIJKLMNOPQRSTUVWXYZ', "consensus_string on metafasta";
is $aln->symbol_chars,'23',"symbol_chars() using metafasta";

BioPerl-1.007002/t/AlignIO/msf.t000444000766000024       123513155576321 16214 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: msf.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 4);
	
	use_ok('Bio::AlignIO::msf');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# MSF
$str = Bio::AlignIO->new(
    '-file' => test_input_file("testaln.msf"));
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, '1433_LYCES/9-246', "msf input test";

$strout = Bio::AlignIO->new(
   '-file' => ">".test_output_file(), 
			    '-format' => 'msf');
$status = $strout->write_aln($aln);
is $status, 1, "msf output test";

BioPerl-1.007002/t/AlignIO/nexml.t000444000766000024       620413155576321 16553 0ustar00cjfieldsstaff000000000000#-*-perl-*-
# $Id$
use strict;

use Bio::Root::Test;
test_begin(-tests => 125,  -requires_modules => [qw(Bio::Phylo)]);
use_ok('Bio::AlignIO::nexml'); # checks that your module is there and loads ok
diag("WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support");
SKIP: {
    skip("NeXML parsing for NeXML v0.9 is currently very experimental support", 124);

    #Read in Data
    ok( my $inAlnStream = Bio::AlignIO->new(-file => test_input_file("nexml","characters.nexml.xml"),
                                            -format => 'nexml'), 'make stream');
        
    #Read in aln objects
    ok( my $aln_obj = $inAlnStream->next_aln(), 'nexml matrix to aln' );
    isa_ok($aln_obj, 'Bio::SimpleAlign', 'obj ok');
    is ($aln_obj->id,   'DNA sequences', 'aln id');
    my $num =0;
    my @expected_seqs = ('ACGCTCGCATCGCATC', 'ACGCTCGCATCGCATC', 'ACGCTCGCATCGCATC');
    #checking sequence objects
    foreach my $seq_obj ($aln_obj->each_seq()) {
        $num++;
        
        is( $seq_obj->alphabet, 'dna', "alphabet" );
        
        TODO: {
            local $TODO = 'primary/display_id broken with NeXML 0.9';
            is( $seq_obj->display_id, "DNA sequences.row_$num", "display_id");
        }
        is( $seq_obj->seq, $expected_seqs[$num-1], "sequence correct");
    }
        
    #Write Data
    diag('Begin tests for write/read roundtrip');
    my $outdata = test_output_file();
    ok( my $outAlnStream = Bio::AlignIO->new(-file => ">$outdata", -format => 'nexml'), 'out stream ok');;
    ok( $outAlnStream->write_aln($aln_obj), 'write nexml');
    close($outdata);
    
    
    #Read in the written file to test roundtrip
    ok( my $inAlnStream2 = Bio::AlignIO->new(-file => $outdata, -format => 'nexml'), 'reopen');
        
    #Read in aln objects
    ok( my $aln_obj2 = $inAlnStream2->next_aln(),'get aln (rt)' );
    isa_ok($aln_obj2, 'Bio::SimpleAlign', 'aln obj (rt)');
    is ($aln_obj2->id, 'DNA sequences', "aln id (rt)");
    $num =0;
    @expected_seqs = ('ACGCTCGCATCGCATC', 'ACGCTCGCATCGCATC', 'ACGCTCGCATCGCATC');
    #checking sequence objects
    foreach my $seq_obj ($aln_obj2->each_seq()) {
        $num++;
        
        is( $seq_obj->alphabet, 'dna', "alphabet (rt)" );
        is( $seq_obj->display_id, "DNA sequences.row_$num", "display_id (rt)");
        is( $seq_obj->seq, $expected_seqs[$num-1], "sequence (rt)");
    }
    #check taxa object
    my %expected_taxa = ('DNA sequences.row_1' => 'Homo sapiens',
                         'DNA sequences.row_2' => 'Pan paniscus',
                         'DNA sequences.row_3' => 'Pan troglodytes');
    my @feats = $aln_obj2->get_all_SeqFeatures();
    foreach my $feat (@feats) {
        if ($feat->has_tag('taxa_id')){
            is ( ($feat->get_tag_values('taxa_id'))[0], 'taxa1', 'taxa id ok' );
            is ( ($feat->get_tag_values('taxa_label'))[0], 'Primary taxa block', 'taxa label ok');
            is ( $feat->get_tag_values('taxon'), 5, 'Number of taxa ok')
        }
        else{
            my $seq_num = ($feat->get_tag_values('id'))[0];
            is ( ($feat->get_tag_values('taxon'))[0], $expected_taxa{$seq_num}, "$seq_num taxon ok" )
        }
    }
}
BioPerl-1.007002/t/AlignIO/nexus.t000444000766000024      1073413155576321 16615 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: nexus.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 43);
	
	use_ok('Bio::AlignIO::nexus');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# NEXUS
$str = Bio::AlignIO->new(
   '-file' => test_input_file('testaln.nexus'),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'Homo_sapiens/1-45';
$strout = Bio::AlignIO->new('-file'  => ">".test_output_file(),
			    '-format' => 'nexus', );
$status = $strout->write_aln($aln);
is $status, 1, "nexus output test";

$str = Bio::AlignIO->new(
   '-file' => test_input_file('Bird_Ovomucoids.nex'),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => test_input_file('basic-ladder.nex'),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => test_input_file('Kingdoms_DNA.nex'),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
  '-file' => test_input_file('char-interleave.nex'),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => test_input_file('Primate_mtDNA.nex'),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => test_input_file("char-matrix-spaces.nex"),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => test_input_file("SPAN_Family4nl.nex"),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => test_input_file("intrablock-comment.nex"),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => test_input_file("SPAN_Family7n.nex"),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => test_input_file("long-names.nex"),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => test_input_file("SPAN_Family8a.nex"),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => test_input_file("multiline-intrablock-comment.nex"),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
  '-file' => test_input_file("Treebase-chlamy-dna.nex"),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
  '-file' => test_input_file("quoted-strings1.nex"),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => test_input_file("UnaSmithHIV-both.nex"),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
  '-file' => test_input_file("quoted-strings2.nex"),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => test_input_file("barns-combined.nex"),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => test_input_file("radical-whitespace.nex"),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
   '-file' => test_input_file("basic-bush.nex"),
			  '-format' => 'nexus');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
$str = Bio::AlignIO->new(
  '-file' => test_input_file("radical-whitespace_02.nex"),
			  '-format' => 'nexus');
BioPerl-1.007002/t/AlignIO/pfam.t000444000766000024       130713155576321 16352 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: pfam.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 5);
	
	use_ok('Bio::AlignIO::pfam');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# PFAM format (no annotation)
$str = Bio::AlignIO->new(
	  '-file' => test_input_file("testaln.pfam"));
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, '1433_LYCES/9-246');

$strout = Bio::AlignIO->new(
   '-file' => ">".test_output_file(), 
			    '-format' => 'pfam');
$status = $strout->write_aln($aln);
is($status, 1, " pfam output test");

BioPerl-1.007002/t/AlignIO/phylip.t000444000766000024       614613155576321 16742 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 20);

	use_ok('Bio::AlignIO::phylip');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# PHYLIP sequential/non-interleaved
$strout = Bio::AlignIO->new('-file'  => test_input_file('noninterleaved.phy'), '-interleaved' => 0,
			    '-format' => 'phylip');
$aln = $strout->next_aln($aln);
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(2)->seq(), 'CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAA'.
   'AGGTAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGACATGAATT'.
   'TGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGGTTTATCAAAGTAAGACAGTATGATCAGA'.
   'TACCCATAGAGATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCCACACCTGTCAATATAATTG'.
   'GAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTT' );

# PHYLIP interleaved with long Ids
$str = Bio::AlignIO->new(
    '-file' => test_input_file("protpars_longid.phy"),
    '-format' => 'phylip',
    'longid' => 1);

$aln = $str->next_aln();
#isa_ok($str,'Bio::AlignIO');
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'S I N F R U  P 0 0 1 /1-84';
is $aln->get_seq_by_pos(2)->get_nse, 'SINFRUP002/1-84';

# PHYLIP interleaved, multiple segments
$str = Bio::AlignIO->new(
    '-file' => test_input_file("protpars.phy"),
    '-format' => 'phylip');

$aln = $str->next_aln();
#isa_ok($str,'Bio::AlignIO');
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'SINFRUP001/1-4940';
# is $aln->get_seq_by_pos(2)->get_nse, 'SINFRUP002/1-84';

# PHYLIP interleaved
$str = Bio::AlignIO->new(
    '-file' => test_input_file("testaln.phylip"),
    '-format' => 'phylip');
$aln = $str->next_aln();
#isa_ok($str,'Bio::AlignIO');
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'Homo_sapie/1-45';

$strout = Bio::AlignIO->new(
    '-file'  => ">".test_output_file(),
    '-format' => 'phylip');
$status = $strout->write_aln($aln);
is $status, 1, "phylip output test";

# check the LocatableSeq start/end/strand etc
my $ls = $aln->get_seq_by_pos(2);
is($ls->display_id, 'Pan_panisc');
is($ls->start, 1);
is($ls->end,47);
is($ls->length,50);

# bug 2984
TODO: {
    local $TODO = 'problems with default strand';
    # shouldn't this be 0?
    is($ls->strand,0);
}

# check to see that newlines between header and sequences are parsed correctly
$str = Bio::AlignIO->new('-file' => test_input_file("codeml45b.mlc"), -format => 'phylip', '-longid' => 1);
$aln = $str->next_aln();
$ls = $aln->get_seq_by_pos(9);
ok($ls->display_id eq "Pop_trich_ch", "newline between header and sequences is parsed correctly");

# bug 123 "Problem with newer versions of AlignIO to write alignment data #123"
my $io = Bio::AlignIO->new(
    -file => test_input_file("ORTHOMCL2345.cluster.aa.fa.aln.aa.phy.txt"),
    -format => 'phylip');
$aln = $io->next_aln();
isa_ok($aln,'Bio::SimpleAlign');

# Alignment file where an id has spaces in it
$io = Bio::AlignIO->new(
    -file => test_input_file("ids-with-spaces.phy"),
    -format => 'phylip');
$aln = $io->next_aln();
isa_ok($aln,'Bio::SimpleAlign');
is($aln->get_seq_by_pos(1)->display_id, 'A_BAD_ID');




BioPerl-1.007002/t/AlignIO/po.t000444000766000024       303413155576321 16044 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: po.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 11);
	
	use_ok('Bio::AlignIO::po');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# POA
# just skip on perl 5.6.0 and earlier as it causes a crash on 
# default perl with OS X 10.2
# fink perl 5.6.0 does not seem to have the problem
# can't figure out what it is so just skip for now
SKIP: {
	skip("skipping due to bug in perl 5.6.0 that comes with OS X 10.2", 10) unless ($^O ne 'darwin' || $] > 5.006);
	
	$str = Bio::AlignIO->new(
			  -file   => test_input_file('testaln.po'),
			  -format => 'po',
			  );
	isa_ok($str, 'Bio::AlignIO');
	$aln = $str->next_aln();
	isa_ok($aln,'Bio::Align::AlignI');
	is $aln->num_sequences, 6;
	
	# output is? i.e. does conversion from clustalw to po give the same alignment?
	$str = Bio::AlignIO->new(
		  '-file'   => test_input_file('testaln.clustalw'),
		  '-format' => 'clustalw');
	isa_ok($str,'Bio::AlignIO');
	$aln = $str->next_aln();
	isa_ok($aln,'Bio::Align::AlignI');
	$strout = Bio::AlignIO->new(
		 '-file'   => ">" . test_output_file(),
		 '-format' => 'po');
	$status = $strout->write_aln($aln);
	is $status, 1, "po output test";
	
	$str = Bio::AlignIO->new(
		 '-file'   => test_input_file('testaln.po'),
		 '-format' => 'po');
	isa_ok($str,'Bio::AlignIO');
	my $aln2 = $str->next_aln();
	isa_ok($aln2,'Bio::Align::AlignI');
	is $aln2->num_sequences, $aln->num_sequences;
	is $aln2->length, $aln->length;
}
BioPerl-1.007002/t/AlignIO/prodom.t000444000766000024       103513155576321 16725 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: prodom.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 3);
	
	use_ok('Bio::AlignIO::prodom');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# PRODOM
$str = Bio::AlignIO->new(
   '-file' => test_input_file("testaln.prodom"),
			   '-format' => 'prodom');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'P04777/1-33', "prodom input test ";

BioPerl-1.007002/t/AlignIO/psi.t000444000766000024       107313155576321 16222 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: psi.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 5);
	
	use_ok('Bio::AlignIO::psi');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# PSI format  
$str  = Bio::AlignIO->new(
    '-file'	=> test_input_file("testaln.psi"),
    '-format'	=> 'psi');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, 'QUERY/1-798');
is($aln->num_sequences, 56);
BioPerl-1.007002/t/AlignIO/selex.t000444000766000024       130513155576321 16545 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: selex.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 4);
	
	use_ok('Bio::AlignIO::selex');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# SELEX
$str = Bio::AlignIO->new(
    '-file' => test_input_file("testaln.selex"),
			   '-format' => 'selex');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'HSFAU/1-518', "selex format test ";

$strout = Bio::AlignIO->new(
   '-file' => ">".test_output_file(), 
			      '-format' => 'selex');
$status = $strout->write_aln($aln);
is $status, 1, "selex output test";
BioPerl-1.007002/t/AlignIO/stockholm.t000444000766000024      1474213155576321 17461 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 87);

	use_ok('Bio::AlignIO::stockholm');
}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# STOCKHOLM (multiple concatenated files)
# Rfam
$str  = Bio::AlignIO->new(
    '-file'	=> test_input_file("rfam_tests.stk"),
    '-format'	=> 'stockholm');
$strout = Bio::AlignIO->new('-file'  => ">".test_output_file(),
		'-format' => 'stockholm', );

isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->source, 'stockholm');
is($aln->get_seq_by_pos(1)->get_nse, 'Z11765.1/1-89');
is($aln->accession, 'RF00006');
is($aln->id, 'Vault');
is($aln->description,'Vault RNA');
# annotation
my ($ann) = $aln->annotation->get_Annotations('alignment_comment');
isa_ok($ann, 'Bio::Annotation::Comment');
is($ann->text,'This family of RNAs are found as part of the enigmatic vault'.
   ' ribonucleoprotein complex. The complex consists of a major vault protein'.
   ' (MVP), two minor vault proteins (VPARP and TEP1), and several small '.
   'untranslated RNA molecules. It has been suggested that the vault complex '.
   'is involved in drug resistance. We have identified a putative novel vault '.
   'RNA on chromosome 5 EMBL:AC005219.','Stockholm annotation');
is($ann->tagname,'alignment_comment','Stockholm annotation');

# test output
$status = $strout->write_aln($aln);
is $status, 1, "stockholm output test";

$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->source, 'stockholm');
is($aln->get_seq_by_pos(1)->get_nse, 'L43844.1/2-149');
is($aln->get_seq_by_pos(1)->version, '1');
is($aln->accession, 'RF00007');
is($aln->id, 'U12');
is($aln->description,'U12 minor spliceosomal RNA');
my @anns = $aln->annotation->get_Annotations('reference');
$ann = shift @anns;
isa_ok($ann, 'Bio::Annotation::Reference', 'Stockholm annotation');
$ann = shift @anns;
is($ann->pubmed,'9149533', 'Stockholm annotation');
is($ann->title,
   'Pre-mRNA splicing: the discovery of a new spliceosome doubles the challenge.',
   'Stockholm annotation');
is($ann->authors,'Tarn WY, Steitz JA;', 'Stockholm annotation');
is($ann->location,'Trends Biochem Sci 1997;22:132-137.', 'Stockholm annotation');
# alignment meta data
my $meta = $aln->consensus_meta;
isa_ok($meta, 'Bio::Seq::MetaI');
my ($name) = $meta->meta_names;
is($name,'SS_cons', 'Rfam meta data');
my $meta_str = $meta->named_meta($name);
is($meta_str, '...<<<<<..........>>>>>........<<<<......<<<<......>>>>>>>>'.
   '<<<<<.......>>>>>...........<<<<<<<...<<<<<<<.....>>>>>>>.>>>>>>>..<<<'.
   '<<<<<<.........>>>>>>>>>...', 'Rfam meta data');
$aln = $str->next_aln();
is($aln->source, 'stockholm');
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, 'AJ295015.1/58-1');
is($aln->get_seq_by_pos(1)->strand, -1);
is($aln->accession, 'RF00008');
is($aln->id, 'Hammerhead_3');
is($aln->description,'Hammerhead ribozyme (type III)');
# alignment meta data
$meta = $aln->consensus_meta;
isa_ok($meta, 'Bio::Seq::MetaI');
($name) = $meta->meta_names;
is($name,'SS_cons', 'Rfam meta data');
$meta_str = $meta->named_meta($name);
is($meta_str, '.<<<<<<..<<<<<.........>>>>>.......<<<<.....................'.
   '...........>>>>...>>>>>>.', 'Rfam meta data');

# STOCKHOLM (Pfam)
$str  = Bio::AlignIO->new(
    '-file'	=> test_input_file("pfam_tests.stk"),
    '-format'	=> 'stockholm');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
is($aln->source, 'stockholm');
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, 'RAD25_SCHPO/5-240');
is($aln->accession, 'PF00244.9');
is($aln->id, '14-3-3');
is($aln->description,'14-3-3 protein');
($ann) = $aln->annotation->get_Annotations('gathering_threshold');
isa_ok($ann, 'Bio::Annotation::SimpleValue');
is($ann->display_text, '25.00 25.00; 25.00 25.00;', 'Pfam annotation');
$aln = $str->next_aln();
is($aln->source, 'stockholm');
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, 'COMB_CLOAB/6-235');
is($aln->accession, 'PF04029.4');
is($aln->id, '2-ph_phosp');
is($aln->description,'2-phosphosulpholactate phosphatase');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->source, 'stockholm');
is($aln->get_seq_by_pos(1)->get_nse, 'Y278_HAEIN/174-219');
is($aln->accession, 'PF03475.3');
is($aln->id, '3-alpha');
is($aln->description,'3-alpha domain');
# alignment meta data
$meta = $aln->consensus_meta;
isa_ok($meta, 'Bio::Seq::MetaI');
my %test_data = ('SA_cons'  => '6000320010013274....3372052026033.108303630350385563',
                 'SS_cons'  => 'SCBHHHHHHHHHTSCC....CHHHHHHHHTSTT.CCHHHHHHHHHHHHHSSC',
                 'seq_cons' => 'plTVtclsclhasc......stphLcphLshss.Lupsa+cohpK+lspshs',);
for my $name ($meta->meta_names) {
    ok(exists $test_data{$name}, 'Pfam aln meta data');
    $meta_str = $meta->named_meta($name);
    is($meta_str, $test_data{$name}, 'Pfam aln meta data');
}
%test_data = ();
# sequence meta data
%test_data = ('SA'  => '6000320010013274....3372052026033.108303630350385563',
              'SS'  => 'SCBHHHHHHHHHTSCC....CHHHHHHHHTSTT.CCHHHHHHHHHHHHHSSC');
for my $seq ($aln->each_seq) {
    for my $name ($seq->meta_names) {
        ok(exists $test_data{$name}, 'Pfam seq meta data');
        is($seq->named_meta($name), $test_data{$name}, 'Pfam seq meta data');
    }
}

# sequence-specific alignments
# these are generally DBLinks. However, simple DBLinks are not RangeI, so these
# are now Target (which now is-a DBLink). Since these are per-seq, these are
# stored in a full-length SeqFeature as annotation. For now only sequences which
# have this annotation have a SeqFeature.

my @feats = $aln->get_SeqFeatures;
is(scalar(@feats),6);
isa_ok($feats[0], 'Bio::SeqFeatureI');
isa_ok($feats[0]->entire_seq, 'Bio::Seq::Meta');

my ($link)  = $feats[0]->annotation->get_Annotations('dblink');
isa_ok($link, 'Bio::AnnotationI');
isa_ok($link, 'Bio::Annotation::DBLink');
is($link->database, 'PDB');
is($link->start, '178');
is($link->end, '224');
is($link->primary_id, '1o65');
is($link->target_id, '1o65');  # if not set, defaults to primary_id
is($link->optional_id, 'A');
($link)  = $feats[3]->annotation->get_Annotations('dblink');
is($link->database, 'PDB');
is($link->start, '178');
is($link->end, '224');
is($link->target_id, '1o67');

# bug #3420

my $in = Bio::AlignIO->new(-file => test_input_file('tiny.stk'),
                            -format => 'stockholm');
$aln = $in->next_aln;
is($aln->id, 'NoName');
is($aln->get_seq_by_id('a')->display_id, 'a');
is($aln->get_seq_by_id('b')->display_id, 'b');
BioPerl-1.007002/t/AlignIO/xmfa.t000444000766000024       373413155576321 16370 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: xmfa.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 30);
	
	use_ok('Bio::AlignIO::xmfa');
}

my $DEBUG = test_debug(); # foo

my ($str,$aln,$strout,$status);

# XMFA
$str = Bio::AlignIO->new(
		 -file => test_input_file("testaln.xmfa"), 
		 -format => 'xmfa');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');

# test seqs

my @test_data = (
    # 1:1-598 + chrY 
    [ 'chrY/1-598', 1, 598, 1, 'chrY', undef],

    # 2:5000-5534 - chr17 
    [ 'chr17/5534-5000', 5000, 5534, -1, 'chr17', undef],

    # 3:19000-19537 - chr7
    [ 'chr7/19537-19000', 19000, 19537, -1, 'chr7', undef],
);

for my $pos (1..3) {
    my $seq = $aln->get_seq_by_pos($pos);
    my @seq_data = @{shift @test_data};
    is $seq->get_nse, shift @seq_data,  "xmfa input test ";
    is $seq->start, shift @seq_data, "xmfa input test for start";
    is $seq->end, shift @seq_data, "xmfa input test for end";
    is $seq->strand, shift @seq_data,  "xmfa strand test";
    is $seq->display_id, shift @seq_data, "xmfa input test for id";
    is $seq->description, shift @seq_data, "xmfa input test for id";
}

# test aln
is $aln->score, 111, 'xmfa alignment score';

$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'chrY/1000-1059', 
  "xmfa input test ";
is $aln->get_seq_by_pos(1)->strand, 1, 
  "xmfa strand";
is ($aln->get_seq_by_pos(2)->description, undef, 
    "xmfa input test for description");
is ($aln->get_seq_by_pos(3)->display_id, 'chr12',
    "xmfa input test for id");
is ($aln->get_seq_by_pos(2)->start, 6000,
    "xmfa input test for end");
is ($aln->get_seq_by_pos(1)->end, 1059,
    "xmfa input test for end");
is ($aln->score, 11, 'xmfa alignment score');

$strout = Bio::AlignIO->new(
   '-file' => ">".test_output_file(), 
			      '-format' => 'xmfa');
$status = $strout->write_aln($aln);
is $status, 1,"xmfa output test";

BioPerl-1.007002/t/Annotation000755000766000024          013155576321 15734 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Annotation/Annotation.t000444000766000024      3347713155576321 20426 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests           => 152,
               -requires_module => 'Data::Stag');

    use_ok('Bio::Annotation::Collection');
    use_ok('Bio::Annotation::DBLink');
    use_ok('Bio::Annotation::Comment');
    use_ok('Bio::Annotation::Reference');
    use_ok('Bio::Annotation::SimpleValue');
    use_ok('Bio::Annotation::Target');
    use_ok('Bio::Annotation::AnnotationFactory');
    use_ok('Bio::Annotation::StructuredValue');
    use_ok('Bio::Annotation::TagTree');
    use_ok('Bio::Annotation::Tree');
}

my $DEBUG = test_debug();

#simple value

my $simple = Bio::Annotation::SimpleValue->new(-tagname => 'colour',
                                               -value   => '1',
                                              );

isa_ok($simple, 'Bio::AnnotationI');
is $simple->display_text, 1;
is $simple->value, 1;
is $simple->tagname, 'colour';

is $simple->value(0), 0;
is $simple->value, 0;
is $simple->display_text, 0;

# link

my $link1 = Bio::Annotation::DBLink->new(-database => 'TSC',
                                         -primary_id => 'TSC0000030',
                                        );
isa_ok($link1,'Bio::AnnotationI');
is $link1->database(), 'TSC';
is $link1->primary_id(), 'TSC0000030';
is $link1->as_text, 'Direct database link to TSC0000030 in database TSC';
my $ac = Bio::Annotation::Collection->new();
isa_ok($ac,'Bio::AnnotationCollectionI');

$ac->add_Annotation('dblink',$link1);
$ac->add_Annotation('dblink',
                    Bio::Annotation::DBLink->new(-database => 'TSC',
                                                 -primary_id => 'HUM_FABV'));

my $comment = Bio::Annotation::Comment->new( '-text' => 'sometext');
is $comment->text, 'sometext';
is $comment->as_text, 'Comment: sometext';
$ac->add_Annotation('comment', $comment);



my $target = Bio::Annotation::Target->new(-target_id  => 'F321966.1',
                                          -start      => 1,
                                          -end        => 200,
                                          -strand     => 1,
                                         );
isa_ok($target,'Bio::AnnotationI');
ok $ac->add_Annotation('target', $target);


my $ref = Bio::Annotation::Reference->new( -authors  => 'author line',
                                           -title    => 'title line',
                                           -location => 'location line',
                                           -start    => 12);
isa_ok($ref,'Bio::AnnotationI');
is $ref->authors, 'author line';
is $ref->title,  'title line';
is $ref->location, 'location line';
is $ref->start, 12;
is $ref->database, 'MEDLINE';
is $ref->as_text, 'Reference: title line';
$ac->add_Annotation('reference', $ref);


my $n = 0;
foreach my $link ( $ac->get_Annotations('dblink') ) {
    is $link->database, 'TSC';
    is $link->tagname(), 'dblink';
    $n++;
}
is ($n, 2);

$n = 0;
my @keys = $ac->get_all_annotation_keys();
is (scalar(@keys), 4);
foreach my $ann ( $ac->get_Annotations() ) {
    shift(@keys) if ($n > 0) && ($ann->tagname ne $keys[0]);
    is $ann->tagname(), $keys[0];
    $n++;
}
is ($n, 5);

$ac->add_Annotation($link1);

$n = 0;
foreach my $link ( $ac->get_Annotations('dblink') ) {
    is $link->tagname(), 'dblink';
    $n++;
}
is ($n, 3);

# annotation of structured simple values (like swissprot''is GN line)
my $ann = Bio::Annotation::StructuredValue->new();
isa_ok($ann, "Bio::AnnotationI");

$ann->add_value([-1], "val1");
is ($ann->value(), "val1");
$ann->value("compat test");
is ($ann->value(), "compat test");
$ann->add_value([-1], "val2");
is ($ann->value(-joins => [" AND "]), "compat test AND val2");
$ann->add_value([0], "val1");
is ($ann->value(-joins => [" AND "]), "val1 AND val2");
$ann->add_value([-1,-1], "val3", "val4");
$ann->add_value([-1,-1], "val5", "val6");
$ann->add_value([-1,-1], "val7");
is ($ann->value(-joins => [" AND "]), "val1 AND val2 AND (val3 AND val4) AND (val5 AND val6) AND val7");
is ($ann->value(-joins => [" AND ", " OR "]), "val1 AND val2 AND (val3 OR val4) AND (val5 OR val6) AND val7");

$n = 1;
foreach ($ann->get_all_values()) {
    is ($_, "val".$n++);
}

# nested collections
my $nested_ac = Bio::Annotation::Collection->new();
$nested_ac->add_Annotation('nested', $ac);

is (scalar($nested_ac->get_Annotations()), 1);
($ac) = $nested_ac->get_Annotations();
isa_ok($ac, "Bio::AnnotationCollectionI");
is (scalar($nested_ac->get_all_Annotations()), 6);
$nested_ac->add_Annotation('gene names', $ann);
is (scalar($nested_ac->get_Annotations()), 2);
is (scalar($nested_ac->get_all_Annotations()), 7);
is (scalar($nested_ac->get_Annotations('dblink')), 0);
my @anns = $nested_ac->get_Annotations('gene names');
isa_ok($anns[0], "Bio::Annotation::StructuredValue");
@anns = map { $_->get_Annotations('dblink');
          } $nested_ac->get_Annotations('nested');
is (scalar(@anns), 3);
is (scalar($nested_ac->flatten_Annotations()), 2);
is (scalar($nested_ac->get_Annotations()), 7);
is (scalar($nested_ac->get_all_Annotations()), 7);

SKIP: {
  test_skip(-tests => 7, -requires_modules => [qw(Bio::Annotation::OntologyTerm)]);
  use_ok('Bio::Annotation::OntologyTerm');
  # OntologyTerm annotation
  my $termann = Bio::Annotation::OntologyTerm->new(-label => 'test case',
                                                   -identifier => 'Ann:00001',
                                                   -ontology => 'dumpster');
  isa_ok($termann->term,'Bio::Ontology::Term');
  is ($termann->term->name, 'test case');
  is ($termann->term->identifier, 'Ann:00001');
  is ($termann->tagname, 'dumpster');
  is ($termann->ontology->name, 'dumpster');
  is ($termann->as_text, "dumpster|test case|");
}

# AnnotatableI
use Bio::Seq;
my $seq = Bio::Seq->new();
SKIP: {
        test_skip(-requires_modules => [qw(Bio::SeqFeature::Annotated URI::Escape)],
                          -tests => 4);
        my $fea = Bio::SeqFeature::Annotated->new();
        isa_ok($fea, "Bio::SeqFeatureI",'isa SeqFeatureI');
        isa_ok($fea, "Bio::AnnotatableI",'isa AnnotatableI');
        $fea = Bio::SeqFeature::Generic->new();
        isa_ok($fea, "Bio::SeqFeatureI",'isa SeqFeatureI');
        isa_ok($fea, "Bio::AnnotatableI",'isa AnnotatableI');
}

# tests for Bio::Annotation::AnnotationFactory

my $factory = Bio::Annotation::AnnotationFactory->new;
isa_ok($factory, 'Bio::Factory::ObjectFactoryI');

# defaults to SimpleValue
$ann = $factory->create_object(-value => 'peroxisome',
                               -tagname => 'cellular component');
isa_ok($ann, 'Bio::Annotation::SimpleValue');

$factory->type('Bio::Annotation::OntologyTerm');

$ann = $factory->create_object(-name => 'peroxisome',
                               -tagname => 'cellular component');
ok(defined $ann);
isa_ok($ann, 'Bio::Annotation::OntologyTerm');

# unset type()
$factory->type(undef);
$ann = $factory->create_object(-text => 'this is a comment');
ok(defined $ann,'Bio::Annotation::Comment');

isa_ok($ann,'Bio::Annotation::Comment');

ok $factory->type('Bio::Annotation::Comment');
$ann = $factory->create_object(-text => 'this is a comment');
ok(defined $ann,'Bio::Annotation::Comment');
isa_ok($ann,'Bio::Annotation::Comment');

# factory guessing the type: Comment
$factory = Bio::Annotation::AnnotationFactory->new();
$ann = $factory->create_object(-text => 'this is a comment');
ok(defined $ann,'Bio::Annotation::Comment');
isa_ok($ann,'Bio::Annotation::Comment');

# factory guessing the type: Target
$factory = Bio::Annotation::AnnotationFactory->new();
$ann = $factory->create_object(-target_id => 'F1234',
                               -start     => 1,
                               -end       => 10 );
ok defined $ann;
isa_ok($ann,'Bio::Annotation::Target');

# factory guessing the type: OntologyTerm
$factory = Bio::Annotation::AnnotationFactory->new();
ok(defined ($ann = $factory->create_object(-name => 'peroxisome',
                                           -tagname => 'cellular component')));
like(ref $ann, qr(Bio::Annotation::OntologyTerm));

# tree
my $tree_filename = test_input_file('longnames.dnd');
my $tree = Bio::TreeIO->new(-file=>$tree_filename)->next_tree();
my $ann_tree = Bio::Annotation::Tree->new(
                                          -tagname  => 'tree',
                                          -tree_obj => $tree,
                                         );

isa_ok($ann_tree, 'Bio::AnnotationI');
$ann_tree->tree_id('test');
is $ann_tree->tree_id(), 'test', "tree_id()";
$ann_tree->tagname('tree');
is $ann_tree->tagname(), 'tree', "tagname()";
use Bio::AlignIO;
my $aln = Bio::AlignIO->new(-file  => test_input_file('longnames.aln'),
                         -format=>'clustalw')->next_aln();
$ac = Bio::Annotation::Collection->new();
$ac->add_Annotation('tree',$ann_tree);
$aln->annotation($ac);
for my $treeblock ( $aln->annotation->get_Annotations('tree') ) {
  my $treeref = $treeblock->tree();
  my @nodes = sort { defined $a->id &&
                       defined $b->id &&
                         $a->id cmp $b->id } $treeref->get_nodes();
  is(@nodes, 26);
  is $nodes[12]->id, 'Skud_Contig1703.7', "add tree to AlignI";
  my $str;
  for my $seq ($aln->each_seq_with_id($nodes[12]->id)) {
    $str = $seq->subseq(1,20);
  }
  is( $str, "-------------MPFAQIV", "get seq from node id");
}

# factory guessing the type: Tree
$factory = Bio::Annotation::AnnotationFactory->new();
$ann = $factory->create_object(-tree_obj => $tree);
ok defined $ann;
isa_ok($ann,'Bio::Annotation::Tree');

#tagtree
my $struct = [ 'genenames' => [
                               ['genename' => [
                                               [ 'Name' => 'CALM1' ],
                                               ['Synonyms'=> 'CAM1'],
                                               ['Synonyms'=> 'CALM'],
                                               ['Synonyms'=> 'CAM' ] ] ],
                               ['genename'=> [
                                              [ 'Name'=> 'CALM2' ],
                                              [ 'Synonyms'=> 'CAM2'],
                                              [ 'Synonyms'=> 'CAMB'] ] ],
                               [ 'genename'=> [
                                               [ 'Name'=> 'CALM3' ],
                                               [ 'Synonyms'=> 'CAM3' ],
                                               [ 'Synonyms'=> 'CAMC' ] ] ]
                              ] ];

my $ann_struct = Bio::Annotation::TagTree->new(-tagname => 'gn',
                                               -value => $struct);

isa_ok($ann_struct, 'Bio::AnnotationI');
my $val = $ann_struct->value;
like($val, qr/Name: CALM1/,'default itext');

# roundtrip
my $ann_struct2 = Bio::Annotation::TagTree->new(-tagname => 'gn',
                                                -value => $val);
is($ann_struct2->value, $val,'roundtrip');

# formats
like($ann_struct2->value, qr/Name: CALM1/,'itext');
$ann_struct2->tagformat('sxpr');
like($ann_struct2->value, qr/\(Name "CALM1"\)/,'spxr');
$ann_struct2->tagformat('indent');
like($ann_struct2->value, qr/Name "CALM1"/,'indent');

SKIP: {
    eval {require XML::Parser::PerlSAX};
    skip ("XML::Parser::PerlSAX rquired for XML",1) if $@;
    $ann_struct2->tagformat('xml');
    like($ann_struct2->value, qr/CALM1<\/Name>/,'xml');
}

# grab Data::Stag nodes, use Data::Stag methods
my @nodes = $ann_struct2->children;
for my $node (@nodes) {
    isa_ok($node, 'Data::Stag::StagI');
    is($node->element, 'genename');
    # add tag-value data to node
    $node->set('foo', 'bar');
    # check output
    like($node->itext, qr/foo:\s+bar/,'child changes');
}

$ann_struct2->tagformat('itext');
like($ann_struct2->value, qr/foo:\s+bar/,'child changes in parent node');

# pass in a Data::Stag node to value()
$ann_struct = Bio::Annotation::TagTree->new(-tagname => 'mytags');
like($ann_struct->value, qr/^\s+:\s+$/xms, 'no tags');
like($ann_struct->value, qr/^\s+:\s+$/xms,'before Stag node');
$ann_struct->value($nodes[0]);
like($ann_struct->value, qr/Name: CALM1/,'after Stag node');
is(ref $ann_struct->node, ref $nodes[0], 'both stag nodes');
isnt($ann_struct->node, $nodes[0], 'different instances');

# pass in another TagTree to value()
$ann_struct = Bio::Annotation::TagTree->new(-tagname => 'mytags');
like($ann_struct->value, qr/^\s+:\s+$/xms,'before TagTree');
$ann_struct->value($ann_struct2);
like($ann_struct->value, qr/Name: CALM2/,'after TagTree');
is(ref $ann_struct->node, ref $ann_struct2->node, 'both stag nodes');
isnt($ann_struct->node, $ann_struct2->node, 'different instances');

# replace the Data::Stag node in the annotation (no copy)
$ann_struct = Bio::Annotation::TagTree->new(-tagname => 'mytags');
like($ann_struct->value, qr/^\s+:\s+$/xms,'before TagTree');
$ann_struct->node($nodes[1]);
like($ann_struct->value, qr/Name: CALM2/,'after TagTree');
is(ref $ann_struct->node, ref $ann_struct2->node, 'stag nodes');
is($ann_struct->node, $nodes[1], 'same instance');
# replace the Data::Stag node in the annotation (use duplicate)
$ann_struct = Bio::Annotation::TagTree->new(-tagname => 'mytags');
like($ann_struct->value, qr/^\s+:\s+$/xms,'before TagTree');
$ann_struct->node($nodes[1],'copy');
like($ann_struct->value, qr/Name: CALM2/,'after TagTree');
is(ref $ann_struct->node, ref $ann_struct2->node, 'stag nodes');
isnt($ann_struct->node, $nodes[1], 'different instance');

#check insertion in to collection
$ann_struct = Bio::Annotation::TagTree->new(-value => $struct);
$ac = Bio::Annotation::Collection->new();

$ac->add_Annotation('genenames',$ann_struct);
my $ct = 0;
for my $tagtree ( $ac->get_Annotations('genenames') ) {
  isa_ok($tagtree, 'Bio::AnnotationI');
  for my $node ($tagtree->children) {
    isa_ok($node, 'Data::Stag::StagI');
    like($node->itext, qr/Name:\s+CALM/,'child changes');
    $ct++;
  }
}
is($ct,3);

# factory guessing the type: TagTree
$factory = Bio::Annotation::AnnotationFactory->new();
$ann = $factory->create_object(-value => $struct);
ok defined $ann;
isa_ok($ann,'Bio::Annotation::TagTree');
BioPerl-1.007002/t/Annotation/AnnotationAdaptor.t000444000766000024       423613155576321 21710 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 23);
	
	use_ok('Bio::SeqFeature::Generic');
	use_ok('Bio::SeqFeature::AnnotationAdaptor');
	use_ok('Bio::Annotation::DBLink');
	use_ok('Bio::Annotation::Comment');
	use_ok('Bio::Annotation::SimpleValue');
}


my $feat = Bio::SeqFeature::Generic->new();
$feat->add_tag_value("tag1", "value of tag1");
$feat->add_tag_value("tag1", "another value of tag1");
$feat->add_tag_value("tag2", "some value for a tag");

my $link1 = Bio::Annotation::DBLink->new(-database => 'TSC',
                                        -primary_id => 'TSC0000030',
                                        -tagname => "tag2"
                                       );
$feat->annotation->add_Annotation($link1);

my $anncoll = Bio::SeqFeature::AnnotationAdaptor->new(-feature => $feat);

is($anncoll->get_num_of_annotations(), 4);
is(scalar($anncoll->get_all_annotation_keys()), 2);

my @anns = $anncoll->get_Annotations("tag1");
my @vals = $feat->get_tag_values("tag1");

is (scalar(@anns), scalar(@vals));
for(my $i = 0; $i < @anns; $i++) {
  is ($anns[$i]->value(), $vals[$i]);
}

@anns = $anncoll->get_Annotations("tag2");
my @fanns = $feat->annotation->get_Annotations("tag2");
@vals = $feat->get_tag_values("tag2");

is (scalar(@fanns), 1);
is (scalar(@anns), 2);
is (scalar(@vals), 1);
is ($anns[0]->value(), $vals[0]);

is ($anns[1]->primary_id(), $fanns[0]->primary_id());

my $comment = Bio::Annotation::Comment->new( '-text' => 'sometext');
$anncoll->add_Annotation('comment', $comment);

@fanns = $feat->annotation->get_Annotations("comment");
is (scalar(@fanns), 1);
is ($fanns[0]->text(), "sometext");

my $tagval = Bio::Annotation::SimpleValue->new(-value => "boring value",
					       -tagname => "tag2");
$anncoll->add_Annotation($tagval);

@anns = $anncoll->get_Annotations("tag2");
@fanns = $feat->annotation->get_Annotations("tag2");
@vals = $feat->get_tag_values("tag2");

is (scalar(@fanns), 1);
is (scalar(@anns), 3);
is (scalar(@vals), 2);
is ($anns[0]->value(), $vals[0]);
is ($anns[1]->value(), $vals[1]);
is ($anns[2]->primary_id(), $fanns[0]->primary_id());
BioPerl-1.007002/t/Assembly000755000766000024          013155576321 15401 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Assembly/ContigSpectrum.t000444000766000024      3565213155576321 20724 0ustar00cjfieldsstaff000000000000use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    test_begin( -tests            => 239,
                -requires_modules => [ 'DB_File',
                                       qw(Bio::Assembly::Tools::ContigSpectrum)] );
    use_ok 'Bio::Assembly::IO';
    use_ok 'Bio::Assembly::Tools::ContigSpectrum';
}


my $in = Bio::Assembly::IO->new(
   -file => test_input_file('contigspectrumtest.tigr'),
   -format => 'tigr'
);
isa_ok $in, 'Bio::Assembly::IO';
my $sc = $in->next_assembly;
isa_ok $sc, 'Bio::Assembly::Scaffold';

# Try all the get/set methods
ok my $csp = Bio::Assembly::Tools::ContigSpectrum->new, 'get/set methods';
isa_ok $csp, 'Bio::Assembly::Tools::ContigSpectrum';
ok $csp->id('asdf');
is $csp->id, 'asdf';
ok $csp->nof_seq(123);
is $csp->nof_seq, 123;
ok $csp->nof_rep(456);
is $csp->nof_rep, 456;
ok $csp->max_size(789);
is $csp->max_size, 789;
ok $csp->nof_overlaps(111);
is $csp->nof_overlaps, 111;
ok $csp->min_overlap(50);
is $csp->min_overlap, 50;
ok $csp->avg_overlap(54.3);
is $csp->avg_overlap, 54.3;
ok $csp->min_identity(89.1);
is $csp->min_identity, 89.1;
ok $csp->avg_identity(98.7);
is $csp->avg_identity, 98.7;
ok $csp->avg_seq_len(123.456);
is $csp->avg_seq_len, 123.456;
ok $csp->eff_asm_params(1);
is $csp->eff_asm_params, 1;

# contig spectrum based on simple spectrum
ok my $spectrum_csp = Bio::Assembly::Tools::ContigSpectrum->new, 'simple spectrum';
ok $spectrum_csp->spectrum({1=>1, 2=>2, 3=>3});
is $spectrum_csp->eff_asm_params, 0;
is $spectrum_csp->nof_seq, 14;
is $spectrum_csp->max_size, 3;
is $spectrum_csp->nof_rep, 1;
is $spectrum_csp->nof_overlaps, 0;
is $spectrum_csp->min_overlap, undef;
is $spectrum_csp->avg_overlap, 0;
is $spectrum_csp->min_identity, undef;
is $spectrum_csp->avg_identity, 0;
is $spectrum_csp->avg_seq_len, 0;
is scalar $spectrum_csp->assembly, 0;

ok my $string = $spectrum_csp->to_string(1);
is $string, '1 2 3';
ok $string = $spectrum_csp->to_string(2);
is $string, "1\t2\t3";
ok $string = $spectrum_csp->to_string(3);
is $string, "1\n2\n3";

# score
my $test_csp;
my $spectrum;
ok $test_csp = Bio::Assembly::Tools::ContigSpectrum->new(-spectrum=>$spectrum), 'contig spectrum score';
is $test_csp->score, undef;
$spectrum = {1=>120};
ok $test_csp = Bio::Assembly::Tools::ContigSpectrum->new(-spectrum=>$spectrum);
is $test_csp->score, 0;
$spectrum = {120=>1};
ok $test_csp = Bio::Assembly::Tools::ContigSpectrum->new(-spectrum=>$spectrum);
is $test_csp->score, 1;
float_is $test_csp->score(240), 0.248953974895397;
$spectrum = {1=>120, 120=>1};
ok $test_csp = Bio::Assembly::Tools::ContigSpectrum->new(-spectrum=>$spectrum);
float_is $test_csp->score, 0.248953974895397;

SKIP: {
   test_skip( -tests => 183, -requires_module => 'Graph::Undirected' ); #####

   # mixed contig spectrum imported from assembly
   ok my $mixed_csp = Bio::Assembly::Tools::ContigSpectrum->new(
      -assembly       => $sc,
      -eff_asm_params => 1 ), 'mixed contig spectrum';
   is_deeply $mixed_csp->spectrum, {1=>0, 2=>3, 6=>1, 9=>1}; # [0 3 0 0 0 1 0 0 1]
   is $mixed_csp->eff_asm_params, 1;
   is $mixed_csp->max_size, 9;
   is $mixed_csp->nof_rep, 1;
   is $mixed_csp->nof_seq, 21;
   float_is $mixed_csp->avg_seq_len, 303.81;
   is $mixed_csp->nof_overlaps, 16;
   is $mixed_csp->min_overlap, 35;
   float_is $mixed_csp->avg_overlap, 155.875;
   float_is $mixed_csp->min_identity, 96.8421;
   float_is $mixed_csp->avg_identity, 98.8826;
   is scalar $mixed_csp->assembly, 1;

   # dissolved contig spectrum
   ok my $dissolved_csp = Bio::Assembly::Tools::ContigSpectrum->new(
      -dissolve => [$mixed_csp, 'ZZZ'] ), 'dissolved contig spectrum';
   is_deeply $dissolved_csp->spectrum, {1=>2, 2=>1}; # [2 1]
   is $dissolved_csp->eff_asm_params, 0;
   is $dissolved_csp->max_size, 2;
   is $dissolved_csp->nof_rep, 1;
   is $dissolved_csp->nof_seq, 4;
   float_is $dissolved_csp->avg_seq_len, 321;
   # eff_asm_params haven't been requested
   is $dissolved_csp->nof_overlaps, 0;
   is $dissolved_csp->min_overlap, undef;
   is $dissolved_csp->avg_overlap, 0;
   is $dissolved_csp->min_identity, undef;
   is $dissolved_csp->avg_identity, 0;

   ok $dissolved_csp = Bio::Assembly::Tools::ContigSpectrum->new(
      -dissolve => [$mixed_csp, 'sdsu'] );
   is_deeply $dissolved_csp->spectrum, {1=>3, 6=>1}; # [3 0 0 0 0 1]
   is $dissolved_csp->eff_asm_params, 0;
   is $dissolved_csp->max_size, 6;
   is $dissolved_csp->nof_rep, 1;
   is $dissolved_csp->nof_seq, 9;
   float_is $dissolved_csp->avg_seq_len, 441.222222222222;
   # eff_asm_params haven't been requested
   is $dissolved_csp->nof_overlaps, 0;
   is $dissolved_csp->min_overlap, undef;
   is $dissolved_csp->avg_overlap, 0;
   is $dissolved_csp->min_identity, undef;
   is $dissolved_csp->avg_identity, 0;

   ok $dissolved_csp = Bio::Assembly::Tools::ContigSpectrum->new(
      -dissolve => [$mixed_csp, 'ABC'] );
   is_deeply $dissolved_csp->spectrum, {1=>2, 6=>1}; # [2 0 0 0 0 1]
   is $dissolved_csp->eff_asm_params, 0;
   is $dissolved_csp->max_size, 6;
   is $dissolved_csp->nof_rep, 1;
   is $dissolved_csp->nof_seq, 8;
   float_is $dissolved_csp->avg_seq_len, 140.625;
   # eff_asm_params haven't been requested
   is $dissolved_csp->nof_overlaps, 0;
   is $dissolved_csp->min_overlap, undef;
   is $dissolved_csp->avg_overlap, 0;
   is $dissolved_csp->min_identity, undef;
   is $dissolved_csp->avg_identity, 0;

   ok $dissolved_csp = Bio::Assembly::Tools::ContigSpectrum->new(
      -min_overlap  => 62,
      -min_identity => 1,
      -dissolve     => [$mixed_csp, 'ABC'] );
   is_deeply $dissolved_csp->spectrum, {1=>2, 6=>1}; # [2 0 0 0 0 1]

   ok $dissolved_csp = Bio::Assembly::Tools::ContigSpectrum->new(
      -min_overlap  => 63,
      -min_identity => 1,
      -dissolve     => [$mixed_csp, 'ABC'] );
   is_deeply $dissolved_csp->spectrum, {1=>3, 5=>1}; # [3 0 0 0 1]

   # after dissolving, the remaining assembly objects should be 3 singlets and 1 6-contig
   my @contigs = ($dissolved_csp->assembly);
   is scalar @contigs, 4;
   my @contig_ids = sort qw( 144 652_1 652_2 652_3 );
   is_deeply [sort map($_->id, @contigs)], \@contig_ids;
   my @contig_sizes = sort qw( 1 1 1 5 );
   is_deeply [sort map($_->num_sequences, @contigs)], \@contig_sizes;
   my @contig_isas = sort qw( Bio::Assembly::Singlet Bio::Assembly::Singlet
   Bio::Assembly::Singlet Bio::Assembly::Contig );
   is_deeply [sort map(ref $_, @contigs)], \@contig_isas;
   my @reads = ($contigs[1])->each_seq;
   my @read_ids = sort qw(ABC|9980040 ABC|9937790 ABC|9956706 ABC|9960711 ABC|9976538);
   is_deeply [sort map($_->id, @reads)], \@read_ids;

   ok $dissolved_csp = Bio::Assembly::Tools::ContigSpectrum->new(
      -min_overlap  => 62,
      -min_identity => 97,
      -dissolve     => [$mixed_csp, 'ABC'] );
   is_deeply $dissolved_csp->spectrum, {1=>2, 6=>1}; # [2 0 0 0 0 1]

   ok $dissolved_csp = Bio::Assembly::Tools::ContigSpectrum->new(
      -min_overlap  => 62,
      -min_identity => 98,
      -dissolve     => [$mixed_csp, 'ABC'] );
   is_deeply $dissolved_csp->spectrum, {1=>2, 6=>1}; # [2 0 0 0 0 1]

   ok $dissolved_csp = Bio::Assembly::Tools::ContigSpectrum->new(
      -dissolve       => [$mixed_csp, 'ABC'],
      -eff_asm_params => 1 );
   is_deeply $dissolved_csp->spectrum, {1=>2, 6=>1}; # [2 0 0 0 0 1]
   is $dissolved_csp->eff_asm_params, 1;
   is $dissolved_csp->max_size, 6;
   is $dissolved_csp->nof_rep, 1;
   is $dissolved_csp->nof_seq, 8;
   float_is $dissolved_csp->avg_seq_len, 140.625;
   is $dissolved_csp->nof_overlaps, 5;
   float_is $dissolved_csp->avg_overlap, 76.8;
   float_is $dissolved_csp->avg_identity, 100.0;
   # min_overlap and min_identity not explicitely specified for the dissolved csp
   # min_overlap and min_identity are thus taken from the mixed csp
   is $dissolved_csp->min_overlap, 35;
   float_is $dissolved_csp->min_identity, 96.8421;

   # cross contig spectrum
   ok my $cross_csp = Bio::Assembly::Tools::ContigSpectrum->new(
      -cross => $mixed_csp), 'cross-contig spectrum';
   is_deeply $cross_csp->spectrum, {1=>7, 2=>2, 9=>1}; # [7 2 0 0 0 0 0 0 1]

   # assembly should have 2 singlets and 1 9-contig
   @contigs = $cross_csp->assembly;
   is scalar @contigs, 3;
   @contig_sizes = sort qw( 2 2 9 );
   is_deeply [sort map($_->num_sequences, @contigs)], \@contig_sizes;
   @contig_isas = sort qw( Bio::Assembly::Contig Bio::Assembly::Contig Bio::Assembly::Contig);
   is_deeply [sort map(ref $_, @contigs)], \@contig_isas;
   @read_ids = sort qw(sdsu|SDSU_RFPERU_006_E04.x01.phd.1 ZZZ|SDSU_RFPERU_010_B05.x01.phd.1);
   is_deeply [sort map($_->id, $contigs[0]->each_seq)], \@read_ids;
   @read_ids = sort qw(sdsu|SDSU_RFPERU_013_H05.x01.phd.1 ABC|SDSU_RFPERU_005_F02.x01.phd.1);
   is_deeply [sort map($_->id, $contigs[1]->each_seq)], \@read_ids;
   @read_ids = sort qw( ZZZ|9962187 ABC|9937790 ABC|9944760 ABC|9956706
           sdsu|9986984 ABC|9960711 ABC|9970175 ABC|9976538 ABC|9980040);
   is_deeply [sort map($_->id, $contigs[2]->each_seq)], \@read_ids;

   # effective assembly params
   ok $cross_csp = Bio::Assembly::Tools::ContigSpectrum->new(
      -cross          => $mixed_csp,
      -eff_asm_params => 1 ), 'cross-contig spectrum';
   is_deeply $cross_csp->spectrum, {1=>7, 2=>2, 9=>1}; # [7 2 0 0 0 0 0 0 1]
   is $cross_csp->nof_rep, 1;
   is $cross_csp->eff_asm_params, 1;
   is $cross_csp->max_size, 9;
   is $cross_csp->nof_seq, 13;
   float_is $cross_csp->avg_seq_len, 206.308;
   is $cross_csp->nof_overlaps, 10;
   float_is $cross_csp->avg_overlap, 76.9;
   float_is $cross_csp->avg_identity, 99.2357;
   # min_overlap and min_identity not explicitly specified for the cross csp
   # min_overlap and min_identity are thus taken from the mixed csp
   is $cross_csp->min_overlap, 35;
   float_is $cross_csp->min_identity, 96.8421;

   # with a specified minimum overlap and identity
   ok $cross_csp = Bio::Assembly::Tools::ContigSpectrum->new(
      -cross          => $mixed_csp,
      -min_overlap    => 50,
      -min_identity   => 98 ), 'cross-contig spectrum';
   is_deeply $cross_csp->spectrum, {1=>3, 2=>1, 7=>1}; # [3 1 0 0 0 0 1]
   is $cross_csp->nof_rep, 1;
   is $cross_csp->eff_asm_params, 0;
   is $cross_csp->max_size, 7;
   is $cross_csp->nof_seq, 9;
   float_is $cross_csp->avg_seq_len, 191.222;
   is $cross_csp->min_overlap, 50;
   float_is $cross_csp->min_identity, 98;

   # sum of contig spectra
   ok my $sum_csp = Bio::Assembly::Tools::ContigSpectrum->new(-eff_asm_params=>1), 'contig spectrum sum';
   ok $sum_csp->add($dissolved_csp);
   ok $sum_csp->add($mixed_csp);
   is_deeply $sum_csp->spectrum, {1=>2, 2=>3, 6=>2, 9=>1}; # [2 3 0 0 0 2 0 0 1]
   is $sum_csp->eff_asm_params, 1;
   is $sum_csp->max_size, 9;
   is $sum_csp->nof_rep, 2;
   is $sum_csp->nof_seq, 29;
   float_is $sum_csp->avg_seq_len, 258.7934;
   is $sum_csp->nof_overlaps, 21;
   is $sum_csp->min_overlap, 35;
   float_is $sum_csp->avg_overlap, 137.0476;
   float_is $sum_csp->min_identity, 96.8421;
   float_is $sum_csp->avg_identity, 99.1487;
   is scalar $sum_csp->assembly, 4;

   # average of contig spectra
   ok my $avg_csp = Bio::Assembly::Tools::ContigSpectrum->new(-eff_asm_params=>1), 'average contig spectrum';
   ok $avg_csp = $avg_csp->average([$dissolved_csp, $mixed_csp]);
   is_deeply $avg_csp->spectrum, {1=>1, 2=>1.5, 6=>1, 9=>0.5}; # [1 1 0 0 0 1 0 0 0.5]
   is $avg_csp->eff_asm_params, 1;
   is $avg_csp->max_size, 9;
   is $avg_csp->nof_rep, 2;
   is $avg_csp->nof_seq, 14.5;
   float_is $avg_csp->avg_seq_len, 258.7934;
   is $avg_csp->nof_overlaps, 10.5;
   is $avg_csp->min_overlap, 35;
   float_is $avg_csp->avg_overlap, 137.0476;
   float_is $avg_csp->min_identity, 96.8421;
   float_is $avg_csp->avg_identity, 99.1487;
   is scalar $avg_csp->assembly, 4;

   # drop assembly info from contig spectrum
   ok $mixed_csp->drop_assembly(), 'drop assembly';
   is scalar $mixed_csp->assembly(), 0;

   # large contig (27 reads)
   $in = Bio::Assembly::IO->new(
      -file   => test_input_file('27-contig_Newbler.ace'),
      -format => 'ace-454'
   );
   isa_ok $in, 'Bio::Assembly::IO';
   $sc = $in->next_assembly;
   isa_ok $sc, 'Bio::Assembly::Scaffold';
   ok my $large_csp = Bio::Assembly::Tools::ContigSpectrum->new(
      -assembly       => $sc,
      -eff_asm_params => 1 ), 'large contig spectrum';
   is scalar $large_csp->assembly(), 1;
   is_deeply $large_csp->spectrum, {1=>0, 27=>1};
   is $large_csp->eff_asm_params, 1;
   is $large_csp->max_size, 27;
   is $large_csp->nof_rep, 1;
   is $large_csp->nof_seq, 27;
   float_is $large_csp->avg_seq_len, 100;
   is $large_csp->nof_overlaps, 26;
   is $large_csp->min_overlap, 54;
   
   # Stochastic test results:
   # Operation returns sometimes 88.76923... and sometimes 88.80769...
   
   cmp_ok($large_csp->avg_overlap, '>=', 85);
   cmp_ok($large_csp->avg_overlap, '<=', 95);
   float_is $large_csp->min_identity, 33.3333;
   cmp_ok($large_csp->avg_identity, '>=', 70, $large_csp->avg_identity);
   cmp_ok($large_csp->avg_identity, '<=', 80, $large_csp->avg_identity);

   ok my $large_xcsp = Bio::Assembly::Tools::ContigSpectrum->new(
      -cross          => $large_csp,
      -eff_asm_params => 1           ), 'large cross-contig spectrum';
   is $large_xcsp->nof_overlaps, 26;
   cmp_ok($large_xcsp->avg_overlap, '>=', 88.7, $large_xcsp->avg_overlap);
   cmp_ok($large_xcsp->avg_overlap, '<=', 88.9, $large_xcsp->avg_overlap);
   is_deeply $large_xcsp->spectrum, {1=>21, 27=>1};

   ok $large_xcsp = Bio::Assembly::Tools::ContigSpectrum->new(
      -cross          => $large_csp,
      -min_overlap    => 100);
   is_deeply $large_xcsp->spectrum, {1=>18, 2=>5, 3=>1, 7=>1};
   my @xcontigs = sort {$a->id cmp $b->id} $large_xcsp->assembly;
   is scalar @xcontigs, 7; # the cross-1-contigs are not included
   my @xcontig_ids = sort qw( contig00001_1 contig00001_2 contig00001_3 contig00001_4
      contig00001_5 contig00001_6 contig00001_7 );
   is_deeply [map($_->id, @xcontigs)], \@xcontig_ids;
   my @xcontig_sizes = sort qw( 2 2 2 2 2 3 7 );
   is_deeply [sort map($_->num_sequences, @xcontigs)], \@xcontig_sizes;

   # Examine largest cross-contig
   my $xcontig = (sort {$b->num_sequences <=> $a->num_sequences} $large_xcsp->assembly)[0];
   is $xcontig->num_sequences, 7;
   is $xcontig->get_seq_coord($xcontig->get_seq_by_name('species1635|5973'))->start, 1;
   is $xcontig->get_seq_coord($xcontig->get_seq_by_name('species158|7890'))->start, 1;
   is $xcontig->get_seq_coord($xcontig->get_seq_by_name('species2742|48'))->end, 140;

   # one contig at a time
   $in = Bio::Assembly::IO->new(
      -file => test_input_file('contigspectrumtest.tigr'),
      -format => 'tigr'
   );
   $sc = $in->next_assembly;
   ok $csp = Bio::Assembly::Tools::ContigSpectrum->new(
      -eff_asm_params => 1 ), 'one contig at a time';
   for my $contig ($sc->all_contigs) {
     ok $csp->assembly($contig);
   }

   is scalar $csp->assembly(), 5;
   is_deeply $csp->spectrum, {1=>0, 2=>3, 6=>1, 9=>1}; # [0 3 0 0 0 1 0 0 1]
   is $csp->eff_asm_params, 1;
   is $csp->max_size, 9;
   is $csp->nof_rep, 5;
   is $csp->nof_seq, 21;
   float_is $csp->avg_seq_len, 303.81;
   is $csp->nof_overlaps, 16;
   is $csp->min_overlap, 35;
   float_is $csp->avg_overlap, 155.875;
   float_is $csp->min_identity, 96.8421;
   float_is $csp->avg_identity, 98.8826;
}
BioPerl-1.007002/t/Assembly/core.t000444000766000024      3731013155576321 16677 0ustar00cjfieldsstaff000000000000use strict;
use warnings;
my %ASSEMBLY_TESTS;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin( -tests => 892,
                -requires_module => 'DB_File' );

    use_ok 'Bio::Seq';
    use_ok 'Bio::LocatableSeq';
    use_ok 'Bio::Seq::Quality';
    use_ok 'Bio::Assembly::IO';
    use_ok 'Bio::Assembly::Singlet';
}
use Bio::Root::IO;

#
# Testing Singlet
#
my ($seq_id, $seq_str, $qual, $start, $end, $strand) = ('seq1', 'CAGT-GGT',
  '0 1 2 3 4 5 6 7', 1, 7, -1, );

my $seq = Bio::PrimarySeq->new(-seq => $seq_str, -id  => $seq_id);
my $singlet_id = 'singlet1';
ok my $singlet = Bio::Assembly::Singlet->new( -id => $singlet_id, -seqref =>
  $seq), 'singlet from Bio::PrimarySeq';
isa_ok $singlet, 'Bio::Assembly::Contig';
isa_ok $singlet, 'Bio::Assembly::Singlet';
is $singlet->id, $singlet_id;
ok my $consensus = $singlet->get_consensus_sequence;
isa_ok $consensus, 'Bio::LocatableSeq';
is $consensus->seq, $seq_str;
is $consensus->start, 1;
is $consensus->end, 7;
is $consensus->strand, 1;
is $singlet->get_consensus_length, 8;
is $singlet->get_consensus_quality, undef;
ok my $seqref = $singlet->seqref;
is $seqref->id, $seq_id;
is $seqref->seq, $seq_str;
is $seqref->start, 1;
is $seqref->end, 7;
is $seqref->length, 8;

$seq = Bio::Seq::Quality->new(-seq => $seq_str, -id => $seq_id, -qual => $qual);
ok $singlet = Bio::Assembly::Singlet->new( -id => $singlet_id, -seqref => $seq),
  'singlet from Bio::Seq::Quality';
is $singlet->get_consensus_length, 8;
ok $consensus = $singlet->get_consensus_quality;
isa_ok $consensus, 'Bio::Seq::QualI';
is join(' ', @{$consensus->qual}), $qual;

$seq = Bio::LocatableSeq->new( -seq => $seq_str, -id => $seq_id, -start =>
  $start, -end => $end, -strand => $strand );
ok $singlet = Bio::Assembly::Singlet->new( -id => $singlet_id, -seqref => $seq),
  'singlet from LocatableSeq';
ok $consensus = $singlet->get_consensus_sequence;
is $consensus->start, 1;
is $consensus->end, 7;
is $consensus->strand, -1;
ok $seqref = $singlet->seqref;
is $seqref->start, 1;
is $seqref->end, 7;
is $seqref->strand, -1;

($start, $end) = (20, 26);
$seq = Bio::LocatableSeq->new( -seq => $seq_str, -id => $seq_id, -start =>
  $start, -end => $end, -strand => $strand );
ok $singlet = Bio::Assembly::Singlet->new( -id => $singlet_id, -seqref => $seq),
  'singlet from LocatableSeq with set coordinates';
ok $consensus = $singlet->get_consensus_sequence;
is $consensus->start, 1;
is $consensus->end, 7;
is $consensus->strand, -1;
ok $seqref = $singlet->seqref;
is $seqref->start, 1;
is $seqref->end, 7;
is $seqref->strand, -1;

#
# Testing Contig
#

#
# Testing IO
#

# ACE variants
ok my $aio = Bio::Assembly::IO->new(
    -file   => test_input_file('assembly_with_singlets.ace'),
    -format => 'ace-consed',
);
is $aio->variant, 'consed', 'consed';
ok $aio = Bio::Assembly::IO->new(
    -file   => test_input_file('assembly_with_singlets.ace'),
    -format => 'ace',
);
is $aio->variant, 'consed';
ok $aio->variant('454');
is $aio->variant, '454';

#
# Some PHRAP input
#

my $in = Bio::Assembly::IO->new(
    -file    => test_input_file('consed_project','edit_dir','test_project.phrap.out'),
    -verbose => -1,
);
isa_ok $in, 'Bio::Assembly::IO';
while (my $contig = $in->next_contig) {
    isa_ok $contig, 'Bio::Assembly::Contig';
}

$in = Bio::Assembly::IO->new(
    -file    => test_input_file('consed_project','edit_dir','test_project.phrap.out'),
    -verbose => -1,
);
isa_ok $in, 'Bio::Assembly::IO';
my $sc;
TODO: {
    local $TODO = "phrap parser doesn't include the sequence string in the sequence objects.";
    $in->verbose(2);
    eval {$sc = $in->next_assembly};
    ok !$@;
}

$in->verbose(-1);
$in = Bio::Assembly::IO->new(
    -file    => test_input_file('consed_project','edit_dir','test_project.phrap.out'),
    -verbose => -1,
);
ok $sc = $in->next_assembly;
isa_ok $sc, 'Bio::Assembly::Scaffold';


#
# Testing Scaffold
#

is $sc->id, "NoName";
is $sc->id('test'), "test";

isa_ok $sc->annotation, 'Bio::AnnotationCollectionI';
is $sc->annotation->get_all_annotation_keys, 0,"no annotations in Annotation collection?";
is $sc->get_nof_contigs, 1;
is $sc->get_nof_sequences_in_contigs, 2;
is $sc->get_nof_singlets, 2, "get_nof_singlets";
is $sc->get_contig_seq_ids, 2, "get_contig_seq_ids";
is $sc->get_contig_ids, 1, "get_contig_ids";
is $sc->get_singlet_ids, 2, "get_singlet_ids";

my @phrap_contigs = $sc->all_contigs();
isa_ok $phrap_contigs[0], "Bio::Assembly::Contig",'the contig is a Bio::Assembly::Contig';
my @singlets = $sc->all_singlets();
isa_ok $singlets[0], "Bio::Assembly::Contig", 'the singlet is a Bio::Assembly::Contig';
isa_ok $singlets[0], "Bio::Assembly::Singlet", 'the singlet is a Bio::Assembly::Singlet';

my @contig_seq_ids;
ok @contig_seq_ids = $sc->get_contig_seq_ids, "get_contig_seq_ids";
is @contig_seq_ids, 2;
for my $contig_seq_id (@contig_seq_ids) {
  ok not $contig_seq_id =~ m/contig/i;
}
my @contig_ids;
ok @contig_ids = $sc->get_contig_ids, "get_contig_ids";
is @contig_ids, 1;
for my $contig_id (@contig_ids) {
  ok not $contig_id =~ m/contig/i;
}
my @singlet_ids;
ok @singlet_ids = $sc->get_singlet_ids, "get_singlet_ids";
is @singlet_ids, 2;
for my $singlet_id (@singlet_ids) {
  ok not $singlet_id =~ m/contig/i;
}
my @all_seq_ids;
ok @all_seq_ids = $sc->get_all_seq_ids, "get_all_seq_ids";
for my $seq_id (@all_seq_ids) {
  ok not $seq_id =~ m/contig/i;
}
is @all_seq_ids, 4;

#
# Testing ContigAnalysis
#

#
# Testing ACE
#

# ACE Consed variant (default)
$aio = Bio::Assembly::IO->new(
    -file   => test_input_file('consed_project','edit_dir','test_project.fasta.screen.ace.2'),
    -format => 'ace',
);

my $assembly = $aio->next_assembly();

my @contigs = $assembly->all_contigs();

my $direction = $contigs[0]->strand;
is $direction, 1;

my $features =  $contigs[0]->get_features_collection;

my @contig_features = $features->features;
is @contig_features, 61, 'contig features'; # 59 contig features + 2 seqfeatures

my @annotations = $features->get_features_by_type('Annotation');
is @annotations, 2;

my $had_tag = 0;
for my $an (@annotations) {
    if ($an->has_tag('extra_info')) {
        $had_tag++;
        is (($an->get_tag_values('extra_info'))[0], "contig extra\ninfo\n");
    }
    elsif ($an->has_tag('comment')){
        $had_tag++;
        is (($an->get_tag_values('comment'))[0], "contig tag\ncomment\n");
    }
}
is $had_tag, 2;

is $assembly->get_nof_contigs, 1;
is $assembly->get_nof_sequences_in_contigs, 2;
is $assembly->get_nof_singlets, 0, "get_nof_singlets";
is $assembly->get_contig_seq_ids, 2, "get_contig_seq_ids";
is $assembly->get_contig_ids, 1, "get_contig_ids";
is $assembly->get_singlet_ids, 0, "get_singlet_ids";

$aio = Bio::Assembly::IO->new(
    -file   => test_input_file('assembly_with_singlets.ace'),
    -format => 'ace',
);

while (my $obj = $aio->next_contig) {
    isa_ok $obj, 'Bio::Assembly::Contig'; # Singlets are contigs too
}

$aio = Bio::Assembly::IO->new(
    -file   => test_input_file('assembly_with_singlets.ace'),
    -format => 'ace',
);

$assembly = $aio->next_assembly();
is $assembly->get_nof_contigs, 3;
my @ace_contigs = $assembly->all_contigs();
my $ace_contig = $ace_contigs[0];
isa_ok $ace_contig, "Bio::Assembly::Contig",'the contig is a Bio::Assembly::Contig';

ok my @test_reads = $ace_contig->get_seq_ids();
is scalar @test_reads, 2;
is $test_reads[0], '5704073';
is $test_reads[1], '5762101';

is $assembly->get_nof_sequences_in_contigs, 6;
is $assembly->get_nof_singlets, 33, "get_nof_singlets";
@singlets = $assembly->all_singlets();
isa_ok $singlets[0], "Bio::Assembly::Contig", 'the singlet is a Bio::Assembly::Contig';
isa_ok $singlets[0], "Bio::Assembly::Singlet", 'the singlet is a Bio::Assembly::Singlet';
ok @contig_seq_ids = $assembly->get_contig_seq_ids, "get_contig_seq_ids";
is @contig_seq_ids, 6;
for my $contig_seq_id (@contig_seq_ids) {
  ok not $contig_seq_id =~ m/contig/i;
}
ok @contig_ids = $assembly->get_contig_ids, "get_contig_ids";
is @contig_ids, 3;
for my $contig_id (@contig_ids) {
  ok $contig_id =~ m/contig/i;
}
ok @singlet_ids = $assembly->get_singlet_ids, "get_singlet_ids";
is @singlet_ids, 33;
for my $singlet_id (@singlet_ids) {
  ok $singlet_id =~ m/contig/i;
}
ok @all_seq_ids = $assembly->get_all_seq_ids, "get_all_seq_ids";
for my $seq_id (@all_seq_ids) {
  ok not $seq_id =~ m/contig/i;
}
is @all_seq_ids, 39;

# bug 2758
ok $aio = Bio::Assembly::IO->new(
    -file   => test_input_file('singlet_w_CT.ace'),
    -format => 'ace',
);

# ACE 454 variant
$aio = Bio::Assembly::IO->new(
    -file   => test_input_file('27-contig_Newbler.ace'),
    -format => 'ace-454',
);
$assembly = $aio->next_assembly();
@contigs = $assembly->all_contigs();
# All read positions should be >0
my $contig = $contigs[0];
my $min_aln_coord = undef;
for my $read ($contig->each_seq) {
   my ($feat) = $contig->get_features_collection->get_features_by_type("_aligned_coord:".$read->id);
   my $aln_coord_start = $feat->location->start;
   if ( (not defined $min_aln_coord) or ($aln_coord_start < $min_aln_coord) ) {
      $min_aln_coord = $aln_coord_start;
   }
}
is $min_aln_coord, 1, '454 ACE variant coordinates check';
# The ends of the consensus should be padded
my $left_pad_length  = 29;
my $sequence_length  = 203;
my $right_pad_length = 81;
my $consensus_length = $left_pad_length + $sequence_length + $right_pad_length;
my $cons_seq  = $contig->get_consensus_sequence->seq;
is length $cons_seq, $consensus_length;
$cons_seq =~ m/^(-*).*?(-*)$/;
is length $1, $left_pad_length, '454 ACE variant consensus check';
is length $2, $right_pad_length;
my $cons_qual = $contig->get_consensus_quality->qual;
is scalar @$cons_qual, $consensus_length;
$cons_qual = join ' ', @{$contig->get_consensus_quality->qual};
my $lpad = $left_pad_length x '0 ';
my $rpad = $right_pad_length x '0 ';
$cons_qual =~ m/^($lpad).*($rpad)$/;
ok defined $1;
ok defined $2;

# Writing ACE files
my $asm_infile  = '27-contig_Newbler.ace';
my $asm_outfile = test_output_file();
my $asm_out = Bio::Assembly::IO->new(
    -file    => ">$asm_outfile",
    -format  =>'ace',
);
my $asm_in;
ok $asm_in = Bio::Assembly::IO->new(
    -file    => test_input_file($asm_infile),
    -format  => 'ace',
    -variant => '454',
)->next_assembly, 'writing in the ACE format';
ok $asm_out->write_assembly( -scaffold => $asm_in, -singlets => 1 );

$asm_infile = 'assembly_with_singlets.ace';
ok $asm_in = Bio::Assembly::IO->new(
    -file   => test_input_file($asm_infile),
    -format => 'ace',
)->next_assembly;
ok $asm_out->write_assembly( -scaffold => $asm_in, -singlets => 1  );

$asm_infile = 'reference_ace.ace';
ok $asm_in = Bio::Assembly::IO->new(
    -file   => test_input_file($asm_infile),
    -format => 'ace',
)->next_assembly;
ok $asm_out->write_assembly( -scaffold => $asm_in, -singlets => 1  );


#
# Testing TIGR format
#

# Importing an assembly

$asm_in = Bio::Assembly::IO->new(
    -file   => test_input_file("sample_dataset.tigr"),
    -format => 'tigr',
);
while (my $obj = $asm_in->next_contig) {
    isa_ok $obj, 'Bio::Assembly::Contig'; # Singlets are contigs too
}

$asm_in = Bio::Assembly::IO->new(
    -file   => test_input_file("sample_dataset.tigr"),
    -format => 'tigr',
);

my $scaf_in = $asm_in->next_assembly;
isa_ok $scaf_in, 'Bio::Assembly::Scaffold';
is $scaf_in->id, 'NoName';
is $scaf_in->get_nof_contigs, 13;
is $scaf_in->get_nof_sequences_in_contigs, 36;
is $scaf_in->get_nof_singlets, 1;
my @contigseqids = sort qw(sdsu|SDSU1_RFPERU_001_A09.x01.phd.1
sdsu|SDSU1_RFPERU_001_B03.x01.phd.1 sdsu|SDSU1_RFPERU_001_B04.x01.phd.1
sdsu|SDSU1_RFPERU_001_E04.x01.phd.1 sdsu|SDSU_RFPERU_002_A01.x01.phd.1
sdsu|SDSU_RFPERU_002_B07.x01.phd.1 sdsu|SDSU_RFPERU_002_C12.x01.phd.1
sdsu|SDSU_RFPERU_002_D08.x01.phd.1 sdsu|SDSU_RFPERU_002_H12.x01.phd.1
sdsu|SDSU_RFPERU_003_G09.x01.phd.1 sdsu|SDSU_RFPERU_004_H12.x01.phd.1
sdsu|SDSU_RFPERU_005_F02.x01.phd.1 sdsu|SDSU_RFPERU_006_D03.x01.phd.1
sdsu|SDSU_RFPERU_006_E04.x01.phd.1 sdsu|SDSU_RFPERU_006_E05.x01.phd.1
sdsu|SDSU_RFPERU_006_H08.x01.phd.1 sdsu|SDSU_RFPERU_007_E09.x01.phd.1
sdsu|SDSU_RFPERU_007_F06.x01.phd.1 sdsu|SDSU_RFPERU_008_B02.x01.phd.1
sdsu|SDSU_RFPERU_009_E07.x01.phd.1 sdsu|SDSU_RFPERU_010_B05.x01.phd.1
sdsu|SDSU_RFPERU_010_B06.x01.phd.1 sdsu|SDSU_RFPERU_010_C09.x01.phd.1
sdsu|SDSU_RFPERU_010_D10.x01.phd.1 sdsu|SDSU_RFPERU_012_H02.x01.phd.1
sdsu|SDSU_RFPERU_013_B05.x01.phd.1 sdsu|SDSU_RFPERU_013_C07.x01.phd.1
sdsu|SDSU_RFPERU_013_C08.x01.phd.1 sdsu|SDSU_RFPERU_013_G10.x01.phd.1
sdsu|SDSU_RFPERU_013_H05.x01.phd.1 sdsu|SDSU_RFPERU_014_H06.x01.phd.1
sdsu|SDSU_RFPERU_015_A05.x01.phd.1 sdsu|SDSU_RFPERU_015_C06.x01.phd.1
sdsu|SDSU_RFPERU_015_E04.x01.phd.1 sdsu|SDSU_RFPERU_015_G04.x01.phd.1
sdsu|SDSU_RFPERU_015_H03.x01.phd.1);
my @contigids     = sort qw(106 144 148 17 185 2 210 36 453 500 613 668 93);
my @singletids    = sort qw(123);
my @singletseqids = sort qw(asdf);
is_deeply [sort $scaf_in->get_contig_seq_ids], \@contigseqids;
is_deeply [sort $scaf_in->get_contig_ids],     \@contigids   ;
is_deeply [sort $scaf_in->get_singlet_ids],    \@singletids  ;
isa_ok $scaf_in->get_seq_by_id('sdsu|SDSU1_RFPERU_001_A09.x01.phd.1'),'Bio::LocatableSeq';
$contig = $scaf_in->get_contig_by_id('106');
isa_ok $contig,'Bio::Assembly::Contig';

# check Contig object SeqFeature::Collection
# should add more specific Contig tests...
my @sfs = $contig->get_features_collection->features; # 5 contig features + 2 seqfeatures
is scalar @sfs, 7;
is $sfs[1]->seq_id(), undef; # should this be undef?
ok $contig->get_features_collection->get_features_by_type('_aligned_coord:sdsu|SDSU_RFPERU_006_E04.x01.phd.1');
isa_ok $scaf_in->annotation, 'Bio::AnnotationCollectionI';
is $scaf_in->annotation->get_all_annotation_keys, 0, "no annotations in Annotation collection?";


# Exporting an assembly
$asm_outfile = test_output_file();
$asm_out = Bio::Assembly::IO->new(
    -file   =>  ">$asm_outfile",
    -format => 'tigr',
);
ok $asm_out->write_assembly( -scaffold => $scaf_in), 'writing in the TIGR format';


#
# Testing maq
# /maj
#
my $file = 'test.maq';
ok $aio = Bio::Assembly::IO->new(
    -file   => test_input_file($file),
    -format => 'maq',
), "init maq IO object";
ok $assembly = $aio->next_assembly, "get maq assy";
is $assembly->get_nof_contigs, 11, "got all contigs";
ok open(my $tf, test_input_file($file)), "read test file as text";
my @lines = <$tf>;
is $assembly->get_nof_contig_seqs, scalar @lines, "recorded all maq reads";
ok !$assembly->get_nof_singlets, "no singlets";

ok $aio = Bio::Assembly::IO->new( -file => test_input_file($file),
                                  -format => 'maq' );
isa_ok $aio, 'Bio::Assembly::IO';
while (my $contig = $aio->next_contig) {
    isa_ok $contig, 'Bio::Assembly::Contig';
}

#
# Testing maq with singlets
#
$file = 'test_singlets.maq';
ok $aio = Bio::Assembly::IO->new(
    -file   => test_input_file($file),
    -format => 'maq',
);
ok $assembly = $aio->next_assembly, "get maq assy";
isa_ok $aio, 'Bio::Assembly::IO';


ok @contig_seq_ids = $assembly->get_contig_seq_ids, "get_contig_seq_ids";
is @contig_seq_ids, 246;
for my $contig_seq_id (@contig_seq_ids) {
  ok not $contig_seq_id =~ m/maq_assy/i;
}

ok @contig_ids = $assembly->get_contig_ids, "get_contig_ids";
is @contig_ids, 37;
for my $contig_id (@contig_ids) {
  ok $contig_id =~ m/maq_assy/i;
}

ok @singlet_ids = $assembly->get_singlet_ids, "get_singlet_ids";
is @singlet_ids, 4;
for my $singlet_id (@singlet_ids) {
  ok $singlet_id =~ m/maq_assy/i;
}

ok @all_seq_ids = $assembly->get_all_seq_ids, "get_all_seq_ids";
for my $seq_id (@all_seq_ids) {
  ok not $seq_id =~ m/maq_assy/i;
}
is @all_seq_ids, 250;

ok $aio = Bio::Assembly::IO->new(
    -file   => test_input_file($file),
    -format => 'maq',
);
while (my $contig = $aio->next_contig) {
    isa_ok $contig, 'Bio::Assembly::Contig';
}

##############################################
# test format() and variant() in Bio::RootIO
##############################################

$in = Bio::Assembly::IO->new(
   -file   => test_input_file('assembly_with_singlets.ace'),
);
is $in->format, 'ace';
is $in->variant, 'consed';

exit;
BioPerl-1.007002/t/Assembly/IO000755000766000024          013155576321 15710 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Assembly/IO/bowtie.t000444000766000024       420013155576321 17517 0ustar00cjfieldsstaff000000000000use strict;
use warnings;
my %ASSEMBLY_TESTS;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin( -tests => 796,
                -requires_modules => [
                    'DB_File',
                    'Bio::DB::Sam',
                    'Bio::Tools::Run::Samtools',
                   ],
               );

    use_ok('Bio::Seq');
    use_ok('Bio::LocatableSeq');
    use_ok('Bio::Seq::Quality');
    use_ok('Bio::Assembly::IO');
    use_ok('Bio::Assembly::Singlet');

}

use Bio::Root::IO;

SKIP: {
    skip("SAMTOOLSDIR not set, skipping", 791) unless exists $ENV{SAMTOOLSDIR};

    my ($aio, $assembly, @contig_seq_ids, @singlet_ids, @contig_ids, @all_seq_ids);

    my $file = 'test.bowtie';
    my $refdb = 'test.ref.fas';
    ok $aio = Bio::Assembly::IO->new( -file => test_input_file($file),
                      -index => test_input_file($refdb),
                      -format => 'bowtie' ), "init bowtie IO object";
    isa_ok($aio, 'Bio::Assembly::IO');
    $aio->_current_refseq_id( ($aio->sam->seq_ids)[0] ); # kludge

    while (my $contig = $aio->next_contig) {
    isa_ok($contig, 'Bio::Assembly::Contig');
    }
    ok $aio = Bio::Assembly::IO->new( -file => test_input_file($file),
                      -index => test_input_file($refdb),
                      -format => 'bowtie' ),"reopen";
    ok $assembly = $aio->next_assembly, "get sam assy";
    is( $assembly->get_nof_contigs, 23, "got all contigs");

    ok(@contig_seq_ids = $assembly->get_contig_seq_ids, "get_contig_seq_ids");
    is(@contig_seq_ids, 312);
    for my $contig_seq_id (@contig_seq_ids) {
    ok ($contig_seq_id =~ m/^SRR/i);
    }
    ok(@contig_ids = $assembly->get_contig_ids, "get_contig_ids");
    is(@contig_ids, 23);
    for my $contig_id (@contig_ids) {
    ok ($contig_id =~ m/sam_assy/i);
    }
    ok(@singlet_ids = $assembly->get_singlet_ids, "get_singlet_ids");
    is(@singlet_ids, 36);
    for my $singlet_id (@singlet_ids) {
    ok ($singlet_id =~ m/^sam_assy/i);
    }
    ok(@all_seq_ids = $assembly->get_all_seq_ids, "get_all_seq_ids");
    for my $seq_id (@all_seq_ids) {
    ok ($seq_id =~ m/^SRR/i);
    }
    is(@all_seq_ids, 348);

}
exit;
BioPerl-1.007002/t/Assembly/IO/sam.t000444000766000024       434513155576321 17020 0ustar00cjfieldsstaff000000000000use strict;
use warnings;
my %ASSEMBLY_TESTS;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin( -tests => 441+5,
                -requires_modules => [
                    'DB_File',
                    'Bio::DB::Sam',
                    'Bio::Tools::Run::Samtools',
                   ],
               );

    use_ok('Bio::Seq');
    use_ok('Bio::LocatableSeq');
    use_ok('Bio::Seq::Quality');
    use_ok('Bio::Assembly::IO');
    use_ok('Bio::Assembly::Singlet');
}

use Bio::Root::IO;

my ($aio, $assembly, @contig_seq_ids, @singlet_ids, @contig_ids, @all_seq_ids);
my $file = 'test.bam';
my $refdb = 'test.ref.fas';
ok $aio = Bio::Assembly::IO->new( -file => test_input_file($file),
                                  -refdb => test_input_file($refdb),
                                  -format => 'sam' ), "init sam IO object";
isa_ok($aio, 'Bio::Assembly::IO');
$aio->_current_refseq_id( ($aio->sam->seq_ids)[0] ); # kludge

while (my $contig = $aio->next_contig) {
    isa_ok($contig, 'Bio::Assembly::Contig');
}
ok $aio = Bio::Assembly::IO->new( -file => test_input_file($file),
                                  -refdb => test_input_file($refdb),
                                  -format => 'sam' ),"reopen";
ok $assembly = $aio->next_assembly, "get sam assy";
cmp_ok( $assembly->get_nof_contigs, '>=', 21, "got all contigs");


ok(@contig_seq_ids = $assembly->get_contig_seq_ids, "get_contig_seq_ids");
is(@contig_seq_ids, 334);
# trashing these for now; not much a test really anyway/maj
# for my $contig_seq_id (@contig_seq_ids) {
#     ok ($contig_seq_id =~ m/^SRR/i);
# }

ok(@contig_ids = $assembly->get_contig_ids, "get_contig_ids");
cmp_ok(@contig_ids, '>=', 21);
my $correct_ids = grep {$_ =~ m/sam_assy/i} @contig_ids;
is($correct_ids, scalar(@contig_ids));

ok(@singlet_ids = $assembly->get_singlet_ids, "get_singlet_ids");
is(@singlet_ids, 35);
# trashing these/maj
# for my $singlet_id (@singlet_ids) {
#     ok ($singlet_id =~ m/^SRR/i);
# }

ok(@all_seq_ids = $assembly->get_all_seq_ids, "get_all_seq_ids");
for my $seq_id (@all_seq_ids) {
    ok ($seq_id =~ m/^SRR/i);
}
is(@all_seq_ids, 369);

for my $f (qw(test.bam.bai test.ref.fas.fai)) {
    my $path = Bio::Root::IO->catfile('t', 'data', $f);
    unlink $path if -e $path
}
BioPerl-1.007002/t/Cluster000755000766000024          013155576321 15243 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Cluster/UniGene.t000444000766000024        40613155576321 17077 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 2);

    use_ok('Bio::Cluster::UniGene');
}

my $clu = Bio::Cluster::UniGene->new();
isa_ok($clu, "Bio::AnnotatableI");
BioPerl-1.007002/t/ClusterIO000755000766000024          013155576321 15473 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/ClusterIO/ClusterIO.t000444000766000024       247213155576321 17673 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {     
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 12,
			   -requires_module => 'Time::HiRes');
    
	use_ok('Bio::ClusterIO');
	use_ok('Bio::Cluster::ClusterFactory');
}

SKIP: {
	test_skip(-tests => 8, -requires_module => 'XML::SAX');
    
	my ($clusterio, $result,$hit,$hsp);
	$clusterio = Bio::ClusterIO->new('-tempfile' => 0,
					'-format' => 'dbsnp',
					'-file'   => test_input_file('LittleChrY.dbsnp.xml'));
    
	$result = $clusterio->next_cluster;
	ok($result);
	is($result->observed, 'C/T');
	is($result->type, 'notwithdrawn');
	ok($result->seq_5);
	ok($result->seq_3);
	my @ss = $result->each_subsnp;
	is scalar @ss,  5;
	is($ss[0]->handle, 'CGAP-GAI');
	is($ss[1]->handle, 'LEE');
	
	# don't know if these were ever meant to work... cjf 3/7/07
	#is($result->heterozygous, 0.208738461136818);
	#is($result->heterozygous_SE, 0.0260274689436777);
}

###################################
# ClusterFactory tests            #
###################################

my $fact = Bio::Cluster::ClusterFactory->new();
# auto-recognize implementation class
my $clu = $fact->create_object(-display_id => 'Hs.2');
isa_ok($clu, "Bio::Cluster::UniGeneI");
$clu = $fact->create_object(-namespace => "UNIGENE");
isa_ok($clu, "Bio::Cluster::UniGeneI");
BioPerl-1.007002/t/ClusterIO/SequenceFamily.t000444000766000024       243013155576321 20726 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests           => 17,
               -requires_module => 'Data::Stag');

    use_ok('Bio::SeqIO');
    use_ok('Bio::Cluster::SequenceFamily');
}

my $seqio= Bio::SeqIO->new('-format' => 'swiss',
                           '-file'   => test_input_file('sequencefamily.dat'));
my @mem;
while(my $seq = $seqio->next_seq){
    push @mem, $seq;
}
my $family = Bio::Cluster::SequenceFamily->new(
    -family_id=>"Family_1",
    -description=>"SomeFamily",
    -annotation_score=>"100",
    -family_score=>"50",
    -version=>"1.0",
    -members=>\@mem,
);
is $family->description, "SomeFamily";
is $family->annotation_score,100;
is $family->size, 5;
is $family->family_id,"Family_1";
is $family->version, "1.0";

$family->add_members($mem[0]);
$family->add_members($mem[1]);
is $family->size, 7;
is $family->cluster_score, "50";
is $family->family_score, "50";

my @members = $family->get_members(-ncbi_taxid=>9606);

foreach my $mem(@members){
    is $mem->species->ncbi_taxid, 9606;
}

@members = $family->get_members(-binomial=>"Homo sapiens");

foreach my $mem(@members){
    is $mem->species->binomial, "Homo sapiens";
}


$family->flush_members();

is $family->size, 0;
BioPerl-1.007002/t/ClusterIO/unigene.t000444000766000024      1755613155576321 17505 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 73);
	
	use_ok('Bio::ClusterIO');
}

my ($str, $unigene); # predeclare variables for strict

$str = Bio::ClusterIO->new('-file' => test_input_file('unigene.data'), '-format' => "unigene");
ok $str, 'new Bio::ClusterIO object defined';

ok ( defined ($unigene = $str->next_cluster()));

# check interface implementations to be sure
isa_ok $unigene, "Bio::Cluster::UniGeneI";
isa_ok $unigene, "Bio::ClusterI";
isa_ok $unigene, "Bio::IdentifiableI";
isa_ok $unigene, "Bio::DescribableI";

# test specific instance of unigene record provided in the unigene.data file
is ($unigene->unigene_id, 'Hs.2');
is ($unigene->title, 'N-acetyltransferase 2 (arylamine N-acetyltransferase)');
is ($unigene->gene, 'NAT2');
is ($unigene->cytoband,'8p22');
is ($unigene->gnm_terminus,'S');
is ($unigene->homol,'YES');
is ($unigene->restr_expr,'liver');
is ($unigene->scount,26);
is (scalar @{ $unigene->locuslink }, 1);
is (scalar @{ $unigene->chromosome }, 1);
is (scalar @{ $unigene->express }, 7);
is (scalar @{ $unigene->sts }, 8);
is (scalar @{ $unigene->txmap }, 0);
is (scalar @{ $unigene->protsim } , 4);
is (scalar @{ $unigene->sequences },26);

is ($unigene->locuslink->[0], '10');
is ($unigene->chromosome->[0], '8');
is ($unigene->express->[0], 'liver');
is ($unigene->sts->[0], 'ACC=G59899 UNISTS=137181');
is ($unigene->protsim->[0], 'ORG=Escherischia coli; PROTGI=16129422; PROTID=ref:NP_415980.1; PCT=24.81; ALN=255');

my ($seq1) = $unigene->next_seq;
is ($seq1->display_id, 'BX095770');

# test recognition of species

SKIP: {
	# TODO? why wouldn't it be available? Bug if not? Remove this skip?
	skip 'species not available', 'species test' unless defined $unigene->species;
	is $unigene->species->binomial, "Homo sapiens" ;
}


# test accessors of interfaces
is  ($seq1->namespace, "GenBank");
is  ($seq1->authority, "NCBI");
is  ($seq1->alphabet, "dna");
my $n = 1; # we've seen already one seq
while($seq1 = $unigene->next_seq()) {
    $n++;
}
is  ($n, 26);
is  ($unigene->size(), 26);
is  (scalar($unigene->get_members()), 26);
is  ($unigene->description, 'N-acetyltransferase 2 (arylamine N-acetyltransferase)');
is  ($unigene->display_id, "Hs.2");
is  ($unigene->namespace, "UniGene");
is  ($unigene->authority, "NCBI");

$unigene->unigene_id('Hs.50');
is ($unigene->unigene_id, 'Hs.50') || diag('unigene_id was ' . $unigene->unigene_id);

$unigene->title('title_test');
is ($unigene->title, 'title_test') || diag('title was ' . $unigene->title);

$unigene->gene('gene_test');
is ($unigene->gene, 'gene_test') || diag('gene was ' . $unigene->gene);

$unigene->cytoband('cytoband_test');
is ($unigene->cytoband, 'cytoband_test') || diag('cytoband was ' . $unigene->cytoband);

$unigene->gnm_terminus('gnm_terminus_test');
is ($unigene->gnm_terminus, 'gnm_terminus_test') || diag('gnm_terminus was ' . $unigene->gnm_terminus);

$unigene->homol('homol_test');
is ($unigene->homol, 'homol_test') || diag('homol was ' . $unigene->homol);

$unigene->restr_expr('restr_expr_test');
is ($unigene->restr_expr, 'restr_expr_test') || diag('restr_expr was ' . $unigene->restr_expr);

$unigene->scount('scount_test');
is ($unigene->scount, 'scount_test') || diag('scount was ' . $unigene->scount);

my $seq = $unigene->next_seq;
$seq = $unigene->next_seq;
isa_ok ($seq, 'Bio::PrimarySeqI') || diag('expected a Bio::PrimarySeq object but got a ' . ref($seq));
my $accession = $seq->accession_number;
is ($accession, 'AI262683');
my $version = $seq->seq_version();
is ($version, 1);

# test the sequence parsing is working
my $ac = $seq->annotation();
my $simple_ann_object;
($simple_ann_object) = $ac->get_Annotations('seqtype');
ok defined $simple_ann_object, 'annotation object defined';
is ($simple_ann_object->value(), 'EST') || diag('seqtype was ' . $simple_ann_object->value);	

# test PERIPHERAL, bug 1708
$seq = $unigene->next_seq;
$accession = $seq->accession_number;
is ($accession, 'CB161982');

my @acs = $seq->annotation->get_Annotations('peripheral');
is  $acs[0]->display_text, 1;

# tests not specific to unigene record provided in the unigene.data file
my @locuslink_test = ( "58473", "5354" );
$unigene->locuslink(\@locuslink_test);
my @locuslink_results;
while (my $locuslink = $unigene->next_locuslink) {
	push @locuslink_results, $locuslink;
}
is(scalar(@locuslink_results), 2) || diag('expected locuslink to have 2 entries but it had ' . scalar(@locuslink_results));
my $locuslink = shift @locuslink_results;
is( $locuslink, '58473') || diag('expected 58473 but got ' . $locuslink);


my @express_test = qw( kidney heart liver spleen );
$unigene->express(\@express_test);
my @express_results;
while (my $tissue = $unigene->next_express) {
	push @express_results, $tissue;
}
is(  scalar(@express_results), 4) || diag('expected express to have 4 entries but it had ' . scalar(@express_results));

my @chromosome_test = ( "7", "11" );
$unigene->chromosome(\@chromosome_test);
my @chromosome_results;
while (my $chromosome = $unigene->next_chromosome) {
	push @chromosome_results, $chromosome;
}
is( scalar(@chromosome_results), 2) || diag('expected chromosome to have 2 entries but it had ' . scalar(@chromosome_results));
my $chromosome = shift @chromosome_results;
is(  $chromosome, '7') || diag('expected 7 but got ' . $chromosome);

my @sts_test = ( "ACC=- NAME=sts-D90276 UNISTS=37687", "ACC=G29786 NAME=SHGC-35230 UNISTS=58455" );
$unigene->sts(\@sts_test);
my @sts_results;
while (my $sts = $unigene->next_sts) {
	push @sts_results, $sts;
}
is(scalar(@sts_results), 2) || diag('expected sts to have 2 entries but it had ' . scalar(@sts_results));
my $sts = shift @sts_results;
is($sts, 'ACC=- NAME=sts-D90276 UNISTS=37687') || diag('expected ACC=- NAME=sts-D90276 UNISTS=37687 but got ' . $sts);

my @txmap_test = ("D19S425-D19S418; MARKER=sts-D90276; RHPANEL=GB4" , "D19S425-D19S418; MARKER=stSG41396; RHPANEL=GB4");
$unigene->txmap(\@txmap_test);
my @txmap_results;
while (my $txmap = $unigene->next_txmap) {
	push @txmap_results, $txmap;
}
is(scalar(@txmap_results), 2) || diag('expected txmap to have 2 entries but it had ' . scalar(@txmap_results));
my $txmap = shift @txmap_results;
is ($txmap, 'D19S425-D19S418; MARKER=sts-D90276; RHPANEL=GB4') || diag('expected D19S425-D19S418; MARKER=sts-D90276; RHPANEL=GB4 but got ' . $txmap);

my @protsim_test = ("ORG=Homo sapiens; PROTGI=107211; PROTID=pir:A40428; PCT=100; ALN=243" , "ORG=Mus musculus; PROTGI=2497288; PROTID=sp:Q61400; PCT=42; ALN=143");
$unigene->protsim(\@protsim_test);
my @protsim_results;
while (my $protsim = $unigene->next_protsim) {
    push @protsim_results, $protsim;
}
is (scalar(@protsim_results), 2) || diag('expected protsim to have 2 entries but it had ' . scalar(@protsim_results));
my $protsim = shift @protsim_results;
is ($protsim, 'ORG=Homo sapiens; PROTGI=107211; PROTID=pir:A40428; PCT=100; ALN=243') || diag('expected ORG=Homo sapiens; PROTGI=107211; PROTID=pir:A40428; PCT=100; ALN=243 but got ' . $protsim);



# do a quick test on Rn record included as the next cluster in the
# test data file because it has version numbers tacked on the end of
# the accession numbers in each seq line - NCBI has started doing this
# now (Sept 2003).

$unigene = $str->next_cluster();
$seq = $unigene->next_seq;
isa_ok ($seq,'Bio::PrimarySeqI') || diag( 'expected a Bio::PrimarySeq object but got a ' . ref($seq));
$version = $seq->seq_version();
is($version, '1');

# next cluster contains a // in the title - yes NCBI did that. Nonetheless,
# this should not trip up the parser:

$unigene = $str->next_cluster();
ok ($unigene, 'next cluster'); # previously this would have been undef
is  ($unigene->unigene_id, "Mm.340763");
is ($unigene->title, 'Transcribed locus, strongly similar to NP_003008.1 splicing factor, arginine/serine-rich 3; splicing factor, arginine//serine-rich, 20-kD [Homo sapiens]');
is ($unigene->homol, 'YES');
is ($unigene->scount, 31);
is (scalar($unigene->get_members()), 31);
BioPerl-1.007002/t/Draw000755000766000024          013155576321 14517 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Draw/Pictogram.t000444000766000024       233313155576321 16767 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: Pictogram.t 15112 2008-12-08 18:12:38Z sendu $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 6,
			   -requires_module => 'SVG 2.26');
	
	use_ok('Bio::Draw::Pictogram');
	use_ok('Bio::SeqIO');
	use_ok('Bio::Matrix::PSM::IO');
}


my $file = test_input_file('pictogram.fa');
my $sio = Bio::SeqIO->new(-file=>$file,-format=>'fasta');
my @seq;
while(my $seq = $sio->next_seq){
  push @seq, $seq;
}
my $picto = Bio::Draw::Pictogram->new(-width=>"800",
									-fontsize=>"80",
									-plot_bits=>1,
									-color=>{'A'=>'red',
											 'G'=>'blue',
											 'C'=>'green',
											 'T'=>'magenta'});
isa_ok $picto,"Bio::Draw::Pictogram";

my $svg = $picto->make_svg(\@seq);
ok $svg->xmlify;

my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'meme', 
                                   -file=> test_input_file('meme.dat'));
$picto = Bio::Draw::Pictogram->new(-width=>"800",
									-normalize=>1,
									-fontsize=>"80",
									-plot_bits=>1,
									-color=>{'A'=>'red',
											 'G'=>'blue',
											 'C'=>'green',
											 'T'=>'magenta'});

my $psm = $psmIO->next_psm;
$svg = $picto->make_svg($psm);
ok $svg->xmlify;
BioPerl-1.007002/t/LiveSeq000755000766000024          013155576321 15172 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/LiveSeq/Chain.t000444000766000024       605213155576321 16541 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$


use strict;

BEGIN { 
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 45);
    
	use_ok('Bio::LiveSeq::Chain');
}

# this script tests Bio::LiveSeq::Chain methods directly since it isn't OO:
# Bio::LiveSeq::Chain->new() isn't expected here.

my $chain = Bio::LiveSeq::Chain::string2chain("abcdefghijklmnopqrstuvwxyz");
ok defined $chain;
is( Bio::LiveSeq::Chain::down_chain2string($chain), 
    "abcdefghijklmnopqrstuvwxyz");
is( Bio::LiveSeq::Chain::down_chain2string($chain,undef,4),
    "abcd"); # default start=1
my ($warning,$output);
eval {
  local $SIG{__WARN__}=sub{ $warning=$_[0]};
  $output=Bio::LiveSeq::Chain::down_chain2string($chain,1,4,6);
};
is (((index($warning,"Warning chain2string: argument LAST:6 overriding LEN:4!")==0)&&($output eq "abcdef")),1);
my $arrayref=Bio::LiveSeq::Chain::down_labels($chain,1,4);
is $arrayref->[1], 2;
$arrayref=Bio::LiveSeq::Chain::up_labels($chain,4,1);
is $arrayref->[1], 3;
$arrayref=Bio::LiveSeq::Chain::up_labels($chain);
is scalar(@{$arrayref}), 26; # total number of labels should be 26
is Bio::LiveSeq::Chain::start($chain), '1';
is Bio::LiveSeq::Chain::end($chain), '26';
ok Bio::LiveSeq::Chain::label_exists($chain,'4');
is Bio::LiveSeq::Chain::label_exists($chain,'28'), '0';
is Bio::LiveSeq::Chain::down_get_pos_of_label($chain,4), '4';
is Bio::LiveSeq::Chain::down_get_pos_of_label($chain,4,4), '1';
is Bio::LiveSeq::Chain::up_get_pos_of_label($chain,26,1), '1';
is Bio::LiveSeq::Chain::down_subchain_length($chain,1,4), '4';
is Bio::LiveSeq::Chain::up_subchain_length($chain,4,1), '4';
ok Bio::LiveSeq::Chain::invert_chain($chain);
ok Bio::LiveSeq::Chain::invert_chain($chain);
is Bio::LiveSeq::Chain::down_get_value_at_pos($chain,4), 'd';
is Bio::LiveSeq::Chain::down_get_value_at_pos($chain,1,4), 'd';
is Bio::LiveSeq::Chain::up_get_value_at_pos($chain,4), 'w';

ok Bio::LiveSeq::Chain::up_set_value_at_pos($chain,'W',4);
is Bio::LiveSeq::Chain::up_get_value_at_pos($chain,4), 'W';

ok Bio::LiveSeq::Chain::down_set_value_at_pos($chain,'D',4); 
is Bio::LiveSeq::Chain::down_get_value_at_pos($chain,4), 'D';

ok Bio::LiveSeq::Chain::set_value_at_label($chain,'d',4);
is Bio::LiveSeq::Chain::get_value_at_label($chain,4), 'd';

is Bio::LiveSeq::Chain::down_get_label_at_pos($chain,1,4), '4';
is Bio::LiveSeq::Chain::up_get_label_at_pos($chain,4), '23';
ok Bio::LiveSeq::Chain::is_downstream($chain,3,4);
is Bio::LiveSeq::Chain::is_downstream($chain,4,3), '0';
ok Bio::LiveSeq::Chain::is_upstream($chain,4,3);
is Bio::LiveSeq::Chain::is_upstream($chain,3,4), '0';
is Bio::LiveSeq::Chain::splice_chain($chain,4,2), 'de';
is Bio::LiveSeq::Chain::splice_chain($chain,7,undef,9), 'ghi';

my @array=Bio::LiveSeq::Chain::praeinsert_string($chain,"ghi",10);
is $array[0],27;
is $array[1],29;

@array=Bio::LiveSeq::Chain::postinsert_string($chain,"de",3);
is $array[0], 30;
is $array[1], 31;
is Bio::LiveSeq::Chain::up_chain2string($chain), "zyxWvutsrqponmlkjihgfedcba";

@array=Bio::LiveSeq::Chain::check_chain($chain);
is $array[0], 1;
is $array[1], 1;
is $array[2], 1;
is $array[3], 1;
BioPerl-1.007002/t/LiveSeq/LiveSeq.t000444000766000024       505113155576321 17065 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$


use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 48,
               -requires_module => 'IO::String');
	
	use_ok('Bio::LiveSeq::IO::BioPerl');
}

my $loader=Bio::LiveSeq::IO::BioPerl->load(-db=>"EMBL", 
					   -file=>test_input_file('factor7.embl'));
ok $loader;
my $gene=$loader->gene2liveseq(-gene_name => "factor7");
ok $gene;
ok ref($gene), "Bio::LiveSeq::Gene";
is $gene->name, "factor7";
is $gene->get_DNA->alphabet, "dna";
is $gene->get_DNA->display_id, "HSCFVII";
is $gene->get_DNA->accession_number, "J02933";
is $gene, $gene->get_DNA->gene;
is $gene->get_DNA->desc, "Human blood coagulation factor VII gene, complete cds.";
is $gene->get_DNA->source, "Homo sapiens";
is $gene->get_DNA->start, 1;
is $gene->get_DNA->end, 12850;
is $gene->maxtranscript->start, 487;
is $gene->maxtranscript->end, 12686;
is $gene->upbound, 487;
is $gene->downbound, 12686;
ok not(defined($gene->get_Repeat_Units));

my @exons   = @{$gene->get_Exons};
my @introns = @{$gene->get_Introns};
is scalar(@exons), 9;
is scalar(@introns), 8;
is $introns[4]->desc, "Intron D";
is $introns[4]->start, 6592;
is $introns[4]->end, 8306;
is $exons[1]->desc, "optional";
is $exons[4]->end, 6591;

my $transcript  = $gene->get_Transcripts->[0];
my $translation = $gene->get_Translations->[0];
is $transcript , $translation->get_Transcript;
is $translation , $transcript->get_Translation;

@exons = $transcript->all_Exons;
is $exons[4]->end , 6591;
is $exons[4]->length , 114;
is $transcript->upstream_seq, "tcaacaggcaggggcagcactgcagagatttcatc";
is substr($transcript->downstream_seq,0,16), "cccagcagccctggcc";
is $transcript->position($transcript->label(666)), 666;
is $transcript->position($transcript->label(666),9419), 95;
is $transcript->labelsubseq(8447,undef,9419), "gt";
is $transcript->labelsubseq(8447,2), "gt";
is $gene->get_DNA->labelsubseq(8447,2), "gg";
is substr($gene->get_DNA->labelsubseq(8447,undef,9419),0,16), "ggtgaccaggcttcat";
is $gene->get_DNA, $transcript->{seq};
my ($nothing,$whichexon) = $transcript->in_which_Exon(9419);
is $whichexon , 7;
is $transcript->frame(9419) , 1;
is $transcript->frame(9420) , 2;
is substr($translation->seq,0,16), "MVSQALRLLCLLLGLQ";
is substr($transcript->seq,0,32), "atggtctcccaggccctcaggctcctctgcct";
ok $transcript->translation_table(2);
is $transcript->translation_table , 2;
is substr($translation->seq,0,16), "MVSQAL*"; # mitochondrial table creates stop codon
is $gene->verbose(2), 2;
ok $gene->delete_Obj(); # to free all memory, deleting circular references
BioPerl-1.007002/t/LiveSeq/Mutation.t000444000766000024       156713155576321 17325 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 19);
	
	use_ok('Bio::LiveSeq::Mutation');
}


my $a = Bio::LiveSeq::Mutation->new();
ok defined $a;

$a->seq('aaa');
is $a->seq, 'aaa';

$a->seqori('ggg');
is $a->seqori, 'ggg';

$a->pos(-4);
is $a->pos, -4;

$a->pos(5);
is $a->pos, 5;

is ($a->len, 3);

$a->len(9);
is ($a->len, 9);

$a->transpos(55);
is $a->transpos, 55;

$a->issue(1);
is $a->issue, 1;

$a->label(57);
is $a->label, '57';

$a->prelabel(57);
is $a->prelabel, '57';

$a->postlabel(57);
is $a->postlabel, '57';

$a->lastlabel(57);
is $a->lastlabel, '57';

#constuctor test
$b = Bio::LiveSeq::Mutation->new('-seq'=>'AC',
				 '-seqori' => 'GG',
				 '-pos' => 5,
				 '-len' => 2,
				 );
ok  defined $b;
is $b->seqori, 'GG';
is $b->len, 2;
is $b->seq, 'AC';
is $b->pos, 5;
BioPerl-1.007002/t/LiveSeq/Mutator.t000444000766000024       415613155576321 17155 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 24,
			   -requires_module => 'IO::String');
	
	use_ok('Bio::LiveSeq::Mutator');
	use_ok('Bio::LiveSeq::IO::BioPerl');
	use_ok('Bio::Variation::IO');
}

$a = Bio::LiveSeq::Mutator->new();
ok $a;

is $a->numbering, 'coding';
ok $a->numbering('coding 1');
is $a->numbering, 'coding 1';

my $mt = Bio::LiveSeq::Mutation->new();
ok $mt->seq('g');
$mt->pos(100);
ok ($a->add_Mutation($mt));
my @each = $a->each_Mutation;
is( (scalar @each), 1 );
my $mt_b = pop @each;
is($mt_b->seq, 'g');
my $filename=test_input_file('ar.embl');
my $loader=Bio::LiveSeq::IO::BioPerl->load('-file' => "$filename");
my $gene_name='AR'; # was G6PD

my $gene=$loader->gene2liveseq('-gene_name' => $gene_name);
ok($gene);
ok $a->gene($gene);

my $results = $a->change_gene();
ok($results);

# bug 1701 - mutations on intron/exon boundaries where codon is split 

$loader = Bio::LiveSeq::IO::BioPerl->load( -db   => 'EMBL',
                                -file => test_input_file('ssp160.embl.1')
                        );
# move across intron/exon boundaries, check expected mutations
my @positions = (3128..3129,3188..3189);
my @bases = (qw(C C T T));
my @expected = (qw(T683T T684P T684I T684T));
my $ct = 0;

for my $pos (@positions) {
    # reset gene
    my $gene = $loader->gene2liveseq( -gene_name => 'ssp160');
    my $mutation = Bio::LiveSeq::Mutation->new( -seq => $bases[$ct],
                                                -pos => $pos,
                          );
    my $mutate = Bio::LiveSeq::Mutator->new( -gene      => $gene,
                                             -numbering => 'entry',
                           );
    
    $mutate->add_Mutation( $mutation );

    my $results = $mutate->change_gene();
    
    ok(defined($results));
    is($expected[$ct], $results->trivname);
    $ct++;
}

my $s;
my $io = IO::String->new($s);
my $out = Bio::Variation::IO->new('-fh'   => $io,
                  '-format' => 'flat'
                  );
ok($out->write($results));
ok ($s=~/DNA/ && $s=~/RNA/ && $s=~/AA/);
BioPerl-1.007002/t/LocalDB000755000766000024          013155576321 15062 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/LocalDB/BioDBGFF.t000444000766000024      3235513155576321 16676 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;
use Module::Build;
use Data::Dumper;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 275);
	
	use_ok('Bio::DB::GFF');
}

my $fasta_files = test_input_file('dbfa');
my $gff_file1   = test_input_file('biodbgff', 'test.gff');
my $gff_file2   = test_input_file('biodbgff', 'test.gff3');

my $build = Module::Build->current;
my $test_dsn = $build->notes('test_dsn');

my $adaptor = $test_dsn ? $test_dsn : 'memory';
$adaptor    = shift if @ARGV;

if ($adaptor =~ /sqlite/i) {
    $adaptor = 'memory';
}

my @args;
if ($adaptor =~ /^dbi/) {
  my $cfg = {};
  $cfg->{dbd_driver} = $build->notes('dbd_driver');
  $cfg->{test_db} = $build->notes('test_db');
  $cfg->{test_host} = $build->notes('test_host');
  $cfg->{test_user} = $build->notes('test_user');
  $cfg->{test_pass} = $build->notes('test_pass');
  $cfg->{test_dsn} = $build->notes('test_dsn');
  
  $adaptor = "dbi::$cfg->{dbd_driver}" if $cfg->{dbd_driver};
  @args = ( '-adaptor'  => $adaptor,
	    '-dsn'     => $cfg->{test_dsn},
	  );
  push @args,('-user' => $cfg->{test_user}) if $cfg->{test_user};
  push @args,('-pass' => $cfg->{test_pass}) if $cfg->{test_pass};
} else {
  @args = ('-adaptor' => $adaptor,
	   '-create'  => 1);
}

push @args,('-aggregators' => ['transcript','processed_transcript']);

SKIP: {
for my $FILE ($gff_file1,$gff_file2) {

  my $db = eval { Bio::DB::GFF->new(@args) };
  skip "DB load failed? Skipping all! $@", 278 if $@;
  ok($db);

  $db->debug(0);
  $db->gff3_name_munging(1);

  # set the preferred groups
  $db->preferred_groups( [ 'transcript', 'gene', 'mRNA' ] );
  my @pg = $db->preferred_groups;
  is(scalar(@pg), 3);
  is($pg[1], 'gene'); 

  # exercise the loader
  ok($db->initialize(1));
  ok($db->load_gff($FILE));
  ok($db->load_fasta($fasta_files));

  # exercise db->types
  my @types = sort $db->types;
  is(scalar @types,11);
  is($types[0],'CDS:confirmed');
  is($types[-1],'transposon:tc1');
  my %types = $db->types('-enumerate'=>1);
  is($types{'transposon:tc1'},2);

  # exercise segment
  my $segment1 = $db->segment('Contig1');

  ok($segment1);
  is($segment1->length,37450);
  is($segment1->start,1);
  is($segment1->end,37450);
  is($segment1->strand,1);
  
  my $segment2  = $db->segment('Contig1',1=>1000);
  is($segment2->length,1000);
  is($segment2->start,1);
  is($segment2->end,1000);
  is($segment2->strand,1);
  
  my $segment3 = $db->segment('Contig1',10=>1);
  is($segment3->start,10);
  is($segment3->end,1);
  is($segment3->strand,-1);

  # exercise attribute fetching
  my @t = $db->fetch_feature_by_name(Transcript => 'trans-1');
  my ($t) = grep {$_->type eq 'transcript:confirmed'} @t;
  is($t->attributes('Note'),'function unknown');
  is(join(' ',sort $t->attributes('Gene')),'abc-1 xyz-2');
  my $att = $t->attributes;
  is(scalar @{$att->{Gene}},2);
  @t = sort {$a->display_name cmp $b->display_name} $db->fetch_feature_by_attribute('Gene'=>'abc-1');
  cmp_ok(@t,'>',0);
  is($t[0], $t);
  my $seg = $db->segment('Contig1');
  @t = $seg->features(-attributes=>{'Gene'=>'abc-1'});
  cmp_ok(@t,'>',0);
  is($seg->feature_count, 17);
  @t = $seg->features(-attributes=>{'Gene'=>'xyz-2',Note=>'Terribly interesting'});
  is(@t,1);

  # exercise dna() a bit
  my $dna = $segment2->dna;
  is(length $dna,1000);
  is(substr($dna,0,10),'gcctaagcct');
  is($segment3->dna,'aggcttaggc');
  is($segment1->dna, $db->dna($segment1->ref));

  # exercise ref()
  my $segment4 = $db->segment('-name'=>'c128.1','-class'=>'Transposon');
  is($segment4->length,1000);
  is($segment4->start,1);
  is($segment4->end,1000);
  is($segment4->ref,'c128.1');
  is($segment4->strand,1);
  ok(!$segment4->absolute);

  $segment4->absolute(1);
  ok($segment4->absolute);
  is($segment4->ref,'Contig1');
  is($segment4->start,5001);
  $segment4->absolute(0);
  my $tmp = $db->segment('Contig1',5001=>6000);
  is($segment4->dna,$tmp->dna);

  $segment4->ref('Contig1');
  is($segment4->ref,'Contig1');
  is($segment4->start,5001);
  is($segment4->end,6000);

  my $segment5 = $db->segment('-name'=>'c128.2','-class'=>'Transposon');
  is($segment5->length,1000);
  is($segment5->start,1);
  is($segment5->end,1000);
  is($segment5->ref,'c128.2');
  is($segment5->strand,1);

  $tmp = $db->segment('Contig1',9000,8001);
  is($segment5->dna,$tmp->dna);
  $segment5->absolute(1);
  is($segment5->strand,-1);

  # rel/rel addressing
  # first two positive strand features
  $segment4 = $db->segment('-name'=>'c128.1','-class'=>'Transposon');
  my $start4 = $segment4->abs_start;
  $segment5  = $db->segment('Transcript' => 'trans-1');
  my $start5 = $segment5->abs_start;
  $segment4->ref($segment5);
  is($segment4->strand,1);
  is($segment4->start,$start4-$start5+1);
  is($segment4->stop,$start4-$start5+$segment4->length);

  $segment4->ref('Transposon' => 'c128.1');
  $segment5->ref('Transcript' => 'trans-1');
  $segment5->ref($segment4);
  is($segment5->start,$start5-$start4+1);

  # now a positive on a negative strand feature
  my $segment6 = $db->segment('Transcript'=>'trans-2');
  my $start6 = $segment6->abs_start;
  is($segment6->strand,1);
  is($segment6->abs_strand,-1);
  $segment6->ref($segment4);
  is($segment6->start,$start6-$start4+1);
  is($segment6->strand,-1);

  $segment4->ref($segment6);
  is($segment4->start,$start6-$start4+1);
  is($segment4->strand,-1);
  is($segment4->ref,$segment6);

  # the reference sequence shouldn't affect the dna
  $segment6 = $db->segment('Transcript'=>'trans-2');
  $dna = $segment6->dna;
  $segment6->ref($segment4);
  is($segment6->dna,$dna);

  # segments should refuse to accept a reference sequence on a foreign segment
  undef $@;
  my $result = eval { $segment6->ref('Contig2') };
  ok(!$result);
  like($@, qr/are on different sequence segments/);

  # types across a segment
  $segment1 = $db->segment('Contig1');
  @types = sort $segment1->types;
  is(scalar @types,6);
  is($types[0],'CDS:confirmed');
  is($types[-1],'transposon:tc1');
  %types = $segment1->types('-enumerate'=>1);
  is($types{'similarity:est'},3);

  # features across a segment
  my @features = $segment1->features('-automerge'=>0);
  is(scalar @features,17);
  my %types_seen;
  foreach (@features) {
    $types_seen{$_->type}++;
  }
  my $inconsistency = 0;
  foreach (keys %types,keys %types_seen) {
    $inconsistency++ unless $types_seen{$_} == $types{$_};
  }
  ok(!$inconsistency);

  @features = sort {$a->start<=>$b->start} @features;

  # make sure that we can use features to get at dna
  is($features[0]->dna,$db->segment('Contig1',$features[0]->start,$features[0]->end)->dna);

  # check three forward features and three reverse features
  # (This depends on the test.gff data)
  for (1..3,-3..-1) {
    $segment2 = $db->segment($features[$_],50,100);
    if ($features[$_]->strand >= 0) {
      is($segment2->dna,$db->segment('Contig1',
				     $features[$_]->start+50-1,
				     $features[$_]->start+100-1)->dna)
    } else {
      is($segment2->dna,$db->segment('Contig1',
				     $features[$_]->start-50+1,
				     $features[$_]->start-100+1)->dna)
    }
  }

  # exercise the aggregator
  my $aggregator = Bio::DB::GFF::Aggregator->new('-method'      => 'aggregated_transcript',
						 '-main_method' => 'transcript',
						 '-sub_parts'   => ['exon','CDS']);
  $db->add_aggregator($aggregator);
  $segment1 = $db->segment('Contig1');
  @features = sort $segment1->features('aggregated_transcript');   # sort so that trans-1 comes first
  is(scalar @features,2);
  cmp_ok($features[0]->Exon, '>', 0);
  cmp_ok($features[0]->Cds,'>', 0);

  # Test that sorting is correct.  The way that test.gff is set up, the lower one is
  # on the + strand and the higher is on the -.
  @features = sort {$a->start <=> $b->start} @features;
  is($features[0]->strand,1);
  is($features[1]->strand,-1);

  my $last = 0;
  $inconsistency = 0;
  foreach ($features[0]->Exon) {
    $inconsistency++ if $_->start > $_->end;
    $inconsistency++ if $last && $_->start < $last;
    $last = $_->start;
  }
  ok(!$inconsistency);

  $inconsistency = $last = 0;
  foreach ($features[1]->Exon) {
    $inconsistency++ if $_->start < $_->end;
    $inconsistency++ if $last && $_->start > $last;
    $last = $_->start;
  }
  ok(!$inconsistency);
  
  # relative addressing in aggregated features
  my $transcript1 = $db->segment($features[0]);
  $transcript1->ref($features[0]);
  my @overlap     = sort {$a->start <=> $b->start } $transcript1->features;
  is(scalar(@overlap),5);
  is($overlap[0]->start,-999);

  $transcript1 = $db->segment('Transcript' => 'trans-1');
  @overlap     = sort {$a->start <=> $b->start } $transcript1->features;
  is($overlap[0]->start,-999);

  # test strandedness of features
  $segment1 = $db->segment('-class' => 'Transcript',
			   '-name'  => 'trans-3',
			   '-start' => 1,
			   '-stop'  => 6000);
  is($segment1->strand,1);
  @overlap  = sort {$a->start <=> $b->start} $segment1->features('transcript');
  is(scalar(@overlap),2);
  is($overlap[0]->name,'trans-3');
  is($overlap[1]->name,'trans-4');
  is($overlap[0]->strand,1);
  is($overlap[1]->strand,-1);

  # testing feature id and group_id
  my $tf = $overlap[0];
  ok(defined $tf->id);
  my $t1 = $db->fetch_feature_by_id($tf->id);
  is($t1->id,$tf->id);

  SKIP: {
    if (defined $tf->group_id) {
      my $t2 = $db->fetch_feature_by_gid($tf->group_id);
      is($t2->group_id,$tf->group_id);
      is($t2->group_id,$t1->group_id);
    } else {
      skip("fetch_feature_by_gid() not implemented by this adaptor",2);
    }
  }

  $segment1 = $db->segment('-class' => 'Transcript',
			   '-name'  => 'trans-4',
			   '-start' => 1,
			   '-stop'  => 6000);
  is($segment1->strand,1);
  @overlap = sort {$a->start <=> $b->start} $segment1->features('transcript');
  is($overlap[0]->name,'trans-4');
  is($overlap[1]->name,'trans-3');
  is($overlap[0]->strand,1);
  is($overlap[1]->strand,-1);

  @overlap = sort {$a->start <=> $b->start} $segment1->features('Component');
  is($overlap[0]->strand,0);

SKIP: {
  # test preferred group assignments
  if ($FILE =~ /\.gff$/) {
    my @gene = $db->get_feature_by_name( gene => 'gene-9' );
    my @mrna = $db->get_feature_by_name( mRNA => 'trans-9' );
    is($gene[0]->ref, 'Contig4');
    is(scalar(@gene), 2);
    is(scalar(@mrna), 1);
  } else {
    skip('preferred groups are not supported by gff3',3);
  }
}

  # test iterator across a segment
  $segment1 = $db->segment('Contig1');
  my $i = $segment1->features('-automerge'=>0,'-iterator'=>1);
  my %strand;
  while (my $s = $i->next_feature) {
    $strand{$s->strand}++;
  }
  is(keys %strand, 3);

  # test iterator across entire database
  $i = $db->features('-automerge'=>0,'-iterator'=>1);
  %strand = ();
  while (my $s = $i->next_feature) {
    $strand{$s->strand}++;
  }
  is(keys %strand, 3);

  # test iterator across a segment, limited by an attribute
  $i = $seg->get_feature_stream(-attributes=>{'Gene'=>'abc-1',Note=>'function unknown'});
  my $count = 0;
  while ($i->next_seq) {
    $count++;
  }
  is($count,2);

  # test that aliases work
  my $st1 = $db->segment(Transcript => 'trans-3');
  ok($st1);
  my $st2 = $db->segment(Transcript => 'trans-18');  # this is an alias!
  ok($st2);
  is($st1,$st2);
  my @transcripts = $st1->features('transcript');
  is(($transcripts[0]->aliases)[0],'trans-18');

  # test truncation
  $db->strict_bounds_checking(1);
  my $tseg = $db->segment(-name=>'trans-1',-class=>'Transcript',-start=>1,-stop=>500);
  ok(!$tseg->truncated);
  $tseg    = $db->segment(-name=>'trans-1',-class=>'Transcript',-start=>1,-stop=>50000);
  ok($tseg->truncated);
  $db->strict_bounds_checking(0);
  $tseg    = $db->segment(-name=>'trans-1',-class=>'Transcript',-start=>1,-stop=>50000);
  ok(!$tseg->truncated);

  # test the processed_transcript aggregator
  $db->clear_aggregators;
  $db->add_aggregator('processed_transcript');
  my @f = $db->fetch_feature_by_name(mRNA => 'trans-8');
  is(scalar @f,1);
  is($f[0]->length,35000-32000+1);
  is(scalar $f[0]->CDS,3);
  is(scalar $f[0]->UTR,2);

  # test deletions
  # segment delete() method
  my $clone = $db->segment(Clone=>'M7.3');
  my $overlapping_feature_count = $clone->features(-range_type =>'overlaps');
  my $contained_feature_count   = $clone->features(-range_type =>'contains');
  is(scalar $clone->delete(-range_type=>'contains'),$contained_feature_count);
  is(scalar $clone->features,$overlapping_feature_count - $contained_feature_count);

  # database delete() method
  is($db->delete(-type=>['mRNA:confirmed','transposon:tc1']),4);
  is($db->delete(-type=>'UTR',-ref=>'Contig29'),undef);
  is($db->delete(-type=>'CDS',-ref=>'AL12345.2',-class=>'Clone'),3);
  is($db->delete_features(1,2,3),3);

  SKIP: {
    $result = eval {
      is($db->delete_groups(1,2,3,4,5),5);
      my @features = $db->get_feature_by_name(Sequence => 'Contig2');
      is($db->delete_groups(@features),1);
      1;
    };
    if (!$result && $@ =~ /not implemented/i) {
      skip("delete_groups() not implemented by this adaptor",2);
    }
  }
  
  SKIP: {
	test_skip(-tests => 1, -excludes_os => 'mswin');
	
	# test ability to pass adaptors across a fork
	if (my $child = open(F,"-|")) { # parent reads from child
		ok(scalar );
		close F;
	}
	else { # in child
		$db->clone;
		my @f = $db->features();
		print @f>0;
		exit 0;
	}
  }

  ok(!defined eval{$db->delete()});
  ok($db->delete(-force=>1));
  is(scalar $db->features,0);
  ok(!$db->segment('Contig1'));

}

}



END {
  unlink $fasta_files."/directory.index";
}
BioPerl-1.007002/t/LocalDB/Fasta.t000444000766000024      3434213155576321 16470 0ustar00cjfieldsstaff000000000000BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin( -tests => 109,
                -requires_modules => [qw(Bio::DB::Fasta Bio::SeqIO)] );
}
use strict;
use warnings;
use Bio::Root::Root;
use File::Copy;
my $DEBUG = test_debug();


# Test Bio::DB::Fasta, but also the underlying module, Bio::DB::IndexedBase

my $test_dir  = setup_temp_dir('dbfa');
my $test_file = test_input_file('dbfa', 'mixed_alphabet.fasta');
my $test_files = [
    test_input_file('dbfa', 'mixed_alphabet.fasta'),
    test_input_file('dbfa', '6.fa')
];


{
    # Test basic functionalities
    ok my $db = Bio::DB::Fasta->new($test_dir, -reindex => 1), 'Index a directory';
    is $db->glob, '*.{fa,FA,fasta,FASTA,fast,FAST,dna,DNA,fna,FNA,faa,FAA,fsa,FSA}';
    isa_ok $db, 'Bio::DB::Fasta';
    is $db->length('CEESC13F'), 389;
    is $db->seq('CEESC13F:1,10'), 'cttgcttgaa';
    is $db->seq('CEESC13F:1-10'), 'cttgcttgaa';
    is $db->seq('CEESC13F:1..10'), 'cttgcttgaa';
    is $db->seq('CEESC13F:1..10/1'), 'cttgcttgaa';
    is $db->seq('CEESC13F:1..10/+1'), 'cttgcttgaa';
    is $db->seq('CEESC13F:1..10/-1'), 'ttcaagcaag';
    is $db->seq('CEESC13F/1'), 'cttgcttgaaaaatttatataaatatttaagagaagaaaaataaataatcgcatctaatgacgtctgtccttgtatccctggtttccattgactggtgcactttcctgtctttgaggacatggacaatattcggcatcagttcctggctctccctcctctcctggtgctccagcagaaccgttctctccattatctcccttgtctccacgtggtccacgctctcctggtgctcctggaataccttgagctccctcgtgccgaattcctgcagcccgggggatccactagttctagagcggccgccaccgcggtgggagctccagcttttgttncctttagtgagggttaatttcgagcttggcgtaatcatggtcatagctgtttcctg';
    is $db->seq('CEESC13F/-1'), 'caggaaacagctatgaccatgattacgccaagctcgaaattaaccctcactaaaggnaacaaaagctggagctcccaccgcggtggcggccgctctagaactagtggatcccccgggctgcaggaattcggcacgagggagctcaaggtattccaggagcaccaggagagcgtggaccacgtggagacaagggagataatggagagaacggttctgctggagcaccaggagaggagggagagccaggaactgatgccgaatattgtccatgtcctcaaagacaggaaagtgcaccagtcaatggaaaccagggatacaaggacagacgtcattagatgcgattatttatttttcttctcttaaatatttatataaatttttcaagcaag';
    is $db->seq('AW057119', 1, 10), 'tcatgttggc';
    is $db->seq('AW057119', 1, 10, 1), 'tcatgttggc';
    is $db->seq('AW057119', 1, 10, -1), 'gccaacatga';
    is $db->seq('AW057119', 10, 1), 'gccaacatga';
    is $db->seq('AW057119', 10, 1, -1), 'tcatgttggc';
    is $db->header('AW057119'), 'AW057119 test description';
    is $db->seq('foobarbaz'), undef;
    is $db->get_Seq_by_id('foobarbaz'), undef;
    is $db->file('AW057119'), '1.fa';
    is $db->file('AW057410'), '3.fa';
    is $db->file('CEESC13F'), '6.fa';

    # Bio::DB::RandomAccessI and Bio::DB::SeqI methods
    ok my $primary_seq = $db->get_Seq_by_id('AW057119');
    ok $primary_seq = $db->get_Seq_by_acc('AW057119');
    ok $primary_seq = $db->get_Seq_by_version('AW057119');
    ok $primary_seq = $db->get_Seq_by_primary_id('AW057119');
    isa_ok $primary_seq, 'Bio::PrimarySeq::Fasta';
    isa_ok $primary_seq, 'Bio::PrimarySeqI';

    # Bio::PrimarySeqI methods
    is $primary_seq->id, 'AW057119';
    is $primary_seq->display_id, 'AW057119';
    like $primary_seq->primary_id, qr/^Bio::PrimarySeq::Fasta=HASH/;
    is $primary_seq->alphabet, 'dna';
    is $primary_seq->accession_number, 'unknown';
    is $primary_seq->is_circular, undef;
    is $primary_seq->subseq(11, 20), 'ttctcggggt';
    is $primary_seq->description, 'test description', 'bug 3126';
    is $primary_seq->seq, 'tcatgttggcttctcggggtttttatggattaatacattttccaaacgattctttgcgccttctgtggtgccgccttctccgaaggaactgacgaaaaatgacgtggatttgctgacaaatccaggcgaggaatatttggacggattgatgaaatggcacggcgacgagcgacccgtgttcaaaagagaggacatttatcgttggtcggatagttttccagaatatcggctaagaatgatttgtctgaaagacacgacaagggtcattgcagtcggtcaatattgttactttgatgctctgaaagaaaggagagcagccattgttcttcttaggattgggatggacggatcctgaatatcgtaatcgggcagttatggagcttcaagcttcgatggcgctggaggagagggatcggtatccgactgccaacgcggcatcgcatccaaataagttcatgaaacgattttggcacatattcaacggcctcaaagagcacgaggacaaaggtcacaaggctgccgctgtttcatacaagagcttctacgacctcanagacatgatcattcctgaaaatctggatgtcagtggtattactgtaaatgatgcacgaaaggtgccacaaagagatataatcaactacgatcaaacatttcatccatatcatcgagaaatggttataatttctcacatgtatgacaatgatgggtttggaaaagtgcgtatgatgaggatggaaatgtacttggaattgtctagcgatgtctttanaccaacaagactgcacattagtcaattatgcagatagcc';
    ok my $trunc = $primary_seq->trunc(11,20);
    isa_ok $trunc, 'Bio::PrimarySeq::Fasta';
    isa_ok $trunc, 'Bio::PrimarySeqI';
    is $trunc->length, 10;
    is $trunc->seq, 'ttctcggggt';
    ok my $rev = $trunc->revcom;
    isa_ok $rev, 'Bio::PrimarySeq::Fasta';
    isa_ok $rev, 'Bio::PrimarySeqI';
    is $rev->seq, 'accccgagaa';
    is $rev->length, 10;
}


{
    # Re-open an existing index.
    # Doing this test properly involves unloading and reloading Bio::DB::Fasta.

    SKIP: {
        test_skip(-tests => 1, -requires_modules => [qw(Class::Unload)]);
        use_ok('Class::Unload');
        Class::Unload->unload( 'Bio::DB::Fasta' );
        Class::Unload->unload( 'Bio::DB::IndexedBase' );
        require Bio::DB::Fasta;
    }

    ok my $db = Bio::DB::Fasta->new($test_dir), 'Re-open an existing index';
    is $db->seq('AW057119', 1, 10), 'tcatgttggc';
}


{
    # Test tied hash access
    my %h;
    ok tie(%h, 'Bio::DB::Fasta', $test_dir), 'Tied hash access';
    ok exists $h{'AW057146'};
    is $h{'AW057146:1,10'} , 'aatgtgtaca'; # in file 1.fa
    is $h{'AW057146:10,1'} , 'tgtacacatt'; # reverse complement
    is $h{'AW057443:11,20'}, 'gaaccgtcag'; # in file 4.fa
}


{
    # Test writing the Bio::PrimarySeq::Fasta objects with SeqIO
    ok my $db = Bio::DB::Fasta->new($test_dir, -reindex => 1), 'Writing with SeqIO';
    my $out = Bio::SeqIO->new(
        -format => 'genbank',
        -file   => '>'.test_output_file()
    );
    my $primary_seq = Bio::Seq->new(-primary_seq => $db->get_Seq_by_acc('AW057119'));
    eval {
        $out->write_seq($primary_seq)
    };
    is $@, '';

    $out = Bio::SeqIO->new(-format => 'embl', -file  => '>'.test_output_file());
    eval {
        $out->write_seq($primary_seq)
    };
    is $@, '';
}


{
    # Test alphabet and reverse-complement RNA
    ok my $db = Bio::DB::Fasta->new( $test_file, -reindex => 1), 'Index a single file';
    is $db->alphabet('gi|352962132|ref|NG_030353.1|'), 'dna';
    is $db->alphabet('gi|352962148|ref|NM_001251825.1|'), 'rna';
    is $db->alphabet('gi|194473622|ref|NP_001123975.1|'), 'protein';
    is $db->alphabet('gi|61679760|pdb|1Y4P|B'), 'protein';
    is $db->alphabet('123'), '';
    is $db->seq('gi|352962148|ref|NM_001251825.1|', 20, 29,  1), 'GUCAGCGUCC';
    is $db->seq('gi|352962148|ref|NM_001251825.1|', 20, 29, -1), 'GGACGCUGAC';

    # Test empty sequence
    is $db->seq('123'), '';

    is $db->file('gi|352962132|ref|NG_030353.1|'), 'mixed_alphabet.fasta';
}


{
    # Test stream
    ok my $db = Bio::DB::Fasta->new( $test_file, -reindex => 1);
    ok my $stream = $db->get_PrimarySeq_stream;
    isa_ok $stream, 'Bio::DB::Indexed::Stream';    
    my $count = 0;
    
    # note use of modified iterator, needed b/c of overloading
    while (defined(my $seq = $stream->next_seq)) {
        $count++;
    }
    is $count, 7;
    
    # bug #170 (Github)
    # retrieve seq with ID of 0
    my $seq = $db->get_Seq_by_id(0);
    isa_ok $seq, 'Bio::PrimarySeq::Fasta';
    is $seq->display_id, 0;
    
    # ActivePerl will not allow deletion if the tie-hash is still active
    $db->DESTROY;
    # Strawberry Perl temporary file
    unlink "$test_file.index" if -e "$test_file.index";
    # ActivePerl temporary files
    unlink "$test_file.index.dir" if -e "$test_file.index.dir";
    unlink "$test_file.index.pag" if -e "$test_file.index.pag";
}


{
    # Concurrent databases (bug #3390)
    ok my $db1 = Bio::DB::Fasta->new( test_input_file('dbfa', '1.fa') );
    ok my $db3 = Bio::DB::Fasta->new( test_input_file('dbfa', '3.fa') );
    ok my $db4 = Bio::DB::Fasta->new( $test_dir );
    ok my $db2 = Bio::DB::Fasta->new( test_input_file('dbfa', '2.fa') );
    is $db4->file('AW057231'), '1.fa';
    is $db2->file('AW057302'), '2.fa';
    is $db4->file('AW057119'), '1.fa';
    is $db3->file('AW057336'), '3.fa';
    is $db1->file('AW057231'), '1.fa';
    is $db4->file('AW057410'), '3.fa';

    # ActivePerl will not allow deletion if the tie-hash is still active
    $db1->DESTROY;
    $db2->DESTROY;
    $db3->DESTROY;
    # Strawberry Perl temporary file
    unlink $db1->index_name if -e $db1->index_name;
    unlink $db2->index_name if -e $db2->index_name;
    unlink $db3->index_name if -e $db3->index_name;
    # ActivePerl temporary files
    unlink $db1->index_name().'.dir' if -e $db1->index_name().'.dir';
    unlink $db2->index_name().'.dir' if -e $db2->index_name().'.dir';
    unlink $db3->index_name().'.dir' if -e $db3->index_name().'.dir';
    unlink $db1->index_name().'.pag' if -e $db1->index_name().'.pag';
    unlink $db2->index_name().'.pag' if -e $db2->index_name().'.pag';
    unlink $db3->index_name().'.pag' if -e $db3->index_name().'.pag';
}


{
    # Test an arbitrary index filename and cleaning
    my $name = 'arbitrary.idx';
    ok my $db = Bio::DB::Fasta->new( $test_file,
        -reindex => 1, -index_name => $name, -clean => 1,
    );
    is $db->index_name, $name;

    # Tied-hash in Strawberry Perl produce $name,
    # while in ActivePerl produce "$name.dir" and "$name.pag"
    if (-e "$name.pag") {
        ok -f "$name.pag";
        # ActivePerl will not allow deletion if the tie-hash is still active
        $db->DESTROY;
        unlink "$name.dir" if -e "$name.dir";
        unlink "$name.pag" if -e "$name.pag";
        ok ! -f "$name.pag";
    }
    else {
        ok -f $name;
        # ActivePerl will not allow deletion if the tie-hash is still active
        $db->DESTROY;
        unlink $name if -e $name;
        ok ! -f $name;
    }
    undef $db;
}


{
    # Test makeid
    ok my $db = Bio::DB::Fasta->new( $test_file,
        -reindex => 1, -clean => 1, -makeid => \&extract_gi,
    ), 'Make single ID';
    is_deeply [sort $db->get_all_primary_ids], ['', 194473622, 352962132, 352962148, 61679760];
    is $db->get_Seq_by_id('gi|352962148|ref|NM_001251825.1|'), undef;
    isa_ok $db->get_Seq_by_id(194473622), 'Bio::PrimarySeqI';
}


{
    # Test makeid that generates several IDs, bug #3389
    ok my $db = Bio::DB::Fasta->new( $test_file,
        -reindex => 1, -clean => 1, -makeid => \&extract_gi_and_ref,
    ), 'Make multiple IDs, bug #3389';
    is_deeply [sort $db->get_all_primary_ids], ['', 194473622, 352962132, 352962148, 61679760, 'NG_030353.1',  'NM_001251825.1', 'NP_001123975.1'];
    is $db->get_Seq_by_id('gi|352962148|ref|NM_001251825.1|'), undef;
    isa_ok $db->get_Seq_by_id('NG_030353.1'), 'Bio::PrimarySeqI';
}


{
    # Test opening set of files and test IDs
    ok my $db = Bio::DB::Fasta->new( $test_files, -reindex => 1), 'Index a set of files';
    ok $db->ids;
    ok $db->get_all_ids;
    my @ids = sort $db->get_all_primary_ids();
    is_deeply \@ids, [ qw(
        0
        1
        123
        CEESC12R
        CEESC13F
        CEESC13R
        CEESC14F
        CEESC14R
        CEESC15F
        CEESC15R
        CEESC15RB
        CEESC16F
        CEESC17F
        CEESC17RB
        CEESC18F
        CEESC18R
        CEESC19F
        CEESC19R
        CEESC20F
        CEESC21F
        CEESC21R
        CEESC22F
        CEESC23F
        CEESC24F
        CEESC25F
        CEESC26F
        CEESC27F
        CEESC28F
        CEESC29F
        CEESC30F
        CEESC32F
        CEESC33F
        CEESC33R
        CEESC34F
        CEESC35R
        CEESC36F
        CEESC37F
        CEESC39F
        CEESC40R
        CEESC41F
        gi|194473622|ref|NP_001123975.1|
        gi|352962132|ref|NG_030353.1|
        gi|352962148|ref|NM_001251825.1|
        gi|61679760|pdb|1Y4P|B
    )];
    like $db->index_name, qr/^fileset_.+\.index$/;

    my $index = $db->index_name;
    # ActivePerl will not allow deletion if the tie-hash is still active
    $db->DESTROY;
    # Strawberry Perl temporary file
    unlink $index if -e $index;
    # ActivePerl temporary files
    unlink "$index.dir" if -e "$index.dir";
    unlink "$index.pag" if -e "$index.pag";
}


{
    # Squash warnings locally
    local $SIG{__WARN__} = sub {};

    # Issue 3172
    my $test_dir = setup_temp_dir('bad_dbfa');
    throws_ok {my $db = Bio::DB::Fasta->new($test_dir, -reindex => 1)}
        qr/FASTA header doesn't match/;

    # Issue 3237
    # Empty lines within a sequence is bad...
    throws_ok {my $db = Bio::DB::Fasta->new(test_input_file('badfasta.fa'), -reindex => 1)}
        qr/Blank lines can only precede header lines/;
}


{
    # Issue 3237 again
    # but empty lines preceding headers are okay, but let's check the seqs just in case
    my $db;
    lives_ok {$db = Bio::DB::Fasta->new(test_input_file('spaced_fasta.fa'), -reindex => 1)};
    is length($db->seq('CEESC39F')), 375, 'length is correct in sequences past spaces';
    is length($db->seq('CEESC13F')), 389;

    is $db->subseq('CEESC39F', 51, 60)  , 'acatatganc', 'subseq is correct';
    is $db->subseq('CEESC13F', 146, 155), 'ggctctccct', 'subseq is correct';

    # Remove temporary test file
    my $outfile = test_input_file('spaced_fasta.fa').'.index';

    # ActivePerl will not allow deletion if the tie-hash is still active
    $db->DESTROY;
    # Strawberry Perl temporary file
    unlink $outfile if -e $outfile;
    # ActivePerl temporary files
    unlink "$outfile.dir" if -e "$outfile.dir";
    unlink "$outfile.pag" if -e "$outfile.pag";
}

exit;


sub extract_gi {
    # Extract GI from RefSeq
    my $header = shift;
    my ($id) = ($header =~ /gi\|(\d+)/m);
    return $id || '';
}


sub extract_gi_and_ref {
    # Extract GI and from RefSeq
    my $header = shift;
    my ($gi)  = ($header =~ /gi\|(\d+)/m);
    $gi ||= '';
    my ($ref) = ($header =~ /ref\|([^|]+)/m);
    $ref ||= '';
    return $gi, $ref;
}


sub setup_temp_dir {
    # this obfuscation is to deal with lockfiles by GDBM_File which can
    # only be created on local filesystems apparently so will cause test
    # to block and then fail when the testdir is on an NFS mounted system

    my $data_dir = shift;

    my $io = Bio::Root::IO->new();
    my $tempdir = test_output_dir();
    my $test_dir = $io->catfile($tempdir, $data_dir);
    mkdir($test_dir); # make the directory
    my $indir = test_input_file($data_dir);
    opendir(my $INDIR,$indir) || die("cannot open dir $indir");
    # effectively do a cp -r but only copy the files that are in there, no subdirs
    for my $file ( map { $io->catfile($indir,$_) } readdir($INDIR) ) {
        next unless (-f $file );
        copy($file, $test_dir);
    }
    closedir($INDIR);
    return $test_dir
}
BioPerl-1.007002/t/LocalDB/Flat.t000444000766000024       726213155576321 16301 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 27,
               -requires_module => 'DB_File');

    use_ok('Bio::DB::Flat');
}

my $verbose = test_debug();

# First of all we need to create an flat db

my $tmpdir = test_output_dir();

my $db = Bio::DB::Flat->new(-directory  => $tmpdir,
                            -index      => 'bdb',
                            -dbname     => 'mydb',
                            -format     => 'fasta',
                            -verbose    => $verbose,
                            -write_flag => 1 );
ok($db);
my $dir = test_input_file('AAC12660.fa');
my $result = $db->build_index(glob($dir));
ok($result);

# Now let's get the sequence out again
my $seq = $db->get_Seq_by_id('AAC12660');
ok($seq);
is($seq->length,504);
undef $db;

$db = Bio::DB::Flat->new(-directory  => $tmpdir,
                         -index      => 'bdb',
                         -format     => 'embl',
                         -dbname     => 'myembl',
                         -verbose    => $verbose,
                         -write_flag => 1 );

$dir= test_input_file('cds_sample.embl');

$result = $db->build_index(glob($dir));

is ($db->get_all_primary_ids, 1);
#is ($db->get_all_accs, 1);
ok($result);
$seq = $db->get_Seq_by_id('EAL24309');
ok($seq);
is($seq->length,192);

# deal with wantarray conditions
$seq = $db->get_Seq_by_acc('CH236947.1');
ok($seq && ref($seq));
is($seq->length,192);

undef $db;

$db = Bio::DB::Flat->new(-directory  => $tmpdir,
                         -index      => 'binarysearch',
                         -format     => 'fasta',
                         -dbname     => 'mybinfa',
                         -verbose    => $verbose,
                         -write_flag => 1
                         );

$dir = test_input_file('dbfa', '1.fa');
$result = $db->build_index($dir);
ok($result);
$seq = $db->get_Seq_by_id('AW057119');
ok($seq);
is($seq->length, 808);
$seq = $db->get_Seq_by_id('AW057118');
ok($seq);
is($seq->length, 299);

undef $db;

SKIP: {
    test_skip(-tests => 4, -requires_module => 'Data::Stag');
    $db = Bio::DB::Flat->new(-directory  => $tmpdir,
                             -index      => 'binarysearch',
                             -format     => 'swiss',
                             -dbname     => 'mybinswiss',
                             -verbose    => $verbose,
                             -write_flag => 1
                             );
    $dir= test_input_file('swiss.dat');
    $result = $db->build_index($dir);

    ok($result);
    $seq = $db->get_Seq_by_id('ACON_CAEEL');
    ok($seq);
    is($seq->length,788);

    $seq = $db->get_Seq_by_id('ACON_CAEEL');
    ok($seq && ref($seq));

    undef $db;
}
$db = Bio::DB::Flat->new(-directory  => $tmpdir,
                         -index      => 'binarysearch',
                         -format     => 'fasta',
                         -dbname     => 'myfasta',
                         -verbose    => $verbose,
                         -write_flag => 1 );

$dir = test_input_file('tmp.fst');
$result = $db->build_index(glob($dir));
ok($result);
$seq = $db->get_Seq_by_id('TEST00004');
is($seq->length,98);

undef $db;

$db = Bio::DB::Flat->new(-directory  => $tmpdir,
                         -index      => 'bdb',
                         -format     => 'fasta',
                         -dbname     => 'mybfasta',
                         -verbose    => $verbose,
                         -write_flag => 1 );

$dir = test_input_file('tmp.fst');
$result = $db->build_index(glob($dir));
ok($result);
for my $id ( qw(TEST00001 TEST00002 TEST00003 TEST00004) ) {
    $seq = $db->get_Seq_by_id($id);
    is($seq->length,98);
}
BioPerl-1.007002/t/LocalDB/Qual.t000444000766000024       720213155576321 16307 0ustar00cjfieldsstaff000000000000BEGIN {     
    use lib '.';
    use Bio::Root::Test;

    test_begin( -tests => 56,
                -requires_module => 'Bio::DB::Qual');

    use_ok('Bio::Root::IO');
    use_ok('File::Copy');
}

my $DEBUG = test_debug();

{

my $test_dbdir = setup_temp_dir('dbqual');

# now use this temporary dir for the db file
ok my $db = Bio::DB::Qual->new($test_dbdir, -reindex => 1);
is $db->glob, '*.{qual,QUAL,qa,QA}';
isa_ok $db, 'Bio::DB::Qual';
ok my @ids = $db->ids;
is scalar(@ids), 15;
@ids = sort {$a <=> $b} @ids;
is $ids[0] , '17601976';
is $ids[14], '17601991';
my $seqid = '17601979';

# direct indexed qual file database access
is ref($db->qual($seqid)), 'ARRAY';
is_deeply $db->qual($seqid), [23, 32, 24, 27, 26, 27, 27, 27, 28, 23, 28, 31, 23, 27];
is $db->length($seqid), 14;
is $db->length($seqid, -1000, 1000), 14; # length() ignores start and stop
is $db->header($seqid), '17601979';
is_deeply $db->qual($seqid, 2, 11), [32, 24, 27, 26, 27, 27, 27, 28, 23, 28];
is_deeply $db->qual($seqid, 2, 11, 1), [32, 24, 27, 26, 27, 27, 27, 28, 23, 28];
is_deeply $db->qual($seqid, 11, 2), [28, 23, 28, 27, 27, 27, 26, 27, 24, 32];
is_deeply $db->qual($seqid, 2, 11, -1), [28, 23, 28, 27, 27, 27, 26, 27, 24, 32];
is_deeply $db->qual($seqid, 11, 2, -1), [32, 24, 27, 26, 27, 27, 27, 28, 23, 28];

# the bioperl  way
is $db->get_Qual_by_id('foobarbaz'), undef;
ok my $obj = $db->get_Qual_by_id($seqid);
isa_ok $obj, 'Bio::Seq::PrimaryQual::Qual';
isa_ok $obj, 'Bio::Seq::QualI';
is ref($obj->qual($seqid)), 'ARRAY';
is $obj->length, 14;
is $obj->id, '17601979';
is $obj->display_id, '17601979';
is $obj->accession_number, 'unknown';
like $obj->primary_id, qr/^Bio::Seq::PrimaryQual::Qual=HASH/;
is $obj->validate_qual( join(' ', @{$obj->qual($seqid)}) ), 1;
is $obj->translate, 0;
is $obj->qualat(12), 31;
is_deeply $obj->subqual(2, 11), [32, 24, 27, 26, 27, 27, 27, 28, 23, 28];
is $obj->header, undef;
is $obj->desc, undef;
ok my $truncobj = $obj->trunc(1,3);
isa_ok $truncobj, 'Bio::Seq::PrimaryQual::Qual';
isa_ok $obj, 'Bio::Seq::QualI';
is ref($truncobj->qual($seqid)), 'ARRAY';
is $truncobj->length, 3;
ok my $revobj = $obj->revcom;
isa_ok $revobj, 'Bio::Seq::PrimaryQual::Qual';
isa_ok $revobj, 'Bio::Seq::PrimaryQual';
is ref($revobj->qual), 'ARRAY';
is $revobj->length, 14;
undef $obj;
undef $truncobj;
undef $revobj;

# using get_PrimarySeq_stream streaming
ok my $stream = $db->get_PrimaryQual_stream;
ok $stream = $db->get_PrimarySeq_stream;
isa_ok $stream, 'Bio::DB::Indexed::Stream';
ok my $streamqual = $stream->next_seq;
isa_ok $streamqual, 'Bio::Seq::PrimaryQual';

# using newFh streaming
ok my $fh = Bio::DB::Qual->newFh($test_dbdir);
my $fhqual = <$fh>;
isa_ok $fhqual, 'Bio::Seq::PrimaryQual';
undef $fh;

# tied-hash access
my (%h,$dna1,$dna2);
ok tie(%h,'Bio::DB::Qual',$test_dbdir);
ok $h{$seqid};
ok $dna1 = $h{"$seqid:1,10"};
ok $dna2 = $h{"$seqid:10,1"};

}



sub setup_temp_dir {
    # this obfuscation is to deal with lockfiles by GDBM_File which can
    # only be created on local filesystems apparently so will cause test
    # to block and then fail when the testdir is on an NFS mounted system

    my $data_dir = shift;

    my $io = Bio::Root::IO->new();
    my $tempdir = test_output_dir();
    my $test_dbdir = $io->catfile($tempdir, $data_dir);
    mkdir($test_dbdir); # make the directory
    my $indir = test_input_file($data_dir);
    opendir(my $INDIR,$indir) || die("cannot open dir $indir");
    # effectively do a cp -r but only copy the files that are in there, no subdirs
    for my $file ( map { $io->catfile($indir,$_) } readdir($INDIR) ) {
        next unless (-f $file );
        copy($file, $test_dbdir);
    }
    closedir($INDIR);
    return $test_dbdir
}
BioPerl-1.007002/t/LocalDB/Registry.t000555000766000024       530013155576321 17215 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 14);
	
	$ENV{OBDA_SEARCH_PATH} = 't/data/registry/flat;t/data/registry/bdb';
	
	use_ok('Bio::DB::Registry');
	use_ok('Bio::DB::Flat');
}

# we need a temp directory t/tmp since t/tmp is specified in the registry files
my $tmpdir = File::Spec->catfile(qw(t tmp));
mkdir($tmpdir,0777);

SKIP: {
	skip "unable to create temp dir '$tmpdir', skipping tests", 12 unless -d $tmpdir;
	
	my $flat = Bio::DB::Flat->new(-directory  => $tmpdir,
					  -dbname     => 'testflat',
					  -format     => 'fasta',
					  -index      => 'binarysearch',
								  -write_flag => 1 );
	my $entries = $flat->build_index(test_input_file('cysprot.fa'));
	is $entries, 7;
	
	SKIP: {
		test_skip(-tests => 2, -requires_modules => [qw(DB_File)]);
		
		my $bdb = Bio::DB::Flat->new(-directory  => $tmpdir,
					 -dbname     => 'testbdb',
					 -format     => 'fasta',
					 -index      => 'bdb',
					 -write_flag => 1 );
		ok defined($bdb);
		$entries = $bdb->build_index(test_input_file('cysprot.fa'));
		is $entries, 7;
	}
	
	SKIP: {
		test_skip(-tests => 9,
                  -requires_modules => [qw(LWP::UserAgent HTTP::Request::Common)],
                  -requires_networking => 1);
		
		my $registry = Bio::DB::Registry->new();
		ok defined($registry);
		my @available_services = $registry->services;
		
		ok grep /testflat/,@available_services;
		my $db = $registry->get_database('testflat');
		ok defined($db);
		my $seq = $db->get_Seq_by_id("ALEU_HORVU");
		ok defined($seq);
		my $sequence = $seq->seq;
		is $sequence, "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA";
	
		SKIP: {
			test_skip(-tests => 4, -requires_modules => [qw(DB_File)]);
			
			ok grep /testbdb/,@available_services;
			$db = $registry->get_database('testbdb');
			ok defined($db);
			$seq = $db->get_Seq_by_id("ALEU_HORVU");
			ok defined($seq);
			$sequence = $seq->seq;
			is $sequence, "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA";
		}
	}
}

END {
	File::Path::rmtree($tmpdir) if ($tmpdir && (-d $tmpdir));
}
BioPerl-1.007002/t/LocalDB/SeqFeature.t000444000766000024      3050313155576321 17471 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;
use constant TEST_COUNT => 116;

BEGIN {
    use lib '.','..','./t/lib';
    use Bio::Root::Test;

    test_begin(-tests           => TEST_COUNT,
               -requires_module => 'DB_File');

    $ENV{ORACLE_HOME} ||= '/home/oracle/Home';
    use_ok('Bio::SeqFeature::Generic');
    use_ok('Bio::DB::SeqFeature::Store');
    use_ok('Bio::DB::SeqFeature::Store::GFF3Loader');
    use_ok('Bio::Root::IO');
    use_ok('Bio::DB::Fasta');
    use_ok('File::Copy');
}

my $DEBUG = test_debug();

my $gff_file = test_input_file('seqfeaturedb','test.gff3');

my (@f,$f,$f2,$sf1,$sf2,$sf3,@s,$s,$seq1,$seq2,$count,$new_features);

my @args = @ARGV;
@args = (-adaptor => 'memory') unless @args;

SKIP: {
my $db = eval { Bio::DB::SeqFeature::Store->new(@args) };
skip "DB load failed? Skipping all! $@", (TEST_COUNT - 6) if $@;
ok($db);

is( $db->isa('Bio::SeqFeature::CollectionI'), 1 );

my $loader = eval { Bio::DB::SeqFeature::Store::GFF3Loader->new(-store=>$db) };
skip "GFF3 loader failed? Skipping all! $@", (TEST_COUNT - 6) if $@;
ok($loader);

$new_features = 0;
SKIP: {
#    skip("skipping memory adaptor-specific tests",27)
#	unless $db->isa('Bio::DB::SeqFeature::Store::memory');


# test adding
    my $n = Bio::SeqFeature::Generic->new(
#	-primary_id => '_some_id',  # you're not allowed to do this!!
	-primary    => 'repeat_123',
	-start      => 23,
	-end        => 512,
	-strand     => '+',
	-display_name => 'My favorite feature'
	);
    ok( my $id = $db->add_features([$n]), 'adding a feature' );
    ok( @f = $db->fetch($n->primary_id));
    is( scalar @f, 1 );
    $f = $f[0];
    is( $f->primary_id, $n->primary_id);

    $f2 = Bio::SeqFeature::Generic->new(
	-start        => 10,
	-end          => 100,
	-strand       => -1,
	-primary      => 'repeat_123', # -primary_tag is a synonym
	-source_tag   => 'repeatmasker',
	-display_name => 'alu family',
	-score        => 1000,
	-tag          => { new => 1,
			   author => 'someone',
			   sillytag => 'this is silly!' }
	);
    ok( $db->store($f2) , 'adding a feature with no primary_id' );
    ok( $f2->primary_id );

# test fetching features
    is( $db->fetch('-1'), undef, 'searching for a feature that shouldnt exist');
    is( $db->get_features_by_type('repeat_123:repeatmasker'), 1, 'simple type' );
    is( $db->get_features_by_type('repeat_123:'), 2, 'base type with colon' );
    is( $db->get_features_by_type('repeat_123'), 2, 'base type alone' );
    is( $db->get_features_by_type('rep.*'), 0, 'queried types are not interpolated' );
    ok( @f = $db->types );
    is( @f, 2 );
    isa_ok($f[0], 'Bio::DB::GFF::Typename');

# test removing features
    ok( $db->delete( $f ), 'feature deletion' );
    is( $db->fetch( $f->primary_id ), undef );
    $db->delete( $f2 );

    ok( $db->store($f, $f2) );

# test adding seqfeatures
    $sf1 = Bio::SeqFeature::Generic->new( -primary=>'seqfeat1', -start=>23, -end=>512 );
    $sf2 = Bio::SeqFeature::Generic->new( -primary=>'seqfeat2', -start=>23, -end=>512 );
    $sf3 = Bio::SeqFeature::Generic->new( -primary=>'seqfeat1', -start=>23, -end=>512, source_tag => 'dna' );
    ok $db->add_features([$sf1, $sf2, $sf3]), 'adding subfeatures';
    is $db->add_SeqFeature($f, $sf1), 1;
    is $db->add_SeqFeature($f, $sf2, $sf3), 2;
    is $db->add_SeqFeature($f, $sf1, $sf2, $sf3), 3;

# test fetching seqfeatures
    is $db->fetch_SeqFeatures($f), 3;
    is $db->fetch_SeqFeatures($f, 'seqfeat2'), 1;
    is $db->fetch_SeqFeatures($f, 'seqfeat1:dna'), 1;
    is $db->fetch_SeqFeatures($f, 'seqfeat1'), 2;
    is $db->fetch_SeqFeatures($f, 'seqfeat1', 'seqfeat2'), 3;
    is $db->fetch_SeqFeatures($f, 'seqfeat4'), 0;

    $new_features = scalar $db->features;
}

# exercise the loader
ok($loader->load($gff_file));

# there should be one gene named 'abc-1'
@f = $db->get_features_by_name('abc-1');
is(@f,1);

$f = $f[0];
# there should be three subfeatures of type "exon" and three of type "CDS"
is($f->get_SeqFeatures('exon'),3);
is($f->get_SeqFeatures('CDS'),3);

# the sequence of feature abc-1 should match the sequence of the first exon at the beginning
$seq1 = $f->seq->seq;
$seq2 = (sort {$a->start<=>$b->start} $f->get_SeqFeatures('exon'))[0]->seq->seq;
is(substr($seq1,0,length $seq2),$seq2);

# sequence lengths should match
is(length $seq1, $f->length);

# if we pull out abc-1 again we should get the same object
($s) = $db->get_features_by_name('abc-1');
is($s, $f);

# test case-sensitivity
($s) = $db->get_features_by_name('Abc-1');
is($s, $f, 'feature names should be case insensitive');

# we should get two objects when we ask for abc-1 using get_features_by_alias
# this also depends on selective subfeature indexing
@f = $db->get_features_by_alias('abc-1');
is(@f,2);

# the two features should be different
isnt($f[0], $f[1]);

# test that targets are working
($f) = $db->get_features_by_name('match1');
ok(defined $f);
$s = $f->target;
ok(defined $s);
ok($s->seq_id  eq 'CEESC13F');
$seq1 = $s->seq->seq;
is(substr($seq1,0,10), 'ttgcgttcgg');

# can we fetch subfeatures?
# gene3.a has the Index=1 attribute, so we should fetch it
($f) = $db->get_features_by_name('gene3.a');
ok($f);

# gene 3.b doesn't have an index, so we shouldn't get it
($f) = $db->get_features_by_name('gene3.b');
ok(!$f);

# test three-tiered genes
($f) = $db->get_features_by_name('gene3');
ok($f);
my @transcripts = $f->get_SeqFeatures;
is(@transcripts, 2);
is($transcripts[0]->method,'mRNA');
is($transcripts[0]->source,'confirmed');

# test that exon #2 is shared between the two transcripts
my @exons1      = $transcripts[0]->get_SeqFeatures('CDS');
is(@exons1, 3);
my @exons2      = $transcripts[1]->get_SeqFeatures('CDS');
my ($shared1)   = grep {$_->display_name||'' eq 'shared_exon'} @exons1;
my ($shared2)   = grep {$_->display_name||'' eq 'shared_exon'} @exons2;
ok($shared1 && $shared2);
is($shared1, $shared2);
is($shared1->primary_id, $shared2->primary_id);

# test attributes
is($shared1->phase, 0);
is($shared1->strand, +1);
is(($f->attributes('expressed'))[0], 'yes');

# test type getting
is (scalar $db->get_features_by_type('transcript'), 4, 'base type');
is (scalar $db->get_features_by_type('transcript:confirmed'), 2, 'base:source type');

# test autoloading
my ($gene3a) = grep { $_->display_name eq 'gene3.a'} @transcripts;
my ($gene3b) = grep { $_->display_name eq 'gene3.b'} @transcripts;
ok($gene3a);
ok($gene3b);
ok($gene3a->Is_expressed);
ok(!$gene3b->Is_expressed);

# the representation of the 3'-UTR in the two transcripts a and b is
# different (not recommended but supported by the GFF3 spec). In the
# first case, there are two 3'UTRs existing as independent
# features. In the second, there is one UTR with a split location.
is($gene3a->Three_prime_UTR, 2);
is($gene3b->Three_prime_UTR, 1);
my ($utr) = $gene3b->Three_prime_UTR;
is($utr->segments, 2);
my $location = $utr->location;
isa_ok($location, 'Bio::Location::Split');
is($location->sub_Location,2);

# ok, test that queries are working properly.
# find all features with the attribute "expressed"
@f = $db->get_features_by_attribute({expressed=>'yes'});
is(@f, 2);

# find all top-level features on Contig3 -- there should be two
@f = $db->get_features_by_location(-seq_id=>'Contig3');
is(@f, 2);

# find all top-level features on Contig3 that overlap a range -- only one
@f = $db->get_features_by_location(-seq_id=>'Contig3',-start=>40000,-end=>50000);
is(@f,1);

# find all top-level features on Contig3 of type 'assembly_component'
@f = $db->features(-seq_id=>'Contig3',-type=>'assembly_component');
is(@f, 1);

# test iteration
@f = $db->features;
is(scalar @f, 27+$new_features);

my $i = $db->get_seq_stream;
ok($i);

my $feature_count = @f;
while ($i->next_seq) { $count++ }
is($feature_count,$count);

# regression test on bug in which get_SeqFeatures('type') did not filter inline segments
@f = $db->get_features_by_name('agt830.3');
ok(@f && !$f[0]->get_SeqFeatures('exon'));
ok(@f && $f[0]->get_SeqFeatures('EST_match'));

# regression test on bug in which the load_id disappeared
is(@f && $f[0]->load_id, 'Match2');

# regress on proper handling of multiple ID features
my ($alignment) = $db->get_features_by_name('agt830.5');
ok($alignment);
is($alignment->target->start,1);
is($alignment->target->end, 654);
is($alignment->get_SeqFeatures, 2);
my $gff3 = $alignment->gff3_string(1);
my @lines = split "\n",$gff3;
is (@lines, 2);
ok("@lines" !~ /Parent=/s);
ok("@lines" =~ /ID=/s);

# regress on multiple parentage
my ($gp)     = $db->get_features_by_name('gparent1');
my ($p1,$p2) = $gp->get_SeqFeatures;
my @c    = sort {$a->start<=>$b->start} $p1->get_SeqFeatures;
is(scalar @c,2);
is($c[0]->phase,0);
is($c[1]->phase,1);
@c    = sort {$a->start<=>$b->start} $p2->get_SeqFeatures;
is(scalar @c,2);
is($c[0]->phase,0);
is($c[1]->phase,1);

 SKIP: {
     test_skip(-tests => 2, -excludes_os => 'mswin');

     if (my $child = open(F,"-|")) { # parent reads from child
	 cmp_ok(scalar ,'>',0);
	 close F;
	 # The challenge is to make sure that the handle
	 # still works in the parent!
	 my @f = $db->features();
	 cmp_ok(scalar @f,'>',0);
     }
     else { # in child
	 $db->clone;
	 my @f = $db->features();
	 my $feature_count = @f;
	 print $feature_count;
	 exit 0;
     }
}


# test the -ignore_seqregion flag

# the original should have a single feature named 'Contig1'
my @f   = $db->get_features_by_name('Contig1');
is(scalar @f,1);

$db     = eval { Bio::DB::SeqFeature::Store->new(@args) };
$loader = eval { Bio::DB::SeqFeature::Store::GFF3Loader->new(-store=>$db,
							     -ignore_seqregion=>1)
               };
$loader->load($gff_file);
@f      = $db->get_features_by_name('Contig1');
is(scalar @f,0);

# test keyword search
my @results = $db->search_notes('interesting');
is(scalar @results,2,'keyword search; 1 term');

@results = $db->search_notes('terribly interesting');
is(scalar @results,2,'keyword search; 2 terms');

# test our ability to substitute a FASTA file for the database
my $fasta_dir = make_fasta_testdir();
my $dbfa = Bio::DB::Fasta->new($fasta_dir, -reindex => 1);
ok($dbfa);

ok(my $contig1=$dbfa->seq('Contig1'));

$db     = Bio::DB::SeqFeature::Store->new(@args,-fasta=>$dbfa);
$loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store=>$db);
ok($loader->load($gff_file));

ok($db->dna_accessor);
my $f = $db->segment('Contig1');
ok($f->dna eq $contig1);

ok(my $contig2 = $dbfa->seq('Contig2'));
($f) = $db->get_feature_by_name('match4');
my $length = $f->length;
ok(substr($contig2,0,$length) eq $f->dna);

# DESTROY for $dbfa sometimes is not being called at script end,
# so call it explicitly to close temporal filehandles
# and allow their deletion
$dbfa->DESTROY;

# Remove temporal database file used for SQLite tests
if ($db->isa('Bio::DB::SeqFeature::Store::DBI::SQLite')) {
    $db->DESTROY;
    unlink $db->{dbh_file};
}


# testing namespaces for mysql and Pg adaptor

 SKIP: {
     my $adaptor;

     for (my $i=0; $i < @args; $i++) {
	 if ($args[$i] eq '-adaptor') {
	     $adaptor = $args[$i+1];
	     last;
	 }
     }

     skip "Namespaces only supported for DBI::mysql and DBI::Pg adaptors", 6, if ($adaptor ne 'DBI::mysql' && $adaptor ne 'DBI::Pg');

     push(@args, ('-namespace', 'bioperl_seqfeature_t_test_schema'));
     $db     = eval { Bio::DB::SeqFeature::Store->new(@args) };
     ok($db);

     $loader = eval { Bio::DB::SeqFeature::Store::GFF3Loader->new(-store=>$db) };
     ok($loader);

     $loader->load($gff_file);

     # there should be one gene named 'abc-1'
     ok( @f = $db->get_features_by_name('abc-1') );
     is(@f,1);

     $f = $f[0];
     # there should be three subfeatures of type "exon" and three of type "CDS"
     is($f->get_SeqFeatures('exon'),3);
     is($f->get_SeqFeatures('CDS'),3);

     $db->remove_namespace();
}


sub make_fasta_testdir {
    # this obfuscation is to deal with lockfiles by GDBM_File which can
    # only be created on local filesystems apparently so will cause test
    # to block and then fail when the testdir is on an NFS mounted system
    my $io = Bio::Root::IO->new(-verbose => $DEBUG);
    my $tempdir = test_output_dir();
    my $test_dbdir = $io->catfile($tempdir, 'dbfa');
    mkdir($test_dbdir); # make the directory
    my $indir = test_input_file('dbfa');
    opendir(INDIR,$indir) || die("cannot open dir $indir");
    # effectively do a cp -r but only copy the files that are in there, no subdirs
    for my $file ( map { $io->catfile($indir,$_) } readdir(INDIR) ) {
	next unless (-f $file );
	copy($file, $test_dbdir);
    }
    closedir(INDIR);
    return $test_dbdir;
}

} # SKIP
BioPerl-1.007002/t/LocalDB/transfac_pro.t000444000766000024      2736713155576321 20124 0ustar00cjfieldsstaff000000000000use strict;
use warnings;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    test_begin(-tests           => 115,
               -requires_module => 'DB_File');
    
    use_ok('Bio::Matrix::PSM::IO');
    use_ok('Bio::DB::TFBS');
    use_ok('Bio::DB::Taxonomy');
}

#*** need to test getting all ids of a certain kind, like $db->get_matrix_ids();
#    but hard to do without a complete tax dump

my $temp_dir = test_output_dir();
my $tax_db = Bio::DB::Taxonomy->new(-source => 'flatfile',
                                    -directory => $temp_dir,
                                    -nodesfile => test_input_file('taxdump', 'nodes.dmp'),
                                    -namesfile => test_input_file('taxdump', 'names.dmp'));

# test transfac pro (local flat files)
{
    ok my $db = Bio::DB::TFBS->new(-source => 'transfac_pro',
                                   -index_dir => $temp_dir,
                                   -dat_dir => test_input_file('transfac_pro'),
                                   -tax_db => $tax_db,
                                   -force => 1);
    
    # reference.dat
    {
        ok my ($ref_id) = $db->get_reference_ids(-pubmed => 16574738);
        is $ref_id, 'RE0047775';
        ok my $ref = $db->get_reference($ref_id);
        isa_ok $ref, 'Bio::Annotation::Reference';
        is $ref->primary_id, 16574738;
        is $ref->pubmed, $ref->primary_id;
        is $ref->database, 'PUBMED';
        is $ref->authors, '..Bet S . ,.u i rMeK ,,d. vWeWk KaS.ee.nyNk mJMMih. a, i P';
        is $ref->location, 'Mc (o0o.. 0n)lnir.do 2E:6l';
        is $ref->title, 'INDD VDGT C1AALEBEI.EIT IYIHLA6ITTE E ANV  ITSL MTRTANYE TM NISP TNBAUTPOIORSL I- NVTOD,MHIRRLINSDX TRPY NO CAELUAOA SNMMNT CED5CTH NII TERTOI2IMTVPEH3DSAI';
        
        my @sites = $db->get_site_ids(-reference => $ref_id);
        is join(' ', sort @sites), 'R19310 R19311 R19312 R19313 R19314 R19315 R19316';
        my @genes = $db->get_gene_ids(-reference => $ref_id);
        is "@genes", 'G036757';
        my @ref_ids = $db->get_reference_ids(-site => 'R19310');
        is "@ref_ids", $ref_id;
        @ref_ids = $db->get_reference_ids(-gene => 'G036757');
        is "@ref_ids", $ref_id;
        
        $ref_id = 'RE0047531';
        my @matrices = $db->get_matrix_ids(-reference => $ref_id);
        is join(' ', sort @matrices), 'M01123 M01124 M01125';
        my @factors = $db->get_factor_ids(-reference => $ref_id);
        like "@factors", qr/T08800/;
        @ref_ids = $db->get_reference_ids(-matrix => 'M01123');
        is join(' ', sort @ref_ids), "$ref_id RE0047626";
        @ref_ids = $db->get_reference_ids(-factor => 'T08800');
        is join(' ', sort @ref_ids), "$ref_id RE0047634 RE0047637 RE0047645";
		
		$ref_id = 'RE0023998';
		my %fragments = map { $_ => 1 } $db->get_fragment_ids(-reference => $ref_id);
		ok $fragments{'FR0002267'};
		@ref_ids = $db->get_reference_ids(-fragment => 'FR0002267');
		is "@ref_ids", $ref_id;
    }
    
    # gene.dat
    {
        ok my ($gene_id) = $db->get_gene_ids(-name => 'P5');
        is $gene_id, 'G000001';
		
		#*** get_genemap with ensembl lookup being fantastically slow
        #ok defined Bio::Map::Gene->set_from_db; # will try and do ensembl lookups for gene info
        #ok my $gene_map = $db->get_genemap($gene_id, 1000);
        #Bio::Tools::Run::Ensembl->_stats;
        #ok $gene_map->isa('Bio::Map::GeneMap');
        #ok $gene_map->unique_id, 'G000001';
        #ok $gene_map->universal_name, 'P5';
        #ok $gene_map->species->scientific_name, 'Adeno-associated virus';
        #my @factors = grep { $_->isa("Bio::Map::TranscriptionFactor") } $gene_map->get_elements;
        #ok @factors, 3;
        
        ($gene_id) = $db->get_gene_ids(-id => 'AAV$P5');
        is $gene_id, 'G000001';
        my @gene_ids = $db->get_gene_ids(-species => '9606');
        is @gene_ids, 5;
        is [sort @gene_ids]->[0], 'G000060'; # in real data this would be G000174, but since our taxdump doesn't have chicken in it, G000060 was changed to human
        ($gene_id) = $db->get_gene_ids(-site => 'R03174');
        is $gene_id, 'G000001';
        ($gene_id) = $db->get_gene_ids(-factor => 'T00267');
        is $gene_id, 'G000060';
		my %gene_ids = map { $_ => 1 } $db->get_gene_ids(-fragment => 'FR0002267');
		ok $gene_ids{'G020751'};
        # get_gene_ids(-reference => ...) already tested
        
        my @site_ids = $db->get_site_ids(-gene => 'G000001');
        is join(' ', sort @site_ids), 'R03174 R03175 R03176';
        my @factor_ids = $db->get_factor_ids(-gene => 'G000060');
        is join(' ', sort @factor_ids), 'T00267 T08293'; # only found for genes that encode factors
		my %fragment_ids = map { $_ => 1 } $db->get_fragment_ids(-gene => 'G020751');
		ok $fragment_ids{'FR0002267'};
        # get_reference_ids(-gene => ...) already tested
    }
    
    # site.dat
    {
        ok my ($site_id) = $db->get_site_ids(-id => 'HS$IFI616_01');
        is $site_id, 'R00001';
        ok my $seq = $db->get_seq($site_id);
        isa_ok $seq, 'Bio::Seq';
        is $seq->id, 'HS$IFI616_01';
        is $seq->accession_number, 'R00001';
        is $seq->seq, 'aGAGACATAAGTgA';
        my $annot = $seq->annotation;
        is [$annot->get_Annotations('relative_start')]->[0]->value, -172;
        is [$annot->get_Annotations('relative_end')]->[0]->value, -98;
        is [$annot->get_Annotations('relative_type')]->[0]->value, 'TSS';
        is [$annot->get_Annotations('relative_to')]->[0]->value, 'G000176';
        is $seq->species, 9606;
        
        my @site_ids = $db->get_site_ids(-species => '9606');
        is @site_ids, 14;
        is [sort @site_ids]->[0], 'R00001';
        # get_site_ids(-gene => ...) already tested
        ($site_id) = $db->get_site_ids(-matrix => 'M00972');
        is $site_id, 'R00001';
        my %site_ids = map { $_ => 1 } $db->get_site_ids(-factor => 'T00428');
        ok $site_ids{R00001};
        # get_site_ids(-reference => ...) already tested
        
        # get_gene_ids(-site => ...) already tested
        my @matrix_ids = $db->get_matrix_ids(-site => 'R00001');
        is "@matrix_ids", 'M00972';
        my @factor_ids = $db->get_factor_ids(-site => 'R00001');
        is "@factor_ids", 'T00428';
        # get_reference_ids(-site => ...) already tested
    }
    
    # matrix.dat
    {
        ok my ($matrix_id) = $db->get_matrix_ids(-id => 'V$E47_01');
        is $matrix_id, 'M00002';
        ok my $matrix = $db->get_matrix($matrix_id);
        isa_ok $matrix, 'Bio::Matrix::PSM::SiteMatrix';
        
        # detailed psm tests
        {
            # Lets try to compress and uncompress the frequencies, see if
            # there is no considerable loss of data.
            my $fA = $matrix->get_compressed_freq('A');
            my @check = Bio::Matrix::PSM::SiteMatrix::_uncompress_string($fA,1,1);
            my @A = $matrix->get_array('A');
            my ($var, $max) = (0, 0);
            for (my $i = 0; $i < @check; $i++) {
                my $diff = abs(abs($check[$i]) - abs($A[$i]));
                $var += $diff;
                $max = $diff if ($diff > $max);
            }
            my $avg = $var / @check;
            cmp_ok $avg, '<', 0.01; # Loss of data under 1 percent
            
            # SiteMatrixI methods
            is $matrix->id, 'V$E47_01';
            is $matrix->accession_number, $matrix_id;
            is $matrix->consensus, 'ATGCATGCATGC';
            is $matrix->IUPAC, 'NNNNNNNNNNNN';
            is $matrix->regexp, '\S\S\S\S\S\S\S\S\S\S\S\S';
            is $matrix->width, 12;
            is $matrix->sites, 5;
            ok ! $matrix->IC;
            ok ! $matrix->e_val;
        }
        
        ok my $aln = $db->get_aln($matrix_id);
        isa_ok $aln, 'Bio::SimpleAlign';
        is $aln->length, 12;
        is $aln->num_residues, 132;
        ok $aln->is_flush;
        is $aln->num_sequences, 11;
        my @ids = qw(R05108 R05109 R05110 R05111 R05112 R05113 R05114 R05115 R05116 R05117 R05118);
        foreach my $seq ($aln->each_alphabetically) {
            is $seq->id, shift(@ids);
        }
        is @ids, 0;
        ok ! $db->get_aln('M00001'); # no seqs in db
        ok $aln = $db->get_aln('M00001', 1); # force to find seqs, store in db
        ok $aln = $db->get_aln('M00001'); # seqs now in db
        is $aln->num_sequences, 5;
		
        ($matrix_id) = $db->get_matrix_ids(-name => 'MyoD');
        is $matrix_id, 'M00001';
        # get_matrix_ids(-site =>  ...) already tested
        my %matrix_ids = map { $_ => 1 } $db->get_matrix_ids(-factor => 'T00526');
        ok $matrix_ids{M00001};
        # get_matrix_ids(-reference => ...) already tested
        
        # get_site_ids(-matrix => ...) already tested
        my @factor_ids = $db->get_factor_ids(-matrix => 'M00001');
        is join(' ', sort @factor_ids), 'T00526 T09177';
        # get_reference_ids(-matrix => ...) already tested
    }
    
	# fragment.dat
	{
		ok my ($fragment_id) = $db->get_fragment_ids(-id => 'FR0002267');
        is $fragment_id, 'FR0002267'; # id and accession are the same for fragments
		ok my $seq = $db->get_fragment($fragment_id);
		isa_ok $seq, 'Bio::SeqI';
        is $seq->id, 'FR0002267';
        is $seq->seq, 'GTCTACAACACTCTTGCGGACGGAGAGCCGAAGAGCAAAGCGTCGCCGGGTAAGACGAACGCTCAAGGGGGTACGAGCAGCGTAACGACGGAAACGGTGACGCCCCGGGATTTGGGGCTCAGCTAGGGTCGCCGAGTAGGGGGCCGCGGGGACAACGGGGGCGACACGCCGCTTTCCCTGCGTCTGTGGAGCCTATGGTACGGCGTAACCGGTTGTGTGATGAACTGTCCAGACCGCACGTAGTCCCAGCGCAAGGTCTATGCCGCCTAGAGGCAAGACGGGCCGTCTCCTACTTAGTAGCCAGCTACGGGGCGTTGGTCCCCTCGGTAGTGCAACTATCCAGCCACGGCGTCCGCCGGGCTGAGCCTCAGCAGAGCTGGGGGGGTATCATTCCGACGCTGTTTAATTCGTCAGCAGGACCCACTACACGCTCTGTCATTCGCCTGAGCAGTTGTAAATTAGCGCGGCGATCTTGCAAGAGACAAGGAGGCGAACCTGGGGTCGGGACGTAAGGACGAACGGCAGTACAGACGCTGGGGGACGCCACGTGCCAGAACCTCTCACGACCGGAGGTTCAACGCTGATTGGGGCGCAACAGAGGGCGGAGCAGCGAGGTGGCGCTGGTGGGATGGGGCGAGACAAACCCAAGCTGACGCCGAAGGGCCCGCGTGGCCGGGCTGGGGCCCGTAGAACGAGGGAATTGTATGCGGCGCCTGAATGGGCGCACCACA';
		is $seq->species, 9606;
		
        # -id -species -gene -factor -reference
        my @fragment_ids = $db->get_fragment_ids(-species => '9606');
        is @fragment_ids, 2;
        is [sort @fragment_ids]->[0], 'FR0000001';
        my %fragment_ids = map { $_ => 1 } $db->get_fragment_ids(-factor => 'T03828');
        ok $fragment_ids{'FR0002267'};
        # get_fragment_ids(-gene => ...) already tested
        # get_fragment_ids(-reference => ...) already tested
        
        my ($factor_id) = $db->get_factor_ids(-fragment => 'FR0002267');
        is $factor_id, 'T03828';
        # get_gene_ids(-fragment => ...) already tested
        # get_reference_ids(-fragment => ...) already tested
	}
	
    # factor.dat
    {
        ok my ($factor_id) = $db->get_factor_ids(-id => 'T00001');
        is $factor_id, 'T00001'; # id and accession are the same for factors
        ok my $factor = $db->get_factor($factor_id);
        isa_ok $factor, 'Bio::Map::TranscriptionFactor';
        is $factor->id, 'T00001';
        is $factor->universal_name, 'AAF';
        is $factor->known_maps, 1;
        my @positions = $factor->get_positions;
        is @positions, 1;
        
        ($factor_id) = $db->get_factor_ids(-name => 'AAF');
        is $factor_id, 'T00001';
        my @factor_ids = $db->get_factor_ids(-species => '9606');
        is @factor_ids, 7;
        is [sort @factor_ids]->[0], 'T00001';
        @factor_ids = $db->get_factor_ids(-interactors => 'T03200');
        is [sort @factor_ids]->[0], 'T00002';
        # get_factor_ids(-gene => ...) already tested
        # get_factor_ids(-site => ...) already tested
        # get_factor_ids(-matrix => ...) already tested
        # get_factor_ids(-fragment => ...) already tested
        # get_factor_ids(-reference => ...) already tested
        
        # get_*_ids(-factor => ...) already tested
    }
}

# how to get something like ok $psmIO->release, '10.2--2006-06-30'; ?
# or all factors, all sites, all matrices, all genes etc.?
BioPerl-1.007002/t/LocalDB/Index000755000766000024          013155576321 16131 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/LocalDB/Index/Blast.t000444000766000024       324313155576321 17522 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 26,
				  -requires_module => 'IO::String');
    
	use_ok('Cwd');
	use_ok('Bio::SearchIO');
	use_ok('Bio::Index::Blast');
}

# BLASTP

my $index = Bio::Index::Blast->new(-filename => 'Wibbl',
											  -write_flag => 1);
ok($index);

$index->make_index(test_input_file('multi_blast.bls'));
($index->dbm_package eq 'SDBM_File') ? 
	(ok(-e "Wibbl.pag" && -e "Wibbl.dir")) :
	(ok(-e "Wibbl"));

foreach my $id ( qw(CATH_RAT PAPA_CARPA) ) {
	my $fh = $index->get_stream($id);
	ok($fh);
	ok( ! eof($fh) );
	my $report = Bio::SearchIO->new(-noclose => 1,
				   -format  => 'blast',
				   -fh      => $fh);
	my $result = $report->next_result;
	like($result->query_name, qr/$id/);
	ok( $result->next_hit);
	
	like( $index->fetch_report($id)->query_name, qr/$id/);
}
# ActivePerl will not allow deletion if the tie-hash is still active
$index->DESTROY;
unlink qw( Wibbl Wibbl.pag Wibbl.dir );

# RPS-BLAST

$index = Bio::Index::Blast->new(-filename => 'Wibbl.index',
										  -write_flag => 1);
ok($index);

$index->make_index(test_input_file('rpsblast.bls'));

foreach my $id ( qw(orf20 orf40) ) {
	my $fh = $index->get_stream($id);
	ok($fh);
	ok( ! eof($fh) );
	my $report = Bio::SearchIO->new(-noclose => 1,
				   -format  => 'blast',
				   -fh      => $fh);
	my $result = $report->next_result;
	like($result->query_name, qr/$id/);
	ok( $result->next_hit);
	
	like( $index->fetch_report($id)->query_name, qr/$id/);
}
# ActivePerl will not allow deletion if the tie-hash is still active
$index->DESTROY;
unlink qw( Wibbl.index Wibbl.index.pag Wibbl.index.dir );
BioPerl-1.007002/t/LocalDB/Index/BlastTable.t000444000766000024       302113155576321 20464 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: Blast.t 16293 2009-10-27 20:03:02Z cjfields $

use strict;

BEGIN {
	use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 27,
		-requires_module => 'IO::String');
    
	use_ok('Cwd');
	use_ok('Bio::SearchIO');
	use_ok('Bio::Index::BlastTable');
}

                       # -m 9                -m 8
my @test_cases = qw(multi.blast.m9      multi.blast.m8);

for my $file (@test_cases) {
    my $index = Bio::Index::BlastTable->new(-filename => 'Wibbl',
                                        -write_flag => 1);
    ok($index);
    $index->id_parser(\&my_id_parser);
    $index->make_index(test_input_file($file));
    ($index->dbm_package eq 'SDBM_File') ? 
        (ok(-e "Wibbl.pag" && -e "Wibbl.dir")) :
        (ok(-e "Wibbl"));
    
    foreach my $id ( qw(SP130_MOUSE IKZF1_MOUSE) ) {
        my $fh = $index->get_stream($id);
        ok($fh);
        ok( ! eof($fh) );
        my $report = Bio::SearchIO->new(-noclose => 1,
                       -format  => 'blasttable',
                       -fh      => $fh);
        my $result = $report->next_result;
        like($result->query_name, qr/$id/);
        ok( $result->next_hit);
        
        like( $index->fetch_report($id)->query_name, qr/$id/);
    }
    # ActivePerl will not allow deletion if the tie-hash is still active
    $index->DESTROY;
    unlink qw( Wibbl Wibbl.pag Wibbl.dir Wibbl.index);
}

# test id_parser
sub my_id_parser {
    if ($_[0] =~ /^\S+\|(\S+)/) {
        return $1;
    } else {
        return;
    }
}
BioPerl-1.007002/t/LocalDB/Index/Index.t000444000766000024      1640013155576321 17543 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
   use lib '.';
   use Bio::Root::Test;
   
   test_begin(-tests => 73,
              -requires_modules => [qw(DB_File
                                       Storable
                                       Fcntl)]);
   
   use_ok('Bio::Index::Fasta');
   use_ok('Bio::Index::Qual');
   use_ok('Bio::Index::SwissPfam');
   use_ok('Bio::Index::EMBL');
   use_ok('Bio::Index::GenBank');
   use_ok('Bio::Index::Stockholm');
   use_ok('Bio::Index::Swissprot');
   use_ok('Bio::Index::Hmmer');
   use_ok('Bio::DB::InMemoryCache');
   use_ok('Bio::DB::InMemoryCache');
}

my $ind = Bio::Index::Fasta->new(-filename => 'Wibbl',
                                 -write_flag => 1,
                                 -verbose => 0);
$ind->make_index(test_input_file('multifa.seq'));
$ind->make_index(test_input_file('seqs.fas'));

ok ( -e "Wibbl" || -e "Wibbl.pag" );
my $seq = $ind->fetch('HSEARLOBE');
is($seq->length,321);
is($seq->primary_id(),'HSEARLOBE');
$seq = $ind->fetch('HSMETOO');
is($seq->length,134);
is($seq->primary_id(),'HSMETOO');
$seq = $ind->fetch('MMWHISK');
is($seq->length,62);
is($seq->primary_id(),'MMWHISK');
$seq = $ind->fetch('gi|238775|bbs|65126');
is($seq->length,70);

my $stream = $ind->get_PrimarySeq_stream();
$seq = $stream->next_seq;
isa_ok $seq, 'Bio::PrimarySeqI';

$ind = Bio::Index::Fasta->new(-filename => 'multifa_index',
                              -write_flag => 1,
                              -verbose => 0);
$ind->make_index(test_input_file('multifa.seq.qual'));

ok ( -e "multifa_index" );

$ind = Bio::Index::Qual->new(-filename => 'multifa_qual_index',
                             -write_flag => 1,
                             -verbose => 0);
$ind->make_index(test_input_file('multifa.seq.qual'));

ok ( -e "multifa_qual_index" );

ok ( defined($seq) );
isa_ok $seq, 'Bio::SeqI';
$seq = $ind->fetch('HSEARLOBE');
is($seq->length,321);
is($seq->primary_id(),'HSEARLOBE');
$seq = $ind->fetch('HSMETOO');
is($seq->length,134);
is($seq->primary_id(),'HSMETOO');
$seq = $ind->fetch('MMWHISK');
is($seq->length,62);
is($seq->primary_id(),'MMWHISK');
$seq = $ind->fetch('NONEXISTENT_SEQ');
ok(! defined $seq);

$ind = Bio::Index::SwissPfam->new(-filename => 'Wibbl2',
                                  -write_flag =>1);
$ind->make_index(test_input_file('swisspfam.data'));

ok ( -e "Wibbl2" || -e "Wibbl2.pag" );

$ind = Bio::Index::EMBL->new(-filename   => 'Wibbl3',
                             -write_flag =>1);
$ind->make_index(test_input_file('test.embl'));
ok ( -e "Wibbl3" || -e "Wibbl3.pag" );
is ($ind->fetch('AL031232')->length, 4870);

SKIP: {
    test_skip(-tests => 5, -requires_module => 'Data::Stag');
    $ind = Bio::Index::Swissprot->new(-filename   => 'Wibbl4',
                                      -write_flag => 1);
    $ind->make_index(test_input_file('roa1.swiss'));
    ok ( -e "Wibbl4" || -e "Wibbl4.pag" );
    $seq = $ind->fetch('ROA1_HUMAN');
    is ($seq->display_id(), 'ROA1_HUMAN');
    $seq = $ind->fetch('P09651');
    is ($seq->display_id(), 'ROA1_HUMAN');

    # test id_parser
    $ind = Bio::Index::Swissprot->new(-filename   => 'Wibbl4',
                                      -write_flag => 1);
    $ind->id_parser(\&get_id);
    $ind->make_index(test_input_file('roa1.swiss'));
    ok ( -e "Wibbl4" || -e "Wibbl4.pag" );
    $seq = $ind->fetch('X12671');
    is ($seq->length,371);
}


my $gb_ind = Bio::Index::GenBank->new(-filename => 'Wibbl5',
                                      -write_flag =>1,
                                      -verbose    => 0);
$gb_ind->make_index(test_input_file('roa1.genbank'));
ok ( -e "Wibbl5" || -e "Wibbl5.pag" );
$seq = $gb_ind->fetch('AI129902');
is ($seq->length, 37);
is ($seq->species->binomial, 'Homo sapiens');
$seq = $gb_ind->fetch(3598416);
is ($seq->seq,"CTCCGCGCCAACTCCCCCCACCCCCCCCCCACACCCC");

my $cache = Bio::DB::InMemoryCache->new( -seqdb => $gb_ind );

ok ( $cache->get_Seq_by_id('AI129902') );

SKIP: {
   test_skip(-tests => 22, -requires_module => 'Bio::DB::FileCache');

   $cache = Bio::DB::FileCache->new(-seqdb => $gb_ind,
                                    -keep  => 1,
                                    -file  => 'filecache.idx');
   # problem:
   my $seq = $cache->get_Seq_by_id('AI129902');
   ok ( $seq);
   is ( $seq->length, 37);
   is ( lc($seq->seq()), 'ctccgcgccaactccccccaccccccccccacacccc');

   my ( $f1 ) = $seq->get_SeqFeatures();
   is ( ($f1->get_tag_values('sex'))[0], 'female');
   is ( ($f1->get_tag_values('lab_host'))[0], 'DH10B');
   my $species = $seq->species;
   ok( $species );
   is( $species->binomial, 'Homo sapiens');
   is( $species->species(), 'sapiens');
   is( $species->genus(), 'Homo');
   # changes in GenBank file SOURCE line
   # this is now the abbreviated name
   ok defined($species->name('abbreviated'));
   is ($species->name('abbreviated')->[0], 'human');

   $cache = undef;
   $cache = Bio::DB::FileCache->new(-seqdb => $gb_ind,
                                    -keep  => 0,
                                    -file  => 'filecache.idx');
   $seq = $cache->get_Seq_by_id('AI129902');
   ok ( $seq);
   is ( $seq->length, 37);
   is ( lc($seq->seq()), 'ctccgcgccaactccccccaccccccccccacacccc');

   ( $f1 ) = $seq->get_SeqFeatures();
   is ( ($f1->get_tag_values('sex'))[0], 'female');
   is ( ($f1->get_tag_values('lab_host'))[0], 'DH10B');
   $species = $seq->species;
   ok( $species );
   is( $species->binomial, 'Homo sapiens');
   is( $species->species(), 'sapiens');
   is( $species->genus(), 'Homo');
   # changes in GenBank file SOURCE line
   # this is now the abbreviated name
   ok defined($species->name('abbreviated'));
   is ($species->name('abbreviated')->[0], 'human');
}

# test id_parser
$gb_ind = Bio::Index::GenBank->new(-filename => 'Wibbl5',
                                   -write_flag =>1,
                                   -verbose    => 0);
$gb_ind->id_parser(\&get_id);
$gb_ind->make_index(test_input_file('roa1.genbank'));
ok ( -e "Wibbl5" || -e "Wibbl5.pag" );
$seq = $gb_ind->fetch('alpha D-globin');
is ($seq->length,141);

# test Stockholm
my $st_ind = Bio::Index::Stockholm->new(-filename => 'Wibbl6',
                                        -write_flag => 1,
                                        -verbose    => 0);
isa_ok $st_ind, 'Bio::Index::Stockholm';
$st_ind->make_index(test_input_file('testaln.stockholm'));
ok ( -e "Wibbl6" );
my $aln = $st_ind->fetch_aln('PF00244');
isa_ok($aln,'Bio::SimpleAlign');

# test Hmmer
my $hmmer_ind = Bio::Index::Hmmer->new(-filename => 'Wibbl7',
                                       -write_flag => 1,
                                       -verbose    => 0);
isa_ok $hmmer_ind, 'Bio::Index::Hmmer';
$hmmer_ind->make_index(test_input_file('hmmpfam_multiresult.out'));
ok ( -e "Wibbl7" );
my $hmm_result = $hmmer_ind->fetch_report('lcl|gi|340783625|Plus1');
is ($hmm_result->query_description, 'megaplasmid, complete sequence [UNKNOWN]');




sub get_id {
   my $line = shift;
   return $1 if ($line =~ /product="([^"]+)"/);
   return $1 if ($line =~ /^DR\s+EMBL;\s+([^;]+)/);
}

END {
   cleanup();
}

sub cleanup {
   for my $root ( qw( Wibbl Wibbl2 Wibbl3 Wibbl4 Wibbl5 Wibbl6 Wibbl7
                      multifa_index multifa_qual_index ) ) {
      unlink $root if( -e $root );
      unlink "$root.pag" if( -e "$root.pag");
      unlink "$root.dir" if( -e "$root.dir");
   }
}
BioPerl-1.007002/t/LocalDB/Taxonomy000755000766000024          013155576321 16700 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/LocalDB/Taxonomy/greengenes.t000444000766000024       503613155576321 21350 0ustar00cjfieldsstaff000000000000use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    test_begin( -tests => 38 );
    use_ok('Bio::DB::Taxonomy');
    use_ok('Bio::Tree::Tree');
}


my ($db, $id, @ids, $node, $node2, $ancestor, @children, %common_names, $tree, @descs);


# Test Bio::DB::Taxonomy::greengenes

ok $db = Bio::DB::Taxonomy->new( -source => 'greengenes' );

isa_ok $db, 'Bio::DB::Taxonomy::greengenes';
isa_ok $db, 'Bio::DB::Taxonomy::list';
isa_ok $db, 'Bio::DB::Taxonomy';

ok $db = Bio::DB::Taxonomy->new(
   -source   => 'greengenes',
   -taxofile => test_input_file('taxonomy', 'greengenes_taxonomy_16S_candiv_gg_2011_1.txt'),
);

@ids = $db->get_taxonid('Homo sapiens');
is scalar @ids, 0;

@ids = $db->get_taxonid('s__Bacteroides uniformis');
is scalar @ids, 1;
$id = $ids[0];

ok $node = $db->get_taxon($id);
is $node->id, $id;
is $node->object_id, $node->id;
is $node->ncbi_taxid, undef;
is $node->rank, 'species';
is $node->parent_id, 'gg6';
is $node->node_name, 's__Bacteroides uniformis';
is $node->scientific_name, $node->node_name;

is ${$node->name('scientific')}[0], $node->node_name;

%common_names = map { $_ => 1 } $node->common_names;
is scalar keys %common_names, 0;

is $node->division, undef;
is $node->genetic_code, undef;
is $node->mitochondrial_genetic_code, undef;

# briefly test some Bio::Tree::NodeI methods
ok $ancestor = $node->ancestor;
is $ancestor->scientific_name, 'g__Bacteroides';

# unless set explicitly, Bio::Taxon doesn't return anything for
# each_Descendent; must ask the database directly
ok @children = $ancestor->db_handle->each_Descendent($ancestor);
is scalar @children, 2;

# do some trickier things...
ok $node2 = $db->get_taxon('gg104');
is $node2->scientific_name, 'o__Synergistales';

# briefly check that we can use some Tree methods
$tree = Bio::Tree::Tree->new();
is $tree->get_lca($node, $node2)->scientific_name, 'k__Bacteria';

# can we actually form a Tree and use other Tree methods?
ok $tree = Bio::Tree::Tree->new(-node => $node);
is $tree->number_nodes, 7;
is $tree->get_nodes, 7;
is $tree->find_node(-rank => 'genus')->scientific_name, 'g__Bacteroides';
is $tree->find_node(-rank => 'class')->scientific_name, 'c__Bacteroidia';

# check that getting the ancestor still works now we have explitly set the
# ancestor by making a Tree
is $node->ancestor->scientific_name, 'g__Bacteroides';

# we can recursively fetch all descendents of a taxon
my $lca = $db->get_taxon( -name => 'f__Enterobacteriaceae' );
ok @descs = $db->each_Descendent($lca);
is scalar @descs, 2;
@descs = $db->get_all_Descendents($lca);
is scalar @descs, 3;


BioPerl-1.007002/t/LocalDB/Taxonomy/silva.t000444000766000024       527113155576321 20345 0ustar00cjfieldsstaff000000000000use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    test_begin( -tests => 42 );
    use_ok('Bio::DB::Taxonomy');
    use_ok('Bio::Tree::Tree');
}


my ($db, $id, @ids, $node, $node2, $ancestor, @children, %common_names, $tree, @descs);


# Test Bio::DB::Taxonomy::silva

ok $db = Bio::DB::Taxonomy->new( -source => 'silva' );

isa_ok $db, 'Bio::DB::Taxonomy::silva';
isa_ok $db, 'Bio::DB::Taxonomy::list';
isa_ok $db, 'Bio::DB::Taxonomy';

ok $db = Bio::DB::Taxonomy->new(
   -source   => 'silva',
   -taxofile => test_input_file('taxonomy', 'silva_SSURef_108_tax_silva_trunc.fasta'),
);

@ids = $db->get_taxonid('Homo sapiens');
is scalar @ids, 0;

@ids = $db->get_taxonid('Rattus norvegicus');
is scalar @ids, 1;
$id = $ids[0];

ok $node = $db->get_taxon($id);
is $node->id, $id;
is $node->object_id, $node->id;
is $node->ncbi_taxid, undef;
is $node->rank, undef;
is $node->parent_id, 'sv72';
is $node->node_name, 'Rattus norvegicus';
is $node->scientific_name, $node->node_name;

is ${$node->name('scientific')}[0], $node->node_name;

# it has a common name in Silva, but Bio::DB::Taxonomy::silva does not record it
%common_names = map { $_ => 1 } $node->common_names;
is scalar keys %common_names, 0;

is $node->division, undef;
is $node->genetic_code, undef;
is $node->mitochondrial_genetic_code, undef;

# briefly test some Bio::Tree::NodeI methods
ok $ancestor = $node->ancestor;
is $ancestor->scientific_name, '';
ok $ancestor = $ancestor->ancestor;
is $ancestor->scientific_name, 'Rattus';
ok $ancestor = $ancestor->ancestor;
is $ancestor->scientific_name, 'Murinae';

# unless set explicitly, Bio::Taxon doesn't return anything for
# each_Descendent; must ask the database directly
@ids = $db->get_taxonid('Metazoa');
is scalar @ids, 1;
$id = $ids[0];
ok $node = $db->get_taxon($id);
ok @children = $node->db_handle->each_Descendent($node);
is scalar @children, 3; # Chordata, Platyhelminthes, Metazoa

# do some trickier things...
ok $node2 = $db->get_taxon('sv112');
is $node2->scientific_name, 'Mucoromycotina';

# briefly check that we can use some Tree methods
$tree = Bio::Tree::Tree->new();
is $tree->get_lca($node, $node2)->scientific_name, 'Eukaryota';

# can we actually form a Tree and use other Tree methods?
ok $tree = Bio::Tree::Tree->new(-node => $node2);
is $tree->number_nodes, 5;
is $tree->get_nodes, 5;

# check that getting the ancestor still works now we have explitly set the
# ancestor by making a Tree
is $node2->ancestor->scientific_name, 'Basal fungal lineages';

# we can recursively fetch all descendents of a taxon
my $lca = $db->get_taxon( -name => 'Liliopsida' );
ok @descs = $db->each_Descendent($lca);
is scalar @descs, 1;
@descs = $db->get_all_Descendents($lca);
is scalar @descs, 9;

BioPerl-1.007002/t/LocalDB/Taxonomy/sqlite.t000444000766000024      1564413155576321 20555 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(
        
        -requires_modules => [qw( 5.010 DB_File DBI DBD::SQLite )]
    );

    use_ok('Bio::DB::Taxonomy');
    use_ok('Bio::Tree::Tree');
}

my $temp_dir = test_output_dir();

# TODO: run basic tests making sure that a database is not regenerated if
# present or unless forced

ok my $db_flatfile = Bio::DB::Taxonomy->new(
    -source    => 'sqlite',
    -nodesfile => test_input_file('taxdump', 'nodes.dmp'),
    -namesfile => test_input_file('taxdump', 'names.dmp'),
);
isa_ok $db_flatfile, 'Bio::DB::Taxonomy::sqlite';
isa_ok $db_flatfile, 'Bio::DB::Taxonomy';

ok my $db = Bio::DB::Taxonomy->new(
    -source    => 'sqlite',
    -directory => $temp_dir,
    -nodesfile => test_input_file('taxdump', 'nodes.dmp'),
    -namesfile => test_input_file('taxdump', 'names.dmp'),
    -force     => 1,
);

my $id;

# taxid data in the nodes.dmp file should be unique, we ignore repeated values
# if seen

is $db->get_num_taxa, 188;

lives_ok {$id = $db->get_taxonid('Homo sapiens')};

is $id, 9606;

## easy test on human, try out the main Taxon methods
my $n;
ok $n = $db->get_taxon(9606);
is $n->id, 9606;
is $n->object_id, $n->id;
is $n->ncbi_taxid, $n->id;
is $n->parent_id, 9605;
is $n->rank, 'species';

is $n->node_name, 'Homo sapiens';
is $n->scientific_name, $n->node_name;
is ${$n->name('scientific')}[0], $n->node_name;

my %common_names = map { $_ => 1 } $n->common_names;
is keys %common_names, 3, ref($db).": common names";
ok exists $common_names{human};
ok exists $common_names{man};

is $n->division, 'Primates';
is $n->genetic_code, 1;
is $n->mitochondrial_genetic_code, 2;

# these are entrez-only, data not available in dmp files
#if ($db eq $db_entrez) {
#    ok defined $n->pub_date;
#    ok defined $n->create_date;
#    ok defined $n->update_date;
#}

# briefly test some Bio::Tree::NodeI methods
ok my $ancestor = $n->ancestor;
is $ancestor->scientific_name, 'Homo';
# unless set explicitly, Bio::Taxon doesn't return anything for
# each_Descendent; must ask the database directly
ok my @children = $ancestor->db_handle->each_Descendent($ancestor);
is @children, 1;

#sleep(3) if $db eq $db_entrez;
#
## do some trickier things...
ok my $n2 = $db->get_Taxonomy_Node('89593');
is $n2->scientific_name, 'Craniata';

# briefly check we can use some Tree methods
my $tree = Bio::Tree::Tree->new();
is $tree->get_lca($n, $n2)->scientific_name, 'Craniata';

# get lineage_nodes
my @nodes = $tree->get_nodes;
is scalar(@nodes), 0;
my @lineage_nodes;
@lineage_nodes = $tree->get_lineage_nodes($n->id); # read ID, only works if nodes have been added to tree
is scalar @lineage_nodes, 0;
@lineage_nodes = $tree->get_lineage_nodes($n);     # node object always works
cmp_ok(scalar @lineage_nodes, '>', 20);

# get lineage string
like($tree->get_lineage_string($n), qr/cellular organisms;Eukaryota/);
like($tree->get_lineage_string($n,'-'), qr/cellular organisms-Eukaryota/);
like($tree->get_lineage_string($n2), qr/cellular organisms;Eukaryota/);

# can we actually form a Tree and use other Tree methods?
ok $tree = Bio::Tree::Tree->new(-node => $n);
cmp_ok($tree->number_nodes, '>', 20);
cmp_ok(scalar($tree->get_nodes), '>', 20);
is $tree->find_node(-rank => 'genus')->scientific_name, 'Homo';

# check that getting the ancestor still works now we have explitly set the
# ancestor by making a Tree
is $n->ancestor->scientific_name, 'Homo';

ok $n = $db->get_Taxonomy_Node('1760');
is $n->scientific_name, 'Actinobacteria (class)';

# entrez isn't as good at searching as flatfile, so we have to special-case
my @ids = sort $db->get_taxonids('Chloroflexi');
is scalar @ids, 1;
is_deeply \@ids, [200795];

# lowercase
@ids = sort $db->get_taxonids('chloroflexi');
is scalar @ids, 1;
is_deeply \@ids, [200795];

# fuzzy match using SQL syntax to match any 'Chloroflexi'
@ids = sort $db->get_taxonids('Chloroflexi%');
is scalar @ids, 2;
is_deeply \@ids, [200795, 32061];

$id = $db->get_taxonids('Chloroflexi (class)');
is($id, 32061);

@ids = $db->get_taxonids('Rhodotorula');
is @ids, 8;
@ids = $db->get_taxonids('Rhodotorula ');
is @ids, 1;
is $ids[0], 231509;

# get_lca should work on nodes from different databases
SKIP: {
    test_skip(-tests => 9, -requires_networking => 1);

    # check that the result is the same as if we are retrieving from the same DB
    # flatfile
    my $h_flat = $db_flatfile->get_taxon(-name => 'Homo');
    my $h_flat2 = $db_flatfile->get_taxon(-name => 'Homo sapiens');
    ok my $tree_functions = Bio::Tree::Tree->new();
    is $tree_functions->get_lca($h_flat, $h_flat2)->scientific_name, 'Homo', 'get_lca() within flatfile db';

    # entrez
    #my $h_entrez;
    #eval { $h_entrez = $db_entrez->get_taxon(-name => 'Homo sapiens');};
    #skip "Unable to connect to entrez database; no network or server busy?", 7 if $@;
    #my $h_entrez2;
    #eval { $h_entrez2 = $db_entrez->get_taxon(-name => 'Homo');};
    #skip "Unable to connect to entrez database; no network or server busy?", 7 if $@;
    #ok $tree_functions = Bio::Tree::Tree->new();
    #is $tree_functions->get_lca($h_entrez, $h_entrez2)->scientific_name, 'Homo', 'get_lca() within entrez db';

    #ok $tree_functions = Bio::Tree::Tree->new();
    # mixing entrez and flatfile
    #TODO:{
    #    local $TODO = 'Mixing databases for get_lca() not working, see bug #3416';
    #    is $tree_functions->get_lca($h_flat, $h_entrez)->scientific_name, 'Homo', 'get_lca() mixing flatfile and remote db';
    #}
    # even though the species taxa for Homo sapiens from list and flat databases
    # have the same internal id, get_lca won't work because they have different
    # roots and descendents
    #$h_list = $db_list->get_taxon(-name => 'Homo sapiens');
    #is $h_list->ancestor->internal_id, $h_flat->internal_id;
    #ok ! $tree_functions->get_lca($h_flat, $h_list);

    # but we can form a tree with the flat node then remove all the ranks we're
    # not interested in and try again
    #$tree = Bio::Tree::Tree->new(-node => $h_flat);
    #$tree->splice(-keep_rank => \@ranks);
    #is $tree->get_lca($h_flat, $h_list)->scientific_name, 'Homo';
}

# Some tests carried over from flatfile and others that would be nice to pass

# ideas from taxonomy2tree.PLS that let us make nice tree, using
# Bio::Tree::TreeFunctionsI methods; this is a weird and trivial example just
# because our test flatfile database only has the full lineage of one species
undef $tree;
for my $name ('Human', 'Hominidae') {
  my $ncbi_id = $db_flatfile->get_taxonid($name);
  if ($ncbi_id) {
    my $node = $db_flatfile->get_taxon(-taxonid => $ncbi_id);

    if ($tree) {
        ok $tree->merge_lineage($node);
    }
    else {
        ok $tree = Bio::Tree::Tree->new(-node => $node);
    }
  }
}
is $tree->get_nodes, 30;
$tree->contract_linear_paths;
my $ids = join(",", map { $_->id } $tree->get_nodes);
is $ids, '131567,9606';

END {
    unlink 'taxonomy.sqlite' if (-e 'taxonomy.sqlite');
}

done_testing();
BioPerl-1.007002/t/Map000755000766000024          013155576321 14337 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Map/Cyto.t000444000766000024      1245213155576321 15623 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 110);
    
    use_ok('Bio::Map::CytoMap');
    use_ok('Bio::Map::CytoPosition');
    use_ok('Bio::Map::CytoMarker');
}

#
# Let's test first the map class : Bio::Map::CytoMap
#

ok my $map = Bio::Map::CytoMap->new(-name  => 'my');
is $map->type, 'cyto'; 
is $map->units, ''; 
is $map->length, 0;
is $map->name, 'my';
is $map->species('human'), 'human';
is $map->species, 'human';
is $map->unique_id, '1';

#
#
# Secondly, we make sure the location calculations in
#           Bio::Map::CytoPosition make sense
#

my($a, $b, $r);
my $string = 'b';
is Bio::Map::CytoPosition::_pad($string, 5, 'z'), 'bzzzz';

ok $a = Bio::Map::CytoPosition->new();
isa_ok $a, 'Bio::Map::CytoPosition';
is $a->cytorange, undef;


$a->verbose(2);
eval {
    is $a->value('C'), 'C'; 
    is $a->cytorange, undef ;
};
ok $@;
$a->verbose(0);

is $a->value('X'), 'X';
$r = $a->cytorange;
isa_ok $r, 'Bio::Range';
is $r->start, 100000000;
is $r->end, 100200000;

$a->value('1p');
is $a->cytorange->start, 1000000;
is $a->cytorange->end, 1100000;

$a->value('2qter');
is $a->cytorange->start, 2200000;
is $a->cytorange->end, 2200000;

$a->value('2qcen');
is $a->cytorange->start, 2100000;
is $a->cytorange->end, 2100000;

eval {
    $a->value('2qcen2');
    $a->cytorange->start;
};
ok 1 if $@;

$a->value('2q22');
is $a->cytorange->start, 2122000;
is $a->cytorange->end, 2122999;

$a->value('2p22');
is $a->cytorange->start, 2077001;
is $a->cytorange->end, 2078000;

$a->value('2p21');
is $a->cytorange->start, 2078001;
is $a->cytorange->end, 2079000;

$a->value('10p22.1-cen');
is $a->cytorange->start, 10022199;
is $a->cytorange->end, 10100000;

eval {
    $a->value('10q22.1-cen');
    $a->cytorange->start;
};
ok 1 if $@;

$a->value('10q22.1-ter');
is $a->cytorange->start, 10122100;
is $a->cytorange->end, 10200000;


eval {
    $a->value('10q22.1-p');
    $a->cytorange->start;
};
ok 1 if $@;

$a->value('10qcen-qter');
is $a->cytorange->start, 10100000;
is $a->cytorange->end, 10200000;

$a->value('10pcen-qter');
is $a->cytorange->start, 10100000;
is $a->cytorange->end, 10200000;

$a->value('10q22.1-q23');
is $a->cytorange->start, 10122100;
is $a->cytorange->end, 10123999;
cmp_ok ($a->cytorange->start, '<', $a->cytorange->end );

$a->value('10p22.1-p23');
is $a->cytorange->start, 10076001;
is $a->cytorange->end,  10077900;
cmp_ok ($a->cytorange->start, '<', $a->cytorange->end );

$a->value('10cen-p23');
is $a->cytorange->start, 10076001;
is $a->cytorange->end, 10100000;
cmp_ok ($a->cytorange->start, '<', $a->cytorange->end );

$a->value('10q22.1-p23');
is $a->cytorange->start, 10076001;
is $a->cytorange->end, 10122199;
cmp_ok ($a->cytorange->start, '<', $a->cytorange->end );

$a->value('10p22.1-q23');
is $a->cytorange->start, 10077801;
is $a->cytorange->end, 10123999;
cmp_ok ($a->cytorange->start, '<', $a->cytorange->end );

$a->value('10q22.1-p22');
is $a->cytorange->start, 10077001 ;
is $a->cytorange->end, 10122199 ;

$b = Bio::Map::CytoPosition->new();
$b->value('10p22-p22.1');
is $b->cytorange->start, 10077801 ;
is $b->cytorange->end, 10078000;
ok $a->cytorange->overlaps($b->cytorange);

$a->value('10p22.1-q23');
is $a->cytorange->start, 10077801;
is $a->cytorange->end, 10123999;
cmp_ok ($a->cytorange->start, '<', $a->cytorange->end );

$a->value('17p13-pter');
is $a->cytorange->start, 17000000;
is $a->cytorange->end, 17087000;
cmp_ok ($a->cytorange->start, '<', $a->cytorange->end );

$a->value('17cen-pter');
is $a->cytorange->start, 17000000;
is $a->cytorange->end, 17100000;
cmp_ok ($a->cytorange->start, '<', $a->cytorange->end );


#-----------------------------------------
#my $s;

sub test {
    my ($s) = @_;
    my $a = Bio::Map::CytoPosition->new();
    $a->value($s);
    $r = $a->cytorange;
    is $a->range2value($r), $s;
}

test '1';
test '2p';
test '3q';
test '4cen';

test '5pter';
test '6qter';
test '7p21';
test '8q11.1';

test '9q13.13-15';
test '10p13.13-q15';
test '11p13.13-qter';
test '12p13.13-qter';
test '13p13.13-14';
test '14p13.13-pter';
test '15cen-q2';
test '16cen-p2';
#test '17cen-pter'; eq 17p
#test '18cen-qter'; eq 18q 


# by now we should be convinced that band conversion to a range works
# so lets try to use it for comparing markers.

ok my $marker1 = Bio::Map::CytoMarker->new();
is $marker1->name('gene1'), 'gene1' ;
ok $marker1->position($map, '10p33.13-q15');

ok my $marker2 = Bio::Map::CytoMarker->new(-name => 'gene2' );
ok $marker2->position($map, '10p10-15');
is $marker1->get_chr, 10;

ok my $marker3 = Bio::Map::CytoMarker->new(-name => '3' );
ok $marker3->position($map, '10p1');

ok my $marker4 = Bio::Map::CytoMarker->new(-name => '4' );
ok $marker4->position($map, '10q2');

#
# Lastly, let's test the comparison methods
#

ok $marker1->equals($marker1);
ok ! $marker1->equals($marker2);

ok $marker3->less_than($marker4);
ok ! $marker3->greater_than($marker4);
ok ! $marker4->less_than($marker3);
ok $marker4->greater_than($marker3);

ok ! $marker4->overlaps($marker3);
ok $marker1->overlaps($marker3);

ok ! $marker4->contains($marker3);
ok $marker1->contains($marker3);

# 
# Test throw() in some private functions
#

eval { Bio::Map::CytoPosition::_pad('string', -1, 'x'); };
like($@, qr/positive integer/);
eval { Bio::Map::CytoPosition::_pad('string', +1, 'toolong'); };
like($@, qr/single character/);

BioPerl-1.007002/t/Map/Linkage.t000444000766000024       354713155576321 16244 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 18);
	
	use_ok('Bio::Map::LinkagePosition');
	use_ok('Bio::Map::Microsatellite');
	use_ok('Bio::Map::LinkageMap');
}

#require_ok('dumpvar.pl');

my $verbose = test_debug();
ok my $map = Bio::Map::LinkageMap->new('-verbose' => $verbose,
				   '-name'    => 'Leviathon',
				   '-type'    => 'Genetic',
				   '-units'   => 'cM',
				   '-species' => "Brassica");
is ref($map), 'Bio::Map::LinkageMap';
is $map->name, 'Leviathon';
is $map->type, 'Genetic';
is $map->units, 'cM';
is $map->species, 'Brassica';
is $map->unique_id, '1';

ok my $position = Bio::Map::LinkagePosition->new('-order' => 2,
						'-map' =>  $map, 
						'-value' => 22.3
						);

is $position->order, 2;
ok my $map2 = $position->map;
is $position->value, 22.3;

ok my $o_usat = Bio::Map::Microsatellite->new('-name'     => "Chad marker",
					     '-position' => $position);

is $o_usat->name, 'Chad marker';
is $o_usat->position, $position ;
ok $map->add_element($o_usat);

#use Data::Dumper; print Dumper($map);
#----------------------------
#ok my $position2 = Bio::Map::LinkagePosition->new(-order => qw(3 4 5),
#						 );
# print("position2 looks like this:\n");
# dumpValue($position2);
#is(($position2->each_position_value('fakemap'))[0], 0);
#is $position2->order, 3;

#-------------
#is($position->order, 2);
#is(($position->each_position_value($map))[0], 22.3);
	# what should be printed if this was ok?
	# ok(1);

#ok my $o_usat = Bio::Map::Microsatellite->new('-name'     => "Chad marker",
#					      '-position' => $position);
#
#is $o_usat->name, 'Chad marker';
#is $o_usat->position, $position ;
#ok $map->add_element($o_usat);
# what should be printed if this is ok?
#dumpValue($map);

# add more tests
# see also t/microsatellite.t and t/linkageposition.t
BioPerl-1.007002/t/Map/Map.t000444000766000024      7300413155576321 15422 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 267);

    use_ok('Bio::Map::SimpleMap');
    use_ok('Bio::Map::Marker');
    use_ok('Bio::Map::Position');
    use_ok('Bio::Map::Relative');
    use_ok('Bio::Map::Mappable');
}

###
# We explicitly test Bio::Map::SimpleMap, Bio::Map::Mappable, Bio::Map::Position,
# Bio::Map::Marker and Bio::Map::Relative.
#
# We implicitly test Bio::Map::MapI, Bio::Map::MappableI, Bio::Map::PositionI,
# and Bio::Map::PositionHandler.
###

# Test map basics
my $map;
{
    ok $map = Bio::Map::SimpleMap->new(-name  => 'my');
    ok $map->type('cyto');
    is $map->type, 'cyto';
    is $map->units, '';
    is $map->length, 0, "Length is ". $map->length;
    is $map->name, 'my';
    is $map->species('human'), 'human';
    is $map->species, 'human';
    is $map->unique_id, '1';
}

# Test marker basics
my $marker;
{
    # make a plane one and add details after
    ok $marker = Bio::Map::Marker->new();
    is $marker->name('gene1'), 'gene1';
    ok $marker->position($map, 100);
    is $marker->position->value, 100;
    is $marker->map, $map;

    # make positions a little easier to add by setting a default map first
    ok my $marker2 = Bio::Map::Marker->new(-name => 'gene3');
    ok $map->add_element($marker2); # one way of setting default
    is $marker2->default_map, $map;
    $marker2 = Bio::Map::Marker->new(-name => 'gene3');
    ok $marker2->default_map($map); # the other way of setting default
    is $marker2->default_map, $map;
    ok $marker2->position(300);
    is $marker2->position->value, 300;
    ok my $position = $marker2->position();
    is $position->value, 300;

    # make one with details set in new()
    ok my $marker3 = Bio::Map::Marker->new(-name => 'gene2', -position => [$map, 200]);
    is $marker3->default_map, $map;
    is $marker3->position->value, 200;

    # make one with multiple positions on multiple maps
    my $map2 = Bio::Map::SimpleMap->new();
    $marker2->positions([[$map, 150], [$map, 200], [$map2, 200], [$map2, 400]]);
    my @p = map($_->numeric, $marker2->each_position);
    is $p[0], 150;
    is $p[1], 200;
    is $p[2], 200;
    is $p[3], 300;
    is $p[4], 400;
    $marker2->purge_positions($map2);
    @p = map($_->numeric, $marker2->each_position);
    is $p[0], 150;
    is $p[1], 200;
    is $p[2], 300;

    # make sure we can add positions with 0 value
    my $map3 = Bio::Map::SimpleMap->new();
    $marker->add_position($map3, 0);
    ok my @positions = $marker->get_positions($map3);
    is @positions, 1;
    is $positions[0]->value, 0;
}

# Test position basics
my $pos;
{
    ok $pos = Bio::Map::Position->new();
    ok $pos->map($map);
    is $pos->map(), $map;
    ok $pos->element($marker);
    is $pos->element(), $marker;

    ok $pos->value('10');
    is $pos->value(), '10';
    is $pos->numeric, 10;
    is $pos->sortable, 10;
    is $pos->start, 10;
    is $pos->end, 10;

    # give a marker a single position with explicit position creation
    ok $pos = Bio::Map::Position->new(-map => $map, -value => 500);
    ok $marker->position($pos);
    ok my $got_pos = $marker->position();
    is $got_pos, $pos;
    is $marker->position->value, 500;

    # add a position
    my $map2 = Bio::Map::SimpleMap->new(-name => 'genethon', -type => 'Genetic');
    my $pos2 = Bio::Map::Position->new(-map => $map2, -value => 100);
    $marker->add_position($pos2);
    ok my @positions = $marker->get_positions($map2);
    is @positions, 1;
    is $positions[0]->value, 100;
}

# Test interaction of Markers and Maps via Positions
{
    # markers know what maps they are on
    $marker->purge_positions;
    is $marker->known_maps, 0;
    $pos->element($marker);
    is $marker->known_maps, 1;
    ok $marker->in_map(1);
    ok $marker->in_map($map);

    # maps know what markers are on themselves
    $map->purge_positions;
    my @els = $map->get_elements;
    is @els, 0;
    $pos->map($map);
    ok my @elements = $map->get_elements;
    is @elements, 1;
    is $elements[0], $marker;

    # positions know what marker they are for and what map they are on
    is $pos->map, $map;
    is $pos->element, $marker;
}

# We can compare Map objects to their own kind
{
    # positions to positions
    {
        ok $pos->equals($pos);
        # these get tested properly when testing Relative, later
    }

    # markers to markers
    {
        ok $marker->equals($marker);
        # these get tested properly when testing Mappables, later
    }

    # maps to maps
    {
        my $human = Bio::Map::SimpleMap->new();
        my $mouse = Bio::Map::SimpleMap->new();
        my $chicken = Bio::Map::SimpleMap->new();
        my $aardvark = Bio::Map::SimpleMap->new();

        # scenario 1: we have information about where some factors bind upstream
        # of a gene in 4 different species. Which factors are found in all the
        # species?
        my $fac1 = Bio::Map::Mappable->new();
        my $pos1 = Bio::Map::Position->new(-map => $human, -element => $fac1);
        my $pos2 = Bio::Map::Position->new(-map => $mouse, -element => $fac1);
        my $pos3 = Bio::Map::Position->new(-map => $chicken, -element => $fac1);
        my $pos4 = Bio::Map::Position->new(-map => $aardvark, -element => $fac1);
        my $fac2 = Bio::Map::Mappable->new();
        my $pos5 = Bio::Map::Position->new(-map => $human, -element => $fac2);
        my $pos6 = Bio::Map::Position->new(-map => $mouse, -element => $fac2);
        my $pos7 = Bio::Map::Position->new(-map => $chicken, -element => $fac2);
        my $fac3 = Bio::Map::Mappable->new();
        my $pos8 = Bio::Map::Position->new(-map => $human, -element => $fac3);
        my $pos9 = Bio::Map::Position->new(-map => $mouse, -element => $fac3);

        # scenario 1 answer:
        ok my @factors = $human->common_elements([$mouse, $chicken, $aardvark]);
        is @factors, 1;
        ok @factors = $human->common_elements([$mouse, $chicken, $aardvark], -min_percent => 50);
        is @factors, 3;
        ok @factors = $human->common_elements([$mouse, $chicken, $aardvark], -min_percent => 50, -min_num => 3);
        is @factors, 2;
        ok @factors = $chicken->common_elements([$mouse, $human, $aardvark], -min_percent => 50, -require_self => 1);
        is @factors, 2;
        ok @factors = Bio::Map::SimpleMap->common_elements([$human, $mouse, $human, $aardvark], -min_percent => 50, -required => [$aardvark]);
        is @factors, 1;
    }
}

# Test relative positions
{
    my $map = Bio::Map::SimpleMap->new();
    my $pos1 = Bio::Map::Position->new(-map => $map, -start => 50, -length => 5);
    my $pos2 = Bio::Map::Position->new(-map => $map, -start => 100, -length => 5);
    ok my $relative = Bio::Map::Relative->new(-position => $pos2);
    ok $pos1->relative($relative);
    is $pos1->start, 50;
    is $pos1->absolute(1), 1;
    is $pos1->start, 150;
    is $pos1->absolute(0), 0;
    ok my $relative2 = Bio::Map::Relative->new(-map => 10);
    my $pos3 = Bio::Map::Position->new(-map => $map, -element => $marker, -start => -5, -length => 5);
    $pos3->relative($relative2);
    my $relative3 = Bio::Map::Relative->new(-position => $pos3);
    is $pos1->start($relative3), 145;
    is $pos1->numeric($relative3), 145;
    is $pos1->end($relative3), 149;

    # Test the RangeI-related methods on relative positions
    {
        my $pos1 = Bio::Map::Position->new(-map => $map, -start => 50, -length => 10);
        my $pos2 = Bio::Map::Position->new(-map => $map, -start => 100, -length => 10);
        my $pos3 = Bio::Map::Position->new(-map => $map, -start => 45, -length => 1);
        my $pos4 = Bio::Map::Position->new(-map => $map, -start => 200, -length => 1);
        my $relative = Bio::Map::Relative->new(-position => $pos3);
        my $relative2 = Bio::Map::Relative->new(-position => $pos4);
        ok ! $pos1->overlaps($pos2);
        $pos1->relative($relative);
        ok $pos1->overlaps($pos2);
        ok $pos2->overlaps($pos1);
        ok $pos1->overlaps($pos2, undef, $relative2);

        # Make sure it works with normal Ranges
        use Bio::Range;
        my $range = Bio::Range->new(-start => 100, -end => 109);
        ok $pos1->overlaps($range);
        ok ! $range->overlaps($pos1);
        $pos1->absolute(1);
        ok $range->overlaps($pos1);
        $pos1->absolute(0);

        # Try the other methods briefly
        ok my $i = $pos1->intersection($pos2); # returns a mappable
        ($i) = $i->get_positions; # but we're just interested in the first (and only) position of mappable
        is $i->toString, '100..104';
        ok $i = $pos1->intersection($pos2, undef, $relative2);
        ($i) = $i->get_positions;
        is $i->toString, '-100..-96';
        is $i->map, $map;
        is $i->relative, $relative2;
        $i->absolute(1);
        is $i->toString, '100..104';

        ok my $u = $pos1->union($pos2);
        ($u) = $u->get_positions;
        is $u->toString, '95..109';
        ok $u = $pos1->union($pos2, $relative2);
        ($u) = $u->get_positions;
        is $u->toString, '-105..-91';
        is $u->map, $map;
        is $u->relative, $relative2;
        $u->absolute(1);
        is $u->toString, '95..109';

        ok ! $pos1->contains($pos2);
        $pos2->end(104);
        ok $pos1->contains($pos2);
        ok $pos1->contains(100);

        ok ! $pos1->equals($pos2);
        $pos2->start(95);
        ok $pos1->equals($pos2);
    }
}

# Test Mappables
{
    ok my $gene = Bio::Map::Mappable->new();
    my $human = Bio::Map::SimpleMap->new();
    my $mouse = Bio::Map::SimpleMap->new();
    ok my $pos1 = Bio::Map::Position->new(-map => $human, -element => $gene, -start => 50, -length => 1000);
    my $pos2 = Bio::Map::Position->new(-map => $mouse, -start => 100, -length => 1000);
    $gene->add_position($pos2);
    my $gene_rel = Bio::Map::Relative->new(-element => $gene);

    # scenario 1a: we know where a TF binds upstream of a gene in human.
    # we use four different programs to predict the site; how good were they?
    # scenaria 1b: to what extent do the predictions and known agree?
    my $factor = Bio::Map::Mappable->new();
    my $pos3 = Bio::Map::Position->new(-map => $human, -element => $factor, -start => -25, -length => 10, -relative => $gene_rel);
    my $perfect_prediction = Bio::Map::Mappable->new();
    my $pos4 = Bio::Map::Position->new(-map => $human, -element => $perfect_prediction, -start => 25, -length => 10);
    my $good_prediction = Bio::Map::Mappable->new();
    my $pos5 = Bio::Map::Position->new(-map => $human, -element => $good_prediction, -start => 24, -length => 10);
    my $ok_prediction = Bio::Map::Mappable->new();
    my $pos6 = Bio::Map::Position->new(-map => $human, -element => $ok_prediction, -start => 20, -length => 10);
    my $bad_prediction = Bio::Map::Mappable->new();
    my $pos7 = Bio::Map::Position->new(-map => $human, -element => $bad_prediction, -start => 10, -length => 10);

    # scenario 2: we have the same program making a prediciton for a site
    # in two different species; is the predicted site conserved in terms of
    # its position relative to the gene?
    my $human_prediction = Bio::Map::Mappable->new();
    my $pos8 = Bio::Map::Position->new(-map => $human, -element => $human_prediction, -start => 25, -length => 10);
    my $mouse_prediction = Bio::Map::Mappable->new();
    my $pos9 = Bio::Map::Position->new(-map => $mouse, -element => $mouse_prediction, -start => 75, -length => 10);

    # Test the RangeI-related methods
    {
        # scenario 1a answers:
        ok $perfect_prediction->equals($factor);
        ok $perfect_prediction->contains($factor);
        ok ! $ok_prediction->equals($factor);
        ok $ok_prediction->overlaps($factor);
        ok ! $bad_prediction->overlaps($factor);
        ok $bad_prediction->less_than($factor);
        ok ! $bad_prediction->greater_than($factor);
        ok $factor->greater_than($bad_prediction);

        # scenario 1b answer:
        my $predictions = [$perfect_prediction, $good_prediction, $ok_prediction, $bad_prediction];
        ok my @groups = $factor->overlapping_groups($predictions, -relative => $gene_rel);
        is @groups, 2;
        is ${$groups[1]}[0], $pos7;
        is ${$groups[0]}[0], $pos6;
        is ${$groups[0]}[1], $pos5;
        is ${$groups[0]}[2]->toString($gene_rel), $pos4->toString($gene_rel);
        is ${$groups[0]}[3]->toString($gene_rel), $pos3->toString($gene_rel);
        ok my $di = $factor->disconnected_intersections($predictions, -relative => $gene_rel, -min_mappables_num => 3);
        my @di = $di->get_positions;
        is @di, 1;
        is $di[0]->toString, '-25..-21';
        ok my $du = $factor->disconnected_unions($predictions, -relative => $gene_rel, -min_mappables_num => 3);
        my @du = $du->get_positions;
        is @du, 1;
        is $du[0]->toString, '-30..-16';

        # test the flags on overlapping_groups a bit more
        @groups = $factor->overlapping_groups($predictions, -relative => $gene_rel, -min_pos_num => 2);
        is @groups, 1;
        @groups = $factor->overlapping_groups($predictions, -relative => $gene_rel, -min_pos_num => 1, -min_mappables_num => 2);
        is @groups, 1;
        @groups = $factor->overlapping_groups($predictions, -relative => $gene_rel, -min_pos_num => 1, -min_mappables_num => 1, -min_mappables_percent => 50);
        is @groups, 1;
        @groups = $factor->overlapping_groups($predictions, -relative => $gene_rel, -min_pos_num => 1, -min_mappables_num => 1, -min_mappables_percent => 5);
        is @groups, 2;
        @groups = $factor->overlapping_groups($predictions, -relative => $gene_rel, -require_self => 1);
        is @groups, 1;
        @groups = $factor->overlapping_groups($predictions, -relative => $gene_rel, -required => [$factor]);
        is @groups, 1;

        # scenario 2 answer:
        ok ! $human_prediction->overlaps($mouse_prediction);
        ok $human_prediction->overlaps($mouse_prediction, -relative => $gene_rel);
    }
}

# complex (multi-mappable, multi-map) test of disconnected_*
# and test Bio::Map::GeneMap, Bio::Map::Gene, Bio::Map::TranscriptionFactor,
# Bio::Map::GeneRelative, Bio::Map::GenePosition and Bio::Map::Prediction
use_ok('Bio::Map::Gene');
use_ok('Bio::Map::GeneMap');
use_ok('Bio::Map::TranscriptionFactor');
use_ok('Bio::Map::GeneRelative');
use_ok('Bio::Map::GenePosition');
use_ok('Bio::Map::Prediction');
{
    my @genes;
    my @predictions;

    $genes[0] = Bio::Map::Gene->get(-universal_name => 'gene1');
    $genes[1] = Bio::Map::Gene->get(-universal_name => 'gene2');
    $genes[2] = Bio::Map::Gene->get(-universal_name => 'gene3');
    Bio::Map::GeneMap->get(-gene => 'gene1',
                           -species => 'species1',
                           -upstream => 1000);
    Bio::Map::GeneMap->get(-gene => 'gene1',
                           -species => 'species2',
                           -upstream => 2000);
    Bio::Map::GeneMap->get(-gene => 'gene2',
                           -species => 'species1',
                           -upstream => 1000);
    Bio::Map::GeneMap->get(-gene => 'gene2',
                           -species => 'species2',
                           -upstream => 2000);
    Bio::Map::GeneMap->get(-gene => 'gene3',
                           -species => 'species1',
                           -upstream => 1000);
    Bio::Map::GeneMap->get(-gene => 'gene3',
                           -species => 'species2',
                           -upstream => 2000);

    $predictions[0] = Bio::Map::Prediction->new(-source => 'meme');
    Bio::Map::Position->new(-element => $predictions[0],
                            -map => Bio::Map::GeneMap->get(-gene => 'gene1', -species => 'species1'),
                            -start => 950,
                            -end => 960);
    Bio::Map::Position->new(-element => $predictions[0],
                            -map => Bio::Map::GeneMap->get(-gene => 'gene1', -species => 'species2'),
                            -start => 1950,
                            -end => 1960);
    Bio::Map::Position->new(-element => $predictions[0],
                            -map => Bio::Map::GeneMap->get(-gene => 'gene2', -species => 'species1'),
                            -start => 955,
                            -end => 965);
    Bio::Map::Position->new(-element => $predictions[0],
                            -map => Bio::Map::GeneMap->get(-gene => 'gene2', -species => 'species2'),
                            -start => 1955,
                            -end => 1965);
    $predictions[1] = Bio::Map::Prediction->new(-source => 'meme');
    Bio::Map::Position->new(-element => $predictions[1],
                            -map => Bio::Map::GeneMap->get(-gene => 'gene1', -species => 'species1'),
                            -start => 950,
                            -end => 960);
    Bio::Map::Position->new(-element => $predictions[1],
                            -map => Bio::Map::GeneMap->get(-gene => 'gene1', -species => 'species2'),
                            -start => 1950,
                            -end => 1960);
    Bio::Map::Position->new(-element => $predictions[1],
                            -map => Bio::Map::GeneMap->get(-gene => 'gene3', -species => 'species1'),
                            -start => 956,
                            -end => 966);
    Bio::Map::Position->new(-element => $predictions[1],
                            -map => Bio::Map::GeneMap->get(-gene => 'gene3', -species => 'species2'),
                            -start => 1956,
                            -end => 1966);

    Bio::Map::Position->new(-element => $predictions[0],
                            -map => Bio::Map::GeneMap->get(-gene => 'gene2', -species => 'species2'),
                            -start => 19850,
                            -end => 19860);
    Bio::Map::Position->new(-element => $predictions[1],
                            -map => Bio::Map::GeneMap->get(-gene => 'gene2', -species => 'species2'),
                            -start => 19850,
                            -end => 19860);

    my $rel = Bio::Map::GeneRelative->new(-gene => 0);
    my $di = Bio::Map::Mappable->disconnected_intersections(\@predictions,
                                                            -min_mappables_percent => 100,
                                                            -min_map_percent => 100,
                                                            -relative => $rel);
    my @positions = $di->get_positions;
    my $expected;
    $expected->{gene1}->{species1} = '-45..-41';
    $expected->{gene1}->{species2} = '-45..-41';
    $expected->{gene2}->{species1} = '-45..-41';
    $expected->{gene2}->{species2} = '-45..-41';
    $expected->{gene3}->{species1} = '-45..-41';
    $expected->{gene3}->{species2} = '-45..-41';
    foreach my $pos (@positions) {
        my $map = $pos->map;
        my $gname = $map ? $map->gene->universal_name : 'n/a';
        my $species = $map ? $map->species : 'n/a';
        if (defined $expected->{$gname}->{$species}) {
            is $expected->{$gname}->{$species}, $pos->toString;
            delete $expected->{$gname}->{$species};
        }
        unless (keys %{$expected->{$gname}} > 0) {
            delete $expected->{$gname};
        }
    }
    is scalar(keys %{$expected}), 0;

    # check we don't have any extraneous positions
    $expected = 8;
    foreach my $map ($genes[0]->known_maps) {
        foreach my $pos ($map->get_positions) {
            $expected--;
        }
    }
    is $expected, 0;
    $expected = 8;
    foreach my $map ($genes[1]->known_maps) {
        foreach my $pos ($map->get_positions) {
            $expected--;
        }
    }
    is $expected, 0;
}

{
	# make some maps that will represent an area around a particular gene in
	# particular species
    ok my $map1 = Bio::Map::GeneMap->get(-gene => 'BRCA2',
                                         -species => 'human',
                                         -description => 'breast cancer 2, early onset');
    ok my $gene = $map1->gene;
	my $map2 = Bio::Map::GeneMap->get(-gene => $gene,
                                      -species => 'mouse',
                                      -upstream => 500);
    is $map1->gene, $map2->gene;
    is $gene->universal_name, 'BRCA2';
    is $gene->description, 'breast cancer 2, early onset';
    is $map1->universal_name, 'BRCA2';
    is $map1->upstream, 1000;
    is $map2->upstream, 500;
    my $map3 = Bio::Map::GeneMap->get(-gene => 'BRCA2', -species => 'human');
    is $map3, $map1;
    is $map3->gene, $gene;

	# model a TF that binds 500bp upstream of the BRCA2 gene in humans and
	# 250bp upstream of BRCA2 in mice
	ok my $rel = Bio::Map::GeneRelative->new(-description => "gene start");
    ok my $tf = Bio::Map::TranscriptionFactor->get(-universal_name => 'tf1');
    is $tf->universal_name, 'tf1';
	Bio::Map::Position->new(-map => $map1,
                            -element => $tf,
                            -start => -450,
                            -length => 10,
                            -relative => $rel);
	Bio::Map::Position->new(-map => $map2,
                            -element => $tf,
                            -start => -200,
                            -length => 10,
                            -relative => $rel);

	# find out all the things that map near BRCA2 in all species
    my %answers = (human => ['human', 'tf1', -450, 'gene start', 551], mouse => ['mouse', 'tf1', -200, 'gene start', 301]);
	foreach my $map ($gene->known_maps) {
        my @answers = @{$answers{$map->species}};
		foreach my $thing ($map->get_elements) {
            next if $thing eq $gene;
            foreach my $pos ($thing->get_positions($map)) {
                is $map->species, shift @answers;
                is $thing->universal_name, shift @answers;
                is $pos->value, shift @answers;
                is $pos->relative->description, shift @answers;
                $pos->absolute(1);
                is $pos->start, shift @answers;
            }
		}
        is @answers, 0;
        delete $answers{$map->species};
	}
    is keys %answers, 0;

    # test getting abolute positions of things relative to things that don't
    # even exist in the map yet: 1st exon of default transcript
    ok $rel = Bio::Map::GeneRelative->new(-exon => [1]);
    my $pos = Bio::Map::Position->new(-map => $map1,
                                      -element => $tf,
                                      -start => 5,
                                      -length => 5,
                                      -relative => $rel);
    is $pos->start, 5;
    is $pos->relative->absolute_conversion($pos), 1006;
    is $pos->start($pos->absolute_relative), 1006;
    $pos->absolute(1);
    is $pos->start, 1006;
    is $pos->end, 1010;

    # now actually add some transcripts, exons, introns, coding etc. and retest
    ok my $trans = Bio::Map::GenePosition->new(-start => 0, -length => 700, -map => $map1, -type => 'transcript');
    ok $gene->add_transcript_position($trans);
    ok my $gene_pos = $gene->position($map1);
    is $gene_pos->start, 1001;
    is $gene_pos->end, 1700; # the gene position is big enough to hold the transcript

    $trans = Bio::Map::GenePosition->new(-start => 100, -length => 800, -map => $map1, -type => 'transcript');
    $gene->add_transcript_position($trans);
    is $gene_pos->end, 1900;
    is $gene->active_transcript($map1), 2;
    my @t_pos = $gene->get_transcript_positions($map1);
    is @t_pos, 2;

    # pos was relative to the active transcript, which has now changed...
    is $pos->start, 1106;

    # make a new one relative to an explicit transcript
    $rel = Bio::Map::GeneRelative->new(-exon => [1, 2]);
    my $pos2 = Bio::Map::Position->new(-map => $map1,
                            -element => $tf,
                            -start => 15,
                            -length => 15,
                            -relative => $rel);
    is $pos2->start, 15;
    $pos2->absolute(1);
    is $pos2->start, 1116;
    is $pos2->end, 1130;

    # which isn't affected by changing the active
    is $gene->active_transcript($map1, 1), 1;
    is $pos->start, 1006;
    is $pos2->start, 1116;

    $map1->get_position_handler->purge_positions($pos2);

    # add some exons to the first transcript
    ok my $exon = Bio::Map::GenePosition->new(-start => 0, -length => 100, -map => $map1, -type => 'exon');
    $gene->add_exon_position($exon, 1);
    is $pos->start, 1006;
    $exon->start(30); # not something you'd normally do; just for demo purposes
    is $exon->relative->absolute_conversion($exon), 1031;
    is $pos->start, 1036;

    # add another exon before the previous one - this will be considered exon 1
    my $exon1 = Bio::Map::GenePosition->new(-start => 0, -length => 20, -map => $map1, -type => 'exon');
    $gene->add_exon_position($exon1, 1);
    is $gene->get_exon_position($map1, 2), $exon;
    ok my @exons = $gene->get_exon_positions($map1);
    is @exons, 2;
    is $exons[0], $exon1;
    is $exons[1], $exon;
    is $pos->start, 1006;

    # add the intervening intron
    ok my $intron = Bio::Map::GenePosition->new(-start => 20, -length => 10, -map => $map1, -type => 'intron');
    ok ! $gene->get_intron_position($map1, 1);
    $gene->add_intron_position($intron, 1);
    is $gene->get_intron_position($map1, 1), $intron;
    ok ! $gene->get_intron_position($map1, 1, 2);
    ok ! $gene->get_intron_position($map1, 2);
    is $gene->get_intron_positions($map1), 1;
    is $intron->relative->absolute_conversion($intron), 1021;

    # like for exon 1, we can be relative to the coding region without
    # defining it
    $rel = Bio::Map::GeneRelative->new(-coding => 0);
    my $pos3 = Bio::Map::Position->new(-map => $map1,
                            -element => $tf,
                            -start => -10,
                            -length => 5,
                            -relative => $rel);
    is $pos3->start, -10;
    $pos3->absolute(1);
    is $pos3->start, 991;

    # add the coding region for transcript 1
    ok my $coding1a = Bio::Map::GenePosition->new(-start => 50, -length => 20, -map => $map1, -type => 'coding');
    $gene->coding_position($coding1a);
    is $pos3->start, 1041;

    # try adding another coding region to the same transcript: we can't, so
    # the existing coding is replaced
    my $coding1b = Bio::Map::GenePosition->new(-start => 60, -length => 20, -map => $map1, -type => 'coding');
    $gene->coding_position($coding1b);
    is $pos3->start, 1051;
    ok ! $coding1a->element;
    # try adding things without using the add_x_position methods of Gene
    #...

    # GenePositions can have sequence
    like $exon->seq, qr/N{70}/;
    my $pos4 = Bio::Map::GenePosition->new(-start => 200, -seq => 'ATGCCCAAAG', -map => $map1, -type => 'exon');
    is $pos4->seq, 'ATGCCCAAAG';
    $gene->add_exon_position($pos4, 1);
    is $gene->get_exon_positions($map1), 3;
    is $pos4->length, 10;
    $pos4->absolute(1);
    is $pos4->end, 1210;
    is $pos4->seq('ATGCC'), 'ATGCC';
    is $pos4->length, 5;
    is $pos4->end, 1205;

    # so can GeneMaps
    my $map4 = Bio::Map::GeneMap->get(-gene => $gene,
                                      -species => 'chicken',
                                      -seq => 'ATGCCCAAAG');
    like $map4->seq, qr/ATGCCCAAAGN{991}/;
    is $map4->subseq(3,6), 'GCCC';
    is $map4->subseq(9,15), 'AGNNNNN'; # subseq is within map but beyond supplied seq, pads with Ns

    # map sequence can be built from the sequence of PositionWithSequences on the map
    my $pos5 = Bio::Map::PositionWithSequence->new(-start => 11, -seq => 'ATG', -map => $map4);
    is $pos5->seq, 'ATG';
    is $map4->subseq(9,15), 'AGATGNN';

    SKIP: {
        test_skip(-tests => 19,
                  -requires_modules => [qw(Bio::Tools::Run::Ensembl Bio::EnsEMBL::Registry XML::Twig)],
                  -requires_networking => 1);

        # make transcript, coding, exon, intron positions on all maps for gene,
        # purging manually added GenePositions
        my $success = $gene->set_from_db;

        skip('Failed to retreive anything from Ensembl; not sure why', 19) unless $success;

        is $gene->get_transcript_position($map1)->toString($pos->absolute_relative), '1001..84737';
        is $gene->get_transcript_position($map2)->toString($pos->absolute_relative), '501..47617';
        is $gene->get_transcript_position($map4)->toString($pos->absolute_relative), '1373..37665';
        like $gene->description($map1), qr/Breast cancer/i;
        is $gene->display_id($map1), 'ENSG00000139618';
        is $gene->display_id($map2), 'ENSMUSG00000041147';
        is $gene->display_id($map4), 'ENSGALG00000017073';
        ok defined($gene->display_xref($map4));
        is $gene->external_name($map1), 'BRCA2';
        is $gene->biotype($map2), 'protein_coding';
        is $gene->source($map4), 'ensembl';

        # we can add to a new map and the database info will be automatically there
        my $species = Bio::Species->new(-name => 'dog');
        $species->db_handle(Bio::DB::Taxonomy->new(-source => 'entrez'));
        my $map5 = Bio::Map::GeneMap->get(-gene => $gene, -species => $species);
        is $gene->display_id($map5), 'ENSCAFG00000006383';

        # now the gene has a database connection, its maps and positions can get sequence
        ok my $seq = $map1->seq;
        is length($seq), 84737;
        is substr($seq, 0, 20), 'TGTTACAGAACCAACGAATT'; # start of upstream
        is substr($seq, -20, 20), 'CTACAAGTATTATTTTACAA'; # end of gene since no downstream
        ok substr($map1->subseq($gene->coding_position($map1)), 0, 3);
        #my $exon1_str = 'GGGCTTGTGGCGCGAGCTTCTGAAACTAGGCGGCAGAGGCGGAGCCGCTGTGGCACTGCTGCGCCTCTGCTGCGCCTCGGGTGTCTTTTGCGGCGGTGGGTCGCCGCCGGGAGAAGCGTGAGGGGACAGA';
        my $exon1_pos = $gene->get_exon_position($map1, 1);
        cmp_ok(length($map1->subseq($exon1_pos)), '>', 20);
        is $exon1_pos->seq, $map1->subseq($exon1_pos);
    }

    # test a gene with multiple transcripts...
    #...
}
BioPerl-1.007002/t/Map/MapIO.t000444000766000024       323613155576321 15632 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {     
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 51);
	
	use_ok('Bio::MapIO');
}

my $verbose = test_debug();

ok my $mapio = Bio::MapIO->new(-verbose => $verbose,
										-format => 'mapmaker',
										-file   => test_input_file('mapmaker.out'));

my $map = $mapio->next_map;

isa_ok($map, 'Bio::Map::MapI');

is $map->units, 'cM';
is $map->type, 'Genetic';
is $map->name('test map'), 'test map'; # map name is unset for this data type

my $count;
foreach my $marker ( $map->each_element ) {
	$count++;
	is($marker->position->order,$count);
}
is $count,18;

ok $mapio = Bio::MapIO->new(-format => 'mapmaker',
									-file   => test_input_file('mapmaker.txt'));

$map = $mapio->next_map;
is $map->length,382.5;

$count = 0;
foreach my $marker ( $map->each_element ) {
	$count++;
	is($marker->position->order,$count);
}
is $count,13;

ok $mapio = Bio::MapIO->new(-format => 'fpc',
									-file   => test_input_file('ctgdemo.fpc'));

$map = $mapio->next_map;

is($map->length, 0);
is($map->version, 7.2);
is($map->modification_user, 'cari');
is($map->group_type, 'Chromosome');
is($map->group_abbr, 'Chr');
is($map->core_exists, 0);

$count = 0;
foreach my $marker ($map->each_markerid) {
	$count++;
}

is($count,150);

# add tests for get_markerobj

$count = 0;
foreach my $clone ($map->each_cloneid) {
	$count++;
}

is($count,618);

# add tests for get_cloneobj

$count = 0;
foreach my $contig ($map->each_contigid) {
	$count++;
}

is($count,2);

# add tests for get_contigobj

# need tests for
# matching_bands
# coincidence_score
# print_contiglist
# print_markerlist
# print_gffstyle
BioPerl-1.007002/t/Map/MicrosatelliteMarker.t000555000766000024       157513155576321 21016 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 8);
	
	use_ok('Bio::Map::SimpleMap');
	use_ok('Bio::Map::Position');
	use_ok('Bio::Map::Microsatellite');
}

my $map = Bio::Map::SimpleMap->new(-units => 'MB',
				  -type  => 'oo-121');
my $position = Bio::Map::Position->new(-map => $map,
				      -value => 20
				      );

my $o_usat = Bio::Map::Microsatellite->new
    (-name=>'Chad Super Marker 2',
     -sequence => 'gctgactgatcatatatatatatatatatatatatatatatcgcgatcgtgatttt',
     -motif => 'at',
     -repeats => 15,
     -repeat_start_position => 12,
     -position => $position,
     );

is($o_usat->get_leading_flank(), "gctgactgatc");
is($o_usat->get_trailing_flank(), "cgcgatcgtgatttt");
is($o_usat->motif(), 'at');
is($o_usat->repeats(), 15);
is($o_usat->repeat_start_position, 12);
BioPerl-1.007002/t/Map/Physical.t000444000766000024      1125213155576321 16456 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 40);
	
    use_ok('Bio::Map::Physical');
    use_ok('Bio::MapIO');
}

ok my $phm = Bio::Map::Physical->new();
is $phm->version(2), 2;
is $phm->version(), 2;
is $phm->modification_user('me'), 'me';
is $phm->modification_user(), 'me';

is $phm->group_type('xx'), 'xx';
is $phm->group_type(), 'xx';

is $phm->group_abbr('xx'), 'xx';
is $phm->group_abbr(), 'xx';

is $phm->core_exists, undef, 'code holds and returns a string, definition requires a boolean';

is $phm->core_exists(3), 1, 'code holds and returns a string, definition requires a boolean';

is $phm->core_exists(1), 1;
is $phm->core_exists(), 1;

my $fpcpath = test_input_file('biofpc.fpc');

# TODO? get Bio::MapIO::fpc to load from a Bio::MapIO call
my $mapio = Bio::MapIO->new(-format => "fpc", -species => 'demo', -readcor => 1, -file => $fpcpath);
my $fobj = $mapio->next_map();

is $fobj->group_abbr(), "Chr";
is $fobj->core_exists(), 1;

test_clones($fobj);
test_contigs($fobj);
test_markers($fobj);

#########################################################

sub test_markers
{
    my $nmrk = 0;
    my $nrem = 0;
    my %types;
    my $nanch = 0;
    my $nfrm = 0;
    my %grps;
    my $pos = 0;
    my @ctgpos;

    my $f = shift;
    foreach my $mid ($f->each_markerid())
    {
        $nmrk++;
        my $mobj = $f->get_markerobj($mid);
        if (not defined $mobj)
        {
            is 1, 0;
            next;
        }
        my @remarks = split /\n/, $mobj->remark();
        $nrem += scalar(@remarks);
        $types{$mobj->type()} = 1;
        if ($mobj->anchor())
        {
            $nanch++;
            $grps{$mobj->group()} = 1;
            $pos += $mobj->global();
        }
        if ($mobj->framework())
        {
            $nfrm++;
        }
        foreach my $ctgid ($f->each_contigid())
        {
            push @ctgpos, $mobj->position($ctgid);
        }
    }
    is $nmrk, 15;
    is $nrem, 17;
    is scalar(keys %types), 2;
    is $nanch, 9;
    is $nfrm, 7;
    is scalar (keys %grps), 4;
    is $pos, 36;
    is @ctgpos, 165;
    my $sum = 0;
    $sum += $_ for @ctgpos;
    is $sum, 1177;
}

#########################################################

sub test_contigs
{
    my $f = shift;
    my $nchr = 0;
    my $nuser = 0;
    my $ntrace = 0;
    my $nctg = 0;
    my $ncb = 0;
    my $psum = 0;
    my %grps;
    
    foreach my $cid ($f->each_contigid())
    {
        $nctg++;
        my $cobj = $f->get_contigobj($cid);
        if (not defined $cobj)
        {
            is 1, 0;
            next;
        }
        if ($cobj->chr_remark() ne "")
        {
            $nchr++;
        }
        if ($cobj->user_remark() eq "test")
        {
            $nuser++;
        }
        if ($cobj->trace_remark() eq "test")
        {
            $ntrace++;
        }
        if ($cid > 0)
        {
            $ncb += ($cobj->range()->end() - $cobj->range()->start() + 1);
        }
        if ($cobj->anchor())
        {
            $psum += $cobj->position(); 
            $grps{$cobj->group()} = 1;
        }
    }
    is $nctg, 11;
    is $nchr, 3;
    is $nuser, 1;
    is $ntrace, 1;
    is $ncb, 880; 
    is $psum, 15.55;
    is scalar(keys %grps), 3;
}

#########################################################

sub test_clones
{
    my $f = shift;
    my $nclones = 0;
    my $nbands = 0;
    my $nrem = 0;
    my %ctgs;
    my $nmrkhits = 0;
    my $nfprem = 0;
    my %stati;
    foreach my $cid ($f->each_cloneid())
    {
        $nclones++;
        my $cobj = $f->get_cloneobj($cid);
        if (not defined $cobj)
        {
            is 1, 0;
            next;
        }
        my $pbands = $cobj->bands();
        $nbands += scalar(@$pbands);
        $ctgs{$cobj->contigid()} = 1;
        if ($cobj->contigid() > 0)
        {
            if (not defined $cobj->range()->start() or 
                not defined $cobj->range()->end() or
                $cobj->range()->end() < $cobj->range()->start())
            {
                is 1, 0;
            }
        }
        foreach my $mid ($cobj->each_markerid())
        {
            $nmrkhits++;
        }
        my @remarks;
        if ($cobj->remark) {
            @remarks = split /\n/, $cobj->remark();
            $nrem += scalar(@remarks);
        }
        if ($cobj->fpc_remark) {
            @remarks = split /\n/, $cobj->fpc_remark();
            $nfprem += scalar(@remarks);
        }
        $stati{$cobj->sequence_status()} = 1 if $cobj->sequence_status;
    }
    is $nclones, 355;
    is $nbands, 9772;
    is scalar(keys %ctgs), 11;
    is $nmrkhits, 46;
    is $nrem, 12;
    is $nfprem, 162;
    is scalar(keys %stati), 5;
}
BioPerl-1.007002/t/Matrix000755000766000024          013155576321 15066 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Matrix/InstanceSite.t000444000766000024       112713155576321 20002 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 6);
	
	use_ok('Bio::Matrix::PSM::InstanceSite');
}

my %params=(-seq=>'TATAAT',-id=>"TATAbox1", -accession_number=>'ENSG00000122304', -mid=>'TB1',
            -desc=>'TATA box, experimentally verified in PRM1 gene',-relpos=>-35, -start=>1965);

ok my $instance = Bio::Matrix::PSM::InstanceSite->new(%params);
is $instance->seq, 'TATAAT';
is $instance->subseq(1,3),'TAT';
is $instance->accession_number, 'ENSG00000122304';
is $instance->end(1970), 1970;
BioPerl-1.007002/t/Matrix/Matrix.t000444000766000024      1050613155576321 16676 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 77);
	
	use_ok('Bio::Matrix::Generic');
	use_ok('Bio::Matrix::IO');
}

my $raw = [ [ 0, 10, 20],
	    [ 2, 17,  4],
	    [ 3,  4,  5] ];

my $matrix = Bio::Matrix::Generic->new(-values => $raw,
				      -matrix_id  => 'fakeid00',
				      -matrix_name=> 'matname',
				      -rownames   => [qw(A B C)],
				      -colnames   => [qw(D E F)] );

is($matrix->matrix_name, 'matname');
is($matrix->matrix_id,   'fakeid00');
is($matrix->entry('A','F'), $raw->[0]->[2]);
my @colE = $matrix->get_column('E');
is($colE[0], $raw->[0]->[1]);
is($colE[1], $raw->[1]->[1]);
is($colE[2], $raw->[2]->[1]);

my @rowC = $matrix->get_row('C');
is($rowC[0], $raw->[2]->[0]);
is($rowC[1], $raw->[2]->[1]);
is($rowC[2], $raw->[2]->[2]);

is($matrix->row_num_for_name('A'),0);
is($matrix->column_num_for_name('D'),0);

is($matrix->row_header(1),'B');
is($matrix->column_header(0),'D');

is($matrix->add_row(1, 'b', [qw(21 13 14)]),4);
is($matrix->add_column(2, 'f', [qw(71 81 14 3)]),4);

is($matrix->add_row(4, 'c', [qw(22 11 17)]),5);
is($matrix->remove_row(4),4);

is($matrix->add_column(4, 'g', [qw(11 10 100 71)]),5);
is($matrix->remove_column(4),4);

is($matrix->row_num_for_name('B'),2);
is($matrix->row_num_for_name('b'),1);

is($matrix->column_num_for_name('D'),0);
is($matrix->column_num_for_name('F'),3);
is($matrix->column_num_for_name('f'),2);

is($matrix->row_header(2),'B');

is($matrix->column_header(3),'F');

is($matrix->get_entry('b', 'f'), 81);


# read in a scoring matrix

my $io = Bio::Matrix::IO->new(-format => 'scoring',
			      -file   => test_input_file('BLOSUM50'));
my $blosum_matrix = $io->next_matrix;
isa_ok($blosum_matrix,'Bio::Matrix::Scoring');
is($blosum_matrix->entropy, 0.4808);
is($blosum_matrix->expected_score, -0.3573);
is($blosum_matrix->scale, '1/3');
is($blosum_matrix->get_entry('*','A'), -5);
is($blosum_matrix->get_entry('V','Y'), -1);
is($blosum_matrix->get_entry('Y','V'), -1);
is($blosum_matrix->get_entry('L','I'), 2);
my @diag = $blosum_matrix->get_diagonal;
is($diag[2],7);
my @row = $blosum_matrix->get_row('D');
is($row[5], $blosum_matrix->get_entry('D','Q'));
is($blosum_matrix->num_rows,24);
is($blosum_matrix->num_columns,24);
 
$io = Bio::Matrix::IO->new(-format => 'scoring',
			   -file   => test_input_file('PAM250'));
my $pam_matrix = $io->next_matrix;
isa_ok($pam_matrix, 'Bio::Matrix::Scoring');
is($pam_matrix->entropy, 0.354);
is($pam_matrix->expected_score, -0.844);
is($pam_matrix->scale, 'ln(2)/3');
is($pam_matrix->num_rows,24);
is($pam_matrix->get_entry('G','*'), -8);
is($pam_matrix->get_entry('V','Y'), -2);
is($pam_matrix->get_entry('Y','V'), -2);
is($pam_matrix->get_entry('L','I'), 2);
@diag = $pam_matrix->get_diagonal;
is($diag[2],2);
@row = $pam_matrix->get_row('D');
is($row[5], $pam_matrix->get_entry('D','Q'));

# test Phylip parsing

$io = Bio::Matrix::IO->new(-format  => 'phylip',
			  -program => 'phylipdist',
			  -file    => test_input_file('phylipdist.out'));

my $phy = $io->next_matrix;
is $phy->program, 'phylipdist';
is $phy->get_entry('Alpha','Beta'), '4.23419';
is $phy->get_entry('Gamma','Alpha'),'3.63330';

my @column =  $phy->get_column('Alpha');
is $column[0], '0.00000';
is $column[1], '4.23419';
is $column[2], '3.63330';
is $column[3], '6.20865';
is $column[4], '3.45431';

@row    = $phy->get_row('Gamma');
is $row[0], '3.63330';
is $row[1], '3.49289';
is $row[2], '0.00000';
is $row[3], '3.68733';
is $row[4], '5.84929';

@diag   = $phy->get_diagonal;

is $diag[0], '0.00000';
is $diag[1], '0.00000';
is $diag[2], '0.00000';
is $diag[3], '0.00000';
is $diag[4], '0.00000';


# test mlagan parsing

$io = Bio::Matrix::IO->new(-format => 'mlagan',
						  -file   => test_input_file('nucmatrix.txt'));

my $mlag = $io->next_matrix;
is $mlag->get_entry('A', 'C'), -150;
is $mlag->get_entry('.', 'A'), 0;
is $mlag->gap_open, -300;
is $mlag->gap_continue, -25;

# test output round-trip
$mlag->entry('A', 'C', -149);
$mlag->gap_open(-150);
$mlag->gap_continue(-5);

my $out = test_output_file();
$io = Bio::Matrix::IO->new(-format => 'mlagan',
						  -file   => ">$out");
$io->write_matrix($mlag);

$io = Bio::Matrix::IO->new(-format => 'mlagan',
						  -file   => $out);
$mlag = $io->next_matrix;
is $mlag->get_entry('A', 'C'), -149;
is $mlag->gap_open, -150;
is $mlag->gap_continue, -5;
BioPerl-1.007002/t/Matrix/ProtMatrix.t000444000766000024      1042513155576321 17543 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$


use strict;

BEGIN {
   use lib '.';
   use Bio::Root::Test;
   
   test_begin(-tests => 14);
   
   use_ok 'Bio::Matrix::PSM::ProtMatrix';
}


my %param = (
   '-id' => 'A. thaliana protein atp1',
   '-e_val' => 0.0001,
   '-ic' => [ '0.28', '0.40', '0.64', '0.68', '0.68', '0.70', '0.72', '0.72' ],
   '-lS' => [ '-2', '3', '-3', '2', '-3', '1', '1', '3' ],
   '-lF' => [ '-1', '-4', '0', '-5', '0', '-5', '-4', '-4' ],
   '-lT' => [ '-1', '1', '0', '1', '-2', '-1', '0', '1' ],
   '-lN' => [ '-3', '-1', '-2', '3', '-5', '5', '-2', '0' ],
   '-lK' => [ '-2', '0', '-3', '2', '-3', '2', '-3', '-1' ],
   '-lY' => [ '-2', '-3', '-3', '-4', '-3', '-4', '-4', '-4' ],
   '-lE' => [ '-3', '4', '-3', '2', '-4', '-2', '-3', '2' ],
   '-lV' => [ '0', '-2', '1', '-4', '1', '-4', '-1', '-3' ],
   '-lQ' => [ '-1', '0', '-2', '3', '-4', '1', '-3', '0' ],
   '-lM' => [ '8', '-3', '8', '-3', '1', '-3', '-3', '-3' ],
   '-lC' => [ '-2', '-3', '-3', '-4', '-3', '-4', '-3', '-3' ],
   '-lL' => [ '1', '-3', '1', '-4', '3', '-4', '-2', '-4' ],
   '-lA' => [ '-2', '1', '-2', '0', '-2', '-2', '2', '2' ],
   '-lW' => [ '-2', '-4', '-3', '-5', '-4', '-5', '-5', '-5' ],
   '-lP' => [ '-3', '-2', '-4', '-3', '-1', '-3', '6', '-3' ],
   '-lH' => [ '-2', '-2', '-3', '-2', '-5', '-2', '-2', '-3' ],
   '-lD' => [ '-4', '-1', '-3', '1', '-3', '-1', '-3', '4' ],
   '-lR' => [ '-2', '-1', '-3', '0', '-4', '4', '-4', '-3' ],
   '-lI' => [ '0', '-3', '0', '-4', '6', '-4', '-2', '-2' ],
   '-lG' => [ '-4', '-2', '-4', '-2', '-5', '-3', '-1', '-2' ],
   '-pS' => [ '0', '33', '0', '16', '1', '12', '11', '25' ],
   '-pF' => [ '0', '0', '2', '0', '3', '0', '0', '0' ],
   '-pT' => [ '0', '8', '7', '10', '1', '2', '7', '8' ],
   '-pN' => [ '0', '0', '2', '13', '0', '36', '1', '4' ],
   '-pK' => [ '0', '5', '0', '13', '1', '15', '0', '2' ],
   '-pY' => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
   '-pE' => [ '0', '41', '1', '12', '0', '0', '0', '15' ],
   '-pV' => [ '0', '3', '9', '0', '2', '0', '3', '1' ],
   '-pQ' => [ '0', '0', '0', '15', '0', '4', '0', '3' ],
   '-pM' => [ '100', '0', '66', '0', '2', '0', '0', '0' ],
   '-pC' => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
   '-pL' => [ '0', '0', '8', '0', '25', '0', '4', '0' ],
   '-pA' => [ '0', '10', '1', '9', '2', '0', '22', '16' ],
   '-pW' => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
   '-pP' => [ '0', '0', '0', '0', '3', '1', '45', '0' ],
   '-pH' => [ '0', '0', '0', '0', '0', '0', '1', '0' ],
   '-pD' => [ '0', '0', '1', '7', '2', '2', '0', '22' ],
   '-pR' => [ '0', '0', '0', '3', '0', '27', '0', '0' ],
   '-pI' => [ '0', '0', '3', '0', '59', '1', '2', '3' ],
   '-pG' => [ '0', '0', '0', '1', '0', '0', '4', '1' ],
);

my $matrix = Bio::Matrix::PSM::ProtMatrix->new(%param);
ok $matrix;

#Simple methods here
is $matrix->IUPAC,'MEMSINPS';

is $matrix->consensus,'MEMSINPS';

is $matrix->width,8;

is $matrix->curpos,0;

is $matrix->get_string('A'), '0100a90200220160';

my %x1 = (
         'base' => 'M', 'prob' => 100, 'rel' => 0,
         'lC' => '-2',
         'pM' => '100',
         'lY' => '-2',
         'lK' => '-2',
         'lR' => '-2',
         'lM' => '8',
         'pP' => '0',
         'lV' => '0',
         'pK' => '0',
         'lH' => '-2',
         'pI' => '0',
         'pT' => '0',
         'lE' => '-3',
         'lN' => '-3',
         'lQ' => '-1',
         'lW' => '-2',
         'pH' => '0',
         'pC' => '0',
         'lI' => '0',
         'pA' => '0',
         'lA' => '-2',
         'pV' => '0',
         'pF' => '0',
         'lS' => '-2',
         'pY' => '0',
         'lL' => '1',
         'lG' => '-4',
         'pE' => '0',
         'pL' => '0',
         'lF' => '-1',
         'pS' => '0',
         'pD' => '0',
         'pN' => '0',
         'lP' => '-3',
         'lT' => '-1',
         'pQ' => '0',
         'pR' => '0',
         'lD' => '-4',
         'pW' => '0',
         'pG' => '0'
);

my %x2 = $matrix->next_pos;
is_deeply \%x1, \%x2;

is $matrix->curpos,1;

ok $matrix->e_val(0.0001);
is $matrix->e_val,0.0001;

#Now some PSM specific methods like regexp and matrix info

my @a = ('0', '10', '1', '9', '2', '0', '22', '16');
is_deeply [$matrix->get_array('A')], \@a;

my $regexp = '[Mm][EeSs][Mm]\.[IiLl][RrNn][AaPp][DdSs]';
is $matrix->regexp, $regexp;
is $matrix->sequence_match_weight('MSMPLRPD'), 33;
BioPerl-1.007002/t/Matrix/ProtPsm.t000444000766000024       457613155576321 17030 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$


use strict;

BEGIN {
   use lib '.';
   use Bio::Root::Test;
   
   test_begin(-tests => 14);
   
   use_ok('Bio::Matrix::PSM::IO');
}

# Test psiblast reading functionality.
my $psmIO =  Bio::Matrix::PSM::IO->new(-format => 'psiblast', 
			      -file   => test_input_file('atp1.matrix'));
ok $psmIO;

my $psm = $psmIO->next_psm;
ok $psm;

# Verify that getting IUPAC sequence is functional
my $IUPAC = 'MEMSINPSEISSIIKEQIENYDTKAEVSEVGTVLSVGDGIARVYGLDNVMAGEMVEFPSGVKGMALNLEEDNVGVVLLGDDTGIKEGDLVKRTGKIVEVPVGEALLGRVVDPLGNPIDAKGPIKTDERRPVEVKAPGIIPRKSVHEPLQTGLKAIDSLVPIGRGQRELIIGDRQTGKTAIAIDTIINQKRINDESTDEGKKVYCIYVAIGQKRSTVAQVVQTLREAGALEYTIIVAATAAAPAPAQYLSAYAGCAIGEAFADNGAAACIIHDDLSRQAVAYAIISLLLRRPPGREAYPGDVFYLHSRLLERAAKLSDELGGGSLTALPIIETQAGDVSAYIPTNVISITDGQIFLETDLFNSGIRPAINVGLSVSRVGSAAQIKAMKKVAGSLKLELAQYRELAAFAQFGSDLDAATQAQLNRGARLTELLKQPQYSPLPVEEQVVILYAGVNGYLDDIPVEDIRDFEKELLEYLKSNHPEILESIRTGKLSDEIEKALKEAIKEFV';
is $psm->IUPAC, $IUPAC;

## Lets try to compress and uncompress the log odds and the
## frequencies, see if there is no considerable loss of data.
SKIP: {
   skip('TODO: Module incomplete',10); 
   my $fA=$psm->get_compressed_freq('A');
   my @check=Bio::Matrix::PSM::SiteMatrix::_uncompress_string($fA,1,1);
   my @A=$psm->get_array('A');
   my ($var,$max) = (0,0);
   
   for (my $i = 0; $i<@check;$i++) {
     my $diff=abs(abs($check[$i])-abs($A[$i]));
     $var += $diff;
     $max=$diff if ($diff>$max);
   }
   my $avg=$var/@check;
   cmp_ok $avg,'<',0.01; #Loss of data under 1 percent
   is $psm->sequence_match_weight('CAGAAAAATAAAATGGCCACCACCC'),2015;
   
   my $lA=$psm->get_compressed_logs('A');
   @check=Bio::Matrix::PSM::SiteMatrix::_uncompress_string($lA,1000,2);
   @A=$psm->get_logs_array('A');
   ($var,$max) = (0,0);
   for (my $i = 0;$i<@check;$i++) {
     my $diff=abs(abs($check[$i])-abs($A[$i]));
     $var += $diff;
     $max=$diff if ($diff>$max);
   }
   $avg=$var/@check;
   cmp_ok $avg,'<',10; #Loss of data under 1 percent
   
   my $matrix=$psm->matrix;
   ok $matrix;
   my $psm2=$psm;
   $psm2->matrix($matrix);
   is $psm,$psm2;
   
   is $IUPAC,'CAGAAAAATWVAATYCCCACCHCCC';
   is $IUPAC,$psm2->IUPAC;
   is $IUPAC,$matrix->IUPAC;
   
   my $instances=$psm->instances;
   ok $instances;
   
   foreach my $instance (@{$instances}) {
     my $id=$instance->primary_id;
     is $instance->strand,1;
     last if (ok $id);
   }
}
BioPerl-1.007002/t/Matrix/SiteMatrix.t000444000766000024       232613155576321 17504 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$


use strict;

BEGIN {
  use lib '.';
  use Bio::Root::Test;
  
  test_begin(-tests => 14);
  
  use_ok('Bio::Matrix::PSM::SiteMatrix');
}

my $score;
my $A='a0501';
my $C='014a0';
my $G='01103';
my $T='08006';
my $eval=0.0001;
my %param=(pA=>$A,pC=>$C,pG=>$G,pT=>$T,e_val=>$eval, correction =>0);
ok my $matrix=Bio::Matrix::PSM::SiteMatrix->new(%param);

#Simple methods here
is $matrix->IUPAC,'ABVCD';

is $matrix->consensus,'ATACT';

is $matrix->width,5;

is $matrix->curpos,0;

is $matrix->get_string('A'),$A;

my %x= (base=>'A',pA=>1,pC=>0,pG=>0,pT=>0,prob=>10,rel=>0, 
        lA=>undef,lC=>undef,lG=>undef,lT=>undef);
my %pos = $matrix->next_pos;
my ($all) = 1;
while(my ($k,$v) = each %x ) {
    my $r =$pos{$k};
    if( ! defined $v && ! defined $r) {
    } elsif($pos{$k} ne $v ) { 
	$all = 0;
	last;
    }
}
ok($all);

is $matrix->curpos,1;

ok $matrix->e_val(0.0001);

is $matrix->e_val,0.0001;

#Now some PSM specific methods like regexp and matrix info
is $matrix->regexp,'[Aa][CcGgTtBb][AaCcGgVv][Cc][AaGgTtDd]';

my @x=(1,0,0.5,0,0.1);
is_deeply [$matrix->get_array('A')], \@x;

@x=qw([Aa] [CcGgTtBb] [AaCcGgVv] [Cc] [AaGgTtDd]);
is_deeply [$matrix->regexp_array], \@x;
BioPerl-1.007002/t/Matrix/IO000755000766000024          013155576321 15375 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Matrix/IO/masta.t000555000766000024       244413155576321 17033 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 16);
	
	use_ok('Bio::Matrix::PSM::IO');
}

#Let's try masta formats here
my $mio =  Bio::Matrix::PSM::IO->new(-format=>'masta', 
				      -file=>test_input_file('masta.dat'));
my $masta_w_dat = test_output_file();
my $wmio=Bio::Matrix::PSM::IO->new(-format=>'masta', 
				      -file=>">".$masta_w_dat);
$wmio->_flush_on_write(1);
ok $mio;
ok $wmio;
my @cons;
my $carry;
while (my $site=$mio->next_matrix) {
	ok $site;
	push @cons,$site->consensus;	
	$carry=$site if ($site->id eq 'm1logs');
} 
is $cons[0],'CAGAAAAATNGAATNCCCACCCCCC';
is $cons[1],'CAGAAAAATAGAATCCCCACCCCCC';
is $cons[2],'CAGAAAAATNNAATNCCCACCNCCC';

$wmio->write_psm($carry,'PWM');
$carry->id('m1freq');
$wmio->write_psm($carry,'PFM');
$carry->id('m1seq');
$wmio->write_psm($carry,'SEQ');
$wmio->DESTROY;
my $chio=Bio::Matrix::PSM::IO->new(-format=>'masta', 
				      -file=>$masta_w_dat);
ok $chio;
my $site=$chio->next_matrix;
is $site->id,'m1logs';
is $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';	
$site=$chio->next_matrix;
is $site->id,'m1freq';
is $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';  
$site=$chio->next_matrix;
is $site->id,'m1seq';
is $site->consensus,'CAGAAAAATAGAATCCCCACCCCCC';
BioPerl-1.007002/t/Matrix/IO/psm.t000444000766000024      1221713155576321 16541 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 63);
	
	use_ok ('Bio::Matrix::PSM::IO');
}

my $mmt= "chr04q	170164	170208	strong	-	0	Motif 3 occurrance in chr04q
chr04q	215755	215799	strong	+	0	Motif 4 occurrance in chr04q
chr04q	532530	532574	strong	+	2	Motif 2 occurrance in chr04q
chr04q	539492	539536	strong	-	1	Motif 1 occurrance in chr04q
chr04q	586113	586157	strong	+	2	Motif 2 occurrance in chr04q
chr04q	698245	698289	strong	-	0	Motif 4 occurrance in chr04q
chr04q	804412	804456	strong	-	0	Motif 3 occurrance in chr04q
chr04q	858870	858914	strong	-	2	Motif 3 occurrance in chr04q
chr04q	861561	861605	strong	-	2	Motif 3 occurrance in chr04q
chr04q	916898	916942	strong	-	1	Motif 1 occurrance in chr04q
chr04q	1146916	1146960	strong	-	0	Motif 1 occurrance in chr04q
chr04q	1315772	1315816	strong	+	1	Motif 1 occurrance in chr04q
chr04q	1636119	1636163	strong	+	2	Motif 3 occurrance in chr04q
chr04q	1636200	1636244	strong	+	2	Motif 1 occurrance in chr04q
chr04q	1636437	1636481	strong	+	2	Motif 4 occurrance in chr04q
chr04q	1637361	1637405	strong	+	2	Motif 2 occurrance in chr04q
chr04q	1652447	1652491	strong	+	1	Motif 4 occurrance in chr04q";
my @mmt=split(/\n/,$mmt);

#Let's try meme here
my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'meme', 
	     -file=>test_input_file('meme.dat'));
ok $psmIO;

my @inputfile=grep(/datafile/i,$psmIO->unstructured);
ok @inputfile;

my $release=$psmIO->release;
ok $release;

my @ids=$psmIO->hid;
is @ids,4;

my %weights=$psmIO->weight;
ok %weights;

my %seq = $psmIO->seq;
is %seq,'0';#Meme doesn't have seq

is $psmIO->version,'3.0';

my $psm = $psmIO->next_psm;
ok $psm;

#Lets try to compress and uncompress the log odds and the frequencies, see if there is no
#considerable loss of data.
my $fA=$psm->get_compressed_freq('A');
my @check=Bio::Matrix::PSM::SiteMatrix::_uncompress_string($fA,1,1);
my @A=$psm->get_array('A');
my ($var,$max) = (0,0);
for (my $i = 0; $i<@check;$i++) {
  my $diff=abs(abs($check[$i])-abs($A[$i]));
  $var += $diff;
  $max=$diff if ($diff>$max);
}
my $avg=$var/@check;
cmp_ok $avg,'<',0.01; #Loss of data under 1 percent
#print $avg,"\n";
is $psm->sequence_match_weight('CAGAAAAATAAAATGGCCACCACCC'),2015;

my $lA=$psm->get_compressed_logs('A');
@check=Bio::Matrix::PSM::SiteMatrix::_uncompress_string($lA,1000,2);
@A=$psm->get_logs_array('A');
($var,$max) = (0,0);
for (my $i = 0;$i<@check;$i++) {
  my $diff=abs(abs($check[$i])-abs($A[$i]));
  $var += $diff;
  $max=$diff if ($diff>$max);
}
$avg=$var/@check;
cmp_ok $avg,'<',10; #Loss of data under 1 percent

my $matrix=$psm->matrix;
ok $matrix;
my $psm2=$psm;
$psm2->matrix($matrix);
is $psm,$psm2;

my %psm_header=$psm->header;
is $psm_header{IC},38.1;
is $psm_header{sites},4;
is $psm_header{width},25;
is $psm_header{e_val},'1.2e-002';


#Quick check if returned object works
my $IUPAC=$psm->IUPAC;
is $IUPAC,'CMKWMAAAKWVAWTYCMCASCHCCM';
is $IUPAC,$psm2->IUPAC;
is $IUPAC,$matrix->IUPAC;

my $instances=$psm->instances;
ok $instances;

foreach my $instance (@{$instances}) {
  my $id=$instance->primary_id;
  is $instance->strand,1;
  last if (ok $id);
}

ok $psm->header('e_val');
#Meme parser should be OK if tests passed


#Now we are going to try transfac

$psmIO =  Bio::Matrix::PSM::IO->new(-format=>'transfac', 
	  -file=> test_input_file('transfac.dat'));
ok $psmIO;

my $version=$psmIO->version;
ok !$version;

is $psmIO->release, '6.4--2002-12-02';

$psm     = $psmIO->next_psm;
ok $psm;

# Lets try to compress and uncompress the the frequencies, see if
# there is no considerable loss of data.
$fA=$psm->get_compressed_freq('A');
@check=Bio::Matrix::PSM::SiteMatrix::_uncompress_string($fA,1,1);
@A=$psm->get_array('A');
($var,$max) = (0,0);
for (my $i = 0; $i<@check;$i++) {
  my $diff=abs(abs($check[$i])-abs($A[$i]));
  $var += $diff;
  $max=$diff if ($diff>$max);
}
$avg=$var/@check;
cmp_ok $avg,'<',0.01; #Loss of data under 1 percent

%weights = $psmIO->weight;
ok !$weights{''};

%seq     = $psmIO->seq;
is scalar keys %seq, 0;

#Quick check if returned object works
$IUPAC   = $psm->IUPAC;
is $IUPAC,'VVDCAKSTGBYD';

#Now we are going to try mast
$psmIO =  Bio::Matrix::PSM::IO->new(-format=>'mast', 
	  -file=>test_input_file('mast.dat'));
ok $psmIO;

@inputfile = grep(/datafile/i,$psmIO->unstructured);
ok !@inputfile;

is( $psmIO->release, '2002/04/02 0:11:59');

@ids     = $psmIO->hid;
is @ids,4;

%weights = $psmIO->weight;
ok !%weights; #Mast doesn't have weights

ok %seq    = $psmIO->seq;

foreach my $id ($psmIO->hid) {
    ok $seq{$id};
}
ok $psm=$psmIO->next_psm;

my %instances=$psmIO->instances;
ok %instances;

is $psmIO->version, '3.0';

my $mmastIO=Bio::Matrix::PSM::IO->new(-format=>'mast',-file=>test_input_file('mixedmast.dat'));

$psm = $mmastIO->next_psm; 
my $lastinstances = $psm->instances();
my $i=0;
foreach my $hit (@$lastinstances) {
    $hit -> end ( $hit-> start () + length ($hit->seq) - 1 ) ; # fix an old bug in InstanceSite.pm
    my $d=join("\t",$hit->{accession_number},$hit -> start () , $hit-> end (),$hit -> score (),
    $hit -> strand == 1 ? '+' : '-' , $hit -> frame,  $hit -> desc ( ));
    is $d,$mmt[$i];
    $i++;
    last if ($hit -> start == 1652447);
}
BioPerl-1.007002/t/Ontology000755000766000024          013155576321 15434 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Ontology/GOterm.t000444000766000024       751313155576321 17161 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;
use warnings;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 62,
               -requires_module => 'Graph::Directed');
	
    use_ok('Bio::Ontology::GOterm');
    use_ok('Bio::Ontology::Ontology');
	use_ok('Bio::Annotation::DBLink');
}

my $obj = Bio::Ontology::GOterm->new();

# note that all *dblink* methods are now deprecated...

isa_ok( $obj,"Bio::Ontology::GOterm");

$obj->init();

like( $obj->to_string(), qr'-- GO id:' );

is( $obj->GO_id( "GO:0003947" ), "GO:0003947" );
is( $obj->GO_id(), "GO:0003947" );


is( $obj->get_dbxrefs(), 0 );

my @dblinks = (Bio::Annotation::DBLink->new(-primary_id => 'dAA'),
				 Bio::Annotation::DBLink->new(-primary_id => 'dAB'));

$obj->add_dbxref( -dbxrefs => \@dblinks );
is( scalar($obj->get_dbxrefs()), 2 );
my @df1 = $obj->get_dbxrefs();
is( $df1[ 0 ]->display_text, "dAA" );
is( $df1[ 1 ]->display_text, "dAB" );
is( $obj->get_dbxrefs(), 2 );

my @df2 = $obj->remove_dbxrefs();
is( $df2[ 0 ]->display_text, "dAA" );
is( $df2[ 1 ]->display_text, "dAB" );

is( $obj->get_dbxrefs(), 0 );
is( $obj->remove_dbxrefs(), 0 );


is( $obj->get_secondary_GO_ids(), 0 );

$obj->add_secondary_GO_id( ( "GO:0000000", "GO:1234567" ) );
is( scalar($obj->get_secondary_GO_ids()), 2 );
my @si1 = $obj->get_secondary_GO_ids();
is( $si1[ 0 ], "GO:0000000" );
is( $si1[ 1 ], "GO:1234567" );
is( $obj->get_secondary_GO_ids(), 2 );

my @si2 = $obj->remove_secondary_GO_ids();
is( $si2[ 0 ], "GO:0000000" );
is( $si2[ 1 ], "GO:1234567" );

is( $obj->get_secondary_GO_ids(), 0 );
is( $obj->remove_secondary_GO_ids(), 0 );



is( $obj->identifier( "0003947" ), "0003947" );
is( $obj->identifier(), "0003947" );

is( $obj->name( "N-acetylgalactosaminyltransferase" ), "N-acetylgalactosaminyltransferase" );
is( $obj->name(), "N-acetylgalactosaminyltransferase" );

is( $obj->definition( "Catalysis of ..." ), "Catalysis of ..." );
is( $obj->definition(), "Catalysis of ..." );

is( $obj->version( "666" ), "666" );
is( $obj->version(), "666" );

ok( $obj->ontology( "category 1 name" ) );
is( $obj->ontology()->name(), "category 1 name" );

my $ont = Bio::Ontology::Ontology->new();
ok( $ont->name( "category 2 name" ) );

ok( $obj->ontology( $ont ) );
is( $obj->ontology()->name(), "category 2 name" );

is( $obj->is_obsolete( 1 ), 1 );
is( $obj->is_obsolete(), 1 );

is( $obj->comment( "Consider the term ..." ), "Consider the term ..." );
is( $obj->comment(), "Consider the term ..." );

is( $obj->get_synonyms(), 0 );

$obj->add_synonym( ( "AA", "AB" ) );
my @al1 = $obj->get_synonyms();
is( scalar(@al1), 2 );
is( $al1[ 0 ], "AA" );
is( $al1[ 1 ], "AB" );

my @al2 = $obj->remove_synonyms();
is( $al2[ 0 ], "AA" );
is( $al2[ 1 ], "AB" );

is( $obj->get_synonyms(), 0 );
is( $obj->remove_synonyms(), 0 );

$obj->add_synonym( ( "AA", "AB" ) );
$obj->add_dbxref( -dbxrefs => \@dblinks );
$obj->add_secondary_GO_id( ( "GO:1234567", "GO:1234567" ) );

$obj->init();
is( $obj->identifier(), undef ); # don't make up identifiers
is( $obj->name(), undef );
is( $obj->definition(), undef );
is( $obj->is_obsolete(), 0 );
is( $obj->comment(), undef );


$obj = Bio::Ontology::GOterm->new( -go_id       => "0016847",
                                   -name        => "1-aminocyclopropane-1-carboxylate synthase",
                                   -definition  => "Catalysis of ...",
                                   -is_obsolete => 0,
                                   -version     => "6.6.6",
                                   -ontology    => "cat",
                                   -comment     => "X" );  

is( $obj->identifier(), "GO:0016847" );
is( $obj->name(), "1-aminocyclopropane-1-carboxylate synthase" );
is( $obj->definition(), "Catalysis of ..." );
is( $obj->is_obsolete(), 0 );
is( $obj->comment(), "X" );
is( $obj->version(), "6.6.6" );
is( $obj->ontology()->name(), "cat" );
BioPerl-1.007002/t/Ontology/GraphAdaptor.t000555000766000024       403313155576321 20335 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 28,
			   -requires_module => 'Graph');
	
    use_ok('Bio::Ontology::SimpleGOEngine::GraphAdaptor');
}

my $g=Bio::Ontology::SimpleGOEngine::GraphAdaptor->new();
my $graph_version=( defined($Graph::VERSION) && $Graph::VERSION >= 0.5 )  ? 'new' : 'old';
my $adaptor_class=$graph_version eq 'new' ? 
  'Bio::Ontology::SimpleGOEngine::GraphAdaptor' : 'Bio::Ontology::SimpleGOEngine::GraphAdaptor02';
is (ref $g, $adaptor_class);

$g->add_vertex('vertex0');
ok($g->has_vertex('vertex0'));
ok(!$g->has_vertex('vertex1'));
my @v=$g->vertices;
is (@v, 1);
is ($v[0],'vertex0');

$g->add_edge('vertex0','vertex1');
ok($g->has_edge('vertex0','vertex1'));
ok(!$g->has_edge('vertex0','vertex'));
my @e=$g->edges;
is (@e, 1);
is ($e[0]->[0],'vertex0');
is ($e[0]->[1],'vertex1');

@e=$g->edges_at('vertex0');
is (@e, 1);
is ($e[0]->[0], 'vertex0');
is ($e[0]->[1], 'vertex1');

@v=$g->predecessors('vertex1');
is (@v, 1);
is ($v[0],'vertex0');

@v=$g->successors('vertex0');
is(@v, 1);
is ($v[0],'vertex1');

@v=$g->source_vertices;
is(@v,1);
is($v[0],'vertex0');

@v=$g->sink_vertices;
is(@v, 1);
is($v[0],'vertex1');

$g->set_vertex_attribute('vertex0','ATTR0','vertex0_ATTR0');
$g->set_vertex_attribute('vertex0','ATTR1','vertex0_ATTR1');
$g->set_vertex_attribute('vertex1','ATTR0','vertex1_ATTR0');
$g->set_vertex_attribute('vertex1','ATTR1','vertex1_ATTR1');
is ($g->get_vertex_attribute('vertex0','ATTR0'),'vertex0_ATTR0');
is ($g->get_vertex_attribute('vertex0','ATTR1'),'vertex0_ATTR1');
is ($g->get_vertex_attribute('vertex1','ATTR0'),'vertex1_ATTR0');
is ($g->get_vertex_attribute('vertex1','ATTR1'),'vertex1_ATTR1');

$g->set_edge_attribute('vertex0','vertex1','ATTR0','vertex0_vertex1_ATTR0');
$g->set_edge_attribute('vertex0','vertex1','ATTR1','vertex0_vertex1_ATTR1');
is ($g->get_edge_attribute('vertex0','vertex1','ATTR0'),'vertex0_vertex1_ATTR0');
is ($g->get_edge_attribute('vertex0','vertex1','ATTR1'),'vertex0_vertex1_ATTR1');   
BioPerl-1.007002/t/Ontology/Ontology.t000444000766000024      1215413155576321 17613 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(
        -tests           => 55,
        -requires_module => 'Graph'
    );

    use_ok('Bio::OntologyIO');
    use_ok('Bio::Ontology::RelationshipType');
}

my $IS_A    = Bio::Ontology::RelationshipType->get_instance("IS_A");
my $PART_OF = Bio::Ontology::RelationshipType->get_instance("PART_OF");

my $parser = Bio::OntologyIO->new(
    -format => "soflat",
    -file   => test_input_file('sofa.ontology')
);

my $ont = $parser->next_ontology();
isa_ok( $ont, 'Bio::Ontology::Ontology' );
is( $ont->name, "Sequence Feature Ontology" );

my @roots = $ont->get_root_terms();
is( scalar(@roots),          1 );
is( $roots[0]->name(),       "Sequence_Feature_Ontology" );
is( $roots[0]->identifier(), "SO:0000000" );

my @terms = $ont->get_child_terms( $roots[0] );
is( scalar(@terms),    1 );
is( $terms[0]->name(), "sofa" );
@terms = $ont->get_child_terms( $terms[0] );
is( scalar(@terms),    1 );
is( $terms[0]->name(), "feature" );
my $featterm = $terms[0];
@terms = $ont->get_child_terms($featterm);
is( scalar(@terms), 10 );

# oligonucleotide has two parents, see whether this is handled
@terms = $ont->get_descendant_terms($featterm);
my ($term) = grep { $_->name() eq "oligonucleotide"; } @terms;
ok $term;

#TODO: {
#	local $TODO = '$term->identifier()';
is( $term->identifier(), "SO:0000696" );

#}

@terms = $ont->get_ancestor_terms($term);
is( scalar(@terms), 7 );
is( scalar( grep { $_->name() eq "remark"; } @terms ),  1 );
is( scalar( grep { $_->name() eq "reagent"; } @terms ), 1 );

# processed_transcript has part-of and is-a children
@terms = $ont->get_descendant_terms($featterm);
($term) = grep { $_->name() eq "processed_transcript"; } @terms;
ok $term;

#TODO: {
#	local $TODO = '$term->identifier()';
is( $term->identifier(), "SO:0000233" );

#}

@terms = $ont->get_child_terms($term);
is( scalar(@terms), 4 );
@terms = $ont->get_child_terms( $term, $PART_OF );
is( scalar(@terms), 2 );
@terms = $ont->get_child_terms( $term, $IS_A );
is( scalar(@terms), 2 );
@terms = $ont->get_child_terms( $term, $PART_OF, $IS_A );
is( scalar(@terms), 4 );

# now all descendants:
@terms = $ont->get_descendant_terms($term);
is( scalar(@terms), 13 );
@terms = $ont->get_descendant_terms( $term, $PART_OF );
is( scalar(@terms), 2 );
@terms = $ont->get_descendant_terms( $term, $IS_A );
is( scalar(@terms), 5 );
@terms = $ont->get_descendant_terms( $term, $PART_OF, $IS_A );
is( scalar(@terms), 13 );

# TF_binding_site has 2 parents and different relationships in the two
# paths up (although the relationships to its two parents are of the
# same type, namely is-a)
@terms = $ont->get_descendant_terms($featterm);
($term) = grep { $_->name() eq "TF_binding_site"; } @terms;
ok $term;

#TODO: {
#	local $TODO = '$term->identifier()';
is( $term->identifier(), "SO:0000235" );

#}

@terms = $ont->get_parent_terms($term);
is( scalar(@terms), 2 );
my ($pterm) = grep { $_->name eq "regulatory_region"; } @terms;
ok $pterm;
@terms = $ont->get_parent_terms( $term, $PART_OF );
is( scalar(@terms), 0 );
@terms = $ont->get_parent_terms( $term, $IS_A );
is( scalar(@terms), 2 );
@terms = $ont->get_parent_terms( $term, $PART_OF, $IS_A );
is( scalar(@terms), 2 );

# now all ancestors:
@terms = $ont->get_ancestor_terms($term);
is( scalar(@terms), 6 );
@terms = $ont->get_ancestor_terms( $term, $PART_OF );
is( scalar(@terms), 0 );
@terms = $ont->get_ancestor_terms( $pterm, $PART_OF );
is( scalar(@terms), 1 );
@terms = $ont->get_ancestor_terms( $term, $IS_A );
is( scalar(@terms), 5 );
@terms = $ont->get_ancestor_terms( $pterm, $IS_A );
is( scalar(@terms), 0 );
@terms = $ont->get_ancestor_terms( $term, $PART_OF, $IS_A );
is( scalar(@terms), 6 );

# pull out all relationships
my @rels = $ont->get_relationships();
my @relset = grep { $_->object_term->name eq "sofa"; } @rels;
is( scalar(@relset), 1 );
@relset = grep { $_->subject_term->name eq "sofa"; } @rels;
is( scalar(@relset), 1 );
@relset = grep { $_->object_term->name eq "feature"; } @rels;
is( scalar(@relset), 10 );
@relset = grep { $_->subject_term->name eq "feature"; } @rels;
is( scalar(@relset), 1 );
@relset = grep { $_->object_term->identifier eq "SO:0000233"; } @rels;
is( scalar(@relset), 4 );
@relset = grep { $_->predicate_term->name eq "IS_A" } @relset;
is( scalar(@relset), 2 );

# relationships for a specific term only
($term) = $ont->find_terms( -identifier => "SO:0000233" );
ok($term);
is( $term->identifier, "SO:0000233" );
is( $term->name,       "processed_transcript" );
@rels = $ont->get_relationships($term);
is( scalar(@rels), 5 );
@relset = grep { $_->predicate_term->name eq "IS_A"; } @rels;
is( scalar(@relset), 3 );
@relset = grep { $_->object_term->identifier eq "SO:0000233"; } @rels;
is( scalar(@relset), 4 );

SKIP: {
    test_skip(-tests    => 3, -requires_module => 'XML::Parser::PerlSAX');
    for my $file (qw/interpro.xml interpro_sample.xml interpro_relationship.xml/) {
        my $parser = Bio::OntologyIO->new(
            -format => "interpro",
            -file   => test_input_file($file),
        );
        ok( $parser->next_ontology, "Interpro XML file $file can be parsed" );
    }
}

BioPerl-1.007002/t/Ontology/OntologyEngine.t000444000766000024      1355413155576321 20746 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

my $ERROR_CLASS;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(
        -tests           => 31,
        -requires_module => 'Graph::Directed'
    );
    
    $ERROR_CLASS = eval "require Error; 1" ? 1 : 0;

    use_ok('Bio::Ontology::Term');
    use_ok('Bio::Ontology::Relationship');
    use_ok('Bio::Ontology::RelationshipType');
    use_ok('Bio::Ontology::SimpleOntologyEngine');
    use_ok('Bio::Ontology::Ontology');
}

my $ont = Bio::Ontology::Ontology->new( -name => "My Ontology" );

my $eng = Bio::Ontology::SimpleOntologyEngine->new();
$ont->engine($eng);
isa_ok( $eng, "Bio::Ontology::OntologyEngineI" );
is( $ont->engine, $eng );

my @terms = (
    [
        -identifier => "IPR000001",
        -name       => "Kringle",
        -definition => "Kringles are autonomous structural domains ...",
        -ontology   => $ont
    ],
    [
        -identifier => "IPR000002",
        -name       => "Cdc20/Fizzy",
        -definition => "The Cdc20/Fizzy region is almost always ...",
        -ontology   => $ont
    ],
    [
        -identifier => "IPR000003",
        -name       => "Retinoid X receptor",
        -definition => "Steroid or nuclear hormone receptors ...",
        -ontology   => $ont
    ],
    [
        -identifier => "IPR000004",
        -name       => "Test4",
        -definition => "Test4 definition ...",
        -ontology   => $ont
    ],
);

for ( my $i = 0 ; $i < @terms ; $i++ ) {
    $terms[$i] = Bio::Ontology::Term->new( @{ $terms[$i] } );
    $ont->add_term( $terms[$i] );
}

my $rel_type  = Bio::Ontology::RelationshipType->get_instance( "IS_A",    $ont );
my $rel_type1 = Bio::Ontology::RelationshipType->get_instance( "PART_OF", $ont );

my @rels = (
    [
        -object_term    => $terms[0],
        -subject_term   => $terms[1],
        -predicate_term => $rel_type,
        -ontology       => $ont,
    ],
    [
        -object_term    => $terms[1],
        -subject_term   => $terms[2],
        -predicate_term => $rel_type,
        -ontology       => $ont,
    ],
    [
        -object_term    => $terms[0],
        -subject_term   => $terms[3],
        -predicate_term => $rel_type,
        -ontology       => $ont,
    ],
    [
        -object_term    => $terms[3],
        -subject_term   => $terms[2],
        -predicate_term => $rel_type,
        -ontology       => $ont,
    ],
);
my @bad_rels = (
    [
        -object_term    => undef,
        -subject_term   => $terms[2],
        -predicate_term => $rel_type,
        -ontology       => $ont,
    ],
    [
        -object_term    => $terms[1],
        -subject_term   => undef,
        -predicate_term => $rel_type,
        -ontology       => $ont,
    ],
    [
        -object_term    => $terms[1],
        -subject_term   => $terms[2],
        -predicate_term => $rel_type,
        -ontology       => $ont,
    ],
);

$bad_rels[0] = Bio::Ontology::Relationship->new( @{ $bad_rels[0] } );
if ($ERROR_CLASS) {
    throws_ok( sub { $ont->add_relationship( $bad_rels[0] ) }, 
    'Bio::Root::Exception',
    'adding a relationship with an undef object term fails');
} else {
    throws_ok( sub { $ont->add_relationship( $bad_rels[0] ) }, qr/Exception/,
              'adding a relationship with an undef object term fails');
}
throws_ok( sub { $ont->add_relationship( $bad_rels[0] ) }, qr/MSG: cannot add relationship, relationship has no object_term/, 'adding a relationship with an undef object term fails');

$bad_rels[1] = Bio::Ontology::Relationship->new( @{ $bad_rels[1] } );
if ($ERROR_CLASS) {
    throws_ok( sub { $ont->add_relationship( $bad_rels[1] ) },
    'Bio::Root::Exception',
    'adding a relationship with an undef subject term fails');
} else {
    throws_ok( sub { $ont->add_relationship( $bad_rels[1] ) },
    qr/Exception/,
    'adding a relationship with an undef subject term fails');
}
throws_ok( sub { $ont->add_relationship( $bad_rels[1] ) }, qr/MSG: cannot add relationship, relationship has no subject_term/, 'adding a relationship with an undef subject term fails');

for ( my $i = 0 ; $i < @rels ; $i++ ) {
    $rels[$i] = Bio::Ontology::Relationship->new( @{ $rels[$i] } );
    $ont->add_relationship( $rels[$i] );
}

my @child_terms =
    sort { $a->identifier() cmp $b->identifier(); } $ont->get_child_terms( $terms[0] );
is( scalar(@child_terms), 2 );
is( $child_terms[0],      $terms[1] );
my @child_terms1 =
    sort { $a->identifier() cmp $b->identifier(); } $ont->get_child_terms( $terms[0], $rel_type );
is( scalar(@child_terms), 2 );
is( $child_terms1[0],     $terms[1] );
is( scalar( $ont->get_child_terms( $terms[0], $rel_type1 ) ), 0 );

my @descendant_terms =
    sort { $a->identifier() cmp $b->identifier(); } $ont->get_descendant_terms( $terms[0] );
is( scalar(@descendant_terms), 3 );
is( $descendant_terms[1],      $terms[2] );

my @descendant_terms1 =
    sort { $a->identifier() cmp $b->identifier(); }
    $ont->get_descendant_terms( $terms[0], $rel_type );
is( $descendant_terms1[1],      $terms[2] );
is( scalar(@descendant_terms1), 3 );
is( scalar( $ont->get_descendant_terms( $terms[0], $rel_type1 ) ), 0 );

my @parent_terms =
    sort { $a->identifier() cmp $b->identifier(); } $ont->get_parent_terms( $terms[1] );
is( scalar(@parent_terms), 1 );
is( $parent_terms[0],      $terms[0] );

my @ancestor_terms =
    sort { $a->identifier() cmp $b->identifier(); } $ont->get_ancestor_terms( $terms[2] );
is( $ancestor_terms[0],      $terms[0] );
is( scalar(@ancestor_terms), 3 );
is( scalar( $ont->get_ancestor_terms( $terms[2], $rel_type ) ),  3 );
is( scalar( $ont->get_ancestor_terms( $terms[2], $rel_type1 ) ), 0 );

my @leaf_terms = $ont->get_leaf_terms();

# print scalar(@leaf_terms)."\n";
is( scalar(@leaf_terms), 1 );
is( $leaf_terms[0],      $terms[2] );

my @root_terms = $ont->get_root_terms();

# print scalar(@root_terms)."\n";
is( scalar(@root_terms), 1 );
is( $root_terms[0],      $terms[0] );

#print $ont->engine->to_string();
BioPerl-1.007002/t/Ontology/OntologyStore.t000444000766000024       140113155576321 20601 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 6,
			   -requires_module => 'Graph',
			   -requires_networking => 1);
	
	use_ok('Bio::Ontology::OntologyStore');
}

ok my $store = Bio::Ontology::OntologyStore->get_instance;
SKIP: {
	my $ontology;
	eval {$ontology = $store->get_ontology(-name => 'Sequence Ontology');};
	skip "Couldn't get sequence ontology, network problems? Skipping these tests", 4 if $@;
	ok(scalar($ontology->get_root_terms()) == 1);
	my($txt) = $ontology->find_terms(-name => 'transcript');
	is $txt->identifier, 'SO:0000673';
	is $txt->name, 'transcript';
	is $txt->definition, 'An RNA synthesized on a DNA or RNA template by an RNA polymerase.';
}
BioPerl-1.007002/t/Ontology/Relationship.t000444000766000024       231113155576321 20414 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 12,
               -requires_module => 'Graph::Directed');
	
    use_ok('Bio::Ontology::Relationship');
    use_ok('Bio::Ontology::GOterm');
    use_ok('Bio::Ontology::RelationshipType');
}

my $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
isa_ok($IS_A, "Bio::Ontology::RelationshipType");

my $parent = Bio::Ontology::GOterm->new();
isa_ok($parent, "Bio::Ontology::GOterm" );

my $child = Bio::Ontology::GOterm->new();
isa_ok($child, "Bio::Ontology::GOterm");

$parent->name( "parent" );

$child->name( "child" );

my $rel = Bio::Ontology::Relationship->new( -identifier        => "16847",
                                            -parent_term       => $parent,
                                            -child_term        => $child,
                                            -relationship_type => $IS_A );

isa_ok($rel, "Bio::Ontology::Relationship");

is( $rel->identifier(), "16847" );

is( $rel->parent_term()->name(), "parent" );

is( $rel->child_term()->name(), "child" );

is( $rel->relationship_type()->name(), "IS_A" );

ok( $rel->to_string() );
BioPerl-1.007002/t/Ontology/RelationshipType.t000444000766000024       351413155576321 21264 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 23,
               -requires_module => 'Graph::Directed');
	
    use_ok('Bio::Ontology::RelationshipType');
    use_ok('Bio::Ontology::Ontology');
}

my $ont = Bio::Ontology::Ontology->new(-name => "relationship type");
  
my $IS_A     = Bio::Ontology::RelationshipType->get_instance("IS_A", $ont);
my $PART_OF  = Bio::Ontology::RelationshipType->get_instance("PART_OF", $ont);
my $CONTAINS = Bio::Ontology::RelationshipType->get_instance("CONTAINS", $ont);
my $FOUND_IN = Bio::Ontology::RelationshipType->get_instance("FOUND_IN", $ont);
my $IS_A2    = Bio::Ontology::RelationshipType->get_instance("IS_A", $ont);

isa_ok($IS_A, "Bio::Ontology::RelationshipType");
isa_ok($IS_A, "Bio::Ontology::TermI");


ok( ! $IS_A->equals( $PART_OF ) );
ok( $IS_A->equals( $IS_A2 ) );
ok( $PART_OF->equals( $PART_OF ) );


is( $IS_A->identifier(), undef ); # don't make up identifiers
is( $IS_A->name(), "IS_A" );
is( $IS_A->definition(), "IS_A relationship predicate (type)" );
is( $IS_A->ontology()->name(), "relationship type" );


is( $PART_OF->identifier(), undef ); # don't make up identifiers
is( $PART_OF->name(), "PART_OF" );
is( $PART_OF->definition(), "PART_OF relationship predicate (type)" );
is( $PART_OF->ontology()->name(), "relationship type" );


is( $CONTAINS->identifier(), undef ); # don't make up identifiers
is( $CONTAINS->name(), "CONTAINS" );
is( $CONTAINS->definition(), "CONTAINS relationship predicate (type)" );
is( $CONTAINS->ontology()->name(), "relationship type" );


is( $FOUND_IN->identifier(), undef ); # don't make up identifiers
is( $FOUND_IN->name(), "FOUND_IN" );
is( $FOUND_IN->definition(), "FOUND_IN relationship predicate (type)" );
is( $FOUND_IN->ontology()->name(), "relationship type" );
BioPerl-1.007002/t/Ontology/Term.t000444000766000024       654213155576321 16674 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 54,
			   -requires_module => 'Graph::Directed');
	
	use_ok('Bio::Ontology::Term');
	use_ok('Bio::Ontology::TermFactory');
	use_ok('Bio::Annotation::DBLink');
}

my $obj = Bio::Ontology::Term->new();

isa_ok $obj, "Bio::Ontology::TermI";

is( $obj->identifier( "0003947" ), "0003947" );
is( $obj->identifier(), "0003947" );

is( $obj->name( "N-acetylgalactosaminyltransferase" ), "N-acetylgalactosaminyltransferase" );
is( $obj->name(), "N-acetylgalactosaminyltransferase" );

is( $obj->definition( "Catalysis of ..." ), "Catalysis of ..." );
is( $obj->definition(), "Catalysis of ..." );

is( $obj->version( "666" ), "666" );
is( $obj->version(), "666" );

ok( $obj->ontology( "category 1 name" ) );
is( $obj->ontology()->name(), "category 1 name" );

my $ont = Bio::Ontology::Ontology->new();
ok( $ont->name( "category 2 name" ) );

ok( $obj->ontology( $ont ) );
is( $obj->ontology()->name(), "category 2 name" );

is( $obj->is_obsolete( 1 ), 1 );
is( $obj->is_obsolete(), 1 );

is( $obj->comment( "Consider the term ..." ), "Consider the term ..." );
is( $obj->comment(), "Consider the term ..." );

is( $obj->get_synonyms(), 0 );

$obj->add_synonym( ( "AA", "AB" ) );
my @al1 = $obj->get_synonyms();
is( scalar(@al1), 2 );
is( $al1[ 0 ], "AA" );
is( $al1[ 1 ], "AB" );

my @al2 = $obj->remove_synonyms();
is( $al2[ 0 ], "AA" );
is( $al2[ 1 ], "AB" );

is( $obj->get_synonyms(), 0 );
is( $obj->remove_synonyms(), 0 );

$obj->add_synonyms( ( "AA", "AB" ) );

is( $obj->identifier(undef), undef );
is( $obj->name(undef), undef );
is( $obj->definition(undef), undef );
is( $obj->is_obsolete(0), 0 );
is( $obj->comment(undef), undef );


$obj = Bio::Ontology::Term->new( 
    -identifier  => "0016847",
    -name        => "1-aminocyclopropane-1-carboxylate synthase",
    -definition  => "Catalysis of ...",
    -is_obsolete => 0,
    -version     => "6.6.6",
    -ontology    => "cat",
    -comment     => "X",
    -dbxrefs    => [
        Bio::Annotation::DBLink->new(-database => 'db1'),
        Bio::Annotation::DBLink->new(-database => 'db2')
    ],
    -references => []
);  

is( $obj->identifier(), "0016847" );
is( $obj->name(), "1-aminocyclopropane-1-carboxylate synthase" );
is( $obj->definition(), "Catalysis of ..." );
is( $obj->is_obsolete(), 0);
is( $obj->comment(), "X" );
is( $obj->version(), "6.6.6" );
is( $obj->ontology()->name(), "cat" );
is( scalar($obj->get_dbxrefs), 2);
is( scalar($obj->get_references), 0);

# test object factory for terms
my $fact = Bio::Ontology::TermFactory->new();
$obj = $fact->create_object(-name => "some ontology term");
isa_ok $obj, "Bio::Ontology::TermI";
is ($obj->name, "some ontology term");

$fact->type("Bio::Ontology::GOterm");
$obj = $fact->create_object(-name => "some ontology term",
			    -identifier => "GO:987654");
isa_ok $obj, "Bio::Ontology::TermI";
isa_ok $obj, "Bio::Ontology::GOterm";
is ($obj->name, "some ontology term");
is ($obj->identifier, "GO:987654");

$fact->type("Bio::Annotation::OntologyTerm");
$obj = $fact->create_object(-name => "some ontology term",
			    -identifier => "GO:987654",
			    -ontology => "nonsense");
isa_ok $obj, "Bio::Ontology::TermI";
isa_ok $obj, "Bio::AnnotationI";
is ($obj->name, "some ontology term");
is ($obj->identifier, "GO:987654");
is ($obj->tagname, "nonsense");
BioPerl-1.007002/t/Ontology/IO000755000766000024          013155576321 15743 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Ontology/IO/go.t000555000766000024      1743513155576321 16727 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 102,
			   -requires_module => 'Graph');
	
	use_ok('Bio::OntologyIO');
}

my $parser = Bio::OntologyIO->new(
                      -format    => "go",
		      -defs_file => test_input_file('GO.defs.test'),
                      # test using -file
		      -file      => test_input_file('component.ontology.test'));


my $IS_A    = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );


my @onts = ();
while(my $ont = $parser->next_ontology()) {
    push(@onts, $ont);
}
is (scalar(@onts), 1);
my $ont = $onts[0];
isa_ok $ont, "Bio::Ontology::OntologyI";
is ($ont->name(), "Gene Ontology");

my $engine = $ont->engine();
isa_ok $engine, "Bio::Ontology::OntologyEngineI";

my $term = $engine->get_terms( "GO:0018897" );

# note that all dblinks are now Bio::Annotation::DBLink instances and that all
# *dblink* methods related to Bio::Ontology::Term are deprecated; this is due to
# inconsistencies in those Bio::Ontology::Term methods. Use *dbxref* methods
# instead

my @dblinks = sort {$a->display_text cmp $b->display_text} ( $term->get_dbxrefs() );
my @synos = sort ( $term->get_synonyms() );

is( $dblinks[ 0 ]->display_text, "MetaCyc:PWY-681" );
is( $dblinks[ 1 ]->display_text, "UM-BBD_pathwayID:dbt" );
is( $synos[ 0 ], "murein sacculus" );
is( $synos[ 1 ], "peptidoglycan" );
is( $term->ontology()->name(), "Gene Ontology" );
is( $term->name(), "dibenzothiophene desulfurization" );


$term = $engine->get_terms( "GO:0004796" );
@dblinks = sort ( $term->get_dbxrefs() );
@synos = sort ( $term->get_synonyms() );
my @sec = sort ( $term->get_secondary_GO_ids() ); 

is( $dblinks[ 0 ]->display_text, "EC:5.3.99.5" );
is( $synos[ 0 ], "cytochrome P450 CYP5" );
is( $sec[ 0 ], "GO:0008400" );
is( $term->ontology()->name(), "Gene Ontology" );
is( $term->name(), "thromboxane-A synthase" );

my @parents = sort goid ( $ont->get_parent_terms( $term ) );
is( @parents, 2 );
is( $parents[ 0 ]->GO_id(), "GO:0015034" );
is( $parents[ 1 ]->GO_id(), "GO:0018895" );


@parents = sort goid ( $ont->get_parent_terms( $term, $PART_OF, $IS_A) );

is( @parents, 2 );
is( $parents[ 0 ]->GO_id(), "GO:0015034" );
is( $parents[ 1 ]->GO_id(), "GO:0018895" );


@parents = sort goid ( $ont->get_parent_terms( "GO:0004796", $IS_A ) );
is( @parents, 2 );
is( $parents[ 0 ]->GO_id(), "GO:0015034" );
is( $parents[ 1 ]->GO_id(), "GO:0018895" );


@parents = sort goid ( $ont->get_parent_terms( "GO:0004796", $PART_OF ) );
is( scalar(@parents), 0 );
my @anc = sort goid ( $ont->get_ancestor_terms( $term ) );
is( scalar(@anc), 3 );
is( $anc[ 0 ]->GO_id(), "GO:0003673" );
is( $anc[ 1 ]->GO_id(), "GO:0015034" );
is( $anc[ 2 ]->GO_id(), "GO:0018895" );


@anc = sort goid ( $ont->get_ancestor_terms( "GO:0004796", $IS_A ) );
is( scalar(@anc), 3 );
is( $anc[ 0 ]->GO_id(), "GO:0003673" );
is( $anc[ 1 ]->GO_id(), "GO:0015034" );
is( $anc[ 2 ]->GO_id(), "GO:0018895" );


@anc = sort goid ( $ont->get_ancestor_terms( "GO:0000666" ) );
is( @anc, 12 );

@anc = sort goid ( $ont->get_ancestor_terms( "GO:0000666", $IS_A ) );
is( @anc, 2 );
is( $anc[ 0 ]->GO_id(), "GO:0005811" );
is( $anc[ 1 ]->GO_id(), "GO:0030481" );

@anc = sort goid ( $ont->get_ancestor_terms( "GO:0000666", $PART_OF ) );
is( @anc, 6 );
is( $anc[ 0 ]->GO_id(), "GO:0005623" );
is( $anc[ 1 ]->GO_id(), "GO:0005625" );
is( $anc[ 2 ]->GO_id(), "GO:0005933" );
is( $anc[ 3 ]->GO_id(), "GO:0005935" );
is( $anc[ 4 ]->GO_id(), "GO:0005937" );
is( $anc[ 5 ]->GO_id(), "GO:0005938" );


my @childs = sort goid ( $ont->get_child_terms( "GO:0005625", $PART_OF ) );
is( @childs, 2 );
is( $childs[ 0 ]->GO_id(), "GO:0000666" );
is( $childs[ 0 ]->name(), "polarisomeX" );
is( $childs[ 1 ]->GO_id(), "GO:0000667" );
is( $childs[ 1 ]->name(), "polarisomeY" );
is( $childs[ 1 ]->ontology()->name(), "Gene Ontology" );


is( $engine->get_terms( "GO:0005625" )->name(), "soluble fraction" ); 


@childs = sort goid ( $ont->get_descendant_terms( "GO:0005624", $IS_A ) );
is( @childs, 6 );
is( $childs[ 0 ]->GO_id(), "GO:0000299" );
is( $childs[ 0 ]->name(), "integral membrane protein of membrane fraction" );
is( $childs[ 1 ]->GO_id(), "GO:0000300" );
is( $childs[ 1 ]->name(), "peripheral membrane protein of membrane fraction" );
is( $childs[ 2 ]->GO_id(), "GO:0005792" );
is( $childs[ 2 ]->name(), "microsome" );
is( $childs[ 3 ]->GO_id(), "GO:0019717" );
is( $childs[ 3 ]->name(), "synaptosome" );
is( $childs[ 4 ]->GO_id(), "GO:0019718" );
is( $childs[ 4 ]->name(), "rough microsome" );
is( $childs[ 5 ]->GO_id(), "GO:0019719" );
is( $childs[ 5 ]->name(), "smooth microsome" );

@childs = sort goid ( $ont->get_descendant_terms( "GO:0005625", $IS_A ) );
is( @childs, 0 );


@childs = sort goid ( $ont->get_descendant_terms( "GO:0005625", $PART_OF ) );
is( @childs, 2 );

my @rels = sort child_goid ( $ont->get_relationships( "GO:0005625" ) );
is( @rels, 3 );
is( $rels[ 0 ]->object_term()->GO_id(), "GO:0005625" );
is( $rels[ 0 ]->subject_term()->GO_id(), "GO:0000666" );
ok( $rels[ 0 ]->predicate_term()->equals( $PART_OF ) );

is( $rels[ 1 ]->object_term()->GO_id(), "GO:0005625" );
is( $rels[ 1 ]->subject_term()->GO_id(), "GO:0000667" );
ok( $rels[ 1 ]->predicate_term()->equals( $PART_OF ) );

is( $rels[ 2 ]->object_term()->GO_id(), "GO:0000267" );
is( $rels[ 2 ]->subject_term()->GO_id(), "GO:0005625" );
ok( $rels[ 2 ]->predicate_term()->equals( $IS_A ) );

# dbxrefs and synonyms are candidates for being falsely picked up by
# overly promiscuous regular expressions as related terms, so we test for
# that here
my @terms = $engine->get_terms( "EC:5.3.99.5" );
is (scalar(@terms), 0);
@terms = $engine->get_terms("MetaCyc:PWY-681","MetaCyc:PWY");
is (scalar(@terms), 0);
@terms = $engine->get_terms("UM-BBD_pathwayID:dbt","BBD_pathwayID:dbt",
                            "UM-BBD_pathwayID:dbt2","BBD_pathwayID:dbt2");
is (scalar(@terms), 0);


ok( $engine->graph() );

ok( $ont->add_term( Bio::Ontology::GOterm->new(-identifier => "GO:0000000")));

ok( $engine->has_term( "GO:0000300" ) );

is( scalar $ont->get_all_terms(), 44 );
is( scalar $ont->get_relationship_types(), 3 );

ok( ! $ont->add_relationship( $rels[ 2 ] ) ); # this edge already exists, cannot add

$rels[ 2 ]->subject_term()->GO_id( "GO:0005938" );
ok( $ont->add_relationship( $rels[ 2 ] ) ); # now it's changed, can add
 

my @roots = $ont->get_root_terms();
is( scalar(@roots), 10 );

my @leafs = $ont->get_leaf_terms();
is( scalar(@leafs), 19 );



$parser = Bio::OntologyIO->new(
                      -format    => "go",
		      -defs_file => test_input_file('GO.defs.test2'),
		      # test using -files
		      -files     => test_input_file('component.ontology.test2'));

$ont = $parser->next_ontology();
ok ($ont);

@roots = $ont->get_root_terms();
is( scalar(@roots), 1 );

@leafs = $ont->get_leaf_terms();
is( scalar(@leafs), 4 );

$parser = Bio::OntologyIO->new(
                      -format    => "go",
		      -file      => test_input_file('mpath.ontology.test'));

ok($parser);
$ont = $parser->next_ontology;
ok($ont);
$engine = $ont->engine;
ok($engine);
$term = $engine->get_terms( "MPATH:30" );
is($term->identifier,"MPATH:30");
is($term->name,"cystic medial necrosis");
is($term->definition,undef);
is((sort $term->get_synonyms)[0],"erdheim disease");
is($ont->get_parent_terms( $term )->name,"tissue specific degenerative process");
is(scalar($ont->get_root_terms()),2);
@anc = $ont->get_ancestor_terms($term);
is(scalar(@anc),4);

#################################################################
# helper functions
#################################################################

sub goid { snum ( $a->GO_id() ) <=> snum ( $b->GO_id() ) }

sub child_goid { snum ( $a->child_term()->GO_id() ) <=> snum ( $b->child_term()->GO_id() ) }

sub snum {
    my $x = shift( @_ );
    $x =~ s/\D+//g;
    return $x;
}
BioPerl-1.007002/t/Ontology/IO/interpro.t000444000766000024      1065713155576321 20160 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 69,
               -requires_modules => [qw(XML::Parser::PerlSAX
                                        XML::Parser
                                        Graph::Directed)]);
    use_ok('Bio::OntologyIO');
}
use Data::Dumper;

my $ipp = Bio::OntologyIO->new( -format          => 'interpro',
                                -file            => test_input_file('interpro_short.xml'),
                                -ontology_engine => 'simple' );
isa_ok ($ipp, 'Bio::OntologyIO::InterProParser');

my $ip;
while(my $ont = $ipp->next_ontology) {
    # there should be only one ontology
    is ($ip, undef);
    $ip = $ont;
}
# we grep for defined values because we don't want a list of undefined values to be pass any test
my @leaves = $ip->get_leaf_terms;
ok( ( grep { defined } map { $_->get_dbxrefs } @leaves), 'get_dbxrefs on leaf terms is non-empty');
ok( ( grep { defined } map { $_->get_dbxrefs('member_list') }       @leaves), 'get_dbxrefs(member_list) on leaf terms is non-empty');
ok( ( grep { defined } map { $_->get_dbxrefs('sec_list') }          @leaves), 'get_dbxrefs(sec_list) on leaf terms is non-empty');
ok( ( grep { defined } map { $_->get_dbxrefs('class_list') }        @leaves), 'get_dbxrefs(class_list) on leaf terms is non-empty');
ok( ( grep { defined } map { $_->get_dbxrefs('pub_list') }          @leaves), 'get_dbxrefs(pub_list) on leaf terms is non-empty');
ok( ( grep { defined } map { $_->get_dbxrefs('example_list') }      @leaves), 'get_dbxrefs(example_list) on leaf terms is non-empty');
ok( ( grep { defined } map { $_->get_dbxrefs('external_doc_list') } @leaves), 'get_dbxrefs(external_doc_list) on leaf terms is non-empty');

ok( ( grep { defined } map { $_->get_members }            @leaves), 'get_members on leaf terms is non-empty');
ok( ( grep { defined } map { $_->class_list }             @leaves), 'class_list on leaf terms is non-empty');
ok( ( grep { defined } map { $_->get_examples }           @leaves), 'get_examples on leaf terms is non-empty');
ok( ( grep { defined } map { $_->get_external_documents } @leaves), 'get_external_documents on leaf terms is non-empty');
ok( ( grep { defined } map { $_->get_references }         @leaves), 'get_references on leaf terms is non-empty');
ok( ( grep { defined } map { $_->protein_count }          @leaves), 'protein_count on leaf terms is non-empty');

# this could greatly be improved (note: @leaves elements currently come in random order)
like( $leaves[0]->to_string, qr/-- InterPro id:/, 'to_string looks reasonable');

# there should be 8 root terms: InterPro Domain, InterPro Family,
# InterPro Repeat, and InterPro PTM (Post Translational Modification),
# Active_site, Binding_site, Conserved_site and Region

my @rt = sort { $a->name cmp $b->name; } $ip->get_root_terms();
is (scalar(@rt), 8, 'There are 8 root InterPro terms');

# every InterPro term should have an ontology,
foreach my $term ($ip->get_leaf_terms, @rt) {
    isa_ok ($term->ontology, 'Bio::Ontology::Ontology');
    is ($term->ontology->name, "InterPro", "term ".$term->name." in ontology InterPro");
}

# there are 10 fully instantiated InterPro terms in total, which should be returned as the leafs
is (scalar($ip->get_leaf_terms), 10);
# roots and leafs together:
is (scalar($ip->get_all_terms), 15);

# descendants and children (synonymous here because of depth 1)
# note that the sort should have placed Domain first and Family second
is (scalar($ip->get_descendant_terms($rt[3])), 4); # 4 InterPro Domains
is (scalar($ip->get_child_terms($rt[3])),      4); # dto.
is (scalar($ip->get_descendant_terms($rt[4])), 3); # 3 Interpro Family
is (scalar($ip->get_child_terms($rt[4])),      3); # dto.

# test for ancestors and parents (synonymous here because of depth 1)
foreach my $t ($ip->get_leaf_terms) {
    # every InterPro term has exactly one parent - namely either
    # Domain, Region, Family, Repeat, or PTM(Post Transl. Modification)

    if (not (   $t->identifier eq "Repeat" or $t->identifier eq "PTM"
             or $t->identifier eq "Region" or $t->identifier =~ '_site' )
        ) {
        is (scalar($ip->get_parent_terms($t)),   1, $t->name . " term has one parent");
        is (scalar($ip->get_ancestor_terms($t)), 1, $t->name . " term has one ancestor");
    }
}

# test for secondary accession map
is(scalar(keys %{$ipp->secondary_accessions_map}), 2, 'secondary accession map has 2 keys');
BioPerl-1.007002/t/Ontology/IO/obo.t000444000766000024      2116713155576321 17073 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 92,
			   -requires_module => 'Graph');
	
	use_ok('Bio::OntologyIO');
	use_ok('Bio::Ontology::RelationshipType');
}

my $IS_A    = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );

my $parser = Bio::OntologyIO->new(
                      -format    => "obo",
		      -file      => test_input_file('so.obo'));

my $ont = $parser->next_ontology();
ok ($ont);
is ($ont->name(), "sequence");

my @roots = $ont->get_root_terms();
is (scalar(@roots), 1);
is ($roots[0]->name(), "Sequence_Ontology");
is ($roots[0]->identifier(), "SO:0000000");

my @terms = sort {$a->name cmp $b->name} $ont->get_child_terms($roots[0]);
is (scalar(@terms), 5);
my ($term) = grep { $_->name() eq "variation_operation"; } @terms;
ok $term;
($term) = grep { $_->name() eq "sequence_attribute"; } @terms;
ok $term;
($term) = grep { $_->name() eq "consequences_of_mutation"; } @terms;
ok $term;
($term) = grep { $_->name() eq "chromosome_variation"; } @terms;
ok $term;
($term) = grep { $_->name() eq "located_sequence_feature"; } @terms;
ok $term;

@terms = sort {$a->name cmp $b->name} $ont->get_child_terms($terms[4]);
is (scalar(@terms), 5);
($term) = grep { $_->name() eq "translocate"; } @terms;
ok $term;
($term) = grep { $_->name() eq "delete"; } @terms;
ok $term;
($term) = grep { $_->name() eq "insert"; } @terms;
ok $term;
($term) = grep { $_->name() eq "substitute"; } @terms;
ok $term;
($term) = grep { $_->name() eq "invert"; } @terms;
ok $term;

my $featterm = $terms[0];
@terms = sort {$a->name cmp $b->name} $ont->get_child_terms($featterm);
is (scalar(@terms), 2);

# substitution has two parents, see whether this is handled
@terms = $ont->find_terms(-name => "substitution");
$term =  $terms[0];
is ($term->name(), "substitution");

# search using obo terms;
@terms = $ont->find_identically_named_terms($term);
is scalar @terms, 1;
@terms = $ont->find_identical_terms($term);
is scalar @terms, 1;
@terms = $ont->find_similar_terms($term);
is scalar @terms, 7;

@terms = $ont->get_ancestor_terms($term);
is (scalar(@terms), 6);
is (scalar(grep { $_->name() eq "region"; } @terms), 1);
is (scalar(grep { $_->name() eq "sequence_variant"; } @terms), 1);

# processed_transcript has part-of and is-a children

@terms = $ont->find_terms(-name => "processed_transcript");;
$term = $terms[0];

@terms = $ont->get_child_terms($term);
is (scalar(@terms), 5);
@terms = $ont->get_child_terms($term, $PART_OF);
is (scalar(@terms), 2);
@terms = $ont->get_child_terms($term, $IS_A);
is (scalar(@terms), 3);
@terms = $ont->get_child_terms($term, $PART_OF, $IS_A);
is (scalar(@terms), 5);

# TF_binding_site has 2 parents and different relationships in the two
# paths up (although the relationships to its two parents are of the
# same type, namely is-a)
@terms = $ont->find_terms(-name => "TF_binding_site");;
$term = $terms[0];

@terms = $ont->get_parent_terms($term);
is (scalar(@terms), 2);
my ($pterm) = grep { $_->name eq "regulatory_region"; } @terms;
ok $pterm;
@terms = $ont->get_parent_terms($term, $PART_OF);
is (scalar(@terms), 0);
@terms = $ont->get_parent_terms($term, $IS_A);
is (scalar(@terms), 2);
@terms = $ont->get_parent_terms($term, $PART_OF, $IS_A);
is (scalar(@terms), 2);


# pull out all relationships
my @rels = $ont->get_relationships();
my @relset = grep { $_->object_term->name eq "Sequence_Ontology"; } @rels;
is (scalar(@relset), 5);
@relset = grep { $_->subject_term->name eq "Sequence_Ontology"; } @rels;
is (scalar(@relset), 0);

# relationships for a specific term only
($term) = $ont->find_terms(-identifier => "SO:0000082");
ok ($term);
is ($term->identifier, "SO:0000082");
is ($term->name, "processed_transcript_attribute");
@rels = $ont->get_relationships($term);
is (scalar(@rels), 5);
@relset = grep { $_->predicate_term->name eq "IS_A"; } @rels;
is (scalar(@relset), 5);
@relset = grep { $_->object_term->identifier eq "SO:0000082"; } @rels;
is (scalar(@relset), 4);
@relset = grep { $_->subject_term->identifier eq "SO:0000082"; } @rels;
is (scalar(@relset), 1);




#### --- testing obo parsers for regulates relationships
my $parser2 = Bio::OntologyIO->new (
	 -format => 'obo',
	 -file => test_input_file('regulation_test.obo'));

isa_ok($parser2,'Bio::OntologyIO', 'got a ontology IO handler');

my @ontologies;
while (my $ont = $parser2->next_ontology()) {
	 isa_ok($ont,'Bio::Ontology::Ontology','got ontology parser2');
	 isa_ok($ont->engine,'Bio::Ontology::OBOEngine','got OBO engine object');
	 push @ontologies,$ont;
}

my $molont = $ontologies[1];
my $bioont = $ontologies[2];
is($ontologies[0]->name(),'gene_ontology','Gene ontology');
is($bioont->name(),'biological_process','biological process');
is($molont->name(),'molecular_function','molecular function');

my ($broot) = $bioont->get_root_terms();
is($broot->name(),'biological_process','Got root');


my ($mroot) = $molont->get_root_terms();
is($mroot->name(),'molecular_function','Got root');


## -- testing newly introduced relationships
is($ontologies[0]->get_relationship_type('REGULATES')->name,'REGULATES','Got regulates
	 from gene_ontology');
is($ontologies[0]->get_relationship_type('POSITIVELY_REGULATES')->name,'POSITIVELY_REGULATES','Got
	 positively regulates from gene_ontology');
is($bioont->get_relationship_type('REGULATES')->name,'REGULATES','Got
	  regulates from biological_process');
is($bioont->get_relationship_type('POSITIVELY_REGULATES')->name,'POSITIVELY_REGULATES','Got
	 positively regulates from biological_process');


## -- getting relationships for various ontologies
my @onto_pred = sort {$a->name cmp $b->name} $ontologies[0]->get_predicate_terms();
my @bio_pred =  sort {$a->name cmp $b->name} $bioont->get_predicate_terms();
is(scalar @onto_pred,6,'Got predicates for gene_ontology');
is(scalar @bio_pred,2,'Got predicates for biological_process');
is($onto_pred[4]->name(),'REGULATES','Got regulates predicate');
is($bio_pred[0]->name(),'POSITIVELY_REGULATES','Got positively regulates predicate');


my @bio_rel = $bioont->get_relationships();
my @mol_rel = $molont->get_relationships();
is(scalar @bio_rel,11,'Got relationships for biological_process');
is(scalar @mol_rel,2,'Got relationships for molecular_function');
is($mol_rel[0]->predicate_term->name(),'IS_A','Got is a relationship from
	 molecular_function');
## ----


## -- testing the regulates relationships between term1s
my $REG = Bio::Ontology::RelationshipType->get_instance('REGULATES');
my $PREG = Bio::Ontology::RelationshipType->get_instance('POSITIVELY_REGULATES');

my ($term1) = $bioont->find_terms(-identifier => 'GO:0050790');
isa_ok($term1,'Bio::Ontology::Term','Got term object');
is($term1->identifier(),'GO:0050790', 'Got term id');
is($term1->name(),'regulation of catalytic activity', 'Got term name');

my ($parent) = $bioont->get_parent_terms($term1,$REG);
isa_ok($parent,'Bio::Ontology::Term','Got regulated object');
is($parent->identifier(),'GO:0003824','Got regulated term1 id'); 

## -- now testing the other way
my ($child) = $bioont->get_child_terms($parent,$REG); 
isa_ok($child,'Bio::Ontology::Term','Got term1 object');
is($child->identifier(),$term1->identifier(),'Got back the child');

my ($term2) = $bioont->find_terms(-identifier => 'GO:0043085');
isa_ok($term2,'Bio::Ontology::Term','Got term object');
is($term2->identifier(),'GO:0043085', 'Got term id');
is($term2->name(),'positive regulation of catalytic activity', 'Got term name');

my ($parent2) = $bioont->get_parent_terms($term2,$PREG);
isa_ok($parent2,'Bio::Ontology::Term','Got regulated object');
is($parent2->identifier(),'GO:0003824','Got regulated term1 id'); 
is($parent->name(),$parent2->name(),'Got identical regulation');


my ($child2) = $bioont->get_child_terms($parent2,$PREG); 
isa_ok($child2,'Bio::Ontology::Term','Got term1 object');
is($child2->identifier(),$term2->identifier(),'Got back the child');



#### --- testing obo parsers for secondary identifiers
my $parser3 = Bio::OntologyIO->new (
	 -format => 'obo',
	 -file => test_input_file('sp_subset.obo'));

isa_ok($parser3,'Bio::OntologyIO', 'got a ontology IO handler');


my $sp_ont = $parser3->next_ontology();
ok ($sp_ont);
is ($sp_ont->name(), "solanaceae_phenotype");

#the term 'plant size has 4 secondary identifiers
@terms = $sp_ont->find_terms(-name => "plant size");
$term =  $terms[0];
is ($term->name(), "plant size");

my @xrefs = $term->get_secondary_ids();
is(scalar(@xrefs) , 4);

my ($xref) = grep { $_ eq "PATO:0000117"; } @xrefs;
ok $xref;
($xref) = grep { $_ eq "PO:0000003"; } @xrefs;
ok $xref;
($xref) = grep { $_ eq "PO:0007130"; } @xrefs;
ok $xref;
($xref) = grep { $_ eq "TO:0000207"; } @xrefs;
ok $xref;


BioPerl-1.007002/t/Phenotype000755000766000024          013155576321 15575 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Phenotype/Correlate.t000444000766000024       234013155576321 20036 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;
BEGIN {
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 17);
    
    use_ok('Bio::Phenotype::Correlate');
    use_ok('Bio::Species');
}

my $mouse = Bio::Species->new();
  
$mouse->classification( qw( musculus Mus ) );

my $co = Bio::Phenotype::Correlate->new( -name        => "4(Tas1r3)",
                                         -description => "mouse correlate of human phenotype MIM 605865",
                                         -species     => $mouse,
                                         -type        => "homolog",
                                         -comment     => "type=homolog is putative" );

isa_ok($co, "Bio::Phenotype::Correlate" );

ok( $co->to_string() );

is( $co->name(), "4(Tas1r3)" );
is( $co->description(), "mouse correlate of human phenotype MIM 605865" );
is( $co->species()->binomial(), "Mus musculus" );
is( $co->type(), "homolog" );
is( $co->comment(), "type=homolog is putative" );

$co->init();

is( $co->name(), "" );
is( $co->description(), "" );
is( $co->type(), "" );
is( $co->comment(), "" );

is( $co->name( "A" ), "A" );
is( $co->description( "B" ), "B" );
is( $co->type( "C" ), "C" );
is( $co->comment( "D" ), "D" );
BioPerl-1.007002/t/Phenotype/MeSH.t000444000766000024       220613155576321 16713 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 24);
	
	use_ok('Bio::Phenotype::MeSH::Term');
	use_ok('Bio::Phenotype::MeSH::Twig');
}
# For tests of Bio::DB::MeSH see t/DB.t

my $verbose = test_debug();

ok my $term = Bio::Phenotype::MeSH::Term->new(-verbose =>$verbose);
is $term->id('D000001'), 'D000001';
is $term->id, 'D000001';
is $term->name('Dietary Fats'), 'Dietary Fats';
is $term->name, 'Dietary Fats';
is $term->description('dietary fats are...'), 'dietary fats are...';
is $term->description, 'dietary fats are...';

ok my $twig = Bio::Phenotype::MeSH::Twig->new(-verbose =>$verbose);
is $twig->parent('Fats'), 'Fats';
is $twig->parent(), 'Fats';


ok $term->add_twig($twig);
is $term->each_twig(), 1;
is $twig->term, $term;

is $twig->add_sister('Bread', 'Candy', 'Cereals'), 3;
is $twig->add_sister('Condiments', 'Dairy Products'), 2;
is $twig->each_sister(), 5;
ok $twig->purge_sisters();
is $twig->each_sister(), 0;

is $twig->add_child('Butter', 'Margarine'), 2;
is $twig->each_child(), 2;
ok $twig->purge_children();
is $twig->each_child(), 0;
BioPerl-1.007002/t/Phenotype/Measure.t000444000766000024       242513155576321 17523 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 21);
	
    use_ok 'Bio::Phenotype::Measure';
}
  
my $measure = Bio::Phenotype::Measure->new( -context     => "height",
                                            -description => "desc",
                                            -start       => 10,
                                            -end         => 150,
                                            -unit        => "cm",
                                            -comment     => "comment" );

isa_ok( $measure, "Bio::Phenotype::Measure" );

ok( $measure->to_string() );

is( $measure->context(), "height" );
is( $measure->description(), "desc" );
is( $measure->start(), 10 );
is( $measure->end(), 150 );
is( $measure->unit(), "cm" );
is( $measure->comment(), "comment" );

$measure->init();

is( $measure->context(), "" );
is( $measure->description(), "" );
is( $measure->start(), "" );
is( $measure->end(), "" );
is( $measure->unit(), "" );
is( $measure->comment(), "" );

is( $measure->context( "A" ), "A" );
is( $measure->description( "B" ), "B" );
is( $measure->start( "C" ), "C" );
is( $measure->end( "D" ), "D" );
is( $measure->unit( "E" ), "E" );
is( $measure->comment( "F" ), "F" );
BioPerl-1.007002/t/Phenotype/MiniMIMentry.t000444000766000024       222213155576321 20436 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 15);
	
    use_ok('Bio::Phenotype::OMIM::MiniMIMentry');
}
  
my  $mm = Bio::Phenotype::OMIM::MiniMIMentry->new( -description  => "The central form of ...",
                                                   -created      => "Victor A. McKusick: 6/4/1986",
                                                   -contributors => "Kelly A. Przylepa - revised: 03/18/2002",
                                                   -edited       => "alopez: 06/03/1997" );

isa_ok( $mm, "Bio::Phenotype::OMIM::MiniMIMentry");

ok( $mm->to_string() );

is( $mm->description(), "The central form of ..." );
is( $mm->created(), "Victor A. McKusick: 6/4/1986" );
is( $mm->contributors(), "Kelly A. Przylepa - revised: 03/18/2002" );
is( $mm->edited(), "alopez: 06/03/1997" );

$mm->init();

is( $mm->description(), "" );
is( $mm->created(), "" );
is( $mm->contributors(), "" );
is( $mm->edited(), "" );


is( $mm->description( "A" ), "A" );
is( $mm->created( "B" ), "B" );
is( $mm->contributors( "C" ), "C" );
is( $mm->edited( "D" ), "D" );
BioPerl-1.007002/t/Phenotype/OMIMentry.t000444000766000024      1701113155576321 17762 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 153);
	
    use_ok('Bio::Phenotype::OMIM::OMIMentry');
    use_ok('Bio::Phenotype::OMIM::MiniMIMentry');
    use_ok('Bio::Species');
    use_ok('Bio::Annotation::Reference');
    use_ok('Bio::Map::CytoPosition');
    use_ok('Bio::Phenotype::Correlate');
    use_ok('Bio::Phenotype::Measure');
    use_ok('Bio::Annotation::DBLink');
}

my $obj = Bio::Phenotype::OMIM::OMIMentry->new();

isa_ok( $obj, "Bio::Phenotype::OMIM::OMIMentry" );

ok( $obj->to_string() );

ok( $obj->MIM_number( "100050" ) );
is( $obj->MIM_number(), "100050" );

ok( $obj->title( "AARSKOG SYNDROME" ) );
is( $obj->title(), "AARSKOG SYNDROME" );


ok( $obj->more_than_two_genes( 1 ) );
is( $obj->more_than_two_genes(), 1 );

ok( $obj->is_separate( 1 ) );
is( $obj->is_separate(), 1 );

ok( $obj->alternative_titles_and_symbols( "AORTIC ANEURYSM, ABDOMINAL" ) );
is( $obj->alternative_titles_and_symbols(), "AORTIC ANEURYSM, ABDOMINAL" );

ok( $obj->mapping_method( "PCR of somatic cell hybrid DNA" ) );
is( $obj->mapping_method(), "PCR of somatic cell hybrid DNA" );

ok( $obj->gene_status( "I" ) );
is( $obj->gene_status(), "I" );


ok( $obj->clinical_symptoms_raw( "Patients with ..." ) );
is( $obj->clinical_symptoms_raw(), "Patients with ..." );


ok( $obj->created( "Victor A. McKusick: 6/4/1986" ) );
is( $obj->created(), "Victor A. McKusick: 6/4/1986" );

ok( $obj->contributors( "Kelly A. Przylepa - revised: 03/18/2002" ) );
is( $obj->contributors(), "Kelly A. Przylepa - revised: 03/18/2002" );

ok( $obj->edited( "alopez: 06/03/1997" ) );
is( $obj->edited(), "alopez: 06/03/1997" );


my $mm = Bio::Phenotype::OMIM::MiniMIMentry->new();

ok( $obj->miniMIM( $mm ) );
is( $obj->miniMIM(), $mm );



my $av1 = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new();
my $av2 = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new();

ok( $av1->description( "dedxsc" ) );

is( $obj->each_AllelicVariant(), 0 );

ok( $obj->add_AllelicVariants( ( $av1, $av2 ) ) );
is( $obj->each_AllelicVariant(), 2 );
my @avs = $obj->each_AllelicVariant();
is( $avs[ 0 ], $av1 );
is( $avs[ 1 ], $av2 );
is( $avs[ 0 ]->description, "dedxsc" );
is( $obj->each_AllelicVariant(), 2 );

my @avs2 = $obj->remove_AllelicVariants();
is( $avs2[ 0 ], $av1 );
is( $avs2[ 1 ], $av2 );

is( $obj->each_AllelicVariant(), 0 );
is( $obj->remove_AllelicVariants(), 0 );






ok( $obj->name( "r1" ) );
is( $obj->name(), "r1" );

ok( $obj->description( "This is ..." ) );
is( $obj->description(), "This is ..." );

my $mouse = Bio::Species->new();
$mouse->classification( qw( musculus Mus ) );
ok( $obj->species( $mouse ) );
is( $obj->species()->binomial(), "Mus musculus" );

ok( $obj->comment( "putative" ) );
is( $obj->comment(), "putative" );



is( $obj->each_gene_symbol(), 0 );

ok( $obj->add_gene_symbols( ( "A", "B" ) ) );
is( $obj->each_gene_symbol(), 2 );
my @gs = $obj->each_gene_symbol();
is( $gs[ 0 ], "A" );
is( $gs[ 1 ], "B" );
is( $obj->each_gene_symbol(), 2 );

my @gs2 = $obj->remove_gene_symbols();
is( $gs2[ 0 ], "A" );
is( $gs2[ 1 ], "B" );

is( $obj->each_gene_symbol(), 0 );
is( $obj->remove_gene_symbols(), 0 );



my $v1 = Bio::Variation::VariantI->new();
my $v2 = Bio::Variation::VariantI->new();

$v1->length( "123" );

is( $obj->each_Variant(), 0 );

ok( $obj->add_Variants( ( $v1, $v2 ) ) );
is( $obj->each_Variant(), 2 );
my @vs = $obj->each_Variant();
is( $vs[ 0 ], $v1 );
is( $vs[ 1 ], $v2 );
is( $vs[ 0 ]->length(), "123" );
is( $obj->each_Variant(), 2 );

my @vs2 = $obj->remove_Variants();
is( $vs2[ 0 ], $v1 );
is( $vs2[ 1 ], $v2 );

is( $obj->each_Variant(), 0 );
is( $obj->remove_Variants(), 0 );




my $r1 = Bio::Annotation::Reference->new();
my $r2 = Bio::Annotation::Reference->new();

$r1->title( "title" );

is( $obj->each_Reference(), 0 );

ok( $obj->add_References( ( $r1, $r2 ) ) );
is( $obj->each_Reference(), 2 );
my @rs = $obj->each_Reference();
is( $rs[ 0 ]->display_text, $r1->display_text,'operator overloading in AnnotationI is deprecated');
is( $rs[ 1 ]->display_text, $r2->display_text,'operator overloading in AnnotationI is deprecated');
is( $rs[ 0 ]->title(), "title" );
is( $obj->each_Reference(), 2 );

my @rs2 = $obj->remove_References();
is( $rs2[ 0 ]->display_text, $r1->display_text,'operator overloading in AnnotationI is deprecated');
is( $rs2[ 1 ]->display_text, $r2->display_text,'operator overloading in AnnotationI is deprecated');

is( $obj->each_Reference(), 0 );
is( $obj->remove_References(), 0 );




my $c1 = Bio::Map::CytoPosition->new();
my $c2 = Bio::Map::CytoPosition->new();

$c1->chr( "12" );

is( $obj->each_CytoPosition(), 0 );

ok( $obj->add_CytoPositions( ( $c1, $c2 ) ) );
is( $obj->each_CytoPosition(), 2 );
my @cs = $obj->each_CytoPosition();
is( $cs[ 0 ], $c1 );
is( $cs[ 1 ], $c2 );
is( $cs[ 0 ]->chr(), "12" );
is( $obj->each_CytoPosition(), 2 );

my @cs2 = $obj->remove_CytoPositions();
is( $cs2[ 0 ], $c1 );
is( $cs2[ 1 ], $c2 );

is( $obj->each_CytoPosition(), 0 );
is( $obj->remove_CytoPositions(), 0 );




my $co1 = Bio::Phenotype::Correlate->new();
my $co2 = Bio::Phenotype::Correlate->new();

ok( $co1->name( "name" ) );

is( $obj->each_Correlate(), 0 );

ok( $obj->add_Correlates( ( $co1, $co2 ) ) );
is( $obj->each_Correlate(), 2 );
my @cos = $obj->each_Correlate();
is( $cos[ 0 ], $co1 );
is( $cos[ 1 ], $co2 );
is( $cos[ 0 ]->name, "name" );
is( $obj->each_Correlate(), 2 );

my @cos2 = $obj->remove_Correlates();
is( $cos2[ 0 ], $co1 );
is( $cos2[ 1 ], $co2 );

is( $obj->each_Correlate(), 0 );
is( $obj->remove_Correlates(), 0 );




my $m1 = Bio::Phenotype::Measure->new();
my $m2 = Bio::Phenotype::Measure->new();

ok( $m1->description( "desc" ) );

is( $obj->each_Measure(), 0 );

ok( $obj->add_Measures( ( $m1, $m2 ) ) );
is( $obj->each_Measure(), 2 );
my @ms = $obj->each_Measure();
is( $ms[ 0 ], $m1 );
is( $ms[ 1 ], $m2 );
is( $ms[ 0 ]->description, "desc" );
is( $obj->each_Measure(), 2 );

my @ms2 = $obj->remove_Measures();
is( $ms2[ 0 ], $m1 );
is( $ms2[ 1 ], $m2 );

is( $obj->each_Measure(), 0 );
is( $obj->remove_Measures(), 0 );



is( $obj->each_keyword(), 0 );

ok( $obj->add_keywords( ( "A", "B" ) ) );
is( $obj->each_keyword(), 2 );
my @ks = $obj->each_keyword();
is( $ks[ 0 ], "A" );
is( $ks[ 1 ], "B" );
is( $obj->each_keyword(), 2 );

my @ks2 = $obj->remove_keywords();
is( $ks2[ 0 ], "A" );
is( $ks2[ 1 ], "B" );

is( $obj->each_keyword(), 0 );
is( $obj->remove_keywords(), 0 );



my $l1 = Bio::Annotation::DBLink->new();
my $l2 = Bio::Annotation::DBLink->new();

ok( $l1->comment( "comment" ) );

is( $obj->each_DBLink(), 0 );

ok( $obj->add_DBLinks( ( $l1, $l2 ) ) );
is( $obj->each_DBLink(), 2 );
my @ls = $obj->each_DBLink();
is( $ls[ 0 ]->display_text, $l1->display_text,'operator overloading in AnnotationI is deprecated');
is( $ls[ 1 ]->display_text, $l2->display_text,'operator overloading in AnnotationI is deprecated');
is( $ls[ 0 ]->comment(), "comment" );
is( $obj->each_DBLink(), 2 );

my @ls2 = $obj->remove_DBLinks();
is( $ls2[ 0 ]->display_text, $l1->display_text,'operator overloading in AnnotationI is deprecated');
is( $ls2[ 1 ]->display_text, $l2->display_text,'operator overloading in AnnotationI is deprecated');

is( $obj->each_DBLink(), 0 );
is( $obj->remove_DBLinks(), 0 );



is( $obj->each_Genotype(), 0 );

ok( $obj->add_Genotypes( ( "A", "B" ) ) );
is( $obj->each_Genotype(), 2 );
my @gts = $obj->each_Genotype();
is( $gts[ 0 ], "A" );
is( $gts[ 1 ], "B" );
is( $obj->each_Genotype(), 2 );

my @gts2 = $obj->remove_Genotypes();
is( $gts2[ 0 ], "A" );
is( $gts2[ 1 ], "B" );

is( $obj->each_Genotype(), 0 );
is( $obj->remove_Genotypes(), 0 );
BioPerl-1.007002/t/Phenotype/OMIMentryAllelicVariant.t000444000766000024       356313155576321 22564 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 27);
	
    use_ok 'Bio::Phenotype::OMIM::OMIMentryAllelicVariant';
}

my $av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new( -number               => ".0001",
                                                             -title                => "ALCOHOL INTOLERANCE",
                                                             -symbol               => "ALDH2*2",
                                                             -description          => "The ALDH2*2-encoded ...",
                                                             -aa_ori               => "GLU",
                                                             -aa_mut               => "LYS",
                                                             -position             => 487,
                                                             -additional_mutations => "IVS4DS, G-A, +1" );  

isa_ok( $av, "Bio::Phenotype::OMIM::OMIMentryAllelicVariant" );

ok( $av->to_string() );

is( $av->number(), ".0001" );
is( $av->title(), "ALCOHOL INTOLERANCE" );
is( $av->symbol(), "ALDH2*2" );
is( $av->description(), "The ALDH2*2-encoded ..." );
is( $av->aa_ori(), "GLU" );
is( $av->aa_mut(), "LYS" );
is( $av->position(), 487 );
is( $av->additional_mutations(), "IVS4DS, G-A, +1" );

$av->init();

is( $av->number(), "" );
is( $av->title(), "" );
is( $av->symbol(), "" );
is( $av->description(), "" );
is( $av->aa_ori(), "" );
is( $av->aa_mut(), "" );
is( $av->position(), "" );
is( $av->additional_mutations(), "" );

is( $av->number( "A" ), "A" );
is( $av->title( "B" ), "B" );
is( $av->symbol( "C" ), "C" );
is( $av->description( "D" ), "D" );
is( $av->aa_ori( "E" ), "E" );
is( $av->aa_mut( "F" ), "F" );
is( $av->position( "G" ), "G" );
is( $av->additional_mutations( "H" ), "H" );
BioPerl-1.007002/t/Phenotype/OMIMparser.t000444000766000024      2345613155576321 20127 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 175);
    
    use_ok('Bio::Phenotype::OMIM::OMIMparser');
}


my $omim_parser = Bio::Phenotype::OMIM::OMIMparser->new( -genemap  => test_input_file('omim_genemap_test'),
                                                         -omimtext => test_input_file('omim_text_test'));

isa_ok( $omim_parser, "Bio::Phenotype::OMIM::OMIMparser");

my $omim_entry = $omim_parser->next_phenotype();

isa_ok($omim_entry, "Bio::Phenotype::OMIM::OMIMentry");

is( $omim_entry->MIM_number(), "100500" );
is( $omim_entry->title(), "*100500 title" );
is( $omim_entry->alternative_titles_and_symbols(), ";;title1;;\ntitle2;;\ntitle3" );
is( $omim_entry->more_than_two_genes(), 0 );
is( $omim_entry->is_separate(), 1 );
is( $omim_entry->description(), undef); # "DESCRIPTION1\nDESCRIPTION2" );
is( $omim_entry->mapping_method(), "M method 1" );
is( $omim_entry->gene_status(), "C" );
is( $omim_entry->comment(), "comment1" );
is( $omim_entry->edited(), undef); # "ed1\ned2\ned3" );
is( $omim_entry->created(), undef); # "cd1\ncd2\ncd3" );
is( $omim_entry->contributors, undef); # "cn1\ncn2\ncn3" );
is( $omim_entry->additional_references(), "sa" );
is( ref($omim_entry->clinical_symptoms()), 'HASH' );
is( $omim_entry->species()->binomial(), "Homo sapiens" );


my $mini_mim = $omim_entry->miniMIM();

isa_ok( $mini_mim,"Bio::Phenotype::OMIM::MiniMIMentry" );
is( $mini_mim->description(), "Mini MIM text" );
is( $mini_mim->created(), "Mini MIM - cd" );
is( $mini_mim->contributors(), "Mini MIM - cn" );
is( $mini_mim->edited(), "Mini MIM - ed" );


my @corrs      = $omim_entry->each_Correlate();

is( $corrs[ 0 ]->name(), "mousecorrelate1" );
is( $corrs[ 0 ]->type(), "OMIM mouse correlate" );
is( $corrs[ 0 ]->species()->binomial(), "Mus musculus" );


my @cps        = $omim_entry->each_CytoPosition();

is( $cps[ 0 ]->value(), "1pter-p36.14" );


my @gss        = $omim_entry->each_gene_symbol();

is( $gss[ 0 ], "gene-symbol1" );


my @refs       = $omim_entry->each_Reference();

is( $refs[ 0 ]->authors(), "Author11, A. A.; Author12, A. A." );
is( $refs[ 0 ]->title(), "Title 1." );
is( $refs[ 0 ]->location(), "Am. J. Med. Genet1. 11 11-111 \(1981\)" );

is( $refs[ 1 ]->authors(), "Author21, A. A.; Author22, A. A." );
is( $refs[ 1 ]->title(), "Title 2." );
is( $refs[ 1 ]->location(), "Am. J. Med. Genet2. 12 22-222 \(1982\)" );

is( $refs[ 2 ]->authors(), "Author31, A. A.; Author32, A. A." );
is( $refs[ 2 ]->title(), "Title 3." );
is( $refs[ 2 ]->location(), "Am. J. Med. Genet3. 13 33-333 \(1983\)" );

is( $refs[ 3 ]->authors(), "" );
is( $refs[ 3 ]->title(), "other reference undef format" );
is( $refs[ 3 ]->location(), "" );



my @avs        = $omim_entry->each_AllelicVariant();

is( $avs[ 0 ]->number(), ".0001" );
is( $avs[ 0 ]->title(), "ALCOHOL INTOLERANCE, ACUTE" );
is( $avs[ 0 ]->symbol(), "ALDH2" );
is( $avs[ 0 ]->description(), "AV1-text" );
is( $avs[ 0 ]->aa_ori(), "GLU" );
is( $avs[ 0 ]->aa_mut(), "LYS" );
is( $avs[ 0 ]->position(), "487" );
is( $avs[ 0 ]->additional_mutations(), "" );


is( $avs[ 1 ]->number(), ".0002" );
is( $avs[ 1 ]->title(), "MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL" );
is( $avs[ 1 ]->symbol(), "CHRNA1" );
is( $avs[ 1 ]->description(), "AV2-text" );
is( $avs[ 1 ]->aa_ori(), "VAL" );
is( $avs[ 1 ]->aa_mut(), "MET" );
is( $avs[ 1 ]->position(), "156" );
is( $avs[ 1 ]->additional_mutations(), "" );


is( $avs[ 2 ]->number(), ".0003" );
is( $avs[ 2 ]->title(), "MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL" );
is( $avs[ 2 ]->symbol(), "CHRNE" );
is( $avs[ 2 ]->description(), "AV2-text a\nAV2-text b" );
is( $avs[ 2 ]->aa_ori(), "ARG" );
is( $avs[ 2 ]->aa_mut(), "LEU" );
is( $avs[ 2 ]->position(), "147" );
is( $avs[ 2 ]->additional_mutations(), "" );


is( $avs[ 3 ]->number(), ".0004" );
is( $avs[ 3 ]->title(), "MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL" );
is( $avs[ 3 ]->symbol(), "CHRNE" );
is( $avs[ 3 ]->description(), "Sieb et al. (2000) found that a brother and sister with congenital\nmyasthenic syndrome (601462) were compound heterozygotes for a deletion\nof 911T and a splicing mutation (IVS4+1G-A; 100725.0007)." );
is( $avs[ 3 ]->aa_ori(), "" );
is( $avs[ 3 ]->aa_mut(), "" );
is( $avs[ 3 ]->position(), "" );
is( $avs[ 3 ]->additional_mutations(), "1-BP DEL, 911T" );


is( $avs[ 4 ]->number(), ".0005" );
is( $avs[ 4 ]->title(), "MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL" );
is( $avs[ 4 ]->symbol(), "CHRNE" );
is( $avs[ 4 ]->description(), "See 100725.0006 and Sieb et al. (2000)." );
is( $avs[ 4 ]->aa_ori(), "" );
is( $avs[ 4 ]->aa_mut(), "" );
is( $avs[ 4 ]->position(), "" );
is( $avs[ 4 ]->additional_mutations(), "IVS4DS, G-A, +1" );



is( $avs[ 5 ]->number(), ".0006" );
is( $avs[ 5 ]->title(), "MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL" );
is( $avs[ 5 ]->symbol(), "CHRNE" );
is( $avs[ 5 ]->description(), "AV6-text" );
is( $avs[ 5 ]->aa_ori(), "" );
is( $avs[ 5 ]->aa_mut(), "" );
is( $avs[ 5 ]->position(), "" );
is( $avs[ 5 ]->additional_mutations(), "1-BP DEL, 1030C" );





my $omim_entry2 = $omim_parser->next_phenotype();


isa_ok( $omim_entry2, "Bio::Phenotype::OMIM::OMIMentry" );

is( $omim_entry2->MIM_number(), "100501" );
is( $omim_entry2->title(), "#100501 second entry" );
is( $omim_entry2->alternative_titles_and_symbols(), ";;title1;;\ntitle2;;\ntitle3" );
is( $omim_entry2->more_than_two_genes(), 1 );
is( $omim_entry2->is_separate(), 0 );
is( $omim_entry2->description(), undef); # "DESCRIPTION1\nDESCRIPTION2" );
is( $omim_entry2->mapping_method(), "M method 2" );
is( $omim_entry2->gene_status(), "C" );
is( $omim_entry2->comment(), "comment2" );
is( $omim_entry2->edited(), undef); # "ed1\ned2\ned3" );
is( $omim_entry2->created(), undef); # "cd1\ncd2\ncd3" );
is( $omim_entry2->contributors(), undef); # "cn1\ncn2\ncn3" );
is( $omim_entry2->additional_references(), "sa" );

my $cs = $omim_entry2->clinical_symptoms();
is( ref($cs), 'HASH' );
is( $omim_entry2->species()->binomial(), "Homo sapiens" );


$mini_mim   = $omim_entry2->miniMIM();

isa_ok( $mini_mim, "Bio::Phenotype::OMIM::MiniMIMentry" );
is( $mini_mim->description(), "Mini MIM text" );
is( $mini_mim->created(), "Mini MIM - cd" );
is( $mini_mim->contributors(), "Mini MIM - cn" );
is( $mini_mim->edited(), "Mini MIM - ed" );


@corrs      = $omim_entry2->each_Correlate();

is( $corrs[ 0 ]->name(), "mousecorrelate2" );
is( $corrs[ 0 ]->type(), "OMIM mouse correlate" );
is( $corrs[ 0 ]->species()->binomial(), "Mus musculus" );


@cps        = $omim_entry2->each_CytoPosition();

is( $cps[ 0 ]->value(), "1pter-p36.15" );


@gss        = $omim_entry2->each_gene_symbol();

is( $gss[ 0 ], "gene-symbol2" );


@refs       = $omim_entry2->each_Reference();

is( $refs[ 0 ]->authors(), "Author11, A. A.; Author12, A. A." );
is( $refs[ 0 ]->title(), "Title 1." );
is( $refs[ 0 ]->location(), "Am. J. Med. Genet1. 11 11-111 \(1981\)" );

is( $refs[ 1 ]->authors(), "Author21, A. A.; Author22, A. A." );
is( $refs[ 1 ]->title(), "Title 2." );
is( $refs[ 1 ]->location(), "Am. J. Med. Genet2. 12 22-222 \(1982\)" );

is( $refs[ 2 ]->authors(), "Author31, A. A.; Author32, A. A." );
is( $refs[ 2 ]->title(), "Title 3." );
is( $refs[ 2 ]->location(), "Am. J. Med. Genet3. 13 33-333 \(1983\)" );

is( $refs[ 3 ]->authors(), "" );
is( $refs[ 3 ]->title(), "other reference undef format" );
is( $refs[ 3 ]->location(), "" );



@avs        = $omim_entry2->each_AllelicVariant();

is( $avs[ 0 ]->number(), ".0001" );
is( $avs[ 0 ]->title(), "ALCOHOL INTOLERANCE, ACUTE" );
is( $avs[ 0 ]->symbol(), "ALDH2" );
is( $avs[ 0 ]->description(), "AV1-text" );
is( $avs[ 0 ]->aa_ori(), "GLU" );
is( $avs[ 0 ]->aa_mut(), "LYS" );
is( $avs[ 0 ]->position(), "487" );
is( $avs[ 0 ]->additional_mutations(), "" );


is( $avs[ 1 ]->number(), ".0002" );
is( $avs[ 1 ]->title(), "MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL" );
is( $avs[ 1 ]->symbol(), "CHRNA1" );
is( $avs[ 1 ]->description(), "AV2-text" );
is( $avs[ 1 ]->aa_ori(), "VAL" );
is( $avs[ 1 ]->aa_mut(), "MET" );
is( $avs[ 1 ]->position(), "156" );
is( $avs[ 1 ]->additional_mutations(), "" );


is( $avs[ 2 ]->number(), ".0003" );
is( $avs[ 2 ]->title(), "MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL" );
is( $avs[ 2 ]->symbol(), "CHRNE" );
is( $avs[ 2 ]->description(), "AV2-text a\nAV2-text b" );
is( $avs[ 2 ]->aa_ori(), "ARG" );
is( $avs[ 2 ]->aa_mut(), "LEU" );
is( $avs[ 2 ]->position(), "147" );
is( $avs[ 2 ]->additional_mutations(), "" );


is( $avs[ 3 ]->number(), ".0004" );
is( $avs[ 3 ]->title(), "MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL" );
is( $avs[ 3 ]->symbol(), "CHRNE" );
is( $avs[ 3 ]->description(), "Sieb et al. (2000) found that a brother and sister with congenital\nmyasthenic syndrome (601462) were compound heterozygotes for a deletion\nof 911T and a splicing mutation (IVS4+1G-A; 100725.0007)." );
is( $avs[ 3 ]->aa_ori(), "" );
is( $avs[ 3 ]->aa_mut(), "" );
is( $avs[ 3 ]->position(), "" );
is( $avs[ 3 ]->additional_mutations(), "1-BP DEL, 911T" );


is( $avs[ 4 ]->number(), ".0005" );
is( $avs[ 4 ]->title(), "MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL" );
is( $avs[ 4 ]->symbol(), "CHRNE" );
is( $avs[ 4 ]->description(), "See 100725.0006 and Sieb et al. (2000)." );
is( $avs[ 4 ]->aa_ori(), "" );
is( $avs[ 4 ]->aa_mut(), "" );
is( $avs[ 4 ]->position(), "" );
is( $avs[ 4 ]->additional_mutations(), "IVS4DS, G-A, +1" );



is( $avs[ 5 ]->number(), ".0006" );
is( $avs[ 5 ]->title(), "MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL" );
is( $avs[ 5 ]->symbol(), "CHRNE" );
is( $avs[ 5 ]->description(), "AV6-text" );
is( $avs[ 5 ]->aa_ori(), "" );
is( $avs[ 5 ]->aa_mut(), "" );
is( $avs[ 5 ]->position(), "" );
is( $avs[ 5 ]->additional_mutations(), "1-BP DEL, 1030C" );


# catch missing linebreak
throws_ok { my $omim_parser = Bio::Phenotype::OMIM::OMIMparser->new(
    -genemap  => test_input_file('omim_genemap_test_linebreak'),
    -omimtext => test_input_file('omim_text_test'));
} qr/linebreak/, 'missing linebreak caught';
BioPerl-1.007002/t/Phenotype/Phenotype.t000444000766000024      1323213155576321 20113 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 116);
	
    use_ok('Bio::Phenotype::Phenotype');
    use_ok('Bio::Species');
    use_ok('Bio::Annotation::Reference');
    use_ok('Bio::Map::CytoPosition');
    use_ok('Bio::Phenotype::Correlate');
    use_ok('Bio::Phenotype::Measure');
    use_ok('Bio::Annotation::DBLink');
}

my $obj = Bio::Phenotype::Phenotype->new();

isa_ok( $obj, "Bio::Phenotype::PhenotypeI" );
isa_ok( $obj, "Bio::Phenotype::Phenotype" );

ok( $obj->name( "r1" ) );
is( $obj->name(), "r1" );

ok( $obj->description( "This is ..." ) );
is( $obj->description(), "This is ..." );

my $mouse = Bio::Species->new();
$mouse->classification( qw( musculus Mus ) );
ok( $obj->species( $mouse ) );
is( $obj->species()->binomial(), "Mus musculus" );

ok( $obj->comment( "putative" ) );
is( $obj->comment(), "putative" );



is( $obj->each_gene_symbol(), 0 );

ok( $obj->add_gene_symbols( ( "A", "B" ) ) );
is( $obj->each_gene_symbol(), 2 );
my @gs = $obj->each_gene_symbol();
is( $gs[ 0 ], "A" );
is( $gs[ 1 ], "B" );
is( $obj->each_gene_symbol(), 2 );

my @gs2 = $obj->remove_gene_symbols();
is( $gs2[ 0 ], "A" );
is( $gs2[ 1 ], "B" );

is( $obj->each_gene_symbol(), 0 );
is( $obj->remove_gene_symbols(), 0 );



my $v1 = Bio::Variation::VariantI->new();
my $v2 = Bio::Variation::VariantI->new();

$v1->length( "123" );

is( $obj->each_Variant(), 0 );

ok( $obj->add_Variants( ( $v1, $v2 ) ) );
is( $obj->each_Variant(), 2 );
my @vs = $obj->each_Variant();
is( $vs[ 0 ], $v1 );
is( $vs[ 1 ], $v2 );
is( $vs[ 0 ]->length(), "123" );
is( $obj->each_Variant(), 2 );

my @vs2 = $obj->remove_Variants();
is( $vs2[ 0 ], $v1 );
is( $vs2[ 1 ], $v2 );

is( $obj->each_Variant(), 0 );
is( $obj->remove_Variants(), 0 );




my $r1 = Bio::Annotation::Reference->new();
my $r2 = Bio::Annotation::Reference->new();

$r1->title( "title" );

is( $obj->each_Reference(), 0 );

ok( $obj->add_References( ( $r1, $r2 ) ) );
is( $obj->each_Reference(), 2 );
my @rs = $obj->each_Reference();
is( $rs[ 0 ]->display_text, $r1->display_text,'operator overloading in AnnotationI is deprecated');
is( $rs[ 1 ]->display_text, $r2->display_text,'operator overloading in AnnotationI is deprecated');
is( $rs[ 0 ]->title(), "title" );
is( $obj->each_Reference(), 2 );

my @rs2 = $obj->remove_References();
is( $rs2[ 0 ]->display_text, $r1->display_text,'operator overloading in AnnotationI is deprecated');
is( $rs2[ 1 ]->display_text, $r2->display_text,'operator overloading in AnnotationI is deprecated');

is( $obj->each_Reference(), 0 );
is( $obj->remove_References(), 0 );




my $c1 = Bio::Map::CytoPosition->new();
my $c2 = Bio::Map::CytoPosition->new();

$c1->chr( "12" );

is( $obj->each_CytoPosition(), 0 );

ok( $obj->add_CytoPositions( ( $c1, $c2 ) ) );
is( $obj->each_CytoPosition(), 2 );
my @cs = $obj->each_CytoPosition();
is( $cs[ 0 ], $c1 );
is( $cs[ 1 ], $c2 );
is( $cs[ 0 ]->chr(), 12 );
is( $obj->each_CytoPosition(), 2 );

my @cs2 = $obj->remove_CytoPositions();
is( $cs2[ 0 ], $c1 );
is( $cs2[ 1 ], $c2 );

is( $obj->each_CytoPosition(), 0 );
is( $obj->remove_CytoPositions(), 0 );




my $co1 = Bio::Phenotype::Correlate->new();
my $co2 = Bio::Phenotype::Correlate->new();

ok( $co1->name( "name" ) );

is( $obj->each_Correlate(), 0 );

ok( $obj->add_Correlates( ( $co1, $co2 ) ) );
is( $obj->each_Correlate(), 2 );
my @cos = $obj->each_Correlate();
is( $cos[ 0 ], $co1 );
is( $cos[ 1 ], $co2 );
is( $cos[ 0 ]->name, "name" );
is( $obj->each_Correlate(), 2 );

my @cos2 = $obj->remove_Correlates();
is( $cos2[ 0 ], $co1 );
is( $cos2[ 1 ], $co2 );

is( $obj->each_Correlate(), 0 );
is( $obj->remove_Correlates(), 0 );




my $m1 = Bio::Phenotype::Measure->new();
my $m2 = Bio::Phenotype::Measure->new();

ok( $m1->description( "desc" ) );

is( $obj->each_Measure(), 0 );

ok( $obj->add_Measures( ( $m1, $m2 ) ) );
is( $obj->each_Measure(), 2 );
my @ms = $obj->each_Measure();
is( $ms[ 0 ], $m1 );
is( $ms[ 1 ], $m2 );
is( $ms[ 0 ]->description, "desc" );
is( $obj->each_Measure(), 2 );

my @ms2 = $obj->remove_Measures();
is( $ms2[ 0 ], $m1 );
is( $ms2[ 1 ], $m2 );

is( $obj->each_Measure(), 0 );
is( $obj->remove_Measures(), 0 );



is( $obj->each_keyword(), 0 );

ok( $obj->add_keywords( ( "A", "B" ) ) );
is( $obj->each_keyword(), 2 );
my @ks = $obj->each_keyword();
is( $ks[ 0 ], "A" );
is( $ks[ 1 ], "B" );
is( $obj->each_keyword(), 2 );

my @ks2 = $obj->remove_keywords();
is( $ks2[ 0 ], "A" );
is( $ks2[ 1 ], "B" );

is( $obj->each_keyword(), 0 );
is( $obj->remove_keywords(), 0 );



my $l1 = Bio::Annotation::DBLink->new();
my $l2 = Bio::Annotation::DBLink->new();

ok( $l1->comment( "comment" ) );

is( $obj->each_DBLink(), 0 );

ok( $obj->add_DBLinks( ( $l1, $l2 ) ) );
is( $obj->each_DBLink(), 2 );
my @ls = $obj->each_DBLink();
is( $ls[ 0 ]->display_text, $l1->display_text,'operator overloading in AnnotationI is deprecated');
is( $ls[ 1 ]->display_text, $l2->display_text,'operator overloading in AnnotationI is deprecated');
is( $ls[ 0 ]->comment(), "comment" );
is( $obj->each_DBLink(), 2 );

my @ls2 = $obj->remove_DBLinks();
is( $ls2[ 0 ]->display_text, $l1->display_text,'operator overloading in AnnotationI is deprecated');
is( $ls2[ 1 ]->display_text, $l2->display_text,'operator overloading in AnnotationI is deprecated');

is( $obj->each_DBLink(), 0 );
is( $obj->remove_DBLinks(), 0 );



is( $obj->each_Genotype(), 0 );

ok( $obj->add_Genotypes( ( "A", "B" ) ) );
is( $obj->each_Genotype(), 2 );
my @gts = $obj->each_Genotype();
is( $gts[ 0 ], "A" );
is( $gts[ 1 ], "B" );
is( $obj->each_Genotype(), 2 );

my @gts2 = $obj->remove_Genotypes();
is( $gts2[ 0 ], "A" );
is( $gts2[ 1 ], "B" );

is( $obj->each_Genotype(), 0 );
is( $obj->remove_Genotypes(), 0 );
BioPerl-1.007002/t/PopGen000755000766000024          013155576321 15012 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/PopGen/Coalescent.t000444000766000024       307513155576321 17421 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 13);
	
	use_ok('Bio::PopGen::Simulation::Coalescent');
	use_ok('Bio::PopGen::Statistics');
	use_ok('Bio::TreeIO');
}

my $ssize = 5;
my $sim = Bio::PopGen::Simulation::Coalescent->new(-sample_size => $ssize);
my $stats = Bio::PopGen::Statistics->new();
my $tree = $sim->next_tree;

is($tree->get_nodes, ($ssize * 2 - 1));

my $FILE1 = test_output_file();
my $treeio = Bio::TreeIO->new(-format => 'newick', -file => ">$FILE1");

$treeio->write_tree($tree);
undef $treeio;

ok(-s $FILE1);
my $mutcount = 100;
$sim->add_Mutations($tree, $mutcount);

my $leaves = [$tree->get_leaf_nodes];
# $stats->verbose(1);
my $pi = $stats->pi($leaves);
is( $pi > 0 , 1, 'pi');


# theta is num seg sites / sum(1/(numsams-1))
my $theta = $stats->theta(scalar @$leaves, $mutcount);
is($theta,48, 'theta');

my $tD = Bio::PopGen::Statistics->tajima_D($leaves);
is(defined $tD,1, 'tajimaD');

my $seg_sites = Bio::PopGen::Statistics->segregating_sites_count($leaves);
is($seg_sites,$mutcount,
   'all the mutations should be polymorphic (by definition)');
my $single = Bio::PopGen::Statistics->singleton_count($leaves);
my $flD = Bio::PopGen::Statistics->fu_and_li_D($leaves,$single);
is(defined $flD,1,'fu and li D');

my $flD_star = $stats->fu_and_li_D_star($leaves);
is(defined $flD_star,1,'fu and li D*');

my $flF = $stats->fu_and_li_F($leaves,$single);
is(defined $flF, 1,'fu and li F');

my $flFstar = $stats->fu_and_li_F_star($leaves);
is(defined $flF, 1,'fu and li F');
BioPerl-1.007002/t/PopGen/HtSNP.t000444000766000024       362213155576321 16273 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 8);
	
    use_ok('Bio::PopGen::HtSNP');
}

my $hap = [
     'acgt?cact',
     'acgt?ca-t',
     'cg?tag?gc',
     'cactcgtgc',
     'cgctcgtgc',
     'cggtag?gc',
     'ac?t?cact',
     ];

my $snp = [qw/s1 s2 s3 s4 s5 s6 s7 s8 s9/];

my $pop = [
     [qw/ uno    0.20/],
     [qw/ dos    0.20/],
     [qw/ tres   0.15/],
     [qw/ cuatro 0.15/],
     [qw/ cinco  0.10/],
     [qw/ seis   0.10/],
     [qw/ siete  0.10/],
       ];

my $obj = Bio::PopGen::HtSNP->new(-haplotype_block => $hap,
                                   -snp_ids         => $snp,
                                   -pattern_freq    => $pop,
);


# check lenght of the haplotype
is($obj->hap_length,9); # length of the haplotype must be 9 

# check silent SNPs
is( (join ' ', @{$obj->silent_snp}) ,'s4'); # the silent snp is in position 4 (counting from 1)

# check degenerated SNPs 
is( (join ' ', @{$obj->deg_snp}) ,'s7 s5 s3'); # degenerate SNPs 

# check useful SNP's
is( (join ' ', @{$obj->useful_snp}) ,'s1 s2 s6 s8 s9'); # degenerate SNPs 

# check the SNP code
is( (join ' ',@{$obj->snp_type_code}),'36 63 36 75 36'); # code for SNPs

# check the HtType 
is( (join ' ',@{$obj->ht_type}),'36 63 75'); # min snp_code 

my $tmp = $obj->deg_pattern();
my $err=0;

foreach my $family (keys %$tmp){
    if ($family eq '0'){
       unless ( (join ' ', @{$tmp->{$family}}) eq '0 6'){
           $err=1;
       }
    }
    if ($family eq '1'){
       unless ( (join ' ', @{$tmp->{$family}}) eq '1'){
           $err=1;
       }
    }
    if ($family eq '2'){
       unless ( (join ' ', @{$tmp->{$family}}) eq '2 4 5'){
           $err=1;
       }
    }
    if ($family eq '3'){
       unless ( (join ' ', @{$tmp->{$family}}) eq '3'){
           $err=1;
       }
    }
}

ok(! $err); # clustering degenerated haplotypes 
BioPerl-1.007002/t/PopGen/MK.t000444000766000024      1400213155576321 15660 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

# This will outline many tests for the population genetics
# objects in the Bio::PopGen namespace

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 46);
    use_ok('Bio::AlignIO');
    use_ok('Bio::PopGen::Statistics');
    use_ok('Bio::PopGen::Utilities');
    
}
my $verbose = test_debug();


# - McDonald Kreitman tests -

my $stats = Bio::PopGen::Statistics->new(-verbose => $verbose);
isa_ok($stats, 'Bio::PopGen::Statistics');
my $alnio = Bio::AlignIO->new(-format => 'fasta',
			    -file   => test_input_file('CG2865.fasaln'));
my $aln = $alnio->next_aln;
isa_ok($aln,'Bio::SimpleAlign');
my $population = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln,
							   -site_model => 'codon',
							   -include_monomorphic => 1);
isa_ok($population,'Bio::PopGen::Population');

my @marker_names = $population->get_marker_names;
my @inds = $population->get_Individuals;

is(scalar @marker_names, 434, 'Marker Names');
is(scalar @inds, 6,'Number of Inds');

my (@ingroup_seqs,@outgroup_seqs1, @outgroup_seqs2);

for my $ind ( $population->get_Individuals ) {
    my $id = $ind->unique_id;
    # do we allow ingroup to be a list as well?
    my $pushed = 0;
    if( $id =~ /sim/ ) {
	push @ingroup_seqs, $ind;
	$pushed++;
    }
    if( ! $pushed ) {
	if( $id =~ /mel/ ) {
	    push @outgroup_seqs1, $ind;
	    $pushed++;
	} elsif( $id =~ /yak/ ) {
	    push @outgroup_seqs2, $ind;
	    $pushed++;
	}
    }
    #    if( ! $pushed ) {
    #	warn("sequence $id was not grouped, ignoring...\n");
    #	    push @ingroup_seqs, $ind;
    #}   
}
is(scalar @ingroup_seqs, 4, 'number of ingroup sequences');
is(scalar @outgroup_seqs1, 1, 'number of outgroup1 sequences');
is(scalar @outgroup_seqs2, 1, 'number of outgroup2 sequences');

my $polarized = 0;

my @counts = $stats->mcdonald_kreitman(-ingroup   => \@ingroup_seqs,
				       -outgroup  => \@outgroup_seqs1,
				       -polarized => $polarized);
is($counts[0], 0, 'NSpoly');
is($counts[1], 1, 'NSfixed');
is($counts[2], 3, 'Spoly');
is($counts[3], 7, 'Sfixed');
my $mk;
 SKIP: {
     test_skip(-tests => 1, 
	       -requires_module => 'Text::NSP::Measures::2D::Fisher2::twotailed');
     skip "Some problem with Bio::PopGen::Statistics::has_twotailed", 1 unless $Bio::PopGen::Statistics::has_twotailed;
     
     $mk = $stats->mcdonald_kreitman_counts(@counts);
     is($mk, 1, 'McDonald Kreitman');
 }
@counts = $stats->mcdonald_kreitman(-ingroup   => \@ingroup_seqs,
				    -outgroup  => \@outgroup_seqs2,
				    -polarized => $polarized);
is($counts[0], 0, 'NSpoly');
is($counts[1], 6, 'NSfixed');
is($counts[2], 3, 'Spoly');
is($counts[3], 16, 'Sfixed');

SKIP: {
	test_skip(-tests => 1, 
			  -requires_module => 'Text::NSP::Measures::2D::Fisher2::twotailed');
	skip "Some problem with Bio::PopGen::Statistics::has_twotailed", 1 unless $Bio::PopGen::Statistics::has_twotailed;
	
    $mk = $stats->mcdonald_kreitman_counts(@counts);
    is(sprintf("%.2f",$mk), 0.55, 'McDonald Kreitman');
}

@counts = $stats->mcdonald_kreitman(-ingroup  => \@ingroup_seqs,
				    -outgroup => [@outgroup_seqs1,
						  @outgroup_seqs2],
				    -polarized=> 1);
is($counts[0], 0, 'NSpoly');
is($counts[1], 1, 'NSfixed');
is($counts[2], 3, 'Spoly');
is($counts[3], 1, 'Sfixed');


# test 2nd aln file
$alnio = Bio::AlignIO->new(-format => 'fasta',
			   -file   => test_input_file('CG11099.fasaln'));
$aln = $alnio->next_aln;
isa_ok($aln,'Bio::SimpleAlign');
$population = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln,
							-site_model => 'codon',
							-include_monomorphic => 1);
isa_ok($population,'Bio::PopGen::Population');

@marker_names = $population->get_marker_names;
@inds = $population->get_Individuals;

is(scalar @marker_names, 378, 'Marker Names');
is(scalar @inds, 7,'Number of Inds');

@ingroup_seqs = ();
@outgroup_seqs1 = ();
@outgroup_seqs2 = ();

for my $ind ( $population->get_Individuals ) {
    my $id = $ind->unique_id;
    # do we allow ingroup to be a list as well?
    my $pushed = 0;
    if( $id =~ /sim/ ) {
	push @ingroup_seqs, $ind;
	$pushed++;
    }
    if( ! $pushed ) {
	if( $id =~ /mel/ ) {
	    push @outgroup_seqs1, $ind;
	    $pushed++;
	} elsif( $id =~ /yak/ ) {
	    push @outgroup_seqs2, $ind;
	    $pushed++;
	}
    }
    #    if( ! $pushed ) {
    #	warn("sequence $id was not grouped, ignoring...\n");
    #	    push @ingroup_seqs, $ind;
    #}   
}
is(scalar @ingroup_seqs, 5, 'number of ingroup sequences');
is(scalar @outgroup_seqs1, 1, 'number of outgroup1 sequences');
is(scalar @outgroup_seqs2, 1, 'number of outgroup2 sequences');

$polarized = 0;

@counts = $stats->mcdonald_kreitman(-ingroup   => \@ingroup_seqs,
				    -outgroup  => \@outgroup_seqs1,
				    -polarized => $polarized);
is($counts[0], 9, 'NSpoly');
is($counts[1], 1, 'NSfixed');
is($counts[2], 26, 'Spoly');
is($counts[3], 17, 'Sfixed');


SKIP: {
	test_skip(-tests => 1, 
			  -requires_module => 'Text::NSP::Measures::2D::Fisher2::twotailed');
	skip "Some problem with Bio::PopGen::Statistics::has_twotailed", 1 unless $Bio::PopGen::Statistics::has_twotailed;
	
    $mk = $stats->mcdonald_kreitman_counts(@counts);
    is(sprintf("%.2f",$mk), 0.14, 'McDonald Kreitman');
}

@counts = $stats->mcdonald_kreitman(-ingroup  => \@ingroup_seqs,
				    -outgroup => \@outgroup_seqs2,
				    -polarized=> $polarized);
is($counts[0], 9, 'NSpoly');
is($counts[1], 10, 'NSfixed');
is($counts[2], 26, 'Spoly');
is($counts[3], 42, 'Sfixed');

SKIP: {
	test_skip(-tests => 1, 
			  -requires_module => 'Text::NSP::Measures::2D::Fisher2::twotailed');
	skip "Some problem with Bio::PopGen::Statistics::has_twotailed", 1 unless $Bio::PopGen::Statistics::has_twotailed;
	
    $mk = $stats->mcdonald_kreitman_counts(@counts);
    is(sprintf("%.2f",$mk), '0.60', 'McDonald Kreitman');
}

@counts = $stats->mcdonald_kreitman(-ingroup  => \@ingroup_seqs,
				    -outgroup => [@outgroup_seqs1,
						  @outgroup_seqs2],
				    -polarized=> 1);
is($counts[0], 6, 'NSpoly');
is($counts[1], 0, 'NSfixed');
is($counts[2], 17, 'Spoly');
is($counts[3], 1, 'Sfixed');
BioPerl-1.007002/t/PopGen/PopGen.t000444000766000024      3661213155576321 16554 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

# This will outline many tests for the population genetics
# objects in the Bio::PopGen namespace

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 105);

    use_ok('IO::String');
    use_ok('Bio::PopGen::Individual');
    use_ok('Bio::PopGen::Genotype');
    use_ok('Bio::PopGen::Population');
    use_ok('Bio::PopGen::IO');
    use_ok('Bio::PopGen::PopStats');
    use_ok('Bio::AlignIO');
    use_ok('Bio::PopGen::Statistics');
    use_ok('Bio::PopGen::Utilities');
}

# test Fu and Li's D using data from the paper

is(sprintf("%.3f",
	   Bio::PopGen::Statistics->fu_and_li_D_counts(24, 18, 9)),
   -1.529);

is(sprintf("%.3f",
	   Bio::PopGen::Statistics->fu_and_li_D_star_counts(24, 18, 10)),
   -1.558);

is(sprintf("%.3f",
	   Bio::PopGen::Statistics->fu_and_li_F_counts(24, 3.16, 18, 9)),
   -1.735);

is(sprintf("%.2f",
	   Bio::PopGen::Statistics->fu_and_li_F_star_counts(24, 3.16, 18, 10)),
   -1.71);

my $FILE1 = test_output_file();

my @individuals = ( Bio::PopGen::Individual->new(-unique_id => '10a'));
ok($individuals[0]);

my @genotypes = ( Bio::PopGen::Genotype->new(-marker_name    => 'Mkr1',
					    -individual_id  => '10a',
					    -alleles => [ qw(A a)]),
		  Bio::PopGen::Genotype->new(-marker_name    => 'Mkr2',
					    -individual_id  => '10a',
					    -alleles => [ qw(B B)]),
		  Bio::PopGen::Genotype->new(-marker_name    => 'Mkr3',
					    -individual_id  => '10a',
					    -alleles => [ qw(A a)]));
is(($genotypes[1]->get_Alleles)[0], 'B');

$individuals[0]->add_Genotype(@genotypes);
is($individuals[0]->get_Genotypes,3);
is($individuals[0]->get_Genotypes(-marker => 'Mkr3')->get_Alleles(),2);
my @alleles = $individuals[0]->get_Genotypes(-marker => 'Mkr2')->get_Alleles();
is($alleles[0], 'B');

					     
my $population = Bio::PopGen::Population->new(-name        => 'TestPop1',
					     -source      => 'testjasondata',
					     -description => 'throw away example',
					     -individuals => \@individuals);

is(scalar ($population->get_Individuals()), 1);
is($population->name, 'TestPop1');
is($population->source, 'testjasondata');
is($population->description, 'throw away example');

my @genotypes2 = ( Bio::PopGen::Genotype->new(-marker_name   => 'Mkr1',
					     -individual_id => '11',
					     -alleles       => [ qw(A A)]),
		   Bio::PopGen::Genotype->new(-marker_name   => 'Mkr2',
					     -individual_id => '11',
					     -alleles       => [ qw(B B)]),
		   Bio::PopGen::Genotype->new(-marker_name   => 'Mkr3',
					     -individual_id => '11',
					     -alleles       => [ qw(a a)]),
		   Bio::PopGen::Genotype->new(-marker_name   => 'Mkr4',
					     -individual_id => '11',
					     -alleles       => [ qw(C C)])
		   );
push @individuals, Bio::PopGen::Individual->new(-genotypes   => \@genotypes2,
					       -unique_id   => '11');
$population->add_Individual($individuals[1]);

is(scalar ($population->get_Individuals()), 2);
my ($found_ind) = $population->get_Individuals(-unique_id => '10a');
is($found_ind->unique_id, '10a');
is(scalar($population->get_Individuals(-marker => 'Mkr4')) , 1);
is(scalar($population->get_Individuals(-marker => 'Mkr3')) , 2);

my @g = $population->get_Genotypes(-marker => 'Mkr4');

is($g[0]->individual_id, '11');
is(($g[0]->get_Alleles())[0], 'C');

my $marker = $population->get_Marker('Mkr3');
ok($marker);

is($marker->marker_coverage, 2);
@alleles = $marker->get_Alleles;
is(@alleles,2);
my %af = $marker->get_Allele_Frequencies();
is($af{'a'}, 0.75);
is($af{'A'}, 0.25);

$population->remove_Individuals('10a');
$marker = $population->get_Marker('Mkr3');
is($marker->marker_coverage, 1);
%af = $marker->get_Allele_Frequencies();

is($af{'a'}, 1);
is($af{'A'}, undef);

# Read in data from a file
my $io = Bio::PopGen::IO->new(-format => 'csv',
			     -file   => test_input_file('popgen_saureus.dat'));

my @inds;
while( my $ind = $io->next_individual ) {
    push @inds, $ind;
}

my @mrsainds = grep { $_->unique_id =~ /^MRSA/ } @inds;
my @mssainds = grep { $_->unique_id =~ /^MSSA/ } @inds;
my @envinds = grep { $_->unique_id =~ /^NC/ } @inds;

is(scalar @mrsainds, 9);
is(scalar @mssainds, 10);
is(scalar @envinds, 5);

my $mrsapop = Bio::PopGen::Population->new(-name        => 'MRSA',
					  -description => 'Resistant S.aureus',
					  -individuals => \@mrsainds);

my $mssapop = Bio::PopGen::Population->new(-name        => 'MSSA',
					  -description =>'Suceptible S.aureus',
					  -individuals => \@mssainds);

my $envpop = Bio::PopGen::Population->new(-name        => 'NC',
					 -description => 'WT isolates',
					  -individuals => \@envinds);

my $stats = Bio::PopGen::PopStats->new(-haploid => 1);
my $fst = $stats->Fst([$mrsapop,$mssapop],[qw(AFLP1)]);
# We're going to check the values against other programs first
is(sprintf("%.3f",$fst),0.077,'mrsa,mssa aflp1'); 
  
$fst = $stats->Fst([$envpop,$mssapop,$mrsapop],[qw(AFLP1 )]);
is(sprintf("%.3f",$fst),0.035,'all pops, aflp1'); 

$fst = $stats->Fst([$mrsapop,$envpop],[qw(AFLP1 AFLP2)]);
is(sprintf("%.3f",$fst),0.046,'mrsa,envpop aflp1,aflp2');

# Read in data from a file
$io = Bio::PopGen::IO->new(-format => 'csv',
			  -file   => test_input_file('popgen_saureus.multidat'));

@inds = ();
while( my $ind = $io->next_individual ) {
    push @inds, $ind;
}

@mrsainds = grep { $_->unique_id =~ /^MRSA/ } @inds;
@mssainds = grep { $_->unique_id =~ /^MSSA/ } @inds;
@envinds = grep { $_->unique_id =~ /^NC/ } @inds;

is(scalar @mrsainds, 7);
is(scalar @mssainds, 10);
is(scalar @envinds, 5);

$mrsapop = Bio::PopGen::Population->new(-name        => 'MRSA',
				       -description => 'Resistant S.aureus',
				       -individuals => \@mrsainds);

$mssapop = Bio::PopGen::Population->new(-name        => 'MSSA',
				       -description =>'Suceptible S.aureus',
				       -individuals => \@mssainds);

$envpop = Bio::PopGen::Population->new(-name        => 'NC',
				      -description => 'WT isolates',
				      -individuals => \@envinds);

$stats = Bio::PopGen::PopStats->new(-haploid => 1);
my @all_bands = map { 'B' . $_ } 1..20;
my @mkr1     = map { 'B' . $_ } 1..13;
my @mkr2     = map { 'B' . $_ } 14..20;

# still wrong ? seems to work now? --sendubala
$fst = $stats->Fst([$mrsapop,$mssapop],[@all_bands ]);
#TODO: {
#    local $TODO = 'Possible bug with Fst() output';
is(sprintf("%.3f",$fst),'-0.001','mssa,mrsa all_bands'); # We're going to check the values against other programs first
#}
$fst = $stats->Fst([$envpop,$mssapop],[ @mkr1 ]);
is(sprintf("%.3f",$fst),0.023,'env,mssa mkr1'); # We're going to check the values against other programs first

$fst = $stats->Fst([$envpop,$mssapop,$mrsapop],[ @all_bands ]);
is(sprintf("%.3f",$fst),0.071,'env,mssa,mrsa all bands'); # We're going to check the values against other programs first

$fst = $stats->Fst([$envpop,$mssapop,$mrsapop],[ @mkr2 ]);
is(sprintf("%.3f",$fst),0.076, 'env,mssa,mrsa mkr2'); # We're going to check the values against other programs first

$fst = $stats->Fst([$mrsapop,$envpop],[@all_bands ]);
is(sprintf("%.3f",$fst),0.241,'mrsa,nc all_bands'); # We're going to check the values against other programs first

# test overall allele freq setting for a population

my $poptst1 = Bio::PopGen::Population->new(-name => 'tst1');
my $poptst2 = Bio::PopGen::Population->new(-name => 'tst2');

$poptst1->set_Allele_Frequency(-frequencies => 
			       { 'marker1' => { 'a' => '0.20',
						'A' => '0.80' },
				 'marker2' => { 'A' => '0.10',
						'B' => '0.20',
						'C' => '0.70' }
			     });

my $mk1 = $poptst1->get_Marker('marker1');
my %f1 = $mk1->get_Allele_Frequencies;
is($f1{'a'}, '0.20');
is($f1{'A'}, '0.80');
my $mk2 = $poptst1->get_Marker('marker2');
my %f2 = $mk2->get_Allele_Frequencies;
is($f2{'C'}, '0.70');

$poptst2->set_Allele_Frequency(-name      => 'marker1',
			       -allele    => 'A',
			       -frequency => '0.60');
$poptst2->set_Allele_Frequency(-name      => 'marker1',
			       -allele    => 'a',
			       -frequency => '0.40');

#TODO: {
#    local $TODO = 'Fst not calculated yet for just allele freqs';
#    ok 0;
#    #$fst = $stats->Fst([$poptst1,$poptst2],[qw(marker1 marker2) ]);
#}

$io = Bio::PopGen::IO->new(-format => 'csv',
			  -file   => ">$FILE1");

$io->write_individual(@inds);
$io->close();
ok( -s $FILE1);
$io = Bio::PopGen::IO->new(-format => 'csv',
			  -file   => ">$FILE1");

$io->write_population(($mssapop,$mrsapop));
$io->close();
ok( -s $FILE1);

$io = Bio::PopGen::IO->new(-format => 'prettybase',
			  -file   => ">$FILE1");

$io->write_individual(@inds);
$io->close();
ok( -s $FILE1);

$io = Bio::PopGen::IO->new(-format => 'prettybase',
			  -file   => ">$FILE1");

$io->write_population(($mssapop,$mrsapop));
$io->close();
ok( -s $FILE1);


# Let's do PopGen::Statistics tests here

$io = Bio::PopGen::IO->new(-format          => 'prettybase',
			  -no_header       => 1,
			  -file            => test_input_file('popstats.prettybase'));
my (@ingroup,@outgroup);
my $sitecount;
while( my $ind = $io->next_individual ) {
    if($ind->unique_id =~ /out/) {
	push @outgroup, $ind;
    } else { 
	push @ingroup, $ind;
	$sitecount = scalar $ind->get_marker_names() unless defined $sitecount;
    }
}
$stats = Bio::PopGen::Statistics->new();

# Real data and values courtesy M.Hahn and DNASP

is($stats->pi(\@ingroup),2);
is(Bio::PopGen::Statistics->pi(\@ingroup,$sitecount),0.4);

is(Bio::PopGen::Statistics->theta(\@ingroup),1.92);
is(Bio::PopGen::Statistics->theta(\@ingroup,$sitecount),0.384);

# Test with a population object
my $ingroup  = Bio::PopGen::Population->new(-individuals => \@ingroup);
my $outgroup = Bio::PopGen::Population->new(-individuals => \@outgroup);

is($stats->pi($ingroup),2);
is(Bio::PopGen::Statistics->pi($ingroup,$sitecount),0.4);

is(Bio::PopGen::Statistics->theta($ingroup),1.92);
is(Bio::PopGen::Statistics->theta($ingroup,$sitecount),0.384);

my $haploidpop = $ingroup->haploid_population;
is(sprintf("%.5f",Bio::PopGen::Statistics->tajima_D($haploidpop)), 0.27345);

# to fix
is(sprintf("%.5f",Bio::PopGen::Statistics->tajima_D(\@ingroup)),0.27345);
is(sprintf("%.5f",Bio::PopGen::Statistics->tajima_D($ingroup)),0.27345);

is(sprintf("%.5f",Bio::PopGen::Statistics->fu_and_li_D_star(\@ingroup)),
   0.27345);
is(sprintf("%.5f",Bio::PopGen::Statistics->fu_and_li_D_star($ingroup)),
   0.27345);

is(sprintf("%.5f",Bio::PopGen::Statistics->fu_and_li_F_star(\@ingroup)),
     0.27834);
is(sprintf("%.5f",Bio::PopGen::Statistics->fu_and_li_F_star($ingroup)),
   0.27834);

is((Bio::PopGen::Statistics->derived_mutations(\@ingroup,\@outgroup))[0], 1);
is((Bio::PopGen::Statistics->derived_mutations($ingroup,\@outgroup))[0], 1);
is((Bio::PopGen::Statistics->derived_mutations(\@ingroup,$outgroup))[0], 1);
is((Bio::PopGen::Statistics->derived_mutations($ingroup,$outgroup))[0], 1);

# expect to have 1 external mutation
@ingroup = $haploidpop->get_Individuals;

is(sprintf("%.5f",Bio::PopGen::Statistics->fu_and_li_D(\@ingroup,1)),0.75653);
is(sprintf("%.5f",Bio::PopGen::Statistics->fu_and_li_D($ingroup,1)),0.75653);

is(sprintf("%.5f",Bio::PopGen::Statistics->fu_and_li_D(\@ingroup,
						       \@outgroup)),0.75653);
is(sprintf("%.5f",Bio::PopGen::Statistics->fu_and_li_D($ingroup,
						       \@outgroup)),0.75653);
is(sprintf("%.5f",Bio::PopGen::Statistics->fu_and_li_D($ingroup,
						       $outgroup)),0.75653);
is(sprintf("%.5f",Bio::PopGen::Statistics->fu_and_li_D(\@ingroup,
						       $outgroup)),0.75653);

is(sprintf("%.5f",Bio::PopGen::Statistics->fu_and_li_F(\@ingroup,1)),
     0.77499);
is(sprintf("%.5f",Bio::PopGen::Statistics->fu_and_li_F($haploidpop,1)),0.77499);
is(sprintf("%.5f",Bio::PopGen::Statistics->fu_and_li_F($ingroup,
						       \@outgroup)),0.77499);
is( sprintf("%.5f",Bio::PopGen::Statistics->fu_and_li_F($ingroup,
							 $outgroup)),0.77499);


# Test composite LD

$io = Bio::PopGen::IO->new(-format => 'prettybase',
			  -file   => test_input_file('compLD_test.prettybase'));

my $pop = $io->next_population;

my %LD = $stats->composite_LD($pop);

is($LD{'01'}->{'02'}->[1], 10);
is($LD{'01'}->{'03'}->[1], 0);
is($LD{'02'}->{'03'}->[1], 0);

# Test composite LD

$io = Bio::PopGen::IO->new(-format => 'prettybase',
			  -file   => test_input_file('compLD_missingtest.prettybase'));

$pop = $io->next_population;

%LD = $stats->composite_LD($pop);

is(sprintf("%.4f",$LD{'ProC9198EA'}->{'ProcR2973EA'}->[0]), -0.0375);
is(sprintf("%.2f",$LD{'ProC9198EA'}->{'ProcR2973EA'}->[1]), 2.56);



# build a population from an alignment

my $alnin = Bio::AlignIO->new(-format => 'clustalw',
			      -file   => test_input_file('T7.aln'));
my $aln = $alnin->next_aln;
$population = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln);
is($population->get_number_individuals,9);
#warn($aln->match_line,"\n");
my $matchline = $aln->match_line;
is( $population->get_marker_names, $matchline =~ tr/ //);
for my $name ( $population->get_marker_names ) {
    my $marker = $population->get_Marker($name); 
#    warn("$name ",join(" ",$marker->get_Alleles()),"\n");
}


# test Rich's phase and hap parsers

$io = Bio::PopGen::IO->new(-format   => 'hapmap',
			  -verbose  => 1,
			  -no_header=> 1,
			  -starting_column => 10,
			  -file     => test_input_file('example.hap'));

# Some IO might support reading in a population at a time

my @population;
while( my $ind = $io->next_individual ) {
    push @population, $ind;
}
is(@population, 90);
is($population[3]->unique_id, 'NA06994');
is($population[3]->get_Genotypes, 34);
$population = Bio::PopGen::Population->new(-individuals => \@population);

is(sprintf("%.3f",$stats->pi($population)),12.266);
# if forced haploid population is called within pi
# need to decide about that...
# is(sprintf("%.3f",$stats->pi($population)),12.266);

is(sprintf("%.3f",$stats->theta($population)),5.548);
#TODO: {
#    local $TODO = 'May be TJd inconsistency, need to recalculate';
    is(sprintf("%.3f",$stats->tajima_D($population)),'2.926');
    is(sprintf("%.3f",$stats->tajima_D($population->haploid_population)),3.468);
#}

# test converting from hapmap to phase
my $string;
my $out = IO::String->new($string);
Bio::PopGen::IO->new(-fh => $out, -format => 'phase')->write_individual($population[0]);
is($string, "1
34
P rs1022827 rs1323262 rs1359058 rs1475202 rs1570473 rs2025307 rs2025308 rs2296049 rs2296050 rs2296054 rs3739586 rs4400444 rs4584192 rs4740849 rs4740850 rs4740851 rs4740866 rs4742215 rs4742219 rs4742220 rs4742222 rs4742223 rs4742225 rs4742227 rs4742236 rs4742292 rs732118 rs732119 rs745876 rs745877 rs881684 rs912174 rs912175 rs962817
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
#NA06985
G C A G G A A A C T C T A C A A T G C A A C G G A A A T A T A A C C
G G T G G A A G G T C T G G G T T T T G G T T G G A A T A T A C G T
");


$io = Bio::PopGen::IO->new(-format => 'phase',
			   -file   => test_input_file('example.phase'));

# Some IO might support reading in a population at a time

@population = ();
while( my $ind = $io->next_individual ) {
    push @population, $ind;
}
is(@population, 3);

# test writing in phase format
$population = Bio::PopGen::Population->new(-individuals => \@population);
$string = '';
$out = IO::String->new($string);
Bio::PopGen::IO->new(-fh => $out, -format => 'phase')->write_population($population);
is($string, "3
5
P 1313 1500 2023 300 5635
SSSMM
#1
1 0 1 12 3
0 1 0 11 3
#2
1 1 1 12 2
0 0 0 12 3
#3
? 0 0 -1 2
? 1 1 -1 13
");

# test diploid data

# bug 2492
{
    my $in = Bio::PopGen::IO->new(-format=>"csv", -fh=>\*DATA);
    my $pop = $in->next_population;
    is(sprintf("%.3f",$stats->pi($pop)),0.833,'Pi on 3-allele data');
    is(sprintf("%.3f",$stats->theta($pop)),0.545,'Theta on 3-allele data');
}
__DATA__
SAMPLE,Site-1
seq_1,G
seq_2,C
seq_3,T
seq_4,G
BioPerl-1.007002/t/PopGen/PopGenSims.t000444000766000024       210513155576321 17356 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

# This will outline tests for the population genetics simulation
# in the Bio::PopGen::Simulation namespace
# Coalescent has its own tests though in t/Coalescent.t

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 23);
	
    use_ok 'Bio::PopGen::Simulation::GeneticDrift';
}

my $sim = Bio::PopGen::Simulation::GeneticDrift->new(-popsize => 40,
						    -alleles => {A => 0.2,
								 B => 0.8});

my (@Afreqs,@Bfreqs);
for my $i (0..9) {
    my %f = $sim->next_generation;
    push @Afreqs, $f{'A'};
    push @Bfreqs, $f{'B'};
    is(($f{'A'}||0) + ($f{'B'}||0), 1, 'Allele freqs should sum to 1');
}

is(@Afreqs, 10);
cmp_ok (($Afreqs[9]||0), '<=', 1, 'All frequencies should be <= 1');

$sim = Bio::PopGen::Simulation::GeneticDrift->new(-popsize => 50,
						 -alleles => {A => 0.2,
							      B => 0.3,
							      C => 0.5,
							  });

for my $i (0..9) {
    my %f = $sim->next_generation;
    is(($f{'A'}||0) + ($f{'B'}||0) + ($f{'C'}||0), 1, 'Allele freqs should sum to 1');
}
BioPerl-1.007002/t/PopGen/TagHaplotype.t000444000766000024       124113155576321 17733 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 3);
	
    use_ok('Bio::PopGen::TagHaplotype');
}

my $hap = [
             [qw/0       0       0/],
             [qw/1       1       1/],
             [qw/0       0       1/],
             [qw/1       2       1/]
          ];

my $obj = Bio::PopGen::TagHaplotype->new(-haplotype_block => $hap);


# check haplotype length 
is( $obj->tag_length ,1); # Tag length for this set must be 1
 
# check the tag list
is( (join ' ', @{($obj->tag_list)->[0]}) ,'1 2'); # the SNPs are 1 and 2 (1 2)

# TODO? is this really enough tests?!
BioPerl-1.007002/t/RemoteDB000755000766000024          013155576321 15263 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/RemoteDB/BioFetch.t000444000766000024       674613155576321 17305 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests               => 36,
               -requires_modules    => [qw(IO::String
                                           LWP::UserAgent)],
               -requires_networking => 1);

    use_ok('Bio::DB::BioFetch');
}

my $verbose = test_debug();

my $dbwarn = "Warning: Couldn't connect to EMBL with Bio::DB::BioFetch!\n";

my ($db,$db2,$seq,$seqio);

SKIP :{
    # get a single seq
    ok defined($db = Bio::DB::BioFetch->new(-verbose => $verbose));
    # get a RefSeq entry
    ok $db->db('refseq');
    eval {
        $seq = $db->get_Seq_by_acc('NM_006732'); # RefSeq VERSION
    };
    skip($dbwarn, 4) if $@;
    isa_ok($seq, 'Bio::SeqI');
    is($seq->accession_number,'NM_006732');
    is($seq->accession_number,'NM_006732');
    is( $seq->length, 3776);
}

SKIP: {
    # EMBL
    $db->db('embl');
    eval {
        $seq = $db->get_Seq_by_acc('J02231');
    };
    skip($dbwarn, 3) if $@;
    isa_ok($seq, 'Bio::SeqI');
    is($seq->id, 'J02231');
    is($seq->length, 200);
}

SKIP: {
    eval {
        $seqio = $db->get_Stream_by_id(['AEE33958']);
    };
    skip($dbwarn, 3) if $@;
    undef $db; # testing to see if we can remove gb
    $seq = $seqio->next_seq();
    isa_ok($seqio, 'Bio::SeqIO');
    isa_ok($seq, 'Bio::SeqI');
    cmp_ok( $seq->length, '>=', 1);
}

SKIP: {
    #swissprot
    ok $db2 = Bio::DB::BioFetch->new(-db => 'swissprot');
    test_skip(-tests => 5, -requires_module => 'Data::Stag');
    eval {
        $seq = $db2->get_Seq_by_id('YNB3_YEAST');
    };
    skip($dbwarn, 5) if $@;
    isa_ok($seq, 'Bio::SeqI');
    is($seq->length, 125);
    is($seq->division, 'YEAST');
    $db2->request_format('fasta');
    eval {
        $seq = $db2->get_Seq_by_acc('P43780');
    };
    skip($dbwarn, 2) if $@;
    isa_ok($seq, 'Bio::SeqI');
    is($seq->length,103);
}

$seq = $seqio = undef;

SKIP: {
    ok $db = Bio::DB::BioFetch->new(-retrievaltype => 'tempfile',
                                    -format        => 'fasta',
                                    -verbose       => $verbose
                                    );
    $db->db('embl');
    eval {
        $seqio = $db->get_Stream_by_id('J00522 AF303112 J02231');
    };
    skip($dbwarn, 7) if $@;
    my %seqs;
    # don't assume anything about the order of the sequences
    while ( my $s = $seqio->next_seq ) {
        isa_ok($s, 'Bio::SeqI');
        my ($type,$x,$name) = split(/\|/,$s->display_id);
        $seqs{$x} = $s->length;
    }
    isa_ok($seqio, 'Bio::SeqIO');
    is($seqs{'J00522'},408);
    is($seqs{'AF303112'},1611);
    is($seqs{'J02231'},200);
}

SKIP: {
    ok $db = Bio::DB::BioFetch->new(-db      => 'embl',
                                    -verbose => $verbose ? $verbose : -1);

    # check contig warning (WebDBSeqI)
    eval {
        $seq = $db->get_Seq_by_acc('NT_006732');
    };
    like($@, qr{contigs are whole chromosome files}, 'contig warning');
    eval {
        $seq = $db->get_Seq_by_acc('NM_006732');
    };
    skip($dbwarn, 2) if $@;
    isa_ok($seq, 'Bio::SeqI');
    is($seq->length,3776);
}

# unisave
SKIP: {
    ok $db = Bio::DB::BioFetch->new(-db      => 'unisave',
                                    -verbose => $verbose ? $verbose : -1);
    eval {
        $seq = $db->get_Seq_by_acc('P14733');
    };
    skip($dbwarn, 4) if $@;
    isa_ok($seq, 'Bio::SeqI');
    is($seq->display_id, 'LMNB1_MOUSE');
    is($seq->accession, 'P14733');
    is($seq->length, 588);
}
BioPerl-1.007002/t/RemoteDB/CUTG.t000555000766000024       656113155576321 16362 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 37,
			   -requires_modules => [qw(IO::String LWP::UserAgent)]);
	
	use_ok('Bio::DB::CUTG');
	use_ok('Bio::CodonUsage::Table');
	use_ok('Bio::CodonUsage::IO');
    use_ok('Bio::SeqIO');
    use_ok('Bio::Tools::SeqStats');
}

my $outfile = test_output_file();
my $verbose = test_debug();

# try reading from file
ok my $io = Bio::CodonUsage::IO->new
  (-file=> test_input_file('MmCT'));
ok  my $cut2 = $io->next_data();
is int($cut2->aa_frequency('LEU')), 10;

# write
ok $io = Bio::CodonUsage::IO->new(-file => ">$outfile");
$io->write_data($cut2);
ok -e $outfile;

# can we read what we've written?
ok $io = Bio::CodonUsage::IO->new(-file => "$outfile");
ok $cut2 = $io->next_data();
is int($cut2->aa_frequency('LEU')), 10;

# now try making a user defined CUT from a sequence
ok my $seqobj = Bio::SeqIO->new (-file =>test_input_file('HUMBETGLOA.fa'),
				                        -format => 'fasta')->next_seq;
is $seqobj->subseq(10,20), 'TTGACACCACT';
ok my $codcont_Ref = Bio::Tools::SeqStats->count_codons($seqobj);
is $codcont_Ref->{'TGA'}, 16;
ok my $cut = Bio::CodonUsage::Table->new(-data=>$codcont_Ref);
is $cut->codon_rel_frequency('CTG'), 0.18;
is $cut->codon_abs_frequency('CTG'), 2.6;
is $cut->codon_count('CTG'), 26;
is $cut->get_coding_gc(1), "39.70";
ok my $ref = $cut->probable_codons(20);

# Examples:
# http://www.kazusa.or.jp/codon/cgi-bin/spsearch.cgi?species=Pan+troglodytes&c=s
# http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=37011&aa=1&style=GCG
# requiring Internet access, set env BIOPERLDEBUG to 1 to run
SKIP: {
	test_skip(-tests => 14, -requires_networking => 1);
	ok my $tool = Bio::WebAgent->new(-verbose => $verbose);
	ok $tool->sleep;
	is $tool->delay(1), 1;
	ok $tool->sleep;

	# get CUT from web
	ok my $db = Bio::DB::CUTG->new();
	$db->verbose($verbose ? $verbose : -1);
	my $cdtable;
	eval {$cdtable = $db->get_request(-sp =>'Pan troglodytes');};
	skip "Server/network problems? Skipping those tests\n$@", 9 if $@;
	
	# tests for Table.pm, the answers seem to change with time, so not specific
	cmp_ok($cdtable->cds_count(), '>', 10);
	cmp_ok(int($cdtable->aa_frequency('LEU')), '>', 1);
	ok $cdtable->get_coding_gc('all');
	cmp_ok($cdtable->codon_rel_frequency('ttc'), '<', 1); 
    
	## now lets enter a non-existent species ans check handling..
	## should default to human...
	my $db2 = Bio::DB::CUTG->new();
	$db2->verbose($verbose ? $verbose : -1);
	eval {$cut2 = $db2->get_request(-sp =>'Wookie magnus');};
	skip "Server/network problems? Skipping those tests\n$@", 5 if $@;
	is $cut2->species(), 'Homo sapiens';
	
	$db = Bio::DB::CUTG->new();
	$db->verbose($verbose ? $verbose : -1);
	eval {$cdtable = $db->get_request(-sp =>'Homo sapiens');};
	skip "Server/network problems? Skipping those tests\n$@", 4 if $@;
	
	# tests for Table.pm, the answers seem to change with time, so not specific
	cmp_ok($cdtable->cds_count(), '>', 10);
	cmp_ok(int($cdtable->aa_frequency('LEU')), '>', 1);
	ok $cdtable->get_coding_gc('all');
	cmp_ok($cdtable->codon_rel_frequency('ttc'), '<', 1); 

	my $db3 = Bio::DB::CUTG->new(-sp =>'Bacillus subtilis', -gc => 1);
	$db3->verbose($verbose ? $verbose : -1);
	my $cut3;
	eval {$cut3 = $db3->get_request();};
	skip "Server/network problems? Skipping those tests\n$@", 5 if $@;
	print $cut3->codon_rel_frequency('ATG');
}
BioPerl-1.007002/t/RemoteDB/EMBL.t000444000766000024       340713155576321 16330 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 16,
               -requires_modules    => [qw(IO::String
                                           LWP::UserAgent
                                           HTTP::Request::Common)],
               -requires_networking => 1);

    use_ok('Bio::DB::EMBL');
}

my $verbose = test_debug();

my ($db,$seq,$seqio);
# get a single seq

$seq = $seqio = undef;

SKIP: { 
    ok defined($db = Bio::DB::EMBL->new(-verbose=>$verbose)); 
    ok(defined($seq = $db->get_Seq_by_acc('J00522')));
    is( $seq->length, 408); 
    ok defined ($db->request_format('fasta'));
	
    eval {ok(defined($seq = $db->get_Seq_by_acc('J02231')))};
	skip('could not connect to embl',2) if $@;
    like( $seq->id, qr/J02231/);
    is( $seq->length, 200); 
    ok( defined($db = Bio::DB::EMBL->new(-verbose=>$verbose, 
					-retrievaltype => 'tempfile')));
    eval {ok(defined($seqio = $db->get_Stream_by_id(['AEE33958'])))};
	skip('could not connect to embl',2) if $@;
    undef $db; # testing to see if we can remove gb
    ok( defined($seq = $seqio->next_seq()));
    cmp_ok( $seq->length, '>=', 1);
}

$seq = $seqio = undef;

SKIP: {
    $db = Bio::DB::EMBL->new(-verbose => $verbose,
			    -retrievaltype => 'tempfile',
			    -format => 'fasta'
			    ); 
    eval{ok( defined($seqio = $db->get_Stream_by_acc(['J00522 AF303112 J02231'])))};
	skip('could not connect to embl',3) if $@;
    my %seqs;
    # don't assume anything about the order of the sequences
    while ( my $s = $seqio->next_seq ) {
		my ($type,$x,$name) = split(/\|/,$s->display_id);
		$seqs{$x} = $s->length;
    }
    is($seqs{'J00522'},408);
    is($seqs{'AF303112'},1611);
    is($seqs{'J02231'},200);
}
BioPerl-1.007002/t/RemoteDB/EntrezGene.t000555000766000024       215413155576321 17660 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 8,
			   -requires_modules => [qw(IO::String
									    LWP::UserAgent
										HTTP::Request::Common
                                        Bio::ASN1::EntrezGene)
                                        ],
			   -requires_networking => 1);
	use_ok('Bio::DB::EntrezGene');
}

my ($gb, $seq, $seqio);

#
# Bio::DB::EntrezGene
#
SKIP: {
	test_skip(-tests => 7);
    ok $gb = Bio::DB::EntrezGene->new(-retrievaltype => 'tempfile', -delay => 0);
    eval {$seqio = $gb->get_Stream_by_id([2,3064]);};
    skip "Couldn't connect to Entrez with Bio::DB::EntrezGene. Skipping those tests", 6 if $@;
    $seq = $seqio->next_seq;
    is $seq->display_id, "A2M";
    is $seq->accession_number, 2;
    $seq = $seqio->next_seq;
    is $seq->display_id, "HTT";
    is $seq->accession_number, 3064;
    eval {$seq = $gb->get_Seq_by_id(6099);};
    skip "Couldn't connect to Entrez with Bio::DB::EntrezGene. Skipping those tests", 2 if $@;
    is $seq->display_id, "RP";
    is $seq->accession_number, 6099;
}
BioPerl-1.007002/t/RemoteDB/GenBank.t000555000766000024      1537313155576321 17146 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
	use Bio::Root::Test;

	test_begin(-tests => 44,
			   -requires_modules => [qw(IO::String
									    LWP::UserAgent
										HTTP::Request::Common)],
			   -requires_networking => 1);

	use_ok('Bio::DB::GenBank');
}

my %expected_lengths = (
    'MUSIGHBA1' => 408,
	'J00522.1' => 408,
    'AF303112'  => 1611,
    'AF303112.1' => 1611,
    'AF041456'  => 1156,
    'CELRABGDI' => 1743,
    'JH374761'  => 38055,
);

my ($gb, $seq, $seqio, $seqin);

#
# Bio::DB::GenBank
#

ok $gb = Bio::DB::GenBank->new('-delay'=>0), 'Bio::DB::GenBank';

# get a single seq
SKIP: {
    eval {$seq = $gb->get_Seq_by_id('J00522');1};
    skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Do you have network access? Skipping GenBank tests: $@", 4 if $@;
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
    eval {$seq = $gb->get_Seq_by_acc('AF303112');};
    skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Transient network problems? Skipping GenBank tests: $@", 3 if $@;
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
    eval {$seq = $gb->get_Seq_by_version('AF303112.1');};
    skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Transient network problems? Skipping GenBank tests: $@", 2 if $@;
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
    eval {$seq = $gb->get_Seq_by_gi('405830');};
    skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Transient network problems? Skipping GenBank tests: $@", 1 if $@;
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
}

$seq = $seqio = undef;

# batch mode
SKIP: {
    eval {$seqio = $gb->get_Stream_by_id([qw(J00522 AF303112 2981014)]);};
    skip "Batch access test failed for Genbank. Skipping those tests", 4 if $@;
    my $done = 0;
    while (my $s = $seqio->next_seq) {
        is $s->length, $expected_lengths{$s->display_id}, $s->display_id;
        $done++;
    }
    skip('No seqs returned', 4) if !$done;
    is $done, 3;
}

$seq = $seqio = undef;

# test the temporary file creation and fasta
ok $gb = Bio::DB::GenBank->new('-format' => 'fasta', '-retrievaltype' => 'tempfile', '-delay' => 0);
SKIP: {
    eval {$seq = $gb->get_Seq_by_id('J00522');};
    skip "Couldn't connect to complete GenBank tests with a tempfile with Bio::DB::GenBank.pm. Skipping those tests", 6 if $@;
    # last part of id holds the key
    is $seq->length, $expected_lengths{(split(/\|/,$seq->display_id))[-1]}, $seq->display_id;
    eval {$seq = $gb->get_Seq_by_acc('AF303112');};
    skip "Couldn't connect to complete GenBank tests with a tempfile with Bio::DB::GenBank.pm. Skipping those tests", 5 if $@;
    # last part of id holds the key
    is $seq->length, $expected_lengths{(split(/\|/,$seq->display_id))[-1]}, $seq->display_id;
    # batch mode requires genbank format
    $gb->request_format("gb");
    eval {$seqio = $gb->get_Stream_by_id([qw(J00522 AF303112 2981014)]);};
    skip "Couldn't connect to complete GenBank batch tests with a tempfile with Bio::DB::GenBank.pm. Skipping those tests", 4 if $@;
    my $done = 0;
    while (my $s = $seqio->next_seq) {
        is $s->length, $expected_lengths{$s->display_id};
        undef $gb; # test the case where the db is gone,
        # but a temp file should remain until seqio goes away.
        $done++;
    }
    skip('No seqs returned', 4) if !$done;
    is $done, 3;
}

$seq = $seqio = undef;

# test pipeline creation
ok $gb = Bio::DB::GenBank->new('-retrievaltype' => 'pipeline', '-delay' => 0);
SKIP: {
    eval {$seq = $gb->get_Seq_by_id('J00522');};
    skip "Couldn't connect to complete GenBank tests with a pipeline with Bio::DB::GenBank.pm. Skipping those tests", 6 if $@;
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
    eval {$seq = $gb->get_Seq_by_acc('AF303112');};
    skip "Couldn't connect to complete GenBank tests with a pipeline with Bio::DB::GenBank.pm. Skipping those tests", 5 if $@;
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
    eval {$seqio = $gb->get_Stream_by_id([qw(J00522 AF303112 2981014)]);};
    skip "Couldn't connect to complete GenBank tests with a pipeline with Bio::DB::GenBank.pm. Skipping those tests", 4 if $@;
    my $done = 0;
    while (my $s = $seqio->next_seq) {
        is $s->length, $expected_lengths{$s->display_id}, $s->display_id;
        undef $gb; # test the case where the db is gone,
        # but the pipeline should remain until seqio goes away
        $done++;
    }
    skip('No seqs returned', 4) if !$done;
    is $done, 3;
}

$seq = $seqio = undef;

# test contig retrieval
ok $gb = Bio::DB::GenBank->new('-delay'  => 0, '-format' => 'gbwithparts');
SKIP: {
    eval {$seq = $gb->get_Seq_by_id('JH374761');};
    skip "Couldn't connect to GenBank with Bio::DB::GenBank.pm. Skipping those tests", 3 if $@;
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
    # now to check that postprocess_data in NCBIHelper catches CONTIG...
    ok $gb = Bio::DB::GenBank->new('-delay' => 0, '-format' => 'gb');
    eval {$seq = $gb->get_Seq_by_id('JH374761');};
    skip "Couldn't connect to GenBank with Bio::DB::GenBank.pm. Skipping those tests", 1 if $@;
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
}

$seq = $seqio = undef;

# bug 1405
my @result;
ok $gb = Bio::DB::GenBank->new(-format => 'Fasta', -seq_start  => 2, -seq_stop   => 7);
SKIP: {
    eval {$seq = $gb->get_Seq_by_acc("A11111");};
    skip "Couldn't connect to complete GenBank tests. Skipping those tests", 15 if $@;
    is $seq->length, 6;
    # complexity tests
    ok $gb = Bio::DB::GenBank->new(-format => 'Fasta', -complexity => 0);
    eval {$seqin = $gb->get_Stream_by_acc("5");};
    skip "Couldn't connect to complete GenBank tests. Skipping those tests", 13 if $@;
    @result = (1136, 'dna', 342, 'protein');
    while ($seq = $seqin->next_seq) {
        is $seq->length, shift(@result);
        is $seq->alphabet, shift(@result);
    }
    is @result, 0;
    # Real batch retrieval using epost/efetch
    # these tests may change if integrated further into Bio::DB::Gen*
    # Currently only useful for retrieving GI's via get_seq_stream
    $gb = Bio::DB::GenBank->new();
    eval {$seqin = $gb->get_seq_stream(-uids => [4887706 ,431229, 147460], -mode => 'batch');};
    skip "Couldn't connect to complete GenBank batchmode epost/efetch tests. Skipping those tests", 8 if $@;
    my %result = ('M59757' => 12611 ,'X76083'=> 3140, 'J01670'=> 1593);
	my $ct = 0;
    while ($seq = $seqin->next_seq) {
		$ct++;
		my $acc = $seq->accession;
        ok exists $result{ $acc };
        is $seq->length, $result{ $acc };
		delete $result{$acc};
    }
    skip('No seqs returned', 8) if !$ct;
	is $ct, 3;
    is %result, 0;
}
BioPerl-1.007002/t/RemoteDB/GenPept.t000555000766000024       501313155576321 17151 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
	use Bio::Root::Test;

	test_begin(-tests => 21,
			   -requires_modules => [qw(IO::String
									    LWP::UserAgent
										HTTP::Request::Common)],
			   -requires_networking => 1);

	use_ok('Bio::DB::GenPept');
}

my %expected_lengths = (
    'AAC06201'  => 353,
    'AAD15290'  => 136,
    'P31383'    => 635,
    '2AAA_YEAST' => 635
);

my ($gb, $seq, $seqio);

#
# Bio::DB::GenPept
#
ok $gb = Bio::DB::GenPept->new();
SKIP: {
    eval {$seqio = $gb->get_seq_stream(-uids => [2981015, 1621261, 195055], -mode => 'batch');};
    skip "Couldn't connect to complete GenPept tests. Skipping those tests", 8 if $@;
    my %result = ('AAC06201' => 353, 'CAB02640' => 193, 'AAD15290' => 136);
    my $ct = 0;
    while ($seq = $seqio->next_seq) {
		$ct++;
		my $acc = $seq->accession;
        ok exists $result{ $acc };
        is $seq->length, $result{ $acc };
		delete $result{$acc};
    }
    skip('No seqs returned', 8) if !$ct;
	is $ct, 3;
    is %result, 0;
}

$seq = $seqio = undef;

ok $gb = Bio::DB::GenPept->new('-delay' => 0);
SKIP: {
    eval {$seq = $gb->get_Seq_by_id('195055');};
    skip "Couldn't connect to Genbank with Bio::DB::GenPept.pm. Skipping those tests", 10 if $@;
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
    eval {$seq = $gb->get_Seq_by_acc('AAC06201');};
    skip "Couldn't connect to Genbank with Bio::DB::GenPept.pm. Skipping those tests", 9 if $@;
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
    eval {$seqio = $gb->get_Stream_by_id([qw(AAC06201 195055)]);};
    skip "Couldn't connect to Genbank with Bio::DB::GenPept.pm. Skipping those tests", 8 if $@;
    my $done = 0;
    while( my $s = $seqio->next_seq ) {
        is $s->length, $expected_lengths{$s->display_id}, $s->display_id;
        $done++;
    }
    skip('No seqs returned', 8) if !$done;
    is $done, 2;
    # swissprot genpept parsing
    eval {$seq = $gb->get_Seq_by_acc('P31383');};
    skip "Couldn't connect to Genbank with Bio::DB::GenPept.pm. Skipping those tests", 5 if $@;
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;

    # test dbsource stuff
    # small chance this might change but hopefully not
    my @annot = $seq->annotation->get_Annotations('dblink');
    cmp_ok(scalar(@annot), '>', 31);
    is $annot[0]->database, 'UniProtKB';
    is $annot[0]->primary_id, '2AAA_YEAST';
    is (($seq->annotation->get_Annotations('swissprot_dates'))[0]->value, 'Jul 1, 1993');
}
BioPerl-1.007002/t/RemoteDB/MeSH.t000555000766000024       154413155576321 16410 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 5,
               -requires_modules => [qw(IO::String
                                        LWP::UserAgent
                                        HTTP::Request::Common)],
               -requires_networking => 1);

    use_ok('Bio::DB::MeSH');
}

#
# Bio::DB::MeSH
#
ok my $mesh = Bio::DB::MeSH->new();
SKIP: {
    my $t;
    eval {$t = $mesh->get_exact_term('Dietary Fats');};
    skip "Couldn't connect to MeSH with Bio::DB::MeSH. Skipping those tests", 3 if $@;
    is $t->each_twig(), 3;

    eval {$t = $mesh->get_exact_term("Sinus Thrombosis, Intracranial");};
    skip "Couldn't connect to MeSH with Bio::DB::MeSH. Skipping those tests", 2 if $@;
    like $t->description, qr/Thrombus/i;
    is $t->id, "D012851";
}
BioPerl-1.007002/t/RemoteDB/RefSeq.t000444000766000024       311713155576321 16774 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 16,
               -requires_modules => [qw(IO::String
                                        LWP::UserAgent
                                        HTTP::Request::Common)]);
    
	use_ok('Bio::DB::RefSeq');
    use_ok('Bio::DB::GenBank');
    use_ok('Bio::DB::EMBL');
}

my $verbose = test_debug() || -1;

my ($db,$seq,$db2,$seq2,$seqio);
# get a single seq

$seq = $seqio = undef;

#test redirection from GenBank and EMBL
#GenBank
ok $db = Bio::DB::GenBank->new('-verbose'=> $verbose, -redirect_refseq => 1);
#EMBL
ok $db2 = Bio::DB::EMBL->new('-verbose'=> $verbose, -redirect_refseq => 1);     

eval {
    $seq = $db->get_Seq_by_acc('NT_006732');
    $seq2 = $db2->get_Seq_by_acc('NT_006732');
};
ok $@;

SKIP: {
    test_skip(-tests => 10, -requires_networking => 1);
    
    eval {
        ok($seq = $db->get_Seq_by_acc('NM_006732'));
        is($seq->length, 3776);
        ok $seq2 = $db2->get_Seq_by_acc('NM_006732');
        is($seq2->length, 3776);
    };
    skip "Warning: Couldn't connect to RefSeq with Bio::DB::RefSeq.pm!", 10 if $@;
    
    eval { 
        ok defined($db = Bio::DB::RefSeq->new(-verbose=>$verbose)); 
        ok(defined($seq = $db->get_Seq_by_acc('NM_006732')));
        is( $seq->length, 3776);
        ok defined ($db->request_format('fasta'));
        ok(defined($seq = $db->get_Seq_by_acc('NM_006732')));
        is( $seq->length, 3776); 
    };
    skip "Warning: Couldn't connect to RefSeq with Bio::DB::RefSeq.pm!", 6 if $@;
}
BioPerl-1.007002/t/RemoteDB/SeqRead_fail.t000444000766000024       255513155576321 20133 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 18,
			   -requires_modules => [qw(IO::String
									    LWP::UserAgent
										HTTP::Request::Common)],
			   -requires_networking => 1);
	
	use_ok('Bio::DB::GenBank');
	use_ok('Bio::DB::GenPept');
	use_ok('Bio::DB::SwissProt');
	use_ok('Bio::DB::RefSeq');
	use_ok('Bio::DB::EMBL');
	use_ok('Bio::DB::BioFetch');
}

my $verbose = test_debug();

sub fetch {
    my ($id, $class) = @_;
    print "###################### $class  ####################################\n" if $verbose;
    my $seq;
    ok defined( my $gb = $class->new('-verbose'       => $verbose,
                                     '-delay'         => 0,
                                     '-retrievaltype' => 'tempfile') ), "defined for $class";

    if ($class eq 'Bio::DB::SwissProt') {
        test_skip(-tests => 1, -requires_module => 'Data::Stag');
        next if $@;
    }

    eval { $seq = $gb->get_Seq_by_id($id) };
    if ($@ || !defined $seq) {
        ok 1, "error or undef for $class";
        return;
    }
    ok 0, "failure for $class";
}

my @classes = qw( Bio::DB::BioFetch Bio::DB::GenBank Bio::DB::GenPept
                  Bio::DB::SwissProt Bio::DB::RefSeq Bio::DB::EMBL );

my $id = 'XXX111';  # nonsense id

for (@classes) {
    fetch($id, $_);
}
BioPerl-1.007002/t/RemoteDB/SeqVersion.t000444000766000024       246613155576321 17713 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(    #-tests => 10,
	-requires_modules => [qw(LWP::UserAgent HTML::TableExtract)]
    );

    use_ok('Bio::DB::SeqVersion');
}

my $DEBUG = $ENV{BIOPERLDEBUG} || 0;

ok my $query = Bio::DB::SeqVersion->new( -type => 'gi' );

SKIP: {
    test_skip( -tests => 8, -requires_networking => 1 );

    throws_ok { $query->get_history('DODGY_ID_WHICH_SHOULD_FAIL') }
    qr/ID likely does not exist|No table found/i, 'throw on bad ID';

    my $latest_gi = $query->get_recent(2);
    is($latest_gi, 2, 'get_recent');
    is($query->get_status(2), 'live');

    my @all_gis = $query->get_all(2);
    cmp_ok(@all_gis, '>=', 8, 'get_all');
    is($query->get_status(2), 'live');

    $latest_gi = $query->get_recent('A00002');
    is($latest_gi, 2, 'get_recent, string');
    is($query->get_status('A00002'), 'live');

    $latest_gi = $query->get_recent(27478738);
    is($latest_gi, 42659163, 'get_recent, integer');
    is($query->get_status(27478738), 'suppressed');

    # check that default type is "gi"
    ok $query = Bio::DB::SeqVersion->new();
    ok my $ref = $query->get_history(3245);
    is($ref->[0]->[0], 578167, 'get_history');
    is($query->get_status('3245'), 'suppressed');
}

done_testing();
BioPerl-1.007002/t/RemoteDB/SwissProt.t000555000766000024       722213155576321 17570 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests               => 23,
               -requires_modules    => [qw(IO::String
                                           LWP::UserAgent
                                           HTTP::Request::Common
                                           Data::Stag)],
               -requires_networking => 1);

    use_ok('Bio::DB::SwissProt');
}

ok my $gb = Bio::DB::SwissProt->new(-retrievaltype => 'pipeline',
                                    -delay         => 0);

my %expected_lengths = (
                        'NDP_MOUSE'   => 131,
                        'NDP_HUMAN'   => 133,
                        'BOLA_HAEIN'  => 103,
                        'YNB3_YEAST'  => 125,
                        'O39869'      => 56,
                        'DEGP_CHLTR'  => 497,
                        'DEGPL_CHLTR' => 497
                        );

my ($seq, $seqio);

SKIP: {
    eval {$seq = $gb->get_Seq_by_id('YNB3_YEAST');};
    skip "Couldn't connect to SwissProt with Bio::DB::SwissProt.pm. Skipping those tests", 14 if $@;
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
    is $seq->division, 'YEAST';

    eval {$seq = $gb->get_Seq_by_acc('P43780');};
    skip "Couldn't connect to SwissProt with Bio::DB::SwissProt.pm. Skipping those tests", 12 if $@;
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
    eval {$seq = $gb->get_Seq_by_acc('O39869');};
    skip "Couldn't connect to SwissProt with Bio::DB::SwissProt.pm. Skipping those tests", 11 if $@;
    is $seq->length, $expected_lengths{$seq->accession_number}, $seq->accession_number;
    is $seq->accession_number, 'O39869';
    is $seq->division, '9PICO';

    # test for bug #958
    eval {$seq = $gb->get_Seq_by_id('P18584');};
    skip "Couldn't connect to SwissProt with Bio::DB::SwissProt.pm. Skipping those tests", 8 if $@;
    ok exists $expected_lengths{$seq->display_id}, 'P18584';
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
    is $seq->division, 'CHLTR';

    ok $gb = Bio::DB::SwissProt->new('-retrievaltype' => 'tempfile', '-delay' => 0);
    eval {$seqio = $gb->get_Stream_by_id(['NDP_MOUSE', 'NDP_HUMAN']);};
    skip "Couldn't connect to SwissProt with Bio::DB::SwissProt.pm. Skipping those tests", 4 if $@;
    undef $gb; # testing to see if we can remove gb
    ok $seq = $seqio->next_seq();
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
    ok $seq = $seqio->next_seq();
    is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
}

# test idtracker() method
ok $gb = Bio::DB::SwissProt->new(-retrievaltype => 'pipeline',
                                 -delay         => 0,
                                 -verbose       => 2);

SKIP: {
    my $map;
    # check old ID
    eval {$map = $gb->id_mapper(-from => 'ACC+ID',
                                -to   => 'ACC',
                                -ids  => [qw(MYOD1_PIG PYRC_YEAST)]
                                )};
    skip("Problem with idtracker(), skipping these tests: $@", 6) if $@;

    cmp_ok(@{$map->{MYOD1_PIG}}, '>=', 1);
    is($map->{MYOD1_PIG}[0], 'P49811');
    cmp_ok(@{$map->{PYRC_YEAST}}, '>=', 1);
    is($map->{PYRC_YEAST}[0], 'P20051');

    eval {$map = $gb->id_mapper(-from => 'ACC+ID',
                                -to   => 'EMBL',
                                -ids  => [qw(PYRC_YEAST)]
                                )};
    skip("Problem with idtracker(), skipping these tests: $@", 2) if $@;

    cmp_ok(@{$map->{PYRC_YEAST}}, '>=', 2);
    like($map->{PYRC_YEAST}[0], qr/^[A-Z0-9]/);
}

1;
BioPerl-1.007002/t/RemoteDB/Taxonomy.t000444000766000024      5016413155576321 17451 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(
        -tests            => 220,
        -requires_modules => [qw(DB_File
                                 LWP::UserAgent
                                 XML::Twig )]
    );

    use_ok('Bio::DB::Taxonomy');
    use_ok('Bio::Tree::Tree');
}

my $temp_dir = test_output_dir();

# we're actually testing Bio::Taxon and Bio::DB::Taxonomy::* here, not
# Bio::Taxonomy

ok my $db_entrez = Bio::DB::Taxonomy->new(-source => 'entrez');
isa_ok $db_entrez, 'Bio::DB::Taxonomy::entrez';
isa_ok $db_entrez, 'Bio::DB::Taxonomy';

ok my $db_flatfile = Bio::DB::Taxonomy->new(
    -source    => 'flatfile',
    -nodesfile => test_input_file('taxdump', 'nodes.dmp'),
    -namesfile => test_input_file('taxdump', 'names.dmp'),
);
isa_ok $db_flatfile, 'Bio::DB::Taxonomy::flatfile';
isa_ok $db_flatfile, 'Bio::DB::Taxonomy';

# By not specifying a '-directory' argument, index files go to a temporary
# folder ($Bio::Root::IO::TEMPDIR, such as 'C:\Users\USER\AppData\Local\Temp'),
# and are implied to be temporary. So test the ability of flatfile->DESTROY to
# remove the temporary index files at object destruction (this also affects files
# in "test_output_dir()", since the folder is created inside the temporary folder)
no warnings qw(once); # silence 'Name "$Bio::Root::IO::TEMPDIR" used only once'
is $db_flatfile->{index_directory}, $Bio::Root::IO::TEMPDIR, 'removal of temporary index files: no -directory';
$db_flatfile->DESTROY;
ok not -e ($db_flatfile->{index_directory} . '/id2names');
ok not -e ($db_flatfile->{index_directory} . '/names2id');
ok not -e ($db_flatfile->{index_directory} . '/nodes');
ok not -e ($db_flatfile->{index_directory} . '/parents');

# Test removal of temporary index files from test_output_dir folder
# (since test_output_dir() =~ m/^$Bio::Root::IO::TEMPDIR/)
ok $db_flatfile = Bio::DB::Taxonomy->new(
    -source    => 'flatfile',
    -directory => $temp_dir,
    -nodesfile => test_input_file('taxdump', 'nodes.dmp'),
    -namesfile => test_input_file('taxdump', 'names.dmp'),
    -force     => 1,
);
is $db_flatfile->{index_directory}, $temp_dir, 'removal of temporary index files: test_output_dir()';
$db_flatfile->DESTROY;
ok not -e ($db_flatfile->{index_directory} . '/id2names');
ok not -e ($db_flatfile->{index_directory} . '/names2id');
ok not -e ($db_flatfile->{index_directory} . '/nodes');
ok not -e ($db_flatfile->{index_directory} . '/parents');

# Generate the object (and the files) again for the remaining tests
ok $db_flatfile = Bio::DB::Taxonomy->new(
    -source    => 'flatfile',
    -directory => $temp_dir,
    -nodesfile => test_input_file('taxdump', 'nodes.dmp'),
    -namesfile => test_input_file('taxdump', 'names.dmp'),
    -force     => 1,
);

my $n;
for my $db ($db_entrez, $db_flatfile) {
    SKIP: {
        test_skip(-tests => 46, -requires_networking => 1) if $db eq $db_entrez;
        my $id;

        if ($db eq $db_entrez) {
           cmp_ok $db->get_num_taxa, '>', 880_000; # 886,907 as of 08-May-2012
        } else {
           is $db->get_num_taxa, 189;
        }

        eval { $id = $db->get_taxonid('Homo sapiens');};
        skip "Unable to connect to entrez database; no network or server busy?", 38 if $@;

        is $id, 9606;

        # easy test on human, try out the main Taxon methods
        ok $n = $db->get_taxon(9606);
        is $n->id, 9606;
        is $n->object_id, $n->id;
        is $n->ncbi_taxid, $n->id;
        is $n->parent_id, 9605;
        is $n->rank, 'species';

        is $n->node_name, 'Homo sapiens';
        is $n->scientific_name, $n->node_name;
        is ${$n->name('scientific')}[0], $n->node_name;

        my %common_names = map { $_ => 1 } $n->common_names;
        cmp_ok keys %common_names, '>=', 3, ref($db).": common names";
        ok exists $common_names{human};
        ok exists $common_names{man};

        is $n->division, 'Primates';
        is $n->genetic_code, 1;
        is $n->mitochondrial_genetic_code, 2;
        # these are entrez-only, data not available in dmp files
        if ($db eq $db_entrez) {
            ok defined $n->pub_date;
            ok defined $n->create_date;
            ok defined $n->update_date;
        }

        # briefly test some Bio::Tree::NodeI methods
        ok my $ancestor = $n->ancestor;
        is $ancestor->scientific_name, 'Homo';
        # unless set explicitly, Bio::Taxon doesn't return anything for
        # each_Descendent; must ask the database directly
        ok my @children = $ancestor->db_handle->each_Descendent($ancestor);
        cmp_ok @children, '>', 0;

        sleep(3) if $db eq $db_entrez;

        # do some trickier things...
        ok my $n2 = $db->get_Taxonomy_Node('89593');
        is $n2->scientific_name, 'Craniata';

        # briefly check we can use some Tree methods
        my $tree = Bio::Tree::Tree->new();
        is $tree->get_lca($n, $n2)->scientific_name, 'Craniata';

        # get lineage_nodes
        my @nodes = $tree->get_nodes;
        is scalar(@nodes), 0;
        my @lineage_nodes;
        @lineage_nodes = $tree->get_lineage_nodes($n->id); # read ID, only works if nodes have been added to tree
        is scalar @lineage_nodes, 0;
        @lineage_nodes = $tree->get_lineage_nodes($n);     # node object always works
        cmp_ok(scalar @lineage_nodes, '>', 20);

        # get lineage string
        like($tree->get_lineage_string($n), qr/cellular organisms;Eukaryota/);
        like($tree->get_lineage_string($n,'-'), qr/cellular organisms-Eukaryota/);
        like($tree->get_lineage_string($n2), qr/cellular organisms;Eukaryota/);

        # can we actually form a Tree and use other Tree methods?
        ok $tree = Bio::Tree::Tree->new(-node => $n);
        cmp_ok($tree->number_nodes, '>', 20);
        cmp_ok(scalar($tree->get_nodes), '>', 20);
        is $tree->find_node(-rank => 'genus')->scientific_name, 'Homo';

        # check that getting the ancestor still works now we have explitly set the
        # ancestor by making a Tree
        is $n->ancestor->scientific_name, 'Homo';

        sleep(3) if $db eq $db_entrez;

        ok $n = $db->get_Taxonomy_Node('1760');
        is $n->scientific_name, 'Actinobacteria';

        sleep(3) if $db eq $db_entrez;

        # entrez isn't as good at searching as flatfile, so we have to special-case
        my @ids = sort $db->get_taxonids('Chloroflexi');
        is scalar @ids, 2;
        is_deeply \@ids, [200795, 32061];

        $id = $db->get_taxonids('Chloroflexi (class)');
        $db eq $db_entrez ? is($id, 'No hit') : is($id, 32061);

        @ids = $db->get_taxonids('Rhodotorula');
        cmp_ok @ids, '>=' , 1;
        if ($db eq $db_entrez) {
            diag(join(",", @ids));
            # From NCBI: Taxid 592558 was merged into taxid 5533 on June 16, 2017
            is( (grep { $_ == 592558 } @ids), 0, 'Value no longer found');
            ok grep { $_ == 5533 } @ids;
        } else {
            # note the locally cached flatfile is out-of-date, but technically
            # correct for testing purposes
            ok grep { $_ == 266791 } @ids;
            ok grep { $_ == 5533 } @ids;
        }
    }
}


# Test the list database

ok my $db_list = Bio::DB::Taxonomy->new(-source => 'list');
isa_ok $db_list, 'Bio::DB::Taxonomy::list';
isa_ok $db_list, 'Bio::DB::Taxonomy';

my @ranks = qw(superkingdom class genus species);
my @h_lineage = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens');
ok $db_list = Bio::DB::Taxonomy->new(
    -source => 'list',
    -names  => \@h_lineage,
    -ranks  => \@ranks,
);
is $db_list->get_num_taxa, 4;

my @taxa;
ok @taxa = map {$db_list->get_taxon(-name=>$_)} @h_lineage;
is_deeply [map {ref($_)} @taxa], [('Bio::Taxon')x4];
is_deeply [map {$_->rank} @taxa], \@ranks, 'Ranks';

@h_lineage = ('Eukaryota', 'Mammalia', 'Homo', 'Homo erectus');
$db_list->add_lineage(-names => \@h_lineage, -ranks => \@ranks);

ok @taxa = map {$db_list->get_taxon(-name=>$_)} @h_lineage;
is_deeply [map {ref($_)} @taxa], [('Bio::Taxon')x4];
is_deeply [map {$_->rank} @taxa], \@ranks, 'Ranks';

# Make a tree
ok my $tree = $db_list->get_tree('Homo sapiens', 'Homo erectus');
isa_ok $tree, 'Bio::Tree::TreeI';
is $tree->number_nodes, 5;
is $tree->total_branch_length, 4;
ok my $node1 = $tree->find_node( -scientific_name => 'Homo sapiens' );
ok my $node2 = $tree->find_node( -scientific_name => 'Homo erectus' );
is $tree->distance($node1, $node2), 2;

ok my $h_list = $db_list->get_taxon(-name => 'Homo sapiens');
ok my $h_flat = $db_flatfile->get_taxon(-name => 'Homo sapiens');

is $h_list->ancestor->scientific_name, 'Homo';

my @names = $h_list->common_names;
is @names, 0;
$h_list->common_names('woman');
@names = $h_list->common_names;
is @names, 1;
@names = $h_flat->common_names;
is @names, 3;

# you can switch to another database when you need more information, which also
# merges information in the node from the two different dbs
$h_list->db_handle($db_flatfile);
@names = $h_list->common_names;
is @names, 4;

# form a tree with the list lineage first, preventing a subsequent database
# change from giving us all those extra ranks
$h_list->db_handle($db_list);
my $ancestors_ancestor = $h_list->ancestor->ancestor;
is $ancestors_ancestor->scientific_name, 'Mammalia';

$tree = Bio::Tree::Tree->new(-node => $h_list);
$h_list->db_handle($db_flatfile);
$ancestors_ancestor = $h_list->ancestor->ancestor;
is $ancestors_ancestor->scientific_name, 'Mammalia';

# or we can get the flatfile database's idea of the ancestors by removing
# ourselves from the tree
is $h_flat->ancestor->ancestor->scientific_name, 'Homo/Pan/Gorilla group';
$h_list->ancestor(undef);
is $h_list->ancestor->ancestor->scientific_name, 'Homo/Pan/Gorilla group';

# get_lca should work on nodes from different databases
SKIP: {
    test_skip(-tests => 9, -requires_networking => 1);

    # check that the result is the same as if we are retrieving from the same DB
    # flatfile
    $h_flat = $db_flatfile->get_taxon(-name => 'Homo');
    my $h_flat2 = $db_flatfile->get_taxon(-name => 'Homo sapiens');
    ok my $tree_functions = Bio::Tree::Tree->new();
    is $tree_functions->get_lca($h_flat, $h_flat2)->scientific_name, 'Homo', 'get_lca() within flatfile db';

    # entrez
    my $h_entrez;
    eval { $h_entrez = $db_entrez->get_taxon(-name => 'Homo sapiens');};
    skip "Unable to connect to entrez database; no network or server busy?", 7 if $@;
    my $h_entrez2;
    eval { $h_entrez2 = $db_entrez->get_taxon(-name => 'Homo');};
    skip "Unable to connect to entrez database; no network or server busy?", 7 if $@;
    ok $tree_functions = Bio::Tree::Tree->new();
    is $tree_functions->get_lca($h_entrez, $h_entrez2)->scientific_name, 'Homo', 'get_lca() within entrez db';

    ok $tree_functions = Bio::Tree::Tree->new();
    # mixing entrez and flatfile
    TODO:{
        local $TODO = 'Mixing databases for get_lca() not working, see bug #3416';
        is $tree_functions->get_lca($h_flat, $h_entrez)->scientific_name, 'Homo', 'get_lca() mixing flatfile and remote db';
    }
    # even though the species taxa for Homo sapiens from list and flat databases
    # have the same internal id, get_lca won't work because they have different
    # roots and descendents
    $h_list = $db_list->get_taxon(-name => 'Homo sapiens');
    is $h_list->ancestor->internal_id, $h_flat->internal_id;
    ok ! $tree_functions->get_lca($h_flat, $h_list);

    # but we can form a tree with the flat node then remove all the ranks we're
    # not interested in and try again
    $tree = Bio::Tree::Tree->new(-node => $h_flat);
    $tree->splice(-keep_rank => \@ranks);
    is $tree->get_lca($h_flat, $h_list)->scientific_name, 'Homo';
}

# ideas from taxonomy2tree.PLS that let us make nice tree, using
# Bio::Tree::TreeFunctionsI methods; this is a weird and trivial example just
# because our test flatfile database only has the full lineage of one species
undef $tree;
for my $name ('Human', 'Hominidae') {
  my $ncbi_id = $db_flatfile->get_taxonid($name);
  if ($ncbi_id) {
    my $node = $db_flatfile->get_taxon(-taxonid => $ncbi_id);

    if ($tree) {
        ok $tree->merge_lineage($node);
    }
    else {
        ok $tree = Bio::Tree::Tree->new(-node => $node);
    }
  }
}
is $tree->get_nodes, 30;
$tree->contract_linear_paths;
my $ids = join(",", map { $_->id } $tree->get_nodes);
is $ids, '131567,9606';

# More thorough tests of merge_lineage
ok my $node = $db_list->get_taxon(-name => 'Eukaryota');
$tree = Bio::Tree::Tree->new(-node => $node);
ok $node = $db_list->get_taxon(-name => 'Homo erectus');
ok $tree->merge_lineage($node);
for my $name ('Eukaryota', 'Mammalia', 'Homo', 'Homo erectus') {
   ok $node = $tree->find_node(-scientific_name => $name);
}

# we can recursively fetch all descendents of a taxon
SKIP: {
    test_skip(-tests => 1, -requires_networking => 1);
    eval {$db_entrez->get_taxon(10090);};
    skip "Unable to connect to entrez database; no network or server busy?", 1 if $@;

    my $lca = $db_entrez->get_taxon(314146);
    my @descs = $db_entrez->get_all_Descendents($lca);
    cmp_ok @descs, '>=', 17;
}

# bug 2461
$db_list = Bio::DB::Taxonomy->new(-source => 'list',
                                  -names => [
(split(/,\s+/, "cellular organisms, Eukaryota, Fungi/Metazoa group,
Metazoa, Eumetazoa, Bilateria, Coelomata, Protostomia, Panarthropoda,
Arthropoda, Mandibulata, Pancrustacea, Hexapoda, Insecta, Dicondylia,
Pterygota, Neoptera, Endopterygota, Diptera, Nematocera, Culicimorpha,
Culicoidea, Culicidae, Anophelinae, Anopheles, Anopheles, Angusticorn,
Anopheles, maculipennis group, maculipennis species complex, Anopheles daciae"))]);

my @taxonids = $db_list->get_taxonids('Anopheles');
is @taxonids, 3, 'List context';

my $taxonid = $db_list->get_taxonids('Anopheles');
isa_ok \$taxonid, 'SCALAR', 'Scalar context';
ok exists { map({$_ => undef} @taxonids) }->{$taxonid};

# but we should still be able to merge in an incomplete lineage of a sister
# species and have the 'tree' remain consistent:

# missing 'no rank' Anopheles
$db_list->add_lineage(-names => [
(split(/,\s+/, "Anophelinae, Anopheles, Anopheles, Angusticorn,
maculipennis group, maculipennis species complex, Anopheles labranchiae"))]);
$node = $db_list->get_taxon(-name => 'Anopheles labranchiae');
is $node->ancestor->ancestor->ancestor->ancestor->ancestor->ancestor->ancestor->scientific_name, 'Anophelinae';
is $node->rank, undef;

# missing 'subgenus' Anopheles
$db_list->add_lineage(-names => [
(split(/,\s+/, "Anophelinae, Anopheles, Angusticorn, Anopheles,
maculipennis group, maculipennis species complex, Anopheles maculipennis"))]);
$node = $db_list->get_taxon(-name => 'Anopheles maculipennis');
is $node->ancestor->ancestor->ancestor->ancestor->ancestor->ancestor->ancestor->scientific_name, 'Anophelinae';

# missing 'no rank' Angusticorn
$db_list->add_lineage(-names => [
(split(/,\s+/, "Anophelinae, Anopheles, Anopheles, Anopheles,
maculipennis group, maculipennis species complex, Anopheles melanoon"))]);
$node = $db_list->get_taxon(-name => 'Anopheles melanoon');
is $node->ancestor->ancestor->ancestor->ancestor->scientific_name, 'Angusticorn';

@taxonids = $db_list->get_taxonids('Anopheles');
is scalar @taxonids, 3;

# bug: duplicate topmost taxa
$db_list = Bio::DB::Taxonomy->new( -source => 'list',
                                   -names => ['Bacteria', 'Tenericutes'] );
$db_list->add_lineage(  -names => ['Bacteria'] );
@taxonids = $db_list->get_taxonids('Bacteria');
is scalar @taxonids, 1;

# Disambiguate between taxa with same name using -names
ok $db_list = Bio::DB::Taxonomy->new( -source => 'list' ), 'DB with ambiguous names';
ok $db_list->add_lineage( -names => ['c__Gammaproteobacteria', 'o__Oceanospirillales', 'f__Alteromonadaceae', 'g__Spongiibacter'] );
ok $db_list->add_lineage( -names => ['c__Gammaproteobacteria', 'o__Alteromonadales'  , 'f__Alteromonadaceae', 'g__Alteromonas'  ] );

ok @taxonids = $db_list->get_taxonids('f__Alteromonadaceae');
is scalar @taxonids, 2; # multiple taxa would match using $db_list->get_taxon(-name => 'f__Alteromonadaceae')

ok $node = $db_list->get_taxon( -names => ['c__Gammaproteobacteria', 'o__Alteromonadales'  , 'f__Alteromonadaceae'] );
is $node->ancestor->node_name, 'o__Alteromonadales';
my $iid = $node->internal_id;

ok $node = $db_list->get_taxon( -names => ['c__Gammaproteobacteria', 'o__Oceanospirillales', 'f__Alteromonadaceae'] );
is $node->ancestor->node_name, 'o__Oceanospirillales';
isnt $node->internal_id, $iid;


# More tests with ambiguous names, internal IDs and multiple databases
my ($node3, $node4, $db_list_2);
ok $db_list = Bio::DB::Taxonomy->new( -source => 'list' );
ok $db_list->add_lineage( -names => [ 'o__Enterobacteriales', 'g__Escherichia' ] );
ok $db_list->add_lineage( -names => [ 'o__Pseudomonadales'  , 'g__Pseudomonas' ] );
ok $db_list->add_lineage( -names => [ 'o__Chroococcales'    , 'g__Microcoleus' ] );
ok $node1 = $db_list->get_taxon( -names => [ 'k__Chroococcales', 'g__Microcoleus' ] );

ok $db_list_2 = Bio::DB::Taxonomy->new( -source => 'list' );
ok $db_list_2->add_lineage( -names => [ 'o__Chroococcales', 'g__Microcoleus' ] );
ok $node2 = $db_list_2->get_taxon( -names => [ 'o__Chroococcales', 'g__Microcoleus' ] );

is $node1->scientific_name, 'g__Microcoleus';
is $node2->scientific_name, 'g__Microcoleus'; # same taxon name
isnt $node1->id, $node2->id;                  # but different dbs and hence taxids
is $node1->internal_id, $node1->internal_id;  # but same cross-database internal ID

ok $db_list->add_lineage( -names => [ 'o__Oscillatoriales' , 'g__Microcoleus' ] );
ok $db_list->add_lineage( -names => [ 'o__Acidobacteriales', 'g__Microcoleus' ] );

ok $node1 = $db_list->get_taxon( -names => [ 'o__Chroococcales', 'g__Microcoleus' ] );
ok $node2 = $db_list->get_taxon( -names => [ 'o__Oscillatoriales'  , 'g__Microcoleus' ] );
ok $node3 = $db_list->get_taxon( -names => [ 'o__Acidobacteriales'    , 'g__Microcoleus' ] );
my @nodes = ($node1, $node2, $node3);

is map({$_->id          => undef} @nodes), 6; # 3 distinct taxids
is map({$_->internal_id => undef} @nodes), 6; # 3 distinct iids

ok $db_list->add_lineage( -names => [ 'o__Chroococcales'  , 'g__Microcoleus' ] );
ok $node2 = $db_list->get_taxon( -names => [ 'o__Chroococcales', 'g__Microcoleus' ] );
is $node2->scientific_name, $node1->scientific_name;
is $node2->id, $node1->id;
is $node2->internal_id, $node1->internal_id;

# tests for #182
SKIP: {
    test_skip(-tests => 12, -requires_networking => 1);

    my $db=Bio::DB::Taxonomy->new(-source=>"entrez");

    my @taxa = qw(viruses Deltavirus unclassified plasmid);

    for my $taxon (@taxa) {
        test_taxid($db, $taxon);
    }

    sub test_taxid {
        my ($db, $taxa) = @_;
        my @taxonids = $db->get_taxonids($taxa);
        cmp_ok(scalar(@taxonids), '>', 0, "Got IDs returned for $taxa:".join(',', @taxonids));
        my $taxon;
        lives_ok { $taxon = $db->get_taxon(-taxonid => pop @taxonids) } "IDs generates a Bio::Taxonomy::Node";
        if (defined $taxon) {
            like( $taxon->scientific_name, qr/$taxa/i, "Name returned matches $taxa");
        } else {
            ok(0, "No taxon object returned for $taxa");
        }
    }
}

# tests for #212
SKIP: {
        test_skip( -tests => 6, -requires_networking => 1 );

        my $db = Bio::DB::Taxonomy->new( -source => "entrez" );

        # String                 | What I expect | What I get
        # ---------------------- | ------------- | ----------
        # 'Lissotriton vulgaris' | 8324          | 8324
        # 'Chlorella vulgaris'   | 3077          | 3077
        # 'Phygadeuon solidus'   | 1763951       | 1763951
        # 'Ovatus'               | 666060        | 666060
        # 'Phygadeuon ovatus'    | "No hit"      | 666060
        # 'Trimorus ovatus'      | "No hit"      | 666060

        my @ids;
        @ids = $db->get_taxonids('Lissotriton vulgaris');
        is $ids[0], 8324, 'Correct: Lissotriton vulgaris';
        @ids = $db->get_taxonids('Chlorella vulgaris');
        is $ids[0], 3077, 'Correct: Chlorella vulgaris';
        @ids = $db->get_taxonids('Phygadeuon solidus');
        is $ids[0], 1763951, 'Correct: Phygadeuon solidus';
        @ids = $db->get_taxonids('Ovatus');
        is $ids[0], 666060, 'Correct: Ovatus';
        @ids = $db->get_taxonids('Phygadeuon ovatus');
        is $ids[0], 'No hit', 'Correct: No hit';
        @ids = $db->get_taxonids('Trimorus ovatus');
        is $ids[0], 'No hit', 'Correct: No hit';
}
BioPerl-1.007002/t/RemoteDB/HIV000755000766000024          013155576321 15711 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/RemoteDB/HIV/HIV.t000555000766000024      1005713155576321 16707 0ustar00cjfieldsstaff000000000000# testing Bio::DB::HIV
#$Id: HIV.t 232 2008-12-11 14:51:51Z maj $#
use strict;
use warnings;

BEGIN {
    use Bio::Root::Test;
    test_begin(
        -tests => 30,
        -requires_modules => [qw(LWP::UserAgent
                                 XML::Simple
                                 HTTP::Request::Common)],
        );
    use_ok('Bio::DB::HIV');
    use_ok('Bio::DB::WebDBSeqI');
    use_ok('Bio::DB::HIV::HIVAnnotProcessor');
}

my $tobj= Bio::DB::HIV->new();

$tobj->ua->timeout(90);

#object tests
isa_ok($tobj, 'Bio::DB::HIV');

#compliance tests
isa_ok($tobj, 'Bio::Root::Root');
can_ok($tobj, qw( get_request postprocess_data ));

#methods
can_ok($tobj, qw( get_seq_stream get_Stream_by_acc get_Stream_by_query _request ));

#internals
can_ok($tobj, qw( lanl_base map_db make_search_if search_ _map_db_uri _make_search_if_uri _search_uri _session_id _sorry ));

# defaults tests
ok($tobj->lanl_base, 'lanl_base set in default object');
ok($tobj->map_db, 'map_db set in default object');
ok($tobj->make_search_if, 'make_search_if set in default object');
ok($tobj->search_, 'search_ set in default object');
ok($tobj->url_base_address, 'url_base_address set in default object');
is(($tobj->request_format)[0], "fasta", 'default sequence request format (fasta)');

#todos
throws_ok { $tobj->get_request('mode'=>'version', 'uids'=>['K03455.1']) } qr/Bio::HIVSorry::Exception/, 'sorry till implemented';

throws_ok {$tobj->get_request('mode'=>'gi', 'uids'=>['1906382'])} qr/Bio::HIVSorry::Exception/, 'sorry till implemented';

#exception tests
my $badq = bless({}, "Not::A::Query");
throws_ok {$tobj->get_Stream_by_query($badq)} qr/HIVQuery required/, 'HIVQuery type exception check';

# network tests
SKIP: {
    test_skip(-tests => 13,
          -requires_networking => 1);
    
    # WebDBSeqI compliance-
    # (this requires network access, since request is built after establishing
    # the LANL session...)
    my $req;
    lives_ok {$req = $tobj->get_request('mode'=>'single','uids'=>['17756'])} 'test connection';
    if ($@) {
        skip("Network problems, skipping all tests", 12)
    }
    isa_ok($req, 'HTTP::Request', 'Object returned from get_request');
    # get_... functionality
    lives_ok { $tobj->get_Seq_by_id('17756') } 'get HXB2 by LANL id';
    if ($@) {
        skip("Network problems, skipping all tests", 10)
    }
    lives_ok { $tobj->get_Seq_by_acc('K03455');} 'get HXB2 by GB accession';
    if ($@) {
        skip("Network problems, skipping all tests", 9)
    }    
    my ($seqio, $hxb2);
    lives_ok { $seqio = $tobj->get_Stream_by_id(['17756']) } 'get HXB2 in a stream';
    if ($@) {
        skip("Network problems, skipping all tests", 8)
    }
	
	# this test seems to fail ~50% of the time (server-side issue), so we tread
	# lightly with an eval and pass regardless, but indicate the problem and
	# skip the rest
	eval { $seqio = $tobj->get_Stream_by_acc(['K03455']) };
    if ($@) {
		ok(1, "Server-side request problem, bypassing...");
        skip("Network problems, skipping all tests", 7)
    } else {
		ok(1, 'get HXB2 in a stream by accession');
	}
    $hxb2 =  $seqio->next_seq;
    is($hxb2->primary_id, 'K03455', 'checking returned stream');
    is($hxb2->alphabet,'dna', 'checking returned stream');
    ok(!($hxb2->seq !~ /atgc/i), 'checking returned sequence');
    #network exceptions
        
    # bad id exception
    throws_ok { $tobj->get_Seq_by_id('XXXXXX') } qr/no sequences found/i, 'bad id exception check';
    # session id exception
    $tobj->_session_id('555-1212');
    throws_ok {$tobj->get_Seq_by_id('17756')} qr/request failed/, 'bad session exception check';
    # bad url exception
    $tobj->_session_id('');
    $tobj->map_db('');
    $tobj->url_base_address('http://socrates_jones_et_cie.us');
    throws_ok {$tobj->get_Seq_by_id('17756')} qr/Connect failed|Session not established/, 'bad url exception check';
    # wrong url exception 
    $tobj->url_base_address('http://fortinbras.us');
    throws_ok {$tobj->get_Seq_by_id('17756')} qr/Session not established/, 'wrong url exception check';
    
# check ..._by_query functions in HIVQuery.t
}


BioPerl-1.007002/t/RemoteDB/HIV/HIVAnnotProcessor.t000555000766000024       203013155576321 21557 0ustar00cjfieldsstaff000000000000# testing Bio::DB::HIVAnnotProcessor.pm
# $Id: HIVAnnotProcessor.t 231 2008-12-11 14:32:00Z maj $
use strict;
use warnings;

BEGIN {
    use Bio::Root::Test;
    test_begin(
	-tests => 11,
	);
    use_ok('Bio::Seq');
    use_ok('Bio::SeqIO');
    use_ok('Bio::DB::HIV::HIVAnnotProcessor');
}

my $tobj = new Bio::DB::HIV::HIVAnnotProcessor();

#object tests
isa_ok($tobj, 'Bio::DB::HIV::HIVAnnotProcessor');

#compliance tests
isa_ok($tobj, 'Bio::Root::Root');
can_ok($tobj, qw( source_stream next_seq write_seq ));

#methods
can_ok($tobj, qw( hiv_query ));

#exception tests
throws_ok {$tobj->hiv_query(bless({},"narb"))} qr/BadParameter/, "bad type set exception";

#stream tests
my $fas = test_output_file();
open my $FAS, '>', $fas or die "Could not write file '$fas': $!\n";
print $FAS ">goob\natcg\n";
close $FAS;
ok( $tobj->source_stream(new Bio::SeqIO(-file=>$fas, -format=>'fasta')), "attach stream");
throws_ok {$tobj->write_seq(new Bio::Seq(-sequence=>"atcg"))} qr/IOException/, "write exception";
ok( $tobj->next_seq, "access stream");
BioPerl-1.007002/t/RemoteDB/HIV/HIVQuery.t000555000766000024      1415113155576321 17734 0ustar00cjfieldsstaff000000000000# testing Bio::DB::Query::HIVQuery
# $Id: HIVQuery.t 232 2008-12-11 14:51:51Z maj $
use strict;
use warnings;

BEGIN {
    use Bio::Root::Test;
    test_begin(
        -tests => 41,
        -requires_modules => [qw(CGI
                                 LWP::UserAgent
                                 XML::Simple )]
    );
    use_ok('Bio::DB::Query::HIVQuery');
    use_ok('Bio::DB::HIV');
    use_ok('Bio::Annotation::Collection');
    use_ok('Bio::Annotation::Comment');
    use_ok('Bio::Annotation::Reference');
    use_ok('Bio::DB::HIV::HIVQueryHelper');

}

my $tobj= new Bio::DB::Query::HIVQuery(-RUN_OPTION=>0);

#object tests
isa_ok($tobj, 'Bio::DB::Query::HIVQuery');

#compliance tests
isa_ok($tobj, 'Bio::Root::Root');
can_ok($tobj, qw( count ids query ));

#methods
can_ok($tobj, qw( 
                  get_annotations_by_ids 
                  get_annotations_by_id 
                  add_annotations_for_id 
                  remove_annotations_for_ids
                  remove_annotations_for_id
                  remove_annotations
                  get_accessions
                  get_accessions_by_ids
                  get_accessions_by_id
                  )
    );
#internals
can_ok($tobj, qw(
                  _do_query
                  _reset
                  _session_id
                  _run_option
                  add_id
                  lanl_base
                  map_db
                  make_search_if
                  search_
                  _map_db_uri
                  _make_search_if_uri
                  _search_uri
                  _schema_file
                  _schema
                  _lanl_query
                  _lanl_response
                  _create_lanl_query
                  _do_lanl_request
                  _parse_lanl_response
                  _parse_query_string
                  _sorry 
                 )
    );

#defaults tests
ok($tobj->_map_db_uri, "_map_db_uri set in default object");
ok($tobj->_make_search_if_uri, "_make_search_if_uri set in default object");
ok($tobj->_search_uri, "_search_uri set in default object");
ok($tobj->_schema_file, "_schema_file set in default object");
ok(defined $tobj->_run_option, "_run_option set in default object");
ok($tobj->{_annotations}, "annotations container available");

# query syntax (no run)
$tobj->_reset;
$tobj->query(['coreceptor'=>['CCR5 CXCR4','CXCR4'], subtype=>['D', 'F'], country=>'Any']);
is($tobj->_do_query(0), 0, 'query syntax check 1');
$tobj->_reset;
$tobj->query({'coreceptor'=>['CCR5 CXCR4','CXCR4'], subtype=>['D', 'F'], country=>'Any'});
is($tobj->_do_query(0), 0, 'query syntax check 2');
$tobj->_reset;
$tobj->query({'query'=>{'coreceptor'=>['CCR5 CXCR4','CXCR4'], subtype=>['D', 'F']}, 'annot'=> ['country']});
is($tobj->_do_query(0),0, 'query syntax check 3');
$tobj->_reset;
$tobj->query("('CCR5 CXCR4', 'CXCR4')[coreceptor] (D F)[subtype] {[country]}");
is($tobj->_do_query(0),0, 'query parser check');

#multiquery parse
$tobj->_reset;
$tobj->query( "(SI[phenotype] ('CCR5 CXCR4')[coreceptor] C[subtype] OR NSI[phenotype] D[subtype]) AND ZA[country]");
is($tobj->_do_query(0),0, 'multiquery parse check');

SKIP: {
	test_skip(-requires_module => 'HTML::Parser', -tests => 3);
	no warnings; # HTML::Parser has an uninited value issue
	use_ok('HTML::Parser');
	use warnings;
	# help test; just tests that file can be written and that tags are in matching 
	# pairs, with reasonable placement of  and 
	my $hlpf = test_output_file();
	my $a = 0;
	my $html = 0;
	my $h = HTML::Parser->new(empty_element_tags => 1,
				  start_h => [sub {$a++; (shift eq 'html') && ($a==1) && $html++;}, "tagname"],
				  end_h   => [sub {$a--; (shift eq 'html') && ($a==0) && $html++;}, "tagname"] );
	ok($tobj->help($hlpf), "help html to file");
	{
		local $/;
		undef $/;
		open my $HP, '<', $hlpf or die "Could not read file '$hlpf': $!\n";
		$h->parse(<$HP>);
		is_deeply([$a, $html], [0, 2], "help html parsed");
		close $HP; # Always explicitly close filehandles
		1;
	}

}

#exceptions tests
#pre-run query exceptions
$tobj->verbose(2);
$tobj->_reset;
$tobj->query( "narb[scroob]" );
throws_ok {$tobj->_do_query} qr/BadParameter/, "bad field exception check";
$tobj->_reset;
$tobj->query( "narb[phenotype]" );
throws_ok {$tobj->_do_query} qr/BadParameter/, "bad match data exception check";
$tobj->_reset;
$tobj->query( [ 'cd4_count'  => "" ] );
throws_ok {$tobj->_do_query} qr/BadParameter/, "empty field not ok exception check";
$tobj->_reset;
$tobj->{_schema} = undef;
throws_ok {$tobj->_do_query} qr/SchemaNotInit/, "uninitialized schema exception check";
throws_ok {$tobj->count} qr/Query not yet run/, "query not run (level 1) warning check";
throws_ok {$tobj->get_annotations_by_id($tobj->ids)} qr/Requires query run/, "query not run (level 2) warning check";



# network tests
SKIP : {
    test_skip(-tests => 10,
          -requires_networking => 1);
    eval {$tobj  = Bio::DB::Query::HIVQuery->new(-QUERY=>"(SI[phenotype] ('CCR5 CXCR4')[coreceptor] C[subtype] OR NSI[phenotype] D[subtype]) AND ZA[country]",-RUN_OPTION=>2)};
    if ($@) {
        diag($@);
        skip("Network problems, skipping all", 10);
    }
    ok($tobj,"live query");
    cmp_ok( $tobj->count, ">=", 12, "enough sequences returned");
# test query object handling of Bio::DB::HIV   
    my ($tdb, $seqio, $seq);
    ok( $tdb = new Bio::DB::HIV, "create Bio::DB::HIV object");
        eval {$seqio = $tdb->get_Stream_by_query($tobj)};
    if ($@) {
        diag($@);
        skip("Network problems, skipping all", 7);
    }
    ok($seqio, "get SeqIO stream from query");
# test HIVAnnotProcessor indirectly
    ok($seq = $seqio->next_seq, "access sequence stream");
    ok($seq->annotation->get_value('Virus'), "'Virus' annotation present");
    like ($seq->annotation->get_value('Virus','phenotype'), qr/SI/, "'Virus' phenotype annotation present");
    like ($seq->annotation->get_value('Virus', 'subtype'), qr/[CD]/, "'Virus' subtype annotation present");
    ok($seq->accession_number, "GenBank accession available");

# exception checks
    $tobj->_reset;
    $tobj->verbose(2);
    $tobj->query( "2BR02B[accession]" );
    throws_ok {$tobj->_do_query(2)} qr/no sequences/i, "no sequences warning check";
}
BioPerl-1.007002/t/RemoteDB/HIV/HIVQueryHelper.t000555000766000024      1004113155576321 21066 0ustar00cjfieldsstaff000000000000#-*-perl-*-
# testing HIVQueryHelper.pm and lanl-schema.xml indirectly
# $Id: HIVQueryHelper.t 231 2008-12-11 14:32:00Z maj $

use strict;
use warnings;

BEGIN {
    use Bio::Root::Test;
    test_begin(
	-tests => 40,
	-requires_modules => [qw( Bio::Root::Root XML::Simple)]
	);
    use_ok('Bio::DB::HIV::HIVQueryHelper');
}


# lanl-schema.xml characteristics as of $Date: 2008-12-11 08:05:24 -0500 (Thu, 11 Dec 2008) $
my ($naliases, $nfields, $ntables) = (165, 97, 14);
my ($Q, $r, $q);
# object tests
isa_ok(new HIVSchema(), "HIVSchema");
isa_ok($Q = new QRY(), "QRY");
isa_ok($r = new R(), "R");
isa_ok($q = new Q(), "Q");

#HIVSchema tests
my $tobj;
ok( $tobj = new HIVSchema(Bio::Root::IO->catfile(qw(Bio DB HIV lanl-schema.xml))), "schema load");

# methods
can_ok( $tobj, qw (
                   tables
                   columns
                   fields
                   options
                   aliases
                   ankh
                   tablepart
                   tbl
                   columnpart
                   col
                   primarykey
                   pk
                   foreignkey
                   fk
                   foreigntable
                   ftbl
                   loadSchema
                   _sfieldh
                   loadHIVSchema
                   ));

# lanl-schema.xml tests
is( scalar $tobj->fields, $nfields, "fields complete");
is( scalar $tobj->tables, $ntables, "tables complete");
is( scalar $tobj->aliases, $naliases, "aliases complete");
my ($tbl, $fld, $col, $als);
ok( ($fld) = grep /sequenceentry.se_sequence/, $tobj->fields, "test field present");
ok( $tbl = $tobj->tablepart($fld), "test field syntax ok");
ok( $col = $tobj->columnpart($fld), "test field syntax ok");
ok( $als = $tobj->aliases($fld), "test alias by field name");
is( $tobj->primarykey($tbl), 'sequenceentry.se_id', "correct primary key for SequenceEntry");
is( scalar $tobj->foreignkey('author'), 2, "correct number of foreign keys for AUthor");
is( $tobj->foreigntable(($tobj->foreignkey('author'))[1]), 'publication', "correct foreign table for au_pub_id");
is_deeply( {$tobj->ankh('seq_sample.ssam_second_receptor')}, 
{'seq_sample.ssam_second_receptor' => {'ankey'=>'coreceptor','antype'=>'Virus'}}, "correct annotation key hash");


#Query parser tests

#methods
can_ok($Q, qw(
              requests
              put_requests
              isnull
              A
              len
              clone
              ));
can_ok($r, qw(
              atoms
              put_atoms
              del_atoms
              fields
              isnull
              A
              len
              clone
              ));
can_ok($q, qw(
              fld
              dta
              A
              clone
              ));
# operations tests
ok($Q->isnull, "null QRY");
ok($r->isnull, "null R (request object)");
ok($q->isnull, "null Q (atomic query object)");

my ($R1, $R2);
ok($R1 = new R( new Q('X', 'a b c') ), "R obj create and init (1)");
ok($R2 = new R( new Q('X', 'a'), new Q('Y', 'u v w') ), "R obj create and init (2)");
ok(R::In($R2, $R1), "R::In");
ok(!R::In($R1, $R2), "!R::In");
ok(R::Eq($R1, $R1->clone), "R::Eq");
my ($Q1, $Q2, $Q3);
ok($Q1 = new QRY( $R1 ), "QRY obj create and init (1)");
ok($Q2 = new QRY( $R2 ), "QRY obj create and init (2)");
ok($Q3 = new QRY( new R( new Q('X', 'a'), new Q('Y', 'w v u'))), "QRY obj create and init (3)");

ok(QRY::Eq($Q1 | $Q1, $Q1), "QRY overload |");
ok(QRY::Eq($Q1 & $Q1,$Q1), "QRY overload &");
ok(QRY::Eq($Q1 & $Q2, $Q3), "QRY nontrivial &"); 

# parse and make query tests

my $pt;
ok($pt=QRY::_parse_q("('odds bodkins', a)[X] m[Y] u[Z] OR 'b'[X] {A B [C] [D]}"), "parse: ('odds bodkins', a)[X] m[Y] u[Z] OR 'b'[X] {A B [C] [D]} ");
is(scalar QRY::_make_q($pt), 2, "make: 2 queries returned");
is_deeply((QRY::_make_q($pt))[0]->{annot}, ['A','B','C','D'], "{annotation fields} parsed correctly");
ok($pt=QRY::_parse_q("('odds bodkins', a)[X] m[Y] u[Z] AND b[X] {A B [C] [D]}"), "parse: ('odds bodkins', a)[X] m[Y] u[Z] AND b[X] {A B [C] [D]} ");
is_deeply((QRY::_make_q($pt))[0],{}, "above query is null");


BioPerl-1.007002/t/RemoteDB/Query000755000766000024          013155576321 16370 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/RemoteDB/Query/GenBank.t000555000766000024       543513155576321 20231 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 18,
			   -requires_modules => [qw(IO::String
									    LWP::UserAgent
										HTTP::Request::Common)],
			   -requires_networking => 1);
	
	use_ok('Bio::DB::Query::GenBank');
	use_ok('Bio::DB::GenBank');
}

my %expected_lengths = (
                        'MUSIGHBA1' => 408,  
                        'AF303112'  => 1611, 
                        'AF041456'  => 1156, 
                        'AY080910'  => 798,  
                        'AY080909'  => 1042, 
                        'AF155220'  => 1172, 
                        'AF442768'  => 2547, 
                        );

my ($gb, $seq, $seqio, $seqin, $query);

# test query facility
ok $query = Bio::DB::Query::GenBank->new('-db'      => 'nucleotide',
                                         '-query'   => 'Onchocerca volvulus[Organism]',
                                         '-mindate' => '2002/1/1',
                                         '-maxdate' => '2002/12/31'), 'Bio::DB::Query::GenBank';
SKIP: {
    cmp_ok $query->count, '>', 0;
    my @ids = $query->ids;
    cmp_ok @ids, '>', 0;
    is @ids, $query->count;
    ok $gb = Bio::DB::GenBank->new('-delay' => 0);
    eval {$seqio = $gb->get_Stream_by_query($query);};
    skip "Couldn't connect to complete GenBank query tests. Skipping those tests", 5 if $@;
    my $done = 0;
    while (my $s = $seqio->next_seq) {
        is $s->length, $expected_lengths{$s->display_id}, $s->display_id;
        undef $gb; # test the case where the db is gone, 
        # but the pipeline should remain until seqio goes away
        $done++;
    }
    skip('No seqs returned', 5) if !$done;
    is $done, 1;
}

$seq = $seqio = undef;

# test query facility (again)
ok $query = Bio::DB::Query::GenBank->new('-db'  => 'nucleotide',
                                         '-ids' => [qw(J00522 AF303112 2981014)]);
SKIP: {
    cmp_ok $query->count, '>', 0;
    my @ids = $query->ids;
    cmp_ok @ids, '>', 0;
    is @ids, $query->count;
    $gb = Bio::DB::GenBank->new('-delay' => 0);
    eval {$seqio = $gb->get_Stream_by_query($query);};
    skip "Couldn't connect to complete GenBank query tests. Skipping those tests: $@", 4 if $@;
    my $done = 0;
    while (my $s = $seqio->next_seq) {
        is $s->length, $expected_lengths{$s->display_id}, $s->display_id;
        $done++;
    }
    skip('No seqs returned', 4) if !$done;
    is $done, 3;
    $seqio->close(); # the key to preventing errors during make test, no idea why
}

$seq = $seqio = undef;

# and yet again, for bug 2133
$query = Bio::DB::Query::GenBank->new('-query'  => 'AF303112',
                                      '-ids' => [qw(J00522 AF303112 2981014)]);
is $query->query, 'J00522[PACC]|AF303112[PACC]|2981014[UID]';
BioPerl-1.007002/t/Restriction000755000766000024          013155576321 16127 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Restriction/Analysis-refac.t000555000766000024      2144013155576321 21336 0ustar00cjfieldsstaff000000000000#-*-perl-*-
# $Id$
use strict;
use warnings;
use Bio::Root::Test;
use Bio::PrimarySeq;

use lib '.';

test_begin(-tests => 91);

use_ok( 'Bio::Restriction::IO' );
use_ok( 'Bio::Restriction::Analysis' );
use_ok('Bio::Restriction::EnzymeCollection');
use_ok('Bio::Restriction::Enzyme');

# recog sites (not nec. cut sites!) in lc

my $seq = new Bio::PrimarySeq(
     -seq        => 'gtcGaagcttAGCAAACGGTTTCTACgacgttatcgtcATTCGGGgcaagcgTCGGCGATTCGGACGTGcacctgcAAAtGCGCGGCgTTAgcgaggtgGCGAgacttttatgtcCCCCTgaagcggttattggTTATATGGTGTTCGTgaccgaTCTAATCCATATTTATTTTTGGCAGTGCtgggtgTTACgacTCGCGA',
     -primary_id => 'test',
     -molecule   => 'dna'
);

# the test enzymes [rebase characterization]: 
# nonambig intrasite cutter: HindIII  [ A^AGCTT        ]
#    ambig intrasite cutter: AasI     [ GACNNNN^NNGTC  ]
# nonambig extrasite cutter: AarI     [ CACCTGC(4/8)   ]
#    ambig extrasite cutter: BceSI    [ SSAAGCG(27/27) ]
#    ambig center    cutter: AjuI     [ (7/12)GAANNNNNNNTTGG(11/6) ]
#    multi extrasite cutter: TaqII    [ GACCGA(11/9),CACCCA(11/9) ]

# the test sequence *cut* (not site) map (recog sites in lc)

#+    AasI(circ)
#+         HindIII                     AasI                      
# 1   CTCGaagcttAGCAAACGGTTTCTACgacgttatcgtcATTCGGGgcaagcgTCGGCGAT  60
#-      IIIdniH                  IsaA      


#+                       BceSI                             AjuI 
#+                       AarI                          AasI
# 61  TCGGACGTGcacctgcAAATGCGCGGCgTTAgcgaggtgGCGAgacttttatgtcCCCCT 120
#-                        IraA                    IsaA            
#-                  ISecB                         IujA      

#+                                                         IIqaT         
#+                             AjuI                TaqII             
# 121 gaagcggttattggTTATATGGTGTTCGTgaccgaTCTAATCCATATTTATTTTTGGCAG 180
#-                    IujA                  IIqaT                 
#-                                                  TaqII          

#+                          
# 181 TGCtgggtgTTACgacTCGCGA 202 
#-              (cric)IsaA   

# so we have +/- cut sites (tpi's, not nt's), in positive strand 
# coordinates:
# HindIII : (5, 9)
# AasI    : (33, 31), (110,108)
# AasI    : (200,202=0) when circularized
# BceSI   : (79, 79)
# AarI    : (80, 84)
# AjuI    : (145, 140) / (113, 108)
# TaqII   : (166, 164) / (174, 172)

ok( my $rebase_io = Bio::Restriction::IO->new(
     -file   => test_input_file('withrefm.906'),
     -format => 'withrefm',
    ), 'read withrefm file');

ok( my $rebase_cln = $rebase_io->read, 'parse withrefm file');

# examples
# ambiguous, nonamibiguous X intrasite, extrasite
ok( my $ninz = $rebase_cln->get_enzyme('HindIII'), 'HindIII: nonambiguous intrasite cutter');
ok( my $nexz = $rebase_cln->get_enzyme('AarI'), 'AarI: nonambiguous extrasite cutter');
ok( my $ainz = $rebase_cln->get_enzyme('AasI'), 'AasI: ambiguous intrasite cutter' );
ok( my $aexz = $rebase_cln->get_enzyme('BceSI'), 'BceSI: ambiguous extrasite cutter' );
# central recognition site: (s/t)[site](m/n)
ok( my $cenz = $rebase_cln->get_enzyme('AjuI'), 'AjuI: cutter with central recog site');
# multisite extrasite:
ok (my $menz = $rebase_cln->get_enzyme('TaqII'), 'TaqII: multi-extrasite cutter');

ok (my $examples = Bio::Restriction::EnzymeCollection->new(
	-enzymes=>[$ninz,$ainz, $ainz, $aexz, $cenz, $menz]
    ) );


# build pretend analysis object to test internals

my $an = {};
bless($an, 'Bio::Restriction::Analysis');
$an->seq($seq);

my ($plus_sites, $minus_sites);
# intrasite cutters

$plus_sites = $an->_make_cuts( $seq->seq, $ninz );
$minus_sites = $an->_make_cuts( $seq->seq, $ninz,'COMP' );
is_deeply( $plus_sites, [5], 'HindIII plus');
is_deeply( $minus_sites, [9], 'HindIII minus');

$plus_sites = $an->_make_cuts(  $seq->seq, $ainz );
$minus_sites = $an->_make_cuts( $seq->seq, $ainz,'COMP' );
is_deeply( $plus_sites, [33, 110], 'AasI plus');
is_deeply( $minus_sites, [31, 108], 'AasI  minus');

# extrasite cutters

$plus_sites = $an->_make_cuts( $seq->seq, $nexz );
$minus_sites = $an->_make_cuts( $seq->seq, $nexz, 'COMP');
is_deeply( $plus_sites, [80], 'AarI plus');
is_deeply( $minus_sites, [84], 'AarI  minus');

$plus_sites = $an->_make_cuts( $seq->seq, $aexz );
$minus_sites = $an->_make_cuts( $seq->seq, $aexz, 'COMP');
is_deeply( $plus_sites, [79], 'BceSI plus');
is_deeply( $minus_sites, [79], 'BceSI  minus');

# central site cutter
$plus_sites = $an->_make_cuts( $seq->seq, $cenz );
$minus_sites = $an->_make_cuts( $seq->seq, $cenz, 'COMP');

is_deeply( $plus_sites, [145, 113], 'AjuI plus');
is_deeply( $minus_sites, [140, 108], 'AjuI minus');

# multisite extrasite cutter
$plus_sites =  $an->_make_cuts( $seq->seq, $menz );
$minus_sites =  $an->_make_cuts( $seq->seq, $menz, 'COMP' );

is_deeply( $plus_sites, [166, 174], 'TaqII plus');
is_deeply( $minus_sites, [164, 172], 'TaqII minus');

# real Analysis object
# start restriction analysis
ok( my $analysis = Bio::Restriction::Analysis->new(
     -seq     => $seq,
     -enzymes => $rebase_cln
    ), "build real B:R::Analysis object");

# retrieve fragment map
my @fm = $analysis->fragment_maps($examples);
is( @fm, 13, '13 fragments');
# circularize
ok( $seq->is_circular(1), 'circularize');
ok( $analysis->cut, 'recut');
@fm = $analysis->fragment_maps($examples);
is_deeply( [$analysis->positions('AasI')], [33, 110, 200], 'circ: AasI
site at origin' );
is( @fm, 13, 'circ: still 13 fragments (cut site at origin)');


# Emmanuel's tests / bug3015

use_ok('Bio::Restriction::IO');
use_ok('Bio::Restriction::Analysis');

#ATGAGCGCTcacgtcACTAG^TTCTAGAGcctcagcAATTC^CGATCccgctcGATTAATGC^TccgcAGCAGCGATATCGAG^CATGGTCATGAgaatgcGGC^ATCGATCGGCATTATATcacgtcAATCGCGTCGCTGCATGCTAGCG
$seq = new Bio::PrimarySeq(
     -seq        => 'ATGAGCGCTcacgtcACTAGTTCTAGAGcctcagcAATTCCGATCccgctcGATTAATGCTccgcAGCAGCGATATCGAGCATGGTCATGAgaatgcGGCATCGATCGGCATTATATcacgtcAATCGCGTCGCTGCATGCTAGCG',
     -primary_id => 'test1',
     -molecule   => 'dna'
);

ok( $rebase_io = Bio::Restriction::IO->new(
     -file   => test_input_file('withrefm.906'),
     -format => 'withrefm',
    ), 'read withrefm file');

ok( $rebase_cln = $rebase_io->read, 'parse withrefm file');

my @enzs = qw/AbeI AccBSI AciI Asp26HI BmgBI/;

# Get the enzymes with back cut site
# 'AbeI'    CCTCAGC(-5/-2) #1
# 'AccBSI'  CCGCTC(-3/-3)  #1
# 'AciI'    CCGC(-3/-1)    #2
# 'Asp26HI' GAATGC(1/-1)   #1
# 'BmgBI'   CACGTC(-3/-3)  #2

ok(my $collection = Bio::Restriction::EnzymeCollection->new(-empty => 1), "Collection initiated");

foreach my $e (@enzs){

    ok(my $enz = $rebase_cln->get_enzyme($e), "$e: found ok into collection");
    $collection->enzymes($enz);
}

$an = { };
bless($an, 'Bio::Restriction::Analysis');
$an->seq($seq);
$an->enzymes($collection);

#Test all types of stuff from the enzyme
my $data = {
   'AbeI'    => { 'p' => [23],
                  'm' => [26],
                  'pos' => 2,
                  'f' => 3,
                  'o' => "5'",
                  's' => 'CC^TCAGC',
                  'r' => 'GCTGAGG',
                  'c' => '-5',
                  'rc' => '-2' },

   'AccBSI'  => { 'p' => [42],
                  'm' => [42],
                  'pos' => 1,
                  'f' => 2,
                  'o' => "blunt",
                  's' => 'CCG^CTC',
                  'r' => 'GAGCGG',
                  'c' => '-3',
                  'rc' => '-3' },

   'AciI'    => { 'p' => [42,58,100],
                  'm' => [44,60,102],
                  'pos' => 6,
                  'f' => 7,
                  'o' => "5'",
                  's' => 'C^CGC',
                  'r' => 'GCGG',
                  'c' => '-3',
                  'rc' => '-1' },

   'Asp26HI' => { 'p' => [98],
                  'm' => [90],
                  'pos' => 1,
                  'f' => 2,
                  'o' => "3'",
                  's' => 'GAATGC',
                  'r' => 'GCATTC',
                  'c' => 7,
                  'rc' => '-1' },

   'BmgBI'   => { 'p' => [6, 114],
                  'm' => [6, 114],
                  'pos' => 2,
                  'f' => 3,
                  'o' => "blunt",
                  's' => 'CAC^GTC',
                  'r' => 'GACGTG',
                  'c' => '-3',
                  'rc' => '-3' },
};

foreach my $e (@enzs){

   my $d = $data->{$e};
   my $z = $rebase_cln->get_enzyme($e);
   my $minus_sites = $an->_make_cuts($seq->seq, $z, 'COMP');
   my $plus_sites  = $an->_make_cuts($seq->seq, $z);

   is_deeply($plus_sites,  $d->{p}, "$e plus");
   is_deeply($minus_sites, $d->{m}, "$e minus");

   ok(scalar($an->fragments($z)) eq $d->{f}, "$e fragment");
   ok(scalar($an->positions($e)) eq $d->{pos}, "$e positions");

   is($z->overhang(), $d->{'o'}, "$e Overhang");
   is($z->name(), "$e", "$e name");
   is($z->site(), $d->{s}, "$e site");
   is($z->revcom_site(), $d->{r}, "$e revcom_site");
   is($z->cut(), $d->{c}, "$e cut");
   is($z->complementary_cut(), $d->{rc}, "$e complementary_cut");
}

BioPerl-1.007002/t/Restriction/Analysis.t000444000766000024      2201513155576321 20254 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$


use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 182);
	
    use_ok('Bio::Restriction::Enzyme');
    use_ok('Bio::Restriction::Enzyme::MultiCut');
    use_ok('Bio::Restriction::Enzyme::MultiSite');
    use_ok('Bio::Restriction::EnzymeCollection');
    use_ok('Bio::Restriction::Analysis');
    use_ok('Bio::SeqIO');
}

#
# Bio::Restriction::Enzyme
#

my ($re, $seq, $iso, %meth, $microbe, $source, @vendors, @refs, $name);
ok $re=Bio::Restriction::Enzyme->new(-enzyme=>'EcoRI', -site=>'G^AATTC');
isa_ok($re, 'Bio::Restriction::EnzymeI');
is $re->cut, 1;
ok ! $re->cut(0);
is $re->complementary_cut, 6;
ok $re->cut(1);

is $re->complementary_cut,5;
is $re->site,'G^AATTC';
ok $seq = $re->seq;
isa_ok($seq, 'Bio::PrimarySeqI');
is $seq->seq, 'GAATTC';
is $re->string,'GAATTC';
is $re->revcom, 'GAATTC';
is $re->recognition_length, 6;
is $re->cutter, 6;
is $re->palindromic, 1;
is $re->overhang, "5'";
is $re->overhang_seq, 'AATT';
is $re->is_ambiguous, 0;

ok $re->compatible_ends($re);

ok $re->isoschizomers('BamHI', 'AvaI'); # not really true :)

is my @isos=$re->isoschizomers, 2;
is $isos[0],'BamHI';
ok $re->purge_isoschizomers;
is scalar($re->isoschizomers), 0;
ok $re->methylation_sites(2,5); # not really true :)
ok %meth = $re->methylation_sites;
is $meth{2}, 5;
ok $re->purge_methylation_sites;
is scalar($re->methylation_sites), 0;


ok $re->microbe('E. coli');
ok $microbe = $re->microbe;
is $microbe, "E. coli";
ok $re->source("Rob"); # not really true :)

ok $source = $re->source;
is $source, "Rob";

ok !$re->vendor;
ok $re->vendors('NEB'); # my favorite
ok @vendors = $re->vendors;
is $vendors[0], "NEB";
$re->purge_vendors;
is scalar($re->vendors), 0;

ok $re->references('Rob et al');
ok @refs = $re->references;
is $refs[0], "Rob et al";
$re->purge_references;
is scalar($re->references), 0;

ok $re->name('BamHI');
ok $name = $re->name;
is $name, "BamHI";

$re->verbose(2);

eval {$re->is_prototype};
ok($@);
like($@, qr/Can't unequivocally assign prototype based on input format alone/, 'bug 2179');
$re->verbose(2);

is $re->is_prototype(0), 0;
is $re->is_prototype, 0;
is $re->is_prototype(1), 1;
is $re->is_prototype, 1;

is $re->prototype_name, $re->name;
ok ! $re->is_prototype(0);
is $re->prototype_name('XxxI'), 'XxxI';
is $re->prototype_name, 'XxxI';


is $re->cutter, 6;
ok $re->seq->seq('RCATGY');
is $re->cutter, 5;

ok my $re2 = $re->clone;
isnt $re, $re2;
is $re->name, $re2->name;

ok $re = Bio::Restriction::Enzyme->new(-enzyme=>'AciI', 
										-site=>'C^CGC');
is $re->palindromic, 0;
is $re->is_palindromic, 0;

#
# Bio::Restriction::Enzyme::MultiSite
#

ok $re=Bio::Restriction::Enzyme::MultiSite->new(-enzyme=>'TaqII',
                                              -site=>'GACCGA',
                                              -cut=>17,
                                              -complementary_cut=>15
                                             );
ok $re2=Bio::Restriction::Enzyme::MultiSite->new(-enzyme=>'TaqII',
                                                -site=>'CACCCA',
                                                -cut=>17,
                                                -complementary_cut=>15
                                               );
isa_ok( $re, 'Bio::Restriction::EnzymeI');
isa_ok( $re2, 'Bio::Restriction::EnzymeI');
ok $re->others($re2);
ok $re2->others($re);

is $re->others, 1;
is $re2->others, 1;

ok my $re3 = $re->clone;
isnt $re, $re3;
is $re->name , $re3->name; # wouldn't this be a circular reference???
#print Dumper $re, $re3;exit;

#
# Bio::Restriction::Enzyme::MultiCut
#
#Hin4I has four cut sites [(8/13)GAYNNNNNVTC(13/8)],

ok $re = Bio::Restriction::Enzyme::MultiCut->new(-enzyme=>'Hin4I',
                                              -site=>'GAYNNNNNVTC',
                                              -cut=>-8,
                                              -complementary_cut=>-13
                                             );
ok $re2 = Bio::Restriction::Enzyme::MultiCut->new(-enzyme=>'Hin4I',
                                               -site=>'GAYNNNNNVTC',
                                               -cut=>13,
                                               -complementary_cut=>8
                                              );
isa_ok($re, 'Bio::Restriction::EnzymeI');
isa_ok($re2, 'Bio::Restriction::EnzymeI');
ok $re->others($re2);
ok $re2->others($re);

ok $re3 = $re->clone;
isnt $re, $re3;
is $re->name, $re3->name;
#print Dumper $re, $re3;exit;

#
# Bio::Restriction::EnzymeCollection
#

my ($collection, $enz, $new_set);

ok $collection = Bio::Restriction::EnzymeCollection->new(-empty=>1);
is $collection->each_enzyme, 0;
# default set
$collection = Bio::Restriction::EnzymeCollection->new;
is $collection->each_enzyme, 532;
is $collection->each_enzyme, 532;

ok $enz = $collection->get_enzyme('AclI');
isa_ok($enz, 'Bio::Restriction::Enzyme');
is my @enzymes=$collection->available_list, 532;

ok $new_set = $collection->blunt_enzymes;
isa_ok($enz, 'Bio::Restriction::Enzyme');
is $new_set->each_enzyme, 114;

#map {print $_->name, ": ", $_->cutter, "\n"; } $collection->each_enzyme;

ok $new_set = $collection->cutters(8);
is $new_set->each_enzyme, 17;

ok $new_set=$collection->cutters(-start => 8, -end => 8);
is $new_set->each_enzyme, 17;

ok $new_set=$collection->cutters(-start => 6, -end => 8);
is $new_set->each_enzyme, 293;

ok $new_set=$collection->cutters(-start => 6, -end => 8,  -exclusive => 1);
is $new_set->each_enzyme, 10;

ok $new_set = $collection->cutters([4,8]);
is $new_set->each_enzyme, 129;

# bug 2128; enhancement request to pass array ref of sizes

#
# Restriction::Analysis
#


ok my $seqio=Bio::SeqIO->new(-file=>test_input_file('dna1.fa'),
                         -format=>'fasta');
ok $seq=$seqio->next_seq;

ok my $ra = Bio::Restriction::Analysis->new(-seq=>$seq);
ok my $uniq = $ra->unique_cutters;

# test most objects
is $ra->unique_cutters->each_enzyme, 42, 'number of unique cutters';
is $ra->fragments('RsaI'), 2, 'number of RsaI fragments';
is $ra->max_cuts, 9, 'number of maximum cutters';
is $ra->zero_cutters->each_enzyme, 477, 'number of zero cutters';
is $ra->cutters->each_enzyme, 55, 'number of cutters';
is $ra->cutters(3)->each_enzyme, 8, 'number of 3x cutters';
is $ra->fragments('MseI'), 4, '4 MseI fragments';
is $ra->cuts_by_enzyme('MseI'), 3, '3 MseI cut sites';

#my $z = $ra->cutters(3);
#my $out=Bio::Restriction::IO->new;
#$out->write($z);


is $ra->fragments('PspEI'), 2, 'expected 2 PspEI fragments';
is $ra->cuts_by_enzyme('PspEI'), 1;
is $ra->cuts_by_enzyme('XxxI'), undef;


is my @ss = $ra->sizes('PspEI'), 2, 'expected 2 sizes for PspEI';
is $ss[0] + $ss[1], $seq->length;

# Issue 3157
$re = Bio::Restriction::Enzyme->new(-enzyme=>'PspEI', -site=>'G^GTNACC');
is @ss = $ra->sizes($re), 2, 'expected 2 sizes for PspEI';
is $ss[0] + $ss[1], $seq->length;

is $ra->fragments('MwoI'), 1, 'not circular expected 1 fragments for MwoI as it doesnt cut';

# circularise the sequence, regenerate the cuts and test again
# note that there is one less fragment now!
ok $seq->is_circular(1);

# we need to regenerate all the cuts
ok $ra->cut;

is $ra->fragments('RsaI'), 1, 'number of RsaI fragments';
is $ra->fragments('MseI'), 3, '3 circular MseI fragments';
is $ra->cuts_by_enzyme('MseI'), 3, '3 circular MseI cut sites';
is $ra->fragments('AciI'), 1, 'number for AciI a non-palindromic enzyme';

is $ra->fragments('MwoI'), 1, '1 fragment for MwoI as it cuts across the circ point';

ok my @rb=($collection->get_enzyme("AluI"), $collection->get_enzyme("MseI"), $collection->get_enzyme("MaeIII"));

# test multiple digests
ok my $rbc=Bio::Restriction::EnzymeCollection->new(-empty=>1);
ok $rbc->enzymes(@rb);
ok $ra->cut('multiple', $rbc);
is $ra->fragments('multiple_digest'),7, '7 fragments in the multiple digest';
is my @pos=$ra->positions('multiple_digest'),7, '7 positions in the multiple digest';
is my @ssm = $ra->sizes('multiple_digest'),7, '7 sizes in the multiple digest';
my $check_len;
map {$check_len+=$_}@ssm;
is $check_len, $seq->length;

# now test the non-palindromic part
# HindI is a non palindromic enzyme that cuts 9 times
is $ra->positions('HindI'), 9, ' expected 9 cuts for HindI';

# now we need to test the fragment maps
# lets do this for HindI
is my @fm=$ra->fragment_maps('HindI'), 9, 'expect 9 fragment maps for HindI';
foreach my $fm (@fm) {
 is exists $fm->{'seq'}, 1, "sequence for ".$fm->{'seq'};
 is exists $fm->{'start'}, 1, "start at ".$fm->{'start'};
 is exists $fm->{'end'}, 1, "end at ".$fm->{'end'};
}

# bug 2139

eval {$re = Bio::Restriction::Enzyme->new(
        -name    => 'Invalid',
        -site    => 'G^AATTE' );};

ok $@;
like($@, qr(Unrecognized characters in site), 'bug 2139');

# 0-pos bug (Elia Stupka)

$seq = Bio::Seq->new(
    -display_name   => 'foo',
    -alphabet       => 'dna',
    -seq            => 'GATCNNNNGATC'
);

$ra = Bio::Restriction::Analysis->new(-seq=>$seq);

is $ra->fragments('HindIII'), 1, 'number of HindIII fragments';
is $ra->fragments('BfuCI'), 2, 'number of EcoRI fragments';

# passing a bad enzyme name

is $ra->fragments('FooBarI'), 1, 'number of RsaI fragments';


BioPerl-1.007002/t/Restriction/Gel.t000444000766000024       145213155576321 17162 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 9);
	
    use_ok('Bio::PrimarySeq');
    use_ok('Bio::Restriction::Analysis');
    use_ok('Bio::Tools::Gel');
}

my $seq1 = Bio::PrimarySeq->new(-id=>'groundhog day',
                                -seq=>'AAAAAAAAAGAATTCTTTTTTTTTTTTTTGAATTCGGGGGGGGGGGGGGGGGGGG');

my $ra=Bio::Restriction::Analysis->new(-seq=>$seq1);
is my @cuts = $ra->fragments('EcoRI'), 3;

ok my $gel = Bio::Tools::Gel->new(-seq=>\@cuts,-dilate=>10);
ok my %bands = $gel->bands;
my @bands = (26, 27, 30);
my $c = 0;
foreach my $band (sort {$b <=> $a} keys %bands){
    #print $band,"\t",  sprintf("%.1f", $bands{$band}), "\n";
    is $bands[$c],  sprintf("%.0f", $bands{$band});
    $c++;
}
BioPerl-1.007002/t/Restriction/IO.t000444000766000024       353313155576321 16764 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin( -tests => 17 );

    use_ok('Bio::Restriction::IO');
}

#
# default enz set
#
ok my $in    = Bio::Restriction::IO->new();
ok my $renzs = $in->read;
is $renzs->each_enzyme, 532;

ok my $e = $renzs->get_enzyme('AccI');
is $e->name, 'AccI';

my $outfile = test_output_file();
ok my $out = Bio::Restriction::IO->new( -format => 'base', -file => ">$outfile" );
TODO: {
    local $TODO = "writing to a file doesn't seem to work? prints to STDOUT!";

    #$out->write($renzs);
    # ok -s $outfile;
    #map {print $_->name, "\t", $_->site, "\t", $_->overhang, "\n"} $renzs->each_enzyme;
}

#
# withrefm, 31
#

ok $in = Bio::Restriction::IO->new(
    -format  => 'withrefm',
    -verbose => 0,
    -file    => test_input_file('rebase.withrefm')
);
ok $renzs = $in->read;
is $renzs->each_enzyme, 11;

#
# itype2, 8
#
#enzyme name [tab] prototype [tab] recognition sequence with cleavage site
#  [tab] methylation site and type [tab] commercial source [tab] references

ok $in = Bio::Restriction::IO->new(
    -format  => 'itype2',
    -verbose => 0,
    -file    => test_input_file('rebase.itype2')
);

ok $renzs = $in->read;
is $renzs->each_enzyme, 16;

ok $out = Bio::Restriction::IO->new( -format => 'base' );

SKIP: {
    test_skip(
        -tests               => 3,
        -requires_module     => 'LWP::UserAgent',
        -requires_networking => 1
    );

    eval {$in = Bio::Restriction::IO->new(-format  => 'prototype',
                                          -current => 1); };
    skip "Couldn't connect to REBASE with Bio::Restriction::IO. Skipping those tests", 3 if $@;

    ok $in = Bio::Restriction::IO->new(
        -format  => 'prototype',
        -current => 1
    );

    ok my $coll = $in->read;
    cmp_ok $coll->each_enzyme, '>=', 307;
}
BioPerl-1.007002/t/Root000755000766000024          013155576321 14545 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Root/Exception.t000444000766000024       277013155576321 17033 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;

BEGIN {
    eval {require Error;};

    use lib qw( . t/lib );
    use Bio::Root::Test;

    test_begin(-tests => 7,
               -requires_module => 'Error');

    use_ok('Bio::Root::TestObject');
}

use Error qw(:try);
$Error::Debug = test_debug();

# Set up a tester object.
ok my $test = Bio::Root::TestObject->new(-verbose => test_debug());

is $test->data('Eeny meeny miney moe.'), 'Eeny meeny miney moe.';

# This demonstrates what will happen if a method defined in an
# interface that is not implemented in the implementating object.

eval {
    try {
        $test->foo();
    }
    catch Bio::Root::NotImplemented with {
        my $err = shift;
        is ref $err, 'Bio::Root::NotImplemented';
    };
};

# TestObject::bar() deliberately throws a Bio::TestException,
# which is defined in TestObject.pm
try {
    $test->bar;
}
catch Bio::TestException with {
    my $err = shift;
    is ref $err, 'Bio::TestException';
};


# Use the non-object-oriented syntax to throw a generic Bio::Root::Exception.
try {
    throw Bio::Root::Exception( "A generic error", 42 );
}
catch Bio::Root::Exception with {
    my $err = shift;
    is ref $err, 'Bio::Root::Exception';
    is $err->value, 42;
};

# Try to call a subroutine that doesn't exist. But because it occurs
# within a try block, the Error module will create a Error::Simple to
# capture it. Handy eh?

try {
    $test->foobar();
}
otherwise {
    my $err = shift;
    is ref $err, 'Error::Simple';
};
BioPerl-1.007002/t/Root/HTTPget.t000444000766000024       552113155576321 16351 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;
use warnings;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 29,
	       -requires_networking => 1);
	
    use_ok('Bio::Root::HTTPget');
}

my $TESTURL = 'http://www.google.com/index.html';

my $TEST_PROXY = 'http://myproxy';

my @TEST_AUTHENTICATION = qw(foo bar);

my ($fh, $proxy);

my @auth;

=head1 Bio::Root::HTTPget comments

This module is a bit schizophrenic in that it is called in three different
ways; as an instance method, a class method, or as an explicit subroutine.

These tests check for all call types.  They are by no means incomplete.

=cut 

# test object method calls
my $obj = Bio::Root::HTTPget->new();

ok defined($obj) && $obj->isa('Bio::Root::Root');

lives_ok {$obj->get($TESTURL)};
lives_ok {$fh = $obj->getFH($TESTURL)};
isa_ok($fh, 'IO::Socket::INET');

undef($fh);

is ($obj->proxy(), undef);
is_deeply([$obj->authentication], []);
$obj->proxy('http', $TEST_PROXY);
$obj->authentication(@TEST_AUTHENTICATION);
is ($obj->proxy(), $TEST_PROXY);
is_deeply([$obj->authentication], \@TEST_AUTHENTICATION);

# test class method calls; note that mixing class and sub calls pollutes the
# class attributes

lives_ok {Bio::Root::HTTPget->get($TESTURL)};
lives_ok {$fh = Bio::Root::HTTPget->getFH($TESTURL)};
isa_ok($fh, 'IO::Socket::INET');

undef($fh);

is (Bio::Root::HTTPget->proxy(), undef);
is_deeply([Bio::Root::HTTPget->authentication], []);
Bio::Root::HTTPget->proxy('http', $TEST_PROXY);
Bio::Root::HTTPget->authentication(@TEST_AUTHENTICATION);
is (Bio::Root::HTTPget->proxy('http'), $TEST_PROXY);
is_deeply([Bio::Root::HTTPget->authentication], \@TEST_AUTHENTICATION);

# test sub calls (not called as method)

lives_ok {Bio::Root::HTTPget::get($TESTURL)};
lives_ok {$fh = Bio::Root::HTTPget::getFH($TESTURL)};
isa_ok($fh, 'IO::Socket::INET');

undef($fh);

# note that mixing class and sub calls pollutes the class attributes, have to
# manually reset
Bio::Root::HTTPget->authentication(undef, undef);

my $old = Bio::Root::HTTPget->clear_proxy('http');
is (Bio::Root::HTTPget::proxy(), undef);
is ($old, $TEST_PROXY);

is_deeply([Bio::Root::HTTPget->authentication], [undef, undef]);
Bio::Root::HTTPget::proxy('http', $TEST_PROXY);
Bio::Root::HTTPget::authentication(@TEST_AUTHENTICATION);
is (Bio::Root::HTTPget::proxy('http'), $TEST_PROXY);
is_deeply([Bio::Root::HTTPget->authentication], \@TEST_AUTHENTICATION);

# check to make sure new instance attributes are not polluted by class attrbutes
# from previous tests

my $newobj = Bio::Root::HTTPget->new();

ok defined($newobj) && $obj->isa('Bio::Root::Root');

is ($newobj->proxy(), undef);
is_deeply([$newobj->authentication], []);
$newobj->proxy('http', $TEST_PROXY);
$newobj->authentication(@TEST_AUTHENTICATION);
is ($newobj->proxy(), $TEST_PROXY);
is_deeply([$newobj->authentication], \@TEST_AUTHENTICATION);
BioPerl-1.007002/t/Root/IO.t000444000766000024      3315213155576321 15422 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;
use warnings;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    test_begin(-tests => 154);
    use_ok 'Bio::Root::IO';
}


ok my $obj = Bio::Root::IO->new();
isa_ok $obj, 'Bio::Root::IO';


#############################################
# tests for exceptions/debugging/verbosity
#############################################

throws_ok { $obj->throw('Testing throw') } qr/Testing throw/, 'Throw';

$obj->verbose(-1);
throws_ok { $obj->throw('Testing throw') } qr/Testing throw/;

eval { $obj->warn('Testing warn') };
ok !$@, 'Warn';

$obj->verbose(1);
throws_ok { $obj->throw('Testing throw') } qr/Testing throw/;

ok my @stack = $obj->stack_trace(), 'Stack trace';
is scalar @stack, 2;

ok my $verbobj = Bio::Root::IO->new( -verbose => 1, -strict => 1 ), 'Verbosity';
is $verbobj->verbose(), 1;

ok $obj->verbose(-1);


#############################################
# tests for finding executables
#############################################

ok my $io = Bio::Root::IO->new();

# An executable file
my $out_file = 'test_file.txt';
my $out_fh;
open  $out_fh, '>', $out_file or die "Could not write file '$out_file': $!\n";
print $out_fh 'test';
close $out_fh;
# -X test file will fail in Windows regardless of chmod,
# because it looks for the executable suffix (like ".exe")
if ($^O =~ m/mswin/i) {
    # An executable file
    my $exec_file = 'test_exec.exe';
    open my $exe_fh, '>', $exec_file or die "Could not write file '$exec_file': $!\n";
    close $exe_fh;
    ok $obj->exists_exe($exec_file), 'executable file';
    unlink $exec_file or die "Could not delete file '$exec_file': $!\n";

    # A not executable file
    ok (! $obj->exists_exe($out_file), 'non-executable file');
    unlink $out_file  or die "Could not delete file '$out_file': $!\n";
}
else {
    # An executable file
    chmod 0777, $out_file or die "Could not change permission of file '$out_file': $!\n";
    ok $obj->exists_exe($out_file), 'executable file';

    # A not executable file
    chmod 0444, $out_file or die "Could not change permission of file '$out_file': $!\n";
    ok (! $obj->exists_exe($out_file), 'non-executable file');
    unlink $out_file or die "Could not delete file '$out_file': $!\n";
}

# An executable dir
my $out_dir = 'test_dir';
mkdir $out_dir or die "Could not write dir '$out_dir': $!\n";
chmod 0777, $out_dir or die "Could not change permission of dir '$out_dir': $!\n";
ok (! $obj->exists_exe($out_dir), 'executable dir');
rmdir $out_dir or die "Could not delete dir '$out_dir': $!\n";


#############################################
# tests for handle read and write abilities
#############################################

# Test catfile

ok my $in_file = Bio::Root::IO->catfile(qw(t data test.waba));
is $in_file, test_input_file('test.waba');

ok my $in_file_2 = Bio::Root::IO->catfile(qw(t data test.txt));

$out_file = test_output_file();


# Test with files

ok my $rio = Bio::Root::IO->new( -input => $in_file ), 'Read from file';
is $rio->file, $in_file;
is_deeply [$rio->cleanfile], [undef, $in_file];
is $rio->mode, 'r';
ok $rio->close;

ok $rio = Bio::Root::IO->new( -file => '<'.$in_file );
is $rio->file, '<'.$in_file;
is_deeply [$rio->cleanfile], ['<', $in_file];
1 while $rio->_readline; # read entire file content
is $rio->mode, 'r';
ok $rio->close;

ok my $wio = Bio::Root::IO->new( -file => ">$out_file" ), 'Write to file';
is $wio->file, ">$out_file";
is_deeply [$wio->cleanfile], ['>', $out_file];
is $wio->mode, 'w';
ok $wio->close;

ok $rio = Bio::Root::IO->new( -file => "+>$out_file" ), 'Read+write to file';
is $rio->file, "+>$out_file";
is_deeply [$rio->cleanfile], ['+>', $out_file];
is $rio->mode, 'rw';
ok $rio->close;


# Test with handles

my $in_fh;
open $in_fh , '<', $in_file  or die "Could not read file '$in_file': $!\n", 'Read from GLOB handle';
ok $rio = Bio::Root::IO->new( -fh => $in_fh );
is $rio->_fh, $in_fh;
is $rio->mode, 'r';
close $in_fh;

open $out_fh, '>', $out_file or die "Could not write file '$out_file': $!\n", 'Write to GLOB handle';
ok $wio = Bio::Root::IO->new( -fh => $out_fh );
is $wio->_fh, $out_fh;
is $wio->mode, 'w';
close $out_fh;

SKIP: {
    eval { require File::Temp; }
       or skip 'could not create File::Temp object, maybe your File::Temp is 10 years old', 4;

    $out_fh = File::Temp->new;
    ok $wio = Bio::Root::IO->new( -fh => $out_fh ), 'Read from File::Temp handle';
    isa_ok $wio, 'Bio::Root::IO';
    is $wio->mode, 'rw', 'is a write handle';
    warnings_like sub { $wio->close }, '', 'no warnings in ->close()';
    ok $wio->close;
}


# Exclusive arguments
open $in_fh , '<', $in_file  or die "Could not read file '$in_file': $!\n", 'Read from GLOB handle';
throws_ok {$rio = Bio::Root::IO->new( -input => $in_file, -fh     => $in_fh     )} qr/Providing both a file and a filehandle for reading/, 'Exclusive arguments';
throws_ok {$rio = Bio::Root::IO->new( -input => $in_file, -file   => $in_file_2 )} qr/Input file given twice/;
throws_ok {$rio = Bio::Root::IO->new( -input => $in_file, -string => 'abcedf'   )} qr/File or filehandle provided with -string/;
throws_ok {$rio = Bio::Root::IO->new( -fh    => $in_fh  , -file   => $in_file   )} qr/Providing both a file and a filehandle for reading/;
throws_ok {$rio = Bio::Root::IO->new( -fh    => $in_fh  , -string => 'abcedf'   )} qr/File or filehandle provided with -string/;
throws_ok {$rio = Bio::Root::IO->new( -file  => $in_file, -string => 'abcedf'   )} qr/File or filehandle provided with -string/;
close $in_fh;

lives_ok  {$rio = Bio::Root::IO->new( -input => $in_file, -file   => $in_file   )} 'Same file';


##############################################
# tests _pushback for multi-line buffering
##############################################

ok $rio = Bio::Root::IO->new( -file => $in_file ), 'Pushback';

ok my $line1 = $rio->_readline;
ok my $line2 = $rio->_readline;

ok $rio->_pushback($line2);
ok $rio->_pushback($line1);

ok my $line3 = $rio->_readline;
ok my $line4 = $rio->_readline;
ok my $line5 = $rio->_readline;

is $line1, $line3;
is $line2, $line4;
isnt $line5, $line4;

ok $rio->close;


##############################################
# test _print and _insert
##############################################

ok my $fio = Bio::Root::IO->new( -file => ">$out_file" );
ok $fio->_print("line 1\n"), '_print';
ok $fio->_print("line 2\n");
ok $fio->_insert("insertion at line 2\n",2), '_insert at middle of file';
ok $fio->_print("line 3\n");
ok $fio->_print("line 4\n");
ok $fio->close;

open my $checkio, '<', $out_file or die "Could not read file '$out_file': $!\n";
my @content = <$checkio>;
close $checkio;
is_deeply \@content, ["line 1\n","insertion at line 2\n","line 2\n","line 3\n","line 4\n"];

ok $fio = Bio::Root::IO->new(-file=>">$out_file");
ok $fio->_insert("insertion at line 1\n",1), '_insert in empty file';
ok $fio->close;

open $checkio, '<', $out_file or die "Could not read file '$out_file': $!\n";
@content = <$checkio>;
close $checkio;
is_deeply \@content, ["insertion at line 1\n"];


##############################################
# test Win vs UNIX line ending
##############################################

{
    ok my $unix_rio = Bio::Root::IO->new(-file => test_input_file('U71225.gb.unix'));
    ok my $win_rio  = Bio::Root::IO->new(-file => test_input_file('U71225.gb.win' ));
    ok my $mac_rio  = Bio::Root::IO->new(-file => test_input_file('U71225.gb.mac' ));

    my $expected = "LOCUS       U71225                  1164 bp    DNA     linear   VRT 27-NOV-2001\n";
    is $unix_rio->_readline, $expected;
    is $win_rio->_readline , $expected;
    like $mac_rio->_readline, qr#^LOCUS.*//\n$#ms;
    # line spans entire file because lines end with "\r" but $/ is "\n"

    $expected = "DEFINITION  Desmognathus quadramaculatus 12S ribosomal RNA gene, partial\n";
    is $unix_rio->_readline, $expected;
    is $win_rio->_readline , $expected;
    is $mac_rio->_readline , undef;

    $expected = "            sequence; tRNA-Val gene, complete sequence; and 16S ribosomal RNA\n";
    is $unix_rio->_readline, $expected;
    is $win_rio->_readline , $expected;
    is $mac_rio->_readline , undef;

    $expected = "            gene, partial sequence, mitochondrial genes for mitochondrial RNAs.\n";
    is $unix_rio->_readline, $expected;
    is $win_rio->_readline , $expected;
    is $mac_rio->_readline , undef;

    $expected = "ACCESSION   U71225\n";
    is $unix_rio->_readline, $expected;
    is $win_rio->_readline , $expected;
    is $mac_rio->_readline , undef;

    # In Windows the "-raw" parameter has no effect, because Perl already discards
    # the '\r' from the line when reading in text mode from the filehandle
    # ($line = <$fh>), and put it back automatically when printing
    if ($^O =~ m/mswin/i) {
        is $win_rio->_readline( -raw => 1) , "VERSION     U71225.1  GI:2804359\n";
    }
    else {
        is $win_rio->_readline( -raw => 1) , "VERSION     U71225.1  GI:2804359\r\n";
    }
    is $win_rio->_readline( -raw => 0) , "KEYWORDS    .\n";
}


##############################################
# test Win vs UNIX line ending using PerlIO::eol
##############################################

SKIP: {
    test_skip(-tests => 20, -requires_module => 'PerlIO::eol');

    local $Bio::Root::IO::HAS_EOL = 1;
    ok my $unix_rio = Bio::Root::IO->new(-file => test_input_file('U71225.gb.unix'));
    ok my $win_rio  = Bio::Root::IO->new(-file => test_input_file('U71225.gb.win' ));
    ok my $mac_rio  = Bio::Root::IO->new(-file => test_input_file('U71225.gb.mac' ));

    my $expected = "LOCUS       U71225                  1164 bp    DNA     linear   VRT 27-NOV-2001\n";
    is $unix_rio->_readline, $expected;
    is $win_rio->_readline , $expected;
    is $mac_rio->_readline , $expected;

    $expected = "DEFINITION  Desmognathus quadramaculatus 12S ribosomal RNA gene, partial\n";
    is $unix_rio->_readline, $expected;
    TODO: {
        local $TODO = "Sporadic test failures when running using PerlIO::eol on Linux w/".
                      "Windows line endings: #";
        is $win_rio->_readline , $expected;
    };
    is $mac_rio->_readline , $expected;

    $expected = "            sequence; tRNA-Val gene, complete sequence; and 16S ribosomal RNA\n";
    is $unix_rio->_readline, $expected;
    TODO: {
        local $TODO = "Sporadic test failures when running using PerlIO::eol on Linux w/".
                      "Windows line endings: #";
        is $win_rio->_readline , $expected;
    };
    is $mac_rio->_readline , $expected;

    $expected = "            gene, partial sequence, mitochondrial genes for mitochondrial RNAs.\n";
    is $unix_rio->_readline, $expected;
    TODO: {
        local $TODO = "Sporadic test failures when running using PerlIO::eol on Linux w/".
                      "Windows line endings: #";
        is $win_rio->_readline , $expected;
    };
    is $mac_rio->_readline , $expected;

    $expected = "ACCESSION   U71225\n";
    is $unix_rio->_readline, $expected;
    TODO: {
        local $TODO = "Sporadic test failures when running using PerlIO::eol on Linux w/".
                      "Windows line endings: #";
        is $win_rio->_readline , $expected;
    };
    is $mac_rio->_readline , $expected;

    # $HAS_EOL ignores -raw
    is $win_rio->_readline( -raw => 1) , "VERSION     U71225.1  GI:2804359\n";
    is $win_rio->_readline( -raw => 0) , "KEYWORDS    .\n";
}


##############################################
# test Path::Class support
##############################################

SKIP: {
    test_skip(-tests => 2, -requires_module => 'Path::Class');
    my $f = sub { Bio::Root::IO->new( -file => Path::Class::file(test_input_file('U71225.gb.unix') ) ) };
    lives_ok(sub { $f->() } , 'Bio::Root::IO->new can handle a Path::Class object');
    isa_ok($f->(), 'Bio::Root::IO');
}


##############################################
# test -string
##############################################

my $teststring = "Foo\nBar\nBaz";
ok $rio = Bio::Root::IO->new(-string => $teststring), 'Read string';

is $rio->mode, 'r';

ok $line1 = $rio->_readline;
is $line1, "Foo\n";

ok $line2 = $rio->_readline;
is $line2, "Bar\n";
ok $rio->_pushback($line2);

ok $line3 = $rio->_readline;
is $line3, "Bar\n";
ok $line3 = $rio->_readline;
is $line3, 'Baz';


##############################################
# test tempfile()
##############################################
{
ok my $obj = Bio::Root::IO->new(-verbose => 0);

isa_ok $obj, 'Bio::Root::IO';

my $TEST_STRING = "Bioperl rocks!\n";

my ($tfh,$tfile);

eval {
    ($tfh, $tfile) = $obj->tempfile();
    isa_ok $tfh, 'GLOB';
    print $tfh $TEST_STRING;
    close $tfh;
    open my $IN, '<', $tfile or die "Could not read file '$tfile': $!\n";
    my $val = join '', <$IN>;
    is $val, $TEST_STRING;
    close $IN;
    ok -e $tfile;
    undef $obj;
};
undef $obj;
if ( $@ ) {
    ok 0;
} else {
    ok ! -e $tfile, 'auto UNLINK => 1';
}

$obj = Bio::Root::IO->new();

eval {
    my $tdir = $obj->tempdir(CLEANUP=>1);
    ok -d $tdir;
    ($tfh, $tfile) = $obj->tempfile(dir => $tdir);
    close $tfh;
    ok -e $tfile;
    undef $obj; # see Bio::Root::IO::_io_cleanup
};

if ( $@ ) {
    ok 0;
} else {
    ok ! -e $tfile, 'tempfile deleted';
}

eval {
    $obj = Bio::Root::IO->new(-verbose => 0);
    ($tfh, $tfile) = $obj->tempfile(UNLINK => 0);
    isa_ok $tfh, 'GLOB';
    close $tfh;
    ok -e $tfile;
    undef $obj; # see Bio::Root::IO::_io_cleanup
};

if ( $@ ) {
   ok 0;
} else {
   ok -e $tfile, 'UNLINK => 0';
}

ok unlink( $tfile) == 1 ;


ok $obj = Bio::Root::IO->new;

# check suffix is applied
my ($fh1, $fn1) = $obj->tempfile(SUFFIX => '.bioperl');
isa_ok $fh1, 'GLOB';
like $fn1, qr/\.bioperl$/, 'tempfile suffix';
ok close $fh1;

# check single return value mode of File::Temp
my $fh2 = $obj->tempfile;
isa_ok $fh2, 'GLOB';
ok $fh2, 'tempfile() in scalar context';
ok close $fh2;
}

BioPerl-1.007002/t/Root/RootI.t000444000766000024      2242313155576321 16146 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 61);

    use_ok 'Bio::Root::Root';
}

ok my $obj = Bio::Root::Root->new();
isa_ok $obj, 'Bio::Root::RootI';

throws_ok { $obj->throw('Testing throw') } qr/Testing throw/;# 'throw failed';

# test throw_not_implemented()
throws_ok { $obj->throw_not_implemented() } qr/EXCEPTION: Bio::Root::NotImplemented/;

{
    package Bio::FooI;
    use base qw(Bio::Root::RootI);
    sub new {
            my $class = shift;
            my $self = {};
            bless $self, ref($class) || $class;
            return $self;
    };
}
$obj = Bio::FooI->new();
throws_ok { $obj->throw_not_implemented() } qr/EXCEPTION /;
$obj = Bio::Root::Root->new();

# doesn't work in perl 5.00405
#my $val;
#eval {
#    my ($tfh,$tfile) = $obj->tempfile();
#    local * STDERR = $tfh;
#    $obj->warn('Testing warn');
#    close $tfh;
#    open(IN, $tfile) or die("cannot open $tfile");
#    $val = join("", ) ;
#    close IN;
#    unlink $tfile;
#};
#ok $val =~ /Testing warn/;
#'verbose(0) warn did not work properly' . $val;

$obj->verbose(-1);
throws_ok { $obj->throw('Testing throw') } qr/Testing throw/;# 'verbose(-1) throw did not work properly' . $@;

lives_ok { $obj->warn('Testing warn') };

$obj->verbose(1);
throws_ok { $obj->throw('Testing throw') } qr/Testing throw/;# 'verbose(1) throw did not work properly' . $@;

# doesn't work in perl 5.00405
#undef $val;
#eval {
#    my ($tfh,$tfile) = $obj->tempfile();
#    local * STDERR = $tfh;
#    $obj->warn('Testing warn');
#    close $tfh;
#    open(IN, $tfile) or die("cannot open $tfile");
#    $val = join("", );
#    close IN;
#    unlink $tfile;
#};
#ok $val =~ /Testing warn/;# 'verbose(1) warn did not work properly' . $val;

my @stack = $obj->stack_trace();
is scalar @stack, 2;

my $verbobj = Bio::Root::Root->new(-verbose=>1,-strict=>1);
is $verbobj->verbose(), 1;

$Bio::Root::Root::DEBUG = 1;
my $seq = Bio::Root::Root->new();
is $seq->verbose, 1;

# test for bug #1343
my @vals = Bio::Root::RootI->_rearrange([qw(apples pears)],
                                        -apples => 'up the',
                                        -pears  => 'stairs');
is shift @vals, 'up the';
is shift @vals, 'stairs';

# test deprecated()

# class method
{
    local $Bio::Root::Root::VERSION = 8.9;
    warning_like{ Bio::Root::Root->deprecated('Test1') } qr/Test1/, 'simple';
    warning_like{ Bio::Root::Root->deprecated(-message => 'Test2') } qr/Test2/;
    warning_like{ Bio::Root::Root->deprecated('Test3', 999.999) } qr/Test3/,
        'warns for versions below current version';
    warning_like{ Bio::Root::Root->deprecated(-message => 'Test4',
                                              -version => 999.999) } qr/Test4/,
        'warns for versions below current version';
    throws_ok{ Bio::Root::Root->deprecated('Test5', 0.001) } qr/Test5/,
        'throws for versions above current version';
    throws_ok{ Bio::Root::Root->deprecated(-message => 'Test6',
                                       -version => 0.001) } qr/Test6/,
        'throws for versions above current version';

    throws_ok{ Bio::Root::Root->deprecated(-message => 'Test6',
                                           -version => $Bio::Root::Root::VERSION) } qr/Test6/,
        'throws for versions equal to current version';

    # object method
    my $root = Bio::Root::Root->new();
    warning_like{ $root->deprecated('Test1') } qr/Test1/, 'simple';
    warning_like{ $root->deprecated(-message => 'Test2') } qr/Test2/, 'simple';
    warning_like{ $root->deprecated('Test3', 999.999) } qr/Test3/,
        'warns for versions below current version';
    warning_like{ $root->deprecated(-message => 'Test4',
                                    -version => 999.999) } qr/Test4/,
                                'warns for versions below current version';
    throws_ok{ $root->deprecated('Test5', 0.001) } qr/Test5/,
      'throws for versions above current version';
    throws_ok{ $root->deprecated(-message => 'Test6',
                                 -version => 0.001) } qr/Test6/,
                             'throws for versions above current version';

}

# tests for _set_from_args()
# Let's not pollute Bio::Root::Root namespace if possible
# Create temp classes instead which inherit Bio::Root::Root, then test

{

    package Bio::Foo1;
    use base qw(Bio::Root::Root);
    our $VERSION = '2.00';
    sub new {
        my $class = shift;
        my $self = {};
        bless $self, ref($class) || $class;

        $self->_set_from_args(\@_);

        return $self;
    };
}

$obj = Bio::Foo1->new(-verbose => 1, t1 => 1, '--Test-2' => 2);
#ok ! $obj->can('t1'), 'arg not callable';

{

    package Bio::Foo2;
    use base qw(Bio::Root::Root);
    sub new {
        my $class = shift;
        my $self = {};
        bless $self, ref($class) || $class;

        $self->_set_from_args(\@_, -create => 1);

        return $self;
    };

}

$obj = Bio::Foo2->new(-verbose => 1, t3 => 1, '--Test-4' => 2);
ok $obj->can('t3'), 'arg callable since method was created';
ok $obj->can('test_4'), 'mal-formed arg callable since method was created with good name';
for my $m (qw(t3 test_4)) {
    can_ok('Bio::Foo2',$m);
    ok ! Bio::Root::Root->can($m), "Methods don't pollute original Bio::Root::Root namespace";
}

{
    package Bio::Foo3;
    use base qw(Bio::Root::Root);
    sub new {
        my $class = shift;
        my $self = {};
        bless $self, ref($class) || $class;

        $self->_set_from_args(\@_, -methods => ['verbose', 't5'], -create => 1);

        return $self;
    };
}

$obj = Bio::Foo3->new(-verbose => 1, t5 => 1, '--Test-6' => 2);
can_ok $obj, 't5';
ok ! $obj->can('test_6'), 'arg not in method list not created';

can_ok ('Bio::Foo3','t5');
ok ! UNIVERSAL::can('Bio::Root::Root','t5'), "Methods don't pollute original Bio::Root::Root namespace";

{
    package Bio::Foo4;
    use base qw(Bio::Root::Root);
    sub new {
            my $class = shift;
            my $self = {};
            bless $self, ref($class) || $class;

            my %args = @_;

            $self->_set_from_args(\%args, -methods => {(verbose => 'v',
                                                        test7 => 't7',
                                                        test_8 => 't8')},
                                          -create => 1);

            return $self;
    };
}

# with synonyms

$obj = Bio::Foo4->new(-verbose => 1, t7 => 1, '--Test-8' => 2);
is $obj->verbose, 1, 'verbose was set correctly';
is $obj->t7, 1, 'synonym was set correctly';
is $obj->test7, 1, 'real method of synonym was set correctly';
is $obj->test_8, 2, 'mal-formed arg correctly resolved to created method';
is $obj->t8, 2, 'synonym of set method was set correctly';

for my $m (qw(t7 test7 test_8 t8)) {
    can_ok 'Bio::Foo4', $m;
    ok ! UNIVERSAL::can('Bio::Root::Root','t7'), "Methods don't pollute original Bio::Root::Root namespace";
}

# test basic Root::clone()

my $clone = $obj->clone;

is $clone->t7, $obj->t7, 'clone';
is $clone->test7, $obj->test7, 'clone';
is $clone->test_8, $obj->test_8, 'clone';
$clone->test_8('xyz');
isnt $clone->test_8, $obj->test_8, 'clone changed, original didn\'t';

# test Root::clone() with parameter passing, only works for methods
# (introspection via can())

my $clone2 = $obj->clone(-t7 => 'foo');

is $clone2->t7, 'foo', 'parameters passed to clone() modify object';
is $obj->t7, 1, 'original is not modified';



# test deprecations using start_version
{
    package Bio::Foo5;
    use base qw(Bio::Root::Root);

    our $v = '18.001';
    our $VERSION = $v;

    sub not_good {
        my $self = shift;
        $self->deprecated(-message => 'This is not good',
                          -warn_version  => $v,
                          -throw_version => $v + 0.001);
    }

    sub not_good2 {
        my $self = shift;
        # note, due to _rearrange, ordering is throw version, then warn version
        $self->deprecated('This is not good',$v + 0.001,$v);
    }

    sub really_not_good {
        my $self = shift;
        $self->deprecated(-message => 'This is really not good',
                          -warn_version  => $v - 0.001,
                          -throw_version => $v,);
    }

    # version is the same as throw_version (and vice versa)
    sub still_very_bad {
        my $self = shift;
        $self->deprecated(-message => 'This is still very bad',
                          -warn_version  => $v - 0.001,
                          -version => $v);
    }

    sub okay_for_now {
        my $self = shift;
        $self->deprecated(-message => 'This is okay for now',
                          -warn_version  => $v + 0.001,
                          -throw_version => $v + 0.002);
    }
}

my $foo = Bio::Foo5->new();

warning_like{ $foo->not_good } qr/This is not good/,
    'warns for versions >= current version';
# this tests the three-arg (non-named) form just to make sure it works, even
# though we probably won't support it
warning_like{ $foo->not_good2 } qr/This is not good/,
    'warns for versions >= current version';

throws_ok { $foo->really_not_good } qr/This is really not good/,
    'throws for versions >= current version';
throws_ok { $foo->still_very_bad } qr/This is still very bad/,
    'throws for versions >= current version';
lives_ok { $foo->okay_for_now } 'No warnings/exceptions below current version';


BioPerl-1.007002/t/Root/RootIO.t000444000766000024        73213155576321 16224 0ustar00cjfieldsstaff000000000000##############################################
# tests http retrieval
##############################################

use strict;
use warnings;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    test_begin(-tests => 3,
	       -requires_networking => 1);
    use_ok 'Bio::Root::IO';
}

my $TESTURL = 'http://www.google.com/index.html';

my $rio;

ok $rio = Bio::Root::IO->new(-url=>$TESTURL), 'default -url method';
lives_ok {$rio = Bio::Root::IO->new(-url=>$TESTURL)};
BioPerl-1.007002/t/Root/Storable.t000444000766000024       436313155576321 16650 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 35);

    use_ok('Bio::Root::Storable');
}

foreach my $mode( "BINARY", "ASCII" ){
    if( $mode eq "ASCII" ){
        no warnings;
        $Bio::Root::Storable::BINARY = 0;
    }

    #------------------------------
    # Test the easy bits that don't need file IO
    my $obj = Bio::Root::Storable->new();
    ok defined($obj) && $obj->isa('Bio::Root::Storable');

    eval { $obj->throw('Testing throw') };
    ok $@ =~ /Testing throw/;   # 'throw failed';

    $obj->{_test}  = "_TEST";   # Provide test attributes
    $obj->{__test} = "__TEST";  #

    my $state = $obj->serialise;
    ok length($state) > 0;

    my $clone = $obj->clone;
    ok defined($clone) and $clone->isa('Bio::Root::Storable');
    ok $clone->{_test} eq "_TEST" && $clone->{__test}  eq "__TEST";

    #------------------------------
    # Test standard file IO
    my $file = $obj->store;
    ok $file && -f $obj->statefile;

    my $retrieved;
    eval { $retrieved = Bio::Root::Storable->retrieve( $file ) };
    ok defined($retrieved) && $retrieved->isa('Bio::Root::Storable');
    ok $retrieved->{_test} eq "_TEST" && ! exists $retrieved->{__test};

    my $skel = $obj->new_retrievable;
    ok defined($skel) && $skel->isa('Bio::Root::Storable');
    ok ! exists $skel->{_test} && ! exists $skel->{__test};
    ok $skel->retrievable;

    eval { $skel->retrieve };
    ok ! $skel->retrievable;
    ok $skel->{_test} eq "_TEST" && ! exists $skel->{__test};

    my $obj2 = Bio::Root::Storable->new();
    $obj2->template('TEST_XXXXXX');
    $obj2->suffix('.state');
    my $file2 = $obj2->store;
    ok $file2 =~ /TEST_\w{6}?\.state$/ and -f $file2;

    #------------------------------
    # Test recursive file IO
    $obj->{_test_lazy} = $obj2;
    $obj->store;
    my $retrieved2;
    eval { $retrieved2 = Bio::Root::Storable->retrieve( $obj->token ) };
    ok $retrieved2->{_test_lazy} && $retrieved2->{_test_lazy}->retrievable;

    #------------------------------
    # Clean up
    # Should only be 2 object files; all others were clones in one way or another
    $obj->remove;
    ok ! -f $obj->statefile;
    $obj2->remove;
    ok ! -f $obj2->statefile;
}
BioPerl-1.007002/t/Root/Utilities.t000444000766000024       614113155576321 17044 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$


use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 56);

    use_ok('Bio::Root::Utilities');
}

# Object creation
my $u = Bio::Root::Utilities->new();
isa_ok($u, 'Bio::Root::Utilities') ;

# month2num() and num2month()

my @month = qw(XXX Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec);
for my $i (1 .. 12) {
  is $u->month2num($month[$i]), $i;
  is $u->num2month($i), $month[$i];
}

# untaint()

is $u->untaint(''), '';
is $u->untaint('nice string'), 'nice string';
is $u->untaint('bad *?&^$! string'), 'bad ';
is $u->untaint( q{100% relaxed&;''\"|*?!~<>^()[]{}$}, 1 ), '100% relaxed';

# mean_stdev()

my($mu,$sd);

($mu,$sd) = $u->mean_stdev();
is $mu, undef;
is $sd, undef;

($mu,$sd) = $u->mean_stdev(42);
is $mu, 42;
is $sd, undef;

($mu,$sd) = $u->mean_stdev(-1,0,1);
is $mu, 0;
is $sd, 1;

# file_date(), file_flavor(), date_format()

my $file = test_input_file('test.txt');
my $file2 = test_input_file('test 2.txt');
my $fdate = $u->file_date($file);
like $fdate ,  qr/\d{4}-\d{2}-\d{2}/, 'file_date()';
ok $u->file_flavor($file), 'unix (\n or 012 or ^J)';

my $date = $u->date_format();
like $date, qr/\d{4}-\d{2}-\d{2}/, 'date format';
my $date2 = $u->date_format('yyyy-mmm-dd', $date);
like $date2 , qr/\d{4}-[a-z]{3}-\d{2}/i, 'date format';
my $date3 = $u->date_format('mdhms');
like $date3 , qr/[a-z]{3}\d{1,2} \d{1,2}:\d{1,2}:\d{1,2}/, 'date format';
my $date4 = $u->date_format('d-m-y', '11/22/60');
like $date4 , qr/\d{1,2}-[a-z]{3}-\d{4}/i, 'date format';
my $date5 = $u->date_format('mdy', '1/5/01');
like $date5 , qr/[a-z]{3} \d{1,2}, \d{4}/i, 'date format';

# External executable-related functions.

my $exe = $u->find_exe('some-weird-thing-no-one-will-have');
ok ! defined $exe ;

# compress() and uncompress() using gzip.
SKIP: {
    my $gzip = $u->find_exe('gzip');
    skip "gzip not found, skipping gzip tests", 12 unless $gzip;
    ok -x $gzip;

    # test compression/decompression of a simple file
    my $zfile = $u->compress($file);

    # In Windows, the folder separator '\' may brake
    # the following qr{}, so change it to '/'
    $zfile =~ s'\\'/'g;
    $file  =~ s'\\'/'g;

    like $zfile, qr/$file.gz|tmp.bioperl.gz/;
    ok -s $zfile;
    if ($zfile =~ /tmp.bioperl.gz/) {
        ok -e $file;
    }
    else {
        ok ! -e $file;
    }
    my $unzfile = $u->uncompress($zfile);
    ok ! -e $zfile;
    ok -e $file;

    # test compression/decompression of a filename with spaces keeping the original intact
    my $zfile2 = $file2.'.gz';
    my $return = $u->compress(-file => $file2, -outfile => $zfile2, -tmp => 1);
    is $return, $zfile2;
    ok -e $zfile2;
    ok -e $file2;
    unlink $file2 or die "Problem deleting $file2: $!\n";
    $return = $u->uncompress(-file => $zfile2, -outfile => $file2, -tmp => 1);
    is $return, $file2;
    ok -e $file2;
    ok -e $zfile2;
    unlink $zfile2 or die "Problem deleting $zfile2: $!\n";
}

# send_mail()

# $u->send_mail(-to=>'sac@bioperl.org',  # <--- your address here!
#               -subj=>'Root-Utilities.t',
#               -msg=>'Hey, your send_mail() method works!');
BioPerl-1.007002/t/SearchIO000755000766000024          013155576321 15257 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/SearchIO/CigarString.t000444000766000024       147013155576321 20017 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$


use strict;

BEGIN {
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 4);
    
	use_ok('Bio::SearchIO');
}

my $searchio = Bio::SearchIO->new(
	 -format => 'blast',
    -file => test_input_file('blast.report')
);

my @hsps = ();
while(my $result = $searchio->next_result){
    while(my $hit = $result->next_hit){
        while(my $hsp = $hit->next_hsp){
            push @hsps, $hsp;
        }
    }
}

my $first_hsp = shift @hsps;
my $first_hsp_cigar_string = '504M'; 
is $first_hsp->cigar_string, $first_hsp_cigar_string;
is $first_hsp->cigar_string, $first_hsp_cigar_string; # fetch from hash

my $second_hsp = $hsps[0];
my $second_hsp_cigar_string = '29M18I22M11I20MD33M4I22M3I25M5I21MI33MD14M';
is $second_hsp->cigar_string, $second_hsp_cigar_string;
BioPerl-1.007002/t/SearchIO/SearchIO.t000444000766000024       221613155576321 17237 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 19);
	
	use_ok('Bio::SearchIO');
}

# only methods defined in Bio::SearchIO should be tested here; all
# parsers should have their own separate SearchIO_*.t test file

# Let's test if _guess_format is doing its job correctly
my %pair = ( 'filename.blast'  => 'blast',
	     'filename.bls'    => 'blast',
	     'f.blx'           => 'blast',
	     'f.tblx'          => 'blast',
	     'fast.bls'        => 'blast',
	     'f.fasta'         => 'fasta',
	     'f.fa'            => 'fasta',
	     'f.fx'            => 'fasta',
	     'f.fy'            => 'fasta',
	     'f.ssearch'       => 'fasta',
	     'f.SSEARCH.m9'    => 'fasta',
	     'f.m9'            => 'fasta',
	     'f.psearch'       => 'fasta',
	     'f.osearch'       => 'fasta',
	     'f.exon'          => 'exonerate',
	     'f.exonerate'     => 'exonerate',
	     'f.blastxml'      => 'blastxml',
	     'f.xml'           => 'blastxml');
while( my ($file,$expformat) = each %pair ) {
    is(Bio::SearchIO->_guess_format($file),$expformat, "$expformat for $file");
}
BioPerl-1.007002/t/SearchIO/SimilarityPair.t000444000766000024       134213155576321 20543 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 12);
	
	use_ok('Bio::SearchIO');
	use_ok('Bio::SeqIO');
}

# test SimilarityPair

ok my $seq = (Bio::SeqIO->new('-format' => 'fasta',
			  '-file' => test_input_file('AAC12660.fa')))->next_seq();
isa_ok $seq, 'Bio::SeqI';
ok my $blast = Bio::SearchIO->new('-file'=>test_input_file('blast.report'), '-format' => 'blast');
isa_ok $blast, 'Bio::SearchIO';
my $r = $blast->next_result;
ok my $hit = $r->next_hit;
isa_ok $hit, 'Bio::Search::Hit::HitI';
ok my $sim_pair = $hit->next_hsp;
isa_ok $sim_pair, 'Bio::SeqFeatureI';
ok $seq->add_SeqFeature($sim_pair);
is $seq->all_SeqFeatures(), 1;
BioPerl-1.007002/t/SearchIO/Tiling.t000444000766000024      3337613155576321 17063 0ustar00cjfieldsstaff000000000000#-*-perl-*-
#$Id$
use strict;
use warnings;
    use vars qw($EXHAUSTIVE $VERBOSE);
BEGIN {
    use lib '.';
    use lib '../..';

    use Bio::Root::Test;
    $EXHAUSTIVE = $ENV{BIOPERL_TILING_EXHAUSTIVE_TESTS};
    $VERBOSE    = $ENV{BIOPERL_TILING_VERBOSE_TESTS};
    test_begin(-tests => ($EXHAUSTIVE ? 6519 : 1141) );
}

use_ok('Bio::Search::Tiling::MapTiling');
use_ok('Bio::Search::Tiling::MapTileUtils');
use_ok('Bio::SearchIO');
use_ok('Bio::Search::Hit::BlastHit');
use_ok('File::Spec');

my ($blio, $result, $hit, $tiling, $hsp);

my @normal_formats = qw( blast  wublast
                         blastn wublastn
                         blastp wublastp
                         multiblast 
                         megablast
                         rpsblast
                         psiblast );
my @xltd_formats  = qw(  blastx wublastx
                         tblastn wutblastn
                         tblastx wutblastx );
                         
                 
# an exhaustive listing of search reports in 
# t/data 
        
my %test_files = (
    'blast' => [qw(
               ecolitst.bls
               frac_problems.blast
               frac_problems2.blast
               frac_problems3.blast
               bl2seq.out
               )],
    'multiblast' => [qw(
               multi_blast.bls
               )],
    'blastn' => [qw(
               a_thaliana.blastn
               bl2seq.blastn
               new_blastn.txt
               hsinsulin.blastcl3.blastn
               )],
    'wublastn' =>[qw(
               brassica_ATH.WUBLASTN
               echofilter.wublastn
               )],
    'blastp' => [qw(
               blastp2215.blast
               no_hsps.blastp
               catalase-webblast.BLASTP
               )],
    'wublastp' => [qw(
               dcr1_sp.WUBLASTP
               ecolitst.wublastp
               contig-by-hand.wublastp
               ecolitst.noseqs.wublastp
               )],
    'blastx' => [qw(
               bl2seq.blastx.out
               )],
    'wublastx' => [qw(
               dnaEbsub_ecoli.wublastx
               )],
    'wublast' => [qw(
               tricky.wublast
               )],
    'tblastn' => [qw(
               tblastn.out
               1ZZ19XR301R-Alignment.tblastn
               )],
    'wutblastn' => [qw(
               dnaEbsub_ecoli.wutblastn
               )],
    'tblastx' => [qw(
               bl2seq.tblastx.out
               HUMBETGLOA.tblastx
               )],
    'wutblastx' => [qw(
               dnaEbsub_ecoli.wutblastx
               )],
    'megablast' => [qw(
               503384.MEGABLAST.2
               )],
    'rpsblast' => [qw(
               ecoli_domains.rpsblast
               )],
    'psiblast' => [qw(
               psiblastreport.out
               )],
    'bug2942'  => [qw(
               bug2942.blastx
               )]
    );

# a subset of search reports for 
# run-o-the-mill regression tests

my %example_files = (
    'blast' => [qw(
               ecolitst.bls
               )],
    'blastn' => [qw(
               a_thaliana.blastn
               )],
    'wublastn' =>[qw(
               brassica_ATH.WUBLASTN
               )],
    'blastp' => [qw(
               no_hsps.blastp
               catalase-webblast.BLASTP
               )],
    'wublastp' => [qw(
               dcr1_sp.WUBLASTP
               )],
    'blastx' => [qw(
               bl2seq.blastx.out
               )],
    'wublastx' => [qw(
               dnaEbsub_ecoli.wublastx
               )],
    'wublast' => [qw(
               tricky.wublast
               )],
    'tblastn' => [qw(
               tblastn.out
               )],
    'wutblastn' => [qw(
               dnaEbsub_ecoli.wutblastn
               )],
    'tblastx' => [qw(
               HUMBETGLOA.tblastx
               )],
    'wutblastx' => [qw(
               dnaEbsub_ecoli.wutblastx
               )],
    'megablast' => [qw(
               503384.MEGABLAST.2
               )]
    );

ok( $blio = new Bio::SearchIO( 
	-file=>test_input_file('dcr1_sp.WUBLASTP'),
	-format=>'blast'), 'parse data file');

$result = $blio->next_result;
while ( $_ = $result->next_hit ) {
    last if $_->name =~ /ASPTN/;
}
ok($hit = $_, 'got test hit');
ok($tiling = Bio::Search::Tiling::MapTiling->new($hit), 'create tiling');


# TilingI compliance

isa_ok($tiling, 'Bio::Search::Tiling::TilingI');
foreach ( qw( next_tiling rewind_tilings identities conserved length ) ) {
    ok( $tiling->$_, "implements '$_'" );
}

# regression test on original calculations

my @orig_id_results = ( 387,388,388,381,382,389 );
my @orig_cn_results = ( 622,619,628,608,611,613 );
my @id_results = (
    $tiling->identities('query', 'exact'),
    $tiling->identities('query', 'est'),
    $tiling->identities('query', 'max'),
    $tiling->identities('subject', 'exact'),
    $tiling->identities('subject', 'est'),
    $tiling->identities('subject', 'max')
    );
my @cn_results = (
    $tiling->conserved('query', 'exact'),
    $tiling->conserved('query', 'est'),
    $tiling->conserved('query', 'max'),
    $tiling->conserved('subject', 'exact'),
    $tiling->conserved('subject', 'est'),
    $tiling->conserved('subject', 'max')
    );
map { $_ = int($_) } @id_results, @cn_results;

is_deeply(\@id_results, \@orig_id_results, 'identities regression test');
is_deeply(\@cn_results, \@orig_cn_results, 'conserved regression test');

# tiling iterator regression tests

my ($qn, $sn)=(0,0);
while ($tiling->next_tiling('query')) {$qn++};
while ($tiling->next_tiling('subject')) {$sn++};
is ($qn, 8, 'tiling iterator regression test(1)');
is ($sn, 128, 'tiling iterator regression test(2)');
$tiling->rewind('subject');
while ($tiling->next_tiling('subject')) {$sn++};
is ($sn, 256, 'tiling iterator regression test(3, rewind)');

diag("Old blast.t tiling tests") if $VERBOSE;

ok($blio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('ecolitst.wublastp')
   ), "ecolitst.wublastp");
$result = $blio->next_result;
$result->next_hit;
$hit = $result->next_hit;
$tiling = Bio::Search::Tiling::MapTiling->new($hit);
# Test HSP contig data returned by SearchUtils::tile_hsps()
# Second hit has two hsps that overlap.

# compare with the contig made by hand for these two contigs
# in t/data/contig-by-hand.wublastp
# (in this made-up file, the hsps from ecolitst.wublastp
#  were aligned and contiged, and Length, Identities, Positives 
#  were counted, by a human (maj) )
	
my $hand_hit = Bio::SearchIO->new(
    -format=>'blast', 
    -file=>test_input_file('contig-by-hand.wublastp')
    )->next_result->next_hit;
my $hand_hsp = $hand_hit->next_hsp;
my @hand_qrng = $hand_hsp->range('query');
my @hand_srng = $hand_hsp->range('hit');
my @hand_matches = $hand_hit->matches;

is(($tiling->range('query'))[0], $hand_qrng[0]);
is(($tiling->range('query'))[1], $hand_qrng[1]);
is(sprintf("%d",$tiling->identities('query')), $hand_matches[0]);
is(sprintf("%d",$tiling->conserved('query')), $hand_matches[1]);
is(($tiling->range('hit'))[0], $hand_srng[0]);
is(($tiling->range('hit'))[1], $hand_srng[1]);
is(sprintf("%d",$tiling->identities('hit')), $hand_matches[0]);
is(sprintf("%d",$tiling->conserved('hit')), $hand_matches[1]);

ok( $blio = Bio::SearchIO->new(
	'-format' => 'blast',
	'-file'   => test_input_file('dnaEbsub_ecoli.wublastx')
    ), "dnaEbsub_ecoli.wublastx");

$hit = $blio->next_result->next_hit;
$tiling = Bio::Search::Tiling::MapTiling->new($hit);
is(sprintf("%.3f",$tiling->frac_identical(-type=>'query',-denom=>'aligned',-context=>'p2')), '0.364');
is(sprintf("%.3f",$tiling->frac_identical(-type=>'hit',-denom=>'aligned',-context=>'all')), '0.366');
is(sprintf("%.3f",$tiling->frac_conserved(-type=>'query',-denom=>'aligned',-context=>'p2')), '0.537');
is(sprintf("%.3f",$tiling->frac_conserved(-type=>'hit',-denom=>'aligned',-context=>'all')), '0.540');
is(sprintf("%.2f",$tiling->frac_aligned_query(-context=>'p2')), '0.62');
is(sprintf("%.2f",$tiling->frac_aligned_hit(-context=>'all')), '0.71');

ok( $blio = Bio::SearchIO->new(
	'-format' => 'blast',
	'-file'   => test_input_file('tricky.wublast')
    ), "tricky.wublast");

$hit = $blio->next_result->next_hit;
$tiling = Bio::Search::Tiling::MapTiling->new($hit);
cmp_ok sprintf("%.3f",$tiling->frac_identical(-denom => 'aligned')), '>', 0.2, 'tricky.wublast(1)';
cmp_ok sprintf("%.3f",$tiling->frac_conserved(-denom => 'aligned')), '<=', 1, 'tricky.wublast(2)';
is(sprintf("%.2f",$tiling->frac_aligned_query), '0.92', 'tricky.wublast(3)');
is(sprintf("%.2f",$tiling->frac_aligned_hit), '0.91','tricky.wublast(4)');

diag("New tiling tests") if $VERBOSE;

# select test file set based on the environment variable
# BIOPERL_TILING_EXHAUSTIVE_TESTS

my $files = ($EXHAUSTIVE ? \%test_files : \%example_files);

foreach my $alg (@normal_formats, @xltd_formats) {
    diag("*******$alg files*******") if ($files->{$alg} && $VERBOSE);
    foreach my $tf (@{$files->{$alg}}) {
	ok( $blio = Bio::SearchIO->new( -format=>'blast', 
					-file=>test_input_file($tf)
	    ), "$tf" );
	$result = $blio->next_result;
	my $hit_count = 0;
	# compare the per-aligned-base identity avg over hsps
	# with frac_identical (bzw, conserved)
	
      HIT:
	while ( $hit = $result->next_hit ) {
	    ++$hit_count;
	    # quiet the "No HSPs" warning with -verbose => -1
	    ok( $tiling = Bio::Search::Tiling::MapTiling->new(-hit=>$hit,-verbose=>-1), "tile $tf hit $hit_count #hsps ".scalar $tiling->hsps );
	    my @hsps = $tiling->hsps;
	    
	    unless (@hsps) {
		diag( "--no hsps for $tf hit $hit_count") if $VERBOSE;
		next HIT;
	    }
	    my ($dpct, $est, $fast,$exact, $max);
	    my $tol = 0.10; # % difference accepted as approx. equal
	    
	    ## loop through contexts:
	    for my $type (qw( query hit )) {
		for my $context ($tiling->contexts($type)) {
		    diag(" --- $type $context ---") if $VERBOSE;
		    if (scalar($tiling->contexts($type, $context)) == 1) {
			# equality
			($dpct, $est, $fast) = $tiling->cmp_frac($type,'identical','aligned', 'est', 'fast', $context);
			is( $est,$fast, substr($type,0,1)." id: est ($est) = fast ($fast)");
			($dpct, $est, $fast) = $tiling->cmp_frac($type,'conserved','aligned', 'est', 'fast', $context);
			is( $est,$fast, substr($type,0,1)." cn: est ($est) = fast ($fast)");
		    }
		    else {
			# comparisons
			($dpct, $est, $fast) = $tiling->cmp_frac($type,'identical','aligned', 'est', 'fast', $context);
#			cmp_ok( $dpct, "<", $tol, 
#				substr($type,0,1)." id: est ($est) ~ fast ($fast)");
			($dpct, $exact, $max) = $tiling->cmp_frac($type,'identical','aligned', 'exact', 'max', $context);
			cmp_ok( abs($exact-$est)/$exact, "<" , $tol, 
				substr($type,0,1)." id: exact ($exact) ~ est ($est)");
			cmp_ok( $exact, "<=" , $max, 
				substr($type,0,1)." id: exact ($exact) <= max ($max)");
			
			($dpct, $est, $fast) = $tiling->cmp_frac($type,'conserved','aligned', 'est', 'fast', $context);
#			cmp_ok( $dpct, "<", $tol, 
#				substr($type,0,1)." cn: est ($est) ~ fast ($fast)");
			($dpct, $exact, $max) = $tiling->cmp_frac($type,'conserved','aligned', 'exact', 'max', $context);
			cmp_ok(  abs($exact-$est)/$exact, "<" , $tol, 
				 substr($type,0,1)." cn: exact ($exact) ~ est ($est)");
			cmp_ok( $exact, "<=" , $max, 
				substr($type,0,1)." cn: exact ($exact) <= max ($max)");
		    }
		}
	    }
	}
    }
}

# bug 2942

my %expected_ranges = ( 'm0' => [7, 11037], #query
			'm1' => [1770, 10865], #query 
			'm2' => [2462, 14599], #query
			'all' => [231, 3563] #subject
    );
$blio = Bio::SearchIO->new( -file=>test_input_file( $test_files{'bug2942'}->[0] ),
			    -format => 'blast' );
$hit = $blio->next_result->next_hit;
$tiling = Bio::Search::Tiling::MapTiling->new($hit);
for ( 'm0', 'm1', 'm2' ) {
    is_deeply( [$tiling->range('query',$_)], $expected_ranges{$_}, "bug2942: query $_: range correct");
}
is_deeply( [$tiling->range('subject', 'all')], $expected_ranges{'all'}, "bug2942: subject all : range correct" );

# test get_tiled_alns

$blio = Bio::SearchIO->new( -file=>test_input_file( 'dcr1_sp.WUBLASTP' ) );
$result = $blio->next_result;
while ($hit = $result->next_hit) {
    last if $hit->name =~ /ASPTN/;
}

$tiling = Bio::Search::Tiling::MapTiling->new($hit);

ok my @alns = $tiling->get_tiled_alns, "get_tiled_alns";
is scalar @alns, 6, "got all alns";

for my $aln ( @alns ) {
    my (@aint, @qint, @sint);
    my $qs = $aln->get_seq_by_id('query');
    my $ss = $aln->get_seq_by_id('subject');
    ok my @qfeats = $qs->get_SeqFeatures;
    foreach (@qfeats) {
	push @aint, [$_->start, $_->end];
	push @qint, [($_->get_tag_values('query_start'))[0],
		     ($_->get_tag_values('query_end'))[0] ];
    }
    is( eval(join('+', map {$$_[1]-$$_[0]+1} @aint)),
	eval(join('+', map {$$_[1]-$$_[0]+1} @qint)), 
	"aln and qfeat lengths correspond" );
    is( $qs->length - $qs->num_gaps('-'), eval(join('+', map {$$_[1]-$$_[0]+1} @qint)), "q length correct");
    ok my @hfeats = $ss->get_SeqFeatures;
    @aint = ();
    ok ( @qfeats == @hfeats, "features on q and s correspond");
    foreach (@hfeats) {
	push @aint, [$_->start, $_->end];
	push @sint, [($_->get_tag_values('subject_start'))[0],
		     ($_->get_tag_values('subject_end'))[0] ];
    }
    is( eval(join('+', map {$$_[1]-$$_[0]+1} @aint)),
	eval(join('+', map {$$_[1]-$$_[0]+1} @sint)), 
	"aln and hfeat lengths correspond" );
    is( $ss->length - $ss->num_gaps('-'), eval(join('+', map {$$_[1]-$$_[0]+1} @sint)), "s length correct");

}
1;



package Bio::Search::Tiling::MapTiling;

sub cmp_frac {
    my ($tiling, $type, $method, $denom, @actions) = @_;
    my ($a, $b);
    my $context = ($actions[2] ? $actions[2] : 'all');
    $a = $tiling->frac(-type=>$type, 
		       -method=>$method, 
		       -denom=>$denom,
		       -action=>$actions[0],
		       -context=>$context);
    $b = $tiling->frac(-type=>$type, 
		       -method=>$method, 
		       -denom=>$denom,
		       -action=>$actions[1],
		       -context=>$context);
    return ( abs($a-$b)/$a, f(5,$a), f(5,$b) );
}

sub f { my ($d,$val) = @_; sprintf("%.${d}f",$val) }       

    

    
1;

BioPerl-1.007002/t/SearchIO/axt.t000444000766000024       203713155576321 16377 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 19);

    use_ok('Bio::SearchIO');
}

my $axtparser = Bio::SearchIO->new(-format => 'axt',
				  -file   => test_input_file('test_data.axt'));

my $result = $axtparser->next_result;
is($result->query_name, 'chr19');

my $hit = $result->next_hit;
is($hit->name, 'chr11');

my $hsp    = $hit->next_hsp;
is($hsp->query->start,3001012);
is($hsp->query->end,3001075);
is($hsp->query->length, 64);
is($hsp->query->strand, 1);

is($hsp->hit->start,70568380);
is($hsp->hit->end,70568443);
is($hsp->hit->length, 64);
is($hsp->hit->strand, -1);

# next HSP returns next alignment, but shouldn't this be the next_hit instead????
# what happens if the hit name changes?

$hsp    = $hit->next_hsp;
is($hsp->query->start,3008279);
is($hsp->query->end,3008357);
is($hsp->query->length, 79);
is($hsp->query->strand, 1);

is($hsp->hit->start,70573976);
is($hsp->hit->end,70574054);
is($hsp->hit->length, 79);
is($hsp->hit->strand, -1);

BioPerl-1.007002/t/SearchIO/blast.t000444000766000024     26317013155576321 16757 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_blast.t 14995 2008-11-16 06:20:00Z cjfields $

use strict;
use warnings;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 1389);

    use_ok('Bio::SearchIO');
}

SKIP: {
    test_skip(-tests => 4, -requires_module => 'Path::Class');


    my $file = Path::Class::file(test_input_file('ecolitst.bls'));
    my $f    = sub { my ($file) = @_; Bio::SearchIO->new( -file   => $file, -format => 'blast') };

    lives_ok(sub { $f->($file) } , 'Bio::SearchIO->new can handle a Path::Class object');
    isa_ok($f->($file), 'Bio::Root::IO');

    $file = Path::Class::dir(File::Spec->catfile(qw/t data/))->file('ecolitst.bls');

    lives_ok(sub { $f->($file) } , 'Bio::SearchIO->new can handle a Path::Class object');
    isa_ok($f->($file), 'Bio::Root::IO');
}

my ( $searchio, $result, $iter, $hit, $hsp );

$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('ecolitst.bls')
);

$result = $searchio->next_result;

like($result->algorithm_reference,
    qr/Gapped BLAST and PSI-BLAST: a new generation of protein database search/
);

is( $result->database_name, 'ecoli.aa', 'database_name()' );
is( $result->database_entries, 4289 );
is( $result->database_letters, 1358990 );

is( $result->algorithm, 'BLASTP' );
like( $result->algorithm_version, qr/^2\.1\.3/ );
like( $result->query_name,
qr/gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I,\s+homoserine dehydrogenase I [Escherichia coli]/
);
is( $result->query_accession,                 'AAC73113.1' );
is( $result->query_gi,                        1786183 );
is( $result->query_length,                    820 );
is( $result->get_statistic('kappa'),          '0.135' );
is( $result->get_statistic('kappa_gapped'),   '0.0410' );
is( $result->get_statistic('lambda'),         '0.319' );
is( $result->get_statistic('lambda_gapped'),  '0.267' );
is( $result->get_statistic('entropy'),        '0.383' );
is( $result->get_statistic('entropy_gapped'), '0.140' );

is( $result->get_statistic('dbletters'),           1358990 );
is( $result->get_statistic('dbentries'),           4289 );
is( $result->get_statistic('effective_hsplength'), 47 );
is( $result->get_statistic('effectivespace'),      894675611 );
is( $result->get_parameter('matrix'),              'BLOSUM62' );
is( $result->get_parameter('gapopen'),             11 );
is( $result->get_parameter('gapext'),              1 );
is( $result->get_statistic('S2'),                  '92' );
is( $result->get_statistic('S2_bits'),             '40.0' );
float_is( $result->get_parameter('expect'), '1.0e-03' );
is( $result->get_statistic('num_extensions'),     '82424' );
is( $result->get_statistic('querylength'),        773 );
is( $result->get_statistic('effectivedblength'),  1157407 );
is( $result->get_statistic('effectivespaceused'), 894675611 );

my @valid = (
    [ 'gb|AAC73113.1|', 820, 'AAC73113', '0',     1567, 4058 ],
    [ 'gb|AAC76922.1|', 810, 'AAC76922', '1e-91', 332,  850 ],
    [ 'gb|AAC76994.1|', 449, 'AAC76994', '3e-47', 184,  467 ]
);
my $count = 0;
while ( $hit = $result->next_hit ) {
    my $d = shift @valid;

    is( $hit->name,      shift @$d );
    is( $hit->length,    shift @$d );
    is( $hit->accession, shift @$d );
    float_is( $hit->significance, shift @$d );
    is( $hit->bits,      shift @$d );
    is( $hit->raw_score, shift @$d );

    if ( $count == 0 ) {
        my $hsps_left = 1;
        while ( my $hsp = $hit->next_hsp ) {
            is( $hsp->query->start,    1 );
            is( $hsp->query->end,      820 );
            is( $hsp->hit->start,      1 );
            is( $hsp->hit->end,        820 );
            is( $hsp->length('total'), 820 );
            is( $hsp->start('hit'),    $hsp->hit->start );
            is( $hsp->end('query'),    $hsp->query->end );
            is( $hsp->strand('sbjct'), $hsp->subject->strand );  # alias for hit
            float_is( $hsp->evalue, 0.0 );
            is( $hsp->score, 4058 );
            is( $hsp->bits,  1567 );
            is( sprintf( "%.2f", $hsp->percent_identity ),        98.29 );
            is( sprintf( "%.4f", $hsp->frac_identical('query') ), 0.9829 );
            is( sprintf( "%.4f", $hsp->frac_identical('hit') ),   0.9829 );
            is( $hsp->gaps, 0 );
            is( $hsp->n,    1 );
            $hsps_left--;
        }
        is( $hsps_left, 0 );
    }
    last if ( $count++ > @valid );
}
is( @valid, 0 );

$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('ecolitst.wublastp')
);

$result = $searchio->next_result;

like($result->algorithm_reference,
     qr/Gish, W. \(1996-2000\)/);

is( $result->database_name,    'ecoli.aa' );
is( $result->database_letters, 1358990 );
is( $result->database_entries, 4289 );
is( $result->algorithm,        'BLASTP' );
like( $result->algorithm_version, qr/^2\.0MP\-WashU/ );
like( $result->query_name,
qr/gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I,\s+homoserine dehydrogenase I [Escherichia coli]/
);
is( $result->query_accession, 'AAC73113.1' );

is( $result->query_length,                          820 );
is( $result->query_gi,                              1786183 );
is( $result->get_statistic('kappa'),                0.136 );
is( $result->get_statistic('lambda'),               0.319 );
is( $result->get_statistic('entropy'),              0.384 );
is( $result->get_statistic('dbletters'),            1358990 );
is( $result->get_statistic('dbentries'),            4289 );
is( $result->get_parameter('matrix'),               'BLOSUM62' );
is( $result->get_statistic('Frame+0_lambda_used'),  '0.319' );
is( $result->get_statistic('Frame+0_kappa_used'),   '0.136' );
is( $result->get_statistic('Frame+0_entropy_used'), '0.384' );

is( $result->get_statistic('Frame+0_lambda_computed'),  '0.319' );
is( $result->get_statistic('Frame+0_kappa_computed'),   '0.136' );
is( $result->get_statistic('Frame+0_entropy_computed'), '0.384' );

is( $result->get_statistic('Frame+0_lambda_gapped'),  '0.244' );
is( $result->get_statistic('Frame+0_kappa_gapped'),   '0.0300' );
is( $result->get_statistic('Frame+0_entropy_gapped'), '0.180' );

@valid = (
    [ 'gb|AAC73113.1|', 820, 'AAC73113', '0',       4141 ],
    [ 'gb|AAC76922.1|', 810, 'AAC76922', '3.1e-86', 844 ],
    [ 'gb|AAC76994.1|', 449, 'AAC76994', '2.8e-47', 483 ]
);
$count = 0;
while ( $hit = $result->next_hit ) {
    my $d = shift @valid;

    if ( $count == 1 ) {

        # Test HSP contig data returned by SearchUtils::tile_hsps()
        # Second hit has two hsps that overlap.

        # compare with the contig made by hand for these two contigs
        # in t/data/contig-by-hand.wublastp
        # (in this made-up file, the hsps from ecolitst.wublastp
        #  were aligned and contiged, and Length, Identities, Positives
        #  were counted, by a human (maj) )

        my $hand_hit = Bio::SearchIO->new(
            -format => 'blast',
            -file   => test_input_file('contig-by-hand.wublastp')
        )->next_result->next_hit;
        my $hand_hsp     = $hand_hit->next_hsp;
        my @hand_qrng    = $hand_hsp->range('query');
        my @hand_srng    = $hand_hsp->range('hit');
        my @hand_matches = $hand_hit->matches;

        my ( $qcontigs, $scontigs ) = Bio::Search::SearchUtils::tile_hsps($hit);

        # Query contigs
        is( $qcontigs->[0]->{'start'}, $hand_qrng[0] );
        is( $qcontigs->[0]->{'stop'},  $hand_qrng[1] );
        is( $qcontigs->[0]->{'iden'},  $hand_matches[0] );
        is( $qcontigs->[0]->{'cons'},  $hand_matches[1] );

        # Subject contigs
        is( $scontigs->[0]->{'start'}, $hand_srng[0] );
        is( $scontigs->[0]->{'stop'},  $hand_srng[1] );
        is( $scontigs->[0]->{'iden'},  $hand_matches[0] );
        is( $scontigs->[0]->{'cons'},  $hand_matches[1] );
    }

    is( $hit->name,      shift @$d );
    is( $hit->length,    shift @$d );
    is( $hit->accession, shift @$d );
    float_is( $hit->significance, shift @$d );
    is( $hit->raw_score, shift @$d );

    if ( $count == 0 ) {
        my $hsps_left = 1;
        while ( my $hsp = $hit->next_hsp ) {
            is( $hsp->query->start,    1 );
            is( $hsp->query->end,      820 );
            is( $hsp->hit->start,      1 );
            is( $hsp->hit->end,        820 );
            is( $hsp->length('total'), 820 );

            float_is( $hsp->evalue, 0.0 );
            float_is( $hsp->pvalue, '0.0' );
            is( $hsp->score,                   4141 );
            is( $hsp->bits,                    1462.8 );
            is( $hsp->percent_identity,        100 );
            is( $hsp->frac_identical('query'), 1.00 );
            is( $hsp->frac_identical('hit'),   1.00 );
            is( $hsp->gaps,                    0 );
            is( $hsp->n,                       1 );
            $hsps_left--;
        }
        is( $hsps_left, 0 );
    }
    last if ( $count++ > @valid );
}
is( @valid, 0 );

# test that add hit really works properly for BLAST objects
# bug 1611
my @hits = $result->hits;
$result->add_hit( $hits[0] );
is( $result->num_hits, @hits + 1 );

# test WU-BLAST -noseqs option
$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('ecolitst.noseqs.wublastp')
);

$result = $searchio->next_result;
is(
    $result->algorithm_reference, 'Gish, W. (1996-2004) http://blast.wustl.edu
'
);
is( $result->database_name,    'ecoli.aa' );
is( $result->database_letters, 1358990 );
is( $result->database_entries, 4289 );
is( $result->algorithm,        'BLASTP' );
like( $result->algorithm_version, qr/^2\.0MP\-WashU/ );
like( $result->query_name,
qr/gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I,\s+homoserine dehydrogenase I [Escherichia coli]/
);
is( $result->query_accession, 'AAC73113.1' );
is( $result->query_gi,        1786183 );

is( $result->query_length,                          820 );
is( $result->get_statistic('kappa'),                0.135 );
is( $result->get_statistic('lambda'),               0.319 );
is( $result->get_statistic('entropy'),              0.384 );
is( $result->get_statistic('dbletters'),            1358990 );
is( $result->get_statistic('dbentries'),            4289 );
is( $result->get_parameter('matrix'),               'BLOSUM62' );
is( $result->get_statistic('Frame+0_lambda_used'),  '0.319' );
is( $result->get_statistic('Frame+0_kappa_used'),   '0.135' );
is( $result->get_statistic('Frame+0_entropy_used'), '0.384' );

is( $result->get_statistic('Frame+0_lambda_computed'),  '0.319' );
is( $result->get_statistic('Frame+0_kappa_computed'),   '0.135' );
is( $result->get_statistic('Frame+0_entropy_computed'), '0.384' );

is( $result->get_statistic('Frame+0_lambda_gapped'),  '0.244' );
is( $result->get_statistic('Frame+0_kappa_gapped'),   '0.0300' );
is( $result->get_statistic('Frame+0_entropy_gapped'), '0.180' );

@valid = (
    [ 'gb|AAC73113.1|', 820, 'AAC73113', '0',       4141 ],
    [ 'gb|AAC76922.1|', 810, 'AAC76922', '6.6e-93', 907 ],
    [ 'gb|AAC76994.1|', 449, 'AAC76994', '2.8e-47', 483 ]
);
$count = 0;
while ( $hit = $result->next_hit ) {
    my $d = shift @valid;

    is( $hit->name,      shift @$d );
    is( $hit->length,    shift @$d );
    is( $hit->accession, shift @$d );
    float_is( $hit->significance, shift @$d );
    is( $hit->raw_score, shift @$d );

    if ( $count == 0 ) {
        my $hsps_left = 1;
        while ( my $hsp = $hit->next_hsp ) {
            is( $hsp->query->start,    1 );
            is( $hsp->query->end,      820 );
            is( $hsp->hit->start,      1 );
            is( $hsp->hit->end,        820 );
            is( $hsp->length('total'), 820 );

            float_is( $hsp->evalue, 0. );
            float_is( $hsp->pvalue, '0.' );
            is( $hsp->score,                   4141 );
            is( $hsp->bits,                    1462.8 );
            is( $hsp->percent_identity,        100 );
            is( $hsp->frac_identical('query'), 1.00 );
            is( $hsp->frac_identical('hit'),   1.00 );
            is( $hsp->gaps,                    0 );
            is( $hsp->n,                       1 );
            $hsps_left--;
        }
        is( $hsps_left, 0 );
    }
    last if ( $count++ > @valid );
}
is( @valid, 0 );

# test tblastx
$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('HUMBETGLOA.tblastx')
);

$result = $searchio->next_result;
like($result->algorithm_reference,qr/Gapped BLAST and PSI-BLAST/);
is( $result->database_name,    'ecoli.nt' );
is( $result->database_letters, 4662239 );
is( $result->database_entries, 400 );
is( $result->algorithm,        'TBLASTX' );
like( $result->algorithm_version, qr/^2\.1\.2/ );
is( $result->query_name, 'HUMBETGLOA' );
is( $result->query_description,
    'Human haplotype C4 beta-globin gene, complete cds.' );
is( $result->query_length,                        3002 );
is( $result->get_statistic('kappa'),              0.135 );
is( $result->get_statistic('lambda'),             0.318 );
is( $result->get_statistic('entropy'),            0.401 );
is( $result->get_statistic('dbletters'),          4662239 );
is( $result->get_statistic('dbentries'),          400 );
is( $result->get_statistic('querylength'),        953 );
is( $result->get_statistic('effectivedblength'),  1535279 );
is( $result->get_statistic('effectivespace'),     1463120887 );
is( $result->get_statistic('effectivespaceused'), 1463120887 );
is( $result->get_statistic('T'),                  13 );
is( $result->get_statistic('X1'),                 16 );
is( $result->get_statistic('X1_bits'),            7.3 );
is( $result->get_statistic('X2'),                 0 );
is( $result->get_statistic('X2_bits'),            '0.0' );
is( $result->get_statistic('S1'),                 41 );
is( $result->get_statistic('S1_bits'),            21.7 );
is( $result->get_statistic('S2'),                 53 );
is( $result->get_statistic('S2_bits'),            27.2 );

is( $result->get_statistic('decayconst'), 0.1 );

is( $result->get_parameter('matrix'), 'BLOSUM62' );

@valid = (
    [ 'gb|AE000479.1|AE000479', 10934, 'AE000479', '0.13', 33.6, 67 ],
    [ 'gb|AE000302.1|AE000302', 10264, 'AE000302', '0.61', 31.3, 62 ],
    [ 'gb|AE000277.1|AE000277', 11653, 'AE000277', '0.84', 30.8, 61 ]
);
$count = 0;

while ( $hit = $result->next_hit ) {
    my $d = shift @valid;
    is( $hit->name,      shift @$d );
    is( $hit->length,    shift @$d );
    is( $hit->accession, shift @$d );
    float_is( $hit->significance, shift @$d );
    is( $hit->bits,      shift @$d );
    is( $hit->raw_score, shift @$d );

    if ( $count == 0 ) {
        my $hsps_left = 1;
        while ( my $hsp = $hit->next_hsp ) {
            is( $hsp->query->start,    1057 );
            is( $hsp->query->end,      1134 );
            is( $hsp->query->strand,   1 );
            is( $hsp->strand('query'), $hsp->query->strand );
            is( $hsp->hit->end,        5893 );
            is( $hsp->hit->start,      5816 );
            is( $hsp->hit->strand,     -1 );
            is( $hsp->strand('sbjct'), $hsp->subject->strand );
            is( $hsp->length('total'), 26 );

            float_is( $hsp->evalue, 0.13 );
            is( $hsp->score, 67 );
            is( $hsp->bits,  33.6 );
            is( sprintf( "%.2f", $hsp->percent_identity ),        42.31 );
            is( sprintf( "%.4f", $hsp->frac_identical('query') ), '0.4231' );
            is( sprintf( "%.4f", $hsp->frac_identical('hit') ),   '0.4231' );
            is( $hsp->query->frame(),  0 );
            is( $hsp->hit->frame(),    1 );
            is( $hsp->gaps,            0 );
            is( $hsp->query_string,    'SAYWSIFPPLGCWWSTLGPRGSLSPL' );
            is( $hsp->hit_string,      'AAVWALFPPVGSQWGCLASQWRTSPL' );
            is( $hsp->homology_string, '+A W++FPP+G  W  L  +   SPL' );

            # changed to reflect positional ambiguities, note extra flag
            is(
                join( ' ', $hsp->seq_inds( 'query', 'nomatch', 1 ) ),
                '1063-1065 1090-1095 1099-1104 1108-1113 1117-1125'
            );
            is(
                join( ' ', $hsp->seq_inds( 'hit', 'nomatch', 1 ) ),
                '5825-5833 5837-5842 5846-5851 5855-5860 5885-5887'
            );
            is( $hsp->ambiguous_seq_inds, 'query/subject' );
            is( $hsp->n,                  1 );
            $hsps_left--;
        }
        is( $hsps_left, 0 );
    }
    last if ( $count++ > @valid );
}
is( @valid, 0 );

# test for MarkW bug in blastN

$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('a_thaliana.blastn')
);

$result = $searchio->next_result;
like($result->algorithm_reference,qr/Gapped BLAST and PSI-BLAST/);
is( $result->rid, '1012577175-3730-28291' );
is( $result->database_name,
'All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,or phase 0, 1 or 2 HTGS sequences) '
);
is( $result->database_letters, 4677375331 );
is( $result->database_entries, 1083200 );
is( $result->algorithm,        'BLASTN' );
like( $result->algorithm_version, qr/^2\.2\.1/ );
is( $result->query_name,                          '' );
is( $result->query_length,                        60 );
is( $result->get_parameter('gapopen'),            5 );
is( $result->get_parameter('gapext'),             2 );
is( $result->get_parameter('ktup'),               undef );
is( $result->get_statistic('querylength'),        41 );
is( $result->get_statistic('effectivedblength'),  4656794531 );
is( $result->get_statistic('effectivespace'),     190928575771 );
is( $result->get_statistic('effectivespaceused'), 190928575771 );

is( $result->get_statistic('lambda'),  1.37 );
is( $result->get_statistic('kappa'),   0.711 );
is( $result->get_statistic('entropy'), 1.31 );
is( $result->get_statistic('T'),       0 );
is( $result->get_statistic('A'),       30 );
is( $result->get_statistic('X1'),      '6' );
is( $result->get_statistic('X1_bits'), 11.9 );
is( $result->get_statistic('X2'),      15 );
is( $result->get_statistic('X2_bits'), 29.7 );
is( $result->get_statistic('S1'),      12 );
is( $result->get_statistic('S1_bits'), 24.3 );
is( $result->get_statistic('S2'),      17 );
is( $result->get_statistic('S2_bits'), 34.2 );

is( $result->get_statistic('dbentries'), 1083200 );

@valid = (
    [ 'gb|AY052359.1|', 2826, 'AY052359', '3e-18', 95.6, 48, 1, 60, '1.0000' ],
    [
        'gb|AC002329.2|AC002329', 76170, 'AC002329', '3e-18', 95.6, 48, 1, 60,
        '1.0000'
    ],
    [
        'gb|AF132318.1|AF132318', 5383, 'AF132318', '0.04', 42.1, 21, 35, 55,
        '0.3500'
    ]
);
$count = 0;

while ( my $hit = $result->next_hit ) {
    my $d = shift @valid;
    is( $hit->name,      shift @$d );
    is( $hit->length,    shift @$d );
    is( $hit->accession, shift @$d );
    float_is( $hit->significance, shift @$d );
    is( $hit->bits,      shift @$d );
    is( $hit->raw_score, shift @$d );
    is( $hit->start,     shift @$d );
    is( $hit->end,       shift @$d );
    is( sprintf( "%.4f", $hit->frac_aligned_query ), shift @$d );

    if ( $count == 0 ) {
        my $hsps_left = 1;
        while ( my $hsp = $hit->next_hsp ) {
            is( $hsp->query->start,    1 );
            is( $hsp->query->end,      60 );
            is( $hsp->query->strand,   1 );
            is( $hsp->hit->start,      154 );
            is( $hsp->hit->end,        212 );
            is( $hsp->hit->strand,     1 );
            is( $hsp->length('total'), 60 );
            float_is( $hsp->evalue, 3e-18 );
            is( $hsp->score, 48 );
            is( $hsp->bits,  95.6 );
            is( sprintf( "%.2f", $hsp->percent_identity ),        96.67 );
            is( sprintf( "%.4f", $hsp->frac_identical('query') ), 0.9667 );
            is( sprintf( "%.4f", $hsp->frac_identical('hit') ),   0.9831 );
            is( $hsp->query->frame(), 0 );
            is( $hsp->hit->frame(),   0 );
            is( $hsp->query->seq_id,  undef );
            is( $hsp->hit->seq_id,    'gb|AY052359.1|' );
            is( $hsp->gaps('query'),  0 );
            is( $hsp->gaps('hit'),    1 );
            is( $hsp->gaps,           1 );
            is( $hsp->query_string,
                'aggaatgctgtttaattggaatcgtacaatggagaatttgacggaaatagaatcaacgat'
            );
            is( $hsp->hit_string,
                'aggaatgctgtttaattggaatca-acaatggagaatttgacggaaatagaatcaacgat'
            );
            is( $hsp->homology_string,
                '|||||||||||||||||||||||  |||||||||||||||||||||||||||||||||||'
            );
            my $aln = $hsp->get_aln;
            is( sprintf( "%.2f", $aln->overall_percentage_identity ), 96.67 );
            is( sprintf( "%.2f", $aln->percentage_identity ),         98.31 );
            is( $hsp->n, 1 );
            $hsps_left--;
        }
        is( $hsps_left, 0 );
    }
    last if ( $count++ > @valid );
}
is( @valid, 0 );

#WU-BlastX test

$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('dnaEbsub_ecoli.wublastx')
);

$result = $searchio->next_result;
is(
    $result->algorithm_reference, 'Gish, W. (1996-2000) http://blast.wustl.edu
Gish, Warren and David J. States (1993).  Identification of protein coding
regions by database similarity search.  Nat. Genet. 3:266-72.
'
);
is( $result->database_name,    'ecoli.aa' );
is( $result->database_letters, 1358990 );
is( $result->database_entries, 4289 );
is( $result->algorithm,        'BLASTX' );
like( $result->algorithm_version, qr/^2\.0MP\-WashU/ );
is( $result->query_name, 'gi|142864|gb|M10040.1|BACDNAE' );
is( $result->query_description,
    'B.subtilis dnaE gene encoding DNA primase, complete cds' );
is( $result->query_accession,         'M10040.1' );
is( $result->query_gi,                142864 );
is( $result->query_length,            2001 );
is( $result->get_parameter('matrix'), 'blosum62' );

is( $result->get_statistic('lambda'),  0.318 );
is( $result->get_statistic('kappa'),   0.135 );
is( $result->get_statistic('entropy'), 0.401 );

is( $result->get_statistic('dbentries'), 4289 );

@valid = ( [ 'gi|1789447|gb|AAC76102.1|', 581, 'AAC76102', '1.1e-74', 671 ] );
$count = 0;

while ( my $hit = $result->next_hit ) {
    my $d = shift @valid;
    is( $hit->name,      shift @$d );
    is( $hit->length,    shift @$d );
    is( $hit->accession, shift @$d );
    float_is( $hit->significance, shift @$d );
    is( $hit->raw_score, shift @$d );
    is( sprintf( "%.4f", $hit->frac_identical('query') ), '0.3640' );
    is( sprintf( "%.4f", $hit->frac_identical('hit') ),   '0.3660' );
    is( sprintf( "%.4f", $hit->frac_conserved('query') ), '0.5370' );
    is( sprintf( "%.4f", $hit->frac_conserved('hit') ),   '0.5400' );
    is( sprintf( "%.4f", $hit->frac_aligned_query ),      '0.6200' );
    is( sprintf( "%.4f", $hit->frac_aligned_hit ),        '0.7100' );

    if ( $count == 0 ) {
        my $hsps_left = 1;
        while ( my $hsp = $hit->next_hsp ) {
            is( $hsp->query->start,    21 );
            is( $hsp->query->end,      1265 );
            is( $hsp->query->strand,   1 );
            is( $hsp->hit->start,      1 );
            is( $hsp->hit->end,        413 );
            is( $hsp->hit->strand,     0 );
            is( $hsp->length('total'), 421 );
            float_is( $hsp->evalue, 1.1e-74 );
            float_is( $hsp->pvalue, '1.1e-74' );
            is( $hsp->score, 671 );
            is( $hsp->bits,  265.8 );
            is( sprintf( "%.2f", $hsp->percent_identity ), 35.87 );

            is( sprintf( "%.4f", $hsp->frac_identical('query') ), 0.3639 );
            is( sprintf( "%.4f", $hsp->frac_identical('hit') ),   0.3656 );
            is( sprintf( "%.4f", $hsp->frac_conserved('query') ), 0.5373 );
            is( sprintf( "%.2f", $hsp->frac_conserved('hit') ),   0.54 );

            is( sprintf( "%.4f", $hsp->frac_identical('hsp') ), 0.3587 );
            is( sprintf( "%.4f", $hsp->frac_conserved('hsp') ), 0.5297 );

            is( $hsp->query->frame(), 2 );
            is( $hsp->hit->frame(),   0 );
            is( $hsp->gaps('query'),  6 );
            is( $hsp->gaps('hit'),    8 );
            is( $hsp->gaps,           14 );
            is( $hsp->query_string,
'MGNRIPDEIVDQVQKSADIVEVIGDYVQLKKQGRNYFGLCPFHGESTPSFSVSPDKQIFHCFGCGAGGNVFSFLRQMEGYSFAESVSHLADKYQIDFPDDITVHSGARP---ESSGEQKMAEAHELLKKFYHHLLINTKEGQEALDYLLSRGFTKELINEFQIGYALDSWDFITKFLVKRGFSEAQMEKAGLLIRREDGSGYFDRFRNRVMFPIHDHHGAVVAFSGRALGSQQPKYMNSPETPLFHKSKLLYNFYKARLHIRKQERAVLFEGFADVYTAVSSDVKESIATMGTSLTDDHVKILRRNVEEIILCYDSDKAGYEATLKASELL---QKKGCKVRVAMIPDGLDPDDYIKKFGGEKFKNDIIDASVTVMAFKMQYFRKGKNLSDEGDRLAYIKDVLKEISTLSGSLEQEVYVKQ'
            );
            is( $hsp->hit_string,
'MAGRIPRVFINDLLARTDIVDLIDARVKLKKQGKNFHACCPFHNEKTPSFTVNGEKQFYHCFGCGAHGNAIDFLMNYDKLEFVETVEELAAMHNLEVPFE----AGSGPSQIERHQRQTLYQLMDGLNTFYQQSL-QQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSY-DRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARM-EQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLR-IYLRQ'
            );
            is( $hsp->homology_string,
'M  RIP   ++ +    DIV++I   V+LKKQG+N+   CPFH E TPSF+V+ +KQ +HCFGCGA GN   FL   +   F E+V  LA  + ++ P +    +G+ P   E    Q + +  + L  FY   L        A  YL  RG + E+I  F IG+A   WD + K       +   +  AG+L+  + G  Y DRFR RVMFPI D  G V+ F GR LG+  PKY+NSPET +FHK + LY  Y+A+    +  R ++ EG+ DV       +  ++A++GTS T DH+++L R    +I CYD D+AG +A  +A E        G ++R   +PDG DPD  ++K G E F+  + + ++ + AF         +LS    R       L  IS + G   + +Y++Q'
            );
            is(
                join( ' ', $hsp->seq_inds( 'query', 'nomatch', 1 ) ),
'24-29 39-47 54-56 60-71 90-98 129-137 150-152 156-158 180-182 192-194 219-221 228-236 243-251 255-263 267-269 279-284 291-296 300-302 309-311 315-317 321-332 342-344 351-362 366-368 372-374 378-383 387-389 393-398 405-413 417-440 444-449 456-461 468-470 474-476 486-491 495-497 510-518 525-527 531-533 537-557 561-569 573-578 594-599 603-605 609-614 618-620 633-635 654-656 660-665 669-671 678-680 684-686 693-695 705-710 738-740 753-755 759-761 768-773 786-797 801-806 810-812 819-821 831-833 840-860 864-869 894-896 900-902 921-923 927-938 945-947 957-959 972-974 981-986 993-995 999-1013 1017-1019 1029-1037 1050-1052 1062-1067 1077-1079 1083-1085 1089-1091 1098-1103 1107-1109 1113-1115 1122-1124 1128-1130 1137-1163 1173-1184 1188-1208 1212-1217 1224-1226 1230-1232 1236-1244 1248-1250'
            );
            is(
                join( ' ', $hsp->seq_inds( 'query', 'mismatch', 1 ) ),
'24-29 39-47 54-56 60-71 90-98 129-137 150-152 156-158 180-182 192-194 219-221 228-236 243-251 255-263 267-269 279-284 291-296 300-302 309-311 315-317 342-344 351-362 366-368 372-374 378-383 387-389 393-398 405-413 420-440 444-449 456-461 468-470 474-476 486-491 495-497 510-518 525-527 531-533 537-557 561-569 573-578 594-599 603-605 609-614 633-635 654-656 660-665 669-671 678-680 684-686 693-695 705-710 738-740 753-755 759-761 768-773 786-797 801-806 810-812 819-821 831-833 840-860 864-869 894-896 900-902 921-923 927-938 945-947 957-959 972-974 981-986 993-995 999-1013 1017-1019 1029-1037 1050-1052 1062-1067 1077-1079 1083-1085 1089-1091 1098-1103 1113-1115 1122-1124 1128-1130 1137-1163 1173-1184 1188-1208 1212-1217 1224-1226 1230-1232 1236-1244'
            );
            is(
                join( ' ', $hsp->seq_inds( 'hit', 'nomatch', 1 ) ),
'2 3 7-9 12 14-17 24-26 37-39 44 46 54 58 67 70-72 75-77 79-81 83 87 88 91 92 94 97 99 104 106-108 110-113 115 117 119 120 122 124 125 128-130 132-138 140 141 144 145 148 150 154 155 157 162-164 167 169 171-177 179-181 183 184 190 191 193 195 196 202 209 211 212 214 217 219 222 226 227 237 242 244 247 248 253-256 258 259 261 264 268 271-277 279 280 289 291 298 300-303 306 310 315 318 319 322 324-331 333 337-339 344 348 349 353 355 357 360 361 364 367 369 372-380 384-387 389-395 397 398 401 403 405-407'
            );
            is(
                join( ' ', $hsp->seq_inds( 'hit', 'mismatch', 1 ) ),
'2 3 7-9 12 14-17 24-26 37-39 44 46 54 58 67 70-72 75-77 79-81 83 87 88 91 92 94 97 99 104 110-113 115 117 119 120 122 124 125 128-130 132-138 140 141 144 145 148 150 154 155 157 162-164 167 169 171-177 179-181 183 184 190 191 193 195 196 202 209 211 212 214 217 219 222 226 227 237 242 244 247 248 253-256 258 259 261 264 268 271-277 279 280 289 291 298 300-303 306 310 315 318 319 322 324 325 329-331 333 337-339 344 348 349 353 355 357 360 361 364 367 369 372-380 384-387 389-395 397 398 401 403 405-407'
            );
            is( join( ' ', $hsp->seq_inds( 'query', 'gaps', 1 ) ), '347 1004' );
            is( join( ' ', $hsp->seq_inds( 'hit', 'gaps', 1 ) ),
                '100 131 197 362 408' );
            is( $hsp->ambiguous_seq_inds, 'query' );
            is( $hsp->n,                  1 );
            $hsps_left--;
        }
        is( $hsps_left, 0 );
    }
    last if ( $count++ > @valid );
}
is( @valid, 0 );

#Trickier WU-Blast
$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('tricky.wublast')
);
$result = $searchio->next_result;
my $hits_left = 1;
while ( my $hit = $result->next_hit ) {

# frac_aligned_hit used to be over 1, frac_identical & frac_conserved are still too wrong
  TODO: {
        local $TODO = 'frac_identical & frac_conserved are still too wrong';
        cmp_ok sprintf( "%.3f", $hit->frac_identical ), '>',  0.9;
        cmp_ok sprintf( "%.3f", $hit->frac_conserved ), '<=', 1;
    }
    is( sprintf( "%.2f", $hit->frac_aligned_query ), '0.92' );
    is( sprintf( "%.2f", $hit->frac_aligned_hit ),   '0.91' );
    $hits_left--;
}
is( $hits_left, 0 );

# More frac_ method testing, this time on ncbi blastn
$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('frac_problems.blast')
);
my @expected = ( "1.000", "0.943" );
while ( my $result = $searchio->next_result ) {
    my $hit = $result->next_hit;
    is( $hit->frac_identical, shift @expected );
}
is( @expected, 0 );

# And even more: frac_aligned_query should never be over 1!
$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('frac_problems2.blast')
);
$result = $searchio->next_result;
$hit    = $result->next_hit;
is $hit->frac_aligned_query, 0.97;

# Also, start and end should be sane
$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('frac_problems3.blast')
);
$result = $searchio->next_result;
$hit    = $result->next_hit;
is $hit->start('sbjct'), 207;
is $hit->end('sbjct'),   1051;

#WU-TBlastN test

$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('dnaEbsub_ecoli.wutblastn')
);

$result = $searchio->next_result;
is(
    $result->algorithm_reference, 'Gish, W. (1996-2000) http://blast.wustl.edu
'
);
is( $result->database_name,    'ecoli.nt' );
is( $result->database_letters, 4662239 );
is( $result->database_entries, 400 );
is( $result->algorithm,        'TBLASTN' );
like( $result->algorithm_version, qr/^2\.0MP\-WashU/ );
is( $result->query_name,              'gi|142865|gb|AAA22406.1|' );
is( $result->query_description,       'DNA primase' );
is( $result->query_accession,         'AAA22406.1' );
is( $result->query_gi,                142865 );
is( $result->query_length,            603 );
is( $result->get_parameter('matrix'), 'blosum62' );

is( $result->get_statistic('lambda'),  '0.320' );
is( $result->get_statistic('kappa'),   0.136 );
is( $result->get_statistic('entropy'), 0.387 );

is( $result->get_statistic('dbentries'), 400 );

@valid =
  ( [ 'gi|1789441|gb|AE000388.1|AE000388', 10334, 'AE000388', '1.4e-73', 671 ]
  );
$count = 0;

while ( my $hit = $result->next_hit ) {
    my $d = shift @valid;
    is( $hit->name,      shift @$d );
    is( $hit->length,    shift @$d );
    is( $hit->accession, shift @$d );
    float_is( $hit->significance, shift @$d );
    is( $hit->raw_score, shift @$d );

    if ( $count == 0 ) {
        my $hsps_left = 1;
        while ( my $hsp = $hit->next_hsp ) {
            is( $hsp->query->start,    1 );
            is( $hsp->query->end,      415 );
            is( $hsp->query->strand,   0 );
            is( $hsp->hit->start,      4778 );
            is( $hsp->hit->end,        6016 );
            is( $hsp->hit->strand,     1 );
            is( $hsp->length('total'), 421 );
            float_is( $hsp->evalue, 1.4e-73 );
            float_is( $hsp->pvalue, 1.4e-73 );
            is( $hsp->score, 671 );
            is( $hsp->bits,  265.8 );
            is( sprintf( "%.2f", $hsp->percent_identity ),        35.87 );
            is( sprintf( "%.4f", $hsp->frac_identical('hit') ),   0.3656 );
            is( sprintf( "%.4f", $hsp->frac_identical('query') ), 0.3639 );
            is( sprintf( "%.4f", $hsp->frac_conserved('hsp') ),   0.5297 );
            is( $hsp->query->frame(), 0 );
            is( $hsp->hit->frame(),   1 );
            is( $hsp->gaps('query'),  6 );
            is( $hsp->gaps('hit'),    8 );
            is( $hsp->gaps,           14 );
            is( $hsp->query_string,
'MGNRIPDEIVDQVQKSADIVEVIGDYVQLKKQGRNYFGLCPFHGESTPSFSVSPDKQIFHCFGCGAGGNVFSFLRQMEGYSFAESVSHLADKYQIDFPDDITVHSGARP---ESSGEQKMAEAHELLKKFYHHLLINTKEGQEALDYLLSRGFTKELINEFQIGYALDSWDFITKFLVKRGFSEAQMEKAGLLIRREDGSGYFDRFRNRVMFPIHDHHGAVVAFSGRALGSQQPKYMNSPETPLFHKSKLLYNFYKARLHIRKQERAVLFEGFADVYTAVSSDVKESIATMGTSLTDDHVKILRRNVEEIILCYDSDKAGYEATLKASELL---QKKGCKVRVAMIPDGLDPDDYIKKFGGEKFKNDIIDASVTVMAFKMQYFRKGKNLSDEGDRLAYIKDVLKEISTLSGSLEQEVYVKQ'
            );
            is( $hsp->hit_string,
'MAGRIPRVFINDLLARTDIVDLIDARVKLKKQGKNFHACCPFHNEKTPSFTVNGEKQFYHCFGCGAHGNAIDFLMNYDKLEFVETVEELAAMHNLEVPFE----AGSGPSQIERHQRQTLYQLMDGLNTFYQQSL-QQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSY-DRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARM-EQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLR-IYLRQ'
            );
            is( $hsp->homology_string,
'M  RIP   ++ +    DIV++I   V+LKKQG+N+   CPFH E TPSF+V+ +KQ +HCFGCGA GN   FL   +   F E+V  LA  + ++ P +    +G+ P   E    Q + +  + L  FY   L        A  YL  RG + E+I  F IG+A   WD + K       +   +  AG+L+  + G  Y DRFR RVMFPI D  G V+ F GR LG+  PKY+NSPET +FHK + LY  Y+A+    +  R ++ EG+ DV       +  ++A++GTS T DH+++L R    +I CYD D+AG +A  +A E        G ++R   +PDG DPD  ++K G E F+  + + ++ + AF         +LS    R       L  IS + G   + +Y++Q'
            );
            is(
                join( ' ', $hsp->seq_inds( 'query', 'nomatch', 1 ) ),
'2 3 7-9 12 14-17 24-26 37-39 44 46 54 58 67 70-72 75-77 79-81 83 87 88 91 92 94 97 99 101-104 108 111-114 116 118 120 121 123 125 126 129-131 133-140 142 143 146 147 150 152 156 157 159 164-166 169 171 173-179 181-183 185 186 192 193 195 197 198 200 205 212 214 215 217 220 222 225 229 230 240 245 247 250 251 256-259 261 262 264 267 271 274-280 282 283 292 294 301 303-306 309 313 318 321 322 325 327-331 333 337-339 344 348 349 353 355 357 360 361 363 365 368 370 373-381 385-388 390-396 398 399 402 404 406-408 410'
            );
            is(
                join( ' ', $hsp->seq_inds( 'hit', 'nomatch', 1 ) ),
'4781-4786 4796-4804 4811-4813 4817-4828 4847-4855 4886-4894 4907-4909 4913-4915 4937-4939 4949-4951 4976-4978 4985-4993 5000-5008 5012-5020 5024-5026 5036-5041 5048-5053 5057-5059 5066-5068 5072-5074 5087-5089 5093-5101 5105-5116 5120-5122 5126-5128 5132-5137 5141-5143 5147-5152 5159-5167 5171-5191 5195-5200 5207-5212 5219-5221 5225-5227 5237-5242 5246-5248 5261-5269 5276-5278 5282-5284 5288-5308 5312-5320 5324-5329 5345-5350 5354-5356 5360-5365 5381-5383 5402-5404 5408-5413 5417-5419 5426-5428 5432-5434 5441-5443 5453-5458 5486-5488 5501-5503 5507-5509 5516-5521 5534-5545 5549-5554 5558-5560 5567-5569 5579-5581 5588-5608 5612-5617 5642-5644 5648-5650 5669-5671 5675-5686 5693-5695 5705-5707 5720-5722 5729-5734 5741-5743 5747-5770 5774-5776 5786-5794 5807-5809 5819-5824 5834-5836 5840-5842 5846-5848 5855-5860 5867-5869 5876-5878 5882-5884 5891-5917 5927-5938 5942-5962 5966-5971 5978-5980 5984-5986 5990-5998'
            );
            is( join( ' ', $hsp->seq_inds( 'query', 'gaps', 1 ) ), '109 328' );
            is( join( ' ', $hsp->seq_inds( 'hit', 'gaps', 1 ) ),
                '5077 5170 5368 5863 6001' );
            is( $hsp->ambiguous_seq_inds, 'subject' );
            is( $hsp->n,                  1 );
            $hsps_left--;
        }
        is( $hsps_left, 0 );
    }
    last if ( $count++ > @valid );
}
is( $count, 1 );

# WU-BLAST TBLASTX
$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('dnaEbsub_ecoli.wutblastx')
);

$result = $searchio->next_result;
is(
    $result->algorithm_reference, 'Gish, W. (1996-2000) http://blast.wustl.edu
'
);
is( $result->database_name,    'ecoli.nt' );
is( $result->database_letters, 4662239 );
is( $result->database_entries, 400 );
is( $result->algorithm,        'TBLASTX' );
like( $result->algorithm_version, qr/^2\.0MP\-WashU/ );
is( $result->query_name, 'gi|142864|gb|M10040.1|BACDNAE' );
is( $result->query_description,
    'B.subtilis dnaE gene encoding DNA primase, complete cds' );
is( $result->query_accession,         'M10040.1' );
is( $result->query_gi,                142864 );
is( $result->query_length,            2001 );
is( $result->get_parameter('matrix'), 'blosum62' );

is( $result->get_statistic('lambda'),    0.318 );
is( $result->get_statistic('kappa'),     0.135 );
is( $result->get_statistic('entropy'),   0.401 );
is( $result->get_statistic('dbentries'), 400 );

@valid = (
    [
        'gi|1789441|gb|AE000388.1|AE000388',
        10334, 'AE000388', '6.4e-70', 318, 148.6
    ],
    [ 'gi|2367383|gb|AE000509.1|AE000509', 10589, 'AE000509', 1, 59, 29.9 ]
);
$count = 0;

while ( my $hit = $result->next_hit ) {
    my $d = shift @valid;
    is( $hit->name,      shift @$d );
    is( $hit->length,    shift @$d );
    is( $hit->accession, shift @$d );

    # using e here to deal with 0.9992 coming out right here as well
    float_is( $hit->significance, shift @$d );
    is( $hit->raw_score, shift @$d );
    is( $hit->bits,      shift @$d );
    if ( $count == 0 ) {
        my $hspcounter = 0;
        while ( my $hsp = $hit->next_hsp ) {
            $hspcounter++;
            if ( $hspcounter == 3 ) {

                # let's actually look at the 3rd HSP
                is( $hsp->query->start,    441 );
                is( $hsp->query->end,      617 );
                is( $hsp->query->strand,   1 );
                is( $hsp->hit->start,      5192 );
                is( $hsp->hit->end,        5368 );
                is( $hsp->hit->strand,     1 );
                is( $hsp->length('total'), 59 );
                float_is( $hsp->evalue, 6.4e-70 );
                float_is( $hsp->pvalue, 6.4e-70 );
                is( $hsp->score, 85 );
                is( $hsp->bits,  41.8 );
                is( sprintf( "%.2f", $hsp->percent_identity ),        '32.20' );
                is( sprintf( "%.3f", $hsp->frac_identical('hit') ),   0.322 );
                is( sprintf( "%.3f", $hsp->frac_identical('query') ), 0.322 );
                is( sprintf( "%.4f", $hsp->frac_conserved('hsp') ),   0.4746 );
                is( $hsp->query->frame(), 2 );
                is( $hsp->hit->frame(),   1 );
                is( $hsp->gaps('query'),  0 );
                is( $hsp->gaps('hit'),    0 );
                is( $hsp->gaps,           0 );
                is( $hsp->n,              1 );
                is( $hsp->query_string,
'ALDYLLSRGFTKELINEFQIGYALDSWDFITKFLVKRGFSEAQMEKAGLLIRREDGSGY'
                );
                is( $hsp->hit_string,
'ARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSY'
                );
                is( $hsp->homology_string,
'A  YL  RG + E+I  F IG+A   WD + K       +   +  AG+L+  + G  Y'
                );
                is(
                    join( ' ', $hsp->seq_inds( 'query', 'nomatch', 1 ) ),
'444-449 456-461 468-470 474-476 486-491 495-497 510-518 525-527 531-533 537-557 561-569 573-578 594-599 603-605 609-614'
                );
                is(
                    join( ' ', $hsp->seq_inds( 'hit', 'nomatch', 1 ) ),
'5195-5200 5207-5212 5219-5221 5225-5227 5237-5242 5246-5248 5261-5269 5276-5278 5282-5284 5288-5308 5312-5320 5324-5329 5345-5350 5354-5356 5360-5365'
                );
                is( $hsp->ambiguous_seq_inds, 'query/subject' );
                last;
            }
        }
        is( $hspcounter, 3 );
    }
    elsif ( $count == 1 ) {
        my $hsps_to_do = 1;
        while ( my $hsp = $hit->next_hsp ) {
            is( $hsp->query->start,    587 );
            is( $hsp->query->end,      706 );
            is( $hsp->query->strand,   -1 );
            is( $hsp->hit->start,      4108 );
            is( $hsp->hit->end,        4227 );
            is( $hsp->hit->strand,     -1 );
            is( $hsp->length('total'), 40 );
            float_is( $hsp->evalue, 7.1 );
            float_is( $hsp->pvalue, '1.00' );
            is( $hsp->score, 59 );
            is( $hsp->bits,  29.9 );
            is( sprintf( "%.2f", $hsp->percent_identity ),        '37.50' );
            is( sprintf( "%.4f", $hsp->frac_identical('hit') ),   '0.3750' );
            is( sprintf( "%.4f", $hsp->frac_identical('query') ), '0.3750' );
            is( sprintf( "%.4f", $hsp->frac_conserved('hsp') ),   '0.4750' );
            is( $hsp->query->frame(), 2 );
            is( $hsp->hit->frame(),   2 );
            is( $hsp->gaps('query'),  0 );
            is( $hsp->gaps('hit'),    0 );
            is( $hsp->gaps,           0 );
            is( $hsp->n,              1 );
            is( $hsp->query_string,
                'WLPRALPEKATTAP**SWIGNMTRFLKRSKYPLPSSRLIR' );
            is( $hsp->hit_string, 'WLSRTTVGSSTVSPRTFWITRMKVKLSSSKVTLPSTKSTR' );
            is( $hsp->homology_string,
                'WL R     +T +P   WI  M   L  SK  LPS++  R' );
            $hsps_to_do--;
            last;
        }
        is( $hsps_to_do, 0 );
    }
    last if ( $count++ > @valid );
}
is( $count, 2 );

# WU-BLAST -echofilter option test (Bug 2388)
$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('echofilter.wublastn')
);

$result = $searchio->next_result;
is(
    $result->algorithm_reference, 'Gish, W. (1996-2006) http://blast.wustl.edu
'
);
is( $result->database_name,    'NM_003201.fa' );
is( $result->database_letters, 1936 );
is( $result->database_entries, 1 );
is( $result->algorithm,        'BLASTN' );
like( $result->algorithm_version, qr/^2\.0MP\-WashU/ );
like( $result->query_name,
qr/ref|NM_003201.1| Homo sapiens transcription factor A, mitochondrial \(TFAM\), mRNA/
);
is( $result->query_accession, 'NM_003201.1' );

is( $result->query_length,               1936 );
is( $result->get_statistic('lambda'),    0.192 );
is( $result->get_statistic('kappa'),     0.182 );
is( $result->get_statistic('entropy'),   0.357 );
is( $result->get_statistic('dbletters'), 1936 );
is( $result->get_statistic('dbentries'), 1 );
is( $result->get_parameter('matrix'),    '+5,-4' );

@valid = ( [ 'ref|NM_003201.1|', 1936, 'NM_003201', '0', 9680 ], );
$count = 0;
while ( $hit = $result->next_hit ) {
    my $d = shift @valid;

    is( $hit->name,      shift @$d );
    is( $hit->length,    shift @$d );
    is( $hit->accession, shift @$d );
    float_is( $hit->significance, shift @$d );
    is( $hit->raw_score, shift @$d );

    if ( $count == 0 ) {
        my $hsps_left = 1;
        while ( my $hsp = $hit->next_hsp ) {
            is( $hsp->query->start,    1 );
            is( $hsp->query->end,      1936 );
            is( $hsp->hit->start,      1 );
            is( $hsp->hit->end,        1936 );
            is( $hsp->length('total'), 1936 );

            float_is( $hsp->evalue, 0. );
            float_is( $hsp->pvalue, '0.' );
            is( $hsp->score,                   9680 );
            is( $hsp->bits,                    1458.4 );
            is( $hsp->percent_identity,        100 );
            is( $hsp->frac_identical('query'), 1.00 );
            is( $hsp->frac_identical('hit'),   1.00 );
            is( $hsp->gaps,                    0 );
            is( $hsp->n,                       1 );
            $hsps_left--;
        }
        is( $hsps_left, 0 );
    }
    last if ( $count++ > @valid );
}
is( @valid, 0 );

# Do a multiblast report test
$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('multi_blast.bls')
);

@expected = qw(CATH_RAT CATL_HUMAN CATL_RAT PAPA_CARPA);
my $results_left = 4;
while ( my $result = $searchio->next_result ) {
    like($result->algorithm_reference, qr/Gapped BLAST and PSI-BLAST/);
    is( $result->query_name, shift @expected, "Multiblast query test" );
    $results_left--;
}
is( $results_left, 0 );

# Test GCGBlast parsing

$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('test.gcgblast')
);
$result = $searchio->next_result();
like($result->algorithm_reference,qr/Gapped BLAST and PSI-BLAST/);
is( $result->query_name,                   '/v0/people/staji002/test.gcg' );
is( $result->algorithm,                    'BLASTP' );
is( $result->algorithm_version,            '2.2.1 [Apr-13-2001]' );
is( $result->database_name,                'pir' );
is( $result->database_entries,             274514 );
is( $result->database_letters,             93460074 );
is( $result->get_statistic('querylength'), 44 );
is( $result->get_statistic('effectivedblength'),  65459646 );
is( $result->get_statistic('effectivespace'),     2880224424 );
is( $result->get_statistic('effectivespaceused'), 2880224424 );

$hit = $result->next_hit;
is( $hit->description, 'F22B7.10 protein - Caenorhabditis elegans' );
is( $hit->name,        'PIR2:S44629' );
is( $hit->length,      628 );
is( $hit->accession,   'PIR2:S44629' );
float_is( $hit->significance, 2e-08 );
is( $hit->raw_score, 136 );
is( $hit->bits,      '57.0' );
$hsp = $hit->next_hsp;
float_is( $hsp->evalue, 2e-08 );
is( $hsp->bits,                    '57.0' );
is( $hsp->score,                   136 );
is( int( $hsp->percent_identity ), 28 );
is( sprintf( "%.2f", $hsp->frac_identical('query') ), 0.29 );
is( $hsp->frac_conserved('total'), 69 / 135 );
is( $hsp->gaps('total'),           8 );
is( $hsp->gaps('hit'),             6 );
is( $hsp->gaps('query'),           2 );

is( $hsp->hit->start,   342 );
is( $hsp->hit->end,     470 );
is( $hsp->query->start, 3 );
is( $hsp->query->end,   135 );

is( $hsp->query_string,
'CAAEFDFMEKETPLRYTKTXXXXXXXXXXXXXXRKIISDMWGVLAKQQTHVRKHQFDHGELVYHALQLLAYTALGILIMRLKLFLTPYMCVMASLICSRQLFGW--LFCKVHPGAIVFVILAAMSIQGSANLQTQ'
);
is( $hsp->hit_string,
'CSAEFDFIQYSTIEKLCGTLLIPLALISLVTFVFNFVKNT-NLLWRNSEEIG----ENGEILYNVVQLCCSTVMAFLIMRLKLFMTPHLCIVAALFANSKLLGGDRISKTIRVSALVGVI-AILFYRGIPNIRQQ'
);
is( $hsp->homology_string,
'C+AEFDF++  T  +   T                 + +   +L +    +     ++GE++Y+ +QL   T +  LIMRLKLF+TP++C++A+L  + +L G   +   +   A+V VI A +  +G  N++ Q'
);

#test all the database accession number formats
$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('testdbaccnums.out')
);
$result = $searchio->next_result;
like($result->algorithm_reference,qr/Gapped BLAST and PSI-BLAST/);
is( $result->rid,                                 '1036160600-011802-21377' );
is( $result->get_statistic('querylength'),        9 );
is( $result->get_statistic('effectivedblength'),  35444647 );
is( $result->get_statistic('effectivespace'),     319001823 );
is( $result->get_statistic('effectivespaceused'), 319001823 );

@valid = (
    [ 'pir||T14789',           'T14789',    'T14789', 'CAB53709', 'AAH01726' ],
    [ 'gb|NP_065733.1|CYT19',  'NP_065733', 'CYT19' ],
    [ 'emb|XP_053690.4|Cyt19', 'XP_053690' ],
    [ 'dbj|NP_056277.2|DKFZP586L0724',      'NP_056277' ],
    [ 'prf||XP_064862.2',                   'XP_064862' ],
    [ 'pdb|BAB13968.1|1',                   'BAB13968' ],
    [ 'sp|Q16478|GLK5_HUMAN',               'Q16478' ],
    [ 'pat|US|NP_002079.2',                 'NP_002079' ],
    [ 'bbs|NP_079463.2|',                   'NP_079463' ],
    [ 'gnl|db1|NP_002444.1',                'NP_002444' ],
    [ 'ref|XP_051877.1|',                   'XP_051877' ],
    [ 'lcl|AAH16829.1|',                    'AAH16829' ],
    [ 'gi|1|gb|NP_065733.1|CYT19',          'NP_065733' ],
    [ 'gi|2|emb|XP_053690.4|Cyt19',         'XP_053690' ],
    [ 'gi|3|dbj|NP_056277.2|DKFZP586L0724', 'NP_056277' ],
    [ 'gi|4|pir||T14789',                   'T14789' ],
    [ 'gi|5|prf||XP_064862.2',              'XP_064862' ],
    [ 'gi|6|pdb|BAB13968.1|1',              'BAB13968' ],
    [ 'gi|7|sp|Q16478|GLK5_HUMAN',          'Q16478' ],
    [ 'gi|8|pat|US|NP_002079.2',            'NP_002079' ],
    [ 'gi|9|bbs|NP_079463.2|',              'NP_079463' ],
    [ 'gi|10|gnl|db1|NP_002444.1',          'NP_002444' ],
    [ 'gi|11|ref|XP_051877.1|',             'XP_051877' ],
    [ 'gi|12|lcl|AAH16829.1|',              'AAH16829' ],
    [ 'MY_test_ID',                         'MY_test_ID' ]
);

$hit = $result->next_hit;
my $d = shift @valid;
is( $hit->name,      shift @$d );
is( $hit->accession, shift @$d );
my @accnums = $hit->each_accession_number;
foreach my $a (@accnums) {
    is( $a, shift @$d );
}
$d   = shift @valid;
$hit = $result->next_hit;
is( $hit->name,      shift @$d );
is( $hit->accession, shift @$d );
is( $hit->locus,     shift @$d );

$hits_left = 23;
while ( $hit = $result->next_hit ) {
    my $d = shift @valid;
    is( $hit->name,      shift @$d );
    is( $hit->accession, shift @$d );
    $hits_left--;
}
is( $hits_left, 0 );

# Parse MEGABLAST

# parse the BLAST-like output
my $infile = test_input_file('503384.MEGABLAST.2');
my $in     = Bio::SearchIO->new(
    -file   => $infile,
    -format => 'blast'
);    # this is megablast blast-like output
my $r        = $in->next_result;
my @dcompare = (
    [
        'Contig3700', 5631, 396, 785, '0.0', 785, '0.0', 396, 639, 12, 8723,
        9434, 1, 4083, 4794, -1
    ],
    [
        'Contig3997', 12734, 335, 664, '0.0', 664, '0.0', 335, 401, 0, 1282,
        1704, 1, 1546, 1968, -1
    ],
    [
        'Contig634', 858, 245, 486, '1e-136', 486,
        '1e-136',    245, 304, 3,   7620,     7941,
        1,           1,   321, -1
    ],
    [
        'Contig1853', 2314, 171,  339, '1e-91', 339,
        '1e-91',      171,  204,  0,   6406,    6620,
        1,            1691, 1905, 1
    ]
);

like($r->algorithm_reference,qr/A greedy algorithm for aligning DNA sequences/);
is( $r->algorithm,                           'MEGABLAST' );
is( $r->query_name,                          '503384' );
is( $r->query_description,                   '11337 bp 2 contigs' );
is( $r->query_length,                        11337 );
is( $r->database_name,                       'cneoA.nt' );
is( $r->database_letters,                    17206226 );
is( $r->database_entries,                    4935 );
is( $r->get_statistic('querylength'),        11318 );
is( $r->get_statistic('effectivedblength'),  17112461 );
is( $r->get_statistic('effectivespace'),     193678833598 );
is( $r->get_statistic('effectivespaceused'), 0 );

$hits_left = 4;
while ( my $hit = $r->next_hit ) {
    my $d = shift @dcompare;
    is( $hit->name,      shift @$d );
    is( $hit->length,    shift @$d );
    is( $hit->raw_score, shift @$d );
    is( $hit->bits,      shift @$d );
    float_is( $hit->significance, shift @$d );

    my $hsp = $hit->next_hsp;
    is( $hsp->bits, shift @$d );
    float_is( $hsp->evalue, shift @$d );
    is( $hsp->score,         shift @$d );
    is( $hsp->num_identical, shift @$d );
    is( $hsp->gaps('total'), shift @$d );
    is( $hsp->query->start,  shift @$d );
    is( $hsp->query->end,    shift @$d );
    is( $hsp->query->strand, shift @$d );
    is( $hsp->hit->start,    shift @$d );
    is( $hsp->hit->end,      shift @$d );
    is( $hsp->hit->strand,   shift @$d );
    is( $hsp->n,             1 );
    $hits_left--;
}
is( $hits_left, 0 );

# Let's test RPS-BLAST

my $parser = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('ecoli_domains.rpsblast')
);

$r = $parser->next_result;
is( $r->algorithm,                           'RPS-BLAST(BLASTP)');
is( $r->algorithm_version,                   '2.2.4 [Aug-26-2002]');
is( $r->algorithm_reference,                 undef );
is( $r->query_name,                          'gi|1786183|gb|AAC73113.1|' );
is( $r->query_gi,                            1786183 );
is( $r->num_hits,                            7 );
is( $r->get_statistic('querylength'),        438 );
is( $r->get_statistic('effectivedblength'),  31988 );
is( $r->get_statistic('effectivespace'),     14010744 );
is( $r->get_statistic('effectivespaceused'), 24054976 );
$hit = $r->next_hit;
is( $hit->name, 'gnl|CDD|3919' );
float_is( $hit->significance, 0.064 );
is( $hit->bits,      28.3 );
is( $hit->raw_score, 63 );
$hsp = $hit->next_hsp;
is( $hsp->query->start, 599 );
is( $hsp->query->end,   655 );
is( $hsp->hit->start,   23 );
is( $hsp->hit->end,     76 );

# Test PSI-BLAST parsing

$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('psiblastreport.out')
);

$result = $searchio->next_result;
like($result->algorithm_reference, qr/Gapped BLAST and PSI-BLAST/);
is( $result->database_name,    '/home/peter/blast/data/swissprot.pr' );
is( $result->database_entries, 88780 );
is( $result->database_letters, 31984247 );

is( $result->algorithm, 'BLASTP' );
like( $result->algorithm_version, qr/^2\.0\.14/ );
is( $result->query_name,             'CYS1_DICDI' );
is( $result->query_length,           343 );
is( $result->get_statistic('kappa'), 0.0491 );
cmp_ok( $result->get_statistic('lambda'),  '==', 0.270 );
cmp_ok( $result->get_statistic('entropy'), '==', 0.230 );
is( $result->get_statistic('dbletters'),           31984247 );
is( $result->get_statistic('dbentries'),           88780 );
is( $result->get_statistic('effective_hsplength'), 49 );
is( $result->get_statistic('querylength'),         294 );
is( $result->get_statistic('effectivedblength'),   27634027 );
is( $result->get_statistic('effectivespace'),      8124403938 );
is( $result->get_statistic('effectivespaceused'),  8124403938 );
is( $result->get_parameter('matrix'),              'BLOSUM62' );
is( $result->get_parameter('gapopen'),             11 );
is( $result->get_parameter('gapext'),              1 );

my @valid_hit_data = (
    [ 'sp|P04988|CYS1_DICDI', 343, 'P04988', '0',     721 ],
    [ 'sp|P43295|A494_ARATH', 313, 'P43295', '1e-75', 281 ],
    [ 'sp|P25804|CYSP_PEA',   363, 'P25804', '1e-74', 278 ]
);
my @valid_iter_data = (
    [ 127, 127, 0,   109, 18, 0, 0,   0, 0 ],
    [ 157, 40,  117, 2,   38, 0, 109, 3, 5 ]
);
my $iter_count = 0;

while ( $iter = $result->next_iteration ) {
    $iter_count++;
    my $di = shift @valid_iter_data;
    is( $iter->number, $iter_count );

    is( $iter->num_hits,                                shift @$di );
    is( $iter->num_hits_new,                            shift @$di );
    is( $iter->num_hits_old,                            shift @$di );
    is( scalar( $iter->newhits_below_threshold ),       shift @$di );
    is( scalar( $iter->newhits_not_below_threshold ),   shift @$di );
    is( scalar( $iter->newhits_unclassified ),          shift @$di );
    is( scalar( $iter->oldhits_below_threshold ),       shift @$di );
    is( scalar( $iter->oldhits_newly_below_threshold ), shift @$di );
    is( scalar( $iter->oldhits_not_below_threshold ),   shift @$di );

    my $hit_count = 0;
    if ( $iter_count == 1 ) {
        while ( $hit = $result->next_hit ) {
            my $d = shift @valid_hit_data;

            is( $hit->name,      shift @$d );
            is( $hit->length,    shift @$d );
            is( $hit->accession, shift @$d );
            float_is( $hit->significance, shift @$d );
            is( $hit->bits, shift @$d );

            if ( $hit_count == 1 ) {
                my $hsps_left = 1;
                while ( my $hsp = $hit->next_hsp ) {
                    is( $hsp->query->start,    32 );
                    is( $hsp->query->end,      340 );
                    is( $hsp->hit->start,      3 );
                    is( $hsp->hit->end,        307 );
                    is( $hsp->length('total'), 316 );
                    is( $hsp->start('hit'),    $hsp->hit->start );
                    is( $hsp->end('query'),    $hsp->query->end );
                    is( $hsp->strand('sbjct'), $hsp->subject->strand )
                      ;    # alias for hit
                    float_is( $hsp->evalue, 1e-75 );
                    is( $hsp->score, 712 );
                    is( $hsp->bits,  281 );
                    is( sprintf( "%.1f", $hsp->percent_identity ), 46.5 );
                    is( sprintf( "%.4f", $hsp->frac_identical('query') ),
                        0.4757 );
                    is( sprintf( "%.3f", $hsp->frac_identical('hit') ), 0.482 );
                    is( $hsp->gaps, 18 );
                    is( $hsp->n,    1 );
                    $hsps_left--;
                }
                is( $hsps_left, 0 );
            }
            last if ( $hit_count++ > @valid_hit_data );
        }
    }
}
is( @valid_hit_data,  0 );
is( @valid_iter_data, 0 );

# Test filtering

$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('ecolitst.bls'),
    '-signif' => 1e-100
);

@valid = qw(gb|AAC73113.1|);
$r     = $searchio->next_result;

while ( my $hit = $r->next_hit ) {
    is( $hit->name, shift @valid );
}

$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('ecolitst.bls'),
    '-score'  => 100
);

@valid = qw(gb|AAC73113.1| gb|AAC76922.1| gb|AAC76994.1|);
$r     = $searchio->next_result;

while ( my $hit = $r->next_hit ) {
    is( $hit->name, shift @valid );
}
is( @valid, 0 );

$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('ecolitst.bls'),
    '-bits'   => 200
);

@valid = qw(gb|AAC73113.1| gb|AAC76922.1|);
$r     = $searchio->next_result;

while ( my $hit = $r->next_hit ) {
    is( $hit->name, shift @valid );
}
is( @valid, 0 );

my $filt_func = sub {
    my $hit = shift;
    $hit->frac_identical('query') >= 0.31;
};

$searchio = Bio::SearchIO->new(
    '-format'     => 'blast',
    '-file'       => test_input_file('ecolitst.bls'),
    '-hit_filter' => $filt_func
);

@valid = qw(gb|AAC73113.1| gb|AAC76994.1|);
$r     = $searchio->next_result;

while ( my $hit = $r->next_hit ) {
    is( $hit->name, shift @valid );
}
is( @valid, 0 );

# bl2seq parsing testing

# this is blastp bl2seq
$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('bl2seq.out')
);
$result = $searchio->next_result;
isa_ok( $result, 'Bio::Search::Result::ResultI' );
is( $result->query_name,                          '' );
is( $result->algorithm,                           'BLASTP' );
is( $result->algorithm_reference,                 undef );
is( $result->get_statistic('querylength'),        320 );
is( $result->get_statistic('effectivedblength'),  339 );
is( $result->get_statistic('effectivespace'),     108480 );
is( $result->get_statistic('effectivespaceused'), 108480 );
$hit = $result->next_hit;
is( $hit->name,   'ALEU_HORVU' );
is( $hit->length, 362 );
$hsp = $hit->next_hsp;
is( $hsp->score,                481 );
is( $hsp->bits,                 191 );
is( int $hsp->percent_identity, 34 );
float_is( $hsp->evalue, 2e-53 );
is( int( $hsp->frac_conserved * $hsp->length ), 167 );
is( $hsp->query->start,                         28 );
is( $hsp->query->end,                           343 );
is( $hsp->hit->start,                           60 );
is( $hsp->hit->end,                             360 );
is( $hsp->gaps,                                 27 );

# this is blastn bl2seq
$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('bl2seq.blastn.rev')
);
$result = $searchio->next_result;
isa_ok( $result, 'Bio::Search::Result::ResultI' );
is( $result->query_name,                          '' );
is( $result->algorithm,                           'BLASTN' );
is( $result->algorithm_reference,                 undef );
is( $result->query_length,                        180 );
is( $result->get_statistic('querylength'),        174 );
is( $result->get_statistic('effectivedblength'),  173 );
is( $result->get_statistic('effectivespace'),     30102 );
is( $result->get_statistic('effectivespaceused'), 30102 );
$hit = $result->next_hit;
is( $hit->length, 179 );
is( $hit->name,   'human' );
$hsp = $hit->next_hsp;
is( $hsp->score,                27 );
is( $hsp->bits,                 '54.0' );
is( int $hsp->percent_identity, 88 );
float_is( $hsp->evalue, 2e-12 );
is( int( $hsp->frac_conserved * $hsp->length ), 83 );
is( $hsp->query->start,                         94 );
is( $hsp->query->end,                           180 );
is( $hsp->query->strand,                        1 );
is( $hsp->hit->strand,                          -1 );
is( $hsp->hit->start,                           1 );
is( $hsp->hit->end,                             94 );
is( $hsp->gaps,                                 7 );
is( $hsp->n,                                    1 );

# this is blastn bl2seq
$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('bl2seq.blastn')
);
$result = $searchio->next_result;
isa_ok( $result, 'Bio::Search::Result::ResultI' );
is( $result->query_name,                          '' );
is( $result->query_length,                        180 );
is( $result->algorithm,                           'BLASTN' );
is( $result->algorithm_reference,                 undef );
is( $result->get_statistic('querylength'),        174 );
is( $result->get_statistic('effectivedblength'),  173 );
is( $result->get_statistic('effectivespace'),     30102 );
is( $result->get_statistic('effectivespaceused'), 30102 );
$hit = $result->next_hit;
is( $hit->name,   'human' );
is( $hit->length, 179 );
$hsp = $hit->next_hsp;
is( $hsp->score,                27 );
is( $hsp->bits,                 '54.0' );
is( int $hsp->percent_identity, 88 );
float_is( $hsp->evalue, 2e-12 );
is( int( $hsp->frac_conserved * $hsp->length ), 83 );
is( $hsp->query->start,                         94 );
is( $hsp->query->end,                           180 );
is( $hsp->query->strand,                        1 );
is( $hsp->hit->strand,                          1 );
is( $hsp->hit->start,                           86 );
is( $hsp->hit->end,                             179 );
is( $hsp->gaps,                                 7 );
is( $hsp->n,                                    1 );

# this is blastn bl2seq+
$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('bl2seq+.blastn')
);
$result = $searchio->next_result;
isa_ok( $result, 'Bio::Search::Result::ResultI' );
is( $result->query_name, 'gi|2695846|emb|Y13255.1|' );
is( $result->query_description,
   'Acipenser baeri mRNA for immunoglobulin heavy chain, clone ScH 3.3'
);
is( $result->query_length,                        606 );
is( $result->algorithm,                          'BLASTN' );
is( $result->algorithm_version,                  '2.2.29+' );
is( $result->algorithm_reference,                 undef );
is( $result->get_statistic('effectivespaceused'), 352836 );
is( $result->get_statistic('kappa'),              0.621 );
is( $result->get_statistic('kappa_gapped'),      '0.460' );
is( $result->get_statistic('lambda'),             1.33 );
is( $result->get_statistic('lambda_gapped'),      1.28 );
is( $result->get_statistic('entropy'),            1.12 );
is( $result->get_statistic('entropy_gapped'),    '0.850' );
$hit = $result->next_hit;
is( $hit->name,   'gi|2695846|emb|Y13255.1|' );
is( $hit->description,
   'Acipenser baeri mRNA for immunoglobulin heavy chain, clone ScH 3.3'
);
is( $hit->length, 606 );
$hsp = $hit->next_hsp;
is( $hsp->score,            606 );
is( $hsp->bits,             1120 );
is( $hsp->percent_identity, 100 );
float_is( $hsp->evalue,    '0.0' );
is( $hsp->query->start,     1 );
is( $hsp->query->end,       606 );
is( $hsp->query->strand,    1 );
is( $hsp->hit->strand,      1 );
is( $hsp->hit->start,       1 );
is( $hsp->hit->end,         606 );
is( $hsp->gaps,             0 );
is( $hsp->n,                1 );

# this is blastp bl2seq
$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('bl2seq.bug940.out')
);
$result = $searchio->next_result;
isa_ok( $result, 'Bio::Search::Result::ResultI' );
is( $result->query_name, 'zinc' );
is( $result->algorithm,  'BLASTP' );
is( $result->query_description,
'finger protein 135 (clone pHZ-17) [Homo sapiens]. neo_id RS.ctg14243-000000.6.0'
);
is( $result->query_length,                        469 );
is( $result->get_statistic('querylength'),        446 );
is( $result->get_statistic('effectivedblength'),  446 );
is( $result->get_statistic('effectivespace'),     198916 );
is( $result->get_statistic('effectivespaceused'), 198916 );
$hit = $result->next_hit;
is( $hit->name,    'gi|4507985|' );
is( $hit->ncbi_gi, 4507985 );
is( $hit->description,
'zinc finger protein 135 (clone pHZ-17) [Homo sapiens]. neo_id RS.ctg14243-000000.6.0'
);
is( $hit->length, 469 );
$hsp = $hit->next_hsp;
is( $hsp->score,                1626 );
is( $hsp->bits,                 637 );
is( int $hsp->percent_identity, 66 );
float_is( $hsp->evalue, 0.0 );
is( int( $hsp->frac_conserved * $hsp->length ), 330 );
is( $hsp->query->start,                         121 );
is( $hsp->query->end,                           469 );
is( $hsp->hit->start,                           1 );
is( $hsp->hit->end,                             469 );
is( $hsp->gaps,                                 120 );
is( $hsp->n,                                    1 );

ok( $hit->next_hsp );    # there is more than one HSP here,
                         # make sure it is parsed at least

# cannot distinguish between blastx and tblastn reports
# so we're only testing a blastx report for now

# this is blastx bl2seq
$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('bl2seq.blastx.out')
);
$result = $searchio->next_result;
isa_ok( $result, 'Bio::Search::Result::ResultI' );
is( $result->query_name, 'AE000111.1' );
is( $result->query_description,
    'Escherichia coli K-12 MG1655 section 1 of 400 of the complete genome' );
is( $result->algorithm,                           'BLASTX' );
is( $result->algorithm_reference,                 undef );
is( $result->query_length,                        720 );
is( $result->get_statistic('querylength'),        undef );
is( $result->get_statistic('effectivedblength'),  787 );
is( $result->get_statistic('effectivespace'),     undef );
is( $result->get_statistic('effectivespaceused'), 162122 );
$hit = $result->next_hit;
is( $hit->name, 'AK1H_ECOLI' );
is( $hit->description,
'P00561 Bifunctional aspartokinase/homoserine dehydrogenase I (AKI-HDI) [Includes: Aspartokinase I ; Homoserine dehydrogenase I ]'
);
is( $hit->length, 820 );
$hsp = $hit->next_hsp;
is( $hsp->score,                634 );
is( $hsp->bits,                 248 );
is( int $hsp->percent_identity, 100 );
float_is( $hsp->evalue, 2e-70 );
is( int( $hsp->frac_conserved * $hsp->length ), 128 );
is( $hsp->query->start,                         1 );
is( $hsp->query->end,                           384 );
is( $hsp->hit->start,                           1 );
is( $hsp->hit->end,                             128 );
is( $hsp->gaps,                                 0 );
is( $hsp->query->frame,                         0 );
is( $hsp->hit->frame,                           0 );
is( $hsp->query->strand,                        -1 );
is( $hsp->hit->strand,                          0 );
is( $hsp->n,                                    1 );

# this is tblastx bl2seq (self against self)
$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('bl2seq.tblastx.out')
);
$result = $searchio->next_result;
isa_ok( $result, 'Bio::Search::Result::ResultI' );
is( $result->query_name,          'Escherichia' );
is( $result->algorithm,           'TBLASTX' );
is( $result->algorithm_reference, undef );
is( $result->query_description,
    'coli K-12 MG1655 section 1 of 400 of the complete genome' );
is( $result->query_length,                        720 );
is( $result->get_statistic('querylength'),        undef );
is( $result->get_statistic('effectivedblength'),  221 );
is( $result->get_statistic('effectivespace'),     undef );
is( $result->get_statistic('effectivespaceused'), 48620 );
$hit = $result->next_hit;
is( $hit->name,    'gi|1786181|gb|AE000111.1|AE000111' );
is( $hit->ncbi_gi, 1786181 );
is( $hit->description,
    'Escherichia coli K-12 MG1655 section 1 of 400 of the complete genome' );
is( $hit->length, 720 );
$hsp = $hit->next_hsp;
is( $hsp->score,                1118 );
is( $hsp->bits,                 515 );
is( int $hsp->percent_identity, 95 );
float_is( $hsp->evalue, 1e-151 );
is( int( $hsp->frac_conserved * $hsp->length ), 229 );
is( $hsp->query->start,                         1 );
is( $hsp->query->end,                           720 );
is( $hsp->hit->start,                           1 );
is( $hsp->hit->end,                             720 );
is( $hsp->gaps,                                 0 );
is( $hsp->query->frame,                         0 );
is( $hsp->hit->frame,                           0 );
is( $hsp->query->strand,                        1 );
is( $hsp->hit->strand,                          1 );
is( $hsp->n,                                    1 );

# this is NCBI tblastn
$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('tblastn.out')
);
$result = $searchio->next_result;
isa_ok( $result, 'Bio::Search::Result::ResultI' );
is( $result->algorithm, 'TBLASTN' );
like($result->algorithm_reference,qr/Gapped BLAST and PSI-BLAST/);
is( $result->get_statistic('querylength'),        102 );
is( $result->get_statistic('effectivedblength'),  4342 );
is( $result->get_statistic('effectivespace'),     442884 );
is( $result->get_statistic('effectivespaceused'), 442884 );
$hit = $result->next_hit;
is( $hit->name, 'gi|10040111|emb|AL390796.6|AL390796' );

# Test Blast parsing with B=0 (WU-BLAST)
$searchio = Bio::SearchIO->new(
    -file   => test_input_file('no_hsps.blastp'),
    -format => 'blast'
);
$result = $searchio->next_result;
like($result->algorithm_reference,qr/Gish, W. \(1996-2003\)/);
is( $result->query_name, 'mgri:MG00189.3' );
$hit = $result->next_hit;
is( $hit->name,        'mgri:MG00189.3' );
is( $hit->description, 'hypothetical protein 6892 8867 +' );
is( $hit->bits,        3098 );
float_is( $hit->significance, 0. );

$hit = $result->next_hit;
is( $hit->name,        'fgram:FG01141.1' );
is( $hit->description, 'hypothetical protein 47007 48803 -' );
is( $hit->bits,        2182 );
float_is( $hit->significance, 4.2e-226 );
is( $result->num_hits, 415 );

# Let's now test if _guess_format is doing its job correctly
my %pair = (
    'filename.blast' => 'blast',
    'filename.bls'   => 'blast',
    'f.blx'          => 'blast',
    'f.tblx'         => 'blast',
    'fast.bls'       => 'blast',
    'f.fasta'        => 'fasta',
    'f.fa'           => 'fasta',
    'f.fx'           => 'fasta',
    'f.fy'           => 'fasta',
    'f.ssearch'      => 'fasta',
    'f.SSEARCH.m9'   => 'fasta',
    'f.m9'           => 'fasta',
    'f.psearch'      => 'fasta',
    'f.osearch'      => 'fasta',
    'f.exon'         => 'exonerate',
    'f.exonerate'    => 'exonerate',
    'f.blastxml'     => 'blastxml',
    'f.xml'          => 'blastxml'
);
while ( my ( $file, $expformat ) = each %pair ) {
    is( Bio::SearchIO->_guess_format($file),
        $expformat, "$expformat for $file" );
}

# Test Wes Barris's reported bug when parsing blastcl3 output which
# has integer overflow

$searchio = Bio::SearchIO->new(
    -file   => test_input_file('hsinsulin.blastcl3.blastn'),
    -format => 'blast'
);
$result = $searchio->next_result;
is( $result->query_name,         'human' );
is( $result->database_letters(), '-24016349' );

# this is of course not the right length, but is the what blastcl3
# reports, the correct value is
is( $result->get_statistic('dbletters'), '192913178' );
is( $result->get_statistic('dbentries'), '1867771' );

# test for links and groups being parsed out of WU-BLAST properly
$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('brassica_ATH.WUBLASTN')
);
ok( $result = $searchio->next_result );
ok( $hit    = $result->next_hit );
ok( $hsp    = $hit->next_hsp );
is( $hsp->links,         '(1)-3-2' );
is( $hsp->query->strand, 1 );
is( $hsp->hit->strand,   1 );
is( $hsp->hsp_group,     '1' );
is( $hsp->n,             1 );
## Web blast result parsing

$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('catalase-webblast.BLASTP')
);
ok( $result = $searchio->next_result );
is( $result->rid, '1118324516-16598-103707467515.BLASTQ1' );
ok( $hit = $result->next_hit );
is( $hit->name,      'gi|40747822|gb|EAA66978.1|', 'full hit name' );
is( $hit->accession, 'EAA66978',                   'hit accession' );
is( $hit->ncbi_gi,   40747822 );
ok( $hsp = $hit->next_hsp );
is( $hsp->query->start, 1,   'query start' );
is( $hsp->query->end,   528, 'query start' );
is( $hsp->n,            1 );

# tests for new BLAST 2.2.13 output
$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('new_blastn.txt')
);

$result = $searchio->next_result;
is( $result->database_name,
'All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)'
);
is( $result->database_entries,  3742891 );
is( $result->database_letters,  16670205594 );
is( $result->algorithm,         'BLASTN' );
is( $result->algorithm_version, '2.2.13 [Nov-27-2005]' );
like($result->algorithm_reference, qr/Gapped BLAST and PSI-BLAST/);
is( $result->rid,                    '1141079027-8324-8848328247.BLASTQ4' );
is( $result->query_name,             'pyrR,' );
is( $result->query_length,           558 );
is( $result->get_statistic('kappa'), '0.711' );
is( $result->get_statistic('kappa_gapped'),        '0.711' );
is( $result->get_statistic('lambda'),              '1.37' );
is( $result->get_statistic('lambda_gapped'),       '1.37' );
is( $result->get_statistic('entropy'),             '1.31' );
is( $result->get_statistic('entropy_gapped'),      '1.31' );
is( $result->get_statistic('dbletters'),           '-509663586' );
is( $result->get_statistic('dbentries'),           3742891 );
is( $result->get_statistic('effective_hsplength'), undef );
is( $result->get_statistic('effectivespace'),      8935230198384 );
is(
    $result->get_statistic(
        'number_of_hsps_better_than_expect_value_cutoff_without_gapping'),
    0
);
is( $result->get_statistic('number_of_hsps_gapped'),              1771 );
is( $result->get_statistic('number_of_hsps_successfully_gapped'), 0 );
is( $result->get_statistic('length_adjustment'),                  22 );
is( $result->get_statistic('querylength'),                        536 );
is( $result->get_statistic('effectivedblength'),                  16670205594 );
is( $result->get_statistic('effectivespaceused'), 8891094027712 );
is( $result->get_parameter('matrix'),             'blastn matrix:1 -3' );
is( $result->get_parameter('gapopen'),            5 );
is( $result->get_parameter('gapext'),             2 );
is( $result->get_statistic('S2'),                 '60' );
is( $result->get_statistic('S2_bits'),            '119.4' );
float_is( $result->get_parameter('expect'), '1e-23' );
is( $result->get_statistic('num_extensions'), '117843' );

@valid = (
    [
        'gi|41400296|gb|AE016958.1|', 4829781, 'AE016958', 41400296, '6e-059',
        119, 236
    ],
    [
        'gi|54013472|dbj|AP006618.1|', 6021225, 'AP006618', 54013472, '4e-026',
        64, 127
    ],
    [
        'gi|57546753|dbj|BA000030.2|', 9025608, 'BA000030', 57546753, '1e-023',
        60, 119
    ]
);
$count = 0;

while ( $hit = $result->next_hit ) {
    my $d = shift @valid;

    is( $hit->name,      shift @$d );
    is( $hit->length,    shift @$d );
    is( $hit->accession, shift @$d );
    is( $hit->ncbi_gi,   shift @$d );
    float_is( $hit->significance, shift @$d );
    is( $hit->raw_score, shift @$d );
    is( $hit->bits,      shift @$d );

    if ( $count == 0 ) {
        my $hsps_left = 1;
        while ( my $hsp = $hit->next_hsp ) {
            is( $hsp->query->start,    262 );
            is( $hsp->query->end,      552 );
            is( $hsp->hit->start,      1166897 );
            is( $hsp->hit->end,        1167187 );
            is( $hsp->length('total'), 291 );
            is( $hsp->hit_features,    'PyrR' );
            is( $hsp->start('hit'),    $hsp->hit->start );
            is( $hsp->end('query'),    $hsp->query->end );
            is( $hsp->strand('sbjct'), $hsp->subject->strand );  # alias for hit
            float_is( $hsp->evalue, 6e-59 );
            is( $hsp->score, 119 );
            is( $hsp->bits,  236 );
            is( sprintf( "%.2f", $hsp->percent_identity ),        85.22 );
            is( sprintf( "%.4f", $hsp->frac_identical('query') ), 0.8522 );
            is( sprintf( "%.4f", $hsp->frac_identical('hit') ),   0.8522 );
            is( $hsp->gaps, 0 );
            is( $hsp->n,    1 );
            $hsps_left--;
        }
        is( $hsps_left, 0 );
    }
    last if ( $count++ > @valid );
}
is( @valid, 0 );

# Bug 2189
$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('blastp2215.blast')
);

$result = $searchio->next_result;
is( $result->database_entries,  4460989 );
is( $result->database_letters,  1533424333 );
is( $result->algorithm,         'BLASTP' );
is( $result->algorithm_version, '2.2.15 [Oct-15-2006]' );
is( $result->rid,               '1169055516-21385-22799250964.BLASTQ4' );
is( $result->query_name,        'gi|15608519|ref|NP_215895.1|' );
is( $result->query_gi,          15608519 );
is( $result->query_length,      193 );
@hits = $result->hits;
is( scalar(@hits),          10 );
is( $hits[1]->accession,    '1W30' );
is( $hits[4]->significance, '2e-72' );
is( $hits[7]->bits,         '254' );
$result = $searchio->next_result;
is( $result->database_entries,  4460989 );
is( $result->database_letters,  1533424333 );
is( $result->algorithm,         'BLASTP' );
is( $result->algorithm_version, '2.2.15 [Oct-15-2006]' );
is( $result->query_name,        'gi|15595598|ref|NP_249092.1|' );
is( $result->query_length,      423 );
@hits = $result->hits;
is( scalar(@hits),          10 );
is( $hits[1]->accession,    'ZP_00972546' );
is( $hits[2]->ncbi_gi,      116054132 );
is( $hits[4]->significance, '0.0' );
is( $hits[7]->bits,         624 );

# Bug 2246
$searchio = Bio::SearchIO->new(
    -format  => 'blast',
    -verbose => -1,
    -file    => test_input_file('bug2246.blast')
);
$result = $searchio->next_result;
is(
    $result->get_statistic(
        'number_of_hsps_better_than_expect_value_cutoff_without_gapping'),
    0
);
is( $result->get_statistic('number_of_hsps_gapped'),              7049 );
is( $result->get_statistic('number_of_hsps_successfully_gapped'), 55 );
is( $result->get_statistic('length_adjustment'),                  125 );
is( $result->get_statistic('querylength'),                        68 );
is( $result->get_statistic('effectivedblength'),                  1045382588 );
is( $result->get_statistic('effectivespace'),                     71086015984 );
is( $result->get_statistic('effectivespaceused'),                 71086015984 );
$hit = $result->next_hit;
is $hit->name,        'UniRef50_Q9X0H5';
is $hit->length,      0;
is $hit->accession,   'UniRef50_Q9X0H5';
is $hit->description, 'Cluster: Histidyl-tRNA synthetase; n=4; Thermoto...';
is $hit->bits,        23;
float_is( $hit->significance, 650 );

# Bug 1986
$searchio = Bio::SearchIO->new(
    -format  => 'blast',
    -verbose => -1,
    -file    => test_input_file('bug1986.blastp')
);
$result = $searchio->next_result;
is( $result->get_statistic('querylength'),        335 );
is( $result->get_statistic('effectivedblength'),  18683311 );
is( $result->get_statistic('effectivespace'),     6258909185 );
is( $result->get_statistic('effectivespaceused'), 6258909185 );
$hit = $result->next_hit;
is $hit->name,      'ENSP00000350182';
is $hit->length,    425;
is $hit->accession, 'ENSP00000350182';
is $hit->description,
'pep:novel clone::BX322644.8:4905:15090:-1 gene:ENSG00000137397 transcript:ENST00000357569';
is $hit->raw_score, 301;
is $hit->bits,      120;
float_is( $hit->significance, 3e-27 );
$hit = $result->next_hit;
is $hit->name,      'ENSP00000327738';
is $hit->length,    468;
is $hit->accession, 'ENSP00000327738';
is $hit->description,
'pep:known-ccds chromosome:NCBI36:4:189297592:189305643:1 gene:ENSG00000184108 transcript:ENST00000332517 CCDS3851.1';
is $hit->raw_score, 289;
is $hit->bits,      115;
float_is( $hit->significance, 8e-26 );

# Bug 1986, pt. 2

# handle at least the first iteration with BLAST searches using databases
# containing non-unique IDs

my $file = test_input_file('bug1986.blast2');
my %unique_accs;
open my $IN, '<', $file or die "Could not read file '$file': $!\n";

while (<$IN>) {
    last if (/^Sequences/);
}
$count = 1;
while (<$IN>) {
    chomp;
    next if m{^\s*$};
    next unless ($_);
    last if m{^>};
    my ($accession) = split(/\s+/);

    #print "Real Hit $count = $accession\n";
    $unique_accs{$accession}++;

    #last if ($count == 10);
    ++$count;
}
close $IN;

is( $count,                      495 );
is( scalar( keys %unique_accs ), 490 );

my %search_accs;

$searchio = Bio::SearchIO->new(
    -format  => 'blast',
    -verbose => -1,
    -file    => $file
);
$result = $searchio->next_result;
$count  = 1;
while ( my $hit = $result->next_hit ) {
    $search_accs{ $hit->accession }++;
    $count++;
}

is( $count,                      495 );
is( scalar( keys %search_accs ), 490 );

is_deeply( \%unique_accs, \%search_accs );

# bug 2391 - long query names

$file = test_input_file('bug2391.megablast');

$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => $file
);
$result = $searchio->next_result;

# data is getting munged up with long names
is( $result->query_name,
    'c6_COX;c6_QBL;6|31508172;31503325;31478402|rs36223351|1|dbSNP|C/G' );
is( $result->query_description, '' );
is( $result->algorithm,         'MEGABLAST' );
is(
    $result->get_statistic(
        'number_of_hsps_better_than_expect_value_cutoff_without_gapping'),
    undef
);
is( $result->get_statistic('number_of_hsps_gapped'),              0 );
is( $result->get_statistic('number_of_hsps_successfully_gapped'), 0 );
is( $result->get_statistic('length_adjustment'),                  16 );
is( $result->get_statistic('querylength'),                        85 );
is( $result->get_statistic('effectivedblength'),                  59358266 );
is( $result->get_statistic('effectivespace'),                     5045452610 );
is( $result->get_statistic('effectivespaceused'),                 5045452610 );

# bug 2399 - catching Expect(n) values

$file = test_input_file('bug2399.tblastn');

$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => $file
);
my $total_n = 0;
while ( my $query = $searchio->next_result ) {
    while ( my $subject = $query->next_hit ) {
        $total_n += grep { $_->n } $subject->hsps;
    }
}
is( $total_n, 80 );    # n = at least 1, so this was changed to reflect that

sub cmp_evalue ($$) {
    my ( $tval, $aval ) = @_;
    is( sprintf( "%g", $tval ), sprintf( "%g", $aval ) );
}

# bug 3064 - All-gap Query/Subject lines for BLAST+ do not have numbering

$file = test_input_file('blast_plus.blastp');

$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => $file
);

my $total_hsps = 0;
while ( my $query = $searchio->next_result ) {
    is( $query->get_statistic('querylength'),        undef );
    is( $query->get_statistic('effectivedblength'),  undef );
    is( $query->get_statistic('effectivespace'),     undef );
    is( $query->get_statistic('effectivespaceused'), 55770 );
    while ( my $subject = $query->next_hit ) {
        while ( my $hsp = $subject->next_hsp ) {
            $total_hsps++;
            if ( $total_hsps == 1 ) {
                is( $hsp->start('query'),         5 );
                is( $hsp->start('hit'),           3 );
                is( $hsp->end('query'),           220 );
                is( $hsp->end('hit'),             308 );
                is( length( $hsp->query_string ), length( $hsp->hit_string ) );
            }
        }
    }
}

is( $total_hsps, 2 );

# BLAST 2.2.20+ output file ZABJ4EA7014.CH878695.1.blast.txt
# Tests SearchIO blast parsing of 'Features in/flanking this part of a subject sequence'
$searchio = Bio::SearchIO->new(
    -format => 'blast',
    -file   => test_input_file('ZABJ4EA7014.CH878695.1.blast.txt')
);

$result = $searchio->next_result;

# Parse BLAST header details
is( $result->algorithm,         'BLASTN' );
is( $result->algorithm_version, '2.2.20+' );
like($result->algorithm_reference, qr/A greedy algorithm for aligning DNA\s+sequences/);
is( $result->database_name,
    'human build 35 genome database (reference assembly only)' );
is( $result->database_entries, 378 );
is( $result->database_letters, 2866055344 );
is( $result->query_name,       'gi|95131563|gb|CH878695.1|' );
is( $result->query_description,
    'Homo sapiens 211000035829648 genomic scaffold' );
is( $result->query_length, 29324 );

# Parse BLAST footer details
is( $result->get_statistic('posted_date'),    'Jul 26, 2007  3:20 PM' );
is( $result->get_statistic('dbletters'),      -1428911948 );
is( $result->get_statistic('lambda'),         '1.33' );
is( $result->get_statistic('kappa'),          '0.621' );
is( $result->get_statistic('entropy'),        '1.12' );
is( $result->get_statistic('lambda_gapped'),  '1.28' );
is( $result->get_statistic('kappa_gapped'),   '0.460' );
is( $result->get_statistic('entropy_gapped'), '0.850' );
is( $result->get_parameter('matrix'),         'blastn matrix:1 -2' );
is( $result->get_parameter('gapopen'),        0 );
is( $result->get_parameter('gapext'),         0 );
is( $result->get_statistic('num_extensions'), 216 );
is( $result->get_statistic('num_successful_extensions'), 216 );
is( $result->get_parameter('expect'),                    '0.01' );
is( $result->get_statistic('seqs_better_than_cutoff'),   10 );
is(
    $result->get_statistic(
        'number_of_hsps_better_than_expect_value_cutoff_without_gapping'),
    0
);
is( $result->get_statistic('number_of_hsps_gapped'),              216 );
is( $result->get_statistic('number_of_hsps_successfully_gapped'), 212 );
is( $result->get_statistic('length_adjustment'),                  34 );
is( $result->get_statistic('querylength'),                        29290 );
is( $result->get_statistic('effectivedblength'),                  2866042492 );
is( $result->get_statistic('effectivespace'),     83946384590680 );
is( $result->get_statistic('effectivespaceused'), 83946384590680 );
is( $result->get_statistic('A'),                  0 );
is( $result->get_statistic('X1'),                 23 );
is( $result->get_statistic('X1_bits'),            '44.2' );
is( $result->get_statistic('X2'),                 32 );
is( $result->get_statistic('X2_bits'),            '59.1' );
is( $result->get_statistic('X3'),                 54 );
is( $result->get_statistic('X3_bits'),            '99.7' );
is( $result->get_statistic('S1'),                 23 );
is( $result->get_statistic('S1_bits'),            '43.6' );
is( $result->get_statistic('S2'),                 29 );
is( $result->get_statistic('S2_bits'),            '54.7' );

# Skip the 1st hit. It doesn't have any 'Features in/flanking this part of subject sequence:'
$hit = $result->next_hit;

# The 2nd hit has hsps with 'Features flanking this part of subject sequence:'
$hit = $result->next_hit;
is( $hit->name,        'gi|51459264|ref|NT_077382.3|Hs1_77431' );
is( $hit->description, 'Homo sapiens chromosome 1 genomic contig' );
is( $hit->length,      237250 );

# In the 2nd hit, look at the 1st hsp
$hsp = $hit->next_hsp;
is( $hsp->hit_features,
"16338 bp at 5' side: PRAME family member 8   11926 bp at 3' side: PRAME family member 9"
);
is( $hsp->bits,          7286 );
is( $hsp->score,         3945 );
is( $hsp->expect,        '0.0' );
is( $hsp->hsp_length,    6145 );
is( $hsp->num_identical, 5437 );
is( int sprintf( "%.2f", $hsp->percent_identity ), 88 );
is( $hsp->gaps,           152 );
is( $hsp->start('query'), 23225 );
is( $hsp->start('sbjct'), 86128 );
is( $hsp->end('query'),   29324 );
is( $hsp->end('sbjct'),   92165 );

# In the 2nd hit, look at the 2nd hsp
$hsp = $hit->next_hsp;
is( $hsp->hit_features,
"25773 bp at 5' side: PRAME family member 3   3198 bp at 3' side: PRAME family member 5"
);
is( $hsp->bits,          4732 );
is( $hsp->score,         2562 );
is( $hsp->expect,        '0.0' );
is( $hsp->hsp_length,    4367 );
is( $hsp->num_identical, 3795 );
is( int sprintf( "%.2f", $hsp->percent_identity ), 86 );
is( $hsp->gaps,           178 );
is( $hsp->start('query'), 23894 );
is( $hsp->start('sbjct'), 37526 );
is( $hsp->end('query'),   28193 );
is( $hsp->end('sbjct'),   41781 );

# In the 2nd hit, look at the 3rd hsp
$hsp = $hit->next_hsp;
is( $hsp->hit_features,
"16338 bp at 5' side: PRAME family member 8   14600 bp at 3' side: PRAME family member 9"
);
is( $hsp->bits,          3825 );
is( $hsp->score,         2071 );
is( $hsp->expect,        '0.0' );
is( $hsp->hsp_length,    3406 );
is( $hsp->num_identical, 2976 );
is( int sprintf( "%.2f", $hsp->percent_identity ), 87 );
is( $hsp->gaps,           89 );
is( $hsp->start('query'), 14528 );
is( $hsp->start('sbjct'), 86128 );
is( $hsp->end('query'),   17886 );
is( $hsp->end('sbjct'),   89491 );

# In the 2nd hit, look at the 4th hsp
$hsp = $hit->next_hsp;
is( $hsp->hit_features,
"29101 bp at 5' side: PRAME family member 8   2120 bp at 3' side: PRAME family member 9"
);
is( $hsp->bits,          3241 );
is( $hsp->score,         1755 );
is( $hsp->expect,        '0.0' );
is( $hsp->hsp_length,    3158 );
is( $hsp->num_identical, 2711 );
is( int sprintf( "%.2f", $hsp->percent_identity ), 85 );
is( $hsp->gaps,           123 );
is( $hsp->start('query'), 23894 );
is( $hsp->start('sbjct'), 98891 );
is( $hsp->end('query'),   27005 );
is( $hsp->end('sbjct'),   101971 );

# In the 2nd hit, look at the 5th hsp
$hsp = $hit->next_hsp;
is( $hsp->hit_features,  "PRAME family member 13" );
is( $hsp->bits,          3142 );
is( $hsp->score,         1701 );
is( $hsp->expect,        '0.0' );
is( $hsp->hsp_length,    2507 );
is( $hsp->num_identical, 2249 );
is( int sprintf( "%.2f", $hsp->percent_identity ), 89 );
is( $hsp->gaps,           63 );
is( $hsp->start('query'), 3255 );
is( $hsp->start('sbjct'), 128516 );
is( $hsp->end('query'),   5720 );
is( $hsp->end('sbjct'),   131000 );

# testing for Bug #3298
$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('multiresult_blastn+.bls')
);

is ($searchio->next_result->algorithm_version, '2.2.25+', "testing Bug 3298");
is ($searchio->next_result->algorithm_version, '2.2.25+', "testing Bug 3298");
is ($searchio->next_result->algorithm_version, '2.2.25+', "testing Bug 3298");

# testing for Bug #3251
$searchio = Bio::SearchIO->new(
    '-format' => 'blast',
    '-file'   => test_input_file('rpsblast_no_hits.bls')
);

is ($searchio->next_result->database_name, 'CDD.v.2.13', "testing Bug 3251");
is ($searchio->next_result->database_name, 'CDD.v.2.13', "testing Bug 3251");
is ($searchio->next_result->database_name, 'CDD.v.2.13', "testing Bug 3251");
BioPerl-1.007002/t/SearchIO/blast_pull.t000444000766000024      3657513155576321 20002 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_blast_pull.t 11525 2007-06-27 10:16:38Z sendu $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 289);
	
	use_ok('Bio::SearchIO');
}


my $searchio = Bio::SearchIO->new(-format => 'blast_pull', -file => test_input_file('new_blastn.txt'));

my $result = $searchio->next_result;
is $result->database_name, 'All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)';
is $result->database_entries, 3742891;
is $result->database_letters, 16670205594;
is $result->algorithm, 'BLASTN';
is $result->algorithm_version, '2.2.13 [Nov-27-2005]';
is $result->query_name, 'pyrR,';
is $result->query_length, 558;
is $result->get_statistic('kappa'), 0.711;
is $result->get_statistic('kappa_gapped'), 0.711;
is $result->get_statistic('lambda'), 1.37;
is $result->get_statistic('lambda_gapped'), 1.37;
is $result->get_statistic('entropy'), 1.31;
is $result->get_statistic('entropy_gapped'), 1.31;
is $result->get_statistic('dbletters'), -509663586;
is $result->get_statistic('dbentries'), 3742891;
is $result->get_statistic('effectivespace'), 8935230198384;
is $result->get_parameter('matrix'), 'blastn matrix:1 -3';
is $result->get_parameter('gapopen'), 5;
is $result->get_parameter('gapext'), 2;
is $result->get_statistic('S2'), 60;
is $result->get_statistic('S2_bits'), 119.4;
float_is $result->get_parameter('expect'), 1e-23;
is $result->get_statistic('num_extensions'), 117843;

my @valid = ( [ 'gi|41400296|gb|AE016958.1|', 4829781, 'AE016958', '6e-059', 236],
	      [ 'gi|54013472|dbj|AP006618.1|', 6021225, 'AP006618', '4e-026', 127],
	      [ 'gi|57546753|dbj|BA000030.2|', 9025608, 'BA000030', '1e-023', 119]);
my $count = 0;
while (my $hit = $result->next_hit ) {
    my $d = shift @valid;

    is $hit->name, shift @$d;
    is $hit->length, shift @$d;
    is $hit->accession, shift @$d;
    float_is($hit->significance, shift @$d);
    is $hit->raw_score, shift @$d;

    if( $count == 0 ) {
        my $hsps_left = 1;
        while( my $hsp = $hit->next_hsp ) {
            is $hsp->query->start, 262;
            is $hsp->query->end, 552;
            is $hsp->hit->start, 1166897;
            is $hsp->hit->end, 1167187;
            is $hsp->length('hsp'), 291;
            is $hsp->start('hit'), $hsp->hit->start;
            is $hsp->end('query'), $hsp->query->end;
            is $hsp->strand('sbjct'), $hsp->subject->strand;# alias for hit
            float_is($hsp->evalue, 6e-59);
            is $hsp->score, 119;
            is $hsp->bits,236;	    	    
            is sprintf("%.1f",$hsp->percent_identity), 85.2;
            is sprintf("%.3f",$hsp->frac_identical('query')), 0.852;
            is sprintf("%.3f",$hsp->frac_identical('hit')), 0.852;
            is $hsp->gaps, 0;
            $hsps_left--;
        }
        is $hsps_left, 0;
    }
    last if( $count++ > @valid );
}
is @valid, 0;

# descriptionless hit
$searchio = Bio::SearchIO->new('-format' => 'blast_pull',
							   '-file' => test_input_file('blast_no_hit_desc.txt'));

$result = $searchio->next_result;
my $hit = $result->next_hit;
is $hit->name, 'chr1';
is $hit->description, '';

# further (NCBI blastn/p) tests taken from SearchIO.t
$searchio = Bio::SearchIO->new('-format' => 'blast_pull',
							   '-file' => test_input_file('ecolitst.bls'));

$result = $searchio->next_result;

is($result->database_name, 'ecoli.aa', 'database_name()');
is($result->database_entries, 4289);
is($result->database_letters, 1358990);

is($result->algorithm, 'BLASTP');
like($result->algorithm_version, qr/^2\.1\.3/);
like($result->query_name, qr/gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I,\s+homoserine dehydrogenase I [Escherichia coli]/);
is($result->query_length, 820);
is($result->get_statistic('kappa'), '0.135');
is($result->get_statistic('kappa_gapped'), '0.0410');
is($result->get_statistic('lambda'), '0.319');
is($result->get_statistic('lambda_gapped'), '0.267');
is($result->get_statistic('entropy'), '0.383');
is($result->get_statistic('entropy_gapped'), '0.140');

is($result->get_statistic('dbletters'), 1358990);
is($result->get_statistic('dbentries'), 4289);
is($result->get_statistic('effective_hsplength'), 47);
is($result->get_statistic('effectivespace'), 894675611);
is($result->get_parameter('matrix'), 'BLOSUM62');
is($result->get_parameter('gapopen'), 11);
is($result->get_parameter('gapext'), 1);
is($result->get_statistic('S2'), '92');
is($result->get_statistic('S2_bits'), '40.0');
float_is($result->get_parameter('expect'), '1.0e-03');
is($result->get_statistic('num_extensions'), '82424');


@valid = ( [ 'gb|AAC73113.1|', 820, 'AAC73113', '0', 1567],
	      [ 'gb|AAC76922.1|', 810, 'AAC76922', '1e-91', 332],
	      [ 'gb|AAC76994.1|', 449, 'AAC76994', '3e-47', 184]);
$count = 0;
while (my $hit = $result->next_hit) {
    my $d = shift @valid;

    is($hit->name, shift @$d);
    is($hit->length, shift @$d);
    is($hit->accession, shift @$d);
    float_is($hit->significance, shift @$d);
    is($hit->raw_score, shift @$d );

    if( $count == 0 ) {
        my $hsps_left = 1;
        while (my $hsp = $hit->next_hsp) {
            is($hsp->query->start, 1);
            is($hsp->query->end, 820);
            is($hsp->hit->start, 1);
            is($hsp->hit->end, 820);
            is($hsp->length('hsp'), 820);
            is($hsp->start('hit'), $hsp->hit->start);
            is($hsp->end('query'), $hsp->query->end);
            is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
            float_is($hsp->evalue, 0.0);
            is($hsp->score, 4058);
            is($hsp->bits,1567);	    	    
            is(sprintf("%.2f",$hsp->percent_identity), 98.29);
            is(sprintf("%.4f",$hsp->frac_identical('query')), 0.9829);
            is(sprintf("%.4f",$hsp->frac_identical('hit')), 0.9829);
            is($hsp->gaps, 0);
            $hsps_left--;
        }
        is($hsps_left, 0);
    }
    last if( $count++ > @valid );
}
is(@valid, 0);

$searchio = Bio::SearchIO->new('-format' => 'blast_pull',
							  '-file'   => test_input_file('a_thaliana.blastn'));

$result = $searchio->next_result;
is($result->database_name, 'All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,or phase 0, 1 or 2 HTGS sequences)');
is($result->database_letters, 4677375331);
is($result->database_entries, 1083200);
is($result->algorithm, 'BLASTN');
like($result->algorithm_version, qr/^2\.2\.1/);
is($result->query_name, '');
is($result->query_length, 60);
is($result->get_parameter('gapopen'), 5);
is($result->get_parameter('gapext'), 2);
is($result->get_parameter('ktup'), undef);

is($result->get_statistic('lambda'), 1.37);
is($result->get_statistic('kappa'), 0.711);
is($result->get_statistic('entropy'),1.31 );
is($result->get_statistic('T'), 0);
is($result->get_statistic('A'), 30);
is($result->get_statistic('X1'), '6');
is($result->get_statistic('X1_bits'), 11.9);
is($result->get_statistic('X2'), 15);
is($result->get_statistic('X2_bits'), 29.7);
is($result->get_statistic('S1'), 12);
is($result->get_statistic('S1_bits'), 24.3);
is($result->get_statistic('S2'), 17);
is($result->get_statistic('S2_bits'), 34.2);

is($result->get_statistic('dbentries'), 1083200);

@valid = ( [ 'gb|AY052359.1|', 2826, 'AY052359', '3e-18', 96, 1, 60, 
	     '1.0000'],
	   [ 'gb|AC002329.2|AC002329', 76170, 'AC002329', '3e-18', 96, 1, 60, 
	     '1.0000' ],
	   [ 'gb|AF132318.1|AF132318', 5383, 'AF132318', '0.04', 42, 35, 55, 
	     '0.3500']);
$count = 0;

while( my $hit = $result->next_hit ) {
    my $d = shift @valid;
    is($hit->name, shift @$d);
    is($hit->length, shift @$d);
    is($hit->accession, shift @$d);
    float_is($hit->significance, shift @$d);
    is($hit->raw_score, shift @$d );
    is($hit->start, shift @$d);
    is($hit->end,shift @$d);    
    is(sprintf("%.4f",$hit->frac_aligned_query), shift @$d);
    if( $count == 0 ) {
        my $hsps_left = 1;
        while( my $hsp = $hit->next_hsp ) {
            is($hsp->query->start, 1);
            is($hsp->query->end, 60);
            is($hsp->query->strand, 1);
            is($hsp->hit->start, 154);
            is($hsp->hit->end, 212);
            is($hsp->hit->strand, 1);
            is($hsp->length('hsp'), 60);	    
            float_is($hsp->evalue, 3e-18);
            is($hsp->score, 48);
            is($hsp->bits,95.6);
            is(sprintf("%.2f",$hsp->percent_identity), 96.67);
            is(sprintf("%.4f",$hsp->frac_identical('query')), 0.9667);
            is(sprintf("%.4f",$hsp->frac_identical('hit')), 0.9831);
            is($hsp->query->frame(), 0);
            is($hsp->hit->frame(), 0);
            is($hsp->query->seq_id, '');
            is($hsp->hit->seq_id, 'gb|AY052359.1|');
            is($hsp->gaps('query'), 0);
            is($hsp->gaps('hit'), 1);
            is($hsp->gaps, 1);
            is($hsp->query_string, 'aggaatgctgtttaattggaatcgtacaatggagaatttgacggaaatagaatcaacgat');
            is($hsp->hit_string, 'aggaatgctgtttaattggaatca-acaatggagaatttgacggaaatagaatcaacgat');
            is($hsp->homology_string, '|||||||||||||||||||||||  |||||||||||||||||||||||||||||||||||');
            is(sprintf("%.2f",$hsp->get_aln->overall_percentage_identity), 96.67);
            is(sprintf("%.2f",$hsp->get_aln->percentage_identity), 98.31);
            $hsps_left--;
        }
        is($hsps_left, 0);
    }
    last if( $count++ > @valid );
} 
is(@valid, 0);

$searchio = Bio::SearchIO->new('-format' => 'blast_pull',
							  '-file'   => test_input_file('frac_problems.blast'));
my @expected = ("1.000", "0.943");
while (my $result = $searchio->next_result) {
    my $hit = $result->next_hit;
	if (@expected == 2) {
		is($hit->frac_identical, shift @expected);
	}
	else {
		TODO: {
			local $TODO = 'frac_identical failing!';
			is($hit->frac_identical, shift @expected);
		}
	}
}
is(@expected, 0);

# And even more: frac_aligned_query should never be over 1!
$searchio = Bio::SearchIO->new('-format' => 'blast_pull',
							  '-file'   => test_input_file('frac_problems2.blast'));
$result = $searchio->next_result;
$hit = $result->next_hit;
is $hit->frac_aligned_query, 0.97;

# Also, start and end should be sane
$searchio = Bio::SearchIO->new('-format' => 'blast_pull',
							  '-file'   => test_input_file('frac_problems3.blast'));
$result = $searchio->next_result;
$hit = $result->next_hit;
is $hit->start('sbjct'), 207;
is $hit->end('sbjct'), 1051;

# Do a multiblast report test
$searchio = Bio::SearchIO->new('-format' => 'blast_pull',
							   '-file'   => test_input_file('multi_blast.bls'));

@expected = qw(CATH_RAT CATL_HUMAN CATL_RAT PAPA_CARPA);
my $results_left = 4;
while( my $result = $searchio->next_result ) {
    is($result->query_name, shift @expected, "Multiblast query test");
    $results_left--;
}
is($results_left, 0);

# Web blast result parsing
$searchio = Bio::SearchIO->new(-format => 'blast_pull',
							   -file   => test_input_file('catalase-webblast.BLASTP'));
ok($result = $searchio->next_result);
ok($hit = $result->next_hit);
is($hit->name, 'gi|40747822|gb|EAA66978.1|', 'full hit name');
is($hit->accession, 'EAA66978', 'hit accession');
ok(my $hsp = $hit->next_hsp);
is($hsp->query->start, 1, 'query start');
is($hsp->query->end, 528, 'query start');

# tests for new BLAST 2.2.13 output
$searchio = Bio::SearchIO->new(-format => 'blast_pull',
							  -file   => test_input_file('new_blastn.txt'));

$result = $searchio->next_result;
is($result->database_name, 'All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)');
is($result->database_entries, 3742891);
is($result->database_letters, 16670205594);
is($result->algorithm, 'BLASTN');
is($result->algorithm_version, '2.2.13 [Nov-27-2005]');
is($result->query_name, 'pyrR,');
is($result->query_length, 558);
is($result->get_statistic('kappa'), '0.711');
is($result->get_statistic('kappa_gapped'), '0.711');
is($result->get_statistic('lambda'), '1.37');
is($result->get_statistic('lambda_gapped'), '1.37');
is($result->get_statistic('entropy'), '1.31');
is($result->get_statistic('entropy_gapped'), '1.31');
is($result->get_statistic('dbletters'), '-509663586');
is($result->get_statistic('dbentries'), 3742891);
is($result->get_statistic('effective_hsplength'), undef);
is($result->get_statistic('effectivespace'), 8935230198384);
is($result->get_parameter('matrix'), 'blastn matrix:1 -3');
is($result->get_parameter('gapopen'), 5);
is($result->get_parameter('gapext'), 2);
is($result->get_statistic('S2'), '60');
is($result->get_statistic('S2_bits'), '119.4');
float_is($result->get_parameter('expect'), '1e-23');
is($result->get_statistic('num_extensions'), '117843');

@valid = ( [ 'gi|41400296|gb|AE016958.1|', 4829781, 'AE016958', '6e-059', 236],
	      [ 'gi|54013472|dbj|AP006618.1|', 6021225, 'AP006618', '4e-026', 127],
	      [ 'gi|57546753|dbj|BA000030.2|', 9025608, 'BA000030', '1e-023', 119]);
$count = 0;
while( $hit = $result->next_hit ) {
    my $d = shift @valid;

    is($hit->name, shift @$d);
    is($hit->length, shift @$d);
    is($hit->accession, shift @$d);
    float_is($hit->significance, shift @$d);
    is($hit->raw_score, shift @$d );

    if( $count == 0 ) {
        my $hsps_left = 1;
        while( my $hsp = $hit->next_hsp ) {
            is($hsp->query->start, 262);
            is($hsp->query->end, 552);
            is($hsp->hit->start, 1166897);
            is($hsp->hit->end, 1167187);
            is($hsp->length('hsp'), 291);
            is($hsp->start('hit'), $hsp->hit->start);
            is($hsp->end('query'), $hsp->query->end);
            is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
            float_is($hsp->evalue, 6e-59);
            is($hsp->score, 119);
            is($hsp->bits,236);	    	    
            is(sprintf("%.2f",$hsp->percent_identity), 85.22);
            is(sprintf("%.4f",$hsp->frac_identical('query')), 0.8522);
            is(sprintf("%.4f",$hsp->frac_identical('hit')), 0.8522);
            is($hsp->gaps, 0);
            $hsps_left--;
        }
        is($hsps_left, 0);
    }
    last if( $count++ > @valid );
}
is(@valid, 0);

# Bug 2189
$searchio = Bio::SearchIO->new(-format => 'blast_pull',
							  -file   => test_input_file('blastp2215.blast'));

$result = $searchio->next_result;
is($result->database_entries, 4460989);
is($result->database_letters, 1533424333);
is($result->algorithm, 'BLASTP');
is($result->algorithm_version, '2.2.15 [Oct-15-2006]');
is($result->query_name, 'gi|15608519|ref|NP_215895.1|');
is($result->query_length, 193);
my @hits = $result->hits;
is(scalar(@hits), 10);
is($hits[1]->accession,'1W30');
float_is($hits[4]->significance,'2e-72');
is($hits[7]->score,'254');
$result = $searchio->next_result;
is($result->database_entries, 4460989);
is($result->database_letters, 1533424333);
is($result->algorithm, 'BLASTP');
is($result->algorithm_version, '2.2.15 [Oct-15-2006]');
is($result->query_name, 'gi|15595598|ref|NP_249092.1|');
is($result->query_length, 423);
@hits = $result->hits;
is(scalar(@hits), 10);
is($hits[1]->accession,'ZP_00972546');
float_is($hits[4]->significance, '0.0');
is($hits[7]->score, 624);

# Bug 2246
$searchio = Bio::SearchIO->new(-format => 'blast_pull',
                               -verbose => -1,
							  -file   => test_input_file('bug2246.blast'));
$result = $searchio->next_result;
$hit = $result->next_hit;
is $hit->name, 'UniRef50_Q9X0H5';
is $hit->length, undef;
is $hit->accession, 'UniRef50_Q9X0H5';
is $hit->description, 'Cluster: Histidyl-tRNA synthetase; n=4; Thermoto...';
is $hit->raw_score, 23;
float_is($hit->significance, 650);

#*** need to /fully/ test a multi-result, multi-hit, multi-hsp report!
BioPerl-1.007002/t/SearchIO/blasttable.t000444000766000024       571013155576321 17721 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO.t 14995 2008-11-16 06:20:00Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 166);
	
	use_ok('Bio::SearchIO');
    use_ok('Bio::Search::SearchUtils');
}

my ($searchio, $result,$iter,$hit,$hsp);

# test blasttable output
my @eqset = qw( c200-vs-yeast.BLASTN.m9);
$searchio = Bio::SearchIO->new(-file => test_input_file('c200-vs-yeast.BLASTN'),
			      -format => 'blast');
$result = $searchio->next_result;
isa_ok($result,'Bio::Search::Result::ResultI');
my %ref = &Bio::Search::SearchUtils::result2hash($result);
is( scalar keys %ref, 67);
$searchio = Bio::SearchIO->new(-file => test_input_file('c200-vs-yeast.BLASTN.m8'),
			      -program_name => 'BLASTN',
			      -format => 'blasttable');
$result = $searchio->next_result;
my %tester = &Bio::Search::SearchUtils::result2hash($result);
is( scalar keys %tester, 67);
foreach my $key ( sort keys %ref ) {
    is($tester{$key}, $ref{$key},$key);
}

# test WU-BLAST blasttable output
$searchio = Bio::SearchIO->new(-file => test_input_file('test1.wublastp'),
			      			   -format => 'blast');
$result = $searchio->next_result;
isa_ok($result,'Bio::Search::Result::ResultI');
my %wuref = &Bio::Search::SearchUtils::result2hash($result);
is( scalar keys %wuref, 31);
$searchio = Bio::SearchIO->new(-file => test_input_file('test1.blasttab3'),
			      -program_name => 'BLASTP',
			      -format => 'blasttable');
$result = $searchio->next_result;
my %wutester = &Bio::Search::SearchUtils::result2hash($result);
is( scalar keys %wutester, 31);
foreach my $key ( sort keys %ref ) {
    is($wutester{$key}, $wuref{$key},$key);
}

# BLAST 2.2.18+ tabular output (has 13 columns instead of 12)
$searchio = Bio::SearchIO->new(-format => 'blasttable',
							  -file   => test_input_file('2008.blasttable'));

while(my $res = $searchio->next_result) {
    is($res->query_name, 'gi|1786183|gb|AAC73113.1|');
    is($res->algorithm, 'BLASTP');
    is($res->algorithm_version, '2.2.18+');
    my $hit = $res->next_hit;
    is($hit->name, 'gi|34395933|sp|P00561.2|AK1H_ECOLI');
    $hit = $res->next_hit;
    is($hit->score, 331, 'hit score');
    is($hit->raw_score, 331, 'hit raw_score');
    my $hsp = $hit->next_hsp;
	isa_ok($hsp, 'Bio::SeqFeatureI');
    is($hsp->bits, 331);
    float_is($hsp->evalue, 2e-91);
    is($hsp->start('hit'), 16);
    is($hsp->end('hit'), 805);
    is($hsp->start('query'), 5);
    is($hsp->end('query'), 812);
    is($hsp->length, 821);
    float_is($hsp->percent_identity, 30.0852618757613, 'fixed bug 3343 (percent identity)');
    is($hsp->gaps, 44, 'side effect of fixing bug 3343 (number of gaps)');
	my $hit_sf = $hsp->hit;
	my $query_sf = $hsp->query;
	isa_ok($hit_sf, 'Bio::SeqFeatureI');
    is($hit_sf->start(), 16);
    is($hit_sf->end(), 805);
    is($hit_sf->strand(), 0);	
	isa_ok($query_sf, 'Bio::SeqFeatureI');
    is($query_sf->start(), 5);
    is($query_sf->end(), 812);
    is($query_sf->strand(), 0);
}
BioPerl-1.007002/t/SearchIO/cross_match.t000444000766000024       352613155576321 20114 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_cross_match.t 11788 2007-12-03 23:37:59Z jason $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 15);
	
	use_ok('Bio::SearchIO');
}

my ($searchio, $result,$iter,$hit,$hsp);

# The cross_match SearchIO parser is not event-based; it directly adds
# information to the relevant Bio::Search objects as the report is parsed.
# The parser currently misses much information present in the report. Also,
# methods expected to work somehow don't (hsp->length('hsp'), for instance).
# Unsure if this parses non-alignment-based cross-match reports accurately
# (see bioperl-live/t/data/consed_project/edit_dir/test_project.screen.out for
# an example).

# Note lots of ResultI/HitI/HSPI methods not tested yet!

$searchio = Bio::SearchIO->new('-format' => 'cross_match',
				  '-file'   => test_input_file('testdata.crossmatch'));

$result = $searchio->next_result;

is($result->algorithm, 'cross_match');
is($result->algorithm_version, '0.990329');

my @valid = ( [ 'msx1_ens2', 0]);
my $count = 0;
while( $hit = $result->next_hit ) {
    my $d = shift @valid;

    is($hit->name, shift @$d);
    is($hit->length, shift @$d);

    if( $count == 0 ) {
        my $hsps_left = 1;
        while( my $hsp = $hit->next_hsp ) {
            is($hsp->query->start, 19);
            is($hsp->query->end, 603);
            is($hsp->hit->start, 2824);
            is($hsp->hit->end, 3409);
            #is($hsp->length('hsp'), 820);  # shouldn't this work?
            is($hsp->start('hit'), $hsp->hit->start);
            is($hsp->end('query'), $hsp->query->end);
            is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
            is($hsp->gaps, 0);
            $hsps_left--;
        }
        is($hsps_left, 0);
    }
    last if( $count++ > @valid );
}

is(@valid, 0);
BioPerl-1.007002/t/SearchIO/erpin.t000444000766000024      1200613155576321 16735 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_erpin.t 14672 2008-04-22 21:42:50Z cjfields $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 91);
    
    use_ok('Bio::SearchIO');
}

my ($searchio, $result, $iter, $hit, $hsp, $algorithm, $meta);

$searchio = Bio::SearchIO->new( -format => 'erpin',
                                -file   => test_input_file('testfile.erpin'),
                                -model => 'stem-loop',
                                -query_acc => 'test',
                                -version => 5.5,
                                -verbose => 2
                               );
$result = $searchio->next_result;
isa_ok($result, 'Bio::Search::Result::ResultI');
$algorithm = $result->algorithm;
is($result->algorithm, 'ERPIN', "Result $algorithm");
is($result->algorithm_reference, undef, "Result $algorithm reference");
is($result->algorithm_version, 5.5, "Result $algorithm version");
is($result->available_parameters, 2, "Result parameters");
is($result->available_statistics, 1, "Result statistics");
is($result->database_entries, '', "Result entries");
is($result->database_letters, '', "Result letters");
is($result->database_name, 'AE016879.fna', "Result database_name");
is($result->num_hits, 1, "Result num_hits");
is($result->program_reference, undef, "Result program_reference");
is($result->query_accession, 'test', "Result query_accession");
is($result->query_description, '40 sequences of length 43', "Result query_description");
is($result->query_name, '/home/Administrator/pyrR.epn', "Result query_name");

$hit = $result->next_hit;
isa_ok($hit, 'Bio::Search::Hit::HitI');
is($hit->accession, 'AE016879.1', "Hit accession");
is($hit->ncbi_gi, '30260185', "Hit GI");
is($hit->algorithm, 'ERPIN', "Hit algorithm");
is($hit->bits, 31.64, "Hit bits");
is($hit->description, 'Bacillus anthracis str. Ames, complete genome',
   "Hit description"); # no hit descs yet
is($hit->length, 0, "Hit length");
is($hit->locus, '', "Hit locus");
is($hit->n, 4, "Hit n");
is($hit->name, 'gi|30260185|gb|AE016879.1|', "Hit name");
is($hit->num_hsps, 4, "Hit num_hsps"); 
is($hit->overlap, 0, "Hit overlap");
is($hit->query_length, undef, "Hit query_length");
is($hit->rank, 1, "Hit rank");
is($hit->raw_score, 31.64, "Hit raw_score");
is($hit->score, 31.64, "Hit score");
float_is($hit->significance, 4.44e-06);

$hsp = $hit->next_hsp;
isa_ok($hsp, 'Bio::Search::HSP::HSPI');
is($hsp->algorithm, 'ERPIN', "HSP algorithm");
float_is($hsp->evalue, 1.68e-05);
isa_ok($hsp->feature1, 'Bio::SeqFeature::Similarity');
isa_ok($hsp->feature2, 'Bio::SeqFeature::Similarity');
is($hsp->frame('query'), 0, "HSP frame");
is($hsp->gaps, 2, "HSP gaps");
isa_ok($hsp->hit, 'Bio::SeqFeature::Similarity', "HSP hit");
is($hsp->hit_string,
   'CTTT.aacc--.CAACC.CCGTGA.GGTTG.a.GAAG',
   "HSP hit_string");
is($hsp->homology_string,
   '',
   "HSP homology_string");
is($hsp->hsp_group, undef, "HSP hsp_group");
is($hsp->hsp_length, 37, "HSP hsp_length");
is($hsp->length, 37, "HSP length");
is($hsp->links, undef, "HSP links");
isa_ok($hsp->query, 'Bio::SeqFeature::Similarity', "HSP query");
is($hsp->query_string,
   '',
   "HSP query_string");
is($hsp->range, 37, "HSP range");
is($hsp->rank, 1, "HSP rank");
float_is($hsp->significance, 1.68e-05);
float_is($hsp->expect, '1.68e-05', "HSP expect");
isa_ok($hsp->seq, 'Bio::LocatableSeq');
is($hsp->seq_str,
   '',
   "HSP seq_str");
is($hsp->start, 1, "HSP start");
is($hsp->custom_score, undef, "HSP custom_score");
is($hsp->meta, undef, "HSP meta");
is($hsp->meta, undef);
is($hsp->meta, undef);
is($hsp->strand('hit'), 1, "HSP strand");
is($hsp->meta, undef);
is($hsp->meta, undef);

# ERPIN lacks sequence for query, will spit back a warning..
eval{$hsp->get_aln};
like($@, qr'Missing query string, can\'t build alignment','ERPIN get_aln warning');

$hsp = $hit->next_hsp;
isa_ok($hsp, 'Bio::Search::HSP::HSPI');
is($hsp->algorithm, 'ERPIN', "HSP algorithm");
float_is($hsp->evalue, 5.61e-05);
isa_ok($hsp->feature1, 'Bio::SeqFeature::Similarity');
isa_ok($hsp->feature2, 'Bio::SeqFeature::Similarity');
is($hsp->frame('query'), 0, "HSP frame");
is($hsp->gaps, 1, "HSP gaps");
isa_ok($hsp->hit, 'Bio::SeqFeature::Similarity', "HSP hit");
is($hsp->hit_string,
   'CTTT.taatt-.CAGTC.CTGTGA.GACCG.g.AAAG',
   "HSP hit_string");
is($hsp->homology_string,
   '',
   "HSP homology_string");
is($hsp->query_string,
   '',
   "HSP query_string");
is($hsp->hsp_group, undef, "HSP hsp_group");
is($hsp->hsp_length, 37, "HSP hsp_length");
is($hsp->length, 37, "HSP length");
is($hsp->links, undef, "HSP links");
isa_ok($hsp->query, 'Bio::SeqFeature::Similarity');
is($hsp->range, 37, "HSP range");
is($hsp->rank, 2, "HSP rank");
float_is($hsp->significance, 5.61e-05);
is($hsp->end, 37, "HSP end");
float_is($hsp->expect, '5.61e-05', "HSP expect");
isa_ok($hsp->seq, 'Bio::LocatableSeq');
is($hsp->seq_str,   '',   "HSP seq_str");
is($hsp->start, 1, "HSP start");
is($hsp->custom_score, undef, "HSP custom_score");
is($hsp->meta, undef);
is($hsp->meta, undef);
is($hsp->strand('hit'), -1, "HSP strand");
BioPerl-1.007002/t/SearchIO/exonerate.t000444000766000024       501113155576321 17570 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_exonerate.t 11525 2007-06-27 10:16:38Z sendu $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin( -tests => 52 );

    use_ok('Bio::SearchIO');
}

my ( $searchio, $result, $hit, $hsp );

$searchio = Bio::SearchIO->new(
    -file   => test_input_file('testdat.exonerate'),
    -format => 'exonerate'
);
my @data = (
    [
        qw(ln27 416 Contig124 939
          293 416 -1
          1   124 1

          107 292 -1
          178 363 1

          66 106 -1
          899 939 1
          )
    ],
    [
        qw(ln74 644 Contig275 1296
          601 644 -1
          901 944 1

          436 600 -1
          998 1162    1

          386 435 -1
          1247 1296 1

          )
    ]
);

my $val;

while ( my $r = $searchio->next_result ) {
    my $d = shift @data;
    is( $r->query_name, shift @$d );
  SKIP: {
        $val = shift @$d;
        skip( 'no query length available in default output', 1 );
        is( $r->query_length, $val );
    }

    my $h = $r->next_hit;
    is( $h->name, shift @$d );
  SKIP: {
        $val = shift @$d;
        skip( 'no hit length available in default output', 1 );
        is( $h->length, $val );
    }
    while ( my $hsp = $h->next_hsp ) {
        is( $hsp->query->start,  shift @$d );
        is( $hsp->query->end,    shift @$d );
        is( $hsp->query->strand, shift @$d );

        is( $hsp->hit->start,  shift @$d );
        is( $hsp->hit->end,    shift @$d );
        is( $hsp->hit->strand, shift @$d );
    }
}

# bug 2346

my @cts = (7, 1, 7);

$searchio = Bio::SearchIO->new(
   -format => 'exonerate',
   -file   => test_input_file('exonerate.output.works'),
);
parse($searchio);

$searchio = Bio::SearchIO->new(
   -format => 'exonerate',
   -file   => test_input_file('exonerate.output.dontwork'),
);
parse($searchio);

$searchio = Bio::SearchIO->new(
   -format => 'exonerate',
   -file   => test_input_file('exonerate.whitespace_before_query.works'),
);
parse($searchio);

sub parse {
    my ($searchio) = @_;
    while( my $r = $searchio->next_result ) {
        my $hsp_ct = 0;
        while(my $hit = $r->next_hit){
            while(my $hsp = $hit->next_hsp){
                $hsp_ct++;
            }
        }
        ok($r->query_name, "query_name");
        is($hsp_ct, shift @cts);
    }
}

$searchio = Bio::SearchIO->new(
    -format => 'exonerate',
    -file   => test_input_file('exonerate.output.negativescore.works'),
);
my $r   = $searchio->next_result;
$hit = $r->next_hit;
is( $hit->score, "-3" );
BioPerl-1.007002/t/SearchIO/fasta.t000444000766000024      6724213155576321 16732 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_fasta.t 14995 2008-11-16 06:20:00Z cjfields $

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 299);
	
	use_ok('Bio::SearchIO');
}

my ($searchio, $result, $hit, $hsp);

# simple FASTA
$searchio = Bio::SearchIO->new(-format => 'fasta',
				 -file   => test_input_file('HUMBETGLOA.FASTA'));
$result = $searchio->next_result;
like($result->database_name, qr/dros_clones.2.5/);
is($result->database_letters, 112936249);
is($result->database_entries, 657);
is($result->algorithm, 'FASTN');
is($result->algorithm_version, '3.3t08');
is($result->query_name, "HUMBETGLOA");
is($result->query_description, "Human haplotype C4 beta-globin gene, complete cds.");
is($result->query_length, 3002);
is($result->get_parameter('gapopen'), -16);
is($result->get_parameter('gapext'), -4);
is($result->get_parameter('ktup'), 6);

is($result->get_statistic('lambda'), 0.0823);
is($result->get_statistic('dbletters'), 112936249);
is($result->get_statistic('dbentries'), 657);

my @valid = ( [ 'BACR21I23', 73982, 'BACR21I23', '0.017', 44.2],
	   [ 'BACR40P19', 73982, 'BACR40P19', '0.017', 44.2],
	   [ 'BACR30L17', 32481, 'BACR30L17', '0.018', 44.1]);
my $count = 0;

while( my $hit = $result->next_hit ) {
    my $d = shift @valid;
    is($hit->name, shift @$d);
    is($hit->length, shift @$d);
    is($hit->accession, shift @$d);
    float_is($hit->significance, shift @$d);
    is($hit->raw_score, shift @$d );
    is($hit->rank, $count + 1);
    if( $count == 0 ) {
        my $hsps_left = 1;
        while( my $hsp = $hit->next_hsp ) {
            is($hsp->query->start, 31);
            is($hsp->query->end, 289);
            is($hsp->query->strand, -1);
            is($hsp->hit->end, 65167);
            is($hsp->hit->start, 64902);
            is($hsp->hit->strand, 1);
            is($hsp->length('total'), 267);	    
            float_is($hsp->evalue, 0.017);
            is($hsp->score, 134.5);
            is($hsp->bits,44.2);
            is(sprintf("%.2f",$hsp->percent_identity), '57.30');
            is(sprintf("%.4f",$hsp->frac_identical('query')), 0.5907); 
            is(sprintf("%.4f",$hsp->frac_identical('hit')), 0.5752);
			# these are really UNGAPPED values not CONSERVED
			# otherwise ident and conserved would be identical for
			# nucleotide alignments
			is(sprintf("%.4f",$hsp->frac_conserved('total')), '0.5918'); 
			is(sprintf("%.4f",$hsp->frac_conserved('query')), '0.6100'); 
			is(sprintf("%.4f",$hsp->frac_conserved('hit')), '0.5940'); 
            is($hsp->query->frame(), 0);
            is($hsp->hit->frame(), 0);
            is($hsp->gaps('query'), 8);
            is($hsp->gaps('hit'),1);
            is($hsp->gaps('total'), 9);
            is($hsp->query_string, 'GATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATATGTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTCATGCATGCTA----ATAAATTATGTCTAAAAATAGAAT---AAATACAAATCAATGTGCTCTGTGCATTA-GTTACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGAGACCTCTTAATGCAGTCAAAAATACAAATAAATAAAAAGTCACTTACAACCCAAAGTGTGACTATCAATGGGGTAATCAGTGGTGTCAAATAGGAGGT');
            is($hsp->hit_string, 'GATGTCCTTGGTGGATTATGGTGTTAGGGTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAATATAATACAAAATATAATACAAAATATAATACAAAATATAATACAAAATATAATACAAAATATAATACAAAATATAATACAAAATATAATATAAAATATAATATAAAATATAATATAAAATAAAATATAAAATAAAATATAAAATAAAATATAAAATAAAATATAAAATAAAATAT-AATATAAAATATAAAATAAAATATAATATAAAATATAATATAAAATATAATATAAAATATAATATAAAATA');
            is($hsp->homology_string, '                              :::::::::::::::::: : ::::: :: : : ::: ::::: ::::::::  ::  :: : :   : : : : :  ::    : :: ::   ::    : ::: :::     :::::: :::   ::::: ::  :::  :    :    : ::   :::  : ::   : :   : : :: :   :: : : :: : :       ::  : : ::: ::: ::  ::::: ::: : :  :: ::   ::: : : : ::: ::   '.' 'x60);
            is(join(' ', $hsp->seq_inds('query', 'nomatch',1)), '33 37 39 41 43 47-49 52 55 56 58 60 64 70 71 74 78 82 84 86 87 90-96 98 100 103 105 107 110-112 114 117 119 121-123 125 127-129 132 134 135 139 140 143 145-148 150-153 155 156 160 161 164 173 180-184 188 192 196-198 201 204 206-209 212 213 215 217 219 221 223-225 227 229 232 233 236 237 246 252 256 258 260 263 269 271');
            is(join(' ', $hsp->seq_inds('query', 'mismatch',1)), '33 37 41 43 47-49 52 55 56 58 60 64 70 71 74 78 82 84 86 87 90-96 98 100 103 105 107 110-112 114 117 119 121-123 125 127-129 132 134 135 139 140 143 145-148 150-153 155 156 160 161 164 173 180-184 188 192 196-198 201 204 206-209 212 213 215 217 219 221 223-225 227 229 232 233 236 237 246 252 256 258 260 263 269 271');
            is(join(' ', $hsp->seq_inds('query', 'conserved',1)), '31 32 34-36 38 40 42 44-46 50 51 53 54 57 59 61-63 65-69 72 73 75-77 79-81 83 85 88 89 97 99 101 102 104 106 108 109 113 115 116 118 120 124 126 130 131 133 136-138 141 142 144 149 154 157-159 162 163 165-172 174-179 185-187 189-191 193-195 199 200 202 203 205 210 211 214 216 218 220 222 226 228 230 231 234 235 238-245 247-251 253-255 257 259 261 262 264-268 270 272-289');
            is(join(' ', $hsp->seq_inds('hit', 'nomatch',1)), '64920 64922 64928 64931 64933 64935 64939 64945 64954 64955 64958 64959 64962 64964 64966-64968 64970 64972 64974 64976 64978 64979 64982-64985 64987 64990 64993-64995 64998-65001 65003 65007 65011-65015 65022 65026-65028 65034 65037 65038 65042 65043 65045-65048 65050-65053 65055 65058-65060 65064 65065 65067 65070-65072 65074 65076-65078 65080 65082 65085 65087-65089 65092 65094 65096 65099 65101 65103-65109 65112 65113 65115 65117 65121 65125 65128 65129 65135 65139 65141 65143 65144 65147 65150-65152 65156 65158 65161 65165');
            is(join(' ', $hsp->seq_inds('hit', 'mismatch',1)), '64920 64922 64928 64931 64933 64935 64939 64945 64954 64955 64958 64959 64962 64964 64966-64968 64970 64972 64974 64976 64978 64979 64982-64985 64987 64990 64993-64995 65003 65007 65011-65015 65022 65034 65037 65038 65042 65043 65045-65048 65050-65053 65055 65059 65060 65064 65065 65067 65070-65072 65074 65076-65078 65080 65082 65085 65087-65089 65092 65094 65096 65099 65101 65103-65109 65112 65113 65115 65117 65121 65125 65128 65129 65135 65139 65141 65143 65144 65147 65150-65152 65156 65158 65161 65165');
            is(join(' ', $hsp->seq_inds('hit', 'conserved',1)), '64902-64919 64921 64923-64927 64929 64930 64932 64934 64936-64938 64940-64944 64946-64953 64956 64957 64960 64961 64963 64965 64969 64971 64973 64975 64977 64980 64981 64986 64988 64989 64991 64992 64996 64997 65002 65004-65006 65008-65010 65016-65021 65023-65025 65029-65033 65035 65036 65039-65041 65044 65049 65054 65056 65057 65061-65063 65066 65068 65069 65073 65075 65079 65081 65083 65084 65086 65090 65091 65093 65095 65097 65098 65100 65102 65110 65111 65114 65116 65118-65120 65122-65124 65126 65127 65130-65134 65136-65138 65140 65142 65145 65146 65148 65149 65153-65155 65157 65159 65160 65162-65164 65166 65167');            
            is(join(' ', $hsp->seq_inds('query', 'gap',1)), '141 170 194');
            is(join(' ', $hsp->seq_inds('hit', 'frameshift')), '');
            is(join(' ', $hsp->seq_inds('query', 'frameshift')), '');
            is($hsp->ambiguous_seq_inds, '');
            # note: the reason this is not the same percent id above
            # is we are calculating average percent id
            is(sprintf("%.2f",$hsp->get_aln->percentage_identity()), '59.30');
            $hsps_left--;
        }
        is($hsps_left, 0);
    }
    last if( $count++ > @valid );
}
is(@valid, 0);

$searchio = Bio::SearchIO->new(-format => 'fasta',
				 -file   => test_input_file('cysprot1.FASTA'));
$result = $searchio->next_result;
like($result->database_name, qr/ecoli.aa/);
is($result->database_letters, 1358987);
is($result->database_entries, 4289);
is($result->algorithm, 'FASTP');
is($result->algorithm_version, '3.3t08');
is($result->query_name, 'CYS1_DICDI');
is($result->query_length, 343);
is($result->get_parameter('gapopen'), -12);
is($result->get_parameter('gapext'), -2);
is($result->get_parameter('ktup'), 2);

is($result->get_statistic('lambda'), 0.1456);
is($result->get_statistic('dbletters'), 1358987);
is($result->get_statistic('dbentries'), 4289);


@valid = ( [ 'gi|1787478|gb|AAC74309.1|', 512, 'AAC74309', 1787478, 1.2, 29.2],
	   [ 'gi|1790635|gb|AAC77148.1|', 251, 'AAC77148', 1790635, 2.1, 27.4],
	   [ 'gi|1786590|gb|AAC73494.1|', 94, 'AAC73494', 1786590, 2.1, 25.9]);
$count = 0;

while( my $hit = $result->next_hit ) {
    my $d = shift @valid;
    is($hit->name, shift @$d);
    is($hit->length, shift @$d);
    is($hit->accession, shift @$d);
    is($hit->ncbi_gi, shift @$d);
    float_is($hit->significance, shift @$d);
    is($hit->raw_score, shift @$d );

    if( $count == 0 ) {
        my $hsps_left = 1;
        while( my $hsp = $hit->next_hsp ) {
            is($hsp->query->start, 125);
            is($hsp->query->end, 305);
            is($hsp->query->strand, 0);
            is($hsp->hit->start, 2);
            is($hsp->hit->end, 181);
            is($hsp->hit->strand, 0);
            is($hsp->length('total'), 188);	    
            float_is($hsp->evalue, 1.2);
            is($hsp->score, 109.2);
            is($hsp->bits,29.2);
            is(sprintf("%.2f",$hsp->percent_identity), 23.94);
            is(sprintf("%.4f",$hsp->frac_identical('query')), 0.2486);
            is(sprintf("%.4f",$hsp->frac_identical('hit')), '0.2500');
            is(sprintf("%.4f",$hsp->frac_conserved('query')), '0.2707');
            is(sprintf("%.4f",$hsp->frac_conserved('hit')), '0.2722');
            # there is slight rounding different here so file says 26.012%
            # but with the rounding this ends up as 0.2606
            is(sprintf("%.4f",$hsp->frac_conserved('total')), '0.2606');
            is($hsp->query->frame(), 0);
            is($hsp->hit->frame(), 0);
            is($hsp->gaps('query'), 7);
            is($hsp->gaps('hit'), 8);
            is($hsp->gaps, 15);
            is($hsp->query_string, 'NKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTT-GNV----EGQHFISQNKLVSLSEQNLVDCDHECME-YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGP-LAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII');
            is($hsp->hit_string, (' 'x29).'MKIRSQVGMVLNLDKCIGCHTCSVTCKNVWTSREGVEYAWFNNVETKPGQGF-PTDWENQEKYKGGWI--RKINGKLQPRMGNRAMLLGKIFANPHLPGIDDYYEPFDFDYQNLHTAPEG----SKSQPIARPRSLITGERMAKIEKGPNWEDDLGGEFDKLAKDKNFDN-IQKAMYSQFENTFMMYLPRLCEHCLNPACVATCPSGAIYKREEDGIVLIDQDKCRGWRMCITGCPYKKIYFNWKSGKSEKCIFCYPRIEAGQPTVCSETC');
            is($hsp->homology_string, '                              . :. :  : :  .: .: . :.:  ::    :: ..   :.. .   :..   : : .: :.:     .  :: :::   :  .  : : ..   :   .     .:.  :. .   .     :.. .     . ::  .:    . .:.  .:: ::   . ...:. :  . ::  .. :   .:                      '.' 'x60);
            # note: the reason this is not the same percent id above
            # is we are calculating average percent id
            is(sprintf("%.2f",$hsp->get_aln->percentage_identity()), 26.01);
            is(join(' ', $hsp->seq_inds('query', 'nomatch',1)), '126 129 131 132 134 136 137 140 143 145 149 154 157-159 163 165-167 171-173 175 177 183-187 189 190 193 197-199 201 202 204 205 207 209 212-214 216-218 220-224 228 229 232 234-236 238-242 246 248-252 254 257 260-263 265 269 270 274 277-279 281 287 289 290 292 295 296 299 301-303');
            is(join(' ', $hsp->seq_inds('query', 'mismatch',1)), '126 129 131 132 134 136 137 140 143 145 149 154 157-159 163 165-167 172 173 175 177 183-185 189 190 193 197-199 201 202 204 205 207 209 212-214 216-218 220-224 228 229 232 234-236 242 246 248-252 254 257 260-263 265 269 270 274 277-279 281 289 290 292 295 296 299 301-303');
            is(join(' ', $hsp->seq_inds('query', 'conserved',1)), '125 127 128 130 133 135 138 139 141 142 144 146-148 150-153 155 156 160-162 164 168-170 174 176 178-182 188 191 192 194-196 200 203 206 208 210 211 215 219 225-227 230 231 233 237 243-245 247 253 255 256 258 259 264 266-268 271-273 275 276 280 282-286 288 291 293 294 297 298 300 304 305');
            is(join(' ', $hsp->seq_inds('hit', 'nomatch',1)), '3 6 8 9 11 13 14 17 20 22 26 27 30-33 36 39-41 45 47-49 53 54 56 58 61 65-67 69 70 73 77-79 81 82 84 85 87 89 92-94 96-98 100-104 108 109 112 114-116 118 122 124-128 130 133 134 137-140 142 146 147 151 154-156 158 165 166 168 171 172 175 177-179');
            is(join(' ', $hsp->seq_inds('hit', 'mismatch',1)), '3 6 8 9 11 13 14 17 20 22 27 36 39-41 45 47-49 53 54 56 58 65-67 69 70 73 77-79 81 82 84 85 87 89 92-94 96-98 100-104 108 109 112 114-116 118 122 124-128 130 133 137-140 142 146 147 151 154-156 158 165 166 168 171 172 175 177-179');
            is(join(' ', $hsp->seq_inds('hit', 'conserved',1)), '2 4 5 7 10 12 15 16 18 19 21 23-25 28 29 34 35 37 38 42-44 46 50-52 55 57 59 60 62-64 68 71 72 74-76 80 83 86 88 90 91 95 99 105-107 110 111 113 117 119-121 123 129 131 132 135 136 141 143-145 148-150 152 153 157 159-164 167 169 170 173 174 176 180 181');
            is(join(' ', $hsp->seq_inds('query', 'gap',1)), '148 151 179 257');
            is(join(' ', $hsp->seq_inds('hit', 'frameshift')), '');
            is(join(' ', $hsp->seq_inds('query', 'frameshift')), '');
            $hsps_left--;
        }
        is($hsps_left, 0);
    }
    last if( $count++ > @valid );
}
is(@valid, 0);

is($result->hits, 8);
$searchio = Bio::SearchIO->new(-format => 'fasta',
				 -file   => test_input_file('cysprot_vs_gadfly.FASTA'));
$result = $searchio->next_result;
like($result->database_name, qr/gadflypep2/);
is($result->database_letters, 7177762);
is($result->database_entries, 14334);
is($result->algorithm, 'FASTP');
is($result->algorithm_version, '3.3t08');
is($result->query_name, 'cysprot.fa');
is($result->query_length, 2385);
is($result->get_parameter('gapopen'), -12);
is($result->get_parameter('gapext'), -2);
is($result->get_parameter('ktup'), 2);
is($result->get_parameter('matrix'), 'BL50');

is($result->get_statistic('lambda'), 0.1397);
is($result->get_statistic('dbletters'), 7177762 );
is($result->get_statistic('dbentries'), 14334);


@valid = ( [ 'Cp1|FBgn0013770|pp-CT20780|FBan0006692', 341, 
	     'FBan0006692', '3.1e-59', 227.8],
	   [ 'CG11459|FBgn0037396|pp-CT28891|FBan0011459', 336, 
	     'FBan0011459', '6.4e-41',  166.9],
	   [ 'CG4847|FBgn0034229|pp-CT15577|FBan0004847', 390, 
	     'FBan0004847',  '2.5e-40', 165.2]);
$count = 0;

while( my $hit = $result->next_hit ) {
    my $d = shift @valid;

    is($hit->name, shift @$d);
    is($hit->length, shift @$d);
    is($hit->accession, shift @$d);
    float_is($hit->significance, shift @$d);
    is($hit->raw_score, shift @$d );

    if( $count == 0 ) {
        my $hsps_left = 1;
        while( my $hsp = $hit->next_hsp ) {
            is($hsp->query->start, 1373);
            is($hsp->query->end, 1706);
            is($hsp->query->strand, 0);
            is($hsp->hit->start, 5);
            is($hsp->hit->end, 341);
            is($hsp->hit->strand, 0);
            is($hsp->length('total'), 345);	    
            float_is($hsp->evalue, 3.1e-59);
            is($hsp->score, 1170.6);
            is($hsp->bits,227.8);
            is(sprintf("%.2f",$hsp->percent_identity), 53.04);
            is(sprintf("%.4f",$hsp->frac_identical('query')), 0.5479);
            is(sprintf("%.4f",$hsp->frac_identical('hit')), '0.5430');
            is($hsp->query->frame(), 0);
            is($hsp->hit->frame(), 0);
            is($hsp->gaps('query'), 11);
            is($hsp->gaps('hit'), 8);
            is($hsp->gaps, 19);
            is($hsp->hit_string, (' 'x26).'MRTAVLLPLLAL----LAVAQA-VSFADVVMEEWHTFKLEHRKNYQDETEERFRLKIFNENKHKIAKHNQRFAEGKVSFKLAVNKYADLLHHEFRQLMNGFNYTLHKQLRAADESFKGVTFISPAHVTLPKSVDWRTKGAVTAVKDQGHCGSCWAFSSTGALEGQHFRKSGVLVSLSEQNLVDCSTKYGNNGCNGGLMDNAFRYIKDNGGIDTEKSYPYEAIDDSCHFNKGTVGATDRGFTDIPQGDEKKMAEAVATVGPVSVAIDASHESFQFYSEGVYNEPQCDAQNLDHGVLVVGFGTDESGED---YWLVKNSWGTTWGDKGFIKMLRNKENQCGIASASSYPLV');
            is($hsp->query_string, 'SNWGNNGYFLIERGKNMCGLAACASYPIPQVMNPTLILAAFCLGIASATLTFDHSLEAQWTKWKAMHNRLY-GMNEEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQ---NRKPR------KGKVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPK-QEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTVMTPLLLLAVLCLGTALATPKFDQTFNAQWHQWKSTHRRLYGTNEE');
            # note: the reason this is not the same percent id above
            # is we are calculating average percent id
            is(sprintf("%.2f",$hsp->get_aln->percentage_identity()), 56.13);
            is(join(' ', $hsp->seq_inds('query', 'nomatch',1)), '1375 1377 1379 1381-1384 1391 1395-1397 1399 1400 1403 1404 1407 1408 1410 1412 1414 1415 1419 1422 1423 1429 1431 1433 1434 1440 1444 1447 1452 1457 1458 1473 1477 1480 1481 1483-1487 1495 1498 1501 1524 1530 1544-1546 1558 1580 1588-1592 1596 1607 1609 1630 1638 1658 1660 1662 1663 1665-1667 1677 1678 1681 1682 1688 1705');
            is(join(' ', $hsp->seq_inds('query', 'mismatch',1)), '1375 1377 1379 1395-1397 1399 1400 1403 1404 1407 1408 1410 1412 1414 1415 1419 1422 1423 1429 1431 1433 1434 1440 1444 1447 1452 1457 1458 1473 1477 1480 1481 1483-1487 1495 1498 1501 1524 1530 1544-1546 1558 1580 1588-1592 1596 1607 1609 1630 1638 1658 1660 1662 1663 1677 1678 1681 1682 1688 1705');
            is(join(' ', $hsp->seq_inds('query', 'conserved',1)), '1373 1374 1376 1378 1380 1385-1390 1392-1394 1398 1401 1402 1405 1406 1409 1411 1413 1416-1418 1420 1421 1424-1428 1430 1432 1435-1439 1441-1443 1445 1446 1448-1451 1453-1456 1459-1472 1474-1476 1478 1479 1482 1488-1494 1496 1497 1499 1500 1502-1523 1525-1529 1531-1543 1547-1557 1559-1579 1581-1587 1593-1595 1597-1606 1608 1610-1629 1631-1637 1639-1657 1659 1661 1664 1668-1676 1679 1680 1683-1687 1689-1704 1706');
            is(join(' ', $hsp->seq_inds('hit', 'nomatch',1)), '7 9 11 22-24 26 27 30 31 34 35 37 39 41-43 47 50 51 57 59 61 62 68 72 75 80 85 86 98-100 104 106-111 114 117 118 120-124 132 135 138 161 167 181-183 195 217 225-229 233 241 245 247 268 276 296 298 300 301 312 313 316 317 323 340');
            is(join(' ', $hsp->seq_inds('hit', 'mismatch',1)), '7 9 11 22-24 26 27 30 31 34 35 37 39 42 43 47 50 51 57 59 61 62 68 72 75 80 85 86 104 114 117 118 120-124 132 135 138 161 167 181-183 195 217 225-229 233 245 247 268 276 296 298 300 301 312 313 316 317 323 340');
            is(join(' ', $hsp->seq_inds('hit', 'conserved',1)), '5 6 8 10 12-21 25 28 29 32 33 36 38 40 44-46 48 49 52-56 58 60 63-67 69-71 73 74 76-79 81-84 87-97 101-103 105 112 113 115 116 119 125-131 133 134 136 137 139-160 162-166 168-180 184-194 196-216 218-224 230-232 234-240 242-244 246 248-267 269-275 277-295 297 299 302-311 314 315 318-322 324-339 341');
            is(join(' ', $hsp->seq_inds('query', 'gap',1)), '1413 1469 1474 1603');
            is(join(' ', $hsp->seq_inds('hit', 'frameshift')), '');
            is(join(' ', $hsp->seq_inds('query', 'frameshift')), '');
            $hsps_left--;
        }
        is($hsps_left, 0);
    }
    last if( $count++ > @valid );
}
is(@valid, 0);
is($result->hits, 21);

# test on TFASTXY
$searchio = Bio::SearchIO->new(-format => 'fasta',
			      -file   => test_input_file('5X_1895.FASTXY'));
$result = $searchio->next_result;
like($result->database_name, qr/yeast_nrpep.fasta/);
is($result->database_letters, 4215311);
is($result->database_entries, 9190);
is($result->algorithm, 'FASTY');
is($result->algorithm_version, '3.4t07');
is($result->query_name, '5X_1895.fa');
is($result->query_length, 7972);
is($result->get_parameter('gapopen'), -14);
is($result->get_parameter('gapext'), -2);
is($result->get_parameter('ktup'), 2);
is($result->get_parameter('matrix'), 'BL50');

is($result->get_statistic('lambda'), 0.1711);
is($result->get_statistic('dbletters'), 4215311);
is($result->get_statistic('dbentries'), 9190);


@valid = ( [ 'NR_SC:SW-YNN2_YEAST', 1056, 'NR_SC:SW-YNN2_YEAST','1.6e-154', '547.0'],
	   [ 'NR_SC:SW-MPCP_YEAST', 311, 'NR_SC:SW-MPCP_YEAST', '1.3e-25', 117.1],
	   [ 'NR_SC:SW-YEO3_YEAST', 300, 'NR_SC:SW-YEO3_YEAST', '5.7e-05', 48.5]);
$count = 0;

while( my $hit = $result->next_hit ) {
    my $d = shift @valid;

    is($hit->name, shift @$d);
    is($hit->length, shift @$d);
    is($hit->accession, shift @$d);
    float_is($hit->significance, shift @$d);
    is($hit->raw_score, shift @$d );

    if ( $count == 1 ) {
        my $hsps_left = 1;
        while( my $hsp = $hit->next_hsp ) {
            is($hsp->query->start, 6947);
            is($hsp->query->end, 7938);
            is($hsp->query->strand, -1);
            is($hsp->hit->start, 19);
            is($hsp->hit->end, 287);
            is($hsp->hit->strand, 0);
            is($hsp->length('total'), 330);
            
            float_is($hsp->evalue, 1.3e-25);
            is($hsp->score, 563.4);
            is($hsp->bits,'117.1');
            is(sprintf("%.2f",$hsp->percent_identity), 54.24);
            is(sprintf("%.4f",$hsp->frac_identical('query')), '0.5413');
            is(sprintf("%.4f",$hsp->frac_identical('hit')), '0.6654');
            is($hsp->query->frame(), 0);
            is($hsp->hit->frame(), 0);
            is($hsp->gaps('query'), 0);
            is($hsp->gaps('hit'), 61);
            is($hsp->gaps, 61);
            is($hsp->query_string, 'RFALAGALGCAVTHGALTPVDVVKTRIQLEPEVYNRVGRFFNSS*GF*EL*GVVLMSQT\KGMVASFRQIIAKEGAGALLTGFGPTAVGYAIQGAFKFGG*VMMSLQITA*SRANLPISYEFWKKKAIDLVGVDKARENRQAIYLGASAIAEFFADIALCPLEATRIRLVSQPSFANGLSGGFLRILREEGPAAFYAGFGPILFKQVPYTMAKFAV*VDRTA*\YQTFG*YYRSYEVAVEKILKATGKSKDSLTGGQLTGLNLTSGLIAGLAAAVISQPADTLLSKINKTKGAPGQSTTSRLVQMAGQLGVSGLFTGMTTRLVMIGTLTAGQ');
            is($hsp->hit_string, 'KFALAGAIGCGSTHSSMVPIDVVKTRIQLEPTVYN-------------------------KGMVGSFKQIIAGEGAGALLTGFGPTLLGYSIQGAFKFGG-------------------YEVFKKFFIDNLGYDTASRYKNSVYMGSAAMAEFLADIALCPLEATRIRLVSQPQFANGLVGGFSRILKEEGIGSFYSGFTPILFKQIPYNIAKFLVFERASEF-YYGFAG------------------PKEKLSSTSTTLLNLLSGLTAGLAAAIVSQPADTLLSKVNKTKKAPGQSTVGLLAQLAKQLGFFGSFAGLPTRLVMVGTLTSLQ');
            is($hsp->homology_string, '.::::::.::. ::....:.::::::::::: :::                         ::::.::.:::: ::::::::::::: .::.:::::::::                   :: .::  :: .: : : . ....:.:..:.:::.:::::::::::::::::::.::::: ::: :::.::: ..::.:: ::::::.::..::: :    .   :  :.                    :..:.. . : ::: ::: ::::::..::::::::::.:::: ::::::.. :.:.: :::  : :.:. :::::.::::. :');
            # note: the reason this is not the same percent id above
            # is we are calculating average percent id
            is(sprintf("%.2f",$hsp->get_aln->overall_percentage_identity()),
               '53.92');
            is(sprintf("%.2f",$hsp->get_aln->average_percentage_identity()),
               '67.29');
            is(join(' ', $hsp->seq_inds('query', 'nomatch',1)), '6950-6952 6986-6988 7001-7003 7007-7012 7022-7024 7040-7042 7067-7069 7139-7141 7151-7153 7163-7165 7169-7171 7175-7177 7196-7255 7262-7267 7272-7277 7281-7292 7296-7298 7341-7343 7365-7367 7389-7391 7401-7403 7524-7526 7530-7532 7536-7538 7542-7544 7551-7553 7560-7565 7575-7577 7584-7640 7680-7682 7722-7724 7762-7833 7843-7845 7903-7905');
            is(join(' ', $hsp->seq_inds('query', 'mismatch',1)), '6950-6952 6986-6988 7001-7003 7007-7012 7022-7024 7040-7042 7067-7069 7139-7141 7151-7153 7163-7165 7169-7171 7175-7177 7196-7198 7253-7255 7262-7267 7272-7277 7281-7292 7296-7298 7341-7343 7365-7367 7389-7391 7401-7403 7524-7526 7530-7532 7536-7538 7542-7544 7551-7553 7560-7565 7575-7577 7680-7682 7722-7724 7843-7845 7903-7905');
            is(join(' ', $hsp->seq_inds('query', 'conserved',1)), '6947-6949 6953-6985 6989-7000 7004-7006 7013-7021 7025-7039 7043-7066 7070-7138 7142-7150 7154-7162 7166-7168 7172-7174 7178-7195 7256-7261 7269-7272 7278-7280 7293-7295 7299-7340 7344-7364 7368-7388 7392-7400 7404-7523 7527-7529 7533-7535 7539-7541 7545-7550 7554-7559 7566-7574 7578-7583 7641-7679 7683-7721 7725-7757 7759-7762 7834-7842 7846-7902 7906-7938');
            is(join(' ', $hsp->seq_inds('query', 'gap',1)), '');
            is(join(' ', $hsp->seq_inds('hit', 'nomatch',1)), '30 50 66 80 96 100 101 104 107 109 111 113 154 158 166 174 189 191-194 196 197 199 200 203 204 211 213 215 219 223 247 256 262 266 267 269 274 286');
            is(join(' ', $hsp->seq_inds('hit', 'mismatch',1)), '30 50 66 80 96 100 101 104 107 109 111 113 154 158 166 174 189 191-194 196 197 199 200 203 204 211 213 215 219 223 247 256 262 266 267 269 274 286');
            is(join(' ', $hsp->seq_inds('hit', 'conserved',1)), '19-29 31-49 51-65 67-79 81-95 97-99 102 103 105 106 108 110 112 114-153 155-157 159-165 167-173 175-188 190 195 198 201 202 205-210 212 214 216-218 220-222 224-246 248-255 257-261 263-265 268 270-273 275-285 287');
            is(join(' ', $hsp->seq_inds('hit', 'gap',1)), '53 93 203');
            is(join(' ', $hsp->seq_inds('query', 'frameshift', 1)), '7271-7273 7761-7763');
            is(join(' ', $hsp->seq_inds('hit', 'frameshift')), '');
            is($hsp->ambiguous_seq_inds, 'query');
            $hsps_left--;
        }
        is($hsps_left, 0);
    }
    last if( $count++ > @valid );
}
is(@valid, 0);
is($result->hits, 58);

# test FASTA v35.04, params encoding changed 
# test on TFASTXY
$searchio = Bio::SearchIO->new(-format => 'fasta',
			      -file   => test_input_file('BOSS_DROME.FASTP_v35_04'));
$result = $searchio->next_result;
like($result->database_name, qr/wormpep190/, 'TFASTXY');
is($result->database_letters, 10449259);
is($result->database_entries, 23771);
is($result->algorithm, 'FASTP');
is($result->algorithm_version, '35.04');
is($result->query_name, 'BOSS_DROME');
is($result->query_length, 896);
is($result->get_parameter('gapopen'), -10);
is($result->get_parameter('gapext'), -2);
is($result->get_parameter('ktup'), 2);
is($result->get_parameter('matrix'), 'BL50');

# wordsize is the same as ktup, not opt width, as we used to parse
# is($result->get_parameter('wordsize'), 16);

# this is the range of the scoring matrix, not a filter (which is meant
# to capture whether xS seg filtering used)
# is($result->get_parameter('filter'), '15:-5');

is($result->get_statistic('lambda'), 0.122629);
is($result->get_statistic('dbletters'), 10449259);
is($result->get_statistic('dbentries'), 23771);
is($result->get_statistic('effectivespace'),23771);

# bug 2473 - fasta3.4 parsing with -U option

$searchio = Bio::SearchIO->new(-format => 'fasta',
							  -file   => test_input_file('bug2473.fasta'));

while(my $res = $searchio->next_result) {
    is($res->query_name, 'total:39860_L:12096_-3:12346_0:617_+3:14801');
    is($res->query_description, '');
    is($res->query_length, 22);
    is($res->algorithm, 'FASTN');
}

# bug 2537

$searchio = Bio::SearchIO->new(
   -format => 'fasta',
   -file   => test_input_file('in.fasta'),
);

while ( my $result = $searchio->next_result() ) {
   while( my $hit = $result->next_hit ) {
      # process the Bio::Search::Hit::HitI object
      while( my $hsp = $hit->next_hsp ) {
         # process the Bio::Search::HSP::HSPI object
         is($hsp->num_identical, 30, "num_identical()");
         is($hsp->num_conserved, 30, "num_conserved()");
      }
   }
}


# bug 2937 and version 35.04
$searchio = Bio::SearchIO->new(
   -format => 'fasta',
   -file   => test_input_file('bug2937.fasta'),
);
ok($searchio, 'bug 2937 and FASTA version 3.5');

while ( my $result = $searchio->next_result() ) {
   is ($result->algorithm_version, '35.04', 'algorithm version');
   is($result->query_name, 'ILTV-miR1', 'query name');
   is($result->query_description, '', 'query description');
   is($result->query_length, 70, 'query length');
   is($result->algorithm, 'FASTN', 'algorithm');
   
   while( my $hit = $result->next_hit ) {
      # process the Bio::Search::Hit::HitI object
      while( my $hsp = $hit->next_hsp ) {
         # process the Bio::Search::HSP::HSPI object
         is($hsp->num_identical, 26, "num_identical()");
         is($hsp->num_conserved, 26, "num_conserved()");
         is($hsp->strand('hit'), '1', 'hsp->strand(hit)');
		 is($hsp->hit->strand, '1', 'hsp->hit->strand');
		 is($hsp->strand('query'), '-1', 'hsp->strand(query)');
		 is($hsp->query->strand, '-1', 'hsp->query->strand');
      }
   }
}
BioPerl-1.007002/t/SearchIO/gmap_f9.t000444000766000024      1143713155576321 17151 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: gmap_f9.t 14995 2008-11-16 06:20:00Z cjfields $

use strict;
use warnings;
BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 54);
    
    use_ok('Bio::SearchIO');
}

my $searchio =
    Bio::SearchIO->new(-format => 'gmap_f9',
               -file   => test_input_file('gmap_f9.txt'));

my $result = $searchio->next_result;
isa_ok($result, 'Bio::Search::Result::GenericResult', 'Did we get a Result?');
is($result->num_hits(), 1, 'Did we get the expected number of hits?');
is($result->algorithm(), 'gmap', 'Did we get the expected algorithm?');
is($result->query_name(), 'NM_004448', 'Did we get the expected query_name?');

my $hit = $result->next_hit;
isa_ok($hit, 'Bio::Search::Hit::GenericHit', 'Did we get a Hit?');
_check_hit($hit, {name => '17',
          length => 4624,
          num_hsps => 27,
          query_length => 4623
         } );

my $hsp = $hit->next_hsp;
_check_hsp($hsp, {algorithm => 'GMAP',
          query_gaps => 1,
          hit_gaps => 0,
          query_length => 310,
          hit_length => 311,
          qseq => 'GGAGGAGGTGGAGGAGGAGG', # first 20 bases
          hseq => 'GGAGGAGGTGGAGGAGGAGG', # ditto
          query => {start => 1,
                end => 310,
                strand => 1},
          hit => {start => 35109780,
              end =>  35110090,
              strand => 1},
          homology_string => 'GGAGGAGGTGGAGGAGGAGG',
          seq_inds_query_gap => [(61)]
         } );

my $searchio_rev =
    Bio::SearchIO->new(-format => 'gmap_f9',
               -file   => test_input_file('gmap_f9-reverse-strand.txt'));
my $result_rev = $searchio_rev->next_result;
isa_ok($result_rev,
       'Bio::Search::Result::GenericResult', 'Did we get a Result?');
is($result_rev->num_hits(), 1, 'Did we get the expected number of hits?');
is($result_rev->algorithm(), 'gmap', 'Did we get the expected algorithm?');
is($result_rev->query_name(),
   'NM_004448', 'Did we get the expected query_name?');

$hit = $result_rev->next_hit;
_check_hit($hit, {name => '17',
          length => 4624,
          num_hsps => 27,
          query_length => 4623
         } );

$hsp = $hit->next_hsp;
_check_hsp($hsp, {algorithm => 'GMAP',
          query_gaps => 0,
          hit_gaps => 0,
          query_length => 974,
          hit_length => 974,
          qseq => 'TAGCTGTTTTCCAAAATATA', # first 20 bases
          hseq => 'TAGCTGTTTTCCAAAATATA', # ditto
          query => {start => 1,
                end => 974,
                strand => 1},
          hit => {start => 35137468,
              end =>  35138441,
              strand => -1},
          homology_string => 'TAGCTGTTTTCCAAAATATA',
          seq_inds_query_gap => [()]
         } );


$searchio =  Bio::SearchIO->new(-format => 'gmap_f9',
                -file   => test_input_file('gmap_f9-multiple_results.txt'));

my $result_count = 0;
while (my $result = $searchio->next_result) {
    $result_count++;
}

is($result_count, 58, "Can we loop over multiple results properly (expecting 58)?");

# bug 3021

$searchio =  Bio::SearchIO->new(-format => 'gmap_f9',
                -file   => test_input_file('bug3021.gmap'));

$result = $searchio->next_result;

is($result->query_name, 'NM_004448', 'simple query_name now caught, bug 3021');

exit(0);

sub _check_hit {
    my ($hit, $info) = @_;

    isa_ok($hit, 'Bio::Search::Hit::HitI');
    is($hit->name, $info->{name}, 'Check the name');
    is($hit->length, $info->{length}, 'Check the hit length');
    is($hit->num_hsps, $info->{num_hsps}, 'Check the number of hsps');
    is($hit->query_length, $info->{query_length}, 'Check the query length');

}

sub _check_hsp {
    my($hsp, $info) = @_;
    isa_ok($hsp, 'Bio::Search::HSP::HSPI');
    is($hsp->algorithm, $info->{algorithm}, 'Check the algorithm');
    is($hsp->gaps('query'), $info->{query_gaps}, 'Count gaps in the query');
    is($hsp->gaps('hit'), $info->{hit_gaps}, 'Count gaps in the hit');
    is($hsp->length('query'), $info->{query_length}, 'Length of the query');
    is($hsp->length('hit'), $info->{hit_length}, 'Length of the hit');
    is(substr($hsp->query_string, 0, 20), $info->{qseq}, 'Query sequence');
    is(substr($hsp->hit_string, 0, 20), $info->{hseq}, 'Hit sequence');
    is($hsp->query->start, $info->{query}->{start}, "Check query start");
    is($hsp->query->end, $info->{query}->{end}, "Check query end");
    is($hsp->query->strand, $info->{query}->{strand}, "Check query end");
    is(substr($hsp->homology_string, 0, 20), $info->{homology_string}, 'Check the homology string');
    is_deeply([$hsp->seq_inds('query', 'gap')], $info->{seq_inds_query_gap}, 'Check seq_inds');
    is($hsp->hit->start, $info->{hit}->{start}, "Check hit start");
    is($hsp->hit->end, $info->{hit}->{end}, "Check hit end");
    is($hsp->hit->strand, $info->{hit}->{strand}, "Check hit end");
}
BioPerl-1.007002/t/SearchIO/hmmer.t000444000766000024     25471213155576321 16764 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;
use warnings;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin( -tests => 824 );

    use_ok('Bio::SearchIO');
}

my $searchio = Bio::SearchIO->new(
    -format => 'hmmer',
    -file   => test_input_file('hmmpfam.out')
);
my $result;

while ( $result = $searchio->next_result ) {
    is( ref($result),
        'Bio::Search::Result::HMMERResult',
        'Check for the correct result reference type'
    );
    is( $result->algorithm,         'HMMPFAM', 'Check algorithm' );
    is( $result->algorithm_version, '2.1.1',   'Check algorithm version' );
    is( $result->hmm_name,          'pfam',    'Check hmm_name' );
    is( $result->sequence_file,
        '/home/birney/src/wise2/example/road.pep',
        'Check sequence_file'
    );

    is( $result->query_name,        'roa1_drome', 'Check query_name' );
    is( $result->query_length,       0,           'Check query_length absence' );
    is( $result->query_description, '',           'Check query_description' );
    is( $result->num_hits(),         2,           'Check num_hits' );
    my ( $hsp, $hit );

    if ( defined( $hit = $result->next_model ) ) {
        is( ref($hit), 'Bio::Search::Hit::HMMERHit',
            'Check for the correct hit reference type' );
        is( $hit->name, 'SEED', 'Check hit name' );
        is( $hit->description,
            '',
            'Check for hit description'
        );
        is( $hit->raw_score,          146.1,   'Check hit raw_score' );
        is( $hit->bits,               0,       'Check hit bits (0)' );
        float_is( $hit->significance, 6.3e-40, 'Check hit significance' );
        is( $hit->num_hsps,           1,       'Check num_hsps' );

        # Query and Hit lengths are usually unknown in HMMER,
        # but sometimes they can be deduced from domain data '[]'
        is( $hit->length,             77,      'Check hit length' );
        is( $hit->frac_aligned_query, undef );
        is( $hit->frac_aligned_hit,  '1.00' );

        is( $hit->matches('cons'), 55, 'Check hit total conserved residues' );
        is( $hit->matches('id'),   22, 'Check hit total identical residues' );
        is( sprintf( "%.3f", $hit->frac_identical('query') ), '0.310' );
        is( sprintf( "%.3f", $hit->frac_identical('hit') ),    0.286 );
        is( sprintf( "%.3f", $hit->frac_identical('total') ),  0.282 );
        is( sprintf( "%.3f", $hit->frac_conserved('query') ),  0.775 );
        is( sprintf( "%.3f", $hit->frac_conserved('hit') ),    0.714 );
        is( sprintf( "%.3f", $hit->frac_conserved('total') ),  0.705 );

        if ( defined( $hsp = $hit->next_domain ) ) {
            is( ref($hsp), 'Bio::Search::HSP::HMMERHSP',
                'Check for correct hsp reference type' );
            is( $hsp->query->seq_id(), 'roa1_drome', 'Check for query seq_id' );
            is( $hsp->hit->seq_id(),   'SEED',       'Check for hit seq_id' );

            is( $hsp->hit->start,   1,       'Check for hit hmmfrom value' );
            is( $hsp->hit->end,     77,      'Check for hit hmm to value' );
            is( $hsp->query->start, 33,      'Check for query alifrom value' );
            is( $hsp->query->end,   103,     'Check for query ali to value' );
            is( $hsp->score,        71.2,    'Check for hsp score' );
            is( $hsp->bits,         0,       'Check for hsp bits (0)' );
            float_is( $hsp->evalue, 2.2e-17, 'Check for hsp c-Evalue' );

            is( $hsp->length('query'), 71, 'Check for hsp query length' );
            is( $hsp->length('hit'),   77, 'Check for hsp hit length' );
            is( $hsp->length('total'), 78, 'Check for hsp total length' );
            is( $hsp->gaps('query'),   7,  'Check for hsp query gaps' );
            is( $hsp->gaps('hit'),     1,  'Check for hsp hit gaps' );
            is( $hsp->gaps('total'),   8,  'Check for hsp total gaps' );

            ($hit->length == 0) ?
                  is( $hsp->{HIT_LENGTH}, $hsp->hit->length, 'Check hit length consistency' )
                : is( $hsp->{HIT_LENGTH}, $hit->length,      'Check hit length consistency' );
            ($result->query_length == 0) ?
                  is( $hsp->{QUERY_LENGTH}, $hsp->query->length,   'Check query length consistency' )
                : is( $hsp->{QUERY_LENGTH}, $result->query_length, 'Check query length consistency' );

            is( $hsp->num_conserved, 55 );
            is( $hsp->num_identical, 22 );
            is( sprintf( "%.2f", $hsp->percent_identity ),         28.21 );
            is( sprintf( "%.3f", $hsp->frac_identical('query') ), '0.310' );
            is( sprintf( "%.3f", $hsp->frac_identical('hit') ),    0.286 );
            is( sprintf( "%.3f", $hsp->frac_identical('total') ),  0.282 );
            is( sprintf( "%.3f", $hsp->frac_conserved('query') ),  0.775 );
            is( sprintf( "%.3f", $hsp->frac_conserved('hit') ),    0.714 );
            is( sprintf( "%.3f", $hsp->frac_conserved('total') ),  0.705 );

            is( $hsp->query_string,
                'LFIGGLDYRTTDENLKAHFEKWGNIVDVVVMKD-----PRTKRSRGFGFITYSHSSMIDEAQK--SRpHKIDGRVVEP',
                'Check for query string'
            );
            is( $hsp->hit_string,
                'lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGfaFVeFeseedAekAlealnG-kelggrklrv',
                'Check for hit string'
            );
            is( $hsp->homology_string,
                'lf+g+L + +t+e Lk++F+k G iv++ +++D     + t++s+Gf+F+++  ++  + A +    +++++gr+++ ',
                'Check for homology string'
            );
            is( length( $hsp->homology_string ),
                length( $hsp->hit_string ),
                'Check if homology string and hit string have an equal length'
            );
            is( length( $hsp->query_string ),
                length( $hsp->homology_string ),
                'Check if query string and homology string have an equal length'
            );
            # This Hmmpfam don't have PP or CS strings, these are tests to check for side effects
            is( $hsp->posterior_string, '' );
            is( $hsp->consensus_string, '' );
        }
    }
    if ( defined( $hit = $result->next_model ) ) {
        is( ref($hit), 'Bio::Search::Hit::HMMERHit',
            'Check for the correct hit reference type' );
        is( $hit->name,              'SEED',    'Check hit name' );
        is( $hit->description,       '',        'Check for hit description' );
        is( $hit->raw_score,          146.1,    'Check hit raw_score' );
        is( $hit->bits,               0,        'Check hit bits (0)' );
        float_is( $hit->significance, 6.3e-040, 'Check hit significance' );
        is( $hit->num_hsps,           1,        'Check num_hsps' );

        # Query and Hit lengths are usually unknown in HMMER,
        # but sometimes they can be deduced from domain data '[]'
        is( $hit->length,             77,      'Check hit length' );
        is( $hit->frac_aligned_query, undef );
        is( $hit->frac_aligned_hit,  '1.00' );

        is( $hit->matches('cons'), 56, 'Check hit total conserved residues' );
        is( $hit->matches('id'),   33, 'Check hit total identical residues' );
        is( sprintf( "%.3f", $hit->frac_identical('query') ),  0.471 );
        is( sprintf( "%.3f", $hit->frac_identical('hit') ),    0.429 );
        is( sprintf( "%.3f", $hit->frac_identical('total') ),  0.429 );
        is( sprintf( "%.3f", $hit->frac_conserved('query') ), '0.800' );
        is( sprintf( "%.3f", $hit->frac_conserved('hit') ),    0.727 );
        is( sprintf( "%.3f", $hit->frac_conserved('total') ),  0.727 );

        if ( defined( $hsp = $hit->next_domain ) ) {
            is( ref($hsp), 'Bio::Search::HSP::HMMERHSP',
                'Check for correct hsp reference type' );
            is( $hsp->query->seq_id(), 'roa1_drome', 'Check for query seq_id' );
            is( $hsp->hit->seq_id(),   'SEED',       'Check for hit seq_id' );

            is( $hsp->hit->start,   1,       'Check for hit hmmfrom value' );
            is( $hsp->hit->end,     77,      'Check for hit hmm to value' );
            is( $hsp->query->start, 124,     'Check for query alifrom value' );
            is( $hsp->query->end,   193,     'Check for query ali to value' );
            is( $hsp->score,        75.5,    'Check for hsp score' );
            is( $hsp->bits,         0,       'Check for hsp bits (0)' );
            float_is( $hsp->evalue, 1.1e-18, 'Check for hsp c-Evalue' );

            is( $hsp->length('query'), 70, 'Check for hsp query length' );
            is( $hsp->length('hit'),   77, 'Check for hsp hit length' );
            is( $hsp->length('total'), 77, 'Check for hsp total length' );
            is( $hsp->gaps('query'),   7,  'Check for hsp query gaps' );
            is( $hsp->gaps('hit'),     0,  'Check for hsp hit gaps' );
            is( $hsp->gaps('total'),   7,  'Check for hsp total gaps' );

            ($hit->length == 0) ?
                  is( $hsp->{HIT_LENGTH}, $hsp->hit->length, 'Check hit length consistency' )
                : is( $hsp->{HIT_LENGTH}, $hit->length,      'Check hit length consistency' );
            ($result->query_length == 0) ?
                  is( $hsp->{QUERY_LENGTH}, $hsp->query->length,   'Check query length consistency' )
                : is( $hsp->{QUERY_LENGTH}, $result->query_length, 'Check query length consistency' );

            is( $hsp->num_conserved, 56 );
            is( $hsp->num_identical, 33 );
            is( sprintf( "%.2f", $hsp->percent_identity ),         42.86 );
            is( sprintf( "%.3f", $hsp->frac_identical('query') ),  0.471 );
            is( sprintf( "%.3f", $hsp->frac_identical('hit') ),    0.429 );
            is( sprintf( "%.3f", $hsp->frac_identical('total') ),  0.429 );
            is( sprintf( "%.3f", $hsp->frac_conserved('query') ), '0.800' );
            is( sprintf( "%.3f", $hsp->frac_conserved('hit') ),    0.727 );
            is( sprintf( "%.3f", $hsp->frac_conserved('total') ),  0.727);

            is( $hsp->query_string,
                'LFVGALKDDHDEQSIRDYFQHFGNIVDINIVID-----KETGKKRGFAFVEFDDYDPVDKVVL--KQHQLNGKMVDV',
                'Check for query string'
            );
            is( $hsp->hit_string,
                'lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGfaFVeFeseedAekAlealnGkelggrklrv',
                'Check for hit string'
            );
            is( $hsp->homology_string,
                'lfVg L  d +e+ ++d+F++fG iv+i+iv+D     ketgk +GfaFVeF++++ ++k +     ++l+g+ + v',
                'Check for homology string'
            );
            is( length( $hsp->homology_string ),
                length( $hsp->hit_string ),
                'Check if homology string and hit string have an equal length'
            );
            is( length( $hsp->query_string ),
                length( $hsp->homology_string ),
                'Check if query string and homology string have an equal length'
            );
        }
        last;
    }
}

$searchio = Bio::SearchIO->new(
    -format => 'hmmer',
    -file   => test_input_file('hmmsearch.out')
);
while ( $result = $searchio->next_result ) {
    is( ref($result),
        'Bio::Search::Result::HMMERResult',
        'Check for the correct result reference type'
    );
    is( $result->algorithm,         'HMMSEARCH',        'Check algorithm' );
    is( $result->algorithm_version, '2.0',              'Check algorithm version' );
    is( $result->hmm_name,          'HMM [SEED]',       'Check hmm_name' );
    is( $result->sequence_file,     'HMM.dbtemp.29591', 'Check sequence_file' );
    is( $result->database_name,     'HMM.dbtemp.29591', 'Check database_name' );

    is( $result->query_name,        'SEED', 'Check query_name' );
    is( $result->query_length,       77,    'Check query_length' );
    is( $result->query_description, '',     'Check query_description' );
    is( $result->num_hits(),         1215,  'Check num_hits' );

    my $hit = $result->next_model;
    is( ref($hit), 'Bio::Search::Hit::HMMERHit',
        'Check for the correct hit reference type' );
    is( $hit->name, 'Q91581', 'Check hit name' );
    is( $hit->description,
        'Q91581 POLYADENYLATION FACTOR 64 KDA SUBUN',
        'Check for hit description'
    );
    is( $hit->raw_score,          119.7, 'Check hit raw_score' );
    is( $hit->bits,               0,     'Check hit bits (0)' );
    float_is( $hit->significance, 2e-31, 'Check hit significance' );
    is( $hit->num_hsps,           1,     'Check num_hsps' );
    is( $hit->length,             0,     'Check hit length' );

    my $hsp = $hit->next_domain;
    is( ref($hsp), 'Bio::Search::HSP::HMMERHSP',
        'Check for correct hsp reference type' );
    is( $hsp->query->seq_id(), 'SEED',   'Check for query seq_id' );
    is( $hsp->hit->seq_id(),   'Q91581', 'Check for hit seq_id' );

    is( $hsp->hit->start,       18,    'Check for hit hmmfrom value' );
    is( $hsp->hit->end,         89,    'Check for hit hmm to value' );
    is( $hsp->query->start,     1,     'Check for query alifrom value' );
    is( $hsp->query->end,       77,    'Check for query ali to value' );
    is( $hsp->score,            119.7, 'Check for hsp score' );
    is( $hsp->bits,             0,     'Check for hsp bits (0)' );
    float_is( $hsp->evalue,     2e-31, 'Check for hsp c-Evalue' );

    is( $hsp->length('query'), 77, 'Check for hsp query length' );
    is( $hsp->length('hit'),   72, 'Check for hsp hit length' );
    is( $hsp->length('total'), 0,  'Check for hsp total length' );
    is( $hsp->gaps('query'),   0,  'Check for hsp query gaps' );
    is( $hsp->gaps('hit'),     0,  'Check for hsp hit gaps' );
    is( $hsp->gaps('total'),   0,  'Check for hsp total gaps' );

    my $example_counter = 0;
    while ($hit = $result->next_model) {
        if ($hit->name eq 'Q61954') {
            $example_counter++;
            if ($example_counter == 1) {
                # Query and Hit lengths are usually unknown in HMMER,
                # but sometimes they can be deduced from domain data '[]'
                is( $hit->length,              153,    'Check hit length' );
                is( $hit->frac_aligned_query, '1.00' );
                is( $hit->frac_aligned_hit,    0.42 );

                $hsp = $hit->next_domain;
                is( $hsp->query->seq_id(), 'SEED',   'Check for query seq_id' );
                is( $hsp->hit->seq_id(),   'Q61954', 'Check for hit seq_id' );

                is( $hsp->hit->start,       26,      'Check for hit hmmfrom value' );
                is( $hsp->hit->end,         89,      'Check for hit hmm to value' );
                is( $hsp->query->start,     1,       'Check for query alifrom value' );
                is( $hsp->query->end,       77,      'Check for query ali to value' );
                is( $hsp->score,            72.9,    'Check for hsp score' );
                is( $hsp->bits,             0,       'Check for hsp bits (0)' );
                float_is( $hsp->evalue,     2.4e-17, 'Check for hsp c-Evalue' );

                is( $hsp->length('query'), 77, 'Check for hsp query length' );
                is( $hsp->length('hit'),   64, 'Check for hsp hit length' );
                is( $hsp->length('total'), 0,  'Check for hsp total length' );
                is( $hsp->gaps('query'),   0,  'Check for hsp query gaps' );
                is( $hsp->gaps('hit'),     0,  'Check for hsp hit gaps' );
                is( $hsp->gaps('total'),   0,  'Check for hsp total gaps' );
            }
            elsif ($example_counter == 2) {
                # Query and Hit lengths are usually unknown in HMMER,
                # but sometimes they can be deduced from domain data '[]'
                is( $hit->length,              153,  'Check hit length' );
                is( $hit->frac_aligned_query, '1.00' );
                is( $hit->frac_aligned_hit,    0.34 );

                $hsp = $hit->next_domain;
                is( $hsp->query->seq_id(), 'SEED',   'Check for query seq_id' );
                is( $hsp->hit->seq_id(),   'Q61954', 'Check for hit seq_id' );

                is( $hsp->hit->start,       102, 'Check for hit hmmfrom value' );
                is( $hsp->hit->end,         153, 'Check for hit hmm to value' );
                is( $hsp->query->start,     1,   'Check for query alifrom value' );
                is( $hsp->query->end,       77,  'Check for query ali to value' );
                is( $hsp->score,            3.3, 'Check for hsp score' );
                is( $hsp->bits,             0,   'Check for hsp bits (0)' );
                float_is( $hsp->evalue,     1.9, 'Check for hsp c-Evalue' );

                is( $hsp->length('query'), 77, 'Check for hsp query length' );
                is( $hsp->length('hit'),   52, 'Check for hsp hit length' );
                is( $hsp->length('total'), 0,  'Check for hsp total length' );
                is( $hsp->gaps('query'),   0,  'Check for hsp query gaps' );
                is( $hsp->gaps('hit'),     0,  'Check for hsp hit gaps' );
                is( $hsp->gaps('total'),   0,  'Check for hsp total gaps' );

                last;
            }
        }
    }
}

$searchio = Bio::SearchIO->new(
    -format => 'hmmer',
    -file   => test_input_file('L77119.hmmer')
);

while ( $result = $searchio->next_result ) {
    is( ref($result),
        'Bio::Search::Result::HMMERResult',
        'Check for the correct result reference type'
    );
    is( $result->algorithm,         'HMMPFAM',    'Check algorithm' );
    is( $result->algorithm_version, '2.2g',       'Check algorithm version' );
    is( $result->hmm_name,          'Pfam',       'Check hmm_name' );
    is( $result->sequence_file,     'L77119.faa', 'Check sequence_file' );

    is( $result->query_name,
        'gi|1522636|gb|AAC37060.1|',
        'Check query_name'
    );
    is( $result->query_length, 0, 'Check query_length absence' );
    is( $result->query_description,
        'M. jannaschii predicted coding region MJECS02 [Methanococcus jannaschii]',
        'Check query_description'
    );
    is( $result->num_hits(), 1, 'Check num_hits' );

    my $hit = $result->next_hit;
    is( ref($hit), 'Bio::Search::Hit::HMMERHit',
        'Check for the correct hit reference type' );
    is( $hit->name, 'Methylase_M', 'Check hit name' );
    is( $hit->description,
        'Type I restriction modification system, M',
        'Check for hit description'
    );
    is( $hit->raw_score,         -105.2,  'Check hit raw_score' );
    is( $hit->bits,               0,      'Check hit bits (0)' );
    float_is( $hit->significance, 0.0022, 'Check hit significance' );
    is( $hit->num_hsps,           1,      'Check num_hsps' );

    # Query and Hit lengths are usually unknown in HMMER,
    # but sometimes they can be deduced from domain data '[]'
    is( $hit->length,             279,    'Check hit length' );
    is( $hit->frac_aligned_query, undef );
    is( $hit->frac_aligned_hit,  '1.00' );

    is( $hit->matches('cons'), 133, 'Check hit total conserved residues' );
    is( $hit->matches('id'),   48,  'Check hit total identical residues' );
    is( sprintf( "%.3f", $hit->frac_identical('query') ), 0.238 );
    is( sprintf( "%.3f", $hit->frac_identical('hit') ),   0.172 );
    is( sprintf( "%.3f", $hit->frac_identical('total') ), 0.171 );
    is( sprintf( "%.3f", $hit->frac_conserved('query') ), 0.658 );
    is( sprintf( "%.3f", $hit->frac_conserved('hit') ),   0.477 );
    is( sprintf( "%.3f", $hit->frac_conserved('total') ), 0.475 );

    my $hsp = $hit->next_hsp;
    is( ref($hsp), 'Bio::Search::HSP::HMMERHSP',
        'Check for correct hsp reference type' );
    is( $hsp->query->seq_id(), 'gi|1522636|gb|AAC37060.1|', 'Check for query seq_id' );
    is( $hsp->hit->seq_id(),   'Methylase_M',               'Check for hit seq_id' );

    is( $hsp->hit->start,   1,      'Check for hit hmmfrom value' );
    is( $hsp->hit->end,     279,    'Check for hit hmm to value' );
    is( $hsp->query->start, 280,    'Check for query alifrom value' );
    is( $hsp->query->end,   481,    'Check for query ali to value' );
    is( $hsp->score,       -105.2,  'Check for hsp score' );
    is( $hsp->bits,         0,      'Check for hsp bits (0)' );
    float_is( $hsp->evalue, 0.0022, 'Check for hsp evalue' );

    is( $hsp->length('query'), 202, 'Check for hsp query length' );
    is( $hsp->length('hit'),   279, 'Check for hsp hit length' );
    is( $hsp->length('total'), 280, 'Check for hsp total length' );
    is( $hsp->gaps('query'),   78,  'Check for hsp query gaps' );
    is( $hsp->gaps('hit'),     1,   'Check for hsp hit gaps' );
    is( $hsp->gaps('total'),   79,  'Check for hsp total gaps' );

    ($hit->length == 0) ?
          is( $hsp->{HIT_LENGTH}, $hsp->hit->length, 'Check hit length consistency' )
        : is( $hsp->{HIT_LENGTH}, $hit->length,      'Check hit length consistency' );
    ($result->query_length == 0) ?
          is( $hsp->{QUERY_LENGTH}, $hsp->query->length,   'Check query length consistency' )
        : is( $hsp->{QUERY_LENGTH}, $result->query_length, 'Check query length consistency' );

    is( $hsp->num_conserved, 133 );
    is( $hsp->num_identical, 48 );
    is( sprintf( "%.2f", $hsp->percent_identity ),        17.14 );
    is( sprintf( "%.3f", $hsp->frac_identical('query') ), 0.238 );
    is( sprintf( "%.3f", $hsp->frac_identical('hit') ),   0.172 );
    is( sprintf( "%.3f", $hsp->frac_identical('total') ), 0.171 );
    is( sprintf( "%.3f", $hsp->frac_conserved('query') ), 0.658 );
    is( sprintf( "%.3f", $hsp->frac_conserved('hit') ),   0.477 );
    is( sprintf( "%.3f", $hsp->frac_conserved('total') ), 0.475 );

    is (length($hsp->homology_string), length($hsp->query_string));

    is( $hsp->hit_string,
        'lrnELentLWavADkLRGsmDaseYKdyVLGLlFlKYiSdkFlerrieieerktdtesepsldyakledqyeqlededlekedfyqkkGvFilPsqlFwdfikeaeknkldedigtdldkifseledqialgypaSeedfkGlfpdldfnsnkLgskaqarnetLtelidlfselelgtPmHNG-dfeelgikDlfGDaYEYLLgkFAeneGKsGGeFYTPqeVSkLiaeiLtigqpsegdfsIYDPAcGSGSLllqaskflgehdgkrnaisyYGQEsn',
        'Check for hiy string'
    );
    is( $hsp->query_string,
        'NTSELDKKKFAVLLMNR--------------LIFIKFLEDK------GIV---------PRDLLRRTYEDY---KKSNVLI-NYYDAY-L----KPLFYEVLNTPEDER--KENIRT-NPYYKDIPYL---N-G-------GLFRSNNV--PNELSFTIKDNEIIGEVINFLERYKFTLSTSEGsEEVELNP-DILGYVYEKLINILAEKGQKGLGAYYTPDEITSYIAKNT-IEPIVVE----------------RFKEIIK--NWKINDINF----ST',
        'Check for query string'
    );
    is( $hsp->homology_string,
        ' ++EL+++  av+   R              L+F K++ dk      +i+         p +   + +++y   ++   ++ ++y ++      + lF++++   e ++  ++++ + +    ++      + +       Glf ++++  ++ +s+   +ne ++e+i+ +++ +++     G++ +el   D++G +YE L+   Ae   K+ G +YTP e++  ia+ + i+  ++                  +++ ++    k+n+i +    s+',
        'Check for homology string'
    );
    is( join( ' ', $hsp->seq_inds( 'query', 'nomatch', 1 ) ),
        '280 288 289 293-295 300 304 311 313-315 317 324-326 332 335 337 344-346 348 355 358-361 364-366 372 379 383-385 389 396 400 404-408 412 416 417 422 426 429-431 434-436 439 441 446 450 451 455 459 460 463 464 468 471 472 478',
        'Check for nomatch indices in query'
    );
    is( join( ' ', $hsp->seq_inds( 'hit', 'nomatch', 1 ) ),
        '1 9 10 14-16 18-31 35 39 42-47 51-59 61 63-65 67 72-74 77-79 82 86 89-94 96 103-105 107 110 111 116 118 120-123 126-131 133 135-141 145 150 151 154 158-160 164 171 175 179-183 187 191-193 198 202 205-207 210-212 215 217 222 226 227 231 233 236 237 240-257 261 264-267 273 275-278',
        'Check for nomatch indices in hit'
    );
    is( join( ' ', $hsp->seq_inds( 'query', 'gap', 1 ) ),
        '296 306 309 321 328 334 335 350 356 366-368 376 417 456 463 470 479',
        'Check for gap indices in query'
    );
    is( join( ' ', $hsp->seq_inds( 'hit', 'gap', 1 ) ),
        '', 'Check for gap indices in hit' );
}

$searchio = Bio::SearchIO->new(
    -format => 'hmmer',
    -file   => test_input_file('cysprot1b.hmmsearch')
);

while ( $result = $searchio->next_result ) {
    is( ref($result),
        'Bio::Search::Result::HMMERResult',
        'Check for the correct result reference type'
    );
    is( $result->algorithm,         'HMMSEARCH', 'Check algorithm' );
    is( $result->algorithm_version, '2.2g',      'Check algorithm version' );
    is( $result->hmm_name,
        'Peptidase_C1.hmm [Peptidase_C1]',
        'Check hmm_name'
    );
    is( $result->database_name,   'cysprot1b.fa', 'Check database_name' );
    is( $result->sequence_file,   'cysprot1b.fa', 'Check sequence_file' );

    is( $result->query_name,      'Peptidase_C1', 'Check query_name' );
    is( $result->query_length,     337,           'Check query_length' );
    is( $result->query_accession, 'PF00112',      'Check query_accession' );
    is( $result->query_description,
        'Papain family cysteine protease',
        'Check query_description'
    );
    is( $result->num_hits(), 4, 'Check num_hits' );

    my $hit = $result->next_hit;
    is( ref($hit), 'Bio::Search::Hit::HMMERHit',
        'Check for the correct hit reference type' );
    is( $hit->name, 'CATL_RAT', 'Check hit name' );
    is( $hit->description,
        '',
        'Check for hit description'
    );
    is( $hit->raw_score,          449.4,  'Check hit raw_score' );
    is( $hit->bits,               0,      'Check hit bits (0)' );
    float_is( $hit->significance, 2e-135, 'Check hit significance' );
    is( $hit->num_hsps,           1,      'Check num_hsps' );

    # Query and Hit lengths are usually unknown in HMMER,
    # but sometimes they can be deduced from domain data '[]'
    is( $hit->length,              0,     'Check hit length absence' );
    is( $hit->frac_aligned_query, '1.00' );
    is( $hit->frac_aligned_hit,    undef );

    is( $hit->matches('cons'), 204, 'Check hit total conserved residues' );
    is( $hit->matches('id'),   131, 'Check hit total identical residues' );
    is( sprintf( "%.3f", $hit->frac_identical('query') ), 0.389 );
    is( sprintf( "%.3f", $hit->frac_identical('hit') ),   0.598 );
    is( sprintf( "%.3f", $hit->frac_identical('total') ), 0.389 );
    is( sprintf( "%.3f", $hit->frac_conserved('query') ), 0.605 );
    is( sprintf( "%.3f", $hit->frac_conserved('hit') ),   0.932 );
    is( sprintf( "%.3f", $hit->frac_conserved('total') ), 0.605 );

    my $hsp = $hit->next_hsp;
    is( ref($hsp), 'Bio::Search::HSP::HMMERHSP',
        'Check for correct hsp reference type' );
    is( $hsp->query->seq_id(), 'Peptidase_C1', 'Check for query seq_id' );
    is( $hsp->hit->seq_id(),   'CATL_RAT',     'Check for hit seq_id' );

    is( $hsp->hit->start,       114,           'Check for hit hmmfrom value' );
    is( $hsp->hit->end,         332,           'Check for hit hmm to value' );
    is( $hsp->query->start,     1,             'Check for query alifrom value' );
    is( $hsp->query->end,       337,           'Check for query ali to value' );
    is( $hsp->score,            449.4,         'Check for hsp score' );
    is( $hsp->bits,             0,             'Check for hsp bits (0)' );
    float_is( $hsp->evalue,     2e-135,        'Check for hsp evalue' );

    is( $hsp->length('query'), 337, 'Check for hsp query length' );
    is( $hsp->length('hit'),   219, 'Check for hsp hit length' );
    is( $hsp->length('total'), 337, 'Check for hsp total length' );
    is( $hsp->gaps('query'),   0,   'Check for hsp query gaps' );
    is( $hsp->gaps('hit'),     118, 'Check for hsp hit gaps' );
    is( $hsp->gaps('total'),   118, 'Check for hsp total gaps' );

    ($hit->length == 0) ?
          is( $hsp->{HIT_LENGTH}, $hsp->hit->length, 'Check hit length consistency' )
        : is( $hsp->{HIT_LENGTH}, $hit->length,      'Check hit length consistency' );
    ($result->query_length == 0) ?
          is( $hsp->{QUERY_LENGTH}, $hsp->query->length,   'Check query length consistency' )
        : is( $hsp->{QUERY_LENGTH}, $result->query_length, 'Check query length consistency' );

    is( $hsp->num_conserved, 204 );
    is( $hsp->num_identical, 131 );
    is( sprintf( "%.2f", $hsp->percent_identity ),        38.87 );
    is( sprintf( "%.3f", $hsp->frac_identical('query') ), 0.389 );
    is( sprintf( "%.3f", $hsp->frac_identical('hit') ),   0.598 );
    is( sprintf( "%.3f", $hsp->frac_identical('total') ), 0.389 );
    is( sprintf( "%.3f", $hsp->frac_conserved('query') ), 0.605 );
    is( sprintf( "%.3f", $hsp->frac_conserved('hit') ),   0.932 );
    is( sprintf( "%.3f", $hsp->frac_conserved('total') ), 0.605 );

    is (length($hsp->homology_string), length($hsp->query_string));

    is( $hsp->hit_string,
        'IPKTVDWRE-KG-CVTPVKNQG-QCGSCWAFSASGCLEGQMFLKT------GKLISLSEQNLVDCSH-DQGNQ------GCNG-GLMDFAFQYIKE-----NGGLDSEESY-----PYE----AKD-------------------GSCKYR-AEYAV-----ANDTGFVDIPQQ-----EKALMKAVATVGPISVAMDASHPS---LQFYSSG-------IYYEP---NCSSK---DLDHGVLVVGYGYEG-T------------------------------------DSNKDKYWLVKNSWGKEWGMDGYIKIAKDRN----NHCGLATAASYPI',
        'Check for hiy string'
    );
    is( $hsp->homology_string,
        '+P+++DWRe kg  VtpVK+QG qCGSCWAFSa g lEg+ ++kt      gkl+sLSEQ+LvDC++ d gn+      GCnG Glmd Af+Yik+     NgGl++E++Y     PY+    +kd                   g+Cky+  + ++     a+++g++d+p++     E+al+ka+a++GP+sVa+das+ s    q+Y+sG       +Y+++    C+++   +LdH+Vl+VGYG e+                                      ++++ +YW+VKNSWG++WG++GY++ia+++n    n+CG+a+ asypi',
        'Check for homology string'
    );
    is( $hsp->query_string,
        'lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgryciktgtkawggklvsLSEQqLvDCdgedygnngesCGyGCnGGGlmdnAfeYikkeqIsnNgGlvtEsdYekgCkPYtdfPCgkdggndtyypCpgkaydpndTgtCkynckknskypktyakikgygdvpynvsTydEealqkalaknGPvsVaidasedskgDFqlYksGendvgyGvYkhtsageCggtpfteLdHAVliVGYGteneggtfdetssskksesgiqvssgsngssgSSgssgapiedkgkdYWIVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi',
        'Check for query string'
    );
    # Hmmsearch2 don't have PP or CS strings, these are tests to check for side effects
    is( $hsp->posterior_string, '' );
    is( $hsp->consensus_string, '' );

    $hit = $result->next_hit;
    is( $hit->name,              'CATL_HUMAN', 'Check hit name' );
    is( $hit->description,       '',           'Check for hit description' );
    is( $hit->raw_score,          444.5,       'Check hit raw_score' );
    is( $hit->bits,               0,           'Check hit bits (0)' );
    float_is( $hit->significance, 6.1e-134,    'Check hit significance' );
}

# test for bug 2632 - CS lines are captured without breaking the parser
$searchio = Bio::SearchIO->new(
    -format => 'hmmer',
    -file   => test_input_file('hmmpfam_cs.out')
);
if (defined ($result = $searchio->next_result) ) {
    my $hit = $result->next_hit;
    my $hsp = $hit->next_hsp;

    is ($hsp->seq_str,                  $hsp->query_string);
    is (length($hsp->seq_str),          length($hsp->query_string));
    is (length($hsp->homology_string),  length($hsp->query_string));
    is (length($hsp->consensus_string), length($hsp->query_string));

    is( $hsp->consensus_string,
        'EEEEEEEEETSSHSBHHHHHHHHHHHHHGGGGSSCSTTSSCECEEEEEEECTCCCHHHHHHHCT----S GC-EEEEEEE-SSHHHHHHHHHHHHHHHHHTT-EEEEEEE--B-GGGS-HHHHHC--EEEEEEEE-TT--HHHHHHCEEEEECHSCHHHHTHHH.    BEEEEEESSEEEEEECC-GGGHHHHBHGGGSTTEEBSEEEEEECESSSSSCTGGGSSCEEECCCTTCEEEEEEEEETTTHHHHHHHHHHTSCCCSSTTCGHHHHCC-SSS-TTSCHHHHHHHHHHHHHHTT--HHHHHHHHS----TT-GGGTST-HHHHHHHHHHHHHHCCHCCEEEEEEETSSEEEEEEETTTSCESEEEEEEEEEE.TTEEEEEESSC',
        'Check for consensus structure string'
    );
    is( $hsp->seq_str,
        'CGV-GFIADVNNVANHKIVVQALEALTCMEHRGACSADRDSGDGAGITTAIPWNLFQKSLQNQNIKFEQnDSVGVGMLFLPAHKLKES--KLIIETVLKEENLEIIGWRLVPTVQEVLGKQAYLNKPHVEQVFCKSSNLSKDRLEQQLFLVRKKIEKYIGINGKDwaheFYICSLSCYTIVYKGMMRSAVLGQFYQDLYHSEYTSSFAIYHRRFSTNTMPKWPLAQPMR---------FVSHNGEINTLLGNLNWMQSREPLLQSKVWKDRIHELKPITNKDNSDSANLDAAVELLIASGRSPEEALMILVPEAFQNQPDFA-NNTEISDFYEYYSGLQEPWDGPALVVFTNGKV-IGATLDRNGL-RPARYVIT----KDNLVIVSSES',
        'Check for hsp seq_str'
    );
    is( $hsp->query_string,
        'CGV-GFIADVNNVANHKIVVQALEALTCMEHRGACSADRDSGDGAGITTAIPWNLFQKSLQNQNIKFEQnDSVGVGMLFLPAHKLKES--KLIIETVLKEENLEIIGWRLVPTVQEVLGKQAYLNKPHVEQVFCKSSNLSKDRLEQQLFLVRKKIEKYIGINGKDwaheFYICSLSCYTIVYKGMMRSAVLGQFYQDLYHSEYTSSFAIYHRRFSTNTMPKWPLAQPMR---------FVSHNGEINTLLGNLNWMQSREPLLQSKVWKDRIHELKPITNKDNSDSANLDAAVELLIASGRSPEEALMILVPEAFQNQPDFA-NNTEISDFYEYYSGLQEPWDGPALVVFTNGKV-IGATLDRNGL-RPARYVIT----KDNLVIVSSES',
        'Check for query string'
    );
    is( $hsp->hit_string,
        'CGvlGfiAhikgkpshkivedaleaLerLeHRGavgADgktGDGAGIltqiPdgFFrevakelGieLpe-gqYAVGmvFLPqdelaraearkifEkiaeeeGLeVLGWReVPvnnsvLGetAlatePvIeQvFvgapsgdgedfErrLyviRkrieksivaenvn----fYiCSLSsrTIVYKGMLtseQLgqFYpDLqderfeSalAivHsRFSTNTfPsWplAQPfRVnslwgggivlAHNGEINTlrgNrnwMraRegvlksplFgddldkLkPIvneggSDSaalDnvlEllvraGRslpeAlMMlIPEAWqnnpdmdkdrpekraFYeylsglmEPWDGPAalvftDGryavgAtLDRNGLTRPaRygiTrdldkDglvvvaSEa',
        'Check for hit string'
    );
    is( $hsp->homology_string,
        'CGv GfiA+ ++ ++hkiv +aleaL+++eHRGa++AD ++GDGAGI t+iP+++F++  ++++i++ ++   +VGm+FLP   l+    + i+E +++ee+Le++GWR VP+  +vLG++A  + P++eQvF+ +++ +++ +E++L+++Rk+iek+i+  + +  ++fYiCSLS++TIVYKGM++s++LgqFY+DL++++++S++Ai+H+RFSTNT+P+WplAQP+R         ++ HNGEINTl gN nwM++Re +l+s++++d++++LkPI n+++SDSa+lD ++Ell+++GRs++eAlM+l+PEA+qn+pd   +++e+ +FYey+sgl+EPWDGPA++vft+G++ +gAtLDRNGL RPaRy+iT    kD+lv+v+SE+',
        'Check for homology string'
    );
}

# Tests for hmmer3 output here
$searchio = Bio::SearchIO->new(
    -format  => 'hmmer',
    -file    => test_input_file('hmmscan.out'),
    -verbose => 1
);
is( ref($searchio), 'Bio::SearchIO::hmmer3',
    'Check if correct searchio object is returned' );
my $counter = 0;
while ( $result = $searchio->next_result ) {
    $counter++;
    if ($counter == 1) {
        is( ref($result),
            'Bio::Search::Result::HMMERResult',
            'Check for the correct result reference type'
        );
        is( $result->algorithm,         'HMMSCAN', 'Check algorithm' );
        is( $result->algorithm_version, '3.0',     'Check algorithm version' );
        is( $result->hmm_name,
            '/data/biodata/HMMerDB/Pfam.hmm',
            'Check hmm_name'
        );
        is( $result->sequence_file,
            'BA000019.orf1.fasta',
            'Check sequence_file'
        );
        is( $result->query_name,        'BA000019.orf1', 'Check query_name' );
        is( $result->query_length,       198,            'Check query_length' );
        is( $result->query_accession,   '',              'Check query_accession' );
        is( $result->query_description, '',              'Check query_description' );
        # 1 hit above and 6 below inclusion threshold
        is( $result->num_hits(), 7, 'Check num_hits' );

        my ( $hsp, $hit );
        if ( $hit = $result->next_model ) {
            is( ref($hit), 'Bio::Search::Hit::HMMERHit',
                'Check for the correct hit reference type' );
            is( $hit->name, 'Peripla_BP_2', 'Check hit name' );
            is( $hit->description,
                'Periplasmic binding protein',
                'Check for hit description'
            );
            is( $hit->raw_score,          105.2, 'Check hit raw_score' );
            is( $hit->bits,               0,     'Check hit bits (0)' );
            float_is( $hit->significance, 6e-30, 'Check hit significance' );
            is( $hit->num_hsps,           1,     'Check num_hsps' );

            # Hit length is usually unknown for HMMSCAN and HMMSEARCH but not for NHMMER.
            # When is not known, sometimes it can be deduced from domain data '[]'
            is( $hit->length,             0,     'Check hit length absence' );
            is( $hit->frac_aligned_query, 0.87 );
            is( $hit->frac_aligned_hit,   undef );

            if ( defined( $hsp = $hit->next_domain ) ) {
                is( ref($hsp), 'Bio::Search::HSP::HMMERHSP',
                    'Check for correct hsp reference type' );
                is( $hsp->hit->seq_id(),   'Peripla_BP_2',  'Check for hit seq_id' );
                is( $hsp->query->seq_id(), 'BA000019.orf1', 'Check for query seq_id' );

                is( $hsp->hit->start,   59,      'Check for hit hmmfrom value' );
                is( $hsp->hit->end,     236,     'Check for hit hmm to value' );
                is( $hsp->query->start, 2,       'Check for query alifrom value' );
                is( $hsp->query->end,   173,     'Check for query ali to value' );
                is( $hsp->score,       '105.0',  'Check for hsp score' );
                is( $hsp->bits,         0,       'Check for hsp bits (0)' );
                float_is( $hsp->evalue, 1.5e-33, 'Check for hsp c-Evalue' );

                is( $hsp->length('query'), 172, 'Check for hsp query length' );
                is( $hsp->length('hit'),   178, 'Check for hsp hit length' );
                is( $hsp->length('total'), 180, 'Check for hsp total length' );
                is( $hsp->gaps('query'),   8,   'Check for hsp query gaps' );
                is( $hsp->gaps('hit'),     2,   'Check for hsp hit gaps' );
                is( $hsp->gaps('total'),   10,  'Check for hsp total gaps' );

                ($hit->length == 0) ?
                      is( $hsp->{HIT_LENGTH}, $hsp->hit->length, 'Check hit length consistency' )
                    : is( $hsp->{HIT_LENGTH}, $hit->length,      'Check hit length consistency' );
                ($result->query_length == 0) ?
                      is( $hsp->{QUERY_LENGTH}, $hsp->query->length,   'Check query length consistency' )
                    : is( $hsp->{QUERY_LENGTH}, $result->query_length, 'Check query length consistency' );

                is( $hsp->num_conserved, 140 );
                is( $hsp->num_identical, 50 );
                is( sprintf( "%.2f", $hsp->percent_identity ),        27.78 );
                is( sprintf( "%.3f", $hsp->frac_identical('query') ), 0.291 );
                is( sprintf( "%.3f", $hsp->frac_identical('hit') ),   0.281 );
                is( sprintf( "%.3f", $hsp->frac_identical('total') ), 0.278 );
                is( sprintf( "%.3f", $hsp->frac_conserved('query') ), 0.814 );
                is( sprintf( "%.3f", $hsp->frac_conserved('hit') ),   0.787 );
                is( sprintf( "%.3f", $hsp->frac_conserved('total') ), 0.778 );

                is (length($hsp->homology_string), length($hsp->query_string));

                is( $hsp->query_string,
                    'LKPDLIIGREYQ---KNIYNQLSNFAPTVLVDWGSF-TSFQDNFRYIAQVLNEEEQGKLVLQQYQKRIRDLQDRMGERlQKIEVSVIGFSGQSIKSLNR-DAVFNQVLDDAGIKRIsIQKNQQERYLEISIENLNKYDADVLFVINE---SKEQLYPDLKNPLWHHLRAVKKQQVYVVNQ',
                    'Check for query string'
                );
                is( $hsp->hit_string,
                    'lkPDlvivsafgalvseieellelgipvvavessstaeslleqirllgellgeedeaeelvaelesridavkaridsl-kpktvlvfgyadegikvvfgsgswvgdlldaaggeni-iaeakgseseeisaEqilaadpdviivsgrgedtktgveelkenplwaelpAvkngrvyllds',
                    'Check for hit string'
                );
                is( $hsp->homology_string,
                    'lkPDl+i+ +++   ++i+++l++ +p+v v+  s+  s+++ +r ++++l+ee++++ + +++++ri+++++r  +  ++ +v+v+g+++ +ik+++  +  ++++ld+ag++ i i++++++ + eis+E+++++d+dv++v       k+ +   ++nplw +l+Avk+++vy++++',
                    'Check for homology string'
                );
                is( $hsp->posterior_string,
                    '8***********...********************9.*****************************************999999999999997777776.5678999999****99777777*************************...77777777899***************9976',
                    'Check for posterior probability string'
                );
            }
        }
    }
    # Check for errors in HSP caused by the existence of 2 hits with the same ID
    elsif ($counter == 2) {
        is( $result->algorithm,         'HMMSCAN', 'Check algorithm' );
        is( $result->algorithm_version, '3.0',     'Check algorithm version' );
        is( $result->hmm_name,
            '/data/biodata/HMMerDB/Pfam.hmm',
            'Check hmm_name'
        );
        is( $result->sequence_file,
            'BA000019.orf1.fasta',
            'Check sequence_file'
        );
        is( $result->query_name,        'lcl|Test_ID.1|P1', 'Check query_name' );
        is( $result->query_length,       463,               'Check query_length' );
        is( $result->query_description, '281521..282909',   'Check query_description' );
        is( $result->num_hits(),         2,                 'Check num_hits' );

        my ( $hsp, $hit );
        my $hit_counter = 0;
        while ( $hit = $result->next_model ) {
            $hit_counter++;
            if ($hit_counter == 1) {
                is( ref($hit), 'Bio::Search::Hit::HMMERHit',
                    'Check for the correct hit reference type' );
                is( $hit->name,        'IS4.original', 'Check hit name' );
                is( $hit->description, '',             'Check for hit description' );
                is( $hit->num_hsps,     1,             'Check num_hsps' );
                if ( defined( $hsp = $hit->next_domain ) ) {
                    is( ref($hsp), 'Bio::Search::HSP::HMMERHSP',
                        'Check for correct hsp reference type' );
                    is( $hsp->hit->seq_id(),   'IS4.original',     'Check for hit seq_id' );
                    is( $hsp->query->seq_id(), 'lcl|Test_ID.1|P1', 'Check for query seq_id' );

                    is( $hsp->hit->start,   315,     'Check for hit hmmfrom value' );
                    is( $hsp->hit->end,     353,     'Check for hit hmm to value' );
                    is( $hsp->query->start, 335,     'Check for query alifrom value' );
                    is( $hsp->query->end,   369,     'Check for query ali to value' );
                    is( $hsp->score,        18.9,    'Check for hsp score' );
                    is( $hsp->bits,         0,       'Check for hsp bits (0)' );
                    float_is( $hsp->evalue, 8.9e-08, 'Check for hsp c-Evalue' );
                }
            }
            elsif ($hit_counter == 2) {
                is( ref($hit), 'Bio::Search::Hit::HMMERHit',
                    'Check for the correct hit reference type' );
                is( $hit->name,        'IS4.original', 'Check hit name' );
                is( $hit->description, '',             'Check for hit description' );
                is( $hit->num_hsps,     1,             'Check num_hsps' );
                if ( defined( $hsp = $hit->next_domain ) ) {
                    is( ref($hsp), 'Bio::Search::HSP::HMMERHSP',
                        'Check for correct hsp reference type' );
                    is( $hsp->hit->seq_id(),   'IS4.original',     'Check for hit seq_id' );
                    is( $hsp->query->seq_id(), 'lcl|Test_ID.1|P1', 'Check for query seq_id' );

                    is( $hsp->hit->start,   315,    'Check for hit hmmfrom value' );
                    is( $hsp->hit->end,     353,    'Check for hit hmm to value' );
                    is( $hsp->query->start, 335,    'Check for query alifrom value' );
                    is( $hsp->query->end,   369,    'Check for query ali to value' );
                    is( $hsp->score,        18.8,   'Check for hsp score' );
                    is( $hsp->bits,         0,      'Check for hsp bits (0)' );
                    float_is( $hsp->evalue, 9e-08,  'Check for hsp c-Evalue' );
                }
            }
        }
    }
}

$searchio = Bio::SearchIO->new(
    -format  => 'hmmer',
    -file    => test_input_file('hmmsearch3.out'),
    -verbose => 1
);
while ( $result = $searchio->next_result ) {
    is( ref($result),
        'Bio::Search::Result::HMMERResult',
        'Check for the correct result reference type'
    );
    is( $result->algorithm,         'HMMSEARCH', 'Check algorithm' );
    is( $result->algorithm_version, '3.0',       'Check algorithm version' );
    is( $result->hmm_name,          'Kv9.hmm',   'Check hmm_name' );
    is( $result->sequence_file,
        '/home/pboutet/Desktop/databases/nr_May26',
        'Check sequence_file'
    );
    is( $result->query_name,        'Kv9', 'Check query_name' );
    is( $result->query_length,      '481', 'Check query_length' );
    is( $result->query_description, '',    'Check query_description' );
    is( $result->num_hits(),        2,     'Check num_hits' );

    while ( my $hit = $result->next_model ) {
    }
}

$searchio = Bio::SearchIO->new(
    -format  => 'hmmer',
    -file    => test_input_file('hmmsearch3_multi.out'),
    -verbose => 1
);
is( ref($searchio), 'Bio::SearchIO::hmmer3',
    'Check if correct searchio object is returned' );
$counter = 0;
while ( $result = $searchio->next_result ) {
    $counter++;
    if ($counter == 1) {
        is( ref($result),
            'Bio::Search::Result::HMMERResult',
            'Check for the correct result reference type'
        );
        is( $result->algorithm,         'HMMSEARCH',             'Check algorithm' );
        is( $result->algorithm_version, '3.0',                   'Check algorithm version' );
        is( $result->hmm_name,          'Pfam-A.hmm',            'Check hmm_name' );
        is( $result->sequence_file,     'test_seqs.seq_raw.txt', 'Check sequence_file' );

        is( $result->query_name,      '1-cysPrx_C', 'Check query_name' );
        is( $result->query_length,     40,          'Check query_length' );
        is( $result->query_accession, 'PF10417.4',  'Check query_accession' );
        is( $result->query_description,
            'C-terminal domain of 1-Cys peroxiredoxin',
            'Check query_description'
        );
        is( $result->num_hits(), 0, 'Check num_hits' );
    }
    elsif ($counter == 2) {
        is( ref($result),
            'Bio::Search::Result::HMMERResult',
            'Check for the correct result reference type'
        );
        is( $result->algorithm,         'HMMSEARCH',             'Check algorithm' );
        is( $result->algorithm_version, '3.0',                   'Check algorithm version' );
        is( $result->hmm_name,          'Pfam-A.hmm',            'Check hmm_name' );
        is( $result->sequence_file,     'test_seqs.seq_raw.txt', 'Check sequence_file' );

        is( $result->query_name,      'DUF4229',   'Check query_name' );
        is( $result->query_length,     69,         'Check query_length' );
        is( $result->query_accession, 'PF14012.1', 'Check query_accession' );
        is( $result->query_description,
            'Protein of unknown function (DUF4229)',
            'Check query_description'
        );
        is( $result->num_hits(), 1, 'Check num_hits' );

        my ( $hsp, $hit );
        if ( $hit = $result->next_model ) {
            is( ref($hit), 'Bio::Search::Hit::HMMERHit',
                'Check for the correct hit reference type' );
            is( $hit->name, 'lcl|Protein_ID1.3|M3', 'Check hit name' );
            is( $hit->description,
                'complement(48376..51420)',
                'Check for hit description'
            );
            is( $hit->raw_score,         -17.8, 'Check hit raw_score' );
            is( $hit->bits,               0,    'Check hit bits (0)' );
            float_is( $hit->significance, 3,    'Check hit significance' );
            is( $hit->num_hsps,           5,    'Check num_hsps' );

            # Check first HSP
            if ( defined( $hsp = $hit->next_domain ) ) {
                is( ref($hsp), 'Bio::Search::HSP::HMMERHSP',
                    'Check for correct hsp reference type' );
                is( $hsp->hit->seq_id(),   'lcl|Protein_ID1.3|M3', 'Check for hit seq_id' );
                is( $hsp->query->seq_id(), 'DUF4229',              'Check for query seq_id' );

                is( $hsp->hit->start,   305, 'Check for hit alifrom value' );
                is( $hsp->hit->end,     311, 'Check for hit ali to value' );
                is( $hsp->query->start, 34,  'Check for query hmmfrom value' );
                is( $hsp->query->end,   40,  'Check for query hmm to value' );
                is( $hsp->score,       -4.3, 'Check for hsp score' );
                is( $hsp->bits,         0,   'Check for hsp bits (0)' );
                float_is( $hsp->evalue, 1,   'Check for hsp c-Evalue' );

                is( $hsp->length('query'), 7, 'Check for hsp query length' );
                is( $hsp->length('hit'),   7, 'Check for hsp hit length' );
                is( $hsp->length('total'), 7, 'Check for hsp total length' );
                is( $hsp->gaps('query'),   0, 'Check for hsp query gaps' );
                is( $hsp->gaps('hit'),     0, 'Check for hsp hit gaps' );
                is( $hsp->gaps('total'),   0, 'Check for hsp total gaps' );

                ($hit->length == 0) ?
                      is( $hsp->{HIT_LENGTH}, $hsp->hit->length, 'Check hit length consistency' )
                    : is( $hsp->{HIT_LENGTH}, $hit->length,      'Check hit length consistency' );
                ($result->query_length == 0) ?
                      is( $hsp->{QUERY_LENGTH}, $hsp->query->length,   'Check query length consistency' )
                    : is( $hsp->{QUERY_LENGTH}, $result->query_length, 'Check query length consistency' );

                is( $hsp->num_conserved, 6 );
                is( $hsp->num_identical, 4 );
                is( sprintf( "%.2f", $hsp->percent_identity ),        57.14 );
                is( sprintf( "%.3f", $hsp->frac_identical('query') ), 0.571 );
                is( sprintf( "%.3f", $hsp->frac_identical('hit') ),   0.571 );
                is( sprintf( "%.3f", $hsp->frac_identical('total') ), 0.571 );
                is( sprintf( "%.3f", $hsp->frac_conserved('query') ), 0.857 );
                is( sprintf( "%.3f", $hsp->frac_conserved('hit') ),   0.857 );
                is( sprintf( "%.3f", $hsp->frac_conserved('total') ), 0.857 );

                is (length($hsp->homology_string), length($hsp->query_string));

                is( $hsp->consensus_string,
                    '',
                    'Check for consensus structure string'
                );
                is( $hsp->query_string,
                    'laallAl',
                    'Check for query string'
                );
                is( $hsp->hit_string,
                    'LAILSAI',
                    'Check for hit string'
                );
                is( $hsp->homology_string,
                    'la+l A+',
                    'Check for homology string'
                );
                is( $hsp->posterior_string,
                    '3333332',
                    'Check for posterior probability string'
                );
            }
        }
    }
    elsif ($counter == 3) {
        is( ref($result),
            'Bio::Search::Result::HMMERResult',
            'Check for the correct result reference type'
        );
        is( $result->algorithm,         'HMMSEARCH',             'Check algorithm' );
        is( $result->algorithm_version, '3.0',                   'Check algorithm version' );
        is( $result->hmm_name,          'Pfam-A.hmm',            'Check hmm_name' );
        is( $result->sequence_file,     'test_seqs.seq_raw.txt', 'Check sequence_file' );

        is( $result->query_name,      'ACR_tran',   'Check query_name' );
        is( $result->query_length,     1021,        'Check query_length' );
        is( $result->query_accession, 'PF00873.14', 'Check query_accession' );
        is( $result->query_description,
            'AcrB/AcrD/AcrF family',
            'Check query_description'
        );
        is( $result->num_hits(), 1, 'Check num_hits' );

        my ( $hsp, $hit );
        if ( $hit = $result->next_model ) {
            is( ref($hit), 'Bio::Search::Hit::HMMERHit',
                'Check for the correct hit reference type' );
            is( $hit->name, 'lcl|Protein_ID1.3|M3', 'Check hit name' );
            is( $hit->description,
                'complement(48376..51420)',
                'Check for hit description'
            );
            is( $hit->raw_score,          616.9,    'Check hit raw_score' );
            is( $hit->bits,               0,        'Check hit bits (0)' );
            float_is( $hit->significance, 9.3e-189, 'Check hit significance' );
            is( $hit->num_hsps,           1,        'Check num_hsps' );

            # Hit length is usually unknown for HMMSCAN and HMMSEARCH but not for NHMMER.
            # When is not known, sometimes it can be deduced from domain data '[]'
            is( $hit->length,             0,        'Check hit length absence' );
            is( $hit->frac_aligned_query, 0.93 );
            is( $hit->frac_aligned_hit,   undef );

            if ( defined( $hsp = $hit->next_domain ) ) {
                is( ref($hsp), 'Bio::Search::HSP::HMMERHSP',
                    'Check for correct hsp reference type' );
                is( $hsp->hit->seq_id(),   'lcl|Protein_ID1.3|M3', 'Check for hit seq_id' );
                is( $hsp->query->seq_id(), 'ACR_tran',             'Check for query seq_id' );

                is( $hsp->hit->start,   11,       'Check for hit alifrom value' );
                is( $hsp->hit->end,     1000,     'Check for hit ali to value' );
                is( $hsp->query->start, 71,       'Check for query hmmfrom value' );
                is( $hsp->query->end,   1021,     'Check for query hmm to value' );
                is( $hsp->score,        616.6,    'Check for hsp score' );
                is( $hsp->bits,         0,        'Check for hsp bits (0)' );
                float_is( $hsp->evalue, 3.9e-189, 'Check for hsp c-Evalue' );

                is( $hsp->length('query'), 951,  'Check for hsp query length' );
                is( $hsp->length('hit'),   990,  'Check for hsp hit length' );
                is( $hsp->length('total'), 1003, 'Check for hsp total length' );
                is( $hsp->gaps('query'),   52,   'Check for hsp query gaps' );
                is( $hsp->gaps('hit'),     13,   'Check for hsp hit gaps' );
                is( $hsp->gaps('total'),   65,   'Check for hsp total gaps' );

                ($hit->length == 0) ?
                      is( $hsp->{HIT_LENGTH}, $hsp->hit->length, 'Check hit length consistency' )
                    : is( $hsp->{HIT_LENGTH}, $hit->length,      'Check hit length consistency' );
                ($result->query_length == 0) ?
                      is( $hsp->{QUERY_LENGTH}, $hsp->query->length,   'Check query length consistency' )
                    : is( $hsp->{QUERY_LENGTH}, $result->query_length, 'Check query length consistency' );

                is( $hsp->num_conserved, 690 );
                is( $hsp->num_identical, 262 );
                is( sprintf( "%.2f", $hsp->percent_identity ),        26.12 );
                is( sprintf( "%.3f", $hsp->frac_identical('query') ), 0.275 );
                is( sprintf( "%.3f", $hsp->frac_identical('hit') ),   0.265 );
                is( sprintf( "%.3f", $hsp->frac_identical('total') ), 0.261 );
                is( sprintf( "%.3f", $hsp->frac_conserved('query') ), 0.726 );
                is( sprintf( "%.3f", $hsp->frac_conserved('hit') ),   0.697 );
                is( sprintf( "%.3f", $hsp->frac_conserved('total') ), 0.688 );

                is (length($hsp->homology_string), length($hsp->query_string));

                is( $hsp->consensus_string,
                    'S-TTEEEEEEEETTSEEEEEEEESTTS-HHHHHHHHHHHHHHHGGGS-HHHHHH-EEEEEEECCECEEEEEEESSSTS-HHHHHHHHHHCTHHHHHTSTTEEEEEESS.--EEEEEEE-HHHHHCTT--HHHHHHHHHHHSSB-EEEECTT-SB-EEEE-SB---SCCHHCT-EEEETTSEEEEHHHCEEEEEEESSSS-EEEETTCEEEEEEEEEETTSBHHHHHHHHHHHHHCCGGGSSTTEEEEEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSHCCCHHHHHHHHHHHHHHHHHHHHTT--EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSS-HHHHHHHHHHHHCCHHHHHHHHHHHHCCGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCS----TT-CC..............................CHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHH.HHHHHCCS-BESS----TSEEEEEEE-STTC-HHHHHHHHHHHHHHHH...TTTTEEEEEEEESESSSS..E........CTTEEEEEEEE--CTTS-SCCCSHHHHHHHHHHHC.CTSTSSEEEEEE-SSSCCCSSSSSEEEEEEE.TSSSCHHHHHHHHHHHHHHHCCSTTEECEEESS-S-EEEEEEEE-HHHHHHCTB-HHHHHHHHHHHHT-..EEEEEEEETTE...EEEEEEEE-GGGSSSGGGGCC-EEEETTSE.EEECGGCEEEEEEEE-SEEEEETTCEEEEEEEEESTTS...-HHHHHHHHHHCCTT..SSTTEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCTSSSTCHHHHTTHHHHHHHHHHHHHHTT--BSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTTBHHHHHHHHHHHHCHHHHHHHHHHHHHCCHHHHTT-STTHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHH',
                    'Check for consensus structure string'
                );
                is( $hsp->query_string,
                    'gldglkyvsSqSseglssitvtFedgtdidiArqqvqnrlqeaknkLPeevqepgiskiktssseilvlavtskdgsltktdlrdlaesnikdqlsrveGVgdvqliGgsekavriwldpqklaklgltltdvvsalkeqnvqvaaGqlegqqeelliraqgrlqsaediekiivksqdgskvrlrDvAkvelgaeeeriaatlngkpavllavkklpganaievvkavkekleelketlPegveivvvydttefvrasieeVvktlleaivLvvlvlflFLqnlratlipaiavPlsllgtfavlkalglsiNlltlfgLvlAiGlvvDdAiVvvEnverkleeegekpleaalksmkeiegalvaialvllavfvPilflgGveGklfrqfaltivlaillsvlvaltltPalcallLkarkeekek..............................gffrefnrlfdalerrYekllekvlrhravvllvalllvvg.slllfvripkeflPeedegvlvtsvqlppgvsleqtekvlkqvekilk...ekpevesvfavtGfafagdta........gqnsakvfisLkpekerkeeektvealierlrkel.ekikganvellapiqlreletlsgvrlelqvklfgddleaLseareqllaalkqlpeladvrseqqedepqlqvkidrekaaalGvsiadinetlstalgg..syvndfieegr...vvkvvvqleedlrsspedlkklyvrnkkgk.mvplsavakieeekgpnsierenglrsveisgevaegd...slgeaeeavekiakqvklPagvgiewtglseqeqeagnsllllvalalllvflvLaalyeslsdpllvlltvPlalvGallalllrglelsviaqvGlilliGlavkNailivefakelrekeglsleeAileaaklRLrPiLMTalaailGvlPLalstGaGselqqplgivvlGGlvtstvLtlllvPvlYvlva',
                    'Check for query string'
                );
                is( $hsp->hit_string,
                    'TVNDIEHIESQSLFGYGIVKIFFQPDVDIRTANAQVTAISQTVLKQMPPGITPPLILNYNAATVPILQLALSSK--VLSEDRIFDLGQNFIRPQLATVRGSAVPSPYGGKVRQIQIDLDPQAMQSKRVSPDDVARALSQQNLVLSPGTEKIGSFEYNVKINDSPDEFTLLNNLPIKNVGGVTIFIHDVAHVRDGFPPQINVVRDDGRRSVLMTILKNGATSTLDIIQGTKELIPKLKETLPNNLVLKVVGDQSIFVKSAISGVVREGTIAGILTSVMILLFLGSWRSTIIISMSIPLAILSAIIFLSLTGNTLNVMTLGGLALAVGMLVDDATVVIENINHHLEM-GKPTTKAIIDAARQIIQPALVSTLSICIVFVPMFSLTGVPRYLFIPMAEAVIFGMLSSFVLSQTFVPTVANKLLKYQTQHFKHehhtdahrpehdpnfkvhrsvkasifqffiNIQQGFEKRFTKVRLVYRSILHFALDHRKKFITLFLGFVIVsCVTLFPLLGKNFFPEVDSGDMKIHIRVQVGTRIEETAKQFDLIENTIRrlvPQNELDTIVDNIGLSVSGINTaysstgtiGPQDGDILIHLNEN------HHPTKEYMKKLRETLpRAFPGVS-FAFLPADITSQILNFGVPAPIDIRVDGPNHDNNLKFVRAILKDIRNVPGIADLRVQQATNYPQFNVDIDRSQAKNYGLTEGDITNSLVATLAGtsQVAPTFWLNNKngvSYPIVIQMPQYKINSLADLANIPITTKESSsMQVLGGLGSIERDQSDSVISHYNIKPSFDIFASLQGRDlgsISGDIETIIQHHHQE--LPKGVSVKLQGQVPIMQDSYRGLSLGLVASIILIYFLVVVNFESWLDPFVIITALPAALAGIVWMLYLTGTTLSVPALTGAIMCMGVATANSILVISFARERLA-IVKDSTQAALEAGYTRFRPVLMTASAMLIGMIPMALGLGDGGEQNAPLGRAVIGGLLLATIATLIFVPVVFSVVH',
                    'Check for hit string'
                );
                is( $hsp->homology_string,
                    ' ++ +++++SqS  g   + + F+ + di  A+ qv++  q + +++P ++++p i   +++  +il+la++sk   l++  + dl ++ i++ql+ v G +    +Gg+ ++++i ldpq++++ +++++dv++al++qn   + G+ +  + e+++++++   +   ++++ +k+  g  + ++DvA+v +g   + ++++ +g   vl+++ k     ++++++  ke +++lketlP+++ ++vv d++ fv+++i+ Vv +  +a +L  ++++lFL+++r+t+i+ +++Pl++l ++++l++ g ++N++tl+gL+lA+G++vDdA Vv+En+  +le+ g+   +a++ ++++i  + + ++l++++vfvP+++l+Gv   lf ++a ++++ +l s +++ t++P ++  lLk + ++ ++                              ++ + f++ f ++   Y+ +l++ l hr+  ++++l +v++ ++ lf+ ++k+f+Pe d g++ ++++++ g+ +e+t+k  + +e++++    ++e + ++   G + +g +         g++ +++ i+L ++      ++  ++ +++lr+ l ++++g++ +++ p +++ +    gv + ++  + g ++++  + ++++l+ ++++p++ad+r++q ++ pq++v+idr +a+++G++  di + l + l g  +++ +f  +++    + +v+q+++ + +s+ dl+++++++k++  m  l+ + +ie+ ++ + i+++n ++s+ i ++++ +d   ++g++e+++++ +++  lP+gv+++ +g+    q ++  l+l ++++++l++++  + +es++dp+++++ +P al+G +  l+l+g++lsv a+ G i+ +G+a  N il+++fa+e  +   ++  +A+lea+ +R+rP+LMTa a+++G++P+al+ G+G e   plg +v+GGl+++t+ tl +vPv++ +v+',
                    'Check for homology string'
                );
                is( $hsp->posterior_string,
                    '578899********************************************************************..*****************************************************************************************************************************************************************************************************************************************************************************.***************************************************************************8776544446799********************9655555578*************************999999887775899******************************************8875446889999999999888774331111111134445555555444......45688999999999945678887.7888999*999************************************************************************8877666655434556776544422279***********************998764889*******************************8876222578999999999888..********************************************************************************************************.888899*****************************************************************9997',
                    'Check for posterior probability string'
                );
            }
        }
    }
}

$searchio = Bio::SearchIO->new(
    -format  => 'hmmer',
    -file    => test_input_file('hmmscan_multi_domain.out'),
    -verbose => 1
);

my @multi_hits = (
    [   'PPC',
        'Bacterial pre-peptidase C-terminal domain',
        '111.0', 3.1e-32, 6,
        [   [ 4,  59, 117,  183,  0.5,  0.16 ],
            [ 12, 58, 347,  388,  -0.6, 0.36 ],
            [ 1,  69, 470,  549,  71.3, 1.3e-23 ],
            [ 15, 25, 582,  603,  -3.2, 2 ],
            [ 13, 36, 987,  1019, -1.1, 0.5 ],
            [ 1,  69, 1087, 1168, 54.4, 2.4e-18 ]
        ]
    ],
    [   'HemolysinCabind',
        'Hemolysin-type calcium-binding repeat (2 copies)',
        '47.9', 4.7e-13, 3,
        [   [ 2, 13, 1214, 1225, 5.9,  0.0026 ],
            [ 1, 18, 1231, 1248, 10.8, 6.8e-5 ],
            [ 4, 18, 1243, 1257, 11.4, 4.3e-05 ]
        ]
    ]
);

while ( $result = $searchio->next_result ) {
    is( ref($result),
        'Bio::Search::Result::HMMERResult',
        'Check for the correct result reference type'
    );
    is( $result->algorithm,         'HMMSCAN', 'Check algorithm' );
    is( $result->algorithm_version, '3.0',     'Check algorithm version' );
    is( $result->hmm_name,
        '/data/biodata/HMMerDB/Pfam-A.hmm',
        'Check hmm_name'
    );
    is( $result->sequence_file, 'BA000019.orf37.fasta',
        'Check sequence_file' );
    is( $result->query_name, 'BA000019.orf37', 'Check query_name' );
    is( $result->query_length, '1418', 'Check query_length' );
    is( $result->query_description, '', 'Check query_description' );
    is( $result->num_hits(),        2,  'Check num_hits' );
    my ( $hsp, $hit );

    while ( $hit = $result->next_model ) {
        if ($hit->name eq 'HemolysinCabind') {
            # Hit length is usually unknown for HMMSCAN and HMMSEARCH but not for NHMMER.
            # When is not known, sometimes it can be deduced from domain data '[]'
            is( $hit->length,             18, 'Check hit length' );
            is( $hit->frac_aligned_query, 0.03 );
            is( $hit->frac_aligned_hit,  '1.00' );
        }
        my @expected = @{ shift @multi_hits };
        is( ref($hit), 'Bio::Search::Hit::HMMERHit',
            'Check for the correct hit reference type' );
        is( $hit->name,        shift @expected, 'Check hit name' );
        is( $hit->description, shift @expected, 'Check for hit description' );
        is( $hit->raw_score,   shift @expected, 'Check hit raw_score' );
        float_is(
            $hit->significance,
            shift @expected,
            'Check hit significance'
        );
        is( $hit->num_hsps, shift @expected, 'Check num_hsps' );
        my @hsp_list = @{ shift @expected };

        while ( defined( $hsp = $hit->next_domain ) ) {
            my @hsp_exp = @{ shift @hsp_list };
            is( ref($hsp), 'Bio::Search::HSP::HMMERHSP',
                'Check for correct hsp reference type' );
            is( $hsp->hit->start,
                shift @hsp_exp,
                'Check for hit envfrom value'
            );
            is( $hsp->hit->end, shift @hsp_exp,
                'Check for hit env to value' );
            is( $hsp->query->start,
                shift @hsp_exp,
                'Check for query hmmfrom value'
            );
            is( $hsp->query->end,
                shift @hsp_exp,
                'Check for query hmm to value'
            );
            is( $hsp->score, shift @hsp_exp, 'Check for hsp score' );
            float_is( $hsp->evalue, shift @hsp_exp,
                'Check for hsp c-Evalue' );
        }
    }
}

$searchio = Bio::SearchIO->new(
    -format  => 'hmmer',
    -file    => test_input_file('hmmscan_sec_struct.out'),
    -verbose => 1
);

@multi_hits = (
    [   'HTH_AraC',
        'Bacterial regulatory helix-turn-helix proteins, AraC family',
        '41.3', 6.7e-11, 2,
        [   [ 'siadiAeevgfSpsyfsrlFkkytGvt', 'SLMELSRQVGLNDCTLKRGFRLVFDTT' ],
            [   'nwsiadiAeevgf-SpsyfsrlFkkytGvtPsqyr',
                'EINISQAARRVGFsSRSYFATAFRKKFGINPKEFL'
            ]
        ]
    ],
    [   'PKSI-KS_m3',
        '', '38.2', 3.8e-12, 2,
        [   [ 'GPSvtVDTACSSSLvA', 'GPSVTVDTLCSSSLVA' ],
            [ 'GPSvtVDTACSSSLv',  'GPNLVIDSACSSALV' ]
        ]
    ],
    [   'DUF746',
        'Domain of Unknown Function (DUF746)',
        '13.9', 0.023, 2,
        [   [   'rllIrlLsqplslaeaadqlgtdegiiak',
                'EILIRNLENPPSLMELSRQVGLNDCTLKR'
            ],
            [ 'plslaeaadqlgtdeg', 'EINISQAARRVGFSSR' ]
        ]
    ]
);

my $result_counter = 0;
while ( $result = $searchio->next_result ) {
    $result_counter++;
    if ($result_counter == 1) {
        is( ref($result),
            'Bio::Search::Result::HMMERResult',
            'Check for the correct result reference type'
        );
        is( $result->algorithm,         'HMMSCAN',             'Check algorithm' );
        is( $result->algorithm_version, '3.0',                 'Check algorithm version' );
        is( $result->hmm_name,          'Pfam-A.hmm',          'Check hmm_name' );
        is( $result->sequence_file,     'BA000019.orf8.fasta', 'Check sequence_file' );
        is( $result->query_name,        'BA000019.orf8',       'Check query_name' );
        is( $result->query_length,       348,                  'Check query_length' );
        is( $result->query_description, '',                    'Check query_description' );
        is( $result->num_hits(),         3,                    'Check num_hits' );
        my ( $hsp, $hit );

        while ( $hit = $result->next_model ) {
            if ($hit->name eq 'PKSI-KS_m3') {
                # Hit length is usually unknown for HMMSCAN and HMMSEARCH but not for NHMMER.
                # When is not known, sometimes it can be deduced from domain data '[]'
                is( $hit->length,             16, 'Check hit length' );
                is( $hit->frac_aligned_query, 0.09 );
                is( $hit->frac_aligned_hit,  '1.00' );
            }
            my @expected = @{ shift @multi_hits };
            is( ref($hit), 'Bio::Search::Hit::HMMERHit',
                'Check for the correct hit reference type' );
            is( $hit->name,        shift @expected, 'Check hit name' );
            is( $hit->description, shift @expected, 'Check for hit description' );
            is( $hit->raw_score,   shift @expected, 'Check hit raw_score' );
            float_is(
                $hit->significance,
                shift @expected,
                'Check hit significance'
            );
            is( $hit->num_hsps, shift @expected, 'Check num_hsps' );
            my @hsp_list = @{ shift @expected };

            while ( defined( $hsp = $hit->next_domain ) ) {
                my @hsp_exp = @{ shift @hsp_list };
                is( ref($hsp), 'Bio::Search::HSP::HMMERHSP',
                    'Check for correct hsp reference type' );
                is( $hsp->hit_string,   shift @hsp_exp, 'Check hit sequence' );
                is( $hsp->query_string, shift @hsp_exp, 'Check query sequence' );
            }
        }
    }
    elsif ($result_counter == 2) {
        is( ref($result),
            'Bio::Search::Result::HMMERResult',
            'Check for the correct result reference type'
        );
        is( $result->algorithm,         'HMMSCAN',                    'Check algorithm' );
        is( $result->algorithm_version, '3.0',                        'Check algorithm version' );
        is( $result->query_name,        'lcl|aorf_00010|P1',          'Check query_name' );
        is( $result->query_length,       132,                         'Check query_length' );
        is( $result->query_description, 'IS481.original transposase', 'Check query_description' );
        is( $result->num_hits(),         1,                           'Check num_hits' );
        my ( $hsp, $hit );

        while ( $hit = $result->next_model ) {
            is( ref($hit), 'Bio::Search::Hit::HMMERHit',
                'Check for the correct hit reference type' );
            is( $hit->name,              'IS481.original.hmm', 'Check hit name' );
            is( $hit->description,       '',                   'Check for hit description' );
            is( $hit->raw_score,         '130.0',              'Check hit raw_score' );
            float_is( $hit->significance, 3.4e-040,            'Check hit significance' );
            is( $hit->num_hsps,           1,                   'Check num_hsps' );

            while ( defined( $hsp = $hit->next_domain ) ) {
                is( ref($hsp), 'Bio::Search::HSP::HMMERHSP',
                    'Check for correct hsp reference type' );
                is( $hsp->query_string,
                    'GEIETAHPSYLGSQDTFYVGNITGAGR----------------------------IYQQTFVDTYSKWDSTKLYTTKTPITAADLLNDRVLSFFA-EQGMGIIRLLTDRSTEYCSKA--ETQDYELCLALNDIEHTKTKVYHPQTNDICRRFHKA',
                    'Check for query string'
                );
                is( $hsp->hit_string,
                    'kRYErdhPgeLvhmDvkklgripdgGgvkighRwrgrtrgrgkrtnqsrnrglgkayvitaiDDhSRfayaeilsdettttaadfllraaayfygkigeeiitrvlTDnGaayrskkrsakhdFqealaelGIkhilTrprsPqTNGKiERFhrT',
                    'Check for hit string'
                );
                is( $hsp->homology_string,
                    '+++E++hP +L+++D++++g+i + G+                            +y++t++D++S+   +++++++t++taad l++ ++ f+   ++++i r lTD+ ++y+sk   ++ d+  +la ++I+h++T++++PqTN ++ RFh+ ',
                    'Check for homology string'
                );
                is( $hsp->posterior_string,
                    '579*******************88888............................****************************************.********************8..**********************************95',
                    'Check for posterior probability string'
                );
            }
        }
    }
}

# Make sure that you can also directly call the hmmer2 and hmmer3 subclasses
$searchio = Bio::SearchIO->new(
    -format => 'hmmer2',
    -file   => test_input_file('hmmpfam.out')
);
is( ref($searchio), 'Bio::SearchIO::hmmer2',
    'Check if loading hmmpfam output via the hmm2 parser directly works' );
is( ref( $searchio->next_result ),
    'Bio::Search::Result::HMMERResult',
    'Check for the correct result reference type'
);

$searchio = Bio::SearchIO->new(
    -format => 'hmmer2',
    -file   => test_input_file('hmmsearch.out')
);
is( ref($searchio), 'Bio::SearchIO::hmmer2',
    'Check if loading hmmsearch2 output via the hmm2 parser directly works' );
is( ref( $searchio->next_result ),
    'Bio::Search::Result::HMMERResult',
    'Check for the correct result reference type'
);

$searchio = Bio::SearchIO->new(
    -format => 'hmmer3',
    -file   => test_input_file('hmmscan.out')
);
is( ref($searchio), 'Bio::SearchIO::hmmer3',
    'Check if loading hmmscan output via the hmm3 parser directly works' );
is( ref( $searchio->next_result ),
    'Bio::Search::Result::HMMERResult',
    'Check for the correct result reference type'
);

$searchio = Bio::SearchIO->new(
    -format => 'hmmer',
    -file   => test_input_file('hmmsearch3.out')
);
is( ref($searchio), 'Bio::SearchIO::hmmer3',
    'Check if loading hmmsearch3 output via the hmm3 parser directly works' );
is( ref( $searchio->next_result ),
    'Bio::Search::Result::HMMERResult',
    'Check for the correct result reference type'
);

# Make sure that you can also specify the -version parameter directly
$searchio = Bio::SearchIO->new(
    -format  => 'hmmer',
    -file    => test_input_file('hmmpfam.out'),
    -version => 2
);
is( ref($searchio), 'Bio::SearchIO::hmmer2',
    'Check if selecting the correct hmmpfam parser using -version works' );
is( ref( $searchio->next_result ),
    'Bio::Search::Result::HMMERResult',
    'Check for the correct result reference type'
);

$searchio = Bio::SearchIO->new(
    -format  => 'hmmer',
    -file    => test_input_file('hmmsearch.out'),
    -version => 2
);
is( ref($searchio), 'Bio::SearchIO::hmmer2',
    'Check if selecting the correct hmmsearch2 parser using -version works' );
is( ref( $searchio->next_result ),
    'Bio::Search::Result::HMMERResult',
    'Check for the correct result reference type'
);

$searchio = Bio::SearchIO->new(
    -format  => 'hmmer3',
    -file    => test_input_file('hmmscan.out'),
    -version => 3
);
is( ref($searchio), 'Bio::SearchIO::hmmer3',
    'Check if selecting the correct hmmscan parser using -version works' );
is( ref( $searchio->next_result ),
    'Bio::Search::Result::HMMERResult',
    'Check for the correct result reference type'
);

$searchio = Bio::SearchIO->new(
    -format  => 'hmmer',
    -file    => test_input_file('hmmsearch3.out'),
    -version => 3
);
is( ref($searchio), 'Bio::SearchIO::hmmer3',
    'Check if selecting the correct hmmsearch3 parser using -version works' );
is( ref( $searchio->next_result ),
    'Bio::Search::Result::HMMERResult',
    'Check for the correct result reference type'
);

my $cat_command = ($^O =~ m/mswin/i) ? 'type' : 'cat';
my $pipestr = "$cat_command " . test_input_file('hmmpfam.out') . " |";
open( my $pipefh, $pipestr );

$searchio = Bio::SearchIO->new(
    -format => 'hmmer',
    -fh     => $pipefh
);
is( ref($searchio), 'Bio::SearchIO::hmmer2',
    'Check if reading from a pipe works' );
$result = $searchio->next_result;
is( ref($result),
    'Bio::Search::Result::HMMERResult',
    'Check for the correct result reference type'
);
is( $result->num_hits(), 2, 'Check num_hits' );

# bug 3376
{
    my $in = Bio::SearchIO->new(
        -format => 'hmmer',
        -file   => test_input_file('pfamOutput-bug3376.out')
    );
    my $result = $in->next_result;
    my $hit    = $result->next_hit;
    my $hsp    = $hit->next_hsp;
    is( $result->query_length, 97, 'Check query_length' );
    is( $hit->length,          95, 'Check hit length' );
    is( $hsp->hit_string,
        'svfqqqqssksttgstvtAiAiAigYRYRYRAvtWnsGsLssGvnDnDnDqqsdgLYtiYYsvtvpssslpsqtviHHHaHkasstkiiikiePr',
        'bug3376'
    );
}
# end bug 3376

# bug 3421 - making sure a full line of dashes in an HSP is parsed correctly
{
    my $in = Bio::SearchIO->new(
        -format => 'hmmer',
        -file   => test_input_file('hmmpfam_HSPdashline.txt')
    );
    my $result = $in->next_result;
    my $hit    = $result->next_hit;
    my $hsp    = $hit->next_hsp;
    is( $hsp->length, '561',
        'bug3421 - Check if can correctly parse an HSP with line full of dashes'
    );
}
# end bug 3421

# bug 3302
{
    my $in = Bio::SearchIO->new(
        -format => 'hmmer',
        -file   => test_input_file('hmmpfam_multiresult.out')
    );
    my $result = $in->next_result;
    $result = $in->next_result;
    my $hit = $result->next_hit;
    is( $hit->name, 'IS66_ORF3.uniq', 'bug3302 - Check if can parse multiresult hmmer' );
}
# end bug 3302

# HMMER 3.1 nhmmer output
{
    my $in = Bio::SearchIO->new(
        -format  => 'hmmer',
        -version => 3,
        -file    => test_input_file('nhmmer-3.1.out')
    );
    my $result = $in->next_result;
    is( $result->algorithm,         'NHMMER', 'Check algorithm' );
    is( $result->algorithm_version, '3.1b1',  'Check nhmmer algorithm version' );
    is( $result->hmm_name,
        '../HMMs/A_HA_H7_CDS_nucleotide.hmm',
        'Check hmm_name'
    );
    is( $result->sequence_file,
        'tmp.fa',
        'Check sequence_file'
    );
    is( $result->query_name,        'A_HA_H7_CDS_nucleotide', 'Check query_name' );
    is( $result->query_length,       1683,                    'Check query_length' );
    is( $result->query_accession,   '',                       'Check query_accession' );
    is( $result->query_description, '',                       'Check query_description' );
    is( $result->num_hits(),         2,                       'Check num_hits' );

    my $hit = $result->next_hit;
    is( ref($hit), 'Bio::Search::Hit::HMMERHit',
        'Check for the correct hit reference type' );
    is( $hit->name,              'seq1',                'Check nhmmer hit name' );
    is( $hit->description,       'Description of seq1', 'Check nhmmer hit description' );
    is( $hit->score,              148.2,                'Check nhmmer hit score' );
    is( $hit->bits,               0,                    'Check nhmmer hit bits (0)' );
    float_is( $hit->significance, 3.2e-48,              'Check nhmmer hit significance' );
    is( $hit->num_hsps,           1,                    'Check num_hsps' );

    # Hit length is usually unknown for HMMSCAN and HMMSEARCH but not for NHMMER.
    # When is not known, sometimes it can be deduced from domain data '[]'
    is( $hit->length,             151,                  'Check nhmmer hit length' );
    is( $hit->frac_aligned_query, 0.09 );
    is( $hit->frac_aligned_hit,  '1.00' );

    my $hsp = $hit->next_hsp;
    is( ref($hsp), 'Bio::Search::HSP::HMMERHSP',
        'Check for correct hsp reference type' );
    is( $hsp->hit->seq_id(),   'seq1',                   'Check for nhmmer hit seq_id' );
    is( $hsp->query->seq_id(), 'A_HA_H7_CDS_nucleotide', 'Check for nhmmer query seq_id' );

    is( $hsp->start('hit'),       1,       'Check nhmmer hsp hit start' );
    is( $hsp->end('hit'),         151,     'Check nhmmer hsp hit end' );
    is( $hsp->start('query'),     258,     'Check nhmmer hsp query start' );
    is( $hsp->end('query'),       411,     'Check nhmmer hsp query end' );
    is( $hsp->strand('hit'),      1,       'Check nhmmer hsp hit strand' );
    is( $hsp->strand('query'),    1,       'Check nhmmer hsp query strand' );
    is( $hsp->score,              148.2,   'Check nhmmer hsp score' );
    is( $hsp->bits,               0,       'Check nhmmer hsp bits (0)' );
    float_is( $hsp->significance, 3.2e-48, 'Check nhmmer hsp evalue' );

    is( $hsp->length('query'), 154, 'Check for hsp query length' );
    is( $hsp->length('hit'),   151, 'Check for hsp hit length' );
    is( $hsp->length('total'), 154, 'Check for hsp total length' );
    is( $hsp->gaps('query'),   0,   'Check for hsp query gaps' );
    is( $hsp->gaps('hit'),     3,   'Check for hsp hit gaps' );
    is( $hsp->gaps('total'),   3,   'Check for hsp total gaps' );

    ($hit->length == 0) ?
          is( $hsp->{HIT_LENGTH}, $hsp->hit->length, 'Check hit length consistency' )
        : is( $hsp->{HIT_LENGTH}, $hit->length,      'Check hit length consistency' );
    ($result->query_length == 0) ?
          is( $hsp->{QUERY_LENGTH}, $hsp->query->length,   'Check query length consistency' )
        : is( $hsp->{QUERY_LENGTH}, $result->query_length, 'Check query length consistency' );

    is( $hsp->num_conserved, 151 );
    is( $hsp->num_identical, 146 );
    is( sprintf( "%.2f", $hsp->percent_identity ),        94.81 );
    is( sprintf( "%.3f", $hsp->frac_identical('query') ), 0.948 );
    is( sprintf( "%.3f", $hsp->frac_identical('hit') ),   0.967 );
    is( sprintf( "%.3f", $hsp->frac_identical('total') ), 0.948 );
    is( sprintf( "%.3f", $hsp->frac_conserved('query') ), 0.981 );
    is( sprintf( "%.3f", $hsp->frac_conserved('hit') ),  '1.000' );
    is( sprintf( "%.3f", $hsp->frac_conserved('total') ), 0.981 );

    is( $hsp->consensus_string,
        '',
        'Check for consensus structure string'
    );
    is( $hsp->query_string,
        'attcctagaattttcagctgatttaattattgagaggcgagaaggaagtaatgatgtctgttatcctgggaaattcgtaaatgaagaagctctgaggcaaattctcagggggtcaggcggaattgacaaggagacaatgggattcacatatagc',
        'Check for nhmmer query string'
    );
    is( $hsp->homology_string,
        'attcctagaattttcagc+gatttaattattgagaggcgagaaggaagt   gatgtctgttatcctgggaaattcgt+aatgaagaagctctgaggcaaattctcaggg+gtcaggcggaattgacaaggagacaatgggattcac+ta+agc',
        'Check for nhmmer homology string'
    );
    is( $hsp->hit_string,
        'ATTCCTAGAATTTTCAGCCGATTTAATTATTGAGAGGCGAGAAGGAAGT---GATGTCTGTTATCCTGGGAAATTCGTGAATGAAGAAGCTCTGAGGCAAATTCTCAGGGAGTCAGGCGGAATTGACAAGGAGACAATGGGATTCACCTACAGC',
        'Check for nhmmer hit string'
    );
    is( $hsp->posterior_string,
       '689*******************************************777...***************************************************************************************************986',
        'Check for nhmmer posterior probability string'
    );
    is( length( $hsp->homology_string ),
        length( $hsp->hit_string ),
        'Check if nhmmer homology string and hit string have an equal length'
    );
    is( length( $hsp->query_string ),
        length( $hsp->homology_string ),
        'Check if nhmmer query string and homology string have an equal length'
    );

    $hit = $result->next_hit;
    is( $hit->name,              'seq2',                'Check nhmmer hit name' );
    is( $hit->description,       'Description of seq2', 'Check nhmmer hit description' );
    is( $hit->score,              38.6,                 'Check nhmmer hit score' );
    is( $hit->bits,               0,                    'Check nhmmer hit bits (0)' );
    float_is( $hit->significance, 3.9e-15,              'Check nhmmer hit significance' );
    is( $hit->length,             60,                   'Check nhmmer hit length' );

    $hsp = $hit->next_hsp;
    is( $hsp->hit->seq_id(),   'seq2',                   'Check for nhmmer hit seq_id' );
    is( $hsp->query->seq_id(), 'A_HA_H7_CDS_nucleotide', 'Check for nhmmer query seq_id' );

    is( $hsp->start('query'),     34,      'Check nhmmer hsp query start' );
    is( $hsp->end('query'),       92,      'Check nhmmer hsp query end' );
    is( $hsp->start('hit'),       1,       'Check nhmmer hsp hit start' );
    is( $hsp->end('hit'),         59,      'Check nhmmer hsp hit end' );
    is( $hsp->strand('hit'),     -1,       'Check nhmmer hsp hit strand' );
    is( $hsp->strand('query'),    1,       'Check nhmmer hsp query strand' );
    is( $hsp->score,              38.6,    'Check nhmmer hsp score' );
    is( $hsp->bits,               0,       'Check nhmmer hsp bits (0)' );
    float_is( $hsp->significance, 3.9e-15, 'Check nhmmer hsp evalue' );

    is( $hsp->length('query'), 59, 'Check for hsp query length' );
    is( $hsp->length('hit'),   59, 'Check for hsp hit length' );
    is( $hsp->length('total'), 59, 'Check for hsp total length' );
    is( $hsp->gaps('query'),   0,  'Check for hsp query gaps' );
    is( $hsp->gaps('hit'),     0,  'Check for hsp hit gaps' );
    is( $hsp->gaps('total'),   0,  'Check for hsp total gaps' );

    ($hit->length == 0) ?
          is( $hsp->{HIT_LENGTH}, $hsp->hit->length, 'Check hit length consistency' )
        : is( $hsp->{HIT_LENGTH}, $hit->length,      'Check hit length consistency' );
    ($result->query_length == 0) ?
          is( $hsp->{QUERY_LENGTH}, $hsp->query->length,   'Check query length consistency' )
        : is( $hsp->{QUERY_LENGTH}, $result->query_length, 'Check query length consistency' );

    is (length($hsp->homology_string), length($hsp->query_string));

    is( $hsp->consensus_string,
        '',
        'Check for consensus structure string'
    );
    is( $hsp->query_string,
        'gtgatgattgcaacaaatgcagacaaaatctgccttgggcaccatgctgtgtcaaacgg',
        'Check for nhmmer query string'
    );
    is( $hsp->homology_string,
        'g+gat+att+c+acaaatgcagacaa atctgccttgggca+catgc+gtgtcaaacgg',
        'Check for nhmmer homology string'
    );
    is( $hsp->hit_string,
        'GCGATCATTCCGACAAATGCAGACAAGATCTGCCTTGGGCATCATGCCGTGTCAAACGG',
        'Check for nhmmer hit string'
    );
    is( $hsp->posterior_string,
        '6899****************************************************986',
        'Check for nhmmer posterior probability string' );
    is( length( $hsp->homology_string ),
        length( $hsp->hit_string ),
        'Check if nhmmer homology string and hit string have an equal length'
    );
    is( length( $hsp->query_string ),
        length( $hsp->homology_string ),
        'Check if nhmmer query string and homology string have an equal length'
    );
}
# end HMMER 3.1 nhmmer output

# Test HIT filtering by SIGNIFICANCE
$searchio = Bio::SearchIO->new(
    '-format' => 'hmmer',
    '-file'   => test_input_file('hmmpfam_cs.out'),
    '-signif' => 1e-100
);
# NOTE: For Hmmer2, if a single model pass the HIT filter
# but it shows 2 domains, it counts as 2 hits (Glu_synthase)
my @valid = qw( GATase_2
                Glu_syn_central
                Glu_synthase
                Glu_synthase
                GXGXG );
$result   = $searchio->next_result;
is( $result->num_hits(), 5, 'Check Significance filtered num_hits' );
while ( my $hit = $result->next_hit ) {
    is( $hit->name, shift @valid, 'Check Significance filtered hit ID' );
}
is( @valid, 0 );

# Test HIT filtering by SCORE
$searchio = Bio::SearchIO->new(
    '-format' => 'hmmer',
    '-file'   => test_input_file('hmmsearch.out'),
    '-score'  => 390
);
# NOTE: This Hmmer2 report top hit (score 393.8) have 4 domains,
# so it count as 4 hits (PAB2_ARATH)
@valid = qw( PAB2_ARATH
             PAB2_ARATH
             PAB2_ARATH
             PAB2_ARATH );
$result   = $searchio->next_result;
is( $result->num_hits(), 4, 'Check Score filtered num_hits' );
while ( my $hit = $result->next_hit ) {
    is( $hit->name, shift @valid, 'Check Score filtered hit ID' );
}
is( @valid, 0 );

# Test HIT filtering by BITS
$searchio = Bio::SearchIO->new(
    '-format' => 'hmmer',
    '-file'   => test_input_file('hmmsearch3_multi.out'),
    '-bits'   => 10
);
# NOTE: No HMMER report use Bits, so this will filter out everything
$result   = $searchio->next_result;
is( $result->num_hits(), 0, 'Check Bits filtered num_hits' );
$result   = $searchio->next_result;
is( $result->num_hits(), 0, 'Check Bits filtered num_hits' );
$result   = $searchio->next_result;
is( $result->num_hits(), 0, 'Check Bits filtered num_hits' );

# Test HIT filtering by HIT_FILTER
my $filt_func = sub {
    my $hit = shift;
    $hit->frac_aligned_query >= 0.20;
};
$searchio = Bio::SearchIO->new(
    '-format'     => 'hmmer',
    '-file'       => test_input_file('hmmscan_multi_domain.out'),
    '-hit_filter' => $filt_func
);
# NOTE: In Hmmer3 reports, the multiple domains of a model are treated
# as HSPs instead of Hits (like it is in Hmmer2 reports)
@valid = qw( PPC );
$result   = $searchio->next_result;
is( $result->num_hits(), 1, 'Check Hit_filter filtered num_hits' );
while ( my $hit = $result->next_hit ) {
    is( $hit->name, shift @valid, 'Check Hit_filter filtered hits ID' );
}
is( @valid, 0 );

# Test for correct parsing of results from query sequences containing stops.
# Without the patch, parsing dies with "Quantifier follows nothing in regex;" error
$searchio = Bio::SearchIO->new(
    '-format' => 'hmmer',
    '-file'   => test_input_file('hmmscan_qry_stop.txt'),
);
eval { $searchio->next_result; };
is( $@, '', 'Correct parsing of alignments with stops' );


# Test for correct parsing of phmmer results
# Without the patch, parsing skips all lines from phmmer output
{
	my $searchio = Bio::SearchIO->new(
		-format => 'hmmer',
		-file   => test_input_file('phmmer.out')
	);
	
	my $result = $searchio->next_result;
	if ( defined $result ) {

		is( $result->algorithm,         'PHMMER',  'Check algorithm' );
		is( $result->query_name,        'A0R3R7',  'Check query_name' );
		is( $result->query_length,       762,      'Check query_length absence' );
		is( $result->query_description, '',        'Check query_description' );
		is( $result->num_hits(),         8,        'Check num_hits' );

		my $hit = $result->next_model;
		if ( defined $hit ) {
			is( $hit->name, 'cath|4_0_0|1vs0A03/639-759', 'query name okay' );
			is( $hit->num_hsps(), 1, 'Check num_hsps' );
		}
	}

}
BioPerl-1.007002/t/SearchIO/hmmer_pull.t000444000766000024      2137013155576321 17770 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_hmmer_pull.t 14984 2008-11-11 18:39:20Z sendu $

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 290);
	
	use_ok('Bio::SearchIO');
}

my $searchio = Bio::SearchIO->new(-format => 'hmmer_pull', -file => test_input_file('hmmpfam_fake.out'), -verbose => -1);
my @data = ([qw(roa1_drome roa2_drome)], [2, 1], [1, 2], [2, 1]);
while (my $result = $searchio->next_result) {
    is ref($result), 'Bio::Search::Result::HmmpfamResult';
    is $result->algorithm, 'HMMPFAM';
    is $result->algorithm_version, '2.1.1';
    is $result->hmm_name, 'pfam';
    is $result->hmm_file, $result->hmm_name;
    is $result->database_name, $result->hmm_name;
    is $result->sequence_file, '/home/birney/src/wise2/example/road.pep';
    is $result->sequence_database, $result->sequence_file;
    is $result->query_name, shift @{$data[0]};
    is $result->num_hits(), shift @{$data[1]};
    is $result->no_hits_found, 0;
    
	is $result->query_accession, '';
    is $result->query_description, '';
    ok ! $result->query_length;
    ok ! $result->database_letters;
    ok ! $result->database_entries;
    is $result->algorithm_reference, '';
    is $result->get_parameter('test'), undef;
    is $result->available_parameters, undef;
    is $result->get_statistic('test'), undef;
    is $result->available_statistics, undef;
    
    my @orig_order = $result->hits;
    is @orig_order, shift @{$data[3]};
	if (@orig_order > 1) {
		isnt $orig_order[0]->name, $orig_order[1]->name;
		$result->sort_hits(sub{$Bio::Search::Result::HmmpfamResult::a->[2]
													<=> 
							   $Bio::Search::Result::HmmpfamResult::b->[2]});
		my @hits = $result->hits;
		is @hits, @orig_order;
		is $hits[0]->name, $orig_order[1]->name;
		$result->sort_hits(sub{$Bio::Search::Result::HmmpfamResult::b->[4]
													<=> 
							   $Bio::Search::Result::HmmpfamResult::a->[4]});
	}
    
    my @hit_data = ([qw(SEED TEST)], [146.1, "5.0"], [6.3e-40, 7.2], [2, 1], [77, undef], [2, 0], [1, 2],
                    ["33 34 36 38 43 45 47 48 51 53 55 57 58 65 68 71 73 74 76 88 98 99 124 125 126 127 129 132 135 140 142 145 146 148 149 151 153 154 156 157 158 159 160 161 164 165 166 167 168 169 170 178 187 189 194", ''],
                    ["1 2 3 4 6 9 11 12 13 15 16 17 19 21 22 23 25 26 28 30 31 33 39 40 41 42 43 44 46 47 48 49 50 51 52 60 61 70 72 73 77", ''],
                    ["1-6 8-13 15-23 25-33 39-56 58-63 67-77", '']);
    while (defined(my $hit = $result->next_model)) {
        is ref($hit), 'Bio::Search::Hit::HmmpfamHit';
        is $hit->name, shift @{$hit_data[0]};
        is $hit->raw_score, shift @{$hit_data[1]};
        is $hit->score, $hit->raw_score;
        float_is $hit->significance, shift @{$hit_data[2]};
        float_is $hit->p, $hit->significance;
        is $hit->num_hsps, shift @{$hit_data[3]};
        is $hit->n, $hit->num_hsps;
        is $hit->algorithm, $result->algorithm;
        is $hit->overlap, 0;
        is $hit->rank, shift @{$hit_data[6]};
        is $hit->tiled_hsps, 0;
        is $hit->strand('query'), 1;
        is $hit->strand('hit'), 1;
        my @strands = $hit->strand;
        is "@strands", "1 1";
        
        is $hit->description, undef;
        is $hit->accession, undef;
        ok ! $hit->locus;
        ok ! $hit->bits;
        ok ! $result->logical_length('query');
        ok ! $result->frame;
        is $hit->each_accession_number, undef;
        
        is $hit->length, shift @{$hit_data[4]};
        is $hit->logical_length('hit'), $hit->length;
		
		if ($result->query_name eq 'roa1_drome') {
			my @inds = $hit->seq_inds('query', 'identical');
			is "@inds", shift @{$hit_data[7]};
			@inds = $hit->seq_inds('hit', 'identical');
			is "@inds", shift @{$hit_data[8]};
			@inds = $hit->seq_inds('hit', 'conserved', 1);
			is "@inds", shift @{$hit_data[9]};
		}
		
		if ($hit->name eq 'SEED') {
			my $best = $hit->hsp('best');
			float_is($best->evalue, 1.1e-18);
			my $worst = $hit->hsp('worst');
			float_is($worst->evalue, 2.2e-17);
			is $hit->start('query'), 33;
			is $hit->start('hit'), 1;
			is $hit->end('query'), 194;
			is $hit->end('hit'), 77;
			my @range = $hit->range('query');
			is "@range", '33 194';
			@range = $hit->range('hit');
			is "@range", '1 77';
			
			if ($hit->query_name eq 'roa1_drome') {
				is $hit->length_aln('query'),142;
				is $hit->length_aln('hit'), 77;
				is $hit->gaps('total'), 14;
				is $hit->gaps('query'), 13;
				is $hit->gaps('hit'), 1;
				is $hit->matches('id'), 41;
				is $hit->matches('cons'), 24;
				is $hit->frac_identical, 0.387;
				is $hit->frac_conserved, 0.169;
				ok ! $hit->frac_aligned_query;
				is $hit->frac_aligned_hit, '1.00';
				is $hit->num_unaligned_hit, 1;
				is $hit->num_unaligned_query, 13;
			}
		}
        
        my @hsps = $hit->hsps;
        is @hsps, shift @{$hit_data[5]};
        
        my @hsp_data = ([1, 1], [77, 77], [33, 124], [103, 194], [71.2, 75.5], [2.2e-17, 1.1e-18],
                        ['LFIGGLDYRTTDENLKAHFEKWGNIVDVVVMKD-----PRTKRSRGFGFITYSHSSMIDEAQK--SRpHKIDGRVVEP',
                         'LFVGALKDDHDEQSIRDYFQHFGNIVDINIVID-----KETGKKRGFAFVEFDDYDPVDKVVL-QKQHQLNGKMVDV'],
						[7, 6],
						['lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGfaFVeFeseedAekAlealnG.kelggrklrv',
                         'lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGfaFVeFeseedAekAlealnGkelggrklrv'],
                        ['lf+g+L + +t+e Lk++F+k G iv++ +++D     + t++s+Gf+F+++  ++  + A +    +++++gr+++ ',
                         'lfVg L  d +e+ ++d+F++fG iv+i+iv+D     ketgk +GfaFVeF++++ ++k +     ++l+g+ + v'],
						[1, 0], [8, 6], [1, 2], ['33 103', '124 194'], [78, 77], [22, 33], [33, 23],
						['0.3099', '0.4648'], ['0.2857', '0.4286'], ['0.2821', '0.4286']);
        
        while (defined(my $hsp = $hit->next_domain)) {
            is ref($hsp), 'Bio::Search::HSP::HmmpfamHSP';
            is $hsp->hit->start, shift @{$hsp_data[0]};
            is $hsp->hit->end, shift @{$hsp_data[1]};
            is $hsp->query->start, shift @{$hsp_data[2]};
            is $hsp->query->end, shift @{$hsp_data[3]};
			is $hsp->start('hit'), $hsp->hit->start;
			is $hsp->end('hit'),$hsp->hit->end;
			is $hsp->start('query'), $hsp->query->start;
			is $hsp->end('query'), $hsp->query->end;
			is $hsp->strand('hit'), 1;
			is $hsp->strand('query'), 1;
            is $hsp->score, shift @{$hsp_data[4]};
			ok ! $hsp->bits;
            float_is($hsp->evalue, shift @{$hsp_data[5]});
			ok ! $hsp->pvalue;
			float_is($hsp->significance, $hsp->evalue);
			is $hsp->algorithm, $result->algorithm;
			is $hsp->rank, shift @{$hsp_data[12]};
			my @range = $hsp->range;
			is "@range", shift @{$hsp_data[13]};
			is $hsp->n, $hit->num_hsps;
			is $hsp->length('query'), 71;
			is $hsp->length('hit'), 77;
			my $locseq = $hsp->seq('hit');
			
			if ($result->query_name eq 'roa1_drome') {
				is ref($locseq), 'Bio::LocatableSeq';
				my $aln = $hsp->get_aln('hit');
				is ref($aln), 'Bio::SimpleAlign';
				is $hsp->query_string, shift @{$hsp_data[6]};
				is $hsp->gaps('query'), shift @{$hsp_data[7]};
				is $hsp->gaps('hit'), shift @{$hsp_data[10]};
				is $hsp->gaps('total'), shift @{$hsp_data[11]};
				is $hsp->hit_string, shift @{$hsp_data[8]};
				is $hsp->homology_string, shift @{$hsp_data[9]};
				is $hsp->seq_str('hit'), $hsp->hit_string;
				is $hsp->seq_str('query'), $hsp->query_string;
				is $hsp->seq_str('homology'), $hsp->homology_string;
				is length($hsp->homology_string), length($hsp->hit_string);
				is length($hsp->query_string), length($hsp->homology_string);
				is $hsp->length('total'), shift @{$hsp_data[14]};
				is $hsp->hsp_length, $hsp->length('total');
				is $hsp->num_identical, shift @{$hsp_data[15]};
				is $hsp->num_conserved, shift @{$hsp_data[16]};
				is $hsp->frac_identical('query'), shift @{$hsp_data[17]};
				is $hsp->frac_identical('hit'), shift @{$hsp_data[18]};
				is $hsp->frac_identical('total'), shift @{$hsp_data[19]};
			}
        }
    }
}

is $searchio->result_count, 2;

# bug revealed by bug 2632 - CS lines were already ignored, but we couldn't
# parse alignments when HSPs weren't in simple order!!
$searchio = Bio::SearchIO->new(-format => 'hmmer_pull', -file => test_input_file('hmmpfam_cs.out'), -verbose => 1);
my $result = $searchio->next_result;
my $hit = $result->next_hit;
my $hsp = $hit->next_hsp;
is $hsp->seq_str, "IPPLLAVGAVHHHLINKGLRQEASILV";

# and another bug revealed: we don't always know the hit length, and
# shouldn't complain about that with a warning
is $hsp->hit->seqlength, 412;

my $count = 0;
while (my $hit = $result->next_hit) {
    $count++;
    next if $count < 6;
    last if $count > 6;
	my $hsp = $hit->next_hsp;
    ok ! $hsp->hit->seqlength;
    #*** not sure how to test for the lack of a warning though...
	# Maybe run an eval with verbose set to 2, then make sure $@ is undef? --cjfields
}
BioPerl-1.007002/t/SearchIO/infernal.t000444000766000024     11544213155576321 17446 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_infernal.t 14672 2008-04-22 21:42:50Z cjfields $

use strict;
use warnings;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 496);

    use_ok('Bio::SearchIO');
}

my ($in, $result, $iter, $hit, $hsp, $algorithm, $meta);

### Infernal v. 1.1 ###
{
    # one query vs one database sequence report
    $in = Bio::SearchIO->new(
        -format  => 'infernal',
        -file    => test_input_file('cmsearch_output.txt')
    );
    $result = $in->next_result;
    isa_ok($result, 'Bio::Search::Result::ResultI');
    is( ref($result), 'Bio::Search::Result::INFERNALResult', 'Check for the correct Result reference type');
    is( $result->algorithm,         'CMSEARCH',    'Check algorithm' );
    is( $result->algorithm_version, '1.1.1',       'Check cmsearch algorithm version' );
    is( $result->cm_name,           'RF00174.cm',  'Check cm_name');
    is( $result->database_name,     'NC_000913.fna','Check database_name' );
    is( $result->database_entries,  1,              'Check database_entries' );
    is( $result->database_letters,  9283304,        'Check database_letters' );
    is( $result->query_name,        'Cobalamin',    'Check query_name' );
    is( $result->query_length,      191,            'Check query_length' );
    is( $result->query_accession,   'RF00174',      'Check query_accession' );
    is( $result->query_description, '',             'Check query_description' );
    is( $result->num_hits(),        2,              'Check num_hits' );

    # 1st hit

    $hit = $result->next_hit;
    is( ref($hit), 'Bio::Search::Hit::ModelHit', 'Check for the correct hit reference type' );
    is( $hit->algorithm, 'CMSEARCH', "Hit algorithm");
    is( $hit->name,              'gi|556503834|ref|NC_000913.3|', 'Check hit name' );
    is( $hit->description,       'Escherichia coli str. K-12 substr. MG1655, complete genome', 'Check hit description' );
    is( $hit->length,             0,       'Check hit length' );
    is( $hit->score,              98.2,    'Check hit score' );
    is( $hit->bits,               98.2,    'Check hit bits' );
    is( $hit->num_hsps,           1,       'Check number of HSPs' );
    float_is( $hit->significance, 8.7e-16, 'Check hit significance' );
    is($hit->rank,                1,       'Check hit rank' );

    $hsp = $hit->next_hsp;
    is( ref($hsp), 'Bio::Search::HSP::ModelHSP', 'Check for correct hsp reference type' );
    isa_ok( $hsp, 'Bio::Search::HSP::HSPI' );
    isa_ok( $hsp->get_aln, 'Bio::Align::AlignI' );
    isa_ok( $hsp->hit,     'Bio::SeqFeature::Similarity', "Check for hsp hit isa seqfeature similarity" );

    is( $hsp->hit->seq_id(),   'gi|556503834|ref|NC_000913.3|', 'Check for HSP hit seq_id' );
    is( $hsp->query->seq_id(), 'Cobalamin', 'Check for HSP query seq_id' );
    is( $hsp->start('query'),     1,       'Check hsp query start' );
    is( $hsp->end('query'),       191,     'Check hsp query end' );
    is( $hsp->start('hit'),       4163384, 'Check hsp hit start' );
    is( $hsp->end('hit'),         4163574, 'Check hsp hit end' );
    is( $hsp->score,              98.2,    'Check hsp score' );
    is( $hsp->bits,               98.2,    'Check hsp bits' );
    float_is( $hsp->significance, 8.7e-16, 'Check hsp evalue' );

    is( $hsp->length('query'), 191, 'Check for hsp query length' );
    is( $hsp->length('hit'),   191, 'Check for hsp hit length' );
    is( $hsp->length,          207, 'Check for hsp total length' );
    is( $hsp->gaps('query'),   16,   'Check for hsp query gaps' );
    is( $hsp->gaps('hit'),     16,   'Check for hsp hit gaps' );
    is( $hsp->gaps,            32,   'Check for hsp total gaps' );
    is( $hsp->strand('hit'),      1,       'Check hsp hit strand' );
    
    # 2nd hit 
     
    $hit = $result->next_hit;
    is( $hit->name,              'gi|556503834|ref|NC_000913.3|',                 'Check hit name' );
    is( $hit->description,       'Escherichia coli str. K-12 substr. MG1655, complete genome','Check hit description' );
    is( $hit->score,              8.4,  'Check hit score' );
    is( $hit->raw_score,          8.4, "Check hit raw_score");
    is( $hit->bits,               8.4,    'Check hit bits' );
    float_is( $hit->significance, 0.63, 'Check hit significance' );
    is( $hit->length,             0,  'Check hit length' );
    is($hit->rank, 2, "Hit rank");

    $hsp = $hit->next_hsp;
    is( $hsp->hit->seq_id(),   'gi|556503834|ref|NC_000913.3|', 'Check for hit seq_id' );
    is( $hsp->query->seq_id(), 'Cobalamin', 'Check for query seq_id' );
    is( $hsp->start('query'),     1,       'Check hsp query start' );
    is( $hsp->end('query'),       191,     'Check hsp query end' );
    is( $hsp->start('hit'),       4593356, 'Check hsp hit start' );
    is( $hsp->end('hit'),         4593565, 'Check hsp hit end' );
    is( $hsp->score,              8.4,     'Check hsp score' );
    is( $hsp->bits,               8.4,     'Check hsp bits' );
    float_is( $hsp->significance, 0.63,    'Check hsp evalue' );

    is( $hsp->gaps('query'),   67,   'Check for hsp query gaps' );
    is( $hsp->gaps('hit'),     48,   'Check for hsp hit gaps' );
    is( $hsp->gaps,            115,   'Check for hsp total gaps' );
    is( $hsp->strand('hit'),      1,       'Check hsp hit strand' );

    is( $hsp->noncanonical_string,
        '               v                                    v             v   v        v       v  v       vvvvvv     vvv    vvv                                   vvv      vvvvvvvvv                                              v  v                    v               ',
        'Check for NC string');
    is( $hsp->meta,
        ':::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_______>>>>>,,<<<____>>>,<<<---<<<<.------<<<<<<-----<<<-<<<<<<_____............................._>>>>>>--->>>>>>>>>----------....................................>>>>----.>>>,,,,)))]]]]]]:::::::::::::::',
        'Check for CS string');
    is( $hsp->query_string,
        'uuaaauugaaacgaugauGGUuccccuuuaaagugaaggguuAAaaGGGAAcccGGUGaaAaUCCgggGCuGcCCCCgCaACuGUAAgcGg.agagcaccccccAauAaGCCACUggcccgcaa.............................gggccGGGAAGGCggggggaaggaaugac....................................cCgcgAGc.CaGGAGACCuGCCaucaguuuuugaaucucc',
        'Check for query string');
    is( $hsp->homology_string,
        '  A AUU+A+++    :UGG  :C +U ++  G     G: +AA : GGAA:  G         C  :+  GCCCCCGC +C GU+A ::     GCA ++ ++ A   GCCA   G+C G                                                                                                  :: +AG+ C GGA AC : CCA:  + + + + AU    ',
        'Check for homology string');
    is( $hsp->hit_string,
        'GGAGAUUAAUCUUUACGUGGG-UCGUUGAUCGG---CUGACGAACCAGGAAGAUGU-------ACGCCAGUGCCCCCGCUGCGGUGACGCAa-CCGCAGAUGAUUAGU-GCCA---GACGG---aaugagugggugguaucaacaauaaaacc-----------------------------aguaaugaucggcgcaaaagaggcgcagaugaagcuGGCAAAGUuCUGGAUACUGCCCACCGACGCAGUCAUGCGA',
        'Check for hit string');
    is( $hsp->posterior_string,
        '*********************.88877554444...5777779*********9996.......7999********************88873.333333333333333.4544...33333...44566655444444444444444444444.............................566666666666666666666666677777777776788899966*******************************',
        'Check for posterior probability string');

    isa_ok($hsp->feature1, 'Bio::SeqFeature::Similarity');
    isa_ok($hsp->feature2, 'Bio::SeqFeature::Similarity');
    ($meta) = $hsp->feature1->get_tag_values('meta');
    is($meta, ':::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_______>>>>>,,<<<____>>>,<<<---<<<<.------<<<<<<-----<<<-<<<<<<_____............................._>>>>>>--->>>>>>>>>----------....................................>>>>----.>>>,,,,)))]]]]]]:::::::::::::::', "Check hsp feature1 get_tag_values");
    ($meta) = $hsp->feature2->get_tag_values('meta');
    is($meta, ':::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_______>>>>>,,<<<____>>>,<<<---<<<<.------<<<<<<-----<<<-<<<<<<_____............................._>>>>>>--->>>>>>>>>----------....................................>>>>----.>>>,,,,)))]]]]]]:::::::::::::::', "Check hsp feature2 get_tag_values");

    $result = $in->next_result;
    is( $result, undef, 'Check for undefined result' );


    # multi query vs multi sequence database report
    $in = Bio::SearchIO->new(
        -format  => 'infernal',
        -file    => test_input_file('cmsearch.multi.out')
    );
      # 1st query
    $result = $in->next_result;
    is( $result->num_hits,   12, 'Check result num_hits - multi report');
    is( $result->query_name, 'tRNA5', 'Check result query_name - multi report');
    $hit = $result->next_hit;
    is( $hit->length,        72, 'Check hit length - multi report' );

      # 2nd query
    $result = $in->next_result;
    is( $result->num_hits,   1, 'Check result#2 num_hits - multi report');
    is( $result->query_name, 'Cobalamin', 'Check result#2 query_name - multi report');
    $hit = $result->next_hit;
    is( $hit->length,        0, 'Check result#2 hit length - multi report' );
    $hsp = $hit->next_hsp;
    is( $hsp->strand('hit'), -1, 'Check result#2 hsp hit strand - multi report');


    # report with no hits
    $in = Bio::SearchIO->new(
        -format  => 'infernal',
        -file    => test_input_file('cmsearch.nohit.out')
    );
    $result = $in->next_result;
    is( $result->cm_name, 'Cobalamin.c.cm', 'Check cm_name' );
    $hit = $result->next_hit;
    is( $hit, undef, 'Check for undefined hit' );

}


### Infernal v. 1.0 ####

my $searchio = Bio::SearchIO->new( -format => 'infernal',
                                -file   => test_input_file('test2.infernal'),
                                -model => 'tRNAtest',
                                -query_acc => 'RF01234',
                                -query_desc => 'tRNA',
                               );

$result = $searchio->next_result;
isa_ok($result, 'Bio::Search::Result::ResultI');
is($result->algorithm, 'CMSEARCH', "Result");
is($result->algorithm_reference, undef, "Result reference");
is($result->algorithm_version, '1.0', "Result version");
is($result->available_parameters, 0, "Result parameters");
is($result->available_statistics, 0, "Result statistics");
is($result->database_entries, '', "Result entries");
is($result->database_letters, 600000, "Result letters");
is($result->database_name, 'tosearch.300Kb.db',
   "Result database_name");
is($result->num_hits, 1, "Result num_hits");
is($result->program_reference, undef, "Result program_reference");
is($result->query_accession, 'RF01234', "Result query_accession");
is($result->query_description, 'tRNA', "Result query_description");
is($result->query_length, 72, "Result query_length");
is($result->query_name, 'trna.5-1', "Result query_name");

$hit = $result->next_hit;

isa_ok($hit, 'Bio::Search::Hit::HitI');
is($hit->ncbi_gi, '', "Hit GI");
is($hit->accession, 'example', "Hit accession");
is($hit->algorithm, 'CMSEARCH', "Hit algorithm");
is($hit->bits, '78.06', "Hit bits");
is($hit->description, '', "Hit description"); # no hit descs yet
is($hit->locus, '', "Hit locus");
is($hit->n, 3, "Hit n");
is($hit->name, 'example', "Hit name");
is($hit->num_hsps, 3, "Hit num_hsps");

# These Bio::Search::Hit::HitI methods are currently unimplemented in
# Bio::Search::Hit::ModelHit; they may be integrated over time but will require
# some reconfiguring for Model-based searches

# these need to be replaced by dies_ok() or warnings_like()
warning_like { $hit->length_aln() }
    qr'length_aln not implemented for Model-based searches',
    "Hit length_aln() not implemented";
warning_like {$hit->num_unaligned_hit}
    qr'num_unaligned_hit/num_unaligned_sbjct not implemented for Model-based searches',
    "Hit num_unaligned_hit() not implemented";
warning_like {$hit->num_unaligned_query}
    qr'num_unaligned_query not implemented for Model-based searches',
    "Hit num_unaligned_query() not implemented";
warning_like {$hit->num_unaligned_sbjct}
    qr'num_unaligned_hit/num_unaligned_sbjct not implemented for Model-based searches',
    "Hit num_unaligned_sbjct() not implemented";
warning_like {$hit->start}
    qr'start not implemented for Model-based searches',
    'Hit start not implemented';
warning_like {$hit->end}
    qr'end not implemented for Model-based searches',
    'Hit end not implemented';
warning_like {$hit->strand}
    qr'strand not implemented for Model-based searches',
    'Hit strand not implemented';
warning_like {$hit->logical_length}
    qr'logical_length not implemented for Model-based searches',
    'Hit logical_length not implemented';
warning_like {$hit->frac_aligned_hit}
    qr'frac_aligned_hit not implemented for Model-based searches',
    'Hit frac_aligned_hit not implemented';
warning_like {$hit->frac_aligned_query}
    qr'frac_aligned_query not implemented for Model-based searches',
    'Hit frac_aligned_query not implemented';
warning_like {$hit->frac_conserved}
    qr'frac_conserved not implemented for Model-based searches',
    'Hit frac_conserved not implemented';
warning_like {$hit->frac_identical}
    qr'frac_identical not implemented for Model-based searches',
    'Hit frac_identical not implemented';
warning_like {$hit->matches}
    qr'matches not implemented for Model-based searches',
    'Hit matches not implemented';
warning_like {$hit->gaps}
    qr'gaps not implemented for Model-based searches',
    'Hit gaps not implemented';
warning_like {$hit->frame}
    qr'frame not implemented for Model-based searches',
    'Hit frame not implemented';
warning_like {$hit->range}
    qr'range not implemented for Model-based searches',
    'Hit range not implemented';
warning_like {$hit->seq_inds}
    qr'seq_inds not implemented for Model-based searches',
    'Hit seq_inds not implemented';

is($hit->length, 0, "Hit length");
is($hit->overlap, 0, "Hit overlap");
is($hit->query_length, 72, "Hit query_length");
is($hit->rank, 1, "Hit rank");
is($hit->raw_score, '78.06', "Hit raw_score");
is($hit->score, '78.06', "Hit score");
float_is($hit->p, '2.906e-26', "Hit p");
float_is($hit->significance, '3.133e-21');

$hsp = $hit->next_hsp;
isa_ok($hsp, 'Bio::Search::HSP::HSPI');
is($hsp->algorithm, 'CMSEARCH', "HSP algorithm");
float_is($hsp->evalue, '3.133e-21');
isa_ok($hsp->feature1, 'Bio::SeqFeature::Similarity');
isa_ok($hsp->feature2, 'Bio::SeqFeature::Similarity');
($meta) = $hsp->feature1->get_tag_values('meta');
is($meta, '(((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):');
($meta) = $hsp->feature2->get_tag_values('meta');
is($meta, '(((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):');

is($hsp->frame('query'), 0, "HSP frame");
is($hsp->gaps, 1, "HSP gaps");
is($hit->length, 0, "Hit length");
isa_ok($hsp->get_aln, 'Bio::Align::AlignI');
isa_ok($hsp->hit, 'Bio::SeqFeature::Similarity', "HSP hit");
is($hsp->hit_string,
   'GCGGAUUUAGCUCAGUuGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA',
   "HSP hit_string");
is($hsp->homology_string,
   'GC::A::UAGC:CAGU GG AG:GCGCCAG:CUG+++A:CUGGAGGUCC:G:GUUCGAU C:C:G::U::GCA',
   "HSP homology_string");
is($hsp->hsp_group, undef, "HSP hsp_group");
is($hsp->hsp_length, 73, "HSP hsp_length");
is($hsp->length, 73, "HSP length");
is($hsp->links, undef, "HSP links");
is($hsp->n, 1, "HSP n");
float_is($hsp->pvalue, 2.906e-26, "HSP pvalue");
isa_ok($hsp->query, 'Bio::SeqFeature::Similarity', "HSP query");
is($hsp->query_string,
   'gCcgacAUaGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUuCcccGUgucgGca',
   "HSP query_string");
is($hsp->range, 72, "HSP range");
is($hsp->rank, 1, "HSP rank");
float_is($hsp->significance, 3.133e-21);
is($hsp->end, 72, "HSP end");
float_is($hsp->expect, '3.133e-21', "HSP expect");

# These Bio::Search::HSP::HSPI methods are currently unimplemented in
# Bio::Search::HSP::ModelHSP; they may be integrated over time but will require
# some reconfiguring for Model-based searches

warning_like {$hsp->seq_inds}
    qr'seq_inds not implemented for Model-based searches',
    'HSP seq_inds not implemented';
warning_like {$hsp->matches}
    qr'matches not implemented for Model-based searches',
    'HSP matches not implemented';
warning_like {$hsp->frac_conserved}
    qr'frac_conserved not implemented for Model-based searches',
    'HSP frac_conserved not implemented';
warning_like {$hsp->frac_identical}
    qr'frac_identical not implemented for Model-based searches',
    'HSP frac_identical not implemented';
warning_like {$hsp->num_conserved}
    qr'num_conserved not implemented for Model-based searches',
    'HSP num_conserved not implemented';
warning_like {$hsp->num_identical}
    qr'num_identical not implemented for Model-based searches',
    'HSP num_identical not implemented';
warning_like {$hsp->percent_identity}
    qr'percent_identity not implemented for Model-based searches',
    'HSP percent_identity not implemented';
warning_like {$hsp->cigar_string}
    qr'cigar_string not implemented for Model-based searches',
    'HSP cigar_string not implemented';
warning_like {$hsp->generate_cigar_string}
    qr'generate_cigar_string not implemented for Model-based searches',
    'HSP cigar_string not implemented';

isa_ok($hsp->seq, 'Bio::LocatableSeq');
is($hsp->seq_str,
   'gCcgacAUaGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUuCcccGUgucgGca',
   "HSP seq_str");
is($hsp->start, 1, "HSP start");
is($hsp->custom_score, undef, "HSP custom_score");
is($hsp->meta,
   '(((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))):',
   "HSP meta");
is($hsp->strand('hit'), 1, "HSP strand");

$hsp = $hit->next_hsp;
isa_ok($hsp, 'Bio::Search::HSP::HSPI');
is($hsp->algorithm, 'CMSEARCH', "HSP algorithm");
float_is($hsp->evalue, 0.6752);
isa_ok($hsp->feature1, 'Bio::SeqFeature::Similarity');
isa_ok($hsp->feature2, 'Bio::SeqFeature::Similarity');
is($hsp->frame('query'), 0, "HSP frame");
is($hsp->gaps, 4, "HSP gaps");
# infernal can return alignment data
isa_ok($hsp->get_aln, 'Bio::Align::AlignI');
isa_ok($hsp->hit, 'Bio::SeqFeature::Similarity', "HSP hit");
is($hsp->hit_string,
   'UCUGCUAUGGCGUAAUGGCCACGCGC----CCAUCAACAAAGAUAUC*[19]*UAACAGGA',
   "HSP hit_string");
is($hsp->homology_string,
   ' C:G :AU+GCG:A+UGG  :CGCGC    C  UCAA +++GA +UC      U: C:G A',
   "HSP homology_string");
is($hsp->hsp_group, undef, "HSP hsp_group");
is($hsp->hsp_length, 73, "HSP hsp_length");
is($hsp->length, 73, "HSP length");
is($hsp->links, undef, "HSP links");
is($hsp->n, 1, "HSP n");
float_is($hsp->pvalue, 6.263e-06, "HSP pvalue");
isa_ok($hsp->query, 'Bio::SeqFeature::Similarity', "HSP query");
is($hsp->query_string,
   'gCcgacAUaGcgcAgUGGuAgcgCgccagccUgucAagcuggAGgUC*[17]*UgucgGca',
   "HSP query_string");
is($hsp->range, 72, "HSP range");
is($hsp->rank, 2, "HSP rank");
float_is($hsp->significance, 0.6752);
is($hsp->end, 72, "HSP end");
float_is($hsp->expect, 0.6752, "HSP expect");
isa_ok($hsp->seq, 'Bio::LocatableSeq');
# this should probably default to the hit string
is($hsp->seq_str,
   'gCcgacAUaGcgcAgUGGuAgcgCgccagccUgucAagcuggAGgUC*[17]*UgucgGca',
   "HSP seq_str");
is($hsp->start, 1, "HSP start");
is($hsp->custom_score, undef, "HSP custom_score");
is($hsp->meta,
   '(((((((,,<<<<_______>>>>,<<<<<_______>>>>>,,,,,~~~~~~))))))):',
   "HSP meta");
is($hsp->strand('hit'), 1, "HSP strand");

### Infernal pre-v. 1.0 ####

$searchio = Bio::SearchIO->new( -format => 'infernal',
                                -file   => test_input_file('test.infernal'),
                                # version is reset to the correct one by parser
                                -version => 0.7,
                                -model => 'Purine',
                                -query_acc => 'RF00167',
                                -query_desc => 'Purine riboswitch',
                                -database => 'b_sub.fas',
                                -hsp_minscore => 40,
                                -convert_meta => 0,
                               );

$result = $searchio->next_result;
isa_ok($result, 'Bio::Search::Result::ResultI');
$algorithm = $result->algorithm;
is($result->algorithm, 'CMSEARCH', "Result $algorithm");
is($result->algorithm_reference, undef, "Result $algorithm reference");
is($result->algorithm_version, 0.7, "Result $algorithm version");
is($result->available_parameters, 0, "Result parameters");
is($result->available_statistics, 0, "Result statistics");
is($result->database_entries, '', "Result entries");
is($result->database_letters, '', "Result letters");
is($result->database_name, 'b_sub.fas', "Result database_name");
is($result->num_hits, 2, "Result num_hits");
is($result->program_reference, undef, "Result program_reference");
is($result->query_accession, 'RF00167', "Result query_accession");
is($result->query_description, 'Purine riboswitch', "Result query_description");
is($result->query_length, 102, "Result query_length");
is($result->query_name, 'Purine', "Result query_name");

$hit = $result->next_hit;

isa_ok($hit, 'Bio::Search::Hit::HitI');
is($hit->ncbi_gi, '2239287', "Hit GI");
is($hit->accession, 'U51115.1', "Hit accession");
is($hit->algorithm, 'CMSEARCH', "Hit algorithm");
is($hit->bits, 81.29, "Hit bits");
is($hit->description, '', "Hit description"); # no hit descs yet
is($hit->locus, 'BSU51115', "Hit locus");
is($hit->n, 2, "Hit n");
is($hit->name, 'gi|2239287|gb|U51115.1|BSU51115', "Hit name");
is($hit->num_hsps, 2, "Hit num_hsps");

# p() works but there are no evalues yet for Infernal output, so catch and check...
warning_like {$hit->p}
    qr'P-value not defined. Using significance\(\) instead',
    "No p values";

is($hit->length, 0, "Hit length");
is($hit->overlap, 0, "Hit overlap");
is($hit->query_length, 102, "Hit query_length");
is($hit->rank, 1, "Hit rank");
is($hit->raw_score, 81.29, "Hit raw_score");
is($hit->score, 81.29, "Hit score");
float_is($hit->significance, undef);

$hsp = $hit->next_hsp;
isa_ok($hsp, 'Bio::Search::HSP::HSPI');
is($hsp->algorithm, 'CMSEARCH', "HSP algorithm");
float_is($hsp->evalue, undef);
isa_ok($hsp->feature1, 'Bio::SeqFeature::Similarity');
isa_ok($hsp->feature2, 'Bio::SeqFeature::Similarity');
($meta) = $hsp->feature1->get_tag_values('meta');
is($meta, ':::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<<<<<_______>>>>>>>,,)))).))))::::::::::::::');
($meta) = $hsp->feature2->get_tag_values('meta');
is($meta, ':::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<<<<<_______>>>>>>>,,)))).))))::::::::::::::');

is($hsp->frame('query'), 0, "HSP frame");
is($hsp->gaps, 1, "HSP gaps");
is($hit->length, 0, "Hit length");
isa_ok($hsp->get_aln, 'Bio::Align::AlignI');
isa_ok($hsp->hit, 'Bio::SeqFeature::Similarity', "HSP hit");
is($hsp->hit_string,
   'CAUGAAAUCAAAACACGACCUCAUAUAAUCUUGGGAAUAUGGCCCAUAAGUUUCUACCCGGCAACCGUAAAUUGCCGGACUAUGcAGGGAAGUGAUCGAUAAA',
   "HSP hit_string");
is($hsp->homology_string,
   ' A+ A+A+ AAAA A   :CUC:UAUAAU: :GGGAAUAUGGCCC: :AGUUUCUACC:GGCAACCGUAAAUUGCC:GACUA:G AG: AA + ++  +++++',
   "HSP homology_string");
is($hsp->hsp_group, undef, "HSP hsp_group");
is($hsp->hsp_length, 103, "HSP hsp_length");
is($hsp->length, 103, "HSP length");
is($hsp->links, undef, "HSP links");
is($hsp->n, 1, "HSP n");
float_is($hsp->pvalue, undef, "HSP pvalue");
isa_ok($hsp->query, 'Bio::SeqFeature::Similarity', "HSP query");
is($hsp->query_string,
   'aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaGgcaaCCGUAAAuugcCuGACUAcG.aGuaAauauuaaauauuu',
   "HSP query_string");
is($hsp->range, 102, "HSP range");
is($hsp->rank, 1, "HSP rank");
float_is($hsp->significance, undef);
is($hsp->end, 102, "HSP end");
float_is($hsp->expect, undef, "HSP expect");

isa_ok($hsp->seq, 'Bio::LocatableSeq');
is($hsp->seq_str,
   'aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaGgcaaCCGUAAAuugcCuGACUAcG.aGuaAauauuaaauauuu',
   "HSP seq_str");
is($hsp->start, 1, "HSP start");
is($hsp->custom_score, undef, "HSP custom_score");
is($hsp->meta,
   ':::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<<<<<_______>>>>>>>,,)))).))))::::::::::::::',
   "HSP meta");
is($hsp->strand('hit'), 1, "HSP strand");

$hsp = $hit->next_hsp;
isa_ok($hsp, 'Bio::Search::HSP::HSPI');
is($hsp->algorithm, 'CMSEARCH', "HSP algorithm");
float_is($hsp->evalue, undef);
isa_ok($hsp->feature1, 'Bio::SeqFeature::Similarity');
isa_ok($hsp->feature2, 'Bio::SeqFeature::Similarity');
is($hsp->frame('query'), 0, "HSP frame");
is($hsp->gaps, 0, "HSP gaps");
# infernal can return alignment data
isa_ok($hsp->get_aln, 'Bio::Align::AlignI');
isa_ok($hsp->hit, 'Bio::SeqFeature::Similarity', "HSP hit");
is($hsp->hit_string,
   'AGAAAUCAAAUAAGAUGAAUUCGUAUAAUCGCGGGAAUAUGGCUCGCAAGUCUCUACCAAGCUACCGUAAAUGGCUUGACUACGUAAACAUUUCUUUCGUUU',
   "HSP hit_string");
is($hsp->homology_string,
   'A AAAU AAA+AA A+   : CGUAUAAU::CG:GAAUAUGGC:CG::AGU UCUACCA:GC ACCGUAAAU GC:UGACUACG :   AU+U +++  UUU',
   "HSP homology_string");
is($hsp->hsp_group, undef, "HSP hsp_group");
is($hsp->hsp_length, 103, "HSP hsp_length");
is($hsp->length, 103, "HSP length");
is($hsp->links, undef, "HSP links");
is($hsp->n, 1, "HSP n");
float_is($hsp->pvalue, undef, "HSP pvalue");
isa_ok($hsp->query, 'Bio::SeqFeature::Similarity', "HSP query");
is($hsp->query_string,
   'aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaGgcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu',
   "HSP query_string");
is($hsp->range, 102, "HSP range");
is($hsp->rank, 2, "HSP rank");
float_is($hsp->significance, undef);
is($hsp->end, 102, "HSP end");
float_is($hsp->expect, undef, "HSP expect");
#is($hsp->matches, 2, "HSP matches");
isa_ok($hsp->seq, 'Bio::LocatableSeq');
# this should probably default to the hit string
is($hsp->seq_str,
   'aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaGgcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu',
   "HSP seq_str");
is($hsp->start, 1, "HSP start");
is($hsp->custom_score, undef, "HSP custom_score");
is($hsp->meta,
   ':::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<<<<<_______>>>>>>>,,))))))))::::::::::::::',
   "HSP meta");
is($hsp->strand('hit'), 1, "HSP strand");

# one more hit...

$hit = $result->next_hit;
isa_ok($hit, 'Bio::Search::Hit::HitI');
is($hit->accession, 'X83878.1', "Hit accession");
is($hit->ncbi_gi, '633168', "Hit GI");
is($hit->algorithm, 'CMSEARCH', "Hit algorithm");
is($hit->bits, 79.36, "Hit bits");
is($hit->description, '', "Hit description"); # no hit descs yet
is($hit->length, 0, "Hit length");
is($hit->locus, '', "Hit locus");
is($hit->n, 1, "Hit n");
is($hit->name, 'gi|633168|emb|X83878.1|', "Hit name");
is($hit->num_hsps, 1, "Hit num_hsps");
is($hit->overlap, 0, "Hit overlap");
is($hit->query_length, 102, "Hit query_length");
is($hit->rank, 2, "Hit rank");
is($hit->raw_score, 79.36, "Hit raw_score");
is($hit->score, 79.36, "Hit score");
float_is($hit->significance, undef);

# one more HSP...

$hsp = $hit->next_hsp;
isa_ok($hsp, 'Bio::Search::HSP::HSPI');
is($hsp->algorithm, 'CMSEARCH', "HSP algorithm");
float_is($hsp->evalue, undef);
isa_ok($hsp->feature1, 'Bio::SeqFeature::Similarity');
isa_ok($hsp->feature2, 'Bio::SeqFeature::Similarity');
is($hsp->frame('query'), 0, "HSP frame");
is($hsp->gaps, 2, "HSP gaps");
isa_ok($hsp->get_aln, 'Bio::Align::AlignI');
isa_ok($hsp->hit, 'Bio::SeqFeature::Similarity', "HSP hit");
is($hsp->hit_string,
   'UUACAAUAUAAUAGGAACACUCAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCA-CCGUAAA-UGUCCGACUAUGGGUGAGCAAUGGAACCGC',
   "HSP hit_string");
is($hsp->homology_string,
   '+ A A++A AA A  AA:AC+C:UAUAAU::CG:G AUAUGGC:CG::AGUUUCUACC:G CA CCGUAAA UG C:GACUA:G+GU:A  A+U  A+    ',
   "HSP homology_string");
is($hsp->hsp_group, undef, "HSP hsp_group");
is($hsp->hsp_length, 103, "HSP hsp_length");
is($hsp->length, 103, "HSP length");
is($hsp->links, undef, "HSP links");
is($hsp->n, 1, "HSP n");
isa_ok($hsp->query, 'Bio::SeqFeature::Similarity', "HSP query");
is($hsp->query_string,
   'aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaGgcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu',
   "HSP query_string");
is($hsp->range, 102, "HSP range");
is($hsp->rank, 1, "HSP rank");
float_is($hsp->significance, undef);
is($hsp->end, 102, "HSP end");
float_is($hsp->expect, undef, "HSP expect");
isa_ok($hsp->seq, 'Bio::LocatableSeq');
is($hsp->seq_str,
   'aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaGgcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu',
   "HSP seq_str");
is($hsp->start, 1, "HSP start");
is($hsp->custom_score, undef, "HSP custom_score");
is($hsp->meta,
   ':::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<<<<<_______>>>>>>>,,))))))))::::::::::::::',
   "HSP meta");
is($hsp->strand('hit'), 1, "HSP strand");

my $symbols = {
            '5-prime'        => '(',
            '3-prime'        => ')',
            'single-strand'  => ':',
            'unknown'        => '?',
            'gap'            => '-'
             # may add more for quartets, triplets
              };

$searchio = Bio::SearchIO->new( -format => 'infernal',
                                -file   => test_input_file('test.infernal'),
                                # version is reset to the correct one by parser
                                -version => 0.7,
                                -model => 'Purine',
                                -query_acc => 'RF00167',
                                -query_desc => 'Purine riboswitch',
                                -database => 'b_sub.fas',
                                -hsp_minscore => 40,
                                -convert_meta => 1,
                                -symbols => $symbols,
                               );

$result = $searchio->next_result;
$hit = $result->next_hit;
$hsp = $hit->next_hsp;
is($hsp->meta,
   ':::::::::::::::::((((((((:::(((((((:::::::)))))))::::::::(((((((:::::::)))))))::))))-))))::::::::::::::',
   "HSP meta gap bug");
$hsp = $hit->next_hsp;
is($hsp->meta,
   ':::::::::::::::::((((((((:::(((((((:::::::)))))))::::::::(((((((:::::::)))))))::))))))))::::::::::::::',
   "HSP meta");
$hit = $result->next_hit;
$hsp = $hit->next_hsp;
is($hsp->meta,
   ':::::::::::::::::((((((((:::(((((((:::::::)))))))::::::::(((((((:::::::)))))))::))))))))::::::::::::::',
   "HSP meta");
($meta) = $hsp->feature1->get_tag_values('meta');
is($meta, ':::::::::::::::::((((((((:::(((((((:::::::)))))))::::::::(((((((:::::::)))))))::))))))))::::::::::::::');
($meta) = $hsp->feature2->get_tag_values('meta');
is($meta, ':::::::::::::::::((((((((:::(((((((:::::::)))))))::::::::(((((((:::::::)))))))::))))))))::::::::::::::');

## Infernal 0.81 parsing ##

$searchio = Bio::SearchIO->new( -format => 'infernal',
                                -file   => test_input_file('purine_v081.infernal'),
                                # version is reset to the correct one by parser
                                -query_acc => 'RF00167',
                                -query_desc => 'Purine riboswitch',
                                -database => 'b_sub.fas',
                                -convert_meta => 0,
                               );

$result = $searchio->next_result;

isa_ok($result, 'Bio::Search::Result::ResultI');
$algorithm = $result->algorithm;
is($result->algorithm, 'CMSEARCH', "Result $algorithm");
is($result->algorithm_reference, undef, "Result $algorithm reference");
is($result->algorithm_version, 0.81, "Result $algorithm version");
is($result->available_parameters, 0, "Result parameters");
is($result->available_statistics, 0, "Result statistics");
is($result->database_entries, '', "Result entries");
is($result->database_letters, '', "Result letters");
is($result->database_name, 'b_sub.fas', "Result database_name");
is($result->num_hits, 3, "Result num_hits");
is($result->program_reference, undef, "Result program_reference");
is($result->query_accession, 'RF00167', "Result query_accession");
is($result->query_description, 'Purine riboswitch', "Result query_description");
is($result->query_length, 102, "Result query_length");
is($result->query_name, 'Purine', "Result query_name");

$hit = $result->next_hit;
isa_ok($hit, 'Bio::Search::Hit::HitI');
is($hit->ncbi_gi, '633168', "Hit GI");
is($hit->accession, 'X83878.1', "Hit accession");
is($hit->algorithm, 'CMSEARCH', "Hit algorithm");
is($hit->bits, 79.36, "Hit bits");
is($hit->description, '', "Hit description"); # no hit descs yet
is($hit->locus, '', "Hit locus");
is($hit->n, 2, "Hit n");
is($hit->name, 'gi|633168|emb|X83878.1|', "Hit name");
is($hit->num_hsps, 2, "Hit num_hsps");

# p() works but there are no evalues yet for Infernal output, so catch and check...
warnings_like {$hit->p} qr'P-value not defined. Using significance\(\) instead',
     "No p values";

is($hit->length, 0, "Hit length");
is($hit->overlap, 0, "Hit overlap");
is($hit->query_length, 102, "Hit query_length");
is($hit->rank, 1, "Hit rank");
is($hit->raw_score, 79.36, "Hit raw_score");
is($hit->score, 79.36, "Hit score");
float_is($hit->significance, 1.945e-07);

$hsp = $hit->next_hsp;
isa_ok($hsp, 'Bio::Search::HSP::HSPI');
is($hsp->algorithm, 'CMSEARCH', "HSP algorithm");
float_is($hsp->evalue, 1.945e-07);
isa_ok($hsp->feature1, 'Bio::SeqFeature::Similarity');
isa_ok($hsp->feature2, 'Bio::SeqFeature::Similarity');
($meta) = $hsp->feature1->get_tag_values('meta');
is($meta, ':::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<<<<<_______>>>>>>>,,))))))))::::::::::::::');
($meta) = $hsp->feature2->get_tag_values('meta');
is($meta, ':::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<<<<<_______>>>>>>>,,))))))))::::::::::::::');

is($hsp->frame('query'), 0, "HSP frame");
is($hsp->gaps, 2, "HSP gaps");
is($hit->length, 0, "Hit length");
isa_ok($hsp->get_aln, 'Bio::Align::AlignI');
isa_ok($hsp->hit, 'Bio::SeqFeature::Similarity', "HSP hit");
is($hsp->hit_string,
   'UUACAAUAUAAUAGGAACACUCAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCA-CCGUAAA-UGUCCGACUAUGGGUGAGCAAUGGAACCGC',
   "HSP hit_string");
is($hsp->homology_string,
   '+ A A++A AA A  AA:AC+C:UAUAAU::CG:G AUAUGGC:CG::AGUUUCUACC:G CA CCGUAAA UG C:GACUA:G+GU:A  A+U  A+    ',
   "HSP homology_string");
is($hsp->hsp_group, undef, "HSP hsp_group");
is($hsp->hsp_length,102, "HSP hsp_length");
is($hsp->length, 102, "HSP length");
is($hsp->links, undef, "HSP links");
is($hsp->n, 1, "HSP n");
float_is($hsp->pvalue, 1.945e-07, "HSP pvalue");
isa_ok($hsp->query, 'Bio::SeqFeature::Similarity', "HSP query");
is($hsp->query_string,
   'aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaGgcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu',
   "HSP query_string");
is($hsp->range, 102, "HSP range");
is($hsp->rank, 1, "HSP rank");
float_is($hsp->significance, 1.945e-07);
is($hsp->end, 102, "HSP end");
float_is($hsp->expect, 1.945e-07, "HSP expect");

isa_ok($hsp->seq, 'Bio::LocatableSeq');
is($hsp->seq_str,
   'aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaGgcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu',
   "HSP seq_str");
is($hsp->start, 1, "HSP start");
is($hsp->custom_score, undef, "HSP custom_score");
is($hsp->meta,
   ':::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<<<<<_______>>>>>>>,,))))))))::::::::::::::',
   "HSP meta");
is($hsp->strand('hit'), 1, "HSP strand");

$hsp = $hit->next_hsp;
isa_ok($hsp, 'Bio::Search::HSP::HSPI');
is($hsp->algorithm, 'CMSEARCH', "HSP algorithm");
float_is($hsp->evalue, 6.802);
isa_ok($hsp->feature1, 'Bio::SeqFeature::Similarity');
isa_ok($hsp->feature2, 'Bio::SeqFeature::Similarity');
is($hsp->frame('query'), 0, "HSP frame");
is($hsp->gaps, 4, "HSP gaps");
# infernal can return alignment data
isa_ok($hsp->get_aln, 'Bio::Align::AlignI');
isa_ok($hsp->hit, 'Bio::SeqFeature::Similarity', "HSP hit");
is($hsp->hit_string,
   'CGUGCGGUUCCAUUGCUCACCCAUA-GUCGGACAU-UUACGG-UGCCCGGUAGAAACUUGCGUGCCAUAUCCACGCGAUUaUAUGAGUGUUCCUAUUAUAUUG',
   "HSP hit_string");
is($hsp->homology_string,
   '  +    +   A    +:AC C:UA  +::: ::   UA GG :: :::GU    AC: G::::CC UA  ::::C :   UA:G GU: +  U+++AUAUU ',
   "HSP homology_string");
is($hsp->hsp_group, undef, "HSP hsp_group");
is($hsp->hsp_length, 102, "HSP hsp_length");
is($hsp->length, 102, "HSP length");
is($hsp->links, undef, "HSP links");
is($hsp->n, 1, "HSP n");
float_is($hsp->pvalue, 0.9989, "HSP pvalue");
isa_ok($hsp->query, 'Bio::SeqFeature::Similarity', "HSP query");
is($hsp->query_string,
   'aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaGgcaaCCGUAAAuugcCuGAC.UAcGaGuaAauauuaaauauuu',
   "HSP query_string");
is($hsp->range, 102, "HSP range");
is($hsp->rank, 2, "HSP rank");
float_is($hsp->significance, 6.802);
is($hsp->end, 102, "HSP end");
float_is($hsp->expect, 6.802, "HSP expect");
#is($hsp->matches, 2, "HSP matches");
isa_ok($hsp->seq, 'Bio::LocatableSeq');
# this should probably default to the hit string
is($hsp->seq_str,
   'aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaGgcaaCCGUAAAuugcCuGAC.UAcGaGuaAauauuaaauauuu',
   "HSP seq_str");
is($hsp->start, 1, "HSP start");
is($hsp->custom_score, undef, "HSP custom_score");
is($hsp->meta,
   ':::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<<<<<_______>>>>>>>,,.))))))))::::::::::::::',
   "HSP meta");
is($hsp->strand('hit'), -1, "HSP strand");

# one more hit...

$hit = $result->next_hit;
isa_ok($hit, 'Bio::Search::Hit::HitI');
is($hit->accession, 'U51115.1', "Hit accession");
is($hit->ncbi_gi, '2239287', "Hit GI");
is($hit->algorithm, 'CMSEARCH', "Hit algorithm");
is($hit->bits, 81.29, "Hit bits");
is($hit->description, '', "Hit description"); # no hit descs yet
is($hit->length, 0, "Hit length");
is($hit->locus, 'BSU51115', "Hit locus");
is($hit->n, 11, "Hit n");
is($hit->name, 'gi|2239287|gb|U51115.1|BSU51115', "Hit name");
is($hit->num_hsps, 11, "Hit num_hsps");
is($hit->overlap, 0, "Hit overlap");
is($hit->query_length, 102, "Hit query_length");
is($hit->rank, 2, "Hit rank");
is($hit->raw_score, 81.29, "Hit raw_score");
is($hit->score, 81.29, "Hit score");
float_is($hit->significance, 1.259e-07);

# one more HSP...

$hsp = $hit->next_hsp;
isa_ok($hsp, 'Bio::Search::HSP::HSPI');
is($hsp->algorithm, 'CMSEARCH', "HSP algorithm");
float_is($hsp->evalue, 1.259e-07);
isa_ok($hsp->feature1, 'Bio::SeqFeature::Similarity');
isa_ok($hsp->feature2, 'Bio::SeqFeature::Similarity');
is($hsp->frame('query'), 0, "HSP frame");
is($hsp->gaps, 0, "HSP gaps");
isa_ok($hsp->get_aln, 'Bio::Align::AlignI');
isa_ok($hsp->hit, 'Bio::SeqFeature::Similarity', "HSP hit");
is($hsp->hit_string,
   'AGAAAUCAAAUAAGAUGAAUUCGUAUAAUCGCGGGAAUAUGGCUCGCAAGUCUCUACCAAGCUACCGUAAAUGGCUUGACUACGUAAACAUUUCUUUCGUUU',
   "HSP hit_string");
is($hsp->homology_string,
   'A AAAU AAA+AA A+   : CGUAUAAU::CG:GAAUAUGGC:CG::AGU UCUACCA:GC ACCGUAAAU GC:UGACUACG :   AU+U +++  UUU',
   "HSP homology_string");
is($hsp->hsp_group, undef, "HSP hsp_group");
is($hsp->hsp_length, 102, "HSP hsp_length");
is($hsp->length, 102, "HSP length");
is($hsp->links, undef, "HSP links");
is($hsp->n, 1, "HSP n");
isa_ok($hsp->query, 'Bio::SeqFeature::Similarity', "HSP query");
is($hsp->query_string,
   'aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaGgcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu',
   "HSP query_string");
is($hsp->range, 102, "HSP range");
is($hsp->rank, 1, "HSP rank");
float_is($hsp->significance, 1.259e-07);
is($hsp->end, 102, "HSP end");
float_is($hsp->expect, 1.259e-07, "HSP expect");
isa_ok($hsp->seq, 'Bio::LocatableSeq');
is($hsp->seq_str,
   'aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaGgcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu',
   "HSP seq_str");
is($hsp->start, 1, "HSP start");
is($hsp->custom_score, undef, "HSP custom_score");
is($hsp->meta,
   ':::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<<<<<_______>>>>>>>,,))))))))::::::::::::::',
   "HSP meta");
is($hsp->strand('hit'), 1, "HSP strand");
BioPerl-1.007002/t/SearchIO/megablast.t000444000766000024       215513155576321 17543 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_megablast.t 14995 2008-11-16 06:20:00Z cjfields $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 31);
    
    use_ok('Bio::SearchIO');
}

my ($searchio, $result, $hit, $hsp);

# this is megablast output type 0 
my $in = Bio::SearchIO->new(-file          => test_input_file('503384.MEGABLAST.0'),
			-report_format => 0,
			-format        => 'megablast'); 
my $r = $in->next_result;
my @dcompare = ( 
	      ['Contig634', 7620, 7941, 1, 1, 321, -1],
	      ['Contig1853', 6406, 6620, 1, 1691, 1905, 1],  
	      ['Contig3700', 8723,9434, 1, 4083, 4794, -1],
	      ['Contig3997', 1282, 1704, 1, 1546, 1968,-1 ],
	      );

is($r->query_name, '503384');

while( my $hit = $r->next_hit ) {
    my $d = shift @dcompare;
    is($hit->name, shift @$d);
    my $hsp = $hit->next_hsp;
    is($hsp->query->start, shift @$d);
    is($hsp->query->end, shift @$d);
    is($hsp->query->strand, shift @$d);
    is($hsp->hit->start, shift @$d);
    is($hsp->hit->end, shift @$d);
    is($hsp->hit->strand, shift @$d);
}
is(@dcompare, 0);

BioPerl-1.007002/t/SearchIO/psl.t000444000766000024       541113155576321 16400 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: UCSCParsers.t 11525 2007-06-27 10:16:38Z sendu $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 53);

    use_ok('Bio::SearchIO');
}

my $pslparser = Bio::SearchIO->new(-format => 'psl',
				  -file   => test_input_file('sbay_c545-yeast.BLASTZ.PSL'));

my $result = $pslparser->next_result;
is($result->query_name, 'I');
is($result->query_length, 230203);

my $hit    = $result->next_hit;
is($hit->name, 'sbay_c545');
is($hit->length, 28791);
my $hsp    = $hit->next_hsp;
is($hsp->query->start,139871);
is($hsp->query->end,141472);
is($hsp->query->length, 1602);
is($hsp->query->strand, 1);
is($hsp->hit->strand, 1);
my $q_gapblocks = $hsp->gap_blocks('query');
is(scalar @$q_gapblocks, 24);
is($q_gapblocks->[0]->[1],45);
is($q_gapblocks->[1]->[1],10);
is($q_gapblocks->[1]->[0],139921);

$hsp       = $hit->next_hsp;
$hsp       = $hit->next_hsp;
is($hsp->hit->start,27302);
is($hsp->hit->end,27468);
is($hsp->hit->length,167);
is($hsp->query->start, 123814);
is($hsp->query->end, 123972);
is($hsp->query->length, 159);
is($hsp->query->strand,-1);

$q_gapblocks = $hsp->gap_blocks('query');
is(scalar @$q_gapblocks, 4);
is($q_gapblocks->[0]->[1],116);
is($q_gapblocks->[1]->[1],4);
is($q_gapblocks->[1]->[0],123856);

#-----------------------------------

$pslparser = Bio::SearchIO->new(-format => 'psl',
			       -file   => test_input_file('blat.psLayout3'));

$result = $pslparser->next_result;
is($result->query_name, 'sequence_10');
is($result->query_length, 1775);

$hit    = $result->next_hit;
is($hit->name, 'sequence_10');
is($hit->length, 1775);
$hsp    = $hit->next_hsp;
is($hsp->query->start,1);
is($hsp->query->end,1775);
is($hsp->query->length,1775);
is($hsp->query->strand,1);
is($hsp->hit->strand,1);
$q_gapblocks = $hsp->gap_blocks('query');
is(scalar @$q_gapblocks, 1);
is($q_gapblocks->[0]->[1],1775);
is($q_gapblocks->[1]->[1],undef);
is($q_gapblocks->[1]->[0],undef);

$hsp       = $hit->next_hsp;
is($hsp->hit->start,841);
is($hsp->hit->end,1244);
is($hsp->query->start, 841);
is($hsp->query->end, 1244);
is($hsp->query->length, 404);
is($hsp->query->strand,-1);
is($hsp->hit->strand,1);

$q_gapblocks = $hsp->gap_blocks('query');
is(scalar @$q_gapblocks, 4);
is($q_gapblocks->[0]->[1],14);
is($q_gapblocks->[1]->[1],21);
is($q_gapblocks->[1]->[0],1152);


is( $hit->next_hsp, undef, 'next_hsp should be undef');
is( $result->next_hit, undef, 'next_hit should be undef');
TODO: {
    local $TODO = "next_result should really return undef, not empty string";
    is( $pslparser->next_result, undef, 'next_result should be undef');
}

# bug 2850

my $searchio = Bio::SearchIO->new(
    -format => 'psl',
    -file   => test_input_file('headerless.psl'),
);

lives_ok { my $result = $searchio->next_result };
BioPerl-1.007002/t/SearchIO/rnamotif.t000444000766000024      1001113155576321 17431 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_rnamotif.t 14672 2008-04-22 21:42:50Z cjfields $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 60);
    
    use_ok('Bio::SearchIO');
}

my ($searchio, $result, $iter, $hit, $hsp, $algorithm, $meta);

#### RNAMotif ####

# regular data

$searchio = Bio::SearchIO->new( -format => 'rnamotif',
                                -file   => test_input_file('trna.strict.rnamotif'),
                                -model => 'trna.descr',
                                -query_acc => 'test',
                                -database => 'gbrna.fas',
                                -verbose => 2
                               );

$result = $searchio->next_result;
isa_ok($result, 'Bio::Search::Result::ResultI');
$algorithm = $result->algorithm;
is($result->algorithm, 'RNAMOTIF', "Result $algorithm");
is($result->algorithm_reference, undef, "Result $algorithm reference");
is($result->algorithm_version, '3.0.3', "Result $algorithm version");
is($result->database_entries, '', "Result entries");
is($result->database_letters, '', "Result letters");
is($result->database_name, 'gbrna.fas', "Result database_name");
is($result->num_hits, 28, "Result num_hits");
is($result->program_reference, undef, "Result program_reference");
is($result->query_accession, 'test', "Result query_accession");
is($result->query_description, 'h5 ss h5 ss h3 ss h5 ss h3 ss h5 ss h3 h3 ss', "Result query_description");
is($result->query_length, 0, "Result query_length");
is($result->query_name, 'trna.strict.descr', "Result query_name");

$hit = $result->next_hit;
isa_ok($hit, 'Bio::Search::Hit::HitI');
is($hit->accession, 'M10671', "Hit accession");
is($hit->ncbi_gi, '173683', "Hit GI");
is($hit->algorithm, 'RNAMOTIF', "Hit algorithm");
is($hit->description, 'Avian oncornavirus Trp-tRNA',
   "Hit description"); # no hit descs yet
is($hit->length, 0, "Hit length");
is($hit->locus, 'ACSTRW', "Hit locus");
is($hit->n, 8, "Hit n");
is($hit->name, 'gi|173683|gb|M10671|ACSTRW', "Hit name");
is($hit->num_hsps, 8, "Hit num_hsps"); 
is($hit->overlap, 0, "Hit overlap");
is($hit->rank, 1, "Hit rank");
is($hit->raw_score, 0, "Hit raw_score");
is($hit->score, 0, "Hit score");
float_is($hit->significance, undef);

$hsp = $hit->next_hsp;
isa_ok($hsp, 'Bio::Search::HSP::HSPI');
is($hsp->algorithm, 'RNAMOTIF', "HSP algorithm");
float_is($hsp->evalue, undef);
isa_ok($hsp->feature1, 'Bio::SeqFeature::Similarity');
isa_ok($hsp->feature2, 'Bio::SeqFeature::Similarity');
is($hsp->frame('query'), 0, "HSP frame");
is($hsp->gaps, 0, "HSP gaps");

# RNAMotif cannot build alignments
eval{$hsp->get_aln};
like($@, qr'Missing query string, can\'t build alignment','RNAMotif get_aln warning');
isa_ok($hsp->hit, 'Bio::SeqFeature::Similarity', "HSP hit");
is($hsp->hit_string,
   'gacctcgtggcgcaacggtagcgcgtctgactccagatcagaaggctgcgtgttcgaatcacgtcggggtcacca',
   "HSP hit_string");
is($hsp->homology_string,
   '',
   "HSP homology_string");
is($hsp->hsp_group, undef, "HSP hsp_group");
is($hsp->hsp_length, 75, "HSP hsp_length");
is($hsp->length, 75, "HSP length");
is($hsp->links, undef, "HSP links");
is($hsp->n, 1,"HSP n");
isa_ok($hsp->query, 'Bio::SeqFeature::Similarity', "HSP query");
is($hsp->query_string,
   '',
   "HSP query_string");
is($hsp->range, 75, "HSP range");
is($hsp->rank, 1, "HSP rank");
float_is($hsp->significance, undef);
is($hsp->end, 75, "HSP end");
float_is($hsp->expect, undef, "HSP expect");
isa_ok($hsp->seq, 'Bio::LocatableSeq');
is($hsp->seq_str,
   '',
   "HSP seq_str");
is($hsp->start, 1, "HSP start");
is($hsp->custom_score, undef, "HSP custom_score");
is($hsp->meta,
   '<<<<<<<..<<<.........>>>.<<<<<.......>>>>>.......<<<<.......>>>>>>>>>>>....',
   "HSP meta");
is($hsp->strand('hit'), 1, "HSP strand");
($meta) = $hsp->feature1->get_tag_values('meta');
is($meta, '<<<<<<<..<<<.........>>>.<<<<<.......>>>>>.......<<<<.......>>>>>>>>>>>....');
($meta) = $hsp->feature2->get_tag_values('meta');
is($meta, '<<<<<<<..<<<.........>>>.<<<<<.......>>>>>.......<<<<.......>>>>>>>>>>>....');

BioPerl-1.007002/t/SearchIO/sim4.t000444000766000024      1073713155576321 16505 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: Sim4.t 11525 2007-06-27 10:16:38Z sendu $

use strict;
BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 102);
	
	use_ok('Bio::SearchIO');
}

# parse align format 0
my $parser = Bio::SearchIO->new(-format => 'sim4',
			       -file   => test_input_file('crypto.sim4-0')
			       );
my $r = $parser->next_result;
is ($r->query_name, 'cn416');
is ($r->query_length, 630);

my $hit = $r->next_hit;
is ($hit->name, 'Contig147');
is ($hit->description, 'Contig147.fa');
is ($hit->length, 1086);

my $hsp = $hit->next_hsp;
is ($hsp->query->start, 36);
is ($hsp->query->end, 132);
is ($hsp->query->strand, 1);
is ($hsp->hit->start, 191);
is ($hsp->hit->end, 286);
is ($hsp->hit->strand, 1);

$hsp = $hit->next_hsp;
is ($hsp->query->start, 133);
is ($hsp->query->end, 191);
is ($hsp->query->strand, 1);
is ($hsp->hit->start, 343);
is ($hsp->hit->end, 401);
is ($hsp->hit->strand, 1);

# parse align format 3
$parser = Bio::SearchIO->new(-format => 'sim4',
			    -file   => test_input_file('crypto.sim4-3')
			    );
$r = $parser->next_result;
is ($r->query_name, 'cn416');
is ($r->query_length, 630);
$hit = $r->next_hit;
is ($hit->name, 'Contig147');
is ($hit->description, 'Contig147.fa');
is ($hit->length, 1086);

$hsp = $hit->next_hsp;
is ($hsp->query->start, 36);
is ($hsp->query->end, 132);
is ($hsp->query->strand, 1);
is ($hsp->hit->start, 191);
is ($hsp->hit->end, 286);
is ($hsp->hit->strand, 1);

$hsp = $hit->next_hsp;
is ($hsp->query->start, 133);
is ($hsp->query->end, 191);
is ($hsp->query->strand, 1);
is ($hsp->hit->start, 343);
is ($hsp->hit->end, 401);
is ($hsp->hit->strand, 1);

# parse align format 4
$parser = Bio::SearchIO->new(-format => 'sim4',
			    -file   => test_input_file('crypto.sim4-4')
			    );
$r = $parser->next_result;
is ($r->query_name, 'cn416');
is ($r->query_length, 630);

$hit = $r->next_hit;
is ($hit->name, 'Contig147');
is ($hit->length, 1086);

$hsp = $hit->next_hsp;
is ($hsp->query->start, 36);
is ($hsp->query->end, 132);
is ($hsp->query->strand, 1);
is ($hsp->hit->start, 191);
is ($hsp->hit->end, 286);
is ($hsp->hit->strand, 1);

$hsp = $hit->next_hsp;
is ($hsp->query->start, 133);
is ($hsp->query->end, 191);
is ($hsp->query->strand, 1);
is ($hsp->hit->start, 343);
is ($hsp->hit->end, 401);
is ($hsp->hit->strand, 1);


# do the other sim4 files
$parser = Bio::SearchIO->new(-format => 'sim4',
			    -file   => test_input_file('sim4.rev')
			    );
$r = $parser->next_result;
is ($r->query_name, '/nfs/disk21/birney/prog/wise2/example/human.rev');
is ($r->query_length, 5368);
$hit = $r->next_hit;
is ($hit->name, 'HSHNCPA1');
is ($hit->description, 'temp.cdna');
is ($hit->length, 1198);

$hsp = $hit->next_hsp;
is ($hsp->query->start, 486);
is ($hsp->query->end, 503);
is ($hsp->query->strand, 1);
is ($hsp->hit->start, 10);
is ($hsp->hit->end, 27);
is ($hsp->hit->strand, -1);

$hsp = $hit->next_hsp;
is ($hsp->query->start, 1048);
is ($hsp->query->end, 1117);
is ($hsp->query->strand, 1);
is ($hsp->hit->start, 194);
is ($hsp->hit->end, 265);
is ($hsp->hit->strand, -1);

# do the other sim4 files fwd
$parser = Bio::SearchIO->new(-format => 'sim4',
			    -file   => test_input_file('sim4.for.for')
			    );
$r = $parser->next_result;
is ($r->query_name, 'human.genomic');
is ($r->query_length, 5368);
$hit = $r->next_hit;
is ($hit->name, 'hs_est');
is ($hit->description, 'est.for');
is ($hit->length, 479);

$hsp = $hit->next_hsp;
is ($hsp->query->start, 695);
is ($hsp->query->end, 813);
is ($hsp->query->strand, 1);
is ($hsp->hit->start, 1);
is ($hsp->hit->end, 119);
is ($hsp->hit->strand, 1);

$hsp = $hit->next_hsp;
is ($hsp->query->start, 1377);
is ($hsp->query->end, 1500);
is ($hsp->query->strand, 1);
is ($hsp->hit->start, 120);
is ($hsp->hit->end, 243);
is ($hsp->hit->strand, 1);

# do the other sim4 files fwd rev
$parser = Bio::SearchIO->new(-format => 'sim4',
			    -file   => test_input_file('sim4.for.rev')
			    );
$r = $parser->next_result;
is ($r->query_name, 'human.genomic');
is ($r->query_length, 5368);
$hit = $r->next_hit;
is ($hit->name, 'REVCOMP');
is ($hit->description, 'hn_est.rev');
is ($hit->length, 479);

$hsp = $hit->next_hsp;
is ($hsp->query->start, 695);
is ($hsp->query->end, 813);
is ($hsp->query->strand, 1);
is ($hsp->hit->start, 1);
is ($hsp->hit->end, 119);
is ($hsp->hit->strand, -1);

$hsp = $hit->next_hsp;
is ($hsp->query->start, 1377);
is ($hsp->query->end, 1500);
is ($hsp->query->strand, 1);
is ($hsp->hit->start, 120);
is ($hsp->hit->end, 243);
is ($hsp->hit->strand, -1);
BioPerl-1.007002/t/SearchIO/waba.t000444000766000024       505513155576321 16520 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: WABA.t 11525 2007-06-27 10:16:38Z sendu $

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 64);
	
    use_ok('Bio::SearchIO');
}

my $wabain = Bio::SearchIO->new(
    -format => 'waba',
    -file   => test_input_file('test.waba')
);

isa_ok($wabain, 'Bio::SearchIO') ;

# These won't look the same as the WABA file because Jim's code is 0 based
# while we (bioperl) are 1 based.
my @results = (
    [
        'U57623',
        'pair1_hs.fa',
        'pair1_mm.fa',
        [
            'U02884',
            3,
            [qw(3833 34 2972 1 243 3688 1 40.9)],
            [qw(4211 3022 6914 1 3705 6848 1 43.7)],
            [qw(2218 7004 9171 1 6892 8712 1 50.3)],
        ],
    ],
    [
        'X57152', 'pair9_hs.fa',
        'pair9_mm.fa', [ 'X80685', 1, [qw(7572 4 5845 1 632 7368 1 46.8)], ],
    ]
);

while ( my $wabar = $wabain->next_result ) {
    my @r = @{ shift @results };
    is( $wabar->query_name,     shift @r, 'query_name'     );
    is( $wabar->query_database, shift @r, 'query database' );
    is( $wabar->database_name,  shift @r, 'database name'  );

    while ( my $wabah = $wabar->next_hit ) {
        my (@h) = @{ shift @r };
        is( $wabah->name, shift @h, 'name' );
        is( $wabah->hsps(), shift @h, 'hsps' );

        while ( my $wabahsp = $wabah->next_hsp ) {
            my (@hsp) = @{ shift @h };
            is( $wabahsp->length('total'),        shift @hsp , 'total length');
            is( $wabahsp->query->start,           shift @hsp , 'start'       );
            is( $wabahsp->query->end,             shift @hsp , 'end'         );
            is( $wabahsp->strand('query'),        shift @hsp , 'strand'      );
            is( $wabahsp->start('hit'),           shift @hsp , 'start'       );
            is( $wabahsp->end('subject'),         shift @hsp , 'end'         );
            is( $wabahsp->subject->strand,        shift @hsp, 'strand'       );
            is( length( $wabahsp->query_string ), $wabahsp->length('total') , 'query string');
            is( length( $wabahsp->hit_string ),   $wabahsp->length('total') , 'hit_string'  );
            is( length( $wabahsp->hmmstate_string ),
                $wabahsp->length('total') , 'hmmstate string');
            my $hs = $wabahsp->hit_string;
            is( $wabahsp->gaps('hit'), $hs =~ tr/\-// );
            my $qs = $wabahsp->query_string;
            is( $wabahsp->gaps('query'), $qs =~ tr/\-// );
            is( sprintf( "%.1f", $wabahsp->percent_identity ), shift @hsp );
        }
    }
}
BioPerl-1.007002/t/SearchIO/wise.t000444000766000024       203013155576321 16543 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_wise.t 11733 2007-10-26 18:22:10Z jason $

use strict;

BEGIN {
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 20);
	
    use_ok('Bio::SearchIO');
}

my $parser = Bio::SearchIO->new(-file => test_input_file('genewise.out'),
			    -format   => 'wise',
			    -wisetype => 'genewise');
my $result = $parser->next_result;
my $hit = $result->next_hit;
is($result->query_name, 'SINFRUP00000067802');
is($hit->name, 'Scaffold_2042.1');

is($hit->score, 2054.68);
my $hsp = $hit->next_hsp;

is($hsp->query->start,22265);
is($hsp->query->end,22396);
is($hsp->query->strand,1);
is($hsp->query->score, 2054.68);

is($hsp->hit->start,1);
is($hsp->hit->end,44);
is($hsp->hit->strand,0);
is($hsp->hit->score, 2054.68);

$hsp = $hit->next_hsp;

is($hsp->query->start,24224);
is($hsp->query->end,24328);

is($hsp->hit->start,45);
is($hsp->hit->end,79);

$hsp = $hit->next_hsp;

is($hsp->query->start,24471);
is($hsp->query->end,24513);

is($hsp->hit->start,80);
is($hsp->hit->end,93);
BioPerl-1.007002/t/SearchIO/Writer000755000766000024          013155576321 16533 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/SearchIO/Writer/GbrowseGFF.t000444000766000024       121513155576321 21007 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 4);
	
    use_ok('Bio::SearchIO');
}

my $in = Bio::SearchIO->new(-format => 'blast',
			    -file   => test_input_file('brassica_ATH.WUBLASTN'));

my $outfile = test_output_file();

my $out = Bio::SearchIO->new(-output_format  => 'GbrowseGFF',
			    -prefix => 'Sequence',
			    -output_cigar   => 1,
			    -output_signif  => 1,
			    -file           => ">$outfile");
ok($out);
while( my $r = $in->next_result ) {
    ok($out->write_result($r));
}

ok(-s $outfile);

# tests checking file output?
BioPerl-1.007002/t/SearchIO/Writer/HSPTableWriter.t000555000766000024       203113155576321 21653 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 8);
    
    use_ok('Bio::SearchIO');
    use_ok('Bio::SearchIO::Writer::HSPTableWriter');
}

my ($searchio, $result, $hit, $hsp);

$searchio = Bio::SearchIO->new('-format' => 'blast',
    '-file'   => test_input_file('HUMBETGLOA.tblastx'));

$result = $searchio->next_result;

isa_ok($result,'Bio::Search::Result::ResultI');
$hit = $result->next_hit;
is($hit->accession, 'AE000479');
is($hit->bits, 33.6);
$hsp = $hit->next_hsp;
is($hit->hsp->bits,$hsp->bits);
isa_ok($hsp->get_aln,'Bio::Align::AlignI');

my $writer = Bio::SearchIO::Writer::HSPTableWriter->new(
-columns => [qw(
    query_name
    query_length
    hit_name
    hit_length
    rank
    frac_identical_query
    expect
    )]  );    

my $outfile = test_output_file();
my $out = Bio::SearchIO->new(-writer => $writer,
             -file   => ">$outfile");
$out->write_result($result, 1);
ok(-s $outfile);

# tests checking file output?
BioPerl-1.007002/t/SearchIO/Writer/HTMLWriter.t000444000766000024       177413155576321 21027 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_HTMLWriter.t 14995 2008-11-16 06:20:00Z cjfields $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 8);
    
    use_ok('Bio::SearchIO');
    use_ok('Bio::SearchIO::Writer::HTMLResultWriter');
}

my ($searchio, $result,$iter,$hit,$hsp);

$searchio = Bio::SearchIO->new('-format' => 'blast',
                   '-file'   => test_input_file('HUMBETGLOA.tblastx'));

$result = $searchio->next_result;

isa_ok($result,'Bio::Search::Result::ResultI');
$hit = $result->next_hit;
is($hit->accession, 'AE000479');
is($hit->bits, 33.6);
$hsp = $hit->next_hsp;
is($hit->hsp->bits,$hsp->bits);
isa_ok($hsp->get_aln,'Bio::Align::AlignI');

my $outfile = test_output_file();
my $writerhtml = Bio::SearchIO::Writer::HTMLResultWriter->new();
my $outhtml = Bio::SearchIO->new(-writer => $writerhtml,
                -file   => ">$outfile");
$outhtml->write_result($result, 1);
ok(-s $outfile);

# tests checking HTML file output?
BioPerl-1.007002/t/SearchIO/Writer/HitTableWriter.t000444000766000024       233713155576321 21753 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_HitTableWriter.t 14995 2008-11-16 06:20:00Z cjfields $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 8);
    
    use_ok('Bio::SearchIO');
    use_ok('Bio::SearchIO::Writer::HitTableWriter');
}

my ($searchio, $result, $hit, $hsp);

$searchio = Bio::SearchIO->new('-format' => 'blast',
    '-file'   => test_input_file('HUMBETGLOA.tblastx'));

$result = $searchio->next_result;

isa_ok($result,'Bio::Search::Result::ResultI');
$hit = $result->next_hit;
is($hit->accession, 'AE000479');
is($hit->bits, 33.6);
$hsp = $hit->next_hsp;
is($hit->hsp->bits,$hsp->bits);
isa_ok($hsp->get_aln,'Bio::Align::AlignI');

my $writer = Bio::SearchIO::Writer::HitTableWriter->new( 
    -columns => [qw(query_name
                    query_length
                    hit_name
                    hit_length
                    bits
                    score
                    frac_identical_query
                    expect
                    )]  );

my $outfile = test_output_file();
my $out = Bio::SearchIO->new(-writer => $writer,
             -file   => ">$outfile");
$out->write_result($result, 1);
ok(-s $outfile);

# tests checking file output?
BioPerl-1.007002/t/SearchIO/Writer/TextWriter.t000444000766000024       175413155576321 21205 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SearchIO_HTMLWriter.t 14995 2008-11-16 06:20:00Z cjfields $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 8);
    
    use_ok('Bio::SearchIO');
    use_ok('Bio::SearchIO::Writer::TextResultWriter');
}

my ($searchio, $result,$iter,$hit,$hsp);

$searchio = Bio::SearchIO->new('-format' => 'blast',
                   '-file'   => test_input_file('HUMBETGLOA.tblastx'));

$result = $searchio->next_result;

isa_ok($result,'Bio::Search::Result::ResultI');
$hit = $result->next_hit;
is($hit->accession, 'AE000479');
is($hit->bits, 33.6);
$hsp = $hit->next_hsp;
is($hit->hsp->bits,$hsp->bits);
isa_ok($hsp->get_aln,'Bio::Align::AlignI');

my $outfile = test_output_file();
my $writertxt = Bio::SearchIO::Writer::TextResultWriter->new();
my $outtxt = Bio::SearchIO->new(-writer => $writertxt,
				 -file   => ">$outfile");
$outtxt->write_result($result, 1);
ok(-s $outfile);
# tests checking Text file output?
BioPerl-1.007002/t/Seq000755000766000024          013155576321 14352 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Seq/DBLink.t000444000766000024       242113155576321 15776 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 131);
	
    use_ok('Bio::SeqIO');
}

my @genbank_files = qw/BK000016-tpa.gbk ay116458.gb ay149291.gb NC_006346.gb ay007676.gb dq519393.gb P35527.gb/;

# bug 2152
#------------------------------------
my $verbose = test_debug();
for my $in ( @genbank_files ) {
    my $infile = test_input_file($in);
    my $seqio = Bio::SeqIO->new(
                            -format  =>'genbank',
                            -verbose => $verbose,
                            -file    => $infile,
    );
    my $seq = $seqio->next_seq;
    my @values = $seq->annotation->get_Annotations('dblink');
    foreach my $value (@values) {
        my $output = $value->display_text;
        ok(defined $output, '"'.$output . '"');          # check value is not empty
        ok(index($output,'::') < 0       , 'no double colon'  );  # these tests seems silly
        ok( substr($output,-1) ne ':'    , 'no trailing colon');  #    but all have been known to occur
        ok(index($output,'  ') < 0       , 'no double space'  );  #
        my @parts = split(/:/,$output, 2);
        ok( scalar(@parts) == 2, 'dblink value is splittable');
    }
}
#------------------------------------
BioPerl-1.007002/t/Seq/EncodedSeq.t000444000766000024       365613155576321 16720 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 37);

    use_ok('Bio::Seq::EncodedSeq');
}


my ($str, $aln, $seq, $loc);

ok $seq = Bio::Seq::EncodedSeq->new(
                 -seq    => '--atg---gta--',
                 -start  => 1,
                 -end    => 6,
                 -strand => 1
                 );
is $seq->alphabet, 'dna';
is $seq->start, 1;
is $seq->end, 6;
is $seq->strand, 1;
is $seq->num_gaps, 1;
is $seq->column_from_residue_number(4), 9;

# this should fail
eval {
    $seq->column_from_residue_number(8);
};
ok $@;

ok $loc = $seq->location_from_column(4);
isa_ok $loc, 'Bio::Location::Simple';
is $loc->to_FTstring, "2";

ok $loc = $seq->location_from_column(6);
isa_ok $loc,'Bio::Location::Simple';
is $loc->start, 3;
is $loc->location_type, 'IN-BETWEEN';
is $loc->to_FTstring, '3^4';

is $loc = $seq->location_from_column(2), undef;

is $seq->encoding, "GGCCCGGGCCCGG";
is $seq->encoding(-explicit => 1), "GGCDEGGGCDEGG";

ok $seq = Bio::Seq::EncodedSeq->new(
                 -seq    => 'atcgta',
                 -start  => 10,
                 -end    => 15,
                 -strand => -1,
                 );
is $seq->encoding('CCGGG'), 'CCGGGCCCC';
is $seq->seq, 'atcg---ta';
is $seq->column_from_residue_number(14), 2;
is $seq->encoding('3C2GCG'), 'CCCGGCGCC';
is $seq->seq, 'at-c--gta';
is $seq->num_gaps, 2;
is $seq->location_from_column(2)->to_FTstring, 14;
is $seq->location_from_column(5)->to_FTstring, "12^13";
is $seq->encoding("B", Bio::Location::Simple->new(-start => 10, -end => 11,
                          -location_type => 'IN-BETWEEN')), 'B';
is $seq->seq, 'at-c--gt-a';
is $seq->encoding, 'CBCCGGCGCC';
is $seq->cds(-nogaps => 1)->seq, 'tacgat';
is $seq->translate->seq, 'YD';
ok $seq = $seq->trunc(4,10); # kinda testing LocatableSeq's new trunc() here as well.
is $seq->seq, 'c--gt-a';
is $seq->encoding, 'CBCCGGC';
BioPerl-1.007002/t/Seq/LargeLocatableSeq.t000444000766000024        77513155576321 20177 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 8);
	
	use_ok('Bio::Seq::LargeLocatableSeq');
}

ok my $llseq  = Bio::Seq::LargeLocatableSeq->new(-seq => 'at-cg',
                                                 -display_id => 'seq1');

isa_ok $llseq, "Bio::Seq::LargeSeqI";

is $llseq->seq, 'at-cg';
is $llseq->add_sequence_as_string('atcc'), 9;

is $llseq->start, 1;

is $llseq->end, 8;
is $llseq->length, 9;
BioPerl-1.007002/t/Seq/LargePSeq.t000444000766000024       564213155576321 16526 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 30);
	
	use_ok('Bio::Seq::LargePrimarySeq');
	use_ok('Bio::Seq::LargeSeq');
	use_ok('Bio::Location::Simple');
	use_ok('Bio::Location::Fuzzy');
	use_ok('Bio::Location::Split');
	use_ok('Bio::SeqIO');
}

my $pseq = Bio::Seq::LargePrimarySeq->new();
ok $pseq;
$pseq->add_sequence_as_string('ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAAT');
$pseq->add_sequence_as_string('GTTTGGGGTTAAACCCCTTTGGGGGGT');

is $pseq->display_id('hello'), 'hello';

is $pseq->seq, 'ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT' , "Sequence is " . $pseq->seq;

is $pseq->subseq(3,7), 'GGGGT', "Subseq is ".$pseq->subseq(3,7);
my $location = Bio::Location::Simple->new(-start => 4, -end => 8,
					 -strand => 1);
is($pseq->subseq($location), 'GGGTG');

my $splitlocation = Bio::Location::Split->new();

$splitlocation->add_sub_Location( Bio::Location::Simple->new('-start' => 1,
							    '-end'   => 15,
							    '-strand' => 1));

$splitlocation->add_sub_Location( Bio::Location::Simple->new('-start' => 21,
							    '-end'   => 27,
							    '-strand' => -1));

is( $pseq->subseq($splitlocation), 'ATGGGGTGGGGTGAACCCCCAA');

my $fuzzy = Bio::Location::Fuzzy->new(-start => '<10',
				     -end   => '18',
				     -strand => 1);

is( $pseq->subseq($fuzzy), 'GGTGAAACC');


is($pseq->trunc(8,15)->seq, 'GGGGTGAA',
    'trunc seq was ' . $pseq->trunc(8,15)->seq);


is $pseq->alphabet('dna'), 'dna'; # so translate will not complain
is $pseq->translate()->seq, 'MGWGETLWGWGKCLGLNPFGG';


my $seq = Bio::Seq::LargeSeq->new(-primaryseq => $pseq );

is $seq->display_id('hello'), 'hello';

is $seq->seq, 'ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT' , "Sequence is " . $seq->seq;

# test SeqIO::fasta (allows LargeSeqI; bug 2490)

SKIP: {
    eval {require IO::String};
    skip "SeqIO output for LargeSeq requires IO::String", 2 if $@;
	my $str;
	my $strobj = IO::String->new($str);
	my $out = Bio::SeqIO->new(-fh => $strobj, -format => 'fasta');
    ok($out->write_seq($seq));
	like($str, qr/>hello\nATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGG\nGGGT/,
		 'output via Bio::SeqIO::fasta');
}						  

is $seq->subseq(3,7), 'GGGGT', "Subseq is ".$seq->subseq(3,7);
is ($seq->trunc(8,15)->seq, 'GGGGTGAA', 
    'trunc seq was ' . $seq->trunc(8,15)->seq);

is $seq->alphabet('dna'), 'dna'; # so translate will not complain
is $seq->translate()->seq, 'MGWGETLWGWGKCLGLNPFGG';

$seq = Bio::Seq::LargeSeq->new( -display_id => 'hello');
$seq->seq('ATGGGGTGGGGT');
is $seq->display_id, 'hello';

is $seq->seq, 'ATGGGGTGGGGT' , "Sequence is " . $seq->seq;

is $seq->subseq(3,7), 'GGGGT', "Subseq is ".$seq->subseq(3,7);
is ($seq->trunc(8,12)->seq, 'GGGGT', 
    'trunc seq was ' . $seq->trunc(8,12)->seq);

is $seq->alphabet('dna'), 'dna'; # so translate will not complain
is $seq->translate()->seq, 'MGWG';
BioPerl-1.007002/t/Seq/LocatableSeq.t000444000766000024      2051413155576321 17255 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 119);

    use_ok('Bio::LocatableSeq');
    use_ok('Bio::AlignIO');
}

my ($str, $aln, $seq, $loc);

# basic tests

ok $seq = Bio::LocatableSeq->new(
                 -seq => '--atg---gta--',
                 -strand => 1,
                 -alphabet => 'dna'
                 );
is $seq->alphabet, 'dna';
is $seq->start, 1;
is $seq->end, 6;
is $seq->strand, 1;
is $seq->num_gaps, 1;
is $seq->column_from_residue_number(4), 9;
is $seq->column_from_residue_number(3), 5;

ok $loc = $seq->location_from_column(4);
isa_ok $loc,'Bio::Location::Simple';
is $loc->to_FTstring, 2;

ok $loc = $seq->location_from_column(6);
isa_ok $loc,'Bio::Location::Simple';
is $loc->start, 3;
is $loc->location_type, 'IN-BETWEEN';
is $loc->to_FTstring, '3^4';

is $loc = $seq->location_from_column(2), undef;
TODO: {
  local $TODO = "Need to fix columns before start of seq w/ start > 1";
  $seq->start(90);
  is $loc = $seq->location_from_column(2), undef;
}

$str = Bio::AlignIO->new(-file=> test_input_file('testaln.pfam'));
ok defined($str);
isa_ok $str,'Bio::AlignIO';
$aln = $str->next_aln();
ok $seq = $aln->get_seq_by_pos(1);
is ref($seq), 'Bio::LocatableSeq';

is $seq->get_nse, '1433_LYCES/9-246';
is $seq->id, '1433_LYCES';

# test invalid sequence

throws_ok{ $seq = Bio::LocatableSeq->new( -seq => '//!\\' ) } qr/.+/;

# test revcom and trunc

$seq = Bio::LocatableSeq->new(
                 -seq => '--atg---gta--',
                 -strand => 1,
                 -alphabet => 'dna'
                 );

my $seq2 = $seq->trunc(1,9);
is $seq2->seq, '--atg---g';
is $seq2->start, 1;
is $seq2->end, 4;
is $seq2->strand, $seq->strand;

$seq2 = $seq->trunc(3,8);
is $seq2->seq, 'atg---';
is $seq2->start, 1;
is $seq2->end, 3;

is $seq->strand(-1), -1;
is $seq->start, 1;
is $seq->end, 6;
$seq2 = $seq->trunc(3,8);
is $seq2->seq, 'atg---';
is $seq2->start, 4;
is $seq2->end, 6;
$seq2 = $seq->revcom();
is $seq2->seq, '--tac---cat--';
is $seq2->start, $seq->start;
is $seq2->end, $seq->end;
is $seq2->strand, $seq->strand * -1;
is $seq2->column_from_residue_number(4), 9;
is $seq2->column_from_residue_number(3), 5;

# test column-mapping for -1 strand sequence
$seq = Bio::LocatableSeq->new(
                 -seq => '--atg---gtaa-',
                 -strand => -1,
                 -alphabet => 'dna'
                 );
is $seq->column_from_residue_number(5),5;
is $seq->column_from_residue_number(4),9;
ok $loc = $seq->location_from_column(4);
isa_ok $loc,'Bio::Location::Simple';
is $loc->to_FTstring, 6;
ok $loc = $seq->location_from_column(6);
isa_ok $loc,'Bio::Location::Simple';
is $loc->start, 4;
is $loc->location_type, 'IN-BETWEEN';
is $loc->to_FTstring, '4^5';


# more tests for trunc() with strand -1


ok $seq = Bio::LocatableSeq->new(
                 -seq => '--atg---gta--',
                 -strand => -1,
                 -alphabet => 'dna'
                 );
is $seq->alphabet, 'dna';
is $seq->start, 1;
is $seq->end, 6;
is $seq->strand, -1;
is $seq->num_gaps, 1;
is $seq->column_from_residue_number(4), 5;


ok $seq2 = $seq->trunc(1,9);
is $seq2->seq, '--atg---g';
is $seq2->start, 3;
is $seq2->end, 6;
is $seq2->strand, $seq->strand;

is $seq->location_from_column(3)->start, 6;
is $seq->location_from_column(11)->start, 1;
is $seq->location_from_column(9)->start, 3;



ok $seq2 = $seq->trunc(7,12);
is $seq2->seq, '--gta-';
is $seq2->start, 1;
is $seq2->end, 3;


ok $seq2 = $seq->trunc(2,6);
is $seq2->seq, '-atg-';
is $seq2->start, 4;
is $seq2->end, 6;

ok $seq2 = $seq->trunc(4,7);
is $seq2->seq, 'tg--';
is $seq2->start, 4;
is $seq2->end, 5;

ok $seq = Bio::LocatableSeq->new();
is $seq->seq, undef;
is $seq->start, undef;
is $seq->end, undef;
my $nse;
eval{$nse = $seq->get_nse};
ok($@);
is ($nse, undef);
$seq->force_nse(1);
eval{$nse = $seq->get_nse};
ok(!$@);
is ($nse, '/0-0');

# test mapping

# mapping only supported for 1 => 1, 3 => 1, or 1 => 3 mapping relationships

eval{$seq = Bio::LocatableSeq->new(
                 -mapping => [40 => 2],
                 );};

ok($@);
like($@, qr/Mapping values other than 1 or 3 are not currently supported/);

eval{$seq = Bio::LocatableSeq->new(
                 -mapping => [3 => 3],
                 );};

ok($@);

# sequence is translated to protein, retains original DNA coordinates
# mapping is 1 residue for every 3 coordinate positions
$seq = Bio::LocatableSeq->new(
                 -seq => 'KKKAIDLVGVDKARENRQAIYLGASAIAEF',
                 -strand => -1,
                 -mapping => [1 => 3],
                 -start => 1,
                 -end => 90,
                 -alphabet => 'dna'
                 );

is $seq->seq, 'KKKAIDLVGVDKARENRQAIYLGASAIAEF';
is $seq->start, 1;
is $seq->end, 90;

# sequence is reverse-translated to DNA, retains original protein coordinates
# mapping is 3 residues for every 1 coordinate positions
$seq = Bio::LocatableSeq->new(
                 -seq => 'aaraaraargcnathgayytngtnggngtngayaargcnmgngaraaymgncargcnathtayytnggngcnwsngcnathgcngartty',
                 -strand => -1,
                 -mapping => [3 => 1],
                 -start => 1,
                 -end => 30,
                 -alphabet => 'protein'
                 );

is $seq->seq, 'aaraaraargcnathgayytngtnggngtngayaargcnmgngaraaymgncargcnathtayytnggngcnwsngcnathgcngartty';
is $seq->start, 1;
is $seq->end, 30;

# frameshifts (FASTA-like)
# support for this is preliminary
# this is a real example from a TFASTY report

$seq = Bio::LocatableSeq->new(
                 -seq => 'MGSSSTDRELLSAADVGRTVSRIAHQIIEKTALDDPAERTRVVLLGIPTRGVILATRLAAKIKEFAGEDVPHGALDITLYRDDLNFKPPRPLEATSIPAF\GGVDDAIVILVDDVLYSGRSVRSALDALRDIGRPRIVQLAVLVDRGHRELPI--/DYVGKNVPTSRSESVHVLLSEHDDRDGVVISK',
                 -strand => 1,
                 -mapping => [1 => 3],
                 -start => 1,
                 -end => 552,
                 -frameshifts => { # position, frameshift
                    298 => -1,
                    455 => 1
                    },
                 -alphabet => 'dna'
                 );

is $seq->seq, 'MGSSSTDRELLSAADVGRTVSRIAHQIIEKTALDDPAERTRVVLLGIPTRGVILATRLAAKIKEFAGEDVPHGALDITLYRDDLNFKPPRPLEATSIPAF\GGVDDAIVILVDDVLYSGRSVRSALDALRDIGRPRIVQLAVLVDRGHRELPI--/DYVGKNVPTSRSESVHVLLSEHDDRDGVVISK';
is $seq->start, 1;
is $seq->end, 552;
$seq->verbose(2);
eval { $seq->end(554);};
ok $@;
like $@, qr/Overriding value \[554\] with value 552/;

lives_ok { $seq = Bio::LocatableSeq->new(
                 -seq => 'LSYC*',
                 -strand => 0,
                 -start => 1,
                 -end => 5,
                 -verbose => 2
                 );} '* is counted in length';

throws_ok { $seq = Bio::LocatableSeq->new(
                 -seq => 'LSYC*',
                 -strand => 0,
                 -start => 1,
                 -end => 6,
                 -verbose => 2
                 );} qr/Overriding value \[6\] with value 5/, '* is counted in length, but end is wrong';

# setting symbols (class variables) - demonstrate scoping issues when using
# globals with and w/o localization.  To be fixed in a future BioPerl version

# see bug 2715
my $temp;

{
    $temp = $Bio::LocatableSeq::GAP_SYMBOLS;
    $Bio::LocatableSeq::GAP_SYMBOLS = '-\?';
    $seq = Bio::LocatableSeq->new(
                     -seq => '??atg-?-gta-?',
                     -strand => 1,
                     -start => 10,
                     -end => 15,
                     -alphabet => 'dna',
                     );
    is $Bio::LocatableSeq::GAP_SYMBOLS, '-\?';    
    is $seq->start, 10;
    is $seq->end, 15;
}

is $Bio::LocatableSeq::GAP_SYMBOLS, '-\?';
is $seq->end(15), 15;
$Bio::LocatableSeq::GAP_SYMBOLS = $temp;
is $Bio::LocatableSeq::GAP_SYMBOLS, '\-\.=~';

{
    local $Bio::LocatableSeq::GAP_SYMBOLS = '-\?';
    $seq = Bio::LocatableSeq->new(
                     -seq => '??atg-?-gta-?',
                     -strand => 1,
                     -start => 10,
                     -end => 15,
                     -alphabet => 'dna',
                     );
    is $Bio::LocatableSeq::GAP_SYMBOLS, '-\?';    
    is $seq->start, 10;
    is $seq->end, 15;
}

is $seq->end, 15;

# note, recalling the end() method uses old $GAP_SYMBOLS, which
# no longer are set (this argues for locally set symbols)
TODO: {
    local $TODO = 'Bio::LocatableSeq global variables have scoping issues';
    is $Bio::LocatableSeq::GAP_SYMBOLS, '-\?';
    # this should be 15 
    isnt $seq->end(19), 19;
}

BioPerl-1.007002/t/Seq/MetaSeq.t000444000766000024      1717613155576321 16267 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 132);
	
	use_ok('Bio::Seq::Meta');
	use_ok('Bio::Seq::Meta::Array');
	use_ok('Bio::SeqIO');
	use_ok('Bio::AlignIO');
	use_ok('Bio::Seq::Quality');
}

my $DEBUG = test_debug();

ok my $seq = Bio::Seq::Meta->new( -seq => "AT-CGATCGA");
is $seq->is_flush, 1;
is $seq->revcom->seq, 'TCGATCG-AT';
is $seq->meta, "";
ok $seq->force_flush(1);
is $seq->meta, "          ";
$seq->seq("AT-CGATCGATT");
is $seq->meta, "            ";
ok not $seq->force_flush(0);

ok $seq = Bio::Seq::Meta::Array->new( -seq => "AT-CGATCGA");
is $seq->is_flush, 1;
is $seq->revcom->seq, 'TCGATCG-AT';
is $seq->meta_text, "";
ok $seq->force_flush(1);
$seq->seq("AT-CGATCGATT");
is $seq->meta_text, "0 0 0 0 0 0 0 0 0 0 0 0";
ok not $seq->force_flush(0);

ok $seq = Bio::Seq::Quality->new( -seq => "AT-CGATCGA");
is $seq->meta_text, "";
ok $seq->force_flush(1);
is $seq->meta_text, "0 0 0 0 0 0 0 0 0 0";
$seq->seq("AT-CGATCGATT");
is $seq->meta_text, "0 0 0 0 0 0 0 0 0 0 0 0";
ok not $seq->force_flush(0);

ok $seq = Bio::Seq::Meta->new
    ( -seq => "",
      -meta => "",
      -alphabet => 'dna',
      -id => 'myid'
    );

# create a sequence object
ok $seq = Bio::Seq::Meta->new( -seq => "AT-CGATCGA",
                               -id => 'test',
                               -verbose => 2,
                               -force_flush => 1
                             );

is $seq->meta, "          ";
is $seq->meta_length, 10;

# Create some random meta values, but gap in the wrong place
my $metastring = "a-abb  bb ";
$seq->meta($metastring);
$seq->verbose(1);

# create some random meta values, but not for the last residue
$metastring = "aa-bb  bb";
ok $seq->meta($metastring), $metastring. " ";

# truncate the sequence by assignment
$seq->force_flush(1);
$seq->seq('AT-CGA');
$seq->alphabet('dna');
is $seq->meta, 'aa-bb ';
is $seq->start, 1;
is $seq->end, 5;
$seq->force_flush(0);

# truncate the sequence with trunc()
is $seq->strand(-1), -1;
ok $seq = $seq->trunc(1,5);
is $seq->start, 2;
is $seq->end, 5;
is $seq->seq, 'AT-CG';
is $seq->meta, 'aa-bb';
is $seq->strand, -1;

# revcom
ok $seq = $seq->revcom;
is $seq->seq, 'CG-AT';
is $seq->meta, 'bb-aa';
is $seq->strand, 1;

# submeta
is $seq->subseq(2,4), 'G-A';
is $seq->submeta(2,4), 'b-a';
is $seq->submeta(2,undef, 'c-c'), 'c-ca';
is $seq->submeta(2,4), 'c-c';
is $seq->meta, 'bc-ca';
is $seq->meta(''), '     ';
is $seq->submeta(2,undef, 'c-c'), 'c-c ';
is $seq->meta, ' c-c ';

# add named meta annotations

my $first = '11-22';
is $seq->named_meta('first', $first), $first;
is $seq->named_meta('first'), $first;

my $second = '[[-]]';
ok $seq->named_meta('second', $second);

# undefined range arguments
is $seq->named_submeta('second', 3, 4), '-]';
is $seq->named_submeta('second', 3), '-]]';
is $seq->named_submeta('second'), '[[-]]';

my @names =  $seq->meta_names;
is @names, 3;
is $names[0], 'DEFAULT';



#
# IO tests
#

sub diff {
    my ($infile, $outfile) = @_;
    my ($in, $out);
    open my $FH_IN, '<', $infile or die "Could not read file '$infile': $!\n";
    $in .= $_ while (<$FH_IN>);
    close $FH_IN;

    open my $FH_OUT, '<', $outfile or die "Could not read file '$outfile': $!\n";
    $out .= $_ while (<$FH_OUT>);
    close $FH_OUT;
    print "|$in||$out|\n" if $DEBUG;
    is $in, $out;
}


# SeqIO
my $str = Bio::SeqIO->new
    ( '-file'=> test_input_file('test.metafasta'),
      '-format' => 'metafasta');
ok  $seq = $str->next_seq;

my $outfile = test_output_file();
my $strout = Bio::SeqIO->new
    ('-file'=> ">". $outfile,
     '-format' => 'metafasta');
ok $strout->write_seq($seq);

diff (test_input_file('test.metafasta'),
      $outfile
     );

# AlignIO

$str = Bio::AlignIO->new
    ( '-file'=> test_input_file('testaln.metafasta'),
      '-format' => 'metafasta');
ok my $aln = $str->next_aln;

$outfile = test_output_file();
$strout = Bio::AlignIO->new
    ('-file'=> ">". $outfile,
     '-format' => 'metafasta');
ok $strout->write_aln($aln);

diff (test_input_file('testaln.metafasta'),
      $outfile
     );

#
##
### tests for Meta::Array
##
#

ok $seq = Bio::Seq::Meta::Array->new
    ( -seq => "",
      -meta => "",
      -alphabet => 'dna',
      -id => 'myid'
    );

# create a sequence object
ok $seq = Bio::Seq::Meta::Array->new( -seq => "AT-CGATCGA",
                                      -id => 'test',
                                      -force_flush => 1,
                                      -verbose => 2
                             );

is $seq->is_flush, 1;
#is $seq->meta_text, "          ";
is $seq->meta_text, '0 0 0 0 0 0 0 0 0 0';

# create some random meta values, but not for the last residue
$metastring = "a a - b b 0 b b 0";
is join (' ',  @{$seq->meta($metastring)}), $metastring. ' 0';
is $seq->meta_text, $metastring. ' 0';

# truncate the sequence by assignment
$seq->seq('AT-CGA');
$seq->alphabet('dna');
is $seq->meta_text, 'a a - b b 0';

# truncate the sequence with trunc()
is $seq->strand(-1), -1;
ok $seq = $seq->trunc(1,5);
is $seq->seq, 'AT-CG';
is $seq->meta_text, 'a a - b b';
is $seq->strand, -1;

#is $seq->length, 5;
#is $seq->meta_length, 6;
#ok $seq->force_flush(1);
#is $seq->meta_length, 5;

# revcom
ok $seq = $seq->revcom;
is $seq->seq, 'CG-AT';
is $seq->meta_text, 'b b - a a';
is $seq->strand, 1;

# submeta

is $seq->subseq(2,4), 'G-A';

is $seq->submeta_text(2,4), 'b - a';
is $seq->submeta_text(2,undef, 'c - c'), 'c - c';
is $seq->submeta_text(2,4), 'c - c';
is $seq->meta_text, 'b c - c a';

is $seq->meta_text(''), '0 0 0 0 0';
is $seq->submeta_text(2,undef, 'c - c'), 'c - c';
is $seq->meta_text, '0 c - c 0';

# add named meta annotations
$first = '1 10 - 222 23';
is $seq->named_meta_text('first', $first), $first;
is $seq->named_meta_text('first'), $first;
$second = '[ [ - ] ]';
ok $seq->named_meta_text('second', $second);

# undefined range arguments
is $seq->named_submeta_text('second', 3, 4), '- ]';
is $seq->named_submeta_text('second', 3), '- ] ]';
is $seq->named_submeta_text('second'), '[ [ - ] ]';

@names =  $seq->meta_names;
is @names, 3;
is $names[0], 'DEFAULT';




#
# testing the forcing of flushed meta values
#




ok $seq = Bio::Seq::Meta->new( -seq =>  "AT-CGATCGA",
                                  -id => 'test',
                                  -verbose => 2
                             );
is $seq->submeta(4, 6, '456'), '456';
is $seq->meta_length, 6;
is $seq->length, 10;

is $seq->meta, "   456";

ok $seq->force_flush(1);
is $seq->meta, "   456    ";
ok $seq->seq('aaatttc');
is $seq->meta, "   456 ";

ok $seq = Bio::Seq::Meta::Array->new( -seq =>  "AT-CGATCGA",
                                  -id => 'test',
                                  -verbose => 2
                             );
is join (' ', @{$seq->submeta(4, 6, '4 5 6')}), '4 5 6';
is $seq->meta_length, 6;
is $seq->length, 10;

is $seq->meta_text, "0 0 0 4 5 6";
ok $seq->force_flush(1);
is $seq->meta_text, "0 0 0 4 5 6 0 0 0 0";

ok $seq->seq('aaatttc');
is $seq->meta_text, "0 0 0 4 5 6 0";
is $seq->meta_length, 7;


ok  $seq = Bio::Seq::Quality->new( -seq =>  "AT-CGATCGA",
                                  -id => 'test',
                                  -verbose => 2
                             );
is join (' ', @{$seq->submeta(4, 6, '4 5 6')}), '4 5 6';
is $seq->meta_length, 6;
is $seq->length, 10;

is $seq->meta_text, "0 0 0 4 5 6";

ok $seq->force_flush(1);

is $seq->meta_text, "0 0 0 4 5 6 0 0 0 0";

ok $seq->seq('aaatttc');
is $seq->meta_text, "0 0 0 4 5 6 0";
is $seq->meta_length, 7;
is $seq->trace_length, 7;
#is $seq->quality_length, 7;

is $seq->is_flush, 1;
is $seq->trace_is_flush, 1;
is $seq->quality_is_flush, 1;

# quality: trace_lengths, trace_is_flush, quality_is_flush
BioPerl-1.007002/t/Seq/PrimaryQual.t000444000766000024      1024213155576321 17161 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 70);

    use_ok('Bio::SeqIO');
    use_ok('Bio::Seq::Quality');
    use_ok('Bio::Seq::PrimaryQual');
}

my $DEBUG = test_debug();
my $verbose = -1 unless $DEBUG;

# redirect STDERR to STDOUT
open (STDERR, ">&STDOUT");

my $string_quals = "10 20 30 40 50 40 30 20 10";
print("Quals are $string_quals\n") if($DEBUG);
ok my $qualobj = Bio::Seq::PrimaryQual->new(
    -qual             => $string_quals,
    -id               => 'QualityFragment-12',
    -accession_number => 'X78121',
);
is $qualobj->display_id, 'QualityFragment-12';
is $qualobj->accession_number, 'X78121';

my @q2 = split / /, $string_quals;
$qualobj = Bio::Seq::PrimaryQual->new(
    -qual             => \@q2,
    -primary_id       => 'chads primary_id',
    -desc             => 'chads desc',
    -accession_number => 'chads accession_number',
    -id               => 'chads id',
    -header           => 'chads header'
);

is $qualobj->primary_id, 'chads primary_id';
isa_ok $qualobj->qual(), 'ARRAY';

my $newqualstring = "50 90 1000 20 12 0 0";

ok $qualobj->qual($newqualstring);
is join(' ', @{$qualobj->qual()}), $newqualstring;

my @newqualarray = split / /,$newqualstring;
ok $qualobj->qual(\@newqualarray);
is join(' ', @{$qualobj->qual()}), $newqualstring;

is $qualobj->validate_qual($string_quals ), 1;
is $qualobj->validate_qual(""            ), 1;
is $qualobj->validate_qual("0"           ), 1;
is $qualobj->validate_qual(undef         ), 1;
is $qualobj->validate_qual("   "         ), 1;
is $qualobj->validate_qual("10 20 30 30" ), 1;
is $qualobj->validate_qual(" 20  9 5   " ), 1;
is $qualobj->validate_qual("+1 9.3 50e-1"), 1;
is $qualobj->validate_qual(" 4"          ), 1;
is $qualobj->validate_qual("chad"        ), 0;
is $qualobj->validate_qual("10 one"      ), 0;

ok $qualobj->qual("10 20 30 30");
ok $qualobj->qual("+1 9.3 50e-1");
throws_ok { $qualobj->qual("chad"); } qr/.+/;
throws_ok { $qualobj->validate_qual("chad", 1) } qr/.+/;

ok $qualobj->qual("4 10");
is $qualobj->length(), 2;

$qualobj->qual("10 20 30 40 50 40 30 20 10");
ok my @subquals = @{$qualobj->subqual(3,6);};
is @subquals, 4;
is "30 20 10", join(' ',@{$qualobj->subqual(7,9)});

throws_ok { $qualobj->subqual(-1,6); } qr/EX/;
ok $qualobj->subqual(1,6);
ok $qualobj->subqual(1,9);
throws_ok { $qualobj->subqual(9,1); } qr/EX/;


is $qualobj->display_id(), "chads id";
is $qualobj->display_id("chads new display_id"), "chads new display_id";
is $qualobj->display_id(), "chads new display_id";

is $qualobj->accession_number(), "chads accession_number";
is $qualobj->accession_number("chads new accession_number"), "chads new accession_number";
is $qualobj->accession_number(), "chads new accession_number";
is $qualobj->primary_id(), "chads primary_id";
is $qualobj->primary_id("chads new primary_id"), "chads new primary_id";
is $qualobj->primary_id(), "chads new primary_id";

is $qualobj->desc(), "chads desc";
is $qualobj->desc("chads new desc"), "chads new desc";
is $qualobj->desc(), "chads new desc";
is $qualobj->display_id(), "chads new display_id";
is $qualobj->display_id("chads new id"), ("chads new id");
is $qualobj->display_id(), "chads new id";

is $qualobj->header(), "chads header";

ok my $in_qual  = Bio::SeqIO->new(
    -file    => test_input_file('qualfile.qual'),
    -format  => 'qual',
    -verbose => $verbose,
);
ok my $pq = $in_qual->next_seq();
is $pq->qual()->[99] , '39'; # spot check boundary
is $pq->qual()->[100], '39'; # spot check boundary

ok my $out_qual = Bio::SeqIO->new(
    -file    => ">".test_output_file(),
    -format  => 'qual',
    -verbose => $verbose,
);
ok $out_qual->write_seq(-source => $pq);

ok my $swq545 = Bio::Seq::Quality->new (
    -seq  => "ATA",
    -qual => $pq
);
ok $out_qual->write_seq(-source => $swq545);

ok $in_qual = Bio::SeqIO->new(
    -file    => test_input_file('qualfile.qual'),
    -format  => 'qual',
    -verbose => $verbose,
);

ok my $out_qual2 = Bio::SeqIO->new(
    -file    => ">".test_output_file(),
    -format  => 'qual',
    -verbose => $verbose,
);

while ( my $batch_qual = $in_qual->next_seq() ) {
    ok $out_qual2->write_seq(-source => $batch_qual);
}

BioPerl-1.007002/t/Seq/PrimarySeq.t000444000766000024      7577313155576321 17033 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;
use Data::Dumper;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    test_begin( -tests => 312 );

    use_ok('Bio::PrimarySeq');
    use_ok('Bio::Location::Simple');
    use_ok('Bio::Location::Fuzzy');
    use_ok('Bio::Location::Split');
}


# Bare object
ok my $seq = Bio::PrimarySeq->new(), 'Bare object';
isa_ok $seq, 'Bio::PrimarySeqI';
is $seq->id, undef;
is $seq->seq, undef;
is $seq->length, 0;
is $seq->alphabet, undef;
is $seq->is_circular, undef;


# Empty sequence
ok $seq = Bio::PrimarySeq->new( -seq => '', -nowarnonempty => 1);
is $seq->seq, '';
is $seq->length, 0;
is $seq->alphabet, undef;


# Basic tests
ok $seq = Bio::PrimarySeq->new(
    '-seq'              => 'TTGGTGGCGTCAACT',
    '-display_id'       => 'new-id',
    '-alphabet'         => 'dna',
    '-accession_number' => 'X677667',
    '-desc'             => 'Sample Bio::Seq object'
);
ok defined $seq;
is $seq->accession_number(), 'X677667';
is $seq->seq(),              'TTGGTGGCGTCAACT';
is $seq->display_id(),       'new-id';
is $seq->alphabet(),         'dna';
is $seq->is_circular(),      undef;
ok $seq->is_circular(1);
is $seq->is_circular(0),     0;

# check IdentifiableI and DescribableI interfaces
isa_ok $seq, 'Bio::IdentifiableI';
isa_ok $seq, 'Bio::DescribableI';

# make sure all methods are implemented
is $seq->authority("bioperl.org"), "bioperl.org";
is $seq->authority, "bioperl.org";
is $seq->namespace("t"), "t";
is $seq->namespace, "t";
is $seq->version(0), 0;
is $seq->version, 0;
is $seq->lsid_string(), "bioperl.org:t:X677667";
is $seq->namespace_string, "t:X677667.0";
is $seq->version(47), 47;
is $seq->version, 47;
is $seq->namespace_string, "t:X677667.47";
is $seq->description, 'Sample Bio::Seq object';
is $seq->display_name, "new-id";


# Test subseq
is $seq->subseq(2, 5), 'TGGT';

is $seq->subseq( -start => 1, -end => 15), 'TTGGTGGCGTCAACT';

my $location = Bio::Location::Simple->new(
    '-start'  => 2,
    '-end'    => 5,
    '-strand' => -1
);
is $seq->subseq($location), 'ACCA';

my $splitlocation = Bio::Location::Split->new();
$splitlocation->add_sub_Location(
    Bio::Location::Simple->new(
        '-start'  => 1,
        '-end'    => 4,
        '-strand' => 1
    )
);

$splitlocation->add_sub_Location(
    Bio::Location::Simple->new(
        '-start'  => 7,
        '-end'    => 12,
        '-strand' => -1
    )
);

is $seq->subseq($splitlocation), 'TTGGTGACGC';

my $fuzzy = Bio::Location::Fuzzy->new(
    -start  => '<3',
    -end    => '8',
    -strand => 1
);

is $seq->subseq($fuzzy), 'GGTGGC';

{
    ok my $seq = Bio::PrimarySeq->new( -seq => 'TT-GTGGCGTCAACT' );
    is $seq->subseq(2, 5, 'nogap'), 'TGT';
    is $seq->subseq( -start => 2, -end => 5, -nogap => 1 ), 'TGT';
    my $location = Bio::Location::Simple->new(
       '-start'  => 2,
       '-end'    => 5,
       '-strand' => 1
    );
    is $seq->subseq( $location, -nogap => 1), 'TGT';

    is $seq->subseq(-start=>2, -end=>5, -replace_with=>'aa'), 'T-GT';
    is $seq->seq, 'TaaGGCGTCAACT';

    throws_ok { $seq->subseq(-start=>2, -end=>5, -replace_with=>'?!'); } qr/.+/;
}

{
    ok my $seq = Bio::PrimarySeq->new( -seq => 'AACCGGTT', -is_circular => 1 );
    is $seq->subseq( -start => 7, -end => 10 ), 'TTAA';
}

### Test for Bug #2936
# Without strand input argument (case: user don't think is necessary)
my $split_loc_obj1 = Bio::Location::Split->new();
$split_loc_obj1->add_sub_Location(
    Bio::Location::Simple->new(
        '-start'  => 1,
        '-end'    => 10
    )
);
$split_loc_obj1->add_sub_Location(
    Bio::Location::Simple->new(
        '-start'  => 20,
        '-end'    => 30
    )
);
# With strand input argument (case: user provides the argument)
my $split_loc_obj2 = Bio::Location::Split->new();
$split_loc_obj2->add_sub_Location(
    Bio::Location::Simple->new(
        '-start'  => 1,
        '-end'    => 10,
        '-strand' => 1
    )
);
$split_loc_obj2->add_sub_Location(
    Bio::Location::Simple->new(
        '-start'  => 20,
        '-end'    => 30,
        '-strand' => 1
    )
);
is $split_loc_obj1->to_FTstring, "join(1..10,20..30)";
is $split_loc_obj2->to_FTstring, "join(1..10,20..30)";
$split_loc_obj1->flip_strand;
$split_loc_obj2->flip_strand;
is $split_loc_obj1->to_FTstring, "complement(join(1..10,20..30))";
is $split_loc_obj2->to_FTstring, "complement(join(1..10,20..30))";
###

# Test trunc
my $trunc = $seq->trunc( 1, 4 );
isa_ok $trunc, 'Bio::PrimarySeqI';
is $trunc->seq(), 'TTGG' or diag( "Expecting TTGG. Got " . $trunc->seq() );

$trunc = $seq->trunc($splitlocation);
isa_ok $trunc, 'Bio::PrimarySeqI' ;
is $trunc->seq(), 'TTGGTGACGC';

$trunc = $seq->trunc($fuzzy);
isa_ok $trunc, 'Bio::PrimarySeqI';
is $trunc->seq(), 'GGTGGC';

my $rev = $seq->revcom();
isa_ok $rev, 'Bio::PrimarySeqI';

is $rev->seq(), 'AGTTGACGCCACCAA'
  or diag( 'revcom() failed, was ' . $rev->seq() );

is $rev->display_id,         'new-id';
is $rev->display_name(),     'new-id';
is $rev->accession_number(), 'X677667';
is $rev->alphabet,           'dna';
is $rev->description,        'Sample Bio::Seq object';
is $rev->is_circular(),      0;
is $rev->version,            47;
is $rev->authority,          'bioperl.org';
is $rev->namespace,          't';
is $rev->namespace_string(), 't:X677667.47';

#
# Translate
#

my $aa = $seq->translate();    # TTG GTG GCG TCA ACT
is $aa->seq, 'LVAST', "Translation: " . $aa->seq;

# tests for non-standard initiator codon coding for
# M by making translate() look for an initiator codon and
# terminator codon ("complete", the 5th argument below)
$seq->seq('TTGGTGGCGTCAACTTAA');    # TTG GTG GCG TCA ACT TAA
$aa = $seq->translate( undef, undef, undef, undef, 1 );
is $aa->seq, 'MVAST', "Translation: " . $aa->seq;

# same test as previous, but using named parameter
$aa = $seq->translate( -complete => 1 );
is $aa->seq, 'MVAST', "Translation: " . $aa->seq;

# find ORF, ignore codons outside the ORF or CDS
$seq->seq('TTTTATGGTGGCGTCAACTTAATTT');    # ATG GTG GCG TCA ACT
$aa = $seq->translate( -orf => 1 );
is $aa->seq, 'MVAST*', "Translation: " . $aa->seq;

# smallest possible ORF
$seq->seq("ggggggatgtagcccc");             # atg tga
$aa = $seq->translate( -orf => 1 );
is $aa->seq, 'M*', "Translation: " . $aa->seq;

# same as previous but complete, so * is removed
$aa = $seq->translate(
    -orf      => 1,
    -complete => 1
);
is $aa->seq, 'M', "Translation: " . $aa->seq;

# ORF without termination codon
# should warn, let's change it into throw for testing
$seq->verbose(2);
$seq->seq("ggggggatgtggcccc");    # atg tgg ccc
eval { $seq->translate( -orf => 1 ); };
like( $@, qr/\batgtggccc\b/i );
$seq->verbose(-1);
$aa = $seq->translate( -orf => 1 );
is $aa->seq, 'MWP', "Translation: MWP";
$seq->verbose(0);

# use non-standard codon table where terminator is read as Q
$seq->seq('ATGGTGGCGTCAACTTAG');    # ATG GTG GCG TCA ACT TAG
$aa = $seq->translate( -codontable_id => 6 );
is $aa->seq, 'MVASTQ' or diag( "Translation: " . $aa->seq );

# insert an odd character instead of terminating with *
$aa = $seq->translate( -terminator => 'X' );
is $aa->seq, 'MVASTX' or diag( "Translation: " . $aa->seq );

# change frame from default
$aa = $seq->translate( -frame => 1 );    # TGG TGG CGT CAA CTT AG
is $aa->seq, 'WWRQL' or diag( "Translation: " . $aa->seq );

$aa = $seq->translate( -frame => 2 );    # GGT GGC GTC AAC TTA G
is $aa->seq, 'GGVNL' or diag( "Translation: " . $aa->seq );

# TTG is initiator in Standard codon table? Afraid so.
$seq->seq("ggggggttgtagcccc");           # ttg tag
$aa = $seq->translate( -orf => 1 );
is $aa->seq, 'L*' or diag( "Translation: " . $aa->seq );

# Replace L at 1st position with M by setting complete to 1
$seq->seq("ggggggttgtagcccc");           # ttg tag
$aa = $seq->translate(
    -orf      => 1,
    -complete => 1
);
is $aa->seq, 'M' or diag( "Translation: " . $aa->seq );

# Ignore non-ATG initiators (e.g. TTG) in codon table
$seq->seq("ggggggttgatgtagcccc");        # atg tag
$aa = $seq->translate(
    -orf      => 1,
    -start    => "atg",
    -complete => 1
);
is $aa->seq, 'M' or diag( "Translation: " . $aa->seq );

# test for character '?' in the sequence string
is $seq->seq('TTGGTGGCG?CAACT'), 'TTGGTGGCG?CAACT';

# issue #105 - when there are starts and stops in both frame 0 and
# frame 1, frame 0 start < frame 1 start, then should return the frame
# 0 ORF per the pod ('the first orf') even if frame 1 stop < frame 0 stop

# Turn off warnings for a few tests
my $verbosity = $seq->verbose();
$seq->verbose(-1);

$seq->seq('ATGAATGTAAATAA');
$aa = $seq->translate( -orf => 1 );
my $aa0 = $seq->translate(-frame => 0);

is $aa->seq, $aa0->seq, "frame 0 start, frame 1 stop < frame 0 stop";
$seq->seq('AAATGAATGTAAATAA');
$aa = $seq->translate( -orf => 1, -frame=>1 );
my $aa2 = $seq->translate(-frame => 2);
is $aa->seq, $aa2->seq, "frame 1 start, frame 2 stop < frame 1 stop";
# Turn 'em back on!
$seq->verbose($verbosity);

# test for some aliases
$seq = Bio::PrimarySeq->new(
    -id          => 'aliasid',
    -description => 'Alias desc'
);
is $seq->description, 'Alias desc';
is $seq->display_id,  'aliasid';

# Test alphabet

ok $seq->seq('actgx');
is $seq->alphabet, 'protein', 'Alphabet';
ok $seq->seq('actge');
is $seq->alphabet, 'protein';
ok $seq->seq('actgf');
is $seq->alphabet, 'protein';
ok $seq->seq('actgi');
is $seq->alphabet, 'protein';
ok $seq->seq('actgj');
is $seq->alphabet, 'protein';
ok $seq->seq('actgl');
is $seq->alphabet, 'protein';
ok $seq->seq('actgo');
is $seq->alphabet, 'protein';
ok $seq->seq('actgp');
is $seq->alphabet, 'protein';
ok $seq->seq('actgq');
is $seq->alphabet, 'protein';
ok $seq->seq('actgz');
is $seq->alphabet, 'protein';
ok $seq->seq('actgn');
is $seq->alphabet, 'dna';
ok $seq->seq('acugn');
is $seq->alphabet, 'rna';
ok $seq->seq('bdhkm');
is $seq->alphabet, 'protein';
ok $seq->seq('rsvwx');
is $seq->alphabet, 'protein';
ok $seq->seq('AAACTYAAAAGAATTGRCGG'); # valid degenerate DNA PCR primer sequence (90% ACGTN)
is $seq->alphabet, 'dna';
ok $seq->seq('AAACTYAAAKGAATTGRCGG'); # another primer previously detected as protein (85% ACGTN)
is $seq->alphabet, 'dna';
ok $seq->seq('YWACTYAAAKGARTTGRCGG'); # 70% ACGTNWSRM. Everything <= 70% is considered a protein
is $seq->alphabet, 'dna';
ok $seq->seq('XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX'); # Bug 2438
is $seq->alphabet, 'protein', 'Bug 2438';
ok $seq->seq('CAGTCXXXXXXXXXXXXXXXXXXXXXXXXXXXCAGCG');
is $seq->alphabet, 'protein';
ok $seq->seq('WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC'); # showed up on MAKER list
is $seq->alphabet, 'dna';

ok $seq->seq('actgn', 'protein'); # accept specified alphabet, no matter what
is $seq->alphabet, 'protein';
ok $seq->seq('bdhkm', 'dna');
is $seq->alphabet, 'dna';


# Bug #2864:

$seq = Bio::PrimarySeq->new( -display_id => 0, -seq => 'GATC' );

is $seq->display_id, 0, "Bug #2864";

# Test that the check for terminators inside the translated protein
# works when the terminator isn't '*':

$seq = Bio::PrimarySeq->new(-seq=>'ATGCTCTAAGCAGGGTAA'); # ML*AG*
eval { $aa = $seq->translate(-complete=>1, -throw=>1, -terminator=>'#') };
my $error = $@;
ok $error =~ /\QTerminator codon inside CDS!\E/, 'Terminator + inside sequence';

$seq = Bio::PrimarySeq->new(-seq=>'ATGCTCGCAGGGTAA'); # MLAG*
$aa = $seq->translate(-complete=>1, -throw=>1, -terminator=>'#');
is $aa->seq, 'MLAG';


# Test length method
ok $seq = Bio::PrimarySeq->new(), 'Length method';
is $seq->length, 0;
ok $seq->length(123);
is $seq->length, 123;

ok $seq = Bio::PrimarySeq->new( -seq => 'ATGCTCTAAGCAGGGTAA' );
is $seq->length, 18;
ok $seq->seq('ATGCTCTAAG');
is $seq->length, 10;
is $seq->seq(undef), undef;
is $seq->length, 0;

ok $seq = Bio::PrimarySeq->new( -length => 123 );
is $seq->length, 123;

ok $seq = Bio::PrimarySeq->new( -seq => 'ATGCTCTAAGCAGGGTAA' );
is $seq->length, 18;
ok $seq->length( $seq->length ); # save memory by removing seq
is $seq->seq( undef ), undef;    # ... but keeping a record of length
is $seq->length, 18;
is $seq->seq, undef;
ok $seq->seq('ACGT');
is $seq->length, 4; # manually-specified length changed when sequence is changed

throws_ok { $seq->length(666); } qr/.+/; # Cannot lie about length


# Sequence validation method
is $seq->validate_seq( undef    ), 1;
is $seq->validate_seq( ''       ), 1;
is $seq->validate_seq( 'acgt'   ), 1;
is $seq->validate_seq( 'ACGT'   ), 1;
is $seq->validate_seq( 'XFRH'   ), 1;
is $seq->validate_seq( '-~'     ), 1; # gap symbols
is $seq->validate_seq( '-.*?=~' ), 1; # other valid symbols
is $seq->validate_seq( '0'      ), 0;
is $seq->validate_seq( '   '    ), 0;
is $seq->validate_seq( 'AAAA$'  ), 0;
is $seq->validate_seq( 'tt&t!'  ), 0;

throws_ok { $seq->validate_seq('tt&t!', 1); } qr/.+/;


# Test direct option (no sequence validation)
throws_ok { $seq = Bio::PrimarySeq->new(-seq => 'A\T$AGQ+T'); } qr/.+/, 'Validation';
ok $seq = Bio::PrimarySeq->new( -seq => 'A\T$AGQ+T', -direct => 1 );
is $seq->seq, 'A\T$AGQ+T';
throws_ok { $seq->seq('NT@/') } qr/.+/;

# Set a sequence by reference
my $string = 'AAAACCCCGGGGTTTT';
ok $seq = Bio::PrimarySeq->new( -ref_to_seq => \$string );
is $seq->seq, 'AAAACCCCGGGGTTTT';


# Test internal PrimarySeqI _find_orfs function and translate( -orf => 'longest' )
{
    my @tests = (
        #tiny test
        ['TTTTATGGTGGCGTCAACTTAATTT',
         [[4,22,18,1]],
        ],

        #bigger test (this is a tomato unigene)
        ['GAAGGCTGGTTCTGAGTTGGATCTATGTTTGATGAAGGGAAGTAGACCGGAGGTCTTGCATCAGCAATATTAGTACCAAATCCAGGTGGAGGCGCATCCTGTCTCCGTTGCATTTCAACTTTCATTTCAGCAATCTGTTGCATCAGTTGCATGATCAATTCATTCTGTTCCACTACAGTGGGCTGAGCGACCACAACGTCAGTAAGACGCCCTTCGTCATTGTTGTCTCCCATAACTGTTTTTCCTTTATCTGAATTTGATCGAGGGAAGGAATCTGTAGGACCTTTCGATCTGGTGAAGTAAGGATGATCTGCCAGCTTTATTGACACAGATCAGTAAAAAGGTACCTGAAAGGTAAAAACAACTCAAAGGCAAATTTGTTAGTGCATATCCAGAGTACAAAATGCTTAATATCGCACATAAAACCGATAAACACACAAGTCGTTTTGTTTGAGGATATCTTAACCCACGAATAAGGACGGATATATATTTTGAACAAACAGGAATTTGTTTGTTTGGCGTTATCTTGGGAAATCTG',
         [[98,254,156,2],[347,476,129,2],[219,303,84,0],[16,73,57,1],[403,454,51,1],[310,358,48,1],[235,280,45,1],[491,536,45,2],[150,186,36,0],[507,537,30,0],[5,32,27,2],[511,538,27,1],[24,45,21,0],[305,326,21,2],[450,465,15,0]],
        ],


       );
    foreach my $test (@tests) {
        my ($test_seq, $orfs) = @$test;
        my @orfs = Bio::PrimarySeqI::_find_orfs_nucleotide(
            undef,
            $test_seq,
            Bio::Tools::CodonTable->new,
            undef,
           ); # ATG GTG GCG TCA ACT
        is_deeply( \@orfs, $orfs, '_find_orfs 1')
            or diag "for $test_seq, _find_orfs returned:\n"
                    .Dumper([map [@$_], @orfs]);

        is_deeply( $orfs->[0],
                   (sort {$b->[2] <=> $a->[2]} @$orfs)[0],
                   'orfs are sorted by descending length'
                  );

        # make sure we get the same sequence by taking the longest orf
        # nucleotide from the test data and translating it, as by
        # calling translate with -orf => 'longest'
        is(
            Bio::PrimarySeq
              ->new( -seq => $test_seq, -id => 'fake_id' )
              ->translate( -orf => 'longest' )
              ->seq,

            Bio::PrimarySeq
              ->new( -seq => substr( $test_seq, $orfs->[0][0], $orfs->[0][2] ),
                     -id => 'foo'
                    )
              ->translate
              ->seq,
            'got correct -orf => "longest" seq',
           );
    }
}

#####
# Extensive location and subsequence tests
ok $seq = Bio::PrimarySeq->new('-seq' => 'AAAAACCCCCGGGGGTTTTT',);
ok $seq->is_circular(1);

# NOTE: "_no_strand" variables tests the possibility that the user didn't set
# Strand for positive coordinates (or the object comes from
# Bio::Factory::FTLocationFactory->from_string)

# Single location
# Coordinates: 1..5 => AAAAA
# Revcom: complement(1..5) => TTTTT
ok my $loc1_strand    = Bio::Location::Simple->new('-start' => 1, '-end' => 5,'-strand' => 1);
ok my $loc1_no_strand = Bio::Location::Simple->new('-start' => 1, '-end' => 5);
is $seq->subseq($loc1_strand),    'AAAAA';
is $seq->subseq($loc1_no_strand), 'AAAAA';
is $loc1_strand->to_FTstring,     '1..5';
is $loc1_no_strand->to_FTstring,  '1..5';
$loc1_strand->flip_strand;
$loc1_no_strand->flip_strand;
is $seq->subseq($loc1_strand),    'TTTTT';
is $seq->subseq($loc1_no_strand), 'TTTTT';
is $loc1_strand->to_FTstring,     'complement(1..5)';
is $loc1_no_strand->to_FTstring,  'complement(1..5)';
is $loc1_strand->length,    5;
is $loc1_no_strand->length, 5;

# Basic split, both locations in positive strand
# Coords: join(6..10,16..20) => CCCCCTTTTT
# Revcom: complement(join(6..10,16..20)) => AAAAAGGGGG
ok my $loc2_strand    = Bio::Location::Split->new();
ok my $loc2_no_strand = Bio::Location::Split->new();
ok $loc2_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 6,  '-end' => 10, '-strand' => 1) );
ok $loc2_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 16, '-end' => 20, '-strand' => 1) );
ok $loc2_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 6,  '-end' => 10) );
ok $loc2_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 16, '-end' => 20) );
is $seq->subseq($loc2_strand),    'CCCCCTTTTT';
is $seq->subseq($loc2_no_strand), 'CCCCCTTTTT';
is $loc2_strand->to_FTstring,     'join(6..10,16..20)';
is $loc2_no_strand->to_FTstring,  'join(6..10,16..20)';
$loc2_strand->flip_strand;
$loc2_no_strand->flip_strand;
is $seq->subseq($loc2_strand),    'AAAAAGGGGG';
is $seq->subseq($loc2_no_strand), 'AAAAAGGGGG';
is $loc2_strand->to_FTstring,     'complement(join(6..10,16..20))';
is $loc2_no_strand->to_FTstring,  'complement(join(6..10,16..20))';
is $loc2_strand->length,    15;
is $loc2_no_strand->length, 15;

# Basic split, both locations in negative strand
# Coords: complement(join(6..10,16..20)) => AAAAAGGGGG
# Revcom: join(6..10,16..20) => CCCCCTTTTT
my $loc3_strand    = Bio::Location::Split->new();
$loc3_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 6,  '-end' => 10, '-strand' => -1) );
$loc3_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 16, '-end' => 20, '-strand' => -1) );
is $seq->subseq($loc3_strand),    'AAAAAGGGGG';
is $loc3_strand->to_FTstring,     'complement(join(6..10,16..20))';
$loc3_strand->flip_strand;
is $seq->subseq($loc3_strand),    'CCCCCTTTTT';
is $loc3_strand->to_FTstring,     'join(6..10,16..20)';
is $loc3_strand->length, 15;

## Cut by origin-split, same strand, single sequence that pass through origin
#Coords: join(16..20,1..2) => TTTTTAA
#Revcom: complement(join(16..20,1..2)) => TTAAAAA
my $loc4_strand    = Bio::Location::Split->new();
my $loc4_no_strand = Bio::Location::Split->new();
$loc4_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 16, '-end' => 20, '-strand' => 1) );
$loc4_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 1,  '-end' => 2,  '-strand' => 1) );
$loc4_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 16, '-end' => 20) );
$loc4_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 1,  '-end' => 2)  );
is $seq->subseq($loc4_strand),    'TTTTTAA';
is $seq->subseq($loc4_no_strand), 'TTTTTAA';
is $loc4_strand->to_FTstring,     'join(16..20,1..2)';
is $loc4_no_strand->to_FTstring,  'join(16..20,1..2)';
$loc4_strand->flip_strand;
$loc4_no_strand->flip_strand;
is $seq->subseq($loc4_strand),    'TTAAAAA';
is $seq->subseq($loc4_no_strand), 'TTAAAAA';
is $loc4_strand->to_FTstring,     'complement(join(16..20,1..2))';
is $loc4_no_strand->to_FTstring,  'complement(join(16..20,1..2))';
is $loc4_strand->length,    7;
is $loc4_no_strand->length, 7;

## Cut by origin-combo split, same strand, 2 sequences with 1st passing through origin
#Coords: join(19..20,1..2,11..13) => TTAAGGG
#Revcom: complement(join(19..20,1..2,11..13)) => CCCTTAA
my $loc5_strand    = Bio::Location::Split->new();
my $loc5_no_strand = Bio::Location::Split->new();
$loc5_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 19, '-end' => 20, '-strand' => 1) );
$loc5_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 1,  '-end' => 2,  '-strand' => 1) );
$loc5_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 11, '-end' => 13, '-strand' => 1) );
$loc5_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 19, '-end' => 20) );
$loc5_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 1,  '-end' => 2)  );
$loc5_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 11, '-end' => 13) );
is $seq->subseq($loc5_strand),    'TTAAGGG';
is $seq->subseq($loc5_no_strand), 'TTAAGGG';
is $loc5_strand->to_FTstring,     'join(19..20,1..2,11..13)';
is $loc5_no_strand->to_FTstring,  'join(19..20,1..2,11..13)';
$loc5_strand->flip_strand;
$loc5_no_strand->flip_strand;
is $seq->subseq($loc5_strand),    'CCCTTAA';
is $seq->subseq($loc5_no_strand), 'CCCTTAA';
is $loc5_strand->to_FTstring,     'complement(join(19..20,1..2,11..13))';
is $loc5_no_strand->to_FTstring,  'complement(join(19..20,1..2,11..13))';
is $loc5_strand->length,    15;
is $loc5_no_strand->length, 15;

## Cut by origin-combo split, same strand, 2 sequences with 2nd passing through origin
#Coords: join(6..10,19..20,1..4) => CCCCCTTAAAA
#Revcom: complement(join(6..10,19..20,1..4)) => TTTTAAGGGGG
my $loc6_strand    = Bio::Location::Split->new();
my $loc6_no_strand = Bio::Location::Split->new();
$loc6_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 6,  '-end' => 10, '-strand' => 1) );
$loc6_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 19, '-end' => 20, '-strand' => 1) );
$loc6_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 1,  '-end' => 4,  '-strand' => 1) );
$loc6_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 6,  '-end' => 10) );
$loc6_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 19, '-end' => 20) );
$loc6_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 1,  '-end' => 4)  );
is $seq->subseq($loc6_strand),    'CCCCCTTAAAA';
is $seq->subseq($loc6_no_strand), 'CCCCCTTAAAA';
is $loc6_strand->to_FTstring,     'join(6..10,19..20,1..4)';
is $loc6_no_strand->to_FTstring,  'join(6..10,19..20,1..4)';
$loc6_strand->flip_strand;
$loc6_no_strand->flip_strand;
is $seq->subseq($loc6_strand),    'TTTTAAGGGGG';
is $seq->subseq($loc6_no_strand), 'TTTTAAGGGGG';
is $loc6_strand->to_FTstring,     'complement(join(6..10,19..20,1..4))';
is $loc6_no_strand->to_FTstring,  'complement(join(6..10,19..20,1..4))';
is $loc6_strand->length,    19;
is $loc6_no_strand->length, 19;

## Trans-splicing, 2 sequences in different strands, 2nd in complement
#Coords: join(6..10,complement(16..20)) => CCCCCAAAAA
#Revcom: join(16..20,complement(6..10)) => TTTTTGGGGG
my $loc7_strand    = Bio::Location::Split->new();
my $loc7_no_strand = Bio::Location::Split->new();
$loc7_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 6,  '-end' => 10, '-strand' =>  1) );
$loc7_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 16, '-end' => 20, '-strand' => -1) );
$loc7_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 6,  '-end' => 10) );
$loc7_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 16, '-end' => 20, '-strand' => -1) );
is $seq->subseq($loc7_strand),    'CCCCCAAAAA';
is $seq->subseq($loc7_no_strand), 'CCCCCAAAAA';
is $loc7_strand->to_FTstring,     'join(6..10,complement(16..20))';
is $loc7_no_strand->to_FTstring,  'join(6..10,complement(16..20))';
$loc7_strand->flip_strand;
$loc7_no_strand->flip_strand;
is $seq->subseq($loc7_strand),    'TTTTTGGGGG';
is $seq->subseq($loc7_no_strand), 'TTTTTGGGGG';
is $loc7_strand->to_FTstring,     'join(16..20,complement(6..10))';
is $loc7_no_strand->to_FTstring,  'join(16..20,complement(6..10))';
is $loc7_strand->length,    10;
is $loc7_no_strand->length, 10;

## Trans-splicing, 2 sequences in different strands, 1st in complement
#Coords: join(complement(16..20),6..10) => AAAAACCCCC
#Revcom: join(complement(6..10),16..20) => GGGGGTTTTT
my $loc8_strand    = Bio::Location::Split->new();
my $loc8_no_strand = Bio::Location::Split->new();
$loc8_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 16, '-end' => 20, '-strand' => -1) );
$loc8_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 6,  '-end' => 10, '-strand' =>  1) );
$loc8_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 16, '-end' => 20, '-strand' => -1) );
$loc8_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 6,  '-end' => 10) );
is $seq->subseq($loc8_strand),    'AAAAACCCCC';
is $seq->subseq($loc8_no_strand), 'AAAAACCCCC';
is $loc8_strand->to_FTstring,     'join(complement(16..20),6..10)';
is $loc8_no_strand->to_FTstring,  'join(complement(16..20),6..10)';
$loc8_strand->flip_strand;
$loc8_no_strand->flip_strand;
is $seq->subseq($loc8_strand),    'GGGGGTTTTT';
is $seq->subseq($loc8_no_strand), 'GGGGGTTTTT';
is $loc8_strand->to_FTstring,     'join(complement(6..10),16..20)';
is $loc8_no_strand->to_FTstring,  'join(complement(6..10),16..20)';
is $loc8_strand->length,    10;
is $loc8_no_strand->length, 10;

## Trans-splicing w/cut by origin, 2 sequences with 1st passing through origin, 2nd in complement
#Coords: join(19..20,1..3,complement(11..13)) => TTAAACCC
#Revcom: join(11..13,complement(1..3),complement(19..20)) => GGGTTTAA
my $loc9_strand    = Bio::Location::Split->new();
my $loc9_no_strand = Bio::Location::Split->new();
$loc9_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 19, '-end' => 20, '-strand' =>  1) );
$loc9_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 1,  '-end' => 3,  '-strand' =>  1) );
$loc9_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 11, '-end' => 13, '-strand' => -1) );
$loc9_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 19, '-end' => 20) );
$loc9_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 1,  '-end' => 3)  );
$loc9_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 11, '-end' => 13, '-strand' => -1) );
is $seq->subseq($loc9_strand),    'TTAAACCC';
is $seq->subseq($loc9_no_strand), 'TTAAACCC';
is $loc9_strand->to_FTstring,     'join(19..20,1..3,complement(11..13))';
is $loc9_no_strand->to_FTstring,  'join(19..20,1..3,complement(11..13))';
$loc9_strand->flip_strand;
$loc9_no_strand->flip_strand;
is $seq->subseq($loc9_strand),    'GGGTTTAA';
is $seq->subseq($loc9_no_strand), 'GGGTTTAA';
is $loc9_strand->to_FTstring,     'join(11..13,complement(1..3),complement(19..20))';
is $loc9_no_strand->to_FTstring,  'join(11..13,complement(1..3),complement(19..20))';
is $loc9_strand->length,    8;
is $loc9_no_strand->length, 8;

## Trans-splicing w/cut by origin, 2 sequences with 1st passing through origin, 1st in complement
#Coords: join(complement(1..3),complement(19..20),11..13) => TTTAAGGG
#Revcom: join(complement(11..13),19..20,1..3) => CCCTTAAA
my $loc10_strand    = Bio::Location::Split->new();
my $loc10_no_strand = Bio::Location::Split->new();
$loc10_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 1,  '-end' => 3,  '-strand' => -1) );
$loc10_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 19, '-end' => 20, '-strand' => -1) );
$loc10_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 11, '-end' => 13, '-strand' =>  1) );
$loc10_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 1,  '-end' => 3,  '-strand' => -1) );
$loc10_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 19, '-end' => 20, '-strand' => -1) );
$loc10_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 11, '-end' => 13) );
is $seq->subseq($loc10_strand),    'TTTAAGGG';
is $seq->subseq($loc10_no_strand), 'TTTAAGGG';
is $loc10_strand->to_FTstring,     'join(complement(1..3),complement(19..20),11..13)';
is $loc10_no_strand->to_FTstring,  'join(complement(1..3),complement(19..20),11..13)';
$loc10_strand->flip_strand;
$loc10_no_strand->flip_strand;
is $seq->subseq($loc10_strand),    'CCCTTAAA';
is $seq->subseq($loc10_no_strand), 'CCCTTAAA';
is $loc10_strand->to_FTstring,     'join(complement(11..13),19..20,1..3)';
is $loc10_no_strand->to_FTstring,  'join(complement(11..13),19..20,1..3)';
is $loc10_strand->length,    8;
is $loc10_no_strand->length, 8;

## Trans-splicing w/cut by origin, 2 sequences with 2nd passing through origin, 2nd in complement
#Coords: join(6..10,complement(1..2),complement(18..20)) => CCCCCTTAAA
#Revcom: join(18..20,1..2,complement(6..10)) => TTTAAGGGGG
my $loc11_strand    = Bio::Location::Split->new();
my $loc11_no_strand = Bio::Location::Split->new();
$loc11_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 6,  '-end' => 10, '-strand' =>  1) );
$loc11_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 1,  '-end' => 2,  '-strand' => -1) );
$loc11_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 18, '-end' => 20, '-strand' => -1) );
$loc11_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 6,  '-end' => 10) );
$loc11_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 1,  '-end' => 2,  '-strand' => -1) );
$loc11_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 18, '-end' => 20, '-strand' => -1) );
is $seq->subseq($loc11_strand),    'CCCCCTTAAA';
is $seq->subseq($loc11_no_strand), 'CCCCCTTAAA';
is $loc11_strand->to_FTstring,     'join(6..10,complement(1..2),complement(18..20))';
is $loc11_no_strand->to_FTstring,  'join(6..10,complement(1..2),complement(18..20))';
$loc11_strand->flip_strand;
$loc11_no_strand->flip_strand;
is $seq->subseq($loc11_strand),    'TTTAAGGGGG';
is $seq->subseq($loc11_no_strand), 'TTTAAGGGGG';
is $loc11_strand->to_FTstring,     'join(18..20,1..2,complement(6..10))';
is $loc11_no_strand->to_FTstring,  'join(18..20,1..2,complement(6..10))';
is $loc11_strand->length,    10;
is $loc11_no_strand->length, 10;

## Trans-splicing w/cut by origin, 2 sequences with 2nd passing through origin, 1st in complement
#Coords: join(complement(6..10),18..20,1..2) => GGGGGTTTAA
#Revcom: join(complement(1..2),complement(18..20),6..10) => TTAAACCCCC
my $loc12_strand    = Bio::Location::Split->new();
my $loc12_no_strand = Bio::Location::Split->new();
$loc12_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 6,  '-end' => 10, '-strand' => -1) );
$loc12_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 18, '-end' => 20, '-strand' =>  1) );
$loc12_strand->add_sub_Location(    Bio::Location::Simple->new('-start'  => 1,  '-end' => 2,  '-strand' =>  1) );
$loc12_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 6,  '-end' => 10, '-strand' => -1) );
$loc12_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 18, '-end' => 20) );
$loc12_no_strand->add_sub_Location( Bio::Location::Simple->new('-start'  => 1,  '-end' => 2)  );
is $seq->subseq($loc12_strand),    'GGGGGTTTAA';
is $seq->subseq($loc12_no_strand), 'GGGGGTTTAA';
is $loc12_strand->to_FTstring,     'join(complement(6..10),18..20,1..2)';
is $loc12_no_strand->to_FTstring,  'join(complement(6..10),18..20,1..2)';
$loc12_strand->flip_strand;
$loc12_no_strand->flip_strand;
is $seq->subseq($loc12_strand),    'TTAAACCCCC';
is $seq->subseq($loc12_no_strand), 'TTAAACCCCC';
is $loc12_strand->to_FTstring,     'join(complement(1..2),complement(18..20),6..10)';
is $loc12_no_strand->to_FTstring,  'join(complement(1..2),complement(18..20),6..10)';
is $loc12_strand->length,    10;
is $loc12_no_strand->length, 10;
BioPerl-1.007002/t/Seq/PrimedSeq.t000555000766000024      1065613155576321 16620 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$


use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 65);

    use_ok('Bio::SeqIO');
    use_ok('Bio::Seq::PrimedSeq');
}

my ($seqio, $seq, $left, $right, $primed_seq, $left_test, $right_test, $annseq, $amplicon, $returnedseq);

$seqio = Bio::SeqIO->new(-file => test_input_file('primedseq.fa'));
$seq   = $seqio->next_seq;

my $expected_amplicon_seq = 'cttttcattctgactgcaacgGGCAATATGTCTCTGTGTGGATTAAAAA'.
'AAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAA'.
'TACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAacgcattagca'.
'ccacc';

my $expected_amplicon_seq2 = 'cttttcattctgactgcaacgTGTCTCTGTGTGGATTAAAAA'.
'AAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAA'.
'TACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAacgcattagca'.
'ccacc';

# Prime with Bio::PrimarySeqI objects and have the primer positions calculated
$left  = Bio::PrimarySeq->new(-id => 123, -seq => 'CTTTTCATTCTGACTGCAACG');
$right = Bio::Seq->new(-seq => 'GGTGGTGCTAATGCGT');
ok $primed_seq = Bio::Seq::PrimedSeq->new(
    -seq          => $seq,
    -left_primer  => $left,
    -right_primer => $right,
), 'Priming the target with sequence objects';

is $primed_seq->isa('Bio::SeqFeature::Generic'), 1;

ok $annseq = $primed_seq->annotated_sequence; # should I check that this is what I think it is, or just be happy?

ok $amplicon = $primed_seq->amplicon;
is $amplicon->seq, $expected_amplicon_seq;
is $amplicon->id, 'Amplicon_from_Test1';
ok $returnedseq = $primed_seq->seq;
is $returnedseq->seq, $seq->seq;
ok $left_test = $primed_seq->get_primer('-left_primer');
isa_ok $left_test, 'Bio::SeqFeature::Primer';
is $left_test->seq->seq, 'CTTTTCATTCTGACTGCAACG';
ok $right_test = $primed_seq->get_primer('-r');
isa_ok $right_test, 'Bio::SeqFeature::Primer';
is $right_test->seq->seq, 'GGTGGTGCTAATGCGT';
ok( ($left_test, $right_test) = $primed_seq->get_primer() );
is $left_test->seq->seq, 'CTTTTCATTCTGACTGCAACG';
is $right_test->seq->seq, 'GGTGGTGCTAATGCGT';
is $left_test->strand, 1;
is $left_test->start, 3;
is $left_test->end, 23;
is $right_test->strand, -1;
is $right_test->start, 195;
is $right_test->end, 210;


# Prime the sequence with Bio::SeqFeature::Primer objects
$left  = Bio::SeqFeature::Primer->new(-id => 123, -seq => 'CTTTTCATTCTGACTGCAACG');
$right = Bio::SeqFeature::Primer->new(-seq => 'GGTGGTGCTAATGCGT');
ok $primed_seq = Bio::Seq::PrimedSeq->new(
    -seq          => $seq,
    -left_primer  => $left,
    -right_primer => $right,
), 'Priming the target with primer objects';
ok $annseq = $primed_seq->annotated_sequence;
ok $amplicon = $primed_seq->amplicon;
is $amplicon->seq, $expected_amplicon_seq;
is $amplicon->id, 'Amplicon_from_Test1';
ok $returnedseq = $primed_seq->seq;
is $returnedseq->seq, $seq->seq;
ok $left_test = $primed_seq->get_primer('left');
is_deeply $left_test, $left;
ok $right_test = $primed_seq->get_primer('r');
is_deeply $right_test, $right;
ok( ($left_test, $right_test) = $primed_seq->get_primer('-both') );
is_deeply $left_test, $left;
is_deeply $right_test, $right;
is $left_test->strand, 1;
is $left_test->start, 3;
is $left_test->end, 23;
is $right_test->strand, -1;
is $right_test->start, 195;
is $right_test->end, 210;


# Prime the sequence with Bio::SeqFeature::Primer objects
$left  = Bio::SeqFeature::Primer->new(
    -id => 123,
    -seq => 'CTTTTCATTCTGACTGCAACG',
    -start => 10,
    -end => 30,
    -strand => 1,
);
$right = Bio::SeqFeature::Primer->new(
    -seq => 'GGTGGTGCTAATGCGT',
    -start => 195,
    -end => 210,
    -strand => -1,
);
ok $primed_seq = Bio::Seq::PrimedSeq->new(
    -seq          => $seq,
    -left_primer  => $left,
    -right_primer => $right,
), 'Priming the target with located primer objects';
ok $annseq = $primed_seq->annotated_sequence;
ok $amplicon = $primed_seq->amplicon;
is $amplicon->seq, $expected_amplicon_seq2;
is $amplicon->id, 'Amplicon_from_Test1';
ok $returnedseq = $primed_seq->seq;
is $returnedseq->seq, $seq->seq;
ok $left_test = $primed_seq->get_primer('left');
is_deeply $left_test, $left;
ok $right_test = $primed_seq->get_primer('r');
is_deeply $right_test, $right;
ok( ($left_test, $right_test) = $primed_seq->get_primer('-both') );
is_deeply $left_test, $left;
is_deeply $right_test, $right;
is $left_test->strand, 1;
is $left_test->start, 10;
is $left_test->end, 30;
is $right_test->strand, -1;
is $right_test->start, 195;
is $right_test->end, 210;
BioPerl-1.007002/t/Seq/Quality.t000444000766000024      3074013155576321 16350 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 85);

    use_ok('Bio::Seq::Quality');
}

use Bio::SeqIO;

my $DEBUG = test_debug();

# create some random sequence object with no id
my $seqobj_broken = Bio::Seq::Quality->
    new( -seq => "ATCGATCGA",
	 );

my $seqobj;
lives_ok {
    $seqobj = Bio::Seq::Quality->
	new( -seq => "ATCGATCGA",
	     -id  => 'QualityFragment-12',
	     -accession_number => 'X78121',
	     );
};


# create some random quality object with the same number of qualities
# and the same identifiers
my $string_quals = "10 20 30 40 50 40 30 20 10";
my $qualobj;
lives_ok {
    $qualobj = Bio::Seq::Quality->
	new( -qual => $string_quals,
	     -id  => 'QualityFragment-12',
	     -accession_number => 'X78121',
	     );
};

# check to see what happens when you construct the Quality object
ok my $swq1 = Bio::Seq::Quality->
    new( -seq => "ATCGATCGA",
	 -id  => 'QualityFragment-12',
	 -accession_number => 'X78121',
	 -qual	=>	$string_quals);


print("Testing various weird constructors...\n") if $DEBUG;
print("\ta) No ids, Sequence object, no quality...\n") if $DEBUG;

# w for weird
my $wswq1;
lives_ok {
    $wswq1 = Bio::Seq::Quality->
	new( -seq  => "ATCGATCGA",
	     -qual => "");
};
print $@ if $DEBUG;


print("\tb) No ids, no sequence, quality object...\n") if $DEBUG;
	# note that you must provide a alphabet for this one.
$wswq1 = Bio::Seq::Quality->
    new( -seq => "",
	 -qual => $string_quals,
	 -alphabet => 'dna'
	 );

print("\tc) Absolutely nothing. (HAHAHAHA)...\n") if $DEBUG;
lives_ok {
    $wswq1 = Bio::Seq::Quality->new( -seq => "",
				     -qual => "",
				     -alphabet => 'dna'
				     );
};


print("\td) Absolutely nothing but an ID\n") if $DEBUG;
lives_ok {
    $wswq1 = Bio::Seq::Quality->
	new( -seq => "",
	     -qual => "",
	     -alphabet => 'dna',
	     -id => 'an object with no sequence and no quality but with an id'
	     );
};

print("\td) No sequence, no quality, no ID...\n") if $DEBUG;
warnings_like {
    $wswq1 = Bio::Seq::Quality->
	new( -seq  =>	"",
	     -qual =>	"",
	     -verbose => 0);
} qr/not guess alphabet/i;

print("Testing various methods and behaviors...\n") if $DEBUG;

print("1. Testing the seq() method...\n") if $DEBUG;
	print("\t1a) get\n") if $DEBUG;
	my $original_seq = $swq1->seq();
	is ($original_seq, "ATCGATCGA");
	print("\t1b) set\n") if $DEBUG;
	ok ($swq1->seq("AAAAAAAAAAAA"));
	print("\t1c) get (again, to make sure the set was done.)\n") if $DEBUG;
	is($swq1->seq(), "AAAAAAAAAAAA");
	print("\tSetting the sequence back to the original value...\n") if $DEBUG;
	$swq1->seq($original_seq);


print("2. Testing the qual() method...\n") if $DEBUG;
	print("\t2a) get\n") if $DEBUG;
	my @qual = @{$swq1->qual()};
	my $str_qual = join(' ',@qual);
	is $str_qual, "10 20 30 40 50 40 30 20 10";
	print("\t2b) set\n") if $DEBUG;
	ok $swq1->qual("10 10 10 10 10");
	print("\t2c) get (again, to make sure the set was done.)\n") if $DEBUG;
	my @qual2 = @{$swq1->qual()};
	my $str_qual2 = join(' ',@qual2);
	is($str_qual2, "10 10 10 10 10 0 0 0 0"); ###!
	print("\tSetting the quality back to the original value...\n") if $DEBUG;
	$swq1->qual($str_qual);

print("3. Testing the length() method...\n") if $DEBUG;
	print("\t3a) When lengths are equal...\n") if $DEBUG;
	is($swq1->length(), 9);	
	print("\t3b) When lengths are different\n") if $DEBUG;
	$swq1->qual("10 10 10 10 10");
	isnt ($swq1->length(), "DIFFERENT");


print("6. Testing the subqual() method...\n") if $DEBUG;
     my $t_subqual = "10 20 30 40 50 60 70 80 90";
     $swq1->qual($t_subqual);
     print("\t6d) Testing the subqual at the start (border condition)\n") if $DEBUG;
     ok ('10 20 30' eq join(' ',@{$swq1->subqual(1,3)}));
     print("\t6d) Testing the subqual at the end (border condition)\n") if $DEBUG;
     ok ('70 80 90' eq join(' ',@{$swq1->subqual(7,9)}));
     print("\t6d) Testing the subqual in the middle\n") if $DEBUG;
     ok ('40 50 60' eq join(' ',@{$swq1->subqual(4,6)}));

print("7. Testing cases where quality is zero...\n") if $DEBUG;
$swq1 = Bio::Seq::Quality->new(-seq =>  'G',
                               -qual => '0',
			       );
my $swq2 = Bio::Seq::Quality->new(-seq =>  'G',
                                  -qual => '65',
				  );
is $swq1->length, $swq2->length;

$swq1 = Bio::Seq::Quality->new(-seq =>  'GC',
                               -qual => '0 0',
			       );
$swq2 = Bio::Seq::Quality->new(-seq =>  'GT',
                               -qual => '65 0',
			       );
my $swq3 = Bio::Seq::Quality->new(-seq =>  'AG',
                               -qual => '0 60',
			       );
is $swq1->length, $swq2->length;
is $swq1->length, $swq3->length;


#
# end of test inherited from seqwithquality.t 
#
#################################################################
#
# testing new functionality
#

my $qual = '0 1 2 3 4 5 6 7 8 9 11 12 13';
my $trace = '0 5 10 15 20 25 30 35 40 45 50 55 60';

ok my $seq = Bio::Seq::Quality->new
    ( -qual => $qual,
      -trace_indices => $trace,
      -seq =>  'atcgatcgatcgt',
      -id  => 'human_id',
      -accession_number => 'S000012',
      -verbose => $DEBUG >= 0 ? $DEBUG : 0
);


print("2. Testing the trace() method...\n") if $DEBUG;
	print("\t2a) get\n") if $DEBUG;
	my @trace = @{$seq->trace()};
	my $str_trace = join(' ',@trace);
	is $str_trace, $trace;
	print("\t2b) set\n") if $DEBUG;
	ok $seq->trace("10 10 10 10 10");
	print("\t2c) get (again, to make sure the set was done.)\n") if $DEBUG;
	my @trace2 = @{$seq->trace()};
	my $str_trace2 = join(' ',@trace2);
	is($str_trace2, "10 10 10 10 10 0 0 0 0 0 0 0 0"); ###!
	print("\tSetting the trace back to the original value...\n") if $DEBUG;
	$seq->trace($trace);



is_deeply $seq->qual, [split / /, $qual];
is_deeply $seq->trace, [split / /, $trace];
is_deeply $seq->trace_indices, [split / /, $trace]; #deprecated

is $seq->qual_text, $qual;
is $seq->trace_text, $trace;

is join (' ', @{$seq->subqual(2, 3)}), '1 2';
is $seq->subqual_text(2, 3), '1 2';
is join (' ', @{$seq->subqual(2, 3, "9 9")}), '9 9';
is $seq->subqual_text(2, 3, "8 8"), '8 8';

is join (' ', @{$seq->subtrace(2, 3)}), '5 10';
is $seq->subtrace_text(2, 3), '5 10';
is join (' ', @{$seq->subtrace(2, 3, "9 9")}), '9 9';
is $seq->subtrace_text(2, 3, "8 8"), '8 8';


is $seq->trace_index_at(5), 20;
is join(' ', @{$seq->sub_trace_index(5,6)}), "20 25";

is $seq->baseat(2), 't';
is $seq->baseat(3), 'c';
is $seq->baseat(4), 'g';
is $seq->baseat(5), 'a';


#############################################
#
# same tests using Seq::Meta::Array methods follow ...
#

my $meta = '0 1 2 3 4 5 6 7 8 9 11 12';
$trace = '0 5 10 15 20 25 30 35 40 45 50 55';
my @trace_array = qw(0 5 10 15 20 25 30 35 40 45 50 55);

ok $seq = Bio::Seq::Quality->new
    ( -meta => $meta,
      -seq =>  'atcgatcgatcg',
      -id  => 'human_id',
      -accession_number => 'S000012',
      -verbose => $DEBUG >= 0 ? $DEBUG : 0
);

$seq->named_meta('trace', \@trace_array);

is_deeply $seq->meta, [split / /, $meta];
is_deeply $seq->named_meta('trace'), [split / /, $trace];

is $seq->meta_text, $meta;
is $seq->named_meta_text('trace'), $trace;

is join (' ', @{$seq->submeta(2, 3)}), '1 2';
is $seq->submeta_text(2, 3), '1 2';
is join (' ', @{$seq->submeta(2, 3, "9 9")}), '9 9';
is $seq->submeta_text(2, 3, "8 8"), '8 8';

is join (' ', @{$seq->named_submeta('trace', 2, 3)}), '5 10';
is $seq->named_submeta_text('trace', 2, 3), '5 10';
is join (' ', @{$seq->named_submeta('trace', 2, 3, "9 9")}), '9 9';
is $seq->named_submeta_text('trace', 2, 3, "8 8"), '8 8';


ok $seq = Bio::Seq::Quality->new(
    -seq => "ATGGGGGTGGTGGTACCCTATGGGGGTGGTGGTACCCT",
    -qual => "10 59 12 75 63 76 84 36 42 10 35 97 81 50 81 53 93 13 38 10 59 12 75 63 76 84 36 42 10 35 97 81 50 81 53 93 13 38",
    -trace_indices => "1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38"
);

my $rev;
ok $rev = $seq->revcom; 
is $rev->seq, 'AGGGTACCACCACCCCCATAGGGTACCACCACCCCCAT';
is $rev->qual_text, "38 13 93 53 81 50 81 97 35 10 42 36 84 76 63 75 12 59 10 38 13 93 53 81 50 81 97 35 10 42 36 84 76 63 75 12 59 10";


# selecting ranges based on quality

# test seq with three high quality regions (13, 12 and 3), one very short (3)
ok $seq = Bio::Seq::Quality->new(
    -seq => "ATGGGGGTGGTGGTACCCTATGGGGGTGGTGGTACCCT",
    -qual => "0 5 10 20 30 40 40 50 50 50 50 50 40 10 10 10 5 5 20 20 30 40 50 44 44 50 50 50 50 50 5 5 40 40 40 40 50 50"
    );


is $seq->threshold, undef;
is $seq->threshold(10), 10;
is $seq->threshold(13), 13;

is $seq->count_clear_ranges, 3;

my $newseq = $seq->get_clear_range;
is $newseq->length, 12;


my @ranges = $seq->get_all_clean_ranges;
is scalar @ranges, 3;
my $min_length = 10;
@ranges = $seq->get_all_clean_ranges($min_length);
is scalar @ranges, 2;

my $seqio = Bio::SeqIO->new(
    -file   => test_input_file('test_clear_range.fastq'),
    -format => 'fastq'
);

while ( my $seq = $seqio->next_seq() ) {
    my $newqualobj;
    lives_ok { $newqualobj = $seq->get_clear_range(0) };
    if ($newqualobj) {
        is($newqualobj->id, $seq->id, 'Bug 2845');
    } else {
        ok(0, "No object returned via get_clear_range()");
    }
}




#############################################
#
# try testing some 'meta morphic relations'
#

## belief; As the threshold is increased, the number of clear ranges
## (ncr) should not decrease.

## belief; As the thrshold is increased, the length of the clear
## ranges (lcr) should not decrease.

## belief; As the threshold is incrazed, the clear range length (clr)
## should not increase. Sorry for the terribe var names.

## belief; The number of clear ranges should vary between zero and
## half the sequence length.

## belief; The length of the clear ranges should vary between zero and
## the sequence length.

## belief; The length of the clear range should vary between zero and
## the sequence length.

## belief; The lenght of the clear range should not be larger than the
## length of hte clear ranges.


my @bases = qw (A T C G a t c g);
my @qualities = 0..65;


## See beliefs above:
my $ncr_thresh_sanity = 0;
my $lcr_thresh_sanity = 0;
my $clr_thresh_sanity = 0;

my $ncr_range_sanity = 0;
my $lcr_range_sanity = 0;
my $clr_range_sanity = 0;

my $final_loss_of_sanity = 0;



## Go time:

for (1..100){
    $seq = join("", map {$bases[rand(@bases)]} 1..1000  );
    $qual = join(" ", map {$qualities[rand(@qualities)]} 1..1000  );
    
    $seq = Bio::Seq::Quality->
	new(
	    -seq => $seq,
	    -qual => $qual,
	    );
    
    $seq->threshold(10);
    my $a_ncr = $seq->count_clear_ranges;
    my $a_lcr = $seq->clear_ranges_length;
    my $a_clr = scalar(@{$seq->get_clear_range->qual});
    
    $ncr_range_sanity ++ if $a_ncr >= 0 && $a_ncr <=  500;
    $lcr_range_sanity ++ if $a_lcr >= 0 && $a_lcr <= 1000;
    $clr_range_sanity ++ if $a_clr >= 0 && $a_clr <= 1000;
    $final_loss_of_sanity ++ if $a_lcr >= $a_clr;

    $seq->threshold(20);
    my $b_ncr = $seq->count_clear_ranges;
    my $b_lcr = $seq->clear_ranges_length;
    my $b_clr = scalar(@{$seq->get_clear_range->qual});

    $ncr_range_sanity ++ if $b_ncr >= 0 && $b_ncr <=  500;
    $lcr_range_sanity ++ if $b_lcr >= 0 && $b_lcr <= 1000;
    $clr_range_sanity ++ if $b_clr >= 0 && $b_clr <= 1000;
    $final_loss_of_sanity ++ if $b_lcr >= $b_clr;


    $seq->threshold(30);
    my $c_ncr = $seq->count_clear_ranges;
    my $c_lcr = $seq->clear_ranges_length;
    my $c_clr = scalar(@{$seq->get_clear_range->qual});

    $ncr_range_sanity ++ if $c_ncr >= 0 && $c_ncr <=  500;
    $lcr_range_sanity ++ if $c_lcr >= 0 && $c_lcr <= 1000;
    $clr_range_sanity ++ if $c_clr >= 0 && $c_clr <= 1000;
    $final_loss_of_sanity ++ if $c_lcr >= $c_clr;
    
    
    
    $ncr_thresh_sanity ++ if 
	$a_ncr <= $b_ncr && 
	$b_ncr <= $c_ncr;
    
    $lcr_thresh_sanity ++ if 
	$a_ncr <= $b_ncr && 
	$b_ncr <= $c_ncr;
    
    $clr_thresh_sanity ++ if
	$a_clr >= $b_clr && 
	$b_clr >= $c_clr;
       
}

is $ncr_thresh_sanity, 100;
is $lcr_thresh_sanity, 100;
is $clr_thresh_sanity, 100;

is $ncr_range_sanity, 300;
is $lcr_range_sanity, 300;
is $clr_range_sanity, 300;

is $final_loss_of_sanity, 300;




## Test the mask sequence function ...

## Ideally we'd at least test each function with each permutation of constructors.

my $x = Bio::Seq::Quality->
    new( -seq => "aaaattttccccgggg",
	 -qual =>"1 1 1 1 2 2 2 2 1 1 1 1 3 3 3 3");

$x->threshold(1); 

is $x->mask_below_threshold, "aaaattttccccgggg";

$x->threshold(2); 

is $x->mask_below_threshold, "XXXXttttXXXXgggg";

$x->threshold(3); 

is $x->mask_below_threshold, "XXXXXXXXXXXXgggg";

$x->threshold(4); 

is $x->mask_below_threshold, "XXXXXXXXXXXXXXXX";

BioPerl-1.007002/t/Seq/Seq.t000444000766000024      1711413155576321 15450 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 76);

    use_ok('Bio::Seq');
    use_ok('Bio::Seq::RichSeq');
    use_ok('Bio::SeqFeature::Generic');
    use_ok('Bio::Species');
    use_ok('Bio::Annotation::SimpleValue');
}

ok my $seq = Bio::Seq->new(-seq=>'ACTGTGGCGTCAACT',
                        -desc=>'Sample Bio::Seq object',
                        -alphabet => 'dna',
                        -is_circular => 1
                       );
isa_ok($seq,"Bio::AnnotatableI");

ok $seq->is_circular;
ok not $seq->is_circular(0);
ok not $seq->is_circular;

my $trunc = $seq->trunc(1,4);
is $trunc->length, 4, 'truncated sequence length';

is $trunc->seq, 'ACTG', 'truncated sequence string';

# test ability to get str function
is $seq->seq(),  'ACTGTGGCGTCAACT' ;

ok $seq = Bio::Seq->new(-seq=>'actgtggcgtcaact',
                        -desc=>'Sample Bio::Seq object',
                        -display_id => 'something',
                        -accession_number => 'accnum',
                        -alphabet => 'dna' );

is uc $seq->alphabet, 'DNA' , 'alphabet';

# basic methods

is $seq->id(), 'something',  "id";
is $seq->accession_number, 'accnum', "accession number";
is $seq->subseq(5, 9),  'tggcg', "subseq";

# check IdentifiableI and DescribableI interfaces
isa_ok $seq, 'Bio::IdentifiableI';
isa_ok $seq, 'Bio::DescribableI';
# make sure all methods are implemented
is $seq->authority("bioperl.org"), "bioperl.org";
is $seq->namespace("t"), "t";
is $seq->version(0), 0;
is $seq->lsid_string(), "bioperl.org:t:accnum";
is $seq->namespace_string(), "t:accnum.0";
is $seq->description(), 'Sample Bio::Seq object';
is $seq->display_name(), "something";

# check that feature accession works regardless of lazy things going on
is scalar($seq->top_SeqFeatures()), 0;
is scalar($seq->flush_SeqFeatures()), 0;

my $newfeat = Bio::SeqFeature::Generic->new( -start => 10,
                                             -end => 12,
                                             -primary => 'silly',
                                             -source => 'stuff');


$seq->add_SeqFeature($newfeat);
is $seq->feature_count, 1;

my $species = Bio::Species->new
    (-verbose => 1,
     -classification => [ qw( sapiens Homo Hominidae
                              Catarrhini Primates Eutheria
                              Mammalia Vertebrata Chordata
                              Metazoa Eukaryota )]);
$seq->species($species);
is $seq->species->binomial, 'Homo sapiens';
$seq->annotation->add_Annotation('description',
                 Bio::Annotation::SimpleValue->new(-value => 'desc-here'));
my ($descr) = $seq->annotation->get_Annotations('description');
is $descr->value(), 'desc-here';
is $descr->tagname(), 'description';

#
#  translation tests
#

my $trans = $seq->translate();
is  $trans->seq(), 'TVAST' , 'translated sequence';

# unambiguous two character codons like 'ACN' and 'GTN' should give out an amino
# acid ...with the addendum that there should be no assumption by the method
# to complete the codon unless specified, using the -complete_codons flag.

$seq->seq('ACTGTGGCGTCAACN');
$trans = $seq->translate();
is $trans->seq(), 'TVAST', 'translated sequence with explicit unambiguous codons';

$seq->seq('ACTGTGGCGTCAAC');
$trans = $seq->translate();
is $trans->seq(), 'TVAS', 'translated sequence with unknown unambiguous codons';

$seq->seq('ACTGTGGCGTCAAC');
$trans = $seq->translate(-complete_codons => 1);
is $trans->seq(), 'TVAST', 'translated sequence with unknown unambiguous codons, completed';

$seq->seq('ACTGTGGCGTCAACA');
$trans = $seq->translate();
is $trans->seq(), 'TVAST', 'translated sequence with unambiguous codons';

$seq->seq('ACTGTGGCGTCAACAG');
$trans = $seq->translate();
is $trans->seq(), 'TVAST', 'translated sequence with unambiguous codons';

$seq->seq('ACTGTGGCGTCAACAGT');
$trans = $seq->translate(-complete_codons => 1);
is $trans->seq(), 'TVASTV', 'translated sequence with unknown unambiguous codons, completed';

$seq->seq('ACTGTGGCGTCAACAGTA');
$trans = $seq->translate();
is $trans->seq(), 'TVASTV', 'translated sequence with unambiguous codons';

$seq->seq('AC');
is $seq->translate(-complete_codons => 1)->seq , 'T', 'translated sequence with unknown unambiguous codons, completed';

#difference between the default and full CDS translation

$seq->seq('atgtggtaa');
$trans = $seq->translate();
is $trans->seq(), 'MW*' , 'translated sequence with stop';

$seq->seq('atgtggtaa');
$trans = $seq->translate(undef,undef,undef,undef,1);
is $trans->seq(), 'MW', 'translated sequence';

#frame
my $string;
my @frames = (0, 1, 2);
foreach my $frame (@frames) {
    $string .= $seq->translate(undef, undef, $frame)->seq;
    $string .= $seq->revcom->translate(undef, undef, $frame)->seq;
}
is $string, 'MW*LPHCGYHVVTT';

#Translating with all codon tables using method defaults
$string = '';
my @codontables = qw( 1 2 3 4 5 6 9 10 11 12 13 14 15 16 21 22 23);
foreach my $ct (@codontables) {
    $string .= $seq->translate(undef, undef, undef, $ct)->seq;
}
is $string, 'MW*MW*MW*MW*MW*MWQMW*MW*MW*MW*MW*MWYMW*MW*MW*MW*MW*';

# CDS translation set to throw an exception for internal stop codons
$seq->seq('atgtggtaataa');
eval {
    $seq->translate(undef, undef, undef, undef, 'CDS' , 'throw');
};
like ($@, qr/EX/);

$seq->seq('atgtggtaataa');
is( $seq->translate('J', '-',)->seq, 'MWJJ');

# tests for RichSeq
ok my $richseq = Bio::Seq::RichSeq->new( -seq => 'atgtggtaataa',
                                      -accession_number => 'AC123',
                                      -alphabet => 'rna',
                                      -molecule => 'mRNA',
                                      -id => 'id1',
                                      -dates => [ '2001/1/1' ],
                                      -pid => '887821',
                                      -keywords => 'JUNK1;JUNK2',
                                      -division => 'Fungi',
                                      -secondary_accessions => 'AC1152' );

is ($richseq->seq, 'atgtggtaataa');
is ($richseq->display_id, 'id1');
is (($richseq->get_dates)[0], '2001/1/1');
is (($richseq->get_secondary_accessions)[0], 'AC1152');
is ($richseq->accession_number, 'AC123');
is ($richseq->alphabet, 'rna');
is ($richseq->molecule, 'mRNA');
is ($richseq->pid, 887821);
is ($richseq->division, 'Fungi');
is ($richseq->keywords, 'JUNK1; JUNK2');
$richseq->seq_version('2');
is ($richseq->seq_version, 2);

# Test adding a feature to a RichSeq type, then
# trunc() and see if the feature vanishes (we shouldn't
# be using clone() for RichSeq types)
$richseq->add_SeqFeature($newfeat);
is $richseq->feature_count, 1;
my $newrichseq = $richseq->trunc(1,5);
is $newrichseq->feature_count, 0, "Don't use clone for trunc of Bio::Seq::RichSeq";
is $newrichseq->length, 5;

# tests for subtle misbehaviors
$seq = Bio::Seq->new(-primary_id => 'blah', -accession_number => 'foo');
is ($seq->accession_number, $seq->primary_seq->accession_number);
is ($seq->primary_id, $seq->primary_seq->primary_id);
$seq->accession_number('blurb');
$seq->primary_id('bar');
is ($seq->accession_number, $seq->primary_seq->accession_number);
is ($seq->primary_id, $seq->primary_seq->primary_id);


# Bug #2864:

$seq = Bio::Seq->new(-display_id => 0, -seq => 'GATC');

is $seq->display_id, 0, "Bug #2864";

# transcribe/rev_transcribe

$seq = Bio::Seq->new( -id => 'seq1', -alphabet=>'dna',
                      -seq=> 'attTcgcatgT' );
ok my $xseq = $seq->transcribe;
is $xseq->alphabet, 'rna';
ok !($xseq->seq =~ /[tT]/);
is $xseq->seq, 'auuUcgcaugU';
ok !$xseq->transcribe;
ok $seq = $xseq->rev_transcribe;
is $seq->seq, 'attTcgcatgT';
is $seq->alphabet, 'dna';
BioPerl-1.007002/t/Seq/SimulatedRead.t000444000766000024      3343513155576321 17447 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;
use warnings;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    test_begin(-tests => 194);

    use_ok('Bio::Seq');
    use_ok('Bio::Seq::Quality');
    use_ok('Bio::PrimarySeq');
    use_ok('Bio::LocatableSeq');
    use_ok('Bio::Seq::SimulatedRead');
}

my $VERBOSE = test_debug();

my ($ref, $ref2, $ref3, $ref4, $ref5, $read, $errors);

$ref = Bio::Seq::Quality->new(-id    => 'human_id',
                               -seq   => 'TAAAAAAACCCC',
                               -qual  => '1 2 3 4 5 6 7 8 9 10 11 12',
                               -trace => '0 5 10 15 20 25 30 35 40 45 50 55',
                               -desc  => 'The human genome' );

$ref2 = Bio::Seq->new(-id   => 'other_genome',
                       -seq  => 'ACGTACGT',
                       -desc => '"Secret" sequence');

$ref3 = Bio::PrimarySeq->new(-seq => 'ACACTGATCTAGCGTCGTGCTAGCTGACGTAGCTGAT' );

$ref4 = Bio::LocatableSeq->new(-id  => 'a_thaliana',
                                -seq => 'CGTATTCTGAGGAGAGCTCT' );


# Basic object

ok $read = Bio::Seq::SimulatedRead->new();
isa_ok $read, 'Bio::Seq::SimulatedRead';
isa_ok $read, 'Bio::LocatableSeq';
isa_ok $read, 'Bio::Seq::Quality';

$errors->{'1'}->{'+'} = 'T';
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors );
is $read->reference, $ref;
ok $read->errors;
is $read->errors->{'1'}->{'+'}->[0], 'T';

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -track => 0 );
is $read->start, 1;
is $read->end, 12;
is $read->seq, 'TAAAAAAACCCC';
is $read->track, 0;
is $read->desc, undef;
is $read->revcom->seq, 'GGGGTTTTTTTA';

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -track => 1 );
is $read->start, 1;
is $read->end, 12;
is $read->seq, 'TAAAAAAACCCC';
is join(' ',@{$read->qual}), '';
is $read->track, 1;
is $read->desc, 'reference=human_id start=1 end=12 strand=+1 description="The human genome"';

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -track => 1, -coord_style => 'bioperl' );
is $read->desc, 'reference=human_id start=1 end=12 strand=+1 description="The human genome"';

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -track => 1, -coord_style => 'genbank' );
is $read->desc, 'reference=human_id position=1..12 description="The human genome"';

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -qual_levels => [30, 10]);
is $read->start, 1;
is $read->end, 12;
is $read->seq, 'TAAAAAAACCCC';
is join(' ', @{$read->qual}), '30 30 30 30 30 30 30 30 30 30 30 30';
is $read->track, 1;
is $read->desc, 'reference=human_id start=1 end=12 strand=+1 description="The human genome"';
is $read->revcom->seq, 'GGGGTTTTTTTA';

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref2 );
is $read->start, 1;
is $read->end, 8;
is $read->seq, 'ACGTACGT';
is join(' ',@{$read->qual}), '';
is $read->desc, 'reference=other_genome start=1 end=8 strand=+1 description="\"Secret\" sequence"';

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref3 );
is $read->start, 1;
is $read->end, 37;
is $read->seq, 'ACACTGATCTAGCGTCGTGCTAGCTGACGTAGCTGAT';
is join(' ',@{$read->qual}), '';
is $read->desc, 'start=1 end=37 strand=+1';

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -strand => -1, -qual_levels => [30, 10]);
is $read->seq, 'GGGGTTTTTTTA';
is join(' ', @{$read->qual}), '30 30 30 30 30 30 30 30 30 30 30 30';
is $read->desc, 'reference=human_id start=1 end=12 strand=-1 description="The human genome"';

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -strand => -1, -qual_levels => [30, 10], -coord_style => 'genbank' );
is $read->desc, 'reference=human_id position=complement(1..12) description="The human genome"';

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -start => 2, -end => 8, -qual_levels => [30, 10]);
is $read->seq, 'AAAAAAA';
is join(' ', @{$read->qual}), '30 30 30 30 30 30 30';
is $read->desc, 'reference=human_id start=2 end=8 strand=+1 description="The human genome"';

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -strand => -1, -start => 2, -end => 8, -qual_levels => [30, 10]);
is $read->seq, 'TTTTTTT';
is join(' ', @{$read->qual}), '30 30 30 30 30 30 30';
is $read->desc, 'reference=human_id start=2 end=8 strand=-1 description="The human genome"';

$errors = {};
$errors->{'6'}->{'+'} = 'GG';
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -strand => -1, -start => 2, -end => 8, -errors => $errors, -qual_levels => [30, 10]);
is $read->start, 2;
is $read->end, 8;
is $read->seq, 'TTTTTTGGT';
is join(' ', @{$read->qual}), '30 30 30 30 30 30 10 10 30';
is $read->desc, 'reference=human_id start=2 end=8 strand=-1 errors=6+G,6+G description="The human genome"';

$errors = {};
$errors->{'6'}->{'+'} = 'GG';
$errors->{'1'}->{'%'} = 'T';
$errors->{'3'}->{'-'} = undef;
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -strand => 1, -start => 2, -end => 8, -errors => $errors, -qual_levels => [30, 10]);
is $read->start, 2;
is $read->end, 8;
is $read->seq, 'TAAAAGGA';
is join(' ', @{$read->qual}), '10 30 30 30 30 10 10 30';
is $read->desc, 'reference=human_id start=2 end=8 strand=+1 errors=1%T,3-,6+G,6+G description="The human genome"';

$errors = {};
$errors->{'6'}->{'+'} = 'GG';
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors, -qual_levels => [30, 10]);
is $read->start, 1;
is $read->end, 12;
is $read->seq, 'TAAAAAGGAACCCC';
is join(' ', @{$read->qual}), '30 30 30 30 30 30 10 10 30 30 30 30 30 30';
is $read->desc, 'reference=human_id start=1 end=12 strand=+1 errors=6+G,6+G description="The human genome"';

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors, -mid => 'ACGT', -errors => $errors, -qual_levels => [30, 10]);
is $read->start, 1;
is $read->end, 12;
is $read->seq, 'ACGTTAGGAAAAAACCCC';
is join(' ', @{$read->qual}), '30 30 30 30 30 30 10 10 30 30 30 30 30 30 30 30 30 30';
is $read->desc, 'reference=human_id start=1 end=12 strand=+1 mid=ACGT errors=6+G,6+G description="The human genome"';

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -mid => 'TTTAAA', -qual_levels => [30, 10]);
is $read->start, 1;
is $read->end, 12;
is $read->seq, 'TTTAAATAAAAAAACCCC';
is join(' ', @{$read->qual}), '30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30';
is $read->desc, 'reference=human_id start=1 end=12 strand=+1 mid=TTTAAA description="The human genome"';

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -mid => '', -qual_levels => []);
is $read->start, 1;
is $read->end, 12;
is $read->seq, 'TAAAAAAACCCC';
is join(' ', @{$read->qual}), '';
is $read->desc, 'reference=human_id start=1 end=12 strand=+1 description="The human genome"';


# Redundant errors

$errors = {};
$errors->{'6'}->{'+'} = ['G', 'G'];
$errors->{'1'}->{'%'} = ['A', 'G', 'T'];
$errors->{'3'}->{'-'} = [undef, undef];
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -strand => 1, -start => 2, -end => 8, -errors => $errors, -qual_levels => [30, 10]), 'redundant errors';
is $read->start, 2;
is $read->end, 8;
is $read->seq, 'TAAAAGGA';
is join(' ', @{$read->qual}), '10 30 30 30 30 10 10 30';
is $read->desc, 'reference=human_id start=2 end=8 strand=+1 errors=1%A,1%G,1%T,3-,3-,6+G,6+G description="The human genome"';


# Specifying errors() after new()

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -mid => '', -qual_levels => []);
is $read->start, 1;
is $read->end, 12;
is $read->seq, 'TAAAAAAACCCC';
is join(' ', @{$read->qual}), '';
is $read->desc, 'reference=human_id start=1 end=12 strand=+1 description="The human genome"';

$errors = {};
ok $read->errors($errors), 'errors()';
is $read->start, 1;
is $read->end, 12;
is $read->seq, 'TAAAAAAACCCC';
is $read->desc, 'reference=human_id start=1 end=12 strand=+1 description="The human genome"';

$errors = {};
$errors->{'6'}->{'+'} = 'GG';
ok $read->errors($errors);
is $read->seq, 'TAAAAAGGAACCCC';
is $read->start, 1;
is $read->end, 12;
is $read->desc, 'reference=human_id start=1 end=12 strand=+1 errors=6+G,6+G description="The human genome"';


# More tracking tests

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -mid => 'ACGT', -qual_levels => [], -coord_style => 'genbank' );
is $read->desc, 'reference=human_id position=1..12 mid=ACGT description="The human genome"';

ok $read->mid('AAAA');
is $read->desc, 'reference=human_id position=1..12 mid=AAAA description="The human genome"';

$errors = {};
$errors->{'6'}->{'+'} = 'GG';
ok $read->errors($errors);
is $read->desc, 'reference=human_id position=1..12 mid=AAAA errors=6+G,6+G description="The human genome"';

ok not($read->track(0)), 'track()';
is $read->track, 0;
is $read->desc, undef;
ok $read->track(1);
is $read->track, 1;
is $read->desc, 'reference=human_id position=1..12 mid=AAAA errors=6+G,6+G description="The human genome"';


# qual_levels() method

ok $read = Bio::Seq::SimulatedRead->new(-verbose => $VERBOSE, );
ok $read->qual_levels([30, 10]), 'qual_levels()';
is join(' ', @{$read->qual_levels}), '30 10';

# reference() method

ok $read->reference($ref), 'reference()';
is $read->reference(), $ref;

# mid() method

ok $read = Bio::Seq::SimulatedRead->new(-verbose => $VERBOSE, ), 'mid()';
ok $read->qual_levels([30, 10]);
ok $read->reference($ref);
ok $read->mid('ACGT');
ok $read->mid, 'ACGT';

is $read->seq, 'ACGTTAAAAAAACCCC';
is join(' ', @{$read->qual}), '30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30';
is $read->desc, 'reference=human_id start=1 end=12 strand=+1 mid=ACGT description="The human genome"';

ok $read->mid('TTTAAA');
ok $read->mid, 'TTTAAA';
is $read->seq, 'TTTAAATAAAAAAACCCC';
is join(' ', @{$read->qual}), '30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30';
is $read->desc, 'reference=human_id start=1 end=12 strand=+1 mid=TTTAAA description="The human genome"';


# Edge case... mutation of the last bases of a simulated read with MID

$errors = {};
$errors->{'18'}->{'%'} = 'T';
$read->errors($errors);
is $read->seq, 'TTTAAATAAAAAAACCCT';


# Try different BioPerl object types

ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref  ), 'Bio::Seq::Quality';
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref2 ), 'Bio::Seq';
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref3 ), 'Bio::PrimarySeq';
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref4 ), 'Bio::LocatableSeq';


# More detailed tests of the error specifications

$errors = {};
$errors->{'0'}->{'-'} = undef;
warning_like {$read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors )}
    qr/Positions of substitutions and deletions have to be strictly positive but got 0/;
is $read->seq, 'TAAAAAAACCCC';

$errors = {};
$errors->{'1'}->{'-'} = undef;
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors );
is $read->seq, 'AAAAAAACCCC';

$errors = {};
$errors->{'12'}->{'-'} = undef;
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors );
is $read->seq, 'TAAAAAAACCC';

$errors = {};
$errors->{'13'}->{'-'} = undef;
warning_like {$read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors )}
    qr/Position 13 is beyond end of read \(12 residues\)/; # there should be a warning too
is $read->seq, 'TAAAAAAACCCC';

$errors = {};
$errors->{'0'}->{'%'} = 'G';
warning_like {$read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors )}
    qr/Positions of substitutions and deletions have to be strictly positive/; # there should be a warning too
is $read->seq, 'TAAAAAAACCCC';

$errors = {};
$errors->{'1'}->{'%'} = 'G';
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors );
is $read->seq, 'GAAAAAAACCCC';

$errors = {};
$errors->{'12'}->{'%'} = 'G';
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors );
is $read->seq, 'TAAAAAAACCCG';

$errors = {};
$errors->{'13'}->{'%'} = 'G';
warning_like { $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors ) }
    qr/Position 13 is beyond end of read \(12 residues\)/; # there should be a warning too
is $read->seq, 'TAAAAAAACCCC';

$errors = {};
$errors->{'0'}->{'+'} = 'A';
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors );
is $read->seq, 'ATAAAAAAACCCC';

$errors = {};
$errors->{'1'}->{'+'} = 'A';
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors );
is $read->seq, 'TAAAAAAAACCCC';

$errors = {};
$errors->{'12'}->{'+'} = 'A';
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors );
is $read->seq, 'TAAAAAAACCCCA';

$errors = {};
$errors->{'13'}->{'+'} = 'A';
warning_like {$read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors ) }
    qr/Position 13 is beyond end of read \(12 residues\)/; # there should be a warning too
is $read->seq, 'TAAAAAAACCCC';

$errors = {};
$errors->{'1'}->{'%'} = 'G';
$errors->{'2'}->{'%'} = 'G';
$errors->{'3'}->{'%'} = 'G';
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors );
is $read->seq, 'GGGAAAAACCCC';

$errors = {};
$errors->{'1'}->{'+'} = 'G';
$errors->{'2'}->{'+'} = 'G';
$errors->{'3'}->{'+'} = 'G';
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors );
is $read->seq, 'TGAGAGAAAAACCCC';

$errors = {};
$errors->{'1'}->{'-'} = undef;
$errors->{'2'}->{'-'} = undef;
$errors->{'3'}->{'-'} = undef;
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors );
is $read->seq, 'AAAAACCCC';

$errors = {};
$errors->{'1'}->{'+'} = 'GGG';
$errors->{'2'}->{'-'} = undef;
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors );
is $read->seq, 'TGGGAAAAAACCCC';

$errors = {};
$errors->{'2'}->{'+'} = 'CC';
$errors->{'2'}->{'-'} = undef;
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors );
is $read->seq, 'TCCAAAAAACCCC';

$errors = {};
$errors->{'2'}->{'%'} = 'C';
$errors->{'2'}->{'-'} = undef;
ok $read = Bio::Seq::SimulatedRead->new(-reference => $ref, -errors => $errors );
is $read->seq, 'TAAAAAACCCC';
BioPerl-1.007002/t/Seq/WithQuality.t000444000766000024      1407313155576321 17205 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 22);
	
	use_ok('Bio::Seq::SeqWithQuality');
	use_ok('Bio::PrimarySeq');
	use_ok('Bio::Seq::PrimaryQual');
}

my $DEBUG = test_debug();

my $verbosity = $DEBUG || -1;

# create some random sequence object with no id
my $seqobj_broken = Bio::PrimarySeq->new( -seq => "ATCGATCGA");

ok my $seqobj = Bio::PrimarySeq->new( -seq => "ATCGATCGA",
                            -id  => 'QualityFragment-12',
                            -accession_number => 'X78121',
                            -verbose => $verbosity);

# create some random quality object with the same number of qualities and the same identifiers
my $string_quals = "10 20 30 40 50 40 30 20 10";
my $indices = "5 10 15 20 25 30 35 40 45";
my $qualobj;
eval {
$qualobj = Bio::Seq::PrimaryQual->new( -qual => $string_quals,
                            -id  => 'QualityFragment-12',
                            -accession_number => 'X78121',
                            -verbose => $verbosity);
};
ok(!$@);


# check to see what happens when you construct the SeqWithQuality object
my $swq1 = Bio::Seq::SeqWithQuality->new( -seq	=>	$seqobj,
                                         -verbose => $verbosity,
					-qual		=>	$qualobj);
ok(!$@);
no warnings;

print("Testing various weird constructors...\n") if $DEBUG;
print("\ta) No ids, Sequence object, no quality...\n") if $DEBUG;
# w for weird
my $wswq1;
eval {
	$wswq1 = Bio::Seq::SeqWithQuality->new( -seq  =>	$seqobj,
                                                -verbose => $verbosity,
						-qual	=>	"");
};
ok(!$@);

print("\tb) No ids, no sequence, quality object...\n") if $DEBUG;
	# note that you must provide a alphabet for this one.
$wswq1 = Bio::Seq::SeqWithQuality->new( -seq => "",
                                        -verbose => $verbosity,
					-qual => $qualobj,
					-alphabet => 'dna'
);
print("\tc) Absolutely nothing. (HAHAHAHA)...\n") if $DEBUG;
eval {
	$wswq1 = Bio::Seq::SeqWithQuality->new( -seq => "",
                                                -verbose => $verbosity,
						-qual => "",
						-alphabet => 'dna'
	);
};
ok(!$@);
print("\td) Absolutely nothing but an ID\n") if $DEBUG;
eval {
	$wswq1 = Bio::Seq::SeqWithQuality->new( -seq => "",
                                                -verbose => $verbosity,
						-qual => "",
						-alphabet => 'dna',
						-id => 'an object with no sequence and no quality but with an id'
	);
};
ok(!$@);

print("\td) No sequence, No quality, No ID...\n") if $DEBUG;

eval {
	$wswq1 = Bio::Seq::SeqWithQuality->new( -seq  =>	"",
                                                -verbose => $verbosity,
							-qual	=>	"");
};
# this should fail without a alphabet
ok($@);

print("Testing various methods and behaviors...\n") if $DEBUG;

print("1. Testing the seq() method...\n") if $DEBUG;
	print("\t1a) get\n") if $DEBUG;
	my $original_seq = $swq1->seq();
	is ($original_seq, "ATCGATCGA");
	print("\t1b) set\n") if $DEBUG;
	ok ($swq1->seq("AAAAAAAAAAAA"));
	print("\t1c) get (again, to make sure the set was done.)\n") if $DEBUG;
	is ($swq1->seq(), "AAAAAAAAAAAA");
	print("\tSetting the sequence back to the original value...\n") if $DEBUG;
	$swq1->seq($original_seq);

print("2. Testing the qual() method...\n") if $DEBUG;
	print("\t2a) get\n") if $DEBUG;
	my @qual = @{$swq1->qual()};
	my $str_qual = join(' ',@qual);
	is ($str_qual, "10 20 30 40 50 40 30 20 10");
	print("\t2b) set\n") if $DEBUG;
	ok ($swq1->qual("10 10 10 10 10"));
	print("\t2c) get (again, to make sure the set was done.)\n") if $DEBUG;
	my @qual2 = @{$swq1->qual()};
	my $str_qual2 = join(' ',@qual2);
	is($str_qual2, "10 10 10 10 10");
	print("\tSetting the quality back to the original value...\n") if $DEBUG;
	$swq1->qual($str_qual);

print("3. Testing the length() method...\n") if $DEBUG;
	print("\t3a) When lengths are equal...\n") if $DEBUG;
	is($swq1->length(), 9);	
	print("\t3b) When lengths are different\n") if $DEBUG;
	$swq1->qual("10 10 10 10 10");
	is($swq1->length(), "DIFFERENT");


print("4. Testing the qual_obj() method...\n") if $DEBUG;
	print("\t4a) Testing qual_obj()...\n") if $DEBUG;
		my $retr_qual_obj = $swq1->qual_obj();
		isa_ok $retr_qual_obj, "Bio::Seq::PrimaryQual";
	print("\t4b) Testing qual_obj(\$ref)...\n") if $DEBUG;
		$swq1->qual_obj($qualobj);

print("5. Testing the seq_obj() method...\n") if $DEBUG;
	print("\t5a) Testing seq_qual_obj()...\n") if $DEBUG;
		my $retr_seq_obj = $swq1->seq_obj();
		isa_ok $retr_seq_obj, "Bio::PrimarySeq";
	print("\t5b) Testing seq_obj(\$ref)...\n") if $DEBUG;
		$swq1->seq_obj($seqobj);

print("6. Testing the subqual() method...\n") if $DEBUG;
     my $t_subqual = "10 20 30 40 50 60 70 80 90";
     $swq1->qual($t_subqual);
     print("\t6d) Testing the subqual at the start (border condition)\n") if $DEBUG;
          # ok ('1 2 3' eq join(' ',@{$swq1->subqual(1,3)}));
     print("\t6d) Testing the subqual at the end (border condition)\n") if $DEBUG;
          # ok ('7 8 9' eq join(' ',@{$swq1->subqual(7,9)}));
     print("\t6d) Testing the subqual in the middle\n") if $DEBUG;
          # ok ('4 5 6' eq join(' ',@{$swq1->subqual(4,6)}));


print("7. Testing cases where quality is zero...\n") if $DEBUG;
$swq1 = Bio::Seq::SeqWithQuality->new(-seq =>  'G',
                                      -qual => '0',
                                      -verbose => $verbosity,
                                     );
my $swq2 = Bio::Seq::SeqWithQuality->new(-seq =>  'G',
                                         -qual => '65',
                                         -verbose => $verbosity,
                                     );
is $swq1->length, $swq2->length;

$swq1 = Bio::Seq::SeqWithQuality->new(-seq =>  'GC',
                                      -verbose => $verbosity,
                                      -qual => '0 0',
                                     );
$swq2 = Bio::Seq::SeqWithQuality->new(-seq =>  'GT',
                                      -verbose => $verbosity,
                                      -qual => '65 0',
                                     );
is $swq1->length, $swq2->length;
BioPerl-1.007002/t/SeqFeature000755000766000024          013155576321 15666 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/SeqFeature/Amplicon.t000444000766000024       346413155576321 17761 0ustar00cjfieldsstaff000000000000use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 21);

    use_ok 'Bio::PrimarySeq';
    use_ok 'Bio::SeqFeature::Primer';
    use_ok 'Bio::SeqFeature::Amplicon';
}

my ($amplicon, $amplicon_seq, $fwd_primer, $rev_primer, $template);


# Basic amplicon object

$amplicon = Bio::SeqFeature::Amplicon->new();
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
isa_ok $amplicon, 'Bio::SeqFeature::SubSeq';


# Amplicon with explicit sequence (sequence string)

ok $amplicon = Bio::SeqFeature::Amplicon->new(
    -seq => 'CCCCCAAAAAGGGGGTTTTT',
);
ok $amplicon_seq = $amplicon->seq;
isa_ok $amplicon_seq, 'Bio::PrimarySeq';
is $amplicon_seq->seq, 'CCCCCAAAAAGGGGGTTTTT';


# Amplicon with explicit sequence (sequence object)

$fwd_primer = Bio::SeqFeature::Primer->new(
    -start  => 1,
    -end    => 4,
    -strand => 1
);

$rev_primer = Bio::SeqFeature::Primer->new(
    -seq    => 'GATTA',
    -start  => 16,
    -end    => 20,
    -strand => -1
);

ok $amplicon = Bio::SeqFeature::Amplicon->new(
    -start      => 1,
    -end        => 20,
    -seq        => Bio::PrimarySeq->new( -seq => 'CCCCCAAAAAGGGGGTTTTT' ),
    -fwd_primer => $fwd_primer,
);

ok $amplicon->rev_primer($rev_primer);

is_deeply $amplicon->fwd_primer(), $fwd_primer;
is_deeply $amplicon->rev_primer(), $rev_primer;

ok $amplicon_seq = $amplicon->seq;
isa_ok $amplicon_seq, 'Bio::PrimarySeq';
is $amplicon_seq->seq, 'CCCCCAAAAAGGGGGTTTTT';


# Amplicon with implicit sequence

$template = Bio::Seq->new( -seq => 'ATCGATCGATCCCCCAAAAAGGGGGTTTTTAGCTAGCTAT');

ok $amplicon = Bio::SeqFeature::Amplicon->new(
    -start  => 11,
    -end    => 30,
    -strand => -1
);

ok $template->add_SeqFeature($amplicon);

ok $amplicon_seq = $amplicon->seq;
isa_ok $amplicon_seq, 'Bio::PrimarySeq';
is $amplicon_seq->seq, 'AAAAACCCCCTTTTTGGGGG';
BioPerl-1.007002/t/SeqFeature/Clone.t000444000766000024       505413155576321 17254 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    use Bio::SeqFeature::Generic;
    use Bio::Location::Split;

    test_begin(-tests => 17);
}

my $DEBUG = test_debug();

my $orig = Bio::SeqFeature::Generic->new(
                                       -start => 40,
                                       -end => 80,
                                       -strand => 1,
                                       -primary => 'exon',
                                       -source  => 'internal',
                                       -tag => {
                                           silly => 20,
                                           new => 1
                                           }
                                       );

# ----------
# Verify simple attributes work and are independent of each other
ok(my $clone = $orig->clone(),                'clone()');
ok($clone->start(140),                        'start() clone set');
is($clone->start(),     140,                  'start() clone get');
is($orig->start(),      40,                   'start() original unchanged');

# ----------
# Verify that arguments passed into clone() are applied to the cloned object
# and that the attributes are still independent.
ok($clone = $orig->clone(-start => 150, -end => 157),   'clone() with arguments');
is($orig->start(),       40,                  'start() orig get');
is($orig->end(),         80,                  'end() orig get');
is($clone->start(),     150,                  'start() clone get');
is($clone->end(),       157,                  'end() clone get');
ok($clone->start(140),                        'start() clone set');
is($clone->start(),     140,                  'start() clone get');
is($orig->start(),       40,                  'start() original unchanged');

# ----------
# Verify that object attributes can be cloned, and are independent after cloning
my $splitlocation = Bio::Location::Split->new();
$splitlocation->add_sub_Location(Bio::Location::Simple->new(
   -start=>1, -end=>30, -strand=>1
));
$splitlocation->add_sub_Location(Bio::Location::Simple->new(
   -start=>50, -end=>61, -strand=>1
));
ok($orig->location($splitlocation),                      'location() Bio::Location::Split');
ok($clone = $orig->clone(),                           'clone()');
ok(($clone->location->sub_Location())[1]->start(51),     'start() clone set');
is(($clone->location->sub_Location())[1]->start,     51, 'start() clone get');
is(($orig->location->sub_Location())[1]->start,      50, 'start() original unchanged');


BioPerl-1.007002/t/SeqFeature/Collection.t000444000766000024      1153113155576321 20324 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(
        -tests => 24,
        -requires_module => 'DB_File'
    );

    use_ok('Bio::SeqFeature::Collection');
    use_ok('Bio::Location::Simple');
    use_ok('Bio::Tools::GFF');
    use_ok('Bio::SeqIO');
}

my $verbose = test_debug();

#First of all we need to create an flat db
my $simple = Bio::SeqIO->new(
    -format => 'genbank',
    -file   =>  test_input_file('AB077698.gb')
);

my @features;
my $seq = $simple->next_seq();
@features = $seq->top_SeqFeatures();
is(scalar @features, 11);

ok my $col = Bio::SeqFeature::Collection->new(-verbose => $verbose);

is($col->add_features( \@features), 11);
my @feat = $col->features_in_range(
    -range => (
        Bio::Location::Simple->new(
            -start  => 100,
            -end    => 300,
            -strand => 1,
        )
    ),
    -contain => 0,
);
is(scalar @feat, 5);
if( $verbose ) {    
    for my $f ( @feat ) {
        print "location: ", $f->location->to_FTstring(), "\n";
    }
}

is(scalar $col->features_in_range(
    -range => (
        Bio::Location::Simple->new(
            -start => 100,
            -end   => 300,
            -strand => -1,
        )
    ),
    -strandmatch => 'ignore',
    -contain => 1,
), 2);

@feat = $col->features_in_range(
    -start => 79,
    -end   => 1145,
    -strand => 1,
    -strandmatch => 'strong',
    -contain => 1
);
is(scalar @feat, 5);
if( $verbose ) {    
    for my $f ( sort { $a->start <=> $b->start} @feat ) {
        print $f->primary_tag, " ", $f->location->to_FTstring(), "\n";
    }
}

is($feat[0]->primary_tag, 'CDS');
ok($feat[0]->has_tag('gene'));

$verbose = 0;
# specify input via -fh or -file
my $gffio = Bio::Tools::GFF->new(
    -file => test_input_file('myco_sites.gff'), 
    -gff_version => 2,
);
@features = ();
# loop over the input stream
while(my $feature = $gffio->next_feature()) {
    # do something with feature
    push @features, $feature;
}
$gffio->close();

is(scalar @features, 412);
$col = Bio::SeqFeature::Collection->new(
    -verbose => $verbose,
    -usefile => 1,
);

ok($col);

is($col->add_features( \@features), 412);

my $r = Bio::Location::Simple->new(
    -start => 67700,
    -end   => 150000,
    -strand => 1,
);

@feat = $col->features_in_range(
    -range => $r,
    -strandmatch => 'ignore',
    -contain => 0,
);

is(scalar @feat, 56);
is($col->feature_count, 412);
my $count = $col->feature_count;
$col->remove_features( [$features[58], $features[60]]);

is( $col->feature_count, 410);
@feat = $col->features_in_range(
    -range => $r,
    -strandmatch => 'ignore',
    -contain => 0,
);
is( scalar @feat, 54);
# add the removed features back in in order to get the collection back to size 

$col->add_features([$features[58], $features[60]]);

# let's randomize so we aren't removing and adding in the same order
# and hopefully randomly deal with a bin's expiration
fy_shuffle(\@features);

for my $f ( @features ) {
    $count--, next unless defined $f;
    $col->remove_features([$f]);
#    ok( $col->feature_count, --$count);
}
is($col->feature_count, 0);

# explicitly destroy old instances above (should clear out any open filehandles
# w/o -keep flag set)
undef $col; 

my $filename = test_output_file();
my $newcollection = Bio::SeqFeature::Collection->new(
    -verbose => $verbose,
    -keep    => 1,
    -file    => $filename,
);
$newcollection->add_features(\@feat);
is($newcollection->feature_count, 54);
undef $newcollection;
ok(-s $filename);
$newcollection = Bio::SeqFeature::Collection->new(
    -verbose => $verbose,
    -file    => $filename,
);
is($newcollection->feature_count, 54);
undef $newcollection;
ok( ! -e $filename);
# without -keep => 1, $filename was deleted as expected.
# to stop Bio::Root::Test complaining that the temp file was already deleted,
# we'll just create it again
open my $TMP, '>', $filename or die "Could not write file '$filename': $!\n";
print $TMP "temp\n";
close $TMP;

if( $verbose ) {
    my @fts =  sort { $a->start <=> $b->start}  
    grep { $r->overlaps($_,'ignore') } @features;
    
    if( $verbose ) {
        for my $f ( @fts ) {
            print $f->primary_tag, "    ", $f->location->to_FTstring(), "\n";
        }
        print "\n";
    }

    my %G = map { ($_,1) } @feat; 
    my $c = 0;
    for my $A ( @fts ) {
        if( ! $G{$A} ) {
            print "missing ", $A->primary_tag, " ", $A->location->to_FTstring(), "\n";
        } else { 
            $c++;
        }
    }
    print "Number of features correctly retrieved $c\n";
    for my $f ( sort { $a->start <=> $b->start} @feat ) {
        print $f->primary_tag, "    ", $f->location->to_FTstring(), "\n";
    }
}

sub fy_shuffle { 
    my $array = shift;
    my $i;
    for( $i = @$array; $i--; ) { 
        my $j = int rand($i+1);
        next if $i==$j;
        @$array[$i,$j] = @$array[$j,$i];
    }
}
BioPerl-1.007002/t/SeqFeature/Computation.t000444000766000024       230013155576321 20505 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 12);

    use_ok('Bio::SeqFeature::Computation');
}

my ($comp_obj1, $comp_obj2, @sft);

ok $comp_obj1 = Bio::SeqFeature::Computation->new(
    -start => 1,
    -end   => 10,
);

is $comp_obj1->computation_id(332), 332, 'computation id';

ok $comp_obj1->add_score_value('P', 33), 'score value';

ok $comp_obj2 = Bio::SeqFeature::Computation->new(
    -start => 2,
    -end   => 10,
);

ok $comp_obj1->add_SeqFeature($comp_obj2, 'exon');
ok @sft = $comp_obj1->get_all_SeqFeature_types();

is $sft[0], 'exon', 'sft[0] is exon';


ok $comp_obj1 = Bio::SeqFeature::Computation->new(
    -start => 10,
    -end => 100,
    -strand => -1,
    -primary => 'repeat',
    -program_name => 'GeneMark',
    -program_date => '12-5-2000',
    -program_version => 'x.y',
    -database_name => 'Arabidopsis',
    -database_date => '12-dec-2000',
    -computation_id => 2231,
    -score    => { no_score => 334 },
);

is $comp_obj1->computation_id, 2231, 'computation id';
ok $comp_obj1->add_score_value('P', 33);
is ( ($comp_obj1->each_score_value('no_score'))[0], '334', 'score value');
BioPerl-1.007002/t/SeqFeature/FeaturePair.t000444000766000024       247613155576321 20430 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 19);

    use_ok('Bio::SeqFeature::Generic');
    use_ok('Bio::SeqFeature::FeaturePair');
}


my ($feat, $feat2, $pair);

ok $pair = Bio::SeqFeature::FeaturePair->new();

ok $feat = Bio::SeqFeature::Generic->new(
    -start => 40,
    -end => 80,
    -strand => 1,
    -primary => 'exon',
    -source => 'internal',
    -display_name => 'my exon feature',
    -tag => {
        silly => 20,
        new => 1
    }
);

ok $feat2 = Bio::SeqFeature::Generic->new(
    -start => 400,
    -end => 440,
    -strand => 1,
    -primary => 'other',
    -source => 'program_a',
    -phase => 1,
    -tag => {
        silly => 20,
        new => 1
    }
);

ok $pair->feature1($feat);
ok $pair->feature2($feat2);

is $pair->feature1, $feat, 'feature1 of pair stored';
is $pair->feature2, $feat2, 'feature2 of pair stored';
is $pair->start, 40, 'feature start';
is $pair->end, 80, 'feature end';
is $pair->primary_tag, 'exon', 'primary tag';
is $pair->source_tag, 'internal', 'source tag';
is $pair->hstart, 400, 'hstart';
is $pair->hend, 440, 'hend';
is $pair->hprimary_tag, 'other', 'hprimary tag';
is $pair->hsource_tag, 'program_a', 'hsource tag';

ok $pair->invert;
is $pair->end, 440, 'inverted end';
BioPerl-1.007002/t/SeqFeature/Gene.t000444000766000024       637613155576321 17102 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 28);

    use_ok('Bio::SeqIO');
    use_ok('Bio::SeqFeature::Gene::Transcript');
    use_ok('Bio::SeqFeature::Gene::UTR');
    use_ok('Bio::SeqFeature::Gene::Exon');
    use_ok('Bio::SeqFeature::Gene::Poly_A_site');
    use_ok('Bio::SeqFeature::Gene::GeneStructure');
    use_ok('Bio::Location::Fuzzy');
}


my ( $seqio, $geneseq, $gene, $transcript, $poly_A_site1, $poly_A_site2,
     $fiveprimeUTR, $exon);

# tests for Bio::SeqFeature::Gene::* objects
# using information from acc: AB077698 as a guide

ok $seqio = Bio::SeqIO->new(
    -format => 'genbank',
    -file   => test_input_file('AB077698.gb'),
);

ok $geneseq = $seqio->next_seq();

ok $gene = Bio::SeqFeature::Gene::GeneStructure->new(
    -primary => 'gene',
    -start   => 1,
    -end     => 2701,
    -strand  => 1,
);

ok $transcript = Bio::SeqFeature::Gene::Transcript->new(
    -primary => 'CDS',
    -start   => 80,
    -end     => 1144,
    -tag     => { 
        'gene' => "CHCR",
        'note' => "Cys3His CCG1-Required Encoded on BAC clone RP5-842K24 (AL050310) The human CHCR (Cys3His CCG1-Required) protein is highly related to EXP/MBNL (Y13829, NM_021038, AF401998) and MBLL (NM_005757,AF061261), which together comprise the human Muscleblind family",
       'codon_start' => 1,
       'protein_id'  => 'BAB85648.1',
    }
);

ok $poly_A_site1 = Bio::SeqFeature::Gene::Poly_A_site->new(
    -primary => 'polyA_site',
    -start => 2660,
    -end   => 2660,
    -tag   => { 
        'note' => "Encoded on BAC clone RP5-842K24 (AL050310); PolyA_site#2 used by CHCR EST clone DKFZp434G2222 (AL133625)"
    }
);

ok $poly_A_site2 = Bio::SeqFeature::Gene::Poly_A_site->new(
    -primary => 'polyA_site',
    -start => 1606,
    -end   => 1606,
    -tag   => { 
        'note' => "Encoded on BAC clone RP5-842K24 (AL050310); PolyA_site#1 used by CHCR EST clone PLACE1010202 (AK002178)",
    }
);

ok $fiveprimeUTR = Bio::SeqFeature::Gene::UTR->new(-primary => "utr5prime");
ok $fiveprimeUTR->location(
    Bio::Location::Fuzzy->new(
        -start => "<1",
        -end   => 79,
    )
);
ok my $threeprimeUTR = Bio::SeqFeature::Gene::UTR->new(
    -primary => "utr3prime",
    -start   => 1145,
    -end     => 2659,
);

# Did a quick est2genome against genomic DNA (this is on Chr X) to
# get the gene structure by hand since it is not in the file
# --Jason

ok $exon = Bio::SeqFeature::Gene::Exon->new(
    -primary => 'exon',
    -start => 80,
    -end   => 177,
);
ok $geneseq->add_SeqFeature($exon);

ok $geneseq->add_SeqFeature($fiveprimeUTR);
ok $geneseq->add_SeqFeature($threeprimeUTR);
ok $geneseq->add_SeqFeature($poly_A_site1);
ok $geneseq->add_SeqFeature($poly_A_site2);

ok $transcript->add_utr($fiveprimeUTR, 'utr5prime');
ok $transcript->add_utr($threeprimeUTR, 'utr3prime');

ok $transcript->add_exon($exon);

# API only supports a single poly-A site per transcript at this point 
$transcript->poly_A_site($poly_A_site2);
$geneseq->add_SeqFeature($transcript);
$gene->add_transcript($transcript);
$geneseq->add_SeqFeature($gene);

my ($t) = $gene->transcripts(); # get 1st transcript
ok(defined $t); 
is($t->mrna->length, 1693, 'mRNA spliced length');
is($gene->utrs, 2, 'has 2 UTRs');


BioPerl-1.007002/t/SeqFeature/Generic.t000444000766000024      2347013155576321 17612 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 364);

    use_ok 'Bio::Seq';
    use_ok 'Bio::SeqIO';
    use_ok 'Bio::SeqFeature::Generic';
}


my ($feat, $str, $feat2, $pair, @sft); 

my $DEBUG = test_debug();

ok $feat = Bio::SeqFeature::Generic->new(
    -start => 40,
    -end => 80,
    -strand => 1,
);
is $feat->primary_tag, '';
is $feat->source_tag, '';
is $feat->display_name, '';

ok $feat = Bio::SeqFeature::Generic->new(
    -start => 40,
    -end => 80,
    -strand => 1,
    -primary => 'exon',
    -source  => 'internal',
    -display_name => 'my exon feature',
    -tag => {
        silly => 20,
        new => 1
    }
);

is $feat->start, 40, 'Start of feature location';
is $feat->end, 80, 'End of feature location';
is $feat->primary_tag, 'exon', 'Primary tag';
is $feat->source_tag, 'internal', 'Source tag';
is $feat->display_name, 'my exon feature', 'Display name';
is $feat->phase, undef, 'Undef phase by default';
is $feat->phase(1), 1, 'Phase accessor returns';
is $feat->phase, 1, 'Phase is persistent';

ok $feat->gff_string();

ok $feat2 = Bio::SeqFeature::Generic->new(
    -start => 400,
    -end => 440,
    -strand => 1,
    -primary => 'other',
    -source  => 'program_a',
        -phase => 1,
        -tag => {
            silly => 20,
            new => 1
        }
);
is $feat2->phase, 1, 'Set phase from constructor';


# Test attaching a SeqFeature::Generic to a Bio::Seq or SeqFeature::Generic
{
    # Make the parent sequence object
    my $seq = Bio::Seq->new(
        -seq        => 'aaaaggggtttt',
        -display_id => 'test',
        -alphabet   => 'dna',
    );
    
    # Make a SeqFeature
    ok my $sf1 = Bio::SeqFeature::Generic->new(
        -start  => 4,
        -end    => 9,
        -strand => 1,
    );
    
    # Add the SeqFeature to the parent
    ok $seq->add_SeqFeature($sf1);
    
    # Test that it gives the correct sequence
    is $sf1->start, 4, 'Start of first seqfeature';
    is $sf1->end, 9, 'End of first seqfeature';
    is $sf1->strand, 1, 'Strand of first seqfeature';
    ok my $sf_seq1 = $sf1->seq;
    is $sf_seq1->seq, 'aggggt', 'Sequence of first seqfeature';

    # Make a second seqfeature on the opposite strand
    ok my $sf2 = Bio::SeqFeature::Generic->new(
        -start  => 4,
        -end    => 9,
        -strand => -1,
    );
    
    # Now add the PrimarySeq to the seqfeature before adding it to the parent
    ok $sf2->attach_seq($seq->primary_seq);
    ok $seq->add_SeqFeature($sf2);
    
    # Test again that we have the correct sequence
    is $sf2->start, 4, 'Start of second seqfeature';
    is $sf2->end, 9, 'End of second seqfeature';
    is $sf2->strand, -1, 'Strand of second seqfeature';
    ok my $sf_seq2 = $sf2->seq;
    is $sf_seq2->seq, 'acccct', 'Sequence of second seqfeature';
}


# Some tests for bug #947

ok my $sfeat = Bio::SeqFeature::Generic->new(-primary => 'test');

ok $sfeat->add_sub_SeqFeature(
    Bio::SeqFeature::Generic->new(
        -start => 2,
        -end   => 4,
        -primary => 'sub1'
    ),
    'EXPAND'
);

ok $sfeat->add_sub_SeqFeature(
    Bio::SeqFeature::Generic->new(
        -start => 6,
        -end   => 8,
        -primary => 'sub2'
    ),
    'EXPAND'
);

is $sfeat->start, 2, 'sfeat start for EXPAND-ED feature (bug #947)';
is $sfeat->end, 8, 'sfeat end for EXPAND-ED feature (bug #947)';

# Some tests to see if we can set a feature to start at 0
ok $sfeat = Bio::SeqFeature::Generic->new(-start => 0, -end => 0 );

ok defined $sfeat->start;
is $sfeat->start, 0, 'Can create feature starting and ending at 0';
ok defined $sfeat->end;
is $sfeat->end, 0, 'Can create feature starting and ending at 0';


# Test for bug when Locations are not created explicitly

ok my $feat1 = Bio::SeqFeature::Generic->new(
    -start => 1,
    -end   => 15,
    -strand=> 1
);

ok $feat2 = Bio::SeqFeature::Generic->new(
    -start => 10,
    -end   => 25,
    -strand=> 1
);

ok my $overlap = $feat1->location->union($feat2->location);
is $overlap->start, 1;
is $overlap->end,   25;

ok my $intersect = $feat1->location->intersection($feat2->location);
is $intersect->start, 10;
is $intersect->end,   15;


# Now let's test spliced_seq
ok my $seqio = Bio::SeqIO->new(
    -file => test_input_file('AY095303S1.gbk'),
    -format  => 'genbank'
);
isa_ok $seqio, 'Bio::SeqIO';
ok my $geneseq = $seqio->next_seq;
isa_ok $geneseq, 'Bio::Seq';
ok my ($CDS) = grep { $_->primary_tag eq 'CDS' } $geneseq->get_SeqFeatures;
my $db;

SKIP: {
    test_skip(-tests => 5,
              -requires_modules => [qw(IO::String
                                       LWP::UserAgent
                                       HTTP::Request::Common)],
              -requires_networking => 1);
    
    use_ok 'Bio::DB::GenBank';
    
    $db = Bio::DB::GenBank->new(-verbose=> $DEBUG);
    $CDS->verbose(-1);
    my $cdsseq = $CDS->spliced_seq(-db => $db,-nosort => 1);
    
    is $cdsseq->subseq(1,76),
       'ATGCAGCCATACGCTTCCGTGAGCGGGCGATGTCTATCTAGACCAGATGCATTGCATGTGATACCGTTTGGGCGAC';
    is $cdsseq->translate->subseq(1,100),
       'MQPYASVSGRCLSRPDALHVIPFGRPLQAIAGRRFVRCFAKGGQPGDKKKLNVTDKLRLGNTPPTLDVLK'.
       'APRPTDAPSAIDDAPSTSGLGLGGGVASPR';
    # Test what happens without 
    $cdsseq = $CDS->spliced_seq(-db => $db,-nosort => 1);    
    is $cdsseq->subseq(1,76), 
       'ATGCAGCCATACGCTTCCGTGAGCGGGCGATGTCTATCTAGACCAGATGCATTGCATGTGATACCGTTTGGGCGAC';
    is $cdsseq->translate->subseq(1,100), 
       'MQPYASVSGRCLSRPDALHVIPFGRPLQAIAGRRFVRCFAKGGQPGDKKKLNVTDKLRLGNTPPTLDVLK'.
       'APRPTDAPSAIDDAPSTSGLGLGGGVASPR';
} 

ok $seqio = Bio::SeqIO->new(
    -file => test_input_file('AF032047.gbk'),
    -format  => 'genbank'
);
isa_ok $seqio, 'Bio::SeqIO';
ok $geneseq = $seqio->next_seq;
isa_ok $geneseq, 'Bio::Seq';
ok( ($CDS) = grep { $_->primary_tag eq 'CDS' } $geneseq->get_SeqFeatures );
SKIP: { 
    test_skip(-tests => 2,
              -requires_modules => [qw(IO::String
                                       LWP::UserAgent
                                       HTTP::Request::Common)],
              -requires_networking => 1);
    
    my $cdsseq = $CDS->spliced_seq( -db => $db, -nosort => 1);
    is $cdsseq->subseq(1,70),
       'ATGGCTCGCTTCGTGGTGGTAGCCCTGCTCGCGCTACTCTCTCTGTCTGGCCTGGAGGCTATCCAGCATG';
    is $cdsseq->translate->seq,
       'MARFVVVALLALLSLSGLEAIQHAPKIQVYSRHPAENGKPNFLNCYVSGFHPSDIEVDLLKNGKKIEKVE'.
       'HSDLSFSKDWSFYLLYYTEFTPNEKDEYACRVSHVTFPTPKTVKWDRTM*';
}


# Trans-spliced 

ok $seqio = Bio::SeqIO->new(
    -format => 'genbank',
    -file => test_input_file('NC_001284.gbk')
);
isa_ok $seqio, 'Bio::SeqIO';
ok my $genome = $seqio->next_seq;

for my $cds (grep { $_->primary_tag eq 'CDS' } $genome->get_SeqFeatures) {
   ok my $spliced = $cds->spliced_seq(-nosort => 1)->translate->seq;
   chop $spliced; # remove stop codon
   is $spliced, ($cds->get_tag_values('translation'))[0], 'spliced_seq translation matches expected';
}

# Spliced_seq phase 
ok my $seq = Bio::SeqIO->new(
    -format => 'fasta',
    -file   => test_input_file('sbay_c127.fas')
)->next_seq;

ok my $sf = Bio::SeqFeature::Generic->new(
    -verbose => -1,
    -start => 263,
    -end => 721,
    -strand => 1,
    -primary => 'splicedgene'
);

ok $sf->attach_seq($seq);

my %phase_check = (
    'TTCAATGACT' => 'FNDFYSMGKS',
    'TCAATGACTT' => 'SMTSIPWVNQ',
    'GTTCAATGAC' => 'VQ*LLFHG*I',
);

for my $phase (-1..3) {
    ok my $sfseq = $sf->spliced_seq(-phase => $phase);
    ok exists $phase_check{$sfseq->subseq(1,10)};
    is $sfseq->translate->subseq(1,10), $phase_check{$sfseq->subseq(1,10)}, 'phase check';
}

# Tags
ok $sf->add_tag_value('note','n1');
ok $sf->add_tag_value('note','n2');
ok $sf->add_tag_value('comment','c1');
is_deeply [sort $sf->get_all_tags()], [sort qw(note comment)] , 'Tags found';
is_deeply [sort $sf->get_tagset_values('note')], [sort qw(n1 n2)] , 'get_tagset_values tag values found';
is_deeply [sort $sf->get_tagset_values(qw(note comment))], [sort qw(c1 n1 n2)] , 'get_tagset_values tag values for multiple tags found';
lives_ok { 
  is_deeply [sort $sf->get_tag_values('note')], [sort qw(n1 n2)] , 'get_tag_values tag values found';
} 'get_tag_values lives with tag';
lives_ok { 
  is_deeply [$sf->get_tagset_values('notag') ], [], 'get_tagset_values no tag values found';
} 'get_tagset_values lives with no tag';
throws_ok { $sf->get_tag_values('notag') } qr/tag value that does not exist/, 'get_tag_values throws with no tag';

# Circular sequence SeqFeature tests
$seq = Bio::SeqIO->new(
    -format => 'genbank',
    -file   => test_input_file('PX1CG.gb')
)->next_seq;

ok $seq->is_circular, 'Phi-X174 genome is circular';

# Retrieving the spliced sequence from any split location requires spliced_seq()

my %sf_data = (
    #       start
    'A'  => [3981, 136, 1, 1542, 'join(3981..5386,1..136)', 'ATGGTTCGTT'],
    'A*' => [4497, 136, 1, 1026, 'join(4497..5386,1..136)', 'ATGAAATCGC'],
    'B'  => [5075, 51,  1, 363,  'join(5075..5386,1..51)',  'ATGGAACAAC'],
);

ok my @split_sfs = grep {
    $_->location->isa('Bio::Location::SplitLocationI')
    } $seq->get_SeqFeatures();

is @split_sfs, 3, 'Only 3 split locations';

for my $sf (@split_sfs) {
    isa_ok $sf->location, 'Bio::Location::SplitLocationI';
    ok my ($tag) = $sf->get_tag_values('product');
    my ($start, $end, $strand, $length, $ftstring, $first_ten) = @{$sf_data{$tag}};
    
    is $sf->location->to_FTstring, $ftstring, 'Feature string';
    is $sf->spliced_seq->subseq(1,10), $first_ten, 'First ten nucleotides';
    is $sf->strand, $strand, 'Strand';
    is $sf->start, $start, 'Start';
    is $sf->end, $end, 'End';
    is $sf->length, $length, 'Expected length';
}

# spliced_seq() on the reverse strand, bug #88 (github)
$seq = Bio::SeqIO->new( -file => test_input_file('AF222649-rc.gbk') )->next_seq;
# All should start with "ATG"
for my $feat ( $seq->get_SeqFeatures('CDS') ) {
    ok $feat->spliced_seq->seq =~ /^ATG/, "Reverse strand is spliced correctly";
}
        

BioPerl-1.007002/t/SeqFeature/Location.t000444000766000024      2107713155576321 20007 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 109);
	
    use_ok('Bio::Location::Simple');
    use_ok('Bio::Location::Split');
    use_ok('Bio::Location::Fuzzy');
    use_ok('Bio::SeqFeature::Generic');
    use_ok('Bio::SeqFeature::SimilarityPair');
    use_ok('Bio::SeqFeature::FeaturePair');
    use_ok('Bio::SeqFeature::Lite');
}

my $simple = Bio::Location::Simple->new('-start' => 10, '-end' => 20,
				       '-strand' => 1, -seq_id => 'my1');
isa_ok($simple, 'Bio::LocationI');
isa_ok($simple, 'Bio::RangeI');

is($simple->start, 10, 'Bio::Location::Simple tests');
is($simple->end, 20);
is($simple->seq_id, 'my1');

my ($loc) = $simple->each_Location();
ok($loc);
is("$loc", "$simple");

my $generic = Bio::SeqFeature::Generic->new('-start' => 5, '-end' => 30, 
					   '-strand' => 1);

isa_ok($generic,'Bio::SeqFeatureI', 'Bio::SeqFeature::Generic' );
isa_ok($generic,'Bio::RangeI');
is($generic->start, 5);
is($generic->end, 30);

my $lite_pos  = Bio::SeqFeature::Lite->new(-start => 1000, -stop => 2000, -strand => '+');
my $lite_neg  = Bio::SeqFeature::Lite->new(-start => 1000, -end  => 2000, -strand => '-');
my $lite_none = Bio::SeqFeature::Lite->new(-start => 1000, -stop => 2000, -strand => '.');
is($lite_pos->strand,  1);
is($lite_neg->strand, -1);
is($lite_neg->end,  2000);
is($lite_neg->stop, 2000);
is($lite_none->strand, 0);

my $similarity = Bio::SeqFeature::SimilarityPair->new();

my $feat1 = Bio::SeqFeature::Generic->new('-start' => 30, '-end' => 43, 
					 '-strand' => -1);
my $feat2 = Bio::SeqFeature::Generic->new('-start' => 80, '-end' => 90, 
					 '-strand' => -1);

my $featpair = Bio::SeqFeature::FeaturePair->new('-feature1' => $feat1,
						'-feature2' => $feat2 );

my $feat3 = Bio::SeqFeature::Generic->new('-start' => 35, '-end' => 50, 
					 '-strand' => -1);

is($featpair->start, 30,'Bio::SeqFeature::FeaturePair tests');
is($featpair->end,  43);

is($featpair->length, 14);

ok($featpair->overlaps($feat3));
ok($generic->overlaps($simple), 'Bio::SeqFeature::Generic tests');
ok($generic->contains($simple));

# fuzzy location tests
my $fuzzy = Bio::Location::Fuzzy->new('-start'  =>'<10', 
				     '-end'    => 20,
				     -strand   =>1, 
				     -seq_id   =>'my2');

is($fuzzy->strand, 1, 'Bio::Location::Fuzzy tests');
is($fuzzy->start, 10);
is($fuzzy->end,20);
ok(!defined $fuzzy->min_start);
is($fuzzy->max_start, 10);
is($fuzzy->min_end, 20);
is($fuzzy->max_end, 20);
is($fuzzy->location_type, 'EXACT');
is($fuzzy->start_pos_type, 'BEFORE');
is($fuzzy->end_pos_type, 'EXACT');
is($fuzzy->seq_id, 'my2');
is($fuzzy->seq_id('my3'), 'my3');

($loc) = $fuzzy->each_Location();
ok($loc);
is("$loc", "$fuzzy");

# split location tests
my $splitlocation = Bio::Location::Split->new();
my $f = Bio::Location::Simple->new(-start  => 13,
				  -end    => 30,
				  -strand => 1);
$splitlocation->add_sub_Location($f);
is($f->start, 13, 'Bio::Location::Split tests');
is($f->min_start, 13);
is($f->max_start,13);


$f = Bio::Location::Simple->new(-start  =>30,
			       -end    =>90,
			       -strand =>1);
$splitlocation->add_sub_Location($f);

$f = Bio::Location::Simple->new(-start  =>11,
			       -end    =>22,
			       -strand =>1);
$splitlocation->add_sub_Location($f);

$f = Bio::Location::Simple->new(-start  =>19,
			       -end    =>20,
			       -strand =>1);

$splitlocation->add_sub_Location($f);

$f = Bio::Location::Fuzzy->new(-start  =>"<50",
			      -end    =>61,
			      -strand =>1);
is($f->start, 50);
ok(! defined $f->min_start);
is($f->max_start, 50);

is(scalar($splitlocation->each_Location()), 4);

$splitlocation->add_sub_Location($f);

# For unsorted split locations like this:
# ('join(13..30,30..90,11..22,19..20,<50..61)'),
# BioPerl will assume Start and End belongs to the
# first and last segments respectively, because sorting
# would break real cases like circular cut by origin features
is($splitlocation->end, 61);
is($splitlocation->start, 13);
is($splitlocation->sub_Location(),5);
# Minimum Start and Maximum End in unsorted sublocations can be
# achieved by asking explicitly sub_Location to sort the segments
my @increase_sort_sublocs = $splitlocation->sub_Location(1);  # Forward sort by Start
my @decrease_sort_sublocs = $splitlocation->sub_Location(-1); # Reverse sort by End
is($increase_sort_sublocs[0]->min_start, 11);
is($decrease_sort_sublocs[0]->max_end,   90);

is($fuzzy->to_FTstring(), '<10..20');
$fuzzy->strand(-1);
is($fuzzy->to_FTstring(), 'complement(<10..20)');
is($simple->to_FTstring(), '10..20');
$simple->strand(-1);
is($simple->to_FTstring(), 'complement(10..20)');
is( $splitlocation->to_FTstring(), 
    'join(13..30,30..90,11..22,19..20,<50..61)');

# test for bug #1074
$f = Bio::Location::Simple->new(-start  => 5,
			       -end    => 12,
			       -strand => -1);
$splitlocation->add_sub_Location($f);
is( $splitlocation->to_FTstring(), 
    'join(13..30,30..90,11..22,19..20,<50..61,complement(5..12))',
	'Bugfix 1074');
$splitlocation->strand(-1);
is( $splitlocation->to_FTstring(), 
    'complement(join(13..30,30..90,11..22,19..20,<50..61,5..12))');

$f = Bio::Location::Fuzzy->new(-start => '45.60',
			      -end   => '75^80');

is($f->to_FTstring(), '(45.60)..(75^80)');
$f->start('20>');
is($f->to_FTstring(), '>20..(75^80)');

# test that even when end < start that length is always positive

$f = Bio::Location::Simple->new(-verbose => -1,
			       -start   => 100, 
			       -end     => 20, 
			       -strand  => 1);

is($f->length, 81, 'Positive length');
is($f->strand,-1);

# test that can call seq_id() on a split location;
$splitlocation = Bio::Location::Split->new(-seq_id => 'mysplit1');
is($splitlocation->seq_id,'mysplit1', 'seq_id() on Bio::Location::Split');
is($splitlocation->seq_id('mysplit2'),'mysplit2');


# Test Bio::Location::Exact

ok(my $exact = Bio::Location::Simple->new(-start    => 10, 
					 -end      => 20,
					 -strand   => 1, 
					 -seq_id   => 'my1'));
isa_ok($exact, 'Bio::LocationI');
isa_ok($exact, 'Bio::RangeI');

is( $exact->start, 10, 'Bio::Location::Simple EXACT');
is( $exact->end, 20);
is( $exact->seq_id, 'my1');
is( $exact->length, 11);
is( $exact->location_type, 'EXACT');

ok ($exact = Bio::Location::Simple->new(-start         => 10, 
				      -end           => 11,
				      -location_type => 'IN-BETWEEN',
				      -strand        => 1, 
				      -seq_id        => 'my2'));

is($exact->start, 10, 'Bio::Location::Simple IN-BETWEEN');
is($exact->end, 11);
is($exact->seq_id, 'my2');
is($exact->length, 0);
is($exact->location_type, 'IN-BETWEEN');

eval {
    $exact = Bio::Location::Simple->new(-start         => 10, 
				       -end           => 12,
				       -location_type => 'IN-BETWEEN');
};
ok( $@, 'Testing error handling' );

# testing error when assigning 10^11 simple location into fuzzy
eval {
    ok $fuzzy = Bio::Location::Fuzzy->new(-start         => 10, 
					 -end           => 11,
					 -location_type => '^',
					 -strand        => 1, 
					 -seq_id        => 'my2');
};
ok( $@ );

$fuzzy = Bio::Location::Fuzzy->new(-location_type => '^',
				  -strand        => 1, 
				  -seq_id        => 'my2');

$fuzzy->start(10);
eval { $fuzzy->end(11) };
ok($@);

$fuzzy = Bio::Location::Fuzzy->new(-location_type => '^',
				  -strand        => 1, 
				  -seq_id        =>'my2');

$fuzzy->end(11);
eval {
    $fuzzy->start(10);
};
ok($@);

# testing coodinate policy modules

use_ok('Bio::Location::WidestCoordPolicy');
use_ok('Bio::Location::NarrowestCoordPolicy');
use_ok('Bio::Location::AvWithinCoordPolicy');

$f = Bio::Location::Fuzzy->new(-start => '40.60',
			      -end   => '80.100');
is $f->start, 40, 'Default coodinate policy';
is $f->end, 100;
is $f->length, 61;
is $f->to_FTstring, '(40.60)..(80.100)';
isa_ok($f->coordinate_policy, 'Bio::Location::WidestCoordPolicy');

# this gives an odd location string; is it legal?
$f->coordinate_policy(Bio::Location::NarrowestCoordPolicy->new());
is $f->start, 60, 'Narrowest coodinate policy';
is $f->end, 80;
is $f->length, 21;
is $f->to_FTstring, '(60.60)..(80.80)';
isa_ok($f->coordinate_policy, 'Bio::Location::NarrowestCoordPolicy');

# this gives an odd location string
$f->coordinate_policy(Bio::Location::AvWithinCoordPolicy->new());
is $f->start, 50, 'Average coodinate policy';
is $f->end, 90;
is $f->length, 41;
is $f->to_FTstring, '(50.60)..(80.90)';
isa_ok($f->coordinate_policy, 'Bio::Location::AvWithinCoordPolicy');

# to complete the circle
$f->coordinate_policy(Bio::Location::WidestCoordPolicy->new());
is $f->start, 40, 'Widest coodinate policy';
is $f->end, 100;
is $f->length, 61;
is $f->to_FTstring, '(40.60)..(80.100)';
isa_ok($f->coordinate_policy, 'Bio::Location::WidestCoordPolicy');
BioPerl-1.007002/t/SeqFeature/LocationFactory.t000444000766000024      2440513155576321 21335 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 325);

    use_ok('Bio::Factory::FTLocationFactory');
}

my $simple_impl = "Bio::Location::Simple";
my $fuzzy_impl  = "Bio::Location::Fuzzy";
my $split_impl  = "Bio::Location::Split";

# Holds strings and results. The latter is an array of expected class name,
# min/max start position and position type, min/max end position and position
# type, location type, the number of locations, and the strand.
#
my %testcases = (
    # note: the following are directly taken from
    # http://www.insdc.org/documents/feature_table.html#3.4.3
    "467"
        => [$simple_impl, 467, 467, "EXACT",
                          467, 467, "EXACT",
                          "EXACT", 1, 1],
    "340..565"
        => [$simple_impl, 340, 340, "EXACT",
                          565, 565, "EXACT",
                          "EXACT", 1, 1],
    "<345..500"
        => [$fuzzy_impl, undef, 345, "BEFORE",
                         500,   500, "EXACT",
                         "EXACT", 1, 1],
    "<1..888"
        => [$fuzzy_impl, undef, 1,   "BEFORE",
                         888,   888, "EXACT",
                         "EXACT", 1, 1],
    "1..>888"
        => [$fuzzy_impl, 1,   1,     "EXACT",
                         888, undef, "AFTER",
                         "EXACT", 1, 1],
    "(102.110)"
        => [$fuzzy_impl, 102, 102, "EXACT",
                         110, 110, "EXACT",
                         "WITHIN", 1, 1],
    "(23.45)..600"
        => [$fuzzy_impl, 23,  45,  "WITHIN",
                         600, 600, "EXACT",
                         "EXACT", 1, 1],
    "(122.133)..(204.221)"
        => [$fuzzy_impl, 122, 133, "WITHIN",
                         204, 221, "WITHIN",
                         "EXACT", 1, 1],
    "123^124"
        => [$simple_impl, 123, 123, "EXACT",
                          124, 124, "EXACT",
                          "IN-BETWEEN", 1, 1],
    "145^177"
        => [$fuzzy_impl, 145, 145, "EXACT",
                         177, 177, "EXACT",
                         "IN-BETWEEN", 1, 1],
    "join(12..78,134..202)"
        => [$split_impl, 12,  12,  "EXACT",
                         202, 202, "EXACT",
                         "EXACT", 2, 1],
    "complement(join(2691..4571,4918..5163))"
        => [$split_impl, 2691, 2691, "EXACT",
                         5163, 5163, "EXACT",
                         "EXACT", 2, -1],
    # Partial frameshifted gene at the end of a contig
    "complement(join(94468..94578,94578..>94889))"
        => [$split_impl, 94468, 94468, "EXACT",
                         94889, undef, "AFTER",
                         "EXACT", 2, -1],
    "complement(34..(122.126))"
        => [$fuzzy_impl, 34,  34,  "EXACT",
                         122, 126, "WITHIN",
                         "EXACT", 1, -1],
    "J00194:100..202"
        => [$simple_impl, 100, 100, "EXACT",
                          202, 202, "EXACT",
                          "EXACT", 1, 1],
    "join(1..100,J00194.1:100..202)"
        => [$split_impl, 1,   1,   "EXACT",
                         100, 100, "EXACT",
                         "EXACT", 2, 1],

    # this variant is not really allowed by the FT definition
    # document but we want to be able to cope with it
    "J00194:(100..202)"
        => [$simple_impl, 100, 100, "EXACT",
                          202, 202, "EXACT",
                          "EXACT", 1, 1],
    "((122.133)..(204.221))"
        => [$fuzzy_impl, 122, 133, "WITHIN",
                         204, 221, "WITHIN",
                         "EXACT", 1, 1],
    "join(AY016290.1:108..185,AY016291.1:1546..1599)"
        => [$split_impl, 108, 108, "EXACT",
                         185, 185, "EXACT",
                         "EXACT", 2, 1],

    # UNCERTAIN locations and positions (Swissprot)
    "?2465..2774"
        => [$fuzzy_impl, 2465, 2465, "UNCERTAIN",
                         2774, 2774, "EXACT",
                         "EXACT", 1, 1],
    "22..?64"
        => [$fuzzy_impl, 22, 22, "EXACT",
                         64, 64, "UNCERTAIN",
                         "EXACT", 1, 1],
    "?22..?64"
        => [$fuzzy_impl, 22, 22, "UNCERTAIN",
                         64, 64, "UNCERTAIN",
                         "EXACT", 1, 1],
    "?..>393"
        => [$fuzzy_impl, undef, undef, "UNCERTAIN",
                         393,   undef, "AFTER",
                         "UNCERTAIN", 1, 1],
    "<1..?"
        => [$fuzzy_impl, undef, 1,     "BEFORE",
                         undef, undef, "UNCERTAIN",
                         "UNCERTAIN", 1, 1],
    "?..536"
        => [$fuzzy_impl, undef, undef, "UNCERTAIN",
                         536,   536,   "EXACT",
                         "UNCERTAIN", 1, 1],
    "1..?"
        => [$fuzzy_impl, 1,     1,     "EXACT",
                         undef, undef, "UNCERTAIN",
                         "UNCERTAIN", 1, 1],
    "?..?"
        => [$fuzzy_impl, undef, undef, "UNCERTAIN",
                         undef, undef, "UNCERTAIN",
                         "UNCERTAIN", 1, 1],
    "?1..12"
        => [$fuzzy_impl, 1,  1,  "UNCERTAIN",
                         12, 12, "EXACT",
                         "EXACT", 1, 1]
);

my $locfac = Bio::Factory::FTLocationFactory->new();
isa_ok($locfac,'Bio::Factory::LocationFactoryI');

# sorting is to keep the order constant from one run to the next
foreach my $locstr (keys %testcases) {
    my $loc = $locfac->from_string($locstr);
    if($locstr eq "join(AY016290.1:108..185,AY016291.1:1546..1599)") {
        $loc->seq_id("AY016295.1");
    }
    if($locstr eq "join(1..100,J00194.1:100..202)") {
        $loc->seq_id("unknown");
    }
    my @res = @{$testcases{$locstr}};
    is(ref($loc), $res[0], $res[0]);
    is($loc->min_start(), $res[1]);
    is($loc->max_start(), $res[2]);
    is($loc->start_pos_type(), $res[3]);
    is($loc->min_end(), $res[4]);
    is($loc->max_end(), $res[5]);
    is($loc->end_pos_type(), $res[6]);
    is($loc->location_type(), $res[7]);
    my @locs = $loc->each_Location();
    is(@locs, $res[8]);
    my $ftstr = $loc->to_FTstring();
    # this is a somewhat ugly hack, but we want clean output from to_FTstring()
    # Umm, then these should really fail, correct?
    # Should we be engineering workarounds for tests?
    $locstr = "J00194:100..202"      if $locstr eq "J00194:(100..202)";
    $locstr = "(122.133)..(204.221)" if $locstr eq "((122.133)..(204.221))";
    # now test
    is($ftstr, $locstr, "Location String: $locstr");
    # test strand production
    is($loc->strand(), $res[9]);
}

SKIP: {
    skip('nested matches in regex only supported in v5.6.1 and higher', 8) unless $^V gt v5.6.0;

    # Tests based on location definition (http://www.insdc.org/documents/feature_table.html#3.4)
    my $string1  = 'complement(join(2691..4571,4918..5163))';
    my $string2  = 'join(complement(4918..5163),complement(2691..4571))';
    my $loc1     = $locfac->from_string($string1);
    my $loc2     = $locfac->from_string($string2);
    my $loc1_str = $loc1->to_FTstring;
    my $loc2_str = $loc2->to_FTstring;
    is($loc1_str, $string1, $string1);
    is($loc2_str, $string1, $string2);
    is($loc1_str, $loc2_str, 'equivalent remote location strings');

    # Test for equivalent reverse strand locations adding one remote component
    $string1  = 'complement(join(TEST0001.1:2691..4571,4918..5163))';
    $string2  = 'join(complement(4918..5163),complement(TEST0001.1:2691..4571))';
    $loc1     = $locfac->from_string($string1);
    $loc2     = $locfac->from_string($string2);
    $loc1_str = $loc1->to_FTstring;
    $loc2_str = $loc2->to_FTstring;
    is($loc1_str, $string1, $string1);
    is($loc2_str, $string1, $string2);
    is($loc1_str, $loc2_str, 'equivalent remote location strings');

    # Test for equivalent reverse strand locations adding two remote components
    $string1  = 'complement(join(TEST0001.1:2691..4571,TEST0008.1:4918..5163))';
    $string2  = 'join(complement(TEST0008.1:4918..5163),complement(TEST0001.1:2691..4571))';
    $loc1     = $locfac->from_string($string1);
    $loc2     = $locfac->from_string($string2);
    $loc1_str = $loc1->to_FTstring;
    $loc2_str = $loc2->to_FTstring;
    is($loc1_str, $string1, $string1);
    is($loc2_str, $string1, $string2);
    is($loc1_str, $loc2_str, 'equivalent remote location strings');

    # bug #1674, #1765, 2101
    # EMBL-like (BAC19856.3 protein)
    # join(20464..20694,21548..22763,join(complement(314652..314672),complement(232596..232990),complement(231520..231669)))
    # GenBank-like
    # join(20464..20694,21548..22763,complement(join(231520..231669,232596..232990,314652..314672)))
    # Note that
    # join(1000..2000,join(3000..4000,join(5000..6000,7000..8000)),9000..10000)
    # is the same as
    # join(1000..2000,3000..4000,5000..6000,7000..8000,9000..10000)

    my @expected = (# intentionally testing same expected string twice
                    # as I am providing two different encodings
                    # that should mean the same thing
    'join(11025..11049,complement(join(315036..315294,251354..251412,241499..241580,239890..240081)))',
    'join(11025..11049,complement(join(315036..315294,251354..251412,241499..241580,239890..240081)))',
    # ditto
    'join(20464..20694,21548..22763,complement(join(231520..231669,232596..232990,314652..314672)))',
    'join(20464..20694,21548..22763,complement(join(231520..231669,232596..232990,314652..314672)))',
    # this is just seen once
    'join(1000..2000,3000..4000,5000..6000,7000..8000,9000..10000)',
    'order(S67862.1:72..75,join(S67863.1:1..788,1..19))'
   );

    for my $locstr (
        'join(11025..11049,join(complement(239890..240081),complement(241499..241580),complement(251354..251412),complement(315036..315294)))',
        'join(11025..11049,complement(join(315036..315294,251354..251412,241499..241580,239890..240081)))',
        'join(20464..20694,21548..22763,complement(join(231520..231669,232596..232990,314652..314672)))',
        'join(20464..20694,21548..22763,join(complement(314652..314672),complement(232596..232990),complement(231520..231669)))',
        'join(1000..2000,join(3000..4000,join(5000..6000,7000..8000)),9000..10000)',
        'order(S67862.1:72..75,join(S67863.1:1..788,1..19))'
       ) {
        my $loc = $locfac->from_string($locstr);
        my $ftstr = $loc->to_FTstring();
        is($ftstr, shift @expected, $locstr);
    }
}
BioPerl-1.007002/t/SeqFeature/Primer.t000444000766000024       573513155576321 17460 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$


use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    test_begin(-tests => 47);
    use_ok('Bio::SeqFeature::Primer');
    use_ok('Bio::PrimarySeq');
}

my ($primer, $primer_seq, $location, $start, $end, $strand, $id, $tm, $tme, $template, $seq);

# Implied primer sequence
$template = Bio::Seq->new( -seq => 'AAAAACCCCCGGGGGTTTTT' );
ok $primer = Bio::SeqFeature::Primer->new( -start => 6, -end => 10 ), 'Implied primer sequence';
isa_ok $primer, 'Bio::SeqFeature::Primer';
isa_ok $primer, 'Bio::SeqFeature::SubSeq';
ok $template->add_SeqFeature($primer); # $primer->attach_seq($template);
ok $primer_seq = $primer->seq;
isa_ok $primer_seq, 'Bio::PrimarySeqI';
is $primer_seq->seq, 'CCCCC';


# Bio::PrimarySeq primer
$template = Bio::Seq->new( -seq => 'AAAAACCCCCGGGGGTTTTT' );
$seq = Bio::PrimarySeq->new(-seq => 'CTTTTCATTCTGACTGCAACG');
ok $primer = Bio::SeqFeature::Primer->new(-seq => $seq), 'PrimarySeq primer';
ok $template->add_SeqFeature($primer); # $primer->attach_seq($template);
ok $primer_seq = $primer->seq;
isa_ok $primer_seq, 'Bio::PrimarySeqI';
is $primer_seq->seq, 'CTTTTCATTCTGACTGCAACG';


# Initialize with a sequence string
ok $primer = Bio::SeqFeature::Primer->new(
    -seq    => 'CTTTTCATTCTGACTGCAACG',
    -start  => 3,
    -id     => 'myid',
);
is $primer->start, 3;
ok $primer_seq = $primer->seq;
is $primer_seq->isa('Bio::PrimarySeqI'), 1;
is $primer_seq->seq, 'CTTTTCATTCTGACTGCAACG';
is $primer_seq->id, 'myid';
is $primer->primary_tag, 'Primer';
ok $primer->display_name('test');
is $primer->display_name, 'test';


# Coordinates
ok $primer->start(2);
is $primer->start, 2;
ok $primer->end(19);
is $primer->end, 19;
ok $primer->strand(-1);
is $primer->strand, -1;
ok $location = $primer->location;
isa_ok $location, 'Bio::LocationI';


# Melting temperatures
ok $tm = $primer->Tm;
is int($tm), 52;
ok $tm = $primer->Tm(-salt => 0.05, -oligo => 0.0000001);
ok $tme = $primer->Tm_estimate;
is int($tme), 58;
ok $tm = $primer->Tm_estimate(-salt => 0.05);


# Legacy
#   * initializing with -sequence
#   * passing a string to location()
{
   local $SIG{'__WARN__'} = sub {  }; # Silence deprecation warnings
   ok $primer = Bio::SeqFeature::Primer->new(
       -sequence => 'CTTTTCATTCTGACTGCAACG',
   );
   ok $location = $primer->location('3,25');
   is $location, '3,25';
}


# Chad's tests
$seq = Bio::Seq->new(
    -seq => 'gcatcgatctagctagcta' ,
    -id  => 'chads_nifty_sequence',
);
$primer = Bio::SeqFeature::Primer->new(
    -seq => $seq,
    -TARGET => '5,3'
);
isa_ok $primer, 'Bio::SeqFeature::Primer';
is $primer->seq->display_id, 'chads_nifty_sequence';
is $primer->seq->seq, 'gcatcgatctagctagcta';
$primer = Bio::SeqFeature::Primer->new(
    -seq => 'aaaaaacgatcgatcgtagctagct',
    -id => 'chads_nifty_primer',
    -TARGET => '5,3',
);
isa_ok $primer, 'Bio::SeqFeature::Primer';
isa_ok $primer->seq(), 'Bio::PrimarySeq';
is $primer->seq->id, 'chads_nifty_primer';
is $primer->seq->seq, 'aaaaaacgatcgatcgtagctagct';






BioPerl-1.007002/t/SeqFeature/Range.t000444000766000024       671613155576321 17256 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 49);
	
    use_ok('Bio::Range');
}

my $range = Bio::Range->new(-start=>10,
                            -end=>20,
						    -strand=>1);

isa_ok($range,'Bio::Range', 'BioRange object');
is($range->strand, 1);

my $range2 = Bio::Range->new(-start=>15,
                             -end=>25,
						     -strand=>1);

isa_ok($range2,'Bio::Range', 'BioRange object');
is($range2->strand, 1);

my $r = Bio::Range->new();
is ( $r->strand(0), 0 ) ;
is ( $r->start(27), 27 );
is ( $r->end(28), 28 ) ;

ok(! defined $r->intersection($range2));

$r = $range->union($range2);
is($r->start, 10);
is($r->end, 25);

$r = $range->intersection($range2);
is ( $r->start, 15  ) ;
is ( $r->end, 20    );
is ( $r->strand, 1  );

# intersection and union can also take lists
my $range3 = Bio::Range->new(-start=>18,-end=>30);
isa_ok($range3,'Bio::Range', 'BioRange object');

$r = $range->intersection([$range2, $range3]);
ok( ( $r->start == 18 ) && ( $r->end == 20 ));
$r = Bio::Range->intersection([$range, $range2, $range3]);
ok($r->start == 18 && $r->end == 20);
$r = $range->union($range2, $range3);
ok( ( $r->start == 10 ) && ( $r->end == 30 ) );
$r = Bio::Range->union($range, $range2, $range3);
ok( ( $r->start == 10 ) && ( $r->end == 30 ) );
$range3->start(21);
ok (! $range->intersection([$range2, $range3]));

ok (! $range->contains($range2));
ok (! $range2->contains($range));
ok ($range->overlaps($range2));
ok ($range2->overlaps($range));

# testing strand
$range3 = Bio::Range->new(-start => 15,
                           -end => 25,
						   -strand => 1);

my $range4 = Bio::Range->new(-start => 15,
						    -end => 25,
							-strand => -1);

isa_ok($range4,'Bio::Range', 'BioRange object');

my $range5 = Bio::Range->new(-start => 15,
                             -end => 25,
						     -strand => 0);

isa_ok($range5,'Bio::Range', 'BioRange object');

my $range6 = Bio::Range->new(-start => 20,
							 -end => 30,
							 -strand => -1);

isa_ok($range6,'Bio::Range', 'BioRange object');

ok $range3->_ignore($range4), ' 1 & -1' ;     
ok $range3->_weak($range3),' 1 & 1 true' ;       
ok $range3->_weak($range5), ' 1 & 0 true' ;       
ok (! $range3->_weak($range4), ' 1 & -1 false' );   
ok $range3->_strong($range3), ' 1 & 1 true' ;     
ok (! $range3->_strong($range5), ' 1 & 0 false' ); 
ok (! $range3->_strong($range4), ' 1 & -1 false' ); 

ok ! ( $range3->overlaps($range4,'weak'));
ok ! ( $range4->overlaps($range3,'weak'));
ok ! ( $range3->overlaps($range4,'strong')); 
ok ! ( $range4->overlaps($range3,'strong')); 

$range3->strand(0);

ok  ( $range3->overlaps($range4,'weak'));
ok  ( $range4->overlaps($range3,'weak')); 
ok ! ( $range3->overlaps($range4,'strong'));
ok ! ( $range4->overlaps($range3,'strong')); 

# if strands are different then intersection() should return 0...
$r = $range3->intersection($range4);
is ( $r->strand, 0 );

# or if both strands are -1 then -1 should be returned
$r = $range6->intersection($range4);
is ( $r->strand, -1 );

# test implemention of offsetStranded:
$r = Bio::Range->new(-start => 30, -end => 40, -strand => -1);
isa_ok($r, 'Bio::Range', 'Bio::Range object') ;
is ($r->offsetStranded(-5,10)->toString, '(20, 45) strand=-1');
is ($r->offsetStranded(+5,-10)->toString, '(30, 40) strand=-1');
$r->strand(1);
is ($r->offsetStranded(-5,10)->toString, '(25, 50) strand=1');
is ($r->offsetStranded(+5,-10)->toString, '(30, 40) strand=1');
BioPerl-1.007002/t/SeqFeature/RangeI.t000444000766000024       614013155576321 17356 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 45);
	
    use_ok('Bio::SeqFeature::Generic');
}

my @funcs = qw(start end length strand overlaps contains
    equals intersection union overlap_extent disconnected_ranges
    offsetStranded subtract);

my $i = 1;
while (my $func = shift @funcs ) {
    $i++;

    # test for presence of method
    ok exists $Bio::RangeI::{$func};
    
    # union get caught in an infinite loop w/o parameters; skip invoke test.
    next if $func eq 'union';
    
    # call to strand complains without a value; skip invoke test.
    next if $func eq 'disconnected_ranges';
    
    # test invocation of method
    eval { $Bio::RangeI::{$func}->(); };
    ok($@);
}

### unit tests for subtract method ###
# contributed by Stephen Montgomery (sm8 at sanger.ac.uk), who also
# wrote the subtract method
my $feature1 =  Bio::SeqFeature::Generic->new( -start => 1, -end =>
1000, -strand => 1);
my $feature2 =  Bio::SeqFeature::Generic->new( -start => 100, -end =>
900, -strand => -1);

my $subtracted = $feature1->subtract($feature2);
ok(defined($subtracted));
is(scalar(@$subtracted), 2);
foreach my $range (@$subtracted) {
    ok($range->start == 1 || $range->start == 901);
    ok($range->end == 99 || $range->end == 1000);
}

$subtracted = $feature2->subtract($feature1);
ok(!defined($subtracted));
$subtracted = $feature1->subtract($feature2, 'weak');
ok(!defined($subtracted));
$subtracted = $feature1->subtract($feature2, 'strong');
ok(!defined($subtracted));

my $feature3 =  Bio::SeqFeature::Generic->new( -start => 500, -end =>
1500, -strand => 1);
$subtracted = $feature1->subtract($feature3);
ok(defined($subtracted));
is scalar(@$subtracted), 1;
my $subtracted_i = @$subtracted[0];
is($subtracted_i->start, 1);
is($subtracted_i->end, 499);


# ---------------
# Added Bio::Location::SplitLocationI support to subtract().  --jhannah 20091018
$feature1 =  Bio::SeqFeature::Generic->new();
$feature2 =  Bio::SeqFeature::Generic->new();
my $loc = Bio::Location::Split->new();
$loc->add_sub_Location(Bio::Location::Simple->new(-start=>100, -end=>200, -strand=>1));
$loc->add_sub_Location(Bio::Location::Simple->new(-start=>300, -end=>400, -strand=>1));
$loc->add_sub_Location(Bio::Location::Simple->new(-start=>500, -end=>600, -strand=>1));
$feature1->location($loc);
$loc = Bio::Location::Split->new();
$loc->add_sub_Location(Bio::Location::Simple->new(-start=>350, -end=>400, -strand=>1));
$loc->add_sub_Location(Bio::Location::Simple->new(-start=>500, -end=>510, -strand=>1));
$feature2->location($loc);
$subtracted = $feature1->subtract($feature2);
is(@$subtracted, 3,                              "subtract() of split features");
is($subtracted->[0]->start, 100,                 "   0 start");
is($subtracted->[0]->end,   200,                 "   0 end");
is($subtracted->[1]->start, 300,                 "   1 start");
is($subtracted->[1]->end,   349,                 "   1 end");
is($subtracted->[2]->start, 511,                 "   2 start");
is($subtracted->[2]->end,   600,                 "   2 end");
# ---------------


BioPerl-1.007002/t/SeqFeature/SeqAnalysisParser.t000444000766000024       400713155576321 21622 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 14);
	
	use_ok('Bio::Factory::SeqAnalysisParserFactory');
	use_ok('Bio::SeqIO');
}

my ($seqio,$seq,$factory,$parser, $gene_seen, $exon_seen);

$seqio = Bio::SeqIO->new('-format'=>'fasta', '-file' => test_input_file('genomic-seq.fasta'));
isa_ok $seqio, 'Bio::SeqIO';
$seq = $seqio->next_seq;
isa_ok $seq, 'Bio::PrimarySeqI';

$factory = Bio::Factory::SeqAnalysisParserFactory->new();

# let's test the genscan factory
$parser = $factory->get_parser(-input => test_input_file('genomic-seq.genscan'),
				  -method => 'genscan');
isa_ok $parser, 'Bio::SeqAnalysisParserI';
while( my $feat = $parser->next_feature() ){
    $seq->add_SeqFeature($feat);
}
($gene_seen, $exon_seen)  = (0,0);
foreach my $feat (  $seq->top_SeqFeatures() ) {
    if( $feat->isa("Bio::Tools::Prediction::Gene") ) {
	foreach my $exon ( $feat->exons ) {
	    $exon_seen++;
	}
	$gene_seen++;
    } 
}
is $exon_seen, 37;
is $gene_seen, 3;

# let's test the mzef factory
$parser = $factory->get_parser(-input => test_input_file('genomic-seq.mzef'),
			       -method=> 'mzef');
$seqio = Bio::SeqIO->new('-format'=>'fasta', '-file' => test_input_file('genomic-seq.fasta'));
ok $seq = $seqio->next_seq();
isa_ok $seq, 'Bio::PrimarySeqI';

isa_ok $parser, 'Bio::SeqAnalysisParserI';
while( my $feat = $parser->next_feature() ){
    $seq->add_SeqFeature($feat);
}
($gene_seen, $exon_seen)  = (0,0);
foreach my $feat (  $seq->top_SeqFeatures() ) {
    if( $feat->isa("Bio::Tools::Prediction::Gene") ) {
	foreach my $exon ( $feat->exons ) { 
	    $exon_seen++;
	}
	$gene_seen++;
    } 
}
is $exon_seen, 23;
is $gene_seen, 1;

# let's test the ePCR factory

$parser = $factory->get_parser(-input => test_input_file('genomic-seq.epcr'),
			       -method => 'epcr');

$seq->flush_SeqFeatures;

isa_ok $parser, 'Bio::SeqAnalysisParserI';
while( my $feat = $parser->next_feature() ){
    $seq->add_SeqFeature($feat);
}

is $seq->top_SeqFeatures(), 7;
BioPerl-1.007002/t/SeqFeature/SubSeq.t000444000766000024       502213155576321 17411 0ustar00cjfieldsstaff000000000000use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 37);

    use_ok 'Bio::PrimarySeq';
    use_ok 'Bio::SeqFeature::SubSeq';
}

my ($subseq, $subseq_seq, $subsubseq, $subsubseq_seq, $template);


# Basic SubSeq object

$subseq = Bio::SeqFeature::SubSeq->new();
isa_ok $subseq, 'Bio::SeqFeature::SubSeq';
isa_ok $subseq, 'Bio::SeqFeature::Generic';
is $subseq->length, undef;


# SubSeq with explicit sequence (sequence string)

ok $subseq = Bio::SeqFeature::SubSeq->new(
    -seq => 'CCCCCAAAAAGGGGGTTTTT',
);
is $subseq->length, 20;
ok $subseq_seq = $subseq->seq;
isa_ok $subseq_seq, 'Bio::PrimarySeq';
is $subseq_seq->seq, 'CCCCCAAAAAGGGGGTTTTT';


# SubSeq with explicit sequence (sequence object)

ok $subseq = Bio::SeqFeature::SubSeq->new(
    -seq => Bio::PrimarySeq->new( -seq => 'CCCCCAAAAAGGGGGTTTTT' ),
);
is $subseq->length, 20;
ok $subseq_seq = $subseq->seq;
isa_ok $subseq_seq, 'Bio::PrimarySeq';
is $subseq_seq->seq, 'CCCCCAAAAAGGGGGTTTTT';


# SubSeq with explicit sequence and coordinates

ok $subseq = Bio::SeqFeature::SubSeq->new(
    -seq    => Bio::PrimarySeq->new( -seq => 'CCCCCAAAAAGGGGGTTTTT' ),
    -start  => 11,
    -end    => 40,
    -strand => -1
);
is $subseq->length, 30;
ok $subseq_seq = $subseq->seq;
isa_ok $subseq_seq, 'Bio::PrimarySeq';
is $subseq_seq->seq, 'CCCCCAAAAAGGGGGTTTTT';


# Subseq with implicit sequence

$template = Bio::Seq->new( -seq => 'ATCGATCGATCCCCCAAAAAGGGGGTTTTTAGCTAGCTAT');

ok $subseq = Bio::SeqFeature::SubSeq->new(
    -start  => 11,
    -end    => 30,
    -strand => -1
);
is $subseq->length, 20;

ok $template->add_SeqFeature($subseq);
ok $subseq_seq = $subseq->seq;
isa_ok $subseq_seq, 'Bio::PrimarySeq';
is $subseq_seq->seq, 'AAAAACCCCCTTTTTGGGGG';


# Subseq with implicit sequence

$template = Bio::Seq->new( -seq => 'ATCGATCGATCCCCCAAAAAGGGGGTTTTTAGCTAGCTAT');

ok $subseq = Bio::SeqFeature::SubSeq->new(
    -start    => 11,
    -end      => 30,
    -strand   => -1,
    -template => $template,
);
is $subseq->length, 20;
ok $subseq_seq = $subseq->seq;
isa_ok $subseq_seq, 'Bio::PrimarySeq';
is $subseq_seq->seq, 'AAAAACCCCCTTTTTGGGGG';


# Sub SubSeq

ok $subsubseq = Bio::SeqFeature::SubSeq->new(
    -start    => 11,
    -end      => 15,
    -strand   => 1,
    -template => $subseq,
);
is $subsubseq->length, 5;
ok $subsubseq_seq = $subsubseq->seq;
isa_ok $subsubseq_seq, 'Bio::PrimarySeq';
is $subsubseq_seq->seq, 'CCCCC';


# One-liner

is( Bio::SeqFeature::SubSeq->new(-start=>11,-end=>30,-strand=>1,-template=>$template)->seq->seq, 'CCCCCAAAAAGGGGGTTTTT' );
BioPerl-1.007002/t/SeqFeature/Unflattener.t000444000766000024      2310613155576321 20521 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 21);

    use_ok('Bio::SeqIO');
    use_ok('Bio::SeqFeature::Tools::Unflattener');
}

my $verbosity = test_debug();

my ($seq, @sfs);
my $unflattener = Bio::SeqFeature::Tools::Unflattener->new;
$unflattener->verbose($verbosity);


if (1) {
    my @path = ("NC_000007-ribosomal-slippage.gb");
    $seq = getseq(@path);

    my @topsfs = $seq->get_SeqFeatures;
    if( $verbosity > 0 ) {
        warn sprintf "TOP:%d\n", scalar(@topsfs);
        write_hier(@topsfs);
    }

    # UNFLATTEN
    @sfs = $unflattener->unflatten_seq(-seq       => $seq,
                                       -use_magic => 1);
    if( $verbosity > 0 ) {
        warn "\n\nPOST PROCESSING:\n";
        write_hier(@sfs);
        warn sprintf "PROCESSED:%d\n", scalar(@sfs);
    }
    is(@sfs, 1995);
}


if (1) {
    my @path = ("ribosome-slippage.gb");
    $seq     = getseq(@path);

    my @topsfs = $seq->get_SeqFeatures;
    if( $verbosity > 0 ) {
        warn sprintf "TOP:%d\n", scalar(@topsfs);
        write_hier(@topsfs);
    }

    # UNFLATTEN
    @sfs = $unflattener->unflatten_seq(-seq       => $seq,
                                       -use_magic => 1);
    if( $verbosity > 0 ) {
        warn "\n\nPOST PROCESSING:\n";
        write_hier(@sfs);
        warn sprintf "PROCESSED:%d\n", scalar(@sfs);
    }
    is(@sfs, 3);
}


if (1) {
    my @path = ("AE003644_Adh-genomic.gb");
    $seq     = getseq(@path);

    is ($seq->accession_number, 'AE003644');
    my @topsfs = $seq->get_SeqFeatures;
    if( $verbosity > 0 ) {
        warn sprintf "TOP:%d\n", scalar(@topsfs);
        write_hier(@topsfs);
    }

    # UNFLATTEN
    @sfs = $unflattener->unflatten_seq(-seq       => $seq,
                                       -group_tag => 'locus_tag');
    if( $verbosity > 0 ) {
        warn "\n\nPOST PROCESSING:\n";
        write_hier(@sfs);
        warn sprintf "PROCESSED:%d\n", scalar(@sfs);
    }
    is(@sfs, 21);
}

# now try again, using a custom subroutine to link together features
$seq = getseq("AE003644_Adh-genomic.gb");
@sfs = $unflattener->unflatten_seq
    (-seq       => $seq,
     -group_tag => 'locus_tag',
     -resolver_method =>
        sub {
             my $self = shift;
             my ($sf, @candidate_container_sfs) = @_;

             if ($sf->has_tag('note')) {
                 my @notes   = $sf->get_tag_values('note');
                 my @trnames = map {/from transcript\s+(.*)/; $1;}
                               @notes;
                 @trnames    = grep {$_} @trnames;

                 my $trname;
                 if (@trnames == 0) {
                     $self->throw("UNRESOLVABLE");
                 }
                 elsif (@trnames == 1) {
                     $trname = $trnames[0];
                 }
                 else {
                     $self->throw("AMBIGUOUS: @trnames");
                 }

                 my @container_sfs =
                     grep {
                           my ($product) =
                                 $_->has_tag('product') ? $_->get_tag_values('product')
                               : ('');
                           $product eq $trname;
                     } @candidate_container_sfs;

                 if (@container_sfs == 0) {
                     $self->throw("UNRESOLVABLE");
                 }
                 elsif (@container_sfs == 1) {
                     # we got it!
                     return ($container_sfs[0]=>0);
                 }
                 else {
                     $self->throw("AMBIGUOUS");
                 }
             }
        });
$unflattener->feature_from_splitloc(-seq => $seq);
if( $verbosity > 0 ) {
    warn "\n\nPOST PROCESSING:\n";
    write_hier(@sfs);
    warn sprintf "PROCESSED2:%d\n", scalar(@sfs);
}
is(@sfs, 21);

# try again; different sequence
# this is an E-Coli seq with no mRNA features;
# we just want to link all features directly with gene

$seq = getseq("D10483.gbk");

# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq       => $seq,
                                   -partonomy => {'*'=>'gene'});
if( $verbosity > 0 ) {
    warn "\n\nPOST PROCESSING:\n";
    write_hier(@sfs);
    warn sprintf "PROCESSED:%d\n", scalar(@sfs);
}
is(@sfs, 98);

# this sequence has no locus_tag or or gene tags
$seq = getseq("AY763288.gb");

# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq       => $seq,
                                   -use_magic => 1);
if( $verbosity > 0 ) {
    warn "\n\nPOST PROCESSING:\n";
    write_hier(@sfs);
    warn sprintf "PROCESSED:%d\n", scalar(@sfs);
}
is(@sfs, 3);

# try again; different sequence - dicistronic gene, mRNA record

$seq = getseq("X98338_Adh-mRNA.gb");

# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq       => $seq,
                                   -partonomy => {'*'=>'gene'});
if( $verbosity > 0 ) {
    warn "\n\nPOST PROCESSING:\n";
    write_hier(@sfs);
    warn sprintf "PROCESSED:%d\n", scalar(@sfs);
}
is(@sfs, 7);

# try again; this sequence has no CDSs but rRNA present

$seq = getseq("no_cds_example.gb");

# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq       => $seq,
                                   -use_magic => 1);
if( $verbosity > 0 ) {
    warn "\n\nPOST PROCESSING:\n";
    write_hier(@sfs);
    warn sprintf "PROCESSED:%d\n", scalar(@sfs);
}

my @all_sfs = $seq->get_all_SeqFeatures;

my @exons = grep { $_-> primary_tag eq 'exon' } @all_sfs ;

is(@exons, 2);


if (1) {
    # this is an arabidopsise gbk record. it has no mRNA features.
    # it has explicit exon/intron records
    my @path = ("ATF14F8.gbk");
    $seq     = getseq(@path);

    is ($seq->accession_number, 'AL391144');
    my @topsfs = $seq->get_SeqFeatures;
    my @cdss   = grep {$_->primary_tag eq 'CDS'} @topsfs;
    my $n      = scalar(@topsfs);
    if( $verbosity > 0 ) {
        warn sprintf "TOP:%d\n", scalar(@topsfs);
        write_hier(@topsfs);
    }

    # UNFLATTEN
    @sfs = $unflattener->unflatten_seq(-seq       => $seq,
                                       -use_magic => 1);
    @sfs = $seq->get_SeqFeatures;
    if( $verbosity > 0 ) {
        warn "\n\nPOST PROCESSING:\n";
        write_hier(@sfs);
        warn sprintf "PROCESSED/TOP:%d\n", scalar(@sfs);
    }
    is(@sfs,28);

    my @allsfs = $seq->get_all_SeqFeatures;
    is(@allsfs,202);

    my @mrnas = grep {$_->primary_tag eq 'mRNA'} @allsfs;
    if( $verbosity > 0 ) {
        warn sprintf "ALL:%d\n",   scalar(@allsfs);
        warn sprintf "mRNAs:%d\n", scalar(@mrnas);
    }
    # relationship between mRNA and CDS should be one-one
    is(@mrnas,@cdss);
}


if (1) {
    # this is a record from FlyBase
    # it has mRNA features, and explicit exon/intron records
    my @path = ("AnnIX-v003.gbk");
    $seq     = getseq(@path);

    my @topsfs = $seq->get_SeqFeatures;
    if( $verbosity > 0 ) {
        warn sprintf "TOP:%d\n", scalar(@topsfs);
        write_hier(@topsfs);
    }

    # UNFLATTEN
    @sfs = $unflattener->unflatten_seq(-seq       => $seq,
                                       -use_magic => 1);
    @sfs = $seq->get_SeqFeatures;
    if( $verbosity > 0 ) {
        warn "\n\nPOST PROCESSING:\n";
        write_hier(@sfs);
        warn sprintf "PROCESSED/TOP:%d\n", scalar(@sfs);
    }
    is scalar(@sfs), 1;

    my @exons = grep {$_->primary_tag eq 'exon'} $seq->get_all_SeqFeatures;
    is scalar(@exons), 6;    # total number of exons per splice

    my %numberh = map {$_->get_tag_values("number") => 1} @exons;
    my @numbers = keys %numberh;
    if( $verbosity > 0 ) {
        warn sprintf "DISTINCT EXONS: %d [@numbers]\n", scalar(@numbers);
    }
    is scalar(@numbers), 6;  # distinct exons
}


if (1) {
    # example of a BAD genbank entry
    my @path = ("dmel_2Lchunk.gb");
    $seq     = getseq(@path);

    my @topsfs = $seq->get_SeqFeatures;
    if( $verbosity > 0 ) {
        warn sprintf "TOP:%d\n", scalar(@topsfs);
        write_hier(@topsfs);
    }

    # UNFLATTEN
    #
    # we EXPECT problems with this erroneous record
    $unflattener->error_threshold(2);
    @sfs = $unflattener->unflatten_seq(-seq       => $seq,
                                       -use_magic => 1);
    @sfs = $seq->get_SeqFeatures;
    if( $verbosity > 0 ) {
        warn "\n\nPOST PROCESSING:\n";
        write_hier(@sfs);
        warn sprintf "PROCESSED/TOP:%d\n", scalar(@sfs);
    }
    is scalar(@sfs), 2;

    my @exons = grep {$_->primary_tag eq 'exon'} $seq->get_all_SeqFeatures;
    is scalar(@exons), 2;    # total number of exons per splice

    my @probs = $unflattener->get_problems;
    $unflattener->report_problems(\*STDERR) if $verbosity > 0;
    $unflattener->clear_problems;
    if( $verbosity > 0 ) {
        warn sprintf "PROBLEMS ENCOUNTERED: %d (EXPECTED: 6)\n", scalar(@probs);
    }
    is scalar(@probs), 6;
}


sub write_hier {
    my @sfs = @_;
    _write_hier(0, @sfs);
}

sub _write_hier {
    my $indent = shift;
    my @sfs = @_;
    foreach my $sf (@sfs) {
        my $label = '?';
        if ($sf->has_tag('gene')) {
            ($label) = $sf->get_tag_values('gene');
        }
        elsif ($sf->has_tag('product')) {
            ($label) = $sf->get_tag_values('product');
        }
        elsif ($sf->has_tag('number')) {
            $label = join("; ", $sf->get_tag_values('number'));
        }
        warn sprintf "%s%s $label\n", '  ' x $indent, $sf->primary_tag;
        my @sub_sfs = $sf->sub_SeqFeature;
        _write_hier($indent+1, @sub_sfs);
    }
}

sub getseq {
    my @path  = @_;
    my $seqio = Bio::SeqIO->new('-file'   => test_input_file(@path),
                                '-format' => 'GenBank');
    $seqio->verbose($verbosity);

    my $seq = $seqio->next_seq();
    return $seq;
}
BioPerl-1.007002/t/SeqIO000755000766000024          013155576321 14602 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/SeqIO/Handler.t000444000766000024     11312413155576321 16543 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests           => 561,
               -requires_module => 'Data::Stag');
	
    use_ok('Bio::SeqIO');
}


my $verbose = test_debug();

################################## GenBank ##################################

my $ast = Bio::SeqIO->new(-format => 'gbdriver' ,
                        -verbose => $verbose,
                        -file => test_input_file("roa1.genbank"));
$ast->verbose($verbose);
my $as = $ast->next_seq();
is $as->molecule, 'mRNA',$as->accession_number;
is $as->alphabet, 'dna';
is($as->primary_id, 3598416);
my @class = $as->species->classification;
is $class[$#class],'Eukaryota';

$ast = Bio::SeqIO->new(-format => 'gbdriver',
                              -verbose => $verbose,
                       -file => test_input_file("NT_021877.gbk"));
$ast->verbose($verbose);
$as = $ast->next_seq();
is $as->molecule, 'DNA',$as->accession_number;
is $as->alphabet, 'dna';
is($as->primary_id, 37539616);
is($as->accession_number, 'NT_021877');

my ($cds) = grep { $_->primary_tag eq 'CDS' } $as->get_SeqFeatures();
is(($cds->get_tag_values('transl_except'))[1],
   '(pos:complement(4224..4226),aa:OTHER)');

# test for a DBSOURCE line
$ast = Bio::SeqIO->new(-format => 'gbdriver',
                              -verbose => $verbose,
                       -file => test_input_file("BAB68554.gb"));
$ast->verbose($verbose);
$as = $ast->next_seq();
is $as->molecule, 'linear',$as->accession_number;;
is $as->alphabet, 'protein';
# Though older GenBank releases indicate SOURCE contains only the common name,
# this is no longer true.  In general, this line will contain an abbreviated
# form of the full organism name (but may contain the full length name),
# as well as the optional common name and organelle.  There is no get/set
# for the abbreviated name but it is accessible via name()
ok defined($as->species->name('abbreviated')->[0]);
is $as->species->name('abbreviated')->[0], 'Aldabra giant tortoise';
is($as->primary_id, 15824047);
my $ac = $as->annotation;
ok defined $ac;
my @dblinks = $ac->get_Annotations('dblink');
is(scalar @dblinks,1);
is($dblinks[0]->database, 'GenBank');
is($dblinks[0]->primary_id, 'AB072353');
is($dblinks[0]->version, '1');
is($dblinks[0]->display_text, 'GenBank:AB072353.1','operator overloading in AnnotationI is deprecated');

# test for multi-line SOURCE
$ast = Bio::SeqIO->new(-format => 'gbdriver',
                              -verbose => $verbose,
                       -file => test_input_file("NC_006346.gb"));
$as = $ast->next_seq;
is $as->species->binomial('FULL'), 'Bolitoglossa n. sp. RLM-2004',$as->accession_number;;
@class = $as->species->classification;
is($class[$#class],'Eukaryota');
is($as->species->common_name,'mushroomtongue salamander');

$ast = Bio::SeqIO->new(-format => 'gbdriver',
                              -verbose => $verbose,
                       -file => test_input_file("U71225.gb"));
$as = $ast->next_seq;
@class = $as->species->classification;
is($class[$#class],'Eukaryota',$as->accession_number);
is $as->species->common_name,'black-bellied salamander';

# test for unusual common name
$ast = Bio::SeqIO->new(-format => 'gbdriver',
                              -verbose => $verbose,
                       -file => test_input_file("AB077698.gb"));
$as = $ast->next_seq;
# again, this is not a common name but is in name('abbreviated')
ok defined($as->species->name('abbreviated')->[0]),$as->accession_number;
is $as->species->name('abbreviated')->[0],'Homo sapiens cDNA to mRNA';

# test for common name with parentheses
$ast = Bio::SeqIO->new(-format => 'gbdriver',
                              -verbose => $verbose,
                       -file => test_input_file("DQ018368.gb"));
$as = $ast->next_seq;
is $as->species->scientific_name,'(Populus tomentosa x P. bolleana) x P. tomentosa var. truncata',
$as->accession_number;;

# test secondary accessions
my $seqio = Bio::SeqIO->new(-format => 'gbdriver',
                                    -verbose => $verbose,
                                    -file => test_input_file('D10483.gbk'));
my $seq = $seqio->next_seq;
my @kw =  $seq->get_keywords;
is(scalar @kw, 118, $seq->accession_number);
is($kw[-1], 'yabO');
my @sec_acc = $seq->get_secondary_accessions();
is(scalar @sec_acc,14);
is($sec_acc[-1], 'X56742');

# bug #1487
my $str = Bio::SeqIO->new(-verbose => $verbose,
                                 -file    => test_input_file('D12555.gbk'));
eval {
    $seq = $str->next_seq;
};

ok(! $@, 'bug 1487');

# bug 1647 rpt_unit sub-feature with multiple parens
$str = Bio::SeqIO->new(-format => 'gbdriver',
                              -verbose => $verbose,
                       -file => test_input_file('mini-AE001405.gb'));
ok($seq = $str->next_seq);
my @rpts = grep { $_->primary_tag eq 'repeat_region' }
  $seq->get_SeqFeatures;
is $#rpts, 2, 'bug 1647';
my @rpt_units = grep {$_->has_tag('rpt_unit')} @rpts;
is $#rpt_units, 0;
is(($rpt_units[0]->get_tag_values('rpt_unit'))[0],'(TG)10;A;(TG)7');

# test bug #1673 , RDB-II genbank files
$str = Bio::SeqIO->new(-format => 'gbdriver',
                              -verbose => $verbose,
                       -file => test_input_file('Mcjanrna_rdbII.gbk')
              );
ok($seq = $str->next_seq, 'bug 1673');
my @refs = $seq->annotation->get_Annotations('reference');
is(@refs, 1);
is($seq->display_id,'Mc.janrrnA');
is($seq->molecule ,'RNA');

$str  = Bio::SeqIO->new(-format => 'gbdriver',
                              -file   => test_input_file("AF165282.gb"),
                              -verbose => $verbose);
$seq = $str->next_seq;
my @features = $seq->all_SeqFeatures();
is(@features, 5, $seq->accession_number);
is($features[0]->start, 1);
is($features[0]->end, 226);
my $location = $features[1]->location;
ok($location->isa('Bio::Location::SplitLocationI'));
my @sublocs = $location->sub_Location();
is(@sublocs, 29);

# version and primary ID - believe it or not, this wasn't working
is ($seq->version, 1);
is ($seq->seq_version, 1);
is ($seq->primary_id, "5734104");

# streaming and Bio::RichSeq creation
my $stream = Bio::SeqIO->new(-file => test_input_file("test.genbank"),
                                      -verbose => $verbose,
                             -format => 'gbdriver');
$stream->verbose($verbose);
my $seqnum = 0;
my $species;
my @cl;
my $lasts;
my @ids = qw(DDU63596 DDU63595 HUMBDNF);
my @tids = (44689, 44689, 9606);
my @tnames = ("Dictyostelium discoideum","Dictyostelium discoideum",
                  "Homo sapiens");
while($seq = $stream->next_seq()) {
    if($seqnum < 3) {
        is $seq->display_id(), $ids[$seqnum];
        $species = $seq->species();
        @cl = $species->classification();
        is( $species->binomial(), $tnames[$seqnum],
             'species parsing incorrect for genbank');
        is( $cl[3] ne $species->genus(), 1,
             'genus duplicated in genbank parsing');
        is( $species->ncbi_taxid, $tids[$seqnum] );
    }
    $seqnum++;
    $lasts = $seq;
}
is($seqnum, 5,'streaming');
is $lasts->display_id(), "HUMBETGLOA";
my ($ref) = $lasts->annotation->get_Annotations('reference');
is($ref->medline, 94173918);
$stream->close();

$stream = Bio::SeqIO->new(-file => test_input_file("test.genbank.noseq"),
                                  -verbose => $verbose,
                                  -format => 'gbdriver' );
$seqnum = 0;
while($seq = $stream->next_seq()) {
    if($seqnum < 3) {
        is $seq->display_id(), $ids[$seqnum];
    } elsif( $seq->display_id eq 'M37762') {
        is( ($seq->get_keywords())[0], 'neurotrophic factor');
    }
    $seqnum++;
}
is $seqnum, 5, "Total number of sequences in test file";

# fuzzy
$seq = Bio::SeqIO->new( -format => 'gbdriver',
                                -verbose => $verbose,
                        -file =>test_input_file("testfuzzy.genbank"));
$seq->verbose($verbose);
ok(defined($as = $seq->next_seq()));

@features = $as->all_SeqFeatures();
is(@features,21,'Fuzzy in');
my $lastfeature = pop @features;
# this is a split location; the root doesn't have strand
is($lastfeature->strand, undef);
$location = $lastfeature->location;
#$location->verbose(-1); # silence the warning of undef seq_id()
# see above; splitlocs roots do not have a strand really
is($location->strand, undef);
is($location->start, 83202);
is($location->end, 84996);

@sublocs = $location->sub_Location();

is(@sublocs, 2);
my $loc = shift @sublocs;
is($loc->start, 83202);
is($loc->end, 83329);
is($loc->strand, -1);

$loc = shift @sublocs;
is($loc->start, 84248);
is($loc->end, 84996);
is($loc->strand,1);

my $outfile = test_output_file();
$seq = Bio::SeqIO->new(-format => 'genbank',
                              -verbose => $verbose,
                       -file=> ">$outfile");
$seq->verbose($verbose);
ok($seq->write_seq($as),'Fuzzy out');

## now genbank ##
$str = Bio::SeqIO->new(-format =>'gbdriver',
                             -verbose => $verbose,
                             -file => test_input_file('BK000016-tpa.gbk'));
$seq = $str->next_seq;
ok(defined $seq, $seq->accession_number);
ok(defined $seq->seq);
is($seq->accession_number, 'BK000016',$seq->accession_number);
is($seq->alphabet, 'dna');
is($seq->display_id, 'BK000016');
is($seq->length, 1162);
is($seq->division, 'ROD');
is($seq->get_dates, 1);
is($seq->keywords, 'Third Party Annotation; TPA');
is($seq->desc, 'TPA: Mus musculus pantothenate kinase 4 mRNA, partial cds.');
is($seq->seq_version, 1);
is($seq->feature_count, 2);
my $spec_obj = $seq->species;
is ($spec_obj->common_name, 'house mouse');
is ($spec_obj->species, 'musculus');
is ($spec_obj->genus, 'Mus');
is ($spec_obj->binomial, 'Mus musculus');
$ac = $seq->annotation;
my $reference =  ($ac->get_Annotations('reference') )[0];
is ($reference->pubmed, '11479594');
is ($reference->medline, '21372465',$seq->accession_number);

# validate that what is written is what is read
my $testfile = test_output_file();
my $out = Bio::SeqIO->new(-file => ">$testfile",
                             -format => 'genbank');
$out->write_seq($seq);
$out->close();

$str = Bio::SeqIO->new(-format =>'gbdriver',
                             -file => $testfile);
$seq = $str->next_seq;
ok(defined $seq,'roundtrip');
ok(defined $seq->seq);
is($seq->accession_number, 'BK000016');
is($seq->alphabet, 'dna');
is($seq->display_id, 'BK000016');
is($seq->length, 1162);
is($seq->division, 'ROD');
is($seq->get_dates, 1);
is($seq->keywords, 'Third Party Annotation; TPA');
is($seq->desc, 'TPA: Mus musculus pantothenate kinase 4 mRNA, partial cds.');
is($seq->seq_version, 1);
is($seq->feature_count, 2);
$spec_obj = $seq->species;
is ($spec_obj->common_name, 'house mouse');
is ($spec_obj->species, 'musculus');
is ($spec_obj->genus, 'Mus');
is ($spec_obj->binomial, 'Mus musculus');
$ac = $seq->annotation;
$reference =  ($ac->get_Annotations('reference') )[0];
is ($reference->pubmed, '11479594');
is ($reference->medline, '21372465');

# write revcomp split location
my $gb = Bio::SeqIO->new(-format => 'gbdriver',
                        -verbose => $verbose,
                        -file   => test_input_file('revcomp_mrna.gb'));
$seq = $gb->next_seq();

$gb = Bio::SeqIO->new(-format => 'genbank',
                     -file   => ">$testfile");

$gb->write_seq($seq);
undef $gb;
ok(! -z $testfile, 'revcomp split location');

# bug 1925, continuation of long ORGANISM line ends up in @classification:
# ORGANISM  Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC
#           9150
#           Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
#           Enterobacteriaceae; Salmonella.
$gb = Bio::SeqIO->new(-format => 'gbdriver',
                     -verbose => $verbose,
                        -file   => test_input_file('NC_006511-short.gbk'));
$seq = $gb->next_seq;
is $seq->species->common_name, undef, "Bug 1925";
is $seq->species->scientific_name, "Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150";
@class = $seq->species->classification;
is $class[$#class], "Bacteria";

# WGS tests
$gb = Bio::SeqIO->new(-format => 'gbdriver',
                      -verbose => $verbose,
                    -file   => test_input_file('O_sat.wgs'));
$seq = $gb->next_seq;

my @tests = ('wgs'        => 'AAAA02000001-AAAA02050231',
            'wgs_scafld' => 'CM000126-CM000137',
            'wgs_scafld' => 'CH398081-CH401163');

my @wgs = map {$seq->annotation->get_Annotations(lc($_))} (qw(WGS WGS_SCAFLD));

my $ct=0;

for my $wgs (@wgs) {
    my ($tagname, $value) = (shift @tests, shift @tests);
    is($wgs->tagname, $tagname, $tagname);
    is($wgs->value, $value);
    $ct++;
}

is ($ct, 3);

# make sure we can retrieve a feature with a primary tag of 'misc_difference'
$gb = Bio::SeqIO->new(-format => 'gbdriver',
                     -verbose => $verbose,
                    -file   => test_input_file('BC000007.gbk'));
$seq = $gb->next_seq;
($cds) = grep { $_->primary_tag eq 'misc_difference' } $seq->get_SeqFeatures;
my @vals = $cds->get_tag_values('gene');
is $vals[0], 'PX19', $seq->accession_number;

# Check that the source,organism section is identical between input and output.
# - test an easy one where organism is species, then two different formats of
# subspecies, then a species with a format that used to be mistaken for
# subspecies, then a bacteria with no genus, and finally a virus with a genus.

# These tests are now somewhat out-of-date since we are moving to a Bio::Taxon-
# based system for verifying taxonomic information.  Right now they just verify
# changes so are really useless; I will change them to verify common name,
# organelle, scientific name, etc.


# output always adds a period (GenBank std), but two of these files do not use them.

foreach my $in ('BK000016-tpa.gbk', 'ay116458.gb', 'ay149291.gb', 'NC_006346.gb', 'ay007676.gb', 'dq519393.gb') {
    my $infile =  test_input_file($in);
	$outfile = test_output_file();
    
    $str = Bio::SeqIO->new(-format =>'genbank',
                          -verbose => $verbose,
                          -file => $infile);
    $seq = $str->next_seq;
    
    $out = Bio::SeqIO->new(-file => $outfile, -format => 'genbank');
    $out->write_seq($seq);
    $out->close();
    
    open my $IN, '<', $infile or die "Could not read file '$infile': $!\n";
    my @in = <$IN>;
    close $IN;
    open my $RESULT, '<', $outfile or die "Could not read file '$outfile': $!\n";
    my $line = 0;
    my $check = 0;
    my $is = 1;
    
    FILECHECK:
    while (my $result = <$RESULT>) {
        if ($result =~ /^KEYWORDS/) {
            $check = 1;
            next;
        }

        if ($result =~ /^REFERENCE/) {
            last FILECHECK;
        }

        if ($check) {
            
            # end periods don't count (not all input files have them)
            $result =~ s{\.$}{};
            $in[$line] =~ s{\.$}{};
            
            if ($result ne $in[$line]) {
                $is = 0;
                last;
            }
        }
    } continue { $line++ }
    close $RESULT;
    
    ok $is, $in;
}

# NB: there should probably be full testing on all lines to ensure that output
# matches input.

# 20061117: problem with *double* colon in some annotation-dblink values
$ct = 0;

foreach my $in ('P35527.gb') {
    my $infile =  test_input_file($in);
    $str = Bio::SeqIO->new(-format =>'genbank',
                         -verbose => $verbose,
                         -file => $infile);
    $seq = $str->next_seq;
    my $ac      = $seq->annotation();      # Bio::AnnotationCollection
    foreach my $key ($ac->get_all_annotation_keys() ) {
        my @values = $ac->get_Annotations($key);
        foreach my $ann (@values) {
            my $value = $ann->display_text;
            $ct++;
            if ($key eq 'dblink') {

                ok (index($value,'::') < 0);   # this should never be true

                ok ($value, $value);   # check value is not empty

                #  print "  ann/", sprintf('%12s  ',$key), '>>>', $value , '<<<', "\n";
                #  print "        index double colon: ",index($value   ,'::'), "\n";

                #  check db name:
                my @parts = split(/:/,$value);
                if ( $parts[0] =~ /^(?:
                        #  not an exhaustive list of databases;
                        #  just the db's referenced in P35527.gb:
                        swissprot | GenBank | GenPept  | HSSP| IntAct | Ensembl | KEGG | HGNC | MIM | ArrayExpress
                                  | GO      | InterPro | Pfam| PRINTS | PROSITE
                                     )$/x )
                {
                    ok 1;
                }
                else {
                    ok 0;
                }
                    ok ( $parts[1], "$parts[0]" );
            }
                # elsif ($key eq 'reference') { }
        }
    }
}

is($ct, 46);

# bug 2195
    
$str = Bio::SeqIO->new(-format =>'gbdriver',
                      -verbose => $verbose,
                      -file => test_input_file('AF305198.gb')
                     );

$species = $str->next_seq->species;

is($species->scientific_name, 'Virginia creeper phytoplasma', 'Bug 2195');
is(join(', ',$species->classification), 'Virginia creeper phytoplasma, '.
   '16SrV (Elm yellows group), Candidatus Phytoplasma, '.
   'Acholeplasmataceae, Acholeplasmatales, Mollicutes, '.
   'Firmicutes, Bacteria', 'Bug 2195');

# bug 2569, PROJECT line support, read and write, round-tripping
    
$str = Bio::SeqIO->new(-format =>'gbdriver',
                      -verbose => $verbose,
                      -file => test_input_file('NC_008536.gb'));

$seq = $str->next_seq;

my $project = ($seq->annotation->get_Annotations('project'))[0];

isa_ok($project, 'Bio::Annotation::SimpleValue');

if ($project) {
	is($project->value, 'GenomeProject:12638');
} else {
	ok(0, "PROJECT not parsed");
}

$outfile = test_output_file();

$gb = Bio::SeqIO->new(-format => 'genbank',
                              -verbose => $verbose,
                       -file=> ">$outfile");

$gb->write_seq($seq);

$str = Bio::SeqIO->new(-format =>'gbdriver',
                      -verbose => $verbose,
                      -file => $outfile);

$seq = $str->next_seq;

$project = ($seq->annotation->get_Annotations('project'))[0];

isa_ok($project, 'Bio::Annotation::SimpleValue');

if ($project) {
	is($project->value, 'GenomeProject:12638');
} else {
	ok(0, "Roundtrip test failed");
}

################################## EMBL ##################################

# Set to -1 for release version, so warnings aren't printed

$ast = Bio::SeqIO->new( -format => 'embldriver',
			   -verbose => $verbose,
			   -file => test_input_file("roa1.dat"));
$ast->verbose($verbose);
$as = $ast->next_seq();
ok defined $as->seq;
is($as->display_id, 'HSHNCPA1');
is($as->accession_number, 'X79536');
is($as->seq_version, 1);
is($as->version, 1);
is($as->desc, 'H.sapiens mRNA for hnRNPcore protein A1');
is($as->molecule, 'RNA');
is($as->alphabet, 'rna');
is(scalar $as->all_SeqFeatures(), 4);
is($as->length, 1198);
is($as->species->binomial(), 'Homo sapiens');
is($as->get_dates, 2);

# EMBL Release 87 changes (8-17-06)

$ast = Bio::SeqIO->new( -format => 'embldriver',
			   -verbose => $verbose,
			   -file => test_input_file("roa1_v2.dat"));
$ast->verbose($verbose);
$as = $ast->next_seq();
ok defined $as->seq;
# accession # same as display name now
is($as->display_id, 'X79536');
is($as->get_dates, 2);
is($as->accession_number, 'X79536');
is($as->seq_version, 1);
is($as->version, 1);
is($as->desc, 'H.sapiens mRNA for hnRNPcore protein A1');
# mRNA instead of RNA
is($as->molecule, 'mRNA');
is($as->alphabet, 'rna');
is(scalar $as->all_SeqFeatures(), 4);
is($as->length, 1198);
is($as->species->binomial(), 'Homo sapiens');

my $ent = Bio::SeqIO->new( -file => test_input_file("test.embl"),
			   -format => 'embldriver');
$seq = $ent->next_seq();

is(defined $seq->seq(), 1,
   'success reading Embl with ^ location and badly split double quotes');
is(scalar $seq->annotation->get_Annotations('reference'), 3);
is($seq->get_dates, 0);

$out = Bio::SeqIO->new(-file=> ">$outfile",
			  -format => 'embl');
is($out->write_seq($seq),1,
   'success writing Embl format with ^ < and > locations');

# embl with no FT
$ent = Bio::SeqIO->new( -file => test_input_file("test.embl"),
			-format => 'embldriver');
$seq = $ent->next_seq();

ok($seq);
is(lc($seq->subseq(1,10)),'gatcagtaga');
is($seq->length, 4870);

# embl with no FH
my $noFH = Bio::SeqIO->new(-file => test_input_file("no_FH.embl"),
			-format => 'embldriver');
$seq = $noFH->next_seq;
is(scalar($seq->get_SeqFeatures), 4);
is($seq->display_id, 'AE000001');
is($seq->get_dates, 0);

# bug 1571
$ent = Bio::SeqIO->new(-format => 'embldriver',
		       -file   => test_input_file('test.embl2sq'));
$seq = $ent->next_seq;
is($seq->length,4870);
is($seq->get_dates, 0);

# embl repbase
$ent = Bio::SeqIO->new(-file => test_input_file("BEL16-LTR_AG.embl"), -format => 'embldriver');
$seq = $ent->next_seq;
is($seq->display_id,'BEL16-LTR_AG');
is($seq->get_dates, 2);

# test secondary accessions in EMBL (bug #1332)
$seqio = Bio::SeqIO->new(-format => 'embldriver',
			   -file => test_input_file('ECAPAH02.embl'));
$seq = $seqio->next_seq;
is($seq->accession_number, 'D10483');
is($seq->seq_version, 2);
my @accs = $seq->get_secondary_accessions();
is($accs[0], 'J01597');
is($accs[-1], 'X56742');
is($seq->get_dates, 2);

### TPA TESTS - Thanks to Richard Adams ###
# test Third Party Annotation entries in EMBL/Gb format 
# to ensure compatability with parsers.
$str = Bio::SeqIO->new(-verbose => $verbose,
                         -format =>'embldriver',
			 -file => test_input_file('BN000066-tpa.embl'));
$seq = $str->next_seq;
ok(defined $seq);
is($seq->accession_number, 'BN000066');
is($seq->alphabet, 'dna');
is($seq->display_id, 'AGA000066');
is($seq->length, 5195);
is($seq->division, 'INV');
is($seq->keywords, 'acetylcholinesterase; achE1 gene; Third Party Annotation; TPA');
is($seq->seq_version, 1);
is($seq->feature_count, 15);
is($seq->get_dates, 2);

$spec_obj = $seq->species;
is ($spec_obj->common_name, 'African malaria mosquito');
is ($spec_obj->species, 'gambiae');
is ($spec_obj->genus, 'Anopheles');
is ($spec_obj->binomial, 'Anopheles gambiae');

$ac = $seq->annotation;
$reference =  ($ac->get_Annotations('reference') )[1];
is ($reference->title,'"A novel acetylcholinesterase gene in mosquitoes codes for the insecticide target and is non-homologous to the ace gene in Drosophila"');
is ($reference->authors,'Weill M., Fort P., Berthomi eu A., Dubois M.P., Pasteur N., Raymond M.');
my $cmmnt =  ($ac->get_Annotations('comment') )[0];
is($cmmnt->text, 'see also AJ488492 for achE-1 from Kisumu strain Third Party Annotation Database: This TPA record uses Anopheles gambiae trace archive data (http://trace.ensembl.org)');


$ent = Bio::SeqIO->new( -file => test_input_file("test.embl"),
                        -format => 'embldriver');
$ent->verbose($verbose);
$seq = $ent->next_seq();
$species = $seq->species();
@cl = $species->classification();
is( $cl[3] ne $species->genus(), 1, 'genus duplication test');
$ent->close();

#
## read-write - test embl writing of a PrimarySeq
#
my $primaryseq = Bio::PrimarySeq->new( -seq => 'AGAGAGAGATA',
                                      -id  => 'myid',
                                      -desc => 'mydescr',
                                      -alphabet => 'DNA',
                                      -accession_number => 'myaccession');

$verbose = -1 unless $ENV{'BIOPERLDEBUG'};  # silence warnings unless we are debuggin

my $embl = Bio::SeqIO->new(-format => 'embl',
                          -verbose => $verbose,
                          -file => ">$outfile");

ok($embl->write_seq($primaryseq));

# this should generate a warning
my $scalar = "test";
eval {
	$embl->write_seq($scalar);
};
ok ($@);

############################## Swiss/UniProt ##############################

$seqio = Bio::SeqIO->new( -verbose => $verbose,
                                     -format => 'swissdriver',
                                     -file   => test_input_file('test.swiss'));

isa_ok($seqio, 'Bio::SeqIO');
$seq = $seqio->next_seq;
my @gns = $seq->annotation->get_Annotations('gene_name');

$outfile = test_output_file();
$seqio = Bio::SeqIO->new( -verbose => $verbose,
                                 -format => 'swiss',
                                 -file   => ">$outfile");

$seqio->write_seq($seq);

# reads it in once again
$seqio = Bio::SeqIO->new( -verbose => $verbose,
                                 -format => 'swissdriver',
                                 -file => $outfile);
    
$seq = $seqio->next_seq;
isa_ok($seq->species, 'Bio::Species');
is($seq->species->ncbi_taxid, 6239);

# version, seq_update, dates (5 tests)
is($seq->version, 40);
my ($ann) = $seq->annotation->get_Annotations('seq_update');
eval {is($ann->display_text, 35,'operator overloading in AnnotationI is deprecated')};
ok(!$@);

my @dates = $seq->get_dates;
my @date_check = qw(01-NOV-1997 01-NOV-1997 16-OCT-2001);

for my $date (@dates) {
    my $expdate = shift @date_check;
    is($date, $expdate,'dates');
}

my @gns2 = $seq->annotation->get_Annotations('gene_name');
# check gene name is preserved (was losing suffix in worm gene names)
ok($#gns2 == 0 && $gns[0]->value eq $gns2[0]->value);

# test swissprot multiple RP lines
$str = Bio::SeqIO->new(-file => test_input_file('P33897'));
$seq = $str->next_seq;
isa_ok($seq, 'Bio::Seq::RichSeqI');
@refs = $seq->annotation->get_Annotations('reference');
is( @refs, 23);
is($refs[20]->rp, 'VARIANTS X-ALD LEU-98; ASP-99; GLU-217; GLN-518; ASP-608; ILE-633 AND PRO-660, AND VARIANT THR-13.');

# version, seq_update, dates (5 tests)
is($seq->version, 44);
($ann) = $seq->annotation->get_Annotations('seq_update');
is($ann->display_text, 28,'operator overloading in AnnotationI is deprecated');
@dates = $seq->get_dates;
@date_check = qw(01-FEB-1994 01-FEB-1994 15-JUN-2004);
for my $date (@dates) {
    is($date, shift @date_check);
}

$ast = Bio::SeqIO->new(-verbose => $verbose,
                                  -format => 'swissdriver' ,
                                  -file => test_input_file("roa1.swiss"));
$as = $ast->next_seq();

ok defined $as->seq;
is($as->id, 'ROA1_HUMAN', "id is ".$as->id);
like($as->primary_id, qr(Bio::PrimarySeq));
is($as->length, 371);
is($as->alphabet, 'protein');
is($as->division, 'HUMAN');
is(scalar $as->all_SeqFeatures(), 16);
is(scalar $as->annotation->get_Annotations('reference'), 11);

# version, seq_update, dates (5 tests)
is($as->version, 35);
($ann) = $as->annotation->get_Annotations('seq_update');
is($ann->display_text, 15,'operator overloading in AnnotationI is deprecated');
@dates = $as->get_dates;
@date_check = qw(01-MAR-1989 01-AUG-1990 01-NOV-1997);
for my $date (@dates) {
    is($date, shift @date_check);
}

($ent,$out) = undef;
($as,$seq) = undef;

$seqio = Bio::SeqIO->new(-format => 'swissdriver' ,
                                 -verbose => $verbose,
                                 -file => test_input_file("swiss.dat"));
$seq = $seqio->next_seq;
isa_ok($seq, 'Bio::Seq::RichSeqI');

# more tests to verify we are actually parsing correctly
like($seq->primary_id, qr(Bio::PrimarySeq));
is($seq->display_id, 'MA32_HUMAN');
is($seq->length, 282);
is($seq->division, 'HUMAN');
is($seq->alphabet, 'protein');
my @f = $seq->all_SeqFeatures();
is(@f, 2);
is($f[1]->primary_tag, 'CHAIN');
is(($f[1]->get_tag_values('description'))[0], 'COMPLEMENT COMPONENT 1, Q SUBCOMPONENT BINDING PROTEIN');

# version, seq_update, dates (5 tests)
is($seq->version, 40);
($ann) = $seq->annotation->get_Annotations('seq_update');
is($ann->display_text, 31,'operator overloading in AnnotationI is deprecated');
@dates = $seq->get_dates;
@date_check = qw(01-FEB-1995 01-FEB-1995 01-OCT-2000);
for my $date (@dates) {
    is($date, shift @date_check);
}

my @genenames = qw(GC1QBP HABP1 SF2P32 C1QBP);
($ann) = $seq->annotation->get_Annotations('gene_name');
# use Data::Stag findval and element name to get values/nodes
foreach my $gn ( $ann->findval('Name') ) {
    ok ($gn, shift(@genenames));
}
foreach my $gn ( $ann->findval('Synonyms') ) {
    ok ($gn, shift(@genenames));
}
like($ann->value, qr/Name: GC1QBP/);

# test for feature locations like ?..N
$seq = $seqio->next_seq();
isa_ok($seq, 'Bio::Seq::RichSeqI');
like($seq->primary_id, qr(Bio::PrimarySeq));
is($seq->display_id, 'ACON_CAEEL');
is($seq->length, 788);
is($seq->division, 'CAEEL');
is($seq->alphabet, 'protein');
is(scalar $seq->all_SeqFeatures(), 5);

foreach my $gn ( $seq->annotation->get_Annotations('gene_name') ) {
    ok ($gn->value, 'F54H12.1');
}

# test species in swissprot -- this can be a n:n nightmare
$seq = $seqio->next_seq();
isa_ok($seq, 'Bio::Seq::RichSeqI');
like($seq->primary_id, qr(Bio::PrimarySeq));
@sec_acc = $seq->get_secondary_accessions();
is($sec_acc[0], 'P29360');
is($sec_acc[1], 'Q63631');
is($seq->accession_number, 'P42655');
@kw = $seq->get_keywords;
is( $kw[0], 'Brain');
is( $kw[1], 'Neurone');
is($kw[3], 'Multigene family');
is($seq->display_id, '143E_HUMAN');

# hybrid names from old sequences are no longer valid, these are chopped
# off at the first organism
is($seq->species->binomial, "Homo sapiens");
is($seq->species->common_name, "Human");
is($seq->species->ncbi_taxid, 9606);

$seq = $seqio->next_seq();
isa_ok($seq, 'Bio::Seq::RichSeqI');
like($seq->primary_id, qr(Bio::PrimarySeq));
is($seq->species->binomial, "Bos taurus");
is($seq->species->common_name, "Bovine");
is($seq->species->ncbi_taxid, 9913);

# multiple genes in swissprot
$seq = $seqio->next_seq();
isa_ok($seq, 'Bio::Seq::RichSeqI');
like($seq->primary_id, qr(Bio::PrimarySeq));

($ann) = $seq->annotation->get_Annotations("gene_name");
@genenames = qw(CALM1 CAM1 CALM CAM CALM2 CAM2 CAMB CALM3 CAM3 CAMC);
my $flatnames = "(CALM1 OR CAM1 OR CALM OR CAM) AND (CALM2 OR CAM2 OR CAMB) AND (CALM3 OR CAM3 OR CAMC)";

my @names = @genenames; # copy array

my @ann_names = $ann->get_all_values();
is(scalar(@ann_names), scalar(@names));

# do this in a layered way (nested tags)
for my $node ($ann->findnode('gene_name')) {
    for my $name ($node->findval('Name')) {
        is($name, shift(@names));
    }
    for my $name ($node->findval('Synonyms')) {
        is($name, shift(@names));
    }
}

is(scalar(@names),0);

# same entry as before, but with the new gene names format
$seqio = Bio::SeqIO->new(-format => 'swissdriver',
                                 -verbose => $verbose,
                         -file => test_input_file("calm.swiss"));
$seq = $seqio->next_seq();
isa_ok($seq, 'Bio::Seq::RichSeqI');
like($seq->primary_id, qr(Bio::PrimarySeq));

($ann) = $seq->annotation->get_Annotations("gene_name");
@names = @genenames; # copy array

my @ann_names2 = $ann->get_all_values(); #emulate StructuredValue's flattened array
is(scalar(@ann_names2), scalar(@names));

for my $node ($ann->findnode('gene_name')) {
    for my $name ($node->findval('Name')) {
        is($name, shift(@names));
    }
    for my $name ($node->findval('Synonyms')) {
        is($name, shift(@names));
    }
}

is(scalar(@names),0);

# test proper parsing of references
my @litrefs = $seq->annotation->get_Annotations('reference');
is(scalar(@litrefs), 17);

my @titles = (
    '"Complete amino acid sequence of human brain calmodulin."',
    '"Multiple divergent mRNAs code for a single human calmodulin."',
    '"Molecular analysis of human and rat calmodulin complementary DNA clones. Evidence for additional active genes in these species."',
    '"Isolation and nucleotide sequence of a cDNA encoding human calmodulin."',
    '"Structure of the human CALM1 calmodulin gene and identification of two CALM1-related pseudogenes CALM1P1 and CALM1P2."',
    undef,
    '"Characterization of the human CALM2 calmodulin gene and comparison of the transcriptional activity of CALM1, CALM2 and CALM3."',
    '"Cloning of human full-length CDSs in BD Creator(TM) system donor vector."',
    '"The DNA sequence and analysis of human chromosome 14."',
    '"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences."',
    '"Alpha-helix nucleation by a calcium-binding peptide loop."',
    '"Solution structure of Ca(2+)-calmodulin reveals flexible hand-like properties of its domains."',
    '"Calmodulin structure refined at 1.7 A resolution."',
    '"Drug binding by calmodulin: crystal structure of a calmodulin-trifluoperazine complex."',
    '"Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin."',
    '"Physiological calcium concentrations regulate calmodulin binding and catalysis of adenylyl cyclase exotoxins."',
    '"Crystal structure of a MARCKS peptide containing the calmodulin-binding domain in complex with Ca2+-calmodulin."',
);

my @locs = (
    "Biochemistry 21:2565-2569(1982).",
    "J. Biol. Chem. 263:17055-17062(1988).",
    "J. Biol. Chem. 262:16663-16670(1987).",
    "Biochem. Int. 9:177-185(1984).",
    "Eur. J. Biochem. 225:71-82(1994).",
    "Submitted (FEB-1995) to the EMBL/GenBank/DDBJ databases.",
    "Cell Calcium 23:323-338(1998).",
    "Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases.",
    "Nature 421:601-607(2003).",
    "Proc. Natl. Acad. Sci. U.S.A. 99:16899-16903(2002).",
    "Proc. Natl. Acad. Sci. U.S.A. 96:903-908(1999).",
    "Nat. Struct. Biol. 8:990-997(2001).",
    "J. Mol. Biol. 228:1177-1192(1992).",
    "Biochemistry 33:15259-15265(1994).",
    "Nature 415:396-402(2002).",
    "EMBO J. 21:6721-6732(2002).",
    "Nat. Struct. Biol. 10:226-231(2003).",
);

my @positions = (
     undef, undef,
    undef, undef,
    undef, undef,
    undef, undef,
    undef, undef,
    undef, undef,
    undef, undef,
    undef, undef,
    undef, undef,
    undef, undef,
    94, 103,
    1, 76,
    undef, undef,
    undef, undef,
    5, 148,
    1, 148,
    undef, undef,
);

foreach my $litref (@litrefs) {
    is($litref->title, shift(@titles));
    is($litref->location, shift(@locs));
    is($litref->start, shift(@positions));
    is($litref->end, shift(@positions));
}

# format parsing changes (pre-rel 9.0)

$seqio = Bio::SeqIO->new( -verbose => $verbose,
                         -format => 'swissdriver',
                         -file   => test_input_file('pre_rel9.swiss'));

ok($seqio);
$seq = $seqio->next_seq;
isa_ok($seq->species, 'Bio::Species');
is($seq->species->ncbi_taxid, "6239");

# version, seq_update, dates (5 tests)
is($seq->version, 44);
($ann) = $seq->annotation->get_Annotations('seq_update');
is($ann->display_text, 1);
@dates = $seq->get_dates;
@date_check = qw(01-NOV-1997 01-NOV-1996 30-MAY-2006 );
for my $date (@dates) {
    is($date, shift @date_check);
}

my @idcheck = qw(Z66513 T22647 Cel.30446 Q06319 Q20772 F54D5.7 WBGene00010052
		 F54D5.7 GO:0005515 IPR006089 IPR006091 IPR006090
		 IPR006092 IPR009075 IPR009100 IPR013764 PF00441
		 PF02770 PF02771 PS00072 PS00073);

for my $dblink ( $seq->annotation->get_Annotations('dblink') ) {
    is($dblink->primary_id, shift @idcheck);
}

$seqio = Bio::SeqIO->new( -verbose => $verbose,
                         -format => 'swissdriver',
                         -file   => test_input_file('pre_rel9.swiss'));

my @namespaces = qw(Swiss-Prot TrEMBL TrEMBL);

while (my $seq = $seqio->next_seq) {
    is($seq->namespace, shift @namespaces);
}

# format parsing changes (rel 9.0, Oct 2006)

$seqio = Bio::SeqIO->new( -verbose => $verbose,
                         -format => 'swissdriver',
                         -file   => test_input_file('rel9.swiss'));

ok($seqio);
$seq = $seqio->next_seq;
isa_ok($seq->species, 'Bio::Species');
is($seq->species->ncbi_taxid, 6239);

is($seq->version, 47);
($ann) = $seq->annotation->get_Annotations('seq_update');
is($ann->display_text, 1,'operator overloading in AnnotationI is deprecated');
@dates = $seq->get_dates;
@date_check = qw(01-NOV-1997 01-NOV-1996 31-OCT-2006 );
for my $date (@dates) {
    is($date, shift @date_check);
}

@idcheck = qw(Z66513 T22647 Cel.30446 Q06319 Q20772 F54D5.7 cel:F54D5.7
         WBGene00010052 F54D5.7 GO:0005515 IPR006089 IPR006091 IPR006090
         IPR006092 IPR009075 IPR013786 IPR009100 IPR013764 PF00441 PF02770
         PF02771 PS00072 PS00073 );

for my $dblink ( $seq->annotation->get_Annotations('dblink') ) {
    is($dblink->primary_id, shift @idcheck);
}

$seqio = Bio::SeqIO->new( -verbose => $verbose,
                         -format => 'swissdriver',
                         -file   => test_input_file('rel9.swiss'));

@namespaces = qw(Swiss-Prot TrEMBL TrEMBL);

while (my $seq = $seqio->next_seq) {
    is($seq->namespace, shift @namespaces);
}

# bug 2288
# Q8GBD3.swiss
$seqio = Bio::SeqIO->new( -verbose => $verbose,
                         -format => 'swiss',
                         -file   => test_input_file('Q8GBD3.swiss'));

while (my $seq = $seqio->next_seq) {
    my $lineage = join(';', $seq->species->classification);
	is ($lineage, 'Acetobacter aceti;Acetobacter subgen. Acetobacter;'.
		'Acetobacter;Acetobacteraceae;Rhodospirillales;Alphaproteobacteria;'.
		'Proteobacteria;Bacteria');
}

# test for GenBank swissprot/UniProt/UniProtKB DBSOURCE line (Bug : RT 44536)
$ast = Bio::SeqIO->new(-format => 'genbank',
                              -verbose => $verbose,
                       -file => test_input_file('P39765.gb'));
$ast->verbose($verbose);
$as = $ast->next_seq();
is $as->molecule, 'PRT',$as->accession_number;;
is $as->alphabet, 'protein';
# Though older GenBank releases indicate SOURCE contains only the common name,
# this is no longer true.  In general, this line will contain an abbreviated
# form of the full organism name (but may contain the full length name),
# as well as the optional common name and organelle.  There is no get/set
# for the abbreviated name but it is accessible via name()
ok defined($as->species->name('abbreviated')->[0]);
is $as->species->name('abbreviated')->[0], 'Bacillus subtilis';
is($as->primary_id, 20141743);
$ac = $as->annotation;
ok defined $ac;
@dblinks = $ac->get_Annotations('dblink');
is(scalar @dblinks,31);
is($dblinks[0]->database, 'UniProtKB');
is($dblinks[0]->primary_id, 'PYRR_BACSU');
is($dblinks[0]->version, undef);
is($dblinks[0]->display_text, 'UniProtKB:PYRR_BACSU','operator overloading in AnnotationI is deprecated');
BioPerl-1.007002/t/SeqIO/MultiFile.t000444000766000024       133713155576321 17022 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 5);

    use_ok 'Bio::SeqIO::MultiFile';
}

my $verbose = test_debug();


# Test multiple files, with a specified format
ok my $mf = Bio::SeqIO::MultiFile->new(
    -format  => 'Fasta' ,
    -verbose => $verbose,
    -files   => [ test_input_file('multi_1.fa'), test_input_file('multi_2.fa')],
);

my $count = 0;
while (my $seq = $mf->next_seq() ) {
    $count++;
}
is $count, 12;


# Automatically determine format
ok $mf = Bio::SeqIO::MultiFile->new(
    -verbose => $verbose,
    -files   => [ test_input_file('multi_1.fa'), test_input_file('multi_2.fa')],
);

is $mf->format, 'fasta';
BioPerl-1.007002/t/SeqIO/Multiple_fasta.t000444000766000024        61013155576321 20052 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 9);
	
	use_ok('Bio::SeqIO');
}

my $in = Bio::SeqIO->new(-file => test_input_file('multifa.seq') , '-format' => 'Fasta');
ok $in;
my $c=0;
while ( my $seq = $in->next_seq() ) {
    ok($seq);
    $c++;
}
is $c,6, "all sequences in the file";
BioPerl-1.007002/t/SeqIO/SeqBuilder.t000444000766000024       730613155576321 17171 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    test_begin(-tests => 137);
    use_ok('Bio::SeqIO');
}

my $verbosity = test_debug;

my ($seqio, $seq); # predeclare variables for strict

# default mode
ok $seqio = Bio::SeqIO->new('-file' => test_input_file('test.genbank'), 
                            '-format' => 'GenBank');
$seqio->verbose($verbosity);

my $numseqs = 0;
my @loci = qw(U63596 U63595 M37762 NT_010368 L26462);
my @numfeas = (3,1,6,3,26);

while ($seq = $seqio->next_seq) {
    is $seq->accession_number, $loci[$numseqs++];
    ok $seq->annotation->get_Annotations;
    is scalar($seq->top_SeqFeatures), $numfeas[$numseqs-1];
    ok $seq->species->binomial;
    ok $seq->seq;
    ok $seq->desc;
    ok $seq->id;
}
is $numseqs, 5;

# minimalistic mode
$seqio = Bio::SeqIO->new('-file' => test_input_file('test.genbank'), 
                         '-format' => 'GenBank');
ok $seqio;
$seqio->verbose($verbosity);
ok my $seqbuilder = $seqio->sequence_builder;
isa_ok $seqbuilder, "Bio::Factory::ObjectBuilderI";
$seqbuilder->want_none;
$seqbuilder->add_wanted_slot('display_id','accession_number','desc');

$numseqs = 0;

while ($seq = $seqio->next_seq) {
    is $seq->accession_number, $loci[$numseqs++];
    is scalar(grep { ! ($_->tagname eq "keyword" ||
                        $_->tagname eq "date_changed" ||
                        $_->tagname eq "secondary_accession"); }
               $seq->annotation->get_Annotations), 0;
    if ($numseqs <= 3) {
        is scalar($seq->top_SeqFeatures), 0;
    }
    else {
        is scalar($seq->top_SeqFeatures), $numfeas[$numseqs-1];
    }
    is $seq->species, undef;
    is $seq->seq, undef;
    ok $seq->desc;
    ok $seq->id;
    # switch on features for the last 2 seqs
    $seqbuilder->add_wanted_slot('features') if $numseqs == 3;
}
is $numseqs, 5;

# everything but no sequence, and no features
$seqio = Bio::SeqIO->new('-file' => test_input_file('test.genbank'), 
                         '-format' => 'GenBank');
ok $seqio;
$seqio->verbose($verbosity);
$seqbuilder = $seqio->sequence_builder;
# want-all is default
$seqbuilder->add_unwanted_slot('seq','features');

$numseqs = 0;

while ($seq = $seqio->next_seq) {
    is $seq->accession_number, $loci[$numseqs++];
    ok scalar($seq->annotation->get_Annotations);
    if ($numseqs <= 3) {
        is scalar($seq->top_SeqFeatures), 0;
    }
    else {
        is scalar($seq->top_SeqFeatures), $numfeas[$numseqs-1];
    }
    ok $seq->species->binomial;
    is $seq->seq, undef;
    ok $seq->desc;
    ok $seq->id;
    # switch on features for the last 2 seqs
    if ($numseqs == 3) {
        $seqbuilder->add_unwanted_slot(
            grep { $_ ne 'features'; } $seqbuilder->remove_unwanted_slots
        );
    }
}
is $numseqs, 5;

# skip sequences less than 100bp or accession like 'NT_*'
$seqio = Bio::SeqIO->new('-file' => test_input_file('test.genbank'), 
                         '-format' => 'GenBank');
ok $seqio;
$seqio->verbose($verbosity);
$seqbuilder = $seqio->sequence_builder;
# we could have as well combined the two conditions into one, but we want to
# test the implicit AND here
$seqbuilder->add_object_condition(sub {
    my $h = shift;
    return 0 if($h->{'-length'} < 100);
    return 1;
});
$seqbuilder->add_object_condition(sub {
    my $h = shift;
    return 0 if($h->{'-display_id'} =~ /^NT_/);
    return 1;
});

$numseqs = 0;
my $i = 0;

while ($seq = $seqio->next_seq) {
    $numseqs++;
    is $seq->accession_number, $loci[$i];
    ok scalar($seq->annotation->get_Annotations);
    is scalar($seq->top_SeqFeatures), $numfeas[$i];
    ok $seq->species->binomial;
    ok $seq->seq;
    ok $seq->desc;
    ok $seq->id;
    $i += 2;
}
is $numseqs, 3;
BioPerl-1.007002/t/SeqIO/SeqIO.t000444000766000024      1231713155576321 16130 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 58);
    
    use_ok 'Bio::SeqIO';
}

my $verbose = test_debug();

my @formats = qw(gcg fasta raw pir tab ace );
# The following files or formats are failing: swiss genbank interpro embl

for my $format (@formats) {
    print "======== $format ========\n" if $verbose;
    my $seq;
    my $str = Bio::SeqIO->new( -file   => test_input_file("test.$format"),
                               -format => $format                          );

    is $str->format(), $format;

    ok $seq = $str->next_seq();
    print "Sequence 1 of 2 from $format stream:\n", $seq->seq, "\n\n" if  $verbose;
    unless ($format eq 'raw') {
        is $seq->id, 'roa1_drome',"ID for format $format";
        is $seq->length, 358;
    }
    
    unless ($format eq 'gcg') { # GCG file can contain only one sequence
        ok $seq = $str->next_seq();
        print "Sequence 2 of 2 from $format stream:\n", $seq->seq, $seq->seq, "\n" if $verbose;
    }
    
    my $outfile = test_output_file();
    my $out = Bio::SeqIO->new( -file   => ">$outfile",
                               -format => $format      );
    ok $out->write_seq($seq);
    if ($format eq 'fasta') {
        my $id_type;
        ok($id_type = $out->preferred_id_type('accession.version'),
            'accession.version');
    }
    
    ok -s $outfile;
}



# from testformats.pl
SKIP: {
    test_skip(-tests => 6, -requires_modules => [qw(Algorithm::Diff
                                                    IO::ScalarArray
                                                    IO::String)]);
    use_ok 'Algorithm::Diff';
    eval "use Algorithm::Diff qw(diff LCS);";
    use_ok 'IO::ScalarArray';
    use_ok 'IO::String';
    
    my %files = ( 
             #'test.embl'      => 'embl',
             #'test.ace'       => 'ace',
              'test.fasta'     => 'fasta',
             #'test.game'      => 'game',
              'test.gcg'       => 'gcg',
             #'test.genbank'   => 'genbank',
              'test.raw'       => 'raw',
             #'test_badlf.gcg' => 'gcg'
              );
    
    while( my ($file, $type) = each %files ) {
        my $filename = test_input_file($file);
        print "processing file $filename\n" if $verbose;
        open my $FILE, '<', $filename or die "Could not read file '$filename': $!\n";
        my @datain = <$FILE>;
        close $FILE;

        my $in = IO::String->new( join('', @datain) );
        my $seqin = Bio::SeqIO->new( -fh     => $in,
                                     -format => $type );
        my $out = IO::String->new();
        my $seqout = Bio::SeqIO->new( -fh     => $out,
                                      -format => $type );
        my $seq;
        while( defined($seq = $seqin->next_seq) ) {
            $seqout->write_seq($seq);
        }
        $seqout->close();
        $seqin->close();
        my $strref = $out->string_ref;
        my @dataout = map { $_."\n"} split(/\n/, $$strref );
        my @diffs = &diff( \@datain, \@dataout);
        is @diffs, 0;
        
        if(@diffs && $verbose) {
            foreach my $d ( @diffs ) {
                foreach my $diff ( @$d ) {
                    chomp($diff->[2]);
                    print $diff->[0], $diff->[1], "\n>", $diff->[2], "\n";
                }
            }
            print "in is \n", join('', @datain), "\n";
            print "out is \n", join('',@dataout), "\n";
        }
    }
}

# simple tests specific to Bio::SeqIO interface (applicable to all SeqIO
# modules)

##############################################
# test format() and variant() in Bio::RootIO
##############################################

my $in = Bio::SeqIO->new(
   -file    => test_input_file('bug2901.fa'),
   -format  => "fasta",
);
is $in->format, 'fasta';
is $in->variant, undef;

$in = Bio::SeqIO->new(
   -file    => test_input_file('fastq', 'illumina_faked.fastq'),
   -format  => "fastq",
   -variant => 'illumina',
);
is $in->format, 'fastq';
is $in->variant, 'illumina';


######################################################
# test format detection from different inputs
######################################################

$in = Bio::SeqIO->new( -file => test_input_file('test.fastq') );
is $in->format, 'fastq';

open my $fh, '<', test_input_file('test.genbank') or die "Could not read file 'test.genbank': $!\n";
$in = Bio::SeqIO->new( -fh => $fh );
is $in->format, 'genbank';
close $fh;

my $string = ">seq\nACGATCG\n";
$in = Bio::SeqIO->new( -string => $string );
is $in->format, 'fasta';


############ EXCEPTION HANDLING ############

TODO: {
    local $TODO = 'file/fh-based tests should be in Bio::Root::IO, see issue #3204';
    throws_ok {
        Bio::SeqIO->new();
    } qr/No file, fh, or string argument provided/, 'Must pass a file or file handle';
}

throws_ok {
    Bio::SeqIO->new(-fh => undef);
} qr/fh argument provided, but with an undefined value/,
    'Must pass a file or file handle';

throws_ok {
    Bio::SeqIO->new(-file => undef);
} qr/file argument provided, but with an undefined value/,
    'Must pass a file or file handle';

throws_ok {
    Bio::SeqIO->new(-file => 'foo.bar');
} qr/Could not read file 'foo.bar':/,
    'Must pass a real file';
BioPerl-1.007002/t/SeqIO/Splicedseq.t000444000766000024      1071113155576321 17240 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 27);

    use_ok('Bio::Seq');
    use_ok('Bio::SeqIO');
}

ok my $str = Bio::SeqIO->new(-file   => test_input_file('U58726.gb'),
                             -format => 'GenBank');
my $seq;
ok ( $seq = $str->next_seq() );

# Here is a cute way to verify the sequence by seeing if the
# the translation matches what is annotated in the file -js
foreach my $ft ( grep { $_->primary_tag eq 'CDS'}
                 $seq->top_SeqFeatures ) {
    if( $ft->has_tag('translation') ) {
        my ($translation) = $ft->get_tag_values('translation');
        my $t = $ft->spliced_seq(-nosort => 1);
        my $pepseq = $t->translate()->seq();
        chop($pepseq); # chop is to remove stop codon
        is($translation, $pepseq);
    }
}

my $stream = Bio::SeqIO->new(-file   => test_input_file('M12730.gb'),
                             -format => 'genbank');
# Jump down to M12730 which lists CDS join(1959..2355,1..92)
while ($seq->accession ne "M12730") {
    $seq = $stream->next_seq;
}
ok(my @features = $seq->get_SeqFeatures(), "get_SeqFeatures()");
my $feat;
foreach my $feat2 ( @features ) {
    next unless ($feat2->primary_tag eq "CDS");
    my @db_xrefs = $feat2->get_tag_values("db_xref");
    if (grep { $_ eq "GI:150830" } @db_xrefs) {
       $feat = $feat2;
       last;
    }
}
my ($protein_seq) = $feat->get_tag_values("translation");
like($protein_seq, qr(^MKERYGTVYKGSQRLIDE.*ANEKQENALYLIIILSRTSIT$),
                   "protein sequence");
my ($nucleotide_seq) = $feat->spliced_seq(-nosort => 1)->seq;
like($nucleotide_seq, qr(^ATGAAAGAAAGATATGGA.*TCAAGGACTAGTATAACATAA$),
                     "nucleotide sequence - correct CDS range");
is(length($nucleotide_seq), 489, "nucleotide length");

#  Test for Fix spliced seq #72
my $str2 = Bio::SeqIO->new(-file   => test_input_file('AF032047.gbk'),
                           -format => 'GenBank');
my @feats = $str2-> next_seq -> get_SeqFeatures;
# feat[1] has 2 exons from remote sequence AF032048.1
my $len_nodb;
warnings_like { $len_nodb = length($feats[1]->spliced_seq()->seq); }
              [ {carped => qr/cannot get remote location for/},
                {carped => qr/cannot get remote location for/}
               ],
              "appropriate warning if db not provided for remote sequence";
ok($len_nodb == 374, "correct number of Ns added if remote sequence not provided");

# Test for cut by origin features
my $seq_obj = Bio::Seq->new(-display_id => 'NC_008309',
                            -seq        => 'AAAAACCCCCGGGGGTTTTT');
$seq_obj->is_circular(1);
my $loc_obj = Bio::Factory::FTLocationFactory->from_string('join(16..20,1..2)');
my $cut_feat = Bio::SeqFeature::Generic->new(-primary_tag => 'CDS',
                                             -location    => $loc_obj,
                                             -tag => { locus_tag  => 'HS_1792',
                                                       product    => 'hypothetical protein',
                                                       protein_id => 'YP_718205.1',
                                                      } );
$seq_obj->add_SeqFeature($cut_feat);
is $cut_feat->seq->seq,         'TTTTTAA', 'cut by origin sequence using $feat->seq';
is $cut_feat->spliced_seq->seq, 'TTTTTAA', 'cut by origin sequence using $feat->spliced_seq';
is $cut_feat->start,             16,       'cut by origin start using $feat->start';
is $cut_feat->end,               2,        'cut by origin end using $feat->end';
is $cut_feat->location->start,   16,       'cut by origin start using $feat->location->start';
is $cut_feat->location->end,     2,        'cut by origin end using $feat->location->end';

SKIP: {
    test_skip(-tests => 3,
              -requires_modules    => [qw(Bio::DB::GenBank
                                          LWP::UserAgent )],
              -requires_networking => 1);
    my $db_in;
    eval {
        ok $db_in = Bio::DB::GenBank->new();
        my $seq_obj = $db_in->get_Seq_by_id('AF032048.1');
    };
    if ($@) {
        print "$@\n";
        skip  "Warning: Problem accessing GenBank entry AF032048.1 "
            . "to test spliced_seq on remote DBs", 2;
    }

    my $len_w_db;
    warning_is { $len_w_db = length($feats[1]->spliced_seq(-db => $db_in)->seq) }
               [],
               "no warnings if GenBank db provided for remote sequence";
    ok($len_w_db == 374, "correct length if remote sequence is provided")
}
BioPerl-1.007002/t/SeqIO/abi.t000444000766000024       273613155576321 15667 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 7,
			   -requires_module => 'Bio::SeqIO::staden::read 1.006');
	
	use_ok('Bio::SeqIO');
}

my $verbose = test_debug();

my $io = Bio::SeqIO->new(-format => 'abi',
								 -verbose => $verbose,
								 -file => test_input_file('test.abi',),
								 -get_trace_data => 1);
my $seq = $io->next_seq;
isa_ok($seq, 'Bio::PrimarySeqI');
is($seq->seq, "GCNTATGACGTGGATTNCGAATTCTNNNNNCGGTAGNNGAAAATCCCCGGNCAAGNTTNNCCCTGCAAANGGAANAANNTGGCCGAGCGCTACGGGCTGATCTGGGTGTGCCTGTTTCCCCCGGCCGGGGGGAGNGATGCAGGACATCCAAGTATCCCGCCNATGGNGGGCTGAGGACGAGGACGGCTTCCATCAGATCAGTGTGCCCGGNCTTCGACATCGGCGGCAGCGCCGCGCGCCAACTGGAAGGCTTCATCGACGTGNAGCATTTTGNCTTCNTGCGCACCGCTACCTTCACCCANCCGGACAAGCGCNAANTGCNGNCCTACACCACCACNGAAACACCGACCGGNTTNAATGCCGATTACCTGAGNNGCGTGGCAAATTATTCGGNGGACNTGCCGCTGNCGGACGTGGACCCGAACTTCCAATGGCTGCGTCATTNCTAGGTGAATCTGCCTTTCACCGCCACGCTCACCATCCACTTCCCGGTGCCGGGCAAGCGGTTGGTGATNATGAATGCCGCCAGACCGGTGTCCAAGCACACCANCCGCCTGNTGGTGCCGATCGNCCGCTAATTTCGACACCCATCTGCCNGNGGGAAGACGTACATGNGTTCAACCTTGCACNTNGTTCNAAAAAAACCNTGCCATGGTGGNAANCGCAAGCGGNCCGGAAATATCNGCCGGNTTGACCCGCNTGNTTGGAAAGTGCATATTCCCCNCCGATNCNCAATTTCGAT");
# trace data points, only added if get_trace_data is invoked
is($seq->get_trace_graph( -trace => 'a' ), 8793); 
is($seq->get_trace_graph( -trace => 't' ), 8793); 
is($seq->get_trace_graph( -trace => 'g' ), 8793); 
is($seq->get_trace_graph( -trace => 'c' ), 8793); BioPerl-1.007002/t/SeqIO/ace.t000444000766000024       273413155576321 15662 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 7);

    use_ok 'Bio::SeqIO';
}

my $verbose = test_debug();

my $t_file = test_input_file('test.ace');
my $before;
{
    local $/ = undef;
    open my $BEFORE, '<', $t_file or die "Could not read file '$t_file': $!\n";
    $before = <$BEFORE>;
    close $BEFORE;
}

my $a_in = Bio::SeqIO->new( -FILE    => $t_file,
                            -verbose => $verbose,
                            -FORMAT  => 'ace' );
my @a_seq;
while (my $a = $a_in->next_seq) {
    push @a_seq, $a;
}

is @a_seq, 3, 'number of sequence objects';

my $esc_name = $a_seq[1]->display_id;
is $esc_name, 'Name; 4% strewn with \ various / escaped characters',
    "unescaping of characters, $esc_name";

is $a_seq[0]->alphabet, 'protein', 'alphabets detected';
is $a_seq[1]->alphabet, 'dna', 'alphabets detected';

my $o_file = test_output_file();
my $a_out = Bio::SeqIO->new( -FILE    => ">$o_file",
                             -verbose => $verbose,
                             -FORMAT  => 'ace' );
my $a_out_ok = 1;
for my $a (@a_seq) {
    $a_out->write_seq($a) or $a_out_ok = 0;
}
undef($a_out);  # Flush to disk
is $a_out_ok,1,'writing sequence';

my $after;
{
    local $/ = undef;
    open my $AFTER, '<', $o_file or die "Could not read file '$o_file': $!\n";
    $after = <$AFTER>;
    close $AFTER;
}

is( ($before and $after and ($before eq $after)), 1, 'test output');
BioPerl-1.007002/t/SeqIO/agave.t000444000766000024       236613155576321 16216 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests               => 8,
			   -requires_module     => 'XML::Writer',
			   -requires_networking => 0,
			  );
	
	use_ok('Bio::SeqIO::agave');
}

my $verbose = test_debug();

TODO: {
	my $format = 'agave';
	todo_skip "No tests for $format format -- no sample file to test against", 7, if 1;

	my $seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test.$format"),
							        -format => $format);
	
	isa_ok($seqio_obj, 'Bio::SeqIO');
	
	my @methods = qw(next_seq write_seq);
	foreach my $method (@methods) {
		can_ok($seqio_obj, $method) || 
			diag "$method method not implemented for $format";	
	}
	
	# checking the first sequence object
	my $seq_obj = $seqio_obj->next_seq();
	isa_ok($seq_obj, 'Bio::Seq');
	my %expected = ('seq'         => '' .
					'length'      => '',
					'primary_id'  => '',
					'description' => qr(),
				   );
	is   ($seq_obj->seq(),         $expected{'seq'},         'sequence');
	is   ($seq_obj->length(),      $expected{'length'},      'length');
	is   ($seq_obj->primary_id(),  $expected{'primary_id'},  'primary_id');
	like ($seq_obj->description(), $expected{'description'}, 'description');
}BioPerl-1.007002/t/SeqIO/alf.t000444000766000024       234013155576321 15665 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests               => 8,
			   -requires_module     => 'Bio::SeqIO::staden::read');
	
	use_ok('Bio::SeqIO::alf');
}

my $verbose = test_debug();

TODO: {
	my $format = 'alf';
	todo_skip "No tests for $format format -- no sample file to test against", 7, if 1;

	my $seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test.$format"),
							        -format => $format);
	
	isa_ok($seqio_obj, 'Bio::SeqIO');
	
	my @methods = qw(next_seq write_seq);
	foreach my $method (@methods) {
		can_ok($seqio_obj, $method) || 
			diag "$method method not implemented for $format";	
	}
	
	# checking the first sequence object
	my $seq_obj = $seqio_obj->next_seq();
	isa_ok($seq_obj, 'Bio::Seq::Quality');
	my %expected = ('seq'         => '' .
					'length'      => '',
					'primary_id'  => '',
					'description' => qr(),
				   );
	is   ($seq_obj->seq(),         $expected{'seq'},         'sequence');
	is   ($seq_obj->length(),      $expected{'length'},      'length');
	is   ($seq_obj->primary_id(),  $expected{'primary_id'},  'primary_id');
	like ($seq_obj->description(), $expected{'description'}, 'description');
}BioPerl-1.007002/t/SeqIO/asciitree.t000444000766000024       157613155576321 17105 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

# `make test'. After `make install' it should work as `perl test.t'

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 2);
	
	use_ok('Bio::SeqIO');
}

my $verbose = test_debug();

# asciitree is a write-only format
my $in = Bio::SeqIO->new(-format => 'genbank',
						-verbose => $verbose,
						-file => test_input_file('AE003644_Adh-genomic.gb'));
my $seq = $in->next_seq;

my $out_file = test_output_file();
my $out = Bio::SeqIO->new(-file => ">".$out_file,
						-verbose => $verbose,
						-format => 'asciitree');
$out->write_seq($seq);

# this is a bug and is failing on some systems like IRIX (not sure why, maybe
# File::Temp?)

if (-s $out_file) {
	ok(1, "File exists, has contents on ".$^O);
} else {
	TODO: {
        local $TODO = "Output doesn't exists on ".$^O;
		ok(-s $out_file);
	}
}
BioPerl-1.007002/t/SeqIO/bsml.t000444000766000024       227613155576321 16070 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 16,
			   -requires_modules => ['XML::DOM']
			  );
	use_ok('XML::DOM');
	use_ok('Bio::SeqIO::bsml');
}

my $verbose = test_debug();

my $str = Bio::SeqIO->new(-format => 'bsml',
			  -verbose => $verbose,
			  -file => test_input_file('U83300.bsml'));
my $seq = $str->next_seq;
isa_ok($seq, 'Bio::Seq::RichSeqI');
my @refs = $seq->annotation->get_Annotations('reference');
is(@refs, 2, 'got correct number of refs');
is($seq->display_id, 'MIVN83300', 'display_id');
is($seq->molecule, 'DNA', 'molecule');
ok(! $seq->is_circular, 'is_circular');
is($seq->get_dates, 2, 'dates');
is($seq->accession_number, 'U83300', 'accession_number');
is($seq->seq_version, 1, 'seq_version');
my @feats = $seq->get_SeqFeatures;
is(@feats, 2, 'got correct number of SeqFeatures');
is($feats[1]->start, 1, 'feature start');
is($feats[1]->end, 946, 'feature end');
is($feats[1]->get_tag_values('db_xref'), 3, 'get_tag_values db_xref');
is($seq->annotation->get_Annotations('reference'), 2, 'get_Annotations reference');
is($seq->annotation->get_Annotations('dblink'), 2, 'get_Annotations dblink');
BioPerl-1.007002/t/SeqIO/bsml_sax.t000444000766000024       172113155576321 16735 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 15,
			   -requires_modules => [qw(XML::SAX
									    XML::SAX::Writer
										XML::SAX::Base)]);
    
	use_ok('Bio::SeqIO');
}

my $verbose = test_debug();

my $str = Bio::SeqIO->new(-format => 'bsml_sax',
			  -verbose => $verbose,
			  -file => test_input_file('U83300.bsml'));
my $seq = $str->next_seq;
isa_ok($seq, 'Bio::Seq::RichSeqI');
my @refs = $seq->annotation->get_Annotations('reference');
is(@refs, 2);
is($seq->display_id,'MIVN83300');
is($seq->molecule ,'dna');
ok(! $seq->is_circular);
is($seq->get_dates,2);
is($seq->accession_number, 'U83300');
is($seq->seq_version,1);
my @feats = $seq->get_SeqFeatures;
is(@feats, 2);
is($feats[1]->start, 1);
is($feats[1]->end, 946);
is($feats[1]->get_tag_values('db_xref'), 3);
is($seq->annotation->get_Annotations('reference'),2);
is($seq->annotation->get_Annotations('dblink'),2);
BioPerl-1.007002/t/SeqIO/chadoxml.t000444000766000024       237413155576321 16731 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests               => 8,
			   -requires_module     => 'XML::Writer',
			   -requires_networking => 0,
			  );
	
	use_ok('Bio::SeqIO::chadoxml');
}

my $verbose = test_debug();

TODO: {
	my $format = 'chadoxml';
	todo_skip "No tests for $format format -- no sample file to test against", 7, if 1;

	my $seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test.$format"),
							        -format => $format);
	
	isa_ok($seqio_obj, 'Bio::SeqIO');
	
	my @methods = qw(next_seq write_seq);
	foreach my $method (@methods) {
		can_ok($seqio_obj, $method) || 
			diag "$method method not implemented for $format";	
	}
	
	# checking the first sequence object
	my $seq_obj = $seqio_obj->next_seq();
	isa_ok($seq_obj, 'Bio::Seq');
	my %expected = ('seq'         => '' .
					'length'      => '',
					'primary_id'  => '',
					'description' => qr(),
				   );
	is   ($seq_obj->seq(),         $expected{'seq'},         'sequence');
	is   ($seq_obj->length(),      $expected{'length'},      'length');
	is   ($seq_obj->primary_id(),  $expected{'primary_id'},  'primary_id');
	like ($seq_obj->description(), $expected{'description'}, 'description');
}BioPerl-1.007002/t/SeqIO/chaos.t000444000766000024       240213155576321 16217 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests               => 8,
               -requires_module     => 'Data::Stag',
               -requires_networking => 0);

    use_ok('Bio::SeqIO::chaos');
}

my $verbose = test_debug();

TODO: {
	my $format = 'chaos';
	todo_skip "No tests for $format format -- no sample file to test against", 7, if 1;

	my $seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test.$format"),
							        -format => $format);
	
	isa_ok($seqio_obj, 'Bio::SeqIO');
	
	my @methods = qw(next_seq write_seq);
	foreach my $method (@methods) {
		can_ok($seqio_obj, $method) || 
			diag "$method method not implemented for $format";	
	}
	
	# checking the first sequence object
	my $seq_obj = $seqio_obj->next_seq();
	isa_ok($seq_obj, 'Bio::Seq');
	my %expected = ('seq'         => '' .
					'length'      => '',
					'primary_id'  => '',
					'description' => qr(),
				   );
	is   ($seq_obj->seq(),         $expected{'seq'},         'sequence');
	is   ($seq_obj->length(),      $expected{'length'},      'length');
	is   ($seq_obj->primary_id(),  $expected{'primary_id'},  'primary_id');
	like ($seq_obj->description(), $expected{'description'}, 'description');
}
BioPerl-1.007002/t/SeqIO/chaosxml.t000444000766000024       116613155576321 16746 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 2,
			   -requires_module => 'Data::Stag');
	
	use_ok('Bio::SeqIO');
}

my $verbose = test_debug();

# currently chaosxml is write-only
my $in = Bio::SeqIO->new(-format => 'genbank',
								 -verbose => $verbose,
								 -file => test_input_file('AE003644_Adh-genomic.gb'));

my $seq = $in->next_seq;

my $out_file = test_output_file();
my $out = Bio::SeqIO->new(-file => ">$out_file",
								  -verbose => $verbose,
								  -format => 'chaosxml');
$out->write_seq($seq);
ok (-e $out_file);
BioPerl-1.007002/t/SeqIO/ctf.t000444000766000024       305513155576321 15703 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 4,
			   -requires_module => 'Bio::SeqIO::staden::read');
    
	use_ok('Bio::SeqIO::ctf');
}

my $verbose = test_debug();

my $seqio_obj = Bio::SeqIO->new(-format => 'ctf',
			 					-verbose => $verbose,
			 					-file => test_input_file('test.ctf'));
isa_ok($seqio_obj, 'Bio::SeqIO');
ok(my $seq = $seqio_obj->next_seq);
is($seq->seq, "GATGATTCCGGCTTCGGACGACTCTAGAGGATCCCCATTTTTATAGTTTTTATCTTGTAATAGATGTTTAGATTTTTCGTTGTAATTATTTTCTTTATTGTTGAAATTAGTATCTCTGGGTAATTTATCATATTCTCTGGAAAATGATTTACTATCACTAGATACTTCATAAGATTTATAATCTTTATTATGAAAATCATCTCTATTTTTCAAATTATTATTATATCTATCAAAGTTTCTGTCTTCATTATATCTATTAGCATATCTATCTTTATCTTTATCCCTATCACTATATCTATCATATGGTTCATCTTGTTCAACCGATCAGACTCGATTCGCCATCGCCTCTAACGGATGGCCGCTCCCCCTCTCATACCTCGCTCCCCTCGACATCCCCCGTCTCGCCACCCTATCCGCCCCCTTCATCACCCCCCCTTATCCACACCCTCACCCCCCGCATCGCGCACCCACGACCACCCGAAGAACCGCCCTTACTCCCAAGTACGCCCCGACCTCCATCACCCTATGCGGTACCACTCCCACCACACCCAGTCCTACTTTCGCCCGCACATCGGCCCCGCTTCAGACAGCTCCCAACTACGCAACCCACGCTTGTTCTTGTTCACACTCGAATACTCGAATCTCTCATTACTCCGCGGACTCCGCCGCACCTGTGCACCATTAACTGTGTAGCGCCTGAACCGGCACCTCTGATTACCACTTCCTCCACCAGCACAGTCCTATTACCGCATGTCGCTCTGCTAAGACAGTGCAAGACTCTGCGGTCGCTCTGACCCGCATCCGCCAGGGCACCTCTCACCCTCGCTGGCCACCCCGCCCCCCTCTCCCTGCCCCTTCATTCCCCCAAACCGCTTTCAACGGGACACACCCCTCCGCGGCGGACCACAACTCGCCGTCGGCCACCACTCACACCTTCCCTCCTCCTTCCCCCACATCACGCCAACCCCGTGGGACGGCTCTCCCGCGGCTACGACGCGCAACCCCCCCTCGCCGCTTCCCCCCCAACTTCCCACGGGCTCCCCTCCGCCCCTTACCCGCGAGGAGCTTCACCCGCGAACCACCTCCCCCCTTTCCCAACAGCACCG");
BioPerl-1.007002/t/SeqIO/embl.t000444000766000024      2765113155576321 16076 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use lib '../..';
    use Bio::Root::Test;

    test_begin(-tests => 100);

    use_ok('Bio::SeqIO::embl');
}

my $verbose = test_debug();

my $ast = Bio::SeqIO->new( -format => 'embl',
                           -verbose => $verbose,
                           -file => test_input_file('roa1.dat'));
$ast->verbose($verbose);
my $as = $ast->next_seq();
ok defined $as->seq;
is($as->display_id, 'HSHNCPA1');
is($as->accession_number, 'X79536');
is($as->seq_version, 1);
is($as->version, 1);
is($as->desc, 'H.sapiens mRNA for hnRNPcore protein A1');
is($as->molecule, 'RNA');
is($as->alphabet, 'rna');
is(scalar $as->all_SeqFeatures(), 4);
is($as->length, 1198);
is($as->species->binomial(), 'Homo sapiens');

# EMBL Release 87 changes (8-17-06)

$ast = Bio::SeqIO->new( -format => 'embl',
                        -verbose => $verbose,
                        -file => test_input_file('roa1_v2.dat'));
$ast->verbose($verbose);
$as = $ast->next_seq();
ok defined $as->seq;
# accession # same as display name now
is($as->display_id, 'X79536'); 
is($as->accession_number, 'X79536');
is($as->seq_version, 1);
is($as->version, 1);
is($as->desc, 'H.sapiens mRNA for hnRNPcore protein A1');
# mRNA instead of RNA
is($as->molecule, 'mRNA');
is($as->alphabet, 'rna');
is(scalar $as->all_SeqFeatures(), 4);
is($as->length, 1198);
is($as->species->binomial(), 'Homo sapiens');

my $ent = Bio::SeqIO->new( -file => test_input_file('test.embl'),
                           -format => 'embl');
my $seq = $ent->next_seq();

is(defined $seq->seq(), 1,
   'success reading Embl with ^ location and badly split double quotes');
is(scalar $seq->annotation->get_Annotations('reference'), 3);

my $out_file = test_output_file();
my $out = Bio::SeqIO->new(-file=> ">$out_file",
                          -format => 'embl');
is($out->write_seq($seq),1,
   'success writing Embl format with ^ < and > locations');

# embl with no FT
$ent = Bio::SeqIO->new( -file => test_input_file('test.embl'),
                        -format => 'embl');
$seq = $ent->next_seq();

ok($seq);
is(lc($seq->subseq(1,10)),'gatcagtaga');
is($seq->length, 4870);

# embl with no FH
my $noFH = Bio::SeqIO->new( -file => test_input_file('no_FH.embl'),
                            -format => 'embl');
is(scalar($noFH->next_seq->get_SeqFeatures), 4);

# bug 1571
$ent = Bio::SeqIO->new( -format => 'embl',
                        -file   => test_input_file('test.embl2sq'));
is($ent->next_seq->length,4877);

# embl repbase
$ent = Bio::SeqIO->new(-file => test_input_file('BEL16-LTR_AG.embl'), -format => 'embl');
$seq = $ent->next_seq;
is($seq->display_id,'BEL16-LTR_AG');

# test secondary accessions in EMBL (bug #1332)
my $seqio = Bio::SeqIO->new( -format => 'embl',
                             -file => test_input_file('ECAPAH02.embl'));
$seq = $seqio->next_seq;
is($seq->accession_number, 'D10483');
is($seq->seq_version, 2);
my @accs = $seq->get_secondary_accessions();
is($accs[0], 'J01597');
is($accs[-1], 'X56742');

### TPA TESTS - Thanks to Richard Adams ###
# test Third Party Annotation entries in EMBL/Gb format 
# to ensure compatability with parsers.
my $str = Bio::SeqIO->new( -format =>'embl',
                           -file => test_input_file('BN000066-tpa.embl'));
$seq = $str->next_seq;
ok(defined $seq);
is($seq->accession_number, 'BN000066');
is($seq->alphabet, 'dna');
is($seq->display_id, 'AGA000066');
is($seq->length, 5195);
is($seq->division, 'INV');
is($seq->get_dates, 2);
is($seq->keywords, 'acetylcholinesterase; achE1 gene; Third Party Annotation; TPA.');
is($seq->seq_version, 1);
is($seq->feature_count, 15);

my $spec_obj = $seq->species;
is ($spec_obj->common_name, 'African malaria mosquito');
is ($spec_obj->species, 'gambiae');
is ($spec_obj->genus, 'Anopheles');
is ($spec_obj->binomial, 'Anopheles gambiae');

my $ac = $seq->annotation;
my $reference =  ($ac->get_Annotations('reference') )[1];
is ($reference->title,'"A novel acetylcholinesterase gene in mosquitoes codes for the insecticide target and is non-homologous to the ace gene in Drosophila"');
is ($reference->authors,'Weill M., Fort P., Berthomi eu A., Dubois M.P., Pasteur N., Raymond M.');
my $cmmnt =  ($ac->get_Annotations('comment') )[0];
is($cmmnt->text, 'see also AJ488492 for achE-1 from Kisumu strain Third Party Annotation Database: This TPA record uses Anopheles gambiae trace archive data (http://trace.ensembl.org) ');


$ent = Bio::SeqIO->new( -file => test_input_file('test.embl'),
                        -format => 'embl');
$ent->verbose($verbose);
$seq = $ent->next_seq();
my $species = $seq->species();
my @cl = $species->classification();
is( $cl[3] ne $species->genus(), 1, 'genus duplication test');
$ent->close();

#
## read-write - test embl writing of a PrimarySeq
#
my $primaryseq = Bio::PrimarySeq->new( -seq => 'AGAGAGAGATA',
                                      -id  => 'myid',
                                      -desc => 'mydescr',
                                      -alphabet => 'DNA',
                                      -accession_number => 'myaccession');



$verbose = -1 unless $ENV{'BIOPERLDEBUG'};  # silence warnings unless we are debuggin

my $embl = Bio::SeqIO->new(-format => 'embl',
                          -verbose => $verbose,
                          -file => ">$out_file");

ok($embl->write_seq($primaryseq));

# this should generate a warning
my $scalar = "test";
eval {
    $embl->write_seq($scalar);
};
ok ($@);

# CDS records
# (which have nonstandard 'PA' and 'OX' tags)
# see http://bioperl.org/pipermail/bioperl-l/2009-February/029252.html
# and the rest of that thread
my $cds_file = Bio::SeqIO->new(-format =>'embl',
                               -file => test_input_file('cds_sample.embl'));
my $cds_seq = $cds_file->next_seq;
ok(defined $cds_seq);
is($cds_seq->display_id, 'EAL24309');
is($cds_seq->accession_number, 'CH236947.1', 'CDS - accession on PA line');
is($cds_seq->alphabet, 'dna');
is($cds_seq->length, 192);
is($cds_seq->species->binomial(), 'Homo sapiens');
is($cds_seq->seq_version, 1);
is($cds_seq->feature_count, 2);
my $cds_annot = $cds_seq->annotation;
ok(defined $cds_annot);
my $cds_dblink = ($cds_annot->get_Annotations('dblink'))[0];
ok(defined $cds_dblink);
is($cds_dblink->tagname, 'dblink', 'CDS - OX tagname');
is($cds_dblink->database, 'NCBI_TaxID', 'CDS - OX database');
is($cds_dblink->primary_id, '9606', 'CDS - OX primary_id');

#bug 2982 - parsing contig descriptions sans sequence data

ok( $embl = Bio::SeqIO->new( -file => test_input_file('bug2982.embl'),
                             -format => 'embl') );
my $i;
for ($i=0; my $seq = $embl->next_seq; $i++) {
    ok !$seq->seq;
    ok ( my $ann = ($seq->annotation->get_Annotations('contig'))[0] );
    like $ann->value, qr/join\(/;
}
is $i, 4;


# bug 3086 - parsing long lines correctly

ok( $embl = Bio::SeqIO->new(-file => test_input_file('bug3086.embl'),
                            -format => 'embl',
                            -verbose => '$verbose') );
$seq = $embl->next_seq;
foreach my $feature ($seq->top_SeqFeatures) {
    if ($feature->has_tag('product')) {
        my ($product) = $feature->get_tag_values('product');
        is($product,
           'bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase',
           'Check if product was parsed correctly');
    }
}

# long labels handled

{
    # Create sequence with feature with a long label qualifier
    my $seq=Bio::Seq->new(-seq=>'actg');
    my $feature=Bio::SeqFeature::Generic->new(-primary=>'CDS', -start=>1, -end=>4);
    $feature->add_tag_value(label=>'1 2 3 4 5 6 7 8 9 a b c d e f g h i j k l m n o p q r');
    $seq->add_SeqFeature($feature);

    # Write EMBL
    my $string;
    open my $str_fh, '>', \$string or skip("Could not write string, skipping", 2);
    
    my $out=Bio::SeqIO->new(-format=>'embl', -fh => $str_fh);
    $out->write_seq($seq);

    # Read EMBL
    my $in=Bio::SeqIO->new(-format=>'embl', -string => $string);
    my $ret=eval { my $embl=$in->next_seq };
    my $error;
    $error=$@ if (!$ret);
    ok($ret, 'Parse long qualifier');
    is($error, undef);
}

# NCBI TaxIDs should roundtrip
{
    my $seq=Bio::Seq->new(-seq=>'actg');
    my $species = Bio::Species->new(-ncbi_taxid => 7165, -classification=>
                                    [ 'Anopheles gambiae', 'Anopheles', 'Culicoidea',
                                      'Nematocera', 'Diptera', 'Endopterygota',
                                      'Neoptera', 'Pterygota', 'Insecta', 'Hexapoda',
                                      'Arthropoda', 'Metazoa', 'Eukaryota' ]);

    $seq->species($species);
    is($seq->species->ncbi_taxid, 7165, 'TaxID set correctly');

    # Write EMBL
    my $string;
    open my $str_fh, '>', \$string or skip("Could not write string, skipping", 2);

    my $out=Bio::SeqIO->new(-format=>'embl', -fh => $str_fh);
    $out->write_seq($seq);

    # Read EMBL
    my $in=Bio::SeqIO->new(-format=>'embl', -string => $string);
    my $embl_seq;
    my $ret=eval { $embl_seq=$in->next_seq };
    my $error;
    $error=$@ if (!$ret);

    # Check that TaxID has roundtripped
    my $embl_species = $embl_seq->species;
    ok(defined $embl_species, "The read sequence has a species object");
    is($embl_species->ncbi_taxid, 7165, "NCBI TaxID has roundtripped");
    is($embl_species->binomial(), 'Anopheles gambiae', "Name has roundtripped");
}

# a taxon db_xref on a source feature should override an OX line
{
    my $seq=Bio::Seq->new(-seq=>'actg');
    my $species = Bio::Species->new(-ncbi_taxid => 7165, -classification=>
                                    [ 'Anopheles gambiae', 'Anopheles', 'Culicoidea',
                                      'Nematocera', 'Diptera', 'Endopterygota',
                                      'Neoptera', 'Pterygota', 'Insecta', 'Hexapoda',
                                      'Arthropoda', 'Metazoa', 'Eukaryota' ]);

    $seq->species($species);
    is($seq->species->ncbi_taxid, 7165, 'TaxID set correctly');

    my $seq_feature = Bio::SeqFeature::Generic->new(-primary=>'source',
                                                    -start => 1,
                                                    -end=> length($seq->seq));

    $seq_feature->add_tag_value('db_xref', 'taxon:9606');
    $seq->add_SeqFeature($seq_feature);

    # Write EMBL
    my $string;
    open my $str_fh, '>', \$string or skip("Could not write string, skipping", 2);

    my $out=Bio::SeqIO->new(-format=>'embl', -fh => $str_fh);
    $out->write_seq($seq);

    # Read EMBL
    my $in=Bio::SeqIO->new(-format=>'embl', -string => $string);
    my $embl_seq;
    my $ret=eval { $embl_seq=$in->next_seq };
    my $error;
    $error=$@ if (!$ret);

    # Check that TaxID has roundtripped
    my $embl_species = $embl_seq->species;
    ok(defined $embl_species, "The read sequence has a species object");
    is($embl_species->ncbi_taxid, 9606, "The taxid of the source feature overrides that of the OX line");
    is($embl_species->binomial(), 'Anopheles gambiae', "Name has roundtripped");
}

# Handle Seq objects that only define an ID, not an accession number
{
    my $seq = Bio::Seq->new(-seq=>'actg', -id=>'test_id');

    my $string;
    open my $str_fh, '>', \$string or skip("Could not write string, skipping", 1);

    my $out = Bio::SeqIO->new(-format=>'embl', -fh=>$str_fh);
    $out->write_seq($seq);

    ok($string =~ m/ID   test_id;/, "The ID field was written correctly");
}

# Test lenient handling of space after '=' sign in qualifiers:
{
    my $ent = Bio::SeqIO->new( -file => test_input_file('test_space.embl'),
                               -format => 'embl');
    my $seq;
    eval { $seq = $ent->next_seq(); };
    my $error=$@;
    is($error, '', 'EMBL format with space after equal sign parses');

    my ($feature)=$seq->all_SeqFeatures;
    is($feature->primary_tag, 'CDS', 'CDS read');

    ok($feature->has_tag('product'), '/product found');

    my ($value)=$feature->get_tag_values('product');
    is($value, 'somewordandt extthatisquite lon gandthereforewraps', 'Qualifier /product value matches');
}
BioPerl-1.007002/t/SeqIO/entrezgene.t000444000766000024      3713213155576321 17320 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 1427,
               -requires_module => 'Bio::ASN1::EntrezGene');

    use_ok('Bio::SeqIO::entrezgene');
}

my @species=('Homo sapiens','Mus musculus', 'Caenorhabditis elegans');
my @pubmed=qw(15461460 15221005 14702039 12477932 8889549 3610142 3458201 2591067);

my %pmed=(1=>8, 
            2=>55,
            3=>1,
            4=>0,
            5=>0,
            6=>0,
            7=>0,
            8=>1,
            9=>32,
            10=>58,
            11=>1,
            12=>76,
            13=>7,
            14=>5,
            15=>13,
            9996=>0,
            11286=>0,
            11287=>5,
            11288=>0,
            11289=>0,
            11293=>0,
            11294=>0,
            11295=>0,
            11296=>0,
            11297=>0,
            11298=>3,
            11299=>0,
            11300=>0,
            11301=>0,
            11302=>9,
            11303=>54,
            11304=>11,
            11305=>3,
            11306=>9,
            171590=>0,
            171591=>0,
            171592=>0,
            171593=>0,
            171594=>0);
            
my %asym=(1=>['A1B', 'ABG', 'GAB', 'HYST2477', 'DKFZp686F0970'],
            2=>['FWP007','S863-7','DKFZp779B086'], 4=>['A12M1'], 5=>['A12M2'],6=>['A12M3'],7=>['A12M4'],
            9=>['AAC1'],10=>['AAC2'],11=>['NATP'],
            12=>['ACT','AACT','MGC88254'],13=>['DAC'],15=>['SNAT','AA-NAT'],
            14=>[''],
            11287=>['A1m','A2m','MAM'],
            11298=>['Nat4','SNAT','Nat-2'],
            11302=>['AATYK','mKIAA0641'],11303=>['Abc1'],
            11304=>['RmP','Abcr','Abc10','D430003I15Rik'],
            11305=>['Abc2','mKIAA1062','D2H0S1474E'],
            11306=>['Abc7'],
            171590=>['Y74C9A.3','CELK05052'],
            171591=>['Y74C9A.2','CELK01753'],
            171592=>['Y74C9A.4a','Y74C9A.4b','CELK08126'],
            171593=>['Y74C9A.5','CELK09643'],
            171594=>['Y48G1C.4','CELK05819']);
            
my @ids=qw(1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
9996
11286
11287
11288
11289
11293
11294
11295
11296
11297
11298
11299
11300
11301
11302
11303
11304
11305
11306
171590
171591
171592
171593
171594);

my @loop_counts = ([1,1,1,1,5,1,12,1,1,1,14,8,16],
				   [1,1,1,1,3,1,40,1,1,1,14,31],
				   [1,1,1,1,0,1,4,1,10,5],
				   [1,1,0,1,1,1,1,7,0],
				   [1,1,0,1,1,1,1,7,0],
				   [1,1,0,1,1,1,1,7,0],
				   [1,1,0,1,1,1,1,7,0],
				   [1,0,1,1,0,1,4,1,1,1,13,0],
				   [1,1,1,1,1,1,33,1,1,1,14,41],
				   [1,1,1,1,1,1,51,1,1,1,14,51],
				   [1,0,1,1,1,1,1,1,10,1],
				   [1,1,1,1,3,1,28,1,1,1,14,33],
				   [1,1,1,1,1,1,17,1,1,1,14,10],
				   [1,1,1,1,0,1,11,1,1,1,13,20],
				   [1,1,1,1,2,1,16,1,1,1,14,23],
				   [1,0,0,0,0,0,0,2,0],
				   [1,0,0,0,0,0,0,3,0],
				   [1,1,1,1,3,1,10,1,13,10],
				   [1,0,0,0,0,0,0,3,0],
				   [1,0,0,0,0,0,0,2,0],
				   [1,0,0,0,0,0,0,3,0],
				   [1,0,0,0,0,0,0,3,0],
				   [1,0,0,0,0,0,0,3,0],
				   [1,0,0,0,0,0,0,2,0],
				   [1,0,0,0,0,0,0,2,0],
				   [1,1,1,1,3,1,9,1,13,5,16],
				   [1,0,0,0,0,0,0,3,0],
				   [1,0,0,0,0,0,0,3,0],
				   [1,0,0,0,0,0,0,2,0],
				   [1,1,1,1,2,1,10,1,12,19],
				   [1,1,1,1,1,1,50,1,13,14],
				   [1,1,1,1,4,1,9,1,13,12],
				   [1,1,1,1,3,1,9,1,13,8,8],
				   [1,1,1,1,1,1,11,1,13,12],
				   [1,1,0,1,2,0,0,1,1,1,1,9,4],
				   [1,1,0,1,2,0,0,1,1,1,1,9,4],
				   [1,1,0,1,3,0,0,1,1,1,1,9,8],
				   [1,1,0,1,2,0,0,1,1,1,1,9,4],
				   [1,1,0,1,2,0,0,1,1,1,1,9,4]);

my $fs='!';
my @revkeys=('Entrez Gene Status','RefSeq status','Official Full Name','chromosome','cyto','Reference','dblink',
'ALIAS_SYMBOL','OntologyTerm','Index terms','Official Symbol','cM','Property');

ok my $eio=Bio::SeqIO->new(-file=>test_input_file('entrezgene.dat'), -format=>'entrezgene', -debug=>'on',-service_record=>'yes');

my ($seq,$struct,$uncapt);
my $num_of_seqs = 0;
while (1) {
	my $seq;
	($seq,$struct,$uncapt)=$eio->next_seq;
	last unless ($seq);
	my @lc = @{$loop_counts[$num_of_seqs]};
	$num_of_seqs++;
	
	#T0: GENERAL TESTS
	ok $seq;
	is ref($struct),'Bio::Cluster::SequenceFamily';
	my $acc=$seq->accession_number;
	
	#T1: ORGANISM
	my $org=$seq->species->binomial;
	is grep(/\b$org\b/,@species),1;
	
	#T2: SUMMARY test
	ok $seq->desc if ($acc eq '1')||($acc eq '2')||($acc eq '11304');
	ok !defined $seq->desc if ($acc eq '171592')||($acc eq '11306');
	
	#Are we supposed to have this in our test?
	ok grep(/\b$acc\b/,@ids);
	
	my $ann=$seq->annotation();
	my $tcount;
	
	#T3: ENTREZGENE STATUS TESTS
	my @egstatus=$ann->get_Annotations('Entrez Gene Status');
	my $loop_count = 0;
	foreach my $status (@egstatus) {
		$loop_count++;
		STATUS: {
			if ($acc==1) {is $status->value,'live'; last STATUS;}
			if ($acc==2) {is $status->value,'live'; last STATUS;}
			if ($acc==4) {is $status->value,'discontinued'; last STATUS;}
			if ($acc==6) {is $status->value,'discontinued'; last STATUS;}
			if ($acc==11288) {is $status->value,'secondary'; last STATUS;}
			if ($acc==11293) {is $status->value,'secondary'; last STATUS;} 
			if ($acc==171594) {is $status->value,'live'; last STATUS;} 
		}
	}
	is $loop_count, shift @lc, "correct number of loops for T3";
	$loop_count = 0;
	
	#T4: REFSEQ STATUS TESTS
	my @refstatus=$ann->get_Annotations('RefSeq status');
	foreach my $status (@refstatus) {
		$loop_count++;
		STATUS: {
			if ($acc==1) {is $status->value,'REVIEWED'; last STATUS;}
			if ($acc==2) {is $status->value,'REVIEWED'; last STATUS;}
			if ($acc==3) {is $status->value,'PROVISIONAL'; last STATUS;}
			if ($acc==4) {is $status->value,'WITHDRAWN'; last STATUS;}
			if ($acc==9) {is $status->value,'VALIDATED'; last STATUS;}
			if ($acc==11300) {is $status->value,''; last STATUS;}
			if ($acc==11306) {is $status->value,'MODEL'; last STATUS;}
			if ($acc==11293) {is $status->value,'secondary'; last STATUS;} 
			if ($acc==171594) {is $status->value,'Reviewed'; last STATUS;} 
		}
	}
	is $loop_count, shift @lc, "correct number of loops for T4";
	$loop_count = 0;
	
	#T5: GENE NAME TESTS
	my @ofname=$ann->get_Annotations('Official Full Name');
	foreach my $name (@ofname) {
		$loop_count++;
		STATUS: {
			if ($acc==10) {is $name->value,'N-acetyltransferase 2 (arylamine N-acetyltransferase)'; last STATUS;}
			if ($acc==13) {is $name->value,'arylacetamide deacetylase (esterase)'; last STATUS;}
			if ($acc==14) {is $name->value,'angio-associated, migratory cell protein'; last STATUS;}
			if ($acc==11287) {is $name->value,'pregnancy zone protein'; last STATUS;}
			if ($acc==11298) {is $name->value,'arylalkylamine N-acetyltransferase'; last STATUS;}
			if ($acc==11304) {is $name->value,'ATP-binding cassette, sub-family A (ABC1), member 4'; last STATUS;}
			if ($acc==11306) {is $name->value,'ATP-binding cassette, sub-family B (MDR/TAP), member 7'; last STATUS;} 
		}
	}
	is $loop_count, shift @lc, "correct number of loops for T5";
	$loop_count = 0;
	
	#T6: CHROMOSOME TESTS
	my @chr=$ann->get_Annotations('chromosome');
	foreach my $chr (@chr) {
		$loop_count++;
		STATUS: {
			if ($acc==5) {is $chr->value,1; last STATUS;}
			if ($acc==6) {is $chr->value,1; last STATUS;}
			if ($acc==7) {is $chr->value,17; last STATUS;}
			if ($acc==11306) {is $chr->value,'X'; last STATUS;}
			if ($acc==11304) {is $chr->value,3; last STATUS;}
			if ($acc==171590) {is $chr->value,'I'; last STATUS;}
			if ($acc==171592) {is $chr->value,'I'; last STATUS;} 
		}
	}
	is $loop_count, shift @lc, "correct number of loops for T6";
	$loop_count = 0;
	
	#T7: GENE SYMBOL ALIAS TESTS
	my @sym=$ann->get_Annotations('ALIAS_SYMBOL');
	foreach my $sym (@sym) {
		$loop_count++;
        my $val = $sym->display_text;
		next if (($val eq '')||!defined($val));
		is grep(/\b$val\b/,@{$asym{$acc}}),1;
	}
	is $loop_count, shift @lc, "correct number of loops for T7";
	$loop_count = 0;
	
	#T8: CYTO LOCATION TESTS
	my @map=$ann->get_Annotations('cyto');
	foreach my $map (@map) {
		$loop_count++;
		STATUS: {
			if ($acc==10) {is $map->value,'8p22'; last STATUS;}
			if ($acc==11) {is $map->value,'8p22'; last STATUS;}
			if ($acc==13) {is $map->value,'3q21.3-q25.2'; last STATUS;}
			if ($acc==11306) {is $map->value,'X C-D'; last STATUS;}
			if ($acc==11305) {is $map->value,'2 A2-B'; last STATUS;}
			if ($acc==11304) {is $map->value,'3 G1'; last STATUS;}
			if ($acc==11303) {is $map->value,'4 A5-B3'; last STATUS;} 
		}
	}
	is $loop_count, shift @lc, "correct number of loops for T8";
	$loop_count = 0;
	
	#T9: REFERENCE NUMBER TEST
	my @refs=$ann->get_Annotations('Reference');
	my $refs=$#refs+1||0;
	is $pmed{$acc},$refs;
	
	my @dblinks=$ann->get_Annotations('dblink');
	my @keys=$ann->get_all_annotation_keys;
	
	#T10: GENERIF AND OTHER DBLINK TESTS
	my @url=qw(HGMD Ensembl KEGG Homologene);#Only validate the URL
	foreach my $dblink (@dblinks) {
		$loop_count++;
		my $dbname=$dblink->database||'';
		DB: {
			if ( $dbname eq 'generif') {#Should have ID and text
				ok $dblink->primary_id;
				ok $dblink->comment->text;
				last DB;
			}
			if ($acc==2) {
				if (($dbname eq 'MIM')&&($dblink->authority)&&($dblink->authority eq 'phenotype')) {
					ok $dblink->optional_id;
					last DB;
				}
				if ($dbname eq 'Evidence viewer') {
					ok $dblink->url; #We may even validate the urls?
					is $dblink->primary_id,2;
					last DB;
				}
				if ($dbname eq 'Model maker') {
					ok $dblink->url; #We may even validate the urls?
					is $dblink->primary_id,2;
					last DB;
				}
				if ($dbname eq 'AceView') {
					ok $dblink->url; #We may even validate the urls?
					is $dblink->primary_id,2;
					last DB; 
				}
				if (grep(/$dbname/,@url)) {
					ok $dblink->url; #We may even validate the urls?
					last DB;
				}
				if ($dbname eq 'GDB') {
					is $dblink->primary_id,'GDB:119639'; #We may even validate the urls?
					last DB;
				}
				if ($dbname eq 'UniGene') {
					ok $dblink->url; #We may even validate the urls?
					is $dblink->primary_id,'Hs.212838';
					last DB;
				}
				if ($dbname eq 'PharmGKB') {
					is $dblink->primary_id,'PA24357';
					last DB;
				}
				if ($dbname eq 'MGC') {
					ok $dblink->url; #We may even validate the urls?
					is $dblink->primary_id,'BC040071';
					last DB;
				}
			}
		}
	}
	is $loop_count, shift @lc, "correct number of loops for T10";
	$loop_count = 0;
	
	#T11: SOME EXTERNAL DATABASE IDS TESTS
	foreach my $key (@keys) {
		$loop_count++;
		next if grep(/\b$key\b/, @revkeys);
		my @all=$ann->get_Annotations($key);
		#Checking xref to some databases- OMIM, Wormbase and HGNC, others later
		my $loop_count_internal = 0;
		foreach my $pid (@all) {
			$loop_count_internal++;
			DBID: {
				if (($acc==8)&&($key eq 'MIM')) {is $pid->value,'108985'; last DBID;}
				if (($acc==9)&&($key eq 'HGNC')) {is $pid->value,'7645'; last DBID;}
				if (($acc==11298)&&($key eq 'MGI')) {is $pid->value,'1328365'; last DBID;}
				if (($acc==171593)&&($key eq 'AceView/WormGenes')) {is $pid->value,'1A502'; last DBID;} 
				if (($acc==171594)&&($key eq 'WormBase')) {is $pid->value,'Y48G1C.4'; last DBID;} 
			}
		}
		is $loop_count_internal, shift @lc, "correct number of loops for T11a";
	}
	is $loop_count, shift @lc, "correct number of loops for T11";
	$loop_count = 0;
	
	#T12: REFERENCE RECORD TEST
	if ($acc==1) {
		foreach my $ref (@refs) {
			$loop_count++;
			my $pmed=$ref->medline;
			is grep(/\b$pmed\b/,@pubmed),1;
		}
		is $loop_count, shift @lc, "correct number of loops for T12";
		$loop_count = 0;
	}
	
	#T13/14: STS Markers and Gene Ontology
	my @syn=('MGI:707739','MPC786');
	my @evid=qw(IEA TAS ISS);
	my (%pmeds,%go);
	$go{11305}=['5524', '16887', '5215', '8203', '6810', '16021' ,'5765'];
	$go{11298}=['8080', '8415', '4060', '16740'];
	$pmeds{11305}=['12466851']; 
	my @types=qw(Function Component Process);
	if (($acc==11305)||($acc==11298)) { #Let's check just this two...
		foreach my $ot ($ann->get_Annotations('OntologyTerm')) {
			$loop_count++;
			if (($ot->term->authority)&&($ot->term->authority eq 'STS marker')) {
				if ($acc==11305) {
					is $ot->name,'AI413825';
					is $ot->term->namespace,'UniSTS';
					is $ot->identifier,158928;
				}
				else {
					is $ot->name,'D11Mit102';
					is $ot->term->namespace,'UniSTS';
					is $ot->identifier,126289;
					foreach my $syn ($ot->get_synonyms) {
						is grep(/\b$syn\b/,@syn),1;
					}
				}
				next;
			}
			my $evid=$ot->comment;
			$evid=~s/evidence: //i;
			my $type=$ot->ontology->name;
			my @ref=$ot->term->get_references;
			my $id=$ot->identifier;
			my $thispmed=$ref[0]->medline if (@ref);
			is grep(/\b$type\b/,@types),1;
			is grep(/\b$id\b/,@{$go{$acc}}),1;
			is grep(/\b$thispmed\b/,@{$pmeds{$acc}}),1 if ($thispmed);
			ok $ot->name;
		}
		is $loop_count, shift @lc, "correct number of loops for T13/14";
		$loop_count = 0;
	}
	
	#T15/16/17: GENOMIC LOCATION TESTS/SEQUENCE TYPES TESTS/CONSERVED DOMAINS TESTS
	my @gffs=('SEQ	entrezgene	gene location	63548355	63556668	.	+	.',
				 'SEQ	entrezgene	genestructure	63548355	63556668	.	+	.',
				 'SEQ	entrezgene	gene location	31124733	31133046	.	+	.',
				 'SEQ	entrezgene	genestructure	31124733	31133046	.	+	.',
				 'SEQ	entrezgene	gene location	8163589	8172398	.	+	.',
				 'SEQ	entrezgene	genestructure	8163589	8172398	.	+	.');
	my @contigs=$struct->get_members;
	my @auth=('mrna','genomic','product','mrna sequence','protein','peptide');#Known types....
	foreach my $contig (@contigs) {
		$loop_count++;
		my $stype=$contig->authority;
		is grep(/^$stype$/i,@auth),1;
		if ($acc==1) {#Do just 1?
			if (($contig->authority eq 'genomic')||($contig->authority eq 'Genomic')) {
				foreach my $sf ($contig->get_SeqFeatures) {
					$sf->source_tag('entrezgene');
					my $gff=$sf->gff_string;
					$gff=~s/[\t\s]+$//g;
					foreach my $gffstr (@gffs) {
						if ($gffstr eq $gff) {
							ok(1);
							last;
						}
					}
				}
			}
			if ($contig->authority eq 'Product') {
				is $contig->id,'NP_570602';
				is $contig->accession_number,21071030;
				foreach my $sf ($contig->get_SeqFeatures) {
				foreach my $dblink ($sf->annotation->get_Annotations('dblink')) {
						my $key=$dblink->{_anchor}?$dblink->{_anchor}:$dblink->optional_id;
						my $db=$dblink->database;
						next unless (($db =~/cdd/i)||($sf->primary_tag=~ /conserved/i));
						my $desc;
						if ($key =~ /:/) {
							($key,$desc)=split(/:/,$key);
						}
						$desc=~s/^\s+//;#THIS SHOULD GO IN entrezgene.pm!!!
						is $desc,'IGc2; Immunoglobulin C-2 Type';
						is $key,'smart00408';
						is $sf->score,103;
						is $db,'CDD';
						is $sf->start,223;
						is $sf->end,282;
				}
				}
			}
		}
	}
	cmp_ok( $loop_count,'>=', shift @lc, "correct number of loops for T15");
	$loop_count = 0;
}
is $num_of_seqs, 39, 'looped through correct number of sequences';


#, -locuslink=>'convert');
#See if we can convert to locuslink
#T18: BACKCOMPATIBILITY TESTS
my @llsp =('OFFICIAL_GENE_NAME','CHR','MAP','OFFICIAL_SYMBOL');
ok my $eio_b=Bio::SeqIO->new(-file=>test_input_file('entrezgene.dat'),-format=>'entrezgene', -debug=>'on',-service_record=>'yes',-locuslink=>'convert');
my $loop_count = 0;
while (my $seq=$eio_b->next_seq) {
    $loop_count++;
    ok $seq;
    my $acc=$seq->accession_number;
    is grep(/\b$acc\b/,@ids),1;
    my $ann=$seq->annotation;
    last if ($acc==4);#3 is enough? and 4 does not have gene name, so....
    foreach my $key (@llsp) {
        my @vals=$ann->get_Annotations($key);
        ok @vals;
    }
}
is $loop_count, 4, "correct number of loops for T18";

# Test for Bug #3453
ok my $eio_c = Bio::SeqIO->new(-format => 'entrezgene',
                               -file   => test_input_file('entrezgene_bug3453.dat') );
my $entry = 0;
while ( my ( $gene, $genestructure, $uncaptured ) = $eio_c->next_seq ) {
    $entry++;
    if ($entry == 1) {
        is $gene->accession_number, 3581;
        is scalar @{ $uncaptured }, 55;
    }
    elsif ($entry == 2) {
        is $gene->accession_number, 56111;
        is scalar @{ $uncaptured }, 32;
    }
}
BioPerl-1.007002/t/SeqIO/excel.t000444000766000024       120613155576321 16223 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests               => 4,
			   -requires_module     => 'Spreadsheet::ParseExcel',
			   -requires_networking => 0,
			  );
	
	use_ok('Bio::SeqIO::excel');
}

my $verbose = test_debug();

my $format = 'excel';
my $seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test.xls"),
						        -format => $format);

isa_ok($seqio_obj, 'Bio::SeqIO');

my @methods = qw(next_seq write_seq);
foreach my $method (@methods) {
	can_ok($seqio_obj, $method) || 
		diag "$method method not implemented for $format";	
}
BioPerl-1.007002/t/SeqIO/exp.t000444000766000024       276013155576321 15725 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 3,
			   -requires_module => 'Bio::SeqIO::staden::read');
	
	use_ok('Bio::SeqIO::exp');
}

my $verbose = test_debug();

my $io = Bio::SeqIO->new(-format => 'exp',
			 -verbose => $verbose,
			 -file => test_input_file('test.exp'));
ok(my $seq = $io->next_seq);
is($seq->seq, "GATGATTCCGGCTTCGGACGACTCTAGAGGATCCCCATTTTTATAGTTTTTATCTTGTAATAGATGTTTAGATTTTTCGTTGTAATTATTTTCTTTATTGTTGAAATTAGTATCTCTGGGTAATTTATCATATTCTCTGGAAAATGATTTACTATCACTAGATACTTCATAAGATTTATAATCTTTATTATGAAAATCATCTCTATTTTTCAAATTATTATTATATCTATCAAAGTTTCTGTCTTCATTATATCTATTAGCATATCTATCTTTATCTTTATCCCTATCACTATATCTATCATATGGTTCATCTTGTTCAACCGATCAGACTCGATTCGCCATCGCCTCTAACGGATGGCCGCTCCCCCTCTCATACCTCGCTCCCCTCGACATCCCCCGTCTCGCCACCCTATCCGCCCCCTTCATCACCCCCCCTTATCCACACCCTCACCCCCCGCATCGCGCACCCACGACCACCCGAAGAACCGCCCTTACTCCCAAGTACGCCCCGACCTCCATCACCCTATGCGGTACCACTCCCACCACACCCAGTCCTACTTTCGCCCGCACATCGGCCCCGCTTCAGACAGCTCCCAACTACGCAACCCACGCTTGTTCTTGTTCACACTCGAATACTCGAATCTCTCATTACTCCGCGGACTCCGCCGCACCTGTGCACCATTAACTGTGTAGCGCCTGAACCGGCACCTCTGATTACCACTTCCTCCACCAGCACAGTCCTATTACCGCATGTCGCTCTGCTAAGACAGTGCAAGACTCTGCGGTCGCTCTGACCCGCATCCGCCAGGGCACCTCTCACCCTCGCTGGCCACCCCGCCCCCCTCTCCCTGCCCCTTCATTCCCCCAAACCGCTTTCAACGGGACACACCCCTCCGCGGCGGACCACAACTCGCCGTCGGCCACCACTCACACCTTCCCTCCTCCTTCCCCCACATCACGCCAACCCCGTGGGACGGCTCTCCCGCGGCTACGACGCGCAACCCCCCCTCGCCGCTTCCCCCCCAACTTCCCACGGGCTCCCCTCCGCCCCTTACCCGCGAGGAGCTTCACCCGCGAACCACCTCCCCCCTTTCCCAACAGCACCG");
BioPerl-1.007002/t/SeqIO/fasta.t000444000766000024      1216213155576321 16244 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests               => 22,
               -requires_modules    => [],
               -requires_networking => 0,
              );

    use_ok('Bio::SeqIO::fasta');
}

my $verbose = test_debug();

my $format = 'fasta';
my $seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test.$format"),
                                -format => $format);

isa_ok($seqio_obj, 'Bio::SeqIO');

my @methods = qw(next_seq write_seq);
foreach my $method (@methods) {
    can_ok($seqio_obj, $method) ||
        diag "$method method not implemented for $format";
}

# checking the first sequence object
my $seq_obj = $seqio_obj->next_seq();
isa_ok($seq_obj, 'Bio::Seq');
my %expected = ('seq'         => 'MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGL' .
                                 'DYRTTDENLKAHEKWGNIVDVVVMKDPRTKRSRGFGFI' .
                                 'TYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPN' .
                                 'AGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDNIVI' .
                                 'DKETGKKRGFAFVEFDDYDPVDKVVLQKQHQLNGKMVD' .
                                 'VKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGN' .
                                 'QNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGY' .
                                 'GGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGY' .
                                 'QQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGN' .
                                 'YGNNQGFNNGGNNRRY',
                'length'      => '358',
                'primary_id'  => 'roa1_drome',
                'description' => qr(Rea guano receptor type III),
               );
is   ($seq_obj->seq(),         $expected{'seq'},         'sequence');
is   ($seq_obj->length(),      $expected{'length'},      'length');
is   ($seq_obj->primary_id(),  $expected{'primary_id'},  'primary_id');
like ($seq_obj->description(), $expected{'description'}, 'description');


# checking the second sequence object
my $seq_obj2  = $seqio_obj->next_seq();
isa_ok($seq_obj2, 'Bio::Seq');
my %expected2 = ('seq'         => 'MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGL' .
                                  'DYRTTDENLKAHEKWGNIVDVVVMKDPTSTSTSTSTST' .
                                  'STSTSTMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPN' .
                                  'AGATVKKLFVGALKDDHDEQSIRDYFQHLLLLLLLDLL' .
                                  'LLDLLLLDLLLFVEFDDYDPVDKVVLQKQHQLNGKMVD' .
                                  'VKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGN' .
                                  'QNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGY' .
                                  'GGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGY' .
                                  'QQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGN' .
                                  'YGNNQGFNNGGNNRRY',
                 'length'      => '358',
                 'primary_id'  => 'roa2_drome',
                 'description' => qr(Rea guano ligand),
                );
is   ($seq_obj2->seq(),         $expected2{'seq'},         'sequence');
is   ($seq_obj2->length(),      $expected2{'length'},      'length');
is   ($seq_obj2->primary_id(),  $expected2{'primary_id'},  'primary_id');
like ($seq_obj2->description(), $expected2{'description'}, 'description');

# from testformats.pl
SKIP: {
    test_skip(-tests => 4, -requires_modules => [qw(Algorithm::Diff
                                                    IO::ScalarArray
                                                    IO::String)]);
    use_ok('Algorithm::Diff');
    eval "use Algorithm::Diff qw(diff LCS);";
    use_ok('IO::ScalarArray');
    use_ok('IO::String');
    
    my ($file, $type) = ("test.$format", $format);
    my $filename = test_input_file($file);
    print "processing file $filename\n" if $verbose;
    open my $FILE, '<', $filename or die "Could not read file '$filename': $!\n";
    my @datain = <$FILE>;
    close $FILE;

    my $in = new IO::String(join('', @datain));
    my $seqin = new Bio::SeqIO( -fh => $in,
                -format => $type);
    my $out = new IO::String;
    my $seqout = new Bio::SeqIO( -fh => $out,
                 -format => $type);
    my $seq;
    while( defined($seq = $seqin->next_seq) ) {
    $seqout->write_seq($seq);
    }
    $seqout->close();
    $seqin->close();
    my $strref = $out->string_ref;
    my @dataout = map { $_."\n"} split(/\n/, $$strref );
    my @diffs = &diff( \@datain, \@dataout);
    is(@diffs, 0, "$format format can round-trip");
    
    if(@diffs && $verbose) {
        foreach my $d ( @diffs ) {
            foreach my $diff ( @$d ) {
                chomp($diff->[2]);
                print $diff->[0], $diff->[1], "\n>", $diff->[2], "\n";
            }
        }
        print "in is \n", join('', @datain), "\n";
        print "out is \n", join('',@dataout), "\n";
    }

}

# bug 1508
# test genbank, gcg, ace against fasta (should throw an exception on each)

for my $file (qw(roa1.genbank test.gcg test.ace test.raw)) {
    my $in = Bio::SeqIO->new(-file   => test_input_file($file),
                             -format => 'fasta');
    throws_ok {$in->next_seq}
        qr/The sequence does not appear to be FASTA format/, "dies with $file";
}
BioPerl-1.007002/t/SeqIO/fastq.t000444000766000024      5212613155576321 16270 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin( -tests => 149 );

    use_ok('Bio::SeqIO::fastq');
    use_ok('Bio::Seq::Quality');
}

my $DEBUG = test_debug();

# simple parsing, data conversion of fastq example files

my %example_files = (
    bug2335               => {
        'variant'       => 'sanger',
        'seq'           => 'TTGGAATGTTGCAAATGGGAGGCAGTTTGAAATACTGAATAGGCCTCATC'.
                           'GAGAATGTGAAGTTTCAGTAAAGACTTGAGGAAGTTGAATGAGCTGATGA'.
                           'ATGGATATATG',
        'qual'          => '31 23 32 23 31 22 27 28 32 24 25 23 30 25 2 21 33 '.
                           '29 9 17 33 27 27 27 25 33 29 9 28 32 27 7 27 21 '.
                           '26 21 27 27 17 26 23 31 23 32 24 27 27 28 27 28 '.
                           '28 27 27 31 23 23 28 27 27 32 23 27 35 30 12 28 '.
                           '27 27 25 33 29 10 27 28 28 33 25 27 27 31 23 34 '.
                           '27 27 32 24 27 30 22 24 28 24 27 28 27 26 28 27 '.
                           '28 32 24 28 33 25 23 27 27 28 27 28 26',
        'display_id'    => 'DS6BPQV01A2G0A',
        'desc'          => undef,
        'count'         => 1
        },
    RT98876             => {
        'variant'       => 'sanger',
        'seq'           => 'CCGCCATTTCTTCAAATCTTTTCTTTTCTTTAGGAGTCATCAATTTCCAT'.
                           'TTCTCTGCACATTTCTTTGAAAATTA',
        'qual'          => '31 34 34 34 34 34 34 34 34 33 34 34 34 34 34 34 '.
                           '34 34 34 34 34 32 32 34 34 34 34 34 34 34 34 34 '.
                           '30 34 34 34 34 34 34 34 34 34 34 34 34 34 32 32 '.
                           '34 34 34 34 34 34 34 34 34 34 34 34 34 34 34 34 '.
                           '34 34 34 34 33 30 30 27 33 34 29 2',
        'display_id'    => 'Illumina_SRR125365.38',
        'desc'          => 's_5_1_0001_qseq_37 length=76',
        'count'         => 1
        },
    test1_sanger            => {
        'variant'       => 'sanger',
        'seq'           => 'TATTGACAATTGTAAGACCACTAAGGATTTTTGGGCGGCAGCGACTTGGA'.
                           'GCTCTTGTAAAAGCGCACTGCGTTCCTTTTCTTTATTCTTTTGATCTTGA'.
                           'GAATCTTCTAAAAATGCCGAAAAGAAATGTTGGGAAGAGAGCGTAATCAG'.
                           'TTTAGAAATGCTCTTGATGGTAGCTTTATGTTGATCCATTCTTCTGCCTC'.
                           'CTTTACGAATAAAATAGAATAAAACTCAAATGACTAATTACCTGTATTTT'.
                           'ACCTAATTTTGTGATAAAATTCAAGAAAATATGTTCGCCTTCAATAATTA'.
                           'TG',
        'qual'          => '37 37 37 37 37 37 37 37 37 37 37 40 38 40 40 37 '.
                           '37 37 39 39 40 39 39 39 39 39 37 33 33 33 33 33 '.
                           '39 39 34 29 28 28 38 39 39 39 39 39 39 37 37 37 '.
                           '37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 '.
                           '37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 38 '.
                           '38 29 29 29 34 38 37 37 33 33 33 33 37 37 37 37 '.
                           '37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 '.
                           '37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 '.
                           '37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 '.
                           '37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 '.
                           '37 37 37 37 37 37 37 37 37 37 37 37 37 37 38 38 '.
                           '38 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 '.
                           '37 37 37 37 37 37 37 37 37 34 34 34 38 38 37 37 '.
                           '37 37 37 37 37 37 37 37 40 40 40 40 38 38 38 38 '.
                           '40 40 40 38 38 38 40 40 40 40 40 40 40 40 40 40 '.
                           '38 38 38 38 38 32 25 25 25 25 30 30 31 32 32 31 '.
                           '31 31 31 31 31 31 31 31 19 19 19 19 19 22 22 31 '.
                           '31 31 31 31 31 31 31 32 32 31 32 31 31 31 31 31 '.
                           '31 25 25 25 28 28 30 30 30 30 30 31 31 32',
        'display_id'    => 'SRR005406.250',
        'desc'          => 'FB9GE3J10F6I2T length=302',
        'count'         => 250
                                },
    test2_solexa            => {
        'variant'       => 'solexa',
        'seq'           => 'GTATTATTTAATGGCATACACTCAA',
        'qual'          => '25 25 25 25 25 25 25 25 25 25 23 25 25 25 25 23 '.
                           '25 23 23 21 23 23 23 17 17',
        'display_id'    => 'SLXA-B3_649_FC8437_R1_1_1_183_714',
        'desc'          => undef,
        'count'         => 5
                                },
    test3_illumina          => {
        'variant'       => 'illumina',
        'seq'           => 'CCAAATCTTGAATTGTAGCTCCCCT',
        'qual'          => '15 19 24 15 17 24 24 24 24 24 19 24 24 21 24 24 '.
                           '20 24 24 24 24 20 18 13 19',
        'display_id'    => 'FC12044_91407_8_200_285_136',
        'desc'          => undef,
        'count'         => 25
                                },
    example                 => {
        'variant'       => 'sanger', # TODO: guessing on the format here...
        'seq'           => 'GTTGCTTCTGGCGTGGGTGGGGGGG',
        'qual'          => '26 26 26 26 26 26 26 26 26 26 26 24 26 22 26 26 '.
                           '13 22 26 18 24 18 18 18 18',
        'display_id'    => 'EAS54_6_R1_2_1_443_348',
        'desc'          => undef,
        'count'         => 3
                                },
    illumina_faked          => {
        'variant'       => 'illumina',
        'seq'           => 'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN',
        'qual'          => '40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 '.
                           '21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0',
        'display_id'    => 'Test',
        'desc'          => 'PHRED qualities from 40 to 0 inclusive',
        'count'         => 1
                                },
    sanger_93               => {
        'variant'       => 'sanger',
        'seq'           => 'ACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGAC'.
                           'TGACTGACTGACTGACTGACTGACTGACTGACTGAN',
        'qual'          => '93 92 91 90 89 88 87 86 85 84 83 82 81 80 79 78 77 76 75 '.
                           '74 73 72 71 70 69 68 67 66 65 64 63 62 61 60 59 58 57 56 '.
                           '55 54 53 52 51 50 49 48 47 46 45 44 43 42 41 40 39 38 37 '.
                           '36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 '.
                           '17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0',
        'display_id'    => 'Test',
        'desc'          => 'PHRED qualities from 93 to 0 inclusive',
        'count'         => 1
                                },
    sanger_faked            => {
        'variant'       => 'sanger',
        'seq'           => 'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN',
        'qual'          => '40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 '.
                           '21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0',
        'display_id'    => 'Test',
        'desc'          => 'PHRED qualities from 40 to 0 inclusive',
        'count'         => 1
                                },
    solexa_example          => {
        'variant'       => 'solexa',
        'seq'           => 'GTATTATTTAATGGCATACACTCAA',
        'qual'          => '25 25 25 25 25 25 25 25 25 25 23 25 25 25 25 23 '.
                           '25 23 23 21 23 23 23 17 17',
        'display_id'    => 'SLXA-B3_649_FC8437_R1_1_1_183_714',
        'desc'          => undef,
        'count'         => 5
                                },
    solexa_faked            => {
        'variant'       => 'solexa',
        'seq'           => 'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN',
        'qual'          => '40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 '.
                           '24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 10 9 '.
                           '8 7 6 5 5 4 4 3 3 2 2 1 1',
        'display_id'    => 'slxa_0001_1_0001_01',
        'desc'          => undef,
        'count'         => 1
                                },
    tricky                  => {
        'variant'       => 'sanger', # TODO: guessing on the format here...
        'seq'           => 'TGGGAGGTTTTATGTGGAAAGCAGCAATGTACAAGA',
        'qual'          => '40 40 40 40 40 40 40 13 40 40 40 40 40 40 16 31 '.
                           '19 19 31 12 22 13 4 27 5 10 14 3 14 4 19 7 10 10 '.
                           '7 4',
        'display_id'    => '071113_EAS56_0053:1:3:990:501',
        'desc'          => undef,
        'count'         => 4
                                },
    evil_wrapping           => {
        'variant'       => 'sanger', # TODO: guessing on the format here...
        'seq'           => 'AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTC'.
                           'AAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGA'.
                           'TGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT',
        'qual'          => '32 26 31 26 4 22 20 30 25 2 27 27 24 36 32 16 '.
                           '26 28 36 32 18 4 33 26 33 26 32 26 33 26 31 26 '.
                           '4 24 36 32 16 36 32 16 36 32 18 4 27 33 26 32 26 '.
                           '23 36 32 15 35 31 18 3 36 32 16 28 33 26 32 26 33 '.
                           '26 33 26 25 28 25 33 26 25 33 25 32 24 25 36 32 '.
                           '15 32 24 27 37 32 23 16 10 5 1 35 30 12 33 26 19 '.
                           '27 25 25 14 27 26 28 25 32 24 23 12 20 30 21 28 '.
                           '34 29 10 23 27 27 18 26 28 19 25 35 32 18 4 27 26 '.
                           '28 23 12 24 13 32 28 8 25 33 28 9',
        'display_id'    => 'SRR014849.203935',
        'desc'          => 'EIXKN4201B4HU6 length=144',
        'count'         => 3
                                },
);

for my $example (sort keys %example_files) {
    my $file = test_input_file('fastq', "$example.fastq");
    my $variant = $example_files{$example}->{variant};
    my $in = Bio::SeqIO->new(-format    => "fastq-$variant",
                             -file      => $file,
                             -verbose   => 2);  #strictest level
    my $ct = 0;
    my $sample_seq;
    eval {
        while (my $seq = $in->next_seq) {
            $ct++;
            $sample_seq = $seq; # always grab the last seq
        }
    };
    ok(!$@, "$example parses");
    is($ct, $example_files{$example}->{count}, "correct num. seqs in $example");
    ok(defined($sample_seq), 'sample sequence obtained');
    if ($sample_seq) {
        isa_ok($sample_seq, 'Bio::Seq::Quality');
        for my $method (qw(seq desc display_id)) {
            is($sample_seq->$method,
               $example_files{$example}->{$method},
               "$method() matches $example");
        }
        is(join(' ', map {sprintf("%.0f", $_)} @{$sample_seq->qual}),
                $example_files{$example}->{qual},
                "qual() matches $example");
        my $truncated = $sample_seq->trunc(1,10);
        is(scalar(@{$truncated->meta}), $truncated->length);
    }
}

# test round-trip and conversions (single file of each type)

my @variants = qw(sanger illumina solexa);

my %conversion = (  # check conversions, particularly solexa
    sanger_93            => {
        'variant'       => 'sanger',
        'to_solexa'     => {
          '-seq' => 'ACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGAN',
          '-qual' => [ (map {62} 0..31),(reverse(1..61)),1 ],
          '-raw_quality' => '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJHGFECB@>;;',
          '-id' => 'Test',
          '-desc' => 'PHRED qualities from 93 to 0 inclusive',
          '-descriptor' => 'Test PHRED qualities from 93 to 0 inclusive'
        },
        'to_illumina'   => {
          '-seq' => 'ACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGAN',
          '-qual' => [ (map {62} 0..31),(reverse(0..61)) ],
          '-raw_quality' => '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@',
          '-id' => 'Test',
          '-desc' => 'PHRED qualities from 93 to 0 inclusive',
          '-descriptor' => 'Test PHRED qualities from 93 to 0 inclusive'
        },
        'to_sanger'     => {
          '-seq' => 'ACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGAN',
          '-qual' => [reverse(0..93)],
          '-raw_quality' => '~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)(\'&%$#"!',
          '-id' => 'Test',
          '-desc' => 'PHRED qualities from 93 to 0 inclusive',
          '-descriptor' => 'Test PHRED qualities from 93 to 0 inclusive'
        },
    },
    solexa_faked            => {
            'variant'       => 'solexa',
        'to_solexa'     => {'-seq' => 'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN',
          '-qual' => [qw(40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 10 9 8 7 6 5 5 4 4 3 3 2 2 1 1)],
          '-raw_quality' => 'hgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;',
          '-id' => 'slxa_0001_1_0001_01',
          '-desc' => '',
          '-descriptor' => 'slxa_0001_1_0001_01'
        },
        'to_illumina'   => {
          '-seq' => 'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN',
          '-qual' => [qw(40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 10 9 8 7 6 5 5 4 4 3 3 2 2 1 1)],
          '-namespace' => 'solexa',
          '-raw_quality' => 'hgfedcba`_^]\\[ZYXWVUTSRQPONMLKJJIHGFEEDDCCBBAA',
          '-id' => 'slxa_0001_1_0001_01',
          '-desc' => '',
          '-descriptor' => 'slxa_0001_1_0001_01'
        },
        'to_sanger'     => {
          '-seq' => 'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN',
          '-qual' => [qw(40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 10 9 8 7 6 5 5 4 4 3 3 2 2 1 1)],
          '-namespace' => 'solexa',
          '-raw_quality' => 'IHGFEDCBA@?>=<;:9876543210/.-,++*)(\'&&%%$$##""',
          '-id' => 'slxa_0001_1_0001_01',
          '-desc' => '',
          '-descriptor' => 'slxa_0001_1_0001_01'
        },
    },
    illumina_faked          => {
        'variant'       => 'illumina',
        'to_solexa'     => {
          '-seq' => 'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN',
          '-qual' => [reverse(1..40), 1],  # round trip from solexa is lossy
          '-namespace' => 'illumina',
          '-raw_quality' => 'hgfedcba`_^]\[ZYXWVUTSRQPONMLKJHGFECB@>;;',
          '-id' => 'Test',
          '-desc' => 'PHRED qualities from 40 to 0 inclusive',
          '-descriptor' => 'Test PHRED qualities from 40 to 0 inclusive'
        },
        'to_illumina'   => {
          '-seq' => 'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN',
          '-qual' => [reverse(0..40)],
          '-raw_quality' => 'hgfedcba`_^]\\[ZYXWVUTSRQPONMLKJIHGFEDCBA@',
          '-id' => 'Test',
          '-desc' => 'PHRED qualities from 40 to 0 inclusive',
          '-descriptor' => 'Test PHRED qualities from 40 to 0 inclusive'
        },
        'to_sanger'     => {
          '-seq' => 'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN',
          '-qual' => [reverse(0..40)],
          '-raw_quality' => 'IHGFEDCBA@?>=<;:9876543210/.-,+*)(\'&%$#"!',
          '-id' => 'Test',
          '-desc' => 'PHRED qualities from 40 to 0 inclusive',
          '-descriptor' => 'Test PHRED qualities from 40 to 0 inclusive'
        }
    },
);

for my $example (sort keys %conversion) {
    my $file = test_input_file('fastq', "$example.fastq");
    my $variant = $conversion{$example}->{variant};
    my $in = Bio::SeqIO->new(-format    => "fastq-$variant",
                             -file      => $file,
                             -verbose   => 2);  #strictest level
    # this both tests the next_dataset method and helps check roundtripping
    my $seq = $in->next_seq;
    for my $newvar (@variants) {
        next unless exists $conversion{$example}->{"to_$newvar"};
        my $outfile = test_output_file();
        Bio::SeqIO->new(-format   => "fastq-$newvar",
                        -file     => ">$outfile",
                        -verbose  => -1)->write_seq($seq);
        my $newdata = Bio::SeqIO->new(-format => "fastq-$newvar",
                                    -file     => $outfile)->next_dataset;
        # round for simple comparison, get around floating pt comparison probs

        if ($newvar eq 'solexa') {
            $newdata->{-qual} = [map {sprintf("%.0f",$_)} @{$newdata->{-qual}}];
        }

        #print Dumper($newdata) if $variant eq 'sanger' && $newvar eq 'illumina';

        $conversion{$example}->{"to_$newvar"}->{'-namespace'} = $newvar;
        is_deeply($newdata, $conversion{$example}->{"to_$newvar"}, "Conversion from $variant to $newvar");
    }
}

# test fastq exception handling

my %error = (
    # file name
    error_diff_ids          => {
        variant         => 'sanger',
        exception       => qr/doesn't\smatch\sseq\sdescriptor/xms,
                                },
    error_long_qual         => {
        variant         => 'sanger',
        exception       => qr/doesn't\smatch\slength\sof\ssequence/xms,
                                },
    error_no_qual           => {
        variant         => 'sanger',
        exception       => qr/Missing\ssequence\sand\/or\squality\sdata/xms,
                                },
    error_qual_del          => {
        variant         => 'sanger',
        exception       => qr/Unknown\ssymbol\swith\sASCII\svalue/xms,
                                },
    error_qual_escape       => {
        variant         => 'sanger',
        exception       => qr/Unknown\ssymbol\swith\sASCII\svalue/xms,
                                },
    error_qual_null         => {
        variant         => 'sanger',
        exception       => qr/Unknown\ssymbol\swith\sASCII\svalue/xms,
                                },
    error_qual_space        => {
        variant         => 'sanger',
        exception       => qr/Unknown\ssymbol\swith\sASCII\svalue/xms,
                                },
    error_qual_tab          => {
        variant         => 'sanger',
        exception       => qr/Unknown\ssymbol\swith\sASCII\svalue/xms,
                                },
    error_qual_unit_sep     => {
        variant         => 'sanger',
        exception       => qr/Unknown\ssymbol\swith\sASCII\svalue/xms,
                                },
    error_qual_vtab         => {
        variant         => 'sanger',
        exception       => qr/Unknown\ssymbol\swith\sASCII\svalue/xms,
                                },
    error_short_qual        => {
        variant         => 'sanger',
        exception       => qr/doesn't\smatch\slength\sof\ssequence/,
                                },
    error_spaces            => {
        variant         => 'sanger',
        exception       => qr/Unknown\ssymbol\swith\sASCII\svalue/xms,
                                },
    error_tabs              => {
        variant         => 'sanger',
        exception       => qr/Unknown\ssymbol\swith\sASCII\svalue/xms,
                                },
    error_trunc_at_plus     => {
        variant         => 'sanger',
        exception       => qr/Missing\ssequence\sand\/or\squality\sdata/xms,
                                },
    error_trunc_at_qual     => {
        variant         => 'sanger',
        exception       => qr/Missing\ssequence\sand\/or\squality\sdata/xms,
                                },
    error_trunc_at_seq      => {
        variant         => 'sanger',
        exception       => qr/Missing\ssequence\sand\/or\squality\sdata/xms,
                                },
    error_trunc_in_title    => {
        variant         => 'sanger',
        exception       => qr/Missing\ssequence\sand\/or\squality\sdata/xms,
                                },
    error_trunc_in_seq      => {
        variant         => 'sanger',
        exception       => qr/Missing\ssequence\sand\/or\squality\sdata/xms,
                                },
    error_trunc_in_plus     => {
        variant         => 'sanger',
        exception       => qr/doesn't\smatch\sseq\s descriptor/xms,
                                },
    error_trunc_in_qual     => {
        variant         => 'sanger',
        exception       => qr/doesn't\smatch\slength\sof\ssequence/xms,
                                },
);

for my $example (sort keys %error) {
    my $file = test_input_file('fastq', "$example.fastq");
    my $variant = $error{$example}->{variant};
    my $in = Bio::SeqIO->new(-format    => "fastq-$variant",
                             -file      => $file,
                             -verbose   => 2);  #strictest level
    my $ct = 0;
    throws_ok {        while (my $seq = $in->next_seq) {
            $ct++;
        } } $error{$example}->{exception}, "Exception caught for $example";
}

# fastq

my $in = Bio::SeqIO->new(-format    => 'fastq',
                         -file      => test_input_file('fastq', 'zero_qual.fastq'),
                         -verbose   => 2);  # strictest level

lives_and {my $seq = $in->next_seq;
           is($seq->seq, 'G');} 'edge case; single 0 in quality fails';



BioPerl-1.007002/t/SeqIO/flybase_chadoxml.t000444000766000024       241413155576321 20431 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests               => 8,
			   -requires_module     => 'XML::Writer',
			   -requires_networking => 0,
			  );
	
	use_ok('Bio::SeqIO::flybase_chadoxml');
}

my $verbose = test_debug();

TODO: {
	my $format = 'flybase_chadoxml';
	todo_skip "No tests for $format format -- no sample file to test against", 7, if 1;

	my $seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test.$format"),
							        -format => $format);
	
	isa_ok($seqio_obj, 'Bio::SeqIO');
	
	my @methods = qw(next_seq write_seq);
	foreach my $method (@methods) {
		can_ok($seqio_obj, $method) || 
			diag "$method method not implemented for $format";	
	}
	
	# checking the first sequence object
	my $seq_obj = $seqio_obj->next_seq();
	isa_ok($seq_obj, 'Bio::Seq');
	my %expected = ('seq'         => '' .
					'length'      => '',
					'primary_id'  => '',
					'description' => qr(),
				   );
	is   ($seq_obj->seq(),         $expected{'seq'},         'sequence');
	is   ($seq_obj->length(),      $expected{'length'},      'length');
	is   ($seq_obj->primary_id(),  $expected{'primary_id'},  'primary_id');
	like ($seq_obj->description(), $expected{'description'}, 'description');
}BioPerl-1.007002/t/SeqIO/game.t000444000766000024       363213155576321 16041 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 24,
		   -requires_modules => [qw(XML::Parser::PerlSAX XML::Writer)]);
    use_ok('Bio::SeqIO::game');
}

my $verbose = test_debug() || -1;
my $str = Bio::SeqIO->new('-file'=> test_input_file('test.game'), 
			  '-format' => 'game',
			  '-verbose' => $verbose);
isa_ok ($str, 'Bio::SeqIO');
my $seq = $str->next_seq();
isa_ok($seq, 'Bio::Seq::RichSeq');

# exercise game parsing
$str = Bio::SeqIO->new(
    -format =>'game',
    -file => test_input_file('test.game')
		      );
$seq = $str->next_seq;
ok(defined $seq);
ok(defined $seq->seq);
is($seq->alphabet, 'dna');
is($seq->display_id, 'L16622');
is($seq->length, 28735);
is($seq->species->binomial, 'Caenorhabditis elegans');
my @feats = $seq->get_SeqFeatures;
is(scalar(@feats), 7);
my $source = grep { $_->primary_tag eq 'source' } @feats;
ok($source);
my @genes = grep { $_->primary_tag eq 'gene' } @feats;
is(scalar(@genes), 3);
ok($genes[0]->has_tag('gene'));
my $gname;
if ( $genes[0]->has_tag('gene') ) {
    ($gname) = $genes[0]->get_tag_values('gene');
}
is($gname, 'C02D5.3');
is($genes[0]->strand, 1);
my $cds   = grep { $_->primary_tag eq 'CDS' } @feats;
is($cds, 3);

# make sure we can read what we write
# test XML-writing
my $testfile = test_output_file();
# map argument is require to write a  element
my $out = Bio::SeqIO->new(-format => 'game', -file => ">$testfile", -map => 1);
$out->write_seq($seq);
$out->close();

$str = Bio::SeqIO->new(-format =>'game', -file => $testfile);
$seq = $str->next_seq;
ok(defined $seq);
ok(defined $seq->seq);
is($seq->alphabet, 'dna');
is($seq->display_id, 'L16622');
is($seq->length, 28735);
is($seq->species->binomial, 'Caenorhabditis elegans');

my $genes = grep { $_->primary_tag eq 'gene' } @feats;
$cds   = grep { $_->primary_tag eq 'CDS' } @feats;
is($genes, 3);
is($cds, 3);
BioPerl-1.007002/t/SeqIO/gbxml.t000444000766000024       337713155576321 16247 0ustar00cjfieldsstaff000000000000use strict;

BEGIN {
   use lib '.';
   use Bio::Root::Test;
   
   test_begin(-tests => 14,
              -requires_modules => [ qw(XML::SAX) ]
              );
   
   use_ok('Bio::SeqIO::gbxml');
}

my $verbose = test_debug();

my $in = Bio::SeqIO->new(-format  => 'gbxml',
                          -verbose => $verbose,
                          # This class can't parse dbEST data yet...
                          # -file    => test_input_file('roa1.gbxml'));
                          # So let's try a  file:
                          -file    => test_input_file('EG352462.gbxml'));
isa_ok($in, 'Bio::SeqIO');
my $seq = $in->next_seq();
is($seq->molecule,   'mRNA',                                            'molecule');
is($seq->alphabet,   'dna',                                             'alphabet');
is($seq->primary_id,  116038450,                                        'primary_id');
is($seq->display_id, 'EG352462',                                        'display_id');
is($seq->version,     1,                                                'version');
is($seq->is_circular, 0,                                                'is_circular');

is(substr($seq->description, 0, 10), 'SAAH-aad23',                      'description');
is(substr($seq->seq,         0, 10), 'aataaaatta',                      'sequence');

my @class = $seq->species->classification;
is($class[$#class],'Eukaryota',                                         'classification');

my ($feat) = $seq->get_SeqFeatures;
is_deeply([ $feat->get_tag_values('clone_lib') ], [ 'Agen 0058' ],      'feat - clone_lib');
is_deeply([ $feat->get_tag_values('db_xref') ],   [ 'taxon:79327' ],    'feat - db_xref');
is_deeply([ $feat->get_tag_values('lab_host') ],  [ 'DH10B cells' ],    'feat - lab_host');



BioPerl-1.007002/t/SeqIO/gcg.t000444000766000024       715213155576321 15671 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests               => 17,
			   -requires_modules    => [],
			   -requires_networking => 0,
			  );
	
	use_ok('Bio::SeqIO::gcg');
}

my $verbose = test_debug();

my $format = 'gcg';
my $seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test.$format"),
						        -format => $format);

isa_ok($seqio_obj, 'Bio::SeqIO');

my @methods = qw(next_seq write_seq);
foreach my $method (@methods) {
	can_ok($seqio_obj, $method) || 
		diag "$method method not implemented for $format";	
}

# checking the first sequence object
my $seq_obj = $seqio_obj->next_seq();
isa_ok($seq_obj, 'Bio::Seq');
isa_ok($seq_obj, 'Bio::Seq::RichSeq');
my %expected = ('seq'         => 'MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGL' .
						   		 'DYRTTDENLKAHEKWGNIVDVVVMKDPRTKRSRGFGFI' .
								 'TYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPN' .
								 'AGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDNIVI' .
								 'DKETGKKRGFAFVEFDDYDPVDKVVLQKQHQLNGKMVD' .
								 'VKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGN' .
								 'QNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGY' .
								 'GGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGY' .
								 'QQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGN' .
								 'YGNNQGFNNGGNNRRY',
				'length'      => '358',
				'primary_id'  => 'roa1_drome',
				'description' => qr(Rea guano receptor type III),
			   );
is   ($seq_obj->seq(),         $expected{'seq'},         'sequence');
is   ($seq_obj->length(),      $expected{'length'},      'length');
TODO: {
	local $TODO = 'possible bug: RichSeq not setting primary_id?';
	is   ($seq_obj->primary_id(),  $expected{'primary_id'},  'primary_id');
}
like ($seq_obj->description(), $expected{'description'}, 'description');

# test DOS linefeeds in gcg parser
my $str = Bio::SeqIO->new(-file => test_input_file('test_badlf.gcg'),
								  -verbose => $verbose,
								  -format => 'GCG');
ok($str);
my $seq = $str->next_seq();
isa_ok ($seq, 'Bio::SeqI');
is(length($seq->seq), $seq->length);
print "Sequence 1 of 1 from GCG stream:\n", $seq->seq, "\n" if( $verbose);



# from testformats.pl
SKIP: {
    test_skip(-tests => 4, -requires_modules => [qw(Algorithm::Diff
                                                    IO::ScalarArray
                                                    IO::String)]);
    use_ok('Algorithm::Diff');
    eval "use Algorithm::Diff qw(diff LCS);";
    use_ok('IO::ScalarArray');
    use_ok('IO::String');
    
    my ($file, $type) = ("test.$format", $format);
    my $filename = test_input_file($file);
    print "processing file $filename\n" if $verbose;
    open my $FILE, '<', $filename or die "Could not read file '$filename': $!\n";
    my @datain = <$FILE>;
    close $FILE;

    my $in = new IO::String(join('', @datain));
    my $seqin = new Bio::SeqIO( -fh => $in,
                -format => $type);
    my $out = new IO::String;
    my $seqout = new Bio::SeqIO( -fh => $out,
                 -format => $type);
    my $seq;
    while( defined($seq = $seqin->next_seq) ) {	
    $seqout->write_seq($seq);
    }
    $seqout->close();
    $seqin->close();
    my $strref = $out->string_ref;
    my @dataout = map { $_."\n"} split(/\n/, $$strref );
    my @diffs = &diff( \@datain, \@dataout);
    is(@diffs, 0, "$format format can round-trip");
    
    if(@diffs && $verbose) {
        foreach my $d ( @diffs ) {
            foreach my $diff ( @$d ) {
                chomp($diff->[2]);
                print $diff->[0], $diff->[1], "\n>", $diff->[2], "\n";
            }
        }
        print "in is \n", join('', @datain), "\n";
        print "out is \n", join('',@dataout), "\n";	
    }

}
BioPerl-1.007002/t/SeqIO/genbank.t000444000766000024      6276113155576321 16565 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    test_begin(-tests => 301);
    use_ok('Bio::SeqIO::genbank');
}

my $verbose = test_debug;

my $ast = Bio::SeqIO->new(-format  => 'genbank' ,
                          -verbose => $verbose,
                          -file    => test_input_file('roa1.genbank'));
isa_ok($ast, 'Bio::SeqIO');
$ast->verbose($verbose);
my $as = $ast->next_seq;
is $as->molecule, 'mRNA',$as->accession_number;
is $as->alphabet, 'dna';
is $as->division, 'EST';
is join(',',$as->get_dates), '27-OCT-1998';
is($as->primary_id, 3598416);
my @class = $as->species->classification;
is $class[$#class],'Eukaryota';

$ast = Bio::SeqIO->new(-format  => 'genbank',
                       -verbose => $verbose,
                       -file    => test_input_file('NT_021877.gbk'));
$ast->verbose($verbose);
$as = $ast->next_seq;
is $as->molecule, 'DNA',$as->accession_number;
is $as->alphabet, 'dna';
is $as->division, 'CON';
is join(',',$as->get_dates), '17-OCT-2003';
is($as->primary_id, 37539616);
is($as->accession_number, 'NT_021877');

my ($cds) = grep { $_->primary_tag eq 'CDS' } $as->get_SeqFeatures;
is(($cds->get_tag_values('transl_except'))[1],
   '(pos:complement(4224..4226),aa:OTHER)');

# test for a DBSOURCE line
$ast = Bio::SeqIO->new(-format  => 'genbank',
                       -verbose => $verbose,
                       -file    => test_input_file('BAB68554.gb'));
$ast->verbose($verbose);
$as = $ast->next_seq;
is $as->molecule, 'PRT',$as->accession_number;
is $as->alphabet, 'protein';
is $as->division, 'VRT';
is join(',',$as->get_dates), '11-APR-2002';
# Though older GenBank releases indicate SOURCE contains only the common name,
# this is no longer true.  In general, this line will contain an abbreviated
# form of the full organism name (but may contain the full length name),
# as well as the optional common name and organelle.  There is no get/set
# for the abbreviated name but it is accessible via name()
ok defined($as->species->name('abbreviated')->[0]);
is $as->species->name('abbreviated')->[0], 'Aldabra giant tortoise';
is($as->primary_id, 15824047);
my $ac = $as->annotation;
ok defined $ac;
my @dblinks = $ac->get_Annotations('dblink');
is(scalar @dblinks,1);
is($dblinks[0]->database, 'GenBank');
is($dblinks[0]->primary_id, 'AB072353');
is($dblinks[0]->version, '1');
is($dblinks[0]->display_text, 'GenBank:AB072353.1','operator overloading in AnnotationI is deprecated');

# test for multi-line SOURCE
$ast = Bio::SeqIO->new(-format  => 'genbank',
                       -verbose => $verbose,
                       -file    => test_input_file('NC_006346.gb'));
$as = $ast->next_seq;
is $as->species->binomial('FULL'), 'Bolitoglossa n. sp. RLM-2004',$as->accession_number;;
@class = $as->species->classification;
is($class[$#class],'Eukaryota');
is($as->species->common_name,'mushroomtongue salamander');

$ast = Bio::SeqIO->new(-format  => 'genbank',
                       -verbose => $verbose,
                       -file    => test_input_file('U71225.gb'));
$as = $ast->next_seq;
@class = $as->species->classification;
is($class[$#class],'Eukaryota',$as->accession_number);
is $as->species->common_name,'black-bellied salamander';

# test for unusual common name
$ast = Bio::SeqIO->new(-format  => 'genbank',
                       -verbose => $verbose,
                       -file    => test_input_file('AB077698.gb'));
$as = $ast->next_seq;
# again, this is not a common name but is in name('abbreviated')
ok defined($as->species->name('abbreviated')->[0]),$as->accession_number;
is $as->species->name('abbreviated')->[0],'Homo sapiens cDNA to mRNA';

# test for common name with parentheses
$ast = Bio::SeqIO->new(-format  => 'genbank',
                       -verbose => $verbose,
                       -file    => test_input_file('DQ018368.gb'));
$as = $ast->next_seq;
is $as->species->scientific_name,'(Populus tomentosa x P. bolleana) x P. tomentosa var. truncata',
$as->accession_number;;

# test secondary accessions
my $seqio = Bio::SeqIO->new(-format  => 'genbank',
                            -verbose => $verbose,
                            -file    => test_input_file('D10483.gbk'));
my $seq = $seqio->next_seq;
my @kw =  $seq->get_keywords;
is(scalar @kw, 118, $seq->accession_number);
is($kw[-1], 'yabO');
my @sec_acc = $seq->get_secondary_accessions;
is(scalar @sec_acc,14);
is($sec_acc[-1], 'X56742');

# bug #1487
my $str = Bio::SeqIO->new(-verbose => $verbose,
                          -file    => test_input_file('D12555.gbk'));
eval {
    $seq = $str->next_seq;
};

ok(! $@, 'bug 1487');

# bug 1647 rpt_unit sub-feature with multiple parens
$str = Bio::SeqIO->new(-format  => 'genbank',
                       -verbose => $verbose,
                       -file    => test_input_file('mini-AE001405.gb'));
ok($seq = $str->next_seq);
my @rpts = grep { $_->primary_tag eq 'repeat_region' }
  $seq->get_SeqFeatures;
is $#rpts, 2, 'bug 1647';
my @rpt_units = grep {$_->has_tag('rpt_unit')} @rpts;
is $#rpt_units, 0;
is(($rpt_units[0]->get_tag_values('rpt_unit'))[0],'(TG)10;A;(TG)7');

# test bug #1673 , RDB-II genbank files
$str = Bio::SeqIO->new(-format  => 'genbank',
                       -verbose => $verbose,
                       -file    => test_input_file('Mcjanrna_rdbII.gbk')
              );
ok($seq = $str->next_seq, 'bug 1673');
my @refs = $seq->annotation->get_Annotations('reference');
is(@refs, 1);
is($seq->display_id,'Mc.janrrnA');
is($seq->molecule ,'RNA');
is $as->division, 'PLN';
is join(',',$as->get_dates), '23-MAY-2005';

$str  = Bio::SeqIO->new(-format  => 'genbank',
                        -file    => test_input_file('AF165282.gb'),
                        -verbose => $verbose);
$seq = $str->next_seq;
my @features = $seq->all_SeqFeatures;
is(@features, 5, $seq->accession_number);
is($features[0]->start, 1);
is($features[0]->end, 226);
my $location = $features[1]->location;
ok($location->isa('Bio::Location::SplitLocationI'));
my @sublocs = $location->sub_Location;
is(@sublocs, 29);

# version and primary ID - believe it or not, this wasn't working
is ($seq->version, 1);
is ($seq->seq_version, 1);
is ($seq->primary_id, "5734104");

# streaming and Bio::RichSeq creation
my $stream = Bio::SeqIO->new(-file    => test_input_file('test.genbank'),
                             -verbose => $verbose,
                             -format  => 'genbank');
$stream->verbose($verbose);
my $seqnum = 0;
my $species;
my @cl;
my $lasts;
my @ids = qw(DDU63596 DDU63595 HUMBDNF);
my @tids = (44689, 44689, 9606);
my @tnames = ("Dictyostelium discoideum",
              "Dictyostelium discoideum",
              "Homo sapiens");
while($seq = $stream->next_seq) {
    if($seqnum < 3) {
        is $seq->display_id, $ids[$seqnum];
        $species = $seq->species;
        @cl = $species->classification;
        is( $species->binomial, $tnames[$seqnum],
            'species parsing incorrect for genbank');
        is( $cl[3] ne $species->genus, 1,
            'genus duplicated in genbank parsing');
        is( $species->ncbi_taxid, $tids[$seqnum] );
    }
    $seqnum++;
    $lasts = $seq;
}
is($seqnum, 5,'streaming');
is $lasts->display_id, "HUMBETGLOA";
my ($ref) = $lasts->annotation->get_Annotations('reference');
is($ref->medline, 94173918);
$stream->close;

$stream = Bio::SeqIO->new(-file    => test_input_file('test.genbank.noseq'),
                          -verbose => $verbose,
                          -format  => 'genbank' );
$seqnum = 0;
while($seq = $stream->next_seq) {
    if($seqnum < 3) {
        is $seq->display_id, $ids[$seqnum];
    }
    elsif( $seq->display_id eq 'M37762') {
        is( ($seq->get_keywords)[0], 'neurotrophic factor');
    }
    $seqnum++;
}
is $seqnum, 5, "Total number of sequences in test file";

# fuzzy
$seq = Bio::SeqIO->new( -file    => test_input_file('testfuzzy.genbank'),
                        -format  => 'genbank',
                        -verbose => $verbose );
ok(defined($as = $seq->next_seq));

@features = $as->all_SeqFeatures;
is(@features,21,'Fuzzy in');
my $lastfeature = pop @features;
# this is a split location; the root doesn't have strand
is($lastfeature->strand, undef);
$location = $lastfeature->location;
#$location->verbose(-1); # silence the warning of undef seq_id()
# see above; splitlocs roots do not have a strand really
is($location->strand, undef);
is($location->start, 83202);
is($location->end, 84996);

@sublocs = $location->sub_Location;

is(@sublocs, 2);
my $loc = shift @sublocs;
is($loc->start, 83202);
is($loc->end, 83329);
is($loc->strand, -1);

$loc = shift @sublocs;
is($loc->start, 84248);
is($loc->end, 84996);
is($loc->strand,1);

$seq = Bio::SeqIO->new(-format  => 'genbank',
                       -verbose => $verbose,
                       -file    => ">" .test_output_file);
$seq->verbose($verbose);
ok($seq->write_seq($as),'Fuzzy out');

## now genbank ##
$str = Bio::SeqIO->new(-format  => 'genbank',
                       -verbose => $verbose,
                       -file    => test_input_file('BK000016-tpa.gbk'));
$seq = $str->next_seq;
ok(defined $seq, $seq->accession_number);
ok(defined $seq->seq);
is($seq->accession_number, 'BK000016',$seq->accession_number);
is($seq->alphabet, 'dna');
is($seq->display_id, 'BK000016');
is($seq->length, 1162);
is($seq->division, 'ROD');
is($seq->get_dates, 1);
is($seq->keywords, 'Third Party Annotation; TPA');
is($seq->desc, 'TPA: Mus musculus pantothenate kinase 4 mRNA, partial cds.');
is($seq->seq_version, 1);
is($seq->feature_count, 2);
my $spec_obj = $seq->species;
is ($spec_obj->common_name, 'house mouse');
is ($spec_obj->species, 'musculus');
is ($spec_obj->genus, 'Mus');
is ($spec_obj->binomial, 'Mus musculus');
$ac = $seq->annotation;
my $reference =  ($ac->get_Annotations('reference') )[0];
is ($reference->pubmed, '11479594');
is ($reference->medline, '21372465',$seq->accession_number);

# validate that what is written is what is read
my $testfile = test_output_file;
my $out = Bio::SeqIO->new(-file   => ">$testfile",
                          -format => 'genbank');
$out->write_seq($seq);
$out->close;

$str = Bio::SeqIO->new(-format => 'genbank',
                       -file   => $testfile);
$seq = $str->next_seq;
ok(defined $seq,'roundtrip');
ok(defined $seq->seq);
is($seq->accession_number, 'BK000016');
is($seq->alphabet, 'dna');
is($seq->display_id, 'BK000016');
is($seq->length, 1162);
is($seq->division, 'ROD');
is($seq->get_dates, 1);
is($seq->keywords, 'Third Party Annotation; TPA');
is($seq->desc, 'TPA: Mus musculus pantothenate kinase 4 mRNA, partial cds.');
is($seq->seq_version, 1);
is($seq->feature_count, 2);
$spec_obj = $seq->species;
is ($spec_obj->common_name, 'house mouse');
is ($spec_obj->species, 'musculus');
is ($spec_obj->genus, 'Mus');
is ($spec_obj->binomial, 'Mus musculus');
$ac = $seq->annotation;
$reference =  ($ac->get_Annotations('reference') )[0];
is ($reference->pubmed, '11479594');
is ($reference->medline, '21372465');

# write revcomp split location
my $gb = Bio::SeqIO->new(-format => 'genbank',
                         # This sequence has an odd LOCUS line which sets off a warning, setting
                         # verbose to -1.
                         # The newest Ensembl seq lacks this.  Maybe update?  cjfields 6-5-07
                         -verbose => $verbose ? $verbose : -1,
                         -file   => test_input_file('revcomp_mrna.gb'));
$seq = $gb->next_seq;

$gb = Bio::SeqIO->new(-format => 'genbank',
                      -file   => ">$testfile");

$gb->write_seq($seq);
undef $gb;
ok(! -z $testfile, 'revcomp split location');

# bug 1925, continuation of long ORGANISM line ends up in @classification:
# ORGANISM  Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC
#           9150
#           Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
#           Enterobacteriaceae; Salmonella.
$gb = Bio::SeqIO->new(-format  => 'genbank',
                      -verbose => $verbose,
                      -file    => test_input_file('NC_006511-short.gbk'));
$seq = $gb->next_seq;
is $seq->species->common_name, undef, "Bug 1925";
is $seq->species->scientific_name, "Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150";
@class = $seq->species->classification;
is $class[$#class], "Bacteria";

# WGS   tests
$gb = Bio::SeqIO->new(-format  => 'genbank',
                      -verbose => $verbose,
                      -file    => test_input_file('O_sat.wgs'));
$seq = $gb->next_seq;

my @tests = ('wgs'        => 'AAAA02000001-AAAA02050231',
             'wgs_scafld' => 'CM000126-CM000137',
             'wgs_scafld' => 'CH398081-CH401163');

my @wgs = map {$seq->annotation->get_Annotations(lc($_))} qw(WGS WGS_SCAFLD);

my $ct=0;

for my $wgs (@wgs) {
    my ($tagname, $value) = (shift @tests, shift @tests);
    is($wgs->tagname, $tagname, $tagname);
    is($wgs->value, $value);
    $ct++;
}

is ($ct, 3);

# make sure we can retrieve a feature with a primary tag of 'misc_difference'
$gb = Bio::SeqIO->new(-format  => 'genbank',
                      -verbose => $verbose,
                      -file    => test_input_file('BC000007.gbk'));
$seq = $gb->next_seq;
($cds) = grep { $_->primary_tag eq 'misc_difference' } $seq->get_SeqFeatures;
my @vals = $cds->get_tag_values('gene');
is $vals[0], 'PX19', $seq->accession_number;

# Check that the source,organism section is identical between input and output.
# - test an easy one where organism is species, then two different formats of
# subspecies, then a species with a format that used to be mistaken for
# subspecies, then a bacteria with no genus, and finally a virus with a genus.

# These tests are now somewhat out-of-date since we are moving to a Bio::Taxon-
# based system for verifying taxonomic information.  Right now they just verify
# changes so are really useless; I will change them to verify common name,
# organelle, scientific name, etc.

my $outfile = test_output_file;

# output always adds a period (GenBank std), but two of these files do not use them.

foreach my $in ('BK000016-tpa.gbk', 'ay116458.gb', 'ay149291.gb', 'NC_006346.gb', 'ay007676.gb', 'dq519393.gb') {
    my $infile =  test_input_file($in);

    $str = Bio::SeqIO->new(-format  => 'genbank',
                           -verbose => $verbose,
                           -file    => $infile);
    $seq = $str->next_seq;

    $out = Bio::SeqIO->new(-file   => ">$outfile",
                           -format => 'genbank');
    $out->write_seq($seq);
    $out->close;

    open my $IN, '<', $infile or die "Could not read file '$infile': $!\n";
    my @in = <$IN>;
    close $IN;

    open my $RESULT, '<', $outfile or die "Could not read file '$outfile': $!\n";
    my $line = 0;
    my $check = 0;
    my $is = 1;

  FILECHECK:
    while (my $result = <$RESULT>) {
        if ($result =~ /^KEYWORDS/) {
            $check = 1;
            next;
        }

        if ($result =~ /^REFERENCE/) {
            last FILECHECK;
        }

        if ($check) {
            # end periods don't count (not all input files have them)
            $result =~ s{\.$}{};
            $in[$line] =~ s{\.$}{};

            if ($result ne $in[$line]) {
                $is = 0;
                last;
            }
        }
    }
    continue {
        $line++;
    }
    close $RESULT;

    ok $is, $in;
}

# NB: there should probably be full testing on all lines to ensure that output
# matches input.

# 20061117: problem with *double* colon in some annotation-dblink values
$ct = 0;

foreach my $in ('P35527.gb') {
    my $infile =  test_input_file($in);
    $str = Bio::SeqIO->new(-format  => 'genbank',
                           -verbose => $verbose,
                           -file    => $infile);
    $seq = $str->next_seq;

    my $ac = $seq->annotation;      # Bio::AnnotationCollection
    foreach my $key ($ac->get_all_annotation_keys ) {
        my @values = $ac->get_Annotations($key);
        foreach my $ann (@values) {
            my $value = $ann->display_text;
            $ct++;
            if ($key eq 'dblink') {
                ok (index($value,'::') < 0);   # this should never be true
                ok ($value, $value);           # check value is not empty

                #  print "  ann/", sprintf('%12s  ',$key), '>>>', $value , '<<<', "\n";
                #  print "        index double colon: ",index($value   ,'::'), "\n";

                #  check db name:
                my @parts = split(/:/,$value);
                if ( $parts[0] =~ /^(?:
                        #  not an exhaustive list of databases;
                        #  just the db's referenced in P35527.gb:
                          swissprot | GenBank | GenPept      | HSSP | IntAct   | Ensembl | KEGG
                        | HGNC      | MIM     | ArrayExpress | GO   | InterPro | Pfam    | PRINTS
                        | PROSITE    )$/x
                ) {
                    ok 1;
                }
                else {
                    ok 0;
                }
                    ok ( $parts[1], "$parts[0]" );
            }
        }
    }
}

is($ct, 46);

# bug 2195

$str = Bio::SeqIO->new(-format  => 'genbank',
                       -verbose => $verbose,
                       -file    => test_input_file('AF305198.gb')
                     );

$species = $str->next_seq->species;

is($species->scientific_name, 'Virginia creeper phytoplasma', 'Bug 2195');
is(join(', ',$species->classification),
     'Virginia creeper phytoplasma, 16SrV (Elm yellows group), '
   . 'Candidatus Phytoplasma, Acholeplasmataceae, Acholeplasmatales, '
   . 'Mollicutes, Firmicutes, Bacteria',
   'Bug 2195');

# bug 2569, PROJECT line support, read and write, round-tripping

$str = Bio::SeqIO->new(-format  => 'genbank',
                       -verbose => $verbose,
                       -file    => test_input_file('NC_008536.gb'));
$seq = $str->next_seq;

my $project = ($seq->annotation->get_Annotations('project'))[0];
isa_ok($project, 'Bio::Annotation::SimpleValue');

if ($project) {
    is($project->value, 'GenomeProject:12638');
}
else {
    ok(0, "PROJECT not parsed");
}

$outfile = test_output_file;
$gb = Bio::SeqIO->new(-format  => 'genbank',
                      -verbose => $verbose,
                      -file    => ">$outfile");
$gb->write_seq($seq);

$str = Bio::SeqIO->new(-format  => 'genbank',
                       -verbose => $verbose,
                       -file    => $outfile);
$seq = $str->next_seq;

$project = ($seq->annotation->get_Annotations('project'))[0];
isa_ok($project, 'Bio::Annotation::SimpleValue');

if ($project) {
    is($project->value, 'GenomeProject:12638');
}
else {
    ok(0, "Roundtrip test failed");
}

# test for swissprot/UniProt/UniProtKB DBSOURCE line (Bug : RT 44536)
$ast = Bio::SeqIO->new(-format  => 'genbank',
                       -verbose => $verbose,
                       -file    => test_input_file('P39765.gb'));
$as = $ast->next_seq;
is $as->molecule, 'PRT',$as->accession_number;
is $as->division, 'BCT',$as->accession_number;
is join(',',$as->get_dates), '03-MAR-2009',$as->accession_number;
is $as->alphabet, 'protein';
# Though older GenBank releases indicate SOURCE contains only the common name,
# this is no longer true.  In general, this line will contain an abbreviated
# form of the full organism name (but may contain the full length name),
# as well as the optional common name and organelle.  There is no get/set
# for the abbreviated name but it is accessible via name()
ok defined($as->species->name('abbreviated')->[0]);
is $as->species->name('abbreviated')->[0], 'Bacillus subtilis';
is($as->primary_id, 20141743);
$ac = $as->annotation;
ok defined $ac;
@dblinks = $ac->get_Annotations('dblink');
is(scalar @dblinks,31);
is($dblinks[0]->database, 'UniProtKB');
is($dblinks[0]->primary_id, 'PYRR_BACSU');
is($dblinks[0]->version, undef);
is($dblinks[0]->display_text, 'UniProtKB:PYRR_BACSU','operator overloading in AnnotationI is deprecated');

#bug 2982 embl/genbank contig handling

$ast = Bio::SeqIO->new( -file   => test_input_file('bug2982.gb'),
                        -format => 'genbank' );
$seq = $ast->next_seq;

ok my @ctg = $seq->annotation->get_Annotations('contig');
like $ctg[0]->value, qr/join\(.*?gap.*?complement/;

# write_seq() and FTHelper duplicate specific tags, need to check a round-trip
$ast = Bio::SeqIO->new(-format  => 'genbank' ,
                       -verbose => $verbose,
                       -file    => test_input_file('singlescore.gbk'));
$as = $ast->next_seq;
($cds) = grep { $_->primary_tag eq 'CDS' } $as->get_SeqFeatures;
my @notes = $cds->get_tag_values('note');
is(scalar @notes, 2);
$testfile = test_output_file;
$out = Bio::SeqIO->new(-file   => ">$testfile",
                       -format => 'genbank');
$out->write_seq($as);
$out->close;
$ast = Bio::SeqIO->new(-format  => 'genbank' ,
                       -verbose => $verbose,
                       -file    => $testfile );
$as = $ast->next_seq;
($cds) = grep { $_->primary_tag eq 'CDS' } $as->get_SeqFeatures;
@notes = $cds->get_tag_values('note');
is(scalar @notes, 2);


#bug 3375
my $in = Bio::SeqIO->new(-format => 'genbank',
                         -file   => test_input_file('NC_002058_multDBLINK_bug3375.gb'));
$seq = $in->next_seq;     # should not throw a warning now
@dblinks = $seq->annotation->get_Annotations('dblink');    # contains 5 dblink references
# testing DBLINK      BioProject: PRJNA15288
is($dblinks[0]->database, 'BioProject', 'bug3375 database is BioProject');
is($dblinks[0]->primary_id, 'PRJNA15288', 'bug3375 primary_id is PRJNA15288');
# testing DBLINK      Project:100,200,300
is($dblinks[3]->database, 'Project');
is($dblinks[3]->primary_id, '300');
# testing DBLINK      NC_002058.3
is($dblinks[4]->database, 'GenBank');
is($dblinks[4]->primary_id, 'NC_002058');
is($dblinks[4]->version, '3');

# long labels handled
{
    # Create sequence with feature with a long label qualifier
    my $seq=Bio::Seq->new(-seq => 'actg',
                          -id  => 'abacab');
    my $feature=Bio::SeqFeature::Generic->new(-primary=>'CDS', -start=>1, -end=>4);
    my $label='1 2 3 4 5 6 7 8 9 a b c d e f g h i j k l m n o p q r';
    $feature->add_tag_value(label => $label);
    $seq->add_SeqFeature($feature);

    # Write genbank
    my $string;
    open my $str_fh, '>', \$string or skip("Could not write string, skipping", 2);
    my $out = Bio::SeqIO->new(-format => 'genbank',
                              -fh     => $str_fh);
    $out->write_seq($seq);

    # Read genbank
    my $in = Bio::SeqIO->new(-format => 'genbank',
                             -string => $string);
    my $genbank = $in->next_seq;
    my ($read_feature) = $genbank->get_SeqFeatures;
    my ($read_label) = $read_feature->get_tag_values('label');
    is($read_label, $label, 'Label is the same');
}

# bug 3448
$in = Bio::SeqIO->new(-format  => 'genbank',
                      -file    => test_input_file('YP_007988852.gp'),
                      -verbose => $verbose);
$seq = $in->next_seq;     # should not throw a warning now
is($seq->length, 205);

my @anns = $seq->annotation->get_Annotations('contig');
is(@anns, 1);
isa_ok($anns[0], 'Bio::Annotation::SimpleValue');
is($anns[0]->value, 'join(WP_015639704.1:1..205)');

is($seq->seq, 'MENRKFGYIRVSSKDQNEGRQLEAMRKIGITERDIYLDKQSGKNFERANYQLLKRIIRKGDI'
            . 'LYIHSLDRFGRNKEEILQEWNDLTKNIEADIVVLDMPLLDTTQYKDSMGTFIADLVLQILSWMAEEERERIRK'
            . 'RQREGIDLALQNGIQFGRSPVVVSDEFKEVYRKWKAKELTAVEAMQEAGVKKTSFYKLVKAHENSIKVNS');

# Genbank files with CONTIG and sequence should print the sequence with write_seq()
$testfile = test_output_file;
$out = Bio::SeqIO->new(-file   => ">$testfile",
                       -format => 'genbank');
$out->write_seq($seq);
$out->close;

$in = Bio::SeqIO->new(-file    => $testfile,
                      -format  => 'genbank',
                      -verbose => $verbose);
$seq = $in->next_seq;
is($seq->length, 205);

@anns = $seq->annotation->get_Annotations('contig');
is(@anns, 1);
isa_ok($anns[0], 'Bio::Annotation::SimpleValue');
is($anns[0]->value, 'join(WP_015639704.1:1..205)');

is($seq->seq, 'MENRKFGYIRVSSKDQNEGRQLEAMRKIGITERDIYLDKQSGKNFERANYQLLKRIIRKGDI'
            . 'LYIHSLDRFGRNKEEILQEWNDLTKNIEADIVVLDMPLLDTTQYKDSMGTFIADLVLQILSWMAEEERERIRK'
            . 'RQREGIDLALQNGIQFGRSPVVVSDEFKEVYRKWKAKELTAVEAMQEAGVKKTSFYKLVKAHENSIKVNS');

$seq = Bio::SeqIO->new(-format => 'genbank',
                       -file   => test_input_file('YP_007988852.gp') )->next_seq;
@features = $seq->remove_SeqFeatures;
is $#features, 10, 'Got 11 features';

$seq = Bio::SeqIO->new(-format => 'genbank',
                       -file   => test_input_file('YP_007988852.gp') )->next_seq;
@features = $seq->remove_SeqFeatures('CDS');
is $#features, 0, 'Got 1 feature';
is $features[0]->primary_tag, 'CDS', 'Correct primary tag for feature';
@features = $seq->remove_SeqFeatures;
is $#features, 9, 'Got 10 features';

# Handle Structured Comments in COMMENT section
$seq = Bio::SeqIO->new(-format => 'genbank',
                       -file   => test_input_file('KF527485.gbk') )->next_seq;
my $comment = ($seq->get_Annotations('comment') )[0];
is($comment->as_text, "Comment: 
##Assembly-Data-START##
Assembly Method :: Lasergene v. 10
Sequencing Technology :: ABI37XL; Sanger dideoxy sequencing
##Assembly-Data-END##",
"Got correct Structured Comment");

$seq = Bio::SeqIO->new(-format => 'genbank',
                       -file   => test_input_file('HM138502.gbk') )->next_seq;
$comment = ($seq->get_Annotations('comment') )[0];
ok( $comment->as_text
        =~ /^Comment: Swine influenza A \(H1N1\) virus isolated during human swine flu outbreak of 2009/,
    "Got correct Structured Comment"
);
ok( $comment->as_text =~ /^##GISAID_EpiFlu\(TM\)Data-START##/m,
    "Got correct Structured Comment" );
ok( $comment->as_text =~ /^Subtype :: H1N1/m,
    "Got correct Structured Comment"
);
ok( $comment->as_text =~ /^##GISAID_EpiFlu\(TM\)Data-END##/m,
    "Got correct Structured Comment" );
BioPerl-1.007002/t/SeqIO/interpro.t000444000766000024       441413155576321 16771 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
  use lib '.';
  use Bio::Root::Test;
  
  test_begin(-tests => 20,
             -requires_module => 'XML::DOM::XPath');
  
  use_ok('Bio::SeqIO::interpro');
}

my $verbose = test_debug();

my $t_file = test_input_file('test.interpro');
my $a_in = Bio::SeqIO->new( -file    => $t_file,
                            -verbose => $verbose,
                            -format  => 'interpro');
isa_ok($a_in, 'Bio::SeqIO');

my $seq = $a_in->next_seq();
ok($seq, 'seq obj is defined');
isa_ok($seq, 'Bio::Seq::RichSeq');
is(scalar( $seq->get_SeqFeatures() ), 6, 'right number of SeqFeatures');

my($feat) = $seq->get_SeqFeatures();
isa_ok($feat,'Bio::SeqFeature::Generic');

is($feat->display_name,'Retinoblastoma-associated protein, B-box', 'display_name()');

ok($seq = $a_in->next_seq(), 'seq object is defined');
is(scalar( $seq->get_SeqFeatures() ),40, 'right number of SeqFeatures');

ok(!($seq = $a_in->next_seq()), 'there is no next_seq (correctly)');

# Bug 1908 (enhancement)
$t_file = test_input_file('interpro_ebi.xml');
my $b_in = Bio::SeqIO->new( -file    => $t_file,
                            -verbose => $verbose,
                            -format  => 'interpro');
$seq = $b_in->next_seq();
ok($seq, 'bug 1908');

my @features = $seq->get_SeqFeatures;
is(scalar @features, 2, 'right number of SeqFeatures');
is($features[0]->primary_tag, 'region', 'primary_tag()');
is($features[0]->display_name, 'Protein of unknown function DUF1021', 'display_name()');
is($features[0]->location->end, 78, 'location->end()');

my @dblinks = $features[0]->annotation->get_Annotations('dblink');
is(scalar @dblinks, 3, 'right number of dblinks');
is($dblinks[1]->primary_id, 'IPR009366', 'first primary_id');
is($dblinks[2]->primary_id, 'PF06257.1', 'second primary_id');

my $other_t_file = test_input_file('test.interpro-go.xml');
my $ipr_in = Bio::SeqIO->new( -file    => $other_t_file,
                              -verbose => $verbose,
                              -format  => 'interpro');

$seq = $ipr_in->next_seq();
@features = $seq->get_SeqFeatures;
@dblinks = $features[0]->annotation->get_Annotations('dblink');
is(scalar @dblinks, 4, 'right number of dblinks');
is($dblinks[3]->primary_id, 'GO:0003677', 'primary_id via dblinks');
BioPerl-1.007002/t/SeqIO/kegg.t000444000766000024       710713155576321 16046 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 16);
	
	use_ok('Bio::SeqIO::kegg');
}

my $verbose = test_debug();

my $io = Bio::SeqIO->new(-format => 'kegg',
								 -verbose => $verbose,
								 -file => test_input_file('AHCYL1.kegg'));
isa_ok($io, 'Bio::SeqIO');
my $kegg = $io->next_seq();
ok($kegg);
isa_ok($kegg, 'Bio::Seq::RichSeq');
is($kegg->accession, '10768');
is($kegg->display_id, 'AHCYL1');
is($kegg->alphabet, 'dna');
is($kegg->seq,'atgtcgatgcctgacgcgatgccgctgcccggggtcggggaggagctgaagcaggccaaggagatcgaggacgccgagaagtactccttcatggccaccgtcaccaaggcgcccaagaagcaaatccagtttgctgatgacatgcaggagttcaccaaattccccaccaaaactggccgaagatctttgtctcgctcgatctcacagtcctccactgacagctacagttcagctgcatcctacacagatagctctgatgatgaggtttctccccgagagaagcagcaaaccaactccaagggcagcagcaatttctgtgtgaagaacatcaagcaggcagaatttggacgccgggagattgagattgcagagcaagacatgtctgctctgatttcactcaggaaacgtgctcagggggagaagcccttggctggtgctaaaatagtgggctgtacacacatcacagcccagacagcggtgttgattgagacactctgtgccctgggggctcagtgccgctggtctgcttgtaacatctactcaactcagaatgaagtagctgcagcactggctgaggctggagttgcagtgttcgcttggaagggcgagtcagaagatgacttctggtggtgtattgaccgctgtgtgaacatggatgggtggcaggccaacatgatcctggatgatgggggagacttaacccactgggtttataagaagtatccaaacgtgtttaagaagatccgaggcattgtggaagagagcgtgactggtgttcacaggctgtatcagctctccaaagctgggaagctctgtgttccggccatgaacgtcaatgattctgttaccaaacagaagtttgataacttgtactgctgccgagaatccattttggatggcctgaagaggaccacagatgtgatgtttggtgggaaacaagtggtggtgtgtggctatggtgaggtaggcaagggctgctgtgctgctctcaaagctcttggagcaattgtctacattaccgaaatcgaccccatctgtgctctgcaggcctgcatggatgggttcagggtggtaaagctaaatgaagtcatccggcaagtcgatgtcgtaataacttgcacaggaaataagaatgtagtgacacgggagcacttggatcgcatgaaaaacagttgtatcgtatgcaatatgggccactccaacacagaaatcgatgtgaccagcctccgcactccggagctgacgtgggagcgagtacgttctcaggtggaccatgtcatctggccagatggcaaacgagttgtcctcctggcagagggtcgtctactcaatttgagctgctccacagttcccacctttgttctgtccatcacagccacaacacaggctttggcactgatagaactctataatgcacccgaggggcgatacaagcaggatgtgtacttgcttcctaagaaaatggatgaatacgttgccagcttgcatctgccatcatttgatgcccaccttacagagctgacagatgaccaagcaaaatatctgggactcaacaaaaatgggccattcaaacctaattattacagatactaa');
ok($kegg->translate->seq);

is(($kegg->annotation->get_Annotations('description'))[0]->text,
   'S-adenosylhomocysteine hydrolase-like 1 [EC:3.3.1.1]');

is(($kegg->annotation->get_Annotations('pathway'))[0]->text,
   'Metabolism; Amino Acid Metabolism; Methionine metabolism');

is( (grep {$_->database eq 'KO'}
     $kegg->annotation->get_Annotations('dblink'))[0]->comment, 
    'adenosylhomocysteinase' );

is( (grep {$_->database eq 'PATH'} 
     $kegg->annotation->get_Annotations('dblink'))[0]->primary_id,
    'hsa00271' );

is( ($kegg->annotation->get_Annotations('aa_seq'))[0]->text,
'MSMPDAMPLPGVGEELKQAKEIEDAEKYSFMATVTKAPKKQIQFADDMQEFTKFPTKTGRRSLSRSISQSSTDSYSSAASYTDSSDDEVSPREKQQTNSKGSSNFCVKNIKQAEFGRREIEIAEQDMSALISLRKRAQGEKPLAGAKIVGCTHITAQTAVLIETLCALGAQCRWSACNIYSTQNEVAAALAEAGVAVFAWKGESEDDFWWCIDRCVNMDGWQANMILDDGGDLTHWVYKKYPNVFKKIRGIVEESVTGVHRLYQLSKAGKLCVPAMNVNDSVTKQKFDNLYCCRESILDGLKRTTDVMFGGKQVVVCGYGEVGKGCCAALKALGAIVYITEIDPICALQACMDGFRVVKLNEVIRQVDVVITCTGNKNVVTREHLDRMKNSCIVCNMGHSNTEIDVTSLRTPELTWERVRSQVDHVIWPDGKRVVLLAEGRLLNLSCSTVPTFVLSITATTQALALIELYNAPEGRYKQDVYLLPKKMDEYVASLHLPSFDAHLTELTDDQAKYLGLNKNGPFKPNYYRY');

is( ($kegg->annotation->get_Annotations('position'))[0]->text, '1:join(26813..26932,50794..50905,52974..53117,54122..54222,54657..
            54759,56523..56617,57185..57291,58104..58220,58427..58490,59255..
            59343,59706..59776,60133..60227,60312..60410,60811..60879,61308..
            61386,62491..62611,63434..63440)');

is($kegg->species->common_name , 'H.sapiens');BioPerl-1.007002/t/SeqIO/largefasta.t000444000766000024       251513155576321 17240 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 16);

    use_ok('Bio::SeqIO::largefasta');
}

my $tmpfile = test_output_file();

my $seqio = Bio::SeqIO->new('-format' => 'largefasta',
                            '-file'   => test_input_file('genomic-seq.fasta'),
                            );
isa_ok($seqio, 'Bio::SeqIO');

my $pseq = $seqio->next_seq();
$pseq->alphabet('dna');
$pseq->desc('this is my description');;
my $plength = $pseq->length();
my $last_3 = $pseq->subseq($plength-3,$plength);

is defined $pseq, 1;
is $plength > 0, 1;
is length($pseq->subseq(100, 299)), 200; 
is $pseq->trunc(100,199)->length(), 100; 
is $pseq->alphabet(), 'dna';
is $pseq->display_id(), 'HSBA536C5';
is $pseq->accession_number(), 'unknown';
is $pseq->desc, 'this is my description';

is open(OUT, '>', $tmpfile), 1;

my $seqout = Bio::SeqIO->new('-format' => 'largefasta',
                             '-fh'     => \*OUT );
is defined $seqout, 1;

is $seqout->write_seq($pseq), 1;
$seqout->close();
close(OUT);
my $seqin = Bio::SeqIO->new('-format' => 'largefasta',
                            '-file'   => $tmpfile);
my $pseq2 = $seqin->next_seq;
is ($plength, $pseq2->length());
is ($pseq->display_id(), $pseq2->display_id());
is ($pseq->desc(), $pseq2->desc());
BioPerl-1.007002/t/SeqIO/lasergene.t000444000766000024       154713155576321 17100 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 13);
	
	use_ok('Bio::SeqIO::lasergene');
}

my $verbose = test_debug();

#
# Positive tests
#

my $io = Bio::SeqIO->new(
  -format => 'lasergene',
  -verbose => $verbose,
  -file => test_input_file('test.lasergene')
);

ok($io);
isa_ok($io, 'Bio::SeqIO');

my $seq;

ok($seq = $io->next_seq);
is($seq->length, 12*3);
is($seq->subseq(1,12), 'ATCGATCGATCG');

ok($seq = $io->next_seq);
is($seq->length, 200);

ok($seq = $io->next_seq);
is($seq->length, 70*5+12);

ok(not defined $io->next_seq);

#
# Negative tests
#

$io = Bio::SeqIO->new(
  -format => 'lasergene',
  -verbose => $verbose,
  -file => test_input_file('test.fasta') # not lasergene!
);

ok($io);

eval { 
  $io->next_seq;
};
like($@, qr/unexpected end of file/i);
BioPerl-1.007002/t/SeqIO/locuslink.t000444000766000024       510313155576321 17126 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 26,
               -requires_module => 'Graph::Directed');
	
	use_ok('Bio::SeqIO::locuslink');
	use_ok('Bio::SeqFeature::Generic');
	use_ok('Bio::SeqFeature::AnnotationAdaptor');
}

my $seqin = Bio::SeqIO->new(-file => test_input_file('test.locuslink'),
			    -format => 'locuslink');
ok $seqin;
isa_ok($seqin, 'Bio::SeqIO');
my $seqout = Bio::SeqIO->new(-file => ">".test_output_file(),
			     -format => 'embl');

# process and write to output
my @seqs = ();

while(my $seq = $seqin->next_seq()) {
    push(@seqs, $seq);
    
    # create an artificial feature to stick the annotation on
    my $fea = Bio::SeqFeature::Generic->new(-start => 1, -end => 9999,
					    -strand => 1,
					    -primary => 'annotation');
    my $ac = Bio::SeqFeature::AnnotationAdaptor->new(-feature => $fea);
    foreach my $k ($seq->annotation->get_all_annotation_keys()) {
	foreach my $ann ($seq->annotation->get_Annotations($k)) {
	    next unless $ann->isa("Bio::Annotation::SimpleValue");
	    $ac->add_Annotation($ann);
	}
    }
    $seq->add_SeqFeature($fea);
    $seqout->write_seq($seq);
}

is (scalar(@seqs), 2);

is ($seqs[0]->desc,
    "amiloride binding protein 1 (amine oxidase (copper-containing))");
is ($seqs[0]->accession, "26");
is ($seqs[0]->display_id, "ABP1");
is ($seqs[0]->species->binomial, "Homo sapiens");


my @dblinks = $seqs[0]->annotation->get_Annotations('dblink');
my %counts = map { ($_->database(),0) } @dblinks;
foreach (@dblinks) { $counts{$_->database()}++; }

is ($counts{GenBank}, 11);
is ($counts{RefSeq}, 4);
is ($counts{UniGene}, 1);
is ($counts{Pfam}, 1);
is ($counts{STS}, 2);
is ($counts{MIM}, 1);
is ($counts{PUBMED}, 6);
is (scalar(@dblinks), 27);

is ($seqs[1]->desc, "v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)");
is ($seqs[1]->display_id, "ABL2");

my $ac = $seqs[1]->annotation;
my @keys = $ac->get_all_annotation_keys();
is (scalar(@keys), 19);

my ($cmt) = $ac->get_Annotations('comment');
is (length($cmt->text), 403);

my @isoforms = qw(a b);
foreach ($ac->get_Annotations('PRODUCT')) {
    is ($_->value,
	"v-abl Abelson murine leukemia viral oncogene homolog 2 isoform ".
	shift(@isoforms));
}

my @goann = ();
foreach my $k (@keys) {
    foreach my $ann ($ac->get_Annotations($k)) {
	next unless $ann->isa("Bio::Ontology::TermI");
	push(@goann, $ann);
    }
}
is (scalar(@goann), 4);
@goann = sort { $a->as_text() cmp $b->as_text() } @goann;
is ($goann[2]->as_text, "cellular component|cytoplasm|");
BioPerl-1.007002/t/SeqIO/mbsout.t000444000766000024      3653313155576321 16467 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
use version;
our $API_VERSION = qv('1.1.3');

use strict;
use File::Path qw(mkpath rmtree);
use Carp;

BEGIN {
    use lib '.';    # for core package test scripts only
    use Bio::Root::Test;

    test_begin(
        -tests               => 74,
        -requires_modules    => [q(Bio::SeqIO::mbsout)],
        -requires_networking => 0
    );

    use_ok('Bio::SeqIO::mbsout');
}

# skip tests if the msout.pm module is too old.
cmp_ok( $Bio::SeqIO::mbsout::API_VERSION,
    '>=', qv('1.1.3'), "Bio::SeqIO::mbsout is at least api version 1.1.3" );

create_dir("mbsout");
test_file_1( 0, "mbsout/mbsout_infile1" );
test_file_2( 0, "mbsout/mbsout_infile2" );
test_file_3( 0, "mbsout/mbsout_infile3" );

sub create_dir {

    my $dir = shift;

    $dir = test_input_file($dir);

    unless ( -d $dir ) {
        mkpath($dir);
    }
}

sub test_file_1 {
##############################################################################
## Test file 1
##############################################################################

    my $gzip   = shift;
    my $infile = shift;
    $infile = test_input_file($infile);

    #print_file1( $infile, $gzip );

    my $file_sequence = $infile;
    if ($gzip) {
        $file_sequence = "gunzip -c <$file_sequence |";
    }
    my $mbsout = Bio::SeqIO->new(
        -file   => "$file_sequence",
        -format => 'mbsout',
    );

    isa_ok( $mbsout, 'Bio::SeqIO::mbsout' );

    my $rh_base_conversion_table = $mbsout->get_base_conversion_table;

    isa_ok( $mbsout, 'Bio::SeqIO::mbsout' );

    my %attributes = (
        RUNS     => 3,
        SEGSITES => 7,
        MBS_INFO_LINE =>
          'command:        mbs 6 -t 0.001 -r 0.00025 -s 5000 2500 -f 3 1 traj ',
        TOT_RUN_HAPS      => 6,
        NEXT_RUN_NUM      => 1,
        LAST_READ_HAP_NUM => 0,
        POSITIONS => [qw(79.1001 80.1001 81.101 82.101 83.10001 84.801 85)],
        CURRENT_RUN_SEGSITES      => 7,
        POP_MUT_PARAM_PER_SITE    => 0.001,
        POP_RECOMB_PARAM_PER_SITE => 0.00025,
        NSITES                    => 5000,
        SELPOS                    => 2500,
        NFILES                    => 3,
        NREPS                     => 1,
        TRAJ_FILENAME             => 'traj'
    );

    foreach my $attribute ( keys %attributes ) {
        my $func = lc($attribute);

        if ( $attribute =~ m/POPS|SEEDS|POSITIONS/ ) {
            $func = ucfirst($func);
        }

        $func = 'get_' . $func;
        my @returns = $mbsout->$func();
        my ( $return, $got );

        # If there were more than one return value, then compare references to
        # arrays instead of scalars
        unless ( @returns > 1 ) {
            $got = shift @returns;
        }
        else { $got = \@returns }

        my $expected = $attributes{$attribute};

        if ( defined $got && defined $expected ) {
            is_deeply( $got, $expected, "Get $attribute" );
        }
        else { is_deeply( $got, $expected, "Get $attribute" ) }
    }

    # Testing next_hap at beginning of run
    my @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $mbsout->get_next_seq );
    my @data_expected = qw(1111111);
    is_deeply( \@data_got, \@data_expected,
        "Get next_hap at beginning of run" );

    # Testing next_hap after beginning of run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $mbsout->get_next_seq );
    @data_expected = qw(5555555);
    is_deeply( \@data_got, \@data_expected,
        "Get next_hap after beginning of run" );

    # Testing next_pop after beginning of pop
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $mbsout->get_next_seq );
    @data_expected = qw(4444444);
    is_deeply( \@data_got, \@data_expected,
        "Get next_pop after beginning of pop" );

    # Testing next_hap
    @data_got      = $mbsout->get_next_hap;
    @data_expected = qw(4444444);
    is_deeply( \@data_got, \@data_expected, "Get next_hap" );

    # Testing next_hap
    @data_got      = $mbsout->get_next_hap;
    @data_expected = qw(5555555);
    is_deeply( \@data_got, \@data_expected, "Get next_hap" );

    # Testing next_run after beginning of run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $mbsout->get_next_run );
    @data_expected = qw(4444444);
    is_deeply( \@data_got, \@data_expected,
        "Get next_run after beginning of run" );

    # Testing next_run at beginning of run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $mbsout->get_next_run );
    @data_expected = qw(5555555 5555555 5555555 1010101 1111111 1515151);
    is_deeply( \@data_got, \@data_expected,
        "Get next_run at beginning of run" );

    # Testing next_run at beginning of run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $mbsout->get_next_run );
    @data_expected = qw(
      1414141
      1414141
      1515151
      1414141
      1515151
      1515151);
    is_deeply( \@data_got, \@data_expected,
        "Get next_run at beginning of run" );

    is( $mbsout->get_next_run_num, undef, 'have all lines been read?' );
}

sub test_file_2 {
##############################################################################
## Test file 2
##############################################################################

    my $gzip   = shift;
    my $infile = shift;
    $infile = test_input_file($infile);

    #print_file2( $infile, $gzip );

    my $file_sequence = $infile;
    if ($gzip) {
        $file_sequence = "gunzip -c <$file_sequence |";
    }

    my $mbsout = Bio::SeqIO->new(
        -file   => "$file_sequence",
        -format => 'mbsout',
    );

    isa_ok( $mbsout, 'Bio::SeqIO::mbsout' );

    my %attributes = (
        RUNS     => 5,
        SEGSITES => 7,
        MBS_INFO_LINE =>
          'command:        mbs 6 -t 0.001 -r 0.00025 -s 5000 2500 -f 5 1 traj ',
        TOT_RUN_HAPS      => 6,
        NEXT_RUN_NUM      => 1,
        LAST_READ_HAP_NUM => 0,
        POSITIONS => [qw(79.1001 80.1001 81.101 82.101 83.10001 84.801 85)],
        CURRENT_RUN_SEGSITES      => 7,
        POP_MUT_PARAM_PER_SITE    => 0.001,
        POP_RECOMB_PARAM_PER_SITE => 0.00025,
        NSITES                    => 5000,
        SELPOS                    => 2500,
        NFILES                    => 5,
        NREPS                     => 1,
        TRAJ_FILENAME             => 'traj'
    );

    foreach my $attribute ( keys %attributes ) {
        my $func = lc($attribute);
        if ( $attribute =~ m/POSITIONS/ ) {
            $func = ucfirst($func);
        }
        elsif ( $attribute =~ m/\_file/ ) {
            $func = q(infile);
        }

        $func = 'get_' . $func;
        my @returns = $mbsout->$func();
        my ( $return, $got );

        # If there were more than one return value, then compare references to
        # arrays instead of scalars
        unless ( @returns > 1 ) {
            $got = shift @returns;
        }
        else { $got = \@returns }

        my $expected = $attributes{$attribute};

        if ( defined $got && defined $expected ) {
            is_deeply( $got, $expected, "Get $attribute" );
        }
        else { is_deeply( $got, $expected, "Get $attribute" ) }
    }

    my $rh_base_conversion_table = $mbsout->get_base_conversion_table;

    # Testing next_hap at beginning of run
    my @data_got      = $mbsout->get_next_hap;
    my @data_expected = qw(1111111);
    is_deeply( \@data_got, \@data_expected,
        "Get next_hap at beginning of run" );

    # Testing next_hap after beginning of run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $mbsout->get_next_seq );
    @data_expected = '5555555';
    is_deeply( \@data_got, \@data_expected,
        "Get next_hap after beginning of run" );

    # Surprise test! testing mbsout::outgroup
    my $outgroup = $mbsout->outgroup;
    is( $outgroup, 0, "Testing mbsout::outgroup" );

    # Testing next_run after beginning of run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $mbsout->get_next_run );
    @data_expected = qw(
      4444444
      4444444
      5555555
      4444444);
    is_deeply( \@data_got, \@data_expected,
        "Get next_run after beginning of run" );

    # Testing next_run after beginning of run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $mbsout->get_next_run );
    @data_expected = qw(
      5555555
      5555555
      5555555
      1010101
      1111111
      1515151);
    is_deeply( \@data_got, \@data_expected,
        "Get next_run after beginning of run" );

    # Testing next_run at beginning of run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $mbsout->get_next_run );
    @data_expected = qw(
      1414141
      1414141
      1515151
      1414141
      1515151
      1515151);
    is_deeply( \@data_got, \@data_expected,
        "Get next_run at beginning of run" );

    # Testing next_hap at beginning of run 2
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $mbsout->get_next_seq );
    @data_expected = '1515151';
    is_deeply( \@data_got, \@data_expected,
        "Get next_hap at beginning of run 2" );

    # Testing next_run after hap
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $mbsout->get_next_run );
    @data_expected = qw(
      5050505
      5151515
      5555555
      5454545
      5454545);
    is_deeply( \@data_got, \@data_expected, "Get next_run after hap" );

    is( $mbsout->get_next_run_num, 5, 'next run should be 5.' );

}

sub test_file_3 {
##############################################################################
## Test file 3
##############################################################################

    my $gzip   = shift;
    my $infile = shift;
    $infile = test_input_file($infile);

    #print_file3( $infile, $gzip );

    my $file_sequence = $infile;
    if ($gzip) {
        $file_sequence = "gunzip -c <$file_sequence |";
    }
    my $mbsout = Bio::SeqIO->new(
        -file   => "$file_sequence",
        -format => 'mbsout',
    );

    isa_ok( $mbsout, 'Bio::SeqIO::mbsout' );

    my $rh_base_conversion_table = $mbsout->get_base_conversion_table;

    my %attributes = (
        RUNS     => 1,
        SEGSITES => 7,
        MBS_INFO_LINE =>
          'command:        mbs 3 -t 0.001 -r 0.00025 -s 5000 2500 -f 1 1 traj ',
        TOT_RUN_HAPS      => 3,
        NEXT_RUN_NUM      => 1,
        LAST_READ_HAP_NUM => 0,
        POSITIONS => [qw(79.1001 80.1001 81.101 82.101 83.10001 84.801 85)],
        CURRENT_RUN_SEGSITES      => 7,
        POP_MUT_PARAM_PER_SITE    => 0.001,
        POP_RECOMB_PARAM_PER_SITE => 0.00025,
        NSITES                    => 5000,
        SELPOS                    => 2500,
        NFILES                    => 1,
        NREPS                     => 1,
        TRAJ_FILENAME             => 'traj'
    );

    foreach my $attribute ( keys %attributes ) {
        my $func = lc($attribute);

        if ( $attribute =~ m/POPS|SEEDS|POSITIONS/ ) {
            $func = ucfirst($func);
        }

        $func = 'get_' . $func;
        my @returns = $mbsout->$func();
        my ( $return, $got );

        # If there were more than one return value, then compare references to
        # arrays instead of scalars
        unless ( @returns > 1 ) {
            $got = shift @returns;
        }
        else { $got = \@returns }

        my $expected = $attributes{$attribute};

        if ( defined $got && defined $expected ) {
            is_deeply( $got, $expected, "Get $attribute" );
        }
        else { is_deeply( $got, $expected, "Get $attribute" ) }
    }

    # Testing next_run at beginning of run
    my @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $mbsout->get_next_run );
    my @data_expected = qw(1111111 5555555 4444444);
    is_deeply( \@data_got, \@data_expected,
        "Get next_run at end/beginning of run" );

    is( $mbsout->get_next_run_num, undef, 'have all lines been read?' );

    # Testing what happens when we read from empty stream
    @data_got      = $mbsout->get_next_run;
    @data_expected = ();
    is_deeply( \@data_got, \@data_expected, "Get next_run at eof" );

    # Testing what happens when we read from empty stream
    @data_got      = $mbsout->get_next_hap;
    @data_expected = undef;
    is_deeply( \@data_got, \@data_expected, "Get next_hap at eof" );

    # Testing what happens when we read from empty stream
    @data_got      = $mbsout->get_next_seq;
    @data_expected = ();
    is_deeply( \@data_got, \@data_expected, "Get next_seq at eof" );

}

sub print_file1 {

    my $destination = shift;
    my $gzip        = shift;

    my $out = <$destination" or croak "Could not write file '$destination': $!\n";

    print $OUT $out;
    close $OUT;
}

sub print_file2 {

    my $destination = shift;
    my $gzip        = shift;

    my $out = <$destination" or croak "Could not write file '$destination': $!\n";

    print $OUT $out;
    close $OUT;
}

sub print_file3 {

    my $destination = shift;
    my $gzip        = shift;

    my $out = <$destination" or croak "Could not write file '$destination': $!\n";

    print $OUT $out;
    close $OUT;
}

sub print_to_file {
    my ( $ra_in, $out ) = @_;
    open my $OUT, '>', $out or croak "\nCould not write outfile '$out': $!\n";
    print $OUT ("@$ra_in");
    close $OUT;
}

sub convert_bases_to_nums {
    my ( $rh_base_conversion_table, @seqs ) = @_;

    my @out_seqstrings;
    foreach my $seq (@seqs) {
        my $seqstring = $seq->seq;
        foreach my $base ( keys %{$rh_base_conversion_table} ) {
            $seqstring =~ s/($base)/$rh_base_conversion_table->{$base}/g;
        }
        push @out_seqstrings, $seqstring;
    }
    return @out_seqstrings;
}
BioPerl-1.007002/t/SeqIO/metafasta.t000444000766000024        77713155576321 17064 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 6);
	
	use_ok('Bio::SeqIO::metafasta');
}

my $verbose = test_debug();

my $io = Bio::SeqIO->new(-format => 'metafasta',
								 -verbose => $verbose,
								 -file => test_input_file('test.metafasta'));

isa_ok($io, 'Bio::SeqIO');
ok(my $seq = $io->next_seq);
isa_ok($seq, 'Bio::Seq::Meta');
is($seq->seq, "ABCDEFHIJKLMNOPQRSTUVWXYZ");
is($seq->display_id,'test');
BioPerl-1.007002/t/SeqIO/msout.t000444000766000024      5074513155576321 16326 0ustar00cjfieldsstaff000000000000#!/usr/bin/perl
use version;
our $API_VERSION = $Bio::SeqIO::msout::API_VERSION;
use strict;
use File::Path qw(mkpath rmtree);

BEGIN {
    use lib '.';    # for core package test scripts only
    use Bio::Root::Test;

    test_begin(
        -tests               => 165,
        -requires_modules    => [q(Bio::SeqIO::msout)],
        -requires_networking => 0
    );

    use_ok('Bio::SeqIO::msout');

}

# skip tests if the msout.pm module is too old.
my $api_version = $Bio::SeqIO::msout::API_VERSION;
cmp_ok( $api_version, '>=', qv('1.1.5'),
    "Bio::SeqIO::msout is at least api version 1.1.5" );

test_file_1( 0, "msout/msout_infile1" );    # 23 tests
test_file_2( 0, "msout/msout_infile2" );    # 22 tests
test_file_3( 0, "msout/msout_infile3" );    # 17 tests

# tests to run for api versions >= 1.1.6
SKIP: {
    skip q($Bio::SeqIO::msout::API_VERSION < 1.1.6), 22
      unless $api_version >= qv('1.1.6');
    test_file_1( 0, q(msout/msout_infile4) );
}

# tests to run for api versions >= 1.1.7
SKIP: {
    skip q($Bio::SeqIO::msout::API_VERSION < 1.1.7), 4
      unless $api_version >= qv('1.1.7');
    bad_test_file_1( 0, q(msout/bad_msout_infile1) ); # 2 tests
    bad_test_file_2( 0, q(msout/bad_msout_infile2) ); # 2 tests
}

# tests to run for api version >= 1.1.8
SKIP: {
    skip q($Bio::SeqIO::msout::API_VERSION < 1.1.8), 75
      unless $api_version >= qv('1.1.8');

    test_file_1( 0, "msout/msout_infile1", 100 );
    test_file_2( 0, "msout/msout_infile2", 10 );
    test_file_1( 0, q(msout/msout_infile4), 100 );
    bad_test_file_1( 0, q(msout/bad_msout_infile1), 1000 );
    bad_test_file_2( 0, q(msout/bad_msout_infile2), 1000 );
    bad_n_sites( 0, q(msout/msout_infile1) ); # 2 tests
}

sub create_dir {

    my $dir = shift;

    $dir = Bio::Root::Test::test_input_file($dir);

    unless ( -d $dir ) {
        mkpath($dir);
    }
}

sub remove_dir {

    my $dir = shift;

    $dir = Bio::Root::Test::test_input_file($dir);

    if ( -d $dir ) {
        rmtree($dir);
    }
    else { warn "Tried to remove $dir, but it does not exist" }
}

sub test_file_1 {
##############################################################################
## Test file 1
##############################################################################

    my $gzip    = shift;
    my $infile  = shift;
    my $n_sites = shift;
    $infile = Bio::Root::Test::test_input_file($infile);

    # the files are now part of the git repo and don't have to be printed
    #    print_file1( $infile, $gzip );

    my $file_sequence = $infile;
    if ($gzip) {
        $file_sequence = "gzip -dc <$file_sequence |";
    }
    my $msout = Bio::SeqIO->new(
        -file    => "$file_sequence",
        -format  => 'msout',
        -n_sites => $n_sites,
    );

    isa_ok( $msout, 'Bio::SeqIO::msout' );

    my $rh_base_conversion_table = $msout->get_base_conversion_table;

    my %attributes = (
        RUNS                 => 3,
        SEGSITES             => 7,
        N_SITES              => $n_sites,
        SEEDS                => [qw(1 1 1)],
        MS_INFO_LINE         => 'ms 6 3 -s 7 -I 3 3 2 1',
        TOT_RUN_HAPS         => 6,
        POPS                 => [qw(3 2 1)],
        NEXT_RUN_NUM         => 1,
        LAST_READ_HAP_NUM    => 0,
        POSITIONS            => [qw(0.01 0.25 0.31 0.35 0.68 0.76 0.85)],
        CURRENT_RUN_SEGSITES => 7
    );

    foreach my $attribute ( keys %attributes ) {
        my $func = lc($attribute);

        if ( $attribute =~ m/POPS|SEEDS|POSITIONS/ ) {
            $func = ucfirst($func);
        }

        $func = 'get_' . $func;
        my @returns = $msout->$func();
        my ( $return, $got );

        # If there were more than one return value, then compare references to
        # arrays instead of scalars
        unless ( @returns > 1 ) {
            $got = shift @returns;
        }
        else { $got = \@returns }

        my $expected = $attributes{$attribute};

        if ( defined $got && defined $expected ) {
            is_deeply( $got, $expected, "Get $attribute" );
        }
        else { is_deeply( $got, $expected, "Get $attribute" ) }
    }

    # Testing next_hap at beginning of run
    my @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_seq );
    my @data_expected;
    if ( !defined($n_sites) ) {
        @data_expected = qw(1111111);
    }
    else {
        @data_expected =
          qw(1000000000000000000000001000001000100000000000000000000000000000000100000001000000001000000000000000);
    }
    is_deeply( \@data_got, \@data_expected,
        "Get next_hap at beginning of run" );

    # Testing next_hap after beginning of run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_seq );
    if ( !defined($n_sites) ) {
        @data_expected = qw(5555555);
    }
    else {
        @data_expected =
          qw(5000000000000000000000005000005000500000000000000000000000000000000500000005000000005000000000000000);
    }
    is_deeply( \@data_got, \@data_expected,
        "Get next_hap after beginning of run" );

    # Surprise test! testing msout::outgroup
    my $outgroup = $msout->outgroup;
    is( $outgroup, 1, "Testing msout::outgroup" );

    # Testing next_pop after beginning of pop
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_pop );
    if ( !defined($n_sites) ) {
        @data_expected = qw(4444444);
    }
    else {
        @data_expected =
          qw(4000000000000000000000004000004000400000000000000000000000000000000400000004000000004000000000000000);
    }
    is_deeply( \@data_got, \@data_expected,
        "Get next_pop after beginning of pop" );

    # Testing next_pop at beginning of pop
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_pop );
    if ( !defined($n_sites) ) {
        @data_expected = qw(4444444 5555555);
    }
    else {
        @data_expected =
          qw(4000000000000000000000004000004000400000000000000000000000000000000400000004000000004000000000000000 5000000000000000000000005000005000500000000000000000000000000000000500000005000000005000000000000000);
    }
    is_deeply( \@data_got, \@data_expected,
        "Get next_pop at beginning of pop" );

    # Testing next_run after beginning of run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_run );
    if ( !defined($n_sites) ) {
        @data_expected = qw(4444444);
    }
    else {
        @data_expected =
          qw(4000000000000000000000004000004000400000000000000000000000000000000400000004000000004000000000000000);
    }
    is_deeply( \@data_got, \@data_expected,
        "Get next_run after beginning of run" );

    # Testing next_pop at beginning of run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_pop );
    if ( !defined($n_sites) ) {
        @data_expected = qw(5555555 5555555 5555555);
    }
    else {
        @data_expected =
          qw(5000000000000000000000005000005000500000000000000000000000000000000500000005000000005000000000000000 5000000000000000000000005000005000500000000000000000000000000000000500000005000000005000000000000000 5000000000000000000000005000005000500000000000000000000000000000000500000005000000005000000000000000);
    }
    is_deeply( \@data_got, \@data_expected,
        "Get next_pop at beginning of run" );

    # Testing next_hap after pop
    @data_got      = $msout->get_next_hap;
    @data_expected = qw(1010101);
    is_deeply( \@data_got, \@data_expected, "Get next_hap after pop" );

    # Testing next_run after pop and hap
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_run );
    if ( !defined($n_sites) ) {
        @data_expected = qw(1111111 1515151);
    }
    else {
        @data_expected =
          qw(1000000000000000000000001000001000100000000000000000000000000000000100000001000000001000000000000000 1000000000000000000000005000001000500000000000000000000000000000000100000005000000001000000000000000);
    }
    is_deeply( \@data_got, \@data_expected, "Get next_run after pop and hap" );

    # Testing next_run at beginning of run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_run );
    if ( !defined($n_sites) ) {
        @data_expected = qw(1414141 1414141 1515151 1414141 1515151 1515151);
    }
    else {
        @data_expected =
          qw(1000000000000000000000004000001000400000000000000000000000000000000100000004000000001000000000000000 1000000000000000000000004000001000400000000000000000000000000000000100000004000000001000000000000000 1000000000000000000000005000001000500000000000000000000000000000000100000005000000001000000000000000 1000000000000000000000004000001000400000000000000000000000000000000100000004000000001000000000000000 1000000000000000000000005000001000500000000000000000000000000000000100000005000000001000000000000000 1000000000000000000000005000001000500000000000000000000000000000000100000005000000001000000000000000);
    }
    is_deeply( \@data_got, \@data_expected,
        "Get next_run at beginning of run" );

    is( $msout->get_next_run_num, undef, 'have all lines been read?' );
}

sub test_file_2 {
##############################################################################
## Test file 2
##############################################################################

    my $gzip    = shift;
    my $infile  = shift;
    my $n_sites = shift;
    $infile = Bio::Root::Test::test_input_file($infile);

    # the files are now part of the git repo and don't have to be printed
    #    print_file2( $infile, $gzip );

    my $file_sequence = $infile;
    if ($gzip) {
        $file_sequence = "gzip -dc <$file_sequence |";
    }

    my $msout = Bio::SeqIO->new(
        -file    => "$file_sequence",
        -format  => 'msout',
        -n_sites => $n_sites,
    );

    isa_ok( $msout, 'Bio::SeqIO::msout' );

    my %attributes = (
        RUNS                 => 3,
        SEGSITES             => 7,
        N_SITES              => $n_sites,
        SEEDS                => [qw(1 1 1)],
        MS_INFO_LINE         => 'ms 6 3',
        TOT_RUN_HAPS         => 6,
        POPS                 => 6,
        NEXT_RUN_NUM         => 1,
        LAST_READ_HAP_NUM    => 0,
        POSITIONS            => [qw(0.01 0.25 0.31 0.35 0.68 0.76 0.85)],
        CURRENT_RUN_SEGSITES => 7
    );

    foreach my $attribute ( keys %attributes ) {
        my $func = lc($attribute);

        if ( $attribute =~ m/POPS|SEEDS|POSITIONS/ ) {
            $func = ucfirst($func);
        }

        $func = 'get_' . $func;
        my @returns = $msout->$func();
        my ( $return, $got );

        # If there were more than one return value, then compare references to
        # arrays instead of scalars
        unless ( @returns > 1 ) {
            $got = shift @returns;
        }
        else { $got = \@returns }

        my $expected = $attributes{$attribute};

        if ( defined $got && defined $expected ) {
            is_deeply( $got, $expected, "Get $attribute" );
        }
        else { is_deeply( $got, $expected, "Get $attribute" ) }
    }

    my $rh_base_conversion_table = $msout->get_base_conversion_table;

    # Testing next_hap at beginning of run
    my @data_got      = $msout->get_next_hap;
    my @data_expected = '1111111';
    is_deeply( \@data_got, \@data_expected,
        "Get next_hap at beginning of run" );

    # Testing next_hap after beginning of run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_seq );
    if ( !defined($n_sites) ) {
        @data_expected = '5555555';
    }
    else {
        @data_expected = '5555055500';
    }
    is_deeply( \@data_got, \@data_expected,
        "Get next_hap after beginning of run" );

    # Surprise test! testing msout::outgroup
    my $outgroup = $msout->outgroup;
    is( $outgroup, 0, "Testing msout::outgroup" );

    # Testing next_pop after beginning of pop
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_pop );
    if ( !defined($n_sites) ) {
        @data_expected = qw(4444444 4444444 5555555 4444444);
    }
    else {
        @data_expected = qw(4444044400 4444044400 5555055500 4444044400);
    }
    is_deeply( \@data_got, \@data_expected,
        "Get next_pop after beginning of pop" );

    # Testing next_pop at beginning of pop/run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_pop );
    if ( !defined($n_sites) ) {
        @data_expected = qw(5555555 5555555 5555555 1010101 1111111 1515151);
    }
    else {
        @data_expected =
          qw(5555055500 5555055500 5555055500 1010010100 1111011100 1515015100);
    }
    is_deeply( \@data_got, \@data_expected,
        "Get next_pop at beginning of pop/run" );

    # Testing next_run at beginning of run
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_run );
    if ( !defined($n_sites) ) {
        @data_expected = qw(1414141 1414141 1515151 1414141 1515151 1515151);
    }
    else {
        @data_expected =
          qw(1414014100 1414014100 1515015100 1414014100 1515015100 1515015100);
    }
    is_deeply( \@data_got, \@data_expected,
        "Get next_run at beginning of run" );

    # Testing next_hap at beginning of run 2
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_seq );
    if ( !defined($n_sites) ) {
        @data_expected = '1515151';
    }
    else {
        @data_expected = '1515015100';
    }
    is_deeply( \@data_got, \@data_expected,
        "Get next_hap at beginning of run 2" );

    # Testing next_run after hap
    @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_run );
    if ( !defined($n_sites) ) {
        @data_expected = qw(5050505 5151515 5555555 5454545 5454545);
    }
    else {
        @data_expected =
          qw(5050050500 5151051500 5555055500 5454054500 5454054500);
    }
    is_deeply( \@data_got, \@data_expected, "Get next_run after hap" );

    is( $msout->get_next_run_num, 5, 'next run should be 5.' );

    # getting the last hap of the file via next hap
    # Testing next_run after hap
    @data_got      = $msout->get_next_hap;
    @data_expected = qw( 5555555 );
    is_deeply( \@data_got, \@data_expected, "Get last hap through next_hap" );

}

sub test_file_3 {
##############################################################################
## Test file 3
##############################################################################

    my $gzip    = shift;
    my $infile  = shift;
    $infile = Bio::Root::Test::test_input_file($infile);

    # the files are now part of the git repo and don't have to be printed
    #    print_file3( $infile, $gzip );

    my $file_sequence = $infile;
    if ($gzip) {
        $file_sequence = "gzip -dc <$file_sequence |";
    }
    my $msout = Bio::SeqIO->new(
        -file   => "$file_sequence",
        -format => 'msout',
    );

    isa_ok( $msout, 'Bio::SeqIO::msout' );

    my $rh_base_conversion_table = $msout->get_base_conversion_table;

    my %attributes = (
        RUNS                 => 1,
        SEGSITES             => 7,
        SEEDS                => [qw(1 1 1)],
        MS_INFO_LINE         => 'ms 3 1',
        TOT_RUN_HAPS         => 3,
        POPS                 => 3,
        NEXT_RUN_NUM         => 1,
        LAST_READ_HAP_NUM    => 0,
        POSITIONS            => [qw(0.01 0.25 0.31 0.35 0.68 0.76 0.85)],
        CURRENT_RUN_SEGSITES => 7
    );

    foreach my $attribute ( keys %attributes ) {
        my $func = lc($attribute);

        if ( $attribute =~ m/POPS|SEEDS|POSITIONS/ ) {
            $func = ucfirst($func);
        }

        $func = 'get_' . $func;
        my @returns = $msout->$func();
        my ( $return, $got );

        # If there were more than one return value, then compare references to
        # arrays instead of scalars
        unless ( @returns > 1 ) {
            $got = shift @returns;
        }
        else { $got = \@returns }

        my $expected = $attributes{$attribute};

        if ( defined $got && defined $expected ) {
            is_deeply( $got, $expected, "Get $attribute" );
        }
        else { is_deeply( $got, $expected, "Get $attribute" ) }
    }

    # Testing next_hap at beginning of run
    my @data_got =
      convert_bases_to_nums( $rh_base_conversion_table, $msout->get_next_pop );
    my @data_expected = qw(1111111 5555555 4444444);
    is_deeply( \@data_got, \@data_expected, "Get next_pop at end of run" );

    is( $msout->get_next_run_num, undef, 'have all lines been read?' );

    # Testing what happens when we read from empty stream
    @data_got      = $msout->get_next_pop;
    @data_expected = ();
    is_deeply( \@data_got, \@data_expected, "Get next_pop at eof" );

    # Testing what happens when we read from empty stream
    @data_got      = $msout->get_next_run;
    @data_expected = ();
    is_deeply( \@data_got, \@data_expected, "Get next_run at eof" );

    # Testing what happens when we read from empty stream
    @data_got      = $msout->get_next_hap;
    @data_expected = undef;
    is_deeply( \@data_got, \@data_expected, "Get next_hap at eof" );

    # Testing what happens when we read from empty stream
    @data_got      = $msout->get_next_seq;
    @data_expected = ();
    is_deeply( \@data_got, \@data_expected, "Get next_seq at eof" );

}

sub print_to_file {
    my ( $ra_in, $out ) = @_;
    open my $OUT, '>', $out or die "\nCould not write outfile '$out': $!\n";
    print $OUT ("@$ra_in");
    close $OUT;
}

sub convert_bases_to_nums {

    my ( $rh_base_conversion_table, @seqs ) = @_;

    my @out_seqstrings;
    foreach my $seq (@seqs) {
        my $seqstring = $seq->seq;
        foreach my $base ( keys %{$rh_base_conversion_table} ) {
            $seqstring =~ s/($base)/$rh_base_conversion_table->{$base}/g;
        }
        push @out_seqstrings, $seqstring;
    }

    return @out_seqstrings;

}

sub bad_test_file_1 {
##############################################################################
## Bad Test file 1
##############################################################################

    # This sub tests to see if msout.pm will catch if the msinfo line's
    # advertized haps are less than are actually in the file

    my $gzip    = shift;
    my $infile  = shift;
    my $n_sites = shift;
    $infile = test_input_file($infile);

    my $file_sequence = $infile;
    if ($gzip) {
        $file_sequence = "gunzip -c <$file_sequence |";
    }
    my $msout = Bio::SeqIO->new(
        -file    => "$file_sequence",
        -format  => 'msout',
        -n_sites => $n_sites,
    );

    isa_ok( $msout, 'Bio::SeqIO::msout' );

    throws_ok { $msout->get_next_run }
qr/msout file has only 2 hap\(s\), which is less than indicated in msinfo line \( 9 \)/,
      q(Caught error in bad msout file 1);

}

sub bad_test_file_2 {
##############################################################################
## Bad Test file 2
##############################################################################

    # This sub tests to see if msout.pm will catch if the msinfo line's
    # advertized haps are more than are actually in the file

    my $gzip    = shift;
    my $infile  = shift;
    my $n_sites = shift;
    $infile = test_input_file($infile);

    my $file_sequence = $infile;
    if ($gzip) {
        $file_sequence = "gunzip -c <$file_sequence |";
    }
    my $msout = Bio::SeqIO->new(
        -file    => "$file_sequence",
        -format  => 'msout',
        -n_sites => $n_sites,
    );

    isa_ok( $msout, 'Bio::SeqIO::msout' );

    throws_ok { $msout->get_next_run }
qr/\'\/\/\' not encountered when expected. There are more haplos in one of the msOUT runs than advertised in the msinfo line/,
      q(Caught error in bad msout file 2);

}

sub bad_n_sites {
##############################################################################
## Bad n_sites
##############################################################################

    # this sub tests if msout.pm dies when n_sites is smaller than segsites
    my $gzip    = shift;
    my $infile  = shift;
    $infile = Bio::Root::Test::test_input_file($infile);

    my $file_sequence = $infile;
    if ($gzip) {
        $file_sequence = "gzip -dc <$file_sequence |";
    }
    my $msout = Bio::SeqIO->new(
            -file    => "$file_sequence",
            -format  => 'msout',
    );

    # test nsites -1
    throws_ok { $msout->set_n_sites(-1) } qr|first argument needs to be a positive integer. argument supplied: -1|;

    # test nsites smaller than next hap
    $msout->set_n_sites(1);
    throws_ok{$msout->get_next_seq} qr/n_sites needs to be at least the number of segsites of every run/, 'too few n_sites failed OK';
    
}
BioPerl-1.007002/t/SeqIO/nexml.t000444000766000024       721713155576321 16256 0ustar00cjfieldsstaff000000000000#-*-perl-*-
# $Id$

use strict;

use Bio::Root::Test;
test_begin(-tests => 126,
	    -requires_modules => [qw(Bio::Phylo)]);
use_ok( 'Bio::PrimarySeq' );
use_ok('Bio::SeqIO::nexml'); # checks that your module is there and loads ok
diag("WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support");
SKIP: {
    skip("NeXML parsing for NeXML v0.9 is currently very experimental support", 124);

#Read Data
ok( my $SeqStream = Bio::SeqIO->new(
                    -file => test_input_file('nexml', 'characters.nexml.xml'),
                    -format => 'nexml'),'stream ok');

#checking first sequence object
ok( my $seq_obj = $SeqStream->next_seq(), 'seq obj' );
isa_ok($seq_obj, 'Bio::Seq');
is( $seq_obj->alphabet, 'dna', "alphabet" );
TODO: {
    local $TODO = 'primary/display_id broken with NeXML 0.9';
    is( $seq_obj->primary_id, 'DNA sequences.seq_1', "primary_id");
    is( $seq_obj->display_id, 'DNA sequences.seq_1', "display_id");
}
is( $seq_obj->seq, 'ACGCTCGCATCGCATC', "sequence");
#check taxa
my %expected_taxa = ('Homo sapiens' => 1,
                     'Pan paniscus' => 1,
                     'Pan troglodytes' => 1,
                     'Gorilla gorilla' => 1,
                     'Pongo pygmaeus' => 1);
my $feat = ($seq_obj->get_SeqFeatures())[0];
is( ($feat->get_tag_values('taxa_id'))[0], 'taxa1', 'taxa id');
is( ($feat->get_tag_values('taxa_label'))[0], 'Primary taxa block', 'taxa label');
is( ($feat->get_tag_values('my_taxon'))[0], 'Homo sapiens', "taxon ok" );
my @taxa = $feat->get_tag_values('taxon');
is( @taxa, 5, 'number of taxa');
foreach my $taxon (@taxa) {
    ok( $expected_taxa{$taxon}, 'taxon ok')	
}

#checking second sequence object
ok( $seq_obj = $SeqStream->next_seq() );
is( $seq_obj->alphabet, 'dna', "alphabet" );
TODO: {
    local $TODO = 'primary/display_id broken with NeXML 0.9';
    is( $seq_obj->primary_id, 'DNA sequences.seq_2', "primary_id");
    is( $seq_obj->display_id, 'DNA sequences.seq_2', "display_id");
}
is( $seq_obj->seq, 'ACGCTCGCATCGCATC', "sequence");
$SeqStream->next_seq();
$SeqStream->next_seq();

#checking fifth sequence object
ok( $seq_obj = $SeqStream->next_seq() );
is( $seq_obj->alphabet, 'rna', "alphabet" );
TODO: {
    local $TODO = 'primary/display_id broken with NeXML 0.9';
    is( $seq_obj->primary_id, 'RNA sequences.seq_2', "primary_id");
    is( $seq_obj->display_id, 'RNA sequences.seq_2', "display_id defaults to primary");
}
is( $seq_obj->seq, 'ACGCUCGCAUCGCAUC', "sequence");

#Write Data
diag('Begin tests for writing seq files');
my $outdata = test_output_file();
ok( my $outSeqStream = Bio::SeqIO->new(-file => ">$outdata",
                                       -format => 'nexml'), 'out stream ok');
ok $outSeqStream->write_seq($seq_obj), 'write nexml seq';
close($outdata);

diag("write_seq support for NeXML 0.9 NYI");

#Read in the out file to test roundtrip
my $inSeqStream = Bio::SeqIO->new(-file => $outdata, -format => 'nexml');

#checking fifth sequence object
ok( my $seq_obj2 = $inSeqStream->next_seq() );
is( $seq_obj2->alphabet, 'rna', "alphabet" );
is( $seq_obj2->primary_id, 'RNA sequences.seq_2', "primary_id");
is( $seq_obj2->display_id, 'RNA sequences.seq_2', "display_id defaults to primary");
is( $seq_obj2->seq, 'ACGCUCGCAUCGCAUC', "sequence");

#check taxa
my $feat1 = ($seq_obj2->get_SeqFeatures())[0];
is( ($feat1->get_tag_values('taxa_id'))[0], 'taxa1', 'taxa id');
is( ($feat1->get_tag_values('taxa_label'))[0], 'Primary taxa block', 'taxa label');
is( ($feat1->get_tag_values('my_taxon'))[0], 'Pan paniscus', "taxon ok" );
my @taxa2 = $feat1->get_tag_values('taxon');
is( @taxa2, 5, 'number of taxa');
foreach my $taxon (@taxa2) {
    ok( $expected_taxa{$taxon}, 'taxon ok')	
}

}
BioPerl-1.007002/t/SeqIO/phd.t000444000766000024      1343213155576321 15722 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 21);
	
	use_ok('Bio::SeqIO::phd');
}

my $DEBUG = test_debug();

print("Checking to see if Bio::Seq::Quality objects can be created from a file...\n") if ($DEBUG);
my $in_phd  = Bio::SeqIO->new('-file' => test_input_file('test.phd'),
			      '-format'  => 'phd',
			      '-verbose' => $DEBUG);
isa_ok($in_phd,'Bio::SeqIO::phd');



my $phd = $in_phd->next_seq();
is($phd->quality_levels,'99',"Did you get the 'QUALITY_LEVELS' comment?");
isa_ok($phd,"Bio::Seq::Quality");


if( $DEBUG ) {
    my $position = 6;
    print("I saw these in phredfile.phd:\n\n");
    print $_->tagname,": ",$_->display_text || 0," \n"
        for ($phd->annotation->get_Annotations('header'));

    print("What is the base at position $position (using subseq)?\n");
    print($phd->subseq($position,$position)."\n");
    print("What is the base at position $position (using baseat)?\n");
    print($phd->baseat($position)."\n");
    print("What is the quality at $position? (using subqual)\n");

my @qualsretr = @{$phd->subqual($position,$position)};
    print($qualsretr[0]."\n");
    print("What is the quality at $position? (using qualat)\n");
    print($phd->qualat($position)."\n");
    print("What is the trace at $position? (using trace_index_at)\n");
    print($phd->trace_index_at($position)."\n");
    print("What is the trace at $position? (using subtrace)\n");
    my @tracesretr = @{$phd->subtrace($position,$position)};
    print($tracesretr[0]."\n");
}

print("OK. Now testing write_phd...\n") if($DEBUG);

my $outfile = test_output_file();
my $out_phd = Bio::SeqIO->new(-file => ">$outfile",
			      '-format' => 'phd');
isa_ok($out_phd,"Bio::SeqIO::phd");

$out_phd->write_seq($phd);

ok( -s $outfile);

# Bug 2120

my @qual = q(9 9 12 12 8 8 9 8 8 8 9);
my @trace = q(113 121 130 145 153 169 177 203 210 218 234);

$in_phd  = Bio::SeqIO->new('-file' => test_input_file('bug2120.phd'),
			      '-format'  => 'phd',
			      '-verbose' => $DEBUG);

my $seq = $in_phd->next_seq;
is($seq->subseq(10,20),'gggggccttat','$seq->subseq()');
my @seq_qual =$seq->subqual_text(10,20);
is_deeply(\@seq_qual,\@qual,'$seq->subqual_tex()');
my @seq_trace = $seq->subtrace_text(10,20);
is_deeply(\@seq_trace,\@trace,'$seq->subqual_tex()');

if($DEBUG) {
    print "\nDefault header ... \n\n";
    use Bio::Seq::Quality;
    my $seq = Bio::Seq::Quality->new('-seq' => 'GAATTC');
    $out_phd->_fh(\*STDOUT);
    $out_phd->write_header($seq);
    print "Complete output\n\n";
    $out_phd->write_seq($seq);
}

print("Testing the header manipulation\n") if($DEBUG);
is($phd->chromat_file(),'ML4924R','$phd->chromat_file()');
$phd->chromat_file('ML4924R.esd');
is($phd->chromat_file(), 'ML4924R.esd','$phd->chromat_file()');
$phd->touch();

# Commented out 1/17/09.
# This isn't exactly a stable regression test as the comparison tests
# localtime() called from two different timepoints. They can differ if the calls
# occurred before and after a change in seconds, for example.

#my $localtime = localtime();
#is($phd->time, "$localtime", $phd->time.':'.$localtime);

if ($DEBUG){
    print "Testing the sequence ...\n";
    print ">",$phd->id," ",$phd->desc,"\n",$phd->seq,"\n";
    my $revcom = $phd->revcom;
    print ">revcom\n",$revcom->seq,"\n";
    print ">revcom_qual at 6\n",$revcom->qualat(6),"\n";
    print ">revcom_trace at 6 !!\n",$revcom->trace_index_at(6),"\n";
    my $trunc = $phd->trunc(10,20);
    print ">TRUNC 10,20\n",$trunc->seq,"\n>qual\n@{$trunc->qual}\n>trace\n@{$trunc->trace}\n";
}

# Multiple seqs in one file

$in_phd  = Bio::SeqIO->new('-file' => test_input_file('multi.phd'),
			      '-format'  => 'phd',
			      '-verbose' => $DEBUG);

@qual = qq(9 9 15 17 17 22 22 25 25 22 22);
@trace = qq(98 105 119 128 143 148 162 173 185 197 202);

$seq = $in_phd->next_seq;
is($seq->id, 'ML4924F');
is($seq->subseq(10,20),'tctcgagggta','$seq->subseq()');
@seq_qual =$seq->subqual_text(10,20);
is_deeply(\@seq_qual,\@qual,'$seq->subqual_tex()');
@seq_trace = $seq->subtrace_text(10,20);
is_deeply(\@seq_trace,\@trace,'$seq->subqual_tex()');

@qual = qq(11 9 6 6 9 19 20 32 34 34 39);
@trace = qq(98 104 122 128 140 147 159 167 178 190 200);

$seq = $in_phd->next_seq;
is($seq->id, 'ML4924R');
is($seq->subseq(10,20),'gcctgcaggta','$seq->subseq()');
@seq_qual =$seq->subqual_text(10,20);
is_deeply(\@seq_qual,\@qual,'$seq->subqual_tex()');
@seq_trace = $seq->subtrace_text(10,20);
is_deeply(\@seq_trace,\@trace,'$seq->subqual_tex()');

#if($DEBUG) {
#    print "\nDefault header ... \n\n";
#    use Bio::Seq::Quality;
#    my $seq = Bio::Seq::Quality->new('-seq' => 'GAATTC');
#    $out_phd->_fh(\*STDOUT);
#    $out_phd->write_header($seq);
#    print "Complete output\n\n";
#    $out_phd->write_seq($seq);
#}

##print("Testing the header manipulation\n") if($DEBUG);
#is($phd->chromat_file(),'ML4924R','$phd->chromat_file()');
#$phd->chromat_file('ML4924R.esd');
#is($phd->chromat_file(), 'ML4924R.esd','$phd->chromat_file()');
#$phd->touch();
#my $localtime = localtime();
#is($phd->time, "$localtime");
#if ($DEBUG){
#    print "Testing the sequence ...\n";
#    print ">",$phd->id," ",$phd->desc,"\n",$phd->seq,"\n";
#    my $revcom = $phd->revcom;
#    print ">revcom\n",$revcom->seq,"\n";
#    print ">revcom_qual at 6\n",$revcom->qualat(6),"\n";
#    print ">revcom_trace at 6 !!\n",$revcom->trace_index_at(6),"\n";
#    my $trunc = $phd->trunc(10,20);
#    print ">TRUNC 10,20\n",$trunc->seq,"\n>qual\n@{$trunc->qual}\n>trace\n@{$trunc->trace}\n";
#}
#

# Whole-read tags in the file
$in_phd  = Bio::SeqIO->new('-file' => test_input_file('multiseq_tags.phd'),
			      '-format'  => 'phd',
			      '-verbose' => $DEBUG);
isa_ok($in_phd,'Bio::SeqIO::phd');
my @seqs = ();
while (my $seq = $in_phd->next_seq){
  push @seqs, $seq;
}
is( scalar @seqs, 2 );
BioPerl-1.007002/t/SeqIO/pir.t000444000766000024       172213155576321 15720 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin( -tests => 12 );

    use_ok('Bio::SeqIO::pir');
}

my $verbose = test_debug();

my $in = Bio::SeqIO->new(
    -file    => test_input_file('seqfile.pir'),
    -verbose => $verbose,
    -format  => 'pir'
);

ok( defined $in, 'new instance is defined ' );
isa_ok( $in, 'Bio::SeqIO' );

my $out = Bio::SeqIO->new(
    -format => 'pir',
    -fh     => \*STDOUT
);

while ( my $seq = $in->next_seq() ) {
    ok( $seq->length > 1, 'checked length' );
    $out->write_seq($seq) if $verbose > 0;
}

# Empty description line
$in = Bio::SeqIO->new(
    -file    => test_input_file('seqfile-no-desc.pir'),
    -verbose => $verbose,
    -format  => 'pir'
);
my $seq = $in->next_seq();
ok( $seq->seq =~ /^MGD/, 'Correct start' );
$seq = $in->next_seq();
ok( $seq->seq =~ /^GDV/, 'Correct start' );
$seq = $in->next_seq();
ok( $seq->seq =~ /^GDV/, 'Correct start' );
BioPerl-1.007002/t/SeqIO/pln.t000444000766000024       303713155576321 15720 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 4,
			   -requires_module => 'Bio::SeqIO::staden::read');
	
    use_ok('Bio::SeqIO::pln');
}

my $verbose = test_debug();

my $io = Bio::SeqIO->new(-format => 'pln',
			 -verbose => $verbose,
			 -file => test_input_file('test.pln'));
ok(my $seq = $io->next_seq);
isa_ok($seq, 'Bio::Seq::Quality');
is($seq->seq, "GATGATTCCGGCTTCGGACGACTCTAGAGGATCCCCATTTTTATAGTTTTTATCTTGTAATAGATGTTTAGATTTTTCGTTGTAATTATTTTCTTTATTGTTGAAATTAGTATCTCTGGGTAATTTATCATATTCTCTGGAAAATGATTTACTATCACTAGATACTTCATAAGATTTATAATCTTTATTATGAAAATCATCTCTATTTTTCAAATTATTATTATATCTATCAAAGTTTCTGTCTTCATTATATCTATTAGCATATCTATCTTTATCTTTATCCCTATCACTATATCTATCATATGGTTCATCTTGTTCAACCGATCAGACTCGATTCGCCATCGCCTCTAACGGATGGCCGCTCCCCCTCTCATACCTCGCTCCCCTCGACATCCCCCGTCTCGCCACCCTATCCGCCCCCTTCATCACCCCCCCTTATCCACACCCTCACCCCCCGCATCGCGCACCCACGACCACCCGAAGAACCGCCCTTACTCCCAAGTACGCCCCGACCTCCATCACCCTATGCGGTACCACTCCCACCACACCCAGTCCTACTTTCGCCCGCACATCGGCCCCGCTTCAGACAGCTCCCAACTACGCAACCCACGCTTGTTCTTGTTCACACTCGAATACTCGAATCTCTCATTACTCCGCGGACTCCGCCGCACCTGTGCACCATTAACTGTGTAGCGCCTGAACCGGCACCTCTGATTACCACTTCCTCCACCAGCACAGTCCTATTACCGCATGTCGCTCTGCTAAGACAGTGCAAGACTCTGCGGTCGCTCTGACCCGCATCCGCCAGGGCACCTCTCACCCTCGCTGGCCACCCCGCCCCCCTCTCCCTGCCCCTTCATTCCCCCAAACCGCTTTCAACGGGACACACCCCTCCGCGGCGGACCACAACTCGCCGTCGGCCACCACTCACACCTTCCCTCCTCCTTCCCCCACATCACGCCAACCCCGTGGGACGGCTCTCCCGCGGCTACGACGCGCAACCCCCCCTCGCCGCTTCCCCCCCAACTTCCCACGGGCTCCCCTCCGCCCCTTACCCGCGAGGAGCTTCACCCGCGAACCACCTCCCCCCTTTCCCAACAGCACCG");
BioPerl-1.007002/t/SeqIO/qual.t000444000766000024       261013155576321 16065 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 18);
	
	use_ok('Bio::SeqIO');
	use_ok('Bio::Seq::PrimaryQual');
}

my $DEBUG = test_debug();

my $in_qual  = Bio::SeqIO->new('-file' => test_input_file('qualfile.qual'),
			       '-format' => 'qual');
ok($in_qual);

my @quals;

my $first = 1;
while ( my $qual = $in_qual->next_seq() ) {
		# ::dumpValue($qual);
	isa_ok($qual, 'Bio::Seq::PrimaryQual');
    @quals = @{$qual->qual()};
    if( $DEBUG ) {
	warn($qual->id()."\n");
	
	warn("(".scalar(@quals).") quality values.\n");
    }
    if( $first ) { 
		is(@quals, 484);
    }
    $first = 0;
}

# in October 2004, Carlos Mauricio La Rota posted a problem with descriptions
# this routine is to test that

@quals = 10..20;
# this one has a forced header
my $seq = Bio::Seq::PrimaryQual->new(
                    -qual =>   \@quals,
                    -header   =>   "Hank is a good cat. I gave him a bath yesterday.");
my $out = Bio::SeqIO->new(-file  =>   ">".test_output_file(),
                         -format   =>   'qual');
# yes, that works
is $seq->header, 'Hank is a good cat. I gave him a bath yesterday.';
@quals = @{$seq->qual()};
is scalar(@quals), 11;
ok $out->write_seq($seq);
$seq->header('');
is $seq->header, '';
$seq->id('Hank1');
is $seq->id, 'Hank1';
# yes, that works
ok $out->write_seq($seq);
BioPerl-1.007002/t/SeqIO/raw.t000444000766000024      1116113155576321 15735 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests               => 25,
			   -requires_modules    => [],
			   -requires_networking => 0,
			  );
	
	use_ok('Bio::SeqIO::raw');
}

my $verbose = test_debug();

my $format = 'raw';
my $seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test.$format"),
						        -format => $format);

isa_ok($seqio_obj, 'Bio::SeqIO');


is $seqio_obj->variant, 'multiple';

my @methods = qw(next_seq write_seq);
foreach my $method (@methods) {
	can_ok($seqio_obj, $method) || 
		diag "$method method not implemented for $format";	
}

# checking the first sequence object
my $seq_obj = $seqio_obj->next_seq();
isa_ok($seq_obj, 'Bio::Seq');
my %expected = ('seq'         => 'MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGL' .
						   		 'DYRTTDENLKAHEKWGNIVDVVVMKDPRTKRSRGFGFI' .
								 'TYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPN' .
								 'AGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDNIVI' .
								 'DKETGKKRGFAFVEFDDYDPVDKVVLQKQHQLNGKMVD' .
								 'VKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGN' .
								 'QNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGY' .
								 'GGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGY' .
								 'QQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGN' .
								 'YGNNQGFNNGGNNRRY',
				'length'      => '358',
			   );
is   ($seq_obj->seq(),         $expected{'seq'},         'sequence');
is   ($seq_obj->length(),      $expected{'length'},      'length');


# checking the second sequence object
my $seq_obj2  = $seqio_obj->next_seq();
isa_ok($seq_obj2, 'Bio::Seq');
my %expected2 = ('seq'         => 'MNKQRGTYSEVSLAQDPKRQQRKLKGNKISISGTKQEI' .
								  'FQVELNLQNASSDHQGNDKTYHCKGLLPPPEKLTAEVL' .
								  'GIICIVLMATVLKTIVLIPCIGVLEQNNFSLNRRMQKA' .
								  'RHCGHCPEEWITYSNSCYYIGKERRTWEERVCWPVLRR' .
								  'TLICFL',
				 'length'      => '158',
			    );
is   ($seq_obj2->seq(),         $expected2{'seq'},         'sequence');
is   ($seq_obj2->length(),      $expected2{'length'},      'length');
	
# from testformats.pl
SKIP: {

    test_skip(-tests => 2,
              -requires_modules => [qw(Algorithm::Diff
                                    IO::ScalarArray
                                    IO::String)]);
    use_ok('Algorithm::Diff', qw(diff LCS));
    
	my ($file, $type) = ("test.$format", $format);
    my $filename = test_input_file($file);
    print "processing file $filename\n" if $verbose;
    open my $FILE, '<', $filename or die "Could not read file '$filename': $!\n";
    my @datain = <$FILE>;
    close $FILE;

    my $in = IO::String->new(join('', @datain));
    my $seqin = Bio::SeqIO->new( -fh => $in,
                -format => $type);
    my $out = IO::String->new;
    my $seqout = Bio::SeqIO->new( -fh => $out,
                 -format => $type);
    my $seq;
    while( defined($seq = $seqin->next_seq) ) {	
        $seqout->write_seq($seq);
    }
    $seqout->close();
    $seqin->close();
    my $strref = $out->string_ref;
    my @dataout = map { $_."\n"} split(/\n/, $$strref );
    my @diffs = &diff( \@datain, \@dataout);
    is(@diffs, 0, "$format format can round-trip");
    
    if(@diffs && $verbose) {
        use Data::Dumper;  # should be safe for 5.005 and greater
        foreach my $d ( @diffs ) {
            print STDERR Dumper $d;
            foreach my $diff ( @$d ) {
                chomp($diff->[2]);
                print $diff->[0], $diff->[1], "\n>", $diff->[2], "\n";
            }
        }
        print "in is \n", join('', @datain), "\n";
        print "out is \n", join('',@dataout), "\n";	
    }
}

# test raw variants
my @seq = qw(MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVV
VMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVK
KLFVGALKDDHDEQSIRDYFQHFGNIVDNIVIDKETGKKRGFAFVEFDDYDPVDKVVLQK
QHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGN
NWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGND
FGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY);

$seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test2.raw"),
						        -format => 'raw');

is($seqio_obj->variant, 'multiple');

my $ct = 0;

while (my $seq = $seqio_obj->next_seq) {
    is($seq->seq, $seq[$ct]);
    $ct++;
}

is($ct, 6);

$seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test2.raw"),
						        -format => 'raw-single');

is($seqio_obj->variant, 'single');

my $seq = $seqio_obj->next_seq;
is($seq->seq, join('', @seq));

$seqio_obj = Bio::SeqIO->new(-file      => test_input_file("test2.raw"),
                            -format     => 'raw',
                            -variant    => 'single');

is($seqio_obj->variant, 'single');

$seq = $seqio_obj->next_seq;
is($seq->seq, join('', @seq));
BioPerl-1.007002/t/SeqIO/scf.t000555000766000024      2026613155576321 15730 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 80);
	
    use_ok('Bio::SeqIO::scf');
    use_ok('Bio::Seq::SequenceTrace');
}

my $verbose = test_debug();

ok my $in_scf = Bio::SeqIO->new(-file => test_input_file('chad100.scf'),
				-format => 'scf',
				-verbose => $verbose);

my $swq = $in_scf->next_seq();

isa_ok($swq,"Bio::Seq::SequenceTrace");

cmp_ok (length($swq->seq()), '>', 10);
my $qualities = join(' ',@{$swq->qual()});

cmp_ok (length($qualities), '>', 10);
my $id = $swq->id();
is ($swq->id(), "ML4942R");

my $a_channel = $swq->trace("a");
cmp_ok (scalar(@$a_channel), '>', 10);
my $c_channel = $swq->trace("c");
cmp_ok (scalar(@$c_channel), '>', 10);
my $g_channel = $swq->trace("g");
cmp_ok (scalar(@$g_channel), '>', 10);
my $t_channel = $swq->trace("t");
cmp_ok (scalar(@$t_channel), '>', 10);

my $ref = $swq->peak_indices();
my @indices = @$ref;
my $indexcount = 761;
is (scalar(@indices), $indexcount);

#use Data::Dumper;
#----------------------------------------
isa_ok $swq->seq_obj, 'Bio::Seq::Quality';
isa_ok $swq->qual_obj, 'Bio::Seq::Quality';
is $swq->alphabet, 'dna', 'alphabet';

is $swq->display_id, 'ML4942R', 'display_id';
like $swq->primary_id, qr/HASH/, 'primary_id is the stringified memory position';
is $swq->primary_id('ABC'), 'ABC', 'set primary_id';

is $swq->accession_number, 'unknown', 'accession_number';
is $swq->desc, undef, 'desc';
is $swq->desc('test'), 'test', 'desc';
is $swq->id, 'ML4942R', 'id';
is $swq->id('test'), 'test', 'id';
is length($swq->seq), $indexcount, 'seq';



my $len = 7; 
my $start = $swq->length-$len+1;
my $end = $swq->length;

is $swq->subseq($start,$end), 'cctcaag', 'subseq';
is $swq->baseat($start), 'c', 'baseat';
is $swq->qualat($start), '18', 'qualat';

is $swq->trace_value_at('a',$start), '482', 'trace_value_at';

TODO: {
    local $TODO = 'documentation and code for accuracies() do not match' if 1;
    is $swq->accuracies('a',$start), '482', 'accuracies';
}
my $qualstring = join(' ',@{$swq->subqual($start,$end)});
is ($qualstring, '18 18 21 15 8 8 8');

my $refs = $swq->sub_peak_index($start,$end);
is @$refs, $len, 'sub_peak_index';
is $swq->peak_index_at($start), 8819, 'peak_index_at';

my $indices_at_end = join(' ',@{$swq->sub_peak_index($start,$end)});
is($indices_at_end, '8819 8831 8843 8853 8862 8873 8891');

my $swq_end = $swq->trace_length();
my $swq_start = $swq_end - $len +1;
my $subtrace_a = join(' ',@{$swq->sub_trace('a',$swq_start,$swq_end)});
is $subtrace_a, '13 3 0 0 75 274 431';

my $swq2 = $swq->sub_trace_object(1,5);
#$traces2->verbose(-1);

isa_ok($swq2, 'Bio::Seq::SequenceTrace');

$swq2->_synthesize_traces(), 1; # this should not be a private method! Heikki
$swq2->set_accuracies(), 1;

is $swq->accuracy_at('a',1), '755', 'accuracy_at';

#----------------------------------------


warn("Now checking version3...\n") if $verbose;
my $in_scf_v3 = Bio::SeqIO->new(-file => test_input_file('version3.scf'),
				-format => 'scf',
				-verbose => $verbose);

my $v3 = $in_scf_v3->next_seq();
isa_ok($v3, 'Bio::Seq::SequenceTrace');
my $ind = $v3->peak_indices();
my @ff = @$ind;

@indices = @{$v3->peak_indices()};
is (scalar(@indices), 1106);

my %header = %{$in_scf_v3->get_header()};
is $header{bases}, 1106;
is $header{samples},  14107;

# is the Bio::Seq::SequenceTrace AnnotatableI?
my $ac = $v3->annotation();

isa_ok($ac,"Bio::Annotation::Collection");

my @name_comments = grep {$_->tagname() eq 'NAME'} 
$ac->get_Annotations('comment');

is $name_comments[0]->as_text(), 'Comment: IIABP1D4373';

# also get comments this way...
$ac = $in_scf_v3->get_comments();

isa_ok($ac,"Bio::Annotation::Collection");

@name_comments = grep {$_->tagname() eq 'NAME'} 
$ac->get_Annotations('comment');

is $name_comments[0]->as_text(), 'Comment: IIABP1D4373';

my @conv_comments = grep {$_->tagname() eq 'CONV'} 
$ac->get_Annotations('comment');

is $conv_comments[0]->as_text(), 'Comment: phred version=0.990722.h';

# is the SequenceTrace object annotated?
my $st_ac = $swq->annotation();

isa_ok ($st_ac, "Bio::Annotation::Collection");

my @ann =   $st_ac->get_Annotations();

is $ann[0]->tagname, 'SIGN';
is $ann[2]->text, 'SRC3700';
is $ann[5]->tagname, 'LANE';
is $ann[5]->text, 89;
is $ann[6]->text, 'phred version=0.980904.e';
is $ann[8]->text, 'ABI 373A or 377';

my $outfile = test_output_file();
my $out_scf = Bio::SeqIO->new(-file => ">$outfile",
			      -format => 'scf',
			      -verbose => $verbose);

# Bug 2196 - commentless scf

my $in = Bio::SeqIO->new(-file => test_input_file('13-pilE-F.scf'),
			 -format => 'scf',
			 -verbose => $verbose);

my $seq = $in->next_seq;

ok ($seq);

isa_ok($seq, 'Bio::Seq::SequenceTrace');

$ac = $seq->annotation;

isa_ok($ac, 'Bio::Annotation::Collection');

@name_comments = grep {$_->tagname() eq 'NAME'} 
$ac->get_Annotations('comment');

is $name_comments[0], undef;

@conv_comments = grep {$_->tagname() eq 'CONV'} 
$ac->get_Annotations('comment');

is $conv_comments[0], undef;

# the new way

warn("Now testing the _writing_ of scfs\n") if $verbose;

$out_scf->write_seq(-target	=>	$v3,
		    -MACH		=>	'CSM sequence-o-matic 5000',
		    -TPSW		=>	'trace processing software',
		    -BCSW		=>	'basecalling software',
		    -DATF		=>	'AM_Version=2.00',
		    -DATN		=>	'a22c.alf',
		    -CONV		=>	'Bioperl-scf.pm');

ok( -s $outfile && ! -z "$outfile" );

# TODO? tests below don't do much

$out_scf = Bio::SeqIO->new(-verbose => 1,
			   -file => ">$outfile",
			   -format => 'scf');

$swq = Bio::Seq::Quality->new(-seq =>'ATCGATCGAA',
			      -qual =>"10 20 30 40 50 20 10 30 40 50",
			      -alphabet =>'dna');

my $trace = Bio::Seq::SequenceTrace->new(-swq => $swq);

$out_scf->write_seq(	-target	        =>	$trace,
			-MACH		=>	'CSM sequence-o-matic 5000',
			-TPSW		=>	'trace processing software',
			-BCSW		=>	'basecalling software',
			-DATF		=>	'AM_Version=2.00',
			-DATN		=>	'a22c.alf',
			-CONV		=>	'Bioperl-scf.pm' );

warn("Trying to write an scf with a subset of a real scf...\n") if $verbose;
$out_scf = Bio::SeqIO->new(-verbose => 1,
			   -file => ">$outfile",
			   -format => 'scf');

$in_scf_v3 = Bio::SeqIO->new(-file => test_input_file('version3.scf'),
			     -format => 'scf',
			     -verbose => $verbose);
$v3 = $in_scf_v3->next_seq();

my $sub_v3 = $v3->sub_trace_object(5,50);

#warn("The subtrace object is this:\n") if $DEBUG;

$out_scf->write_seq(-target => $sub_v3 );

my $in_scf_v2 = Bio::SeqIO->new(-file => test_input_file('version2.scf'),
				-format => 'scf',
				-verbose => $verbose);
$v3 = $in_scf_v2->next_seq();
ok($v3);

$out_scf = Bio::SeqIO->new(-file   => ">$outfile",
                           -format => "scf");
$out_scf->write_seq( -target  => $v3,
                     -version => 2 );

# simple round trip tests (bug 2881)

my %file_map = (
	# filename         # write_seq args
	'chad100.scf'	=> 1,
	'13-pilE-F.scf' => 1,
	'version2.scf'  => 1,
	'version3.scf'  => 1
	);

for my $f (sort keys %file_map) {
	my $outfile = test_output_file();
	my $in = Bio::SeqIO->new(-file => test_input_file($f),
							 -format => 'scf');
	my $out = Bio::SeqIO->new(-file => ">$outfile",
							 -format => 'scf');
	
	my $seq1 = $in->next_seq();
	isa_ok($seq1, 'Bio::Seq::SequenceTrace');
	
	ok($out->write_seq(-target => $seq1));
	
	my $in2 = Bio::SeqIO->new(-file => "<$outfile",
							  -format => 'scf');
	my $seq2 = $in2->next_seq();
	isa_ok($seq2, 'Bio::Seq::SequenceTrace');
	if ($seq1->display_id) {
		TODO: {
			local $TODO = "display_id doesn't round trip yet";
			is($seq1->display_id, $seq2->display_id, 'display_id matches');
		}
	}
	is_deeply($seq1->qual, $seq2->qual, 'qual scores match');
}

# synthesizing traces roundtrip (bug 2881):

my @sequences=('A',
               'ATGGAGCTCATCAAAGAATCGACTCATATATCCATCCCTGAACGGCTGACTCACATTAATGGTTGA');
foreach my $sequence (@sequences) {
    my $qualstr=join ' ', map { 65 } (1 .. length($sequence));
    my $seq_qual=Bio::Seq::Quality->new(-seq=>$sequence, -qual=>$qualstr);

    my $outfile=test_output_file();
    my $out=Bio::SeqIO->new(-file=>">$outfile", -format=>'scf');
    $out->write_seq(-target=>$seq_qual);

    my $in=Bio::SeqIO->new(-file=>$outfile, -format=>'scf');
    my $in_seq=$in->next_seq();

    is_deeply($seq_qual, $in_seq->{swq}, 'Bio::Sequence::Quality matches');
}

BioPerl-1.007002/t/SeqIO/seqxml.t000444000766000024      2107513155576321 16462 0ustar00cjfieldsstaff000000000000#-*-perl-*-
# $Id$

use strict;

BEGIN {
    use Bio::Root::Test;
    test_begin(
        -tests            => 61,
        -requires_modules => [qw(XML::LibXML XML::LibXML::Reader XML::Writer)]
    );

    use_ok('Bio::SeqIO');
}
use_ok('Bio::PrimarySeq');

my $verbose = test_debug();

SKIP: {

    # XML library version checks
    if ( 1000 * $] < 5008 ) {
        skip( "Reader interface only supported in Perl >= 5.8", 96 );
    }
    elsif ( XML::LibXML::LIBXML_VERSION() <= 20620 ) {
        skip( "Reader not supported for libxml2 <= 2.6.20", 96 );
    }

    if ($verbose) {
        diag( "libxml version: ", XML::LibXML::LIBXML_VERSION() );
    }

    # checks that your module is there and loads ok
    use_ok('Bio::SeqIO::seqxml');

    # read data
    ok(
        my $seq_stream = Bio::SeqIO->new(
            -file    => test_input_file("seqxml.xml"),
            -format  => 'seqxml',
            -verbose => $verbose,
        ),
        'stream ok',
    );

    # check metadata
    is( $seq_stream->seqXMLversion, '0.3',     'seqXML version' );
    is( $seq_stream->source,        'Ensembl', 'source' );
    is( $seq_stream->sourceVersion, '56',      'source version' );

    # now get and check the sequence entry itself
    my $seq_obj = $seq_stream->next_seq;
    isa_ok( $seq_obj, 'Bio::Seq' );
    is( $seq_obj->display_id, 'ENST00000308775',           'display id' );
    is( $seq_obj->primary_id, 'ENST00000308775',           'primary id' );
    is( $seq_obj->desc,       'dystroglycan 1',            'description' );
    is( $seq_obj->seq,        'AAGGC----UGAUGUC.....ACAU', 'sequence' );
    is( $seq_obj->length,     25,                          'length' );

    my ($source) = $seq_obj->get_Annotations('source');
    if ($source) { is($source->value, 'Ensembl', 'entry source'); }

    # species
    isa_ok( $seq_obj->species, 'Bio::Species', 'species' );
    is( $seq_obj->species->node_name,    'Homo sapiens', 'species name' );
    is( $seq_obj->species->ncbi_taxid, '9606',         'NCBI tax id' );

    # alternative IDs
    my @dblinks = $seq_obj->get_Annotations('dblink');
    my $dblink  = shift @dblinks;
    isa_ok( $dblink, 'Bio::Annotation::DBLink' );
    is( $dblink->database,   'RefSeq',   'dblink source' );
    is( $dblink->primary_id, 'NM_004393', 'dblink ID' );

    # properties
    my @annotations = $seq_obj->get_Annotations();
    foreach my $annot_obj (@annotations) {
        next if ( $annot_obj->tagname eq 'dblink' );
        next if ( $annot_obj->tagname eq 'source' );        
        isa_ok( $annot_obj, 'Bio::Annotation::SimpleValue' );
        if ( $annot_obj->tagname eq 'has_splice_variants' ) {
            is( $annot_obj->value, undef, 'boolean property' );
        }
        elsif ( $annot_obj->tagname eq 'prediction_method' ) {
            is( $annot_obj->value, 'manual curation', 'property with value' );
        }
    }

    # write data
    my $outfile = test_output_file();
    ok(
        my $seq_writer = Bio::SeqIO->new(
            -file          => ">$outfile",
            -format        => 'seqxml',
            -verbose       => $verbose,
            -source        => 'Ensembl',
            -sourceVersion => '56',
            -seqXMLversion => '0.3',
        ),
        'writer ok',
    );
    $seq_writer->flush;    # to make sure output is written to file
    ok( -s $outfile, 'outfile is created' );

    # check metadata
    is( $seq_writer->seqXMLversion, '0.3',     'seqXML version' );
    is( $seq_writer->source,        'Ensembl', 'source' );
    is( $seq_writer->sourceVersion, '56',      'source version' );
    is( $seq_writer->schemaLocation, 'http://www.seqxml.org/0.3/seqxml.xsd', 'schemaLocation' );

    # write one sequence entry to file
    $seq_writer->write_seq($seq_obj);
    $seq_writer->close;
    if ( $verbose > 0 ) {
        diag("writing first seqXML outfile");
        diag(`cat $outfile`);
    }

    # verify written data by roundtripping it
    {
        my $new_in = Bio::SeqIO->new(
            -file   => $outfile,
            -format => 'seqxml'
        );

        my $new_seqobj = $new_in->next_seq;
        isa_ok( $new_seqobj, 'Bio::Seq' );
        is( $new_seqobj->display_id, 'ENST00000308775', 'display id' );
        is( $new_seqobj->primary_id, 'ENST00000308775', 'primary id' );
        is( $new_seqobj->desc,       'dystroglycan 1',  'description' );
        is( $new_seqobj->seq, 'AAGGC----UGAUGUC.....ACAU', 'sequence' );
        is( $new_seqobj->length, 25, 'length' );

        my ($new_source) = $new_seqobj->get_Annotations('source');
        if ($new_source) { is($new_source->value, 'Ensembl', 'entry source'); }


        # species
        isa_ok( $new_seqobj->species, 'Bio::Species', 'species' );
        is( $new_seqobj->species->node_name,    'Homo sapiens', 'species name' );
        is( $new_seqobj->species->ncbi_taxid, '9606',         'NCBI tax id' );

        # alternative IDs
        my @dblinks = $new_seqobj->get_Annotations('dblink');
        my $dblink  = shift @dblinks;
        isa_ok( $dblink, 'Bio::Annotation::DBLink' );
        is( $dblink->database,   'RefSeq',   'dblink source' );
        is( $dblink->primary_id, 'NM_004393', 'dblink ID' );

        # properties
        my @annotations = $new_seqobj->get_Annotations();
        foreach my $annot_obj (@annotations) {
            next if ( $annot_obj->tagname eq 'dblink' );
            next if ( $annot_obj->tagname eq 'source' );
            isa_ok( $annot_obj, 'Bio::Annotation::SimpleValue' );
            if ( $annot_obj->tagname eq 'has_splice_variants' ) {
                is( $annot_obj->value, undef, 'boolean property' );
            }
            elsif ( $annot_obj->tagname eq 'prediction_method' ) {
                is(
                    $annot_obj->value,
                    'manual curation',
                    'property with value'
                );
            }
        }
    }

    # write data from a Seq object created from a fasta file
    {
        # forcing a Bio::Seq to be created
        # due to SeqIO::fasta creating a PrimarySeq by default
        # as of r16838
        my $factory = Bio::Seq::SeqFactory->new(-type => 'Bio::Seq');
        
        my $seq_stream = Bio::SeqIO->new(
            -file   => test_input_file("test.fasta"),
            -format => 'fasta',
            -seqfactory => $factory,
        );

        my $outfile = test_output_file();
        my $writer  = Bio::SeqIO->new(
            -file   => ">$outfile",
            -format => 'seqxml'
        );
        $writer->flush;
        ok( -s $outfile, 'outfile is created' );

        while ( my $seq_obj = $seq_stream->next_seq ) {
            $writer->write_seq($seq_obj);
        }
        $writer->close;
        if ( $verbose > 0 ) {
            diag(`cat $outfile`);
        }

        # now read that newly made seqxml back in
        my $in = Bio::SeqIO->new(
            -file   => $outfile,
            -format => 'seqxml'
        );

        # check header
        is( $in->seqXMLversion, '0.3', 'seqXML version' );
        is( $in->source,        undef, 'source' );
        is( $in->sourceVersion, undef, 'source version' );

        # check first sequence entry
        my $seqxml_obj = $in->next_seq;
        is( $seqxml_obj->display_id, 'roa1_drome', 'display id' );
        is( $seqxml_obj->primary_id, 'roa1_drome', 'primary id' );
        is( $seqxml_obj->desc, 'Rea guano receptor type III >> 0.1',
            'description' );
        is(
            $seqxml_obj->seq,
'MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVVVMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDNIVIDKETGKKRGFAFVEFDDYDPVDKVVLQKQHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY',
            'sequence'
        );
        is( $seqxml_obj->length, 358, 'length' );

        # check second sequence entry
        my $seqxml_obj2 = $in->next_seq;
        is( $seqxml_obj2->display_id, 'roa2_drome',       'display id' );
        is( $seqxml_obj2->primary_id, 'roa2_drome',       'primary id' );
        is( $seqxml_obj2->desc,       'Rea guano ligand', 'description' );
        is(
            $seqxml_obj2->seq,
'MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVVVMKDPTSTSTSTSTSTSTSTSTMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVKKLFVGALKDDHDEQSIRDYFQHLLLLLLLDLLLLDLLLLDLLLFVEFDDYDPVDKVVLQKQHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY',
            'sequence'
        );
        is( $seqxml_obj2->length, 358, 'length' );

    }

}
BioPerl-1.007002/t/SeqIO/strider.t000444000766000024       240013155576321 16574 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests               => 8,
			   -requires_module    => 'Convert::Binary::C',
			   -requires_networking => 0,
			  );
	
	use_ok('Bio::SeqIO::strider');
}

my $verbose = test_debug();

TODO: {
	my $format = 'strider';
	todo_skip "No tests for $format format -- no sample file to test against", 7, if 1;

	my $seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test.$format"),
							        -format => $format);
	
	isa_ok($seqio_obj, 'Bio::SeqIO');
	
	my @methods = qw(next_seq write_seq);
	foreach my $method (@methods) {
		can_ok($seqio_obj, $method) || 
			diag "$method method not implemented for $format";	
	}
	
	# checking the first sequence object
	my $seq_obj = $seqio_obj->next_seq();
	isa_ok($seq_obj, 'Bio::Seq');
	my %expected = ('seq'         => '' .
					'length'      => '',
					'primary_id'  => '',
					'description' => qr(),
				   );
	is   ($seq_obj->seq(),         $expected{'seq'},         'sequence');
	is   ($seq_obj->length(),      $expected{'length'},      'length');
	is   ($seq_obj->primary_id(),  $expected{'primary_id'},  'primary_id');
	like ($seq_obj->description(), $expected{'description'}, 'description');
}BioPerl-1.007002/t/SeqIO/swiss.t000444000766000024      3707613155576321 16331 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests           => 247,
               -requires_module => 'Data::Stag');

    use_ok('Bio::SeqIO::swiss');
}

use Bio::Annotation::SimpleValue;

my $verbose = test_debug();

my $seqio = Bio::SeqIO->new( -verbose => $verbose,
                                     -format => 'swiss',
                                     -file   => test_input_file('test.swiss'));

isa_ok($seqio, 'Bio::SeqIO');
my $seq = $seqio->next_seq;
my @gns = $seq->annotation->get_Annotations('gene_name');

my $outfile = test_output_file();
$seqio = Bio::SeqIO->new( -verbose => $verbose,
                                 -format => 'swiss',
                                 -file   => ">$outfile");

$seqio->write_seq($seq);

# reads it in once again
$seqio = Bio::SeqIO->new( -verbose => $verbose,
                                 -format => 'swiss',
                                 -file => $outfile);

$seq = $seqio->next_seq;
isa_ok($seq->species, 'Bio::Species');
is($seq->species->ncbi_taxid, 6239);

# version, seq_update, dates (5 tests)
is($seq->version, 40);
my ($ann) = $seq->annotation->get_Annotations('seq_update');
is($ann->display_text, 35,'operator overloading in AnnotationI is deprecated');

my @dates = $seq->get_dates;
my @date_check = qw(01-NOV-1997 01-NOV-1997 16-OCT-2001);

for my $date (@dates) {
    my $expdate = shift @date_check;
    if ($expdate) {
        is($date, $expdate,'dates');
    } else {
        is($date, $expdate);
    }
}

my @gns2 = $seq->annotation->get_Annotations('gene_name');
# check gene name is preserved (was losing suffix in worm gene names)
ok($#gns2 == 0 && $gns[0]->value eq $gns2[0]->value);

# test swissprot multiple RP lines
my $str = Bio::SeqIO->new(-file => test_input_file('P33897'));
$seq = $str->next_seq;
isa_ok($seq, 'Bio::Seq::RichSeqI');
my @refs = $seq->annotation->get_Annotations('reference');
is( @refs, 23);
is($refs[20]->rp, 'VARIANTS X-ALD LEU-98; ASP-99; GLU-217; GLN-518; ASP-608; ILE-633 AND PRO-660, AND VARIANT THR-13.');

# version, seq_update, dates (5 tests)
is($seq->version, 44);
($ann) = $seq->annotation->get_Annotations('seq_update');
is($ann->display_text, 28,'operator overloading in AnnotationI is deprecated');
@dates = $seq->get_dates;
@date_check = qw(01-FEB-1994 01-FEB-1994 15-JUN-2004);
for my $date (@dates) {
    is($date, shift @date_check);
}

my $ast = Bio::SeqIO->new(-verbose => $verbose,
                                  -format => 'swiss' ,
                                  -file => test_input_file('roa1.swiss'));
my $as = $ast->next_seq();

ok defined $as->seq;
is($as->id, 'ROA1_HUMAN', "id is ".$as->id);
like($as->primary_id, qr(Bio::PrimarySeq));
is($as->length, 371);
is($as->alphabet, 'protein');
is($as->division, 'HUMAN');
is(scalar $as->all_SeqFeatures(), 16);
is(scalar $as->annotation->get_Annotations('reference'), 11);

# version, seq_update, dates (6 tests)
is($as->version, 35);
($ann) = $as->annotation->get_Annotations('seq_update');
is($ann->display_text, 15,'operator overloading in AnnotationI is deprecated');
@dates = $as->get_dates;
@date_check = qw(01-MAR-1989 01-AUG-1990 01-NOV-1997);
for my $date (@dates) {
    is($date, shift @date_check);
}
($ann) = $as->annotation->get_Annotations('evidence');
is($ann->value,"1: Evidence at protein level");


my ($ent,$out) = undef;
($as,$seq) = undef;

$seqio = Bio::SeqIO->new(-format => 'swiss' ,
                                 -verbose => $verbose,
                                 -file => test_input_file('swiss.dat'));
$seq = $seqio->next_seq;
isa_ok($seq, 'Bio::Seq::RichSeqI');

# more tests to verify we are actually parsing correctly
like($seq->primary_id, qr(Bio::PrimarySeq));
is($seq->display_id, 'MA32_HUMAN');
is($seq->length, 282);
is($seq->division, 'HUMAN');
is($seq->alphabet, 'protein');
my @f = $seq->all_SeqFeatures();
is(@f, 2);
is($f[1]->primary_tag, 'CHAIN');
is(($f[1]->get_tag_values('description'))[0], 'COMPLEMENT COMPONENT 1, Q SUBCOMPONENT BINDING PROTEIN');

# version, seq_update, dates (5 tests)
is($seq->version, 40);
($ann) = $seq->annotation->get_Annotations('seq_update');
is($ann->display_text, 31,'operator overloading in AnnotationI is deprecated');
@dates = $seq->get_dates;
@date_check = qw(01-FEB-1995 01-FEB-1995 01-OCT-2000);
for my $date (@dates) {
    is($date, shift @date_check);
}

my @genenames = qw(GC1QBP HABP1 SF2P32 C1QBP);
($ann) = $seq->annotation->get_Annotations('gene_name');
# use Data::Stag findval and element name to get values/nodes
foreach my $gn ( $ann->findval('Name') ) {
    ok ($gn, shift(@genenames));
}
foreach my $gn ( $ann->findval('Synonyms') ) {
    ok ($gn, shift(@genenames));
}
like($ann->value, qr/Name: GC1QBP/);

# test for feature locations like ?..N
$seq = $seqio->next_seq();
isa_ok($seq, 'Bio::Seq::RichSeqI');
like($seq->primary_id, qr(Bio::PrimarySeq));
is($seq->display_id, 'ACON_CAEEL');
is($seq->length, 788);
is($seq->division, 'CAEEL');
is($seq->alphabet, 'protein');
is(scalar $seq->all_SeqFeatures(), 5);

foreach my $gn ( $seq->annotation->get_Annotations('gene_name') ) {
    ok ($gn->value, 'F54H12.1');
}

# test species in swissprot -- this can be a n:n nightmare
$seq = $seqio->next_seq();
isa_ok($seq, 'Bio::Seq::RichSeqI');
like($seq->primary_id, qr(Bio::PrimarySeq));
my @sec_acc = $seq->get_secondary_accessions();
is($sec_acc[0], 'P29360');
is($sec_acc[1], 'Q63631');
is($seq->accession_number, 'P42655');
my @kw = $seq->get_keywords;
is( $kw[0], 'Brain');
is( $kw[1], 'Neurone');
is($kw[3], 'Multigene family');
is($seq->display_id, '143E_HUMAN');
is($seq->species->binomial, "Homo sapiens");
is($seq->species->common_name, "Human");
is($seq->species->ncbi_taxid, 9606);

$seq = $seqio->next_seq();
isa_ok($seq, 'Bio::Seq::RichSeqI');
like($seq->primary_id, qr(Bio::PrimarySeq));
is($seq->species->binomial, "Bos taurus");
is($seq->species->common_name, "Bovine");
is($seq->species->ncbi_taxid, 9913);

# multiple genes in swissprot
$seq = $seqio->next_seq();
isa_ok($seq, 'Bio::Seq::RichSeqI');
like($seq->primary_id, qr(Bio::PrimarySeq));

($ann) = $seq->annotation->get_Annotations("gene_name");
@genenames = qw(CALM1 CAM1 CALM CAM CALM2 CAM2 CAMB CALM3 CAM3 CAMC);
my $flatnames = "(CALM1 OR CAM1 OR CALM OR CAM) AND (CALM2 OR CAM2 OR CAMB) AND (CALM3 OR CAM3 OR CAMC)";

my @names = @genenames; # copy array

my @ann_names = $ann->get_all_values();
is(scalar(@ann_names), scalar(@names));

# do this in a layered way (nested tags)
for my $node ($ann->findnode('gene_name')) {
    for my $name ($node->findval('Name')) {
        is($name, shift(@names));
    }
    for my $name ($node->findval('Synonyms')) {
        is($name, shift(@names));
    }
}

is(scalar(@names),0);

# same entry as before, but with the new gene names format
$seqio = Bio::SeqIO->new(-format => 'swiss',
                                 -verbose => $verbose,
                         -file => test_input_file('calm.swiss'));
$seq = $seqio->next_seq();
isa_ok($seq, 'Bio::Seq::RichSeqI');
like($seq->primary_id, qr(Bio::PrimarySeq));
($ann) = $seq->annotation->get_Annotations("gene_name");
@names = @genenames; # copy array

my @ann_names2 = $ann->get_all_values(); #emulate StructuredValue's flattened array
is(scalar(@ann_names2), scalar(@names));

for my $node ($ann->findnode('gene_name')) {
    for my $name ($node->findval('Name')) {
        is($name, shift(@names));
    }
    for my $name ($node->findval('Synonyms')) {
        is($name, shift(@names));
    }
}

is(scalar(@names),0);

# test proper parsing of references
my @litrefs = $seq->annotation->get_Annotations('reference');
is(scalar(@litrefs), 17);

my @titles = (
    '"Complete amino acid sequence of human brain calmodulin."',
    '"Multiple divergent mRNAs code for a single human calmodulin."',
    '"Molecular analysis of human and rat calmodulin complementary DNA clones. Evidence for additional active genes in these species."',
    '"Isolation and nucleotide sequence of a cDNA encoding human calmodulin."',
    '"Structure of the human CALM1 calmodulin gene and identification of two CALM1-related pseudogenes CALM1P1 and CALM1P2."',
    undef,
    '"Characterization of the human CALM2 calmodulin gene and comparison of the transcriptional activity of CALM1, CALM2 and CALM3."',
    '"Cloning of human full-length CDSs in BD Creator(TM) system donor vector."',
    '"The DNA sequence and analysis of human chromosome 14."',
    '"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences."',
    '"Alpha-helix nucleation by a calcium-binding peptide loop."',
    '"Solution structure of Ca(2+)-calmodulin reveals flexible hand-like properties of its domains."',
    '"Calmodulin structure refined at 1.7 A resolution."',
    '"Drug binding by calmodulin: crystal structure of a calmodulin-trifluoperazine complex."',
    '"Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin."',
    '"Physiological calcium concentrations regulate calmodulin binding and catalysis of adenylyl cyclase exotoxins."',
    '"Crystal structure of a MARCKS peptide containing the calmodulin-binding domain in complex with Ca2+-calmodulin."',
);

my @locs = (
    "Biochemistry 21:2565-2569(1982).",
    "J. Biol. Chem. 263:17055-17062(1988).",
    "J. Biol. Chem. 262:16663-16670(1987).",
    "Biochem. Int. 9:177-185(1984).",
    "Eur. J. Biochem. 225:71-82(1994).",
    "Submitted (FEB-1995) to the EMBL/GenBank/DDBJ databases.",
    "Cell Calcium 23:323-338(1998).",
    "Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases.",
    "Nature 421:601-607(2003).",
    "Proc. Natl. Acad. Sci. U.S.A. 99:16899-16903(2002).",
    "Proc. Natl. Acad. Sci. U.S.A. 96:903-908(1999).",
    "Nat. Struct. Biol. 8:990-997(2001).",
    "J. Mol. Biol. 228:1177-1192(1992).",
    "Biochemistry 33:15259-15265(1994).",
    "Nature 415:396-402(2002).",
    "EMBO J. 21:6721-6732(2002).",
    "Nat. Struct. Biol. 10:226-231(2003).",
);

my @positions = (
     undef, undef,
    undef, undef,
    undef, undef,
    undef, undef,
    undef, undef,
    undef, undef,
    undef, undef,
    undef, undef,
    undef, undef,
    undef, undef,
    94, 103,
    1, 76,
    undef, undef,
    undef, undef,
    5, 148,
    1, 148,
    undef, undef,
);

foreach my $litref (@litrefs) {
    is($litref->title, shift(@titles));
    is($litref->location, shift(@locs));
    is($litref->start, shift(@positions));
    is($litref->end, shift(@positions));
}

# format parsing changes (pre-rel 9.0)

$seqio = Bio::SeqIO->new( -verbose => $verbose,
                         -format => 'swiss',
                         -file   => test_input_file('pre_rel9.swiss'));

ok($seqio);
$seq = $seqio->next_seq;
isa_ok($seq->species, 'Bio::Species');
is($seq->species->ncbi_taxid, "6239");

# version, seq_update, dates (5 tests)
is($seq->version, 44);
($ann) = $seq->annotation->get_Annotations('seq_update');
is($ann->display_text, 1,'operator overloading in AnnotationI is deprecated');
@dates = $seq->get_dates;
@date_check = qw(01-NOV-1997 01-NOV-1996 30-MAY-2006 );
for my $date (@dates) {
    is($date, shift @date_check);
}

my @idcheck = qw(Z66513 T22647 Cel.30446 Q06319 Q20772 F54D5.7 WBGene00010052
		 F54D5.7 GO:0005515 IPR006089 IPR006091 IPR006090
		 IPR006092 IPR009075 IPR009100 IPR013764 PF00441
		 PF02770 PF02771 PS00072 PS00073);

for my $dblink ( $seq->annotation->get_Annotations('dblink') ) {
    is($dblink->primary_id, shift @idcheck);
}

$seqio = Bio::SeqIO->new( -verbose => $verbose,
                         -format => 'swiss',
                         -file   => test_input_file('pre_rel9.swiss'));

my @namespaces = qw(Swiss-Prot TrEMBL TrEMBL);

while (my $seq = $seqio->next_seq) {
    is($seq->namespace, shift @namespaces);
}

# format parsing changes (rel 9.0, Oct 2006)

$seqio = Bio::SeqIO->new( -verbose => $verbose,
                         -format => 'swiss',
                         -file   => test_input_file('rel9.swiss'));

ok($seqio);
$seq = $seqio->next_seq;
isa_ok($seq->species, 'Bio::Species');
is($seq->species->ncbi_taxid, 6239);

is($seq->version, 47);
($ann) = $seq->annotation->get_Annotations('seq_update');
is($ann->display_text, 1,'operator overloading in AnnotationI is deprecated');
@dates = $seq->get_dates;
@date_check = qw(01-NOV-1997 01-NOV-1996 31-OCT-2006 );
for my $date (@dates) {
    is($date, shift @date_check);
}

@idcheck = qw(Z66513 T22647 Cel.30446 Q06319 Q20772 F54D5.7 cel:F54D5.7
         WBGene00010052 F54D5.7 GO:0005515 IPR006089 IPR006091 IPR006090
         IPR006092 IPR009075 IPR013786 IPR009100 IPR013764 PF00441 PF02770
         PF02771 PS00072 PS00073 );

for my $dblink ( $seq->annotation->get_Annotations('dblink') ) {
    is($dblink->primary_id, shift @idcheck);
}

$seqio = Bio::SeqIO->new( -verbose => $verbose,
                         -format => 'swiss',
                         -file   => test_input_file('rel9.swiss'));

@namespaces = qw(Swiss-Prot TrEMBL TrEMBL);

while (my $seq = $seqio->next_seq) {
    is($seq->namespace, shift @namespaces);
}

# bug 2288
# Q8GBD3.swiss
$seqio = Bio::SeqIO->new( -verbose => $verbose,
                         -format => 'swiss',
                         -file   => test_input_file('Q8GBD3.swiss'));

while (my $seq = $seqio->next_seq) {
    my $lineage = join(';', $seq->species->classification);
	is ($lineage, 'Acetobacter aceti;Acetobacter subgen. Acetobacter;'.
		'Acetobacter;Acetobacteraceae;Rhodospirillales;Alphaproteobacteria;'.
		'Proteobacteria;Bacteria');
}

# Test for roundtrippability swiss->fasta->swiss
# 1. Swiss -> Fasta
$seqio = Bio::SeqIO->new(
    -verbose => $verbose,
    -format  => 'swiss',
    -file    => test_input_file('test.swiss'),
);
my $fasta_output = test_output_file();
my $seqio_out = Bio::SeqIO->new(
    -verbose => $verbose,
    -format  => 'fasta',
    -file    => ">$fasta_output",
);

my $seq_first = $seqio->next_seq();
$seqio_out->write_seq( $seq_first );

# 2. Fasta -> Swiss
my $swiss_output = test_output_file();
$seqio = Bio::SeqIO->new(
    -verbose => $verbose,
    -format  => 'fasta',
    -file    => $fasta_output,
);
$seqio_out = Bio::SeqIO->new(
    -verbose => $verbose,
    -format  => 'swiss',
    -file    => ">$swiss_output",
);
my $seq_second = $seqio->next_seq();
is( $seq_second->id,  $seq_first->id,  'Converting to fasta seqids match');
is( $seq_second->seq, $seq_first->seq, 'Converting to fasta sequences match');
$seqio_out->write_seq( $seq_second );

# 3. Check that we can open and read the resulting swiss-prot file

$seqio = Bio::SeqIO->new(
    -verbose => $verbose,
    -format  => 'swiss',
    -file    => $swiss_output,
);
my $seq_third;
SKIP: {
    skip "Can't parse generated swissprot file", 1
        unless lives_ok( sub {$seq_third = $seqio->next_seq()}, 'Can parse generated swiss' );
    is( $seq_third->id,  $seq_first->id,  'Roundtrip, seqids match');
    is( $seq_third->seq, $seq_first->seq, 'Roundtrip, sequences match');
};

# bug 3153

# the default type for gene_name is Bio::Annotation::TagTree, but we need to
# allow Bio::Annotation::SimpleValue as well for output (even though we will not
# support parsing it)

$seqio = Bio::SeqIO->new(-format => 'swiss',
                         -file =>  test_input_file('test.swiss'));

$seq = $seqio->next_seq;

$seq->annotation->remove_Annotations('gene_name');

$seq->add_Annotation('gene_name',
        Bio::Annotation::SimpleValue->new(-name   => 'foo', -value  => 'bar'));

$outfile = test_output_file();

my $seqout = Bio::SeqIO->new(-format => 'swiss',
                             -file   => ">$outfile");

lives_ok {$seqout->write_seq($seq)};

$seqout->close;

open my $swissfh, '<', $outfile or die "Could not read file '$outfile': $!\n";

my $seen_gn;
while (<$swissfh>) {
    if (/^GN\s+(\S+)/) {
        $seen_gn = $1;
        last
    }
}
close $swissfh;

is $seen_gn, 'bar';
BioPerl-1.007002/t/SeqIO/tab.t000444000766000024       105513155576321 15673 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 8);
	
	use_ok('Bio::SeqIO::tab');
}

my $verbose = test_debug();

my $io = Bio::SeqIO->new(-format => 'tab',
								 -verbose => $verbose,
								 -file => test_input_file('test.tab'));
isa_ok($io, 'Bio::SeqIO');

while (my $seq = $io->next_seq) {
	ok ( $seq && defined $seq, 'seq is defined' ) ;
	is ( $seq->length, 358, 'check seq length'  ) ;
	like ($seq->display_id, qr/^roa\d_drome$/, 'check matching' );
}
BioPerl-1.007002/t/SeqIO/table.t000444000766000024      1364213155576321 16241 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 463,
			   -requires_module => 'IO::Scalar');
	
	use_ok('Bio::Tools::CodonTable');
	use_ok('Bio::SeqIO::table');
}

my @names = qw(A6
               A6r
               A6ps1
               A6ps2
               CaMK2d
               CaMKK2
               AMPKa1
               AMPKa2
               MARK3
               MARK2);
my @accs = qw(SK001
              SK512
              SK752
              SK766
              SK703
              SK482
              SK032
              SK033
              SK096
              SK120);
my @num_anns = (5, 5, 5, 5, 6, 7, 7, 7, 7, 7);
my @psg = (0, 0, 1, 1, 0, 0, 0, 0, 0, 0);
my @rs = (0, 0, 0, 0, 1, 1, 1, 1, 1, 1);

ok my $seqin = Bio::SeqIO->new(-file => test_input_file("test.tsv"),
			    -format  => 'table',
                            -species => "Homo sapiens",
                            -delim   => "\t",
                            -header  => 1,
                            -display_id => 1,
                            -accession_number => 2,
                            -seq => 7,
                            -annotation => 1,
                            -trim => 1);
run_tests([@names],[@accs],[@num_anns],[@psg],[@rs]);

$seqin->close();

ok $seqin = Bio::SeqIO->new(-file => test_input_file("test.tsv"),
                         -format  => 'table',
                         -species => "Homo sapiens",
                         -delim   => "\t",
                         -header  => 1,
                         -display_id => 1,
                         -accession_number => 2,
                         -seq => 7,
                         -colnames => "[Family,Subfamily,Pseudogene?,Protein,Novelty]",
                         -trim => 1);
run_tests([@names],[@accs],[4,4,4,4,4,5,5,5,5,5],[@psg],[@rs]);

$seqin->close();

ok $seqin = Bio::SeqIO->new(-file => test_input_file("test.tsv"),
                         -format  => 'table',
                         -species => "Homo sapiens",
                         -delim   => "\t",
                         -header  => 1,
                         -display_id => 1,
                         -accession_number => 2,
                         -seq => 7,
                         -annotation => "[4,5,6,8,10]",
                         -trim => 1);
run_tests([@names],[@accs],[4,4,4,4,4,5,5,5,5,5],[@psg],[@rs]);

# Tests to check that 'description' is read from 'table' format
ok $seqin = Bio::SeqIO->new(
    -file   => test_input_file("test-1.tab"),
    -format => 'table',
    -header => 1,
    -display_id => 1, 
    -accession_number => 1, 
    -seq => 3, 
    -desc => 2
);
ok($seqin);
my $seq = $seqin->next_seq;
ok($seq);
is( $seq->desc, 'd1');
is( $seq->display_id, 'n1');
is( $seq->seq, 'aaaa');
$seq = $seqin->next_seq;
ok($seq);
is( $seq->desc, 'd2');
is( $seq->display_id, 'n2');
is( $seq->seq, 'tttt');

$seqin->close();

# Tests to check that we can _not_ write to 'table' format
ok $seqin = Bio::SeqIO->new(
    -file   => test_input_file("test-1.tab.gb"),
    -format => 'genbank'
);
ok($seqin);
my $seq = $seqin->next_seq;
ok($seq);
my $tmpfile = test_output_file();
my $seqout = Bio::SeqIO->new( -format => 'table', -file => ">$tmpfile" );
# dies_ok not available
# dies_ok { $seqout->write_seq($seq) } "write_seq() not implemented";

# Need Spreadsheet::ParseExcel installed for testing Excel format
SKIP: {
	test_skip(-tests => 112, -requires_module => 'Spreadsheet::ParseExcel');

	ok $seqin = Bio::SeqIO->new(-file => test_input_file("test.xls"),
							 -format  => 'excel',
							 -species => "Homo sapiens",
							 -header  => 1,
							 -display_id => 1,
							 -accession_number => 2,
							 -seq => 7,
							 -annotation => 1,
							 -trim => 1);
	run_tests([@names],[@accs],[@num_anns],[@psg],[@rs]);
	
	$seqin->close();
}

sub run_tests {
    my ($names_,$accs_,$num_anns_,$psg_,$rs_) = @_;

    my @names = @$names_;
    my @accs = @$accs_;
    my @num_anns = @$num_anns_;
    my @psg = @$psg_;
    my @rs = @$rs_;

    my $n = 0;
    my $translator = Bio::Tools::CodonTable->new(-id => 1);
    while (my $seq = $seqin->next_seq()) {
        $n++;
        is ($seq->display_id, shift(@names));
        is ($seq->accession_number, shift(@accs));
        ok ($seq->species);
        is ($seq->species->binomial, "Homo sapiens");
        my @anns = $seq->annotation->get_Annotations();
        is (scalar(@anns), shift(@num_anns));
        @anns = grep { $_->value eq "Y"; 
                     } $seq->annotation->get_Annotations("Pseudogene?");
        is (scalar(@anns), shift(@psg));
        
        # check sequences and that they translate to what we expect
        if (($n >= 5) && ($seq->display_id ne "MARK3")) {
            my $dna = $seq->seq;
            my $protein = "";
            my $frame = 0;
            while ($frame <= 2) {
                my $inframe = substr($dna,$frame);
                # translate to protein
                my $protseq = $translator->translate($inframe);
                # chop off everything after the stop and before the first Met
                while ($protseq =~ /(M[^\*]+)/g) {
                    $protein = $1 if length($1) > length($protein);
                }
                $frame++;
            }
            # retrieve expected result from annotation and compare
            my ($protann) = $seq->annotation->get_Annotations("Protein");
            ok (defined $protann);
            is ($protein, $protann->value);
        }
        
        @anns = grep { $_->value eq "Known - Refseq"; 
                     } $seq->annotation->get_Annotations("Novelty");
        is (scalar(@anns), shift(@rs));
        @anns = $seq->annotation->get_Annotations("Subfamily");
        is (scalar(@anns), ($n <= 5) ? 0 : 1);
        @anns = $seq->annotation->get_Annotations("Family");
        is (scalar(@anns), 1);
        is (substr($anns[0]->value,0,4), ($n <= 4) ? "A6" : "CAMK");    
    }
    
    is ($n, 10);
}
BioPerl-1.007002/t/SeqIO/tigr.t000444000766000024       235613155576321 16077 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests               => 8,
			   -requires_module     => 'Error',
			   -requires_networking => 0,
			  );
	
	use_ok('Bio::SeqIO::tigr');
}

my $verbose = test_debug();

TODO: {
	my $format = 'tigr';
	todo_skip "No tests for $format format -- no sample file to test against", 7, if 1;

	my $seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test.$format"),
							        -format => $format);
	
	isa_ok($seqio_obj, 'Bio::SeqIO');
	
	my @methods = qw(next_seq write_seq);
	foreach my $method (@methods) {
		can_ok($seqio_obj, $method) || 
			diag "$method method not implemented for $format";	
	}
	
	# checking the first sequence object
	my $seq_obj = $seqio_obj->next_seq();
	isa_ok($seq_obj, 'Bio::Seq');
	my %expected = ('seq'         => '' .
					'length'      => '',
					'primary_id'  => '',
					'description' => qr(),
				   );
	is   ($seq_obj->seq(),         $expected{'seq'},         'sequence');
	is   ($seq_obj->length(),      $expected{'length'},      'length');
	is   ($seq_obj->primary_id(),  $expected{'primary_id'},  'primary_id');
	like ($seq_obj->description(), $expected{'description'}, 'description');
}BioPerl-1.007002/t/SeqIO/tigrxml.t000444000766000024       473513155576321 16623 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 49,
			   -requires_modules => [qw(XML::SAX XML::SAX::Writer)]);
	
	use_ok('Bio::SeqIO::tigrxml');
}

my $verbose = test_debug();

my $ast = Bio::SeqIO->new(-format => 'tigrxml' ,
			  -verbose => $verbose,
			  -file => test_input_file('test.tigrxml'));
isa_ok($ast, 'Bio::SeqIO');
$ast->verbose($verbose);
ok my $as = $ast->next_seq();
is($as->display_id, 'chr9');

my $first = 1;
for my $f ( sort { $a->start * $a->strand <=> $b->start * $b->strand } $as->get_SeqFeatures ) {
    ok($f);

    my ($name);
    for my $tag ( qw(Parent ID) ) {
	if( $f->has_tag($tag) ) {
	    ($name) = $f->get_tag_values($tag);
	    last;
	}
    }
    if( $name eq '162.t00500' || $name eq '162.m02638' ) {
	if( $f->primary_tag eq 'gene' ) {
	    is($f->start, 185408);
	    is($f->end, 187155);
	    # warn($f->gff_string, "\n");
	} elsif( $f->primary_tag eq 'mRNA' ) { 
	    is($f->start, 185408); # the values list for COORD are start/end of CDS not whole transcript
	    is($f->end, 187155);    
	    is($f->strand, 1);
	} elsif( $f->primary_tag eq "five_prime_UTR" ) {
	    my ($id) = $f->get_tag_values('ID');
	    if( $id =~ /UTR1$/ ) {
		is($f->start, 185408);
		is($f->end,   185433);
	    } elsif( $id =~ /UTR2$/ ) {
		is($f->start, 185487);
		is($f->end,   185793);
	    } else {
		ok(0, 'expected only two UTRS');
	    }	    
	} elsif( $f->primary_tag eq "three_prime_UTR" ) {
	    is($f->start, 187042);
	    is($f->end, 187155);
	} elsif( $f->primary_tag eq 'CDS' ) {
	    is($f->start, 185794);
	    is($f->end, 187041);
	}
    } elsif ( $name eq '162.t00448' || $name eq '162.m02967' ) {
	if( $f->primary_tag eq 'gene' ) {
	    is($f->start, 59343);
	    is($f->end, 61061);
	} elsif( $f->primary_tag eq 'mRNA' ) { 
	    is($f->start, 59343); # the values list for COORD are start/end of CDS not whole transcript
	    is($f->end, 61061);    
	    is($f->strand, -1);
	} elsif( $f->primary_tag eq "five_prime_UTR" ) {
	    my ($id) = $f->get_tag_values('ID');
	    is($f->start, 60834);
	    is($f->end, 61061);
	    is($f->strand, -1);
	} elsif( $f->primary_tag eq "three_prime_UTR" ) {
	    is($f->start, 59343);
	    is($f->end,   59632);
	    is($f->strand, -1);
	} elsif( $f->primary_tag eq 'CDS' ) {
	    if( $first ) { 
		is($f->start, 60801);
		is($f->end,   60833);
		is($f->strand, -1);
		$first = 0;
	    }
	}
    } else { 
	ok(0, "unexpected name '$name'\n");
    }
}
BioPerl-1.007002/t/SeqIO/tinyseq.t000555000766000024       226313155576321 16626 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 16,
               -requires_modules => [qw(XML::Parser::PerlSAX XML::Writer)]);

    use_ok('Bio::SeqIO::tinyseq');
}

my $file    = test_input_file('test.tseq');
my $outfile = test_output_file();

my $instream = Bio::SeqIO->new( -file    => $file,
                                -format  => 'tinyseq' );

my $outstream = Bio::SeqIO->new( -file   => ">$outfile",
                                 -format => 'tinyseq' );

my $seq = $instream->next_seq;
ok(defined $seq);
ok(defined $seq->seq);
is($seq->length, 5830);
is($seq->accession_number,'NM_002253');
ok($seq->species);
is($seq->species->binomial, 'Homo sapiens');
is($seq->species->ncbi_taxid, 9606);
$outstream->write_seq($seq);
undef $outstream;

ok(-s $outfile);

my $reread = Bio::SeqIO->new( -file   => $outfile,
                              -format => 'tinyseq' );

my $seq2 = $reread->next_seq;

ok($seq2);
ok($seq2->seq);
is($seq2->length, 5830);
is($seq2->accession_number, 'NM_002253');
ok($seq2->species);
is($seq2->species->binomial, 'Homo sapiens');
is($seq2->species->ncbi_taxid, 9606);
BioPerl-1.007002/t/SeqIO/ztr.t000444000766000024       277513155576321 15756 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 3,
			   -requires_module => 'Bio::SeqIO::staden::read');
	
	use_ok('Bio::SeqIO::ztr');
}

my $verbose = test_debug();

my $io = Bio::SeqIO->new(-format => 'ztr',
			 -verbose => $verbose,
			 -file => test_input_file('test.ztr'));
ok(my $seq = $io->next_seq);
is($seq->seq, "GATGATTCCGGCTTCGGACGACTCTAGAGGATCCCCATTTTTATAGTTTTTATCTTGTAATAGATGTTTAGATTTTTCGTTGTAATTATTTTCTTTATTGTTGAAATTAGTATCTCTGGGTAATTTATCATATTCTCTGGAAAATGATTTACTATCACTAGATACTTCATAAGATTTATAATCTTTATTATGAAAATCATCTCTATTTTTCAAATTATTATTATATCTATCAAAGTTTCTGTCTTCATTATATCTATTAGCATATCTATCTTTATCTTTATCCCTATCACTATATCTATCATATGGTTCATCTTGTTCAACCGATCAGACTCGATTCGCCATCGCCTCTAACGGATGGCCGCTCCCCCTCTCATACCTCGCTCCCCTCGACATCCCCCGTCTCGCCACCCTATCCGCCCCCTTCATCACCCCCCCTTATCCACACCCTCACCCCCCGCATCGCGCACCCACGACCACCCGAAGAACCGCCCTTACTCCCAAGTACGCCCCGACCTCCATCACCCTATGCGGTACCACTCCCACCACACCCAGTCCTACTTTCGCCCGCACATCGGCCCCGCTTCAGACAGCTCCCAACTACGCAACCCACGCTTGTTCTTGTTCACACTCGAATACTCGAATCTCTCATTACTCCGCGGACTCCGCCGCACCTGTGCACCATTAACTGTGTAGCGCCTGAACCGGCACCTCTGATTACCACTTCCTCCACCAGCACAGTCCTATTACCGCATGTCGCTCTGCTAAGACAGTGCAAGACTCTGCGGTCGCTCTGACCCGCATCCGCCAGGGCACCTCTCACCCTCGCTGGCCACCCCGCCCCCCTCTCCCTGCCCCTTCATTCCCCCAAACCGCTTTCAACGGGACACACCCCTCCGCGGCGGACCACAACTCGCCGTCGGCCACCACTCACACCTTCCCTCCTCCTTCCCCCACATCACGCCAACCCCGTGGGACGGCTCTCCCGCGGCTACGACGCGCAACCCCCCCTCGCCGCTTCCCCCCCAACTTCCCACGGGCTCCCCTCCGCCCCTTACCCGCGAGGAGCTTCACCCGCGAACCACCTCCCCCCTTTCCCAACAGCACCG");
BioPerl-1.007002/t/SeqTools000755000766000024          013155576321 15373 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/SeqTools/Backtranslate.t000444000766000024       141613155576321 20475 0ustar00cjfieldsstaff000000000000use strict;
use warnings;

BEGIN {
    use Bio::Root::Test;
    test_begin( -tests => 8, -requires_module => 'List::MoreUtils');
}

use_ok 'Bio::Tools::SeqPattern::Backtranslate';

can_ok 'Bio::Tools::SeqPattern::Backtranslate', '_reverse_translate_motif';

my @data;
while () {
    chomp;
    push @data, [split];
}

foreach my $line (@data) {
    if ( $line->[1] ) {
        is _reverse_translate_motif( $line->[0] ), $line->[1];
    } else {
        throws_ok { _reverse_translate_motif( $line->[0] ) }
        qr/syntax token/;
    }
}

__DATA__
MAEELKAVAP ATGGCNGARGARYTNAARGCNGTNGCNCCN
LKGHB[WhYq]Q YTNAARGGNCAYRAYYRNCAR
(LK){2,3}[^GHB][WHYQ]Q (YTNAAR){2,3}HBNYRNCAR
LK[^GHB][WHYQ]Q YTNAARHBNYRNCAR
(LK){2,3}[^GHB][WHYQ]QX.X (YTNAAR){2,3}HBNYRNCARNNNNNNNNN
/&%/&%(/)(/%
BioPerl-1.007002/t/SeqTools/CodonTable.t000444000766000024      2021613155576321 17750 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 84);

    use_ok('Bio::Tools::CodonTable');
    use_ok('Bio::CodonUsage::IO');
}

# create a table object by giving an ID
my $DEBUG = test_debug();
my $myCodonTable = Bio::Tools::CodonTable -> new ( -id => 16);
ok defined $myCodonTable;
isa_ok $myCodonTable, 'Bio::Tools::CodonTable';

# defaults to ID 1 "Standard"
$myCodonTable = Bio::Tools::CodonTable->new();
is $myCodonTable->id(), 1;

# invalid table should produce a warn and set default table (1)
my $stderr = '';
{
    # capture stderr output
    local *STDERR;
    open STDERR, '>', \$stderr;
    $myCodonTable->id(99);
}
like $stderr, qr/Not a valid codon table ID/;
is $myCodonTable->id, 1;

# change codon table
$myCodonTable->id(10);
is $myCodonTable->id, 10;
is $myCodonTable->name(), 'Euplotid Nuclear';

# enumerate tables as object method
my $table = $myCodonTable->tables();
cmp_ok (keys %{$table}, '>=', 19); # currently 19 known tables
is $table->{11}, 'Bacterial, Archaeal and Plant Plastid';

# enumerate tables as class method
$table = Bio::Tools::CodonTable->tables;
cmp_ok (values %{$table}, '>=', 19); # currently 19 known tables
is $table->{23}, 'Thraustochytrium Mitochondrial';

# translate codons
$myCodonTable->id(1);

eval {
    $myCodonTable->translate();
};
ok ($@ =~ /EX/) ;

# Automatically completing translation of incomplete codons is no longer default
# behavior b/c of inconsistent behavior compared with Bio::PrimarySeq::translate
# and unexpected side effects (e.g. what if the last few bases isn't supposed to
# be translated). To re-establish this, pass a second argument to the method.

is $myCodonTable->translate(''), '';

my @ii  = qw(ACT acu ATN gt ytr sar);
my @res = qw(T   T   X   V  L   Z  );
my $test = 1;
for my $i (0..$#ii) {
    if ($res[$i] ne $myCodonTable->translate($ii[$i], 1) ) {
        $test = 0;
        print $ii[$i], ": |", $res[$i], "| ne |",
        $myCodonTable->translate($ii[$i], 1), "|\n" if( $DEBUG);
        last ;
    }
}
ok ($test);
is $myCodonTable->translate('ag'), '';
is $myCodonTable->translate('ag',1), '';

is $myCodonTable->translate('jj'), '';
is $myCodonTable->translate('jj',1), '';

is $myCodonTable->translate('jjg'), 'X';
is $myCodonTable->translate('jjg',1), 'X';

is $myCodonTable->translate('gt'), '';
is $myCodonTable->translate('gt',1), 'V';

is $myCodonTable->translate('g'), '';
is $myCodonTable->translate('g',1), '';

# a more comprehensive test on ambiguous codes
my $seq = <translate($ii[$i]) ) {
        $test = 0;
        print $ii[$i], ": |", $res[$i], "| ne |",
        $myCodonTable->translate($ii[$i]),  "| @ $i\n" if( $DEBUG);
        last ;
    }
}
ok $test;

# reverse translate amino acids

is $myCodonTable->revtranslate('U'), 0;
is $myCodonTable->revtranslate('O'), 0;
is $myCodonTable->revtranslate('J'), 9;
is $myCodonTable->revtranslate('I'), 3;
my @RNA_codons = $myCodonTable->revtranslate('M', 'RNA');
is $RNA_codons[0], 'aug'; # test RNA output

@ii = qw(A l ACN Thr sER ter Glx);
@res = (
    [qw(gct gcc gca gcg)],
    [qw(ggc gga ggg act acc aca acg)],
    [qw(tct tcc tca tcg agt agc)],
    [qw(act acc aca acg)],
    [qw(tct tcc tca tcg agt agc)],
    [qw(taa tag tga)],
    [qw(gaa gag caa cag)]
    );

$test = 1;
 TESTING: {
     for my $i (0..$#ii) {
         my @codonres = $myCodonTable->revtranslate($ii[$i]);
         for my $j (0..$#codonres) {
             if ($codonres[$j] ne $res[$i][$j]) {
                 $test = 0;
                 print $ii[$i], ': ', $codonres[$j], " ne ",
                 $res[$i][$j], "\n" if( $DEBUG);
                 last TESTING;
             }
         }
     }
 }
ok $test;

# boolean tests
$myCodonTable->id(1); # Standard table

ok $myCodonTable->is_start_codon('ATG'), 'is_start_codon, ATG';
is $myCodonTable->is_start_codon('GGH'), 0, 'is_start_codon, GGH';
ok $myCodonTable->is_start_codon('HTG'), 'is_start_codon, HTG';
is $myCodonTable->is_start_codon('CCC'), 0, 'is_start_codon, CCC';

ok $myCodonTable->is_ter_codon('UAG'), 'is_ter_codon, U should map to T, UAG';
ok $myCodonTable->is_ter_codon('TaG'), 'is_ter_codon,TaG';
ok $myCodonTable->is_ter_codon('TaR'), 'is_ter_codon,TaR';
ok $myCodonTable->is_ter_codon('tRa'), 'is_ter_codon,tRa';
is $myCodonTable->is_ter_codon('ttA'), 0, 'is_ter_codon,ttA';

# Ambiguous codons should fail
is $myCodonTable->is_ter_codon('NNN'), 0, 'is_ter_codon, ambiguous codons should fail, NNN';
is $myCodonTable->is_ter_codon('TAN'), 0, 'is_ter_codon, ambiguous codons should fail, TAN';
is $myCodonTable->is_ter_codon('CC'), 0, 'is_ter_codon, incomplete codons should fail, CC';

ok $myCodonTable->is_unknown_codon('jAG');
ok $myCodonTable->is_unknown_codon('jg');
is $myCodonTable->is_unknown_codon('UAG'), 0;

is $myCodonTable->translate_strict('ATG'), 'M';

#
# adding a custom codon table
#

my @custom_table =
    ( 'test1',
      'FFLLSSSSYY**CC*WLLLL**PPHHQQR*RRIIIMT*TT*NKKSSRRV*VVAA*ADDEE*GGG'
    );

ok my $custct = $myCodonTable->add_table(@custom_table);
is $custct, 26;
is $myCodonTable->translate('atgaaraayacmacracwacka'), 'MKNTTTT';
ok $myCodonTable->id($custct);
is $myCodonTable->translate('atgaaraayacmacracwacka'), 'MKXXTTT';

# test doing this via Bio::PrimarySeq object

use Bio::PrimarySeq;
ok $seq = Bio::PrimarySeq->new(-seq=>'atgaaraayacmacracwacka', -alphabet=>'dna');
is $seq->translate()->seq, 'MKNTTTT';
is $seq->translate(undef, undef, undef, undef, undef, undef, $myCodonTable)->seq, 'MKXXTTT';

# test gapped translated

ok $seq = Bio::PrimarySeq->new(-seq      => 'atg---aar------aay',
                               -alphabet => 'dna');
is $seq->translate->seq, 'M-K--N';

ok $seq = Bio::PrimarySeq->new(-seq =>'ASDFGHKL');
is $myCodonTable->reverse_translate_all($seq), 'GCBWSNGAYTTYGGVCAYAARYTN';
ok $seq = Bio::PrimarySeq->new(-seq => 'ASXFHKL');
is $myCodonTable->reverse_translate_all($seq), 'GCBWSNNNNTTYCAYAARYTN';

#
# test reverse_translate_best(), requires a Bio::CodonUsage::Table object
#

ok $seq = Bio::PrimarySeq->new(-seq =>'ACDEFGHIKLMNPQRSTVWYX');
ok my $io = Bio::CodonUsage::IO->new(-file => test_input_file('MmCT'));
ok my $cut = $io->next_data();
is $myCodonTable->reverse_translate_best($seq,$cut), 'GCCTGCGACGAGTTCGGCCACATCAAGCTGATGAACCCCCAGCGCTCCACCGTGTGGTACNNN';
is $myCodonTable->reverse_translate_all($seq, $cut, 15), 'GCNTGYGAYGARTTYGGVCAYATYAARCTSATGAAYCCNCARMGVWSYACHGTSTGGTAYNNN';

#
# test 'Strict' table, requires a Bio::CodonUsage::Table object
#

$myCodonTable = Bio::Tools::CodonTable->new(); # Default Standard table

#  boolean tests
is $myCodonTable->is_start_codon('ATG'), 1;
is $myCodonTable->is_start_codon('GTG'), 0;
is $myCodonTable->is_start_codon('TTG'), 1;
is $myCodonTable->is_start_codon('CTG'), 1;
is $myCodonTable->is_start_codon('CCC'), 0;

$myCodonTable->id(0); # Special 'Strict' table (ATG-only start)

is $myCodonTable->is_start_codon('ATG'), 1;
is $myCodonTable->is_start_codon('GTG'), 0;
is $myCodonTable->is_start_codon('TTG'), 0;
is $myCodonTable->is_start_codon('CTG'), 0;
is $myCodonTable->is_start_codon('CCC'), 0;

# Pterobranchia Mitochondrial codon table
$myCodonTable->id(24);
is $myCodonTable->is_start_codon('GTG'), 1;
is $myCodonTable->is_start_codon('CTG'), 1;
is $myCodonTable->translate_strict('TGA'), 'W';

# Candidate Division SR1 and Gracilibacteria codon table
$myCodonTable->id(25);
is $myCodonTable->is_start_codon('GTG'), 1;
is $myCodonTable->is_start_codon('CTG'), 0;
is $myCodonTable->translate_strict('TGA'), 'G';
BioPerl-1.007002/t/SeqTools/ECnumber.t000444000766000024       307013155576321 17415 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 27);
	
    use_ok('Bio::Tools::ECnumber');
}



my $EC1 = Bio::Tools::ECnumber->new( -ec_string => " EC  01. 02.03.00022  ",
                                     -comment   => "is 1.2.3.22" );


my $EC2 = Bio::Tools::ECnumber->new( -ec_string => "ec:1.2.3.-",
                                     -comment   => "is 1.2.3.-" );


my $EC3 = $EC1->copy();

isa_ok( $EC1,"Bio::Tools::ECnumber" );

isa_ok( $EC3,"Bio::Tools::ECnumber");

is( $EC1->EC_string(), "1.2.3.22" );

is( $EC1->EC_string(), "1.2.3.22" );

is( $EC1->to_string(), "1.2.3.22" );

is( $EC1->comment(),   "is 1.2.3.22" );

is( $EC1->enzyme_class(), "1" );

is( $EC1->sub_class(), "2" );

is( $EC1->sub_sub_class(), "3" );

is( $EC1->serial_number(), "22" );

ok( $EC3->is_equal( $EC1 ) );

ok( $EC3->is_equal( "1.2.3.22" ) );

ok( ! $EC3->is_equal( "1.2.3.-" ) );

ok( ! $EC3->is_equal( "1.2.3.23" ) );

ok( $EC1->is_member( $EC2 ) );

ok( $EC1->is_member( "1.2.3.-" ) );

$EC1->init();

ok( $EC2->is_member( $EC1 ) );

is( $EC1->to_string(), "-.-.-.-" );

$EC1->enzyme_class( 44 );

$EC1->sub_class( "033" );

$EC1->sub_sub_class( 22 );

$EC1->serial_number( "-" );

is( $EC1->to_string(), "44.33.22.-" );

ok( ! $EC1->is_member( "44.33.23.-" ) );

ok( ! $EC1->is_member( "44.33.22.1" ) );

ok( $EC1->is_member( "-.-.-.-" ) );

ok( $EC1->is_member( "44.-.-.-" ) );

ok( $EC1->is_member( "44.33.-.-" ) );

ok( $EC1->is_member( "EC 44.33.22.-" ) );

ok( ! $EC1->is_member( "45.33.22.-" ) );
BioPerl-1.007002/t/SeqTools/GuessSeqFormat.t000444000766000024       562013155576321 20630 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
   
    test_begin(-tests => 105);
   
    use_ok 'Bio::Tools::GuessSeqFormat';
    use_ok 'Bio::SeqIO';
    use_ok 'Bio::AlignIO';
}


ok my $guesser = Bio::Tools::GuessSeqFormat->new;
isa_ok $guesser, 'Bio::Tools::GuessSeqFormat';


#
# Test guesser interfaces
#

# 1/ File guess
ok $guesser = Bio::Tools::GuessSeqFormat->new(
    -file => test_input_file('test.fasta'),
), 'File input';
is $guesser->guess, 'fasta';

# 2/ String guess
my $string = ">test1 no comment
agtgctagctagctagctagct
>test2 no comment
gtagttatgc
";
ok $guesser = Bio::Tools::GuessSeqFormat->new(
    -text => $string,
), 'String input';
is $guesser->guess, 'fasta';

# 3/ Filehandle guess
SKIP: {
    test_skip(-tests => 2, -requires_modules => [qw(IO::String)]);
    require IO::String;
    my $fh = IO::String->new($string);
    ok $guesser = Bio::Tools::GuessSeqFormat->new(
        -fh => $fh,
    ), 'Filehandle input';
    is $guesser->guess, 'fasta';
}


#
# Test behavior with unknown format
#

is $guesser = Bio::Tools::GuessSeqFormat->new(
    -file => test_input_file('test.waba'), # Bio::SearchIO::waba
)->guess, undef, 'Unknown file format';

throws_ok {
    Bio::SeqIO->new( -file=>test_input_file('test.waba') );
} qr/Could not guess format/;


#
# Test SeqIO formats
#

my @fmts = qw{ace embl fasta fastq game gcg genbank pir raw swiss tab};

for my $fmt (@fmts) {
    SKIP: {
        test_skip(
            -tests => 4,
            -requires_modules => [qw(XML::Writer XML::Parser::PerlSAX)]
        ) if $fmt eq 'game';
        test_skip(
            -tests => 4,
            -requires_module  => 'Data::Stag'
        ) if $fmt eq 'swiss';

        my $guess = Bio::Tools::GuessSeqFormat->new(
            -file => test_input_file("test.$fmt"),
        )->guess;
        is $guess, $fmt, "$fmt format";

        ok my $input = Bio::SeqIO->new( -file=>test_input_file("test.$fmt") );
        ok my $seq = $input->next_seq();
        isa_ok $seq, 'Bio::PrimarySeqI';
    }
}


#
# Test AlignIO formats
#

@fmts = qw{clustalw fasta fastq mase mega msf nexus pfam phylip prodom selex stockholm};
my %skip_module = map {$_=>1} qw{ fastq };

for my $fmt (@fmts) {
    my $guess = Bio::Tools::GuessSeqFormat->new(
        -file => test_input_file("testaln.$fmt")
    )->guess;
    is $guess, $fmt, "$fmt format";
    next if $skip_module{$fmt};

    ok my $input = Bio::AlignIO->new( -file=>test_input_file("testaln.$fmt") );
    ok my $seq = $input->next_aln();
    isa_ok $seq, 'Bio::Align::AlignI';
}


#
# Other formats
#

my %fmts = (
   blast    => test_input_file('blastp2215.blast'),
   gcgblast => test_input_file('test.gcgblast'),
   vcf      => test_input_file('example.vcf'),
);

while (my ($fmt, $file) = each %fmts) {
    my $guess = Bio::Tools::GuessSeqFormat->new(
        -file => $file,
    )->guess;
    is $guess, $fmt, "$fmt format";
}
BioPerl-1.007002/t/SeqTools/OddCodes.t000444000766000024       173013155576321 17402 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 11);
	
	use_ok('Bio::PrimarySeq');
	use_ok('Bio::Tools::OddCodes');
}

my ($seqobj, $oddcode_obj);

$seqobj = Bio::PrimarySeq->new('-seq'=>'ABCDEFGHIJKLMNOPQRSTUVWXYZ',
			       '-alphabet'=>'protein', 
			       '-id'=>'test');
$oddcode_obj  =  Bio::Tools::OddCodes->new('-seq' => $seqobj);

isa_ok $oddcode_obj, 'Bio::Tools::OddCodes';

is ${$oddcode_obj->structural()}, 'ABAEEIAEIJEIIEOAEEAAUIAXAZ';
is ${$oddcode_obj->chemical()}, 'LBSAARLCLJCLSMOIMCHHULRXRZ';
is ${$oddcode_obj->functional()}, 'HBPAAHPCHJCHHPOHPCPPUHHXPZ';
is ${$oddcode_obj->charge()}, 'NBNAANNCNJCNNNONNCNNUNNXNZ';
is ${$oddcode_obj->hydrophobic()}, 'IBOOOIOOIJOIIOOIOOOOUIIXOZ';
is ${$oddcode_obj->Dayhoff()}, 'CBADDGCEFJEFFDOCDECCUFGXGZ';
is ${$oddcode_obj->Sneath()}, 'CBEFFHCHAJGADDOCDGEEUAHXHZ';
is ${$oddcode_obj->Stanfel()}, 'ABACCDAEAJEAACOACEAAUADXDZ';
BioPerl-1.007002/t/SeqTools/SeqPattern.t000444000766000024       435113155576321 20006 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 28);
	
	use_ok('Bio::Tools::SeqPattern');
}

my ( $pattern,$pattern_obj,$pattern_obj2, $pattern_obj3);

$pattern     = '(CCCCT)N{1,200}(agyyg)N{1,80}(ag)';
ok $pattern_obj = Bio::Tools::SeqPattern->new(-SEQ =>$pattern, -TYPE =>'dna');
isa_ok $pattern_obj, 'Bio::Tools::SeqPattern';

$pattern_obj2  = $pattern_obj->revcom();
is $pattern_obj2->str, '(CT)N(CRRCT){1,80}N(AGGGG){1,200}';

$pattern_obj3 = $pattern_obj->revcom(1);
is $pattern_obj3->str, '(CT).{1,80}(C[GA][GA]CT).(AGGGG){1,200}';

$pattern     = '(CCCCT)N{1,200}(agyyg)N{1,80}(bb)'; # test protein object expand
ok $pattern_obj = Bio::Tools::SeqPattern->new(-SEQ =>$pattern, -TYPE =>'protein');
isa_ok $pattern_obj, 'Bio::Tools::SeqPattern';

is $pattern_obj2->expand, '(CT).(C[AG][AG]CT){1,80}.(AGGGG){1,200}';

# amino patterns

$pattern = 'ABZH';
$pattern_obj2 = Bio::Tools::SeqPattern->new(-SEQ =>$pattern, 
					   -TYPE =>'amino');
is $pattern_obj2->expand, 'A[EQ][DN]H';

SKIP: {
    test_skip(-tests => 19, -requires_module => 'List::MoreUtils');
    # Test reverse complement
    my $rev_pattern = $pattern_obj2->backtranslate;
    isa_ok $rev_pattern, 'Bio::Tools::SeqPattern';
    is $rev_pattern->str, 'GCNRAYSARCAY';

    # Test exceptions.
    throws_ok { $pattern_obj2->revcom  } qr/revcom for .+ sequence types/;
    throws_ok { $rev_pattern->backtranslate } qr/backtranslate for .+ sequence types/;

    # Test reverse translation more thoroughly
    
    my @data;
    while () {
       chomp;
       push @data, [ split ];
    }
    
    foreach my $line (@data) {
        my $pattern_obj = Bio::Tools::SeqPattern->new(
            -SEQ  => $line->[0],
            -TYPE => 'amino',
        );
    
        isa_ok $pattern_obj, 'Bio::Tools::SeqPattern';
    
        my $backtranslate = $pattern_obj->backtranslate;
        isa_ok $backtranslate, 'Bio::Tools::SeqPattern';
        is $backtranslate->str, $line->[1],
    }
}

__DATA__
MAEELKAVAP ATGGCNGARGARYTNAARGCNGTNGCNCCN
LKGHB[WhYq]Q YTNAARGGNCAYRAYYRNCAR
(LK){2,3}[^GHB][WHYQ]Q (YTNAAR){2,3}HBNYRNCAR
LK[^GHB][WHYQ]Q YTNAARHBNYRNCAR
(LK){2,3}[^GHB][WHYQ]QX.X (YTNAAR){2,3}HBNYRNCARNNNNNNNNN
BioPerl-1.007002/t/SeqTools/SeqStats.t000444000766000024      1064513155576321 17512 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SeqStats.t 11525 2007-06-27 10:16:38Z sendu $

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 47);
	
	use_ok('Bio::SeqIO');
	use_ok('Bio::Tools::SeqStats');
}

my ($seqobj, $count, $seqobj_stats, $wt);

my $str = Bio::SeqIO->new(-file=> test_input_file('multifa.seq'), '-format' => 'Fasta');
$seqobj = $str->next_seq();
ok defined $seqobj, 'new Bio::Root::IO object';

my $seq_stats  =  Bio::Tools::SeqStats->new('-seq' => $seqobj);
ok defined $seq_stats && $seq_stats, 'new Bio::Tools:SeqStats object';

# eg for DNA sequence
my $hash_ref = $seq_stats->count_monomers();  
is ( $hash_ref->{'A'}, 80 , 'count_monomers()');

$hash_ref = $seq_stats-> count_codons();  
ok defined $hash_ref && $hash_ref , 'count_codons()';

my $weight = $seq_stats->get_mol_wt();
ok defined $weight && $weight , 'get_mol_wt()' ;

$seqobj = Bio::PrimarySeq->new(-seq=>'ACTGTGGCGTCAACTG',
			       -alphabet=>'dna', -id=>'test');
ok $seqobj_stats = Bio::Tools::SeqStats->new(-seq=>$seqobj);
isa_ok $seqobj_stats, 'Bio::Tools::SeqStats';

$count = $seqobj_stats->count_monomers();  # for DNA sequence
is $count->{'A'}, 3;
is $count->{'C'}, 4;
is $count->{'G'}, 5;
is $count->{'T'}, 4;

$count = $seqobj_stats->count_codons();
is $count->{'ACT'}, 2;
is $count->{'GTG'}, 1;
is $count->{'GCG'}, 1;
is $count->{'TCA'}, 1;

$seqobj = Bio::PrimarySeq->new(-seq=>'ACTACTTCA', -alphabet=>'dna',
			       -id=>'test');
$seqobj_stats  =  Bio::Tools::SeqStats->new('-seq' => $seqobj);
$wt = $seqobj_stats->get_mol_wt();  # for DNA sequence
is &round($$wt[0]), 2738 ;

$seqobj = Bio::PrimarySeq->new(-seq=>'ACXACNNCA',
			       -alphabet=>'dna', -id=>'test');
$wt = Bio::Tools::SeqStats->get_mol_wt($seqobj);
is &round($$wt[0]), 2693;
is &round($$wt[1]), 2813;

$seqobj = Bio::PrimarySeq->new(-seq=>'ACTGTGGCGTCAACTG',
			       -alphabet=>'dna', -id=>'test');
$count = Bio::Tools::SeqStats->count_monomers($seqobj);  # for DNA sequence
is $count->{'A'}, 3;
is $count->{'C'}, 4;
is $count->{'G'}, 5;
is $count->{'T'}, 4;

# protein

$seqobj = Bio::PrimarySeq->new(-seq=>'MQSERGITIDISLWKFETSKYYVT',
                               -alphabet=>'protein', -id=>'test');
$seqobj_stats  =  Bio::Tools::SeqStats->new('-seq' => $seqobj);
$count = $seqobj_stats->count_monomers();  # for amino sequence
is $$count{'M'}, 1;
is $$count{'I'}, 3;
is $$count{'Y'}, 2;
is $$count{'T'}, 3;
$wt = Bio::Tools::SeqStats->get_mol_wt($seqobj);
is int $$wt[0], 2896;
is int $$wt[1], 2896;

# Issue 3185: https://redmine.open-bio.org/issues/3185

$seqobj = Bio::PrimarySeq->new(-seq=>'MQSERGITIDISLWKFETSKYYVT*',
                               -alphabet=>'protein', -id=>'test');
is($seqobj->seq, 'MQSERGITIDISLWKFETSKYYVT*');
$seqobj_stats  =  Bio::Tools::SeqStats->new('-seq' => $seqobj);
$wt = Bio::Tools::SeqStats->get_mol_wt($seqobj);
is int $$wt[0], 2896;
is int $$wt[1], 2896;

# selenocysteine
ok $seqobj = Bio::PrimarySeq->new(-seq=>'MQSERGITIDISLWKFETSKYYVT',
                                  -alphabet=>'protein');
$wt = Bio::Tools::SeqStats->get_mol_wt($seqobj);
is &round($$wt[0]), 2896 ;

# RNA

$seqobj = Bio::PrimarySeq->new(-seq=>'UYXUYNNYU', -alphabet=>'rna');
$wt = Bio::Tools::SeqStats->get_mol_wt($seqobj);
is &round($$wt[0]), 2768;
is &round($$wt[1]), 2891;

ok $seqobj = Bio::PrimarySeq->new(-seq=>'TGCCGTGTGTGCTGCTGCT', -alphabet=>'rna');
$wt = Bio::Tools::SeqStats->get_mol_wt($seqobj);
is &round($$wt[0]), 6104 ;

#
# hydropathicity aka "gravy" score
#

# normal seq (should succeed)
ok $seqobj = Bio::PrimarySeq->new(-seq=>'MSFVLVAPDMLATAAADVVQIGSAVSAGS',
                                  -alphabet=>'protein');
my $gravy = Bio::Tools::SeqStats->hydropathicity($seqobj);
is int($gravy*1000), 1224;  # check to nearest 0.1%

# ambiguous sequence (should fail)
ok $seqobj = Bio::PrimarySeq->new(-seq=>'XXXB**BS', -alphabet=>'protein');
eval { Bio::Tools::SeqStats->hydropathicity($seqobj) };
like $@, qr/ambiguous amino acids/i;

# empty sequence (should fail)
ok $seqobj = Bio::PrimarySeq->new(-seq=>'', -alphabet=>'protein');
eval { Bio::Tools::SeqStats->hydropathicity($seqobj) };
like $@, qr/hydropathicity not defined/i;

# DNA sequence (should fail)
ok $seqobj = Bio::PrimarySeq->new(-seq=>'GATTACA', -alphabet=>'dna');
eval { Bio::Tools::SeqStats->hydropathicity($seqobj) };
like $@, qr/only meaningful for protein/;


#
# Extra functions
#

# perl does not have an explicit rounding function
sub round { return int ((shift @_) + 0.5 ) }

BioPerl-1.007002/t/SeqTools/SeqUtils.t000444000766000024      6211213155576321 17510 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
#    use List::MoreUtils qw(uniq);
    use Bio::Root::Test;
    
    test_begin(-tests => 133);

    use_ok('Bio::PrimarySeq');
    use_ok('Bio::SeqUtils');
    use_ok('Bio::LiveSeq::Mutation');
    use_ok('Bio::SeqFeature::Generic');
    use_ok('Bio::Annotation::SimpleValue');
    use_ok('Bio::Annotation::Collection');
    use_ok('Bio::Annotation::Comment');
}

my ($seq, $util, $ascii, $ascii_aa, $ascii3);

# Entire alphabet now IUPAC-endorsed and used in GenBank (Oct 2006)          
$ascii =    'ABCDEFGHIJKLMNOPQRSTUVWXYZ';
$ascii_aa = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ';

$ascii3 = 
    'AlaAsxCysAspGluPheGlyHisIleXleLysLeuMetAsnPylProGlnArgSerThrSecValTrpXaaTyrGlx';

$seq = Bio::PrimarySeq->new('-seq'=> $ascii,
                            '-alphabet'=>'protein', 
                            '-id'=>'test');

# one letter amino acid code to three letter code
ok $util = Bio::SeqUtils->new();
is $util->seq3($seq), $ascii3;

#using anonymous hash
is (Bio::SeqUtils->seq3($seq), $ascii3); 
is (Bio::SeqUtils->seq3($seq, undef, ','), 
    'Ala,Asx,Cys,Asp,Glu,Phe,Gly,His,Ile,Xle,Lys,'.
    'Leu,Met,Asn,Pyl,Pro,Gln,Arg,Ser,Thr,Sec,Val,Trp,Xaa,Tyr,Glx');

$seq->seq('asd-KJJK-');
is (Bio::SeqUtils->seq3($seq, '-', ':'), 
    'Ala:Ser:Asp:Ter:Lys:Xle:Xle:Lys:Ter');

# three letter amino acid code to one letter code
ok (Bio::SeqUtils->seq3in($seq, 'AlaPYHCysAspGlu')); 
is $seq->seq, 'AXCDE';
is (Bio::SeqUtils->seq3in($seq, $ascii3)->seq, $ascii_aa);

#
# Tests for multiframe translations
#

$seq = Bio::PrimarySeq->new('-seq'=> 'agctgctgatcggattgtgatggctggatggcttgggatgctgg',
                            '-alphabet'=>'dna', 
                            '-id'=>'test2');

my @a = $util->translate_3frames($seq);
is scalar @a, 3;
#foreach $a (@a) {
#    print 'ID: ', $a->id, ' ', $a->seq, "\n";
#}

@a = $util->translate_6frames($seq);
is scalar @a, 6;
#foreach $a (@a) {
#    print 'ID: ', $a->id, ' ', $a->seq, "\n";
#}

#
# test for valid AA return
#

my @valid_aa = sort Bio::SeqUtils->valid_aa;
is(@valid_aa, 27);
is($valid_aa[1], 'A');

@valid_aa = sort Bio::SeqUtils->valid_aa(1);
is(@valid_aa, 27);
is ($valid_aa[1], 'Arg');

my %valid_aa = Bio::SeqUtils->valid_aa(2);
is keys %valid_aa, 54;
is($valid_aa{'C'}, 'Cys');
is( $valid_aa{'Cys'}, 'C');


#
# Mutate
#

my $string1 = 'aggt';
$seq = Bio::PrimarySeq->new('-seq'=> 'aggt',
                            '-alphabet'=>'dna',
                            '-id'=>'test3');

# point
Bio::SeqUtils->mutate($seq,
                      Bio::LiveSeq::Mutation->new(-seq => 'c',
                                                  -pos => 3
                                                 )
                     );
is $seq->seq, 'agct';

# insertion and deletion
my @mutations = (
                 Bio::LiveSeq::Mutation->new(-seq => 'tt',
                                             -pos => 2,
                                             -len => 0
                                            ),
                 Bio::LiveSeq::Mutation->new(-pos => 2,
                                             -len => 2
                                            )
);

Bio::SeqUtils->mutate($seq, @mutations);
is $seq->seq, 'agct';

# insertion to the end of the sequence
Bio::SeqUtils->mutate($seq,
                      Bio::LiveSeq::Mutation->new(-seq => 'aa',
                                                  -pos => 5,
                                                  -len => 0
                                                 )
                     );
is $seq->seq, 'agctaa';



#
# testing Bio::SeqUtils->cat
#

# PrimarySeqs

my $primseq1 = Bio::PrimarySeq->new(-id => 1, -seq => 'acgt', -description => 'master');
my $primseq2 = Bio::PrimarySeq->new(-id => 2, -seq => 'tgca');

Bio::SeqUtils->cat($primseq1, $primseq2);
is $primseq1->seq, 'acgttgca';
is $primseq1->description, 'master';

#should work for Bio::LocatableSeq
#should work for Bio::Seq::MetaI Seqs?


# Bio::SeqI

my $seq1 = Bio::Seq->new(-id => 1, -seq => 'aaaa', -description => 'first');
my $seq2 = Bio::Seq->new(-id => 2, -seq => 'tttt', -description => 'second');
my $seq3 = Bio::Seq->new(-id => 3, -seq => 'cccc', -description => 'third');


#  annotations
my $ac2 = Bio::Annotation::Collection->new();
my $simple1 = Bio::Annotation::SimpleValue->new(
                                                -tagname => 'colour',
                                                -value   => 'blue'
                                               ), ;
my $simple2 = Bio::Annotation::SimpleValue->new(
                                                -tagname => 'colour',
                                                -value   => 'black'
                                               ), ;
$ac2->add_Annotation('simple',$simple1);
$ac2->add_Annotation('simple',$simple2);
$seq2->annotation($ac2);

my $ac3 = Bio::Annotation::Collection->new();
my $simple3 = Bio::Annotation::SimpleValue->new(
                                                -tagname => 'colour',
                                                -value   => 'red'
                                               );
$ac3->add_Annotation('simple',$simple3);
$seq3->annotation($ac3);


ok (Bio::SeqUtils->cat($seq1, $seq2, $seq3));
is $seq1->seq, 'aaaattttcccc';
is scalar $seq1->annotation->get_Annotations, 3;


# seq features
my $ft2 = Bio::SeqFeature::Generic->new( -start => 1,
                                         -end => 4,
                                         -strand => 1,
                                         -primary => 'source',
                                         -tag     => {note => 'note2'},
                                       );


my $ft3 = Bio::SeqFeature::Generic->new( -start => 3,
                                         -end => 3,
                                         -strand => 1,
                                         -primary => 'hotspot',
                                         -tag     => {note => ['note3a','note3b'],
                                                      comment => 'c1'},
                                       );

$seq2->add_SeqFeature($ft2);
$seq2->add_SeqFeature($ft3);

my $seq1_length = $seq1->length;
ok (Bio::SeqUtils->cat($seq1, $seq2));
is $seq1->seq, 'aaaattttcccctttt';
is scalar $seq1->annotation->get_Annotations, 5;
is_deeply([uniq_sort(map{$_->get_all_tags}$seq1->get_SeqFeatures)], [sort qw(note comment)], 'cat - has expected tags');
is_deeply([sort map{$_->get_tagset_values('note')}$seq1->get_SeqFeatures], [sort qw(note2 note3a note3b)], 'cat - has expected tag values');
my @tags;
lives_ok {
  @tags = map{$_->get_tag_values(q(note))}$seq1->get_SeqFeatures ;
} 'cat - note tag transfered (no throw)';
cmp_ok(scalar(@tags),'==',3, 'cat - note tag values transfered (correct count)') ;
my ($ft3_precat) = grep ($_->primary_tag eq 'hotspot', $seq2->get_SeqFeatures);
is ($ft3_precat->start, 3, "get correct start of feature before 'cat'");
my ($ft3_cat) = grep ($_->primary_tag eq 'hotspot', $seq1->get_SeqFeatures);
is ($ft3_cat->start, 3+$seq1_length, "get correct start of feature after 'cat'");


my $protseq = Bio::PrimarySeq->new(-id => 2, -seq => 'MVTF'); # protein seq

throws_ok {
    Bio::SeqUtils->cat($seq1, $protseq);
} qr/different alphabets:/, 'different alphabets' ;


#
# evolve()
#

$seq = Bio::PrimarySeq->new('-seq'=> 'aaaaaaaaaa',
                            '-id'=>'test');



$util = Bio::SeqUtils->new(-verbose => 0);
ok my $newseq = $util->evolve($seq, 60, 4);

#  annotations

$seq2 = Bio::Seq->new(-id => 2, -seq => 'ggttaaaa', -description => 'second');
$ac3 = Bio::Annotation::Collection->new();
$simple3 = Bio::Annotation::SimpleValue->new(
                                                -tagname => 'colour',
                                                -value   => 'red'
                                            );
$ac3->add_Annotation('simple',$simple3);
$seq2->annotation($ac3);
$ft2 = Bio::SeqFeature::Generic->new( -start => 1,
                                      -end => 4,
                                      -strand => 1,
                                      -primary => 'source',
                                      -tag     => {note => 'note2'},
                                    );


$ft3 = Bio::SeqFeature::Generic->new( -start => 5,
                                      -end => 8,
                                      -strand => -1,
                                      -primary => 'hotspot',
                                      -tag     => {note => ['note3a','note3b'], 
                                                   comment => 'c1'},
                                    );

my $ft4 = Bio::SeqFeature::Generic->new(-primary => 'CDS');
$ft4->location(Bio::Location::Fuzzy->new(-start=>'<1',
					 -end=>5,
					 -strand=>-1));

$seq2->add_SeqFeature($ft2);
$seq2->add_SeqFeature($ft3);
$seq2->add_SeqFeature($ft4);

my $trunc=Bio::SeqUtils->trunc_with_features($seq2, 2, 7);
is $trunc->seq, 'gttaaa';
my @feat=$trunc->get_SeqFeatures;
is $feat[0]->location->to_FTstring, '<1..3';
is $feat[1]->location->to_FTstring, 'complement(4..>6)';
is $feat[2]->location->to_FTstring, 'complement(<1..4)';
is_deeply([uniq_sort(map{$_->get_all_tags}$trunc->get_SeqFeatures)], [sort qw(note comment)], 'trunc_with_features - has expected tags');
is_deeply([sort map{$_->get_tagset_values('note')}$trunc->get_SeqFeatures], [sort qw(note2 note3a note3b)], 'trunc_with_features - has expected tag values');

my $revcom=Bio::SeqUtils->revcom_with_features($seq2);
is $revcom->seq, 'ttttaacc';
my ($rf1) = $revcom->get_SeqFeatures('hotspot');
is $rf1->primary_tag, $ft3->primary_tag, 'primary_tag matches original feature...';
is $rf1->location->to_FTstring, '1..4', 'but tagged sf is now revcom';

my ($rf2) = $revcom->get_SeqFeatures('source');
is $rf2->primary_tag, $ft2->primary_tag, 'primary_tag matches original feature...';
is $rf2->location->to_FTstring, 'complement(5..8)', 'but tagged sf is now revcom';

my ($rf3) = $revcom->get_SeqFeatures('CDS');
is $rf3->primary_tag, $ft4->primary_tag, 'primary_tag matches original feature...';
is $rf3->location->to_FTstring, '4..>8', 'but tagged sf is now revcom';

is_deeply([uniq_sort(map{$_->get_all_tags}$revcom->get_SeqFeatures)], [sort qw(note comment)], 'revcom_with_features - has expected tags');
is_deeply([sort map{$_->get_tagset_values('note')}$revcom->get_SeqFeatures], [sort qw(note2 note3a note3b)], 'revcom_with_features - has expected tag values');
# check circularity
isnt($revcom->is_circular, 1, 'still not circular');
$seq3 = Bio::Seq->new(-id => 3, -seq => 'ggttaaaa', -description => 'third', -is_circular => 1);
is(Bio::SeqUtils->revcom_with_features($seq3)->is_circular, 1, 'still circular');


# delete, insert and ligate
# prepare some sequence objects
my $seq_obj = Bio::Seq->new( 
  -seq =>'aaaaaaaaaaccccccccccggggggggggtttttttttt',
  -display_id => 'seq1',
  -desc       => 'some sequence for testing'
); 
my $subfeat1 = Bio::SeqFeature::Generic->new(
  -primary_tag => 'sf1',
  -seq_id      => 'seq1',
  -start       => 2,
  -end         => 12
);

my $subfeat2 = Bio::SeqFeature::Generic->new(
  -primary_tag => 'sf2',
  -seq_id      => 'seq1',
  -start       => 14,
  -end         => 16
);
my $subfeat3 = Bio::SeqFeature::Generic->new(
  -primary_tag => 'sf3',
  -seq_id      => 'seq1',
  -start       => 21,
  -end         => 25
);

my $composite_feat1 = Bio::SeqFeature::Generic->new(
  -primary_tag => 'comp_feat1',
  -seq_id      => 'seq1',
  -start       => 2,
  -end         => 30
);
my $coll_sf = Bio::Annotation::Collection->new;
$coll_sf->add_Annotation(
  'comment', Bio::Annotation::Comment->new( '-text' => 'a comment on sf1')
);
$subfeat1->annotation($coll_sf);

$composite_feat1->add_SeqFeature( $subfeat1);
$composite_feat1->add_SeqFeature( $subfeat2);
$composite_feat1->add_SeqFeature( $subfeat3);
my $feature1 = Bio::SeqFeature::Generic->new(
  -primary_tag => 'feat1',
  -seq_id      => 'seq1',
  -start       => 2,
  -end         => 25
);
my $feature2 = Bio::SeqFeature::Generic->new(
  -primary_tag => 'feat2',
  -seq_id      => 'seq1',
  -start       => 15,
  -end         => 25,
  -strand      => -1,
);
my $feature3 = Bio::SeqFeature::Generic->new(
  -primary_tag => 'feat3',
  -seq_id      => 'seq1',
  -start       => 30,
  -end         => 40
);
my $feature4 = Bio::SeqFeature::Generic->new(
  -primary_tag => 'feat4',
  -seq_id      => 'seq1',
  -start       => 1,
  -end         => 10
);
my $feature5 = Bio::SeqFeature::Generic->new(
  -primary_tag => 'feat5',
  -seq_id      => 'seq1',
  -start       => 11,
  -end         => 20
);

my $feature6 = Bio::SeqFeature::Generic->new(
  -primary_tag => 'feat6',
  -seq_id      => 'seq1',
  -start       => 11,
  -end         => 25
);
$seq_obj->add_SeqFeature( $composite_feat1, $feature1, $feature2, $feature3, $feature4, $feature5, $feature6);

my $coll = Bio::Annotation::Collection->new;
$coll->add_Annotation(
  'comment', Bio::Annotation::Comment->new( '-text' => 'a comment on the whole sequence')
);
$seq_obj->annotation($coll);


my $fragment_obj = Bio::Seq->new( 
  -seq =>'atatatatat',
  -display_id => 'fragment1',
  -desc       => 'some fragment to insert'
); 
my $frag_feature1 = Bio::SeqFeature::Generic->new(
  -primary_tag => 'frag_feat1',
  -seq_id      => 'fragment1',
  -start       => 2,
  -end         => 4,
  -strand      => -1,
);
$fragment_obj->add_SeqFeature( $frag_feature1 );
my $frag_coll = Bio::Annotation::Collection->new;
$frag_coll->add_Annotation(
  'comment', Bio::Annotation::Comment->new( '-text' => 'a comment on the fragment')
);
$fragment_obj->annotation($frag_coll);

# delete
my $product;
lives_ok(
  sub {
    $product = Bio::SeqUtils->delete( $seq_obj, 11, 20 );
  },
  "No error thrown when deleting a segment of the sequence"
);

my ($seq_obj_comment) = $seq_obj->annotation->get_Annotations('comment');
my ($product_comment) = $product->annotation->get_Annotations('comment');
is( $seq_obj_comment, $product_comment, 'annotation of whole sequence has been moved to new molecule');

ok( 
  grep ($_ eq 'deletion of 10bp', 
    map ($_->get_tag_values('note'), 
      grep ($_->primary_tag eq 'misc_feature', $product->get_SeqFeatures)
    )
  ),
  "the product has an additional 'misc_feature' and the note specifies the lengths of the deletion'"
);

my ($composite_feat1_del) = grep ($_->primary_tag eq 'comp_feat1', $product->get_SeqFeatures);
ok ($composite_feat1_del, "The composite feature is still present");
isa_ok( $composite_feat1_del, 'Bio::SeqFeature::Generic');
isa_ok( $composite_feat1_del->location, 'Bio::Location::Split', "a composite feature that spanned the deletion site has been split up, Location");

is( $composite_feat1_del->get_SeqFeatures, 2, 'one of the sub-eatures of the composite feature has been deleted completely');
my ($subfeat1_del) = grep ($_->primary_tag eq 'sf1', $composite_feat1_del->get_SeqFeatures);
ok ($subfeat1_del, "sub-feature 1 of the composite feature is still present");
is ($subfeat1->end, 12, "the original end of sf1 is 12");
is ($subfeat1_del->end, 10, "after deletion, the end of sf1 is 1nt before the deletion site");
is ($subfeat1->location->end_pos_type, 'EXACT', 'the original end location of sf1 EXACT');

my ($subfeat1_comment) = $subfeat1->annotation->get_Annotations('comment');
my ($subfeat1_del_comment) = $subfeat1_del->annotation->get_Annotations('comment');
is( $subfeat1_comment, $subfeat1_del_comment, 'annotation of subeature 1 has been moved to new molecule');

my ($feature1_del) = grep ($_->primary_tag eq 'feat1', $product->get_SeqFeatures);
ok ($feature1_del, "feature1 is till present");
isa_ok( $feature1_del->location, 'Bio::Location::Split', 'feature1 location has now been split by the deletion and location object');
is( my @feature1_del_sublocs = $feature1_del->location->each_Location, 2, 'feature1 has two locations after the deletion');
is( $feature1_del_sublocs[0]->start, 2, 'feature1 start is unaffected by the deletion');
is( $feature1_del_sublocs[0]->end, 10, 'feature1 end of first split is 1nt before deletion site');
is( $feature1_del_sublocs[1]->start, 11, 'feature1 start of second split is 1nt after deletion site');
is( $feature1_del_sublocs[1]->end, 15, 'feature1 end of second split has been adjusted correctly');
my @fd1_notes = $feature1_del->get_tag_values('note');
is( @fd1_notes,1, 'split feature now has a note');
is (shift @fd1_notes, '10bp internal deletion between pos 10 and 11', 'got the expected note about length and position of deletion');

my ($feature3_del) = grep ($_->primary_tag eq 'feat3', $product->get_SeqFeatures);
ok ($feature3_del, "feature3 is till present");
is_deeply ( [$feature3_del->start, $feature3_del->end], [$feature3->start - 10, $feature3->end - 10], 'a feature downstream of the deletion site is shifted entirely by 10nt to the left');

my ($feature4_del) = grep ($_->primary_tag eq 'feat4', $product->get_SeqFeatures);
ok ($feature4_del, "feature4 is till present");
is_deeply ( [$feature4_del->start, $feature4_del->end], [$feature4->start, $feature4->end], 'a feature upstream of the deletion site is not repositioned by the deletion');

my ($feature2_del) = grep ($_->primary_tag eq 'feat2', $product->get_SeqFeatures);
ok ($feature2_del, "feature2 is till present");
is ( $feature2_del->start, 11, 'start pos of a feature that started in the deletion site has been altered accordingly');
my @fd2_notes = $feature2_del->get_tag_values('note');
is( @fd2_notes,1, 'feature 2 now has a note');
is (shift @fd2_notes, "6bp deleted from feature 3' end", "note added to feature2 about deletion at 3' end");

ok (!grep ($_->primary_tag eq 'feat5', $product->get_SeqFeatures), 'a feature that was completely positioned inside the deletion site is not present on the new molecule');

my ($feature6_del) = grep ($_->primary_tag eq 'feat6', $product->get_SeqFeatures);
ok ($feature6_del, "feature6 is till present");
is ( $feature6_del->start, 11, 'start pos of a feature that started in the deletion site has been altered accordingly');
is ( $feature6_del->end, 15, 'end pos of a feature that started in the deletion site has been altered accordingly');


# insert
lives_ok(
  sub {
    $product = Bio::SeqUtils->insert( $seq_obj, $fragment_obj, 10 );
  },
  "No error thrown when inserting a fragment into recipient sequence"
);
($seq_obj_comment) = $seq_obj->annotation->get_Annotations('comment');
($product_comment) = $product->annotation->get_Annotations('comment');
is( $seq_obj_comment, $product_comment, 'annotation of whole sequence has been moved to new molecule');

my ($composite_feat1_ins) = grep ($_->primary_tag eq 'comp_feat1', $product->get_SeqFeatures);
ok ($composite_feat1_ins, "The composite feature is still present");
isa_ok( $composite_feat1_ins, 'Bio::SeqFeature::Generic');
isa_ok( $composite_feat1_ins->location, 'Bio::Location::Split', "a composite feature that spanned the insertion site has been split up, Location");
is( $composite_feat1_ins->get_SeqFeatures, 3, 'all of the parts of the composite feature are still present');

my ($subfeat1_ins) = grep ($_->primary_tag eq 'sf1', $composite_feat1_ins->get_SeqFeatures);
ok ($subfeat1_ins, "sub-feature 1 of the composite feature is still present");
is ($subfeat1->end, 12, "the original end of sf1 is 12");
is ($subfeat1_ins->end, $subfeat1->end + $fragment_obj->length, "after insertion, the end of sf1 has been shifted by the length of the insertion");
isa_ok( $subfeat1_ins->location, 'Bio::Location::Split', 'sub-feature 1 (spans insertion site) is now split up and');
is_deeply (
  [$subfeat1->location->end_pos_type, $subfeat1->location->start_pos_type],
  [$subfeat1_ins->location->end_pos_type, $subfeat1_ins->location->start_pos_type],
  'the start and end position types of sub-feature1 have not changed'
);
($subfeat1_comment) = $subfeat1->annotation->get_Annotations('comment');
my ($subfeat1_ins_comment) = $subfeat1_ins->annotation->get_Annotations('comment');
is( $subfeat1_comment, $subfeat1_ins_comment, 'annotation of subeature 1 has been moved to new molecule');
my @sf1ins_notes = $subfeat1_ins->get_tag_values('note');
is( @sf1ins_notes,1, 'split feature now has a note');
is (shift @sf1ins_notes, '10bp internal insertion between pos 10 and 21', 'got the expected note about length and position of insertion');

my ($feature3_ins) = grep ($_->primary_tag eq 'feat3', $product->get_SeqFeatures);
ok ($feature3_ins, "feature3 is till present");
is_deeply ( 
  [$feature3_ins->start, $feature3_ins->end],
  [$feature3->start + $fragment_obj->length, $feature3->end + $fragment_obj->length],
  'a feature downstream of the insertion site is shifted entirely to the left by the length of the insertion');

my ($feature4_ins) = grep ($_->primary_tag eq 'feat4', $product->get_SeqFeatures);
ok ($feature4_ins, "feature4 is till present");
is_deeply ( [$feature4_ins->start, $feature4_ins->end], [$feature4->start, $feature4->end], 'a feature upstream of the insertion site is not repositioned');

my ($frag_feature1_ins) = grep ($_->primary_tag eq 'frag_feat1', $product->get_SeqFeatures);
ok( $frag_feature1_ins, 'a feature on the inserted fragment is present on the product molecule');
is_deeply (
  [$frag_feature1_ins->start, $frag_feature1_ins->end],
  [12, 14],
  'position of the feature on the insert has been adjusted to product coordinates'
);
is( $frag_feature1_ins->strand, $frag_feature1->strand, 'strand of the feature on insert has not changed');
like( $product->desc, qr/some fragment to insert/, 'desctription of the product contains description of the fragment');
like( $product->desc, qr/some sequence for testing/, 'desctription of the product contains description of the recipient');

ok( 
  grep ($_ eq 'inserted fragment', 
    map ($_->get_tag_values('note'), 
      grep ($_->primary_tag eq 'misc_feature', $product->get_SeqFeatures)
    )
  ),
  "the product has an additional 'misc_feature' with note='inserted fragment'"
);

# ligate
lives_ok(
  sub {
    $product = Bio::SeqUtils->ligate( 
      -recipient => $seq_obj, 
      -fragment  => $fragment_obj, 
      -left      => 10, 
      -right     => 31,
      -flip      => 1
    ); 
  },
  "No error thrown using 'ligate' of fragment into recipient"
);

is ($product->length, 30, 'product has the expected length');
is ($product->subseq(11,20), 'atatatatat', 'the sequence of the fragment is inserted into the product');

my ($inserted_fragment_feature) = grep( 
  grep($_ eq 'inserted fragment', $_->get_tag_values('note')),
  grep( $_->has_tag('note'), $product->get_SeqFeatures)
);

ok($inserted_fragment_feature, 'we have a feature annotating the ligated fragment');
is_deeply ( 
  [$inserted_fragment_feature->start, $inserted_fragment_feature->end],
  [11, 20],
  'coordinates of the feature annotating the ligated feature are correct'
);

my ($fragment_feat_lig) = grep ($_->primary_tag eq 'frag_feat1', $product->get_SeqFeatures);
ok( $fragment_feat_lig, 'the fragment feature1 is now a feature of the product');
is_deeply( [$fragment_feat_lig->start, $fragment_feat_lig->end], [17,19], 'start and end of a feature on the fragment are correct after insertion with "flip" option');

# test clone_obj option (create new objects via clone not 'new')
my $foo_seq_obj = Bio::Seq::Foo->new( 
  -seq =>'aaaaaaaaaaccccccccccggggggggggtttttttttt',
  -display_id => 'seq1',
  -desc       => 'some sequence for testing'
);
for ($composite_feat1, $feature1, $feature2, $feature3, $feature4, $feature5) {
    $foo_seq_obj->add_SeqFeature( $_ );
}
$foo_seq_obj->annotation($coll);

dies_ok(
  sub {
    $product = Bio::SeqUtils->delete( $foo_seq_obj, 11, 20, { clone_obj => 0} );
  },
  "Trying to delete from an object of a custom Bio::Seq subclass that doesn't allow calling 'new' throws an error"
);

lives_ok(
  sub {
    $product = Bio::SeqUtils->delete( $foo_seq_obj, 11, 20, { clone_obj => 1} );
  },
  "Deleting from Bio::Seq::Foo does not throw an error when using the 'clone_obj' option to clone instead of calling 'new'"
);

isa_ok( $product, 'Bio::Seq::Foo');

# just repeat some of the tests for the cloned feature
ok( 
  grep ($_ eq 'deletion of 10bp', 
    map ($_->get_tag_values('note'), 
      grep ($_->primary_tag eq 'misc_feature', $product->get_SeqFeatures)
    )
  ),
  "the product has an additional 'misc_feature' and the note specifies the lengths of the deletion'"
);
($composite_feat1_del) = grep ($_->primary_tag eq 'comp_feat1', $product->get_SeqFeatures);
ok ($composite_feat1_del, "The composite feature is still present");
isa_ok( $composite_feat1_del, 'Bio::SeqFeature::Generic');
isa_ok( $composite_feat1_del->location, 'Bio::Location::Split', "a composite feature that spanned the deletion site has been split up, Location");

# ligate with clone_obj
dies_ok(
  sub {
    $product = Bio::SeqUtils->ligate( 
      -recipient => $foo_seq_obj, 
      -fragment  => $fragment_obj, 
      -left      => 10, 
      -right     => 31,
      -flip      => 1
    ); 
  },
  "'ligate' without clone_obj option dies with a Bio::Seq::Foo object that can't call new"
);

lives_ok(
  sub {
    $product = Bio::SeqUtils->ligate( 
      -recipient => $foo_seq_obj, 
      -fragment  => $fragment_obj, 
      -left      => 10, 
      -right     => 31,
      -flip      => 1,
      -clone_obj => 1,
    ); 
  },
  "'ligate' with clone_obj option works with a Bio::Seq::Foo object that can't call new"
);

sub uniq_sort {
    my @args = @_;
    my %uniq;
    @args = sort @args;
    @uniq{@args} = (0..$#args);
    return sort {$uniq{$a} <=> $uniq{$b}} keys %uniq;
}

package Bio::Seq::Foo;

use base 'Bio::Seq';

sub can_call_new { 0 }
BioPerl-1.007002/t/SeqTools/SeqWords.t000444000766000024       314213155576321 17464 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: SeqWords.t 11525 2007-06-27 10:16:38Z sendu $

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 22);
	
	use_ok('Bio::SeqIO');
	use_ok('Bio::Tools::SeqWords');
}

my ($seqobj, $count, $seqobj_stats, $wt);

my $str = Bio::SeqIO->new(-file=> test_input_file('multifa.seq'), '-format' => 'Fasta');
$seqobj= $str->next_seq();
ok defined $seqobj, 'new Bio::Root::IO object';

my $words = Bio::Tools::SeqWords->new('-seq' => $seqobj);
my $hash = $words->count_words(6);
ok (defined $words, 'new Bio::Tools::SeqWords object');
ok (defined $hash, 'count_words');

$seqobj = Bio::PrimarySeq->new(-seq=>'ACTGTGGCGTCAACTGACTGGC',
			       -alphabet=>'dna', -id=>'test');
ok $seqobj_stats  =  Bio::Tools::SeqWords->new(-seq=>$seqobj);
isa_ok $seqobj_stats, 'Bio::Tools::SeqWords';

$count = $seqobj_stats->count_words(4);
is $count->{'ACTG'}, 3;
is $count->{'TGGC'}, 1;
is $count->{'GTCA'}, 1;

$count = $seqobj_stats->count_overlap_words(4);
is $count->{'ACTG'}, 3;
is $count->{'TGGC'}, 2;
is $count->{'GTCA'}, 1;
is $count->{'GTGG'}, 1;

# now test a protein
$seqobj = Bio::PrimarySeq->new(-seq=>'MQSERGITIDISLWKFETSKYYVTIDISSLWKF',
                               -alphabet=>'protein', -id=>'test');
ok $seqobj_stats  =  Bio::Tools::SeqWords->new('-seq' => $seqobj);
isa_ok $seqobj_stats, 'Bio::Tools::SeqWords';

$count = $seqobj_stats->count_words(4);
is $count->{'MQSE'}, 1;
is $count->{'LWKF'}, 1;
is $count->{'IDIS'}, 2;

$count = $seqobj_stats->count_overlap_words(4);
is $count->{'MQSE'}, 1;
is $count->{'LWKF'}, 2;
is $count->{'IDIS'}, 2;
BioPerl-1.007002/t/Structure000755000766000024          013155576321 15622 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Structure/IO.t000444000766000024       415513155576321 16460 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 14);
	
	use_ok('Bio::Structure::IO');
}

#
# test reading PDB format - single model, single chain
#
my $pdb_file = test_input_file('1BPT.pdb');
ok my $structin = Bio::Structure::IO->new(-file => $pdb_file, 
										  -format => 'pdb');
ok my $struc = $structin->next_structure;
isa_ok $struc, "Bio::Structure::Entry";

# some basic checks, Structure objects are tested in Structure.t
my ($chain) = $struc->chain;
is($struc->residue, 97);
my ($atom) = $struc->get_atom_by_serial(367);
is($atom->id, "NZ");
is($struc->parent($atom)->id, "LYS-46");
my ($ann) = $struc->annotation->get_Annotations("author");
is($ann->as_text,
	"Value: D.HOUSSET,A.WLODAWER,F.TAO,J.FUCHS,C.WOODWARD              ");
($ann) = $struc->annotation->get_Annotations("header");
is($ann->as_text,
	"Value: PROTEINASE INHIBITOR (TRYPSIN)          11-DEC-91   1BPT");
my $pseq = $struc->seqres;
is($pseq->subseq(1,20), "RPDFCLEPPYTGPCKARIIR");

#
# test reading PDB format - single model, multiple chains
#
$pdb_file = test_input_file('1A3I.pdb');
$structin = Bio::Structure::IO->new(-file => $pdb_file, 
									-format => 'pdb');
$struc = $structin->next_structure;

my ($chaincount,$rescount,$atomcount);
for my $chain ($struc->get_chains) {
	$chaincount++;
   for my $res ($struc->get_residues($chain)) {
		$rescount++;
      for my $atom ($struc->get_atoms($res)) {
			$atomcount++;
		}
   }
}

is($chaincount, 4);  # 3 polypeptides and a group of hetero-atoms
is($rescount, 60);   # amino acid residues and solvent molecules
is($atomcount, 171); # ATOM and HETATM

#
# test reading PDB format - multiple models, single chain
#
#$pdb_file = test_input_file('1A11.pdb');
# TODO?

#
# test reading PDB format - chains with ATOMs plus HETATMs
#
#$pdb_file = test_input_file('8HVP.pdb');
# TODO?

#
# test writing PDB format
#
my $out_file = test_output_file();
my $structout = Bio::Structure::IO->new(-file => ">$out_file", 
                                        -format => 'PDB');
$structout->write_structure($struc);
ok -s $out_file;
BioPerl-1.007002/t/Structure/Structure.t000444000766000024       603613155576321 20151 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 51);
	
	use_ok('Bio::Structure::Entry');
	use_ok('Bio::Structure::Model');
	use_ok('Bio::Structure::Chain');
	use_ok('Bio::Structure::Residue');
	use_ok('Bio::Structure::Atom');
}

ok my $entry = Bio::Structure::Entry->new;
isa_ok $entry, 'Bio::Structure::Entry';

ok my $model = Bio::Structure::Model->new;
isa_ok $model, 'Bio::Structure::Model';

ok my $chain = Bio::Structure::Chain->new;
isa_ok $chain, 'Bio::Structure::Chain';

ok my $residue = Bio::Structure::Residue->new;
isa_ok $residue, 'Bio::Structure::Residue';

ok my $atom = Bio::Structure::Atom->new;
isa_ok $atom, 'Bio::Structure::Atom';

# adding/removing to Entry
my $m1 = Bio::Structure::Model->new;
$entry->model($m1);
is $entry->model,1;
my $m2 = Bio::Structure::Model->new;
$entry->add_model($m2);
is $entry->get_models, 2;

$entry->model($m2);
is $entry->model, 1;
my @m = ($m1, $m2);
$entry->model(\@m);
is $entry->model, 2;

# does $m2 gest orphaned
$entry->model($m1);
is $entry->parent($m2), undef;


# adding/removing to Model 
my $c1 = Bio::Structure::Chain->new;
$entry->add_chain($model,$c1);
is $entry->get_chains($model),1;
my $c2 = Bio::Structure::Chain->new;
$entry->add_chain($model,$c2);
is $entry->get_chains($model), 2;
isa_ok $entry->parent($c1), 'Bio::Structure::Model';
is $entry->parent($c1), $entry->parent($c2);


# adding/removing to Chain 
my $r1 = Bio::Structure::Residue->new;
$entry->add_residue($chain,$r1);
is $entry->get_residues($chain),1;
my $r2 = Bio::Structure::Residue->new;
$entry->add_residue($chain,$r2);
is $entry->get_residues($chain), 2;

isa_ok $entry->parent($r2), 'Bio::Structure::Chain';
is $entry->parent($r1), $entry->parent($r2);

# adding/removing to Residue 
$entry->add_atom($residue,$atom);
is $entry->get_atoms($residue),1;
my $a2 = Bio::Structure::Atom->new;
my $a3 = Bio::Structure::Atom->new;
my $a4 = Bio::Structure::Atom->new;
my $a5 = Bio::Structure::Atom->new;
my $a6 = Bio::Structure::Atom->new;
$entry->add_atom($residue,$a2);
is $entry->get_atoms($residue), 2;

my @a = ($a3, $a4, $a5);
$entry->add_atom($r2,\@a);
is $entry->get_atoms($r2), 3;

isa_ok $entry->parent($a2), 'Bio::Structure::Residue';
is $entry->parent($a3), $entry->parent($a5);


$atom->x(10.234);
is $atom->x, 10.234;
my $y = 12.345;
$atom->y($y);
is $atom->y, $y;
my $z = $atom->x - $y;
$atom->z($z);
is $atom->z, -2.111;
my @xyz = $atom->xyz;
is (scalar (@xyz), 3);

is $xyz[0], 10.234;
is $xyz[1], 12.345;
is $xyz[2], -2.111;

ok my $e2 = Bio::Structure::Entry->new(-id => "Entry 2");
is $e2->id, "Entry 2";
ok my $m3 = Bio::Structure::Model->new(-id => "Model 2");
is $m3->id, "Model 2";
ok my $c3 = Bio::Structure::Chain->new(-id => "Chain 2");
is $c3->id, "Chain 2";
ok my $r3 = Bio::Structure::Residue->new(-id => "Residue 2");
is $r3->id, "Residue 2";
ok $a2 = Bio::Structure::Atom->new(-id => "Atom 2");
is $a2->id, "Atom 2";

$entry->add_atom($r3,$a6);
$entry->add_residue($c3,$r3);
is $entry->parent( $entry->parent($a6) )->id , "Chain 2";
BioPerl-1.007002/t/Tools000755000766000024          013155576321 14722 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Tools/AmpliconSearch.t000444000766000024      3102613155576321 20156 0ustar00cjfieldsstaff000000000000BEGIN {     
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 185);

    use_ok 'Bio::PrimarySeq';
    use_ok 'Bio::SeqFeature::Primer';
    use_ok 'Bio::Tools::AmpliconSearch';
}


my ($search, $amplicon, $seq, $seq2, $forward, $forward2, $reverse, $reverse2,
    $primer, $primer_seq, $annotated, $num_feats, $template_seq, $rna);


# Basic object

ok $search = Bio::Tools::AmpliconSearch->new(), 'Basic';
isa_ok $search, 'Bio::Tools::AmpliconSearch';


# Forward primer only

$seq = Bio::PrimarySeq->new(
   -seq => 'acgAAACTTAAAGGAATTGACGGacgtacgtacgtGTACACACCGCCCGTacgtac',
);

$rna = Bio::PrimarySeq->new(
   -seq => 'acgAAACUUAAAGGAAUUGACGGacguacguacguGUACACACCGCCCGUacguac',
);


$forward = Bio::PrimarySeq->new(
   -seq => 'AAACTTAAAGGAATTGACGG',
);
ok $search = Bio::Tools::AmpliconSearch->new(
   -template       => $seq,
   -fwd_primer     => $forward,
   -attach_primers => 1,
), 'Forward primer only';
is $search->fwd_primer->seq, 'AAACTTAAAGGAATTGACGG';
is $search->rev_primer, undef;
ok $template_seq = $search->template;
isa_ok $template_seq, 'Bio::Seq';
is $template_seq->seq, 'acgAAACTTAAAGGAATTGACGGacgtacgtacgtGTACACACCGCCCGTacgtac';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 4;
is $amplicon->end, 56;
is $amplicon->strand, 1;
is $amplicon->seq->seq, 'AAACTTAAAGGAATTGACGGacgtacgtacgtGTACACACCGCCCGTacgtac';
ok $primer = $amplicon->fwd_primer;
ok $primer_seq = $primer->seq;
is $primer_seq->seq, 'AAACTTAAAGGAATTGACGG';
is $primer->start, 4;
is $primer->end, 23;
is $primer->strand, 1;
is $amplicon = $search->next_amplicon, undef;


# Reverse primer only

$seq = Bio::PrimarySeq->new(
   -seq => 'acgAAACTTAAAGGAATTGACGGacgtacgtacgtGTACACACCGCCCGTacgtac',
);
$reverse = Bio::SeqFeature::Primer->new(
   -seq => 'ACGGGCGGTGTGTAC',
);
ok $search = Bio::Tools::AmpliconSearch->new(
   -template       => $seq,
   -rev_primer     => $reverse,
   -attach_primers => 0,
), 'Reverse primer only';
is $search->fwd_primer, undef;
is $search->rev_primer->seq->seq, 'ACGGGCGGTGTGTAC';
is $search->template->seq, 'acgAAACTTAAAGGAATTGACGGacgtacgtacgtGTACACACCGCCCGTacgtac';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 1;
is $amplicon->end, 50;
is $amplicon->strand, 1;
is $amplicon->seq->seq, 'acgAAACTTAAAGGAATTGACGGacgtacgtacgtGTACACACCGCCCGT';
is $amplicon->fwd_primer, undef;
is $amplicon->rev_primer, undef;
is $search->next_amplicon, undef;


# Forward and reverse primers, no amplicon

$seq = Bio::PrimarySeq->new(
   -seq => 'acgAAACTTAAAGGAATTGACGGacgtacgtacgtGTACACACCGCCCGTacgtac',
);
$forward = Bio::PrimarySeq->new(
   -seq => 'AAACTTAAAGGAATTGACGG',
);
$reverse = Bio::PrimarySeq->new(
   -seq => 'CCCCCCCCCC',
);
ok $search = Bio::Tools::AmpliconSearch->new(
   -template   => $seq,
   -fwd_primer => $forward,
   -rev_primer => $reverse,
), 'Two primers, no match';
is $search->fwd_primer->seq, 'AAACTTAAAGGAATTGACGG';
is $search->rev_primer->seq, 'CCCCCCCCCC';
is $search->template->seq, 'acgAAACTTAAAGGAATTGACGGacgtacgtacgtGTACACACCGCCCGTacgtac';
is $search->next_amplicon, undef;


# Degenerate forward and reverse primers from file, single amplicon

ok $search = Bio::Tools::AmpliconSearch->new(
   -template    => $seq,
   -primer_file => test_input_file('forward_reverse_primers.fa'),
), 'Two degenerate primers from a file';
is $search->fwd_primer->seq, 'AAACTYAAAKGAATTGRCGG';
is $search->rev_primer->seq, 'ACGGGCGGTGTGTRC';
is $search->template->seq, 'acgAAACTTAAAGGAATTGACGGacgtacgtacgtGTACACACCGCCCGTacgtac';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 4;
is $amplicon->end, 50;
is $amplicon->strand, 1;
is $amplicon->seq->seq, 'AAACTTAAAGGAATTGACGGacgtacgtacgtGTACACACCGCCCGT';
is $search->next_amplicon, undef;


# Same thing but with RNA template

ok $search = Bio::Tools::AmpliconSearch->new(
   -template    => $rna,
   -primer_file => test_input_file('forward_reverse_primers.fa'),
), 'RNA template';
is $search->fwd_primer->seq, 'AAACTYAAAKGAATTGRCGG';
is $search->rev_primer->seq, 'ACGGGCGGTGTGTRC';
is $search->template->seq, 'acgAAACUUAAAGGAAUUGACGGacguacguacguGUACACACCGCCCGUacguac';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 4;
is $amplicon->end, 50;
is $amplicon->strand, 1;
is $amplicon->seq->seq, 'AAACUUAAAGGAAUUGACGGacguacguacguGUACACACCGCCCGU';
is $search->next_amplicon, undef;


# Forward primer only, in sequence file

ok $search = Bio::Tools::AmpliconSearch->new(
   -primer_file => test_input_file('forward_primer.fa'),
), 'Forward primer from file';
ok $search->template($seq);
is $search->fwd_primer->seq, 'AAACTTAAAGGAATTGACGG';
is $search->rev_primer, undef;
ok $template_seq = $search->template;
isa_ok $template_seq, 'Bio::Seq';
is $template_seq->seq, 'acgAAACTTAAAGGAATTGACGGacgtacgtacgtGTACACACCGCCCGTacgtac';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 4;
is $amplicon->end, 56;
is $amplicon->strand, 1;
is $amplicon->seq->seq, 'AAACTTAAAGGAATTGACGGacgtacgtacgtGTACACACCGCCCGTacgtac';
is $amplicon = $search->next_amplicon, undef;


# Multiple amplicons

$seq = Bio::PrimarySeq->new(
   -seq => 'acgtaCCCCacgtacgtacTTTTTTacgtaCCCCacgtaTTTTTTacgtacgtac',
);
$forward = Bio::PrimarySeq->new(
   -seq => 'CCCC',
);
$reverse = Bio::PrimarySeq->new(
   -seq => 'AAAAAA',
);
ok $search = Bio::Tools::AmpliconSearch->new(
   -template   => $seq,
   -fwd_primer => $forward,
   -rev_primer => $reverse,
), 'Multiple amplicons';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 6;
is $amplicon->end, 25;
is $amplicon->strand, 1;
is $amplicon->seq->seq, 'CCCCacgtacgtacTTTTTT';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 31;
is $amplicon->end, 45;
is $amplicon->strand, 1;
is $amplicon->seq->seq, 'CCCCacgtaTTTTTT';
is $search->next_amplicon, undef;


# Amplicon on reverse strand

$seq = Bio::PrimarySeq->new(
   # Reverse-complement of previous sequence... should have same amplicons
   -seq => 'gtacgtacgtAAAAAAtacgtGGGGtacgtAAAAAAgtacgtacgtGGGGtacgt',
);
$forward = Bio::PrimarySeq->new(
   -seq => 'CCCC',
);
$reverse = Bio::PrimarySeq->new(
   -seq => 'AAAAAA',
);
ok $search = Bio::Tools::AmpliconSearch->new(
   -template   => $seq,
   -fwd_primer => $forward,
   -rev_primer => $reverse,
), 'Amplicon on reverse strand';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 11;
is $amplicon->end, 25;
is $amplicon->strand, -1;
is $amplicon->seq->seq, 'CCCCacgtaTTTTTT';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 31;
is $amplicon->end, 50;
is $amplicon->strand, -1;
is $amplicon->seq->seq, 'CCCCacgtacgtacTTTTTT';
is $search->next_amplicon, undef;


# Overlapping amplicons (1)

$seq = Bio::PrimarySeq->new(
   -seq => 'acgtaCCCCacgtacgtacgtacgCCCCacgtaTTTTTTacgtacgtac',
);
$forward = Bio::PrimarySeq->new(
   -seq => 'CCCC',
);
$reverse = Bio::PrimarySeq->new(
   -seq => 'AAAAAA',
);
ok $search = Bio::Tools::AmpliconSearch->new(
   -template   => $seq,
   -fwd_primer => $forward,
   -rev_primer => $reverse,
), 'Overlapping amplicons (1)';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 25;
is $amplicon->end, 39;
is $amplicon->strand, 1;
is $amplicon->seq->seq, 'CCCCacgtaTTTTTT';
is $search->next_amplicon, undef;


# Overlapping amplicons (2)

$seq = Bio::PrimarySeq->new(
   -seq => 'acgtaCCCCacgtacgtacgtacgTTTTTTacgtaTTTTTTacgtacgtac',
);
$forward = Bio::PrimarySeq->new(
   -seq => 'CCCC',
);
$reverse = Bio::PrimarySeq->new(
   -seq => 'AAAAAA',
);
ok $search = Bio::Tools::AmpliconSearch->new(
   -template   => $seq,
   -fwd_primer => $forward,
   -rev_primer => $reverse,
), 'Overlapping amplicons (2)';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 6;
is $amplicon->end, 30;
is $amplicon->strand, 1;
is $amplicon->seq->seq, 'CCCCacgtacgtacgtacgTTTTTT';
is $search->next_amplicon, undef;


# Overlapping amplicons (3)

$seq = Bio::PrimarySeq->new(
   -seq => 'acgtaCCCCacgtacgCCCCacgtacgaTTTTTTacgtaTTTTTTaaaaaaaaaa',
);
$forward = Bio::PrimarySeq->new(
   -seq => 'CCCC',
);
$reverse = Bio::PrimarySeq->new(
   -seq => 'AAAAAA',
);
ok $search = Bio::Tools::AmpliconSearch->new(
   -template   => $seq,
   -fwd_primer => $forward,
   -rev_primer => $reverse,
), 'Overlapping amplicons (3)';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 17;
is $amplicon->end, 34;
is $amplicon->strand, 1;
is $amplicon->seq->seq, 'CCCCacgtacgaTTTTTT';
is $search->next_amplicon, undef;


# Amplicons on both strands

$seq = Bio::PrimarySeq->new(
   -seq => 'acgtaCCCCacgtaacgtaTTTTTTacAAAAAAgtGGGGacgtaacgta',
);
$forward = Bio::PrimarySeq->new(
   -seq => 'CCCC',
);
$reverse = Bio::PrimarySeq->new(
   -seq => 'AAAAAA',
);
ok $search = Bio::Tools::AmpliconSearch->new(
   -template   => $seq,
   -fwd_primer => $forward,
   -rev_primer => $reverse,
), 'Amplicons on both strands';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 6;
is $amplicon->end, 25;
is $amplicon->strand, 1;
is $amplicon->seq->seq, 'CCCCacgtaacgtaTTTTTT';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 28;
is $amplicon->end, 39;
is $amplicon->strand, -1;
is $amplicon->seq->seq, 'CCCCacTTTTTT';
is $search->next_amplicon, undef;


# Overlapping amplicons on both strands

$seq = Bio::PrimarySeq->new(
   -seq => 'acgtaCCCCacgtacgtacagAAAAAATTTTTTacgtGGGGacgtacgtac',
);
$forward = Bio::PrimarySeq->new(
   -seq => 'CCCC',
);
$reverse = Bio::PrimarySeq->new(
   -seq => 'AAAAAA',
);
ok $search = Bio::Tools::AmpliconSearch->new(
   -template   => $seq,
   -fwd_primer => $forward,
   -rev_primer => $reverse,
), 'Overlapping amplicons on both strands';
ok $amplicon = $search->next_amplicon;
isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
is $amplicon->start, 22;
is $amplicon->end, 41;
is $amplicon->strand, -1;
is $amplicon->seq->seq, 'CCCCacgtAAAAAATTTTTT';
is $search->next_amplicon, undef;


# Annotate template

$seq = Bio::PrimarySeq->new(
   -seq => 'acgtaCCCCacgtacgtacTTTTTTacAAAAAAgtGGGGacgtacgtac',
);
$forward = Bio::PrimarySeq->new(
   -seq => 'CCCC',
);
$reverse = Bio::PrimarySeq->new(
   -seq => 'AAAAAA',
);
ok $search = Bio::Tools::AmpliconSearch->new(
   -template   => $seq,
   -fwd_primer => $forward,
   -rev_primer => $reverse,
), 'Annotated template';
ok $annotated = $search->annotate_template;
isa_ok $annotated, 'Bio::Seq';
$num_feats = 0;
for my $feat ( $annotated->get_SeqFeatures ) {
   $num_feats++;
   isa_ok $feat, 'Bio::SeqFeature::Amplicon';
}
is $num_feats, 2;
is $search->next_amplicon, undef;


# Update primers

$seq = Bio::PrimarySeq->new(
   -seq => 'acgtaCCCCacgtacgtacTTTTTTacCTCTCTgtTGTGTGacgtacgtac',
);
$forward = Bio::PrimarySeq->new(
   -seq => 'CTCTCT',
);
$reverse = Bio::PrimarySeq->new(
   -seq => 'CACACA',
);
$forward2 = Bio::PrimarySeq->new(
   -seq => 'CCCC',
);
$reverse2 = Bio::PrimarySeq->new(
   -seq => 'AAAAAA',
);
ok $search = Bio::Tools::AmpliconSearch->new(
   -template   => $seq,
), 'Update primers';
ok $search->fwd_primer($forward);
is $search->fwd_primer->seq, 'CTCTCT';
ok $search->rev_primer($reverse);
is $search->rev_primer->seq, 'CACACA';
ok $amplicon = $search->next_amplicon;
is $amplicon->seq->seq, 'CTCTCTgtTGTGTG';
is $search->next_amplicon, undef;
ok $search->fwd_primer($forward2);
ok $search->rev_primer($reverse2);
is $search->fwd_primer->seq, 'CCCC';
is $search->rev_primer->seq, 'AAAAAA';
ok $amplicon = $search->next_amplicon;
is $amplicon->seq->seq, 'CCCCacgtacgtacTTTTTT';
is $search->next_amplicon, undef;


# Update template

$seq = Bio::PrimarySeq->new(
   -seq => 'acgtaCCCCacgtacgtacTTTTTTa',
);
$seq2 = Bio::PrimarySeq->new(
   -seq => 'aCCCCgaTTTTTTgacgtacgtac',
);
$forward = Bio::PrimarySeq->new(
   -seq => 'CCCC',
);
$reverse = Bio::PrimarySeq->new(
   -seq => 'AAAAAA',
);
ok $search = Bio::Tools::AmpliconSearch->new(
   -fwd_primer => $forward,
   -rev_primer => $reverse,
), 'Update template';
ok $search->template($seq);
is $search->template->seq, 'acgtaCCCCacgtacgtacTTTTTTa';
ok $amplicon = $search->next_amplicon;
is $amplicon->seq->seq, 'CCCCacgtacgtacTTTTTT';
is $search->next_amplicon, undef;
ok $search->template($seq2);
is $search->template->seq, 'aCCCCgaTTTTTTgacgtacgtac';
ok $amplicon = $search->next_amplicon;
is $amplicon->seq->seq, 'CCCCgaTTTTTT';
is $search->next_amplicon, undef;

BioPerl-1.007002/t/Tools/Est2Genome.t000444000766000024       427113155576321 17220 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 61);
	
	use_ok('Bio::Tools::Est2Genome');
}

my $parser = Bio::Tools::Est2Genome->new(-file   => test_input_file('hs_est.est2genome'));

ok($parser);
my $feature_set = $parser->parse_next_gene;
like(ref($feature_set), qr/ARRAY/i );

is(scalar @$feature_set, 7);
my @exons = grep { $_->primary_tag eq 'Exon' } @$feature_set;
my @introns = grep { $_->primary_tag eq 'Intron' } @$feature_set;

my @expected_exons = ( [695,813,1,1,119,1],
		       [1377,1493,1,120,236,1],
		       [1789,1935,1,237,382,1],
		       [2084,2180,1,383,479,1]);
my @expected_introns = ( [814,1376,1],
			 [1494,1788,1],
			 [1936,2083,1] );

foreach my $e ( @exons ) {
    my $test_e = shift @expected_exons;
    my $i = 0;
    is($e->query->start, $test_e->[$i++]);
    is($e->query->end, $test_e->[$i++]);
    is($e->query->strand, $test_e->[$i++]);

    is($e->hit->start, $test_e->[$i++]);
    is($e->hit->end, $test_e->[$i++]);
    is($e->hit->strand, $test_e->[$i++]);
}
ok(! @expected_exons);
foreach my $intron ( @introns ) {
    my $test_i = shift @expected_introns;
    my $i = 0;
    is($intron->start, $test_i->[$i++]);
    is($intron->end, $test_i->[$i++]);
    is($intron->strand, $test_i->[$i++]);
}
ok(! @expected_introns);

$parser = Bio::Tools::Est2Genome->new(-file   => test_input_file('hs_est.est2genome'));

ok($parser);
my $gene = $parser->parse_next_gene(1);
@expected_exons = ( [695,813,1,1,119,1],
		       [1377,1493,1,120,236,1],
		       [1789,1935,1,237,382,1],
		       [2084,2180,1,383,479,1]);
@expected_introns = ( [814,1376,1],
			 [1494,1788,1],
			 [1936,2083,1] );

foreach my $trans($gene->transcripts){
   my @exons = $trans->exons;
   foreach my $e(@exons){
    my $test_e = shift @expected_exons;
    my $i = 0;
    is($e->start, $test_e->[$i++]);
    is($e->end, $test_e->[$i++]);
    is($e->strand, $test_e->[$i++]);
  }
  my @introns = $trans->introns;
  foreach my $intron ( @introns ) {
    my $test_i = shift @expected_introns;
    my $i = 0;
    is($intron->start, $test_i->[$i++]);
    is($intron->end, $test_i->[$i++]);
    is($intron->strand, $test_i->[$i++]);
  }
}
BioPerl-1.007002/t/Tools/FootPrinter.t000444000766000024       214713155576321 17523 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 27);
	
	use_ok('Bio::Tools::FootPrinter');
}

my $inputfilename= test_input_file('footprinter.out');
my $parser = Bio::Tools::FootPrinter->new(-file => $inputfilename);
my @sub;
my @species = qw(TETRAODON CHICKEN MOUSE HAMSTER HUMAN PIG);
while (my $feat = $parser->next_feature){
    is($feat->seq_id, shift @species);
    foreach my $sub ($feat->sub_SeqFeature){
      push @sub,$sub;
    }
}

is $sub[0]->seq_id, 'TETRAODON-motif1';
is $sub[0]->start,352;
is $sub[0]->end,362;
is $sub[0]->seq->seq,'tacaggatgca';
is $sub[1]->seq_id, 'TETRAODON-motif2';
is $sub[1]->start,363;
is $sub[1]->end,373;
is $sub[1]->seq->seq,'ccatatttgga';

is $sub[2]->seq_id, 'CHICKEN-motif1';
is $sub[2]->start,363;
is $sub[2]->end,373;
is $sub[2]->seq->seq,'cacaggatgta';

is $sub[3]->seq_id, 'CHICKEN-motif2';
is $sub[3]->start,376;
is $sub[3]->end,386;
is $sub[3]->seq->seq,'ccatataagga';

is $sub[4]->seq_id, 'MOUSE-motif1';
is $sub[4]->start,234;
is $sub[4]->end,243;
is $sub[4]->seq->seq,'cacaggatgt';
BioPerl-1.007002/t/Tools/GFF.t000444000766000024       613313155576321 15651 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 34);
	
    use_ok('Bio::Tools::GFF');
    use_ok('Bio::SeqFeature::Generic');
}

my $feat = Bio::SeqFeature::Generic->new( -start => 10, -end => 100,
				-strand => -1, -primary => 'repeat',
				-source => 'repeatmasker',
				-score  => 1000,
				-tag    => {
				    new => 1,
				    author => 'someone',
				    sillytag => 'this is silly!;breakfast' } );
ok($feat);

my ($out1, $out2) = (test_output_file(), test_output_file());
my $gff1out = Bio::Tools::GFF->new(-gff_version => 1, -file => ">$out1");
ok($gff1out);
my $gff2out = Bio::Tools::GFF->new(-gff_version => 2, -file => ">$out2");
ok($gff2out);

$gff1out->write_feature($feat);
$gff2out->write_feature($feat);

$gff1out->close();
$gff2out->close();

my $gff1in = Bio::Tools::GFF->new(-gff_version => 1,  -file => "$out1");
ok($gff1in);
my $gff2in = Bio::Tools::GFF->new(-gff_version => 2, -file => "$out2");
ok($gff2in);

my $feat1 = $gff1in->next_feature();
ok($feat1);
is($feat1->start, $feat->start);
is($feat1->end, $feat->end);
is($feat1->primary_tag, $feat->primary_tag);
is($feat1->score, $feat->score);

my $feat2 = $gff2in->next_feature();
ok($feat2);
is($feat2->start, $feat->start);
is($feat2->end, $feat->end);
is($feat2->primary_tag, $feat->primary_tag);
is($feat2->score, $feat->score);
is(($feat2->get_tag_values('sillytag'))[0], 'this is silly!;breakfast');

#test sequence-region parsing
$gff2in = Bio::Tools::GFF->new(-gff_version => 2, -file => test_input_file('hg16_chroms.gff'));
is($gff2in->next_feature(),undef);
my $seq = $gff2in->next_segment;
is($seq->display_id, 'chr1');
is($seq->end, 246127941);
is($seq->start, 1);


# GFF3
SKIP: {
	test_skip(-tests => 12, -requires_module => 'IO::String');
    my $str = IO::String->new;
    my $gffout = Bio::Tools::GFF->new(-fh => $str, -gff_version => 3);
    my $feat_test = Bio::SeqFeature::Generic->new
    (-primary_tag => 'tag',
     -source_tag  => 'exon',
     -seq_id      => 'testseq',
     -score       => undef,
     -start       => 10,
     -end         => 120,
     -strand      => 1,
     -tag         => { 
         'bungle' => 'jungle;mumble',
         'lion'   => 'snake=tree'
         });
    $feat_test->add_tag_value('giant_squid', 'lakeshore manor');
    $gffout->write_feature($feat_test);
    seek($str,0,0);
    my $in = Bio::Tools::GFF->new(-fh          => $str,
                 -gff_version => 3);
    my $f_recon = $in->next_feature;
    is($f_recon->primary_tag, $feat_test->primary_tag);
    is($f_recon->source_tag,  $feat_test->source_tag);
    is($f_recon->score, $feat_test->score);
    is($f_recon->start, $feat_test->start);
    is($f_recon->end, $feat_test->end);
    is($f_recon->strand, $feat_test->strand);
    for my $tag ( $feat_test->get_all_tags ) {
        ok($f_recon->has_tag($tag));
        if( $f_recon->has_tag($tag) ) {
            my @v = $feat_test->get_tag_values($tag);
            my @g = $f_recon->get_tag_values($tag);
            while( @v && @g ) {
               is(shift @v, shift @g);
            }
        }
    }
}
BioPerl-1.007002/t/Tools/Geneid.t000444000766000024       341313155576321 16440 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 26);
	
    use_ok('Bio::Tools::Geneid');
}

my $inputfilename = test_input_file('geneid_1.0.out');
my $parser = Bio::Tools::Geneid->new(-file => $inputfilename);
my @genes;

while (my $gene= $parser->next_prediction)
{
    push(@genes, $gene);
}

my @transcripts = $genes[0]->transcripts;
my @exons = $transcripts[0]->exons;

is($transcripts[0]->seq_id, '10');
is($exons[0]->seq_id, '10');
is($transcripts[0]->source_tag, 'geneid');
is($exons[0]->source_tag, 'geneid');
is($transcripts[0]->primary_tag, 'transcript');
is($exons[0]->primary_tag, 'Initial');

is(scalar($transcripts[0]->exons), 2);
is($transcripts[0]->start, 6090);
is($transcripts[0]->end, 7276);
is($transcripts[0]->score, 36.87);
is($transcripts[0]->strand, 1);
is($exons[0]->start, 6090);
is($exons[0]->end, 6155);
is($exons[0]->score, '1.40');
is($exons[0]->strand, 1);

my ($type) = $exons[0]->get_tag_values('Type');
is($type, 'Initial');

my ($phase) = $exons[0]->get_tag_values('phase');
is($phase, 0);

my ($end_phase) = $exons[0]->get_tag_values('end_phase');
is($end_phase, 0);

my ($start_signal_score) = $exons[0]->get_tag_values('start_signal_score');
is($start_signal_score, 2.15);

my ($end_signal_score) = $exons[0]->get_tag_values('end_signal_score');
is($end_signal_score, 3.63);

my ($coding_potential_score) = $exons[0]->get_tag_values('coding_potential_score');
is($coding_potential_score, 12.34);

my ($homology_score) = $exons[0]->get_tag_values('homology_score');
is($homology_score, '0.00');

is(scalar(@genes), 3);

@transcripts = $genes[1]->transcripts;
is(scalar($transcripts[0]->exons), 5);

@transcripts = $genes[2]->transcripts;
is(scalar($transcripts[0]->exons), 1);
BioPerl-1.007002/t/Tools/Genewise.t000444000766000024       362013155576321 17013 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: Genewise.t 11733 2007-10-26 18:22:10Z jason $

use strict;

BEGIN {
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 33);
	
    use_ok('Bio::Tools::Genewise');
}

my $inputfilename= test_input_file('genewise.out');
my $parser = Bio::Tools::Genewise->new(-file => $inputfilename);
my @gene;
while (my $gene= $parser->next_prediction){
    push @gene, $gene;
}
my @t = $gene[0]->transcripts;
my @e = $t[0]->exons;

is ($t[0]->seq_id, 'Scaffold_2042.1');
is ($e[0]->seq_id, 'Scaffold_2042.1');
is ($t[0]->source_tag, 'genewise');
is ($e[0]->source_tag, 'genewise');
is ($t[0]->primary_tag, 'transcript');
is ($e[0]->primary_tag, 'exon');

is (scalar($t[0]->exons), 18);
is ($t[0]->start, 22265);
is ($t[0]->end, 37062);
is ($e[0]->start,22265);
is ($e[0]->end, 22396);
my ($phase) = $e[0]->get_tag_values('phase');
is ($phase,0);
my ($sf)= $e[0]->get_tag_values('supporting_feature');
is ($sf->feature1->seq_id,'Scaffold_2042.1');
is ($sf->feature1->start,22265);
is ($sf->feature1->end,22396);
is ($sf->feature2->seq_id,'SINFRUP00000067802');
is ($sf->feature2->start,1);
is ($sf->feature2->end,44);
is ($sf->feature1->end,22396);

open my $FH, '<', $inputfilename or die "Could not read file '$inputfilename': $!\n";
$parser = Bio::Tools::Genewise->new(-fh => $FH);
while (my $gene = $parser->next_prediction){
    push @gene, $gene;
}
@t = $gene[0]->transcripts;
@e = $t[0]->exons;

is (scalar($t[0]->exons), 18);
is ($t[0]->start, 22265);
is ($t[0]->end, 37062);
is ($e[0]->start,22265);
is ($e[0]->end, 22396);
($phase) = $e[0]->get_tag_values('phase');
is ($phase,0);
($sf)= $e[0]->get_tag_values('supporting_feature');
is ($sf->feature1->seq_id,'Scaffold_2042.1');
is ($sf->feature1->start,22265);
is ($sf->feature1->end,22396);
is ($sf->feature2->seq_id,'SINFRUP00000067802');
is ($sf->feature2->start,1);
is ($sf->feature2->end,44);
is ($sf->feature1->end,22396);
BioPerl-1.007002/t/Tools/Genomewise.t000444000766000024       261713155576321 17354 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: Genomewise.t 11525 2007-06-27 10:16:38Z sendu $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 21);
	
    use_ok('Bio::Tools::Genomewise');
}

my $inputfilename = test_input_file("genomewise.out");
my $parser = Bio::Tools::Genomewise->new(-file => $inputfilename);
my @gene;
while (my $gene= $parser->next_prediction){
    push @gene, $gene;
}
my @t = $gene[0]->transcripts;
my @e = $t[0]->exons;

is ($t[0]->source_tag, 'genomewise');
is ($e[0]->source_tag, 'genomewise');
is ($t[0]->primary_tag, 'transcript');
is ($e[0]->primary_tag, 'exon');

is (scalar($t[0]->exons), 5);
is ($t[0]->start, 4761);
is ($t[0]->end, 6713);
is ($e[0]->start,4761);
is ($e[0]->end, 4874);
my ($phase) = $e[0]->get_tag_values('phase');
is ($phase,0);

open my $FH, '<', $inputfilename or die "Could not read file '$inputfilename': $!\n";
$parser = Bio::Tools::Genomewise->new(-fh => $FH);
while (my $gene= $parser->next_prediction){
    push @gene, $gene;
}
@t = $gene[1]->transcripts;
@e = $t[0]->exons;

is ($t[0]->source_tag, 'genomewise');
is ($e[0]->source_tag, 'genomewise');
is ($t[0]->primary_tag, 'transcript');
is ($e[0]->primary_tag, 'exon');

is (scalar($t[0]->exons), 3);
is ($t[0]->start, 9862);
is ($t[0]->end, 10316);
is ($e[1]->start,10024);
is ($e[1]->end, 10211);

($phase) = $e[2]->get_tag_values('phase');
is ($phase,2);
BioPerl-1.007002/t/Tools/Genpred.t000444000766000024      2304713155576321 16656 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 185);

    use_ok('Bio::Tools::Fgenesh');
    use_ok('Bio::Tools::Genscan');
    use_ok('Bio::Tools::Genemark');
    use_ok('Bio::Tools::Glimmer');
    use_ok('Bio::Tools::MZEF');  
    use_ok('Bio::SeqIO');
}

# Genscan report
my $genscan = Bio::Tools::Genscan->new('-file' => test_input_file('genomic-seq.genscan'));
ok $genscan;

# original sequence
my $seqin = Bio::SeqIO->new('-file' => test_input_file('genomic-seq.fasta'),
			    '-format' => "fasta");
ok $seqin;
my $seq = $seqin->next_seq();
$seqin->close();
ok $seq;

# scan through the report
my $fea;
my $pred_num = 0;
my ($prtseq, $cds, $tr_cds);
while(my $gene = $genscan->next_prediction()) {
    $gene->attach_seq($seq) if $seq;
    $pred_num++;

    if($pred_num == 1) {
	$fea = ($gene->exons())[0];
	is $fea->strand(), -1, 
	     "strand match (".$fea->strand()."  and -1)";
	$fea = ($gene->poly_A_site());
	is $fea->score(), 1.05, 
             "score match (".$fea->score()." and 1.05)";
    }
    if($pred_num == 2) {
	$fea = ($gene->exons("Initial"))[0];
	is $fea->strand(), 1, 
	"strand match (".$fea->strand()." and 1)";
	is $fea->score(), 4.46, 
             "score match (".$fea->score()." and 4.46)";
    }
    if($pred_num == 3) {
	my @exons = $gene->exons("Initial");
	is scalar(@exons), 0, 
	     "initial exons ".scalar(@exons);
	$fea = ($gene->exons())[0];
	is $fea->score(),  1.74, 
             "score match ".$fea->score();
    }
    if($seq) {
	$prtseq = $gene->predicted_protein()->seq();
        $cds = $gene->cds();
	ok($cds);
	$tr_cds = $cds->translate()->seq();
	$tr_cds =~ s/\*$//;
	is( lc($prtseq), lc($tr_cds),
	    "predicted and extracted protein seqs match");
    }
}

# Genscan report with no genes predicted
my $null_genscan = Bio::Tools::Genscan->new('-file' => test_input_file('no-genes.genscan'));
ok $null_genscan;
my $no_gene = $null_genscan->next_prediction;
my @exons = $no_gene->exons;
is($#exons,-1);

# MZEF report
my $mzef = Bio::Tools::MZEF->new('-file' => test_input_file('genomic-seq.mzef'));
ok $mzef;

my $exon_num = 0;
my $gene = $mzef->next_prediction();

is($gene->exons, 23);

# Genemark testing
my $genemark = Bio::Tools::Genemark->new('-file' => test_input_file('genemark.out'));

my $gmgene = $genemark->next_prediction();
is $gmgene->seq_id(), "Hvrn.contig8";
is $genemark->analysis_date(), "Thu Mar 22 10:25:00 2001";

my $i = 0;
my @num_exons = (1,5,2,1,9,5,3,2,3,2,1,2,7);
while($gmgene = $genemark->next_prediction()) {
    $i++;
    my @gmexons = $gmgene->exons();
    is scalar(@gmexons), $num_exons[$i];

    if($i == 5) {
	my $gmstart = $gmexons[0]->start();
	is $gmstart, 23000;

	my $gmend = $gmexons[0]->end();
	is $gmend, 23061;
    }
}

# Genemark testing (prokaryotic gene fragment)
$genemark = Bio::Tools::Genemark->new('-file'    => test_input_file('genemark-fragment.out'),
                                         '-seqname' => 'AAVN02000021.1');

$gmgene = $genemark->next_prediction();
is $gmgene->seq_id(), 'AAVN02000021.1','Genemark tests';
is $gmgene->start(), 2;
is $gmgene->end(), 214;
is $gmgene->strand(), '1';
my ($gmexon) = $gmgene->exons();
isa_ok $gmexon->location(), 'Bio::Location::Fuzzy';
is $gmexon->location->start_pos_type(), 'BEFORE';
is $gmexon->location->max_start(), 2;
is $gmexon->location->end_pos_type(), 'EXACT';
is $gmexon->location->end(), 214;

$gmgene = $genemark->next_prediction();
is $gmgene->seq_id(), 'AAVN02000021.1';
is $gmgene->start, 459;
is $gmgene->end, 596;
is $gmgene->strand(), '1';
($gmexon) = $gmgene->exons();
isa_ok $gmexon->location, 'Bio::Location::Fuzzy';
is $gmexon->location->start_pos_type(), 'EXACT';
is $gmexon->location->start(), 459;
is $gmexon->location->end_pos_type(), 'AFTER';
is $gmexon->location->min_end(), 596;

# Glimmer testing (GlimmerM)
my $glimmer_m = Bio::Tools::Glimmer->new('-file' => test_input_file('GlimmerM.out'));
$gmgene = $glimmer_m->next_prediction;

ok($gmgene);
is($gmgene->seq_id, 'gi|23613028|ref|NC_004326.1|');
is($gmgene->source_tag, 'GlimmerM_3.0');
is($gmgene->primary_tag, 'transcript');
is(($gmgene->get_tag_values('Group'))[0], 'GenePrediction1');
my @glim_exons = $gmgene->exons;
is(scalar (@glim_exons), 1);
is($glim_exons[0]->start, 461);
is($glim_exons[0]->end, 523);
is($glim_exons[0]->strand, -1);
is(($glim_exons[0]->get_tag_values('Group'))[0], 'GenePrediction1');

@num_exons = (0,1,3,1,4,2,5,2,8,3,5);
$i = 1;
while($gmgene = $glimmer_m->next_prediction()) {
    $i++;
    is(($gmgene->get_tag_values('Group'))[0],"GenePrediction$i");
    @glim_exons = $gmgene->exons();    
    is scalar(@glim_exons), $num_exons[$i];
    if($i == 5) {
	is $glim_exons[1]->start, 23910;
	is $glim_exons[1]->end, 23956;
	is $glim_exons[1]->strand, 1;
    }
}

# Glimmer testing (GlimmerHMM)
my $glimmer_hmm = Bio::Tools::Glimmer->new('-file' => test_input_file('GlimmerHMM.out'));
my $ghmmgene = $glimmer_hmm->next_prediction;

ok($ghmmgene);
is($ghmmgene->seq_id, 'gi|23613028|ref|NC_004326.1|');
is($ghmmgene->source_tag, 'GlimmerHMM');
is($ghmmgene->primary_tag, 'transcript');
is($ghmmgene->exons, 1);

@num_exons = qw(0 1 2 4 2 2 1 1 1 2 2 2 10 4 1 1); # only first few tested
$i = 1;
while ($ghmmgene = $glimmer_hmm->next_prediction) {
  $i++;
  my @ghmm_exons = $ghmmgene->exons;    
  is(scalar(@ghmm_exons), $num_exons[$i]) if $i <= $#num_exons;
  if ($i == 9) {
    is( $ghmm_exons[1]->start, 5538 );
    is( $ghmm_exons[1]->end,   5647 );
    cmp_ok( $ghmm_exons[1]->strand, '>', 0  );
  }
}
is($i, 44);

# Glimmer testing (Glimmer 2.X)
my $glimmer_2 = Bio::Tools::Glimmer->new('-file' => test_input_file('Glimmer2.out'),
										 '-seqname' => 'BCTDNA',
										 '-seqlength' => 29940,);
my $g2gene = $glimmer_2->next_prediction;

ok($g2gene);
is($g2gene->seq_id, 'BCTDNA');
is($g2gene->source_tag, 'Glimmer_2.X');
is($g2gene->primary_tag, 'gene');
is($g2gene->start, 292);
is($g2gene->end, 1623);
is($g2gene->frame, 0);
is($g2gene->strand, 1);

$i = 1;
while ($g2gene = $glimmer_2->next_prediction) {
    $i++;
    if ($i == 2) {
        is($g2gene->start, 2230);
        is($g2gene->end, 2349);
        is($g2gene->strand, -1);
        is($g2gene->frame, 0);		
	} elsif ($i == 25) {
        isa_ok($g2gene->location, 'Bio::Location::SplitLocationI');
        my @sublocations = $g2gene->location->sub_Location();
        is(scalar (@sublocations), 2);
        is($sublocations[0]->start, 29263);
        is($sublocations[0]->end, 29940);
        is($sublocations[1]->start, 1);
        is($sublocations[1]->end, 9);
        is($g2gene->strand, 1);
        is($g2gene->frame, 0);
    }
}
is($i, 25);


# Glimmer testing (Glimmer 3.X)
my $glimmer_3 = Bio::Tools::Glimmer->new('-file' => test_input_file('Glimmer3.predict'),
										 '-detail' => test_input_file('Glimmer3.detail'));
my $g3gene = $glimmer_3->next_prediction;

ok($g3gene);
is($g3gene->seq_id, 'BCTDNA');
is($g3gene->source_tag, 'Glimmer_3.X');
is($g3gene->primary_tag, 'gene');
is($g3gene->score, '9.60');
isa_ok($g3gene->location, 'Bio::Location::SplitLocationI');
my @sublocations = $g3gene->location->sub_Location();
is(scalar (@sublocations), 2);
is($sublocations[0]->start, 29263);
is($sublocations[0]->end, 29940);
is($sublocations[1]->start, 1);
is($sublocations[1]->end, 9);
is($g3gene->frame, 0);

$i = 1;
while ($g3gene = $glimmer_3->next_prediction) {
    $i++;
    if ($i == 13) {
        is($g3gene->start, 13804);
        is($g3gene->end, 14781);
        is($g3gene->strand, -1);
        is($g3gene->frame, 0);
        is($g3gene->score, '5.51');
		
        my ($orfid) = $g3gene->has_tag('Group') ? $g3gene->get_tag_values('Group') : undef;
        is($orfid, 'GenePrediction_00015');
    }
}
is($i, 27);

# Glimmer 3.X (prokaryotic gene fragment)
my $glimmer_3a = Bio::Tools::Glimmer->new(
                                         '-file'   => test_input_file('glimmer3-fragment.predict'),
                                         '-detail' => test_input_file('glimmer3-fragment.detail'), 
                                        );
my $g3gene_a = $glimmer_3a->next_prediction;

ok($g3gene_a);

isa_ok $g3gene_a->location(), 'Bio::Location::Fuzzy';
is $g3gene_a->location->start_pos_type(), 'BEFORE';
is $g3gene_a->location->max_start(), 1;
is $g3gene_a->location->end_pos_type(), 'EXACT';
is $g3gene_a->location->end(), 674;
is $g3gene_a->frame(), 2;

for (1..3) { $g3gene_a = $glimmer_3a->next_prediction; }

isa_ok $g3gene_a->location(), 'Bio::Location::Fuzzy';
is $g3gene_a->location->start_pos_type(), 'EXACT';
is $g3gene_a->location->start(), 2677;
is $g3gene_a->frame(), 0;
is $g3gene_a->location->end_pos_type(), 'AFTER';
is $g3gene_a->location->min_end(), 2932;
is $g3gene_a->score, '5.63';

# Fgenesh
my $fgh = Bio::Tools::Fgenesh->new(
                                   '-file' => test_input_file('fgenesh.out'),
                                  );

my $fghgene = $fgh->next_prediction();

ok($fghgene);
is($fghgene->seq_id, 'gi|1914348|emb|Z81551.1|');
is($fghgene->source_tag, 'Fgenesh');
is($fghgene->start(), 29);
is($fghgene->end(), 1869);
cmp_ok($fghgene->strand(), '<', 0);

$i = 0;
@num_exons = (2,5,4,8);

while ($fghgene = $fgh->next_prediction()) {

    $i++;
    my @fghexons = $fghgene->exons();
    is(scalar(@fghexons), $num_exons[$i]);

    if ($i == 2) {
        cmp_ok($fghexons[0]->strand(), '>', 0);
        is($fghexons[0]->primary_tag(), 'InitialExon');
        is($fghexons[0]->start(), 14778);
        is($fghexons[0]->end(), 15104);
        cmp_ok($fghexons[3]->strand(), '>', 0);
        is($fghexons[3]->primary_tag(), 'TerminalExon');        
        is($fghexons[3]->start(), 16988);
        is($fghexons[3]->end(), 17212);
    }

}

is($i, 3);
BioPerl-1.007002/t/Tools/Hmmer.t000444000766000024       534213155576321 16320 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: Hmmer.t 14989 2008-11-11 19:52:02Z cjfields $

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 29);
	
	use_ok('Bio::Tools::HMMER::Domain');
	use_ok('Bio::Tools::HMMER::Set');
	use_ok('Bio::Tools::HMMER::Results');
}

my ($domain,$set,$homol,$rev,$res,$dom,@doms);
$domain = Bio::Tools::HMMER::Domain->new(-verbose=>1);

is ref($domain), 'Bio::Tools::HMMER::Domain';

$domain->start(50);
$domain->end(200);
$domain->hstart(10);
$domain->hend(100);
$domain->seqbits(50);
$domain->bits(20);
$domain->evalue(0.0001);
$domain->seq_id('silly');


# test that we can get out forward and reverse homol_SeqFeatures
$homol = $domain->feature2();
is $homol->start(), 10;

$rev = $domain;

is $rev->start(), 50;

$set = Bio::Tools::HMMER::Set->new();
$set->add_Domain($domain);

@doms = $set->each_Domain();
$dom = shift @doms;

is $dom->start(), 50;

$set->bits(300);
$set->evalue(0.0001);
$set->name('sillyname');
$set->desc('a desc');
$set->accession('fakeaccesssion');
is $set->bits(), 300;
is $set->evalue(), 0.0001;
is $set->name(), 'sillyname';
is $set->desc, 'a desc';
is $set->accession, 'fakeaccesssion';

$res = Bio::Tools::HMMER::Results->new( -file => test_input_file('hmmsearch.out') , -type => 'hmmsearch');
my $seen =0;
is $res->hmmfile, "HMM";
is $res->seqfile, "HMM.dbtemp.29591";

my $first = 0;
foreach $set ( $res->each_Set) {
    foreach $domain ( $set->each_Domain ) {
    #print STDERR "Got domain ",$domain->seq_id," start ",$domain->start," end ",$domain->end,"\n";
    # do nothing for the moment
      $seen = 1;
  }
}
is $seen, 1;

is $res->number, 1215;

$res = Bio::Tools::HMMER::Results->new( -file => test_input_file('hmmpfam.out') , 
					-type => 'hmmpfam');

is ($res->number, 2);

# parse HMM 2.2 files

$res = Bio::Tools::HMMER::Results->new( -file => test_input_file('L77119.hmmer'),
					-type => 'hmmpfam');
$seen =0;
is $res->hmmfile, 'Pfam';
is $res->seqfile, 'L77119.faa';
foreach $set ( $res->each_Set) {
    # only one set anyways

    is($set->name, 'gi|1522636|gb|AAC37060.1|');
    is($set->desc, 'M. jannaschii predicted coding region MJECS02 [Methanococcus jannaschii]');
    is($set->accession, '[none]');
    foreach $domain ( $set->each_Domain ) {
	#print STDERR "Got domain ",$domain->seq_id," start ",$domain->start," end ",$domain->end,"\n";
    # do nothing for the moment
	is($domain->start, 280);
	is($domain->end, 481);
	is($domain->bits, -105.2);
	is($domain->evalue, 0.0022 );
    }
}
is ($res->number, 1);

# test for bugs #(1189,1034,1172)
$res = Bio::Tools::HMMER::Results->new( -file => test_input_file('hmmsearch.out') , 
					-type => 'hmmsearch');
my $res2 = $res->filter_on_cutoff(100,50);
ok($res2);
is($res2->number, 604);
BioPerl-1.007002/t/Tools/IUPAC.t000444000766000024       352613155576321 16113 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 46);

    use_ok('Bio::Tools::IUPAC');
    use_ok('Bio::Seq');
    use_ok('Bio::PrimarySeq');
}


# IUPAC sequences and regular expressions

my $ambiseq = Bio::Seq->new(
    -seq      => 'ARTCGTTGN',
    -alphabet => 'dna',
);

my $ambiprimaryseq = Bio::Seq->new(
    -seq      => 'ARTCGTTGN',
    -alphabet => 'dna',
);

ok my $iupac = Bio::Tools::IUPAC->new( -seq => $ambiprimaryseq );

ok $iupac = Bio::Tools::IUPAC->new( -seq => $ambiseq );

ok my $regexp = $iupac->regexp, 'Regexp';
is $regexp, 'A[AGR]TCGTTG[ACGTBDHKMNRSVWY]';

$regexp = $iupac->regexp(1);
is $regexp, 'A[AGR][TU]CG[TU][TU]G[ACGTUBDHKMNRSVWY]', 'Regexp';


is $iupac->count(), 8, 'Count';

my @seqs;
while (my $uniqueseq = $iupac->next_seq()) {
    push @seqs, $uniqueseq->seq;
    is $uniqueseq->isa('Bio::PrimarySeqI'), 1;
    like $uniqueseq->seq, qr/$regexp/i;
}

@seqs = sort @seqs;
is_deeply \@seqs, [ 'AATCGTTGA', 'AATCGTTGC', 'AATCGTTGG', 'AATCGTTGT',
                    'AGTCGTTGA', 'AGTCGTTGC', 'AGTCGTTGG', 'AGTCGTTGT' ];

like $ambiseq->seq, qr/$regexp/i, 'Regexp matches ambiguous sequences';
like 'ARTCGTTGW', qr/$regexp/i;


# IUPAC code methods

my %iupac;
ok %iupac = $iupac->iupac_iub(), 'Nucleic IUPAC';
ok exists $iupac{'A'};
ok not exists $iupac{'Z'};

ok %iupac = $iupac->iupac_iub_amb();
ok exists $iupac{'N'};
ok not exists $iupac{'A'};

ok %iupac = $iupac->iupac_rev_iub();

ok %iupac = $iupac->iupac_iup(), 'Proteic IUPAC';
ok exists $iupac{'A'};
ok exists $iupac{'Z'};

ok %iupac = $iupac->iupac_iup_amb();
ok exists $iupac{'B'};
ok not exists $iupac{'A'};

ok %iupac = $iupac->iupac();
ok not(exists $iupac{'Z'});

ok %iupac = $iupac->iupac_amb();
ok not(exists $iupac{'A'});

ok %iupac = Bio::Tools::IUPAC->new->iupac_iup;

BioPerl-1.007002/t/Tools/Lucy.t000555000766000024       236313155576321 16167 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 22);
	
    use_ok('Bio::Tools::Lucy');
}

my @params = (adv_stderr => 1, seqfile => test_input_file('lucy.seq'), rev_desig => 'R'); 
# Bio::Tools::Lucy will find .qual, .info, and .stderr files in this folder 

my $lucyObj = Bio::Tools::Lucy->new(@params);
isa_ok $lucyObj,'Bio::Tools::Lucy';
ok $lucyObj->seqfile();
$lucyObj->adv_stderr(1);
my $stderr = $lucyObj->adv_stderr();
ok $stderr;
my $names =$lucyObj->get_sequence_names();
ok $names;
my $seq = shift @$names;
is $seq, 'TaLr1010B10R';
is $lucyObj->length_raw("$seq"), 1060;
is $lucyObj->length_clear("$seq"), 420;
is $lucyObj->start_clear("$seq"), 86;
is $lucyObj->end_clear("$seq"), 505;
ok $lucyObj->avg_quality("$seq");
ok $lucyObj->full_length("$seq");
ok $lucyObj->polyA("$seq");
is $lucyObj->direction("$seq"), 'R';
ok $lucyObj->per_GC("$seq");
ok $lucyObj->sequence("$seq");
ok $lucyObj->quality("$seq");
my $seqObj = $lucyObj->get_Seq_Obj("$seq");
ok $seqObj;
my $seqObjs = $lucyObj->get_Seq_Objs();
ok $seqObjs;

my $rejects = $lucyObj->get_rejects();
ok $rejects;
my ($key) = (sort keys %$rejects);
is $key, 'TaLr1011A07R';
is $rejects->{$key}, 'Q'; 
BioPerl-1.007002/t/Tools/Match.t000444000766000024       267213155576321 16307 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: Match.t,v 1.15 2007/06/27 10:16:38 sendu Exp $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 38,
			   -requires_module => 'URI::Escape');
	
    use_ok('Bio::Tools::Match');
}

ok my $parser = Bio::Tools::Match->new(-file => test_input_file('match.output'));

my $count = 0;
my @expected = ([qw(4338 4349 1.000 0.945 V$MYOD_01)],
                [qw(7390 7401 1.000 0.932 V$MYOD_01)],
                [qw(8503 8514 1.000 0.941 V$MYOD_01)],
                [qw(8767 8778 1.000 0.937 V$MYOD_01)],
                [qw(33 47 0.693 0.779 V$E47_01)]);
while (my $feat = $parser->next_result) {
    $count++;
    my @exp = @{shift(@expected)};
    
    isa_ok $feat, 'Bio::SeqFeature::Generic';
    is $feat->source_tag, 'transfac_match', 'correct source';
    is $feat->start, shift(@exp), 'feature start correct';
    is $feat->end, shift(@exp), 'feature end correct';
    
    my $core_score = $feat->score;
    my $matrix_score = ($feat->annotation->get_Annotations('matrix_score'))[0]->value;
    my $matrix_id = ($feat->annotation->get_Annotations('matrix_id'))[0]->value;
    
    is $core_score, shift(@exp), 'feature core score correct';
    is $matrix_score, shift(@exp), 'feature matrix score correct';
    is $matrix_id, shift(@exp), 'feature matrix id correct';
    
    last if $count == 5;
}

is $count, 5, "correct number of results managed to get tested";
BioPerl-1.007002/t/Tools/Primer3.t000555000766000024       260013155576321 16566 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$


use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 14);

    use_ok('Bio::Tools::Primer3');
}

my ($p3, $num, $primer);

ok $p3 = Bio::Tools::Primer3->new(-file => test_input_file('primer3_output.txt'));
ok $num = $p3->number_of_results;
is $num, 5 or diag "Got $num";
ok $num = $p3->all_results;
is defined $num, 1 or diag "Can't get all results";
ok $num = $p3->primer_results(1);
is defined $num, 1 or diag "Can't get results for 1";
ok $primer = $p3->next_primer;
isa_ok $primer, "Bio::Seq::PrimedSeq" or diag
  "reference for primer stream is not right";

# get the left primer
my $left_primer = $primer->get_primer('left');

# get the sequence for that primer. This is a test to verify behavior 
# on the bioperl list in or about 050315
my $seqobj = $left_primer->seq();

my $seq = $seqobj->seq();

my $other_left_primer = $primer->get_primer();

# a different way to access the primers in the stream
my $alt = $p3->primer_results(0,'PRIMER_LEFT_INPUT');

# next one
ok $primer = $p3->next_primer;
# get the left primer
my $left_primer_seq = $primer->get_primer('left')->seq;
is $left_primer_seq->seq, "GAGGGTAACACGCTGGTCAT";

# bug 2862
ok $p3 = Bio::Tools::Primer3->new(-file => test_input_file('bug2862.pmr'));
$num = 0;
while ($p3->next_primer) { $num++ };
is $p3->number_of_results, $num, 'bug 2862';
BioPerl-1.007002/t/Tools/Promoterwise.t000444000766000024       121513155576321 17742 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 7);
	
    use_ok('Bio::Tools::Promoterwise');
}

my $file = test_input_file('promoterwise.out');
my $parser = Bio::Tools::Promoterwise->new(-file=>$file);
isa_ok $parser,'Bio::Tools::Promoterwise';
my @fp;
while (my $fp = $parser->next_result){
  push @fp,$fp;
}
my $first = $fp[0]->feature1;
my $second = $fp[0]->feature2;

my @sub = $first->sub_SeqFeature;
my @sub2 = $second->sub_SeqFeature;

is $sub[0]->start,4;
is $sub2[0]->start,29;
is $sub[0]->end,18;
is $sub2[0]->end,43;
is $sub[0]->score,1596.49
BioPerl-1.007002/t/Tools/PrositeScan.t000444000766000024       265013155576321 17501 0ustar00cjfieldsstaff000000000000use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 3);

    use_ok('Bio::Tools::PrositeScan');
    use_ok('Bio::SeqFeature::FeaturePair');
}

# Note: data generated by running
#
#   ./ps_scan.pl --pfscan ./pfscan -d prosite.dat -o fasta \
#       t/data/test.fasta > t/data/ps_scan/out.PrositeScan
#
# followed by a manual removal of some of the output to simplify the test.

subtest "Predictions" => sub {
    my $factory = Bio::Tools::PrositeScan->new(
          '-file'   => test_input_file('ps_scan/out.PrositeScan'),
          '-format' => 'fasta'
    );

    my $expected_matches = [
        { seq_id => 'roa1_drome', coords => [253, 256], psac => 'PS00001', subseq => 'NNSF' },
        { seq_id => 'roa1_drome', coords => [270, 273], psac => 'PS00001', subseq => 'NNSW' },
        { seq_id => 'roa2_drome', coords => [344, 349], psac => 'PS00008', subseq => 'GNNQGF' },
        { seq_id => 'roa2_drome', coords => [217, 355], psac => 'PS50321', subseq => re(qr/NR.{135}NN/) },
    ];

    my $actual_matches = [];
    while( my $match = $factory->next_prediction ) {
        push @$actual_matches, {
            seq_id  =>   $match->seq_id,
            coords  => [ $match->start, $match->end ],
            psac    =>   $match->hseq_id,
            subseq  =>   $match->feature1->seq->seq,
        };
    }

    cmp_deeply( $actual_matches, $expected_matches, 'Comparing parsed prediction input' );
};
BioPerl-1.007002/t/Tools/Pseudowise.t000555000766000024       210113155576321 17370 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 21);
	
	use_ok('Bio::Tools::Pseudowise');
}


my $inputfilename= test_input_file('pseudowise.out');
my $parser = Bio::Tools::Pseudowise->new(-file => $inputfilename);
my @gene;
while (my $gene= $parser->next_prediction){
    push @gene, $gene;
}
my ($g) = @gene;
my @e = $g->sub_SeqFeature;

is ($g->primary_tag, 'pseudogene');
is ($g->source_tag, 'pseudowise');

is(($g->get_tag_values('Synonymous'))[0],7);
is(($g->get_tag_values('Nonsynonymous'))[0],18);
is(($g->get_tag_values('Ka/Ks'))[0],2.57);
is(($g->get_tag_values('Unlikely'))[0],0);
is(($g->get_tag_values('Identical'))[0],5);
is(($g->get_tag_values('Stop'))[0],0);
is(($g->get_tag_values('Total codons'))[0],30);
is(($g->get_tag_values('Frameshift'))[0],0);
is(($g->get_tag_values('Intron'))[0],1);

is($g->start,163);
is($g->end,626);
is($g->strand,1);
is($e[0]->start, 163);
is($e[0]->end,213);
is($e[0]->strand,1);
is($e[1]->start,585);
is($e[1]->end,626);
is($e[1]->strand,1);
BioPerl-1.007002/t/Tools/QRNA.t000444000766000024       345513155576321 16014 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 30);
	
	use_ok('Bio::Tools::QRNA');
}

my $inputfilename= test_input_file('ecoli-trna-qrna.out');
ok my $parser = Bio::Tools::QRNA->new(-file => $inputfilename);

my $rnacount = 0;
while( my $f = $parser->next_feature ) {
    if( $f->primary_tag eq 'RNA' ) { # winning model is primary tag
	if( ! $rnacount ) { # 1st time through let's test
	    is($f->feature1->start,4);
	    is($f->feature1->end,  70);
	    is($f->score, 22.147);
	    is($f->feature1->seq_id,'DA0780-1-');
	    
	    is($f->feature2->start, 4);
	    is($f->feature2->end,  70);
	    is($f->feature2->seq_id, 'ECOLI-3979754-');
	    is(($f->get_tag_values('alignment_len'))[0], 70);
	    is(($f->get_tag_values('alignment_pid'))[0], '72.86');
	    is(($f->get_tag_values('COD_score'))[0], '16.954');
	    is(($f->get_tag_values('COD_logoddspost'))[0], '-4.365');
	    is(($f->get_tag_values('OTH_score'))[0], '21.319');
	    is(($f->get_tag_values('OTH_logoddspost'))[0], '0.000');
	}
	$rnacount++;
    }
}
is($rnacount, 21);
$inputfilename= test_input_file('qrna-relloc.out');
$parser = Bio::Tools::QRNA->new(-file => $inputfilename);

my $qrna = $parser->next_feature;
is($qrna->primary_tag, 'COD');
is($qrna->source_tag, 'qrna');
is($qrna->feature1->seq_id, 'Contig1');
is($qrna->feature2->seq_id, 'chr5.pseudo');
is($qrna->feature1->start, 24732);
is($qrna->feature1->end, 24881);

is($qrna->feature2->start, 527251);
is($qrna->feature2->end, 527400);

is($parser->seq_file,'tst.out');
is($parser->RNA_model, '/mix_tied_linux.cfg');
is($parser->PAM_model, 'BLOSUM62 scaled by 1.000');
is($parser->program_name, 'qrna');
is($parser->program_version, '1.2b');
is($parser->program_date, 'Tue Dec 18 15:04:38 CST 2001');
BioPerl-1.007002/t/Tools/RandDistFunctions.t000444000766000024        66213155576321 20631 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 5);
	
    use_ok('Bio::Tools::RandomDistFunctions');
}


ok my $dist = Bio::Tools::RandomDistFunctions->new();

ok($dist->rand_exponentional_distribution(1.0));
ok($dist->rand_geometric_distribution(0.9));
ok($dist->rand_normal_distribution);

# TODO? these tests seem pretty pointless!
BioPerl-1.007002/t/Tools/RepeatMasker.t000444000766000024       336213155576321 17633 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 28);

    use_ok('Bio::Tools::RepeatMasker');
}

my $inputfilename = test_input_file('repeatmasker.fa.out');
my $parser = Bio::Tools::RepeatMasker->new(-file => $inputfilename);

{
    my $rpt = $parser->next_result;
    is ($rpt->feature1->seq_id, "contig11600");
    is ($rpt->feature1->start, 1337);
    is ($rpt->feature1->end, 1407);
    is ($rpt->feature1->strand, 1);
    is ($rpt->feature1->primary_tag, "Simple_repeat");
    is ($rpt->feature1->source_tag, "RepeatMasker");
    is (scalar $rpt->feature1->get_tag_values('Target'), 3);
    is ($rpt->feature2->seq_id, "(TTAGGG)n");
    is ($rpt->feature2->start, 2);
    is ($rpt->feature2->end, 76);
    is ($rpt->feature1->primary_tag, "Simple_repeat");
    is ($rpt->feature1->source_tag, "RepeatMasker");
    is (scalar $rpt->feature2->get_tag_values('Target'), 3);
}

$parser->next_result for 1,2,3;

{
    my $rpt = $parser->next_result;
    is ($rpt->feature1->seq_id, "SL2.30ch10");
    is ($rpt->feature1->start, 38849);
    is ($rpt->feature1->end, 38940);
    is ($rpt->feature1->strand, -1);
    is ($rpt->feature1->primary_tag, "LTR");
    is ($rpt->feature1->source_tag, "RepeatMasker");
    is_deeply ( [ $rpt->feature1->get_tag_values('Target') ], ['LTR_PGSC0003DMS000000301_448',10681,10775] );
    is ($rpt->feature2->seq_id, "LTR_PGSC0003DMS000000301_448");
    is ($rpt->feature2->start, 10681);
    is ($rpt->feature2->end, 10775);
    is ($rpt->feature2->strand, -1);
    is ($rpt->feature1->primary_tag, "LTR");
    is ($rpt->feature1->source_tag, "RepeatMasker");
    is_deeply ([$rpt->feature2->get_tag_values('Target')],['SL2.30ch10',38849,38940]);
}

BioPerl-1.007002/t/Tools/Seg.t000444000766000024       217513155576321 15767 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 15);
	
	use_ok('Bio::Tools::Seg');
}

my ($infile, $parser) ;

$infile = test_input_file('seg.out');
ok ($parser = Bio::Tools::Seg->new(-file=>$infile), 'parser defined') ;

my @feat;
while ( my $feat = $parser->next_result ) {
	push @feat, $feat;
}

is scalar(@feat), 3;

# seq 0
#>LBL_0012(32-46) complexity=2.47 (12/2.20/2.50)
#gdggwtfegwggppe

# seq 1
#>LBL_0012(66-80) complexity=2.31 (12/2.20/2.50)
#kfssrasakavakks

# seq 2
#>LBL_0012(123-138) complexity=2.31 (12/2.20/2.50)
#svivsqsqgvvkgvgv

my $raa_testdata = [
	[ 'LBL_0012', 32, 46, 2.47   ],
	[ 'LBL_0012', 66, 80, 2.31   ],
	[ 'LBL_0012', 123, 138, 2.31 ],
] ;

for (0..( scalar(@feat)-1 )) {
	is ( $feat[$_]->seq_id, $raa_testdata->[$_]->[0], "seq id for seq $_ identified" ) ;
	is ( $feat[$_]->start,  $raa_testdata->[$_]->[1], "start for seq $_ identified"  ) ;
	is ( $feat[$_]->end,    $raa_testdata->[$_]->[2], "end for seq $_ identified"    ) ;
	is ( $feat[$_]->score,  $raa_testdata->[$_]->[3], "score for seq $_ identified"  ) ;
}
BioPerl-1.007002/t/Tools/SiRNA.t000444000766000024       243513155576321 16164 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 11);
	
	use_ok('Bio::Tools::SiRNA');
	use_ok('Bio::Seq');
	use_ok('Bio::SeqIO');
}

my $DEBUG = test_debug();

my $input = Bio::SeqIO->new( -file 	=> test_input_file('NM_002254.gb'),
			     -format 	=> 'Genbank' );
my $seq = $input->next_seq;

isa_ok( $input, 'Bio::SeqIO' ) ;


#object creation
my $sirna = Bio::Tools::SiRNA->new( -target 	=> $seq,
                                     );
isa_ok( $sirna, 'Bio::Tools::SiRNA' ) ;

# first test - cds only
my @pairs = $sirna->design;
is ( scalar(@pairs), 62, "CDS only: got ". scalar(@pairs) );


# next test - include 3prime utr
my @feats = $seq->remove_SeqFeatures;
foreach my $feat (@feats) {
    $seq->add_SeqFeature($feat) unless
	($feat->primary_tag eq 'Target' or $feat->isa('Bio::SeqFeature::SiRNA::Pair'));
}
ok( $sirna->include_3pr(1) ) ;
@pairs = $sirna->design;
print "With 3p UTR: got ",scalar(@pairs),"\n" if $DEBUG;
is( scalar(@pairs), 124 );


#third test - naked sequence
my $newseq = Bio::Seq->new( -seq => $seq->seq);
isa_ok($newseq, 'Bio::Seq') ;

ok( $sirna->target($newseq) );
@pairs = $sirna->design;
print "Bare sequence: got ",scalar(@pairs),"\n" if $DEBUG;
is ( scalar(@pairs),  126 ) ;
BioPerl-1.007002/t/Tools/Sigcleave.t000444000766000024       176613155576321 17160 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 18);
	
	use_ok('Bio::PrimarySeq');
	use_ok('Bio::Tools::Sigcleave');
}

#load n-terminus of MGR5_HUMAN as test seq
my $protein = "MVLLLILSVLLLKEDVRGSAQSSERRVVAHMPGDIIIGALFSVHHQPTVDKVHERKCGAVREQYGI";

ok my $seq= Bio::PrimarySeq->new(-seq => $protein);

ok my $sig = Bio::Tools::Sigcleave->new();
ok $sig->seq($seq);
ok my $sout = $sig->seq;
is $sout->seq, $protein;
is $sig->threshold, 3.5;
is $sig->threshold(5), 5;
is $sig->matrix, 'eucaryotic';
is $sig->matrix('procaryotic'), 'procaryotic';
is $sig->matrix('eucaryotic'), 'eucaryotic';

like $sig->pretty_print, qr/Maximum score 7/;
ok my %results = $sig->signals;

is $results{9}, 5.2, "unable to get raw sigcleave results";


$sig = Bio::Tools::Sigcleave->new(-seq=>$protein,
				 -threshold=>5);
ok %results = $sig->signals;
is $results{9}, 5.2, "unable to get raw sigcleave results";
is $sig->result_count, 5;
BioPerl-1.007002/t/Tools/Signalp.t000444000766000024       214013155576321 16636 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 11);
	
    use_ok('Bio::Tools::Signalp');
}

# global setting

my $verbose = test_debug();

# shared variables

my $infile;
my $parser;
my @feat;

# negative example without "YES" features

ok $infile = test_input_file('signalp.negative.out');
ok $parser = Bio::Tools::Signalp->new(-file=>$infile, -verbose=>$verbose);

while ( my $feat = $parser->next_result ) {
  push @feat, $feat;
}
is @feat, 0;
is $parser->_seqname, 'my_fasta_id';
is $parser->_fact1,   'NO';

# positive example with "YES" features

ok $infile = test_input_file('signalp.positive.out');
ok $parser = Bio::Tools::Signalp->new(-file=>$infile, -verbose=>$verbose);

#
#  The current module does NOT parse stuff properly
#  It is probably from version 2 but version 3 is used today
#  This has to be investigated!!!! --Torsten
#  FIXME / TODO? / BUG / *** 
# 

while ( my $feat = $parser->next_result ) {
  push @feat, $feat;
}
is @feat , 1;
is $parser->_seqname, 'my_fasta_id';
is $parser->_fact1,   'YES';
BioPerl-1.007002/t/Tools/Sim4.t000444000766000024       311013155576321 16053 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: Sim4.t 11525 2007-06-27 10:16:38Z sendu $

use strict;
BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 27);
	
	use_ok('Bio::Tools::Sim4::Results');
}

my $sim4 = Bio::Tools::Sim4::Results->new(-file=> test_input_file('sim4.rev'), -estisfirst=>0);
ok ( $sim4, 'new Sim4 results instance') ;


my $exonset = $sim4->next_exonset;
my @exons = $exonset->sub_SeqFeature(); 

is (scalar(@exons), 10);

my $exon = 1;
is $exons[$exon]->est_hit()->seq_id(), 'HSHNCPA1';
like($exons[$exon]->seq_id(), qr/human/);
is $exons[$exon]->strand(), -1;
is $exons[$exon]->start(), 1048;
is $exons[$exon]->end(), 1117;
is $exons[$exon]->score, 93;
is $exons[$exon]->est_hit()->seqlength(), 1198;


$sim4 = Bio::Tools::Sim4::Results->new(-file=> test_input_file('sim4.for.for'), -estisfirst=>0);
ok ( $sim4, 'new Sim4 results instance') ;

$exonset = $sim4->next_exonset;
@exons = $exonset->sub_SeqFeature(); 

is (scalar(@exons), 4);

$exon = 1;
is $exons[$exon]->est_hit()->seq_id(), 'hs_est';
is $exons[$exon]->seq_id(), 'human';
is $exons[$exon]->strand(), 1;
is $exons[$exon]->start(), 1377;
is $exons[$exon]->end(), 1500;
is $exons[$exon]->score, 99;
is $exons[$exon]->est_hit()->seqlength(), 479;

ok($sim4->next_exonset);
@exons = $exonset->sub_SeqFeature();

is $exons[$exon]->est_hit()->seq_id(), 'hs_est';
is $exons[$exon]->seq_id(), 'human';
is $exons[$exon]->strand(), 1;
is $exons[$exon]->est_hit->start(), 120;
is $exons[$exon]->est_hit->end(), 243;
is $exons[$exon]->score, 99;
is $exons[$exon]->est_hit()->seqlength(), 479;
BioPerl-1.007002/t/Tools/TandemRepeatsFinder.t000444000766000024      2351313155576321 21154 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 66);
	
	use_ok('Bio::Tools::TandemRepeatsFinder');
}

# first, open empty output file
# make sure no results get returned
my $trf =
   Bio::Tools::TandemRepeatsFinder->new( -file => test_input_file('tandem_repeats_finder.noresults')
  );
ok $trf,"Parser created  successfully" ;
my $feat = $trf->next_result;
ok( !defined($feat), "empty results file correctly returns no results" );


# now check some results
$trf =
   Bio::Tools::TandemRepeatsFinder->new( -file => test_input_file('tandem_repeats_finder.dat')
  );
ok $trf,"Second parser created  successfully" ;
my $feat1 = $trf->next_result();

# these are the parameters that should be parsed from 
# the following line:
# Parameters: 2 7 7 80 10 50 12
my $expected_run_parameters = {
                match_weight    => 2,
                mismatch_weight => 7,
                indel_weight    => 7,
                match_prob      => 80,
                indel_prob      => 10,
                min_score       => 50,
                max_period_size => 12
};

# test feature properties
is ( $feat1->seq_id(),      "DDB0169550",             "seq_id for first result correctly parsed");
is ( $feat1->start(),       13936,                    "start for first result correctly parsed");
is ( $feat1->end(),         13960,                    "end for first result correctly parsed");
is ( $feat1->source_tag(),  'Tandem Repeats Finder',  "source tag for first result correctly parsed");
is ( $feat1->primary_tag(), 'tandem repeat',          "primary tag for first result correctly parsed");
is ( $feat1->score(),       50,                       "score for first result correctly parsed");

# test tag values
# all of the data other than start, end, score, and seq_id 
# is stored in tags
my ($seqence_description) = $feat1->get_tag_values( 'sequence_description' );
is ( $seqence_description, "|Masked Chromosomal Sequence| on chromosome: M", "sequence description correctly parsed.");
my ($parameters) = $feat1->get_tag_values( 'run_parameters' );
is_deeply ( $parameters, $expected_run_parameters ,"correctly parsed all run parameters");
my ($period_size) = $feat1->get_tag_values( 'period_size' );
is ( $period_size, 12 ,"correctly parsed period_size for first result");
my ($copy_number) = $feat1->get_tag_values( 'copy_number' );
is ( $copy_number, 2.1 ,"correctly parsed copy_number for first result");
my ($consensus_size) = $feat1->get_tag_values( 'consensus_size' );
is ( $consensus_size, 12 ,"correctly parsed consensus_size for first result");
my ($percent_matches) = $feat1->get_tag_values( 'percent_matches' );
is ( $percent_matches, 100 ,"correctly parsed percent_matches for first result");
my ($percent_indels) = $feat1->get_tag_values( 'percent_indels' );
is ( $percent_indels, 0 ,"correctly parsed percent_indels for first result");
my ($percent_a) = $feat1->get_tag_values( 'percent_a' );
is ( $percent_a, 16 ,"correctly parsed percent_a for first result");
my ($percent_c) = $feat1->get_tag_values( 'percent_c' );
is ( $percent_c, 8 ,"correctly parsed percent_c for first result");
my ($percent_g) = $feat1->get_tag_values( 'percent_g' );
is ( $percent_g, 52 ,"correctly parsed percent_g for first result");
my ($percent_t) = $feat1->get_tag_values( 'percent_t' );
is ( $percent_t, 24 ,"correctly parsed percent_t for first result");
my ($entropy) = $feat1->get_tag_values( 'entropy' );
is ( $entropy, "1.70", "correctly parsed entropy for first result");
my ($repeat_sequence) = $feat1->get_tag_values( 'repeat_sequence' );
is ( $repeat_sequence, "GGCGTAATGGGTGGCGTAATGGGTG", "correctly parsed repeat_sequence for first result");
my ($consensus_sequence) = $feat1->get_tag_values( 'consensus_sequence' );
is ( $consensus_sequence, "GGCGTAATGGGT", "correctly parsed consensus_sequence for first result");

# for the next result just check the sequence _id, start, and end
my $feat2 = $trf->next_result();
is ( $feat2->seq_id(),      "DDB0169550",        "seq_id for second result correctly parsed");
is ( $feat2->start(),       "16937",             "start for second result correctly parsed");
is ( $feat2->end(),         "16965",             "end for second result correctly parsed");
is ( $feat2->source_tag(),  'Tandem Repeats Finder',  "source tag for first result correctly parsed");
is ( $feat2->primary_tag(), 'tandem repeat',          "primary tag for first result correctly parsed");
is ( $feat2->score(),       58,                       "score for first result correctly parsed");

# test tag values
# all of the data other than start, end, score, and seq_id 
# is stored in tags
($seqence_description) = $feat2->get_tag_values( 'sequence_description' );
is ( $seqence_description, "|Masked Chromosomal Sequence| on chromosome: M", "sequence description correctly parsed.");

($parameters) = $feat2->get_tag_values( 'run_parameters' );
is_deeply ( $parameters, $expected_run_parameters ,"correctly reatained all run parameters for second feature");
($period_size) = $feat2->get_tag_values( 'period_size' );
is ( $period_size, 9 ,"correctly parsed period_size for second result");
($copy_number) = $feat2->get_tag_values( 'copy_number' );
is ( $copy_number, "3.2" ,"correctly parsed copy_number for second result");
($consensus_size) = $feat2->get_tag_values( 'consensus_size' );
is ( $consensus_size, 9 ,"correctly parsed consensus_size for second result");
($percent_matches) = $feat2->get_tag_values( 'percent_matches' );
is ( $percent_matches, 100 ,"correctly parsed percent_matches for second result");
($percent_indels) = $feat2->get_tag_values( 'percent_indels' );
is ( $percent_indels, 0 ,"correctly parsed percent_indels for second result");
($percent_a) = $feat2->get_tag_values( 'percent_a' );
is ( $percent_a, 44 ,"correctly parsed percent_a for second result");
($percent_c) = $feat2->get_tag_values( 'percent_c' );
is ( $percent_c, 0 ,"correctly parsed percent_c for second result");
($percent_g) = $feat2->get_tag_values( 'percent_g' );
is ( $percent_g, 10 ,"correctly parsed percent_g for second result");
($percent_t) = $feat2->get_tag_values( 'percent_t' );
is ( $percent_t, 44 ,"correctly parsed percent_t for second result");
($entropy) = $feat2->get_tag_values( 'entropy' );
is ( $entropy, "1.38", "correctly parsed entropy for second result");
($repeat_sequence) = $feat2->get_tag_values( 'repeat_sequence' );
is ( $repeat_sequence, "TATATAGTATATATAGTATATATAGTATA", "correctly parsed repeat_sequence for second result");
($consensus_sequence) = $feat2->get_tag_values( 'consensus_sequence' );
is ( $consensus_sequence, "TATATAGTA", "correctly parsed consensus_sequence for second result");

# now, check the full results again for last result (on a different sequence).
my $feat3 = $trf->next_result();
# test feature properties
is ( $feat3->seq_id(),      "DDB0215018",             "seq_id for first result correctly parsed");
is ( $feat3->start(),       1649,                    "start for first result correctly parsed");
is ( $feat3->end(),         1679,                    "end for first result correctly parsed");
is ( $feat3->source_tag(),  'Tandem Repeats Finder',  "source tag for first result correctly parsed");
is ( $feat3->primary_tag(), 'tandem repeat',          "primary tag for first result correctly parsed");
is ( $feat3->score(),       62,                       "score for first result correctly parsed");

# test tag values
# all of the data other than start, end, score, and seq_id 
# is stored in tags
($seqence_description) = $feat3->get_tag_values( 'sequence_description' );
is ( $seqence_description, "|Masked Chromosomal Sequence| on chromosome: 2F", "sequence description correctly parsed.");

($parameters) = $feat3->get_tag_values( 'run_parameters' );
is_deeply ( $parameters, $expected_run_parameters ,"correctly reatained all run parameters for third feature");
($period_size) = $feat3->get_tag_values( 'period_size' );
is ( $period_size, 1 ,"correctly parsed period_size for third result");
($copy_number) = $feat3->get_tag_values( 'copy_number' );
is ( $copy_number, "31.0" ,"correctly parsed copy_number for third result");
($consensus_size) = $feat3->get_tag_values( 'consensus_size' );
is ( $consensus_size, 1 ,"correctly parsed consensus_size for third result");
($percent_matches) = $feat3->get_tag_values( 'percent_matches' );
is ( $percent_matches, 100 ,"correctly parsed percent_matches for third result");
($percent_indels) = $feat3->get_tag_values( 'percent_indels' );
is ( $percent_indels, 0 ,"correctly parsed percent_indels for third result");
($percent_a) = $feat3->get_tag_values( 'percent_a' );
is ( $percent_a, 0 ,"correctly parsed percent_a for third result");
($percent_c) = $feat3->get_tag_values( 'percent_c' );
is ( $percent_c, 0 ,"correctly parsed percent_c for third result");
($percent_g) = $feat3->get_tag_values( 'percent_g' );
is ( $percent_g, 0 ,"correctly parsed percent_g for third result");
($percent_t) = $feat3->get_tag_values( 'percent_t' );
is ( $percent_t, 100 ,"correctly parsed percent_t for third result");
($entropy) = $feat3->get_tag_values( 'entropy' );
is ( $entropy, "0.00", "correctly parsed entropy for third result");
($repeat_sequence) = $feat3->get_tag_values( 'repeat_sequence' );
is ( $repeat_sequence, "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT", "correctly parsed repeat_sequence for third result");
($consensus_sequence) = $feat3->get_tag_values( 'consensus_sequence' );
is ( $consensus_sequence, "T", "correctly parsed consensus_sequence for third result");

my $empty_feat = $trf->next_result();
ok( !defined($empty_feat), "correctly return undef when no features are left" );


 $trf =
   Bio::Tools::TandemRepeatsFinder->new( -file => test_input_file('tandem_repeats_finder_no_desc.dat')
  );

my $feat_with_seqid = $trf->next_result();
#ensuring that we can parse out seq_id in the file even in the absent of description
is( $feat_with_seqid->seq_id(),"DDB0169550", "Correctly parsed seq_id even if description does not exist" );
BioPerl-1.007002/t/Tools/TargetP.t000444000766000024      1135713155576321 16641 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 124);
	
	use_ok('Bio::Tools::TargetP');
}

my $targetp = Bio::Tools::TargetP->new(
				       -file => test_input_file('targetp.out')
				      );

ok($targetp);

my $items = {
	     '1' => {
		     'id' => 'BC1G_00001.1',
		     'len' => '173',
		     'mTP' => '0.393',
		     'SP'  => '0.024',
		     'other' => '0.683',
		     'loc'   => '_',
		     'RC'    => '4',
		     'tplen' => undef,
		    },
	     '2' => {
		     'id' => 'BC1G_00002.1',
		     'len' => '120',
		     'mTP' => '0.619',
		     'SP'  => '0.040',
		     'other' => '0.458',
		     'loc'   => 'M',
		     'RC'    => '5',
		     'tplen' => '97',
		    },
	     '3' => {
		     'id' => 'BC1G_00003.1',
		     'len' => '323',
		     'mTP' => '0.094',
		     'SP'  => '0.895',
		     'other' => '0.027',
		     'loc'   => 'S',
		     'RC'    => '1',
		     'tplen' => '21',
		    },
	     '4' => {
		     'id' => 'BC1G_00004.1',
		     'len' => '361',
		     'mTP' => '0.402',
		     'SP'  => '0.072',
		     'other' => '0.479',
		     'loc'   => '_',
		     'RC'    => '5',
		     'tplen' => undef,
		    },
	     '5' => {
		     'id' => 'BC1G_00005.1',
		     'len' => '244',
		     'mTP' => '0.526',
		     'SP'  => '0.035',
		     'other' => '0.548',
		     'loc'   => '_',
		     'RC'    => '5',
		     'tplen' => undef,
		    },
	     '6' => {
		     'id' => 'BC1G_00006.1',
		     'len' => '35',
		     'mTP' => '0.234',
		     'SP'  => '0.036',
		     'other' => '0.819',
		     'loc'   => '_',
		     'RC'    => '3',
		     'tplen' => undef,
		    },
	     '7' => {
		     'id' => 'BC1G_00007.1',
		     'len' => '73',
		     'mTP' => '0.292',
		     'SP'  => '0.127',
		     'other' => '0.431',
		     'loc'   => '_',
		     'RC'    => '5',
		     'tplen' => undef,
		    },
	     '8' => {
		     'id' => 'BC1G_00008.1',
		     'len' => '349',
		     'mTP' => '0.088',
		     'SP'  => '0.958',
		     'other' => '0.078',
		     'loc'   => 'S',
		     'RC'    => '1',
		     'tplen' => '82',
		    },
	     '9' => {
		     'id' => 'BC1G_00009.1',
		     'len' => '514',
		     'mTP' => '0.183',
		     'SP'  => '0.102',
		     'other' => '0.735',
		     'loc'   => '_',
		     'RC'    => '3',
		     'tplen' => undef,
		    },
	     '10' => {
		     'id' => 'BC1G_00010.1',
		     'len' => '440',
		     'mTP' => '0.114',
		     'SP'  => '0.088',
		     'other' => '0.865',
		     'loc'   => '_',
		     'RC'    => '2',
		     'tplen' => undef,
		    },
	     '11' => {
		     'id' => 'BC1G_04501.1',
		     'len' => '215',
		     'mTP' => '0.185',
		     'SP'  => '0.038',
		     'other' => '0.843',
		     'loc'   => '_',
		     'RC'    => '2',
		     'tplen' => undef,
		    },
	     '12' => {
		     'id' => 'BC1G_04502.1',
		     'len' => '395',
		     'mTP' => '0.118',
		     'SP'  => '0.164',
		     'other' => '0.825',
		     'loc'   => '_',
		     'RC'    => '2',
		     'tplen' => undef,
		    },
	     '13' => {
		     'id' => 'BC1G_04503.1',
		     'len' => '199',
		     'mTP' => '0.515',
		     'SP'  => '0.062',
		     'other' => '0.436',
		     'loc'   => 'M',
		     'RC'    => '5',
		     'tplen' => '20',
		    },
	     '14' => {
		     'id' => 'BC1G_04504.1',
		     'len' => '220',
		     'mTP' => '0.440',
		     'SP'  => '0.030',
		     'other' => '0.707',
		     'loc'   => '_',
		     'RC'    => '4',
		     'tplen' => undef,
		    },
	     '15' => {
		     'id' => 'BC1G_04505.1',
		     'len' => '67',
		     'mTP' => '0.382',
		     'SP'  => '0.049',
		     'other' => '0.610',
		     'loc'   => '_',
		     'RC'    => '4',
		     'tplen' => undef,
		    },
	    };
	
my $i = 1;
$targetp->_parse_results();

is($targetp->network(), 'NON-PLANT');
is($targetp->analysis_method_version(), "v1.1");

while(my $feat = $targetp->next_prediction()){

    is($feat->seq_id(), $items->{$i}->{id}, "good SeqID");
    is($feat->length(), $items->{$i}->{len}, "good Seqlength");
    is(($feat->get_tag_values('mitochondrionCutOff'))[0], $items->{$i}->{mTP}, "correct Mitochondrion cutoff");
    is(($feat->get_tag_values('signalPeptideCutOff'))[0], $items->{$i}->{SP}, "correct signalpPeptide cutoff");
    is(($feat->get_tag_values('otherCutOff'))[0], $items->{$i}->{other}, "correct other cutoff");
    is(($feat->get_tag_values('location'))[0], $targetp->_toString_location($items->{$i}->{loc}), "correct location");
    is(($feat->get_tag_values('reliabilityClass'))[0], $items->{$i}->{RC}, "correct Reliability class score");
    
	if ($feat->has_tag('signalPeptideLength')) {
		is(($feat->get_tag_values('signalPeptideLength'))[0], $items->{$i}->{tplen}, "correct peptide signal length")
	} else {
		is($feat->has_tag('signalPeptideLength'), '', "No peptide signal length reported")
	}
    $i++;
}
BioPerl-1.007002/t/Tools/Tmhmm.t000444000766000024       132413155576321 16326 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 12);
	
	use_ok('Bio::Tools::Tmhmm');
}

my $infile = test_input_file('tmhmm.out');

ok my $parser = Bio::Tools::Tmhmm->new(-file=>$infile), 'new()';

my @feat;
while ( my $feat = $parser->next_result ) {
  push @feat, $feat;
}

is @feat, 3, 'got 3 feat';

is $feat[0]->seq_id,      'my_sequence_id';
is $feat[0]->source_tag,  'TMHMM2.0';
is $feat[0]->primary_tag, 'transmembrane';


my $raa_test_data = [
  [ 54, 76],
  [116, 138],
  [151, 173],
];

for (0..(scalar(@feat)-1)) {
	is $feat[$_]->start, $raa_test_data->[$_]->[0];
	is $feat[$_]->end, $raa_test_data->[$_]->[1];
}
BioPerl-1.007002/t/Tools/ePCR.t000444000766000024       155313155576321 16041 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$


BEGIN {     
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 27);
	
    use_ok('Bio::Tools::EPCR');
    use_ok('Bio::SeqIO');
}

my $DEBUG = test_debug();

my $seqio = Bio::SeqIO->new('-format' => 'fasta', '-file' => test_input_file('genomic-seq.fasta'));

my $seq = $seqio->next_seq;
ok($seq);
my $epcr = Bio::Tools::EPCR->new( '-file' => test_input_file('genomic-seq.epcr'));
ok ($epcr);
my %strand;
while( defined(my $feature = $epcr->next_feature) ) {
    ok($feature);
    ok($feature->start);
    ok($feature->end);
    $seq->add_SeqFeature($feature);
    $strand{$feature->strand} ++;
}
is ($strand{1},  3, 'got 3 forward strand ePCR hits');
is ($strand{-1}, 3, 'got 3 reverse strand ePCR hits');

if( $DEBUG ) {
    $seqio = Bio::SeqIO->new('-format' => 'genbank' );
    $seqio->write_seq($seq);
}
BioPerl-1.007002/t/Tools/pICalculator.t000555000766000024       217613155576321 17637 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 38);
	
    use_ok('Bio::Seq');
    use_ok('Bio::Tools::pICalculator');
}

my @results = (12.999052267583,12.99700393539,12.9905348815881,12.9701609055248,12.9065486239062,12.7131376670492,12.1681721433832,10.8960154975975,8.82939162036317,6.81329734996812,5.58311842185452,4.87361913724596,4.11053952923425,3.00644711484741,1.91237900622079,1.19755236429121,0.669596284738213,0.0571988207175853,-0.584285455699191,-1.14218959353989,-1.79865831607402,-2.74360327055112,-3.87361697725167,-4.91494976791445,-6.01005299841696,-7.43711791135299,-8.77859455006782,-9.53905973773058,-9.84470802408586);

my $protein = "MVLLLILSVLLLKEDVRGSAQSSERRVVAHMPGDIIIGALFSVHHQPTVDKVHERKCGAVREQYGI";
ok my $seq = Bio::Seq->new(-seq => $protein);
is $seq->seq, $protein;
ok my $pep = $seq->seq;
ok my $calc = Bio::Tools::pICalculator->new(-places => 2);
ok $calc->seq($seq);
ok my $iep = $calc->iep;
for ( my $x = 0 ; $x <= 14 ; $x += .5 ) {
   float_is($calc->charge_at_pH($x), $results[(2 * $x)]);
}
is ($calc->iep,8.54);
BioPerl-1.007002/t/Tools/tRNAscanSE.t000444000766000024       177413155576321 17156 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 14);
	
	use_ok('Bio::Tools::tRNAscanSE');
}

my $verbose = test_debug();

my $parser = Bio::Tools::tRNAscanSE->new(-verbose => $verbose,
					 -file => test_input_file('yeast.tRNAscanSE'));

isa_ok($parser, 'Bio::Tools::tRNAscanSE') ;

my @genes;
while( my $gene = $parser->next_prediction ) {
    push @genes, $gene;
}

is (scalar(@genes), 287);
is($genes[2]->seq_id, 'I', 'seq_id');
my ($codon) = $genes[2]->get_tag_values('Codon');
is($codon, 'TTG', 'codon');
is($genes[2]->start, 181135, 'start');
is($genes[2]->end, 181248, 'end');
is($genes[2]->strand, 1, 'strand');

my @exons = $genes[2]->get_SeqFeatures ;
is ( scalar(@exons), 2, 'exons' );
is($exons[0]->end,181172, 'end' ); 
is($exons[0]->start,$genes[2]->start, 'start'); 
is($exons[1]->start,181205, 'start'); 
is($exons[1]->end,$genes[2]->end, 'end'); 
is($exons[0]->seq_id, $genes[2]->seq_id, 'seq_id');
BioPerl-1.007002/t/Tools/Alignment000755000766000024          013155576321 16640 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Tools/Alignment/Consed.t000555000766000024       564113155576321 20406 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

#####
#
# this script simply tests parsing ace* files
# - it cares nothing about the chromat_dir,phd_dir,edit_dir types of things
#
#####

use strict;

BEGIN {
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 15);
    
	use_ok('Bio::Tools::Alignment::Consed');
}

my $DEBUG = test_debug();

# scope some variables
my($o_consed,@singlets,@singletons,@pairs,@doublets,@multiplets,$invoker);

# instantiate a new object
my $passed_in_acefile = test_input_file('acefile.ace.1');
$o_consed = Bio::Tools::Alignment::Consed->new(-acefile => $passed_in_acefile);
ok defined $o_consed, 'new CSM::Consed object was created';

$o_consed->verbose($DEBUG);

isa_ok($o_consed,'Bio::Tools::Alignment::Consed');

isnt($o_consed->set_singlets(), 1,  'singlets can be successfully set');
	
@singlets = $o_consed->get_singlets();
is (scalar(@singlets), 65, 'singlets can be retrieved');

isnt ($o_consed->set_doublets(), 1, 'doublets can be set');

ok @doublets = $o_consed->get_doublets(), 'doublets can be retreived';

print(scalar(@doublets)." doublets were found\n") if ($DEBUG > 0);
is (scalar(@doublets), 45, 'doublets can be retrieved');

@pairs = $o_consed->get_pairs();
is (scalar(@pairs),1, 'pairs can be retrieved');

@multiplets = $o_consed->get_multiplets();
is (scalar(@multiplets), 4, 'multiplets can be retrieved');

@singletons = $o_consed->get_singletons();
is (scalar(@singletons), 3, 'singletons can be retrieved');
my($total_object_sequences, $total_grep_sequences);
is($total_grep_sequences = $o_consed->count_sequences_with_grep(), 179, 'how many sequences there are in the acefile _and_ in the singlets file');

is($total_object_sequences = $o_consed->sum_lets("total_only"),179, 'statistics from the Bio::Tools::Alignment::Consed object to compare the total number of sequences accounted for there to the number of sequences found via grep');
print("Match?\n") if($DEBUG > 0) ;
is ($total_object_sequences, $total_grep_sequences);

print("These are the statistics. Look right? ".$o_consed->sum_lets()."\n") if($DEBUG > 0);
is($o_consed->sum_lets(),'Singt/singn/doub/pair/mult/total : 65,3,45(90),1(2),4(19),179');

print("Dumping out the hash in a compact way...\n")if($DEBUG > 0)  ;
$o_consed->dump_hash_compact() if($DEBUG > 0)  ;

# print("Dumping out the hash in an ugly way...\n");
# $o_consed->dump_hash();

sub allele_script {
	my($a,$trunc,$rev);
	ok defined $a,
	isa_ok $a, 'Bio::Variation::Allele';
	
	is $a->accession_number(), 'X677667';
	is $a->seq(), 'ACTGACTGACTG';
	is $a->display_id(),'new-id' ;
	is $a->desc, 'Sample Bio::Seq object';
	is $a->moltype(), 'dna';

	ok defined($trunc = $a->trunc(1,4));
	is $trunc->seq(), 'ACTG', "Expecting ACTG. Got ". $trunc->seq();

	ok defined($rev = $a->revcom());
	is $rev->seq(), 'CAGTCAGTCAGT';

	$a->is_reference(1);
	ok $a->is_reference;

	$a->repeat_unit('ACTG');
	is $a->repeat_unit, 'ACTG';
	
	$a->repeat_count(3);
	is $a->repeat_count, 3;
}
BioPerl-1.007002/t/Tools/Analysis000755000766000024          013155576321 16505 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Tools/Analysis/DNA000755000766000024          013155576321 17107 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Tools/Analysis/DNA/ESEfinder.t000444000766000024       255313155576321 21242 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 13,
			   -requires_modules => [qw(IO::String
										LWP::UserAgent
										Bio::WebAgent
										HTML::HeadParser
										HTTP::Request::Common)],
			   -requires_networking => 1);
	
	use_ok('Bio::Tools::Analysis::DNA::ESEfinder');
	use_ok('Data::Dumper');
	use_ok('Bio::PrimarySeq');
}

#######all these tests work with 1ary seq########
my $seq = Bio::PrimarySeq->new(-id=>'bioperl',
                               -seq=>'atcgatgctatgcatgctatgggtgtgattcgatgcgactgttcatcgtagccccccccccccccctttt');
ok my $tool = Bio::Tools::Analysis::DNA::ESEfinder->new(-seq => $seq);

SKIP: {
	eval {$tool->run;};
	skip "Could not connect to ESEfinder server, skipping those tests", 9 if $@;
    ok my @res = $tool->result('Bio::SeqFeatureI');
	ok @res > 0;
    ok my $raw = $tool->result('');
    ok my $parsed = $tool->result('parsed');
    ok my $meta = $tool->result('all');
    is $parsed->[0][1], 41;
	
	SKIP: {
		test_skip(-tests => 3, -requires_module => 'Bio::Seq::Meta::Array');
		is $meta->{'seq'}, "atcgatgctatgcatgctatgggtgtgattcgatgcgactgttcatcgtagccccccccccccccctttt";
		is $meta->named_submeta_text('ESEfinder_SRp55', 1,2), "-3.221149 -1.602223";
		is $meta->seq, "atcgatgctatgcatgctatgggtgtgattcgatgcgactgttcatcgtagccccccccccccccctttt";
	}
}
BioPerl-1.007002/t/Tools/Analysis/Protein000755000766000024          013155576321 20125 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Tools/Analysis/Protein/Domcut.t000444000766000024       442213155576321 21704 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
	use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 26,
			   -requires_modules => [qw(IO::String
									    LWP::UserAgent)],
			   -requires_networking => 1);
	
	use_ok('Bio::PrimarySeq');
	use_ok('Bio::Tools::Analysis::Protein::Domcut');
}

my $verbose = test_debug();

ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);

SKIP: {
	######## test using PrimarySeq object ##############
	my $seq = Bio::PrimarySeq->new(-seq        => 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQPPPPPPPPPPPPPDQRS',
								   -display_id => 'test2');
	
	ok $tool = Bio::Tools::Analysis::Protein::Domcut->new( -seq=>$seq);
	ok $tool->run ();
	if ($tool->status eq 'TERMINATED_BY_ERROR') {
		skip('Problem with DomCut run, check status', 21);
	}
	
	ok my $raw    = $tool->result('');
	ok my $parsed = $tool->result('parsed');
	is ($parsed->[23]{'score'}, '-0.209');
	my @res       = $tool->result('Bio::SeqFeatureI');
	if (scalar @res > 0) {
		ok 1;
	} else {
		skip('No network access - could not connect to Domcut server', 18);
	}
	ok my $meta = $tool->result('meta');
	
	SKIP: {
		test_skip(-tests => 2, -requires_module => 'Bio::Seq::Meta::Array');
		is($meta->named_submeta_text('Domcut', 1,2), "0.068 0.053");
		is ($meta->seq, "MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQPPPPPPPPPPPPPDQRS");
	}
	
	########## test using Bio::Seq object ##############
	ok my $tool2 = Bio::WebAgent->new(-verbose =>$verbose);
	
	ok my $seq2  = Bio::Seq->new(-seq => 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS',
				 -display_id => 'test2');
	
	ok $tool2 = Bio::Tools::Analysis::Protein::Domcut->new( -seq=>$seq2->primary_seq);
	ok $tool2->run ();
	
	@res = $tool2->result('Bio::SeqFeatureI');
	
	if (scalar @res > 0) {
		ok 1;
	} else {
		skip('No network access - could not connect to Domcut server', 10);
	}
	
	ok my $parsed2 = $tool2->result('parsed');
	is ($parsed2->[23]{'score'}, '-0.209');
	
	ok my $meta2 = $tool2->result('meta');
	
	is($meta2->named_submeta_text('Domcut', 1,2), "0.068 0.053");
	is ($meta2->seq, "MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS");
	
	ok my $seq4 = Bio::Seq->new();
	ok $seq2->primary_seq($meta2);
	for (@res) {
		ok $seq2->add_SeqFeature($_);
	}
	ok $seq2->primary_seq->named_submeta_text('Domcut', 1,2);
}
BioPerl-1.007002/t/Tools/Analysis/Protein/ELM.t000555000766000024       312413155576321 21067 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;
BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests               => 16,
               -requires_modules    => [qw(IO::String
                                           LWP::UserAgent
                                           HTML::HeadParser
                                           Data::Stag)],
               -requires_networking => 1);

    use_ok('Bio::Tools::Analysis::Protein::ELM');
    use_ok('Bio::SeqIO');
    use_ok('Bio::WebAgent');
}

my $verbose = test_debug();

ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);

my $seqio=Bio::SeqIO->new( -verbose => $verbose,
                  -format => 'swiss',
                  -file   => test_input_file('swiss.dat'));

my $seq = $seqio->next_seq();
ok $tool = Bio::Tools::Analysis::Protein::ELM->new( 
					-seq=>$seq->primary_seq), 'new object';
ok $tool->compartment(['golgi', 'er']), 'set compartment';
ok my $cmp = $tool->compartment(), 'get compartment';
is $cmp->[1], 'GO:0005783', 'check compartment';
ok $tool->species(9606), 'set species()';
is $tool->species, 9606, 'get species()';;

my $req_status = $tool->run();

ok $req_status, 'run';

is $tool->status(), 'TERMINATED_BY_ERROR';

SKIP: {
    skip "Bad run() status, possible time out or error so skipping tests", 4 if !$req_status or $tool->status eq 'TERMINATED_BY_ERROR';
 
    ok my $raw = $tool->result('');
    print $raw if $verbose;
    ok my $parsed = $tool->result('parsed');
    
    is $parsed->{'CLV_NRD_NRD_1'}{'locus'}[0], '54-56';
    ok my @res = $tool->result('Bio::SeqFeatureI');
};
BioPerl-1.007002/t/Tools/Analysis/Protein/GOR4.t000444000766000024       254513155576321 21170 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 0,
               -requires_modules => [qw(IO::String
                                        LWP::UserAgent)],
               -requires_networking => 1);
    
    use_ok("Bio::Seq");
    use_ok("Bio::Tools::Analysis::Protein::GOR4");
}

my $seq = Bio::Seq->new(-seq => 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS',
                        -display_id => 'test2');
ok my $tool = Bio::Tools::Analysis::Protein::GOR4->new(-seq=>$seq->primary_seq);

SKIP: {
    ok $tool->run();
    skip "Skipping tests since we got terminated by a server error", 9 if $tool->status eq 'TERMINATED_BY_ERROR';
    ok my $raw    = $tool->result('');
    ok my $parsed = $tool->result('parsed');
    
    is $parsed->[0]{'coil'}, '56';
    my @res = sort {$a->start <=> $b->start} $tool->result('Bio::SeqFeatureI');
    if (scalar @res > 0) {
        ok 1;
    }
    else {
        skip 'No results - could not connect to GOR4 server?', 6;
    }
    is $res[0]->start, 1;
    is $res[0]->end, 7;
    ok my $meta = $tool->result('meta');
    
    test_skip(-tests => 2, -requires_module => 'Bio::Seq::Meta::Array');
    is $meta->named_submeta_text('GOR4_coil',1,2), '56 195';
    is $meta->seq, 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS';
}
BioPerl-1.007002/t/Tools/Analysis/Protein/HNN.t000444000766000024       265513155576321 21102 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 0,
               -requires_modules => [qw(IO::String
                                        LWP::UserAgent)],
               -requires_networking => 1);

    use_ok("Bio::Seq");
    use_ok("Bio::Tools::Analysis::Protein::HNN");
}

my $seq = Bio::Seq->new(-seq => 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS',
                        -display_id => 'test2');
ok my $tool = Bio::Tools::Analysis::Protein::HNN->new(-seq=>$seq->primary_seq);

SKIP: {
    ok $tool->run();
    skip "Skipping tests since we got terminated by a server error", 9 if $tool->status eq 'TERMINATED_BY_ERROR';
    ok my $raw    = $tool->result('');
    ok my $parsed = $tool->result('parsed');
    is $parsed->[0]{'coil'}, '1000';
    my @res = $tool->result('Bio::SeqFeatureI');
    if (scalar @res > 0) {
        ok 1;
    }
    else {
        skip 'No results - could not connect to HNN server?', 6;
    }

    ok my $meta   = $tool->result('meta');
    ok my $seqobj = Bio::Seq->new(-primary_seq => $meta, display_id=>"a");
    for ( $tool->result('Bio::SeqFeatureI') ) {
        ok $seqobj->add_SeqFeature($_);
    }

    test_skip(-tests => 2, -requires_module => 'Bio::Seq::Meta::Array');
    is $meta->named_submeta_text('HNN_helix',1,2), '0 111';
    is $meta->seq, 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS';
}
BioPerl-1.007002/t/Tools/Analysis/Protein/NetPhos.t000444000766000024       240013155576321 22023 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;

BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 14,
			   -requires_modules => [qw(IO::String LWP::UserAgent)],
			   -requires_networking => 1);
	
	use_ok('Bio::Tools::Analysis::Protein::NetPhos');
	use_ok('Bio::PrimarySeq');
	use_ok('Bio::WebAgent');
}

my $verbose = test_debug();

ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);

ok $tool->sleep;
is $tool->delay(1), 1;
ok $tool->sleep;
ok $tool->timeout(120); # LWP::UserAgent method
is $tool->url('http://a.b.c/'), 'http://a.b.c/';


my $seq = Bio::PrimarySeq->new(-id=>'bioperl',
							   -seq=>'ABCDEFGHIJKLLKJFHSAKNDJFPSINCSJNDSKNSN');

ok $tool = Bio::Tools::Analysis::Protein::NetPhos->new(-verbose =>$verbose);
$tool->timeout(15);

ok $tool->run ( {seq=>$seq, threshold=>0.9} );
SKIP: {
	if ($tool->status eq 'TERMINATED_BY_ERROR') {
		skip "Running of the tool was terminated by an error, probably network/ NetPhos server error", 3;
	}
	my @res = $tool->result('Bio::SeqFeatureI');
	unless (@res) {
		skip "Didn't get any results from NetPhos server, probable network/server error", 3;
	}
	#new tests her in v 1.2
	ok my $raw = $tool->result('');
	ok my $parsed = $tool->result('parsed');
	is $parsed->[0][1], '0.934';
}
BioPerl-1.007002/t/Tools/Analysis/Protein/Scansite.t000555000766000024       243313155576321 22225 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests            => 14,
               -requires_modules => [qw(IO::String
                                        LWP::UserAgent
                                        Data::Stag)]);

    use_ok('Bio::Tools::Analysis::Protein::Scansite');
    use_ok('Bio::SeqIO');
    use_ok('Bio::WebAgent');
}

my $verbose = test_debug();

ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);


my $seqio=Bio::SeqIO->new( -verbose => $verbose,
                  -format => 'swiss',
                  -file   => test_input_file('swiss.dat'));

my $seq = $seqio->next_seq();
ok $tool = Bio::Tools::Analysis::Protein::Scansite->new( 
					-seq=>$seq->primary_seq);
ok $tool->stringency('Low');
is $tool->stringency(), 'Low';
is $tool->protein_id(), $tool->seq->display_id();

SKIP: {
	test_skip(-tests => 6, -requires_networking => 2);
	ok $tool->run();
	skip "Something wrong with server? Terminated by error, skipping tests", 5 if $tool->status eq 'TERMINATED_BY_ERROR';
	ok my $raw = $tool->result('');
	print $raw if $verbose;
	ok my $parsed = $tool->result('parsed');
	is $parsed->[0]{'site'}, 'T101';
	ok my @res = $tool->result('Bio::SeqFeatureI');
	is $res[0]->start, 101;
}
BioPerl-1.007002/t/Tools/Analysis/Protein/Sopma.t000444000766000024       303513155576321 21527 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests => 0,
               -requires_modules => [qw(IO::String
                                        LWP::UserAgent)],
               -requires_networking => 1);

    use_ok('Bio::PrimarySeq');
    use_ok('Bio::Tools::Analysis::Protein::Sopma');
}

my $verbose = test_debug();

ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);

my $seq = Bio::PrimarySeq->new(
    -seq => 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS',
    -display_id => 'test2'
);
ok $tool = Bio::Tools::Analysis::Protein::Sopma->new( -seq=>$seq,
                                                     #-verbose => $verbose,
                                                      -window_width => 15);

SKIP: {
    ok $tool->run();
    skip "Tool was terminated by some error: problem connecting to server?", 11 if $tool->status eq 'TERMINATED_BY_ERROR';

    ok my $raw    = $tool->result('');
    ok my $parsed = $tool->result('parsed');
    is ($parsed->[0]{'helix'}, '102');
    ok my @res  = $tool->result('Bio::SeqFeatureI');
    ok my $meta = $tool->result('meta', "ww15");

    ok $tool->window_width(21);
    ok $tool->clear();
    ok $tool->run;
    ok my $meta2 = $tool->result('meta', "ww21");

    SKIP: {
        test_skip(-tests => 2, -requires_module => 'Bio::Seq::Meta::Array');
        is $meta->named_submeta_text('Sopma_helix|ww15',1,2), '102 195';
        is $meta->seq, 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS';
    }
}
BioPerl-1.007002/t/Tools/EMBOSS000755000766000024          013155576321 15712 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Tools/EMBOSS/Palindrome.t000444000766000024       157713155576321 20340 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 13);
	
	use_ok('Bio::Tools::EMBOSS::Palindrome');
	use_ok('Bio::Tools::GFF');
}

my $DEBUG = test_debug();

my $parser = Bio::Tools::EMBOSS::Palindrome->new(-file => test_input_file('humts1.pal'));

my $seq = $parser->next_seq;
ok($seq);
is($seq->display_id, 'HUMTS1');
is($seq->length, 18596);
my @features = $seq->get_SeqFeatures();
is(scalar @features, 23);

is($features[0]->feature1->start, 126);
is($features[0]->feature1->end, 142);
is($features[0]->feature1->strand, 1);
is($features[0]->feature1->seq_id, 'HUMTS1');


is($features[0]->feature2->start, 201);
is($features[0]->feature2->end, 217);
is($features[0]->feature2->strand, -1);

if( $DEBUG ) {
    my $out = Bio::Tools::GFF->new(-gff_version => 2);
    $out->write_feature($features[0]);
}
BioPerl-1.007002/t/Tools/Phylo000755000766000024          013155576321 16015 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Tools/Phylo/Gerp.t000444000766000024       235013155576321 17234 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: gerp.t,v 1.15 2007/06/27 10:16:38 sendu Exp $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 33,
			   -requires_module => 'URI::Escape');
	
    use_ok('Bio::Tools::Phylo::Gerp');
}

ok my $parser = Bio::Tools::Phylo::Gerp->new(-file => test_input_file('ENr111.mfa.example.elems'));

my $count = 0;
my @expected = ([qw(334180 334352 449 1.03744e-165)],
                [qw(337735 337915 458.2 5.02405e-164)],
                [qw(262604 262861 473.1 3.64789e-117)],
                [qw(285427 285608 386.1 8.42494e-113)],
                [qw(309563 309744 383.6 2.88895e-111)]);
while (my $feat = $parser->next_result) {
    $count++;
    my @exp = @{shift(@expected)};
    
    isa_ok $feat, 'Bio::SeqFeature::Generic';
    is $feat->source_tag, 'GERP', 'correct source';
    is $feat->start, shift(@exp), 'feature start correct';
    is $feat->end, shift(@exp), 'feature end correct';
    is $feat->score, shift(@exp), 'feature score correct';
    my ($p_value) = $feat->annotation->get_Annotations('pvalue');
    is ref $p_value ? $p_value->value : $p_value, shift(@exp), 'feature pvalue correct';
}

is $count, 5, "correct number of results parsed out";
BioPerl-1.007002/t/Tools/Phylo/Molphy.t000444000766000024       225613155576321 17614 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 18,
			   -requires_module => 'IO::String');
	
	use_ok('Bio::Tools::Phylo::Molphy');
}

my $verbose = test_debug();

my $inmolphy = Bio::Tools::Phylo::Molphy->new(-file => test_input_file('lysozyme6.simple.protml'));
ok($inmolphy);
my $r = $inmolphy->next_result;
ok($r);
is($r->model, 'JTT');
is($r->search_space,50);
my @trees;
while( my $t = $r->next_tree ) { 
    push @trees, $t;
}
is(@trees,5);
 $inmolphy = Bio::Tools::Phylo::Molphy->new(-file => test_input_file('lysozyme6.protml'));
ok($inmolphy);
$r = $inmolphy->next_result;
is($r->model, 'JTT');
is($r->search_space,50);
@trees = ();
while( my $t = $r->next_tree ) { 
    push @trees, $t;
}
is(@trees,5);

is($trees[0]->score, -1047.8);
is($trees[-1]->id, 9);

my $tpm = $r->transition_probability_matrix;
is($tpm->{'Val'}->{'Val'}, -122884);
is($tpm->{'Ala'}->{'Arg'}, 2710);

my $sub_mat = $r->substitution_matrix;
is($sub_mat->{'Val'}->{'Tyr'}, 50);
is($sub_mat->{'Arg'}->{'Ile'}, 72);
is($sub_mat->{'Met'}->{'Met'}, '');

my %fmat = $r->residue_frequencies();
is($fmat{'D'}->[0], 0.052);
BioPerl-1.007002/t/Tools/Phylo/Phylip000755000766000024          013155576321 17262 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Tools/Phylo/Phylip/ProtDist.t000444000766000024       451113155576321 21355 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 47);
	
    use_ok('Bio::Tools::Phylo::Phylip::ProtDist');
}

my $inputfilename= test_input_file('phylipdist.out');
my $tool= Bio::Tools::Phylo::Phylip::ProtDist->new(-file => $inputfilename);
my $phy = $tool->next_matrix;
is(@{$phy->names}, 5);
is $phy->get_entry('Alpha','Beta'), '4.23419';
is $phy->get_entry('Gamma','Alpha'),'3.63330';
my @column =  $phy->get_column('Alpha');
is $column[0], '0.00000';
is $column[1], '4.23419';
is $column[2], '3.63330';
is $column[3], '6.20865';
is $column[4], '3.45431';

my @row    = $phy->get_row('Gamma');
is $row[0], '3.63330';
is $row[1], '3.49289';
is $row[2], '0.00000';
is $row[3], '3.68733';
is $row[4], '5.84929';

my @diag   = $phy->get_diagonal;


is $diag[0], '0.00000';
is $diag[1], '0.00000';
is $diag[2], '0.00000';
is $diag[3], '0.00000';
is $diag[4], '0.00000';

my $matrix =<print_matrix , $matrix;

# now parse Phylip 3.6 output

$inputfilename= test_input_file('phylipdist-36.out');
$tool= Bio::Tools::Phylo::Phylip::ProtDist->new(-file => $inputfilename);
$phy = $tool->next_matrix;

is(@{$phy->names}, 39);
is $phy->get_entry('CBG01299','CBG00435'), '4.7793';
is $phy->get_entry('CBG22788','CBG22521'),'5.3195';
is $phy->get_entry('CBG01466', 'CBG01473'), '3.3944';

@row = $phy->get_row('CBG01473');
is(scalar @row, 39);
@column =  $phy->get_column('CBG01300');
is $column[0], '0.0817';
is $column[1], '0.0000';
is $column[2], '0.0950';
is $column[3], '0.3111';
is $column[37], '4.7190';
is $column[38], '4.7592';

@row    = $phy->get_row('CBG17433');
is $row[0], '4.8451';
is $row[1], '4.5982';
is $row[2], '4.0620';
is $row[3], '5.9673';
is $row[4], '4.6224';
is $row[5], '5.1993';
is $row[6], '5.4427';
is $row[7], '4.2783';

@diag   = $phy->get_diagonal;

is $diag[0], '0.0000';
is $diag[1], '0.0000';
is $diag[2], '0.0000';
is $diag[3], '0.0000';
is $diag[4], '0.0000';
is $diag[5], '0.0000';
is $diag[37], '0.0000';
is $diag[38], '0.0000';
BioPerl-1.007002/t/Tools/Run000755000766000024          013155576321 15466 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Tools/Run/RemoteBlast.t000444000766000024      2105213155576321 20251 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests               => 21,
               -requires_modules    => [qw(IO::String
                                           LWP::UserAgent)],
               -requires_networking => 1);

    use_ok('Bio::Tools::Run::RemoteBlast');
}

my $prog  = 'blastp';
my $db    = 'swissprot';
my $e_val = '1e-10';
my $v     = test_debug();

SKIP: {
    my $remote_blast
        = Bio::Tools::Run::RemoteBlast->new(-verbose => $v,
                                            -prog    => $prog,
                                            -data    => $db,
                                            -expect  => $e_val,
                                            );
    $remote_blast->submit_parameter('ENTREZ_QUERY', 'Escherichia coli[ORGN]');

    my $inputfilename = test_input_file('ecolitst.fa');
    ok( -e $inputfilename);
    ok(1, 'Text BLAST');

    my $attempt = 1;
    my $status;
    eval{
        $status = $remote_blast->submit_blast($inputfilename);
    };

    ok($status,'BLAST text output submitted');
    skip("Error accessing remote BLAST interface: $@", 5) if $@;

    cmp_ok($remote_blast->get_rtoe, '>', 0, "Estimated retrieval time");
    diag("Time remaining: ".$remote_blast->get_rtoe) if $v;

    my @rids = $remote_blast->each_rid;
    is(@rids, 1, 'should only be one RID');
    skip("Wrong number of RIDs: ".scalar(@rids), 3) if @rids != 1;

    diag("Retrieving $rids[0]...\n") if $v;
    my $max_attempts = 20;
    my $rc;
    while (defined($rc = $remote_blast->retrieve_blast($rids[0]))) {
        if ( !ref($rc) ) {
            if ( $rc < 0 ) {
                skip("need a better solution for when 'Server failed to return any data'",3);
            }
            sleep 30;
            diag("Retrieval attempt: $attempt\n") if $v;
            $attempt++ < $max_attempts ? next : last;
        }
        else {
            last;
        }
    }

    if ($rc) {
        ok(1,'retrieve_blast succeeded');
        $remote_blast->remove_rid($rids[0]);
        my $count = 0;
        isa_ok($rc, 'Bio::SearchIO');
        while (my $result = $rc->next_result) {
            while ( my $hit = $result->next_hit ) {
                $count++;
                next unless ( $v > 0);
                print "sbjct name is ", $hit->name, "\n";
                while ( my $hsp = $hit->next_hsp ) {
                    print "score is ", $hsp->bits, "\n";
                }
            }
        }
        is($count, 3, 'HSPs returned');
    }
    elsif ($attempt > $max_attempts) {
        # have a test fail here (there should not be repeated failed attempts to
        # get reports)
        ok(0,'Exceeded maximum attempts on server to retrieve report');
        diag("Timeout, did not return report after ".($attempt - 1)." attempts");
        skip('Remote server timeout problems', 2);
    }
    else {
        # have a test fail here (whatever is returned should be eval as true and
        # be a SearchIO)
        ok(0,"Other problem on remote server, no report returned: $rc");
        skip('Possible remote server problems', 2);
    }
}

SKIP: {
    # test blasttable
    my $remote_blast
        = Bio::Tools::Run::RemoteBlast->new(-verbose    => $v,
                                            -prog       => $prog,
                                            -data       => $db,
                                            -readmethod => 'blasttable',
                                            -expect     => $e_val,
                                            );
    $remote_blast->submit_parameter('ENTREZ_QUERY', 'Escherichia coli[ORGN]');
    $remote_blast->retrieve_parameter('ALIGNMENT_VIEW', 'Tabular');

    my $inputfilename = test_input_file('ecolitst.fa');
    my $attempt = 1;

    my $status;
    eval{
        $status = $remote_blast->submit_blast($inputfilename);
    };

    ok($status,'Tabular BLAST submitted');
    skip("Error accessing remote BLAST interface: $@", 5) if $@;

    cmp_ok($remote_blast->get_rtoe, '>', 0, "Estimated retrieval time");
    diag("Time remaining: ".$remote_blast->get_rtoe) if $v;

    my @rids = $remote_blast->each_rid;
    is(@rids, 1, 'should only be one RID');
    skip("Wrong number of RIDs: ".scalar(@rids), 3) if @rids != 1;

    diag("waiting [$rids[0]]...") if $v;
    my $max_attempts = 20;
    my $rc;
    while (defined($rc = $remote_blast->retrieve_blast($rids[0]))) {
        if ( !ref($rc) ) {
            if ( $rc < 0 ) {
                skip("need a better solution for when 'Server failed to return any data'",3);
            }
            sleep 30;
            diag("Retrieval attempt: $attempt") if $v;
            $attempt++ < $max_attempts ? next : last;
        }
        else {
            last;
        }
    }

    if ($rc) {
        ok(1,'retrieve_blast succeeded');
        $remote_blast->remove_rid($rids[0]);
        my $count = 0;
        isa_ok($rc, 'Bio::SearchIO');
        while (my $result = $rc->next_result) {
            while ( my $hit = $result->next_hit ) {
                $count++;
                next unless ( $v > 0);
                print "sbjct name is ", $hit->name, "\n";
                while ( my $hsp = $hit->next_hsp ) {
                    print "score is ", $hsp->bits, "\n";
                }
            }
        }
        is($count, 3, 'HSPs returned');
    }
    elsif ($attempt > $max_attempts) {
        # have a test fail here (there should not be repeated failed attempts to
        # get reports)
        ok(0,'Exceeded maximum attempts on server to retrieve report');
        diag("Timeout, did not return report after ".($attempt - 1)." attempts");
        skip('Remote server timeout problems', 2);
    }
    else {
        # have a test fail here (whatever is returned should be eval as true and
        # be a SearchIO)
        ok(0,"Other problem on remote server, no report returned: $rc");
        skip('Possible remote server problems', 2);
    }
}

SKIP: {
    test_skip(-tests           => 6,
              -requires_module => 'Bio::SearchIO::blastxml');

    my $remote_blast
        = Bio::Tools::Run::RemoteBlast->new(-prog       => $prog,
                                            -data       => $db,
                                            -readmethod => 'xml',
                                            -expect     => $e_val,
                                            );
    $remote_blast->submit_parameter('ENTREZ_QUERY',
                                    'Escherichia coli[ORGN]');
    $remote_blast->retrieve_parameter('FORMAT_TYPE', 'XML');

    my $inputfilename = test_input_file('ecolitst.fa');
    my $attempt = 1;

    my $status;
    eval{
        $status = $remote_blast->submit_blast($inputfilename);
    };

    ok($status,'XML BLAST submitted');
    skip("Error accessing remote BLAST interface: $@", 5) if $@;

    cmp_ok($remote_blast->get_rtoe, '>', 0, "Estimated retrieval time");
    diag("Time remaining: ".$remote_blast->get_rtoe) if $v;

    my @rids = $remote_blast->each_rid;
    is(@rids, 1, 'should only be one RID');
    skip("Wrong number of RIDs: ".scalar(@rids), 3) if @rids != 1;

    diag("waiting [$rids[0]]...") if $v;
    # This blast usually takes 2x time compared to the other two
    my $max_attempts = 30;
    my $rc;
    while (defined($rc = $remote_blast->retrieve_blast($rids[0]))) {
        if ( !ref($rc) ) {
            if ( $rc < 0 ) {
                skip("need a better solution for when 'Server failed to return any data'",3);
            }
            sleep 30;
            diag("Retrieval attempt: $attempt") if $v;
            $attempt++ < $max_attempts ? next : last;
        }
        else {
            last;
        }
    }

    if ($rc) {
        ok(1,'retrieve_blast succeeded');
        $remote_blast->remove_rid($rids[0]);
        my $count = 0;
        isa_ok($rc, 'Bio::SearchIO');
        while (my $result = $rc->next_result) {
            while ( my $hit = $result->next_hit ) {
                $count++;
            }
        }
        is($count, 3, 'HSPs returned');
    }
    elsif ($attempt > $max_attempts) {
        # have a test fail here (there should not be repeated failed attempts to
        # get reports)
        ok(0,'Exceeded maximum attempts on server to retrieve report');
        diag("Timeout, did not return report after ".($attempt - 1)." attempts");
        skip('Remote server timeout problems', 2);
    }
    else {
        # have a test fail here (whatever is returned should be eval as true and
        # be a SearchIO)
        ok(0,"Other problem on remote server, no report returned: $rc");
        skip('Possible remote server problems', 2);
    }
}
BioPerl-1.007002/t/Tools/Run/RemoteBlast_rpsblast.t000444000766000024       716313155576321 22152 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

# malcolm_cook@stowers.org: this test is in a separate file from
# RemoteBlast.t (on which it is modelled) since there is some sort of
# side-effecting between the multiple remote blasts that is causing
# this test to fail, if it comes last, or the other test to fail, if
# this one comes first.  THIS IS A BUG EITHER IN REMOTE BLAST OR MY
# UNDERSTANDING, i.e. of how to initialize it.

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;

    test_begin(-tests               => 7,
               -requires_modules    => [qw(IO::String
                                           LWP::UserAgent)],
               -requires_networking => 1);

    use_ok('Bio::Tools::Run::RemoteBlast');
}

my $v = test_debug();
my $inputfilename = test_input_file('ecolitst.fa');
ok( -e $inputfilename);

my $remote_rpsblast
    = Bio::Tools::Run::RemoteBlast->new(-verbose    => test_debug(),
                                        -prog       => 'blastp',
                                        -data       => 'cdd',
                                        -readmethod => 'blasttable',
                                        -expect     => '1e-10',
                                        );
$remote_rpsblast->retrieve_parameter('ALIGNMENT_VIEW', 'Tabular');

# This is the key to getting job run using rpsblast:
$Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast';

my $attempt = 1;

SKIP: {
    my $status;
    eval{
        $status = $remote_rpsblast->submit_blast($inputfilename);
    };

    ok($status,'rpsblast blasttable submitted');
    skip("Error accessing remote BLAST interface: $@", 4) if $@;

    my @rids = $remote_rpsblast->each_rid;
    is(@rids, 1, 'should only be one RID');
    skip("Wrong number of RIDs: ".scalar(@rids), 3) if @rids != 1;

    diag("Retrieving $rids[0]...\n") if $v;
    my $rc;
    while (defined($rc = $remote_rpsblast->retrieve_blast($rids[0]))) {
        if ( !ref($rc) ) {
            if ( $rc < 0 ) {
                skip("need a better solution for when 'Server failed to return any data'",2);
            }
            sleep 5;
            diag("Retrieval attempt: $attempt\n") if $v;
            $attempt++ < 10 ? next : last;
        }
        else {
            last;
        }
    }
    $remote_rpsblast->remove_rid($rids[0]);

    if ($rc) {
        ok(1,'retrieve_blast succeeded');
        $remote_rpsblast->remove_rid($rids[0]);
        my $count = 0;
        isa_ok($rc, 'Bio::SearchIO');
        
        while (my $result = $rc->next_result) {
            while ( my $hit = $result->next_hit ) {
                $count++;
                next unless ( $v > 0);
                print "sbjct name is ", $hit->name, "\n";
                while ( my $hsp = $hit->next_hsp ) {
                    print "score is ", $hsp->bits, "\n";
                }
            }
        }
        cmp_ok($count, '>=', 45, 'HSPs returned');
    }
    elsif ($attempt > 10) {
        # have a test fail here (there should not be repeated failed attempts to
        # get reports)
        ok(0,'Exceeded maximum attempts on server to retrieve report');
        diag("Timeout, did not return report after ".($attempt - 1)." attempts");
        skip('Remote server timeout problems', 2);
    }
    else {
        # have a test fail here (whatever is returned should be eval as true and
        # be a SearchIO)
        ok(0,"Other problem on remote server, no report returned: $rc");
        skip('Possible remote server problems', 2);
    }
}

# To be a good citizen, we should restore the default NCBI service
# ('plain') for future tests
$Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'plain';
BioPerl-1.007002/t/Tools/Signalp000755000766000024          013155576321 16317 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Tools/Signalp/ExtendedSignalp.t000444000766000024      3133413155576321 21743 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;
use Data::Dumper;
BEGIN {
	use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 185);
	
    use_ok('Bio::Tools::Signalp::ExtendedSignalp');
}

###############################################
### TESTS ON SUMMARY OUTPUT FORMAT (NN+HMM) ###
###############################################

my $res = {
	   '1' => {
	           'id'     => 'BC1G_00003.1',
                   'pred'   => 'Signal peptide',
		   'nnpred' => 'signal-peptide',
                   'end'    => '22',
                   'prob'   => '0.999',
                   'anchor' => '0.000',
		  },
        '2' => {
		   'id'     => 'BC1G_00008.1',
                   'pred'   => 'Non-secretory protein',
		   'nnpred' => 'signal-peptide',
                   'end'    => '83',
                   'prob'   => '0.222',
                   'anchor' => '0.067',
		  },
	  };

# Test on filtered results
my $facts   = [qw(maxS D)];
my $in      = test_input_file("signalp.summary");
my $signalp = Bio::Tools::Signalp::ExtendedSignalp->new(
							-file => $in,
							-factors => $facts,
						       );

ok($signalp);
my $i = 1;

while(my $feat = $signalp->next_feature()){
    #print Dumper($feat);
    is($feat->seq_id(), $res->{$i}->{id});
    is($feat->end(), $res->{$i}->{end});
    is(($feat->get_tag_values('peptideProb'))[0], $res->{$i}->{prob});
    is(($feat->get_tag_values('anchorProb'))[0], $res->{$i}->{anchor});
    is(($feat->get_tag_values('signalpPrediction'))[0], $res->{$i}->{pred});
    is(($feat->get_tag_values('nnPrediction'))[0], $res->{$i}->{nnpred});
    $i++;
}

# Tests without filters.
# It should by default only parses results with Ymax and meanS to mimic default behavior
# from Bio::Tools::Signalp
$res = {
	'1' => {
		'id'     => 'BC1G_00003.1',
		'pred'   => 'Signal peptide',
		'end'    => '22',
		'prob'   => '0.999',
		'anchor' => '0.000',
	       },
	'2' => {
		'id'     => 'BC1G_00008.1',
		'pred'   => 'Non-secretory protein',
		'end'    => '83',
		'prob'   => '0.222',
		'anchor' => '0.067',
	       },
       };

#No filters required
$signalp = Bio::Tools::Signalp::ExtendedSignalp->new(
						     -file => $in
						    );
ok($signalp);
$i = 1;

while(my $feat = $signalp->next_feature()){
    is($feat->seq_id(), $res->{$i}->{id});
    is($feat->end(), $res->{$i}->{end});
    is(($feat->get_tag_values('peptideProb'))[0], $res->{$i}->{prob});
    is(($feat->get_tag_values('anchorProb'))[0], $res->{$i}->{anchor});
    is(($feat->get_tag_values('signalpPrediction'))[0], $res->{$i}->{pred});
    $i++;
}

#############################################
### TESTS ON SHORT OUTPUT FORMAT (NN+HMM) ###
#############################################

$res = {
	'1' => {
		'id'     => 'BC1G_00003.1',
		'pred'   => 'Signal peptide',
		'nnpred' => 'signal-peptide',
		'end'    => '22',
	       },
	'2' => {
		'id'     => 'BC1G_00008.1',
		'nnpred' => 'signal-peptide',
		'pred'   => 'Non-secretory protein',
		'end'    => '83',
	       },
	'3' => {
		'id'     => 'BC1G_00009.1',
		'nnpred' => 'signal-peptide',
		'pred'   => 'Non-secretory protein',
		'end'    => '28',
		},
	'4' => {
		'id'     => 'BC1G_00010.1',
		'nnpred' => 'signal-peptide',
		'pred'   => 'Non-secretory protein',
		'end'    => '15',
		},

       };

# Test on filtered results
$facts   = [qw(maxC)];
$in      = test_input_file("signalp.short");
$signalp = Bio::Tools::Signalp::ExtendedSignalp->new(
						     -file => $in,
						     -factors => $facts,
						    );

ok($signalp);
$i = 1;

while(my $feat = $signalp->next_feature()){
    is($feat->seq_id(), $res->{$i}->{id});
    is($feat->end(), $res->{$i}->{end});
    is(($feat->get_tag_values('signalpPrediction'))[0], $res->{$i}->{pred});
    is(($feat->get_tag_values('nnPrediction'))[0], $res->{$i}->{nnpred});
    $i++;
}

# Tests without filters.
# It should by default only parses results with Ymax and meanS to mimic default behavior
# from GPI::Bio::Tools::Signalp
$res = {
	'1' => {
		'id'     => 'BC1G_00003.1',
		'pred'   => 'Signal peptide',
        'prob' => 0.999,
		'nnpred' => 'signal-peptide',
		'end'    => '22',
	       },
	'2' => {
		'id'     => 'BC1G_00008.1',
		'pred'   => 'Non-secretory protein',
        'prob' => 0.222,
		'nnpred' => 'signal-peptide',
		'end'    => '83',
	       },
       };

#No filters required
$signalp = Bio::Tools::Signalp::ExtendedSignalp->new(
						     -file => $in
						    );
ok($signalp);
$i = 1;

while(my $feat = $signalp->next_feature()){
    is($feat->seq_id(), $res->{$i}->{id});
    is($feat->end(), $res->{$i}->{end});
    is(($feat->get_tag_values('peptideProb'))[0], $res->{$i}->{prob});
    is(($feat->get_tag_values('anchorProb'))[0], $res->{$i}->{anchor});
    is(($feat->get_tag_values('signalpPrediction'))[0], $res->{$i}->{pred});
    is(($feat->get_tag_values('nnPrediction'))[0], $res->{$i}->{nnpred});
    $i++;
}


###########################################
### TESTS ON SUMMARY OUTPUT FORMAT (NN) ###
###########################################

$res = {
	'1' => {
		'id'     => 'BC1G_00003.1',
		'nnpred' => 'signal-peptide',
		'end'    => '22',
	       },
	'2' => {
		'id'     => 'BC1G_00008.1',
		'nnpred' => 'signal-peptide',
		'end'    => '83',
	       },
       };

# Test on filtered results BROKEN
$facts   = [qw(maxC)];
$in      = test_input_file("signalp.nn.summary");
$signalp = Bio::Tools::Signalp::ExtendedSignalp->new(
						     -file => $in,
						     -factors => $facts,
						    );

ok($signalp);
$i = 1;

while(my $feat = $signalp->next_feature()){

    is($feat->seq_id(), $res->{$i}->{id});
    is($feat->end(), $res->{$i}->{end});
    is(($feat->get_tag_values('nnPrediction'))[0], $res->{$i}->{nnpred});
    $i++;
}
# Tests without filters.
# It should by default only parses results with Ymax and meanS to mimic default behavior
# from GPI::Bio::Tools::Signalp
$res = {
	'1' => {
		'id'     => 'BC1G_00003.1',
		'nnpred' => 'signal-peptide',
		'end'    => '22',
	       },
	'2' => {
		'id'     => 'BC1G_00008.1',
		'nnpred' => 'signal-peptide',
		'end'    => '83',
	       },
	'3' => {
		'id'     => 'BC1G_00009.1',
		'nnpred' => 'signal-peptide',
		'end'    => '28',
		},
	'4' => {
		'id'     => 'BC1G_00010.1',
		'nnpred' => 'signal-peptide',
		'end'    => '15',
		},
       };

#No filters required BROKEN
$signalp = Bio::Tools::Signalp::ExtendedSignalp->new(
						     -file => $in
						    );
ok($signalp);
$i = 1;

while(my $feat = $signalp->next_feature()){

    is($feat->seq_id(), $res->{$i}->{id});
    is($feat->end(), $res->{$i}->{end});
    is(($feat->get_tag_values('nnPrediction'))[0], $res->{$i}->{nnpred});
    $i++;
}


############################################
### TESTS ON SUMMARY OUTPUT FORMAT (HMM) ###
############################################

$res = {
	'1' => {
		'id'     => 'BC1G_00002.1',
		'prob'   => '0.000',
		'anchor' => '0.000',
		'cleav'  => '0.000',
		'pred'   => 'Non-secretory protein',
		'end'    => '22',
	       },
	'2' => {
		'id'     => 'BC1G_00003.1',
		'prob'   => '0.999',
		'anchor' => '0.000',
		'cleav'  => '0.973',
		'pred'   => 'Signal peptide',
		'end'    => '22',
	       },
	'3' => {
		'id'     => 'BC1G_00004.1',
		'prob'   => '0.003',
		'anchor' => '0.000',
		'cleav'  => '0.001',
		'pred'   => 'Non-secretory protein',
		'end'    => '19',
	       },
	'4' => {
		'id'     => 'BC1G_00005.1',
		'prob'   => '0.008',
		'anchor' => '0.000',
		'cleav'  => '0.007',
		'pred'   => 'Non-secretory protein',
		'end'    => '22',
		},
	'5' => {
		'id'     => 'BC1G_00006.1',
		'prob'   => '0.000',
		'anchor' => '0.000',
		'cleav'  => '0.000',
		'pred'   => 'Non-secretory protein',
		'end'    => '23',
		},
	'6' => {
		'id'     => 'BC1G_00007.1',
		'prob'   => '0.240',
		'anchor' => '0.000',
		'cleav'  => '0.228',
		'pred'   => 'Non-secretory protein',
		'end'    => '22',
		},
	'7' => {
		'id'     => 'BC1G_00008.1',
		'prob'   => '0.222',
		'anchor' => '0.067',
		'cleav'  => '0.061',
		'pred'   => 'Non-secretory protein',
		'end'    => '22',
		},
	'8' => {
		'id'     => 'BC1G_00009.1',
		'prob'   => '0.000',
		'anchor' => '0.000',
		'cleav'  => '0.000',
		'pred'   => 'Non-secretory protein',
		'end'    => '20',
		},
       };

# It is impossible to filter with hmm output...
$in      = test_input_file("signalp.hmm.summary");
$signalp = Bio::Tools::Signalp::ExtendedSignalp->new(
						     -file => $in,
						    );

ok($signalp);
$i = 1;

while(my $feat = $signalp->next_feature()){
    is($feat->seq_id(), $res->{$i}->{id});
    is($feat->end(), $res->{$i}->{end});
    is(($feat->get_tag_values('peptideProb'))[0], $res->{$i}->{prob});
    is(($feat->get_tag_values('anchorProb'))[0], $res->{$i}->{anchor});
    is(($feat->get_tag_values('signalpPrediction'))[0], $res->{$i}->{pred});
    is(($feat->get_tag_values('cleavageSiteProb'))[0], $res->{$i}->{cleav});
    $i++;
}

#########################################
### TESTS ON SHORT OUTPUT FORMAT (NN) ###
#########################################

$res = {
	'1' => {
		'id'     => 'BC1G_00003.1',
		'nnpred' => 'signal-peptide',
		'yprob'  => '0.866',
		'dprob'  => '0.902',
		'cprob'  => '0.934',
		'end'    => '22',
	       },
	'2' => {
		'id'     => 'BC1G_00008.1',
		'yprob'  => '0.383',
		'dprob'  => '0.436',
		'cprob'  => '0.576',
		'nnpred' => 'signal-peptide',
		'end'    => '83',
	       },
       };

# Test on filtered results
$facts   = [qw(maxY)];
$in      = test_input_file("signalp.nn.short");
$signalp = Bio::Tools::Signalp::ExtendedSignalp->new(
						     -file => $in,
						     -factors => $facts,
						    );

ok($signalp);
$i = 1;

while(my $feat = $signalp->next_feature()){
    is($feat->seq_id(), $res->{$i}->{id});
    is($feat->end(), $res->{$i}->{end});
    is(($feat->get_tag_values('maxCprob'))[0], $res->{$i}->{cprob});
    is(($feat->get_tag_values('Dprob'))[0], $res->{$i}->{dprob});
    is(($feat->get_tag_values('maxYprob'))[0], $res->{$i}->{yprob});
    is(($feat->get_tag_values('nnPrediction'))[0], $res->{$i}->{nnpred});
    $i++;
}
# Tests without filters.
# It should by default only parses results with Ymax and meanS to mimic default behavior
# from GPI::Bio::Tools::Signalp
$res = {
	'1' => {
		'id'     => 'BC1G_00003.1',
		'nnpred' => 'signal-peptide',
		'yprob'  => '0.866',
		'dprob'  => '0.902',
		'cprob'  => '0.934',
		'end'    => '22',
	       },
	'2' => {
		'id'     => 'BC1G_00008.1',
		'yprob'  => '0.383',
		'dprob'  => '0.436',
		'cprob'  => '0.576',
		'nnpred' => 'signal-peptide',
		'end'    => '83',
	       },
       };

#No filters required
$signalp = Bio::Tools::Signalp::ExtendedSignalp->new(
						     -file => $in
						    );
ok($signalp);
$i = 1;

while(my $feat = $signalp->next_feature()){
    is($feat->seq_id(), $res->{$i}->{id});
    is($feat->end(), $res->{$i}->{end});
    is(($feat->get_tag_values('maxCprob'))[0], $res->{$i}->{cprob});
    is(($feat->get_tag_values('Dprob'))[0], $res->{$i}->{dprob});
    is(($feat->get_tag_values('maxYprob'))[0], $res->{$i}->{yprob});
    is(($feat->get_tag_values('nnPrediction'))[0], $res->{$i}->{nnpred});
    $i++;
}

##########################################
### TESTS ON SHORT OUTPUT FORMAT (HMM) ###
##########################################

$res = {
	'1' => {
		'id'     => 'BC1G_00002.1',
		'prob'   => '0.000',
		'cleav'  => '0.000',
		'pred'   => 'Non-secretory protein',
		'end'    => '22',
	       },
	'2' => {
		'id'     => 'BC1G_00003.1',
		'prob'   => '0.999',
		'cleav'  => '0.973',
		'pred'   => 'Signal peptide',
		'end'    => '22',
	       },
	'3' => {
		'id'     => 'BC1G_00004.1',
		'prob'   => '0.003',
		'cleav'  => '0.001',
		'pred'   => 'Non-secretory protein',
		'end'    => '19',
	       },
	'4' => {
		'id'     => 'BC1G_00005.1',
		'prob'   => '0.008',
		'cleav'  => '0.007',
		'pred'   => 'Non-secretory protein',
		'end'    => '22',
		},
	'5' => {
		'id'     => 'BC1G_00006.1',
		'prob'   => '0.000',
		'cleav'  => '0.000',
		'pred'   => 'Non-secretory protein',
		'end'    => '23',
		},
	'6' => {
		'id'     => 'BC1G_00007.1',
		'prob'   => '0.240',
		'cleav'  => '0.228',
		'pred'   => 'Non-secretory protein',
		'end'    => '22',
		},
	'7' => {
		'id'     => 'BC1G_00008.1',
		'prob'   => '0.222',
		'cleav'  => '0.061',
		'pred'   => 'Non-secretory protein',
		'end'    => '22',
		},
	'8' => {
		'id'     => 'BC1G_00009.1',
		'prob'   => '0.000',
		'cleav'  => '0.000',
		'pred'   => 'Non-secretory protein',
		'end'    => '20',
		},
       };

# No filters available with hmm on short output
$in      = test_input_file("signalp.hmm.short");
$signalp = Bio::Tools::Signalp::ExtendedSignalp->new(
						     -file => $in,
						    );

ok($signalp);
$i = 1;

while(my $feat = $signalp->next_feature()){
    is($feat->seq_id(), $res->{$i}->{id});
    is($feat->end(), $res->{$i}->{end});
    is(($feat->get_tag_values('peptideProb'))[0], $res->{$i}->{prob});
    is(($feat->get_tag_values('cleavageSiteProb'))[0], $res->{$i}->{cleav});
    is(($feat->get_tag_values('signalpPrediction'))[0], $res->{$i}->{pred});
    $i++;
}


exit 0;
BioPerl-1.007002/t/Tools/Spidey000755000766000024          013155576321 16157 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Tools/Spidey/Spidey.t000444000766000024       271213155576321 17740 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {     
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 26);
	
	use_ok('Bio::Tools::Spidey::Results');
}

ok my $spidey = Bio::Tools::Spidey::Results->new(-file=> test_input_file('spidey.noalignment'),
                                                 -verbose => -1);

$spidey->close();

my $exonset = $spidey->next_exonset;
ok(!defined($exonset));

$spidey = Bio::Tools::Spidey::Results->new(-file=> test_input_file('spidey.test1'));
$exonset = $spidey->next_exonset;
my @exons = $exonset->sub_SeqFeature(); 
is @exons, 6;

is $spidey->genomic_dna_length(), 145732769;
is $spidey->splicesites(), 4;
is $spidey->est_coverage(), 100;
is $spidey->overall_percentage_id(), 99.7;
is $spidey->missing_mrna_ends(), 'neither';

is $exonset->seq_id(), 'lcl|chr2';
is $exonset->start(), 36356457;
is $exonset->end(), 36375798;

my $exon = 0;
is $exons[$exon]->est_hit()->seq_id(), 'lcl|tmpseq_0';
is $exons[$exon]->start(), 36375691;
is $exons[$exon]->end(), 36375798;
is $exons[$exon]->strand(), -1;
is $exons[$exon]->est_hit()->start(), 1;
is $exons[$exon]->est_hit()->end(), 108;
is $exons[$exon]->donor(), 1;
is $exons[$exon]->acceptor(), 0;

$exon = 1;
is $exons[$exon]->start(), 36369345;
is $exons[$exon]->end(), 36369492;
is $exons[$exon]->est_hit()->start(), 109;
is $exons[$exon]->est_hit()->end(), 256;
is $exons[$exon]->donor(), 0;
is $exons[$exon]->acceptor(), 1;

$spidey->close();
BioPerl-1.007002/t/Tree000755000766000024          013155576321 14521 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Tree/Compatible.t000555000766000024       347713155576321 17140 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
  use lib '.';
  use Bio::Root::Test;
  
  test_begin(-tests => 5,
			 -requires_module => 'Set::Scalar');
  
  use_ok('Bio::Tree::Compatible');
  use_ok('Bio::TreeIO');
}

# these tests are done with direct access to Bio::Tree::Compatible methods,
# instead of via creating a Bio::Tree::Compatible->new() object or similar...
# the docs seem to indicate that is normally possible? TODO?

my $in = Bio::TreeIO->new(-format => 'newick',
						  -fh     => \*DATA);

# the common labels of (((A,B)C,D),(E,F,G)); and ((A,B)H,E,(J,(K)G)I);
# are [A,B,E,G]

my $t1 = $in->next_tree;
my $t2 = $in->next_tree;
my $common = Bio::Tree::Compatible::common_labels($t1,$t2);
my $labels = Set::Scalar->new(qw(A B E G));
ok($common->is_equal($labels));

# the topological restrictions of (((A,B)C,D),(E,F,G)); and
# ((A,B)H,E,(J,(K)G)I); to their common labels, [A,B,E,G], are,
# respectively, ((A,B),(E,G)); and ((A,B),E,(G));

Bio::Tree::Compatible::topological_restriction($t1,$common);
Bio::Tree::Compatible::topological_restriction($t2,$common);
my $t3 = $in->next_tree;
my $t4 = $in->next_tree;
# ok($t1->is_equal($t3)); # is_equal method missing in Bio::Tree::Tree
# ok($t2->is_equal($t4)); # is_equal method missing in Bio::Tree::Tree

# the topological restrictions of (((A,B)C,D),(E,F,G)); and
# ((A,B)H,E,(J,(K)G)I); to their common labels, [A,B,E,G], are
# compatible

my ($incompat, $ilabels, $inodes) = Bio::Tree::Compatible::is_compatible($t3,$t4);
ok(!$incompat);

# (((B,A),C),D); and ((A,(D,B)),C); are incompatible

my $t5 = $in->next_tree;
my $t6 = $in->next_tree;
($incompat, $ilabels, $inodes) = Bio::Tree::Compatible::is_compatible($t5,$t6);
ok($incompat);

__DATA__
(((A,B)C,D),(E,F,G));
((A,B)H,E,(J,(K)G)I);
((A,B),(E,G));
((A,B),E,(G));
(((B,A),C),D);
((A,(D,B)),C);
BioPerl-1.007002/t/Tree/Node.t000444000766000024       654413155576321 15741 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
  use lib '.';
  use Bio::Root::Test;
  use File::Temp qw(tempfile);
  test_begin( -tests => 40 );
  use_ok('Bio::Tree::Node');
  use_ok('Bio::Tree::AlleleNode');
  use_ok('Bio::TreeIO');
}

my $node1 = Bio::Tree::Node->new();
my $node2 = Bio::Tree::Node->new();
ok( $node1->is_Leaf() );
is( $node1->ancestor, undef );

# tests for tags
ok !$node1->has_tag('test');
is $node1->add_tag_value( 'test', 'a' ), 1;
ok $node1->has_tag('test');
is $node1->add_tag_value( 'test', 'b' ), 2;
my @tags = $node1->get_tag_values('test');
is scalar @tags, 2;
is scalar $node1->get_tag_values('test'), 'a', 'retrieve the first value';

is $node1->remove_tag('test2'), 0;
is $node1->remove_tag('test'),  1;
ok !$node1->has_tag('test');
is $node1->set_tag_value( 'test', ( 'a', 'b', 'c' ) ), 3;
is $node1->remove_all_tags(), undef;
ok !$node1->has_tag('test');

my $pnode = Bio::Tree::Node->new();
$pnode->add_Descendent($node1);
is( $node1->ancestor, $pnode );
$pnode->add_Descendent($node2);
is( $node2->ancestor, $pnode );

ok( !$pnode->is_Leaf );

my $phylo_node = Bio::Tree::Node->new(
  -bootstrap => 0.25,
  -id        => 'ADH_BOV',
  -desc      => 'Taxon 1'
);
$node1->add_Descendent($phylo_node);
ok( !$node1->is_Leaf );
is( $phylo_node->ancestor,    $node1 );
is( $phylo_node->id,          'ADH_BOV' );
is( $phylo_node->bootstrap,   0.25 );
is( $phylo_node->description, 'Taxon 1' );

is $phylo_node->ancestor($node2), $node2;
ok $node1->is_Leaf;
is my @descs = $node2->each_Descendent, 1;
is $descs[0], $phylo_node;

my $allele_node = Bio::Tree::AlleleNode->new();
$allele_node->add_Genotype(
  Bio::PopGen::Genotype->new(
    -marker_name => 'm1',
    -alleles     => [0]
  )
);
$allele_node->add_Genotype(
  Bio::PopGen::Genotype->new(
    -marker_name => 'm3',
    -alleles     => [ 1, 1 ]
  )
);
$allele_node->add_Genotype(
  Bio::PopGen::Genotype->new(
    -marker_name => 'm4',
    -alleles     => [ 0, 4 ]
  )
);
ok($allele_node);
my @mkrs = $allele_node->get_marker_names;

is( @mkrs, 3 );
my ($m3) = $allele_node->get_Genotypes( -marker => 'm3' );
is( $m3->get_Alleles, 2 );
my ($a1) = $allele_node->get_Genotypes( -marker => 'm1' )->get_Alleles;
is( $a1, 0 );

my ( $a2, $a3 ) = $allele_node->get_Genotypes( -marker => 'm4' )->get_Alleles;
is( $a2, 0 );
is( $a3, 4 );

# bug 2877
my $str = "(A:52,(B:46,C:50):11,D:70)68"; 
my $in = Bio::TreeIO->new(
  -internal_node_id => 'bootstrap',
  -format => 'nhx',
  -string => $str,
);
my $t = $in->next_tree;
  my $s;
  my $old_root = $t->get_root_node();
  my ($b) = $t->find_node( -id => "B" );
  my $b_anc = $b->ancestor;

  my $r = $b->create_node_on_branch( -FRACTION => 0.5 );
  $r->id('fake');

  # before reroot
  is( $t->as_text('newick',$in->params), "(A:52,(C:50,(B:23)fake:23):11,D:70)68;", 'with fake node' );

  # after reroot
  $t->reroot($r);
  is( $t->as_text('newick',$in->params), "(B:23,(C:50,(A:52,D:70)68:11):23)fake;",
    "after reroot on fake node" );
  $t->reroot($b);

  is( $t->as_text('newick',$in->params), "(((C:50,(A:52,D:70)68:11):23)fake:23)B;", "reroot on B" );

  $t->reroot($b_anc);
  $t->splice( -remove_id => 'fake' );

  is(
    $t->as_text('newick',$in->params),
    "(B:23,C:50,(A:52,D:70)68:11);",
    "remove fake node, reroot on former B anc"
  );
  $t->reroot($old_root);
  is( $t->as_text('newick',$in->params), "(A:52,(B:23,C:50):11,D:70)68;", "roundtrip" );
BioPerl-1.007002/t/Tree/RandomTreeFactory.t000444000766000024       116313155576321 20434 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 5);
    
	use_ok('Bio::Tree::RandomFactory');
    use_ok('Bio::TreeIO');
    use_ok('Bio::Tree::Statistics');
}

my $FILE1 = test_output_file();
 
my $ssize = 5;
my $factory = Bio::Tree::RandomFactory->new(-sample_size => $ssize);
my $stats = Bio::Tree::Statistics->new();

my $tree = $factory->next_tree;

is($tree->get_nodes, ($ssize * 2 - 1));

my $treeio = Bio::TreeIO->new(-format => 'newick', -file => ">$FILE1");

$treeio->write_tree($tree);
undef $treeio;

ok(-s $FILE1);
BioPerl-1.007002/t/Tree/Tree.t000444000766000024      3135313155576321 15767 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    test_begin(-tests => 66);
    use_ok('Bio::TreeIO');
}

my $verbose = test_debug();

my $treeio = Bio::TreeIO->new(-verbose => $verbose,
                              -format => 'nhx',
                              -file   => test_input_file('test.nhx'));
my $tree = $treeio->next_tree;

# tests for tags
ok ! $tree->has_tag('test');
is $tree->add_tag_value('test','a'), 1;
ok $tree->has_tag('test');
is $tree->add_tag_value('test','b'), 2;
my @tags = $tree->get_tag_values('test');
is scalar @tags, 2;
is scalar $tree->get_tag_values('test'), 'a', 'retrieve the first value';
is $tree->remove_tag('test2'), 0;
is $tree->remove_tag('test'), 1;
ok ! $tree->has_tag('test');
is $tree->set_tag_value('test',('a','b','c')), 3;
is $tree->remove_all_tags(), undef;
ok ! $tree->has_tag('test');


my @nodes = $tree->find_node('ADH2');
is(@nodes, 2,'Number of nodes that have ADH2 as name');

if( $verbose ) {
    $treeio = Bio::TreeIO->new(-verbose => $verbose,
                               -format => 'nhx',
                              );
    $treeio->write_tree($tree);
    print "nodes are: \n",
    join(", ", map {  $_->id . ":". (defined $_->branch_length ? 
                                     $_->branch_length : '' ) } @nodes), "\n";
}

$treeio = Bio::TreeIO->new(-format => 'newick',
                           -file   => test_input_file('test.nh'));
$tree = $treeio->next_tree;


if( $verbose ) { 
    my $out = Bio::TreeIO->new(-format => 'tabtree');
    
    $out->write_tree($tree);
}

my @hADH = ( $tree->find_node('hADH1'),
             $tree->find_node('hADH2') );
my ($n4) = $tree->find_node('yADH4');

is($tree->is_monophyletic(-nodes    => \@hADH,
                          -outgroup => $n4),1,'Test Monophyly');

my @mixgroup = ( $tree->find_node('hADH1'),
                 $tree->find_node('yADH2'),
                 $tree->find_node('yADH3'),
                 );

my ($iADHX) = $tree->find_node('iADHX');

# test height
is($iADHX->height, 0,'Height');
is($iADHX->depth,0.22,'Depth');
isnt( $tree->is_monophyletic(-nodes   => \@mixgroup,
                             -outgroup=> $iADHX),1, 'non-monophyletic group');

# binary tree?
is $tree->is_binary, 0, 'not a binary tree';
is scalar $tree->get_nodes, 12, '12 nodes';
$tree->verbose(-1);
$tree->force_binary;
is $tree->is_binary, 1, 'after force_binary() it is';
is scalar $tree->get_nodes, 17, 'and there are more nodes (17)';

my $in = Bio::TreeIO->new(-format => 'newick',
                          -fh     => \*DATA);
$tree = $in->next_tree;
my ($a,$b,$c,$d) = ( $tree->find_node('A'),
                     $tree->find_node('B'),
                     $tree->find_node('C'),
                     $tree->find_node('D'));

is($tree->is_monophyletic(-nodes => [$b,$c],
                          -outgroup => $d),1, 'B,C are Monophyletic');

is($tree->is_monophyletic(-nodes => [$b,$a],
                          -outgroup => $d),1,'A,B are Monophyletic');

$tree = $in->next_tree;
my ($e,$f,$i);
($a,$b,$c,$d,$e,$f,$i) = ( $tree->find_node('A'),
                           $tree->find_node('B'),
                           $tree->find_node('C'),
                           $tree->find_node('D'),
                           $tree->find_node('E'),
                           $tree->find_node('F'),
                           $tree->find_node('I'),
                           );
isnt( $tree->is_monophyletic(-nodes => [$b,$f],
                             -outgroup => $d),1,'B,F are not Monophyletic' );

is($tree->is_monophyletic(-nodes => [$b,$a],
                          -outgroup => $f),1, 'A,B are Monophyletic');

# test for paraphyly

isnt(  $tree->is_paraphyletic(-nodes => [$a,$b,$c],
                              -outgroup => $d), 1,'A,B,C are not Monophyletic w D as outgroup');

is(  $tree->is_paraphyletic(-nodes => [$a,$f,$e],
                            -outgroup => $i), 1, 'A,F,E are monophyletic with I as outgroup');


# test for rerooting the tree
my $out = Bio::TreeIO->new(-format => 'newick', 
                           -fh => \*STDERR, 
                           -noclose => 1);
$tree = $in->next_tree;
$tree->verbose( -1 ) unless $verbose;
my $node_cnt_orig = scalar($tree->get_nodes);
# reroot on an internal node: should work fine
$a = $tree->find_node('A');
# removing node_count checks because re-rooting can change the
# number of internal nodes (if it is done correctly)
my $total_length_orig = $tree->total_branch_length;
is $tree->total_branch_length, $tree->subtree_length, 
    "subtree_length() without attributes is an alias to total_branch_lenght()";
cmp_ok($total_length_orig, '>',$tree->subtree_length($a->ancestor), 
       'Length of the tree is larger that lenght of a subtree');
$out->write_tree($tree) if $verbose;
is($tree->reroot($a),1, 'Can re-root with A as outgroup');
$out->write_tree($tree) if $verbose;
is($node_cnt_orig, scalar($tree->get_nodes), 'Count the number of nodes');
my $total_length_new = $tree->total_branch_length;
my $eps = 0.001 * $total_length_new; # tolerance for checking length
warn("orig total len ", $total_length_orig, "\n") if $verbose;
warn("new  total len ", $tree->total_branch_length,"\n") if $verbose;
# according to retree in phylip these branch lengths actually get larger
# go figure...
# this should be fixed now/maj
ok(($total_length_orig >= $tree->total_branch_length - $eps) &&
   ($total_length_orig <= $tree->total_branch_length + $eps),'same length');

# prob with below: rerooted tree on node A at line 146; so $a IS root
#/maj is($tree->get_root_node, $a->ancestor, "Root node is A's ancestor");
is($tree->get_root_node, $a, "Root node is A");

# former test expected the old behavior of reroot; here is the new
# test/maj
my $desc = ($a->each_Descendent)[0];
my $newroot = $desc->create_node_on_branch(-FRACTION=>0.5, -ANNOT=>{-id=>'newroot'});
$tree->reroot($newroot);
is($tree->get_root_node, $a->ancestor, "Root node is A's ancestor");

# try to reroot on an internal, will result in there being 1 less node
# Rerooting should be an invariant operation with respect to node number!/maj
# the test show that it now is, because the secret removal of nodes 
# no longer occurs

$a = $tree->find_node('C')->ancestor;
$out->write_tree($tree) if $verbose;
is($tree->reroot($a),1, "Can reroot with C's ancsestor");
$out->write_tree($tree) if $verbose;
#/maj is($node_cnt_orig, scalar($tree->get_nodes), 'Check to see that node count is correct after an internal node was removed after this re-rooting');
# but we did add a new node at line 166, so
is($node_cnt_orig+1, scalar($tree->get_nodes), 'Node count correct');
warn("orig total len ", $total_length_orig, "\n") if $verbose;
warn("new  total len ", $tree->total_branch_length,"\n") if $verbose;
cmp_ok($total_length_orig, '>=', $tree->total_branch_length - $eps, 
       'Total original branch length is what it is supposed to be');
# branch length should also be invariant w/r to rerooting...
cmp_ok($total_length_orig, '<=',$tree->total_branch_length + $eps, 
       'Updated total branch length after the reroot');
# again, we rerooted ON THE NODE, so $a IS the root./maj
is($tree->get_root_node, $a, 'Make sure root is really what we asked for');

# try to reroot on new root: should fail
#/maj  $a = $tree->get_root_node;
isnt( $tree->reroot($a),1, 'Testing for failed re-rerooting');

# try a more realistic tree
$tree = $in->next_tree;
$a = $tree->find_node('VV');
$node_cnt_orig = scalar($tree->get_nodes);
$total_length_orig = $tree->total_branch_length;
$out->write_tree($tree) if $verbose;
is($tree->reroot($a),1, 'Test that rooting succeeded'); #mod /maj
$out->write_tree($tree) if $verbose;
# node number should be invariant after reroot/maj
is($node_cnt_orig, scalar($tree->get_nodes), 'Test that re-rooted tree has proper number of nodes after re-rooting'); #mod /maj
$total_length_new = $tree->total_branch_length;
$eps = 0.001 * $total_length_new;    # tolerance for checking length
cmp_ok($total_length_orig, '>=', $tree->total_branch_length - $eps, 'Branch length before rerooting');
cmp_ok($total_length_orig, '<=', $tree->total_branch_length + $eps, 
       'Branch length after rerooting');
is($tree->get_root_node, $a,'Root is really the ancestor we asked for'); #mod /maj

# BFS and DFS search testing
$treeio = Bio::TreeIO->new(-verbose => $verbose,
                           -format  => 'newick',
                           -file    => test_input_file('test.nh'));
$tree = $treeio->next_tree;
my ($ct,$n) = (0);
my $let = ord('A');
for $n (  $tree->get_leaf_nodes ) {
    $n->id(chr($let++));
}

for $n ( grep {! $_->is_Leaf } $tree->get_nodes ) {
    $n->id($ct++);
}
# enable for debugging
Bio::TreeIO->new(-format => 'newick')->write_tree($tree) if( $verbose );

my $BFSorder = join(",", map { $_->id } ( $tree->get_nodes(-order => 'b')));
is($BFSorder, '0,1,3,2,C,D,E,F,G,H,A,B', 'BFS traversal order');
my $DFSorder = join(",", map { $_->id } ( $tree->get_nodes(-order => 'd')));
is($DFSorder, '0,1,2,A,B,C,D,3,E,F,G,H', 'DFS travfersal order');


# test some Bio::Tree::TreeFunctionI methods
#find_node tested extensively already
$tree->remove_Node('H');
$DFSorder = join(",", map { $_->id } ( $tree->get_nodes(-order => 'd')));
is($DFSorder, '0,1,2,A,B,C,D,3,E,F,G', 'DFS traversal after removing H');
$tree->splice(-remove_id => 'G');
$DFSorder = join(",", map { $_->id } ( $tree->get_nodes(-order => 'd')));
is($DFSorder, '0,1,2,A,B,C,D,3,E,F', 'DFS traversal after removing G');
$tree->splice(-remove_id => [('E', 'F')], -keep_id => 'F');
$DFSorder = join(",", map { $_->id } ( $tree->get_nodes(-order => 'd')));
# the node '3' is not explicitly removed, so it should still be there
# I suspect that it disappeared before was due to the previously
# automatic removal of internal degree 2 nodes../maj
is($DFSorder, '0,1,2,A,B,C,D,3,F', 'DFS traversal after removing E');
$tree->splice(-keep_id => [qw(0 1 2 A B C D)]);
$DFSorder = join(",", map { $_->id } ( $tree->get_nodes(-order => 'd')));
is($DFSorder, '0,1,2,A,B,C,D', 'DFS after removing all but 0,1,2,A,B,C,D');
#get_lineage_nodes, get_lineage_string, get_lca, merge_lineage, contract_linear_paths tested in Taxonomy.t


# try out the id to bootstrap copy method
$treeio = Bio::TreeIO->new(-format => 'newick',
                           -file   => test_input_file('bootstrap.tre'));
$tree = $treeio->next_tree;
my ($test_node) = $tree->find_node(-id => 'A');
is($test_node->ancestor->id, 90,'Testing bootstrap copy');
is($test_node->ancestor->ancestor->id, '25','Testing bootstrap copy');
is($test_node->ancestor->ancestor->ancestor->id, '0','Testing bootstrap copy');
$tree->move_id_to_bootstrap;
is($test_node->ancestor->id, '','Testing bootstrap copy');
is($test_node->ancestor->bootstrap, '90', 'Testing bootstrap copy');
is($test_node->ancestor->ancestor->id, '', 'Testing bootstrap copy');
is($test_node->ancestor->ancestor->bootstrap, '25', 'Testing bootstrap copy');
is($test_node->ancestor->ancestor->ancestor->bootstrap, '0','Testing bootstrap copy');

# change TreeIO to parse 
$treeio = Bio::TreeIO->new(-format => 'newick',
                           -file   => test_input_file('bootstrap.tre'),
                           -internal_node_id => 'bootstrap');
$tree = $treeio->next_tree;
($test_node) = $tree->find_node(-id => 'A');
is($test_node->ancestor->id, '','Testing auto-boostrap copy during parse');
is($test_node->ancestor->ancestor->id, '',
   'Testing auto-boostrap copy during parse');
is($test_node->ancestor->bootstrap, '90',
   'Testing auto-boostrap copy during parse');
is($test_node->ancestor->ancestor->bootstrap, '25', 
   'Testing auto-boostrap copy during parse');

# return an empty array when no nodes are found
ok $tree = Bio::Tree::Tree->new();
@nodes = $tree->get_nodes;
is scalar @nodes, 0;


__DATA__
(D,(C,(A,B)));
(I,((D,(C,(A,B)x)y),(E,(F,G))));
(((A:0.3,B:2.1):0.45,C:0.7),D:4);
(A:0.031162,((((((B:0.022910,C:0.002796):0.010713,(D:0.015277,E:0.020484):0.005336):0.005588,((F:0.013293,(G:0.018374,H:0.003108):0.005318):0.006047,I:0.014607):0.001677):0.004196,(((((J:0.003307,K:0.001523):0.011884,L:0.006960):0.006514,((M:0.001683,N:0.000100):0.002226,O:0.007085):0.014649):0.008004,P:0.037422):0.005201,(Q:0.000805,R:0.000100):0.015280):0.005736):0.004612,S:0.042283):0.017979,(T:0.006883,U:0.016655):0.040226):0.014239,((((((V:0.000726,W:0.000100):0.028490,((((X:0.011182,Y:0.001407):0.005293,Z:0.011175):0.004701,AA:0.007825):0.016256,BB:0.029618):0.008146):0.004279,CC:0.035012):0.060215,((((((DD:0.014933,(EE:0.008148,FF:0.000100):0.015458):0.003891,GG:0.010996):0.001489,(HH:0.000100,II:0.000100):0.054265):0.003253,JJ:0.019722):0.013796,((KK:0.001960,LL:0.004924):0.013034,MM:0.010071):0.043273):0.011912,(NN:0.031543,OO:0.018307):0.059182):0.026517):0.011087,((PP:0.000100,QQ:0.002916):0.067214,(RR:0.064486,SS:0.013444):0.011613):0.050846):0.015644,((TT:0.000100,UU:0.009287):0.072710,(VV:0.009242,WW:0.009690):0.035346):0.042993):0.060365);
BioPerl-1.007002/t/Tree/TreeIO.t000444000766000024      2165413155576321 16222 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 78);
    
    use_ok('Bio::TreeIO');
}

my $verbose = test_debug();

ok my $treeio = Bio::TreeIO->new(-verbose => $verbose,
                 -format => 'newick',
                 -file   => test_input_file('cysprot1b.newick'));

my $tree = $treeio->next_tree;
isa_ok($tree, 'Bio::Tree::TreeI');

my @nodes = $tree->get_nodes;
is(@nodes, 6);
my ($rat) = $tree->find_node('CATL_RAT');
ok($rat);
is($rat->branch_length, '0.12788');
# move the id to the bootstap
is($rat->ancestor->bootstrap($rat->ancestor->id), '95');
$rat->ancestor->id('');
# maybe this can be auto-detected, but then can't distinguish
# between internal node labels and bootstraps...
is($rat->ancestor->bootstrap, '95');
is($rat->ancestor->branch_length, '0.18794');
is($rat->ancestor->id, '');

if ($verbose) {
    foreach my $node ( $tree->get_root_node()->each_Descendent() ) {
        print "node: ", $node->to_string(), "\n";
        my @ch = $node->each_Descendent();
        if( @ch ) {
            print "\tchildren are: \n";
            foreach my $node ( $node->each_Descendent() ) {
                print "\t\t ", $node->to_string(), "\n";
            }
        }
    }
}

my $FILE1 = test_output_file();
$treeio = Bio::TreeIO->new(-verbose => $verbose,
              -format => 'newick',
              -file   => ">$FILE1");
$treeio->write_tree($tree);
undef $treeio;
ok( -s $FILE1 );
$treeio = Bio::TreeIO->new(-verbose => $verbose,
              -format => 'newick',
              -file   => test_input_file('LOAD_Ccd1.dnd'));
ok($treeio);
$tree = $treeio->next_tree;

isa_ok($tree,'Bio::Tree::TreeI');

@nodes = $tree->get_nodes;
is(@nodes, 52);

if( $verbose ) { 
    foreach my $node ( @nodes ) {
        print "node: ", $node->to_string(), "\n";
        my @ch = $node->each_Descendent();
        if( @ch ) {
            print "\tchildren are: \n";
            foreach my $node ( $node->each_Descendent() ) {
                print "\t\t ", $node->to_string(), "\n";
            }
        }
    }
}

is($tree->total_branch_length, 7.12148);
my $FILE2 = test_output_file();
$treeio = Bio::TreeIO->new(-verbose => $verbose,
              -format => 'newick', 
              -file   => ">$FILE2");
$treeio->write_tree($tree);
undef $treeio;
ok(-s $FILE2);
$treeio = Bio::TreeIO->new(-verbose => $verbose,
              -format  => 'newick',
              -file    => test_input_file('hs_fugu.newick'));
$tree = $treeio->next_tree();
@nodes = $tree->get_nodes();
is(@nodes, 5);
# no relable order for the bottom nodes because they have no branchlen
my @vals = qw(SINFRUP0000006110);
my $saw = 0;
foreach my $node ( $tree->get_root_node()->each_Descendent() ) {
    foreach my $v ( @vals ) {
       if( defined $node->id && 
           $node->id eq $v ){ $saw = 1; last; }
    }
    last if $saw;
}
is($saw, 1, "Saw $vals[0] as expected");
if( $verbose ) {
    foreach my $node ( @nodes ) {
        print "\t", $node->id, "\n" if $node->id;
    }
}

$treeio = Bio::TreeIO->new(-format => 'newick', 
                                  -fh => \*DATA);
my $treeout = Bio::TreeIO->new(-format => 'tabtree');
my $treeout2 = Bio::TreeIO->new(-format => 'newick');

$tree = $treeio->next_tree;

if( $verbose > 0  ) {
    $treeout->write_tree($tree);
    $treeout2->write_tree($tree);
}

$treeio = Bio::TreeIO->new(-verbose => $verbose,
              -file   => test_input_file('test.nhx'));

SKIP: {
    test_skip(-tests => 2, -requires_module => 'SVG::Graph');
    my $FILE3 = test_output_file();
    my $treeout3 = Bio::TreeIO->new(-format => 'svggraph',
                                             -file => ">$FILE3");
    ok($treeout3);
    eval {$treeout3->write_tree($tree);};
    ok (-s $FILE3);
}

ok($treeio);
$tree = $treeio->next_tree;

isa_ok($tree, 'Bio::Tree::TreeI');

@nodes = $tree->get_nodes;
is(@nodes, 12, "Total Nodes");

my $adhy = $tree->find_node('ADHY');
is($adhy->branch_length, 0.1);
is(($adhy->get_tag_values('S'))[0], 'nematode');
is(($adhy->get_tag_values('E'))[0], '1.1.1.1');

# try lintree parsing
$treeio = Bio::TreeIO->new(-format => 'lintree',
                  -file   => test_input_file('crab.njb'));

my (@leaves, $node);
while( $tree = $treeio->next_tree ) {

    isa_ok($tree, 'Bio::Tree::TreeI');

    @nodes = $tree->get_nodes;

    @leaves = $tree->get_leaf_nodes;
    is(@leaves, 13);
#/maj   is(@nodes, 25);
    is(@nodes, 24); # this is clear from the datafile and counting \maj
    ($node) = $tree->find_node(-id => '18');
    ok($node);
    is($node->id, '18');
    is($node->branch_length, '0.030579');
    is($node->bootstrap, 998);
}

$treeio = Bio::TreeIO->new(-format => 'lintree',
               -file   => test_input_file('crab.nj'));

$tree = $treeio->next_tree;

isa_ok($tree, 'Bio::Tree::TreeI');

@nodes = $tree->get_nodes;
@leaves = $tree->get_leaf_nodes;
is(@leaves, 13);
#/maj is(@nodes, 25);
is(@nodes, 24); #/maj
($node) = $tree->find_node('18');
is($node->id, '18');
is($node->branch_length, '0.028117');

($node) = $tree->find_node(-id => 'C-vittat');
is($node->id, 'C-vittat');
is($node->branch_length, '0.087619');
is($node->ancestor->id, '14');

$treeio = Bio::TreeIO->new(-format => 'lintree',
              -file   => test_input_file('crab.dat.cn'));

$tree = $treeio->next_tree;

isa_ok($tree, 'Bio::Tree::TreeI');

@nodes = $tree->get_nodes;
@leaves = $tree->get_leaf_nodes;
is(@leaves, 13, "Leaf nodes");

#/maj is(@nodes, 25, "All nodes");
is(@nodes, 24, "All nodes"); 
($node) = $tree->find_node('18');
is($node->id, '18');

is($node->branch_length, '0.029044');

($node) = $tree->find_node(-id => 'C-vittat');
is($node->id, 'C-vittat');
is($node->branch_length, '0.097855');
is($node->ancestor->id, '14');

SKIP: {
    test_skip(-tests => 8, -requires_module => 'IO::String');
    
    # test nexus tree parsing
    $treeio = Bio::TreeIO->new(-format => 'nexus',
                               -verbose => $verbose,
                   -file   => test_input_file('urease.tre.nexus'));
    
    $tree = $treeio->next_tree;
    ok($tree);
    is($tree->id, 'PAUP_1');
    is($tree->get_leaf_nodes, 6);
    ($node) = $tree->find_node(-id => 'Spombe');
    is($node->branch_length,0.221404);
    
    # test nexus MrBayes tree parsing
    $treeio = Bio::TreeIO->new(-format => 'nexus',
                   -file   => test_input_file('adh.mb_tree.nexus'));
    
    $tree = $treeio->next_tree;
    my $ct = 1; 
    ok($tree);
    is($tree->id, 'rep.1');
    is($tree->get_leaf_nodes, 54);
    ($node) = $tree->find_node(-id => 'd.madeirensis');
    is($node->branch_length,0.039223);
    while ($tree = $treeio->next_tree) {
        $ct++;
    }
    is($ct,13,'bug 2356');
}

# bug #1854
# process no-newlined tree
$treeio = Bio::TreeIO->new(-format => 'nexus',
                           -verbose => $verbose,
               -file   => test_input_file('tree_nonewline.nexus'));

$tree = $treeio->next_tree;
ok($tree);
ok($tree->find_node('TRXHomo'));


# parse trees with scores

$treeio = Bio::TreeIO->new(-format => 'newick',
               -file   => test_input_file('puzzle.tre'));
$tree = $treeio->next_tree;
ok($tree);
is($tree->score, '-2673.059726');

# bug #2205
# process trees with node IDs containing spaces
$treeio = Bio::TreeIO->new(-format => 'nexus',
                           -verbose => $verbose,
               -file   => test_input_file('spaces.nex'));

$tree = $treeio->next_tree;

my @nodeids = ("'Allium drummondii'", "'Allium cernuum'",'A.cyaneum');

ok($tree);
for my $node ($tree->get_leaf_nodes) {
    is($node->id, shift @nodeids);      
}

# bug #2221
# process tree with names containing quoted commas

$tree = $treeio->next_tree;

@nodeids = ("'Allium drummondii, USA'", "'Allium drummondii, Russia'",'A.cyaneum');

ok($tree);
for my $node ($tree->get_leaf_nodes) {
    is($node->id, shift @nodeids);      
}

# bug #2221
# process tree with names containing quoted commas on one line

$tree = $treeio->next_tree;

@nodeids = ("'Allium drummondii, Russia'", "'Allium drummondii, USA'",'A.cyaneum');

ok($tree);
for my $node ($tree->get_leaf_nodes) {
    is($node->id, shift @nodeids);      
}

# bug #2869
#

# proper way (Tree isn't GC'd)
$tree = Bio::TreeIO->new(-format => 'newick',
               -verbose => $verbose,
               -file   => test_input_file('bug2869.tree'))->next_tree;

my $root = $tree->get_root_node;

isa_ok($root, 'Bio::Tree::NodeI');

my $total1 = 0;
for my $child ($root->get_Descendents) {
    $total1++;
}

is($total1, 198);

undef $tree; # GC

$root = Bio::TreeIO->new(-format => 'newick',
               -verbose => $verbose,
               -file   => test_input_file('bug2869.tree'),
               -no_cleanup => 1)->next_tree->get_root_node;

isa_ok($root, 'Bio::Tree::NodeI');

TODO: {
    local $TODO = 'The nodes are garbage-collected away b/c Tree isn\'t retained in memory';
    my $total2 = 0;
    for my $child ($root->get_Descendents) {
        $total2++;
    }
    
    is($total2, $total1);
}

__DATA__
(((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1);
BioPerl-1.007002/t/Tree/TreeStatistics.t000444000766000024      1102213155576321 20031 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: RandomTreeFactory.t 11525 2007-06-27 10:16:38Z sendu $

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 42);

    use_ok('Bio::TreeIO');
    use_ok('Bio::Tree::Statistics');
}


use Data::Dumper;
my $in = Bio::TreeIO->new(-format => 'nexus',
                          -file   => test_input_file('traittree.nexus'));
my $tree = $in->next_tree;
my $node = $tree->find_node(-id => 'N14');


my $stats = Bio::Tree::Statistics->new();
is $stats->cherries($tree), 8, 'cherries';
is $stats->cherries($tree, $node), 4, 'cherries';

# traits
my $key = $tree->add_trait(test_input_file('traits.tab'), 4);
is $key, undef, 'read traits'; # exceeded column number

$key = $tree->add_trait(test_input_file('traits.tab'), 2, 1);
is $key, 'disp'; # one leaf has a missing trait value, but ignore it

$key = $tree->add_trait(test_input_file('traits.tab'), 3);
is $key, 'intermediate';

is $stats->ps($tree, $key), 4, 'parsimony score';
is $stats->ps($tree, $key, $node), 1, 'subtree parsimony score';

my $node_i = $tree->find_node(-id => 'N10');
my @values = sort $node_i->get_tag_values('ps_trait');
ok eq_set (\@values, ['red', 'blue']), 'ps value';

is $stats->fitch_down($tree), 1, 'fitch_down';
is $node_i->get_tag_values('ps_trait'), 'red', 'ps value after fitch_down';



$node_i = $tree->find_node(-id => '2'); # leaf
is $stats->persistence($tree, $node_i), 1, 'persistence of a leaf';

$node_i = $tree->find_node(-id => 'N1');
is $stats->persistence($tree, $node_i), 1, 'persistence of an internal node value ';

$node_i = $tree->find_node(-id => 'N13');
is $stats->persistence($tree, $node_i), 3,  'persistence of an internal node value';

$node_i = $tree->find_node(-id => 'N6');
is $stats->persistence($tree, $node_i), 2,  'persistence of an internal node value';

my $value;

$node_i = $tree->find_node(-id => '1');
is $stats->count_subclusters($tree, $node_i), 0,  'leaf node: number of clusters = 0 ';

$node_i = $tree->find_node(-id => 'N3');
is $stats->count_subclusters($tree, $node_i), 1,  'number of clusters ';

$node_i = $tree->find_node(-id => 'N14');
is $stats->count_subclusters($tree, $node_i), 1,  'number of clusters ';

$node_i = $tree->find_node(-id => 'N7');
is $stats->count_subclusters($tree, $node_i), 2,  'number of clusters ';



$node_i = $tree->find_node(-id => 'N12');
is $stats->count_leaves($tree, $node_i), 2,  'number of leaves in phylotype ';

$node_i = $tree->find_node(-id => 'N13');
is $stats->count_leaves($tree, $node_i), 4,  'number of leaves in phylotype ';

$node_i = $tree->find_node(-id => 'N14');
is $stats->count_leaves($tree, $node_i), 6,  'number of leaves in phylotype ';

$node_i = $tree->find_node(-id => 'N7');
is $stats->count_leaves($tree, $node_i), 6,  'number of leaves in phylotype ';



$node_i = $tree->find_node(-id => 'N4');
is $stats->phylotype_length($tree, $node_i), 1,  'phylotype length';

$node_i = $tree->find_node(-id => 'N6');
is $stats->phylotype_length($tree, $node_i), 5,  'phylotype length';

$node_i = $tree->find_node(-id => 'N7');
is $stats->phylotype_length($tree, $node_i), 12,  'phylotype length';

$node_i = $tree->find_node(-id => 'N13');
is $stats->phylotype_length($tree, $node_i), 6,  'phylotype length';

$node_i = $tree->find_node(-id => 'N14');
is $stats->phylotype_length($tree, $node_i), 11,  'phylotype length';


$node_i = $tree->find_node(-id => 'N4');
is $stats->sum_of_leaf_distances($tree, $node_i), 1,  'sum of leaf distances';

$node_i = $tree->find_node(-id => 'N6');
is $stats->sum_of_leaf_distances($tree, $node_i), 6,  'sum of leaf distances';

$node_i = $tree->find_node(-id => 'N7');
is $stats->sum_of_leaf_distances($tree, $node_i), 18,  'sum of leaf distances';

$node_i = $tree->find_node(-id => 'N13');
is $stats->sum_of_leaf_distances($tree, $node_i), 8,  'sum of leaf distances';

$node_i = $tree->find_node(-id => 'N14');
is $stats->sum_of_leaf_distances($tree, $node_i), 18,  'sum of leaf distances';



is sprintf ("%.3f", $stats->genetic_diversity($tree, $node_i)), '3.000',  'genetic diversity'; 

is sprintf ("%.3f", $stats->statratio($tree, $node_i)), '0.333',  'separation'; 


is $stats->ai($tree, $key), 0.628906, 'association index';
is $stats->ai($tree, $key, $node), 0.062500, 'subtree association index';

my $mc = $stats->mc($tree, $key);
is ($mc->{blue}, 2, 'monophyletic clade size');
is ($mc->{red}, 4, 'monophyletic clade size');
$node = $tree->find_node(-id => 'N10');
$mc = $stats->mc($tree, $key, $node);
is ($mc->{blue}, 2, 'monophyletic clade size');
is ($mc->{red}, 2, 'monophyletic clade size');


BioPerl-1.007002/t/Tree/PhyloNetwork000755000766000024          013155576321 17166 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Tree/PhyloNetwork/Factory.t000444000766000024       663613155576321 21132 0ustar00cjfieldsstaff000000000000# $Id$
# -*-Perl-*-

use strict;

BEGIN {
  use lib '.';
  use Bio::Root::Test;

  test_begin(-tests => 70,
	     -requires_modules => [qw(Bio::PhyloNetwork
				      Bio::PhyloNetwork::TreeFactory)]);

  use_ok('Bio::PhyloNetwork::Factory');
}

my $factory = Bio::PhyloNetwork::Factory->new(-numleaves=>3);
isa_ok($factory,'Bio::PhyloNetwork::Factory');

my @nets;

while (my $net=$factory->next_network()) {
  push @nets,$net;
}

is(scalar @nets,66,'factory');

my @netsbk;

foreach my $enw () {
  my $net = Bio::PhyloNetwork->new(-eNewick=>$enw);
  push @netsbk,$net;
}
is(scalar @netsbk,66,'seen all the data lines');

foreach my $net (@nets) {
  my $found=0;
  foreach my $netbk (@netsbk) {
    if ($net->mu_distance($netbk)==0) {
      $found = 1;
      last;
    }
  }
  ok($found,'found');
}

__DATA__
((l1,l3),l2); 
(#H1,(#H1,(l1,l3))); (l2)#H1; 
(#H1,(#H1,((#H2,l1),#H2))); (l2)#H1; (l3)#H2; 
(#H1,(#H2,(#H1,(#H2,l1)))); (l2)#H1; (l3)#H2; 
(#H1,(#H1,(#H2,l1))); ((#H2,l2))#H1; (l3)#H2; 
(#H1,(#H1,((#H2,l3),#H2))); (l2)#H1; (l1)#H2; 
(#H1,(#H2,(#H1,(l3,#H2)))); (l2)#H1; (l1)#H2; 
(#H1,(#H1,(l3,#H2))); ((#H2,l2))#H1; (l1)#H2; 
(#H1,(l1,(l3,#H1))); (l2)#H1; 
((((l3,#H1),#H2),#H2),#H1); (l2)#H1; (l1)#H2; 
(#H1,((#H1,l3),#H2)); ((l2,#H2))#H1; (l1)#H2; 
(#H1,(#H2,(#H2,l1))); (l2)#H1; ((#H1,l3))#H2; 
(#H1,(l3,(l1,#H1))); (l2)#H1; 
((((l1,#H1),#H2),#H2),#H1); (l2)#H1; (l3)#H2; 
(#H1,((#H1,l1),#H2)); ((l2,#H2))#H1; (l3)#H2; 
(#H1,(#H2,(#H2,l3))); (l2)#H1; ((#H1,l1))#H2; 
(#H1,(l2,#H1)); ((l1,l3))#H1; 
((#H1,(l2,#H2)),#H1); ((#H2,l1))#H1; (l3)#H2; 
(#H1,(#H1,l2)); ((#H2,(#H2,l1)))#H1; (l3)#H2; 
(#H1,(#H2,(#H1,l2))); ((#H2,l1))#H1; (l3)#H2; 
((#H1,(l2,#H2)),#H1); ((#H2,l3))#H1; (l1)#H2; 
(#H1,(#H1,l2)); ((#H2,(#H2,l3)))#H1; (l1)#H2; 
(#H1,(#H2,(#H1,l2))); ((l3,#H2))#H1; (l1)#H2; 
((l2,#H1),(l1,#H1)); (l3)#H1; 
(l2,(#H1,(l1,#H1))); (l3)#H1; 
((l2,#H1),(l3,#H1)); (l1)#H1; 
(l2,(#H1,(l3,#H1))); (l1)#H1; 
(l1,(l3,l2)); 
(l1,(#H1,(#H1,l3))); (l2)#H1; 
((#H1,((#H1,l3),#H2)),#H2); (l2)#H1; (l1)#H2; 
((#H1,(#H1,(#H2,l3))),#H2); (l2)#H1; (l1)#H2; 
(#H2,(#H2,(#H1,(#H1,l3)))); (l2)#H1; (l1)#H2; 
((#H1,(l3,#H1)),#H2); ((#H2,l2))#H1; (l1)#H2; 
(#H2,(#H2,l1)); (l2)#H1; (((l3,#H1),#H1))#H2; 
((l1,#H1),(l3,#H1)); (l2)#H1; 
((#H1,(l1,#H2)),#H2); (l2)#H1; ((#H1,l3))#H2; 
(#H2,(#H2,(#H1,l1))); (l2)#H1; ((#H1,l3))#H2; 
(#H2,(#H2,(#H1,l3))); (l2)#H1; ((#H1,l1))#H2; 
(#H2,(#H1,(l3,#H2))); (l2)#H1; ((#H1,l1))#H2; 
(#H1,(l1,#H1)); ((l3,l2))#H1; 
(#H1,(l1,#H1)); ((#H2,(#H2,l2)))#H1; (l3)#H2; 
(l1,(#H1,(l2,#H1))); (l3)#H1; 
((#H1,(#H1,(#H2,l2))),#H2); (l3)#H1; (l1)#H2; 
(#H2,(((l2,#H1),#H1),#H2)); (l3)#H1; (l1)#H2; 
(#H2,(((l2,#H1),#H2),#H1)); (l3)#H1; (l1)#H2; 
((#H1,(#H1,l2)),#H2); ((l3,#H2))#H1; (l1)#H2; 
(#H1,(l3,(l2,#H1))); (l1)#H1; 
(#H1,(#H1,(l2,l3))); (l1)#H1; 
(#H1,((l3,#H1),l2)); (l1)#H1; 
((l1,l2),l3); 
(#H1,(#H1,(l1,l2))); (l3)#H1; 
(#H1,(#H1,((#H2,l1),#H2))); (l3)#H1; (l2)#H2; 
(#H1,(#H2,(#H1,(#H2,l1)))); (l3)#H1; (l2)#H2; 
(#H1,(#H1,((#H2,l2),#H2))); (l3)#H1; (l1)#H2; 
(#H1,(#H2,(#H1,(l2,#H2)))); (l3)#H1; (l1)#H2; 
(#H1,(l1,(l2,#H1))); (l3)#H1; 
((((l2,#H1),#H2),#H2),#H1); (l3)#H1; (l1)#H2; 
(#H1,(#H2,(#H2,l1))); (l3)#H1; ((#H1,l2))#H2; 
(#H1,(l2,(l1,#H1))); (l3)#H1; 
((((l1,#H1),#H2),#H2),#H1); (l3)#H1; (l2)#H2; 
(#H1,(#H2,(#H2,l2))); (l3)#H1; ((#H1,l1))#H2; 
(#H1,(l3,#H1)); ((l1,l2))#H1; 
(#H1,(#H1,l3)); ((#H2,(#H2,l1)))#H1; (l2)#H2; 
(#H1,(#H1,l3)); ((#H2,(#H2,l2)))#H1; (l1)#H2; 
(l3,(#H1,(l1,#H1))); (l2)#H1; 
(l3,(#H1,(l2,#H1))); (l1)#H1; 
BioPerl-1.007002/t/Tree/PhyloNetwork/GraphViz.t000444000766000024        71313155576321 21223 0ustar00cjfieldsstaff000000000000# $Id$
use strict;

BEGIN {
  use lib '.';
  use Bio::Root::Test;

  test_begin(-tests => 3,
	     -requires_modules => [qw(Bio::PhyloNetwork
				      GraphViz)]);

  use_ok('Bio::PhyloNetwork::GraphViz');
}

my $net=Bio::PhyloNetwork->new(-eNewick=>'((H1,(H1,(H2,l))),H2)t0; (some long label)H1; ("quoted label")H2;');

my $gv=Bio::PhyloNetwork::GraphViz->new(-net=>$net,-short_labels=>1);
isa_ok($gv,'Bio::PhyloNetwork::GraphViz');
isa_ok($gv,'GraphViz');
BioPerl-1.007002/t/Tree/PhyloNetwork/MuVector.t000444000766000024       146013155576321 21255 0ustar00cjfieldsstaff000000000000# $Id$
use strict;

BEGIN {
  use lib '.';
  use Bio::Root::Test;

  test_begin(-tests => 8);

  use_ok('Bio::PhyloNetwork::muVector');
}

my $vec1=Bio::PhyloNetwork::muVector->new(4);
my $vec2=Bio::PhyloNetwork::muVector->new([1,2,3,4]);
isa_ok($vec1,'Bio::PhyloNetwork::muVector');
isa_ok($vec1,'Bio::PhyloNetwork::muVector');

my $vec3=-1*$vec2;
my $vec4=$vec3+$vec2;

is($vec4 cmp $vec1,0,'arithmetic');
ok($vec2->display() eq "(1 2 3 4)",'display');
ok($vec2->is_positive(),'is_positive');

my $vec5=Bio::PhyloNetwork::muVector->new([2,3,5,0,77]);
my $vec6=Bio::PhyloNetwork::muVector->new([2,3,4,5,-7]);

ok($vec5->geq_poset($vec6) == 0,'geq_poset');

my $vec7=Bio::PhyloNetwork::muVector->new([2,3,5,0,77]);
my $vec8=Bio::PhyloNetwork::muVector->new([2,3,4,-1,-7]);

ok($vec7->geq_poset($vec8),'geq_poset');

BioPerl-1.007002/t/Tree/PhyloNetwork/PhyloNetwork.t000444000766000024       530113155576321 22154 0ustar00cjfieldsstaff000000000000# $Id$
# -*-Perl-*-
use strict;

BEGIN {
  use lib '.';
  use Bio::Root::Test;

  test_begin(-tests => 30,
	     -requires_modules => [qw(Graph::Directed
				      Bio::Tree::Node
				      Bio::TreeIO
				      IO::String
				      Array::Compare
				      Algorithm::Munkres
				      Bio::PhyloNetwork::muVector)]);

  use_ok('Bio::PhyloNetwork');
}

my $net = Bio::PhyloNetwork->new(-eNewick=>'((#H1,(#H2,l2)T),#H2)r; ((#H3,l1))#H1; ((#H3,(l3,#H1)))#H2; (l4)#H3;');

isa_ok($net, 'Bio::PhyloNetwork');

ok($net->is_leaf('l1'),'is_leaf');
ok($net->is_tree_node('T'),'is_tree_node');
ok($net->is_hybrid_node('#1'),'is_hybrid_node');
ok($net->is_root('r'),'is_root');
ok($net->is_tree_child(),'is_tree_child');

is(scalar $net->nodes(),13,'nodes');
is(scalar $net->leaves(),4,'leaves');
is(scalar $net->internal_nodes(),9,'internal_nodes');
is(scalar $net->edges(),15,'edges');
is(scalar $net->tree_edges(),9,'tree_edges');
is(scalar $net->hybrid_edges(),6,'hybrid_edges');

my %mudata = $net->mudata();
ok(($mudata{'r'} cmp 
    Bio::PhyloNetwork::muVector->new([3,1,2,5]))==0,'mudata');

my $net2 = Bio::PhyloNetwork->new(-mudata=>\%mudata,
				  -leaves=>[qw(l1 l2 l3 l4)]);
is($net->mu_distance($net2),0,'build from mudata');

my %heights=$net->heights;
is($heights{'r'},9,'heights');

my $net3 = Bio::PhyloNetwork->new(-eNewick=>'r=(l2,((l1,(#H1,l4)),#H1)); #H1=(l3);');
is($net->mu_distance($net3),12,'mu_distance');

my $net4 = Bio::PhyloNetwork->new(-eNewick=>'((1,#H1)t1,(#H1,3))r; (2)#H1');
ok($net4->is_time_consistent(),'time_consistent');

my %time=$net4->temporal_representation();
ok($time{'t1'} == $time{'#1'},'temporal_representation');

my $net5 = Bio::PhyloNetwork->new(-eNewick=>'((1,#H1)x,(#H1,3)); (2)#H1;');
my %tripartitions=$net5->tripartitions();
ok($tripartitions{'x'}  eq 'ABC','tripartitions');
ok($tripartitions{'#1'} eq 'CAC','tripartitions');

my $net6=Bio::PhyloNetwork->new(-eNewick=>'(1,(2,3))');
ok(abs($net5->tripartition_error($net6)-0.2678)<0.0001,'tripartition_error');

my ($w,$alignR,$weightsR)=$net->optimal_alignment($net3);
my %align=%{$alignR};
my %weights=%{$weightsR};

is($w,8,'weight (manhattan)');
ok($align{'T'} eq 'r','optimal_alignment (manhattan)');
my ($w2,$alignR2,$weightR2)= $net->optimal_alignment($net3,
						     -metric=>'Hamming');
is($w2,6.125,'weight (hamming)');

my %align2=%$alignR2;
ok($align2{'T'} eq 'r','optimal_alignment (hamming)');
my $enw=$net->eNewick();
my $enwf=$net->eNewick_full();


$net5=Bio::PhyloNetwork->new(-eNewick=>$enw);
ok($net->mu_distance($net5) == 0,'eNewick');

$net6=Bio::PhyloNetwork->new(-eNewick=>$enwf);
ok($net->mu_distance($net6) == 0,'eNewick_full');

my @trees=$net->explode();
is(scalar @trees,8,'explode');
isa_ok($trees[0],'Bio::Tree::Tree');
BioPerl-1.007002/t/Tree/PhyloNetwork/RandomFactory.t000444000766000024       666213155576321 22272 0ustar00cjfieldsstaff000000000000# $Id$
# -*-Perl-*-
use strict;

BEGIN {
  use lib '.';
  use Bio::Root::Test;

  test_begin(-tests => 70,
	     -requires_modules => [qw(Bio::PhyloNetwork
				      Bio::Tree::RandomFactory)]);

  use_ok('Bio::PhyloNetwork::RandomFactory');
}

my $factory=Bio::PhyloNetwork::RandomFactory->new(-numleaves=>3,-norepeat=>1);
isa_ok($factory,'Bio::PhyloNetwork::RandomFactory');

my @nets;
for (my $i=0; $i<66; $i++) {
  my $net=$factory->next_network();
  push @nets,$net;
}

is(scalar @nets,66,'random factory');

my @netsbk;

foreach my $enw () {
  my $net=Bio::PhyloNetwork->new(-eNewick=>$enw);
  push @netsbk,$net;
}
is(scalar @netsbk,66);

foreach my $net (@nets) {
  my $found=0;
  foreach my $netbk (@netsbk) {
    if ($net->mu_distance($netbk)==0) {
      $found=1;
      last;
    }
  }
  ok($found,'found');
}

__DATA__
((l1,l3),l2); 
(#H1,(#H1,(l1,l3))); (l2)#H1; 
(#H1,(#H1,((#H2,l1),#H2))); (l2)#H1; (l3)#H2; 
(#H1,(#H2,(#H1,(#H2,l1)))); (l2)#H1; (l3)#H2; 
(#H1,(#H1,(#H2,l1))); ((#H2,l2))#H1; (l3)#H2; 
(#H1,(#H1,((#H2,l3),#H2))); (l2)#H1; (l1)#H2; 
(#H1,(#H2,(#H1,(l3,#H2)))); (l2)#H1; (l1)#H2; 
(#H1,(#H1,(l3,#H2))); ((#H2,l2))#H1; (l1)#H2; 
(#H1,(l1,(l3,#H1))); (l2)#H1; 
((((l3,#H1),#H2),#H2),#H1); (l2)#H1; (l1)#H2; 
(#H1,((#H1,l3),#H2)); ((l2,#H2))#H1; (l1)#H2; 
(#H1,(#H2,(#H2,l1))); (l2)#H1; ((#H1,l3))#H2; 
(#H1,(l3,(l1,#H1))); (l2)#H1; 
((((l1,#H1),#H2),#H2),#H1); (l2)#H1; (l3)#H2; 
(#H1,((#H1,l1),#H2)); ((l2,#H2))#H1; (l3)#H2; 
(#H1,(#H2,(#H2,l3))); (l2)#H1; ((#H1,l1))#H2; 
(#H1,(l2,#H1)); ((l1,l3))#H1; 
((#H1,(l2,#H2)),#H1); ((#H2,l1))#H1; (l3)#H2; 
(#H1,(#H1,l2)); ((#H2,(#H2,l1)))#H1; (l3)#H2; 
(#H1,(#H2,(#H1,l2))); ((#H2,l1))#H1; (l3)#H2; 
((#H1,(l2,#H2)),#H1); ((#H2,l3))#H1; (l1)#H2; 
(#H1,(#H1,l2)); ((#H2,(#H2,l3)))#H1; (l1)#H2; 
(#H1,(#H2,(#H1,l2))); ((l3,#H2))#H1; (l1)#H2; 
((l2,#H1),(l1,#H1)); (l3)#H1; 
(l2,(#H1,(l1,#H1))); (l3)#H1; 
((l2,#H1),(l3,#H1)); (l1)#H1; 
(l2,(#H1,(l3,#H1))); (l1)#H1; 
(l1,(l3,l2)); 
(l1,(#H1,(#H1,l3))); (l2)#H1; 
((#H1,((#H1,l3),#H2)),#H2); (l2)#H1; (l1)#H2; 
((#H1,(#H1,(#H2,l3))),#H2); (l2)#H1; (l1)#H2; 
(#H2,(#H2,(#H1,(#H1,l3)))); (l2)#H1; (l1)#H2; 
((#H1,(l3,#H1)),#H2); ((#H2,l2))#H1; (l1)#H2; 
(#H2,(#H2,l1)); (l2)#H1; (((l3,#H1),#H1))#H2; 
((l1,#H1),(l3,#H1)); (l2)#H1; 
((#H1,(l1,#H2)),#H2); (l2)#H1; ((#H1,l3))#H2; 
(#H2,(#H2,(#H1,l1))); (l2)#H1; ((#H1,l3))#H2; 
(#H2,(#H2,(#H1,l3))); (l2)#H1; ((#H1,l1))#H2; 
(#H2,(#H1,(l3,#H2))); (l2)#H1; ((#H1,l1))#H2; 
(#H1,(l1,#H1)); ((l3,l2))#H1; 
(#H1,(l1,#H1)); ((#H2,(#H2,l2)))#H1; (l3)#H2; 
(l1,(#H1,(l2,#H1))); (l3)#H1; 
((#H1,(#H1,(#H2,l2))),#H2); (l3)#H1; (l1)#H2; 
(#H2,(((l2,#H1),#H1),#H2)); (l3)#H1; (l1)#H2; 
(#H2,(((l2,#H1),#H2),#H1)); (l3)#H1; (l1)#H2; 
((#H1,(#H1,l2)),#H2); ((l3,#H2))#H1; (l1)#H2; 
(#H1,(l3,(l2,#H1))); (l1)#H1; 
(#H1,(#H1,(l2,l3))); (l1)#H1; 
(#H1,((l3,#H1),l2)); (l1)#H1; 
((l1,l2),l3); 
(#H1,(#H1,(l1,l2))); (l3)#H1; 
(#H1,(#H1,((#H2,l1),#H2))); (l3)#H1; (l2)#H2; 
(#H1,(#H2,(#H1,(#H2,l1)))); (l3)#H1; (l2)#H2; 
(#H1,(#H1,((#H2,l2),#H2))); (l3)#H1; (l1)#H2; 
(#H1,(#H2,(#H1,(l2,#H2)))); (l3)#H1; (l1)#H2; 
(#H1,(l1,(l2,#H1))); (l3)#H1; 
((((l2,#H1),#H2),#H2),#H1); (l3)#H1; (l1)#H2; 
(#H1,(#H2,(#H2,l1))); (l3)#H1; ((#H1,l2))#H2; 
(#H1,(l2,(l1,#H1))); (l3)#H1; 
((((l1,#H1),#H2),#H2),#H1); (l3)#H1; (l2)#H2; 
(#H1,(#H2,(#H2,l2))); (l3)#H1; ((#H1,l1))#H2; 
(#H1,(l3,#H1)); ((l1,l2))#H1; 
(#H1,(#H1,l3)); ((#H2,(#H2,l1)))#H1; (l2)#H2; 
(#H1,(#H1,l3)); ((#H2,(#H2,l2)))#H1; (l1)#H2; 
(l3,(#H1,(l1,#H1))); (l2)#H1; 
(l3,(#H1,(l2,#H1))); (l1)#H1; 
BioPerl-1.007002/t/Tree/PhyloNetwork/TreeFactory.t000444000766000024       207513155576321 21743 0ustar00cjfieldsstaff000000000000# $Id$
# -*-Perl-*-
use strict;

BEGIN {
  use lib '.';
  use Bio::Root::Test;

  test_begin(-tests => 19,
	     -requires_modules => [qw(Bio::PhyloNetwork)]);

  use_ok('Bio::PhyloNetwork::TreeFactory');
}

my $factory=Bio::PhyloNetwork::TreeFactory->new(-numleaves=>4);
isa_ok($factory,'Bio::PhyloNetwork::TreeFactory');

my @nets;

while (my $net=$factory->next_network()) {
  push @nets,$net;
}

is(scalar @nets,15,'tree factory');

my @netsbk;

foreach my $enw () {
  my $net=Bio::PhyloNetwork->new(-eNewick=>$enw);
  push @netsbk,$net;
}
is(scalar @netsbk,15,'seen all the data lines');

foreach my $net (@nets) {
  my $found=0;
  foreach my $netbk (@netsbk) {
    if ($net->mu_distance($netbk)==0) {
      $found=1;
      last;
    }
  }
  ok($found,'found');
}

__DATA__
(l2,((l1,l4),l3)); 
((l1,l3),(l2,l4)); 
((l1,(l3,l4)),l2); 
(l4,(l2,(l1,l3))); 
((l4,(l3,l1)),l2); 
((l2,l3),(l1,l4)); 
(l1,((l2,l4),l3)); 
(l1,((l3,l4),l2)); 
(l4,(l1,(l2,l3))); 
(l1,((l3,l2),l4)); 
(l3,((l1,l4),l2)); 
((l1,(l2,l4)),l3); 
((l1,l2),(l3,l4)); 
((l4,(l2,l1)),l3); 
(l4,(l3,(l1,l2))); 
BioPerl-1.007002/t/Tree/TreeIO000755000766000024          013155576321 15650 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Tree/TreeIO/lintree.t000444000766000024       352313155576321 17637 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: TreeIO.t 14580 2008-03-01 17:01:30Z cjfields $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 24);
    use_ok('Bio::TreeIO');
}

my $verbose = test_debug();

# try lintree parsing
my $treeio = Bio::TreeIO->new(-format => 'lintree',
			      -file   => test_input_file('crab.njb'));

my ($tree, @leaves, $node);
while( $tree = $treeio->next_tree ) {

    isa_ok($tree, 'Bio::Tree::TreeI');

    my @nodes = $tree->get_nodes;

    @leaves = $tree->get_leaf_nodes;
    is(@leaves, 13);
#\maj    is(@nodes, 25);
    is(@nodes, 24);
    ($node) = $tree->find_node(-id => '18');
    ok($node);
    is($node->id, '18');
    is($node->branch_length, '0.030579');
    is($node->bootstrap, 998);
}

$treeio = Bio::TreeIO->new(-format => 'lintree',
			   -file   => test_input_file('crab.nj'));

$tree = $treeio->next_tree;

isa_ok($tree, 'Bio::Tree::TreeI');

my @nodes = $tree->get_nodes;
@leaves = $tree->get_leaf_nodes;
is(@leaves, 13);
#/maj is(@nodes, 25);
is(@nodes, 24); #/maj
($node) = $tree->find_node('18');
is($node->id, '18');
is($node->branch_length, '0.028117');

($node) = $tree->find_node(-id => 'C-vittat');
is($node->id, 'C-vittat');
is($node->branch_length, '0.087619');
is($node->ancestor->id, '14');

$treeio = Bio::TreeIO->new(-format => 'lintree',
			  -file   => test_input_file('crab.dat.cn'));

$tree = $treeio->next_tree;

isa_ok($tree, 'Bio::Tree::TreeI');

@nodes = $tree->get_nodes;
@leaves = $tree->get_leaf_nodes;
is(@leaves, 13, "Leaf nodes");

#/maj is(@nodes, 25, "All nodes");
is(@nodes, 24, "All nodes"); #/maj
($node) = $tree->find_node('18');
is($node->id, '18');

is($node->branch_length, '0.029044');

($node) = $tree->find_node(-id => 'C-vittat');
is($node->id, 'C-vittat');
is($node->branch_length, '0.097855');
is($node->ancestor->id, '14');
BioPerl-1.007002/t/Tree/TreeIO/newick.t000444000766000024      1441213155576321 17474 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: TreeIO.t 14580 2008-03-01 17:01:30Z cjfields $

use strict;

BEGIN {
  use lib '.';
  use Bio::Root::Test;
    
  test_begin(-tests => 51);

  use_ok('Bio::TreeIO');
}

my $verbose = test_debug();

ok my $treeio = Bio::TreeIO->new(-verbose => $verbose,
                                 -format => 'newick',
                                 -file => test_input_file('cysprot1b.newick'));

my $tree = $treeio->next_tree;
isa_ok($tree, 'Bio::Tree::TreeI');

my @nodes = $tree->get_nodes;
is(@nodes, 6);
my ($rat) = $tree->find_node('CATL_RAT');
ok($rat);
is($rat->branch_length, '0.12788');
# move the id to the bootstap
is($rat->ancestor->bootstrap($rat->ancestor->id), '95');
$rat->ancestor->id('');
# maybe this can be auto-detected, but then can't distinguish
# between internal node labels and bootstraps...
is($rat->ancestor->bootstrap, '95');
is($rat->ancestor->branch_length, '0.18794');
is($rat->ancestor->id, '');

if ($verbose) {
	foreach my $node ( $tree->get_root_node()->each_Descendent() ) {
		print "node: ", $node->to_string(), "\n";
		my @ch = $node->each_Descendent();
		if( @ch ) {
			print "\tchildren are: \n";
			foreach my $node ( $node->each_Descendent() ) {
				print "\t\t ", $node->to_string(), "\n";
			}
		}
	}
}

my $FILE1 = test_output_file();
$treeio = Bio::TreeIO->new(-verbose => $verbose,
			  -format => 'newick',
			  -file   => ">$FILE1");
$treeio->write_tree($tree);
undef $treeio;
ok( -s $FILE1 );
$treeio = Bio::TreeIO->new(-verbose => $verbose,
			  -format => 'newick',
			  -file   => test_input_file('LOAD_Ccd1.dnd'));
ok($treeio);
$tree = $treeio->next_tree;

isa_ok($tree,'Bio::Tree::TreeI');

@nodes = $tree->get_nodes;
is(@nodes, 52);

if( $verbose ) { 
	foreach my $node ( @nodes ) {
		print "node: ", $node->to_string(), "\n";
		my @ch = $node->each_Descendent();
		if( @ch ) {
			print "\tchildren are: \n";
			foreach my $node ( $node->each_Descendent() ) {
				print "\t\t ", $node->to_string(), "\n";
			}
		}
	}
}

is($tree->total_branch_length, 7.12148);
my $FILE2 = test_output_file();
$treeio = Bio::TreeIO->new(-verbose => $verbose,
			  -format => 'newick', 
			  -file   => ">$FILE2");
$treeio->write_tree($tree);
undef $treeio;
ok(-s $FILE2);
$treeio = Bio::TreeIO->new(-verbose => $verbose,
			  -format  => 'newick',
			  -file    => test_input_file('hs_fugu.newick'));
$tree = $treeio->next_tree();
@nodes = $tree->get_nodes();
is(@nodes, 5);
# no relable order for the bottom nodes because they have no branchlen
my @vals = qw(SINFRUP0000006110);
my $saw = 0;
foreach my $node ( $tree->get_root_node()->each_Descendent() ) {
	foreach my $v ( @vals ) {
	   if( defined $node->id && 
	       $node->id eq $v ){ $saw = 1; last; }
	}
	last if $saw;
}
is($saw, 1, "Saw $vals[0] as expected");
if( $verbose ) {
	foreach my $node ( @nodes ) {
		print "\t", $node->id, "\n" if $node->id;
	}
}

# parse trees with scores

$treeio = Bio::TreeIO->new(-format => 'newick',
			   -file   => test_input_file('puzzle.tre'));
$tree = $treeio->next_tree;
ok($tree);
is($tree->score, '-2673.059726');


# no semi-colon

$treeio = Bio::TreeIO->new(-format => 'newick', 
			   -file=> test_input_file('semicolon.newick'));
$tree = $treeio->next_tree;
ok($tree);
is($tree->get_nodes, 15);

$treeio = Bio::TreeIO->new(-format => 'newick', 
			   -file=> test_input_file('no_semicolon.newick'));
$tree = $treeio->next_tree;
ok($tree);
is($tree->get_nodes, 15);

# initial AMPHORA2 tests
$treeio = Bio::TreeIO->new(-format => 'newick',
			   -file=> test_input_file('amphora.newick'));
$tree = $treeio->next_tree;
ok($tree);
is($tree->get_nodes, 5);

test_roundtrip('((a,b),c);','Round trip: simple newick');
test_roundtrip('(a:1,b:2,c:3,d:4)TEST:1.2345;','Round trip: Root node branch length');
test_roundtrip('(a:1,b:2,c:3,d:4):1.2345;','Round trip: Root node branch length');
test_roundtrip('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;','Round trip: from Wikipedia');
test_roundtrip('(a:1,b:2):0.0;','Branch length on root');
test_roundtrip('(a:1,b:2):0.001;','Tiny branch length on root');
test_roundtrip('(a:0,b:00):0.0;','Zero branch lenghts');

# From Wikipedia:
test_roundtrip('(,,(,));','wkp blank tree');
test_roundtrip('(A,B,(C,D));','wkp only leaves labeled');
test_roundtrip('(A,B,(C,D)E)F;','wkp all nodes labeled');
test_roundtrip('(:0.1,:0.2,(:0.3,:0.4):0.5);','wkp branch lengths, no labels');
test_roundtrip('(:0.1,:0.2,(:0.3,:0.4):0.5):0.0;','wkp branch lengths, including root');
test_roundtrip('(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);','wkp distances and leaf names');
test_roundtrip('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;','wkp distances and all names');
test_roundtrip('((B:0.2,(C:0.3,D:0.4)E:0.5)F:0.1)A;','wkp rooted on leaf node');

# From the PHYLIP site:
test_roundtrip('(B,(A,C,E),D);','phylip simple tree');
test_roundtrip('(,(,,),);','phylip no labels');
test_roundtrip('(B:6.0,(A:5.0,C:3.0,E:4.0):5.0,D:11.0);','phylip w/ branch lengths');
test_roundtrip('(B:6.0,(A:5.0,C:3.0,E:4.0)Ancestor1:5.0,D:11.0);','phylip w/ internal label');
test_roundtrip('((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700,seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201,weasel:18.87953):2.09460):3.87382,dog:25.46154);','phylip raccoon tree');
test_roundtrip('(Bovine:0.69395,(Gibbon:0.36079,(Orang:0.33636,(Gorilla:0.17147,(Chimp:0.19268,Human:0.11927):0.08386):0.06124):0.15057):0.54939,Mouse:1.21460):0.10;','phylip mammal tree');
test_roundtrip('(Bovine:0.69395,(Hylobates:0.36079,(Pongo:0.33636,(G._Gorilla:0.17147,(P._paniscus:0.19268,H._sapiens:0.11927):0.08386):0.06124):0.15057):0.54939,Rodent:1.21460);','phylip mammal tree w/ underbars');
test_roundtrip('A;','phylip single node');
test_roundtrip('((A,B),(C,D));','phylip_quartet');
test_roundtrip('(Alpha,Beta,Gamma,Delta,,Epsilon,,,);','phylip greek');

sub test_roundtrip {
  my $string = shift;
  my $desc = shift;

  my $in = Bio::TreeIO->new(-format => 'newick',
                            -string => $string,
                            -verbose => $verbose
                            );
  my $out = '';
  eval {
    my $t = $in->next_tree;
    $out = $t->as_text('newick');
  };
  return is($out,$string,$desc);
}

sub read_file {
  my $file = shift;
  open my $IN, '<', $file or die "Could not read file '$file': $!\n";
  my (@lines) = <$IN>;
  close $IN;

  @lines = map {$_ =~ s/\\n//g} @lines;
  return join("",@lines);
}
BioPerl-1.007002/t/Tree/TreeIO/nexml.t000444000766000024       567713155576321 17334 0ustar00cjfieldsstaff000000000000#-*-perl-*-
# $Id$

use strict;
use Bio::Root::Test;
test_begin( -tests            => 46,
           # TODO: seeing perl version-dependent fails on perl 5.10 with
           # Travis-CI; skip but needs debugging
            -requires_modules => [qw(5.012 Bio::Phylo XML::Twig)]);

use_ok( 'Bio::Tree::Tree' );
use_ok( 'Bio::TreeIO' );
use_ok('Bio::TreeIO::nexml'); # checks that your module is there and loads ok

diag("WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support");

#Read in Data
ok( my $TreeStream = Bio::TreeIO->new(-file   => test_input_file('nexml','trees.nexml.xml'),
                                      -format => 'nexml') );

#Checking first tree object
ok( my $tree_obj = $TreeStream->next_tree(), 'tree obj read' );
isa_ok($tree_obj, 'Bio::Tree::Tree');
is( $tree_obj->get_root_node()->id(), 'n1', "root node");
my @nodes = $tree_obj->get_nodes();
is( @nodes, 9, "number of nodes");
ok ( my $node7 = $tree_obj->find_node('n7') );
is( $node7->branch_length, 0.3247, "branch length");
is( $node7->ancestor->id, 'n3', 'anc id');
is( $node7->ancestor->branch_length, '0.34534', 'anc bl');

#Check leaf nodes and taxa
my %expected_leaves = ('n8' => 'bird',
                       'n9' => 'worm',
                       'n5' => 'dog',
                       'n6' => 'mouse',
                       'n2' => 'human'
);
ok( my @leaves = $tree_obj->get_leaf_nodes() );
is( @leaves, 5, "number of leaf nodes");
foreach my $leaf (@leaves) {
    my $leafID = $leaf->id();
    ok( exists $expected_leaves{$leaf->id()}, "$leafID exists" );
    is( $leaf->get_tag_values('taxon'), $expected_leaves{$leaf->id()}, "$leafID taxon");
}

#Write data
diag('Begin tests for writing tree files');
my $outdata = test_output_file();
ok( my $outTreeStream = Bio::TreeIO->new(-file   => ">$outdata",
                                         -format => 'nexml'),
   'out stream');
ok( $outTreeStream->write_tree($tree_obj), 'write tree');
$outTreeStream->close;


#Read in the out file to test roundtrip
my $inTreeStream = Bio::TreeIO->new(-file   => $outdata,
                                    -format => 'nexml');

#Checking first tree object
ok($tree_obj = $inTreeStream->next_tree(), 'read tree obj (rt)' );
isa_ok($tree_obj, 'Bio::Tree::Tree');
is( $tree_obj->get_root_node()->id(), 'n1', "root node (rt)");
my @outnodes = $tree_obj->get_nodes();
is( @outnodes, 9, "number of nodes (rt)");
ok ( $node7 = $tree_obj->find_node('n7') );
is( $node7->branch_length, 0.3247, "branch length (rt)");
is( $node7->ancestor->id, 'n3','anc id (rt)');
is( $node7->ancestor->branch_length, '0.34534', 'anc bl (rt)');

#Check leaf nodes and taxa
ok( my @outleaves = $tree_obj->get_leaf_nodes() );
is( @outleaves, 5, "number of leaf nodes (rt)");
foreach my $leaf (@outleaves) {
    my $leafID = $leaf->id();
    ok( exists $expected_leaves{$leaf->id()}, "$leafID exists (rt)"  );
    is( $leaf->get_tag_values('taxon'), $expected_leaves{$leaf->id()}, "$leafID taxon (rt)");
}
$inTreeStream->close;
BioPerl-1.007002/t/Tree/TreeIO/nexus.t000444000766000024       443713155576321 17344 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: TreeIO.t 14580 2008-03-01 17:01:30Z cjfields $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 24);
    use_ok('Bio::TreeIO');
}

my $verbose = test_debug();


SKIP: {
    test_skip(-tests => 8, -requires_module => 'IO::String');
	
    # test nexus tree parsing
    my $treeio = Bio::TreeIO->new(-format => 'nexus',
				  -verbose => $verbose,
				  -file   => test_input_file('urease.tre.nexus'));
    
    my $tree = $treeio->next_tree;
    ok($tree);
    is($tree->id, 'PAUP_1');
    is($tree->get_leaf_nodes, 6);
    my ($node) = $tree->find_node(-id => 'Spombe');
    is($node->branch_length,0.221404);
    
    # test nexus MrBayes tree parsing
    $treeio = Bio::TreeIO->new(-format => 'nexus',
			       -file   => test_input_file('adh.mb_tree.nexus'));
    
    $tree = $treeio->next_tree;
	my $ct = 1; 
    ok($tree);
    is($tree->id, 'rep.1');
    is($tree->get_leaf_nodes, 54);
    ($node) = $tree->find_node(-id => 'd.madeirensis');
    is($node->branch_length,0.039223);
	while ($tree = $treeio->next_tree) {
		$ct++;
	}
	is($ct,13,'bug 2356');
}


# bug #1854
# process no-newlined tree
my $treeio = Bio::TreeIO->new(-format => 'nexus',
			      -verbose => $verbose,
			      -file   => test_input_file('tree_nonewline.nexus'));

my $tree = $treeio->next_tree;
ok($tree);
ok($tree->find_node('TRXHomo'));

# bug #2205
# process trees with node IDs containing spaces
$treeio = Bio::TreeIO->new(-format => 'nexus',
			   -verbose => $verbose,
			   -file   => test_input_file('spaces.nex'));

$tree = $treeio->next_tree;

my @nodeids = ("'Allium drummondii'", "'Allium cernuum'",'A.cyaneum');

ok($tree);
for my $node ($tree->get_leaf_nodes) {
	is($node->id, shift @nodeids);		
}

# bug #2221
# process tree with names containing quoted commas

$tree = $treeio->next_tree;

@nodeids = ("'Allium drummondii, USA'", "'Allium drummondii, Russia'",'A.cyaneum');

ok($tree);
for my $node ($tree->get_leaf_nodes) {
	is($node->id, shift @nodeids);		
}

# bug #2221
# process tree with names containing quoted commas on one line

$tree = $treeio->next_tree;

@nodeids = ("'Allium drummondii, Russia'", "'Allium drummondii, USA'",'A.cyaneum');

ok($tree);
for my $node ($tree->get_leaf_nodes) {
	is($node->id, shift @nodeids);		
}
BioPerl-1.007002/t/Tree/TreeIO/nhx.t000444000766000024       743213155576321 16775 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: TreeIO.t 14580 2008-03-01 17:01:30Z cjfields $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    use File::Temp qw(tempfile);
    
    test_begin(-tests => 19);
    use_ok('Bio::TreeIO');
}

my $verbose = 0; #test_debug();
my $nl = qr/\n/;
my $cr = qr/\r/;

my $treeio = Bio::TreeIO->new(
  -format => 'nhx',
  -verbose => $verbose,
  -file   => test_input_file('test.nhx'),
  );
my $tree;
ok($treeio);
$tree = $treeio->next_tree;
isa_ok($tree, 'Bio::Tree::TreeI');

my @nodes = $tree->get_nodes;
is(@nodes, 12, "Total Nodes");
#print STDERR "TREE: ".$tree->as_text('nhx')."\n";

my $adhy = $tree->find_node('ADHY');
is($adhy->branch_length, 0.1);
is(($adhy->get_tag_values('S'))[0], 'nematode');
is(($adhy->get_tag_values('E'))[0], '1.1.1.1');

test_roundtrip('((a,b),c);','simple newick');
test_roundtrip('((x:0.05,y:0.06),a:0.1[&&NHX:G=dummy]);','bug 1471 test');
test_roundtrip('((x:0.05[&&NHX:label=x],y:0.06)[&&NHX:label=int_node],a:0.1[&&NHX:label=a]);','different combinations of label, NHX, and branch length');

test_roundtrip('(a:1,b:2,c:3,d:4)TEST:1.2345;','doot node branch length');
test_roundtrip('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;','Example from Wikipedia');

test_roundtrip('(((ADH2:0.1[&&NHX:E=1.1.1.1:S=human],ADH1:0.11[&&NHX:E=1.1.1.1:S=human]):0.05[&&NHX:B=100:D=Y:E=1.1.1.1:S=Primates],ADHY:0.1[&&NHX:E=1.1.1.1:S=nematode],ADHX:0.12[&&NHX:E=1.1.1.1:S=insect]):0.1[&&NHX:D=N:E=1.1.1.1:S=Metazoa],(ADH4:0.09[&&NHX:E=1.1.1.1:S=yeast],ADH3:0.13[&&NHX:E=1.1.1.1:S=yeast],ADH2:0.12[&&NHX:E=1.1.1.1:S=yeast],ADH1:0.11[&&NHX:E=1.1.1.1:S=yeast]):0.1[&&NHX:S=Fungi])[&&NHX:D=N:E=1.1.1.1];','ADH NHX tree');
test_roundtrip('(gene1_Hu[&&NHX:S=Hu_Homo_sapiens],(gene2_Hu[&&NHX:S=Hu_Homo_sapiens],gene2_Mu[&&NHX:S=Mu_Mus_musculus]));','notung nhx example http://www.cs.cmu.edu/~aiton/split/Manual-2.6.master014.html');
test_roundtrip('(cow_gene1,(mouse_gene2,cow_gene2)[&&NHX:B=100]);','notung nhx bootstrap http://www.cs.cmu.edu/~aiton/split/Manual-2.6.master014.html');

# Read in some larger trees from data files...
test_roundtrip(read_file(test_input_file('nhx-bacteria.nhx')),'r-sig-phylo mailing list http://www.mail-archive.com/r-sig-phylo@r-project.org/msg00516.html');
test_roundtrip(read_file(test_input_file('ex1.nucl.nhx')),'treebest example nhx');
# Note: these files aren't reproduced exactly in their online form. We need to round-trip them once
# before including them in the test, because the ordering of annotation keys is not a well-defined
# part of the NHX format. Since nhx.pm sorts the keys before output, once they've been through
# one time, the ordering becomes stable.
test_roundtrip(read_file(test_input_file('wellcome_tol.nhx')),'Wellcome Trust ToL (from http://iphylo.blogspot.com/2009/02/thoughts-on-wellcome-interactive-tree.html)');

# Uncomment to run (takes a long time!!)
#test_roundtrip(read_file(test_input_file('tol-2010-02-18.nhx')),'Tolweb.org converted to NHX');

test_roundtrip(read_file(test_input_file('biorecipe.nhx')),'Biorecipes NHX file (http://www.biorecipes.com/Orthologues/StatusPage/pics/TreeEukaryota.nt)');

sub test_roundtrip {
  my $string = shift;
  my $desc = shift;

  my $in = Bio::TreeIO->new(-format => 'nhx',
                            -string => $string,
                            -verbose => $verbose
                            );
  
  my $t = $in->next_tree;
  my $out;
  if (defined $t) {
    $out = $t->as_text('nhx');
  }

  $desc = "Roundtrip: $desc";
  return is($out,$string,$desc);
}

sub read_file {
  my $file = shift;
  local $/=undef;
  my $string;
  open my $IN, '<', $file or die "Could not read file '$file': $!\n";
  binmode $IN;
  $string = <$IN>;
  close $IN;
  $string =~ s/$nl//g;
  $string =~ s/$cr//g; # For files with Windows line-endings
  #print STDERR "STR: $string\n";
  return $string;
}
BioPerl-1.007002/t/Tree/TreeIO/phyloxml.t000444000766000024      5053613155576321 20077 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl

use strict;
use warnings;

BEGIN {
	use lib '.';
	use Bio::Root::Test;
  
	test_begin(-tests => 98,
			   -requires_modules => [qw(XML::LibXML XML::LibXML::Reader)]);
	
	use_ok('Bio::TreeIO');
}

my $verbose = test_debug();

SKIP: {
  if (1000*$] < 5008) {
    skip("Reader interface only supported in Perl >= 5.8",96);
  } elsif (XML::LibXML::LIBXML_VERSION() <= 20620) {
    skip("Reader not supported for libxml2 <= 2.6.20",96);
  }
  use_ok('Bio::TreeIO::phyloxml');
  
  if ($verbose) {
	diag("libxml version: ", XML::LibXML::LIBXML_VERSION()); 
  }
  
  ok my $treeio = Bio::TreeIO->new(
			 -verbose => $verbose,
				   -format => 'phyloxml',
				   -file   => test_input_file('phyloxml_examples.xml'));
  
  # tree1: clade and attribute
  #   
  {
	if ($verbose > 0) {
	  diag("\ntree1: clade and attribute");
	}
	my $tree = $treeio->next_tree;
	isa_ok($tree, 'Bio::Tree::TreeI');
	is($tree->id, 'example from Prof. Joe Felsenstein\'s book "Inferring Phylogenies"');
	is($tree->get_tag_values('description'), 'phyloXML allows to use either a "branch_length" attribute or element to indicate branch lengths.');
	if ($verbose > 0) {
	  diag("tree id: ",$tree->id);
	  diag("tree description: ", $tree->get_tag_values('description'));
	}
	is($tree->get_tag_values('rooted'), 'true');
	my @nodes = $tree->get_nodes;
	is(@nodes, 5);
	my ($A) = $tree->find_node('A');
	ok($A);
	is($A->branch_length, '0.102');
	if ($verbose > 0) {
	  diag("node A: branch_length ", $A->branch_length);
	}
	is($A->ancestor->id, '');
	is($A->ancestor->branch_length, '0.06');
	my $leaves_string = $tree->simplify_to_leaves_string();
	if ($verbose > 0) {
	  diag($leaves_string);
	}
	is($leaves_string, '((A,B),C)');
  
  # write_tree
	if ($verbose > 0) {
	  diag("\ntest write_tree");
	}
	my $FILE1 = test_output_file();
	my $treeout = Bio::TreeIO->new(-verbose => $verbose,
		-format => 'phyloxml',
		-file   => ">$FILE1");
	$treeout->write_tree($tree);
	ok -s $FILE1;
	if ($verbose > 0) {
	  diag(`cat $FILE1`);
	}
  }
  
  # tree2: branch_length
  # 
  {
	if ($verbose > 0) {
	  diag("\ntree2: branch_length");
	}
	my $tree = $treeio->next_tree;
	isa_ok($tree, 'Bio::Tree::TreeI');
	if ($verbose > 0) {
	  diag("tree id: ",$tree->id);
	}
	my @nodes = $tree->get_nodes;
	is(@nodes, 5);
	my $A = $tree->find_node('A');
	ok($A);
	is($A->branch_length, '0.102');
	if ($verbose > 0) {
	  diag("node A: branch_length ", $A->branch_length);
	}
	is($A->ancestor->id, '');
	is($A->ancestor->branch_length, '0.06');
	my $leaves_string = $tree->simplify_to_leaves_string();
	if ($verbose > 0) {
	  diag($leaves_string);
	}
	is($leaves_string, '((A,B),C)');
  
  # write_tree
	if ($verbose > 0) {
	  diag("\ntest write_tree");
	}
	my $FILE1 = test_output_file();
	my $treeout = Bio::TreeIO->new(-verbose => $verbose,
		-format => 'phyloxml',
		-file   => ">$FILE1");
	$treeout->write_tree($tree);
	ok -s $FILE1;
	if ($verbose > 0) {
	  diag(`cat $FILE1`);
	}
  }
  
  # tree3: confidence (bootstrap)
  # 
  {
	if ($verbose > 0) {
	  diag("\ntree3: confidence (bootstrap)");
	}
	my $tree = $treeio->next_tree;
	isa_ok($tree, 'Bio::Tree::TreeI');
	if ($verbose > 0) {
	  diag("tree id: ",$tree->id);
	}
	my $AB = $tree->find_node('AB');
	ok($AB);
	is($AB->bootstrap, '89');
	if ($verbose > 0) {
	  diag("node AB: bootstrap ", $AB->bootstrap);
	}
	my $leaves_string = $tree->simplify_to_leaves_string();
	if ($verbose > 0) {
	  diag($leaves_string);
	}
	is($leaves_string, '((A,B),C)');
  
  # write_tree
	if ($verbose > 0) {
	  diag("\ntest write_tree");
	}
	my $FILE1 = test_output_file();
	my $treeout = Bio::TreeIO->new(-verbose => $verbose,
		-format => 'phyloxml',
		-file   => ">$FILE1");
	$treeout->write_tree($tree);
	ok -s $FILE1;
	if ($verbose > 0) {
	  diag(`cat $FILE1`);
	}
  }
  
  # tree4: species and sequence
  #    
  {
	if ($verbose > 0) {
	  diag("\ntree4: taxonomy and sequence");
	}
	my $tree = $treeio->next_tree;
	isa_ok($tree, 'Bio::Tree::TreeI');
	if ($verbose > 0) {
	  diag("tree id: ",$tree->id);
	}
	my $C = $tree->find_node('C');
	my ($ac) = $C->annotation->get_Annotations('taxonomy');
	isa_ok( $ac, 'Bio::Annotation::Collection');
	my ($ac2) = $ac->get_Annotations('scientific_name');
	isa_ok( $ac2, 'Bio::Annotation::Collection');
	my ($scientificname) = $ac2->get_Annotations('_text');
	is($scientificname->value, 'C. elegans');
	if ($verbose > 0) {
	  diag( "Node C Scientific Name: ",$scientificname->value);
	}
	my ($ac3) = $C->annotation->get_nested_Annotations(-keys=>['scientific_name'], -recursive=>1);
	isa_ok( $ac3, 'Bio::Annotation::Collection');
	($scientificname) = $ac2->get_Annotations('_text');
	is($scientificname->value, 'C. elegans');
	if ($verbose > 0) {
	  diag( "Node C Scientific Name: ",$scientificname->value);
	}
	my ($seq) = @{$C->sequence};
	isa_ok( $seq, 'Bio::SeqI');
	my ($seqac) = $seq->annotation;
	isa_ok( $seqac, 'Bio::Annotation::Collection');
	my ($descac) = $seqac->get_nested_Annotations(-keys=>['desc'], -recursive=>1);
	my ($desc) = $descac->get_Annotations('_text');
	is($desc->value, 'alcohol dehydrogenase');
	if ($verbose > 0) {
	  diag( "Node C Sequence description: ",$desc->value);
	}
	($descac) = $seqac->get_nested_Annotations(-keys=>['desc'], -recursive=>1);
	
  # write_tree
	if ($verbose > 0) {
	  diag("\ntest write_tree");
	}
	my $FILE1 = test_output_file();
	my $treeout = Bio::TreeIO->new(-verbose => $verbose,
		-format => 'phyloxml',
		-file   => ">$FILE1");
	$treeout->write_tree($tree);
	ok -s $FILE1;
	if ($verbose > 0) {
	  diag(`cat $FILE1`);
	}
  }
  
  # tree5: homolog relationship and sequence relationship
  #      
  #  
  {
	if ($verbose > 0) {
	  diag("\ntree5: events and relations");
	}
	my $tree = $treeio->next_tree;
	isa_ok($tree, 'Bio::Tree::TreeI');
	if ($verbose > 0) {
	  diag("tree id: ",$tree->id);
	}
	my $node = $tree->get_root_node;
	my ($speciationsac) = $node->annotation->get_nested_Annotations(-keys=>['speciations'], -recursive=>1);
	my ($speciationval) = $speciationsac->get_Annotations('_text');
	is($speciationval->value, '1');
	if ($verbose > 0) {
	  diag("root node speciation event: ", $speciationval->value);
	}
	my @children = ($node);
	for (@children) {
	  push @children, $_->each_Descendent();
	}
	my @leaves = ();
	for (@children) {
	  push @leaves, $_ if $_->is_Leaf;
	}
	my ($z) = $leaves[0];
	my $z_seq = $z->sequence->[0];
	isa_ok ($z_seq, 'Bio::SeqI');
	my ($z_id) = $z_seq->annotation->get_nested_Annotations('-keys'=>['id_source'], '-recursive'=>1);
	my ($z_id_text) = $z_id->value;
	my @seq_rels = $z_seq->annotation->get_nested_Annotations('-keys'=>['sequence_relation'], '-recursive'=>1);
	foreach my $rel (@seq_rels) {
	  isa_ok($rel, 'Bio::Annotation::Relation');
	  is ($rel->tagname, 'sequence_relation');
	  my $seqto = $rel->to;
	  isa_ok ($seqto, 'Bio::SeqI');
	  my ($seqto_id) = $seqto->annotation->get_nested_Annotations('-keys'=>['id_source'], '-recursive'=>1);
	  my $seqto_text = $seqto_id->value;
	  if ($verbose > 0) {
		diag( "node ", $z_id_text, " has ", $rel->type, " relation to ", $seqto_text);
	  }
	}
	my ($x) = $leaves[1];
	
  
  # write_tree
	if ($verbose > 0) {
	  diag("\ntest write_tree");
	}
	my $FILE1 = test_output_file();
	my $treeout = Bio::TreeIO->new(-verbose => $verbose,
		-format => 'phyloxml',
		-file   => ">$FILE1");
	$treeout->write_tree($tree);
	ok -s $FILE1;
	if ($verbose > 0) {
	  diag(`cat $FILE1`);
	}
  }
  
  # tree6: detailed sequence data
  #   
  {
	if ($verbose > 0) {
	  diag("\ntree6: detailed sequence annotation");
	}
	my $tree = $treeio->next_tree;
	isa_ok($tree, 'Bio::Tree::TreeI');
	if ($verbose > 0) {
	  diag("tree id: ",$tree->id);
	}
	my @children = ($tree->get_root_node);
	for (@children) {
	  push @children, $_->each_Descendent();
	}
	my @leaves = ();
	for (@children) {
	  push @leaves, $_ if $_->is_Leaf;
	}
	my ($z) = $leaves[0];
	my $z_seq = $z->sequence->[0];
	isa_ok ($z_seq, 'Bio::SeqI');
	my ($z_seqname) = $z_seq->annotation->get_nested_Annotations('-keys'=>['name'], '-recursive'=>1); 
	my ($z_seqname_text) = $z_seqname->get_Annotations('_text');
	is ($z_seqname_text->value, 'NADH-dependent butanol dehydrogenase B');
	my ($z_molseq) = $z_seq->seq;
	is ($z_molseq, 'MVDFEYSIPTRIFFGKDKINVLGRELKKYGSKVLIVYGGGSIKRNGIYDK');
	if ($verbose > 0) {
	  diag("Sequence ", $z_seqname_text->value, " is ", $z_molseq);
	}
	my ($z_seqname_text2) = $treeio->read_annotation('-obj'=>$z_seq, '-path'=>'name');
	is ($z_seqname_text->value, $z_seqname_text2);
	my ($y) = $leaves[1];
	my $y_seq = $y->sequence->[0];
	isa_ok ($y_seq, 'Bio::SeqI');

  # add attribute id_source
  $treeio->add_attribute(
        '-obj' => $z_seq,
        '-attr' => "id_source = \"A\""
        );
  $treeio->add_attribute(
        '-obj' => $y_seq,
        '-attr' => "id_source = \"B\""
        );
 
  # add sequence relation
  $treeio->add_phyloXML_annotation(
          '-obj'=>$tree,
          '-xml'=>''
          );      
 
  # write_tree
	if ($verbose > 0) {
	  diag("\ntest write_tree");
	}
	my $FILE1 = test_output_file();
	my $treeout = Bio::TreeIO->new(-verbose => $verbose,
		-format => 'phyloxml',
		-file   => ">$FILE1");
	$treeout->write_tree($tree);
	ok -s $FILE1;
	if ($verbose > 0) {
	  diag(`cat $FILE1`);
	}
  }
  
  # tree7: network
  #  @id_source & @id_ref
  {
	if ($verbose > 0) {
	  diag("\ntree7: network using id_source/id_ref");
	}
	my $tree = $treeio->next_tree;
	isa_ok($tree, 'Bio::Tree::TreeI');
	if ($verbose > 0) {
	  diag("tree id: ",$tree->id);
	}
	my @children = ($tree->get_root_node);
	for (@children) {
	  push @children, $_->each_Descendent();
	}
	my @leaves = ();
	for (@children) {
	  push @leaves, $_ if $_->is_Leaf;
	}
	my ($c) = $leaves[0];
	my ($c_id) = $c->annotation->get_nested_Annotations('-keys'=>['id_source'], '-recursive'=>1);
	my @clade_rels = $c->annotation->get_nested_Annotations('-keys'=>['clade_relation'], '-recursive'=>1);
	foreach my $rel (@clade_rels) {
	  isa_ok($rel, 'Bio::Annotation::Relation');
	  is ($rel->tagname, 'clade_relation');
	  my $nodeto = $rel->to;
	  isa_ok ($nodeto, 'Bio::Tree::AnnotatableNode');
	  my ($nodeto_id) = $nodeto->annotation->get_nested_Annotations('-keys'=>['id_source'], '-recursive'=>1);
	  is ($nodeto_id->value, 'b');
	  my ($nodeto_id2) = $treeio->read_annotation('-obj'=>$nodeto, '-path'=>'id_source', '-attr'=>1);
	  is ($nodeto_id->value, $nodeto_id2);
	  if ($verbose > 0) {
		diag( "node ", $c_id->value, " has ", $rel->type, " relation to ", $nodeto_id->value);
	  }
	}
  
  # write_tree
	if ($verbose > 0) {
	  diag("\ntest write_tree");
	}
	my $FILE1 = test_output_file();
	my $treeout = Bio::TreeIO->new(-verbose => $verbose,
		-format => 'phyloxml',
		-file   => ">$FILE1");
	$treeout->write_tree($tree);
	ok -s $FILE1;
	if ($verbose > 0) {
	  diag(`cat $FILE1`);
	}
  }
  
  # tree8: property elements
  # 
  {
	if ($verbose > 0) {
	  diag("\ntree8: property");
	}
	my $tree = $treeio->next_tree;
	isa_ok($tree, 'Bio::Tree::TreeI');
	if ($verbose > 0) {
	  diag("tree id: ",$tree->id);
	}
	my ($A) = $tree->find_node('A');
	isa_ok($A, 'Bio::Tree::AnnotatableNode');
	my ($ac) = $A->annotation();
	isa_ok($ac, 'Bio::AnnotationCollectionI');
	my (@annotations) = $ac->get_Annotations('property');
	isa_ok( $annotations[0], 'Bio::Annotation::Collection');
	diag("property:",$annotations[0]) if $verbose;
	my (@keys) = $annotations[0]->get_all_annotation_keys();
	diag("keys:",@keys) if $verbose;
	my (@value) = $annotations[0]->get_Annotations('_text');
	is($value[0]->value, ' 1200 ');
	if ($verbose > 0) {
	  diag( "Annotation NOAA:depth ",$value[0]->value);
	}
	my $leaves_string = $tree->simplify_to_leaves_string();
	if ($verbose > 0) {
	  diag($leaves_string);
	}
	is($leaves_string, '((A,B),C)');
  
  # write_tree
	if ($verbose > 0) {
	  diag("\ntest write_tree");
	}
	my $FILE1 = test_output_file();
	my $treeout = Bio::TreeIO->new(-verbose => $verbose,
		-format => 'phyloxml',
		-file   => ">$FILE1");
	$treeout->write_tree($tree);
	ok -s $FILE1;
	if ($verbose > 0) {
	  diag(`cat $FILE1`);
	}
  }
  
  # tree9: property outside tree topology using id refs
  #  @id_source @id_ref
  {
	if ($verbose > 0) {
	  diag("\ntree9: property using id_source/id_ref");
	}
	my $tree = $treeio->next_tree;
	isa_ok($tree, 'Bio::Tree::TreeI');
	if ($verbose > 0) {
	  diag("tree id: ",$tree->id);
	}
	my $A = $tree->find_node('A');
	isa_ok($A, 'Bio::Tree::AnnotatableNode');
	my $ac = $A->annotation();
	isa_ok($ac, 'Bio::AnnotationCollectionI');
	my @annotations = $ac->get_Annotations('property');
	isa_ok( $annotations[0], 'Bio::Annotation::Collection');
	my @value = $annotations[0]->get_Annotations('_text');
	is($value[0]->value, ' 1200 ');
	if ($verbose > 0) {
	  diag( "Annotation NOAA:depth ",$value[0]->value);
	}
	my $leaves_string = $tree->simplify_to_leaves_string();
	if ($verbose > 0) {
	  diag($leaves_string);
	}
	is($leaves_string, '((A,B),C)');
  
  # write_tree
	if ($verbose > 0) {
	  diag("\ntest write_tree");
	}
	my $FILE1 = test_output_file();
	my $treeout = Bio::TreeIO->new(-verbose => $verbose,
		-format => 'phyloxml',
		-file   => ">$FILE1");
	$treeout->write_tree($tree);
	ok -s $FILE1;
	if ($verbose > 0) {
	  diag(`cat $FILE1`);
	}
  }
  
  # tree10: detailed taxonomy and distribution
  #     
  {
	if ($verbose > 0) {
	  diag("\ntree10: taxonomy and distribution");
	}
	my $tree = $treeio->next_tree;
	isa_ok($tree, 'Bio::Tree::TreeI');
	if ($verbose > 0) {
	  diag("tree id: ",$tree->id);
	}
	my $node = $tree->get_root_node;
	my @leaves;
	my @children = ($node);
	for (@children) {
	  push @children, $_->each_Descendent();
	}
	for (@children) {
	  push @leaves, $_ if $_->is_Leaf;
	}
	my ($A) = $leaves[0];
	my ($scientificname) = $A->annotation->get_nested_Annotations('-keys'=>['scientific_name'], '-recursive'=>1);
	my ($scientificname_text) = $scientificname->get_Annotations('_text');
	my ($commonname) = $A->annotation->get_nested_Annotations('-keys'=>['common_name'], '-recursive'=>1); 
	my ($commonname_text) = $commonname->get_Annotations('_text');
	my ($rank) = $A->annotation->get_nested_Annotations('-keys'=>['rank'], '-recursive'=>1); 
	my ($rank_text) = $rank->get_Annotations('_text');
	if ($verbose > 0) {
	  diag("node rank is ", $rank_text->value);
	  diag("node scientific name is ", $scientificname_text->value);
	  diag("node common name is ", $commonname_text->value);
	}
	my ($distribution) = $A->annotation->get_nested_Annotations('-keys'=>['distribution'], '-recursive'=>1);
	my ($desc) = $distribution->get_Annotations('desc');
	my ($desc_text) = $desc->get_Annotations('_text');
	if ($verbose > 0) {
	  diag("node distribution is ", $desc_text->value);
	} 
	
  # write_tree
	if ($verbose > 0) {
	  diag("\ntest write_tree");
	}
	my $FILE1 = test_output_file();
	my $treeout = Bio::TreeIO->new(-verbose => $verbose,
		-format => 'phyloxml',
		-file   => ">$FILE1");
	$treeout->write_tree($tree);
	ok -s $FILE1;
	if ($verbose > 0) {
	  diag(`cat $FILE1`);
	}
  }
  
  # tree11: phylogeographic information
  #     
  {
	if ($verbose > 0) {
	  diag("\ntree11: phylogenographic information");
	}
	my $tree = $treeio->next_tree;
	isa_ok($tree, 'Bio::Tree::TreeI');
	if ($verbose > 0) {
	  diag("tree id: ",$tree->id);
	}
	my $node = $tree->get_root_node;
	my @leaves;
	my @children = ($node);
	for (@children) {
	  push @children, $_->each_Descendent();
	}
	for (@children) {
	  push @leaves, $_ if $_->is_Leaf;
	}
	my ($D) = $leaves[0];
	my ($point) = $treeio->read_annotation('-obj'=>$D, '-path'=>'distribution/point/geodetic_datum', '-attr'=>1);
	is ($point, 'WGS84');
	my ($lat) =  $treeio->read_annotation('-obj'=>$D, '-path'=>'distribution/point/lat');
	my ($long) =  $treeio->read_annotation('-obj'=>$D, '-path'=>'distribution/point/long');
	my ($alt) =  $treeio->read_annotation('-obj'=>$D, '-path'=>'distribution/point/alt');
	is ($lat, '32.880933');
	is ($long, '-117.217543');
	is ($alt, '104');
	if ($verbose > 0) {
	  diag("node distribution lat: $lat long $long alt $alt");
	}
	
	
  # write_tree
	if ($verbose > 0) {
	  diag("\ntest write_tree");
	}
	my $FILE1 = test_output_file();
	my $treeout = Bio::TreeIO->new(-verbose => $verbose,
		-format => 'phyloxml',
		-file   => ">$FILE1");
	$treeout->write_tree($tree);
	ok -s $FILE1;
	if ($verbose > 0) {
	  diag(`cat $FILE1`);
	}
  }
  
  # tree12: date information
  #   
  {
	if ($verbose > 0) {
	  diag("\ntree12: date");
	}
	my $tree = $treeio->next_tree;
	isa_ok($tree, 'Bio::Tree::TreeI');
	if ($verbose > 0) {
	  diag("tree id: ",$tree->id);
	}
	my $node = $tree->get_root_node;
	my @leaves;
	my @children = ($node);
	for (@children) {
	  push @children, $_->each_Descendent();
	}
	for (@children) {
	  push @leaves, $_ if $_->is_Leaf;
	}
  my ($D) = $tree->find_node(-id => 'A');
	my ($dateunit) =  $treeio->read_annotation('-obj'=>$D, '-path'=>'date/unit', '-attr'=>1);
	my ($datemin) =  $treeio->read_annotation('-obj'=>$D, '-path'=>'date/minimum' );
	my ($datemax) =  $treeio->read_annotation('-obj'=>$D, '-path'=>'date/maximum' );
	my ($datevalue) =  $treeio->read_annotation('-obj'=>$D, '-path'=>'date/value');
	is ($dateunit, 'mya');
	is ($datemin, '416.0');
	is ($datemax, '443.7');
	is ($datevalue, '425');
	if ($verbose > 0) {
	  diag("node date unit: $dateunit min $datemin max $datemax value $datevalue");
	}
  
  # write_tree
	if ($verbose > 0) {
	  diag("\ntest write_tree");
	}
	my $FILE1 = test_output_file();
	my $treeout = Bio::TreeIO->new(-verbose => $verbose,
		-format => 'phyloxml',
		-file   => ">$FILE1");
	$treeout->write_tree($tree);
	ok -s $FILE1;
	if ($verbose > 0) {
	  diag(`cat $FILE1`);
	}
  }
  
  # tree13: alignment outside 
  #   
  {
	if ($verbose > 0) {
	  diag("\ntree13: alignment outside  ");
	}
	my $tree = $treeio->next_tree;
	isa_ok($tree, 'Bio::Tree::TreeI');
	if ($verbose > 0) {
	  diag("tree id: ",$tree->id);
	}
	my $leaves_string = $tree->simplify_to_leaves_string();
	if ($verbose > 0) {
	  diag($leaves_string);
	}
	is($leaves_string, '((A,B),C)');
  
  # add annotation in phyloxml
	if ($verbose > 0) {
	  diag("test add annotation in phyloXML format");
	}
	my $node = $tree->get_root_node;
	my @leaves;
	my @children = ($node);
	for (@children) {
	  push @children, $_->each_Descendent();
	}
	for (@children) {
	  push @leaves, $_ if $_->is_Leaf;
	}
	my ($D) = $leaves[0];
	isa_ok($D, 'Bio::Tree::AnnotatableNode');
	$treeio->add_phyloXML_annotation(
			  -obj => $D, 
			  -xml => "            D
			  
				 my date
				 manymany million years
			  
  "
			  );
	my ($dateunit) =  $treeio->read_annotation('-obj'=>$D, '-path'=>'date/unit', '-attr'=>1);
	my ($datevalue) =  $treeio->read_annotation('-obj'=>$D, '-path'=>'date/value');
	is ($dateunit, 'mya');
	is ($datevalue, 'manymany million years');
  
  # write_tree
	if ($verbose > 0) {
	  diag("\ntest write_tree");
	}
	my $FILE1 = test_output_file();
	my $treeout = Bio::TreeIO->new(-verbose => $verbose,
		-format => 'phyloxml',
		-file   => ">$FILE1");
	$treeout->write_tree($tree);
	ok -s $FILE1;
	if ($verbose > 0) {
	  diag(`cat $FILE1`);
	}
  }
  
  
  # tree14: convert between nhx and phyloxml
  # convert between nhx-phyloxml
  {
	if ($verbose > 0) {
	  diag("\n test translation between nhx and phyloxml");
	}
	ok my $nhxio = Bio::TreeIO->new(
		-verbose => $verbose,
		-format => 'nhx',
		-file   => test_input_file('test.nhx'));
	my $tree = $nhxio->next_tree;
	isa_ok($tree, 'Bio::Tree::TreeI');
	my $FILE1 = test_output_file();
	my $phyloxmlio = Bio::TreeIO->new(-verbose => $verbose,
		-format => 'phyloxml',
		-file   => ">$FILE1");
	$phyloxmlio->write_tree($tree);
	ok -s $FILE1;
	if ($verbose > 0) {
	  diag(`cat $FILE1`);
	}
  }

  # to-do 1. validation
TODO: {
  local $TODO = 'validation not implemented yet';

  my $xsd = "http://www.phyloxml.org/1.10/phyloxml.xsd";
#  for my $XSD ($xsd, XML::LibXML::Schema->new(location => $xsd)) {
#    {
#      my $reader = new XML::LibXML::Reader(
#  location => "test/schema/demo.xml",
#  Schema => $XSD,
#       );
#      ok($reader->finish, "validate using ".(ref($XSD) ? 'XML::LibXML::Schema' : 'Schema file'));
#    }
#    {
#      my $reader = new XML::LibXML::Reader(
#  location => "test/schema/invaliddemo.xml",
#  Schema => $XSD,
#       );
#      eval { $reader->finish };
#      ok($@, "catch validation error for ".(ref($XSD) ? 'XML::LibXML::Schema' : 'Schema file'));
#    }
#
#  }

} 
  
}
BioPerl-1.007002/t/Tree/TreeIO/svggraph.t000444000766000024       121413155576321 20011 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: TreeIO.t 14580 2008-03-01 17:01:30Z cjfields $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 4);
    use_ok('Bio::TreeIO');
}

my $verbose = test_debug();

my $treeio = Bio::TreeIO->new(-verbose => $verbose,
			  -file   => test_input_file('test.nhx'));
my $tree = $treeio->next_tree;

SKIP: {
	test_skip(-tests => 3, -requires_module => 'SVG::Graph');
	my $FILE3 = test_output_file();
	my $treeout3 = Bio::TreeIO->new(-format => 'svggraph',
					-file => ">$FILE3");
	ok($treeout3);
	eval {$treeout3->write_tree($tree);};
	ok(!$@);
	ok (-s $FILE3);
}
BioPerl-1.007002/t/Tree/TreeIO/tabtree.t000444000766000024       353113155576321 17622 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id: TreeIO.t 14580 2008-03-01 17:01:30Z cjfields $

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 24);
    use_ok('Bio::TreeIO');
}

my $verbose = test_debug();

# try lintree parsing
my $treeio = Bio::TreeIO->new(-format => 'lintree',
			      -file   => test_input_file('crab.njb'));

my ($tree, @leaves, $node);
while( $tree = $treeio->next_tree ) {

    isa_ok($tree, 'Bio::Tree::TreeI');

    my @nodes = $tree->get_nodes;

    @leaves = $tree->get_leaf_nodes;
    is(@leaves, 13);
#/maj    is(@nodes, 25);
    is(@nodes, 24); #/maj
    ($node) = $tree->find_node(-id => '18');
    ok($node);
    is($node->id, '18');
    is($node->branch_length, '0.030579');
    is($node->bootstrap, 998);
}

$treeio = Bio::TreeIO->new(-format => 'lintree',
			   -file   => test_input_file('crab.nj'));

$tree = $treeio->next_tree;

isa_ok($tree, 'Bio::Tree::TreeI');

my @nodes = $tree->get_nodes;
@leaves = $tree->get_leaf_nodes;
is(@leaves, 13);
#/maj is(@nodes, 25);
is(@nodes, 24); #/maj
($node) = $tree->find_node('18');
is($node->id, '18');
is($node->branch_length, '0.028117');

($node) = $tree->find_node(-id => 'C-vittat');
is($node->id, 'C-vittat');
is($node->branch_length, '0.087619');
is($node->ancestor->id, '14');

$treeio = Bio::TreeIO->new(-format => 'lintree',
			  -file   => test_input_file('crab.dat.cn'));

$tree = $treeio->next_tree;

isa_ok($tree, 'Bio::Tree::TreeI');

@nodes = $tree->get_nodes;
@leaves = $tree->get_leaf_nodes;
is(@leaves, 13, "Leaf nodes");

#/maj is(@nodes, 25, "All nodes");
is(@nodes, 24, "All nodes"); #/maj
($node) = $tree->find_node('18');
is($node->id, '18');

is($node->branch_length, '0.029044');

($node) = $tree->find_node(-id => 'C-vittat');
is($node->id, 'C-vittat');
is($node->branch_length, '0.097855');
is($node->ancestor->id, '14');
BioPerl-1.007002/t/Variation000755000766000024          013155576321 15556 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/Variation/AAChange.t000444000766000024       347413155576321 17477 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 27);
	
	use_ok('Bio::Variation::Allele');
	use_ok('Bio::Variation::AAChange');
	use_ok('Bio::Variation::RNAChange');
}


ok my $obj = Bio::Variation::AAChange->new();
isa_ok $obj, 'Bio::Variation::AAChange';

$obj->start(3);           
is $obj->start, 3;

$obj->end(3); 
is $obj->end, 3;

$obj->length(3);

is $obj->length, 3;

$obj->strand('1');  
is $obj->strand, '1';

is $obj->primary_tag, 'Variation';

$obj->source_tag('source');
is $obj->source_tag, 'source';

$obj->frame(2);   
is $obj->frame,2;

$obj->score(2);   
is $obj->score, 2;

$obj->isMutation(1); 
ok $obj->isMutation;

my $a1 = Bio::Variation::Allele->new(-seq => 'V');
$obj->allele_ori($a1);

is $obj->allele_ori->seq, 'V';

my $a2 = Bio::Variation::Allele->new('-seq' => 'A');
$obj->add_Allele($a2);

is $obj->allele_mut->seq, 'A';

is $obj->similarity_score, 0;

$obj->upStreamSeq('upStreamSeq'); 
is $obj->upStreamSeq, 'upStreamSeq';

$obj->dnStreamSeq('dnStreamSeq'); 
is $obj->dnStreamSeq, 'dnStreamSeq' ;

is $obj->label, 'substitution, conservative';

$obj->status('proven'); 
is $obj->status, 'proven';

$obj->proof('experimental'); 
is $obj->proof, 'experimental';

$obj->region('region'); 
is $obj->region, 'region';

$obj->region_value('region_value'); 
is $obj->region_value, 'region_value';

$obj->numbering('coding'); 
is $obj->numbering, 'coding';

my $obj2 = Bio::Variation::RNAChange->new(-start => 7, 
					  -end => 7,
					  -cds_end => 100,
					  -codon_pos => 1,
					  -upStreamSeq => 'acgcgcgcgc',
					  -dnStreamSeq => 'acgcgcgcgc'
					  );
$obj2->label('missense');
$obj->RNAChange($obj2);

is $obj->trivname, 'V3A', "Trivial name is [". $obj->trivname. "]";

$obj->mut_number(2);
is $obj->mut_number, 2;
BioPerl-1.007002/t/Variation/AAReverseMutate.t000444000766000024       173713155576321 21105 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 16);
	
	use_ok('Bio::Variation::AAReverseMutate');
}

my $obj = Bio::Variation::AAReverseMutate->new
    ('-aa_ori' => 'F', 
     '-aa_mut' => 'S'
     );
ok defined $obj;
isa_ok($obj, 'Bio::Variation::AAReverseMutate');

is $obj->aa_ori, 'F';

is $obj->aa_mut, 'S';

my @points = $obj->each_Variant;
# F>S has two solutions
is scalar @points, 2;

$obj->codon_ori('ttc');
ok defined $obj;

#now there should be only one left
@points = $obj->each_Variant;
is scalar @points, 1;

$obj->codon_table(3);
is $obj->codon_table, 3;

#Check the returned object
my $rna = pop @points;
isa_ok($rna, 'Bio::Variation::RNAChange');

is $rna->length, 1;
is $rna->allele_ori->seq, 't';
is $rna->allele_mut->seq, 'c';

is $rna->codon_ori, 'ttc', "Codon_ori is |". $rna->codon_ori. "|";

is $rna->codon_pos, 2;

$obj->codon_table(11);
is $obj->codon_table, 11;
BioPerl-1.007002/t/Variation/Allele.t000444000766000024       157113155576321 17302 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$


use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 14);
	
	use_ok('Bio::Variation::Allele');	
}

my($a,$trunc,$rev);

$a = Bio::Variation::Allele->new(-seq=>'ACTGACTGACTG',
			-display_id => 'new-id',
			-alphabet => 'dna',
			-accession_number => 'X677667',
                        -desc=>'Sample Bio::Seq object');
isa_ok($a, 'Bio::Variation::Allele');

is $a->accession_number(), 'X677667';
is $a->seq(), 'ACTGACTGACTG';
is $a->display_id(),'new-id' ;
is $a->desc, 'Sample Bio::Seq object';
is $a->alphabet(), 'dna';

ok defined($trunc = $a->trunc(1,4));
is $trunc->seq(), 'ACTG';

ok defined($rev = $a->revcom());
is $rev->seq(), 'CAGTCAGTCAGT';

$a->is_reference(1);
ok $a->is_reference;

$a->repeat_unit('ACTG');
is $a->repeat_unit, 'ACTG';

$a->repeat_count(3);
is $a->repeat_count, 3;
BioPerl-1.007002/t/Variation/DNAMutation.t000444000766000024       460513155576321 20230 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
	use Bio::Root::Test;
	
	test_begin(-tests => 37);
	
	use_ok('Bio::Variation::DNAMutation');
	use_ok('Bio::Variation::Allele');
}

my($obj,$a1,$a2,$obj2);
$obj = Bio::Variation::DNAMutation -> new;

ok defined $obj;

$obj->start(3);           
is $obj->start, 3;

$obj->end(3); 
is $obj->end, 3;

$obj->length(2);
is $obj->length, 2;

$obj->strand('1');  
is $obj->strand, '1';

is $obj->primary_tag, 'Variation';

$obj->source_tag('source');
is $obj->source_tag, 'source';

$obj->frame(2);   
is $obj->frame,2;

$obj->score(2);   
is $obj->score, 2;

if( $obj->can('dna_mut') ) {
	#test gff string
    $obj->dna_mut('dna_mut'); 
    is( $obj->dna_mut,'dna_mut');
}

$a1 = Bio::Variation::Allele->new(-seq => 'c');
$obj->allele_ori($a1);
 
is $obj->allele_ori->seq, 'c';

$a2 = Bio::Variation::Allele->new('-seq' => 'g');
$obj->allele_mut($a2);

is $obj->allele_mut->seq, 'g';

$obj->upStreamSeq('agcacctcccggcgccagtttgctg'); 
is $obj->upStreamSeq, 'agcacctcccggcgccagtttgctg';

$obj->dnStreamSeq('tgctgcagcagcagcagcagcagca'); 
is $obj->dnStreamSeq, 'tgctgcagcagcagcagcagcagca';


is $obj->label, 'point, transversion' ;

$obj->status('proven'); 
is $obj->status, 'proven';


$obj->proof('experimental'); 
is $obj->proof, 'experimental';


is $obj->restriction_changes, '-BbvI, +BstXI, -Fnu4HI, -TseI';

$obj->region('region'); 
is $obj->region, 'region';

$obj->region_value('region_value'); 
is $obj->region_value, 'region_value';

$obj->region_dist(-5); 
is $obj->region_dist, -5;

$obj->numbering('coding'); 
is $obj->numbering, 'coding';

ok not $obj->CpG;

$obj->mut_number(2);
is $obj->mut_number, 2;


ok defined ($obj2 = Bio::Variation::DNAMutation -> new
	    ('-mut_number' => 2));

is $obj2->mut_number, 2;


$obj->isMutation(1); 
ok $obj->isMutation;

$obj->add_Allele($a1);
$obj->add_Allele($a2);

is scalar ($obj->each_Allele), 2;


$obj = Bio::Variation::DNAMutation->new
    ('-start'         => 23,
     '-end'           => 24,
     '-length'        => 2,
     '-upStreamSeq'   => 'gt',
     '-dnStreamSeq'   => 'at',
     '-proof'         => 'experimental',
     '-isMutation'    => 1,
     '-mut_number'    => 2
     );

is $obj->start(), 23;
is $obj->end(), 24;
is $obj->length(), 2;
is $obj->upStreamSeq(), 'gt';
is $obj->dnStreamSeq(), 'at';
is $obj->proof(), 'experimental';
is $obj->mut_number(), 2;
ok $obj->isMutation;
BioPerl-1.007002/t/Variation/RNAChange.t000444000766000024       417213155576321 17632 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 31);
	
	use_ok('Bio::Variation::Allele');
	use_ok('Bio::Variation::RNAChange');
	use_ok('Bio::Variation::AAChange');
}

ok my $obj = Bio::Variation::RNAChange->new();

$obj->start(4);           
is $obj->start, 4;

$obj->end(4); 
is $obj->end, 4;

$obj->length(1);

is $obj->length, 1;

$obj->strand('1');  
is $obj->strand, '1';

is ($obj->primary_tag, 'Variation' );

$obj->source_tag('source');
is ($obj->source_tag, 'source' );

$obj->frame(2);   
is ($obj->frame, 2 );

$obj->score(2);   
is ($obj->score, 2 );

#test gff string
#$obj->dna_mut('dna_mut'); 
#if ($obj->dna_mut eq 'dna_mut' ) {
#    print "ok 11\n";  
#} else {
#    print "not ok 11\n";
#}

my $a1 = Bio::Variation::Allele->new(-seq => 'g');
$obj->allele_ori($a1);

is( $obj->allele_ori->seq, 'g' );

my $a2 = Bio::Variation::Allele->new('-seq' => 'a');
$obj->allele_mut($a2);

is($obj->allele_mut->seq, 'a' );

$obj->upStreamSeq('gaagattcagccaagctcaaggatg'); 
is ($obj->upStreamSeq, 'gaagattcagccaagctcaaggatg' );

$obj->cds_end(1000); 
is ($obj->cds_end, 1000 );

$obj->dnStreamSeq('aagtgcagttagggctgggaagggt'); 
is ($obj->dnStreamSeq, 'aagtgcagttagggctgggaagggt' );

$obj->codon_pos(1); 
is ($obj->codon_pos, 1 );

my $obj3 = Bio::Variation::AAChange->new();
$obj3->start(2);
$obj->AAChange($obj3);
$obj3->allele_ori($a1);
$obj3->allele_mut($a2);

is ($obj->label, 'missense' , "label is". $obj->label);


$obj->status('proven'); 
is ($obj->status, 'proven' );

$obj->proof('experimental'); 
is ($obj->proof, 'experimental' );
is ($obj->restriction_changes, '-BccI' );

$obj->region('coding'); 
is ($obj->region, 'coding' );
$obj->numbering('coding'); 
is ($obj->numbering, 'coding' );

is ($obj->codon_ori, 'gaa', "Codon_ori is |". $obj->codon_ori. "|");

is($obj->codon_mut, 'aaa' , "Codon_mut is |". $obj->codon_mut. "|");


$obj->codon_pos(1); 
is ($obj->codon_pos, 1 );
is( $obj->codon_table, 1 );

$obj->codon_table(3);
is ( $obj->codon_table, 3 );

$obj->mut_number(2);
is ( $obj->mut_number, 2 );

$obj->verbose(2);
is ( $obj->verbose, 2 );
BioPerl-1.007002/t/Variation/SNP.t000444000766000024       121513155576321 16537 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 13);
	
	use_ok('Bio::Variation::SNP');
}

my($a);

#
# SNP
#

ok $a = Bio::Variation::SNP->new();
is $a->id('123'), 123;
eval { $a->di('123'); };
ok $@;
is $a->validated('by-cluster'), 'by-cluster';
my @alleles = ('A', 'T');
is $a->validated(\@alleles), \@alleles;
is $a->desc('abc'), 'abc'; # Bio::Variation::Allele method
is $a->chromosome('X'), 'X'; # Bio::Variation::Allele method
ok my $s = $a->add_subsnp;
ok $s->is_subsnp;
is $s->handle('HGBASE'), 'HGBASE';
ok $a->add_subsnp;
is $a->each_subsnp, 2;
BioPerl-1.007002/t/Variation/SeqDiff.t000444000766000024       436113155576321 17425 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 44);
	
	use_ok('Bio::Variation::SeqDiff');
	use_ok('Bio::Variation::DNAMutation');
	use_ok('Bio::Variation::Allele');
}

my ($obj, $mm, $aa, $dna, $m);

ok $obj = Bio::Variation::SeqDiff->new();

ok $obj->id('id');
is $obj->id, 'id';

ok $obj->sysname('sysname');
is $obj->sysname, 'sysname';

$obj->trivname('trivname'); 
is $obj->trivname, 'trivname';

ok $obj->chromosome('chr');
is $obj->chromosome, 'chr';

ok $obj->description('desc');
is $obj->description, 'desc';

ok $obj->numbering('numbering');
is $obj->numbering, 'numbering';

ok $obj->offset(100);
is $obj->offset, 100;
#                  12345678901234567890
ok $obj->dna_ori ('gctgctgatcgatcgtagctagctag');
is $obj->dna_ori, 'gctgctgatcgatcgtagctagctag';

# generate mutated DNA seq from the mutation
ok $m = Bio::Variation::DNAMutation->new(-isMutation => 1, -start=>14, -end=>14);
ok $a = Bio::Variation::Allele->new(-seq=>'c');
$b = Bio::Variation::Allele->new(-seq=>'g');
ok $m->allele_ori($a);
ok $m->allele_mut($b);
ok $obj->add_Variant($m);
my $m2 = Bio::Variation::DNAMutation->new(-isMutation => 1, -start=>19, -end=>19);
my $a2 = Bio::Variation::Allele->new(-seq=>'c');
my $b2 = Bio::Variation::Allele->new(-seq=>'g');
$m2->allele_ori($a2);
$m2->allele_mut($b2);
$obj->add_Variant($m2);

#ok $obj->dna_mut('gctgctgatcggtcgtagctagctag');
is $obj->dna_mut, 'gctgctgatcgatggtaggtagctag';

ok $obj->rna_ori('gctgctgatcgatcgtagctagctag');
is $obj->rna_ori, 'gctgctgatcgatcgtagctagctag';

$obj->rna_mut('gctgctgatcgatcgtagctagctag'); 
is $obj->rna_mut, 'gctgctgatcgatcgtagctagctag';

ok $obj->aa_ori('MHYTRD');
is $obj->aa_ori, 'MHYTRD';

ok $obj->aa_mut('MHGTRD');
is $obj->aa_mut, 'MHGTRD';

foreach $mm ( $obj->each_Variant ) {
    $mm->primary_tag('a');
    isa_ok($mm,'Bio::Variation::VariantI');
}


ok $obj->gene_symbol('fos');
is $obj->gene_symbol, 'fos';

ok $obj->rna_offset(10);
is $obj->rna_offset, 10;

ok $obj->rna_id('transcript#3');
is $obj->rna_id, 'transcript#3';

ok $dna = $obj->seqobj('dna_ori');
isa_ok($dna,'Bio::PrimarySeq');

$obj->aa_mut(''); 
$aa = $obj->seqobj('aa_mut');
ok not defined $aa;

eval {
    $dna = $obj->seqobj('dna_ri');
};
ok $@;
BioPerl-1.007002/t/Variation/Variation_IO.t000444000766000024       512213155576321 20423 0ustar00cjfieldsstaff000000000000# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 26,
			   -requires_modules => ['Text::Wrap 98', 'XML::Writer']);
	
	use_ok('Bio::Variation::IO');
}

sub io {
    my ($t_file, $o_file, $out_format) = @_; 
    my $res;
	
    my ($o_ext) = $out_format eq 'flat' ? 'dat' : 'xml';
    my ($o_format) = $out_format;
    my ($t_name) = $t_file =~ /(.*)....$/;
	
    my( $before );
    {
        local $/ = undef;
        open my $BEFORE, '<', "$t_name.$o_ext" or die "Could not read file '$t_name.$o_ext': $!\n";
        $before = <$BEFORE>;
        close $BEFORE;
    }

    ok $before;#"Error in reading input file [$t_name.$o_ext]";

    my $in = Bio::Variation::IO->new( -file => $t_file);
    my  @entries ;
    while (my $e = $in->next) {
        push @entries, $e;
    }
    my $count = scalar @entries;
    cmp_ok @entries, '>', 0;# "No SeqDiff objects [$count]";

    my $out = Bio::Variation::IO->new( -FILE => ">$o_file", 
				       -FORMAT => $o_format);
    my $out_ok = 1;
    foreach my $e (@entries) {
        $out->write($e) or $out_ok = 0;
    }
    undef($out);  # Flush to disk
    ok $out_ok;#  "error writing variants";

    my( $after );
    {
        local $/ = undef;
        open my $AFTER, '<', $o_file or die "Could not read file '$o_file': $!\n";
        $after = <$AFTER>;
        close $AFTER;
    }

    ok $after;# "Error in reading in again the output file [$o_file]";
    is $before, $after, "test output file compared to input";
    print STDERR `diff $t_file $o_file` if $before ne $after;
}

io  (test_input_file('mutations.dat'), 
     test_output_file(), 'flat'); #1..5
io  (test_input_file('polymorphism.dat'), 
     test_output_file(), 'flat'); #6..10

SKIP: {
	test_skip(-tests => 15, -requires_modules => [qw(XML::Twig
												     XML::Writer
												     IO::String)]);

	eval {
		if( $XML::Writer::VERSION >= 0.5 ) { 
		io  (test_input_file('mutations.xml'), 
			 test_output_file(), 'xml'); #10..12
		} else { 
		io  (test_input_file('mutations.old.xml'), 
			 test_output_file(), 'xml'); #10..12
		}
	};
	
	eval {
		if( $XML::Writer::VERSION >= 0.5 ) { 
		io  (test_input_file('polymorphism.xml'), 
			 test_output_file(), 'xml'); #13..14
		} else { 
		io  (test_input_file('polymorphism.old.xml'), 
			 test_output_file(), 'xml'); #13..14
	
		}
	};
	
	eval { 
		if( $XML::Writer::VERSION >= 0.5 ) { 
		io  (test_input_file('mutations.dat'), 
			 test_output_file(), 'xml'); #15..25
		} else { 
		io  (test_input_file('mutations.old.dat'), 
			 test_output_file(), 'xml'); #15..25
		}
	};
}
BioPerl-1.007002/t/data000755000766000024          013155576322 14534 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/01_basic.xml000444000766000024       703613155576321 17001 0ustar00cjfieldsstaff000000000000


    
    
    
    
    
    
  
  
    
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    
  
  
    
      
        
        
        
        
        
        
        
        
        
        
        
        
          
          
          
          
          
          
          
          
          
          
          
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
    
  

BioPerl-1.007002/t/data/02_dogfish_dict_cdao_lsid_taxrefs.xml000444000766000024      1024213155576321 24115 0ustar00cjfieldsstaff000000000000
  
     
     
      
        
          
            
          
        
      
      
     
      
      
      
  
  
    
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    
  
  
    
      
        
        
        
        
        
        
        
        
        
        
        
        
          
          
          
          
          
          
          
          
          
          
          
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
    
  

BioPerl-1.007002/t/data/02_dogfish_no_taxrefs.xml000444000766000024       762413155576321 21577 0ustar00cjfieldsstaff000000000000
  
     
      
     
      
      
      
  
  
    
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    
  
  
    
      
        
        
        
        
        
        
        
        
        
        
        
        
          
          
          
          
          
          
          
          
          
          
          
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
    
  

BioPerl-1.007002/t/data/02_dogfish_rdfa_2_cdao_lsid_taxrefs.xml000444000766000024      1001213155576321 24322 0ustar00cjfieldsstaff000000000000

  
     
    
     
      
      
      
   
  
    
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    
  
  
    
      
        
        
        
        
        
        
        
        
        
        
        
        
          
          
          
          
          
          
          
          
          
          
          
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
    
  

BioPerl-1.007002/t/data/02_dogfish_rdfa_tdwg_lsid_taxrefs.xml000444000766000024      1032713155576321 24151 0ustar00cjfieldsstaff000000000000
  
     
    
      
        
          Squalus
          glaucus
        
      
    
     
      
      
      
  
  
    
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    
  
  
    
      
        
        
        
        
        
        
        
        
        
        
        
        
          
          
          
          
          
          
          
          
          
          
          
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
    
  

BioPerl-1.007002/t/data/02_mackerel_dict_cdao_lsid_taxrefs.xml000444000766000024       775613155576321 24255 0ustar00cjfieldsstaff000000000000
  
      
      
     
    
      
        
          
            
          
        
      
    
      
      
  
  
    
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    
  
  
    
      
        
        
        
        
        
        
        
        
        
        
        
        
          
          
          
          
          
          
          
          
          
          
          
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
    
  

BioPerl-1.007002/t/data/02_mackerel_no_taxrefs.xml000444000766000024       735213155576321 21735 0ustar00cjfieldsstaff000000000000
  
      
      
     
      
      
      
  
  
    
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    
  
  
    
      
        
        
        
        
        
        
        
        
        
        
        
        
          
          
          
          
          
          
          
          
          
          
          
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
    
  

BioPerl-1.007002/t/data/02_mackerel_rdfa_2_cdao_lsid_taxrefs.xml000444000766000024       754213155576321 24460 0ustar00cjfieldsstaff000000000000
  
      
      
     
    
      
      
  
  
    
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    
  
  
    
      
        
        
        
        
        
        
        
        
        
        
        
        
          
          
          
          
          
          
          
          
          
          
          
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
    
  

BioPerl-1.007002/t/data/02_mackerel_rdfa_tdwg_lsid_taxrefs.xml000444000766000024      1007613155576321 24312 0ustar00cjfieldsstaff000000000000
  
      
      
     
    
      
        
          Scomber
          glaucus
        
      
    
      
      
  
  
    
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    
  
  
    
      
        
        
        
        
        
        
        
        
        
        
        
        
          
          
          
          
          
          
          
          
          
          
          
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
    
  

BioPerl-1.007002/t/data/03_bootstraps.xml000444000766000024       776113155576321 20127 0ustar00cjfieldsstaff000000000000


    
    
    
    
    
    
  
  
    
      
      
      
      
      
      
      
      
      
      
      
      
      
      
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BioPerl-1.007002/t/data/03_bootstraps_in_tag.xml000444000766000024       761613155576321 21447 0ustar00cjfieldsstaff000000000000


    
    
    
    
    
    
  
  
    
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    
  
  
    
      
        
        
        
        
        
        
        
        
        
        
        
        
          
          
          
          
          
          
          
          
          
          
          
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
    
  

BioPerl-1.007002/t/data/04_labeled_ancestors.xml000444000766000024       716613155576321 21400 0ustar00cjfieldsstaff000000000000


    
    
    
    
    
    
  
  
    
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    
  
  
    
      
        
        
        
        
        
        
        
        
        
        
        
        
          
          
          
          
          
          
          
          
          
          
          
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
    
  

BioPerl-1.007002/t/data/05_ancestral_states.xml000444000766000024      1103513155576321 21275 0ustar00cjfieldsstaff000000000000


    
    
    
    
    
    
  
  
    
      
        
          
        
      
      
      
        
          
        
      
      
        
          
        
      
      
        
          
        
      
      
        
          
        
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    
  
  
    
      
        
        
        
        
        
        
        
        
        
        
        
        
          
          
          
          
          
          
          
          
          
          
          
        
      
      
    
    
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
      
        
      
    
  

BioPerl-1.007002/t/data/13-pilE-F.scf000444000766000024     55524613155576321 16743 0ustar00cjfieldsstaff000000000000.scf!Ù„«€3.00¶Z#L$7I]fz£¸Åáõ"ARdv…”¥ºÑëù!:Mc{†˜ª¾Òçò-DZnƒ™©ºÏãö-@Uk|“¡µÌäñ0BXd{¥¹Éàô4IZn‚•ª¾Ïæù"7H^r”ª¿Óçü';O_tˆ›¯ÀØñ			,	=	T	j	}		£	·	Ê	á	ö


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/)ê2xá(â“ÿÿÿÿ©xppHœêà™œêðêj½xP"xÿÿÿÿÏx¸x¬a;l²{;ló}b;lppHó}ðêÈA@lüêBioPerl-1.007002/t/data/1A11.pdb000444000766000024    117517413155576321 16062 0ustar00cjfieldsstaff000000000000HEADER    ACETYLCHOLINE RECEPTOR                  19-DEC-97   1A11              
TITLE     NMR STRUCTURE OF MEMBRANE SPANNING SEGMENT 2 OF THE                   
TITLE    2 ACETYLCHOLINE RECEPTOR IN DPC MICELLES, 10 STRUCTURES                
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: ACETYLCHOLINE RECEPTOR M2;                                 
COMPND   3 CHAIN: NULL;                                                         
COMPND   4 SYNONYM: ACHR M2;                                                    
COMPND   5 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;                              
SOURCE   3 ORGANISM_COMMON: RAT;                                                
SOURCE   4 ORGAN: BRAIN;                                                        
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_STRAIN: BL21;                                      
SOURCE   7 EXPRESSION_SYSTEM_PLASMID: PGEX FUSION                               
KEYWDS    ACETYLCHOLINE RECEPTOR, M2, MICELLE                                   
EXPDTA    NMR, 10 STRUCTURES                                                    
AUTHOR    J.J.GESELL,W.SUN,M.MONTAL,S.J.OPELLA                                  
REVDAT   1   08-APR-98 1A11    0                                                
JRNL        AUTH   S.J.OPELLA,J.GESELL,A.P.VALENTE,F.M.MARASSI,                 
JRNL        AUTH 2 M.OBLATT-MONTAL,W.SUN,A.FERRER-MONTIEL,M.MONTAL              
JRNL        TITL   STRUCTURAL STUDIES OF THE PORE-LINING SEGMENTS OF            
JRNL        TITL 2 NEUROTRANSMITTER-GATED CHANNELS                              
JRNL        REF    CHEMTRACTS: BIOCHEM.MOL.      V.  10   153 1997              
JRNL        REF  2 BIOL.                                                        
JRNL        REFN   ASTM CMBIE5  US ISSN 1045-2680                 2176          
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR 3.1                                           
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE                 
REMARK   3  FOUND IN THE JRNL CITATION ABOVE.                                   
REMARK   4                                                                      
REMARK   4 1A11 COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996                        
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 313                                
REMARK 210  PH                             : 5.5                                
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : HMQC-NOESY, HMQC-TOCSY,            
REMARK 210   HNCA, HNCOCA, HNHA                                                 
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600, 750                           
REMARK 210  SPECTROMETER MODEL             : DMX600, DMX750                     
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : X-PLOR                             
REMARK 210   METHOD USED                   : DISTANCE GEOMETRY,                 
REMARK 210   SIMULATED ANNEALING                                                
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 30                                 
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 10                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : LOWEST ENERGY                      
REMARK 210                                                                      
REMARK 210 REMARK:                                                              
REMARK 210 IONIC_STRENGTH: 450MM DPC                                            
REMARK 210 PRESSURE: 1 ATM                                                      
REMARK 210 SOLVENT SYSTEM: WATER                                                
REMARK 210                                                                      
REMARK 210 HNCA AND HNCOCA WERE USED TO OBTAIN BACKBONE RESONANCE               
REMARK 210 ASSIGNMENTS.  15N AND 13C EDITED HMQC-NOESY SPECTRA WERE             
REMARK 210 USED TO TABULATE NOE RESTRAINTS.  AN HNHA SPECTRUM WAS               
REMARK 210 TO OBTAIN HNCAH COUPLING CONSTANTS.                                  
REMARK 215                                                                      
REMARK 215 NMR STUDY                                                            
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION           
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT                
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON              
REMARK 215 THESE RECORDS ARE MEANINGLESS.                                       
REMARK 999                                                                      
REMARK 999 SEQUENCE                                                             
REMARK 999 1A11       SWS     P25110       1 -   273 NOT IN ATOMS LIST          
REMARK 999 1A11       SWS     P25110     299 -   517 NOT IN ATOMS LIST          
DBREF  1A11      1    25  SWS    P25110   ACHD_RAT       274    298             
SEQADV 1A11 GLY      1  SWS  P25110    CYS   274 CONFLICT                       
SEQADV 1A11 SER      2  SWS  P25110    GLY   275 CONFLICT                       
SEQADV 1A11 MET      5  SWS  P25110    THR   278 CONFLICT                       
SEQADV 1A11 THR      7  SWS  P25110    VAL   280 CONFLICT                       
SEQADV 1A11 ALA     16  SWS  P25110    SER   289 CONFLICT                       
SEQADV 1A11 THR     22  SWS  P25110    ILE   295 CONFLICT                       
SEQADV 1A11 GLN     24  SWS  P25110    LYS   297 CONFLICT                       
SEQRES   1     25  GLY SER GLU LYS MET SER THR ALA ILE SER VAL LEU LEU          
SEQRES   2     25  ALA GLN ALA VAL PHE LEU LEU LEU THR SER GLN ARG              
HELIX    1   1 SER      2  SER     23  1                                  22    
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      1.000000  0.000000  0.000000        0.00000                         
SCALE2      0.000000  1.000000  0.000000        0.00000                         
SCALE3      0.000000  0.000000  1.000000        0.00000                         
MODEL        1                                                                  
ATOM      1  N   GLY     1      15.933   2.572  -9.465  1.00  0.00           N  
ATOM      2  CA  GLY     1      15.248   3.793  -8.849  1.00  0.00           C  
ATOM      3  C   GLY     1      14.402   4.670  -9.708  1.00  0.00           C  
ATOM      4  O   GLY     1      13.527   4.207 -10.413  1.00  0.00           O  
ATOM      5 1H   GLY     1      16.550   2.876 -10.244  1.00  0.00           H  
ATOM      6 2H   GLY     1      16.502   2.091  -8.738  1.00  0.00           H  
ATOM      7 3H   GLY     1      15.212   1.917  -9.829  1.00  0.00           H  
ATOM      8 1HA  GLY     1      14.396   3.552  -8.438  1.00  0.00           H  
ATOM      9 2HA  GLY     1      16.004   4.260  -8.092  1.00  0.00           H  
ATOM     10  N   SER     2      14.637   5.953  -9.674  1.00  0.00           N  
ATOM     11  CA  SER     2      13.825   6.883 -10.510  1.00  0.00           C  
ATOM     12  C   SER     2      12.385   6.909  -9.995  1.00  0.00           C  
ATOM     13  O   SER     2      12.011   6.147  -9.125  1.00  0.00           O  
ATOM     14  CB  SER     2      13.840   6.409 -11.963  1.00  0.00           C  
ATOM     15  OG  SER     2      13.830   7.539 -12.826  1.00  0.00           O  
ATOM     16  H   SER     2      15.348   6.305  -9.099  1.00  0.00           H  
ATOM     17  HA  SER     2      14.245   7.878 -10.452  1.00  0.00           H  
ATOM     18 1HB  SER     2      14.731   5.831 -12.147  1.00  0.00           H  
ATOM     19 2HB  SER     2      12.970   5.794 -12.150  1.00  0.00           H  
ATOM     20  HG  SER     2      13.081   7.454 -13.419  1.00  0.00           H  
ATOM     21  N   GLU     3      11.572   7.782 -10.525  1.00  0.00           N  
ATOM     22  CA  GLU     3      10.156   7.859 -10.065  1.00  0.00           C  
ATOM     23  C   GLU     3       9.466   6.514 -10.300  1.00  0.00           C  
ATOM     24  O   GLU     3       8.448   6.217  -9.708  1.00  0.00           O  
ATOM     25  CB  GLU     3       9.424   8.950 -10.848  1.00  0.00           C  
ATOM     26  CG  GLU     3       9.409   8.589 -12.334  1.00  0.00           C  
ATOM     27  CD  GLU     3       9.028   9.823 -13.154  1.00  0.00           C  
ATOM     28  OE1 GLU     3       7.864  10.186 -13.137  1.00  0.00           O  
ATOM     29  OE2 GLU     3       9.909  10.385 -13.784  1.00  0.00           O  
ATOM     30  H   GLU     3      11.893   8.388 -11.225  1.00  0.00           H  
ATOM     31  HA  GLU     3      10.133   8.095  -9.011  1.00  0.00           H  
ATOM     32 1HB  GLU     3       8.409   9.033 -10.486  1.00  0.00           H  
ATOM     33 2HB  GLU     3       9.932   9.893 -10.713  1.00  0.00           H  
ATOM     34 1HG  GLU     3      10.390   8.247 -12.630  1.00  0.00           H  
ATOM     35 2HG  GLU     3       8.686   7.807 -12.507  1.00  0.00           H  
ATOM     36  N   LYS     4      10.011   5.698 -11.161  1.00  0.00           N  
ATOM     37  CA  LYS     4       9.385   4.373 -11.430  1.00  0.00           C  
ATOM     38  C   LYS     4       9.476   3.506 -10.174  1.00  0.00           C  
ATOM     39  O   LYS     4       8.477   3.109  -9.607  1.00  0.00           O  
ATOM     40  CB  LYS     4      10.116   3.686 -12.585  1.00  0.00           C  
ATOM     41  CG  LYS     4       9.392   3.987 -13.898  1.00  0.00           C  
ATOM     42  CD  LYS     4       9.734   5.407 -14.356  1.00  0.00           C  
ATOM     43  CE  LYS     4       9.186   5.637 -15.765  1.00  0.00           C  
ATOM     44  NZ  LYS     4      10.318   5.708 -16.733  1.00  0.00           N  
ATOM     45  H   LYS     4      10.833   5.956 -11.628  1.00  0.00           H  
ATOM     46  HA  LYS     4       8.347   4.514 -11.694  1.00  0.00           H  
ATOM     47 1HB  LYS     4      11.131   4.055 -12.639  1.00  0.00           H  
ATOM     48 2HB  LYS     4      10.129   2.619 -12.419  1.00  0.00           H  
ATOM     49 1HG  LYS     4       9.704   3.279 -14.652  1.00  0.00           H  
ATOM     50 2HG  LYS     4       8.326   3.906 -13.748  1.00  0.00           H  
ATOM     51 1HD  LYS     4       9.290   6.121 -13.676  1.00  0.00           H  
ATOM     52 2HD  LYS     4      10.806   5.535 -14.363  1.00  0.00           H  
ATOM     53 1HE  LYS     4       8.531   4.821 -16.036  1.00  0.00           H  
ATOM     54 2HE  LYS     4       8.633   6.564 -15.790  1.00  0.00           H  
ATOM     55 1HZ  LYS     4      11.214   5.546 -16.232  1.00  0.00           H  
ATOM     56 2HZ  LYS     4      10.195   4.979 -17.464  1.00  0.00           H  
ATOM     57 3HZ  LYS     4      10.333   6.648 -17.179  1.00  0.00           H  
ATOM     58  N   MET     5      10.667   3.212  -9.730  1.00  0.00           N  
ATOM     59  CA  MET     5      10.817   2.375  -8.507  1.00  0.00           C  
ATOM     60  C   MET     5      10.231   3.125  -7.310  1.00  0.00           C  
ATOM     61  O   MET     5       9.942   2.546  -6.281  1.00  0.00           O  
ATOM     62  CB  MET     5      12.300   2.093  -8.259  1.00  0.00           C  
ATOM     63  CG  MET     5      12.474   0.643  -7.803  1.00  0.00           C  
ATOM     64  SD  MET     5      13.033   0.615  -6.081  1.00  0.00           S  
ATOM     65  CE  MET     5      14.531  -0.366  -6.347  1.00  0.00           C  
ATOM     66  H   MET     5      11.461   3.544 -10.198  1.00  0.00           H  
ATOM     67  HA  MET     5      10.290   1.442  -8.642  1.00  0.00           H  
ATOM     68 1HB  MET     5      12.854   2.254  -9.171  1.00  0.00           H  
ATOM     69 2HB  MET     5      12.669   2.757  -7.491  1.00  0.00           H  
ATOM     70 1HG  MET     5      11.531   0.125  -7.883  1.00  0.00           H  
ATOM     71 2HG  MET     5      13.208   0.155  -8.428  1.00  0.00           H  
ATOM     72 1HE  MET     5      14.648  -0.564  -7.404  1.00  0.00           H  
ATOM     73 2HE  MET     5      15.389   0.181  -5.982  1.00  0.00           H  
ATOM     74 3HE  MET     5      14.450  -1.300  -5.816  1.00  0.00           H  
ATOM     75  N   SER     6      10.055   4.411  -7.436  1.00  0.00           N  
ATOM     76  CA  SER     6       9.488   5.201  -6.309  1.00  0.00           C  
ATOM     77  C   SER     6       7.971   4.999  -6.259  1.00  0.00           C  
ATOM     78  O   SER     6       7.371   4.988  -5.202  1.00  0.00           O  
ATOM     79  CB  SER     6       9.798   6.683  -6.522  1.00  0.00           C  
ATOM     80  OG  SER     6       9.626   7.380  -5.295  1.00  0.00           O  
ATOM     81  H   SER     6      10.295   4.858  -8.276  1.00  0.00           H  
ATOM     82  HA  SER     6       9.926   4.870  -5.380  1.00  0.00           H  
ATOM     83 1HB  SER     6      10.818   6.795  -6.853  1.00  0.00           H  
ATOM     84 2HB  SER     6       9.132   7.084  -7.274  1.00  0.00           H  
ATOM     85  HG  SER     6      10.254   7.025  -4.662  1.00  0.00           H  
ATOM     86  N   THR     7       7.349   4.835  -7.394  1.00  0.00           N  
ATOM     87  CA  THR     7       5.873   4.632  -7.414  1.00  0.00           C  
ATOM     88  C   THR     7       5.562   3.154  -7.171  1.00  0.00           C  
ATOM     89  O   THR     7       4.458   2.792  -6.815  1.00  0.00           O  
ATOM     90  CB  THR     7       5.317   5.058  -8.775  1.00  0.00           C  
ATOM     91  OG1 THR     7       6.248   4.712  -9.792  1.00  0.00           O  
ATOM     92  CG2 THR     7       5.087   6.570  -8.782  1.00  0.00           C  
ATOM     93  H   THR     7       7.852   4.843  -8.235  1.00  0.00           H  
ATOM     94  HA  THR     7       5.417   5.229  -6.636  1.00  0.00           H  
ATOM     95  HB  THR     7       4.381   4.554  -8.956  1.00  0.00           H  
ATOM     96  HG1 THR     7       5.969   5.138 -10.606  1.00  0.00           H  
ATOM     97 1HG2 THR     7       4.638   6.870  -7.847  1.00  0.00           H  
ATOM     98 2HG2 THR     7       6.031   7.077  -8.909  1.00  0.00           H  
ATOM     99 3HG2 THR     7       4.427   6.829  -9.598  1.00  0.00           H  
ATOM    100  N   ALA     8       6.530   2.298  -7.352  1.00  0.00           N  
ATOM    101  CA  ALA     8       6.294   0.848  -7.125  1.00  0.00           C  
ATOM    102  C   ALA     8       6.505   0.543  -5.645  1.00  0.00           C  
ATOM    103  O   ALA     8       5.770  -0.210  -5.037  1.00  0.00           O  
ATOM    104  CB  ALA     8       7.279   0.031  -7.962  1.00  0.00           C  
ATOM    105  H   ALA     8       7.416   2.609  -7.630  1.00  0.00           H  
ATOM    106  HA  ALA     8       5.282   0.597  -7.404  1.00  0.00           H  
ATOM    107 1HB  ALA     8       8.123   0.649  -8.228  1.00  0.00           H  
ATOM    108 2HB  ALA     8       7.619  -0.818  -7.390  1.00  0.00           H  
ATOM    109 3HB  ALA     8       6.789  -0.313  -8.861  1.00  0.00           H  
ATOM    110  N   ILE     9       7.510   1.131  -5.059  1.00  0.00           N  
ATOM    111  CA  ILE     9       7.779   0.884  -3.620  1.00  0.00           C  
ATOM    112  C   ILE     9       6.757   1.641  -2.774  1.00  0.00           C  
ATOM    113  O   ILE     9       6.393   1.212  -1.701  1.00  0.00           O  
ATOM    114  CB  ILE     9       9.190   1.359  -3.268  1.00  0.00           C  
ATOM    115  CG1 ILE     9       9.314   2.855  -3.562  1.00  0.00           C  
ATOM    116  CG2 ILE     9      10.212   0.591  -4.109  1.00  0.00           C  
ATOM    117  CD1 ILE     9       9.457   3.623  -2.247  1.00  0.00           C  
ATOM    118  H   ILE     9       8.087   1.736  -5.570  1.00  0.00           H  
ATOM    119  HA  ILE     9       7.693  -0.172  -3.420  1.00  0.00           H  
ATOM    120  HB  ILE     9       9.379   1.178  -2.220  1.00  0.00           H  
ATOM    121 1HG1 ILE     9      10.183   3.030  -4.179  1.00  0.00           H  
ATOM    122 2HG1 ILE     9       8.431   3.195  -4.081  1.00  0.00           H  
ATOM    123 1HG2 ILE     9       9.697   0.013  -4.862  1.00  0.00           H  
ATOM    124 2HG2 ILE     9      10.883   1.289  -4.586  1.00  0.00           H  
ATOM    125 3HG2 ILE     9      10.777  -0.073  -3.470  1.00  0.00           H  
ATOM    126 1HD1 ILE     9      10.205   3.147  -1.631  1.00  0.00           H  
ATOM    127 2HD1 ILE     9       9.757   4.640  -2.454  1.00  0.00           H  
ATOM    128 3HD1 ILE     9       8.510   3.626  -1.726  1.00  0.00           H  
ATOM    129  N   SER    10       6.283   2.761  -3.250  1.00  0.00           N  
ATOM    130  CA  SER    10       5.278   3.530  -2.465  1.00  0.00           C  
ATOM    131  C   SER    10       3.914   2.861  -2.617  1.00  0.00           C  
ATOM    132  O   SER    10       3.209   2.640  -1.653  1.00  0.00           O  
ATOM    133  CB  SER    10       5.206   4.965  -2.986  1.00  0.00           C  
ATOM    134  OG  SER    10       5.884   5.827  -2.082  1.00  0.00           O  
ATOM    135  H   SER    10       6.582   3.092  -4.123  1.00  0.00           H  
ATOM    136  HA  SER    10       5.561   3.534  -1.423  1.00  0.00           H  
ATOM    137 1HB  SER    10       5.676   5.025  -3.953  1.00  0.00           H  
ATOM    138 2HB  SER    10       4.168   5.264  -3.073  1.00  0.00           H  
ATOM    139  HG  SER    10       6.543   5.307  -1.615  1.00  0.00           H  
ATOM    140  N   VAL    11       3.538   2.529  -3.822  1.00  0.00           N  
ATOM    141  CA  VAL    11       2.224   1.866  -4.032  1.00  0.00           C  
ATOM    142  C   VAL    11       2.216   0.535  -3.277  1.00  0.00           C  
ATOM    143  O   VAL    11       1.182   0.048  -2.867  1.00  0.00           O  
ATOM    144  CB  VAL    11       2.012   1.616  -5.526  1.00  0.00           C  
ATOM    145  CG1 VAL    11       0.862   0.625  -5.727  1.00  0.00           C  
ATOM    146  CG2 VAL    11       1.667   2.938  -6.217  1.00  0.00           C  
ATOM    147  H   VAL    11       4.125   2.710  -4.586  1.00  0.00           H  
ATOM    148  HA  VAL    11       1.435   2.499  -3.654  1.00  0.00           H  
ATOM    149  HB  VAL    11       2.917   1.209  -5.956  1.00  0.00           H  
ATOM    150 1HG1 VAL    11       0.068   0.850  -5.031  1.00  0.00           H  
ATOM    151 2HG1 VAL    11       0.491   0.705  -6.737  1.00  0.00           H  
ATOM    152 3HG1 VAL    11       1.219  -0.379  -5.552  1.00  0.00           H  
ATOM    153 1HG2 VAL    11       1.797   3.752  -5.519  1.00  0.00           H  
ATOM    154 2HG2 VAL    11       2.320   3.083  -7.065  1.00  0.00           H  
ATOM    155 3HG2 VAL    11       0.641   2.912  -6.553  1.00  0.00           H  
ATOM    156  N   LEU    12       3.367  -0.056  -3.086  1.00  0.00           N  
ATOM    157  CA  LEU    12       3.423  -1.350  -2.354  1.00  0.00           C  
ATOM    158  C   LEU    12       2.879  -1.157  -0.937  1.00  0.00           C  
ATOM    159  O   LEU    12       2.063  -1.926  -0.466  1.00  0.00           O  
ATOM    160  CB  LEU    12       4.872  -1.833  -2.286  1.00  0.00           C  
ATOM    161  CG  LEU    12       5.136  -2.814  -3.429  1.00  0.00           C  
ATOM    162  CD1 LEU    12       6.604  -3.243  -3.406  1.00  0.00           C  
ATOM    163  CD2 LEU    12       4.242  -4.044  -3.259  1.00  0.00           C  
ATOM    164  H   LEU    12       4.193   0.353  -3.423  1.00  0.00           H  
ATOM    165  HA  LEU    12       2.823  -2.083  -2.872  1.00  0.00           H  
ATOM    166 1HB  LEU    12       5.538  -0.987  -2.374  1.00  0.00           H  
ATOM    167 2HB  LEU    12       5.042  -2.329  -1.342  1.00  0.00           H  
ATOM    168  HG  LEU    12       4.917  -2.333  -4.372  1.00  0.00           H  
ATOM    169 1HD1 LEU    12       6.943  -3.313  -2.383  1.00  0.00           H  
ATOM    170 2HD1 LEU    12       6.704  -4.206  -3.886  1.00  0.00           H  
ATOM    171 3HD1 LEU    12       7.201  -2.513  -3.934  1.00  0.00           H  
ATOM    172 1HD2 LEU    12       4.200  -4.318  -2.216  1.00  0.00           H  
ATOM    173 2HD2 LEU    12       3.246  -3.817  -3.612  1.00  0.00           H  
ATOM    174 3HD2 LEU    12       4.647  -4.866  -3.832  1.00  0.00           H  
ATOM    175  N   LEU    13       3.318  -0.134  -0.251  1.00  0.00           N  
ATOM    176  CA  LEU    13       2.814   0.099   1.134  1.00  0.00           C  
ATOM    177  C   LEU    13       1.360   0.568   1.069  1.00  0.00           C  
ATOM    178  O   LEU    13       0.541   0.198   1.885  1.00  0.00           O  
ATOM    179  CB  LEU    13       3.658   1.176   1.825  1.00  0.00           C  
ATOM    180  CG  LEU    13       5.082   0.662   2.070  1.00  0.00           C  
ATOM    181  CD1 LEU    13       5.045  -0.794   2.541  1.00  0.00           C  
ATOM    182  CD2 LEU    13       5.881   0.759   0.771  1.00  0.00           C  
ATOM    183  H   LEU    13       3.973   0.480  -0.646  1.00  0.00           H  
ATOM    184  HA  LEU    13       2.869  -0.820   1.697  1.00  0.00           H  
ATOM    185 1HB  LEU    13       3.699   2.055   1.197  1.00  0.00           H  
ATOM    186 2HB  LEU    13       3.205   1.433   2.770  1.00  0.00           H  
ATOM    187  HG  LEU    13       5.554   1.270   2.829  1.00  0.00           H  
ATOM    188 1HD1 LEU    13       4.267  -0.915   3.280  1.00  0.00           H  
ATOM    189 2HD1 LEU    13       4.844  -1.439   1.698  1.00  0.00           H  
ATOM    190 3HD1 LEU    13       5.998  -1.056   2.975  1.00  0.00           H  
ATOM    191 1HD2 LEU    13       5.409   1.473   0.114  1.00  0.00           H  
ATOM    192 2HD2 LEU    13       6.888   1.083   0.991  1.00  0.00           H  
ATOM    193 3HD2 LEU    13       5.909  -0.208   0.293  1.00  0.00           H  
ATOM    194  N   ALA    14       1.037   1.386   0.104  1.00  0.00           N  
ATOM    195  CA  ALA    14      -0.362   1.885  -0.014  1.00  0.00           C  
ATOM    196  C   ALA    14      -1.338   0.718   0.143  1.00  0.00           C  
ATOM    197  O   ALA    14      -2.271   0.777   0.920  1.00  0.00           O  
ATOM    198  CB  ALA    14      -0.556   2.534  -1.386  1.00  0.00           C  
ATOM    199  H   ALA    14       1.715   1.673  -0.541  1.00  0.00           H  
ATOM    200  HA  ALA    14      -0.548   2.616   0.759  1.00  0.00           H  
ATOM    201 1HB  ALA    14       0.300   2.321  -2.010  1.00  0.00           H  
ATOM    202 2HB  ALA    14      -1.447   2.137  -1.850  1.00  0.00           H  
ATOM    203 3HB  ALA    14      -0.658   3.602  -1.267  1.00  0.00           H  
ATOM    204  N   GLN    15      -1.135  -0.341  -0.591  1.00  0.00           N  
ATOM    205  CA  GLN    15      -2.055  -1.510  -0.487  1.00  0.00           C  
ATOM    206  C   GLN    15      -1.875  -2.190   0.873  1.00  0.00           C  
ATOM    207  O   GLN    15      -2.832  -2.497   1.556  1.00  0.00           O  
ATOM    208  CB  GLN    15      -1.731  -2.509  -1.601  1.00  0.00           C  
ATOM    209  CG  GLN    15      -2.937  -2.645  -2.533  1.00  0.00           C  
ATOM    210  CD  GLN    15      -3.686  -3.940  -2.215  1.00  0.00           C  
ATOM    211  OE1 GLN    15      -4.235  -4.089  -1.142  1.00  0.00           O  
ATOM    212  NE2 GLN    15      -3.730  -4.890  -3.109  1.00  0.00           N  
ATOM    213  H   GLN    15      -0.379  -0.368  -1.213  1.00  0.00           H  
ATOM    214  HA  GLN    15      -3.076  -1.175  -0.591  1.00  0.00           H  
ATOM    215 1HB  GLN    15      -0.879  -2.157  -2.164  1.00  0.00           H  
ATOM    216 2HB  GLN    15      -1.505  -3.471  -1.168  1.00  0.00           H  
ATOM    217 1HG  GLN    15      -3.598  -1.802  -2.392  1.00  0.00           H  
ATOM    218 2HG  GLN    15      -2.598  -2.669  -3.558  1.00  0.00           H  
ATOM    219 1HE2 GLN    15      -4.208  -5.723  -2.914  1.00  0.00           H  
ATOM    220 2HE2 GLN    15      -3.287  -4.771  -3.975  1.00  0.00           H  
ATOM    221  N   ALA    16      -0.655  -2.432   1.265  1.00  0.00           N  
ATOM    222  CA  ALA    16      -0.404  -3.099   2.575  1.00  0.00           C  
ATOM    223  C   ALA    16      -1.338  -2.527   3.645  1.00  0.00           C  
ATOM    224  O   ALA    16      -2.023  -3.255   4.336  1.00  0.00           O  
ATOM    225  CB  ALA    16       1.050  -2.865   2.991  1.00  0.00           C  
ATOM    226  H   ALA    16       0.100  -2.180   0.693  1.00  0.00           H  
ATOM    227  HA  ALA    16      -0.580  -4.160   2.476  1.00  0.00           H  
ATOM    228 1HB  ALA    16       1.263  -1.805   2.976  1.00  0.00           H  
ATOM    229 2HB  ALA    16       1.205  -3.248   3.988  1.00  0.00           H  
ATOM    230 3HB  ALA    16       1.708  -3.374   2.303  1.00  0.00           H  
ATOM    231  N   VAL    17      -1.365  -1.231   3.797  1.00  0.00           N  
ATOM    232  CA  VAL    17      -2.249  -0.619   4.831  1.00  0.00           C  
ATOM    233  C   VAL    17      -3.673  -0.484   4.286  1.00  0.00           C  
ATOM    234  O   VAL    17      -4.628  -0.423   5.033  1.00  0.00           O  
ATOM    235  CB  VAL    17      -1.713   0.766   5.202  1.00  0.00           C  
ATOM    236  CG1 VAL    17      -2.561   1.358   6.329  1.00  0.00           C  
ATOM    237  CG2 VAL    17      -0.261   0.642   5.670  1.00  0.00           C  
ATOM    238  H   VAL    17      -0.801  -0.660   3.236  1.00  0.00           H  
ATOM    239  HA  VAL    17      -2.260  -1.245   5.710  1.00  0.00           H  
ATOM    240  HB  VAL    17      -1.760   1.413   4.338  1.00  0.00           H  
ATOM    241 1HG1 VAL    17      -3.591   1.063   6.199  1.00  0.00           H  
ATOM    242 2HG1 VAL    17      -2.200   0.994   7.280  1.00  0.00           H  
ATOM    243 3HG1 VAL    17      -2.489   2.435   6.306  1.00  0.00           H  
ATOM    244 1HG2 VAL    17      -0.107  -0.330   6.114  1.00  0.00           H  
ATOM    245 2HG2 VAL    17       0.402   0.760   4.825  1.00  0.00           H  
ATOM    246 3HG2 VAL    17      -0.052   1.409   6.401  1.00  0.00           H  
ATOM    247  N   PHE    18      -3.825  -0.436   2.992  1.00  0.00           N  
ATOM    248  CA  PHE    18      -5.189  -0.304   2.406  1.00  0.00           C  
ATOM    249  C   PHE    18      -6.092  -1.405   2.965  1.00  0.00           C  
ATOM    250  O   PHE    18      -7.064  -1.141   3.643  1.00  0.00           O  
ATOM    251  CB  PHE    18      -5.106  -0.438   0.885  1.00  0.00           C  
ATOM    252  CG  PHE    18      -6.146   0.447   0.241  1.00  0.00           C  
ATOM    253  CD1 PHE    18      -5.969   1.835   0.221  1.00  0.00           C  
ATOM    254  CD2 PHE    18      -7.285  -0.122  -0.340  1.00  0.00           C  
ATOM    255  CE1 PHE    18      -6.932   2.655  -0.379  1.00  0.00           C  
ATOM    256  CE2 PHE    18      -8.249   0.698  -0.940  1.00  0.00           C  
ATOM    257  CZ  PHE    18      -8.072   2.087  -0.959  1.00  0.00           C  
ATOM    258  H   PHE    18      -3.042  -0.485   2.404  1.00  0.00           H  
ATOM    259  HA  PHE    18      -5.599   0.662   2.660  1.00  0.00           H  
ATOM    260 1HB  PHE    18      -4.123  -0.140   0.552  1.00  0.00           H  
ATOM    261 2HB  PHE    18      -5.283  -1.466   0.605  1.00  0.00           H  
ATOM    262  HD1 PHE    18      -5.089   2.274   0.669  1.00  0.00           H  
ATOM    263  HD2 PHE    18      -7.422  -1.193  -0.325  1.00  0.00           H  
ATOM    264  HE1 PHE    18      -6.795   3.726  -0.393  1.00  0.00           H  
ATOM    265  HE2 PHE    18      -9.128   0.259  -1.388  1.00  0.00           H  
ATOM    266  HZ  PHE    18      -8.815   2.720  -1.422  1.00  0.00           H  
ATOM    267  N   LEU    19      -5.775  -2.640   2.685  1.00  0.00           N  
ATOM    268  CA  LEU    19      -6.613  -3.758   3.200  1.00  0.00           C  
ATOM    269  C   LEU    19      -6.606  -3.735   4.730  1.00  0.00           C  
ATOM    270  O   LEU    19      -7.561  -4.124   5.371  1.00  0.00           O  
ATOM    271  CB  LEU    19      -6.047  -5.092   2.704  1.00  0.00           C  
ATOM    272  CG  LEU    19      -5.837  -5.028   1.190  1.00  0.00           C  
ATOM    273  CD1 LEU    19      -5.401  -6.400   0.673  1.00  0.00           C  
ATOM    274  CD2 LEU    19      -7.148  -4.624   0.511  1.00  0.00           C  
ATOM    275  H   LEU    19      -4.986  -2.831   2.137  1.00  0.00           H  
ATOM    276  HA  LEU    19      -7.626  -3.642   2.844  1.00  0.00           H  
ATOM    277 1HB  LEU    19      -5.103  -5.286   3.191  1.00  0.00           H  
ATOM    278 2HB  LEU    19      -6.741  -5.886   2.935  1.00  0.00           H  
ATOM    279  HG  LEU    19      -5.073  -4.299   0.962  1.00  0.00           H  
ATOM    280 1HD1 LEU    19      -5.007  -6.985   1.491  1.00  0.00           H  
ATOM    281 2HD1 LEU    19      -6.250  -6.910   0.242  1.00  0.00           H  
ATOM    282 3HD1 LEU    19      -4.636  -6.275  -0.079  1.00  0.00           H  
ATOM    283 1HD2 LEU    19      -7.479  -3.674   0.906  1.00  0.00           H  
ATOM    284 2HD2 LEU    19      -6.992  -4.536  -0.553  1.00  0.00           H  
ATOM    285 3HD2 LEU    19      -7.901  -5.375   0.705  1.00  0.00           H  
ATOM    286  N   LEU    20      -5.536  -3.277   5.320  1.00  0.00           N  
ATOM    287  CA  LEU    20      -5.469  -3.225   6.806  1.00  0.00           C  
ATOM    288  C   LEU    20      -6.577  -2.310   7.332  1.00  0.00           C  
ATOM    289  O   LEU    20      -7.113  -2.516   8.402  1.00  0.00           O  
ATOM    290  CB  LEU    20      -4.106  -2.678   7.238  1.00  0.00           C  
ATOM    291  CG  LEU    20      -3.842  -3.056   8.697  1.00  0.00           C  
ATOM    292  CD1 LEU    20      -3.948  -4.574   8.861  1.00  0.00           C  
ATOM    293  CD2 LEU    20      -2.437  -2.599   9.096  1.00  0.00           C  
ATOM    294  H   LEU    20      -4.777  -2.965   4.783  1.00  0.00           H  
ATOM    295  HA  LEU    20      -5.603  -4.219   7.208  1.00  0.00           H  
ATOM    296 1HB  LEU    20      -3.334  -3.099   6.610  1.00  0.00           H  
ATOM    297 2HB  LEU    20      -4.103  -1.604   7.142  1.00  0.00           H  
ATOM    298  HG  LEU    20      -4.573  -2.575   9.331  1.00  0.00           H  
ATOM    299 1HD1 LEU    20      -3.614  -5.058   7.955  1.00  0.00           H  
ATOM    300 2HD1 LEU    20      -3.330  -4.891   9.688  1.00  0.00           H  
ATOM    301 3HD1 LEU    20      -4.976  -4.844   9.056  1.00  0.00           H  
ATOM    302 1HD2 LEU    20      -1.877  -2.341   8.209  1.00  0.00           H  
ATOM    303 2HD2 LEU    20      -2.510  -1.736   9.740  1.00  0.00           H  
ATOM    304 3HD2 LEU    20      -1.933  -3.398   9.620  1.00  0.00           H  
ATOM    305  N   LEU    21      -6.923  -1.297   6.584  1.00  0.00           N  
ATOM    306  CA  LEU    21      -7.994  -0.367   7.039  1.00  0.00           C  
ATOM    307  C   LEU    21      -9.364  -0.982   6.748  1.00  0.00           C  
ATOM    308  O   LEU    21     -10.155  -1.209   7.642  1.00  0.00           O  
ATOM    309  CB  LEU    21      -7.867   0.964   6.291  1.00  0.00           C  
ATOM    310  CG  LEU    21      -8.987   1.906   6.732  1.00  0.00           C  
ATOM    311  CD1 LEU    21      -8.587   2.601   8.034  1.00  0.00           C  
ATOM    312  CD2 LEU    21      -9.227   2.958   5.647  1.00  0.00           C  
ATOM    313  H   LEU    21      -6.478  -1.148   5.723  1.00  0.00           H  
ATOM    314  HA  LEU    21      -7.895  -0.193   8.100  1.00  0.00           H  
ATOM    315 1HB  LEU    21      -6.910   1.412   6.513  1.00  0.00           H  
ATOM    316 2HB  LEU    21      -7.945   0.789   5.228  1.00  0.00           H  
ATOM    317  HG  LEU    21      -9.893   1.338   6.893  1.00  0.00           H  
ATOM    318 1HD1 LEU    21      -7.718   2.112   8.451  1.00  0.00           H  
ATOM    319 2HD1 LEU    21      -8.356   3.637   7.833  1.00  0.00           H  
ATOM    320 3HD1 LEU    21      -9.404   2.545   8.738  1.00  0.00           H  
ATOM    321 1HD2 LEU    21      -8.317   3.111   5.086  1.00  0.00           H  
ATOM    322 2HD2 LEU    21     -10.007   2.618   4.982  1.00  0.00           H  
ATOM    323 3HD2 LEU    21      -9.526   3.889   6.108  1.00  0.00           H  
ATOM    324  N   THR    22      -9.651  -1.251   5.504  1.00  0.00           N  
ATOM    325  CA  THR    22     -10.971  -1.848   5.154  1.00  0.00           C  
ATOM    326  C   THR    22     -11.292  -2.997   6.113  1.00  0.00           C  
ATOM    327  O   THR    22     -12.434  -3.228   6.458  1.00  0.00           O  
ATOM    328  CB  THR    22     -10.922  -2.381   3.720  1.00  0.00           C  
ATOM    329  OG1 THR    22      -9.763  -3.186   3.556  1.00  0.00           O  
ATOM    330  CG2 THR    22     -10.876  -1.207   2.740  1.00  0.00           C  
ATOM    331  H   THR    22      -8.998  -1.058   4.798  1.00  0.00           H  
ATOM    332  HA  THR    22     -11.738  -1.092   5.230  1.00  0.00           H  
ATOM    333  HB  THR    22     -11.803  -2.972   3.525  1.00  0.00           H  
ATOM    334  HG1 THR    22      -9.520  -3.170   2.628  1.00  0.00           H  
ATOM    335 1HG2 THR    22     -10.880  -0.277   3.289  1.00  0.00           H  
ATOM    336 2HG2 THR    22      -9.976  -1.270   2.145  1.00  0.00           H  
ATOM    337 3HG2 THR    22     -11.739  -1.246   2.092  1.00  0.00           H  
ATOM    338  N   SER    23     -10.296  -3.722   6.543  1.00  0.00           N  
ATOM    339  CA  SER    23     -10.547  -4.858   7.475  1.00  0.00           C  
ATOM    340  C   SER    23     -10.857  -4.319   8.874  1.00  0.00           C  
ATOM    341  O   SER    23     -11.807  -4.729   9.510  1.00  0.00           O  
ATOM    342  CB  SER    23      -9.306  -5.747   7.539  1.00  0.00           C  
ATOM    343  OG  SER    23      -9.694  -7.105   7.374  1.00  0.00           O  
ATOM    344  H   SER    23      -9.382  -3.521   6.250  1.00  0.00           H  
ATOM    345  HA  SER    23     -11.385  -5.437   7.119  1.00  0.00           H  
ATOM    346 1HB  SER    23      -8.623  -5.475   6.752  1.00  0.00           H  
ATOM    347 2HB  SER    23      -8.819  -5.617   8.497  1.00  0.00           H  
ATOM    348  HG  SER    23      -8.986  -7.561   6.913  1.00  0.00           H  
ATOM    349  N   GLN    24     -10.063  -3.404   9.358  1.00  0.00           N  
ATOM    350  CA  GLN    24     -10.312  -2.843  10.714  1.00  0.00           C  
ATOM    351  C   GLN    24     -11.356  -1.726  10.624  1.00  0.00           C  
ATOM    352  O   GLN    24     -11.574  -0.991  11.566  1.00  0.00           O  
ATOM    353  CB  GLN    24      -9.006  -2.280  11.274  1.00  0.00           C  
ATOM    354  CG  GLN    24      -7.913  -3.347  11.192  1.00  0.00           C  
ATOM    355  CD  GLN    24      -8.257  -4.506  12.128  1.00  0.00           C  
ATOM    356  OE1 GLN    24      -8.854  -5.481  11.713  1.00  0.00           O  
ATOM    357  NE2 GLN    24      -7.906  -4.442  13.382  1.00  0.00           N  
ATOM    358  H   GLN    24      -9.301  -3.087   8.831  1.00  0.00           H  
ATOM    359  HA  GLN    24     -10.676  -3.625  11.365  1.00  0.00           H  
ATOM    360 1HB  GLN    24      -8.711  -1.417  10.695  1.00  0.00           H  
ATOM    361 2HB  GLN    24      -9.150  -1.992  12.303  1.00  0.00           H  
ATOM    362 1HG  GLN    24      -7.841  -3.711  10.177  1.00  0.00           H  
ATOM    363 2HG  GLN    24      -6.968  -2.917  11.487  1.00  0.00           H  
ATOM    364 1HE2 GLN    24      -8.122  -5.181  13.990  1.00  0.00           H  
ATOM    365 2HE2 GLN    24      -7.427  -3.657  13.717  1.00  0.00           H  
ATOM    366  N   ARG    25     -12.002  -1.593   9.498  1.00  0.00           N  
ATOM    367  CA  ARG    25     -13.030  -0.525   9.350  1.00  0.00           C  
ATOM    368  C   ARG    25     -14.278  -1.110   8.687  1.00  0.00           C  
ATOM    369  O   ARG    25     -15.290  -0.429   8.670  1.00  0.00           O  
ATOM    370  CB  ARG    25     -12.473   0.604   8.480  1.00  0.00           C  
ATOM    371  CG  ARG    25     -12.008   1.756   9.370  1.00  0.00           C  
ATOM    372  CD  ARG    25     -13.227   2.465   9.965  1.00  0.00           C  
ATOM    373  NE  ARG    25     -12.793   3.340  11.090  1.00  0.00           N  
ATOM    374  CZ  ARG    25     -13.195   3.089  12.306  1.00  0.00           C  
ATOM    375  NH1 ARG    25     -12.406   2.467  13.138  1.00  0.00           N  
ATOM    376  NH2 ARG    25     -14.385   3.463  12.689  1.00  0.00           N  
ATOM    377  OXT ARG    25     -14.200  -2.229   8.207  1.00  0.00           O  
ATOM    378  H   ARG    25     -11.812  -2.195   8.749  1.00  0.00           H  
ATOM    379  HA  ARG    25     -13.288  -0.136  10.324  1.00  0.00           H  
ATOM    380 1HB  ARG    25     -11.637   0.235   7.904  1.00  0.00           H  
ATOM    381 2HB  ARG    25     -13.243   0.957   7.810  1.00  0.00           H  
ATOM    382 1HG  ARG    25     -11.390   1.369  10.168  1.00  0.00           H  
ATOM    383 2HG  ARG    25     -11.438   2.459   8.782  1.00  0.00           H  
ATOM    384 1HD  ARG    25     -13.701   3.065   9.203  1.00  0.00           H  
ATOM    385 2HD  ARG    25     -13.928   1.729  10.331  1.00  0.00           H  
ATOM    386  HE  ARG    25     -12.207   4.105  10.916  1.00  0.00           H  
ATOM    387 1HH1 ARG    25     -11.493   2.181  12.844  1.00  0.00           H  
ATOM    388 2HH1 ARG    25     -12.714   2.276  14.070  1.00  0.00           H  
ATOM    389 1HH2 ARG    25     -14.989   3.942  12.051  1.00  0.00           H  
ATOM    390 2HH2 ARG    25     -14.694   3.271  13.621  1.00  0.00           H  
TER     391      ARG    25                                                      
ENDMDL                                                                          
MODEL        2                                                                  
ATOM    392  N   GLY     1      16.481   4.923  -4.827  1.00  0.00           N  
ATOM    393  CA  GLY     1      16.036   3.978  -5.946  1.00  0.00           C  
ATOM    394  C   GLY     1      15.368   4.536  -7.157  1.00  0.00           C  
ATOM    395  O   GLY     1      14.605   3.863  -7.821  1.00  0.00           O  
ATOM    396 1H   GLY     1      17.036   5.703  -5.232  1.00  0.00           H  
ATOM    397 2H   GLY     1      15.643   5.307  -4.344  1.00  0.00           H  
ATOM    398 3H   GLY     1      17.064   4.399  -4.144  1.00  0.00           H  
ATOM    399 1HA  GLY     1      16.767   3.796  -6.564  1.00  0.00           H  
ATOM    400 2HA  GLY     1      15.621   3.016  -5.432  1.00  0.00           H  
ATOM    401  N   SER     2      15.634   5.773  -7.479  1.00  0.00           N  
ATOM    402  CA  SER     2      14.997   6.384  -8.680  1.00  0.00           C  
ATOM    403  C   SER     2      13.485   6.484  -8.463  1.00  0.00           C  
ATOM    404  O   SER     2      12.918   5.781  -7.651  1.00  0.00           O  
ATOM    405  CB  SER     2      15.279   5.513  -9.904  1.00  0.00           C  
ATOM    406  OG  SER     2      16.590   4.972  -9.801  1.00  0.00           O  
ATOM    407  H   SER     2      16.253   6.300  -6.931  1.00  0.00           H  
ATOM    408  HA  SER     2      15.404   7.372  -8.840  1.00  0.00           H  
ATOM    409 1HB  SER     2      14.565   4.707  -9.946  1.00  0.00           H  
ATOM    410 2HB  SER     2      15.194   6.114 -10.800  1.00  0.00           H  
ATOM    411  HG  SER     2      16.723   4.375 -10.540  1.00  0.00           H  
ATOM    412  N   GLU     3      12.828   7.353  -9.183  1.00  0.00           N  
ATOM    413  CA  GLU     3      11.354   7.495  -9.017  1.00  0.00           C  
ATOM    414  C   GLU     3      10.670   6.174  -9.371  1.00  0.00           C  
ATOM    415  O   GLU     3       9.507   5.969  -9.084  1.00  0.00           O  
ATOM    416  CB  GLU     3      10.839   8.600  -9.944  1.00  0.00           C  
ATOM    417  CG  GLU     3       9.488   9.106  -9.433  1.00  0.00           C  
ATOM    418  CD  GLU     3       9.704  10.354  -8.574  1.00  0.00           C  
ATOM    419  OE1 GLU     3      10.507  10.286  -7.659  1.00  0.00           O  
ATOM    420  OE2 GLU     3       9.061  11.355  -8.846  1.00  0.00           O  
ATOM    421  H   GLU     3      13.304   7.911  -9.833  1.00  0.00           H  
ATOM    422  HA  GLU     3      11.131   7.754  -7.992  1.00  0.00           H  
ATOM    423 1HB  GLU     3      11.547   9.415  -9.961  1.00  0.00           H  
ATOM    424 2HB  GLU     3      10.719   8.206 -10.942  1.00  0.00           H  
ATOM    425 1HG  GLU     3       8.854   9.352 -10.273  1.00  0.00           H  
ATOM    426 2HG  GLU     3       9.018   8.340  -8.838  1.00  0.00           H  
ATOM    427  N   LYS     4      11.382   5.274  -9.992  1.00  0.00           N  
ATOM    428  CA  LYS     4      10.770   3.967 -10.364  1.00  0.00           C  
ATOM    429  C   LYS     4      10.603   3.106  -9.111  1.00  0.00           C  
ATOM    430  O   LYS     4       9.530   2.614  -8.823  1.00  0.00           O  
ATOM    431  CB  LYS     4      11.677   3.244 -11.364  1.00  0.00           C  
ATOM    432  CG  LYS     4      11.878   4.120 -12.601  1.00  0.00           C  
ATOM    433  CD  LYS     4      13.299   4.688 -12.601  1.00  0.00           C  
ATOM    434  CE  LYS     4      13.404   5.802 -13.643  1.00  0.00           C  
ATOM    435  NZ  LYS     4      14.363   6.838 -13.167  1.00  0.00           N  
ATOM    436  H   LYS     4      12.319   5.458 -10.215  1.00  0.00           H  
ATOM    437  HA  LYS     4       9.803   4.139 -10.814  1.00  0.00           H  
ATOM    438 1HB  LYS     4      12.633   3.045 -10.902  1.00  0.00           H  
ATOM    439 2HB  LYS     4      11.217   2.312 -11.655  1.00  0.00           H  
ATOM    440 1HG  LYS     4      11.727   3.525 -13.490  1.00  0.00           H  
ATOM    441 2HG  LYS     4      11.168   4.933 -12.586  1.00  0.00           H  
ATOM    442 1HD  LYS     4      13.527   5.084 -11.622  1.00  0.00           H  
ATOM    443 2HD  LYS     4      14.000   3.902 -12.844  1.00  0.00           H  
ATOM    444 1HE  LYS     4      13.754   5.389 -14.578  1.00  0.00           H  
ATOM    445 2HE  LYS     4      12.432   6.251 -13.789  1.00  0.00           H  
ATOM    446 1HZ  LYS     4      14.077   7.168 -12.223  1.00  0.00           H  
ATOM    447 2HZ  LYS     4      15.317   6.430 -13.115  1.00  0.00           H  
ATOM    448 3HZ  LYS     4      14.364   7.640 -13.830  1.00  0.00           H  
ATOM    449  N   MET     5      11.657   2.915  -8.366  1.00  0.00           N  
ATOM    450  CA  MET     5      11.561   2.083  -7.134  1.00  0.00           C  
ATOM    451  C   MET     5      10.733   2.819  -6.080  1.00  0.00           C  
ATOM    452  O   MET     5      10.184   2.219  -5.177  1.00  0.00           O  
ATOM    453  CB  MET     5      12.966   1.824  -6.587  1.00  0.00           C  
ATOM    454  CG  MET     5      13.021   0.429  -5.965  1.00  0.00           C  
ATOM    455  SD  MET     5      12.772   0.555  -4.177  1.00  0.00           S  
ATOM    456  CE  MET     5      14.219  -0.410  -3.678  1.00  0.00           C  
ATOM    457  H   MET     5      12.514   3.320  -8.618  1.00  0.00           H  
ATOM    458  HA  MET     5      11.088   1.141  -7.371  1.00  0.00           H  
ATOM    459 1HB  MET     5      13.684   1.890  -7.391  1.00  0.00           H  
ATOM    460 2HB  MET     5      13.200   2.561  -5.834  1.00  0.00           H  
ATOM    461 1HG  MET     5      12.246  -0.188  -6.394  1.00  0.00           H  
ATOM    462 2HG  MET     5      13.985  -0.016  -6.163  1.00  0.00           H  
ATOM    463 1HE  MET     5      14.356  -1.233  -4.366  1.00  0.00           H  
ATOM    464 2HE  MET     5      15.094   0.224  -3.688  1.00  0.00           H  
ATOM    465 3HE  MET     5      14.069  -0.799  -2.684  1.00  0.00           H  
ATOM    466  N   SER     6      10.642   4.116  -6.182  1.00  0.00           N  
ATOM    467  CA  SER     6       9.853   4.889  -5.181  1.00  0.00           C  
ATOM    468  C   SER     6       8.363   4.808  -5.525  1.00  0.00           C  
ATOM    469  O   SER     6       7.514   4.816  -4.654  1.00  0.00           O  
ATOM    470  CB  SER     6      10.301   6.351  -5.200  1.00  0.00           C  
ATOM    471  OG  SER     6       9.533   7.090  -4.259  1.00  0.00           O  
ATOM    472  H   SER     6      11.094   4.583  -6.915  1.00  0.00           H  
ATOM    473  HA  SER     6      10.017   4.476  -4.197  1.00  0.00           H  
ATOM    474 1HB  SER     6      11.343   6.413  -4.935  1.00  0.00           H  
ATOM    475 2HB  SER     6      10.161   6.756  -6.193  1.00  0.00           H  
ATOM    476  HG  SER     6       9.847   6.868  -3.380  1.00  0.00           H  
ATOM    477  N   THR     7       8.040   4.728  -6.786  1.00  0.00           N  
ATOM    478  CA  THR     7       6.606   4.648  -7.182  1.00  0.00           C  
ATOM    479  C   THR     7       6.129   3.202  -7.051  1.00  0.00           C  
ATOM    480  O   THR     7       4.948   2.935  -6.939  1.00  0.00           O  
ATOM    481  CB  THR     7       6.451   5.110  -8.631  1.00  0.00           C  
ATOM    482  OG1 THR     7       7.571   4.672  -9.389  1.00  0.00           O  
ATOM    483  CG2 THR     7       6.369   6.636  -8.676  1.00  0.00           C  
ATOM    484  H   THR     7       8.739   4.719  -7.472  1.00  0.00           H  
ATOM    485  HA  THR     7       6.017   5.282  -6.535  1.00  0.00           H  
ATOM    486  HB  THR     7       5.547   4.693  -9.049  1.00  0.00           H  
ATOM    487  HG1 THR     7       7.250   4.094 -10.086  1.00  0.00           H  
ATOM    488 1HG2 THR     7       6.049   7.008  -7.714  1.00  0.00           H  
ATOM    489 2HG2 THR     7       7.342   7.042  -8.912  1.00  0.00           H  
ATOM    490 3HG2 THR     7       5.660   6.937  -9.433  1.00  0.00           H  
ATOM    491  N   ALA     8       7.039   2.268  -7.054  1.00  0.00           N  
ATOM    492  CA  ALA     8       6.641   0.842  -6.921  1.00  0.00           C  
ATOM    493  C   ALA     8       6.483   0.520  -5.439  1.00  0.00           C  
ATOM    494  O   ALA     8       5.561  -0.157  -5.031  1.00  0.00           O  
ATOM    495  CB  ALA     8       7.726  -0.047  -7.530  1.00  0.00           C  
ATOM    496  H   ALA     8       7.984   2.505  -7.133  1.00  0.00           H  
ATOM    497  HA  ALA     8       5.705   0.677  -7.430  1.00  0.00           H  
ATOM    498 1HB  ALA     8       8.684   0.446  -7.446  1.00  0.00           H  
ATOM    499 2HB  ALA     8       7.757  -0.988  -7.004  1.00  0.00           H  
ATOM    500 3HB  ALA     8       7.503  -0.224  -8.572  1.00  0.00           H  
ATOM    501  N   ILE     9       7.371   1.019  -4.630  1.00  0.00           N  
ATOM    502  CA  ILE     9       7.271   0.761  -3.171  1.00  0.00           C  
ATOM    503  C   ILE     9       6.054   1.507  -2.627  1.00  0.00           C  
ATOM    504  O   ILE     9       5.396   1.060  -1.708  1.00  0.00           O  
ATOM    505  CB  ILE     9       8.535   1.263  -2.475  1.00  0.00           C  
ATOM    506  CG1 ILE     9       8.713   2.756  -2.763  1.00  0.00           C  
ATOM    507  CG2 ILE     9       9.748   0.495  -3.003  1.00  0.00           C  
ATOM    508  CD1 ILE     9       8.165   3.571  -1.590  1.00  0.00           C  
ATOM    509  H   ILE     9       8.099   1.572  -4.981  1.00  0.00           H  
ATOM    510  HA  ILE     9       7.156  -0.297  -3.000  1.00  0.00           H  
ATOM    511  HB  ILE     9       8.446   1.108  -1.410  1.00  0.00           H  
ATOM    512 1HG1 ILE     9       9.763   2.973  -2.896  1.00  0.00           H  
ATOM    513 2HG1 ILE     9       8.175   3.015  -3.663  1.00  0.00           H  
ATOM    514 1HG2 ILE     9       9.588   0.241  -4.041  1.00  0.00           H  
ATOM    515 2HG2 ILE     9      10.630   1.111  -2.915  1.00  0.00           H  
ATOM    516 3HG2 ILE     9       9.880  -0.409  -2.427  1.00  0.00           H  
ATOM    517 1HD1 ILE     9       7.211   3.167  -1.286  1.00  0.00           H  
ATOM    518 2HD1 ILE     9       8.858   3.522  -0.763  1.00  0.00           H  
ATOM    519 3HD1 ILE     9       8.040   4.600  -1.895  1.00  0.00           H  
ATOM    520  N   SER    10       5.747   2.641  -3.197  1.00  0.00           N  
ATOM    521  CA  SER    10       4.569   3.419  -2.726  1.00  0.00           C  
ATOM    522  C   SER    10       3.291   2.651  -3.065  1.00  0.00           C  
ATOM    523  O   SER    10       2.449   2.424  -2.220  1.00  0.00           O  
ATOM    524  CB  SER    10       4.547   4.780  -3.421  1.00  0.00           C  
ATOM    525  OG  SER    10       5.669   5.543  -2.998  1.00  0.00           O  
ATOM    526  H   SER    10       6.291   2.978  -3.940  1.00  0.00           H  
ATOM    527  HA  SER    10       4.633   3.560  -1.658  1.00  0.00           H  
ATOM    528 1HB  SER    10       4.594   4.643  -4.489  1.00  0.00           H  
ATOM    529 2HB  SER    10       3.630   5.297  -3.168  1.00  0.00           H  
ATOM    530  HG  SER    10       6.372   4.931  -2.764  1.00  0.00           H  
ATOM    531  N   VAL    11       3.141   2.244  -4.297  1.00  0.00           N  
ATOM    532  CA  VAL    11       1.918   1.487  -4.686  1.00  0.00           C  
ATOM    533  C   VAL    11       1.762   0.275  -3.765  1.00  0.00           C  
ATOM    534  O   VAL    11       0.665  -0.125  -3.431  1.00  0.00           O  
ATOM    535  CB  VAL    11       2.050   1.019  -6.139  1.00  0.00           C  
ATOM    536  CG1 VAL    11       1.008  -0.063  -6.433  1.00  0.00           C  
ATOM    537  CG2 VAL    11       1.821   2.208  -7.076  1.00  0.00           C  
ATOM    538  H   VAL    11       3.834   2.435  -4.965  1.00  0.00           H  
ATOM    539  HA  VAL    11       1.053   2.126  -4.591  1.00  0.00           H  
ATOM    540  HB  VAL    11       3.041   0.618  -6.300  1.00  0.00           H  
ATOM    541 1HG1 VAL    11       0.318  -0.134  -5.604  1.00  0.00           H  
ATOM    542 2HG1 VAL    11       0.466   0.193  -7.331  1.00  0.00           H  
ATOM    543 3HG1 VAL    11       1.504  -1.013  -6.570  1.00  0.00           H  
ATOM    544 1HG2 VAL    11       1.207   2.944  -6.578  1.00  0.00           H  
ATOM    545 2HG2 VAL    11       2.771   2.649  -7.338  1.00  0.00           H  
ATOM    546 3HG2 VAL    11       1.322   1.869  -7.972  1.00  0.00           H  
ATOM    547  N   LEU    12       2.852  -0.313  -3.351  1.00  0.00           N  
ATOM    548  CA  LEU    12       2.764  -1.497  -2.451  1.00  0.00           C  
ATOM    549  C   LEU    12       2.077  -1.095  -1.144  1.00  0.00           C  
ATOM    550  O   LEU    12       1.191  -1.772  -0.662  1.00  0.00           O  
ATOM    551  CB  LEU    12       4.172  -2.014  -2.148  1.00  0.00           C  
ATOM    552  CG  LEU    12       4.711  -2.775  -3.360  1.00  0.00           C  
ATOM    553  CD1 LEU    12       6.172  -3.155  -3.115  1.00  0.00           C  
ATOM    554  CD2 LEU    12       3.883  -4.045  -3.572  1.00  0.00           C  
ATOM    555  H   LEU    12       3.729   0.025  -3.633  1.00  0.00           H  
ATOM    556  HA  LEU    12       2.192  -2.275  -2.935  1.00  0.00           H  
ATOM    557 1HB  LEU    12       4.822  -1.177  -1.930  1.00  0.00           H  
ATOM    558 2HB  LEU    12       4.138  -2.674  -1.296  1.00  0.00           H  
ATOM    559  HG  LEU    12       4.645  -2.148  -4.237  1.00  0.00           H  
ATOM    560 1HD1 LEU    12       6.719  -2.286  -2.783  1.00  0.00           H  
ATOM    561 2HD1 LEU    12       6.222  -3.922  -2.356  1.00  0.00           H  
ATOM    562 3HD1 LEU    12       6.606  -3.527  -4.031  1.00  0.00           H  
ATOM    563 1HD2 LEU    12       2.994  -4.001  -2.963  1.00  0.00           H  
ATOM    564 2HD2 LEU    12       3.605  -4.124  -4.612  1.00  0.00           H  
ATOM    565 3HD2 LEU    12       4.470  -4.908  -3.291  1.00  0.00           H  
ATOM    566  N   LEU    13       2.480   0.003  -0.565  1.00  0.00           N  
ATOM    567  CA  LEU    13       1.849   0.446   0.715  1.00  0.00           C  
ATOM    568  C   LEU    13       0.433   0.945   0.428  1.00  0.00           C  
ATOM    569  O   LEU    13      -0.406   1.003   1.304  1.00  0.00           O  
ATOM    570  CB  LEU    13       2.663   1.584   1.346  1.00  0.00           C  
ATOM    571  CG  LEU    13       4.116   1.532   0.866  1.00  0.00           C  
ATOM    572  CD1 LEU    13       4.973   2.439   1.747  1.00  0.00           C  
ATOM    573  CD2 LEU    13       4.635   0.095   0.952  1.00  0.00           C  
ATOM    574  H   LEU    13       3.197   0.533  -0.969  1.00  0.00           H  
ATOM    575  HA  LEU    13       1.804  -0.388   1.400  1.00  0.00           H  
ATOM    576 1HB  LEU    13       2.228   2.532   1.066  1.00  0.00           H  
ATOM    577 2HB  LEU    13       2.639   1.485   2.421  1.00  0.00           H  
ATOM    578  HG  LEU    13       4.169   1.876  -0.156  1.00  0.00           H  
ATOM    579 1HD1 LEU    13       4.356   2.881   2.515  1.00  0.00           H  
ATOM    580 2HD1 LEU    13       5.758   1.857   2.204  1.00  0.00           H  
ATOM    581 3HD1 LEU    13       5.409   3.220   1.141  1.00  0.00           H  
ATOM    582 1HD2 LEU    13       3.884  -0.532   1.410  1.00  0.00           H  
ATOM    583 2HD2 LEU    13       4.851  -0.269  -0.042  1.00  0.00           H  
ATOM    584 3HD2 LEU    13       5.536   0.071   1.547  1.00  0.00           H  
ATOM    585  N   ALA    14       0.165   1.312  -0.792  1.00  0.00           N  
ATOM    586  CA  ALA    14      -1.195   1.812  -1.139  1.00  0.00           C  
ATOM    587  C   ALA    14      -2.227   0.707  -0.903  1.00  0.00           C  
ATOM    588  O   ALA    14      -3.097   0.825  -0.064  1.00  0.00           O  
ATOM    589  CB  ALA    14      -1.224   2.233  -2.609  1.00  0.00           C  
ATOM    590  H   ALA    14       0.861   1.261  -1.480  1.00  0.00           H  
ATOM    591  HA  ALA    14      -1.433   2.663  -0.518  1.00  0.00           H  
ATOM    592 1HB  ALA    14      -0.433   2.944  -2.795  1.00  0.00           H  
ATOM    593 2HB  ALA    14      -1.082   1.365  -3.235  1.00  0.00           H  
ATOM    594 3HB  ALA    14      -2.178   2.687  -2.835  1.00  0.00           H  
ATOM    595  N   GLN    15      -2.140  -0.368  -1.640  1.00  0.00           N  
ATOM    596  CA  GLN    15      -3.119  -1.477  -1.460  1.00  0.00           C  
ATOM    597  C   GLN    15      -2.831  -2.212  -0.148  1.00  0.00           C  
ATOM    598  O   GLN    15      -3.694  -2.855   0.416  1.00  0.00           O  
ATOM    599  CB  GLN    15      -2.999  -2.456  -2.629  1.00  0.00           C  
ATOM    600  CG  GLN    15      -3.790  -1.923  -3.826  1.00  0.00           C  
ATOM    601  CD  GLN    15      -3.390  -2.692  -5.086  1.00  0.00           C  
ATOM    602  OE1 GLN    15      -2.608  -3.619  -5.023  1.00  0.00           O  
ATOM    603  NE2 GLN    15      -3.898  -2.344  -6.236  1.00  0.00           N  
ATOM    604  H   GLN    15      -1.432  -0.443  -2.314  1.00  0.00           H  
ATOM    605  HA  GLN    15      -4.120  -1.072  -1.433  1.00  0.00           H  
ATOM    606 1HB  GLN    15      -1.958  -2.562  -2.904  1.00  0.00           H  
ATOM    607 2HB  GLN    15      -3.395  -3.417  -2.338  1.00  0.00           H  
ATOM    608 1HG  GLN    15      -4.848  -2.052  -3.643  1.00  0.00           H  
ATOM    609 2HG  GLN    15      -3.573  -0.874  -3.962  1.00  0.00           H  
ATOM    610 1HE2 GLN    15      -3.648  -2.829  -7.049  1.00  0.00           H  
ATOM    611 2HE2 GLN    15      -4.529  -1.595  -6.286  1.00  0.00           H  
ATOM    612  N   ALA    16      -1.624  -2.124   0.342  1.00  0.00           N  
ATOM    613  CA  ALA    16      -1.283  -2.820   1.616  1.00  0.00           C  
ATOM    614  C   ALA    16      -1.935  -2.088   2.791  1.00  0.00           C  
ATOM    615  O   ALA    16      -2.884  -2.562   3.381  1.00  0.00           O  
ATOM    616  CB  ALA    16       0.236  -2.830   1.801  1.00  0.00           C  
ATOM    617  H   ALA    16      -0.942  -1.602  -0.129  1.00  0.00           H  
ATOM    618  HA  ALA    16      -1.647  -3.836   1.579  1.00  0.00           H  
ATOM    619 1HB  ALA    16       0.657  -1.935   1.366  1.00  0.00           H  
ATOM    620 2HB  ALA    16       0.471  -2.865   2.854  1.00  0.00           H  
ATOM    621 3HB  ALA    16       0.653  -3.698   1.311  1.00  0.00           H  
ATOM    622  N   VAL    17      -1.430  -0.935   3.137  1.00  0.00           N  
ATOM    623  CA  VAL    17      -2.015  -0.170   4.276  1.00  0.00           C  
ATOM    624  C   VAL    17      -3.510   0.056   4.035  1.00  0.00           C  
ATOM    625  O   VAL    17      -4.281   0.205   4.961  1.00  0.00           O  
ATOM    626  CB  VAL    17      -1.310   1.182   4.389  1.00  0.00           C  
ATOM    627  CG1 VAL    17      -2.077   2.082   5.358  1.00  0.00           C  
ATOM    628  CG2 VAL    17       0.114   0.971   4.908  1.00  0.00           C  
ATOM    629  H   VAL    17      -0.662  -0.575   2.649  1.00  0.00           H  
ATOM    630  HA  VAL    17      -1.877  -0.725   5.192  1.00  0.00           H  
ATOM    631  HB  VAL    17      -1.274   1.651   3.416  1.00  0.00           H  
ATOM    632 1HG1 VAL    17      -3.116   2.124   5.065  1.00  0.00           H  
ATOM    633 2HG1 VAL    17      -2.002   1.681   6.359  1.00  0.00           H  
ATOM    634 3HG1 VAL    17      -1.656   3.076   5.337  1.00  0.00           H  
ATOM    635 1HG2 VAL    17       0.453  -0.018   4.638  1.00  0.00           H  
ATOM    636 2HG2 VAL    17       0.770   1.710   4.470  1.00  0.00           H  
ATOM    637 3HG2 VAL    17       0.124   1.074   5.983  1.00  0.00           H  
ATOM    638  N   PHE    18      -3.922   0.088   2.798  1.00  0.00           N  
ATOM    639  CA  PHE    18      -5.365   0.311   2.497  1.00  0.00           C  
ATOM    640  C   PHE    18      -6.197  -0.845   3.062  1.00  0.00           C  
ATOM    641  O   PHE    18      -7.036  -0.656   3.919  1.00  0.00           O  
ATOM    642  CB  PHE    18      -5.556   0.387   0.978  1.00  0.00           C  
ATOM    643  CG  PHE    18      -7.024   0.278   0.641  1.00  0.00           C  
ATOM    644  CD1 PHE    18      -7.987   0.759   1.537  1.00  0.00           C  
ATOM    645  CD2 PHE    18      -7.423  -0.304  -0.568  1.00  0.00           C  
ATOM    646  CE1 PHE    18      -9.348   0.656   1.223  1.00  0.00           C  
ATOM    647  CE2 PHE    18      -8.783  -0.406  -0.882  1.00  0.00           C  
ATOM    648  CZ  PHE    18      -9.745   0.073   0.014  1.00  0.00           C  
ATOM    649  H   PHE    18      -3.282  -0.030   2.066  1.00  0.00           H  
ATOM    650  HA  PHE    18      -5.686   1.239   2.945  1.00  0.00           H  
ATOM    651 1HB  PHE    18      -5.172   1.330   0.617  1.00  0.00           H  
ATOM    652 2HB  PHE    18      -5.018  -0.423   0.508  1.00  0.00           H  
ATOM    653  HD1 PHE    18      -7.681   1.208   2.470  1.00  0.00           H  
ATOM    654  HD2 PHE    18      -6.680  -0.674  -1.259  1.00  0.00           H  
ATOM    655  HE1 PHE    18     -10.091   1.026   1.915  1.00  0.00           H  
ATOM    656  HE2 PHE    18      -9.090  -0.856  -1.815  1.00  0.00           H  
ATOM    657  HZ  PHE    18     -10.795  -0.005  -0.228  1.00  0.00           H  
ATOM    658  N   LEU    19      -5.979  -2.037   2.579  1.00  0.00           N  
ATOM    659  CA  LEU    19      -6.765  -3.200   3.080  1.00  0.00           C  
ATOM    660  C   LEU    19      -6.378  -3.509   4.529  1.00  0.00           C  
ATOM    661  O   LEU    19      -7.086  -4.200   5.233  1.00  0.00           O  
ATOM    662  CB  LEU    19      -6.481  -4.418   2.201  1.00  0.00           C  
ATOM    663  CG  LEU    19      -7.062  -4.183   0.808  1.00  0.00           C  
ATOM    664  CD1 LEU    19      -6.748  -5.383  -0.087  1.00  0.00           C  
ATOM    665  CD2 LEU    19      -8.579  -4.009   0.911  1.00  0.00           C  
ATOM    666  H   LEU    19      -5.302  -2.167   1.882  1.00  0.00           H  
ATOM    667  HA  LEU    19      -7.818  -2.965   3.035  1.00  0.00           H  
ATOM    668 1HB  LEU    19      -5.413  -4.568   2.127  1.00  0.00           H  
ATOM    669 2HB  LEU    19      -6.939  -5.293   2.637  1.00  0.00           H  
ATOM    670  HG  LEU    19      -6.624  -3.291   0.380  1.00  0.00           H  
ATOM    671 1HD1 LEU    19      -6.925  -6.296   0.460  1.00  0.00           H  
ATOM    672 2HD1 LEU    19      -7.383  -5.357  -0.961  1.00  0.00           H  
ATOM    673 3HD1 LEU    19      -5.713  -5.342  -0.393  1.00  0.00           H  
ATOM    674 1HD2 LEU    19      -8.952  -4.592   1.741  1.00  0.00           H  
ATOM    675 2HD2 LEU    19      -8.812  -2.966   1.068  1.00  0.00           H  
ATOM    676 3HD2 LEU    19      -9.044  -4.348  -0.003  1.00  0.00           H  
ATOM    677  N   LEU    20      -5.264  -3.004   4.984  1.00  0.00           N  
ATOM    678  CA  LEU    20      -4.848  -3.275   6.389  1.00  0.00           C  
ATOM    679  C   LEU    20      -5.818  -2.579   7.345  1.00  0.00           C  
ATOM    680  O   LEU    20      -6.359  -3.186   8.246  1.00  0.00           O  
ATOM    681  CB  LEU    20      -3.432  -2.744   6.619  1.00  0.00           C  
ATOM    682  CG  LEU    20      -2.776  -3.523   7.760  1.00  0.00           C  
ATOM    683  CD1 LEU    20      -3.647  -3.425   9.014  1.00  0.00           C  
ATOM    684  CD2 LEU    20      -2.627  -4.992   7.357  1.00  0.00           C  
ATOM    685  H   LEU    20      -4.706  -2.445   4.404  1.00  0.00           H  
ATOM    686  HA  LEU    20      -4.868  -4.340   6.570  1.00  0.00           H  
ATOM    687 1HB  LEU    20      -2.850  -2.868   5.717  1.00  0.00           H  
ATOM    688 2HB  LEU    20      -3.477  -1.698   6.878  1.00  0.00           H  
ATOM    689  HG  LEU    20      -1.800  -3.104   7.967  1.00  0.00           H  
ATOM    690 1HD1 LEU    20      -4.060  -2.430   9.089  1.00  0.00           H  
ATOM    691 2HD1 LEU    20      -4.451  -4.144   8.949  1.00  0.00           H  
ATOM    692 3HD1 LEU    20      -3.048  -3.632   9.887  1.00  0.00           H  
ATOM    693 1HD2 LEU    20      -2.760  -5.088   6.289  1.00  0.00           H  
ATOM    694 2HD2 LEU    20      -1.644  -5.344   7.630  1.00  0.00           H  
ATOM    695 3HD2 LEU    20      -3.374  -5.583   7.867  1.00  0.00           H  
ATOM    696  N   LEU    21      -6.044  -1.308   7.151  1.00  0.00           N  
ATOM    697  CA  LEU    21      -6.983  -0.574   8.046  1.00  0.00           C  
ATOM    698  C   LEU    21      -8.401  -1.107   7.835  1.00  0.00           C  
ATOM    699  O   LEU    21      -9.116  -1.385   8.778  1.00  0.00           O  
ATOM    700  CB  LEU    21      -6.943   0.919   7.713  1.00  0.00           C  
ATOM    701  CG  LEU    21      -7.964   1.663   8.575  1.00  0.00           C  
ATOM    702  CD1 LEU    21      -7.586   1.524  10.050  1.00  0.00           C  
ATOM    703  CD2 LEU    21      -7.972   3.144   8.188  1.00  0.00           C  
ATOM    704  H   LEU    21      -5.599  -0.838   6.416  1.00  0.00           H  
ATOM    705  HA  LEU    21      -6.691  -0.722   9.074  1.00  0.00           H  
ATOM    706 1HB  LEU    21      -5.954   1.306   7.912  1.00  0.00           H  
ATOM    707 2HB  LEU    21      -7.183   1.062   6.670  1.00  0.00           H  
ATOM    708  HG  LEU    21      -8.946   1.242   8.413  1.00  0.00           H  
ATOM    709 1HD1 LEU    21      -6.548   1.789  10.182  1.00  0.00           H  
ATOM    710 2HD1 LEU    21      -8.204   2.182  10.643  1.00  0.00           H  
ATOM    711 3HD1 LEU    21      -7.741   0.503  10.367  1.00  0.00           H  
ATOM    712 1HD2 LEU    21      -8.009   3.234   7.112  1.00  0.00           H  
ATOM    713 2HD2 LEU    21      -8.838   3.625   8.619  1.00  0.00           H  
ATOM    714 3HD2 LEU    21      -7.075   3.618   8.558  1.00  0.00           H  
ATOM    715  N   THR    22      -8.814  -1.257   6.605  1.00  0.00           N  
ATOM    716  CA  THR    22     -10.185  -1.778   6.338  1.00  0.00           C  
ATOM    717  C   THR    22     -10.259  -3.244   6.768  1.00  0.00           C  
ATOM    718  O   THR    22     -11.326  -3.810   6.898  1.00  0.00           O  
ATOM    719  CB  THR    22     -10.494  -1.668   4.843  1.00  0.00           C  
ATOM    720  OG1 THR    22      -9.636  -0.700   4.254  1.00  0.00           O  
ATOM    721  CG2 THR    22     -11.951  -1.246   4.649  1.00  0.00           C  
ATOM    722  H   THR    22      -8.221  -1.030   5.857  1.00  0.00           H  
ATOM    723  HA  THR    22     -10.905  -1.199   6.899  1.00  0.00           H  
ATOM    724  HB  THR    22     -10.334  -2.625   4.371  1.00  0.00           H  
ATOM    725  HG1 THR    22      -9.986  -0.483   3.387  1.00  0.00           H  
ATOM    726 1HG2 THR    22     -12.211  -0.501   5.386  1.00  0.00           H  
ATOM    727 2HG2 THR    22     -12.078  -0.834   3.660  1.00  0.00           H  
ATOM    728 3HG2 THR    22     -12.593  -2.106   4.767  1.00  0.00           H  
ATOM    729  N   SER    23      -9.132  -3.863   6.990  1.00  0.00           N  
ATOM    730  CA  SER    23      -9.134  -5.291   7.411  1.00  0.00           C  
ATOM    731  C   SER    23      -9.466  -5.383   8.902  1.00  0.00           C  
ATOM    732  O   SER    23     -10.509  -5.875   9.285  1.00  0.00           O  
ATOM    733  CB  SER    23      -7.754  -5.901   7.156  1.00  0.00           C  
ATOM    734  OG  SER    23      -7.745  -6.526   5.879  1.00  0.00           O  
ATOM    735  H   SER    23      -8.282  -3.386   6.879  1.00  0.00           H  
ATOM    736  HA  SER    23      -9.877  -5.832   6.843  1.00  0.00           H  
ATOM    737 1HB  SER    23      -7.007  -5.126   7.177  1.00  0.00           H  
ATOM    738 2HB  SER    23      -7.537  -6.629   7.927  1.00  0.00           H  
ATOM    739  HG  SER    23      -7.509  -7.448   6.002  1.00  0.00           H  
ATOM    740  N   GLN    24      -8.587  -4.916   9.745  1.00  0.00           N  
ATOM    741  CA  GLN    24      -8.852  -4.978  11.210  1.00  0.00           C  
ATOM    742  C   GLN    24      -9.824  -3.862  11.606  1.00  0.00           C  
ATOM    743  O   GLN    24     -10.231  -3.758  12.745  1.00  0.00           O  
ATOM    744  CB  GLN    24      -7.537  -4.802  11.969  1.00  0.00           C  
ATOM    745  CG  GLN    24      -6.500  -5.792  11.432  1.00  0.00           C  
ATOM    746  CD  GLN    24      -5.476  -6.104  12.524  1.00  0.00           C  
ATOM    747  OE1 GLN    24      -4.828  -7.130  12.488  1.00  0.00           O  
ATOM    748  NE2 GLN    24      -5.302  -5.256  13.500  1.00  0.00           N  
ATOM    749  H   GLN    24      -7.751  -4.525   9.417  1.00  0.00           H  
ATOM    750  HA  GLN    24      -9.285  -5.937  11.457  1.00  0.00           H  
ATOM    751 1HB  GLN    24      -7.176  -3.793  11.833  1.00  0.00           H  
ATOM    752 2HB  GLN    24      -7.699  -4.989  13.019  1.00  0.00           H  
ATOM    753 1HG  GLN    24      -6.997  -6.703  11.130  1.00  0.00           H  
ATOM    754 2HG  GLN    24      -5.996  -5.358  10.581  1.00  0.00           H  
ATOM    755 1HE2 GLN    24      -5.825  -4.427  13.529  1.00  0.00           H  
ATOM    756 2HE2 GLN    24      -4.648  -5.447  14.205  1.00  0.00           H  
ATOM    757  N   ARG    25     -10.198  -3.027  10.675  1.00  0.00           N  
ATOM    758  CA  ARG    25     -11.143  -1.922  11.003  1.00  0.00           C  
ATOM    759  C   ARG    25     -12.049  -1.652   9.801  1.00  0.00           C  
ATOM    760  O   ARG    25     -13.030  -2.362   9.652  1.00  0.00           O  
ATOM    761  CB  ARG    25     -10.351  -0.656  11.338  1.00  0.00           C  
ATOM    762  CG  ARG    25     -10.705  -0.189  12.752  1.00  0.00           C  
ATOM    763  CD  ARG    25      -9.587  -0.587  13.715  1.00  0.00           C  
ATOM    764  NE  ARG    25      -8.725   0.596  13.994  1.00  0.00           N  
ATOM    765  CZ  ARG    25      -7.545   0.432  14.527  1.00  0.00           C  
ATOM    766  NH1 ARG    25      -7.227  -0.712  15.067  1.00  0.00           N  
ATOM    767  NH2 ARG    25      -6.683   1.412  14.519  1.00  0.00           N  
ATOM    768  OXT ARG    25     -11.747  -0.739   9.051  1.00  0.00           O  
ATOM    769  H   ARG    25      -9.860  -3.126   9.761  1.00  0.00           H  
ATOM    770  HA  ARG    25     -11.746  -2.205  11.853  1.00  0.00           H  
ATOM    771 1HB  ARG    25      -9.293  -0.869  11.282  1.00  0.00           H  
ATOM    772 2HB  ARG    25     -10.600   0.121  10.632  1.00  0.00           H  
ATOM    773 1HG  ARG    25     -10.820   0.886  12.757  1.00  0.00           H  
ATOM    774 2HG  ARG    25     -11.629  -0.653  13.064  1.00  0.00           H  
ATOM    775 1HD  ARG    25     -10.017  -0.945  14.639  1.00  0.00           H  
ATOM    776 2HD  ARG    25      -8.990  -1.370  13.270  1.00  0.00           H  
ATOM    777  HE  ARG    25      -9.044   1.497  13.776  1.00  0.00           H  
ATOM    778 1HH1 ARG    25      -7.888  -1.463  15.072  1.00  0.00           H  
ATOM    779 2HH1 ARG    25      -6.324  -0.838  15.476  1.00  0.00           H  
ATOM    780 1HH2 ARG    25      -6.927   2.288  14.105  1.00  0.00           H  
ATOM    781 2HH2 ARG    25      -5.780   1.285  14.928  1.00  0.00           H  
TER     782      ARG    25                                                      
ENDMDL                                                                          
MODEL        3                                                                  
ATOM    783  N   GLY     1      17.294   2.900  -8.114  1.00  0.00           N  
ATOM    784  CA  GLY     1      15.844   3.111  -8.549  1.00  0.00           C  
ATOM    785  C   GLY     1      15.346   4.497  -8.779  1.00  0.00           C  
ATOM    786  O   GLY     1      14.493   4.730  -9.613  1.00  0.00           O  
ATOM    787 1H   GLY     1      17.917   3.517  -8.673  1.00  0.00           H  
ATOM    788 2H   GLY     1      17.391   3.134  -7.106  1.00  0.00           H  
ATOM    789 3H   GLY     1      17.561   1.907  -8.268  1.00  0.00           H  
ATOM    790 1HA  GLY     1      15.747   3.029  -9.516  1.00  0.00           H  
ATOM    791 2HA  GLY     1      15.196   2.340  -7.957  1.00  0.00           H  
ATOM    792  N   SER     2      15.859   5.450  -8.050  1.00  0.00           N  
ATOM    793  CA  SER     2      15.404   6.857  -8.231  1.00  0.00           C  
ATOM    794  C   SER     2      13.950   6.984  -7.773  1.00  0.00           C  
ATOM    795  O   SER     2      13.426   6.124  -7.093  1.00  0.00           O  
ATOM    796  CB  SER     2      15.508   7.246  -9.706  1.00  0.00           C  
ATOM    797  OG  SER     2      15.662   8.656  -9.811  1.00  0.00           O  
ATOM    798  H   SER     2      16.546   5.239  -7.382  1.00  0.00           H  
ATOM    799  HA  SER     2      16.025   7.515  -7.640  1.00  0.00           H  
ATOM    800 1HB  SER     2      16.364   6.763 -10.148  1.00  0.00           H  
ATOM    801 2HB  SER     2      14.612   6.931 -10.225  1.00  0.00           H  
ATOM    802  HG  SER     2      16.580   8.869  -9.631  1.00  0.00           H  
ATOM    803  N   GLU     3      13.292   8.049  -8.142  1.00  0.00           N  
ATOM    804  CA  GLU     3      11.872   8.225  -7.730  1.00  0.00           C  
ATOM    805  C   GLU     3      11.002   7.209  -8.471  1.00  0.00           C  
ATOM    806  O   GLU     3       9.861   6.981  -8.119  1.00  0.00           O  
ATOM    807  CB  GLU     3      11.412   9.642  -8.073  1.00  0.00           C  
ATOM    808  CG  GLU     3      11.580   9.882  -9.574  1.00  0.00           C  
ATOM    809  CD  GLU     3      10.265  10.399 -10.161  1.00  0.00           C  
ATOM    810  OE1 GLU     3       9.446   9.578 -10.540  1.00  0.00           O  
ATOM    811  OE2 GLU     3      10.100  11.606 -10.223  1.00  0.00           O  
ATOM    812  H   GLU     3      13.731   8.730  -8.692  1.00  0.00           H  
ATOM    813  HA  GLU     3      11.785   8.065  -6.665  1.00  0.00           H  
ATOM    814 1HB  GLU     3      10.372   9.760  -7.803  1.00  0.00           H  
ATOM    815 2HB  GLU     3      12.009  10.358  -7.527  1.00  0.00           H  
ATOM    816 1HG  GLU     3      12.360  10.613  -9.737  1.00  0.00           H  
ATOM    817 2HG  GLU     3      11.848   8.956 -10.058  1.00  0.00           H  
ATOM    818  N   LYS     4      11.531   6.593  -9.493  1.00  0.00           N  
ATOM    819  CA  LYS     4      10.735   5.589 -10.251  1.00  0.00           C  
ATOM    820  C   LYS     4      10.544   4.340  -9.389  1.00  0.00           C  
ATOM    821  O   LYS     4       9.444   4.010  -8.991  1.00  0.00           O  
ATOM    822  CB  LYS     4      11.472   5.219 -11.540  1.00  0.00           C  
ATOM    823  CG  LYS     4      10.803   5.915 -12.727  1.00  0.00           C  
ATOM    824  CD  LYS     4      11.055   7.420 -12.643  1.00  0.00           C  
ATOM    825  CE  LYS     4      10.219   8.138 -13.704  1.00  0.00           C  
ATOM    826  NZ  LYS     4      10.995   8.226 -14.973  1.00  0.00           N  
ATOM    827  H   LYS     4      12.455   6.788  -9.758  1.00  0.00           H  
ATOM    828  HA  LYS     4       9.770   6.008 -10.496  1.00  0.00           H  
ATOM    829 1HB  LYS     4      12.502   5.536 -11.469  1.00  0.00           H  
ATOM    830 2HB  LYS     4      11.432   4.149 -11.683  1.00  0.00           H  
ATOM    831 1HG  LYS     4      11.213   5.530 -13.648  1.00  0.00           H  
ATOM    832 2HG  LYS     4       9.739   5.728 -12.700  1.00  0.00           H  
ATOM    833 1HD  LYS     4      10.777   7.778 -11.660  1.00  0.00           H  
ATOM    834 2HD  LYS     4      12.102   7.620 -12.815  1.00  0.00           H  
ATOM    835 1HE  LYS     4       9.307   7.586 -13.878  1.00  0.00           H  
ATOM    836 2HE  LYS     4       9.977   9.133 -13.361  1.00  0.00           H  
ATOM    837 1HZ  LYS     4      11.988   7.976 -14.792  1.00  0.00           H  
ATOM    838 2HZ  LYS     4      10.596   7.566 -15.671  1.00  0.00           H  
ATOM    839 3HZ  LYS     4      10.943   9.197 -15.345  1.00  0.00           H  
ATOM    840  N   MET     5      11.608   3.643  -9.091  1.00  0.00           N  
ATOM    841  CA  MET     5      11.480   2.422  -8.247  1.00  0.00           C  
ATOM    842  C   MET     5      10.933   2.817  -6.875  1.00  0.00           C  
ATOM    843  O   MET     5      10.316   2.027  -6.188  1.00  0.00           O  
ATOM    844  CB  MET     5      12.852   1.762  -8.083  1.00  0.00           C  
ATOM    845  CG  MET     5      12.669   0.314  -7.624  1.00  0.00           C  
ATOM    846  SD  MET     5      14.023  -0.146  -6.515  1.00  0.00           S  
ATOM    847  CE  MET     5      13.735  -1.932  -6.542  1.00  0.00           C  
ATOM    848  H   MET     5      12.488   3.927  -9.416  1.00  0.00           H  
ATOM    849  HA  MET     5      10.800   1.728  -8.720  1.00  0.00           H  
ATOM    850 1HB  MET     5      13.373   1.777  -9.030  1.00  0.00           H  
ATOM    851 2HB  MET     5      13.426   2.303  -7.346  1.00  0.00           H  
ATOM    852 1HG  MET     5      11.728   0.218  -7.102  1.00  0.00           H  
ATOM    853 2HG  MET     5      12.671  -0.339  -8.483  1.00  0.00           H  
ATOM    854 1HE  MET     5      13.310  -2.214  -7.493  1.00  0.00           H  
ATOM    855 2HE  MET     5      14.674  -2.448  -6.403  1.00  0.00           H  
ATOM    856 3HE  MET     5      13.050  -2.197  -5.749  1.00  0.00           H  
ATOM    857  N   SER     6      11.149   4.039  -6.473  1.00  0.00           N  
ATOM    858  CA  SER     6      10.638   4.489  -5.147  1.00  0.00           C  
ATOM    859  C   SER     6       9.124   4.696  -5.234  1.00  0.00           C  
ATOM    860  O   SER     6       8.404   4.510  -4.272  1.00  0.00           O  
ATOM    861  CB  SER     6      11.316   5.805  -4.761  1.00  0.00           C  
ATOM    862  OG  SER     6      10.447   6.890  -5.065  1.00  0.00           O  
ATOM    863  H   SER     6      11.646   4.663  -7.044  1.00  0.00           H  
ATOM    864  HA  SER     6      10.858   3.739  -4.402  1.00  0.00           H  
ATOM    865 1HB  SER     6      11.529   5.806  -3.705  1.00  0.00           H  
ATOM    866 2HB  SER     6      12.241   5.906  -5.313  1.00  0.00           H  
ATOM    867  HG  SER     6       9.918   7.072  -4.284  1.00  0.00           H  
ATOM    868  N   THR     7       8.636   5.074  -6.384  1.00  0.00           N  
ATOM    869  CA  THR     7       7.170   5.287  -6.539  1.00  0.00           C  
ATOM    870  C   THR     7       6.488   3.931  -6.710  1.00  0.00           C  
ATOM    871  O   THR     7       5.307   3.779  -6.466  1.00  0.00           O  
ATOM    872  CB  THR     7       6.909   6.150  -7.775  1.00  0.00           C  
ATOM    873  OG1 THR     7       7.537   7.414  -7.611  1.00  0.00           O  
ATOM    874  CG2 THR     7       5.403   6.346  -7.955  1.00  0.00           C  
ATOM    875  H   THR     7       9.233   5.211  -7.148  1.00  0.00           H  
ATOM    876  HA  THR     7       6.779   5.781  -5.661  1.00  0.00           H  
ATOM    877  HB  THR     7       7.310   5.659  -8.648  1.00  0.00           H  
ATOM    878  HG1 THR     7       7.195   8.005  -8.285  1.00  0.00           H  
ATOM    879 1HG2 THR     7       4.898   6.133  -7.025  1.00  0.00           H  
ATOM    880 2HG2 THR     7       5.205   7.366  -8.248  1.00  0.00           H  
ATOM    881 3HG2 THR     7       5.042   5.676  -8.722  1.00  0.00           H  
ATOM    882  N   ALA     8       7.230   2.941  -7.119  1.00  0.00           N  
ATOM    883  CA  ALA     8       6.640   1.592  -7.296  1.00  0.00           C  
ATOM    884  C   ALA     8       6.558   0.924  -5.928  1.00  0.00           C  
ATOM    885  O   ALA     8       5.608   0.237  -5.608  1.00  0.00           O  
ATOM    886  CB  ALA     8       7.532   0.767  -8.225  1.00  0.00           C  
ATOM    887  H   ALA     8       8.184   3.083  -7.297  1.00  0.00           H  
ATOM    888  HA  ALA     8       5.651   1.679  -7.719  1.00  0.00           H  
ATOM    889 1HB  ALA     8       7.723   1.328  -9.129  1.00  0.00           H  
ATOM    890 2HB  ALA     8       8.466   0.555  -7.730  1.00  0.00           H  
ATOM    891 3HB  ALA     8       7.035  -0.158  -8.473  1.00  0.00           H  
ATOM    892  N   ILE     9       7.550   1.142  -5.112  1.00  0.00           N  
ATOM    893  CA  ILE     9       7.539   0.542  -3.756  1.00  0.00           C  
ATOM    894  C   ILE     9       6.414   1.185  -2.945  1.00  0.00           C  
ATOM    895  O   ILE     9       5.740   0.535  -2.171  1.00  0.00           O  
ATOM    896  CB  ILE     9       8.884   0.797  -3.072  1.00  0.00           C  
ATOM    897  CG1 ILE     9       9.176   2.299  -3.060  1.00  0.00           C  
ATOM    898  CG2 ILE     9       9.989   0.072  -3.840  1.00  0.00           C  
ATOM    899  CD1 ILE     9      10.384   2.577  -2.161  1.00  0.00           C  
ATOM    900  H   ILE     9       8.297   1.710  -5.391  1.00  0.00           H  
ATOM    901  HA  ILE     9       7.367  -0.519  -3.835  1.00  0.00           H  
ATOM    902  HB  ILE     9       8.847   0.427  -2.057  1.00  0.00           H  
ATOM    903 1HG1 ILE     9       9.391   2.631  -4.066  1.00  0.00           H  
ATOM    904 2HG1 ILE     9       8.318   2.831  -2.681  1.00  0.00           H  
ATOM    905 1HG2 ILE     9       9.699  -0.032  -4.875  1.00  0.00           H  
ATOM    906 2HG2 ILE     9      10.903   0.645  -3.780  1.00  0.00           H  
ATOM    907 3HG2 ILE     9      10.147  -0.905  -3.409  1.00  0.00           H  
ATOM    908 1HD1 ILE     9      10.330   1.950  -1.283  1.00  0.00           H  
ATOM    909 2HD1 ILE     9      11.293   2.362  -2.702  1.00  0.00           H  
ATOM    910 3HD1 ILE     9      10.380   3.615  -1.864  1.00  0.00           H  
ATOM    911  N   SER    10       6.199   2.460  -3.128  1.00  0.00           N  
ATOM    912  CA  SER    10       5.110   3.148  -2.381  1.00  0.00           C  
ATOM    913  C   SER    10       3.761   2.614  -2.863  1.00  0.00           C  
ATOM    914  O   SER    10       2.843   2.425  -2.090  1.00  0.00           O  
ATOM    915  CB  SER    10       5.183   4.654  -2.639  1.00  0.00           C  
ATOM    916  OG  SER    10       6.519   5.098  -2.452  1.00  0.00           O  
ATOM    917  H   SER    10       6.750   2.964  -3.765  1.00  0.00           H  
ATOM    918  HA  SER    10       5.218   2.955  -1.324  1.00  0.00           H  
ATOM    919 1HB  SER    10       4.877   4.863  -3.650  1.00  0.00           H  
ATOM    920 2HB  SER    10       4.522   5.167  -1.952  1.00  0.00           H  
ATOM    921  HG  SER    10       6.512   6.059  -2.430  1.00  0.00           H  
ATOM    922  N   VAL    11       3.634   2.367  -4.138  1.00  0.00           N  
ATOM    923  CA  VAL    11       2.347   1.841  -4.673  1.00  0.00           C  
ATOM    924  C   VAL    11       2.020   0.511  -3.989  1.00  0.00           C  
ATOM    925  O   VAL    11       0.881   0.234  -3.666  1.00  0.00           O  
ATOM    926  CB  VAL    11       2.476   1.628  -6.183  1.00  0.00           C  
ATOM    927  CG1 VAL    11       1.207   0.965  -6.722  1.00  0.00           C  
ATOM    928  CG2 VAL    11       2.672   2.980  -6.872  1.00  0.00           C  
ATOM    929  H   VAL    11       4.389   2.525  -4.745  1.00  0.00           H  
ATOM    930  HA  VAL    11       1.557   2.551  -4.474  1.00  0.00           H  
ATOM    931  HB  VAL    11       3.326   0.993  -6.385  1.00  0.00           H  
ATOM    932 1HG1 VAL    11       0.342   1.515  -6.384  1.00  0.00           H  
ATOM    933 2HG1 VAL    11       1.233   0.963  -7.802  1.00  0.00           H  
ATOM    934 3HG1 VAL    11       1.151  -0.052  -6.361  1.00  0.00           H  
ATOM    935 1HG2 VAL    11       2.704   3.762  -6.127  1.00  0.00           H  
ATOM    936 2HG2 VAL    11       3.599   2.972  -7.426  1.00  0.00           H  
ATOM    937 3HG2 VAL    11       1.850   3.161  -7.549  1.00  0.00           H  
ATOM    938  N   LEU    12       3.006  -0.314  -3.759  1.00  0.00           N  
ATOM    939  CA  LEU    12       2.740  -1.618  -3.087  1.00  0.00           C  
ATOM    940  C   LEU    12       2.177  -1.355  -1.687  1.00  0.00           C  
ATOM    941  O   LEU    12       1.213  -1.966  -1.267  1.00  0.00           O  
ATOM    942  CB  LEU    12       4.044  -2.413  -2.973  1.00  0.00           C  
ATOM    943  CG  LEU    12       4.195  -3.326  -4.191  1.00  0.00           C  
ATOM    944  CD1 LEU    12       5.679  -3.617  -4.426  1.00  0.00           C  
ATOM    945  CD2 LEU    12       3.453  -4.640  -3.937  1.00  0.00           C  
ATOM    946  H   LEU    12       3.921  -0.073  -4.023  1.00  0.00           H  
ATOM    947  HA  LEU    12       2.022  -2.182  -3.664  1.00  0.00           H  
ATOM    948 1HB  LEU    12       4.879  -1.730  -2.928  1.00  0.00           H  
ATOM    949 2HB  LEU    12       4.022  -3.014  -2.076  1.00  0.00           H  
ATOM    950  HG  LEU    12       3.781  -2.837  -5.061  1.00  0.00           H  
ATOM    951 1HD1 LEU    12       6.160  -3.822  -3.482  1.00  0.00           H  
ATOM    952 2HD1 LEU    12       5.779  -4.475  -5.076  1.00  0.00           H  
ATOM    953 3HD1 LEU    12       6.144  -2.759  -4.889  1.00  0.00           H  
ATOM    954 1HD2 LEU    12       2.996  -4.613  -2.959  1.00  0.00           H  
ATOM    955 2HD2 LEU    12       2.689  -4.773  -4.688  1.00  0.00           H  
ATOM    956 3HD2 LEU    12       4.150  -5.463  -3.986  1.00  0.00           H  
ATOM    957  N   LEU    13       2.772  -0.446  -0.965  1.00  0.00           N  
ATOM    958  CA  LEU    13       2.272  -0.136   0.408  1.00  0.00           C  
ATOM    959  C   LEU    13       0.883   0.495   0.305  1.00  0.00           C  
ATOM    960  O   LEU    13       0.085   0.415   1.217  1.00  0.00           O  
ATOM    961  CB  LEU    13       3.220   0.847   1.109  1.00  0.00           C  
ATOM    962  CG  LEU    13       4.639   0.708   0.550  1.00  0.00           C  
ATOM    963  CD1 LEU    13       5.625   1.405   1.484  1.00  0.00           C  
ATOM    964  CD2 LEU    13       5.003  -0.775   0.435  1.00  0.00           C  
ATOM    965  H   LEU    13       3.544   0.035  -1.327  1.00  0.00           H  
ATOM    966  HA  LEU    13       2.211  -1.049   0.981  1.00  0.00           H  
ATOM    967 1HB  LEU    13       2.870   1.857   0.950  1.00  0.00           H  
ATOM    968 2HB  LEU    13       3.233   0.635   2.168  1.00  0.00           H  
ATOM    969  HG  LEU    13       4.686   1.170  -0.427  1.00  0.00           H  
ATOM    970 1HD1 LEU    13       5.215   1.436   2.482  1.00  0.00           H  
ATOM    971 2HD1 LEU    13       6.557   0.862   1.493  1.00  0.00           H  
ATOM    972 3HD1 LEU    13       5.798   2.413   1.135  1.00  0.00           H  
ATOM    973 1HD2 LEU    13       4.226  -1.372   0.890  1.00  0.00           H  
ATOM    974 2HD2 LEU    13       5.096  -1.044  -0.609  1.00  0.00           H  
ATOM    975 3HD2 LEU    13       5.939  -0.957   0.938  1.00  0.00           H  
ATOM    976  N   ALA    14       0.593   1.122  -0.801  1.00  0.00           N  
ATOM    977  CA  ALA    14      -0.742   1.761  -0.971  1.00  0.00           C  
ATOM    978  C   ALA    14      -1.838   0.753  -0.614  1.00  0.00           C  
ATOM    979  O   ALA    14      -2.476   0.851   0.418  1.00  0.00           O  
ATOM    980  CB  ALA    14      -0.908   2.206  -2.427  1.00  0.00           C  
ATOM    981  H   ALA    14       1.256   1.172  -1.522  1.00  0.00           H  
ATOM    982  HA  ALA    14      -0.816   2.619  -0.320  1.00  0.00           H  
ATOM    983 1HB  ALA    14      -0.796   1.353  -3.080  1.00  0.00           H  
ATOM    984 2HB  ALA    14      -1.888   2.637  -2.563  1.00  0.00           H  
ATOM    985 3HB  ALA    14      -0.155   2.943  -2.665  1.00  0.00           H  
ATOM    986  N   GLN    15      -2.061  -0.218  -1.455  1.00  0.00           N  
ATOM    987  CA  GLN    15      -3.112  -1.231  -1.159  1.00  0.00           C  
ATOM    988  C   GLN    15      -2.794  -1.921   0.169  1.00  0.00           C  
ATOM    989  O   GLN    15      -3.677  -2.255   0.933  1.00  0.00           O  
ATOM    990  CB  GLN    15      -3.148  -2.274  -2.280  1.00  0.00           C  
ATOM    991  CG  GLN    15      -1.904  -3.162  -2.191  1.00  0.00           C  
ATOM    992  CD  GLN    15      -1.905  -4.155  -3.355  1.00  0.00           C  
ATOM    993  OE1 GLN    15      -2.341  -5.279  -3.209  1.00  0.00           O  
ATOM    994  NE2 GLN    15      -1.430  -3.784  -4.512  1.00  0.00           N  
ATOM    995  H   GLN    15      -1.536  -0.283  -2.279  1.00  0.00           H  
ATOM    996  HA  GLN    15      -4.074  -0.743  -1.091  1.00  0.00           H  
ATOM    997 1HB  GLN    15      -4.034  -2.882  -2.177  1.00  0.00           H  
ATOM    998 2HB  GLN    15      -3.163  -1.773  -3.237  1.00  0.00           H  
ATOM    999 1HG  GLN    15      -1.018  -2.546  -2.242  1.00  0.00           H  
ATOM   1000 2HG  GLN    15      -1.914  -3.703  -1.258  1.00  0.00           H  
ATOM   1001 1HE2 GLN    15      -1.426  -4.412  -5.264  1.00  0.00           H  
ATOM   1002 2HE2 GLN    15      -1.079  -2.876  -4.629  1.00  0.00           H  
ATOM   1003  N   ALA    16      -1.538  -2.141   0.447  1.00  0.00           N  
ATOM   1004  CA  ALA    16      -1.164  -2.812   1.724  1.00  0.00           C  
ATOM   1005  C   ALA    16      -1.896  -2.143   2.891  1.00  0.00           C  
ATOM   1006  O   ALA    16      -2.329  -2.797   3.818  1.00  0.00           O  
ATOM   1007  CB  ALA    16       0.348  -2.700   1.932  1.00  0.00           C  
ATOM   1008  H   ALA    16      -0.840  -1.865  -0.185  1.00  0.00           H  
ATOM   1009  HA  ALA    16      -1.443  -3.853   1.675  1.00  0.00           H  
ATOM   1010 1HB  ALA    16       0.839  -2.616   0.973  1.00  0.00           H  
ATOM   1011 2HB  ALA    16       0.566  -1.825   2.525  1.00  0.00           H  
ATOM   1012 3HB  ALA    16       0.707  -3.580   2.444  1.00  0.00           H  
ATOM   1013  N   VAL    17      -2.039  -0.846   2.854  1.00  0.00           N  
ATOM   1014  CA  VAL    17      -2.743  -0.143   3.964  1.00  0.00           C  
ATOM   1015  C   VAL    17      -4.257  -0.261   3.771  1.00  0.00           C  
ATOM   1016  O   VAL    17      -5.005  -0.379   4.719  1.00  0.00           O  
ATOM   1017  CB  VAL    17      -2.343   1.334   3.968  1.00  0.00           C  
ATOM   1018  CG1 VAL    17      -3.279   2.116   4.893  1.00  0.00           C  
ATOM   1019  CG2 VAL    17      -0.904   1.466   4.471  1.00  0.00           C  
ATOM   1020  H   VAL    17      -1.682  -0.336   2.097  1.00  0.00           H  
ATOM   1021  HA  VAL    17      -2.465  -0.592   4.907  1.00  0.00           H  
ATOM   1022  HB  VAL    17      -2.415   1.729   2.965  1.00  0.00           H  
ATOM   1023 1HG1 VAL    17      -4.298   2.003   4.552  1.00  0.00           H  
ATOM   1024 2HG1 VAL    17      -3.191   1.734   5.899  1.00  0.00           H  
ATOM   1025 3HG1 VAL    17      -3.008   3.161   4.879  1.00  0.00           H  
ATOM   1026 1HG2 VAL    17      -0.699   0.682   5.184  1.00  0.00           H  
ATOM   1027 2HG2 VAL    17      -0.222   1.380   3.636  1.00  0.00           H  
ATOM   1028 3HG2 VAL    17      -0.774   2.427   4.944  1.00  0.00           H  
ATOM   1029  N   PHE    18      -4.712  -0.226   2.550  1.00  0.00           N  
ATOM   1030  CA  PHE    18      -6.178  -0.333   2.291  1.00  0.00           C  
ATOM   1031  C   PHE    18      -6.755  -1.518   3.071  1.00  0.00           C  
ATOM   1032  O   PHE    18      -7.667  -1.370   3.865  1.00  0.00           O  
ATOM   1033  CB  PHE    18      -6.415  -0.539   0.795  1.00  0.00           C  
ATOM   1034  CG  PHE    18      -7.544   0.350   0.337  1.00  0.00           C  
ATOM   1035  CD1 PHE    18      -8.577   0.685   1.223  1.00  0.00           C  
ATOM   1036  CD2 PHE    18      -7.560   0.842  -0.974  1.00  0.00           C  
ATOM   1037  CE1 PHE    18      -9.624   1.510   0.796  1.00  0.00           C  
ATOM   1038  CE2 PHE    18      -8.608   1.667  -1.399  1.00  0.00           C  
ATOM   1039  CZ  PHE    18      -9.639   2.001  -0.514  1.00  0.00           C  
ATOM   1040  H   PHE    18      -4.088  -0.126   1.800  1.00  0.00           H  
ATOM   1041  HA  PHE    18      -6.666   0.577   2.610  1.00  0.00           H  
ATOM   1042 1HB  PHE    18      -5.516  -0.289   0.251  1.00  0.00           H  
ATOM   1043 2HB  PHE    18      -6.674  -1.571   0.609  1.00  0.00           H  
ATOM   1044  HD1 PHE    18      -8.563   0.306   2.234  1.00  0.00           H  
ATOM   1045  HD2 PHE    18      -6.763   0.584  -1.655  1.00  0.00           H  
ATOM   1046  HE1 PHE    18     -10.419   1.768   1.479  1.00  0.00           H  
ATOM   1047  HE2 PHE    18      -8.619   2.046  -2.410  1.00  0.00           H  
ATOM   1048  HZ  PHE    18     -10.447   2.637  -0.843  1.00  0.00           H  
ATOM   1049  N   LEU    19      -6.232  -2.695   2.857  1.00  0.00           N  
ATOM   1050  CA  LEU    19      -6.753  -3.879   3.596  1.00  0.00           C  
ATOM   1051  C   LEU    19      -6.557  -3.647   5.093  1.00  0.00           C  
ATOM   1052  O   LEU    19      -7.313  -4.128   5.914  1.00  0.00           O  
ATOM   1053  CB  LEU    19      -5.988  -5.134   3.166  1.00  0.00           C  
ATOM   1054  CG  LEU    19      -4.560  -5.076   3.713  1.00  0.00           C  
ATOM   1055  CD1 LEU    19      -4.482  -5.852   5.030  1.00  0.00           C  
ATOM   1056  CD2 LEU    19      -3.601  -5.703   2.698  1.00  0.00           C  
ATOM   1057  H   LEU    19      -5.497  -2.799   2.218  1.00  0.00           H  
ATOM   1058  HA  LEU    19      -7.805  -4.005   3.383  1.00  0.00           H  
ATOM   1059 1HB  LEU    19      -6.487  -6.010   3.553  1.00  0.00           H  
ATOM   1060 2HB  LEU    19      -5.955  -5.186   2.088  1.00  0.00           H  
ATOM   1061  HG  LEU    19      -4.281  -4.046   3.885  1.00  0.00           H  
ATOM   1062 1HD1 LEU    19      -5.188  -5.437   5.735  1.00  0.00           H  
ATOM   1063 2HD1 LEU    19      -4.718  -6.891   4.852  1.00  0.00           H  
ATOM   1064 3HD1 LEU    19      -3.483  -5.774   5.434  1.00  0.00           H  
ATOM   1065 1HD2 LEU    19      -3.733  -5.228   1.737  1.00  0.00           H  
ATOM   1066 2HD2 LEU    19      -2.583  -5.565   3.031  1.00  0.00           H  
ATOM   1067 3HD2 LEU    19      -3.811  -6.758   2.609  1.00  0.00           H  
ATOM   1068  N   LEU    20      -5.548  -2.901   5.449  1.00  0.00           N  
ATOM   1069  CA  LEU    20      -5.293  -2.620   6.888  1.00  0.00           C  
ATOM   1070  C   LEU    20      -6.445  -1.787   7.449  1.00  0.00           C  
ATOM   1071  O   LEU    20      -6.783  -1.876   8.613  1.00  0.00           O  
ATOM   1072  CB  LEU    20      -3.984  -1.843   7.025  1.00  0.00           C  
ATOM   1073  CG  LEU    20      -3.106  -2.510   8.083  1.00  0.00           C  
ATOM   1074  CD1 LEU    20      -3.931  -2.757   9.347  1.00  0.00           C  
ATOM   1075  CD2 LEU    20      -2.589  -3.846   7.546  1.00  0.00           C  
ATOM   1076  H   LEU    20      -4.958  -2.519   4.766  1.00  0.00           H  
ATOM   1077  HA  LEU    20      -5.221  -3.551   7.432  1.00  0.00           H  
ATOM   1078 1HB  LEU    20      -3.468  -1.841   6.074  1.00  0.00           H  
ATOM   1079 2HB  LEU    20      -4.197  -0.826   7.321  1.00  0.00           H  
ATOM   1080  HG  LEU    20      -2.271  -1.867   8.319  1.00  0.00           H  
ATOM   1081 1HD1 LEU    20      -4.629  -1.946   9.485  1.00  0.00           H  
ATOM   1082 2HD1 LEU    20      -4.474  -3.686   9.247  1.00  0.00           H  
ATOM   1083 3HD1 LEU    20      -3.272  -2.816  10.201  1.00  0.00           H  
ATOM   1084 1HD2 LEU    20      -3.101  -4.086   6.624  1.00  0.00           H  
ATOM   1085 2HD2 LEU    20      -1.527  -3.773   7.359  1.00  0.00           H  
ATOM   1086 3HD2 LEU    20      -2.773  -4.624   8.272  1.00  0.00           H  
ATOM   1087  N   LEU    21      -7.056  -0.981   6.624  1.00  0.00           N  
ATOM   1088  CA  LEU    21      -8.192  -0.144   7.099  1.00  0.00           C  
ATOM   1089  C   LEU    21      -9.399  -1.044   7.353  1.00  0.00           C  
ATOM   1090  O   LEU    21     -10.008  -1.005   8.403  1.00  0.00           O  
ATOM   1091  CB  LEU    21      -8.550   0.894   6.032  1.00  0.00           C  
ATOM   1092  CG  LEU    21      -7.282   1.354   5.308  1.00  0.00           C  
ATOM   1093  CD1 LEU    21      -7.581   2.633   4.524  1.00  0.00           C  
ATOM   1094  CD2 LEU    21      -6.176   1.631   6.331  1.00  0.00           C  
ATOM   1095  H   LEU    21      -6.769  -0.930   5.691  1.00  0.00           H  
ATOM   1096  HA  LEU    21      -7.915   0.358   8.015  1.00  0.00           H  
ATOM   1097 1HB  LEU    21      -9.231   0.453   5.318  1.00  0.00           H  
ATOM   1098 2HB  LEU    21      -9.022   1.744   6.501  1.00  0.00           H  
ATOM   1099  HG  LEU    21      -6.959   0.582   4.624  1.00  0.00           H  
ATOM   1100 1HD1 LEU    21      -8.650   2.775   4.463  1.00  0.00           H  
ATOM   1101 2HD1 LEU    21      -7.135   3.478   5.029  1.00  0.00           H  
ATOM   1102 3HD1 LEU    21      -7.170   2.550   3.528  1.00  0.00           H  
ATOM   1103 1HD2 LEU    21      -6.621   1.866   7.286  1.00  0.00           H  
ATOM   1104 2HD2 LEU    21      -5.551   0.755   6.430  1.00  0.00           H  
ATOM   1105 3HD2 LEU    21      -5.577   2.465   5.997  1.00  0.00           H  
ATOM   1106  N   THR    22      -9.749  -1.855   6.396  1.00  0.00           N  
ATOM   1107  CA  THR    22     -10.918  -2.759   6.579  1.00  0.00           C  
ATOM   1108  C   THR    22     -10.541  -3.899   7.531  1.00  0.00           C  
ATOM   1109  O   THR    22     -11.369  -4.707   7.902  1.00  0.00           O  
ATOM   1110  CB  THR    22     -11.331  -3.337   5.224  1.00  0.00           C  
ATOM   1111  OG1 THR    22     -10.167  -3.658   4.473  1.00  0.00           O  
ATOM   1112  CG2 THR    22     -12.167  -2.306   4.462  1.00  0.00           C  
ATOM   1113  H   THR    22      -9.242  -1.870   5.554  1.00  0.00           H  
ATOM   1114  HA  THR    22     -11.742  -2.200   6.997  1.00  0.00           H  
ATOM   1115  HB  THR    22     -11.918  -4.229   5.376  1.00  0.00           H  
ATOM   1116  HG1 THR    22     -10.010  -2.946   3.847  1.00  0.00           H  
ATOM   1117 1HG2 THR    22     -12.875  -1.848   5.135  1.00  0.00           H  
ATOM   1118 2HG2 THR    22     -11.517  -1.547   4.052  1.00  0.00           H  
ATOM   1119 3HG2 THR    22     -12.698  -2.796   3.659  1.00  0.00           H  
ATOM   1120  N   SER    23      -9.300  -3.971   7.929  1.00  0.00           N  
ATOM   1121  CA  SER    23      -8.877  -5.061   8.854  1.00  0.00           C  
ATOM   1122  C   SER    23      -9.161  -4.650  10.301  1.00  0.00           C  
ATOM   1123  O   SER    23      -9.931  -5.283  10.997  1.00  0.00           O  
ATOM   1124  CB  SER    23      -7.380  -5.319   8.687  1.00  0.00           C  
ATOM   1125  OG  SER    23      -7.180  -6.656   8.248  1.00  0.00           O  
ATOM   1126  H   SER    23      -8.645  -3.310   7.618  1.00  0.00           H  
ATOM   1127  HA  SER    23      -9.424  -5.961   8.623  1.00  0.00           H  
ATOM   1128 1HB  SER    23      -6.973  -4.641   7.954  1.00  0.00           H  
ATOM   1129 2HB  SER    23      -6.880  -5.162   9.636  1.00  0.00           H  
ATOM   1130  HG  SER    23      -7.461  -6.712   7.332  1.00  0.00           H  
ATOM   1131  N   GLN    24      -8.543  -3.597  10.763  1.00  0.00           N  
ATOM   1132  CA  GLN    24      -8.771  -3.150  12.161  1.00  0.00           C  
ATOM   1133  C   GLN    24     -10.150  -2.482  12.259  1.00  0.00           C  
ATOM   1134  O   GLN    24     -10.833  -2.597  13.258  1.00  0.00           O  
ATOM   1135  CB  GLN    24      -7.650  -2.166  12.551  1.00  0.00           C  
ATOM   1136  CG  GLN    24      -8.187  -1.066  13.469  1.00  0.00           C  
ATOM   1137  CD  GLN    24      -7.017  -0.330  14.126  1.00  0.00           C  
ATOM   1138  OE1 GLN    24      -5.872  -0.691  13.934  1.00  0.00           O  
ATOM   1139  NE2 GLN    24      -7.257   0.695  14.896  1.00  0.00           N  
ATOM   1140  H   GLN    24      -7.925  -3.100  10.190  1.00  0.00           H  
ATOM   1141  HA  GLN    24      -8.742  -4.006  12.820  1.00  0.00           H  
ATOM   1142 1HB  GLN    24      -6.868  -2.705  13.064  1.00  0.00           H  
ATOM   1143 2HB  GLN    24      -7.245  -1.717  11.657  1.00  0.00           H  
ATOM   1144 1HG  GLN    24      -8.771  -0.369  12.885  1.00  0.00           H  
ATOM   1145 2HG  GLN    24      -8.808  -1.506  14.232  1.00  0.00           H  
ATOM   1146 1HE2 GLN    24      -6.515   1.175  15.319  1.00  0.00           H  
ATOM   1147 2HE2 GLN    24      -8.180   0.986  15.051  1.00  0.00           H  
ATOM   1148  N   ARG    25     -10.564  -1.791  11.229  1.00  0.00           N  
ATOM   1149  CA  ARG    25     -11.894  -1.122  11.261  1.00  0.00           C  
ATOM   1150  C   ARG    25     -12.114  -0.478  12.631  1.00  0.00           C  
ATOM   1151  O   ARG    25     -12.959  -0.966  13.364  1.00  0.00           O  
ATOM   1152  CB  ARG    25     -12.982  -2.162  10.999  1.00  0.00           C  
ATOM   1153  CG  ARG    25     -14.357  -1.552  11.281  1.00  0.00           C  
ATOM   1154  CD  ARG    25     -15.262  -1.753  10.066  1.00  0.00           C  
ATOM   1155  NE  ARG    25     -16.689  -1.663  10.488  1.00  0.00           N  
ATOM   1156  CZ  ARG    25     -17.624  -1.476   9.595  1.00  0.00           C  
ATOM   1157  NH1 ARG    25     -17.575  -0.438   8.804  1.00  0.00           N  
ATOM   1158  NH2 ARG    25     -18.608  -2.328   9.492  1.00  0.00           N  
ATOM   1159  OXT ARG    25     -11.433   0.490  12.924  1.00  0.00           O  
ATOM   1160  H   ARG    25     -10.002  -1.718  10.433  1.00  0.00           H  
ATOM   1161  HA  ARG    25     -11.933  -0.361  10.496  1.00  0.00           H  
ATOM   1162 1HB  ARG    25     -12.930  -2.480   9.967  1.00  0.00           H  
ATOM   1163 2HB  ARG    25     -12.826  -3.012  11.646  1.00  0.00           H  
ATOM   1164 1HG  ARG    25     -14.794  -2.036  12.142  1.00  0.00           H  
ATOM   1165 2HG  ARG    25     -14.249  -0.496  11.478  1.00  0.00           H  
ATOM   1166 1HD  ARG    25     -15.056  -0.987   9.333  1.00  0.00           H  
ATOM   1167 2HD  ARG    25     -15.075  -2.725   9.633  1.00  0.00           H  
ATOM   1168  HE  ARG    25     -16.925  -1.745  11.435  1.00  0.00           H  
ATOM   1169 1HH1 ARG    25     -16.822   0.215   8.882  1.00  0.00           H  
ATOM   1170 2HH1 ARG    25     -18.291  -0.296   8.121  1.00  0.00           H  
ATOM   1171 1HH2 ARG    25     -18.647  -3.123  10.098  1.00  0.00           H  
ATOM   1172 2HH2 ARG    25     -19.324  -2.185   8.810  1.00  0.00           H  
TER    1173      ARG    25                                                      
ENDMDL                                                                          
MODEL        4                                                                  
ATOM   1174  N   GLY     1      14.467  -2.646  -9.742  1.00  0.00           N  
ATOM   1175  CA  GLY     1      13.304  -1.738 -10.143  1.00  0.00           C  
ATOM   1176  C   GLY     1      13.580  -0.331 -10.550  1.00  0.00           C  
ATOM   1177  O   GLY     1      12.896   0.228 -11.385  1.00  0.00           O  
ATOM   1178 1H   GLY     1      15.345  -2.297 -10.177  1.00  0.00           H  
ATOM   1179 2H   GLY     1      14.568  -2.645  -8.707  1.00  0.00           H  
ATOM   1180 3H   GLY     1      14.279  -3.615 -10.070  1.00  0.00           H  
ATOM   1181 1HA  GLY     1      13.073  -1.853 -11.083  1.00  0.00           H  
ATOM   1182 2HA  GLY     1      12.419  -1.980  -9.421  1.00  0.00           H  
ATOM   1183  N   SER     2      14.581   0.279  -9.975  1.00  0.00           N  
ATOM   1184  CA  SER     2      14.904   1.687 -10.341  1.00  0.00           C  
ATOM   1185  C   SER     2      13.689   2.577 -10.073  1.00  0.00           C  
ATOM   1186  O   SER     2      12.914   2.332  -9.170  1.00  0.00           O  
ATOM   1187  CB  SER     2      15.271   1.757 -11.825  1.00  0.00           C  
ATOM   1188  OG  SER     2      15.981   0.581 -12.188  1.00  0.00           O  
ATOM   1189  H   SER     2      15.120  -0.190  -9.304  1.00  0.00           H  
ATOM   1190  HA  SER     2      15.739   2.031  -9.748  1.00  0.00           H  
ATOM   1191 1HB  SER     2      14.373   1.825 -12.416  1.00  0.00           H  
ATOM   1192 2HB  SER     2      15.883   2.630 -12.002  1.00  0.00           H  
ATOM   1193  HG  SER     2      16.430   0.251 -11.406  1.00  0.00           H  
ATOM   1194  N   GLU     3      13.514   3.610 -10.852  1.00  0.00           N  
ATOM   1195  CA  GLU     3      12.348   4.513 -10.642  1.00  0.00           C  
ATOM   1196  C   GLU     3      11.071   3.680 -10.536  1.00  0.00           C  
ATOM   1197  O   GLU     3      10.204   3.954  -9.731  1.00  0.00           O  
ATOM   1198  CB  GLU     3      12.231   5.475 -11.825  1.00  0.00           C  
ATOM   1199  CG  GLU     3      12.746   6.856 -11.414  1.00  0.00           C  
ATOM   1200  CD  GLU     3      11.719   7.536 -10.507  1.00  0.00           C  
ATOM   1201  OE1 GLU     3      10.622   7.794 -10.976  1.00  0.00           O  
ATOM   1202  OE2 GLU     3      12.045   7.786  -9.359  1.00  0.00           O  
ATOM   1203  H   GLU     3      14.150   3.792 -11.575  1.00  0.00           H  
ATOM   1204  HA  GLU     3      12.488   5.077  -9.732  1.00  0.00           H  
ATOM   1205 1HB  GLU     3      12.818   5.102 -12.652  1.00  0.00           H  
ATOM   1206 2HB  GLU     3      11.196   5.554 -12.124  1.00  0.00           H  
ATOM   1207 1HG  GLU     3      13.681   6.747 -10.882  1.00  0.00           H  
ATOM   1208 2HG  GLU     3      12.901   7.460 -12.295  1.00  0.00           H  
ATOM   1209  N   LYS     4      10.948   2.662 -11.344  1.00  0.00           N  
ATOM   1210  CA  LYS     4       9.728   1.810 -11.286  1.00  0.00           C  
ATOM   1211  C   LYS     4       9.563   1.260  -9.870  1.00  0.00           C  
ATOM   1212  O   LYS     4       8.488   1.289  -9.303  1.00  0.00           O  
ATOM   1213  CB  LYS     4       9.870   0.650 -12.273  1.00  0.00           C  
ATOM   1214  CG  LYS     4      10.383   1.180 -13.613  1.00  0.00           C  
ATOM   1215  CD  LYS     4      11.718   0.513 -13.949  1.00  0.00           C  
ATOM   1216  CE  LYS     4      11.752   0.153 -15.435  1.00  0.00           C  
ATOM   1217  NZ  LYS     4      11.160  -1.200 -15.632  1.00  0.00           N  
ATOM   1218  H   LYS     4      11.659   2.457 -11.986  1.00  0.00           H  
ATOM   1219  HA  LYS     4       8.862   2.402 -11.547  1.00  0.00           H  
ATOM   1220 1HB  LYS     4      10.569  -0.073 -11.880  1.00  0.00           H  
ATOM   1221 2HB  LYS     4       8.908   0.179 -12.419  1.00  0.00           H  
ATOM   1222 1HG  LYS     4       9.663   0.958 -14.388  1.00  0.00           H  
ATOM   1223 2HG  LYS     4      10.524   2.249 -13.548  1.00  0.00           H  
ATOM   1224 1HD  LYS     4      12.527   1.193 -13.724  1.00  0.00           H  
ATOM   1225 2HD  LYS     4      11.829  -0.386 -13.361  1.00  0.00           H  
ATOM   1226 1HE  LYS     4      11.181   0.880 -15.994  1.00  0.00           H  
ATOM   1227 2HE  LYS     4      12.774   0.153 -15.782  1.00  0.00           H  
ATOM   1228 1HZ  LYS     4      10.212  -1.229 -15.209  1.00  0.00           H  
ATOM   1229 2HZ  LYS     4      11.092  -1.404 -16.650  1.00  0.00           H  
ATOM   1230 3HZ  LYS     4      11.764  -1.913 -15.176  1.00  0.00           H  
ATOM   1231  N   MET     5      10.621   0.761  -9.291  1.00  0.00           N  
ATOM   1232  CA  MET     5      10.525   0.212  -7.909  1.00  0.00           C  
ATOM   1233  C   MET     5      10.263   1.355  -6.928  1.00  0.00           C  
ATOM   1234  O   MET     5       9.792   1.145  -5.828  1.00  0.00           O  
ATOM   1235  CB  MET     5      11.838  -0.483  -7.541  1.00  0.00           C  
ATOM   1236  CG  MET     5      11.564  -1.955  -7.224  1.00  0.00           C  
ATOM   1237  SD  MET     5      10.796  -2.087  -5.591  1.00  0.00           S  
ATOM   1238  CE  MET     5      12.316  -1.980  -4.616  1.00  0.00           C  
ATOM   1239  H   MET     5      11.479   0.748  -9.764  1.00  0.00           H  
ATOM   1240  HA  MET     5       9.713  -0.499  -7.860  1.00  0.00           H  
ATOM   1241 1HB  MET     5      12.527  -0.414  -8.371  1.00  0.00           H  
ATOM   1242 2HB  MET     5      12.267  -0.005  -6.674  1.00  0.00           H  
ATOM   1243 1HG  MET     5      10.899  -2.366  -7.970  1.00  0.00           H  
ATOM   1244 2HG  MET     5      12.494  -2.503  -7.230  1.00  0.00           H  
ATOM   1245 1HE  MET     5      12.924  -1.170  -4.984  1.00  0.00           H  
ATOM   1246 2HE  MET     5      12.066  -1.800  -3.579  1.00  0.00           H  
ATOM   1247 3HE  MET     5      12.865  -2.908  -4.703  1.00  0.00           H  
ATOM   1248  N   SER     6      10.564   2.564  -7.318  1.00  0.00           N  
ATOM   1249  CA  SER     6      10.332   3.723  -6.410  1.00  0.00           C  
ATOM   1250  C   SER     6       8.833   4.014  -6.334  1.00  0.00           C  
ATOM   1251  O   SER     6       8.273   4.178  -5.267  1.00  0.00           O  
ATOM   1252  CB  SER     6      11.061   4.950  -6.955  1.00  0.00           C  
ATOM   1253  OG  SER     6      12.296   4.544  -7.532  1.00  0.00           O  
ATOM   1254  H   SER     6      10.943   2.710  -8.210  1.00  0.00           H  
ATOM   1255  HA  SER     6      10.704   3.489  -5.423  1.00  0.00           H  
ATOM   1256 1HB  SER     6      10.457   5.425  -7.710  1.00  0.00           H  
ATOM   1257 2HB  SER     6      11.241   5.648  -6.148  1.00  0.00           H  
ATOM   1258  HG  SER     6      12.777   4.034  -6.876  1.00  0.00           H  
ATOM   1259  N   THR     7       8.175   4.071  -7.459  1.00  0.00           N  
ATOM   1260  CA  THR     7       6.712   4.342  -7.450  1.00  0.00           C  
ATOM   1261  C   THR     7       5.981   3.067  -7.036  1.00  0.00           C  
ATOM   1262  O   THR     7       4.829   3.093  -6.648  1.00  0.00           O  
ATOM   1263  CB  THR     7       6.259   4.765  -8.850  1.00  0.00           C  
ATOM   1264  OG1 THR     7       5.966   3.606  -9.622  1.00  0.00           O  
ATOM   1265  CG2 THR     7       7.375   5.569  -9.522  1.00  0.00           C  
ATOM   1266  H   THR     7       8.642   3.926  -8.308  1.00  0.00           H  
ATOM   1267  HA  THR     7       6.494   5.130  -6.745  1.00  0.00           H  
ATOM   1268  HB  THR     7       5.376   5.378  -8.772  1.00  0.00           H  
ATOM   1269  HG1 THR     7       6.539   3.602 -10.393  1.00  0.00           H  
ATOM   1270 1HG2 THR     7       8.116   5.842  -8.785  1.00  0.00           H  
ATOM   1271 2HG2 THR     7       7.836   4.970 -10.292  1.00  0.00           H  
ATOM   1272 3HG2 THR     7       6.959   6.464  -9.961  1.00  0.00           H  
ATOM   1273  N   ALA     8       6.653   1.953  -7.107  1.00  0.00           N  
ATOM   1274  CA  ALA     8       6.019   0.670  -6.710  1.00  0.00           C  
ATOM   1275  C   ALA     8       6.130   0.518  -5.197  1.00  0.00           C  
ATOM   1276  O   ALA     8       5.280  -0.067  -4.555  1.00  0.00           O  
ATOM   1277  CB  ALA     8       6.743  -0.486  -7.399  1.00  0.00           C  
ATOM   1278  H   ALA     8       7.583   1.961  -7.414  1.00  0.00           H  
ATOM   1279  HA  ALA     8       4.978   0.674  -7.000  1.00  0.00           H  
ATOM   1280 1HB  ALA     8       6.869  -0.258  -8.446  1.00  0.00           H  
ATOM   1281 2HB  ALA     8       7.712  -0.625  -6.942  1.00  0.00           H  
ATOM   1282 3HB  ALA     8       6.162  -1.389  -7.294  1.00  0.00           H  
ATOM   1283  N   ILE     9       7.171   1.052  -4.619  1.00  0.00           N  
ATOM   1284  CA  ILE     9       7.335   0.950  -3.145  1.00  0.00           C  
ATOM   1285  C   ILE     9       6.387   1.942  -2.471  1.00  0.00           C  
ATOM   1286  O   ILE     9       5.853   1.684  -1.412  1.00  0.00           O  
ATOM   1287  CB  ILE     9       8.782   1.269  -2.760  1.00  0.00           C  
ATOM   1288  CG1 ILE     9       9.166   2.652  -3.296  1.00  0.00           C  
ATOM   1289  CG2 ILE     9       9.712   0.214  -3.361  1.00  0.00           C  
ATOM   1290  CD1 ILE     9      10.368   3.183  -2.513  1.00  0.00           C  
ATOM   1291  H   ILE     9       7.840   1.526  -5.155  1.00  0.00           H  
ATOM   1292  HA  ILE     9       7.090  -0.053  -2.828  1.00  0.00           H  
ATOM   1293  HB  ILE     9       8.877   1.259  -1.684  1.00  0.00           H  
ATOM   1294 1HG1 ILE     9       9.422   2.575  -4.342  1.00  0.00           H  
ATOM   1295 2HG1 ILE     9       8.336   3.330  -3.177  1.00  0.00           H  
ATOM   1296 1HG2 ILE     9       9.277  -0.173  -4.271  1.00  0.00           H  
ATOM   1297 2HG2 ILE     9      10.670   0.664  -3.583  1.00  0.00           H  
ATOM   1298 3HG2 ILE     9       9.847  -0.591  -2.655  1.00  0.00           H  
ATOM   1299 1HD1 ILE     9      10.458   2.645  -1.581  1.00  0.00           H  
ATOM   1300 2HD1 ILE     9      11.267   3.045  -3.096  1.00  0.00           H  
ATOM   1301 3HD1 ILE     9      10.229   4.235  -2.309  1.00  0.00           H  
ATOM   1302  N   SER    10       6.166   3.074  -3.083  1.00  0.00           N  
ATOM   1303  CA  SER    10       5.241   4.074  -2.479  1.00  0.00           C  
ATOM   1304  C   SER    10       3.816   3.532  -2.557  1.00  0.00           C  
ATOM   1305  O   SER    10       3.135   3.398  -1.559  1.00  0.00           O  
ATOM   1306  CB  SER    10       5.330   5.399  -3.241  1.00  0.00           C  
ATOM   1307  OG  SER    10       6.077   5.212  -4.435  1.00  0.00           O  
ATOM   1308  H   SER    10       6.601   3.262  -3.942  1.00  0.00           H  
ATOM   1309  HA  SER    10       5.507   4.230  -1.443  1.00  0.00           H  
ATOM   1310 1HB  SER    10       4.340   5.738  -3.494  1.00  0.00           H  
ATOM   1311 2HB  SER    10       5.811   6.140  -2.616  1.00  0.00           H  
ATOM   1312  HG  SER    10       5.957   5.990  -4.985  1.00  0.00           H  
ATOM   1313  N   VAL    11       3.359   3.204  -3.735  1.00  0.00           N  
ATOM   1314  CA  VAL    11       1.983   2.654  -3.865  1.00  0.00           C  
ATOM   1315  C   VAL    11       1.900   1.359  -3.057  1.00  0.00           C  
ATOM   1316  O   VAL    11       0.846   0.962  -2.605  1.00  0.00           O  
ATOM   1317  CB  VAL    11       1.677   2.367  -5.336  1.00  0.00           C  
ATOM   1318  CG1 VAL    11       0.216   1.932  -5.476  1.00  0.00           C  
ATOM   1319  CG2 VAL    11       1.912   3.632  -6.164  1.00  0.00           C  
ATOM   1320  H   VAL    11       3.925   3.307  -4.530  1.00  0.00           H  
ATOM   1321  HA  VAL    11       1.271   3.369  -3.478  1.00  0.00           H  
ATOM   1322  HB  VAL    11       2.323   1.576  -5.690  1.00  0.00           H  
ATOM   1323 1HG1 VAL    11      -0.420   2.644  -4.971  1.00  0.00           H  
ATOM   1324 2HG1 VAL    11      -0.048   1.891  -6.522  1.00  0.00           H  
ATOM   1325 3HG1 VAL    11       0.088   0.955  -5.034  1.00  0.00           H  
ATOM   1326 1HG2 VAL    11       2.276   4.420  -5.521  1.00  0.00           H  
ATOM   1327 2HG2 VAL    11       2.642   3.428  -6.933  1.00  0.00           H  
ATOM   1328 3HG2 VAL    11       0.984   3.940  -6.621  1.00  0.00           H  
ATOM   1329  N   LEU    12       3.015   0.702  -2.863  1.00  0.00           N  
ATOM   1330  CA  LEU    12       3.011  -0.561  -2.074  1.00  0.00           C  
ATOM   1331  C   LEU    12       2.527  -0.263  -0.654  1.00  0.00           C  
ATOM   1332  O   LEU    12       1.698  -0.964  -0.109  1.00  0.00           O  
ATOM   1333  CB  LEU    12       4.432  -1.131  -2.017  1.00  0.00           C  
ATOM   1334  CG  LEU    12       4.597  -2.206  -3.091  1.00  0.00           C  
ATOM   1335  CD1 LEU    12       6.087  -2.474  -3.321  1.00  0.00           C  
ATOM   1336  CD2 LEU    12       3.916  -3.497  -2.629  1.00  0.00           C  
ATOM   1337  H   LEU    12       3.855   1.046  -3.231  1.00  0.00           H  
ATOM   1338  HA  LEU    12       2.351  -1.278  -2.540  1.00  0.00           H  
ATOM   1339 1HB  LEU    12       5.144  -0.337  -2.190  1.00  0.00           H  
ATOM   1340 2HB  LEU    12       4.606  -1.565  -1.045  1.00  0.00           H  
ATOM   1341  HG  LEU    12       4.146  -1.866  -4.013  1.00  0.00           H  
ATOM   1342 1HD1 LEU    12       6.637  -2.242  -2.421  1.00  0.00           H  
ATOM   1343 2HD1 LEU    12       6.231  -3.514  -3.572  1.00  0.00           H  
ATOM   1344 3HD1 LEU    12       6.443  -1.856  -4.130  1.00  0.00           H  
ATOM   1345 1HD2 LEU    12       3.323  -3.295  -1.749  1.00  0.00           H  
ATOM   1346 2HD2 LEU    12       3.276  -3.868  -3.416  1.00  0.00           H  
ATOM   1347 3HD2 LEU    12       4.666  -4.237  -2.396  1.00  0.00           H  
ATOM   1348  N   LEU    13       3.040   0.775  -0.051  1.00  0.00           N  
ATOM   1349  CA  LEU    13       2.614   1.123   1.333  1.00  0.00           C  
ATOM   1350  C   LEU    13       1.200   1.705   1.300  1.00  0.00           C  
ATOM   1351  O   LEU    13       0.477   1.664   2.275  1.00  0.00           O  
ATOM   1352  CB  LEU    13       3.579   2.164   1.909  1.00  0.00           C  
ATOM   1353  CG  LEU    13       4.904   1.503   2.317  1.00  0.00           C  
ATOM   1354  CD1 LEU    13       5.252   0.355   1.361  1.00  0.00           C  
ATOM   1355  CD2 LEU    13       6.017   2.551   2.266  1.00  0.00           C  
ATOM   1356  H   LEU    13       3.710   1.329  -0.510  1.00  0.00           H  
ATOM   1357  HA  LEU    13       2.628   0.238   1.950  1.00  0.00           H  
ATOM   1358 1HB  LEU    13       3.773   2.921   1.163  1.00  0.00           H  
ATOM   1359 2HB  LEU    13       3.130   2.625   2.776  1.00  0.00           H  
ATOM   1360  HG  LEU    13       4.818   1.119   3.323  1.00  0.00           H  
ATOM   1361 1HD1 LEU    13       5.248   0.719   0.345  1.00  0.00           H  
ATOM   1362 2HD1 LEU    13       6.231  -0.030   1.601  1.00  0.00           H  
ATOM   1363 3HD1 LEU    13       4.520  -0.433   1.462  1.00  0.00           H  
ATOM   1364 1HD2 LEU    13       5.613   3.516   2.538  1.00  0.00           H  
ATOM   1365 2HD2 LEU    13       6.800   2.279   2.956  1.00  0.00           H  
ATOM   1366 3HD2 LEU    13       6.418   2.600   1.264  1.00  0.00           H  
ATOM   1367  N   ALA    14       0.803   2.250   0.185  1.00  0.00           N  
ATOM   1368  CA  ALA    14      -0.563   2.840   0.087  1.00  0.00           C  
ATOM   1369  C   ALA    14      -1.612   1.724   0.125  1.00  0.00           C  
ATOM   1370  O   ALA    14      -2.407   1.638   1.038  1.00  0.00           O  
ATOM   1371  CB  ALA    14      -0.691   3.613  -1.227  1.00  0.00           C  
ATOM   1372  H   ALA    14       1.404   2.276  -0.589  1.00  0.00           H  
ATOM   1373  HA  ALA    14      -0.725   3.512   0.916  1.00  0.00           H  
ATOM   1374 1HB  ALA    14       0.195   3.458  -1.823  1.00  0.00           H  
ATOM   1375 2HB  ALA    14      -1.556   3.260  -1.769  1.00  0.00           H  
ATOM   1376 3HB  ALA    14      -0.804   4.666  -1.015  1.00  0.00           H  
ATOM   1377  N   GLN    15      -1.621   0.874  -0.865  1.00  0.00           N  
ATOM   1378  CA  GLN    15      -2.621  -0.233  -0.892  1.00  0.00           C  
ATOM   1379  C   GLN    15      -2.471  -1.099   0.362  1.00  0.00           C  
ATOM   1380  O   GLN    15      -3.441  -1.436   1.010  1.00  0.00           O  
ATOM   1381  CB  GLN    15      -2.395  -1.092  -2.137  1.00  0.00           C  
ATOM   1382  CG  GLN    15      -3.744  -1.427  -2.777  1.00  0.00           C  
ATOM   1383  CD  GLN    15      -3.732  -1.001  -4.247  1.00  0.00           C  
ATOM   1384  OE1 GLN    15      -3.853   0.168  -4.554  1.00  0.00           O  
ATOM   1385  NE2 GLN    15      -3.589  -1.908  -5.174  1.00  0.00           N  
ATOM   1386  H   GLN    15      -0.975   0.965  -1.594  1.00  0.00           H  
ATOM   1387  HA  GLN    15      -3.616   0.185  -0.922  1.00  0.00           H  
ATOM   1388 1HB  GLN    15      -1.786  -0.548  -2.845  1.00  0.00           H  
ATOM   1389 2HB  GLN    15      -1.895  -2.007  -1.859  1.00  0.00           H  
ATOM   1390 1HG  GLN    15      -3.920  -2.490  -2.710  1.00  0.00           H  
ATOM   1391 2HG  GLN    15      -4.529  -0.896  -2.258  1.00  0.00           H  
ATOM   1392 1HE2 GLN    15      -3.580  -1.647  -6.119  1.00  0.00           H  
ATOM   1393 2HE2 GLN    15      -3.491  -2.851  -4.926  1.00  0.00           H  
ATOM   1394  N   ALA    16      -1.268  -1.463   0.711  1.00  0.00           N  
ATOM   1395  CA  ALA    16      -1.073  -2.306   1.924  1.00  0.00           C  
ATOM   1396  C   ALA    16      -1.837  -1.686   3.096  1.00  0.00           C  
ATOM   1397  O   ALA    16      -2.245  -2.366   4.016  1.00  0.00           O  
ATOM   1398  CB  ALA    16       0.417  -2.382   2.265  1.00  0.00           C  
ATOM   1399  H   ALA    16      -0.494  -1.183   0.177  1.00  0.00           H  
ATOM   1400  HA  ALA    16      -1.451  -3.300   1.735  1.00  0.00           H  
ATOM   1401 1HB  ALA    16       0.944  -1.587   1.757  1.00  0.00           H  
ATOM   1402 2HB  ALA    16       0.548  -2.277   3.332  1.00  0.00           H  
ATOM   1403 3HB  ALA    16       0.811  -3.336   1.947  1.00  0.00           H  
ATOM   1404  N   VAL    17      -2.036  -0.396   3.066  1.00  0.00           N  
ATOM   1405  CA  VAL    17      -2.776   0.273   4.174  1.00  0.00           C  
ATOM   1406  C   VAL    17      -4.281   0.189   3.909  1.00  0.00           C  
ATOM   1407  O   VAL    17      -5.075   0.069   4.820  1.00  0.00           O  
ATOM   1408  CB  VAL    17      -2.354   1.741   4.257  1.00  0.00           C  
ATOM   1409  CG1 VAL    17      -3.306   2.495   5.186  1.00  0.00           C  
ATOM   1410  CG2 VAL    17      -0.929   1.832   4.807  1.00  0.00           C  
ATOM   1411  H   VAL    17      -1.699   0.133   2.314  1.00  0.00           H  
ATOM   1412  HA  VAL    17      -2.547  -0.221   5.107  1.00  0.00           H  
ATOM   1413  HB  VAL    17      -2.389   2.181   3.270  1.00  0.00           H  
ATOM   1414 1HG1 VAL    17      -4.018   1.803   5.610  1.00  0.00           H  
ATOM   1415 2HG1 VAL    17      -2.740   2.960   5.980  1.00  0.00           H  
ATOM   1416 3HG1 VAL    17      -3.830   3.254   4.625  1.00  0.00           H  
ATOM   1417 1HG2 VAL    17      -0.295   1.130   4.284  1.00  0.00           H  
ATOM   1418 2HG2 VAL    17      -0.551   2.833   4.665  1.00  0.00           H  
ATOM   1419 3HG2 VAL    17      -0.934   1.595   5.861  1.00  0.00           H  
ATOM   1420  N   PHE    18      -4.680   0.254   2.667  1.00  0.00           N  
ATOM   1421  CA  PHE    18      -6.133   0.179   2.345  1.00  0.00           C  
ATOM   1422  C   PHE    18      -6.677  -1.189   2.762  1.00  0.00           C  
ATOM   1423  O   PHE    18      -7.545  -1.293   3.606  1.00  0.00           O  
ATOM   1424  CB  PHE    18      -6.331   0.369   0.840  1.00  0.00           C  
ATOM   1425  CG  PHE    18      -7.039   1.677   0.584  1.00  0.00           C  
ATOM   1426  CD1 PHE    18      -8.436   1.741   0.651  1.00  0.00           C  
ATOM   1427  CD2 PHE    18      -6.299   2.826   0.279  1.00  0.00           C  
ATOM   1428  CE1 PHE    18      -9.093   2.954   0.413  1.00  0.00           C  
ATOM   1429  CE2 PHE    18      -6.956   4.039   0.041  1.00  0.00           C  
ATOM   1430  CZ  PHE    18      -8.353   4.103   0.106  1.00  0.00           C  
ATOM   1431  H   PHE    18      -4.023   0.353   1.947  1.00  0.00           H  
ATOM   1432  HA  PHE    18      -6.662   0.955   2.879  1.00  0.00           H  
ATOM   1433 1HB  PHE    18      -5.367   0.378   0.350  1.00  0.00           H  
ATOM   1434 2HB  PHE    18      -6.926  -0.444   0.450  1.00  0.00           H  
ATOM   1435  HD1 PHE    18      -9.006   0.855   0.887  1.00  0.00           H  
ATOM   1436  HD2 PHE    18      -5.221   2.776   0.227  1.00  0.00           H  
ATOM   1437  HE1 PHE    18     -10.171   3.003   0.463  1.00  0.00           H  
ATOM   1438  HE2 PHE    18      -6.386   4.924  -0.195  1.00  0.00           H  
ATOM   1439  HZ  PHE    18      -8.860   5.038  -0.077  1.00  0.00           H  
ATOM   1440  N   LEU    19      -6.169  -2.242   2.179  1.00  0.00           N  
ATOM   1441  CA  LEU    19      -6.655  -3.601   2.548  1.00  0.00           C  
ATOM   1442  C   LEU    19      -6.392  -3.840   4.035  1.00  0.00           C  
ATOM   1443  O   LEU    19      -7.134  -4.531   4.705  1.00  0.00           O  
ATOM   1444  CB  LEU    19      -5.910  -4.652   1.721  1.00  0.00           C  
ATOM   1445  CG  LEU    19      -6.264  -4.485   0.243  1.00  0.00           C  
ATOM   1446  CD1 LEU    19      -5.438  -5.464  -0.594  1.00  0.00           C  
ATOM   1447  CD2 LEU    19      -7.753  -4.774   0.040  1.00  0.00           C  
ATOM   1448  H   LEU    19      -5.468  -2.137   1.503  1.00  0.00           H  
ATOM   1449  HA  LEU    19      -7.715  -3.671   2.353  1.00  0.00           H  
ATOM   1450 1HB  LEU    19      -4.845  -4.526   1.854  1.00  0.00           H  
ATOM   1451 2HB  LEU    19      -6.200  -5.639   2.048  1.00  0.00           H  
ATOM   1452  HG  LEU    19      -6.045  -3.474  -0.068  1.00  0.00           H  
ATOM   1453 1HD1 LEU    19      -5.284  -6.375  -0.033  1.00  0.00           H  
ATOM   1454 2HD1 LEU    19      -5.964  -5.689  -1.510  1.00  0.00           H  
ATOM   1455 3HD1 LEU    19      -4.482  -5.020  -0.827  1.00  0.00           H  
ATOM   1456 1HD2 LEU    19      -8.183  -5.119   0.969  1.00  0.00           H  
ATOM   1457 2HD2 LEU    19      -8.255  -3.871  -0.275  1.00  0.00           H  
ATOM   1458 3HD2 LEU    19      -7.872  -5.535  -0.717  1.00  0.00           H  
ATOM   1459  N   LEU    20      -5.342  -3.268   4.558  1.00  0.00           N  
ATOM   1460  CA  LEU    20      -5.034  -3.456   6.003  1.00  0.00           C  
ATOM   1461  C   LEU    20      -6.090  -2.730   6.837  1.00  0.00           C  
ATOM   1462  O   LEU    20      -6.374  -3.101   7.959  1.00  0.00           O  
ATOM   1463  CB  LEU    20      -3.651  -2.877   6.309  1.00  0.00           C  
ATOM   1464  CG  LEU    20      -3.365  -3.001   7.805  1.00  0.00           C  
ATOM   1465  CD1 LEU    20      -2.688  -4.343   8.086  1.00  0.00           C  
ATOM   1466  CD2 LEU    20      -2.438  -1.863   8.240  1.00  0.00           C  
ATOM   1467  H   LEU    20      -4.758  -2.711   4.001  1.00  0.00           H  
ATOM   1468  HA  LEU    20      -5.046  -4.511   6.240  1.00  0.00           H  
ATOM   1469 1HB  LEU    20      -2.901  -3.421   5.751  1.00  0.00           H  
ATOM   1470 2HB  LEU    20      -3.626  -1.836   6.024  1.00  0.00           H  
ATOM   1471  HG  LEU    20      -4.293  -2.942   8.356  1.00  0.00           H  
ATOM   1472 1HD1 LEU    20      -2.759  -4.972   7.211  1.00  0.00           H  
ATOM   1473 2HD1 LEU    20      -1.649  -4.179   8.329  1.00  0.00           H  
ATOM   1474 3HD1 LEU    20      -3.180  -4.827   8.917  1.00  0.00           H  
ATOM   1475 1HD2 LEU    20      -2.560  -1.024   7.572  1.00  0.00           H  
ATOM   1476 2HD2 LEU    20      -2.685  -1.560   9.247  1.00  0.00           H  
ATOM   1477 3HD2 LEU    20      -1.413  -2.202   8.208  1.00  0.00           H  
ATOM   1478  N   LEU    21      -6.678  -1.701   6.292  1.00  0.00           N  
ATOM   1479  CA  LEU    21      -7.720  -0.948   7.044  1.00  0.00           C  
ATOM   1480  C   LEU    21      -8.984  -1.802   7.144  1.00  0.00           C  
ATOM   1481  O   LEU    21      -9.522  -2.008   8.214  1.00  0.00           O  
ATOM   1482  CB  LEU    21      -8.042   0.351   6.304  1.00  0.00           C  
ATOM   1483  CG  LEU    21      -9.269   1.009   6.935  1.00  0.00           C  
ATOM   1484  CD1 LEU    21      -9.061   1.136   8.445  1.00  0.00           C  
ATOM   1485  CD2 LEU    21      -9.467   2.400   6.329  1.00  0.00           C  
ATOM   1486  H   LEU    21      -6.435  -1.425   5.384  1.00  0.00           H  
ATOM   1487  HA  LEU    21      -7.357  -0.721   8.034  1.00  0.00           H  
ATOM   1488 1HB  LEU    21      -7.198   1.022   6.373  1.00  0.00           H  
ATOM   1489 2HB  LEU    21      -8.245   0.134   5.267  1.00  0.00           H  
ATOM   1490  HG  LEU    21     -10.142   0.402   6.742  1.00  0.00           H  
ATOM   1491 1HD1 LEU    21      -8.034   0.907   8.687  1.00  0.00           H  
ATOM   1492 2HD1 LEU    21      -9.288   2.145   8.756  1.00  0.00           H  
ATOM   1493 3HD1 LEU    21      -9.714   0.445   8.958  1.00  0.00           H  
ATOM   1494 1HD2 LEU    21      -8.934   2.462   5.392  1.00  0.00           H  
ATOM   1495 2HD2 LEU    21     -10.519   2.572   6.157  1.00  0.00           H  
ATOM   1496 3HD2 LEU    21      -9.087   3.147   7.010  1.00  0.00           H  
ATOM   1497  N   THR    22      -9.461  -2.301   6.038  1.00  0.00           N  
ATOM   1498  CA  THR    22     -10.687  -3.144   6.072  1.00  0.00           C  
ATOM   1499  C   THR    22     -10.350  -4.495   6.703  1.00  0.00           C  
ATOM   1500  O   THR    22     -11.222  -5.257   7.071  1.00  0.00           O  
ATOM   1501  CB  THR    22     -11.200  -3.356   4.645  1.00  0.00           C  
ATOM   1502  OG1 THR    22     -12.427  -4.072   4.688  1.00  0.00           O  
ATOM   1503  CG2 THR    22     -10.172  -4.151   3.840  1.00  0.00           C  
ATOM   1504  H   THR    22      -9.010  -2.125   5.186  1.00  0.00           H  
ATOM   1505  HA  THR    22     -11.448  -2.651   6.660  1.00  0.00           H  
ATOM   1506  HB  THR    22     -11.359  -2.398   4.174  1.00  0.00           H  
ATOM   1507  HG1 THR    22     -12.861  -3.867   5.520  1.00  0.00           H  
ATOM   1508 1HG2 THR    22      -9.512  -4.675   4.516  1.00  0.00           H  
ATOM   1509 2HG2 THR    22     -10.681  -4.864   3.209  1.00  0.00           H  
ATOM   1510 3HG2 THR    22      -9.595  -3.475   3.225  1.00  0.00           H  
ATOM   1511  N   SER    23      -9.087  -4.797   6.835  1.00  0.00           N  
ATOM   1512  CA  SER    23      -8.689  -6.096   7.446  1.00  0.00           C  
ATOM   1513  C   SER    23      -8.860  -6.016   8.964  1.00  0.00           C  
ATOM   1514  O   SER    23      -9.327  -6.943   9.595  1.00  0.00           O  
ATOM   1515  CB  SER    23      -7.226  -6.387   7.113  1.00  0.00           C  
ATOM   1516  OG  SER    23      -7.164  -7.235   5.974  1.00  0.00           O  
ATOM   1517  H   SER    23      -8.400  -4.166   6.534  1.00  0.00           H  
ATOM   1518  HA  SER    23      -9.313  -6.885   7.053  1.00  0.00           H  
ATOM   1519 1HB  SER    23      -6.712  -5.465   6.897  1.00  0.00           H  
ATOM   1520 2HB  SER    23      -6.754  -6.869   7.959  1.00  0.00           H  
ATOM   1521  HG  SER    23      -7.961  -7.770   5.960  1.00  0.00           H  
ATOM   1522  N   GLN    24      -8.490  -4.913   9.553  1.00  0.00           N  
ATOM   1523  CA  GLN    24      -8.633  -4.767  11.024  1.00  0.00           C  
ATOM   1524  C   GLN    24     -10.092  -4.424  11.348  1.00  0.00           C  
ATOM   1525  O   GLN    24     -10.576  -4.679  12.432  1.00  0.00           O  
ATOM   1526  CB  GLN    24      -7.688  -3.650  11.501  1.00  0.00           C  
ATOM   1527  CG  GLN    24      -8.281  -2.923  12.711  1.00  0.00           C  
ATOM   1528  CD  GLN    24      -7.154  -2.351  13.571  1.00  0.00           C  
ATOM   1529  OE1 GLN    24      -6.051  -2.859  13.565  1.00  0.00           O  
ATOM   1530  NE2 GLN    24      -7.386  -1.304  14.316  1.00  0.00           N  
ATOM   1531  H   GLN    24      -8.119  -4.175   9.028  1.00  0.00           H  
ATOM   1532  HA  GLN    24      -8.366  -5.697  11.506  1.00  0.00           H  
ATOM   1533 1HB  GLN    24      -6.737  -4.081  11.777  1.00  0.00           H  
ATOM   1534 2HB  GLN    24      -7.540  -2.942  10.699  1.00  0.00           H  
ATOM   1535 1HG  GLN    24      -8.918  -2.120  12.367  1.00  0.00           H  
ATOM   1536 2HG  GLN    24      -8.863  -3.618  13.295  1.00  0.00           H  
ATOM   1537 1HE2 GLN    24      -6.671  -0.931  14.871  1.00  0.00           H  
ATOM   1538 2HE2 GLN    24      -8.276  -0.894  14.320  1.00  0.00           H  
ATOM   1539  N   ARG    25     -10.793  -3.847  10.412  1.00  0.00           N  
ATOM   1540  CA  ARG    25     -12.216  -3.485  10.663  1.00  0.00           C  
ATOM   1541  C   ARG    25     -13.118  -4.664  10.291  1.00  0.00           C  
ATOM   1542  O   ARG    25     -13.190  -4.982   9.116  1.00  0.00           O  
ATOM   1543  CB  ARG    25     -12.588  -2.270   9.812  1.00  0.00           C  
ATOM   1544  CG  ARG    25     -12.498  -1.004  10.665  1.00  0.00           C  
ATOM   1545  CD  ARG    25     -13.853  -0.298  10.674  1.00  0.00           C  
ATOM   1546  NE  ARG    25     -14.432  -0.352  12.045  1.00  0.00           N  
ATOM   1547  CZ  ARG    25     -14.884  -1.480  12.519  1.00  0.00           C  
ATOM   1548  NH1 ARG    25     -15.709  -2.202  11.810  1.00  0.00           N  
ATOM   1549  NH2 ARG    25     -14.510  -1.888  13.701  1.00  0.00           N  
ATOM   1550  OXT ARG    25     -13.723  -5.227  11.189  1.00  0.00           O  
ATOM   1551  H   ARG    25     -10.384  -3.648   9.543  1.00  0.00           H  
ATOM   1552  HA  ARG    25     -12.347  -3.247  11.708  1.00  0.00           H  
ATOM   1553 1HB  ARG    25     -11.906  -2.193   8.979  1.00  0.00           H  
ATOM   1554 2HB  ARG    25     -13.597  -2.383   9.446  1.00  0.00           H  
ATOM   1555 1HG  ARG    25     -12.222  -1.269  11.676  1.00  0.00           H  
ATOM   1556 2HG  ARG    25     -11.752  -0.342  10.250  1.00  0.00           H  
ATOM   1557 1HD  ARG    25     -13.726   0.732  10.376  1.00  0.00           H  
ATOM   1558 2HD  ARG    25     -14.520  -0.791   9.981  1.00  0.00           H  
ATOM   1559  HE  ARG    25     -14.475   0.462  12.591  1.00  0.00           H  
ATOM   1560 1HH1 ARG    25     -15.996  -1.889  10.904  1.00  0.00           H  
ATOM   1561 2HH1 ARG    25     -16.056  -3.067  12.173  1.00  0.00           H  
ATOM   1562 1HH2 ARG    25     -13.877  -1.336  14.243  1.00  0.00           H  
ATOM   1563 2HH2 ARG    25     -14.855  -2.754  14.064  1.00  0.00           H  
TER    1564      ARG    25                                                      
ENDMDL                                                                          
MODEL        5                                                                  
ATOM   1565  N   GLY     1      16.815   2.235  -5.715  1.00  0.00           N  
ATOM   1566  CA  GLY     1      15.942   1.905  -6.926  1.00  0.00           C  
ATOM   1567  C   GLY     1      15.450   3.008  -7.802  1.00  0.00           C  
ATOM   1568  O   GLY     1      14.431   2.887  -8.452  1.00  0.00           O  
ATOM   1569 1H   GLY     1      16.464   3.103  -5.262  1.00  0.00           H  
ATOM   1570 2H   GLY     1      16.776   1.448  -5.036  1.00  0.00           H  
ATOM   1571 3H   GLY     1      17.796   2.377  -6.024  1.00  0.00           H  
ATOM   1572 1HA  GLY     1      16.486   1.675  -7.701  1.00  0.00           H  
ATOM   1573 2HA  GLY     1      15.222   1.045  -6.602  1.00  0.00           H  
ATOM   1574  N   SER     2      16.155   4.106  -7.843  1.00  0.00           N  
ATOM   1575  CA  SER     2      15.713   5.241  -8.701  1.00  0.00           C  
ATOM   1576  C   SER     2      14.299   5.665  -8.298  1.00  0.00           C  
ATOM   1577  O   SER     2      13.570   4.914  -7.680  1.00  0.00           O  
ATOM   1578  CB  SER     2      15.716   4.805 -10.166  1.00  0.00           C  
ATOM   1579  OG  SER     2      17.059   4.664 -10.610  1.00  0.00           O  
ATOM   1580  H   SER     2      16.975   4.184  -7.311  1.00  0.00           H  
ATOM   1581  HA  SER     2      16.388   6.075  -8.573  1.00  0.00           H  
ATOM   1582 1HB  SER     2      15.211   3.858 -10.263  1.00  0.00           H  
ATOM   1583 2HB  SER     2      15.204   5.547 -10.764  1.00  0.00           H  
ATOM   1584  HG  SER     2      17.412   5.543 -10.770  1.00  0.00           H  
ATOM   1585  N   GLU     3      13.905   6.860  -8.640  1.00  0.00           N  
ATOM   1586  CA  GLU     3      12.538   7.327  -8.272  1.00  0.00           C  
ATOM   1587  C   GLU     3      11.496   6.376  -8.864  1.00  0.00           C  
ATOM   1588  O   GLU     3      10.351   6.363  -8.458  1.00  0.00           O  
ATOM   1589  CB  GLU     3      12.314   8.739  -8.818  1.00  0.00           C  
ATOM   1590  CG  GLU     3      12.771   9.767  -7.781  1.00  0.00           C  
ATOM   1591  CD  GLU     3      12.388  11.173  -8.249  1.00  0.00           C  
ATOM   1592  OE1 GLU     3      11.396  11.292  -8.949  1.00  0.00           O  
ATOM   1593  OE2 GLU     3      13.093  12.104  -7.900  1.00  0.00           O  
ATOM   1594  H   GLU     3      14.507   7.451  -9.138  1.00  0.00           H  
ATOM   1595  HA  GLU     3      12.441   7.339  -7.196  1.00  0.00           H  
ATOM   1596 1HB  GLU     3      12.883   8.866  -9.728  1.00  0.00           H  
ATOM   1597 2HB  GLU     3      11.264   8.881  -9.026  1.00  0.00           H  
ATOM   1598 1HG  GLU     3      12.295   9.559  -6.833  1.00  0.00           H  
ATOM   1599 2HG  GLU     3      13.843   9.709  -7.664  1.00  0.00           H  
ATOM   1600  N   LYS     4      11.883   5.575  -9.820  1.00  0.00           N  
ATOM   1601  CA  LYS     4      10.913   4.624 -10.432  1.00  0.00           C  
ATOM   1602  C   LYS     4      10.674   3.460  -9.469  1.00  0.00           C  
ATOM   1603  O   LYS     4       9.597   3.297  -8.932  1.00  0.00           O  
ATOM   1604  CB  LYS     4      11.480   4.090 -11.748  1.00  0.00           C  
ATOM   1605  CG  LYS     4      11.261   5.124 -12.852  1.00  0.00           C  
ATOM   1606  CD  LYS     4      12.353   6.192 -12.771  1.00  0.00           C  
ATOM   1607  CE  LYS     4      12.958   6.409 -14.158  1.00  0.00           C  
ATOM   1608  NZ  LYS     4      11.948   7.052 -15.044  1.00  0.00           N  
ATOM   1609  H   LYS     4      12.812   5.598 -10.132  1.00  0.00           H  
ATOM   1610  HA  LYS     4       9.980   5.132 -10.620  1.00  0.00           H  
ATOM   1611 1HB  LYS     4      12.537   3.901 -11.634  1.00  0.00           H  
ATOM   1612 2HB  LYS     4      10.976   3.171 -12.011  1.00  0.00           H  
ATOM   1613 1HG  LYS     4      11.301   4.637 -13.816  1.00  0.00           H  
ATOM   1614 2HG  LYS     4      10.295   5.589 -12.723  1.00  0.00           H  
ATOM   1615 1HD  LYS     4      11.925   7.118 -12.414  1.00  0.00           H  
ATOM   1616 2HD  LYS     4      13.124   5.866 -12.090  1.00  0.00           H  
ATOM   1617 1HE  LYS     4      13.824   7.049 -14.076  1.00  0.00           H  
ATOM   1618 2HE  LYS     4      13.251   5.458 -14.576  1.00  0.00           H  
ATOM   1619 1HZ  LYS     4      10.995   6.748 -14.763  1.00  0.00           H  
ATOM   1620 2HZ  LYS     4      12.019   8.085 -14.959  1.00  0.00           H  
ATOM   1621 3HZ  LYS     4      12.126   6.772 -16.031  1.00  0.00           H  
ATOM   1622  N   MET     5      11.673   2.651  -9.241  1.00  0.00           N  
ATOM   1623  CA  MET     5      11.500   1.504  -8.307  1.00  0.00           C  
ATOM   1624  C   MET     5      11.039   2.030  -6.948  1.00  0.00           C  
ATOM   1625  O   MET     5      10.503   1.301  -6.137  1.00  0.00           O  
ATOM   1626  CB  MET     5      12.833   0.770  -8.148  1.00  0.00           C  
ATOM   1627  CG  MET     5      12.573  -0.694  -7.784  1.00  0.00           C  
ATOM   1628  SD  MET     5      13.996  -1.354  -6.881  1.00  0.00           S  
ATOM   1629  CE  MET     5      13.548  -3.103  -6.996  1.00  0.00           C  
ATOM   1630  H   MET     5      12.536   2.802  -9.679  1.00  0.00           H  
ATOM   1631  HA  MET     5      10.758   0.826  -8.703  1.00  0.00           H  
ATOM   1632 1HB  MET     5      13.383   0.817  -9.078  1.00  0.00           H  
ATOM   1633 2HB  MET     5      13.411   1.237  -7.364  1.00  0.00           H  
ATOM   1634 1HG  MET     5      11.691  -0.760  -7.165  1.00  0.00           H  
ATOM   1635 2HG  MET     5      12.423  -1.268  -8.687  1.00  0.00           H  
ATOM   1636 1HE  MET     5      12.504  -3.189  -7.264  1.00  0.00           H  
ATOM   1637 2HE  MET     5      14.151  -3.582  -7.751  1.00  0.00           H  
ATOM   1638 3HE  MET     5      13.722  -3.581  -6.041  1.00  0.00           H  
ATOM   1639  N   SER     6      11.243   3.293  -6.695  1.00  0.00           N  
ATOM   1640  CA  SER     6      10.817   3.872  -5.390  1.00  0.00           C  
ATOM   1641  C   SER     6       9.330   4.227  -5.457  1.00  0.00           C  
ATOM   1642  O   SER     6       8.612   4.118  -4.483  1.00  0.00           O  
ATOM   1643  CB  SER     6      11.632   5.134  -5.104  1.00  0.00           C  
ATOM   1644  OG  SER     6      11.746   5.308  -3.698  1.00  0.00           O  
ATOM   1645  H   SER     6      11.677   3.862  -7.364  1.00  0.00           H  
ATOM   1646  HA  SER     6      10.981   3.151  -4.605  1.00  0.00           H  
ATOM   1647 1HB  SER     6      12.615   5.034  -5.530  1.00  0.00           H  
ATOM   1648 2HB  SER     6      11.135   5.989  -5.544  1.00  0.00           H  
ATOM   1649  HG  SER     6      10.860   5.342  -3.331  1.00  0.00           H  
ATOM   1650  N   THR     7       8.860   4.639  -6.603  1.00  0.00           N  
ATOM   1651  CA  THR     7       7.418   4.990  -6.732  1.00  0.00           C  
ATOM   1652  C   THR     7       6.608   3.699  -6.823  1.00  0.00           C  
ATOM   1653  O   THR     7       5.411   3.684  -6.610  1.00  0.00           O  
ATOM   1654  CB  THR     7       7.203   5.823  -7.998  1.00  0.00           C  
ATOM   1655  OG1 THR     7       5.877   6.335  -8.004  1.00  0.00           O  
ATOM   1656  CG2 THR     7       7.421   4.950  -9.234  1.00  0.00           C  
ATOM   1657  H   THR     7       9.453   4.709  -7.380  1.00  0.00           H  
ATOM   1658  HA  THR     7       7.104   5.555  -5.867  1.00  0.00           H  
ATOM   1659  HB  THR     7       7.904   6.642  -8.013  1.00  0.00           H  
ATOM   1660  HG1 THR     7       5.883   7.180  -7.549  1.00  0.00           H  
ATOM   1661 1HG2 THR     7       7.596   3.929  -8.928  1.00  0.00           H  
ATOM   1662 2HG2 THR     7       6.545   4.992  -9.864  1.00  0.00           H  
ATOM   1663 3HG2 THR     7       8.277   5.312  -9.784  1.00  0.00           H  
ATOM   1664  N   ALA     8       7.261   2.611  -7.125  1.00  0.00           N  
ATOM   1665  CA  ALA     8       6.548   1.313  -7.218  1.00  0.00           C  
ATOM   1666  C   ALA     8       6.397   0.751  -5.810  1.00  0.00           C  
ATOM   1667  O   ALA     8       5.378   0.195  -5.452  1.00  0.00           O  
ATOM   1668  CB  ALA     8       7.364   0.347  -8.076  1.00  0.00           C  
ATOM   1669  H   ALA     8       8.227   2.647  -7.278  1.00  0.00           H  
ATOM   1670  HA  ALA     8       5.574   1.462  -7.657  1.00  0.00           H  
ATOM   1671 1HB  ALA     8       8.392   0.678  -8.110  1.00  0.00           H  
ATOM   1672 2HB  ALA     8       7.318  -0.642  -7.649  1.00  0.00           H  
ATOM   1673 3HB  ALA     8       6.960   0.328  -9.078  1.00  0.00           H  
ATOM   1674  N   ILE     9       7.407   0.912  -5.001  1.00  0.00           N  
ATOM   1675  CA  ILE     9       7.326   0.410  -3.608  1.00  0.00           C  
ATOM   1676  C   ILE     9       6.312   1.264  -2.846  1.00  0.00           C  
ATOM   1677  O   ILE     9       5.642   0.801  -1.948  1.00  0.00           O  
ATOM   1678  CB  ILE     9       8.699   0.517  -2.942  1.00  0.00           C  
ATOM   1679  CG1 ILE     9       9.172   1.971  -2.987  1.00  0.00           C  
ATOM   1680  CG2 ILE     9       9.701  -0.366  -3.686  1.00  0.00           C  
ATOM   1681  CD1 ILE     9      10.348   2.154  -2.026  1.00  0.00           C  
ATOM   1682  H   ILE     9       8.211   1.377  -5.310  1.00  0.00           H  
ATOM   1683  HA  ILE     9       7.002  -0.618  -3.614  1.00  0.00           H  
ATOM   1684  HB  ILE     9       8.627   0.192  -1.913  1.00  0.00           H  
ATOM   1685 1HG1 ILE     9       9.485   2.215  -3.992  1.00  0.00           H  
ATOM   1686 2HG1 ILE     9       8.364   2.623  -2.692  1.00  0.00           H  
ATOM   1687 1HG2 ILE     9       9.326  -0.580  -4.677  1.00  0.00           H  
ATOM   1688 2HG2 ILE     9      10.646   0.150  -3.763  1.00  0.00           H  
ATOM   1689 3HG2 ILE     9       9.837  -1.290  -3.145  1.00  0.00           H  
ATOM   1690 1HD1 ILE     9      10.365   1.339  -1.318  1.00  0.00           H  
ATOM   1691 2HD1 ILE     9      11.272   2.164  -2.585  1.00  0.00           H  
ATOM   1692 3HD1 ILE     9      10.238   3.089  -1.496  1.00  0.00           H  
ATOM   1693  N   SER    10       6.191   2.512  -3.211  1.00  0.00           N  
ATOM   1694  CA  SER    10       5.213   3.398  -2.521  1.00  0.00           C  
ATOM   1695  C   SER    10       3.796   2.927  -2.844  1.00  0.00           C  
ATOM   1696  O   SER    10       3.001   2.669  -1.960  1.00  0.00           O  
ATOM   1697  CB  SER    10       5.397   4.836  -3.007  1.00  0.00           C  
ATOM   1698  OG  SER    10       6.672   5.311  -2.598  1.00  0.00           O  
ATOM   1699  H   SER    10       6.737   2.864  -3.947  1.00  0.00           H  
ATOM   1700  HA  SER    10       5.376   3.353  -1.455  1.00  0.00           H  
ATOM   1701 1HB  SER    10       5.335   4.867  -4.082  1.00  0.00           H  
ATOM   1702 2HB  SER    10       4.617   5.459  -2.587  1.00  0.00           H  
ATOM   1703  HG  SER    10       7.068   5.776  -3.339  1.00  0.00           H  
ATOM   1704  N   VAL    11       3.471   2.804  -4.102  1.00  0.00           N  
ATOM   1705  CA  VAL    11       2.106   2.341  -4.474  1.00  0.00           C  
ATOM   1706  C   VAL    11       1.805   1.035  -3.735  1.00  0.00           C  
ATOM   1707  O   VAL    11       0.688   0.780  -3.332  1.00  0.00           O  
ATOM   1708  CB  VAL    11       2.035   2.101  -5.984  1.00  0.00           C  
ATOM   1709  CG1 VAL    11       0.714   1.413  -6.331  1.00  0.00           C  
ATOM   1710  CG2 VAL    11       2.117   3.441  -6.719  1.00  0.00           C  
ATOM   1711  H   VAL    11       4.127   3.011  -4.802  1.00  0.00           H  
ATOM   1712  HA  VAL    11       1.380   3.090  -4.192  1.00  0.00           H  
ATOM   1713  HB  VAL    11       2.859   1.471  -6.287  1.00  0.00           H  
ATOM   1714 1HG1 VAL    11       0.627   0.493  -5.772  1.00  0.00           H  
ATOM   1715 2HG1 VAL    11      -0.108   2.066  -6.079  1.00  0.00           H  
ATOM   1716 3HG1 VAL    11       0.689   1.194  -7.389  1.00  0.00           H  
ATOM   1717 1HG2 VAL    11       2.624   4.164  -6.097  1.00  0.00           H  
ATOM   1718 2HG2 VAL    11       2.663   3.313  -7.642  1.00  0.00           H  
ATOM   1719 3HG2 VAL    11       1.119   3.792  -6.938  1.00  0.00           H  
ATOM   1720  N   LEU    12       2.796   0.207  -3.549  1.00  0.00           N  
ATOM   1721  CA  LEU    12       2.565  -1.076  -2.828  1.00  0.00           C  
ATOM   1722  C   LEU    12       2.023  -0.776  -1.429  1.00  0.00           C  
ATOM   1723  O   LEU    12       0.967  -1.239  -1.048  1.00  0.00           O  
ATOM   1724  CB  LEU    12       3.884  -1.841  -2.710  1.00  0.00           C  
ATOM   1725  CG  LEU    12       4.006  -2.834  -3.867  1.00  0.00           C  
ATOM   1726  CD1 LEU    12       5.461  -3.290  -3.997  1.00  0.00           C  
ATOM   1727  CD2 LEU    12       3.116  -4.048  -3.593  1.00  0.00           C  
ATOM   1728  H   LEU    12       3.691   0.431  -3.877  1.00  0.00           H  
ATOM   1729  HA  LEU    12       1.848  -1.672  -3.374  1.00  0.00           H  
ATOM   1730 1HB  LEU    12       4.708  -1.143  -2.745  1.00  0.00           H  
ATOM   1731 2HB  LEU    12       3.905  -2.378  -1.773  1.00  0.00           H  
ATOM   1732  HG  LEU    12       3.695  -2.356  -4.785  1.00  0.00           H  
ATOM   1733 1HD1 LEU    12       6.039  -2.885  -3.180  1.00  0.00           H  
ATOM   1734 2HD1 LEU    12       5.503  -4.368  -3.969  1.00  0.00           H  
ATOM   1735 3HD1 LEU    12       5.866  -2.937  -4.934  1.00  0.00           H  
ATOM   1736 1HD2 LEU    12       2.184  -3.720  -3.154  1.00  0.00           H  
ATOM   1737 2HD2 LEU    12       2.915  -4.564  -4.520  1.00  0.00           H  
ATOM   1738 3HD2 LEU    12       3.619  -4.717  -2.911  1.00  0.00           H  
ATOM   1739  N   LEU    13       2.736   0.002  -0.661  1.00  0.00           N  
ATOM   1740  CA  LEU    13       2.259   0.335   0.710  1.00  0.00           C  
ATOM   1741  C   LEU    13       0.852   0.922   0.624  1.00  0.00           C  
ATOM   1742  O   LEU    13       0.056   0.789   1.531  1.00  0.00           O  
ATOM   1743  CB  LEU    13       3.202   1.363   1.339  1.00  0.00           C  
ATOM   1744  CG  LEU    13       4.452   0.662   1.877  1.00  0.00           C  
ATOM   1745  CD1 LEU    13       4.931  -0.394   0.878  1.00  0.00           C  
ATOM   1746  CD2 LEU    13       5.557   1.699   2.085  1.00  0.00           C  
ATOM   1747  H   LEU    13       3.585   0.370  -0.987  1.00  0.00           H  
ATOM   1748  HA  LEU    13       2.242  -0.559   1.315  1.00  0.00           H  
ATOM   1749 1HB  LEU    13       3.491   2.089   0.593  1.00  0.00           H  
ATOM   1750 2HB  LEU    13       2.696   1.865   2.151  1.00  0.00           H  
ATOM   1751  HG  LEU    13       4.221   0.187   2.821  1.00  0.00           H  
ATOM   1752 1HD1 LEU    13       4.150  -1.124   0.723  1.00  0.00           H  
ATOM   1753 2HD1 LEU    13       5.169   0.081  -0.059  1.00  0.00           H  
ATOM   1754 3HD1 LEU    13       5.810  -0.886   1.266  1.00  0.00           H  
ATOM   1755 1HD2 LEU    13       5.121   2.688   2.109  1.00  0.00           H  
ATOM   1756 2HD2 LEU    13       6.064   1.506   3.018  1.00  0.00           H  
ATOM   1757 3HD2 LEU    13       6.264   1.639   1.271  1.00  0.00           H  
ATOM   1758  N   ALA    14       0.541   1.573  -0.462  1.00  0.00           N  
ATOM   1759  CA  ALA    14      -0.817   2.172  -0.613  1.00  0.00           C  
ATOM   1760  C   ALA    14      -1.878   1.080  -0.458  1.00  0.00           C  
ATOM   1761  O   ALA    14      -2.612   1.046   0.512  1.00  0.00           O  
ATOM   1762  CB  ALA    14      -0.943   2.815  -1.995  1.00  0.00           C  
ATOM   1763  H   ALA    14       1.202   1.668  -1.179  1.00  0.00           H  
ATOM   1764  HA  ALA    14      -0.963   2.923   0.148  1.00  0.00           H  
ATOM   1765 1HB  ALA    14      -0.152   3.540  -2.129  1.00  0.00           H  
ATOM   1766 2HB  ALA    14      -0.865   2.054  -2.755  1.00  0.00           H  
ATOM   1767 3HB  ALA    14      -1.899   3.309  -2.076  1.00  0.00           H  
ATOM   1768  N   GLN    15      -1.969   0.186  -1.406  1.00  0.00           N  
ATOM   1769  CA  GLN    15      -2.987  -0.899  -1.307  1.00  0.00           C  
ATOM   1770  C   GLN    15      -2.854  -1.596   0.050  1.00  0.00           C  
ATOM   1771  O   GLN    15      -3.793  -2.181   0.553  1.00  0.00           O  
ATOM   1772  CB  GLN    15      -2.770  -1.915  -2.433  1.00  0.00           C  
ATOM   1773  CG  GLN    15      -1.551  -2.787  -2.120  1.00  0.00           C  
ATOM   1774  CD  GLN    15      -1.248  -3.690  -3.318  1.00  0.00           C  
ATOM   1775  OE1 GLN    15      -1.308  -4.898  -3.212  1.00  0.00           O  
ATOM   1776  NE2 GLN    15      -0.926  -3.150  -4.461  1.00  0.00           N  
ATOM   1777  H   GLN    15      -1.370   0.228  -2.180  1.00  0.00           H  
ATOM   1778  HA  GLN    15      -3.974  -0.472  -1.394  1.00  0.00           H  
ATOM   1779 1HB  GLN    15      -3.646  -2.542  -2.525  1.00  0.00           H  
ATOM   1780 2HB  GLN    15      -2.605  -1.390  -3.363  1.00  0.00           H  
ATOM   1781 1HG  GLN    15      -0.699  -2.155  -1.922  1.00  0.00           H  
ATOM   1782 2HG  GLN    15      -1.758  -3.398  -1.255  1.00  0.00           H  
ATOM   1783 1HE2 GLN    15      -0.730  -3.720  -5.235  1.00  0.00           H  
ATOM   1784 2HE2 GLN    15      -0.879  -2.175  -4.547  1.00  0.00           H  
ATOM   1785  N   ALA    16      -1.695  -1.537   0.645  1.00  0.00           N  
ATOM   1786  CA  ALA    16      -1.502  -2.193   1.969  1.00  0.00           C  
ATOM   1787  C   ALA    16      -2.349  -1.475   3.022  1.00  0.00           C  
ATOM   1788  O   ALA    16      -3.014  -2.097   3.827  1.00  0.00           O  
ATOM   1789  CB  ALA    16      -0.027  -2.118   2.365  1.00  0.00           C  
ATOM   1790  H   ALA    16      -0.951  -1.059   0.222  1.00  0.00           H  
ATOM   1791  HA  ALA    16      -1.806  -3.227   1.906  1.00  0.00           H  
ATOM   1792 1HB  ALA    16       0.588  -2.220   1.483  1.00  0.00           H  
ATOM   1793 2HB  ALA    16       0.172  -1.166   2.834  1.00  0.00           H  
ATOM   1794 3HB  ALA    16       0.200  -2.916   3.057  1.00  0.00           H  
ATOM   1795  N   VAL    17      -2.333  -0.170   3.022  1.00  0.00           N  
ATOM   1796  CA  VAL    17      -3.140   0.584   4.023  1.00  0.00           C  
ATOM   1797  C   VAL    17      -4.624   0.300   3.795  1.00  0.00           C  
ATOM   1798  O   VAL    17      -5.382   0.124   4.729  1.00  0.00           O  
ATOM   1799  CB  VAL    17      -2.877   2.084   3.868  1.00  0.00           C  
ATOM   1800  CG1 VAL    17      -3.742   2.857   4.864  1.00  0.00           C  
ATOM   1801  CG2 VAL    17      -1.400   2.377   4.143  1.00  0.00           C  
ATOM   1802  H   VAL    17      -1.794   0.314   2.365  1.00  0.00           H  
ATOM   1803  HA  VAL    17      -2.861   0.271   5.019  1.00  0.00           H  
ATOM   1804  HB  VAL    17      -3.127   2.390   2.862  1.00  0.00           H  
ATOM   1805 1HG1 VAL    17      -4.174   2.169   5.576  1.00  0.00           H  
ATOM   1806 2HG1 VAL    17      -3.132   3.579   5.385  1.00  0.00           H  
ATOM   1807 3HG1 VAL    17      -4.533   3.368   4.335  1.00  0.00           H  
ATOM   1808 1HG2 VAL    17      -0.860   1.446   4.234  1.00  0.00           H  
ATOM   1809 2HG2 VAL    17      -0.989   2.953   3.327  1.00  0.00           H  
ATOM   1810 3HG2 VAL    17      -1.310   2.937   5.062  1.00  0.00           H  
ATOM   1811  N   PHE    18      -5.047   0.251   2.562  1.00  0.00           N  
ATOM   1812  CA  PHE    18      -6.485  -0.026   2.280  1.00  0.00           C  
ATOM   1813  C   PHE    18      -6.897  -1.325   2.975  1.00  0.00           C  
ATOM   1814  O   PHE    18      -7.751  -1.337   3.842  1.00  0.00           O  
ATOM   1815  CB  PHE    18      -6.688  -0.163   0.769  1.00  0.00           C  
ATOM   1816  CG  PHE    18      -8.151  -0.389   0.470  1.00  0.00           C  
ATOM   1817  CD1 PHE    18      -9.088   0.611   0.757  1.00  0.00           C  
ATOM   1818  CD2 PHE    18      -8.570  -1.598  -0.097  1.00  0.00           C  
ATOM   1819  CE1 PHE    18     -10.444   0.401   0.477  1.00  0.00           C  
ATOM   1820  CE2 PHE    18      -9.926  -1.809  -0.376  1.00  0.00           C  
ATOM   1821  CZ  PHE    18     -10.863  -0.809  -0.089  1.00  0.00           C  
ATOM   1822  H   PHE    18      -4.420   0.395   1.822  1.00  0.00           H  
ATOM   1823  HA  PHE    18      -7.089   0.789   2.652  1.00  0.00           H  
ATOM   1824 1HB  PHE    18      -6.357   0.740   0.278  1.00  0.00           H  
ATOM   1825 2HB  PHE    18      -6.114  -1.002   0.404  1.00  0.00           H  
ATOM   1826  HD1 PHE    18      -8.765   1.544   1.194  1.00  0.00           H  
ATOM   1827  HD2 PHE    18      -7.847  -2.370  -0.318  1.00  0.00           H  
ATOM   1828  HE1 PHE    18     -11.166   1.173   0.698  1.00  0.00           H  
ATOM   1829  HE2 PHE    18     -10.249  -2.742  -0.814  1.00  0.00           H  
ATOM   1830  HZ  PHE    18     -11.908  -0.971  -0.306  1.00  0.00           H  
ATOM   1831  N   LEU    19      -6.296  -2.423   2.603  1.00  0.00           N  
ATOM   1832  CA  LEU    19      -6.651  -3.721   3.244  1.00  0.00           C  
ATOM   1833  C   LEU    19      -6.276  -3.673   4.727  1.00  0.00           C  
ATOM   1834  O   LEU    19      -6.749  -4.461   5.522  1.00  0.00           O  
ATOM   1835  CB  LEU    19      -5.885  -4.855   2.556  1.00  0.00           C  
ATOM   1836  CG  LEU    19      -4.412  -4.808   2.968  1.00  0.00           C  
ATOM   1837  CD1 LEU    19      -4.205  -5.660   4.222  1.00  0.00           C  
ATOM   1838  CD2 LEU    19      -3.547  -5.355   1.832  1.00  0.00           C  
ATOM   1839  H   LEU    19      -5.609  -2.392   1.904  1.00  0.00           H  
ATOM   1840  HA  LEU    19      -7.713  -3.891   3.146  1.00  0.00           H  
ATOM   1841 1HB  LEU    19      -6.312  -5.804   2.849  1.00  0.00           H  
ATOM   1842 2HB  LEU    19      -5.961  -4.742   1.484  1.00  0.00           H  
ATOM   1843  HG  LEU    19      -4.130  -3.786   3.179  1.00  0.00           H  
ATOM   1844 1HD1 LEU    19      -5.161  -5.859   4.685  1.00  0.00           H  
ATOM   1845 2HD1 LEU    19      -3.737  -6.595   3.949  1.00  0.00           H  
ATOM   1846 3HD1 LEU    19      -3.571  -5.131   4.917  1.00  0.00           H  
ATOM   1847 1HD2 LEU    19      -3.861  -4.917   0.896  1.00  0.00           H  
ATOM   1848 2HD2 LEU    19      -2.512  -5.106   2.015  1.00  0.00           H  
ATOM   1849 3HD2 LEU    19      -3.656  -6.429   1.781  1.00  0.00           H  
ATOM   1850  N   LEU    20      -5.429  -2.755   5.105  1.00  0.00           N  
ATOM   1851  CA  LEU    20      -5.023  -2.656   6.534  1.00  0.00           C  
ATOM   1852  C   LEU    20      -6.192  -2.114   7.360  1.00  0.00           C  
ATOM   1853  O   LEU    20      -6.394  -2.499   8.494  1.00  0.00           O  
ATOM   1854  CB  LEU    20      -3.827  -1.709   6.659  1.00  0.00           C  
ATOM   1855  CG  LEU    20      -3.383  -1.635   8.121  1.00  0.00           C  
ATOM   1856  CD1 LEU    20      -2.484  -2.829   8.445  1.00  0.00           C  
ATOM   1857  CD2 LEU    20      -2.608  -0.335   8.351  1.00  0.00           C  
ATOM   1858  H   LEU    20      -5.060  -2.129   4.447  1.00  0.00           H  
ATOM   1859  HA  LEU    20      -4.747  -3.635   6.899  1.00  0.00           H  
ATOM   1860 1HB  LEU    20      -3.010  -2.079   6.054  1.00  0.00           H  
ATOM   1861 2HB  LEU    20      -4.110  -0.724   6.320  1.00  0.00           H  
ATOM   1862  HG  LEU    20      -4.254  -1.655   8.763  1.00  0.00           H  
ATOM   1863 1HD1 LEU    20      -1.806  -3.002   7.623  1.00  0.00           H  
ATOM   1864 2HD1 LEU    20      -1.918  -2.620   9.341  1.00  0.00           H  
ATOM   1865 3HD1 LEU    20      -3.094  -3.707   8.601  1.00  0.00           H  
ATOM   1866 1HD2 LEU    20      -2.981   0.430   7.687  1.00  0.00           H  
ATOM   1867 2HD2 LEU    20      -2.735  -0.016   9.375  1.00  0.00           H  
ATOM   1868 3HD2 LEU    20      -1.558  -0.503   8.154  1.00  0.00           H  
ATOM   1869  N   LEU    21      -6.964  -1.225   6.799  1.00  0.00           N  
ATOM   1870  CA  LEU    21      -8.119  -0.661   7.552  1.00  0.00           C  
ATOM   1871  C   LEU    21      -9.262  -1.677   7.569  1.00  0.00           C  
ATOM   1872  O   LEU    21      -9.913  -1.878   8.574  1.00  0.00           O  
ATOM   1873  CB  LEU    21      -8.593   0.626   6.873  1.00  0.00           C  
ATOM   1874  CG  LEU    21      -9.909   1.080   7.504  1.00  0.00           C  
ATOM   1875  CD1 LEU    21      -9.704   1.306   9.003  1.00  0.00           C  
ATOM   1876  CD2 LEU    21     -10.366   2.385   6.850  1.00  0.00           C  
ATOM   1877  H   LEU    21      -6.785  -0.928   5.882  1.00  0.00           H  
ATOM   1878  HA  LEU    21      -7.816  -0.442   8.565  1.00  0.00           H  
ATOM   1879 1HB  LEU    21      -7.847   1.396   7.000  1.00  0.00           H  
ATOM   1880 2HB  LEU    21      -8.745   0.441   5.820  1.00  0.00           H  
ATOM   1881  HG  LEU    21     -10.662   0.318   7.355  1.00  0.00           H  
ATOM   1882 1HD1 LEU    21      -8.678   1.096   9.261  1.00  0.00           H  
ATOM   1883 2HD1 LEU    21      -9.934   2.332   9.246  1.00  0.00           H  
ATOM   1884 3HD1 LEU    21     -10.358   0.649   9.558  1.00  0.00           H  
ATOM   1885 1HD2 LEU    21     -10.476   2.236   5.785  1.00  0.00           H  
ATOM   1886 2HD2 LEU    21     -11.313   2.688   7.271  1.00  0.00           H  
ATOM   1887 3HD2 LEU    21      -9.630   3.156   7.031  1.00  0.00           H  
ATOM   1888  N   THR    22      -9.512  -2.318   6.460  1.00  0.00           N  
ATOM   1889  CA  THR    22     -10.615  -3.320   6.412  1.00  0.00           C  
ATOM   1890  C   THR    22     -10.262  -4.515   7.303  1.00  0.00           C  
ATOM   1891  O   THR    22     -11.128  -5.216   7.787  1.00  0.00           O  
ATOM   1892  CB  THR    22     -10.806  -3.801   4.971  1.00  0.00           C  
ATOM   1893  OG1 THR    22      -9.893  -4.854   4.699  1.00  0.00           O  
ATOM   1894  CG2 THR    22     -10.552  -2.641   4.006  1.00  0.00           C  
ATOM   1895  H   THR    22      -8.975  -2.141   5.658  1.00  0.00           H  
ATOM   1896  HA  THR    22     -11.529  -2.866   6.764  1.00  0.00           H  
ATOM   1897  HB  THR    22     -11.817  -4.157   4.840  1.00  0.00           H  
ATOM   1898  HG1 THR    22     -10.357  -5.687   4.813  1.00  0.00           H  
ATOM   1899 1HG2 THR    22     -10.930  -1.726   4.436  1.00  0.00           H  
ATOM   1900 2HG2 THR    22      -9.491  -2.545   3.830  1.00  0.00           H  
ATOM   1901 3HG2 THR    22     -11.057  -2.835   3.071  1.00  0.00           H  
ATOM   1902  N   SER    23      -8.997  -4.753   7.518  1.00  0.00           N  
ATOM   1903  CA  SER    23      -8.590  -5.906   8.372  1.00  0.00           C  
ATOM   1904  C   SER    23      -8.605  -5.491   9.846  1.00  0.00           C  
ATOM   1905  O   SER    23      -8.904  -6.281  10.718  1.00  0.00           O  
ATOM   1906  CB  SER    23      -7.180  -6.351   7.986  1.00  0.00           C  
ATOM   1907  OG  SER    23      -7.247  -7.620   7.348  1.00  0.00           O  
ATOM   1908  H   SER    23      -8.315  -4.178   7.114  1.00  0.00           H  
ATOM   1909  HA  SER    23      -9.279  -6.724   8.224  1.00  0.00           H  
ATOM   1910 1HB  SER    23      -6.747  -5.635   7.307  1.00  0.00           H  
ATOM   1911 2HB  SER    23      -6.568  -6.415   8.876  1.00  0.00           H  
ATOM   1912  HG  SER    23      -6.612  -8.200   7.775  1.00  0.00           H  
ATOM   1913  N   GLN    24      -8.278  -4.259  10.133  1.00  0.00           N  
ATOM   1914  CA  GLN    24      -8.271  -3.805  11.553  1.00  0.00           C  
ATOM   1915  C   GLN    24      -9.702  -3.511  12.008  1.00  0.00           C  
ATOM   1916  O   GLN    24      -9.977  -3.401  13.186  1.00  0.00           O  
ATOM   1917  CB  GLN    24      -7.426  -2.537  11.679  1.00  0.00           C  
ATOM   1918  CG  GLN    24      -6.111  -2.868  12.390  1.00  0.00           C  
ATOM   1919  CD  GLN    24      -4.987  -2.002  11.817  1.00  0.00           C  
ATOM   1920  OE1 GLN    24      -5.177  -0.829  11.563  1.00  0.00           O  
ATOM   1921  NE2 GLN    24      -3.815  -2.534  11.601  1.00  0.00           N  
ATOM   1922  H   GLN    24      -8.036  -3.636   9.417  1.00  0.00           H  
ATOM   1923  HA  GLN    24      -7.849  -4.580  12.175  1.00  0.00           H  
ATOM   1924 1HB  GLN    24      -7.215  -2.144  10.695  1.00  0.00           H  
ATOM   1925 2HB  GLN    24      -7.966  -1.799  12.253  1.00  0.00           H  
ATOM   1926 1HG  GLN    24      -6.214  -2.673  13.447  1.00  0.00           H  
ATOM   1927 2HG  GLN    24      -5.872  -3.910  12.237  1.00  0.00           H  
ATOM   1928 1HE2 GLN    24      -3.089  -1.988  11.236  1.00  0.00           H  
ATOM   1929 2HE2 GLN    24      -3.662  -3.479  11.806  1.00  0.00           H  
ATOM   1930  N   ARG    25     -10.616  -3.382  11.086  1.00  0.00           N  
ATOM   1931  CA  ARG    25     -12.026  -3.095  11.474  1.00  0.00           C  
ATOM   1932  C   ARG    25     -12.841  -4.389  11.435  1.00  0.00           C  
ATOM   1933  O   ARG    25     -13.999  -4.349  11.817  1.00  0.00           O  
ATOM   1934  CB  ARG    25     -12.627  -2.083  10.495  1.00  0.00           C  
ATOM   1935  CG  ARG    25     -13.772  -1.333  11.177  1.00  0.00           C  
ATOM   1936  CD  ARG    25     -13.279   0.039  11.642  1.00  0.00           C  
ATOM   1937  NE  ARG    25     -12.848   0.836  10.459  1.00  0.00           N  
ATOM   1938  CZ  ARG    25     -12.757   2.135  10.545  1.00  0.00           C  
ATOM   1939  NH1 ARG    25     -12.610   2.703  11.711  1.00  0.00           N  
ATOM   1940  NH2 ARG    25     -12.813   2.865   9.466  1.00  0.00           N  
ATOM   1941  OXT ARG    25     -12.293  -5.399  11.026  1.00  0.00           O  
ATOM   1942  H   ARG    25     -10.375  -3.473  10.141  1.00  0.00           H  
ATOM   1943  HA  ARG    25     -12.048  -2.685  12.472  1.00  0.00           H  
ATOM   1944 1HB  ARG    25     -11.865  -1.380  10.191  1.00  0.00           H  
ATOM   1945 2HB  ARG    25     -13.006  -2.602   9.628  1.00  0.00           H  
ATOM   1946 1HG  ARG    25     -14.585  -1.206  10.478  1.00  0.00           H  
ATOM   1947 2HG  ARG    25     -14.115  -1.898  12.031  1.00  0.00           H  
ATOM   1948 1HD  ARG    25     -14.078   0.555  12.152  1.00  0.00           H  
ATOM   1949 2HD  ARG    25     -12.444  -0.087  12.315  1.00  0.00           H  
ATOM   1950  HE  ARG    25     -12.634   0.385   9.616  1.00  0.00           H  
ATOM   1951 1HH1 ARG    25     -12.568   2.143  12.539  1.00  0.00           H  
ATOM   1952 2HH1 ARG    25     -12.539   3.698  11.776  1.00  0.00           H  
ATOM   1953 1HH2 ARG    25     -12.928   2.431   8.573  1.00  0.00           H  
ATOM   1954 2HH2 ARG    25     -12.742   3.861   9.532  1.00  0.00           H  
TER    1955      ARG    25                                                      
ENDMDL                                                                          
MODEL        6                                                                  
ATOM   1956  N   GLY     1      14.522   7.109 -14.316  1.00  0.00           N  
ATOM   1957  CA  GLY     1      13.576   6.049 -13.753  1.00  0.00           C  
ATOM   1958  C   GLY     1      13.511   5.838 -12.279  1.00  0.00           C  
ATOM   1959  O   GLY     1      12.711   5.067 -11.787  1.00  0.00           O  
ATOM   1960 1H   GLY     1      14.426   7.987 -13.767  1.00  0.00           H  
ATOM   1961 2H   GLY     1      15.503   6.768 -14.252  1.00  0.00           H  
ATOM   1962 3H   GLY     1      14.283   7.294 -15.312  1.00  0.00           H  
ATOM   1963 1HA  GLY     1      12.675   6.403 -13.636  1.00  0.00           H  
ATOM   1964 2HA  GLY     1      13.616   5.136 -14.480  1.00  0.00           H  
ATOM   1965  N   SER     2      14.345   6.515 -11.538  1.00  0.00           N  
ATOM   1966  CA  SER     2      14.332   6.350 -10.057  1.00  0.00           C  
ATOM   1967  C   SER     2      12.939   6.680  -9.517  1.00  0.00           C  
ATOM   1968  O   SER     2      12.397   5.969  -8.694  1.00  0.00           O  
ATOM   1969  CB  SER     2      15.357   7.297  -9.432  1.00  0.00           C  
ATOM   1970  OG  SER     2      16.624   7.087 -10.041  1.00  0.00           O  
ATOM   1971  H   SER     2      14.981   7.132 -11.956  1.00  0.00           H  
ATOM   1972  HA  SER     2      14.584   5.330  -9.806  1.00  0.00           H  
ATOM   1973 1HB  SER     2      15.051   8.318  -9.592  1.00  0.00           H  
ATOM   1974 2HB  SER     2      15.420   7.106  -8.369  1.00  0.00           H  
ATOM   1975  HG  SER     2      17.177   7.847  -9.841  1.00  0.00           H  
ATOM   1976  N   GLU     3      12.356   7.755  -9.973  1.00  0.00           N  
ATOM   1977  CA  GLU     3      10.999   8.131  -9.482  1.00  0.00           C  
ATOM   1978  C   GLU     3      10.025   6.978  -9.734  1.00  0.00           C  
ATOM   1979  O   GLU     3       9.148   6.709  -8.937  1.00  0.00           O  
ATOM   1980  CB  GLU     3      10.515   9.378 -10.224  1.00  0.00           C  
ATOM   1981  CG  GLU     3       9.942  10.379  -9.220  1.00  0.00           C  
ATOM   1982  CD  GLU     3       9.323  11.559  -9.970  1.00  0.00           C  
ATOM   1983  OE1 GLU     3       9.977  12.077 -10.861  1.00  0.00           O  
ATOM   1984  OE2 GLU     3       8.207  11.925  -9.642  1.00  0.00           O  
ATOM   1985  H   GLU     3      12.810   8.316 -10.635  1.00  0.00           H  
ATOM   1986  HA  GLU     3      11.044   8.338  -8.423  1.00  0.00           H  
ATOM   1987 1HB  GLU     3      11.346   9.828 -10.749  1.00  0.00           H  
ATOM   1988 2HB  GLU     3       9.748   9.101 -10.932  1.00  0.00           H  
ATOM   1989 1HG  GLU     3       9.184   9.893  -8.621  1.00  0.00           H  
ATOM   1990 2HG  GLU     3      10.733  10.737  -8.577  1.00  0.00           H  
ATOM   1991  N   LYS     4      10.171   6.295 -10.836  1.00  0.00           N  
ATOM   1992  CA  LYS     4       9.250   5.162 -11.134  1.00  0.00           C  
ATOM   1993  C   LYS     4       9.461   4.054 -10.101  1.00  0.00           C  
ATOM   1994  O   LYS     4       8.540   3.638  -9.427  1.00  0.00           O  
ATOM   1995  CB  LYS     4       9.541   4.614 -12.534  1.00  0.00           C  
ATOM   1996  CG  LYS     4       9.862   5.768 -13.489  1.00  0.00           C  
ATOM   1997  CD  LYS     4       8.845   6.896 -13.299  1.00  0.00           C  
ATOM   1998  CE  LYS     4       8.183   7.221 -14.639  1.00  0.00           C  
ATOM   1999  NZ  LYS     4       8.055   8.698 -14.784  1.00  0.00           N  
ATOM   2000  H   LYS     4      10.884   6.527 -11.466  1.00  0.00           H  
ATOM   2001  HA  LYS     4       8.229   5.505 -11.086  1.00  0.00           H  
ATOM   2002 1HB  LYS     4      10.384   3.941 -12.488  1.00  0.00           H  
ATOM   2003 2HB  LYS     4       8.676   4.081 -12.898  1.00  0.00           H  
ATOM   2004 1HG  LYS     4      10.855   6.140 -13.283  1.00  0.00           H  
ATOM   2005 2HG  LYS     4       9.816   5.415 -14.508  1.00  0.00           H  
ATOM   2006 1HD  LYS     4       8.091   6.585 -12.591  1.00  0.00           H  
ATOM   2007 2HD  LYS     4       9.348   7.775 -12.926  1.00  0.00           H  
ATOM   2008 1HE  LYS     4       8.790   6.831 -15.443  1.00  0.00           H  
ATOM   2009 2HE  LYS     4       7.203   6.768 -14.675  1.00  0.00           H  
ATOM   2010 1HZ  LYS     4       8.986   9.142 -14.643  1.00  0.00           H  
ATOM   2011 2HZ  LYS     4       7.703   8.924 -15.735  1.00  0.00           H  
ATOM   2012 3HZ  LYS     4       7.388   9.061 -14.074  1.00  0.00           H  
ATOM   2013  N   MET     5      10.667   3.574  -9.969  1.00  0.00           N  
ATOM   2014  CA  MET     5      10.929   2.495  -8.976  1.00  0.00           C  
ATOM   2015  C   MET     5      10.517   2.981  -7.585  1.00  0.00           C  
ATOM   2016  O   MET     5      10.309   2.199  -6.680  1.00  0.00           O  
ATOM   2017  CB  MET     5      12.419   2.146  -8.980  1.00  0.00           C  
ATOM   2018  CG  MET     5      12.679   1.026  -9.990  1.00  0.00           C  
ATOM   2019  SD  MET     5      13.008  -0.519  -9.107  1.00  0.00           S  
ATOM   2020  CE  MET     5      11.291  -0.913  -8.691  1.00  0.00           C  
ATOM   2021  H   MET     5      11.398   3.922 -10.521  1.00  0.00           H  
ATOM   2022  HA  MET     5      10.353   1.619  -9.237  1.00  0.00           H  
ATOM   2023 1HB  MET     5      12.993   3.020  -9.253  1.00  0.00           H  
ATOM   2024 2HB  MET     5      12.713   1.815  -7.995  1.00  0.00           H  
ATOM   2025 1HG  MET     5      11.811   0.903 -10.621  1.00  0.00           H  
ATOM   2026 2HG  MET     5      13.533   1.282 -10.598  1.00  0.00           H  
ATOM   2027 1HE  MET     5      10.631  -0.435  -9.396  1.00  0.00           H  
ATOM   2028 2HE  MET     5      11.149  -1.984  -8.735  1.00  0.00           H  
ATOM   2029 3HE  MET     5      11.072  -0.555  -7.695  1.00  0.00           H  
ATOM   2030  N   SER     6      10.393   4.269  -7.410  1.00  0.00           N  
ATOM   2031  CA  SER     6       9.991   4.807  -6.081  1.00  0.00           C  
ATOM   2032  C   SER     6       8.464   4.795  -5.968  1.00  0.00           C  
ATOM   2033  O   SER     6       7.912   4.631  -4.897  1.00  0.00           O  
ATOM   2034  CB  SER     6      10.501   6.241  -5.935  1.00  0.00           C  
ATOM   2035  OG  SER     6      10.243   6.699  -4.614  1.00  0.00           O  
ATOM   2036  H   SER     6      10.563   4.882  -8.156  1.00  0.00           H  
ATOM   2037  HA  SER     6      10.414   4.192  -5.300  1.00  0.00           H  
ATOM   2038 1HB  SER     6      11.561   6.270  -6.119  1.00  0.00           H  
ATOM   2039 2HB  SER     6       9.997   6.876  -6.652  1.00  0.00           H  
ATOM   2040  HG  SER     6      10.546   6.025  -4.002  1.00  0.00           H  
ATOM   2041  N   THR     7       7.777   4.964  -7.065  1.00  0.00           N  
ATOM   2042  CA  THR     7       6.287   4.959  -7.018  1.00  0.00           C  
ATOM   2043  C   THR     7       5.791   3.515  -7.006  1.00  0.00           C  
ATOM   2044  O   THR     7       4.651   3.240  -6.682  1.00  0.00           O  
ATOM   2045  CB  THR     7       5.731   5.682  -8.247  1.00  0.00           C  
ATOM   2046  OG1 THR     7       6.290   6.985  -8.322  1.00  0.00           O  
ATOM   2047  CG2 THR     7       4.208   5.782  -8.135  1.00  0.00           C  
ATOM   2048  H   THR     7       8.240   5.089  -7.919  1.00  0.00           H  
ATOM   2049  HA  THR     7       5.954   5.463  -6.122  1.00  0.00           H  
ATOM   2050  HB  THR     7       5.986   5.128  -9.137  1.00  0.00           H  
ATOM   2051  HG1 THR     7       5.614   7.580  -8.655  1.00  0.00           H  
ATOM   2052 1HG2 THR     7       3.924   5.789  -7.092  1.00  0.00           H  
ATOM   2053 2HG2 THR     7       3.871   6.694  -8.606  1.00  0.00           H  
ATOM   2054 3HG2 THR     7       3.754   4.933  -8.626  1.00  0.00           H  
ATOM   2055  N   ALA     8       6.642   2.588  -7.344  1.00  0.00           N  
ATOM   2056  CA  ALA     8       6.229   1.161  -7.341  1.00  0.00           C  
ATOM   2057  C   ALA     8       6.401   0.620  -5.927  1.00  0.00           C  
ATOM   2058  O   ALA     8       5.531  -0.036  -5.384  1.00  0.00           O  
ATOM   2059  CB  ALA     8       7.113   0.373  -8.309  1.00  0.00           C  
ATOM   2060  H   ALA     8       7.558   2.829  -7.588  1.00  0.00           H  
ATOM   2061  HA  ALA     8       5.197   1.080  -7.638  1.00  0.00           H  
ATOM   2062 1HB  ALA     8       8.101   0.810  -8.331  1.00  0.00           H  
ATOM   2063 2HB  ALA     8       7.180  -0.653  -7.981  1.00  0.00           H  
ATOM   2064 3HB  ALA     8       6.682   0.409  -9.299  1.00  0.00           H  
ATOM   2065  N   ILE     9       7.516   0.909  -5.322  1.00  0.00           N  
ATOM   2066  CA  ILE     9       7.751   0.434  -3.937  1.00  0.00           C  
ATOM   2067  C   ILE     9       6.803   1.181  -2.999  1.00  0.00           C  
ATOM   2068  O   ILE     9       6.411   0.679  -1.965  1.00  0.00           O  
ATOM   2069  CB  ILE     9       9.203   0.710  -3.539  1.00  0.00           C  
ATOM   2070  CG1 ILE     9       9.475   2.215  -3.599  1.00  0.00           C  
ATOM   2071  CG2 ILE     9      10.141  -0.012  -4.507  1.00  0.00           C  
ATOM   2072  CD1 ILE     9      10.123   2.669  -2.290  1.00  0.00           C  
ATOM   2073  H   ILE     9       8.193   1.451  -5.778  1.00  0.00           H  
ATOM   2074  HA  ILE     9       7.553  -0.624  -3.884  1.00  0.00           H  
ATOM   2075  HB  ILE     9       9.375   0.349  -2.534  1.00  0.00           H  
ATOM   2076 1HG1 ILE     9      10.143   2.426  -4.422  1.00  0.00           H  
ATOM   2077 2HG1 ILE     9       8.548   2.745  -3.742  1.00  0.00           H  
ATOM   2078 1HG2 ILE     9       9.572  -0.699  -5.115  1.00  0.00           H  
ATOM   2079 2HG2 ILE     9      10.628   0.713  -5.144  1.00  0.00           H  
ATOM   2080 3HG2 ILE     9      10.886  -0.558  -3.947  1.00  0.00           H  
ATOM   2081 1HD1 ILE     9      10.099   1.860  -1.576  1.00  0.00           H  
ATOM   2082 2HD1 ILE     9      11.148   2.956  -2.474  1.00  0.00           H  
ATOM   2083 3HD1 ILE     9       9.579   3.515  -1.894  1.00  0.00           H  
ATOM   2084  N   SER    10       6.420   2.375  -3.364  1.00  0.00           N  
ATOM   2085  CA  SER    10       5.486   3.154  -2.509  1.00  0.00           C  
ATOM   2086  C   SER    10       4.078   2.581  -2.668  1.00  0.00           C  
ATOM   2087  O   SER    10       3.322   2.491  -1.723  1.00  0.00           O  
ATOM   2088  CB  SER    10       5.494   4.620  -2.945  1.00  0.00           C  
ATOM   2089  OG  SER    10       6.117   5.406  -1.938  1.00  0.00           O  
ATOM   2090  H   SER    10       6.741   2.756  -4.209  1.00  0.00           H  
ATOM   2091  HA  SER    10       5.792   3.081  -1.476  1.00  0.00           H  
ATOM   2092 1HB  SER    10       6.046   4.721  -3.865  1.00  0.00           H  
ATOM   2093 2HB  SER    10       4.477   4.953  -3.101  1.00  0.00           H  
ATOM   2094  HG  SER    10       7.008   5.611  -2.229  1.00  0.00           H  
ATOM   2095  N   VAL    11       3.724   2.182  -3.861  1.00  0.00           N  
ATOM   2096  CA  VAL    11       2.370   1.604  -4.080  1.00  0.00           C  
ATOM   2097  C   VAL    11       2.211   0.363  -3.200  1.00  0.00           C  
ATOM   2098  O   VAL    11       1.166   0.122  -2.630  1.00  0.00           O  
ATOM   2099  CB  VAL    11       2.211   1.210  -5.551  1.00  0.00           C  
ATOM   2100  CG1 VAL    11       0.978   0.318  -5.716  1.00  0.00           C  
ATOM   2101  CG2 VAL    11       2.040   2.472  -6.399  1.00  0.00           C  
ATOM   2102  H   VAL    11       4.353   2.258  -4.610  1.00  0.00           H  
ATOM   2103  HA  VAL    11       1.617   2.333  -3.816  1.00  0.00           H  
ATOM   2104  HB  VAL    11       3.090   0.673  -5.877  1.00  0.00           H  
ATOM   2105 1HG1 VAL    11       0.352   0.405  -4.841  1.00  0.00           H  
ATOM   2106 2HG1 VAL    11       0.423   0.628  -6.589  1.00  0.00           H  
ATOM   2107 3HG1 VAL    11       1.291  -0.709  -5.835  1.00  0.00           H  
ATOM   2108 1HG2 VAL    11       2.287   3.340  -5.806  1.00  0.00           H  
ATOM   2109 2HG2 VAL    11       2.697   2.423  -7.256  1.00  0.00           H  
ATOM   2110 3HG2 VAL    11       1.015   2.545  -6.734  1.00  0.00           H  
ATOM   2111  N   LEU    12       3.245  -0.426  -3.084  1.00  0.00           N  
ATOM   2112  CA  LEU    12       3.156  -1.649  -2.238  1.00  0.00           C  
ATOM   2113  C   LEU    12       2.668  -1.268  -0.838  1.00  0.00           C  
ATOM   2114  O   LEU    12       1.834  -1.934  -0.258  1.00  0.00           O  
ATOM   2115  CB  LEU    12       4.536  -2.300  -2.138  1.00  0.00           C  
ATOM   2116  CG  LEU    12       4.950  -2.827  -3.512  1.00  0.00           C  
ATOM   2117  CD1 LEU    12       6.449  -3.133  -3.511  1.00  0.00           C  
ATOM   2118  CD2 LEU    12       4.170  -4.106  -3.823  1.00  0.00           C  
ATOM   2119  H   LEU    12       4.082  -0.213  -3.552  1.00  0.00           H  
ATOM   2120  HA  LEU    12       2.461  -2.345  -2.685  1.00  0.00           H  
ATOM   2121 1HB  LEU    12       5.255  -1.569  -1.799  1.00  0.00           H  
ATOM   2122 2HB  LEU    12       4.498  -3.121  -1.437  1.00  0.00           H  
ATOM   2123  HG  LEU    12       4.737  -2.080  -4.263  1.00  0.00           H  
ATOM   2124 1HD1 LEU    12       6.868  -2.879  -2.549  1.00  0.00           H  
ATOM   2125 2HD1 LEU    12       6.602  -4.185  -3.705  1.00  0.00           H  
ATOM   2126 3HD1 LEU    12       6.936  -2.552  -4.280  1.00  0.00           H  
ATOM   2127 1HD2 LEU    12       3.189  -4.047  -3.375  1.00  0.00           H  
ATOM   2128 2HD2 LEU    12       4.069  -4.216  -4.893  1.00  0.00           H  
ATOM   2129 3HD2 LEU    12       4.699  -4.957  -3.422  1.00  0.00           H  
ATOM   2130  N   LEU    13       3.182  -0.200  -0.291  1.00  0.00           N  
ATOM   2131  CA  LEU    13       2.747   0.223   1.070  1.00  0.00           C  
ATOM   2132  C   LEU    13       1.317   0.767   1.002  1.00  0.00           C  
ATOM   2133  O   LEU    13       0.510   0.530   1.878  1.00  0.00           O  
ATOM   2134  CB  LEU    13       3.681   1.320   1.590  1.00  0.00           C  
ATOM   2135  CG  LEU    13       5.055   0.724   1.909  1.00  0.00           C  
ATOM   2136  CD1 LEU    13       4.886  -0.561   2.723  1.00  0.00           C  
ATOM   2137  CD2 LEU    13       5.789   0.409   0.604  1.00  0.00           C  
ATOM   2138  H   LEU    13       3.853   0.325  -0.776  1.00  0.00           H  
ATOM   2139  HA  LEU    13       2.776  -0.624   1.738  1.00  0.00           H  
ATOM   2140 1HB  LEU    13       3.789   2.086   0.837  1.00  0.00           H  
ATOM   2141 2HB  LEU    13       3.264   1.753   2.487  1.00  0.00           H  
ATOM   2142  HG  LEU    13       5.630   1.437   2.482  1.00  0.00           H  
ATOM   2143 1HD1 LEU    13       3.938  -0.539   3.238  1.00  0.00           H  
ATOM   2144 2HD1 LEU    13       4.916  -1.413   2.059  1.00  0.00           H  
ATOM   2145 3HD1 LEU    13       5.687  -0.640   3.443  1.00  0.00           H  
ATOM   2146 1HD2 LEU    13       5.687   1.242  -0.075  1.00  0.00           H  
ATOM   2147 2HD2 LEU    13       6.836   0.239   0.811  1.00  0.00           H  
ATOM   2148 3HD2 LEU    13       5.363  -0.476   0.155  1.00  0.00           H  
ATOM   2149  N   ALA    14       0.998   1.495  -0.033  1.00  0.00           N  
ATOM   2150  CA  ALA    14      -0.377   2.055  -0.158  1.00  0.00           C  
ATOM   2151  C   ALA    14      -1.404   0.942   0.058  1.00  0.00           C  
ATOM   2152  O   ALA    14      -2.312   1.070   0.857  1.00  0.00           O  
ATOM   2153  CB  ALA    14      -0.557   2.650  -1.557  1.00  0.00           C  
ATOM   2154  H   ALA    14       1.665   1.675  -0.729  1.00  0.00           H  
ATOM   2155  HA  ALA    14      -0.521   2.827   0.582  1.00  0.00           H  
ATOM   2156 1HB  ALA    14       0.399   2.696  -2.056  1.00  0.00           H  
ATOM   2157 2HB  ALA    14      -1.232   2.029  -2.128  1.00  0.00           H  
ATOM   2158 3HB  ALA    14      -0.969   3.646  -1.475  1.00  0.00           H  
ATOM   2159  N   GLN    15      -1.271  -0.146  -0.648  1.00  0.00           N  
ATOM   2160  CA  GLN    15      -2.242  -1.265  -0.484  1.00  0.00           C  
ATOM   2161  C   GLN    15      -2.082  -1.883   0.906  1.00  0.00           C  
ATOM   2162  O   GLN    15      -3.047  -2.241   1.552  1.00  0.00           O  
ATOM   2163  CB  GLN    15      -1.973  -2.330  -1.550  1.00  0.00           C  
ATOM   2164  CG  GLN    15      -3.146  -3.312  -1.598  1.00  0.00           C  
ATOM   2165  CD  GLN    15      -3.820  -3.235  -2.969  1.00  0.00           C  
ATOM   2166  OE1 GLN    15      -5.014  -3.022  -3.060  1.00  0.00           O  
ATOM   2167  NE2 GLN    15      -3.103  -3.402  -4.047  1.00  0.00           N  
ATOM   2168  H   GLN    15      -0.534  -0.227  -1.288  1.00  0.00           H  
ATOM   2169  HA  GLN    15      -3.247  -0.889  -0.597  1.00  0.00           H  
ATOM   2170 1HB  GLN    15      -1.860  -1.854  -2.513  1.00  0.00           H  
ATOM   2171 2HB  GLN    15      -1.068  -2.865  -1.304  1.00  0.00           H  
ATOM   2172 1HG  GLN    15      -2.781  -4.316  -1.431  1.00  0.00           H  
ATOM   2173 2HG  GLN    15      -3.861  -3.056  -0.832  1.00  0.00           H  
ATOM   2174 1HE2 GLN    15      -3.528  -3.355  -4.929  1.00  0.00           H  
ATOM   2175 2HE2 GLN    15      -2.142  -3.574  -3.974  1.00  0.00           H  
ATOM   2176  N   ALA    16      -0.870  -2.014   1.372  1.00  0.00           N  
ATOM   2177  CA  ALA    16      -0.650  -2.613   2.719  1.00  0.00           C  
ATOM   2178  C   ALA    16      -1.538  -1.907   3.746  1.00  0.00           C  
ATOM   2179  O   ALA    16      -2.116  -2.532   4.613  1.00  0.00           O  
ATOM   2180  CB  ALA    16       0.819  -2.447   3.115  1.00  0.00           C  
ATOM   2181  H   ALA    16      -0.104  -1.721   0.835  1.00  0.00           H  
ATOM   2182  HA  ALA    16      -0.897  -3.664   2.690  1.00  0.00           H  
ATOM   2183 1HB  ALA    16       1.421  -2.334   2.225  1.00  0.00           H  
ATOM   2184 2HB  ALA    16       0.928  -1.572   3.737  1.00  0.00           H  
ATOM   2185 3HB  ALA    16       1.145  -3.321   3.661  1.00  0.00           H  
ATOM   2186  N   VAL    17      -1.651  -0.611   3.657  1.00  0.00           N  
ATOM   2187  CA  VAL    17      -2.503   0.130   4.630  1.00  0.00           C  
ATOM   2188  C   VAL    17      -3.966   0.045   4.193  1.00  0.00           C  
ATOM   2189  O   VAL    17      -4.871   0.131   4.999  1.00  0.00           O  
ATOM   2190  CB  VAL    17      -2.069   1.596   4.675  1.00  0.00           C  
ATOM   2191  CG1 VAL    17      -2.959   2.360   5.656  1.00  0.00           C  
ATOM   2192  CG2 VAL    17      -0.613   1.682   5.137  1.00  0.00           C  
ATOM   2193  H   VAL    17      -1.177  -0.125   2.951  1.00  0.00           H  
ATOM   2194  HA  VAL    17      -2.394  -0.309   5.610  1.00  0.00           H  
ATOM   2195  HB  VAL    17      -2.163   2.030   3.690  1.00  0.00           H  
ATOM   2196 1HG1 VAL    17      -3.942   1.912   5.675  1.00  0.00           H  
ATOM   2197 2HG1 VAL    17      -2.525   2.319   6.644  1.00  0.00           H  
ATOM   2198 3HG1 VAL    17      -3.039   3.391   5.342  1.00  0.00           H  
ATOM   2199 1HG2 VAL    17      -0.212   0.685   5.254  1.00  0.00           H  
ATOM   2200 2HG2 VAL    17      -0.032   2.218   4.402  1.00  0.00           H  
ATOM   2201 3HG2 VAL    17      -0.565   2.202   6.083  1.00  0.00           H  
ATOM   2202  N   PHE    18      -4.205  -0.125   2.922  1.00  0.00           N  
ATOM   2203  CA  PHE    18      -5.609  -0.217   2.434  1.00  0.00           C  
ATOM   2204  C   PHE    18      -6.280  -1.452   3.041  1.00  0.00           C  
ATOM   2205  O   PHE    18      -7.213  -1.349   3.811  1.00  0.00           O  
ATOM   2206  CB  PHE    18      -5.612  -0.333   0.909  1.00  0.00           C  
ATOM   2207  CG  PHE    18      -6.786   0.432   0.349  1.00  0.00           C  
ATOM   2208  CD1 PHE    18      -8.087   0.116   0.759  1.00  0.00           C  
ATOM   2209  CD2 PHE    18      -6.575   1.456  -0.582  1.00  0.00           C  
ATOM   2210  CE1 PHE    18      -9.176   0.824   0.239  1.00  0.00           C  
ATOM   2211  CE2 PHE    18      -7.664   2.164  -1.101  1.00  0.00           C  
ATOM   2212  CZ  PHE    18      -8.965   1.849  -0.691  1.00  0.00           C  
ATOM   2213  H   PHE    18      -3.461  -0.193   2.288  1.00  0.00           H  
ATOM   2214  HA  PHE    18      -6.152   0.669   2.730  1.00  0.00           H  
ATOM   2215 1HB  PHE    18      -4.694   0.077   0.516  1.00  0.00           H  
ATOM   2216 2HB  PHE    18      -5.693  -1.372   0.628  1.00  0.00           H  
ATOM   2217  HD1 PHE    18      -8.249  -0.674   1.477  1.00  0.00           H  
ATOM   2218  HD2 PHE    18      -5.572   1.699  -0.898  1.00  0.00           H  
ATOM   2219  HE1 PHE    18     -10.180   0.581   0.557  1.00  0.00           H  
ATOM   2220  HE2 PHE    18      -7.501   2.955  -1.819  1.00  0.00           H  
ATOM   2221  HZ  PHE    18      -9.805   2.396  -1.092  1.00  0.00           H  
ATOM   2222  N   LEU    19      -5.810  -2.620   2.697  1.00  0.00           N  
ATOM   2223  CA  LEU    19      -6.419  -3.861   3.253  1.00  0.00           C  
ATOM   2224  C   LEU    19      -6.446  -3.781   4.781  1.00  0.00           C  
ATOM   2225  O   LEU    19      -7.185  -4.488   5.437  1.00  0.00           O  
ATOM   2226  CB  LEU    19      -5.591  -5.072   2.822  1.00  0.00           C  
ATOM   2227  CG  LEU    19      -4.172  -4.941   3.378  1.00  0.00           C  
ATOM   2228  CD1 LEU    19      -4.073  -5.685   4.710  1.00  0.00           C  
ATOM   2229  CD2 LEU    19      -3.178  -5.546   2.383  1.00  0.00           C  
ATOM   2230  H   LEU    19      -5.056  -2.681   2.075  1.00  0.00           H  
ATOM   2231  HA  LEU    19      -7.427  -3.964   2.880  1.00  0.00           H  
ATOM   2232 1HB  LEU    19      -6.047  -5.974   3.202  1.00  0.00           H  
ATOM   2233 2HB  LEU    19      -5.550  -5.115   1.744  1.00  0.00           H  
ATOM   2234  HG  LEU    19      -3.940  -3.897   3.531  1.00  0.00           H  
ATOM   2235 1HD1 LEU    19      -4.989  -5.550   5.267  1.00  0.00           H  
ATOM   2236 2HD1 LEU    19      -3.917  -6.737   4.524  1.00  0.00           H  
ATOM   2237 3HD1 LEU    19      -3.244  -5.294   5.281  1.00  0.00           H  
ATOM   2238 1HD2 LEU    19      -3.555  -6.494   2.029  1.00  0.00           H  
ATOM   2239 2HD2 LEU    19      -3.051  -4.874   1.547  1.00  0.00           H  
ATOM   2240 3HD2 LEU    19      -2.227  -5.696   2.871  1.00  0.00           H  
ATOM   2241  N   LEU    20      -5.641  -2.929   5.356  1.00  0.00           N  
ATOM   2242  CA  LEU    20      -5.618  -2.808   6.841  1.00  0.00           C  
ATOM   2243  C   LEU    20      -6.890  -2.105   7.322  1.00  0.00           C  
ATOM   2244  O   LEU    20      -7.597  -2.600   8.176  1.00  0.00           O  
ATOM   2245  CB  LEU    20      -4.394  -1.994   7.267  1.00  0.00           C  
ATOM   2246  CG  LEU    20      -3.540  -2.821   8.229  1.00  0.00           C  
ATOM   2247  CD1 LEU    20      -2.059  -2.578   7.934  1.00  0.00           C  
ATOM   2248  CD2 LEU    20      -3.848  -2.404   9.669  1.00  0.00           C  
ATOM   2249  H   LEU    20      -5.050  -2.370   4.810  1.00  0.00           H  
ATOM   2250  HA  LEU    20      -5.563  -3.793   7.280  1.00  0.00           H  
ATOM   2251 1HB  LEU    20      -3.811  -1.738   6.394  1.00  0.00           H  
ATOM   2252 2HB  LEU    20      -4.718  -1.090   7.762  1.00  0.00           H  
ATOM   2253  HG  LEU    20      -3.766  -3.869   8.098  1.00  0.00           H  
ATOM   2254 1HD1 LEU    20      -1.895  -2.600   6.867  1.00  0.00           H  
ATOM   2255 2HD1 LEU    20      -1.768  -1.614   8.324  1.00  0.00           H  
ATOM   2256 3HD1 LEU    20      -1.467  -3.350   8.405  1.00  0.00           H  
ATOM   2257 1HD2 LEU    20      -4.550  -1.584   9.664  1.00  0.00           H  
ATOM   2258 2HD2 LEU    20      -4.275  -3.241  10.202  1.00  0.00           H  
ATOM   2259 3HD2 LEU    20      -2.935  -2.095  10.156  1.00  0.00           H  
ATOM   2260  N   LEU    21      -7.184  -0.953   6.784  1.00  0.00           N  
ATOM   2261  CA  LEU    21      -8.407  -0.218   7.217  1.00  0.00           C  
ATOM   2262  C   LEU    21      -9.654  -1.013   6.818  1.00  0.00           C  
ATOM   2263  O   LEU    21     -10.670  -0.963   7.482  1.00  0.00           O  
ATOM   2264  CB  LEU    21      -8.439   1.161   6.552  1.00  0.00           C  
ATOM   2265  CG  LEU    21      -8.824   1.019   5.078  1.00  0.00           C  
ATOM   2266  CD1 LEU    21     -10.345   1.101   4.936  1.00  0.00           C  
ATOM   2267  CD2 LEU    21      -8.176   2.145   4.272  1.00  0.00           C  
ATOM   2268  H   LEU    21      -6.598  -0.568   6.099  1.00  0.00           H  
ATOM   2269  HA  LEU    21      -8.390  -0.098   8.290  1.00  0.00           H  
ATOM   2270 1HB  LEU    21      -9.164   1.785   7.055  1.00  0.00           H  
ATOM   2271 2HB  LEU    21      -7.463   1.617   6.623  1.00  0.00           H  
ATOM   2272  HG  LEU    21      -8.481   0.063   4.708  1.00  0.00           H  
ATOM   2273 1HD1 LEU    21     -10.755   1.647   5.774  1.00  0.00           H  
ATOM   2274 2HD1 LEU    21     -10.593   1.613   4.018  1.00  0.00           H  
ATOM   2275 3HD1 LEU    21     -10.760   0.106   4.918  1.00  0.00           H  
ATOM   2276 1HD2 LEU    21      -8.081   3.024   4.893  1.00  0.00           H  
ATOM   2277 2HD2 LEU    21      -7.198   1.833   3.938  1.00  0.00           H  
ATOM   2278 3HD2 LEU    21      -8.792   2.375   3.416  1.00  0.00           H  
ATOM   2279  N   THR    22      -9.586  -1.745   5.740  1.00  0.00           N  
ATOM   2280  CA  THR    22     -10.770  -2.540   5.304  1.00  0.00           C  
ATOM   2281  C   THR    22     -10.977  -3.715   6.262  1.00  0.00           C  
ATOM   2282  O   THR    22     -12.091  -4.104   6.549  1.00  0.00           O  
ATOM   2283  CB  THR    22     -10.535  -3.072   3.889  1.00  0.00           C  
ATOM   2284  OG1 THR    22      -9.282  -3.737   3.838  1.00  0.00           O  
ATOM   2285  CG2 THR    22     -10.542  -1.910   2.894  1.00  0.00           C  
ATOM   2286  H   THR    22      -8.758  -1.773   5.217  1.00  0.00           H  
ATOM   2287  HA  THR    22     -11.648  -1.910   5.311  1.00  0.00           H  
ATOM   2288  HB  THR    22     -11.321  -3.765   3.630  1.00  0.00           H  
ATOM   2289  HG1 THR    22      -9.332  -4.509   4.407  1.00  0.00           H  
ATOM   2290 1HG2 THR    22      -9.862  -1.143   3.233  1.00  0.00           H  
ATOM   2291 2HG2 THR    22     -10.229  -2.266   1.924  1.00  0.00           H  
ATOM   2292 3HG2 THR    22     -11.539  -1.502   2.824  1.00  0.00           H  
ATOM   2293  N   SER    23      -9.913  -4.285   6.756  1.00  0.00           N  
ATOM   2294  CA  SER    23     -10.052  -5.434   7.693  1.00  0.00           C  
ATOM   2295  C   SER    23     -10.689  -4.955   8.998  1.00  0.00           C  
ATOM   2296  O   SER    23     -11.684  -5.487   9.445  1.00  0.00           O  
ATOM   2297  CB  SER    23      -8.672  -6.025   7.985  1.00  0.00           C  
ATOM   2298  OG  SER    23      -8.827  -7.295   8.603  1.00  0.00           O  
ATOM   2299  H   SER    23      -9.022  -3.957   6.511  1.00  0.00           H  
ATOM   2300  HA  SER    23     -10.678  -6.190   7.243  1.00  0.00           H  
ATOM   2301 1HB  SER    23      -8.126  -6.143   7.063  1.00  0.00           H  
ATOM   2302 2HB  SER    23      -8.127  -5.358   8.640  1.00  0.00           H  
ATOM   2303  HG  SER    23      -9.459  -7.201   9.319  1.00  0.00           H  
ATOM   2304  N   GLN    24     -10.123  -3.952   9.612  1.00  0.00           N  
ATOM   2305  CA  GLN    24     -10.699  -3.441  10.888  1.00  0.00           C  
ATOM   2306  C   GLN    24     -12.071  -2.821  10.615  1.00  0.00           C  
ATOM   2307  O   GLN    24     -12.874  -2.650  11.510  1.00  0.00           O  
ATOM   2308  CB  GLN    24      -9.767  -2.380  11.480  1.00  0.00           C  
ATOM   2309  CG  GLN    24      -9.728  -1.161  10.557  1.00  0.00           C  
ATOM   2310  CD  GLN    24      -9.853   0.115  11.391  1.00  0.00           C  
ATOM   2311  OE1 GLN    24     -10.482   1.067  10.975  1.00  0.00           O  
ATOM   2312  NE2 GLN    24      -9.275   0.174  12.560  1.00  0.00           N  
ATOM   2313  H   GLN    24      -9.319  -3.535   9.235  1.00  0.00           H  
ATOM   2314  HA  GLN    24     -10.805  -4.257  11.588  1.00  0.00           H  
ATOM   2315 1HB  GLN    24     -10.132  -2.085  12.453  1.00  0.00           H  
ATOM   2316 2HB  GLN    24      -8.773  -2.790  11.577  1.00  0.00           H  
ATOM   2317 1HG  GLN    24      -8.791  -1.149  10.017  1.00  0.00           H  
ATOM   2318 2HG  GLN    24     -10.547  -1.213   9.856  1.00  0.00           H  
ATOM   2319 1HE2 GLN    24      -9.350   0.988  13.102  1.00  0.00           H  
ATOM   2320 2HE2 GLN    24      -8.768  -0.593  12.896  1.00  0.00           H  
ATOM   2321  N   ARG    25     -12.348  -2.485   9.384  1.00  0.00           N  
ATOM   2322  CA  ARG    25     -13.670  -1.879   9.056  1.00  0.00           C  
ATOM   2323  C   ARG    25     -14.492  -2.867   8.228  1.00  0.00           C  
ATOM   2324  O   ARG    25     -14.477  -4.043   8.556  1.00  0.00           O  
ATOM   2325  CB  ARG    25     -13.459  -0.593   8.253  1.00  0.00           C  
ATOM   2326  CG  ARG    25     -14.682   0.313   8.409  1.00  0.00           C  
ATOM   2327  CD  ARG    25     -14.514   1.555   7.532  1.00  0.00           C  
ATOM   2328  NE  ARG    25     -14.617   2.779   8.377  1.00  0.00           N  
ATOM   2329  CZ  ARG    25     -13.576   3.205   9.040  1.00  0.00           C  
ATOM   2330  NH1 ARG    25     -13.357   2.781  10.255  1.00  0.00           N  
ATOM   2331  NH2 ARG    25     -12.755   4.057   8.488  1.00  0.00           N  
ATOM   2332  OXT ARG    25     -15.125  -2.433   7.279  1.00  0.00           O  
ATOM   2333  H   ARG    25     -11.687  -2.633   8.676  1.00  0.00           H  
ATOM   2334  HA  ARG    25     -14.197  -1.650   9.971  1.00  0.00           H  
ATOM   2335 1HB  ARG    25     -12.581  -0.081   8.619  1.00  0.00           H  
ATOM   2336 2HB  ARG    25     -13.325  -0.838   7.210  1.00  0.00           H  
ATOM   2337 1HG  ARG    25     -15.569  -0.225   8.106  1.00  0.00           H  
ATOM   2338 2HG  ARG    25     -14.779   0.614   9.442  1.00  0.00           H  
ATOM   2339 1HD  ARG    25     -13.547   1.530   7.052  1.00  0.00           H  
ATOM   2340 2HD  ARG    25     -15.289   1.572   6.779  1.00  0.00           H  
ATOM   2341  HE  ARG    25     -15.467   3.264   8.436  1.00  0.00           H  
ATOM   2342 1HH1 ARG    25     -13.987   2.128  10.677  1.00  0.00           H  
ATOM   2343 2HH1 ARG    25     -12.561   3.109  10.763  1.00  0.00           H  
ATOM   2344 1HH2 ARG    25     -12.924   4.384   7.559  1.00  0.00           H  
ATOM   2345 2HH2 ARG    25     -11.958   4.382   8.997  1.00  0.00           H  
TER    2346      ARG    25                                                      
ENDMDL                                                                          
MODEL        7                                                                  
ATOM   2347  N   GLY     1      16.431   1.053 -12.751  1.00  0.00           N  
ATOM   2348  CA  GLY     1      15.090   1.313 -12.065  1.00  0.00           C  
ATOM   2349  C   GLY     1      15.068   1.961 -10.723  1.00  0.00           C  
ATOM   2350  O   GLY     1      14.501   1.443  -9.782  1.00  0.00           O  
ATOM   2351 1H   GLY     1      17.206   1.281 -12.094  1.00  0.00           H  
ATOM   2352 2H   GLY     1      16.492   0.052 -13.025  1.00  0.00           H  
ATOM   2353 3H   GLY     1      16.510   1.649 -13.599  1.00  0.00           H  
ATOM   2354 1HA  GLY     1      14.699   2.156 -12.361  1.00  0.00           H  
ATOM   2355 2HA  GLY     1      14.410   0.392 -12.289  1.00  0.00           H  
ATOM   2356  N   SER     2      15.681   3.107 -10.597  1.00  0.00           N  
ATOM   2357  CA  SER     2      15.694   3.803  -9.279  1.00  0.00           C  
ATOM   2358  C   SER     2      14.330   4.448  -9.026  1.00  0.00           C  
ATOM   2359  O   SER     2      13.482   3.888  -8.359  1.00  0.00           O  
ATOM   2360  CB  SER     2      16.774   4.886  -9.286  1.00  0.00           C  
ATOM   2361  OG  SER     2      16.610   5.720  -8.148  1.00  0.00           O  
ATOM   2362  H   SER     2      16.133   3.508 -11.367  1.00  0.00           H  
ATOM   2363  HA  SER     2      15.907   3.090  -8.497  1.00  0.00           H  
ATOM   2364 1HB  SER     2      17.748   4.426  -9.253  1.00  0.00           H  
ATOM   2365 2HB  SER     2      16.686   5.474 -10.191  1.00  0.00           H  
ATOM   2366  HG  SER     2      17.430   5.706  -7.648  1.00  0.00           H  
ATOM   2367  N   GLU     3      14.110   5.623  -9.551  1.00  0.00           N  
ATOM   2368  CA  GLU     3      12.800   6.300  -9.338  1.00  0.00           C  
ATOM   2369  C   GLU     3      11.666   5.312  -9.614  1.00  0.00           C  
ATOM   2370  O   GLU     3      10.598   5.403  -9.043  1.00  0.00           O  
ATOM   2371  CB  GLU     3      12.681   7.493 -10.290  1.00  0.00           C  
ATOM   2372  CG  GLU     3      12.986   7.040 -11.720  1.00  0.00           C  
ATOM   2373  CD  GLU     3      13.318   8.259 -12.581  1.00  0.00           C  
ATOM   2374  OE1 GLU     3      13.420   9.341 -12.029  1.00  0.00           O  
ATOM   2375  OE2 GLU     3      13.465   8.090 -13.782  1.00  0.00           O  
ATOM   2376  H   GLU     3      14.807   6.060 -10.085  1.00  0.00           H  
ATOM   2377  HA  GLU     3      12.736   6.647  -8.317  1.00  0.00           H  
ATOM   2378 1HB  GLU     3      11.677   7.891 -10.244  1.00  0.00           H  
ATOM   2379 2HB  GLU     3      13.385   8.257 -10.000  1.00  0.00           H  
ATOM   2380 1HG  GLU     3      13.828   6.363 -11.711  1.00  0.00           H  
ATOM   2381 2HG  GLU     3      12.123   6.536 -12.130  1.00  0.00           H  
ATOM   2382  N   LYS     4      11.889   4.366 -10.484  1.00  0.00           N  
ATOM   2383  CA  LYS     4      10.822   3.372 -10.792  1.00  0.00           C  
ATOM   2384  C   LYS     4      10.511   2.558  -9.535  1.00  0.00           C  
ATOM   2385  O   LYS     4       9.394   2.534  -9.061  1.00  0.00           O  
ATOM   2386  CB  LYS     4      11.304   2.436 -11.902  1.00  0.00           C  
ATOM   2387  CG  LYS     4      10.651   2.836 -13.227  1.00  0.00           C  
ATOM   2388  CD  LYS     4      11.147   4.224 -13.642  1.00  0.00           C  
ATOM   2389  CE  LYS     4      11.536   4.203 -15.121  1.00  0.00           C  
ATOM   2390  NZ  LYS     4      11.476   5.586 -15.671  1.00  0.00           N  
ATOM   2391  H   LYS     4      12.758   4.309 -10.934  1.00  0.00           H  
ATOM   2392  HA  LYS     4       9.932   3.889 -11.117  1.00  0.00           H  
ATOM   2393 1HB  LYS     4      12.379   2.509 -11.993  1.00  0.00           H  
ATOM   2394 2HB  LYS     4      11.031   1.420 -11.661  1.00  0.00           H  
ATOM   2395 1HG  LYS     4      10.912   2.116 -13.988  1.00  0.00           H  
ATOM   2396 2HG  LYS     4       9.578   2.861 -13.106  1.00  0.00           H  
ATOM   2397 1HD  LYS     4      10.361   4.948 -13.484  1.00  0.00           H  
ATOM   2398 2HD  LYS     4      12.008   4.490 -13.048  1.00  0.00           H  
ATOM   2399 1HE  LYS     4      12.540   3.819 -15.223  1.00  0.00           H  
ATOM   2400 2HE  LYS     4      10.852   3.569 -15.664  1.00  0.00           H  
ATOM   2401 1HZ  LYS     4      10.535   5.991 -15.488  1.00  0.00           H  
ATOM   2402 2HZ  LYS     4      12.202   6.174 -15.214  1.00  0.00           H  
ATOM   2403 3HZ  LYS     4      11.649   5.561 -16.696  1.00  0.00           H  
ATOM   2404  N   MET     5      11.492   1.891  -8.991  1.00  0.00           N  
ATOM   2405  CA  MET     5      11.251   1.082  -7.762  1.00  0.00           C  
ATOM   2406  C   MET     5      10.652   1.977  -6.676  1.00  0.00           C  
ATOM   2407  O   MET     5       9.975   1.515  -5.780  1.00  0.00           O  
ATOM   2408  CB  MET     5      12.576   0.496  -7.270  1.00  0.00           C  
ATOM   2409  CG  MET     5      12.469  -1.030  -7.212  1.00  0.00           C  
ATOM   2410  SD  MET     5      11.903  -1.533  -5.568  1.00  0.00           S  
ATOM   2411  CE  MET     5      10.915  -2.956  -6.091  1.00  0.00           C  
ATOM   2412  H   MET     5      12.387   1.924  -9.387  1.00  0.00           H  
ATOM   2413  HA  MET     5      10.563   0.280  -7.989  1.00  0.00           H  
ATOM   2414 1HB  MET     5      13.368   0.777  -7.948  1.00  0.00           H  
ATOM   2415 2HB  MET     5      12.794   0.877  -6.283  1.00  0.00           H  
ATOM   2416 1HG  MET     5      11.762  -1.369  -7.955  1.00  0.00           H  
ATOM   2417 2HG  MET     5      13.437  -1.466  -7.410  1.00  0.00           H  
ATOM   2418 1HE  MET     5      10.180  -2.640  -6.813  1.00  0.00           H  
ATOM   2419 2HE  MET     5      11.562  -3.697  -6.541  1.00  0.00           H  
ATOM   2420 3HE  MET     5      10.415  -3.381  -5.233  1.00  0.00           H  
ATOM   2421  N   SER     6      10.893   3.259  -6.749  1.00  0.00           N  
ATOM   2422  CA  SER     6      10.334   4.181  -5.721  1.00  0.00           C  
ATOM   2423  C   SER     6       8.821   4.302  -5.916  1.00  0.00           C  
ATOM   2424  O   SER     6       8.067   4.384  -4.968  1.00  0.00           O  
ATOM   2425  CB  SER     6      10.980   5.559  -5.863  1.00  0.00           C  
ATOM   2426  OG  SER     6      10.980   6.210  -4.598  1.00  0.00           O  
ATOM   2427  H   SER     6      11.440   3.614  -7.481  1.00  0.00           H  
ATOM   2428  HA  SER     6      10.540   3.787  -4.736  1.00  0.00           H  
ATOM   2429 1HB  SER     6      11.995   5.450  -6.205  1.00  0.00           H  
ATOM   2430 2HB  SER     6      10.421   6.145  -6.581  1.00  0.00           H  
ATOM   2431  HG  SER     6      10.136   6.038  -4.176  1.00  0.00           H  
ATOM   2432  N   THR     7       8.370   4.303  -7.142  1.00  0.00           N  
ATOM   2433  CA  THR     7       6.906   4.409  -7.396  1.00  0.00           C  
ATOM   2434  C   THR     7       6.264   3.044  -7.156  1.00  0.00           C  
ATOM   2435  O   THR     7       5.066   2.926  -6.989  1.00  0.00           O  
ATOM   2436  CB  THR     7       6.664   4.843  -8.845  1.00  0.00           C  
ATOM   2437  OG1 THR     7       7.909   5.144  -9.461  1.00  0.00           O  
ATOM   2438  CG2 THR     7       5.768   6.081  -8.866  1.00  0.00           C  
ATOM   2439  H   THR     7       8.994   4.227  -7.894  1.00  0.00           H  
ATOM   2440  HA  THR     7       6.473   5.136  -6.723  1.00  0.00           H  
ATOM   2441  HB  THR     7       6.180   4.043  -9.384  1.00  0.00           H  
ATOM   2442  HG1 THR     7       8.171   4.387  -9.988  1.00  0.00           H  
ATOM   2443 1HG2 THR     7       6.197   6.847  -8.237  1.00  0.00           H  
ATOM   2444 2HG2 THR     7       5.687   6.449  -9.879  1.00  0.00           H  
ATOM   2445 3HG2 THR     7       4.785   5.821  -8.499  1.00  0.00           H  
ATOM   2446  N   ALA     8       7.060   2.012  -7.128  1.00  0.00           N  
ATOM   2447  CA  ALA     8       6.513   0.652  -6.891  1.00  0.00           C  
ATOM   2448  C   ALA     8       6.372   0.437  -5.387  1.00  0.00           C  
ATOM   2449  O   ALA     8       5.449  -0.199  -4.920  1.00  0.00           O  
ATOM   2450  CB  ALA     8       7.470  -0.389  -7.472  1.00  0.00           C  
ATOM   2451  H   ALA     8       8.023   2.133  -7.255  1.00  0.00           H  
ATOM   2452  HA  ALA     8       5.546   0.562  -7.362  1.00  0.00           H  
ATOM   2453 1HB  ALA     8       7.676  -0.149  -8.505  1.00  0.00           H  
ATOM   2454 2HB  ALA     8       8.393  -0.381  -6.911  1.00  0.00           H  
ATOM   2455 3HB  ALA     8       7.018  -1.368  -7.413  1.00  0.00           H  
ATOM   2456  N   ILE     9       7.280   0.978  -4.623  1.00  0.00           N  
ATOM   2457  CA  ILE     9       7.199   0.819  -3.149  1.00  0.00           C  
ATOM   2458  C   ILE     9       6.110   1.745  -2.609  1.00  0.00           C  
ATOM   2459  O   ILE     9       5.480   1.464  -1.610  1.00  0.00           O  
ATOM   2460  CB  ILE     9       8.543   1.184  -2.513  1.00  0.00           C  
ATOM   2461  CG1 ILE     9       8.910   2.622  -2.888  1.00  0.00           C  
ATOM   2462  CG2 ILE     9       9.627   0.233  -3.022  1.00  0.00           C  
ATOM   2463  CD1 ILE     9       9.859   3.198  -1.837  1.00  0.00           C  
ATOM   2464  H   ILE     9       8.011   1.495  -5.022  1.00  0.00           H  
ATOM   2465  HA  ILE     9       6.955  -0.204  -2.912  1.00  0.00           H  
ATOM   2466  HB  ILE     9       8.466   1.099  -1.438  1.00  0.00           H  
ATOM   2467 1HG1 ILE     9       9.392   2.628  -3.853  1.00  0.00           H  
ATOM   2468 2HG1 ILE     9       8.014   3.223  -2.929  1.00  0.00           H  
ATOM   2469 1HG2 ILE     9       9.615   0.215  -4.101  1.00  0.00           H  
ATOM   2470 2HG2 ILE     9      10.593   0.572  -2.678  1.00  0.00           H  
ATOM   2471 3HG2 ILE     9       9.440  -0.761  -2.643  1.00  0.00           H  
ATOM   2472 1HD1 ILE     9      10.603   2.458  -1.578  1.00  0.00           H  
ATOM   2473 2HD1 ILE     9      10.347   4.075  -2.235  1.00  0.00           H  
ATOM   2474 3HD1 ILE     9       9.298   3.468  -0.954  1.00  0.00           H  
ATOM   2475  N   SER    10       5.881   2.849  -3.266  1.00  0.00           N  
ATOM   2476  CA  SER    10       4.829   3.792  -2.793  1.00  0.00           C  
ATOM   2477  C   SER    10       3.451   3.200  -3.091  1.00  0.00           C  
ATOM   2478  O   SER    10       2.582   3.175  -2.242  1.00  0.00           O  
ATOM   2479  CB  SER    10       4.981   5.131  -3.517  1.00  0.00           C  
ATOM   2480  OG  SER    10       4.513   4.999  -4.852  1.00  0.00           O  
ATOM   2481  H   SER    10       6.399   3.056  -4.072  1.00  0.00           H  
ATOM   2482  HA  SER    10       4.933   3.941  -1.729  1.00  0.00           H  
ATOM   2483 1HB  SER    10       4.402   5.884  -3.010  1.00  0.00           H  
ATOM   2484 2HB  SER    10       6.024   5.422  -3.518  1.00  0.00           H  
ATOM   2485  HG  SER    10       5.127   5.458  -5.429  1.00  0.00           H  
ATOM   2486  N   VAL    11       3.244   2.718  -4.286  1.00  0.00           N  
ATOM   2487  CA  VAL    11       1.920   2.123  -4.624  1.00  0.00           C  
ATOM   2488  C   VAL    11       1.680   0.896  -3.742  1.00  0.00           C  
ATOM   2489  O   VAL    11       0.561   0.583  -3.389  1.00  0.00           O  
ATOM   2490  CB  VAL    11       1.904   1.703  -6.095  1.00  0.00           C  
ATOM   2491  CG1 VAL    11       0.650   0.871  -6.374  1.00  0.00           C  
ATOM   2492  CG2 VAL    11       1.893   2.950  -6.983  1.00  0.00           C  
ATOM   2493  H   VAL    11       3.958   2.742  -4.958  1.00  0.00           H  
ATOM   2494  HA  VAL    11       1.142   2.852  -4.448  1.00  0.00           H  
ATOM   2495  HB  VAL    11       2.782   1.112  -6.311  1.00  0.00           H  
ATOM   2496 1HG1 VAL    11      -0.217   1.385  -5.983  1.00  0.00           H  
ATOM   2497 2HG1 VAL    11       0.537   0.735  -7.439  1.00  0.00           H  
ATOM   2498 3HG1 VAL    11       0.743  -0.091  -5.894  1.00  0.00           H  
ATOM   2499 1HG2 VAL    11       1.259   3.703  -6.539  1.00  0.00           H  
ATOM   2500 2HG2 VAL    11       2.897   3.334  -7.077  1.00  0.00           H  
ATOM   2501 3HG2 VAL    11       1.514   2.692  -7.962  1.00  0.00           H  
ATOM   2502  N   LEU    12       2.724   0.200  -3.382  1.00  0.00           N  
ATOM   2503  CA  LEU    12       2.556  -1.006  -2.521  1.00  0.00           C  
ATOM   2504  C   LEU    12       2.058  -0.578  -1.140  1.00  0.00           C  
ATOM   2505  O   LEU    12       1.098  -1.114  -0.623  1.00  0.00           O  
ATOM   2506  CB  LEU    12       3.900  -1.725  -2.379  1.00  0.00           C  
ATOM   2507  CG  LEU    12       4.085  -2.699  -3.543  1.00  0.00           C  
ATOM   2508  CD1 LEU    12       5.577  -2.921  -3.791  1.00  0.00           C  
ATOM   2509  CD2 LEU    12       3.422  -4.035  -3.200  1.00  0.00           C  
ATOM   2510  H   LEU    12       3.620   0.470  -3.677  1.00  0.00           H  
ATOM   2511  HA  LEU    12       1.837  -1.673  -2.973  1.00  0.00           H  
ATOM   2512 1HB  LEU    12       4.699  -0.998  -2.386  1.00  0.00           H  
ATOM   2513 2HB  LEU    12       3.918  -2.271  -1.448  1.00  0.00           H  
ATOM   2514  HG  LEU    12       3.629  -2.287  -4.431  1.00  0.00           H  
ATOM   2515 1HD1 LEU    12       6.130  -2.052  -3.465  1.00  0.00           H  
ATOM   2516 2HD1 LEU    12       5.910  -3.787  -3.237  1.00  0.00           H  
ATOM   2517 3HD1 LEU    12       5.747  -3.081  -4.845  1.00  0.00           H  
ATOM   2518 1HD2 LEU    12       3.525  -4.226  -2.140  1.00  0.00           H  
ATOM   2519 2HD2 LEU    12       2.374  -3.993  -3.457  1.00  0.00           H  
ATOM   2520 3HD2 LEU    12       3.899  -4.828  -3.756  1.00  0.00           H  
ATOM   2521  N   LEU    13       2.700   0.387  -0.538  1.00  0.00           N  
ATOM   2522  CA  LEU    13       2.257   0.848   0.806  1.00  0.00           C  
ATOM   2523  C   LEU    13       0.845   1.419   0.700  1.00  0.00           C  
ATOM   2524  O   LEU    13       0.092   1.435   1.654  1.00  0.00           O  
ATOM   2525  CB  LEU    13       3.213   1.935   1.305  1.00  0.00           C  
ATOM   2526  CG  LEU    13       4.494   1.302   1.868  1.00  0.00           C  
ATOM   2527  CD1 LEU    13       4.860   0.040   1.076  1.00  0.00           C  
ATOM   2528  CD2 LEU    13       5.636   2.314   1.758  1.00  0.00           C  
ATOM   2529  H   LEU    13       3.471   0.811  -0.973  1.00  0.00           H  
ATOM   2530  HA  LEU    13       2.262   0.017   1.495  1.00  0.00           H  
ATOM   2531 1HB  LEU    13       3.469   2.589   0.484  1.00  0.00           H  
ATOM   2532 2HB  LEU    13       2.730   2.508   2.081  1.00  0.00           H  
ATOM   2533  HG  LEU    13       4.342   1.043   2.904  1.00  0.00           H  
ATOM   2534 1HD1 LEU    13       4.955   0.284   0.030  1.00  0.00           H  
ATOM   2535 2HD1 LEU    13       5.796  -0.356   1.440  1.00  0.00           H  
ATOM   2536 3HD1 LEU    13       4.083  -0.701   1.202  1.00  0.00           H  
ATOM   2537 1HD2 LEU    13       5.444   2.984   0.932  1.00  0.00           H  
ATOM   2538 2HD2 LEU    13       5.704   2.881   2.673  1.00  0.00           H  
ATOM   2539 3HD2 LEU    13       6.566   1.791   1.588  1.00  0.00           H  
ATOM   2540  N   ALA    14       0.482   1.887  -0.460  1.00  0.00           N  
ATOM   2541  CA  ALA    14      -0.882   2.459  -0.644  1.00  0.00           C  
ATOM   2542  C   ALA    14      -1.932   1.393  -0.324  1.00  0.00           C  
ATOM   2543  O   ALA    14      -2.578   1.435   0.704  1.00  0.00           O  
ATOM   2544  CB  ALA    14      -1.047   2.920  -2.093  1.00  0.00           C  
ATOM   2545  H   ALA    14       1.109   1.863  -1.214  1.00  0.00           H  
ATOM   2546  HA  ALA    14      -1.010   3.302   0.019  1.00  0.00           H  
ATOM   2547 1HB  ALA    14      -0.088   2.900  -2.589  1.00  0.00           H  
ATOM   2548 2HB  ALA    14      -1.731   2.258  -2.606  1.00  0.00           H  
ATOM   2549 3HB  ALA    14      -1.439   3.926  -2.110  1.00  0.00           H  
ATOM   2550  N   GLN    15      -2.107   0.438  -1.196  1.00  0.00           N  
ATOM   2551  CA  GLN    15      -3.117  -0.627  -0.938  1.00  0.00           C  
ATOM   2552  C   GLN    15      -2.676  -1.473   0.258  1.00  0.00           C  
ATOM   2553  O   GLN    15      -3.435  -2.260   0.787  1.00  0.00           O  
ATOM   2554  CB  GLN    15      -3.247  -1.520  -2.174  1.00  0.00           C  
ATOM   2555  CG  GLN    15      -4.634  -2.165  -2.196  1.00  0.00           C  
ATOM   2556  CD  GLN    15      -5.535  -1.404  -3.171  1.00  0.00           C  
ATOM   2557  OE1 GLN    15      -5.748  -0.218  -3.020  1.00  0.00           O  
ATOM   2558  NE2 GLN    15      -6.077  -2.043  -4.171  1.00  0.00           N  
ATOM   2559  H   GLN    15      -1.576   0.422  -2.020  1.00  0.00           H  
ATOM   2560  HA  GLN    15      -4.072  -0.172  -0.723  1.00  0.00           H  
ATOM   2561 1HB  GLN    15      -3.112  -0.923  -3.064  1.00  0.00           H  
ATOM   2562 2HB  GLN    15      -2.493  -2.293  -2.142  1.00  0.00           H  
ATOM   2563 1HG  GLN    15      -4.547  -3.195  -2.512  1.00  0.00           H  
ATOM   2564 2HG  GLN    15      -5.065  -2.126  -1.206  1.00  0.00           H  
ATOM   2565 1HE2 GLN    15      -6.656  -1.566  -4.802  1.00  0.00           H  
ATOM   2566 2HE2 GLN    15      -5.905  -3.000  -4.294  1.00  0.00           H  
ATOM   2567  N   ALA    16      -1.455  -1.315   0.691  1.00  0.00           N  
ATOM   2568  CA  ALA    16      -0.973  -2.109   1.856  1.00  0.00           C  
ATOM   2569  C   ALA    16      -1.725  -1.666   3.112  1.00  0.00           C  
ATOM   2570  O   ALA    16      -2.533  -2.395   3.654  1.00  0.00           O  
ATOM   2571  CB  ALA    16       0.526  -1.875   2.050  1.00  0.00           C  
ATOM   2572  H   ALA    16      -0.857  -0.674   0.254  1.00  0.00           H  
ATOM   2573  HA  ALA    16      -1.155  -3.158   1.678  1.00  0.00           H  
ATOM   2574 1HB  ALA    16       0.716  -0.815   2.137  1.00  0.00           H  
ATOM   2575 2HB  ALA    16       0.856  -2.374   2.949  1.00  0.00           H  
ATOM   2576 3HB  ALA    16       1.065  -2.268   1.201  1.00  0.00           H  
ATOM   2577  N   VAL    17      -1.472  -0.473   3.574  1.00  0.00           N  
ATOM   2578  CA  VAL    17      -2.179   0.021   4.788  1.00  0.00           C  
ATOM   2579  C   VAL    17      -3.677   0.110   4.493  1.00  0.00           C  
ATOM   2580  O   VAL    17      -4.504  -0.027   5.373  1.00  0.00           O  
ATOM   2581  CB  VAL    17      -1.646   1.406   5.159  1.00  0.00           C  
ATOM   2582  CG1 VAL    17      -2.502   2.001   6.278  1.00  0.00           C  
ATOM   2583  CG2 VAL    17      -0.197   1.282   5.635  1.00  0.00           C  
ATOM   2584  H   VAL    17      -0.821   0.101   3.119  1.00  0.00           H  
ATOM   2585  HA  VAL    17      -2.011  -0.663   5.607  1.00  0.00           H  
ATOM   2586  HB  VAL    17      -1.689   2.051   4.293  1.00  0.00           H  
ATOM   2587 1HG1 VAL    17      -3.001   1.204   6.811  1.00  0.00           H  
ATOM   2588 2HG1 VAL    17      -1.870   2.550   6.962  1.00  0.00           H  
ATOM   2589 3HG1 VAL    17      -3.238   2.667   5.853  1.00  0.00           H  
ATOM   2590 1HG2 VAL    17       0.097   0.243   5.624  1.00  0.00           H  
ATOM   2591 2HG2 VAL    17       0.447   1.846   4.977  1.00  0.00           H  
ATOM   2592 3HG2 VAL    17      -0.114   1.670   6.639  1.00  0.00           H  
ATOM   2593  N   PHE    18      -4.030   0.334   3.257  1.00  0.00           N  
ATOM   2594  CA  PHE    18      -5.473   0.427   2.899  1.00  0.00           C  
ATOM   2595  C   PHE    18      -6.173  -0.877   3.281  1.00  0.00           C  
ATOM   2596  O   PHE    18      -6.983  -0.916   4.187  1.00  0.00           O  
ATOM   2597  CB  PHE    18      -5.608   0.656   1.392  1.00  0.00           C  
ATOM   2598  CG  PHE    18      -6.644   1.724   1.135  1.00  0.00           C  
ATOM   2599  CD1 PHE    18      -6.300   3.076   1.255  1.00  0.00           C  
ATOM   2600  CD2 PHE    18      -7.947   1.362   0.777  1.00  0.00           C  
ATOM   2601  CE1 PHE    18      -7.260   4.066   1.016  1.00  0.00           C  
ATOM   2602  CE2 PHE    18      -8.907   2.352   0.538  1.00  0.00           C  
ATOM   2603  CZ  PHE    18      -8.564   3.704   0.657  1.00  0.00           C  
ATOM   2604  H   PHE    18      -3.346   0.438   2.564  1.00  0.00           H  
ATOM   2605  HA  PHE    18      -5.925   1.251   3.432  1.00  0.00           H  
ATOM   2606 1HB  PHE    18      -4.657   0.972   0.989  1.00  0.00           H  
ATOM   2607 2HB  PHE    18      -5.915  -0.262   0.915  1.00  0.00           H  
ATOM   2608  HD1 PHE    18      -5.293   3.355   1.531  1.00  0.00           H  
ATOM   2609  HD2 PHE    18      -8.212   0.320   0.685  1.00  0.00           H  
ATOM   2610  HE1 PHE    18      -6.995   5.109   1.109  1.00  0.00           H  
ATOM   2611  HE2 PHE    18      -9.913   2.073   0.262  1.00  0.00           H  
ATOM   2612  HZ  PHE    18      -9.305   4.467   0.474  1.00  0.00           H  
ATOM   2613  N   LEU    19      -5.865  -1.947   2.601  1.00  0.00           N  
ATOM   2614  CA  LEU    19      -6.512  -3.246   2.932  1.00  0.00           C  
ATOM   2615  C   LEU    19      -6.318  -3.542   4.420  1.00  0.00           C  
ATOM   2616  O   LEU    19      -7.042  -4.319   5.009  1.00  0.00           O  
ATOM   2617  CB  LEU    19      -5.877  -4.362   2.099  1.00  0.00           C  
ATOM   2618  CG  LEU    19      -4.460  -4.634   2.604  1.00  0.00           C  
ATOM   2619  CD1 LEU    19      -4.516  -5.609   3.780  1.00  0.00           C  
ATOM   2620  CD2 LEU    19      -3.627  -5.243   1.474  1.00  0.00           C  
ATOM   2621  H   LEU    19      -5.207  -1.896   1.876  1.00  0.00           H  
ATOM   2622  HA  LEU    19      -7.568  -3.189   2.711  1.00  0.00           H  
ATOM   2623 1HB  LEU    19      -6.470  -5.260   2.189  1.00  0.00           H  
ATOM   2624 2HB  LEU    19      -5.837  -4.060   1.063  1.00  0.00           H  
ATOM   2625  HG  LEU    19      -4.010  -3.706   2.926  1.00  0.00           H  
ATOM   2626 1HD1 LEU    19      -5.540  -5.896   3.961  1.00  0.00           H  
ATOM   2627 2HD1 LEU    19      -3.931  -6.487   3.547  1.00  0.00           H  
ATOM   2628 3HD1 LEU    19      -4.114  -5.132   4.662  1.00  0.00           H  
ATOM   2629 1HD2 LEU    19      -3.595  -4.558   0.640  1.00  0.00           H  
ATOM   2630 2HD2 LEU    19      -2.622  -5.428   1.827  1.00  0.00           H  
ATOM   2631 3HD2 LEU    19      -4.074  -6.175   1.159  1.00  0.00           H  
ATOM   2632  N   LEU    20      -5.347  -2.922   5.036  1.00  0.00           N  
ATOM   2633  CA  LEU    20      -5.115  -3.163   6.488  1.00  0.00           C  
ATOM   2634  C   LEU    20      -6.322  -2.656   7.277  1.00  0.00           C  
ATOM   2635  O   LEU    20      -6.848  -3.340   8.133  1.00  0.00           O  
ATOM   2636  CB  LEU    20      -3.857  -2.417   6.939  1.00  0.00           C  
ATOM   2637  CG  LEU    20      -3.387  -2.977   8.283  1.00  0.00           C  
ATOM   2638  CD1 LEU    20      -1.901  -3.326   8.201  1.00  0.00           C  
ATOM   2639  CD2 LEU    20      -3.603  -1.927   9.376  1.00  0.00           C  
ATOM   2640  H   LEU    20      -4.775  -2.295   4.545  1.00  0.00           H  
ATOM   2641  HA  LEU    20      -4.988  -4.223   6.661  1.00  0.00           H  
ATOM   2642 1HB  LEU    20      -3.078  -2.545   6.201  1.00  0.00           H  
ATOM   2643 2HB  LEU    20      -4.082  -1.366   7.048  1.00  0.00           H  
ATOM   2644  HG  LEU    20      -3.952  -3.867   8.519  1.00  0.00           H  
ATOM   2645 1HD1 LEU    20      -1.560  -3.211   7.183  1.00  0.00           H  
ATOM   2646 2HD1 LEU    20      -1.339  -2.666   8.845  1.00  0.00           H  
ATOM   2647 3HD1 LEU    20      -1.753  -4.348   8.516  1.00  0.00           H  
ATOM   2648 1HD2 LEU    20      -4.377  -1.240   9.068  1.00  0.00           H  
ATOM   2649 2HD2 LEU    20      -3.900  -2.417  10.292  1.00  0.00           H  
ATOM   2650 3HD2 LEU    20      -2.683  -1.385   9.540  1.00  0.00           H  
ATOM   2651  N   LEU    21      -6.771  -1.466   6.989  1.00  0.00           N  
ATOM   2652  CA  LEU    21      -7.953  -0.923   7.716  1.00  0.00           C  
ATOM   2653  C   LEU    21      -9.168  -1.784   7.380  1.00  0.00           C  
ATOM   2654  O   LEU    21      -9.968  -2.113   8.233  1.00  0.00           O  
ATOM   2655  CB  LEU    21      -8.219   0.525   7.288  1.00  0.00           C  
ATOM   2656  CG  LEU    21      -6.900   1.238   6.979  1.00  0.00           C  
ATOM   2657  CD1 LEU    21      -7.156   2.740   6.831  1.00  0.00           C  
ATOM   2658  CD2 LEU    21      -5.906   1.008   8.123  1.00  0.00           C  
ATOM   2659  H   LEU    21      -6.338  -0.937   6.290  1.00  0.00           H  
ATOM   2660  HA  LEU    21      -7.769  -0.959   8.780  1.00  0.00           H  
ATOM   2661 1HB  LEU    21      -8.843   0.528   6.405  1.00  0.00           H  
ATOM   2662 2HB  LEU    21      -8.727   1.047   8.086  1.00  0.00           H  
ATOM   2663  HG  LEU    21      -6.490   0.854   6.057  1.00  0.00           H  
ATOM   2664 1HD1 LEU    21      -8.175   2.960   7.111  1.00  0.00           H  
ATOM   2665 2HD1 LEU    21      -6.481   3.285   7.473  1.00  0.00           H  
ATOM   2666 3HD1 LEU    21      -6.992   3.034   5.804  1.00  0.00           H  
ATOM   2667 1HD2 LEU    21      -5.918  -0.032   8.411  1.00  0.00           H  
ATOM   2668 2HD2 LEU    21      -4.913   1.279   7.798  1.00  0.00           H  
ATOM   2669 3HD2 LEU    21      -6.186   1.618   8.969  1.00  0.00           H  
ATOM   2670  N   THR    22      -9.305  -2.160   6.138  1.00  0.00           N  
ATOM   2671  CA  THR    22     -10.463  -3.009   5.741  1.00  0.00           C  
ATOM   2672  C   THR    22     -10.376  -4.347   6.476  1.00  0.00           C  
ATOM   2673  O   THR    22     -11.373  -4.993   6.731  1.00  0.00           O  
ATOM   2674  CB  THR    22     -10.426  -3.255   4.230  1.00  0.00           C  
ATOM   2675  OG1 THR    22     -10.647  -2.028   3.547  1.00  0.00           O  
ATOM   2676  CG2 THR    22     -11.515  -4.258   3.849  1.00  0.00           C  
ATOM   2677  H   THR    22      -8.642  -1.886   5.467  1.00  0.00           H  
ATOM   2678  HA  THR    22     -11.383  -2.510   6.004  1.00  0.00           H  
ATOM   2679  HB  THR    22      -9.461  -3.652   3.952  1.00  0.00           H  
ATOM   2680  HG1 THR    22     -10.454  -2.166   2.617  1.00  0.00           H  
ATOM   2681 1HG2 THR    22     -12.267  -4.283   4.622  1.00  0.00           H  
ATOM   2682 2HG2 THR    22     -11.968  -3.960   2.915  1.00  0.00           H  
ATOM   2683 3HG2 THR    22     -11.078  -5.240   3.739  1.00  0.00           H  
ATOM   2684  N   SER    23      -9.189  -4.764   6.823  1.00  0.00           N  
ATOM   2685  CA  SER    23      -9.034  -6.056   7.547  1.00  0.00           C  
ATOM   2686  C   SER    23      -9.580  -5.906   8.968  1.00  0.00           C  
ATOM   2687  O   SER    23     -10.299  -6.753   9.460  1.00  0.00           O  
ATOM   2688  CB  SER    23      -7.552  -6.432   7.603  1.00  0.00           C  
ATOM   2689  OG  SER    23      -7.365  -7.700   6.988  1.00  0.00           O  
ATOM   2690  H   SER    23      -8.399  -4.225   6.610  1.00  0.00           H  
ATOM   2691  HA  SER    23      -9.583  -6.828   7.029  1.00  0.00           H  
ATOM   2692 1HB  SER    23      -6.971  -5.694   7.078  1.00  0.00           H  
ATOM   2693 2HB  SER    23      -7.231  -6.471   8.636  1.00  0.00           H  
ATOM   2694  HG  SER    23      -8.176  -8.202   7.091  1.00  0.00           H  
ATOM   2695  N   GLN    24      -9.249  -4.830   9.629  1.00  0.00           N  
ATOM   2696  CA  GLN    24      -9.755  -4.620  11.014  1.00  0.00           C  
ATOM   2697  C   GLN    24     -11.255  -4.330  10.959  1.00  0.00           C  
ATOM   2698  O   GLN    24     -11.953  -4.415  11.950  1.00  0.00           O  
ATOM   2699  CB  GLN    24      -9.031  -3.430  11.649  1.00  0.00           C  
ATOM   2700  CG  GLN    24      -7.853  -3.931  12.487  1.00  0.00           C  
ATOM   2701  CD  GLN    24      -6.798  -4.549  11.569  1.00  0.00           C  
ATOM   2702  OE1 GLN    24      -7.110  -5.377  10.736  1.00  0.00           O  
ATOM   2703  NE2 GLN    24      -5.552  -4.178  11.686  1.00  0.00           N  
ATOM   2704  H   GLN    24      -8.672  -4.157   9.211  1.00  0.00           H  
ATOM   2705  HA  GLN    24      -9.579  -5.508  11.603  1.00  0.00           H  
ATOM   2706 1HB  GLN    24      -8.667  -2.774  10.872  1.00  0.00           H  
ATOM   2707 2HB  GLN    24      -9.716  -2.889  12.284  1.00  0.00           H  
ATOM   2708 1HG  GLN    24      -7.420  -3.103  13.030  1.00  0.00           H  
ATOM   2709 2HG  GLN    24      -8.201  -4.677  13.187  1.00  0.00           H  
ATOM   2710 1HE2 GLN    24      -4.867  -4.570  11.103  1.00  0.00           H  
ATOM   2711 2HE2 GLN    24      -5.301  -3.511  12.356  1.00  0.00           H  
ATOM   2712  N   ARG    25     -11.755  -3.984   9.804  1.00  0.00           N  
ATOM   2713  CA  ARG    25     -13.208  -3.683   9.679  1.00  0.00           C  
ATOM   2714  C   ARG    25     -13.669  -3.984   8.251  1.00  0.00           C  
ATOM   2715  O   ARG    25     -13.689  -5.149   7.890  1.00  0.00           O  
ATOM   2716  CB  ARG    25     -13.447  -2.205   9.991  1.00  0.00           C  
ATOM   2717  CG  ARG    25     -14.937  -1.971  10.248  1.00  0.00           C  
ATOM   2718  CD  ARG    25     -15.255  -0.485  10.078  1.00  0.00           C  
ATOM   2719  NE  ARG    25     -14.358   0.318  10.957  1.00  0.00           N  
ATOM   2720  CZ  ARG    25     -14.812   0.815  12.074  1.00  0.00           C  
ATOM   2721  NH1 ARG    25     -15.070   0.028  13.082  1.00  0.00           N  
ATOM   2722  NH2 ARG    25     -15.008   2.100  12.185  1.00  0.00           N  
ATOM   2723  OXT ARG    25     -13.994  -3.045   7.545  1.00  0.00           O  
ATOM   2724  H   ARG    25     -11.172  -3.919   9.018  1.00  0.00           H  
ATOM   2725  HA  ARG    25     -13.765  -4.293  10.374  1.00  0.00           H  
ATOM   2726 1HB  ARG    25     -12.880  -1.927  10.868  1.00  0.00           H  
ATOM   2727 2HB  ARG    25     -13.130  -1.605   9.152  1.00  0.00           H  
ATOM   2728 1HG  ARG    25     -15.518  -2.548   9.543  1.00  0.00           H  
ATOM   2729 2HG  ARG    25     -15.181  -2.277  11.254  1.00  0.00           H  
ATOM   2730 1HD  ARG    25     -15.101  -0.199   9.048  1.00  0.00           H  
ATOM   2731 2HD  ARG    25     -16.284  -0.304  10.351  1.00  0.00           H  
ATOM   2732  HE  ARG    25     -13.426   0.471  10.695  1.00  0.00           H  
ATOM   2733 1HH1 ARG    25     -14.920  -0.957  12.998  1.00  0.00           H  
ATOM   2734 2HH1 ARG    25     -15.418   0.408  13.938  1.00  0.00           H  
ATOM   2735 1HH2 ARG    25     -14.810   2.705  11.414  1.00  0.00           H  
ATOM   2736 2HH2 ARG    25     -15.357   2.480  13.042  1.00  0.00           H  
TER    2737      ARG    25                                                      
ENDMDL                                                                          
MODEL        8                                                                  
ATOM   2738  N   GLY     1      16.516   1.283 -12.918  1.00  0.00           N  
ATOM   2739  CA  GLY     1      15.094   1.484 -12.396  1.00  0.00           C  
ATOM   2740  C   GLY     1      14.882   1.808 -10.956  1.00  0.00           C  
ATOM   2741  O   GLY     1      14.030   1.240 -10.302  1.00  0.00           O  
ATOM   2742 1H   GLY     1      17.172   1.204 -12.113  1.00  0.00           H  
ATOM   2743 2H   GLY     1      16.558   0.414 -13.487  1.00  0.00           H  
ATOM   2744 3H   GLY     1      16.788   2.096 -13.507  1.00  0.00           H  
ATOM   2745 1HA  GLY     1      14.789   2.399 -12.537  1.00  0.00           H  
ATOM   2746 2HA  GLY     1      14.421   0.692 -12.928  1.00  0.00           H  
ATOM   2747  N   SER     2      15.646   2.722 -10.424  1.00  0.00           N  
ATOM   2748  CA  SER     2      15.483   3.088  -8.989  1.00  0.00           C  
ATOM   2749  C   SER     2      14.271   4.006  -8.828  1.00  0.00           C  
ATOM   2750  O   SER     2      13.416   3.782  -7.994  1.00  0.00           O  
ATOM   2751  CB  SER     2      16.739   3.813  -8.502  1.00  0.00           C  
ATOM   2752  OG  SER     2      16.573   5.212  -8.689  1.00  0.00           O  
ATOM   2753  H   SER     2      16.330   3.166 -10.969  1.00  0.00           H  
ATOM   2754  HA  SER     2      15.337   2.192  -8.403  1.00  0.00           H  
ATOM   2755 1HB  SER     2      16.890   3.611  -7.454  1.00  0.00           H  
ATOM   2756 2HB  SER     2      17.596   3.462  -9.061  1.00  0.00           H  
ATOM   2757  HG  SER     2      15.957   5.530  -8.025  1.00  0.00           H  
ATOM   2758  N   GLU     3      14.189   5.042  -9.618  1.00  0.00           N  
ATOM   2759  CA  GLU     3      13.031   5.974  -9.507  1.00  0.00           C  
ATOM   2760  C   GLU     3      11.735   5.210  -9.791  1.00  0.00           C  
ATOM   2761  O   GLU     3      10.719   5.442  -9.166  1.00  0.00           O  
ATOM   2762  CB  GLU     3      13.188   7.110 -10.520  1.00  0.00           C  
ATOM   2763  CG  GLU     3      14.509   7.840 -10.268  1.00  0.00           C  
ATOM   2764  CD  GLU     3      15.101   8.302 -11.601  1.00  0.00           C  
ATOM   2765  OE1 GLU     3      14.332   8.524 -12.524  1.00  0.00           O  
ATOM   2766  OE2 GLU     3      16.311   8.428 -11.678  1.00  0.00           O  
ATOM   2767  H   GLU     3      14.888   5.207 -10.284  1.00  0.00           H  
ATOM   2768  HA  GLU     3      12.995   6.384  -8.508  1.00  0.00           H  
ATOM   2769 1HB  GLU     3      13.186   6.703 -11.521  1.00  0.00           H  
ATOM   2770 2HB  GLU     3      12.369   7.804 -10.412  1.00  0.00           H  
ATOM   2771 1HG  GLU     3      14.330   8.699  -9.636  1.00  0.00           H  
ATOM   2772 2HG  GLU     3      15.203   7.173  -9.781  1.00  0.00           H  
ATOM   2773  N   LYS     4      11.761   4.301 -10.726  1.00  0.00           N  
ATOM   2774  CA  LYS     4      10.531   3.525 -11.043  1.00  0.00           C  
ATOM   2775  C   LYS     4      10.218   2.581  -9.881  1.00  0.00           C  
ATOM   2776  O   LYS     4       9.102   2.511  -9.405  1.00  0.00           O  
ATOM   2777  CB  LYS     4      10.755   2.710 -12.319  1.00  0.00           C  
ATOM   2778  CG  LYS     4      10.393   3.560 -13.538  1.00  0.00           C  
ATOM   2779  CD  LYS     4      11.301   4.790 -13.592  1.00  0.00           C  
ATOM   2780  CE  LYS     4      11.330   5.344 -15.018  1.00  0.00           C  
ATOM   2781  NZ  LYS     4       9.974   5.834 -15.390  1.00  0.00           N  
ATOM   2782  H   LYS     4      12.591   4.126 -11.217  1.00  0.00           H  
ATOM   2783  HA  LYS     4       9.703   4.204 -11.189  1.00  0.00           H  
ATOM   2784 1HB  LYS     4      11.793   2.417 -12.380  1.00  0.00           H  
ATOM   2785 2HB  LYS     4      10.132   1.829 -12.299  1.00  0.00           H  
ATOM   2786 1HG  LYS     4      10.523   2.975 -14.437  1.00  0.00           H  
ATOM   2787 2HG  LYS     4       9.364   3.879 -13.462  1.00  0.00           H  
ATOM   2788 1HD  LYS     4      10.924   5.547 -12.919  1.00  0.00           H  
ATOM   2789 2HD  LYS     4      12.302   4.512 -13.296  1.00  0.00           H  
ATOM   2790 1HE  LYS     4      12.036   6.160 -15.073  1.00  0.00           H  
ATOM   2791 2HE  LYS     4      11.631   4.563 -15.700  1.00  0.00           H  
ATOM   2792 1HZ  LYS     4       9.567   6.367 -14.594  1.00  0.00           H  
ATOM   2793 2HZ  LYS     4      10.044   6.453 -16.222  1.00  0.00           H  
ATOM   2794 3HZ  LYS     4       9.361   5.025 -15.615  1.00  0.00           H  
ATOM   2795  N   MET     5      11.199   1.856  -9.414  1.00  0.00           N  
ATOM   2796  CA  MET     5      10.961   0.922  -8.279  1.00  0.00           C  
ATOM   2797  C   MET     5      10.619   1.727  -7.025  1.00  0.00           C  
ATOM   2798  O   MET     5      10.082   1.208  -6.068  1.00  0.00           O  
ATOM   2799  CB  MET     5      12.224   0.093  -8.027  1.00  0.00           C  
ATOM   2800  CG  MET     5      12.078  -1.275  -8.696  1.00  0.00           C  
ATOM   2801  SD  MET     5      12.329  -1.106 -10.482  1.00  0.00           S  
ATOM   2802  CE  MET     5      10.586  -0.955 -10.943  1.00  0.00           C  
ATOM   2803  H   MET     5      12.093   1.929  -9.809  1.00  0.00           H  
ATOM   2804  HA  MET     5      10.140   0.263  -8.520  1.00  0.00           H  
ATOM   2805 1HB  MET     5      13.080   0.608  -8.440  1.00  0.00           H  
ATOM   2806 2HB  MET     5      12.360  -0.040  -6.966  1.00  0.00           H  
ATOM   2807 1HG  MET     5      12.815  -1.953  -8.293  1.00  0.00           H  
ATOM   2808 2HG  MET     5      11.089  -1.665  -8.508  1.00  0.00           H  
ATOM   2809 1HE  MET     5      10.129  -0.162 -10.366  1.00  0.00           H  
ATOM   2810 2HE  MET     5      10.512  -0.726 -11.998  1.00  0.00           H  
ATOM   2811 3HE  MET     5      10.076  -1.883 -10.742  1.00  0.00           H  
ATOM   2812  N   SER     6      10.926   2.996  -7.025  1.00  0.00           N  
ATOM   2813  CA  SER     6      10.615   3.838  -5.836  1.00  0.00           C  
ATOM   2814  C   SER     6       9.138   4.232  -5.872  1.00  0.00           C  
ATOM   2815  O   SER     6       8.480   4.315  -4.854  1.00  0.00           O  
ATOM   2816  CB  SER     6      11.480   5.099  -5.863  1.00  0.00           C  
ATOM   2817  OG  SER     6      12.118   5.257  -4.603  1.00  0.00           O  
ATOM   2818  H   SER     6      11.356   3.396  -7.809  1.00  0.00           H  
ATOM   2819  HA  SER     6      10.818   3.279  -4.935  1.00  0.00           H  
ATOM   2820 1HB  SER     6      12.231   5.007  -6.630  1.00  0.00           H  
ATOM   2821 2HB  SER     6      10.857   5.958  -6.073  1.00  0.00           H  
ATOM   2822  HG  SER     6      12.449   4.398  -4.329  1.00  0.00           H  
ATOM   2823  N   THR     7       8.610   4.467  -7.042  1.00  0.00           N  
ATOM   2824  CA  THR     7       7.176   4.848  -7.150  1.00  0.00           C  
ATOM   2825  C   THR     7       6.321   3.586  -7.067  1.00  0.00           C  
ATOM   2826  O   THR     7       5.151   3.633  -6.744  1.00  0.00           O  
ATOM   2827  CB  THR     7       6.932   5.547  -8.488  1.00  0.00           C  
ATOM   2828  OG1 THR     7       7.782   6.681  -8.590  1.00  0.00           O  
ATOM   2829  CG2 THR     7       5.471   5.992  -8.577  1.00  0.00           C  
ATOM   2830  H   THR     7       9.157   4.385  -7.851  1.00  0.00           H  
ATOM   2831  HA  THR     7       6.917   5.514  -6.340  1.00  0.00           H  
ATOM   2832  HB  THR     7       7.144   4.864  -9.297  1.00  0.00           H  
ATOM   2833  HG1 THR     7       8.258   6.622  -9.422  1.00  0.00           H  
ATOM   2834 1HG2 THR     7       5.120   6.272  -7.595  1.00  0.00           H  
ATOM   2835 2HG2 THR     7       5.392   6.838  -9.244  1.00  0.00           H  
ATOM   2836 3HG2 THR     7       4.869   5.178  -8.956  1.00  0.00           H  
ATOM   2837  N   ALA     8       6.902   2.453  -7.350  1.00  0.00           N  
ATOM   2838  CA  ALA     8       6.135   1.183  -7.282  1.00  0.00           C  
ATOM   2839  C   ALA     8       6.154   0.673  -5.844  1.00  0.00           C  
ATOM   2840  O   ALA     8       5.175   0.154  -5.343  1.00  0.00           O  
ATOM   2841  CB  ALA     8       6.782   0.149  -8.205  1.00  0.00           C  
ATOM   2842  H   ALA     8       7.850   2.438  -7.598  1.00  0.00           H  
ATOM   2843  HA  ALA     8       5.117   1.359  -7.589  1.00  0.00           H  
ATOM   2844 1HB  ALA     8       7.556   0.623  -8.789  1.00  0.00           H  
ATOM   2845 2HB  ALA     8       7.211  -0.645  -7.612  1.00  0.00           H  
ATOM   2846 3HB  ALA     8       6.032  -0.261  -8.866  1.00  0.00           H  
ATOM   2847  N   ILE     9       7.259   0.829  -5.172  1.00  0.00           N  
ATOM   2848  CA  ILE     9       7.337   0.361  -3.765  1.00  0.00           C  
ATOM   2849  C   ILE     9       6.485   1.280  -2.889  1.00  0.00           C  
ATOM   2850  O   ILE     9       5.913   0.858  -1.904  1.00  0.00           O  
ATOM   2851  CB  ILE     9       8.791   0.385  -3.287  1.00  0.00           C  
ATOM   2852  CG1 ILE     9       9.359   1.798  -3.425  1.00  0.00           C  
ATOM   2853  CG2 ILE     9       9.620  -0.581  -4.134  1.00  0.00           C  
ATOM   2854  CD1 ILE     9       9.642   2.372  -2.037  1.00  0.00           C  
ATOM   2855  H   ILE     9       8.033   1.257  -5.593  1.00  0.00           H  
ATOM   2856  HA  ILE     9       6.955  -0.646  -3.704  1.00  0.00           H  
ATOM   2857  HB  ILE     9       8.833   0.078  -2.251  1.00  0.00           H  
ATOM   2858 1HG1 ILE     9      10.277   1.761  -3.995  1.00  0.00           H  
ATOM   2859 2HG1 ILE     9       8.646   2.427  -3.934  1.00  0.00           H  
ATOM   2860 1HG2 ILE     9       9.268  -0.557  -5.156  1.00  0.00           H  
ATOM   2861 2HG2 ILE     9      10.658  -0.284  -4.107  1.00  0.00           H  
ATOM   2862 3HG2 ILE     9       9.522  -1.582  -3.743  1.00  0.00           H  
ATOM   2863 1HD1 ILE     9       9.412   1.631  -1.287  1.00  0.00           H  
ATOM   2864 2HD1 ILE     9      10.686   2.644  -1.966  1.00  0.00           H  
ATOM   2865 3HD1 ILE     9       9.031   3.247  -1.878  1.00  0.00           H  
ATOM   2866  N   SER    10       6.383   2.532  -3.246  1.00  0.00           N  
ATOM   2867  CA  SER    10       5.553   3.468  -2.439  1.00  0.00           C  
ATOM   2868  C   SER    10       4.077   3.131  -2.658  1.00  0.00           C  
ATOM   2869  O   SER    10       3.346   2.860  -1.724  1.00  0.00           O  
ATOM   2870  CB  SER    10       5.826   4.907  -2.881  1.00  0.00           C  
ATOM   2871  OG  SER    10       4.598   5.621  -2.956  1.00  0.00           O  
ATOM   2872  H   SER    10       6.843   2.854  -4.051  1.00  0.00           H  
ATOM   2873  HA  SER    10       5.796   3.357  -1.393  1.00  0.00           H  
ATOM   2874 1HB  SER    10       6.473   5.388  -2.166  1.00  0.00           H  
ATOM   2875 2HB  SER    10       6.309   4.898  -3.850  1.00  0.00           H  
ATOM   2876  HG  SER    10       4.302   5.794  -2.059  1.00  0.00           H  
ATOM   2877  N   VAL    11       3.635   3.128  -3.887  1.00  0.00           N  
ATOM   2878  CA  VAL    11       2.211   2.791  -4.158  1.00  0.00           C  
ATOM   2879  C   VAL    11       1.892   1.448  -3.500  1.00  0.00           C  
ATOM   2880  O   VAL    11       0.763   1.169  -3.149  1.00  0.00           O  
ATOM   2881  CB  VAL    11       1.984   2.692  -5.670  1.00  0.00           C  
ATOM   2882  CG1 VAL    11       0.635   2.025  -5.943  1.00  0.00           C  
ATOM   2883  CG2 VAL    11       1.988   4.097  -6.278  1.00  0.00           C  
ATOM   2884  H   VAL    11       4.241   3.338  -4.629  1.00  0.00           H  
ATOM   2885  HA  VAL    11       1.570   3.557  -3.743  1.00  0.00           H  
ATOM   2886  HB  VAL    11       2.774   2.103  -6.114  1.00  0.00           H  
ATOM   2887 1HG1 VAL    11      -0.131   2.508  -5.356  1.00  0.00           H  
ATOM   2888 2HG1 VAL    11       0.395   2.115  -6.992  1.00  0.00           H  
ATOM   2889 3HG1 VAL    11       0.689   0.980  -5.674  1.00  0.00           H  
ATOM   2890 1HG2 VAL    11       1.233   4.701  -5.796  1.00  0.00           H  
ATOM   2891 2HG2 VAL    11       2.957   4.550  -6.133  1.00  0.00           H  
ATOM   2892 3HG2 VAL    11       1.775   4.032  -7.335  1.00  0.00           H  
ATOM   2893  N   LEU    12       2.885   0.618  -3.321  1.00  0.00           N  
ATOM   2894  CA  LEU    12       2.641  -0.700  -2.674  1.00  0.00           C  
ATOM   2895  C   LEU    12       2.189  -0.469  -1.231  1.00  0.00           C  
ATOM   2896  O   LEU    12       1.106  -0.858  -0.841  1.00  0.00           O  
ATOM   2897  CB  LEU    12       3.928  -1.524  -2.683  1.00  0.00           C  
ATOM   2898  CG  LEU    12       3.983  -2.368  -3.958  1.00  0.00           C  
ATOM   2899  CD1 LEU    12       5.307  -3.132  -4.008  1.00  0.00           C  
ATOM   2900  CD2 LEU    12       2.819  -3.362  -3.962  1.00  0.00           C  
ATOM   2901  H   LEU    12       3.791   0.864  -3.606  1.00  0.00           H  
ATOM   2902  HA  LEU    12       1.869  -1.229  -3.213  1.00  0.00           H  
ATOM   2903 1HB  LEU    12       4.780  -0.861  -2.651  1.00  0.00           H  
ATOM   2904 2HB  LEU    12       3.945  -2.175  -1.821  1.00  0.00           H  
ATOM   2905  HG  LEU    12       3.910  -1.721  -4.819  1.00  0.00           H  
ATOM   2906 1HD1 LEU    12       5.833  -3.004  -3.073  1.00  0.00           H  
ATOM   2907 2HD1 LEU    12       5.111  -4.182  -4.169  1.00  0.00           H  
ATOM   2908 3HD1 LEU    12       5.913  -2.751  -4.817  1.00  0.00           H  
ATOM   2909 1HD2 LEU    12       2.296  -3.310  -3.019  1.00  0.00           H  
ATOM   2910 2HD2 LEU    12       2.139  -3.117  -4.764  1.00  0.00           H  
ATOM   2911 3HD2 LEU    12       3.200  -4.362  -4.107  1.00  0.00           H  
ATOM   2912  N   LEU    13       3.005   0.172  -0.435  1.00  0.00           N  
ATOM   2913  CA  LEU    13       2.606   0.432   0.976  1.00  0.00           C  
ATOM   2914  C   LEU    13       1.196   1.022   0.986  1.00  0.00           C  
ATOM   2915  O   LEU    13       0.438   0.836   1.918  1.00  0.00           O  
ATOM   2916  CB  LEU    13       3.582   1.426   1.612  1.00  0.00           C  
ATOM   2917  CG  LEU    13       4.840   0.686   2.071  1.00  0.00           C  
ATOM   2918  CD1 LEU    13       4.446  -0.467   2.994  1.00  0.00           C  
ATOM   2919  CD2 LEU    13       5.578   0.132   0.851  1.00  0.00           C  
ATOM   2920  H   LEU    13       3.873   0.486  -0.767  1.00  0.00           H  
ATOM   2921  HA  LEU    13       2.616  -0.494   1.532  1.00  0.00           H  
ATOM   2922 1HB  LEU    13       3.852   2.180   0.885  1.00  0.00           H  
ATOM   2923 2HB  LEU    13       3.113   1.897   2.461  1.00  0.00           H  
ATOM   2924  HG  LEU    13       5.484   1.370   2.605  1.00  0.00           H  
ATOM   2925 1HD1 LEU    13       3.395  -0.397   3.229  1.00  0.00           H  
ATOM   2926 2HD1 LEU    13       4.643  -1.407   2.499  1.00  0.00           H  
ATOM   2927 3HD1 LEU    13       5.023  -0.411   3.905  1.00  0.00           H  
ATOM   2928 1HD2 LEU    13       5.831   0.944   0.185  1.00  0.00           H  
ATOM   2929 2HD2 LEU    13       6.482  -0.364   1.171  1.00  0.00           H  
ATOM   2930 3HD2 LEU    13       4.944  -0.573   0.336  1.00  0.00           H  
ATOM   2931  N   ALA    14       0.839   1.728  -0.053  1.00  0.00           N  
ATOM   2932  CA  ALA    14      -0.521   2.329  -0.118  1.00  0.00           C  
ATOM   2933  C   ALA    14      -1.569   1.212  -0.114  1.00  0.00           C  
ATOM   2934  O   ALA    14      -2.444   1.170   0.729  1.00  0.00           O  
ATOM   2935  CB  ALA    14      -0.648   3.148  -1.406  1.00  0.00           C  
ATOM   2936  H   ALA    14       1.469   1.859  -0.794  1.00  0.00           H  
ATOM   2937  HA  ALA    14      -0.674   2.972   0.735  1.00  0.00           H  
ATOM   2938 1HB  ALA    14       0.316   3.563  -1.664  1.00  0.00           H  
ATOM   2939 2HB  ALA    14      -0.990   2.510  -2.207  1.00  0.00           H  
ATOM   2940 3HB  ALA    14      -1.356   3.949  -1.256  1.00  0.00           H  
ATOM   2941  N   GLN    15      -1.485   0.304  -1.049  1.00  0.00           N  
ATOM   2942  CA  GLN    15      -2.473  -0.810  -1.099  1.00  0.00           C  
ATOM   2943  C   GLN    15      -2.545  -1.490   0.269  1.00  0.00           C  
ATOM   2944  O   GLN    15      -3.584  -1.962   0.686  1.00  0.00           O  
ATOM   2945  CB  GLN    15      -2.033  -1.832  -2.151  1.00  0.00           C  
ATOM   2946  CG  GLN    15      -2.985  -1.780  -3.347  1.00  0.00           C  
ATOM   2947  CD  GLN    15      -2.272  -2.319  -4.590  1.00  0.00           C  
ATOM   2948  OE1 GLN    15      -2.263  -1.679  -5.623  1.00  0.00           O  
ATOM   2949  NE2 GLN    15      -1.671  -3.476  -4.534  1.00  0.00           N  
ATOM   2950  H   GLN    15      -0.770   0.356  -1.717  1.00  0.00           H  
ATOM   2951  HA  GLN    15      -3.445  -0.421  -1.360  1.00  0.00           H  
ATOM   2952 1HB  GLN    15      -1.029  -1.602  -2.478  1.00  0.00           H  
ATOM   2953 2HB  GLN    15      -2.052  -2.822  -1.721  1.00  0.00           H  
ATOM   2954 1HG  GLN    15      -3.856  -2.384  -3.140  1.00  0.00           H  
ATOM   2955 2HG  GLN    15      -3.288  -0.759  -3.522  1.00  0.00           H  
ATOM   2956 1HE2 GLN    15      -1.213  -3.829  -5.325  1.00  0.00           H  
ATOM   2957 2HE2 GLN    15      -1.679  -3.992  -3.700  1.00  0.00           H  
ATOM   2958  N   ALA    16      -1.446  -1.547   0.971  1.00  0.00           N  
ATOM   2959  CA  ALA    16      -1.449  -2.199   2.312  1.00  0.00           C  
ATOM   2960  C   ALA    16      -2.325  -1.393   3.273  1.00  0.00           C  
ATOM   2961  O   ALA    16      -3.083  -1.944   4.047  1.00  0.00           O  
ATOM   2962  CB  ALA    16      -0.020  -2.256   2.854  1.00  0.00           C  
ATOM   2963  H   ALA    16      -0.618  -1.163   0.617  1.00  0.00           H  
ATOM   2964  HA  ALA    16      -1.840  -3.202   2.223  1.00  0.00           H  
ATOM   2965 1HB  ALA    16       0.378  -1.254   2.925  1.00  0.00           H  
ATOM   2966 2HB  ALA    16      -0.024  -2.712   3.833  1.00  0.00           H  
ATOM   2967 3HB  ALA    16       0.596  -2.840   2.187  1.00  0.00           H  
ATOM   2968  N   VAL    17      -2.226  -0.094   3.233  1.00  0.00           N  
ATOM   2969  CA  VAL    17      -3.052   0.744   4.147  1.00  0.00           C  
ATOM   2970  C   VAL    17      -4.535   0.464   3.896  1.00  0.00           C  
ATOM   2971  O   VAL    17      -5.322   0.363   4.818  1.00  0.00           O  
ATOM   2972  CB  VAL    17      -2.756   2.223   3.887  1.00  0.00           C  
ATOM   2973  CG1 VAL    17      -3.778   3.088   4.628  1.00  0.00           C  
ATOM   2974  CG2 VAL    17      -1.350   2.555   4.391  1.00  0.00           C  
ATOM   2975  H   VAL    17      -1.608   0.332   2.603  1.00  0.00           H  
ATOM   2976  HA  VAL    17      -2.809   0.503   5.171  1.00  0.00           H  
ATOM   2977  HB  VAL    17      -2.818   2.421   2.827  1.00  0.00           H  
ATOM   2978 1HG1 VAL    17      -3.922   2.700   5.626  1.00  0.00           H  
ATOM   2979 2HG1 VAL    17      -3.414   4.103   4.686  1.00  0.00           H  
ATOM   2980 3HG1 VAL    17      -4.718   3.071   4.095  1.00  0.00           H  
ATOM   2981 1HG2 VAL    17      -1.082   1.876   5.187  1.00  0.00           H  
ATOM   2982 2HG2 VAL    17      -0.644   2.456   3.581  1.00  0.00           H  
ATOM   2983 3HG2 VAL    17      -1.331   3.569   4.762  1.00  0.00           H  
ATOM   2984  N   PHE    18      -4.926   0.333   2.658  1.00  0.00           N  
ATOM   2985  CA  PHE    18      -6.358   0.055   2.355  1.00  0.00           C  
ATOM   2986  C   PHE    18      -6.758  -1.278   2.991  1.00  0.00           C  
ATOM   2987  O   PHE    18      -7.682  -1.350   3.780  1.00  0.00           O  
ATOM   2988  CB  PHE    18      -6.553  -0.021   0.838  1.00  0.00           C  
ATOM   2989  CG  PHE    18      -8.029  -0.054   0.518  1.00  0.00           C  
ATOM   2990  CD1 PHE    18      -8.810   1.095   0.697  1.00  0.00           C  
ATOM   2991  CD2 PHE    18      -8.616  -1.231   0.039  1.00  0.00           C  
ATOM   2992  CE1 PHE    18     -10.178   1.065   0.398  1.00  0.00           C  
ATOM   2993  CE2 PHE    18      -9.982  -1.261  -0.260  1.00  0.00           C  
ATOM   2994  CZ  PHE    18     -10.765  -0.113  -0.081  1.00  0.00           C  
ATOM   2995  H   PHE    18      -4.276   0.414   1.928  1.00  0.00           H  
ATOM   2996  HA  PHE    18      -6.972   0.846   2.759  1.00  0.00           H  
ATOM   2997 1HB  PHE    18      -6.103   0.845   0.375  1.00  0.00           H  
ATOM   2998 2HB  PHE    18      -6.084  -0.917   0.461  1.00  0.00           H  
ATOM   2999  HD1 PHE    18      -8.359   2.004   1.067  1.00  0.00           H  
ATOM   3000  HD2 PHE    18      -8.013  -2.117  -0.099  1.00  0.00           H  
ATOM   3001  HE1 PHE    18     -10.781   1.950   0.536  1.00  0.00           H  
ATOM   3002  HE2 PHE    18     -10.435  -2.170  -0.630  1.00  0.00           H  
ATOM   3003  HZ  PHE    18     -11.820  -0.137  -0.312  1.00  0.00           H  
ATOM   3004  N   LEU    19      -6.067  -2.333   2.661  1.00  0.00           N  
ATOM   3005  CA  LEU    19      -6.404  -3.659   3.250  1.00  0.00           C  
ATOM   3006  C   LEU    19      -6.227  -3.598   4.769  1.00  0.00           C  
ATOM   3007  O   LEU    19      -6.704  -4.446   5.495  1.00  0.00           O  
ATOM   3008  CB  LEU    19      -5.475  -4.727   2.669  1.00  0.00           C  
ATOM   3009  CG  LEU    19      -5.572  -4.713   1.143  1.00  0.00           C  
ATOM   3010  CD1 LEU    19      -4.187  -4.964   0.540  1.00  0.00           C  
ATOM   3011  CD2 LEU    19      -6.533  -5.814   0.686  1.00  0.00           C  
ATOM   3012  H   LEU    19      -5.324  -2.254   2.027  1.00  0.00           H  
ATOM   3013  HA  LEU    19      -7.429  -3.907   3.017  1.00  0.00           H  
ATOM   3014 1HB  LEU    19      -4.457  -4.520   2.968  1.00  0.00           H  
ATOM   3015 2HB  LEU    19      -5.769  -5.699   3.038  1.00  0.00           H  
ATOM   3016  HG  LEU    19      -5.939  -3.752   0.813  1.00  0.00           H  
ATOM   3017 1HD1 LEU    19      -3.478  -4.270   0.967  1.00  0.00           H  
ATOM   3018 2HD1 LEU    19      -3.879  -5.975   0.758  1.00  0.00           H  
ATOM   3019 3HD1 LEU    19      -4.229  -4.823  -0.529  1.00  0.00           H  
ATOM   3020 1HD2 LEU    19      -7.222  -6.045   1.484  1.00  0.00           H  
ATOM   3021 2HD2 LEU    19      -7.085  -5.475  -0.179  1.00  0.00           H  
ATOM   3022 3HD2 LEU    19      -5.970  -6.699   0.428  1.00  0.00           H  
ATOM   3023  N   LEU    20      -5.546  -2.596   5.255  1.00  0.00           N  
ATOM   3024  CA  LEU    20      -5.342  -2.478   6.726  1.00  0.00           C  
ATOM   3025  C   LEU    20      -6.672  -2.117   7.390  1.00  0.00           C  
ATOM   3026  O   LEU    20      -7.099  -2.754   8.333  1.00  0.00           O  
ATOM   3027  CB  LEU    20      -4.313  -1.382   7.014  1.00  0.00           C  
ATOM   3028  CG  LEU    20      -4.045  -1.310   8.518  1.00  0.00           C  
ATOM   3029  CD1 LEU    20      -3.061  -2.412   8.916  1.00  0.00           C  
ATOM   3030  CD2 LEU    20      -3.447   0.055   8.863  1.00  0.00           C  
ATOM   3031  H   LEU    20      -5.172  -1.918   4.653  1.00  0.00           H  
ATOM   3032  HA  LEU    20      -4.987  -3.419   7.118  1.00  0.00           H  
ATOM   3033 1HB  LEU    20      -3.394  -1.608   6.493  1.00  0.00           H  
ATOM   3034 2HB  LEU    20      -4.695  -0.431   6.673  1.00  0.00           H  
ATOM   3035  HG  LEU    20      -4.973  -1.447   9.056  1.00  0.00           H  
ATOM   3036 1HD1 LEU    20      -3.348  -3.339   8.445  1.00  0.00           H  
ATOM   3037 2HD1 LEU    20      -2.066  -2.138   8.596  1.00  0.00           H  
ATOM   3038 3HD1 LEU    20      -3.072  -2.534   9.990  1.00  0.00           H  
ATOM   3039 1HD2 LEU    20      -2.524   0.191   8.319  1.00  0.00           H  
ATOM   3040 2HD2 LEU    20      -4.146   0.832   8.590  1.00  0.00           H  
ATOM   3041 3HD2 LEU    20      -3.251   0.104   9.923  1.00  0.00           H  
ATOM   3042  N   LEU    21      -7.333  -1.103   6.902  1.00  0.00           N  
ATOM   3043  CA  LEU    21      -8.637  -0.708   7.505  1.00  0.00           C  
ATOM   3044  C   LEU    21      -9.669  -1.805   7.236  1.00  0.00           C  
ATOM   3045  O   LEU    21     -10.604  -1.988   7.990  1.00  0.00           O  
ATOM   3046  CB  LEU    21      -9.111   0.608   6.884  1.00  0.00           C  
ATOM   3047  CG  LEU    21      -9.572   0.360   5.448  1.00  0.00           C  
ATOM   3048  CD1 LEU    21     -11.101   0.358   5.395  1.00  0.00           C  
ATOM   3049  CD2 LEU    21      -9.034   1.470   4.542  1.00  0.00           C  
ATOM   3050  H   LEU    21      -6.973  -0.604   6.139  1.00  0.00           H  
ATOM   3051  HA  LEU    21      -8.516  -0.580   8.571  1.00  0.00           H  
ATOM   3052 1HB  LEU    21      -9.933   1.004   7.463  1.00  0.00           H  
ATOM   3053 2HB  LEU    21      -8.298   1.319   6.881  1.00  0.00           H  
ATOM   3054  HG  LEU    21      -9.199  -0.596   5.110  1.00  0.00           H  
ATOM   3055 1HD1 LEU    21     -11.494   0.651   6.358  1.00  0.00           H  
ATOM   3056 2HD1 LEU    21     -11.437   1.055   4.642  1.00  0.00           H  
ATOM   3057 3HD1 LEU    21     -11.451  -0.633   5.151  1.00  0.00           H  
ATOM   3058 1HD2 LEU    21      -8.252   2.008   5.057  1.00  0.00           H  
ATOM   3059 2HD2 LEU    21      -8.635   1.034   3.637  1.00  0.00           H  
ATOM   3060 3HD2 LEU    21      -9.834   2.150   4.290  1.00  0.00           H  
ATOM   3061  N   THR    22      -9.505  -2.540   6.168  1.00  0.00           N  
ATOM   3062  CA  THR    22     -10.477  -3.628   5.857  1.00  0.00           C  
ATOM   3063  C   THR    22     -10.119  -4.879   6.663  1.00  0.00           C  
ATOM   3064  O   THR    22     -10.938  -5.752   6.867  1.00  0.00           O  
ATOM   3065  CB  THR    22     -10.417  -3.955   4.362  1.00  0.00           C  
ATOM   3066  OG1 THR    22     -10.667  -2.777   3.609  1.00  0.00           O  
ATOM   3067  CG2 THR    22     -11.471  -5.012   4.028  1.00  0.00           C  
ATOM   3068  H   THR    22      -8.742  -2.378   5.574  1.00  0.00           H  
ATOM   3069  HA  THR    22     -11.474  -3.304   6.115  1.00  0.00           H  
ATOM   3070  HB  THR    22      -9.439  -4.339   4.116  1.00  0.00           H  
ATOM   3071  HG1 THR    22     -10.311  -2.908   2.727  1.00  0.00           H  
ATOM   3072 1HG2 THR    22     -11.761  -5.529   4.930  1.00  0.00           H  
ATOM   3073 2HG2 THR    22     -12.336  -4.534   3.594  1.00  0.00           H  
ATOM   3074 3HG2 THR    22     -11.060  -5.721   3.323  1.00  0.00           H  
ATOM   3075  N   SER    23      -8.899  -4.973   7.120  1.00  0.00           N  
ATOM   3076  CA  SER    23      -8.489  -6.170   7.909  1.00  0.00           C  
ATOM   3077  C   SER    23      -8.929  -5.998   9.365  1.00  0.00           C  
ATOM   3078  O   SER    23      -9.625  -6.828   9.916  1.00  0.00           O  
ATOM   3079  CB  SER    23      -6.969  -6.322   7.848  1.00  0.00           C  
ATOM   3080  OG  SER    23      -6.606  -6.892   6.598  1.00  0.00           O  
ATOM   3081  H   SER    23      -8.253  -4.259   6.943  1.00  0.00           H  
ATOM   3082  HA  SER    23      -8.956  -7.051   7.495  1.00  0.00           H  
ATOM   3083 1HB  SER    23      -6.504  -5.355   7.946  1.00  0.00           H  
ATOM   3084 2HB  SER    23      -6.639  -6.961   8.657  1.00  0.00           H  
ATOM   3085  HG  SER    23      -7.231  -6.582   5.939  1.00  0.00           H  
ATOM   3086  N   GLN    24      -8.531  -4.926   9.994  1.00  0.00           N  
ATOM   3087  CA  GLN    24      -8.928  -4.701  11.409  1.00  0.00           C  
ATOM   3088  C   GLN    24     -10.371  -4.199  11.451  1.00  0.00           C  
ATOM   3089  O   GLN    24     -11.081  -4.402  12.416  1.00  0.00           O  
ATOM   3090  CB  GLN    24      -8.003  -3.654  12.032  1.00  0.00           C  
ATOM   3091  CG  GLN    24      -8.207  -2.310  11.330  1.00  0.00           C  
ATOM   3092  CD  GLN    24      -8.772  -1.294  12.322  1.00  0.00           C  
ATOM   3093  OE1 GLN    24      -9.877  -1.448  12.805  1.00  0.00           O  
ATOM   3094  NE2 GLN    24      -8.057  -0.254  12.650  1.00  0.00           N  
ATOM   3095  H   GLN    24      -7.973  -4.267   9.532  1.00  0.00           H  
ATOM   3096  HA  GLN    24      -8.850  -5.626  11.960  1.00  0.00           H  
ATOM   3097 1HB  GLN    24      -8.233  -3.551  13.082  1.00  0.00           H  
ATOM   3098 2HB  GLN    24      -6.978  -3.966  11.915  1.00  0.00           H  
ATOM   3099 1HG  GLN    24      -7.260  -1.955  10.951  1.00  0.00           H  
ATOM   3100 2HG  GLN    24      -8.899  -2.433  10.511  1.00  0.00           H  
ATOM   3101 1HE2 GLN    24      -8.409   0.404  13.285  1.00  0.00           H  
ATOM   3102 2HE2 GLN    24      -7.166  -0.130  12.260  1.00  0.00           H  
ATOM   3103  N   ARG    25     -10.809  -3.554  10.403  1.00  0.00           N  
ATOM   3104  CA  ARG    25     -12.204  -3.041  10.361  1.00  0.00           C  
ATOM   3105  C   ARG    25     -12.591  -2.468  11.727  1.00  0.00           C  
ATOM   3106  O   ARG    25     -12.333  -1.296  11.949  1.00  0.00           O  
ATOM   3107  CB  ARG    25     -13.140  -4.190   9.999  1.00  0.00           C  
ATOM   3108  CG  ARG    25     -14.568  -3.663   9.848  1.00  0.00           C  
ATOM   3109  CD  ARG    25     -15.269  -4.406   8.708  1.00  0.00           C  
ATOM   3110  NE  ARG    25     -16.378  -5.232   9.262  1.00  0.00           N  
ATOM   3111  CZ  ARG    25     -17.618  -4.921   8.998  1.00  0.00           C  
ATOM   3112  NH1 ARG    25     -18.049  -3.711   9.228  1.00  0.00           N  
ATOM   3113  NH2 ARG    25     -18.427  -5.820   8.506  1.00  0.00           N  
ATOM   3114  OXT ARG    25     -13.135  -3.210  12.526  1.00  0.00           O  
ATOM   3115  H   ARG    25     -10.220  -3.416   9.636  1.00  0.00           H  
ATOM   3116  HA  ARG    25     -12.281  -2.267   9.613  1.00  0.00           H  
ATOM   3117 1HB  ARG    25     -12.815  -4.632   9.068  1.00  0.00           H  
ATOM   3118 2HB  ARG    25     -13.111  -4.934  10.779  1.00  0.00           H  
ATOM   3119 1HG  ARG    25     -15.110  -3.821  10.769  1.00  0.00           H  
ATOM   3120 2HG  ARG    25     -14.540  -2.607   9.622  1.00  0.00           H  
ATOM   3121 1HD  ARG    25     -15.669  -3.691   8.004  1.00  0.00           H  
ATOM   3122 2HD  ARG    25     -14.558  -5.046   8.206  1.00  0.00           H  
ATOM   3123  HE  ARG    25     -16.177  -6.010   9.823  1.00  0.00           H  
ATOM   3124 1HH1 ARG    25     -17.430  -3.023   9.605  1.00  0.00           H  
ATOM   3125 2HH1 ARG    25     -19.000  -3.472   9.027  1.00  0.00           H  
ATOM   3126 1HH2 ARG    25     -18.095  -6.747   8.331  1.00  0.00           H  
ATOM   3127 2HH2 ARG    25     -19.376  -5.582   8.304  1.00  0.00           H  
TER    3128      ARG    25                                                      
ENDMDL                                                                          
MODEL        9                                                                  
ATOM   3129  N   GLY     1      12.763  -1.936 -12.970  1.00  0.00           N  
ATOM   3130  CA  GLY     1      12.611  -0.676 -12.119  1.00  0.00           C  
ATOM   3131  C   GLY     1      12.141   0.588 -12.754  1.00  0.00           C  
ATOM   3132  O   GLY     1      11.047   0.663 -13.276  1.00  0.00           O  
ATOM   3133 1H   GLY     1      11.869  -2.130 -13.465  1.00  0.00           H  
ATOM   3134 2H   GLY     1      13.521  -1.794 -13.668  1.00  0.00           H  
ATOM   3135 3H   GLY     1      13.002  -2.742 -12.357  1.00  0.00           H  
ATOM   3136 1HA  GLY     1      11.744  -0.652 -11.679  1.00  0.00           H  
ATOM   3137 2HA  GLY     1      13.504  -0.663 -11.367  1.00  0.00           H  
ATOM   3138  N   SER     2      12.953   1.609 -12.730  1.00  0.00           N  
ATOM   3139  CA  SER     2      12.547   2.901 -13.353  1.00  0.00           C  
ATOM   3140  C   SER     2      11.453   3.566 -12.514  1.00  0.00           C  
ATOM   3141  O   SER     2      11.072   3.082 -11.465  1.00  0.00           O  
ATOM   3142  CB  SER     2      12.018   2.641 -14.763  1.00  0.00           C  
ATOM   3143  OG  SER     2      12.582   1.435 -15.261  1.00  0.00           O  
ATOM   3144  H   SER     2      13.832   1.526 -12.305  1.00  0.00           H  
ATOM   3145  HA  SER     2      13.404   3.557 -13.408  1.00  0.00           H  
ATOM   3146 1HB  SER     2      10.946   2.546 -14.735  1.00  0.00           H  
ATOM   3147 2HB  SER     2      12.287   3.469 -15.406  1.00  0.00           H  
ATOM   3148  HG  SER     2      12.117   1.201 -16.068  1.00  0.00           H  
ATOM   3149  N   GLU     3      10.944   4.678 -12.973  1.00  0.00           N  
ATOM   3150  CA  GLU     3       9.876   5.383 -12.214  1.00  0.00           C  
ATOM   3151  C   GLU     3       8.805   4.381 -11.784  1.00  0.00           C  
ATOM   3152  O   GLU     3       8.163   4.544 -10.766  1.00  0.00           O  
ATOM   3153  CB  GLU     3       9.243   6.454 -13.105  1.00  0.00           C  
ATOM   3154  CG  GLU     3      10.197   7.643 -13.231  1.00  0.00           C  
ATOM   3155  CD  GLU     3      10.056   8.266 -14.621  1.00  0.00           C  
ATOM   3156  OE1 GLU     3      10.430   7.615 -15.581  1.00  0.00           O  
ATOM   3157  OE2 GLU     3       9.576   9.385 -14.701  1.00  0.00           O  
ATOM   3158  H   GLU     3      11.268   5.048 -13.821  1.00  0.00           H  
ATOM   3159  HA  GLU     3      10.304   5.851 -11.340  1.00  0.00           H  
ATOM   3160 1HB  GLU     3       9.052   6.039 -14.084  1.00  0.00           H  
ATOM   3161 2HB  GLU     3       8.313   6.784 -12.667  1.00  0.00           H  
ATOM   3162 1HG  GLU     3       9.954   8.380 -12.479  1.00  0.00           H  
ATOM   3163 2HG  GLU     3      11.213   7.307 -13.091  1.00  0.00           H  
ATOM   3164  N   LYS     4       8.606   3.343 -12.550  1.00  0.00           N  
ATOM   3165  CA  LYS     4       7.575   2.333 -12.179  1.00  0.00           C  
ATOM   3166  C   LYS     4       7.914   1.741 -10.811  1.00  0.00           C  
ATOM   3167  O   LYS     4       7.139   1.823  -9.879  1.00  0.00           O  
ATOM   3168  CB  LYS     4       7.550   1.219 -13.227  1.00  0.00           C  
ATOM   3169  CG  LYS     4       6.405   1.470 -14.211  1.00  0.00           C  
ATOM   3170  CD  LYS     4       6.690   2.741 -15.013  1.00  0.00           C  
ATOM   3171  CE  LYS     4       6.385   2.492 -16.492  1.00  0.00           C  
ATOM   3172  NZ  LYS     4       7.605   2.762 -17.304  1.00  0.00           N  
ATOM   3173  H   LYS     4       9.133   3.228 -13.367  1.00  0.00           H  
ATOM   3174  HA  LYS     4       6.606   2.808 -12.135  1.00  0.00           H  
ATOM   3175 1HB  LYS     4       8.488   1.205 -13.760  1.00  0.00           H  
ATOM   3176 2HB  LYS     4       7.399   0.268 -12.738  1.00  0.00           H  
ATOM   3177 1HG  LYS     4       6.318   0.629 -14.884  1.00  0.00           H  
ATOM   3178 2HG  LYS     4       5.481   1.592 -13.665  1.00  0.00           H  
ATOM   3179 1HD  LYS     4       6.069   3.545 -14.646  1.00  0.00           H  
ATOM   3180 2HD  LYS     4       7.730   3.010 -14.903  1.00  0.00           H  
ATOM   3181 1HE  LYS     4       6.082   1.465 -16.628  1.00  0.00           H  
ATOM   3182 2HE  LYS     4       5.588   3.148 -16.809  1.00  0.00           H  
ATOM   3183 1HZ  LYS     4       8.438   2.373 -16.819  1.00  0.00           H  
ATOM   3184 2HZ  LYS     4       7.508   2.313 -18.236  1.00  0.00           H  
ATOM   3185 3HZ  LYS     4       7.720   3.790 -17.424  1.00  0.00           H  
ATOM   3186  N   MET     5       9.068   1.145 -10.680  1.00  0.00           N  
ATOM   3187  CA  MET     5       9.455   0.551  -9.370  1.00  0.00           C  
ATOM   3188  C   MET     5       9.334   1.610  -8.274  1.00  0.00           C  
ATOM   3189  O   MET     5       9.067   1.302  -7.129  1.00  0.00           O  
ATOM   3190  CB  MET     5      10.900   0.053  -9.439  1.00  0.00           C  
ATOM   3191  CG  MET     5      10.914  -1.472  -9.597  1.00  0.00           C  
ATOM   3192  SD  MET     5       9.764  -1.965 -10.908  1.00  0.00           S  
ATOM   3193  CE  MET     5       8.997  -3.347 -10.028  1.00  0.00           C  
ATOM   3194  H   MET     5       9.681   1.091 -11.445  1.00  0.00           H  
ATOM   3195  HA  MET     5       8.799  -0.277  -9.144  1.00  0.00           H  
ATOM   3196 1HB  MET     5      11.397   0.509 -10.284  1.00  0.00           H  
ATOM   3197 2HB  MET     5      11.416   0.322  -8.531  1.00  0.00           H  
ATOM   3198 1HG  MET     5      11.912  -1.796  -9.855  1.00  0.00           H  
ATOM   3199 2HG  MET     5      10.617  -1.931  -8.666  1.00  0.00           H  
ATOM   3200 1HE  MET     5       8.549  -2.986  -9.112  1.00  0.00           H  
ATOM   3201 2HE  MET     5       8.233  -3.789 -10.648  1.00  0.00           H  
ATOM   3202 3HE  MET     5       9.748  -4.089  -9.800  1.00  0.00           H  
ATOM   3203  N   SER     6       9.529   2.855  -8.609  1.00  0.00           N  
ATOM   3204  CA  SER     6       9.422   3.928  -7.579  1.00  0.00           C  
ATOM   3205  C   SER     6       7.956   4.099  -7.171  1.00  0.00           C  
ATOM   3206  O   SER     6       7.645   4.350  -6.022  1.00  0.00           O  
ATOM   3207  CB  SER     6       9.949   5.242  -8.154  1.00  0.00           C  
ATOM   3208  OG  SER     6      10.159   6.168  -7.095  1.00  0.00           O  
ATOM   3209  H   SER     6       9.746   3.087  -9.539  1.00  0.00           H  
ATOM   3210  HA  SER     6      10.006   3.653  -6.713  1.00  0.00           H  
ATOM   3211 1HB  SER     6      10.883   5.068  -8.661  1.00  0.00           H  
ATOM   3212 2HB  SER     6       9.229   5.641  -8.856  1.00  0.00           H  
ATOM   3213  HG  SER     6       9.303   6.387  -6.720  1.00  0.00           H  
ATOM   3214  N   THR     7       7.052   3.958  -8.103  1.00  0.00           N  
ATOM   3215  CA  THR     7       5.608   4.109  -7.771  1.00  0.00           C  
ATOM   3216  C   THR     7       5.104   2.815  -7.136  1.00  0.00           C  
ATOM   3217  O   THR     7       4.072   2.784  -6.494  1.00  0.00           O  
ATOM   3218  CB  THR     7       4.816   4.395  -9.049  1.00  0.00           C  
ATOM   3219  OG1 THR     7       5.098   5.714  -9.493  1.00  0.00           O  
ATOM   3220  CG2 THR     7       3.319   4.258  -8.769  1.00  0.00           C  
ATOM   3221  H   THR     7       7.323   3.749  -9.019  1.00  0.00           H  
ATOM   3222  HA  THR     7       5.480   4.927  -7.076  1.00  0.00           H  
ATOM   3223  HB  THR     7       5.100   3.688  -9.814  1.00  0.00           H  
ATOM   3224  HG1 THR     7       5.389   5.664 -10.406  1.00  0.00           H  
ATOM   3225 1HG2 THR     7       3.149   4.277  -7.702  1.00  0.00           H  
ATOM   3226 2HG2 THR     7       2.789   5.076  -9.232  1.00  0.00           H  
ATOM   3227 3HG2 THR     7       2.961   3.322  -9.173  1.00  0.00           H  
ATOM   3228  N   ALA     8       5.831   1.748  -7.306  1.00  0.00           N  
ATOM   3229  CA  ALA     8       5.407   0.455  -6.709  1.00  0.00           C  
ATOM   3230  C   ALA     8       5.907   0.392  -5.268  1.00  0.00           C  
ATOM   3231  O   ALA     8       5.277  -0.181  -4.402  1.00  0.00           O  
ATOM   3232  CB  ALA     8       6.008  -0.697  -7.515  1.00  0.00           C  
ATOM   3233  H   ALA     8       6.663   1.799  -7.820  1.00  0.00           H  
ATOM   3234  HA  ALA     8       4.330   0.385  -6.723  1.00  0.00           H  
ATOM   3235 1HB  ALA     8       6.822  -0.325  -8.121  1.00  0.00           H  
ATOM   3236 2HB  ALA     8       6.380  -1.453  -6.839  1.00  0.00           H  
ATOM   3237 3HB  ALA     8       5.250  -1.125  -8.153  1.00  0.00           H  
ATOM   3238  N   ILE     9       7.038   0.986  -5.008  1.00  0.00           N  
ATOM   3239  CA  ILE     9       7.588   0.973  -3.625  1.00  0.00           C  
ATOM   3240  C   ILE     9       6.762   1.910  -2.744  1.00  0.00           C  
ATOM   3241  O   ILE     9       6.422   1.584  -1.625  1.00  0.00           O  
ATOM   3242  CB  ILE     9       9.046   1.439  -3.644  1.00  0.00           C  
ATOM   3243  CG1 ILE     9       9.144   2.802  -4.339  1.00  0.00           C  
ATOM   3244  CG2 ILE     9       9.900   0.423  -4.404  1.00  0.00           C  
ATOM   3245  CD1 ILE     9      10.597   3.280  -4.322  1.00  0.00           C  
ATOM   3246  H   ILE     9       7.523   1.444  -5.723  1.00  0.00           H  
ATOM   3247  HA  ILE     9       7.535  -0.029  -3.230  1.00  0.00           H  
ATOM   3248  HB  ILE     9       9.409   1.525  -2.629  1.00  0.00           H  
ATOM   3249 1HG1 ILE     9       8.807   2.711  -5.361  1.00  0.00           H  
ATOM   3250 2HG1 ILE     9       8.526   3.517  -3.817  1.00  0.00           H  
ATOM   3251 1HG2 ILE     9       9.447   0.216  -5.362  1.00  0.00           H  
ATOM   3252 2HG2 ILE     9      10.892   0.824  -4.553  1.00  0.00           H  
ATOM   3253 3HG2 ILE     9       9.966  -0.492  -3.831  1.00  0.00           H  
ATOM   3254 1HD1 ILE     9      10.983   3.227  -3.315  1.00  0.00           H  
ATOM   3255 2HD1 ILE     9      11.191   2.650  -4.969  1.00  0.00           H  
ATOM   3256 3HD1 ILE     9      10.645   4.301  -4.673  1.00  0.00           H  
ATOM   3257  N   SER    10       6.429   3.069  -3.242  1.00  0.00           N  
ATOM   3258  CA  SER    10       5.618   4.016  -2.427  1.00  0.00           C  
ATOM   3259  C   SER    10       4.199   3.465  -2.295  1.00  0.00           C  
ATOM   3260  O   SER    10       3.652   3.382  -1.214  1.00  0.00           O  
ATOM   3261  CB  SER    10       5.579   5.381  -3.115  1.00  0.00           C  
ATOM   3262  OG  SER    10       5.786   6.400  -2.147  1.00  0.00           O  
ATOM   3263  H   SER    10       6.707   3.315  -4.150  1.00  0.00           H  
ATOM   3264  HA  SER    10       6.057   4.115  -1.446  1.00  0.00           H  
ATOM   3265 1HB  SER    10       6.357   5.434  -3.858  1.00  0.00           H  
ATOM   3266 2HB  SER    10       4.617   5.514  -3.593  1.00  0.00           H  
ATOM   3267  HG  SER    10       6.519   6.133  -1.586  1.00  0.00           H  
ATOM   3268  N   VAL    11       3.601   3.079  -3.387  1.00  0.00           N  
ATOM   3269  CA  VAL    11       2.223   2.523  -3.322  1.00  0.00           C  
ATOM   3270  C   VAL    11       2.238   1.259  -2.461  1.00  0.00           C  
ATOM   3271  O   VAL    11       1.234   0.864  -1.904  1.00  0.00           O  
ATOM   3272  CB  VAL    11       1.744   2.177  -4.733  1.00  0.00           C  
ATOM   3273  CG1 VAL    11       0.387   1.475  -4.657  1.00  0.00           C  
ATOM   3274  CG2 VAL    11       1.607   3.461  -5.554  1.00  0.00           C  
ATOM   3275  H   VAL    11       4.062   3.148  -4.250  1.00  0.00           H  
ATOM   3276  HA  VAL    11       1.558   3.253  -2.882  1.00  0.00           H  
ATOM   3277  HB  VAL    11       2.462   1.520  -5.205  1.00  0.00           H  
ATOM   3278 1HG1 VAL    11       0.120   1.317  -3.623  1.00  0.00           H  
ATOM   3279 2HG1 VAL    11      -0.362   2.090  -5.132  1.00  0.00           H  
ATOM   3280 3HG1 VAL    11       0.445   0.523  -5.164  1.00  0.00           H  
ATOM   3281 1HG2 VAL    11       2.528   4.025  -5.498  1.00  0.00           H  
ATOM   3282 2HG2 VAL    11       1.401   3.210  -6.584  1.00  0.00           H  
ATOM   3283 3HG2 VAL    11       0.798   4.057  -5.159  1.00  0.00           H  
ATOM   3284  N   LEU    12       3.374   0.624  -2.343  1.00  0.00           N  
ATOM   3285  CA  LEU    12       3.452  -0.609  -1.512  1.00  0.00           C  
ATOM   3286  C   LEU    12       3.193  -0.249  -0.049  1.00  0.00           C  
ATOM   3287  O   LEU    12       2.381  -0.861   0.616  1.00  0.00           O  
ATOM   3288  CB  LEU    12       4.846  -1.228  -1.646  1.00  0.00           C  
ATOM   3289  CG  LEU    12       4.840  -2.263  -2.773  1.00  0.00           C  
ATOM   3290  CD1 LEU    12       6.242  -2.374  -3.374  1.00  0.00           C  
ATOM   3291  CD2 LEU    12       4.420  -3.625  -2.211  1.00  0.00           C  
ATOM   3292  H   LEU    12       4.175   0.961  -2.797  1.00  0.00           H  
ATOM   3293  HA  LEU    12       2.709  -1.318  -1.849  1.00  0.00           H  
ATOM   3294 1HB  LEU    12       5.563  -0.452  -1.872  1.00  0.00           H  
ATOM   3295 2HB  LEU    12       5.115  -1.710  -0.719  1.00  0.00           H  
ATOM   3296  HG  LEU    12       4.142  -1.956  -3.538  1.00  0.00           H  
ATOM   3297 1HD1 LEU    12       6.923  -1.750  -2.815  1.00  0.00           H  
ATOM   3298 2HD1 LEU    12       6.573  -3.400  -3.327  1.00  0.00           H  
ATOM   3299 3HD1 LEU    12       6.219  -2.050  -4.403  1.00  0.00           H  
ATOM   3300 1HD2 LEU    12       5.091  -3.907  -1.414  1.00  0.00           H  
ATOM   3301 2HD2 LEU    12       3.412  -3.561  -1.828  1.00  0.00           H  
ATOM   3302 3HD2 LEU    12       4.460  -4.366  -2.995  1.00  0.00           H  
ATOM   3303  N   LEU    13       3.875   0.742   0.457  1.00  0.00           N  
ATOM   3304  CA  LEU    13       3.660   1.141   1.877  1.00  0.00           C  
ATOM   3305  C   LEU    13       2.231   1.661   2.036  1.00  0.00           C  
ATOM   3306  O   LEU    13       1.640   1.577   3.094  1.00  0.00           O  
ATOM   3307  CB  LEU    13       4.649   2.245   2.271  1.00  0.00           C  
ATOM   3308  CG  LEU    13       5.936   2.123   1.449  1.00  0.00           C  
ATOM   3309  CD1 LEU    13       7.041   2.944   2.109  1.00  0.00           C  
ATOM   3310  CD2 LEU    13       6.366   0.654   1.377  1.00  0.00           C  
ATOM   3311  H   LEU    13       4.523   1.226  -0.099  1.00  0.00           H  
ATOM   3312  HA  LEU    13       3.803   0.283   2.518  1.00  0.00           H  
ATOM   3313 1HB  LEU    13       4.198   3.210   2.088  1.00  0.00           H  
ATOM   3314 2HB  LEU    13       4.887   2.154   3.320  1.00  0.00           H  
ATOM   3315  HG  LEU    13       5.761   2.498   0.450  1.00  0.00           H  
ATOM   3316 1HD1 LEU    13       6.642   3.450   2.977  1.00  0.00           H  
ATOM   3317 2HD1 LEU    13       7.843   2.290   2.411  1.00  0.00           H  
ATOM   3318 3HD1 LEU    13       7.414   3.674   1.407  1.00  0.00           H  
ATOM   3319 1HD2 LEU    13       5.888   0.100   2.172  1.00  0.00           H  
ATOM   3320 2HD2 LEU    13       6.072   0.240   0.424  1.00  0.00           H  
ATOM   3321 3HD2 LEU    13       7.438   0.587   1.485  1.00  0.00           H  
ATOM   3322  N   ALA    14       1.675   2.201   0.987  1.00  0.00           N  
ATOM   3323  CA  ALA    14       0.285   2.732   1.066  1.00  0.00           C  
ATOM   3324  C   ALA    14      -0.710   1.570   1.009  1.00  0.00           C  
ATOM   3325  O   ALA    14      -1.819   1.667   1.493  1.00  0.00           O  
ATOM   3326  CB  ALA    14       0.035   3.674  -0.113  1.00  0.00           C  
ATOM   3327  H   ALA    14       2.174   2.258   0.146  1.00  0.00           H  
ATOM   3328  HA  ALA    14       0.157   3.272   1.992  1.00  0.00           H  
ATOM   3329 1HB  ALA    14       0.981   3.995  -0.523  1.00  0.00           H  
ATOM   3330 2HB  ALA    14      -0.529   3.156  -0.874  1.00  0.00           H  
ATOM   3331 3HB  ALA    14      -0.522   4.534   0.225  1.00  0.00           H  
ATOM   3332  N   GLN    15      -0.322   0.473   0.419  1.00  0.00           N  
ATOM   3333  CA  GLN    15      -1.246  -0.691   0.330  1.00  0.00           C  
ATOM   3334  C   GLN    15      -1.250  -1.442   1.662  1.00  0.00           C  
ATOM   3335  O   GLN    15      -2.217  -2.081   2.023  1.00  0.00           O  
ATOM   3336  CB  GLN    15      -0.778  -1.631  -0.784  1.00  0.00           C  
ATOM   3337  CG  GLN    15      -1.781  -1.594  -1.940  1.00  0.00           C  
ATOM   3338  CD  GLN    15      -1.960  -0.150  -2.413  1.00  0.00           C  
ATOM   3339  OE1 GLN    15      -1.486   0.773  -1.782  1.00  0.00           O  
ATOM   3340  NE2 GLN    15      -2.630   0.086  -3.509  1.00  0.00           N  
ATOM   3341  H   GLN    15       0.577   0.415   0.034  1.00  0.00           H  
ATOM   3342  HA  GLN    15      -2.245  -0.343   0.110  1.00  0.00           H  
ATOM   3343 1HB  GLN    15       0.192  -1.314  -1.138  1.00  0.00           H  
ATOM   3344 2HB  GLN    15      -0.711  -2.639  -0.402  1.00  0.00           H  
ATOM   3345 1HG  GLN    15      -1.413  -2.199  -2.756  1.00  0.00           H  
ATOM   3346 2HG  GLN    15      -2.731  -1.980  -1.604  1.00  0.00           H  
ATOM   3347 1HE2 GLN    15      -2.750   1.006  -3.821  1.00  0.00           H  
ATOM   3348 2HE2 GLN    15      -3.013  -0.658  -4.019  1.00  0.00           H  
ATOM   3349  N   ALA    16      -0.174  -1.372   2.394  1.00  0.00           N  
ATOM   3350  CA  ALA    16      -0.115  -2.082   3.702  1.00  0.00           C  
ATOM   3351  C   ALA    16      -1.279  -1.626   4.587  1.00  0.00           C  
ATOM   3352  O   ALA    16      -1.980  -2.429   5.169  1.00  0.00           O  
ATOM   3353  CB  ALA    16       1.209  -1.761   4.399  1.00  0.00           C  
ATOM   3354  H   ALA    16       0.598  -0.852   2.084  1.00  0.00           H  
ATOM   3355  HA  ALA    16      -0.186  -3.147   3.537  1.00  0.00           H  
ATOM   3356 1HB  ALA    16       1.755  -1.035   3.815  1.00  0.00           H  
ATOM   3357 2HB  ALA    16       1.011  -1.358   5.380  1.00  0.00           H  
ATOM   3358 3HB  ALA    16       1.795  -2.664   4.490  1.00  0.00           H  
ATOM   3359  N   VAL    17      -1.490  -0.342   4.693  1.00  0.00           N  
ATOM   3360  CA  VAL    17      -2.605   0.161   5.543  1.00  0.00           C  
ATOM   3361  C   VAL    17      -3.912   0.141   4.746  1.00  0.00           C  
ATOM   3362  O   VAL    17      -4.983  -0.023   5.296  1.00  0.00           O  
ATOM   3363  CB  VAL    17      -2.302   1.594   5.985  1.00  0.00           C  
ATOM   3364  CG1 VAL    17      -3.249   1.989   7.120  1.00  0.00           C  
ATOM   3365  CG2 VAL    17      -0.856   1.681   6.475  1.00  0.00           C  
ATOM   3366  H   VAL    17      -0.912   0.290   4.216  1.00  0.00           H  
ATOM   3367  HA  VAL    17      -2.706  -0.469   6.414  1.00  0.00           H  
ATOM   3368  HB  VAL    17      -2.443   2.265   5.150  1.00  0.00           H  
ATOM   3369 1HG1 VAL    17      -4.264   1.747   6.844  1.00  0.00           H  
ATOM   3370 2HG1 VAL    17      -2.981   1.450   8.017  1.00  0.00           H  
ATOM   3371 3HG1 VAL    17      -3.170   3.051   7.302  1.00  0.00           H  
ATOM   3372 1HG2 VAL    17      -0.618   0.798   7.050  1.00  0.00           H  
ATOM   3373 2HG2 VAL    17      -0.192   1.748   5.625  1.00  0.00           H  
ATOM   3374 3HG2 VAL    17      -0.737   2.557   7.095  1.00  0.00           H  
ATOM   3375  N   PHE    18      -3.836   0.309   3.455  1.00  0.00           N  
ATOM   3376  CA  PHE    18      -5.075   0.303   2.629  1.00  0.00           C  
ATOM   3377  C   PHE    18      -5.828  -1.013   2.842  1.00  0.00           C  
ATOM   3378  O   PHE    18      -6.948  -1.030   3.312  1.00  0.00           O  
ATOM   3379  CB  PHE    18      -4.704   0.444   1.151  1.00  0.00           C  
ATOM   3380  CG  PHE    18      -5.616   1.455   0.499  1.00  0.00           C  
ATOM   3381  CD1 PHE    18      -5.638   2.777   0.960  1.00  0.00           C  
ATOM   3382  CD2 PHE    18      -6.441   1.070  -0.565  1.00  0.00           C  
ATOM   3383  CE1 PHE    18      -6.483   3.714   0.355  1.00  0.00           C  
ATOM   3384  CE2 PHE    18      -7.286   2.008  -1.169  1.00  0.00           C  
ATOM   3385  CZ  PHE    18      -7.308   3.331  -0.709  1.00  0.00           C  
ATOM   3386  H   PHE    18      -2.963   0.442   3.029  1.00  0.00           H  
ATOM   3387  HA  PHE    18      -5.706   1.129   2.921  1.00  0.00           H  
ATOM   3388 1HB  PHE    18      -3.680   0.777   1.068  1.00  0.00           H  
ATOM   3389 2HB  PHE    18      -4.815  -0.510   0.659  1.00  0.00           H  
ATOM   3390  HD1 PHE    18      -5.002   3.073   1.781  1.00  0.00           H  
ATOM   3391  HD2 PHE    18      -6.423   0.051  -0.920  1.00  0.00           H  
ATOM   3392  HE1 PHE    18      -6.500   4.734   0.711  1.00  0.00           H  
ATOM   3393  HE2 PHE    18      -7.922   1.712  -1.991  1.00  0.00           H  
ATOM   3394  HZ  PHE    18      -7.959   4.054  -1.175  1.00  0.00           H  
ATOM   3395  N   LEU    19      -5.220  -2.116   2.498  1.00  0.00           N  
ATOM   3396  CA  LEU    19      -5.902  -3.428   2.679  1.00  0.00           C  
ATOM   3397  C   LEU    19      -6.251  -3.624   4.156  1.00  0.00           C  
ATOM   3398  O   LEU    19      -7.203  -4.297   4.495  1.00  0.00           O  
ATOM   3399  CB  LEU    19      -4.972  -4.551   2.218  1.00  0.00           C  
ATOM   3400  CG  LEU    19      -4.832  -4.502   0.696  1.00  0.00           C  
ATOM   3401  CD1 LEU    19      -3.772  -5.510   0.247  1.00  0.00           C  
ATOM   3402  CD2 LEU    19      -6.173  -4.854   0.048  1.00  0.00           C  
ATOM   3403  H   LEU    19      -4.318  -2.080   2.119  1.00  0.00           H  
ATOM   3404  HA  LEU    19      -6.808  -3.446   2.091  1.00  0.00           H  
ATOM   3405 1HB  LEU    19      -4.002  -4.427   2.676  1.00  0.00           H  
ATOM   3406 2HB  LEU    19      -5.387  -5.505   2.508  1.00  0.00           H  
ATOM   3407  HG  LEU    19      -4.534  -3.508   0.394  1.00  0.00           H  
ATOM   3408 1HD1 LEU    19      -3.725  -6.323   0.956  1.00  0.00           H  
ATOM   3409 2HD1 LEU    19      -4.030  -5.896  -0.728  1.00  0.00           H  
ATOM   3410 3HD1 LEU    19      -2.809  -5.021   0.197  1.00  0.00           H  
ATOM   3411 1HD2 LEU    19      -6.956  -4.798   0.791  1.00  0.00           H  
ATOM   3412 2HD2 LEU    19      -6.382  -4.155  -0.748  1.00  0.00           H  
ATOM   3413 3HD2 LEU    19      -6.128  -5.855  -0.354  1.00  0.00           H  
ATOM   3414  N   LEU    20      -5.489  -3.037   5.039  1.00  0.00           N  
ATOM   3415  CA  LEU    20      -5.782  -3.189   6.492  1.00  0.00           C  
ATOM   3416  C   LEU    20      -7.224  -2.756   6.764  1.00  0.00           C  
ATOM   3417  O   LEU    20      -8.020  -3.506   7.295  1.00  0.00           O  
ATOM   3418  CB  LEU    20      -4.824  -2.312   7.301  1.00  0.00           C  
ATOM   3419  CG  LEU    20      -4.471  -3.016   8.612  1.00  0.00           C  
ATOM   3420  CD1 LEU    20      -3.578  -4.221   8.319  1.00  0.00           C  
ATOM   3421  CD2 LEU    20      -3.728  -2.043   9.529  1.00  0.00           C  
ATOM   3422  H   LEU    20      -4.726  -2.496   4.746  1.00  0.00           H  
ATOM   3423  HA  LEU    20      -5.656  -4.222   6.780  1.00  0.00           H  
ATOM   3424 1HB  LEU    20      -3.924  -2.140   6.729  1.00  0.00           H  
ATOM   3425 2HB  LEU    20      -5.299  -1.366   7.519  1.00  0.00           H  
ATOM   3426  HG  LEU    20      -5.378  -3.349   9.096  1.00  0.00           H  
ATOM   3427 1HD1 LEU    20      -3.866  -4.663   7.376  1.00  0.00           H  
ATOM   3428 2HD1 LEU    20      -2.547  -3.901   8.266  1.00  0.00           H  
ATOM   3429 3HD1 LEU    20      -3.688  -4.951   9.107  1.00  0.00           H  
ATOM   3430 1HD2 LEU    20      -2.862  -1.653   9.014  1.00  0.00           H  
ATOM   3431 2HD2 LEU    20      -4.384  -1.227   9.796  1.00  0.00           H  
ATOM   3432 3HD2 LEU    20      -3.413  -2.559  10.423  1.00  0.00           H  
ATOM   3433  N   LEU    21      -7.568  -1.551   6.401  1.00  0.00           N  
ATOM   3434  CA  LEU    21      -8.957  -1.071   6.635  1.00  0.00           C  
ATOM   3435  C   LEU    21      -9.936  -1.978   5.889  1.00  0.00           C  
ATOM   3436  O   LEU    21     -10.857  -2.522   6.466  1.00  0.00           O  
ATOM   3437  CB  LEU    21      -9.097   0.363   6.121  1.00  0.00           C  
ATOM   3438  CG  LEU    21     -10.516   0.865   6.389  1.00  0.00           C  
ATOM   3439  CD1 LEU    21     -10.636   1.297   7.852  1.00  0.00           C  
ATOM   3440  CD2 LEU    21     -10.812   2.061   5.481  1.00  0.00           C  
ATOM   3441  H   LEU    21      -6.911  -0.962   5.972  1.00  0.00           H  
ATOM   3442  HA  LEU    21      -9.174  -1.098   7.692  1.00  0.00           H  
ATOM   3443 1HB  LEU    21      -8.387   0.999   6.629  1.00  0.00           H  
ATOM   3444 2HB  LEU    21      -8.905   0.385   5.058  1.00  0.00           H  
ATOM   3445  HG  LEU    21     -11.222   0.074   6.188  1.00  0.00           H  
ATOM   3446 1HD1 LEU    21      -9.901   0.772   8.443  1.00  0.00           H  
ATOM   3447 2HD1 LEU    21     -10.467   2.360   7.928  1.00  0.00           H  
ATOM   3448 3HD1 LEU    21     -11.625   1.062   8.216  1.00  0.00           H  
ATOM   3449 1HD2 LEU    21     -10.343   1.907   4.520  1.00  0.00           H  
ATOM   3450 2HD2 LEU    21     -11.880   2.158   5.350  1.00  0.00           H  
ATOM   3451 3HD2 LEU    21     -10.421   2.961   5.932  1.00  0.00           H  
ATOM   3452  N   THR    22      -9.743  -2.151   4.609  1.00  0.00           N  
ATOM   3453  CA  THR    22     -10.662  -3.028   3.832  1.00  0.00           C  
ATOM   3454  C   THR    22     -10.866  -4.342   4.588  1.00  0.00           C  
ATOM   3455  O   THR    22     -11.889  -4.985   4.472  1.00  0.00           O  
ATOM   3456  CB  THR    22     -10.052  -3.318   2.458  1.00  0.00           C  
ATOM   3457  OG1 THR    22      -8.810  -3.988   2.626  1.00  0.00           O  
ATOM   3458  CG2 THR    22      -9.827  -2.004   1.710  1.00  0.00           C  
ATOM   3459  H   THR    22      -8.992  -1.707   4.162  1.00  0.00           H  
ATOM   3460  HA  THR    22     -11.614  -2.533   3.706  1.00  0.00           H  
ATOM   3461  HB  THR    22     -10.724  -3.941   1.890  1.00  0.00           H  
ATOM   3462  HG1 THR    22      -8.928  -4.901   2.354  1.00  0.00           H  
ATOM   3463 1HG2 THR    22     -10.053  -1.174   2.363  1.00  0.00           H  
ATOM   3464 2HG2 THR    22      -8.798  -1.942   1.391  1.00  0.00           H  
ATOM   3465 3HG2 THR    22     -10.475  -1.967   0.846  1.00  0.00           H  
ATOM   3466  N   SER    23      -9.896  -4.742   5.366  1.00  0.00           N  
ATOM   3467  CA  SER    23     -10.033  -6.011   6.133  1.00  0.00           C  
ATOM   3468  C   SER    23     -11.057  -5.819   7.252  1.00  0.00           C  
ATOM   3469  O   SER    23     -11.984  -6.590   7.399  1.00  0.00           O  
ATOM   3470  CB  SER    23      -8.680  -6.389   6.738  1.00  0.00           C  
ATOM   3471  OG  SER    23      -8.740  -7.724   7.225  1.00  0.00           O  
ATOM   3472  H   SER    23      -9.080  -4.206   5.447  1.00  0.00           H  
ATOM   3473  HA  SER    23     -10.365  -6.798   5.472  1.00  0.00           H  
ATOM   3474 1HB  SER    23      -7.915  -6.321   5.984  1.00  0.00           H  
ATOM   3475 2HB  SER    23      -8.447  -5.709   7.547  1.00  0.00           H  
ATOM   3476  HG  SER    23      -9.395  -8.199   6.709  1.00  0.00           H  
ATOM   3477  N   GLN    24     -10.900  -4.791   8.041  1.00  0.00           N  
ATOM   3478  CA  GLN    24     -11.866  -4.547   9.147  1.00  0.00           C  
ATOM   3479  C   GLN    24     -13.232  -4.191   8.557  1.00  0.00           C  
ATOM   3480  O   GLN    24     -14.223  -4.124   9.257  1.00  0.00           O  
ATOM   3481  CB  GLN    24     -11.367  -3.388  10.012  1.00  0.00           C  
ATOM   3482  CG  GLN    24     -10.664  -3.942  11.253  1.00  0.00           C  
ATOM   3483  CD  GLN    24     -10.704  -2.900  12.371  1.00  0.00           C  
ATOM   3484  OE1 GLN    24     -11.202  -3.165  13.447  1.00  0.00           O  
ATOM   3485  NE2 GLN    24     -10.197  -1.716  12.162  1.00  0.00           N  
ATOM   3486  H   GLN    24     -10.146  -4.179   7.903  1.00  0.00           H  
ATOM   3487  HA  GLN    24     -11.954  -5.437   9.752  1.00  0.00           H  
ATOM   3488 1HB  GLN    24     -10.673  -2.786   9.443  1.00  0.00           H  
ATOM   3489 2HB  GLN    24     -12.206  -2.780  10.318  1.00  0.00           H  
ATOM   3490 1HG  GLN    24     -11.166  -4.842  11.579  1.00  0.00           H  
ATOM   3491 2HG  GLN    24      -9.637  -4.170  11.012  1.00  0.00           H  
ATOM   3492 1HE2 GLN    24     -10.217  -1.041  12.871  1.00  0.00           H  
ATOM   3493 2HE2 GLN    24      -9.795  -1.502  11.293  1.00  0.00           H  
ATOM   3494  N   ARG    25     -13.294  -3.963   7.273  1.00  0.00           N  
ATOM   3495  CA  ARG    25     -14.596  -3.613   6.641  1.00  0.00           C  
ATOM   3496  C   ARG    25     -15.306  -4.893   6.192  1.00  0.00           C  
ATOM   3497  O   ARG    25     -15.229  -5.207   5.016  1.00  0.00           O  
ATOM   3498  CB  ARG    25     -14.348  -2.715   5.427  1.00  0.00           C  
ATOM   3499  CG  ARG    25     -15.368  -1.573   5.419  1.00  0.00           C  
ATOM   3500  CD  ARG    25     -15.792  -1.278   3.978  1.00  0.00           C  
ATOM   3501  NE  ARG    25     -17.265  -1.064   3.928  1.00  0.00           N  
ATOM   3502  CZ  ARG    25     -17.802  -0.063   4.570  1.00  0.00           C  
ATOM   3503  NH1 ARG    25     -18.507  -0.280   5.646  1.00  0.00           N  
ATOM   3504  NH2 ARG    25     -17.631   1.157   4.137  1.00  0.00           N  
ATOM   3505  OXT ARG    25     -15.912  -5.537   7.032  1.00  0.00           O  
ATOM   3506  H   ARG    25     -12.483  -4.022   6.726  1.00  0.00           H  
ATOM   3507  HA  ARG    25     -15.215  -3.090   7.356  1.00  0.00           H  
ATOM   3508 1HB  ARG    25     -13.350  -2.307   5.480  1.00  0.00           H  
ATOM   3509 2HB  ARG    25     -14.454  -3.295   4.523  1.00  0.00           H  
ATOM   3510 1HG  ARG    25     -16.233  -1.859   5.999  1.00  0.00           H  
ATOM   3511 2HG  ARG    25     -14.922  -0.689   5.848  1.00  0.00           H  
ATOM   3512 1HD  ARG    25     -15.287  -0.390   3.629  1.00  0.00           H  
ATOM   3513 2HD  ARG    25     -15.527  -2.114   3.347  1.00  0.00           H  
ATOM   3514  HE  ARG    25     -17.833  -1.675   3.413  1.00  0.00           H  
ATOM   3515 1HH1 ARG    25     -18.638  -1.214   5.978  1.00  0.00           H  
ATOM   3516 2HH1 ARG    25     -18.918   0.488   6.138  1.00  0.00           H  
ATOM   3517 1HH2 ARG    25     -17.091   1.323   3.312  1.00  0.00           H  
ATOM   3518 2HH2 ARG    25     -18.041   1.924   4.630  1.00  0.00           H  
TER    3519      ARG    25                                                      
ENDMDL                                                                          
MODEL       10                                                                  
ATOM   3520  N   GLY     1      16.683   2.046  -8.868  1.00  0.00           N  
ATOM   3521  CA  GLY     1      15.286   2.014  -9.487  1.00  0.00           C  
ATOM   3522  C   GLY     1      14.709   3.267 -10.054  1.00  0.00           C  
ATOM   3523  O   GLY     1      13.652   3.257 -10.653  1.00  0.00           O  
ATOM   3524 1H   GLY     1      17.287   2.694  -9.410  1.00  0.00           H  
ATOM   3525 2H   GLY     1      16.619   2.374  -7.883  1.00  0.00           H  
ATOM   3526 3H   GLY     1      17.094   1.090  -8.889  1.00  0.00           H  
ATOM   3527 1HA  GLY     1      15.318   1.733 -10.420  1.00  0.00           H  
ATOM   3528 2HA  GLY     1      14.635   1.310  -8.821  1.00  0.00           H  
ATOM   3529  N   SER     2      15.381   4.372  -9.883  1.00  0.00           N  
ATOM   3530  CA  SER     2      14.859   5.659 -10.426  1.00  0.00           C  
ATOM   3531  C   SER     2      13.542   6.011  -9.729  1.00  0.00           C  
ATOM   3532  O   SER     2      12.997   5.228  -8.978  1.00  0.00           O  
ATOM   3533  CB  SER     2      14.620   5.521 -11.930  1.00  0.00           C  
ATOM   3534  OG  SER     2      15.846   5.192 -12.571  1.00  0.00           O  
ATOM   3535  H   SER     2      16.232   4.357  -9.395  1.00  0.00           H  
ATOM   3536  HA  SER     2      15.579   6.442 -10.247  1.00  0.00           H  
ATOM   3537 1HB  SER     2      13.902   4.740 -12.115  1.00  0.00           H  
ATOM   3538 2HB  SER     2      14.238   6.455 -12.319  1.00  0.00           H  
ATOM   3539  HG  SER     2      15.736   5.337 -13.514  1.00  0.00           H  
ATOM   3540  N   GLU     3      13.032   7.188  -9.970  1.00  0.00           N  
ATOM   3541  CA  GLU     3      11.752   7.594  -9.321  1.00  0.00           C  
ATOM   3542  C   GLU     3      10.645   6.615  -9.712  1.00  0.00           C  
ATOM   3543  O   GLU     3       9.648   6.486  -9.031  1.00  0.00           O  
ATOM   3544  CB  GLU     3      11.373   9.004  -9.781  1.00  0.00           C  
ATOM   3545  CG  GLU     3      10.769   9.784  -8.610  1.00  0.00           C  
ATOM   3546  CD  GLU     3      11.890  10.438  -7.801  1.00  0.00           C  
ATOM   3547  OE1 GLU     3      12.651  11.194  -8.384  1.00  0.00           O  
ATOM   3548  OE2 GLU     3      11.968  10.174  -6.613  1.00  0.00           O  
ATOM   3549  H   GLU     3      13.489   7.806 -10.577  1.00  0.00           H  
ATOM   3550  HA  GLU     3      11.876   7.588  -8.248  1.00  0.00           H  
ATOM   3551 1HB  GLU     3      12.255   9.515 -10.137  1.00  0.00           H  
ATOM   3552 2HB  GLU     3      10.649   8.940 -10.579  1.00  0.00           H  
ATOM   3553 1HG  GLU     3      10.105  10.546  -8.990  1.00  0.00           H  
ATOM   3554 2HG  GLU     3      10.217   9.109  -7.975  1.00  0.00           H  
ATOM   3555  N   LYS     4      10.809   5.924 -10.807  1.00  0.00           N  
ATOM   3556  CA  LYS     4       9.763   4.955 -11.239  1.00  0.00           C  
ATOM   3557  C   LYS     4       9.649   3.834 -10.204  1.00  0.00           C  
ATOM   3558  O   LYS     4       8.598   3.601  -9.639  1.00  0.00           O  
ATOM   3559  CB  LYS     4      10.146   4.363 -12.598  1.00  0.00           C  
ATOM   3560  CG  LYS     4      10.007   5.439 -13.677  1.00  0.00           C  
ATOM   3561  CD  LYS     4      11.395   5.945 -14.079  1.00  0.00           C  
ATOM   3562  CE  LYS     4      11.290   6.747 -15.377  1.00  0.00           C  
ATOM   3563  NZ  LYS     4      11.674   5.884 -16.530  1.00  0.00           N  
ATOM   3564  H   LYS     4      11.621   6.043 -11.345  1.00  0.00           H  
ATOM   3565  HA  LYS     4       8.815   5.464 -11.322  1.00  0.00           H  
ATOM   3566 1HB  LYS     4      11.167   4.014 -12.564  1.00  0.00           H  
ATOM   3567 2HB  LYS     4       9.490   3.538 -12.828  1.00  0.00           H  
ATOM   3568 1HG  LYS     4       9.512   5.020 -14.541  1.00  0.00           H  
ATOM   3569 2HG  LYS     4       9.424   6.262 -13.292  1.00  0.00           H  
ATOM   3570 1HD  LYS     4      11.788   6.576 -13.293  1.00  0.00           H  
ATOM   3571 2HD  LYS     4      12.054   5.104 -14.229  1.00  0.00           H  
ATOM   3572 1HE  LYS     4      10.274   7.090 -15.506  1.00  0.00           H  
ATOM   3573 2HE  LYS     4      11.953   7.599 -15.329  1.00  0.00           H  
ATOM   3574 1HZ  LYS     4      12.323   5.140 -16.205  1.00  0.00           H  
ATOM   3575 2HZ  LYS     4      10.820   5.447 -16.935  1.00  0.00           H  
ATOM   3576 3HZ  LYS     4      12.145   6.461 -17.254  1.00  0.00           H  
ATOM   3577  N   MET     5      10.723   3.136  -9.948  1.00  0.00           N  
ATOM   3578  CA  MET     5      10.673   2.035  -8.946  1.00  0.00           C  
ATOM   3579  C   MET     5      10.385   2.617  -7.562  1.00  0.00           C  
ATOM   3580  O   MET     5       9.928   1.931  -6.671  1.00  0.00           O  
ATOM   3581  CB  MET     5      12.016   1.303  -8.921  1.00  0.00           C  
ATOM   3582  CG  MET     5      11.791  -0.163  -8.547  1.00  0.00           C  
ATOM   3583  SD  MET     5      12.095  -1.209  -9.992  1.00  0.00           S  
ATOM   3584  CE  MET     5      13.031  -2.504  -9.144  1.00  0.00           C  
ATOM   3585  H   MET     5      11.562   3.340 -10.411  1.00  0.00           H  
ATOM   3586  HA  MET     5       9.890   1.340  -9.215  1.00  0.00           H  
ATOM   3587 1HB  MET     5      12.476   1.361  -9.898  1.00  0.00           H  
ATOM   3588 2HB  MET     5      12.664   1.764  -8.190  1.00  0.00           H  
ATOM   3589 1HG  MET     5      12.468  -0.440  -7.753  1.00  0.00           H  
ATOM   3590 2HG  MET     5      10.773  -0.297  -8.214  1.00  0.00           H  
ATOM   3591 1HE  MET     5      13.257  -2.188  -8.139  1.00  0.00           H  
ATOM   3592 2HE  MET     5      12.442  -3.410  -9.110  1.00  0.00           H  
ATOM   3593 3HE  MET     5      13.954  -2.687  -9.677  1.00  0.00           H  
ATOM   3594  N   SER     6      10.650   3.882  -7.376  1.00  0.00           N  
ATOM   3595  CA  SER     6      10.389   4.509  -6.051  1.00  0.00           C  
ATOM   3596  C   SER     6       8.883   4.700  -5.867  1.00  0.00           C  
ATOM   3597  O   SER     6       8.354   4.543  -4.784  1.00  0.00           O  
ATOM   3598  CB  SER     6      11.087   5.869  -5.988  1.00  0.00           C  
ATOM   3599  OG  SER     6      11.217   6.270  -4.631  1.00  0.00           O  
ATOM   3600  H   SER     6      11.017   4.419  -8.109  1.00  0.00           H  
ATOM   3601  HA  SER     6      10.771   3.872  -5.267  1.00  0.00           H  
ATOM   3602 1HB  SER     6      12.065   5.793  -6.432  1.00  0.00           H  
ATOM   3603 2HB  SER     6      10.502   6.597  -6.536  1.00  0.00           H  
ATOM   3604  HG  SER     6      11.349   5.482  -4.099  1.00  0.00           H  
ATOM   3605  N   THR     7       8.186   5.030  -6.920  1.00  0.00           N  
ATOM   3606  CA  THR     7       6.714   5.223  -6.806  1.00  0.00           C  
ATOM   3607  C   THR     7       6.034   3.857  -6.838  1.00  0.00           C  
ATOM   3608  O   THR     7       4.901   3.703  -6.426  1.00  0.00           O  
ATOM   3609  CB  THR     7       6.213   6.079  -7.972  1.00  0.00           C  
ATOM   3610  OG1 THR     7       7.059   5.888  -9.098  1.00  0.00           O  
ATOM   3611  CG2 THR     7       6.227   7.553  -7.565  1.00  0.00           C  
ATOM   3612  H   THR     7       8.630   5.144  -7.786  1.00  0.00           H  
ATOM   3613  HA  THR     7       6.488   5.716  -5.871  1.00  0.00           H  
ATOM   3614  HB  THR     7       5.205   5.790  -8.225  1.00  0.00           H  
ATOM   3615  HG1 THR     7       7.083   6.711  -9.593  1.00  0.00           H  
ATOM   3616 1HG2 THR     7       6.913   7.693  -6.741  1.00  0.00           H  
ATOM   3617 2HG2 THR     7       6.545   8.156  -8.404  1.00  0.00           H  
ATOM   3618 3HG2 THR     7       5.235   7.853  -7.262  1.00  0.00           H  
ATOM   3619  N   ALA     8       6.726   2.858  -7.313  1.00  0.00           N  
ATOM   3620  CA  ALA     8       6.130   1.498  -7.360  1.00  0.00           C  
ATOM   3621  C   ALA     8       6.294   0.850  -5.988  1.00  0.00           C  
ATOM   3622  O   ALA     8       5.477   0.059  -5.559  1.00  0.00           O  
ATOM   3623  CB  ALA     8       6.855   0.658  -8.415  1.00  0.00           C  
ATOM   3624  H   ALA     8       7.642   3.002  -7.628  1.00  0.00           H  
ATOM   3625  HA  ALA     8       5.082   1.567  -7.607  1.00  0.00           H  
ATOM   3626 1HB  ALA     8       7.294   1.311  -9.156  1.00  0.00           H  
ATOM   3627 2HB  ALA     8       7.631   0.077  -7.941  1.00  0.00           H  
ATOM   3628 3HB  ALA     8       6.149  -0.004  -8.893  1.00  0.00           H  
ATOM   3629  N   ILE     9       7.342   1.194  -5.291  1.00  0.00           N  
ATOM   3630  CA  ILE     9       7.558   0.614  -3.940  1.00  0.00           C  
ATOM   3631  C   ILE     9       6.594   1.279  -2.960  1.00  0.00           C  
ATOM   3632  O   ILE     9       6.023   0.637  -2.101  1.00  0.00           O  
ATOM   3633  CB  ILE     9       9.000   0.864  -3.496  1.00  0.00           C  
ATOM   3634  CG1 ILE     9       9.314   2.359  -3.590  1.00  0.00           C  
ATOM   3635  CG2 ILE     9       9.956   0.087  -4.403  1.00  0.00           C  
ATOM   3636  CD1 ILE     9      10.686   2.633  -2.972  1.00  0.00           C  
ATOM   3637  H   ILE     9       7.980   1.842  -5.655  1.00  0.00           H  
ATOM   3638  HA  ILE     9       7.366  -0.448  -3.971  1.00  0.00           H  
ATOM   3639  HB  ILE     9       9.124   0.532  -2.474  1.00  0.00           H  
ATOM   3640 1HG1 ILE     9       9.316   2.662  -4.628  1.00  0.00           H  
ATOM   3641 2HG1 ILE     9       8.563   2.919  -3.053  1.00  0.00           H  
ATOM   3642 1HG2 ILE     9       9.679   0.245  -5.436  1.00  0.00           H  
ATOM   3643 2HG2 ILE     9      10.966   0.436  -4.244  1.00  0.00           H  
ATOM   3644 3HG2 ILE     9       9.898  -0.966  -4.172  1.00  0.00           H  
ATOM   3645 1HD1 ILE     9      11.319   1.769  -3.102  1.00  0.00           H  
ATOM   3646 2HD1 ILE     9      11.136   3.486  -3.460  1.00  0.00           H  
ATOM   3647 3HD1 ILE     9      10.571   2.842  -1.919  1.00  0.00           H  
ATOM   3648  N   SER    10       6.397   2.563  -3.091  1.00  0.00           N  
ATOM   3649  CA  SER    10       5.458   3.266  -2.176  1.00  0.00           C  
ATOM   3650  C   SER    10       4.038   2.786  -2.469  1.00  0.00           C  
ATOM   3651  O   SER    10       3.229   2.631  -1.577  1.00  0.00           O  
ATOM   3652  CB  SER    10       5.550   4.775  -2.404  1.00  0.00           C  
ATOM   3653  OG  SER    10       4.251   5.344  -2.306  1.00  0.00           O  
ATOM   3654  H   SER    10       6.860   3.062  -3.797  1.00  0.00           H  
ATOM   3655  HA  SER    10       5.712   3.036  -1.151  1.00  0.00           H  
ATOM   3656 1HB  SER    10       6.188   5.216  -1.658  1.00  0.00           H  
ATOM   3657 2HB  SER    10       5.964   4.964  -3.386  1.00  0.00           H  
ATOM   3658  HG  SER    10       4.308   6.262  -2.576  1.00  0.00           H  
ATOM   3659  N   VAL    11       3.733   2.540  -3.715  1.00  0.00           N  
ATOM   3660  CA  VAL    11       2.370   2.056  -4.065  1.00  0.00           C  
ATOM   3661  C   VAL    11       2.123   0.733  -3.340  1.00  0.00           C  
ATOM   3662  O   VAL    11       1.083   0.522  -2.747  1.00  0.00           O  
ATOM   3663  CB  VAL    11       2.278   1.844  -5.581  1.00  0.00           C  
ATOM   3664  CG1 VAL    11       1.068   0.966  -5.911  1.00  0.00           C  
ATOM   3665  CG2 VAL    11       2.122   3.198  -6.274  1.00  0.00           C  
ATOM   3666  H   VAL    11       4.406   2.664  -4.418  1.00  0.00           H  
ATOM   3667  HA  VAL    11       1.636   2.783  -3.754  1.00  0.00           H  
ATOM   3668  HB  VAL    11       3.179   1.360  -5.931  1.00  0.00           H  
ATOM   3669 1HG1 VAL    11       0.192   1.360  -5.420  1.00  0.00           H  
ATOM   3670 2HG1 VAL    11       0.909   0.959  -6.979  1.00  0.00           H  
ATOM   3671 3HG1 VAL    11       1.251  -0.042  -5.568  1.00  0.00           H  
ATOM   3672 1HG2 VAL    11       2.638   3.957  -5.706  1.00  0.00           H  
ATOM   3673 2HG2 VAL    11       2.542   3.144  -7.268  1.00  0.00           H  
ATOM   3674 3HG2 VAL    11       1.074   3.450  -6.341  1.00  0.00           H  
ATOM   3675  N   LEU    12       3.075  -0.159  -3.377  1.00  0.00           N  
ATOM   3676  CA  LEU    12       2.898  -1.461  -2.682  1.00  0.00           C  
ATOM   3677  C   LEU    12       2.458  -1.204  -1.241  1.00  0.00           C  
ATOM   3678  O   LEU    12       1.435  -1.688  -0.799  1.00  0.00           O  
ATOM   3679  CB  LEU    12       4.223  -2.228  -2.688  1.00  0.00           C  
ATOM   3680  CG  LEU    12       4.409  -2.916  -4.041  1.00  0.00           C  
ATOM   3681  CD1 LEU    12       5.898  -3.159  -4.290  1.00  0.00           C  
ATOM   3682  CD2 LEU    12       3.669  -4.254  -4.038  1.00  0.00           C  
ATOM   3683  H   LEU    12       3.909   0.033  -3.857  1.00  0.00           H  
ATOM   3684  HA  LEU    12       2.143  -2.042  -3.192  1.00  0.00           H  
ATOM   3685 1HB  LEU    12       5.038  -1.538  -2.519  1.00  0.00           H  
ATOM   3686 2HB  LEU    12       4.212  -2.972  -1.906  1.00  0.00           H  
ATOM   3687  HG  LEU    12       4.011  -2.285  -4.824  1.00  0.00           H  
ATOM   3688 1HD1 LEU    12       6.469  -2.762  -3.464  1.00  0.00           H  
ATOM   3689 2HD1 LEU    12       6.079  -4.220  -4.377  1.00  0.00           H  
ATOM   3690 3HD1 LEU    12       6.195  -2.667  -5.204  1.00  0.00           H  
ATOM   3691 1HD2 LEU    12       3.751  -4.709  -3.062  1.00  0.00           H  
ATOM   3692 2HD2 LEU    12       2.627  -4.091  -4.271  1.00  0.00           H  
ATOM   3693 3HD2 LEU    12       4.104  -4.909  -4.778  1.00  0.00           H  
ATOM   3694  N   LEU    13       3.215  -0.436  -0.505  1.00  0.00           N  
ATOM   3695  CA  LEU    13       2.827  -0.144   0.902  1.00  0.00           C  
ATOM   3696  C   LEU    13       1.434   0.486   0.912  1.00  0.00           C  
ATOM   3697  O   LEU    13       0.662   0.299   1.831  1.00  0.00           O  
ATOM   3698  CB  LEU    13       3.837   0.823   1.521  1.00  0.00           C  
ATOM   3699  CG  LEU    13       5.096   0.055   1.926  1.00  0.00           C  
ATOM   3700  CD1 LEU    13       4.710  -1.116   2.830  1.00  0.00           C  
ATOM   3701  CD2 LEU    13       5.791  -0.481   0.671  1.00  0.00           C  
ATOM   3702  H   LEU    13       4.034  -0.047  -0.878  1.00  0.00           H  
ATOM   3703  HA  LEU    13       2.810  -1.064   1.469  1.00  0.00           H  
ATOM   3704 1HB  LEU    13       4.094   1.585   0.800  1.00  0.00           H  
ATOM   3705 2HB  LEU    13       3.403   1.286   2.396  1.00  0.00           H  
ATOM   3706  HG  LEU    13       5.766   0.715   2.457  1.00  0.00           H  
ATOM   3707 1HD1 LEU    13       3.958  -0.793   3.535  1.00  0.00           H  
ATOM   3708 2HD1 LEU    13       4.316  -1.921   2.228  1.00  0.00           H  
ATOM   3709 3HD1 LEU    13       5.582  -1.459   3.367  1.00  0.00           H  
ATOM   3710 1HD2 LEU    13       5.989   0.336  -0.007  1.00  0.00           H  
ATOM   3711 2HD2 LEU    13       6.721  -0.952   0.948  1.00  0.00           H  
ATOM   3712 3HD2 LEU    13       5.152  -1.204   0.187  1.00  0.00           H  
ATOM   3713  N   ALA    14       1.103   1.225  -0.112  1.00  0.00           N  
ATOM   3714  CA  ALA    14      -0.243   1.858  -0.168  1.00  0.00           C  
ATOM   3715  C   ALA    14      -1.307   0.774   0.002  1.00  0.00           C  
ATOM   3716  O   ALA    14      -2.127   0.829   0.896  1.00  0.00           O  
ATOM   3717  CB  ALA    14      -0.424   2.552  -1.520  1.00  0.00           C  
ATOM   3718  H   ALA    14       1.737   1.357  -0.847  1.00  0.00           H  
ATOM   3719  HA  ALA    14      -0.335   2.583   0.628  1.00  0.00           H  
ATOM   3720 1HB  ALA    14       0.452   3.144  -1.740  1.00  0.00           H  
ATOM   3721 2HB  ALA    14      -0.559   1.808  -2.291  1.00  0.00           H  
ATOM   3722 3HB  ALA    14      -1.292   3.193  -1.483  1.00  0.00           H  
ATOM   3723  N   GLN    15      -1.294  -0.218  -0.847  1.00  0.00           N  
ATOM   3724  CA  GLN    15      -2.298  -1.310  -0.726  1.00  0.00           C  
ATOM   3725  C   GLN    15      -2.156  -1.964   0.649  1.00  0.00           C  
ATOM   3726  O   GLN    15      -3.117  -2.428   1.229  1.00  0.00           O  
ATOM   3727  CB  GLN    15      -2.054  -2.353  -1.819  1.00  0.00           C  
ATOM   3728  CG  GLN    15      -2.915  -2.023  -3.039  1.00  0.00           C  
ATOM   3729  CD  GLN    15      -4.091  -3.001  -3.117  1.00  0.00           C  
ATOM   3730  OE1 GLN    15      -3.988  -4.044  -3.733  1.00  0.00           O  
ATOM   3731  NE2 GLN    15      -5.210  -2.706  -2.516  1.00  0.00           N  
ATOM   3732  H   GLN    15      -0.619  -0.248  -1.557  1.00  0.00           H  
ATOM   3733  HA  GLN    15      -3.292  -0.901  -0.831  1.00  0.00           H  
ATOM   3734 1HB  GLN    15      -1.011  -2.342  -2.100  1.00  0.00           H  
ATOM   3735 2HB  GLN    15      -2.319  -3.331  -1.447  1.00  0.00           H  
ATOM   3736 1HG  GLN    15      -3.291  -1.014  -2.954  1.00  0.00           H  
ATOM   3737 2HG  GLN    15      -2.319  -2.110  -3.935  1.00  0.00           H  
ATOM   3738 1HE2 GLN    15      -5.967  -3.326  -2.560  1.00  0.00           H  
ATOM   3739 2HE2 GLN    15      -5.293  -1.864  -2.021  1.00  0.00           H  
ATOM   3740  N   ALA    16      -0.962  -1.997   1.179  1.00  0.00           N  
ATOM   3741  CA  ALA    16      -0.758  -2.611   2.520  1.00  0.00           C  
ATOM   3742  C   ALA    16      -1.614  -1.864   3.543  1.00  0.00           C  
ATOM   3743  O   ALA    16      -2.164  -2.448   4.455  1.00  0.00           O  
ATOM   3744  CB  ALA    16       0.718  -2.507   2.913  1.00  0.00           C  
ATOM   3745  H   ALA    16      -0.201  -1.612   0.696  1.00  0.00           H  
ATOM   3746  HA  ALA    16      -1.053  -3.650   2.491  1.00  0.00           H  
ATOM   3747 1HB  ALA    16       1.292  -2.155   2.068  1.00  0.00           H  
ATOM   3748 2HB  ALA    16       0.824  -1.815   3.735  1.00  0.00           H  
ATOM   3749 3HB  ALA    16       1.080  -3.479   3.214  1.00  0.00           H  
ATOM   3750  N   VAL    17      -1.740  -0.573   3.390  1.00  0.00           N  
ATOM   3751  CA  VAL    17      -2.569   0.213   4.343  1.00  0.00           C  
ATOM   3752  C   VAL    17      -4.044   0.023   3.988  1.00  0.00           C  
ATOM   3753  O   VAL    17      -4.905   0.020   4.845  1.00  0.00           O  
ATOM   3754  CB  VAL    17      -2.201   1.694   4.243  1.00  0.00           C  
ATOM   3755  CG1 VAL    17      -3.030   2.496   5.249  1.00  0.00           C  
ATOM   3756  CG2 VAL    17      -0.714   1.871   4.554  1.00  0.00           C  
ATOM   3757  H   VAL    17      -1.294  -0.123   2.642  1.00  0.00           H  
ATOM   3758  HA  VAL    17      -2.392  -0.137   5.350  1.00  0.00           H  
ATOM   3759  HB  VAL    17      -2.407   2.049   3.243  1.00  0.00           H  
ATOM   3760 1HG1 VAL    17      -2.938   2.050   6.228  1.00  0.00           H  
ATOM   3761 2HG1 VAL    17      -2.669   3.514   5.281  1.00  0.00           H  
ATOM   3762 3HG1 VAL    17      -4.067   2.491   4.947  1.00  0.00           H  
ATOM   3763 1HG2 VAL    17      -0.396   1.097   5.238  1.00  0.00           H  
ATOM   3764 2HG2 VAL    17      -0.144   1.800   3.641  1.00  0.00           H  
ATOM   3765 3HG2 VAL    17      -0.554   2.839   5.006  1.00  0.00           H  
ATOM   3766  N   PHE    18      -4.339  -0.146   2.727  1.00  0.00           N  
ATOM   3767  CA  PHE    18      -5.755  -0.348   2.310  1.00  0.00           C  
ATOM   3768  C   PHE    18      -6.316  -1.573   3.034  1.00  0.00           C  
ATOM   3769  O   PHE    18      -7.273  -1.482   3.776  1.00  0.00           O  
ATOM   3770  CB  PHE    18      -5.813  -0.573   0.797  1.00  0.00           C  
ATOM   3771  CG  PHE    18      -7.239  -0.846   0.379  1.00  0.00           C  
ATOM   3772  CD1 PHE    18      -7.748  -2.149   0.436  1.00  0.00           C  
ATOM   3773  CD2 PHE    18      -8.051   0.205  -0.071  1.00  0.00           C  
ATOM   3774  CE1 PHE    18      -9.069  -2.402   0.045  1.00  0.00           C  
ATOM   3775  CE2 PHE    18      -9.371  -0.050  -0.462  1.00  0.00           C  
ATOM   3776  CZ  PHE    18      -9.880  -1.353  -0.405  1.00  0.00           C  
ATOM   3777  H   PHE    18      -3.625  -0.148   2.055  1.00  0.00           H  
ATOM   3778  HA  PHE    18      -6.336   0.525   2.570  1.00  0.00           H  
ATOM   3779 1HB  PHE    18      -5.451   0.308   0.290  1.00  0.00           H  
ATOM   3780 2HB  PHE    18      -5.196  -1.419   0.536  1.00  0.00           H  
ATOM   3781  HD1 PHE    18      -7.123  -2.958   0.783  1.00  0.00           H  
ATOM   3782  HD2 PHE    18      -7.659   1.210  -0.114  1.00  0.00           H  
ATOM   3783  HE1 PHE    18      -9.461  -3.407   0.088  1.00  0.00           H  
ATOM   3784  HE2 PHE    18      -9.996   0.759  -0.808  1.00  0.00           H  
ATOM   3785  HZ  PHE    18     -10.898  -1.549  -0.707  1.00  0.00           H  
ATOM   3786  N   LEU    19      -5.720  -2.718   2.833  1.00  0.00           N  
ATOM   3787  CA  LEU    19      -6.217  -3.941   3.522  1.00  0.00           C  
ATOM   3788  C   LEU    19      -6.304  -3.661   5.024  1.00  0.00           C  
ATOM   3789  O   LEU    19      -7.027  -4.313   5.749  1.00  0.00           O  
ATOM   3790  CB  LEU    19      -5.248  -5.101   3.274  1.00  0.00           C  
ATOM   3791  CG  LEU    19      -5.092  -5.324   1.767  1.00  0.00           C  
ATOM   3792  CD1 LEU    19      -3.610  -5.475   1.421  1.00  0.00           C  
ATOM   3793  CD2 LEU    19      -5.841  -6.594   1.359  1.00  0.00           C  
ATOM   3794  H   LEU    19      -4.944  -2.772   2.238  1.00  0.00           H  
ATOM   3795  HA  LEU    19      -7.195  -4.199   3.144  1.00  0.00           H  
ATOM   3796 1HB  LEU    19      -4.286  -4.865   3.705  1.00  0.00           H  
ATOM   3797 2HB  LEU    19      -5.637  -6.000   3.729  1.00  0.00           H  
ATOM   3798  HG  LEU    19      -5.500  -4.476   1.235  1.00  0.00           H  
ATOM   3799 1HD1 LEU    19      -3.023  -5.441   2.327  1.00  0.00           H  
ATOM   3800 2HD1 LEU    19      -3.452  -6.421   0.925  1.00  0.00           H  
ATOM   3801 3HD1 LEU    19      -3.309  -4.670   0.766  1.00  0.00           H  
ATOM   3802 1HD2 LEU    19      -5.916  -7.257   2.209  1.00  0.00           H  
ATOM   3803 2HD2 LEU    19      -6.832  -6.334   1.017  1.00  0.00           H  
ATOM   3804 3HD2 LEU    19      -5.304  -7.089   0.564  1.00  0.00           H  
ATOM   3805  N   LEU    20      -5.571  -2.686   5.492  1.00  0.00           N  
ATOM   3806  CA  LEU    20      -5.609  -2.352   6.944  1.00  0.00           C  
ATOM   3807  C   LEU    20      -6.993  -1.810   7.301  1.00  0.00           C  
ATOM   3808  O   LEU    20      -7.656  -2.308   8.188  1.00  0.00           O  
ATOM   3809  CB  LEU    20      -4.552  -1.289   7.251  1.00  0.00           C  
ATOM   3810  CG  LEU    20      -4.150  -1.374   8.724  1.00  0.00           C  
ATOM   3811  CD1 LEU    20      -2.922  -0.496   8.971  1.00  0.00           C  
ATOM   3812  CD2 LEU    20      -5.308  -0.883   9.596  1.00  0.00           C  
ATOM   3813  H   LEU    20      -4.998  -2.171   4.886  1.00  0.00           H  
ATOM   3814  HA  LEU    20      -5.408  -3.241   7.524  1.00  0.00           H  
ATOM   3815 1HB  LEU    20      -3.684  -1.455   6.629  1.00  0.00           H  
ATOM   3816 2HB  LEU    20      -4.958  -0.309   7.047  1.00  0.00           H  
ATOM   3817  HG  LEU    20      -3.917  -2.399   8.975  1.00  0.00           H  
ATOM   3818 1HD1 LEU    20      -3.003   0.409   8.388  1.00  0.00           H  
ATOM   3819 2HD1 LEU    20      -2.864  -0.245  10.019  1.00  0.00           H  
ATOM   3820 3HD1 LEU    20      -2.031  -1.034   8.680  1.00  0.00           H  
ATOM   3821 1HD2 LEU    20      -5.935  -0.217   9.022  1.00  0.00           H  
ATOM   3822 2HD2 LEU    20      -5.892  -1.729   9.930  1.00  0.00           H  
ATOM   3823 3HD2 LEU    20      -4.914  -0.356  10.453  1.00  0.00           H  
ATOM   3824  N   LEU    21      -7.437  -0.794   6.612  1.00  0.00           N  
ATOM   3825  CA  LEU    21      -8.779  -0.225   6.910  1.00  0.00           C  
ATOM   3826  C   LEU    21      -9.848  -1.275   6.600  1.00  0.00           C  
ATOM   3827  O   LEU    21     -10.928  -1.262   7.158  1.00  0.00           O  
ATOM   3828  CB  LEU    21      -9.008   1.027   6.054  1.00  0.00           C  
ATOM   3829  CG  LEU    21      -9.379   0.623   4.624  1.00  0.00           C  
ATOM   3830  CD1 LEU    21     -10.902   0.576   4.488  1.00  0.00           C  
ATOM   3831  CD2 LEU    21      -8.812   1.649   3.641  1.00  0.00           C  
ATOM   3832  H   LEU    21      -6.887  -0.408   5.898  1.00  0.00           H  
ATOM   3833  HA  LEU    21      -8.830   0.041   7.956  1.00  0.00           H  
ATOM   3834 1HB  LEU    21      -9.810   1.612   6.480  1.00  0.00           H  
ATOM   3835 2HB  LEU    21      -8.105   1.618   6.034  1.00  0.00           H  
ATOM   3836  HG  LEU    21      -8.967  -0.353   4.409  1.00  0.00           H  
ATOM   3837 1HD1 LEU    21     -11.357   0.830   5.433  1.00  0.00           H  
ATOM   3838 2HD1 LEU    21     -11.218   1.283   3.736  1.00  0.00           H  
ATOM   3839 3HD1 LEU    21     -11.206  -0.419   4.196  1.00  0.00           H  
ATOM   3840 1HD2 LEU    21      -7.762   1.802   3.845  1.00  0.00           H  
ATOM   3841 2HD2 LEU    21      -8.934   1.287   2.631  1.00  0.00           H  
ATOM   3842 3HD2 LEU    21      -9.339   2.586   3.753  1.00  0.00           H  
ATOM   3843  N   THR    22      -9.553  -2.187   5.714  1.00  0.00           N  
ATOM   3844  CA  THR    22     -10.545  -3.240   5.366  1.00  0.00           C  
ATOM   3845  C   THR    22     -10.833  -4.094   6.603  1.00  0.00           C  
ATOM   3846  O   THR    22     -11.971  -4.330   6.956  1.00  0.00           O  
ATOM   3847  CB  THR    22      -9.981  -4.127   4.254  1.00  0.00           C  
ATOM   3848  OG1 THR    22      -9.205  -3.333   3.367  1.00  0.00           O  
ATOM   3849  CG2 THR    22     -11.131  -4.780   3.486  1.00  0.00           C  
ATOM   3850  H   THR    22      -8.674  -2.178   5.278  1.00  0.00           H  
ATOM   3851  HA  THR    22     -11.460  -2.776   5.028  1.00  0.00           H  
ATOM   3852  HB  THR    22      -9.360  -4.895   4.686  1.00  0.00           H  
ATOM   3853  HG1 THR    22      -9.788  -2.689   2.957  1.00  0.00           H  
ATOM   3854 1HG2 THR    22     -12.072  -4.498   3.938  1.00  0.00           H  
ATOM   3855 2HG2 THR    22     -11.111  -4.448   2.458  1.00  0.00           H  
ATOM   3856 3HG2 THR    22     -11.022  -5.853   3.521  1.00  0.00           H  
ATOM   3857  N   SER    23      -9.808  -4.554   7.269  1.00  0.00           N  
ATOM   3858  CA  SER    23     -10.027  -5.387   8.484  1.00  0.00           C  
ATOM   3859  C   SER    23     -10.629  -4.516   9.588  1.00  0.00           C  
ATOM   3860  O   SER    23     -11.600  -4.882  10.221  1.00  0.00           O  
ATOM   3861  CB  SER    23      -8.691  -5.963   8.958  1.00  0.00           C  
ATOM   3862  OG  SER    23      -7.643  -5.071   8.602  1.00  0.00           O  
ATOM   3863  H   SER    23      -8.897  -4.351   6.971  1.00  0.00           H  
ATOM   3864  HA  SER    23     -10.706  -6.193   8.251  1.00  0.00           H  
ATOM   3865 1HB  SER    23      -8.707  -6.083  10.028  1.00  0.00           H  
ATOM   3866 2HB  SER    23      -8.532  -6.927   8.493  1.00  0.00           H  
ATOM   3867  HG  SER    23      -6.978  -5.104   9.293  1.00  0.00           H  
ATOM   3868  N   GLN    24     -10.062  -3.364   9.822  1.00  0.00           N  
ATOM   3869  CA  GLN    24     -10.607  -2.470  10.882  1.00  0.00           C  
ATOM   3870  C   GLN    24     -11.941  -1.881  10.414  1.00  0.00           C  
ATOM   3871  O   GLN    24     -12.618  -1.192  11.151  1.00  0.00           O  
ATOM   3872  CB  GLN    24      -9.615  -1.337  11.153  1.00  0.00           C  
ATOM   3873  CG  GLN    24      -8.342  -1.906  11.782  1.00  0.00           C  
ATOM   3874  CD  GLN    24      -8.711  -2.782  12.980  1.00  0.00           C  
ATOM   3875  OE1 GLN    24      -8.958  -3.963  12.831  1.00  0.00           O  
ATOM   3876  NE2 GLN    24      -8.758  -2.253  14.171  1.00  0.00           N  
ATOM   3877  H   GLN    24      -9.282  -3.086   9.299  1.00  0.00           H  
ATOM   3878  HA  GLN    24     -10.762  -3.039  11.787  1.00  0.00           H  
ATOM   3879 1HB  GLN    24      -9.369  -0.844  10.223  1.00  0.00           H  
ATOM   3880 2HB  GLN    24     -10.061  -0.623  11.830  1.00  0.00           H  
ATOM   3881 1HG  GLN    24      -7.814  -2.499  11.050  1.00  0.00           H  
ATOM   3882 2HG  GLN    24      -7.711  -1.096  12.113  1.00  0.00           H  
ATOM   3883 1HE2 GLN    24      -8.992  -2.806  14.945  1.00  0.00           H  
ATOM   3884 2HE2 GLN    24      -8.558  -1.301  14.292  1.00  0.00           H  
ATOM   3885  N   ARG    25     -12.324  -2.146   9.194  1.00  0.00           N  
ATOM   3886  CA  ARG    25     -13.613  -1.600   8.681  1.00  0.00           C  
ATOM   3887  C   ARG    25     -14.293  -2.645   7.795  1.00  0.00           C  
ATOM   3888  O   ARG    25     -15.267  -3.230   8.242  1.00  0.00           O  
ATOM   3889  CB  ARG    25     -13.341  -0.336   7.862  1.00  0.00           C  
ATOM   3890  CG  ARG    25     -14.572   0.571   7.899  1.00  0.00           C  
ATOM   3891  CD  ARG    25     -14.146   1.999   8.248  1.00  0.00           C  
ATOM   3892  NE  ARG    25     -15.342   2.888   8.251  1.00  0.00           N  
ATOM   3893  CZ  ARG    25     -15.540   3.721   7.266  1.00  0.00           C  
ATOM   3894  NH1 ARG    25     -15.476   3.299   6.033  1.00  0.00           N  
ATOM   3895  NH2 ARG    25     -15.804   4.975   7.514  1.00  0.00           N  
ATOM   3896  OXT ARG    25     -13.829  -2.842   6.683  1.00  0.00           O  
ATOM   3897  H   ARG    25     -11.765  -2.704   8.614  1.00  0.00           H  
ATOM   3898  HA  ARG    25     -14.257  -1.360   9.514  1.00  0.00           H  
ATOM   3899 1HB  ARG    25     -12.494   0.188   8.279  1.00  0.00           H  
ATOM   3900 2HB  ARG    25     -13.128  -0.609   6.840  1.00  0.00           H  
ATOM   3901 1HG  ARG    25     -15.054   0.564   6.932  1.00  0.00           H  
ATOM   3902 2HG  ARG    25     -15.263   0.211   8.647  1.00  0.00           H  
ATOM   3903 1HD  ARG    25     -13.688   2.008   9.226  1.00  0.00           H  
ATOM   3904 2HD  ARG    25     -13.436   2.352   7.515  1.00  0.00           H  
ATOM   3905  HE  ARG    25     -15.981   2.847   8.993  1.00  0.00           H  
ATOM   3906 1HH1 ARG    25     -15.274   2.338   5.844  1.00  0.00           H  
ATOM   3907 2HH1 ARG    25     -15.628   3.936   5.278  1.00  0.00           H  
ATOM   3908 1HH2 ARG    25     -15.855   5.298   8.459  1.00  0.00           H  
ATOM   3909 2HH2 ARG    25     -15.953   5.613   6.759  1.00  0.00           H  
TER    3910      ARG    25                                                      
ENDMDL                                                                          
MASTER       52    0    0    1    0    0    0    6 3900   10    0    2          
END                                                                             
BioPerl-1.007002/t/data/1A3I.pdb000444000766000024     10764613155576321 16072 0ustar00cjfieldsstaff000000000000HEADER    EXTRACELLULAR MATRIX                    22-JAN-98   1A3I              
TITLE     X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE               
TITLE    2 PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY)                    
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: COLLAGEN-LIKE PEPTIDE;                                     
COMPND   3 CHAIN: A, B, C;                                                      
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES                                                       
KEYWDS    COLLAGEN, EXTRACELLULAR MATRIX                                        
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    R.Z.KRAMER,L.VITAGLIANO,J.BELLA,R.BERISIO,L.MAZZARELLA,               
AUTHOR   2 B.BRODSKY,A.ZAGARI,H.M.BERMAN                                        
REVDAT   2   23-JUN-99 1A3I    1       JRNL                                     
REVDAT   1   06-MAY-98 1A3I    0                                                
JRNL        AUTH   R.Z.KRAMER,L.VITAGLIANO,J.BELLA,R.BERISIO,                   
JRNL        AUTH 2 L.MAZZARELLA,B.BRODSKY,A.ZAGARI,H.M.BERMAN                   
JRNL        TITL   X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A                    
JRNL        TITL 2 COLLAGEN-LIKE PEPTIDE WITH THE REPEATING SEQUENCE            
JRNL        TITL 3 (PRO-PRO-GLY)                                                
JRNL        REF    J.MOL.BIOL.                   V. 280   623 1998              
JRNL        REFN   ASTM JMOBAK  UK ISSN 0022-2836                 0070          
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. 1.97 ANGSTROMS.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR 3.1                                           
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 8.                             
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 2.                             
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 1000000.                       
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.1                            
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 76.7                           
REMARK   3   NUMBER OF REFLECTIONS             : 861                            
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : NULL                            
REMARK   3   FREE R VALUE TEST SET SELECTION  : NULL                            
REMARK   3   R VALUE            (WORKING SET) : 0.181                           
REMARK   3   FREE R VALUE                     : NULL                            
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL                            
REMARK   3   FREE R VALUE TEST SET COUNT      : NULL                            
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL                            
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 10                           
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.97                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.04                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 63.3                         
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 69.                          
REMARK   3   BIN R VALUE           (WORKING SET) : 0.22                         
REMARK   3   BIN FREE R VALUE                    : NULL                         
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : NULL                         
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL                         
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 126                                     
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 0                                       
REMARK   3   SOLVENT ATOMS            : 45                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 15.9                           
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : NULL                                                 
REMARK   3    B22 (A**2) : NULL                                                 
REMARK   3    B33 (A**2) : NULL                                                 
REMARK   3    B12 (A**2) : NULL                                                 
REMARK   3    B13 (A**2) : NULL                                                 
REMARK   3    B23 (A**2) : NULL                                                 
REMARK   3                                                                      
REMARK   3  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL                            
REMARK   3   ESD FROM SIGMAA              (A) : NULL                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.01                            
REMARK   3   BOND ANGLES            (DEGREES) : 2.07                            
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL                            
REMARK   3   IMPROPER ANGLES        (DEGREES) : 2.11                            
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : GROUP                                     
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  NCS MODEL : NONE                                                    
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT          
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL                 
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  PARAMETER FILE  1  : PARHCSDX.PRO                                   
REMARK   3  PARAMETER FILE  2  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : TOPHCSDX.PRO                                   
REMARK   3  TOPOLOGY FILE  2   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: DUE TO THE QUASI-INFINITE,                
REMARK   3  AVERAGED NATURE OF THE TRIPLE HELIX, DURING REFINEMENT              
REMARK   3  COVALENT BONDS ARE NECESSARY TO JOIN THE MOLECULE WITH              
REMARK   3  ITS SYMMETRY MATES BOTH ABOVE IT AND BELOW IT ALONG THE             
REMARK   3  HELICAL AXIS AND TIGHT REFINEMENT CONSTRAINTS WERE                  
REMARK   3  MAINTAINED.                                                         
REMARK   4                                                                      
REMARK   4 1A3I COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996                        
REMARK   6                                                                      
REMARK   6 THE 21 RESIDUE ASYMMETRIC UNIT CORRESPONDS TO ONE                    
REMARK   6 TRIPLE-HELICAL REPEAT AND IS SMALLER THAN THE ENTIRE 90              
REMARK   6 RESIDUE PEPTIDE DUE TO TRANSLATIONAL DISORDER ALONG THE              
REMARK   6 HELICAL AXIS.  THE RESULT IS A POLYMER-LIKE STRUCTURE WITH           
REMARK   6 NO DEFINED ENDS.                                                     
REMARK   7                                                                      
REMARK   7 THE POLYMER STRUCTURE IS FORMED BY CONTINUATION OF THE               
REMARK   7 CHAINS USING THE SYMMETRY-RELATED MOLECULES ALONG THE                
REMARK   7 HELICAL AXIS.  THE TVECT RECORD BELOW PRESENTS THE                   
REMARK   7 TRANSLATION THAT WILL GENERATE THE POLYMER.  NOTE:                   
REMARK   7 THEREFORE, CLOSE CONTACTS BETWEEN SYMMETRY-RELATED                   
REMARK   7 MOLECULES ARE INTENTIONAL AND NECESSARY.  INTERCHAIN                 
REMARK   7 HYDROGEN BONDING AT THE END OF CHAINS ALSO UTILIZES                  
REMARK   7 SYMMETRY-RELATED MOLECULES.                                          
REMARK   8                                                                      
REMARK   8 THE ENTIRE 30 RESIDUE LONG PEPTIDE CAN BE GENERATED FROM             
REMARK   8 THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE FOLLOWING              
REMARK   8 TRANSLATIONS (USING FRACTIONAL COORDINATES):                         
REMARK   8 CHAIN A: TRANSLATE RESIDUES 1 - 9 BY (0 0 1), (0 0 2), AND           
REMARK   8          (0 0 3) AND RESIDUES 7 - 9 BY (0 0 4).                      
REMARK   8 CHAIN B: TRANSLATE RESIDUES 31 - 36 BY (0 0 1), (0 0 2),             
REMARK   8          AND (0 0 3).                                                
REMARK   8 CHAIN C: TRANSLATE RESIDUES 61 - 66 BY (0 0 1), (0 0 2),             
REMARK   8          AND (0 0 3) AND RESIDUES 64 - 66 BY (004).                  
REMARK   8 THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 90 RESIDUES,          
REMARK   8 30 IN EACH CHAIN.                                                    
REMARK   9                                                                      
REMARK   9 HYDROGEN BONDS BETWEEN PEPTIDE CHAINS FOLLOW THE RICH AND            
REMARK   9 CRICK MODEL II FOR COLLAGEN.                                         
REMARK  10                                                                      
REMARK  10 THE UNIT CELL AXES WERE CHOSEN TO COINCIDE WITH A                    
REMARK  10 PREVIOUS STRUCTURE DETERMINATION (OKUYAMA 1981) OF THIS              
REMARK  10 PEPTIDE.                                                             
REMARK  11                                                                      
REMARK  11 FOR EACH CHAIN, RESIDUE NUMBERING CORRESPONDS TO THE ENTIRE          
REMARK  11 MOLECULE RATHER THAN THE SHORTER ASYMMETRIC UNIT.                    
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : OCT-1991                           
REMARK 200  TEMPERATURE           (KELVIN) : 259.0                              
REMARK 200  PH                             : NULL                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : N                                  
REMARK 200  RADIATION SOURCE               : NULL                               
REMARK 200  BEAMLINE                       : NULL                               
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.542                              
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CAD4 DIFFRACTOMETER                
REMARK 200  DETECTOR MANUFACTURER          : ENRAF-NONIUS                       
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOLEN                              
REMARK 200  DATA SCALING SOFTWARE          : NULL                               
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 1136                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.97                               
REMARK 200  RESOLUTION RANGE LOW       (A) : INFINITY                           
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.                                 
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.5                               
REMARK 200  DATA REDUNDANCY                : NULL                               
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200   FOR THE DATA SET  : NULL                               
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.2                      
REMARK 200  COMPLETENESS FOR SHELL     (%) : 98.                                
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200   FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR                    
REMARK 200    REPLACEMENT                                                       
REMARK 200 SOFTWARE USED: LALS                                                  
REMARK 200 STARTING MODEL: IDEALIZED SEVEN-FOLD TRIPLE-HELIX                    
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): NULL                                      
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PEPTIDE WAS CRYSTALLIZED FROM            
REMARK 280 4.0 MG/ML PEPTIDE IN 10% ACETIC ACID, 0.1% SODIUM AZIDE,             
REMARK 280 AND 3.0% PEG400.                                                     
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                       
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   1/2-X,-Y,1/2+Z                                          
REMARK 290       3555   -X,1/2+Y,1/2-Z                                          
REMARK 290       4555   1/2+X,1/2-Y,-Z                                          
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       13.40986            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       10.09000            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       13.14510            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       10.09000            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       13.40986            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       13.14510            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 THIS ENTRY IS RELATED TO PDB ENTRY 1A3J.                             
DBREF  1A3I A    1     9  PDB    1A3I     1A3I             1      9             
DBREF  1A3I B   31    36  PDB    1A3I     1A3I            31     36             
DBREF  1A3I C   61    66  PDB    1A3I     1A3I            61     66             
SEQRES   1 A    9  PRO PRO GLY PRO PRO GLY PRO PRO GLY                          
SEQRES   1 B    6  PRO PRO GLY PRO PRO GLY                                      
SEQRES   1 C    6  PRO PRO GLY PRO PRO GLY                                      
HET    ACY    401       4                                                       
HET    ACY    402       4                                                       
HETNAM     ACY ACETIC ACID                                                      
FORMUL   4  ACY    2(C2 H4 O2)                                                  
FORMUL   5  HOH   *37(H2 O1)                                                    
LINK         N   PRO C  61                 C   GLY A   9            1556        
LINK         N   PRO A   1                 C   GLY B  36            1556        
LINK         N   PRO B  31                 C   GLY C  66            1556        
CRYST1   26.820   26.290   20.180  90.00  90.00  90.00 P 21 21 21    4          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      0.037286  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.038037  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.049554        0.00000                         
TVECT    1   0.00000   0.00000  20.18000                                        
ATOM      1  N   PRO A   1       8.316  21.206  21.530  1.00 17.44           N  
ATOM      2  CA  PRO A   1       7.608  20.729  20.336  1.00 17.44           C  
ATOM      3  C   PRO A   1       8.487  20.707  19.092  1.00 17.44           C  
ATOM      4  O   PRO A   1       9.466  21.457  19.005  1.00 17.44           O  
ATOM      5  CB  PRO A   1       6.460  21.723  20.211  1.00 22.26           C  
ATOM      6  CG  PRO A   1       7.110  23.002  20.661  1.00 22.26           C  
ATOM      7  CD  PRO A   1       7.873  22.569  21.889  1.00 22.26           C  
ATOM      8  N   PRO A   2       8.177  19.849  18.107  1.00 13.49           N  
ATOM      9  CA  PRO A   2       9.057  19.896  16.936  1.00 13.49           C  
ATOM     10  C   PRO A   2       9.087  21.308  16.377  1.00 13.49           C  
ATOM     11  O   PRO A   2       8.318  22.186  16.816  1.00 13.49           O  
ATOM     12  CB  PRO A   2       8.426  18.899  15.970  1.00 18.26           C  
ATOM     13  CG  PRO A   2       7.776  17.914  16.886  1.00 18.26           C  
ATOM     14  CD  PRO A   2       7.166  18.797  17.954  1.00 18.26           C  
ATOM     15  N   GLY A   3       9.981  21.517  15.426  1.00 12.07           N  
ATOM     16  CA  GLY A   3      10.060  22.799  14.777  1.00 12.07           C  
ATOM     17  C   GLY A   3       9.119  22.720  13.589  1.00 12.07           C  
ATOM     18  O   GLY A   3       8.531  21.655  13.334  1.00 12.07           O  
ATOM     19  N   PRO A   4       8.954  23.832  12.847  1.00 14.22           N  
ATOM     20  CA  PRO A   4       8.095  23.907  11.675  1.00 14.22           C  
ATOM     21  C   PRO A   4       8.733  23.310  10.437  1.00 14.22           C  
ATOM     22  O   PRO A   4       9.963  23.078  10.402  1.00 14.22           O  
ATOM     23  CB  PRO A   4       7.863  25.403  11.527  1.00  8.61           C  
ATOM     24  CG  PRO A   4       9.218  25.934  11.895  1.00  8.61           C  
ATOM     25  CD  PRO A   4       9.530  25.158  13.143  1.00  8.61           C  
ATOM     26  N   PRO A   5       7.918  23.027   9.412  1.00 14.03           N  
ATOM     27  CA  PRO A   5       8.416  22.493   8.135  1.00 14.03           C  
ATOM     28  C   PRO A   5       9.621  23.306   7.672  1.00 14.03           C  
ATOM     29  O   PRO A   5       9.876  24.379   8.181  1.00 14.03           O  
ATOM     30  CB  PRO A   5       7.229  22.641   7.193  1.00 10.90           C  
ATOM     31  CG  PRO A   5       6.082  22.382   8.123  1.00 10.90           C  
ATOM     32  CD  PRO A   5       6.452  23.069   9.415  1.00 10.90           C  
ATOM     33  N   GLY A   6      10.369  22.765   6.725  1.00 10.80           N  
ATOM     34  CA  GLY A   6      11.517  23.464   6.204  1.00 10.80           C  
ATOM     35  C   GLY A   6      11.139  24.138   4.928  1.00 10.80           C  
ATOM     36  O   GLY A   6      10.028  23.948   4.418  1.00 10.80           O  
ATOM     37  N   PRO A   7      12.050  24.922   4.355  1.00 11.55           N  
ATOM     38  CA  PRO A   7      11.797  25.641   3.111  1.00 11.55           C  
ATOM     39  C   PRO A   7      11.484  24.709   1.970  1.00 11.55           C  
ATOM     40  O   PRO A   7      11.783  23.500   2.038  1.00 11.55           O  
ATOM     41  CB  PRO A   7      13.091  26.440   2.901  1.00 10.61           C  
ATOM     42  CG  PRO A   7      14.119  25.540   3.516  1.00 10.61           C  
ATOM     43  CD  PRO A   7      13.456  25.102   4.796  1.00 10.61           C  
ATOM     44  N   PRO A   8      10.853  25.225   0.900  1.00 14.31           N  
ATOM     45  CA  PRO A   8      10.571  24.322  -0.220  1.00 14.31           C  
ATOM     46  C   PRO A   8      11.897  23.973  -0.901  1.00 14.31           C  
ATOM     47  O   PRO A   8      12.973  24.425  -0.473  1.00 14.31           O  
ATOM     48  CB  PRO A   8       9.623  25.131  -1.124  1.00 16.14           C  
ATOM     49  CG  PRO A   8       9.080  26.188  -0.206  1.00 16.14           C  
ATOM     50  CD  PRO A   8      10.279  26.556   0.633  1.00 16.14           C  
ATOM     51  N   GLY A   9      11.816  23.125  -1.918  1.00 11.65           N  
ATOM     52  CA  GLY A   9      12.996  22.720  -2.639  1.00 11.65           C  
ATOM     53  C   GLY A   9      13.234  23.577  -3.852  1.00 11.65           C  
ATOM     54  O   GLY A   9      12.433  24.459  -4.180  1.00 11.65           O  
TER      55      GLY A   9                                                      
ATOM     56  N   PRO B  31      12.731  18.403  18.599  1.00  8.71           N  
ATOM     57  CA  PRO B  31      13.374  17.891  17.389  1.00  8.71           C  
ATOM     58  C   PRO B  31      13.142  18.745  16.166  1.00  8.71           C  
ATOM     59  O   PRO B  31      12.207  19.526  16.121  1.00  8.71           O  
ATOM     60  CB  PRO B  31      12.784  16.471  17.255  1.00 15.38           C  
ATOM     61  CG  PRO B  31      11.434  16.598  17.873  1.00 15.38           C  
ATOM     62  CD  PRO B  31      11.660  17.490  19.065  1.00 15.38           C  
ATOM     63  N   PRO B  32      14.011  18.647  15.178  1.00 13.67           N  
ATOM     64  CA  PRO B  32      13.833  19.426  13.967  1.00 13.67           C  
ATOM     65  C   PRO B  32      12.523  19.099  13.336  1.00 13.67           C  
ATOM     66  O   PRO B  32      12.038  17.968  13.473  1.00 13.67           O  
ATOM     67  CB  PRO B  32      15.025  19.023  13.125  1.00  9.03           C  
ATOM     68  CG  PRO B  32      16.077  18.799  14.163  1.00  9.03           C  
ATOM     69  CD  PRO B  32      15.320  17.975  15.152  1.00  9.03           C  
ATOM     70  N   GLY B  33      11.928  20.070  12.640  1.00 14.26           N  
ATOM     71  CA  GLY B  33      10.661  19.801  12.008  1.00 14.26           C  
ATOM     72  C   GLY B  33      10.802  18.911  10.797  1.00 14.26           C  
ATOM     73  O   GLY B  33      11.882  18.368  10.516  1.00 14.26           O  
ATOM     74  N   PRO B  34       9.708  18.736  10.046  1.00 11.50           N  
ATOM     75  CA  PRO B  34       9.665  17.922   8.836  1.00 11.50           C  
ATOM     76  C   PRO B  34      10.227  18.620   7.654  1.00 11.50           C  
ATOM     77  O   PRO B  34      10.284  19.836   7.639  1.00 11.50           O  
ATOM     78  CB  PRO B  34       8.192  17.649   8.657  1.00  9.66           C  
ATOM     79  CG  PRO B  34       7.586  18.930   9.132  1.00  9.66           C  
ATOM     80  CD  PRO B  34       8.350  19.245  10.373  1.00  9.66           C  
ATOM     81  N   PRO B  35      10.677  17.860   6.651  1.00 16.25           N  
ATOM     82  CA  PRO B  35      11.228  18.392   5.413  1.00 16.25           C  
ATOM     83  C   PRO B  35      10.219  19.317   4.794  1.00 16.25           C  
ATOM     84  O   PRO B  35       9.010  19.249   5.127  1.00 16.25           O  
ATOM     85  CB  PRO B  35      11.468  17.160   4.542  1.00 10.89           C  
ATOM     86  CG  PRO B  35      11.668  16.066   5.531  1.00 10.89           C  
ATOM     87  CD  PRO B  35      10.798  16.385   6.703  1.00 10.89           C  
ATOM     88  N   GLY B  36      10.709  20.223   3.948  1.00 19.34           N  
ATOM     89  CA  GLY B  36       9.836  21.154   3.260  1.00 19.34           C  
ATOM     90  C   GLY B  36       9.207  20.491   2.050  1.00 19.34           C  
ATOM     91  O   GLY B  36       9.565  19.355   1.710  1.00 19.34           O  
TER      92      GLY B  36                                                      
ATOM     93  N   PRO C  61      14.309  23.332  15.622  1.00 10.63           N  
ATOM     94  CA  PRO C  61      14.643  24.095  14.422  1.00 10.63           C  
ATOM     95  C   PRO C  61      13.859  23.751  13.161  1.00 10.63           C  
ATOM     96  O   PRO C  61      13.189  22.726  13.091  1.00 10.63           O  
ATOM     97  CB  PRO C  61      16.144  23.846  14.270  1.00 19.41           C  
ATOM     98  CG  PRO C  61      16.308  22.475  14.820  1.00 19.41           C  
ATOM     99  CD  PRO C  61      15.451  22.510  16.056  1.00 19.41           C  
ATOM    100  N   PRO C  62      13.910  24.631  12.163  1.00 15.75           N  
ATOM    101  CA  PRO C  62      13.234  24.402  10.876  1.00 15.75           C  
ATOM    102  C   PRO C  62      13.686  23.039  10.262  1.00 15.75           C  
ATOM    103  O   PRO C  62      14.874  22.653  10.369  1.00 15.75           O  
ATOM    104  CB  PRO C  62      13.668  25.600  10.024  1.00  9.87           C  
ATOM    105  CG  PRO C  62      13.859  26.675  11.052  1.00  9.87           C  
ATOM    106  CD  PRO C  62      14.515  25.976  12.213  1.00  9.87           C  
ATOM    107  N   GLY C  63      12.761  22.316   9.639  1.00 16.50           N  
ATOM    108  CA  GLY C  63      13.167  21.066   9.028  1.00 16.50           C  
ATOM    109  C   GLY C  63      14.105  21.312   7.849  1.00 16.50           C  
ATOM    110  O   GLY C  63      14.435  22.472   7.518  1.00 16.50           O  
ATOM    111  N   PRO C  64      14.571  20.246   7.184  1.00 15.53           N  
ATOM    112  CA  PRO C  64      15.458  20.417   6.037  1.00 15.53           C  
ATOM    113  C   PRO C  64      14.684  20.927   4.823  1.00 15.53           C  
ATOM    114  O   PRO C  64      13.463  20.829   4.772  1.00 15.53           O  
ATOM    115  CB  PRO C  64      16.001  19.018   5.816  1.00  5.63           C  
ATOM    116  CG  PRO C  64      14.806  18.201   6.163  1.00  5.63           C  
ATOM    117  CD  PRO C  64      14.354  18.810   7.450  1.00  5.63           C  
ATOM    118  N   PRO C  65      15.378  21.485   3.840  1.00 10.50           N  
ATOM    119  CA  PRO C  65      14.622  21.927   2.689  1.00 10.50           C  
ATOM    120  C   PRO C  65      14.079  20.706   1.955  1.00 10.50           C  
ATOM    121  O   PRO C  65      14.505  19.531   2.221  1.00 10.50           O  
ATOM    122  CB  PRO C  65      15.615  22.734   1.892  1.00 11.55           C  
ATOM    123  CG  PRO C  65      16.951  22.189   2.279  1.00 11.55           C  
ATOM    124  CD  PRO C  65      16.808  21.850   3.742  1.00 11.55           C  
ATOM    125  N   GLY C  66      13.102  20.952   1.076  1.00  9.96           N  
ATOM    126  CA  GLY C  66      12.479  19.874   0.334  1.00  9.96           C  
ATOM    127  C   GLY C  66      13.226  19.430  -0.900  1.00  9.96           C  
ATOM    128  O   GLY C  66      14.206  20.054  -1.286  1.00  9.96           O  
TER     129      GLY C  66                                                      
HETATM  130  C   ACY   401       3.682  22.541  11.236  1.00 21.19           C  
HETATM  131  O   ACY   401       2.807  23.097  10.553  1.00 21.19           O  
HETATM  132  OXT ACY   401       4.306  23.101  12.291  1.00 21.19           O  
HETATM  133  CH3 ACY   401       4.134  21.141  10.915  1.00 21.19           C  
HETATM  134  C   ACY   402      19.091  22.160   7.837  1.00 38.32           C  
HETATM  135  O   ACY   402      19.334  21.755   6.694  1.00 38.32           O  
HETATM  136  OXT ACY   402      18.633  21.338   8.768  1.00 38.32           O  
HETATM  137  CH3 ACY   402      19.293  23.618   8.266  1.00 38.32           C  
HETATM  138  O   HOH   101       5.594  21.889  15.805  1.00 28.97           O  
HETATM  139  O   HOH   102       7.355  25.253  16.293  1.00 22.47           O  
HETATM  140  O   HOH   103       6.457  20.993  12.327  1.00 29.02           O  
HETATM  141  O   HOH   104       7.423  26.270   8.119  1.00 30.44           O  
HETATM  142  O   HOH   105      11.373  26.588   6.950  1.00 23.32           O  
HETATM  143  O   HOH   106       7.408  25.371   4.091  1.00  5.05           O  
HETATM  144  O   HOH   107      13.153  27.296  -0.172  1.00 21.02           O  
HETATM  145  O   HOH   108      15.664  24.810  -1.390  1.00 11.17           O  
HETATM  146  O   HOH   109      12.152  26.921  -4.540  1.00  9.23           O  
HETATM  147  O   HOH   111      13.443  15.615  12.881  1.00 13.59           O  
HETATM  148  O   HOH   112       9.758  16.818  12.994  1.00 27.99           O  
HETATM  149  O   HOH   113      12.963  16.325   9.228  1.00 23.25           O  
HETATM  150  O   HOH   115       5.878  20.610   4.485  1.00 24.12           O  
HETATM  151  O   HOH   116       8.848  16.145   2.532  1.00 47.48           O  
HETATM  152  O   HOH   121      18.638  24.296  11.397  1.00 27.03           O  
HETATM  153  O   HOH   122      16.444  20.463  10.447  1.00 25.94           O  
HETATM  154  O   HOH   123      16.295  24.230   6.930  1.00 19.70           O  
HETATM  155  O   HOH   124      17.331  17.619   2.413  1.00 31.73           O  
HETATM  156  O   HOH   125      13.985  16.977   0.817  1.00 53.43           O  
HETATM  157  O   HOH   126      16.914  19.363  -0.910  1.00  9.43           O  
HETATM  158  O   HOH   201       5.473  23.666   4.098  1.00 14.40           O  
HETATM  159  O   HOH   202      21.595  24.992   9.644  1.00 17.29           O  
HETATM  160  O   HOH   204       4.187  25.027   5.974  1.00  7.43           O  
HETATM  161  O   HOH   205      13.466  14.688   2.583  1.00  7.90           O  
HETATM  162  O   HOH   208      16.622  16.376  -0.560  1.00 22.05           O  
HETATM  163  O   HOH   209      17.417  23.063  -0.970  1.00 23.97           O  
HETATM  164  O   HOH   210      17.034  27.356   9.718  1.00 20.07           O  
HETATM  165  O   HOH   218       3.280  23.836   8.294  1.00 17.32           O  
HETATM  166  O   HOH   220      16.159  26.500  -3.605  1.00 26.00           O  
HETATM  167  O   HOH   241      17.060  26.756   1.465  1.00 16.81           O  
HETATM  168  O   HOH   242       6.144  15.504   5.728  1.00 23.11           O  
HETATM  169  O   HOH   243      18.532  26.812  12.585  1.00 13.40           O  
HETATM  170  O   HOH   244       9.783  28.384   5.130  1.00 21.62           O  
HETATM  171  O   HOH   245      10.552  28.648  13.053  1.00 23.05           O  
HETATM  172  O   HOH   246       9.269  14.976  15.672  1.00 28.60           O  
HETATM  173  O   HOH   247       6.015  15.569  15.283  1.00 26.87           O  
HETATM  174  O   HOH   248      20.598  27.021   8.450  1.00 22.69           O  
CONECT  130  131  132  133                                                      
CONECT  131  130                                                                
CONECT  132  130                                                                
CONECT  133  130                                                                
CONECT  134  135  136  137                                                      
CONECT  135  134                                                                
CONECT  136  134                                                                
CONECT  137  134                                                                
MASTER      226    0    2    0    0    0    0    6  171    3    8    3          
END                                                                             
BioPerl-1.007002/t/data/1BPT.pdb000555000766000024     13717213155576321 16143 0ustar00cjfieldsstaff000000000000HEADER    PROTEINASE INHIBITOR (TRYPSIN)          11-DEC-91   1BPT      1BPT   2
COMPND    BOVINE PANCREATIC TRYPSIN INHIBITOR (/BPTI$) MUTANT (TYR 23   1BPT   3
COMPND   2 REPLACED BY ALA) (/Y23A$)                                    1BPT   4
SOURCE    BOVINE (BOS $TAURUS) PANCREAS                                 1BPT   5
AUTHOR    D.HOUSSET,A.WLODAWER,F.TAO,J.FUCHS,C.WOODWARD                 1BPT   6
REVDAT   1   15-JAN-93 1BPT    0                                        1BPT   7
JRNL        AUTH   A.T.DANISHEFSKY,D.HOUSSET,K.-S.KIM,F.TAO,J.FUCHS,    1BPT   8
JRNL        AUTH 2 C.WOODWARD,A.WLODAWER                                1BPT   9
JRNL        TITL   CREVICE-FORMING MUTANTS OF BPTI: CRYSTAL STRUCTURES  1BPT  10
JRNL        TITL 2 OF F22A, Y23A, N43G, AND F45A                        1BPT  11
JRNL        REF    TO BE PUBLISHED                                      1BPT  12
JRNL        REFN                                                   353  1BPT  13
REMARK   1                                                              1BPT  14
REMARK   1 REFERENCE 1                                                  1BPT  15
REMARK   1  AUTH   K.S.KIM,F.TAO,J.FUCHS,A.T.DANISHEFSKY,D.HOUSSET,     1BPT  16
REMARK   1  AUTH 2 A.WLODAWER,C.WOODWARD                                1BPT  17
REMARK   1  TITL   CREVICE-FORMING MUTANTS OF BPTI: STABILITY CHANGES   1BPT  18
REMARK   1  TITL 2 AND NEW HYDROPHOBIC SURFACE                          1BPT  19
REMARK   1  REF    TO BE PUBLISHED                                      1BPT  20
REMARK   1  REFN                                                   353  1BPT  21
REMARK   1 REFERENCE 2                                                  1BPT  22
REMARK   1  AUTH   D.HOUSSET,K.-*S.KIM,J.FUCHS,C.WOODWARD,A.WLODAWER    1BPT  23
REMARK   1  TITL   CRYSTAL STRUCTURE OF A /Y35G$ MUTANT OF BOVINE       1BPT  24
REMARK   1  TITL 2 PANCREATIC TRYPSIN INHIBITOR                         1BPT  25
REMARK   1  REF    J.MOL.BIOL.                   V. 220   757 1991      1BPT  26
REMARK   1  REFN   ASTM JMOBAK  UK ISSN 0022-2836                  070  1BPT  27
REMARK   1 REFERENCE 3                                                  1BPT  28
REMARK   1  AUTH   C.EIGENBROT,M.RANDAL,A.A.KOSSIAKOFF                  1BPT  29
REMARK   1  TITL   STRUCTURAL EFFECTS INDUCED BY REMOVAL OF A           1BPT  30
REMARK   1  TITL 2 DISULFIDE-BRIDGE. THE X-RAY STRUCTURE OF THE         1BPT  31
REMARK   1  TITL 3 /C30A(SLASH)C51A$ MUTANT OF BASIC PANCREATIC         1BPT  32
REMARK   1  TITL 4 TRYPSIN INHIBITOR AT 1.6 ANGSTROMS                   1BPT  33
REMARK   1  REF    PROTEIN ENG.                  V.   3   591 1990      1BPT  34
REMARK   1  REFN   ASTM PRENE9  UK ISSN 0269-2139                  859  1BPT  35
REMARK   1 REFERENCE 4                                                  1BPT  36
REMARK   1  AUTH   T.R.HYNES,M.RANDAL,L.A.KENNEDY,C.EIGENBROT,          1BPT  37
REMARK   1  AUTH 2 A.A.KOSSIAKOFF                                       1BPT  38
REMARK   1  TITL   X-RAY CRYSTAL STRUCTURE OF THE PROTEASE INHIBITOR    1BPT  39
REMARK   1  TITL 2 DOMAIN OF ALZHEIMER'S AMYLOID BETA-*PROTEIN          1BPT  40
REMARK   1  TITL 3 PRECURSOR                                            1BPT  41
REMARK   1  REF    BIOCHEMISTRY                  V.  29 10018 1990      1BPT  42
REMARK   1  REFN   ASTM BICHAW  US ISSN 0006-2960                  033  1BPT  43
REMARK   1 REFERENCE 5                                                  1BPT  44
REMARK   1  AUTH   A.WLODAWER,J.NACHMAN,G.L.GILLILAND,W.GALLAGHER       1BPT  45
REMARK   1  AUTH 2 C.WOODWARD                                           1BPT  46
REMARK   1  TITL   STRUCTURE OF FORM /III$ CRYSTALS OF BOVINE           1BPT  47
REMARK   1  TITL 2 PANCREATIC TRYPSIN INHIBITOR.                        1BPT  48
REMARK   1  REF    J.MOL.BIOL.                   V. 198   469 1987      1BPT  49
REMARK   1  REFN   ASTM JMOBAK  UK ISSN 0022-2836                  070  1BPT  50
REMARK   1 REFERENCE 6                                                  1BPT  51
REMARK   1  AUTH   A.WLODAWER,J.WALTER,R.HUBER,L.SJOLIN                 1BPT  52
REMARK   1  TITL   STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR.    1BPT  53
REMARK   1  TITL 2 RESULTS OF JOINT NEUTRON AND X-RAY REFINEMENT OF     1BPT  54
REMARK   1  TITL 3 CRYSTAL FORM /II$                                    1BPT  55
REMARK   1  REF    J.MOL.BIOL.                   V. 180   307 1984      1BPT  56
REMARK   1  REFN   ASTM JMOBAK  UK ISSN 0022-2836                  070  1BPT  57
REMARK   1 REFERENCE 7                                                  1BPT  58
REMARK   1  AUTH   A.WLODAWER,J.DEISENHOFER,R.HUBER                     1BPT  59
REMARK   1  TITL   COMPARISON OF TWO HIGHLY REFINED STRUCTURES OF       1BPT  60
REMARK   1  TITL 2 BOVINE PANCREATIC TRYPSIN INHIBITOR                  1BPT  61
REMARK   1  REF    J.MOL.BIOL.                   V. 193   145 1987      1BPT  62
REMARK   1  REFN   ASTM JMOBAK  UK ISSN 0022-2836                  070  1BPT  63
REMARK   1 REFERENCE 8                                                  1BPT  64
REMARK   1  AUTH   J.WALTER,R.HUBER                                     1BPT  65
REMARK   1  TITL   PANCREATIC TRYPSIN INHIBITOR. A NEW CRYSTAL FORM     1BPT  66
REMARK   1  TITL 2 AND ITS ANALYSIS                                     1BPT  67
REMARK   1  REF    J.MOL.BIOL.                   V. 167   911 1983      1BPT  68
REMARK   1  REFN   ASTM JMOBAK  UK ISSN 0022-2836                  070  1BPT  69
REMARK   2                                                              1BPT  70
REMARK   2 RESOLUTION. 2.0  ANGSTROMS.                                  1BPT  71
REMARK   3                                                              1BPT  72
REMARK   3 REFINEMENT.                                                  1BPT  73
REMARK   3   PROGRAM                    XPLOR                           1BPT  74
REMARK   3   AUTHORS                    BRUENGER                        1BPT  75
REMARK   3   R VALUE                    0.165                           1BPT  76
REMARK   3   RMSD BOND DISTANCES        0.018  ANGSTROMS                1BPT  77
REMARK   4                                                              1BPT  78
REMARK   4 THERE WAS NO DENSITY FOR THE FINAL TWO CARBOXY-TERMINAL      1BPT  79
REMARK   4 RESIDUES (GLY 57 AND ALA 58) IN THE FINAL MAPS.              1BPT  80
REMARK   5                                                              1BPT  81
REMARK   5 COORDINATES FOR 40 WATER MOLECULES ARE GIVEN FOLLOWING THE   1BPT  82
REMARK   5 MAIN BODY OF THE PROTEIN.  THE NOMENCLATURE OF THE WATER     1BPT  83
REMARK   5 MOLECULES IS THAT OF THE DEPOSITORS.                         1BPT  84
SEQRES   1     58  ARG PRO ASP PHE CYS LEU GLU PRO PRO TYR THR GLY PRO  1BPT  85
SEQRES   2     58  CYS LYS ALA ARG ILE ILE ARG TYR PHE ALA ASN ALA LYS  1BPT  86
SEQRES   3     58  ALA GLY LEU CYS GLN THR PHE VAL TYR GLY GLY CYS ARG  1BPT  87
SEQRES   4     58  ALA LYS ARG ASN ASN PHE LYS SER ALA GLU ASP CYS MET  1BPT  88
SEQRES   5     58  ARG THR CYS GLY GLY ALA                              1BPT  89
HET    PO4     70       5     PHOSPHATE ION                             1BPT  90
FORMUL   2  PO4    O4 P1 --                                             1BPT  91
FORMUL   3  HOH   *40(H2 O1)                                            1BPT  92
HELIX    1  H1 PRO      2  GLU      7  5 ALL DONORS,ACCEPTORS INCLUDED  1BPT  93
HELIX    2  H2 SER     47  GLY     56  1 ALL DONORS,ACCEPTORS INCLUDED  1BPT  94
SHEET    1  S1 3 LEU    29  TYR    35  0                                1BPT  95
SHEET    2  S1 3 ILE    18  ASN    24 -1  N  ILE    18   O  TYR    35   1BPT  96
SHEET    3  S1 3 PHE    45  PHE    45 -1  N  PHE    45   O  TYR    21   1BPT  97
SSBOND   1 CYS      5    CYS     55                                     1BPT  98
SSBOND   2 CYS     14    CYS     38                                     1BPT  99
SSBOND   3 CYS     30    CYS     51                                     1BPT 100
CRYST1   69.469   23.346   29.188  90.00  90.00  90.00 P 21 21 21    4  1BPT 101
ORIGX1      1.000000  0.000000  0.000000        0.00000                 1BPT 102
ORIGX2      0.000000  1.000000  0.000000        0.00000                 1BPT 103
ORIGX3      0.000000  0.000000  1.000000        0.00000                 1BPT 104
SCALE1      0.014395  0.000000  0.000000        0.00000                 1BPT 105
SCALE2      0.000000  0.042834  0.000000        0.00000                 1BPT 106
SCALE3      0.000000  0.000000  0.034261        0.00000                 1BPT 107
ATOM      1  N   ARG     1      29.292  13.212 -12.751  1.00 33.78      1BPT 108
ATOM      2  CA  ARG     1      29.057  12.019 -11.946  1.00 27.63      1BPT 109
ATOM      3  C   ARG     1      30.419  11.466 -11.478  1.00 29.64      1BPT 110
ATOM      4  O   ARG     1      31.064  10.670 -12.174  1.00 27.67      1BPT 111
ATOM      5  CB  ARG     1      28.297  10.939 -12.700  1.00 28.82      1BPT 112
ATOM      6  CG  ARG     1      27.925   9.695 -11.892  1.00 25.04      1BPT 113
ATOM      7  CD  ARG     1      26.990  10.102 -10.814  1.00 36.35      1BPT 114
ATOM      8  NE  ARG     1      25.671   9.509 -10.875  1.00 43.70      1BPT 115
ATOM      9  CZ  ARG     1      25.299   8.414 -10.207  1.00 44.64      1BPT 116
ATOM     10  NH1 ARG     1      26.105   7.749  -9.392  1.00 44.80      1BPT 117
ATOM     11  NH2 ARG     1      24.055   7.949 -10.340  1.00 51.16      1BPT 118
ATOM     12  N   PRO     2      30.790  11.942 -10.291  1.00 26.52      1BPT 119
ATOM     13  CA  PRO     2      32.005  11.512  -9.585  1.00 25.70      1BPT 120
ATOM     14  C   PRO     2      32.010   9.993  -9.473  1.00 22.30      1BPT 121
ATOM     15  O   PRO     2      30.968   9.316  -9.390  1.00 22.80      1BPT 122
ATOM     16  CB  PRO     2      31.892  12.166  -8.209  1.00 25.93      1BPT 123
ATOM     17  CG  PRO     2      31.000  13.378  -8.442  1.00 26.12      1BPT 124
ATOM     18  CD  PRO     2      29.997  12.890  -9.480  1.00 27.15      1BPT 125
ATOM     19  N   ASP     3      33.188   9.438  -9.467  1.00 21.36      1BPT 126
ATOM     20  CA  ASP     3      33.386   7.984  -9.444  1.00 21.85      1BPT 127
ATOM     21  C   ASP     3      32.859   7.313  -8.187  1.00 18.86      1BPT 128
ATOM     22  O   ASP     3      32.477   6.121  -8.298  1.00  9.03      1BPT 129
ATOM     23  CB  ASP     3      34.849   7.659  -9.800  1.00 30.83      1BPT 130
ATOM     24  CG  ASP     3      35.257   8.386 -11.083  1.00 41.90      1BPT 131
ATOM     25  OD1 ASP     3      34.882   7.832 -12.153  1.00 42.04      1BPT 132
ATOM     26  OD2 ASP     3      35.864   9.473 -10.980  1.00 43.78      1BPT 133
ATOM     27  N   PHE     4      32.841   8.042  -7.067  1.00 14.13      1BPT 134
ATOM     28  CA  PHE     4      32.406   7.481  -5.780  1.00 12.89      1BPT 135
ATOM     29  C   PHE     4      30.894   7.286  -5.768  1.00 12.89      1BPT 136
ATOM     30  O   PHE     4      30.393   6.509  -4.938  1.00 12.42      1BPT 137
ATOM     31  CB  PHE     4      32.998   8.208  -4.578  1.00 13.83      1BPT 138
ATOM     32  CG  PHE     4      32.588   9.662  -4.482  1.00 10.93      1BPT 139
ATOM     33  CD1 PHE     4      31.311   9.973  -3.991  1.00 12.72      1BPT 140
ATOM     34  CD2 PHE     4      33.414  10.650  -4.951  1.00 13.53      1BPT 141
ATOM     35  CE1 PHE     4      30.896  11.308  -3.928  1.00 15.82      1BPT 142
ATOM     36  CE2 PHE     4      33.041  12.001  -4.878  1.00 14.51      1BPT 143
ATOM     37  CZ  PHE     4      31.765  12.300  -4.388  1.00 10.66      1BPT 144
ATOM     38  N   CYS     5      30.213   7.889  -6.711  1.00 11.30      1BPT 145
ATOM     39  CA  CYS     5      28.751   7.756  -6.894  1.00  8.91      1BPT 146
ATOM     40  C   CYS     5      28.333   6.353  -7.318  1.00  9.64      1BPT 147
ATOM     41  O   CYS     5      27.197   5.876  -7.108  1.00  7.73      1BPT 148
ATOM     42  CB  CYS     5      28.387   8.851  -7.898  1.00 11.12      1BPT 149
ATOM     43  SG  CYS     5      28.579  10.549  -7.280  1.00 12.16      1BPT 150
ATOM     44  N   LEU     6      29.193   5.558  -7.897  1.00  4.74      1BPT 151
ATOM     45  CA  LEU     6      29.077   4.189  -8.326  1.00  6.59      1BPT 152
ATOM     46  C   LEU     6      29.483   3.225  -7.187  1.00  9.26      1BPT 153
ATOM     47  O   LEU     6      29.266   1.982  -7.343  1.00 13.32      1BPT 154
ATOM     48  CB  LEU     6      29.823   3.914  -9.616  1.00 11.74      1BPT 155
ATOM     49  CG  LEU     6      29.250   4.089 -11.024  1.00 15.14      1BPT 156
ATOM     50  CD1 LEU     6      28.437   5.346 -11.272  1.00 16.39      1BPT 157
ATOM     51  CD2 LEU     6      30.480   4.138 -11.961  1.00 10.37      1BPT 158
ATOM     52  N   GLU     7      29.975   3.690  -6.075  1.00  9.37      1BPT 159
ATOM     53  CA  GLU     7      30.343   2.830  -4.930  1.00 13.11      1BPT 160
ATOM     54  C   GLU     7      29.096   2.241  -4.249  1.00 10.70      1BPT 161
ATOM     55  O   GLU     7      28.116   2.999  -4.165  1.00  9.68      1BPT 162
ATOM     56  CB  GLU     7      30.967   3.613  -3.776  1.00 19.20      1BPT 163
ATOM     57  CG  GLU     7      32.359   3.902  -3.452  1.00 23.47      1BPT 164
ATOM     58  CD  GLU     7      32.867   5.001  -2.582  1.00 27.28      1BPT 165
ATOM     59  OE1 GLU     7      32.230   5.418  -1.584  1.00 20.35      1BPT 166
ATOM     60  OE2 GLU     7      33.979   5.507  -2.848  1.00 29.04      1BPT 167
ATOM     61  N   PRO     8      29.242   1.021  -3.736  1.00 10.63      1BPT 168
ATOM     62  CA  PRO     8      28.178   0.413  -2.939  1.00 11.56      1BPT 169
ATOM     63  C   PRO     8      28.214   1.124  -1.566  1.00  8.44      1BPT 170
ATOM     64  O   PRO     8      29.236   1.677  -1.137  1.00  6.60      1BPT 171
ATOM     65  CB  PRO     8      28.549  -1.058  -2.811  1.00 11.83      1BPT 172
ATOM     66  CG  PRO     8      30.015  -1.151  -3.101  1.00 11.19      1BPT 173
ATOM     67  CD  PRO     8      30.413   0.125  -3.811  1.00 10.52      1BPT 174
ATOM     68  N   PRO     9      27.095   1.120  -0.895  1.00  8.82      1BPT 175
ATOM     69  CA  PRO     9      27.024   1.732   0.456  1.00  7.22      1BPT 176
ATOM     70  C   PRO     9      27.918   0.926   1.409  1.00  8.58      1BPT 177
ATOM     71  O   PRO     9      28.136  -0.308   1.289  1.00  9.21      1BPT 178
ATOM     72  CB  PRO     9      25.565   1.704   0.830  1.00  8.50      1BPT 179
ATOM     73  CG  PRO     9      24.820   0.922  -0.252  1.00  8.80      1BPT 180
ATOM     74  CD  PRO     9      25.831   0.488  -1.289  1.00  8.43      1BPT 181
ATOM     75  N   TYR    10      28.489   1.597   2.363  1.00  5.10      1BPT 182
ATOM     76  CA  TYR    10      29.355   0.981   3.369  1.00  7.77      1BPT 183
ATOM     77  C   TYR    10      28.862   1.292   4.801  1.00  6.47      1BPT 184
ATOM     78  O   TYR    10      29.004   2.426   5.260  1.00  5.08      1BPT 185
ATOM     79  CB  TYR    10      30.776   1.548   3.188  1.00 10.29      1BPT 186
ATOM     80  CG  TYR    10      31.812   0.865   4.029  1.00  3.16      1BPT 187
ATOM     81  CD1 TYR    10      32.181  -0.458   3.705  1.00  8.41      1BPT 188
ATOM     82  CD2 TYR    10      32.424   1.521   5.086  1.00  6.18      1BPT 189
ATOM     83  CE1 TYR    10      33.149  -1.084   4.464  1.00 15.04      1BPT 190
ATOM     84  CE2 TYR    10      33.412   0.896   5.832  1.00  6.33      1BPT 191
ATOM     85  CZ  TYR    10      33.728  -0.425   5.565  1.00  8.46      1BPT 192
ATOM     86  OH  TYR    10      34.706  -1.029   6.302  1.00 18.91      1BPT 193
ATOM     87  N   THR    11      28.424   0.231   5.434  1.00  6.57      1BPT 194
ATOM     88  CA  THR    11      27.936   0.236   6.812  1.00  8.79      1BPT 195
ATOM     89  C   THR    11      29.135   0.441   7.754  1.00 11.72      1BPT 196
ATOM     90  O   THR    11      29.083   1.299   8.664  1.00  8.91      1BPT 197
ATOM     91  CB  THR    11      27.128  -1.066   7.132  1.00  9.23      1BPT 198
ATOM     92  OG1 THR    11      25.915  -0.877   6.315  1.00 11.90      1BPT 199
ATOM     93  CG2 THR    11      26.632  -1.251   8.598  1.00  9.84      1BPT 200
ATOM     94  N   GLY    12      30.177  -0.374   7.495  1.00  7.42      1BPT 201
ATOM     95  CA  GLY    12      31.386  -0.224   8.306  1.00  5.96      1BPT 202
ATOM     96  C   GLY    12      31.203  -1.147   9.527  1.00 12.57      1BPT 203
ATOM     97  O   GLY    12      30.172  -1.792   9.683  1.00  8.90      1BPT 204
ATOM     98  N   PRO    13      32.259  -1.145  10.334  1.00  9.49      1BPT 205
ATOM     99  CA  PRO    13      32.384  -1.978  11.478  1.00 11.26      1BPT 206
ATOM    100  C   PRO    13      31.761  -1.570  12.787  1.00 10.42      1BPT 207
ATOM    101  O   PRO    13      31.739  -2.455  13.698  1.00  9.05      1BPT 208
ATOM    102  CB  PRO    13      33.930  -2.112  11.625  1.00 12.73      1BPT 209
ATOM    103  CG  PRO    13      34.418  -0.761  11.150  1.00 12.37      1BPT 210
ATOM    104  CD  PRO    13      33.504  -0.375  10.028  1.00  9.04      1BPT 211
ATOM    105  N   CYS    14      31.284  -0.361  12.916  1.00  9.07      1BPT 212
ATOM    106  CA  CYS    14      30.645   0.049  14.197  1.00 10.05      1BPT 213
ATOM    107  C   CYS    14      29.209  -0.417  14.208  1.00 13.02      1BPT 214
ATOM    108  O   CYS    14      28.598  -0.805  13.198  1.00 11.90      1BPT 215
ATOM    109  CB  CYS    14      30.904   1.510  14.446  1.00  7.60      1BPT 216
ATOM    110  SG  CYS    14      32.618   1.798  14.807  1.00 11.36      1BPT 217
ATOM    111  N   LYS    15      28.649  -0.419  15.375  1.00 15.92      1BPT 218
ATOM    112  CA  LYS    15      27.336  -0.923  15.756  1.00 15.34      1BPT 219
ATOM    113  C   LYS    15      26.228   0.042  16.097  1.00 15.21      1BPT 220
ATOM    114  O   LYS    15      25.303  -0.309  16.854  1.00 19.24      1BPT 221
ATOM    115  CB  LYS    15      27.580  -1.878  16.945  1.00 11.46      1BPT 222
ATOM    116  CG  LYS    15      27.956  -3.321  16.572  1.00 19.41      1BPT 223
ATOM    117  CD  LYS    15      29.204  -3.436  15.742  1.00 19.90      1BPT 224
ATOM    118  CE  LYS    15      29.694  -4.836  15.472  1.00 20.37      1BPT 225
ATOM    119  NZ  LYS    15      30.440  -5.364  16.680  1.00 25.63      1BPT 226
ATOM    120  N   ALA    16      26.223   1.260  15.569  1.00 11.74      1BPT 227
ATOM    121  CA  ALA    16      25.109   2.169  15.768  1.00  7.48      1BPT 228
ATOM    122  C   ALA    16      24.174   1.935  14.571  1.00  4.01      1BPT 229
ATOM    123  O   ALA    16      24.497   1.277  13.592  1.00  5.07      1BPT 230
ATOM    124  CB  ALA    16      25.536   3.634  15.859  1.00  5.63      1BPT 231
ATOM    125  N   ARG    17      22.998   2.500  14.683  1.00  8.74      1BPT 232
ATOM    126  CA  ARG    17      21.990   2.475  13.592  1.00 11.74      1BPT 233
ATOM    127  C   ARG    17      21.767   3.981  13.235  1.00  7.15      1BPT 234
ATOM    128  O   ARG    17      21.022   4.658  13.964  1.00 10.78      1BPT 235
ATOM    129  CB  ARG    17      20.614   1.926  13.959  1.00  6.42      1BPT 236
ATOM    130  CG  ARG    17      20.105   0.880  12.983  1.00 15.99      1BPT 237
ATOM    131  CD  ARG    17      19.624  -0.289  13.808  1.00  9.00      1BPT 238
ATOM    132  NE  ARG    17      18.355   0.098  14.439  1.00 18.94      1BPT 239
ATOM    133  CZ  ARG    17      17.708  -0.673  15.324  1.00 17.07      1BPT 240
ATOM    134  NH1 ARG    17      18.221  -1.843  15.720  1.00 10.96      1BPT 241
ATOM    135  NH2 ARG    17      16.495  -0.327  15.731  1.00 15.74      1BPT 242
ATOM    136  N   ILE    18      22.497   4.428  12.250  1.00  8.62      1BPT 243
ATOM    137  CA  ILE    18      22.423   5.788  11.715  1.00 10.26      1BPT 244
ATOM    138  C   ILE    18      21.950   5.730  10.266  1.00  9.38      1BPT 245
ATOM    139  O   ILE    18      22.480   5.004   9.421  1.00  8.61      1BPT 246
ATOM    140  CB  ILE    18      23.762   6.554  11.785  1.00 13.44      1BPT 247
ATOM    141  CG1 ILE    18      24.274   6.512  13.260  1.00 10.02      1BPT 248
ATOM    142  CG2 ILE    18      23.602   8.014  11.254  1.00 10.50      1BPT 249
ATOM    143  CD1 ILE    18      25.764   6.903  13.344  1.00 10.74      1BPT 250
ATOM    144  N   ILE    19      20.867   6.472  10.022  1.00 15.71      1BPT 251
ATOM    145  CA  ILE    19      20.335   6.459   8.640  1.00 13.86      1BPT 252
ATOM    146  C   ILE    19      20.970   7.606   7.855  1.00 13.32      1BPT 253
ATOM    147  O   ILE    19      20.910   8.763   8.262  1.00 11.39      1BPT 254
ATOM    148  CB  ILE    19      18.788   6.485   8.581  1.00 13.72      1BPT 255
ATOM    149  CG1 ILE    19      18.252   5.154   9.150  1.00  6.44      1BPT 256
ATOM    150  CG2 ILE    19      18.282   6.719   7.120  1.00 12.60      1BPT 257
ATOM    151  CD1 ILE    19      18.299   5.180  10.698  1.00 16.15      1BPT 258
ATOM    152  N   ARG    20      21.588   7.204   6.751  1.00 11.35      1BPT 259
ATOM    153  CA  ARG    20      22.236   8.068   5.785  1.00  9.74      1BPT 260
ATOM    154  C   ARG    20      21.695   7.783   4.382  1.00  6.30      1BPT 261
ATOM    155  O   ARG    20      20.944   6.791   4.218  1.00  9.59      1BPT 262
ATOM    156  CB  ARG    20      23.771   7.817   5.751  1.00  9.39      1BPT 263
ATOM    157  CG  ARG    20      24.296   7.949   7.188  1.00  2.00      1BPT 264
ATOM    158  CD  ARG    20      24.046   9.346   7.751  1.00 11.19      1BPT 265
ATOM    159  NE  ARG    20      25.357   9.939   7.653  1.00 16.42      1BPT 266
ATOM    160  CZ  ARG    20      26.326  10.113   8.491  1.00 17.82      1BPT 267
ATOM    161  NH1 ARG    20      26.238  10.069   9.811  1.00 20.52      1BPT 268
ATOM    162  NH2 ARG    20      27.584  10.026   7.945  1.00 11.96      1BPT 269
ATOM    163  N   TYR    21      22.153   8.566   3.449  1.00  3.50      1BPT 270
ATOM    164  CA  TYR    21      21.802   8.399   2.032  1.00  4.17      1BPT 271
ATOM    165  C   TYR    21      23.053   8.021   1.197  1.00  9.33      1BPT 272
ATOM    166  O   TYR    21      24.153   8.520   1.489  1.00  9.71      1BPT 273
ATOM    167  CB  TYR    21      21.233   9.689   1.363  1.00  2.47      1BPT 274
ATOM    168  CG  TYR    21      19.856   9.977   1.902  1.00  5.78      1BPT 275
ATOM    169  CD1 TYR    21      18.714   9.405   1.346  1.00  8.74      1BPT 276
ATOM    170  CD2 TYR    21      19.722  10.802   3.013  1.00  5.70      1BPT 277
ATOM    171  CE1 TYR    21      17.462   9.666   1.913  1.00  8.01      1BPT 278
ATOM    172  CE2 TYR    21      18.482  11.081   3.558  1.00 11.15      1BPT 279
ATOM    173  CZ  TYR    21      17.360  10.496   2.999  1.00  9.06      1BPT 280
ATOM    174  OH  TYR    21      16.131  10.758   3.524  1.00 17.41      1BPT 281
ATOM    175  N   PHE    22      22.829   7.168   0.207  1.00  4.91      1BPT 282
ATOM    176  CA  PHE    22      23.752   6.692  -0.783  1.00  4.40      1BPT 283
ATOM    177  C   PHE    22      23.022   6.846  -2.150  1.00  7.34      1BPT 284
ATOM    178  O   PHE    22      21.797   6.782  -2.278  1.00  6.82      1BPT 285
ATOM    179  CB  PHE    22      24.275   5.290  -0.661  1.00  2.00      1BPT 286
ATOM    180  CG  PHE    22      23.364   4.150  -0.996  1.00  5.18      1BPT 287
ATOM    181  CD1 PHE    22      22.275   3.834  -0.223  1.00  2.00      1BPT 288
ATOM    182  CD2 PHE    22      23.583   3.377  -2.136  1.00  5.44      1BPT 289
ATOM    183  CE1 PHE    22      21.466   2.719  -0.446  1.00  6.36      1BPT 290
ATOM    184  CE2 PHE    22      22.782   2.296  -2.447  1.00  5.66      1BPT 291
ATOM    185  CZ  PHE    22      21.709   1.949  -1.597  1.00 10.45      1BPT 292
ATOM    186  N   ALA    23      23.845   7.069  -3.162  1.00  9.17      1BPT 293
ATOM    187  CA  ALA    23      23.410   7.217  -4.539  1.00  7.19      1BPT 294
ATOM    188  C   ALA    23      23.463   5.773  -5.115  1.00  9.37      1BPT 295
ATOM    189  O   ALA    23      24.506   5.134  -4.936  1.00  8.29      1BPT 296
ATOM    190  CB  ALA    23      24.352   8.087  -5.360  1.00  4.05      1BPT 297
ATOM    191  N   ASN    24      22.400   5.354  -5.693  1.00  7.55      1BPT 298
ATOM    192  CA  ASN    24      22.126   4.088  -6.326  1.00 15.15      1BPT 299
ATOM    193  C   ASN    24      22.120   4.301  -7.848  1.00 14.72      1BPT 300
ATOM    194  O   ASN    24      21.083   4.569  -8.463  1.00 22.72      1BPT 301
ATOM    195  CB  ASN    24      20.788   3.517  -5.804  1.00 19.37      1BPT 302
ATOM    196  CG  ASN    24      20.802   1.994  -5.932  1.00 26.23      1BPT 303
ATOM    197  OD1 ASN    24      21.039   1.448  -7.013  1.00 21.38      1BPT 304
ATOM    198  ND2 ASN    24      20.644   1.338  -4.770  1.00 31.83      1BPT 305
ATOM    199  N   ALA    25      23.301   4.247  -8.411  1.00 17.58      1BPT 306
ATOM    200  CA  ALA    25      23.706   4.425  -9.774  1.00 17.08      1BPT 307
ATOM    201  C   ALA    25      22.839   3.573 -10.736  1.00 21.07      1BPT 308
ATOM    202  O   ALA    25      22.702   3.982 -11.887  1.00 16.65      1BPT 309
ATOM    203  CB  ALA    25      25.187   4.093  -9.933  1.00 11.69      1BPT 310
ATOM    204  N   LYS    26      22.312   2.473 -10.242  1.00 19.28      1BPT 311
ATOM    205  CA  LYS    26      21.466   1.487 -10.891  1.00 22.03      1BPT 312
ATOM    206  C   LYS    26      20.014   1.952 -10.989  1.00 24.09      1BPT 313
ATOM    207  O   LYS    26      19.442   1.857 -12.084  1.00 23.97      1BPT 314
ATOM    208  CB  LYS    26      21.491   0.169 -10.130  1.00 22.95      1BPT 315
ATOM    209  CG  LYS    26      21.106  -1.100 -10.859  1.00 28.77      1BPT 316
ATOM    210  CD  LYS    26      22.013  -1.383 -12.055  1.00 29.92      1BPT 317
ATOM    211  CE  LYS    26      22.610  -2.772 -11.994  1.00 25.89      1BPT 318
ATOM    212  NZ  LYS    26      23.796  -2.860 -12.900  1.00 25.18      1BPT 319
ATOM    213  N   ALA    27      19.497   2.488  -9.874  1.00 22.92      1BPT 320
ATOM    214  CA  ALA    27      18.103   2.961  -9.823  1.00 19.83      1BPT 321
ATOM    215  C   ALA    27      17.967   4.434 -10.123  1.00 20.29      1BPT 322
ATOM    216  O   ALA    27      16.824   4.929 -10.240  1.00 23.87      1BPT 323
ATOM    217  CB  ALA    27      17.441   2.549  -8.518  1.00 16.72      1BPT 324
ATOM    218  N   GLY    28      19.057   5.153 -10.273  1.00 16.11      1BPT 325
ATOM    219  CA  GLY    28      19.062   6.550 -10.586  1.00 17.38      1BPT 326
ATOM    220  C   GLY    28      18.483   7.415  -9.466  1.00 18.84      1BPT 327
ATOM    221  O   GLY    28      18.119   8.579  -9.690  1.00 16.95      1BPT 328
ATOM    222  N   LEU    29      18.443   6.832  -8.287  1.00 21.25      1BPT 329
ATOM    223  CA  LEU    29      17.947   7.407  -7.024  1.00 21.57      1BPT 330
ATOM    224  C   LEU    29      18.945   7.497  -5.866  1.00 18.12      1BPT 331
ATOM    225  O   LEU    29      19.896   6.727  -5.858  1.00 21.34      1BPT 332
ATOM    226  CB  LEU    29      17.024   6.228  -6.528  1.00 23.29      1BPT 333
ATOM    227  CG  LEU    29      15.567   6.158  -6.693  1.00 19.66      1BPT 334
ATOM    228  CD1 LEU    29      15.044   6.893  -7.909  1.00 21.45      1BPT 335
ATOM    229  CD2 LEU    29      15.225   4.662  -6.813  1.00 20.64      1BPT 336
ATOM    230  N   CYS    30      18.644   8.243  -4.834  1.00 15.30      1BPT 337
ATOM    231  CA  CYS    30      19.386   8.332  -3.584  1.00 13.07      1BPT 338
ATOM    232  C   CYS    30      18.461   7.549  -2.587  1.00 11.85      1BPT 339
ATOM    233  O   CYS    30      17.266   7.847  -2.545  1.00  9.49      1BPT 340
ATOM    234  CB  CYS    30      19.618   9.746  -3.030  1.00  7.99      1BPT 341
ATOM    235  SG  CYS    30      20.895  10.605  -3.992  1.00 11.01      1BPT 342
ATOM    236  N   GLN    31      19.006   6.552  -1.970  1.00  8.48      1BPT 343
ATOM    237  CA  GLN    31      18.317   5.700  -1.038  1.00  6.54      1BPT 344
ATOM    238  C   GLN    31      19.100   5.705   0.281  1.00  5.06      1BPT 345
ATOM    239  O   GLN    31      20.258   6.027   0.325  1.00 10.97      1BPT 346
ATOM    240  CB  GLN    31      18.127   4.265  -1.486  1.00  6.08      1BPT 347
ATOM    241  CG  GLN    31      17.649   4.129  -2.917  1.00 10.54      1BPT 348
ATOM    242  CD  GLN    31      17.592   2.652  -3.291  1.00 15.80      1BPT 349
ATOM    243  OE1 GLN    31      18.591   1.933  -3.214  1.00 13.15      1BPT 350
ATOM    244  NE2 GLN    31      16.345   2.282  -3.638  1.00 16.64      1BPT 351
ATOM    245  N   THR    32      18.377   5.323   1.264  1.00  6.87      1BPT 352
ATOM    246  CA  THR    32      18.655   5.165   2.680  1.00  7.62      1BPT 353
ATOM    247  C   THR    32      19.331   3.843   2.925  1.00  4.54      1BPT 354
ATOM    248  O   THR    32      19.028   2.743   2.403  1.00  9.34      1BPT 355
ATOM    249  CB  THR    32      17.212   5.330   3.366  1.00 11.68      1BPT 356
ATOM    250  OG1 THR    32      17.146   6.586   4.121  1.00 16.76      1BPT 357
ATOM    251  CG2 THR    32      16.592   4.169   4.025  1.00 11.13      1BPT 358
ATOM    252  N   PHE    33      20.325   3.905   3.792  1.00  6.01      1BPT 359
ATOM    253  CA  PHE    33      21.049   2.679   4.214  1.00  5.51      1BPT 360
ATOM    254  C   PHE    33      21.391   2.964   5.697  1.00  5.03      1BPT 361
ATOM    255  O   PHE    33      21.307   4.127   6.134  1.00  2.00      1BPT 362
ATOM    256  CB  PHE    33      22.237   2.311   3.301  1.00  6.21      1BPT 363
ATOM    257  CG  PHE    33      23.481   3.115   3.586  1.00  7.37      1BPT 364
ATOM    258  CD1 PHE    33      23.551   4.451   3.178  1.00  3.42      1BPT 365
ATOM    259  CD2 PHE    33      24.548   2.490   4.242  1.00  5.10      1BPT 366
ATOM    260  CE1 PHE    33      24.689   5.209   3.481  1.00  4.87      1BPT 367
ATOM    261  CE2 PHE    33      25.680   3.270   4.545  1.00  3.64      1BPT 368
ATOM    262  CZ  PHE    33      25.736   4.604   4.188  1.00  4.11      1BPT 369
ATOM    263  N   VAL    34      21.791   1.844   6.303  1.00  7.77      1BPT 370
ATOM    264  CA  VAL    34      22.179   1.847   7.727  1.00  7.30      1BPT 371
ATOM    265  C   VAL    34      23.698   2.016   7.870  1.00  5.82      1BPT 372
ATOM    266  O   VAL    34      24.383   1.128   7.464  1.00  7.30      1BPT 373
ATOM    267  CB  VAL    34      21.710   0.602   8.491  1.00 12.10      1BPT 374
ATOM    268  CG1 VAL    34      22.162   0.650   9.973  1.00  9.39      1BPT 375
ATOM    269  CG2 VAL    34      20.174   0.525   8.409  1.00 15.65      1BPT 376
ATOM    270  N   TYR    35      24.091   3.158   8.410  1.00  5.38      1BPT 377
ATOM    271  CA  TYR    35      25.512   3.474   8.630  1.00  4.86      1BPT 378
ATOM    272  C   TYR    35      25.853   3.141  10.089  1.00  6.21      1BPT 379
ATOM    273  O   TYR    35      25.096   3.564  11.002  1.00  5.98      1BPT 380
ATOM    274  CB  TYR    35      25.736   4.938   8.236  1.00  5.98      1BPT 381
ATOM    275  CG  TYR    35      27.123   5.423   8.667  1.00  8.66      1BPT 382
ATOM    276  CD1 TYR    35      28.268   4.755   8.295  1.00  5.52      1BPT 383
ATOM    277  CD2 TYR    35      27.254   6.531   9.488  1.00  5.03      1BPT 384
ATOM    278  CE1 TYR    35      29.512   5.168   8.668  1.00  4.71      1BPT 385
ATOM    279  CE2 TYR    35      28.510   6.966   9.884  1.00  5.81      1BPT 386
ATOM    280  CZ  TYR    35      29.623   6.289   9.481  1.00  3.57      1BPT 387
ATOM    281  OH  TYR    35      30.830   6.742   9.901  1.00 13.53      1BPT 388
ATOM    282  N   GLY    36      26.877   2.383  10.299  1.00  9.83      1BPT 389
ATOM    283  CA  GLY    36      27.457   1.871  11.546  1.00 11.89      1BPT 390
ATOM    284  C   GLY    36      28.028   2.897  12.527  1.00 10.62      1BPT 391
ATOM    285  O   GLY    36      28.257   2.623  13.728  1.00  6.24      1BPT 392
ATOM    286  N   GLY    37      28.306   4.113  12.087  1.00 10.90      1BPT 393
ATOM    287  CA  GLY    37      28.806   5.132  13.062  1.00  8.57      1BPT 394
ATOM    288  C   GLY    37      30.264   5.436  12.901  1.00 11.39      1BPT 395
ATOM    289  O   GLY    37      30.788   6.346  13.587  1.00 12.05      1BPT 396
ATOM    290  N   CYS    38      30.958   4.608  12.100  1.00 11.97      1BPT 397
ATOM    291  CA  CYS    38      32.402   4.846  11.895  1.00 10.71      1BPT 398
ATOM    292  C   CYS    38      32.879   4.309  10.558  1.00  7.26      1BPT 399
ATOM    293  O   CYS    38      32.377   3.284  10.069  1.00 10.85      1BPT 400
ATOM    294  CB  CYS    38      33.254   4.254  13.025  1.00  5.40      1BPT 401
ATOM    295  SG  CYS    38      33.463   2.472  13.064  1.00 11.31      1BPT 402
ATOM    296  N   ARG    39      33.888   5.024  10.044  1.00  7.90      1BPT 403
ATOM    297  CA  ARG    39      34.612   4.645   8.827  1.00  9.16      1BPT 404
ATOM    298  C   ARG    39      33.852   4.820   7.536  1.00  5.75      1BPT 405
ATOM    299  O   ARG    39      33.993   4.050   6.590  1.00  7.37      1BPT 406
ATOM    300  CB  ARG    39      35.284   3.233   8.942  1.00 13.97      1BPT 407
ATOM    301  CG  ARG    39      36.652   3.311   9.588  1.00 23.19      1BPT 408
ATOM    302  CD  ARG    39      37.108   2.346  10.584  1.00 26.99      1BPT 409
ATOM    303  NE  ARG    39      37.383   1.012  10.071  1.00 34.96      1BPT 410
ATOM    304  CZ  ARG    39      38.017   0.015  10.712  1.00 34.64      1BPT 411
ATOM    305  NH1 ARG    39      38.490   0.185  11.953  1.00 32.55      1BPT 412
ATOM    306  NH2 ARG    39      38.178  -1.162  10.082  1.00 31.33      1BPT 413
ATOM    307  N   ALA    40      33.087   5.902   7.525  1.00  6.82      1BPT 414
ATOM    308  CA  ALA    40      32.280   6.346   6.408  1.00  6.05      1BPT 415
ATOM    309  C   ALA    40      33.174   6.463   5.167  1.00 10.08      1BPT 416
ATOM    310  O   ALA    40      34.349   6.857   5.267  1.00  9.96      1BPT 417
ATOM    311  CB  ALA    40      31.763   7.754   6.764  1.00  2.00      1BPT 418
ATOM    312  N   LYS    41      32.572   6.106   4.046  1.00  8.14      1BPT 419
ATOM    313  CA  LYS    41      33.210   6.218   2.716  1.00  6.07      1BPT 420
ATOM    314  C   LYS    41      32.548   7.399   2.044  1.00 12.83      1BPT 421
ATOM    315  O   LYS    41      31.646   8.090   2.693  1.00 10.68      1BPT 422
ATOM    316  CB  LYS    41      33.223   4.867   2.018  1.00 10.37      1BPT 423
ATOM    317  CG  LYS    41      34.398   4.021   2.455  1.00 16.66      1BPT 424
ATOM    318  CD  LYS    41      34.882   2.814   1.760  1.00 24.01      1BPT 425
ATOM    319  CE  LYS    41      35.299   2.810   0.338  1.00 30.41      1BPT 426
ATOM    320  NZ  LYS    41      36.465   3.643  -0.102  1.00 35.07      1BPT 427
ATOM    321  N   ARG    42      32.884   7.785   0.815  1.00 10.98      1BPT 428
ATOM    322  CA  ARG    42      32.283   8.966   0.211  1.00  9.54      1BPT 429
ATOM    323  C   ARG    42      30.805   8.864  -0.204  1.00  6.66      1BPT 430
ATOM    324  O   ARG    42      30.082   9.903  -0.070  1.00  3.97      1BPT 431
ATOM    325  CB  ARG    42      33.012   9.583  -0.935  1.00 15.86      1BPT 432
ATOM    326  CG  ARG    42      34.425  10.106  -0.842  1.00 20.34      1BPT 433
ATOM    327  CD  ARG    42      35.312   9.161  -1.625  1.00 22.25      1BPT 434
ATOM    328  NE  ARG    42      36.086   9.790  -2.633  1.00 21.50      1BPT 435
ATOM    329  CZ  ARG    42      36.767   9.117  -3.589  1.00 27.18      1BPT 436
ATOM    330  NH1 ARG    42      36.779   7.793  -3.734  1.00 24.88      1BPT 437
ATOM    331  NH2 ARG    42      37.511   9.871  -4.403  1.00 23.05      1BPT 438
ATOM    332  N   ASN    43      30.347   7.774  -0.685  1.00  4.96      1BPT 439
ATOM    333  CA  ASN    43      28.913   7.618  -1.084  1.00  5.93      1BPT 440
ATOM    334  C   ASN    43      28.074   7.439   0.214  1.00  6.01      1BPT 441
ATOM    335  O   ASN    43      27.554   6.351   0.508  1.00  5.41      1BPT 442
ATOM    336  CB  ASN    43      28.824   6.464  -2.040  1.00  2.00      1BPT 443
ATOM    337  CG  ASN    43      27.504   6.530  -2.797  1.00  3.64      1BPT 444
ATOM    338  OD1 ASN    43      26.760   7.532  -2.643  1.00  2.67      1BPT 445
ATOM    339  ND2 ASN    43      27.301   5.537  -3.633  1.00  4.58      1BPT 446
ATOM    340  N   ASN    44      27.999   8.522   0.982  1.00  9.31      1BPT 447
ATOM    341  CA  ASN    44      27.314   8.619   2.297  1.00  2.00      1BPT 448
ATOM    342  C   ASN    44      26.927  10.073   2.517  1.00  4.30      1BPT 449
ATOM    343  O   ASN    44      27.772  10.923   2.793  1.00  4.82      1BPT 450
ATOM    344  CB  ASN    44      28.276   8.091   3.338  1.00  8.38      1BPT 451
ATOM    345  CG  ASN    44      27.789   8.066   4.782  1.00  2.00      1BPT 452
ATOM    346  OD1 ASN    44      28.115   7.107   5.498  1.00  3.04      1BPT 453
ATOM    347  ND2 ASN    44      27.094   9.111   5.123  1.00  7.22      1BPT 454
ATOM    348  N   PHE    45      25.640  10.394   2.440  1.00  6.11      1BPT 455
ATOM    349  CA  PHE    45      25.077  11.713   2.604  1.00  6.35      1BPT 456
ATOM    350  C   PHE    45      24.138  11.761   3.822  1.00  5.91      1BPT 457
ATOM    351  O   PHE    45      23.569  10.743   4.220  1.00  7.40      1BPT 458
ATOM    352  CB  PHE    45      24.338  12.182   1.306  1.00  6.75      1BPT 459
ATOM    353  CG  PHE    45      25.243  12.109   0.104  1.00  8.57      1BPT 460
ATOM    354  CD1 PHE    45      26.165  13.134  -0.110  1.00  4.49      1BPT 461
ATOM    355  CD2 PHE    45      25.243  10.988  -0.731  1.00  7.57      1BPT 462
ATOM    356  CE1 PHE    45      27.037  13.057  -1.206  1.00  5.81      1BPT 463
ATOM    357  CE2 PHE    45      26.116  10.886  -1.828  1.00  6.32      1BPT 464
ATOM    358  CZ  PHE    45      27.017  11.915  -2.031  1.00  5.88      1BPT 465
ATOM    359  N   LYS    46      24.017  12.955   4.372  1.00  5.18      1BPT 466
ATOM    360  CA  LYS    46      23.137  13.170   5.515  1.00  7.22      1BPT 467
ATOM    361  C   LYS    46      21.747  13.494   5.037  1.00  8.50      1BPT 468
ATOM    362  O   LYS    46      20.775  13.277   5.777  1.00  8.81      1BPT 469
ATOM    363  CB  LYS    46      23.719  14.097   6.569  1.00 17.67      1BPT 470
ATOM    364  CG  LYS    46      24.807  13.401   7.450  1.00 17.14      1BPT 471
ATOM    365  CD  LYS    46      25.667  14.430   8.162  1.00 22.39      1BPT 472
ATOM    366  CE  LYS    46      26.849  13.763   8.823  1.00 33.75      1BPT 473
ATOM    367  NZ  LYS    46      27.771  13.182   7.778  1.00 39.51      1BPT 474
ATOM    368  N   SER    47      21.567  13.946   3.793  1.00  6.62      1BPT 475
ATOM    369  CA  SER    47      20.237  14.215   3.241  1.00  7.92      1BPT 476
ATOM    370  C   SER    47      20.291  13.788   1.753  1.00  9.35      1BPT 477
ATOM    371  O   SER    47      21.389  13.808   1.198  1.00  6.05      1BPT 478
ATOM    372  CB  SER    47      19.755  15.634   3.248  1.00  8.12      1BPT 479
ATOM    373  OG  SER    47      20.635  16.520   2.615  1.00 10.87      1BPT 480
ATOM    374  N   ALA    48      19.110  13.576   1.248  1.00 13.39      1BPT 481
ATOM    375  CA  ALA    48      18.819  13.216  -0.137  1.00 14.31      1BPT 482
ATOM    376  C   ALA    48      19.222  14.327  -1.097  1.00  9.87      1BPT 483
ATOM    377  O   ALA    48      19.693  14.049  -2.219  1.00 10.59      1BPT 484
ATOM    378  CB  ALA    48      17.317  12.910  -0.257  1.00 14.70      1BPT 485
ATOM    379  N   GLU    49      19.096  15.564  -0.717  1.00 12.65      1BPT 486
ATOM    380  CA  GLU    49      19.425  16.790  -1.459  1.00 16.19      1BPT 487
ATOM    381  C   GLU    49      20.919  16.933  -1.769  1.00 13.71      1BPT 488
ATOM    382  O   GLU    49      21.385  17.262  -2.881  1.00 12.61      1BPT 489
ATOM    383  CB  GLU    49      18.987  18.000  -0.638  1.00 24.93      1BPT 490
ATOM    384  CG  GLU    49      19.603  19.360  -0.977  1.00 32.70      1BPT 491
ATOM    385  CD  GLU    49      18.593  20.478  -0.869  1.00 33.74      1BPT 492
ATOM    386  OE1 GLU    49      17.501  20.301  -0.357  1.00 37.68      1BPT 493
ATOM    387  OE2 GLU    49      19.011  21.524  -1.382  1.00 40.58      1BPT 494
ATOM    388  N   ASP    50      21.678  16.685  -0.752  1.00  8.77      1BPT 495
ATOM    389  CA  ASP    50      23.154  16.618  -0.749  1.00  5.33      1BPT 496
ATOM    390  C   ASP    50      23.557  15.495  -1.741  1.00  7.91      1BPT 497
ATOM    391  O   ASP    50      24.418  15.687  -2.574  1.00 10.59      1BPT 498
ATOM    392  CB  ASP    50      23.469  16.208   0.652  1.00  7.72      1BPT 499
ATOM    393  CG  ASP    50      24.677  16.768   1.310  1.00 22.77      1BPT 500
ATOM    394  OD1 ASP    50      25.784  16.205   1.218  1.00 29.45      1BPT 501
ATOM    395  OD2 ASP    50      24.437  17.805   1.976  1.00 27.42      1BPT 502
ATOM    396  N   CYS    51      22.889  14.372  -1.606  1.00  7.15      1BPT 503
ATOM    397  CA  CYS    51      23.118  13.191  -2.471  1.00  9.78      1BPT 504
ATOM    398  C   CYS    51      22.817  13.463  -3.927  1.00 10.99      1BPT 505
ATOM    399  O   CYS    51      23.624  13.202  -4.878  1.00 10.34      1BPT 506
ATOM    400  CB  CYS    51      22.338  12.044  -1.832  1.00  7.72      1BPT 507
ATOM    401  SG  CYS    51      22.556  10.517  -2.797  1.00  9.28      1BPT 508
ATOM    402  N   MET    52      21.658  14.043  -4.168  1.00 11.69      1BPT 509
ATOM    403  CA  MET    52      21.202  14.431  -5.526  1.00 18.65      1BPT 510
ATOM    404  C   MET    52      22.077  15.525  -6.147  1.00 19.65      1BPT 511
ATOM    405  O   MET    52      22.331  15.528  -7.377  1.00 21.47      1BPT 512
ATOM    406  CB  MET    52      19.733  14.888  -5.520  1.00 18.64      1BPT 513
ATOM    407  CG  MET    52      18.820  13.802  -5.029  1.00 25.08      1BPT 514
ATOM    408  SD  MET    52      18.593  12.518  -6.298  1.00 36.21      1BPT 515
ATOM    409  CE  MET    52      17.140  13.185  -7.164  1.00 31.81      1BPT 516
ATOM    410  N   ARG    53      22.488  16.491  -5.340  1.00 15.68      1BPT 517
ATOM    411  CA  ARG    53      23.357  17.550  -5.895  1.00 14.21      1BPT 518
ATOM    412  C   ARG    53      24.665  16.936  -6.309  1.00 16.12      1BPT 519
ATOM    413  O   ARG    53      25.128  17.198  -7.444  1.00 20.73      1BPT 520
ATOM    414  CB  ARG    53      23.476  18.743  -4.963  1.00 18.66      1BPT 521
ATOM    415  CG  ARG    53      24.712  19.585  -4.904  1.00 20.71      1BPT 522
ATOM    416  CD  ARG    53      24.526  20.881  -4.194  1.00 20.48      1BPT 523
ATOM    417  NE  ARG    53      24.137  20.759  -2.782  1.00 23.67      1BPT 524
ATOM    418  CZ  ARG    53      22.949  21.116  -2.283  1.00 19.89      1BPT 525
ATOM    419  NH1 ARG    53      21.956  21.580  -3.045  1.00 21.51      1BPT 526
ATOM    420  NH2 ARG    53      22.797  21.076  -0.984  1.00 19.67      1BPT 527
ATOM    421  N   THR    54      25.282  16.106  -5.486  1.00 15.94      1BPT 528
ATOM    422  CA  THR    54      26.565  15.457  -5.745  1.00 15.33      1BPT 529
ATOM    423  C   THR    54      26.567  14.390  -6.831  1.00 14.34      1BPT 530
ATOM    424  O   THR    54      27.430  14.320  -7.727  1.00 15.03      1BPT 531
ATOM    425  CB  THR    54      27.103  14.813  -4.378  1.00 15.64      1BPT 532
ATOM    426  OG1 THR    54      26.939  15.842  -3.350  1.00 14.11      1BPT 533
ATOM    427  CG2 THR    54      28.533  14.325  -4.493  1.00 13.03      1BPT 534
ATOM    428  N   CYS    55      25.605  13.478  -6.742  1.00 14.03      1BPT 535
ATOM    429  CA  CYS    55      25.487  12.381  -7.678  1.00 18.90      1BPT 536
ATOM    430  C   CYS    55      24.327  12.243  -8.624  1.00 14.94      1BPT 537
ATOM    431  O   CYS    55      24.416  11.321  -9.464  1.00 17.17      1BPT 538
ATOM    432  CB  CYS    55      25.558  11.073  -6.799  1.00 13.60      1BPT 539
ATOM    433  SG  CYS    55      27.108  10.842  -5.962  1.00 11.32      1BPT 540
ATOM    434  N   GLY    56      23.250  12.959  -8.573  1.00 21.33      1BPT 541
ATOM    435  CA  GLY    56      22.055  12.828  -9.404  1.00 21.71      1BPT 542
ATOM    436  C   GLY    56      22.203  13.318 -10.815  1.00 29.25      1BPT 543
ATOM    437  O   GLY    56      22.062  14.551 -11.007  1.00 36.32      1BPT 544
TER     438      GLY    56                                              1BPT 545
HETATM  439  P   PO4    70      30.706  10.577  10.314  1.00 40.72      1BPT 546
HETATM  440  O1  PO4    70      31.880  11.494  10.318  1.00 40.10      1BPT 547
HETATM  441  O2  PO4    70      29.700  11.094  11.269  1.00 36.93      1BPT 548
HETATM  442  O3  PO4    70      30.132  10.507   8.949  1.00 36.50      1BPT 549
HETATM  443  O4  PO4    70      31.190   9.240  10.783  1.00 33.43      1BPT 550
HETATM  444  O   HOH    80      20.819  13.100   8.431  1.00 24.07      1BPT 551
HETATM  445  O   HOH   102      30.510   0.396  17.550  1.00 19.35      1BPT 552
HETATM  446  O   HOH   110      35.009   6.459  -0.855  1.00 12.67      1BPT 553
HETATM  447  O   HOH   111      30.611   3.654  -0.155  1.00 13.18      1BPT 554
HETATM  448  O   HOH   112      28.828   4.406   1.730  1.00  8.47      1BPT 555
HETATM  449  O   HOH   113      29.841   4.909   4.406  1.00  7.19      1BPT 556
HETATM  450  O   HOH   117      21.848  -0.746   5.060  1.00 16.62      1BPT 557
HETATM  451  O   HOH   119      21.823   5.979 -12.630  1.00 24.84      1BPT 558
HETATM  452  O   HOH   122      30.511   1.654  10.647  1.00  7.89      1BPT 559
HETATM  453  O   HOH   138      25.621  15.094   3.493  1.00 23.48      1BPT 560
HETATM  454  O   HOH   143      26.160   3.139  -5.420  1.00 34.25      1BPT 561
HETATM  455  O   HOH   145      33.316   1.413  18.097  1.00 25.90      1BPT 562
HETATM  456  O   HOH   159      28.583  -2.632   3.791  1.00 39.81      1BPT 563
HETATM  457  O   HOH   160      33.706   3.567  -8.762  1.00 24.53      1BPT 564
HETATM  458  O   HOH   200      14.641   3.645 -11.171  1.00 43.15      1BPT 565
HETATM  459  O   HOH   203      36.110   7.939   7.187  1.00 26.10      1BPT 566
HETATM  460  O   HOH   204      37.573   6.383   4.119  1.00 34.45      1BPT 567
HETATM  461  O   HOH   205      17.114   1.480   5.071  1.00 25.78      1BPT 568
HETATM  462  O   HOH   210      29.293  -0.141  -8.753  1.00 31.97      1BPT 569
HETATM  463  O   HOH   220      38.003  -0.043   7.446  1.00 39.37      1BPT 570
HETATM  464  O   HOH   310      27.894  18.497  -3.763  1.00 43.65      1BPT 571
HETATM  465  O   HOH   400      21.958   7.437  -8.430  1.00 19.20      1BPT 572
HETATM  466  O   HOH   401      31.962   7.677 -12.750  1.00 38.68      1BPT 573
HETATM  467  O   HOH   402      17.664   6.716 -13.231  1.00 33.38      1BPT 574
HETATM  468  O   HOH   403      13.919   2.897  -4.054  1.00 16.38      1BPT 575
HETATM  469  O   HOH   404      21.409  17.309  -9.673  1.00 36.53      1BPT 576
HETATM  470  O   HOH   405      13.834   0.430  16.064  1.00 32.73      1BPT 577
HETATM  471  O   HOH   406      28.339  15.647 -11.514  1.00 41.64      1BPT 578
HETATM  472  O   HOH   407      15.124   9.979  -1.705  1.00 32.62      1BPT 579
HETATM  473  O   HOH   408      15.714   0.107  18.383  1.00 27.81      1BPT 580
HETATM  474  O   HOH   409      28.278  14.368 -14.656  1.00 28.15      1BPT 581
HETATM  475  O   HOH   410      15.105   5.054   0.515  1.00 23.38      1BPT 582
HETATM  476  O   HOH   411      23.761  -2.671   7.342  1.00 35.33      1BPT 583
HETATM  477  O   HOH   412      32.010  -0.303  -0.690  1.00 43.06      1BPT 584
HETATM  478  O   HOH   413      25.967  19.801  -1.055  1.00 37.89      1BPT 585
HETATM  479  O   HOH   414      35.741   2.717  -2.480  1.00 39.48      1BPT 586
HETATM  480  O   HOH   415      22.383  20.755   1.804  1.00 31.50      1BPT 587
HETATM  481  O   HOH   416      26.289  11.963 -15.860  1.00 40.37      1BPT 588
HETATM  482  O   HOH   417      28.681  15.680  -0.316  1.00 48.97      1BPT 589
HETATM  483  O   HOH   418      28.804  19.336  -6.207  1.00 36.73      1BPT 590
CONECT   43   42  433                                                   1BPT 591
CONECT  110  109  295                                                   1BPT 592
CONECT  235  234  401                                                   1BPT 593
CONECT  295  110  294                                                   1BPT 594
CONECT  401  235  400                                                   1BPT 595
CONECT  433   43  432                                                   1BPT 596
CONECT  439  440  441  442  443                                         1BPT 597
CONECT  440  439                                                        1BPT 598
CONECT  441  439                                                        1BPT 599
CONECT  442  439                                                        1BPT 600
CONECT  443  439                                                        1BPT 601
MASTER       71    0    1    2    3    0    0    6  482    1   11    5  1BPT 602
END                                                                     1BPT 603
BioPerl-1.007002/t/data/1ZZ19XR301R-Alignment.tblastn000555000766000024    743324413155576321 21717 0ustar00cjfieldsstaff000000000000TBLASTN 2.2.20+
Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro
A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and
David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new
generation of protein database search programs", Nucleic
Acids Res. 25:3389-3402.


RID: 1ZZ19XR301R


Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
           8,818,151 sequences; 27,400,875,368 total letters
Query= gi|5032311|ref|NP_004013.1| dystrophin Dp140ab isoform [Homo sapiens]
Length=1230


                                                                   Score     E
Sequences producing significant alignments:                       (Bits)  Value

ref|NM_004022.2|  Homo sapiens dystrophin (DMD), transcript va...  2544    0.0   
dbj|AB208836.1|  Homo sapiens mRNA for dystrophin Dp427c isofo...  2538    0.0   
ref|NM_004021.2|  Homo sapiens dystrophin (DMD), transcript va...  2534    0.0   
gb|BC150141.1|  Homo sapiens dystrophin, mRNA (cDNA clone IMAG...  2531    0.0   
ref|NM_004010.3|  Homo sapiens dystrophin (DMD), transcript va...  2486    0.0   
ref|NM_004009.3|  Homo sapiens dystrophin (DMD), transcript va...  2486    0.0   
ref|NM_004007.2|  Homo sapiens dystrophin (DMD), transcript va...  2486    0.0   
ref|NM_004006.2|  Homo sapiens dystrophin (DMD), transcript va...  2486    0.0   
ref|NM_000109.3|  Homo sapiens dystrophin (DMD), transcript va...  2486    0.0   
gb|EU048698.1|  Shuttle vector phcAd.DYS-FL, complete sequence     2486    0.0   
gb|M18533.1|HUMDYS  Homo sapiens dystrophin (DMD) mRNA, comple...  2486    0.0   
emb|X14298.1|  Human mRNA for dystrophin                           2486    0.0   
gb|BC111836.3|  Synthetic construct Homo sapiens clone IMAGE:4...  2485    0.0   
gb|BC118002.1|  Synthetic construct Homo sapiens clone IMAGE:4...  2485    0.0   
gb|BC111934.1|  Synthetic construct Homo sapiens clone IMAGE:4...  2485    0.0   
gb|BC111587.2|  Synthetic construct Homo sapiens clone IMAGE:4...  2485    0.0   
ref|NM_004012.3|  Homo sapiens dystrophin (DMD), transcript va...  2484    0.0   
ref|NM_004011.3|  Homo sapiens dystrophin (DMD), transcript va...  2484    0.0   
ref|NM_004013.2|  Homo sapiens dystrophin (DMD), transcript va...  2469    0.0   
gb|BC127103.1|  Homo sapiens dystrophin, mRNA (cDNA clone IMAG...  2467    0.0   
ref|XR_022800.1|  PREDICTED: Pan troglodytes dystrophin (DMD),...  2450    0.0   
ref|XM_850502.1|  PREDICTED: Canis familiaris hypothetical pro...  2449    0.0   
emb|AJ865385.1|  Sus scrofa mRNA for dystrophin variant Dp427 ...  2447    0.0   
ref|XM_001488124.2|  PREDICTED: Equus caballus similar to dyst...  2443    0.0   
gb|AF070485.1|  Canis familiaris dystrophin mRNA, complete cds     2429    0.0   
ref|NM_007868.5|  Mus musculus dystrophin, muscular dystrophy ...  2414    0.0   
gb|M68859.1|MUSDYSA  Mouse dystrophin mRNA, complete cds           2414    0.0   
ref|XM_001379309.1|  PREDICTED: Monodelphis domestica similar ...  2325    0.0   
emb|X13369.1|  Chicken mRNA for dystrophin (Duchenne muscular ...  2182    0.0   
ref|XM_002191629.1|  PREDICTED: Taeniopygia guttata dystrophin...  2078    0.0   
ref|NM_004023.2|  Homo sapiens dystrophin (DMD), transcript va...  1975    0.0   
ref|NM_004020.2|  Homo sapiens dystrophin (DMD), transcript va...  1955    0.0   
ref|NM_004014.2|  Homo sapiens dystrophin (DMD), transcript va...  1905    0.0   
ref|XM_001096400.1|  PREDICTED: Macaca mulatta similar to dyst...  1707    0.0   
gb|AF339031.1|AF339031  Danio rerio dystrophin (dmd) mRNA, par...  1583    0.0   
gb|BC085236.1|  Mus musculus dystrophin, muscular dystrophy, m...  1519    0.0   
ref|XM_419648.2|  PREDICTED: Gallus gallus utrophin (homologou...  1508    0.0   
ref|XM_518782.2|  PREDICTED: Pan troglodytes utrophin, transcr...  1498    0.0   
ref|XM_001172875.1|  PREDICTED: Pan troglodytes utrophin, tran...  1498    0.0   
ref|XM_001172869.1|  PREDICTED: Pan troglodytes utrophin, tran...  1498    0.0   
ref|XM_001506948.1|  PREDICTED: Ornithorhynchus anatinus simil...  1495    0.0   
gb|M37645.1|FSCDYSTRO  Torpedo californica dystrophin mRNA, 3'...  1493    0.0   
ref|XR_054516.1|  PREDICTED: Taeniopygia guttata misc_RNA (LOC...  1491    0.0   
ref|XM_001380994.1|  PREDICTED: Monodelphis domestica similar ...  1481    0.0   
ref|NM_007124.2|  Homo sapiens utrophin (UTRN), mRNA               1470    0.0   
emb|X69086.1|  H.sapiens mRNA for utrophin                         1470    0.0   
ref|XM_001788161.1|  PREDICTED: Bos taurus similar to putative...  1467    0.0   
emb|AJ002967.1|  Rattus norvegicus mRNA for utrophin               1467    0.0   
ref|XR_010548.1|  PREDICTED: Macaca mulatta utrophin (UTRN), mRNA  1459    0.0   
gb|AY095485.1|  Canis familiaris utrophin mRNA, complete cds       1457    0.0   
ref|XM_001915985.1|  PREDICTED: Equus caballus similar to utro...  1451    0.0   
ref|NM_011682.4|  Mus musculus utrophin (Utrn), mRNA               1438    0.0   
emb|Y12229.1|  M.musculus mRNA for utrophin                        1438    0.0   
gb|M92650.1|HUMDMDXX  Human Duchenne muscular dystrophy (DMD) ...  1299    0.0   
ref|NM_004018.2|  Homo sapiens dystrophin (DMD), transcript va...  1298    0.0   
emb|CR859102.1|  Pongo abelii mRNA; cDNA DKFZp459C1629 (from c...  1295    0.0   
ref|NM_001005244.1|  Rattus norvegicus dystrophin, muscular dy...  1294    0.0   
gb|AY326948.1|  Rattus norvegicus dystrophin Dp71ab (Dmd) mRNA...  1290    0.0   
gb|BC094758.1|  Homo sapiens dystrophin, mRNA (cDNA clone IMAG...  1287    0.0   
gb|BC028720.1|  Homo sapiens dystrophin, mRNA (cDNA clone IMAG...  1287    0.0   
ref|NM_004016.2|  Homo sapiens dystrophin (DMD), transcript va...  1286    0.0   
emb|CR858847.1|  Pongo abelii mRNA; cDNA DKFZp469A0710 (from c...  1266    0.0   
emb|X83506.1|  M.musculus mRNA for G-utrophin                      1237    0.0   
emb|CR848277.2|  Xenopus tropicalis finished cDNA, clone TNeu1...  1236    0.0   
gb|BC080941.1|  Xenopus tropicalis dystrophin, mRNA (cDNA clon...  1236    0.0   
ref|NM_004017.2|  Homo sapiens dystrophin (DMD), transcript va...  1235    0.0   
ref|NM_012698.2|  Rattus norvegicus dystrophin, muscular dystr...  1234    0.0   
gb|BC149235.1|  Bos taurus dystrophin, mRNA (cDNA clone MGC:15...  1230    0.0   
gb|BC070078.1|  Homo sapiens dystrophin, mRNA (cDNA clone IMAG...  1230    0.0   
gb|AY326947.1|  Rattus norvegicus dystrophin Dp71a (Dmd) mRNA,...  1229    0.0   
ref|NM_004015.2|  Homo sapiens dystrophin (DMD), transcript va...  1224    0.0   
dbj|AK036936.1|  Mus musculus adult female vagina cDNA, RIKEN ...  1223    0.0   
gb|BC082429.1|  Xenopus laevis dystrophin, mRNA (cDNA clone MG...  1220    0.0   
gb|BC136240.1|  Xenopus tropicalis cDNA clone IMAGE:7661888, c...  1142    0.0   
dbj|AK159639.1|  Mus musculus osteoclast-like cell cDNA, RIKEN...  1104    0.0   
emb|X99702.1|  S.caniculua mRNA for dystrophin                     1100    0.0   
emb|X99700.1|  X.laevis mRNA for dystrophin                        1100    0.0   
ref|XM_002227549.1|  Branchiostoma floridae hypothetical prote...  1096    0.0   
gb|AF304204.1|AF304204  Strongylocentrotus purpuratus dystroph...  1093    0.0   
ref|XM_001918785.1|  PREDICTED: Danio rerio hypothetical LOC79...  1092    0.0   
gb|BC095190.1|  Danio rerio dystrophin, mRNA (cDNA clone MGC:1...  1091    0.0   
ref|XM_001060977.1|  PREDICTED: Rattus norvegicus similar to d...  1081    0.0   
gb|U43517.2|SCU43517  Scyliorhinus canicula dystrophin-related...  1078    0.0   
ref|XM_002187321.1|  PREDICTED: Taeniopygia guttata similar to...  1025    0.0   
gb|U43519.1|HSU43519  Human dystrophin-related protein 2 (DRP2...  1005    0.0   
ref|XM_001493019.2|  PREDICTED: Equus caballus dystrophin rela...  1003    0.0   
dbj|AK295843.1|  Homo sapiens cDNA FLJ52301 complete cds, high...  1002    0.0   
gb|BC162218.1|  Danio rerio dystrophin related protein 2, mRNA...  1002    0.0   
ref|XM_001092374.1|  PREDICTED: Macaca mulatta dystrophin rela...  1001    0.0   
ref|NM_001939.2|  Homo sapiens dystrophin related protein 2 (D...  1001    0.0   
gb|BC111695.1|  Homo sapiens dystrophin related protein 2, mRN...  1001    0.0   
gb|DQ443728.1|  Danio rerio dystrophin-related protein 2 (DRP2...  1001    0.0   
dbj|AB384915.1|  Synthetic construct DNA, clone: pF1KB4196, Ho...  1000    0.0   
dbj|AK289825.1|  Homo sapiens cDNA FLJ75585 complete cds, high...   999    0.0   
gb|AF195788.1|AF195788  Rattus norvegicus dystrophin-related p...   996    0.0   
gb|AF195787.1|AF195787  Rattus norvegicus dystrophin-related p...   996    0.0   
ref|XM_538105.2|  PREDICTED: Canis familiaris similar to Dystr...   994    0.0   
dbj|AK158102.1|  Mus musculus adult inner ear cDNA, RIKEN full...   993    0.0   
ref|NM_010078.3|  Mus musculus dystrophin related protein 2 (D...   991    0.0   
gb|BC125347.1|  Mus musculus dystrophin related protein 2, mRN...   991    0.0   
gb|BC125345.1|  Mus musculus dystrophin related protein 2, mRN...   991    0.0   
ref|XM_001364344.1|  PREDICTED: Monodelphis domestica similar ...   991    0.0   
ref|XM_617584.4|  PREDICTED: Bos taurus similar to dystrophin ...   991    0.0   
dbj|AK081426.1|  Mus musculus 16 days embryo head cDNA, RIKEN ...   989    0.0   
tpg|BK005803.1|  TPA: TPA_inf: Ornithorhynchus anatinus dystro...   981    0.0   
emb|AJ223356.1|  Strongylocentrotus purpuratus mRNA for SuDp98...   973    0.0   
ref|XR_023213.1|  PREDICTED: Pan troglodytes similar to dystro...   953    0.0   
gb|BC136034.1|  Xenopus tropicalis dystrophin related protein ...   929    0.0   
ref|XM_001342272.2|  PREDICTED: Danio rerio similar to dystrop...   929    0.0   
ref|XM_001863085.1|  Culex quinquefasciatus dystrophin major m...   912    0.0   
ref|NM_001043259.1|  Drosophila melanogaster dystrophin (Dys),...   903    0.0   
gb|AF277386.1|AF277386  Drosophila melanogaster dystrophin-lik...   903    0.0   
ref|XM_001954777.1|  Drosophila ananassae GF16554 (Dana\GF1655...   894    0.0   
ref|NM_001043257.1|  Drosophila melanogaster dystrophin (Dys),...   894    0.0   
gb|AF297644.1|AF297644  Drosophila melanogaster dystrophin-lik...   892    0.0   
ref|NM_001043263.1|  Drosophila melanogaster dystrophin (Dys),...   892    0.0   
ref|NM_001043261.1|  Drosophila melanogaster dystrophin (Dys),...   892    0.0   
ref|NM_001043258.1|  Drosophila melanogaster dystrophin (Dys),...   892    0.0   
ref|XM_394154.3|  PREDICTED: Apis mellifera similar to dystrop...   890    0.0   
ref|XM_001946756.1|  PREDICTED: Acyrthosiphon pisum similar to...   863    0.0   
ref|NM_001043256.1|  Drosophila melanogaster dystrophin (Dys),...   863    0.0   
gb|DQ440978.1|  Petromyzon marinus dystrophin mRNA, partial cds     862    0.0   
ref|XM_001979487.1|  Drosophila erecta GG23350 (Dere\GG23350),...   862    0.0   
ref|XM_002072801.1|  Drosophila willistoni GK13817 (Dwil\GK138...   853    0.0   
ref|XM_001996213.1|  Drosophila grimshawi GH22298 (Dgri\GH2229...   852    0.0   
ref|XM_001999329.1|  Drosophila mojavensis GI23105 (Dmoj\GI231...   849    0.0   
ref|XM_002054550.1|  Drosophila virilis GJ22727 (Dvir\GJ22727)...   848    0.0   
gb|AF300294.1|AF300294  Drosophila melanogaster dystrophin-lik...   846    0.0   
ref|XM_002096289.1|  Drosophila yakuba GE25609 (Dyak\GE25609),...   842    0.0   
emb|X99703.1|  S.caniculua mRNA for utrophin                        842    0.0   
ref|XM_319450.4|  Anopheles gambiae str. PEST AGAP010261-PA (A...   829    0.0   
ref|XM_002212045.1|  Branchiostoma floridae hypothetical prote...   819    0.0   
gb|DQ440977.1|  Myxine glutinosa dystrophin mRNA, partial cds       810    0.0   
ref|NM_001043260.1|  Drosophila melanogaster dystrophin (Dys),...   803    0.0   
gb|AY875639.1|  Drosophila melanogaster Dp205 mRNA, complete cds    802    0.0   
ref|XM_001633110.1|  Nematostella vectensis predicted protein ...   794    0.0   
gb|EU293093.1|  Synthetic construct murine micro utrophin delt...   790    0.0   
emb|X99757.1|  D.melanogaster mRNA for dystrophin                   788    0.0   
gb|DQ440979.1|  Lampetra planeri dystrophin mRNA, partial cds       770    0.0   
dbj|AK035043.1|  Mus musculus 12 days embryo embryonic body be...   739    0.0   
ref|XM_962494.2|  PREDICTED: Tribolium castaneum similar to dy...   758    0.0   
emb|X99701.1|  X.laevis mRNA for utrophin                           745    0.0   
ref|NM_001005246.1|  Rattus norvegicus dystrophin, muscular dy...   731    0.0   
dbj|AK299936.1|  Homo sapiens cDNA FLJ60143 complete cds, high...   731    0.0   
gb|AY326949.1|  Rattus norvegicus dystrophin Dp71c (Dmd) mRNA,...   729    0.0   
dbj|AK087829.1|  Mus musculus 2 days pregnant adult female ova...   724    0.0   
dbj|AK075809.1|  Mus musculus 10 day old male pancreas cDNA, R...   724    0.0   
ref|NM_004019.2|  Homo sapiens dystrophin (DMD), transcript va...   723    0.0   
emb|X69767.1|  R.norvegicus mRNA for APO-dystrophin-3               719    0.0   
ref|XM_694837.3|  PREDICTED: Danio rerio similar to putative u...   711    0.0   
gb|AF339032.1|AF339032  Danio rerio dystrophin variant Dp71 (d...   689    0.0   
emb|X15488.1|  Human mRNA fragment for dystrophin-related protein   689    0.0   
dbj|AB209305.1|  Homo sapiens mRNA for dystrophin related prot...   683    0.0   
emb|X99736.1|  B.lanceolatum mRNA for dystrophin-like protein       669    0.0   
ref|NM_001043262.1|  Drosophila melanogaster dystrophin (Dys),...   664    0.0   
gb|BT010020.1|  Drosophila melanogaster RE11449 full insert cDNA    664    0.0   
ref|XM_002102789.1|  Drosophila simulans GD19295 (Dsim\GD19295...   662    0.0   
ref|XM_002043269.1|  Drosophila sechellia GM26846 (Dsec\GM2684...   658    0.0   
ref|XM_001652092.1|  Aedes aegypti dystrophin partial mRNA          657    0.0   
gb|BC036095.1|  Homo sapiens cDNA clone IMAGE:5300319, contain...   421    0.0   
dbj|AK149002.1|  Mus musculus 2 days neonate sympathetic gangl...   648    0.0   
ref|XM_002138048.1|  Drosophila pseudoobscura pseudoobscura GA...   645    0.0   
ref|XM_002019869.1|  Drosophila persimilis GL12656 (Dper\GL126...   644    0.0   
ref|XM_001096514.1|  PREDICTED: Macaca mulatta dystrophin (DMD...   630    2e-177
ref|XM_002162901.1|  PREDICTED: Hydra magnipapillata similar t...   629    3e-177
gb|U43518.1|GSU43518  Gobius sp. dystrophin-related protein 2 ...   626    3e-176
emb|X99737.1|  Asteroidea sp. mRNA for dystrophin-like protein      625    5e-176
gb|U43520.1|MMU43520  Mus musculus dystrophin-related protein ...   625    7e-176
ref|XM_001900989.1|  Brugia malayi Zinc finger, ZZ type family...   623    2e-175
emb|X99738.1|  Pectinidae sp. mRNA for dystrophin-like protein      621    7e-175
dbj|AK173373.1|  Ciona intestinalis cDNA, clone:cicl022e20, fu...   607    1e-170
dbj|AK222319.1|  Ciona intestinalis cDNA, clone:cibd066b03, fu...   606    2e-170
ref|XM_002129566.1|  PREDICTED: Ciona intestinalis similar to ...   605    5e-170
ref|XM_695636.3|  PREDICTED: Danio rerio similar to putative u...   581    1e-162
ref|XR_026973.1|  PREDICTED: Gallus gallus similar to dystroph...   570    2e-159
emb|AJ012469.1|  Caenorhabditis elegans mRNA for DYS-1 protein...   561    6e-157
ref|NM_060545.5|  Caenorhabditis elegans DYStrophin related fa...   561    9e-157
dbj|AK013510.1|  Mus musculus adult male hippocampus cDNA, RIK...   540    2e-150
emb|CU688550.1|  Synthetic construct Homo sapiens gateway clon...   535    6e-149
ref|XM_002116057.1|  Trichoplax adhaerens hypothetical protein...   508    1e-140
gb|BC060605.1|  Mus musculus dystrophin related protein 2, mRN...   496    2e-137
emb|X99756.1|  Ciona intestinalis mRNA for dystrophin               454    2e-124
dbj|AK173384.1|  Ciona intestinalis cDNA, clone:cieg020h09, fu...   252    8e-113
gb|EZ022163.1|  TSA: Acropora millepora SeqIndex3528, mRNA seq...   342    1e-90 
emb|CU688551.1|  Synthetic construct Homo sapiens gateway clon...   328    1e-86 
ref|XM_001256720.2|  PREDICTED: Bos taurus similar to dystroph...   320    3e-84 
ref|XM_001637080.1|  Nematostella vectensis predicted protein ...   315    7e-83 
ref|XM_002237128.1|  Branchiostoma floridae hypothetical prote...   312    8e-82 
ref|XM_696118.3|  PREDICTED: Danio rerio similar to putative u...   302    7e-79 
gb|EZ014006.1|  TSA: Acropora millepora SeqIndex16792, mRNA se...   189    3e-78 
ref|XM_002189011.1|  PREDICTED: Taeniopygia guttata similar to...   299    7e-78 
gb|AY566609.1|  Canis familiaris dystrophin Dp71 isoform (DMD)...   288    1e-74 
ref|XM_002237465.1|  Branchiostoma floridae hypothetical prote...   279    7e-72 
dbj|AB011666.1|  Rattus norvegicus mRNA for utrophin, partial cds   257    3e-65 
gb|DQ831005.1|  Danio rerio G-utrophin pseudogene mRNA, partia...   246    6e-62 
dbj|AK034383.1|  Mus musculus adult male diencephalon cDNA, RI...   245    1e-61 
ref|XM_002114182.1|  Trichoplax adhaerens hypothetical protein...   243    5e-61 
gb|DQ431250.1|  Schistosoma mansoni dystrophin mRNA, partial cds    232    1e-57 
gb|AF435589.1|AF435589  Eptatretus stouti dystrophin-like prot...   226    9e-56 
gb|AE014297.2|  Drosophila melanogaster chromosome 3R, complet...   170    1e-54 
gb|AC008192.8|AC008192  Drosophila melanogaster, chromosome 3R...   170    1e-54 
gb|AC007815.7|AC007815  Drosophila melanogaster, chromosome 3R...   170    1e-54 
ref|XM_001742610.1|  Monosiga brevicollis MX1 predicted protei...   217    3e-53 
gb|L06945.1|FSCTYRDYS  Torpedo californica postsynaptic membra...   210    4e-51 
ref|XM_001368984.1|  PREDICTED: Monodelphis domestica similar ...   209    6e-51 
ref|XM_001515642.1|  PREDICTED: Ornithorhynchus anatinus simil...   206    5e-50 
ref|XM_001369015.1|  PREDICTED: Monodelphis domestica similar ...   206    5e-50 
gb|DQ516343.1|  Danio rerio alpha-dystrobrevin splice variant ...   206    1e-49 
gb|DQ516344.1|  Danio rerio alpha-dystrobrevin splice variant ...   204    2e-49 
ref|XM_001515599.1|  PREDICTED: Ornithorhynchus anatinus simil...   204    3e-49 
ref|NM_032975.3|  Homo sapiens dystrobrevin, alpha (DTNA), tra...   202    9e-49 
ref|XM_001368953.1|  PREDICTED: Monodelphis domestica similar ...   201    3e-48 
ref|XM_001359998.2|  Drosophila pseudoobscura pseudoobscura GA...   200    5e-48 
ref|XM_002019867.1|  Drosophila persimilis GL12655 (Dper\GL126...   200    5e-48 
ref|XM_001639844.1|  Nematostella vectensis predicted protein ...   199    8e-48 
dbj|AB209102.1|  Homo sapiens mRNA for dystrobrevin alpha isof...   199    8e-48 
dbj|AB463020.1|  Synthetic construct DNA, clone: pF1KB3754, Ho...   199    9e-48 
gb|EU831672.1|  Synthetic construct Homo sapiens clone HAIB:10...   199    1e-47 
emb|AL833285.1|  Homo sapiens mRNA; cDNA DKFZp451O128 (from cl...   197    3e-47 
dbj|AK147359.1|  Mus musculus cDNA, RIKEN full-length enriched...   196    5e-47 
dbj|AK147279.1|  Mus musculus cDNA, RIKEN full-length enriched...   196    6e-47 
gb|EU831587.1|  Synthetic construct Homo sapiens clone HAIB:10...   196    8e-47 
ref|NM_207650.3|  Mus musculus dystrobrevin alpha (Dtna), tran...   194    4e-46 
gb|BC040364.1|  Mus musculus dystrobrevin alpha, mRNA (cDNA cl...   194    4e-46 
ref|XM_002212046.1|  Branchiostoma floridae hypothetical prote...   193    4e-46 
gb|AY525164.1|  Gallus gallus clone Dp71shoA putative short dy...   193    5e-46 
dbj|AK131649.1|  Mus musculus adult male cerebellum cDNA, RIKE...   193    5e-46 
gb|AF063193.1|AF063193  Gallus gallus dystrophin mRNA, partial...   193    5e-46 
gb|U46744.1|HSU46744  Human dystrobrevin-alpha mRNA, complete cds   192    8e-46 
ref|XM_001369093.1|  PREDICTED: Monodelphis domestica similar ...   192    1e-45 
ref|XM_613774.4|  PREDICTED: Bos taurus similar to dystrobrevi...   191    2e-45 
ref|XM_001054487.1|  PREDICTED: Rattus norvegicus similar to d...   191    2e-45 
ref|XM_001054433.1|  PREDICTED: Rattus norvegicus similar to d...   191    2e-45 
ref|XM_001054380.1|  PREDICTED: Rattus norvegicus similar to d...   191    2e-45 
ref|XM_001054793.1|  PREDICTED: Rattus norvegicus similar to d...   191    2e-45 
gb|AF082741.1|AF082741  Gallus gallus dystrophin mRNA, alterna...   191    3e-45 
gb|BC068718.1|  Xenopus laevis hypothetical protein MGC81161, ...   190    5e-45 
gb|BC121459.1|  Xenopus tropicalis dystrobrevin alpha, mRNA (c...   189    6e-45 
ref|XM_419187.2|  PREDICTED: Gallus gallus similar to dystrobr...   189    7e-45 
gb|BC050765.1|  Mus musculus dystrobrevin alpha, mRNA (cDNA cl...   189    8e-45 
ref|XM_002196755.1|  PREDICTED: Taeniopygia guttata similar to...   189    1e-44 
emb|X95226.1|  M.musculus mRNA for dystrobrevin (clone m24)         189    1e-44 
ref|XM_001054655.1|  PREDICTED: Rattus norvegicus similar to d...   188    2e-44 
ref|NM_033148.2|  Homo sapiens dystrobrevin, beta (DTNB), tran...   188    2e-44 
emb|Y12712.1|  Homo sapiens mRNA for brain dystrobrevin B           188    2e-44 
dbj|AK308410.1|  Homo sapiens cDNA, FLJ98358                        175    2e-44 
ref|XM_001515647.1|  PREDICTED: Ornithorhynchus anatinus simil...   187    2e-44 
emb|CR619470.1|  full-length cDNA clone CS0DK002YG20 of HeLa c...   187    3e-44 
ref|XM_961904.2|  PREDICTED: Tribolium castaneum similar to dy...   187    4e-44 
ref|XM_001788826.1|  PREDICTED: Bos taurus dystrobrevin, alpha...   186    8e-44 
gb|BT009805.1|  Homo sapiens dystrobrevin, beta mRNA, complete...   186    8e-44 
gb|AY889125.1|  Synthetic construct Homo sapiens clone FLH1098...   186    8e-44 
gb|AY889124.1|  Synthetic construct Homo sapiens clone FLH1098...   186    8e-44 
gb|AY889123.1|  Synthetic construct Homo sapiens clone FLH1098...   186    8e-44 
ref|NM_183361.1|  Homo sapiens dystrobrevin, beta (DTNB), tran...   186    1e-43 
gb|BC016655.1|  Homo sapiens dystrobrevin, beta, mRNA (cDNA cl...   186    1e-43 
ref|XM_547610.2|  PREDICTED: Canis familiaris similar to dystr...   185    2e-43 
gb|U26744.1|HSU26744  Human dystrobrevin-gamma mRNA, complete cds   184    2e-43 
emb|X95227.1|  M.musculus mRNA for dystrobrevin (clone m32)         184    2e-43 
ref|NM_032979.4|  Homo sapiens dystrobrevin, alpha (DTNA), tra...   184    3e-43 
dbj|AK019477.1|  Mus musculus 0 day neonate skin cDNA, RIKEN f...   184    3e-43 
gb|DQ516346.1|  Danio rerio gamma-dystrobrevin (GDTN) mRNA, co...   184    3e-43 
ref|XM_512087.2|  PREDICTED: Pan troglodytes dystrobrevin alph...   184    3e-43 
ref|XM_001495981.1|  PREDICTED: Equus caballus dystrobrevin, a...   184    3e-43 
ref|XM_001369068.1|  PREDICTED: Monodelphis domestica similar ...   184    4e-43 
ref|NM_001390.4|  Homo sapiens dystrobrevin, alpha (DTNA), tra...   184    4e-43 
ref|XM_001054112.1|  PREDICTED: Rattus norvegicus similar to d...   183    5e-43 
ref|XM_001102769.1|  PREDICTED: Macaca mulatta similar to dyst...   183    6e-43 
ref|XM_001369046.1|  PREDICTED: Monodelphis domestica similar ...   182    8e-43 
emb|X65468.1|  R.norvegicus mRNA for apodystrophin-I                182    8e-43 
ref|XM_001054548.1|  PREDICTED: Rattus norvegicus similar to d...   182    9e-43 
gb|L05649.1|HUMDYSTR15  Homo sapiens dystrophin (DMD) gene, ex...   182    1e-42 
dbj|AK291156.1|  Homo sapiens cDNA FLJ77455 complete cds, high...   181    3e-42 
gb|AC079177.21|  Homo sapiens Xp BAC RP11-147B14 (Roswell Park...   180    4e-42 
ref|XM_001054600.1|  PREDICTED: Rattus norvegicus similar to d...   180    5e-42 
ref|XM_001843534.1|  Culex quinquefasciatus dystrobrevin, mRNA      178    2e-41 
ref|XM_001650730.1|  Aedes aegypti dystrobrevin partial mRNA        178    2e-41 
ref|XM_001975870.1|  Drosophila erecta GG20305 (Dere\GG20305),...   177    2e-41 
ref|XM_002004299.1|  Drosophila mojavensis GI19671 (Dmoj\GI196...   177    2e-41 
ref|NM_001032237.1|  Drosophila melanogaster Dystrobrevin-like...   177    3e-41 
ref|NM_165905.2|  Drosophila melanogaster Dystrobrevin-like (D...   177    3e-41 
ref|XM_002081157.1|  Drosophila simulans GD10888 (Dsim\GD10888...   177    3e-41 
ref|NM_165904.1|  Drosophila melanogaster Dystrobrevin-like (D...   177    4e-41 
ref|NM_001032236.1|  Drosophila melanogaster Dystrobrevin-like...   177    4e-41 
ref|XM_002091011.1|  Drosophila yakuba GE12465 (Dyak\GE12465),...   177    4e-41 
gb|AF277387.2|AF277387  Drosophila melanogaster dystrobrevin-l...   177    4e-41 
ref|XM_001604052.1|  PREDICTED: Nasonia vitripennis similar to...   177    5e-41 
ref|NM_078988.2|  Drosophila melanogaster Dystrobrevin-like (D...   177    5e-41 
ref|XM_001958633.1|  Drosophila ananassae GF12513 (Dana\GF1251...   176    5e-41 
ref|XM_002059767.1|  Drosophila virilis GJ15037 (Dvir\GJ15037)...   176    6e-41 
ref|NM_001103817.1|  Drosophila melanogaster Dystrobrevin-like...   175    1e-40 
gb|DQ516345.1|  Danio rerio beta-dystrobrevin (BDTN) mRNA, com...   175    1e-40 
ref|XM_002033526.1|  Drosophila sechellia GM21392 (Dsec\GM2139...   175    1e-40 
ref|XM_395141.3|  PREDICTED: Apis mellifera similar to Dystrob...   175    1e-40 
ref|XM_001191124.1|  PREDICTED: Strongylocentrotus purpuratus ...   175    1e-40 
ref|XM_792154.2|  PREDICTED: Strongylocentrotus purpuratus sim...   175    1e-40 
ref|XM_002187356.1|  PREDICTED: Taeniopygia guttata similar to...   174    2e-40 
ref|XM_001987489.1|  Drosophila grimshawi GH21967 (Dgri\GH2196...   174    2e-40 
ref|XM_001948373.1|  PREDICTED: Acyrthosiphon pisum similar to...   174    3e-40 
emb|BX323090.7|  Zebrafish DNA sequence from clone CH211-274B7...   101    1e-39 
emb|AL645857.11|  Mouse DNA sequence from clone RP23-167N2 on ...   171    3e-39 
gb|AY423026.1|  Danio rerio dystrobrevin, beta (DTNB) mRNA, co...   170    4e-39 
ref|XM_001054726.1|  PREDICTED: Rattus norvegicus similar to d...   170    4e-39 
gb|M86899.1|HUMDYST16  H.sapiens dystrophin gene, exon 75           170    4e-39 
ref|XM_001089125.1|  PREDICTED: Macaca mulatta similar to dyst...   170    5e-39 
gb|AC193904.3|  Pan troglodytes BAC clone CH251-277B20 from ch...   169    9e-39 
emb|CT573323.2|  CH251-58D24, complete sequence                     169    9e-39 
gb|AC078958.30|  Homo sapiens X BAC RP11-609C15 (Roswell Park ...   169    9e-39 
emb|CT573090.2|  RP43-052E01, complete sequence                     169    9e-39 
emb|AL645477.8|  Mouse DNA sequence from clone RP23-155L18 on ...   168    2e-38 
ref|XM_001361515.2|  Drosophila pseudoobscura pseudoobscura GA...   167    5e-38 
ref|XM_001502889.1|  PREDICTED: Equus caballus dystrobrevin, b...   166    6e-38 
ref|XM_540111.2|  PREDICTED: Canis familiaris similar to dystr...   166    1e-37 
emb|AJ003007.1|  Mus musculus mRNA for beta-dystrobrevin            166    1e-37 
ref|NM_001391.5|  Homo sapiens dystrobrevin, alpha (DTNA), tra...   165    1e-37 
dbj|AK043436.1|  Mus musculus 7 days neonate cerebellum cDNA, ...   165    1e-37 
gb|BC030924.1|  Mus musculus dystrobrevin, beta, mRNA (cDNA cl...   165    2e-37 
gb|DQ160290.1|  Homo sapiens dystrobrevin beta isoform 6 (DTNB...   164    2e-37 
emb|Y15718.1|  Homo sapiens mRNA for dystrobrevin B DTN-B2          164    2e-37 
emb|Y15722.1|  Homo sapiens mRNA for dystrobrevin B DTN-B1          164    2e-37 
ref|XM_001621487.1|  Nematostella vectensis predicted protein ...   164    3e-37 
gb|AF143543.1|AF143543  Mus musculus alpha-dystrobrevin 2a mRN...   164    3e-37 
gb|AF143544.1|AF143544  Mus musculus alpha-dystrobrevin 2b mRN...   164    3e-37 
ref|XM_515336.2|  PREDICTED: Pan troglodytes dystrobrevin, bet...   164    3e-37 
dbj|AK300019.1|  Homo sapiens cDNA FLJ60874 complete cds, high...   164    3e-37 
ref|NM_021907.3|  Homo sapiens dystrobrevin, beta (DTNB), tran...   164    3e-37 
ref|NM_033147.2|  Homo sapiens dystrobrevin, beta (DTNB), tran...   164    3e-37 
ref|NM_183360.1|  Homo sapiens dystrobrevin, beta (DTNB), tran...   164    3e-37 
gb|AF022728.1|AF022728  Homo sapiens beta-dystrobrevin (BDTN) ...   164    3e-37 
gb|BC081889.1|  Rattus norvegicus dystrobrevin, beta, mRNA (cD...   164    4e-37 
emb|Y15742.1|  Mus musculus mRNA for dystrobrevin B, partial        163    5e-37 
gb|BC049366.1|  Homo sapiens dystrobrevin, beta, mRNA (cDNA cl...   163    7e-37 
gb|U46745.1|HSU46745  Human dystrobrevin-beta mRNA, complete cds    163    7e-37 
ref|NM_058459.4|  Caenorhabditis elegans DYstroBrevin homolog ...   162    8e-37 
emb|AJ131742.1|  Caenorhabditis elegans mRNA for dystrobrevin       162    9e-37 
ref|XM_001380100.1|  PREDICTED: Monodelphis domestica similar ...   162    9e-37 
ref|NM_032978.6|  Homo sapiens dystrobrevin, alpha (DTNA), tra...   162    1e-36 
dbj|AK301386.1|  Homo sapiens cDNA FLJ58632 complete cds, high...   162    1e-36 
ref|XM_001667709.1|  Caenorhabditis briggsae hypothetical prot...   161    2e-36 
ref|XM_001054053.1|  PREDICTED: Rattus norvegicus similar to d...   161    3e-36 
ref|XM_001054243.1|  PREDICTED: Rattus norvegicus similar to d...   160    3e-36 
tpd|BR000175.1|  TPA: TPA_exp: Ciona intestinalis Ci-ZF(ZZ)-4 ...   159    8e-36 
gb|DQ516347.1|  Homo sapiens dystrotelin mRNA, complete cds         158    2e-35 
dbj|AK020881.1|  Mus musculus adult retina cDNA, RIKEN full-le...   158    2e-35 
ref|XM_001787345.1|  PREDICTED: Bos taurus similar to Dystrote...   154    4e-34 
gb|S60973.1|  dystrophin {out-of-frame deletion of exon 50} [h...   154    4e-34 
gb|M63072.1|HUMDMDC  Human Duchenne muscular dystrophy protein...   154    4e-34 
gb|BC046265.1|  Xenopus laevis dystrobrevin, alpha, mRNA (cDNA...   151    2e-33 
emb|AJ544617.1|  Takifugu rubripes dmd gene for putative dystr...   150    4e-33 
ref|XM_002245696.1|  Branchiostoma floridae hypothetical prote...   150    5e-33 
gb|EF120476.1|  Schistosoma bovis dystrophin mRNA, partial cds      149    7e-33 
emb|AJ544616.1|  Takifugu rubripes dmd gene for putative dystr...   149    8e-33 
gb|EF120477.1|  Schistosoma haematobium dystrophin mRNA, parti...   149    8e-33 
gb|AC093167.11|  Homo sapiens Xp BAC RP11-593P4 (Roswell Park ...   146    9e-32 
gb|AF213438.1|AF213438  Homo sapiens dystrophin (DMD) gene, ex...   146    9e-32 
gb|AC193238.3|  Pan troglodytes BAC clone CH251-308A5 from chr...   145    1e-31 
emb|CT476801.2|  RP43-004N07, complete sequence                     145    1e-31 
emb|CR972866.3|  RP43-009N23, complete sequence                     145    1e-31 
emb|CT485784.2|  RP43-026J01, complete sequence                     145    1e-31 
ref|XM_002017724.1|  Drosophila persimilis GL17134 (Dper\GL171...   144    2e-31 
gb|AC193178.3|  Pan troglodytes BAC clone CH251-299A18 from ch...   143    7e-31 
emb|CU302226.2|  CH251-299A18, complete sequence                    143    7e-31 
gb|BC150093.1|  Bos taurus cDNA clone IMAGE:8324137                 142    1e-30 
ref|XM_001918076.1|  PREDICTED: Equus caballus dystrotelin (DY...   142    1e-30 
gb|M86889.1|HUMDYST06  H.sapiens dystrophin gene, exon 65           142    1e-30 
dbj|AK083752.1|  Mus musculus 9 days embryo whole body cDNA, R...   141    2e-30 
gb|BC078203.1|  Danio rerio dystrobrevin, gamma, mRNA (cDNA cl...   141    2e-30 
gb|S62620.1|  (mdx3Cv)=dystrophin gene {5'region, alternativel...   140    3e-30 
ref|XM_002066076.1|  Drosophila willistoni GK22187 (Dwil\GK221...   140    7e-30 
gb|AF043067.1|AF043067  Gallus gallus dystrophin mRNA, alterna...   139    1e-29 
emb|AJ720148.1|  Gallus gallus mRNA for hypothetical protein, ...   138    2e-29 
gb|BT011443.1|  Drosophila melanogaster RE48865 full insert cDNA    137    3e-29 
gb|AF533682.1|  Homo sapiens IL1RAPL1/dystrophin fusion protei...   137    3e-29 
gb|DQ443726.1|  Danio rerio dystrotelin mRNA, complete cds          137    3e-29 
gb|BC118294.1|  Bos taurus dystrobrevin, alpha, mRNA (cDNA clo...   137    6e-29 
ref|NM_010087.3|  Mus musculus dystrobrevin alpha (Dtna), tran...   135    1e-28 
dbj|AK003829.2|  Mus musculus 18-day embryo whole body cDNA, R...   135    1e-28 
gb|AF143542.1|AF143542  Mus musculus alpha-dystrobrevin 3 mRNA...   135    1e-28 
gb|BT006937.1|  Homo sapiens dystrobrevin, alpha mRNA, complet...   135    2e-28 
ref|NM_001392.4|  Homo sapiens dystrobrevin, alpha (DTNA), tra...   135    2e-28 
gb|U26742.1|HSU26742  Human dystrobrevin-delta mRNA, complete cds   135    2e-28 
gb|EU831619.1|  Synthetic construct Homo sapiens clone HAIB:10...   135    2e-28 
emb|AJ009668.1|  Homo sapiens mRNA for alpha-dystrobrevin-3         135    2e-28 
ref|NM_001128175.1|  Homo sapiens dystrobrevin, alpha (DTNA), ...   134    2e-28 
gb|BC005300.1|  Homo sapiens dystrobrevin, alpha, mRNA (cDNA c...   134    2e-28 
emb|CR611269.1|  full-length cDNA clone CS0DN002YF11 of Adult ...   134    3e-28 
gb|BT007812.1|  Synthetic construct Homo sapiens dystrobrevin,...   134    3e-28 
gb|EU831705.1|  Synthetic construct Homo sapiens clone HAIB:10...   134    3e-28 
ref|XM_426570.2|  PREDICTED: Gallus gallus similar to dystroph...   134    4e-28 
emb|BX004756.7|  Zebrafish DNA sequence from clone CH211-59A4 ...   133    5e-28 
gb|AC094963.9|  Rattus norvegicus X BAC CH230-6L20 (Children's...   132    2e-27 
gb|M86892.1|HUMDYST09  H.sapiens dystrophin gene, exon 68           130    5e-27 
gb|DQ443727.1|  Mus musculus dystrotelin mRNA, complete cds         130    5e-27 
ref|XM_001606073.1|  PREDICTED: Nasonia vitripennis similar to...   130    6e-27 
emb|AL806516.4|  Mouse DNA sequence from clone RP23-453N20 on ...   130    7e-27 
emb|AJ544612.1|  Takifugu rubripes dmd gene for putative dystr...  78.2    9e-27 
gb|AF213440.1|AF213440  Homo sapiens dystrophin (DMD) gene, ex...   129    1e-26 
gb|AC079175.24|  Homo sapiens Xp BAC RP11-122N14 (Roswell Park...   129    1e-26 
gb|AY525165.1|  Gallus gallus clone Dp71shoB putative short dy...   128    2e-26 
ref|XM_001892815.1|  Brugia malayi Zinc finger, ZZ type family...   128    2e-26 
gb|EF473649.1|  Danio rerio utrophin-like mRNA, partial sequence    127    5e-26 
dbj|AB171279.1|  Macaca fascicularis brain cDNA clone: QorA-13...   113    7e-26 
dbj|AK094494.1|  Homo sapiens cDNA FLJ37175 fis, clone BRACE20...  79.3    4e-25 
emb|AJ544620.1|  Takifugu rubripes utrn gene for putative utro...  95.5    9e-25 
gb|AC152831.2|  Ornithorhynchus anatinus chromosome UNK clone ...  73.6    2e-24 
gb|DQ788696.1|  Danio rerio utrophin isoform G mRNA, partial c...   121    3e-24 
dbj|AK240524.1|  Sus scrofa mRNA, clone:UTR010089D01, expresse...   120    5e-24 
gb|L05647.1|HUMDYSTR13  Homo sapiens dystrophin (DMD) gene, ex...   120    6e-24 
dbj|AK294357.1|  Homo sapiens cDNA FLJ57272 complete cds, high...   107    7e-24 
gb|DQ431251.1|  Schistosoma mansoni dystrobrevin mRNA, complet...   118    3e-23 
gb|M86891.1|HUMDYST08  H.sapiens dystrophin gene, exon 67           117    5e-23 
emb|AL844151.3|  Mouse DNA sequence from clone RP23-73O7 on ch...   116    6e-23 
emb|CR622461.1|  full-length cDNA clone CS0DB006YJ19 of Neurob...   116    8e-23 
gb|AC156952.22|  Mus musculus 10 BAC RP24-385D2 (Roswell Park ...   115    2e-22 
gb|AC153893.3|  Mus musculus 10 BAC RP23-124O20 (Roswell Park ...   115    2e-22 
gb|L04186.1|HUMDYSDMD  Homo sapiens dystrophin (DMD) gene, exo...   114    2e-22 
gb|L22094.1|MUSUTROPH  Mouse utrophin (Dmd1) gene, one complet...   114    3e-22 
gb|AC079864.22|  Homo sapiens Xp BAC RP11-662G16 (Roswell Park...   114    3e-22 
gb|AF213436.1|AF213436  Homo sapiens dystrophin (DMD) gene, ex...   114    3e-22 
emb|X51934.1|  Human dystrophin gene, exon 51 with flanking se...   114    3e-22 
gb|M65035.1|HUMDYSGP  Human dystrophin gene deletion junction ...   114    3e-22 
emb|AL357149.13|  Human DNA sequence from clone RP11-352E13 on...   114    3e-22 
emb|X16089.1|  Human Cf56a/Cf23a region DNA for an exon of Duc...   114    4e-22 
gb|S38776.1|  Homo sapiens dystrophin (DMD) mRNA, partial cds,...   112    1e-21 
emb|CR954286.2|  Pan troglodytes chromosome X BAC RP43-001A02,...   112    1e-21 
emb|AL513184.7|  Human DNA sequence from clone RP11-386H19 on ...   112    2e-21 
gb|AC187490.2|  Rhesus macaque BAC clone CH250-77H12 from chro...   111    2e-21 
gb|AY390386.1|  Rattus norvegicus dystrophin-related mRNA, par...   111    3e-21 
emb|Z81522.1|  Caenorhabditis elegans Cosmid F32B4, complete s...   110    3e-21 
gb|AC112800.6|  Rattus norvegicus X BAC CH230-275F1 (Children'...   110    4e-21 
gb|DQ788695.1|  Danio rerio dystrophin isoform Dp116 mRNA, par...   110    4e-21 
gb|AF213439.1|AF213439  Homo sapiens dystrophin (DMD) gene, ex...   109    1e-20 
gb|M86898.1|HUMDYST15  H.sapiens dystrophin gene, exon 74           107    3e-20 
gb|U01229.1|U01229  Torpedo californica dystrophin mRNA, parti...   107    4e-20 
dbj|AK296450.1|  Homo sapiens cDNA FLJ56097 complete cds, high...   107    6e-20 
gb|AC192936.3|  Pan troglodytes BAC clone CH251-433G11 from ch...   103    5e-19 
emb|CR955037.3|  Pan troglodytes chromosome X BAC RP43-016I09,...   103    5e-19 
gb|M86884.1|HUMDYST01  H.sapiens dystrophin gene, exon 60           103    5e-19 
ref|XM_968674.2|  PREDICTED: Tribolium castaneum similar to ka...   102    1e-18 
gb|AE013599.4|  Drosophila melanogaster chromosome 2R, complet...  81.6    1e-18 
gb|AC007356.8|AC007356  Drosophila melanogaster, chromosome 2R...  81.6    1e-18 
gb|AC007476.5|AC007476  Drosophila melanogaster, chromosome 2R...  81.6    1e-18 
emb|Z11860.1|  H.sapiens gene encoding dystrophin, exon 60          101    2e-18 
ref|XM_001946815.1|  PREDICTED: Acyrthosiphon pisum similar to...   101    3e-18 
gb|AF213442.1|AF213442  Homo sapiens dystrophin (DMD) gene, ex...   101    3e-18 
gb|M86894.1|HUMDYST11  H.sapiens dystrophin gene, exon 70           101    3e-18 
ref|XM_001195605.1|  PREDICTED: Strongylocentrotus purpuratus ...  98.6    2e-17 
emb|CT027835.13|  Zebrafish DNA sequence from clone CH211-66E1...  97.8    3e-17 
emb|BX510641.9|  Zebrafish DNA sequence from clone CH211-106M9...  97.4    4e-17 
emb|BX511121.15|  Zebrafish DNA sequence from clone DKEYP-110A...  97.4    5e-17 
gb|M86893.1|HUMDYST10  H.sapiens dystrophin gene, exon 69          96.3    1e-16 
ref|XM_001365106.1|  PREDICTED: Monodelphis domestica similar ...  95.5    2e-16 
gb|AF070567.1|AF070567  Homo sapiens clone 24544 beta-dystrobr...  92.8    1e-15 
ref|XM_001515580.1|  PREDICTED: Ornithorhynchus anatinus simil...  92.8    1e-15 
ref|XM_001084824.1|  PREDICTED: Macaca mulatta similar to dyst...  92.8    1e-15 
dbj|AK294174.1|  Homo sapiens cDNA FLJ60475 complete cds, high...  92.4    1e-15 
dbj|AK225724.1|  Homo sapiens mRNA for dystrobrevin, beta isof...  92.4    1e-15 
ref|XM_002221469.1|  Branchiostoma floridae hypothetical prote...  92.0    2e-15 
emb|AL672064.17|  Mouse DNA sequence from clone RP23-91G19 on ...  90.5    5e-15 
ref|XM_002221736.1|  Branchiostoma floridae hypothetical prote...  90.1    6e-15 
ref|XM_001505526.1|  PREDICTED: Ornithorhynchus anatinus simil...  89.7    9e-15 
ref|XM_002205053.1|  Branchiostoma floridae hypothetical prote...  89.4    1e-14 
ref|XM_684808.3|  PREDICTED: Danio rerio similar to dystonin (...  89.0    2e-14 
emb|Z68331.3|  Human DNA sequence from clone GHc-521F8 on chro...  88.6    2e-14 
gb|AC194760.4|  Pan troglodytes BAC clone CH251-694P16 from ch...  88.2    2e-14 
ref|XR_024528.1|  PREDICTED: Pan troglodytes similar to dyston...  88.2    3e-14 
dbj|AB018271.2|  Homo sapiens mRNA for KIAA0728 protein, parti...  88.2    3e-14 
ref|NM_001144771.1|  Homo sapiens dystonin (DST), transcript v...  87.8    4e-14 
ref|NM_001144770.1|  Homo sapiens dystonin (DST), transcript v...  87.8    4e-14 
ref|NM_001144769.1|  Homo sapiens dystonin (DST), transcript v...  87.8    4e-14 
ref|NM_183380.2|  Homo sapiens dystonin (DST), transcript vari...  87.8    4e-14 
ref|NM_015548.3|  Homo sapiens dystonin (DST), transcript vari...  87.8    4e-14 
ref|XM_001995054.1|  Drosophila grimshawi GH22959 (Dgri\GH2295...  87.4    4e-14 
gb|AF213443.1|AF213443  Homo sapiens dystrophin (DMD) gene, ex...  87.4    4e-14 
gb|AF400226.1|  Homo sapiens bullous pemphigoid antigen 1 eA (...  86.7    7e-14 
emb|CU677663.1|  Synthetic construct Homo sapiens gateway clon...  86.7    8e-14 
ref|XM_001252266.1|  PREDICTED: Bos taurus similar to dystonin...  86.3    1e-13 
ref|XM_615341.3|  PREDICTED: Bos taurus similar to dystonin, t...  86.3    1e-13 
ref|XM_861695.1|  PREDICTED: Canis familiaris dystonin, transc...  86.3    1e-13 
emb|AJ544618.1|  Takifugu rubripes utrn gene for putative utro...  65.1    1e-13 
ref|XM_861613.1|  PREDICTED: Canis familiaris dystonin, transc...  85.9    1e-13 
ref|XM_861601.1|  PREDICTED: Canis familiaris dystonin, transc...  85.9    1e-13 
ref|XM_861627.1|  PREDICTED: Canis familiaris dystonin, transc...  85.9    1e-13 
ref|XM_861585.1|  PREDICTED: Canis familiaris dystonin, transc...  85.9    1e-13 
ref|XM_861669.1|  PREDICTED: Canis familiaris dystonin, transc...  85.9    1e-13 
ref|XM_861540.1|  PREDICTED: Canis familiaris dystonin, transc...  85.9    1e-13 
ref|XM_861682.1|  PREDICTED: Canis familiaris dystonin, transc...  85.9    1e-13 
ref|XM_861654.1|  PREDICTED: Canis familiaris dystonin, transc...  85.9    1e-13 
ref|XM_532183.2|  PREDICTED: Canis familiaris dystonin, transc...  85.9    1e-13 
ref|XM_861733.1|  PREDICTED: Canis familiaris dystonin, transc...  85.5    2e-13 
ref|XM_861720.1|  PREDICTED: Canis familiaris dystonin, transc...  85.5    2e-13 
ref|XM_861709.1|  PREDICTED: Canis familiaris dystonin, transc...  85.5    2e-13 
ref|XM_861528.1|  PREDICTED: Canis familiaris dystonin, transc...  85.5    2e-13 
ref|NM_001144187.1|  Drosophila melanogaster short stop (shot)...  85.5    2e-13 
gb|M86900.1|HUMDYST17  H.sapiens dystrophin gene, exon 76          85.5    2e-13 
dbj|AK157158.1|  Mus musculus activated spleen cDNA, RIKEN ful...  85.1    2e-13 
ref|NM_001144188.1|  Drosophila melanogaster short stop (shot)...  85.1    2e-13 
ref|NM_001144185.1|  Drosophila melanogaster short stop (shot)...  85.1    2e-13 
ref|NM_166019.1|  Drosophila melanogaster short stop (shot), t...  85.1    3e-13 

ALIGNMENTS
>ref|NM_004022.2| Homo sapiens dystrophin (DMD), transcript variant D140ab, mRNA
Length=7339

 Score = 2544 bits (6593),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1230/1230 (100%), Positives = 1230/1230 (100%), Gaps = 0/1230 (0%)
 Frame = +1

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  1042  MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  1221

Query  61    EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
             EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  1222  EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  1401

Query  121   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
             DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  1402  DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  1581

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  1582  NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  1761

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
             FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  1762  FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  1941

Query  301   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
             KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  1942  KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  2121

Query  361   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
             LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  2122  LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  2301

Query  421   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
             LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  2302  LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  2481

Query  481   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
             EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  2482  EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  2661

Query  541   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
             QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  2662  QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  2841

Query  601   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
             WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  2842  WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  3021

Query  661   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
             LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  3022  LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  3201

Query  721   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
             WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  3202  WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  3381

Query  781   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
             SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  3382  SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  3561

Query  841   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
             VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  3562  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  3741

Query  901   TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT  960
             TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT
Sbjct  3742  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT  3921

Query  961   HSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQ  1020
             HSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQ
Sbjct  3922  HSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQ  4101

Query  1021  ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSP  1080
             ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSP
Sbjct  4102  ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSP  4281

Query  1081  RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSS  1140
             RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSS
Sbjct  4282  RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSS  4461

Query  1141  PSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGH  1200
             PSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGH
Sbjct  4462  PSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGH  4641

Query  1201  NVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             NVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  4642  NVGSLFHMADDLGRAMESLVSVMTDEEGAE  4731


 Score = 55.5 bits (132),  Expect = 2e-04, Method: Compositional matrix adjust.
 Identities = 51/206 (24%), Positives = 99/206 (48%), Gaps = 15/206 (7%)
 Frame = +1

Query  164  KQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAA  223
            K+L   + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  
Sbjct  97   KELQDGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKR  276

Query  224  LEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQG  283
            LEE   +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG
Sbjct  277  LEEQKNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG  456

Query  284  EIEAHTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEA  342
                   +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA
Sbjct  457  -------ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEA  615

Query  343  SSDQWKRLHLSLQE-------LLVWL  361
                  +L   L++       LL+WL
Sbjct  616  QIKDLGQLEKKLEDLEEQLNHLLLWL  693


>dbj|AB208836.1| Homo sapiens mRNA for dystrophin Dp427c isoform variant protein
Length=6801

 Score = 2538 bits (6579),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1229/1230 (99%), Positives = 1230/1230 (100%), Gaps = 0/1230 (0%)
 Frame = +3

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  489   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  668

Query  61    EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
             EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  669   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  848

Query  121   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
             DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  849   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  1028

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  1029  NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  1208

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
             FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  1209  FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  1388

Query  301   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
             KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  1389  KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  1568

Query  361   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
             LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  1569  LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  1748

Query  421   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
             LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERL+ELQ
Sbjct  1749  LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLRELQ  1928

Query  481   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
             EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  1929  EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  2108

Query  541   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
             QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  2109  QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  2288

Query  601   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
             WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  2289  WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  2468

Query  661   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
             LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  2469  LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  2648

Query  721   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
             WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  2649  WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  2828

Query  781   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
             SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  2829  SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  3008

Query  841   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
             VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  3009  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  3188

Query  901   TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT  960
             TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT
Sbjct  3189  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT  3368

Query  961   HSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQ  1020
             HSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQ
Sbjct  3369  HSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQ  3548

Query  1021  ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSP  1080
             ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSP
Sbjct  3549  ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSP  3728

Query  1081  RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSS  1140
             RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSS
Sbjct  3729  RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSS  3908

Query  1141  PSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGH  1200
             PSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGH
Sbjct  3909  PSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGH  4088

Query  1201  NVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             NVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  4089  NVGSLFHMADDLGRAMESLVSVMTDEEGAE  4178


>ref|NM_004021.2| Homo sapiens dystrophin (DMD), transcript variant Dp140b, mRNA
Length=7378

 Score = 2534 bits (6569),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1230/1243 (98%), Positives = 1230/1243 (98%), Gaps = 13/1243 (1%)
 Frame = +1

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  1042  MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  1221

Query  61    EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
             EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  1222  EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  1401

Query  121   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
             DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  1402  DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  1581

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  1582  NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  1761

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
             FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  1762  FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  1941

Query  301   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
             KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  1942  KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  2121

Query  361   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
             LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  2122  LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  2301

Query  421   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
             LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  2302  LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  2481

Query  481   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
             EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  2482  EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  2661

Query  541   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
             QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  2662  QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  2841

Query  601   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
             WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  2842  WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  3021

Query  661   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
             LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  3022  LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  3201

Query  721   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
             WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  3202  WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  3381

Query  781   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
             SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  3382  SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  3561

Query  841   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
             VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  3562  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  3741

Query  901   TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
             TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  3742  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  3921

Query  949   -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
              PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  3922  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  4101

Query  1008  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
             QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  4102  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  4281

Query  1068  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
             SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  4282  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  4461

Query  1128  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
             QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  4462  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  4641

Query  1188  EQLNNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             EQLNNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  4642  EQLNNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  4770


 Score = 55.8 bits (133),  Expect = 2e-04, Method: Compositional matrix adjust.
 Identities = 51/206 (24%), Positives = 99/206 (48%), Gaps = 15/206 (7%)
 Frame = +1

Query  164  KQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAA  223
            K+L   + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  
Sbjct  97   KELQDGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKR  276

Query  224  LEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQG  283
            LEE   +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG
Sbjct  277  LEEQKNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG  456

Query  284  EIEAHTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEA  342
                   +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA
Sbjct  457  -------ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEA  615

Query  343  SSDQWKRLHLSLQE-------LLVWL  361
                  +L   L++       LL+WL
Sbjct  616  QIKDLGQLEKKLEDLEEQLNHLLLWL  693


>gb|BC150141.1| Homo sapiens dystrophin, mRNA (cDNA clone IMAGE:40124455), complete 
cds
Length=4733

 Score = 2531 bits (6560),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1230/1243 (98%), Positives = 1230/1243 (98%), Gaps = 13/1243 (1%)
 Frame = +2

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  566   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  745

Query  61    EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
             EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  746   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  925

Query  121   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
             DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  926   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  1105

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  1106  NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  1285

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
             FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  1286  FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  1465

Query  301   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
             KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  1466  KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  1645

Query  361   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
             LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  1646  LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  1825

Query  421   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
             LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  1826  LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  2005

Query  481   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
             EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  2006  EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  2185

Query  541   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
             QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  2186  QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  2365

Query  601   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
             WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  2366  WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  2545

Query  661   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
             LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  2546  LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  2725

Query  721   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
             WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  2726  WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  2905

Query  781   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
             SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  2906  SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  3085

Query  841   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
             VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  3086  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  3265

Query  901   TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
             TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  3266  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  3445

Query  949   -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
              PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  3446  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  3625

Query  1008  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
             QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  3626  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  3805

Query  1068  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
             SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  3806  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  3985

Query  1128  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
             QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  3986  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  4165

Query  1188  EQLNNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             EQLNNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  4166  EQLNNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  4294


>ref|NM_004010.3| Homo sapiens dystrophin (DMD), transcript variant Dp427p2, mRNA
Length=14083

 Score = 2486 bits (6443),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1200/1215 (98%), Positives = 1200/1215 (98%), Gaps = 13/1215 (1%)
 Frame = +2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  7715   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  7894

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  7895   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  8074

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  8075   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  8254

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  8255   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  8434

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  8435   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  8614

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8615   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8794

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8795   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8974

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  8975   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  9154

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  9155   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  9334

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9335   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  9514

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9515   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9694

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9695   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9874

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9875   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  10054

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  10055  SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  10234

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  10235  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10414

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10415  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10594

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10595  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10774

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10775  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10954

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10955  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  11134

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  11135  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  11314

Query  1188   EQLNNSFPSSRGHNV  1202
              EQLNNSFPSSRG N 
Sbjct  11315  EQLNNSFPSSRGRNT  11359


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +1

Query  1198   RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  11377  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  11475


 Score = 59.3 bits (142),  Expect = 1e-05, Method: Compositional matrix adjust.
 Identities = 81/382 (21%), Positives = 175/382 (45%), Gaps = 54/382 (14%)
 Frame = +2

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  L  ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  6320  VPSTYLTEI----------THVSQALLEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  6457

Query  61    E---QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +   Q+     ++I + +    +++    R  + + + ++  QW++V +  ++R+ + + 
Sbjct  6458  KDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFDR  6637

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  6638  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  6781

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  LEE 
Sbjct  6782  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQ  6961

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG    
Sbjct  6962  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG----  7129

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  7130  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKD  7300

Query  347   WKRLHLSLQE-------LLVWL  361
               +L   L++       LL+WL
Sbjct  7301  LGQLEKKLEDLEEQLNHLLLWL  7366


 Score = 46.2 bits (108),  Expect = 0.12, Method: Compositional matrix adjust.
 Identities = 91/422 (21%), Positives = 180/422 (42%), Gaps = 48/422 (11%)
 Frame = +2

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ E + L   L++ Q+ +   +    ++ +   ++ +RK     E I   W+ +
Sbjct  3251  EIMEQRLGELQALQSSLQEQQSGLYYLSTTVKEMSKKAPSEISRKYQSEFEEIEGRWKKL  3430

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               ++ E    LEE    L++    ++    W+ E         D   KE    L DS+ +
Sbjct  3431  SSQLVEHCQKLEEQMNKLRKIQNHIQTLKKWMAEV--------DVFLKEEWPALGDSEIL  3586

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L  +I+      ++++E  QKI    E  + A  L+  L  +N +W  + +
Sbjct  3587  KKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEAE-PEFASRLETELKELNTQWDHMCQ  3763

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFP-----AVQKQN  385
             +    +  L+   ++   L   L E+  W+ Q +++ L R      DF       +QK  
Sbjct  3764  QVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLER------DFEYKTPDELQKAV  3925

Query  386   DVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLR  445
             +  +  K E + KE  +    E+V   + + P    E L +E   L      Q +   L 
Sbjct  3926  EEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTT--NYQWLCTRLN  4099

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
              + + +   W       A W     E L  L++  +  +E++ KL+  E I G  + + +
Sbjct  4100  GKCKTLEEVW-------ACWH----ELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISE  4246

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
             +L DSL++ +             ++N + +  LA+ LT  G+     N   LE  N+RW+
Sbjct  4247  VL-DSLENLMRHS----------EDNPNQIRILAQTLTDGGVMDELIN-EELETFNSRWR  4390

Query  566   LL  567
              L
Sbjct  4391  EL  4396


 Score = 44.3 bits (103),  Expect = 0.40, Method: Compositional matrix adjust.
 Identities = 79/356 (22%), Positives = 155/356 (43%), Gaps = 42/356 (11%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             L  W++ +D  +K +   +GD E + + + + +  + D++  +P L  +    Q +KN+ 
Sbjct  3512  LKKWMAEVDVFLKEEWPALGDSEILKKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEA  3691

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               + A  + T+ ++ +  QWD + + +  R++ L   L+ +    +   E  + + QA  
Sbjct  3692  EPEFASRLETE-LKELNTQWDHMCQQVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAE-  3865

Query  142   KLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS--ADDT  196
               E + E  +   T D +QK + E K+  ++ +Q +  V +  +    ++      A + 
Sbjct  3866  --EEYLERDFEYKTPDELQKAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEA  4039

Query  197   RKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE----TTA  252
              K  + T   N  W  +  R++ +   LEE      +    LEK   WL E E    TT 
Sbjct  4040  LKKELETLTTNYQW--LCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEFKLKTTE  4213

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
             N+   A   E + E    ++ LM+                H+ D  +Q  + +   +D  
Sbjct  4214  NIPGGA---EEISEVLDSLENLMR----------------HSEDNPNQIRILAQTLTDGG  4336

Query  313   V---LLQRRLDNMNFKWSELRKKSLNIRSHLEAS----SDQWKRLHLSLQELLVWL  361
             V   L+   L+  N +W EL ++++  +  LE S     +  K LHL +QE L ++
Sbjct  4337  VMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEKSLHL-IQESLTFI  4501


 Score = 43.5 bits (101),  Expect = 0.82, Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 42/281 (14%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  5081  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVL  5260

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q ++ +    T+W+ 
Sbjct  5261  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHI----TKWI-  5419

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  +L   +  VD   D A  L
Sbjct  5420  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAELNDIRPKVDSTRDQAANL  5557

Query  188   LRDYSADDTRK-VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             + +   D  RK V      +N  + +I  R+   +A++    + L+QF  D++K L  L 
Sbjct  5558  MAN-RGDHCRKLVEPQISELNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-  5725

Query  247   EAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
             EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  5726  EAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRI  5848


>ref|NM_004009.3| Homo sapiens dystrophin (DMD), transcript variant Dp427p1, mRNA
Length=14000

 Score = 2486 bits (6443),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1200/1215 (98%), Positives = 1200/1215 (98%), Gaps = 13/1215 (1%)
 Frame = +3

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  7632   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  7811

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  7812   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  7991

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  7992   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  8171

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  8172   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  8351

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  8352   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  8531

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8532   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8711

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8712   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8891

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  8892   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  9071

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  9072   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  9251

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9252   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  9431

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9432   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9611

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9612   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9791

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9792   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9971

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9972   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  10151

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  10152  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10331

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10332  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10511

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10512  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10691

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10692  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10871

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10872  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  11051

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  11052  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  11231

Query  1188   EQLNNSFPSSRGHNV  1202
              EQLNNSFPSSRG N 
Sbjct  11232  EQLNNSFPSSRGRNT  11276


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +2

Query  1198   RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  11294  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  11392


 Score = 59.3 bits (142),  Expect = 1e-05, Method: Compositional matrix adjust.
 Identities = 81/382 (21%), Positives = 175/382 (45%), Gaps = 54/382 (14%)
 Frame = +3

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  L  ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  6237  VPSTYLTEI----------THVSQALLEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  6374

Query  61    E---QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +   Q+     ++I + +    +++    R  + + + ++  QW++V +  ++R+ + + 
Sbjct  6375  KDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFDR  6554

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  6555  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  6698

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  LEE 
Sbjct  6699  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQ  6878

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG    
Sbjct  6879  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG----  7046

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  7047  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKD  7217

Query  347   WKRLHLSLQE-------LLVWL  361
               +L   L++       LL+WL
Sbjct  7218  LGQLEKKLEDLEEQLNHLLLWL  7283


 Score = 46.2 bits (108),  Expect = 0.12, Method: Compositional matrix adjust.
 Identities = 91/422 (21%), Positives = 180/422 (42%), Gaps = 48/422 (11%)
 Frame = +3

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ E + L   L++ Q+ +   +    ++ +   ++ +RK     E I   W+ +
Sbjct  3168  EIMEQRLGELQALQSSLQEQQSGLYYLSTTVKEMSKKAPSEISRKYQSEFEEIEGRWKKL  3347

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               ++ E    LEE    L++    ++    W+ E         D   KE    L DS+ +
Sbjct  3348  SSQLVEHCQKLEEQMNKLRKIQNHIQTLKKWMAEV--------DVFLKEEWPALGDSEIL  3503

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L  +I+      ++++E  QKI    E  + A  L+  L  +N +W  + +
Sbjct  3504  KKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEAE-PEFASRLETELKELNTQWDHMCQ  3680

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFP-----AVQKQN  385
             +    +  L+   ++   L   L E+  W+ Q +++ L R      DF       +QK  
Sbjct  3681  QVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLER------DFEYKTPDELQKAV  3842

Query  386   DVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLR  445
             +  +  K E + KE  +    E+V   + + P    E L +E   L      Q +   L 
Sbjct  3843  EEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTT--NYQWLCTRLN  4016

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
              + + +   W       A W     E L  L++  +  +E++ KL+  E I G  + + +
Sbjct  4017  GKCKTLEEVW-------ACWH----ELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISE  4163

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
             +L DSL++ +             ++N + +  LA+ LT  G+     N   LE  N+RW+
Sbjct  4164  VL-DSLENLMRHS----------EDNPNQIRILAQTLTDGGVMDELIN-EELETFNSRWR  4307

Query  566   LL  567
              L
Sbjct  4308  EL  4313


 Score = 44.3 bits (103),  Expect = 0.40, Method: Compositional matrix adjust.
 Identities = 79/356 (22%), Positives = 155/356 (43%), Gaps = 42/356 (11%)
 Frame = +3

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             L  W++ +D  +K +   +GD E + + + + +  + D++  +P L  +    Q +KN+ 
Sbjct  3429  LKKWMAEVDVFLKEEWPALGDSEILKKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEA  3608

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               + A  + T+ ++ +  QWD + + +  R++ L   L+ +    +   E  + + QA  
Sbjct  3609  EPEFASRLETE-LKELNTQWDHMCQQVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAE-  3782

Query  142   KLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS--ADDT  196
               E + E  +   T D +QK + E K+  ++ +Q +  V +  +    ++      A + 
Sbjct  3783  --EEYLERDFEYKTPDELQKAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEA  3956

Query  197   RKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE----TTA  252
              K  + T   N  W  +  R++ +   LEE      +    LEK   WL E E    TT 
Sbjct  3957  LKKELETLTTNYQW--LCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEFKLKTTE  4130

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
             N+   A   E + E    ++ LM+                H+ D  +Q  + +   +D  
Sbjct  4131  NIPGGA---EEISEVLDSLENLMR----------------HSEDNPNQIRILAQTLTDGG  4253

Query  313   V---LLQRRLDNMNFKWSELRKKSLNIRSHLEAS----SDQWKRLHLSLQELLVWL  361
             V   L+   L+  N +W EL ++++  +  LE S     +  K LHL +QE L ++
Sbjct  4254  VMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEKSLHL-IQESLTFI  4418


 Score = 43.5 bits (101),  Expect = 0.82, Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 42/281 (14%)
 Frame = +3

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  4998  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVL  5177

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q ++ +    T+W+ 
Sbjct  5178  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHI----TKWI-  5336

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  +L   +  VD   D A  L
Sbjct  5337  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAELNDIRPKVDSTRDQAANL  5474

Query  188   LRDYSADDTRK-VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             + +   D  RK V      +N  + +I  R+   +A++    + L+QF  D++K L  L 
Sbjct  5475  MAN-RGDHCRKLVEPQISELNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-  5642

Query  247   EAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
             EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  5643  EAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRI  5765


>ref|NM_004007.2| Homo sapiens dystrophin (DMD), transcript variant Dp427l, mRNA
Length=13764

 Score = 2486 bits (6443),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1200/1215 (98%), Positives = 1200/1215 (98%), Gaps = 13/1215 (1%)
 Frame = +1

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  7396   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  7575

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  7576   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  7755

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  7756   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  7935

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  7936   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  8115

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  8116   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  8295

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8296   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8475

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8476   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8655

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  8656   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  8835

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  8836   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  9015

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9016   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  9195

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9196   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9375

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9376   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9555

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9556   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9735

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9736   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  9915

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  9916   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10095

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10096  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10275

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10276  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10455

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10456  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10635

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10636  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10815

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  10816  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  10995

Query  1188   EQLNNSFPSSRGHNV  1202
              EQLNNSFPSSRG N 
Sbjct  10996  EQLNNSFPSSRGRNT  11040


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +3

Query  1198   RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  11058  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  11156


 Score = 59.3 bits (142),  Expect = 1e-05, Method: Compositional matrix adjust.
 Identities = 81/382 (21%), Positives = 175/382 (45%), Gaps = 54/382 (14%)
 Frame = +1

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  L  ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  6001  VPSTYLTEI----------THVSQALLEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  6138

Query  61    E---QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +   Q+     ++I + +    +++    R  + + + ++  QW++V +  ++R+ + + 
Sbjct  6139  KDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFDR  6318

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  6319  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  6462

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  LEE 
Sbjct  6463  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQ  6642

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG    
Sbjct  6643  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG----  6810

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  6811  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKD  6981

Query  347   WKRLHLSLQE-------LLVWL  361
               +L   L++       LL+WL
Sbjct  6982  LGQLEKKLEDLEEQLNHLLLWL  7047


 Score = 46.2 bits (108),  Expect = 0.12, Method: Compositional matrix adjust.
 Identities = 91/422 (21%), Positives = 180/422 (42%), Gaps = 48/422 (11%)
 Frame = +1

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ E + L   L++ Q+ +   +    ++ +   ++ +RK     E I   W+ +
Sbjct  2932  EIMEQRLGELQALQSSLQEQQSGLYYLSTTVKEMSKKAPSEISRKYQSEFEEIEGRWKKL  3111

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               ++ E    LEE    L++    ++    W+ E         D   KE    L DS+ +
Sbjct  3112  SSQLVEHCQKLEEQMNKLRKIQNHIQTLKKWMAEV--------DVFLKEEWPALGDSEIL  3267

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L  +I+      ++++E  QKI    E  + A  L+  L  +N +W  + +
Sbjct  3268  KKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEAE-PEFASRLETELKELNTQWDHMCQ  3444

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFP-----AVQKQN  385
             +    +  L+   ++   L   L E+  W+ Q +++ L R      DF       +QK  
Sbjct  3445  QVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLER------DFEYKTPDELQKAV  3606

Query  386   DVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLR  445
             +  +  K E + KE  +    E+V   + + P    E L +E   L      Q +   L 
Sbjct  3607  EEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTT--NYQWLCTRLN  3780

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
              + + +   W       A W     E L  L++  +  +E++ KL+  E I G  + + +
Sbjct  3781  GKCKTLEEVW-------ACWH----ELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISE  3927

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
             +L DSL++ +             ++N + +  LA+ LT  G+     N   LE  N+RW+
Sbjct  3928  VL-DSLENLMRHS----------EDNPNQIRILAQTLTDGGVMDELIN-EELETFNSRWR  4071

Query  566   LL  567
              L
Sbjct  4072  EL  4077


 Score = 44.3 bits (103),  Expect = 0.40, Method: Compositional matrix adjust.
 Identities = 79/356 (22%), Positives = 155/356 (43%), Gaps = 42/356 (11%)
 Frame = +1

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             L  W++ +D  +K +   +GD E + + + + +  + D++  +P L  +    Q +KN+ 
Sbjct  3193  LKKWMAEVDVFLKEEWPALGDSEILKKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEA  3372

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               + A  + T+ ++ +  QWD + + +  R++ L   L+ +    +   E  + + QA  
Sbjct  3373  EPEFASRLETE-LKELNTQWDHMCQQVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAE-  3546

Query  142   KLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS--ADDT  196
               E + E  +   T D +QK + E K+  ++ +Q +  V +  +    ++      A + 
Sbjct  3547  --EEYLERDFEYKTPDELQKAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEA  3720

Query  197   RKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE----TTA  252
              K  + T   N  W  +  R++ +   LEE      +    LEK   WL E E    TT 
Sbjct  3721  LKKELETLTTNYQW--LCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEFKLKTTE  3894

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
             N+   A   E + E    ++ LM+                H+ D  +Q  + +   +D  
Sbjct  3895  NIPGGA---EEISEVLDSLENLMR----------------HSEDNPNQIRILAQTLTDGG  4017

Query  313   V---LLQRRLDNMNFKWSELRKKSLNIRSHLEAS----SDQWKRLHLSLQELLVWL  361
             V   L+   L+  N +W EL ++++  +  LE S     +  K LHL +QE L ++
Sbjct  4018  VMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEKSLHL-IQESLTFI  4182


 Score = 43.5 bits (101),  Expect = 0.82, Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 42/281 (14%)
 Frame = +1

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  4762  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVL  4941

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q ++ +    T+W+ 
Sbjct  4942  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHI----TKWI-  5100

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  +L   +  VD   D A  L
Sbjct  5101  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAELNDIRPKVDSTRDQAANL  5238

Query  188   LRDYSADDTRK-VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             + +   D  RK V      +N  + +I  R+   +A++    + L+QF  D++K L  L 
Sbjct  5239  MAN-RGDHCRKLVEPQISELNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-  5406

Query  247   EAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
             EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  5407  EAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRI  5529


>ref|NM_004006.2| Homo sapiens dystrophin (DMD), transcript variant Dp427m, mRNA
Length=13993

 Score = 2486 bits (6443),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1200/1215 (98%), Positives = 1200/1215 (98%), Gaps = 13/1215 (1%)
 Frame = +2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  7625   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  7804

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  7805   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  7984

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  7985   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  8164

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  8165   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  8344

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  8345   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  8524

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8525   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8704

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8705   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8884

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  8885   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  9064

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  9065   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  9244

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9245   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  9424

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9425   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9604

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9605   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9784

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9785   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9964

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9965   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  10144

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  10145  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10324

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10325  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10504

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10505  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10684

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10685  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10864

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10865  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  11044

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  11045  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  11224

Query  1188   EQLNNSFPSSRGHNV  1202
              EQLNNSFPSSRG N 
Sbjct  11225  EQLNNSFPSSRGRNT  11269


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +1

Query  1198   RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  11287  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  11385


 Score = 59.3 bits (142),  Expect = 1e-05, Method: Compositional matrix adjust.
 Identities = 81/382 (21%), Positives = 175/382 (45%), Gaps = 54/382 (14%)
 Frame = +2

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  L  ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  6230  VPSTYLTEI----------THVSQALLEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  6367

Query  61    E---QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +   Q+     ++I + +    +++    R  + + + ++  QW++V +  ++R+ + + 
Sbjct  6368  KDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFDR  6547

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  6548  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  6691

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  LEE 
Sbjct  6692  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQ  6871

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG    
Sbjct  6872  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG----  7039

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  7040  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKD  7210

Query  347   WKRLHLSLQE-------LLVWL  361
               +L   L++       LL+WL
Sbjct  7211  LGQLEKKLEDLEEQLNHLLLWL  7276


 Score = 46.2 bits (108),  Expect = 0.12, Method: Compositional matrix adjust.
 Identities = 91/422 (21%), Positives = 180/422 (42%), Gaps = 48/422 (11%)
 Frame = +2

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ E + L   L++ Q+ +   +    ++ +   ++ +RK     E I   W+ +
Sbjct  3161  EIMEQRLGELQALQSSLQEQQSGLYYLSTTVKEMSKKAPSEISRKYQSEFEEIEGRWKKL  3340

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               ++ E    LEE    L++    ++    W+ E         D   KE    L DS+ +
Sbjct  3341  SSQLVEHCQKLEEQMNKLRKIQNHIQTLKKWMAEV--------DVFLKEEWPALGDSEIL  3496

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L  +I+      ++++E  QKI    E  + A  L+  L  +N +W  + +
Sbjct  3497  KKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEAE-PEFASRLETELKELNTQWDHMCQ  3673

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFP-----AVQKQN  385
             +    +  L+   ++   L   L E+  W+ Q +++ L R      DF       +QK  
Sbjct  3674  QVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLER------DFEYKTPDELQKAV  3835

Query  386   DVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLR  445
             +  +  K E + KE  +    E+V   + + P    E L +E   L      Q +   L 
Sbjct  3836  EEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTT--NYQWLCTRLN  4009

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
              + + +   W       A W     E L  L++  +  +E++ KL+  E I G  + + +
Sbjct  4010  GKCKTLEEVW-------ACWH----ELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISE  4156

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
             +L DSL++ +             ++N + +  LA+ LT  G+     N   LE  N+RW+
Sbjct  4157  VL-DSLENLMRHS----------EDNPNQIRILAQTLTDGGVMDELIN-EELETFNSRWR  4300

Query  566   LL  567
              L
Sbjct  4301  EL  4306


 Score = 44.3 bits (103),  Expect = 0.40, Method: Compositional matrix adjust.
 Identities = 79/356 (22%), Positives = 155/356 (43%), Gaps = 42/356 (11%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             L  W++ +D  +K +   +GD E + + + + +  + D++  +P L  +    Q +KN+ 
Sbjct  3422  LKKWMAEVDVFLKEEWPALGDSEILKKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEA  3601

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               + A  + T+ ++ +  QWD + + +  R++ L   L+ +    +   E  + + QA  
Sbjct  3602  EPEFASRLETE-LKELNTQWDHMCQQVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAE-  3775

Query  142   KLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS--ADDT  196
               E + E  +   T D +QK + E K+  ++ +Q +  V +  +    ++      A + 
Sbjct  3776  --EEYLERDFEYKTPDELQKAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEA  3949

Query  197   RKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE----TTA  252
              K  + T   N  W  +  R++ +   LEE      +    LEK   WL E E    TT 
Sbjct  3950  LKKELETLTTNYQW--LCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEFKLKTTE  4123

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
             N+   A   E + E    ++ LM+                H+ D  +Q  + +   +D  
Sbjct  4124  NIPGGA---EEISEVLDSLENLMR----------------HSEDNPNQIRILAQTLTDGG  4246

Query  313   V---LLQRRLDNMNFKWSELRKKSLNIRSHLEAS----SDQWKRLHLSLQELLVWL  361
             V   L+   L+  N +W EL ++++  +  LE S     +  K LHL +QE L ++
Sbjct  4247  VMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEKSLHL-IQESLTFI  4411


 Score = 43.5 bits (101),  Expect = 0.82, Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 42/281 (14%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  4991  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVL  5170

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q ++ +    T+W+ 
Sbjct  5171  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHI----TKWI-  5329

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  +L   +  VD   D A  L
Sbjct  5330  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAELNDIRPKVDSTRDQAANL  5467

Query  188   LRDYSADDTRK-VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             + +   D  RK V      +N  + +I  R+   +A++    + L+QF  D++K L  L 
Sbjct  5468  MAN-RGDHCRKLVEPQISELNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-  5635

Query  247   EAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
             EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  5636  EAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRI  5758


>ref|NM_000109.3| Homo sapiens dystrophin (DMD), transcript variant Dp427c, mRNA
Length=14069

 Score = 2486 bits (6443),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1200/1215 (98%), Positives = 1200/1215 (98%), Gaps = 13/1215 (1%)
 Frame = +3

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  7701   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  7880

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  7881   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  8060

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  8061   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  8240

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  8241   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  8420

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  8421   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  8600

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8601   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8780

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8781   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8960

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  8961   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  9140

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  9141   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  9320

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9321   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  9500

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9501   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9680

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9681   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9860

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9861   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  10040

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  10041  SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  10220

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  10221  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10400

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10401  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10580

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10581  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10760

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10761  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10940

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10941  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  11120

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  11121  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  11300

Query  1188   EQLNNSFPSSRGHNV  1202
              EQLNNSFPSSRG N 
Sbjct  11301  EQLNNSFPSSRGRNT  11345


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +2

Query  1198   RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  11363  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  11461


 Score = 59.3 bits (142),  Expect = 1e-05, Method: Compositional matrix adjust.
 Identities = 81/382 (21%), Positives = 175/382 (45%), Gaps = 54/382 (14%)
 Frame = +3

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  L  ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  6306  VPSTYLTEI----------THVSQALLEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  6443

Query  61    E---QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +   Q+     ++I + +    +++    R  + + + ++  QW++V +  ++R+ + + 
Sbjct  6444  KDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFDR  6623

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  6624  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  6767

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  LEE 
Sbjct  6768  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQ  6947

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG    
Sbjct  6948  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG----  7115

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  7116  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKD  7286

Query  347   WKRLHLSLQE-------LLVWL  361
               +L   L++       LL+WL
Sbjct  7287  LGQLEKKLEDLEEQLNHLLLWL  7352


 Score = 46.2 bits (108),  Expect = 0.12, Method: Compositional matrix adjust.
 Identities = 91/422 (21%), Positives = 180/422 (42%), Gaps = 48/422 (11%)
 Frame = +3

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ E + L   L++ Q+ +   +    ++ +   ++ +RK     E I   W+ +
Sbjct  3237  EIMEQRLGELQALQSSLQEQQSGLYYLSTTVKEMSKKAPSEISRKYQSEFEEIEGRWKKL  3416

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               ++ E    LEE    L++    ++    W+ E         D   KE    L DS+ +
Sbjct  3417  SSQLVEHCQKLEEQMNKLRKIQNHIQTLKKWMAEV--------DVFLKEEWPALGDSEIL  3572

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L  +I+      ++++E  QKI    E  + A  L+  L  +N +W  + +
Sbjct  3573  KKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEAE-PEFASRLETELKELNTQWDHMCQ  3749

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFP-----AVQKQN  385
             +    +  L+   ++   L   L E+  W+ Q +++ L R      DF       +QK  
Sbjct  3750  QVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLER------DFEYKTPDELQKAV  3911

Query  386   DVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLR  445
             +  +  K E + KE  +    E+V   + + P    E L +E   L      Q +   L 
Sbjct  3912  EEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTT--NYQWLCTRLN  4085

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
              + + +   W       A W     E L  L++  +  +E++ KL+  E I G  + + +
Sbjct  4086  GKCKTLEEVW-------ACWH----ELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISE  4232

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
             +L DSL++ +             ++N + +  LA+ LT  G+     N   LE  N+RW+
Sbjct  4233  VL-DSLENLMRHS----------EDNPNQIRILAQTLTDGGVMDELIN-EELETFNSRWR  4376

Query  566   LL  567
              L
Sbjct  4377  EL  4382


 Score = 44.3 bits (103),  Expect = 0.40, Method: Compositional matrix adjust.
 Identities = 79/356 (22%), Positives = 155/356 (43%), Gaps = 42/356 (11%)
 Frame = +3

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             L  W++ +D  +K +   +GD E + + + + +  + D++  +P L  +    Q +KN+ 
Sbjct  3498  LKKWMAEVDVFLKEEWPALGDSEILKKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEA  3677

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               + A  + T+ ++ +  QWD + + +  R++ L   L+ +    +   E  + + QA  
Sbjct  3678  EPEFASRLETE-LKELNTQWDHMCQQVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAE-  3851

Query  142   KLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS--ADDT  196
               E + E  +   T D +QK + E K+  ++ +Q +  V +  +    ++      A + 
Sbjct  3852  --EEYLERDFEYKTPDELQKAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEA  4025

Query  197   RKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE----TTA  252
              K  + T   N  W  +  R++ +   LEE      +    LEK   WL E E    TT 
Sbjct  4026  LKKELETLTTNYQW--LCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEFKLKTTE  4199

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
             N+   A   E + E    ++ LM+                H+ D  +Q  + +   +D  
Sbjct  4200  NIPGGA---EEISEVLDSLENLMR----------------HSEDNPNQIRILAQTLTDGG  4322

Query  313   V---LLQRRLDNMNFKWSELRKKSLNIRSHLEAS----SDQWKRLHLSLQELLVWL  361
             V   L+   L+  N +W EL ++++  +  LE S     +  K LHL +QE L ++
Sbjct  4323  VMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEKSLHL-IQESLTFI  4487


 Score = 43.5 bits (101),  Expect = 0.82, Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 42/281 (14%)
 Frame = +3

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  5067  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVL  5246

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q ++ +    T+W+ 
Sbjct  5247  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHI----TKWI-  5405

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  +L   +  VD   D A  L
Sbjct  5406  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAELNDIRPKVDSTRDQAANL  5543

Query  188   LRDYSADDTRK-VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             + +   D  RK V      +N  + +I  R+   +A++    + L+QF  D++K L  L 
Sbjct  5544  MAN-RGDHCRKLVEPQISELNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-  5711

Query  247   EAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
             EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  5712  EAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRI  5834


>gb|EU048698.1| Shuttle vector phcAd.DYS-FL, complete sequence
Length=30440

 Score = 2486 bits (6443),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1200/1215 (98%), Positives = 1200/1215 (98%), Gaps = 13/1215 (1%)
 Frame = -2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  11656  MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  11477

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  11476  EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  11297

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  11296  DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  11117

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  11116  NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  10937

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  10936  FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  10757

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  10756  KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  10577

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  10576  LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  10397

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  10396  LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  10217

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  10216  EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  10037

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  10036  QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  9857

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9856   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9677

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9676   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9497

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9496   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9317

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9316   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  9137

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  9136   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  8957

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  8956   TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  8777

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  8776   APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  8597

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  8596   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  8417

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  8416   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  8237

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  8236   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  8057

Query  1188   EQLNNSFPSSRGHNV  1202
              EQLNNSFPSSRG N 
Sbjct  8056   EQLNNSFPSSRGRNT  8012


 Score = 59.3 bits (142),  Expect = 1e-05, Method: Compositional matrix adjust.
 Identities = 81/382 (21%), Positives = 175/382 (45%), Gaps = 54/382 (14%)
 Frame = -2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              +PS+ + E+          T ++  L  ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  13051  VPSTYLTEI----------THVSQALLEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  12914

Query  61     E---QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
              +   Q+     ++I + +    +++    R  + + + ++  QW++V +  ++R+ + + 
Sbjct  12913  KDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFDR  12734

Query  118    M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                         +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  12733  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  12590

Query  168    KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
                + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  LEE 
Sbjct  12589  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQ  12410

Query  228    HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
                +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG    
Sbjct  12409  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG----  12242

Query  288    HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                 +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  12241  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKD  12071

Query  347    WKRLHLSLQE-------LLVWL  361
                +L   L++       LL+WL
Sbjct  12070  LGQLEKKLEDLEEQLNHLLLWL  12005


 Score = 45.8 bits (107),  Expect = 0.13, Method: Compositional matrix adjust.
 Identities = 91/422 (21%), Positives = 180/422 (42%), Gaps = 48/422 (11%)
 Frame = -2

Query  154    DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
              + +++++ E + L   L++ Q+ +   +    ++ +   ++ +RK     E I   W+ +
Sbjct  16120  EIMEQRLGELQALQSSLQEQQSGLYYLSTTVKEMSKKAPSEISRKYQSEFEEIEGRWKKL  15941

Query  214    HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
                ++ E    LEE    L++    ++    W+ E         D   KE    L DS+ +
Sbjct  15940  SSQLVEHCQKLEEQMNKLRKIQNHIQTLKKWMAEV--------DVFLKEEWPALGDSEIL  15785

Query  272    KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
              K+ +KQ + L  +I+      ++++E  QKI    E  + A  L+  L  +N +W  + +
Sbjct  15784  KKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEAE-PEFASRLETELKELNTQWDHMCQ  15608

Query  332    KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFP-----AVQKQN  385
              +    +  L+   ++   L   L E+  W+ Q +++ L R      DF       +QK  
Sbjct  15607  QVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLER------DFEYKTPDELQKAV  15446

Query  386    DVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLR  445
              +  +  K E + KE  +    E+V   + + P    E L +E   L      Q +   L 
Sbjct  15445  EEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTT--NYQWLCTRLN  15272

Query  446    KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
               + + +   W       A W     E L  L++  +  +E++ KL+  E I G  + + +
Sbjct  15271  GKCKTLEEVW-------ACWH----ELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISE  15125

Query  506    LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
              +L DSL++ +             ++N + +  LA+ LT  G+     N   LE  N+RW+
Sbjct  15124  VL-DSLENLMRHS----------EDNPNQIRILAQTLTDGGVMDELIN-EELETFNSRWR  14981

Query  566    LL  567
               L
Sbjct  14980  EL  14975


 Score = 44.3 bits (103),  Expect = 0.41, Method: Compositional matrix adjust.
 Identities = 79/356 (22%), Positives = 155/356 (43%), Gaps = 42/356 (11%)
 Frame = -2

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              L  W++ +D  +K +   +GD E + + + + +  + D++  +P L  +    Q +KN+ 
Sbjct  15859  LKKWMAEVDVFLKEEWPALGDSEILKKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEA  15680

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
                + A  + T+ ++ +  QWD + + +  R++ L   L+ +    +   E  + + QA  
Sbjct  15679  EPEFASRLETE-LKELNTQWDHMCQQVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAE-  15506

Query  142    KLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS--ADDT  196
                E + E  +   T D +QK + E K+  ++ +Q +  V +  +    ++      A + 
Sbjct  15505  --EEYLERDFEYKTPDELQKAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEA  15332

Query  197    RKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE----TTA  252
               K  + T   N  W  +  R++ +   LEE      +    LEK   WL E E    TT 
Sbjct  15331  LKKELETLTTNYQW--LCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEFKLKTTE  15158

Query  253    NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
              N+   A   E + E    ++ LM+                H+ D  +Q  + +   +D  
Sbjct  15157  NIPGGA---EEISEVLDSLENLMR----------------HSEDNPNQIRILAQTLTDGG  15035

Query  313    V---LLQRRLDNMNFKWSELRKKSLNIRSHLEAS----SDQWKRLHLSLQELLVWL  361
              V   L+   L+  N +W EL ++++  +  LE S     +  K LHL +QE L ++
Sbjct  15034  VMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEKSLHL-IQESLTFI  14870


 Score = 43.1 bits (100),  Expect = 0.86, Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 42/281 (14%)
 Frame = -2

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  14290  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVL  14111

Query  82     SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
                +E  T++ D++  + + W               E Q+H++   Q ++ +    T+W+ 
Sbjct  14110  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHI----TKWI-  13952

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                 +A+ +L       ES K+ P      Q+K    K+L  +L   +  VD   D A  L
Sbjct  13951  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAELNDIRPKVDSTRDQAANL  13814

Query  188    LRDYSADDTRK-VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
              + +   D  RK V      +N  + +I  R+   +A++    + L+QF  D++K L  L 
Sbjct  13813  MAN-RGDHCRKLVEPQISELNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-  13646

Query  247    EAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
              EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  13645  EAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRI  13523


>gb|M18533.1|HUMDYS Homo sapiens dystrophin (DMD) mRNA, complete cds
Length=13957

 Score = 2486 bits (6443),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1200/1215 (98%), Positives = 1200/1215 (98%), Gaps = 13/1215 (1%)
 Frame = +2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  7589   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  7768

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  7769   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  7948

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  7949   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  8128

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  8129   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  8308

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  8309   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  8488

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8489   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8668

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8669   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8848

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  8849   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  9028

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  9029   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  9208

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9209   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  9388

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9389   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9568

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9569   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9748

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9749   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9928

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9929   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  10108

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  10109  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10288

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10289  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10468

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10469  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10648

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10649  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10828

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10829  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  11008

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  11009  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  11188

Query  1188   EQLNNSFPSSRGHNV  1202
              EQLNNSFPSSRG N 
Sbjct  11189  EQLNNSFPSSRGRNT  11233


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +1

Query  1198   RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  11251  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  11349


 Score = 59.3 bits (142),  Expect = 1e-05, Method: Compositional matrix adjust.
 Identities = 81/382 (21%), Positives = 175/382 (45%), Gaps = 54/382 (14%)
 Frame = +2

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  L  ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  6194  VPSTYLTEI----------THVSQALLEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  6331

Query  61    E---QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +   Q+     ++I + +    +++    R  + + + ++  QW++V +  ++R+ + + 
Sbjct  6332  KDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFDR  6511

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  6512  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  6655

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  LEE 
Sbjct  6656  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQ  6835

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG    
Sbjct  6836  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG----  7003

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  7004  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKD  7174

Query  347   WKRLHLSLQE-------LLVWL  361
               +L   L++       LL+WL
Sbjct  7175  LGQLEKKLEDLEEQLNHLLLWL  7240


 Score = 45.8 bits (107),  Expect = 0.13, Method: Compositional matrix adjust.
 Identities = 91/422 (21%), Positives = 180/422 (42%), Gaps = 48/422 (11%)
 Frame = +2

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ E + L   L++ Q+ +   +    ++ +   ++ +RK     E I   W+ +
Sbjct  3125  EIMEQRLGELQALQSSLQEQQSGLYYLSTTVKEMSKKAPSEISRKYQSEFEEIEGRWKKL  3304

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               ++ E    LEE    L++    ++    W+ E         D   KE    L DS+ +
Sbjct  3305  SSQLVEHCQKLEEQMNKLRKIQNHIQTLKKWMAEV--------DVFLKEEWPALGDSEIL  3460

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L  +I+      ++++E  QKI    E  + A  L+  L  +N +W  + +
Sbjct  3461  KKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEAE-PEFASRLETELKELNTQWDHMCQ  3637

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFP-----AVQKQN  385
             +    +  L+   ++   L   L E+  W+ Q +++ L R      DF       +QK  
Sbjct  3638  QVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLER------DFEYKTPDELQKAV  3799

Query  386   DVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLR  445
             +  +  K E + KE  +    E+V   + + P    E L +E   L      Q +   L 
Sbjct  3800  EEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTT--NYQWLCTRLN  3973

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
              + + +   W       A W     E L  L++  +  +E++ KL+  E I G  + + +
Sbjct  3974  GKCKTLEEVW-------ACWH----ELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISE  4120

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
             +L DSL++ +             ++N + +  LA+ LT  G+     N   LE  N+RW+
Sbjct  4121  VL-DSLENLMRHS----------EDNPNQIRILAQTLTDGGVMDELIN-EELETFNSRWR  4264

Query  566   LL  567
              L
Sbjct  4265  EL  4270


 Score = 44.3 bits (103),  Expect = 0.41, Method: Compositional matrix adjust.
 Identities = 79/356 (22%), Positives = 155/356 (43%), Gaps = 42/356 (11%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             L  W++ +D  +K +   +GD E + + + + +  + D++  +P L  +    Q +KN+ 
Sbjct  3386  LKKWMAEVDVFLKEEWPALGDSEILKKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEA  3565

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               + A  + T+ ++ +  QWD + + +  R++ L   L+ +    +   E  + + QA  
Sbjct  3566  EPEFASRLETE-LKELNTQWDHMCQQVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAE-  3739

Query  142   KLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS--ADDT  196
               E + E  +   T D +QK + E K+  ++ +Q +  V +  +    ++      A + 
Sbjct  3740  --EEYLERDFEYKTPDELQKAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEA  3913

Query  197   RKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE----TTA  252
              K  + T   N  W  +  R++ +   LEE      +    LEK   WL E E    TT 
Sbjct  3914  LKKELETLTTNYQW--LCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEFKLKTTE  4087

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
             N+   A   E + E    ++ LM+                H+ D  +Q  + +   +D  
Sbjct  4088  NIPGGA---EEISEVLDSLENLMR----------------HSEDNPNQIRILAQTLTDGG  4210

Query  313   V---LLQRRLDNMNFKWSELRKKSLNIRSHLEAS----SDQWKRLHLSLQELLVWL  361
             V   L+   L+  N +W EL ++++  +  LE S     +  K LHL +QE L ++
Sbjct  4211  VMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEKSLHL-IQESLTFI  4375


 Score = 43.1 bits (100),  Expect = 0.86, Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 42/281 (14%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  4955  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVL  5134

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q ++ +    T+W+ 
Sbjct  5135  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHI----TKWI-  5293

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  +L   +  VD   D A  L
Sbjct  5294  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAELNDIRPKVDSTRDQAANL  5431

Query  188   LRDYSADDTRK-VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             + +   D  RK V      +N  + +I  R+   +A++    + L+QF  D++K L  L 
Sbjct  5432  MAN-RGDHCRKLVEPQISELNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-  5599

Query  247   EAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
             EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  5600  EAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRI  5722


>emb|X14298.1| Human mRNA for dystrophin
Length=12446

 Score = 2486 bits (6442),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1200/1215 (98%), Positives = 1200/1215 (98%), Gaps = 13/1215 (1%)
 Frame = +3

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  7479   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  7658

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  7659   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  7838

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  7839   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  8018

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  8019   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  8198

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  8199   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  8378

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8379   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8558

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8559   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8738

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  8739   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  8918

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  8919   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  9098

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9099   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  9278

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9279   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9458

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9459   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9638

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9639   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9818

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9819   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  9998

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  9999   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10178

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10179  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10358

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10359  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10538

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10539  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10718

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10719  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10898

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  10899  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  11078

Query  1188   EQLNNSFPSSRGHNV  1202
              EQLNNSFPSSRG N 
Sbjct  11079  EQLNNSFPSSRGRNT  11123


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +2

Query  1198   RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  11141  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  11239


 Score = 59.7 bits (143),  Expect = 1e-05, Method: Compositional matrix adjust.
 Identities = 81/382 (21%), Positives = 175/382 (45%), Gaps = 54/382 (14%)
 Frame = +3

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  L  ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  6084  VPSTYLTEI----------THVSQALLEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  6221

Query  61    E---QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +   Q+     ++I + +    +++    R  + + + ++  QW++V +  ++R+ + + 
Sbjct  6222  KDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFDR  6401

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  6402  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  6545

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  LEE 
Sbjct  6546  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQ  6725

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG    
Sbjct  6726  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG----  6893

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  6894  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKD  7064

Query  347   WKRLHLSLQE-------LLVWL  361
               +L   L++       LL+WL
Sbjct  7065  LGQLEKKLEDLEEQLNHLLLWL  7130


 Score = 46.6 bits (109),  Expect = 0.078, Method: Compositional matrix adjust.
 Identities = 91/423 (21%), Positives = 182/423 (43%), Gaps = 50/423 (11%)
 Frame = +3

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ E + L   L++ Q+ +   +    ++ +   ++ +RK     E I   W+ +
Sbjct  3015  EIMEQRLGELQALQSSLQEQQSGLYYLSTTVKEMSKKAPSEISRKYQSEFEEIEGRWKKL  3194

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               ++ E    LEE    L++    ++    W+ E         D   KE    L DS+ +
Sbjct  3195  SSQLVEHCQKLEEQMNKLRKIQNHIQTLKKWMAEV--------DVFLKEEWPALGDSEIL  3350

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L  +I+      ++++E  QKI    E  + A  L+  L  +N +W  + +
Sbjct  3351  KKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEAE-PEFASRLETELKELNTQWDHMCQ  3527

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFPAVQKQNDVHRA  390
             +    +  L+   ++   L   L E+  W+ Q +++ L R      DF   +  +++ +A
Sbjct  3528  QVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLER------DF-EYKTPDELQKA  3686

Query  391   F------KRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLL  444
             F      K E + KE  +    E+V   + + P    E L +E   L      Q +   L
Sbjct  3687  FEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTT--NYQWLCTRL  3860

Query  445   RKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVG  504
               + + +   W       A W     E L  L++  +  +E++ KL+  E I G  + + 
Sbjct  3861  NGKCKTLEEVW-------ACWH----ELLSYLEKANKWLNEVEFKLKTTENIPGGAEEIS  4007

Query  505   DLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRW  564
             ++L DSL++ +             ++N + +  LA+ LT  G+     N   LE  N+RW
Sbjct  4008  EVL-DSLENLMRHS----------EDNPNQIRILAQTLTDGGVMDELIN-EELETFNSRW  4151

Query  565   KLL  567
             + L
Sbjct  4152  REL  4160


 Score = 44.7 bits (104),  Expect = 0.35, Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 134/281 (47%), Gaps = 42/281 (14%)
 Frame = +3

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  4845  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVL  5024

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q ++ +    T+W+ 
Sbjct  5025  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHI----TKWI-  5183

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  +L   +  VD   D A  L
Sbjct  5184  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAELNDIRPKVDSTRDQAANL  5321

Query  188   LRDYSADDTRK-VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             + ++  D  RK V      +N  + +I  R+   +A++    + L+QF  D++K L  L 
Sbjct  5322  MANH-GDHCRKLVEPQISELNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-  5489

Query  247   EAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
             EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  5490  EAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRI  5612


 Score = 42.4 bits (98),  Expect = 1.6, Method: Compositional matrix adjust.
 Identities = 72/334 (21%), Positives = 143/334 (42%), Gaps = 37/334 (11%)
 Frame = +3

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             L  W++ +D  +K +   +GD E + + + + +  + D++  +P L  +    Q +KN+ 
Sbjct  3276  LKKWMAEVDVFLKEEWPALGDSEILKKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEA  3455

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               + A  + T+ ++ +  QWD + + +  R++ L   L+ +    +   E  + + QA  
Sbjct  3456  EPEFASRLETE-LKELNTQWDHMCQQVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAE-  3629

Query  142   KLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS--ADDT  196
               E + E  +   T D +QK   E K+  ++ +Q +  V +  +    ++      A + 
Sbjct  3630  --EEYLERDFEYKTPDELQKAFEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEA  3803

Query  197   RKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE----TTA  252
              K  + T   N  W  +  R++ +   LEE      +    LEK   WL E E    TT 
Sbjct  3804  LKKELETLTTNYQW--LCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEFKLKTTE  3977

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
             N+   A   E + E    ++ LM+                H+ D  +Q  + +   +D  
Sbjct  3978  NIPGGA---EEISEVLDSLENLMR----------------HSEDNPNQIRILAQTLTDGG  4100

Query  313   V---LLQRRLDNMNFKWSELRKKSLNIRSHLEAS  343
             V   L+   L+  N +W EL ++++  +  LE S
Sbjct  4101  VMDELINEELETFNSRWRELHEEAVRRQKLLEQS  4202


>gb|BC111836.3| Synthetic construct Homo sapiens clone IMAGE:40080640, MGC:133428 
DMD protein (DMD) mRNA, encodes complete protein
Length=11116

 Score = 2485 bits (6441),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1201/1226 (97%), Positives = 1203/1226 (98%), Gaps = 13/1226 (1%)
 Frame = +2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  7415   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  7594

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  7595   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  7774

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  7775   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  7954

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  7955   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  8134

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  8135   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  8314

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8315   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8494

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8495   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8674

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERL+ELQ
Sbjct  8675   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLRELQ  8854

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  8855   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  9034

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9035   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  9214

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9215   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9394

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9395   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9574

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9575   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9754

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9755   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  9934

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  9935   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10114

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10115  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10294

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10295  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10474

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10475  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10654

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10655  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10834

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  10835  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  11014

Query  1188   EQLNNSFPSSRGHNVGSLFHMADDLG  1213
              EQLNNSFPSSRG N        D +G
Sbjct  11015  EQLNNSFPSSRGRNTPGKPMREDTMG  11092


 Score = 59.7 bits (143),  Expect = 9e-06, Method: Compositional matrix adjust.
 Identities = 81/382 (21%), Positives = 175/382 (45%), Gaps = 54/382 (14%)
 Frame = +2

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  L  ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  6020  VPSTYLTEI----------THVSQALLEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  6157

Query  61    E---QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +   Q+     ++I + +    +++    R  + + + ++  QW++V +  ++R+ + + 
Sbjct  6158  KDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFDR  6337

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  6338  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  6481

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  LEE 
Sbjct  6482  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQ  6661

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG    
Sbjct  6662  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG----  6829

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  6830  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKD  7000

Query  347   WKRLHLSLQE-------LLVWL  361
               +L   L++       LL+WL
Sbjct  7001  LGQLEKKLEDLEEQLNHLLLWL  7066


 Score = 46.6 bits (109),  Expect = 0.096, Method: Compositional matrix adjust.
 Identities = 91/422 (21%), Positives = 180/422 (42%), Gaps = 48/422 (11%)
 Frame = +2

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ E + L   L++ Q+ +   +    ++ +   ++ +RK     E I   W+ +
Sbjct  2951  EIMEQRLGELQALQSSLQEQQSGLYYLSTTVKEMSKKAPSEISRKYQSEFEEIEGRWKKL  3130

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               ++ E    LEE    L++    ++    W+ E         D   KE    L DS+ +
Sbjct  3131  SSQLVEHCQKLEEQMNKLRKIQNHIQTLKKWMAEV--------DVFLKEEWPALGDSEIL  3286

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L  +I+      ++++E  QKI    E  + A  L+  L  +N +W  + +
Sbjct  3287  KKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEAE-PEFASRLETELKELNTQWDHMCQ  3463

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFP-----AVQKQN  385
             +    +  L+   ++   L   L E+  W+ Q +++ L R      DF       +QK  
Sbjct  3464  QVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLER------DFEYKTPDELQKAV  3625

Query  386   DVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLR  445
             +  +  K E + KE  +    E+V   + + P    E L +E   L      Q +   L 
Sbjct  3626  EEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTT--NYQWLCTRLN  3799

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
              + + +   W       A W     E L  L++  +  +E++ KL+  E I G  + + +
Sbjct  3800  GKCKTLEEVW-------ACWH----ELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISE  3946

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
             +L DSL++ +             ++N + +  LA+ LT  G+     N   LE  N+RW+
Sbjct  3947  VL-DSLENLMRHS----------EDNPNQIRILAQTLTDGGVMDELIN-EELETFNSRWR  4090

Query  566   LL  567
              L
Sbjct  4091  EL  4096


 Score = 44.7 bits (104),  Expect = 0.32, Method: Compositional matrix adjust.
 Identities = 79/356 (22%), Positives = 155/356 (43%), Gaps = 42/356 (11%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             L  W++ +D  +K +   +GD E + + + + +  + D++  +P L  +    Q +KN+ 
Sbjct  3212  LKKWMAEVDVFLKEEWPALGDSEILKKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEA  3391

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               + A  + T+ ++ +  QWD + + +  R++ L   L+ +    +   E  + + QA  
Sbjct  3392  EPEFASRLETE-LKELNTQWDHMCQQVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAE-  3565

Query  142   KLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS--ADDT  196
               E + E  +   T D +QK + E K+  ++ +Q +  V +  +    ++      A + 
Sbjct  3566  --EEYLERDFEYKTPDELQKAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEA  3739

Query  197   RKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE----TTA  252
              K  + T   N  W  +  R++ +   LEE      +    LEK   WL E E    TT 
Sbjct  3740  LKKELETLTTNYQW--LCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEFKLKTTE  3913

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
             N+   A   E + E    ++ LM+                H+ D  +Q  + +   +D  
Sbjct  3914  NIPGGA---EEISEVLDSLENLMR----------------HSEDNPNQIRILAQTLTDGG  4036

Query  313   V---LLQRRLDNMNFKWSELRKKSLNIRSHLEAS----SDQWKRLHLSLQELLVWL  361
             V   L+   L+  N +W EL ++++  +  LE S     +  K LHL +QE L ++
Sbjct  4037  VMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEKSLHL-IQESLTFI  4201


 Score = 43.5 bits (101),  Expect = 0.71, Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 42/281 (14%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  4781  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVL  4960

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q ++ +    T+W+ 
Sbjct  4961  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHI----TKWI-  5119

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  +L   +  VD   D A  L
Sbjct  5120  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAELNDIRPKVDSTRDQAANL  5257

Query  188   LRDYSADDTRK-VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             + +   D  RK V      +N  + +I  R+   +A++    + L+QF  D++K L  L 
Sbjct  5258  MAN-RGDHCRKLVEPQISELNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-  5425

Query  247   EAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
             EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  5426  EAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRI  5548


>gb|BC118002.1| Synthetic construct Homo sapiens clone IMAGE:40080832, MGC:133386 
DMD protein (DMD) mRNA, encodes complete protein
Length=11116

 Score = 2485 bits (6441),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1201/1226 (97%), Positives = 1203/1226 (98%), Gaps = 13/1226 (1%)
 Frame = +2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  7415   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  7594

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  7595   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  7774

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  7775   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  7954

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  7955   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  8134

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  8135   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  8314

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8315   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8494

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8495   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8674

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERL+ELQ
Sbjct  8675   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLRELQ  8854

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  8855   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  9034

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9035   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  9214

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9215   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9394

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9395   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9574

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9575   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9754

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9755   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  9934

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  9935   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10114

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10115  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10294

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10295  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10474

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10475  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10654

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10655  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10834

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  10835  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  11014

Query  1188   EQLNNSFPSSRGHNVGSLFHMADDLG  1213
              EQLNNSFPSSRG N        D +G
Sbjct  11015  EQLNNSFPSSRGRNTPGKPMREDTMG  11092


 Score = 59.7 bits (143),  Expect = 9e-06, Method: Compositional matrix adjust.
 Identities = 81/382 (21%), Positives = 175/382 (45%), Gaps = 54/382 (14%)
 Frame = +2

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  L  ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  6020  VPSTYLTEI----------THVSQALLEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  6157

Query  61    E---QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +   Q+     ++I + +    +++    R  + + + ++  QW++V +  ++R+ + + 
Sbjct  6158  KDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFDR  6337

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  6338  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  6481

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  LEE 
Sbjct  6482  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQ  6661

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG    
Sbjct  6662  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG----  6829

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  6830  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKD  7000

Query  347   WKRLHLSLQE-------LLVWL  361
               +L   L++       LL+WL
Sbjct  7001  LGQLEKKLEDLEEQLNHLLLWL  7066


 Score = 46.6 bits (109),  Expect = 0.096, Method: Compositional matrix adjust.
 Identities = 91/422 (21%), Positives = 180/422 (42%), Gaps = 48/422 (11%)
 Frame = +2

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ E + L   L++ Q+ +   +    ++ +   ++ +RK     E I   W+ +
Sbjct  2951  EIMEQRLGELQALQSSLQEQQSGLYYLSTTVKEMSKKAPSEISRKYQSEFEEIEGRWKKL  3130

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               ++ E    LEE    L++    ++    W+ E         D   KE    L DS+ +
Sbjct  3131  SSQLVEHCQKLEEQMNKLRKIQNHIQTLKKWMAEV--------DVFLKEEWPALGDSEIL  3286

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L  +I+      ++++E  QKI    E  + A  L+  L  +N +W  + +
Sbjct  3287  KKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEAE-PEFASRLETELKELNTQWDHMCQ  3463

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFP-----AVQKQN  385
             +    +  L+   ++   L   L E+  W+ Q +++ L R      DF       +QK  
Sbjct  3464  QVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLER------DFEYKTPDELQKAV  3625

Query  386   DVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLR  445
             +  +  K E + KE  +    E+V   + + P    E L +E   L      Q +   L 
Sbjct  3626  EEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTT--NYQWLCTRLN  3799

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
              + + +   W       A W     E L  L++  +  +E++ KL+  E I G  + + +
Sbjct  3800  GKCKTLEEVW-------ACWH----ELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISE  3946

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
             +L DSL++ +             ++N + +  LA+ LT  G+     N   LE  N+RW+
Sbjct  3947  VL-DSLENLMRHS----------EDNPNQIRILAQTLTDGGVMDELIN-EELETFNSRWR  4090

Query  566   LL  567
              L
Sbjct  4091  EL  4096


 Score = 44.7 bits (104),  Expect = 0.32, Method: Compositional matrix adjust.
 Identities = 79/356 (22%), Positives = 155/356 (43%), Gaps = 42/356 (11%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             L  W++ +D  +K +   +GD E + + + + +  + D++  +P L  +    Q +KN+ 
Sbjct  3212  LKKWMAEVDVFLKEEWPALGDSEILKKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEA  3391

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               + A  + T+ ++ +  QWD + + +  R++ L   L+ +    +   E  + + QA  
Sbjct  3392  EPEFASRLETE-LKELNTQWDHMCQQVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAE-  3565

Query  142   KLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS--ADDT  196
               E + E  +   T D +QK + E K+  ++ +Q +  V +  +    ++      A + 
Sbjct  3566  --EEYLERDFEYKTPDELQKAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEA  3739

Query  197   RKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE----TTA  252
              K  + T   N  W  +  R++ +   LEE      +    LEK   WL E E    TT 
Sbjct  3740  LKKELETLTTNYQW--LCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEFKLKTTE  3913

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
             N+   A   E + E    ++ LM+                H+ D  +Q  + +   +D  
Sbjct  3914  NIPGGA---EEISEVLDSLENLMR----------------HSEDNPNQIRILAQTLTDGG  4036

Query  313   V---LLQRRLDNMNFKWSELRKKSLNIRSHLEAS----SDQWKRLHLSLQELLVWL  361
             V   L+   L+  N +W EL ++++  +  LE S     +  K LHL +QE L ++
Sbjct  4037  VMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEKSLHL-IQESLTFI  4201


 Score = 43.5 bits (101),  Expect = 0.71, Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 42/281 (14%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  4781  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVL  4960

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q ++ +    T+W+ 
Sbjct  4961  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHI----TKWI-  5119

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  +L   +  VD   D A  L
Sbjct  5120  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAELNDIRPKVDSTRDQAANL  5257

Query  188   LRDYSADDTRK-VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             + +   D  RK V      +N  + +I  R+   +A++    + L+QF  D++K L  L 
Sbjct  5258  MAN-RGDHCRKLVEPQISELNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-  5425

Query  247   EAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
             EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  5426  EAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRI  5548


>gb|BC111934.1| Synthetic construct Homo sapiens clone IMAGE:40080736, MGC:133449 
DMD protein (DMD) mRNA, encodes complete protein
Length=11116

 Score = 2485 bits (6441),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1201/1226 (97%), Positives = 1203/1226 (98%), Gaps = 13/1226 (1%)
 Frame = +2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  7415   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  7594

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  7595   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  7774

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  7775   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  7954

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  7955   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  8134

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  8135   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  8314

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8315   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8494

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8495   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8674

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERL+ELQ
Sbjct  8675   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLRELQ  8854

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  8855   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  9034

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9035   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  9214

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9215   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9394

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9395   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9574

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9575   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9754

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9755   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  9934

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  9935   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10114

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10115  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10294

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10295  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10474

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10475  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10654

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10655  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10834

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  10835  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  11014

Query  1188   EQLNNSFPSSRGHNVGSLFHMADDLG  1213
              EQLNNSFPSSRG N        D +G
Sbjct  11015  EQLNNSFPSSRGRNTPGKPMREDTMG  11092


 Score = 59.7 bits (143),  Expect = 9e-06, Method: Compositional matrix adjust.
 Identities = 81/382 (21%), Positives = 175/382 (45%), Gaps = 54/382 (14%)
 Frame = +2

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  L  ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  6020  VPSTYLTEI----------THVSQALLEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  6157

Query  61    E---QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +   Q+     ++I + +    +++    R  + + + ++  QW++V +  ++R+ + + 
Sbjct  6158  KDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFDR  6337

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  6338  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  6481

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  LEE 
Sbjct  6482  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQ  6661

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG    
Sbjct  6662  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG----  6829

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  6830  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKD  7000

Query  347   WKRLHLSLQE-------LLVWL  361
               +L   L++       LL+WL
Sbjct  7001  LGQLEKKLEDLEEQLNHLLLWL  7066


 Score = 46.6 bits (109),  Expect = 0.096, Method: Compositional matrix adjust.
 Identities = 91/422 (21%), Positives = 180/422 (42%), Gaps = 48/422 (11%)
 Frame = +2

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ E + L   L++ Q+ +   +    ++ +   ++ +RK     E I   W+ +
Sbjct  2951  EIMEQRLGELQALQSSLQEQQSGLYYLSTTVKEMSKKAPSEISRKYQSEFEEIEGRWKKL  3130

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               ++ E    LEE    L++    ++    W+ E         D   KE    L DS+ +
Sbjct  3131  SSQLVEHCQKLEEQMNKLRKIQNHIQTLKKWMAEV--------DVFLKEEWPALGDSEIL  3286

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L  +I+      ++++E  QKI    E  + A  L+  L  +N +W  + +
Sbjct  3287  KKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEAE-PEFASRLETELKELNTQWDHMCQ  3463

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFP-----AVQKQN  385
             +    +  L+   ++   L   L E+  W+ Q +++ L R      DF       +QK  
Sbjct  3464  QVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLER------DFEYKTPDELQKAV  3625

Query  386   DVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLR  445
             +  +  K E + KE  +    E+V   + + P    E L +E   L      Q +   L 
Sbjct  3626  EEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTT--NYQWLCTRLN  3799

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
              + + +   W       A W     E L  L++  +  +E++ KL+  E I G  + + +
Sbjct  3800  GKCKTLEEVW-------ACWH----ELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISE  3946

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
             +L DSL++ +             ++N + +  LA+ LT  G+     N   LE  N+RW+
Sbjct  3947  VL-DSLENLMRHS----------EDNPNQIRILAQTLTDGGVMDELIN-EELETFNSRWR  4090

Query  566   LL  567
              L
Sbjct  4091  EL  4096


 Score = 44.7 bits (104),  Expect = 0.32, Method: Compositional matrix adjust.
 Identities = 79/356 (22%), Positives = 155/356 (43%), Gaps = 42/356 (11%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             L  W++ +D  +K +   +GD E + + + + +  + D++  +P L  +    Q +KN+ 
Sbjct  3212  LKKWMAEVDVFLKEEWPALGDSEILKKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEA  3391

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               + A  + T+ ++ +  QWD + + +  R++ L   L+ +    +   E  + + QA  
Sbjct  3392  EPEFASRLETE-LKELNTQWDHMCQQVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAE-  3565

Query  142   KLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS--ADDT  196
               E + E  +   T D +QK + E K+  ++ +Q +  V +  +    ++      A + 
Sbjct  3566  --EEYLERDFEYKTPDELQKAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEA  3739

Query  197   RKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE----TTA  252
              K  + T   N  W  +  R++ +   LEE      +    LEK   WL E E    TT 
Sbjct  3740  LKKELETLTTNYQW--LCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEFKLKTTE  3913

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
             N+   A   E + E    ++ LM+                H+ D  +Q  + +   +D  
Sbjct  3914  NIPGGA---EEISEVLDSLENLMR----------------HSEDNPNQIRILAQTLTDGG  4036

Query  313   V---LLQRRLDNMNFKWSELRKKSLNIRSHLEAS----SDQWKRLHLSLQELLVWL  361
             V   L+   L+  N +W EL ++++  +  LE S     +  K LHL +QE L ++
Sbjct  4037  VMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEKSLHL-IQESLTFI  4201


 Score = 43.5 bits (101),  Expect = 0.71, Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 42/281 (14%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  4781  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVL  4960

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q ++ +    T+W+ 
Sbjct  4961  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHI----TKWI-  5119

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  +L   +  VD   D A  L
Sbjct  5120  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAELNDIRPKVDSTRDQAANL  5257

Query  188   LRDYSADDTRK-VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             + +   D  RK V      +N  + +I  R+   +A++    + L+QF  D++K L  L 
Sbjct  5258  MAN-RGDHCRKLVEPQISELNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-  5425

Query  247   EAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
             EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  5426  EAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRI  5548


>gb|BC111587.2| Synthetic construct Homo sapiens clone IMAGE:40080544, MGC:133407 
DMD protein (DMD) mRNA, encodes complete protein
Length=11119

 Score = 2485 bits (6440),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1199/1215 (98%), Positives = 1200/1215 (98%), Gaps = 13/1215 (1%)
 Frame = +2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  7415   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  7594

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  7595   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  7774

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  7775   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  7954

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  7955   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  8134

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  8135   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  8314

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8315   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8494

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8495   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8674

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERL+ELQ
Sbjct  8675   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLRELQ  8854

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  8855   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  9034

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9035   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  9214

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9215   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9394

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9395   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9574

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9575   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9754

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9755   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  9934

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  9935   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10114

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10115  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10294

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10295  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10474

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10475  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10654

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10655  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10834

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  10835  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  11014

Query  1188   EQLNNSFPSSRGHNV  1202
              EQLNNSFPSSRG N 
Sbjct  11015  EQLNNSFPSSRGRNT  11059


 Score = 59.3 bits (142),  Expect = 1e-05, Method: Compositional matrix adjust.
 Identities = 81/382 (21%), Positives = 175/382 (45%), Gaps = 54/382 (14%)
 Frame = +2

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  L  ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  6020  VPSTYLTEI----------THVSQALLEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  6157

Query  61    E---QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +   Q+     ++I + +    +++    R  + + + ++  QW++V +  ++R+ + + 
Sbjct  6158  KDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFDR  6337

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  6338  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  6481

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  LEE 
Sbjct  6482  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQ  6661

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG    
Sbjct  6662  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG----  6829

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  6830  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKD  7000

Query  347   WKRLHLSLQE-------LLVWL  361
               +L   L++       LL+WL
Sbjct  7001  LGQLEKKLEDLEEQLNHLLLWL  7066


 Score = 46.2 bits (108),  Expect = 0.13, Method: Compositional matrix adjust.
 Identities = 91/422 (21%), Positives = 180/422 (42%), Gaps = 48/422 (11%)
 Frame = +2

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ E + L   L++ Q+ +   +    ++ +   ++ +RK     E I   W+ +
Sbjct  2951  EIMEQRLGELQALQSSLQEQQSGLYYLSTTVKEMSKKAPSEISRKYQSEFEEIEGRWKKL  3130

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               ++ E    LEE    L++    ++    W+ E         D   KE    L DS+ +
Sbjct  3131  SSQLVEHCQKLEEQMNKLRKIQNHIQTLKKWMAEV--------DVFLKEEWPALGDSEIL  3286

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L  +I+      ++++E  QKI    E  + A  L+  L  +N +W  + +
Sbjct  3287  KKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEAE-PEFASRLETELKELNTQWDHMCQ  3463

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFP-----AVQKQN  385
             +    +  L+   ++   L   L E+  W+ Q +++ L R      DF       +QK  
Sbjct  3464  QVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLER------DFEYKTPDELQKAV  3625

Query  386   DVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLR  445
             +  +  K E + KE  +    E+V   + + P    E L +E   L      Q +   L 
Sbjct  3626  EEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTT--NYQWLCTRLN  3799

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
              + + +   W       A W     E L  L++  +  +E++ KL+  E I G  + + +
Sbjct  3800  GKCKTLEEVW-------ACWH----ELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISE  3946

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
             +L DSL++ +             ++N + +  LA+ LT  G+     N   LE  N+RW+
Sbjct  3947  VL-DSLENLMRHS----------EDNPNQIRILAQTLTDGGVMDELIN-EELETFNSRWR  4090

Query  566   LL  567
              L
Sbjct  4091  EL  4096


 Score = 44.3 bits (103),  Expect = 0.40, Method: Compositional matrix adjust.
 Identities = 79/356 (22%), Positives = 155/356 (43%), Gaps = 42/356 (11%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             L  W++ +D  +K +   +GD E + + + + +  + D++  +P L  +    Q +KN+ 
Sbjct  3212  LKKWMAEVDVFLKEEWPALGDSEILKKQLKQCRLLVSDIQTIQPSLNSVNEGGQKIKNEA  3391

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               + A  + T+ ++ +  QWD + + +  R++ L   L+ +    +   E  + + QA  
Sbjct  3392  EPEFASRLETE-LKELNTQWDHMCQQVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAE-  3565

Query  142   KLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS--ADDT  196
               E + E  +   T D +QK + E K+  ++ +Q +  V +  +    ++      A + 
Sbjct  3566  --EEYLERDFEYKTPDELQKAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEA  3739

Query  197   RKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE----TTA  252
              K  + T   N  W  +  R++ +   LEE      +    LEK   WL E E    TT 
Sbjct  3740  LKKELETLTTNYQW--LCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEFKLKTTE  3913

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
             N+   A   E + E    ++ LM+                H+ D  +Q  + +   +D  
Sbjct  3914  NIPGGA---EEISEVLDSLENLMR----------------HSEDNPNQIRILAQTLTDGG  4036

Query  313   V---LLQRRLDNMNFKWSELRKKSLNIRSHLEAS----SDQWKRLHLSLQELLVWL  361
             V   L+   L+  N +W EL ++++  +  LE S     +  K LHL +QE L ++
Sbjct  4037  VMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQETEKSLHL-IQESLTFI  4201


 Score = 43.1 bits (100),  Expect = 0.85, Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 42/281 (14%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  4781  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVL  4960

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q ++ +    T+W+ 
Sbjct  4961  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHI----TKWI-  5119

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  +L   +  VD   D A  L
Sbjct  5120  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAELNDIRPKVDSTRDQAANL  5257

Query  188   LRDYSADDTRK-VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             + +   D  RK V      +N  + +I  R+   +A++    + L+QF  D++K L  L 
Sbjct  5258  MAN-RGDHCRKLVEPQISELNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-  5425

Query  247   EAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
             EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  5426  EAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRI  5548


>ref|NM_004012.3| Homo sapiens dystrophin (DMD), transcript variant Dp260-2, mRNA
Length=9914

 Score = 2484 bits (6439),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1200/1215 (98%), Positives = 1200/1215 (98%), Gaps = 13/1215 (1%)
 Frame = +3

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  3546  MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  3725

Query  61    EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
             EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  3726  EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  3905

Query  121   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
             DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  3906  DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  4085

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  4086  NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  4265

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
             FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  4266  FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  4445

Query  301   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
             KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  4446  KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  4625

Query  361   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
             LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  4626  LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  4805

Query  421   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
             LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  4806  LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  4985

Query  481   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
             EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  4986  EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  5165

Query  541   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
             QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  5166  QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  5345

Query  601   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
             WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  5346  WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  5525

Query  661   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
             LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  5526  LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  5705

Query  721   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
             WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  5706  WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  5885

Query  781   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
             SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  5886  SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  6065

Query  841   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
             VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  6066  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  6245

Query  901   TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
             TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  6246  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  6425

Query  949   -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
              PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  6426  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  6605

Query  1008  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
             QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  6606  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  6785

Query  1068  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
             SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  6786  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  6965

Query  1128  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
             QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  6966  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  7145

Query  1188  EQLNNSFPSSRGHNV  1202
             EQLNNSFPSSRG N 
Sbjct  7146  EQLNNSFPSSRGRNT  7190


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +2

Query  1198  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  7208  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  7306


 Score = 60.5 bits (145),  Expect = 6e-06, Method: Compositional matrix adjust.
 Identities = 81/382 (21%), Positives = 175/382 (45%), Gaps = 54/382 (14%)
 Frame = +3

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  L  ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  2151  VPSTYLTEI----------THVSQALLEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  2288

Query  61    E---QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +   Q+     ++I + +    +++    R  + + + ++  QW++V +  ++R+ + + 
Sbjct  2289  KDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFDR  2468

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  2469  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  2612

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  LEE 
Sbjct  2613  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQ  2792

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG    
Sbjct  2793  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG----  2960

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  2961  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKD  3131

Query  347   WKRLHLSLQE-------LLVWL  361
               +L   L++       LL+WL
Sbjct  3132  LGQLEKKLEDLEEQLNHLLLWL  3197


 Score = 44.3 bits (103),  Expect = 0.47, Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 42/281 (14%)
 Frame = +3

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  912   LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVL  1091

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q ++ +    T+W+ 
Sbjct  1092  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHI----TKWI-  1250

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  +L   +  VD   D A  L
Sbjct  1251  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAELNDIRPKVDSTRDQAANL  1388

Query  188   LRDYSADDTRK-VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             + +   D  RK V      +N  + +I  R+   +A++    + L+QF  D++K L  L 
Sbjct  1389  MAN-RGDHCRKLVEPQISELNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-  1556

Query  247   EAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
             EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  1557  EAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRI  1679


>ref|NM_004011.3| Homo sapiens dystrophin (DMD), transcript variant Dp260-1, mRNA
Length=9771

 Score = 2484 bits (6439),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1200/1215 (98%), Positives = 1200/1215 (98%), Gaps = 13/1215 (1%)
 Frame = +1

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  3403  MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  3582

Query  61    EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
             EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  3583  EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  3762

Query  121   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
             DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  3763  DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  3942

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  3943  NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  4122

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
             FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  4123  FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  4302

Query  301   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
             KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  4303  KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  4482

Query  361   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
             LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  4483  LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  4662

Query  421   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
             LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  4663  LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  4842

Query  481   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
             EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  4843  EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  5022

Query  541   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
             QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  5023  QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  5202

Query  601   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
             WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  5203  WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  5382

Query  661   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
             LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  5383  LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  5562

Query  721   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
             WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  5563  WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  5742

Query  781   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
             SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  5743  SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  5922

Query  841   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
             VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  5923  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  6102

Query  901   TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
             TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  6103  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  6282

Query  949   -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
              PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  6283  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  6462

Query  1008  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
             QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  6463  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  6642

Query  1068  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
             SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  6643  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  6822

Query  1128  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
             QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  6823  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  7002

Query  1188  EQLNNSFPSSRGHNV  1202
             EQLNNSFPSSRG N 
Sbjct  7003  EQLNNSFPSSRGRNT  7047


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +3

Query  1198  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  7065  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  7163


 Score = 60.5 bits (145),  Expect = 6e-06, Method: Compositional matrix adjust.
 Identities = 81/382 (21%), Positives = 175/382 (45%), Gaps = 54/382 (14%)
 Frame = +1

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  L  ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  2008  VPSTYLTEI----------THVSQALLEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  2145

Query  61    E---QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +   Q+     ++I + +    +++    R  + + + ++  QW++V +  ++R+ + + 
Sbjct  2146  KDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGRFDR  2325

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  2326  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  2469

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  LEE 
Sbjct  2470  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRLEEQ  2649

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG    
Sbjct  2650  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG----  2817

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  2818  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEAQIKD  2988

Query  347   WKRLHLSLQE-------LLVWL  361
               +L   L++       LL+WL
Sbjct  2989  LGQLEKKLEDLEEQLNHLLLWL  3054


 Score = 44.3 bits (103),  Expect = 0.47, Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 42/281 (14%)
 Frame = +1

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  769   LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSITEVGEALKTVL  948

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q ++ +    T+W+ 
Sbjct  949   GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDHI----TKWI-  1107

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  +L   +  VD   D A  L
Sbjct  1108  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAELNDIRPKVDSTRDQAANL  1245

Query  188   LRDYSADDTRK-VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             + +   D  RK V      +N  + +I  R+   +A++    + L+QF  D++K L  L 
Sbjct  1246  MAN-RGDHCRKLVEPQISELNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-  1413

Query  247   EAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
             EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  1414  EAEIQQGVNLKEEDFNKDMNEDNEGTVKELLQRGDNLQQRI  1536


>ref|NM_004013.2| Homo sapiens dystrophin (DMD), transcript variant Dp140, mRNA
Length=7410

 Score = 2469 bits (6400),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1200/1215 (98%), Positives = 1200/1215 (98%), Gaps = 13/1215 (1%)
 Frame = +1

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  1042  MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  1221

Query  61    EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
             EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  1222  EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  1401

Query  121   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
             DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  1402  DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  1581

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  1582  NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  1761

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
             FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  1762  FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  1941

Query  301   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
             KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  1942  KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  2121

Query  361   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
             LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  2122  LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  2301

Query  421   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
             LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  2302  LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  2481

Query  481   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
             EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  2482  EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  2661

Query  541   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
             QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  2662  QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  2841

Query  601   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
             WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  2842  WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  3021

Query  661   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
             LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  3022  LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  3201

Query  721   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
             WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  3202  WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  3381

Query  781   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
             SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  3382  SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  3561

Query  841   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
             VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  3562  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  3741

Query  901   TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
             TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  3742  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  3921

Query  949   -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
              PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  3922  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  4101

Query  1008  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
             QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  4102  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  4281

Query  1068  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
             SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  4282  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  4461

Query  1128  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
             QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  4462  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  4641

Query  1188  EQLNNSFPSSRGHNV  1202
             EQLNNSFPSSRG N 
Sbjct  4642  EQLNNSFPSSRGRNT  4686


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +3

Query  1198  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  4704  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  4802


 Score = 55.8 bits (133),  Expect = 2e-04, Method: Compositional matrix adjust.
 Identities = 51/206 (24%), Positives = 99/206 (48%), Gaps = 15/206 (7%)
 Frame = +1

Query  164  KQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAA  223
            K+L   + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  
Sbjct  97   KELQDGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKR  276

Query  224  LEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQG  283
            LEE   +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG
Sbjct  277  LEEQKNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG  456

Query  284  EIEAHTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEA  342
                   +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA
Sbjct  457  -------ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEA  615

Query  343  SSDQWKRLHLSLQE-------LLVWL  361
                  +L   L++       LL+WL
Sbjct  616  QIKDLGQLEKKLEDLEEQLNHLLLWL  693


>gb|BC127103.1| Homo sapiens dystrophin, mRNA (cDNA clone IMAGE:40124458), complete 
cds
Length=4767

 Score = 2467 bits (6393),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1200/1215 (98%), Positives = 1200/1215 (98%), Gaps = 13/1215 (1%)
 Frame = +2

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  566   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  745

Query  61    EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
             EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  746   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  925

Query  121   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
             DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  926   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  1105

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  1106  NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  1285

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
             FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  1286  FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  1465

Query  301   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
             KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  1466  KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  1645

Query  361   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
             LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  1646  LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  1825

Query  421   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
             LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  1826  LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  2005

Query  481   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
             EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  2006  EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  2185

Query  541   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
             QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  2186  QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  2365

Query  601   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
             WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  2366  WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  2545

Query  661   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
             LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  2546  LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  2725

Query  721   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
             WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  2726  WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  2905

Query  781   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
             SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  2906  SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  3085

Query  841   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
             VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  3086  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  3265

Query  901   TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
             TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  3266  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  3445

Query  949   -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
              PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  3446  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  3625

Query  1008  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
             QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  3626  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  3805

Query  1068  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
             SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  3806  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  3985

Query  1128  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
             QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM
Sbjct  3986  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  4165

Query  1188  EQLNNSFPSSRGHNV  1202
             EQLNNSFPSSRG N 
Sbjct  4166  EQLNNSFPSSRGRNT  4210


 Score = 69.3 bits (168),  Expect = 1e-08, Method: Composition-based stats.
 Identities = 33/35 (94%), Positives = 34/35 (97%), Gaps = 0/35 (0%)
 Frame = +1

Query  1196  SSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             + RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  4222  NERGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  4326


>ref|XR_022800.1| PREDICTED: Pan troglodytes dystrophin (DMD), mRNA
Length=9503

 Score = 2450 bits (6349),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1195/1224 (97%), Positives = 1197/1224 (97%), Gaps = 22/1224 (1%)
 Frame = +1

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             MPSSLMLEVPALADFNRAWTELTDWLSLLD+VIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  3166  MPSSLMLEVPALADFNRAWTELTDWLSLLDRVIKSQRVMVGDLEDINEMIIKQKATMQDL  3345

Query  61    EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
             EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  3346  EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  3525

Query  121   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
             DSTQWLEAKEEAEQVLGQARAKLESWKEGPYT+DAIQKKITETKQLAKDLRQWQ NVDVA
Sbjct  3526  DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTIDAIQKKITETKQLAKDLRQWQINVDVA  3705

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             NDLALKLLRDYSADDTRKVHMITENINASW SIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  3706  NDLALKLLRDYSADDTRKVHMITENINASWGSIHKRVSEREAALEETHRLLQQFPLDLEK  3885

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
             FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTD YHNLDENSQ
Sbjct  3886  FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDAYHNLDENSQ  4065

Query  301   KI---------LRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
             KI         LRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH
Sbjct  4066  KICEIPGSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  4245

Query  352   LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
             LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI
Sbjct  4246  LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  4425

Query  412   FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
             FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE
Sbjct  4426  FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  4605

Query  472   TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
             TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN
Sbjct  4606  TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  4785

Query  532   VSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQH  591
             VSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQH
Sbjct  4786  VSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQH  4965

Query  592   FLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMK  651
             FLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMK
Sbjct  4966  FLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMK  5145

Query  652   LRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNV  711
             LRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNV
Sbjct  5146  LRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNV  5325

Query  712   PLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQ  771
             PLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQ
Sbjct  5326  PLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQ  5505

Query  772   RRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQS  831
             RRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQS
Sbjct  5506  RRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQS  5685

Query  832   MVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHK  891
             MVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHK
Sbjct  5686  MVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHK  5865

Query  892   MHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET---  948
             MHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET   
Sbjct  5866  MHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVT  6045

Query  949   ----------PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLL  998
                       PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLL
Sbjct  6046  LINFWPVDSAPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLL  6225

Query  999   IQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQH  1058
             IQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQH
Sbjct  6226  IQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQH  6405

Query  1059  EHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLH  1118
             EHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLH
Sbjct  6406  EHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLH  6585

Query  1119  RLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQD  1178
             RLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQD
Sbjct  6586  RLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQD  6765

Query  1179  TSTGLEEVMEQLNNSFPSSRGHNV  1202
             TSTGLEEVMEQLNNSFPSSRG N 
Sbjct  6766  TSTGLEEVMEQLNNSFPSSRGRNT  6837


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +3

Query  1198  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  6855  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  6953


 Score = 45.1 bits (105),  Expect = 0.23, Method: Compositional matrix adjust.
 Identities = 41/185 (22%), Positives = 83/185 (44%), Gaps = 19/185 (10%)
 Frame = +1

Query  164   KQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAA  223
             K +   L+Q    +D+ +      L+  +  +  K+      ++  W  ++K   +R+  
Sbjct  1900  KNIKDSLQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQLDFQWEKVNKMYKDRQGR  2079

Query  224   LEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQW--QDL  281
              + +    ++F  D++ F  WLTEAE          RK ++ E+ +  K    +W  ++L
Sbjct  2080  FDRSVEKWRRFHYDIKIFNQWLTEAE-------QFLRKTQIPENWEHAK---YKWYLKEL  2229

Query  282   QGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSEL------RKKSLN  335
             Q  I     V   L+   ++I++      DA +LQ +L ++N +W E+      RKK ++
Sbjct  2230  QDGIGQRQTVVRALNATGEEIIQQ-SSKTDASILQEKLGSLNLRWQEVCKQLSDRKKRVD  2406

Query  336   IRSHL  340
                H+
Sbjct  2407  AHKHI  2421


>ref|XM_850502.1| PREDICTED: Canis familiaris hypothetical protein LOC606758 (LOC606758), 
mRNA
Length=13507

 Score = 2449 bits (6348),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1175/1215 (96%), Positives = 1192/1215 (98%), Gaps = 13/1215 (1%)
 Frame = +3

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSL+LEVPALADFNRAWTELTDWLSLLD+VIKSQRVMVGDLEDINEMIIKQKAT+QDL
Sbjct  7275   MPSSLLLEVPALADFNRAWTELTDWLSLLDRVIKSQRVMVGDLEDINEMIIKQKATLQDL  7454

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQ+QWDEVQEHLQNRRQQLNEMLK
Sbjct  7455   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQSQWDEVQEHLQNRRQQLNEMLK  7634

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKE PYTVDAIQKKITETKQLAKDLRQWQ NVDVA
Sbjct  7635   DSTQWLEAKEEAEQVLGQARAKLESWKEAPYTVDAIQKKITETKQLAKDLRQWQINVDVA  7814

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASW SIHKR+SEREAALEETHRLLQQFPLDLEK
Sbjct  7815   NDLALKLLRDYSADDTRKVHMITENINASWASIHKRLSEREAALEETHRLLQQFPLDLEK  7994

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDAT KERLLEDSKGV+ELMKQWQDLQGEIEAHTD+YHNLDEN Q
Sbjct  7995   FLAWLTEAETTANVLQDATHKERLLEDSKGVRELMKQWQDLQGEIEAHTDIYHNLDENGQ  8174

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              K+LRSLEGSDDA LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8175   KVLRSLEGSDDAALLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8354

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8355   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8534

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNT+WEKLN+HSADWQRKIDE LERLQELQ
Sbjct  8535   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTQWEKLNVHSADWQRKIDEALERLQELQ  8714

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEI PLKENVS+VNDLAR
Sbjct  8715   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEITPLKENVSYVNDLAR  8894

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNL+TLEDLNTRWKLLQVA+EDR+RQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  8895   QLTTLGIQLSPYNLNTLEDLNTRWKLLQVAIEDRIRQLHEAHRDFGPASQHFLSTSVQGP  9074

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9075   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9254

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQ+INCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9255   LDLLSLSAACDALDQHNLKQNDQPMDILQVINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9434

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9435   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9614

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9615   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  9794

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  9795   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  9974

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  9975   TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10154

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10155  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10334

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10335  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10514

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10515  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10694

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTS+SMGEEDLLSPPQDTSTGLEEVM
Sbjct  10695  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSESMGEEDLLSPPQDTSTGLEEVM  10874

Query  1188   EQLNNSFPSSRGHNV  1202
              EQLN+SFPSSRG N 
Sbjct  10875  EQLNHSFPSSRGRNT  10919


 Score = 70.1 bits (170),  Expect = 8e-09, Method: Compositional matrix adjust.
 Identities = 32/33 (96%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +2

Query  1198   RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              RGHNVGSLFH+ADDLGRAMESLVSVMTDEEGAE
Sbjct  10937  RGHNVGSLFHLADDLGRAMESLVSVMTDEEGAE  11035


 Score = 69.7 bits (169),  Expect = 9e-09, Method: Compositional matrix adjust.
 Identities = 83/375 (22%), Positives = 168/375 (44%), Gaps = 47/375 (12%)
 Frame = +3

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  LS +++++ +  +   D ED+     KQ+ +++++
Sbjct  5901  VPSTYLTEI----------THVSQALSEVEELLNAPDLCAQDFEDL----FKQEESLKNI  6038

Query  61    EQRRPQLEELITAAQNLKNK---TSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +    Q+   I    N K     ++    R  + + + R+  QW+ V    ++R+ + + 
Sbjct  6039  KDSLQQISGRIDIIHNKKTAALHSATPAERAKLQEALSRLDFQWERVNNMYKDRQGRFDR  6218

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  6219  SVEKWRRFHYDMKILNQWLT---EAEQFLKKTQIP-ENWEHAKYK--------WYLKELQ  6362

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q Q+ V V N    ++++  S  D   +     ++N  W+ + K+++ER+  LEE 
Sbjct  6363  DGIGQRQSVVRVLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLAERKKRLEEQ  6542

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  D+ +F+ WL EA+  AN+  +   +++L       KE ++Q + L  E+  
Sbjct  6543  KNILSEFQRDVNEFVLWLEEADNVANIPLEPGNEQQL-------KEKLEQVKLLAEELPL  6701

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  6702  RQGILKQLNETGGTVLVSAPLSPEEQDKLENKLKQTNLQWIKVSRNLPEKQEEIEAHVKD  6881

Query  347   WKRLHLSLQELLVWL  361
               +L   L  LL+WL
Sbjct  6882  LGQLEEQLNHLLLWL  6926


 Score = 45.1 bits (105),  Expect = 0.28, Method: Compositional matrix adjust.
 Identities = 78/346 (22%), Positives = 145/346 (41%), Gaps = 33/346 (9%)
 Frame = +3

Query  12    LADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELI  71
             L  +  A  E+  WL   +  +++Q  +  D+E++ E     +  M DL   + ++  ++
Sbjct  933   LDSYQTALEEVLSWLLSAEDALQAQGEISNDVEEVKEQFHTHEGYMMDLTSHQGRVGNVL  1112

Query  72    TAAQNL--------KNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQL-NEMLKDS  122
                  L          +T  QE   ++  R E ++    E Q +L      L N+ LK+ 
Sbjct  1113  QLGSQLIGTGKLSEDEETEVQEQMNLLNSRWECLRVASMEKQSNLHKVLMDLQNQQLKEL  1292

Query  123   TQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVAND  182
               WL   EE  +       K+E    GP  ++ +++++ + K L +DL Q Q  V+    
Sbjct  1293  NDWLTKTEERTR-------KMEKEPLGP-DIEDLKRQVQQHKVLQEDLEQEQVRVNSLTH  1448

Query  183   LALKLLRDYSADD--TRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             + + +  D S+ D  T  +    + +   W +I +   +R   L++     Q+F  +   
Sbjct  1449  MVVVV--DESSGDHATAALEEQLKVLGDRWANICRWTEDRWVLLQDILLKWQRFTEEQCL  1622

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
             F AWL+E E   N +     K     D   V   +++   L+ ++E        L   +Q
Sbjct  1623  FSAWLSEKEDAVNKIHTTGFK-----DQSEVLSNLQKLAVLKTDLEKKKQTMDKLCSLNQ  1787

Query  301   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
              +L +L+ +  A  ++  LDN   +W  L +K       LE SS Q
Sbjct  1788  DLLSALKNTVVAHKMEAWLDNFAQRWDNLVQK-------LEKSSAQ  1904


 Score = 43.5 bits (101),  Expect = 0.83, Method: Compositional matrix adjust.
 Identities = 72/283 (25%), Positives = 134/283 (47%), Gaps = 46/283 (16%)
 Frame = +3

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  4662  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSVTEVGEALKTVL  4841

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E   ++ D++  + + W               E Q+H++N  Q ++ +    T W  
Sbjct  4842  GKKE--MLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMENFDQNVDYI----TNW--  4997

Query  128   AKEEAEQVLGQARAKL-ESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALK  186
                     + QA A L ES K+ P      Q+K    K+L  ++   +  VD   D A  
Sbjct  4998  --------IIQADALLDESEKKKP------QQKEDILKRLKAEMNDIRPKVDSTRDQAAN  5135

Query  187   LLRDYSADDTRKV--HMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAW  244
             L+ +   D  RKV    I+E +N  + +I  R+   +A++    + L+QF  D++K L  
Sbjct  5136  LMAN-RGDHCRKVVEPKISE-LNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEP  5303

Query  245   LTEAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
             L EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  5304  L-EAEIQQGVNLKEEDFNKDMSEDNEGTVKELLQRGDNLQQRI  5429


 Score = 41.2 bits (95),  Expect = 3.4, Method: Compositional matrix adjust.
 Identities = 66/332 (19%), Positives = 141/332 (42%), Gaps = 33/332 (9%)
 Frame = +3

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             L  W++ +D  +K +   +GD E +   + + +  + D++  +P L  +   AQ +KN+ 
Sbjct  3093  LKKWITEVDVFLKEEWPALGDSEILKRQLKQCRLLVNDIQTIQPSLNSVNEGAQKMKNEA  3272

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               + A  + T+ +  +  QWD +   +  R++ L   L  +    +   E  + + QA  
Sbjct  3273  EPEFAGRLETE-LRELNTQWDYMCRQVYARKEALKGGLDKTVSLQKDLSEMHEWMTQAE-  3446

Query  142   KLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRK  198
               E + E  +   T D +Q  + E K+  ++ +Q +  V +  +    ++          
Sbjct  3447  --EEYLERDFEYKTPDELQTAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPAAQEA  3620

Query  199   VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE----TTANV  254
             +    + +  +++ +  R++ +   LEE      +    LEK   WL+E E    TT N+
Sbjct  3621  LKKELDTLTTNYQWLCTRLNGKCKTLEEVWACWHELLSYLEKANKWLSEVEVKLKTTENI  3800

Query  255   LQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAV-  313
                          S G +E+ +    L+  ++      H+ D  +Q  + +   +D  V 
Sbjct  3801  -------------SGGAEEIAEVLDSLENLMQ------HSEDNPNQIRILAQTLTDGGVM  3923

Query  314   --LLQRRLDNMNFKWSELRKKSLNIRSHLEAS  343
               L+   L+  N +W EL ++++  +  LE S
Sbjct  3924  DELINEELETFNSRWRELHEEAVRRQKLLEQS  4019


 Score = 40.0 bits (92),  Expect = 9.0, Method: Compositional matrix adjust.
 Identities = 35/150 (23%), Positives = 77/150 (51%), Gaps = 4/150 (2%)
 Frame = +3

Query  420   GLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQEL  479
             GL  L    +E+  +    +++R  + + EE+   W+KL+    +  +K++E + +L+++
Sbjct  2895  GLNYLSTTVKEMSKKAPLSDISRKYQSEFEEIEGRWKKLSSQLVEHCQKLEEQMAKLRKI  3074

Query  480   QEATDELDLKLRQAEV-IKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDL  538
             Q     L   + + +V +K  W  +GD  I  L+  L++ + L  +I  ++ +++ VN+ 
Sbjct  3075  QNHIKTLKKWITEVDVFLKEEWPALGDSEI--LKRQLKQCRLLVNDIQTIQPSLNSVNEG  3248

Query  539   ARQLTTLGIQLSPYNLST-LEDLNTRWKLL  567
             A+++           L T L +LNT+W  +
Sbjct  3249  AQKMKNEAEPEFAGRLETELRELNTQWDYM  3338


>emb|AJ865385.1| Sus scrofa mRNA for dystrophin variant Dp427 (dmd gene)
Length=11470

 Score = 2447 bits (6342),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1175/1215 (96%), Positives = 1190/1215 (97%), Gaps = 13/1215 (1%)
 Frame = +2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSL+LEVPALADFNRAWTELTDWLSLLD+VIKSQRVMVGDLEDINEMIIKQKAT+QDL
Sbjct  7541   MPSSLLLEVPALADFNRAWTELTDWLSLLDRVIKSQRVMVGDLEDINEMIIKQKATLQDL  7720

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQ+QWDEVQEHLQNRRQQLNEMLK
Sbjct  7721   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQSQWDEVQEHLQNRRQQLNEMLK  7900

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKEGPYT+DAIQ+KITETKQLAKDLRQWQ NVDVA
Sbjct  7901   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTMDAIQRKITETKQLAKDLRQWQINVDVA  8080

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASW +IHKR+SERE  LEETHRLLQQFPLDLEK
Sbjct  8081   NDLALKLLRDYSADDTRKVHMITENINASWANIHKRLSERETVLEETHRLLQQFPLDLEK  8260

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDAT KERLLEDSKGV+ELMKQWQDLQGEIEAHTD+YHNLDEN Q
Sbjct  8261   FLAWLTEAETTANVLQDATHKERLLEDSKGVRELMKQWQDLQGEIEAHTDIYHNLDENGQ  8440

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSDDA+LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8441   KILRSLEGSDDAILLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8620

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGD PAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8621   LQLKDDELSRQAPIGGDCPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8800

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE LERLQELQ
Sbjct  8801   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDEALERLQELQ  8980

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGE APLKENVSHVNDLAR
Sbjct  8981   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEKAPLKENVSHVNDLAR  9160

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR+RQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9161   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRIRQLHEAHRDFGPASQHFLSTSVQGP  9340

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9341   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9520

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTT+YDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9521   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTVYDRLEQEHNNLVNVPLCVDMCLN  9700

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGI+SLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9701   WLLNVYDTGRTGRIRVLSFKTGIVSLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9880

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9881   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  10060

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  10061  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10240

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10241  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10420

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10421  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10600

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10601  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10780

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ LEDHNKQLESQLHRLRQLLEQP
Sbjct  10781  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQTLEDHNKQLESQLHRLRQLLEQP  10960

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTS+SMGEEDLLSPPQDTSTGLEEVM
Sbjct  10961  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSESMGEEDLLSPPQDTSTGLEEVM  11140

Query  1188   EQLNNSFPSSRGHNV  1202
              EQLNNSFPSSRG N 
Sbjct  11141  EQLNNSFPSSRGRNT  11185


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/35 (94%), Positives = 34/35 (97%), Gaps = 0/35 (0%)
 Frame = +1

Query  1196   SSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              S RGHNVGSLFH+ADDLGRAMESLVSVMTDEEGAE
Sbjct  11197  SERGHNVGSLFHLADDLGRAMESLVSVMTDEEGAE  11301


 Score = 66.2 bits (160),  Expect = 9e-08, Method: Compositional matrix adjust.
 Identities = 82/375 (21%), Positives = 169/375 (45%), Gaps = 47/375 (12%)
 Frame = +2

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  LS ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  6167  VPSAYLTEI----------THVSQALSEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  6304

Query  61    EQRRPQLEELITAAQNLKN---KTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +    Q+   +    N K    +++    RT + + + ++  QW+ V +  ++R+ + + 
Sbjct  6305  KDSLQQISGRVDIIHNKKTAGLQSATPVERTRLQEALSQLDFQWERVNKMYKDRQGKFDR  6484

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAE  L + +   E+W+   Y            K+L 
Sbjct  6485  SVEKWRRFHYDMKIFNQWLT---EAEHFLKKTQIP-ENWEHAKYK--------WYLKELQ  6628

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V V N    ++++  S  D   +     ++N  W+ + K+++ER+  LEE 
Sbjct  6629  DGIGQRQTIVRVLNATGEEVIQQSSKTDASILQEKLGSLNLRWQEVCKQLAERKKRLEEQ  6808

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+   +V  +   +++L E  + +K L ++    QG ++ 
Sbjct  6809  KNILSEFQRDLNEFVLWLEEADNITSVALEPGNEQQLKEKLEEIKLLAEELPLRQGTLK-  6985

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                    L+E    +L S   S ++   ++ +L   N +W ++ +     +  +EA    
Sbjct  6986  ------QLNETGGTVLVSAPISPEEQDKIENKLKQTNLQWIKVSRILPEKQGEIEAHIKD  7147

Query  347   WKRLHLSLQELLVWL  361
               +    L  LLVWL
Sbjct  7148  LGQFEEQLNHLLVWL  7192


 Score = 47.4 bits (111),  Expect = 0.048, Method: Compositional matrix adjust.
 Identities = 42/205 (20%), Positives = 92/205 (44%), Gaps = 13/205 (6%)
 Frame = +2

Query  164   KQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAA  223
             K +   L+Q    VD+ ++     L+  +  +  ++      ++  W  ++K   +R+  
Sbjct  6296  KNIKDSLQQISGRVDIIHNKKTAGLQSATPVERTRLQEALSQLDFQWERVNKMYKDRQGK  6475

Query  224   LEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQW--QDL  281
              + +    ++F  D++ F  WLTEAE          +K ++ E+ +  K    +W  ++L
Sbjct  6476  FDRSVEKWRRFHYDMKIFNQWLTEAE-------HFLKKTQIPENWEHAK---YKWYLKEL  6625

Query  282   QGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLE  341
             Q  I     +   L+   +++++      DA +LQ +L ++N +W E+ K+    +  LE
Sbjct  6626  QDGIGQRQTIVRVLNATGEEVIQQ-SSKTDASILQEKLGSLNLRWQEVCKQLAERKKRLE  6802

Query  342   ASSDQWKRLHLSLQELLVWLQLKDD  366
                +        L E ++WL+  D+
Sbjct  6803  EQKNILSEFQRDLNEFVLWLEEADN  6877


 Score = 45.8 bits (107),  Expect = 0.16, Method: Compositional matrix adjust.
 Identities = 71/282 (25%), Positives = 138/282 (48%), Gaps = 44/282 (15%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  ++  KAT +++E+++  L+ +    + LK   
Sbjct  4928  LTEWLAATDTELTKRSAVEGMPSNLDSEVVWGKATQKEIEKQKFHLKSISEIGEALKMVL  5107

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++N  Q ++ +    T+W+ 
Sbjct  5108  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMENFDQNVDHI----TKWI-  5266

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  ++   +  VD   D A  L
Sbjct  5267  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAEMNDMRPKVDSTRDQAANL  5404

Query  188   LRDYSADDTRKV--HMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWL  245
             + +   D  RKV    I+E +N  + +I  R+   +A++    + L+QF  D++K L  L
Sbjct  5405  MAN-RGDHCRKVIEPKISE-LNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL  5572

Query  246   TEAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
              EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  5573  -EAEIQQGVNLKEEDFNKDMSEDNEGTVKELLQRGDNLQQRI  5695


 Score = 44.7 bits (104),  Expect = 0.36, Method: Compositional matrix adjust.
 Identities = 81/355 (22%), Positives = 147/355 (41%), Gaps = 33/355 (9%)
 Frame = +2

Query  3     SSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQ  62
             SSL+     L  +  A  E+  WL   +  +++Q  +  D+E++ E     +  M DL  
Sbjct  1175  SSLLETEVNLDSYQTALEEVLSWLLSAEDTLQAQGEISNDVEEVKEQFHTHEGYMMDLTS  1354

Query  63    RRPQLEELITAAQNLKNK--------TSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQ  114
              + ++  ++     L  K        T  QE   ++  R E ++    E Q +L      
Sbjct  1355  HQGRIGSVLQLGSQLIGKGKLSEDEETEVQEQMNLLNSRWECLRVASVEKQSNLHKVLMD  1534

Query  115   L-NEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
             L N+ LK+   WL   EE  +       K+E    GP  ++ ++ +I + K L +DL Q 
Sbjct  1535  LQNQQLKELNDWLTKTEEKTR-------KMEKEPLGP-DLEDLKHQIQQHKVLQEDLEQE  1690

Query  174   QTNVDVANDLALKLLRDYSADD--TRKVHMITENINASWRSIHKRVSEREAALEETHRLL  231
             Q  V+    + + +  D S+ D  T  +    + +   W +I +   +R   L++     
Sbjct  1691  QVRVNSLTHMVVVV--DESSGDHATAALEEQLKVLGDRWANICRWTEDRWVLLQDILLKW  1864

Query  232   QQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDV  291
             Q+F  +   F  WL+E E   N +     K     D   +   +++   L+ ++E     
Sbjct  1865  QRFTEEQCLFSTWLSEKEDALNKIHTTGFK-----DQGEMLSSLQKLAVLKTDLEKKKQT  2029

Query  292   YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                L   +Q +L +L+ +  A  ++  LDN   +W  L +K       LE SS Q
Sbjct  2030  MDKLSSLNQDLLSTLKNTLVAQKMEAWLDNFAQRWDNLVQK-------LEKSSTQ  2173


>ref|XM_001488124.2| PREDICTED: Equus caballus similar to dystrophin (LOC100051515), 
mRNA
Length=11148

 Score = 2443 bits (6332),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1185/1270 (93%), Positives = 1200/1270 (94%), Gaps = 65/1270 (5%)
 Frame = +1

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSL+LEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKAT+QDL
Sbjct  7411   MPSSLLLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATLQDL  7590

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQ+QWDEVQEHLQNRRQQLNEMLK
Sbjct  7591   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQSQWDEVQEHLQNRRQQLNEMLK  7770

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKEGPYT+DAIQ+KITETKQLAKDLRQWQ NVDVA
Sbjct  7771   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTMDAIQRKITETKQLAKDLRQWQINVDVA  7950

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASW SIHKRVSE+EAALEETHRLLQQFPLDLEK
Sbjct  7951   NDLALKLLRDYSADDTRKVHMITENINASWASIHKRVSEQEAALEETHRLLQQFPLDLEK  8130

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDAT KERLLEDSKGV+ELMKQWQDLQGEIEAHTD+YHNLDEN Q
Sbjct  8131   FLAWLTEAETTANVLQDATHKERLLEDSKGVRELMKQWQDLQGEIEAHTDIYHNLDENGQ  8310

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSDDA++LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8311   KILRSLEGSDDAIVLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8490

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8491   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8670

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE LERLQELQ
Sbjct  8671   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDEALERLQELQ  8850

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  8851   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  9030

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR+RQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9031   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRIRQLHEAHRDFGPASQHFLSTSVQGP  9210

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSL                         
Sbjct  9211   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSL-------------------------  9315

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              +DLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEH+NLVNVPLCVDMCLN
Sbjct  9316   VDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHSNLVNVPLCVDMCLN  9495

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9496   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9675

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9676   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  9855

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  9856   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10035

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10036  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10215

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10216  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10395

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQH+HKGLSPLP
Sbjct  10396  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHDHKGLSPLP  10575

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10576  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10755

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTS+SMGEEDLLSPPQDTSTGLEEVM
Sbjct  10756  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSESMGEEDLLSPPQDTSTGLEEVM  10935

Query  1188   EQLNNSFPSSRG---------------------------HNVGSLFHMADDLGRAMESLV  1220
              EQLNNSFPSSRG                           HNVGSLFHMADDLGRAMESLV
Sbjct  10936  EQLNNSFPSSRGRNTPGKPMRELIADARILLVSASPTHRHNVGSLFHMADDLGRAMESLV  11115

Query  1221   SVMTDEEGAE  1230
              SVMTDEEGAE
Sbjct  11116  SVMTDEEGAE  11145


 Score = 70.5 bits (171),  Expect = 5e-09, Method: Compositional matrix adjust.
 Identities = 84/375 (22%), Positives = 167/375 (44%), Gaps = 47/375 (12%)
 Frame = +1

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  LS ++Q++ +  +   D ED+     KQ+ +++++
Sbjct  6037  VPSTYLTEI----------THVSQALSEVEQLLNAPDLRAKDFEDL----FKQEESLKNI  6174

Query  61    EQRRPQLEELITAAQNLKN---KTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +    Q+   I    N K    +++    R  + + + ++  QW+ V +  ++R+ + + 
Sbjct  6175  KDNLQQISGRIDVIHNKKTAALQSATPAERAKLQEALSQLDFQWESVNKVYKDRQGRFDR  6354

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  6355  SVEKWRRFHYDMKIFNQWLT---EAEQFLKKTQIP-ENWEHAKYK--------WYLKELQ  6498

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V V N    ++++  S  D   +     ++N  W+ + K+++ER+  LEE 
Sbjct  6499  DGIGQRQTVVRVLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLAERKKRLEEQ  6678

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+   +V  +   +++L       KE + Q + L  E+  
Sbjct  6679  KNILSEFQRDLNEFVLWLEEADNVTSVPLEPGNEQQL-------KEKLDQVKLLAEELPL  6837

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S +D   L+ +L   N +W ++ +     +  +EA    
Sbjct  6838  RQGILKQLNETGGTVLVSAPISPEDQDKLENKLKQTNLQWIKVSRDLPEKQGEIEAHIKD  7017

Query  347   WKRLHLSLQELLVWL  361
               +    L  LL+WL
Sbjct  7018  LGQFEEQLNHLLLWL  7062


 Score = 50.4 bits (119),  Expect = 0.005, Method: Compositional matrix adjust.
 Identities = 115/545 (21%), Positives = 230/545 (42%), Gaps = 53/545 (9%)
 Frame = +1

Query  33    IKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITD  92
             +K+Q +   +   I   +   K  +  L   +PQ+E L   +  LK K   Q    +  D
Sbjct  2608  LKTQPITTSEPTAIKSQLKICKDEVSRLSALQPQIERLKIQSIALKEK--GQGPMFLDAD  2781

Query  93    RIERIQNQWDEVQEHLQNRRQQLNEMLKD--STQWLEAKEEAEQVLGQARAKLESWKEGP  150
              +    N +++V   +Q R ++L  +      T++ E        + Q+  KL   +   
Sbjct  2782  FVA-FTNHFNQVFADVQAREKELQTIFDALPPTRYQETMSTILTWIQQSETKLSIPQVTV  2958

Query  151   YTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASW  210
                + +++++ E + L   L++ Q+ ++  +    ++ +   ++ +RK     E++   W
Sbjct  2959  TEYEIMEQRLGELQALQSSLQEQQSGLNYLSTTVKEMSKKAPSEISRKYQSEFEDVEGRW  3138

Query  211   RSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDS  268
             + +  ++ E    LEE    L++    ++    W+ E         D   KE    L DS
Sbjct  3139  KKLSSQLVEHSQKLEEQIAKLRKIQNHIKTLKKWMAEV--------DVFLKEEWPALGDS  3294

Query  269   KGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSE  328
             + +K+ +KQ + L  +I+      ++++E  QKI    E  + A  L+  L  +N +W  
Sbjct  3295  EILKKQLKQCRLLVNDIQTIQPSLNSVNEGGQKIKNEAE-PEFASRLETELGELNTQWDH  3471

Query  329   LRKKSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFP-----AVQ  382
             + ++    +  L+   D+   L   L E+  W+ Q +++ L R      DF       +Q
Sbjct  3472  MCRQVYARKEALKGGLDKTVSLQKDLSEMHEWMTQAEEEYLER------DFEYKTPDELQ  3633

Query  383   KQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTR  442
             K  +  +  K E + KE  +    E+V   + + P    E L +E   L      Q +  
Sbjct  3634  KAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPTAQEALKKELDTLTT--NYQWLCT  3807

Query  443   LLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQP  502
              L  + + +   W       A W     E L  L++  +  +E++ KL+  E I G  + 
Sbjct  3808  RLNGKCKTLEEVW-------ACWH----ELLSYLEKANKWLNEVEFKLKTTENIPGEPEE  3954

Query  503   VGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNT  562
             + ++L DSL++ ++            ++N + +  LA+ LT  G+     N   LE  N+
Sbjct  3955  ISEVL-DSLENLMQHS----------EDNPNQIRILAQTLTDGGVMDELIN-EELETFNS  4098

Query  563   RWKLL  567
             RW+ L
Sbjct  4099  RWREL  4113


 Score = 43.1 bits (100),  Expect = 0.87, Method: Compositional matrix adjust.
 Identities = 70/282 (24%), Positives = 135/282 (47%), Gaps = 44/282 (15%)
 Frame = +1

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  4798  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSVTELGEALKTVL  4977

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q ++ +    T W+ 
Sbjct  4978  GKKE--TLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQHVDHI----TNWI-  5136

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                +A+ +L       ES K+ P      Q+K    K+L  ++   +  VD   D A  L
Sbjct  5137  --IQADTLLD------ESEKKKP------QQKEDVLKRLKAEMNDMRPKVDSTRDQAANL  5274

Query  188   LRDYSADDTRKV--HMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWL  245
             + +   D  RKV    I+E +N  + +I  R+   +A++    + L+QF  D++K L  L
Sbjct  5275  MAN-RGDHCRKVVEPKISE-LNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL  5442

Query  246   TEAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
              EAE    V L++    + + ED++G VKEL+++  +LQ  I
Sbjct  5443  -EAEIQQGVNLKEEDFNKDMSEDNEGTVKELLQRGDNLQQRI  5565


 Score = 41.6 bits (96),  Expect = 2.6, Method: Compositional matrix adjust.
 Identities = 80/359 (22%), Positives = 148/359 (41%), Gaps = 43/359 (11%)
 Frame = +1

Query  3     SSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQ  62
             SSLM    +L  +  A  E+  WL   +  +++Q  +  D+E++ E     +  M DL  
Sbjct  1051  SSLMETEVSLDSYQTALEEVLSWLLSAEDTLQAQGEISNDVEEVKEQFHTHEGYMMDLTS  1230

Query  63    RRPQLEELITAAQNL--------KNKTSNQEARTIITDRIERIQNQWDEVQEH-----LQ  109
              + ++  ++     L          K S +    +I D   R+ +       H     LQ
Sbjct  1231  HQGRVGNVLQLGSQLVGTGKLSEDEKLSTRTMDLLIQDGCLRVASMEKIFSLHKVLMDLQ  1410

Query  110   NRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKD  169
             N++      LK+  +WL   EE  +       K+E    GP  ++A++ +I + K L +D
Sbjct  1411  NKQ------LKELNEWLTKTEERTK-------KMEKEPLGP-DLEALKHQIQQHKVLQED  1548

Query  170   LRQWQTNVDVANDLALKLLRDYSADD--TRKVHMITENINASWRSIHKRVSEREAALEET  227
             L Q Q  V+    + + +  D S+ D  T  +    + +   W +I +   +R   L++ 
Sbjct  1549  LEQEQVRVNSLTHMVVVV--DESSGDHATAALEEQLKVLGDRWANICRWTEDRWVLLQDI  1722

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
                 Q+F  +   F  WL+E E   N +     K     D   +   +++   L+ ++E 
Sbjct  1723  LLKWQRFTEEQCLFSTWLSEKEDAVNKIHTTGFK-----DQSEMLYSLQKLAVLKTDLEK  1887

Query  288   HTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                    L   +Q +L +L+ +  A  ++  LD+   +W  L +K       LE SS Q
Sbjct  1888  KKQTMDKLCSLNQDLLSTLKNTSVAQKMEAWLDSFAQRWDNLVQK-------LEKSSAQ  2043


>gb|AF070485.1| Canis familiaris dystrophin mRNA, complete cds
Length=13887

 Score = 2429 bits (6296),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1166/1215 (95%), Positives = 1186/1215 (97%), Gaps = 13/1215 (1%)
 Frame = +2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSL+LEVPALADFNRAWTELTDWLSLLD+VIKSQRVMVGDLEDINEMIIKQKAT+QDL
Sbjct  7655   MPSSLLLEVPALADFNRAWTELTDWLSLLDRVIKSQRVMVGDLEDINEMIIKQKATLQDL  7834

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQ+QWDEVQEHLQNRR QL EMLK
Sbjct  7835   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQSQWDEVQEHLQNRRLQLTEMLK  8014

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQVLGQARAKLESWKE PYTVDAIQKKITETKQLAKDLRQWQ NVDVA
Sbjct  8015   DSTQWLEAKEEAEQVLGQARAKLESWKEAPYTVDAIQKKITETKQLAKDLRQWQINVDVA  8194

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENINASW SIHKR+SEREAALEETHRLLQQFPLDLEK
Sbjct  8195   NDLALKLLRDYSADDTRKVHMITENINASWASIHKRLSEREAALEETHRLLQQFPLDLEK  8374

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDAT KERLLEDSKGV+ELMKQWQDLQGEIEAHTD+YHNLDEN Q
Sbjct  8375   FLAWLTEAETTANVLQDATHKERLLEDSKGVRELMKQWQDLQGEIEAHTDIYHNLDENGQ  8554

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              K+LRSLEGSDDA LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8555   KVLRSLEGSDDAALLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8734

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8735   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8914

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNT+WEKLN+HSADWQRKIDE LERLQELQ
Sbjct  8915   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTQWEKLNVHSADWQRKIDEALERLQELQ  9094

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEI PLKENVS+VNDLAR
Sbjct  9095   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEITPLKENVSYVNDLAR  9274

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNL+TLEDLNTRWKLLQVA+EDR+RQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9275   QLTTLGIQLSPYNLNTLEDLNTRWKLLQVAIEDRIRQLHEAHRDFGPASQHFLSTSVQGP  9454

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9455   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9634

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQ+INCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9635   LDLLSLSAACDALDQHNLKQNDQPMDILQVINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9814

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9815   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9994

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9995   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  10174

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  10175  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10354

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10355  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10534

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRL +MENSNGSYLNDSISPNESIDDEHLLIQHY +SLN
Sbjct  10535  APASSPQLSHDDTHSRIEHYASRLKKMENSNGSYLNDSISPNESIDDEHLLIQHYWRSLN  10714

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              Q+SPLSQPRSPAQILISLESEERGELERILADLE  NRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10715  QESPLSQPRSPAQILISLESEERGELERILADLEGRNRNLQAEYDRLKQQHEHKGLSPLP  10894

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10895  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  11074

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTS+SMGEEDLLSPPQDTSTGLEEVM
Sbjct  11075  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSESMGEEDLLSPPQDTSTGLEEVM  11254

Query  1188   EQLNNSFPSSRGHNV  1202
              EQLN+SFPSSRG N 
Sbjct  11255  EQLNHSFPSSRGRNT  11299


 Score = 70.1 bits (170),  Expect = 8e-09, Method: Compositional matrix adjust.
 Identities = 83/375 (22%), Positives = 168/375 (44%), Gaps = 47/375 (12%)
 Frame = +2

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             +PS+ + E+          T ++  LS +++++ +  +   D ED+     KQ+ +++++
Sbjct  6281  VPSTYLTEI----------THVSQALSEVEELLNAPDLCAQDFEDL----FKQEESLKNI  6418

Query  61    EQRRPQLEELITAAQNLKNK---TSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
             +    Q+   I    N K     ++    R  + + + R+  QW+ V    ++R+ + + 
Sbjct  6419  KDSLQQISGRIDIIHNKKTAALHSATPAERAKLQEALSRLDFQWERVNNMYKDRQGRFDR  6598

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  6599  SVEKWRRFHYDMKILNQWLT---EAEQFLKKTQIP-ENWEHAKYK--------WYLKELQ  6742

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q Q+ V V N    ++++  S  D   +     ++N  W+ + K+++ER+  LEE 
Sbjct  6743  DGIGQRQSVVRVLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLAERKKRLEEQ  6922

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  D+ +F+ WL EA+  AN+  +   +++L       KE ++Q + L  E+  
Sbjct  6923  KNILSEFQRDVNEFVLWLEEADNVANIPLEPGNEQQL-------KEKLEQVKLLAEELPL  7081

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  7082  RQGILKQLNETGGTVLVSAPLSPEEQDKLENKLKQTNLQWIKVSRNLPEKQEEIEAHVKD  7261

Query  347   WKRLHLSLQELLVWL  361
               +L   L  LL+WL
Sbjct  7262  LGQLEEQLNHLLLWL  7306


 Score = 70.1 bits (170),  Expect = 8e-09, Method: Compositional matrix adjust.
 Identities = 32/33 (96%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +1

Query  1198   RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              RGHNVGSLFH+ADDLGRAMESLVSVMTDEEGAE
Sbjct  11317  RGHNVGSLFHLADDLGRAMESLVSVMTDEEGAE  11415


 Score = 45.4 bits (106),  Expect = 0.22, Method: Compositional matrix adjust.
 Identities = 78/346 (22%), Positives = 145/346 (41%), Gaps = 33/346 (9%)
 Frame = +2

Query  12    LADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELI  71
             L  +  A  E+  WL   +  +++Q  +  D+E++ E     +  M DL   + ++  ++
Sbjct  1313  LDSYQTALEEVLSWLLSAEDALQAQGEISNDVEEVKEQFHTHEGYMMDLTSHQGRVGNVL  1492

Query  72    TAAQNL--------KNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQL-NEMLKDS  122
                  L          +T  QE   ++  R E ++    E Q +L      L N+ LK+ 
Sbjct  1493  QLGSQLIGTGKLSEDEETEVQEQMNLLNSRWECLRVASMEKQSNLHKVLMDLQNQQLKEL  1672

Query  123   TQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVAND  182
               WL   EE  +       K+E    GP  ++ +++++ + K L +DL Q Q  V+    
Sbjct  1673  NDWLTKTEERTR-------KMEKEPLGP-DIEDLKRQVQQHKVLQEDLEQEQVRVNSLTH  1828

Query  183   LALKLLRDYSADD--TRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             + + +  D S+ D  T  +    + +   W +I +   +R   L++     Q+F  +   
Sbjct  1829  MVVVV--DESSGDHATAALEEQLKVLGDRWANICRWTEDRWVLLQDILLKWQRFTEEQCL  2002

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
             F AWL+E E   N +     K     D   V   +++   L+ ++E        L   +Q
Sbjct  2003  FSAWLSEKEDAVNKIHTTGFK-----DQSEVLSNLQKLAVLKTDLEKKKQTMDKLCSLNQ  2167

Query  301   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
              +L +L+ +  A  ++  LDN   +W  L +K       LE SS Q
Sbjct  2168  DLLSALKNTVVAHKMEAWLDNFAQRWDNLVQK-------LEKSSAQ  2284


 Score = 41.6 bits (96),  Expect = 2.6, Method: Compositional matrix adjust.
 Identities = 66/332 (19%), Positives = 141/332 (42%), Gaps = 33/332 (9%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             L  W++ +D  +K +   +GD E +   + + +  + D++  +P L  +   AQ +KN+ 
Sbjct  3473  LKKWITEVDVFLKEEWPALGDSEILKRQLKQCRLLVNDIQTIQPSLNSVNEGAQKMKNEA  3652

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               + A  + T+ +  +  QWD +   +  R++ L   L  +    +   E  + + QA  
Sbjct  3653  EPEFAGRLETE-LRELNTQWDYMCRQVYARKEALKGGLDKTVSLQKDLSEMHEWMTQAE-  3826

Query  142   KLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRK  198
               E + E  +   T D +Q  + E K+  ++ +Q +  V +  +    ++          
Sbjct  3827  --EEYLERDFEYKTPDELQTAVEEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPAAQEA  4000

Query  199   VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE----TTANV  254
             +    + +  +++ +  R++ +   LEE      +    LEK   WL+E E    TT N+
Sbjct  4001  LKKELDTLTTNYQWLCTRLNGKCKTLEEVWACWHELLSYLEKANKWLSEVEVKLKTTENI  4180

Query  255   LQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAV-  313
                          S G +E+ +    L+  ++      H+ D  +Q  + +   +D  V 
Sbjct  4181  -------------SGGAEEIAEVLDSLENLMQ------HSEDNPNQIRILAQTLTDGGVM  4303

Query  314   --LLQRRLDNMNFKWSELRKKSLNIRSHLEAS  343
               L+   L+  N +W EL ++++  +  LE S
Sbjct  4304  DELINEELETFNSRWRELHEEAVRRQKLLEQS  4399


 Score = 41.6 bits (96),  Expect = 3.0, Method: Compositional matrix adjust.
 Identities = 69/269 (25%), Positives = 129/269 (47%), Gaps = 18/269 (6%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    + LK   
Sbjct  5042  LTEWLAATDMELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKVHLKSVTEVGEALKTVL  5221

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               +E   ++ D++  + + W  V    +     L E  K    + +  +     + QA A
Sbjct  5222  GKKE--MLVEDKLSLLNSNWIAVTSRAEEWLNLLLEYQKHMETFDQNVDYITNWIIQADA  5395

Query  142   KL-ESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKV-  199
              L ES K+ P      Q+K    K+L  ++   +  VD   D A  L+ +   D  RKV 
Sbjct  5396  LLDESEKKKP------QQKEDILKRLKAEMNDIRPKVDSTRDQAANLMAN-RGDHCRKVV  5554

Query  200   -HMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANV-LQD  257
                I+E +N  + +I  R+   +A++    + L+QF  D++K L  L EAE    V L++
Sbjct  5555  EPKISE-LNHRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL-EAEIQQGVNLKE  5722

Query  258   ATRKERLLEDSKG-VKELMKQWQDLQGEI  285
                 + + ED++G VKEL+++  +LQ  I
Sbjct  5723  EDFNKDMSEDNEGTVKELLQRGDNLQQRI  5809


 Score = 40.0 bits (92),  Expect = 8.8, Method: Compositional matrix adjust.
 Identities = 35/147 (23%), Positives = 76/147 (51%), Gaps = 4/147 (2%)
 Frame = +2

Query  420   GLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQEL  479
             GL  L    +E+  +    +++R  + + EE+   W+KL+    +  +K++E + +L+++
Sbjct  3275  GLNYLSTTVKEMSKKAPLSDISRKYQSEFEEIEGRWKKLSSQLVEHCQKLEEQMAKLRKI  3454

Query  480   QEATDELDLKLRQAEV-IKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDL  538
             Q     L   + + +V +K  W  +GD  I  L+  L++ + L  +I  ++ +++ VN+ 
Sbjct  3455  QNHIKTLKKWITEVDVFLKEEWPALGDSEI--LKRQLKQCRLLVNDIQTIQPSLNSVNEG  3628

Query  539   ARQLTTLGIQLSPYNLST-LEDLNTRW  564
             A+++           L T L +LNT+W
Sbjct  3629  AQKMKNEAEPEFAGRLETELRELNTQW  3709


>ref|NM_007868.5| Mus musculus dystrophin, muscular dystrophy (Dmd), mRNA
Length=13857

 Score = 2414 bits (6257),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1159/1215 (95%), Positives = 1182/1215 (97%), Gaps = 13/1215 (1%)
 Frame = +2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSL+LEVPALADFNRAWTELTDWLSLLD+VIKSQRVMVGDLEDINEMIIKQKAT+QDL
Sbjct  7607   MPSSLLLEVPALADFNRAWTELTDWLSLLDRVIKSQRVMVGDLEDINEMIIKQKATLQDL  7786

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQ QWDEVQE LQNRRQQLNEMLK
Sbjct  7787   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQIQWDEVQEQLQNRRQQLNEMLK  7966

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQV+GQ R KL+SWKEGP+TVDAIQKKITETKQLAKDLRQ Q +VDVA
Sbjct  7967   DSTQWLEAKEEAEQVIGQVRGKLDSWKEGPHTVDAIQKKITETKQLAKDLRQRQISVDVA  8146

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENIN SW +IHKRVSE+EAALEETHRLLQQFPLDLEK
Sbjct  8147   NDLALKLLRDYSADDTRKVHMITENINTSWGNIHKRVSEQEAALEETHRLLQQFPLDLEK  8326

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FL+W+TEAETTANVLQDA+RKE+LLEDS+GV+ELMK WQDLQGEIE HTD+YHNLDEN Q
Sbjct  8327   FLSWITEAETTANVLQDASRKEKLLEDSRGVRELMKPWQDLQGEIETHTDIYHNLDENGQ  8506

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSD+A LLQRRLDNMNFKWSEL+KKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8507   KILRSLEGSDEAPLLQRRLDNMNFKWSELQKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8686

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQND+HRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8687   LQLKDDELSRQAPIGGDFPAVQKQNDIHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8866

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVN EW+KLNL SADWQRKIDE LERLQELQ
Sbjct  8867   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNAEWDKLNLRSADWQRKIDEALERLQELQ  9046

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EA DELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENV+ VNDLA 
Sbjct  9047   EAADELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVNRVNDLAH  9226

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRW+LLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9227   QLTTLGIQLSPYNLSTLEDLNTRWRLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  9406

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9407   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9586

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9587   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9766

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9767   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9946

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9947   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  10126

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  10127  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10306

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10307  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10486

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10487  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10666

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10667  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10846

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10847  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  11026

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTS+SMGEEDLLSPPQDTSTGLEEVM
Sbjct  11027  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSESMGEEDLLSPPQDTSTGLEEVM  11206

Query  1188   EQLNNSFPSSRGHNV  1202
              EQLNNSFPSSRG N 
Sbjct  11207  EQLNNSFPSSRGRNA  11251


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +1

Query  1198   RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  11269  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  11367


 Score = 48.9 bits (115),  Expect = 0.019, Method: Compositional matrix adjust.
 Identities = 67/327 (20%), Positives = 139/327 (42%), Gaps = 30/327 (9%)
 Frame = +2

Query  164   KQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAA  223
             K +  +L+Q    +D+ +      L+  ++ +  KV      ++     +H+   ER+  
Sbjct  6368  KNIKDNLQQISGRIDIIHKKKTAALQSATSMEKVKVQEAVAQMDFQGEKLHRMYKERQGR  6547

Query  224   LEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQG  283
              + +    + F  D++ F  WL E E      Q+    E         K  +K+ QD  G
Sbjct  6548  FDRSVEKWRHFHYDMKVFNQWLNEVEQFFKKTQNPENWEH-----AKYKWYLKELQDGIG  6712

Query  284   EIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEAS  343
             + +A   V   L+   ++I++      D  +LQ +L +++ +W ++ K+    R  +E  
Sbjct  6713  QRQA---VVRTLNATGEEIIQQ-SSKTDVNILQEKLGSLSLRWHDICKELAERRKRIEEQ  6880

Query  344   SDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIM  403
              +        L E ++WL+  D+      P+ GD   +++Q +  +    EL  ++ ++ 
Sbjct  6881  KNVLSEFQRDLNEFVLWLEEADN--IAITPL-GDEQQLKEQLEQVKLLAEELPLRQGILK  7051

Query  404   STLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSA  463
                ET    L   P+              PEE+ +     L K+ ++ N +W K++    
Sbjct  7052  QLNETGGAVLVSAPIR-------------PEEQDK-----LEKKLKQTNLQWIKVSRALP  7177

Query  464   DWQRKIDETLERLQELQEATDELDLKL  490
             + Q +++  L+  ++L+E  D L L L
Sbjct  7178  EKQGELEVHLKDFRQLEEQLDHLLLWL  7258


 Score = 47.8 bits (112),  Expect = 0.037, Method: Compositional matrix adjust.
 Identities = 95/429 (22%), Positives = 182/429 (42%), Gaps = 45/429 (10%)
 Frame = +2

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ + + L   L++ Q   +  +D   ++ +   ++  +K     E I   W+ +
Sbjct  3170  EIMEERLGKLQALQSSLKEQQNGFNYLSDTVKEMAKKAPSEICQKYLSEFEEIEGHWKKL  3349

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               ++ E    LEE    L++F   ++    W+ E         D   KE    L D++ +
Sbjct  3350  SSQLVESCQKLEEHMNKLRKFQNHIKTLQKWMAEV--------DVFLKEEWPALGDAEIL  3505

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L G+I+      ++++E  QKI +S    + A  L+  L  +N +W  + +
Sbjct  3506  KKQLKQCRLLVGDIQTIQPSLNSVNEGGQKI-KSEAELEFASRLETELRELNTQWDHICR  3682

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFPAVQKQNDVHRA  390
             +    +  L+A  D+   L   L E+  W+ Q +++ L R               ++ RA
Sbjct  3683  QVYTRKEALKAGLDKTVSLQKDLSEMHEWMTQAEEEYLERDFEYKTPDELQTAVEEMKRA  3862

Query  391   FKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEE  450
              K E   KE  +    ETV   +   P    E L +E   L      Q +   L  + + 
Sbjct  3863  -KEEALQKETKVKLLTETVNSVIAHAPPSAQEALKKELETLTT--NYQWLCTRLNGKCKT  4033

Query  451   VNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLL--I  508
             +   W       A W     E L  L++  +  +E++LKL+  E +    + + ++L  +
Sbjct  4034  LEEVW-------ACWH----ELLSYLEKANKWLNEVELKLKTMENVPAGPEEITEVLESL  4180

Query  509   DSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQ  568
             ++L  H E             EN + +  LA+ LT  G+     N   LE  N+RW+ L 
Sbjct  4181  ENLMHHSE-------------ENPNQIRLLAQTLTDGGVMDELIN-EELETFNSRWRELH  4318

Query  569   VAVEDRVRQ  577
                E+ VR+
Sbjct  4319  ---EEAVRK  4336


 Score = 45.1 bits (105),  Expect = 0.24, Method: Compositional matrix adjust.
 Identities = 76/367 (20%), Positives = 156/367 (42%), Gaps = 31/367 (8%)
 Frame = +2

Query  12    LADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELI  71
             L  F      L  W++ +D  +K +   +GD E + + + + +  + D++  +P L  + 
Sbjct  3401  LRKFQNHIKTLQKWMAEVDVFLKEEWPALGDAEILKKQLKQCRLLVGDIQTIQPSLNSVN  3580

Query  72    TAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEE  131
                Q +K++   + A  + T+ +  +  QWD +   +  R++ L   L  +    +   E
Sbjct  3581  EGGQKIKSEAELEFASRLETE-LRELNTQWDHICRQVYTRKEALKAGLDKTVSLQKDLSE  3757

Query  132   AEQVLGQARAKLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLL  188
               + + QA    E + E  +   T D +Q  + E K+  ++  Q +T V +  +    ++
Sbjct  3758  MHEWMTQAE---EEYLERDFEYKTPDELQTAVEEMKRAKEEALQKETKVKLLTETVNSVI  3928

Query  189   RDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
                  SA +  K  + T   N  W  +  R++ +   LEE      +    LEK   WL 
Sbjct  3929  AHAPPSAQEALKKELETLTTNYQW--LCTRLNGKCKTLEEVWACWHELLSYLEKANKWLN  4102

Query  247   EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKI-LRS  305
             E E     +++            G +E+ +  + L+       ++ H+ +EN  +I L +
Sbjct  4103  EVELKLKTMENV---------PAGPEEITEVLESLE-------NLMHHSEENPNQIRLLA  4234

Query  306   LEGSDDAV---LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQ  362
                +D  V   L+   L+  N +W EL ++++  +  LE S    + +  SL  +   L+
Sbjct  4235  QTLTDGGVMDELINEELETFNSRWRELHEEAVRKQKLLEQSIQSAQEIEKSLHLIQESLE  4414

Query  363   LKDDELS  369
               D +L+
Sbjct  4415  FIDKQLA  4435


 Score = 44.3 bits (103),  Expect = 0.41, Method: Compositional matrix adjust.
 Identities = 70/282 (24%), Positives = 137/282 (48%), Gaps = 44/282 (15%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    ++LK   
Sbjct  5000  LTEWLAATDTELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKAHLKSVTELGESLKMVL  5179

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q + ++    T+W+ 
Sbjct  5180  GKKE--TLVEDKLSLLNSNWIAVTSRVEEWLNLLLEYQKHMETFDQNIEQI----TKWI-  5338

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                 A+++L       ES K+ P      Q+K    K+L  ++   +  VD   D A KL
Sbjct  5339  --IHADELLD------ESEKKKP------QQKEDILKRLKAEMNDMRPKVDSTRDQAAKL  5476

Query  188   LRDYSADDTRKV--HMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWL  245
             + +   D  RKV    I+E +N  + +I  R+   +A++    + L+QF  D++K L  L
Sbjct  5477  MAN-RGDHCRKVVEPQISE-LNRRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL  5644

Query  246   TEAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
              EAE    V L++    + + ED++G V EL+++  +LQ  I
Sbjct  5645  -EAEIQQGVNLKEEDFNKDMSEDNEGTVNELLQRGDNLQQRI  5767


>gb|M68859.1|MUSDYSA Mouse dystrophin mRNA, complete cds
Length=13815

 Score = 2414 bits (6257),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1159/1215 (95%), Positives = 1182/1215 (97%), Gaps = 13/1215 (1%)
 Frame = +2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSL+LEVPALADFNRAWTELTDWLSLLD+VIKSQRVMVGDLEDINEMIIKQKAT+QDL
Sbjct  7580   MPSSLLLEVPALADFNRAWTELTDWLSLLDRVIKSQRVMVGDLEDINEMIIKQKATLQDL  7759

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQ QWDEVQE LQNRRQQLNEMLK
Sbjct  7760   EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQIQWDEVQEQLQNRRQQLNEMLK  7939

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAKEEAEQV+GQ R KL+SWKEGP+TVDAIQKKITETKQLAKDLRQ Q +VDVA
Sbjct  7940   DSTQWLEAKEEAEQVIGQVRGKLDSWKEGPHTVDAIQKKITETKQLAKDLRQRQISVDVA  8119

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLALKLLRDYSADDTRKVHMITENIN SW +IHKRVSE+EAALEETHRLLQQFPLDLEK
Sbjct  8120   NDLALKLLRDYSADDTRKVHMITENINTSWGNIHKRVSEQEAALEETHRLLQQFPLDLEK  8299

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FL+W+TEAETTANVLQDA+RKE+LLEDS+GV+ELMK WQDLQGEIE HTD+YHNLDEN Q
Sbjct  8300   FLSWITEAETTANVLQDASRKEKLLEDSRGVRELMKPWQDLQGEIETHTDIYHNLDENGQ  8479

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGSD+A LLQRRLDNMNFKWSEL+KKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  8480   KILRSLEGSDEAPLLQRRLDNMNFKWSELQKKSLNIRSHLEASSDQWKRLHLSLQELLVW  8659

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGDFPAVQKQND+HRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  8660   LQLKDDELSRQAPIGGDFPAVQKQNDIHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  8839

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEKLYQEPRELPPEERAQNVTRLLRKQAEEVN EW+KLNL SADWQRKIDE LERLQELQ
Sbjct  8840   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNAEWDKLNLRSADWQRKIDEALERLQELQ  9019

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EA DELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENV+ VNDLA 
Sbjct  9020   EAADELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVNRVNDLAH  9199

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTTLGIQLSPYNLSTLEDLNTRW+LLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  9200   QLTTLGIQLSPYNLSTLEDLNTRWRLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  9379

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9380   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9559

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9560   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9739

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9740   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9919

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9920   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  10099

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  10100  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10279

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10280  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10459

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10460  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10639

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10640  QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10819

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10820  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10999

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTS+SMGEEDLLSPPQDTSTGLEEVM
Sbjct  11000  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSESMGEEDLLSPPQDTSTGLEEVM  11179

Query  1188   EQLNNSFPSSRGHNV  1202
              EQLNNSFPSSRG N 
Sbjct  11180  EQLNNSFPSSRGRNA  11224


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +1

Query  1198   RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  11242  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  11340


 Score = 48.9 bits (115),  Expect = 0.019, Method: Compositional matrix adjust.
 Identities = 67/327 (20%), Positives = 139/327 (42%), Gaps = 30/327 (9%)
 Frame = +2

Query  164   KQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAA  223
             K +  +L+Q    +D+ +      L+  ++ +  KV      ++     +H+   ER+  
Sbjct  6341  KNIKDNLQQISGRIDIIHKKKTAALQSATSMEKVKVQEAVAQMDFQGEKLHRMYKERQGR  6520

Query  224   LEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQG  283
              + +    + F  D++ F  WL E E      Q+    E         K  +K+ QD  G
Sbjct  6521  FDRSVEKWRHFHYDMKVFNQWLNEVEQFFKKTQNPENWEH-----AKYKWYLKELQDGIG  6685

Query  284   EIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEAS  343
             + +A   V   L+   ++I++      D  +LQ +L +++ +W ++ K+    R  +E  
Sbjct  6686  QRQA---VVRTLNATGEEIIQQ-SSKTDVNILQEKLGSLSLRWHDICKELAERRKRIEEQ  6853

Query  344   SDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIM  403
              +        L E ++WL+  D+      P+ GD   +++Q +  +    EL  ++ ++ 
Sbjct  6854  KNVLSEFQRDLNEFVLWLEEADN--IAITPL-GDEQQLKEQLEQVKLLAEELPLRQGILK  7024

Query  404   STLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSA  463
                ET    L   P+              PEE+ +     L K+ ++ N +W K++    
Sbjct  7025  QLNETGGAVLVSAPIR-------------PEEQDK-----LEKKLKQTNLQWIKVSRALP  7150

Query  464   DWQRKIDETLERLQELQEATDELDLKL  490
             + Q +++  L+  ++L+E  D L L L
Sbjct  7151  EKQGELEVHLKDFRQLEEQLDHLLLWL  7231


 Score = 47.8 bits (112),  Expect = 0.037, Method: Compositional matrix adjust.
 Identities = 95/429 (22%), Positives = 182/429 (42%), Gaps = 45/429 (10%)
 Frame = +2

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ + + L   L++ Q   +  +D   ++ +   ++  +K     E I   W+ +
Sbjct  3143  EIMEERLGKLQALQSSLKEQQNGFNYLSDTVKEMAKKAPSEICQKYLSEFEEIEGHWKKL  3322

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               ++ E    LEE    L++F   ++    W+ E         D   KE    L D++ +
Sbjct  3323  SSQLVESCQKLEEHMNKLRKFQNHIKTLQKWMAEV--------DVFLKEEWPALGDAEIL  3478

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L G+I+      ++++E  QKI +S    + A  L+  L  +N +W  + +
Sbjct  3479  KKQLKQCRLLVGDIQTIQPSLNSVNEGGQKI-KSEAELEFASRLETELRELNTQWDHICR  3655

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFPAVQKQNDVHRA  390
             +    +  L+A  D+   L   L E+  W+ Q +++ L R               ++ RA
Sbjct  3656  QVYTRKEALKAGLDKTVSLQKDLSEMHEWMTQAEEEYLERDFEYKTPDELQTAVEEMKRA  3835

Query  391   FKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEE  450
              K E   KE  +    ETV   +   P    E L +E   L      Q +   L  + + 
Sbjct  3836  -KEEALQKETKVKLLTETVNSVIAHAPPSAQEALKKELETLTT--NYQWLCTRLNGKCKT  4006

Query  451   VNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLL--I  508
             +   W       A W     E L  L++  +  +E++LKL+  E +    + + ++L  +
Sbjct  4007  LEEVW-------ACWH----ELLSYLEKANKWLNEVELKLKTMENVPAGPEEITEVLESL  4153

Query  509   DSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQ  568
             ++L  H E             EN + +  LA+ LT  G+     N   LE  N+RW+ L 
Sbjct  4154  ENLMHHSE-------------ENPNQIRLLAQTLTDGGVMDELIN-EELETFNSRWRELH  4291

Query  569   VAVEDRVRQ  577
                E+ VR+
Sbjct  4292  ---EEAVRK  4309


 Score = 45.1 bits (105),  Expect = 0.24, Method: Compositional matrix adjust.
 Identities = 76/367 (20%), Positives = 156/367 (42%), Gaps = 31/367 (8%)
 Frame = +2

Query  12    LADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELI  71
             L  F      L  W++ +D  +K +   +GD E + + + + +  + D++  +P L  + 
Sbjct  3374  LRKFQNHIKTLQKWMAEVDVFLKEEWPALGDAEILKKQLKQCRLLVGDIQTIQPSLNSVN  3553

Query  72    TAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEE  131
                Q +K++   + A  + T+ +  +  QWD +   +  R++ L   L  +    +   E
Sbjct  3554  EGGQKIKSEAELEFASRLETE-LRELNTQWDHICRQVYTRKEALKAGLDKTVSLQKDLSE  3730

Query  132   AEQVLGQARAKLESWKEGPY---TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLL  188
               + + QA    E + E  +   T D +Q  + E K+  ++  Q +T V +  +    ++
Sbjct  3731  MHEWMTQAE---EEYLERDFEYKTPDELQTAVEEMKRAKEEALQKETKVKLLTETVNSVI  3901

Query  189   RDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
                  SA +  K  + T   N  W  +  R++ +   LEE      +    LEK   WL 
Sbjct  3902  AHAPPSAQEALKKELETLTTNYQW--LCTRLNGKCKTLEEVWACWHELLSYLEKANKWLN  4075

Query  247   EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKI-LRS  305
             E E     +++            G +E+ +  + L+       ++ H+ +EN  +I L +
Sbjct  4076  EVELKLKTMENV---------PAGPEEITEVLESLE-------NLMHHSEENPNQIRLLA  4207

Query  306   LEGSDDAV---LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQ  362
                +D  V   L+   L+  N +W EL ++++  +  LE S    + +  SL  +   L+
Sbjct  4208  QTLTDGGVMDELINEELETFNSRWRELHEEAVRKQKLLEQSIQSAQEIEKSLHLIQESLE  4387

Query  363   LKDDELS  369
               D +L+
Sbjct  4388  FIDKQLA  4408


 Score = 44.3 bits (103),  Expect = 0.41, Method: Compositional matrix adjust.
 Identities = 70/282 (24%), Positives = 137/282 (48%), Gaps = 44/282 (15%)
 Frame = +2

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  +   KAT +++E+++  L+ +    ++LK   
Sbjct  4973  LTEWLAATDTELTKRSAVEGMPSNLDSEVAWGKATQKEIEKQKAHLKSVTELGESLKMVL  5152

Query  82    SNQEARTIITDRIERIQNQWD--------------EVQEHLQNRRQQLNEMLKDSTQWLE  127
               +E  T++ D++  + + W               E Q+H++   Q + ++    T+W+ 
Sbjct  5153  GKKE--TLVEDKLSLLNSNWIAVTSRVEEWLNLLLEYQKHMETFDQNIEQI----TKWI-  5311

Query  128   AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                 A+++L       ES K+ P      Q+K    K+L  ++   +  VD   D A KL
Sbjct  5312  --IHADELLD------ESEKKKP------QQKEDILKRLKAEMNDMRPKVDSTRDQAAKL  5449

Query  188   LRDYSADDTRKV--HMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWL  245
             + +   D  RKV    I+E +N  + +I  R+   +A++    + L+QF  D++K L  L
Sbjct  5450  MAN-RGDHCRKVVEPQISE-LNRRFAAISHRIKTGKASI--PLKELEQFNSDIQKLLEPL  5617

Query  246   TEAETTANV-LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
              EAE    V L++    + + ED++G V EL+++  +LQ  I
Sbjct  5618  -EAEIQQGVNLKEEDFNKDMSEDNEGTVNELLQRGDNLQQRI  5740


>ref|XM_001379309.1| PREDICTED: Monodelphis domestica similar to T cell antigen receptor 
alpha chain VJC region (LOC100029652), mRNA
Length=11307

 Score = 2325 bits (6026),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1112/1216 (91%), Positives = 1165/1216 (95%), Gaps = 14/1216 (1%)
 Frame = +1

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSSL+LEVPALADFN+AWTELTDWLSLLD+VIK+QRVMVGDLEDIN+MIIKQKAT+QDL
Sbjct  7345   MPSSLLLEVPALADFNKAWTELTDWLSLLDRVIKTQRVMVGDLEDINDMIIKQKATLQDL  7524

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQLEELITAAQNLKNKT NQEARTIITDRIE+IQ+QWDEVQEHLQ RRQQLNEMLK
Sbjct  7525   EQRRPQLEELITAAQNLKNKTGNQEARTIITDRIEKIQSQWDEVQEHLQRRRQQLNEMLK  7704

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DS QWLEAK+EAE  L +A+ KLESWKE PYT++ I+K+ TETKQLAKDLRQWQ NVDVA
Sbjct  7705   DSAQWLEAKKEAEWTLEKAKTKLESWKEIPYTMEGIRKQSTETKQLAKDLRQWQINVDVA  7884

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              NDLA KLLRDYS DDTRKV MIT+NINA+W  I+KRV+EREAALE  HRLLQQFPLDLEK
Sbjct  7885   NDLARKLLRDYSTDDTRKVQMITDNINATWADINKRVNEREAALEAAHRLLQQFPLDLEK  8064

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDAT KER+LED+KGV+ELMKQWQDLQGEIEAHTD++HNLDEN Q
Sbjct  8065   FLAWLTEAETTANVLQDATHKERILEDTKGVRELMKQWQDLQGEIEAHTDIFHNLDENGQ  8244

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KIL+SLEGSDDAVLL+RRLDNMNFKWSELRKKSLNIRSHLE SSDQWKRLHLSLQELLVW
Sbjct  8245   KILKSLEGSDDAVLLKRRLDNMNFKWSELRKKSLNIRSHLEVSSDQWKRLHLSLQELLVW  8424

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLKDDELSRQAPIGGD+PAVQ+QND+HRAFKRELKTKEPVI STLETVRIFL+E+PLE 
Sbjct  8425   LQLKDDELSRQAPIGGDYPAVQQQNDIHRAFKRELKTKEPVITSTLETVRIFLSEKPLEE  8604

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEK YQEPRELPPEERA NVTRLLRKQA+EVN+EWEKLNLHS DWQ+KIDE L RLQ+LQ
Sbjct  8605   LEKHYQEPRELPPEERAHNVTRLLRKQADEVNSEWEKLNLHSVDWQKKIDEALGRLQDLQ  8784

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EA DELDLKLRQAEV++GSWQPVGDLLIDSLQ+HLEKVKALRGEIAPL+EN++HVN LAR
Sbjct  8785   EAMDELDLKLRQAEVMRGSWQPVGDLLIDSLQEHLEKVKALRGEIAPLEENINHVNGLAR  8964

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QLTT GIQLSPYNL++LEDLNTRWKLL VA+++R+RQLHEAHRDFGP SQHFLSTSVQGP
Sbjct  8965   QLTTSGIQLSPYNLNSLEDLNTRWKLLLVAIDERIRQLHEAHRDFGPTSQHFLSTSVQGP  9144

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9145   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9324

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9325   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9504

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTG+ISLCKAHLEDKYRYLFKQVASS GFCDQRRLGLLLHD
Sbjct  9505   WLLNVYDTGRTGRIRVLSFKTGVISLCKAHLEDKYRYLFKQVASSMGFCDQRRLGLLLHD  9684

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9685   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  9864

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  9865   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10044

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET            
Sbjct  10045  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDS  10224

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN
Sbjct  10225  APASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  10404

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
              Q+SPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP
Sbjct  10405  QESPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  10584

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPEMMP SPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10585  SPPEMMPISPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10764

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLS-PPQDTSTGLEEV  1186
              QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTS++MGE+DLLS PPQDTSTGLEEV
Sbjct  10765  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSETMGEDDLLSPPPQDTSTGLEEV  10944

Query  1187   MEQLNNSFPSSRGHNV  1202
              MEQLNNSFPS+RG N 
Sbjct  10945  MEQLNNSFPSTRGRNA  10992


 Score = 60.8 bits (146),  Expect = 5e-06, Method: Compositional matrix adjust.
 Identities = 25/28 (89%), Positives = 28/28 (100%), Gaps = 0/28 (0%)
 Frame = +1

Query  1199   GHNVGSLFHMADDLGRAMESLVSVMTDE  1226
              GHNVG+LFHMADDLGRAME+LV+VMTDE
Sbjct  11212  GHNVGNLFHMADDLGRAMETLVTVMTDE  11295


 Score = 57.0 bits (136),  Expect = 7e-05, Method: Compositional matrix adjust.
 Identities = 119/543 (21%), Positives = 224/543 (41%), Gaps = 56/543 (10%)
 Frame = +1

Query  64    RPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKD--  121
             +PQ+E L   +  LK K   ++    +        N + +V   LQ R +QL   L    
Sbjct  2635  QPQVERLKIQSIALKEK---EQGPMFLDADFVAFTNHFKQVLSDLQAREKQLQTTLDSLP  2805

Query  122   STQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVAN  181
              T +LE        + Q+  KL   +      + +++++ E K L   L++ Q  +++  
Sbjct  2806  PTHYLEMVNTILMCIQQSETKLSIPQVTVTEYEIMEQRLRELKALQSSLQEQQPGLNLLT  2985

Query  182   DLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKF  241
                 ++ +    +  +K  +  E I   W+ +  ++ E    LEE    LQQF  D++  
Sbjct  2986  TTVEEMSKTAPPEINKKYQLELEGIQIRWKKLSSQLVEHCQKLEEHMTKLQQFQNDIKTL  3165

Query  242   LAWLTEAETTANVLQDATRKER--LLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENS  299
               W+ E         D   KE    L DS+ +++ ++Q   L  +I+       +++E  
Sbjct  3166  KKWMAEV--------DVFLKEEWPALGDSEALEKQLEQCTVLVNDIQTIHPSLVSVNEVG  3321

Query  300   QKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLV  359
             QKI    E    A  ++  L  +N +W  + +++   +  L+   D+   L   L E+  
Sbjct  3322  QKIQNEAE-PQFASKVKTELKELNAQWDHICQQARAKKEALKGGLDKTVSLRKDLSEMHE  3498

Query  360   WLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLE  419
             W+   ++E   +         +QK  D  ++ K E + KE  +    +++  F+   P  
Sbjct  3499  WITQAEEEYLERDFEYKTPEELQKAVDELKSAKEEAQQKEVKVKLLTDSMNNFIARAPPV  3678

Query  420   GLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQEL  479
               + L +E   L       N  RL  +    +N + + L    A W     E L  L+  
Sbjct  3679  AHDALKKELDTL-----ITNYQRLCSR----LNGKCKTLEEVWACWC----ELLSYLEAE  3819

Query  480   QEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLA  539
              +  +E+++KL+  E I G  + + ++L     D LE++      +    +N + + +LA
Sbjct  3820  NKWLNEVEIKLKATENIPGGAEEISEVL-----DSLERL------MRHPDDNRNQIRELA  3966

Query  540   RQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQG  599
             + LT  G+     N   LE  N+RW+ L    ++ VR+            Q FL  S+Q 
Sbjct  3967  QTLTDGGVLDELIN-EKLEKFNSRWEELH---QEAVRR------------QKFLEQSIQS  4098

Query  600   PWE  602
               E
Sbjct  4099  AQE  4107


 Score = 48.9 bits (115),  Expect = 0.018, Method: Compositional matrix adjust.
 Identities = 69/273 (25%), Positives = 134/273 (49%), Gaps = 26/273 (9%)
 Frame = +1

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  I   KAT +++E+R+PQL+ +     +LK   
Sbjct  4732  LTEWLAATDTELTKRSAVEGMPANLDAEIAWGKATQKEIEKRQPQLKIITDLGTSLKIVL  4911

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
               +E   ++ D++  +++ W  V     +R ++   +L +  + +E  +E         A
Sbjct  4912  GKKE--NLVDDKLSLLKSNWIAV----TSRAEEWLNLLLEYQKHMETFDE-------NVA  5052

Query  142   KLESW-KEGPYTVDAIQKKITETKQ-----LAKDLRQWQTNVDVANDLALKLLRDYSADD  195
              + +W       +D  +KK T+ K+     L  +L   +  VD  +D A+ L+ +   D 
Sbjct  5053  HITAWISHAEILLDESEKKKTQQKEDVLKCLKAELNDMRPKVDSTHDQAINLMTN-RGDH  5229

Query  196   TRKV-HMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANV  254
              RKV       +N  + +I +R+   +A++    + L+QF  D++K L  L EAE    V
Sbjct  5230  CRKVIEPKLSELNHRFAAISQRIKTGKASI--PLKELEQFNSDIQKLLEPL-EAEIQQGV  5400

Query  255   -LQDATRKERLLEDSKG-VKELMKQWQDLQGEI  285
              L++    + + ED++G VKEL+++   LQ  I
Sbjct  5401  NLKEEDFNKDMSEDNEGTVKELLQRGDTLQQRI  5499


 Score = 48.9 bits (115),  Expect = 0.020, Method: Compositional matrix adjust.
 Identities = 80/372 (21%), Positives = 161/372 (43%), Gaps = 45/372 (12%)
 Frame = +1

Query  7     LEVPA--LADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRR  64
             L VP+  LA+ +R    +T  +S  + ++ +  +   D ED+     KQ+  ++ ++   
Sbjct  5965  LYVPSTYLAEIHR----VTQNISEAEFLLNTPDLCAKDFEDL----FKQEECLKKVKDNL  6120

Query  65    PQLEELITAAQNLKNKTSNQEAR----TIITDRIERIQNQWDEVQEHLQNRRQQLNEM--  118
              ++   +    N K  T+ Q A     T I + + ++ +QW++V    ++R+ + +    
Sbjct  6121  QRISNQVEVIHN-KKTTALQNATPMEATKIKEALTQLNSQWEKVNNIYKDRQGRFDRSVE  6297

Query  119   --------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDL  170
                     +K   QWL    EAEQ L + +         P  +D  + +    K+L   +
Sbjct  6298  KWRRFHYDMKIFNQWLT---EAEQFLDKTK--------HPDNLDHAKYRWY-LKELQDGI  6441

Query  171   RQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRL  230
              + QT V        +++   S  D   +    + +N  W+ + ++++ER+  LEE   +
Sbjct  6442  NRQQTVVKELTVTGEEIIGQSSKGDASILEDKLDYLNVRWQEVCRQLAERKKRLEEQKNI  6621

Query  231   LQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTD  290
             L +F  DL +F+ WL EAE+  N   +   +++L    + VK  +++    QG       
Sbjct  6622  LSEFEGDLNEFILWLKEAESIVNTPLEPGNEQQLKNTLEKVKLRVEELPGRQG-------  6780

Query  291   VYHNLDENSQKILRSLEGSDDAV-LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKR  349
             +   L+E   K L S   + + +  L+ R    N +W ++ K     +  +E     + +
Sbjct  6781  ILKQLNETGGKALISETINPEELDKLENRRKEANLQWIKISKDLPEKQKEIEVLLKNFVQ  6960

Query  350   LHLSLQELLVWL  361
                 L  L +WL
Sbjct  6961  FEEELHHLTLWL  6996


>emb|X13369.1| Chicken mRNA for dystrophin (Duchenne muscular dystrophy gene 
homolog)
Length=13575

 Score = 2182 bits (5654),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1038/1202 (86%), Positives = 1118/1202 (93%), Gaps = 9/1202 (0%)
 Frame = +1

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSS++LEVPALADFN+AW ELTDWLS LD+ IK+QRV VGDL+DIN+MIIKQKA MQDL
Sbjct  7522   MPSSVLLEVPALADFNKAWAELTDWLSRLDREIKAQRVTVGDLDDINDMIIKQKANMQDL  7701

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQL+ELITAAQNLKNKTSNQEARTIITDRIE+IQ+QWD+V  +LQNRRQQL+EM K
Sbjct  7702   EQRRPQLDELITAAQNLKNKTSNQEARTIITDRIEKIQSQWDDVHGYLQNRRQQLHEMQK  7881

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAK+EAEQVL QA+AKLESWKE  YTV+A++K+ +E KQ +K++RQWQ N++  
Sbjct  7882   DSTQWLEAKQEAEQVLEQAKAKLESWKEISYTVEALKKQNSELKQFSKEIRQWQMNIEGV  8061

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              ND+ALK +RDYSADDTRKV ++T+NINA+W +I+KRVSEREAALE    +LQ+F LDLEK
Sbjct  8062   NDVALKPVRDYSADDTRKVELMTDNINATWATINKRVSEREAALESALLMLQEFYLDLEK  8241

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDAT KE+ LED + V+ELMKQWQDLQ EI+AHTD++HNLDEN Q
Sbjct  8242   FLAWLTEAETTANVLQDATHKEKTLEDPQMVRELMKQWQDLQAEIDAHTDIFHNLDENGQ  8421

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGS+DAVLLQRRLDNMNF+WSELRKKSLNIRSHLEAS+DQWKRLHLSLQELL W
Sbjct  8422   KILRSLEGSEDAVLLQRRLDNMNFRWSELRKKSLNIRSHLEASTDQWKRLHLSLQELLAW  8601

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLK+DEL +QAPIGGD P VQKQNDVHR FKRELKTKEPVIM+ LETVR+FL +QP+EG
Sbjct  8602   LQLKEDELKQQAPIGGDIPTVQKQNDVHRTFKRELKTKEPVIMNALETVRLFLADQPVEG  8781

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              LEK+Y EPR+L PEERAQNVT++LR+QA++V TEW+KLNL SADWQ+KID+ LERLQ LQ
Sbjct  8782   LEKVYPEPRDLSPEERAQNVTKVLRRQADDVRTEWDKLNLRSADWQKKIDDALERLQGLQ  8961

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EA DELDLKLRQAE  KGSWQPVGDLLIDSLQDHLEKVK  R E+ PLKE V  VN+LA 
Sbjct  8962   EAMDELDLKLRQAEAFKGSWQPVGDLLIDSLQDHLEKVKVYRAEMVPLKEKVHQVNELAH  9141

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              +     IQLSPY LS LEDLNTRWK+LQVA+++R+RQLHEAHRDFGP SQHFL+TSVQGP
Sbjct  9142   RFAPPDIQLSPYTLSCLEDLNTRWKVLQVAIDERIRQLHEAHRDFGPTSQHFLTTSVQGP  9321

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9322   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9501

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLL+LSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9502   LDLLNLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9681

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTG++SLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9682   WLLNVYDTGRTGRIRVLSFKTGVVSLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9861

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9862   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  10041

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  10042  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  10221

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT  960
              TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETP +       D 
Sbjct  10222  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVD-  10398

Query  961    HSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQ  1020
                      S LAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQ+SPLSQPRSPAQ
Sbjct  10399  --------SALAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQESPLSQPRSPAQ  10554

Query  1021   ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSP  1080
              ILISLESEERGELERILADLEEENRNLQAEYDRLKQQH+HKGLSPLPSPPEMMP SPQSP
Sbjct  10555  ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHDHKGLSPLPSPPEMMPVSPQSP  10734

Query  1081   RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSS  1140
              RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQA+AKVNGTT+SS
Sbjct  10735  RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQADAKVNGTTLSS  10914

Query  1141   PSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGH  1200
              PSTSLQRSDSSQPMLLRVVGSQTS++MGE+DLLSPPQDTSTGLEEVMEQLNNSFPSSRG 
Sbjct  10915  PSTSLQRSDSSQPMLLRVVGSQTSETMGEDDLLSPPQDTSTGLEEVMEQLNNSFPSSRGR  11094

Query  1201   NV  1202
              N 
Sbjct  11095  NA  11100


 Score = 62.4 bits (150),  Expect = 1e-06, Method: Compositional matrix adjust.
 Identities = 27/33 (81%), Positives = 31/33 (93%), Gaps = 0/33 (0%)
 Frame = +3

Query  1195   PSSRGHNVGSLFHMADDLGRAMESLVSVMTDEE  1227
               S RGHNVGSLFHMADDLGRAME+LV+VMTD++
Sbjct  11109  ASERGHNVGSLFHMADDLGRAMETLVTVMTDDK  11207


 Score = 53.5 bits (127),  Expect = 7e-04, Method: Compositional matrix adjust.
 Identities = 112/523 (21%), Positives = 218/523 (41%), Gaps = 43/523 (8%)
 Frame = +1

Query  64    RPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDST  123
             +PQ+E L   +Q LK K   ++    +   +    + + ++   +  R +QL  +  DS 
Sbjct  2806  QPQIERLKAQSQALKEK---EQCPVFLDADLAAFTSHFKQILADMHTREKQLQTIF-DSL  2973

Query  124   QWLEAKEEAEQVLG---QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
                  K+    +L    Q+  K+          + +++++ E K L   L++ Q  +   
Sbjct  2974  PPARYKDTVTTILSWIQQSETKVSIPPVAVAEYEIMEQRLGELKALQSSLQEQQKGLKYL  3153

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             N     L R   A+ ++K     E I   W+ +  ++ E    LE+    LQ+F  D + 
Sbjct  3154  NTTVEDLSRKAPAEVSQKYRSEVELIVGRWKKLSSQLVEHCQKLEDLMTKLQRFQNDTKT  3333

Query  241   FLAWLTEAETTANVLQDATRKER--LLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDEN  298
                W+ E         D   KE    L DS+ +++ ++Q   L  +I+      ++++E 
Sbjct  3334  LKKWMAEV--------DVFLKEEWPALGDSEALEKQLEQCTALVNDIQTIQPSLNSVNEI  3489

Query  299   SQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELL  358
              +K+ R  E  + A  +   L ++N +W  + +++   ++ L+   D+   L   L E+ 
Sbjct  3490  GKKMKREAE-PEFASRIATELKDLNAQWEHICQQAHAKKAALKGGLDKTVSLRKDLSEMH  3666

Query  359   VWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPL  418
              W+   ++E   +         +QK  +  +  K +   KE  +    ++V  F+ + P 
Sbjct  3667  EWITQAEEEYLERDFEYKTPEELQKAVEELKRAKEDAMQKEVKVKLITDSVNNFIAKAPP  3846

Query  419   EGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQE  478
                E L +E   L      Q +   L  + + +   W       A W     E L  L  
Sbjct  3847  AANEALKKELDVLITS--YQRLCSRLNGKCKTLEEVW-------ACWH----ELLSYLDA  3987

Query  479   LQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDL  538
               +  +E++LKL+  E I+G  + + + L     D LE++      +   ++N + + +L
Sbjct  3988  ENKWLNEVELKLKATENIQGGAEEISESL-----DSLERL------MRHPEDNRNQIREL  4134

Query  539   ARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEA  581
             A+ LT  GI     N   LE  NTRW+ LQ     R + L ++
Sbjct  4135  AQTLTDGGILDELIN-EKLEKFNTRWEELQQEAVRRQKSLEQS  4260


 Score = 50.4 bits (119),  Expect = 0.006, Method: Compositional matrix adjust.
 Identities = 84/347 (24%), Positives = 159/347 (45%), Gaps = 43/347 (12%)
 Frame = +1

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  I   KAT +++E+R+ QL+ +    +NLK   
Sbjct  4903  LTEWLAATDVELTKRSAVQGMPSNLDAEIAWGKATRKEIEKRQVQLKNICDLGENLKTVL  5082

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEE--AEQVLGQA  139
               +E  +++ D++  + + W  V     +R ++   +L +  + +EA ++  A       
Sbjct  5083  KGKE--SLVEDKLSLLNSNWIAV----TSRAEEWLNLLMEYQKHMEAFDQKVANVTTWIY  5244

Query  140   RAKL---ESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDT  196
             RA++   ES K+ P      Q+K    K+L  +L      VD   D A+ L+ +   D  
Sbjct  5245  RAEILLDESDKQKP------QQKEETLKRLKAELNDMHPKVDSVRDQAVDLMTN-RGDHC  5403

Query  197   RKV-HMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWL-TEAETTANV  254
             RKV       +N  + +I +R+   +  +    + L+QF  D++K L  L  E +   N+
Sbjct  5404  RKVIEPKLSELNHRFAAISQRIKSGKPFI--PLKELEQFDFDIQKLLEPLEVEIQQGVNL  5577

Query  255   LQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVL  314
              ++   K+   +D   VKEL+++   LQ  I          DE  ++ ++  +      L
Sbjct  5578  KEEDFNKDMSEDDESTVKELLQRGDTLQKRI---------TDERKREEIKIKQQ-----L  5715

Query  315   LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWL  361
             LQ + + +    S+ RKK+L I       S QW +      +L+ WL
Sbjct  5716  LQTKHNALKDLRSQRRKKALEI-------SHQWYQYKRQADDLMTWL  5835


 Score = 48.5 bits (114),  Expect = 0.023, Method: Compositional matrix adjust.
 Identities = 42/179 (23%), Positives = 82/179 (45%), Gaps = 29/179 (16%)
 Frame = +1

Query  90    ITDRIERIQNQWDEVQEHLQNRRQQLNEM----------LKDSTQWLEAKEEAEQVLGQA  139
             I D++ ++ +QW++V +  ++R+ + ++           +K   +WL   EE       +
Sbjct  6376  IQDKLTQLNSQWEKVNKMYRDRQARFDKSKEKWRLFHCEMKSFNEWLTETEEK-----LS  6540

Query  140   RAKLESWKEGPYTVDAIQKKITETKQLAKDLR----QWQTNVDVANDLALKLLRDYSADD  195
             RA++E+   G            +TKQ  ++L+    + QT V   N    +++   SA D
Sbjct  6541  RAQIEAGDVGH----------VKTKQFLQELQDGIGRQQTVVKTLNVTGEEIIEQSSAAD  6690

Query  196   TRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANV  254
                +     N+N  W+ I +++ E+   +EE   +L +F  DL K + WL E E    +
Sbjct  6691  ANVLKEQLGNLNTRWQEICRQLVEKRKRIEEEKNILSEFQEDLNKLILWLEETENVIAI  6867


 Score = 40.4 bits (93),  Expect = 6.5, Method: Compositional matrix adjust.
 Identities = 78/362 (21%), Positives = 144/362 (39%), Gaps = 45/362 (12%)
 Frame = +1

Query  231   LQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTD  290
             L  +   LE+ L WL  AE       D +       D + VKE     +    E+ AH  
Sbjct  1177  LDSYQTALEEVLTWLLSAEDALQAQGDIS------SDVEVVKEQFHTHEGFMMELTAHQG  1338

Query  291   VYHNLDENSQKILRSLEGSDDAV-LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKR  349
                N+ +   ++L   + SDD    +Q +++ +N +W  LR  S+  +S+L        +
Sbjct  1339  RVGNVLQVGSQLLAMGKLSDDEENEIQEQMNLLNSRWESLRVASMEKQSNLH-------K  1497

Query  350   LHLSLQ-----ELLVWLQLKDDELSRQA---PIGGDFPAVQKQNDVHRAFKRELKTKEPV  401
             + + LQ     +L  WL  K +E +++    P+G D   +++Q + H+AF+ +L+ ++  
Sbjct  1498  ILMDLQNQQLAQLADWL-TKTEERTKKIDSEPLGPDLEDLKRQVEEHKAFQDDLEQEQVK  1674

Query  402   IMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLH  461
             + S    V +                      E      T  L +Q +   + W  +   
Sbjct  1675  VNSLTHMVVVV--------------------DENSGDKATAALEEQLQHFGSRWAAICRW  1794

Query  462   SADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKAL  521
             + D    + + L + Q   E     D  L + E      Q       + +   L K+  L
Sbjct  1795  TEDRWVLLQDILRKWQHFAEEQCLFDAWLTEKEGSLSKIQTSDFKDENEMLTSLRKLAIL  1974

Query  522   RGEIAPLKENVSHVNDLARQL--TTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLH  579
             +G+I   K+ +S +  L+R L        ++    S LE+   RW  L   +E   +Q+ 
Sbjct  1975  KGDIEMKKQMMSKLKSLSRDLLVAVKNKAVAQKLESRLENFAQRWDSLVQKLESDSKQVS  2154

Query  580   EA  581
             +A
Sbjct  2155  QA  2160


>ref|XM_002191629.1| PREDICTED: Taeniopygia guttata dystrophin (LOC100228890), mRNA
Length=11801

 Score = 2078 bits (5384),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 1004/1202 (83%), Positives = 1084/1202 (90%), Gaps = 37/1202 (3%)
 Frame = +1

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              MPSS++LEVPALADFN+AW ELTDWLS LD+ IKSQRV VGDL+DIN+MIIKQKA +QDL
Sbjct  7402   MPSSVLLEVPALADFNKAWAELTDWLSRLDREIKSQRVKVGDLDDINDMIIKQKAILQDL  7581

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQRRPQL+ELITAAQNLKNKTSNQEARTIITDRIE+IQ+QWDEV  +LQ+RRQQL EMLK
Sbjct  7582   EQRRPQLDELITAAQNLKNKTSNQEARTIITDRIEKIQSQWDEVHGYLQSRRQQLQEMLK  7761

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DSTQWLEAK EAEQVL QA+AKLESWKE  YTV+A++K+ TE KQ +K++RQWQ NVDVA
Sbjct  7762   DSTQWLEAKREAEQVLEQAKAKLESWKEISYTVEALKKQNTELKQFSKEIRQWQINVDVA  7941

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              ND+ALKLLRDYSADDTRKV ++T++INASW +I+KRV EREAALE   R+LQQF LDLEK
Sbjct  7942   NDMALKLLRDYSADDTRKVQLMTDSINASWAAINKRVCEREAALESALRMLQQFYLDLEK  8121

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FLAWLTEAETTANVLQDAT KE+ LED+K V++LMKQWQ+LQ EI+AHTD++H+LDEN Q
Sbjct  8122   FLAWLTEAETTANVLQDATHKEKTLEDAKMVRDLMKQWQELQAEIDAHTDIFHSLDENGQ  8301

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              KILRSLEGS+DA LLQRRLDNMN +WSELRKKSLNIRSHLEAS+DQWKRLHLSLQELL W
Sbjct  8302   KILRSLEGSEDATLLQRRLDNMNLRWSELRKKSLNIRSHLEASTDQWKRLHLSLQELLAW  8481

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              LQLK+DEL +QAPIGGD P VQKQND+HR FKRELKTKEPVI S LETVRIF+ EQP+E 
Sbjct  8482   LQLKEDELKQQAPIGGDLPTVQKQNDIHRTFKRELKTKEPVIRSALETVRIFVAEQPVEA  8661

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              +EK+  EPR+L PEERA N+T+LL++QA+EV TEW+KLNL SADWQ+KID+ LERLQ LQ
Sbjct  8662   VEKVCPEPRDLSPEERAHNITKLLQRQADEVRTEWDKLNLQSADWQKKIDDALERLQGLQ  8841

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
              EA DELDLKLRQAE  KGSWQPVGDLLIDSLQDHLEKVK  R E+ PLKE V HVN+LA 
Sbjct  8842   EAMDELDLKLRQAEAFKGSWQPVGDLLIDSLQDHLEKVKVYRAELVPLKEKVHHVNELAH  9021

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              + T   IQLS YNLS +EDLNTRWK+LQVAV++R++QLHEAHRDFGP SQHFL+TSVQGP
Sbjct  9022   RFTPPDIQLSQYNLSCVEDLNTRWKVLQVAVDERIKQLHEAHRDFGPTSQHFLTTSVQGP  9201

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  9202   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  9381

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  9382   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  9561

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTGRIRVLSFKTG++SLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  9562   WLLNVYDTGRTGRIRVLSFKTGVVSLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  9741

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  9742   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  9921

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPIIGFRYR                            +  + 
Sbjct  9922   VAAAETAKHQAKCNICKECPIIGFRYR----------------------------LSPFQ  10017

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT  960
              T TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETP +       D 
Sbjct  10018  TRTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVD-  10194

Query  961    HSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQ  1020
                      S LAEMEN+NGSYLNDSISPNESIDDEHLLIQHYCQSLNQ+SPLSQP+SPAQ
Sbjct  10195  --------SALAEMENTNGSYLNDSISPNESIDDEHLLIQHYCQSLNQESPLSQPQSPAQ  10350

Query  1021   ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSP  1080
              ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMP SPQSP
Sbjct  10351  ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPVSPQSP  10530

Query  1081   RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSS  1140
              RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQA+AKVNGTT+SS
Sbjct  10531  RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQADAKVNGTTLSS  10710

Query  1141   PSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGH  1200
              PSTSLQRS SSQPMLLRVVGSQTS++MGE++LLSPPQDTSTGLEEVMEQLNNSFPSSRG 
Sbjct  10711  PSTSLQRSGSSQPMLLRVVGSQTSETMGEDELLSPPQDTSTGLEEVMEQLNNSFPSSRGR  10890

Query  1201   NV  1202
              N 
Sbjct  10891  NA  10896


 Score = 62.8 bits (151),  Expect = 1e-06, Method: Compositional matrix adjust.
 Identities = 27/32 (84%), Positives = 31/32 (96%), Gaps = 0/32 (0%)
 Frame = +3

Query  1196   SSRGHNVGSLFHMADDLGRAMESLVSVMTDEE  1227
              S RGHNVGSLFHMADDLGRAME+LV+VMTD++
Sbjct  10908  SERGHNVGSLFHMADDLGRAMETLVTVMTDDK  11003


 Score = 57.0 bits (136),  Expect = 7e-05, Method: Compositional matrix adjust.
 Identities = 116/529 (21%), Positives = 228/529 (43%), Gaps = 55/529 (10%)
 Frame = +1

Query  64    RPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDST  123
             +PQ+E L   +Q LK K   ++A   +   +    + + ++   +  R +QL  +  DS 
Sbjct  2686  QPQIERLKAQSQALKEK---EQAPVFLDADLAAFTSHFKQIFADMHAREKQLQTIF-DSL  2853

Query  124   QWLEAKEEAEQVL---GQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
                  KE    +L    Q+  KL + +      + +++++ E K L   L++ Q  +   
Sbjct  2854  PPAHYKETMNTILVWMQQSETKLSTPQVAIAEYEIMEQRLREFKALQSSLQEQQKGLTYL  3033

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             +     L R    + ++      E +   W+ +  +++E    LEE    LQ+F  D   
Sbjct  3034  STTVEDLSRKAPTEVSQSYRSEVEVVLGRWKKLSAQLAEHCQRLEERMTKLQRFQNDTRT  3213

Query  241   FLAWLTEAETTANVLQDATRKER--LLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDEN  298
                W+ E         D   KE    L DS+ +++ ++Q   L  +I+      ++++E 
Sbjct  3214  LKKWMAEV--------DVFLKEEWPALGDSEALEKQLEQCTALVNDIQTIQPSLNSVNET  3369

Query  299   SQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELL  358
              +K ++S    + A  ++  L ++N +W  + +++   ++ L+   D+   L   L E+ 
Sbjct  3370  GKK-MKSEAEPEFASRIESELKDLNAQWDHICQQAYAKKAALKGGLDKTVSLRKDLSEMH  3546

Query  359   VWL-QLKDDELSRQAPIGGDFP-----AVQKQNDVHRAFKRELKTKEPVIMSTLETVRIF  412
              W+ Q +++ L R      DF       +QK  +  +  K E   KE  +    ++V  F
Sbjct  3547  EWITQAEEEYLER------DFEYKTPDELQKAVEELKRAKEEALQKEVKVKLITDSVNNF  3708

Query  413   LTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDET  472
             + + P    E L +E   L    + Q  +RL        N +W+ L    A W+    E 
Sbjct  3709  IAKAPPAAHEALKKELDVLITSYQ-QLCSRL--------NGKWKTLEEVWACWR----EL  3849

Query  473   LERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENV  532
             L  L    +  +E+++KL+  E ++G  + + + L     D LE++      +   ++N 
Sbjct  3850  LSYLDAENKWLNEIEMKLKATENVQGGAEEISECL-----DSLERL------MRHPEDNR  3996

Query  533   SHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEA  581
             + + +LA+ LT  GI     N   LE  N+RW+ LQ     R + L ++
Sbjct  3997  NQIRELAQTLTDGGILDELIN-EKLEKFNSRWEELQQEAVRRQKSLEQS  4140


 Score = 55.1 bits (131),  Expect = 2e-04, Method: Compositional matrix adjust.
 Identities = 83/348 (23%), Positives = 159/348 (45%), Gaps = 52/348 (14%)
 Frame = +1

Query  273   ELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKK  332
             E +K  +D  G ++ H ++ +N    + + +   E ++    +Q +L  +NF+W +L K 
Sbjct  6142  ECLKSIKDSLGRLQGHVEIVNNKKTAALQNVTPKEAAN----IQEKLTQLNFEWEKLNKM  6309

Query  333   SLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFK  392
               + ++  + S ++W+  H  ++    WL   +++LSR     GD   V+      + F 
Sbjct  6310  YRDRQARFDKSLEKWQIFHSDMKRFNHWLNETEEKLSRAQIEAGDVGLVKT-----KQFI  6474

Query  393   RELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVN  452
             +EL+         +   + F+      G E +         E+ ++   ++L++Q E +N
Sbjct  6475  QELQ-------DGIGQQQTFVKTLNATGEEII---------EQSSKADAKVLKEQLESLN  6606

Query  453   TEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQ  512
               W+++     + +++I+E    L E QE  ++L L L +A+ I     P+ +   D L+
Sbjct  6607  NRWKEICRQLVEKKKRIEEEKNILSEFQEDLNKLILWLEEADNIICI--PLEEGNEDQLR  6780

Query  513   DHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNL---------STLEDLNTR  563
             D L KVK   GE+ P K  +  +N+      T GI L   +L         STL++ N R
Sbjct  6781  DCLSKVKLRVGELPPHKGILKRLNE------TGGIALGSASLNPDKKHKLESTLKEANHR  6942

Query  564   WKLLQVA--VEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNK  609
               LL+V+  + D+ +++    +DF    Q         PW   I+P K
Sbjct  6943  --LLKVSKDLPDKQKEIEILLKDFVELDQQLNQVI---PW---ITPVK  7062


 Score = 48.1 bits (113),  Expect = 0.033, Method: Compositional matrix adjust.
 Identities = 91/389 (23%), Positives = 171/389 (43%), Gaps = 53/389 (13%)
 Frame = +1

Query  22    LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             LT+WL+  D  +  +  + G   +++  I   KAT +++E+R+ QL+ +    +NLK   
Sbjct  4783  LTEWLAATDAELTKRSAVQGMPRNLDAEIAWGKATRKEIEKRQVQLKSISDLGENLKAVM  4962

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEE--AEQVLGQA  139
               +E  +++ D++  + + W  V     +R ++   +L +  + +EA ++  A       
Sbjct  4963  KGKE--SLVDDKLSLLNSNWKAV----TSRAEEWFNLLLEYQKHMEAFDQNVANVTTWMY  5124

Query  140   RAKL---ESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDT  196
             RA++   ES K+ P      Q+K    K+L  +L      VD   D A  L+ +      
Sbjct  5125  RAEILLDESDKQKP------QQKEEILKRLKAELNDIHPKVDSVRDQARDLMANRGEHCR  5286

Query  197   RKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWL-TEAETTANVL  255
             + V      +N    +I +R+   +  +    + L+QF  D++K L  L  E +   N+ 
Sbjct  5287  KVVEPKLSELNQRLAAISQRIKSVKPFI--PLKELEQFDFDIQKMLEPLEVEIQQGVNLK  5460

Query  256   QDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLD-ENSQKILRSLEGSDDAVL  314
             ++   K+   ED   VKEL+++   LQ  +   TD     + +  Q++LR+   +   + 
Sbjct  5461  EEDFNKDMSEEDESTVKELLQRGDRLQKGV---TDEKKREEIKTKQQLLRTKHNALKDLR  5631

Query  315   LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELS-----  369
              QR            RKK+L I       S QW +      +L+ WL   + +L+     
Sbjct  5632  AQR------------RKKALEI-------SHQWYQYKRQADDLMTWLDDIEKKLAGLPDH  5754

Query  370   ----RQAPIGGDFPAVQKQ-NDVHRAFKR  393
                 +   IGG+    ++  N VHR  +R
Sbjct  5755  KDEQKLKEIGGELEKKKEDLNAVHRQAER  5841


 Score = 39.7 bits (91),  Expect = 9.4, Method: Compositional matrix adjust.
 Identities = 47/194 (24%), Positives = 94/194 (48%), Gaps = 24/194 (12%)
 Frame = +1

Query  231   LQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTD  290
             L+ +   LE+ L WL  AE       D +       D + VKE     +    E+ AH  
Sbjct  1057  LENYQTALEEVLTWLLSAEDALQAQGDISN------DVEVVKEQFHTHEGFMMELTAHQG  1218

Query  291   VYHNLDENSQKILRSLEGSDDAV-LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKR  349
                N+ +   ++L + + SD+    +Q +++ +N +W  LR  S+  +S+L        +
Sbjct  1219  RVGNVLQVGSQLLSTGKLSDEEENEIQEQMNLLNSRWESLRVASMEKQSNLH-------K  1377

Query  350   LHLSLQ-----ELLVWLQLKDDELSRQA---PIGGDFPAVQKQNDVHRAFKRELKTKEPV  401
             + + LQ     +L  WL  K +E +++    P+G D   +++Q + H+AF+ +L+ +E V
Sbjct  1378  ILMDLQNQQLAQLADWL-TKTEERTKKTDLEPLGPDLEDLKRQIEEHKAFQEDLE-QEQV  1551

Query  402   IMSTLETVRIFLTE  415
              +++L  + + + E
Sbjct  1552  KVNSLTHMVVVVDE  1593


>ref|NM_004023.2| Homo sapiens dystrophin (DMD), transcript variant Dp140bc, mRNA
Length=7048

 Score = 1975 bits (5116),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 972/1060 (91%), Positives = 989/1060 (93%), Gaps = 39/1060 (3%)
 Frame = +1

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  1042  MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  1221

Query  61    EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
             EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  1222  EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  1401

Query  121   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
             DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  1402  DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  1581

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  1582  NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  1761

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
             FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  1762  FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  1941

Query  301   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
             KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  1942  KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  2121

Query  361   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
             LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  2122  LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  2301

Query  421   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
             LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  2302  LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  2481

Query  481   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
             EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  2482  EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  2661

Query  541   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
             QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  2662  QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  2841

Query  601   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
             WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  2842  WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  3021

Query  661   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
             LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  3022  LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  3201

Query  721   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
             WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  3202  WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  3381

Query  781   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
             SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  3382  SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  3561

Query  841   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
             VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  3562  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  3741

Query  901   TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT  960
             TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET   + Q  +D  
Sbjct  3742  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET---NLQAEYDRL  3912

Query  961   HSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQ  1020
               + EH               L+   SP E +                  P S P+SP  
Sbjct  3913  KQQHEHKG-------------LSPLPSPPEMM------------------PTS-PQSPRD  3996

Query  1021  ILISLES----EERGELERILADLEEENRNLQAEYDRLKQ  1056
               +  E+    + +G LE  +  LE+ N+ L+++  RL+Q
Sbjct  3997  AELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQ  4116


 Score =  375 bits (964),  Expect = 6e-101, Method: Compositional matrix adjust.
 Identities = 185/185 (100%), Positives = 185/185 (100%), Gaps = 0/185 (0%)
 Frame = +1

Query  1046  NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQI  1105
             NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQI
Sbjct  3886  NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQI  4065

Query  1106  LEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSD  1165
             LEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSD
Sbjct  4066  LEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSD  4245

Query  1166  SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTD  1225
             SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTD
Sbjct  4246  SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTD  4425

Query  1226  EEGAE  1230
             EEGAE
Sbjct  4426  EEGAE  4440


 Score = 55.5 bits (132),  Expect = 2e-04, Method: Compositional matrix adjust.
 Identities = 51/206 (24%), Positives = 99/206 (48%), Gaps = 15/206 (7%)
 Frame = +1

Query  164  KQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAA  223
            K+L   + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  
Sbjct  97   KELQDGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKR  276

Query  224  LEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQG  283
            LEE   +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG
Sbjct  277  LEEQKNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG  456

Query  284  EIEAHTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEA  342
                   +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA
Sbjct  457  -------ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEA  615

Query  343  SSDQWKRLHLSLQE-------LLVWL  361
                  +L   L++       LL+WL
Sbjct  616  QIKDLGQLEKKLEDLEEQLNHLLLWL  693


>ref|NM_004020.2| Homo sapiens dystrophin (DMD), transcript variant Dp140c, mRNA
Length=7050

 Score = 1955 bits (5065),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 938/940 (99%), Positives = 939/940 (99%), Gaps = 0/940 (0%)
 Frame = +1

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  1042  MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  1221

Query  61    EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
             EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  1222  EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  1401

Query  121   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
             DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA
Sbjct  1402  DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  1581

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK
Sbjct  1582  NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  1761

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
             FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ
Sbjct  1762  FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  1941

Query  301   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
             KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  1942  KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  2121

Query  361   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
             LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  2122  LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  2301

Query  421   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
             LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ
Sbjct  2302  LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  2481

Query  481   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
             EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR
Sbjct  2482  EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  2661

Query  541   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
             QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP
Sbjct  2662  QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  2841

Query  601   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
             WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  2842  WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  3021

Query  661   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
             LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  3022  LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  3201

Query  721   WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
             WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD
Sbjct  3202  WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  3381

Query  781   SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
             SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR
Sbjct  3382  SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  3561

Query  841   VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
             VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC
Sbjct  3562  VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  3741

Query  901   TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTV  940
             TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQ +
Sbjct  3742  TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQNL  3861


 Score =  314 bits (804),  Expect(2) = 4e-97, Method: Compositional matrix adjust.
 Identities = 155/158 (98%), Positives = 156/158 (98%), Gaps = 0/158 (0%)
 Frame = +1

Query  1045  RNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ  1104
             +NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ
Sbjct  3853  QNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ  4032

Query  1105  ILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTS  1164
             ILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTS
Sbjct  4033  ILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTS  4212

Query  1165  DSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             DSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG N 
Sbjct  4213  DSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGRNT  4326


 Score = 71.6 bits (174),  Expect(2) = 4e-97, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +3

Query  1198  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  4344  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  4442


 Score = 55.1 bits (131),  Expect = 2e-04, Method: Compositional matrix adjust.
 Identities = 51/206 (24%), Positives = 99/206 (48%), Gaps = 15/206 (7%)
 Frame = +1

Query  164  KQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAA  223
            K+L   + Q QT V   N    ++++  S  D   +     ++N  W+ + K++S+R+  
Sbjct  97   KELQDGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSDRKKR  276

Query  224  LEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQG  283
            LEE   +L +F  DL +F+ WL EA+  A++  +  ++++L E  + VK L+++    QG
Sbjct  277  LEEQKNILSEFQRDLNEFVLWLEEADNIASIPLEPGKEQQLKEKLEQVKLLVEELPLRQG  456

Query  284  EIEAHTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEA  342
                   +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA
Sbjct  457  -------ILKQLNETGGPVLVSAPISPEEQDKLENKLKQTNLQWIKVSRALPEKQGEIEA  615

Query  343  SSDQWKRLHLSLQE-------LLVWL  361
                  +L   L++       LL+WL
Sbjct  616  QIKDLGQLEKKLEDLEEQLNHLLLWL  693


>ref|NM_004014.2| Homo sapiens dystrophin (DMD), transcript variant Dp116, mRNA
Length=5623

 Score = 1905 bits (4934),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 921/937 (98%), Positives = 922/937 (98%), Gaps = 13/937 (1%)
 Frame = +2

Query  279   QDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRS  338
             +DLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRS
Sbjct  89    KDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRS  268

Query  339   HLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTK  398
             HLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTK
Sbjct  269   HLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTK  448

Query  399   EPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKL  458
             EPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKL
Sbjct  449   EPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKL  628

Query  459   NLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKV  518
             NLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKV
Sbjct  629   NLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKV  808

Query  519   KALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQL  578
             KALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQL
Sbjct  809   KALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQL  988

Query  579   HEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADL  638
             HEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADL
Sbjct  989   HEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADL  1168

Query  639   NNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIY  698
             NNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIY
Sbjct  1169  NNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIY  1348

Query  699   DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYL  758
             DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYL
Sbjct  1349  DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYL  1528

Query  759   FKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEA  818
             FKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEA
Sbjct  1529  FKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEA  1708

Query  819   ALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQ  878
             ALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQ
Sbjct  1709  ALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQ  1888

Query  879   SCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQ  938
             SCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQ
Sbjct  1889  SCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQ  2068

Query  939   TVLEGDNMET-------------PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDS  985
             TVLEGDNMET             PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDS
Sbjct  2069  TVLEGDNMETPVTLINFWPVDSAPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDS  2248

Query  986   ISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
             ISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR
Sbjct  2249  ISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  2428

Query  1046  NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQI  1105
             NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQI
Sbjct  2429  NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQI  2608

Query  1106  LEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSD  1165
             LEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSD
Sbjct  2609  LEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSD  2788

Query  1166  SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG N 
Sbjct  2789  SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGRNT  2899


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +1

Query  1198  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  2917  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  3015


>ref|XM_001096400.1| PREDICTED: Macaca mulatta similar to dystrophin Dp140b isoform 
(LOC707966), partial mRNA
Length=3242

 Score = 1707 bits (4420),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 820/854 (96%), Positives = 831/854 (97%), Gaps = 13/854 (1%)
 Frame = +1

Query  390   AFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAE  449
             AFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAE
Sbjct  1     AFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAE  180

Query  450   EVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLID  509
             EVNTEWEKLNLHS DWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLID
Sbjct  181   EVNTEWEKLNLHSTDWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLID  360

Query  510   SLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV  569
             SLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV
Sbjct  361   SLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV  540

Query  570   AVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMT  629
             AVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMT
Sbjct  541   AVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMT  720

Query  630   ELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQ  689
             ELYQSL  L+++++S  R  ++LR L  +LC+DLLSLSAACDALDQHNLKQNDQPMDILQ
Sbjct  721   ELYQSLGFLHSIKYSLLRMLLELRALSSSLCMDLLSLSAACDALDQHNLKQNDQPMDILQ  900

Query  690   IINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKA  749
             IINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKA
Sbjct  901   IINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKA  1080

Query  750   HLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF  809
             HLEDKYRYLFKQV+SSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF
Sbjct  1081  HLEDKYRYLFKQVSSSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF  1260

Query  810   ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
             ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL
Sbjct  1261  ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  1440

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKH  929
             KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKH
Sbjct  1441  KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKH  1620

Query  930   PRMGYLPVQTVLEGDNMET-------------PASSPQLSHDDTHSRIEHYASRLAEMEN  976
             PRMGYLPVQTVLEGDNMET             PASSPQLSHDDTHSRIEHYASRLAEMEN
Sbjct  1621  PRMGYLPVQTVLEGDNMETPVTLINFWPVDSAPASSPQLSHDDTHSRIEHYASRLAEMEN  1800

Query  977   SNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERI  1036
             SNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERI
Sbjct  1801  SNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERI  1980

Query  1037  LADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHK  1096
             LADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHK
Sbjct  1981  LADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHK  2160

Query  1097  GRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLL  1156
             GRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLL
Sbjct  2161  GRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLL  2340

Query  1157  RVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGRAM  1216
             RVVGSQTSDSMGEED+LSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGRAM
Sbjct  2341  RVVGSQTSDSMGEEDVLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGRAM  2520

Query  1217  ESLVSVMTDEEGAE  1230
             ESLVSVMTDEEGAE
Sbjct  2521  ESLVSVMTDEEGAE  2562


>gb|AF339031.1|AF339031 Danio rerio dystrophin (dmd) mRNA, partial cds, alternatively 
spliced
Length=3521

 Score = 1583 bits (4099),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 768/1119 (68%), Positives = 910/1119 (81%), Gaps = 44/1119 (3%)
 Frame = +2

Query  96    RIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDA  155
             R    W++    L  R   L  M KDS+ WLEA++  E ++ +A  KLESWK+  ++V+ 
Sbjct  2     RFCRHWEDSHAKLTARVLTLQNMYKDSSDWLEARKRVEPLIKKANEKLESWKKVSHSVED  181

Query  156   IQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHK  215
             ++ +  + KQL+KDL+QWQT ++V N+LA KLL  Y+ DDT KV  +TE++N +W +I K
Sbjct  182   LKGQNADVKQLSKDLQQWQTQMNVTNELANKLLTLYADDDTSKVKQMTESMNLAWANIKK  361

Query  216   RVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELM  275
             R  ++EA LE   R LQ + LDLEKFL WLTEAETTANVLQDAT KE LLE+   V+ L+
Sbjct  362   RAGDKEADLEAGLRQLQHYYLDLEKFLNWLTEAETTANVLQDATFKEGLLENPATVRHLL  541

Query  276   KQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLN  335
             +QWQDLQ EI+AH + YH+LDEN  +I+ SLEG+D+AV+LQ+RLD+M  +W EL  K ++
Sbjct  542   EQWQDLQAEIDAHRETYHSLDENGHRIVSSLEGTDNAVVLQKRLDDMGQRWHELCNKVMS  721

Query  336   IRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKREL  395
             IR +L+A  DQWK LH+SLQELL WLQLK +EL +Q P+GGD P V +Q   H+AF+REL
Sbjct  722   IRPYLDAGVDQWKHLHMSLQELLNWLQLKREELEKQKPVGGDVPTVHQQLLTHKAFRREL  901

Query  396   KTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEP--RELPPEERAQNVTRLLRKQAEEVNT  453
               KEPVI  TL+  + FL E P EGL+   Q P  +++ PEER QNV R+LRK+ E+V  
Sbjct  902   GAKEPVINGTLDNAKTFLAEMPREGLK---QRPGQKDVSPEERVQNVGRILRKEVEDVTV  1072

Query  454   EWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQD  513
              W+ L   S DWQ++++  LERL ELQ+A D+LD KLRQAE +K SW+PVG+LL+D LQ+
Sbjct  1073  RWKNLGAASVDWQQQLELALERLMELQDAQDQLDYKLRQAESVKNSWKPVGELLVDDLQN  1252

Query  514   HLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVED  573
             H+++VKA + EIAP+++NV+HVN LA       IQLSP NLS ++DLN RW+LLQ+++E+
Sbjct  1253  HIDRVKAFQEEIAPIQDNVNHVNQLASTFRPSDIQLSPDNLSRIDDLNMRWRLLQISIEE  1432

Query  574   RVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQ  633
              + QL  A +D GP SQ+FL  SV+ P ER+ISPN VPYYINH+TQTTCWDHPKM ELYQ
Sbjct  1433  HLSQLTTAFKDLGP-SQNFLHASVESPLERSISPNNVPYYINHQTQTTCWDHPKMAELYQ  1609

Query  634   SLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINC  693
             SLADLNNVRFSAYRTAMKLRR+QKALCLDLLS+ AAC+A +QHNLKQN+Q MDI+Q+INC
Sbjct  1610  SLADLNNVRFSAYRTAMKLRRMQKALCLDLLSMPAACEAFEQHNLKQNEQFMDIVQVINC  1789

Query  694   LTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLED  753
             LT+IYDRLEQ+H++LVNVPLCVDMCLNWLLNVYDTGR G+IR LSFKTGIISLCKAHLED
Sbjct  1790  LTSIYDRLEQQHSSLVNVPLCVDMCLNWLLNVYDTGRAGKIRTLSFKTGIISLCKAHLED  1969

Query  754   KYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNK  813
             KYR+LF++VAS+TGFCDQRRLGLLLHD+IQIPRQLGEVASFGGSNIEPSVRSCFQFANNK
Sbjct  1970  KYRFLFREVASATGFCDQRRLGLLLHDAIQIPRQLGEVASFGGSNIEPSVRSCFQFANNK  2149

Query  814   PEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFN  873
             PE+EA++FLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFN
Sbjct  2150  PELEASVFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFN  2329

Query  874   YDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMG  933
             YDICQSCFFSGRVAKGHKM YPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMG
Sbjct  2330  YDICQSCFFSGRVAKGHKMQYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMG  2509

Query  934   YLPVQTVLEGDNMET-------------PASSPQLSHDDTHSRIEHYASRLAEMENSNGS  980
             YLPVQT+LEGDNMET             PASSPQLSHDDTHSRIEHYASR          
Sbjct  2510  YLPVQTILEGDNMETPVTLINFWPVDHPPASSPQLSHDDTHSRIEHYASR----------  2659

Query  981   YLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADL  1040
                         DDEHLLIQHYCQSLNQ SPLSQP+SPAQILIS+E+EE+GELER+L DL
Sbjct  2660  ------------DDEHLLIQHYCQSLNQGSPLSQPQSPAQILISMETEEKGELERVLNDL  2803

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E+ENR LQAEYDRLK+ H+HKGLSPLPSPP+M+P SPQSPRDAELIAEAKLLRQHKGRLE
Sbjct  2804  EQENRKLQAEYDRLKKAHDHKGLSPLPSPPQMLPVSPQSPRDAELIAEAKLLRQHKGRLE  2983

Query  1101  ARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVG  1160
             ARMQILEDHNKQLESQL RLRQLLE  Q E+KVNGT +SSPST+  RSD+S    LRV  
Sbjct  2984  ARMQILEDHNKQLESQLTRLRQLLE--QTESKVNGTALSSPSTASPRSDTSLAS-LRVAA  3154

Query  1161  SQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
             SQT+++MG+++L SP QD STGLE+V+EQLNNSFP S+G
Sbjct  3155  SQTTETMGDDELSSPTQDASTGLEDVIEQLNNSFPHSQG  3271


 Score = 50.1 bits (118),  Expect = 0.007, Method: Compositional matrix adjust.
 Identities = 22/32 (68%), Positives = 27/32 (84%), Gaps = 0/32 (0%)
 Frame = +1

Query  1196  SSRGHNVGSLFHMADDLGRAMESLVSVMTDEE  1227
             S RG NVGSLFHM D++G AMESLV V+T+E+
Sbjct  3286  SMRGPNVGSLFHMVDNIGHAMESLVHVITEEQ  3381


 Score = 43.9 bits (102),  Expect = 0.51, Method: Compositional matrix adjust.
 Identities = 51/232 (21%), Positives = 101/232 (43%), Gaps = 30/232 (12%)
 Frame = +2

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA------  74
             EL +WL L  + ++ Q+ + GD+  +++ ++  KA  ++L  + P +   +  A      
Sbjct  782   ELLNWLQLKREELEKQKPVGGDVPTVHQQLLTHKAFRRELGAKEPVINGTLDNAKTFLAE  961

Query  75    ---QNLKNKTSN---------QEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDS  122
                + LK +            Q    I+   +E +  +W  +     + +QQL   L+  
Sbjct  962   MPREGLKQRPGQKDVSPEERVQNVGRILRKEVEDVTVRWKNLGAASVDWQQQLELALERL  1141

Query  123   TQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVAN  181
              +  +A+++ +  L QA +   SWK  G   VD +Q  I   K   +++   Q NV+  N
Sbjct  1142  MELQDAQDQLDYKLRQAESVKNSWKPVGELLVDDLQNHIDRVKAFQEEIAPIQDNVNHVN  1321

Query  182   DLALKLLRD---YSADDTRKVHMITENINASWR----SIHKRVSEREAALEE  226
              LA          S D+  ++    +++N  WR    SI + +S+   A ++
Sbjct  1322  QLASTFRPSDIQLSPDNLSRI----DDLNMRWRLLQISIEEHLSQLTTAFKD  1465


>gb|BC085236.1| Mus musculus dystrophin, muscular dystrophy, mRNA (cDNA clone 
IMAGE:5357162), partial cds
Length=2509

 Score = 1519 bits (3932),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 722/749 (96%), Positives = 737/749 (98%), Gaps = 0/749 (0%)
 Frame = +1

Query  200   HMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDAT  259
             HMITENIN SW +IHKRVSE+EAALEETHRLLQQFPLDLEKFL+W+TEAETTANVLQDA+
Sbjct  1     HMITENINTSWGNIHKRVSEQEAALEETHRLLQQFPLDLEKFLSWITEAETTANVLQDAS  180

Query  260   RKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRL  319
             RKE+LLEDS+GV+ELMK WQDLQGEIE HTD+YHNLDEN QKILRSLEGSD+A LLQRRL
Sbjct  181   RKEKLLEDSRGVRELMKPWQDLQGEIETHTDIYHNLDENGQKILRSLEGSDEAPLLQRRL  360

Query  320   DNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFP  379
             DNMNFKWSEL+KKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFP
Sbjct  361   DNMNFKWSELQKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFP  540

Query  380   AVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQN  439
             AVQKQND+HRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQN
Sbjct  541   AVQKQNDIHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQN  720

Query  440   VTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGS  499
             VTRLLRKQAEEVN EW+KLNL SADWQRKIDE LERLQELQEA DELDLKLRQAEVIKGS
Sbjct  721   VTRLLRKQAEEVNAEWDKLNLRSADWQRKIDEALERLQELQEAADELDLKLRQAEVIKGS  900

Query  500   WQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLED  559
             WQPVGDLLIDSLQDHLEKVKALRGEIAPLKENV+ VNDLA QLTTLGIQLSPYNLSTLED
Sbjct  901   WQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVNRVNDLAHQLTTLGIQLSPYNLSTLED  1080

Query  560   LNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQ  619
             LNTRW+LLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQ
Sbjct  1081  LNTRWRLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQ  1260

Query  620   TTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK  679
             TTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK
Sbjct  1261  TTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK  1440

Query  680   QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSF  739
             QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSF
Sbjct  1441  QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSF  1620

Query  740   KTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNI  799
             KTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNI
Sbjct  1621  KTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNI  1800

Query  800   EPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKEC  859
             EPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKEC
Sbjct  1801  EPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKEC  1980

Query  860   PIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNK  919
             PIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNK
Sbjct  1981  PIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNK  2160

Query  920   FRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
             FRTKRYFAKHPRMGYLPVQTVLEGDNMET
Sbjct  2161  FRTKRYFAKHPRMGYLPVQTVLEGDNMET  2247


>ref|XM_419648.2| PREDICTED: Gallus gallus utrophin (homologous to dystrophin) 
(UTRN), mRNA
Length=8538

 Score = 1508 bits (3903),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 731/1213 (60%), Positives = 925/1213 (76%), Gaps = 37/1213 (3%)
 Frame = +1

Query  7     LEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQ  66
             LE+ A AD ++  TEL +WL L+DQ++KS  V VG+ E+IN  I + K T  DL+QR PQ
Sbjct  4795  LELSAPADLDKTTTELAEWLVLIDQMLKSNIVTVGNAEEINRTIARMKVTKADLDQRHPQ  4974

Query  67    LEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWL  126
             L+ + T AQNLKNKTS+ + RT+IT+++E+++NQWD  Q  ++ R+QQL  ML DS QW 
Sbjct  4975  LDSVFTLAQNLKNKTSSSDIRTVITEKLEKVKNQWDNTQHGVEVRQQQLKYMLSDSMQWD  5154

Query  127   EAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALK  186
             E ++E E ++ Q   +L   ++ P   +A+ K+I++ K L  DL +    V   NDL+ K
Sbjct  5155  EQRKEMEHLMEQCEIRLRMLQQAPK--EALIKQISDNKLLVHDLHRGDITVAAFNDLSNK  5328

Query  187   LLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             LLR+Y  DDTR+V   T+ +N  W ++++R  +R+  LE   + +Q    DLE FL WL 
Sbjct  5329  LLREYRDDDTRRVKETTDQMNTCWVNLNQRAVDRQNFLETELKTVQTSCKDLESFLKWLQ  5508

Query  247   EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL  306
             EAETT NVL DA R+E   +DS  V+EL KQ QD+Q EI+AH D++ ++D N QK++++L
Sbjct  5509  EAETTVNVLADAARRENTAQDSACVRELRKQMQDIQAEIDAHNDIFKSIDGNRQKMVKAL  5688

Query  307   EGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDD  366
               S++A LLQ RLD+MN +W++L+ KS NIR+HLEAS+++W RL  SL+EL+ WL +KD+
Sbjct  5689  GNSEEAALLQHRLDDMNQRWNDLKVKSANIRAHLEASAEKWNRLLTSLEELIKWLNMKDE  5868

Query  367   ELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQ  426
             EL +Q PIGGD P +Q+Q D  +A +RELK KE  I++ ++  RIFL +QP+EG E    
Sbjct  5869  ELKKQMPIGGDVPTLQQQYDHCKALRRELKDKEQTILNAVDQARIFLADQPIEGPE----  6036

Query  427   EPR-------ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQEL  479
             EPR       EL PEE+A  + + +RKQ+ EV  +WE LN  ++ WQ+++D+ LE+L++L
Sbjct  6037  EPRRSVHSKTELTPEEKAMRIAKAMRKQSSEVKEKWENLNASASIWQKQVDKALEKLKDL  6216

Query  480   QEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLA  539
             Q A D+LD  L++AE ++  W+PVGDLLIDSL DH+EK  A R EIAP+   V  VNDL+
Sbjct  6217  QCAMDDLDADLKEAENVRNGWKPVGDLLIDSLPDHIEKTTAFREEIAPINLKVKTVNDLS  6396

Query  540   RQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQG  599
              QL+ L +  S      L+DLN RWKLLQV+VEDR++QL EAHRDFGPASQHFLSTSVQ 
Sbjct  6397  SQLSPLDLYPSLKMSCQLDDLNMRWKLLQVSVEDRLKQLQEAHRDFGPASQHFLSTSVQF  6576

Query  600   PWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKAL  659
             PW+R++S NKVPYYINHETQTTCWDHPKMT+L+QSLADLNNVRFSAYRTA+K+RRLQKAL
Sbjct  6577  PWQRSVSHNKVPYYINHETQTTCWDHPKMTDLFQSLADLNNVRFSAYRTAIKIRRLQKAL  6756

Query  660   CLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCL  719
             CLDLL L+   +   QH L QNDQ + +  +I+CLTTIY  LE++HN++VNVPLCVDMCL
Sbjct  6757  CLDLLELNTTTEIFKQHKLSQNDQLVGVQDVISCLTTIYSGLEEKHNDMVNVPLCVDMCL  6936

Query  720   NWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLH  779
             NWLLNVYD+GRTG+IRV S K G++SL K  LE+KYRYLFK+V+  T  CDQR+LGLLLH
Sbjct  6937  NWLLNVYDSGRTGKIRVQSLKIGLMSLSKGLLEEKYRYLFKEVSGPTEMCDQRQLGLLLH  7116

Query  780   DSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLH  839
             D+IQIPRQLGEVA+FGGSNIEPSVRSCFQ  +NKPEI    F+DWM LEPQSMVWLPVLH
Sbjct  7117  DAIQIPRQLGEVAAFGGSNIEPSVRSCFQQNHNKPEITVKQFIDWMHLEPQSMVWLPVLH  7296

Query  840   RVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
             RVAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEY
Sbjct  7297  RVAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEY  7476

Query  900   CTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-----------  948
             C PTTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ET           
Sbjct  7477  CIPTTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMWPEQ  7656

Query  949   --PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSL  1006
               P+ SPQL HDDTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH LIQ YCQ+L
Sbjct  7657  YDPSQSPQLFHDDTHSRIEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHALIQQYCQTL  7836

Query  1007  NQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPL  1066
               +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE R+LQ EY++LK+QH  +G++PL
Sbjct  7837  GGESPVSQPQSPAQILKSVEKEERGELERIIADLEEEQRSLQIEYEQLKEQHLRRGINPL  8016

Query  1067  PSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ  1126
              SPP+ + +   +  DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ
Sbjct  8017  ASPPDSIVSPQHASEDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ  8196

Query  1127  PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSM---GEEDLLSPPQDTSTGL  1183
             P+++++VNG   +SP TS Q S    P+       +TS      GE DLL PP DT+T L
Sbjct  8197  PESDSRVNG---ASPCTSPQHSALGYPL-----DQETSSQFHQAGEYDLLVPPHDTNTDL  8352

Query  1184  EEVMEQLNNSFPS  1196
              +VMEQ+N++FP+
Sbjct  8353  TDVMEQINSTFPA  8391


 Score = 53.1 bits (126),  Expect = 0.001, Method: Compositional matrix adjust.
 Identities = 83/387 (21%), Positives = 166/387 (42%), Gaps = 50/387 (12%)
 Frame = +1

Query  10    PALADFNRAWTELTDWLSLLDQVIKSQRVMVG------------------DLE----DIN  47
             P LA+ NR + +++       Q IKS +++VG                  DL+    DI 
Sbjct  3304  PKLAELNRNFEKVS-------QHIKSAKMLVGQERLPVMSEPREVRVGFPDLDKFESDIQ  3462

Query  48    EM--IIKQKATMQD----LEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQW  101
              M  ++++   + +    L+Q R Q+EE++     L  +      R  I  ++  +Q ++
Sbjct  3463  NMLKVVEKHQELSEGDEKLDQERAQIEEVLQRGGQLLQQPMEDNKREKIRMQLVLLQTKY  3642

Query  102   DEVQEHLQNRRQQLNEMLKDSTQWLEAKE--EAEQVLGQARAKLESWKEGPYTVDAIQKK  159
             + VQ     +R + +      TQ   A+   E  +VL  A A +E    GP     I + 
Sbjct  3643  NNVQAVAVQQRLKGHFATGVRTQPFSAEYLVEINKVL-LAMADVELLLNGPELNTGIYED  3819

Query  160   ITETKQLAKDLR----QWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHK  215
              +  +   K+++    +    + V ++    ++ + S  +  ++      +NA W  I++
Sbjct  3820  FSTQEDALKNVKDILDKLGDQIAVIHEKQPDVILEASGPEAIQIGDALTQLNAEWDRINR  3999

Query  216   RVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELM  275
               ++R+ + +      +QF  DL     W+TEAE    +L DA    R  +DS  ++   
Sbjct  4000  MYNDRKCSFDRAIEAWRQFHCDLNDLSQWITEAE---GLLADA----RGPDDSLDLQTAG  4158

Query  276   KQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLN  335
                Q+L+  + +H      L+   + I++ L  +D +  LQ +L  +N +W  +  + ++
Sbjct  4159  LHQQELEEGVHSHQSSVLALNRTGEGIIQKLSATDGS-FLQEKLAGLNRRWKAITAEVMD  4335

Query  336   IRSHLEASSDQWKRLHLSLQELLVWLQ  362
              +  L+  + Q       L EL  WL+
Sbjct  4336  RQQRLKGENQQLIDYRKKLDELRCWLE  4416


>ref|XM_518782.2| PREDICTED: Pan troglodytes utrophin, transcript variant 3 (UTRN), 
mRNA
Length=12385

 Score = 1498 bits (3877),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 728/1209 (60%), Positives = 923/1209 (76%), Gaps = 31/1209 (2%)
 Frame = +2

Query  8      EVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQL  67
              E+   AD ++  TEL DWL L+DQ++KS  V VGD+E+IN+ + + K T  DLEQR PQL
Sbjct  6731   EISIPADLDKTITELADWLVLIDQMLKSNIVTVGDVEEINKTVSRMKITKADLEQRHPQL  6910

Query  68     EELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
              + + T AQNLKNK S+ + RT IT+++ER++NQWD  Q  ++ R+QQL +M+ DS QW +
Sbjct  6911   DYVFTLAQNLKNKASSSDVRTAITEKLERVKNQWDGTQHGVELRQQQLEDMIIDSLQWDD  7090

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
               +EE E+++ +  A+L   ++     D + K+I++ + L ++L      V   +++  KL
Sbjct  7091   HREETEELMRKYEARLYILQQARR--DPLTKQISDNQILLQELGPGDGIVMAFDNVLQKL  7264

Query  188    LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
              L +Y +DDTR V   TE +  SW ++ + +++R+ ALE   R +Q    DLE FL W+ E
Sbjct  7265   LEEYGSDDTRNVKETTEYLKTSWINLKQSIADRQNALEAEWRTVQASRRDLENFLKWIQE  7444

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
              AETT NVL DA+ +E  L+DS   +EL +Q QD+Q EI+AH D++ ++D N QK++++L 
Sbjct  7445   AETTVNVLADASNRENALQDSILARELKQQMQDIQAEIDAHNDIFKSIDGNRQKMVKALG  7624

Query  308    GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
               S++A +LQ RLD+MN +W++L+ KS +IR+HLEAS+++W RL +SL+EL+ WL +KD+E
Sbjct  7625   NSEEATMLQHRLDDMNQRWNDLKAKSASIRAHLEASAEKWNRLLMSLEELIKWLNMKDEE  7804

Query  368    LSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQE  427
              L +Q PIGGD PA+Q Q D  +A +RELK KE  +++ ++  R+FL +QP+E  E    E
Sbjct  7805   LKKQMPIGGDVPALQLQYDHCKALRRELKEKEYSVLNAVDQARVFLADQPIEAPE----E  7972

Query  428    PR-------ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              PR       EL PEERAQ + + +RKQ+ EV  +WE LN  +++WQ+++D+ LE+L++LQ
Sbjct  7973   PRRNLQSKTELTPEERAQKIAKAMRKQSSEVKEKWESLNAVTSNWQKQVDKALEKLRDLQ  8152

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
               A D+LD  +++AE ++  W+PVGDLLIDSLQDH+EK+ A R EIAP+   V  VNDL+ 
Sbjct  8153   GAMDDLDADMKEAESVRNGWKPVGDLLIDSLQDHIEKIMAFREEIAPINFKVKTVNDLSS  8332

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QL+ L +  S      L+DLN RWKLLQV+V+DR++QL EAHRDFGP+SQHFLSTSVQ P
Sbjct  8333   QLSPLDLHPSLKMSRQLDDLNMRWKLLQVSVDDRLKQLQEAHRDFGPSSQHFLSTSVQLP  8512

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              W+R+IS NKVPYYINH+TQTTCWDHPKMTEL+QSLADLNNVRFSAYRTA+K+RRLQKALC
Sbjct  8513   WQRSISHNKVPYYINHQTQTTCWDHPKMTELFQSLADLNNVRFSAYRTAIKIRRLQKALC  8692

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLL LS   +   QH L QNDQ + +  +INCLTT YD LEQ H +LVNVPLCVDMCLN
Sbjct  8693   LDLLELSTTNEIFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQMHKDLVNVPLCVDMCLN  8872

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTG+IRV S K G++SL K  LE+KYRYLFK+VA  T  CDQR+LGLLLHD
Sbjct  8873   WLLNVYDTGRTGKIRVQSLKIGLMSLSKGLLEEKYRYLFKEVAGPTEMCDQRQLGLLLHD  9052

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              +IQIPRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWMRLEPQSMVWLPVLHR
Sbjct  9053   AIQIPRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKEFIDWMRLEPQSMVWLPVLHR  9232

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC
Sbjct  9233   VAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYC  9412

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPAS---------  951
               PTTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ETP +         
Sbjct  9413   IPTTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMWPEHY  9592

Query  952    ----SPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
                  SPQL HDDTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH LIQ YCQ+L 
Sbjct  9593   DPSQSPQLFHDDTHSRIEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHALIQQYCQTLG  9772

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
               +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE RNLQ EY++LK QH  +GL P+ 
Sbjct  9773   GESPVSQPQSPAQILKSVEKEERGELERIIADLEEEQRNLQVEYEQLKDQHLRRGL-PVG  9949

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPE + +   +  D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  9950   SPPESIVSPHHTSEDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10129

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              ++++++NG    SP  S Q S  S  +     G Q   + G EDLL+PP DTST L EVM
Sbjct  10130  ESDSRINGV---SPWASPQHSALSYSLDPDASGPQFHQAAG-EDLLAPPHDTSTDLTEVM  10297

Query  1188   EQLNNSFPS  1196
              EQ++N+FPS
Sbjct  10298  EQIHNTFPS  10324


 Score = 47.0 bits (110),  Expect = 0.075, Method: Compositional matrix adjust.
 Identities = 113/514 (21%), Positives = 219/514 (42%), Gaps = 78/514 (15%)
 Frame = +2

Query  7     LEVPALADFNRAWTELTDWLSLLDQVIKSQRVM-VGDLEDINEMIIKQKATMQDLEQRRP  65
             +++ A   F+    EL +W+      I++  +     ++D +EM  K KA  ++  +R P
Sbjct  2111  VDIEAKKKFDAISAELLNWILKSKTAIQTTEIKEYMKMQDTSEMKKKLKALEKEQRERIP  2290

Query  66    QLEELITAAQNLKNKTSNQEARTI-ITDRIERIQNQWDEVQEHLQN--RRQQLNEMLKDS  122
             + +EL    Q L  +   +   T  I + +E++ ++W  V +HL++  R+ QL E   D 
Sbjct  2291  RADELNQTGQILVEQMGKEGLPTEEIKNVLEKVSSEWKNVSQHLEDIERKIQLQE---DI  2461

Query  123   TQWLEAKEEAEQVLGQAR--AKLESWKEG-----PYTVDAIQKKITETKQLAKDLRQWQT  175
               + +  +E E+VL       K  S  E      P   D+ Q+++T       +L     
Sbjct  2462  NAYFKQLDELEKVLKTKEEWVKHTSISESSRQSLPSLKDSCQRELT-------NLLGLHP  2620

Query  176   NVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALE----------  225
              +++A      L+   SA D   V    ++    ++++ + V +R+  LE          
Sbjct  2621  KIEMARASCSALMSQPSAPDF--VQRGFDSFLGCYQAVQEAVEDRQQHLENELKGQPGHA  2794

Query  226   --ETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQG  283
               ET + L+    D E       +A+ + NVL D  + E+ L++ K + E++        
Sbjct  2795  YLETLKTLKDVLDDSE------NKAQASLNVLNDLAKVEKALQEKKTLDEIL--------  2932

Query  284   EIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELR---KKSLNIRSHL  340
               E      H L E ++ + +++   D   L ++  D++  KW++L+    K L++   L
Sbjct  2933  --ENQKPALHKLAEETKALEKNVH-PDVEKLYKQEFDDVQGKWNKLKVLVSKDLHL---L  3094

Query  341   EASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEP  400
             E  + + +        +  W+    D L +Q    GD   +Q+Q D   AF  E++T E 
Sbjct  3095  EEIALKLRAFEADSTVIEKWMDGVKDFLVKQQAAQGDDAGLQRQLDQCSAFVNEIETIES  3274

Query  401   VIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNL  460
               +  ++ +   L   P+ G++   Q              TRL   Q     T+ EKL+ 
Sbjct  3275  S-LKNMKEIETNLRSGPVAGIKTWVQ--------------TRLGDYQ-----TQLEKLSK  3394

Query  461   HSADWQRKIDETLERLQELQEATDELDLKLRQAE  494
                  + ++ E+ E+   L++   E+   + QAE
Sbjct  3395  EITTQKSRLSESQEKAANLKKDLAEMQEWMTQAE  3496


 Score = 44.3 bits (103),  Expect = 0.43, Method: Compositional matrix adjust.
 Identities = 38/156 (24%), Positives = 68/156 (43%), Gaps = 8/156 (5%)
 Frame = +2

Query  206   INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
             +NA W  I++  S+R+   +      +QF  DL     W+TEAE    +L D       L
Sbjct  5918  LNAKWDRINRMYSDRKGCFDRAMEEWRQFHCDLNDLTQWITEAE---ELLVDTCAPGGSL  6088

Query  266   EDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFK  325
             +  K         Q+L+  I +H   +  L+     I++ L  +D +  L+ +L  +N +
Sbjct  6089  DLEKA----RIHQQELEVGISSHQPSFAALNRTGDGIVQKLSQADGS-FLKDKLAGLNQR  6253

Query  326   WSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWL  361
             W  +  +  + +  L+  S Q       L E++ WL
Sbjct  6254  WDAIVAEVKDRQPRLKGESKQVMEYRHQLDEIICWL  6361


>ref|XM_001172875.1| PREDICTED: Pan troglodytes utrophin, transcript variant 2 (UTRN), 
mRNA
Length=12634

 Score = 1498 bits (3877),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 728/1209 (60%), Positives = 923/1209 (76%), Gaps = 31/1209 (2%)
 Frame = +2

Query  8      EVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQL  67
              E+   AD ++  TEL DWL L+DQ++KS  V VGD+E+IN+ + + K T  DLEQR PQL
Sbjct  6980   EISIPADLDKTITELADWLVLIDQMLKSNIVTVGDVEEINKTVSRMKITKADLEQRHPQL  7159

Query  68     EELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
              + + T AQNLKNK S+ + RT IT+++ER++NQWD  Q  ++ R+QQL +M+ DS QW +
Sbjct  7160   DYVFTLAQNLKNKASSSDVRTAITEKLERVKNQWDGTQHGVELRQQQLEDMIIDSLQWDD  7339

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
               +EE E+++ +  A+L   ++     D + K+I++ + L ++L      V   +++  KL
Sbjct  7340   HREETEELMRKYEARLYILQQARR--DPLTKQISDNQILLQELGPGDGIVMAFDNVLQKL  7513

Query  188    LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
              L +Y +DDTR V   TE +  SW ++ + +++R+ ALE   R +Q    DLE FL W+ E
Sbjct  7514   LEEYGSDDTRNVKETTEYLKTSWINLKQSIADRQNALEAEWRTVQASRRDLENFLKWIQE  7693

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
              AETT NVL DA+ +E  L+DS   +EL +Q QD+Q EI+AH D++ ++D N QK++++L 
Sbjct  7694   AETTVNVLADASNRENALQDSILARELKQQMQDIQAEIDAHNDIFKSIDGNRQKMVKALG  7873

Query  308    GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
               S++A +LQ RLD+MN +W++L+ KS +IR+HLEAS+++W RL +SL+EL+ WL +KD+E
Sbjct  7874   NSEEATMLQHRLDDMNQRWNDLKAKSASIRAHLEASAEKWNRLLMSLEELIKWLNMKDEE  8053

Query  368    LSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQE  427
              L +Q PIGGD PA+Q Q D  +A +RELK KE  +++ ++  R+FL +QP+E  E    E
Sbjct  8054   LKKQMPIGGDVPALQLQYDHCKALRRELKEKEYSVLNAVDQARVFLADQPIEAPE----E  8221

Query  428    PR-------ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              PR       EL PEERAQ + + +RKQ+ EV  +WE LN  +++WQ+++D+ LE+L++LQ
Sbjct  8222   PRRNLQSKTELTPEERAQKIAKAMRKQSSEVKEKWESLNAVTSNWQKQVDKALEKLRDLQ  8401

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
               A D+LD  +++AE ++  W+PVGDLLIDSLQDH+EK+ A R EIAP+   V  VNDL+ 
Sbjct  8402   GAMDDLDADMKEAESVRNGWKPVGDLLIDSLQDHIEKIMAFREEIAPINFKVKTVNDLSS  8581

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QL+ L +  S      L+DLN RWKLLQV+V+DR++QL EAHRDFGP+SQHFLSTSVQ P
Sbjct  8582   QLSPLDLHPSLKMSRQLDDLNMRWKLLQVSVDDRLKQLQEAHRDFGPSSQHFLSTSVQLP  8761

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              W+R+IS NKVPYYINH+TQTTCWDHPKMTEL+QSLADLNNVRFSAYRTA+K+RRLQKALC
Sbjct  8762   WQRSISHNKVPYYINHQTQTTCWDHPKMTELFQSLADLNNVRFSAYRTAIKIRRLQKALC  8941

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLL LS   +   QH L QNDQ + +  +INCLTT YD LEQ H +LVNVPLCVDMCLN
Sbjct  8942   LDLLELSTTNEIFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQMHKDLVNVPLCVDMCLN  9121

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTG+IRV S K G++SL K  LE+KYRYLFK+VA  T  CDQR+LGLLLHD
Sbjct  9122   WLLNVYDTGRTGKIRVQSLKIGLMSLSKGLLEEKYRYLFKEVAGPTEMCDQRQLGLLLHD  9301

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              +IQIPRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWMRLEPQSMVWLPVLHR
Sbjct  9302   AIQIPRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKEFIDWMRLEPQSMVWLPVLHR  9481

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC
Sbjct  9482   VAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYC  9661

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPAS---------  951
               PTTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ETP +         
Sbjct  9662   IPTTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMWPEHY  9841

Query  952    ----SPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
                  SPQL HDDTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH LIQ YCQ+L 
Sbjct  9842   DPSQSPQLFHDDTHSRIEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHALIQQYCQTLG  10021

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
               +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE RNLQ EY++LK QH  +GL P+ 
Sbjct  10022  GESPVSQPQSPAQILKSVEKEERGELERIIADLEEEQRNLQVEYEQLKDQHLRRGL-PVG  10198

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPE + +   +  D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10199  SPPESIVSPHHTSEDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10378

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              ++++++NG    SP  S Q S  S  +     G Q   + G EDLL+PP DTST L EVM
Sbjct  10379  ESDSRINGV---SPWASPQHSALSYSLDPDASGPQFHQAAG-EDLLAPPHDTSTDLTEVM  10546

Query  1188   EQLNNSFPS  1196
              EQ++N+FPS
Sbjct  10547  EQIHNTFPS  10573


 Score = 47.0 bits (110),  Expect = 0.075, Method: Compositional matrix adjust.
 Identities = 113/514 (21%), Positives = 219/514 (42%), Gaps = 78/514 (15%)
 Frame = +2

Query  7     LEVPALADFNRAWTELTDWLSLLDQVIKSQRVM-VGDLEDINEMIIKQKATMQDLEQRRP  65
             +++ A   F+    EL +W+      I++  +     ++D +EM  K KA  ++  +R P
Sbjct  2360  VDIEAKKKFDAISAELLNWILKSKTAIQTTEIKEYMKMQDTSEMKKKLKALEKEQRERIP  2539

Query  66    QLEELITAAQNLKNKTSNQEARTI-ITDRIERIQNQWDEVQEHLQN--RRQQLNEMLKDS  122
             + +EL    Q L  +   +   T  I + +E++ ++W  V +HL++  R+ QL E   D 
Sbjct  2540  RADELNQTGQILVEQMGKEGLPTEEIKNVLEKVSSEWKNVSQHLEDIERKIQLQE---DI  2710

Query  123   TQWLEAKEEAEQVLGQAR--AKLESWKEG-----PYTVDAIQKKITETKQLAKDLRQWQT  175
               + +  +E E+VL       K  S  E      P   D+ Q+++T       +L     
Sbjct  2711  NAYFKQLDELEKVLKTKEEWVKHTSISESSRQSLPSLKDSCQRELT-------NLLGLHP  2869

Query  176   NVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALE----------  225
              +++A      L+   SA D   V    ++    ++++ + V +R+  LE          
Sbjct  2870  KIEMARASCSALMSQPSAPDF--VQRGFDSFLGCYQAVQEAVEDRQQHLENELKGQPGHA  3043

Query  226   --ETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQG  283
               ET + L+    D E       +A+ + NVL D  + E+ L++ K + E++        
Sbjct  3044  YLETLKTLKDVLDDSE------NKAQASLNVLNDLAKVEKALQEKKTLDEIL--------  3181

Query  284   EIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELR---KKSLNIRSHL  340
               E      H L E ++ + +++   D   L ++  D++  KW++L+    K L++   L
Sbjct  3182  --ENQKPALHKLAEETKALEKNVH-PDVEKLYKQEFDDVQGKWNKLKVLVSKDLHL---L  3343

Query  341   EASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEP  400
             E  + + +        +  W+    D L +Q    GD   +Q+Q D   AF  E++T E 
Sbjct  3344  EEIALKLRAFEADSTVIEKWMDGVKDFLVKQQAAQGDDAGLQRQLDQCSAFVNEIETIES  3523

Query  401   VIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNL  460
               +  ++ +   L   P+ G++   Q              TRL   Q     T+ EKL+ 
Sbjct  3524  S-LKNMKEIETNLRSGPVAGIKTWVQ--------------TRLGDYQ-----TQLEKLSK  3643

Query  461   HSADWQRKIDETLERLQELQEATDELDLKLRQAE  494
                  + ++ E+ E+   L++   E+   + QAE
Sbjct  3644  EITTQKSRLSESQEKAANLKKDLAEMQEWMTQAE  3745


 Score = 44.3 bits (103),  Expect = 0.43, Method: Compositional matrix adjust.
 Identities = 38/156 (24%), Positives = 68/156 (43%), Gaps = 8/156 (5%)
 Frame = +2

Query  206   INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
             +NA W  I++  S+R+   +      +QF  DL     W+TEAE    +L D       L
Sbjct  6167  LNAKWDRINRMYSDRKGCFDRAMEEWRQFHCDLNDLTQWITEAE---ELLVDTCAPGGSL  6337

Query  266   EDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFK  325
             +  K         Q+L+  I +H   +  L+     I++ L  +D +  L+ +L  +N +
Sbjct  6338  DLEKA----RIHQQELEVGISSHQPSFAALNRTGDGIVQKLSQADGS-FLKDKLAGLNQR  6502

Query  326   WSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWL  361
             W  +  +  + +  L+  S Q       L E++ WL
Sbjct  6503  WDAIVAEVKDRQPRLKGESKQVMEYRHQLDEIICWL  6610


>ref|XM_001172869.1| PREDICTED: Pan troglodytes utrophin, transcript variant 1 (UTRN), 
mRNA
Length=12748

 Score = 1498 bits (3877),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 728/1209 (60%), Positives = 923/1209 (76%), Gaps = 31/1209 (2%)
 Frame = +2

Query  8      EVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQL  67
              E+   AD ++  TEL DWL L+DQ++KS  V VGD+E+IN+ + + K T  DLEQR PQL
Sbjct  7094   EISIPADLDKTITELADWLVLIDQMLKSNIVTVGDVEEINKTVSRMKITKADLEQRHPQL  7273

Query  68     EELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
              + + T AQNLKNK S+ + RT IT+++ER++NQWD  Q  ++ R+QQL +M+ DS QW +
Sbjct  7274   DYVFTLAQNLKNKASSSDVRTAITEKLERVKNQWDGTQHGVELRQQQLEDMIIDSLQWDD  7453

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
               +EE E+++ +  A+L   ++     D + K+I++ + L ++L      V   +++  KL
Sbjct  7454   HREETEELMRKYEARLYILQQARR--DPLTKQISDNQILLQELGPGDGIVMAFDNVLQKL  7627

Query  188    LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
              L +Y +DDTR V   TE +  SW ++ + +++R+ ALE   R +Q    DLE FL W+ E
Sbjct  7628   LEEYGSDDTRNVKETTEYLKTSWINLKQSIADRQNALEAEWRTVQASRRDLENFLKWIQE  7807

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
              AETT NVL DA+ +E  L+DS   +EL +Q QD+Q EI+AH D++ ++D N QK++++L 
Sbjct  7808   AETTVNVLADASNRENALQDSILARELKQQMQDIQAEIDAHNDIFKSIDGNRQKMVKALG  7987

Query  308    GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
               S++A +LQ RLD+MN +W++L+ KS +IR+HLEAS+++W RL +SL+EL+ WL +KD+E
Sbjct  7988   NSEEATMLQHRLDDMNQRWNDLKAKSASIRAHLEASAEKWNRLLMSLEELIKWLNMKDEE  8167

Query  368    LSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQE  427
              L +Q PIGGD PA+Q Q D  +A +RELK KE  +++ ++  R+FL +QP+E  E    E
Sbjct  8168   LKKQMPIGGDVPALQLQYDHCKALRRELKEKEYSVLNAVDQARVFLADQPIEAPE----E  8335

Query  428    PR-------ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              PR       EL PEERAQ + + +RKQ+ EV  +WE LN  +++WQ+++D+ LE+L++LQ
Sbjct  8336   PRRNLQSKTELTPEERAQKIAKAMRKQSSEVKEKWESLNAVTSNWQKQVDKALEKLRDLQ  8515

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
               A D+LD  +++AE ++  W+PVGDLLIDSLQDH+EK+ A R EIAP+   V  VNDL+ 
Sbjct  8516   GAMDDLDADMKEAESVRNGWKPVGDLLIDSLQDHIEKIMAFREEIAPINFKVKTVNDLSS  8695

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QL+ L +  S      L+DLN RWKLLQV+V+DR++QL EAHRDFGP+SQHFLSTSVQ P
Sbjct  8696   QLSPLDLHPSLKMSRQLDDLNMRWKLLQVSVDDRLKQLQEAHRDFGPSSQHFLSTSVQLP  8875

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              W+R+IS NKVPYYINH+TQTTCWDHPKMTEL+QSLADLNNVRFSAYRTA+K+RRLQKALC
Sbjct  8876   WQRSISHNKVPYYINHQTQTTCWDHPKMTELFQSLADLNNVRFSAYRTAIKIRRLQKALC  9055

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLL LS   +   QH L QNDQ + +  +INCLTT YD LEQ H +LVNVPLCVDMCLN
Sbjct  9056   LDLLELSTTNEIFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQMHKDLVNVPLCVDMCLN  9235

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTG+IRV S K G++SL K  LE+KYRYLFK+VA  T  CDQR+LGLLLHD
Sbjct  9236   WLLNVYDTGRTGKIRVQSLKIGLMSLSKGLLEEKYRYLFKEVAGPTEMCDQRQLGLLLHD  9415

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              +IQIPRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWMRLEPQSMVWLPVLHR
Sbjct  9416   AIQIPRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKEFIDWMRLEPQSMVWLPVLHR  9595

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC
Sbjct  9596   VAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYC  9775

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPAS---------  951
               PTTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ETP +         
Sbjct  9776   IPTTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMWPEHY  9955

Query  952    ----SPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
                  SPQL HDDTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH LIQ YCQ+L 
Sbjct  9956   DPSQSPQLFHDDTHSRIEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHALIQQYCQTLG  10135

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
               +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE RNLQ EY++LK QH  +GL P+ 
Sbjct  10136  GESPVSQPQSPAQILKSVEKEERGELERIIADLEEEQRNLQVEYEQLKDQHLRRGL-PVG  10312

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPE + +   +  D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  10313  SPPESIVSPHHTSEDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10492

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              ++++++NG    SP  S Q S  S  +     G Q   + G EDLL+PP DTST L EVM
Sbjct  10493  ESDSRINGV---SPWASPQHSALSYSLDPDASGPQFHQAAG-EDLLAPPHDTSTDLTEVM  10660

Query  1188   EQLNNSFPS  1196
              EQ++N+FPS
Sbjct  10661  EQIHNTFPS  10687


 Score = 47.0 bits (110),  Expect = 0.075, Method: Compositional matrix adjust.
 Identities = 113/514 (21%), Positives = 219/514 (42%), Gaps = 78/514 (15%)
 Frame = +2

Query  7     LEVPALADFNRAWTELTDWLSLLDQVIKSQRVM-VGDLEDINEMIIKQKATMQDLEQRRP  65
             +++ A   F+    EL +W+      I++  +     ++D +EM  K KA  ++  +R P
Sbjct  2474  VDIEAKKKFDAISAELLNWILKSKTAIQTTEIKEYMKMQDTSEMKKKLKALEKEQRERIP  2653

Query  66    QLEELITAAQNLKNKTSNQEARTI-ITDRIERIQNQWDEVQEHLQN--RRQQLNEMLKDS  122
             + +EL    Q L  +   +   T  I + +E++ ++W  V +HL++  R+ QL E   D 
Sbjct  2654  RADELNQTGQILVEQMGKEGLPTEEIKNVLEKVSSEWKNVSQHLEDIERKIQLQE---DI  2824

Query  123   TQWLEAKEEAEQVLGQAR--AKLESWKEG-----PYTVDAIQKKITETKQLAKDLRQWQT  175
               + +  +E E+VL       K  S  E      P   D+ Q+++T       +L     
Sbjct  2825  NAYFKQLDELEKVLKTKEEWVKHTSISESSRQSLPSLKDSCQRELT-------NLLGLHP  2983

Query  176   NVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALE----------  225
              +++A      L+   SA D   V    ++    ++++ + V +R+  LE          
Sbjct  2984  KIEMARASCSALMSQPSAPDF--VQRGFDSFLGCYQAVQEAVEDRQQHLENELKGQPGHA  3157

Query  226   --ETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQG  283
               ET + L+    D E       +A+ + NVL D  + E+ L++ K + E++        
Sbjct  3158  YLETLKTLKDVLDDSE------NKAQASLNVLNDLAKVEKALQEKKTLDEIL--------  3295

Query  284   EIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELR---KKSLNIRSHL  340
               E      H L E ++ + +++   D   L ++  D++  KW++L+    K L++   L
Sbjct  3296  --ENQKPALHKLAEETKALEKNVH-PDVEKLYKQEFDDVQGKWNKLKVLVSKDLHL---L  3457

Query  341   EASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEP  400
             E  + + +        +  W+    D L +Q    GD   +Q+Q D   AF  E++T E 
Sbjct  3458  EEIALKLRAFEADSTVIEKWMDGVKDFLVKQQAAQGDDAGLQRQLDQCSAFVNEIETIES  3637

Query  401   VIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNL  460
               +  ++ +   L   P+ G++   Q              TRL   Q     T+ EKL+ 
Sbjct  3638  S-LKNMKEIETNLRSGPVAGIKTWVQ--------------TRLGDYQ-----TQLEKLSK  3757

Query  461   HSADWQRKIDETLERLQELQEATDELDLKLRQAE  494
                  + ++ E+ E+   L++   E+   + QAE
Sbjct  3758  EITTQKSRLSESQEKAANLKKDLAEMQEWMTQAE  3859


 Score = 44.3 bits (103),  Expect = 0.43, Method: Compositional matrix adjust.
 Identities = 38/156 (24%), Positives = 68/156 (43%), Gaps = 8/156 (5%)
 Frame = +2

Query  206   INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
             +NA W  I++  S+R+   +      +QF  DL     W+TEAE    +L D       L
Sbjct  6281  LNAKWDRINRMYSDRKGCFDRAMEEWRQFHCDLNDLTQWITEAE---ELLVDTCAPGGSL  6451

Query  266   EDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFK  325
             +  K         Q+L+  I +H   +  L+     I++ L  +D +  L+ +L  +N +
Sbjct  6452  DLEKA----RIHQQELEVGISSHQPSFAALNRTGDGIVQKLSQADGS-FLKDKLAGLNQR  6616

Query  326   WSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWL  361
             W  +  +  + +  L+  S Q       L E++ WL
Sbjct  6617  WDAIVAEVKDRQPRLKGESKQVMEYRHQLDEIICWL  6724


>ref|XM_001506948.1| PREDICTED: Ornithorhynchus anatinus similar to utrophin (homologous 
to dystrophin), (LOC100075517), mRNA
Length=10299

 Score = 1495 bits (3870),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 735/1221 (60%), Positives = 931/1221 (76%), Gaps = 35/1221 (2%)
 Frame = +1

Query  3      SSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQ  62
              + L LE+   AD ++  TEL DWL L+DQ++KS  V VG  E+IN+ I + K TM DLEQ
Sbjct  6523   TQLALELSLPADLDKTTTELADWLILIDQMLKSNIVTVGSAEEINQTIARMKITMADLEQ  6702

Query  63     RRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDS  122
              R PQL+ + T AQNLKNKTS+ + RT IT+++E+++NQWD  Q  ++ R+QQL +ML DS
Sbjct  6703   RHPQLDSVFTLAQNLKNKTSSSDVRTAITEKLEKVKNQWDNTQHGVEVRQQQLQDMLSDS  6882

Query  123    TQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVAND  182
               QW + ++E EQ+      +  +  + P   + + K++ E K LA+++ + +  +   ND
Sbjct  6883   LQWNDQRQETEQLFRHYEVRFHTLLQAPK--EPLVKQLPENKVLAQEMHRGEITIAAFND  7056

Query  183    LALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFL  242
              L+ KLLRDYS DDTRKV   T+++N SW ++++ + +R+ ALE   R LQ    DLE FL
Sbjct  7057   LSKKLLRDYSEDDTRKVKETTDHLNTSWINLNQSIGDRQNALEAELRTLQASLKDLEIFL  7236

Query  243    AWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKI  302
               W+ EAETT NVL DA+++E  L+D   ++E  KQ +D+Q EI+AH D++ ++D N QK+
Sbjct  7237   KWMQEAETTVNVLADASQRENALQDDVLMREFKKQMKDIQAEIDAHNDIFKSIDGNRQKM  7416

Query  303    LRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQ  362
              +++L  SD+A LLQ RLD+MN +W++L+ KS +IR+HLEAS+++W RL  SL+EL+ WL 
Sbjct  7417   VKALGNSDEAALLQHRLDDMNQRWNDLKAKSASIRAHLEASAEKWNRLLASLEELVKWLN  7596

Query  363    LKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLE  422
              LKD+EL++Q PIGGD PA+Q+Q D  +A +RELK KE  +++ ++  R+FL +QP+EGLE
Sbjct  7597   LKDEELNQQMPIGGDVPALQQQYDHCKALRRELKDKEQTVLNAVDQARVFLADQPVEGLE  7776

Query  423    ---KLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQEL  479
                 +  Q   EL PEE+AQ + + +RKQ+ EV  +WE LN  ++ WQ+++D+ LE+L++L
Sbjct  7777   ESRRHLQSKTELTPEEKAQRIAKTMRKQSSEVKGKWESLNAVTSSWQKQVDKALEKLKDL  7956

Query  480    QEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLA  539
              Q A D+LD  +++AE ++  W+PVGDLLIDSLQDH++K  A R EIAP+   V  VNDL+
Sbjct  7957   QGAMDDLDADMKEAETVRNGWKPVGDLLIDSLQDHIDKTTAFREEIAPISLKVKTVNDLS  8136

Query  540    RQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQG  599
               QL+ L +  S      L+DLN RWKLLQV+VEDR++QL EAHRDFGP+SQHFLSTSVQ 
Sbjct  8137   SQLSPLDLHPSLKMSRQLDDLNMRWKLLQVSVEDRLKQLQEAHRDFGPSSQHFLSTSVQL  8316

Query  600    PWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKAL  659
              PW+R++S NKVPYYINH+TQTTCWDHPKMTEL+QSLADLNNVRFSAYRTA+K+RRLQKAL
Sbjct  8317   PWQRSVSHNKVPYYINHQTQTTCWDHPKMTELFQSLADLNNVRFSAYRTAIKIRRLQKAL  8496

Query  660    CLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCL  719
              CLDLL L+   +   QH L QNDQ + +  +INCLTT YD LEQ+H +LVNVPLCVDMCL
Sbjct  8497   CLDLLELNTTNEVFQQHKLNQNDQLLSVPDVINCLTTTYDGLEQKHKDLVNVPLCVDMCL  8676

Query  720    NWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLH  779
              NWLLNVYDTGRTG+IRV S K G+ISL K  LE+KYRYLFK+VA  T  CDQR+LGLLLH
Sbjct  8677   NWLLNVYDTGRTGKIRVQSLKIGLISLSKGLLEEKYRYLFKEVAGPTEMCDQRQLGLLLH  8856

Query  780    DSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLH  839
              D+IQIPRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWMRLEPQS+VWLPVLH
Sbjct  8857   DAIQIPRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEINVKQFIDWMRLEPQSVVWLPVLH  9036

Query  840    RVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
              RVAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEY
Sbjct  9037   RVAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEY  9216

Query  900    CTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-----------  948
              C PTTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ET           
Sbjct  9217   CIPTTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMWPEQ  9396

Query  949    --PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSL  1006
                P+ SPQL HDDTHSRIE YA+RLA+ME +NGS L DS S   S++DEH LI  YCQ+L
Sbjct  9397   YDPSQSPQLFHDDTHSRIEQYATRLAQMERTNGSLLTDSSSTTGSVEDEHSLIHQYCQTL  9576

Query  1007   NQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPL  1066
                +SP+SQP+SPAQIL S+E EERGELERI++DLEEE R LQ EY++LK+QH  +G+SPL
Sbjct  9577   GGESPVSQPQSPAQILKSVEREERGELERIISDLEEEQRILQVEYEQLKEQHLKRGISPL  9756

Query  1067   PSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ  1126
               SPP+ + +      D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ
Sbjct  9757   SSPPDSVVSPQHLSGDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ  9936

Query  1127   PQAEAKVNGTTV-SSP-----STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTS  1180
              P++ A++NG +  SSP     S SL +  SSQ         QT+     +DLL PPQ TS
Sbjct  9937   PESNARINGISPWSSPQHSALSYSLDQDPSSQ-------FQQTA----ADDLLVPPQPTS  10083

Query  1181   TGLEEVMEQLNNSFPSSRGHN  1201
              T L +VMEQ+N++FPS   H 
Sbjct  10084  TDLTDVMEQINSTFPSCHSHG  10146


>gb|M37645.1|FSCDYSTRO Torpedo californica dystrophin mRNA, 3' end
Length=2654

 Score = 1493 bits (3865),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 721/869 (82%), Positives = 787/869 (90%), Gaps = 13/869 (1%)
 Frame = +3

Query  343   SSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVI  402
             S +QWKRL +SLQ+ L W+ LK+DEL RQ PIGGD P V +QNDVHR FKRELK KEPV+
Sbjct  3     SGEQWKRLQISLQDFLTWMNLKNDELRRQMPIGGDAPTVCQQNDVHRIFKRELKAKEPVV  182

Query  403   MSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHS  462
             MS L+TV +FL +  +   E L   PRE  PEE  QNV + +RK AEEV  EW+KL+  S
Sbjct  183   MSALDTVHLFLADPAIRAPESLLTGPREKIPEENIQNVAKRIRKYAEEVKVEWDKLSNRS  362

Query  463   ADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALR  522
              DWQ++IDE L+RL ELQ++ DEL+LKLRQAE IK +WQPVGDLLIDSLQDH+EKVK  R
Sbjct  363   VDWQKRIDEALKRLLELQDSMDELNLKLRQAEAIKDTWQPVGDLLIDSLQDHIEKVKVFR  542

Query  523   GEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAH  582
              EIAP+KENV+H+NDLA Q T   IQLSPYNL+ LEDLNTRWKLLQV++++ ++QLHEAH
Sbjct  543   AEIAPMKENVTHMNDLASQFTPPDIQLSPYNLNQLEDLNTRWKLLQVSIDELLKQLHEAH  722

Query  583   RDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVR  642
             RDFGP SQHFLSTSVQGPWERAISPNKVPYYINH+TQTTCWDHPKMTELYQSLADLNNVR
Sbjct  723   RDFGPTSQHFLSTSVQGPWERAISPNKVPYYINHQTQTTCWDHPKMTELYQSLADLNNVR  902

Query  643   FSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLE  702
             FSAYRTAMKLRRLQKALCLDLLSL +AC+A DQHNLKQNDQ +DIL+IINCLT+IYDRLE
Sbjct  903   FSAYRTAMKLRRLQKALCLDLLSLPSACEAFDQHNLKQNDQLLDILEIINCLTSIYDRLE  1082

Query  703   QEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQV  762
             QEH+NLVNVPLCVDMCLNWLLNVYDTGRTG+IRVLSFK+GI+S+CKAHLEDKYRYLFKQV
Sbjct  1083  QEHSNLVNVPLCVDMCLNWLLNVYDTGRTGKIRVLSFKSGIMSMCKAHLEDKYRYLFKQV  1262

Query  763   ASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFL  822
             AS TGFCDQRRLGLLLH++IQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFL
Sbjct  1263  ASPTGFCDQRRLGLLLHEAIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFL  1442

Query  823   DWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFF  882
             DWMRLEPQS+VW+PVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYD+CQSCFF
Sbjct  1443  DWMRLEPQSLVWMPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDVCQSCFF  1622

Query  883   SGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLE  942
             SGR AKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLE
Sbjct  1623  SGRTAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLE  1802

Query  943   GDNMET-------------PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPN  989
             GDN+ET             PASSPQLSHDDTHSRIEHY SRLAEMEN NGSYLNDSISPN
Sbjct  1803  GDNLETPVTLINFWPVDYEPASSPQLSHDDTHSRIEHYLSRLAEMENRNGSYLNDSISPN  1982

Query  990   ESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQA  1049
             ESIDDEHLLIQHYCQSLNQ+SPLSQPRSPAQILISLESEERGELERILADLE+ENRNLQ+
Sbjct  1983  ESIDDEHLLIQHYCQSLNQESPLSQPRSPAQILISLESEERGELERILADLEDENRNLQS  2162

Query  1050  EYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDH  1109
             EY++LKQQH+HKGLSPLPSPPEMMP SPQSPRDAELIAEAKLLRQHKGRLEARMQILEDH
Sbjct  2163  EYEKLKQQHDHKGLSPLPSPPEMMPISPQSPRDAELIAEAKLLRQHKGRLEARMQILEDH  2342

Query  1110  NKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGE  1169
             NKQLESQLHRLRQLLEQPQAE +VNGT+VSSPSTS QRSDSSQP+LL  VGSQTS  +GE
Sbjct  2343  NKQLESQLHRLRQLLEQPQAEVRVNGTSVSSPSTSSQRSDSSQPVLLHGVGSQTSGILGE  2522

Query  1170  EDLLSPPQDTSTGLEEVMEQLNNSFPSSR  1198
             +DLLS PQ TS+ LE+VMEQL++SFPSS+
Sbjct  2523  DDLLSAPQSTSSELEDVMEQLSSSFPSSQ  2609


>ref|XR_054516.1| PREDICTED: Taeniopygia guttata misc_RNA (LOC100220254), miscRNA
Length=10323

 Score = 1491 bits (3859),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 726/1217 (59%), Positives = 921/1217 (75%), Gaps = 31/1217 (2%)
 Frame = +1

Query  7      LEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQ  66
              LE+ A AD ++  TEL DWL L+DQ++KS  V VG+ E+IN  I + K T  D++ R PQ
Sbjct  6691   LELSAPADLDKTRTELADWLVLIDQMLKSNIVTVGNTEEINRTIARMKITNADMDHRHPQ  6870

Query  67     LEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWL  126
              L+ + T AQNLKNKTS+ + RT IT+++E+++NQWD  Q  ++ R+QQL  ML DS QW 
Sbjct  6871   LDSVFTLAQNLKNKTSSSDIRTEITEKMEQLKNQWDNTQHSVEVRQQQLKHMLADSLQWH  7050

Query  127    EAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALK  186
              E + E E ++ Q   +L    + P   + + K+I ++K L +DL +    V   NDL+ K
Sbjct  7051   EQRREMEHLMEQCEIRLRVLLQAPK--EMLTKQIADSKLLVQDLHRGDITVAAFNDLSNK  7224

Query  187    LLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
              LLR+Y  DD+RKV   T+ +N  W ++++R  +R+  LE   + +Q    DLE FL WL 
Sbjct  7225   LLREYRDDDSRKVKETTDQMNTCWVNLNQRAVDRQNFLETEMKTVQASHKDLESFLKWLQ  7404

Query  247    EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL  306
              EAETT NVL DA  +E+  +DS  ++EL KQ QD+Q EI+AH D++ ++D N QK++++L
Sbjct  7405   EAETTVNVLADAFEREKTAQDSVYIRELRKQMQDIQAEIDAHNDIFKSIDGNRQKMVKAL  7584

Query  307    EGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDD  366
                S++A LLQ RLD+MN +W++L+ KS NI++HLEAS+++W RL  SL+EL+ WL  KD+
Sbjct  7585   GNSEEAALLQHRLDDMNQRWNDLKAKSANIKAHLEASAEKWNRLLTSLEELIKWLNTKDE  7764

Query  367    ELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQ  426
              EL +Q P+GGD P +Q+Q D  +A +RELK KE  +++ ++  R+FL  QP+EG E    
Sbjct  7765   ELKKQMPVGGDVPTLQQQYDHCKALRRELKDKEQTVLNAVDQARVFLANQPIEGPE----  7932

Query  427    EPR-------ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQEL  479
              EPR       EL PEE+A  + + +RKQ+ EV  +WE LN  ++ WQ+++D+ LE+L++L
Sbjct  7933   EPRRSLHSKTELTPEEKALKIAKAMRKQSSEVKEKWENLNASASIWQKQVDKALEKLKDL  8112

Query  480    QEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLA  539
              Q A D+LD  L++AE ++  W+PVGDLLIDSL DH+EK  A R EIAP+   V  VNDL+
Sbjct  8113   QCAMDDLDADLKEAENVRNGWKPVGDLLIDSLPDHIEKTTAFREEIAPINLKVKTVNDLS  8292

Query  540    RQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQG  599
               QL+ L +  S      L+DLN RWKLLQV+VEDR++QL EAHRDFGPASQHFLSTSVQ 
Sbjct  8293   SQLSPLDLYPSLKMSRQLDDLNMRWKLLQVSVEDRLKQLQEAHRDFGPASQHFLSTSVQF  8472

Query  600    PWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKAL  659
              PW+R++S NKVPYYINHETQTTCWDHPKMT+L+QSLADLNNVRFSAYRTA+K+RRLQKAL
Sbjct  8473   PWQRSVSHNKVPYYINHETQTTCWDHPKMTDLFQSLADLNNVRFSAYRTAIKIRRLQKAL  8652

Query  660    CLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCL  719
              CLDLL L+   +   QH L QNDQ + +  +I+CLTTIY  LE++H ++VNVPLCVDMCL
Sbjct  8653   CLDLLDLNTTSEVFKQHKLSQNDQLIGVQDVISCLTTIYSGLEEKHKDMVNVPLCVDMCL  8832

Query  720    NWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLH  779
              NWLLNVYD+GRTG+IRV S K G++SL K  LE+KYRYLFK+VA  T  CDQR+LGLLLH
Sbjct  8833   NWLLNVYDSGRTGKIRVQSLKIGLMSLSKGLLEEKYRYLFKEVAGPTEMCDQRQLGLLLH  9012

Query  780    DSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLH  839
              D+IQIPRQLGEVA+FGGSNIEPSVRSCFQ  +NKPEI    F+DWMRLEPQSMVWLPVLH
Sbjct  9013   DAIQIPRQLGEVAAFGGSNIEPSVRSCFQQNHNKPEITVKQFIDWMRLEPQSMVWLPVLH  9192

Query  840    RVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
              RVAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEY
Sbjct  9193   RVAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEY  9372

Query  900    CTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-----------  948
              C PTTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ET           
Sbjct  9373   CIPTTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMWPEQ  9552

Query  949    --PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSL  1006
                P+ SPQL HDDTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH LIQ YCQ+L
Sbjct  9553   YDPSQSPQLFHDDTHSRIEQYATRLAQMERTNGSFLMDSSSTTGSVEDEHALIQQYCQTL  9732

Query  1007   NQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPL  1066
                +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE R+LQ EY++LK+QH  +G++PL
Sbjct  9733   GGESPVSQPQSPAQILKSVEKEERGELERIIADLEEEQRSLQIEYEQLKEQHLRRGINPL  9912

Query  1067   PSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ  1126
               SPP+ + +   +  DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ
Sbjct  9913   ASPPDSIVSPQHASEDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ  10092

Query  1127   PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEV  1186
              P+++++VNG   +SP  S QRS    P L +   SQ   + G +DLL PP DT+T L +V
Sbjct  10093  PESDSRVNG---ASPCASPQRSALGFP-LEQDTSSQFHQTAG-DDLLVPPHDTNTDLTDV  10257

Query  1187   MEQLNNSFPSSRGHNVG  1203
              MEQ+NN+FP+      G
Sbjct  10258  MEQINNTFPACCSSFTG  10308


 Score = 50.1 bits (118),  Expect = 0.008, Method: Compositional matrix adjust.
 Identities = 38/158 (24%), Positives = 74/158 (46%), Gaps = 10/158 (6%)
 Frame = +1

Query  206   INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
             +NA W  I++  ++R+   +    + +QF  DL     W+ EAE    +L DA   +  L
Sbjct  5881  LNAEWDRINRMYNDRKCCFDRAIEVWRQFHCDLNDLSHWIAEAE---ELLADARGPDGSL  6051

Query  266   E-DSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNF  324
             E  + G+ +     Q+L+  + +H      L+   + I++ L  +D +  LQ +L  +N 
Sbjct  6052  ELQAAGLHQ-----QELEEGVSSHQTSISALNRTGEGIIQKLSATDGS-FLQEKLAGLNR  6213

Query  325   KWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQ  362
             +W  +  + ++ +  L+  + Q       L EL  WL+
Sbjct  6214  RWKAITTEVMDRQQRLKGENQQLIEYRKKLDELRCWLE  6327


 Score = 42.0 bits (97),  Expect = 1.9, Method: Compositional matrix adjust.
 Identities = 54/254 (21%), Positives = 110/254 (43%), Gaps = 17/254 (6%)
 Frame = +1

Query  12    LADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELI  71
             L  +  A  E+  WL   +   + Q  + GD+E++ E     +  M +L   +  +  ++
Sbjct  973   LDSYQVALEEVLTWLLSAEDAFREQEEISGDVEEVKEQFSTHEGFMMELTAHQSSVGNVL  1152

Query  72    TAAQNLKNKTS-NQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKD--------S  122
              A   L  + S + E    I +++  + ++W+E++    +R+ +L++ML +         
Sbjct  1153  QAGNQLVAQGSLSPEEEFEIQEQMLLLNSRWEELRVESMDRQSRLHDMLMELQKQQLQQL  1332

Query  123   TQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVAND  182
             + WL   EE  Q       K+ES +     ++++QK++ E K L  DL   Q  V+    
Sbjct  1333  SDWLTVTEERIQ-------KMES-QLLAEDLESLQKQLEEHKSLQSDLEAEQVKVNSLTH  1488

Query  183   LALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFL  242
             + + +        T  +    + +   W ++ +   +R   L+E   L Q+   +     
Sbjct  1489  MVVIVDESSGESATAILEEQLQRLGERWTAVCRWTEDRRVKLQEIQLLWQELLEEQCLLK  1668

Query  243   AWLTEAETTANVLQ  256
             AWLTE E   + +Q
Sbjct  1669  AWLTEKEEALSKVQ  1710


>ref|XM_001380994.1| PREDICTED: Monodelphis domestica similar to utrophin (homologous 
to dystrophin), (LOC100031882), mRNA
Length=10395

 Score = 1481 bits (3835),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 735/1219 (60%), Positives = 929/1219 (76%), Gaps = 44/1219 (3%)
 Frame = +1

Query  4      SLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQR  63
              SL L VPA  D ++  TEL DWL L+DQ++KS  V VG+ E+I + I + K T  DLEQR
Sbjct  6670   SLELSVPA--DLDKTTTELADWLVLIDQMLKSNIVTVGNAEEIKQTIERMKITKADLEQR  6843

Query  64     RPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDST  123
               PQL+ + T AQNLKNKTS+ + RT IT+++E+++NQWD  Q  +  R+QQL +ML DS 
Sbjct  6844   HPQLDYVFTLAQNLKNKTSSSDIRTAITEKLEKVKNQWDNTQHGVDVRQQQLQDMLVDSE  7023

Query  124    QWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDL  183
              QW + +EE E+++ Q  AK+ S  + P   + + ++++E K L ++L + +  +   ++L
Sbjct  7024   QWNDLREETEELITQHEAKVHSVLKVPK--EPLIRQLSENKMLIQELNKGEVTMAAFSNL  7197

Query  184    ALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLA  243
                KLLRDYS DDTRKV+   +++NASW ++++ + +R+ ALE   R +Q    DLE FL 
Sbjct  7198   LKKLLRDYSGDDTRKVNETYDHLNASWINLNQSLCDRQNALEAELRTVQASLKDLESFLK  7377

Query  244    WLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKIL  303
              W+ EAETT NVL DA ++E  L+D+  VKEL KQ QD+Q EI+AH D++ ++D N QK++
Sbjct  7378   WMPEAETTVNVLADAAQRENALQDAGLVKELRKQIQDIQAEIDAHNDIFKSIDGNRQKMV  7557

Query  304    RSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQL  363
              ++L  SD+A LLQ RLD+MN +W++L+ KS +IR+HLEAS+++W RL  SL+EL+ WL +
Sbjct  7558   KALGNSDEAALLQHRLDDMNQRWNDLKAKSASIRAHLEASAEKWNRLLTSLEELIKWLNM  7737

Query  364    KDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEK  423
              KDDEL +Q PIGGD PA+Q Q D  +A +RELK KE  I++ ++  R+FL +QP+E  + 
Sbjct  7738   KDDELKKQMPIGGDVPALQLQYDHCKALRRELKEKEHSILNAVDQARVFLADQPIEAPD-  7914

Query  424    LYQEPR-------ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERL  476
                 EPR       EL PEE+AQ + + +RKQ+ EV  +WE LN  ++ WQ+++D+ LE+L
Sbjct  7915   ---EPRRNLQSKIELTPEEKAQKIAKAMRKQSSEVKEKWENLNAVTSSWQKQVDKALEKL  8085

Query  477    QELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVN  536
              ++LQ A D+LD  L++AE ++  W+PVGDLLIDSLQDH+EK  A R EIAP+   V  VN
Sbjct  8086   RDLQGAMDDLDADLKEAETVRNGWKPVGDLLIDSLQDHIEKTTAFREEIAPINLKVKTVN  8265

Query  537    DLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTS  596
              DL+ QL+ L +  S      L+DLN RWKLLQV+VEDR++QL EAHRDFGP+SQHFLSTS
Sbjct  8266   DLSSQLSPLDLHPSLKMSRQLDDLNMRWKLLQVSVEDRLKQLQEAHRDFGPSSQHFLSTS  8445

Query  597    VQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQ  656
              VQ PW+R++S NKVPYYINH+TQTTCWDHPKMTEL+QSL DLNNVRFSAYRTA+K+RRLQ
Sbjct  8446   VQLPWQRSVSHNKVPYYINHQTQTTCWDHPKMTELFQSLGDLNNVRFSAYRTAIKIRRLQ  8625

Query  657    KALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVD  716
              KALCLDLL L+   +   QH L QNDQ +++  +INCLTT YD LEQ H +LVNVPLCVD
Sbjct  8626   KALCLDLLELNTTNEIFKQHKLNQNDQLLNVPDVINCLTTTYDGLEQSHKDLVNVPLCVD  8805

Query  717    MCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGL  776
              MCLNWLLNVYDTGRTG+IRV S K G++SL K  LE+KYR LFK+VA  T  CDQR+LGL
Sbjct  8806   MCLNWLLNVYDTGRTGKIRVQSLKIGLMSLSKGLLEEKYRCLFKEVAGPTEMCDQRQLGL  8985

Query  777    LLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLP  836
              LLHD+IQIPRQLGEVA+FGGSNIEPSVRSCFQ  +NKPEI    F+DWMRLEPQSMVWLP
Sbjct  8986   LLHDAIQIPRQLGEVAAFGGSNIEPSVRSCFQQNHNKPEISVKEFIDWMRLEPQSMVWLP  9165

Query  837    VLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPM  896
              VLHRVAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPM
Sbjct  9166   VLHRVAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPM  9345

Query  897    VEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET--------  948
              VEYC PTTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ET        
Sbjct  9346   VEYCIPTTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMW  9525

Query  949    -----PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYC  1003
                   P+ SPQL HDDTHSRIE YASRLA+ME +NGS+L DS S   S++DEH LIQ YC
Sbjct  9526   PEQYDPSQSPQLFHDDTHSRIEQYASRLAQMERTNGSFLTDSSSTTGSVEDEHALIQQYC  9705

Query  1004   QSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGL  1063
              Q+L  +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE R+LQ EY++LK+QH  + +
Sbjct  9706   QTLGGESPVSQPQSPAQILKSVEREERGELERIIADLEEEQRSLQVEYEQLKEQHLRRAM  9885

Query  1064   SPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQL  1123
              SPL SPP+ +     +  D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQL
Sbjct  9886   SPLSSPPDSIAPPHHTAEDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQL  10065

Query  1124   LEQPQAEAKVNGTTV-SSP-----STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQ  1177
              LEQP+++A++NG +  SSP       SL +  SSQP               ++DLL PP 
Sbjct  10066  LEQPESDARINGVSPWSSPQHSALGYSLDQDSSSQPF----------HCSAKDDLLVPPH  10215

Query  1178   DTSTGLEEVMEQLNNSFPS  1196
              +TST L +VMEQ++++FPS
Sbjct  10216  NTSTDLTDVMEQIHSTFPS  10272


 Score = 46.6 bits (109),  Expect = 0.094, Method: Compositional matrix adjust.
 Identities = 107/509 (21%), Positives = 214/509 (42%), Gaps = 68/509 (13%)
 Frame = +1

Query  7     LEVPALADFNRAWTELTDWLSLLDQVIKSQRVM-VGDLEDINEMIIKQKATMQDLEQRRP  65
             +++ A   F+   TEL +W+S  +  I++  +       D  +M  K K   ++  +R P
Sbjct  2053  VDLDAKKKFDAVSTELLNWISKSNSAIQAIDIKEYKKTRDTLDMKKKLKVLEKEQTERIP  2232

Query  66    QLEELITAAQNL-----KNKTSNQEARTIITDRIERIQNQWDEVQEHLQN--RRQQL---  115
             +L EL    QNL     K   S  + + ++    E++Q++W +V  +L++  R+ QL   
Sbjct  2233  KLNELKHRGQNLLEQMGKEGISADDVKKVL----EKVQSEWKDVVWNLEDVSRKIQLQDD  2400

Query  116   -NEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQ  174
              N   KD  +  +A +E E+ +  +     + + GP   D  Q ++T    L        
Sbjct  2401  INTFFKDLDELEKAIKEKEEWVENSSIADTTQQFGPNLKDTCQWELTHLLSLG-------  2559

Query  175   TNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQF  234
               +++ +   + L+   SA     +    E+    ++S+ + + E +  LE+    L+  
Sbjct  2560  PQIEMMSSSCMALMSQPSAPSF--IQKSLESFIDRYKSVQQNLEECQKQLEKD---LKSQ  2724

Query  235   PLD-----LEKFLAWLTEAET----TANVLQDATRKERLLEDSKGVKELMKQWQDLQGEI  285
             P D     L+     L E+E     + N L D +  E+ L++ + ++++++  + L G++
Sbjct  2725  PGDDYLQTLKTVKDVLNESENKTQISLNALNDLSEVEKALQEKRALEQILEDQKPLLGKL  2904

Query  286   EAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSD  345
             E  T           K L      D     +   +N+  KW  L+ +       LE    
Sbjct  2905  EEET-----------KTLEQGAPHDIKNKYRHEFENVQGKWDRLKARVSKDIHLLEEIIP  3051

Query  346   QWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMST  405
             + +      + +  W+    D L ++  I GD   +Q+Q D  R F  E++T +   +  
Sbjct  3052  KLRVFEADSKVIEKWINGVKDFLMKEQAIQGDSEGLQRQLDQCRVFVNEMETIDSS-LKE  3228

Query  406   LETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADW  465
             ++ +   L   P+ G++   Q              T L+  Q++     WEK +   A  
Sbjct  3229  MKEIESALRSHPVAGVKTWVQ--------------TILVDHQSQ-----WEKFSKQIAIQ  3351

Query  466   QRKIDETLERLQELQEATDELDLKLRQAE  494
             + K+ E+ E+   L++   E+   + QAE
Sbjct  3352  KNKLSESQEKAMNLKKDLAEMQEWMTQAE  3438


>ref|NM_007124.2| Homo sapiens utrophin (UTRN), mRNA
Length=12436

 Score = 1470 bits (3805),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 726/1209 (60%), Positives = 922/1209 (76%), Gaps = 31/1209 (2%)
 Frame = +3

Query  8      EVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQL  67
              E+   AD ++  TEL DWL L+DQ++KS  V VGD+E+IN+ + + K T  DLEQR PQL
Sbjct  6762   EISIPADLDKTITELADWLVLIDQMLKSNIVTVGDVEEINKTVSRMKITKADLEQRHPQL  6941

Query  68     EELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
              + + T AQNLKNK S+ + RT IT+++ER++NQWD  Q  ++ R+QQL +M+ DS QW +
Sbjct  6942   DYVFTLAQNLKNKASSSDMRTAITEKLERVKNQWDGTQHGVELRQQQLEDMIIDSLQWDD  7121

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
               +EE E+++ +  A+L   ++     D + K+I++ + L ++L      V   +++  KL
Sbjct  7122   HREETEELMRKYEARLYILQQARR--DPLTKQISDNQILLQELGPGDGIVMAFDNVLQKL  7295

Query  188    LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
              L +Y +DDTR V   TE +  SW ++ + +++R+ ALE   R +Q    DLE FL W+ E
Sbjct  7296   LEEYGSDDTRNVKETTEYLKTSWINLKQSIADRQNALEAEWRTVQASRRDLENFLKWIQE  7475

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
              AETT NVL DA+ +E  L+DS   +EL +Q QD+Q EI+AH D++ ++D N QK++++L 
Sbjct  7476   AETTVNVLVDASHRENALQDSILARELKQQMQDIQAEIDAHNDIFKSIDGNRQKMVKALG  7655

Query  308    GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
               S++A +LQ RLD+MN +W++L+ KS +IR+HLEAS+++W RL +SL+EL+ WL +KD+E
Sbjct  7656   NSEEATMLQHRLDDMNQRWNDLKAKSASIRAHLEASAEKWNRLLMSLEELIKWLNMKDEE  7835

Query  368    LSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQE  427
              L +Q PIGGD PA+Q Q D  +A +RELK KE  +++ ++  R+FL +QP+E  E    E
Sbjct  7836   LKKQMPIGGDVPALQLQYDHCKALRRELKEKEYSVLNAVDQARVFLADQPIEAPE----E  8003

Query  428    PR-------ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              PR       EL PEERAQ + + +RKQ+ EV  +WE LN  +++WQ+++D+ LE+L++LQ
Sbjct  8004   PRRNLQSKTELTPEERAQKIAKAMRKQSSEVKEKWESLNAVTSNWQKQVDKALEKLRDLQ  8183

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
               A D+LD  +++AE ++  W+PVGDLLIDSLQDH+EK+ A R EIAP+   V  VNDL+ 
Sbjct  8184   GAMDDLDADMKEAESVRNGWKPVGDLLIDSLQDHIEKIMAFREEIAPINFKVKTVNDLSS  8363

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QL+ L +  S      L+DLN RWKLLQV+V+DR++QL EAHRDFGP+SQHFLSTSVQ P
Sbjct  8364   QLSPLDLHPSLKMSRQLDDLNMRWKLLQVSVDDRLKQLQEAHRDFGPSSQHFLSTSVQLP  8543

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              W+R+IS NKVPYYINH+TQTTCWDHPKMTEL+QSLADLNNVRFSAYRTA+K+RRLQKALC
Sbjct  8544   WQRSISHNKVPYYINHQTQTTCWDHPKMTELFQSLADLNNVRFSAYRTAIKIRRLQKALC  8723

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLL LS   +   QH L QNDQ + +  +INCLTT YD LEQ H +LVNVPLCVDMCLN
Sbjct  8724   LDLLELSTTNEIFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQMHKDLVNVPLCVDMCLN  8903

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTG+IRV S K G++SL K  LE+KYRYLFK+VA  T  CDQR+LGLLLHD
Sbjct  8904   WLLNVYDTGRTGKIRVQSLKIGLMSLSKGLLEEKYRYLFKEVAGPTEMCDQRQLGLLLHD  9083

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              +IQIPRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWM LEPQSMVWLPVLHR
Sbjct  9084   AIQIPRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKEFIDWMHLEPQSMVWLPVLHR  9263

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC
Sbjct  9264   VAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYC  9443

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPAS---------  951
               PTTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ETP +         
Sbjct  9444   IPTTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMWPEHY  9623

Query  952    ----SPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
                  SPQL HDDTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH LIQ YCQ+L 
Sbjct  9624   DPSQSPQLFHDDTHSRIEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHALIQQYCQTLG  9803

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
               +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE RNLQ EY++LK QH  +GL P+ 
Sbjct  9804   GESPVSQPQSPAQILKSVEREERGELERIIADLEEEQRNLQVEYEQLKDQHLRRGL-PVG  9980

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPE + +   +  D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  9981   SPPESIISPHHTSEDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10160

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              ++++++NG    SP  S Q S  S  +     G Q   + G EDLL+PP DTST L EVM
Sbjct  10161  ESDSRINGV---SPWASPQHSALSYSLDPDASGPQFHQAAG-EDLLAPPHDTSTDLTEVM  10328

Query  1188   EQLNNSFPS  1196
              EQ++++FPS
Sbjct  10329  EQIHSTFPS  10355


 Score = 46.6 bits (109),  Expect = 0.084, Method: Compositional matrix adjust.
 Identities = 113/514 (21%), Positives = 219/514 (42%), Gaps = 78/514 (15%)
 Frame = +3

Query  7     LEVPALADFNRAWTELTDWLSLLDQVIKSQRVM-VGDLEDINEMIIKQKATMQDLEQRRP  65
             +++ A   F+    EL +W+      I++  +     ++D +EM  K KA  ++  +R P
Sbjct  2142  VDIEAKKKFDAISAELLNWILKWKTAIQTTEIKEYMKMQDTSEMKKKLKALEKEQRERIP  2321

Query  66    QLEELITAAQNLKNKTSNQEARTI-ITDRIERIQNQWDEVQEHLQN--RRQQLNEMLKDS  122
             + +EL    Q L  +   +   T  I + +E++ ++W  V +HL++  R+ QL E   D 
Sbjct  2322  RADELNQTGQILVEQMGKEGLPTEEIKNVLEKVSSEWKNVSQHLEDLERKIQLQE---DI  2492

Query  123   TQWLEAKEEAEQVLGQAR--AKLESWKEG-----PYTVDAIQKKITETKQLAKDLRQWQT  175
               + +  +E E+V+       K  S  E      P   D+ Q+++T       +L     
Sbjct  2493  NAYFKQLDELEKVIKTKEEWVKHTSISESSRQSLPSLKDSCQRELT-------NLLGLHP  2651

Query  176   NVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALE----------  225
              +++A      L+   SA D   V    ++    ++++ + V +R+  LE          
Sbjct  2652  KIEMARASCSALMSQPSAPDF--VQRGFDSFLGRYQAVQEAVEDRQQHLENELKGQPGHA  2825

Query  226   --ETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQG  283
               ET + L+    D E       +A+ + NVL D  + E+ L++ K + E++        
Sbjct  2826  YLETLKTLKDVLNDSE------NKAQVSLNVLNDLAKVEKALQEKKTLDEIL--------  2963

Query  284   EIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELR---KKSLNIRSHL  340
               E      H L E ++ + +++   D   L ++  D++  KW++L+    K L++   L
Sbjct  2964  --ENQKPALHKLAEETKALEKNVH-PDVEKLYKQEFDDVQGKWNKLKVLVSKDLHL---L  3125

Query  341   EASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEP  400
             E  +   +        +  W+    D L +Q    GD   +Q+Q D   AF  E++T E 
Sbjct  3126  EEIALTLRAFEADSTVIEKWMDGVKDFLMKQQAAQGDDAGLQRQLDQCSAFVNEIETIES  3305

Query  401   VIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNL  460
               +  ++ +   L   P+ G++   Q              TRL   Q     T+ EKL+ 
Sbjct  3306  S-LKNMKEIETNLRSGPVAGIKTWVQ--------------TRLGDYQ-----TQLEKLSK  3425

Query  461   HSADWQRKIDETLERLQELQEATDELDLKLRQAE  494
               A  + ++ E+ E+   L++   E+   + QAE
Sbjct  3426  EIATQKSRLSESQEKAANLKKDLAEMQEWMTQAE  3527


 Score = 45.8 bits (107),  Expect = 0.17, Method: Compositional matrix adjust.
 Identities = 38/156 (24%), Positives = 69/156 (44%), Gaps = 8/156 (5%)
 Frame = +3

Query  206   INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
             +NA W  I++  S+R+   +      +QF  DL     W+TEAE    +L D       L
Sbjct  5949  LNAKWDRINRMYSDRKGCFDRAMEEWRQFHCDLNDLTQWITEAE---ELLVDTCAPGGSL  6119

Query  266   EDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFK  325
             +  K         Q+L+  I +H   +  L+     I++ L  +D +  L+ +L  +N +
Sbjct  6120  DLEKA----RIHQQELEVGISSHQPSFAALNRTGDGIVQKLSQADGS-FLKEKLAGLNQR  6284

Query  326   WSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWL  361
             W  +  +  + +  L+  S Q  +    L E++ WL
Sbjct  6285  WDAIVAEVKDRQPRLKGESKQVMKYRHQLDEIICWL  6392


>emb|X69086.1| H.sapiens mRNA for utrophin
Length=10302

 Score = 1470 bits (3805),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 726/1209 (60%), Positives = 922/1209 (76%), Gaps = 31/1209 (2%)
 Frame = +1

Query  8      EVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQL  67
              E+   AD ++  TEL DWL L+DQ++KS  V VGD+E+IN+ + + K T  DLEQR PQL
Sbjct  6670   EISIPADLDKTITELADWLVLIDQMLKSNIVTVGDVEEINKTVSRMKITKADLEQRHPQL  6849

Query  68     EELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
              + + T AQNLKNK S+ + RT IT+++ER++NQWD  Q  ++ R+QQL +M+ DS QW +
Sbjct  6850   DYVFTLAQNLKNKASSSDMRTAITEKLERVKNQWDGTQHGVELRQQQLEDMIIDSLQWDD  7029

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
               +EE E+++ +  A+L   ++     D + K+I++ + L ++L      V   +++  KL
Sbjct  7030   HREETEELMRKYEARLYILQQARR--DPLTKQISDNQILLQELGPGDGIVMAFDNVLQKL  7203

Query  188    LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
              L +Y +DDTR V   TE +  SW ++ + +++R+ ALE   R +Q    DLE FL W+ E
Sbjct  7204   LEEYGSDDTRNVKETTEYLKTSWINLKQSIADRQNALEAEWRTVQASRRDLENFLKWIQE  7383

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
              AETT NVL DA+ +E  L+DS   +EL +Q QD+Q EI+AH D++ ++D N QK++++L 
Sbjct  7384   AETTVNVLVDASHRENALQDSILARELKQQMQDIQAEIDAHNDIFKSIDGNRQKMVKALG  7563

Query  308    GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
               S++A +LQ RLD+MN +W++L+ KS +IR+HLEAS+++W RL +SL+EL+ WL +KD+E
Sbjct  7564   NSEEATMLQHRLDDMNQRWNDLKAKSASIRAHLEASAEKWNRLLMSLEELIKWLNMKDEE  7743

Query  368    LSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQE  427
              L +Q PIGGD PA+Q Q D  +A +RELK KE  +++ ++  R+FL +QP+E  E    E
Sbjct  7744   LKKQMPIGGDVPALQLQYDHCKALRRELKEKEYSVLNAVDQARVFLADQPIEAPE----E  7911

Query  428    PR-------ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              PR       EL PEERAQ + + +RKQ+ EV  +WE LN  +++WQ+++D+ LE+L++LQ
Sbjct  7912   PRRNLQSKTELTPEERAQKIAKAMRKQSSEVKEKWESLNAVTSNWQKQVDKALEKLRDLQ  8091

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
               A D+LD  +++AE ++  W+PVGDLLIDSLQDH+EK+ A R EIAP+   V  VNDL+ 
Sbjct  8092   GAMDDLDADMKEAESVRNGWKPVGDLLIDSLQDHIEKIMAFREEIAPINFKVKTVNDLSS  8271

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QL+ L +  S      L+DLN RWKLLQV+V+DR++QL EAHRDFGP+SQHFLSTSVQ P
Sbjct  8272   QLSPLDLHPSLKMSRQLDDLNMRWKLLQVSVDDRLKQLQEAHRDFGPSSQHFLSTSVQLP  8451

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              W+R+IS NKVPYYINH+TQTTCWDHPKMTEL+QSLADLNNVRFSAYRTA+K+RRLQKALC
Sbjct  8452   WQRSISHNKVPYYINHQTQTTCWDHPKMTELFQSLADLNNVRFSAYRTAIKIRRLQKALC  8631

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLL LS   +   QH L QNDQ + +  +INCLTT YD LEQ H +LVNVPLCVDMCLN
Sbjct  8632   LDLLELSTTNEIFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQMHKDLVNVPLCVDMCLN  8811

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTG+IRV S K G++SL K  LE+KYRYLFK+VA  T  CDQR+LGLLLHD
Sbjct  8812   WLLNVYDTGRTGKIRVQSLKIGLMSLSKGLLEEKYRYLFKEVAGPTEMCDQRQLGLLLHD  8991

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              +IQIPRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWM LEPQSMVWLPVLHR
Sbjct  8992   AIQIPRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKEFIDWMHLEPQSMVWLPVLHR  9171

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC
Sbjct  9172   VAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYC  9351

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPAS---------  951
               PTTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ETP +         
Sbjct  9352   IPTTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMWPEHY  9531

Query  952    ----SPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
                  SPQL HDDTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH LIQ YCQ+L 
Sbjct  9532   DPSQSPQLFHDDTHSRIEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHALIQQYCQTLG  9711

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
               +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE RNLQ EY++LK QH  +GL P+ 
Sbjct  9712   GESPVSQPQSPAQILKSVEREERGELERIIADLEEEQRNLQVEYEQLKDQHLRRGL-PVG  9888

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPE + +   +  D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  9889   SPPESIISPHHTSEDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10068

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              ++++++NG    SP  S Q S  S  +     G Q   + G EDLL+PP DTST L EVM
Sbjct  10069  ESDSRINGV---SPWASPQHSALSYSLDPDASGPQFHQAAG-EDLLAPPHDTSTDLTEVM  10236

Query  1188   EQLNNSFPS  1196
              EQ++++FPS
Sbjct  10237  EQIHSTFPS  10263


 Score = 46.6 bits (109),  Expect = 0.083, Method: Compositional matrix adjust.
 Identities = 113/514 (21%), Positives = 219/514 (42%), Gaps = 78/514 (15%)
 Frame = +1

Query  7     LEVPALADFNRAWTELTDWLSLLDQVIKSQRVM-VGDLEDINEMIIKQKATMQDLEQRRP  65
             +++ A   F+    EL +W+      I++  +     ++D +EM  K KA  ++  +R P
Sbjct  2050  VDIEAKKKFDAISAELLNWILKWKTAIQTTEIKEYMKMQDTSEMKKKLKALEKEQRERIP  2229

Query  66    QLEELITAAQNLKNKTSNQEARTI-ITDRIERIQNQWDEVQEHLQN--RRQQLNEMLKDS  122
             + +EL    Q L  +   +   T  I + +E++ ++W  V +HL++  R+ QL E   D 
Sbjct  2230  RADELNQTGQILVEQMGKEGLPTEEIKNVLEKVSSEWKNVSQHLEDLERKIQLQE---DI  2400

Query  123   TQWLEAKEEAEQVLGQAR--AKLESWKEG-----PYTVDAIQKKITETKQLAKDLRQWQT  175
               + +  +E E+V+       K  S  E      P   D+ Q+++T       +L     
Sbjct  2401  NAYFKQLDELEKVIKTKEEWVKHTSISESSRQSLPSLKDSCQRELT-------NLLGLHP  2559

Query  176   NVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALE----------  225
              +++A      L+   SA D   V    ++    ++++ + V +R+  LE          
Sbjct  2560  KIEMARASCSALMSQPSAPDF--VQRGFDSFLGRYQAVQEAVEDRQQHLENELKGQPGHA  2733

Query  226   --ETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQG  283
               ET + L+    D E       +A+ + NVL D  + E+ L++ K + E++        
Sbjct  2734  YLETLKTLKDVLNDSE------NKAQVSLNVLNDLAKVEKALQEKKTLDEIL--------  2871

Query  284   EIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELR---KKSLNIRSHL  340
               E      H L E ++ + +++   D   L ++  D++  KW++L+    K L++   L
Sbjct  2872  --ENQKPALHKLAEETKALEKNVH-PDVEKLYKQEFDDVQGKWNKLKVLVSKDLHL---L  3033

Query  341   EASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEP  400
             E  +   +        +  W+    D L +Q    GD   +Q+Q D   AF  E++T E 
Sbjct  3034  EEIALTLRAFEADSTVIEKWMDGVKDFLMKQQAAQGDDAGLQRQLDQCSAFVNEIETIES  3213

Query  401   VIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNL  460
               +  ++ +   L   P+ G++   Q              TRL   Q     T+ EKL+ 
Sbjct  3214  S-LKNMKEIETNLRSGPVAGIKTWVQ--------------TRLGDYQ-----TQLEKLSK  3333

Query  461   HSADWQRKIDETLERLQELQEATDELDLKLRQAE  494
               A  + ++ E+ E+   L++   E+   + QAE
Sbjct  3334  EIATQKSRLSESQEKAANLKKDLAEMQEWMTQAE  3435


 Score = 45.8 bits (107),  Expect = 0.17, Method: Compositional matrix adjust.
 Identities = 38/156 (24%), Positives = 69/156 (44%), Gaps = 8/156 (5%)
 Frame = +1

Query  206   INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
             +NA W  I++  S+R+   +      +QF  DL     W+TEAE    +L D       L
Sbjct  5857  LNAKWDRINRMYSDRKGCFDRAMEEWRQFHCDLNDLTQWITEAE---ELLVDTCAPGGSL  6027

Query  266   EDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFK  325
             +  K         Q+L+  I +H   +  L+     I++ L  +D +  L+ +L  +N +
Sbjct  6028  DLEKA----RIHQQELEVGISSHQPSFAALNRTGDGIVQKLSQADGS-FLKEKLAGLNQR  6192

Query  326   WSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWL  361
             W  +  +  + +  L+  S Q  +    L E++ WL
Sbjct  6193  WDAIVAEVKDRQPRLKGESKQVMKYRHQLDEIICWL  6300


>ref|XM_001788161.1| PREDICTED: Bos taurus similar to putative utrophin (LOC534358), 
mRNA
Length=11203

 Score = 1467 bits (3798),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 722/1219 (59%), Positives = 926/1219 (75%), Gaps = 36/1219 (2%)
 Frame = +1

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
              +PS    E+   AD ++  TEL DWL L+DQ++KS  V VGD+E+IN+ I + K T  DL
Sbjct  6901   VPSPRASEISVPADLDKTITELADWLVLIDQMLKSNIVTVGDVEEINKTISRMKITKADL  7080

Query  61     EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
              EQR PQL+ + T AQNLKNK S+ + RT IT+++E+++NQWD  Q  ++ RRQQL +M+ 
Sbjct  7081   EQRHPQLDYVFTLAQNLKNKASSSDVRTAITEKLEKVKNQWDNTQHGVELRRQQLEDMII  7260

Query  121    DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              DS QW + +EE E+++ +  A+L   ++     D + K+I++++ L ++L      V   
Sbjct  7261   DSLQWDDHREETEELMRKYEARLYILQQARR--DPLVKQISDSQMLLQELAAGDGVVMAF  7434

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              +++  KLL +Y +DDTR V   TE +  SW ++ + +++R++ALE   R +Q    DLE 
Sbjct  7435   DNVLQKLLEEYGSDDTRNVKETTEYLKTSWINLKQSIADRQSALEAELRTVQSSRKDLEN  7614

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              FL W+ EAETT NVL DA+++E  L+D+   +EL +Q QD+Q EI+AH D++ ++D N Q
Sbjct  7615   FLKWIQEAETTVNVLADASQRENALQDTVLARELTQQMQDIQAEIDAHNDIFKSIDGNRQ  7794

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
              K++++L  S++A +LQ RLD+MN +W++L+ KS +IR+HLEAS+++W RL  SL+EL+ W
Sbjct  7795   KMVKALGNSEEATMLQHRLDDMNQRWNDLKAKSASIRAHLEASAEKWNRLLTSLEELIKW  7974

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              L +KD+EL +Q P+GGD PA+Q Q D  +A +RELK KE  +++ ++  R+FL +QP+E 
Sbjct  7975   LNMKDEELKKQMPVGGDVPALQLQYDHCKALRRELKEKEYSVLNAIDQARVFLADQPIEA  8154

Query  421    LEKLYQEPR-------ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
               E    EPR       EL PEE+AQ + + +RKQ+ EV  +WE LN  ++ WQ+++D+ L
Sbjct  8155   PE----EPRRNLQSKTELTPEEKAQKIAKAMRKQSSEVKEKWETLNAVTSSWQKQVDKAL  8322

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVS  533
              E+L++LQ A D+LD  L++AE ++  W+PVGDLLIDSLQDH+EK  A R EIAP+   V 
Sbjct  8323   EKLRDLQGAMDDLDADLKEAEAVRNGWKPVGDLLIDSLQDHIEKTMAFREEIAPINLKVK  8502

Query  534    HVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFL  593
               +NDL+ QL+ L +  S      L+DLN RWKLLQV+V+DR++QL EAHRDFGP+SQHFL
Sbjct  8503   TMNDLSSQLSPLDLHPSLKMSRQLDDLNMRWKLLQVSVDDRLKQLQEAHRDFGPSSQHFL  8682

Query  594    STSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLR  653
              STSVQ PW+R+IS NKVPYYINH+TQTTCWDHPKMTEL+QSLADLNNVRFSAYRTA+K+R
Sbjct  8683   STSVQLPWQRSISHNKVPYYINHQTQTTCWDHPKMTELFQSLADLNNVRFSAYRTAIKIR  8862

Query  654    RLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPL  713
              RLQKALCLDLL L+   +  +QH L QNDQ + +  +INCLTT YD LEQ H NLVNVPL
Sbjct  8863   RLQKALCLDLLELNTTNEVFEQHKLNQNDQLLSVPDVINCLTTTYDGLEQMHKNLVNVPL  9042

Query  714    CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRR  773
              CVDMCLNWLLNVYDTGRTG+IRV S K G+I+L K  LE+KYRYLFK+VA  T  CDQR+
Sbjct  9043   CVDMCLNWLLNVYDTGRTGKIRVQSLKIGLIALSKGLLEEKYRYLFKEVAGPTEMCDQRQ  9222

Query  774    LGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMV  833
              LGLLLHD+IQIPRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWMRLEPQSMV
Sbjct  9223   LGLLLHDAIQIPRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKEFIDWMRLEPQSMV  9402

Query  834    WLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMH  893
              WLPVLHRVAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+H
Sbjct  9403   WLPVLHRVAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLH  9582

Query  894    YPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPAS--  951
              YPMVEYC PTTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ETP +  
Sbjct  9583   YPMVEYCIPTTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLI  9762

Query  952    -----------SPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQ  1000
                         SPQL HDDTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH LIQ
Sbjct  9763   SMWPEHYDPSQSPQLFHDDTHSRIEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHALIQ  9942

Query  1001   HYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEH  1060
               YCQ+L  +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE RNLQ EY++LK+QH  
Sbjct  9943   QYCQTLGGESPVSQPQSPAQILKSVEREERGELERIIADLEEEQRNLQVEYEQLKEQHLR  10122

Query  1061   KGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRL  1120
              +GL P+ SPP+ + +   +  D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRL
Sbjct  10123  RGL-PVGSPPDSVVSPHHTSEDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRL  10299

Query  1121   RQLLEQPQAEAKVNGTT--VSSPSTSLQRSDSSQPMLLRVVGSQTSDS-MGEEDLLSPPQ  1177
              RQLLEQP++++++NG +   S   ++L  S    P      G Q   +    E+ L+PP 
Sbjct  10300  RQLLEQPESDSQINGVSPWASPQQSALNYSLDPDP------GPQFHQAGTAAEESLAPPH  10461

Query  1178   DTSTGLEEVMEQLNNSFPS  1196
              DTST L EVMEQ+N++FPS
Sbjct  10462  DTSTDLTEVMEQINSTFPS  10518


 Score = 43.1 bits (100),  Expect = 1.1, Method: Compositional matrix adjust.
 Identities = 37/156 (23%), Positives = 68/156 (43%), Gaps = 8/156 (5%)
 Frame = +1

Query  206   INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
             +NA W  I++  ++R+   +      +QF  DL     W+TEAE    +L      +  L
Sbjct  6109  LNAKWDRINRMYNDRKGYFDRAVEEWRQFHCDLNDLTHWITEAE---ELLAGTFAPDGGL  6279

Query  266   EDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFK  325
             +  K         Q+L+  I +H   +  L+     I++ L  +D +  L+ +L  +N +
Sbjct  6280  DLEKA----RIHQQELEEGISSHQPSFAALNRTGDGIIQKLSPTDGS-FLKDKLAGLNQR  6444

Query  326   WSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWL  361
             W  +  +  + R  L+  S Q       L E++ WL
Sbjct  6445  WGAITAEVKDRRPRLKGESKQVMDYRKRLDEIICWL  6552


>emb|AJ002967.1| Rattus norvegicus mRNA for utrophin
Length=10705

 Score = 1467 bits (3797),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 714/1207 (59%), Positives = 914/1207 (75%), Gaps = 28/1207 (2%)
 Frame = +3

Query  8      EVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQL  67
              E+   AD ++  TEL DWL L+DQ++KS  V VGD+++IN+ + + K T  DLEQR PQL
Sbjct  6819   EISVPADLDKTITELADWLVLIDQMLKSNIVTVGDVKEINKTVSRMKITKADLEQRHPQL  6998

Query  68     EELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
              + + T AQNLKNK S+ + RT IT ++E+++ QW+  Q  ++ RRQQL +M+ DS QW +
Sbjct  6999   DFVFTLAQNLKNKASSSDLRTAITGKLEKLKTQWESTQHGVELRRQQLEDMVVDSLQWDD  7178

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
               +EE E+++ +  A+    ++     D + K++++ + L ++L      +   +++  KL
Sbjct  7179   HREETEELMRKHEARFYMLQQARR--DPLSKQVSDNQLLLQELGSGDGVIMAFDNVLQKL  7352

Query  188    LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
              L +YS+DDTR V   TE +  SW ++ + +++R++ALE   R +Q    DLE F+ WL E
Sbjct  7353   LEEYSSDDTRNVEETTEYLKTSWINLKQSIADRQSALEAELRTVQTSRRDLENFVKWLQE  7532

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
              AETTANVL DA+++E  L+DS   ++L +Q  D+Q EI+AH D++ ++D N QK++++L 
Sbjct  7533   AETTANVLADASQRENALQDSVLARQLRQQMLDIQAEIDAHNDIFKSIDGNRQKMVKALG  7712

Query  308    GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
               S++A +LQ RLD+MN +W++L+ KS +IR+HLEAS+++W RL  SL+EL+ WL +KD+E
Sbjct  7713   NSEEATMLQHRLDDMNQRWNDLKAKSASIRAHLEASAEKWNRLLASLEELIKWLNMKDEE  7892

Query  368    LSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQE  427
              L +Q PIGGD PA+Q Q D  +  +RELK KE  +++ ++  R+FL +QP+E  E+  + 
Sbjct  7893   LKKQMPIGGDVPALQLQYDHCKVLRRELKEKEYSVLNAVDQARVFLADQPIEAPEEPRRN  8072

Query  428    PR---ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATD  484
              P+   EL PEERAQ + + +RKQ+ EV  +WE LN  ++ WQ+++ + LE+L++LQ A D
Sbjct  8073   PQSKTELTPEERAQKIAKAMRKQSSEVREKWESLNAVTSTWQKQVGKALEKLRDLQGAVD  8252

Query  485    ELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTT  544
              +LD  +++ E ++  W+PVGDLLIDSLQDH+EK  A R EIAP+   V  +NDL+ QL+ 
Sbjct  8253   DLDADMKEVEAVRNGWKPVGDLLIDSLQDHIEKTLAFREEIAPINLKVKTMNDLSSQLSP  8432

Query  545    LGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERA  604
              L +  SP     L+DLN RWKLLQV+VEDR++QL EAHRDFGP SQHFLSTSVQ PW+R+
Sbjct  8433   LDLHPSPKMSRQLDDLNMRWKLLQVSVEDRLKQLQEAHRDFGPCSQHFLSTSVQLPWQRS  8612

Query  605    ISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLL  664
              IS NKVPYYINH+TQTTCWDHPKMTEL+QSL DLNNVRFSAYRTA+K+RRLQKALCLDLL
Sbjct  8613   ISHNKVPYYINHQTQTTCWDHPKMTELFQSLGDLNNVRFSAYRTAIKIRRLQKALCLDLL  8792

Query  665    SLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLN  724
               L+   +   QH L QNDQ + +  +INCLTT YD LEQ H +LVNVPLCVDMCLNWLLN
Sbjct  8793   ELNTTNEVFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQLHKDLVNVPLCVDMCLNWLLN  8972

Query  725    VYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQI  784
              VYDTGRTG+IRV S K G++SL K  LE+KYR LFK+VA  T  CDQR+LGLLLHD+IQI
Sbjct  8973   VYDTGRTGKIRVQSLKIGLMSLSKGLLEEKYRCLFKEVAGPTEMCDQRQLGLLLHDAIQI  9152

Query  785    PRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAA  844
              PRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWMRLEPQSMVWLPVLHRVAAA
Sbjct  9153   PRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKEFIDWMRLEPQSMVWLPVLHRVAAA  9332

Query  845    ETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
              ETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC PTT
Sbjct  9333   ETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYCIPTT  9512

Query  905    SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPAS-------------  951
              SGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ETP +             
Sbjct  9513   SGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMWPEHYDPSQ  9692

Query  952    SPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSP  1011
              SPQL HDDTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH LIQ YCQ+L  +SP
Sbjct  9693   SPQLFHDDTHSRIEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHALIQQYCQTLGGESP  9872

Query  1012   LSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPE  1071
              +SQP+SPAQIL S+E EERGELERI+ADLEEE RNLQ EY++LK+QH  +GL PL SPP+
Sbjct  9873   VSQPQSPAQILKSVEKEERGELERIIADLEEEQRNLQVEYEQLKEQHLRRGL-PLGSPPD  10049

Query  1072   MMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEA  1131
               + +   +  D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP +++
Sbjct  10050  SIVSPHHTSEDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPDSDS  10229

Query  1132   KVNGTT--VSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQ  1189
              ++NG +   S    SL  S    P      G Q S     EDLL+PP DTST L +VMEQ
Sbjct  10230  RINGVSPWASPQHPSLSYSLDPDP------GPQ-SHQAASEDLLAPPHDTSTDLTDVMEQ  10388

Query  1190   LNNSFPS  1196
              LN++FPS
Sbjct  10389  LNSTFPS  10409


 Score = 46.6 bits (109),  Expect = 0.085, Method: Compositional matrix adjust.
 Identities = 37/156 (23%), Positives = 74/156 (47%), Gaps = 8/156 (5%)
 Frame = +3

Query  206   INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
             +NA W  +++  S+R  +        +QF  DL+    WL+EAE   ++L      +  L
Sbjct  6015  LNAKWDRVNRLYSDRRGSFARAVEEWKQFHCDLDDLTQWLSEAE---DLLVGTCAPDGSL  6185

Query  266   EDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFK  325
             +  K     +    +L+  + +H     ++++  + I++ L  SD A  L+ +L ++N +
Sbjct  6186  DLEKARTHQL----ELEDGLSSHQPCLIDVNQKGEDIVQRLRPSD-ASFLKDKLASLNQR  6350

Query  326   WSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWL  361
             WS L  +  +++  L+  S Q       L E++ WL
Sbjct  6351  WSALVAEVKDLQPRLKGESKQVSGYRKRLDEVVCWL  6458


>ref|XR_010548.1| PREDICTED: Macaca mulatta utrophin (UTRN), mRNA
Length=12319

 Score = 1459 bits (3778),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 724/1209 (59%), Positives = 922/1209 (76%), Gaps = 31/1209 (2%)
 Frame = +2

Query  8      EVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQL  67
              E+   AD ++  TEL DWL L+DQ++KS  V VGD+E+IN+ + + K T  DLEQR PQL
Sbjct  6674   EISIPADLDKTITELADWLVLIDQMLKSNIVTVGDVEEINKTVSRMKITKADLEQRHPQL  6853

Query  68     EELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
              + + T AQNLKNK S+ + RT IT+++ER++NQWD  Q  ++ R+QQL +M+ DS QW +
Sbjct  6854   DYVFTLAQNLKNKASSSDVRTAITEKLERVKNQWDGTQHGVELRQQQLEDMIIDSLQWDD  7033

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
               +EE E+++ +  A+L   ++     D + K+I++ + L ++L      V   +++  KL
Sbjct  7034   HREETEELMRKHEARLYILQQSRR--DPLTKQISDNQILLQELGPGDGIVMAFDNILQKL  7207

Query  188    LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
              L +Y  DDTR V   TE +  SW ++ + +++R+ ALE   R +Q    DLE FL W+ E
Sbjct  7208   LEEYGNDDTRNVKETTEYLKTSWINLKQSIADRQNALEAEWRTVQASRGDLENFLKWIQE  7387

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
              AETT NVL DA+ +E  L+DS   +EL +Q QD+Q EI+AH D++ ++D N QK++++L 
Sbjct  7388   AETTVNVLADASHRENALQDSILARELKQQMQDIQAEIDAHNDIFKSIDGNRQKMVKALG  7567

Query  308    GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
               S++A +LQ RLD+MN +W++L+ KS +IR+HLEAS+++W RL +SL+EL+ WL +KD+E
Sbjct  7568   NSEEATMLQHRLDDMNQRWNDLKAKSASIRAHLEASAEKWNRLLMSLEELIKWLNMKDEE  7747

Query  368    LSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQE  427
              L +Q PIGGD PA+Q Q D  +A +RELK KE  +++ ++  R+FL +QP+E  E    E
Sbjct  7748   LKKQMPIGGDVPALQLQYDHCKALRRELKEKEHSVLNAVDQARVFLADQPIEAPE----E  7915

Query  428    PR-------ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              PR       EL PEE+AQ + + +RKQ+ EV  +WE LN  +++WQ+++D+ LE+L++LQ
Sbjct  7916   PRRNLQSKTELTPEEKAQKIAKAMRKQSSEVKEKWESLNAVTSNWQKQVDKALEKLRDLQ  8095

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
               A D+LD  +++AE ++  W+PVGDLLIDSLQDH+EK+ A R EIAP+   V  VNDL+ 
Sbjct  8096   GAMDDLDADMKEAESVRNGWKPVGDLLIDSLQDHIEKIMAFREEIAPINLKVKTVNDLSS  8275

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QL+ L +  S      L+DLN RWKLLQV+V+DR++QL EAHRDFGP+SQHFLSTSVQ P
Sbjct  8276   QLSPLDLHPSLKMSRQLDDLNMRWKLLQVSVDDRLKQLQEAHRDFGPSSQHFLSTSVQLP  8455

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              W+R+IS NKVPYYINH+TQTTCWDHPKMTEL+QSLADLNNVRFSAYRTA+K+RRLQKALC
Sbjct  8456   WQRSISHNKVPYYINHQTQTTCWDHPKMTELFQSLADLNNVRFSAYRTAIKIRRLQKALC  8635

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLL LS   +   QH L QNDQ + +  +INCLTT YD LEQ H +LVNVPLCVDMCLN
Sbjct  8636   LDLLELSTTNEIFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQMHKDLVNVPLCVDMCLN  8815

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTG+IRV S K G++SL K  LE+KYRYLFK+VA  T  CDQR+LGLLLHD
Sbjct  8816   WLLNVYDTGRTGKIRVQSLKIGLMSLSKGLLEEKYRYLFKEVAGPTEMCDQRQLGLLLHD  8995

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              +IQIPRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWMRLEPQSMVWLPVLHR
Sbjct  8996   AIQIPRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKEFIDWMRLEPQSMVWLPVLHR  9175

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC
Sbjct  9176   VAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYC  9355

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPAS---------  951
               PTTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ETP +         
Sbjct  9356   IPTTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMWPEHY  9535

Query  952    ----SPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
                  SPQL ++DTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH LIQ YCQ+L 
Sbjct  9536   DPSQSPQLFYEDTHSRIEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHALIQQYCQTLG  9715

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
               +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE RNLQ EY++LK QH  +G  P+ 
Sbjct  9716   GESPVSQPQSPAQILKSVEREERGELERIIADLEEEQRNLQVEYEQLKDQHLRRGF-PVG  9892

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPPE + +   +  D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  9893   SPPESIVSPHHTSEDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10072

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
              +++ ++NG    SP  S Q S  S  + L   G+Q   + G EDLL+PP DTST L EVM
Sbjct  10073  ESDTRINGV---SPWASPQHSALSYSLDLDASGAQFHQAAG-EDLLAPPHDTSTDLTEVM  10240

Query  1188   EQLNNSFPS  1196
              EQ++++FPS
Sbjct  10241  EQIHSTFPS  10267


 Score = 42.4 bits (98),  Expect = 1.5, Method: Compositional matrix adjust.
 Identities = 37/156 (23%), Positives = 67/156 (42%), Gaps = 8/156 (5%)
 Frame = +2

Query  206   INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
             +NA W  I++  S+R+   +      +QF  DL     W+TEAE    +L D       L
Sbjct  5861  LNAKWDRINRMYSDRKGYFDRAMEEWRQFHCDLNDLTQWITEAE---ELLVDTCAPGGSL  6031

Query  266   EDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFK  325
             +  K         Q+L+  I +H   +  L+     I++ L  +D +  L+ +L  +N +
Sbjct  6032  DLEKA----RIHQQELEEGISSHRPSFAALNRTGDGIVQKLSQADGS-FLKDKLAGLNQR  6196

Query  326   WSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWL  361
             W  +  +  + +  L+  S Q       L  ++ WL
Sbjct  6197  WDAIIAEVKDRQPRLKGESKQVMEYRHQLDGIICWL  6304


 Score = 42.0 bits (97),  Expect = 2.0, Method: Compositional matrix adjust.
 Identities = 112/518 (21%), Positives = 224/518 (43%), Gaps = 86/518 (16%)
 Frame = +1

Query  7     LEVPALADFNRAWTELTDWLSLLDQVIKSQRVM-VGDLEDINEMIIKQKATMQDLEQRRP  65
             +++ A   F+    EL +W+      I++  +     ++D +EM  K KA  ++  +R P
Sbjct  2050  VDIEAKKKFDAVSAELLNWILKSKPAIQTTEIKEYMKMQDTSEMKKKLKALEKEQRERIP  2229

Query  66    QLEELITAAQNLKNKTSNQEARTI-ITDRIERIQNQWDEVQEHLQN--RRQQLNEMLKDS  122
             + +EL    Q L  +   +   T  I + +E++ ++W  V +HL++  R+ QL E   D 
Sbjct  2230  RADELNQTGQILVEQMGKEGLPTEEIKNVLEKVLSEWKNVSQHLKDLERKIQLQE---DI  2400

Query  123   TQWLEAKEEAEQVLGQARAKLE-------SWKEGPYTVDAIQKKITETKQLAKDLRQWQT  175
               + +  +E E+V+      ++       SW+  P   D+ Q+++T       +L     
Sbjct  2401  NAYFKQLDELEKVIKTKEEWVKHTSVSESSWQSLPSLKDSCQRELT-------NLLGLHP  2559

Query  176   NVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEE------THR  229
              +++A      L    SA D   V    ++    ++++ + + +R+  LE        H 
Sbjct  2560  KIEMARASCSALKSQPSAPDF--VQRGFDSFLGRYQAVQQALKDRQQQLENELKGQPGHA  2733

Query  230   LLQQFPLDLEKFLAWLTE--AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
              L+   L   KF+   +E  A+T+ +VL D  + E+ L++ K + E++          E 
Sbjct  2734  YLE--TLKTLKFVLNDSENKAQTSLSVLDDPAKVEKALQEKKALDEIL----------EN  2877

Query  288   HTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELR-----------KKSLNI  336
                  H L E ++ + +++   D   L ++  D++  KW++L+           + +L +
Sbjct  2878  QKPTLHKLAEETKALEKNVH-PDVEKLYKQEFDDVQGKWNKLKVLVSKDLHLLEEITLKL  3054

Query  337   RSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELK  396
             R+  EA S   +R          W+    D L +Q    G+   +Q+Q D   AF  E++
Sbjct  3055  RA-FEADSTVIER----------WMDGVKDFLMKQQAARGNNADLQRQLDQCSAFVNEIE  3201

Query  397   TKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWE  456
             T E   +  ++ +   L   P+ G++   Q              TRL      +  T+ E
Sbjct  3202  TIESS-LKNMKEIETNLRSGPIAGIKTWVQ--------------TRL-----SDYQTQLE  3321

Query  457   KLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAE  494
             KL+   A  + ++ E+ E+   L++   E+   + QAE
Sbjct  3322  KLSKEIATQKSRLSESQEKAANLKKDLAEMQEWMTQAE  3435


>gb|AY095485.1| Canis familiaris utrophin mRNA, complete cds
Length=10299

 Score = 1457 bits (3773),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 719/1216 (59%), Positives = 919/1216 (75%), Gaps = 46/1216 (3%)
 Frame = +1

Query  8      EVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQL  67
              E+   AD ++  TEL DWL L+DQ++KS  V VGD+E+IN+ + + K T  DLEQR PQL
Sbjct  6670   EISIPADLDKTITELADWLVLIDQMLKSNIVTVGDIEEINKTVSRMKITKSDLEQRHPQL  6849

Query  68     EELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
              + + T AQNLKNK S+ + RT IT+++E+++NQWD  Q  ++ R+QQL +M+ DS QW +
Sbjct  6850   DYVFTLAQNLKNKASSSDVRTAITEKLEKVKNQWDSTQHGVELRQQQLEDMIIDSIQWDD  7029

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
               KEE E+++ +  A+L   ++     D + K+I++ + L ++L      +   +++  KL
Sbjct  7030   HKEETEELMRKYEARLYILQQARR--DPLIKQISDNQILLQELGPGDGIIMAFDNVLQKL  7203

Query  188    LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
              L +Y +DDTR V   TE +  SW ++ + +++R+ ALE   R +Q    DLE FL W+ E
Sbjct  7204   LEEYGSDDTRNVKETTEYLKTSWINLKQSITDRQCALEAELRAVQASRRDLENFLKWIQE  7383

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
              AETT NVL DA+++E  L+D+   +EL +Q QD+Q EI+AH D++ ++D N QK++++L 
Sbjct  7384   AETTVNVLADASQRENALQDTLLARELTQQMQDIQAEIDAHNDIFKSIDGNRQKMVKALG  7563

Query  308    GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
               S++A +LQ RLD+MN +W++L+ KS +IR+HLEAS+++W RL  SL+EL+ WL +KD+E
Sbjct  7564   NSEEATMLQHRLDDMNQRWNDLKAKSASIRAHLEASAEKWNRLLTSLEELIKWLNIKDEE  7743

Query  368    LSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQE  427
              L  Q PIGGD PA+Q Q D  +A +RELK KE  +++ ++  R+FL +QP+E  E    E
Sbjct  7744   LQNQMPIGGDVPALQLQYDHCKALRRELKEKEYSVLNAIDQARVFLADQPIEAPE----E  7911

Query  428    PR-------ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              PR       EL PEERAQ + + +RKQ+ EV  +WE LN  +++WQ+++D+ LE+L++LQ
Sbjct  7912   PRRDLQSKTELTPEERAQKIAKAMRKQSSEVKEKWESLNAVTSNWQKQVDKALEKLRDLQ  8091

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
               A D+LD+ +++AE ++  W+PVGDLLIDSLQDH+EK  A R EIAP+   V  VNDL+ 
Sbjct  8092   GAMDDLDVDMKEAEAVRNGWKPVGDLLIDSLQDHIEKTMAFREEIAPINLKVKTVNDLSS  8271

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QL+ L +  S      L+DLN RWKLLQV+V+DR++QL EAHRD GP+SQHFLSTSVQ P
Sbjct  8272   QLSPLDLHPSLKMSRQLDDLNMRWKLLQVSVDDRLKQLQEAHRDLGPSSQHFLSTSVQLP  8451

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              W+R+IS NKVPYYINH+TQTTCWDHPKMTEL+QSLADLNNVRFSAYRTA+K+RRLQKALC
Sbjct  8452   WQRSISHNKVPYYINHQTQTTCWDHPKMTELFQSLADLNNVRFSAYRTAIKIRRLQKALC  8631

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLL L+   +   QH L QNDQ + +  +INCLTT YD LEQ H +LVNVPLCVDMCLN
Sbjct  8632   LDLLELNTTNEVFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQMHMDLVNVPLCVDMCLN  8811

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTG+IRV S K G++SL K  LE+KYRYLFK+VA  T  CDQR+LGLLLHD
Sbjct  8812   WLLNVYDTGRTGKIRVQSLKIGLMSLSKGLLEEKYRYLFKEVAGPTEMCDQRQLGLLLHD  8991

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              +IQIPRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWMRLEPQSMVWLPVLHR
Sbjct  8992   AIQIPRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKDFIDWMRLEPQSMVWLPVLHR  9171

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC
Sbjct  9172   VAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYC  9351

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPAS---------  951
               PTT GEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ETP +         
Sbjct  9352   IPTTPGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPVTLISMWPEHY  9531

Query  952    ----SPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
                  SPQL HDDTHSRIE YA+RLA+ME +NGS++ DS S   S++DEH LIQ YCQ+L 
Sbjct  9532   DPSQSPQLFHDDTHSRIEQYATRLAQMERTNGSFVTDSSSTTGSVEDEHALIQQYCQTLG  9711

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
               +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE RNLQ EY++LK+QH  +GL P+ 
Sbjct  9712   GESPVSQPQSPAQILKSVEREERGELERIIADLEEEQRNLQVEYEQLKEQHLRRGL-PVG  9888

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPP+ + +   +  D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP
Sbjct  9889   SPPDSVVSPHHTSEDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  10068

Query  1128   QAEAKVNGTTVSSPSTSLQRSDSS-------QPMLLRVVGSQTSDSMGEEDLLSPPQDTS  1180
              ++++++NG    SP  S Q+S  S        P   + V          EDLL+PP DTS
Sbjct  10069  ESDSRINGV---SPWASPQQSALSYSLDPDPDPQFHQAVA---------EDLLAPPHDTS  10212

Query  1181   TGLEEVMEQLNNSFPS  1196
              T L E MEQ+N++FPS
Sbjct  10213  TDLTEFMEQINSTFPS  10260


 Score = 46.2 bits (108),  Expect = 0.10, Method: Compositional matrix adjust.
 Identities = 102/479 (21%), Positives = 207/479 (43%), Gaps = 67/479 (13%)
 Frame = +1

Query  7     LEVPALADFNRAWTELTDWLSLLDQVIKSQRVM-VGDLEDINEMIIKQKATMQDLEQRRP  65
             +++ A   F+ A  EL + +      I++  +     +++ +EM  K K   ++  +R P
Sbjct  2050  VDIEAKKKFDAASAELLNCILKSKTAIQAAEIKGYKKMQETSEMKKKLKGLQKEQTERSP  2229

Query  66    QLEELITAAQNLKNKTSNQEARTI-ITDRIERIQNQWDEVQEHLQN--RRQQLNEMLKDS  122
             +L+EL    Q L  +   +   T  I + +E++ ++W ++ +HL++  R+ QL E   D 
Sbjct  2230  RLDELNQTGQVLLEQMGKEGIPTEEIKNVLEKVFSEWKDISQHLEDLARKIQLQE---DI  2400

Query  123   TQWLEAKEEAEQVLGQARAKLESWKEGPYT----------VDAIQKKITETKQLAKDLRQ  172
               + +  ++ E+++   + K E  K  P+            D+ Q+++T       DL  
Sbjct  2401  NAYFKQLDDLEKIV---KTKEEWVKHTPFLEAPQRPSPSLKDSCQRELT-------DLLG  2550

Query  173   WQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALE-------  225
                 +++A    L L     A D   V    E++   ++++ + +  R+  LE       
Sbjct  2551  LHPKIEMARAYCLALKSRPLAPDF--VQQGFESLLGRYQAVRQELEHRQQQLENELKSQP  2724

Query  226   -----ETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD  280
                  ET + L+    D E      ++A+T+ NVL D T+ E+ L++ K + E++     
Sbjct  2725  GRAYLETLKTLKNTLNDSE------SKAQTSLNVLNDLTKLEKALQEKKALDEIL-----  2871

Query  281   LQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHL  340
                  E      + L E ++ + +++   D   + ++  D++  KW++L+ K       L
Sbjct  2872  -----ENQRPTLYTLAEETKALEKTV-SPDVEKMYKQEFDDVQGKWNKLKVKVSKDLHLL  3033

Query  341   EASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEP  400
             E  + + +      + +  W+    D +  QA +  D   +Q Q D    F  E++T E 
Sbjct  3034  EEITSKLRAFEADSKVIEKWMDGVKDFMKEQA-VQRDAEGLQSQLDQCCGFVNEIETVES  3210

Query  401   VIMSTLETVRIFLTEQPLEGLE-----KL--YQEPRELPPEERAQNVTRLLRKQAEEVN  452
               +  ++ +   L   P+ G++     KL  YQ   E   +E A    RL   Q + VN
Sbjct  3211  S-LKDMKEIETNLRSYPVAGIKTWMQTKLVDYQTQLEKFSKEIAIQKNRLSESQEKAVN  3384


 Score = 40.8 bits (94),  Expect = 4.3, Method: Compositional matrix adjust.
 Identities = 55/273 (20%), Positives = 117/273 (42%), Gaps = 21/273 (7%)
 Frame = +1

Query  2     PSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLE  61
             PS++      L  +  A  E+  WL   +   + Q  +  D+E++ E     +A M +L 
Sbjct  901   PSTVTEVDTDLDSYQIALEEVLTWLLSAEDTFQEQDDISDDVEEVKEQFTTHEAFMMELT  1080

Query  62    QRRPQLEELITAAQNLKNK-TSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEML-  119
               +  +  ++ A   L  + T + E    I +++  +  +W+ ++    NR+ +L+++L 
Sbjct  1081  AHQSSVGSVLQAGNQLITQGTLSDEEEFEIQEQMTLLNARWEALRVDSMNRQSRLHDVLM  1260

Query  120   -------KDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVD--AIQKKITETKQLAKDL  170
                    +  + WL   EE          +++  +  P   D  ++QK + + K+L  DL
Sbjct  1261  ELQKKQLQQLSAWLTLTEE----------RIQKMETCPLDDDLKSLQKLLEDHKRLQNDL  1410

Query  171   RQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRL  230
                Q  V+    + + +  +     T  +    + +   W ++ +   ER + L+E + L
Sbjct  1411  EAEQVKVNSLTHMVVIVDENSGESATAVLEDQLQKLGERWTAVCRWTEERWSRLQEINIL  1590

Query  231   LQQFPLDLEKFLAWLTEAETTANVLQDATRKER  263
              Q+   +     AWLTE E   N +Q +  K++
Sbjct  1591  WQELLEEQCLLKAWLTEKEEALNKVQTSNFKDQ  1689


>ref|XM_001915985.1| PREDICTED: Equus caballus similar to utrophin (LOC100066683), 
mRNA
Length=10494

 Score = 1451 bits (3755),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 720/1211 (59%), Positives = 915/1211 (75%), Gaps = 36/1211 (2%)
 Frame = +1

Query  8      EVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQL  67
              E+   AD ++  TEL DWL L+DQ++KS  V VGD+E+IN+ + + K T  DLEQR PQL
Sbjct  6673   EISIPADLDKTITELADWLVLIDQMLKSNIVTVGDVEEINKTVSRMKITRADLEQRHPQL  6852

Query  68     EELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
              + + T AQNLKNK S+ + RT IT+++ER++NQWD  Q  ++ R+QQL +M+ DS QW +
Sbjct  6853   DYVFTLAQNLKNKASSSDVRTAITEKLERVKNQWDGTQHGVELRQQQLEDMIVDSRQWDD  7032

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
               +EE E+++ +  A+L   ++     D + K+I++ + L ++L      V   +++  KL
Sbjct  7033   HREETEELMRKYEARLYMLQQA--RKDPLVKQISDNQILLQELGPGDGIVMAFDNVLQKL  7206

Query  188    LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
              L +Y +DDTR V   TE +  SW ++ + +++R++ALE   R +Q    DLE FL WL E
Sbjct  7207   LEEYGSDDTRNVKETTEYLKTSWINLKQSITDRQSALEAELRTVQASRKDLENFLKWLQE  7386

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
              AETT NVL DA+ +E  L+D+   +EL +Q QD+Q EI+AH D++ ++D N QK++++L 
Sbjct  7387   AETTVNVLADASEREDALQDTVLARELTQQMQDIQAEIDAHNDIFKSIDGNRQKMVKALG  7566

Query  308    GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
               S++A +LQ RLD+MN +W++L+ KS +IR+HLEAS+++W RL  SL+EL+ WL +KD+E
Sbjct  7567   NSEEATMLQHRLDDMNQRWNDLKAKSASIRAHLEASAEKWNRLLTSLEELIKWLNMKDEE  7746

Query  368    LSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQE  427
              L +Q PIGGD PA+Q Q D  +A +RELK KE  +++ ++  R+FL +QP+E  E    E
Sbjct  7747   LKKQMPIGGDVPALQLQYDHCKALRRELKEKEYSVLNAIDQARVFLADQPIEAPE----E  7914

Query  428    PR-------ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
              PR       EL PEERAQ + + +RKQ+ EV  +WE LN  + +WQ+++D+ LE+L++LQ
Sbjct  7915   PRRNLQSKTELTPEERAQKIAKAMRKQSSEVKEKWESLNAVTNNWQKQVDKALEKLRDLQ  8094

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
               A D+LD  L++AE ++  W+PVGDLLIDSLQDH+EK  A R EIAP+   V  VNDL+ 
Sbjct  8095   GAMDDLDADLKEAEAVRNGWKPVGDLLIDSLQDHIEKTMAFREEIAPINLKVKTVNDLSS  8274

Query  541    QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGP  600
              QL+ L +  S      L+DLN RWKLLQV+V DR++QL EAHRDFGP SQHFLS SVQ P
Sbjct  8275   QLSPLDLHPSLKMSRQLDDLNMRWKLLQVSVGDRLKQLQEAHRDFGPPSQHFLSASVQLP  8454

Query  601    WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
              W+R+IS NKVPYYINH+TQTTCWDHPKMTEL+QSLADLNNVRFSAYRTA+K+RRLQKALC
Sbjct  8455   WQRSISHNKVPYYINHQTQTTCWDHPKMTELFQSLADLNNVRFSAYRTAIKIRRLQKALC  8634

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              LDLL L+   +   QH L QNDQ + +  +INCLTT YD LEQ H  LVNVPLCVDMCLN
Sbjct  8635   LDLLELNTTNEVFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQMHKELVNVPLCVDMCLN  8814

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD  780
              WLLNVYDTGRTG+IRV S K G++SL K  LE+KYRYLFK+VA  T  CDQR+LGLLLHD
Sbjct  8815   WLLNVYDTGRTGKIRVQSLKIGLMSLSKGLLEEKYRYLFKEVAGPTEMCDQRQLGLLLHD  8994

Query  781    SIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHR  840
              +IQIPRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWMRLEPQSMVWLPVLHR
Sbjct  8995   AIQIPRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKEFIDWMRLEPQSMVWLPVLHR  9174

Query  841    VAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC  900
              VAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC
Sbjct  9175   VAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYC  9354

Query  901    TPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET------------  948
               PTTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+E             
Sbjct  9355   IPTTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLEAPITLISMWPEHY  9534

Query  949    -PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN  1007
               P+  PQL HDDTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH LIQ YCQ+L 
Sbjct  9535   DPSQFPQLFHDDTHSRIEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHALIQQYCQTLG  9714

Query  1008   QDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
               +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE RNLQ EY++LK+QH  +GL P+ 
Sbjct  9715   GESPVSQPQSPAQILKSVEREERGELERIIADLEEEQRNLQVEYEQLKEQHLRRGL-PVG  9891

Query  1068   SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              SPP+ + +   +  D+ELIAEAKLLRQHKGRLEARMQILE+HNKQLESQLHRLRQLLEQP
Sbjct  9892   SPPDSVASPHHTAEDSELIAEAKLLRQHKGRLEARMQILEEHNKQLESQLHRLRQLLEQP  10071

Query  1128   QAEAKVNGTT--VSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEE  1185
              ++++++NG +   S   ++L  S    P      G Q   +   EDLL+PP DTST L E
Sbjct  10072  ESDSRINGVSPWASPQQSALSYSLDPDP------GPQFHQAAA-EDLLAPPHDTSTDLTE  10230

Query  1186   VMEQLNNSFPS  1196
              VMEQ+N++FPS
Sbjct  10231  VMEQINSTFPS  10263


>ref|NM_011682.4| Mus musculus utrophin (Utrn), mRNA
Length=12382

 Score = 1438 bits (3723),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 708/1208 (58%), Positives = 918/1208 (75%), Gaps = 28/1208 (2%)
 Frame = +3

Query  7      LEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQ  66
              LE+   AD ++  TEL DWL L+DQ++KS  V VGD+++IN+ + + K T  DLEQR PQ
Sbjct  6750   LEISVPADLDKTITELADWLVLIDQMLKSNIVTVGDVKEINKTVSRMKITKADLEQRHPQ  6929

Query  67     LEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWL  126
              L+ + T AQNLKNK S+ + RT IT+++E+++ QW+  Q  ++ RRQQL +M+ DS QW 
Sbjct  6930   LDCVFTLAQNLKNKASSSDVRTAITEKLEKLKTQWESTQHGVELRRQQLEDMVVDSLQWD  7109

Query  127    EAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALK  186
              + +EE E+++ +  A+    ++     D + K++++ + L ++L      +   +++  K
Sbjct  7110   DHREETEELMRKYEARFYMLQQARR--DPLSKQVSDNQLLLQELGSGDGVIMAFDNVLQK  7283

Query  187    LLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
              LL +YS DDTR V   TE +  SW ++ + +++R++ALE   + +Q    DLE F+ WL 
Sbjct  7284   LLEEYSGDDTRNVEETTEYLKTSWVNLKQSIADRQSALEAELQTVQTSRRDLENFVKWLQ  7463

Query  247    EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL  306
              EAETTANVL DA+++E  L+DS   ++L +Q  D+Q EI+AH D++ ++D N QK++++L
Sbjct  7464   EAETTANVLADASQRENALQDSVLARQLRQQMLDIQAEIDAHNDIFKSIDGNRQKMVKAL  7643

Query  307    EGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDD  366
                S++A +LQ RLD+MN +W++L+ KS +IR+HLEAS+++W RL  SL+EL+ WL +KD+
Sbjct  7644   GNSEEATMLQHRLDDMNQRWNDLKAKSASIRAHLEASAEKWNRLLASLEELIKWLNMKDE  7823

Query  367    ELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQ  426
              EL +Q PIGGD PA+Q Q D  +  +RELK KE  +++ ++  R+FL +QP+E  E+  +
Sbjct  7824   ELKKQMPIGGDVPALQLQYDHCKVLRRELKEKEYSVLNAVDQARVFLADQPIEAPEEPRR  8003

Query  427    EPR---ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEAT  483
               P+   EL PEERAQ + + +RKQ+ EV  +WE LN  +++WQ+++ + LE+L++LQ A 
Sbjct  8004   NPQSKTELTPEERAQKIAKAMRKQSSEVREKWENLNAVTSNWQKQVGKALEKLRDLQGAM  8183

Query  484    DELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLT  543
              D+LD  +++ E ++  W+PVGDLLIDSLQDH+EK  A R EIAP+   V  +NDL+ QL+
Sbjct  8184   DDLDADMKEVEAVRNGWKPVGDLLIDSLQDHIEKTLAFREEIAPINLKVKTMNDLSSQLS  8363

Query  544    TLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWER  603
               L +  S      L+DLN RWKLLQV+V+DR++QL EAHRDFGP+SQHFLSTSVQ PW+R
Sbjct  8364   PLDLHPSLKMSRQLDDLNMRWKLLQVSVDDRLKQLQEAHRDFGPSSQHFLSTSVQLPWQR  8543

Query  604    AISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL  663
              +IS NKVPYYINH+TQTTCWDHPKMTEL+QSLADLNNVRFSAYRTA+K+RRLQKALCLDL
Sbjct  8544   SISHNKVPYYINHQTQTTCWDHPKMTELFQSLADLNNVRFSAYRTAIKIRRLQKALCLDL  8723

Query  664    LSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLL  723
              L L+   +   QH L QNDQ + +  +INCLTT YD LEQ H +LVNVPLCVDMCLNWLL
Sbjct  8724   LELNTTNEVFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQLHKDLVNVPLCVDMCLNWLL  8903

Query  724    NVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQ  783
              NVYDTGRTG+IRV S K G++SL K  LE+KYR LFK+VA  T  CDQR+LGLLLHD+IQ
Sbjct  8904   NVYDTGRTGKIRVQSLKIGLMSLSKGLLEEKYRCLFKEVAGPTEMCDQRQLGLLLHDAIQ  9083

Query  784    IPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAA  843
              IPRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWM LEPQSMVWLPVLHRVAA
Sbjct  9084   IPRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKEFIDWMHLEPQSMVWLPVLHRVAA  9263

Query  844    AETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT  903
              AETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC PT
Sbjct  9264   AETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYCIPT  9443

Query  904    TSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPAS------------  951
              TSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ETP +            
Sbjct  9444   TSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMWPEHYDPS  9623

Query  952    -SPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDS  1010
               SPQL HDDTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH LIQ YCQ+L  +S
Sbjct  9624   QSPQLFHDDTHSRIEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHALIQQYCQTLGGES  9803

Query  1011   PLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPP  1070
              P+SQP+SPAQIL S+E EERGELERI+ADLEEE RNLQ EY++LK+QH  +GL P+ SPP
Sbjct  9804   PVSQPQSPAQILKSVEREERGELERIIADLEEEQRNLQVEYEQLKEQHLRRGL-PVGSPP  9980

Query  1071   EMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAE  1130
              + + +   +  D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP ++
Sbjct  9981   DSIVSPHHTSEDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPDSD  10160

Query  1131   AKVNGTT--VSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVME  1188
              +++NG +   S   ++L  S  + P      G Q   +   EDLL+PP DTST L +VME
Sbjct  10161  SRINGVSPWASPQHSALSYSLDTDP------GPQFHQA-ASEDLLAPPHDTSTDLTDVME  10319

Query  1189   QLNNSFPS  1196
              Q+N++FPS
Sbjct  10320  QINSTFPS  10343


 Score = 42.7 bits (99),  Expect = 1.2, Method: Compositional matrix adjust.
 Identities = 47/198 (23%), Positives = 92/198 (46%), Gaps = 11/198 (5%)
 Frame = +3

Query  218   SEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQ  277
             +E  + + E    L  + + LE+ L WL  AE T     D +      +D + VKE    
Sbjct  981   AETPSTVTEVDMDLDSYQIALEEVLTWLLSAEDTFQEQDDIS------DDVEEVKEQFAT  1142

Query  278   WQDLQGEIEAH-TDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNI  336
              +    E+ AH + V   L   +Q + +     ++   +Q ++  +N +W  LR +S+  
Sbjct  1143  HETFMMELTAHQSSVGSVLQAGNQLMTQGTLSEEEEFEIQEQMTLLNARWEALRVESMER  1322

Query  337   RSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRAFKRE  394
             +S L  +  + ++  L  Q+L  WL L ++ + +    P+G D P++QK    H++ + +
Sbjct  1323  QSRLHDALMELQKKQL--QQLSSWLALTEERIQKMESLPLGDDLPSLQKLLQEHKSLQND  1496

Query  395   LKTKEPVIMSTLETVRIF  412
             L+ ++  + S    V I 
Sbjct  1497  LEAEQVKVNSLTHMVVIV  1550


>emb|Y12229.1| M.musculus mRNA for utrophin
Length=11096

 Score = 1438 bits (3723),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 708/1208 (58%), Positives = 918/1208 (75%), Gaps = 28/1208 (2%)
 Frame = +1

Query  7      LEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQ  66
              LE+   AD ++  TEL DWL L+DQ++KS  V VGD+++IN+ + + K T  DLEQR PQ
Sbjct  6658   LEISVPADLDKTITELADWLVLIDQMLKSNIVTVGDVKEINKTVSRMKITKADLEQRHPQ  6837

Query  67     LEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWL  126
              L+ + T AQNLKNK S+ + RT IT+++E+++ QW+  Q  ++ RRQQL +M+ DS QW 
Sbjct  6838   LDCVFTLAQNLKNKASSSDVRTAITEKLEKLKTQWESTQHGVELRRQQLEDMVVDSLQWD  7017

Query  127    EAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALK  186
              + +EE E+++ +  A+    ++     D + K++++ + L ++L      +   +++  K
Sbjct  7018   DHREETEELMRKYEARFYMLQQARR--DPLSKQVSDNQLLLQELGSGDGVIMAFDNVLQK  7191

Query  187    LLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
              LL +YS DDTR V   TE +  SW ++ + +++R++ALE   + +Q    DLE F+ WL 
Sbjct  7192   LLEEYSGDDTRNVEETTEYLKTSWVNLKQSIADRQSALEAELQTVQTSRRDLENFVKWLQ  7371

Query  247    EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL  306
              EAETTANVL DA+++E  L+DS   ++L +Q  D+Q EI+AH D++ ++D N QK++++L
Sbjct  7372   EAETTANVLADASQRENALQDSVLARQLRQQMLDIQAEIDAHNDIFKSIDGNRQKMVKAL  7551

Query  307    EGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDD  366
                S++A +LQ RLD+MN +W++L+ KS +IR+HLEAS+++W RL  SL+EL+ WL +KD+
Sbjct  7552   GNSEEATMLQHRLDDMNQRWNDLKAKSASIRAHLEASAEKWNRLLASLEELIKWLNMKDE  7731

Query  367    ELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQ  426
              EL +Q PIGGD PA+Q Q D  +  +RELK KE  +++ ++  R+FL +QP+E  E+  +
Sbjct  7732   ELKKQMPIGGDVPALQLQYDHCKVLRRELKEKEYSVLNAVDQARVFLADQPIEAPEEPRR  7911

Query  427    EPR---ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEAT  483
               P+   EL PEERAQ + + +RKQ+ EV  +WE LN  +++WQ+++ + LE+L++LQ A 
Sbjct  7912   NPQSKTELTPEERAQKIAKAMRKQSSEVREKWENLNAVTSNWQKQVGKALEKLRDLQGAM  8091

Query  484    DELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLT  543
              D+LD  +++ E ++  W+PVGDLLIDSLQDH+EK  A R EIAP+   V  +NDL+ QL+
Sbjct  8092   DDLDADMKEVEAVRNGWKPVGDLLIDSLQDHIEKTLAFREEIAPINLKVKTMNDLSSQLS  8271

Query  544    TLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWER  603
               L +  S      L+DLN RWKLLQV+V+DR++QL EAHRDFGP+SQHFLSTSVQ PW+R
Sbjct  8272   PLDLHPSLKMSRQLDDLNMRWKLLQVSVDDRLKQLQEAHRDFGPSSQHFLSTSVQLPWQR  8451

Query  604    AISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL  663
              +IS NKVPYYINH+TQTTCWDHPKMTEL+QSLADLNNVRFSAYRTA+K+RRLQKALCLDL
Sbjct  8452   SISHNKVPYYINHQTQTTCWDHPKMTELFQSLADLNNVRFSAYRTAIKIRRLQKALCLDL  8631

Query  664    LSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLL  723
              L L+   +   QH L QNDQ + +  +INCLTT YD LEQ H +LVNVPLCVDMCLNWLL
Sbjct  8632   LELNTTNEVFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQLHKDLVNVPLCVDMCLNWLL  8811

Query  724    NVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQ  783
              NVYDTGRTG+IRV S K G++SL K  LE+KYR LFK+VA  T  CDQR+LGLLLHD+IQ
Sbjct  8812   NVYDTGRTGKIRVQSLKIGLMSLSKGLLEEKYRCLFKEVAGPTEMCDQRQLGLLLHDAIQ  8991

Query  784    IPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAA  843
              IPRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWM LEPQSMVWLPVLHRVAA
Sbjct  8992   IPRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKEFIDWMHLEPQSMVWLPVLHRVAA  9171

Query  844    AETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT  903
              AETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC PT
Sbjct  9172   AETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYCIPT  9351

Query  904    TSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPAS------------  951
              TSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ETP +            
Sbjct  9352   TSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMWPEHYDPS  9531

Query  952    -SPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDS  1010
               SPQL HDDTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH LIQ YCQ+L  +S
Sbjct  9532   QSPQLFHDDTHSRIEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHALIQQYCQTLGGES  9711

Query  1011   PLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPP  1070
              P+SQP+SPAQIL S+E EERGELERI+ADLEEE RNLQ EY++LK+QH  +GL P+ SPP
Sbjct  9712   PVSQPQSPAQILKSVEREERGELERIIADLEEEQRNLQVEYEQLKEQHLRRGL-PVGSPP  9888

Query  1071   EMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAE  1130
              + + +   +  D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP ++
Sbjct  9889   DSIVSPHHTSEDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPDSD  10068

Query  1131   AKVNGTT--VSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVME  1188
              +++NG +   S   ++L  S  + P      G Q   +   EDLL+PP DTST L +VME
Sbjct  10069  SRINGVSPWASPQHSALSYSLDTDP------GPQFHQA-ASEDLLAPPHDTSTDLTDVME  10227

Query  1189   QLNNSFPS  1196
              Q+N++FPS
Sbjct  10228  QINSTFPS  10251


 Score = 47.8 bits (112),  Expect = 0.036, Method: Compositional matrix adjust.
 Identities = 45/185 (24%), Positives = 87/185 (47%), Gaps = 11/185 (5%)
 Frame = +1

Query  231   LQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAH-T  289
             L  + + LE+ L WL  AE T     D +      +D + VKE     +    E+ AH +
Sbjct  931   LDSYQIALEEVLTWLLSAEDTFQEQHDIS------DDVEEVKEQFATHETFMMELTAHQS  1092

Query  290   DVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKR  349
              V   L   +Q + +     ++   +Q ++  +N +W  LR +S+  +S L  +  + ++
Sbjct  1093  SVGSVLQAGNQLMTQGTLSREEEFEIQEQMTLLNARWEALRVESMERQSRLHDALMELQK  1272

Query  350   LHLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLE  407
               L  Q+L  WL L ++ + +    P+G D P++QK    H++ + +L+ ++  + S   
Sbjct  1273  KQL--QQLSSWLALTEERIQKMESLPLGDDLPSLQKLLQEHKSLQNDLEAEQVKVNSLTH  1446

Query  408   TVRIF  412
              V I 
Sbjct  1447  MVVIV  1461


>gb|M92650.1|HUMDMDXX Human Duchenne muscular dystrophy (DMD) mRNA, complete cds
Length=2110

 Score = 1299 bits (3361),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 615/616 (99%), Positives = 615/616 (99%), Gaps = 0/616 (0%)
 Frame = +2

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  71    GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  250

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  251   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  430

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  431   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  610

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  611   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  790

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  791   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  970

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM
Sbjct  971   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  1150

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1034
             ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE
Sbjct  1151  ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1330

Query  1035  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ
Sbjct  1331  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1510

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1154
             HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM
Sbjct  1511  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1690

Query  1155  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR  1214
             LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR
Sbjct  1691  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR  1870

Query  1215  AMESLVSVMTDEEGAE  1230
             AMESLVSVMTDEEGAE
Sbjct  1871  AMESLVSVMTDEEGAE  1918


>ref|NM_004018.2| Homo sapiens dystrophin (DMD), transcript variant Dp71ab, mRNA
Length=4552

 Score = 1298 bits (3359),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 615/616 (99%), Positives = 615/616 (99%), Gaps = 0/616 (0%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  97    GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  276

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  277   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  456

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  457   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  636

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  637   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  816

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  817   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  996

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM
Sbjct  997   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  1176

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1034
             ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE
Sbjct  1177  ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1356

Query  1035  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ
Sbjct  1357  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1536

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1154
             HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM
Sbjct  1537  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1716

Query  1155  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR  1214
             LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR
Sbjct  1717  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR  1896

Query  1215  AMESLVSVMTDEEGAE  1230
             AMESLVSVMTDEEGAE
Sbjct  1897  AMESLVSVMTDEEGAE  1944


>emb|CR859102.1| Pongo abelii mRNA; cDNA DKFZp459C1629 (from clone DKFZp459C1629)
Length=4563

 Score = 1295 bits (3351),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 613/616 (99%), Positives = 614/616 (99%), Gaps = 0/616 (0%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  118   GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  297

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  298   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  477

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  478   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  657

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  658   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  837

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  838   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  1017

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM
Sbjct  1018  VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  1197

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1034
             ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE
Sbjct  1198  ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1377

Query  1035  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ
Sbjct  1378  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1557

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1154
             HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPS SLQRSDSSQPM
Sbjct  1558  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSASLQRSDSSQPM  1737

Query  1155  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR  1214
             LLRVVGSQTSDSMGE+DLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR
Sbjct  1738  LLRVVGSQTSDSMGEDDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR  1917

Query  1215  AMESLVSVMTDEEGAE  1230
             AMESLVSVMTDEEGAE
Sbjct  1918  AMESLVSVMTDEEGAE  1965


>ref|NM_001005244.1| Rattus norvegicus dystrophin, muscular dystrophy (Dmd), transcript 
variant Dp71ab, mRNA
Length=2297

 Score = 1294 bits (3348),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 613/616 (99%), Positives = 614/616 (99%), Gaps = 0/616 (0%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  109   GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  288

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  289   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  468

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  469   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  648

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  649   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  828

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  829   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  1008

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM
Sbjct  1009  VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  1188

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1034
             ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE
Sbjct  1189  ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1368

Query  1035  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ
Sbjct  1369  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1548

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1154
             HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM
Sbjct  1549  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1728

Query  1155  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR  1214
             LLRVVGSQTS+SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR
Sbjct  1729  LLRVVGSQTSESMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR  1908

Query  1215  AMESLVSVMTDEEGAE  1230
             AMESLVSVM DEEGAE
Sbjct  1909  AMESLVSVMIDEEGAE  1956


>gb|AY326948.1| Rattus norvegicus dystrophin Dp71ab (Dmd) mRNA, complete cds; 
alternatively spliced
Length=1914

 Score = 1290 bits (3339),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 611/616 (99%), Positives = 613/616 (99%), Gaps = 0/616 (0%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  46    GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  225

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  226   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  405

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  406   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  585

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANN PEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  586   GGSNIEPSVRSCFQFANNNPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  765

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  766   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  945

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM
Sbjct  946   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  1125

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1034
             ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE
Sbjct  1126  ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1305

Query  1035  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             RILADLEEEN+NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ
Sbjct  1306  RILADLEEENQNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1485

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1154
             HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM
Sbjct  1486  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1665

Query  1155  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR  1214
             LLRVVGSQTS+SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR
Sbjct  1666  LLRVVGSQTSESMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGR  1845

Query  1215  AMESLVSVMTDEEGAE  1230
             AMESLVSVM DEEGAE
Sbjct  1846  AMESLVSVMIDEEGAE  1893


>gb|BC094758.1| Homo sapiens dystrophin, mRNA (cDNA clone IMAGE:30336570), complete 
cds
Length=4621

 Score = 1287 bits (3331),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 615/629 (97%), Positives = 615/629 (97%), Gaps = 13/629 (2%)
 Frame = +3

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  111   GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  290

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  291   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  470

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  471   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  650

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  651   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  830

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  831   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  1010

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-------------PASSPQLSHDDTH  961
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET             PASSPQLSHDDTH
Sbjct  1011  VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDSAPASSPQLSHDDTH  1190

Query  962   SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI  1021
             SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI
Sbjct  1191  SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI  1370

Query  1022  LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR  1081
             LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR
Sbjct  1371  LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR  1550

Query  1082  DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP  1141
             DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP
Sbjct  1551  DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP  1730

Query  1142  STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHN  1201
             STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHN
Sbjct  1731  STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHN  1910

Query  1202  VGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             VGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  1911  VGSLFHMADDLGRAMESLVSVMTDEEGAE  1997


>gb|BC028720.1| Homo sapiens dystrophin, mRNA (cDNA clone IMAGE:4822807), complete 
cds
Length=4658

 Score = 1287 bits (3330),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 615/629 (97%), Positives = 615/629 (97%), Gaps = 13/629 (2%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  148   GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  327

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  328   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  507

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  508   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  687

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  688   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  867

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  868   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  1047

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-------------PASSPQLSHDDTH  961
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET             PASSPQLSHDDTH
Sbjct  1048  VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDSAPASSPQLSHDDTH  1227

Query  962   SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI  1021
             SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI
Sbjct  1228  SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI  1407

Query  1022  LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR  1081
             LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR
Sbjct  1408  LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR  1587

Query  1082  DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP  1141
             DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP
Sbjct  1588  DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP  1767

Query  1142  STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHN  1201
             STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHN
Sbjct  1768  STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHN  1947

Query  1202  VGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             VGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  1948  VGSLFHMADDLGRAMESLVSVMTDEEGAE  2034


>ref|NM_004016.2| Homo sapiens dystrophin (DMD), transcript variant Dp71b, mRNA
Length=4591

 Score = 1286 bits (3328),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 615/629 (97%), Positives = 615/629 (97%), Gaps = 13/629 (2%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  97    GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  276

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  277   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  456

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  457   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  636

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  637   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  816

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  817   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  996

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-------------PASSPQLSHDDTH  961
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET             PASSPQLSHDDTH
Sbjct  997   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDSAPASSPQLSHDDTH  1176

Query  962   SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI  1021
             SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI
Sbjct  1177  SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI  1356

Query  1022  LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR  1081
             LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR
Sbjct  1357  LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR  1536

Query  1082  DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP  1141
             DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP
Sbjct  1537  DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP  1716

Query  1142  STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHN  1201
             STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHN
Sbjct  1717  STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHN  1896

Query  1202  VGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             VGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  1897  VGSLFHMADDLGRAMESLVSVMTDEEGAE  1983


>emb|CR858847.1| Pongo abelii mRNA; cDNA DKFZp469A0710 (from clone DKFZp469A0710)
Length=5043

 Score = 1266 bits (3276),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 614/934 (65%), Positives = 755/934 (80%), Gaps = 17/934 (1%)
 Frame = +3

Query  271   VKELMKQWQ-DLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSEL  329
             ++EL+ +++ D+Q EI+AH D++ ++D N QK++++L  S++A +LQ RLD+MN +W++L
Sbjct  174   LRELLTKFEKDIQAEIDAHNDIFKSIDGNRQKMVKALGNSEEATMLQHRLDDMNQRWNDL  353

Query  330   RKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHR  389
             + KS +IR+HLEAS+++W RL +SL+EL+ WL +KD+EL +Q PIGGD PA+Q Q D  +
Sbjct  354   KAKSASIRAHLEASAEKWNRLLMSLEELIKWLNMKDEELKKQMPIGGDIPALQLQYDHCK  533

Query  390   AFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPR-------ELPPEERAQNVTR  442
             A +RELK KE  I++ ++  R+FL +QP+E  E    EPR       EL PEERAQ + +
Sbjct  534   ALRRELKEKEYSILNAVDQARVFLADQPIEAPE----EPRRNLQSKTELTPEERAQKIAK  701

Query  443   LLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQP  502
              +RKQ+ E+  +WE LN  +++WQ+++D+ LE+L++LQ A D+LD  +++AE ++  W+P
Sbjct  702   AMRKQSSELKEKWESLNAVTSNWQKQVDKALEKLRDLQGAMDDLDADMKEAESVRNGWKP  881

Query  503   VGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNT  562
             VGDLLIDSLQDH+EK+ A R EIAP+   V  VNDL+ QL+ L +  S      L+DLN 
Sbjct  882   VGDLLIDSLQDHIEKIMAFREEIAPINFKVKTVNDLSSQLSPLDLHPSLKMSRQLDDLNM  1061

Query  563   RWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTC  622
             RWKLLQV+V+DR++QL EAHRDFGP+SQHFLSTSVQ PW+R+IS NKVPYYINH+TQTTC
Sbjct  1062  RWKLLQVSVDDRLKQLQEAHRDFGPSSQHFLSTSVQLPWQRSISHNKVPYYINHQTQTTC  1241

Query  623   WDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND  682
             WDHPKMTEL+QSLADLNNVRFSAYRTA+K+RRLQKALCLDLL LS   +   QH L QND
Sbjct  1242  WDHPKMTELFQSLADLNNVRFSAYRTAIKIRRLQKALCLDLLELSTTIEIFKQHKLNQND  1421

Query  683   QPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTG  742
             Q + +  +INCLTT YD LEQ H +LVNVPLCVDMCLNWLLNVYDTGRTG+IRV S K G
Sbjct  1422  QLLSVPDVINCLTTTYDGLEQMHKDLVNVPLCVDMCLNWLLNVYDTGRTGKIRVQSLKIG  1601

Query  743   IISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPS  802
             ++SL K  LE+KYRYLFK+VA  T  CDQR+LGLLLHD+IQIPRQLGEVA+FGGSNIEPS
Sbjct  1602  LMSLSKGLLEEKYRYLFKEVAGPTEMCDQRQLGLLLHDAIQIPRQLGEVAAFGGSNIEPS  1781

Query  803   VRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPII  862
             VRSCFQ  NNKPEI    F+DWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI+
Sbjct  1782  VRSCFQQNNNKPEISVKEFIDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIV  1961

Query  863   GFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRT  922
             GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC PTTSGEDVRDF KVLKNKFR+
Sbjct  1962  GFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYCIPTTSGEDVRDFTKVLKNKFRS  2141

Query  923   KRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYL  982
             K+YFAKHPR+GYLPVQTVLEGDN+ETP+ SPQL HDDTHSRIE YA+RLA+ME +NGS+L
Sbjct  2142  KKYFAKHPRLGYLPVQTVLEGDNLETPSQSPQLLHDDTHSRIEQYATRLAQMERTNGSFL  2321

Query  983   NDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEE  1042
              DS S   S++DEH LIQ YCQ+L  +SP+SQP+SPAQIL S+E EERGELERI+ADLEE
Sbjct  2322  TDSSSTTGSVEDEHALIQQYCQTLGGESPVSQPQSPAQILKSVEREERGELERIIADLEE  2501

Query  1043  ENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEAR  1102
             E  NLQ EY++LK QH  +GL P+ SPPE + +   +  D+ELIAEAKLLRQHKGRLEAR
Sbjct  2502  EQGNLQVEYEQLKDQHLRRGL-PVGSPPESIVSPHHTSEDSELIAEAKLLRQHKGRLEAR  2678

Query  1103  MQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQ  1162
             MQILEDHNKQLESQLHRLRQLLEQP++++++NG    SP  S Q S  S  +     G Q
Sbjct  2679  MQILEDHNKQLESQLHRLRQLLEQPESDSRINGV---SPWASPQHSARSYSLDPDASGPQ  2849

Query  1163  TSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPS  1196
                + G EDLL+PP DTST L EVMEQ++++FPS
Sbjct  2850  FHQAAG-EDLLAPPHDTSTDLTEVMEQIHSTFPS  2948


>emb|X83506.1| M.musculus mRNA for G-utrophin
Length=3161

 Score = 1237 bits (3200),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 605/955 (63%), Positives = 751/955 (78%), Gaps = 29/955 (3%)
 Frame = +3

Query  260   RKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRL  319
             R +R+   S   ++L K   D+Q EI+AH D++ ++D N QK++++L  S++A +LQ RL
Sbjct  291   RLQRMAVSSPRYQKLCK---DIQAEIDAHNDIFKSIDGNRQKMVKALGNSEEATMLQHRL  461

Query  320   DNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFP  379
             D+MN +W++L+ KS +IR+HLEAS+++W RL  SL+EL+ WL +KD+EL +Q PIGGD P
Sbjct  462   DDMNQRWNDLKAKSASIRAHLEASAEKWNRLLASLEELIKWLNMKDEELKKQMPIGGDVP  641

Query  380   AVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPR---ELPPEER  436
             A+Q Q D  +  +RELK KE  +++ ++  R+FL +QP+E  E+  + P+   EL PEER
Sbjct  642   ALQLQYDHCKVLRRELKEKEYSVLNAVDQARVFLADQPIEAPEEPRRNPQSKTELTPEER  821

Query  437   AQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVI  496
             AQ + + +RKQ+ EV  +WE LN  +++WQ+++ + LE+L++LQ A D+LD  +++ E +
Sbjct  822   AQKIAKAMRKQSSEVREKWENLNAVTSNWQKQVGKALEKLRDLQGAMDDLDADMKEVEAV  1001

Query  497   KGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLST  556
             +  W+PVGDLLIDSLQDH+EK  A R EIAP+   V  +NDL+ QL+ L +  S      
Sbjct  1002  RNGWKPVGDLLIDSLQDHIEKTLAFREEIAPINLKVKTMNDLSSQLSPLDLHPSLKMSRQ  1181

Query  557   LEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINH  616
             L+DLN RWKLLQV+V+DR++QL EAHRDFGP+SQHFLSTSVQ PW+R+IS NKVPYYINH
Sbjct  1182  LDDLNMRWKLLQVSVDDRLKQLQEAHRDFGPSSQHFLSTSVQLPWQRSISHNKVPYYINH  1361

Query  617   ETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH  676
             +TQTTCWDHPKMTEL+QSLADLNNVRFSAYRTA+K+RRLQKALCLDLL L+   +   QH
Sbjct  1362  QTQTTCWDHPKMTELFQSLADLNNVRFSAYRTAIKIRRLQKALCLDLLELNTTNEVFKQH  1541

Query  677   NLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRV  736
              L QNDQ + +  +INCLTT YD LEQ H +LVNVPLCVDMCLNWLLNVYDTGRTG+IRV
Sbjct  1542  KLNQNDQLLSVPDVINCLTTTYDGLEQLHKDLVNVPLCVDMCLNWLLNVYDTGRTGKIRV  1721

Query  737   LSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGG  796
              S K G++SL K  LE+KYR LFK+VA  T  CDQR+LGLLLHD+IQIPRQLGEVA+FGG
Sbjct  1722  QSLKIGLMSLSKGLLEEKYRCLFKEVAGPTEMCDQRQLGLLLHDAIQIPRQLGEVAAFGG  1901

Query  797   SNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNIC  856
             SNIEPSVRSCFQ  NNKPEI    F+DWM LEPQSMVWLPVLHRVAAAETAKHQAKCNIC
Sbjct  1902  SNIEPSVRSCFQQNNNKPEISVKEFIDWMHLEPQSMVWLPVLHRVAAAETAKHQAKCNIC  2081

Query  857   KECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVL  916
             KECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC PTTSGEDVRDF KVL
Sbjct  2082  KECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYCIPTTSGEDVRDFTKVL  2261

Query  917   KNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPAS-------------SPQLSHDDTHSR  963
             KNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ETP +             SPQL HDDTHSR
Sbjct  2262  KNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMWPEHYDPSQSPQLFHDDTHSR  2441

Query  964   IEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILI  1023
             IE YA+RLA+ME +NGS+L DS S   S++DEH LIQ YCQ+L  +SP+SQP+SPAQIL 
Sbjct  2442  IEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHALIQQYCQTLGGESPVSQPQSPAQILK  2621

Query  1024  SLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDA  1083
             S+E EERGELERI+ADLEEE RNLQ EY++LK+QH  +GL P+ SPP+ + +   +  D+
Sbjct  2622  SVEREERGELERIIADLEEEQRNLQVEYEQLKEQHLRRGL-PVGSPPDSIVSPHHTSEDS  2798

Query  1084  ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTT--VSSP  1141
             ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP +++++NG +   S  
Sbjct  2799  ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPDSDSRINGVSPWASPQ  2978

Query  1142  STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPS  1196
              ++L  S  + P      G Q   +   EDLL+PP DTST L +VMEQ+N++FPS
Sbjct  2979  HSALSYSLDTDP------GPQFHQA-ASEDLLAPPHDTSTDLTDVMEQINSTFPS  3122


>emb|CR848277.2| Xenopus tropicalis finished cDNA, clone TNeu143c03
Length=2368

 Score = 1236 bits (3198),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 586/640 (91%), Positives = 611/640 (95%), Gaps = 13/640 (2%)
 Frame = +1

Query  604   AISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL  663
             ++SP        HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL
Sbjct  67    SLSPAMRELLKGHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL  246

Query  664   LSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLL  723
             L LSAAC+ALDQHNLKQNDQ MDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLL
Sbjct  247   LGLSAACEALDQHNLKQNDQLMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLL  426

Query  724   NVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQ  783
             NVYDTGRTGRIRVLSFKTG+ISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD+IQ
Sbjct  427   NVYDTGRTGRIRVLSFKTGVISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDAIQ  606

Query  784   IPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAA  843
             IPRQLGEVASFGGSNIEPSVRSCFQ+ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAA
Sbjct  607   IPRQLGEVASFGGSNIEPSVRSCFQYANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAA  786

Query  844   AETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT  903
             AETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT
Sbjct  787   AETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT  966

Query  904   TSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-------------PA  950
             TSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET             PA
Sbjct  967   TSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDSAPA  1146

Query  951   SSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDS  1010
             SSPQLSHDDTHSRIEHYASRLAEMEN+NGSYLNDSISPNESIDDEHLLIQHYCQSLNQ+S
Sbjct  1147  SSPQLSHDDTHSRIEHYASRLAEMENTNGSYLNDSISPNESIDDEHLLIQHYCQSLNQES  1326

Query  1011  PLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPP  1070
             PLSQPRSPAQILISLESEERGELERILADLEEEN+NLQ+EYDRLK+QH+HKGLSPLPSPP
Sbjct  1327  PLSQPRSPAQILISLESEERGELERILADLEEENKNLQSEYDRLKEQHDHKGLSPLPSPP  1506

Query  1071  EMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAE  1130
             EMMP+SPQS RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAE
Sbjct  1507  EMMPSSPQSQRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAE  1686

Query  1131  AKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQL  1190
             AKVNGTT SSP++SLQRS+SSQPMLLRVVGSQTS+SMGE+DLLSPP D+STGLE+VMEQL
Sbjct  1687  AKVNGTTYSSPTSSLQRSESSQPMLLRVVGSQTSESMGEDDLLSPPHDSSTGLEDVMEQL  1866

Query  1191  NNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             NNSFP++RG NVGSLFHMADDLGRAME+LV+VMTD+E  E
Sbjct  1867  NNSFPTARGTNVGSLFHMADDLGRAMETLVTVMTDDEVLE  1986


>gb|BC080941.1| Xenopus tropicalis dystrophin, mRNA (cDNA clone MGC:79631 IMAGE:6979993), 
complete cds
Length=2367

 Score = 1236 bits (3198),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 586/640 (91%), Positives = 611/640 (95%), Gaps = 13/640 (2%)
 Frame = +3

Query  604   AISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL  663
             ++SP        HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL
Sbjct  153   SLSPAMRELLKGHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL  332

Query  664   LSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLL  723
             L LSAAC+ALDQHNLKQNDQ MDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLL
Sbjct  333   LGLSAACEALDQHNLKQNDQLMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLL  512

Query  724   NVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQ  783
             NVYDTGRTGRIRVLSFKTG+ISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD+IQ
Sbjct  513   NVYDTGRTGRIRVLSFKTGVISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDAIQ  692

Query  784   IPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAA  843
             IPRQLGEVASFGGSNIEPSVRSCFQ+ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAA
Sbjct  693   IPRQLGEVASFGGSNIEPSVRSCFQYANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAA  872

Query  844   AETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT  903
             AETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT
Sbjct  873   AETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT  1052

Query  904   TSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-------------PA  950
             TSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET             PA
Sbjct  1053  TSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDSAPA  1232

Query  951   SSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDS  1010
             SSPQLSHDDTHSRIEHYASRLAEMEN+NGSYLNDSISPNESIDDEHLLIQHYCQSLNQ+S
Sbjct  1233  SSPQLSHDDTHSRIEHYASRLAEMENTNGSYLNDSISPNESIDDEHLLIQHYCQSLNQES  1412

Query  1011  PLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPP  1070
             PLSQPRSPAQILISLESEERGELERILADLEEEN+NLQ+EYDRLK+QH+HKGLSPLPSPP
Sbjct  1413  PLSQPRSPAQILISLESEERGELERILADLEEENKNLQSEYDRLKEQHDHKGLSPLPSPP  1592

Query  1071  EMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAE  1130
             EMMP+SPQS RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAE
Sbjct  1593  EMMPSSPQSQRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAE  1772

Query  1131  AKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQL  1190
             AKVNGTT SSP++SLQRS+SSQPMLLRVVGSQTS+SMGE+DLLSPP D+STGLE+VMEQL
Sbjct  1773  AKVNGTTYSSPTSSLQRSESSQPMLLRVVGSQTSESMGEDDLLSPPHDSSTGLEDVMEQL  1952

Query  1191  NNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             NNSFP++RG NVGSLFHMADDLGRAME+LV+VMTD+E  E
Sbjct  1953  NNSFPTARGTNVGSLFHMADDLGRAMETLVTVMTDDEVLE  2072


>ref|NM_004017.2| Homo sapiens dystrophin (DMD), transcript variant Dp71a, mRNA
Length=4584

 Score = 1235 bits (3195),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 585/588 (99%), Positives = 585/588 (99%), Gaps = 0/588 (0%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  97    GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  276

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  277   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  456

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  457   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  636

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  637   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  816

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  817   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  996

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM
Sbjct  997   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  1176

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1034
             ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE
Sbjct  1177  ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1356

Query  1035  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ
Sbjct  1357  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1536

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1154
             HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM
Sbjct  1537  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1716

Query  1155  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG N 
Sbjct  1717  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGRNT  1860


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +3

Query  1198  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  1878  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1976


>ref|NM_012698.2| Rattus norvegicus dystrophin, muscular dystrophy (Dmd), transcript 
variant Dp71a, mRNA
Length=2329

 Score = 1234 bits (3194),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 584/588 (99%), Positives = 585/588 (99%), Gaps = 0/588 (0%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  109   GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  288

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  289   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  468

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  469   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  648

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  649   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  828

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  829   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  1008

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM
Sbjct  1009  VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  1188

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1034
             ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE
Sbjct  1189  ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1368

Query  1035  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ
Sbjct  1369  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1548

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1154
             HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM
Sbjct  1549  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1728

Query  1155  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             LLRVVGSQTS+SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG N 
Sbjct  1729  LLRVVGSQTSESMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGRNA  1872


 Score = 67.8 bits (164),  Expect = 3e-08, Method: Composition-based stats.
 Identities = 32/35 (91%), Positives = 33/35 (94%), Gaps = 0/35 (0%)
 Frame = +3

Query  1196  SSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             + RGHNVGSLFHMADDLGRAMESLVSVM DEEGAE
Sbjct  1884  NERGHNVGSLFHMADDLGRAMESLVSVMIDEEGAE  1988


>gb|BC149235.1| Bos taurus dystrophin, mRNA (cDNA clone MGC:155049 IMAGE:8466545), 
complete cds
Length=2333

 Score = 1230 bits (3182),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 581/588 (98%), Positives = 585/588 (99%), Gaps = 0/588 (0%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  106   GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  285

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  286   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  465

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  466   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  645

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  646   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  825

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  826   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  1005

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM
Sbjct  1006  VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  1185

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1034
             ENS+GSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE
Sbjct  1186  ENSSGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1365

Query  1035  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             RILADLEEENRNLQAEYDRLK+QHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ
Sbjct  1366  RILADLEEENRNLQAEYDRLKEQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1545

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1154
             HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM
Sbjct  1546  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1725

Query  1155  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             LLRVVGSQTS+SMGEEDLLSPPQD+STGLEEVMEQLNNSFPSSRG N 
Sbjct  1726  LLRVVGSQTSESMGEEDLLSPPQDSSTGLEEVMEQLNNSFPSSRGRNT  1869


 Score = 67.8 bits (164),  Expect = 3e-08, Method: Composition-based stats.
 Identities = 32/35 (91%), Positives = 34/35 (97%), Gaps = 0/35 (0%)
 Frame = +3

Query  1196  SSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             + RGHNVGSLFH+ADDLGRAMESLVSVMTDEEGAE
Sbjct  1881  NERGHNVGSLFHLADDLGRAMESLVSVMTDEEGAE  1985


>gb|BC070078.1| Homo sapiens dystrophin, mRNA (cDNA clone IMAGE:5262850), complete 
cds
Length=4598

 Score = 1230 bits (3182),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 583/588 (99%), Positives = 584/588 (99%), Gaps = 0/588 (0%)
 Frame = +2

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  98    GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  277

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  278   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  457

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  458   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  637

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  638   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  817

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  818   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  997

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM
Sbjct  998   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  1177

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1034
             ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE
Sbjct  1178  ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1357

Query  1035  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPS PEM+PTSPQSPRDAELIAEAKLLRQ
Sbjct  1358  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSTPEMVPTSPQSPRDAELIAEAKLLRQ  1537

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1154
             HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM
Sbjct  1538  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1717

Query  1155  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG N 
Sbjct  1718  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGRNT  1861


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +1

Query  1198  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  1879  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1977


>gb|AY326947.1| Rattus norvegicus dystrophin Dp71a (Dmd) mRNA, complete cds; 
alternatively spliced
Length=1858

 Score = 1229 bits (3181),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 582/588 (98%), Positives = 584/588 (99%), Gaps = 0/588 (0%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  46    GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  225

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  226   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  405

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  406   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  585

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANN PEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  586   GGSNIEPSVRSCFQFANNNPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  765

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  766   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  945

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM
Sbjct  946   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  1125

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1034
             ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE
Sbjct  1126  ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1305

Query  1035  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             RILADLEEEN+NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ
Sbjct  1306  RILADLEEENQNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1485

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1154
             HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM
Sbjct  1486  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1665

Query  1155  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             LLRVVGSQTS+SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG N 
Sbjct  1666  LLRVVGSQTSESMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGRNA  1809


>ref|NM_004015.2| Homo sapiens dystrophin (DMD), transcript variant Dp71, mRNA
Length=4623

 Score = 1224 bits (3166),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 585/601 (97%), Positives = 585/601 (97%), Gaps = 13/601 (2%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  97    GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  276

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  277   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  456

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  457   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  636

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  637   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  816

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  817   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  996

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-------------PASSPQLSHDDTH  961
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET             PASSPQLSHDDTH
Sbjct  997   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDSAPASSPQLSHDDTH  1176

Query  962   SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI  1021
             SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI
Sbjct  1177  SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI  1356

Query  1022  LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR  1081
             LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR
Sbjct  1357  LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR  1536

Query  1082  DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP  1141
             DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP
Sbjct  1537  DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP  1716

Query  1142  STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHN  1201
             STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG N
Sbjct  1717  STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGRN  1896

Query  1202  V  1202
              
Sbjct  1897  T  1899


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +3

Query  1198  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  1917  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  2015


>dbj|AK036936.1| Mus musculus adult female vagina cDNA, RIKEN full-length enriched 
library, clone:9930028B14 product:dystrophin, muscular 
dystrophy, full insert sequence
Length=4437

 Score = 1223 bits (3164),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 584/601 (97%), Positives = 585/601 (97%), Gaps = 13/601 (2%)
 Frame = +2

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  47    GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  226

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  227   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  406

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  407   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  586

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  587   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  766

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  767   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  946

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-------------PASSPQLSHDDTH  961
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET             PASSPQLSHDDTH
Sbjct  947   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDSAPASSPQLSHDDTH  1126

Query  962   SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI  1021
             SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI
Sbjct  1127  SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI  1306

Query  1022  LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR  1081
             LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR
Sbjct  1307  LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR  1486

Query  1082  DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP  1141
             DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP
Sbjct  1487  DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP  1666

Query  1142  STSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHN  1201
             STSLQRSDSSQPMLLRVVGSQTS+SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG N
Sbjct  1667  STSLQRSDSSQPMLLRVVGSQTSESMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGRN  1846

Query  1202  V  1202
              
Sbjct  1847  A  1849


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +1

Query  1198  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  1867  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1965


>gb|BC082429.1| Xenopus laevis dystrophin, mRNA (cDNA clone MGC:83347 IMAGE:6865319), 
complete cds
Length=2263

 Score = 1220 bits (3156),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 582/640 (90%), Positives = 606/640 (94%), Gaps = 14/640 (2%)
 Frame = +3

Query  604   AISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL  663
             ++SP        HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL
Sbjct  66    SLSPAMRELLKGHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL  245

Query  664   LSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLL  723
             L LSAAC+ALDQHNLKQNDQ MDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLL
Sbjct  246   LGLSAACEALDQHNLKQNDQLMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLL  425

Query  724   NVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQ  783
             NVYDTGRTGRIRVLSFKTG+ISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD+IQ
Sbjct  426   NVYDTGRTGRIRVLSFKTGVISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDAIQ  605

Query  784   IPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAA  843
             IPRQLGEVASFGGSNIEPSVRSCFQ+ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAA
Sbjct  606   IPRQLGEVASFGGSNIEPSVRSCFQYANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAA  785

Query  844   AETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT  903
             AETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT
Sbjct  786   AETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT  965

Query  904   TSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-------------PA  950
             TSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET             PA
Sbjct  966   TSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDSAPA  1145

Query  951   SSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDS  1010
             SSPQLSHDDTH RIEHYASRLAEMEN+NGSYLNDSISPNESIDDEHLLIQHYCQSLNQ+S
Sbjct  1146  SSPQLSHDDTHLRIEHYASRLAEMENTNGSYLNDSISPNESIDDEHLLIQHYCQSLNQES  1325

Query  1011  PLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPP  1070
             PLSQPRSPAQILISLESEERGELERILADLEEEN+NLQ EYDRLK+QH+HKGLSPLPSPP
Sbjct  1326  PLSQPRSPAQILISLESEERGELERILADLEEENKNLQTEYDRLKEQHDHKGLSPLPSPP  1505

Query  1071  EMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAE  1130
             EMMP+SPQS RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAE
Sbjct  1506  EMMPSSPQSQRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAE  1685

Query  1131  AKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQL  1190
             +KVNGTT SSP+ SLQRS+S+QPMLLRVVGSQTS+SMGE+DLLS P D+STGLEEVMEQL
Sbjct  1686  SKVNGTTYSSPTPSLQRSESNQPMLLRVVGSQTSESMGEDDLLS-PHDSSTGLEEVMEQL  1862

Query  1191  NNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             NNSFP++RG NVGSLFHM DDLGRAME+LV+VMTD+E  E
Sbjct  1863  NNSFPTARGTNVGSLFHMVDDLGRAMETLVTVMTDDEVLE  1982


>gb|BC136240.1| Xenopus tropicalis cDNA clone IMAGE:7661888, containing frame-shift 
errors
Length=2437

 Score = 1142 bits (2953),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 543/599 (90%), Positives = 567/599 (94%), Gaps = 9/599 (1%)
 Frame = +3

Query  604   AISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL  663
             ++SP        HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL
Sbjct  141   SLSPAMRELLKGHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL  320

Query  664   LSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLL  723
             L LSAAC+ALDQHNLKQNDQ MDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLL
Sbjct  321   LGLSAACEALDQHNLKQNDQLMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLL  500

Query  724   NVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQ  783
             NVYDTGRTGRIRVLSFKTG+ISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHD+IQ
Sbjct  501   NVYDTGRTGRIRVLSFKTGVISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDAIQ  680

Query  784   IPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAA  843
             IPRQLGEVASFGGSNIEPSVRSCFQ+ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAA
Sbjct  681   IPRQLGEVASFGGSNIEPSVRSCFQYANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAA  860

Query  844   AETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT  903
             AETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT
Sbjct  861   AETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT  1040

Query  904   TSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSR  963
             TSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETP +       D    
Sbjct  1041  TSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVD----  1208

Query  964   IEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILI  1023
                  S LAEMEN+NGSYLNDSISPNESIDDEHLLIQHYCQSLNQ+SPLSQPRSPAQILI
Sbjct  1209  -----SALAEMENTNGSYLNDSISPNESIDDEHLLIQHYCQSLNQESPLSQPRSPAQILI  1373

Query  1024  SLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDA  1083
             SLESEERGELERILADLEEEN+NLQ+EYDRLK+QH+HKGLSPLPSPPEMMP+SPQS RDA
Sbjct  1374  SLESEERGELERILADLEEENKNLQSEYDRLKEQHDHKGLSPLPSPPEMMPSSPQSQRDA  1553

Query  1084  ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPST  1143
             ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTT SSP++
Sbjct  1554  ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTYSSPTS  1733

Query  1144  SLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             SLQRS+SSQPMLLRVVGSQTS+SMGE+DLLSPP D+STGLE+VMEQLNNSFP++RG +V
Sbjct  1734  SLQRSESSQPMLLRVVGSQTSESMGEDDLLSPPHDSSTGLEDVMEQLNNSFPTARGRSV  1910


 Score = 57.4 bits (137),  Expect = 5e-05, Method: Composition-based stats.
 Identities = 27/35 (77%), Positives = 31/35 (88%), Gaps = 0/35 (0%)
 Frame = +2

Query  1196  SSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             + RG NVGSLFHMADDLGRAME+LV+VMTD+E  E
Sbjct  1922  NERGTNVGSLFHMADDLGRAMETLVTVMTDDEVLE  2026


>dbj|AK159639.1| Mus musculus osteoclast-like cell cDNA, RIKEN full-length enriched 
library, clone:I420026N21 product:dystrophin, muscular 
dystrophy, full insert sequence
Length=2839

 Score = 1104 bits (2855),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 528/545 (96%), Positives = 529/545 (97%), Gaps = 13/545 (2%)
 Frame = +3

Query  671   DALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGR  730
             DALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGR
Sbjct  3     DALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGR  182

Query  731   TGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGE  790
             TGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGE
Sbjct  183   TGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGE  362

Query  791   VASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQ  850
             VASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQ
Sbjct  363   VASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQ  542

Query  851   AKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVR  910
             AKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVR
Sbjct  543   AKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVR  722

Query  911   DFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-------------PASSPQLSH  957
             DFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET             PASSPQLSH
Sbjct  723   DFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDSAPASSPQLSH  902

Query  958   DDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRS  1017
             DDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRS
Sbjct  903   DDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRS  1082

Query  1018  PAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSP  1077
             PAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSP
Sbjct  1083  PAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSP  1262

Query  1078  QSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTT  1137
             QSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTT
Sbjct  1263  QSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTT  1442

Query  1138  VSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSS  1197
             VSSPSTSLQRSDSSQPMLLRVVGSQTS+SMGEEDLLSPPQDTSTGLEEVMEQLN SFPSS
Sbjct  1443  VSSPSTSLQRSDSSQPMLLRVVGSQTSESMGEEDLLSPPQDTSTGLEEVMEQLNKSFPSS  1622

Query  1198  RGHNV  1202
             RG N 
Sbjct  1623  RGRNA  1637


 Score = 71.6 bits (174),  Expect = 3e-09, Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%), Gaps = 0/33 (0%)
 Frame = +2

Query  1198  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  1655  RGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1753


>emb|X99702.1| S.caniculua mRNA for dystrophin
Length=1993

 Score = 1100 bits (2846),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 536/587 (91%), Positives = 560/587 (95%), Gaps = 13/587 (2%)
 Frame = +1

Query  625   HPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQP  684
             HPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSL +AC+A DQHNLKQNDQ 
Sbjct  1     HPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLPSACEAFDQHNLKQNDQL  180

Query  685   MDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGII  744
             MDIL+IINCLT+IYDRLEQEH+NLVNVPLCVDMCLNWLLNVYDTGRTG+IRVLSFK+GI+
Sbjct  181   MDILEIINCLTSIYDRLEQEHSNLVNVPLCVDMCLNWLLNVYDTGRTGKIRVLSFKSGIM  360

Query  745   SLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVR  804
             SLCKAHLEDKYRYLFKQVAS TGFCDQRRLGLLLHD+IQIPRQLGEVASFGGSNIEPSVR
Sbjct  361   SLCKAHLEDKYRYLFKQVASPTGFCDQRRLGLLLHDAIQIPRQLGEVASFGGSNIEPSVR  540

Query  805   SCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGF  864
             SCFQFANNKPE+EAALFLDWMRLEPQSMVW+PVLHRVAAAETAKHQAKCNICKECPIIGF
Sbjct  541   SCFQFANNKPEVEAALFLDWMRLEPQSMVWMPVLHRVAAAETAKHQAKCNICKECPIIGF  720

Query  865   RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKR  924
             RYRSLKHFNYD+CQSCFFSGR AKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKR
Sbjct  721   RYRSLKHFNYDVCQSCFFSGRTAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKR  900

Query  925   YFAKHPRMGYLPVQTVLEGDNMET-------------PASSPQLSHDDTHSRIEHYASRL  971
             YFAKHPRMGYLPVQTVLEGDN+ET             PASSPQLSHDDTHSRIEHYASRL
Sbjct  901   YFAKHPRMGYLPVQTVLEGDNLETPVTLINFWPVDYEPASSPQLSHDDTHSRIEHYASRL  1080

Query  972   AEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERG  1031
             AEMEN NGSYLNDSISPNESIDDEHLLIQHYCQSLNQ+SPLSQPRSPAQILISLESEERG
Sbjct  1081  AEMENRNGSYLNDSISPNESIDDEHLLIQHYCQSLNQESPLSQPRSPAQILISLESEERG  1260

Query  1032  ELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKL  1091
             ELERILADLE+ENRNLQ+EY+RLKQQH+HKGLSPLPSPPEMMP SPQSPRDAELIAEAKL
Sbjct  1261  ELERILADLEDENRNLQSEYERLKQQHDHKGLSPLPSPPEMMPISPQSPRDAELIAEAKL  1440

Query  1092  LRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSS  1151
             LRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQ E +VNGTTVSSPSTS QRSDSS
Sbjct  1441  LRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQTEVRVNGTTVSSPSTSSQRSDSS  1620

Query  1152  QPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSR  1198
             QP+LL  VGSQTS +MGE++LLSPPQ T+TGLEEVMEQLNNSFPSSR
Sbjct  1621  QPVLLHGVGSQTSGTMGEDELLSPPQGTTTGLEEVMEQLNNSFPSSR  1761


 Score = 60.1 bits (144),  Expect = 8e-06, Method: Composition-based stats.
 Identities = 27/35 (77%), Positives = 32/35 (91%), Gaps = 0/35 (0%)
 Frame = +3

Query  1196  SSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             S RG+NVGSLFHM DDLGRAME+LV++MTD+E AE
Sbjct  1785  SERGNNVGSLFHMVDDLGRAMETLVTIMTDDETAE  1889


>emb|X99700.1| X.laevis mRNA for dystrophin
Length=1961

 Score = 1100 bits (2845),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 525/577 (90%), Positives = 547/577 (94%), Gaps = 9/577 (1%)
 Frame = +1

Query  626   PKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPM  685
             PKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLL LSAAC+ALDQ+NLKQNDQ M
Sbjct  1     PKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLGLSAACEALDQYNLKQNDQLM  180

Query  686   DILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIIS  745
             DILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTG+IS
Sbjct  181   DILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGVIS  360

Query  746   LCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRS  805
             LCKAHLEDKYRYLFKQVASSTG+CDQRRLGLLLHD+IQIPRQLGEVASFGGSNIEPSVRS
Sbjct  361   LCKAHLEDKYRYLFKQVASSTGYCDQRRLGLLLHDAIQIPRQLGEVASFGGSNIEPSVRS  540

Query  806   CFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFR  865
             CFQ+ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFR
Sbjct  541   CFQYANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFR  720

Query  866   YRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRY  925
             YRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRY
Sbjct  721   YRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRY  900

Query  926   FAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDS  985
             FAKHPRMGYLPVQTVLEGDNMETP +       D         S LAEMEN+NGSYLNDS
Sbjct  901   FAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVD---------SALAEMENTNGSYLNDS  1053

Query  986   ISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
             ISPNESIDDEHLLIQHYCQSLNQ+SPLSQPRSPAQILISLESEERGELERILADLEEEN+
Sbjct  1054  ISPNESIDDEHLLIQHYCQSLNQESPLSQPRSPAQILISLESEERGELERILADLEEENK  1233

Query  1046  NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQI  1105
             NLQAEYDRLK+QH+HKGLSPLP+PPEMMP SPQS RDAELIAEAKLLRQHKGRLEARMQI
Sbjct  1234  NLQAEYDRLKEQHDHKGLSPLPTPPEMMPPSPQSQRDAELIAEAKLLRQHKGRLEARMQI  1413

Query  1106  LEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSD  1165
             LEDHNKQLESQLHRLRQLLEQPQAE+KVNGTT SSP+ SLQRS+S+QPMLLRVVGSQTS+
Sbjct  1414  LEDHNKQLESQLHRLRQLLEQPQAESKVNGTTYSSPTPSLQRSESNQPMLLRVVGSQTSE  1593

Query  1166  SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             SMGE+D L  P D+STGLEEVMEQLNNSFP++RG  V
Sbjct  1594  SMGEDDRLLSPHDSSTGLEEVMEQLNNSFPTARGRIV  1704


 Score = 55.8 bits (133),  Expect = 1e-04, Method: Composition-based stats.
 Identities = 26/35 (74%), Positives = 30/35 (85%), Gaps = 0/35 (0%)
 Frame = +3

Query  1196  SSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             + RG NVGSLFHM DDLGRAME+LV+VMTD+E  E
Sbjct  1716  NERGTNVGSLFHMVDDLGRAMETLVTVMTDDEVLE  1820


>ref|XM_002227549.1| Branchiostoma floridae hypothetical protein (BRAFLDRAFT_125744) 
mRNA, complete cds
Length=6396

 Score = 1096 bits (2834),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 576/1057 (54%), Positives = 738/1057 (69%), Gaps = 104/1057 (9%)
 Frame = +1

Query  264   LLEDSKGVKE-LMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNM  322
             ++E +  VK+ L+K  QDLQ EI+AH DV+ +L++  + IL+S+E  +DA +LQRRL+NM
Sbjct  2332  MIELTFSVKDMLLKFEQDLQAEIDAHQDVWSSLNDTGRHILQSIEHCEDAQMLQRRLENM  2511

Query  323   NFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQ  382
             N +W+ LR KSL+IR  LEA+ +QW +L ++LQ+L+ W  +K+DEL+R  P+GGD   VQ
Sbjct  2512  NDRWTALRSKSLDIRQRLEANIEQWNQLLITLQDLIEWCGIKEDELTRMQPVGGDLNTVQ  2691

Query  383   KQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLY-----------------  425
             +Q   H+ F++ ++ K P+I ++LET + +L EQ  +    L                  
Sbjct  2692  QQQADHKLFRQSVEDKRPLIETSLETGKEYLVEQGEDSRSTLNTSGDSQISATSLSDELS  2871

Query  426   --QEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEAT  483
               ++   L PEE+A+ + R L++Q + +  +W +L   S  WQ++ID+   +L++L +A 
Sbjct  2872  TEEDKVGLTPEEQAKEIARNLKRQVKTLTDKWAQLQGRSDIWQKRIDDVQNKLRQLHDAM  3051

Query  484   DELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLT  543
             ++L  KL + E +K SW PVGDL+ID+LQD ++ VKA + +IAP++ NV + N+LA    
Sbjct  3052  NDLSGKLHEGETLKASWLPVGDLIIDNLQDQIDDVKAFQAQIAPIQSNVDYTNNLANSFP  3231

Query  544   TLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWER  603
              + +QLS  NL+ LEDLNTRW+LLQV+ +DR++QL EA RDFGP SQHFLSTSV+G WER
Sbjct  3232  PMDVQLSSSNLNRLEDLNTRWRLLQVSAQDRLKQLEEALRDFGPNSQHFLSTSVEGTWER  3411

Query  604   AISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL  663
             A++ NKVPYYINH T+TT WDHPKMTEL+QSLADLN+VRFSAYRTAMKLRRLQKALCLDL
Sbjct  3412  AVAANKVPYYINHTTETTSWDHPKMTELFQSLADLNDVRFSAYRTAMKLRRLQKALCLDL  3591

Query  664   LSLSAACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWL  722
             LS++ A DA DQH L+ QND+ MD+++IINCLTTIYD LEQ+H NLVNVPLCVDMCLNWL
Sbjct  3592  LSMNNAIDAFDQHGLRGQNDRLMDVIEIINCLTTIYDNLEQDHGNLVNVPLCVDMCLNWL  3771

Query  723   LNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSI  782
             LNVYDTGR+G+IRVLSFK GIISLC+AHLEDKYR+ F+ +A +TGF DQR+LGLLLHD I
Sbjct  3772  LNVYDTGRSGKIRVLSFKVGIISLCRAHLEDKYRFNFRLIAEATGFADQRKLGLLLHDLI  3951

Query  783   QIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVA  842
             Q+PRQLGE+ASFGGSNIEPSVRSCF+ A  KPEIEAA FLDWM+ EPQSMVWLPVLHR+A
Sbjct  3952  QVPRQLGEIASFGGSNIEPSVRSCFERAGGKPEIEAAHFLDWMKQEPQSMVWLPVLHRLA  4131

Query  843   AAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTP  902
             AAETAKHQAKCNICKE PI+GFRYR L+ FN+D+CQSCF SGR AKGHK+ +PM EYCT 
Sbjct  4132  AAETAKHQAKCNICKEYPIVGFRYRCLRCFNFDMCQSCFLSGRKAKGHKLSHPMQEYCTA  4311

Query  903   TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET--------------  948
             TTSGEDVRDFAKV++NKFR+K+   KHPR+GYLPVQTVLEGDN+ET              
Sbjct  4312  TTSGEDVRDFAKVVRNKFRSKKSLKKHPRLGYLPVQTVLEGDNLETPLVLWRYEQVTPDR  4491

Query  949   -------------PASSPQLS-HDDTHSRIEHYASRLAEMENSNGSY-----LNDSISPN  989
                          P+SSPQ +   D HSR+E YASRLAE+E S  S      +  ++S  
Sbjct  4492  EEPPRHLHIEERQPSSSPQQAVSQDMHSRLELYASRLAEVEQSMNSMSSSSDIWTTVSST  4671

Query  990   ESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQA  1049
             +      ++I          S   +P+SPAQI+++++ E+R ELE ++ DLEEENRNLQ 
Sbjct  4672  KIRGSLRVIIAVL-------SGKEKPKSPAQIVVAIDQEQRAELEAMIKDLEEENRNLQM  4830

Query  1050  EYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDH  1109
             EY+RLK Q + +     PS P+  P S +  RD ELIAEAKLLRQHKGRLEARMQILEDH
Sbjct  4831  EYERLKIQKQQQ-----PS-PQAEPRS-EVNRDNELIAEAKLLRQHKGRLEARMQILEDH  4989

Query  1110  NKQLESQLHRLRQLLEQPQAE-----------AKVNGTTVSSPSTSLQRSD--SSQPMLL  1156
             N+QLE+QL RLRQLLEQPQ++              N  T SS   SL  +   S  P   
Sbjct  4990  NRQLEAQLQRLRQLLEQPQSDRSPTSHTSSSSHTPNEVTPSSSQGSLPGNTPPSRAPRFP  5169

Query  1157  RVV-GSQTSDSM--GEEDL------LSPP---------QDTSTGLEEVMEQLNNSFPSSR  1198
                 G    D    G  D+       +PP         Q     LEEVM ++N+SFP   
Sbjct  5170  TTTNGLPNGDGAVNGAADIRVQGATRTPPPLRDGQRRQQTPEEQLEEVMREVNSSFPPDS  5349

Query  1199  GH-----NVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              H      VGSLF+MA DL +A+  LV+VMT+E+G E
Sbjct  5350  NHTQGKNTVGSLFNMAGDLNKAVGKLVTVMTNEDGTE  5460


 Score =  196 bits (499),  Expect = 5e-47, Method: Compositional matrix adjust.
 Identities = 100/248 (40%), Positives = 156/248 (62%), Gaps = 1/248 (0%)
 Frame = +1

Query  8     EVPAL-ADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQ  66
             ++P++  DF+++  EL DWL LLD ++KSQ V VGD+E+I EMIIKQK  + DL+ ++PQ
Sbjct  808   DMPSMYPDFDKSVAELRDWLMLLDHMLKSQIVTVGDVEEIEEMIIKQKTVLNDLDVKKPQ  987

Query  67    LEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWL  126
             L+ ++ A + L         + ++ ++++RIQ QWDE    +  R+++L+ ML D   W 
Sbjct  988   LDTVVAAGRRLIQTADTDSDKQLLKEKVDRIQEQWDEASTRVGARKRELDNMLTDCHHWD  1167

Query  127   EAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALK  186
             E +E+  + L QA  ++E   E   TVD + K+I + K+   +LRQWQ +++  NDLA K
Sbjct  1168  ELREDVSRWLEQAEQQVEHDSEVGQTVDVLDKQIAQHKEFMDNLRQWQPSIEAVNDLAQK  1347

Query  187   LLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             L+ DYS DDT K+  + + IN  W+ ++ R  ER+  L+     LQ+F L LE+FLAWL+
Sbjct  1348  LISDYSNDDTSKIKQMIDRINGRWQQLNNRCRERQQNLKNALEKLQKFSLQLEEFLAWLS  1527

Query  247   EAETTANV  254
             EAE    V
Sbjct  1528  EAEAAMEV  1551


>gb|AF304204.1|AF304204 Strongylocentrotus purpuratus dystrophin-like protein mRNA, complete 
cds
Length=12315

 Score = 1093 bits (2827),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 581/1267 (45%), Positives = 826/1267 (65%), Gaps = 63/1267 (4%)
 Frame = +1

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              D ++   EL DWL LL+++++ Q V VGDLE+I  MI+KQK+ +QDL+ + PQL+EL+  
Sbjct  8518   DVDKVVAELRDWLMLLERMLRLQVVTVGDLEEIENMIMKQKSHIQDLDMKHPQLKELVER  8697

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE  133
              A++++ +T+N+  + ++ +++ R+   W+  ++   +R  QL  M+ DS ++ +  +E  
Sbjct  8698   AKSIQEETANEGDKRLLHEKMARLLELWEGAEKRATHRAGQLETMMTDSQRFHQLTQELL  8877

Query  134    QVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSA  193
                L +    L+ +      +  +Q ++   K   +++ QW+  +D  N+   +L  +Y  
Sbjct  8878   TWLSKMEGTLDRYPPVAQDMLMLQAQLMAQKGFLEEVEQWKPCLDAVNENGDRLGLEYKD  9057

Query  194    DDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTAN  253
              DDT K+  + + +N  W +I  R + R   +EET + +Q     L +F AWL   E   +
Sbjct  9058   DDTSKIKHVLDGVNQRWANICDRSNVRLGKIEETEQSMQDIDSQLSEFTAWLDSVEGPLS  9237

Query  254    VLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAV  313
               L   T  +   ED   V+  ++Q QDLQ EIEAH  +  +L+++  K ++  +  D++ 
Sbjct  9238   SLYSQTEDKADREDRDRVRVWLQQQQDLQAEIEAHHSILSSLNQSGVKAVQDADSPDESH  9417

Query  314    LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAP  373
               LQ++LD +N +W+ +  +S  IR  LEA++++W  L  + +EL+ W++LK+D+L ++ P
Sbjct  9418   TLQKKLDTVNHRWTNIHDRSAEIRKRLEANAEEWNNLVRATEELVRWIRLKEDDLIKRQP  9597

Query  374    IGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPP  433
              +GGD+ ++Q+Q   H+ ++++L+ K+  +   L+   ++L EQ    L+ L  E     P
Sbjct  9598   VGGDYNSIQQQISDHKVYRQQLEEKQSAVERNLQMGSLYLAEQ--RDLD-LLSEKELTGP  9768

Query  434    EERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQA  493
              E  A N+   L+    ++   W KLN+ S +WQ K+DE   ++  L +A D+L  +L +A
Sbjct  9769   EAEAHNIVHKLKDSVTDLQDSWNKLNIKSENWQHKLDEMSTKMLALHQAMDKLSSRLHEA  9948

Query  494    EVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYN  553
              E  +  W PVGDL+IDSL  HL ++++ +   +P+ +++  V  +A       + LS  N
Sbjct  9949   EATRSRWLPVGDLIIDSLPQHLAELRSFQDYYSPIHDDLEKVTQMAGHFPAQQVSLSTVN  10128

Query  554    LSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYY  613
                 LED+  RWK LQ+A+++R R L+EA RDFGP SQHFL  SVQ PWERA++ NKVPY+
Sbjct  10129  QGRLEDIVRRWKTLQLAIDERARLLNEALRDFGPQSQHFLRASVQHPWERAVAANKVPYF  10308

Query  614    INHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDAL  673
              INH T+TT WDHP+MTEL+ SL DLN V+FSAYRT MKLRRLQK+LCL LL+L++A    
Sbjct  10309  INHGTETTHWDHPRMTELFHSLFDLNAVKFSAYRTGMKLRRLQKSLCLYLLNLASAESIF  10488

Query  674    DQHNL-KQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTG  732
               QH L   ND+ +D+ +II CL T+Y+ L  +H  +VNVP CVDMCLNWLLNVYDT R+G
Sbjct  10489  TQHELVSGNDRTLDVTEIITCLATVYENLAMDHPGMVNVPQCVDMCLNWLLNVYDTVRSG  10668

Query  733    RIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVA  792
              RIRVL+FK GI+ LC AHLEDKYR++ + VA   G  DQR LGLLLHD +QIPRQLGEVA
Sbjct  10669  RIRVLAFKVGIVMLCNAHLEDKYRFICRFVADKNGMIDQRGLGLLLHDCVQIPRQLGEVA  10848

Query  793    SFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK  852
              SFGGSNIEPSVRSCF    +KP IE A FL WM+LEPQSMVW+PVLHRVAA+ETAKHQAK
Sbjct  10849  SFGGSNIEPSVRSCFNMTGSKPLIEPAQFLAWMKLEPQSMVWMPVLHRVAASETAKHQAK  11028

Query  853    CNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDF  912
              CNICKECPI+G RYR LK FN+D+CQSCFFSGR AK HK+ +PM EYCT TTSGEDVRDF
Sbjct  11029  CNICKECPIVGLRYRCLKCFNFDLCQSCFFSGRKAKTHKLSHPMQEYCTTTTSGEDVRDF  11208

Query  913    AKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQ-LSHDDTHSRIEHYASRL  971
              AKV++NKF++KRY+ KHPR+GYLPVQ+VLEGD++E+P ++PQ +++ DTH+R+E YA+RL
Sbjct  11209  AKVVRNKFKSKRYYRKHPRVGYLPVQSVLEGDDLESPITTPQHMANQDTHTRLELYANRL  11388

Query  972    AEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERG  1031
              AE+E S G+ LN   S    ++DEH LI HYC SL  D   + P SPAQI++S+++E R 
Sbjct  11389  AEVE-SQGT-LN---SVPTDLEDEHQLIAHYCHSLGGDVS-TVPNSPAQIVVSIDAEHRP  11550

Query  1032   ELERILADLEEENRNLQAEYDRLK--QQHEHKGLSPLPSPPEMMPTSPQSP-RDAELIAE  1088
              +LE  + +LE+ENR L +E + LK  +  + K  + L +      TS +SP RDAEL+AE
Sbjct  11551  DLESQINELEDENRTLLSELETLKTLRSEDVKRAAELAASSGDERTSGRSPGRDAELVAE  11730

Query  1089   AKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQ-AEAKVNGTTVSSPSTSLQR  1147
              AKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLLEQPQ   A    ++ ++P+ S   
Sbjct  11731  AKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLEQPQDKSASQVSSSKTTPAVSPTS  11910

Query  1148   SDSSQPMLLRV-------------VGSQTSDSMGEE-----DLLSPPQDT----------  1179
              S SS     R+                  SD  GEE        +PP             
Sbjct  11911  SISSASKAKRIQHPIAIETRTNGGTSDYDSDMAGEEYNNHPSPHTPPHLKDDHHHHHHLH  12090

Query  1180   -------------STGLEEVMEQLNNSFPSSR-----GHN-VGSLFHMADDLGRAMESLV  1220
                              L++V+++LNN FP        G N VGSL HMAD++G+A+++LV
Sbjct  12091  QGGGAANGVQAKGKVDLDKVIQELNN-FPDGAKNGNVGQNSVGSLLHMADNIGKAVDTLV  12267

Query  1221   SVMTDEE  1227
              +VM+DEE
Sbjct  12268  TVMSDEE  12288


 Score = 58.9 bits (141),  Expect = 2e-05, Method: Compositional matrix adjust.
 Identities = 114/579 (19%), Positives = 239/579 (41%), Gaps = 68/579 (11%)
 Frame = +1

Query  25    WLSLLDQVIKSQRVMVG---DLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
             W    +Q  + +R M G    ++D  E   K KA    +E++R ++++L   AQ L    
Sbjct  6688  WYQFKNQTDQMERRMEGVDEQMKDGMEDEEKMKAIQGQIEEKRQEIQKLNQNAQQLNTDG  6867

Query  82    SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEML---------KDSTQW----LEA  128
             + Q A  ++     R+  QW E+++     R+ + E +         K S ++    +E 
Sbjct  6868  ARQVAEPVML----RMNTQWREIEQRFAQFRKPVREEVFVERTITEVKTSFKFEKTTIEQ  7035

Query  129   KEEAEQ------VLGQARAKLESW--KEGPYTVDAIQKKITET--------KQLAKDLRQ  172
             K  +E       +L +A A  +     +G   V  +     E+        K + + L  
Sbjct  7036  KSGSEPPADFSPLLAEANALCDRVVDTQGILKVPELTGAAFESFSVQEDHLKAIKESLDD  7215

Query  173   WQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQ  232
                +++   +    ++    A   +++  + + +  +W+ +++   ER    +      +
Sbjct  7216  LAPSIESVKEREHVVVSQVGATQRKEIQDVMDRLRENWQRLNREYEERHGQFQRCFDQWR  7395

Query  233   QFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVY  292
             QF  D+    +WL+EAE    ++QD+ R +  L     +++  K    L+  I  H  + 
Sbjct  7396  QFHCDMRDLASWLSEAE---RMIQDSKRADGRLH----IEKACKHQPVLEEGIATHQAMV  7554

Query  293   HNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHL  352
              +L+ N + I+ +   S D  +LQ +L+ +N +W  +  +  + +   E S ++ +    
Sbjct  7555  ASLNSNGEDIV-AQSSSVDGGMLQEKLEGLNARWKSVCAEVASWKDRFEFSPEKVEAFME  7731

Query  353   SLQELLVWLQLKDDELSRQA-PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
                 L  WL      +  QA P+  D  A ++     +  + +L+ K        E+V+I
Sbjct  7732  ECSHLQQWLSECQALIRPQAQPVPADATAFKELILKIKEREEDLQQKADEKQRIEESVQI  7911

Query  412   FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
              L+   +               +ER  ++    +K+ E +   WEK++     ++ +++E
Sbjct  7912  LLSGGSIS--------------QERGISI----KKETEALFKLWEKVSGTIPKFRAQLEE  8037

Query  472   TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDH-LEKVKALRGEIAPLKE  530
              LE+ +   E   ++   ++    +  +  PVG    +  QD  +   K +   +   +E
Sbjct  8038  KLEKTEAFLEELQQMRAWVQATMDVLETQGPVGSATSNDEQDSVVVDPKTMNEALKARQE  8217

Query  531   NVSHVNDLARQLT----TLGIQLSPYNLSTLEDLNTRWK  565
             N+  +N L  QLT        QL+      +E LNT W+
Sbjct  8218  NMDSINRLNTQLTAEAQAASRQLADPLREDVERLNTDWE  8334


 Score = 57.4 bits (137),  Expect = 5e-05, Method: Compositional matrix adjust.
 Identities = 69/356 (19%), Positives = 157/356 (44%), Gaps = 30/356 (8%)
 Frame = +1

Query  13    ADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLE----  68
             A +  A   LT WL+ + + +K + + V DL+++ + + + K     + ++R   +    
Sbjct  3358  ARYLEALKALTQWLASVQEALKEEEIFVSDLDELEDQLQRYKEVETTIGEQRSSYDYVNR  3537

Query  69    ---ELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQW  125
                EL+ AA     +TS Q A  I  D + ++   W++V    ++R+  L+  + +   W
Sbjct  3538  TGKELVVAA-----RTSKQ-AENIQKD-VTQLNRNWEDVTRLCEDRKALLDRSINELRLW  3696

Query  126   LEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLAL  185
             L+        +        + +     +D ++ ++ ++K L  D++  Q+N+D   +   
Sbjct  3697  LDEVSGLTSWMDDLDVFFTAEEVAMGDIDVLKDQLDQSKCLEDDIKTLQSNMDNILETGE  3876

Query  186   KLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWL  245
             +L+RD     + +     ++++  W+ +    +E    L E ++  Q    +++   + L
Sbjct  3877  RLIRDGDPAFSSRTRGELDDLHQRWKRVTGLATEHRTNLTEAYQRCQTLKANMQDLGSCL  4056

Query  246   TEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRS  305
                E   +       K+  ++D   ++  +K++     E+EA   V   + E ++K+ +S
Sbjct  4057  DRCEADLD-----PGKKFSIQDPAEIQTQLKKYMSALEELEAKEKVITEIQEVAEKVNQS  4221

Query  306   LEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWL  361
                S+   L++R        W+ +R +       L  +S  WKRL   L E ++W+
Sbjct  4222  ---SEVKTLVER--------WTVMRAQVTAKHKILSDASGSWKRLKQMLTEEVIWM  4356


 Score = 45.8 bits (107),  Expect = 0.15, Method: Compositional matrix adjust.
 Identities = 78/402 (19%), Positives = 156/402 (38%), Gaps = 46/402 (11%)
 Frame = +1

Query  87    RTIITDRIERIQNQWDEVQEHLQNRRQQLNEM----------LKDSTQWLEAKEEAEQVL  136
             R  I D ++R++  W  +    + R  Q              ++D   WL   E   Q  
Sbjct  7285  RKEIQDVMDRLRENWQRLNREYEERHGQFQRCFDQWRQFHCDMRDLASWLSEAERMIQDS  7464

Query  137   GQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDT  196
              +A  +L            I+K       L + +   Q  V   N     ++   S+ D 
Sbjct  7465  KRADGRLH-----------IEKACKHQPVLEEGIATHQAMVASLNSNGEDIVAQSSSVDG  7611

Query  197   RKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQ  256
               +    E +NA W+S+   V+  +   E +   ++ F  +      WL+E +       
Sbjct  7612  GMLQEKLEGLNARWKSVCAEVASWKDRFEFSPEKVEAFMEECSHLQQWLSECQALIR---  7782

Query  257   DATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQ  316
                + + +  D+   KEL+ + ++ + +++   D    ++E+ Q +L     S +  +  
Sbjct  7783  --PQAQPVPADATAFKELILKIKEREEDLQQKADEKQRIEESVQILLSGGSISQERGISI  7956

Query  317   RRLDNMNFK-WSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIG  375
             ++     FK W ++       R+ LE   ++ +     LQ++  W+Q   D L  Q P+G
Sbjct  7957  KKETEALFKLWEKVSGTIPKFRAQLEEKLEKTEAFLEELQQMRAWVQATMDVLETQGPVG  8136

Query  376   GDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEE  435
                      ND   +   + KT    + +  E          ++ + +L  +   L  E 
Sbjct  8137  S-----ATSNDEQDSVVVDPKTMNEALKARQEN---------MDSINRLNTQ---LTAEA  8265

Query  436   RA--QNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLER  475
             +A  + +   LR+  E +NT+WE++   +A  + + D  LER
Sbjct  8266  QAASRQLADPLREDVERLNTDWERIRYLAAHLRPRSDVELER  8391


 Score = 41.2 bits (95),  Expect = 3.3, Method: Compositional matrix adjust.
 Identities = 77/377 (20%), Positives = 170/377 (45%), Gaps = 30/377 (7%)
 Frame = +1

Query  42    DLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQ-  100
             DLE + E +  Q+  MQ L+Q R +  EL   A +++  ++   A       + R  N+ 
Sbjct  3094  DLEPVTEDL--QRIKMQ-LDQCRAKQTELAINASHMERLSTTAAALVTFDSTLSRSTNRD  3264

Query  101   -------WDEVQEHLQNRRQQLNEMLKDS--TQWLEAKEEAEQVLGQARAKLESWKEGPY  151
                    WD  +EHL  R + L E +  +   ++LEA +   Q L   +  L+  +    
Sbjct  3265  LKEFRHLWDTTREHLDEREKLLTEAMNSAPPARYLEALKALTQWLASVQEALKEEEIFVS  3444

Query  152   TVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENI---NA  208
              +D ++ ++   K++   + + +++ D  N    +L+   +A  +++   I +++   N 
Sbjct  3445  DLDELEDQLQRYKEVETTIGEQRSSYDYVNRTGKELV--VAARTSKQAENIQKDVTQLNR  3618

Query  209   SWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDS  268
             +W  + +   +R+A L+ +   L+ +  ++    +W+ + +         T +E  + D 
Sbjct  3619  NWEDVTRLCEDRKALLDRSINELRLWLDEVSGLTSWMDDLDVF------FTAEEVAMGDI  3780

Query  269   KGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRR--LDNMNFKW  326
               +K+ + Q + L+ +I+       N+ E  ++++R     D A   + R  LD+++ +W
Sbjct  3781  DVLKDQLDQSKCLEDDIKTLQSNMDNILETGERLIRD---GDPAFSSRTRGELDDLHQRW  3951

Query  327   SELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPA-VQKQN  385
               +   +   R++L  +  + + L  ++Q+L   L   + +L          PA +Q Q 
Sbjct  3952  KRVTGLATEHRTNLTEAYQRCQTLKANMQDLGSCLDRCEADLDPGKKFSIQDPAEIQTQL  4131

Query  386   DVHRAFKRELKTKEPVI  402
               + +   EL+ KE VI
Sbjct  4132  KKYMSALEELEAKEKVI  4182


>ref|XM_001918785.1| PREDICTED: Danio rerio hypothetical LOC794967 (LOC794967), mRNA
Length=2105

 Score = 1092 bits (2825),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 506/585 (86%), Positives = 555/585 (94%), Gaps = 3/585 (0%)
 Frame = +2

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
             NH+TQTTCWDHPKM ELYQSLADLNNVRFSAYRTAMKLRR+QKALCLDLLS+ AAC+A +
Sbjct  140   NHQTQTTCWDHPKMAELYQSLADLNNVRFSAYRTAMKLRRMQKALCLDLLSMPAACEAFE  319

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQN+Q MDI+Q+INCLT+IYDRLEQ+H++LVNVPLCVDMCLNWLLNVYDTGR G+I
Sbjct  320   QHNLKQNEQFMDIVQVINCLTSIYDRLEQQHSSLVNVPLCVDMCLNWLLNVYDTGRAGKI  499

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             R LSFKTGIISLCKAHLEDKYR+LF++VAS+TGFCDQRRLGLLLHD+IQIPRQLGEVASF
Sbjct  500   RTLSFKTGIISLCKAHLEDKYRFLFREVASATGFCDQRRLGLLLHDAIQIPRQLGEVASF  679

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPE+EA++FLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  680   GGSNIEPSVRSCFQFANNKPELEASVFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  859

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKM YPMVEYCTPTTSGEDVRDFAK
Sbjct  860   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMQYPMVEYCTPTTSGEDVRDFAK  1039

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRTKRYFAKHPRMGYLPVQT+LEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM
Sbjct  1040  VLKNKFRTKRYFAKHPRMGYLPVQTILEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  1219

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1034
             EN NGSY+ND++SPNES+DDEHLLIQHYCQSLNQ SPLSQP+SPAQILIS+E+EE+GELE
Sbjct  1220  ENRNGSYVNDNVSPNESMDDEHLLIQHYCQSLNQGSPLSQPQSPAQILISMETEEKGELE  1399

Query  1035  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             R+L DLE+ENR LQAEYDRLK+ H+HKGLSPLPSPP+M+P SPQSPRDAELIAEAKLLRQ
Sbjct  1400  RVLNDLEQENRKLQAEYDRLKKAHDHKGLSPLPSPPQMLPVSPQSPRDAELIAEAKLLRQ  1579

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1154
             HKGRLEARMQILEDHNKQLESQL RLRQLLE  Q E+KVNGT +SSPST+  RSD+S   
Sbjct  1580  HKGRLEARMQILEDHNKQLESQLTRLRQLLE--QTESKVNGTALSSPSTASPRSDTSLAS  1753

Query  1155  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
              LRV  SQT+++MG+++L SP QD STGLE+V+EQLNNSFP S+G
Sbjct  1754  -LRVAASQTTETMGDDELSSPTQDASTGLEDVIEQLNNSFPHSQG  1885


 Score = 50.1 bits (118),  Expect = 0.007, Method: Compositional matrix adjust.
 Identities = 22/32 (68%), Positives = 27/32 (84%), Gaps = 0/32 (0%)
 Frame = +1

Query  1196  SSRGHNVGSLFHMADDLGRAMESLVSVMTDEE  1227
             S RG NVGSLFHM D++G AMESLV V+T+E+
Sbjct  1900  SMRGPNVGSLFHMVDNIGHAMESLVHVITEEQ  1995


>gb|BC095190.1| Danio rerio dystrophin, mRNA (cDNA clone MGC:110165 IMAGE:7290297), 
complete cds
Length=2137

 Score = 1091 bits (2822),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 505/585 (86%), Positives = 555/585 (94%), Gaps = 3/585 (0%)
 Frame = +2

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
             NH+TQTTCWDHPKM ELYQSLADLNNVRFSAYRTAMKLRR+QKALCLDLLS+ AAC+A +
Sbjct  140   NHQTQTTCWDHPKMAELYQSLADLNNVRFSAYRTAMKLRRMQKALCLDLLSMPAACEAFE  319

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQN+Q MDI+Q+INCLT+IYDRLEQ+H++LVNVPLCVDMCLNWLLNVYDTGR G+I
Sbjct  320   QHNLKQNEQFMDIVQVINCLTSIYDRLEQQHSSLVNVPLCVDMCLNWLLNVYDTGRAGKI  499

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             R LSFKTGIISLCKAHLEDKYR+LF++VAS+TGFCDQRRLGLLLHD+IQIPRQLGEVASF
Sbjct  500   RTLSFKTGIISLCKAHLEDKYRFLFREVASATGFCDQRRLGLLLHDAIQIPRQLGEVASF  679

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPE+EA++FLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  680   GGSNIEPSVRSCFQFANNKPELEASVFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  859

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKM YPMVEYCTPTTSGEDVRDFAK
Sbjct  860   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMQYPMVEYCTPTTSGEDVRDFAK  1039

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRT+RYFAKHPRMGYLPVQT+LEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM
Sbjct  1040  VLKNKFRTERYFAKHPRMGYLPVQTILEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  1219

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELE  1034
             EN NGSY+ND++SPNES+DDEHLLIQHYCQSLNQ SPLSQP+SPAQILIS+E+EE+GELE
Sbjct  1220  ENRNGSYVNDNVSPNESMDDEHLLIQHYCQSLNQGSPLSQPQSPAQILISMETEEKGELE  1399

Query  1035  RILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             R+L DLE+ENR LQAEYDRLK+ H+HKGLSPLPSPP+M+P SPQSPRDAELIAEAKLLRQ
Sbjct  1400  RVLYDLEQENRKLQAEYDRLKKAHDHKGLSPLPSPPQMLPVSPQSPRDAELIAEAKLLRQ  1579

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1154
             HKGRLEARMQILEDHNKQLESQL RLRQLLE  Q E+KVNGT +SSPST+  RSD+S   
Sbjct  1580  HKGRLEARMQILEDHNKQLESQLTRLRQLLE--QTESKVNGTALSSPSTASPRSDTSLAS  1753

Query  1155  LLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
              LRV  SQT+++MG+++L SP QD STGLE+V+EQLNNSFP S+G
Sbjct  1754  -LRVAASQTTETMGDDELSSPTQDASTGLEDVIEQLNNSFPHSQG  1885


 Score = 50.1 bits (118),  Expect = 0.007, Method: Compositional matrix adjust.
 Identities = 22/32 (68%), Positives = 27/32 (84%), Gaps = 0/32 (0%)
 Frame = +1

Query  1196  SSRGHNVGSLFHMADDLGRAMESLVSVMTDEE  1227
             S RG NVGSLFHM D++G AMESLV V+T+E+
Sbjct  1900  SMRGPNVGSLFHMVDNIGHAMESLVHVITEEQ  1995


>ref|XM_001060977.1| PREDICTED: Rattus norvegicus similar to dystrophin, muscular 
dystrophy (LOC682316), mRNA
Length=7725

 Score = 1081 bits (2796),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 534/573 (93%), Positives = 553/573 (96%), Gaps = 0/573 (0%)
 Frame = +1

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             MPSSL+LEVPALADFNRAWTELTDWLSLLD+VIKSQRVMVGDLEDINEMIIKQKAT+QDL
Sbjct  6001  MPSSLLLEVPALADFNRAWTELTDWLSLLDRVIKSQRVMVGDLEDINEMIIKQKATLQDL  6180

Query  61    EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
             EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQ QWDEVQE LQNRRQQLNEMLK
Sbjct  6181  EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQIQWDEVQEQLQNRRQQLNEMLK  6360

Query  121   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
             DSTQWLEAKEEAEQV+GQAR KL+SWKEGP+T+DAIQKKITETKQLAKDLRQ Q NVDVA
Sbjct  6361  DSTQWLEAKEEAEQVIGQARGKLDSWKEGPHTMDAIQKKITETKQLAKDLRQRQINVDVA  6540

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             NDLALKLLRDYSADDTRKVHMITENIN SW +I KRVSEREAALEET RLLQQFPLDLEK
Sbjct  6541  NDLALKLLRDYSADDTRKVHMITENINTSWGNILKRVSEREAALEETQRLLQQFPLDLEK  6720

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
             FLAW+TEAETTANVLQDA+RKE+LLEDS+GV+ELMK WQDLQGEIEAHTD+YHNLDEN Q
Sbjct  6721  FLAWITEAETTANVLQDASRKEKLLEDSRGVRELMKPWQDLQGEIEAHTDIYHNLDENGQ  6900

Query  301   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
             KILRSLEGSD+A LLQRRLDNMNFKWSELRKKSLNIRSHLE SSDQWKRLHLSLQELLVW
Sbjct  6901  KILRSLEGSDEAPLLQRRLDNMNFKWSELRKKSLNIRSHLEVSSDQWKRLHLSLQELLVW  7080

Query  361   LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
             LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG
Sbjct  7081  LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  7260

Query  421   LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
             LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEW+KLNLHSADWQRKIDE LERLQELQ
Sbjct  7261  LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWDKLNLHSADWQRKIDEALERLQELQ  7440

Query  481   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLAR  540
             EA DELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENV+HVNDLA 
Sbjct  7441  EAADELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVNHVNDLAH  7620

Query  541   QLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVED  573
              LTTLGIQLSPYNLS LEDLNTRW+LLQ  V+D
Sbjct  7621  HLTTLGIQLSPYNLSILEDLNTRWRLLQSVVQD  7719


 Score = 41.6 bits (96),  Expect = 2.7, Method: Compositional matrix adjust.
 Identities = 75/371 (20%), Positives = 157/371 (42%), Gaps = 52/371 (14%)
 Frame = +1

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ + + L   L++ Q   +  N    ++ +   ++ ++K     E +   W+ +
Sbjct  2173  EIMEERLGKLQALQSSLKEQQNGFNYLNATVKEIAKKAPSEISQKYQSEFEEVEGRWKKL  2352

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               ++ E    LEE    L++F    +    W+ E         D   KE    L D++ +
Sbjct  2353  STQLVEHCQKLEEHMNKLRKFQNHKKTLQKWMAEV--------DVFLKEEWPALGDAEIL  2508

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L G+I+      ++++E  QKI +S    + A  L++ L  +N +W  + +
Sbjct  2509  KKQLKQCRLLVGDIQTIQPSLNSVNEGGQKI-KSEAEFEFASRLEKELKELNTQWDHICR  2685

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFPAVQKQNDVHRA  390
             +    +  L+A  D+   L   L E+  W+ Q +++ L R               ++ RA
Sbjct  2686  QVYTRKEALKAGLDKTVSLQKDLSEMHEWMTQAEEEYLERDFEYKTPDELQTAVEEMKRA  2865

Query  391   FKRELKTKEPVIMSTLETVRIFLTEQP-------------------------------LE  419
              K E   KE  +    ETV   +++ P                               LE
Sbjct  2866  -KEEALQKEAKVKLLTETVNSVISQAPPAAQEALKKELETLTTNYQWLCTRLNGKCKTLE  3042

Query  420   GLEKLYQEPRELPPEER--AQNVT------RLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
              LE L     E P + R  AQ +T       L+ ++ E  N+ W +L+  +   Q+ +++
Sbjct  3043  SLENLMHHSEENPNQIRLLAQTLTDGGVMDELINEELETFNSRWRELHEEAVRKQKLLEQ  3222

Query  472   TLERLQELQEA  482
             +++  QE++++
Sbjct  3223  SIQSAQEIEKS  3255


>gb|U43517.2|SCU43517 Scyliorhinus canicula dystrophin-related protein 2 (DRP2) mRNA, 
partial cds
Length=2502

 Score = 1078 bits (2789),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 520/831 (62%), Positives = 650/831 (78%), Gaps = 3/831 (0%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  WSE++KKS NIR+ LEA SD   +L LSLQE++ WL LKD+ELS Q P  GD  AV
Sbjct  19    MNLCWSEIKKKSQNIRARLEALSDHSGKLQLSLQEIIDWLTLKDEELSEQLPFTGDVDAV  198

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q+ N+ H AF  ++KTK P I++TLE+ + FL++ PL   E+  Q+ +++ P+++ QNV+
Sbjct  199   QRYNEFHSAFMEDVKTKGPFILATLESAQAFLSQHPLVETEEPAQD-KDMSPKQKIQNVS  375

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL+    D  R I+ T+ERL ELQ A DEL L L QAE ++ SW+
Sbjct  376   RFIWKQANVSSEMWEKLSARCIDRHRHIERTMERLLELQGAMDELSLALDQAEAVRDSWE  555

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
              VGDL IDSLQ+H+E  K  + E+  LK+ ++  NDLA QL    + LS  N   LE+L 
Sbjct  556   TVGDLFIDSLQEHIEPTKVFKEELGALKDGMTIANDLAHQLAISDVHLSTENTQRLEELT  735

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
             +RW+ LQ ++E+R++QL +AHRDFGP SQHFLSTSVQ PWERAISPNKVPYYINH+ QTT
Sbjct  736   SRWQALQTSIEERLKQLQDAHRDFGPGSQHFLSTSVQVPWERAISPNKVPYYINHQGQTT  915

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQSLA LNN++FSAYRTAMKLRR+QKAL LDLLS+++A +   Q+ L+Q+
Sbjct  916   CWDHPKMTELYQSLAALNNIKFSAYRTAMKLRRVQKALRLDLLSMASASNIFTQYKLQQS  1095

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             DQ +D+L+II CLT +YD LEQE   +VNVPL VDMCLNWLLNVYDTGR G+IRVLSFKT
Sbjct  1096  DQTIDVLEIIQCLTAMYDHLEQERGIIVNVPLSVDMCLNWLLNVYDTGRNGKIRVLSFKT  1275

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GII+LC + +E+KY+YL+KQV+ ST  CDQR L LLLH++IQIPRQLGEVASFGGSN+E 
Sbjct  1276  GIITLCNSEVEEKYQYLYKQVSDSTSLCDQRHLSLLLHEAIQIPRQLGEVASFGGSNVES  1455

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F N++P IEA  FL+WMRLEPQSMVWLPVLHR+  AE AKHQAKC+ICK+CPI
Sbjct  1456  SVRSCFRFVNDQPIIEATHFLEWMRLEPQSMVWLPVLHRLITAEAAKHQAKCHICKQCPI  1635

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KGHK+ YP++EYC PTTSGE+VRDFAK LKNKFR
Sbjct  1636  KGFRYRSLKQFNVDICQTCFLTGRASKGHKLRYPIMEYCAPTTSGENVRDFAKTLKNKFR  1815

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             TK+YF+KHP+ GYLPVQ+V++GD+++TPASSP L H DTHSRIEHYASRLAEME+ N S+
Sbjct  1816  TKQYFSKHPQRGYLPVQSVMDGDSIDTPASSPMLPHADTHSRIEHYASRLAEMESKNCSF  1995

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLE  1041
              + S+SP+ES+DDE L++Q++    +QDS  +   +P Q+L  L++EE+ ELE I+  LE
Sbjct  1996  FSGSLSPDESVDDEQLIVQYFSPETDQDSLQNPSHNPNQLLSVLDTEEKTELEAIIGHLE  2175

Query  1042  EENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEA  1101
              ENR LQ EY RLK QHE   +S   S  E  P+SP SPRD EL+AEA+LLRQHK RLE 
Sbjct  2176  HENRILQEEYRRLKWQHEEAAIS--SSVKEGSPSSPLSPRDTELLAEARLLRQHKTRLET  2349

Query  1102  RMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQ  1152
             RMQILEDHNKQLESQL RLR+LL QPQ +++ NG+T SS S S   SD++Q
Sbjct  2350  RMQILEDHNKQLESQLKRLRELLLQPQQDSEKNGSTASSASPSSHHSDNNQ  2502


 Score = 60.5 bits (145),  Expect = 6e-06, Method: Compositional matrix adjust.
 Identities = 54/234 (23%), Positives = 104/234 (44%), Gaps = 32/234 (13%)
 Frame = +1

Query  21   ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
            E+ DWL+L D+ +  Q    GD++ +        A M+D++ + P +   + +AQ   ++
Sbjct  121  EIIDWLTLKDEELSEQLPFTGDVDAVQRYNEFHSAFMEDVKTKGPFILATLESAQAFLSQ  300

Query  81   TSNQEARTIITDR----IERIQN--------------QWDEVQEHLQNRRQQLNEMLKDS  122
                E      D+     ++IQN               W+++     +R + +   ++  
Sbjct  301  HPLVETEEPAQDKDMSPKQKIQNVSRFIWKQANVSSEMWEKLSARCIDRHRHIERTMERL  480

Query  123  TQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVAN  181
             +   A +E    L QA A  +SW+  G   +D++Q+ I  TK   ++L   +  + +AN
Sbjct  481  LELQGAMDELSLALDQAEAVRDSWETVGDLFIDSLQEHIEPTKVFKEELGALKDGMTIAN  660

Query  182  DLALKLLRDYSADDTRKVHMITEN------INASWRSIHKRVSEREAALEETHR  229
            DLA +L           VH+ TEN      + + W+++   + ER   L++ HR
Sbjct  661  DLAHQLA-------ISDVHLSTENTQRLEELTSRWQALQTSIEERLKQLQDAHR  801


>ref|XM_002187321.1| PREDICTED: Taeniopygia guttata similar to Dystrophin related 
protein 2 (LOC100222379), mRNA
Length=2703

 Score = 1025 bits (2649),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 491/880 (55%), Positives = 661/880 (75%), Gaps = 14/880 (1%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS ++R+ LEA SD   +L + LQE++ WL  KD+ELS Q P+ GD   V
Sbjct  82    MNLCWNEIKKKSHSLRARLEAFSDHSGKLQVPLQEIIDWLGQKDEELSAQLPLRGDVLLV  261

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K++ P I S LE+ + FL++ P E LE+   E +++ P  R QN++
Sbjct  262   QQEKETHTAFMEEVKSRGPYIYSVLESAQAFLSQHPFEELEEPTLESKDVSPRHRIQNIS  441

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE+L E++ A +EL + L QAE ++ +W+
Sbjct  442   RFVWKQANVASELWEKLTARCVDQHRHIERTLEQLLEIKGAMEELSMTLDQAESVRETWE  621

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++  K  + E++P+K+ V  VNDLA QL    + L   N  TLE +N
Sbjct  622   PIGDLFIDSLPEHIQSTKLFKEELSPVKDGVKVVNDLAHQLAISDVHLCMENSRTLEQIN  801

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
             TRWK LQ ++ +R++QL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTT
Sbjct  802   TRWKQLQASINERLKQLQDAHRDFGPGSQHFLSSSVQVPWERAISPNKVPYYINHQAQTT  981

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LD+++L+ A +  ++H+L+ +
Sbjct  982   CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDMVTLATALEIFNEHDLQPS  1161

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             D+ MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1162  DRAMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1341

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K++YLF QVA++ G CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1342  GIACLCGTEVKEKFQYLFSQVANAGGLCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEP  1521

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             S+RSCF+F+N K  IEA+ FL+W  LEPQSMVWL VLHRVA AE  KHQ KC++C++CPI
Sbjct  1522  SIRSCFRFSNGKSAIEASQFLEWANLEPQSMVWLAVLHRVAMAEQVKHQTKCSVCRQCPI  1701

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  1702  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  1881

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K+YF+KHP+ GYLPVQ+VLE D  ETPASSP L H DTHSRIEH+ASRLAEME+ N S+
Sbjct  1882  SKQYFSKHPQRGYLPVQSVLEADFSETPASSPMLPHADTHSRIEHFASRLAEMESQNCSF  2061

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLS--QPRSPAQILISLESEERGELERILAD  1039
              +DS+SP++S+D++  L++H        SP++  +P    Q+   L  +++GELER+LA 
Sbjct  2062  FSDSLSPDDSLDEDQYLLRH-------SSPITDREPGGSQQLPGGLNMDDKGELERVLAH  2220

Query  1040  LEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRL  1099
             LE+ENR LQ E  RLK QH+    S  PS     P S Q PR+ EL+AEA++LRQHK RL
Sbjct  2221  LEDENRILQGELRRLKWQHDEAVES--PSLATGSPGSVQDPRNEELLAEARILRQHKSRL  2394

Query  1100  EARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVV  1159
             E RMQILEDHNKQLESQLHRLR+LL QP AE++ NG+  SS ++S  +S+ SQ    +  
Sbjct  2395  ETRMQILEDHNKQLESQLHRLRELLLQPPAESEGNGSAASSLASSPHQSEGSQA---KEK  2565

Query  1160  GSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
                T D+   +++ +  Q+ S  LE++ME+L ++FP+SRG
Sbjct  2566  EHNTPDTETADEVEAKTQEVSMCLEDIMEKLRSAFPTSRG  2685


 Score = 57.8 bits (138),  Expect = 4e-05, Method: Compositional matrix adjust.
 Identities = 55/235 (23%), Positives = 104/235 (44%), Gaps = 33/235 (14%)
 Frame = +1

Query  21   ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
            E+ DWL   D+ + +Q  + GD+  + +      A M++++ R P +  ++ +AQ   ++
Sbjct  184  EIIDWLGQKDEELSAQLPLRGDVLLVQQEKETHTAFMEEVKSRGPYIYSVLESAQAFLSQ  363

Query  81   TSNQEAR--TIITDRI---ERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
               +E    T+ +  +    RIQN               W+++     ++ + +   L+ 
Sbjct  364  HPFEELEEPTLESKDVSPRHRIQNISRFVWKQANVASELWEKLTARCVDQHRHIERTLEQ  543

Query  122  STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              +   A EE    L QA +  E+W+  G   +D++ + I  TK   ++L   +  V V 
Sbjct  544  LLEIKGAMEELSMTLDQAESVRETWEPIGDLFIDSLPEHIQSTKLFKEELSPVKDGVKVV  723

Query  181  NDLALKLLRDYSADDTRKVHMITEN------INASWRSIHKRVSEREAALEETHR  229
            NDLA +L           VH+  EN      IN  W+ +   ++ER   L++ HR
Sbjct  724  NDLAHQLA-------ISDVHLCMENSRTLEQINTRWKQLQASINERLKQLQDAHR  867


>gb|U43519.1|HSU43519 Human dystrophin-related protein 2 (DRP2) mRNA, complete cds
Length=3499

 Score = 1005 bits (2598),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 498/884 (56%), Positives = 656/884 (74%), Gaps = 16/884 (1%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L LQE++ WL  KD+ELS Q P+ GD   V
Sbjct  553   MNLCWNEIKKKSHNLRARLEAFSDHSGKLQLPLQEIIDWLSQKDEELSAQLPLQGDVALV  732

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K++ P I S LE+ + FL++ P E LE+ + E ++  P++R QN++
Sbjct  733   QQEKETHAAFMEEVKSRAPYIYSVLESAQAFLSQHPFEELEEPHSESKDTSPKQRIQNLS  912

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE+L E+Q A +EL   L QAE ++ +W+
Sbjct  913   RFVWKQATVASELWEKLTARCVDQHRHIERTLEQLLEIQGAMEELSTTLSQAEGVRATWE  1092

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  1093  PIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLVNDLAHQLAISDVHLSMENSQALEQIN  1272

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQ +V++R++QL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTT
Sbjct  1273  VRWKQLQASVDERLKQLQDAHRDFGPGSQHFLSSSVQVPWERAISPNKVPYYINHQAQTT  1452

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1453  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1632

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1633  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1812

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1813  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEP  1992

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWLPVLHRV  AE  KHQ KC+IC++CPI
Sbjct  1993  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLPVLHRVTIAEQVKHQTKCSICRQCPI  2172

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  2173  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2352

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K YF+KHP+ GYLPVQ+VLE D  ETPASSP   H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2353  SKHYFSKHPQRGYLPVQSVLEADYSETPASSPMWPHADTHSRIEHFASRLAEMESQNCSF  2532

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GEL++ILA
Sbjct  2533  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSVATESKGELQKILA  2688

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
              LE+ENR LQ E  RLK QHE    +  PS  +    +    R+ EL+AEA++LRQHK R
Sbjct  2689  HLEDENRILQGELRRLKWQHEEAAEA--PSLADGSTEAATDHRNEELLAEARILRQHKSR  2862

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RMQILEDHNKQLESQL RLR+LL QP  E+  +G+  SS ++S Q+S+ S P   R 
Sbjct  2863  LETRMQILEDHNKQLESQLQRLRELLLQPPTESDGSGSAGSSLASSPQQSEGSHP---RE  3033

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
              G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  3034  KGQTTPDTEAADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  3165


 Score = 55.8 bits (133),  Expect = 1e-04, Method: Compositional matrix adjust.
 Identities = 53/235 (22%), Positives = 100/235 (42%), Gaps = 33/235 (14%)
 Frame = +1

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ R P +  ++ +AQ   ++
Sbjct  655   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSRAPYIYSVLESAQAFLSQ  834

Query  81    TSNQE-----ARTIITDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E     + +  T   +RIQN               W+++     ++ + +   L+ 
Sbjct  835   HPFEELEEPHSESKDTSPKQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIERTLEQ  1014

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  1015  LLEIQGAMEELSTTLSQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLV  1194

Query  181   NDLALKLLRDYSADDTRKVHMITEN------INASWRSIHKRVSEREAALEETHR  229
             NDLA +L           VH+  EN      IN  W+ +   V ER   L++ HR
Sbjct  1195  NDLAHQLA-------ISDVHLSMENSQALEQINVRWKQLQASVDERLKQLQDAHR  1338


>ref|XM_001493019.2| PREDICTED: Equus caballus dystrophin related protein 2 (DRP2), 
mRNA
Length=3631

 Score = 1003 bits (2592),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 497/883 (56%), Positives = 655/883 (74%), Gaps = 14/883 (1%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L LQE++ WL  KD+ELS Q P+ GD   V
Sbjct  550   MNLCWNEIKKKSHNLRARLEAFSDHSGKLQLPLQEIIDWLSQKDEELSAQLPLRGDVALV  729

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  ++K++ P I S LE+ + FL++ P E LE+ + E ++  P +R QN++
Sbjct  730   QQEKETHAAFMEDVKSRGPYIYSVLESAQAFLSQHPFEELEEPHSESKDTSPRQRIQNLS  909

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE+L E+Q A +EL   L QAE ++ +W+
Sbjct  910   RFVWKQATVASELWEKLTARCVDQHRHIERTLEQLLEIQGAMEELSTTLTQAEGVRATWE  1089

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  1090  PIGDLFIDSLPEHIQALKLFKEEFSPMKDGVKLVNDLAHQLAISDVHLSMENSRALEQIN  1269

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQ +V +R++QL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTT
Sbjct  1270  VRWKQLQGSVGERLKQLQDAHRDFGPGSQHFLSSSVQVPWERAISPNKVPYYINHQAQTT  1449

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1450  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1629

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1630  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1809

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1810  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEP  1989

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1990  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  2169

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  2170  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2349

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K YF+KHP+ GYLPVQ+VLE D  ETPASSP L H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2350  SKHYFSKHPQRGYLPVQSVLEADYSETPASSPMLPHADTHSRIEHFASRLAEMESQNCSF  2529

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLS--QPRSPAQILISLESEERGELERILAD  1039
              NDS+SP++SID++  L++H        SP++  +P    Q   S+ +E +GELE+ILA 
Sbjct  2530  FNDSLSPDDSIDEDQYLLRH-------SSPITDREPGFGQQAPCSMATESKGELEKILAH  2688

Query  1040  LEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRL  1099
             LE+ENR LQ E  RLK QHE    +  P+  +      Q  R+ EL+AEA++LRQHK RL
Sbjct  2689  LEDENRILQGELRRLKWQHEEAAEA--PTLADGSAEVAQDHRNEELLAEARILRQHKSRL  2862

Query  1100  EARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVV  1159
             E RMQILEDHNKQLESQL RLR+LL QP  E++ NG+  SS ++S Q+S+SS P   +  
Sbjct  2863  ETRMQILEDHNKQLESQLQRLRELLLQPPTESEGNGSAGSSLASSPQQSESSHP---QEK  3033

Query  1160  GSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  3034  GQTTPDTEAADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  3162


 Score = 56.6 bits (135),  Expect = 8e-05, Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 100/235 (42%), Gaps = 33/235 (14%)
 Frame = +1

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M+D++ R P +  ++ +AQ   ++
Sbjct  652   EIIDWLSQKDEELSAQLPLRGDVALVQQEKETHAAFMEDVKSRGPYIYSVLESAQAFLSQ  831

Query  81    TSNQE-----ARTIITDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E     + +  T   +RIQN               W+++     ++ + +   L+ 
Sbjct  832   HPFEELEEPHSESKDTSPRQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIERTLEQ  1011

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  1012  LLEIQGAMEELSTTLTQAEGVRATWEPIGDLFIDSLPEHIQALKLFKEEFSPMKDGVKLV  1191

Query  181   NDLALKLLRDYSADDTRKVHMITEN------INASWRSIHKRVSEREAALEETHR  229
             NDLA +L           VH+  EN      IN  W+ +   V ER   L++ HR
Sbjct  1192  NDLAHQLA-------ISDVHLSMENSRALEQINVRWKQLQGSVGERLKQLQDAHR  1335


>dbj|AK295843.1| Homo sapiens cDNA FLJ52301 complete cds, highly similar to Dystrophin-related 
protein 2
Length=2921

 Score = 1002 bits (2590),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 497/884 (56%), Positives = 654/884 (73%), Gaps = 16/884 (1%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L LQE++ WL  KD+ELS Q P+ GD   V
Sbjct  190   MNLCWNEIKKKSHNLRARLEAFSDHSGKLQLPLQEIIDWLSQKDEELSAQLPLQGDVALV  369

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K++ P I S LE+ + FL++ P E LE+ + E ++  P++R QN++
Sbjct  370   QQEKETHAAFMEEVKSRGPYIYSVLESAQAFLSQHPFEELEEPHSESKDTSPKQRIQNLS  549

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE+L E+Q A +EL   L QAE ++ +W+
Sbjct  550   RFVWKQATVASELWEKLTARCVDQHRHIERTLEQLLEIQGAMEELSTTLSQAEGVRATWE  729

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  730   PIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLVNDLAHQLAISDVHLSMENSQALEQIN  909

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQ +V +R++QL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTT
Sbjct  910   VRWKQLQASVSERLKQLQDAHRDFGPGSQHFLSSSVQVPWERAISPNKVPYYINHQAQTT  1089

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1090  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1269

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1270  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1449

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1450  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEP  1629

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1630  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  1809

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  1810  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  1989

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K YF+KHP+ GYLPVQ+VLE D  ETPASSP   H DTHSRIEH+ASRLAEME+ N S+
Sbjct  1990  SKHYFSKHPQRGYLPVQSVLEADYSETPASSPMWPHADTHSRIEHFASRLAEMESQNCSF  2169

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GEL++ILA
Sbjct  2170  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSVATESKGELQKILA  2325

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
              LE+ENR LQ E  RLK QHE    +  PS  +    +    R+ EL+AEA++LRQHK R
Sbjct  2326  HLEDENRILQGELRRLKWQHEEAAEA--PSLADGSTEAATDHRNEELLAEARILRQHKSR  2499

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RMQILEDHNKQLESQL RLR+LL QP  E+  +G+  SS ++S Q+S+ S P   R 
Sbjct  2500  LETRMQILEDHNKQLESQLQRLRELLLQPPTESDGSGSAGSSLASSPQQSEGSHP---RE  2670

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
              G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  2671  KGQTTPDTEAADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  2802


 Score = 57.0 bits (136),  Expect = 7e-05, Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 101/235 (42%), Gaps = 33/235 (14%)
 Frame = +1

Query  21   ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
            E+ DWLS  D+ + +Q  + GD+  + +      A M++++ R P +  ++ +AQ   ++
Sbjct  292  EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSRGPYIYSVLESAQAFLSQ  471

Query  81   TSNQE-----ARTIITDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
               +E     + +  T   +RIQN               W+++     ++ + +   L+ 
Sbjct  472  HPFEELEEPHSESKDTSPKQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIERTLEQ  651

Query  122  STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  652  LLEIQGAMEELSTTLSQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLV  831

Query  181  NDLALKLLRDYSADDTRKVHMITEN------INASWRSIHKRVSEREAALEETHR  229
            NDLA +L           VH+  EN      IN  W+ +   VSER   L++ HR
Sbjct  832  NDLAHQLA-------ISDVHLSMENSQALEQINVRWKQLQASVSERLKQLQDAHR  975


>gb|BC162218.1| Danio rerio dystrophin related protein 2, mRNA (cDNA clone MGC:193759 
IMAGE:9037842), complete cds
Length=2716

 Score = 1002 bits (2590),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 496/878 (56%), Positives = 640/878 (72%), Gaps = 13/878 (1%)
 Frame = +2

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E+++KS NIR  LEA SD   +L LSLQE++ WL  KD+ELS Q PIGGD  AV
Sbjct  92    MNLCWNEIKRKSHNIRVRLEAFSDNSGKLQLSLQEIIEWLTAKDEELSEQLPIGGDVGAV  271

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q Q + H+AF  ++K++ P I S LE+ + FL + P +  E+   + +E+ P  R  NV+
Sbjct  272   QHQREFHQAFMEDVKSRGPYIYSVLESAQTFLAQHPFQEPEETLPDGKEVSPRRRMLNVS  451

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R ++ TLERL ++Q A +EL   L QAE ++ +W+
Sbjct  452   RSVWKQANVASDLWEKLTARCVDRHRHMERTLERLLQIQAAMEELAAALEQAEGVRDAWE  631

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             PVGDL IDSLQDH++  K  + E++ +KE + H+NDLA +L    + LS  N   LE LN
Sbjct  632   PVGDLFIDSLQDHIDATKLFKEELSQVKEGMKHINDLAHELAISDVHLSMDNARALEHLN  811

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWKLLQ ++E+R++QL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTT
Sbjct  812   NRWKLLQGSIEERLKQLQDAHRDFGPGSQHFLSSSVQIPWERAISPNKVPYYINHQAQTT  991

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLR +QKAL LDL  LS+  D   +  L+  
Sbjct  992   CWDHPKMTELYQALADLNNIKFSAYRTAMKLRHVQKALRLDLFKLSSVVDVFREQELQHG  1171

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+ LT++Y+RLE+E + L+N+PLCVDMCLNWLLNVYD+GR G++RVLSFK 
Sbjct  1172  EHVMDVVEVIHALTSLYERLEEERSVLINIPLCVDMCLNWLLNVYDSGRNGKMRVLSFKM  1351

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             G++ LC A +++KY+YLF+QV    G  DQ+ L LLLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1352  GLVILCNADIQEKYKYLFRQVCGPGGLTDQKHLSLLLHEAIQVPRQLGEVAAFGGSNVEP  1531

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+  + K  IE + FL+WM LEPQS+VWLPVLHRV  AETAKHQA+C ICK+CPI
Sbjct  1532  SVRSCFRMVSGKSAIELSHFLEWMSLEPQSVVWLPVLHRVTVAETAKHQARCYICKQCPI  1711

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR  KG K+HYP++EY TPTTSGE +RDFAK LKNKFR
Sbjct  1712  KGFRYRSLKQFNVDICQTCFLTGRTTKGKKLHYPIMEYYTPTTSGEKMRDFAKTLKNKFR  1891

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K+YF+KHP+ GYLPVQ+VLE ++ ETP SSP+L H DTHSRIEH+ASRLAEMEN N S+
Sbjct  1892  SKQYFSKHPQRGYLPVQSVLEVESSETPCSSPRLPHADTHSRIEHFASRLAEMENQNCSF  2071

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLE  1041
               DS+SP+ES+D++  L++H   SL QDSP         +L  L+ ++R EL+R L  LE
Sbjct  2072  FTDSLSPDESLDEDQYLLRHSSPSLEQDSP------HGLMLAQLDCQDREELQRTLHRLE  2233

Query  1042  EENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEA  1101
              ENR LQ EY RLK +HE    S  P   E  P SP   +D EL+AEA++LRQHK RLE 
Sbjct  2234  NENRVLQGEYRRLKWKHEEAAAS--PQLLESGPGSPPGQQDEELLAEARVLRQHKTRLET  2407

Query  1102  RMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGS  1161
             RMQILEDHNKQLESQL RLR+LL QP+ +++ NG+  SS S+ +      +P        
Sbjct  2408  RMQILEDHNKQLESQLRRLRELLLQPKDDSEANGSAPSSLSSPVSGGHQGEP-----PSR  2572

Query  1162  QTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
             +T+D+    + L   QDT   L++V+EQL N FPS  G
Sbjct  2573  ETTDTEAAGEDLDHEQDTVLQLQQVIEQLRNVFPSEPG  2686


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 56/232 (24%), Positives = 103/232 (44%), Gaps = 27/232 (11%)
 Frame = +2

Query  21   ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
            E+ +WL+  D+ +  Q  + GD+  +       +A M+D++ R P +  ++ +AQ    +
Sbjct  194  EIIEWLTAKDEELSEQLPIGGDVGAVQHQREFHQAFMEDVKSRGPYIYSVLESAQTFLAQ  373

Query  81   TSNQEARTIITDRIE-----RIQNQ--------------WDEVQEHLQNRRQQLNEMLKD  121
               QE    + D  E     R+ N               W+++     +R + +   L+ 
Sbjct  374  HPFQEPEETLPDGKEVSPRRRMLNVSRSVWKQANVASDLWEKLTARCVDRHRHMERTLER  553

Query  122  STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              Q   A EE    L QA    ++W+  G   +D++Q  I  TK   ++L Q +  +   
Sbjct  554  LLQIQAAMEELAAALEQAEGVRDAWEPVGDLFIDSLQDHIDATKLFKEELSQVKEGMKHI  733

Query  181  NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
            NDLA +L + D   S D+ R +    E++N  W+ +   + ER   L++ HR
Sbjct  734  NDLAHELAISDVHLSMDNARAL----EHLNNRWKLLQGSIEERLKQLQDAHR  877


>ref|XM_001092374.1| PREDICTED: Macaca mulatta dystrophin related protein 2 (DRP2), 
mRNA
Length=5387

 Score = 1001 bits (2589),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 499/886 (56%), Positives = 653/886 (73%), Gaps = 20/886 (2%)
 Frame = +3

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L LQE++ WL  KD+ELS Q P+ GD   V
Sbjct  759   MNLCWNEIKKKSHNLRARLEAFSDHSGKLQLPLQEIIDWLSQKDEELSAQLPLQGDVALV  938

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K++ P I S LE+ + FL++ P E LE+ + E ++  P+ R QN++
Sbjct  939   QQEKETHAAFMEEVKSRGPYIYSVLESAQAFLSQHPFEELEEPHSESKDTSPKRRIQNLS  1118

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE+L E+Q A +EL   L QAE ++ +W+
Sbjct  1119  RFVWKQATVASELWEKLTARCVDQHRHIERTLEQLLEIQGAMEELSTTLSQAEGVRATWE  1298

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  1299  PIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLVNDLAHQLAISDVHLSMENSHALEQIN  1478

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQ +V +R++QL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTT
Sbjct  1479  VRWKQLQASVSERLKQLQDAHRDFGPGSQHFLSSSVQVPWERAISPNKVPYYINHQAQTT  1658

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1659  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1838

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1839  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  2018

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  2019  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEP  2198

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  2199  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  2378

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  2379  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2558

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K YF+KHP+ GYLPVQ+VLE D  ETPASSP L H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2559  SKHYFSKHPQRGYLPVQSVLEADYSETPASSPMLPHADTHSRIEHFASRLAEMESQNCSF  2738

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GEL++ILA
Sbjct  2739  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSVATESKGELQKILA  2894

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPL--PSPPEMMPTSPQSPRDAELIAEAKLLRQHK  1096
              LE+ENR LQ E  RLK QHE    +P       E  P      R+ EL+AEA++LRQHK
Sbjct  2895  HLEDENRILQGELRRLKWQHEEAAEAPTLADGSTEAAPDH----RNEELLAEARILRQHK  3062

Query  1097  GRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLL  1156
              RLE RMQILEDHNKQLESQL RLR+LL QP  E+  +G+  SS ++S Q+S+ S P   
Sbjct  3063  SRLETRMQILEDHNKQLESQLQRLRELLLQPPTESDGSGSAGSSLASSPQQSEGSHP---  3233

Query  1157  RVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             R  G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  3234  REKGQTTPDTEAADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  3371


 Score = 57.0 bits (136),  Expect = 7e-05, Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 100/235 (42%), Gaps = 33/235 (14%)
 Frame = +3

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ R P +  ++ +AQ   ++
Sbjct  861   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSRGPYIYSVLESAQAFLSQ  1040

Query  81    TSNQE-----ARTIITDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E     + +  T    RIQN               W+++     ++ + +   L+ 
Sbjct  1041  HPFEELEEPHSESKDTSPKRRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIERTLEQ  1220

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  1221  LLEIQGAMEELSTTLSQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLV  1400

Query  181   NDLALKLLRDYSADDTRKVHMITEN------INASWRSIHKRVSEREAALEETHR  229
             NDLA +L           VH+  EN      IN  W+ +   VSER   L++ HR
Sbjct  1401  NDLAHQLA-------ISDVHLSMENSHALEQINVRWKQLQASVSERLKQLQDAHR  1544


>ref|NM_001939.2| Homo sapiens dystrophin related protein 2 (DRP2), mRNA
Length=7118

 Score = 1001 bits (2588),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 497/884 (56%), Positives = 654/884 (73%), Gaps = 16/884 (1%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L LQE++ WL  KD+ELS Q P+ GD   V
Sbjct  604   MNLCWNEIKKKSHNLRARLEAFSDHSGKLQLPLQEIIDWLSQKDEELSAQLPLQGDVALV  783

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K++ P I S LE+ + FL++ P E LE+ + E ++  P++R QN++
Sbjct  784   QQEKETHAAFMEEVKSRGPYIYSVLESAQAFLSQHPFEELEEPHSESKDTSPKQRIQNLS  963

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE+L E+Q A +EL   L QAE ++ +W+
Sbjct  964   RFVWKQATVASELWEKLTARCVDQHRHIERTLEQLLEIQGAMEELSTTLSQAEGVRATWE  1143

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  1144  PIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLVNDLAHQLAISDVHLSMENSQALEQIN  1323

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQ +V +R++QL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTT
Sbjct  1324  VRWKQLQASVSERLKQLQDAHRDFGPGSQHFLSSSVQVPWERAISPNKVPYYINHQAQTT  1503

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1504  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1683

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1684  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1863

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1864  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEP  2043

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  2044  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  2223

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  2224  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2403

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K YF+KHP+ GYLPVQ+VLE D  ETPASSP   H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2404  SKHYFSKHPQRGYLPVQSVLEADYSETPASSPMWPHADTHSRIEHFASRLAEMESQNCSF  2583

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GEL++ILA
Sbjct  2584  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSVATESKGELQKILA  2739

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
              LE+ENR LQ E  RLK QHE    +  PS  +    +    R+ EL+AEA++LRQHK R
Sbjct  2740  HLEDENRILQGELRRLKWQHEEAAEA--PSLADGSTEAATDHRNEELLAEARILRQHKSR  2913

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RMQILEDHNKQLESQL RLR+LL QP  E+  +G+  SS ++S Q+S+ S P   R 
Sbjct  2914  LETRMQILEDHNKQLESQLQRLRELLLQPPTESDGSGSAGSSLASSPQQSEGSHP---RE  3084

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
              G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  3085  KGQTTPDTEAADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  3216


 Score = 57.4 bits (137),  Expect = 5e-05, Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 101/235 (42%), Gaps = 33/235 (14%)
 Frame = +1

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ R P +  ++ +AQ   ++
Sbjct  706   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSRGPYIYSVLESAQAFLSQ  885

Query  81    TSNQE-----ARTIITDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E     + +  T   +RIQN               W+++     ++ + +   L+ 
Sbjct  886   HPFEELEEPHSESKDTSPKQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIERTLEQ  1065

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  1066  LLEIQGAMEELSTTLSQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLV  1245

Query  181   NDLALKLLRDYSADDTRKVHMITEN------INASWRSIHKRVSEREAALEETHR  229
             NDLA +L           VH+  EN      IN  W+ +   VSER   L++ HR
Sbjct  1246  NDLAHQLA-------ISDVHLSMENSQALEQINVRWKQLQASVSERLKQLQDAHR  1389


>gb|BC111695.1| Homo sapiens dystrophin related protein 2, mRNA (cDNA clone MGC:133255 
IMAGE:40036070), complete cds
Length=3191

 Score = 1001 bits (2588),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 497/884 (56%), Positives = 654/884 (73%), Gaps = 16/884 (1%)
 Frame = +3

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L LQE++ WL  KD+ELS Q P+ GD   V
Sbjct  441   MNLCWNEIKKKSHNLRARLEAFSDHSGKLQLPLQEIIDWLSQKDEELSAQLPLQGDVALV  620

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K++ P I S LE+ + FL++ P E LE+ + E ++  P++R QN++
Sbjct  621   QQEKETHAAFMEEVKSRGPYIYSVLESAQAFLSQHPFEELEEPHSESKDTSPKQRIQNLS  800

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE+L E+Q A +EL   L QAE ++ +W+
Sbjct  801   RFVWKQATVASELWEKLTARCVDQHRHIERTLEQLLEIQGAMEELSTTLSQAEGVRATWE  980

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  981   PIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLVNDLAHQLAISDVHLSMENSQALEQIN  1160

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQ +V +R++QL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTT
Sbjct  1161  VRWKQLQASVSERLKQLQDAHRDFGPGSQHFLSSSVQVPWERAISPNKVPYYINHQAQTT  1340

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1341  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1520

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1521  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1700

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1701  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEP  1880

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1881  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  2060

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  2061  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2240

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K YF+KHP+ GYLPVQ+VLE D  ETPASSP   H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2241  SKHYFSKHPQRGYLPVQSVLEADYSETPASSPMWPHADTHSRIEHFASRLAEMESQNCSF  2420

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GEL++ILA
Sbjct  2421  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSVATESKGELQKILA  2576

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
              LE+ENR LQ E  RLK QHE    +  PS  +    +    R+ EL+AEA++LRQHK R
Sbjct  2577  HLEDENRILQGELRRLKWQHEEAAEA--PSLADGSTEAATDHRNEELLAEARILRQHKSR  2750

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RMQILEDHNKQLESQL RLR+LL QP  E+  +G+  SS ++S Q+S+ S P   R 
Sbjct  2751  LETRMQILEDHNKQLESQLQRLRELLLQPPTESDGSGSAGSSLASSPQQSEGSHP---RE  2921

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
              G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  2922  KGQTTPDTEAADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  3053


 Score = 57.4 bits (137),  Expect = 5e-05, Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 101/235 (42%), Gaps = 33/235 (14%)
 Frame = +3

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ R P +  ++ +AQ   ++
Sbjct  543   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSRGPYIYSVLESAQAFLSQ  722

Query  81    TSNQE-----ARTIITDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E     + +  T   +RIQN               W+++     ++ + +   L+ 
Sbjct  723   HPFEELEEPHSESKDTSPKQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIERTLEQ  902

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  903   LLEIQGAMEELSTTLSQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLV  1082

Query  181   NDLALKLLRDYSADDTRKVHMITEN------INASWRSIHKRVSEREAALEETHR  229
             NDLA +L           VH+  EN      IN  W+ +   VSER   L++ HR
Sbjct  1083  NDLAHQLA-------ISDVHLSMENSQALEQINVRWKQLQASVSERLKQLQDAHR  1226


>gb|DQ443728.1| Danio rerio dystrophin-related protein 2 (DRP2) mRNA, complete 
cds
Length=2979

 Score = 1001 bits (2587),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 496/878 (56%), Positives = 640/878 (72%), Gaps = 13/878 (1%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E+++KS NIR  LEA SD   +L LSLQE++ WL  KD+ELS Q PIGGD  AV
Sbjct  304   MNLCWNEIKRKSHNIRVRLEAFSDNSGKLQLSLQEIIEWLTAKDEELSEQLPIGGDVGAV  483

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q Q + H+AF  ++K++ P I S LE+ + FL + P +  E+   + +E+ P  R  NV+
Sbjct  484   QHQREFHQAFMEDVKSRGPYIYSVLESAQTFLAQHPFQEPEETLPDGKEVSPRRRMLNVS  663

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R ++ TLERL ++Q A +EL   L QAE ++ +W+
Sbjct  664   RSVWKQANVASDLWEKLTARCVDRHRHMERTLERLLQIQAAMEELAAALEQAEGVRDAWE  843

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             PVGDL IDSLQDH++  K  + E++ +KE + H+NDLA +L    + LS  N   LE LN
Sbjct  844   PVGDLFIDSLQDHIDATKLFKEELSQVKEGMKHINDLAHELAISDVHLSMDNARALEHLN  1023

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWKLLQ ++E+R++QL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTT
Sbjct  1024  NRWKLLQGSIEERLKQLQDAHRDFGPGSQHFLSSSVQIPWERAISPNKVPYYINHQAQTT  1203

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLR +QKAL LDL  LS+  D   +  L+  
Sbjct  1204  CWDHPKMTELYQALADLNNIKFSAYRTAMKLRHVQKALRLDLFKLSSVVDVFREQELQHG  1383

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+ LT++Y+RLE+E + L+N+PLCVDMCLNWLLNVYD+GR G++RVLSFK 
Sbjct  1384  EHVMDVVEVIHALTSLYERLEEERSVLINIPLCVDMCLNWLLNVYDSGRNGKMRVLSFKM  1563

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             G++ LC A +++KY+YLF+QV    G  DQ+ L LLLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1564  GLVILCNADIQEKYKYLFRQVCGPGGLTDQKHLSLLLHEAIQVPRQLGEVAAFGGSNVEP  1743

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+  + K  IE + FL+WM LEPQS+VWLPVLHRV  AETAKHQA+C ICK+CPI
Sbjct  1744  SVRSCFRMVSGKSAIELSHFLEWMSLEPQSVVWLPVLHRVTVAETAKHQARCYICKQCPI  1923

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR  KG K+HYP++EY TPTTSGE +RDFAK LKNKFR
Sbjct  1924  KGFRYRSLKQFNVDICQTCFLTGRTTKGKKLHYPIMEYYTPTTSGEKMRDFAKTLKNKFR  2103

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K+YF+KHP+ GYLPVQ+VLE ++ ETP SSP+L H DTHSRIEH+ASRLAEMEN N S+
Sbjct  2104  SKQYFSKHPQRGYLPVQSVLEVESSETPCSSPRLPHADTHSRIEHFASRLAEMENQNCSF  2283

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLE  1041
               DS+SP+ES+D++  L++H   SL QDSP         +L  L+ ++R EL+R L  LE
Sbjct  2284  FTDSLSPDESLDEDQYLLRHSSPSLEQDSP------HGLMLAQLDCQDREELQRTLHRLE  2445

Query  1042  EENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEA  1101
              ENR LQ EY RLK +HE    S  P   E  P SP   +D EL+AEA++LRQHK RLE 
Sbjct  2446  NENRVLQGEYRRLKWKHEEAAAS--PQLLESGPGSPPGQQDEELLAEARVLRQHKTRLET  2619

Query  1102  RMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGS  1161
             RMQILEDHNKQLESQL RLR+LL QP+ +++ NG+  SS S+ +      +P        
Sbjct  2620  RMQILEDHNKQLESQLRRLRELLLQPKDDSEANGSAPSSLSSPVSGGHQGEP-----PSR  2784

Query  1162  QTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
             +T+D+    + L   QDT   L++V+EQL N FPS  G
Sbjct  2785  ETTDTEAAGEDLDHEQDTVLQLQQVIEQLRNVFPSEPG  2898


 Score = 52.4 bits (124),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 56/232 (24%), Positives = 103/232 (44%), Gaps = 27/232 (11%)
 Frame = +1

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ +WL+  D+ +  Q  + GD+  +       +A M+D++ R P +  ++ +AQ    +
Sbjct  406   EIIEWLTAKDEELSEQLPIGGDVGAVQHQREFHQAFMEDVKSRGPYIYSVLESAQTFLAQ  585

Query  81    TSNQEARTIITDRIE-----RIQNQ--------------WDEVQEHLQNRRQQLNEMLKD  121
                QE    + D  E     R+ N               W+++     +R + +   L+ 
Sbjct  586   HPFQEPEETLPDGKEVSPRRRMLNVSRSVWKQANVASDLWEKLTARCVDRHRHMERTLER  765

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               Q   A EE    L QA    ++W+  G   +D++Q  I  TK   ++L Q +  +   
Sbjct  766   LLQIQAAMEELAAALEQAEGVRDAWEPVGDLFIDSLQDHIDATKLFKEELSQVKEGMKHI  945

Query  181   NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             NDLA +L + D   S D+ R +    E++N  W+ +   + ER   L++ HR
Sbjct  946   NDLAHELAISDVHLSMDNARAL----EHLNNRWKLLQGSIEERLKQLQDAHR  1089


>dbj|AB384915.1| Synthetic construct DNA, clone: pF1KB4196, Homo sapiens DRP2 
gene for dystrophin-related protein 2, complete cds, without 
stop codon, in Flexi system
Length=2888

 Score = 1000 bits (2585),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 497/884 (56%), Positives = 654/884 (73%), Gaps = 16/884 (1%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L LQE++ WL  KD+ELS Q P+ GD   V
Sbjct  244   MNLCWNEIKKKSHNLRARLEAFSDHSGKLQLPLQEIIDWLSQKDEELSAQLPLQGDVALV  423

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K++ P I S LE+ + FL++ P E LE+ + E ++  P++R QN++
Sbjct  424   QQEKETHAAFMEEVKSRGPYIYSVLESAQAFLSQHPFEELEEPHSESKDTSPKQRIQNLS  603

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE+L E+Q A +EL   L QAE ++ +W+
Sbjct  604   RFVWKQATVASELWEKLTARCVDQHRHIERTLEQLLEIQGAMEELSTTLSQAEGVRATWE  783

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  784   PIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLVNDLAHQLAISDVHLSMENSQALEQIN  963

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQ +V +R++QL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTT
Sbjct  964   VRWKQLQASVSERLKQLQDAHRDFGPGSQHFLSSSVQVPWERAISPNKVPYYINHQAQTT  1143

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1144  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1323

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1324  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1503

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1504  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEP  1683

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1684  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  1863

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  1864  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2043

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K YF+KHP+ GYLPVQ+VLE D  ETPASSP   H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2044  SKHYFSKHPQRGYLPVQSVLEADYSETPASSPMWPHADTHSRIEHFASRLAEMESQNCSF  2223

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GEL++ILA
Sbjct  2224  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSVATESKGELQKILA  2379

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
              LE+ENR LQ E  RLK QHE    +  PS  +    +    R+ EL+AEA++LRQHK R
Sbjct  2380  HLEDENRILQGELRRLKWQHEEAAEA--PSLADGSTEAATDHRNEELLAEARILRQHKSR  2553

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RMQILEDHNKQLESQL RLR+LL QP  E+  +G+  SS ++S Q+S+ S P   R 
Sbjct  2554  LETRMQILEDHNKQLESQLQRLRELLLQPPTESDGSGSAGSSLASSPQQSEGSHP---RE  2724

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
              G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  2725  KGQTTPDTEAADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  2856


 Score = 57.4 bits (137),  Expect = 5e-05, Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 101/235 (42%), Gaps = 33/235 (14%)
 Frame = +1

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ R P +  ++ +AQ   ++
Sbjct  346   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSRGPYIYSVLESAQAFLSQ  525

Query  81    TSNQE-----ARTIITDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E     + +  T   +RIQN               W+++     ++ + +   L+ 
Sbjct  526   HPFEELEEPHSESKDTSPKQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIERTLEQ  705

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  706   LLEIQGAMEELSTTLSQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLV  885

Query  181   NDLALKLLRDYSADDTRKVHMITEN------INASWRSIHKRVSEREAALEETHR  229
             NDLA +L           VH+  EN      IN  W+ +   VSER   L++ HR
Sbjct  886   NDLAHQLA-------ISDVHLSMENSQALEQINVRWKQLQASVSERLKQLQDAHR  1029


>dbj|AK289825.1| Homo sapiens cDNA FLJ75585 complete cds, highly similar to Homo 
sapiens dystrophin related protein 2 (DRP2), mRNA
Length=3581

 Score =  999 bits (2584),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 496/884 (56%), Positives = 653/884 (73%), Gaps = 16/884 (1%)
 Frame = +3

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L LQE++ WL  KD+ELS Q P+ GD   V
Sbjct  492   MNLCWNEIKKKSHNLRARLEAFSDHSGKLQLPLQEIIDWLSQKDEELSAQLPLQGDVALV  671

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K++ P I S LE+ + FL++ P E LE+ + E ++  P++R QN++
Sbjct  672   QQEKETHAAFMEEVKSRGPYIYSVLESAQAFLSQHPFEELEEPHSESKDTSPKQRIQNLS  851

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE+L E+Q A +EL   L QA  ++ +W+
Sbjct  852   RFVWKQATVASELWEKLTARCVDQHRHIERTLEQLLEIQGAMEELSTTLSQAGGVRATWE  1031

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  1032  PIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLVNDLAHQLAISDVHLSMENSQALEQIN  1211

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQ +V +R++QL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTT
Sbjct  1212  VRWKQLQASVSERLKQLQDAHRDFGPGSQHFLSSSVQVPWERAISPNKVPYYINHQAQTT  1391

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1392  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1571

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1572  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1751

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1752  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEP  1931

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1932  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  2111

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  2112  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2291

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K YF+KHP+ GYLPVQ+VLE D  ETPASSP   H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2292  SKHYFSKHPQRGYLPVQSVLEADYSETPASSPMWPHADTHSRIEHFASRLAEMESQNCSF  2471

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GEL++ILA
Sbjct  2472  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSVATESKGELQKILA  2627

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
              LE+ENR LQ E  RLK QHE    +  PS  +    +    R+ EL+AEA++LRQHK R
Sbjct  2628  HLEDENRILQGELRRLKWQHEEAAEA--PSLADGSTEAATDHRNEELLAEARILRQHKSR  2801

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RMQILEDHNKQLESQL RLR+LL QP  E+  +G+  SS ++S Q+S+ S P   R 
Sbjct  2802  LETRMQILEDHNKQLESQLQRLRELLLQPPTESDGSGSAGSSLASSPQQSEGSHP---RE  2972

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
              G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  2973  KGQTTPDTEAADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  3104


 Score = 57.0 bits (136),  Expect = 7e-05, Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 101/235 (42%), Gaps = 33/235 (14%)
 Frame = +3

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ R P +  ++ +AQ   ++
Sbjct  594   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSRGPYIYSVLESAQAFLSQ  773

Query  81    TSNQE-----ARTIITDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E     + +  T   +RIQN               W+++     ++ + +   L+ 
Sbjct  774   HPFEELEEPHSESKDTSPKQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIERTLEQ  953

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  954   LLEIQGAMEELSTTLSQAGGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLV  1133

Query  181   NDLALKLLRDYSADDTRKVHMITEN------INASWRSIHKRVSEREAALEETHR  229
             NDLA +L           VH+  EN      IN  W+ +   VSER   L++ HR
Sbjct  1134  NDLAHQLA-------ISDVHLSMENSQALEQINVRWKQLQASVSERLKQLQDAHR  1277


>gb|AF195788.1|AF195788 Rattus norvegicus dystrophin-related protein 2 B-form splice 
variant (Drp2) mRNA, complete cds
Length=3073

 Score =  996 bits (2576),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 502/884 (56%), Positives = 654/884 (73%), Gaps = 16/884 (1%)
 Frame = +2

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L LQE++ WL  KD+ELS Q P+ GD   V
Sbjct  434   MNLCWNEIKKKSHNLRARLEAFSDHSGKLQLPLQEIIDWLSQKDEELSAQLPLQGDVALV  613

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K+K P I S LE+ + FL++ P E LE+ + E ++  P +R QN++
Sbjct  614   QQEKETHAAFMEEVKSKGPYIYSVLESAQAFLSQHPFEELEESHSESKDTSPRQRIQNLS  793

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE L E+Q A +EL   L QAE ++ +W+
Sbjct  794   RFVWKQATVASELWEKLTARCVDQHRHIEHTLEHLLEIQGAMEELSSTLTQAEGVRATWE  973

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  974   PIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLVNDLAHQLAISDVHLSMENSRALEQIN  1153

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQV+V +R++QL +AHRDFGP SQHFLSTSVQ PWERAISPNKVPYYINH+ QTT
Sbjct  1154  VRWKQLQVSVAERLKQLQDAHRDFGPGSQHFLSTSVQVPWERAISPNKVPYYINHQAQTT  1333

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1334  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1513

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1514  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1693

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1694  GIACLCGTEVKEKLQYLFSQVANSGSKCDQRHLGALLHEAIQVPRQLGEVAAFGGSNVEP  1873

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1874  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTVAEQVKHQTKCSICRQCPI  2053

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  2054  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2233

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K+YF+KHP+ GYLPVQ+VLE D  ETPASSP L H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2234  SKQYFSKHPQRGYLPVQSVLESDCSETPASSPMLPHADTHSRIEHFASRLAEMESQNCSF  2413

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GELE+ILA
Sbjct  2414  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSMATESKGELEKILA  2569

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
              LE+ENR LQ E  RLK QHE    +P  +  E    +    R+ EL+AEA++LRQHK R
Sbjct  2570  HLEDENRILQGELRRLKWQHEEAVEAPTLA--EGSAEATPDHRNEELLAEARILRQHKSR  2743

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RMQILEDHNKQLESQL RLR+LL QP  E+  NG+  SS ++S ++S+ S P   R 
Sbjct  2744  LETRMQILEDHNKQLESQLQRLRELLLQPPTESDGNGSAGSSLASSPRQSEGSHP---RE  2914

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
              G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  2915  KGQTTPDTEAADDVGSKSQDVSHSLEDIMEKLRHAFPSVRSSDV  3046


 Score = 50.8 bits (120),  Expect = 0.005, Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 103/232 (44%), Gaps = 27/232 (11%)
 Frame = +2

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ + P +  ++ +AQ   ++
Sbjct  536   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSKGPYIYSVLESAQAFLSQ  715

Query  81    TSNQEARTII-----TDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E          T   +RIQN               W+++     ++ + +   L+ 
Sbjct  716   HPFEELEESHSESKDTSPRQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIEHTLEH  895

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  896   LLEIQGAMEELSSTLTQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLV  1075

Query  181   NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             NDLA +L + D   S +++R +    E IN  W+ +   V+ER   L++ HR
Sbjct  1076  NDLAHQLAISDVHLSMENSRAL----EQINVRWKQLQVSVAERLKQLQDAHR  1219


>gb|AF195787.1|AF195787 Rattus norvegicus dystrophin-related protein 2 A-form splice 
variant (Drp2) mRNA, complete cds
Length=3140

 Score =  996 bits (2576),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 502/884 (56%), Positives = 654/884 (73%), Gaps = 16/884 (1%)
 Frame = +3

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L LQE++ WL  KD+ELS Q P+ GD   V
Sbjct  501   MNLCWNEIKKKSHNLRARLEAFSDHSGKLQLPLQEIIDWLSQKDEELSAQLPLQGDVALV  680

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K+K P I S LE+ + FL++ P E LE+ + E ++  P +R QN++
Sbjct  681   QQEKETHAAFMEEVKSKGPYIYSVLESAQAFLSQHPFEELEESHSESKDTSPRQRIQNLS  860

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE L E+Q A +EL   L QAE ++ +W+
Sbjct  861   RFVWKQATVASELWEKLTARCVDQHRHIEHTLEHLLEIQGAMEELSSTLTQAEGVRATWE  1040

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  1041  PIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLVNDLAHQLAISDVHLSMENSRALEQIN  1220

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQV+V +R++QL +AHRDFGP SQHFLSTSVQ PWERAISPNKVPYYINH+ QTT
Sbjct  1221  VRWKQLQVSVAERLKQLQDAHRDFGPGSQHFLSTSVQVPWERAISPNKVPYYINHQAQTT  1400

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1401  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1580

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1581  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1760

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1761  GIACLCGTEVKEKLQYLFSQVANSGSKCDQRHLGALLHEAIQVPRQLGEVAAFGGSNVEP  1940

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1941  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTVAEQVKHQTKCSICRQCPI  2120

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  2121  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2300

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K+YF+KHP+ GYLPVQ+VLE D  ETPASSP L H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2301  SKQYFSKHPQRGYLPVQSVLESDCSETPASSPMLPHADTHSRIEHFASRLAEMESQNCSF  2480

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GELE+ILA
Sbjct  2481  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSMATESKGELEKILA  2636

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
              LE+ENR LQ E  RLK QHE    +P  +  E    +    R+ EL+AEA++LRQHK R
Sbjct  2637  HLEDENRILQGELRRLKWQHEEAVEAPTLA--EGSAEATPDHRNEELLAEARILRQHKSR  2810

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RMQILEDHNKQLESQL RLR+LL QP  E+  NG+  SS ++S ++S+ S P   R 
Sbjct  2811  LETRMQILEDHNKQLESQLQRLRELLLQPPTESDGNGSAGSSLASSPRQSEGSHP---RE  2981

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
              G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  2982  KGQTTPDTEAADDVGSKSQDVSHSLEDIMEKLRHAFPSVRSSDV  3113


 Score = 50.8 bits (120),  Expect = 0.005, Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 103/232 (44%), Gaps = 27/232 (11%)
 Frame = +3

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ + P +  ++ +AQ   ++
Sbjct  603   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSKGPYIYSVLESAQAFLSQ  782

Query  81    TSNQEARTII-----TDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E          T   +RIQN               W+++     ++ + +   L+ 
Sbjct  783   HPFEELEESHSESKDTSPRQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIEHTLEH  962

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  963   LLEIQGAMEELSSTLTQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLV  1142

Query  181   NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             NDLA +L + D   S +++R +    E IN  W+ +   V+ER   L++ HR
Sbjct  1143  NDLAHQLAISDVHLSMENSRAL----EQINVRWKQLQVSVAERLKQLQDAHR  1286


>ref|XM_538105.2| PREDICTED: Canis familiaris similar to Dystrophin-related protein 
2 (LOC480984), mRNA
Length=2874

 Score =  994 bits (2571),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 495/881 (56%), Positives = 652/881 (74%), Gaps = 10/881 (1%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L LQE++ WL  KD+ELS Q P+ GD   V
Sbjct  235   MNLCWNEIKKKSHNLRARLEAFSDHSGKLQLPLQEIIDWLSQKDEELSAQLPLQGDVALV  414

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  ++K++ P I S LE+ + FL++ P E LE+   E ++  P +R QN++
Sbjct  415   QQEKETHAAFMEDVKSRGPYIYSVLESAQAFLSQHPFEELEEPRSESKDTSPRQRIQNLS  594

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE+L E+Q A +EL   L QAE ++ +W+
Sbjct  595   RFVWKQATVASELWEKLTARCVDQHRHIEHTLEQLLEIQGAMEELSNTLTQAEGVRATWE  774

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  775   PIGDLFIDSLPEHIQALKLFKEEFSPMKDGVKLVNDLAHQLAISDVHLSMENSRALEQIN  954

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQV++ +R++QL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTT
Sbjct  955   IRWKQLQVSIGERLKQLQDAHRDFGPGSQHFLSSSVQVPWERAISPNKVPYYINHQAQTT  1134

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1135  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1314

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD+++II+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1315  EHVMDVVEIIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1494

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1495  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEP  1674

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1675  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  1854

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  1855  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2034

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K YF+KHP+ GYLPVQ+VLE D  ET ASSP L H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2035  SKHYFSKHPQRGYLPVQSVLEADYSETLASSPMLPHADTHSRIEHFASRLAEMESQNCSF  2214

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLE  1041
              NDS+SP++SID++  L++H C  +    P    ++P     S+ +E +G+LE+ILA LE
Sbjct  2215  FNDSLSPDDSIDEDQYLLRH-CSPITDREPTFGQQAPC----SMATENKGDLEKILAHLE  2379

Query  1042  EENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEA  1101
             +ENR LQ+E  RLK QHE    +  P+  E      Q  R+ EL+AEA++LRQHK RLE 
Sbjct  2380  DENRILQSELRRLKWQHEEAVEA--PTLAEGSAELAQDHRNEELLAEARILRQHKSRLET  2553

Query  1102  RMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGS  1161
             RMQILEDHNKQLESQL RLR+LL QP  E+  NG+  SS ++S Q+S+ S P   +  G 
Sbjct  2554  RMQILEDHNKQLESQLQRLRELLLQPPTESDGNGSASSSLASSPQQSEGSHP---QEKGQ  2724

Query  1162  QTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
              T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  2725  TTPDTEAADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  2847


 Score = 55.8 bits (133),  Expect = 2e-04, Method: Compositional matrix adjust.
 Identities = 53/232 (22%), Positives = 104/232 (44%), Gaps = 27/232 (11%)
 Frame = +1

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M+D++ R P +  ++ +AQ   ++
Sbjct  337   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEDVKSRGPYIYSVLESAQAFLSQ  516

Query  81    TSNQE-----ARTIITDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E     + +  T   +RIQN               W+++     ++ + +   L+ 
Sbjct  517   HPFEELEEPRSESKDTSPRQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIEHTLEQ  696

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  697   LLEIQGAMEELSNTLTQAEGVRATWEPIGDLFIDSLPEHIQALKLFKEEFSPMKDGVKLV  876

Query  181   NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             NDLA +L + D   S +++R +    E IN  W+ +   + ER   L++ HR
Sbjct  877   NDLAHQLAISDVHLSMENSRAL----EQINIRWKQLQVSIGERLKQLQDAHR  1020


>dbj|AK158102.1| Mus musculus adult inner ear cDNA, RIKEN full-length enriched 
library, clone:F930029B12 product:dystrophin related protein 
2, full insert sequence
Length=3827

 Score =  993 bits (2567),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 502/886 (56%), Positives = 654/886 (73%), Gaps = 20/886 (2%)
 Frame = +3

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L L+E++ WL  KD+ELS Q P+ GD   V
Sbjct  273   MNLCWNEIKKKSHNLRARLEAFSDLSGKLQLPLREIIDWLSQKDEELSAQLPLQGDVALV  452

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K+K P I S LE+ + FL++ P E LE+   E ++  P +R QN++
Sbjct  453   QQEKETHAAFMEEVKSKGPYISSVLESAQAFLSQHPFEELEESQSESKDTSPRQRIQNLS  632

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE L E+Q A +EL   L QAE ++ +W+
Sbjct  633   RFVWKQATVASELWEKLTARCVDQHRHIEHTLEHLLEIQGAMEELSSTLTQAEGVRATWE  812

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  813   PIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLVNDLAHQLAISDVHLSMENSRALEQIN  992

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQV+V +R++QL +AHRDFGP SQHFLSTSVQ PWERAISPNKVPYYINH+ QTT
Sbjct  993   IRWKQLQVSVAERLKQLQDAHRDFGPGSQHFLSTSVQVPWERAISPNKVPYYINHQAQTT  1172

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1173  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1352

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1353  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1532

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1533  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGALLHEAIQVPRQLGEVAAFGGSNVEP  1712

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1713  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  1892

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  1893  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2072

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K+YF+KHP+ GYLPVQ+VLE D  ETPASSP L H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2073  SKQYFSKHPQRGYLPVQSVLESDCSETPASSPMLPHADTHSRIEHFASRLAEMESQNCSF  2252

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GELE+ILA
Sbjct  2253  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSMATESKGELEKILA  2408

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSP--LPSPPEMMPTSPQSPRDAELIAEAKLLRQHK  1096
              LE+ENR LQ E  RLK QHE    +P  +    E  P      R+ EL+AEA++LRQHK
Sbjct  2409  HLEDENRILQGELRRLKWQHEEAAEAPTLVEGSAEATPDH----RNEELLAEARILRQHK  2576

Query  1097  GRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLL  1156
              RLE RMQILEDHNKQLESQL RLR+LL QP +E+  NG+  SS ++S ++S+ S P   
Sbjct  2577  SRLETRMQILEDHNKQLESQLQRLRELLLQPPSESDGNGSAGSSLASSPRQSEGSHP---  2747

Query  1157  RVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             R  G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  2748  REKGQTTPDTEVADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  2885


 Score = 50.8 bits (120),  Expect = 0.005, Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 103/232 (44%), Gaps = 27/232 (11%)
 Frame = +3

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ + P +  ++ +AQ   ++
Sbjct  375   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSKGPYISSVLESAQAFLSQ  554

Query  81    TSNQEARTII-----TDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E          T   +RIQN               W+++     ++ + +   L+ 
Sbjct  555   HPFEELEESQSESKDTSPRQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIEHTLEH  734

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  735   LLEIQGAMEELSSTLTQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLV  914

Query  181   NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             NDLA +L + D   S +++R +    E IN  W+ +   V+ER   L++ HR
Sbjct  915   NDLAHQLAISDVHLSMENSRAL----EQINIRWKQLQVSVAERLKQLQDAHR  1058


>ref|NM_010078.3| Mus musculus dystrophin related protein 2 (Drp2), mRNA
Length=6983

 Score =  991 bits (2563),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 502/886 (56%), Positives = 654/886 (73%), Gaps = 20/886 (2%)
 Frame = +3

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L L+E++ WL  KD+ELS Q P+ GD   V
Sbjct  471   MNLCWNEIKKKSHNLRARLEAFSDLSGKLQLPLREIIDWLSQKDEELSAQLPLQGDVALV  650

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K+K P I S LE+ + FL++ P E LE+   E ++  P +R QN++
Sbjct  651   QQEKETHAAFMEEVKSKGPYISSVLESAQAFLSQHPFEELEESQSESKDTSPRQRIQNLS  830

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE L E+Q A +EL   L QAE ++ +W+
Sbjct  831   RFVWKQATVASELWEKLTARCVDQHRHIEHTLEHLLEIQGAMEELSSTLTQAEGVRATWE  1010

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  1011  PIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLVNDLAHQLAISDVHLSMENSRALEQIN  1190

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQV+V +R++QL +AHRDFGP SQHFLSTSVQ PWERAISPNKVPYYINH+ QTT
Sbjct  1191  IRWKQLQVSVAERLKQLQDAHRDFGPGSQHFLSTSVQVPWERAISPNKVPYYINHQAQTT  1370

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1371  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1550

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1551  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1730

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1731  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGALLHEAIQVPRQLGEVAAFGGSNVEP  1910

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1911  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  2090

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  2091  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2270

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K+YF+KHP+ GYLPVQ+VLE D  ETPASSP L H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2271  SKQYFSKHPQRGYLPVQSVLESDCSETPASSPMLPHADTHSRIEHFASRLAEMESQNCSF  2450

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GELE+ILA
Sbjct  2451  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSMATESKGELEKILA  2606

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSP--LPSPPEMMPTSPQSPRDAELIAEAKLLRQHK  1096
              LE+ENR LQ E  RLK QHE    +P  +    E  P      R+ EL+AEA++LRQHK
Sbjct  2607  HLEDENRILQGELRRLKWQHEEAAEAPTLVEGSAEATPDH----RNEELLAEARILRQHK  2774

Query  1097  GRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLL  1156
              RLE RMQILEDHNKQLESQL RLR+LL QP +E+  NG+  SS ++S ++S+ S P   
Sbjct  2775  SRLETRMQILEDHNKQLESQLQRLRELLLQPPSESDGNGSAGSSLASSPRQSEGSHP---  2945

Query  1157  RVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             R  G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  2946  REKGQTTPDTEVADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  3083


 Score = 50.8 bits (120),  Expect = 0.005, Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 103/232 (44%), Gaps = 27/232 (11%)
 Frame = +3

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ + P +  ++ +AQ   ++
Sbjct  573   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSKGPYISSVLESAQAFLSQ  752

Query  81    TSNQEARTII-----TDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E          T   +RIQN               W+++     ++ + +   L+ 
Sbjct  753   HPFEELEESQSESKDTSPRQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIEHTLEH  932

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  933   LLEIQGAMEELSSTLTQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLV  1112

Query  181   NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             NDLA +L + D   S +++R +    E IN  W+ +   V+ER   L++ HR
Sbjct  1113  NDLAHQLAISDVHLSMENSRAL----EQINIRWKQLQVSVAERLKQLQDAHR  1256


>gb|BC125347.1| Mus musculus dystrophin related protein 2, mRNA (cDNA clone MGC:159050 
IMAGE:40129862), complete cds
Length=3150

 Score =  991 bits (2563),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 502/886 (56%), Positives = 654/886 (73%), Gaps = 20/886 (2%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L L+E++ WL  KD+ELS Q P+ GD   V
Sbjct  331   MNLCWNEIKKKSHNLRARLEAFSDLSGKLQLPLREIIDWLSQKDEELSAQLPLQGDVALV  510

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K+K P I S LE+ + FL++ P E LE+   E ++  P +R QN++
Sbjct  511   QQEKETHAAFMEEVKSKGPYISSVLESAQAFLSQHPFEELEESQSESKDTSPRQRIQNLS  690

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE L E+Q A +EL   L QAE ++ +W+
Sbjct  691   RFVWKQATVASELWEKLTARCVDQHRHIEHTLEHLLEIQGAMEELSSTLTQAEGVRATWE  870

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  871   PIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLVNDLAHQLAISDVHLSMENSRALEQIN  1050

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQV+V +R++QL +AHRDFGP SQHFLSTSVQ PWERAISPNKVPYYINH+ QTT
Sbjct  1051  IRWKQLQVSVAERLKQLQDAHRDFGPGSQHFLSTSVQVPWERAISPNKVPYYINHQAQTT  1230

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1231  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1410

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1411  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1590

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1591  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGALLHEAIQVPRQLGEVAAFGGSNVEP  1770

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1771  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  1950

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  1951  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2130

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K+YF+KHP+ GYLPVQ+VLE D  ETPASSP L H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2131  SKQYFSKHPQRGYLPVQSVLESDCSETPASSPMLPHADTHSRIEHFASRLAEMESQNCSF  2310

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GELE+ILA
Sbjct  2311  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSMATESKGELEKILA  2466

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSP--LPSPPEMMPTSPQSPRDAELIAEAKLLRQHK  1096
              LE+ENR LQ E  RLK QHE    +P  +    E  P      R+ EL+AEA++LRQHK
Sbjct  2467  HLEDENRILQGELRRLKWQHEEAAEAPTLVEGSAEATPDH----RNEELLAEARILRQHK  2634

Query  1097  GRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLL  1156
              RLE RMQILEDHNKQLESQL RLR+LL QP +E+  NG+  SS ++S ++S+ S P   
Sbjct  2635  SRLETRMQILEDHNKQLESQLQRLRELLLQPPSESDGNGSAGSSLASSPRQSEGSHP---  2805

Query  1157  RVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             R  G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  2806  REKGQTTPDTEVADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  2943


 Score = 50.8 bits (120),  Expect = 0.005, Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 103/232 (44%), Gaps = 27/232 (11%)
 Frame = +1

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ + P +  ++ +AQ   ++
Sbjct  433   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSKGPYISSVLESAQAFLSQ  612

Query  81    TSNQEARTII-----TDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E          T   +RIQN               W+++     ++ + +   L+ 
Sbjct  613   HPFEELEESQSESKDTSPRQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIEHTLEH  792

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  793   LLEIQGAMEELSSTLTQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLV  972

Query  181   NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             NDLA +L + D   S +++R +    E IN  W+ +   V+ER   L++ HR
Sbjct  973   NDLAHQLAISDVHLSMENSRAL----EQINIRWKQLQVSVAERLKQLQDAHR  1116


>gb|BC125345.1| Mus musculus dystrophin related protein 2, mRNA (cDNA clone MGC:159048 
IMAGE:40129860), complete cds
Length=3147

 Score =  991 bits (2563),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 502/886 (56%), Positives = 654/886 (73%), Gaps = 20/886 (2%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L L+E++ WL  KD+ELS Q P+ GD   V
Sbjct  331   MNLCWNEIKKKSHNLRARLEAFSDLSGKLQLPLREIIDWLSQKDEELSAQLPLQGDVALV  510

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K+K P I S LE+ + FL++ P E LE+   E ++  P +R QN++
Sbjct  511   QQEKETHAAFMEEVKSKGPYISSVLESAQAFLSQHPFEELEESQSESKDTSPRQRIQNLS  690

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE L E+Q A +EL   L QAE ++ +W+
Sbjct  691   RFVWKQATVASELWEKLTARCVDQHRHIEHTLEHLLEIQGAMEELSSTLTQAEGVRATWE  870

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  871   PIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLVNDLAHQLAISDVHLSMENSRALEQIN  1050

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQV+V +R++QL +AHRDFGP SQHFLSTSVQ PWERAISPNKVPYYINH+ QTT
Sbjct  1051  IRWKQLQVSVAERLKQLQDAHRDFGPGSQHFLSTSVQVPWERAISPNKVPYYINHQAQTT  1230

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1231  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1410

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1411  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1590

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1591  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGALLHEAIQVPRQLGEVAAFGGSNVEP  1770

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1771  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  1950

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  1951  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2130

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K+YF+KHP+ GYLPVQ+VLE D  ETPASSP L H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2131  SKQYFSKHPQRGYLPVQSVLESDCSETPASSPMLPHADTHSRIEHFASRLAEMESQNCSF  2310

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GELE+ILA
Sbjct  2311  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSMATESKGELEKILA  2466

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSP--LPSPPEMMPTSPQSPRDAELIAEAKLLRQHK  1096
              LE+ENR LQ E  RLK QHE    +P  +    E  P      R+ EL+AEA++LRQHK
Sbjct  2467  HLEDENRILQGELRRLKWQHEEAAEAPTLVEGSAEATPDH----RNEELLAEARILRQHK  2634

Query  1097  GRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLL  1156
              RLE RMQILEDHNKQLESQL RLR+LL QP +E+  NG+  SS ++S ++S+ S P   
Sbjct  2635  SRLETRMQILEDHNKQLESQLQRLRELLLQPPSESDGNGSAGSSLASSPRQSEGSHP---  2805

Query  1157  RVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             R  G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  2806  REKGQTTPDTEVADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  2943


 Score = 50.8 bits (120),  Expect = 0.005, Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 103/232 (44%), Gaps = 27/232 (11%)
 Frame = +1

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ + P +  ++ +AQ   ++
Sbjct  433   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSKGPYISSVLESAQAFLSQ  612

Query  81    TSNQEARTII-----TDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E          T   +RIQN               W+++     ++ + +   L+ 
Sbjct  613   HPFEELEESQSESKDTSPRQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIEHTLEH  792

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  793   LLEIQGAMEELSSTLTQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLV  972

Query  181   NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             NDLA +L + D   S +++R +    E IN  W+ +   V+ER   L++ HR
Sbjct  973   NDLAHQLAISDVHLSMENSRAL----EQINIRWKQLQVSVAERLKQLQDAHR  1116


>ref|XM_001364344.1| PREDICTED: Monodelphis domestica similar to FLJ46266 protein 
(LOC100015841), mRNA
Length=2838

 Score =  991 bits (2561),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 495/883 (56%), Positives = 651/883 (73%), Gaps = 20/883 (2%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L   LQE++ WL  KD+ELS Q P+ G    V
Sbjct  217   MNLCWNEIKKKSHNLRARLEAFSDPSGKLQPPLQEIIDWLSQKDEELSAQLPLQGAVALV  396

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             QK+ + H AF  E+K++ P I S LE+ + FL++ P E LE+ + E ++    ++ QN++
Sbjct  397   QKEKETHSAFMEEVKSRGPYIYSVLESAQAFLSQHPFEELEEPHCENKDASARQKIQNLS  576

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE+L E+Q A  EL   L QAE I+ +W+
Sbjct  577   RFVWKQATVASELWEKLTARCVDQHRHIERTLEQLLEIQGAMGELGSTLTQAEGIRATWE  756

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K    E++P+KE V  VN+LA QL    + LS  N   LE +N
Sbjct  757   PIGDLFIDSLPEHIQAIKLFTEELSPVKEGVKLVNELAHQLAISDVHLSMENSRALEQIN  936

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
             TRWK LQ +V +R++QL +AHRDFGP SQHFLSTSVQ PWERAISPNKVPYYINH+ QTT
Sbjct  937   TRWKQLQASVNERLKQLQDAHRDFGPGSQHFLSTSVQVPWERAISPNKVPYYINHQAQTT  1116

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H L+ +
Sbjct  1117  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLNTALEIFNEHELQPS  1296

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT++Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1297  EHVMDVVEVIHCLTSLYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1476

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K++YLF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1477  GIACLCGTEVKEKFQYLFSQVATSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEP  1656

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEAA FL+W  LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1657  SVRSCFRFSTGKPVIEAAQFLEWANLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  1836

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E+VRDFA  LKNKFR
Sbjct  1837  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENVRDFATTLKNKFR  2016

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K+YF+KHP+ GYLPVQ+VLE D  E PASSP L H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2017  SKQYFSKHPQRGYLPVQSVLEADYSEPPASSPMLPHSDTHSRIEHFASRLAEMESQNCSF  2196

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLS--QPRSPAQILISLESEERGELERILAD  1039
              NDS+SP++SID++  L++H        SP++  +P    Q   ++ ++++GELE+ILA 
Sbjct  2197  FNDSLSPDDSIDEDQYLLRH-------SSPITDREPTFGQQAQSTIIADDKGELEKILAH  2355

Query  1040  LEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRL  1099
             LE+ENR LQ E  RLK QHE      +  PPE+     Q PR+ EL+AEA+LLRQHK RL
Sbjct  2356  LEDENRILQGELRRLKWQHEEA----VEGPPEVA----QDPRNEELLAEARLLRQHKSRL  2511

Query  1100  EARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVV  1159
             E RMQILEDHN+QLESQL RLR+LL QP  E++ NG+  SS ++S Q+S+ S     +  
Sbjct  2512  ETRMQILEDHNRQLESQLLRLRELLLQPPPESEGNGSGGSSLASSPQQSEGSHS---QEK  2682

Query  1160  GSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
                T D+   +D+    QD S  LE++ME+L ++FP+ R  +V
Sbjct  2683  EHTTPDTEAADDMGQKSQDVSLCLEDIMEKLRHAFPNVRSPDV  2811


 Score = 45.4 bits (106),  Expect = 0.17, Method: Compositional matrix adjust.
 Identities = 50/232 (21%), Positives = 102/232 (43%), Gaps = 27/232 (11%)
 Frame = +1

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + G +  + +      A M++++ R P +  ++ +AQ   ++
Sbjct  319   EIIDWLSQKDEELSAQLPLQGAVALVQKEKETHSAFMEEVKSRGPYIYSVLESAQAFLSQ  498

Query  81    TSNQE------------ARTIITDRIERIQNQ-------WDEVQEHLQNRRQQLNEMLKD  121
                +E            AR  I +    +  Q       W+++     ++ + +   L+ 
Sbjct  499   HPFEELEEPHCENKDASARQKIQNLSRFVWKQATVASELWEKLTARCVDQHRHIERTLEQ  678

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A  E    L QA     +W+  G   +D++ + I   K   ++L   +  V + 
Sbjct  679   LLEIQGAMGELGSTLTQAEGIRATWEPIGDLFIDSLPEHIQAIKLFTEELSPVKEGVKLV  858

Query  181   NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             N+LA +L + D   S +++R +    E IN  W+ +   V+ER   L++ HR
Sbjct  859   NELAHQLAISDVHLSMENSRAL----EQINTRWKQLQASVNERLKQLQDAHR  1002


>ref|XM_617584.4| PREDICTED: Bos taurus similar to dystrophin related protein 2 
(DRP2), mRNA
Length=3129

 Score =  991 bits (2561),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 498/898 (55%), Positives = 660/898 (73%), Gaps = 18/898 (2%)
 Frame = +3

Query  310   DDAVLLQRRLD--NMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
             + +V+  R L+   MN  W+E++KKS N+R+ LEA SD   +L L LQE++ WL  KD+E
Sbjct  258   NGSVVAARTLEPPAMNLCWNEIKKKSHNLRARLEAFSDHSGKLQLPLQEIIDWLSQKDEE  437

Query  368   LSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQE  427
             LS Q P+ GD   VQ++ + H AF  ++K++ P I S LE+ + FL++ P + LE+   E
Sbjct  438   LSAQLPLQGDVVLVQQEKETHAAFMEDVKSRGPYIYSVLESAQAFLSQHPFDELEEPRSE  617

Query  428   PRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELD  487
              ++  P +R QN++R + KQA   +  WEKL     D  R I+ TLE+L E+Q A +EL+
Sbjct  618   SKDTSPRQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIERTLEQLLEIQGAMEELN  797

Query  488   LKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGI  547
               L QAE ++ +W+P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    +
Sbjct  798   ATLTQAEGVRATWEPIGDLFIDSLPEHIQALKLFKEEFSPMKDGVKLVNDLAHQLAISDV  977

Query  548   QLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISP  607
              LS  N   LE +N RWK LQV+V +R++QL +AHRDFGP SQHFLS+SVQ PWERAISP
Sbjct  978   HLSMENSRALEQINIRWKQLQVSVGERLKQLQDAHRDFGPGSQHFLSSSVQVPWERAISP  1157

Query  608   NKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLS  667
             NKVPYYINH+ QTTCWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+
Sbjct  1158  NKVPYYINHQAQTTCWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLT  1337

Query  668   AACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYD  727
              A +  ++H+L+ ++  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D
Sbjct  1338  TALEIFNEHDLQASEHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFD  1517

Query  728   TGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQ  787
             +GR+G++R LSFKTGI  LC   +++K +YLF QVA+S   CDQR LG+LLH++IQ+PRQ
Sbjct  1518  SGRSGKMRALSFKTGIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGVLLHEAIQVPRQ  1697

Query  788   LGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETA  847
             LGEVA+FGGSN+EPSVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  
Sbjct  1698  LGEVAAFGGSNVEPSVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQV  1877

Query  848   KHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGE  907
             KHQ KC+IC++CPI GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E
Sbjct  1878  KHQTKCSICRQCPIKGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSE  2057

Query  908   DVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHY  967
             ++RDFA  LKNKFR+K YF+KHP+ GYLPVQ+VLE D  ETPASSP L H DTHSRIEH+
Sbjct  2058  NMRDFATTLKNKFRSKHYFSKHPQRGYLPVQSVLEADYNETPASSPMLPHADTHSRIEHF  2237

Query  968   ASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILIS  1024
             ASRLAEME+ N S+ NDS+SP++SID++  L++H        SP++  R PA   Q   +
Sbjct  2238  ASRLAEMESQNCSFFNDSLSPDDSIDEDQYLLRH-------SSPVTD-REPAFRQQAPHN  2393

Query  1025  LESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAE  1084
             + +  +GELE+ILA LE+ENR LQ E  RLK QHE    + +P+  E      Q   + E
Sbjct  2394  MATGSKGELEKILAHLEDENRILQGELRRLKWQHEEA--TEVPALTEGSAEVAQGHCNEE  2567

Query  1085  LIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTS  1144
             L+AEA++LRQHK RLE RMQILEDHNKQLESQL RLR+LL QP  E+  NG+  SS ++S
Sbjct  2568  LLAEARILRQHKSRLETRMQILEDHNKQLESQLQRLRELLLQPPIESNGNGSAGSSLASS  2747

Query  1145  LQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
              Q+S+ S P   +  G  T D+   +D+    QD S  LE++ME+L ++FPS R  +V
Sbjct  2748  PQQSEGSHP---QEKGQTTPDTEAADDVGLKSQDVSLCLEDIMEKLRHAFPSVRSSDV  2912


 Score = 54.3 bits (129),  Expect = 5e-04, Method: Compositional matrix adjust.
 Identities = 54/232 (23%), Positives = 103/232 (44%), Gaps = 27/232 (11%)
 Frame = +3

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M+D++ R P +  ++ +AQ   ++
Sbjct  402   EIIDWLSQKDEELSAQLPLQGDVVLVQQEKETHAAFMEDVKSRGPYIYSVLESAQAFLSQ  581

Query  81    TSNQE-----ARTIITDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                 E     + +  T   +RIQN               W+++     ++ + +   L+ 
Sbjct  582   HPFDELEEPRSESKDTSPRQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIERTLEQ  761

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  762   LLEIQGAMEELNATLTQAEGVRATWEPIGDLFIDSLPEHIQALKLFKEEFSPMKDGVKLV  941

Query  181   NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             NDLA +L + D   S +++R +    E IN  W+ +   V ER   L++ HR
Sbjct  942   NDLAHQLAISDVHLSMENSRAL----EQINIRWKQLQVSVGERLKQLQDAHR  1085


>dbj|AK081426.1| Mus musculus 16 days embryo head cDNA, RIKEN full-length enriched 
library, clone:C130016K19 product:dystrophin related protein 
2, full insert sequence
Length=3753

 Score =  989 bits (2558),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 501/886 (56%), Positives = 653/886 (73%), Gaps = 20/886 (2%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L L+E++ WL  KD+ELS Q P+ GD   V
Sbjct  415   MNLCWNEIKKKSHNLRARLEAFSDLSGKLQLPLREIIDWLSQKDEELSAQLPLQGDVALV  594

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K+K P I S LE+ + FL++ P E LE+   E ++  P +R QN++
Sbjct  595   QQEKETHAAFMEEVKSKGPYISSVLESAQAFLSQHPFEELEESQSESKDTSPRQRIQNLS  774

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE L E+Q A +EL   L QAE ++ +W+
Sbjct  775   RFVWKQATVASELWEKLTARCVDQHRHIEHTLEHLLEIQGAMEELSSTLTQAEGVRATWE  954

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  955   PIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLVNDLAHQLAISDVHLSMENSRALEQIN  1134

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQV+V +R++QL +AHRDFGP SQHFLSTSVQ PWERA SPNKVPYYINH+ QTT
Sbjct  1135  IRWKQLQVSVAERLKQLQDAHRDFGPGSQHFLSTSVQVPWERAFSPNKVPYYINHQAQTT  1314

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1315  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1494

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1495  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1674

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1675  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGALLHEAIQVPRQLGEVAAFGGSNVEP  1854

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1855  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  2034

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  2035  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2214

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K+YF+KHP+ GYLPVQ+VLE D  ETPASSP L H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2215  SKQYFSKHPQRGYLPVQSVLESDCSETPASSPMLPHADTHSRIEHFASRLAEMESQNCSF  2394

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GELE+ILA
Sbjct  2395  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSMATESKGELEKILA  2550

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSP--LPSPPEMMPTSPQSPRDAELIAEAKLLRQHK  1096
              LE+ENR LQ E  RLK QHE    +P  +    E  P      R+ EL+AEA++LRQHK
Sbjct  2551  HLEDENRILQGELRRLKWQHEEAAEAPTLVEGSAEATPDH----RNEELLAEARILRQHK  2718

Query  1097  GRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLL  1156
              RLE RMQILEDHNKQLESQL RLR+LL QP +E+  NG+  SS ++S ++S+ S P   
Sbjct  2719  SRLETRMQILEDHNKQLESQLQRLRELLLQPPSESDGNGSAGSSLASSPRQSEGSHP---  2889

Query  1157  RVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             R  G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  2890  REKGQTTPDTEVADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  3027


 Score = 50.8 bits (120),  Expect = 0.005, Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 103/232 (44%), Gaps = 27/232 (11%)
 Frame = +1

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ + P +  ++ +AQ   ++
Sbjct  517   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSKGPYISSVLESAQAFLSQ  696

Query  81    TSNQEARTII-----TDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E          T   +RIQN               W+++     ++ + +   L+ 
Sbjct  697   HPFEELEESQSESKDTSPRQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIEHTLEH  876

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  877   LLEIQGAMEELSSTLTQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLV  1056

Query  181   NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             NDLA +L + D   S +++R +    E IN  W+ +   V+ER   L++ HR
Sbjct  1057  NDLAHQLAISDVHLSMENSRAL----EQINIRWKQLQVSVAERLKQLQDAHR  1200


>tpg|BK005803.1| TPA_inf: Ornithorhynchus anatinus dystrophin-related protein 
2 (DRP2) mRNA, complete cds
Length=2950

 Score =  981 bits (2535),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 493/880 (56%), Positives = 640/880 (72%), Gaps = 15/880 (1%)
 Frame = +1

Query  321   NMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPA  380
             +MN  WSE++KKS ++R+ LEA SDQ  +L   LQE++ WL  KD+ELS Q P+ GD   
Sbjct  262   DMNLCWSEIKKKSHSLRARLEAFSDQSGKLQAPLQEIVDWLGHKDEELSAQLPLRGDVAL  441

Query  381   VQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNV  440
             VQ++ + H AF  E+K + P I S LE+ + FL + P E LE+   E R++ P  R QN 
Sbjct  442   VQQEKETHAAFMEEVKARGPYIYSVLESAQTFLAQHPFEELEEPQTEGRDVSPRLRGQNG  621

Query  441   TRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSW  500
             +RL+ KQA   +  WEKL     D  R I+ TLE+L +++ A +ELD  L QAE ++ +W
Sbjct  622   SRLVWKQATVASELWEKLTARCVDQHRHIERTLEQLLDVRRAMEELDASLGQAEGVRATW  801

Query  501   QPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDL  560
             +P+GDL IDSL DH++  K  + E++P+K+ V  VND A QL    + LS  N   LE +
Sbjct  802   EPIGDLFIDSLPDHIQTTKLFKEELSPMKDGVKLVNDRAHQLAISDVHLSMENSRALEQI  981

Query  561   NTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQT  620
             NTRWK LQ +V +R++QL +AHRDFGP SQHFL+TSVQ PWERAISPNKVPYYINH+ QT
Sbjct  982   NTRWKQLQTSVSERLKQLQDAHRDFGPGSQHFLATSVQVPWERAISPNKVPYYINHQAQT  1161

Query  621   TCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQ  680
             TCWDHPKMTELYQ+LA+LNN++FSAYRTAMKLRR+QKAL LDL+ LS A +  ++H L+ 
Sbjct  1162  TCWDHPKMTELYQTLAELNNIKFSAYRTAMKLRRVQKALRLDLVPLSTALEIFNEHELQP  1341

Query  681   NDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFK  740
              +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNVYD+GR+G++R LSFK
Sbjct  1342  GEHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMTLNWLLNVYDSGRSGKMRALSFK  1521

Query  741   TGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIE  800
             TGI  LC   +++K++YLF QVA   G CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+E
Sbjct  1522  TGIACLCGTDVKEKFQYLFSQVAHPGGLCDQRHLGILLHEAIQVPRQLGEVAAFGGSNVE  1701

Query  801   PSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECP  860
             PS+RSCF+F+  KP +E A FL+W  LEPQSMVWL VLHRVA AE  KHQ KC++C+ CP
Sbjct  1702  PSIRSCFRFSTGKPVVEVAQFLEWANLEPQSMVWLAVLHRVALAEPVKHQTKCSVCRHCP  1881

Query  861   IIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKF  920
             I GFRYRSLK FN DICQ CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKF
Sbjct  1882  IKGFRYRSLKQFNVDICQMCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKF  2061

Query  921   RTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGS  980
             R+K YF++HP+ GYLPVQ+VLE D  ETPASSP L H DTHSRIEH+ASRLAEME+ N S
Sbjct  2062  RSKHYFSRHPQRGYLPVQSVLEADFSETPASSPVLPHADTHSRIEHFASRLAEMESQNCS  2241

Query  981   YLNDSISPNESIDDEHLLIQHYCQSLNQDSPLS--QPRSPAQILISLESEE-RGELERIL  1037
             + NDS SP++SID++  L++H        SP++  +P    Q   S   EE +G LE+IL
Sbjct  2242  FFNDSQSPDDSIDEDQYLLRH-------SSPITDREPAGGQQAQGSPPGEEDKGTLEKIL  2400

Query  1038  ADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKG  1097
             A LE+ENR LQ E  RLK QHE  G +P  +     P + Q P + EL+AEA++LRQHK 
Sbjct  2401  AHLEDENRILQGELRRLKWQHEEAGEAPPLA--AGTPEAAQDPHNEELLAEARILRQHKS  2574

Query  1098  RLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLR  1157
             RLE RMQILEDHNKQLESQL RLR+LL QP A+    G+  SS ++S Q S+ S     R
Sbjct  2575  RLETRMQILEDHNKQLESQLQRLRELLLQPPADLDGTGSAGSSLASSPQPSEGSH---AR  2745

Query  1158  VVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSS  1197
                  T D+   +++++  QD S  LE++ME+L N+FP++
Sbjct  2746  EREHNTPDTEVADEIVAKSQDVSLCLEDIMEKLRNAFPNA  2865


 Score = 57.4 bits (137),  Expect = 5e-05, Method: Compositional matrix adjust.
 Identities = 56/249 (22%), Positives = 101/249 (40%), Gaps = 36/249 (14%)
 Frame = +1

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRP---------------  65
             E+ DWL   D+ + +Q  + GD+  + +      A M++++ R P               
Sbjct  367   EIVDWLGHKDEELSAQLPLRGDVALVQQEKETHAAFMEEVKARGPYIYSVLESAQTFLAQ  546

Query  66    ----QLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKD  121
                 +LEE  T  +++  +   Q    ++  +       W+++     ++ + +   L+ 
Sbjct  547   HPFEELEEPQTEGRDVSPRLRGQNGSRLVWKQATVASELWEKLTARCVDQHRHIERTLEQ  726

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
                   A EE +  LGQA     +W+  G   +D++   I  TK   ++L   +  V + 
Sbjct  727   LLDVRRAMEELDASLGQAEGVRATWEPIGDLFIDSLPDHIQTTKLFKEELSPMKDGVKLV  906

Query  181   NDLALKLLRDYSADDTRKVHMITEN------INASWRSIHKRVSEREAALEETHRLLQQF  234
             ND A +L           VH+  EN      IN  W+ +   VSER   L++ HR    F
Sbjct  907   NDRAHQLA-------ISDVHLSMENSRALEQINTRWKQLQTSVSERLKQLQDAHR---DF  1056

Query  235   PLDLEKFLA  243
                 + FLA
Sbjct  1057  GPGSQHFLA  1083


>emb|AJ223356.1| Strongylocentrotus purpuratus mRNA for SuDp98 protein
Length=3650

 Score =  973 bits (2514),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 504/1001 (50%), Positives = 681/1001 (68%), Gaps = 63/1001 (6%)
 Frame = +1

Query  280   DLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSH  339
             DLQ EIEAH  +  +L+++  K ++  +  D++  LQ++LD +N +W+ +  +S  IR  
Sbjct  601   DLQAEIEAHHSILSSLNQSGVKAVQDADSPDESHTLQKKLDTVNHRWTNIHDRSAEIRKR  780

Query  340   LEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKE  399
             LEA++++W  L  + +EL+ W++LK+D+L ++ P+GGD+ ++Q+Q   H+ ++++L+ K+
Sbjct  781   LEANAEEWNNLVRATEELVRWIRLKEDDLIKRQPVGGDYNSIQQQISDHKVYRQQLEEKQ  960

Query  400   PVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLN  459
               +   L+   ++L EQ    L+ L  E     PE  A N+   L+    ++   W KLN
Sbjct  961   SAVERNLQMGSLYLAEQ--RDLD-LLSEKELTGPEAEAHNIVHKLKDSVTDLQDSWNKLN  1131

Query  460   LHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVK  519
             + S +WQ K+DE   ++  L +A D+L  +L +AE  +  W PVGDL+IDSL  HL +++
Sbjct  1132  IKSENWQHKLDEMSTKMLALHQAMDKLSSRLHEAEATRSRWLPVGDLIIDSLPQHLAELR  1311

Query  520   ALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLH  579
             + +   +P+ +++  V  +A       + LS  N   LED+  RWK LQ+A+++R R L+
Sbjct  1312  SFQDYYSPIHDDLEKVTQMAGHFPAQQVSLSTVNQGRLEDIVRRWKTLQLAIDERARLLN  1491

Query  580   EAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLN  639
             EA RDFGP SQHFL  SVQ PWERA++ NKVPY+INH T+TT WDHP+MTEL+ SL DLN
Sbjct  1492  EALRDFGPQSQHFLRASVQHPWERAVAANKVPYFINHGTETTHWDHPRMTELFHSLFDLN  1671

Query  640   NVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNL-KQNDQPMDILQIINCLTTIY  698
              V+FSAYRT MKLRRLQK+LCL LL+L++A     QH L   ND+ +D+ +II CL T+Y
Sbjct  1672  AVKFSAYRTGMKLRRLQKSLCLYLLNLASAESIFTQHELVSGNDRTLDVTEIITCLATVY  1851

Query  699   DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYL  758
             + L  +H  +VNVP CVDMCLNWLLNVYDT R+GRIRVL+FK GI+ LC AHLEDKYR++
Sbjct  1852  ENLAMDHPGMVNVPQCVDMCLNWLLNVYDTVRSGRIRVLAFKVGIVMLCNAHLEDKYRFI  2031

Query  759   FKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEA  818
              + VA   G  DQR LGLLLHD +QIPRQLGEVASFGGSNIEPSVRSCF    +KP IE 
Sbjct  2032  CRFVADKNGMIDQRGLGLLLHDCVQIPRQLGEVASFGGSNIEPSVRSCFNMTGSKPLIEP  2211

Query  819   ALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQ  878
             A FL WM+LEPQSMVW+PVLHRVAA+ETAKHQAKCNICKECPI+G RYR LK FN+D+CQ
Sbjct  2212  AQFLAWMKLEPQSMVWMPVLHRVAASETAKHQAKCNICKECPIVGLRYRCLKCFNFDLCQ  2391

Query  879   SCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQ  938
             SCFFSGR AK HK+ +PM EYCT TTSGEDVRDFAKV++NKF++KRY+ KHPR+GYLPVQ
Sbjct  2392  SCFFSGRKAKTHKLSHPMQEYCTTTTSGEDVRDFAKVVRNKFKSKRYYRKHPRVGYLPVQ  2571

Query  939   TVLEGDNMETPASSPQ-LSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHL  997
             +VLEGD++E+P ++PQ +++ DTH+R+E YA+RLAE+E S G+ LN   S    ++DEH 
Sbjct  2572  SVLEGDDLESPITTPQHMANQDTHTRLELYANRLAEVE-SQGT-LN---SVPTDLEDEHQ  2736

Query  998   LIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLK--  1055
             LI HYC SL  D   + P SPAQI++S+++E R +LE  + +LE+ENR L +E + LK  
Sbjct  2737  LIAHYCHSLGGDVS-TVPNSPAQIVVSIDAEHRPDLESQINELEDENRTLLSELETLKTL  2913

Query  1056  QQHEHKGLSPLPSPPEMMPTSPQSP-RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLE  1114
             +  + K  + L +      TS +SP RDAEL+AEAKLLRQHKGRLEARMQILEDHN+QLE
Sbjct  2914  RSEDVKRAAELAASSGDERTSGRSPGRDAELVAEAKLLRQHKGRLEARMQILEDHNRQLE  3093

Query  1115  SQLHRLRQLLEQPQ-AEAKVNGTTVSSPSTSLQRSDSSQPMLLRV-------------VG  1160
             +QL RLRQLLEQPQ   A    ++ ++P+ S   S SS     R+               
Sbjct  3094  AQLQRLRQLLEQPQDKSASQVSSSKTTPAVSPTSSISSASKAKRIQHPIAIETRTNGGTS  3273

Query  1161  SQTSDSMGEEDLLSPPQDT----------------------------STGLEEVMEQLNN  1192
                SD  GEE    P   T                               L++V+++LNN
Sbjct  3274  DYDSDMAGEEYNNHPSPHTPPHLKDDHHHHHHLHQGGGAANGVQAKGKVDLDKVIQELNN  3453

Query  1193  SFP-----SSRGHN-VGSLFHMADDLGRAMESLVSVMTDEE  1227
              FP      + G N VGSL HMAD++G+A+++LV+VM+DEE
Sbjct  3454  -FPDGAKNGNVGQNSVGSLLHMADNIGKAVDTLVTVMSDEE  3573


>ref|XR_023213.1| PREDICTED: Pan troglodytes similar to dystrophin related protein 
2 (DRP2), mRNA
Length=4697

 Score =  953 bits (2463),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 482/884 (54%), Positives = 637/884 (72%), Gaps = 16/884 (1%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R      S     L  SL+ +   +      +    P+  D    
Sbjct  274   MNLCWNEIKKKSHNLRFQPTYFSPN*G*LCKSLKSIFFSVDRLSLAVCACLPLQTDNMLS  453

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             +K+ D  RAF  E+K++ P I S LE+ + FL++ P E LE+ + E ++  P++R QN++
Sbjct  454   EKKPDTKRAFMEEVKSRGPYIYSVLESAQAFLSQHPFEELEEPHSESKDTSPKQRIQNLS  633

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE+L E+Q A +EL   L QAE ++ +W+
Sbjct  634   RFVWKQATVASELWEKLTARCVDQHRHIERTLEQLLEIQGAMEELSTTLSQAEGVRATWE  813

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  814   PIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLVNDLAHQLAISDVHLSMENSQALEQIN  993

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQ +V +R++QL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTT
Sbjct  994   VRWKQLQASVSERLKQLQDAHRDFGPGSQHFLSSSVQVPWERAISPNKVPYYINHQAQTT  1173

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1174  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1353

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1354  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1533

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI  LC   +++K +YLF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EP
Sbjct  1534  GIACLCGTEVKEKLQYLFSQVANSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEP  1713

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI
Sbjct  1714  SVRSCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPI  1893

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR
Sbjct  1894  KGFRYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFR  2073

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             +K YF+KHP+ GYLPVQ+VLE D  ETPASSP   H DTHSRIEH+ASRLAEME+ N S+
Sbjct  2074  SKHYFSKHPQRGYLPVQSVLEADYSETPASSPMWPHADTHSRIEHFASRLAEMESQNCSF  2253

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILA  1038
              NDS+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GEL++ILA
Sbjct  2254  FNDSLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSVATESKGELQKILA  2409

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
              LE+ENR LQ E  RLK QHE    +  PS  +    +    R+ EL+AEA++LRQHK R
Sbjct  2410  HLEDENRILQGELRRLKWQHEEAAEA--PSLADGSTEAAPDHRNEELLAEARILRQHKSR  2583

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RMQILEDHNKQLESQL RLR+LL QP  E+  +G+  SS ++S Q+S+ S P   R 
Sbjct  2584  LETRMQILEDHNKQLESQLQRLRELLLQPPTESDGSGSAGSSLASSPQQSEGSHP---RE  2754

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
              G  T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  2755  KGQTTPDTEAADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  2886


 Score = 44.7 bits (104),  Expect = 0.36, Method: Compositional matrix adjust.
 Identities = 45/203 (22%), Positives = 86/203 (42%), Gaps = 33/203 (16%)
 Frame = +1

Query  53    QKATMQDLEQRRPQLEELITAAQNLKNKTSNQE-----ARTIITDRIERIQNQ-------  100
             ++A M++++ R P +  ++ +AQ   ++   +E     + +  T   +RIQN        
Sbjct  472   KRAFMEEVKSRGPYIYSVLESAQAFLSQHPFEELEEPHSESKDTSPKQRIQNLSRFVWKQ  651

Query  101   -------WDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKE-GPYT  152
                    W+++     ++ + +   L+   +   A EE    L QA     +W+  G   
Sbjct  652   ATVASELWEKLTARCVDQHRHIERTLEQLLEIQGAMEELSTTLSQAEGVRATWEPIGDLF  831

Query  153   VDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITEN------I  206
             +D++ + I   K   ++    +  V + NDLA +L           VH+  EN      I
Sbjct  832   IDSLPEHIQAIKLFKEEFSPMKDGVKLVNDLAHQLA-------ISDVHLSMENSQALEQI  990

Query  207   NASWRSIHKRVSEREAALEETHR  229
             N  W+ +   VSER   L++ HR
Sbjct  991   NVRWKQLQASVSERLKQLQDAHR  1059


>gb|BC136034.1| Xenopus tropicalis dystrophin related protein 2, mRNA (cDNA clone 
MGC:122572 IMAGE:7656069), complete cds
Length=4546

 Score =  929 bits (2402),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 470/885 (53%), Positives = 624/885 (70%), Gaps = 16/885 (1%)
 Frame = +2

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS ++R+ LEA SD   +LH  LQE++ WL  KD+ELS Q P+ GD  +V
Sbjct  197   MNLCWNEIKKKSQSLRARLEAFSDPTLKLHPPLQEIIDWLGQKDEELSAQLPLRGDLSSV  376

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q+  D H  F  E+K++ P I S LE+ + FLT+ P    E+   + ++  P  +A+ ++
Sbjct  377   QQAKDKHVTFMEEVKSRGPYIYSVLESAQTFLTQHPFSDEEEDATQGKDSSPRSKAETLS  556

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             RLL KQA   +  W++L   S D  R ++ TLE++QEL  +  E    + Q E ++ SW+
Sbjct  557   RLLWKQASVASELWDRLTARSLDQHRHLERTLEQIQELGISMKEAGDSIGQGESVQASWE  736

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL DH++  K  + E++P+K+ V   NDLA QL    + LS  N   LE++N
Sbjct  737   PIGDLFIDSLPDHIQTTKLFKEELSPIKDMVKLANDLAHQLALCDVHLSMENARELENIN  916

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
             +RWK LQ +V +R+RQL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTT
Sbjct  917   SRWKQLQTSVGERLRQLQDAHRDFGPESQHFLSSSVQVPWERAISPNKVPYYINHQAQTT  1096

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+L DLNN++FSAYRTAMKLRR+QKAL LDL++L           L+  
Sbjct  1097  CWDHPKMTELYQALGDLNNIKFSAYRTAMKLRRVQKALRLDLVTLPLLTQIFTCDTLQSP  1276

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             ++ +D+L +I CL+++Y+RLE+E   LVNVPLCVD+ LNWLLNV+D  R GRIRVLSFK 
Sbjct  1277  ERNLDVLDVIRCLSSLYERLEEERGLLVNVPLCVDLTLNWLLNVFDGARNGRIRVLSFKA  1456

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
             GI+SLC   ++ K +YLF QVAS    CDQR+LGLLLH++IQIPRQLGEVA+FGGSN+EP
Sbjct  1457  GIVSLCDCDVKGKLQYLFSQVASPGNTCDQRQLGLLLHEAIQIPRQLGEVAAFGGSNVEP  1636

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
             SVRSCF+F N    +E A FL+W  LEPQSMVWLPVLHRV  AET KHQAKC++CK+CP+
Sbjct  1637  SVRSCFRFGNGTAHLELAQFLEWGCLEPQSMVWLPVLHRVTLAETVKHQAKCSVCKQCPM  1816

Query  862   IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
              GFRYRSLK F  DICQSCF +G+  K +K+HYP++EY TPTTSGE +RDFA  LKNKFR
Sbjct  1817  KGFRYRSLKQFGVDICQSCFLTGQAGKVNKLHYPIMEYYTPTTSGEKMRDFATTLKNKFR  1996

Query  922   TKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSY  981
             T++YF++HP+ GYLPVQ+VLE +  +TPASSP L H DTHSRIEH+ASRLAEME+ N S+
Sbjct  1997  TRQYFSRHPQRGYLPVQSVLEAEVADTPASSPMLPHADTHSRIEHFASRLAEMESQNCSF  2176

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLE  1041
               DS+SP++S+D++  L++H     ++D P + P+ P  +      EE+GELE+ILA LE
Sbjct  2177  FTDSLSPDDSLDEDQYLLRHSSPITDRD-PSNTPQIPGNL---NPEEEQGELEKILAHLE  2344

Query  1042  EENRNLQAEYDRLKQQHEHKG-LSPLPS-PPEMMPTSPQSPRDAELIAEAKLLRQHKGRL  1099
              ENR LQ E  RLK QH   G +S L    P++        +  EL++EA++LR HK RL
Sbjct  2345  HENRILQGELKRLKWQHAEAGEVSALGEVSPDVGGNGVGEAQSEELLSEARILRHHKNRL  2524

Query  1100  EARMQILEDHNKQLESQLHRLRQLLEQPQA-EAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             E RMQILEDHNKQLESQL RLR+LL QP   E K + ++ S  S S   ++ +       
Sbjct  2525  ETRMQILEDHNKQLESQLRRLRELLLQPNTDEGKPSSSSSSPDSQSKCPAEGN-------  2683

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVG  1203
               + T D+   +D+ S  ++    LE++ME+L N+FP++   ++ 
Sbjct  2684  --AGTPDTEAADDVESRTREVGLCLEDIMEKLRNAFPNTTDSDIA  2812


 Score = 61.2 bits (147),  Expect = 4e-06, Method: Compositional matrix adjust.
 Identities = 56/232 (24%), Positives = 105/232 (45%), Gaps = 27/232 (11%)
 Frame = +2

Query  21   ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNL---  77
            E+ DWL   D+ + +Q  + GDL  + +   K    M++++ R P +  ++ +AQ     
Sbjct  299  EIIDWLGQKDEELSAQLPLRGDLSSVQQAKDKHVTFMEEVKSRGPYIYSVLESAQTFLTQ  478

Query  78   -------------KNKTSNQEART---IITDRIERIQNQWDEVQEHLQNRRQQLNEMLKD  121
                         K+ +   +A T   ++  +       WD +     ++ + L   L+ 
Sbjct  479  HPFSDEEEDATQGKDSSPRSKAETLSRLLWKQASVASELWDRLTARSLDQHRHLERTLEQ  658

Query  122  STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              +   + +EA   +GQ  +   SW+  G   +D++   I  TK   ++L   +  V +A
Sbjct  659  IQELGISMKEAGDSIGQGESVQASWEPIGDLFIDSLPDHIQTTKLFKEELSPIKDMVKLA  838

Query  181  NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
            NDLA +L L D   S ++ R++    ENIN+ W+ +   V ER   L++ HR
Sbjct  839  NDLAHQLALCDVHLSMENAREL----ENINSRWKQLQTSVGERLRQLQDAHR  982


>ref|XM_001342272.2| PREDICTED: Danio rerio similar to dystrophin related protein 
2 (LOC100002550), mRNA
Length=2496

 Score =  929 bits (2401),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 458/810 (56%), Positives = 592/810 (73%), Gaps = 13/810 (1%)
 Frame = +1

Query  390   AFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAE  449
             AF  ++K++ P I S LE+ + FL + P +  E+   + +E+ P  R  NV+R + KQA 
Sbjct  25    AFMEDVKSRGPYIYSVLESAQTFLAQHPFQEPEETLPDGKEVSPRRRMLNVSRSVWKQAN  204

Query  450   EVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLID  509
               +  WEKL     D  R ++ TLERL ++Q A +EL   L QAE ++ +W+PVGDL ID
Sbjct  205   VASDLWEKLTARCVDRHRHMERTLERLLQIQAAMEELAAALEQAEGVRDAWEPVGDLFID  384

Query  510   SLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV  569
             SLQDH++  K  + E++ +KE + H+NDLA +L    + LS  N   LE LN RWKLLQ 
Sbjct  385   SLQDHIDATKLFKEELSQVKEGMKHINDLAHELAISDVHLSMDNARALEHLNNRWKLLQG  564

Query  570   AVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMT  629
             ++E+R++QL +AHRDFGP SQHFLS+SVQ PWERAISPNKVPYYINH+ QTTCWDHPKMT
Sbjct  565   SIEERLKQLQDAHRDFGPGSQHFLSSSVQIPWERAISPNKVPYYINHQAQTTCWDHPKMT  744

Query  630   ELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQ  689
             ELYQ+LADLNN++FSAYRTAMKLR +QKAL LDL  LS+  D   +  L+  +  MD+++
Sbjct  745   ELYQALADLNNIKFSAYRTAMKLRHVQKALRLDLFKLSSVVDVFREQELQHGEHVMDVVE  924

Query  690   IINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKA  749
             +I+ LT++Y+RLE+E + L+N+PLCVDMCLNWLLNVYD+GR G++RVLSFK G++ LC A
Sbjct  925   VIHALTSLYERLEEERSVLINIPLCVDMCLNWLLNVYDSGRNGKMRVLSFKMGLVILCNA  1104

Query  750   HLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF  809
              +++KY+YLF+QV    G  DQ+ L LLLH++IQ+PRQLGEVA+FGGSN+EPSVRSCF+ 
Sbjct  1105  DIQEKYKYLFRQVCGPGGLTDQKHLSLLLHEAIQVPRQLGEVAAFGGSNVEPSVRSCFRM  1284

Query  810   ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + K  IE + FL+WM LEPQS+VWLPVLHRV  AETAKHQA+C ICK+CPI GFRYRSL
Sbjct  1285  VSGKSAIELSHFLEWMSLEPQSVVWLPVLHRVTVAETAKHQARCYICKQCPIKGFRYRSL  1464

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKH  929
             K FN DICQ+CF +GR  KG K+HYP++EY TPTTSGE +RDFAK LKNKFR+K+YF+KH
Sbjct  1465  KQFNVDICQTCFLTGRTTKGKKLHYPIMEYYTPTTSGEKMRDFAKTLKNKFRSKQYFSKH  1644

Query  930   PRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPN  989
             P+ GYLPVQ+VLE ++ ETP SSP+L H DTHSRIEH+ASRLAEMEN N S+  DS+SP+
Sbjct  1645  PQRGYLPVQSVLEVESSETPCSSPRLPHADTHSRIEHFASRLAEMENQNCSFFTDSLSPD  1824

Query  990   ESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQA  1049
             ES+D++  L++H   SL QDSP         +L  L+ ++R EL+R L  LE ENR LQ 
Sbjct  1825  ESLDEDQYLLRHSSPSLEQDSP------HGLMLAQLDCQDREELQRTLHRLENENRVLQG  1986

Query  1050  EYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDH  1109
             EY RLK +HE    S  P   E  P SP   +D EL+AEA++LRQHK RLE RMQILEDH
Sbjct  1987  EYRRLKWKHEEAAAS--PQLLESGPGSPPGQQDEELLAEARVLRQHKTRLETRMQILEDH  2160

Query  1110  NKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGE  1169
             NKQLESQL RLR+LL QP+ +++ NG+  SS S+ +      +P        +T+D+   
Sbjct  2161  NKQLESQLRRLRELLLQPKDDSEANGSAPSSLSSPVSGGHQGEP-----PSRETTDTEAA  2325

Query  1170  EDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
              + L   QDT   L++V+EQL N FPS  G
Sbjct  2326  GEDLDHEQDTVLQLQQVIEQLRNVFPSEPG  2415


>ref|XM_001863085.1| Culex quinquefasciatus dystrophin major muscle, mRNA
Length=10440

 Score =  912 bits (2358),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 530/1295 (40%), Positives = 778/1295 (60%), Gaps = 126/1295 (9%)
 Frame = +1

Query  17     RAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQN  76
              ++ +++ +WL L  +++    V+ GD + +   I K K T++ LE ++ Q++E++T   N
Sbjct  6637   QSMSQIANWLQLEHELLNKHCVVFGDTDMMLSAIEKGKNTIKQLENKKAQIDEIVTVVDN  6816

Query  77     LKNKTSNQ--EARTII----------------TDRI------ERIQNQWDEVQEHLQNRR  112
              LK+ T+ Q  E +                   T++I       R+++QW++  + +  R+
Sbjct  6817   LKSDTNYQYLENKDFYLMFYSFCCSPSQHVSKTNQIYHFLVATRMRDQWEDTSQSVLERK  6996

Query  113    QQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQ  172
               QL  ML DS ++   + + E  L +  ++ E       T D ++ +  E K    +L Q
Sbjct  6997   SQLTAMLGDSQRYEAKRIDIESWLNRMESRSERMGVVATTADVLEIQQKEQKSFHAELHQ  7176

Query  173    WQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQ  232
              ++ ++++ N L  KL+  Y +DDT ++  +TE++N  + +++  V  R  +L      LQ
Sbjct  7177   YKHHIELFNQLTQKLIAVYPSDDTSRIKRMTESVNLRYNNLNNAVISRGKSLHAAVHSLQ  7356

Query  233    QFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKG-VKELMKQWQDLQGEIEAHTDV  291
               F   L++FL WL+EAE+             L E+++  +      ++DLQ EIE+H  +
Sbjct  7357   SFDKSLDQFLGWLSEAES-------------LCENTESEIDRNPHSFKDLQSEIESHRII  7497

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
              Y  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ KS+ IR+ LE++S+ W  L 
Sbjct  7498   YERLDSTGKKLLGSLTSQEDAVMLQRRLDEMNQRWNHLKFKSVAIRNRLESNSEHWNALL  7677

Query  352    LSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETV  409
              LSL+EL  W+  KD EL+     P+ GD  ++QKQ D HRAF+R+L+ K PV+ + L T 
Sbjct  7678   LSLRELTEWVIRKDTELTSLGLGPMKGDAASLQKQTDDHRAFRRQLEDKRPVVENNLLTG  7857

Query  410    RIFLTEQP----LEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADW  465
              R ++ ++P        E +  E R L  EE+ + +TR +R++  +++ +W  L   S +W
Sbjct  7858   RQYIAKEPPLSDTSDSEAIDSESRYLSAEEQNKELTRSIRREVSKLSEQWNHLIDRSDNW  8037

Query  466    QRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ-PVGDLLIDSLQDHLEKVKALRGE  524
              + +++E + ++++ Q+  D+L  ++  AE +  SW  PV          HL+++K     
Sbjct  8038   KHRLEEYMTKMRQFQKVLDDLSSRVASAETLTQSWTTPVTTADSAEQMQHLQRLKDKMTT  8217

Query  525    IAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------VR  576
                 L ++    N+     T   + +    L+ LEDLNTR KLL +A+++R          
Sbjct  8218   AGALLDDC---NEQQGFFTANHVLVPNQCLAKLEDLNTRMKLLHIAMDERHKILIANGAN  8388

Query  577    QLHEAHRDFGPASQHFLST-----------SVQGPWERAISPNKVPYYINHETQTTCWDH  625
              Q   A  D G  S H +ST           SV+ PWERAI+P  VPYYINHE + T WDH
Sbjct  8389   QSSTADPD-GNKSTHGISTGTIGPIPNLATSVKPPWERAITPANVPYYINHERENTHWDH  8565

Query  626    PKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQP  684
              P+M EL +SLADLN+VRFSAYRTA+KLR +QK L  D L+++ A ++ D+H L+ QND+ 
Sbjct  8566   PEMIELMKSLADLNDVRFSAYRTALKLRTVQKRLAFDRLTMNVAIESFDRHGLRAQNDKL  8745

Query  685    MDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGII  744
              +DI  +   L ++Y  +E      +++PL +D+ +NW+LNVYD+ RTG+IRVLSFK G+I
Sbjct  8746   IDIPDMTTVLHSLYVTIEP-----IDMPLMLDLAINWILNVYDSQRTGQIRVLSFKVGLI  8910

Query  745    SLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVR  804
               LCK HLE+KYRYLF+ +A      DQR+LGLLLHD IQ+PRQLGEVA+FGGSNIEPSVR
Sbjct  8911   LLCKGHLEEKYRYLFRLIADLEKKVDQRKLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVR  9090

Query  805    SCFQFA----NNKP---EIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICK  857
              SCF+ A    N +P    IEA  FL+W++ EPQS+VWLPVLHR+ AAE AKHQAKCNICK
Sbjct  9091   SCFERAGVNQNGEPLETAIEAQHFLNWLQHEPQSLVWLPVLHRLVAAEAAKHQAKCNICK  9270

Query  858    ECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLK  917
              E PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF + L+
Sbjct  9271   EYPIVGFRYRCLKCFNFDMCQKCFFLGRNAKNHKLSHPMHEYCTTTTSTEDVRDFTRALR  9450

Query  918    NKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLAE  973
              NKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ       +D HSR+E YASRLA+
Sbjct  9451   NKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHGAHTLQNDMHSRLEMYASRLAQ  9630

Query  974    MENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGEL  1033
              +E    S    S +P+   DDEH LI  YCQSL  +     P+SP Q++ ++++E+R EL
Sbjct  9631   VEYGTRS----SSTPDS--DDEHQLIAQYCQSLPNNGG---PKSPIQVMAAMDAEQREEL  9783

Query  1034   ERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLR  1093
              E ++ DLE+EN +LQAEY+RLK +      + + +P E       +    +++AEAKLLR
Sbjct  9784   EAMIKDLEDENSSLQAEYERLKSKQ-----TSITTPDE---NQAGANGGNDMVAEAKLLR  9939

Query  1094   QHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQP  1153
              QHKGRLEARMQILEDHN+QLE+QL RLRQLL++P        +T+ + S +  + ++  P
Sbjct  9940   QHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEPN---NSKASTLQTRSVTASQLNTESP  10110

Query  1154   MLLRVVGSQTSDSMGEEDLLSPP--------------QDTSTGLEEVMEQLNN---SFPS  1196
              +  +  G     S  E    S                 D       V +  NN   SF S
Sbjct  10111  VKFQQNGHHDQKSSLENGTSSGSFHNNAGISGLSSGGGDNDRSKPGVGKNENNIGVSFAS  10290

Query  1197   SRGHNV----GSLFHMADDLGRAMESLVSVMTDEE  1227
              S          SL HMA DL +A+E LV+V+T++E
Sbjct  10291  SDARPPPPPHTSLLHMAGDLNKAVEELVNVITEQE  10395


>ref|NM_001043259.1| Drosophila melanogaster dystrophin (Dys), transcript variant 
C, mRNA
Length=10554

 Score =  903 bits (2333),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 500/1161 (43%), Positives = 719/1161 (61%), Gaps = 80/1161 (6%)
 Frame = +1

Query  13    ADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELIT  72
               F+++  +++DWL+    +IK Q V+V D + +   I KQ+  +++L+ ++PQL EL+ 
Sbjct  6109  GSFDKSVLQISDWLTWEQNMIKIQSVLVDDGDAVRLAIEKQEKVLRELKMKKPQLNELVH  6288

Query  73    AAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEA  132
              A+ LK     Q+    + +++ R++  WDE  + +  R  QL  ML DS ++   + E 
Sbjct  6289  TAEVLKGDVKRQQ----LQEKVTRLREHWDETSQCVLQRAAQLKNMLSDSQRFEAKRLEL  6456

Query  133   EQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS  192
             E+ L +   + E       T D ++ +  E K    +L Q + + D+ N+L  KL+  Y 
Sbjct  6457  EKWLARMEQRAERMGTIATTADILEAQQKEQKSFHAELHQNKQHFDIFNELTQKLIAVYP  6636

Query  193   ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
              DDT ++  +TE IN  + +++  V  R   L      LQ F   +++FLA+L+E ET  
Sbjct  6637  NDDTTRIKKMTEVINQRYANLNSGVINRGKQLHAAVHSLQSFDRAMDQFLAFLSETETLC  6816

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
                +    +  L+            ++DLQ EIE H  VY  LD   +K+L SL   +DA
Sbjct  6817  ENAESDIERNPLM------------FKDLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDA  6960

Query  313   VLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA  372
             V+LQRRLD MN +W+ L+ KS+ IR+ LE++S+ W  L LSL+EL  W+  KD ELS   
Sbjct  6961  VMLQRRLDEMNQRWNNLKSKSIAIRNRLESNSEHWNALLLSLRELTEWVIRKDTELSTLG  7140

Query  373   --PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPL-----EGLEKLY  425
               P+ GD  ++QKQ D H+AF+R+L+ K P++ S L + R ++  +       +      
Sbjct  7141  LGPVRGDAVSLQKQLDDHKAFRRQLEDKRPIVESNLTSGRQYIANEAAVSDTSDTEANHD  7320

Query  426   QEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDE  485
              + R +  EE+++ +TR +R++  +++ +W  L   S +W+ ++DE + ++++ Q+  ++
Sbjct  7321  SDSRYMSAEEQSRELTRSIRREVGKLSEQWNNLIDRSDNWKHRLDEYMTKMRQFQKILED  7500

Query  486   LDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTL  545
             L  ++  AE  K SW P     +    + +++++ LR ++      +   N+     T  
Sbjct  7501  LSSRVALAEQTKTSWLPPSS--VGEANEQMQQLQRLRDKMTTASALLDDCNEQQSFFTAN  7674

Query  546   GIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------VRQLHEAHRD---------FGPA  588
              + +    LS LEDLNTR KLLQ+A+++R         +Q HE   D          GP 
Sbjct  7675  QVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCQAGAQQTHENGDDGRTTSNSGTIGPL  7854

Query  589   SQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRT  648
                 L  SV+ PWERA +   VPYYI+HE +TT WDHP+M EL + LADLN +RFSAYRT
Sbjct  7855  PN--LGQSVKPPWERATTAANVPYYIDHERETTHWDHPEMIELMKGLADLNEIRFSAYRT  8028

Query  649   AMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNN  707
             AMKLR +QK L LD +S+S AC++ D+H L+ QND+ +DI  +   L ++Y  +++    
Sbjct  8029  AMKLRSVQKRLALDRISMSTACESFDRHGLRAQNDKLIDIPDMTTVLHSLYVTIDK----  8196

Query  708   LVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTG  767
              +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ LCK HLE+KYRYLF+ VA +  
Sbjct  8197  -IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVLLCKGHLEEKYRYLFRLVADTDR  8373

Query  768   FCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA---------NNKPEIEA  818
               DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRSC + A         N    IE 
Sbjct  8374  RADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRSCLEQAGISQEAIDGNQDISIEL  8553

Query  819   ALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQ  878
               FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNICKE PI+GFRYR LK FN+D+CQ
Sbjct  8554  QHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNICKEYPIVGFRYRCLKCFNFDMCQ  8733

Query  879   SCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQ  938
              CFF GR AK HK+ +PM EYCT TTS EDVRDF + LKNKF++++YF KHPR+GYLPVQ
Sbjct  8734  KCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQ  8913

Query  939   TVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDD  994
             +VLEGD +E+PA SPQ +     +D HSR+E YASRLA++E     Y     +     DD
Sbjct  8914  SVLEGDALESPAPSPQHTTHQLQNDMHSRLEMYASRLAQVE-----YGGTGSNSTPDSDD  9078

Query  995   EHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRL  1054
             EH LI  YCQ+L   S  S P+SP Q++ ++++E+R ELE I+ DLEEEN NLQAEY +L
Sbjct  9079  EHQLIAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREELEAIIRDLEEENANLQAEYQQL  9258

Query  1055  KQQHEHKGLSPLP--------SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQIL  1106
               + +    S +P        S   M   S Q  +  +++AEAKLLRQHKGRLEARMQIL
Sbjct  9259  CSKEQ----SGMPEDSNGMQHSSSSMTGLSGQGEQGQDMMAEAKLLRQHKGRLEARMQIL  9426

Query  1107  EDHNKQLESQLHRLRQLLEQP  1127
             EDHN+QLE+QL RLRQLL++P
Sbjct  9427  EDHNRQLEAQLQRLRQLLDEP  9489


>gb|AF277386.1|AF277386 Drosophila melanogaster dystrophin-like protein DYS (Dys) mRNA, 
complete cds
Length=10181

 Score =  903 bits (2333),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 500/1161 (43%), Positives = 719/1161 (61%), Gaps = 80/1161 (6%)
 Frame = +2

Query  13    ADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELIT  72
               F+++  +++DWL+    +IK Q V+V D + +   I KQ+  +++L+ ++PQL EL+ 
Sbjct  5720  GSFDKSVLQISDWLTWEQNMIKIQSVLVDDGDAVRLAIEKQEKVLRELKMKKPQLNELVH  5899

Query  73    AAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEA  132
              A+ LK     Q+    + +++ R++  WDE  + +  R  QL  ML DS ++   + E 
Sbjct  5900  TAEVLKGDVKRQQ----LQEKVTRLREHWDETSQCVLQRAAQLKNMLSDSQRFEAKRLEL  6067

Query  133   EQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS  192
             E+ L +   + E       T D ++ +  E K    +L Q + + D+ N+L  KL+  Y 
Sbjct  6068  EKWLARMEQRAERMGTIATTADILEAQQKEQKSFHAELHQNKQHFDIFNELTQKLIAVYP  6247

Query  193   ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
              DDT ++  +TE IN  + +++  V  R   L      LQ F   +++FLA+L+E ET  
Sbjct  6248  NDDTTRIKKMTEVINQRYANLNSGVINRGKQLHAAVHSLQSFDRAMDQFLAFLSETETLC  6427

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
                +    +  L+            ++DLQ EIE H  VY  LD   +K+L SL   +DA
Sbjct  6428  ENAESDIERNPLM------------FKDLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDA  6571

Query  313   VLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA  372
             V+LQRRLD MN +W+ L+ KS+ IR+ LE++S+ W  L LSL+EL  W+  KD ELS   
Sbjct  6572  VMLQRRLDEMNQRWNNLKSKSIAIRNRLESNSEHWNALLLSLRELTEWVIRKDTELSTLG  6751

Query  373   --PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPL-----EGLEKLY  425
               P+ GD  ++QKQ D H+AF+R+L+ K P++ S L + R ++  +       +      
Sbjct  6752  LGPVRGDAVSLQKQLDDHKAFRRQLEDKRPIVESNLTSGRQYIANEAAVSDTSDTEANHD  6931

Query  426   QEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDE  485
              + R +  EE+++ +TR +R++  +++ +W  L   S +W+ ++DE + ++++ Q+  ++
Sbjct  6932  SDSRYMSAEEQSRELTRSIRREVGKLSEQWNNLIDRSDNWKHRLDEYMTKMRQFQKILED  7111

Query  486   LDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTL  545
             L  ++  AE  K SW P     +    + +++++ LR ++      +   N+     T  
Sbjct  7112  LSSRVALAEQTKTSWLPPSS--VGEANEQMQQLQRLRDKMTTASALLDDCNEQQSFFTAN  7285

Query  546   GIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------VRQLHEAHRD---------FGPA  588
              + +    LS LEDLNTR KLLQ+A+++R         +Q HE   D          GP 
Sbjct  7286  QVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCQAGAQQTHENGDDGRTTSNSGTIGPL  7465

Query  589   SQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRT  648
                 L  SV+ PWERA +   VPYYI+HE +TT WDHP+M EL + LADLN +RFSAYRT
Sbjct  7466  PN--LGQSVKPPWERATTAANVPYYIDHERETTHWDHPEMIELMKGLADLNEIRFSAYRT  7639

Query  649   AMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNN  707
             AMKLR +QK L LD +S+S AC++ D+H L+ QND+ +DI  +   L ++Y  +++    
Sbjct  7640  AMKLRSVQKRLALDRISMSTACESFDRHGLRAQNDKLIDIPDMTTVLHSLYVTIDK----  7807

Query  708   LVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTG  767
              +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ LCK HLE+KYRYLF+ VA +  
Sbjct  7808  -IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVLLCKGHLEEKYRYLFRLVADTDR  7984

Query  768   FCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA---------NNKPEIEA  818
               DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRSC + A         N    IE 
Sbjct  7985  RADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRSCLEQAGISQEAIDGNQDISIEL  8164

Query  819   ALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQ  878
               FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNICKE PI+GFRYR LK FN+D+CQ
Sbjct  8165  QHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNICKEYPIVGFRYRCLKCFNFDMCQ  8344

Query  879   SCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQ  938
              CFF GR AK HK+ +PM EYCT TTS EDVRDF + LKNKF++++YF KHPR+GYLPVQ
Sbjct  8345  KCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQ  8524

Query  939   TVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDD  994
             +VLEGD +E+PA SPQ +     +D HSR+E YASRLA++E     Y     +     DD
Sbjct  8525  SVLEGDALESPAPSPQHTTHQLQNDMHSRLEMYASRLAQVE-----YGGTGSNSTPDSDD  8689

Query  995   EHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRL  1054
             EH LI  YCQ+L   S  S P+SP Q++ ++++E+R ELE I+ DLEEEN NLQAEY +L
Sbjct  8690  EHQLIAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREELEAIIRDLEEENANLQAEYQQL  8869

Query  1055  KQQHEHKGLSPLP--------SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQIL  1106
               + +    S +P        S   M   S Q  +  +++AEAKLLRQHKGRLEARMQIL
Sbjct  8870  CSKEQ----SGMPEDSNGMQHSSSSMTGLSGQGEQGQDMMAEAKLLRQHKGRLEARMQIL  9037

Query  1107  EDHNKQLESQLHRLRQLLEQP  1127
             EDHN+QLE+QL RLRQLL++P
Sbjct  9038  EDHNRQLEAQLQRLRQLLDEP  9100


>ref|XM_001954777.1| Drosophila ananassae GF16554 (Dana\GF16554), mRNA
Length=10494

 Score =  894 bits (2310),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 504/1178 (42%), Positives = 722/1178 (61%), Gaps = 91/1178 (7%)
 Frame = +1

Query  13     ADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELIT  72
                F+++  +++DWL+    +IK Q V+V D++ +   I KQ+  +++L+ ++PQL EL+ 
Sbjct  6718   GSFDKSVLQISDWLTWEQNMIKIQSVLVDDVDAVRLAIEKQEKVLRELKMKKPQLNELVH  6897

Query  73     AAQNLKNKTSNQE-----------ARTIITD--------RIERIQNQWDEVQEHLQNRRQ  113
               A+ LK+    Q+           A     D        ++ R++  WDE  + +  R  
Sbjct  6898   TAEVLKSDVKRQQLQEKELKQFSLAPHCSADLDYMRCCLKVTRLREHWDETSQCVLQRAA  7077

Query  114    QLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
              QL  ML DS ++   + E E+ L +   + E       T D ++ +  E K    +L Q 
Sbjct  7078   QLKNMLSDSQRFEAKRVELEKWLTRMEQRAERMGTIATTADILEAQQKEQKSFHAELHQN  7257

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              + + D+ N+L  KL+  Y  DDT ++  +TE IN  + +++  V  R   L      LQ 
Sbjct  7258   KQHFDLFNELTQKLIAVYPNDDTTRIKKMTEAINQRYANLNNGVINRGKQLHAAVHNLQS  7437

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYH  293
              F   +++FLA+L+E ET     +    +  L+            ++DLQ EIE H  VY 
Sbjct  7438   FDRAMDQFLAFLSETETLCENAESDIERNPLM------------FKDLQSEIETHRVVYD  7581

Query  294    NLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS  353
               LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ KS+ IR+ LE++S+ W  L LS
Sbjct  7582   RLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSKSIAIRNRLESNSEHWNALLLS  7761

Query  354    LQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
              L+EL  W+  KD ELS     P+ GD  ++QKQ D H+AF+R+L+ K P++ S L + R 
Sbjct  7762   LRELTEWVIRKDTELSTLGLGPVRGDAASLQKQLDDHKAFRRQLEDKRPIVESNLTSGRQ  7941

Query  412    FLTEQPL-----EGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQ  466
              ++  +       +       + R L  EE+++ +TR +R++  +++ +W  L   S +W+
Sbjct  7942   YIANEAAVSDTSDSEANHDSDSRYLSAEEQSRELTRSIRREVGKLSEQWNNLIDRSDNWK  8121

Query  467    RKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIA  526
               ++DE + ++++ Q+  ++L  ++  AE  K SW P     +    + +++++ LR ++ 
Sbjct  8122   HRLDEYMTKMRQFQKILEDLSSRVALAEQTKTSWLPPAS--VGEANEQMQQLQRLRDKMT  8295

Query  527    PLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------VRQL  578
                   +   N+     T   + +    LS LEDLNTR KLLQ+A+++R         +Q 
Sbjct  8296   TASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCQNGAQQS  8475

Query  579    HEAHRD---------FGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMT  629
              HE   D          GP     L  SV+ PWERA +   VPYYI+HE +TT WDHP+M 
Sbjct  8476   HENGDDGRTTSNSGTIGPLPN--LGQSVKPPWERATTSANVPYYIDHERETTHWDHPEMI  8649

Query  630    ELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPMDIL  688
              EL + LADLN +RFSAYRTAMKLR +QK L LD +S++ AC++ D+H L+ QND+ +DI 
Sbjct  8650   ELMKGLADLNEIRFSAYRTAMKLRSVQKRLALDRISMATACESFDRHGLRAQNDKLIDIP  8829

Query  689    QIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCK  748
               +   L ++Y  +++     +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ LCK
Sbjct  8830   DMTTVLHSLYVTIDK-----IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVLLCK  8994

Query  749    AHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
               HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRSC +
Sbjct  8995   GHLEEKYRYLFRLVADTERRADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRSCLE  9174

Query  809    FA---------NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKEC  859
               A         N +  IE   FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNICKE 
Sbjct  9175   QAGISQEAIDGNQEISIELQHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNICKEY  9354

Query  860    PIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNK  919
              PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF + LKNK
Sbjct  9355   PIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFGRALKNK  9534

Query  920    FRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLAEME  975
              F++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ +      D HSR+E YASRLA++E
Sbjct  9535   FKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQSDMHSRLEMYASRLAQVE  9714

Query  976    NSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELER  1035
                   Y     +     DDEH LI  YCQ+L   S  S P+SP Q++ ++++E+R ELE 
Sbjct  9715   -----YGGTGSNSTPDSDDEHQLIAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREELEA  9879

Query  1036   ILADLEEENRNLQAEYDRL--KQQ----HEHKGLSPLPSPPEMMPTSPQSPRDAELIAEA  1089
              I+ DLEEEN NLQAEY +L  KQQ     +  G+    S   M   S Q  +  +++AEA
Sbjct  9880   IIRDLEEENANLQAEYQQLCSKQQSGTPEDSNGMQ--HSSSSMTGLSGQGEQGQDMMAEA  10053

Query  1090   KLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              KLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  10054  KLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  10167


>ref|NM_001043257.1| Drosophila melanogaster dystrophin (Dys), transcript variant 
H, mRNA
Length=11967

 Score =  894 bits (2309),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 502/1180 (42%), Positives = 719/1180 (60%), Gaps = 95/1180 (8%)
 Frame = +1

Query  13     ADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELIT  72
                F+++  +++DWL+    +IK Q V+V D + +   I KQ+  +++L+ ++PQL EL+ 
Sbjct  7150   GSFDKSVLQISDWLTWEQNMIKIQSVLVDDGDAVRLAIEKQEKVLRELKMKKPQLNELVH  7329

Query  73     AAQNLKNKTSNQE-----------ARTIITD--------RIERIQNQWDEVQEHLQNRRQ  113
               A+ LK     Q+           A     D        ++ R++  WDE  + +  R  
Sbjct  7330   TAEVLKGDVKRQQLQEKELKQFSLAPHCSADLDYMRCCLKVTRLREHWDETSQCVLQRAA  7509

Query  114    QLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
              QL  ML DS ++   + E E+ L +   + E       T D ++ +  E K    +L Q 
Sbjct  7510   QLKNMLSDSQRFEAKRLELEKWLARMEQRAERMGTIATTADILEAQQKEQKSFHAELHQN  7689

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              + + D+ N+L  KL+  Y  DDT ++  +TE IN  + +++  V  R   L      LQ 
Sbjct  7690   KQHFDIFNELTQKLIAVYPNDDTTRIKKMTEVINQRYANLNSGVINRGKQLHAAVHSLQS  7869

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYH  293
              F   +++FLA+L+E ET     +    +  L+            ++DLQ EIE H  VY 
Sbjct  7870   FDRAMDQFLAFLSETETLCENAESDIERNPLM------------FKDLQSEIETHRVVYD  8013

Query  294    NLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS  353
               LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ KS+ IR+ LE++S+ W  L LS
Sbjct  8014   RLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSKSIAIRNRLESNSEHWNALLLS  8193

Query  354    LQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
              L+EL  W+  KD ELS     P+ GD  ++QKQ D H+AF+R+L+ K P++ S L + R 
Sbjct  8194   LRELTEWVIRKDTELSTLGLGPVRGDAVSLQKQLDDHKAFRRQLEDKRPIVESNLTSGRQ  8373

Query  412    FLTEQPL-----EGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQ  466
              ++  +       +       + R +  EE+++ +TR +R++  +++ +W  L   S +W+
Sbjct  8374   YIANEAAVSDTSDTEANHDSDSRYMSAEEQSRELTRSIRREVGKLSEQWNNLIDRSDNWK  8553

Query  467    RKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIA  526
               ++DE + ++++ Q+  ++L  ++  AE  K SW P     +    + +++++ LR ++ 
Sbjct  8554   HRLDEYMTKMRQFQKILEDLSSRVALAEQTKTSWLPPSS--VGEANEQMQQLQRLRDKMT  8727

Query  527    PLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------VRQL  578
                   +   N+     T   + +    LS LEDLNTR KLLQ+A+++R         +Q 
Sbjct  8728   TASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCQAGAQQT  8907

Query  579    HEAHRD---------FGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMT  629
              HE   D          GP     L  SV+ PWERA +   VPYYI+HE +TT WDHP+M 
Sbjct  8908   HENGDDGRTTSNSGTIGPLPN--LGQSVKPPWERATTAANVPYYIDHERETTHWDHPEMI  9081

Query  630    ELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPMDIL  688
              EL + LADLN +RFSAYRTAMKLR +QK L LD +S+S AC++ D+H L+ QND+ +DI 
Sbjct  9082   ELMKGLADLNEIRFSAYRTAMKLRSVQKRLALDRISMSTACESFDRHGLRAQNDKLIDIP  9261

Query  689    QIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCK  748
               +   L ++Y  +++     +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ LCK
Sbjct  9262   DMTTVLHSLYVTIDK-----IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVLLCK  9426

Query  749    AHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
               HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRSC +
Sbjct  9427   GHLEEKYRYLFRLVADTDRRADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRSCLE  9606

Query  809    FA---------NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKEC  859
               A         N    IE   FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNICKE 
Sbjct  9607   QAGISQEAIDGNQDISIELQHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNICKEY  9786

Query  860    PIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNK  919
              PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF + LKNK
Sbjct  9787   PIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFTRALKNK  9966

Query  920    FRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLAEME  975
              F++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ +     +D HSR+E YASRLA++E
Sbjct  9967   FKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQNDMHSRLEMYASRLAQVE  10146

Query  976    NSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELER  1035
                   Y     +     DDEH LI  YCQ+L   S  S P+SP Q++ ++++E+R ELE 
Sbjct  10147  -----YGGTGSNSTPDSDDEHQLIAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREELEA  10311

Query  1036   ILADLEEENRNLQAEYDRLKQQHEHKGLSPLP--------SPPEMMPTSPQSPRDAELIA  1087
              I+ DLEEEN NLQAEY +L  + +    S +P        S   M   S Q  +  +++A
Sbjct  10312  IIRDLEEENANLQAEYQQLCSKEQ----SGMPEDSNGMQHSSSSMTGLSGQGEQGQDMMA  10479

Query  1088   EAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              EAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  10480  EAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  10599


>gb|AF297644.1|AF297644 Drosophila melanogaster dystrophin-like protein DLP2 mRNA, complete 
cds
Length=11000

 Score =  892 bits (2306),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 505/1183 (42%), Positives = 721/1183 (60%), Gaps = 96/1183 (8%)
 Frame = +1

Query  11     ALA-DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEE  69
              ALA  F+++  +++DWL+    +IK Q V+V D + +   I KQ+  +++L+ ++PQL E
Sbjct  7141   ALAGSFDKSVLQISDWLTWEQNMIKIQSVLVDDGDAVRLAIEKQEKVLRELKMKKPQLNE  7320

Query  70     LITAAQNLKNKTSNQE-----------ARTIITD--------RIERIQNQWDEVQEHLQN  110
              L+  A+ LK     Q+           A     D        ++ R++  WDE  + +  
Sbjct  7321   LVHTAEVLKGDVKRQQLQEKELKQFSLAPHCSADLDYMRCCLKVTRLREHWDETSQCVLQ  7500

Query  111    RRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDL  170
              R  QL  ML DS ++   + E E+ L +   + E       T D ++ +  E K    +L
Sbjct  7501   RAAQLKNMLSDSQRFEAKRLELEKWLARMEQRAERMGTIATTADILEAQQKEQKSFHAEL  7680

Query  171    RQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRL  230
               Q + + D+ N+L  KL+  Y  DDT ++  +TE IN  + +++  V  R   L      
Sbjct  7681   HQNKQHFDIFNELTQKLIAVYPNDDTTRIKKMTEVINQRYANLNSGVINRGKQLHAAVHS  7860

Query  231    LQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTD  290
              LQ F   +++FLA+L+E ET     +    +  L+            ++DLQ EIE H  
Sbjct  7861   LQSFDRAMDQFLAFLSETETLCENAESDIERNPLM------------FKDLQSEIETHRV  8004

Query  291    VYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRL  350
              VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ KS+ IR+ LE++S+ W  L
Sbjct  8005   VYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSKSIAIRNRLESNSEHWNAL  8184

Query  351    HLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
               LSL+EL  W+  KD ELS     P+ GD  ++QKQ D H+AF+R+L+ K P++ S L +
Sbjct  8185   LLSLRELTEWVIRKDTELSTLGLGPVRGDAASLQKQLDDHKAFRRQLEDKRPIVESNLTS  8364

Query  409    VRIFLTEQPL-----EGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSA  463
               R ++  +       +       + R +  EE+++ + R +R++  +++ +W  L   S 
Sbjct  8365   GRQYIANEAAVSDTSDTEANHDSDSRYMSAEEQSRELRRSIRREVGKLSEQWNNLLDRSD  8544

Query  464    DWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRG  523
              +W+ ++DE + ++++ Q+  ++L  ++  AE  K SW P     +    + +++++ LR 
Sbjct  8545   NWKHRLDEYMTKMRQFQKILEDLSSRVALAEQTKTSWLPPSS--VGEANEQMQQLQRLRD  8718

Query  524    EIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------V  575
              ++      +   N+     T   + +    LS LEDLNTR KLLQ+A+++R         
Sbjct  8719   KMTTASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCQAGA  8898

Query  576    RQLHEAHRD---------FGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHP  626
              +Q HE   D          GP     L  SV+ PWERA +   VPYYI+HE QTT WDHP
Sbjct  8899   QQTHENGDDGRTTSNSGTIGPLPN--LGQSVKPPWERATTAANVPYYIDHERQTTHWDHP  9072

Query  627    KMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPM  685
              +M EL + LADLN +RFSAYRTAMKLR +QK L LD +S+S AC++ D+H L+ QND+ +
Sbjct  9073   EMIELMKGLADLNEIRFSAYRTAMKLRSVQKRLALDRISMSTACESFDRHGLRAQNDKLI  9252

Query  686    DILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIIS  745
              DI  +   L ++Y  +++     +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ 
Sbjct  9253   DIPDMTTVLHSLYVTIDK-----IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVL  9417

Query  746    LCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRS  805
              LCK HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRS
Sbjct  9418   LCKGHLEEKYRYLFRLVADTDRRADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRS  9597

Query  806    CFQFA---------NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNIC  856
              C + A         N    IE   FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNIC
Sbjct  9598   CLEQAGISQEAIDGNQDISIELQHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNIC  9777

Query  857    KECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVL  916
              KE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF + L
Sbjct  9778   KEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFTRAL  9957

Query  917    KNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLA  972
              KNKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ +     +D HSR+E YASRLA
Sbjct  9958   KNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQNDMHSRLEMYASRLA  10137

Query  973    EMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGE  1032
              ++E     Y     +     DDEH LI  YCQ+L   S  S P+SP Q++ ++++E+R E
Sbjct  10138  QVE-----YGGTGSNSTPDSDDEHQLIAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREE  10302

Query  1033   LERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP--------SPPEMMPTSPQSPRDAE  1084
              LE I+ DLEEEN NLQAEY +L  + +    S +P        S   M   S Q  +  +
Sbjct  10303  LEAIIRDLEEENANLQAEYQQLCSKEQ----SGMPEDSNGMQHSSSSMTGLSGQGEQGQD  10470

Query  1085   LIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              ++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  10471  MMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  10599


>ref|NM_001043263.1| Drosophila melanogaster dystrophin (Dys), transcript variant 
F, mRNA
Length=11588

 Score =  892 bits (2305),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 505/1183 (42%), Positives = 722/1183 (61%), Gaps = 96/1183 (8%)
 Frame = +3

Query  11     ALA-DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEE  69
              ALA  F+++  +++DWL+    +IK Q V+V D + +   I KQ+  +++L+ ++PQL E
Sbjct  7065   ALAGSFDKSVLQISDWLTWEQNMIKIQSVLVDDGDAVRLAIEKQEKVLRELKMKKPQLNE  7244

Query  70     LITAAQNLKNKTSNQE-----------ARTIITD--------RIERIQNQWDEVQEHLQN  110
              L+  A+ LK     Q+           A     D        ++ R++  WDE  + +  
Sbjct  7245   LVHTAEVLKGDVKRQQLQEKELKQFSLAPHCSADLDYMRCCLKVTRLREHWDETSQCVLQ  7424

Query  111    RRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDL  170
              R  QL  ML DS ++   + E E+ L +   + E       T D ++ +  E K    +L
Sbjct  7425   RAAQLKNMLSDSQRFEAKRLELEKWLARMEQRAERMGTIATTADILEAQQKEQKSFHAEL  7604

Query  171    RQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRL  230
               Q + + D+ N+L  KL+  Y  DDT ++  +TE IN  + +++  V  R   L      
Sbjct  7605   HQNKQHFDIFNELTQKLIAVYPNDDTTRIKKMTEVINQRYANLNSGVINRGKQLHAAVHS  7784

Query  231    LQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTD  290
              LQ F   +++FLA+L+E ET     +    +  L+            ++DLQ EIE H  
Sbjct  7785   LQSFDRAMDQFLAFLSETETLCENAESDIERNPLM------------FKDLQSEIETHRV  7928

Query  291    VYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRL  350
              VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ KS+ IR+ LE++S+ W  L
Sbjct  7929   VYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSKSIAIRNRLESNSEHWNAL  8108

Query  351    HLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
               LSL+EL  W+  KD ELS     P+ GD  ++QKQ D H+AF+R+L+ K P++ S L +
Sbjct  8109   LLSLRELTEWVIRKDTELSTLGLGPVRGDAVSLQKQLDDHKAFRRQLEDKRPIVESNLTS  8288

Query  409    VRIFLTEQPL-----EGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSA  463
               R ++  +       +       + R +  EE+++ +TR +R++  +++ +W  L   S 
Sbjct  8289   GRQYIANEAAVSDTSDTEANHDSDSRYMSAEEQSRELTRSIRREVGKLSEQWNNLIDRSD  8468

Query  464    DWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRG  523
              +W+ ++DE + ++++ Q+  ++L  ++  AE  K SW P     +    + +++++ LR 
Sbjct  8469   NWKHRLDEYMTKMRQFQKILEDLSSRVALAEQTKTSWLPPSS--VGEANEQMQQLQRLRD  8642

Query  524    EIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------V  575
              ++      +   N+     T   + +    LS LEDLNTR KLLQ+A+++R         
Sbjct  8643   KMTTASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCQAGA  8822

Query  576    RQLHEAHRD---------FGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHP  626
              +Q HE   D          GP     L  SV+ PWERA +   VPYYI+HE +TT WDHP
Sbjct  8823   QQTHENGDDGRTTSNSGTIGPLPN--LGQSVKPPWERATTAANVPYYIDHERETTHWDHP  8996

Query  627    KMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPM  685
              +M EL + LADLN +RFSAYRTAMKLR +QK L LD +S+S AC++ D+H L+ QND+ +
Sbjct  8997   EMIELMKGLADLNEIRFSAYRTAMKLRSVQKRLALDRISMSTACESFDRHGLRAQNDKLI  9176

Query  686    DILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIIS  745
              DI  +   L ++Y  +++     +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ 
Sbjct  9177   DIPDMTTVLHSLYVTIDK-----IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVL  9341

Query  746    LCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRS  805
              LCK HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRS
Sbjct  9342   LCKGHLEEKYRYLFRLVADTDRRADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRS  9521

Query  806    CFQFA---------NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNIC  856
              C + A         N    IE   FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNIC
Sbjct  9522   CLEQAGISQEAIDGNQDISIELQHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNIC  9701

Query  857    KECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVL  916
              KE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF + L
Sbjct  9702   KEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFTRAL  9881

Query  917    KNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLA  972
              KNKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ +     +D HSR+E YASRLA
Sbjct  9882   KNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQNDMHSRLEMYASRLA  10061

Query  973    EMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGE  1032
              ++E     Y     +     DDEH LI  YCQ+L   S  S P+SP Q++ ++++E+R E
Sbjct  10062  QVE-----YGGTGSNSTPDSDDEHQLIAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREE  10226

Query  1033   LERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP--------SPPEMMPTSPQSPRDAE  1084
              LE I+ DLEEEN NLQAEY +L  + +    S +P        S   M   S Q  +  +
Sbjct  10227  LEAIIRDLEEENANLQAEYQQLCSKEQ----SGMPEDSNGMQHSSSSMTGLSGQGEQGQD  10394

Query  1085   LIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              ++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  10395  MMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  10523


>ref|NM_001043261.1| Drosophila melanogaster dystrophin (Dys), transcript variant 
G, mRNA
Length=11377

 Score =  892 bits (2305),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 505/1183 (42%), Positives = 722/1183 (61%), Gaps = 96/1183 (8%)
 Frame = +2

Query  11     ALA-DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEE  69
              ALA  F+++  +++DWL+    +IK Q V+V D + +   I KQ+  +++L+ ++PQL E
Sbjct  6854   ALAGSFDKSVLQISDWLTWEQNMIKIQSVLVDDGDAVRLAIEKQEKVLRELKMKKPQLNE  7033

Query  70     LITAAQNLKNKTSNQE-----------ARTIITD--------RIERIQNQWDEVQEHLQN  110
              L+  A+ LK     Q+           A     D        ++ R++  WDE  + +  
Sbjct  7034   LVHTAEVLKGDVKRQQLQEKELKQFSLAPHCSADLDYMRCCLKVTRLREHWDETSQCVLQ  7213

Query  111    RRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDL  170
              R  QL  ML DS ++   + E E+ L +   + E       T D ++ +  E K    +L
Sbjct  7214   RAAQLKNMLSDSQRFEAKRLELEKWLARMEQRAERMGTIATTADILEAQQKEQKSFHAEL  7393

Query  171    RQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRL  230
               Q + + D+ N+L  KL+  Y  DDT ++  +TE IN  + +++  V  R   L      
Sbjct  7394   HQNKQHFDIFNELTQKLIAVYPNDDTTRIKKMTEVINQRYANLNSGVINRGKQLHAAVHS  7573

Query  231    LQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTD  290
              LQ F   +++FLA+L+E ET     +    +  L+            ++DLQ EIE H  
Sbjct  7574   LQSFDRAMDQFLAFLSETETLCENAESDIERNPLM------------FKDLQSEIETHRV  7717

Query  291    VYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRL  350
              VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ KS+ IR+ LE++S+ W  L
Sbjct  7718   VYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSKSIAIRNRLESNSEHWNAL  7897

Query  351    HLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
               LSL+EL  W+  KD ELS     P+ GD  ++QKQ D H+AF+R+L+ K P++ S L +
Sbjct  7898   LLSLRELTEWVIRKDTELSTLGLGPVRGDAVSLQKQLDDHKAFRRQLEDKRPIVESNLTS  8077

Query  409    VRIFLTEQPL-----EGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSA  463
               R ++  +       +       + R +  EE+++ +TR +R++  +++ +W  L   S 
Sbjct  8078   GRQYIANEAAVSDTSDTEANHDSDSRYMSAEEQSRELTRSIRREVGKLSEQWNNLIDRSD  8257

Query  464    DWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRG  523
              +W+ ++DE + ++++ Q+  ++L  ++  AE  K SW P     +    + +++++ LR 
Sbjct  8258   NWKHRLDEYMTKMRQFQKILEDLSSRVALAEQTKTSWLPPSS--VGEANEQMQQLQRLRD  8431

Query  524    EIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------V  575
              ++      +   N+     T   + +    LS LEDLNTR KLLQ+A+++R         
Sbjct  8432   KMTTASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCQAGA  8611

Query  576    RQLHEAHRD---------FGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHP  626
              +Q HE   D          GP     L  SV+ PWERA +   VPYYI+HE +TT WDHP
Sbjct  8612   QQTHENGDDGRTTSNSGTIGPLPN--LGQSVKPPWERATTAANVPYYIDHERETTHWDHP  8785

Query  627    KMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPM  685
              +M EL + LADLN +RFSAYRTAMKLR +QK L LD +S+S AC++ D+H L+ QND+ +
Sbjct  8786   EMIELMKGLADLNEIRFSAYRTAMKLRSVQKRLALDRISMSTACESFDRHGLRAQNDKLI  8965

Query  686    DILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIIS  745
              DI  +   L ++Y  +++     +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ 
Sbjct  8966   DIPDMTTVLHSLYVTIDK-----IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVL  9130

Query  746    LCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRS  805
              LCK HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRS
Sbjct  9131   LCKGHLEEKYRYLFRLVADTDRRADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRS  9310

Query  806    CFQFA---------NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNIC  856
              C + A         N    IE   FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNIC
Sbjct  9311   CLEQAGISQEAIDGNQDISIELQHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNIC  9490

Query  857    KECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVL  916
              KE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF + L
Sbjct  9491   KEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFTRAL  9670

Query  917    KNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLA  972
              KNKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ +     +D HSR+E YASRLA
Sbjct  9671   KNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQNDMHSRLEMYASRLA  9850

Query  973    EMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGE  1032
              ++E     Y     +     DDEH LI  YCQ+L   S  S P+SP Q++ ++++E+R E
Sbjct  9851   QVE-----YGGTGSNSTPDSDDEHQLIAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREE  10015

Query  1033   LERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP--------SPPEMMPTSPQSPRDAE  1084
              LE I+ DLEEEN NLQAEY +L  + +    S +P        S   M   S Q  +  +
Sbjct  10016  LEAIIRDLEEENANLQAEYQQLCSKEQ----SGMPEDSNGMQHSSSSMTGLSGQGEQGQD  10183

Query  1085   LIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              ++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  10184  MMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  10312


>ref|NM_001043258.1| Drosophila melanogaster dystrophin (Dys), transcript variant 
A, mRNA
Length=11000

 Score =  892 bits (2305),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 505/1183 (42%), Positives = 722/1183 (61%), Gaps = 96/1183 (8%)
 Frame = +1

Query  11     ALA-DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEE  69
              ALA  F+++  +++DWL+    +IK Q V+V D + +   I KQ+  +++L+ ++PQL E
Sbjct  7141   ALAGSFDKSVLQISDWLTWEQNMIKIQSVLVDDGDAVRLAIEKQEKVLRELKMKKPQLNE  7320

Query  70     LITAAQNLKNKTSNQE-----------ARTIITD--------RIERIQNQWDEVQEHLQN  110
              L+  A+ LK     Q+           A     D        ++ R++  WDE  + +  
Sbjct  7321   LVHTAEVLKGDVKRQQLQEKELKQFSLAPHCSADLDYMRCCLKVTRLREHWDETSQCVLQ  7500

Query  111    RRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDL  170
              R  QL  ML DS ++   + E E+ L +   + E       T D ++ +  E K    +L
Sbjct  7501   RAAQLKNMLSDSQRFEAKRLELEKWLARMEQRAERMGTIATTADILEAQQKEQKSFHAEL  7680

Query  171    RQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRL  230
               Q + + D+ N+L  KL+  Y  DDT ++  +TE IN  + +++  V  R   L      
Sbjct  7681   HQNKQHFDIFNELTQKLIAVYPNDDTTRIKKMTEVINQRYANLNSGVINRGKQLHAAVHS  7860

Query  231    LQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTD  290
              LQ F   +++FLA+L+E ET     +    +  L+            ++DLQ EIE H  
Sbjct  7861   LQSFDRAMDQFLAFLSETETLCENAESDIERNPLM------------FKDLQSEIETHRV  8004

Query  291    VYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRL  350
              VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ KS+ IR+ LE++S+ W  L
Sbjct  8005   VYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSKSIAIRNRLESNSEHWNAL  8184

Query  351    HLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
               LSL+EL  W+  KD ELS     P+ GD  ++QKQ D H+AF+R+L+ K P++ S L +
Sbjct  8185   LLSLRELTEWVIRKDTELSTLGLGPVRGDAVSLQKQLDDHKAFRRQLEDKRPIVESNLTS  8364

Query  409    VRIFLTEQPL-----EGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSA  463
               R ++  +       +       + R +  EE+++ +TR +R++  +++ +W  L   S 
Sbjct  8365   GRQYIANEAAVSDTSDTEANHDSDSRYMSAEEQSRELTRSIRREVGKLSEQWNNLIDRSD  8544

Query  464    DWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRG  523
              +W+ ++DE + ++++ Q+  ++L  ++  AE  K SW P     +    + +++++ LR 
Sbjct  8545   NWKHRLDEYMTKMRQFQKILEDLSSRVALAEQTKTSWLPPSS--VGEANEQMQQLQRLRD  8718

Query  524    EIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------V  575
              ++      +   N+     T   + +    LS LEDLNTR KLLQ+A+++R         
Sbjct  8719   KMTTASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCQAGA  8898

Query  576    RQLHEAHRD---------FGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHP  626
              +Q HE   D          GP     L  SV+ PWERA +   VPYYI+HE +TT WDHP
Sbjct  8899   QQTHENGDDGRTTSNSGTIGPLPN--LGQSVKPPWERATTAANVPYYIDHERETTHWDHP  9072

Query  627    KMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPM  685
              +M EL + LADLN +RFSAYRTAMKLR +QK L LD +S+S AC++ D+H L+ QND+ +
Sbjct  9073   EMIELMKGLADLNEIRFSAYRTAMKLRSVQKRLALDRISMSTACESFDRHGLRAQNDKLI  9252

Query  686    DILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIIS  745
              DI  +   L ++Y  +++     +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ 
Sbjct  9253   DIPDMTTVLHSLYVTIDK-----IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVL  9417

Query  746    LCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRS  805
              LCK HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRS
Sbjct  9418   LCKGHLEEKYRYLFRLVADTDRRADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRS  9597

Query  806    CFQFA---------NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNIC  856
              C + A         N    IE   FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNIC
Sbjct  9598   CLEQAGISQEAIDGNQDISIELQHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNIC  9777

Query  857    KECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVL  916
              KE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF + L
Sbjct  9778   KEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFTRAL  9957

Query  917    KNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLA  972
              KNKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ +     +D HSR+E YASRLA
Sbjct  9958   KNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQNDMHSRLEMYASRLA  10137

Query  973    EMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGE  1032
              ++E     Y     +     DDEH LI  YCQ+L   S  S P+SP Q++ ++++E+R E
Sbjct  10138  QVE-----YGGTGSNSTPDSDDEHQLIAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREE  10302

Query  1033   LERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP--------SPPEMMPTSPQSPRDAE  1084
              LE I+ DLEEEN NLQAEY +L  + +    S +P        S   M   S Q  +  +
Sbjct  10303  LEAIIRDLEEENANLQAEYQQLCSKEQ----SGMPEDSNGMQHSSSSMTGLSGQGEQGQD  10470

Query  1085   LIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              ++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  10471  MMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  10599


>ref|XM_394154.3| PREDICTED: Apis mellifera similar to dystrophin CG31175-PA, isoform 
A (LOC410677), mRNA
Length=2922

 Score =  890 bits (2301),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 480/977 (49%), Positives = 645/977 (66%), Gaps = 68/977 (6%)
 Frame = +1

Query  280   DLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSH  339
             DLQ EIE H DVY +L+   +K+L SL   DDAV+LQRRLD MN +W  L+ KS+ IR+ 
Sbjct  61    DLQSEIETHRDVYTSLNGTGRKLLSSLASQDDAVMLQRRLDEMNQRWHHLKAKSMAIRNR  240

Query  340   LEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKE  399
             LE++++ W  L LSL+EL+ W+  KD EL+   P+ GD  A+QKQ D HR F+R+L+ K 
Sbjct  241   LESNTEHWNALLLSLRELIEWVIRKDTELTGLGPVCGDVAALQKQEDDHRGFRRQLEDKR  420

Query  400   PVIMSTLETVRIFLTEQP-------------LEGLEKLYQEPRELPPEERAQNVTRLLRK  446
             P++ + L + R ++  +P             L+G  + Y+       EE+A+ +TR +R+
Sbjct  421   PIVENNLLSGRQYIANEPPLSDTSDSEAGRELDGDSRGYRSA-----EEQARELTRSIRR  585

Query  447   QAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDL  506
             +  +++ +W  L   S  W+RK+D+T+ +L+  +E    L    +  + +K  W    D+
Sbjct  586   EVNKLSEQWNALIERSDAWKRKLDDTIGKLRVFREILLFLRDNNKLLKNLKDPWTRFKDI  765

Query  507   ---------LIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLT-TLGIQLSPYNLST  556
                       ++S++D        R   + LK      N +    T     ++SP     
Sbjct  766   GKRRRRSCISLNSVRD--------RSNRSLLK--TVDCNKIQTLFTRNENSEISPCEAKF  915

Query  557   LEDLNTRWKLLQVAVEDRVRQLHEAHRDFG-PASQHFLSTSVQGPWERAISPNKVPYYIN  615
                   RWK+LQVAV++R + L    +D   P SQ FL++SV+ PWERA++P KVPYYIN
Sbjct  916   FACFR-RWKVLQVAVDERYKLLSGFGKDGSTPGSQAFLASSVEPPWERALTPAKVPYYIN  1092

Query  616   HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQ  675
             H+++TT WDHPKM EL  SLADLN VRFSAYRTAMKLR +QK LCLD+LSLS A +  D 
Sbjct  1093  HQSETTHWDHPKMIELMSSLADLNEVRFSAYRTAMKLRTVQKRLCLDMLSLSTALEQFDS  1272

Query  676   HNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             H L+ QND+ +DI  ++  LT++Y+ +  ++   V+VPLC+D+ +NWLLNVYD+ RTG+I
Sbjct  1273  HGLRAQNDKLIDIPDMVTVLTSLYEVITADNPTQVSVPLCIDLAINWLLNVYDSQRTGQI  1452

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFK G++ LCK HLE+KYRYLF+ +A      DQR+LGLLLHD IQ+PRQLGEVA+F
Sbjct  1453  RVLSFKVGLVLLCKGHLEEKYRYLFRLIADPNRLVDQRKLGLLLHDCIQVPRQLGEVAAF  1632

Query  795   GGSNIEPSVRSCFQFAN-NKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKC  853
             GGSNIEPSVRSCF+ A  +K EIEA  FL W++ EPQSMVWLPVLHR++AAE+AKHQAKC
Sbjct  1633  GGSNIEPSVRSCFEKAGKDKNEIEAVHFLSWLQQEPQSMVWLPVLHRLSAAESAKHQAKC  1812

Query  854   NICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFA  913
             NICKE PIIGFRYR LK FN+D+CQ+CFFSGR AK HK+ +PM EYCT TTSGEDVRDF 
Sbjct  1813  NICKEYPIIGFRYRCLKCFNFDMCQNCFFSGRKAKNHKLTHPMQEYCTATTSGEDVRDFT  1992

Query  914   KVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS--HDDTHSRIEHYASRL  971
             + L+NKF++KRYF KHPR+GYLPVQTVLEGD +E+PA SPQ S    D HSR+E YASRL
Sbjct  1993  RALRNKFKSKRYFKKHPRVGYLPVQTVLEGDALESPAPSPQHSSLSQDMHSRLEMYASRL  2172

Query  972   AEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERG  1031
             AE+E S       + +P+   DDEH LI HYCQSLN    ++ PRSP Q++ ++++E+R 
Sbjct  2173  AEVELSR---TRSNSTPDS--DDEHQLIAHYCQSLNGGDNVNVPRSPVQVMAAIDAEQRE  2337

Query  1032  ELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKL  1091
             ELE ++ +LEEEN  LQAEY+RL+ + +  G +P        P       D ++IAEAKL
Sbjct  2338  ELEAMIRELEEENATLQAEYERLRSK-QTPGSTPEDGHGNRQP-------DCDMIAEAKL  2493

Query  1092  LRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSS  1151
             LRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P A +     T+ + S +  +  + 
Sbjct  2494  LRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEPNASSPSKTGTLQTRSVTASQLATD  2673

Query  1152  QPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSR-GHNVGSLFHMAD  1210
              P  +        DS G          ++ G    +E+      S    HNVG+L HMA 
Sbjct  2674  SPAKM---NGHYHDSPG-------GGGSNEGRVSSLERPPPPPHSHSVAHNVGNLLHMAG  2823

Query  1211  DLGRAMESLVSVMTDEE  1227
             DLG+A+  LV+VMT E+
Sbjct  2824  DLGKAVGELVTVMTSED  2874


>ref|XM_001946756.1| PREDICTED: Acyrthosiphon pisum similar to dystrophin CG34157-PD 
(LOC100168806), mRNA
Length=3738

 Score =  863 bits (2230),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 460/977 (47%), Positives = 642/977 (65%), Gaps = 69/977 (7%)
 Frame = +1

Query  279   QDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRS  338
             ++LQ E+E  +   ++LD + +K+L SL   +DAV+LQRRL+ MN +W++L+ +S+ IR+
Sbjct  913   KELQQEMETKSQSLNSLDTSGRKLLGSLSSQEDAVMLQRRLEEMNQRWNQLKNRSVTIRN  1092

Query  339   HLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTK  398
              LE +++ W  L LSL+EL+ W+  KD E+S   P+G D   +QKQ D HR F+R+L+ K
Sbjct  1093  RLENNTEHWNTLLLSLRELVEWVIKKDTEISSFGPLGNDLVTLQKQQDDHRGFRRQLEEK  1272

Query  399   EPVIMSTLETVRIFLTEQPL-------EGLEKLYQEPRELPPEERAQNVTRLLRKQAEEV  451
              PVI S L + R ++  +         E +            EE+A+++T  L+++   V
Sbjct  1273  RPVIDSNLRSGRQYINNESQIASAVKNEEINNTGDSRGYRSAEEQARDLTISLKREVLRV  1452

Query  452   NTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSL  511
             + +W  L   S  WQR ++++++++Q  Q+  ++   KL   E +  SW P  +   DS 
Sbjct  1453  SEQWNSLLQRSDQWQRSLNDSIKKMQVFQKGLEDCTSKLASVEAMYKSW-PASNT-GDST  1626

Query  512   QDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAV  571
             +  L++++     + P++  +  VND A  L +  + +S  N + L+D+N RWK+LQ+A+
Sbjct  1627  KG-LQELRQFGDRLNPVQRLLEEVNDQASILASNNVTISVSNKNMLQDINNRWKVLQLAM  1803

Query  572   EDRVRQLHEAHRDF-------GPASQH------FLSTSVQGPWERAISPNKVPYYINHET  618
             +DR +Q+ +  ++         PAS         LS SV+ PW+R I+PNKVPYYINH+ 
Sbjct  1804  DDRYKQIRDTGKNTISNSNGTSPASHSEASTSLLLSGSVEPPWKREITPNKVPYYINHKC  1983

Query  619   QTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNL  678
             ++T WDHPKM EL  SL++ N+VRFSAYRTAMKLR +QK + LDLL+L AA +A D H L
Sbjct  1984  ESTNWDHPKMMELMSSLSEFNDVRFSAYRTAMKLRTVQKRMSLDLLTLEAALEAFDNHGL  2163

Query  679   K-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVL  737
             + QND+ + + +++  L +I+D L  +H +LV+VPLC+D+ LNWLLNVYD+ RTG+IRVL
Sbjct  2164  RAQNDKLITVSEMLTILGSIFDTLASQHPSLVHVPLCLDLSLNWLLNVYDSQRTGQIRVL  2343

Query  738   SFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGS  797
             SFK G++ LCK HLE+KYRYLF+ +A      DQR+LGLLLHD IQ+PRQLGEVASFGGS
Sbjct  2344  SFKVGLVLLCKGHLEEKYRYLFRLIADPNRQVDQRKLGLLLHDCIQLPRQLGEVASFGGS  2523

Query  798   NIEPSVRSCFQFAN-NKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNIC  856
             NIEPSVRSCFQ A  +K  IEA  FL W++ EPQSMVWL VLHR+A AE+AKHQAKCNIC
Sbjct  2524  NIEPSVRSCFQKAGKDKTVIEAMHFLVWLQQEPQSMVWLAVLHRLAEAESAKHQAKCNIC  2703

Query  857   KECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVL  916
             K  PIIGFRYR LK FN+D+CQSCFFSGR AK HK+ +PM EYCT TTSGEDVRDF + L
Sbjct  2704  KTYPIIGFRYRCLKCFNFDMCQSCFFSGRKAKHHKLTHPMQEYCTTTTSGEDVRDFTRAL  2883

Query  917   KNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD-----DTHSRIEHYASRL  971
             +NKF++KRYF KHPR+GYLPVQ+VLEGD +E+P+ SPQ S+      D H+R+E YASRL
Sbjct  2884  RNKFKSKRYFKKHPRVGYLPVQSVLEGDALESPSPSPQHSNTPSTIPDVHNRLEMYASRL  3063

Query  972   AEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPL--SQPRSPAQILISLESEE  1029
             AE+E     Y   S S  +S +DEH LI  YCQSLN  S    S PRSP QI++++++++
Sbjct  3064  AEVE-----YRARSNSTPDS-EDEHHLIAQYCQSLNGGSETLPSVPRSPVQIMVAIDADQ  3225

Query  1030  RGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEA  1089
             R ELE ++ +LE+EN +LQ EY++LK     KG   +          P +  + ++++EA
Sbjct  3226  RHELETMIKELEDENTHLQEEYEKLKTGTGSKGSYNI---------MPNNNGEVDMVSEA  3378

Query  1090  KLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSD  1149
             ++LRQHKGRLEARMQILEDHN+QLE+QL RLRQLLE+P         T  + S ++ +  
Sbjct  3379  RMLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLEEP--------ATFQTRSVTVSQLA  3534

Query  1150  SSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMA  1209
                PM        +SD  G          +       +E+       +  H VG+L HMA
Sbjct  3535  CDSPM------QNSSDKSGNW--------SENNSRNTLERPPPPPIPASHHAVGNLHHMA  3672

Query  1210  DDLGRAMESLVSVMTDE  1226
              DLG+ +  LV+VMT E
Sbjct  3673  GDLGKVVTELVTVMTTE  3723


>ref|NM_001043256.1| Drosophila melanogaster dystrophin (Dys), transcript variant 
B, mRNA
Length=5153

 Score =  863 bits (2229),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 477/1081 (44%), Positives = 673/1081 (62%), Gaps = 76/1081 (7%)
 Frame = +1

Query  93    RIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYT  152
             ++ R++  WDE  + +  R  QL  ML DS ++   + E E+ L +   + E       T
Sbjct  1600  QVTRLREHWDETSQCVLQRAAQLKNMLSDSQRFEAKRLELEKWLARMEQRAERMGTIATT  1779

Query  153   VDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRS  212
              D ++ +  E K    +L Q + + D+ N+L  KL+  Y  DDT ++  +TE IN  + +
Sbjct  1780  ADILEAQQKEQKSFHAELHQNKQHFDIFNELTQKLIAVYPNDDTTRIKKMTEVINQRYAN  1959

Query  213   IHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVK  272
             ++  V  R   L      LQ F   +++FLA+L+E ET     +    +  L+       
Sbjct  1960  LNSGVINRGKQLHAAVHSLQSFDRAMDQFLAFLSETETLCENAESDIERNPLM-------  2118

Query  273   ELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKK  332
                  ++DLQ EIE H  VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ K
Sbjct  2119  -----FKDLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSK  2283

Query  333   SLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRA  390
             S+ IR+ LE++S+ W  L LSL+EL  W+  KD ELS     P+ GD  ++QKQ D H+A
Sbjct  2284  SIAIRNRLESNSEHWNALLLSLRELTEWVIRKDTELSTLGLGPVRGDAVSLQKQLDDHKA  2463

Query  391   FKRELKTKEPVIMSTLETVRIFLTEQPL-----EGLEKLYQEPRELPPEERAQNVTRLLR  445
             F+R+L+ K P++ S L + R ++  +       +       + R +  EE+++ +TR +R
Sbjct  2464  FRRQLEDKRPIVESNLTSGRQYIANEAAVSDTSDTEANHDSDSRYMSAEEQSRELTRSIR  2643

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
             ++  +++ +W  L   S +W+ ++DE + ++++ Q+  ++L  ++  AE  K SW P   
Sbjct  2644  REVGKLSEQWNNLIDRSDNWKHRLDEYMTKMRQFQKILEDLSSRVALAEQTKTSWLPPSS  2823

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
               +    + +++++ LR ++      +   N+     T   + +    LS LEDLNTR K
Sbjct  2824  --VGEANEQMQQLQRLRDKMTTASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTRMK  2997

Query  566   LLQVAVEDR--------VRQLHEAHRD---------FGPASQHFLSTSVQGPWERAISPN  608
             LLQ+A+++R         +Q HE   D          GP     L  SV+ PWERA +  
Sbjct  2998  LLQIAMDERQKVLCQAGAQQTHENGDDGRTTSNSGTIGPLPN--LGQSVKPPWERATTAA  3171

Query  609   KVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSA  668
              VPYYI+HE +TT WDHP+M EL + LADLN +RFSAYRTAMKLR +QK L LD +S+S 
Sbjct  3172  NVPYYIDHERETTHWDHPEMIELMKGLADLNEIRFSAYRTAMKLRSVQKRLALDRISMST  3351

Query  669   ACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYD  727
             AC++ D+H L+ QND+ +DI  +   L ++Y  +++     +++ L +D+ +NW+LNVYD
Sbjct  3352  ACESFDRHGLRAQNDKLIDIPDMTTVLHSLYVTIDK-----IDLTLMLDLAINWILNVYD  3516

Query  728   TGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQ  787
             + RTG+IRVLSFK G++ LCK HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PRQ
Sbjct  3517  SQRTGQIRVLSFKVGLVLLCKGHLEEKYRYLFRLVADTDRRADQRRLGLLLHDCIQVPRQ  3696

Query  788   LGEVASFGGSNIEPSVRSCFQFA---------NNKPEIEAALFLDWMRLEPQSMVWLPVL  838
             LGEVA+FGGSNIEPSVRSC + A         N    IE   FL W++ EPQS+VWLPVL
Sbjct  3697  LGEVAAFGGSNIEPSVRSCLEQAGISQEAIDGNQDISIELQHFLGWLQHEPQSLVWLPVL  3876

Query  839   HRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVE  898
             HR+AAAE AKHQAKCNICKE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM E
Sbjct  3877  HRLAAAEAAKHQAKCNICKEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHE  4056

Query  899   YCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS--  956
             YCT TTS EDVRDF + LKNKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ +  
Sbjct  4057  YCTTTTSTEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTTH  4236

Query  957   --HDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                +D HSR+E YASRLA++E     Y     +     DDEH LI  YCQ+L   S  S 
Sbjct  4237  QLQNDMHSRLEMYASRLAQVE-----YGGTGSNSTPDSDDEHQLIAQYCQALPGTSNGSA  4401

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP-------  1067
             P+SP Q++ ++++E+R ELE I+ DLEEEN NLQAEY +L  + +    S +P       
Sbjct  4402  PKSPVQVMAAMDAEQREELEAIIRDLEEENANLQAEYQQLCSKEQ----SGMPEDSNGMQ  4569

Query  1068  -SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ  1126
              S   M   S Q  +  +++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++
Sbjct  4570  HSSSSMTGLSGQGEQGQDMMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDE  4749

Query  1127  P  1127
             P
Sbjct  4750  P  4752


>gb|DQ440978.1| Petromyzon marinus dystrophin mRNA, partial cds
Length=2319

 Score =  862 bits (2228),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 423/624 (67%), Positives = 491/624 (78%), Gaps = 49/624 (7%)
 Frame = +3

Query  623   WDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND  682
             WDHPKMTELYQSL+DLNNVRFSAYRTAMKLRRLQKALCLDL+SL A  +  +Q  LKQND
Sbjct  9     WDHPKMTELYQSLSDLNNVRFSAYRTAMKLRRLQKALCLDLVSLDALTNVFEQSGLKQND  188

Query  683   QPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTG  742
             + MD+ + + CLTTIY  LE++H++LVN+PLCVDMCLNWLLNVYDTGR G+IR LSFKTG
Sbjct  189   RLMDVSEAVGCLTTIYQGLERKHSDLVNLPLCVDMCLNWLLNVYDTGRGGKIRELSFKTG  368

Query  743   IISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPS  802
             ++SL  AHLEDKYR+LFKQVAS +G CDQRRLGL+LHD++QIPRQLGEVASFGGSNIEPS
Sbjct  369   LVSLSNAHLEDKYRFLFKQVASVSGLCDQRRLGLMLHDAVQIPRQLGEVASFGGSNIEPS  548

Query  803   VRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPII  862
             VRSCFQFAN +PEIEA +FL+WMR+EPQSMVWLPVLHRVAA+ETAKHQAKCNICKECPI+
Sbjct  549   VRSCFQFANGRPEIEATMFLEWMRMEPQSMVWLPVLHRVAASETAKHQAKCNICKECPIV  728

Query  863   GFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRT  922
             GFRYRSLKHFNYD+CQSCFFSGR AKGHK+ YPMVEYCTPTTSGED+RDFAKVLKNKF++
Sbjct  729   GFRYRSLKHFNYDVCQSCFFSGRTAKGHKLSYPMVEYCTPTTSGEDIRDFAKVLKNKFKS  908

Query  923   KRYFAKHPRMGYLPVQTVLEGDNMETPAS-------------SPQLSHDDTHSRIEHYAS  969
             K+YF KHPR+GYLPVQTVLEGD++ETP +             SPQLS++DTH+RIEH AS
Sbjct  909   KKYFEKHPRIGYLPVQTVLEGDDLETPVTVIRLVPVALAPSPSPQLSNEDTHARIEHLAS  1088

Query  970   RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEE  1029
             RLAEME  NGS+LNDS SPNES++DEHLLIQHYCQSL+ +SP SQP+SPAQILISL+S+E
Sbjct  1089  RLAEMEFKNGSFLNDS-SPNESLEDEHLLIQHYCQSLSGESPGSQPQSPAQILISLDSQE  1265

Query  1030  RGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEA  1089
             R ELERIL DLE+ENR+LQ+EYDRL+Q+    GL  L   P  MP  P+SPRD+ELIAEA
Sbjct  1266  RSELERILRDLEDENRSLQSEYDRLRQKQGLGGLGALLLAPPTMP--PESPRDSELIAEA  1439

Query  1090  KLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTV---SSPSTSLQ  1146
             KLLRQHKGRLEARM+ILEDHN+QLESQL RLRQLL+QPQ E +VNGT       P     
Sbjct  1440  KLLRQHKGRLEARMRILEDHNRQLESQLIRLRQLLDQPQQEGRVNGTPALPSPPPPPPPP  1619

Query  1147  RSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLF  1206
               + S P+           S G    L PP+ T                   G +VG+  
Sbjct  1620  PQEESHPL-----------SNGGPGGLRPPEPT-------------------GDDVGTAV  1709

Query  1207  HMADDLGRAMESLVSVMTDEEGAE  1230
                +D    + S++    D  G E
Sbjct  1710  PTNEDTAGGLTSVLPAQQDTPGGE  1781


>ref|XM_001979487.1| Drosophila erecta GG23350 (Dere\GG23350), mRNA
Length=5085

 Score =  862 bits (2227),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 476/1081 (44%), Positives = 673/1081 (62%), Gaps = 76/1081 (7%)
 Frame = +1

Query  93    RIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYT  152
             ++ R++  WDE  + +  R  QL  ML DS ++   + E E+ L +   + E       T
Sbjct  1609  KVTRLREHWDETSQCVLQRAAQLKNMLSDSQRFEAKRLELEKWLARMEQRAERMGTIATT  1788

Query  153   VDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRS  212
              D ++ +  E K    +L Q + + D+ N+L  KL+  Y  DDT ++  +TE IN  + +
Sbjct  1789  ADILEAQQKEQKSFHAELHQNKQHFDIFNELTQKLIAVYPNDDTTRIKKMTEVINQRYAN  1968

Query  213   IHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVK  272
             ++  V  R   L      LQ F   +++FLA+L+E ET     +    +  L+       
Sbjct  1969  LNNGVINRGKQLHAAVHSLQSFDRAMDQFLAFLSETETLCENAESDIERNPLM-------  2127

Query  273   ELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKK  332
                  ++DLQ EIE H  VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ K
Sbjct  2128  -----FKDLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSK  2292

Query  333   SLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRA  390
             S+ IR+ LE++S+ W  L LSL+EL  W+  KD ELS     P+ GD  ++QKQ D H+A
Sbjct  2293  SIAIRNRLESNSEHWNALLLSLRELTEWVIRKDTELSTLGLGPVRGDAASLQKQLDDHKA  2472

Query  391   FKRELKTKEPVIMSTLETVRIFLTEQPL-----EGLEKLYQEPRELPPEERAQNVTRLLR  445
             F+R+L+ K P++ S L + R ++  +       +       + R +  EE+++ +TR +R
Sbjct  2473  FRRQLEDKRPIVESNLTSGRQYIANEAAVSDTSDTEANHDSDSRYMSAEEQSRELTRSIR  2652

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
             ++  +++ +W  L   S +W+ ++DE + ++++ Q+  ++L  ++  AE  K +W P   
Sbjct  2653  REVGKLSEQWNNLIDRSDNWKHRLDEYMTKMRQFQKILEDLSSRVALAEQTKTAWLPPSS  2832

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
               +    + +++++ LR ++      +   N+     T   + +    LS LEDLNTR K
Sbjct  2833  --VGEANEQMQQLQRLRDKMTTASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTRMK  3006

Query  566   LLQVAVEDR--------VRQLHEAHRD---------FGPASQHFLSTSVQGPWERAISPN  608
             LLQ+A+++R         +Q HE   D          GP     L  SV+ PWERA +  
Sbjct  3007  LLQIAMDERQKVLCQAGAQQTHENGDDGRTTSNSGTIGPLPN--LGQSVKPPWERATTAA  3180

Query  609   KVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSA  668
              VPYYI+HE +TT WDHP+M EL + LADLN +RFSAYRTAMKLR +QK L LD +S+S 
Sbjct  3181  NVPYYIDHERETTHWDHPEMIELMKGLADLNEIRFSAYRTAMKLRSVQKRLALDRISMST  3360

Query  669   ACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYD  727
             AC++ D+H L+ QND+ +DI  +   L ++Y  +++     +++ L +D+ +NW+LNVYD
Sbjct  3361  ACESFDRHGLRAQNDKLIDIPDMTTVLHSLYVTIDK-----IDLTLMLDLAINWILNVYD  3525

Query  728   TGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQ  787
             + RTG+IRVLSFK G++ LCK HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PRQ
Sbjct  3526  SQRTGQIRVLSFKVGLVLLCKGHLEEKYRYLFRLVADTDRRADQRRLGLLLHDCIQVPRQ  3705

Query  788   LGEVASFGGSNIEPSVRSCFQFA---------NNKPEIEAALFLDWMRLEPQSMVWLPVL  838
             LGEVA+FGGSNIEPSVRSC + A         N    IE   FL W++ EPQS+VWLPVL
Sbjct  3706  LGEVAAFGGSNIEPSVRSCLEQAGISQEAIDGNQDISIELLHFLGWLQHEPQSLVWLPVL  3885

Query  839   HRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVE  898
             HR+AAAE AKHQAKCNICKE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM E
Sbjct  3886  HRLAAAEAAKHQAKCNICKEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHE  4065

Query  899   YCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS--  956
             YCT TTS EDVRDF + LKNKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ +  
Sbjct  4066  YCTTTTSTEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTTH  4245

Query  957   --HDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                +D HSR+E YASRLA++E     Y     +     DDEH LI  YCQ+L   S  S 
Sbjct  4246  QLQNDMHSRLEMYASRLAQVE-----YGGTGSNSTPDSDDEHQLIAQYCQALPGTSNGSA  4410

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP-------  1067
             P+SP Q++ ++++E+R ELE I+ DLEEEN NLQAEY +L  + +    S +P       
Sbjct  4411  PKSPVQVMAAMDAEQREELEAIIRDLEEENANLQAEYQQLCSKEQ----SGMPEDSNGMQ  4578

Query  1068  -SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ  1126
              S   M   S Q  +  +++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++
Sbjct  4579  HSSSSMTGLSGQGEQGQDMMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDE  4758

Query  1127  P  1127
             P
Sbjct  4759  P  4761


>ref|XM_002072801.1| Drosophila willistoni GK13817 (Dwil\GK13817), mRNA
Length=5103

 Score =  853 bits (2204),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 475/1082 (43%), Positives = 673/1082 (62%), Gaps = 73/1082 (6%)
 Frame = +1

Query  93    RIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYT  152
             ++ R++  WDE  + +  R  QL  ML DS ++   + E E+ LG+   + E       T
Sbjct  1555  QVTRLREHWDETSQCVLQRAAQLKNMLSDSQRFEAKRLELEKWLGRMEQRAERMGSIATT  1734

Query  153   VDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRS  212
              D ++ +  E K    +L Q + + ++ NDL  KL+  Y  DDT ++  +TE +N  + +
Sbjct  1735  ADILEAQQKEQKSFHAELHQNKQHFELFNDLTQKLIAVYPNDDTTRIKKLTEVVNQRYAN  1914

Query  213   IHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVK  272
             ++  V  R   L      LQ F   +++FLA+L+E ET     +    +  L+       
Sbjct  1915  LNNGVVNRGKQLHAAVHSLQSFDRAMDQFLAFLSETETLCENAESDIERNPLM-------  2073

Query  273   ELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKK  332
                  ++DLQ EIE H  VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ K
Sbjct  2074  -----FKDLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSK  2238

Query  333   SLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRA  390
             S+ IR+ LE++S+ W  L LSL+EL  W+  K+ ELS     P+ GD  ++QKQ D H+A
Sbjct  2239  SIAIRNRLESNSEHWNALLLSLRELTEWVIRKETELSTLGLGPVRGDAASLQKQLDDHKA  2418

Query  391   FKRELKTKEPVIMSTLETVRIFLTEQP----LEGLEKLY-QEPRELPPEERAQNVTRLLR  445
             F+R+L+ K P++ S L + R ++  +         E  +  + R +  EE+++ +TR +R
Sbjct  2419  FRRQLEDKRPIVESNLTSGRQYIANEAAVSDTSDTEAAHDSDSRYMSAEEQSRELTRSIR  2598

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
             ++  +++ +W  L   S +W+ ++DE + ++++ Q+  ++L  ++  AE  + SW  V  
Sbjct  2599  REVGKLSEQWNNLIDKSDNWKHRLDEYMTKMRQFQKILEDLSSRVALAEQTQNSW--VTP  2772

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
                    D +++++ LR ++      +   N+     T   + +    LS LEDLNTR K
Sbjct  2773  SSTGEANDQMQQLQRLRDKMTTASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTRMK  2952

Query  566   LLQVAVEDRVRQL--------HEAHRD---------FGPASQHFLSTSVQGPWERAISPN  608
             LLQ+A+++R + L        HE   D          GP     L  SV+ PWERA + +
Sbjct  2953  LLQIAMDERQKILCQAGAQHTHENGDDGRNTSNSGTIGPLPN--LGQSVKPPWERATTAS  3126

Query  609   KVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSA  668
              VPYYI+HE +TT WDHP+M EL + LADLN +RFSAYRTAMKLR +QK L LD +S++ 
Sbjct  3127  NVPYYIDHERETTHWDHPEMIELMKGLADLNEIRFSAYRTAMKLRSVQKRLALDRISMAT  3306

Query  669   ACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYD  727
             AC++ D+H L+ QND+ +DI  +   L ++Y  +++     +++ L +D+ +NW+LNVYD
Sbjct  3307  ACESFDRHGLRAQNDKLIDIPDMTTVLHSLYVTIDK-----IDLTLMLDLAINWILNVYD  3471

Query  728   TGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQ  787
             + RTG+IRVLSFK G++ LC+ HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PRQ
Sbjct  3472  SQRTGQIRVLSFKVGLVLLCRGHLEEKYRYLFRLVADTERRADQRRLGLLLHDCIQVPRQ  3651

Query  788   LGEVASFGGSNIEPSVRSCFQFA---------NNKPEIEAALFLDWMRLEPQSMVWLPVL  838
             LGEVA+FGGSNIEPSVRSC + A         N    IE   FL W++ EPQS+VWLPVL
Sbjct  3652  LGEVAAFGGSNIEPSVRSCLEQAGISQEAIDGNQDISIELQHFLGWLQHEPQSLVWLPVL  3831

Query  839   HRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVE  898
             HR+AAAE AKHQAKCNICKE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM E
Sbjct  3832  HRLAAAEAAKHQAKCNICKEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHE  4011

Query  899   YCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS--  956
             YCT TTS EDVRDF + LKNKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ +  
Sbjct  4012  YCTTTTSTEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTTH  4191

Query  957   --HDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPL--  1012
                +D HSR+E YASRLA++E     Y     +     DDEH LI  YCQ+L  +     
Sbjct  4192  QLQNDMHSRLEMYASRLAQVE-----YGGTGSNSTPDSDDEHQLIAQYCQALPANGATNG  4356

Query  1013  -SQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRL--KQQH----EHKGLSP  1065
              S P+SP Q++ ++++E+R ELE I+ DLEEEN NLQAEY +L  KQQ     +  G   
Sbjct  4357  ASAPKSPVQVMAAMDAEQREELEAIIRDLEEENANLQAEYQQLCSKQQSGTPDDSSGGMQ  4536

Query  1066  LPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLE  1125
                   M   S Q     +++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL+
Sbjct  4537  HSGSSSMTGLSNQGEHGQDMMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLD  4716

Query  1126  QP  1127
             +P
Sbjct  4717  EP  4722


>ref|XM_001996213.1| Drosophila grimshawi GH22298 (Dgri\GH22298), mRNA
Length=5103

 Score =  852 bits (2200),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 474/1099 (43%), Positives = 685/1099 (62%), Gaps = 76/1099 (6%)
 Frame = +1

Query  93    RIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYT  152
             ++ R++  WDE  + +  R  QL  ML DS ++   + E E+ L +   + E       T
Sbjct  1636  QVTRLREHWDETSQCVLQRAGQLKNMLSDSQRFEAKRLELEKWLARMEQRAERMGTIATT  1815

Query  153   VDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRS  212
              D ++ +  E K    +L Q + + ++ ++L  KL+  Y  DDT ++  +TE IN  + +
Sbjct  1816  ADILEAQQKEQKSFHAELHQNKQHFELFSELTQKLIAVYPNDDTSRIKKMTEAINQRYSN  1995

Query  213   IHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVK  272
             ++  V  R   L      LQ F   +++FLA+L+E ET     +    +  L+       
Sbjct  1996  LNNGVVNRGKQLHAAVHSLQMFDRAMDQFLAFLSETETLCENAESDIERNPLM-------  2154

Query  273   ELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKK  332
                  ++DLQ EIE H  VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ K
Sbjct  2155  -----FKDLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSK  2319

Query  333   SLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRA  390
             S+ IR+ LE++S+ W  L LSL+EL  W+  KD ELS     P+ GD  ++QKQ D H+A
Sbjct  2320  SIAIRNRLESNSEHWNALLLSLRELTEWVIRKDTELSTLGLGPVRGDAASLQKQLDDHKA  2499

Query  391   FKRELKTKEPVIMSTLETVRIFL-TEQPLEGLEKLY----QEPRELPPEERAQNVTRLLR  445
             F+R+L+ K P++ S L + R ++ +E P+            + R +  EE+++ + R +R
Sbjct  2500  FRRQLEDKRPIVESNLTSGRQYIASEAPISDTSDTEAPHDSDSRYMTAEEQSRELARSIR  2679

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ-PVG  504
             ++  +++ +W  L   S +W+ ++DE + ++++ Q+  ++L  ++  AE  K +WQ P  
Sbjct  2680  REVGKLSEQWNNLIDRSDNWKHRLDEYMTKMRQFQKVLEDLSSRVALAEQTKNAWQTPTS  2859

Query  505   DLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRW  564
                +D   + +++++ LR ++      +   N+     T   + +    LS LEDLNTR 
Sbjct  2860  ---VDEANEQMQQLQRLRDKMTTASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTRM  3030

Query  565   KLLQVAVEDRVRQLHEAHRD-----------------FGPASQHFLSTSVQGPWERAISP  607
             KLLQ+A+++R + L +A  +                  GP     L  SV+ PWERA + 
Sbjct  3031  KLLQIAMDERQKVLCQAGANHTHENGDEGRNTSNSGTIGPLPN--LGQSVKPPWERATTA  3204

Query  608   NKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLS  667
               VPYYI+HE +TT WDHP+M EL + LADLN +RFSAYRTAMKLR +Q  L LD +S++
Sbjct  3205  ANVPYYIDHERETTHWDHPEMIELMKGLADLNEIRFSAYRTAMKLRAVQTRLALDRISMA  3384

Query  668   AACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVY  726
              AC++ D+H L+ QND+ +DI  +   L ++Y  +++     +++ L +D+ +NW+LNVY
Sbjct  3385  TACESFDRHGLRAQNDKLIDIPDMTTVLHSLYVTIDK-----IDLTLMLDLAINWILNVY  3549

Query  727   DTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPR  786
             D+ RTG+IRVLSFK G++ LC+ HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PR
Sbjct  3550  DSQRTGQIRVLSFKVGLVLLCRGHLEEKYRYLFRLVADTERRADQRRLGLLLHDCIQVPR  3729

Query  787   QLGEVASFGGSNIEPSVRSCFQFA---------NNKPEIEAALFLDWMRLEPQSMVWLPV  837
             QLGEVA+FGGSNIEPSVRSC + A         N +  IE   FL W++ EPQS+VWLPV
Sbjct  3730  QLGEVAAFGGSNIEPSVRSCLEQAGISQETIDGNQEISIELQHFLGWLQHEPQSLVWLPV  3909

Query  838   LHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMV  897
             LHR+AAAE AKHQAKCNICKE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM 
Sbjct  3910  LHRLAAAEAAKHQAKCNICKEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMH  4089

Query  898   EYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS-  956
             EYCT TTS EDVRDF + LKNKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ + 
Sbjct  4090  EYCTTTTSTEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTT  4269

Query  957   ---HDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLS  1013
                  D HSR+E YASRLA++E     Y     +     DDEH LI  YCQ+L  ++  S
Sbjct  4270  HQLQSDMHSRLEMYASRLAQVE-----YGGTGSNSTPDSDDEHQLIAQYCQALPTNNG-S  4431

Query  1014  QPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRL--KQQH----EHKGLSPLP  1067
              P+SP Q++ ++++E+R ELE I+ DLEEEN NLQAEY +L  KQQ     +  G+    
Sbjct  4432  APKSPVQVMAAMDAEQREELEAIIRDLEEENSNLQAEYQQLCSKQQSGTPDDSNGMQHSS  4611

Query  1068  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
             S    + +  +  +D  ++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  4612  SSTAGLASQGEHGQD--MMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  4785

Query  1128  QAEAKVNGTTV-SSPSTSL  1145
                     + + S+P ++L
Sbjct  4786  NGGGSATSSGLPSAPGSAL  4842


>ref|XM_001999329.1| Drosophila mojavensis GI23105 (Dmoj\GI23105), mRNA
Length=5001

 Score =  849 bits (2193),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 500/1181 (42%), Positives = 712/1181 (60%), Gaps = 108/1181 (9%)
 Frame = +1

Query  94    IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
             + R++  WDE  + +  R  QL  ML DS ++   + E E  L +   + E       T 
Sbjct  1531  VTRLREHWDETSQCVLQRAAQLKSMLSDSQRFEAKRVELEMWLARMEQRAERMGTVATTA  1710

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             D ++ +  E K    +L Q + + D+ ++L  KL+  Y  DDT +V  +TE+IN  + ++
Sbjct  1711  DILEAQQKEQKSFHAELHQNKQHFDLFSELTQKLIAVYPNDDTSRVKKMTESINQRYTNL  1890

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA-NVLQDATRKERLLEDSKGVK  272
             +  V  R   L    + LQ F   +++FLA+L+E ET   N   D  R   +        
Sbjct  1891  NNGVINRGKLLHAAVQDLQSFDRKMDQFLAFLSETETLCENAESDIDRNPMM--------  2046

Query  273   ELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKK  332
                  ++DLQ EIE H  VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ K
Sbjct  2047  -----FKDLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSK  2211

Query  333   SLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRA  390
             S+ IR+ LE++S+ W  L LSL+EL  W+  KD ELS     P+ GD  ++QKQ D H+A
Sbjct  2212  SIAIRNRLESNSEHWNALLLSLRELTEWVIRKDTELSSLGLGPVRGDAASLQKQLDDHKA  2391

Query  391   FKRELKTKEPVIMSTLETVRIFL-TEQPLEGLEKLY----QEPRELPPEERAQNVTRLLR  445
             F+R+L+ K P++ S L + R ++ +E P+            + R +  EE+++ + R +R
Sbjct  2392  FRRQLEDKRPIVESNLTSGRQYIASETPVSDTSDTEAAHDSDSRYMSAEEQSRELARSIR  2571

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
             ++  +++ +W  L   S +W+ ++DE + ++++ Q+  ++L  ++  AE  + +WQ    
Sbjct  2572  REVGKLSEQWNNLIDRSDNWKHRLDEYMTKMRQFQKVLEDLTSRVALAEQTQLTWQTPSS  2751

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
               +    + +++++ LR ++      +   N+     T   + +    LS LEDLNTR K
Sbjct  2752  --VGEANEQMQQLQRLRDKMTTASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTRMK  2925

Query  566   LLQVAVEDRVRQL--------HEAHRD---------FGPASQHFLSTSVQGPWERAISPN  608
             LLQ+A+++R + L        HE   D          GP     L  SV+ PWERA +  
Sbjct  2926  LLQIAMDERQKVLCQAGANNAHENGDDGRTTSNSGTIGPLPN--LGQSVKPPWERATTAA  3099

Query  609   KVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSA  668
              VPYYI+HE +TT WDHP+M EL + LADLN +RFSAYRTAMKLR +QK L LD +S++ 
Sbjct  3100  NVPYYIDHERETTHWDHPEMIELMKGLADLNEIRFSAYRTAMKLRAVQKRLALDRISMAT  3279

Query  669   ACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYD  727
             AC++ D+H L+ QND+ +DI  +   L ++Y  +++     +++ L +D+ +NW+LNVYD
Sbjct  3280  ACESFDRHGLRAQNDKLIDIPDMTTVLHSLYVTIDK-----IDLTLMLDLAINWILNVYD  3444

Query  728   TGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQ  787
             + RTG+IRVLSFK G++ LCK HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PRQ
Sbjct  3445  SQRTGQIRVLSFKVGLVLLCKGHLEEKYRYLFRLVADTDRRADQRRLGLLLHDCIQVPRQ  3624

Query  788   LGEVASFGGSNIEPSVRSCFQFA---------NNKPEIEAALFLDWMRLEPQSMVWLPVL  838
             LGEVA+FGGSNIEPSVRSC + A         N +  IE   FL W++ EPQS+VWLPVL
Sbjct  3625  LGEVAAFGGSNIEPSVRSCLEQAGISQEAIDGNQEISIELQHFLGWLQHEPQSLVWLPVL  3804

Query  839   HRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVE  898
             HR+AAAE AKHQAKCNICKE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM E
Sbjct  3805  HRLAAAEAAKHQAKCNICKEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHE  3984

Query  899   YCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQ-LSH  957
             YCT TTS EDVRDF + LKNKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ  SH
Sbjct  3985  YCTTTTSTEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTSH  4164

Query  958   ---DDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                +D HSR+E YASRLA++E     Y     +     DDEH LI  YCQ+L   +  S 
Sbjct  4165  QLQNDMHSRLEMYASRLAQVE-----YGGTGSNSTPDSDDEHQLIAQYCQALPATNG-SA  4326

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRL--KQQH----EHKGLSPLPS  1068
             P+SP Q++ ++++E+R ELE I+ DLEEEN NLQAEY +L  KQQ     E  G+    S
Sbjct  4327  PKSPVQVMAAMDAEQREELEAIIRDLEEENANLQAEYQQLCTKQQSGTPDESNGMH-HSS  4503

Query  1069  PPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQ  1128
                M   S Q     +++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P 
Sbjct  4504  SSSMTGLSSQGEHGQDMMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEPN  4683

Query  1129  AEAKVNGTTV--SSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEV  1186
                    ++   S+P ++L    +S+P  L+      S                      
Sbjct  4684  GGGSSATSSGLPSAPGSAL----NSKPNTLQTRSVTAS----------------------  4785

Query  1187  MEQLNNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEE  1227
               QLN   P+      G   H +    +A ++LV+V+T++E
Sbjct  4786  --QLNTDSPAKMNQQNGHYDHTS----KAADNLVTVITEQE  4890


>ref|XM_002054550.1| Drosophila virilis GJ22727 (Dvir\GJ22727), mRNA
Length=4995

 Score =  848 bits (2190),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 480/1102 (43%), Positives = 681/1102 (61%), Gaps = 91/1102 (8%)
 Frame = +1

Query  93    RIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYT  152
             ++ R++  WDE  + +  R  QL  ML DS ++   + E E+ LG+   + E       T
Sbjct  1522  QVTRLREHWDETSQCVLQRAAQLKNMLSDSQRFEAKRLELEKWLGRMEQRAERMGTVATT  1701

Query  153   VDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRS  212
              D ++ +  E K    +L Q + + ++ +DL  KL+  Y  DDT ++  +TE +N  + +
Sbjct  1702  ADILEAQQKEQKSFHAELHQNKQHFELFSDLTQKLIAVYPNDDTTRIKKMTEALNQRYSN  1881

Query  213   IHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA-NVLQDATRKERLLEDSKGV  271
             ++  V  R   L      LQ F   +++FLA+L+E ET   N   D  R   +       
Sbjct  1882  LNNGVINRGKQLHAAVHSLQSFDRAMDQFLAFLSEMETLCENAESDVERNPMM-------  2040

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
                   ++DLQ EIE H  VY  LD   +K+L SL   +DAV+LQ RLD MN +W+ L+ 
Sbjct  2041  ------FKDLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDAVMLQHRLDEMNQRWNNLKS  2202

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHR  389
             KS+ IR+ LE++S+ W  L LSL+EL  W+  KD ELS     P+ GD  ++QKQ D H+
Sbjct  2203  KSIAIRNRLESNSEHWHALLLSLRELTEWVIRKDTELSSLGLGPVRGDAASLQKQLDDHK  2382

Query  390   AFKRELKTKEPVIMSTLETVRIFL-TEQPLEGLEKLY----QEPRELPPEERAQNVTRLL  444
             AF+R+L+ K P++ S L + R ++ +E P+            + R +  EE+++ + R +
Sbjct  2383  AFRRQLEDKRPIVESNLTSGRQYIASEAPVSDTSDTEAAHDSDSRYMSAEEQSRELARSI  2562

Query  445   RKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ-PV  503
             R++  +++ +W  L   S +W+ ++DE + ++++ Q+  ++L  ++  AE  K +WQ P 
Sbjct  2563  RREVGKLSEQWNNLIDRSDNWKHRLDEYMTKMRQFQKVLEDLSSRVALAEQTKNAWQTPT  2742

Query  504   GDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTR  563
                 +    + +++++ LR ++      +   N+     T   + +    LS LEDLNTR
Sbjct  2743  S---VGEANEQMQQLQRLRDKMTTASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTR  2913

Query  564   WKLLQVAVEDRVRQL--------HEAHRD---------FGPASQHFLSTSVQGPWERAIS  606
              KLLQ+A+++R + L        HE   D          GP     L  SV+ PWERA +
Sbjct  2914  MKLLQIAMDERQKVLCQAGANHTHENGDDGRNTSNSGTIGPLPN--LGQSVKPPWERATT  3087

Query  607   PNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSL  666
                VPYYI+HE +TT WDHP+M EL + LADLN +RFSAYRTAMKLR +QK L LD +S+
Sbjct  3088  AANVPYYIDHERETTHWDHPEMIELMKGLADLNEIRFSAYRTAMKLRAVQKRLALDRISM  3267

Query  667   SAACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNV  725
             + AC++ D+H L+ QND+ +DI  +   L ++Y  +++     +++ L +D+ +NW+LNV
Sbjct  3268  ATACESFDRHGLRAQNDKLIDIPDMTTVLHSLYVTIDK-----IDLTLMLDLAINWILNV  3432

Query  726   YDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIP  785
             YD+ RTG+IRVLSFK G++ LC+ HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+P
Sbjct  3433  YDSQRTGQIRVLSFKVGLVLLCRGHLEEKYRYLFRLVADTERRADQRRLGLLLHDCIQVP  3612

Query  786   RQLGEVASFGGSNIEPSVRSCFQFA---------NNKPEIEAALFLDWMRLEPQSMVWLP  836
             RQLGEVA+FGGSNIEPSVRSC + A         N +  IE   FL W++ EPQS+VWLP
Sbjct  3613  RQLGEVAAFGGSNIEPSVRSCLEQAGISQEAIDGNQEISIELQHFLGWLQHEPQSLVWLP  3792

Query  837   VLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPM  896
             VLHR+AAAE A+HQAKCNICKE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM
Sbjct  3793  VLHRLAAAEAARHQAKCNICKEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPM  3972

Query  897   VEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS  956
              EYCT TTS EDVRDF + LKNKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ +
Sbjct  3973  HEYCTTTTSTEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHT  4152

Query  957   ----HDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPL  1012
                   D HSR+E YASRLA++E     Y     +     DDEH LI  YCQ+L  ++  
Sbjct  4153  THQLQSDMHSRLEMYASRLAQVE-----YGGTGSNSTPDSDDEHQLIAQYCQALPTNNG-  4314

Query  1013  SQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRL--KQQHEHKGLSPLPSPP  1070
             S P+SP Q++ ++++E+R ELE I+ DLEEEN NLQAEY +L  KQQ      S  P   
Sbjct  4315  SAPKSPVQVMAAMDAEQREELEAIIRDLEEENANLQAEYQQLCSKQQ------SGTPDES  4476

Query  1071  EMM--------PTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQ  1122
               M          S Q     +++AEAKLLRQHKGRLE+RMQILEDHN+QLE+QL RLRQ
Sbjct  4477  NGMQHSSSSMTGLSSQGEHGQDMMAEAKLLRQHKGRLESRMQILEDHNRQLEAQLQRLRQ  4656

Query  1123  LLEQPQAEAKVNGTTVSSPSTS  1144
             LL++P      NG   SS ++S
Sbjct  4657  LLDEP------NGGGCSSANSS  4704


>gb|AF300294.1|AF300294 Drosophila melanogaster dystrophin-like protein DLP186 mRNA, 
complete cds, alternatively spliced
Length=5153

 Score =  846 bits (2185),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 473/1081 (43%), Positives = 669/1081 (61%), Gaps = 76/1081 (7%)
 Frame = +1

Query  93    RIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYT  152
             ++ R++  WDE  + +  R  QL  ML DS ++   + E E+ L +   + E       T
Sbjct  1600  QVTRLREHWDETSQCVLQRAAQLKNMLSDSQRFEAKRLELEKWLARMEQRAERMGTIATT  1779

Query  153   VDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRS  212
              D ++ +  E K    +L Q + + D+ N+L  KL+  Y  DDT ++  +TE IN  + +
Sbjct  1780  ADILEAQQKEQKSFHAELHQNKQHFDIFNELTQKLIAVYPNDDTTRIKKMTEVINQRYAN  1959

Query  213   IHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVK  272
             ++  V  R   L      LQ F   +++FLA+L+E ET     +    +  L+       
Sbjct  1960  LNSGVINRGKQLHAAVHSLQSFDRAMDQFLAFLSETETLCENAESDIERNPLM-------  2118

Query  273   ELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKK  332
                  ++DLQ EIE H  VY+ LD   +K+L SL   +DAV+LQRRLD MN +W++LR K
Sbjct  2119  -----FKDLQSEIETHRVVYNRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNDLRSK  2283

Query  333   SLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRA  390
             S+ +R+ LE++S+ W  L LSL+EL  W+  KD ELS     P+  D  ++QKQ D H+A
Sbjct  2284  SIAMRNRLESNSEHWNALLLSLRELTEWVIRKDSELSTLGLGPVLTDAASLQKQLDDHKA  2463

Query  391   FKRELKTKEPVIMSTLETVRIFLTEQPL-----EGLEKLYQEPRELPPEERAQNVTRLLR  445
             F+R+L+ K P++ S L + R ++  +       +       + R +  EE+++ + R +R
Sbjct  2464  FRRQLEDKRPIVESNLTSGRQYIANEAAVSDTSDTEANHDSDSRYMSAEEQSRELRRSIR  2643

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
             ++  +++ +W  L   S +W+ ++DE + ++++ Q+  ++L  ++  AE  K SW P   
Sbjct  2644  REVGKLSEQWNNLLDRSDNWKHRLDEYMTKMRQFQKILEDLSSRVALAEQTKTSWLPPSS  2823

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
               +    + +++++ LR ++      +   N+     T   + +    LS LEDLNTR K
Sbjct  2824  --VGEANEQMQQLQRLRDKMTTASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTRMK  2997

Query  566   LLQVAVEDR--------VRQLHEAHRD---------FGPASQHFLSTSVQGPWERAISPN  608
             LLQ+A+++R         +Q HE   D          GP     L  SV+ PWERA +  
Sbjct  2998  LLQIAMDERQKVLCQAGAQQTHENGDDGRTTSNSGTIGPLPN--LGQSVKPPWERATTAA  3171

Query  609   KVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSA  668
              VPYYI+HE QTT WDHP+M EL + LADLN +RFSAYRTAMKLR +QK L LD +S+S 
Sbjct  3172  NVPYYIDHERQTTHWDHPEMIELMKGLADLNEIRFSAYRTAMKLRSVQKRLALDRISMST  3351

Query  669   ACDALDQH-NLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYD  727
             AC++ D+     QND+ +DI  +   L ++Y  +++     +++ L +D+ +NW+LNVYD
Sbjct  3352  ACESFDRTWPACQNDELIDIPDMTTVLHSLYVTIDE-----IDLTLMLDLAINWILNVYD  3516

Query  728   TGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQ  787
             + RTG+IRVLSFK G++ LCK HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PRQ
Sbjct  3517  SQRTGQIRVLSFKVGLVLLCKGHLEEKYRYLFRLVADTDRRADQRRLGLLLHDCIQVPRQ  3696

Query  788   LGEVASFGGSNIEPSVRSCFQFA---------NNKPEIEAALFLDWMRLEPQSMVWLPVL  838
             LGEVA+FGGSNIEPSVRSC + A         N    IE   FL W++ EPQS+VWLPVL
Sbjct  3697  LGEVAAFGGSNIEPSVRSCLEQAGISQEAIDGNQDISIELQHFLGWLQHEPQSLVWLPVL  3876

Query  839   HRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVE  898
             HR+AAAE AKHQAKCNICKE PI+ FRYR LK FN+D+CQ CFF GR AK HK+ +PM E
Sbjct  3877  HRLAAAEAAKHQAKCNICKEYPIVLFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHE  4056

Query  899   YCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS--  956
             YCT TTS EDVRDF + LKNKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ +  
Sbjct  4057  YCTTTTSTEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTTH  4236

Query  957   --HDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                +D HSR+E YASRLA++E     Y     +     DDEH LI  YCQ+L   S  S 
Sbjct  4237  QLQNDMHSRLEMYASRLAQVE-----YGGTGSNSTPDSDDEHQLIAQYCQALPGTSNGSA  4401

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP-------  1067
             P+SP Q++ ++++E+R ELE I+ DLEEEN NLQAEY +L  + +    S +P       
Sbjct  4402  PKSPVQVMAAMDAEQREELEAIIRDLEEENANLQAEYQQLCSKEQ----SGMPEDSNGMQ  4569

Query  1068  -SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ  1126
              S   M   S Q  +  +++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++
Sbjct  4570  HSSSSMTGLSGQGEQGQDMMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDE  4749

Query  1127  P  1127
             P
Sbjct  4750  P  4752


>ref|XM_002096289.1| Drosophila yakuba GE25609 (Dyak\GE25609), mRNA
Length=5403

 Score =  842 bits (2176),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 489/1161 (42%), Positives = 698/1161 (60%), Gaps = 87/1161 (7%)
 Frame = +1

Query  15    FNRAWTELTDWLSLLDQVIKSQRV-MVGDLEDINEMIIK-QKATMQDLEQRRPQLEELIT  72
             F     EL  WL+ ++Q  +++R+  +    DI E   K QK+   +L Q +   +    
Sbjct  1717  FEAKRLELEKWLARMEQ--RAERMGTIATTADILEAQQKEQKSFHAELHQNKQHFDIFNE  1890

Query  73    AAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEA  132
               Q L     N +  T I    E I  ++  +   + NR +QL+  +     +  A ++ 
Sbjct  1891  LTQKLIAVYPNDDT-TRIKKMTEVINQRYANLNNGVINRGKQLHAAVHSLQSFDRAMDQF  2067

Query  133   EQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS  192
                L +     E+ +        I++     K    +L Q + + D+ N+L  KL+  Y 
Sbjct  2068  LAFLSETETLCENAESD------IERNPLMFKSFHAELHQNKQHFDIFNELTQKLIAVYP  2229

Query  193   ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
              DDT ++  +TE IN  + +++  V  R   L      LQ F   +++FLA+L+E ET  
Sbjct  2230  NDDTTRIKKMTEVINQRYANLNNGVINRGKQLHAAVHSLQSFDRAMDQFLAFLSETETLC  2409

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
                +    +  L+            ++DLQ EIE H  VY  LD   +K+L SL   +DA
Sbjct  2410  ENAESDIERNPLM------------FKDLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDA  2553

Query  313   VLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA  372
             V+LQRRLD MN +W+ L+ KS+ IR+ LE++S+ W  L LSL+EL  W+  KD ELS   
Sbjct  2554  VMLQRRLDEMNQRWNNLKSKSIAIRNRLESNSEHWNALLLSLRELTEWVIRKDTELSTLG  2733

Query  373   --PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPL-----EGLEKLY  425
               P+ GD  ++QKQ D H+AF+R+L+ K P++ S L + R ++  +       +      
Sbjct  2734  LGPVRGDAASLQKQLDDHKAFRRQLEDKRPIVESNLTSGRQYIANEAAVSDTSDTEANHD  2913

Query  426   QEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDE  485
              + R +  EE+++ +TR +R++  +++ +W  L   S +W+ ++DE + ++++ Q+  ++
Sbjct  2914  SDSRYMSAEEQSRELTRSIRREVGKLSEQWNNLIDRSDNWKHRLDEYMTKMRQFQKILED  3093

Query  486   LDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTL  545
             L  ++  AE  K SW P     +    + +++++ LR ++      +   N+     T  
Sbjct  3094  LSSRVALAEQTKTSWLPPSS--VGEANEQMQQLQRLRDKMTTASALLDDCNEQQSFFTAN  3267

Query  546   GIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------VRQLHEAHRD---------FGPA  588
              + +    LS LEDLNTR KLLQ+A+++R         +Q HE   D          GP 
Sbjct  3268  QVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCQAGAQQTHENGDDGRTTSNSGTIGPL  3447

Query  589   SQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRT  648
                 L  SV+ PWERA +   VPYYI+HE +TT WDHP+M EL + LADLN +RFSAYRT
Sbjct  3448  PN--LGQSVKPPWERATTAANVPYYIDHERETTHWDHPEMIELMKGLADLNEIRFSAYRT  3621

Query  649   AMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNN  707
             AMKLR +QK L LD +S+S AC++ D+H L+ QND+ +DI  +   L ++Y  +++    
Sbjct  3622  AMKLRSVQKRLALDRISMSTACESFDRHGLRAQNDKLIDIPDMTTVLHSLYVTIDK----  3789

Query  708   LVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTG  767
              +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ LCK HLE+KYRYLF+ VA +  
Sbjct  3790  -IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVLLCKGHLEEKYRYLFRLVADTDR  3966

Query  768   FCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA---------NNKPEIEA  818
               DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRSC + A         N    IE 
Sbjct  3967  RADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRSCLEQAGISQEAIDGNQDISIEL  4146

Query  819   ALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQ  878
               FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNICKE PI+GFRYR LK FN+D+CQ
Sbjct  4147  QHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNICKEYPIVGFRYRCLKCFNFDMCQ  4326

Query  879   SCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQ  938
              CFF GR AK HK+ +PM EYCT TTS EDVRDF + LKNKF++++YF KHPR+GYLPVQ
Sbjct  4327  KCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQ  4506

Query  939   TVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDD  994
             +VLEGD +E+PA SPQ +     +D HSR+E YASRLA++E     Y     +     DD
Sbjct  4507  SVLEGDALESPAPSPQHTTHQLQNDMHSRLEMYASRLAQVE-----YGGTGSNSTPDSDD  4671

Query  995   EHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRL  1054
             EH LI  YCQ+L   S  S P+SP Q++ ++++E+R ELE I+ DLEEEN NLQAEY +L
Sbjct  4672  EHQLIAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREELEAIIRDLEEENANLQAEYQQL  4851

Query  1055  KQQHEHKGLSPLP--------SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQIL  1106
               + +    S +P        S   M   S Q  +  +++AEAKLLRQHKGRLEARMQIL
Sbjct  4852  CSKEQ----SGMPEDSNGMQHSSSSMTGLSGQGEQGQDMMAEAKLLRQHKGRLEARMQIL  5019

Query  1107  EDHNKQLESQLHRLRQLLEQP  1127
             EDHN+QLE+QL RLRQLL++P
Sbjct  5020  EDHNRQLEAQLQRLRQLLDEP  5082


>emb|X99703.1| S.caniculua mRNA for utrophin
Length=1737

 Score =  842 bits (2174),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 406/583 (69%), Positives = 471/583 (80%), Gaps = 22/583 (3%)
 Frame = +1

Query  626   PKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPM  685
             PKM EL+ SL DLNNVRFSAYRTAMK+RRLQKALCLDLL L  A     QH L QN Q +
Sbjct  1     PKMVELFHSLGDLNNVRFSAYRTAMKIRRLQKALCLDLLELHTAQCIFAQHKLIQNVQLL  180

Query  686   DILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIIS  745
             ++ ++INCLTTIYD LEQ+H +LVNVPLCVDMCLNWLLNV+DTGR+GR+ VLS K G++ 
Sbjct  181   NVTEVINCLTTIYDGLEQKHKDLVNVPLCVDMCLNWLLNVFDTGRSGRVGVLSLKIGLMC  360

Query  746   LCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRS  805
             L K HLE+KY YLFKQVA ST  CDQR L LLLHD++QIPRQLGE+ASFGGSNIEPSVRS
Sbjct  361   LSKGHLEEKYTYLFKQVAESTDSCDQRSLSLLLHDAVQIPRQLGEIASFGGSNIEPSVRS  540

Query  806   CFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFR  865
             CFQ   NK EI+A  F++WMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI+GFR
Sbjct  541   CFQHGQNKSEIDAKQFVEWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIVGFR  720

Query  866   YRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRY  925
             YRSLKHFNYDICQSCFFSGR AKGHK+ YPMVEYCTPTTSGEDVRDF KVLKNKFR+K+Y
Sbjct  721   YRSLKHFNYDICQSCFFSGRTAKGHKLQYPMVEYCTPTTSGEDVRDFTKVLKNKFRSKKY  900

Query  926   FAKHPRMGYLPVQTVLEGDNMETPAS-------------SPQLSHDDTHSRIEHYASRLA  972
             FAKHPR+GYLPVQTVLEG+N+E P +             SPQLS DDTHSRIEHYA+RLA
Sbjct  901   FAKHPRLGYLPVQTVLEGENLEIPVTLISMWPEQYDPTQSPQLSQDDTHSRIEHYANRLA  1080

Query  973   EMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGE  1032
             +ME +NGS L DS S   S++DEH+LIQ YC +L ++SP+SQP+SP QIL S+E EER E
Sbjct  1081  QMERTNGSLLTDSSSTTGSVEDEHILIQQYCLTLGRESPISQPQSPVQILKSVEKEERSE  1260

Query  1033  LERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLL  1092
             LE I+A+LEEE RNLQAEY+RLKQQ   + + PLPSP   + ++ Q+  DAEL+AEAKLL
Sbjct  1261  LEFIIANLEEEQRNLQAEYERLKQQQILRDIKPLPSP--TLSSNQQNYHDAELLAEAKLL  1434

Query  1093  RQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQ  1152
             RQHKGRLEARMQILEDHNKQLESQL RLR+LLE+P  E+K+NG T  SP+ S Q +++ Q
Sbjct  1435  RQHKGRLEARMQILEDHNKQLESQLCRLRKLLEEPLTESKLNGVTAVSPTASFQLAENGQ  1614

Query  1153  PMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFP  1195
                     SQT      +DLL PPQDT+T L +V E++ +SFP
Sbjct  1615  -TCNEDFSSQT------DDLLIPPQDTNTDLTDVEEEIKSSFP  1722


>ref|XM_319450.4| Anopheles gambiae str. PEST AGAP010261-PA (AgaP_AGAP010261) mRNA, 
complete cds
Length=3477

 Score =  829 bits (2142),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 469/1095 (42%), Positives = 663/1095 (60%), Gaps = 96/1095 (8%)
 Frame = +1

Query  96    RIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDA  155
             R++ QW++  + +  R+ QL  ML DS ++   + E +  L +     E       T D 
Sbjct  94    RMKEQWEDTNQSVMQRKTQLTAMLGDSQRYEAKRLEIDAWLSRMETITERMGPVATTADV  273

Query  156   IQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHK  215
             +  +  E K    +L ++   +++ N L  KL+  Y  DDT ++  +TE+IN  + +++ 
Sbjct  274   LDIQQKEQKSFHAELHKFNHQIELFNQLTQKLISVYQCDDTSRIKRMTESINLRYNNLNN  453

Query  216   RVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA-NVLQDATRKERLLEDSKGVKEL  274
              +  R   L      LQ F    E+FL WL+EAE+   N   +A R    L         
Sbjct  454   SIISRGKQLHAAIHSLQTFDRTFEQFLGWLSEAESLCENTETEAERNPHCL---------  606

Query  275   MKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSL  334
                 +DLQ EI+A+  VY  LD   +K+LRSL   +DAV+LQ +LD MN +W+ L  +S 
Sbjct  607   ----KDLQSEIDANRKVYEGLDNTGRKLLRSLTSQEDAVMLQHKLDEMNQRWNHLNSRSA  774

Query  335   NIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRAFK  392
              IR+ LE++SD W  L LS +EL  W+  K+ EL+      I GD  ++Q Q D H+AF+
Sbjct  775   AIRNRLESNSDHWNALLLSSRELTEWVIRKNTELTSIGFGSINGDSNSLQMQLDEHKAFR  954

Query  393   RELKTKEPVIMSTLETVRIFLT-EQPLEGLE--KLYQEPRELPPEERAQNVTRLLRKQAE  449
             R+L  K  +I + L   R +++ E PL      +   E   +  EE+ + ++R +R++  
Sbjct  955   RQLDDKRSIIENNLMNGRQYISNESPLSDASDSEAIDETMYISTEEQNRILSRSIRREVN  1134

Query  450   EVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ-PV-GDLL  507
             +++ +W  L      W+ ++DE + ++++ Q+  ++L  ++  AE I  SW  P  G   
Sbjct  1135  KLSEQWSLLIERCDKWKHRLDENITKMRQFQKILEDLSSRVASAETITHSWTTPAPGSDT  1314

Query  508   IDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL  567
              + +Q HL+++K        L ++ +   +         I  SPY L+ LED+NTR KLL
Sbjct  1315  TEEMQ-HLQRLKDKLTTANALLDDCNEQQNFFSSCRV--IVPSPY-LAKLEDINTRMKLL  1482

Query  568   QVAVEDRVRQL----------------HEAHRDF--------GPASQHFLSTSVQGPWER  603
              +AVE+R + L                HE    F        G ++   L  SVQ PWER
Sbjct  1483  HIAVEERFKVLQQSMQTTAEDGIVGSHHEEGSKFSKPLHIAPGSSTVPNLEKSVQIPWER  1662

Query  604   AISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL  663
             A++P  VPYYINHE ++T WDHP+M EL +SLADLN VRFSAYRTA+KLR +QK L  D 
Sbjct  1663  AVTPANVPYYINHERESTHWDHPEMIELMKSLADLNEVRFSAYRTALKLRTVQKKLAFDR  1842

Query  664   LSLSAACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWL  722
             L++S A +  D++ L+ QND+ +DI  +   L ++Y  LE      ++  + +D+ +NW+
Sbjct  1843  LNMSVAIEIFDRYGLRAQNDKLIDIPDMTTILNSLYTTLEP-----IDRAVMLDLAINWV  2007

Query  723   LNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSI  782
             LNVYD+ RTG+IRVLSFK G+I LC+ HLE+KYRYLF+ +A      DQR++GLLLHD I
Sbjct  2008  LNVYDSQRTGQIRVLSFKVGLILLCRGHLEEKYRYLFRLIADLEKKVDQRKMGLLLHDCI  2187

Query  783   QIPRQLGEVASFGGSNIEPSVRSCFQFANN--------KPEIEAALFLDWMRLEPQSMVW  834
             Q+PRQLGEVA+FGGSNIEPSVRSCF+ A          +  IEA  FL W++ EPQS+VW
Sbjct  2188  QVPRQLGEVAAFGGSNIEPSVRSCFELAGGVNQNGELTETAIEAQHFLSWLQHEPQSIVW  2367

Query  835   LPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHY  894
             LPVLHR+ AAETAKHQAKCNICKE PI GFRYR LK FN+D+CQ CFF+GR  K HK+ +
Sbjct  2368  LPVLHRLVAAETAKHQAKCNICKEYPIEGFRYRCLKCFNFDMCQKCFFTGRSTKNHKLSH  2547

Query  895   PMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQ  954
             PM EYCT  TS EDVRDF + L+NKF++++YF KHPR+GYLPVQ+VLEGD +E+P  SPQ
Sbjct  2548  PMHEYCTTATSTEDVRDFTRALRNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPIPSPQ  2727

Query  955   LS----HDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDS  1010
                    +D HSR+E YASRLA++E    S    + +P+   DDEH LI  YCQ+L   +
Sbjct  2728  HGTHTLQNDMHSRLEMYASRLAQVECGTRS----NSTPDS--DDEHQLIAQYCQALPAAN  2889

Query  1011  PLSQ------PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLS  1064
              +        P+SP Q++ ++E+E+R ELE ++ +LEEEN NLQAEY++LK +   K  +
Sbjct  2890  AVGTSTGSGGPKSPVQVMAAMEAEQREELETMIKELEEENANLQAEYEKLKAK---KTST  3060

Query  1065  PLPSPPEMMPTSPQSPRDA-------------ELIAEAKLLRQHKGRLEARMQILEDHNK  1111
             P+ +P E   T P S  +A             +++ EAKLLRQHKGRLEARMQILEDHNK
Sbjct  3061  PITTPDEGYKT-PTSTSNAIVSSVTTSSSGGSDMVTEAKLLRQHKGRLEARMQILEDHNK  3237

Query  1112  QLESQLHRLRQLLEQ  1126
             QLE+QL RLRQLL +
Sbjct  3238  QLEAQLQRLRQLLHE  3282


>ref|XM_002212045.1| Branchiostoma floridae hypothetical protein (BRAFLDRAFT_278584) 
mRNA, complete cds
Length=1878

 Score =  819 bits (2115),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 408/621 (65%), Positives = 483/621 (77%), Gaps = 13/621 (2%)
 Frame = +1

Query  616   HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQ  675
             H T+TT WDHPKMTEL+QSLADLN+VRFSAYRTAMKLRRLQKALCLDLLS++ A DA DQ
Sbjct  1     HTTETTSWDHPKMTELFQSLADLNDVRFSAYRTAMKLRRLQKALCLDLLSMNNAIDAFDQ  180

Query  676   HNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             H L+ QND+ MD+++IINCLTTIYD LEQ+H NLVNVPLCVDMCLNWLLNVYDTGR+G+I
Sbjct  181   HGLRGQNDRLMDVIEIINCLTTIYDNLEQDHGNLVNVPLCVDMCLNWLLNVYDTGRSGKI  360

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFK GIISLC+AHLEDKYR+ F+ +A +TGF DQR+LGLLLHD IQ+PRQLGE+ASF
Sbjct  361   RVLSFKVGIISLCRAHLEDKYRFNFRLIAEATGFADQRKLGLLLHDLIQVPRQLGEIASF  540

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCF+ A  KPEIEAA FLDWM+ EPQSMVWLPVLHR+AAAETAKHQAKCN
Sbjct  541   GGSNIEPSVRSCFERAGGKPEIEAAHFLDWMKQEPQSMVWLPVLHRLAAAETAKHQAKCN  720

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKE PI+GFRYR L+ FN+D+CQSCF SGR AKGHK+ +PM EYCT TTSGEDVRDFAK
Sbjct  721   ICKEYPIVGFRYRCLRCFNFDMCQSCFLSGRKAKGHKLSHPMQEYCTATTSGEDVRDFAK  900

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS-HDDTHSRIEHYASRLAE  973
             V++NKFR+K+   KHPR+GYLPVQTVLEGDN+ETP+SSPQ +   D HSR+E YASR   
Sbjct  901   VVRNKFRSKKSLKKHPRLGYLPVQTVLEGDNLETPSSSPQQAVSQDMHSRLELYASRYEN  1080

Query  974   MENSNGSYLNDSISPNESI-DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGE  1032
             +      +++  I+P     +DEH LIQ YCQSL  DS +  P+SPAQI+++++ E+R E
Sbjct  1081  LSYFIFFHVDSKIAPILFYREDEHTLIQQYCQSLGGDSGVVSPKSPAQIVVAIDQEQRAE  1260

Query  1033  LERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLL  1092
             LE ++ DLEEENRNLQ EY+RLK Q + +     PS P+  P S +  RD ELIAEAKLL
Sbjct  1261  LEAMIKDLEEENRNLQMEYERLKIQKQQQ-----PS-PQAEPRS-EVNRDNELIAEAKLL  1419

Query  1093  RQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ--PQAEAKVNGTTVS-SPSTSLQRSD  1149
             RQHKGRLEARMQILEDHN+QLE+QL RLRQLLEQ  P     VN   +S + S ++ R  
Sbjct  1420  RQHKGRLEARMQILEDHNRQLEAQLQRLRQLLEQQSPHGSGSVNCCAMSHTLSLTIHRCS  1599

Query  1150  SSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMA  1209
                   L  VG  T       D     Q     LEEVM ++N+SFP    H  GSLF+MA
Sbjct  1600  IRLSQSLARVGRATRTPPPLRDGQRRQQTPEEQLEEVMREVNSSFPPDSNHTQGSLFNMA  1779

Query  1210  DDLGRAMESLVSVMTDEEGAE  1230
              DL +A+  LV+VMT+E+G E
Sbjct  1780  GDLNKAVGKLVTVMTNEDGTE  1842


>gb|DQ440977.1| Myxine glutinosa dystrophin mRNA, partial cds
Length=1840

 Score =  810 bits (2092),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 392/522 (75%), Positives = 453/522 (86%), Gaps = 14/522 (2%)
 Frame = +1

Query  624   DHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ  683
             DHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSL AA    ++  LKQND+
Sbjct  1     DHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLEAAAGVFEKGVLKQNDR  180

Query  684   PMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGI  743
              MD  +I++ L  +Y  +E+ H++LVNVPLCVDMCLNWLLNVYDTGR G+IR LSFKTG+
Sbjct  181   LMDTSEIVDGLNDMYQGMERRHSDLVNVPLCVDMCLNWLLNVYDTGRGGKIRELSFKTGL  360

Query  744   ISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSV  803
             + +  AHLEDKYR+LFKQVAS  GFCDQRRLGLLLHD++QIPRQLGEVASFGGSNIEPSV
Sbjct  361   VCMSNAHLEDKYRFLFKQVASPQGFCDQRRLGLLLHDAVQIPRQLGEVASFGGSNIEPSV  540

Query  804   RSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIG  863
             RSCFQFAN +PEIEA  FL+WMRLEPQSMVWLPVLHRVAA+ETAKHQAKCNICKECPI+G
Sbjct  541   RSCFQFANGRPEIEAPSFLEWMRLEPQSMVWLPVLHRVAASETAKHQAKCNICKECPIVG  720

Query  864   FRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTK  923
             FRYRSLKHFN+D+CQS FFSGR AKGH+++YPMVEYCTPTTSGED++DFAKV KNKF++K
Sbjct  721   FRYRSLKHFNHDVCQSRFFSGRTAKGHRLNYPMVEYCTPTTSGEDIKDFAKVFKNKFKSK  900

Query  924   RYFAKHPRMGYLPVQTVLEGDNMETPAS---------SP--QLSHDDTHSRIEHYASRLA  972
             +YF +HPR+GYLPVQTVLEGD++ETP +         SP  QLS++DTH+RIEH ASRLA
Sbjct  901   KYFERHPRIGYLPVQTVLEGDDLETPNTLIRLVPYEPSPTQQLSNEDTHARIEHLASRLA  1080

Query  973   EMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGE  1032
             EME  NGSYL DS SPNES++DEHLLIQHYCQSL+ +SP SQP+SPAQILISLE++ER E
Sbjct  1081  EMEFKNGSYLIDS-SPNESLEDEHLLIQHYCQSLSGESPGSQPQSPAQILISLENQERSE  1257

Query  1033  LERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLL  1092
             LERIL DLEEENR+LQ EY+RL+++ E +GL PL          P+SPRD+ELIAEAKLL
Sbjct  1258  LERILRDLEEENRSLQNEYERLRRKQEKEGLGPLLP--MPPSMPPESPRDSELIAEAKLL  1431

Query  1093  RQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVN  1134
             RQHKGRLE RMQ+LE+HN+QLESQL RLRQLL+QPQ E ++N
Sbjct  1432  RQHKGRLEGRMQVLEEHNRQLESQLCRLRQLLDQPQGEGRLN  1557


>ref|NM_001043260.1| Drosophila melanogaster dystrophin (Dys), transcript variant 
D, mRNA
Length=6600

 Score =  803 bits (2073),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 430/895 (48%), Positives = 588/895 (65%), Gaps = 64/895 (7%)
 Frame = +1

Query  279   QDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRS  338
             QDLQ EIE H  VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ KS+ IR+
Sbjct  2905  QDLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSKSIAIRN  3084

Query  339   HLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRAFKRELK  396
              LE++S+ W  L LSL+EL  W+  KD ELS     P+ GD  ++QKQ D H+AF+R+L+
Sbjct  3085  RLESNSEHWNALLLSLRELTEWVIRKDTELSTLGLGPVRGDAVSLQKQLDDHKAFRRQLE  3264

Query  397   TKEPVIMSTLETVRIFLTEQPL-----EGLEKLYQEPRELPPEERAQNVTRLLRKQAEEV  451
              K P++ S L + R ++  +       +       + R +  EE+++ +TR +R++  ++
Sbjct  3265  DKRPIVESNLTSGRQYIANEAAVSDTSDTEANHDSDSRYMSAEEQSRELTRSIRREVGKL  3444

Query  452   NTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSL  511
             + +W  L   S +W+ ++DE + ++++ Q+  ++L  ++  AE  K SW P     +   
Sbjct  3445  SEQWNNLIDRSDNWKHRLDEYMTKMRQFQKILEDLSSRVALAEQTKTSWLPPSS--VGEA  3618

Query  512   QDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAV  571
              + +++++ LR ++      +   N+     T   + +    LS LEDLNTR KLLQ+A+
Sbjct  3619  NEQMQQLQRLRDKMTTASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTRMKLLQIAM  3798

Query  572   EDR--------VRQLHEAHRD---------FGPASQHFLSTSVQGPWERAISPNKVPYYI  614
             ++R         +Q HE   D          GP     L  SV+ PWERA +   VPYYI
Sbjct  3799  DERQKVLCQAGAQQTHENGDDGRTTSNSGTIGPLPN--LGQSVKPPWERATTAANVPYYI  3972

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
             +HE +TT WDHP+M EL + LADLN +RFSAYRTAMKLR +QK L LD +S+S AC++ D
Sbjct  3973  DHERETTHWDHPEMIELMKGLADLNEIRFSAYRTAMKLRSVQKRLALDRISMSTACESFD  4152

Query  675   QHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGR  733
             +H L+ QND+ +DI  +   L ++Y  +++     +++ L +D+ +NW+LNVYD+ RTG+
Sbjct  4153  RHGLRAQNDKLIDIPDMTTVLHSLYVTIDK-----IDLTLMLDLAINWILNVYDSQRTGQ  4317

Query  734   IRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVAS  793
             IRVLSFK G++ LCK HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+
Sbjct  4318  IRVLSFKVGLVLLCKGHLEEKYRYLFRLVADTDRRADQRRLGLLLHDCIQVPRQLGEVAA  4497

Query  794   FGGSNIEPSVRSCFQFA---------NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAA  844
             FGGSNIEPSVRSC + A         N    IE   FL W++ EPQS+VWLPVLHR+AAA
Sbjct  4498  FGGSNIEPSVRSCLEQAGISQEAIDGNQDISIELQHFLGWLQHEPQSLVWLPVLHRLAAA  4677

Query  845   ETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
             E AKHQAKCNICKE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM EYCT TT
Sbjct  4678  EAAKHQAKCNICKEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTTTT  4857

Query  905   SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDT  960
             S EDVRDF + LKNKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ +     +D 
Sbjct  4858  STEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQNDM  5037

Query  961   HSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQ  1020
             HSR+E YASRLA++E     Y     +     DDEH LI  YCQ+L   S  S P+SP Q
Sbjct  5038  HSRLEMYASRLAQVE-----YGGTGSNSTPDSDDEHQLIAQYCQALPGTSNGSAPKSPVQ  5202

Query  1021  ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP--------SPPEM  1072
             ++ ++++E+R ELE I+ DLEEEN NLQAEY +L  + +    S +P        S   M
Sbjct  5203  VMAAMDAEQREELEAIIRDLEEENANLQAEYQQLCSKEQ----SGMPEDSNGMQHSSSSM  5370

Query  1073  MPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
                S Q  +  +++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  5371  TGLSGQGEQGQDMMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  5535


>gb|AY875639.1| Drosophila melanogaster Dp205 mRNA, complete cds
Length=5862

 Score =  802 bits (2071),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 430/895 (48%), Positives = 587/895 (65%), Gaps = 64/895 (7%)
 Frame = +1

Query  279   QDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRS  338
             QDLQ EIE H  VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ KS+ IR+
Sbjct  2905  QDLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSKSIAIRN  3084

Query  339   HLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRAFKRELK  396
              LE++S+ W  L LSL+EL  W+  KD ELS     P+ GD  ++QKQ D H+AF+R+L+
Sbjct  3085  RLESNSEHWNALLLSLRELTEWVIRKDTELSTLGLGPVRGDAASLQKQLDDHKAFRRQLE  3264

Query  397   TKEPVIMSTLETVRIFLTEQPL-----EGLEKLYQEPRELPPEERAQNVTRLLRKQAEEV  451
              K P++ S L + R ++  +       +       + R +  EE+++ + R +R++  ++
Sbjct  3265  DKRPIVESNLTSGRQYIANEAAVSDTSDTEANHDSDSRYMSAEEQSRELRRSIRREVGKL  3444

Query  452   NTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSL  511
             + +W  L   S +W+ ++DE + ++++ Q+  ++L  ++  AE  K SW P     +   
Sbjct  3445  SEQWNNLLDRSDNWKHRLDEYMTKMRQFQKILEDLSSRVALAEQTKTSWLPPSS--VGEA  3618

Query  512   QDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAV  571
              + +++++ LR ++      +   N+     T   + +    LS LEDLNTR KLLQ+A+
Sbjct  3619  NEQMQQLQRLRDKMTTASALLDDCNEQQSFFTANQVLVPTPCLSKLEDLNTRMKLLQIAM  3798

Query  572   EDR--------VRQLHEAHRD---------FGPASQHFLSTSVQGPWERAISPNKVPYYI  614
             ++R         +Q HE   D          GP     L  SV+ PWERA +   VPYYI
Sbjct  3799  DERQKVLCQAGAQQTHENGDDGRTTSNSGTIGPLPN--LGQSVKPPWERATTAANVPYYI  3972

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
             +HE QTT WDHP+M EL + LADLN +RFSAYRTAMKLR +QK L LD +S+S AC++ D
Sbjct  3973  DHERQTTHWDHPEMIELMKGLADLNEIRFSAYRTAMKLRSVQKRLALDRISMSTACESFD  4152

Query  675   QHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGR  733
             +H L+ QND+ +DI  +   L ++Y  +++     +++ L +D+ +NW+LNVYD+ RTG+
Sbjct  4153  RHGLRAQNDKLIDIPDMTTVLHSLYVTIDK-----IDLTLMLDLAINWILNVYDSQRTGQ  4317

Query  734   IRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVAS  793
             IRVLSFK G++ LCK HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+
Sbjct  4318  IRVLSFKVGLVLLCKGHLEEKYRYLFRLVADTDRRADQRRLGLLLHDCIQVPRQLGEVAA  4497

Query  794   FGGSNIEPSVRSCFQFA---------NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAA  844
             FGGSNIEPSVRSC + A         N    IE   FL W++ EPQS+VWLPVLHR+AAA
Sbjct  4498  FGGSNIEPSVRSCLEQAGISQEAIDGNQDISIELQHFLGWLQHEPQSLVWLPVLHRLAAA  4677

Query  845   ETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
             E AKHQAKCNICKE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +PM EYCT TT
Sbjct  4678  EAAKHQAKCNICKEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTTTT  4857

Query  905   SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDT  960
             S EDVRDF + LKNKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ +     +D 
Sbjct  4858  STEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQNDM  5037

Query  961   HSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQ  1020
             HSR+E YASRLA++E     Y     +     DDEH LI  YCQ+L   S  S P+SP Q
Sbjct  5038  HSRLEMYASRLAQVE-----YGGTGSNSTPDSDDEHQLIAQYCQALPGTSNGSAPKSPVQ  5202

Query  1021  ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP--------SPPEM  1072
             ++ ++++E+R ELE I+ DLEEEN NLQAEY +L  + +    S +P        S   M
Sbjct  5203  VMAAMDAEQREELEAIIRDLEEENANLQAEYQQLCSKEQ----SGMPEDSNGMQHSSSSM  5370

Query  1073  MPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
                S Q  +  +++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  5371  TGLSGQGEQGQDMMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  5535


>ref|XM_001633110.1| Nematostella vectensis predicted protein (NEMVEDRAFT_v1g105253) 
partial mRNA
Length=2559

 Score =  794 bits (2050),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 406/868 (46%), Positives = 585/868 (67%), Gaps = 26/868 (2%)
 Frame = +1

Query  280   DLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSH  339
             +L+ +I  H +++ +L+EN   I+  +E  D    +Q +LD+MN +W  L  ++++IR  
Sbjct  1     NLEEDINNHQEMFASLNENGHHIMTEMEPGDTLTAVQSKLDDMNDRWQSLNVRTIDIRDR  180

Query  340   LEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKE  399
             LE ++ +W++L + LQE+L W+   D+E++ Q PIGGD  A Q QN+ H+AFK ++  + 
Sbjct  181   LEETATEWRQLLMDLQEILEWISRADEEITSQQPIGGDLEAAQNQNEQHQAFKGKVNVRR  360

Query  400   PVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLN  459
              V+   L++ R F+ +   E       +  +  P  R   V   L+ Q E V+  W  L 
Sbjct  361   LVVDRALDSGRRFMDDYRAERTA----DTEDTTPRGR---VAGNLQHQLEVVSDRWSALC  519

Query  460   LHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVK  519
               S +WQ+++DE L R Q LQ   +E+D +L +AEV +  W PV DL+I+SL + +E++K
Sbjct  520   QRSEEWQKQVDEALRRFQLLQSQMEEIDARLTEAEVARAGWTPVQDLVIESLNEQMEELK  699

Query  520   ALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLH  579
              L+  IA L+     +++    L   GI +S    + ++ L  RWK LQ+ +  R   L 
Sbjct  700   LLQDRIAALQHMFEQMSNTEGDLRRRGINISANLQNRIDQLYRRWKQLQLQMIQRQNALQ  879

Query  580   EAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLN  639
             +A+ D    S   L+ SV  PWERA++ NKVPYYINH+T+TT WDHPKMTELY  +A+LN
Sbjct  880   DAYADVDTGSIQALAASVDPPWERAVAVNKVPYYINHKTETTQWDHPKMTELYHQIAELN  1059

Query  640   NVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQ--NDQPMDILQIINCLTTI  697
             ++++SAYRTAMKLR +QKA  LDL++L+    A  QHNL +  ND  + + ++++ L T+
Sbjct  1060  DIKYSAYRTAMKLRCIQKATKLDLVTLNNLSSAFVQHNLSKARNDALIGVAEMVDTLHTV  1239

Query  698   YDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRY  757
             +D +E   +N VN  + +D+ LNWLLNVYD+GR G+IR+LSFK G++ LC+AHL+DKY Y
Sbjct  1240  FDNIEVGFDN-VNPAINIDLTLNWLLNVYDSGRVGKIRLLSFKIGLVCLCRAHLDDKYNY  1416

Query  758   LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIE  817
             LFK VA + G  D ++LGLLLHDS+Q+PRQLGE+A+FGGSNIEPSVRSCF+ A  K  I+
Sbjct  1417  LFKLVADNDGKMDHKQLGLLLHDSLQVPRQLGEIAAFGGSNIEPSVRSCFEKAREKERID  1596

Query  818   AALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDIC  877
                F+ W+  EPQS+VWLP LHR+AA+E  KH+AKC+ICKE PI+GFR+R LK FNYD+C
Sbjct  1597  PTQFVYWLSAEPQSIVWLPTLHRLAASEAVKHKAKCSICKEYPIVGFRFRCLKCFNYDLC  1776

Query  878   QSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHP-RMGYLP  936
             QSCF+SGR++  H++ +P+ +YC  TTSGEDV+DF  +++NKF+ ++Y    P ++GYLP
Sbjct  1777  QSCFWSGRISHEHRLTHPVHQYCLSTTSGEDVKDFLSMVRNKFKARKYKKNPPKKLGYLP  1956

Query  937   VQTVLEGDNMETPAS-SPQLS-HDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDD  994
             +QTV+EG N+E P S +PQ + +++ H+R+  +A+RLAE E+  G Y     SP + +D+
Sbjct  1957  IQTVMEGGNLEAPPSMTPQQNVNNEVHNRLGMFANRLAEAESDGGKY-----SP-KPMDE  2118

Query  995   EHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRN-LQAEYDR  1053
             EH LI  YCQSL     +SQPRSP QI++SL++ E+ +LE  +  LE+ENR  LQ+EY+R
Sbjct  2119  EHQLIAQYCQSLKNVCFVSQPRSPTQIVMSLDANEKDDLESEIGKLEDENRYPLQSEYER  2298

Query  1054  LKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQL  1113
             LK   +        S    + T  QS RD EL+ EAKLLRQHKGRLEARMQ+LEDHN+QL
Sbjct  2299  LKSMRDADH-----SSDGDLSTGSQS-RDTELLTEAKLLRQHKGRLEARMQVLEDHNRQL  2460

Query  1114  ESQLHRLRQLLEQPQAEAKVNGTTVSSP  1141
             E+QL RLRQLL+Q +  +    TT S P
Sbjct  2461  EAQLQRLRQLLDQVRTGSLWYHTTGSLP  2544


>gb|EU293093.1| Synthetic construct murine micro utrophin delta H2-R21 (utrn) 
gene, complete cds
Length=3495

 Score =  790 bits (2039),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 359/484 (74%), Positives = 410/484 (84%), Gaps = 0/484 (0%)
 Frame = +1

Query  467   RKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIA  526
             R+I   LE+L++LQ A D+LD  +++ E ++  W+PVGDLLIDSLQDH+EK  A R EIA
Sbjct  2038  RQIHVDLEKLRDLQGAMDDLDADMKEVEAVRNGWKPVGDLLIDSLQDHIEKTLAFREEIA  2217

Query  527   PLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFG  586
             P+   V  +NDL+ QL+ L +  S      L+DLN RWKLLQV+V+DR++QL EAHRDFG
Sbjct  2218  PINLKVKTMNDLSSQLSPLDLHPSLKMSRQLDDLNMRWKLLQVSVDDRLKQLQEAHRDFG  2397

Query  587   PASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAY  646
             P+SQHFLSTSVQ PW+R+IS NKVPYYINH+TQTTCWDHPKMTEL+QSLADLNNVRFSAY
Sbjct  2398  PSSQHFLSTSVQLPWQRSISHNKVPYYINHQTQTTCWDHPKMTELFQSLADLNNVRFSAY  2577

Query  647   RTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHN  706
             RTA+K+RRLQKALCLDLL L+   +   QH L QNDQ + +  +INCLTT YD LEQ H 
Sbjct  2578  RTAIKIRRLQKALCLDLLELNTTNEVFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQLHK  2757

Query  707   NLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASST  766
             +LVNVPLCVDMCLNWLLNVYDTGRTG+IRV S K G++SL K  LE+KYR LFK+VA  T
Sbjct  2758  DLVNVPLCVDMCLNWLLNVYDTGRTGKIRVQSLKIGLMSLSKGLLEEKYRCLFKEVAGPT  2937

Query  767   GFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMR  826
               CDQR+LGLLLHD+IQIPRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWM 
Sbjct  2938  EMCDQRQLGLLLHDAIQIPRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKEFIDWMH  3117

Query  827   LEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRV  886
             LEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR 
Sbjct  3118  LEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRT  3297

Query  887   AKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNM  946
             AKGHK+HYPMVEYC PTTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+
Sbjct  3298  AKGHKLHYPMVEYCIPTTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNL  3477

Query  947   ETPA  950
             ET A
Sbjct  3478  ETQA  3489


>emb|X99757.1| D.melanogaster mRNA for dystrophin
Length=2962

 Score =  788 bits (2034),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 441/946 (46%), Positives = 600/946 (63%), Gaps = 82/946 (8%)
 Frame = +1

Query  231   LQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTD  290
             LQ F   +++FLA+L+E ET     +    +  L+            ++DLQ EIE H  
Sbjct  19    LQSFDRAMDQFLAFLSETETLCENAESDIERNPLM------------FKDLQSEIETHRV  162

Query  291   VYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRL  350
             VY  LD   +K+L SL   +DAV+LQRRLD MN +W++LR KS+ +R+ LE++S+ W  L
Sbjct  163   VYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNDLRSKSIAMRNRLESNSEHWNAL  342

Query  351   HLSLQELLVWLQLKDDELSRQA--PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
              LSL+EL  W+  KD ELS     P+  D  ++QKQ D H+AF+R+L+ K P++ S L +
Sbjct  343   LLSLRELTEWVIRKDSELSTLGLGPVLTDAASLQKQLDDHKAFRRQLEDKRPIVESNLTS  522

Query  409   VRIFLTEQPL-----EGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSA  463
              R ++  +       +       + R +  EE+++ + R +R++  +++ +W  L   S 
Sbjct  523   GRQYIANEAAVSDTSDTEANHDSDSRYMSAEEQSRELRRSIRREVGKLSEQWNNLLDRSD  702

Query  464   DWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQP---VGDLLIDSLQDHLEKVKA  520
             +W+ ++DE L ++++ QE  ++L  ++  AE  K SW P   VG+ +             
Sbjct  703   NWKHRLDEYLTKMRQFQEILEDLSSRVALAEQTKTSWLPPSSVGEAI-----SRCNSCSR  867

Query  521   LRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR---VRQ  577
             LR ++      +   N+     T   + +    LS LEDLNTR KLLQ+A+++R   +RQ
Sbjct  868   LRDKMTTASALLDDCNEQQSFFTANEVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLRQ  1047

Query  578   LHEAHRD--------------FGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCW  623
             +  + R                GP     L  SV+ PWERA +   VPYYI+HE QTT W
Sbjct  1048  VEPSRRTRGGDDGRTTSNSGTIGPLPN--LGQSVKPPWERATTAANVPYYIDHERQTTHW  1221

Query  624   DHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH-NLKQND  682
             DHP+M EL + LADLN +RFSAYRTAMKLR +QK L LD +S+S AC++ D+     QND
Sbjct  1222  DHPEMIELMKGLADLNEIRFSAYRTAMKLRSVQKRLALDRISMSTACESFDRTWPACQND  1401

Query  683   QPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTG  742
             + +DI  +   L ++Y  +++     +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G
Sbjct  1402  ELIDIPDMTTVLHSLYVTIDE-----IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVG  1566

Query  743   IISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPS  802
             ++ LCK HLE+KYRYLF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPS
Sbjct  1567  LVLLCKGHLEEKYRYLFRLVADTDRRADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPS  1746

Query  803   VRSCFQFA---------NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKC  853
             VRSC + A         N    IE   FL W++ EPQS+VWLPVLHR+AAAE AKHQAKC
Sbjct  1747  VRSCLEQAGISQEAIDGNQDISIELQHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKC  1926

Query  854   NICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFA  913
             NICKE PI+ FRYR LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF 
Sbjct  1927  NICKEYPIVLFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFT  2106

Query  914   KVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYAS  969
             + LKNKF++++YF KHPR+GYLPVQ+VLEGD +E+PA SPQ +     +D HSR+E YAS
Sbjct  2107  RALKNKFKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQNDMHSRLEMYAS  2286

Query  970   RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEE  1029
             RLA++E     Y     +     DDEH LI  YCQ+L   S  S P+SP Q++ ++++E+
Sbjct  2287  RLAQVE-----YGGTGSNSTPDSDDEHQLIAQYCQALPGTSNGSAPKSPVQVMAAMDAEQ  2451

Query  1030  RGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP--------SPPEMMPTSPQSPR  1081
             R ELE I+ DLEEEN NLQAEY    QQ   K  S +P        S   M   S Q  +
Sbjct  2452  REELEAIIRDLEEENANLQAEY----QQLCSKEQSGMPEDSNGMQHSSSSMTGLSGQGEQ  2619

Query  1082  DAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
               +++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  2620  GQDMMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  2757


>gb|DQ440979.1| Lampetra planeri dystrophin mRNA, partial cds
Length=1401

 Score =  770 bits (1988),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 359/471 (76%), Positives = 413/471 (87%), Gaps = 18/471 (3%)
 Frame = +1

Query  643   FSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLE  702
             FSAYRTAMKLRRLQKALCLDL+SL A  +  +Q  LKQND+ MD+ + + CLTTIY  LE
Sbjct  1     FSAYRTAMKLRRLQKALCLDLVSLDALTNVFEQSGLKQNDRLMDVSEAVGCLTTIYQGLE  180

Query  703   QEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQV  762
             ++H++LVN+PLCVDMCLNWLLNVYDTGR G+IR LSFKTG++SL  AHLEDKYR+LFKQV
Sbjct  181   RKHSDLVNLPLCVDMCLNWLLNVYDTGRGGKIRELSFKTGLVSLSNAHLEDKYRFLFKQV  360

Query  763   ASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFL  822
             AS  G CDQRRLGL+LHD++QIPRQLGEVASFGGSNIEPSVRSCFQFAN +PEIEA +FL
Sbjct  361   ASVAGLCDQRRLGLMLHDAVQIPRQLGEVASFGGSNIEPSVRSCFQFANGRPEIEATMFL  540

Query  823   DWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFF  882
             +WMR+EPQSMVWLPVLHRVAA+ETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFF
Sbjct  541   EWMRMEPQSMVWLPVLHRVAASETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFF  720

Query  883   SGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLE  942
             SGR AKGHK+ YPMVEYCTPTTSGED+RDFAKVLKNKF++K+YF KHPR+GYLPVQTVLE
Sbjct  721   SGRTAKGHKLSYPMVEYCTPTTSGEDIRDFAKVLKNKFKSKKYFEKHPRIGYLPVQTVLE  900

Query  943   GDNMETPAS-------------SPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPN  989
             GD++ETP +             SPQLS++DTH+RIEH ASRLAEME  NGS+LNDS SPN
Sbjct  901   GDDLETPVTVIRLVPVALAPSPSPQLSNEDTHARIEHLASRLAEMEFKNGSFLNDS-SPN  1077

Query  990   ESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQA  1049
             ES++DEHLLIQHYCQSL+ +SP SQP+SPAQILISL+S+ER ELERIL DLE+ENR+LQ+
Sbjct  1078  ESLEDEHLLIQHYCQSLSGESPGSQPQSPAQILISLDSQERSELERILRDLEDENRSLQS  1257

Query  1050  EYDRLKQQHEHKGLSP-LPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRL  1099
             EYDRL+Q+ E  GL   LP+PP M    P+SPRD+ELIAEAKLLRQHKGRL
Sbjct  1258  EYDRLRQKQELGGLGALLPAPPTM---PPESPRDSELIAEAKLLRQHKGRL  1401


>dbj|AK035043.1| Mus musculus 12 days embryo embryonic body between diaphragm 
region and neck cDNA, RIKEN full-length enriched library, clone:9430078L05 
product:utrophin, full insert sequence
Length=4087

 Score =  739 bits (1907),  Expect(2) = 0.0, Method: Compositional matrix adjust.
 Identities = 359/484 (74%), Positives = 405/484 (83%), Gaps = 14/484 (2%)
 Frame = +1

Query  651   KLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVN  710
             K+RRLQKALCLDLL L+   +   QH L QNDQ + +  +INCLTT YD LEQ H +LVN
Sbjct  1     KIRRLQKALCLDLLELNTTNEVFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQLHKDLVN  180

Query  711   VPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCD  770
             VPLCVDMCLNWLLNVYDTGRTG+IRV S K G++SL K  LE+KYR LFK+VA  T  CD
Sbjct  181   VPLCVDMCLNWLLNVYDTGRTGKIRVQSLKIGLMSLSKGLLEEKYRCLFKEVAGPTEMCD  360

Query  771   QRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQ  830
             QR+LGLLLHD+IQIPRQLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWM LEPQ
Sbjct  361   QRQLGLLLHDAIQIPRQLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKEFIDWMHLEPQ  540

Query  831   SMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGH  890
             SMVWLPVLHRVAAAETAKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGH
Sbjct  541   SMVWLPVLHRVAAAETAKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGH  720

Query  891   KMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPA  950
             K+HYPMVEYC PTTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ETP 
Sbjct  721   KLHYPMVEYCIPTTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPI  900

Query  951   S-------------SPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHL  997
             +             SPQL HDDTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH 
Sbjct  901   TLISMWPEHYDPSQSPQLFHDDTHSRIEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHA  1080

Query  998   LIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQ  1057
             LIQ YCQ+L  +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE RNLQ EY++LK+Q
Sbjct  1081  LIQQYCQTLGGESPVSQPQSPAQILKSVEREERGELERIIADLEEEQRNLQVEYEQLKEQ  1260

Query  1058  HEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQL  1117
             H  +GL P+ SPP+ + +   +  D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQL
Sbjct  1261  HLRRGL-PVGSPPDSIVSPHHTSEDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQL  1437

Query  1118  HRLR  1121
             HRLR
Sbjct  1438  HRLR  1449


 Score = 45.1 bits (105),  Expect(2) = 0.0, Method: Compositional matrix adjust.
 Identities = 31/72 (43%), Positives = 43/72 (59%), Gaps = 5/72 (6%)
 Frame = +2

Query  1125  EQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLE  1184
              +P +++++NG    SP  S Q S  S   L    G Q   +   EDLL+PP DTST L 
Sbjct  1460  SRPDSDSRINGV---SPWASPQHSALSY-SLDTDPGPQFHQA-ASEDLLAPPHDTSTDLT  1624

Query  1185  EVMEQLNNSFPS  1196
             +VMEQ+N++FPS
Sbjct  1625  DVMEQINSTFPS  1660


>ref|XM_962494.2| PREDICTED: Tribolium castaneum similar to dystrophin major muscle 
(LOC655939), mRNA
Length=2915

 Score =  758 bits (1958),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 431/1016 (42%), Positives = 611/1016 (60%), Gaps = 93/1016 (9%)
 Frame = +3

Query  115   LNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQ  174
             L  M K    +   + E E  L +  A+L S     +T D ++ ++ E K L  +L Q++
Sbjct  36    LATMQKKEESFEHKRLELEAWLQRMEARLASMAAVGHTADVLEVQLREQKGLHAELHQFK  215

Query  175   TNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQF  234
               ++  N L  +L+  +  +DT +     E IN  +  +   V  R   L      LQ  
Sbjct  216   AQIEAFNQLTQRLITAHQHEDTSRYKKTAEYINQHYIRLDACVINRGKLLHSALSSLQNL  395

Query  235   PLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHN  294
                L+KFLAWL+EAE+    L+      R             Q ++LQ ++E     +  
Sbjct  396   DRSLDKFLAWLSEAESVVETLEGDAESRRA----------AHQLKELQADVERQAPAHAA  545

Query  295   LDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSL  354
             L  ++  +L ++   +DA++LQ + D M  +W  L+ ++ ++R+ LE ++D W  L LSL
Sbjct  546   LRSSNLALLGTM-APEDALMLQLKGDEMERRWQALKTRTSDLRNRLEHNADYWNALLLSL  722

Query  355   QELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLT  414
             +EL  W+  KD EL   A          +Q+D HRAF+++L+ K P++ ++L + R F+ 
Sbjct  723   RELTEWVIRKDTELGLAA----------RQDD-HRAFRQQLEDKRPLVEASLRSARQFVA  869

Query  415   EQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLE  474
               P                   +  + R LR++  +++ +W  L   S     + ++   
Sbjct  870   GDP-------------------SGELARNLRRELVKLSDKWNALIDKSDQLAARFEQNTI  992

Query  475   RLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSH  534
             +L++L    +E    + + E    SW   G       ++ L  ++ L  ++  L+ ++  
Sbjct  993   KLKQLTLNLEEASAAVSRLERATLSWS--GPRSAAEARELLASLRNLETQLPQLQRSLEE  1166

Query  535   VNDLARQLTTLGIQLSPYNLST-LEDLNTRWKLLQVAVEDRVRQLHEAHR-DFGPASQHF  592
                   Q  +LG  L P NL+T LED + R + LQ A+ +R  QL    + +  P     
Sbjct  1167  ARI---QAASLGNAL-PNNLATQLEDCSARCRALQAAIRERREQLTSTTQGEISPGP---  1325

Query  593   LSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKL  652
               +SVQ PWER+ +PNKVPYYINH T+TT WDHP+M EL  SL  LN VRFSAYRTA+KL
Sbjct  1326  --SSVQPPWERSTTPNKVPYYINHSTETTHWDHPQMLELATSLLQLNEVRFSAYRTALKL  1499

Query  653   RRLQKALCLDLLSLSAACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNV  711
             R +QK LCLDL+S++ A +A D H L+ QND+ +D+  +I  L  IY         LV+V
Sbjct  1500  RAIQKKLCLDLVSINGASEAFDLHGLRGQNDKLLDVADMILVLRAIYATAASLQPALVDV  1679

Query  712   PLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQ  771
             PLCVD+ LNWLLNVYD+ RTG++RVLSFK G+  L K HLEDKYRYLF+ +A      DQ
Sbjct  1680  PLCVDLALNWLLNVYDSQRTGQLRVLSFKVGLTLLSKGHLEDKYRYLFRLIADPQQKADQ  1859

Query  772   RRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQS  831
             R+LGLLLHD +Q+PRQLGEVA+FGGSNIEPSVRSC      + ++E   FL W++ EPQS
Sbjct  1860  RKLGLLLHDVLQVPRQLGEVAAFGGSNIEPSVRSCL---GEREDLEVTHFLAWLKQEPQS  2030

Query  832   MVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHK  891
             +VWLPVLHR+AAAETAKHQAKCN CK+ PI+G RYR LK FN+D+CQSCFF+GR+ KGHK
Sbjct  2031  LVWLPVLHRLAAAETAKHQAKCNSCKQYPIVGLRYRCLKCFNFDMCQSCFFAGRLTKGHK  2210

Query  892   MHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPAS  951
             + +PM EYC  TTS ED+RDF K LKNKF++KRYF KHPR+GYLPV++VLEGD +E+P +
Sbjct  2211  LSHPMHEYCAATTSVEDMRDFTKALKNKFKSKRYFTKHPRVGYLPVRSVLEGDELESPVA  2390

Query  952   SPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSP  1011
             SPQ  H+D HSR+E YASRLAE+E         + SP    +DEH LI  YCQ++     
Sbjct  2391  SPQ--HNDMHSRLEIYASRLAEVELR-------AASP----EDEHRLIADYCQTIE----  2519

Query  1012  LSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPE  1071
                P SP Q+++ ++ E+R EL+ ++ +LE EN  L+ EY++L+     +G +P P  P+
Sbjct  2520  --GPGSPGQLMLVIDEEQRAELQEMITELEAENAALRQEYEQLQ-----RGATPHPPQPQ  2678

Query  1072  MMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
                         +++AEA+LLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  2679  H-----------DVLAEARLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  2813


>emb|X99701.1| X.laevis mRNA for utrophin
Length=1482

 Score =  745 bits (1923),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 356/494 (72%), Positives = 411/494 (83%), Gaps = 13/494 (2%)
 Frame = +1

Query  626   PKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPM  685
             PKMTEL+QSL DLNNVRFSAYRTAMK+RRLQKALCLDLL L+       QH L QN+Q +
Sbjct  1     PKMTELFQSLGDLNNVRFSAYRTAMKIRRLQKALCLDLLDLTTTHSVFKQHELNQNNQLL  180

Query  686   DILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIIS  745
              + ++IN LTTIYD LEQ+H  LVNVPLCV+MCLNWLLNVYDTGRTG++RVLS K G++ 
Sbjct  181   SVPEVINVLTTIYDGLEQKHKELVNVPLCVEMCLNWLLNVYDTGRTGKLRVLSLKIGLMC  360

Query  746   LCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRS  805
             L K  LE+KYR+LFK+V  +   CDQR+L L+LHD+IQIPRQLGEVA+FGGSNIEPSVRS
Sbjct  361   LSKGLLEEKYRHLFKEVCGAGDTCDQRQLSLMLHDAIQIPRQLGEVAAFGGSNIEPSVRS  540

Query  806   CFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFR  865
             CFQ A NKPEI+   F++WMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI+GFR
Sbjct  541   CFQHAQNKPEIDVNHFIEWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIVGFR  720

Query  866   YRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRY  925
             YRSLKHFNYD+CQSCFFSGR AKGHK+H+PMVEYCTPTTSGEDVRDFAKVLKNKFR+K+Y
Sbjct  721   YRSLKHFNYDVCQSCFFSGRTAKGHKLHHPMVEYCTPTTSGEDVRDFAKVLKNKFRSKKY  900

Query  926   FAKHPRMGYLPVQTVLEGDNMETPAS-------------SPQLSHDDTHSRIEHYASRLA  972
             F KHPR+GYLPVQTVLEGDNMETP +             SP+L HDDTHSRIE YASRLA
Sbjct  901   FDKHPRLGYLPVQTVLEGDNMETPITLISMWPDQFDGMHSPELLHDDTHSRIEQYASRLA  1080

Query  973   EMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGE  1032
             +ME +NGS   D+ S   S++DEH LIQ +C +L  DSP+ QP+SPAQIL S+E EERGE
Sbjct  1081  QMERTNGSLFTDNSSATGSMEDEHALIQQFCHTLGGDSPIGQPQSPAQILKSVEKEERGE  1260

Query  1033  LERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLL  1092
             L+RI+ADLEEE RNL+ EY++LK QH  +GL+P  SPP+ + +   +  DAELIAEAKLL
Sbjct  1261  LDRIIADLEEEQRNLKVEYEQLKAQHLRRGLTPPSSPPDSVISLQHASEDAELIAEAKLL  1440

Query  1093  RQHKGRLEARMQIL  1106
             RQHKGRLEARMQIL
Sbjct  1441  RQHKGRLEARMQIL  1482


>ref|NM_001005246.1| Rattus norvegicus dystrophin, muscular dystrophy (Dmd), transcript 
variant Dp71c, mRNA
Length=2038

 Score =  731 bits (1888),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 356/446 (79%), Positives = 375/446 (84%), Gaps = 39/446 (8%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  109   GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  288

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  289   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  468

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  469   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  648

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  649   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  828

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  829   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  1008

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET   + Q  +D    + EH        
Sbjct  1009  VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET---NLQAEYDRLKQQHEHKG------  1161

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSP--AQIL--ISLESEER  1030
                    L+   SP E +                    + P+SP  A+++    L  + +
Sbjct  1162  -------LSPLPSPPEMMP-------------------TSPQSPRDAELIAEAKLLRQHK  1263

Query  1031  GELERILADLEEENRNLQAEYDRLKQ  1056
             G LE  +  LE+ N+ L+++  RL+Q
Sbjct  1264  GRLEARMQILEDHNKQLESQLHRLRQ  1341


 Score =  311 bits (798),  Expect(2) = 3e-95, Method: Compositional matrix adjust.
 Identities = 154/157 (98%), Positives = 155/157 (98%), Gaps = 0/157 (0%)
 Frame = +1

Query  1046  NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQI  1105
             NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQI
Sbjct  1111  NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQI  1290

Query  1106  LEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSD  1165
             LEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTS+
Sbjct  1291  LEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSE  1470

Query  1166  SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG N 
Sbjct  1471  SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGRNA  1581


 Score = 67.8 bits (164),  Expect(2) = 3e-95, Method: Composition-based stats.
 Identities = 32/35 (91%), Positives = 33/35 (94%), Gaps = 0/35 (0%)
 Frame = +3

Query  1196  SSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             + RGHNVGSLFHMADDLGRAMESLVSVM DEEGAE
Sbjct  1593  NERGHNVGSLFHMADDLGRAMESLVSVMIDEEGAE  1697


>dbj|AK299936.1| Homo sapiens cDNA FLJ60143 complete cds, highly similar to Homo 
sapiens dystrophin, transcript variant Dp140bc, mRNA
Length=1858

 Score =  731 bits (1887),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 356/446 (79%), Positives = 375/446 (84%), Gaps = 39/446 (8%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  139   GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  318

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  319   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  498

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  499   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  678

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  679   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  858

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  859   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  1038

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET   + Q  +D    + EH        
Sbjct  1039  VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET---NLQAEYDRLKQQHEHKG------  1191

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSP--AQIL--ISLESEER  1030
                    L+   SP E +                    + P+SP  A+++    L  + +
Sbjct  1192  -------LSPLPSPPEMMP-------------------TSPQSPRDAELIAEAKLLRQHK  1293

Query  1031  GELERILADLEEENRNLQAEYDRLKQ  1056
             G LE  +  LE+ N+ L+++  RL+Q
Sbjct  1294  GRLEARMQILEDHNKQLESQLHRLRQ  1371


 Score =  375 bits (962),  Expect = 1e-100, Method: Compositional matrix adjust.
 Identities = 188/193 (97%), Positives = 189/193 (97%), Gaps = 2/193 (1%)
 Frame = +1

Query  1040  LEEEN--RNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKG  1097
             LE +N   NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKG
Sbjct  1117  LEGDNMETNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKG  1296

Query  1098  RLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLR  1157
             RLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLR
Sbjct  1297  RLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLR  1476

Query  1158  VVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGRAME  1217
             VVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGRAME
Sbjct  1477  VVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGRAME  1656

Query  1218  SLVSVMTDEEGAE  1230
             SLVSVMTDEEGAE
Sbjct  1657  SLVSVMTDEEGAE  1695


>gb|AY326949.1| Rattus norvegicus dystrophin Dp71c (Dmd) mRNA, complete cds; 
alternatively spliced
Length=1567

 Score =  729 bits (1883),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 355/446 (79%), Positives = 374/446 (83%), Gaps = 39/446 (8%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  46    GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  225

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  226   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  405

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  406   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  585

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANN PEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  586   GGSNIEPSVRSCFQFANNNPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  765

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  766   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  945

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEM  974
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET   + Q  +D    + EH        
Sbjct  946   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET---NLQAEYDRLKQQHEHKG------  1098

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSP--AQIL--ISLESEER  1030
                    L+   SP E +                    + P+SP  A+++    L  + +
Sbjct  1099  -------LSPLPSPPEMMP-------------------TSPQSPRDAELIAEAKLLRQHK  1200

Query  1031  GELERILADLEEENRNLQAEYDRLKQ  1056
             G LE  +  LE+ N+ L+++  RL+Q
Sbjct  1201  GRLEARMQILEDHNKQLESQLHRLRQ  1278


 Score =  312 bits (799),  Expect(2) = 2e-83, Method: Compositional matrix adjust.
 Identities = 154/157 (98%), Positives = 155/157 (98%), Gaps = 0/157 (0%)
 Frame = +1

Query  1046  NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQI  1105
             NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQI
Sbjct  1048  NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQI  1227

Query  1106  LEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSD  1165
             LEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTS+
Sbjct  1228  LEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSE  1407

Query  1166  SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
             SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG N 
Sbjct  1408  SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGRNA  1518


 Score = 27.7 bits (60),  Expect(2) = 2e-83, Method: Composition-based stats.
 Identities = 10/12 (83%), Positives = 11/12 (91%), Gaps = 0/12 (0%)
 Frame = +3

Query  1196  SSRGHNVGSLFH  1207
             + RGHNVGSLFH
Sbjct  1530  NERGHNVGSLFH  1565


>dbj|AK087829.1| Mus musculus 2 days pregnant adult female ovary cDNA, RIKEN full-length 
enriched library, clone:E330026B12 product:dystrophin, 
muscular dystrophy, full insert sequence
Length=1298

 Score =  724 bits (1869),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 333/334 (99%), Positives = 333/334 (99%), Gaps = 0/334 (0%)
 Frame = +3

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  138   GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  317

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  318   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  497

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  498   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  677

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  678   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  857

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  858   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  1037

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET
Sbjct  1038  VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  1139


>dbj|AK075809.1| Mus musculus 10 day old male pancreas cDNA, RIKEN full-length 
enriched library, clone:1810074E05 product:dystrophin, muscular 
dystrophy, full insert sequence
Length=1384

 Score =  724 bits (1869),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 333/334 (99%), Positives = 333/334 (99%), Gaps = 0/334 (0%)
 Frame = +3

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  138   GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  317

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  318   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  497

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  498   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  677

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  678   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  857

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  858   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  1037

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET
Sbjct  1038  VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  1139


>ref|NM_004019.2| Homo sapiens dystrophin (DMD), transcript variant Dp40, mRNA
Length=1571

 Score =  723 bits (1867),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 333/334 (99%), Positives = 333/334 (99%), Gaps = 0/334 (0%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  97    GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  276

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  277   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  456

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  457   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  636

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  637   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  816

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  817   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  996

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET
Sbjct  997   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  1098


>emb|X69767.1| R.norvegicus mRNA for APO-dystrophin-3
Length=1240

 Score =  719 bits (1856),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 331/334 (99%), Positives = 332/334 (99%), Gaps = 0/334 (0%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  124   GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  303

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQII CLTTIYDRLEQEHNNLVNVPLCVD+CLNWLLNVYDTGRTGRI
Sbjct  304   QHNLKQNDQPMDILQIIYCLTTIYDRLEQEHNNLVNVPLCVDVCLNWLLNVYDTGRTGRI  483

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  484   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  663

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  664   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  843

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK
Sbjct  844   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  1023

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
             VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET
Sbjct  1024  VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  1125


>ref|XM_694837.3| PREDICTED: Danio rerio similar to putative utrophin (LOC571265), 
mRNA
Length=3112

 Score =  711 bits (1836),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 397/746 (53%), Positives = 486/746 (65%), Gaps = 111/746 (14%)
 Frame = +1

Query  430   ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLK  489
             EL PEE+AQ V + +RKQ  EV   W++L  H+  WQ +++  L++LQ+LQ + D+LDL+
Sbjct  43    ELTPEEKAQRVAKAIRKQTAEVCERWDRLTGHAGTWQEQVERALDKLQDLQSSMDQLDLR  222

Query  490   LRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQL  549
             L QAE +K  WQPVGDLLIDSLQDH++K  A R E++PLK++V  VNDLA QLT L +QL
Sbjct  223   LAQAEELKAGWQPVGDLLIDSLQDHIDKTTAFREEVSPLKKDVGAVNDLAAQLTPLDVQL  402

Query  550   SPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNK  609
             S      L++LN RWKLLQ+      R+                      P  R   P  
Sbjct  403   SSTTNRQLDNLNMRWKLLQLQCSCPGRE----------------------PCPRIKCP--  510

Query  610   VPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAA  669
                       TT  D          L DL   +    +  + +   Q ++   +  L++ 
Sbjct  511   ----------TTSMD----------LLDLGVAQSMFQQHKLTVNSQQLSVPEIINCLTSV  630

Query  670   CDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTG  729
              D L+Q +    + P+ +   +N L  +YD                            TG
Sbjct  631   YDGLEQEHKDLVNVPLCVDMSLNWLLNVYD----------------------------TG  726

Query  730   RTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLG  789
             R+G+IRVLS K G++SLCK HLE+KY+ LF QVAS+ G CDQR+LGLLLHD+IQIPRQLG
Sbjct  727   RSGKIRVLSMKIGLLSLCKGHLEEKYKCLFNQVASAGGTCDQRQLGLLLHDAIQIPRQLG  906

Query  790   EVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKH  849
             EVA+FGGSNIEPSVRSCFQ   NK E+E   F+DWMRLEPQSMVWLPVLHRVAAAETAKH
Sbjct  907   EVAAFGGSNIEPSVRSCFQHVTNKVELEPRQFIDWMRLEPQSMVWLPVLHRVAAAETAKH  1086

Query  850   QAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDV  909
             QAKCNICKE PI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK++YPMVEYCTPTTSGED+
Sbjct  1087  QAKCNICKEFPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLNYPMVEYCTPTTSGEDM  1266

Query  910   RDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYAS  969
             RDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDNMET   SPQL HDDTHSRI  YA+
Sbjct  1267  RDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNMETLCPSPQLPHDDTHSRIGEYAN  1446

Query  970   RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSL-NQDSPLSQP-------------  1015
             RLA+ME SNGS   DS S   S+D+EH LI  YCQ+L  + S  SQP             
Sbjct  1447  RLAQMERSNGSLPTDSSSATGSMDEEHALILQYCQTLGGEGSSFSQPQSPAHINRTPAHN  1626

Query  1016  --------RSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLP  1067
                     +SPAQIL ++E EERGELERI+A LE++ R LQ EY+ L+ Q+         
Sbjct  1627  THSPSYLLQSPAQILQAVEREERGELERIIARLEDDQRVLQREYEELRFQYGQP------  1788

Query  1068  SPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
                     +  +P +A+L+AEAKLLRQHKGRLEARMQILEDHNKQLESQL+RLRQLL QP
Sbjct  1789  ----GAAAASGAPDEADLLAEAKLLRQHKGRLEARMQILEDHNKQLESQLYRLRQLLHQP  1956

Query  1128  QAEAKVNGTTVSSPSTSLQRSDSSQP  1153
             +    +NGT   S S+SL +  + QP
Sbjct  1957  E----LNGT---SSSSSLHQDAAGQP  2013


>gb|AF339032.1|AF339032 Danio rerio dystrophin variant Dp71 (dmd) mRNA, partial cds, 
alternatively spliced
Length=1195

 Score =  689 bits (1778),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 313/356 (87%), Positives = 336/356 (94%), Gaps = 13/356 (3%)
 Frame = +3

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
             NH+TQTTCWDHPKM ELYQSLADLNNVRFSAYRTAMKLRR+QKALCLDLLS+ AAC+A +
Sbjct  126   NHQTQTTCWDHPKMAELYQSLADLNNVRFSAYRTAMKLRRMQKALCLDLLSMPAACEAFE  305

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQN+Q MDI+Q+INCLT+IYDRLEQ+H++LVNVPLCVDMCLNWLLNVYDTGR G+I
Sbjct  306   QHNLKQNEQFMDIVQVINCLTSIYDRLEQQHSSLVNVPLCVDMCLNWLLNVYDTGRAGKI  485

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             R LSFKTGIISLCKAHLEDKYR+LF++VAS+TGFCDQRRLGLLLHD+IQIPRQLGEVASF
Sbjct  486   RTLSFKTGIISLCKAHLEDKYRFLFREVASATGFCDQRRLGLLLHDAIQIPRQLGEVASF  665

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPE+EA++FLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  666   GGSNIEPSVRSCFQFANNKPELEASVFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  845

Query  855   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAK  914
             ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKM YPMVEYCTPTTSGEDVRDFAK
Sbjct  846   ICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMQYPMVEYCTPTTSGEDVRDFAK  1025

Query  915   VLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-------------PASSPQLSH  957
             VLKNKFRTKRYF+KHPRMGYLPVQT+LEGDNMET             PASSPQLSH
Sbjct  1026  VLKNKFRTKRYFSKHPRMGYLPVQTILEGDNMETPVTLINFWPVDHPPASSPQLSH  1193


>emb|X15488.1| Human mRNA fragment for dystrophin-related protein
Length=1470

 Score =  689 bits (1777),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 345/483 (71%), Positives = 395/483 (81%), Gaps = 18/483 (3%)
 Frame = +1

Query  727   DTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPR  786
             DTGRTG+IRV S K G++SL K  LE+KYRYLFK+VA  T  CDQR+LGLLLHD+IQIPR
Sbjct  1     DTGRTGKIRVQSLKIGLMSLSKGLLEEKYRYLFKEVAGPTEMCDQRQLGLLLHDAIQIPR  180

Query  787   QLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAET  846
             QLGEVA+FGGSNIEPSVRSCFQ  NNKPEI    F+DWM LEPQSMVWLPVLHRVAAAET
Sbjct  181   QLGEVAAFGGSNIEPSVRSCFQQNNNKPEISVKEFIDWMHLEPQSMVWLPVLHRVAAAET  360

Query  847   AKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSG  906
             AKHQAKCNICKECPI+GFRYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC PTTSG
Sbjct  361   AKHQAKCNICKECPIVGFRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYCIPTTSG  540

Query  907   EDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-------------PASSP  953
             EDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ET             P+ SP
Sbjct  541   EDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLETPITLISMWPEHYDPSQSP  720

Query  954   QLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLS  1013
             QL HDDTHSRIE YA+RLA+ME +NGS+L DS S   S++DEH LIQ YCQ+L  +SP+S
Sbjct  721   QLFHDDTHSRIEQYATRLAQMERTNGSFLTDSSSTTGSVEDEHALIQQYCQTLGGESPVS  900

Query  1014  QPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMM  1073
             QP+SPAQIL S+E EERGELERI+ADLEEE RNLQ EY++LK QH  +GL P+ SPPE +
Sbjct  901   QPQSPAQILKSVEREERGELERIIADLEEEQRNLQVEYEQLKDQHLRRGL-PVGSPPESI  1077

Query  1074  PTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKV  1133
              +   +  D+ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP++++++
Sbjct  1078  ISPHHTSEDSELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPESDSRI  1257

Query  1134  NGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNS  1193
             NG    SP  S Q S  S  +     G Q   + G EDLL+PP DTST L EVMEQ++++
Sbjct  1258  NGV---SPWASPQHSALSYSLDPDASGPQFHQAAG-EDLLAPPHDTSTDLTEVMEQIHST  1425

Query  1194  FPS  1196
             FPS
Sbjct  1426  FPS  1434


>dbj|AB209305.1| Homo sapiens mRNA for dystrophin related protein 2 variant protein
Length=5714

 Score =  683 bits (1762),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 344/581 (59%), Positives = 445/581 (76%), Gaps = 16/581 (2%)
 Frame = +2

Query  625   HPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQP  684
             HPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ ++  
Sbjct  110   HPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQASEHV  289

Query  685   MDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGII  744
             MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKTGI 
Sbjct  290   MDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKTGIA  469

Query  745   SLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVR  804
              LC   +++K +YLF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EPSVR
Sbjct  470   CLCGTEVKEKLQYLFSQVANSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEPSVR  649

Query  805   SCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGF  864
             SCF+F+  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI GF
Sbjct  650   SCFRFSTGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPIKGF  829

Query  865   RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKR  924
             RYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR+K 
Sbjct  830   RYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFRSKH  1009

Query  925   YFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLND  984
             YF+KHP+ GYLPVQ+VLE D  ETPASSP   H DTHSRIEH+ASRLAEME+ N S+ ND
Sbjct  1010  YFSKHPQRGYLPVQSVLEADYSETPASSPMWPHADTHSRIEHFASRLAEMESQNCSFFND  1189

Query  985   SISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILADLE  1041
             S+SP++SID++  L++H        SP++  R PA   Q   S+ +E +GEL++ILA LE
Sbjct  1190  SLSPDDSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSVATESKGELQKILAHLE  1345

Query  1042  EENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEA  1101
             +ENR LQ E  RLK QHE    +  PS  +    +    R+ EL+AEA++LRQHK RLE 
Sbjct  1346  DENRILQGELRRLKWQHEEAAEA--PSLADGSTEAATDHRNEELLAEARILRQHKSRLET  1519

Query  1102  RMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGS  1161
             RMQILEDHNKQLESQL RLR+LL QP  E+  +G+  SS ++S Q+S+ S P   R  G 
Sbjct  1520  RMQILEDHNKQLESQLQRLRELLLQPPTESDGSGSAGSSLASSPQQSEGSHP---REKGQ  1690

Query  1162  QTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
              T D+   +D+ S  QD S  LE++ME+L ++FPS R  +V
Sbjct  1691  TTPDTEAADDVGSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  1813


>emb|X99736.1| B.lanceolatum mRNA for dystrophin-like protein
Length=1338

 Score =  669 bits (1727),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 334/476 (70%), Positives = 389/476 (81%), Gaps = 33/476 (6%)
 Frame = +1

Query  626   PKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPM  685
             PKMTEL+QSLADLN+VRFSAYRTAMKLRRLQKALCLDLLS++ A DA             
Sbjct  4     PKMTELFQSLADLNDVRFSAYRTAMKLRRLQKALCLDLLSMNNAIDA-------------  144

Query  686   DILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIIS  745
                +IINCLTTIYD LEQ+H NLVNVPLCVDMCLNWLLNVYDTGR+G+IRVLSFK GIIS
Sbjct  145   ---EIINCLTTIYDNLEQDHGNLVNVPLCVDMCLNWLLNVYDTGRSGKIRVLSFKVGIIS  315

Query  746   LCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNI-EPSVR  804
             LC+AHLEDKYR+ F+ +A +TGF DQR+LGLLLHD IQ+PRQLGE+ASFGGSNI EPSVR
Sbjct  316   LCRAHLEDKYRFNFRLIAEATGFADQRKLGLLLHDLIQVPRQLGEIASFGGSNIIEPSVR  495

Query  805   SCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGF  864
             SCF+ A  KPEIEAA FLDWM+ EPQSMVWLPVLHR+AAAETAKHQAKCNICKE PI+GF
Sbjct  496   SCFERAGGKPEIEAAHFLDWMKQEPQSMVWLPVLHRLAAAETAKHQAKCNICKEYPIVGF  675

Query  865   RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKR  924
             RYR L+ FN+D+CQSCF SGR AKGHK+ +PM EYCT TTSGEDVRDFAKV++NKFR+K+
Sbjct  676   RYRCLRCFNFDMCQSCFLSGRKAKGHKLSHPMQEYCTATTSGEDVRDFAKVVRNKFRSKK  855

Query  925   YFAKHPRMGYLPVQTVLEGDNMETPASSPQLS-HDDTHSRIEHYASRLAEMENSNGSYLN  983
                KHPR+GYLPVQTVLEGDN+ETP+SSPQ +   D HSR+E YASRLAE+E S      
Sbjct  856   SLKKHPRLGYLPVQTVLEGDNLETPSSSPQQAVSQDMHSRLELYASRLAEVEQS-----M  1020

Query  984   DSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEE  1043
             +S+S +  ++DEH LIQ YCQSL  DS +  P+SPAQI+++++ E+R ELE ++ DLEEE
Sbjct  1021  NSMSSSSDMEDEHTLIQQYCQSLGGDSGV--PKSPAQIVVAIDQEQRAELEAVIKDLEEE  1194

Query  1044  NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRL  1099
             NRNL+ EY+RLK Q + +     PSP E  P S +  RD ELIAEAKLLRQHKGRL
Sbjct  1195  NRNLRMEYERLKIQKQQQ-----PSPHE--PKS-EVNRDNELIAEAKLLRQHKGRL  1338


>ref|NM_001043262.1| Drosophila melanogaster dystrophin (Dys), transcript variant 
E, mRNA
Length=4529

 Score =  664 bits (1714),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 353/693 (50%), Positives = 465/693 (67%), Gaps = 57/693 (8%)
 Frame = +3

Query  474   ERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVS  533
             E++++ Q+  ++L  ++  AE  K SW P     +    + +++++ LR ++      + 
Sbjct  1440  EKMRQFQKILEDLSSRVALAEQTKTSWLPPSS--VGEANEQMQQLQRLRDKMTTASALLD  1613

Query  534   HVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------VRQLHEAHRD-  584
               N+     T   + +    LS LEDLNTR KLLQ+A+++R         +Q HE   D 
Sbjct  1614  DCNEQQSFFTANQVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCQAGAQQTHENGDDG  1793

Query  585   --------FGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLA  636
                      GP     L  SV+ PWERA +   VPYYI+HE +TT WDHP+M EL + LA
Sbjct  1794  RTTSNSGTIGPLPN--LGQSVKPPWERATTAANVPYYIDHERETTHWDHPEMIELMKGLA  1967

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPMDILQIINCLT  695
             DLN +RFSAYRTAMKLR +QK L LD +S+S AC++ D+H L+ QND+ +DI  +   L 
Sbjct  1968  DLNEIRFSAYRTAMKLRSVQKRLALDRISMSTACESFDRHGLRAQNDKLIDIPDMTTVLH  2147

Query  696   TIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKY  755
             ++Y  +++     +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ LCK HLE+KY
Sbjct  2148  SLYVTIDK-----IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVLLCKGHLEEKY  2312

Query  756   RYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA-----  810
             RYLF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRSC + A     
Sbjct  2313  RYLFRLVADTDRRADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRSCLEQAGISQE  2492

Query  811   ----NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRY  866
                 N    IE   FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNICKE PI+GFRY
Sbjct  2493  AIDGNQDISIELQHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNICKEYPIVGFRY  2672

Query  867   RSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYF  926
             R LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF + LKNKF++++YF
Sbjct  2673  RCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFTRALKNKFKSRKYF  2852

Query  927   AKHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLAEMENSNGSYL  982
              KHPR+GYLPVQ+VLEGD +E+PA SPQ +     +D HSR+E YASRLA++E     Y 
Sbjct  2853  KKHPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQNDMHSRLEMYASRLAQVE-----YG  3017

Query  983   NDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEE  1042
                 +     DDEH LI  YCQ+L   S  S P+SP Q++ ++++E+R ELE I+ DLEE
Sbjct  3018  GTGSNSTPDSDDEHQLIAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREELEAIIRDLEE  3197

Query  1043  ENRNLQAEYDRLKQQHEHKGLSPLP--------SPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             EN NLQAEY +L  + +    S +P        S   M   S Q  +  +++AEAKLLRQ
Sbjct  3198  ENANLQAEYQQLCSKEQ----SGMPEDSNGMQHSSSSMTGLSGQGEQGQDMMAEAKLLRQ  3365

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
             HKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  3366  HKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  3464


>gb|BT010020.1| Drosophila melanogaster RE11449 full insert cDNA
Length=4541

 Score =  664 bits (1714),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 353/693 (50%), Positives = 465/693 (67%), Gaps = 57/693 (8%)
 Frame = +3

Query  474   ERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVS  533
             E++++ Q+  ++L  ++  AE  K SW P     +    + +++++ LR ++      + 
Sbjct  1440  EKMRQFQKILEDLSSRVALAEQTKTSWLPPSS--VGEANEQMQQLQRLRDKMTTASALLD  1613

Query  534   HVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------VRQLHEAHRD-  584
               N+     T   + +    LS LEDLNTR KLLQ+A+++R         +Q HE   D 
Sbjct  1614  DCNEQQSFFTANQVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCQAGAQQTHENGDDG  1793

Query  585   --------FGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLA  636
                      GP     L  SV+ PWERA +   VPYYI+HE +TT WDHP+M EL + LA
Sbjct  1794  RTTSNSGTIGPLPN--LGQSVKPPWERATTAANVPYYIDHERETTHWDHPEMIELMKGLA  1967

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPMDILQIINCLT  695
             DLN +RFSAYRTAMKLR +QK L LD +S+S AC++ D+H L+ QND+ +DI  +   L 
Sbjct  1968  DLNEIRFSAYRTAMKLRSVQKRLALDRISMSTACESFDRHGLRAQNDKLIDIPDMTTVLH  2147

Query  696   TIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKY  755
             ++Y  +++     +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ LCK HLE+KY
Sbjct  2148  SLYVTIDK-----IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVLLCKGHLEEKY  2312

Query  756   RYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA-----  810
             RYLF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRSC + A     
Sbjct  2313  RYLFRLVADTDRRADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRSCLEQAGISQE  2492

Query  811   ----NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRY  866
                 N    IE   FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNICKE PI+GFRY
Sbjct  2493  AIDGNQDISIELQHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNICKEYPIVGFRY  2672

Query  867   RSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYF  926
             R LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF + LKNKF++++YF
Sbjct  2673  RCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFTRALKNKFKSRKYF  2852

Query  927   AKHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLAEMENSNGSYL  982
              KHPR+GYLPVQ+VLEGD +E+PA SPQ +     +D HSR+E YASRLA++E     Y 
Sbjct  2853  KKHPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQNDMHSRLEMYASRLAQVE-----YG  3017

Query  983   NDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEE  1042
                 +     DDEH LI  YCQ+L   S  S P+SP Q++ ++++E+R ELE I+ DLEE
Sbjct  3018  GTGSNSTPDSDDEHQLIAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREELEAIIRDLEE  3197

Query  1043  ENRNLQAEYDRLKQQHEHKGLSPLP--------SPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             EN NLQAEY +L  + +    S +P        S   M   S Q  +  +++AEAKLLRQ
Sbjct  3198  ENANLQAEYQQLCSKEQ----SGMPEDSNGMQHSSSSMTGLSGQGEQGQDMMAEAKLLRQ  3365

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
             HKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  3366  HKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  3464


>ref|XM_002102789.1| Drosophila simulans GD19295 (Dsim\GD19295), mRNA
Length=2346

 Score =  662 bits (1709),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 352/691 (50%), Positives = 463/691 (67%), Gaps = 57/691 (8%)
 Frame = +1

Query  476   LQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHV  535
             +++ Q+  ++L  ++  AE  K SW P     +    + +++++ LR ++      +   
Sbjct  1     MRQFQKILEDLSSRVALAEQTKTSWLPPSS--VGEANEQMQQLQRLRDKMTTASALLDDC  174

Query  536   NDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------VRQLHEAHRD---  584
             N+     T   + +    LS LEDLNTR KLLQ+A+++R         +Q HE   D   
Sbjct  175   NEQQSFFTANQVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCQAGAQQTHENGDDGRT  354

Query  585   ------FGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADL  638
                    GP     L  SV+ PWERA +   VPYYI+HE +TT WDHP+M EL + LADL
Sbjct  355   TSNSGTIGPLPN--LGQSVKPPWERATTAANVPYYIDHERETTHWDHPEMIELMKGLADL  528

Query  639   NNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPMDILQIINCLTTI  697
             N +RFSAYRTAMKLR +QK L LD +S+S AC++ D+H L+ QND+ +DI  +   L ++
Sbjct  529   NEIRFSAYRTAMKLRSVQKRLALDRISMSTACESFDRHGLRAQNDKLIDIPDMTTVLHSL  708

Query  698   YDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRY  757
             Y  +++     +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ LC+ HLE+KYRY
Sbjct  709   YVTIDK-----IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVLLCRGHLEEKYRY  873

Query  758   LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA-------  810
             LF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRSC + A       
Sbjct  874   LFRLVADTDRRADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRSCLEQAGISQEAI  1053

Query  811   --NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               N    IE   FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNICKE PI+GFRYR 
Sbjct  1054  DGNQDISIELQHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNICKEYPIVGFRYRC  1233

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK  928
             LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF + LKNKF++++YF K
Sbjct  1234  LKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFTRALKNKFKSRKYFKK  1413

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLAEMENSNGSYLND  984
             HPR+GYLPVQ+VLEGD +E+PA SPQ +     +D HSR+E YASRLA++E     Y   
Sbjct  1414  HPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQNDMHSRLEMYASRLAQVE-----YGGT  1578

Query  985   SISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEEN  1044
               +     DDEH LI  YCQ+L   S  S P+SP Q++ ++++E+R ELE I+ DLEEEN
Sbjct  1579  GSNSTPDSDDEHQLIAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREELEAIIRDLEEEN  1758

Query  1045  RNLQAEYDRLKQQHEHKGLSPLP--------SPPEMMPTSPQSPRDAELIAEAKLLRQHK  1096
              NLQAEY +L  + +    S LP        S   M   S Q  +  +++AEAKLLRQHK
Sbjct  1759  ANLQAEYQQLCSKEQ----SGLPEDSNGMQHSSSSMTGLSGQGEQGQDMMAEAKLLRQHK  1926

Query  1097  GRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
             GRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  1927  GRLEARMQILEDHNRQLEAQLQRLRQLLDEP  2019


>ref|XM_002043269.1| Drosophila sechellia GM26846 (Dsec\GM26846), mRNA
Length=2346

 Score =  658 bits (1698),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 350/691 (50%), Positives = 462/691 (66%), Gaps = 57/691 (8%)
 Frame = +1

Query  476   LQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHV  535
             +++ Q+  ++L  ++  AE  K SW P     +    + +++++ L  ++      +   
Sbjct  1     MRQFQKILEDLSSRVALAEQTKTSWLPPSS--VGEANEQMQQLQRLMDKMTTASALLDDC  174

Query  536   NDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------VRQLHEAHRD---  584
             N+     T   + +    LS LEDLNTR KLL++A+++R         +Q HE   D   
Sbjct  175   NEQQSFFTANQVLVPTPCLSKLEDLNTRMKLLKIAMDERQKVLCQAGAQQTHENGDDGRT  354

Query  585   ------FGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADL  638
                    GP     L  SV+ PWERA +   VPYYI+HE +TT WDHP+M EL + LADL
Sbjct  355   TSNSGTIGPLPN--LGQSVKPPWERATTAANVPYYIDHERETTHWDHPEMIELMKGLADL  528

Query  639   NNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPMDILQIINCLTTI  697
             N +RFSAYRTAMKLR +QK L LD +S+S AC++ D+H L+ QND+ +DI  +   L ++
Sbjct  529   NEIRFSAYRTAMKLRSVQKRLALDRISMSTACESFDRHGLRAQNDKLIDIPDMTTVLHSL  708

Query  698   YDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRY  757
             Y  +++     +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ LC+ HLE+KYRY
Sbjct  709   YVTIDK-----IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVLLCRGHLEEKYRY  873

Query  758   LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA-------  810
             LF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRSC + A       
Sbjct  874   LFRLVADTDRRADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRSCLEQAGISQEAI  1053

Query  811   --NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               N    IE   FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNICKE PI+GFRYR 
Sbjct  1054  DGNQDISIELQHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNICKEYPIVGFRYRC  1233

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK  928
             LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF + LKNKF++++YF K
Sbjct  1234  LKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFTRALKNKFKSRKYFKK  1413

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLAEMENSNGSYLND  984
             HPR+GYLPVQ+VLEGD +E+PA SPQ +     +D HSR+E YASRLA++E     Y   
Sbjct  1414  HPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQNDMHSRLEMYASRLAQVE-----YGGT  1578

Query  985   SISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEEN  1044
               +     DDEH LI  YCQ+L   S  S P+SP Q++ ++++E+R ELE I+ DLEEEN
Sbjct  1579  GSNSTPDSDDEHQLIAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREELEAIIRDLEEEN  1758

Query  1045  RNLQAEYDRLKQQHEHKGLSPLP--------SPPEMMPTSPQSPRDAELIAEAKLLRQHK  1096
              NLQAEY +L  + +    S LP        S   M   S Q  +  +++AEAKLLRQHK
Sbjct  1759  ANLQAEYQQLCSKEQ----SGLPEDSNGMQHSSSSMTGLSGQGEQGQDMMAEAKLLRQHK  1926

Query  1097  GRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
             GRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  1927  GRLEARMQILEDHNRQLEAQLQRLRQLLDEP  2019


>ref|XM_001652092.1| Aedes aegypti dystrophin partial mRNA
Length=2127

 Score =  657 bits (1694),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 353/731 (48%), Positives = 478/731 (65%), Gaps = 64/731 (8%)
 Frame = +1

Query  473   LERLQELQEATDELDLKLRQAEVIKGSW-QPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
             + ++++ Q+  ++L  ++  AE +  SW  P           HL+++K        L ++
Sbjct  1     MYKMRQFQKVLEDLGSRVASAETLIKSWTSPSSATDAAEQMQHLQRLKDKMTTAGALLDD  180

Query  532   VSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRD-------  584
                 N+     T   + +    L+ LEDLNTR KLL +A+++R + L     +       
Sbjct  181   C---NEQQSFFTANHVLVPNQCLAKLEDLNTRMKLLHIAMDERHKVLVAGGANQPSASDA  351

Query  585   -------------FGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTEL  631
                           GP     L+ SV+ PWERA +P  VPYYINHE + T WDHP+M EL
Sbjct  352   DGNKSMQGVSSGTIGPIPN--LAMSVKPPWERATTPANVPYYINHERENTHWDHPEMIEL  525

Query  632   YQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPMDILQI  690
              +SLADLN VRFSAYRTA+KLR +QK L  D ++++ A ++ D+H L+ QND+ +DI  +
Sbjct  526   MKSLADLNEVRFSAYRTALKLRTVQKRLAFDRIAMNVAIESFDRHGLRAQNDKLIDIPDM  705

Query  691   INCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
                L ++Y  +E      +++PL +D+ +NW+LNVYD+ RTG+IRVLSFK G+I LCK H
Sbjct  706   TTVLHSLYVTIEP-----IDMPLMLDLAINWILNVYDSQRTGQIRVLSFKVGLILLCKGH  870

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             LE+KYRYLF+ +A      DQR+LGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRSCF+ A
Sbjct  871   LEEKYRYLFRLIADLEKKVDQRKLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRSCFERA  1050

Query  811   --NNKPE-----IEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIG  863
               N   E     IEA  FL+W++ EPQS+VWLPVLHR+ AAE AKHQAKCNICKE PI+G
Sbjct  1051  GVNQNGELIETAIEAQHFLNWLQHEPQSLVWLPVLHRLVAAEAAKHQAKCNICKEYPIVG  1230

Query  864   FRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTK  923
             FRYR LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF + L+NKF+++
Sbjct  1231  FRYRCLKCFNFDMCQRCFFLGRNAKNHKLSHPMHEYCTTTTSTEDVRDFTRALRNKFKSR  1410

Query  924   RYFAKHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLAEMENSNG  979
             +YF KHPR+GYLPVQ+VLEGD +E+PA SPQ       +D HSR+E YASRLA++E    
Sbjct  1411  KYFKKHPRVGYLPVQSVLEGDALESPAPSPQHGTHTLQNDMHSRLEMYASRLAQVE----  1578

Query  980   SYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILAD  1039
              Y   S S  +S DDEH LI  YCQSL  +     P+SP Q++ ++++E+R ELE ++ D
Sbjct  1579  -YGTRSNSTPDS-DDEHQLIAQYCQSLPNN---GGPKSPVQVMAAMDAEQREELEAMIKD  1743

Query  1040  LEEENRNLQAEYDRLKQQHEHKGLSPLPSPPE----MMPTSPQSPRDAELIAEAKLLRQH  1095
             LEEEN +LQAEY+RLK +      +P+ +P +       T      + +++AEAKLLRQH
Sbjct  1744  LEEENASLQAEYERLKSKQ-----TPITTPDDSQMGQTGTGGNVGDNLDMMAEAKLLRQH  1908

Query  1096  KGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPML  1155
             KGRLEARMQILEDHN+QLE+QL RLRQLL++P        +T+ + S +  + ++  P  
Sbjct  1909  KGRLEARMQILEDHNRQLEAQLQRLRQLLDEPNTS---KASTLQTRSVTASQLNTESPAK  2079

Query  1156  LRVVGSQTSDS  1166
             L+  G    +S
Sbjct  2080  LQQNGHYDQNS  2112


>gb|BC036095.1| Homo sapiens cDNA clone IMAGE:5300319, containing frame-shift 
errors
Length=3051

 Score =  421 bits (1083),  Expect(2) = 0.0, Method: Compositional matrix adjust.
 Identities = 186/275 (67%), Positives = 233/275 (84%), Gaps = 0/275 (0%)
 Frame = +3

Query  591   HFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAM  650
             H  STSVQ PWERAISPNKVPYYINH+ QTTCWDHPKMTELYQ+LADLNN++FSAYRTAM
Sbjct  1476  HPRSTSVQVPWERAISPNKVPYYINHQAQTTCWDHPKMTELYQTLADLNNIKFSAYRTAM  1655

Query  651   KLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVN  710
             KLRR+QKAL LDL++L+ A +  ++H+L+ ++  MD++++I+CLT +Y+RLE+E   LVN
Sbjct  1656  KLRRVQKALRLDLVTLTTALEIFNEHDLQASEHVMDVVEVIHCLTALYERLEEERGILVN  1835

Query  711   VPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCD  770
             VPLCVDM LNWLLNV+D+GR+G++R LSFKTGI  LC   +++K +YLF QVA+S   CD
Sbjct  1836  VPLCVDMSLNWLLNVFDSGRSGKMRALSFKTGIACLCGTEVKEKLQYLFSQVANSGSQCD  2015

Query  771   QRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQ  830
             QR LG+LLH++IQ+P QLGEVA+FGGSN+EPSVRSCF+F+  KP IEA+ FL+W+ LEPQ
Sbjct  2016  QRHLGVLLHEAIQVPHQLGEVAAFGGSNVEPSVRSCFRFSTGKPVIEASQFLEWVNLEPQ  2195

Query  831   SMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFR  865
             SMVWL VLHRV  AE  KHQ KC+IC++CPI GFR
Sbjct  2196  SMVWLAVLHRVTIAEQVKHQTKCSICRQCPIKGFR  2300


 Score =  258 bits (658),  Expect(2) = 0.0, Method: Compositional matrix adjust.
 Identities = 127/275 (46%), Positives = 182/275 (66%), Gaps = 0/275 (0%)
 Frame = +1

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L LQE++ WL  KD+ELS Q P+ GD   V
Sbjct  553   MNLCWNEIKKKSHNLRARLEAFSDHSGKLQLPLQEIIDWLSQKDEELSAQLPLQGDVALV  732

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K++ P I S LE+ + FL++ P E LE+ + E ++  P++R QN++
Sbjct  733   QQEKETHAAFMEEVKSRGPYIYSVLESAQAFLSQHPFEELEEPHSESKDTSPKQRIQNLS  912

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE+L E+Q A +EL   L QAE ++ +W+
Sbjct  913   RFVWKQATVASELWEKLTARCVDQHRHIERTLEQLLEIQGAMEELSTTLSQAEGVRATWE  1092

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  1093  PIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLVNDLAHQLAISDVHLSMENSQALEQIN  1272

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTS  596
              RWK LQ +V +R++QL +AHRDFGP SQHFLS +
Sbjct  1273  VRWKQLQASVSERLKQLQDAHRDFGPGSQHFLSCT  1377


 Score = 55.5 bits (132),  Expect = 2e-04, Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 101/235 (42%), Gaps = 33/235 (14%)
 Frame = +1

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ R P +  ++ +AQ   ++
Sbjct  655   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSRGPYIYSVLESAQAFLSQ  834

Query  81    TSNQE-----ARTIITDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E     + +  T   +RIQN               W+++     ++ + +   L+ 
Sbjct  835   HPFEELEEPHSESKDTSPKQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIERTLEQ  1014

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  1015  LLEIQGAMEELSTTLSQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPMKDGVKLV  1194

Query  181   NDLALKLLRDYSADDTRKVHMITEN------INASWRSIHKRVSEREAALEETHR  229
             NDLA +L           VH+  EN      IN  W+ +   VSER   L++ HR
Sbjct  1195  NDLAHQLA-------ISDVHLSMENSQALEQINVRWKQLQASVSERLKQLQDAHR  1338


>dbj|AK149002.1| Mus musculus 2 days neonate sympathetic ganglion cDNA, RIKEN 
full-length enriched library, clone:7120474D01 product:dystrophin, 
muscular dystrophy, full insert sequence
Length=2146

 Score =  648 bits (1671),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 318/336 (94%), Positives = 326/336 (97%), Gaps = 0/336 (0%)
 Frame = +3

Query  279   QDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRS  338
             +DLQGEIE HTD+YHNLDEN QKILRSLEGSD+A LLQRRLDNMNFKWSEL+KKSLNIRS
Sbjct  195   KDLQGEIETHTDIYHNLDENGQKILRSLEGSDEAPLLQRRLDNMNFKWSELQKKSLNIRS  374

Query  339   HLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTK  398
             HLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQND+HRAFKRELKTK
Sbjct  375   HLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDIHRAFKRELKTK  554

Query  399   EPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKL  458
             EPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLR QAEEVN EW+KL
Sbjct  555   EPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRNQAEEVNAEWDKL  734

Query  459   NLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKV  518
             NL SADWQRKIDE LERLQELQEA DELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKV
Sbjct  735   NLRSADWQRKIDEALERLQELQEAADELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKV  914

Query  519   KALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQL  578
             KALRGEIAPLKENV+ VNDLA QLTTLGIQLSPYNLSTLEDLNTRW+LLQVAVEDRVRQL
Sbjct  915   KALRGEIAPLKENVNRVNDLAHQLTTLGIQLSPYNLSTLEDLNTRWRLLQVAVEDRVRQL  1094

Query  579   HEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYI  614
             HEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYI
Sbjct  1095  HEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYI  1202


 Score = 49.3 bits (116),  Expect = 0.014, Method: Compositional matrix adjust.
 Identities = 59/235 (25%), Positives = 101/235 (42%), Gaps = 33/235 (14%)
 Frame = +3

Query  21    ELTDWLSLLDQVIKSQRVMVGDL------EDIN-----EMIIKQKATMQDLEQRR-----  64
             EL  WL L D  +  Q  + GD        DI+     E+  K+   M  LE  R     
Sbjct  426   ELLVWLQLKDDELSRQAPIGGDFPAVQKQNDIHRAFKRELKTKEPVIMSTLETVRIFLTE  605

Query  65    ---PQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKD  121
                  LE+L    + L  +   Q    ++ ++ E +  +WD++     + +++++E L+ 
Sbjct  606   QPLEGLEKLYQEPRELPPEERAQNVTRLLRNQAEEVNAEWDKLNLRSADWQRKIDEALER  785

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +  EA +E +  L QA     SW+  G   +D++Q  + + K L  ++   + NV+  
Sbjct  786   LQELQEAADELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVNRV  965

Query  181   NDLALKL------LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             NDLA +L      L  Y+           E++N  WR +   V +R   L E HR
Sbjct  966   NDLAHQLTTLGIQLSPYNLS-------TLEDLNTRWRLLQVAVEDRVRQLHEAHR  1109


>ref|XM_002138048.1| Drosophila pseudoobscura pseudoobscura GA27582 (Dpse\GA27582), 
mRNA
Length=2388

 Score =  645 bits (1665),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 349/712 (49%), Positives = 470/712 (66%), Gaps = 56/712 (7%)
 Frame = +1

Query  475   RLQELQEATDELDLKLRQAEVIKGSW-QPVGDLLIDSLQDHLEKVKALRGEIAPLKENVS  533
             ++++ Q+  ++L  ++  AE  K SW  PV    +    + +++++ LR ++      + 
Sbjct  1     KMRQFQKILEDLSSRVALAEQTKNSWLSPVS---VGEANEQMQQLQRLRDKMTTASALLD  171

Query  534   HVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------VRQLHEAHRD-  584
               N+     T   + +    LS LEDLNTR KLLQ+A+++R         +Q HE   D 
Sbjct  172   DCNEQQSFFTANQVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCAAGAQQAHENGDDG  351

Query  585   --------FGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLA  636
                      GP     L  SV+ PWERA +   VPYYI+HE +TT WDHP M EL + LA
Sbjct  352   RNTSNSGTIGPLPN--LGQSVKPPWERATTAANVPYYIDHERETTHWDHPDMIELMKGLA  525

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPMDILQIINCLT  695
             DLN +RFSAYRTAMKLR +QK L LD ++++ AC++ D+H L+ QND+ +DI  +   L 
Sbjct  526   DLNEIRFSAYRTAMKLRSVQKRLALDRITMATACESFDRHGLRAQNDKLIDIPDMTTVLH  705

Query  696   TIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKY  755
             ++Y  +++     +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ LCK HLE+KY
Sbjct  706   SLYVTIDK-----IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVLLCKGHLEEKY  870

Query  756   RYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA-----  810
             RYLF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRSC + A     
Sbjct  871   RYLFRLVADTERRADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRSCLEQAGISQE  1050

Query  811   ----NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRY  866
                 N +  IE   FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNICKE PI+GFRY
Sbjct  1051  AIDGNQEISIELQHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNICKEYPIVGFRY  1230

Query  867   RSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYF  926
             R LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF + LKNKF++++YF
Sbjct  1231  RCLKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTATTSTEDVRDFTRALKNKFKSRKYF  1410

Query  927   AKHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLAEMENSNGSYL  982
              KHPR+GYLPVQ+VLEGD +E+PA SPQ +      D H+R+E YASRLA++E     Y 
Sbjct  1411  KKHPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQSDMHTRLEMYASRLAQVE-----YG  1575

Query  983   NDSISPNESIDDEHLLIQHYCQSL-NQDSPLSQPRSPAQILISLESEERGELERILADLE  1041
                 +     DDEH LI  YCQ+L    +  S P+SP Q++ ++++E+R ELE I+ DLE
Sbjct  1576  GTGSNSTPDSDDEHQLIAQYCQALPGTSNGSSAPKSPVQVMAAMDAEQREELEAIIRDLE  1755

Query  1042  EENRNLQAEYDRL--KQQH-----EHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQ  1094
             EEN NLQAEY +L  KQQ       +       S         Q  +  +++AEA+LLRQ
Sbjct  1756  EENANLQAEYQQLCTKQQSGTPDDTNGMQHSSSSSMSGGLGGGQGEQGQDMMAEAQLLRQ  1935

Query  1095  HKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTV-SSPSTSL  1145
             HKGRLEARM+ILEDHN+QLE+QL RLRQLL++P   +    + + S+P ++L
Sbjct  1936  HKGRLEARMRILEDHNRQLEAQLQRLRQLLDEPNGGSSATSSGLPSAPGSAL  2091


>ref|XM_002019869.1| Drosophila persimilis GL12656 (Dper\GL12656), mRNA
Length=2667

 Score =  644 bits (1662),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 349/711 (49%), Positives = 469/711 (65%), Gaps = 56/711 (7%)
 Frame = +1

Query  476   LQELQEATDELDLKLRQAEVIKGSW-QPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSH  534
             +++ Q+  ++L  ++  AE  K SW  PV    +    + +++++ LR ++      +  
Sbjct  1     MRQFQKILEDLSSRVALAEQTKNSWLSPVS---VGEANEQMQQLQRLRDKMTTASALLDD  171

Query  535   VNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDR--------VRQLHEAHRD--  584
              N+     T   + +    LS LEDLNTR KLLQ+A+++R         +Q HE   D  
Sbjct  172   CNEQQSFFTANQVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCAAGAQQAHENGDDGR  351

Query  585   -------FGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLAD  637
                     GP     L  SV+ PWERA +   VPYYI+HE +TT WDHP M EL + LAD
Sbjct  352   NTSNSGTIGPLPN--LGQSVKPPWERATTAANVPYYIDHERETTHWDHPDMIELMKGLAD  525

Query  638   LNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPMDILQIINCLTT  696
             LN +RFSAYRTAMKLR +QK L LD ++++ AC++ D+H L+ QND+ +DI  +   L +
Sbjct  526   LNEIRFSAYRTAMKLRSVQKRLALDRITMATACESFDRHGLRAQNDKLIDIPDMTTVLHS  705

Query  697   IYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYR  756
             +Y  +++     +++ L +D+ +NW+LNVYD+ RTG+IRVLSFK G++ LCK HLE+KYR
Sbjct  706   LYVTIDK-----IDLTLMLDLAINWILNVYDSQRTGQIRVLSFKVGLVLLCKGHLEEKYR  870

Query  757   YLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA------  810
             YLF+ VA +    DQRRLGLLLHD IQ+PRQLGEVA+FGGSNIEPSVRSC + A      
Sbjct  871   YLFRLVADTERRADQRRLGLLLHDCIQVPRQLGEVAAFGGSNIEPSVRSCLEQAGISQEA  1050

Query  811   ---NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYR  867
                N +  IE   FL W++ EPQS+VWLPVLHR+AAAE AKHQAKCNICKE PI+GFRYR
Sbjct  1051  IDGNQEISIELQHFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNICKEYPIVGFRYR  1230

Query  868   SLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA  927
              LK FN+D+CQ CFF GR AK HK+ +PM EYCT TTS EDVRDF + LKNKF++++YF 
Sbjct  1231  CLKCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTATTSTEDVRDFTRALKNKFKSRKYFK  1410

Query  928   KHPRMGYLPVQTVLEGDNMETPASSPQLS----HDDTHSRIEHYASRLAEMENSNGSYLN  983
             KHPR+GYLPVQ+VLEGD +E+PA SPQ +      D H+R+E YASRLA++E     Y  
Sbjct  1411  KHPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQSDMHTRLEMYASRLAQVE-----YGG  1575

Query  984   DSISPNESIDDEHLLIQHYCQSL-NQDSPLSQPRSPAQILISLESEERGELERILADLEE  1042
                +     DDEH LI  YCQ+L    +  S P+SP Q++ ++++E+R ELE I+ DLEE
Sbjct  1576  TGSNSTPDSDDEHQLIAQYCQALPGTSNGSSAPKSPVQVMAAMDAEQREELEAIIRDLEE  1755

Query  1043  ENRNLQAEYDRL--KQQH-----EHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQH  1095
             EN NLQAEY +L  KQQ       +       S         Q  +  +++AEA+LLRQH
Sbjct  1756  ENANLQAEYQQLCTKQQSGTPDDTNGMQHSSSSSMSGGLGGGQGEQGQDMMAEAQLLRQH  1935

Query  1096  KGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTV-SSPSTSL  1145
             KGRLEARM+ILEDHN+QLE+QL RLRQLL++P   +    + + S+P ++L
Sbjct  1936  KGRLEARMRILEDHNRQLEAQLQRLRQLLDEPNGGSSATSSGLPSAPGSAL  2088


>ref|XM_001096514.1| PREDICTED: Macaca mulatta dystrophin (DMD), partial mRNA
Length=7542

 Score =  630 bits (1624),  Expect = 2e-177, Method: Compositional matrix adjust.
 Identities = 323/389 (83%), Positives = 335/389 (86%), Gaps = 37/389 (9%)
 Frame = +1

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
             MPSSLMLEVPALADFNRAWTELT+WLSLL +VIKSQRVMVGDLEDINEMIIKQKAT+QDL
Sbjct  6487  MPSSLMLEVPALADFNRAWTELTEWLSLLGRVIKSQRVMVGDLEDINEMIIKQKATVQDL  6666

Query  61    EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  120
             EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK
Sbjct  6667  EQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK  6846

Query  121   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
             DSTQWLEAKEEAEQVLGQARAKLESWKEGPYT+DAIQKKITETKQLAKDLRQWQ NVDVA
Sbjct  6847  DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTIDAIQKKITETKQLAKDLRQWQINVDVA  7026

Query  181   NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
             NDLALKLLRDYSADDTRKVHMITENINASW SIHKR+     A+++      +F L +  
Sbjct  7027  NDLALKLLRDYSADDTRKVHMITENINASWGSIHKRI-----AMQQDQCCSPRFKLKM--  7185

Query  241   FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
                                    L   +  VK       DLQGEIEAHTDVYHNLDENSQ
Sbjct  7186  -----------------------LHRKTYHVK-------DLQGEIEAHTDVYHNLDENSQ  7275

Query  301   KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
             K+LRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW
Sbjct  7276  KVLRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  7455

Query  361   LQLKDDELSRQAPIGGDFPAVQKQNDVHR  389
             LQLKDDELSRQ PIGGDFPAVQKQNDVHR
Sbjct  7456  LQLKDDELSRQTPIGGDFPAVQKQNDVHR  7542


 Score = 60.5 bits (145),  Expect = 5e-06, Method: Compositional matrix adjust.
 Identities = 99/480 (20%), Positives = 211/480 (43%), Gaps = 82/480 (17%)
 Frame = +1

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQ--  58
             +PS+ + E+          T ++  LS ++Q++ +  +   D ED+     KQ+ +++  
Sbjct  5092  VPSTYLTEI----------THVSQALSEVEQLLNAPDLCAKDFEDL----FKQEESLKNI  5229

Query  59    -DLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNE  117
              D+ Q+     ++I + +    +++    R  + + + +I  QW++V +  ++R+ + + 
Sbjct  5230  KDILQQSSGRIDIIHSKKTAALQSATPVERVKLQEALSQIDFQWEKVNKMYKDRQGRFDR  5409

Query  118   M----------LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLA  167
                        +K   QWL    EAEQ L + +   E+W+   Y            K+L 
Sbjct  5410  SVEKWRRFHYDIKIFNQWLT---EAEQFLRKTQIP-ENWEHAKYK--------WYLKELQ  5553

Query  168   KDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEET  227
               + Q QT V   N    ++++  S  D   +     ++N  W+ + K++SER+  LEE 
Sbjct  5554  DGIGQRQTVVRTLNATGEEIIQQSSKTDASILQEKLGSLNLRWQEVCKQLSERKKRLEEQ  5733

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEA  287
               +L +F  DL +F+ WL EA+  A++  +   +++L E  + VK L+++    QG    
Sbjct  5734  KNILSEFQRDLNEFVLWLEEADNIASIPLEPGNEQQLKEKLEQVKLLVEELPLRQG----  5901

Query  288   HTDVYHNLDENSQKILRSLEGS-DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQ  346
                +   L+E    +L S   S ++   L+ +L   N +W ++ +     +  +EA    
Sbjct  5902  ---ILKQLNETGGPVLVSAPISPEEQDKLENKLKRTNLQWIKVSRALPEKQGEIEAQIKD  6072

Query  347   WKRLHLSLQE-------LLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKE  399
               +L   L++       LL+WL    ++L        + P   K+ ++       ++ K+
Sbjct  6073  LGQLEKKLEDLEEQLNHLLLWLSPIRNQLEIYNQPNQEGPFDIKETEIA------VQAKQ  6234

Query  400   PVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLN  459
             P +   L   + F  E+P                       T+ ++++ E++++EW+ +N
Sbjct  6235  PDVEGILSKGQHFYKEKP----------------------ATQPVKRKLEDLSSEWKTVN  6348


 Score = 46.6 bits (109),  Expect = 0.080, Method: Compositional matrix adjust.
 Identities = 91/424 (21%), Positives = 183/424 (43%), Gaps = 52/424 (12%)
 Frame = +1

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
             + +++++ E + L   L++ Q+ ++  +    ++ +   ++ +RK  +  E I   W+ +
Sbjct  2023  EIMEQRLGELQVLQSSLQEQQSGLNYLSTTVKEMSKKAPSEISRKYQLEFEEIETRWKKL  2202

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER--LLEDSKGV  271
               +++E    LEE    L++    ++    W+ E         D   KE    L DS+ +
Sbjct  2203  SSQLAEHCQKLEEQMNKLRKIQNHIQTLKKWMAEV--------DVFLKEEWPALGDSEIL  2358

Query  272   KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
             K+ +KQ + L  +I+      ++++E  QKI    E  + A+ L+  L  +N +W  + +
Sbjct  2359  KKQLKQCRLLVNDIQTIQPSLNSVNEGGQKIKNEAE-PEFALRLEIELKELNTQWDHMCQ  2535

Query  332   KSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFP-----AVQKQN  385
             +    +  L+   ++   L   L E+  W+ Q +++ L R      DF       +QK  
Sbjct  2536  QVYARKEALKGGLEKTVSLQKDLSEMHEWMTQAEEEYLER------DFEYKTPDELQKAV  2697

Query  386   DVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLR  445
             +  +  K E + KE  +    E+V   + + P    E L +E   L      Q +   L 
Sbjct  2698  EEMKRAKEEAQQKEAKVKLLTESVNSVIAQAPPVAQEALKKELETLTT--NYQWLCTRLN  2871

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
              + + +   W       A W     E L  L++  +  +E++ KL+  E I G  + + +
Sbjct  2872  GKCKTLEEVW-------ACWH----ELLSYLEKANKWLNEVEFKLKTTENIPGGAEEISE  3018

Query  506   LL--IDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTR  563
             +L  +++L  H E             +N + +  LA+ LT  G+     N   LE  N+R
Sbjct  3019  VLHSLENLMQHSE-------------DNPNQIRILAQTLTDGGVMDELIN-EELETFNSR  3156

Query  564   WKLL  567
             W+ L
Sbjct  3157  WREL  3168


>ref|XM_002162901.1| PREDICTED: Hydra magnipapillata similar to dystrophin Dp140ab 
(LOC100213780), mRNA
Length=8310

 Score =  629 bits (1622),  Expect = 3e-177, Method: Compositional matrix adjust.
 Identities = 338/738 (45%), Positives = 479/738 (64%), Gaps = 54/738 (7%)
 Frame = +2

Query  472   TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
             T E + +L +  D+L+ +L+ AE  K  W P  D   +++   LE+ K     +  L+  
Sbjct  6170  TDELVNKLVKEIDDLNNRLKDAENRKNLWNPTSDFNCENVNKALEETKVFNDSVTSLEPY  6349

Query  532   VSHVNDLARQL-TTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEA-HRDFGPAS  589
             +  +N   + L  + G+ L       +++   RW  LQ   E R   L+   + D    S
Sbjct  6350  IDSINGKVKALKVSYGVDLGQKQ-KQVDEFLQRWSKLQSECEQRHNMLNNILNNDQDKQS  6526

Query  590   QHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTA  649
             Q  L  SV  PWER+ S NKVPYYINH T+ T WDHPKMTELY +LA+LN+V+F+AYRT+
Sbjct  6527  Q--LQGSVSPPWERSCSLNKVPYYINHTTKVTQWDHPKMTELYNTLAELNDVKFAAYRTS  6700

Query  650   MKLRRLQKALCLDLLSL-SAACDALDQHNLKQN-DQPMDILQIINCLTTIYDRLEQEHNN  707
             MKLR +QKA CLDL+ + + A  A  +H++  N D  +D+ +++  L T++  ++     
Sbjct  6701  MKLRCIQKACCLDLVDMDNVAIKAFQRHDITANKDSLIDVGEMVAVLLTMFGNIDPTRKE  6880

Query  708   LVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTG  767
              + VP CVD+ LNWLLNV+D+GR G++RVLSFK  I+ LC+A LE+K++YLF+Q+A S+G
Sbjct  6881  AIVVPQCVDLTLNWLLNVFDSGRIGKLRVLSFKIAIVLLCRAKLENKWKYLFEQIADSSG  7060

Query  768   FCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRL  827
               D ++LGLLLHD +QIPRQLGE+A+FGGSNIEPS RSCF+ A N   IE   FL+W   
Sbjct  7061  HADSKKLGLLLHDCVQIPRQLGEIAAFGGSNIEPSARSCFEKAKNPTVIEVNNFLEWTSA  7240

Query  828   EPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVA  887
             EPQS+VW+ VLHR+AAAETAKH AKC ICK+ PI+GFRYR LK FNYD+CQ+CF+SGRV+
Sbjct  7241  EPQSLVWMTVLHRLAAAETAKHDAKCGICKDFPIVGFRYRCLKCFNYDLCQNCFWSGRVS  7420

Query  888   KGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHP-RMGYLPVQTVLEGDNM  946
             K H++ +PM +Y   TT+GED+ DF K++KNKF+++RY ++ P ++GYLPVQT++EG ++
Sbjct  7421  KSHRLTHPMHQYSLATTAGEDMSDFVKLMKNKFKSRRYRSRPPKKLGYLPVQTIMEGSSI  7600

Query  947   ETPA--SSPQLSHDDTHSRIEHYAS--RLAEMENSNGSYLNDSISPNESIDDEHLLIQHY  1002
             ETP+  SSP +           Y S  R +  E+ N   ++D       I++EH LIQH 
Sbjct  7601  ETPSVPSSPNIKFS--------YLSNDRSSSPESENYRMVDD-------INEEHRLIQHM  7735

Query  1003  CQSL-NQDSPLSQPRSPAQILISLESEERGELER----ILADLEEENRNLQAEYDRLKQQ  1057
             C+SL ++DS L   +SP+ IL SL+ EE+ ++ +    I++DLEEE+R L++EY+RLK  
Sbjct  7736  CRSLSSEDSRLLPLKSPSAILASLDIEEKIDIAQSVNDIISDLEEEHRALESEYNRLKNM  7915

Query  1058  HEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQL  1117
               +              ++P+S  D+ELIAEA+LLRQHK RLEARMQILE HNKQLE+QL
Sbjct  7916  RAN-------------GSNPRSSSDSELIAEAQLLRQHKVRLEARMQILEHHNKQLEAQL  8056

Query  1118  HRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQ  1177
              RLRQLL+QPQ++  V  +   +P+ +   S    P L R   S T+        L+   
Sbjct  8057  QRLRQLLDQPQSDRSVQSSAGVTPTLTPSSSYHGSPELGRRDYSFTNGYS-----LTNAM  8221

Query  1178  DTSTGLEEVMEQLNNSFP  1195
             D    +++V  Q+ N+FP
Sbjct  8222  D----IQQVTNQIENAFP  8263


 Score =  150 bits (380),  Expect = 4e-33, Method: Compositional matrix adjust.
 Identities = 115/473 (24%), Positives = 232/473 (49%), Gaps = 25/473 (5%)
 Frame = +2

Query  4     SLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQR  63
             S +L+   +  F++   EL D L L++Q +K   + VGD +DI   + K  A  Q++  R
Sbjct  4037  SEVLQEDKINKFDKNVAELHDVLKLIEQKLKGFTLNVGDPDDIELAVQKHNAIQQEVNNR  4216

Query  64    RPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDST  123
             R  LE++I     L   + N+       D+I +++ +WD V + +++++    ++ +D  
Sbjct  4217  RGDLEDVIEMGAALTMNSKNESFNYATDDKITKLKERWDIVSKKIESQKAMFEQLNRDLR  4396

Query  124   QWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDL  183
             +      + +  + +A ++L    +   TV   Q+++    +   ++R+ QT+       
Sbjct  4397  RCNLIITQVDNWIHKAGSQLNERLKVGSTV--FQEELLAFSEQFNNVRK-QTD-------  4546

Query  184   ALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLA  243
                +L+ YS+ D        + +  +W  +  + + R+ +L+E    +  F  ++   L 
Sbjct  4547  --DILQTYSSLDLTSFKGKCKEMMQAWSDLDTKSNIRQQSLQEALDNILVFHKNMIGALT  4720

Query  244   WLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKIL  303
             WL+ AE+    L D+  +    ED+  ++EL ++   L+ +I  H  ++ +L++   +I+
Sbjct  4721  WLSSAESKVAEL-DSLFEASQTEDNTDLEELQQEMLALEEDIALHQAMFQSLNDTGNQIM  4897

Query  304   RSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQL  363
               LE  +    LQ +LD+MN +W+ L  + ++IR  +   + +W++L   +QE++ WL  
Sbjct  4898  MDLEQGEVRTALQSKLDDMNDRWNSLGLRVVDIRDRMADGTGEWRQLLFDMQEIVDWLLR  5077

Query  364   KDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEK  423
                EL+ Q P+G D   ++ Q++ H+AFK +L  ++ VI   L+  R FL +  +  L  
Sbjct  5078  AGQELNSQQPVGSDISTIKHQHENHQAFKGKLLVRQVVIKQVLDQGRNFLMKHQVHELAS  5257

Query  424   LYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERL  476
                         R  N+   +++Q E + T+W+ L  +S  WQ  ID  LE  
Sbjct  5258  ------------REDNIVSSVQEQIEHIETQWQLLMSNSEKWQVTIDTVLENF  5380


>gb|U43518.1|GSU43518 Gobius sp. dystrophin-related protein 2 (DRP2) mRNA, partial 
cds
Length=1440

 Score =  626 bits (1614),  Expect = 3e-176, Method: Compositional matrix adjust.
 Identities = 294/481 (61%), Positives = 376/481 (78%), Gaps = 4/481 (0%)
 Frame = +1

Query  625   HPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQP  684
             HPKMTELYQ+LADLNN++FSAYRTAMKLRR+QK L LDL+ LS+  +   + +L+Q +  
Sbjct  1     HPKMTELYQALADLNNIKFSAYRTAMKLRRVQKVLRLDLVGLSSLAEVFREQDLQQPEHI  180

Query  685   MDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGII  744
             MD++++I+ LT +Y+RLE+E + +VN+PLCVDMCLNWLLNVYD+ R G+IRVLSFK G++
Sbjct  181   MDVVEVIHGLTALYERLEEERSIMVNIPLCVDMCLNWLLNVYDSPRNGKIRVLSFKMGLV  360

Query  745   SLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVR  804
             SLC   +++KY+YLF+QVA   G  DQR L +LLH++IQIPRQLGEVA+FGGSN+EPSVR
Sbjct  361   SLCNEDVQEKYKYLFRQVACPAGTTDQRHLSMLLHEAIQIPRQLGEVAAFGGSNVEPSVR  540

Query  805   SCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGF  864
             SCF+ A +K  IE + FL+W  LEPQSMVWLPVLHRVAAAE+ KHQAKC++CK+CPI GF
Sbjct  541   SCFRVAPSKATIEVSHFLEWTSLEPQSMVWLPVLHRVAAAESTKHQAKCSVCKQCPIKGF  720

Query  865   RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKR  924
             RYRSLK FN DICQ+CF +GR  KG K+HYP++EY TPTTSGE +RDFAK LKNKFR+K+
Sbjct  721   RYRSLKQFNVDICQTCFLTGRTTKGKKLHYPIMEYYTPTTSGEKMRDFAKTLKNKFRSKQ  900

Query  925   YFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLND  984
             YF+KHP+ GYLPVQ+VLE +  ETP SSP+L H DTHSRIEHYASRLAEME+ N S+  D
Sbjct  901   YFSKHPQRGYLPVQSVLEAEASETPCSSPRLPHADTHSRIEHYASRLAEMESQNCSFFTD  1080

Query  985   SISPNESIDDEHLLIQHYCQSLNQDSPLSQ-PRSPAQILISLESEERGELERILADLEEE  1043
             S+SP+ES+D++  L++H   +L  DSPL+Q    PA+  ++      GEL+R LA LE E
Sbjct  1081  SLSPDESLDEDQYLLRHSSPALEPDSPLAQHAPGPARAQVAHPGPP-GELQRTLARLENE  1257

Query  1044  NRNLQAEYDRLKQQHEHKGLSPL--PSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEA  1101
             NR L+ EY RLK +HE     P+   +  E + +     +D EL+AEA++LRQHK RLE 
Sbjct  1258  NRVLENEYRRLKWKHEEAASVPMLTEAGEEGLGSPTGGAQDEELLAEARVLRQHKSRLET  1437

Query  1102  R  1102
             R
Sbjct  1438  R  1440


>emb|X99737.1| Asteroidea sp. mRNA for dystrophin-like protein
Length=1413

 Score =  625 bits (1612),  Expect = 5e-176, Method: Compositional matrix adjust.
 Identities = 305/481 (63%), Positives = 377/481 (78%), Gaps = 14/481 (2%)
 Frame = +1

Query  625   HPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNL--KQND  682
             HPKMTEL+QSL DLN+V+FSAYRTAMKLR+LQKALC DLLS+++A     QH +     D
Sbjct  1     HPKMTELFQSLGDLNDVKFSAYRTAMKLRKLQKALCFDLLSMNSADRIFQQHEVLSSCTD  180

Query  683   QPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTG  742
             + +D+ +II  LT++Y+ +  +H NLV VP CVDMCLNWLLNVYDT R+GR+R LSFK  
Sbjct  181   RTLDVNEIITLLTSVYENITSDHPNLVVVPQCVDMCLNWLLNVYDTVRSGRMRALSFKLA  360

Query  743   IISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPS  802
             II L KAHLEDKYRY+ + VA++ GF DQR LGLLLHD IQIPRQLGEVASFGGSNIEPS
Sbjct  361   IIILSKAHLEDKYRYIVRCVANNNGFIDQRGLGLLLHDCIQIPRQLGEVASFGGSNIEPS  540

Query  803   VRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPII  862
             VRSCF  +  K  IE   FL WM+LEPQSMVW+PVLHR+AA ETAKHQAKCN+CKE PI+
Sbjct  541   VRSCFNMSGGKSHIEPPQFLAWMKLEPQSMVWMPVLHRMAAGETAKHQAKCNVCKEFPIV  720

Query  863   GFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRT  922
             G RYR LK FN+ +CQ+CFFSGRV+K HK  +PM EYCT TTSGEDVRDFAKV++NKF++
Sbjct  721   GLRYRCLKCFNFYMCQNCFFSGRVSKNHKHSHPMQEYCTTTTSGEDVRDFAKVVRNKFKS  900

Query  923   KRYFAKHPRMGYLPVQTVLEGDNMETPASSP-QLSHDDTHSRIEHYASRLAEMENSNGSY  981
             KRY+ KHPR+GYLPVQ+VLEGD++E+P +SP Q++++D H+R+E YASRLAE+E  +GS+
Sbjct  901   KRYYQKHPRVGYLPVQSVLEGDDLESPVTSPQQMANEDMHTRLELYASRLAEVEE-HGSF  1077

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLE  1041
             L    +P+  +DDEH LI  YCQSL  D   S PRSPAQI++++ES++RGELE  +  LE
Sbjct  1078  L----TPSPDLDDEHQLIAQYCQSLGGDVS-SVPRSPAQIVVAIESDQRGELENQILILE  1242

Query  1042  EENRNLQAEYDRLKQ-QHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             EENR L AE DRL+  +++    + + S  +       SP D EL+AEAKLLRQHKGRLE
Sbjct  1243  EENRTLLAELDRLRALRYDDHTRAEVSSEEDFR----HSPADTELVAEAKLLRQHKGRLE  1410

Query  1101  A  1101
             A
Sbjct  1411  A  1413


>gb|U43520.1|MMU43520 Mus musculus dystrophin-related protein 2 (DRP2) mRNA, partial 
cds
Length=1428

 Score =  625 bits (1611),  Expect = 7e-176, Method: Compositional matrix adjust.
 Identities = 298/488 (61%), Positives = 380/488 (77%), Gaps = 21/488 (4%)
 Frame = +1

Query  634   SLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINC  693
             +LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ ++  MD++++I+C
Sbjct  1     TLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQASEHVMDVVEVIHC  180

Query  694   LTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLED  753
             LT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKTGI  LC   +++
Sbjct  181   LTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKTGIACLCGTEVKE  360

Query  754   KYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNK  813
             K +YLF QVA+S   CDQR LG LLH++IQ+PRQLGEVA+FGGSN+EPSVRSCF+F+  K
Sbjct  361   KLQYLFSQVANSGSQCDQRHLGALLHEAIQVPRQLGEVAAFGGSNVEPSVRSCFRFSTGK  540

Query  814   PEIEAALFLDWMRLEPQSMVWLP----VLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
             P IEA+ FL+W+ LEPQSMVWL     VLHRV  AE  KHQ KC+IC++CPI GFRYRSL
Sbjct  541   PVIEASQFLEWVNLEPQSMVWLAVLHRVLHRVTIAEQVKHQTKCSICRQCPIKGFRYRSL  720

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKH  929
             K FN DICQ+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR+K+YF+KH
Sbjct  721   KQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFRSKQYFSKH  900

Query  930   PRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPN  989
             P+ GYLPVQ+VLE D  ETPASSP L H DTHSRIEH+ASRLAEME+ N S+ NDS+SP+
Sbjct  901   PQRGYLPVQSVLESDCSETPASSPMLPHADTHSRIEHFASRLAEMESQNCSFFNDSLSPD  1080

Query  990   ESIDDEHLLIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILADLEEENRN  1046
             +SID++  L++H        SP++  R PA   Q   S+ +E +GELE+ILA LE+ENR 
Sbjct  1081  DSIDEDQYLLRH-------SSPITD-REPAFGQQAPCSMATESKGELEKILAHLEDENRI  1236

Query  1047  LQAEYDRLKQQHEHKGLSP--LPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ  1104
             LQ E  RLK QHE    +P  +    E  P      R+ EL+AEA++LRQHK RLE RMQ
Sbjct  1237  LQGELRRLKWQHEEAAEAPTLVEGSAEATPDH----RNEELLAEARILRQHKSRLETRMQ  1404

Query  1105  ILEDHNKQ  1112
             ILEDHNKQ
Sbjct  1405  ILEDHNKQ  1428


>ref|XM_001900989.1| Brugia malayi Zinc finger, ZZ type family protein partial mRNA
Length=4851

 Score =  623 bits (1607),  Expect = 2e-175, Method: Compositional matrix adjust.
 Identities = 400/1222 (32%), Positives = 642/1222 (52%), Gaps = 110/1222 (9%)
 Frame = +1

Query  38    VMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERI  97
             V + D E I   +I+ +A +  L+ R   L  ++  +QN            ++ +R E +
Sbjct  1360  VDLADSESIRNAVIQMQAFIDQLKMRYLDLIRILDESQN-----------KVVRERSEVM  1506

Query  98    QNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKL-ESWKEGPYTVDAI  156
               + + +    Q R+  L +ML++S  W + ++     L   + ++ +  K     +  +
Sbjct  1507  TVECNRILGECQRRKMTLTKMLEESRAWDKLRKSLSTWLANVQERVADGSKVDAADLQTL  1686

Query  157   QKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  216
             +++++E + +A+   + +  +D  N+ +  LL +Y AD+   +      +NA W   +  
Sbjct  1687  KQELSEIQGIAEIAGEMKFKMDELNECSNALLDNYRADEGHNLSHTISRLNALWSKFNDN  1866

Query  217   VSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMK  276
             V  R A LE   R    F   LE+   W+   E +   L + T   ++L+DS   K+ ++
Sbjct  1867  VRIRRAVLEAALRARSDFYSSLEQLEEWMNSVEMSLVELNEMTINTQMLKDSVKRKKWIE  2046

Query  277   QWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNI  336
               + ++ ++ AH DV  ++++   ++   +E   +   L+ RL +++ +W  L   +  I
Sbjct  2047  DEKSIRADMNAHKDVIGSVEDMGAQLTCRVEDLKEREHLKERLSHIDIRWRHLVGLADAI  2226

Query  337   RSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELK  396
             R+ L  + ++W++L   L E L W + +   L  + P+GG    VQ+Q    +  + E+K
Sbjct  2227  RTRLMNAQEEWEKLFTQLAENLFWAEAQSKALLEEQPVGGSLARVQEQTSFVQKLEHEMK  2406

Query  397   TKEPVIMSTLETVRIFLTEQPL--------------EGLEKLYQEPRELPPEERAQNVTR  442
              ++  +   +     +L +  L              E  +  Y E  EL      + V  
Sbjct  2407  LRQRDVDECITLAHSYLMQHDLRPRTRSTSVLSPDKENGQYFYDENAEL------RRVGI  2568

Query  443   LLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQP  502
              ++  ++ +  EW +L      W   I +   ++++L  A  E  L L   E      +P
Sbjct  2569  QIKSDSDRLVQEWNELREQLNAWAYIIHDANAKMEKLASAIAECQLALSNMEERMEQLRP  2748

Query  503   VGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNT  562
             + +L ++ L   +++ + L+  +A  +  V   ND + QL    I+LS    + L+ +N 
Sbjct  2749  IEELRLEELTAAVDESEQLKEYLARTRIYVDDANDWSGQLLASDIELSSEPSAQLKSIND  2928

Query  563   RWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAIS-PNKVPYYINHETQTT  621
             R   L+  +  R   L  A  DFGP+SQHFL  SVQ PW+RA+S  N++PYYINHET+ T
Sbjct  2929  RITKLKSDLRIRTAALERAMTDFGPSSQHFLRDSVQAPWQRAVSTSNQLPYYINHETEVT  3108

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
              WDHP M E+ + L   N V+FSAYRTAMKLR +QK LCLDLL+L     +L   N    
Sbjct  3109  QWDHPAMVEIMEELTTFNQVKFSAYRTAMKLRAIQKRLCLDLLTLEDIDLSLQALNSMLG  3288

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLV-NVPLCVDMCLNWLLNVYDTGRTGRIRVLSFK  740
             +Q + +   + CL  +++  ++++  L+ ++PL VD+ LN++LNVYD  R   +R+ SF+
Sbjct  3289  EQCLSMKDAVMCLVPLFETAQEKYPKLIHSIPLAVDLLLNFVLNVYDPARDCIMRIFSFR  3468

Query  741   TGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIE  800
               + +LC ++LEDKYRYL++ +A++ G  DQ++L LLL+D I IPR  GE A+FGGSN+E
Sbjct  3469  VLLATLCNSNLEDKYRYLYQLIANNEGV-DQKKLALLLYDIIHIPRFFGEAAAFGGSNVE  3645

Query  801   PSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECP  860
             PSVRSCF+ A     I    FL+W++ EPQS+VWLPV+HR+A+AE AKHQAKCN+CK  P
Sbjct  3646  PSVRSCFETAKYPRLISVDEFLNWLKKEPQSIVWLPVMHRLASAEFAKHQAKCNVCKMFP  3825

Query  861   IIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKF  920
             IIG RYR L+ FN D+CQ+CFFS R+AK HK+ +P+ EYC PTTSGEDVRDF  +++NK 
Sbjct  3826  IIGLRYRCLRCFNVDVCQNCFFSQRLAKNHKLSHPIQEYCLPTTSGEDVRDFGLIVRNKL  4005

Query  921   RTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDD-THSRIEHYASRLAEMENSNG  979
             R+K       R+GYLPVQTV EG  +ET   +P     +  H+RI+  A RL   +  NG
Sbjct  4006  RSK----SKTRIGYLPVQTVDEGPPLETGNVTPANPFTEPVHNRIQLCARRLWRAQGENG  4173

Query  980   SYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILAD  1039
             + +  S    E +                   +++ +SP Q+L  +E   + EL+++L  
Sbjct  4174  TPIPASNDTGEEM----------------RMSMTELKSPLQLLSQVEQMHKEELDQVLHK  4305

Query  1040  LEEENRNLQAEYDRLKQQHEHKGLSP----------LPSPPEMMPTSPQSPR-----DAE  1084
             L+ ENR L+ E +R ++     G +P            S  + M T    P      D +
Sbjct  4306  LQHENRELKKEIERRRKLGNAVGSTPNLTRGSNAAMSRSVTDNMGTGRSVPSLSSSGDDQ  4485

Query  1085  LIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTS  1144
             L+ EA LLRQHK RLE R +ILE+ N+QLE+QL RLR ++ Q Q     N          
Sbjct  4486  LLREAYLLRQHKERLEQRSRILEEQNRQLETQLARLRTVIAQQQNAGSEN----------  4635

Query  1145  LQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGS  1204
              + S   +P        ++S++  EED          G+E            +R + + S
Sbjct  4636  -KESGPEEP--------ESSEASAEED---------EGIE----------YDTRPNRMNS  4731

Query  1205  LFHMADDLGRAMES-LVSVMTD  1225
             L    D LGRAM+S +VSV+ D
Sbjct  4732  LIASVDQLGRAMQSFVVSVVND  4797


>emb|X99738.1| Pectinidae sp. mRNA for dystrophin-like protein
Length=1431

 Score =  621 bits (1602),  Expect = 7e-175, Method: Compositional matrix adjust.
 Identities = 304/490 (62%), Positives = 390/490 (79%), Gaps = 20/490 (4%)
 Frame = +1

Query  625   HPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQ  683
             HP MT+L Q+LADLNN+RF+AYRTAMKLR LQK L LDLL+++ A +A D HNL+ +ND 
Sbjct  1     HPMMTDLMQALADLNNIRFAAYRTAMKLRMLQKKLRLDLLAINVAVEAFDHHNLRGRNDS  180

Query  684   PMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGI  743
              M+++++INCL+T+YD +  EH +LVNVPLCVD+ LNW+LNVYD  R+G++RVLS K GI
Sbjct  181   LMNVIEMINCLSTMYDNVSVEHPDLVNVPLCVDLVLNWVLNVYDIARSGKVRVLSLKVGI  360

Query  744   ISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSV  803
             I +C  HL+DKYR+LF+ +A + GF DQRRLGLLLHDS+Q+PRQLGEVASFGGSNIEPSV
Sbjct  361   ILMCNGHLDDKYRFLFRLIADTNGFSDQRRLGLLLHDSMQVPRQLGEVASFGGSNIEPSV  540

Query  804   RSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIG  863
             RSCF+ AN +PEI+A  FL+W+++EPQS+VWLPVLHR+AA+ETAKHQAKCNICKE PI+G
Sbjct  541   RSCFEKANGRPEIQATHFLEWLKMEPQSLVWLPVLHRLAASETAKHQAKCNICKEFPIVG  720

Query  864   FRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTK  923
             FRYR L+ FN+D+CQ+CFFSGR AK H++ +PM EYCT TTSGEDVRDF K+L+NKF+TK
Sbjct  721   FRYRCLRCFNFDVCQNCFFSGRKAKTHELSHPMQEYCTATTSGEDVRDFTKMLRNKFKTK  900

Query  924   RYFAKHPRMGYLPVQTVLEGDNMETPASSPQ--LSHDDTHSRIEHYASRLAEMENSNGSY  981
             ++F KHPR+G+LPVQTVLEGD +E+P+ SPQ  +S  D HSR+E YA+RLAE+E    S 
Sbjct  901   KHFKKHPRLGFLPVQTVLEGDVLESPSPSPQHSISSQDMHSRLELYANRLAEVEQRQASS  1080

Query  982   LNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLE  1041
               DS       DDEH LI  YCQSLN ++  +  +SP QI+++++S+++ ELE ++ DLE
Sbjct  1081  TPDS-------DDEHNLIAQYCQSLNGNTSHTL-KSPMQIMMAVDSDQKSELEAMIKDLE  1236

Query  1042  EENRNLQAEYDRLKQQHEHK----GLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKG  1097
             EEN+ LQ EYDRLKQ +E +    GL  +         +     DAE+IAEAKLLRQHKG
Sbjct  1237  EENKTLQQEYDRLKQANELRENGNGLEEVDD-----DNNSNVDMDAEMIAEAKLLRQHKG  1401

Query  1098  RLEARMQILE  1107
             RLE+RM+ILE
Sbjct  1402  RLESRMKILE  1431


>dbj|AK173373.1| Ciona intestinalis cDNA, clone:cicl022e20, full insert sequence
Length=2819

 Score =  607 bits (1566),  Expect = 1e-170, Method: Compositional matrix adjust.
 Identities = 337/825 (40%), Positives = 497/825 (60%), Gaps = 59/825 (7%)
 Frame = +1

Query  345   DQWKRLHLSLQELLVWLQLKDDELSR-QAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIM  403
             +QW+ +   L+ L+ WL++K+++ ++       D  A+ +    H     EL+ K  VI 
Sbjct  28    EQWEDIASILEGLVDWLKVKNEDTNKIMMQCVADAEALTQFRSQHEILDGELEAKCAVID  207

Query  404   STLETVRIFLTEQPLEGLEKLYQEPRELPPEE-RAQNVTRLLRKQAEEVNTEWEKLNLHS  462
              +L+ V   + +         +QE  E P +  R   + R+    A E+   W+     S
Sbjct  208   RSLKAVDAIVIQ---------HQEQAEYPDKYVRPMQLARI-STLASELREVWKVTQKKS  357

Query  463   ADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKAL-  521
                +  I++ L  ++EL     +  L L+  E  K  W  VG+L I++LQ H++ +K   
Sbjct  358   VQLKLHINKLLPAVEELNLLLRKCYLMLQNIERTKEDWVGVGELPIEALQVHIKNMKLFQ  537

Query  522   RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEA  581
             +  + P+  N+  +         + +Q +P     ++++  RWK++QV   +R +QL +A
Sbjct  538   KNYMDPIAVNMEKLKSAILYFHEMKMQFTPDTKKKMDEVEMRWKVMQVYCSERTKQLLDA  717

Query  582   HRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNV  641
              RDFGP SQ FL++SV+G WERA++ NKVPYYINH++++T WDHPKM EL +S+ DLN+V
Sbjct  718   ARDFGPNSQLFLTSSVEGAWERAVAENKVPYYINHKSKSTSWDHPKMAELMESMLDLNDV  897

Query  642   RFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN-DQP-----MDILQIINCLT  695
             RF+AYRT+MKL+RLQKALCLDLL+L  A DA  QH L  + D P     +++L II CLT
Sbjct  898   RFTAYRTSMKLQRLQKALCLDLLNLDTAVDAFTQHKLNISIDNPHVKDDVNVLDIITCLT  1077

Query  696   TIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKY  755
             TIYD LE+EH  LVNVPLCVDMCLNWLLNVYDT R+  I   SF TGI S+C + +E+KY
Sbjct  1078  TIYDALEREHKTLVNVPLCVDMCLNWLLNVYDTKRSSTISTRSFITGITSMCNSPIEEKY  1257

Query  756   RYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPE  815
             +Y+F+Q+    GF D+ +LG L+ D + IP+QLGE  +FGG N   SV SCFQ    +PE
Sbjct  1258  KYVFQQIGMPAGFTDRVKLGDLIKDFMLIPKQLGESEAFGGCNPHASVCSCFQLVGRRPE  1437

Query  816   IEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYD  875
             I+AA F+DWM+LEPQS+VWLPVLHR+ +AE   H A+C++C+ECPI+GFRYRSL+HF +D
Sbjct  1438  IDAAQFIDWMKLEPQSLVWLPVLHRLISAENVSHPARCSVCRECPIVGFRYRSLRHFKHD  1617

Query  876   ICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYL  935
             ICQSCFFSGRVAK +K  YP+VEYCTPTTS E++RDF K+LKNK R K   +K  R+GYL
Sbjct  1618  ICQSCFFSGRVAKNNKFCYPIVEYCTPTTSTENIRDFTKILKNKLRNKSRSSK--RIGYL  1791

Query  936   PVQTVLEGDNMETP-----------ASSPQLSH--DDTHSRIEHYASRLAEMENSNGSYL  982
             PV+T    D+ E P            S  Q +   ++TH +IE YA  LA++++  G   
Sbjct  1792  PVKT----DDKEDPNDDGTNDVIDGGSDDQTNGGANETHEKIEEYARILADLDDETG---  1950

Query  983   NDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEE  1042
                + P   +D+E   I  YC +L +D   +       I  S  S  R +L      ++E
Sbjct  1951  ---VQP--PLDEEQEYILEYCGALTEDKSPTIFTHQEDIFSSKAS--RSDLPSP-PRIKE  2106

Query  1043  ENRNLQ-AEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEA  1101
              N  +  ++   + +QH   G  P          S +     +L+ EAK+L+ H  R++ 
Sbjct  2107  VNVAIHDSKPYSVAKQHNDAGNQP--------HVSSRLSNGPDLMIEAKILQHHSSRIDT  2262

Query  1102  RMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTV-SSPSTSL  1145
             +M++LE+HN+ +++QL  L+ L+   +  ++ + + +  SPS  +
Sbjct  2263  QMKMLENHNESIKNQLQELKMLMNDSETSSEHSMSHIFESPSVHI  2397


>dbj|AK222319.1| Ciona intestinalis cDNA, clone:cibd066b03, full insert sequence
Length=2811

 Score =  606 bits (1563),  Expect = 2e-170, Method: Compositional matrix adjust.
 Identities = 339/835 (40%), Positives = 499/835 (59%), Gaps = 59/835 (7%)
 Frame = +3

Query  335   NIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSR-QAPIGGDFPAVQKQNDVHRAFKR  393
             + R+   +  +QW+ +   L+ L+ WL++K+++ ++       D  A+ +    H     
Sbjct  3     SCRATFLSMMEQWEDIASILEGLVDWLKVKNEDTNKIMMQCVADAEALTQFRSQHEILDG  182

Query  394   ELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEE-RAQNVTRLLRKQAEEVN  452
             EL+ K  VI  +L+ V   + +         +QE  E P +  R   + R+    A E+ 
Sbjct  183   ELEAKCAVIDRSLKAVDAIVIQ---------HQEQAEYPDKYVRPMQLARI-STLASELR  332

Query  453   TEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQ  512
               W+     S   +  I++ L  ++EL     +  L L+  E  K  W  VG+L I++LQ
Sbjct  333   EVWKVTQKKSVQLKLHINKLLPAVEELNLLLRKCYLMLQNIERTKEDWVGVGELPIEALQ  512

Query  513   DHLEKVKAL-RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAV  571
              H++ +K   +  + P+  N+  +         + +Q +P     ++++  RWK++QV  
Sbjct  513   VHIKNMKLFQKNYMDPIAVNMEKLKSAILYFHEMKMQFTPDTKKKMDEVEMRWKVMQVYC  692

Query  572   EDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTEL  631
              +R +QL +A RDFGP SQ FL++SV+G WERA++ NKVPYYINH++++T WDHPKM EL
Sbjct  693   SERTKQLLDAARDFGPNSQLFLTSSVEGAWERAVAENKVPYYINHKSKSTSWDHPKMAEL  872

Query  632   YQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN-DQP-----M  685
              +S+ DLN+VRF+AYRT+MKL+RLQKALCLDLL+L  A DA  QH L  + D P     +
Sbjct  873   MESMLDLNDVRFTAYRTSMKLQRLQKALCLDLLNLDTAVDAFTQHKLNISIDNPHVKDDV  1052

Query  686   DILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIIS  745
             ++L +I CLTTIYD LE+EH  LVNVPLCVDMCLNWLLNVYDT R+  I   SF TGI S
Sbjct  1053  NVLDMITCLTTIYDALEREHKTLVNVPLCVDMCLNWLLNVYDTKRSSTISTRSFITGITS  1232

Query  746   LCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRS  805
             +C + +E+KY+Y+F+Q+    GF D+ +LG L+ D + IP+QLGE  +FGG N   SV S
Sbjct  1233  MCNSPIEEKYKYVFQQIGMPAGFTDRVKLGDLIKDFMLIPKQLGESEAFGGCNPHASVCS  1412

Query  806   CFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFR  865
             CFQ    +PEI+AA F+DWM+LEPQS+VWLPVLHR+ +AE   H A+C++C+ECPI+GFR
Sbjct  1413  CFQLVGRRPEIDAAQFIDWMKLEPQSLVWLPVLHRLISAENVSHPARCSVCRECPIVGFR  1592

Query  866   YRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRY  925
             YRSL+HF +DICQSCFFSGRVAK +K  YP+VEYCTPTTS E++RDF K+LKNK R K  
Sbjct  1593  YRSLRHFKHDICQSCFFSGRVAKNNKFCYPIVEYCTPTTSTENIRDFTKILKNKLRNKSR  1772

Query  926   FAKHPRMGYLPVQTVLEGDNMETP-----------ASSPQLSH--DDTHSRIEHYASRLA  972
              AK  R+GYLPV+T    D+ E P            S  Q +   ++TH +IE YA  LA
Sbjct  1773  SAK--RIGYLPVKT----DDKEDPNDDVTNDVIDGGSDDQTNGGANETHEKIEEYARILA  1934

Query  973   EMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGE  1032
             ++++  G      + P   +D+E   I  YC +L +D   +       I  S  S  R +
Sbjct  1935  DLDDETG------VQP--PLDEEQECILEYCGALTEDKSPTIFTHQEDIFSSKAS--RSD  2084

Query  1033  LERILADLEEENRNLQAEYDRL-KQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKL  1091
             L      ++E N  +      L  +QH   G  P          S +     +L+ EAK+
Sbjct  2085  LPSP-PRIKEVNVAIHDSKPYLVAKQHIDAGNQP--------HVSSRLSNGPDLMIEAKI  2237

Query  1092  LRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTV-SSPSTSL  1145
             L+ H  R++ +M++LE+HN+ +++QL  L+ L+   +  ++ + + +  SPS  +
Sbjct  2238  LQHHSSRIDTQMKMLENHNESIKNQLQELKMLMNDSETSSEHSMSHIFESPSVHI  2402


>ref|XM_002129566.1| PREDICTED: Ciona intestinalis similar to dystrophin (LOC100183361), 
mRNA
Length=2802

 Score =  605 bits (1560),  Expect = 5e-170, Method: Compositional matrix adjust.
 Identities = 334/825 (40%), Positives = 494/825 (59%), Gaps = 59/825 (7%)
 Frame = +3

Query  345   DQWKRLHLSLQELLVWLQLKDDELSR-QAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIM  403
             +QW+ +   L+ L+ WL++K+++ ++       D  A+ +    H     EL+ K  VI 
Sbjct  39    EQWEDIASILEGLIDWLKVKNEDTNKIMMQCVADAEALTQFRSQHEILDGELEAKCAVID  218

Query  404   STLETVRIFLTEQPLEGLEKLYQEPRELPPEE-RAQNVTRLLRKQAEEVNTEWEKLNLHS  462
              +L+ V   + +         +QE  E P +  R   + R+    A E+   W+     S
Sbjct  219   RSLKAVDAIVIQ---------HQEQAEYPDKYVRPMQLARI-STLASELREVWKVTQKKS  368

Query  463   ADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKAL-  521
                +  I++ L  ++EL     +  + L+  E  K  W  VG+L I++LQ H++ +K   
Sbjct  369   VQLKLHINKLLPAVEELNLLLRKCYIMLQNIERTKEDWVGVGELPIEALQVHIKNMKLFQ  548

Query  522   RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEA  581
             +  + P+  N+  +         + +Q +P     ++++  RWK++QV   +R +QL +A
Sbjct  549   KNYMDPIAVNMEKLKSAILYFHEMKMQFTPDTKKKMDEVEMRWKVMQVYCSERTKQLLDA  728

Query  582   HRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNV  641
              RDFGP SQ FL++SV+G WERA++ NKVPYYINH++++T WDHPKM EL +S+ DLN+V
Sbjct  729   ARDFGPNSQLFLTSSVEGAWERAVAENKVPYYINHKSKSTSWDHPKMAELMESMLDLNDV  908

Query  642   RFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN-DQP-----MDILQIINCLT  695
             RF+AYRT+MKL+RLQKALCLDLL+L  A DA  QH L  + D P     +++L +I CLT
Sbjct  909   RFTAYRTSMKLQRLQKALCLDLLNLDTAVDAFTQHKLNISIDNPHVKDDVNVLDMITCLT  1088

Query  696   TIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKY  755
             TIYD LE+EH  LVNVPLCVDMCLNWLLNVYDT R+  I   SF TGI S+C + +E+KY
Sbjct  1089  TIYDALEREHKTLVNVPLCVDMCLNWLLNVYDTKRSSTISTRSFITGITSMCNSPIEEKY  1268

Query  756   RYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPE  815
             +Y+F+Q+    GF D+ +LG L+ D + IP+QLGE  +FGG N   SV SCFQ    +PE
Sbjct  1269  KYVFQQIGMPAGFTDRVKLGDLIKDFMLIPKQLGESEAFGGCNPHASVCSCFQLVGRRPE  1448

Query  816   IEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYD  875
             I+AA F+DWM+LEPQS+VWLPVLHR+ +AE   H A+C++C+ECPI+GFRYRSL+HF +D
Sbjct  1449  IDAAQFIDWMKLEPQSLVWLPVLHRLISAENVSHPARCSVCRECPIVGFRYRSLRHFKHD  1628

Query  876   ICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYL  935
             ICQSCFFSGRVAK +K  YP+VEYCTPTTS E++RDF K+LKNK R K   AK  R+GYL
Sbjct  1629  ICQSCFFSGRVAKNNKFCYPIVEYCTPTTSTENIRDFTKILKNKLRNKSRSAK--RIGYL  1802

Query  936   PVQTVLEGDNMETPASS-------------PQLSHDDTHSRIEHYASRLAEMENSNGSYL  982
             PV+T    D+ E P                     ++TH +IE YA  LA++++  G   
Sbjct  1803  PVKT----DDKEDPNDDGTNDVIDGGIDDQTNGGANETHEKIEEYARILADLDDETG---  1961

Query  983   NDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEE  1042
                + P   +D+E   I  YC +L +D   +       I  S  S  R +L      ++E
Sbjct  1962  ---VQP--PLDEEQECILEYCGALTEDKSPTIFTHQEDIFSSKAS--RSDLPSP-PRIKE  2117

Query  1043  ENRNLQ-AEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEA  1101
              N  +  ++   + +QH   G  P          S +     +L+ EAK+L+ H  R++ 
Sbjct  2118  VNVAIHDSKPYSVAKQHNDAGNQP--------HVSSRLSNGPDLMIEAKILQHHSSRIDT  2273

Query  1102  RMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTV-SSPSTSL  1145
             +M++LE+HN+ +++QL  L+ L+   +  ++ + + +  SPS  +
Sbjct  2274  QMKMLENHNESIKNQLQELKMLMNDSETSSEHSMSHIFESPSVHI  2408


>ref|XM_695636.3| PREDICTED: Danio rerio similar to putative utrophin (LOC571987), 
mRNA
Length=1395

 Score =  581 bits (1497),  Expect = 1e-162, Method: Compositional matrix adjust.
 Identities = 286/515 (55%), Positives = 359/515 (69%), Gaps = 54/515 (10%)
 Frame = +1

Query  434   EERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQA  493
             EE+ + +   ++ Q  EV   WE+ ++ +  +Q++ID  L +L+ LQ+A ++L+L L + 
Sbjct  10    EEKIRRLAEAVQDQVCEVQQIWEQFSVQTVSFQQQIDWALGKLRNLQDAMNQLELGLVEM  189

Query  494   EVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYN  553
             E    +W      +++ + D +E                         + TLG Q  P  
Sbjct  190   E--NENWPSEEQGMVNCVLDSVEN------------------------MGTLGSQ-HP--  282

Query  554   LSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYY  613
                 +   T  +LL                     S  FLS SVQ PW+RA+  N VPYY
Sbjct  283   ----QSSQTERRLL---------------------SHDFLSDSVQFPWQRAVFHNDVPYY  387

Query  614   INHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDAL  673
             INHE Q+T WDHP+MT+L+QS+ADL++VRFSAYRTAMK RRLQKALCLDLL LS A    
Sbjct  388   INHEQQSTSWDHPEMTQLFQSMADLSHVRFSAYRTAMKSRRLQKALCLDLLELSIAQSVF  567

Query  674   DQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGR  733
             DQHNL  N Q ++I  IINCL TIY  L+Q H +LVNVPLCVDMCLNWLL VYD+GR+G+
Sbjct  568   DQHNLTHNGQLLEIPGIINCLCTIYCELQQVHPDLVNVPLCVDMCLNWLLKVYDSGRSGK  747

Query  734   IRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVAS  793
             ++VLS K G+ SL K  ++DKY+YLF QVAS+ G C QR+L LLLH+SIQIP QLGE A+
Sbjct  748   VQVLSMKIGLFSLSKGPIKDKYKYLFAQVASAAGVCTQRQLELLLHNSIQIPHQLGEAAA  927

Query  794   FGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKC  853
             FGGSN+EPSVRSCFQ+   +  IE   F+DWM LEPQSMVWLPVLHRV AAETAKHQAKC
Sbjct  928   FGGSNMEPSVRSCFQYVGRQDVIELQQFVDWMHLEPQSMVWLPVLHRVTAAETAKHQAKC  1107

Query  854   NICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFA  913
             NICKECP++GFRYRSLKHFNY++CQ+CFFSGR++K H +  PMVEYCTPTTSGEDVRDF 
Sbjct  1108  NICKECPMVGFRYRSLKHFNYNVCQTCFFSGRISKDHHLSDPMVEYCTPTTSGEDVRDFT  1287

Query  914   KVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
             KVLKNKFR+K+YF KHPR+GYLPVQT+LE ++ +T
Sbjct  1288  KVLKNKFRSKKYFTKHPRLGYLPVQTILEEEHSDT  1392


>ref|XR_026973.1| PREDICTED: Gallus gallus similar to dystrophin-related protein 
2 A-form splice (LOC422193), mRNA
Length=2953

 Score =  570 bits (1468),  Expect = 2e-159, Method: Compositional matrix adjust.
 Identities = 266/495 (53%), Positives = 358/495 (72%), Gaps = 18/495 (3%)
 Frame = +1

Query  410   RIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKI  469
             R FL++ P E L +     ++  P  R QN++R + KQA   +  WEKL     D  R I
Sbjct  787   RPFLSQHPFEELGEPTFRKQDASPRHRIQNISRFVWKQANVASELWEKLTARCVDQHRHI  966

Query  470   DETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLK  529
             + TLE+L E++ A +EL   L QAE ++ +W+P+GDL IDSL +H++  K  + E++P+K
Sbjct  967   ERTLEQLLEIKGAMEELSTALDQAESVRETWEPIGDLFIDSLPEHIQSTKLFKEELSPMK  1146

Query  530   ENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFG--P  587
             + V  VNDLA QL    + LS  N  +LE +NTRWK LQV          E   D G  P
Sbjct  1147  DGVKVVNDLAHQLAISDVHLSMENSRSLEQINTRWKQLQV-------M*GEVGSDGGHLP  1305

Query  588   ASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYR  647
             A    +S  +   W R      V +   H+ QTTCWDHPKMTELYQ+LADLNN++FSAYR
Sbjct  1306  APVALISVRI---WIR------VGWRYGHQAQTTCWDHPKMTELYQTLADLNNIKFSAYR  1458

Query  648   TAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNN  707
             TAMKLRR+QKAL LD+++L+ A +  ++H+L+ +D+ MD++++I+CLT++Y+RLE+E   
Sbjct  1459  TAMKLRRVQKALRLDMVTLATALEIFNEHDLQPSDRAMDVVEVIHCLTSLYERLEEERGI  1638

Query  708   LVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTG  767
             LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKTGI  LC   +++K++YLF QVA++ G
Sbjct  1639  LVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKTGIACLCGTEVKEKFQYLFSQVANAGG  1818

Query  768   FCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRL  827
              CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EPS+RSCF+F++ KP IEAA FL+W  L
Sbjct  1819  LCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEPSIRSCFRFSHGKPAIEAAQFLEWANL  1998

Query  828   EPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVA  887
             EPQSMVWL VLHRV  AE  KHQ KC++C++CPI GFRYRSLK FN DICQ+CF +GR +
Sbjct  1999  EPQSMVWLAVLHRVTMAEQVKHQTKCSVCRQCPIKGFRYRSLKQFNVDICQTCFLTGRAS  2178

Query  888   KGHKMHYPMVEYCTP  902
             KG+K+HYP++EY TP
Sbjct  2179  KGNKLHYPIMEYYTP  2223


 Score =  160 bits (405),  Expect = 4e-36, Method: Compositional matrix adjust.
 Identities = 102/214 (47%), Positives = 138/214 (64%), Gaps = 14/214 (6%)
 Frame = +1

Query  993   DDEHLLIQHYCQSLNQDSPLS--QPRSPAQILISLESEERGELERILADLEEENRNLQAE  1050
             DD+  L++H        SP++  +P    Q+  SL  +++GELERILA LE+ENR LQ E
Sbjct  2269  DDDQYLLRH-------SSPITDREPAGSQQVPGSLPMDDKGELERILAHLEDENRILQGE  2427

Query  1051  YDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHN  1110
               RLK QH+    SP  +     P S Q PR+ EL+AEA++LRQHK RLE RMQILEDHN
Sbjct  2428  LRRLKWQHDEAVESPTLATGS--PESVQDPRNEELLAEARILRQHKSRLETRMQILEDHN  2601

Query  1111  KQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEE  1170
             KQLESQLHRLR+LL QP AE+  NG+  SS ++S  +S+  QP   R     T D+   +
Sbjct  2602  KQLESQLHRLRELLLQPPAESNGNGSAASSLASSPHQSEGGQP---RDKEHDTPDTEAAD  2772

Query  1171  DLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGS  1204
             ++ +  Q+ S  LE++ME+L ++FP+SRG  V S
Sbjct  2773  EVEAKTQEVSVCLEDIMEKLRSAFPNSRGTRVKS  2874


 Score = 91.7 bits (226),  Expect = 2e-15, Method: Compositional matrix adjust.
 Identities = 47/113 (41%), Positives = 72/113 (63%), Gaps = 1/113 (0%)
 Frame = +3

Query  322  MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
            MN  W+E++KKS ++R+ LEA SD   +L + LQE++ WL  KD+ELS Q P+ GD   V
Sbjct  522  MNLCWNEIKKKSHSLRARLEAFSDHSGKLQVPLQEIIDWLGQKDEELSAQLPLRGDVLLV  701

Query  382  QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKL-YQEPRELPP  433
            Q++ + H AF  E+K++ P I S LE+ + F    P+ G  +  +Q+ R +PP
Sbjct  702  QQEKETHAAFMEEVKSRGPYIYSVLESAQAFPLPAPI*GTGRANFQKARCVPP  860


>emb|AJ012469.1| Caenorhabditis elegans mRNA for DYS-1 protein, partial
Length=11025

 Score =  561 bits (1447),  Expect = 6e-157, Method: Compositional matrix adjust.
 Identities = 380/1209 (31%), Positives = 618/1209 (51%), Gaps = 112/1209 (9%)
 Frame = +1

Query  62     QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKD  121
              Q R Q  +L+T    ++    N E R +I ++I  I  Q               NE  ++
Sbjct  7606   QVRQQAAQLLT---EMRRTIENCEKRCLILNQISDIARQ---------------NEASRN  7731

Query  122    STQ-WLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
                + WL++   A  V+G+ R +         + + +++++   +++ + L + +  +   
Sbjct  7732   EMELWLKS---ASDVIGERRVE-------ELSEEVVRQELQVLERVVEQLTERKDKMAEI  7881

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              N  A K++  Y+ D+   +  +   +N SW   +  +  R A LE + R  + F   L +
Sbjct  7882   NSQANKIVDTYTKDEAHNLSHLLSRLNMSWTKFNDNIRIRRAVLEASLRSXRDFHSALSE  8061

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              F  WL+  E   + L   T   + ++D+   K   + ++ L  E+ AH DV  ++++  +
Sbjct  8062   FEKWLSRQEDNCSKLSADTSNHQAIKDTSKRKNWTQSFKTLNAELNAHEDVMKSVEKMGK  8241

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
               +  SLE  ++ V L +R+     +W+ LRK +  I   LE +  +W++L   L +LL W
Sbjct  8242   MLAESLESGNEKVELLKRVGETTRRWTALRKTTNEIGERLEKAEQEWEKLSDGLADLLSW  8421

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              ++ K   +  + P GG   AV +Q    +  +RE+++K     ST+E    FL +  L  
Sbjct  8422   VEAKKQAIMDEQPTGGSLSAVMQQASFVKGLQREIESKTANYKSTVEEAHSFLMQHDLRP  8601

Query  421    -------LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                     L+  Y++      E+R + +   +    E +   W +L +    W + +   +
Sbjct  8602   KLHSPHVLDDDYEKEELANLEQRRRGLE--INANCERLKKNWAELGIEVESWDKLVQHAM  8775

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVS  533
              +RLQEL+    E  L L  +E    + + V  + ++ L+   E+   +   I  ++  V 
Sbjct  8776   QRLQELERNLAECQLHLTSSENEIETMKAVEKIHLEDLKIAREETDQISKRIDEVRLFVD  8955

Query  534    HVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFL  593
               VND A +L    ++L  +    +E +N R+  L+ A+  R   +  A  DFGP S+HFL
Sbjct  8956   DVNDAAARLLAEDLKLDEHAKGQIEHVNKRYSTLKRAIRIRQAAVRNAASDFGPTSEHFL  9135

Query  594    STSVQGPWERAIS-PNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKL  652
              + SV  PW+RAIS  N +PYYI   ++ T W+HP   E+ + L+  N V+F AYRTAMKL
Sbjct  9136   NQSVTLPWQRAISKSNLLPYYIEQTSEKTQWEHPVWVEIVKELSQFNRVKFLAYRTAMKL  9315

Query  653    RRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLV-NV  711
              R LQK LCLDL+ L+    A  +      ++   +  ++  L  +Y+ L  ++ N V +V
Sbjct  9316   RALQKRLCLDLVDLTLLEKAFVRLKGLSAEECPGLEGMVCALLPMYEALHAKYPNQVQSV  9495

Query  712    PLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQ  771
               L VD+C+N+LLN++D  R G +RVLSFK  +I      LE+KYRYLFK V S  G   Q
Sbjct  9496   SLAVDICINFLLNLFDQSRDGIMRVLSFKIAMIVFSNIPLEEKYRYLFKLV-SQDGHATQ  9672

Query  772    RRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQS  831
              +++ LLL+D I IPR +GE A+FGG+N+EPSVRSCF+     P I    F+DW++ EPQS
Sbjct  9673   KQIALLLYDLIHIPRLVGESAAFGGTNVEPSVRSCFETVRLAPTISEGAFIDWVKKEPQS  9852

Query  832    MVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHK  891
              +VWL V+HR+  +E+ KH +KCN+CK  PIIG RYR L  FN D+CQ+CFFS R AK H+
Sbjct  9853   IVWLAVMHRLVISESTKHASKCNVCKMFPIIGIRYRCLTCFNCDLCQNCFFSQRTAKSHR  10032

Query  892    MHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-PA  950
               ++PM EYC  TTS +D RDFAK+++NKFR     A   + GYLP+    EG  +   PA
Sbjct  10033  TNHPMQEYCEKTTSSDDARDFAKMIRNKFR-----ASKRQKGYLPIDVAEEGIPLTCPPA  10197

Query  951    SSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDS  1010
                   + +  ++      + LA++   +G               EH+             
Sbjct  10198  KVTNQATEQMNADTSQMTAHLAKLSAEHGG------------GAEHM------------E  10305

Query  1011   PLSQPRSPAQILISLESEERGELERILADLEEENRNLQA------------EYDRLKQQH  1058
              P+   +SP QI+  +E  +R E++++L  L+ EN+ L+             E DR  ++H
Sbjct  10306  PV---QSPLQIINQVEQLQRDEMDQMLHRLQFENKQLRKELEWKRGAASTMEIDRSSKRH  10476

Query  1059   EHK-------GLSPLPSPPEMMP-TSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHN  1110
              + +       G  PL +   ++   S QS  D  ++ EAK LR HK RLE R +ILE  N
Sbjct  10477  QERHQSESRGGTLPLRNGRSVVSLKSTQSQND--VMDEAKALRLHKQRLEHRSRILEQQN  10650

Query  1111   KQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEE  1170
              +QLE QL RL+++++  + +A ++       + SL R    QP       S ++ ++   
Sbjct  10651  EQLEMQLQRLKKVIDAQKQQAPLS-------TNSLLRGSHHQPWSPERARSGSASTLDRG  10809

Query  1171   DLLSP-----PQDTSTGLEEVMEQLNNSFPSSRGHNVG---SLFHMADDLGRAMESL-VS  1221
               ++S       +    G E+  ++   +    RG +VG   +L    DDLG+AMESL VS
Sbjct  10810  LIVSSRHQEQAEAAGGGAEDSSDEAGGAGGGPRGSSVGQMQNLMTACDDLGKAMESLVVS  10989

Query  1222   VMTDEEGAE  1230
              V+ D +  E
Sbjct  10990  VVYDSDDEE  11016


>ref|NM_060545.5| Caenorhabditis elegans DYStrophin related family member (dys-1) 
(dys-1) mRNA, complete cds
Length=11025

 Score =  561 bits (1446),  Expect = 9e-157, Method: Compositional matrix adjust.
 Identities = 380/1209 (31%), Positives = 618/1209 (51%), Gaps = 112/1209 (9%)
 Frame = +1

Query  62     QRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKD  121
              Q R Q  +L+T    ++    N E R +I ++I  I  Q               NE  ++
Sbjct  7606   QVRQQAAQLLT---EMRRTIENCEKRCLILNQISDIARQ---------------NEASRN  7731

Query  122    STQ-WLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
                + WL++   A  V+G+ R +         + + +++++   +++ + L + +  +   
Sbjct  7732   EMELWLKS---ASDVIGERRVE-------ELSEEVVRQELQVLERVVEQLTERKDKMAEI  7881

Query  181    NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEK  240
              N  A K++  Y+ D+   +  +   +N SW   +  +  R A LE + R  + F   L +
Sbjct  7882   NSQANKIVDTYTKDEAHNLSHLLSRLNMSWTKFNDNIRIRRAVLEASLRSRRDFHSALSE  8061

Query  241    FLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQ  300
              F  WL+  E   + L   T   + ++D+   K   + ++ L  E+ AH DV  ++++  +
Sbjct  8062   FEKWLSRQEDNCSKLSADTSNHQAIKDTSKRKNWTQSFKTLNAELNAHEDVMKSVEKMGK  8241

Query  301    KILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
               +  SLE  ++ V L +R+     +W+ LRK +  I   LE +  +W++L   L +LL W
Sbjct  8242   MLAESLESGNEKVELLKRVGETTRRWTALRKTTNEIGERLEKAEQEWEKLSDGLADLLSW  8421

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              ++ K   +  + P GG   AV +Q    +  +RE+++K     ST+E    FL +  L  
Sbjct  8422   VEAKKQAIMDEQPTGGSLSAVMQQASFVKGLQREIESKTANYKSTVEEAHSFLMQHDLRP  8601

Query  421    -------LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                     L+  Y++      E+R + +   +    E +   W +L +    W + +   +
Sbjct  8602   KLHSPHVLDDDYEKEELANLEQRRRGLE--INANCERLKKNWAELGIEVESWDKLVQHAM  8775

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVS  533
              +RLQEL+    E  L L  +E    + + V  + ++ L+   E+   +   I  ++  V 
Sbjct  8776   QRLQELERNLAECQLHLTSSENEIETMKAVEKIHLEDLKIAREETDQISKRIDEVRLFVD  8955

Query  534    HVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFL  593
               VND A +L    ++L  +    +E +N R+  L+ A+  R   +  A  DFGP S+HFL
Sbjct  8956   DVNDAAARLLAEDLKLDEHAKGQIEHVNKRYSTLKRAIRIRQAAVRNAASDFGPTSEHFL  9135

Query  594    STSVQGPWERAIS-PNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKL  652
              + SV  PW+RAIS  N +PYYI   ++ T W+HP   E+ + L+  N V+F AYRTAMKL
Sbjct  9136   NQSVTLPWQRAISKSNLLPYYIEQTSEKTQWEHPVWVEIVKELSQFNRVKFLAYRTAMKL  9315

Query  653    RRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLV-NV  711
              R LQK LCLDL+ L+    A  +      ++   +  ++  L  +Y+ L  ++ N V +V
Sbjct  9316   RALQKRLCLDLVDLTLLEKAFVRLKGLSAEECPGLEGMVCALLPMYEALHAKYPNQVQSV  9495

Query  712    PLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQ  771
               L VD+C+N+LLN++D  R G +RVLSFK  +I      LE+KYRYLFK V S  G   Q
Sbjct  9496   SLAVDICINFLLNLFDQSRDGIMRVLSFKIAMIVFSNIPLEEKYRYLFKLV-SQDGHATQ  9672

Query  772    RRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQS  831
              +++ LLL+D I IPR +GE A+FGG+N+EPSVRSCF+     P I    F+DW++ EPQS
Sbjct  9673   KQIALLLYDLIHIPRLVGESAAFGGTNVEPSVRSCFETVRLAPTISEGAFIDWVKKEPQS  9852

Query  832    MVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHK  891
              +VWL V+HR+  +E+ KH +KCN+CK  PIIG RYR L  FN D+CQ+CFFS R AK H+
Sbjct  9853   IVWLAVMHRLVISESTKHASKCNVCKMFPIIGIRYRCLTCFNCDLCQNCFFSQRTAKSHR  10032

Query  892    MHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET-PA  950
               ++PM EYC  TTS +D RDFAK+++NKFR     A   + GYLP+    EG  +   PA
Sbjct  10033  TNHPMQEYCEKTTSSDDARDFAKMIRNKFR-----ASKRQKGYLPIDVAEEGIPLTCPPA  10197

Query  951    SSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDS  1010
                   + +  ++      + LA++   +G               EH+             
Sbjct  10198  KVTNQATEQMNADTSQMTAHLAKLSAEHGG------------GAEHM------------E  10305

Query  1011   PLSQPRSPAQILISLESEERGELERILADLEEENRNLQA------------EYDRLKQQH  1058
              P+   +SP QI+  +E  +R E++++L  L+ EN+ L+             E DR  ++H
Sbjct  10306  PV---QSPLQIINQVEQLQRDEMDQMLHRLQFENKQLRKELEWKRGAASTMEIDRSSKRH  10476

Query  1059   EHK-------GLSPLPSPPEMMP-TSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHN  1110
              + +       G  PL +   ++   S QS  D  ++ EAK LR HK RLE R +ILE  N
Sbjct  10477  QERHQSESRGGTLPLRNGRSVVSLKSTQSQND--VMDEAKALRLHKQRLEHRSRILEQQN  10650

Query  1111   KQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEE  1170
              +QLE QL RL+++++  + +A ++       + SL R    QP       S ++ ++   
Sbjct  10651  EQLEMQLQRLKKVIDAQKQQAPLS-------TNSLLRGSHHQPWSPERARSGSASTLDRG  10809

Query  1171   DLLSP-----PQDTSTGLEEVMEQLNNSFPSSRGHNVG---SLFHMADDLGRAMESL-VS  1221
               ++S       +    G E+  ++   +    RG +VG   +L    DDLG+AMESL VS
Sbjct  10810  LIVSSRHQEQAEAAGGGAEDSSDEAGGAGGGPRGSSVGQMQNLMTACDDLGKAMESLVVS  10989

Query  1222   VMTDEEGAE  1230
              V+ D +  E
Sbjct  10990  VVYDSDDEE  11016


>dbj|AK013510.1| Mus musculus adult male hippocampus cDNA, RIKEN full-length enriched 
library, clone:2900010C03 product:dystrophin, muscular 
dystrophy, full insert sequence
Length=2135

 Score =  540 bits (1391),  Expect = 2e-150, Method: Compositional matrix adjust.
 Identities = 251/252 (99%), Positives = 251/252 (99%), Gaps = 0/252 (0%)
 Frame = +1

Query  615  NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
             HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  142  GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  321

Query  675  QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
            QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  322  QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  501

Query  735  RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
            RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  502  RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  681

Query  795  GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
            GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  682  GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  861

Query  855  ICKECPIIGFRY  866
            ICKECPIIGFRY
Sbjct  862  ICKECPIIGFRY  897


>emb|CU688550.1| Synthetic construct Homo sapiens gateway clone IMAGE:100018376 
5' read DMD mRNA
Length=1227

 Score =  535 bits (1378),  Expect = 6e-149, Method: Compositional matrix adjust.
 Identities = 274/345 (79%), Positives = 286/345 (82%), Gaps = 10/345 (2%)
 Frame = +2

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  674
              HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD
Sbjct  35    GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALD  214

Query  675   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  734
             QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI
Sbjct  215   QHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRI  394

Query  735   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  794
             RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF
Sbjct  395   RVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASF  574

Query  795   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  854
             GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN
Sbjct  575   GGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCN  754

Query  855   ICKECPIIGFRYRSLKHF-NYDICQSCFFS-GRVAKGHKMHYPMVEYCTP--TTSGEDVR  910
             IC+ECPI     +  K        QSCFF    + K  KM         P     G+  +
Sbjct  755   ICQECPIHWI*VQESKAL*LMTSAQSCFFFWSSLQKAIKMPLSHGGNNAPPDYLRGKKFQ  934

Query  911   DFAKVL-KNKF-RTKRYFAKH-PRMGYLP-VQTVL--EGDNMETP  949
             +FA+   KNKF + K YF K  P++ +L  VQ      G  M+TP
Sbjct  935   EFAQGN*KNKFSKPKGYFGKTPPKLAFLVQVQNCF*KGGTTMKTP  1069


>ref|XM_002116057.1| Trichoplax adhaerens hypothetical protein, mRNA
Length=2508

 Score =  508 bits (1307),  Expect = 1e-140, Method: Compositional matrix adjust.
 Identities = 267/743 (35%), Positives = 419/743 (56%), Gaps = 12/743 (1%)
 Frame = +1

Query  206   INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
             IN   R  ++R+  RE  L +       F   LE  L WL   + T N    + +     
Sbjct  43    INFGLRLFNRRLKAREMRLLDAIDCFSNFNSHLENALIWLVGIDNTLNKFHSSVKTSS--  216

Query  266   EDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFK  325
              D   +K   + +Q+L+ EI+ H  +   + +   ++   L   D+  +L+ ++  +   
Sbjct  217   RDPIMIKYQEENYQNLRKEIQDHESIMSQIIKAGNRVNPDL-NEDEEKVLKDKIVKLQDD  393

Query  326   WSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQN  385
             W+ L++  ++I   +E    QW  L  +L++L  WL   +DEL+ + P+ GD  A+Q+QN
Sbjct  394   WARLQEDIIDIGVIIEEHCRQWNELQSNLRKLNEWLLQVNDELAAEEPLKGDLHALQQQN  573

Query  386   DVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLR  445
             +     +  L T +P++  TLE+  ++   Q     E  Y +  + P  E        L+
Sbjct  574   ENLLDIRSRLATHQPLVEETLESGSLYAKSQDDRTQEDQYGDIDQQPMVE--------LK  729

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGD  505
                  +   W  ++  + DWQ  +D+T+    EL     E   +L   E  + SW    D
Sbjct  730   GLLALLGDRWNSVSKRADDWQTLLDKTILEFNELTSLMREAVSQLLSCEKKRLSWVSPRD  909

Query  506   LLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWK  565
             +  ++L   L+ +K+ R  I   + N+ ++  L   +   GI L+   +    D+N RW 
Sbjct  910   INSENLSSQLQDLKSFRESIQKNRPNIENIKRLYFSIGKKGITLNRVIIDQYSDINRRWA  1089

Query  566   LLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDH  625
              L  + + R+ +L E        S H    + + PWE++++ N VPYY+NHE + T WDH
Sbjct  1090  DLTRSEQIRIDELKEFRDTTTEVSHHQSEVTSKPPWEKSLTVNNVPYYVNHEKKVTQWDH  1269

Query  626   PKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQP  684
             P+MTE+Y  L + N ++++AYRTAMKLR+LQK L L+ + L++   A     L+ +ND  
Sbjct  1270  PQMTEIYDLLVNNNFIKYAAYRTAMKLRKLQKCLFLNFIELNSLKTAFQDSGLRFKNDAY  1449

Query  685   MDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGII  744
             +DI  I   L  +Y+R+  +  +   +PL  D+ +NWLLNVYD  RTG+IR+LS + G++
Sbjct  1450  IDINDIYKLLNIVYERINNKKFSRKKIPLYKDLVVNWLLNVYDVPRTGKIRILSLRIGLV  1629

Query  745   SLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVR  804
              LC A LE+KYRY+F  +A   G  D+ RLGL LHD +QIPRQLGEVA+FGGSNIEPS+R
Sbjct  1630  ILCNAPLEEKYRYMFNLIARHDGCTDKARLGLFLHDCLQIPRQLGEVAAFGGSNIEPSIR  1809

Query  805   SCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGF  864
             SC +  N++  + +  FLDWM  EPQSMVWLPV+HR++AAE   HQ +C++CK     G 
Sbjct  1810  SCLETGNSEEFVGSVQFLDWMLAEPQSMVWLPVMHRISAAENVSHQTRCSVCKTAAFKGL  1989

Query  865   RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKR  924
             RYR L+ FN+D+CQ+CFF G   KGHK  + M EYC  +++G+D +DF K ++NK +TK 
Sbjct  1990  RYRCLECFNFDMCQACFFKGETCKGHKSSHQMQEYCLESSTGDDAKDFFKFVRNKLKTKS  2169

Query  925   YFAKHPRMGYLPVQTVLEGDNME  947
                +  ++GYLP+Q+V+EGD++E
Sbjct  2170  MRRRSRKLGYLPLQSVVEGDSVE  2238


>gb|BC060605.1| Mus musculus dystrophin related protein 2, mRNA (cDNA clone IMAGE:5719555), 
partial cds
Length=4416

 Score =  496 bits (1278),  Expect = 2e-137, Method: Compositional matrix adjust.
 Identities = 265/450 (58%), Positives = 334/450 (74%), Gaps = 20/450 (4%)
 Frame = +3

Query  758   LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIE  817
             LF QVA+S   CDQR LG LLH++IQ+PRQLGEVA+FGGSN+EPSVRSCF+F+  KP IE
Sbjct  2358  LFSQVANSGSQCDQRHLGALLHEAIQVPRQLGEVAAFGGSNVEPSVRSCFRFSTGKPVIE  2537

Query  818   AALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDIC  877
             A+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI GFRYRSLK FN DIC
Sbjct  2538  ASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPIKGFRYRSLKQFNVDIC  2717

Query  878   QSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPV  937
             Q+CF +GR +KG+K+HYP++EY TPTTS E++RDFA  LKNKFR+K+YF+KHP+ GYLPV
Sbjct  2718  QTCFLTGRASKGNKLHYPIMEYYTPTTSSENMRDFATTLKNKFRSKQYFSKHPQRGYLPV  2897

Query  938   QTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHL  997
             Q+VLE D  ETPASSP L H DTHSRIEH+ASRLAEME+ N S+ NDS+SP++SID++  
Sbjct  2898  QSVLESDCSETPASSPMLPHADTHSRIEHFASRLAEMESQNCSFFNDSLSPDDSIDEDQY  3077

Query  998   LIQHYCQSLNQDSPLSQPRSPA---QILISLESEERGELERILADLEEENRNLQAEYDRL  1054
             L++H        SP++  R PA   Q   S+ +E +GELE+ILA LE+ENR LQ E  RL
Sbjct  3078  LLRH-------SSPITD-REPAFGQQAPCSMATESKGELEKILAHLEDENRILQGELRRL  3233

Query  1055  KQQHEHKGLSP--LPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQ  1112
             K QHE    +P  +    E  P      R+ EL+AEA++LRQHK RLE RMQILEDHNKQ
Sbjct  3234  KWQHEEAAEAPTLVEGSAEATPDH----RNEELLAEARILRQHKSRLETRMQILEDHNKQ  3401

Query  1113  LESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDL  1172
             LESQL RLR+LL QP +E+  NG+  SS ++S ++S+ S P   R  G  T D+   +D+
Sbjct  3402  LESQLQRLRELLLQPPSESDGNGSAGSSLASSPRQSEGSHP---REKGQTTPDTEVADDV  3572

Query  1173  LSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
              S  QD S  LE++ME+L ++FPS R  +V
Sbjct  3573  GSKSQDVSLCLEDIMEKLRHAFPSVRSSDV  3662


 Score =  491 bits (1265),  Expect = 8e-136, Method: Compositional matrix adjust.
 Identities = 236/433 (54%), Positives = 318/433 (73%), Gaps = 0/433 (0%)
 Frame = +2

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L L+E++ WL  KD+ELS Q P+ GD   V
Sbjct  242   MNLCWNEIKKKSHNLRARLEAFSDLSGKLQLPLREIIDWLSQKDEELSAQLPLQGDVALV  421

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K+K P I S LE+ + FL++ P E LE+   E ++  P +R QN++
Sbjct  422   QQEKETHAAFMEEVKSKGPYISSVLESAQAFLSQHPFEELEESQSESKDTSPRQRIQNLS  601

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE L E+Q A +EL   L QAE ++ +W+
Sbjct  602   RFVWKQATVASELWEKLTARCVDQHRHIEHTLEHLLEIQGAMEELSSTLTQAEGVRATWE  781

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  782   PIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLVNDLAHQLAISDVHLSMENSRALEQIN  961

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
              RWK LQV+V +R++QL +AHRDFGP SQHFLSTSVQ PWERAISPNKVPYYINH+ QTT
Sbjct  962   IRWKQLQVSVAERLKQLQDAHRDFGPGSQHFLSTSVQVPWERAISPNKVPYYINHQAQTT  1141

Query  622   CWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN  681
             CWDHPKMTELYQ+LADLNN++FSAYRTAMKLRR+QKAL LDL++L+ A +  ++H+L+ +
Sbjct  1142  CWDHPKMTELYQTLADLNNIKFSAYRTAMKLRRVQKALRLDLVTLTTALEIFNEHDLQAS  1321

Query  682   DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LNWLLNV+D+GR+G++R LSFKT
Sbjct  1322  EHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLNWLLNVFDSGRSGKMRALSFKT  1501

Query  742   GIISLCKAHLEDK  754
             GI  LC   +++K
Sbjct  1502  GIACLCGTEVKEK  1540


 Score = 50.1 bits (118),  Expect = 0.007, Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 103/232 (44%), Gaps = 27/232 (11%)
 Frame = +2

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ + P +  ++ +AQ   ++
Sbjct  344   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSKGPYISSVLESAQAFLSQ  523

Query  81    TSNQEARTII-----TDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E          T   +RIQN               W+++     ++ + +   L+ 
Sbjct  524   HPFEELEESQSESKDTSPRQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIEHTLEH  703

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  704   LLEIQGAMEELSSTLTQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLV  883

Query  181   NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             NDLA +L + D   S +++R +    E IN  W+ +   V+ER   L++ HR
Sbjct  884   NDLAHQLAISDVHLSMENSRAL----EQINIRWKQLQVSVAERLKQLQDAHR  1027


>emb|X99756.1| Ciona intestinalis mRNA for dystrophin
Length=1729

 Score =  454 bits (1167),  Expect = 2e-124, Method: Compositional matrix adjust.
 Identities = 246/548 (44%), Positives = 342/548 (62%), Gaps = 60/548 (10%)
 Frame = +1

Query  625   HPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQN-DQ  683
             HPKM EL +S+ DLN+VRF+AYRT+MKL+RLQKALCLDLL+L  A DA  QH L  + D 
Sbjct  1     HPKMAELMESMLDLNDVRFTAYRTSMKLQRLQKALCLDLLNLDTAIDAFTQHKLNISIDN  180

Query  684   P-----MDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLS  738
             P     +++L +I CLTTIYD LE+EH  LVNVPLCVDMCLNWLLNVYDT R+  I   S
Sbjct  181   PHVKDDVNVLDMITCLTTIYDALEREHKTLVNVPLCVDMCLNWLLNVYDTKRSSTISTRS  360

Query  739   FKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSN  798
             F TGI S+C +H+E+KY+Y+FKQ+    GF D+ +LG L+ D + IP+QLGE  +FGG N
Sbjct  361   FITGITSMCNSHIEEKYKYVFKQIGMPAGFTDRVKLGDLIKDFMLIPKQLGESEAFGGCN  540

Query  799   IEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKE  858
                SV SCFQ    +PEI+AA F+DWM+LEPQS+VWLPVLHR+ +AE   H A+C++C+ 
Sbjct  541   PHASVCSCFQLVGRRPEIDAAQFIDWMKLEPQSLVWLPVLHRLISAENVSHPARCSVCRS  720

Query  859   CPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKN  918
              PI+ FRYRSL+HF + ICQSCFFSGRVAK +K  YP+VEYCTPTTS E++RDF K+LKN
Sbjct  721   -PIV-FRYRSLRHFKHYICQSCFFSGRVAKNNKFCYPIVEYCTPTTSTENIRDFTKILKN  894

Query  919   KFRTKRYFAKHPRMGYLPVQT-------------VLEGDNMETPASSPQLSHDDTHSRIE  965
             K R K   AK  R+GYLPV+T             V++G + +          ++TH +IE
Sbjct  895   KLRKKSRSAK--RIGYLPVKTDDKEETNDDVTDDVIDGGSDDQTNGGA----NETHEKIE  1056

Query  966   HYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISL  1025
              YA  LA++++  G            +D+E   I  Y  +L +D      +SP    I  
Sbjct  1057  EYARILADLDDETGV--------QAPLDEEQECILEYRGALTED------KSPT---IFT  1185

Query  1026  ESEERGELERILADLEEENR----NLQAEYDR---LKQQHEHKGLSPLPSPPEMMPTSPQ  1078
               E+    +   +DL    R    N+     +   + +QH + G  P          S +
Sbjct  1186  HQEDIFSSKASGSDLPSPPRIKEVNVAIHESKPYSVAKQHNNAGNHP--------HVSSR  1341

Query  1079  SPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTV  1138
                  +L+ EAK+L+ H  R++ +M++LE+HN+ +++QL  L+ L+   +  ++ + + +
Sbjct  1342  LSNGPDLMIEAKILQHHSSRIDTQMKMLENHNESIKNQLQELKMLMNDSETSSEHSMSDI  1521

Query  1139  -SSPSTSL  1145
               SPS  +
Sbjct  1522  FESPSVHI  1545


>dbj|AK173384.1| Ciona intestinalis cDNA, clone:cieg020h09, full insert sequence
Length=1879

 Score =  252 bits (643),  Expect(2) = 8e-113, Method: Compositional matrix adjust.
 Identities = 120/203 (59%), Positives = 150/203 (73%), Gaps = 6/203 (2%)
 Frame = +2

Query  649  AMKLRRLQKALCLDLLSLSAACDALDQHNLKQN-DQP-----MDILQIINCLTTIYDRLE  702
            +MKL+RLQKALCLDLL+L  A DA  QH L  + D P     M++L +I CLTTIYD LE
Sbjct  2    SMKLQRLQKALCLDLLNLDTAVDAFTQHKLNISIDNPHVKDDMNVLDMITCLTTIYDALE  181

Query  703  QEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQV  762
            +EH  LVNVPLCVDMCLNWLLNVYDT R+  I   SF TGI S+C + +E+KY+Y+F+Q+
Sbjct  182  REHKTLVNVPLCVDMCLNWLLNVYDTRRSSTISTRSFITGITSMCNSPIEEKYKYVFQQI  361

Query  763  ASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFL  822
                GF D+ +LG L+ D + IP+QLGE  +FGG N   SV SCFQ    +PEI+AA F+
Sbjct  362  GMPAGFTDRVKLGDLIKDFMLIPKQLGESEAFGGCNPHASVCSCFQLVGRRPEIDAAQFI  541

Query  823  DWMRLEPQSMVWLPVLHRVAAAE  845
            DWM+LEPQS+VWLPVLHR+ +AE
Sbjct  542  DWMKLEPQSLVWLPVLHRLISAE  610


 Score =  186 bits (471),  Expect(2) = 8e-113, Method: Compositional matrix adjust.
 Identities = 112/290 (38%), Positives = 165/290 (56%), Gaps = 39/290 (13%)
 Frame = +1

Query  849   HQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGED  908
             H A+C++C+ECPI+GFRYRSL+HF +DICQSCFFSGRVAK +K  YP+VEYCTPTTS E+
Sbjct  619   HPARCSVCRECPIVGFRYRSLRHFKHDICQSCFFSGRVAKNNKFCYPIVEYCTPTTSTEN  798

Query  909   VRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASS-------------PQL  955
             +RDF K+LKNK R K   AK  R+GYLPV+T    D+ E P                   
Sbjct  799   IRDFTKILKNKLRNKSRSAK--RIGYLPVKT----DDKEDPNDDGTNDVIDGGIDDQTNG  960

Query  956   SHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQP  1015
               ++TH +IE YA  LA++++  G      + P   +D+E   I  YC +L +D   +  
Sbjct  961   GANETHEKIEEYARILADLDDETG------VQP--PLDEEQECILEYCGALTEDKSPTIF  1116

Query  1016  RSPAQILISLESEERGELERILADLEEENRNLQ-AEYDRLKQQHEHKGLSPLPSPPEMMP  1074
                  I  S  S  R +L      ++E N  +  ++   + +QH   G  P  S    + 
Sbjct  1117  THQEDIFSSKAS--RSDLPS-PPRIKEVNVAIHDSKAYSVAKQHNDAGNQPHVS--SRLS  1281

Query  1075  TSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLL  1124
               P      +L+ EAK+L+ H  R++ +M++LE+HN+ +++QL  L+ L+
Sbjct  1282  NGP------DLMIEAKILQHHSSRIDTQMKMLENHNESIKNQLQELKMLM  1413


>gb|EZ022163.1| TSA: Acropora millepora SeqIndex3528, mRNA sequence
Length=1268

 Score =  342 bits (876),  Expect = 1e-90, Method: Compositional matrix adjust.
 Identities = 165/383 (43%), Positives = 249/383 (65%), Gaps = 11/383 (2%)
 Frame = +1

Query  601   WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
             WER+ + N +PYYINHET+TT WDHP+M  L + +  L+N++++AYRTAMKLR +QK   
Sbjct  94    WERSETTNGIPYYINHETETTQWDHPEMISLMEEIEGLSNIKYAAYRTAMKLRTIQKKTQ  273

Query  661   LDLLSLSAACDALDQHNLKQN--DQPMDILQIINCLTTIYDRLEQEHNN-LVNVPLCVDM  717
             L L+ L  A  +L +  +K    +  +   ++   +T I+     + N+ L++V L  ++
Sbjct  274   LYLVDLRVAKASLVEEGIKDGYIEGNLSTAEVHKIITAIFINQTGDRNSQLIDVSLASEL  453

Query  718   CLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLL  777
              LNW+LNVYD GR G + +LS K G+  +    +++KYRYLF Q +++ GF D +RL L 
Sbjct  454   VLNWILNVYDPGRMGFVPILSLKVGLAVMSSEKVQEKYRYLFSQFSNNHGFLDSKRLKLF  633

Query  778   LHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPV  837
             L + +QIP+ + E ASF GS++EP+VR+C +  +    +    F++WM  EPQ++VWLP 
Sbjct  634   LQEMLQIPKHIYESASFSGSSVEPAVRNCLEGVSIPERVSFEEFIEWMIAEPQTVVWLPT  813

Query  838   LHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMV  897
             LHR+A +ET KH+AKCN+CK  PI+GFRYR LK FN+D+CQ CF+SGRV+K HK+ +P  
Sbjct  814   LHRLAVSETVKHEAKCNVCKMYPIVGFRYRCLKCFNFDLCQGCFWSGRVSKQHKIGHPTQ  993

Query  898   EYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--KHPRMG-YLPV----QTVLEGDNMETP-  949
             EYC  +T  ED++DFAKV++NK   K+     +HP  G ++P+        EG+  ++  
Sbjct  994   EYCLVSTQKEDIKDFAKVMRNKVSKKKKKKTPEHPSKGRFIPIDMEDAAPSEGEYEDSVD  1173

Query  950   ASSPQLSHDDTHSRIEHYASRLA  972
               S   +   TH ++E YA+RLA
Sbjct  1174  VGSAVKAFPGTHDKLESYAARLA  1242


>emb|CU688551.1| Synthetic construct Homo sapiens gateway clone IMAGE:100018376 
3' read DMD mRNA
Length=1192

 Score =  328 bits (841),  Expect = 1e-86, Method: Compositional matrix adjust.
 Identities = 187/255 (73%), Positives = 198/255 (77%), Gaps = 17/255 (6%)
 Frame = -2

Query  985   SISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEEN  1044
             SISP ESID E L  QH CQSLNQDSPLSQP SPAQILISLESEERG         E  +
Sbjct  759   SISPYESIDGELL*FQHSCQSLNQDSPLSQPCSPAQILISLESEERG------GARENPS  598

Query  1045  RNLQAEYDRLKQQHEHKGLSPLPSP-PEMMPT---SPQSPRDAELIAEAKLLRQH-----  1095
             R+   + +   +    K  +    P P  +P+    P  PR   +++   LLR       
Sbjct  597   RS*GRKQESASRI*PSKAAART*RPVPTAVPS*NECPPLPRVPGMLS--SLLRPSYCVNT  424

Query  1096  KGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPML  1155
             KGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPML
Sbjct  423   KGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPML  244

Query  1156  LRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGRA  1215
             LRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGRA
Sbjct  243   LRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGRA  64

Query  1216  MESLVSVMTDEEGAE  1230
             MESLVSVMTDEEGAE
Sbjct  63    MESLVSVMTDEEGAE  19


>ref|XM_001256720.2| PREDICTED: Bos taurus similar to dystrophin Dp260-1 (LOC790177), 
partial mRNA
Length=462

 Score =  320 bits (821),  Expect = 3e-84, Method: Compositional matrix adjust.
 Identities = 150/152 (98%), Positives = 151/152 (99%), Gaps = 0/152 (0%)
 Frame = +1

Query  658  ALCLDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDM  717
            AL +DLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDM
Sbjct  7    ALAVDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDM  186

Query  718  CLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLL  777
            CLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLL
Sbjct  187  CLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLL  366

Query  778  LHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF  809
            LHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF
Sbjct  367  LHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF  462


>ref|XM_001637080.1| Nematostella vectensis predicted protein (NEMVEDRAFT_v1g93170) 
partial mRNA
Length=948

 Score =  315 bits (808),  Expect = 7e-83, Method: Compositional matrix adjust.
 Identities = 143/316 (45%), Positives = 213/316 (67%), Gaps = 7/316 (2%)
 Frame = +1

Query  616  HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQ  675
            HET+ T WDHP M +L Q LA+LNN++++AYRTAMKLR + K   L L+ +      LD+
Sbjct  1    HETEKTQWDHPAMIQLMQDLAELNNIKYAAYRTAMKLRAIHKKTQLYLVEIPILTATLDE  180

Query  676  HNL--KQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGR  733
             ++     ++ + I +    +T ++     +  + +++P+  D+ LN +LN+YD GRTG 
Sbjct  181  EDVPDGYTEKALSIPEASKIITALFINQNGDRQDFIDIPMASDLTLNLMLNIYDPGRTGY  360

Query  734  IRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVAS  793
            I+ LS K GI  LC A L+DKYRYLF+Q+ +S    D++RL L L + +QIP+ + E   
Sbjct  361  IQALSLKIGISLLCAAKLQDKYRYLFRQMCNSRAVLDRKRLTLFLQECLQIPKYIYESTI  540

Query  794  FGGSNIEPSVRSCFQFANNKPEIEAAL-----FLDWMRLEPQSMVWLPVLHRVAAAETAK  848
            F G+++EP+V++CF+  +    +E  L     F++WM  EPQ++VWLP LHR+A +ET K
Sbjct  541  FSGTSVEPAVKNCFETVSFTYTLEVELQKFKSFMEWMVAEPQTIVWLPTLHRLAVSETVK  720

Query  849  HQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGED  908
            H+AKCNICK  PI+GFRYR LK FN+D+CQ CF++GRV+KGHK+ +P  EYC   +  ED
Sbjct  721  HEAKCNICKMYPIVGFRYRCLKCFNFDLCQGCFWAGRVSKGHKIGHPTQEYCLAPSQKED  900

Query  909  VRDFAKVLKNKFRTKR  924
            ++DFAKV++NK   K+
Sbjct  901  IKDFAKVMRNKVSKKK  948


>ref|XM_002237128.1| Branchiostoma floridae hypothetical protein (BRAFLDRAFT_129067) 
mRNA, complete cds
Length=2067

 Score =  312 bits (799),  Expect = 8e-82, Method: Compositional matrix adjust.
 Identities = 181/489 (37%), Positives = 271/489 (55%), Gaps = 59/489 (12%)
 Frame = +1

Query  638   LNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK-QNDQPMDILQIINCLTT  696
             LN+++++AYR AMKLR +QK   L  + L       ++HNL+   D  +D++ + + ++ 
Sbjct  28    LNDIKYAAYRMAMKLRAVQKICDLHFVDLKTVVSVFERHNLRGHRDSVVDVMDLYDIISD  207

Query  697   IYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYR  756
             I+    ++  + +++ L  D+ LNW+LNVYDT RTG IRV S K G++ LC   L +KY 
Sbjct  208   IFVMSNKDRPDFIDIELASDLTLNWILNVYDTNRTGCIRVPSVKVGLVVLCSGLLSEKYT  387

Query  757   YLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEI  816
             YLF+  +  +G   ++ L  LL D +Q+  QL E  SFG  ++   V SC +        
Sbjct  388   YLFQLFSDHSGMMSRKSLSGLLQDMLQMTDQLYERPSFG--SVSAGVASCLEGTLGTGVT  561

Query  817   EAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDI  876
             E   FL W+  EPQ++VWLP LHRVA+AE+ KHQAKCNICK CPI+GFRYR LK +NYD+
Sbjct  562   EDH-FLQWLMAEPQTVVWLPTLHRVASAESVKHQAKCNICKVCPILGFRYRCLKCYNYDL  738

Query  877   CQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLP  936
             CQ+CFF GR ++ HK+ +P+ EYCT T+S ED + FA+ ++N   TKRY  K  +  +LP
Sbjct  739   CQNCFFVGRSSRSHKLSHPIQEYCTQTSSKEDAKAFARTVRNNV-TKRYKKKKNKSNFLP  915

Query  937   VQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEH  996
             V    E D   T + +   S  D H  +   A+RLA+ME+        S+ P +      
Sbjct  916   VHGYREDD---TDSLADTQSEADMHGMLGRLATRLADMES--------SLPPTK------  1044

Query  997   LLIQHYCQSLNQDSP----LSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYD  1052
                        Q SP      +P  P Q++++L  EER ELE I+ DLE E  +L  + +
Sbjct  1045  ------VSRPQQTSPKLMQRQRPSPPEQVVVNLAPEERLELEDIIHDLEAEKDDLLDDIN  1206

Query  1053  RLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQ  1112
              ++ Q    G                            +++  + RL+A++++LE HN+Q
Sbjct  1207  EMRTQRSEAG---------------------------SVIQDEQERLQAQVEVLESHNRQ  1305

Query  1113  LESQLHRLR  1121
             LE QL + R
Sbjct  1306  LELQLEKYR  1332


>ref|XM_696118.3| PREDICTED: Danio rerio similar to putative utrophin (LOC572406), 
partial mRNA
Length=7901

 Score =  302 bits (774),  Expect = 7e-79, Method: Compositional matrix adjust.
 Identities = 164/393 (41%), Positives = 261/393 (66%), Gaps = 2/393 (0%)
 Frame = +1

Query  13    ADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELIT  72
             ++ ++  TEL DWL L+ Q++KS  V +GD ++I   I + + T  DLEQR PQLE++IT
Sbjct  6604  SELHQTATELADWLLLIHQMLKSNIVTLGDKDEIRTTIGRLQVTKGDLEQRHPQLEDIIT  6783

Query  73    AAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEA  132
              AQN+KNKTSN + RT I++++E++++QWD  Q  ++ R  QL+ M+  S QW E + + 
Sbjct  6784  LAQNIKNKTSNLDVRTSISEKLEKVRSQWDSTQHGVETRLLQLDHMIGHSDQWEEQRRKV  6963

Query  133   EQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS  192
             + ++GQ   +L +  +   + + + K+I++ K   ++L + Q +V   N+L+ +LL+DY+
Sbjct  6964  KALIGQNELRLNNLLQ--QSREPLTKQISDNKAFLQELSRGQESVSAFNELSNQLLQDYA  7137

Query  193   ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
              DDTRKV  + +  N SW SI+ R S+R+AAL+   + +Q    +LE FL WL E+ETT 
Sbjct  7138  NDDTRKVKEVMDTHNNSWNSINNRASDRQAALDLDLKSVQTSLRELELFLKWLHESETTV  7317

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
             NVL DA ++E L +DS   K+L  Q +D+Q EIEAH DV+ +++ N  K++++L  S++A
Sbjct  7318  NVLSDAAQREGLSQDSAHNKQLKSQLEDIQAEIEAHNDVFRSVEGNKLKMVKALGSSEEA  7497

Query  313   VLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA  372
             V LQ+RLD+MN +WS+L+ KS NIR+HLEAS+++W RL   L++L  W+ LKD+EL++Q 
Sbjct  7498  VFLQQRLDDMNQRWSDLKAKSANIRAHLEASAERWNRLLSVLEDLSRWIGLKDEELNKQM  7677

Query  373   PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMST  405
             PIGGD P + +Q       + E++    V  S 
Sbjct  7678  PIGGDVPTLLQQQTHGMDIQAEIEAHNDVFRSV  7776


 Score = 69.7 bits (169),  Expect = 1e-08, Method: Compositional matrix adjust.
 Identities = 75/314 (23%), Positives = 139/314 (44%), Gaps = 42/314 (13%)
 Frame = +1

Query  44    EDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDE  103
             E + + I   KA +Q+L + +  +      +  L    +N + R +  + ++   N W+ 
Sbjct  7021  EPLTKQISDNKAFLQELSRGQESVSAFNELSNQLLQDYANDDTRKV-KEVMDTHNNSWNS  7197

Query  104   VQEHLQNRRQQLNEMLKDST----------QWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
             +     +R+  L+  LK             +WL   E    VL  A     + +EG    
Sbjct  7198  INNRASDRQAALDLDLKSVQTSLRELELFLKWLHESETTVNVLSDA-----AQREG----  7350

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDL-------ALKLLRDY-SADDTRKVHMITEN  205
               + +     KQL   L   Q  ++  ND+        LK+++   S+++   +    ++
Sbjct  7351  --LSQDSAHNKQLKSQLEDIQAEIEAHNDVFRSVEGNKLKMVKALGSSEEAVFLQQRLDD  7524

Query  206   INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
             +N  W  +  + +   A LE +     +    LE    W+   +   N         + +
Sbjct  7525  MNQRWSDLKAKSANIRAHLEASAERWNRLLSVLEDLSRWIGLKDEELN---------KQM  7677

Query  266   EDSKGVKELMKQ---WQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNM  322
                  V  L++Q     D+Q EIEAH DV+ +++ N  K++++L GS++AV LQ+RLD+M
Sbjct  7678  PIGGDVPTLLQQQTHGMDIQAEIEAHNDVFRSVEGNKLKMVKALGGSEEAVFLQQRLDDM  7857

Query  323   NFKWSELRKKSLNI  336
             N +WS+L+ KS NI
Sbjct  7858  NQRWSDLKAKSANI  7899


>gb|EZ014006.1| TSA: Acropora millepora SeqIndex16792, mRNA sequence
Length=1833

 Score =  189 bits (481),  Expect(2) = 3e-78, Method: Compositional matrix adjust.
 Identities = 117/222 (52%), Positives = 157/222 (70%), Gaps = 15/222 (6%)
 Frame = +2

Query  904   TSGEDVRDFAKVLKNKFRTKRYFAKHPR-MGYLPVQTVLEGDNMETPA-SSPQ--LSHDD  959
              SGEDV DF  +++NKF+ +RY  K PR +GYLP+QTV+EG N+ETP+  SPQ  ++H+ 
Sbjct  266   NSGEDVLDFFAMVRNKFKKRRYKNKPPRKLGYLPIQTVMEGGNLETPSMPSPQQNVNHE-  442

Query  960   THSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPA  1019
              H+R+  +A RLAE E+  GS  +       S+D+EH LI  YCQSL  D+    P+SP 
Sbjct  443   VHNRLGMFAHRLAEAESEGGSKYDP-----HSLDEEHQLIAQYCQSLKSDT-TEAPKSPT  604

Query  1020  QILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQS  1079
             QI+++L++ E+ +LE  L  LEEENR+LQ EY+RL+   +    S  PS  +  P  PQ+
Sbjct  605   QIVMALDAVEKDDLEAELLKLEEENRDLQEEYERLRSIRDQ---SLPPSDSDTSPGGPQN  775

Query  1080  PRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLR  1121
              RD+EL+AEAKLLRQHKGRLEARMQ+LEDHN+QLE+QL RLR
Sbjct  776   -RDSELLAEAKLLRQHKGRLEARMQVLEDHNRQLEAQLQRLR  898


 Score =  132 bits (333),  Expect(2) = 3e-78, Method: Compositional matrix adjust.
 Identities = 56/89 (62%), Positives = 73/89 (82%), Gaps = 0/89 (0%)
 Frame = +3

Query  816  IEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYD  875
            I+ A FL W+ +EPQS+VWLP LHR+AA+E  KH+AKC+ICKE PI+GFR+R LK FNYD
Sbjct  3    IDCAQFLVWLSVEPQSIVWLPTLHRLAASEAVKHKAKCSICKEYPIVGFRFRCLKCFNYD  182

Query  876  ICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
            +CQSCF+SGRV+  H++ +PM +YC  TT
Sbjct  183  LCQSCFWSGRVSHEHRLTHPMHQYCLSTT  269


 Score = 46.6 bits (109),  Expect = 0.077, Method: Compositional matrix adjust.
 Identities = 25/49 (51%), Positives = 35/49 (71%), Gaps = 3/49 (6%)
 Frame = +3

Query  1183  LEEVMEQLNNSFPSSR--GHNVGSLFHMADDLGRAMESLVSVMT-DEEG  1228
             L+EVM ++N+SFP+ +     VG LF  A D+ +A+ESLV VMT D+EG
Sbjct  1140  LKEVMSKINSSFPADQQNADPVGHLFATAKDVNKAVESLVQVMTSDDEG  1286


>ref|XM_002189011.1| PREDICTED: Taeniopygia guttata similar to dystrophin Dp71c (LOC100218005), 
mRNA
Length=549

 Score =  299 bits (765),  Expect = 7e-78, Method: Compositional matrix adjust.
 Identities = 146/154 (94%), Positives = 152/154 (98%), Gaps = 0/154 (0%)
 Frame = +1

Query  1046  NLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQI  1105
             NLQAEYDRLKQQHEHKGLSPLPSPPEMMP SPQSPRDAELIAEAKLLRQHKGRLEARMQI
Sbjct  28    NLQAEYDRLKQQHEHKGLSPLPSPPEMMPVSPQSPRDAELIAEAKLLRQHKGRLEARMQI  207

Query  1106  LEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSD  1165
             LEDHNKQLESQLHRLRQLLEQPQA+AKVNGTT+SSPSTSLQRS SSQPMLLRVVGSQTS+
Sbjct  208   LEDHNKQLESQLHRLRQLLEQPQADAKVNGTTLSSPSTSLQRSGSSQPMLLRVVGSQTSE  387

Query  1166  SMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
             +MGE++LLSPPQDTSTGLEEVMEQLNNSFPSSRG
Sbjct  388   TMGEDELLSPPQDTSTGLEEVMEQLNNSFPSSRG  489


>gb|AY566609.1| Canis familiaris dystrophin Dp71 isoform (DMD) mRNA, partial 
cds
Length=468

 Score =  288 bits (737),  Expect = 1e-74, Method: Compositional matrix adjust.
 Identities = 134/135 (99%), Positives = 135/135 (100%), Gaps = 0/135 (0%)
 Frame = +2

Query  616  HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQ  675
            HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQ
Sbjct  62   HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQ  241

Query  676  HNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIR  735
            HNLKQNDQPMDILQ+INCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIR
Sbjct  242  HNLKQNDQPMDILQVINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIR  421

Query  736  VLSFKTGIISLCKAH  750
            VLSFKTGIISLCKAH
Sbjct  422  VLSFKTGIISLCKAH  466


>ref|XM_002237465.1| Branchiostoma floridae hypothetical protein (BRAFLDRAFT_137716) 
mRNA, partial cds
Length=969

 Score =  279 bits (714),  Expect = 7e-72, Method: Compositional matrix adjust.
 Identities = 143/333 (42%), Positives = 209/333 (62%), Gaps = 14/333 (4%)
 Frame = +1

Query  614  INHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDAL  673
             +H+T+ T WDHP + E  + L  LN+++++AYR AMKLR +QK   L  + L       
Sbjct  7    FSHQTERTQWDHPLLAETLEQLDGLNDIKYAAYRMAMKLRAVQKRCDLHFVDLKTVVSVF  186

Query  674  DQHNLKQN-DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTG  732
            ++HNL+ + D  +D++ + + ++ I+    ++  + +++ L  D+ LNW+LNVYDT RTG
Sbjct  187  ERHNLRSHRDSVVDVMDLYDIISDIFVMSNKDRPDFIDIELASDLTLNWILNVYDTNRTG  366

Query  733  RIRVLSFKTGIISLCKAHLEDKYRY-LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEV  791
             IRV S K G++ LC   L +  R  LF+Q +  +G   ++ L  LL D +Q+  QL E 
Sbjct  367  CIRVPSVKVGLVVLCSGLLSENTRVNLFQQFSDHSGMMSRKSLSGLLQDMLQVRNQLYER  546

Query  792  ASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQA  851
             SFG  ++   V SC         +E   FL W+  EPQ++VWLP LHRVA+AE+ KHQA
Sbjct  547  PSFG--SVSAGVASC---------LEGDHFLQWLMAEPQTLVWLPTLHRVASAESVKHQA  693

Query  852  KCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRD  911
            KCNICK CPI+GFRYR LK +NYD+CQ+CFF GR ++ HK+ +P+ EYCT T+S ED + 
Sbjct  694  KCNICKVCPILGFRYRCLKCYNYDLCQNCFFVGRSSRSHKLSHPIQEYCTQTSSKEDAKA  873

Query  912  FAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGD  944
            FA+ ++N   TKRY  K  +  +LPV    E D
Sbjct  874  FARTVRNNV-TKRYKKKKNKSNFLPVHGYREDD  969


>dbj|AB011666.1| Rattus norvegicus mRNA for utrophin, partial cds
Length=506

 Score =  257 bits (657),  Expect = 3e-65, Method: Compositional matrix adjust.
 Identities = 121/168 (72%), Positives = 138/168 (82%), Gaps = 0/168 (0%)
 Frame = +1

Query  617  ETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH  676
            +TQTTCWDHPKMTEL+QSL DLNNVRFSAYRTA+K+RRLQK LCLDLL L+   +   QH
Sbjct  1    QTQTTCWDHPKMTELFQSLGDLNNVRFSAYRTAIKIRRLQKTLCLDLLELNTTNEVFKQH  180

Query  677  NLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRV  736
             L QNDQ + +  +INCLTT YD LEQ H +LVNVPLCVDMCLNWLLNVYDTGRTG+IRV
Sbjct  181  KLNQNDQLLSVPDVINCLTTTYDGLEQLHKDLVNVPLCVDMCLNWLLNVYDTGRTGKIRV  360

Query  737  LSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQI  784
             S K G++SL K  LE+KYR LFK+VA  T  CDQR+LGLLLHD+IQI
Sbjct  361  QSLKIGLMSLSKGLLEEKYRCLFKEVAGPTEMCDQRQLGLLLHDAIQI  504


>gb|DQ831005.1| Danio rerio G-utrophin pseudogene mRNA, partial sequence
Length=532

 Score =  246 bits (628),  Expect = 6e-62, Method: Composition-based stats.
 Identities = 106/144 (73%), Positives = 125/144 (86%), Gaps = 0/144 (0%)
 Frame = +2

Query  816  IEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYD  875
            IE   F+DWM LEPQSMVWLPVLHRV AAETAKHQAKCNICKECP++GFRYRSLKHFNY+
Sbjct  92   IELQQFVDWMHLEPQSMVWLPVLHRVTAAETAKHQAKCNICKECPMVGFRYRSLKHFNYN  271

Query  876  ICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYL  935
            +CQ+CFFSGR++K H +  PMVEYCTPTTSGEDVRDF KVLKNKFR+K+YF KHPR+GYL
Sbjct  272  VCQTCFFSGRISKDHHLSDPMVEYCTPTTSGEDVRDFTKVLKNKFRSKKYFTKHPRLGYL  451

Query  936  PVQTVLEGDNMETPASSPQLSHDD  959
            PVQT+LE ++ +TP +   +  +D
Sbjct  452  PVQTILEEEHSDTPVAFVSMCPED  523


 Score = 44.7 bits (104),  Expect = 0.35, Method: Composition-based stats.
 Identities = 21/24 (87%), Positives = 23/24 (95%), Gaps = 0/24 (0%)
 Frame = +1

Query  637  DLNNVRFSAYRTAMKLRRLQKALC  660
            DL++VRFSAYRTAMK RRLQKALC
Sbjct  1    DLSHVRFSAYRTAMKSRRLQKALC  72


>dbj|AK034383.1| Mus musculus adult male diencephalon cDNA, RIKEN full-length 
enriched library, clone:9330185F14 product:inferred: dystrophin-related 
protein 2 A-form splice variant {Rattus norvegicus}, 
full insert sequence
Length=1541

 Score =  245 bits (626),  Expect = 1e-61, Method: Compositional matrix adjust.
 Identities = 128/274 (46%), Positives = 180/274 (65%), Gaps = 0/274 (0%)
 Frame = +3

Query  322   MNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
             MN  W+E++KKS N+R+ LEA SD   +L L L+E++ WL  KD+ELS Q P+ GD   V
Sbjct  414   MNLCWNEIKKKSHNLRARLEAFSDLSGKLQLPLREIIDWLSQKDEELSAQLPLQGDVALV  593

Query  382   QKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVT  441
             Q++ + H AF  E+K+K P I S LE+ + FL++ P E LE+   E ++  P +R QN++
Sbjct  594   QQEKETHAAFMEEVKSKGPYISSVLESAQAFLSQHPFEELEESQSESKDTSPRQRIQNLS  773

Query  442   RLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQ  501
             R + KQA   +  WEKL     D  R I+ TLE L E+Q A +EL   L QAE ++ +W+
Sbjct  774   RFVWKQATVASELWEKLTARCVDQHRHIEHTLEHLLEIQGAMEELSSTLTQAEGVRATWE  953

Query  502   PVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLN  561
             P+GDL IDSL +H++ +K  + E +P+K+ V  VNDLA QL    + LS  N   LE +N
Sbjct  954   PIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLVNDLAHQLAISDVHLSMENSRALEQIN  1133

Query  562   TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLST  595
              RWK LQV+V +R++QL +AHRDFGP SQHFLS+
Sbjct  1134  IRWKQLQVSVAERLKQLQDAHRDFGPGSQHFLSS  1235


 Score = 48.9 bits (115),  Expect = 0.016, Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 103/232 (44%), Gaps = 27/232 (11%)
 Frame = +3

Query  21    ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
             E+ DWLS  D+ + +Q  + GD+  + +      A M++++ + P +  ++ +AQ   ++
Sbjct  516   EIIDWLSQKDEELSAQLPLQGDVALVQQEKETHAAFMEEVKSKGPYISSVLESAQAFLSQ  695

Query  81    TSNQEARTII-----TDRIERIQN--------------QWDEVQEHLQNRRQQLNEMLKD  121
                +E          T   +RIQN               W+++     ++ + +   L+ 
Sbjct  696   HPFEELEESQSESKDTSPRQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIEHTLEH  875

Query  122   STQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
               +   A EE    L QA     +W+  G   +D++ + I   K   ++    +  V + 
Sbjct  876   LLEIQGAMEELSSTLTQAEGVRATWEPIGDLFIDSLPEHIQAIKLFKEEFSPVKDGVKLV  1055

Query  181   NDLALKL-LRDY--SADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             NDLA +L + D   S +++R +    E IN  W+ +   V+ER   L++ HR
Sbjct  1056  NDLAHQLAISDVHLSMENSRAL----EQINIRWKQLQVSVAERLKQLQDAHR  1199


>ref|XM_002114182.1| Trichoplax adhaerens hypothetical protein, mRNA
Length=1203

 Score =  243 bits (620),  Expect = 5e-61, Method: Compositional matrix adjust.
 Identities = 126/331 (38%), Positives = 198/331 (59%), Gaps = 8/331 (2%)
 Frame = +1

Query  615   NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKAL-CLDLLSLSAACDAL  673
             +H+T  T WDHP  T++ + +  LN ++F+AYRTA+K+R +Q+    ++ L L +  D L
Sbjct  16    SHKTCRTQWDHPTTTDILREIDQLNYIKFAAYRTAIKMRIIQQRFDKVEFLRLLSVFDQL  195

Query  674   DQHNLKQND----QPMDILQIINCLTTIYDRLEQEHN-NLVNVPLCVDMCLNWLLNVYDT  728
                  + +D    Q M++L + N L  ++ +    ++  L N  L  D+ LN+ LN++D 
Sbjct  196   GYGTQQSSDDDEVQDMNVLDLENILVKLFSQPTLANDIELANPLLSTDLALNFALNIFDR  375

Query  729   GRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQL  788
              R+G++++ + K  +  +CK +L DKY++LFK +A+   F +   L  LL   +QI   +
Sbjct  376   DRSGKLKLTAIKIFLTVMCKGYLRDKYQFLFKLIANRGKFANAEGLESLLSQLMQIVSYI  555

Query  789   GEVASFGG-SNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETA  847
              E  SFGG  +I+ +V++C+  A +   I+   F  W+  EPQ++VWL  + RV AAE  
Sbjct  556   KEDPSFGGIHSIQNAVKNCYDKAAHPSVIKEEEFTQWVLEEPQTIVWLSTMERVIAAENV  735

Query  848   KHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGE  907
              H  KC ICK+ PI+G R++SLK FN+DICQ+CF SG+  K HK   P  EYC  TTS E
Sbjct  736   VHDVKCGICKKTPIVGLRFKSLKKFNFDICQNCFLSGKSGKHHKAGDPTQEYCVATTSKE  915

Query  908   DVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQ  938
              V+DFA+  +NK  TKRY  K  +  Y+ ++
Sbjct  916   GVKDFARTFRNKV-TKRYKRKAAKPRYICIE  1005


>gb|DQ431250.1| Schistosoma mansoni dystrophin mRNA, partial cds
Length=3834

 Score =  232 bits (591),  Expect = 1e-57, Method: Compositional matrix adjust.
 Identities = 99/229 (43%), Positives = 145/229 (63%), Gaps = 16/229 (6%)
 Frame = +3

Query  711   VPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCD  770
             V +CVD+ LNWLLNVYD  R G IRVLSFK  +  +  A+L++KYRYLF  ++   G  D
Sbjct  921   VNVCVDLILNWLLNVYDRMRCGTIRVLSFKVALALMSMANLDEKYRYLFSLISDRDGCVD  1100

Query  771   QRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ----------------FANNKP  814
             ++RLG LL++ + IPR LGE   FG  +    V++CFQ                  ++KP
Sbjct  1101  EQRLGALLYECVLIPRNLGETGQFGNEDFNQYVKTCFQQVLEISKHSDKIDGTLTYHSKP  1280

Query  815   EIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNY  874
                   FL W+RL PQ + WLP+LHR+A +E   H  +C +C   P+IG RYR L+  N+
Sbjct  1281  SARIVHFLTWLRLNPQMLTWLPLLHRLALSEQVIHHIRCTVCHNQPLIGLRYRCLRCLNF  1460

Query  875   DICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTK  923
             D+CQ CFF+GR ++ HK+ +PM EYC+ +TS +  +DF ++++N+FR++
Sbjct  1461  DMCQQCFFAGRTSRNHKLTHPMQEYCSHSTSTDSFKDFTRIVRNRFRSR  1607


 Score = 99.0 bits (245),  Expect = 1e-17, Method: Compositional matrix adjust.
 Identities = 58/139 (41%), Positives = 79/139 (56%), Gaps = 18/139 (12%)
 Frame = +3

Query  596  SVQGPWERAISPN--KVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLR  653
            SV+ PWER + P+  +VPYY NHETQ T WDHP + +L +S+   N VRFS YRT +KLR
Sbjct  3    SVRLPWERCVHPSGTQVPYYKNHETQETQWDHPILCDLMKSMKQFNTVRFSDYRTGLKLR  182

Query  654  RLQKALCLDLLSLSAACDALDQHNLKQN-DQPMDILQIINCLTTIYDRLEQEHNNLVNVP  712
            RLQK LC D +S+S   + L      Q    PM   Q     T  +DR       +++VP
Sbjct  183  RLQKELCFDSISISIVAECLKHIGHSQTLSNPMLGQQT----TDPFDR-------MISVP  329

Query  713  LCVDMCLNWLLNVYDTGRT  731
              +D    +LL +++  RT
Sbjct  330  QIID----YLLQLFNHTRT  374


 Score = 56.6 bits (135),  Expect = 8e-05, Method: Compositional matrix adjust.
 Identities = 33/80 (41%), Positives = 49/80 (61%), Gaps = 9/80 (11%)
 Frame = +3

Query  1088  EAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQR  1147
             E++LL +HKGRLEARM +LE+HN+QLE QL RLRQ L        V+G +   P   L  
Sbjct  3267  ESRLLWEHKGRLEARMVMLEEHNRQLEQQLQRLRQYL--------VSGNSAPDP-IPLHN  3419

Query  1148  SDSSQPMLLRVVGSQTSDSM  1167
             ++ +   +   +G+Q + S+
Sbjct  3420  TNPTGEFVHGAIGNQNNVSI  3479


>gb|AF435589.1|AF435589 Eptatretus stouti dystrophin-like protein mRNA, partial cds
Length=811

 Score =  226 bits (575),  Expect = 9e-56, Method: Compositional matrix adjust.
 Identities = 127/183 (69%), Positives = 147/183 (80%), Gaps = 3/183 (1%)
 Frame = +1

Query  959   DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSP  1018
             DTH+RIEH ASRLAEME  NGSYL DS SPNES++DEHLLIQHY QSL+ +SP SQP SP
Sbjct  1     DTHARIEHLASRLAEMEFKNGSYLIDS-SPNESLEDEHLLIQHYRQSLSGESPGSQPHSP  177

Query  1019  AQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQ  1078
             AQILISLE++ER ELERIL DLEEENR+LQ EY+RL+++ E +GL  L          P+
Sbjct  178   AQILISLENQERSELERILRDLEEENRSLQNEYERLRKKQEKEGLGHLLP--MPPTMPPE  351

Query  1079  SPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTV  1138
             SPRD+ELIAEAKLLRQHKGRLEAR Q+LE+HN+QLESQL RLRQLL+QPQ E    G  +
Sbjct  352   SPRDSELIAEAKLLRQHKGRLEARTQVLEEHNRQLESQLCRLRQLLDQPQGEGGSTGGPL  531

Query  1139  SSP  1141
              SP
Sbjct  532   HSP  540


>gb|AE014297.2| Drosophila melanogaster chromosome 3R, complete sequence
Length=27905053

 Features in this part of subject sequence:
   dystrophin, isoform F
   dystrophin, isoform H

 Score =  170 bits (430),  Expect(2) = 1e-54, Method: Compositional matrix adjust.
 Identities = 85/130 (65%), Positives = 98/130 (75%), Gaps = 9/130 (6%)
 Frame = +2

Query  784       IPRQLGEVASFGGSNIEPSVRSCFQFA---------NNKPEIEAALFLDWMRLEPQSMVW  834
                 +PRQLGEVA+FGGSNIEPSVRSC + A         N    IE   FL W++ EPQS+VW
Sbjct  15417380  VPRQLGEVAAFGGSNIEPSVRSCLEQAGISQEAIDGNQDISIELQHFLGWLQHEPQSLVW  15417559

Query  835       LPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHY  894
                 LPVLHR+AAAE AKHQAKCNICKE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +
Sbjct  15417560  LPVLHRLAAAEAAKHQAKCNICKEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTH  15417739

Query  895       PMVEYCTPTT  904
                 PM EYCT  +
Sbjct  15417740  PMHEYCTTVS  15417769


 Features in this part of subject sequence:
   dystrophin, isoform F
   dystrophin, isoform H

 Score = 73.9 bits (180),  Expect(2) = 1e-54, Method: Compositional matrix adjust.
 Identities = 34/60 (56%), Positives = 46/60 (76%), Gaps = 2/60 (3%)
 Frame = +3

Query  903       TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGD--NMETPASSPQLSHDDT  960
                 TTS EDVRDF + LKNKF++++YF KHPR+GYLPVQ+VLEG   N+ T +   ++ H +T
Sbjct  15417831  TTSTEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQSVLEGKFPNLRTLSI*IKILHSET  15418010


 Features in this part of subject sequence:
   dystrophin, isoform F
   dystrophin, isoform H

 Score =  130 bits (326),  Expect(2) = 4e-42, Method: Compositional matrix adjust.
 Identities = 63/126 (50%), Positives = 92/126 (73%), Gaps = 6/126 (4%)
 Frame = +3

Query  661       LDLLSLSAACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCL  719
                 LD +S+S AC++ D+H L+ QND+ +DI  +   L ++Y  +++     +++ L +D+ +
Sbjct  15416682  LDRISMSTACESFDRHGLRAQNDKLIDIPDMTTVLHSLYVTIDK-----IDLTLMLDLAI  15416846

Query  720       NWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLH  779
                 NW+LNVYD+ RTG+IRVLSFK G++ LCK HLE+KYRYLF+ VA +    DQRRLGLLLH
Sbjct  15416847  NWILNVYDSQRTGQIRVLSFKVGLVLLCKGHLEEKYRYLFRLVADTDRRADQRRLGLLLH  15417026

Query  780       DSIQIP  785
                 D IQ+ 
Sbjct  15417027  DCIQVS  15417044


 Features in this part of subject sequence:
   dystrophin, isoform F
   dystrophin, isoform H

 Score = 72.0 bits (175),  Expect(2) = 4e-42, Method: Compositional matrix adjust.
 Identities = 34/55 (61%), Positives = 42/55 (76%), Gaps = 0/55 (0%)
 Frame = +1

Query  605       ISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKAL  659
                 I+ +K   Y +HE +TT WDHP+M EL + LADLN +RFSAYRTAMKLR +QK L
Sbjct  15416449  INLSKPTLYYSHERETTHWDHPEMIELMKGLADLNEIRFSAYRTAMKLRSVQKRL  15416613


 Features in this part of subject sequence:
   dystrophin, isoform F
   dystrophin, isoform H

 Score =  101 bits (252),  Expect = 2e-18, Method: Compositional matrix adjust.
 Identities = 56/116 (48%), Positives = 75/116 (64%), Gaps = 9/116 (7%)
 Frame = +1

Query  943       GDNMETPASSPQLS----HDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLL  998
                 GD +E+PA SPQ +     +D HSR+E YASRLA++E     Y     +     DDEH L
Sbjct  15418051  GDALESPAPSPQHTTHQLQNDMHSRLEMYASRLAQVE-----YGGTGSNSTPDSDDEHQL  15418215

Query  999       IQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRL  1054
                 I  YCQ+L   S  S P+SP Q++ ++++E+R ELE I+ DLEEEN NLQAEY +L
Sbjct  15418216  IAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREELEAIIRDLEEENANLQAEYQQL  15418383


 Features in this part of subject sequence:
   dystrophin, isoform F
   dystrophin, isoform H

 Score = 78.2 bits (191),  Expect = 3e-11, Method: Compositional matrix adjust.
 Identities = 36/44 (81%), Positives = 43/44 (97%), Gaps = 0/44 (0%)
 Frame = +3

Query  1084      ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
                 +++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  15418545  DMMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  15418676


 Features in this part of subject sequence:
   dystrophin, isoform F
   dystrophin, isoform H

 Score = 64.3 bits (155),  Expect = 4e-07, Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 40/58 (68%), Gaps = 0/58 (0%)
 Frame = +2

Query  280       DLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIR  337
                 DLQ EIE H  VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ KS+ IR
Sbjct  15380540  DLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSKSIAIR  15380713


 Features in this part of subject sequence:
   dystrophin, isoform F
   dystrophin, isoform H

 Score = 40.0 bits (92),  Expect = 7.5, Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 32/50 (64%), Gaps = 2/50 (4%)
 Frame = +2

Query  337       RSHLEASSDQWKRLHLSLQELLVWLQLKDDELSR--QAPIGGDFPAVQKQ  384
                 R+ LE++S+ W  L LSL+EL  W+  KD ELS     P+ GD  ++QKQ
Sbjct  15384134  RNRLESNSEHWNALLLSLRELTEWVIRKDTELSTLGLGPVRGDAVSLQKQ  15384283


>gb|AC008192.8|AC008192 Drosophila melanogaster, chromosome 3R, region 92A-92A, BAC clone 
BACR12P10, complete sequence
Length=186686

 Score =  170 bits (430),  Expect(2) = 1e-54, Method: Compositional matrix adjust.
 Identities = 85/130 (65%), Positives = 98/130 (75%), Gaps = 9/130 (6%)
 Frame = +2

Query  784     IPRQLGEVASFGGSNIEPSVRSCFQFA---------NNKPEIEAALFLDWMRLEPQSMVW  834
               +PRQLGEVA+FGGSNIEPSVRSC + A         N    IE   FL W++ EPQS+VW
Sbjct  185882  VPRQLGEVAAFGGSNIEPSVRSCLEQAGISQEAIDGNQDISIELQHFLGWLQHEPQSLVW  186061

Query  835     LPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHY  894
               LPVLHR+AAAE AKHQAKCNICKE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +
Sbjct  186062  LPVLHRLAAAEAAKHQAKCNICKEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTH  186241

Query  895     PMVEYCTPTT  904
               PM EYCT  +
Sbjct  186242  PMHEYCTTVS  186271


 Score = 73.9 bits (180),  Expect(2) = 1e-54, Method: Compositional matrix adjust.
 Identities = 34/60 (56%), Positives = 46/60 (76%), Gaps = 2/60 (3%)
 Frame = +3

Query  903     TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGD--NMETPASSPQLSHDDT  960
               TTS EDVRDF + LKNKF++++YF KHPR+GYLPVQ+VLEG   N+ T +   ++ H +T
Sbjct  186333  TTSTEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQSVLEGKFPNLRTLSI*IKILHSET  186512


 Score =  130 bits (326),  Expect(2) = 4e-42, Method: Compositional matrix adjust.
 Identities = 63/126 (50%), Positives = 92/126 (73%), Gaps = 6/126 (4%)
 Frame = +3

Query  661     LDLLSLSAACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCL  719
               LD +S+S AC++ D+H L+ QND+ +DI  +   L ++Y  +++     +++ L +D+ +
Sbjct  185184  LDRISMSTACESFDRHGLRAQNDKLIDIPDMTTVLHSLYVTIDK-----IDLTLMLDLAI  185348

Query  720     NWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLH  779
               NW+LNVYD+ RTG+IRVLSFK G++ LCK HLE+KYRYLF+ VA +    DQRRLGLLLH
Sbjct  185349  NWILNVYDSQRTGQIRVLSFKVGLVLLCKGHLEEKYRYLFRLVADTDRRADQRRLGLLLH  185528

Query  780     DSIQIP  785
               D IQ+ 
Sbjct  185529  DCIQVS  185546


 Score = 72.0 bits (175),  Expect(2) = 4e-42, Method: Compositional matrix adjust.
 Identities = 34/55 (61%), Positives = 42/55 (76%), Gaps = 0/55 (0%)
 Frame = +1

Query  605     ISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKAL  659
               I+ +K   Y +HE +TT WDHP+M EL + LADLN +RFSAYRTAMKLR +QK L
Sbjct  184951  INLSKPTLYYSHERETTHWDHPEMIELMKGLADLNEIRFSAYRTAMKLRSVQKRL  185115


 Score = 64.3 bits (155),  Expect = 4e-07, Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 40/58 (68%), Gaps = 0/58 (0%)
 Frame = +2

Query  280     DLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIR  337
               DLQ EIE H  VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ KS+ IR
Sbjct  149042  DLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSKSIAIR  149215


 Score = 40.0 bits (92),  Expect = 7.5, Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 32/50 (64%), Gaps = 2/50 (4%)
 Frame = +2

Query  337     RSHLEASSDQWKRLHLSLQELLVWLQLKDDELSR--QAPIGGDFPAVQKQ  384
               R+ LE++S+ W  L LSL+EL  W+  KD ELS     P+ GD  ++QKQ
Sbjct  152636  RNRLESNSEHWNALLLSLRELTEWVIRKDTELSTLGLGPVRGDAVSLQKQ  152785


>gb|AC007815.7|AC007815 Drosophila melanogaster, chromosome 3R, region 92B-92B, BAC clone 
BACR07I18, complete sequence
Length=159413

 Score =  170 bits (430),  Expect(2) = 1e-54, Method: Compositional matrix adjust.
 Identities = 85/130 (65%), Positives = 98/130 (75%), Gaps = 9/130 (6%)
 Frame = +1

Query  784    IPRQLGEVASFGGSNIEPSVRSCFQFA---------NNKPEIEAALFLDWMRLEPQSMVW  834
              +PRQLGEVA+FGGSNIEPSVRSC + A         N    IE   FL W++ EPQS+VW
Sbjct  14887  VPRQLGEVAAFGGSNIEPSVRSCLEQAGISQEAIDGNQDISIELQHFLGWLQHEPQSLVW  15066

Query  835    LPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHY  894
              LPVLHR+AAAE AKHQAKCNICKE PI+GFRYR LK FN+D+CQ CFF GR AK HK+ +
Sbjct  15067  LPVLHRLAAAEAAKHQAKCNICKEYPIVGFRYRCLKCFNFDMCQKCFFFGRNAKNHKLTH  15246

Query  895    PMVEYCTPTT  904
              PM EYCT  +
Sbjct  15247  PMHEYCTTVS  15276


 Score = 73.9 bits (180),  Expect(2) = 1e-54, Method: Compositional matrix adjust.
 Identities = 34/60 (56%), Positives = 46/60 (76%), Gaps = 2/60 (3%)
 Frame = +2

Query  903    TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGD--NMETPASSPQLSHDDT  960
              TTS EDVRDF + LKNKF++++YF KHPR+GYLPVQ+VLEG   N+ T +   ++ H +T
Sbjct  15338  TTSTEDVRDFTRALKNKFKSRKYFKKHPRVGYLPVQSVLEGKFPNLRTLSI*IKILHSET  15517


 Score =  130 bits (326),  Expect(2) = 4e-42, Method: Compositional matrix adjust.
 Identities = 63/126 (50%), Positives = 92/126 (73%), Gaps = 6/126 (4%)
 Frame = +2

Query  661    LDLLSLSAACDALDQHNLK-QNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCL  719
              LD +S+S AC++ D+H L+ QND+ +DI  +   L ++Y  +++     +++ L +D+ +
Sbjct  14189  LDRISMSTACESFDRHGLRAQNDKLIDIPDMTTVLHSLYVTIDK-----IDLTLMLDLAI  14353

Query  720    NWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLH  779
              NW+LNVYD+ RTG+IRVLSFK G++ LCK HLE+KYRYLF+ VA +    DQRRLGLLLH
Sbjct  14354  NWILNVYDSQRTGQIRVLSFKVGLVLLCKGHLEEKYRYLFRLVADTDRRADQRRLGLLLH  14533

Query  780    DSIQIP  785
              D IQ+ 
Sbjct  14534  DCIQVS  14551


 Score = 72.0 bits (175),  Expect(2) = 4e-42, Method: Compositional matrix adjust.
 Identities = 34/55 (61%), Positives = 42/55 (76%), Gaps = 0/55 (0%)
 Frame = +3

Query  605    ISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKAL  659
              I+ +K   Y +HE +TT WDHP+M EL + LADLN +RFSAYRTAMKLR +QK L
Sbjct  13956  INLSKPTLYYSHERETTHWDHPEMIELMKGLADLNEIRFSAYRTAMKLRSVQKRL  14120


 Score =  101 bits (252),  Expect = 2e-18, Method: Compositional matrix adjust.
 Identities = 56/116 (48%), Positives = 75/116 (64%), Gaps = 9/116 (7%)
 Frame = +3

Query  943    GDNMETPASSPQLS----HDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLL  998
              GD +E+PA SPQ +     +D HSR+E YASRLA++E     Y     +     DDEH L
Sbjct  15558  GDALESPAPSPQHTTHQLQNDMHSRLEMYASRLAQVE-----YGGTGSNSTPDSDDEHQL  15722

Query  999    IQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRL  1054
              I  YCQ+L   S  S P+SP Q++ ++++E+R ELE I+ DLEEEN NLQAEY +L
Sbjct  15723  IAQYCQALPGTSNGSAPKSPVQVMAAMDAEQREELEAIIRDLEEENANLQAEYQQL  15890


 Score = 78.2 bits (191),  Expect = 3e-11, Method: Compositional matrix adjust.
 Identities = 36/44 (81%), Positives = 43/44 (97%), Gaps = 0/44 (0%)
 Frame = +2

Query  1084   ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQP  1127
              +++AEAKLLRQHKGRLEARMQILEDHN+QLE+QL RLRQLL++P
Sbjct  16052  DMMAEAKLLRQHKGRLEARMQILEDHNRQLEAQLQRLRQLLDEP  16183


>ref|XM_001742610.1| Monosiga brevicollis MX1 predicted protein MONBRDRAFT_22129 mRNA, 
complete cds
Length=3036

 Score =  217 bits (552),  Expect = 3e-53, Method: Compositional matrix adjust.
 Identities = 157/586 (26%), Positives = 279/586 (47%), Gaps = 66/586 (11%)
 Frame = +1

Query  587   PASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAY  646
             PA +  +   +   W +A++ +  PYYINHET+ T W  P++    Q L+  +++R +AY
Sbjct  139   PARKSMIGEPLPHGWAKALTDSGTPYYINHETRVTQWVDPRLQSCLQELSAHDDIRLAAY  318

Query  647   RTAMKLRRLQKALCLDLLSLSAACDA---LDQHNLKQNDQPMDILQIINCLTTIYDRLEQ  703
             RTA+KLR +Q  L +  + L  A +A   LD H+   + Q +D  ++   L  +Y  L  
Sbjct  319   RTAIKLRDVQVYLRMSQIKLPTALNAFYALDVHSDYSSGQQIDAEEMAVVLMEMYADLPH  498

Query  704   EHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVA  763
                N       V++ ++ +L +YD  R+G I + +F+T +  L  + +E+KYR+LF    
Sbjct  499   PQRN-------VEVMISMMLKIYDRNRSGHISLQAFQTALTLLSVSWIEEKYRFLFTIYD  657

Query  764   SS-TGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPS--VRSCFQFANNK-----PE  815
             ++   F    +L  LL   + +P  + E  +F  +   P       F+    +      +
Sbjct  658   TNQDDFITVEQLTQLLRHVVGLPNGIREAYAFCPTKEFPEQEAHRVFELERERNGAAATQ  837

Query  816   IEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYD  875
             I    F+++   +P+ ++WLPV+HRVAA E +KH+  C +CK  PIIGFRY+++   + D
Sbjct  838   ISLNTFVNYCMTDPRPLLWLPVMHRVAATENSKHETTCCVCKMYPIIGFRYKNMTSMDRD  1017

Query  876   ICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYL  935
             +CQ C+++GR   GHK  + + EYC  +T+ +D +DF   +K K   K+           
Sbjct  1018  VCQECYWTGREGNGHKASHEVKEYCFSSTARQDAKDFFGRIKRKMTKKKADESEAARTAR  1197

Query  936   PVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDE  995
               + V        P + P++S    + +     +   ++ +     L+  ++    + DE
Sbjct  1198  AAKPV--------PVAEPRMSVAVPYEQALQEPAEGDDVVDHADVGLSHGVA---GLQDE  1344

Query  996   HLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNL-----QAE  1050
             H LIQ     L        P S   ++++LE+E++  L R++ +L+ ENR L      +E
Sbjct  1345  HDLIQEMAAQLKAADDEGGPVS--TMVVNLETEQKLHLLRVIDELDAENRQLLQRLMDSE  1518

Query  1051  YDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHN  1110
              DR+ +  E     P+           +  RDA               ++ R+  L + N
Sbjct  1519  RDRVAELQE-----PV--------AGDEGVRDA---------------MQGRINDLNERN  1614

Query  1111  KQLESQLHRLRQLL-EQPQAEAKVNGT-TVSSPSTSLQRSDSSQPM  1154
             + L  QL RL+ +L     A+   N    V++P+  L R+ +   M
Sbjct  1615  RDLVDQLTRLQAMLVASGMAQGHDNDNEQVNAPAYELARAGTHDDM  1752


>gb|L06945.1|FSCTYRDYS Torpedo californica postsynaptic membrane protein mRNA, complete 
cds
Length=4615

 Score =  210 bits (535),  Expect = 4e-51, Method: Compositional matrix adjust.
 Identities = 180/628 (28%), Positives = 300/628 (47%), Gaps = 68/628 (10%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND--QPMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   + L+ +    +A  ++ L   D    + + ++   +
Sbjct  211   DLDCIRLSTYRTACKLRFVQKKCNVHLVDVWNVIEAFRENGLNTMDPNAELSVARLEAII  390

Query  695   TTIYDRLEQEHNNL--VNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             + I  +L +   N   +NV   V + LN+LL  YD    G+I V + K  + ++C   + 
Sbjct  391   SAILYQLNKRMPNTHQINVEQSVSLLLNFLLAAYDGEGHGKISVFAVKVVLATICGGKIL  570

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E + RSCF   + 
Sbjct  571   DKLRYIFSQISDSNGVMINAKFDQFLREVLKLPTSVFEGPSFGYT--EQASRSCF---SQ  735

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VW+P++HR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  736   QKKVTLNSFLDTLMSDPPPQCLVWIPLMHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  915

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRD-FAKVLKNKFRTKRYFAKH  929
               NY +CQ CF+ G  +  H   + M EY +  +  + + +  +K L      +     +
Sbjct  916   CHNYQLCQDCFWRGHASGSHSNQHQMKEYTSWKSPAKKITNALSKSLSCASSHEPLHPIY  1095

Query  930   PRMGYLPVQTVLEGDNMETPASSPQLSHDD--THSRIE----------HY----ASRLAE  973
             P     P+           P+ +P   +D   +HS I           HY    A RL +
Sbjct  1096  PDQPEKPLNLA-----HVVPSRTPPNMNDTMFSHSVITSGSPSPNKRLHYSLDIADRLGD  1260

Query  974   MENSNGSYLNDSI--------SPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISL  1025
                  G Y+N  +        SPN  +D+EH LI  Y   L  ++  SQ R+P+ +  ++
Sbjct  1261  EHVLIGLYINLLLNNSSRVLDSPNR-MDEEHRLIARYAARLAAEAASSQQRAPSDLTSTI  1437

Query  1026  ESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAEL  1085
             ++ +  +  +++A+LE +NR +  E  RL+ +HE     P P   +  PT         L
Sbjct  1438  DANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------L  1581

Query  1086  IAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLL--EQPQAEAKVNGTTVSSPST  1143
             +AE +LLRQ K  LE RM  L++  ++L  QL  L +LL  E+ + E +  G+  SSPS 
Sbjct  1582  LAELRLLRQRKDELEQRMSALQESRRELMVQLEGLMKLLKEEEMRQETQGTGSPRSSPSH  1761

Query  1144  SLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-  1202
             ++ RS    PM +R   + ++ +         PQD+ TG   V   +  +F  S   N+ 
Sbjct  1762  TISRS-VPIPMPIRSTSTCSTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLR  1908

Query  1203  GSLFHMADDLGRAMESLVSVMTDEEGAE  1230
               L   AD +   M SLV  +  E G+E
Sbjct  1909  NDLLVAADSITNTMSSLVKELNSEAGSE  1992


>ref|XM_001368984.1| PREDICTED: Monodelphis domestica similar to dystrobrevin, alpha,, 
transcript variant 2 (LOC100023710), mRNA
Length=2061

 Score =  209 bits (533),  Expect = 6e-51, Method: Compositional matrix adjust.
 Identities = 183/614 (29%), Positives = 296/614 (48%), Gaps = 74/614 (12%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  76    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  255

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  256   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  435

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R  L L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  436   DKLRYIFSMISDSSGVMVYGRYDLFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  600

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601   QKKVTLNAFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G  +  H   + M EY +        +  AK L N        A   
Sbjct  781   CHNYQLCQDCFWRGHASGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  939

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYL  982
                HP     P + +     ++T    P  S +DT   HS           + +S   ++
Sbjct  940   EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPFI  1086

Query  983   NDSI--SPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERIL  1037
               S+  SPN  +D+EH LI  Y   L  ++  +QP   R P+ I  ++++ +  +  +++
Sbjct  1087  TRSMLDSPNR-LDEEHRLIARYAARLAAETSSTQPSQQRGPSDISFTIDANK--QQRQLI  1257

Query  1038  ADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKG  1097
             A+LE +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K 
Sbjct  1258  AELENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKD  1407

Query  1098  RLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLR  1157
              LE RM  L++  ++L  QL  L +LL+   A     G+  SSPS ++ R     PM +R
Sbjct  1408  ELEQRMSALQESRRELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIR  1563

Query  1158  VVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAM  1216
                + ++ +         PQD+ TG   V   +  +F  S   N+   L   AD +   M
Sbjct  1564  SASACSTPTHT-------PQDSLTG---VGGDVQEAFAQSTRRNLRNDLLVAADSITNTM  1713

Query  1217  ESLVSVMTDEEGAE  1230
              SLV  +  E G+E
Sbjct  1714  SSLVKELNSEVGSE  1755


>ref|XM_001515642.1| PREDICTED: Ornithorhynchus anatinus similar to dystrobrevin, 
alpha,, transcript variant 2 (LOC100079727), mRNA
Length=2061

 Score =  206 bits (525),  Expect = 5e-50, Method: Compositional matrix adjust.
 Identities = 183/614 (29%), Positives = 295/614 (48%), Gaps = 74/614 (12%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  76    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNVELNVARLEAVL  255

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  256   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  435

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R  L L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  436   DKLRYIFSMISDSSGVMVYGRYDLFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  600

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601   QKKVTLNAFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G  +  H   + M EY +        +  AK L N        A   
Sbjct  781   CHNYQLCQDCFWRGHASGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  939

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYL  982
                HP     P + +     ++T    P  S +DT   HS           + +S   ++
Sbjct  940   EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPFI  1086

Query  983   NDSI--SPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERIL  1037
               S+  SPN  +D+EH LI  Y   L  ++  SQP   R  + I  ++++ +  +  +++
Sbjct  1087  TRSMLDSPNR-LDEEHRLIARYAARLAAETSSSQPGQQRGASDISFTIDANK--QQRQLI  1257

Query  1038  ADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKG  1097
             A+LE +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K 
Sbjct  1258  AELENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKD  1407

Query  1098  RLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLR  1157
              LE RM  L++  ++L  QL  L +LL+   A     G+  SSPS ++ R     PM +R
Sbjct  1408  ELEQRMSALQESRRELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIR  1563

Query  1158  VVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAM  1216
                + ++ +         PQD+ TG   V   +  +F  S   N+   L   AD +   M
Sbjct  1564  SASTCSTPTHT-------PQDSLTG---VGGDVQEAFAQSARRNLRNDLLVAADSITNTM  1713

Query  1217  ESLVSVMTDEEGAE  1230
              SLV  +  E G+E
Sbjct  1714  SSLVKELNSEVGSE  1755


>ref|XM_001369015.1| PREDICTED: Monodelphis domestica similar to dystrobrevin, alpha,, 
transcript variant 3 (LOC100023710), mRNA
Length=2052

 Score =  206 bits (525),  Expect = 5e-50, Method: Compositional matrix adjust.
 Identities = 182/611 (29%), Positives = 293/611 (47%), Gaps = 71/611 (11%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  76    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  255

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  256   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  435

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R  L L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  436   DKLRYIFSMISDSSGVMVYGRYDLFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  600

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601   QKKVTLNAFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--K  928
               NY +CQ CF+ G  +  H   + M EY +        +  AK L N        A  +
Sbjct  781   CHNYQLCQDCFWRGHASGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  939

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLNDS  985
              P     P Q     +        P  S +DT   HS           + +S   ++  S
Sbjct  940   EPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITRS  1086

Query  986   I--SPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADL  1040
             +  SPN  +D+EH LI  Y   L  ++  +QP   R P+ I  ++++ +  +  +++A+L
Sbjct  1087  MLDSPNR-LDEEHRLIARYAARLAAETSSTQPSQQRGPSDISFTIDANK--QQRQLIAEL  1257

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE
Sbjct  1258  ENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELE  1407

Query  1101  ARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVG  1160
              RM  L++  ++L  QL  L +LL+   A     G+  SSPS ++ R     PM +R   
Sbjct  1408  QRMSALQESRRELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIRSAS  1563

Query  1161  SQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESL  1219
             + ++ +         PQD+ TG   V   +  +F  S   N+   L   AD +   M SL
Sbjct  1564  ACSTPTHT-------PQDSLTG---VGGDVQEAFAQSTRRNLRNDLLVAADSITNTMSSL  1713

Query  1220  VSVMTDEEGAE  1230
             V  +  E G+E
Sbjct  1714  VKELNSEVGSE  1746


>gb|DQ516343.1| Danio rerio alpha-dystrobrevin splice variant 1 (ADTN) mRNA, 
complete cds, alternatively spliced
Length=2342

 Score =  206 bits (523),  Expect = 1e-49, Method: Compositional matrix adjust.
 Identities = 184/648 (28%), Positives = 296/648 (45%), Gaps = 83/648 (12%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIINCL  694
             DL+++R S YRTA KLR +QK   L L+ +    +   ++ L   + +    +  +   L
Sbjct  76    DLDSIRLSTYRTACKLRFIQKRCNLHLVDIWNIIEVFRENRLNSVELNTEFSVSHLQAIL  255

Query  695   TTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + +NV   +   LN+LL  YD    G+I     K  + +LC   + 
Sbjct  256   STIFQQLNKRLPTTHQINVDQSISYLLNFLLTAYDQEGVGKISAFVMKMALATLCGGKIL  435

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F Q++   G     +    L + +++P  + E  SFG +  E S RSCF     
Sbjct  436   DKLRYIFSQISDPNGLMIYSQFDQFLREVLKVPVSVFEGPSFGYT--EQSTRSCFP---Q  600

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++   +FLD    +P  Q +VWLP++HR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601   EKKVTLNVFLDTFMSDPPPQCLVWLPLMHRLANVENVFHPVECSYCHSQSMMGFRYRCQQ  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRD-FAKVLK-NKFRTKRY--F  926
               NY +CQ CF+ G  +  H   + M EY +  +  + + D  +K L     R   Y  F
Sbjct  781   CDNYQLCQECFWRGHASGSHSNQHQMKEYMSWKSPAKKLSDALSKSLSCAASREPAYPQF  960

Query  927   AKHPRMG-----YLPVQTVLEGD----NMETPAS----SPQLSHDDTH-----SRIE---  965
             +  P         +P + V  G+    +   P+S    S + +HD+T+     SR     
Sbjct  961   SDTPEKTLNLNHIVPPRPVATGNEYMLSHSMPSSGNPYSSKAAHDETNQMKLFSRTTPDL  1140

Query  966   ----------HYASRLAEMENSNGSYLN---------DSISPNESIDDEHLLIQHYCQSL  1006
                         A RLA+     G Y+N            S N+  DDEH LI  Y   L
Sbjct  1141  LKGKGVQYSLDIADRLADEHILIGLYVNLLQKERSCFQHSSKNQ--DDEHCLIARYASRL  1314

Query  1007  NQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPL  1066
               D   ++ R P  I + L+S ++    +++A+LE +N+ +  E  RL+QQHE     PL
Sbjct  1315  AADEVAAKGRVPTDISLCLDSNKQQ--RQLIAELENKNKEILQEIQRLRQQHEEASQPPL  1488

Query  1067  PSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ  1126
                        ++ ++  L+AE +LLRQ K  LE RM  L++  ++L  QL +L  LL+ 
Sbjct  1489  ----------DKNQQNPMLLAELRLLRQRKEELEQRMSALQESRRELMVQLEQLMLLLKN  1638

Query  1127  PQAEAKVNGT---TVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGL  1183
                      +   T+S+   SL  + +  PM ++     T+ S         PQD+  GL
Sbjct  1639  QGPGPSPRSSPSHTLSASVQSLSGNSTPIPMPVQSTSGNTTPSQT-------PQDSLMGL  1797

Query  1184  EEVMEQLNNSFPSSRGHNVGS-LFHMADDLGRAMESLVSVMTDEEGAE  1230
                ++Q   +F      N+ S L   AD +   M SLV  +  E G E
Sbjct  1798  GGEVQQ---AFAQGSRRNLRSDLLVAADSITNTMSSLVKELNSEAGNE  1932


>gb|DQ516344.1| Danio rerio alpha-dystrobrevin splice variant 2 (ADTN) mRNA, 
complete cds, alternatively spliced
Length=2354

 Score =  204 bits (519),  Expect = 2e-49, Method: Compositional matrix adjust.
 Identities = 186/652 (28%), Positives = 297/652 (45%), Gaps = 87/652 (13%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIINCL  694
             DL+++R S YRTA KLR +QK   L L+ +    +   ++ L   + +    +  +   L
Sbjct  76    DLDSIRLSTYRTACKLRFIQKRCNLHLVDIWNIIEVFRENRLNSVELNTEFSVSHLQAIL  255

Query  695   TTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + +NV   +   LN+LL  YD    G+I     K  + +LC   + 
Sbjct  256   STIFQQLNKRLPTTHQINVDQSISYLLNFLLTAYDQEGVGKISAFVMKMALATLCGGKIL  435

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F Q++   G     +    L + +++P  + E  SFG +  E S RSCF     
Sbjct  436   DKLRYIFSQISDPNGLMIYSQFDQFLREVLKVPVSVFEGPSFGYT--EQSTRSCFP---Q  600

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++   +FLD    +P  Q +VWLP++HR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601   EKKVTLNVFLDTFMSDPPPQCLVWLPLMHRLANVENVFHPVECSYCHSQSMMGFRYRCQQ  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRD-FAKVLK-NKFRTKRY--F  926
               NY +CQ CF+ G  +  H   + M EY +  +  + + D  +K L     R   Y  F
Sbjct  781   CDNYQLCQECFWRGHASGSHSNQHQMKEYMSWKSPAKKLSDALSKSLSCAASREPAYPQF  960

Query  927   AKHPR--------MGYLPVQTVLEGD----NMETPAS----SPQLSHDDTH-----SRIE  965
             +  P         +G  P + V  G+    +   P+S    S + +HD+T+     SR  
Sbjct  961   SDTPEKTLNLNHIVGTWPPRPVATGNEYMLSHSMPSSGNPYSSKAAHDETNQMKLFSRTT  1140

Query  966   -------------HYASRLAEMENSNGSYLN---------DSISPNESIDDEHLLIQHYC  1003
                            A RLA+     G Y+N            S N+  DDEH LI  Y 
Sbjct  1141  PDLLKGKGVQYSLDIADRLADEHILIGLYVNLLQKERSCFQHSSKNQ--DDEHCLIARYA  1314

Query  1004  QSLNQDSPLSQP-RSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKG  1062
               L  D   +Q  R P  I + L+S +  +  +++A+LE +N+ +  E  RL+QQHE   
Sbjct  1315  SRLAADEVAAQKGRVPTDISLCLDSNK--QQRQLIAELENKNKEILQEIQRLRQQHEEAS  1488

Query  1063  LSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQ  1122
               PL           ++ ++  L+AE +LLRQ K  LE RM  L++  ++L  QL +L  
Sbjct  1489  QPPL----------DKNQQNPMLLAELRLLRQRKEELEQRMSALQESRRELMVQLEQLML  1638

Query  1123  LLEQPQAEAKVNGT---TVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDT  1179
             LL+          +   T+S+   SL  + +  PM ++     T+ S         PQD+
Sbjct  1639  LLKNQGPGPSPRSSPSHTLSASVQSLSGNSTPIPMPVQSTSGNTTPS-------QTPQDS  1797

Query  1180  STGLEEVMEQLNNSFPSSRGHNVGS-LFHMADDLGRAMESLVSVMTDEEGAE  1230
               GL   ++Q   +F      N+ S L   AD +   M SLV  +  E G E
Sbjct  1798  LMGLGGEVQQ---AFAQGSRRNLRSDLLVAADSITNTMSSLVKELNSEAGNE  1944


>ref|XM_001515599.1| PREDICTED: Ornithorhynchus anatinus similar to dystrobrevin, 
alpha,, transcript variant 1 (LOC100079727), mRNA
Length=2052

 Score =  204 bits (518),  Expect = 3e-49, Method: Compositional matrix adjust.
 Identities = 182/611 (29%), Positives = 292/611 (47%), Gaps = 71/611 (11%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  76    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNVELNVARLEAVL  255

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  256   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  435

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R  L L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  436   DKLRYIFSMISDSSGVMVYGRYDLFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  600

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601   QKKVTLNAFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--K  928
               NY +CQ CF+ G  +  H   + M EY +        +  AK L N        A  +
Sbjct  781   CHNYQLCQDCFWRGHASGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  939

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLNDS  985
              P     P Q     +        P  S +DT   HS           + +S   ++  S
Sbjct  940   EPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITRS  1086

Query  986   I--SPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADL  1040
             +  SPN  +D+EH LI  Y   L  ++  SQP   R  + I  ++++ +  +  +++A+L
Sbjct  1087  MLDSPNR-LDEEHRLIARYAARLAAETSSSQPGQQRGASDISFTIDANK--QQRQLIAEL  1257

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE
Sbjct  1258  ENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELE  1407

Query  1101  ARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVG  1160
              RM  L++  ++L  QL  L +LL+   A     G+  SSPS ++ R     PM +R   
Sbjct  1408  QRMSALQESRRELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIRSAS  1563

Query  1161  SQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESL  1219
             + ++ +         PQD+ TG   V   +  +F  S   N+   L   AD +   M SL
Sbjct  1564  TCSTPTHT-------PQDSLTG---VGGDVQEAFAQSARRNLRNDLLVAADSITNTMSSL  1713

Query  1220  VSVMTDEEGAE  1230
             V  +  E G+E
Sbjct  1714  VKELNSEVGSE  1746


>ref|NM_032975.3| Homo sapiens dystrobrevin, alpha (DTNA), transcript variant 2, 
mRNA
Length=6537

 Score =  202 bits (514),  Expect = 9e-49, Method: Compositional matrix adjust.
 Identities = 182/614 (29%), Positives = 293/614 (47%), Gaps = 74/614 (12%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  427   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  603

Query  694   LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
             L+TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  604   LSTIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  783

Query  752   EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  784   MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  948

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  949   QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  1128

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK-  928
             +  NY +CQ CF+ G     H   + M EY +        +  AK L N        A  
Sbjct  1129  QCHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASS  1287

Query  929   ----HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSY  981
                 HP     P + +     ++T    P  S +DT   HS           + +S   +
Sbjct  1288  REPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPF  1434

Query  982   LNDS-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERIL  1037
             +  S +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++
Sbjct  1435  ITRSMLESSNRLDEEHRLIARYAARLAAESSSSQPPQQRSAPDISFTIDANK--QQRQLI  1608

Query  1038  ADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKG  1097
             A+LE +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K 
Sbjct  1609  AELENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKD  1758

Query  1098  RLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLR  1157
              LE RM  L++  ++L  QL  L +LL+   A     G+  SSPS ++ R     PM +R
Sbjct  1759  ELEQRMSALQESRRELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIR  1914

Query  1158  VVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAM  1216
                + ++ +         PQD+ TG   V   +  +F  S   N+   L   AD +   M
Sbjct  1915  SASACSTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLRNDLLVAADSITNTM  2064

Query  1217  ESLVSVMTDEEGAE  1230
              SLV  +  E G+E
Sbjct  2065  SSLVKELNSEVGSE  2106


>ref|XM_001368953.1| PREDICTED: Monodelphis domestica similar to dystrobrevin, alpha,, 
transcript variant 1 (LOC100023710), mRNA
Length=2232

 Score =  201 bits (510),  Expect = 3e-48, Method: Compositional matrix adjust.
 Identities = 192/662 (29%), Positives = 305/662 (46%), Gaps = 113/662 (17%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  76    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  255

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  256   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  435

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R  L L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  436   DKLRYIFSMISDSSGVMVYGRYDLFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  600

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601   QKKVTLNAFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G  +  H   + M EY +        +  AK L N        A   
Sbjct  781   CHNYQLCQDCFWRGHASGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  939

Query  929   ---HPRMGYLPVQTVLEGDNMET------------------PAS-SPQLSHDDTHSRIE-  965
                HP     P + +     ++T                  P+S SP ++   +H   E 
Sbjct  940   EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHSVPSSGSPFITRSSSHKNTEV  1119

Query  966   -------------------HY----ASRLAE----------MENSNGSYLNDSISPNESI  992
                                HY    A RLA+          M  SN S + D  SPN  +
Sbjct  1120  EQSKLLARAAPIFLKGKGLHYSLDVADRLADEHVLIGLYVNMLQSNPSRMLD--SPNR-L  1290

Query  993   DDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQA  1049
             D+EH LI  Y   L  ++  +QP   R P+ I  ++++ +  +  +++A+LE +NR +  
Sbjct  1291  DEEHRLIARYAARLAAETSSTQPSQQRGPSDISFTIDANK--QQRQLIAELENKNREILQ  1464

Query  1050  EYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDH  1109
             E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++ 
Sbjct  1465  EIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQES  1614

Query  1110  NKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGE  1169
              ++L  QL  L +LL+   A     G+  SSPS ++ R     PM +R   + ++ +   
Sbjct  1615  RRELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIRSASACSTPTHT-  1767

Query  1170  EDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESLVSVMTDEEG  1228
                   PQD+ TG   V   +  +F  S   N+   L   AD +   M SLV  +  E G
Sbjct  1768  ------PQDSLTG---VGGDVQEAFAQSTRRNLRNDLLVAADSITNTMSSLVKELNSEVG  1920

Query  1229  AE  1230
             +E
Sbjct  1921  SE  1926


>ref|XM_001359998.2| Drosophila pseudoobscura pseudoobscura GA20280 (Dpse\GA20280), 
mRNA
Length=3141

 Score =  200 bits (508),  Expect = 5e-48, Method: Compositional matrix adjust.
 Identities = 125/388 (32%), Positives = 210/388 (54%), Gaps = 19/388 (4%)
 Frame = +1

Query  93    RIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYT  152
             ++ R++  WDE Q+ +  R  QL  ML DS ++   + E E+ L +   + E       T
Sbjct  1669  KVTRLREHWDETQQCVLQRAAQLKTMLSDSQRFEAKRLELEKWLARMEQRAERMGTIATT  1848

Query  153   VDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRS  212
              D ++ +  E K    +L Q + + D+ N+L  KL+  Y  DDT ++  +TE +N  + +
Sbjct  1849  ADILEAQQKEQKSFHAELHQNKQHFDIFNELTQKLIAVYPNDDTSRIKKMTEVVNQRYSN  2028

Query  213   IHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVK  272
             ++  V  R   L      LQ F   +++FLA+L+E ET     +    +  L+       
Sbjct  2029  LNNGVINRGKQLHAAVHSLQSFDRAMDQFLAFLSETETLCENAESEIDRNPLM-------  2187

Query  273   ELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKK  332
                  ++DLQ EIE H  VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ K
Sbjct  2188  -----FKDLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSK  2352

Query  333   SLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSR--QAPIGGDFPAVQKQNDVHRA  390
             S+ IR+ LE++S+ W  L LSL+EL  W+  KD ELS     P+ GD  ++QKQ D H+A
Sbjct  2353  SIAIRNRLESNSEHWNALLLSLRELTEWVIRKDTELSTLGLGPVRGDAASLQKQLDDHKA  2532

Query  391   FKRELKTKEPVIMSTLETVRIFLTEQPL-----EGLEKLYQEPRELPPEERAQNVTRLLR  445
             F+R+L+ K P++ S L + R ++  +       +       + R +  EE+++ +TR +R
Sbjct  2533  FRRQLEDKRPIVESNLTSGRQYIANEAAVSDTSDTEANHDSDSRYMSAEEQSRELTRSIR  2712

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETL  473
             ++  +++ +W  L   S +W+ ++DE +
Sbjct  2713  REVGKLSEQWNNLIDRSDNWKHRLDEYM  2796


>ref|XM_002019867.1| Drosophila persimilis GL12655 (Dper\GL12655), mRNA
Length=3138

 Score =  200 bits (508),  Expect = 5e-48, Method: Compositional matrix adjust.
 Identities = 125/388 (32%), Positives = 210/388 (54%), Gaps = 19/388 (4%)
 Frame = +1

Query  93    RIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYT  152
             ++ R++  WDE Q+ +  R  QL  ML DS ++   + E E+ L +   + E       T
Sbjct  1666  KVTRLREHWDETQQCVLQRAAQLKTMLSDSQRFEAKRLELEKWLARMEQRAERMGTIATT  1845

Query  153   VDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRS  212
              D ++ +  E K    +L Q + + D+ N+L  KL+  Y  DDT ++  +TE +N  + +
Sbjct  1846  ADILEAQQKEQKSFHAELHQNKQHFDIFNELTQKLIAVYPNDDTSRIKKMTEVVNQRYSN  2025

Query  213   IHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVK  272
             ++  V  R   L      LQ F   +++FLA+L+E ET     +    +  L+       
Sbjct  2026  LNNGVINRGKQLHAAVHSLQSFDRAMDQFLAFLSETETLCENAESEIDRNPLM-------  2184

Query  273   ELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKK  332
                  ++DLQ EIE H  VY  LD   +K+L SL   +DAV+LQRRLD MN +W+ L+ K
Sbjct  2185  -----FKDLQSEIETHRVVYDRLDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSK  2349

Query  333   SLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSR--QAPIGGDFPAVQKQNDVHRA  390
             S+ IR+ LE++S+ W  L LSL+EL  W+  KD ELS     P+ GD  ++QKQ D H+A
Sbjct  2350  SIAIRNRLESNSEHWNALLLSLRELTEWVIRKDTELSTLGLGPVRGDAASLQKQLDDHKA  2529

Query  391   FKRELKTKEPVIMSTLETVRIFLTEQPL-----EGLEKLYQEPRELPPEERAQNVTRLLR  445
             F+R+L+ K P++ S L + R ++  +       +       + R +  EE+++ +TR +R
Sbjct  2530  FRRQLEDKRPIVESNLTSGRQYIANEAAVSDTSDTEANHDSDSRYMSAEEQSRELTRSIR  2709

Query  446   KQAEEVNTEWEKLNLHSADWQRKIDETL  473
             ++  +++ +W  L   S +W+ ++DE +
Sbjct  2710  REVGKLSEQWNNLIDRSDNWKHRLDEYM  2793


>ref|XM_001639844.1| Nematostella vectensis predicted protein (NEMVEDRAFT_v1g85254) 
partial mRNA
Length=1782

 Score =  199 bits (506),  Expect = 8e-48, Method: Compositional matrix adjust.
 Identities = 155/520 (29%), Positives = 248/520 (47%), Gaps = 49/520 (9%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDI--LQIINCL  694
             + + +RF++YRTA KL+ +QK   L L+ +    +A  ++ L   D   ++  L++   +
Sbjct  4     NFDTIRFASYRTAAKLQFIQKKTNLHLVDVYNMIEAFRENGLNTLDHNTELHELRLEAIV  183

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++I+     RL   HN  V+V   + +  NWLL  YD+   GRIRVLS KT + S+C   
Sbjct  184   SSIFYALNKRLPTTHN--VDVERSISLVTNWLLYAYDSDAIGRIRVLSVKTALSSMCYGR  357

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY F Q+  + G  +  +    L + +Q+P  +GE  +FG +    S+    Q  
Sbjct  358   LVDKLRYHFSQIEDNNGMLNFPKFEAYLRELLQLPASVGEAPTFGFTEDVASIFFKPQGP  537

Query  811   NNKPEIEAALFLDWM--RLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
              ++   +   FL+ +  +  P    WL  L ++  A   +HQ  C +CK  P++GFRY+ 
Sbjct  538   LDRQRTQLVHFLECVMNKEPPPPYAWLSTLQKMNNAAKTEHQVACQVCKNKPVVGFRYKC  717

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCT--PTTSGEDVRDFAKVLKNKFRTKRY-  925
             L  +NY +CQ CF+ G+V++ HK  + M EY T      G  +R  +K L    + KR  
Sbjct  718   LHCYNYVLCQDCFWRGKVSQHHKTDHDMREYSTWNAGEKGSSLR--SKFLCGSGKKKRPS  891

Query  926   ---FAKHPRMGYL--------PVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAE-  973
                F + P             P+ + L G N  T       S +   S +    ++L++ 
Sbjct  892   LPDFPREPEPSRTLDMTNIVPPLPSDLSGPNNATSDYVTSPSPESVVSNVSSNPTKLSDE  1071

Query  974   ---MENSNG-----SYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISL  1025
                +  S+G      YL   I  +  +DDEH LI  Y   L +   + +  SPA     L
Sbjct  1072  VTCVNLSSGFWCWIFYLYYLILFSCRMDDEHKLISRYAARLVR---VHKTFSPATSSSEL  1242

Query  1026  ESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAEL  1085
               +   E   ++  LE +NR L  E  RL+ +H+           E   ++ Q  ++ EL
Sbjct  1243  SIDANKEQRELIQTLENKNRLLLKEIRRLRDEHD-----------EASKSAAQLAQNPEL  1389

Query  1086  IAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLE  1125
             +AE KLLRQ K  LE RM  L++  ++L  QL  L  LL+
Sbjct  1390  LAELKLLRQRKDELELRMSALQESRRELMVQLEGLMNLLK  1509


>dbj|AB209102.1| Homo sapiens mRNA for dystrobrevin alpha isoform 2 variant protein
Length=6015

 Score =  199 bits (506),  Expect = 8e-48, Method: Compositional matrix adjust.
 Identities = 181/611 (29%), Positives = 290/611 (47%), Gaps = 71/611 (11%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  376   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  552

Query  694   LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
             L+TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  553   LSTIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  732

Query  752   EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  733   MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  897

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  898   QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  1077

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--  927
             +  NY +CQ CF+ G     H   + M EY +        +  AK L N        A  
Sbjct  1078  QCHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASS  1236

Query  928   KHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLND  984
             + P     P Q     +        P  S +DT   HS           + +S   ++  
Sbjct  1237  REPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITR  1383

Query  985   S-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADL  1040
             S +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+L
Sbjct  1384  SMLESSNRLDEEHRLIARYAARLAAESSSSQPPQQRSAPDISFTIDANK--QQRQLIAEL  1557

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE
Sbjct  1558  ENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELE  1707

Query  1101  ARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVG  1160
              RM  L++  ++L  QL  L +LL+   A     G+  SSPS ++ R     PM +R   
Sbjct  1708  QRMSALQESRRELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIRSAS  1863

Query  1161  SQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESL  1219
             + ++ +         PQD+ TG   V   +  +F  S   N+   L   AD +   M SL
Sbjct  1864  ACSTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLRNDLLVAADSITNTMSSL  2013

Query  1220  VSVMTDEEGAE  1230
             V  +  E G+E
Sbjct  2014  VKELNSEVGSE  2046


>dbj|AB463020.1| Synthetic construct DNA, clone: pF1KB3754, Homo sapiens DTNA 
gene for dystrobrevin, alpha, without stop codon, in Flexi system
Length=2066

 Score =  199 bits (506),  Expect = 9e-48, Method: Compositional matrix adjust.
 Identities = 181/611 (29%), Positives = 290/611 (47%), Gaps = 71/611 (11%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  85    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  261

Query  694   LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
             L+TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  262   LSTIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  441

Query  752   EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  442   MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  606

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  607   QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  786

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--  927
             +  NY +CQ CF+ G     H   + M EY +        +  AK L N        A  
Sbjct  787   QCHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASS  945

Query  928   KHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLND  984
             + P     P Q     +        P  S +DT   HS           + +S   ++  
Sbjct  946   REPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITR  1092

Query  985   S-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADL  1040
             S +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+L
Sbjct  1093  SMLESSNRLDEEHRLIARYAARLAAESSSSQPPQQRSAPDISFTIDANK--QQRQLIAEL  1266

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE
Sbjct  1267  ENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELE  1416

Query  1101  ARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVG  1160
              RM  L++  ++L  QL  L +LL+   A     G+  SSPS ++ R     PM +R   
Sbjct  1417  QRMSALQESRRELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIRSAS  1572

Query  1161  SQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESL  1219
             + ++ +         PQD+ TG   V   +  +F  S   N+   L   AD +   M SL
Sbjct  1573  ACSTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLRNDLLVAADSITNTMSSL  1722

Query  1220  VSVMTDEEGAE  1230
             V  +  E G+E
Sbjct  1723  VKELNSEVGSE  1755


>gb|EU831672.1| Synthetic construct Homo sapiens clone HAIB:100066701; DKFZo003A0620 
dystrobrevin, alpha protein (DTNA) gene, encodes complete 
protein
Length=2116

 Score =  199 bits (505),  Expect = 1e-47, Method: Compositional matrix adjust.
 Identities = 180/613 (29%), Positives = 292/613 (47%), Gaps = 68/613 (11%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  98    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  274

Query  694   LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
             L+ I+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  275   LSAIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  454

Query  752   EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  455   MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  619

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  620   QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  799

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--  927
             +  NY +CQ CF+ G     H   + M EY +        +  AK L N        A  
Sbjct  800   QCHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASS  958

Query  928   KHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLND  984
             + P     P Q     +        P  S +DT   HS           + +S   ++  
Sbjct  959   REPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITR  1105

Query  985   S-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADL  1040
             S +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++++  +  +++A+L
Sbjct  1106  SMLESSNRLDEEHRLIARYAARLAAESSSSQPPQQRSAPDISFTIDADK--QQRQLIAEL  1279

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE
Sbjct  1280  ENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELE  1429

Query  1101  ARMQILEDHNKQLESQLHRLRQLL--EQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
              RM  L++  ++L  QL  L +LL  E+ +   +  G+  SSPS ++ R     PM +R 
Sbjct  1430  QRMSALQESRRELMVQLEGLMKLLKEEELKQGTQGAGSPRSSPSHTISRPI---PMPIRS  1600

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAME  1217
               + ++ +         PQD+ TG   V   +  +F  S   N+   L   AD +   M 
Sbjct  1601  ASACSTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLRNDLLVAADSITNTMS  1750

Query  1218  SLVSVMTDEEGAE  1230
             SLV  +  E G+E
Sbjct  1751  SLVKELNSEVGSE  1789


>emb|AL833285.1| Homo sapiens mRNA; cDNA DKFZp451O128 (from clone DKFZp451O128)
Length=6066

 Score =  197 bits (502),  Expect = 3e-47, Method: Compositional matrix adjust.
 Identities = 180/613 (29%), Positives = 291/613 (47%), Gaps = 68/613 (11%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  383   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  559

Query  694   LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
             L+ I+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  560   LSAIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  739

Query  752   EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  740   MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  904

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  905   QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  1084

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--  927
             +  NY +CQ CF+ G     H   + M EY +        +  AK L N        A  
Sbjct  1085  QCHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASS  1243

Query  928   KHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLND  984
             + P     P Q     +        P  S +DT   HS           + +S   ++  
Sbjct  1244  REPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITR  1390

Query  985   S-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADL  1040
             S +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+L
Sbjct  1391  SMLESSNRLDEEHRLIARYAARLAAESSSSQPPQQRSAPDISFTIDANK--QQRQLIAEL  1564

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE
Sbjct  1565  ENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELE  1714

Query  1101  ARMQILEDHNKQLESQLHRLRQLL--EQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
              RM  L++  ++L  QL  L +LL  E+ +   +  G+  SSPS ++ R     PM +R 
Sbjct  1715  QRMSALQESRRELMVQLEGLMKLLKEEELKQGTQGAGSPRSSPSHTISRPI---PMPIRS  1885

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAME  1217
               + ++ +         PQD+ TG   V   +  +F  S   N+   L   AD +   M 
Sbjct  1886  ASACSTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLRNDLLVAADSITNTMS  2035

Query  1218  SLVSVMTDEEGAE  1230
             SLV  +  E G+E
Sbjct  2036  SLVKELNSEVGSE  2074


>dbj|AK147359.1| Mus musculus cDNA, RIKEN full-length enriched library, clone:M5C1020E04 
product:dystrobrevin alpha, full insert sequence
Length=6171

 Score =  196 bits (499),  Expect = 5e-47, Method: Compositional matrix adjust.
 Identities = 178/613 (29%), Positives = 290/613 (47%), Gaps = 72/613 (11%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  256   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  435

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  436   STIFYQLNKSMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  615

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  616   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  780

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  781   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  960

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  961   CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1119

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYL  982
                HP     P + +     ++T    P  S +DT   HS           + +S   ++
Sbjct  1120  EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPFI  1266

Query  983   NDS-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILA  1038
               S +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++A
Sbjct  1267  TRSMLESSNRLDEEHRLIARYAARLAAESSSSQPTQQRSAPDISFTIDANK--QQRQLIA  1440

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
             +LE +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  
Sbjct  1441  ELENKNREILQEIQRLRVEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDE  1590

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RM  L++  ++L  QL  L +LL+   A      +  SSPS ++ R     PM +R 
Sbjct  1591  LEQRMSALQESRRELMVQLEGLMKLLKTQGA-----SSPRSSPSHTISRPI---PMPIRS  1746

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGS-LFHMADDLGRAME  1217
               +  + +         PQD+ TG   V   +  +F  S   N+ S L   AD +   M 
Sbjct  1747  ASACPTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLRSDLLVAADSITNTMS  1896

Query  1218  SLVSVMTDEEGAE  1230
             SLV  +  E  +E
Sbjct  1897  SLVKELNSEVASE  1935


>dbj|AK147279.1| Mus musculus cDNA, RIKEN full-length enriched library, clone:M5C1006A05 
product:dystrobrevin alpha, full insert sequence
Length=6282

 Score =  196 bits (499),  Expect = 6e-47, Method: Compositional matrix adjust.
 Identities = 180/613 (29%), Positives = 289/613 (47%), Gaps = 72/613 (11%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  367   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  546

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  547   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  726

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  727   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  891

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  892   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1071

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  1072  CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1230

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYL  982
                HP     P + +     ++T    P  S +DT   HS           + +S   ++
Sbjct  1231  EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPFI  1377

Query  983   NDS-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILA  1038
               S +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++A
Sbjct  1378  TRSMLESSNRLDEEHRLIARYAARLAAESSSSQPTQQRSAPDISFTIDANK--QQRQLIA  1551

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
             +LE +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  
Sbjct  1552  ELENKNREILQEIQRLRVEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDE  1701

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RM  L++  ++L  QL  L +LL+   A      +  SSPS ++ R     PM +R 
Sbjct  1702  LEQRMSALQESRRELMVQLEGLMKLLKTQGA-----SSPRSSPSHTISRPI---PMPIRS  1857

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGS-LFHMADDLGRAME  1217
               +  + +         PQD+ TG   V   +  +F  S   N+ S L   AD +   M 
Sbjct  1858  ASACPTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLRSDLLVAADSITNTMS  2007

Query  1218  SLVSVMTDEEGAE  1230
             SLV  +  E  +E
Sbjct  2008  SLVKELNSEVASE  2046


>gb|EU831587.1| Synthetic construct Homo sapiens clone HAIB:100066616; DKFZo007A0619 
dystrobrevin, alpha protein (DTNA) gene, encodes complete 
protein
Length=2116

 Score =  196 bits (497),  Expect = 8e-47, Method: Compositional matrix adjust.
 Identities = 180/613 (29%), Positives = 290/613 (47%), Gaps = 68/613 (11%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  98    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  274

Query  694   LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
             L+ I+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  275   LSAIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  454

Query  752   EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  455   MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  619

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  620   QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  799

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--  927
             +  NY +CQ CF+ G     H   + M EY +        +  AK L N        A  
Sbjct  800   QCHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASS  958

Query  928   KHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLND  984
             + P     P Q     +        P  S +DT   HS           + +S   ++  
Sbjct  959   REPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITR  1105

Query  985   S-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADL  1040
             S +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ +  +  ++ A+L
Sbjct  1106  SMLESSNRLDEEHRLIARYAARLAAESSSSQPPQQRSAPDISFTIDANK--QQRQLTAEL  1279

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE
Sbjct  1280  ENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELE  1429

Query  1101  ARMQILEDHNKQLESQLHRLRQLL--EQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
              RM  L++  ++L  QL  L +LL  E+ +   +  G+  SSPS ++ R     PM +R 
Sbjct  1430  QRMSALQESRRELMVQLEGLMKLLKEEELKQGTQGAGSPRSSPSHTISRPI---PMPIRS  1600

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAME  1217
               + ++ +         PQD+ TG   V   +  +F  S   N+   L   AD +   M 
Sbjct  1601  ASACSTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLRNDLLVAADSITNTMS  1750

Query  1218  SLVSVMTDEEGAE  1230
             SLV  +  E G+E
Sbjct  1751  SLVKELNSEVGSE  1789


>ref|NM_207650.3| Mus musculus dystrobrevin alpha (Dtna), transcript variant 1, 
mRNA
Length=6321

 Score =  194 bits (492),  Expect = 4e-46, Method: Compositional matrix adjust.
 Identities = 179/610 (29%), Positives = 286/610 (46%), Gaps = 69/610 (11%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  415   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  594

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  595   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  774

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  775   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  939

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  940   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1119

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--K  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A  +
Sbjct  1120  CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1278

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLNDS  985
              P     P Q     +        P  S +DT   HS           + +S   ++  S
Sbjct  1279  EPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITRS  1425

Query  986   -ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLE  1041
              +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+LE
Sbjct  1426  MLESSNRLDEEHRLIARYAARLAAESSSSQPTQQRSAPDISFTIDANK--QQRQLIAELE  1599

Query  1042  EENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEA  1101
              +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE 
Sbjct  1600  NKNREILQEIQRLRVEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQ  1749

Query  1102  RMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGS  1161
             RM  L++  ++L  QL  L +LL+   A      +  SSPS ++ R     PM +R   +
Sbjct  1750  RMSALQESRRELMVQLEGLMKLLKTQGA-----SSPRSSPSHTISRPI---PMPIRSASA  1905

Query  1162  QTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGS-LFHMADDLGRAMESLV  1220
               + +         PQD+ TG   V   +  +F  S   N+ S L   AD +   M SLV
Sbjct  1906  CPTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLRSDLLVAADSITNTMSSLV  2055

Query  1221  SVMTDEEGAE  1230
               +  E  +E
Sbjct  2056  KELNSEVASE  2085


>gb|BC040364.1| Mus musculus dystrobrevin alpha, mRNA (cDNA clone MGC:25316 IMAGE:4505583), 
complete cds
Length=3195

 Score =  194 bits (492),  Expect = 4e-46, Method: Compositional matrix adjust.
 Identities = 179/610 (29%), Positives = 286/610 (46%), Gaps = 69/610 (11%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  388   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  567

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  568   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  747

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  748   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  912

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  913   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1092

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--K  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A  +
Sbjct  1093  CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1251

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLNDS  985
              P     P Q     +        P  S +DT   HS           + +S   ++  S
Sbjct  1252  EPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITRS  1398

Query  986   -ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLE  1041
              +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+LE
Sbjct  1399  MLESSNRLDEEHRLIARYAARLAAESSSSQPTQQRSAPDISFTIDANK--QQRQLIAELE  1572

Query  1042  EENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEA  1101
              +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE 
Sbjct  1573  NKNREILQEIQRLRVEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQ  1722

Query  1102  RMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGS  1161
             RM  L++  ++L  QL  L +LL+   A      +  SSPS ++ R     PM +R   +
Sbjct  1723  RMSALQESRRELMVQLEGLMKLLKTQGA-----SSPRSSPSHTISRPI---PMPIRSASA  1878

Query  1162  QTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGS-LFHMADDLGRAMESLV  1220
               + +         PQD+ TG   V   +  +F  S   N+ S L   AD +   M SLV
Sbjct  1879  CPTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLRSDLLVAADSITNTMSSLV  2028

Query  1221  SVMTDEEGAE  1230
               +  E  +E
Sbjct  2029  KELNSEVASE  2058


>ref|XM_002212046.1| Branchiostoma floridae hypothetical protein (BRAFLDRAFT_74425) 
mRNA, complete cds
Length=2184

 Score =  193 bits (491),  Expect = 4e-46, Method: Compositional matrix adjust.
 Identities = 99/245 (40%), Positives = 155/245 (63%), Gaps = 1/245 (0%)
 Frame = +1

Query  8     EVPAL-ADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQ  66
             ++P++  DF+++  EL DWL LLD ++KSQ V VGD+E+I EMIIKQK  + DL+ ++PQ
Sbjct  1357  DMPSMYPDFDKSVAELRDWLMLLDHMLKSQIVTVGDVEEIEEMIIKQKTVLNDLDVKKPQ  1536

Query  67    LEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWL  126
             L+ ++ A + L         + ++ ++++RIQ QWDE    +  R+++L+ ML D   W 
Sbjct  1537  LDTVVAAGRRLIQTADTDSDKQLLKEKVDRIQEQWDEASTRVGARKRELDNMLTDCHHWD  1716

Query  127   EAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALK  186
             E +E+  + L QA  ++E   E   TVD + K+I + K+   +LRQWQ +++  NDLA K
Sbjct  1717  ELREDVSRWLEQAEQQVEHDSEVGQTVDVLDKQIAQHKEFMDNLRQWQPSIEAVNDLAQK  1896

Query  187   LLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             L+ DYS DDT K+  + + IN  W+ ++ R  ER+  L+     LQ+F L LE+FLAWL+
Sbjct  1897  LISDYSNDDTSKIKQMIDRINGRWQQLNNRCRERQQNLKNALEKLQKFSLQLEEFLAWLS  2076

Query  247   EAETT  251
             EAE  
Sbjct  2077  EAEAA  2091


 Score = 50.8 bits (120),  Expect = 0.005, Method: Compositional matrix adjust.
 Identities = 74/287 (25%), Positives = 125/287 (43%), Gaps = 34/287 (11%)
 Frame = +1

Query  281  LQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHL  340
            LQ  IE H      L+ N Q+I+     S DA LL+ +LD +N +W  L  +  + +  L
Sbjct  106  LQDGIEKHRKQVEGLNANGQEIVEQC-TSIDATLLREKLDGLNRRWRVLCAEVNDRKERL  282

Query  341  EASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEP  400
            E +S Q +     + ELL WL+  +  L++Q       PA + Q       +  L+  + 
Sbjct  283  EEASMQTEEFQEEIDELLFWLEDTEGILNKQV-----CPADEDQ------LEEALEKVKD  429

Query  401  VIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNL  460
             +   LE V++    +  EG+      P E    E A    ++  +  E +  +     +
Sbjct  430  QLEEALEKVKV--RHRQTEGILNKQMCPTEEDQLEEALEKVKVRHRHTEGIRNK----QV  591

Query  461  HSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKA  520
              AD             +L+EA +++ ++ RQ E I        D   D L++ LEKVK 
Sbjct  592  CPAD-----------EDQLEEALEKVKVRHRQTEGILNKQVCPADE--DQLEEALEKVKD  732

Query  521  LRGEIAPLKENVSHVNDLA-RQLTTLGIQ--LSPYNLSTLEDLNTRW  564
               ++   ++NV+ +N    R +TT G    L       +++LNTRW
Sbjct  733  KENDLGSRQDNVNTINQTGNRIMTTPGASKALVSNVKKKVDNLNTRW  873


>gb|AY525164.1| Gallus gallus clone Dp71shoA putative short dystrophin mRNA, 
partial cds
Length=277

 Score =  193 bits (491),  Expect = 5e-46, Method: Compositional matrix adjust.
 Identities = 85/92 (92%), Positives = 91/92 (98%), Gaps = 0/92 (0%)
 Frame = +2

Query  562  TRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTT  621
            TRWK+LQVA+++R+RQLHEAHRDFGP SQHFL+TSVQGPWERAISPNKVPYYINHETQTT
Sbjct  2    TRWKVLQVAIDERIRQLHEAHRDFGPTSQHFLTTSVQGPWERAISPNKVPYYINHETQTT  181

Query  622  CWDHPKMTELYQSLADLNNVRFSAYRTAMKLR  653
            CWDHPKMTELYQSLADLNNVRFSAYRTAMKLR
Sbjct  182  CWDHPKMTELYQSLADLNNVRFSAYRTAMKLR  277


>dbj|AK131649.1| Mus musculus adult male cerebellum cDNA, RIKEN full-length enriched 
library, clone:1520403D02 product:dystrobrevin alpha, 
full insert sequence
Length=2983

 Score =  193 bits (491),  Expect = 5e-46, Method: Compositional matrix adjust.
 Identities = 177/610 (29%), Positives = 287/610 (47%), Gaps = 69/610 (11%)
 Frame = +3

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  192   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  371

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  372   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  551

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  552   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  716

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  717   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  896

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--K  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A  +
Sbjct  897   CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1055

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLNDS  985
              P     P Q     +        P  S +DT   HS           + +S   ++  S
Sbjct  1056  EPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITRS  1202

Query  986   -ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLE  1041
              +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+LE
Sbjct  1203  MLESSNRLDEEHRLIARYAARLAAESSSSQPTQQRSAPDISFTIDANK--QQRQLIAELE  1376

Query  1042  EENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEA  1101
              +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  LE 
Sbjct  1377  NKNREILQEIQRLRVEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELEQ  1526

Query  1102  RMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGS  1161
             RM  L++  ++L  QL  L +LL+   A      +  SSPS ++ R     PM +R   +
Sbjct  1527  RMSALQESRRELMVQLEGLMKLLKTQGA-----SSPRSSPSHTISRPI---PMPIRSASA  1682

Query  1162  QTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGS-LFHMADDLGRAMESLV  1220
               + +         PQD+ TG   V   +  +F  S   N+ S L   AD +   M SLV
Sbjct  1683  CPTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLRSDLLVAADSITNTMSSLV  1832

Query  1221  SVMTDEEGAE  1230
               +  E  +E
Sbjct  1833  KELNSEVASE  1862


>gb|AF063193.1|AF063193 Gallus gallus dystrophin mRNA, partial cds
Length=321

 Score =  193 bits (490),  Expect = 5e-46, Method: Compositional matrix adjust.
 Identities = 94/107 (87%), Positives = 94/107 (87%), Gaps = 13/107 (12%)
 Frame = +1

Query  898  EYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET---------  948
            EYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET         
Sbjct  1    EYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWP  180

Query  949  ----PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNES  991
                PASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNES
Sbjct  181  VDSAPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNES  321


>gb|U46744.1|HSU46744 Human dystrobrevin-alpha mRNA, complete cds
Length=2518

 Score =  192 bits (489),  Expect = 8e-46, Method: Compositional matrix adjust.
 Identities = 178/614 (28%), Positives = 287/614 (46%), Gaps = 74/614 (12%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  140   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  316

Query  694   LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
             L+TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  317   LSTIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  496

Query  752   EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  497   MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  661

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  662   QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  841

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK-  928
             +  NY +CQ CF+ G     H   + M EY +        +  AK L N        A  
Sbjct  842   QCHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASS  1000

Query  929   ----HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSY  981
                 HP     P + +     ++T    P  S +DT   HS           + +S   +
Sbjct  1001  REPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPF  1147

Query  982   LNDS-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERIL  1037
             +  S +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++
Sbjct  1148  ITRSMLESSNRLDEEHRLIARYAARLAAESSSSQPPQQRSAPDISFTIDANK--QQRQLI  1321

Query  1038  ADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKG  1097
             A+LE +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K 
Sbjct  1322  AELENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKD  1471

Query  1098  RLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLR  1157
              LE RM  L++  ++L  QL  L +LL       K  G+     S+         PM +R
Sbjct  1472  ELEQRMSALQESRRELMVQLEGLMKLL-------KTQGSGTHR-SSRSHSISRPIPMPIR  1627

Query  1158  VVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAM  1216
                + ++ +         PQD+ TG   V   +  +F  S   N+   L   AD +   M
Sbjct  1628  SASACSTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLRNDLLVAADSITNTM  1777

Query  1217  ESLVSVMTDEEGAE  1230
              SLV  +  E G+E
Sbjct  1778  SSLVKELNSEVGSE  1819


>ref|XM_001369093.1| PREDICTED: Monodelphis domestica similar to dystrobrevin, alpha,, 
transcript variant 6 (LOC100023710), mRNA
Length=1542

 Score =  192 bits (487),  Expect = 1e-45, Method: Compositional matrix adjust.
 Identities = 155/517 (29%), Positives = 257/517 (49%), Gaps = 55/517 (10%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  76    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  255

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  256   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  435

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R  L L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  436   DKLRYIFSMISDSSGVMVYGRYDLFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  600

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601   QKKVTLNAFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G  +  H   + M EY +        +  AK L N        A   
Sbjct  781   CHNYQLCQDCFWRGHASGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  939

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYL  982
                HP     P + +     ++T    P  S +DT   HS           + +S   ++
Sbjct  940   EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPFI  1086

Query  983   NDSI--SPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERIL  1037
               S+  SPN  +D+EH LI  Y   L  ++  +QP   R P+ I  ++++ +  +  +++
Sbjct  1087  TRSMLDSPNR-LDEEHRLIARYAARLAAETSSTQPSQQRGPSDISFTIDANK--QQRQLI  1257

Query  1038  ADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKG  1097
             A+LE +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K 
Sbjct  1258  AELENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKD  1407

Query  1098  RLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVN  1134
              LE RM  L++  ++L  QL  L +LL++ + +  V+
Sbjct  1408  ELEQRMSALQESRRELMVQLEGLMKLLKEEELKQGVS  1518


>ref|XM_613774.4| PREDICTED: Bos taurus similar to dystrobrevin, beta, transcript 
variant 1 (DTNB), mRNA
Length=2241

 Score =  191 bits (486),  Expect = 2e-45, Method: Compositional matrix adjust.
 Identities = 170/621 (27%), Positives = 282/621 (45%), Gaps = 80/621 (12%)
 Frame = +3

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  81    NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHSTEISVSRLETVI  260

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  261   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  434

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  435   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  602

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  603   -QQKKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  779

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTTSGEDV  909
              +  NY +CQ+CF+ G  +  H   + M E+                   C PT      
Sbjct  780   QQCHNYQLCQNCFWRGHASGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHP  959

Query  910   RDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD------DTHSR  963
               F +  +            P                 TP    Q S D      D H+ 
Sbjct  960   -VFPEQPEKPLDLANIVPPRPPTNLNDTMVSHMSSGAPTPTKRLQYSQDIPSHLADEHAL  1136

Query  964   IEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILI  1023
             I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  +  R P  +  
Sbjct  1137  IASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NMTRPPTDLSF  1289

Query  1024  SLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDA  1083
             + ++ +  +  +++A+LE +NR +  E  RL+ +HE              PT  ++ ++ 
Sbjct  1290  NFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNP  1433

Query  1084  ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLL---EQPQAEAKVNGTTVSS  1140
              L+AE +LLRQ K  LE RM  L++  ++L  QL  L +LL   EQ QA A+  G+  +S
Sbjct  1434  TLLAELRLLRQRKDELEQRMSALQESRRELMVQLEGLMKLLKEEEQKQA-AQATGSPHTS  1610

Query  1141  PSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGH  1200
             P+    R     PM +R   + ++ +         PQD  +G+   M++   +F      
Sbjct  1611  PTHGGGRPI---PMPVRSTSAGSTPTHC-------PQDPLSGVGGDMQE---AFAQGTRR  1751

Query  1201  NV-GSLFHMADDLGRAMESLV  1220
             N+   L   AD +   M SLV
Sbjct  1752  NLRNDLLVAADSITNTMSSLV  1814


>ref|XM_001054487.1| PREDICTED: Rattus norvegicus similar to dystrobrevin alpha isoform 
1 (predicted), transcript variant 6 (RGD1561985_predicted), 
mRNA
Length=3485

 Score =  191 bits (485),  Expect = 2e-45, Method: Compositional matrix adjust.
 Identities = 163/565 (28%), Positives = 273/565 (48%), Gaps = 68/565 (12%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  409   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  588

Query  695   TTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +T++ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  589   STMFYQLNKRMPSTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  768

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  769   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  933

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  934   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1113

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  1114  CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1272

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYL  982
                HP     P + +     ++T    P  S +DT   HS           + +S   ++
Sbjct  1273  EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPFI  1419

Query  983   NDS-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILA  1038
               S +  +  +D+EH LI  Y   L  +S  SQP   RS   +  ++++ +  +  +++A
Sbjct  1420  TRSMLESSNRLDEEHRLIARYAARLAAESSSSQPTQQRSAPDVSFTIDANK--QQRQLIA  1593

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
             +LE +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  
Sbjct  1594  ELENKNREILQEIQRLRVEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDE  1743

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RM  L++  ++L  QL  L +LL+   A     G+  SSPS ++ R     PM +R 
Sbjct  1744  LEQRMSALQESRRELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIRS  1899

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGL  1183
               + ++ +         PQD+ TG+
Sbjct  1900  TSACSTPAYT-------PQDSLTGV  1953


>ref|XM_001054433.1| PREDICTED: Rattus norvegicus similar to dystrobrevin alpha isoform 
1 (predicted), transcript variant 5 (RGD1561985_predicted), 
mRNA
Length=3497

 Score =  191 bits (485),  Expect = 2e-45, Method: Compositional matrix adjust.
 Identities = 163/565 (28%), Positives = 273/565 (48%), Gaps = 68/565 (12%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  421   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  600

Query  695   TTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +T++ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  601   STMFYQLNKRMPSTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  780

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  781   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  945

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  946   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1125

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  1126  CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1284

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYL  982
                HP     P + +     ++T    P  S +DT   HS           + +S   ++
Sbjct  1285  EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPFI  1431

Query  983   NDS-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILA  1038
               S +  +  +D+EH LI  Y   L  +S  SQP   RS   +  ++++ +  +  +++A
Sbjct  1432  TRSMLESSNRLDEEHRLIARYAARLAAESSSSQPTQQRSAPDVSFTIDANK--QQRQLIA  1605

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
             +LE +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  
Sbjct  1606  ELENKNREILQEIQRLRVEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDE  1755

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RM  L++  ++L  QL  L +LL+   A     G+  SSPS ++ R     PM +R 
Sbjct  1756  LEQRMSALQESRRELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIRS  1911

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGL  1183
               + ++ +         PQD+ TG+
Sbjct  1912  TSACSTPAYT-------PQDSLTGV  1965


>ref|XM_001054380.1| PREDICTED: Rattus norvegicus similar to dystrobrevin alpha isoform 
1 (predicted), transcript variant 4 (RGD1561985_predicted), 
mRNA
Length=3404

 Score =  191 bits (485),  Expect = 2e-45, Method: Compositional matrix adjust.
 Identities = 163/565 (28%), Positives = 273/565 (48%), Gaps = 68/565 (12%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  328   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  507

Query  695   TTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +T++ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  508   STMFYQLNKRMPSTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  687

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  688   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  852

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  853   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1032

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  1033  CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1191

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYL  982
                HP     P + +     ++T    P  S +DT   HS           + +S   ++
Sbjct  1192  EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPFI  1338

Query  983   NDS-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILA  1038
               S +  +  +D+EH LI  Y   L  +S  SQP   RS   +  ++++ +  +  +++A
Sbjct  1339  TRSMLESSNRLDEEHRLIARYAARLAAESSSSQPTQQRSAPDVSFTIDANK--QQRQLIA  1512

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
             +LE +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  
Sbjct  1513  ELENKNREILQEIQRLRVEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDE  1662

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RM  L++  ++L  QL  L +LL+   A     G+  SSPS ++ R     PM +R 
Sbjct  1663  LEQRMSALQESRRELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIRS  1818

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGL  1183
               + ++ +         PQD+ TG+
Sbjct  1819  TSACSTPAYT-------PQDSLTGV  1872


>ref|XM_001054793.1| PREDICTED: Rattus norvegicus similar to dystrobrevin alpha isoform 
1 (predicted), transcript variant 11 (RGD1561985_predicted), 
mRNA
Length=3333

 Score =  191 bits (485),  Expect = 2e-45, Method: Compositional matrix adjust.
 Identities = 163/565 (28%), Positives = 273/565 (48%), Gaps = 68/565 (12%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  257   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  436

Query  695   TTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +T++ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  437   STMFYQLNKRMPSTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  616

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  617   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  781

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  782   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  961

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  962   CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1120

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYL  982
                HP     P + +     ++T    P  S +DT   HS           + +S   ++
Sbjct  1121  EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPFI  1267

Query  983   NDS-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILA  1038
               S +  +  +D+EH LI  Y   L  +S  SQP   RS   +  ++++ +  +  +++A
Sbjct  1268  TRSMLESSNRLDEEHRLIARYAARLAAESSSSQPTQQRSAPDVSFTIDANK--QQRQLIA  1441

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
             +LE +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  
Sbjct  1442  ELENKNREILQEIQRLRVEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDE  1591

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE RM  L++  ++L  QL  L +LL+   A     G+  SSPS ++ R     PM +R 
Sbjct  1592  LEQRMSALQESRRELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIRS  1747

Query  1159  VGSQTSDSMGEEDLLSPPQDTSTGL  1183
               + ++ +         PQD+ TG+
Sbjct  1748  TSACSTPAYT-------PQDSLTGV  1801


>gb|AF082741.1|AF082741 Gallus gallus dystrophin mRNA, alternatively spliced, partial 
cds
Length=509

 Score =  191 bits (484),  Expect = 3e-45, Method: Compositional matrix adjust.
 Identities = 91/100 (91%), Positives = 100/100 (100%), Gaps = 0/100 (0%)
 Frame = +1

Query  1128  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVM  1187
             QA+AKVNGTT+SSPSTSLQRSDSSQPMLLRVVGSQTS++MGE+DLLSPPQDTSTGLEEVM
Sbjct  1     QADAKVNGTTLSSPSTSLQRSDSSQPMLLRVVGSQTSETMGEDDLLSPPQDTSTGLEEVM  180

Query  1188  EQLNNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEE  1227
             EQLNNSFPSSRGHNVGSLFHMADDLGRAME+LV+VMTD++
Sbjct  181   EQLNNSFPSSRGHNVGSLFHMADDLGRAMETLVTVMTDDK  300


>gb|BC068718.1| Xenopus laevis hypothetical protein MGC81161, mRNA (cDNA clone 
MGC:81161 IMAGE:6318045), complete cds
Length=3932

 Score =  190 bits (482),  Expect = 5e-45, Method: Compositional matrix adjust.
 Identities = 142/492 (28%), Positives = 235/492 (47%), Gaps = 37/492 (7%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRT+ KLR +QK   L L+ +    +AL +++L   D    +++ ++   L
Sbjct  205   DLDRIRLSTYRTSCKLRFVQKKGNLHLVDVWNIIEALRENSLNNVDPNVELNVARLEAVL  384

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + +NV   + + LN+LL  YD    G+I + + K  + +LC   + 
Sbjct  385   STIFYQLNKRMPTTHQINVEQSISLMLNFLLAAYDLEGHGKITLFAVKMALATLCGGKIM  564

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY++  ++ S G     R    L + +++P  + E  SFG +  E + RSCF   + 
Sbjct  565   DKLRYIYSMISDSNGVMVYERYDQFLREVLKLPTAVFEGPSFGYT--EQAARSCF---SQ  729

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  730   QKKVTLNSFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  909

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHP  930
               NY +CQ CF+ G  +  H   + M EY   T+     +  +  L           + P
Sbjct  910   CHNYQLCQDCFWRGHASGSHNNQHQMKEY---TSWKSPAKKLSTALSKSLSCAS--NREP  1074

Query  931   RMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNE  990
                  P Q     +        P  S +D         +  ++   S+GS   + I P+ 
Sbjct  1075  LHPMFPDQPEKPLNLAHIVPPRPVNSMND---------NIFSQSVPSSGSPFTNKIMPDS  1227

Query  991   S--IDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQ  1048
                +D+EH LI  Y   L  ++  SQ +  A   IS   +   +  +++A+LE +NR + 
Sbjct  1228  PSRLDEEHRLIARYAARLAAENSSSQVQQRAGTDISFTIDANKQQRQLIAELENKNREIL  1407

Query  1049  AEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILED  1108
              E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++
Sbjct  1408  QEIQRLRIEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQE  1557

Query  1109  HNKQLESQLHRL  1120
               ++L  QL  L
Sbjct  1558  SRRELMVQLEGL  1593


>gb|BC121459.1| Xenopus tropicalis dystrobrevin alpha, mRNA (cDNA clone MGC:146484 
IMAGE:7793528), complete cds
Length=2499

 Score =  189 bits (481),  Expect = 6e-45, Method: Compositional matrix adjust.
 Identities = 140/491 (28%), Positives = 236/491 (48%), Gaps = 38/491 (7%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL +++L   D    +++ ++   L
Sbjct  245   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNIIEALRENSLNNVDPNVELNVARLEAVL  424

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +T++ +L +     + +NV   + + LN+LL  YD+   G+I V + K  + +LC   + 
Sbjct  425   STVFFQLNKRMPTTHQINVEQSISLMLNFLLTAYDSEGHGKITVFAVKMALATLCGGKIM  604

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY++  ++ + G     R    L + +++P  + E  SFG +  E + RSCF   + 
Sbjct  605   DKLRYIYSMISDTNGMMVYGRYDQFLREVLKLPTAIFEGPSFGYT--EQAARSCF---SQ  769

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  770   QKKVTLNSFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  949

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK-H  929
               NY +CQ CF+ G  +  H   + M EY   T+     +  +  L             H
Sbjct  950   CHNYQLCQDCFWRGHASGSHSNQHQMKEY---TSWKSPAKKLSTALSKSLSCASSREPLH  1120

Query  930   PRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSI---  986
             P     P + +     ++T    P  S +D         +  +     +GS   + I   
Sbjct  1121  PMFPDQPEKPLNLAHIVDTWPPRPVTSMND---------NIFSHSVPCSGSPFTNKIMLD  1273

Query  987   SPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRN  1046
             SP+  +D+EH LI  Y   L  ++  +Q +      IS   +   +  +++A+LE +NR 
Sbjct  1274  SPSR-LDEEHRLIARYAARLAAENSSAQAQQRGGADISFTIDANKQQRQLIAELENKNRE  1450

Query  1047  LQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQIL  1106
             +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L
Sbjct  1451  ILQEIQRLRIEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSAL  1600

Query  1107  EDHNKQLESQL  1117
             ++  ++L  QL
Sbjct  1601  QESRRELMVQL  1633


>ref|XM_419187.2| PREDICTED: Gallus gallus similar to dystrobrevin alpha (LOC421104), 
mRNA
Length=3293

 Score =  189 bits (481),  Expect = 7e-45, Method: Compositional matrix adjust.
 Identities = 184/657 (28%), Positives = 299/657 (45%), Gaps = 104/657 (15%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQP--MDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   +
Sbjct  76    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPSIELNVARLEAVI  255

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + +NV   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  256   STIFYQLNKRMPTTHQINVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  435

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     +  L L + +++P  + E  SFG +  E S +SCF   + 
Sbjct  436   DKLRYIFSMISDSSGVMVYGKYDLFLREVLKLPTAVFEGPSFGYT--EQSAKSCF---SQ  600

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601   QKKVTLNTFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G  +  H   + M EY +        +  AK L N        A   
Sbjct  781   CHNYQLCQDCFWRGHASGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  939

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HS--RIEHYASRLAEMENSN--  978
                HP     P + +     ++T    P  S +DT   HS      +A+R +  +N++  
Sbjct  940   EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHSVPSGSPFANRSSPSKNTDVE  1119

Query  979   --------------GSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLS-----------  1013
                           G  L  S+   + + DEH+LI  Y   L Q +P             
Sbjct  1120  QSKLLARAAPAFLKGKGLQYSLDVADRLADEHVLIGLYVNML-QSNPARVLDSASRLDEE  1296

Query  1014  -------QPRSPAQILISLESEERGELE------------RILADLEEENRNLQAEYDRL  1054
                      R  A+   S ++++RG  +            +++A+LE +NR +  E  RL
Sbjct  1297  HKLIARYAARLAAETSSSQQAQQRGAADISFTIDANKQQRQLIAELENKNREILQEIQRL  1476

Query  1055  KQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLE  1114
             + +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  ++L 
Sbjct  1477  RLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRRELM  1626

Query  1115  SQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLS  1174
              QL  L +LL+   A     G+  SSPS ++ R     PM +R   + ++ +        
Sbjct  1627  VQLEGLMKLLKTQGA-----GSPRSSPSHTISR---PIPMPIRSASACSTPTHT------  1764

Query  1175  PPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              PQD+ TG   V   +  +F  S   N+   L   AD +   M SLV  +  E G+E
Sbjct  1765  -PQDSLTG---VGGDVQEAFAQSARRNLRNDLLVAADSITNTMSSLVKELNSEVGSE  1923


>gb|BC050765.1| Mus musculus dystrobrevin alpha, mRNA (cDNA clone MGC:58284 IMAGE:6533769), 
complete cds
Length=2716

 Score =  189 bits (480),  Expect = 8e-45, Method: Compositional matrix adjust.
 Identities = 176/611 (28%), Positives = 283/611 (46%), Gaps = 68/611 (11%)
 Frame = +3

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  207   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  386

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  387   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  566

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  567   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  731

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  732   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  911

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--K  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A  +
Sbjct  912   CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1070

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLNDS  985
              P     P Q     +        P  S +DT   HS           + +S   ++  S
Sbjct  1071  EPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITRS  1217

Query  986   -ISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQIL----ISLESEERGELERILADL  1040
              +  +  +D+EH LI  Y   L  +S  S  + P Q      IS   +   +  +++A+L
Sbjct  1218  MLESSNRLDEEHRLIARYAARLAAESSSSVLQQPTQQRSAPDISFTIDANKQQRQLIAEL  1397

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  LE
Sbjct  1398  ENKNREILQEIQRLRVEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELE  1547

Query  1101  ARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVG  1160
              RM  L++  ++L  QL  L +LL+   A      +  SSPS ++ R     PM +R   
Sbjct  1548  QRMSALQESRRELMVQLEGLMKLLKTQGA-----SSPRSSPSHTISRPI---PMPIRSAS  1703

Query  1161  SQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGS-LFHMADDLGRAMESL  1219
             +  + +         PQD+ TG   V   +  +F  S   N+ S L   AD +   M SL
Sbjct  1704  ACPTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLRSDLLVAADSITNTMSSL  1853

Query  1220  VSVMTDEEGAE  1230
             V  +  E  +E
Sbjct  1854  VKELNSEVASE  1886


>ref|XM_002196755.1| PREDICTED: Taeniopygia guttata similar to dystrobrevin, alpha 
(LOC100230673), mRNA
Length=2576

 Score =  189 bits (479),  Expect = 1e-44, Method: Compositional matrix adjust.
 Identities = 185/654 (28%), Positives = 294/654 (44%), Gaps = 101/654 (15%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQP--MDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   +
Sbjct  76    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPSIELNVARLEAVI  255

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + +NV   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  256   STIFYQLNKRMPTTHQINVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  435

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R  + L + +++P  + E  SFG +  E S +SCF   + 
Sbjct  436   DKLRYIFSMISDSSGMMVYGRYDMFLREVLKLPTAVFEGPSFGYT--EQSAKSCF---SQ  600

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601   QKKVTLNTFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--K  928
               NY +CQ CF+ G  +  H   + M EY +        +  AK L N        A  +
Sbjct  781   CHNYQLCQDCFWRGHASGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  939

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HS--RIEHYASRLAEMENS------  977
              P     P Q     +        P  S +DT   HS      +A+R +  +N+      
Sbjct  940   EPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHSVPSGSPFANRSSPSKNTEVEQNK  1119

Query  978   ----------NGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLS--------------  1013
                        G  L  S+   + + DEH+LI  Y   L Q SP                
Sbjct  1120  LLARAAPAFLKGKGLQYSLDVADRLADEHVLIGVYVNML-QSSPARVLDSASRLDEEHKL  1296

Query  1014  ----QPRSPAQILISLESEERG------------ELERILADLEEENRNLQAEYDRLKQQ  1057
                   R  A+   S  S++RG            +  +++A+LE +NR +  E  RL+ +
Sbjct  1297  IARYAARLAAETSSSQPSQQRGASDISFTIDANKQQRQLIAELENKNREILQEIQRLRLE  1476

Query  1058  HEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQL  1117
             HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  ++L  QL
Sbjct  1477  HEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRRELMVQL  1626

Query  1118  HRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQ  1177
               L +LL+   A     G+  SSPS ++ R     PM +R   + ++ +         PQ
Sbjct  1627  EGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIRSASACSTPTHA-------PQ  1761

Query  1178  DTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             D+ TG   V   +  +F  S   N+   L   AD +   M SLV  +  E G+E
Sbjct  1762  DSLTG---VGGDVQEAFAQSARRNLRNDLLVAADSITNTMSSLVKELNSEVGSE  1914


>emb|X95226.1| M.musculus mRNA for dystrobrevin (clone m24)
Length=2607

 Score =  189 bits (479),  Expect = 1e-44, Method: Compositional matrix adjust.
 Identities = 181/611 (29%), Positives = 288/611 (47%), Gaps = 65/611 (10%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  121   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  300

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  301   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  480

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  481   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  645

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  646   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  825

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--K  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A  +
Sbjct  826   CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  984

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLNDS  985
              P     P Q     +        P  S +DT   HS           + +S   ++  S
Sbjct  985   EPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITRS  1131

Query  986   -ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLE  1041
              +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+LE
Sbjct  1132  MLESSNRLDEEHRLIARYAARLAAESSSSQPTQQRSAPDISFTIDANK--QQRQLIAELE  1305

Query  1042  EENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEA  1101
              +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE 
Sbjct  1306  NKNREILQEIQRLRVEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQ  1455

Query  1102  RMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQ-PMLLRVVG  1160
             RM  L++  ++L  QL  L +LL++   E    GT  SSP +S   + S   PM +R   
Sbjct  1456  RMSALQESRRELMVQLEGLMKLLKE---EELKQGTRASSPRSSPSHTISRPIPMPIRSAS  1626

Query  1161  SQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGS-LFHMADDLGRAMESL  1219
             +  + +         PQD+ TG   V   +  +F  S   N+ S L   AD +   M SL
Sbjct  1627  ACPTPTHT-------PQDSLTG---VGGDVQEAFAQSSRRNLRSDLLVAADSITNTMSSL  1776

Query  1220  VSVMTDEEGAE  1230
             V  +  E  +E
Sbjct  1777  VKELNSEVASE  1809


>ref|XM_001054655.1| PREDICTED: Rattus norvegicus similar to dystrobrevin alpha isoform 
1 (predicted), transcript variant 9 (RGD1561985_predicted), 
mRNA
Length=3324

 Score =  188 bits (478),  Expect = 2e-44, Method: Compositional matrix adjust.
 Identities = 159/560 (28%), Positives = 268/560 (47%), Gaps = 61/560 (10%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  257   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  436

Query  695   TTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +T++ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  437   STMFYQLNKRMPSTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  616

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  617   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  781

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  782   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  961

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHP  930
               NY +CQ CF+ G     H   + M EY   T+     +     L          ++ P
Sbjct  962   CHNYQLCQDCFWRGHAGGSHSNQHQMKEY---TSWKSPAKKLTNALSKSLSCAS--SREP  1126

Query  931   RMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLNDS-I  986
                  P Q     +        P  S +DT   HS           + +S   ++  S +
Sbjct  1127  LHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITRSML  1273

Query  987   SPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEE  1043
               +  +D+EH LI  Y   L  +S  SQP   RS   +  ++++ +  +  +++A+LE +
Sbjct  1274  ESSNRLDEEHRLIARYAARLAAESSSSQPTQQRSAPDVSFTIDANK--QQRQLIAELENK  1447

Query  1044  NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  1103
             NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  LE RM
Sbjct  1448  NREILQEIQRLRVEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELEQRM  1597

Query  1104  QILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQT  1163
               L++  ++L  QL  L +LL+   A     G+  SSPS ++ R     PM +R   + +
Sbjct  1598  SALQESRRELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIRSTSACS  1753

Query  1164  SDSMGEEDLLSPPQDTSTGL  1183
             + +         PQD+ TG+
Sbjct  1754  TPAYT-------PQDSLTGV  1792


>ref|NM_033148.2| Homo sapiens dystrobrevin, beta (DTNB), transcript variant 3, 
mRNA
Length=2314

 Score =  188 bits (477),  Expect = 2e-44, Method: Compositional matrix adjust.
 Identities = 154/557 (27%), Positives = 266/557 (47%), Gaps = 65/557 (11%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  326   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  505

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  506   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  679

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  680   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  847

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  848   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  1024

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK  928
              +  NY +CQ+CF+ G     H   + M E+          +  AK L +          
Sbjct  1025  QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEH-------SSWKSPAKKLSHAISKS-----  1168

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSI-S  987
                +G +P +        E P     L+H             L  M ++  S+++  + +
Sbjct  1169  ---LGCVPTREPPHPVFPEQPEKPLDLAHIVP-------PRPLTNMNDTMVSHMSSGVPT  1318

Query  988   PNESI-------DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADL  1040
             P +S+       D+EH LI  Y   L  ++  +  R P  +  + ++ +  +  +++A+L
Sbjct  1319  PTKSVLDSPSRLDEEHRLIARYAARLAAEAG-NVTRPPTDLSFNFDANK--QQRQLIAEL  1489

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  LE
Sbjct  1490  ENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELE  1639

Query  1101  ARMQILEDHNKQLESQLHRLRQLL---EQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLR  1157
              RM  L++  ++L  QL  L +LL   EQ QA A+  G+  +SP+    R     PM +R
Sbjct  1640  QRMSALQESRRELMVQLEELMKLLKEEEQKQA-AQATGSPHTSPTHGGGR---PMPMPVR  1807

Query  1158  VVGSQTSDSMGEEDLLS  1174
                + ++ +   +D LS
Sbjct  1808  STSAGSTPTHCPQDSLS  1858


>emb|Y12712.1| Homo sapiens mRNA for brain dystrobrevin B
Length=2247

 Score =  188 bits (477),  Expect = 2e-44, Method: Compositional matrix adjust.
 Identities = 154/557 (27%), Positives = 266/557 (47%), Gaps = 65/557 (11%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  259   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  438

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  439   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  612

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  613   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  780

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  781   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  957

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK  928
              +  NY +CQ+CF+ G     H   + M E+          +  AK L +          
Sbjct  958   QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEH-------SSWKSPAKKLSHAISKS-----  1101

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSI-S  987
                +G +P +        E P     L+H             L  M ++  S+++  + +
Sbjct  1102  ---LGCVPTREPPHPVFPEQPEKPLDLAHIVP-------PRPLTNMNDTMVSHMSSGVPT  1251

Query  988   PNESI-------DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADL  1040
             P +S+       D+EH LI  Y   L  ++  +  R P  +  + ++ +  +  +++A+L
Sbjct  1252  PTKSVLDSPSRLDEEHRLIARYAARLAAEAG-NVTRPPTDLSFNFDANK--QQRQLIAEL  1422

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  LE
Sbjct  1423  ENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELE  1572

Query  1101  ARMQILEDHNKQLESQLHRLRQLL---EQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLR  1157
              RM  L++  ++L  QL  L +LL   EQ QA A+  G+  +SP+    R     PM +R
Sbjct  1573  QRMSALQESRRELMVQLEELMKLLKEEEQKQA-AQATGSPHTSPTHGGGR---PMPMPVR  1740

Query  1158  VVGSQTSDSMGEEDLLS  1174
                + ++ +   +D LS
Sbjct  1741  STSAGSTPTHCPQDSLS  1791


>dbj|AK308410.1| Homo sapiens cDNA, FLJ98358
Length=2681

 Score =  175 bits (444),  Expect(2) = 2e-44, Method: Compositional matrix adjust.
 Identities = 149/511 (29%), Positives = 236/511 (46%), Gaps = 65/511 (12%)
 Frame = +1

Query  732   GRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEV  791
             G+I V + K  + +LC   + DK RY+F  ++ S+G     R    L + +++P  + E 
Sbjct  700   GKISVFAVKMALATLCGGKIMDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEG  879

Query  792   ASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKH  849
              SFG +  E S RSCF   + + ++    FLD +  +P  Q +VWLP+LHR+A  E   H
Sbjct  880   PSFGYT--EQSARSCF---SQQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFH  1044

Query  850   QAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDV  909
               +C+ C    ++GFRYR  +  NY +CQ CF+ G     H   + M EY +        
Sbjct  1045  PVECSYCHSESMMGFRYRCQQCHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------W  1203

Query  910   RDFAKVLKNKFRTKRYFA--KHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRI  964
             +  AK L N        A  + P     P Q     +        P  S +DT   HS  
Sbjct  1204  KSPAKKLTNALSKSLSCASSREPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS--  1377

Query  965   EHYASRLAEMENSNGSYLNDS-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQ  1020
                      + +S   ++  S +  +  +D+EH LI  Y   L  +S  SQP   RS   
Sbjct  1378  ---------VPSSGSPFITRSMLESSNRLDEEHRLIARYAARLAAESSSSQPPQQRSAPD  1530

Query  1021  ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSP  1080
             I  ++++ +  +  +++A+LE +NR +  E  RL+ +HE              PT  ++ 
Sbjct  1531  ISFTIDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QPTPEKAQ  1674

Query  1081  RDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSS  1140
             ++  L+AE +LLRQ K  LE RM  L++  ++L  QL  L +LL+   A     G+  SS
Sbjct  1675  QNPTLLAELRLLRQRKDELEQRMSALQESRRELMVQLEGLMKLLKTQGA-----GSPRSS  1839

Query  1141  PSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGH  1200
             PS ++ R     PM +R   + ++ +         PQD+ TG   V   +  +F  S   
Sbjct  1840  PSHTISRPI---PMPIRSASACSTPTHT-------PQDSLTG---VGGDVQEAFAQSSRR  1980

Query  1201  NV-GSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             N+   L   AD +   M SLV  +  E G+E
Sbjct  1981  NLRNDLLVAADSITNTMSSLVKELNSEVGSE  2073


 Score = 33.9 bits (76),  Expect(2) = 2e-44, Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 2/64 (3%)
 Frame = +3

Query  637  DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND--QPMDILQIINCL  694
            DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  402  DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTELNVSRLEAVL  581

Query  695  TTIY  698
            +TI+
Sbjct  582  STIF  593


>ref|XM_001515647.1| PREDICTED: Ornithorhynchus anatinus similar to dystrobrevin, 
alpha,, transcript variant 3 (LOC100079727), mRNA
Length=2232

 Score =  187 bits (476),  Expect = 2e-44, Method: Compositional matrix adjust.
 Identities = 185/659 (28%), Positives = 296/659 (44%), Gaps = 107/659 (16%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  76    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNVELNVARLEAVL  255

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  256   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  435

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R  L L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  436   DKLRYIFSMISDSSGVMVYGRYDLFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  600

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601   QKKVTLNAFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G  +  H   + M EY +        +  AK L N        A   
Sbjct  781   CHNYQLCQDCFWRGHASGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  939

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT------HSRIEHYASRLAEMENS--  977
                HP     P + +     ++T    P  S +DT       S    + +R +  +N+  
Sbjct  940   EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHSVPSSGSPFITRSSPHQNNEV  1119

Query  978   --------------NGSYLNDSISPNESIDDEHLLIQHYCQSLNQ------DSP------  1011
                            G  L  S+   + + DEH LI  Y   L        DSP      
Sbjct  1120  EQNKLLARAAPSFLKGKGLQYSLDVADRLADEHGLIGLYVNMLQSNPSRMLDSPNRLDEE  1299

Query  1012  ----------------LSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYD  1052
                              SQP   R  + I  ++++ +  +  +++A+LE +NR +  E  
Sbjct  1300  HRLIARYAARLAAETSSSQPGQQRGASDISFTIDANK--QQRQLIAELENKNREILQEIQ  1473

Query  1053  RLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQ  1112
             RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  ++
Sbjct  1474  RLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRRE  1623

Query  1113  LESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDL  1172
             L  QL  L +LL+   A     G+  SSPS ++ R     PM +R   + ++ +      
Sbjct  1624  LMVQLEGLMKLLKTQGA-----GSPRSSPSHTISR---PIPMPIRSASTCSTPTHT----  1767

Query  1173  LSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESLVSVMTDEEGAE  1230
                PQD+ TG   V   +  +F  S   N+   L   AD +   M SLV  +  E G+E
Sbjct  1768  ---PQDSLTG---VGGDVQEAFAQSARRNLRNDLLVAADSITNTMSSLVKELNSEVGSE  1926


>emb|CR619470.1| full-length cDNA clone CS0DK002YG20 of HeLa cells Cot 25-normalized 
of Homo sapiens (human)
Length=2275

 Score =  187 bits (475),  Expect = 3e-44, Method: Compositional matrix adjust.
 Identities = 161/601 (26%), Positives = 279/601 (46%), Gaps = 77/601 (12%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  253   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  432

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  433   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  606

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  607   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  774

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  775   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  951

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK  928
              +  NY +CQ+CF+ G     H   + M E+          +  AK L +          
Sbjct  952   QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEH-------SSWKSPAKKLSHAISKS-----  1095

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSI-S  987
                +G +P +        E P     L+H             L  M ++  S+++  + +
Sbjct  1096  ---LGCVPTREPPHPVFPEQPEKPLDLAHIVP-------PRPLTNMNDTMVSHMSSGVPT  1245

Query  988   PNESI-------DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADL  1040
             P +S+       D+EH LI  Y   L  ++  +  R P  +  + ++ +  +  +++A+L
Sbjct  1246  PTKSVLDSPSRLDEEHRLIARYAARLAAEAG-NVTRPPTDLSFNFDANK--QQRQLIAEL  1416

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  LE
Sbjct  1417  ENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELE  1566

Query  1101  ARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVG  1160
              RM  L++  ++L  QL  L +LL     +A+  G+  +SP+    R     PM +R   
Sbjct  1567  QRMSALQESRRELMVQLEELMKLL-----KAQATGSPHTSPTHGGGR---PMPMPVRSTS  1722

Query  1161  SQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESL  1219
             + ++ +         PQD+ +G   V   +  +F      N+   L   AD +   M SL
Sbjct  1723  AGSTPTHC-------PQDSLSG---VGGDVQEAFAQGTRRNLRNDLLVAADSITNTMSSL  1872

Query  1220  V  1220
             V
Sbjct  1873  V  1875


>ref|XM_961904.2| PREDICTED: Tribolium castaneum similar to dystrobrevin (LOC655364), 
mRNA
Length=2358

 Score =  187 bits (474),  Expect = 4e-44, Method: Compositional matrix adjust.
 Identities = 162/578 (28%), Positives = 270/578 (46%), Gaps = 58/578 (10%)
 Frame = +1

Query  641   VRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIINCLTTIY  698
             +RF++YRTA KLR +QK + L  + +    +A  +  L   +    + + ++   L ++Y
Sbjct  85    IRFASYRTATKLRFIQKKVSLHAVDIWNVIEAFREQGLHALEPSSELSVARLETLLCSLY  264

Query  699   DRLEQEH--NNLVNVPLCVDMCLNWLLNVYDT-GRTGRIRVLSFKTGIISLCKAHLEDKY  755
               L +        +V +C  + LNWLL  Y T    G+IRV S K  + +LC   L DK 
Sbjct  265   HSLNKRAPPTQQAHVDVCSSLLLNWLLAAYATVDNVGKIRVFSIKVALATLCAGKLMDKL  444

Query  756   RYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPE  815
             RY+F Q++ S G   Q R    L + + +P  + E  +F   N   S+ +     N K  
Sbjct  445   RYIFSQISDSNGLLIQWRFNEYLQEVLALPAAVYESPTF---NYTDSLANSIFNPNVK--  609

Query  816   IEAALFLDWMRLEPQ--SMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFN  873
             I    FLD +  +P    +VWLP+LHR+A  E   H  +C+ C+     GFRYR  K  +
Sbjct  610   ITVNDFLDTLMSDPGPPCLVWLPLLHRIANVENVIHPTQCDACQRENFSGFRYRCQKCPH  789

Query  874   YDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKH--PR  931
             Y +CQ CF+ GRV   H + + + EY + + S    +   + L+  FR      K+  PR
Sbjct  790   YTLCQDCFWKGRVTAPHTLDHQVKEYSSFSPS----KTIGQSLRKSFRCVPDKQKNNLPR  957

Query  932   MGYLPVQTVLEGDNMETPASSPQLSHD---DTHSRIEHYASRLAEMENSNGSYLNDSISP  988
                 P +T L   ++  P  SP  SH+   D ++   H+   +  +++ + +   DS   
Sbjct  958   FPEQPEKT-LNLSHIVPP--SPIPSHNGFPDGNNFTSHFDG-MGSLDSRSTARSLDS---  1116

Query  989   NESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQ  1048
               + DDEH ++  Y   L Q++     R P++  + ++S  R + E +++ LE +NR + 
Sbjct  1117  --ARDDEHKMLARYAARLAQEARSGMGRVPSEACLGMDS-TRAQRE-LISQLEAKNREIM  1284

Query  1049  AEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILED  1108
              E  RL++Q E             +  S     +  L+ E + LR  K  LE  +  L+D
Sbjct  1285  REIARLRRQQE-------------LENSGHGTENPALMNELRALRMRKDELETHLTTLQD  1425

Query  1109  HNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLL-RVVGSQTSDSM  1167
               +QL  QL  L ++L+  Q+  +      S+P++S  RS  S P+L      +Q   S 
Sbjct  1426  SRRQLMIQLEGLMKMLKNHQSSPR------STPNSS-PRSTKSPPLLPGGAPATQPPRSA  1584

Query  1168  GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSL  1205
              +  +  PP + S       E+     P+  GH +G +
Sbjct  1585  PQTPMSMPPTNNSIVTVSQAER-----PTHVGHPMGGI  1683


>ref|XM_001788826.1| PREDICTED: Bos taurus dystrobrevin, alpha (DTNA), mRNA
Length=6242

 Score =  186 bits (472),  Expect = 8e-44, Method: Compositional matrix adjust.
 Identities = 185/659 (28%), Positives = 295/659 (44%), Gaps = 107/659 (16%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPM--DILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D  M  ++ ++   L
Sbjct  410   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNVDPNMELNVARLEAVL  589

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + + V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  590   STIFYQLNKRMPTTHQIQVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  769

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  770   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  934

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  935   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMLGFRYRCQQ  1114

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  1115  CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1273

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRL--------AEM  974
                HP     P + +     ++T    P  S +DT   HS     +  +        +E+
Sbjct  1274  EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSEV  1453

Query  975   ENS-----------NGSYLNDSISPNESIDDEHL--------------------------  997
             E S            G  +  S++  + + DEH+                          
Sbjct  1454  EQSKLLARAAPALLKGKGIKYSLNVADRLADEHVLIGLYVNMLRNNPSCMLESSNRLDEE  1633

Query  998   --LIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYD  1052
               LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+LE +NR +  E  
Sbjct  1634  HRLIARYAARLAAESTSSQPTQQRSAPDISFTIDANK--QQRQLIAELENKNREILQEIQ  1807

Query  1053  RLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQ  1112
             RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  ++
Sbjct  1808  RLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRRE  1957

Query  1113  LESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDL  1172
             L  QL  L +LL+   A     G+  SSPS ++ R     PM +R   + ++ +      
Sbjct  1958  LMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPVRSASACSTPT------  2095

Query  1173  LSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESLVSVMTDEEGAE  1230
                PQD+ TG   V   +  +F  S   N+   L   AD +   M SLV  +  E G+E
Sbjct  2096  -PTPQDSLTG---VGGDVQEAFAQSSRRNLRNDLLVAADSITNTMSSLVKELNSEVGSE  2260


>gb|BT009805.1| Homo sapiens dystrobrevin, beta mRNA, complete cds
Length=1683

 Score =  186 bits (471),  Expect = 8e-44, Method: Compositional matrix adjust.
 Identities = 150/554 (27%), Positives = 263/554 (47%), Gaps = 66/554 (11%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  76    NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  255

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  256   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  429

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  430   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  597

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  598   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  774

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK  928
              +  NY +CQ+CF+ G     H   + M E+          +  AK L +          
Sbjct  775   QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEH-------SSWKSPAKKLSHAISKS-----  918

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSI-S  987
                +G +P +        E P     L+H             L  M ++  S+++  + +
Sbjct  919   ---LGCVPTREPPHPVFPEQPEKPLDLAHIVP-------PRPLTNMNDTMVSHMSSGVPT  1068

Query  988   PNESI-------DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADL  1040
             P +S+       D+EH LI  Y   L  ++  +  R P  +  + ++ +  +  +++A+L
Sbjct  1069  PTKSVLDSPSRLDEEHRLIARYAARLAAEAG-NVTRPPTDLSFNFDANK--QQRQLIAEL  1239

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  LE
Sbjct  1240  ENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELE  1389

Query  1101  ARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVG  1160
              RM  L++  ++L  QL  L +LL     +A+  G+  +SP+    R     PM +R   
Sbjct  1390  QRMSALQESRRELMVQLEELMKLL-----KAQATGSPHTSPTHGGGR---PMPMPVRSTS  1545

Query  1161  SQTSDSMGEEDLLS  1174
             + ++ +   +D LS
Sbjct  1546  AGSTPTHCPQDSLS  1587


>gb|AY889125.1| Synthetic construct Homo sapiens clone FLH109815.01X dystrobrevin 
beta (DTNB) mRNA, complete cds
Length=1683

 Score =  186 bits (471),  Expect = 8e-44, Method: Compositional matrix adjust.
 Identities = 150/554 (27%), Positives = 263/554 (47%), Gaps = 66/554 (11%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  76    NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  255

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  256   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  429

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  430   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  597

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  598   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  774

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK  928
              +  NY +CQ+CF+ G     H   + M E+          +  AK L +          
Sbjct  775   QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEH-------SSWKSPAKKLSHAISKS-----  918

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSI-S  987
                +G +P +        E P     L+H             L  M ++  S+++  + +
Sbjct  919   ---LGCVPTREPPHPVFPEQPEKPLDLAHIVP-------PRPLTNMNDTMVSHMSSGVPT  1068

Query  988   PNESI-------DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADL  1040
             P +S+       D+EH LI  Y   L  ++  +  R P  +  + ++ +  +  +++A+L
Sbjct  1069  PTKSVLDSPSRLDEEHRLIARYAARLAAEAG-NVTRPPTDLSFNFDANK--QQRQLIAEL  1239

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  LE
Sbjct  1240  ENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELE  1389

Query  1101  ARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVG  1160
              RM  L++  ++L  QL  L +LL     +A+  G+  +SP+    R     PM +R   
Sbjct  1390  QRMSALQESRRELMVQLEELMKLL-----KAQATGSPHTSPTHGGGR---PMPMPVRSTS  1545

Query  1161  SQTSDSMGEEDLLS  1174
             + ++ +   +D LS
Sbjct  1546  AGSTPTHCPQDSLS  1587


>gb|AY889124.1| Synthetic construct Homo sapiens clone FLH109814.01X dystrobrevin 
beta (DTNB) mRNA, complete cds
Length=1683

 Score =  186 bits (471),  Expect = 8e-44, Method: Compositional matrix adjust.
 Identities = 150/554 (27%), Positives = 263/554 (47%), Gaps = 66/554 (11%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  76    NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  255

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  256   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  429

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  430   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  597

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  598   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  774

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK  928
              +  NY +CQ+CF+ G     H   + M E+          +  AK L +          
Sbjct  775   QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEH-------SSWKSPAKKLSHAISKS-----  918

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSI-S  987
                +G +P +        E P     L+H             L  M ++  S+++  + +
Sbjct  919   ---LGCVPTREPPHPVFPEQPEKPLDLAHIVP-------PRPLTNMNDTMVSHMSSGVPT  1068

Query  988   PNESI-------DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADL  1040
             P +S+       D+EH LI  Y   L  ++  +  R P  +  + ++ +  +  +++A+L
Sbjct  1069  PTKSVLDSPSRLDEEHRLIARYAARLAAEAG-NVTRPPTDLSFNFDANK--QQRQLIAEL  1239

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  LE
Sbjct  1240  ENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELE  1389

Query  1101  ARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVG  1160
              RM  L++  ++L  QL  L +LL     +A+  G+  +SP+    R     PM +R   
Sbjct  1390  QRMSALQESRRELMVQLEELMKLL-----KAQATGSPHTSPTHGGGR---PMPMPVRSTS  1545

Query  1161  SQTSDSMGEEDLLS  1174
             + ++ +   +D LS
Sbjct  1546  AGSTPTHCPQDSLS  1587


>gb|AY889123.1| Synthetic construct Homo sapiens clone FLH109811.01X dystrobrevin 
beta (DTNB) mRNA, complete cds
Length=1683

 Score =  186 bits (471),  Expect = 8e-44, Method: Compositional matrix adjust.
 Identities = 150/554 (27%), Positives = 263/554 (47%), Gaps = 66/554 (11%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  76    NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  255

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  256   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  429

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  430   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  597

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  598   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  774

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK  928
              +  NY +CQ+CF+ G     H   + M E+          +  AK L +          
Sbjct  775   QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEH-------SSWKSPAKKLSHAISKS-----  918

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSI-S  987
                +G +P +        E P     L+H             L  M ++  S+++  + +
Sbjct  919   ---LGCVPTREPPHPVFPEQPEKPLDLAHIVP-------PRPLTNMNDTMVSHMSSGVPT  1068

Query  988   PNESI-------DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADL  1040
             P +S+       D+EH LI  Y   L  ++  +  R P  +  + ++ +  +  +++A+L
Sbjct  1069  PTKSVLDSPSRLDEEHRLIARYAARLAAEAG-NVTRPPTDLSFNFDANK--QQRQLIAEL  1239

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  LE
Sbjct  1240  ENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELE  1389

Query  1101  ARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVG  1160
              RM  L++  ++L  QL  L +LL     +A+  G+  +SP+    R     PM +R   
Sbjct  1390  QRMSALQESRRELMVQLEELMKLL-----KAQATGSPHTSPTHGGGR---PMPMPVRSTS  1545

Query  1161  SQTSDSMGEEDLLS  1174
             + ++ +   +D LS
Sbjct  1546  AGSTPTHCPQDSLS  1587


>ref|NM_183361.1| Homo sapiens dystrobrevin, beta (DTNB), transcript variant 5, 
mRNA
Length=2315

 Score =  186 bits (471),  Expect = 1e-43, Method: Compositional matrix adjust.
 Identities = 150/554 (27%), Positives = 263/554 (47%), Gaps = 66/554 (11%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  326   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  505

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  506   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  679

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  680   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  847

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  848   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  1024

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK  928
              +  NY +CQ+CF+ G     H   + M E+          +  AK L +          
Sbjct  1025  QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEH-------SSWKSPAKKLSHAISKS-----  1168

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSI-S  987
                +G +P +        E P     L+H             L  M ++  S+++  + +
Sbjct  1169  ---LGCVPTREPPHPVFPEQPEKPLDLAHIVP-------PRPLTNMNDTMVSHMSSGVPT  1318

Query  988   PNESI-------DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADL  1040
             P +S+       D+EH LI  Y   L  ++  +  R P  +  + ++ +  +  +++A+L
Sbjct  1319  PTKSVLDSPSRLDEEHRLIARYAARLAAEAG-NVTRPPTDLSFNFDANK--QQRQLIAEL  1489

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  LE
Sbjct  1490  ENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELE  1639

Query  1101  ARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVG  1160
              RM  L++  ++L  QL  L +LL     +A+  G+  +SP+    R     PM +R   
Sbjct  1640  QRMSALQESRRELMVQLEELMKLL-----KAQATGSPHTSPTHGGGR---PMPMPVRSTS  1795

Query  1161  SQTSDSMGEEDLLS  1174
             + ++ +   +D LS
Sbjct  1796  AGSTPTHCPQDSLS  1837


>gb|BC016655.1| Homo sapiens dystrobrevin, beta, mRNA (cDNA clone MGC:17163 IMAGE:3868207), 
complete cds
Length=2221

 Score =  186 bits (471),  Expect = 1e-43, Method: Compositional matrix adjust.
 Identities = 150/554 (27%), Positives = 263/554 (47%), Gaps = 66/554 (11%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  232   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  411

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  412   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  585

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  586   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  753

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  754   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  930

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK  928
              +  NY +CQ+CF+ G     H   + M E+          +  AK L +          
Sbjct  931   QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEH-------SSWKSPAKKLSHAISKS-----  1074

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSI-S  987
                +G +P +        E P     L+H             L  M ++  S+++  + +
Sbjct  1075  ---LGCVPTREPPHPVFPEQPEKPLDLAHIVP-------PRPLTNMNDTMVSHMSSGVPT  1224

Query  988   PNESI-------DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADL  1040
             P +S+       D+EH LI  Y   L  ++  +  R P  +  + ++ +  +  +++A+L
Sbjct  1225  PTKSVLDSPSRLDEEHRLIARYAARLAAEAG-NVTRPPTDLSFNFDANK--QQRQLIAEL  1395

Query  1041  EEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLE  1100
             E +NR +  E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  LE
Sbjct  1396  ENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELE  1545

Query  1101  ARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVG  1160
              RM  L++  ++L  QL  L +LL     +A+  G+  +SP+    R     PM +R   
Sbjct  1546  QRMSALQESRRELMVQLEELMKLL-----KAQATGSPHTSPTHGGGR---PMPMPVRSTS  1701

Query  1161  SQTSDSMGEEDLLS  1174
             + ++ +   +D LS
Sbjct  1702  AGSTPTHCPQDSLS  1743


>ref|XM_547610.2| PREDICTED: Canis familiaris similar to dystrobrevin alpha isoform 
1 (LOC490488), mRNA
Length=2571

 Score =  185 bits (469),  Expect = 2e-43, Method: Compositional matrix adjust.
 Identities = 183/659 (27%), Positives = 294/659 (44%), Gaps = 107/659 (16%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMD--ILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D  ++  + ++   L
Sbjct  253   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELSVARLEAVL  432

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + + V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  433   STIFYQLNKRMPTTHQIQVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  612

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  613   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  777

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  778   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  957

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  958   CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1116

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT------HSRIEHYASRLAEMENS--  977
                HP     P + +     ++T    P  S +DT       S    + +R +  ++S  
Sbjct  1117  EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSEV  1296

Query  978   --------------NGSYLNDSISPNESIDDEHLL-------------------------  998
                            G  +  S++  + + DEH+L                         
Sbjct  1297  EQNKLLARAAPAFLKGKGIQYSLNVADRLADEHVLIGLYVNRLRNNPSCMLESSNRLDEE  1476

Query  999   ---IQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYD  1052
                I  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+LE +NR +  E  
Sbjct  1477  HRLIARYAARLAAESTSSQPTQQRSAPDISFTIDANK--QQRQLIAELENKNREILQEIQ  1650

Query  1053  RLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQ  1112
             RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  ++
Sbjct  1651  RLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRRE  1800

Query  1113  LESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDL  1172
             L  QL  L +LL+   A     G+  SSPS ++ R     PM +R   + +S +      
Sbjct  1801  LMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPVRSASACSSPAHT----  1944

Query  1173  LSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESLVSVMTDEEGAE  1230
                PQD+ TG   V   +  +F  S   N+   L   AD +   M SLV  +  E G+E
Sbjct  1945  ---PQDSLTG---VGGDVQEAFAQSSRRNLRNDLLVAADSITNTMSSLVKELNSEVGSE  2103


>gb|U26744.1|HSU26744 Human dystrobrevin-gamma mRNA, complete cds
Length=2419

 Score =  184 bits (468),  Expect = 2e-43, Method: Compositional matrix adjust.
 Identities = 153/516 (29%), Positives = 253/516 (49%), Gaps = 53/516 (10%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND--QPMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  134   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTELNVSRLEAVL  313

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  314   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  493

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P ++ E  SFG +  E S RSCF   + 
Sbjct  494   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTEVLEGPSFGYT--EQSARSCF---SQ  658

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  659   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  838

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  839   CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  997

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYL  982
                HP     P + +     ++T    P  S +DT   HS           + +S   ++
Sbjct  998   EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPFI  1144

Query  983   NDS-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILA  1038
               S +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ ++    +++A
Sbjct  1145  TRSMLESSNRLDEEHRLIARYAARLAAESSSSQPPQQRSAPDISFTIDANKQQ--RQLIA  1318

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
             +LE +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  
Sbjct  1319  ELENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDE  1468

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVN  1134
             LE RM  L++  ++L  QL  L +LL++ + +  V+
Sbjct  1469  LEQRMSALQESRRELMVQLEGLMKLLKEEELKQGVS  1576


>emb|X95227.1| M.musculus mRNA for dystrobrevin (clone m32)
Length=1883

 Score =  184 bits (467),  Expect = 2e-43, Method: Compositional matrix adjust.
 Identities = 153/516 (29%), Positives = 252/516 (48%), Gaps = 53/516 (10%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  251   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  430

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  431   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  610

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  611   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  775

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  776   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPLECSYCHSESMMGFRYRCQQ  955

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  956   CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1114

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYL  982
                HP     P + +     ++T    P  S +DT   HS           + +S   ++
Sbjct  1115  EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPFI  1261

Query  983   NDS-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILA  1038
               S +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++A
Sbjct  1262  TRSMLESSNRLDEEHRLIARYAARLAAESSSSQPTQQRSAPDISFTIDANK--QQRQLIA  1435

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
             +LE +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  
Sbjct  1436  ELENKNREILQEIQRLRVEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDE  1585

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVN  1134
             LE RM  L++  ++L  QL  L +LL++ + +  V+
Sbjct  1586  LEQRMSALQESRRELMVQLEGLMKLLKEEELKQGVS  1693


>ref|NM_032979.4| Homo sapiens dystrobrevin, alpha (DTNA), transcript variant 5, 
mRNA
Length=4553

 Score =  184 bits (467),  Expect = 3e-43, Method: Compositional matrix adjust.
 Identities = 153/516 (29%), Positives = 252/516 (48%), Gaps = 53/516 (10%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND--QPMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  427   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTELNVSRLEAVL  606

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  607   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  786

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  787   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  951

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  952   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1131

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  1132  CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1290

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYL  982
                HP     P + +     ++T    P  S +DT   HS           + +S   ++
Sbjct  1291  EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPFI  1437

Query  983   NDS-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILA  1038
               S +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ ++    +++A
Sbjct  1438  TRSMLESSNRLDEEHRLIARYAARLAAESSSSQPPQQRSAPDISFTIDANKQQ--RQLIA  1611

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
             +LE +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  
Sbjct  1612  ELENKNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDE  1761

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVN  1134
             LE RM  L++  ++L  QL  L +LL++ + +  V+
Sbjct  1762  LEQRMSALQESRRELMVQLEGLMKLLKEEELKQGVS  1869


>dbj|AK019477.1| Mus musculus 0 day neonate skin cDNA, RIKEN full-length enriched 
library, clone:4631433M03 product:dystrobrevin alpha, full 
insert sequence
Length=3861

 Score =  184 bits (467),  Expect = 3e-43, Method: Compositional matrix adjust.
 Identities = 180/658 (27%), Positives = 294/658 (44%), Gaps = 101/658 (15%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  563   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  742

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  743   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  922

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  923   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  1087

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    I+GFRYR  +
Sbjct  1088  QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESIMGFRYRCQQ  1267

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--K  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A  +
Sbjct  1268  CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1426

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT------HSRIEHYASRLAEMENS-----  977
              P     P Q     +        P  S +DT       S    + +R +  ++S     
Sbjct  1427  EPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSEVEQN  1606

Query  978   -----------NGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPL--------------  1012
                         G  +  S++  + + DEH+LI  Y   L  D P               
Sbjct  1607  KMLARAAPAFLKGRGIQYSLNVADRLADEHVLIGLYVNMLRNDPPCMLESSNRLDEEHRL  1786

Query  1013  --------------SQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYDRLK  1055
                           SQP   RS   I  ++++ +  +  +++A+LE +NR +  E  RL+
Sbjct  1787  IARYAARLAAESSSSQPTQQRSAPDISFTIDANK--QQRQLIAELENKNREILQEIQRLR  1960

Query  1056  QQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLES  1115
              +HE              PT  ++ ++  L+AE +LLRQ K  LE RM  L++  ++L  
Sbjct  1961  VEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELEQRMSALQESRRELMV  2110

Query  1116  QLHRLRQLLEQPQAEAKVNGTTV--SSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLL  1173
             QL  L +LL++ + +    G +   SSPS ++ R     PM +R   +  + +       
Sbjct  2111  QLEGLMKLLKEEELKQGTQGASSPRSSPSHTISRPI---PMPIRSASACPTPTHT-----  2266

Query  1174  SPPQDTSTGLEEVMEQLNNSFPSSRGHNVGS-LFHMADDLGRAMESLVSVMTDEEGAE  1230
               PQD+ TG   V   +  +F  S   N+ S L   AD +   M SLV  +  E  +E
Sbjct  2267  --PQDSLTG---VGGDVQEAFAQSSRRNLRSDLLVAADSITNTMSSLVKELNSEVASE  2425


>gb|DQ516346.1| Danio rerio gamma-dystrobrevin (GDTN) mRNA, complete cds
Length=2570

 Score =  184 bits (467),  Expect = 3e-43, Method: Compositional matrix adjust.
 Identities = 170/619 (27%), Positives = 280/619 (45%), Gaps = 64/619 (10%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCL-DLLSLSAACDALDQHNLKQND--QPMDILQIINC  693
             + + +R S YRTA KLR +QK   L  L+ +    +A   + L   D    + + ++   
Sbjct  103   NYDTIRLSTYRTACKLRFVQKKCNLMHLVDVWNMIEAFRDNGLNTLDVCTEISVARLETI  282

Query  694   LTTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
             LT IY +L +     + ++V     + LN++   +DT   GR+ V S K  +  LC   L
Sbjct  283   LTCIYQQLNKRLPTTHQISVQHNTSLLLNFMATAHDTDAQGRLTVFSVKMMLSVLCGGKL  462

Query  752   EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              DK RY+F Q++ S G  +  +    L +++++P  + E  SFG   ++   RSCF    
Sbjct  463   VDKLRYIFSQISDSHGAMEMSKFDHFLREALKLPAAVFEGPSFG--YLDHLARSCFP---  627

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + ++   +FLD +  +P  Q ++WLP++HR+   E   H   C+ C+   + GFRYR  
Sbjct  628   QQKKVMLNMFLDALMSDPPPQCLIWLPLVHRMGNVENVHHPVSCSFCRSDGMTGFRYRCQ  807

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYC---TPTTS-GEDVRDFAKVLKNKFRTKRY  925
             + FNY +CQ+CF+ G  +  H  H+ M E+    +P    G  +      + ++  +   
Sbjct  808   QCFNYQLCQNCFWRGHASGNHSNHHEMKEHSSWKSPVKKLGRAISKSLGCVPSREPSHPI  987

Query  926   FAKHPR-----MGYLPVQTVLEGDNMETPASSPQLSHDDTHSR---IEHYASRLAEMENS  977
             + ++P         +P + +    NM  PA  P LS   + ++       A R+ E    
Sbjct  988   YPEYPEKPLNLSNIVPPRPI---GNMNEPA--PPLSTGSSPTKRLPTLAAAQRMNEEHAL  1152

Query  978   NGSYLNDSISPNESI------DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERG  1031
               +Y+N   S   ++      D+EH LI  Y   L  D P    R PA        ++R 
Sbjct  1153  IAAYVNKLQSSPRALDSPVRSDEEHKLIARYASRLATD-PGHTAR-PADFSYDTNKQQR-  1323

Query  1032  ELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKL  1091
                 ++  LE +NR +  E  RL+ +HE +   P P   +  PT         L+AE + 
Sbjct  1324  ---ELIMQLENKNREILQEIQRLRVEHE-QACQPTPERVQQNPT---------LLAELRQ  1464

Query  1092  LRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSS  1151
             LRQ K  LE RM  L++  ++L  QL  L +LL     +A+  G   SSPS +  R   S
Sbjct  1465  LRQRKDELEQRMSSLQESRRELMVQLEGLMKLL-----KAQAAG---SSPSHASPR---S  1611

Query  1152  QPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADD  1211
              PM +R   S  + +         PQD+  G+   +++  +  P     N   L   AD 
Sbjct  1612  MPMPIRSPSSGPAPTYTGHTPTHGPQDSLAGVGGDVQEAFSQGPRRNLRN--DLLVAADS  1785

Query  1212  LGRAMESLVSVMTDEEGAE  1230
             +   M SLV  +   E  +
Sbjct  1786  ITNTMSSLVKELNSAEDGD  1842


>ref|XM_512087.2| PREDICTED: Pan troglodytes dystrobrevin alpha (DTNA), mRNA
Length=4928

 Score =  184 bits (466),  Expect = 3e-43, Method: Compositional matrix adjust.
 Identities = 183/660 (27%), Positives = 297/660 (45%), Gaps = 109/660 (16%)
 Frame = +3

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  291   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  467

Query  694   LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
             L+TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  468   LSTIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  647

Query  752   EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  648   MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  812

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  813   QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  992

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK-  928
             +  NY +CQ CF+ G     H   + M EY +        +  AK L N        A  
Sbjct  993   QCHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASS  1151

Query  929   ----HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT------HSRIEHYASRLAEMENS-  977
                 HP     P + +     ++T    P  S +DT       S    + +R +  ++S 
Sbjct  1152  REPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSE  1331

Query  978   ---------------NGSYLNDSISPNESIDDEHLL------------------------  998
                             G  +  S++  + + DEH+L                        
Sbjct  1332  VEQNKLLARAAPAFLKGKGIQYSLNVADRLADEHVLIGLYVNMLRNNPSCMLESSNRLDE  1511

Query  999   ----IQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEY  1051
                 I  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+LE +NR +  E 
Sbjct  1512  EHRLIARYAARLAAESSSSQPPQQRSAPDISFTIDANK--QQRQLIAELENKNREILQEI  1685

Query  1052  DRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNK  1111
              RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  +
Sbjct  1686  QRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRR  1835

Query  1112  QLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEED  1171
             +L  QL  L +LL+   A     G+  SSPS ++ R     PM +R   + ++ +     
Sbjct  1836  ELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIRSASACSTPTHT---  1982

Query  1172  LLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESLVSVMTDEEGAE  1230
                 PQD+ TG   V   +  +F  S   N+   L   AD +   M SLV  +  E G+E
Sbjct  1983  ----PQDSLTG---VGGDVQEAFAQSSRRNLRNDLLVAADSITNTMSSLVKELNSEVGSE  2141


>ref|XM_001495981.1| PREDICTED: Equus caballus dystrobrevin, alpha, transcript variant 
2 (DTNA), mRNA
Length=2232

 Score =  184 bits (466),  Expect = 3e-43, Method: Compositional matrix adjust.
 Identities = 182/659 (27%), Positives = 294/659 (44%), Gaps = 107/659 (16%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  76    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  255

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + + V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  256   STIFYQLNKRMPTTHQIQVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  435

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  436   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  600

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  781   CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  939

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT------HSRIEHYASRLAEMENS--  977
                HP     P + +     ++T    P  S +DT       S    + +R +  ++S  
Sbjct  940   EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSEV  1119

Query  978   --------------NGSYLNDSISPNESIDDEHLL-------------------------  998
                            G  +  S++  + + DEH+L                         
Sbjct  1120  EQNKLLARAAPAFLKGKGIQYSLNVADRLADEHVLIGLYVNMLRNNPSCMLESSNRLDEE  1299

Query  999   ---IQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYD  1052
                I  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+LE +NR +  E  
Sbjct  1300  HRLIARYAARLAAESTSSQPTQQRSAPDISFTIDANK--QQRQLIAELENKNREILQEIQ  1473

Query  1053  RLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQ  1112
             RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  ++
Sbjct  1474  RLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRRE  1623

Query  1113  LESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDL  1172
             L  QL  L +LL+   A     G+  SSPS ++ R     PM +R   + ++ +      
Sbjct  1624  LMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPVRSASACSTPTHT----  1767

Query  1173  LSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESLVSVMTDEEGAE  1230
                PQD+ TG   V   +  +F  S   N+   L   AD +   M SLV  +  E G+E
Sbjct  1768  ---PQDSLTG---VGGDVQEAFAQSSRRNLRNDLLVAADSITNTMSSLVKELNSEAGSE  1926


>ref|XM_001369068.1| PREDICTED: Monodelphis domestica similar to dystrobrevin, alpha,, 
transcript variant 5 (LOC100023710), mRNA
Length=1704

 Score =  184 bits (466),  Expect = 4e-43, Method: Compositional matrix adjust.
 Identities = 164/562 (29%), Positives = 266/562 (47%), Gaps = 91/562 (16%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  76    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  255

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  256   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  435

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R  L L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  436   DKLRYIFSMISDSSGVMVYGRYDLFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  600

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601   QKKVTLNAFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G  +  H   + M EY +        +  AK L N        A   
Sbjct  781   CHNYQLCQDCFWRGHASGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  939

Query  929   ---HPRMG-----------YLPVQTVLEGDNM----ETPAS-SPQLSHDDTHSRIE----  965
                HP               +P + V   ++       P+S SP ++   +H   E    
Sbjct  940   EPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHSVPSSGSPFITRSSSHKNTEVEQS  1119

Query  966   ----------------HY----ASRLAE----------MENSNGSYLNDSISPNESIDDE  995
                             HY    A RLA+          M  SN S + D  SPN  +D+E
Sbjct  1120  KLLARAAPIFLKGKGLHYSLDVADRLADEHVLIGLYVNMLQSNPSRMLD--SPNR-LDEE  1290

Query  996   HLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYD  1052
             H LI  Y   L  ++  +QP   R P+ I  ++++ +  +  +++A+LE +NR +  E  
Sbjct  1291  HRLIARYAARLAAETSSTQPSQQRGPSDISFTIDANK--QQRQLIAELENKNREILQEIQ  1464

Query  1053  RLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQ  1112
             RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  ++
Sbjct  1465  RLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRRE  1614

Query  1113  LESQLHRLRQLLEQPQAEAKVN  1134
             L  QL  L +LL++ + +  V+
Sbjct  1615  LMVQLEGLMKLLKEEELKQGVS  1680


>ref|NM_001390.4| Homo sapiens dystrobrevin, alpha (DTNA), transcript variant 1, 
mRNA
Length=6358

 Score =  184 bits (466),  Expect = 4e-43, Method: Compositional matrix adjust.
 Identities = 183/660 (27%), Positives = 297/660 (45%), Gaps = 109/660 (16%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  77    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  253

Query  694   LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
             L+TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  254   LSTIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  433

Query  752   EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  434   MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  598

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  599   QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  778

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK-  928
             +  NY +CQ CF+ G     H   + M EY +        +  AK L N        A  
Sbjct  779   QCHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASS  937

Query  929   ----HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT------HSRIEHYASRLAEMENS-  977
                 HP     P + +     ++T    P  S +DT       S    + +R +  ++S 
Sbjct  938   REPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSE  1117

Query  978   ---------------NGSYLNDSISPNESIDDEHLL------------------------  998
                             G  +  S++  + + DEH+L                        
Sbjct  1118  VEQNKLLARAAPAFLKGKGIQYSLNVADRLADEHVLIGLYVNMLRNNPSCMLESSNRLDE  1297

Query  999   ----IQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEY  1051
                 I  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+LE +NR +  E 
Sbjct  1298  EHRLIARYAARLAAESSSSQPPQQRSAPDISFTIDANK--QQRQLIAELENKNREILQEI  1471

Query  1052  DRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNK  1111
              RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  +
Sbjct  1472  QRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRR  1621

Query  1112  QLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEED  1171
             +L  QL  L +LL+   A     G+  SSPS ++ R     PM +R   + ++ +     
Sbjct  1622  ELMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIRSASACSTPTHT---  1768

Query  1172  LLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESLVSVMTDEEGAE  1230
                 PQD+ TG   V   +  +F  S   N+   L   AD +   M SLV  +  E G+E
Sbjct  1769  ----PQDSLTG---VGGDVQEAFAQSSRRNLRNDLLVAADSITNTMSSLVKELNSEVGSE  1927


>ref|XM_001054112.1| PREDICTED: Rattus norvegicus similar to dystrobrevin alpha isoform 
1 (predicted), transcript variant 2 (RGD1561985_predicted), 
mRNA
Length=2039

 Score =  183 bits (464),  Expect = 5e-43, Method: Compositional matrix adjust.
 Identities = 151/516 (29%), Positives = 252/516 (48%), Gaps = 53/516 (10%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  409   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  588

Query  695   TTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +T++ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  589   STMFYQLNKRMPSTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  768

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  769   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  933

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  934   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1113

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  1114  CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1272

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYL  982
                HP     P + +     ++T    P  S +DT   HS           + +S   ++
Sbjct  1273  EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHS-----------VPSSGSPFI  1419

Query  983   NDS-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILA  1038
               S +  +  +D+EH LI  Y   L  +S  SQP   RS   +  ++++ +  +  +++A
Sbjct  1420  TRSMLESSNRLDEEHRLIARYAARLAAESSSSQPTQQRSAPDVSFTIDANK--QQRQLIA  1593

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
             +LE +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  
Sbjct  1594  ELENKNREILQEIQRLRVEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDE  1743

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVN  1134
             LE RM  L++  ++L  QL  L +LL++ + +  V+
Sbjct  1744  LEQRMSALQESRRELMVQLEGLMKLLKEEELKQGVS  1851


>ref|XM_001102769.1| PREDICTED: Macaca mulatta similar to dystrobrevin alpha isoform 
1 (LOC707887), mRNA
Length=6588

 Score =  183 bits (464),  Expect = 6e-43, Method: Compositional matrix adjust.
 Identities = 182/659 (27%), Positives = 295/659 (44%), Gaps = 107/659 (16%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  326   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVSRLEAVL  505

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  506   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  685

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  686   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  850

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  851   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1030

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  1031  CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1189

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT------HSRIEHYASRLAEMENS--  977
                HP     P + +     ++T    P  S +DT       S    + +R +  ++S  
Sbjct  1190  EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSEV  1369

Query  978   --------------NGSYLNDSISPNESIDDEHLL-------------------------  998
                            G  +  S++  + + DEH+L                         
Sbjct  1370  EQNKLLARAAPAFLKGKGIQYSLNVADRLADEHVLIGLYVNMLRNNPSCMLESSNRLDEE  1549

Query  999   ---IQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYD  1052
                I  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+LE +NR +  E  
Sbjct  1550  HRLIARYAARLAAESSSSQPTQQRSAPDISFTIDANK--QQRQLIAELENKNREILQEIQ  1723

Query  1053  RLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQ  1112
             RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  ++
Sbjct  1724  RLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRRE  1873

Query  1113  LESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDL  1172
             L  QL  L +LL+   A     G+  SSPS ++ R     PM +R   + ++ +      
Sbjct  1874  LMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPVRSASACSTPTHT----  2017

Query  1173  LSPPQDTSTGLEEVMEQLNNSFPSSRGHNV-GSLFHMADDLGRAMESLVSVMTDEEGAE  1230
                PQD+ TG   V   +  +F  S   N+   L   AD +   M SLV  +  E G+E
Sbjct  2018  ---PQDSLTG---VGGDVQEAFAQSSRRNLRNDLLVAADSITNTMSSLVKELNSEVGSE  2176


>ref|XM_001369046.1| PREDICTED: Monodelphis domestica similar to dystrobrevin, alpha,, 
transcript variant 4 (LOC100023710), mRNA
Length=1713

 Score =  182 bits (463),  Expect = 8e-43, Method: Compositional matrix adjust.
 Identities = 164/565 (29%), Positives = 266/565 (47%), Gaps = 94/565 (16%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  76    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  255

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  256   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  435

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R  L L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  436   DKLRYIFSMISDSSGVMVYGRYDLFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  600

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601   QKKVTLNAFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G  +  H   + M EY +        +  AK L N        A   
Sbjct  781   CHNYQLCQDCFWRGHASGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  939

Query  929   ---HPRMGYLPVQTVLEGDNMET------------------PAS-SPQLSHDDTHSRIE-  965
                HP     P + +     ++T                  P+S SP ++   +H   E 
Sbjct  940   EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHSVPSSGSPFITRSSSHKNTEV  1119

Query  966   -------------------HY----ASRLAE----------MENSNGSYLNDSISPNESI  992
                                HY    A RLA+          M  SN S + D  SPN  +
Sbjct  1120  EQSKLLARAAPIFLKGKGLHYSLDVADRLADEHVLIGLYVNMLQSNPSRMLD--SPNR-L  1290

Query  993   DDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQA  1049
             D+EH LI  Y   L  ++  +QP   R P+ I  ++++ +  +  +++A+LE +NR +  
Sbjct  1291  DEEHRLIARYAARLAAETSSTQPSQQRGPSDISFTIDANK--QQRQLIAELENKNREILQ  1464

Query  1050  EYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDH  1109
             E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++ 
Sbjct  1465  EIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQES  1614

Query  1110  NKQLESQLHRLRQLLEQPQAEAKVN  1134
              ++L  QL  L +LL++ + +  V+
Sbjct  1615  RRELMVQLEGLMKLLKEEELKQGVS  1689


>emb|X65468.1| R.norvegicus mRNA for apodystrophin-I
Length=384

 Score =  182 bits (463),  Expect = 8e-43, Method: Compositional matrix adjust.
 Identities = 86/86 (100%), Positives = 86/86 (100%), Gaps = 0/86 (0%)
 Frame = +1

Query  616  HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQ  675
            HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQ
Sbjct  127  HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQ  306

Query  676  HNLKQNDQPMDILQIINCLTTIYDRL  701
            HNLKQNDQPMDILQIINCLTTIYDRL
Sbjct  307  HNLKQNDQPMDILQIINCLTTIYDRL  384


>ref|XM_001054548.1| PREDICTED: Rattus norvegicus similar to dystrobrevin alpha isoform 
1 (predicted), transcript variant 7 (RGD1561985_predicted), 
mRNA
Length=3402

 Score =  182 bits (462),  Expect = 9e-43, Method: Compositional matrix adjust.
 Identities = 164/588 (27%), Positives = 271/588 (46%), Gaps = 91/588 (15%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  257   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  436

Query  695   TTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +T++ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  437   STMFYQLNKRMPSTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  616

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  617   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  781

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  782   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  961

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--K  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A  +
Sbjct  962   CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1120

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLNDS  985
              P     P Q     +        P  S +DT   HS           + +S   ++  S
Sbjct  1121  EPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITRS  1267

Query  986   ISPNES---------------------------IDDEHLLIQHYCQSLNQDSPLSQP---  1015
               P +S                           +D+EH LI  Y   L  +S  SQP   
Sbjct  1268  SPPKDSEVEQNKILARAAPAFLKGKGMLESSNRLDEEHRLIARYAARLAAESSSSQPTQQ  1447

Query  1016  RSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPT  1075
             RS   +  ++++ +  +  +++A+LE +NR +  E  RL+ +HE              PT
Sbjct  1448  RSAPDVSFTIDANK--QQRQLIAELENKNREILQEIQRLRVEHEQAS----------QPT  1591

Query  1076  SPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNG  1135
               ++ ++  L+AE +LLRQ K  LE RM  L++  ++L  QL  L +LL+   A     G
Sbjct  1592  PEKAQQNPTLLAELRLLRQRKDELEQRMSALQESRRELMVQLEGLMKLLKTQGA-----G  1756

Query  1136  TTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGL  1183
             +  SSPS ++ R     PM +R   + ++ +         PQD+ TG+
Sbjct  1757  SPRSSPSHTISRPI---PMPIRSTSACSTPAYT-------PQDSLTGV  1870


>gb|L05649.1|HUMDYSTR15 Homo sapiens dystrophin (DMD) gene, exon 59
Length=500

 Score =  182 bits (462),  Expect = 1e-42, Method: Compositional matrix adjust.
 Identities = 92/101 (91%), Positives = 94/101 (93%), Gaps = 0/101 (0%)
 Frame = +1

Query  420  GLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQEL  479
            GL+  +    ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQEL
Sbjct  181  GLKPCHIANLELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQEL  360

Query  480  QEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKA  520
            QEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVK 
Sbjct  361  QEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKV  483


>dbj|AK291156.1| Homo sapiens cDNA FLJ77455 complete cds, highly similar to Homo 
sapiens dystrobrevin, alpha (DTNA), transcript variant 5, 
mRNA
Length=1869

 Score =  181 bits (459),  Expect = 3e-42, Method: Compositional matrix adjust.
 Identities = 150/512 (29%), Positives = 249/512 (48%), Gaps = 48/512 (9%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  226   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  402

Query  694   LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
             L+TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  403   LSTIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  582

Query  752   EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  583   MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  747

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  748   QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  927

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKH  929
             +  NY +CQ CF+ G     H   + M EY   T+     +     L          ++ 
Sbjct  928   QCHNYQLCQDCFWRGHAGGSHSNQHQMKEY---TSWKSPAKKLTNALSKSLSCAS--SRE  1092

Query  930   PRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSRIEHYASRLAEMENSNGSYLNDS-  985
             P     P Q     +        P  S +DT   HS           + +S   ++  S 
Sbjct  1093  PLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-----------VPSSGSPFITRSM  1239

Query  986   ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEE  1042
             +  +  +D+EH LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+LE 
Sbjct  1240  LESSNRLDEEHRLIARYAARLAAESSSSQPPQQRSAPDISFTIDANK--QQRQLIAELEN  1413

Query  1043  ENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEAR  1102
             +NR +  E  RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE R
Sbjct  1414  KNREILQEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQR  1563

Query  1103  MQILEDHNKQLESQLHRLRQLLEQPQAEAKVN  1134
             M  L++  ++L  QL  L +LL++ + +  V+
Sbjct  1564  MSALQESRRELMVQLEGLMKLLKEEELKQGVS  1659


>gb|AC079177.21| Homo sapiens Xp BAC RP11-147B14 (Roswell Park Cancer Institute 
Human BAC Library) complete sequence
Length=155533

 Score =  180 bits (457),  Expect = 4e-42, Method: Compositional matrix adjust.
 Identities = 91/101 (90%), Positives = 94/101 (93%), Gaps = 0/101 (0%)
 Frame = -1

Query  420     GLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQEL  479
               GL+  +    ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERL+EL
Sbjct  132907  GLKPCHIANLELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLREL  132728

Query  480     QEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKA  520
               QEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVK 
Sbjct  132727  QEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKV  132605


 Score =  111 bits (278),  Expect = 2e-21, Method: Compositional matrix adjust.
 Identities = 53/55 (96%), Positives = 53/55 (96%), Gaps = 0/55 (0%)
 Frame = -3

Query  336     IRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRA  390
                RSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHR 
Sbjct  151451  FRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRV  151287


 Score =  103 bits (257),  Expect = 5e-19, Method: Compositional matrix adjust.
 Identities = 50/52 (96%), Positives = 52/52 (100%), Gaps = 0/52 (0%)
 Frame = -2

Query  519    KALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVA  570
              +ALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV+
Sbjct  99132  QALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVS  98977


 Score = 84.3 bits (207),  Expect = 4e-13, Method: Compositional matrix adjust.
 Identities = 40/43 (93%), Positives = 42/43 (97%), Gaps = 0/43 (0%)
 Frame = -2

Query  387     VHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPR  429
               + +AFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPR
Sbjct  133614  ISQAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPR  133486


 Score = 60.5 bits (145),  Expect = 6e-06, Method: Compositional matrix adjust.
 Identities = 27/28 (96%), Positives = 28/28 (100%), Gaps = 0/28 (0%)
 Frame = -1

Query  568   QVAVEDRVRQLHEAHRDFGPASQHFLST  595
             QVAVEDRVRQLHEAHRDFGPASQHFLS+
Sbjct  3139  QVAVEDRVRQLHEAHRDFGPASQHFLSS  3056


>ref|XM_001054600.1| PREDICTED: Rattus norvegicus similar to dystrobrevin alpha isoform 
1 (predicted), transcript variant 8 (RGD1561985_predicted), 
mRNA
Length=3504

 Score =  180 bits (456),  Expect = 5e-42, Method: Compositional matrix adjust.
 Identities = 170/611 (27%), Positives = 279/611 (45%), Gaps = 103/611 (16%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  257   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  436

Query  695   TTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +T++ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  437   STMFYQLNKRMPSTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  616

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  617   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  781

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  782   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  961

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK--  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A   
Sbjct  962   CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1120

Query  929   ---HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---------------------HSRI  964
                HP     P + +     ++T    P  S +DT                      S +
Sbjct  1121  EPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSEV  1300

Query  965   E------------------HY----ASRLAEMENSNGSYLN-------DSISPNESIDDE  995
             E                  HY    A RLA+     G Y+N         +  +  +D+E
Sbjct  1301  EQNKILARAAPAFLKGKGIHYSLNVADRLADEHVLIGLYVNMLRNNPSCMLESSNRLDEE  1480

Query  996   HLLIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYD  1052
             H LI  Y   L  +S  SQP   RS   +  ++++ +  +  +++A+LE +NR +  E  
Sbjct  1481  HRLIARYAARLAAESSSSQPTQQRSAPDVSFTIDANK--QQRQLIAELENKNREILQEIQ  1654

Query  1053  RLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQ  1112
             RL+ +HE              PT  ++ ++  L+AE +LLRQ K  LE RM  L++  ++
Sbjct  1655  RLRVEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELEQRMSALQESRRE  1804

Query  1113  LESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDL  1172
             L  QL  L +LL+   A     G+  SSPS ++ R     PM +R   + ++ +      
Sbjct  1805  LMVQLEGLMKLLKTQGA-----GSPRSSPSHTISRPI---PMPIRSTSACSTPAYT----  1948

Query  1173  LSPPQDTSTGL  1183
                PQD+ TG+
Sbjct  1949  ---PQDSLTGV  1972


>ref|XM_001843534.1| Culex quinquefasciatus dystrobrevin, mRNA
Length=1989

 Score =  178 bits (451),  Expect = 2e-41, Method: Compositional matrix adjust.
 Identities = 153/545 (28%), Positives = 254/545 (46%), Gaps = 61/545 (11%)
 Frame = +1

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK----QNDQPMDILQI  690
             +   + +RF++YRTA KLR +QK+  L L+ +    +A  ++ L     QN+  +  L+ 
Sbjct  43    IQSFDTIRFASYRTACKLRYVQKSTNLHLVDIWNVIEAFRENGLNTLEPQNEVSVSRLET  222

Query  691   INCLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCK  748
             +  ++++Y  L +       VP+     + LNWLL  Y    +G+IRV S K  +  +C 
Sbjct  223   L--VSSLYHNLNKRLPPTQQVPVDSKASLLLNWLLAAYSGDNSGKIRVFSIKVALAIMCA  396

Query  749   AHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
               + DK RY+F Q++   G     +LG  L + + +P  + E  +F   + + ++ S   
Sbjct  397   GKMVDKLRYVFSQISDGAGQLIHWKLGDFLREVLALPAAVFESPTF---HYQEALESEIF  567

Query  809   FANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
                NK  +   +        P  +VWL +LHR+A  ET  H   C++C      GFRYR 
Sbjct  568   PVENKITVNDFMAALMSEPGPSCLVWLSLLHRLATVETVVHPTICSVCLRENFTGFRYRC  747

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRT--KRYF  926
              +   Y +CQ CF+ GRV+  H+  + + EY +  +  + +      L+  FR   ++  
Sbjct  748   QRCHAYQLCQDCFWQGRVSLNHQNDHEVKEYSSYKSPSKQI---GHSLRKSFRCVPEKPN  918

Query  927   AKHPRMGYLPVQTVLEGDNMETPASSPQLSHD--------------DTHSRIEHYASRLA  972
                PR    P +T L   ++  P  SP  SH+              D  S ++  A+ L+
Sbjct  919   QVLPRFPEQPEKT-LNLSHIVPP--SPLPSHNGFNDGGGAMIPGMYDRSSTLDSRATGLS  1089

Query  973   EMENSNGSYLN---DSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEE  1029
                +SNG+ +           S D+EH LI  Y   L Q+S      +P  + I L+S  
Sbjct  1090  --LDSNGTSVTRGGGGGGGANSNDEEHRLIARYAARLAQESRTPGGSAPDPVQIGLDS-S  1260

Query  1030  RGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEA  1089
             R + E I+  LE +N+ +  E  +L++Q E + +            +P+SP    L+ E 
Sbjct  1261  RAQRELIM-QLESKNKEIMREIQKLRRQQEAEQV------------APESP---ALMTEL  1392

Query  1090  KLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSD  1149
             + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q ++    T  SSP     RS 
Sbjct  1393  RALRQRKGELEGHLGALQDSRRQLMGQLEGLMRMLKNHQTQSP-RSTPNSSP-----RSG  1554

Query  1150  SSQPM  1154
              S P+
Sbjct  1555  KSPPL  1569


>ref|XM_001650730.1| Aedes aegypti dystrobrevin partial mRNA
Length=1998

 Score =  178 bits (451),  Expect = 2e-41, Method: Compositional matrix adjust.
 Identities = 147/536 (27%), Positives = 249/536 (46%), Gaps = 50/536 (9%)
 Frame = +1

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK----QNDQPMDILQI  690
             +   + +RF++YRTA KLR +QK+  L L+ +    +A  ++ L     QN+  +  L+ 
Sbjct  124   IQSFDTIRFASYRTACKLRYVQKSTNLHLVDIWNVIEAFRENGLNTLEHQNEVSVSRLET  303

Query  691   INCLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCK  748
             +  ++++Y  L +       VP+     + LNWLL  Y    +G+IRV S K  +  +C 
Sbjct  304   L--VSSLYHNLNKRLPPTQQVPVDSKASLLLNWLLAAYSGDNSGKIRVFSIKVALAIMCA  477

Query  749   AHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
               + DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  + S   
Sbjct  478   GKMVDKLRYIFSQISDGAGQLIHWKLGDFLREVLALPAAVFESPTF---HYQEGLESEIF  648

Query  809   FANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
                NK  +   + +      P  +VWL +LHR+A  E   H   C++C      GFRYR 
Sbjct  649   PVENKITVNDFMAVLMSEPGPACLVWLSLLHRLATVEAVVHPTICSVCLRENFTGFRYRC  828

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRT--KRYF  926
              +   Y +CQ CF+ GRV+  H+  + + EY +  +  + +      L+  FR   ++  
Sbjct  829   QRCHAYQLCQDCFWQGRVSLNHQNDHEVKEYSSYKSPSKQI---GHSLRKSFRCVPEKPN  999

Query  927   AKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEME--------NSN  978
                PR    P +T L   ++  P+  P  +       I     R + ++        +SN
Sbjct  1000  QVLPRFPEQPEKT-LNLSHIVPPSPLPSHNGFQDGGMIPGMYDRSSTLDSRGTGLSLDSN  1176

Query  979   GSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILA  1038
             G+ +    +   S D+EH LI  Y   L Q+S      +P  + I L+S  R + E I+ 
Sbjct  1177  GTSVTRGGA--NSNDEEHRLIARYAARLAQESRTPGSSAPDPVQIGLDS-SRAQRELIM-  1344

Query  1039  DLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
              LE +N+ +  E  +L++Q E +         ++ P SP       L+ E + LRQ KG 
Sbjct  1345  QLESKNKEIMREIQKLRRQQEAE---------QVQPESP------ALMNELRALRQRKGE  1479

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPM  1154
             LE  +  L+D  +QL +QL  L ++L+  Q ++    T  SSP     RS  S P+
Sbjct  1480  LEGHLGALQDSRRQLMAQLEGLMRMLKNHQTQSP-RSTPNSSP-----RSGKSPPL  1629


>ref|XM_001975870.1| Drosophila erecta GG20305 (Dere\GG20305), mRNA
Length=2184

 Score =  177 bits (450),  Expect = 2e-41, Method: Compositional matrix adjust.
 Identities = 139/550 (25%), Positives = 243/550 (44%), Gaps = 59/550 (10%)
 Frame = +1

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  43    LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  222

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  223   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  402

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +      A
Sbjct  403   LVDKLRYIFSQISDGAGQMVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPA  573

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP++HR+A  ET  H   C++C +    GFRYR  +
Sbjct  574   ENKVTVNDFMATLMSEPGPSCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQR  753

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDV-----RDFAKVLKNKFRTKRY  925
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +     + F  V +   +    
Sbjct  754   CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQIGHSLRKSFRCVPEKTVQVLPR  933

Query  926   FAKHPRM-----------------GYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYA  968
             F   P                   G+     ++ G + + P    Q    D  S ++  A
Sbjct  934   FPDQPEKTLNLSHIVPPSPLPSHNGFSDPSGLVHGHHGQHPGLPGQHGLFDRSSTLDSRA  1113

Query  969   S-RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI---LIS  1024
             + R  +  +         ++   + D+EH LI  Y   L Q++     R+P+ +      
Sbjct  1114  TGRSLDSASGTAGTTMSRVAAASANDEEHRLIARYAARLAQEN-----RAPSNLPDNATP  1278

Query  1025  LESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAE  1084
             + ++       ++A LE +N+ +  E  RL++Q E               T   +P +  
Sbjct  1279  IGTDNSRAQRELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENPA  1413

Query  1085  LIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTS  1144
             LI E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP   
Sbjct  1414  LINELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP---  1581

Query  1145  LQRSDSSQPM  1154
               RS  S PM
Sbjct  1582  --RSGKSPPM  1605


>ref|XM_002004299.1| Drosophila mojavensis GI19671 (Dmoj\GI19671), mRNA
Length=2367

 Score =  177 bits (450),  Expect = 2e-41, Method: Compositional matrix adjust.
 Identities = 143/545 (26%), Positives = 245/545 (44%), Gaps = 56/545 (10%)
 Frame = +1

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK----QNDQPMDILQI  690
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L     Q+D  + + ++
Sbjct  43    LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSD--VSVARL  216

Query  691   INCLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCK  748
                ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C 
Sbjct  217   ETLVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYSSDNSGKIRVFSIKVALATMCS  396

Query  749   AHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
               L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +     
Sbjct  397   GKLVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKDGLEEEIF  567

Query  809   FANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
              A NK  +   +        P  +VWLP+LHR+A  ET  H   C++C +    GFRYR 
Sbjct  568   PAENKVTVNDFMATLMSEPGPSCLVWLPLLHRLATVETIVHPTICSVCHKENFTGFRYRC  747

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR-----TK  923
              +   Y +CQ CF+ G+ +  H+  + + EY +  +  + +      L+  FR     T 
Sbjct  748   QRCHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQI---GHSLRKSFRCVPEKTT  918

Query  924   RYFAKHPRMG--------YLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEME  975
             +   + P            +P   +   +    PA                   R + ++
Sbjct  919   QVLPRFPDQPEKTLNLSHIVPPSPLPSHNGFSDPALGHLHGPGPGPGHHPGIFDRSSTLD  1098

Query  976   N-SNGSYLNDSIS---PNESIDDEHLLIQHYCQSLNQD--SPLSQPRSPAQILISLESEE  1029
             + + G  L+ ++S      + D+EH LI  Y   L Q+  +P + P   A+ +  + ++ 
Sbjct  1099  SRATGRSLDTTMSRVAAASANDEEHRLIARYAARLAQENRAPSNMPN--AESITPIGTDN  1272

Query  1030  RGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEA  1089
                   ++A LE +N+ +  E  RL++Q E               T   +P +  LI E 
Sbjct  1273  SRAQRELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENPALINEL  1407

Query  1090  KLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSD  1149
             + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP     RS 
Sbjct  1408  RALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP-----RSG  1569

Query  1150  SSQPM  1154
              S PM
Sbjct  1570  KSPPM  1584


>ref|NM_001032237.1| Drosophila melanogaster Dystrobrevin-like (Dyb), transcript variant 
D, mRNA
Length=3387

 Score =  177 bits (450),  Expect = 3e-41, Method: Compositional matrix adjust.
 Identities = 141/549 (25%), Positives = 241/549 (43%), Gaps = 57/549 (10%)
 Frame = +3

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  606   LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  785

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  786   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  965

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +      A
Sbjct  966   LVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPA  1136

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP++HR+A  ET  H   C++C +    GFRYR  +
Sbjct  1137  ENKVTVNDFMATLMSEPGPSCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQR  1316

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDV-----RDFAKVLKNKFRTKRY  925
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +     + F  V +   +    
Sbjct  1317  CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQIGHSLRKSFRCVPEKTVQVLPR  1496

Query  926   FAKHPRM-----------------GYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYA  968
             F   P                   G+     ++ G +   P    Q    D  S ++  A
Sbjct  1497  FPDQPEKTLNLSHIVPPSPLPSHNGFSDPSGLVHGHHGPHPGLPGQHGLFDRSSTLDSRA  1676

Query  969   S-RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQD--SPLSQPRSPAQILISL  1025
             + R  +  +         ++   + D+EH LI  Y   L Q+  +P + P +   I    
Sbjct  1677  TGRSLDSASGTAGTTMSRVAAASANDEEHRLIARYAARLAQENRAPSNLPDNATPIGTDN  1856

Query  1026  ESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAEL  1085
                +R     ++A LE +N+ +  E  RL++Q E               T   +P +  L
Sbjct  1857  SRAQR----ELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENPAL  1979

Query  1086  IAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSL  1145
             I E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP    
Sbjct  1980  INELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP----  2144

Query  1146  QRSDSSQPM  1154
              RS  S PM
Sbjct  2145  -RSGKSPPM  2168


>ref|NM_165905.2| Drosophila melanogaster Dystrobrevin-like (Dyb), transcript variant 
C, mRNA
Length=2851

 Score =  177 bits (450),  Expect = 3e-41, Method: Compositional matrix adjust.
 Identities = 141/549 (25%), Positives = 241/549 (43%), Gaps = 57/549 (10%)
 Frame = +2

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  125   LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  304

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  305   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  484

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +      A
Sbjct  485   LVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPA  655

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP++HR+A  ET  H   C++C +    GFRYR  +
Sbjct  656   ENKVTVNDFMATLMSEPGPSCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQR  835

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDV-----RDFAKVLKNKFRTKRY  925
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +     + F  V +   +    
Sbjct  836   CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQIGHSLRKSFRCVPEKTVQVLPR  1015

Query  926   FAKHPRM-----------------GYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYA  968
             F   P                   G+     ++ G +   P    Q    D  S ++  A
Sbjct  1016  FPDQPEKTLNLSHIVPPSPLPSHNGFSDPSGLVHGHHGPHPGLPGQHGLFDRSSTLDSRA  1195

Query  969   S-RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQD--SPLSQPRSPAQILISL  1025
             + R  +  +         ++   + D+EH LI  Y   L Q+  +P + P +   I    
Sbjct  1196  TGRSLDSASGTAGTTMSRVAAASANDEEHRLIARYAARLAQENRAPSNLPDNATPIGTDN  1375

Query  1026  ESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAEL  1085
                +R     ++A LE +N+ +  E  RL++Q E               T   +P +  L
Sbjct  1376  SRAQR----ELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENPAL  1498

Query  1086  IAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSL  1145
             I E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP    
Sbjct  1499  INELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP----  1663

Query  1146  QRSDSSQPM  1154
              RS  S PM
Sbjct  1664  -RSGKSPPM  1687


>ref|XM_002081157.1| Drosophila simulans GD10888 (Dsim\GD10888), mRNA
Length=2226

 Score =  177 bits (449),  Expect = 3e-41, Method: Compositional matrix adjust.
 Identities = 139/550 (25%), Positives = 242/550 (44%), Gaps = 59/550 (10%)
 Frame = +1

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  70    LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  249

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  250   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  429

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +      A
Sbjct  430   LVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPA  600

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP++HR+A  ET  H   C++C +    GFRYR  +
Sbjct  601   ENKVTVNDFMATLMSEPGPSCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQR  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDV-----RDFAKVLKNKFRTKRY  925
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +     + F  V +   +    
Sbjct  781   CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQIGHSLRKSFRCVPEKTVQVLPR  960

Query  926   FAKHPRM-----------------GYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYA  968
             F   P                   G+     ++ G +   P    Q    D  S ++  A
Sbjct  961   FPDQPEKTLNLSHIVPPSPLPSHNGFSDPSGLVHGHHGPHPGLPGQHGLFDRSSTLDSRA  1140

Query  969   S-RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI---LIS  1024
             + R  +  +         ++   + D+EH LI  Y   L Q++     R+P+ +      
Sbjct  1141  TGRSLDSASGTAGTTMSRVAAASANDEEHRLIARYAARLAQEN-----RAPSNLPDNATP  1305

Query  1025  LESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAE  1084
             + ++       ++A LE +N+ +  E  RL++Q E               T   +P +  
Sbjct  1306  IGTDNSRAQRELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENPA  1440

Query  1085  LIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTS  1144
             LI E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP   
Sbjct  1441  LINELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP---  1608

Query  1145  LQRSDSSQPM  1154
               RS  S PM
Sbjct  1609  --RSGKSPPM  1632


>ref|NM_165904.1| Drosophila melanogaster Dystrobrevin-like (Dyb), transcript variant 
A, mRNA
Length=3332

 Score =  177 bits (448),  Expect = 4e-41, Method: Compositional matrix adjust.
 Identities = 139/550 (25%), Positives = 242/550 (44%), Gaps = 59/550 (10%)
 Frame = +3

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  606   LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  785

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  786   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  965

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +      A
Sbjct  966   LVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPA  1136

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP++HR+A  ET  H   C++C +    GFRYR  +
Sbjct  1137  ENKVTVNDFMATLMSEPGPSCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQR  1316

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDV-----RDFAKVLKNKFRTKRY  925
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +     + F  V +   +    
Sbjct  1317  CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQIGHSLRKSFRCVPEKTVQVLPR  1496

Query  926   FAKHPRM-----------------GYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYA  968
             F   P                   G+     ++ G +   P    Q    D  S ++  A
Sbjct  1497  FPDQPEKTLNLSHIVPPSPLPSHNGFSDPSGLVHGHHGPHPGLPGQHGLFDRSSTLDSRA  1676

Query  969   S-RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI---LIS  1024
             + R  +  +         ++   + D+EH LI  Y   L Q++     R+P+ +      
Sbjct  1677  TGRSLDSASGTAGTTMSRVAAASANDEEHRLIARYAARLAQEN-----RAPSNLPDNATP  1841

Query  1025  LESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAE  1084
             + ++       ++A LE +N+ +  E  RL++Q E               T   +P +  
Sbjct  1842  IGTDNSRAQRELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENPA  1976

Query  1085  LIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTS  1144
             LI E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP   
Sbjct  1977  LINELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP---  2144

Query  1145  LQRSDSSQPM  1154
               RS  S PM
Sbjct  2145  --RSGKSPPM  2168


>ref|NM_001032236.1| Drosophila melanogaster Dystrobrevin-like (Dyb), transcript variant 
E, mRNA
Length=3511

 Score =  177 bits (448),  Expect = 4e-41, Method: Compositional matrix adjust.
 Identities = 139/550 (25%), Positives = 242/550 (44%), Gaps = 59/550 (10%)
 Frame = +3

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  606   LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  785

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  786   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  965

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +      A
Sbjct  966   LVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPA  1136

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP++HR+A  ET  H   C++C +    GFRYR  +
Sbjct  1137  ENKVTVNDFMATLMSEPGPSCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQR  1316

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDV-----RDFAKVLKNKFRTKRY  925
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +     + F  V +   +    
Sbjct  1317  CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQIGHSLRKSFRCVPEKTVQVLPR  1496

Query  926   FAKHPRM-----------------GYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYA  968
             F   P                   G+     ++ G +   P    Q    D  S ++  A
Sbjct  1497  FPDQPEKTLNLSHIVPPSPLPSHNGFSDPSGLVHGHHGPHPGLPGQHGLFDRSSTLDSRA  1676

Query  969   S-RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI---LIS  1024
             + R  +  +         ++   + D+EH LI  Y   L Q++     R+P+ +      
Sbjct  1677  TGRSLDSASGTAGTTMSRVAAASANDEEHRLIARYAARLAQEN-----RAPSNLPDNATP  1841

Query  1025  LESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAE  1084
             + ++       ++A LE +N+ +  E  RL++Q E               T   +P +  
Sbjct  1842  IGTDNSRAQRELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENPA  1976

Query  1085  LIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTS  1144
             LI E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP   
Sbjct  1977  LINELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP---  2144

Query  1145  LQRSDSSQPM  1154
               RS  S PM
Sbjct  2145  --RSGKSPPM  2168


>ref|XM_002091011.1| Drosophila yakuba GE12465 (Dyak\GE12465), mRNA
Length=2208

 Score =  177 bits (448),  Expect = 4e-41, Method: Compositional matrix adjust.
 Identities = 139/550 (25%), Positives = 242/550 (44%), Gaps = 59/550 (10%)
 Frame = +1

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  43    LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  222

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  223   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  402

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +      A
Sbjct  403   LVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPA  573

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP++HR+A  ET  H   C++C +    GFRYR  +
Sbjct  574   ENKVTVNDFMATLMSEPGPSCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQR  753

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDV-----RDFAKVLKNKFRTKRY  925
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +     + F  V +   +    
Sbjct  754   CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQIGHSLRKSFRCVPEKTVQVLPR  933

Query  926   FAKHPRM-----------------GYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYA  968
             F   P                   G+     ++ G +   P    Q    D  S ++  A
Sbjct  934   FPDQPEKTLNLSHIVPPSPLPSHNGFSDPSGLVHGHHGPHPGLPGQHGLFDRSSTLDSRA  1113

Query  969   S-RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI---LIS  1024
             + R  +  +         ++   + D+EH LI  Y   L Q++     R+P+ +      
Sbjct  1114  TGRSLDSASGTAGTTMSRVAAASANDEEHRLIARYAARLAQEN-----RAPSNLPDNATP  1278

Query  1025  LESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAE  1084
             + ++       ++A LE +N+ +  E  RL++Q E               T   +P +  
Sbjct  1279  IGTDNSRAQRELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENPA  1413

Query  1085  LIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTS  1144
             LI E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP   
Sbjct  1414  LINELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP---  1581

Query  1145  LQRSDSSQPM  1154
               RS  S PM
Sbjct  1582  --RSGKSPPM  1605


>gb|AF277387.2|AF277387 Drosophila melanogaster dystrobrevin-like protein DYB (Dyb) mRNA, 
complete cds
Length=2818

 Score =  177 bits (448),  Expect = 4e-41, Method: Compositional matrix adjust.
 Identities = 140/551 (25%), Positives = 245/551 (44%), Gaps = 61/551 (11%)
 Frame = +2

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  92    LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  271

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  272   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  451

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +      A
Sbjct  452   LVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPA  622

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP++HR+A  ET  H   C++C +    GFRYR  +
Sbjct  623   ENKVTVNDFMATLMSEPGPSCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQR  802

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDV-----RDFAKVLKNKFRTKRY  925
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +     + F  V +   +    
Sbjct  803   CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQIGHSLRKSFRCVPEKTVQVLPR  982

Query  926   FAKHPRM-----------------GYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYA  968
             F   P                   G+     ++ G +   P    Q    D  S ++  A
Sbjct  983   FPDQPEKTLNLSHIVPPSPLPSHNGFSDPSGLVHGHHGPHPGLPGQHGLFDRSSTLDSRA  1162

Query  969   S--RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI---LI  1023
             +   L     + G+ ++  ++   + D+EH LI  Y   L Q++     R+P+ +     
Sbjct  1163  TGRSLDSARGTAGTTMS-RVAAASANDEEHRLIARYAARLAQEN-----RAPSNLPDNAT  1324

Query  1024  SLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDA  1083
              + ++       ++A LE +N+ +  E  RL++Q E               T   +P + 
Sbjct  1325  PIGTDNSRAQRELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENP  1459

Query  1084  ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPST  1143
              LI E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP  
Sbjct  1460  ALINELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP--  1630

Query  1144  SLQRSDSSQPM  1154
                RS  S PM
Sbjct  1631  ---RSGKSPPM  1654


>ref|XM_001604052.1| PREDICTED: Nasonia vitripennis similar to dystrobrevin-like protein 
DYB (LOC100120463), mRNA
Length=3042

 Score =  177 bits (448),  Expect = 5e-41, Method: Compositional matrix adjust.
 Identities = 148/546 (27%), Positives = 249/546 (45%), Gaps = 67/546 (12%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIINCL  694
             + + +RF++YRTA KLR +QK + L  + +    +A  +++L   +    + + ++   L
Sbjct  883   NFDIIRFASYRTACKLRFIQKKVNLHNVDIWNVIEAFRENSLNTLEPSSTLSVSRLETLL  1062

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             ++++  L +    +    V     + +NWLL  Y +G   +I V S K  + +LC   L 
Sbjct  1063  SSLFHALNKRVPISQQAKVDATTALLMNWLLASYTSGENSKISVFSVKVALATLCAGKLM  1242

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK+RY+F Q+    G     R    L + + +P  + E  SFG S+    + S    +N 
Sbjct  1243  DKFRYIFSQITDGNGHMIHWRFADYLKEVLALPAAVYESPSFGYSD---GLASSIFPSNA  1413

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             K  I    FLD +  EP    ++WLP+ HR+AA E+  H   C+ C      GFRYR  K
Sbjct  1414  K--ITVNDFLDTLMSEPGPHCLIWLPLYHRMAAVESVTHPIMCDACHRENFTGFRYRCQK  1587

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYC---TPTTS-GEDVRDFAKVLKNKFRTK-RY  925
               +Y +CQ CF+ G+V+  H   +   EY    +P+   G  +R   + + +K R     
Sbjct  1588  CHSYQLCQDCFWRGKVSGTHNNDHETREYSSFKSPSKQIGHSLRKSFRCVPDKGRNSLPR  1767

Query  926   FAKHPRMG-----YLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGS  980
             F + P         +P   +   +    P            SR     S L  M+++   
Sbjct  1768  FPEQPEKTLDLSHIVPPSPIPSHNGFPDPGFMGPFDSGSLDSR-----STLRSMDSAR--  1926

Query  981   YLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADL  1040
                        +DDEH LI  Y Q L+Q++  +Q R+P+ + ++     R + E +++ L
Sbjct  1927  -----------VDDEHKLIAIYAQRLSQEA-RTQSRAPSDVNLAAIDPSRAQRE-LISQL  2067

Query  1041  EEENRNLQAEYDRLKQQH--EHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGR  1098
             E +N+ +  E  RL++Q   E  GL                  +  L++E + LRQ K  
Sbjct  2068  EAKNKEIMREITRLRRQQEIEAAGL-----------------ENPALMSELRALRQRKDE  2196

Query  1099  LEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRV  1158
             LE+ +  L+D  +QL  QL  L ++L+  QA  +      S+P++S  RS  S P+    
Sbjct  2197  LESHLATLQDSRRQLMVQLEGLMKMLKIHQASPR------STPNSS-PRSTKSPPLPPGA  2355

Query  1159  VGSQTS  1164
             V S  S
Sbjct  2356  VPSSRS  2373


>ref|NM_078988.2| Drosophila melanogaster Dystrobrevin-like (Dyb), transcript variant 
B, mRNA
Length=2818

 Score =  177 bits (448),  Expect = 5e-41, Method: Compositional matrix adjust.
 Identities = 139/550 (25%), Positives = 242/550 (44%), Gaps = 59/550 (10%)
 Frame = +2

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  92    LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  271

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  272   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  451

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +      A
Sbjct  452   LVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPA  622

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP++HR+A  ET  H   C++C +    GFRYR  +
Sbjct  623   ENKVTVNDFMATLMSEPGPSCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQR  802

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDV-----RDFAKVLKNKFRTKRY  925
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +     + F  V +   +    
Sbjct  803   CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQIGHSLRKSFRCVPEKTVQVLPR  982

Query  926   FAKHPRM-----------------GYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYA  968
             F   P                   G+     ++ G +   P    Q    D  S ++  A
Sbjct  983   FPDQPEKTLNLSHIVPPSPLPSHNGFSDPSGLVHGHHGPHPGLPGQHGLFDRSSTLDSRA  1162

Query  969   S-RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI---LIS  1024
             + R  +  +         ++   + D+EH LI  Y   L Q++     R+P+ +      
Sbjct  1163  TGRSLDSASGTAGTTMSRVAAASANDEEHRLIARYAARLAQEN-----RAPSNLPDNATP  1327

Query  1025  LESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAE  1084
             + ++       ++A LE +N+ +  E  RL++Q E               T   +P +  
Sbjct  1328  IGTDNSRAQRELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENPA  1462

Query  1085  LIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTS  1144
             LI E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP   
Sbjct  1463  LINELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP---  1630

Query  1145  LQRSDSSQPM  1154
               RS  S PM
Sbjct  1631  --RSGKSPPM  1654


>ref|XM_001958633.1| Drosophila ananassae GF12513 (Dana\GF12513), mRNA
Length=2145

 Score =  176 bits (447),  Expect = 5e-41, Method: Compositional matrix adjust.
 Identities = 139/534 (26%), Positives = 246/534 (46%), Gaps = 55/534 (10%)
 Frame = +1

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  43    LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  222

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  223   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  402

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +      A
Sbjct  403   LVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPA  573

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP++HR+A  ET  H   C++C +    GFRYR  +
Sbjct  574   ENKVTVNDFMATLMSEPGPSCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQR  753

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR-----TKRY  925
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +      L+  FR     T + 
Sbjct  754   CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQI---GHSLRKSFRCVPEKTTQV  924

Query  926   FAKHP-------RMGYLPVQTVLEGDNMETPASSPQL-----SHD----DTHSRIEHYAS  969
               + P        + ++   + L   N  +  S P L      H     D  S ++  A+
Sbjct  925   LPRFPDQPEKTLNLSHIVPPSPLPSHNGFSDPSGPGLVPGHHGHPPGLFDRSSTLDSRAT  1104

Query  970   RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQD--SPLSQPRSPAQILISLES  1027
               + ++++ G+ ++  ++   + D+EH LI  Y   L Q+  +P + P +   I      
Sbjct  1105  GRS-LDSATGTTMS-RVAAASANDEEHRLIARYAARLAQENRAPSNLPDNATPIGTDNSR  1278

Query  1028  EERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIA  1087
              +R     ++A LE +N+ +  E  RL++Q E               T   +P +  LI 
Sbjct  1279  AQR----ELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENPALIN  1401

Query  1088  EAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP  1141
             E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP
Sbjct  1402  ELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP  1560


>ref|XM_002059767.1| Drosophila virilis GJ15037 (Dvir\GJ15037), mRNA
Length=2379

 Score =  176 bits (447),  Expect = 6e-41, Method: Compositional matrix adjust.
 Identities = 151/565 (26%), Positives = 255/565 (45%), Gaps = 67/565 (11%)
 Frame = +1

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK----QNDQPMDILQI  690
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L     Q+D  + + ++
Sbjct  46    LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSD--VSVARL  219

Query  691   INCLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCK  748
                ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C 
Sbjct  220   ETLVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCS  399

Query  749   AHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
               L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +     
Sbjct  400   GKLVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKDGLEEEIF  570

Query  809   FANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
              A NK  +   +        P  +VWLP+LHR+A  ET  H   C++C +    GFRYR 
Sbjct  571   PAENKVTVNDFMATLMSEPGPSCLVWLPLLHRLATVETIVHPTICSVCHKENFTGFRYRC  750

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRT--KRYF  926
              +   Y +CQ CF+ G+ +  H+  + + EY +  +  + +      L+  FR   ++  
Sbjct  751   QRCHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQI---GHSLRKSFRCVPEKTT  921

Query  927   AKHPRMGYLPVQTVLEGDNMETPA--------SSPQLSH---------DDTHSRIEHYAS  969
                PR    P +T L   ++  P+        S P L H                     
Sbjct  922   QVLPRFPDQPEKT-LNLSHIVPPSPLPSHNGFSDPTLGHLHGPGPGSGSGPGPGHPGIFD  1098

Query  970   RLAEMEN-SNGSYLNDSIS---PNESIDDEHLLIQHYCQSLNQD--SPLSQPRSPAQILI  1023
             R + +++ + G  L+ ++S      + D+EH LI  Y   L Q+  +P + P   A+ + 
Sbjct  1099  RSSTLDSRATGRSLDTTMSRVAAASANDEEHRLIARYAARLAQENRAPSNMPN--AESIT  1272

Query  1024  SLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDA  1083
              + ++       ++A LE +N+ +  E  RL++Q E               T   +P + 
Sbjct  1273  PIGTDNSRAQRELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENP  1407

Query  1084  ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPST  1143
              LI E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP  
Sbjct  1408  ALINELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP--  1578

Query  1144  SLQRSDSSQPMLLRVVGSQTSDSMG  1168
                RS  S PM     G   + S G
Sbjct  1579  ---RSGKSPPM----PGGTATTSAG  1632


>ref|NM_001103817.1| Drosophila melanogaster Dystrobrevin-like (Dyb), transcript variant 
F, mRNA
Length=3014

 Score =  175 bits (444),  Expect = 1e-40, Method: Compositional matrix adjust.
 Identities = 142/550 (25%), Positives = 244/550 (44%), Gaps = 59/550 (10%)
 Frame = +3

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  606   LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  785

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  786   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  965

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +      A
Sbjct  966   LVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPA  1136

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP++HR+A  ET  H   C++C +    GFRYR  +
Sbjct  1137  ENKVTVNDFMATLMSEPGPSCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQR  1316

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDV-----RDFAKVLKNKFRTKRY  925
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +     + F  V +   +    
Sbjct  1317  CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQIGHSLRKSFRCVPEKTVQVLPR  1496

Query  926   FAKHPRM-----------------GYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYA  968
             F   P                   G+     ++ G +   P    Q    D  S ++  A
Sbjct  1497  FPDQPEKTLNLSHIVPPSPLPSHNGFSDPSGLVHGHHGPHPGLPGQHGLFDRSSTLDSRA  1676

Query  969   S--RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQD--SPLSQPRSPAQILIS  1024
             +   L     + G+ ++  ++   + D+EH LI  Y   L Q+  +P + P +   I   
Sbjct  1677  TGRSLDSASGTAGTTMS-RVAAASANDEEHRLIARYAARLAQENRAPSNLPDNATPIGTD  1853

Query  1025  LESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAE  1084
                 +R     ++A LE +N+ +  E  RL++Q E               T   +P +  
Sbjct  1854  NSRAQR----ELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENPA  1976

Query  1085  LIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTS  1144
             LI E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP   
Sbjct  1977  LINELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP---  2144

Query  1145  LQRSDSSQPM  1154
               RS  S PM
Sbjct  2145  --RSGKSPPM  2168


>gb|DQ516345.1| Danio rerio beta-dystrobrevin (BDTN) mRNA, complete cds
Length=2204

 Score =  175 bits (444),  Expect = 1e-40, Method: Compositional matrix adjust.
 Identities = 154/593 (25%), Positives = 271/593 (45%), Gaps = 86/593 (14%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D    +++ ++   L
Sbjct  76    NFDVIRLSTYRTACKLRFVQKRCNLHLVDVWNMIEAFRDNGLSTLDHNAEINVSRLETIL  255

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++I+     RL   H   +NV   + + LN+++  YD+   G++ V + K  + ++C   
Sbjct  256   SSIFYQLNKRLPTTHQ--INVEQSIGLLLNFIVATYDSEGHGKLTVFAMKAMLATMCGGK  429

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  430   ILDKLRYVFSQISDSNGVMVFAKFDQFLREVLKLPTAVFEGPSFGYT--EHSVRTCFP--  597

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I    FLD +  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  598   -QQKKILLNTFLDVLMADPPPQCLVWLPLMHRLANVENVFHPVECSYCRSESMMGFRYRC  774

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK  928
              +   Y +CQSCF+ G  +  H   + M E+          +  AK L +        A 
Sbjct  775   QQCHGYQLCQSCFWRGHASGPHSNQHQMKEH-------SSWKSPAKKLSH--------AI  909

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISP  988
                +G +P+         E P           H      A R  ++ ++       ++  
Sbjct  910   SKSLGCMPIG--------EPP-----------HPVFPEAAERPQDLAHTT------TLES  1014

Query  989   NESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQ  1048
                +D+EH LI  Y   L  ++  S    P+ +  + ++ +  +  +++A+LE +NR + 
Sbjct  1015  PSRLDEEHRLIARYAARLAAEASNSTQCPPSDLSFNFDANK--QQRQLIAELENKNREIL  1188

Query  1049  AEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILED  1108
              E  RL+ +HE     P P   +  PT         L+AE +LLR  K  LE RM  L++
Sbjct  1189  QEIQRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRHRKDELERRMSALQE  1338

Query  1109  HNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMG  1168
               ++L  QL  L +LL+          T  S  S+    +  + PM +R   + ++ +  
Sbjct  1339  SRRELMVQLEGLMRLLKA--------QTGTSPHSSPSHSASCTMPMPIRSTSAGSTPT--  1488

Query  1169  EEDLLSPPQDTSTGL-EEVMEQLNNSFPSSRGHNVGSLFHMADDLGRAMESLV  1220
                    PQD   G+ ++V++  +   P +  ++   L   AD +   M SLV
Sbjct  1489  -----HTPQDCLAGVGDDVLDAFSQGVPRNLRND---LLVAADSITNTMSSLV  1623


>ref|XM_002033526.1| Drosophila sechellia GM21392 (Dsec\GM21392), mRNA
Length=2511

 Score =  175 bits (444),  Expect = 1e-40, Method: Compositional matrix adjust.
 Identities = 141/550 (25%), Positives = 243/550 (44%), Gaps = 59/550 (10%)
 Frame = +1

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  70    LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  249

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  250   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  429

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +       
Sbjct  430   LVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPT  600

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP++HR+A  ET  H   C++C +    GFRYR  +
Sbjct  601   ENKVTVNDFMATLMSEPGPSCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQR  780

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDV-----RDFAKVLKNKFRTKRY  925
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +     + F  V +   +    
Sbjct  781   CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQIGHSLRKSFRCVPEKTVQVLPR  960

Query  926   FAKHPRM-----------------GYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYA  968
             F   P                   G+     ++ G +   P    Q    D  S ++  A
Sbjct  961   FPDQPEKTLNLSHIVPPSPLPSHNGFSDPSGLVHGHHGPHPGLPGQHGLFDRSSTLDSRA  1140

Query  969   S--RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQD--SPLSQPRSPAQILIS  1024
             +   L     + G+ ++  ++   + D+EH LI  Y   L Q+  +P + P +   I   
Sbjct  1141  TGRSLDSASGTAGTTMS-RVAAASANDEEHRLIARYAARLAQENRAPSNLPDNATPIGTD  1317

Query  1025  LESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAE  1084
                 +R     ++A LE +N+ +  E  RL++Q E               T   +P +  
Sbjct  1318  NSRAQR----ELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENPA  1440

Query  1085  LIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTS  1144
             LI E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP   
Sbjct  1441  LINELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP---  1608

Query  1145  LQRSDSSQPM  1154
               RS  S PM
Sbjct  1609  --RSGKSPPM  1632


>ref|XM_395141.3| PREDICTED: Apis mellifera similar to Dystrobrevin-like CG8529-PA, 
isoform A, transcript variant 1 (LOC411673), partial mRNA
Length=3816

 Score =  175 bits (444),  Expect = 1e-40, Method: Compositional matrix adjust.
 Identities = 150/536 (27%), Positives = 251/536 (46%), Gaps = 47/536 (8%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIINCL  694
             + + +RF++YRTA KLR +QK + L  + +    +A  ++ L   +    + + ++   L
Sbjct  112   NFDTIRFASYRTACKLRFIQKKVHLHNVDIWNVIEAFRENGLNTLEPSSTLGVSRLETLL  291

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             ++++  L +    +    V     + +NWL+  Y TG   +I V S K  + +LC   L 
Sbjct  292   SSLFHALNKRVPVSQQAKVDATTALLMNWLIAAYTTGENNKISVFSVKVALATLCAGKLM  471

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK+RY++ Q++ S G     R    L + + +   + E  SFG S  E    S F   N+
Sbjct  472   DKFRYIYSQISDSNGHMIHWRFSEYLKEVLSLTAAVYESPSFGYS--EGLANSIFP-QNS  642

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             K  +    FLD +  +P    ++WLP+ HR+AA ET  H   C+ C +    GFRYR  K
Sbjct  643   KVTVND--FLDTLMSDPGPHCLIWLPLYHRMAAVETVAHPVMCDACHKENFTGFRYRCQK  816

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKH-  929
               +Y +CQ CF+ G+V+  H   +   EY +  +  + +      L+  FR      K+ 
Sbjct  817   CHSYQLCQDCFWRGKVSGTHNNDHETREYSSFKSPSKQI---GHSLRKSFRCVPEKGKNS  987

Query  930   -PRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISP  988
              PR    P +T L+  ++  P  SP  SH+               M++ +     DS   
Sbjct  988   LPRFPEQPEKT-LDLSHIVPP--SPLPSHNGFPDPGFMAPFDSGSMDSRSTLRSMDS---  1149

Query  989   NESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQ  1048
                +DDEH LI  Y Q L Q++  +  R+P+   ++     R + E +++ LE +N+ + 
Sbjct  1150  -SRLDDEHKLIARYAQRLAQEA-RTMGRTPSDANLASLDASRAQRE-LISQLEAKNKEIM  1320

Query  1049  AEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILED  1108
              E  RL++Q E +    L +P               L++E + LRQ K  LE  +  L+D
Sbjct  1321  REIARLRRQQEIEAAG-LENP--------------ALMSELRALRQRKDELETHLATLQD  1455

Query  1109  HNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTS  1164
               +QL  QL  L ++L+  QA  +      S+P++S  RS  S P+    V S  S
Sbjct  1456  SRRQLMVQLEGLMKMLKNHQASPR------STPNSS-PRSTKSPPLPPGAVPSSRS  1602


>ref|XM_001191124.1| PREDICTED: Strongylocentrotus purpuratus similar to dystrobrevin 
alpha isoform 2 variant (LOC592642), mRNA
Length=2184

 Score =  175 bits (444),  Expect = 1e-40, Method: Compositional matrix adjust.
 Identities = 151/526 (28%), Positives = 237/526 (45%), Gaps = 74/526 (14%)
 Frame = +1

Query  694   LTTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKA  749
             L++IY     RL   H   +NV   + +  N+L   YD G TG++ V + K  + +LC  
Sbjct  226   LSSIYYQLNKRLPAVHQ--INVDQFLSLLCNFLQTAYDDGATGKMTVFALKVALSTLCAG  399

Query  750   HLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF  809
              L DK RY+F Q++   G     +    L   +Q+P  + E  SFG    E + ++CF  
Sbjct  400   KLSDKLRYIFSQISDGNGILIHSKFDEYLKLVLQLPTAVFEGPSFGYD--ENTAKACFG-  570

Query  810   ANNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYR  867
             AN +  +    FLD +  EP  Q ++WL ++HR++  E   H  +C+ C    ++GFRY+
Sbjct  571   ANRRVTLND--FLDTVLAEPGPQCLMWLSLMHRMSNVENVFHPVECSHCHSDSMMGFRYK  744

Query  868   SLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA  927
               +  NY +CQ+CF+ G  +  H   + M EY   ++     +   K LK  F++     
Sbjct  745   CQRCSNYQLCQNCFWRGYTSGNHSTDHEMKEY---SSYKSPAKKMGKALKKPFKSP---L  906

Query  928   KHPRMGYLP--VQTVLEGDNMETPASSPQLSHDDTHS-RIEHYASRLAEMENSNGSYLND  984
             K PR+ + P   +  L+  ++  P+    L++D   S RI        +M NS  S    
Sbjct  907   KQPRVQHYPEEPERPLDLSHIVPPSPITILTYDSPDSTRILRTEEDFKKMNNSLDS----  1074

Query  985   SISPNESIDDEHLLIQHYCQSLNQDS--PLSQPRSPAQILISLESEERGELERILADLEE  1042
                    +DDEH LI  Y   L   S  P S P  P  +  + E  E      ++  LE 
Sbjct  1075  -----ARLDDEHRLIARYAARLANASANPNSGPELPPGLDANREQRE------LIMQLES  1221

Query  1043  ENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEAR  1102
             +NR +  E  RL+Q+H+                S  S R+  L+AE +LLRQ K  LE R
Sbjct  1222  KNREIMREIQRLRQEHDEA------------VRSSHSQRNPTLLAELRLLRQRKDELELR  1365

Query  1103  MQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTS------LQRSDSSQPMLL  1156
             M  L++  ++L  QL  L +LL       K +G+  +SP+ S      L    S+QP   
Sbjct  1366  MAALQESRRELMVQLEGLMKLL-------KNHGSPRNSPNHSPRPNQPLTPGSSTQPSRA  1524

Query  1157  RVV------GSQTSDSMGE----EDLLSPPQDTSTGLEEVMEQLNN  1192
                      G QT  + G      DLL      +  +  ++ +LN+
Sbjct  1525  ATTTDTVRNGEQTGGTTGSRSLRNDLLVAADSVTNAMSSLVRELNS  1662


>ref|XM_792154.2| PREDICTED: Strongylocentrotus purpuratus similar to dystrobrevin 
alpha isoform 2 variant (LOC592642), mRNA
Length=2184

 Score =  175 bits (444),  Expect = 1e-40, Method: Compositional matrix adjust.
 Identities = 151/526 (28%), Positives = 237/526 (45%), Gaps = 74/526 (14%)
 Frame = +1

Query  694   LTTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKA  749
             L++IY     RL   H   +NV   + +  N+L   YD G TG++ V + K  + +LC  
Sbjct  226   LSSIYYQLNKRLPAVHQ--INVDQFLSLLCNFLQTAYDDGATGKMTVFALKVALSTLCAG  399

Query  750   HLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF  809
              L DK RY+F Q++   G     +    L   +Q+P  + E  SFG    E + ++CF  
Sbjct  400   KLSDKLRYIFSQISDGNGILIHSKFDEYLKLVLQLPTAVFEGPSFGYD--ENTAKACFG-  570

Query  810   ANNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYR  867
             AN +  +    FLD +  EP  Q ++WL ++HR++  E   H  +C+ C    ++GFRY+
Sbjct  571   ANRRVTLND--FLDTVLAEPGPQCLMWLSLMHRMSNVENVFHPVECSHCHSDSMMGFRYK  744

Query  868   SLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA  927
               +  NY +CQ+CF+ G  +  H   + M EY   ++     +   K LK  F++     
Sbjct  745   CQRCSNYQLCQNCFWRGYTSGNHSTDHEMKEY---SSYKSPAKKMGKALKKPFKSP---L  906

Query  928   KHPRMGYLP--VQTVLEGDNMETPASSPQLSHDDTHS-RIEHYASRLAEMENSNGSYLND  984
             K PR+ + P   +  L+  ++  P+    L++D   S RI        +M NS  S    
Sbjct  907   KQPRVQHYPEEPERPLDLSHIVPPSPITILTYDSPDSTRILRTEEDFKKMNNSLDS----  1074

Query  985   SISPNESIDDEHLLIQHYCQSLNQDS--PLSQPRSPAQILISLESEERGELERILADLEE  1042
                    +DDEH LI  Y   L   S  P S P  P  +  + E  E      ++  LE 
Sbjct  1075  -----ARLDDEHRLIARYAARLANASANPNSGPELPPGLDANREQRE------LIMQLES  1221

Query  1043  ENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEAR  1102
             +NR +  E  RL+Q+H+                S  S R+  L+AE +LLRQ K  LE R
Sbjct  1222  KNREIMREIQRLRQEHDEA------------VRSSHSQRNPTLLAELRLLRQRKDELELR  1365

Query  1103  MQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTS------LQRSDSSQPMLL  1156
             M  L++  ++L  QL  L +LL       K +G+  +SP+ S      L    S+QP   
Sbjct  1366  MAALQESRRELMVQLEGLMKLL-------KNHGSPRNSPNHSPRPNQPLTPGSSTQPSRA  1524

Query  1157  RVV------GSQTSDSMGE----EDLLSPPQDTSTGLEEVMEQLNN  1192
                      G QT  + G      DLL      +  +  ++ +LN+
Sbjct  1525  ATTTDTVRNGEQTGGTTGSRSLRNDLLVAADSVTNAMSSLVRELNS  1662


>ref|XM_002187356.1| PREDICTED: Taeniopygia guttata similar to dystrotelin (LOC100224327), 
mRNA
Length=1701

 Score =  174 bits (442),  Expect = 2e-40, Method: Compositional matrix adjust.
 Identities = 100/291 (34%), Positives = 153/291 (52%), Gaps = 8/291 (2%)
 Frame = +1

Query  638  LNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ-PMDILQIINCLTT  696
             ++V  S YRTA+KLR +Q+   LDL+ +S     L     ++ +Q  +++ QI   L  
Sbjct  25   FSDVESSVYRTALKLRSVQRLCQLDLIDVSLIQHILSSEQRQREEQISLNMQQISRMLMK  204

Query  697  IYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYR  756
            ++ R   E    V+ P   +  L  L+ +YD   TG ++  S    +ISL    L  KYR
Sbjct  205  LFQRARLEKPGQVD-PRAAEFTLGLLIAMYDRSGTGYVKTRSAAAALISLSGDTLLAKYR  381

Query  757  YLFKQVASSTG---FCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNK  813
              F+  A   G         L  LL D  QIP  +GE  +   S +E ++  CF    N 
Sbjct  382  AFFQFYAVHDGKETLITCSALRSLLRDLNQIPAIVGEGCTL--SCVEIAIHDCFHGVLNA  555

Query  814  PEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFN  873
              +E   FL W+R EP  ++WLP  +R++A E   HQA+C +CK  PI G RYR LK  N
Sbjct  556  AIVEEK-FLSWLRSEPALLLWLPTCYRLSAMEMVSHQARCRVCKVFPITGIRYRCLKCLN  732

Query  874  YDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKR  924
            +D+CQ+CFF+GR+ K HK  +P+VE+C   ++  + + F + ++N    +R
Sbjct  733  FDLCQACFFTGRLCKPHKRSHPVVEHCVQMSAKANAKHFLRTIRNNLFQER  885


>ref|XM_001987489.1| Drosophila grimshawi GH21967 (Dgri\GH21967), mRNA
Length=2469

 Score =  174 bits (442),  Expect = 2e-40, Method: Compositional matrix adjust.
 Identities = 143/534 (26%), Positives = 246/534 (46%), Gaps = 56/534 (10%)
 Frame = +1

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK----QNDQPMDILQI  690
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L     Q+D  + + ++
Sbjct  43    LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSD--VSVARL  216

Query  691   INCLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCK  748
                ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C 
Sbjct  217   ETLVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCS  396

Query  749   AHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
               L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +     
Sbjct  397   GKLVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIF  567

Query  809   FANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
              A NK  +   +        P  +VWLP+LHR+A  ET  H   C++C +    GFRYR 
Sbjct  568   PAENKVTVNDFMATLMSEPGPSCLVWLPLLHRLATVETIVHPTICSVCHKENFTGFRYRC  747

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRT--KRYF  926
              +   Y +CQ CF+ G+ +  H+  + + EY +  +  + +      L+  FR   ++  
Sbjct  748   QRCHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQI---GHSLRKSFRCVPEKTT  918

Query  927   AKHPRMGYLPVQTVLEGDNMETPASSPQLSHDD-------------THSRIEHYASRLAE  973
                PR    P +T L   ++  P  SP  SH+                        R + 
Sbjct  919   QVLPRFPDQPEKT-LNLSHIVPP--SPLPSHNGFSDPALAHLHGPGPGPGHSGIFDRSST  1089

Query  974   MEN-SNGSYLNDSIS---PNESIDDEHLLIQHYCQSLNQD--SPLSQPRSPAQILISLES  1027
             +++ + G  L+ ++S      + D+EH LI  Y   L Q+  +P + P   A+ +  + +
Sbjct  1090  LDSRATGRSLDTTMSRVAAASANDEEHRLIARYAARLAQENRAPSNMPN--AESITPIGT  1263

Query  1028  EERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIA  1087
             +       ++A LE +N+ +  E  RL++Q E               T   +P +  LI 
Sbjct  1264  DNSRAQRELIAQLESKNKEIMREIARLRRQQE---------------TEQMAPENPALIN  1398

Query  1088  EAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSP  1141
             E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  SSP
Sbjct  1399  ELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNSSP  1557


>ref|XM_001948373.1| PREDICTED: Acyrthosiphon pisum similar to Dystrobrevin-like CG8529-PF 
(LOC100163134), mRNA
Length=2267

 Score =  174 bits (441),  Expect = 3e-40, Method: Compositional matrix adjust.
 Identities = 143/520 (27%), Positives = 245/520 (47%), Gaps = 60/520 (11%)
 Frame = +3

Query  641   VRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIINCLTTIY  698
             +RF++YRTA KLR +QK + L ++ +    +A  ++ L   ++   +++ +    +T++Y
Sbjct  315   IRFASYRTACKLRYVQKKVYLHMIDIWNVIEAFRENGLNTLESHVEVNVSKFETLITSLY  494

Query  699   DRLE-----QEHNNLVNVPLCVDMCLNWLLNVYDTGRT-GRIRVLSFKTGIISLCKAHLE  752
               L      Q+H   V+  L   + LNW+++VY    T GRIRVLS K  ++++C   L 
Sbjct  495   LNLNKRLPTQQH---VHDDLLTTILLNWIMSVYSANDTMGRIRVLSIKVALVTMCSGKLM  665

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSN-IEPSVRSCFQFAN  811
             DK RY+F Q+    G     +    L + + +P  + E  SF  ++ I   +     F+ 
Sbjct  666   DKLRYIFSQICDQNGHMVAWKFREYLQEVLVLPSAVYESPSFHYTDQISAEI-----FSG  830

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
             N  ++    F+D M  +P    +VWLP+LHR+A  E   H   C+ C+     GFRYR  
Sbjct  831   NG-KVTVNDFMDSMMSDPGPACLVWLPLLHRLANVENVTHPISCDACRRDNFTGFRYRCQ  1007

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRT--KRYFA  927
             K  N+ +CQ CF+ GRVA  H + + + EY   T+     +     L+  FR   ++  A
Sbjct  1008  KCHNFQMCQECFWRGRVASSHTIEHDVKEY---TSYKSPSKQIGHSLRKSFRCVPEKEKA  1178

Query  928   KHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSIS  987
               PR    P +T+    N+        L   +  S +   +S+   +++   S   D  +
Sbjct  1179  NIPRFPEEPEKTI----NLSHIIPPSPLPCHNGFSELS-ISSQFNTLDSKTSSRSPDKRT  1343

Query  988   PN---ESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEEN  1044
              +    S+DDEH LI  Y   L  +         A+++  + ++       ++  LE +N
Sbjct  1344  MSLDYTSMDDEHKLIARYAARLAAE---------AKVVSCIIAQ-----RELIIQLESKN  1481

Query  1045  RNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ  1104
             R +  E  +L++Q E +G             S  S  +  L++E + LR  K  LE+ + 
Sbjct  1482  REIMKEISKLRKQQEMEGF-----------CSGYSEDNPALMSELRALRNRKHELESHLT  1628

Query  1105  ILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTS  1144
              L+D  +QL  QL  L +LL+  Q   +   T  SSP ++
Sbjct  1629  SLQDSRRQLMDQLEGLMKLLKNHQGSPR--STPNSSPRST  1742


>emb|BX323090.7| Zebrafish DNA sequence from clone CH211-274B7 in linkage group 
1, complete sequence
Length=166353

 Score =  101 bits (251),  Expect(2) = 1e-39, Method: Compositional matrix adjust.
 Identities = 45/46 (97%), Positives = 46/46 (100%), Gaps = 0/46 (0%)
 Frame = +3

Query  903     TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
               TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQT+LEGDNMET
Sbjct  117315  TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTILEGDNMET  117452


 Score = 92.4 bits (228),  Expect(2) = 1e-39, Method: Compositional matrix adjust.
 Identities = 37/41 (90%), Positives = 39/41 (95%), Gaps = 0/41 (0%)
 Frame = +1

Query  864     FRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
               +RYRSLKHFNYDICQSCFFSGRVAKGHKM YPMVEYCTP +
Sbjct  117082  YRYRSLKHFNYDICQSCFFSGRVAKGHKMQYPMVEYCTPVS  117204


 Score =  150 bits (380),  Expect = 3e-33, Method: Compositional matrix adjust.
 Identities = 74/82 (90%), Positives = 78/82 (95%), Gaps = 0/82 (0%)
 Frame = +2

Query  1045    RNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ  1104
               R LQAEYDRLK+ H+HKGLSPLPSPP+M+P SPQSPRDAELIAEAKLLRQHKGRLEARMQ
Sbjct  134822  RKLQAEYDRLKKAHDHKGLSPLPSPPQMLPVSPQSPRDAELIAEAKLLRQHKGRLEARMQ  135001

Query  1105    ILEDHNKQLESQLHRLRQLLEQ  1126
               ILEDHNKQLESQL RLRQLLEQ
Sbjct  135002  ILEDHNKQLESQLTRLRQLLEQ  135067


 Score =  135 bits (340),  Expect = 2e-28, Method: Compositional matrix adjust.
 Identities = 71/160 (44%), Positives = 97/160 (60%), Gaps = 28/160 (17%)
 Frame = +3

Query  389    RAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEK------------LYQEPR-------  429
              +AF+REL  KEPVI  TL+  + FL E P EGL++             Y   R       
Sbjct  74820  QAFRRELGAKEPVINGTLDNAKTFLAEMPREGLKQRPGQKGIAFVLPFYTYSRYNHRL*P  74999

Query  430    ---------ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
                       ++ PEER QNV R+LRK+ E+V   W+ L   S DWQ++++  LERL ELQ
Sbjct  75000  VFLPLM*CADVSPEERVQNVGRILRKEVEDVTVRWKNLGAASVDWQQQLELALERLMELQ  75179

Query  481    EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKA  520
              +A D+LD KLRQAE +K SW+PVG+LL+D LQ+H+++VK 
Sbjct  75180  DAQDQLDYKLRQAESVKNSWKPVGELLVDDLQNHIDRVKV  75299


 Score =  126 bits (316),  Expect = 1e-25, Method: Compositional matrix adjust.
 Identities = 55/68 (80%), Positives = 64/68 (94%), Gaps = 1/68 (1%)
 Frame = +1

Query  810     ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS-  868
               ANNKPE+EA++FLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRY   
Sbjct  114835  ANNKPELEASVFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYGPF  115014

Query  869     LKHFNYDI  876
               L+++++ +
Sbjct  115015  LQYYSFRV  115038


 Score =  122 bits (307),  Expect = 1e-24, Method: Compositional matrix adjust.
 Identities = 59/97 (60%), Positives = 73/97 (75%), Gaps = 17/97 (17%)
 Frame = +3

Query  661     LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
               +DLLS+ AAC+A +QHNLKQN+Q MDI+Q+INCLT+IYDRLEQ+H++LVNVPLCVDMCLN
Sbjct  102840  VDLLSMPAACEAFEQHNLKQNEQFMDIVQVINCLTSIYDRLEQQHSSLVNVPLCVDMCLN  103019

Query  721     WLLNVYDT-----------------GRTGRIRVLSFK  740
               WLLNVYDT                    G+IR+L F+
Sbjct  103020  WLLNVYDTYV*PVYYCCFACLNGSLFTRGKIRLLCFQ  103130


 Score =  110 bits (275),  Expect = 4e-21, Method: Compositional matrix adjust.
 Identities = 49/55 (89%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = +2

Query  758     LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
               LF++VAS+TGFCDQRRLGLLLHD+IQIPRQLGEVASFGGSNIEPSVRSCFQF +N
Sbjct  112436  LFREVASATGFCDQRRLGLLLHDAIQIPRQLGEVASFGGSNIEPSVRSCFQFVSN  112600


 Score = 96.7 bits (239),  Expect = 8e-17, Method: Compositional matrix adjust.
 Identities = 45/53 (84%), Positives = 51/53 (96%), Gaps = 0/53 (0%)
 Frame = +3

Query  993     DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
               DDEHLLIQHYCQSLNQ SPLSQP+SPAQILIS+E+EE+GELER+L DLE+ENR
Sbjct  128427  DDEHLLIQHYCQSLNQGSPLSQPQSPAQILISMETEEKGELERVLNDLEQENR  128585


 Score = 60.8 bits (146),  Expect(2) = 3e-15, Method: Compositional matrix adjust.
 Identities = 29/53 (54%), Positives = 41/53 (77%), Gaps = 0/53 (0%)
 Frame = +1

Query  164    KQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  216
              +QL+KDL+QWQT ++V N+LA KLL  Y+ DDT KV  +TE++N +W +I KR
Sbjct  61951  QQLSKDLQQWQTQMNVTNELANKLLTLYADDDTSKVKQMTESMNLAWANIKKR  62109


 Score = 50.8 bits (120),  Expect(2) = 3e-15, Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 43/71 (60%), Gaps = 0/71 (0%)
 Frame = +2

Query  94     IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
              +E++Q  W++    L  R   L  M KDS+ WLEA++  E ++ +A  KLESWK+  ++V
Sbjct  61667  VEKLQAHWEDSHAKLTARVLTLQNMYKDSSDWLEARKRVEPLIKKANEKLESWKKVSHSV  61846

Query  154    DAIQKKITETK  164
              + ++ +  + K
Sbjct  61847  EDLKGQNADVK  61879


 Score = 80.9 bits (198),  Expect = 4e-12, Method: Compositional matrix adjust.
 Identities = 37/67 (55%), Positives = 51/67 (76%), Gaps = 0/67 (0%)
 Frame = +2

Query  271    VKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELR  330
              V +L   WQDLQ EI+AH + YH+LDEN  +I+ SLEG+D+AV+LQ+RLD+M  +W EL 
Sbjct  70259  VCDLF*SWQDLQAEIDAHRETYHSLDENGHRIVSSLEGTDNAVVLQKRLDDMGQRWHELC  70438

Query  331    KKSLNIR  337
               K ++IR
Sbjct  70439  NKVMSIR  70459


 Score = 76.3 bits (186),  Expect = 1e-10, Method: Compositional matrix adjust.
 Identities = 40/63 (63%), Positives = 47/63 (74%), Gaps = 0/63 (0%)
 Frame = +1

Query  217    VSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMK  276
                ++EA LE   R LQ + LDLEKFL WLTEAETTANVLQDAT KE LLE+   V+ L++
Sbjct  63910  AGDKEADLEAGLRQLQHYYLDLEKFLNWLTEAETTANVLQDATFKEGLLENPATVRHLLE  64089

Query  277    QWQ  279
              QWQ
Sbjct  64090  QWQ  64098


 Score = 70.1 bits (170),  Expect = 8e-09, Method: Compositional matrix adjust.
 Identities = 32/63 (50%), Positives = 44/63 (69%), Gaps = 0/63 (0%)
 Frame = +1

Query  336    IRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKREL  395
              +R +L+A  DQWK LH+SLQELL WLQLK +EL +Q P+GGD P V +Q   H+    ++
Sbjct  71902  LRPYLDAGVDQWKHLHMSLQELLNWLQLKREELEKQKPVGGDVPTVHQQLLTHKVSPGQI  72081

Query  396    KTK  398
              + K
Sbjct  72082  QFK  72090


 Score = 65.5 bits (158),  Expect = 2e-07, Method: Compositional matrix adjust.
 Identities = 28/46 (60%), Positives = 38/46 (82%), Gaps = 0/46 (0%)
 Frame = +1

Query  10     PALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKA  55
               AL  FN++WTEL DWL+LLD ++++QRVMVGDL++INEM +K K 
Sbjct  58012  AALDKFNKSWTELDDWLALLDHMVQTQRVMVGDLDEINEMTVKLKV  58149


 Score = 61.6 bits (148),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 29/51 (56%), Positives = 38/51 (74%), Gaps = 0/51 (0%)
 Frame = +1

Query  519    KALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV  569
              +A + EIAP+++NV+HVN LA       IQLSP NLS ++DLN RW+LLQV
Sbjct  78775  QAFQEEIAPIQDNVNHVNQLASTFRPSDIQLSPDNLSRIDDLNMRWRLLQV  78927


 Score = 58.2 bits (139),  Expect = 3e-05, Method: Compositional matrix adjust.
 Identities = 26/31 (83%), Positives = 27/31 (87%), Gaps = 0/31 (0%)
 Frame = +1

Query  729     GRTGRIRVLSFKTGIISLCKAHLEDKYRYLF  759
               GR G+IR LSFKTGIISLCKAHLEDKYR  F
Sbjct  109951  GRAGKIRTLSFKTGIISLCKAHLEDKYRCKF  110043


 Score = 55.1 bits (131),  Expect = 3e-04, Method: Compositional matrix adjust.
 Identities = 26/35 (74%), Positives = 28/35 (80%), Gaps = 0/35 (0%)
 Frame = +1

Query  636     ADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAAC  670
               ADLNNVRFSAYRTAMKLRR+QKALC     L+  C
Sbjct  100579  ADLNNVRFSAYRTAMKLRRMQKALCCKSTPLTFYC  100683


 Score = 54.7 bits (130),  Expect = 3e-04, Method: Compositional matrix adjust.
 Identities = 26/40 (65%), Positives = 32/40 (80%), Gaps = 0/40 (0%)
 Frame = +3

Query  54     KATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  93
              ++ +QD+EQR PQL + ITAAQNLKNKT+N E R  ITDR
Sbjct  59928  QSALQDMEQRCPQLNKQITAAQNLKNKTNNPETRATITDR  60047


 Score = 53.5 bits (127),  Expect = 8e-04, Method: Compositional matrix adjust.
 Identities = 23/34 (67%), Positives = 28/34 (82%), Gaps = 0/34 (0%)
 Frame = +2

Query  1194    FPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEE  1227
               FPS  G NVGSLFHM D++G AMESLV V+T+E+
Sbjct  151334  FPSPSGPNVGSLFHMVDNIGHAMESLVHVITEEQ  151435


 Score = 49.7 bits (117),  Expect = 0.010, Method: Compositional matrix adjust.
 Identities = 23/26 (88%), Positives = 24/26 (92%), Gaps = 0/26 (0%)
 Frame = +3

Query  945     NMETPASSPQLSHDDTHSRIEHYASR  970
               +M  PASSPQLSHDDTHSRIEHYASR
Sbjct  122844  SMLRPASSPQLSHDDTHSRIEHYASR  122921


 Score = 48.9 bits (115),  Expect = 0.016, Method: Compositional matrix adjust.
 Identities = 22/32 (68%), Positives = 28/32 (87%), Gaps = 0/32 (0%)
 Frame = +2

Query  1168    GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
               G+++L SP QD STGLE+V+EQLNNSFP S+G
Sbjct  147566  GDDELSSPTQDASTGLEDVIEQLNNSFPHSQG  147661


 Score = 47.0 bits (110),  Expect = 0.064, Method: Compositional matrix adjust.
 Identities = 25/43 (58%), Positives = 33/43 (76%), Gaps = 1/43 (2%)
 Frame = +2

Query  1127    PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGE  1169
               PQ E+KVNGT +SSPST+  RSD+S    LRV  SQT+++MG+
Sbjct  141356  PQTESKVNGTALSSPSTASPRSDTSL-ASLRVAASQTTETMGK  141481


 Score = 47.0 bits (110),  Expect = 0.069, Method: Compositional matrix adjust.
 Identities = 19/25 (76%), Positives = 22/25 (88%), Gaps = 0/25 (0%)
 Frame = +1

Query  616    HETQTTCWDHPKMTELYQSLADLNN  640
              H+TQTTCWDHPKM ELYQSL  L++
Sbjct  98158  HQTQTTCWDHPKMAELYQSLGWLDS  98232


 Score = 42.7 bits (99),  Expect = 1.4, Method: Compositional matrix adjust.
 Identities = 18/23 (78%), Positives = 22/23 (95%), Gaps = 0/23 (0%)
 Frame = +2

Query  970     RLAEMENSNGSYLNDSISPNESI  992
               RLAEMEN NGSY+ND++SPNES+
Sbjct  126248  RLAEMENRNGSYVNDNVSPNESM  126316


>emb|AL645857.11| Mouse DNA sequence from clone RP23-167N2 on chromosome X Contains 
part of the Dmd gene for dystrophin muscular dystrophy, 
complete sequence
Length=137904

 Score =  171 bits (432),  Expect = 3e-39, Method: Compositional matrix adjust.
 Identities = 86/92 (93%), Positives = 87/92 (94%), Gaps = 0/92 (0%)
 Frame = +2

Query  430    ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLK  489
              ELPPEERAQNVTRLLRKQAEEVN EW+KLNL SADWQRKIDE LERLQELQEA DELDLK
Sbjct  39110  ELPPEERAQNVTRLLRKQAEEVNAEWDKLNLRSADWQRKIDEALERLQELQEAADELDLK  39289

Query  490    LRQAEVIKGSWQPVGDLLIDSLQDHLEKVKAL  521
              LRQAEVIKGSWQPVGDLLIDSLQDHLEKVK L
Sbjct  39290  LRQAEVIKGSWQPVGDLLIDSLQDHLEKVKVL  39385


 Score =  111 bits (277),  Expect = 3e-21, Method: Compositional matrix adjust.
 Identities = 52/55 (94%), Positives = 53/55 (96%), Gaps = 0/55 (0%)
 Frame = +1

Query  336   IRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRA  390
              RSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQND+HR 
Sbjct  2998  FRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDIHRV  3162


 Score = 95.5 bits (236),  Expect = 2e-16, Method: Compositional matrix adjust.
 Identities = 46/52 (88%), Positives = 49/52 (94%), Gaps = 0/52 (0%)
 Frame = +3

Query  520    ALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAV  571
              ALRGEIAPLKENV+ VNDLA QLTTLGIQLSPYNLSTLEDLNTRW+LLQV +
Sbjct  69732  ALRGEIAPLKENVNRVNDLAHQLTTLGIQLSPYNLSTLEDLNTRWRLLQVGM  69887


 Score = 84.3 bits (207),  Expect = 4e-13, Method: Compositional matrix adjust.
 Identities = 40/43 (93%), Positives = 42/43 (97%), Gaps = 0/43 (0%)
 Frame = +3

Query  387    VHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPR  429
              + +AFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPR
Sbjct  38373  ISQAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPR  38501


>gb|AY423026.1| Danio rerio dystrobrevin, beta (DTNB) mRNA, complete cds
Length=3069

 Score =  170 bits (431),  Expect = 4e-39, Method: Compositional matrix adjust.
 Identities = 154/568 (27%), Positives = 256/568 (45%), Gaps = 61/568 (10%)
 Frame = +1

Query  685   MDILQIINCLTTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTG  742
             + + ++   LT IY +L +     + ++V     + LN++   +DT   GR+ V S K  
Sbjct  172   ISVARLETILTCIYQQLNKRLPTTHQISVQHNTSLLLNFMATAHDTDAQGRLTVFSVKMM  351

Query  743   IISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPS  802
             +  LC   L DK RY+F Q++ S G  +  +    L +++++P  + E  SFG   ++  
Sbjct  352   LSVLCGGKLVDKLRYIFSQISDSHGAMEMSKFDHFLREALKLPAAVFEGPSFG--YLDHL  525

Query  803   VRSCFQFANNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECP  860
              RSCF     + ++   +FLD +  +P  Q ++WLP++HR+   E   H   C+ C+   
Sbjct  526   ARSCFP---QQKKVMLNMFLDALMSDPPPQCLIWLPLVHRMGNVENVHHPVSCSFCRSDG  696

Query  861   IIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYC---TPTTS-GEDVRDFAKVL  916
             + GFRYR  + FNY +CQ+CF+ G  +  H  H+ M E+    +P    G  +      +
Sbjct  697   MTGFRYRCQQCFNYQLCQNCFWRGHASGNHSNHHEMKEHSSWKSPVKKLGRAISKSLGCV  876

Query  917   KNKFRTKRYFAKHPR-----MGYLPVQTVLEGDNMETPASSPQLSHDDTHSR---IEHYA  968
              ++  +   + ++P         +P + +    NM  PA  P LS   + ++       A
Sbjct  877   PSREPSHPIYPEYPEKPLNLSNIVPPRPI---GNMNEPA--PPLSTGSSPTKRLPTLAAA  1041

Query  969   SRLAEMENSNGSYLNDSISPNESI------DDEHLLIQHYCQSLNQDSPLSQPRSPAQIL  1022
              R+ E      +Y+N   S   ++      D+EH LI  Y   L  D P    R PA   
Sbjct  1042  QRMNEEHALIAAYVNKLQSSPRALDSPVRSDEEHKLIARYASRLATD-PGHTAR-PADFS  1215

Query  1023  ISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRD  1082
                  ++R     ++  LE +NR +  E  RL+ +HE +   P P   +  PT       
Sbjct  1216  YDTNKQQR----ELIMQLENKNREILQEIQRLRVEHE-QACQPTPERVQQNPT-------  1359

Query  1083  AELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPS  1142
               L+AE + LRQ K  LE RM  L++  ++L  QL  L +LL     +A+  G   SSPS
Sbjct  1360  --LLAELRQLRQRKDELEQRMSSLQESRRELMVQLEGLMKLL-----KAQAAG---SSPS  1509

Query  1143  TSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
              +  R   S PM +R   S  + +         PQD+  G+   +++  +  P     N 
Sbjct  1510  HASPR---SMPMPIRSPSSGPAPTYTGHTPTHGPQDSLAGVGGDVQEAFSQGPRRNLRN-  1677

Query  1203  GSLFHMADDLGRAMESLVSVMTDEEGAE  1230
               L   AD +   M SLV  +   E  +
Sbjct  1678  -DLLVAADSITNTMSSLVKELNSAEDGD  1758


>ref|XM_001054726.1| PREDICTED: Rattus norvegicus similar to dystrobrevin alpha isoform 
1 (predicted), transcript variant 10 (RGD1561985_predicted), 
mRNA
Length=3516

 Score =  170 bits (431),  Expect = 4e-39, Method: Compositional matrix adjust.
 Identities = 163/610 (26%), Positives = 277/610 (45%), Gaps = 97/610 (15%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  257   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  436

Query  695   TTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +T++ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  437   STMFYQLNKRMPSTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  616

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  617   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  781

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  782   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  961

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFA--K  928
               NY +CQ CF+ G     H   + M EY +        +  AK L N        A  +
Sbjct  962   CHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASSR  1120

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT------HSRIEHYASRLAEMENS-----  977
              P     P Q     +        P  S +DT       S    + +R +  ++S     
Sbjct  1121  EPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSEVEQN  1300

Query  978   -----------NGSYLNDSISPNESIDDEHLLI---------------------------  999
                         G  ++ S++  + + DEH+LI                           
Sbjct  1301  KILARAAPAFLKGKGIHYSLNVADRLADEHVLIGLYVNMLRNNPSCMLESSNRLDEEHRL  1480

Query  1000  -QHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYDRLK  1055
                Y   L  +S  SQP   RS   +  ++++ +  +  +++A+LE +NR +  E  RL+
Sbjct  1481  IARYAARLAAESSSSQPTQQRSAPDVSFTIDANK--QQRQLIAELENKNREILQEIQRLR  1654

Query  1056  QQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLES  1115
              +HE              PT  ++ ++  L+AE +LLRQ K  LE RM  L++  ++L  
Sbjct  1655  VEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELEQRMSALQESRRELMV  1804

Query  1116  QLHRLRQLL--EQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLL  1173
             QL  L +LL  E+ +   +  G+  SSPS ++ R     PM +R   + ++ +       
Sbjct  1805  QLEGLMKLLKEEELKQGTQGAGSPRSSPSHTISRPI---PMPIRSTSACSTPAYT-----  1960

Query  1174  SPPQDTSTGL  1183
               PQD+ TG+
Sbjct  1961  --PQDSLTGV  1984


>gb|M86899.1|HUMDYST16 H.sapiens dystrophin gene, exon 75
Length=365

 Score =  170 bits (431),  Expect = 4e-39, Method: Compositional matrix adjust.
 Identities = 87/102 (85%), Positives = 89/102 (87%), Gaps = 0/102 (0%)
 Frame = +1

Query  1044  NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  1103
             NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM
Sbjct  28    NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  207

Query  1104  QILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSL  1145
             QILEDHNKQLESQLHRLRQLLEQ + E     T +    T L
Sbjct  208   QILEDHNKQLESQLHRLRQLLEQVRREMGFLQTFIFPS*TKL  333


>ref|XM_001089125.1| PREDICTED: Macaca mulatta similar to dystrophin related protein 
2 (LOC700789), partial mRNA
Length=325

 Score =  170 bits (430),  Expect = 5e-39, Method: Composition-based stats.
 Identities = 75/107 (70%), Positives = 90/107 (84%), Gaps = 0/107 (0%)
 Frame = +3

Query  758  LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIE  817
            LF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EPSVRSCF+F+  KP IE
Sbjct  3    LFSQVANSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEPSVRSCFRFSTGKPVIE  182

Query  818  AALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGF  864
            A+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI GF
Sbjct  183  ASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPIKGF  323


>gb|AC193904.3| Pan troglodytes BAC clone CH251-277B20 from chromosome x, complete 
sequence
Length=146903

 Score =  169 bits (428),  Expect = 9e-39, Method: Compositional matrix adjust.
 Identities = 83/83 (100%), Positives = 83/83 (100%), Gaps = 0/83 (0%)
 Frame = -3

Query  1044   NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  1103
              NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM
Sbjct  70176  NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  69997

Query  1104   QILEDHNKQLESQLHRLRQLLEQ  1126
              QILEDHNKQLESQLHRLRQLLEQ
Sbjct  69996  QILEDHNKQLESQLHRLRQLLEQ  69928


 Score =  143 bits (360),  Expect = 7e-31, Method: Compositional matrix adjust.
 Identities = 67/68 (98%), Positives = 68/68 (100%), Gaps = 0/68 (0%)
 Frame = -2

Query  661     LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
               +DLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  132121  VDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  131942

Query  721     WLLNVYDT  728
               WLLNVYDT
Sbjct  131941  WLLNVYDT  131918


 Score =  132 bits (331),  Expect = 2e-27, Method: Compositional matrix adjust.
 Identities = 62/74 (83%), Positives = 63/74 (85%), Gaps = 0/74 (0%)
 Frame = -3

Query  793     SFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK  852
               SF  S   PS+      ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK
Sbjct  105534  SFLSSFCPPSLSLLSLQANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK  105355

Query  853     CNICKECPIIGFRY  866
               CNICKECPIIGFRY
Sbjct  105354  CNICKECPIIGFRY  105313


 Score =  115 bits (288),  Expect = 1e-22, Method: Compositional matrix adjust.
 Identities = 53/58 (91%), Positives = 54/58 (93%), Gaps = 0/58 (0%)
 Frame = -1

Query  758     LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPE  815
               LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF +  P 
Sbjct  126551  LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFVSYSPS  126378


 Score =  107 bits (268),  Expect = 3e-20, Method: Compositional matrix adjust.
 Identities = 54/55 (98%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = -3

Query  991    SIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
              S DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR
Sbjct  92283  SRDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  92119


 Score =  102 bits (253),  Expect = 2e-18, Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 53/61 (86%), Gaps = 5/61 (8%)
 Frame = -3

Query  893     HYPMVEYCTP-----TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  947
               ++P++   +P     TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME
Sbjct  101427  NHPVLNLISP*SPF*TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  101248

Query  948     T  948
               T
Sbjct  101247  T  101245


 Score = 92.8 bits (229),  Expect = 1e-15, Method: Compositional matrix adjust.
 Identities = 38/40 (95%), Positives = 39/40 (97%), Gaps = 0/40 (0%)
 Frame = -2

Query  865     RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
               RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTP +
Sbjct  103060  RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPVS  102941


 Score = 85.5 bits (210),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 42/43 (97%), Positives = 43/43 (100%), Gaps = 0/43 (0%)
 Frame = -3

Query  1127   PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGE  1169
              PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMG+
Sbjct  69069  PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGK  68941


 Score = 70.1 bits (170),  Expect = 8e-09, Method: Compositional matrix adjust.
 Identities = 34/37 (91%), Positives = 34/37 (91%), Gaps = 3/37 (8%)
 Frame = -1

Query  1194   FPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              FP   GHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  44657  FP---GHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  44556


 Score = 68.6 bits (166),  Expect = 2e-08, Method: Compositional matrix adjust.
 Identities = 32/32 (100%), Positives = 32/32 (100%), Gaps = 0/32 (0%)
 Frame = -3

Query  1168   GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
              GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG
Sbjct  56856  GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  56761


 Score = 63.5 bits (153),  Expect = 6e-07, Method: Compositional matrix adjust.
 Identities = 29/34 (85%), Positives = 32/34 (94%), Gaps = 0/34 (0%)
 Frame = -3

Query  723     LNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYR  756
               L +++ GRTGRIRVLSFKTGIISLCKAHLEDKYR
Sbjct  129108  LILHNRGRTGRIRVLSFKTGIISLCKAHLEDKYR  129007


 Score = 54.3 bits (129),  Expect = 4e-04, Method: Compositional matrix adjust.
 Identities = 25/25 (100%), Positives = 25/25 (100%), Gaps = 0/25 (0%)
 Frame = -2

Query  636     ADLNNVRFSAYRTAMKLRRLQKALC  660
               ADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  145489  ADLNNVRFSAYRTAMKLRRLQKALC  145415


 Score = 52.8 bits (125),  Expect = 0.001, Method: Compositional matrix adjust.
 Identities = 25/32 (78%), Positives = 28/32 (87%), Gaps = 0/32 (0%)
 Frame = -1

Query  970    RLAEMENSNGSYLNDSISPNESIDDEHLLIQH  1001
              RLAEMENSNGSYLNDSISPNES+   HL +Q+
Sbjct  95084  RLAEMENSNGSYLNDSISPNESM*VSHLFLQN  94989


 Score = 48.9 bits (115),  Expect = 0.019, Method: Compositional matrix adjust.
 Identities = 22/23 (95%), Positives = 22/23 (95%), Gaps = 0/23 (0%)
 Frame = -1

Query  949    PASSPQLSHDDTHSRIEHYASRL  971
              PASSPQLSHDDTHSRIEHYASR 
Sbjct  96269  PASSPQLSHDDTHSRIEHYASRY  96201


>emb|CT573323.2| CH251-58D24, complete sequence
Length=66462

 Score =  169 bits (428),  Expect = 9e-39, Method: Compositional matrix adjust.
 Identities = 83/83 (100%), Positives = 83/83 (100%), Gaps = 0/83 (0%)
 Frame = +3

Query  1044   NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  1103
              NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM
Sbjct  41238  NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  41417

Query  1104   QILEDHNKQLESQLHRLRQLLEQ  1126
              QILEDHNKQLESQLHRLRQLLEQ
Sbjct  41418  QILEDHNKQLESQLHRLRQLLEQ  41486


 Score =  132 bits (331),  Expect = 2e-27, Method: Compositional matrix adjust.
 Identities = 62/74 (83%), Positives = 63/74 (85%), Gaps = 0/74 (0%)
 Frame = +1

Query  793   SFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK  852
             SF  S   PS+      ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK
Sbjct  5881  SFLSSFCPPSLSLLSLQANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK  6060

Query  853   CNICKECPIIGFRY  866
             CNICKECPIIGFRY
Sbjct  6061  CNICKECPIIGFRY  6102


 Score =  107 bits (268),  Expect = 3e-20, Method: Compositional matrix adjust.
 Identities = 54/55 (98%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = +3

Query  991    SIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
              S DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR
Sbjct  19131  SRDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  19295


 Score =  102 bits (253),  Expect = 2e-18, Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 53/61 (86%), Gaps = 5/61 (8%)
 Frame = +1

Query  893    HYPMVEYCTP-----TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  947
              ++P++   +P     TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME
Sbjct  9988   NHPVLNLISP*SPF*TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  10167

Query  948    T  948
              T
Sbjct  10168  T  10170


 Score = 92.8 bits (229),  Expect = 1e-15, Method: Compositional matrix adjust.
 Identities = 38/40 (95%), Positives = 39/40 (97%), Gaps = 0/40 (0%)
 Frame = +3

Query  865   RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
             RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTP +
Sbjct  8355  RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPVS  8474


 Score = 85.5 bits (210),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 42/43 (97%), Positives = 43/43 (100%), Gaps = 0/43 (0%)
 Frame = +3

Query  1127   PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGE  1169
              PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMG+
Sbjct  42345  PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGK  42473


 Score = 68.6 bits (166),  Expect = 2e-08, Method: Compositional matrix adjust.
 Identities = 32/32 (100%), Positives = 32/32 (100%), Gaps = 0/32 (0%)
 Frame = +2

Query  1168   GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
              GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG
Sbjct  54560  GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  54655


 Score = 52.8 bits (125),  Expect = 0.001, Method: Compositional matrix adjust.
 Identities = 25/32 (78%), Positives = 28/32 (87%), Gaps = 0/32 (0%)
 Frame = +2

Query  970    RLAEMENSNGSYLNDSISPNESIDDEHLLIQH  1001
              RLAEMENSNGSYLNDSISPNES+   HL +Q+
Sbjct  16331  RLAEMENSNGSYLNDSISPNESM*VSHLFLQN  16426


 Score = 48.9 bits (115),  Expect = 0.019, Method: Compositional matrix adjust.
 Identities = 22/23 (95%), Positives = 22/23 (95%), Gaps = 0/23 (0%)
 Frame = +2

Query  949    PASSPQLSHDDTHSRIEHYASRL  971
              PASSPQLSHDDTHSRIEHYASR 
Sbjct  15146  PASSPQLSHDDTHSRIEHYASRY  15214


>gb|AC078958.30| Homo sapiens X BAC RP11-609C15 (Roswell Park Cancer Institute 
Human BAC Library) complete sequence
Length=187547

 Score =  169 bits (428),  Expect = 9e-39, Method: Compositional matrix adjust.
 Identities = 83/83 (100%), Positives = 83/83 (100%), Gaps = 0/83 (0%)
 Frame = -2

Query  1044   NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  1103
              NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM
Sbjct  19936  NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  19757

Query  1104   QILEDHNKQLESQLHRLRQLLEQ  1126
              QILEDHNKQLESQLHRLRQLLEQ
Sbjct  19756  QILEDHNKQLESQLHRLRQLLEQ  19688


 Score =  142 bits (357),  Expect = 1e-30, Method: Compositional matrix adjust.
 Identities = 67/68 (98%), Positives = 68/68 (100%), Gaps = 0/68 (0%)
 Frame = -3

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              +DLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  82113  VDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  81934

Query  721    WLLNVYDT  728
              WLLNVYDT
Sbjct  81933  WLLNVYDT  81910


 Score =  130 bits (327),  Expect = 4e-27, Method: Compositional matrix adjust.
 Identities = 65/90 (72%), Positives = 69/90 (76%), Gaps = 6/90 (6%)
 Frame = -3

Query  777    LLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLP  836
              L++ S  I      + SF  S   PS+      ANNKPEIEAALFLDWMRLEPQSMVWLP
Sbjct  55398  LIYTSFAI------LPSFLSSFCPPSLSLLSLQANNKPEIEAALFLDWMRLEPQSMVWLP  55237

Query  837    VLHRVAAAETAKHQAKCNICKECPIIGFRY  866
              VLHRVAAAETAKHQAKCNICKECPIIGFRY
Sbjct  55236  VLHRVAAAETAKHQAKCNICKECPIIGFRY  55147


 Score =  115 bits (288),  Expect = 1e-22, Method: Compositional matrix adjust.
 Identities = 53/58 (91%), Positives = 54/58 (93%), Gaps = 0/58 (0%)
 Frame = -1

Query  758    LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPE  815
              LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF +  P 
Sbjct  76529  LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFVSYSPS  76356


 Score =  107 bits (268),  Expect = 3e-20, Method: Compositional matrix adjust.
 Identities = 54/55 (98%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = -2

Query  991    SIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
              S DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR
Sbjct  42019  SRDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  41855


 Score =  102 bits (253),  Expect = 2e-18, Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 53/61 (86%), Gaps = 5/61 (8%)
 Frame = -1

Query  893    HYPMVEYCTP-----TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  947
              ++P++   +P     TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME
Sbjct  51263  NHPVLNLISP*SPF*TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  51084

Query  948    T  948
              T
Sbjct  51083  T  51081


 Score = 92.8 bits (229),  Expect = 1e-15, Method: Compositional matrix adjust.
 Identities = 38/40 (95%), Positives = 39/40 (97%), Gaps = 0/40 (0%)
 Frame = -3

Query  865    RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
              RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTP +
Sbjct  52896  RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPVS  52777


 Score = 85.5 bits (210),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 42/43 (97%), Positives = 43/43 (100%), Gaps = 0/43 (0%)
 Frame = -1

Query  1127   PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGE  1169
              PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMG+
Sbjct  18827  PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGK  18699


 Score = 68.6 bits (166),  Expect = 2e-08, Method: Compositional matrix adjust.
 Identities = 32/32 (100%), Positives = 32/32 (100%), Gaps = 0/32 (0%)
 Frame = -1

Query  1168  GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
             GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG
Sbjct  6608  GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  6513


 Score = 63.5 bits (153),  Expect = 6e-07, Method: Compositional matrix adjust.
 Identities = 29/34 (85%), Positives = 32/34 (94%), Gaps = 0/34 (0%)
 Frame = -1

Query  723    LNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYR  756
              L +++ GRTGRIRVLSFKTGIISLCKAHLEDKYR
Sbjct  79097  LILHNRGRTGRIRVLSFKTGIISLCKAHLEDKYR  78996


 Score = 54.3 bits (129),  Expect = 4e-04, Method: Compositional matrix adjust.
 Identities = 25/25 (100%), Positives = 25/25 (100%), Gaps = 0/25 (0%)
 Frame = -3

Query  636    ADLNNVRFSAYRTAMKLRRLQKALC  660
              ADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  95535  ADLNNVRFSAYRTAMKLRRLQKALC  95461


 Score = 52.8 bits (125),  Expect = 0.001, Method: Compositional matrix adjust.
 Identities = 25/32 (78%), Positives = 28/32 (87%), Gaps = 0/32 (0%)
 Frame = -1

Query  970    RLAEMENSNGSYLNDSISPNESIDDEHLLIQH  1001
              RLAEMENSNGSYLNDSISPNES+   HL +Q+
Sbjct  44828  RLAEMENSNGSYLNDSISPNESM*VSHLFLQN  44733


 Score = 50.8 bits (120),  Expect = 0.005, Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 26/35 (74%), Gaps = 3/35 (8%)
 Frame = -3

Query  605     ISPNKVPYYI---NHETQTTCWDHPKMTELYQSLA  636
               I   KV  Y+   +HETQTTCWDHPKMTELYQSL 
Sbjct  133470  IVNAKVFLYVLCFSHETQTTCWDHPKMTELYQSLG  133366


 Score = 48.9 bits (115),  Expect = 0.019, Method: Compositional matrix adjust.
 Identities = 22/23 (95%), Positives = 22/23 (95%), Gaps = 0/23 (0%)
 Frame = -1

Query  949    PASSPQLSHDDTHSRIEHYASRL  971
              PASSPQLSHDDTHSRIEHYASR 
Sbjct  46016  PASSPQLSHDDTHSRIEHYASRY  45948


>emb|CT573090.2| RP43-052E01, complete sequence
Length=161118

 Score =  169 bits (428),  Expect = 9e-39, Method: Compositional matrix adjust.
 Identities = 83/83 (100%), Positives = 83/83 (100%), Gaps = 0/83 (0%)
 Frame = +3

Query  1044   NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  1103
              NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM
Sbjct  61539  NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  61718

Query  1104   QILEDHNKQLESQLHRLRQLLEQ  1126
              QILEDHNKQLESQLHRLRQLLEQ
Sbjct  61719  QILEDHNKQLESQLHRLRQLLEQ  61787


 Score =  132 bits (331),  Expect = 2e-27, Method: Compositional matrix adjust.
 Identities = 62/74 (83%), Positives = 63/74 (85%), Gaps = 0/74 (0%)
 Frame = +3

Query  793    SFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK  852
              SF  S   PS+      ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK
Sbjct  26127  SFLSSFCPPSLSLLSLQANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK  26306

Query  853    CNICKECPIIGFRY  866
              CNICKECPIIGFRY
Sbjct  26307  CNICKECPIIGFRY  26348


 Score =  115 bits (288),  Expect = 1e-22, Method: Compositional matrix adjust.
 Identities = 53/58 (91%), Positives = 54/58 (93%), Gaps = 0/58 (0%)
 Frame = +3

Query  758   LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPE  815
             LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF +  P 
Sbjct  5070  LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFVSYSPS  5243


 Score =  107 bits (268),  Expect = 3e-20, Method: Compositional matrix adjust.
 Identities = 54/55 (98%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = +3

Query  991    SIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
              S DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR
Sbjct  39447  SRDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  39611


 Score =  102 bits (253),  Expect = 2e-18, Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 53/61 (86%), Gaps = 5/61 (8%)
 Frame = +3

Query  893    HYPMVEYCTP-----TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  947
              ++P++   +P     TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME
Sbjct  30234  NHPVLNLISP*SPF*TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  30413

Query  948    T  948
              T
Sbjct  30414  T  30416


 Score = 92.8 bits (229),  Expect = 1e-15, Method: Compositional matrix adjust.
 Identities = 38/40 (95%), Positives = 39/40 (97%), Gaps = 0/40 (0%)
 Frame = +2

Query  865    RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
              RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTP +
Sbjct  28601  RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPVS  28720


 Score = 85.5 bits (210),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 42/43 (97%), Positives = 43/43 (100%), Gaps = 0/43 (0%)
 Frame = +3

Query  1127   PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGE  1169
              PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMG+
Sbjct  62646  PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGK  62774


 Score = 70.1 bits (170),  Expect = 8e-09, Method: Compositional matrix adjust.
 Identities = 34/37 (91%), Positives = 34/37 (91%), Gaps = 3/37 (8%)
 Frame = +1

Query  1194   FPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              FP   GHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  87091  FP---GHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  87192


 Score = 68.6 bits (166),  Expect = 2e-08, Method: Compositional matrix adjust.
 Identities = 32/32 (100%), Positives = 32/32 (100%), Gaps = 0/32 (0%)
 Frame = +2

Query  1168   GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
              GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG
Sbjct  74852  GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  74947


 Score = 63.5 bits (153),  Expect = 6e-07, Method: Compositional matrix adjust.
 Identities = 29/34 (85%), Positives = 32/34 (94%), Gaps = 0/34 (0%)
 Frame = +1

Query  723   LNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYR  756
             L +++ GRTGRIRVLSFKTGIISLCKAHLEDKYR
Sbjct  2509  LILHNRGRTGRIRVLSFKTGIISLCKAHLEDKYR  2610


 Score = 52.8 bits (125),  Expect = 0.001, Method: Compositional matrix adjust.
 Identities = 25/32 (78%), Positives = 28/32 (87%), Gaps = 0/32 (0%)
 Frame = +1

Query  970    RLAEMENSNGSYLNDSISPNESIDDEHLLIQH  1001
              RLAEMENSNGSYLNDSISPNES+   HL +Q+
Sbjct  36646  RLAEMENSNGSYLNDSISPNESM*VSHLFLQN  36741


 Score = 48.9 bits (115),  Expect = 0.019, Method: Compositional matrix adjust.
 Identities = 22/23 (95%), Positives = 22/23 (95%), Gaps = 0/23 (0%)
 Frame = +2

Query  949    PASSPQLSHDDTHSRIEHYASRL  971
              PASSPQLSHDDTHSRIEHYASR 
Sbjct  35465  PASSPQLSHDDTHSRIEHYASRY  35533


>emb|AL645477.8| Mouse DNA sequence from clone RP23-155L18 on chromosome X Contains 
the 3' end of the Dmd gene for dystrophin muscular dystrophy, 
a novel pseudogene similar to family with sequence similarity 
112 member A FAM112A (Homo sapiens), a ribosomal protein 
S6 (Rps6) pseudogene and the gene for a novel protein 
similar to ferritin, heavy polypeptide 1 FTH1 (Homo sapiens), 
complete sequence
Length=189131

 Score =  168 bits (426),  Expect = 2e-38, Method: Compositional matrix adjust.
 Identities = 82/82 (100%), Positives = 82/82 (100%), Gaps = 0/82 (0%)
 Frame = +3

Query  1045   RNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ  1104
              RNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ
Sbjct  89193  RNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ  89372

Query  1105   ILEDHNKQLESQLHRLRQLLEQ  1126
              ILEDHNKQLESQLHRLRQLLEQ
Sbjct  89373  ILEDHNKQLESQLHRLRQLLEQ  89438


 Score =  144 bits (364),  Expect = 2e-31, Method: Compositional matrix adjust.
 Identities = 67/68 (98%), Positives = 68/68 (100%), Gaps = 0/68 (0%)
 Frame = +2

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              +DLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  16634  VDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  16813

Query  721    WLLNVYDT  728
              WLLNVYDT
Sbjct  16814  WLLNVYDT  16837


 Score =  128 bits (321),  Expect = 2e-26, Method: Compositional matrix adjust.
 Identities = 58/60 (96%), Positives = 58/60 (96%), Gaps = 0/60 (0%)
 Frame = +2

Query  807    FQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRY  866
              F  ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRY
Sbjct  50810  FSQANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRY  50989


 Score =  113 bits (282),  Expect = 7e-22, Method: Compositional matrix adjust.
 Identities = 52/54 (96%), Positives = 53/54 (98%), Gaps = 0/54 (0%)
 Frame = +1

Query  758    LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF +
Sbjct  21436  LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFVS  21597


 Score =  107 bits (268),  Expect = 3e-20, Method: Compositional matrix adjust.
 Identities = 54/55 (98%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = +1

Query  991    SIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
              S DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR
Sbjct  64513  SRDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  64677


 Score =  101 bits (252),  Expect = 2e-18, Method: Compositional matrix adjust.
 Identities = 46/46 (100%), Positives = 46/46 (100%), Gaps = 0/46 (0%)
 Frame = +2

Query  903    TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
              TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET
Sbjct  55520  TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  55657


 Score = 93.2 bits (230),  Expect = 9e-16, Method: Compositional matrix adjust.
 Identities = 39/43 (90%), Positives = 40/43 (93%), Gaps = 0/43 (0%)
 Frame = +1

Query  862    IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
              I  RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTP +
Sbjct  53206  IFIRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPVS  53334


 Score = 83.6 bits (205),  Expect = 7e-13, Method: Compositional matrix adjust.
 Identities = 41/43 (95%), Positives = 43/43 (100%), Gaps = 0/43 (0%)
 Frame = +1

Query  1127   PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGE  1169
              PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTS+SMG+
Sbjct  90190  PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSESMGK  90318


 Score = 70.5 bits (171),  Expect = 6e-09, Method: Compositional matrix adjust.
 Identities = 35/41 (85%), Positives = 36/41 (87%), Gaps = 3/41 (7%)
 Frame = +3

Query  1190    LNNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
               L+  FP   GHNVGSLFHMADDLGRAMESLVSVMTDEEGAE
Sbjct  113943  LSLCFP---GHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  114056


 Score = 69.7 bits (169),  Expect = 1e-08, Method: Compositional matrix adjust.
 Identities = 32/35 (91%), Positives = 34/35 (97%), Gaps = 0/35 (0%)
 Frame = +1

Query  1168    GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNV  1202
               GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG ++
Sbjct  102100  GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGKDL  102204


 Score = 63.5 bits (153),  Expect = 7e-07, Method: Compositional matrix adjust.
 Identities = 29/34 (85%), Positives = 32/34 (94%), Gaps = 0/34 (0%)
 Frame = +1

Query  723    LNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYR  756
              L +++ GRTGRIRVLSFKTGIISLCKAHLEDKYR
Sbjct  19054  LLLHNRGRTGRIRVLSFKTGIISLCKAHLEDKYR  19155


 Score = 54.7 bits (130),  Expect = 3e-04, Method: Compositional matrix adjust.
 Identities = 25/25 (100%), Positives = 25/25 (100%), Gaps = 0/25 (0%)
 Frame = +2

Query  636   ADLNNVRFSAYRTAMKLRRLQKALC  660
             ADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  1307  ADLNNVRFSAYRTAMKLRRLQKALC  1381


 Score = 51.6 bits (122),  Expect = 0.003, Method: Compositional matrix adjust.
 Identities = 25/32 (78%), Positives = 28/32 (87%), Gaps = 0/32 (0%)
 Frame = +1

Query  970    RLAEMENSNGSYLNDSISPNESIDDEHLLIQH  1001
              RLAEMENSNGSYLNDSISPNES+   HL +Q+
Sbjct  61702  RLAEMENSNGSYLNDSISPNESM*VWHLFLQN  61797


 Score = 48.9 bits (115),  Expect = 0.019, Method: Compositional matrix adjust.
 Identities = 22/23 (95%), Positives = 22/23 (95%), Gaps = 0/23 (0%)
 Frame = +1

Query  949    PASSPQLSHDDTHSRIEHYASRL  971
              PASSPQLSHDDTHSRIEHYASR 
Sbjct  60622  PASSPQLSHDDTHSRIEHYASRY  60690


>ref|XM_001361515.2| Drosophila pseudoobscura pseudoobscura GA21140 (Dpse\GA21140), 
mRNA
Length=2445

 Score =  167 bits (422),  Expect = 5e-38, Method: Compositional matrix adjust.
 Identities = 144/542 (26%), Positives = 240/542 (44%), Gaps = 63/542 (11%)
 Frame = +1

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  43    LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  222

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  223   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  402

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +      A
Sbjct  403   LVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPA  573

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP+LHR+A  ET  H   C++C +    GFRYR  +
Sbjct  574   ENKVTVNDFMATLMSEPGPSCLVWLPLLHRLATVETIVHPTICSVCHKENFTGFRYRCQR  753

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRT--KRYFAK  928
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +      L+  FR   ++    
Sbjct  754   CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQI---GHSLRKSFRCVPEKTTQV  924

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSH----DDTHSRIEHYASRLAEMENSNGSYLND  984
              PR    P +T L   ++  P  SP  SH    D T +    +   L        S L D
Sbjct  925   LPRFPDQPEKT-LNLSHIVPP--SPLPSHNGFNDPTLALAGVHHGHLPPGIFDRSSTL-D  1092

Query  985   SISPNESI-------------------------DDEHLLIQHYCQSLNQDSPLSQPRSPA  1019
             S +   SI                         D+EH LI  Y   L Q++    P + +
Sbjct  1093  SRATGRSIDSANCTGGGGGGGTTISRLAAASANDEEHRLIARYAARLAQEN--RAPSNMS  1266

Query  1020  QILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQS  1079
             +    + ++       ++A LE +N+ +  E  RL++Q E               T   +
Sbjct  1267  ESATPIGTDNSRAQRELIAQLESKNKEIMREIARLRRQQE---------------TEQMA  1401

Query  1080  PRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVS  1139
             P +  LI E + LRQ KG LE  +  L+D  +QL  QL  L ++L+  Q  A    T  S
Sbjct  1402  PENPALINELRALRQRKGELEGHLGALQDSRRQLMEQLEGLMRMLKN-QQTASPRSTPNS  1578

Query  1140  SP  1141
             SP
Sbjct  1579  SP  1584


>ref|XM_001502889.1| PREDICTED: Equus caballus dystrobrevin, beta (DTNB), mRNA
Length=2219

 Score =  166 bits (421),  Expect = 6e-38, Method: Compositional matrix adjust.
 Identities = 138/502 (27%), Positives = 232/502 (46%), Gaps = 80/502 (15%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  76    NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  255

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  256   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  429

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  430   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  597

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  598   -QQKKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  774

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT-----  904
              +  NY +CQ+CF+ G  +  H   + M E+                   C PT      
Sbjct  775   QQCHNYQLCQNCFWRGHASGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHP  954

Query  905   ----SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD--  958
                   E   D A ++  +  T         M    V  +  G  + TP    Q S D  
Sbjct  955   VFPEQPEKPLDLANIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDRP  1104

Query  959   ----DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                 D H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  + 
Sbjct  1105  RHLADEHALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NM  1257

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMP  1074
              R P  +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              P
Sbjct  1258  TRPPTDLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QP  1401

Query  1075  TSPQSPRDAELIAEAKLLRQHK  1096
             T  ++ ++  L+AE +LLRQ K
Sbjct  1402  TPEKAQQNPTLLAELRLLRQRK  1467


>ref|XM_540111.2| PREDICTED: Canis familiaris similar to dystrobrevin, beta isoform 
1 (LOC482997), mRNA
Length=2013

 Score =  166 bits (419),  Expect = 1e-37, Method: Compositional matrix adjust.
 Identities = 135/502 (26%), Positives = 229/502 (45%), Gaps = 80/502 (15%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  76    NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHSTEISVSRLETVI  255

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             +++Y     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  256   SSLYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  429

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  430   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  597

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  598   -QQKKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  774

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT-----  904
              +  NY +CQ+CF+ G  +  H   + M E+                   C PT      
Sbjct  775   QQCHNYQLCQNCFWRGHASGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHP  954

Query  905   ----SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD--  958
                   E   D A ++  +          P               + TP    Q S D  
Sbjct  955   VFPEQPEKPLDLANIVPPR----------PLANMNDTMVSHMSSGVPTPTKRLQYSQDIP  1104

Query  959   ----DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                 D H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  + 
Sbjct  1105  SHLADEHALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NM  1257

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMP  1074
              R PA +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              P
Sbjct  1258  TRPPADLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QP  1401

Query  1075  TSPQSPRDAELIAEAKLLRQHK  1096
             T  ++ ++  L+AE +LLRQ K
Sbjct  1402  TPEKAQQNPTLLAELRLLRQRK  1467


>emb|AJ003007.1| Mus musculus mRNA for beta-dystrobrevin
Length=2428

 Score =  166 bits (419),  Expect = 1e-37, Method: Compositional matrix adjust.
 Identities = 135/493 (27%), Positives = 237/493 (48%), Gaps = 62/493 (12%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  202   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHSTEISVSRLETVI  381

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  382   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMVAAYDSEGRGKLTVFSVKAMLATMCGGK  555

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +L   L +++++P  + E  SFG +  E +VR+CF   
Sbjct  556   MLDKLRYIFSQMSDSNGLMMFGKLDQFLKEALKLPTAVFEGPSFGYT--EHAVRTCFP--  723

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C    ++GFRYR 
Sbjct  724   -QQKKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCHCESMMGFRYRC  900

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGED----VRDFAKVLKNKFRTKR  924
              +  NY +CQ+CF+ G  +  H   + M E+ +  +  +     +      + ++     
Sbjct  901   QQCHNYQLCQNCFWRGHASGAHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPSREPPHP  1080

Query  925   YFAKHPR----MGYL----PVQ----TVLE--GDNMETPASSPQLSHD------DTHSRI  964
              F + P     + +L    P+     TV+      + TP    Q S D      D H+ I
Sbjct  1081  VFPEQPEKPLDLAHLVPPRPLTNMNDTVVSHMSSGVPTPTKRLQYSQDMPNLLADEHALI  1260

Query  965   EHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSP-LSQPRSPAQILI  1023
               Y +RL      + + + DS S    +D+EH LI  Y   L  ++  +++P + A    
Sbjct  1261  ASYVARL-----QHCTRVLDSPS---RLDEEHRLIARYAARLAAEAGNMTRPPTDASFNF  1416

Query  1024  SLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDA  1083
                 ++R    +++A+LE +NR +  E  RL+ +HE              PT  ++ ++ 
Sbjct  1417  DANKQQR----QLIAELENKNREILQEIQRLRLEHEQA----------FQPTPEKAQQNP  1554

Query  1084  ELIAEAKLLRQHK  1096
              L+AE +LLRQ K
Sbjct  1555  MLLAELRLLRQRK  1593


>ref|NM_001391.5| Homo sapiens dystrobrevin, alpha (DTNA), transcript variant 3, 
mRNA
Length=4374

 Score =  165 bits (418),  Expect = 1e-37, Method: Compositional matrix adjust.
 Identities = 155/563 (27%), Positives = 258/563 (45%), Gaps = 90/563 (15%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  77    DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  253

Query  694   LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
             L+TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  254   LSTIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  433

Query  752   EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  434   MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  598

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  599   QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  778

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK-  928
             +  NY +CQ CF+ G     H   + M EY +        +  AK L N        A  
Sbjct  779   QCHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------WKSPAKKLTNALSKSLSCASS  937

Query  929   ----HPRMGYLPVQTVLEGDNMETPASSPQLSHDDT------HSRIEHYASRLAEMENS-  977
                 HP     P + +     ++T    P  S +DT       S    + +R +  ++S 
Sbjct  938   REPLHPMFPDQPEKPLNLAHIVDTWPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSE  1117

Query  978   ---------------NGSYLNDSISPNESIDDEHL-------------------------  997
                             G  +  S++  + + DEH+                         
Sbjct  1118  VEQNKLLARAAPAFLKGKGIQYSLNVADRLADEHVLIGLYVNMLRNNPSCMLESSNRLDE  1297

Query  998   ---LIQHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEY  1051
                LI  Y   L  +S  SQP   RS   I  ++++ +  +  +++A+LE +NR +  E 
Sbjct  1298  EHRLIARYAARLAAESSSSQPPQQRSAPDISFTIDANK--QQRQLIAELENKNREILQEI  1471

Query  1052  DRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNK  1111
              RL+ +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  +
Sbjct  1472  QRLRLEHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRR  1621

Query  1112  QLESQLHRLRQLLEQPQAEAKVN  1134
             +L  QL  L +LL++ + +  V+
Sbjct  1622  ELMVQLEGLMKLLKEEELKQGVS  1690


>dbj|AK043436.1| Mus musculus 7 days neonate cerebellum cDNA, RIKEN full-length 
enriched library, clone:A730095I17 product:dystrobrevin, beta, 
full insert sequence
Length=2359

 Score =  165 bits (418),  Expect = 1e-37, Method: Compositional matrix adjust.
 Identities = 135/493 (27%), Positives = 237/493 (48%), Gaps = 62/493 (12%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  292   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHSTEISVSRLETVI  471

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  472   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMVAAYDSEGRGKLTVFSVKAMLATMCGGK  645

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +L   L +++++P  + E  SFG +  E +VR+CF   
Sbjct  646   MLDKLRYIFSQMSDSNGLMMFGKLDQFLKEALKLPTAVFEGPSFGYT--EHAVRTCFP--  813

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C    ++GFRYR 
Sbjct  814   -QQKKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCHCESMMGFRYRC  990

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGED----VRDFAKVLKNKFRTKR  924
              +  NY +CQ+CF+ G  +  H   + M E+ +  +  +     +      + ++     
Sbjct  991   QQCHNYQLCQNCFWRGHASGAHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPSREPPHP  1170

Query  925   YFAKHPR----MGYL----PVQ----TVLE--GDNMETPASSPQLSHD------DTHSRI  964
              F + P     + +L    P+     TV+      + TP    Q S D      D H+ I
Sbjct  1171  VFPEQPEKPLDLAHLVPPRPLTNMNDTVVSHMSSGVPTPTKRLQYSQDMPNLLADEHALI  1350

Query  965   EHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSP-LSQPRSPAQILI  1023
               Y +RL      + + + DS S    +D+EH LI  Y   L  ++  +++P + A    
Sbjct  1351  ASYVARL-----QHCTRVLDSPS---RLDEEHRLIARYAARLAAEAGNMTRPPTDASFNF  1506

Query  1024  SLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDA  1083
                 ++R    +++A+LE +NR +  E  RL+ +HE              PT  ++ ++ 
Sbjct  1507  DANKQQR----QLIAELENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNP  1644

Query  1084  ELIAEAKLLRQHK  1096
              L+AE +LLRQ K
Sbjct  1645  MLLAELRLLRQRK  1683


>gb|BC030924.1| Mus musculus dystrobrevin, beta, mRNA (cDNA clone MGC:31669 IMAGE:4910166), 
complete cds
Length=2329

 Score =  165 bits (417),  Expect = 2e-37, Method: Compositional matrix adjust.
 Identities = 135/493 (27%), Positives = 237/493 (48%), Gaps = 62/493 (12%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  269   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHSTEISVSRLETVI  448

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  449   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMVAAYDSEGRGKLTVFSVKAMLATMCGGK  622

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +L   L +++++P  + E  SFG +  E +VR+CF   
Sbjct  623   MLDKLRYIFSQMSDSNGLMMFGKLDQFLKEALKLPTAVFEGPSFGYT--EHAVRTCFP--  790

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C    ++GFRYR 
Sbjct  791   -QQKKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCHCESMMGFRYRC  967

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGED----VRDFAKVLKNKFRTKR  924
              +  NY +CQ+CF+ G  +  H   + M E+ +  +  +     +      + ++     
Sbjct  968   QQCHNYQLCQNCFWRGHASGAHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPSREPPHP  1147

Query  925   YFAKHPR----MGYL----PVQ----TVLE--GDNMETPASSPQLSHD------DTHSRI  964
              F + P     + +L    P+     TV+      + TP    Q S D      D H+ I
Sbjct  1148  VFPEQPEKPLDLAHLVPPRPLTNMNDTVVSHMSSGVPTPTKRLQYSQDMPNLLADEHALI  1327

Query  965   EHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSP-LSQPRSPAQILI  1023
               Y +RL      + + + DS S    +D+EH LI  Y   L  ++  +++P + A    
Sbjct  1328  ASYVARL-----QHCTRVLDSPS---RLDEEHRLIARYAARLAAEAGNMTRPPTDASFNF  1483

Query  1024  SLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDA  1083
                 ++R    +++A+LE +NR +  E  RL+ +HE              PT  ++ ++ 
Sbjct  1484  DANKQQR----QLIAELENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNP  1621

Query  1084  ELIAEAKLLRQHK  1096
              L+AE +LLRQ K
Sbjct  1622  MLLAELRLLRQRK  1660


>gb|DQ160290.1| Homo sapiens dystrobrevin beta isoform 6 (DTNB) mRNA, complete 
cds
Length=1809

 Score =  164 bits (416),  Expect = 2e-37, Method: Compositional matrix adjust.
 Identities = 138/502 (27%), Positives = 231/502 (46%), Gaps = 80/502 (15%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  76    NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  255

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  256   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  429

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  430   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  597

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  598   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  774

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT-----  904
              +  NY +CQ+CF+ G     H   + M E+                   C PT      
Sbjct  775   QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHP  954

Query  905   ----SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD--  958
                   E   D A ++  +  T         M    V  +  G  + TP    Q S D  
Sbjct  955   VFPEQPEKPLDLAHIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDIP  1104

Query  959   ----DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                 D H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  + 
Sbjct  1105  SHLADEHALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NV  1257

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMP  1074
              R P  +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              P
Sbjct  1258  TRPPTDLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QP  1401

Query  1075  TSPQSPRDAELIAEAKLLRQHK  1096
             T  ++ ++  L+AE +LLRQ K
Sbjct  1402  TPEKAQQNPTLLAELRLLRQRK  1467


>emb|Y15718.1| Homo sapiens mRNA for dystrobrevin B DTN-B2
Length=2573

 Score =  164 bits (416),  Expect = 2e-37, Method: Compositional matrix adjust.
 Identities = 138/502 (27%), Positives = 231/502 (46%), Gaps = 80/502 (15%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  76    NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  255

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  256   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  429

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  430   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  597

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  598   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  774

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT-----  904
              +  NY +CQ+CF+ G     H   + M E+                   C PT      
Sbjct  775   QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHP  954

Query  905   ----SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD--  958
                   E   D A ++  +  T         M    V  +  G  + TP    Q S D  
Sbjct  955   VFPEQPEKPLDLAHIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDIP  1104

Query  959   ----DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                 D H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  + 
Sbjct  1105  SHLADEHALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NV  1257

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMP  1074
              R P  +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              P
Sbjct  1258  TRPPTDLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QP  1401

Query  1075  TSPQSPRDAELIAEAKLLRQHK  1096
             T  ++ ++  L+AE +LLRQ K
Sbjct  1402  TPEKAQQNPTLLAELRLLRQRK  1467


>emb|Y15722.1| Homo sapiens mRNA for dystrobrevin B DTN-B1
Length=2244

 Score =  164 bits (416),  Expect = 2e-37, Method: Compositional matrix adjust.
 Identities = 138/502 (27%), Positives = 231/502 (46%), Gaps = 80/502 (15%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  76    NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  255

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  256   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  429

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  430   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  597

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  598   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  774

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT-----  904
              +  NY +CQ+CF+ G     H   + M E+                   C PT      
Sbjct  775   QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHP  954

Query  905   ----SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD--  958
                   E   D A ++  +  T         M    V  +  G  + TP    Q S D  
Sbjct  955   VFPEQPEKPLDLAHIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDIP  1104

Query  959   ----DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                 D H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  + 
Sbjct  1105  SHLADEHALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NV  1257

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMP  1074
              R P  +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              P
Sbjct  1258  TRPPTDLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QP  1401

Query  1075  TSPQSPRDAELIAEAKLLRQHK  1096
             T  ++ ++  L+AE +LLRQ K
Sbjct  1402  TPEKAQQNPTLLAELRLLRQRK  1467


>ref|XM_001621487.1| Nematostella vectensis predicted protein (NEMVEDRAFT_v1g221874) 
partial mRNA
Length=588

 Score =  164 bits (415),  Expect = 3e-37, Method: Compositional matrix adjust.
 Identities = 77/185 (41%), Positives = 119/185 (64%), Gaps = 2/185 (1%)
 Frame = +1

Query  601  WERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
            WER+ + + +PYYINHET+ T WDHP M +L Q LA+LNN++++AYRTAMKLR + K   
Sbjct  34   WERSETTSGIPYYINHETEKTQWDHPAMIQLMQDLAELNNIKYAAYRTAMKLRAIHKKTQ  213

Query  661  LDLLSLSAACDALDQHNLKQN--DQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMC  718
            L L+ +      LD+ ++     ++ + I +    +T ++     +  + +++P+  D+ 
Sbjct  214  LYLVEIPILTATLDEEDVPDGYTEKALSIPEASKIITALFINQNGDRQDFIDIPMASDLT  393

Query  719  LNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLL  778
            LN +LN+YD GRTG I+ LS K GI  LC A L+DKYRYLF+Q+ +S    D++RL L L
Sbjct  394  LNLMLNIYDPGRTGYIQALSLKIGISLLCAAKLQDKYRYLFRQMCNSRAVLDRKRLTLFL  573

Query  779  HDSIQ  783
             + +Q
Sbjct  574  QECLQ  588


>gb|AF143543.1|AF143543 Mus musculus alpha-dystrobrevin 2a mRNA, complete cds
Length=3144

 Score =  164 bits (415),  Expect = 3e-37, Method: Compositional matrix adjust.
 Identities = 149/549 (27%), Positives = 247/549 (44%), Gaps = 81/549 (14%)
 Frame = +3

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  357   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  536

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  537   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  716

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  717   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  881

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  882   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1061

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHP  930
               NY +CQ CF+ G     H   + M EY   T+     +     L          ++ P
Sbjct  1062  CHNYQLCQDCFWRGHAGGSHSNQHQMKEY---TSWKSPAKKLTNALSKSLSCAS--SREP  1226

Query  931   RMGYLPVQTVLEGDNMETPASSPQLSHDDT------HSRIEHYASRLAEMENS-------  977
                  P Q     +        P  S +DT       S    + +R +  ++S       
Sbjct  1227  LHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSEVEQNKM  1406

Query  978   ---------NGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPL----------------  1012
                       G  +  S++  + + DEH+LI  Y   L  + P                 
Sbjct  1407  LARAAPAFLKGRGIQYSLNVADRLADEHVLIGLYVNMLRNNPPCMLESSNRLDEEHRLIA  1586

Query  1013  ------------SQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQ  1057
                         SQP   RS   I  ++++ +  +  +++A+LE +NR +  E  RL+ +
Sbjct  1587  RYAARLAAESSSSQPTQQRSAPDISFTIDANK--QQRQLIAELENKNREILQEIQRLRVE  1760

Query  1058  HEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQL  1117
             HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  ++L  QL
Sbjct  1761  HEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRRELMVQL  1910

Query  1118  HRLRQLLEQ  1126
               L +LL++
Sbjct  1911  EGLMKLLKE  1937


>gb|AF143544.1|AF143544 Mus musculus alpha-dystrobrevin 2b mRNA, complete cds
Length=1969

 Score =  164 bits (415),  Expect = 3e-37, Method: Compositional matrix adjust.
 Identities = 147/549 (26%), Positives = 248/549 (45%), Gaps = 81/549 (14%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  266   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  445

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  446   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  625

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  626   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  790

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  791   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCPQ  970

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHP  930
               NY +CQ CF+ G     H   + M EY   T+     +     L          ++ P
Sbjct  971   CHNYQLCQDCFWRGHAGGSHSNQHQMKEY---TSWKSPAKKLTNALSKSLSCAS--SREP  1135

Query  931   RMGYLPVQTVLEGDNMETPASSPQLSHDDT------HSRIEHYASRLAEMENS-------  977
                  P Q     +        P  S +DT       S    + +R +  ++S       
Sbjct  1136  LHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSEVEQNKM  1315

Query  978   ---------NGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPL----------------  1012
                       G  +  S++  + + DEH+LI  Y   L  + P                 
Sbjct  1316  LARAAPAFLKGRGIQYSLNVADRLADEHVLIGLYVNMLRNNPPCMLESSNRLDEEHRLIA  1495

Query  1013  ------------SQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQ  1057
                         SQP   RS   I  ++++ +  +  +++A+LE +NR +  E  RL+ +
Sbjct  1496  RYAARLAAESSSSQPTQQRSAPDISFTIDANK--QQRQLIAELENKNREILQEIQRLRVE  1669

Query  1058  HEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQL  1117
             HE              PT  ++ ++  L+AE +LLRQ K  LE RM  L++  ++L  QL
Sbjct  1670  HEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELEQRMSALQESRRELMVQL  1819

Query  1118  HRLRQLLEQ  1126
               L +LL++
Sbjct  1820  EGLMKLLKE  1846


>ref|XM_515336.2| PREDICTED: Pan troglodytes dystrobrevin, beta (DTNB), mRNA
Length=2487

 Score =  164 bits (415),  Expect = 3e-37, Method: Compositional matrix adjust.
 Identities = 138/502 (27%), Positives = 231/502 (46%), Gaps = 80/502 (15%)
 Frame = +3

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  339   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  518

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  519   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  692

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  693   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  860

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  861   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  1037

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT-----  904
              +  NY +CQ+CF+ G     H   + M E+                   C PT      
Sbjct  1038  QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHP  1217

Query  905   ----SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD--  958
                   E   D A ++  +  T         M    V  +  G  + TP    Q S D  
Sbjct  1218  VFPEQPEKPLDLAHIVPPRPLTN--------MNDTVVSHMSSG--VPTPTKRLQYSQDIP  1367

Query  959   ----DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                 D H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  + 
Sbjct  1368  SHLADEHALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NV  1520

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMP  1074
              R P  +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              P
Sbjct  1521  TRPPTDLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QP  1664

Query  1075  TSPQSPRDAELIAEAKLLRQHK  1096
             T  ++ ++  L+AE +LLRQ K
Sbjct  1665  TPEKAQQNPTLLAELRLLRQRK  1730


>dbj|AK300019.1| Homo sapiens cDNA FLJ60874 complete cds, highly similar to Dystrobrevin 
beta
Length=2050

 Score =  164 bits (414),  Expect = 3e-37, Method: Compositional matrix adjust.
 Identities = 138/502 (27%), Positives = 231/502 (46%), Gaps = 80/502 (15%)
 Frame = +3

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  216   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  395

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  396   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  569

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  570   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  737

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  738   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  914

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT-----  904
              +  NY +CQ+CF+ G     H   + M E+                   C PT      
Sbjct  915   QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHP  1094

Query  905   ----SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD--  958
                   E   D A ++  +  T         M    V  +  G  + TP    Q S D  
Sbjct  1095  VFPEQPEKPLDLAHIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDIP  1244

Query  959   ----DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                 D H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  + 
Sbjct  1245  SHLADEHALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NV  1397

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMP  1074
              R P  +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              P
Sbjct  1398  TRPPTDLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QP  1541

Query  1075  TSPQSPRDAELIAEAKLLRQHK  1096
             T  ++ ++  L+AE +LLRQ K
Sbjct  1542  TPEKAQQNPTLLAELRLLRQRK  1607


>ref|NM_021907.3| Homo sapiens dystrobrevin, beta (DTNB), transcript variant 1, 
mRNA
Length=2496

 Score =  164 bits (414),  Expect = 3e-37, Method: Compositional matrix adjust.
 Identities = 138/502 (27%), Positives = 231/502 (46%), Gaps = 80/502 (15%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  326   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  505

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  506   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  679

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  680   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  847

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  848   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  1024

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT-----  904
              +  NY +CQ+CF+ G     H   + M E+                   C PT      
Sbjct  1025  QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHP  1204

Query  905   ----SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD--  958
                   E   D A ++  +  T         M    V  +  G  + TP    Q S D  
Sbjct  1205  VFPEQPEKPLDLAHIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDIP  1354

Query  959   ----DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                 D H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  + 
Sbjct  1355  SHLADEHALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NV  1507

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMP  1074
              R P  +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              P
Sbjct  1508  TRPPTDLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QP  1651

Query  1075  TSPQSPRDAELIAEAKLLRQHK  1096
             T  ++ ++  L+AE +LLRQ K
Sbjct  1652  TPEKAQQNPTLLAELRLLRQRK  1717


>ref|NM_033147.2| Homo sapiens dystrobrevin, beta (DTNB), transcript variant 2, 
mRNA
Length=2406

 Score =  164 bits (414),  Expect = 3e-37, Method: Compositional matrix adjust.
 Identities = 138/502 (27%), Positives = 231/502 (46%), Gaps = 80/502 (15%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  326   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  505

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  506   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  679

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  680   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  847

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  848   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  1024

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT-----  904
              +  NY +CQ+CF+ G     H   + M E+                   C PT      
Sbjct  1025  QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHP  1204

Query  905   ----SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD--  958
                   E   D A ++  +  T         M    V  +  G  + TP    Q S D  
Sbjct  1205  VFPEQPEKPLDLAHIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDIP  1354

Query  959   ----DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                 D H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  + 
Sbjct  1355  SHLADEHALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NV  1507

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMP  1074
              R P  +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              P
Sbjct  1508  TRPPTDLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QP  1651

Query  1075  TSPQSPRDAELIAEAKLLRQHK  1096
             T  ++ ++  L+AE +LLRQ K
Sbjct  1652  TPEKAQQNPTLLAELRLLRQRK  1717


>ref|NM_183360.1| Homo sapiens dystrobrevin, beta (DTNB), transcript variant 4, 
mRNA
Length=2433

 Score =  164 bits (414),  Expect = 3e-37, Method: Compositional matrix adjust.
 Identities = 138/502 (27%), Positives = 231/502 (46%), Gaps = 80/502 (15%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  326   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  505

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  506   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  679

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  680   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  847

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  848   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  1024

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT-----  904
              +  NY +CQ+CF+ G     H   + M E+                   C PT      
Sbjct  1025  QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHP  1204

Query  905   ----SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD--  958
                   E   D A ++  +  T         M    V  +  G  + TP    Q S D  
Sbjct  1205  VFPEQPEKPLDLAHIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDIP  1354

Query  959   ----DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                 D H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  + 
Sbjct  1355  SHLADEHALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NV  1507

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMP  1074
              R P  +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              P
Sbjct  1508  TRPPTDLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QP  1651

Query  1075  TSPQSPRDAELIAEAKLLRQHK  1096
             T  ++ ++  L+AE +LLRQ K
Sbjct  1652  TPEKAQQNPTLLAELRLLRQRK  1717


>gb|AF022728.1|AF022728 Homo sapiens beta-dystrobrevin (BDTN) mRNA, complete cds
Length=2407

 Score =  164 bits (414),  Expect = 3e-37, Method: Compositional matrix adjust.
 Identities = 138/502 (27%), Positives = 231/502 (46%), Gaps = 80/502 (15%)
 Frame = +3

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  237   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  416

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  417   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  590

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  591   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  758

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  759   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  935

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT-----  904
              +  NY +CQ+CF+ G     H   + M E+                   C PT      
Sbjct  936   QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHP  1115

Query  905   ----SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD--  958
                   E   D A ++  +  T         M    V  +  G  + TP    Q S D  
Sbjct  1116  VFPEQPEKPLDLAHIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDIP  1265

Query  959   ----DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                 D H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  + 
Sbjct  1266  SHLADEHALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NV  1418

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMP  1074
              R P  +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              P
Sbjct  1419  TRPPTDLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QP  1562

Query  1075  TSPQSPRDAELIAEAKLLRQHK  1096
             T  ++ ++  L+AE +LLRQ K
Sbjct  1563  TPEKAQQNPTLLAELRLLRQRK  1628


>gb|BC081889.1| Rattus norvegicus dystrobrevin, beta, mRNA (cDNA clone MGC:93784 
IMAGE:7109493), complete cds
Length=3431

 Score =  164 bits (414),  Expect = 4e-37, Method: Compositional matrix adjust.
 Identities = 137/498 (27%), Positives = 231/498 (46%), Gaps = 76/498 (15%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  362   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHATEISVSRLETVI  541

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   +NV   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  542   SSIYYQLNKRLPSTHQ--INVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  715

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +L   L +++++P  + E  SFG +  E +VR+CF   
Sbjct  716   MLDKLRYIFSQMSDSNGLMMFGKLDQFLKEALKLPTAVFEGPSFGYT--EHAVRTCFP--  883

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C    ++GFRYR 
Sbjct  884   -QQKKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCHCESMMGFRYRC  1060

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT-----  904
              +  NY +CQ+CF+ G     H   + M E                    C P+      
Sbjct  1061  QQCHNYQLCQNCFWRGHAGGPHSNQHQMKELSSWKSPAKKLSHAISKSLGCVPSREPPHP  1240

Query  905   ----SGEDVRDFAKVLKNKFRTKR--YFAKHPRMGY-LPVQTVLEGDNMETPASSPQLSH  957
                   E   D A ++  +  T        H   G   P + +  G +M      P L  
Sbjct  1241  VFPEQPEKPLDLAHIVPPRPLTNMNDTMVSHMSSGVPTPTKRLQYGQDM------PNLLA  1402

Query  958   DDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSP-LSQPR  1016
             D+ H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  +++P 
Sbjct  1403  DE-HALIASYVARL-----QHCTRVLDSPS---RLDEEHRLIARYAARLAAEAGNMTRPP  1555

Query  1017  SPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTS  1076
             + A        ++R    +++A+LE +NR +  E  RL+ +HE              PT 
Sbjct  1556  TDASFNFDANKQQR----QLIAELENKNREILQEIQRLRLEHEQAS----------QPTP  1693

Query  1077  PQSPRDAELIAEAKLLRQ  1094
              ++ ++  L+AE +LLRQ
Sbjct  1694  EKAQQNPTLLAELRLLRQ  1747


>emb|Y15742.1| Mus musculus mRNA for dystrobrevin B, partial
Length=2192

 Score =  163 bits (413),  Expect = 5e-37, Method: Compositional matrix adjust.
 Identities = 134/493 (27%), Positives = 236/493 (47%), Gaps = 62/493 (12%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  166   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHSTEISVSRLETVI  345

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  346   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMVAAYDSEGRGKLTVFSVKAMLATMCGGK  519

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +L   L +++++P  + E  SFG +  E +VR+CF   
Sbjct  520   MLDKLRYIFSQMSDSNGLMMFGKLDQFLKEALKLPTAVFEGPSFGYT--EHAVRTCFP--  687

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C    ++GFRYR 
Sbjct  688   -QQKKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCHCESMMGFRYRC  864

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGED----VRDFAKVLKNKFRTKR  924
              +  NY +CQ+CF+ G  +  H   + M E+ +  +  +     +      + ++     
Sbjct  865   QQCHNYQLCQNCFWRGHASGAHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPSREPPHP  1044

Query  925   YFAKHPR----MGYL----PVQ----TVLE--GDNMETPASSPQLSHD------DTHSRI  964
              F + P     + +L    P+     TV+      + TP    Q S D      D H+ I
Sbjct  1045  VFPEQPEKPLDLAHLVPPRPLTNMNDTVVSHMSSGVPTPTKRLQYSQDMPNLLADEHALI  1224

Query  965   EHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHY-CQSLNQDSPLSQPRSPAQILI  1023
               Y +RL      + + + DS S    +D+EH LI  Y  +   +   +++P + A    
Sbjct  1225  ASYVARL-----QHCTRVLDSPS---RLDEEHRLIARYAARPAAEAGNMTRPPTDASFNF  1380

Query  1024  SLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDA  1083
                 ++R    +++A+LE +NR +  E  RL+ +HE              PT  ++ ++ 
Sbjct  1381  DANKQQR----QLIAELENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNP  1518

Query  1084  ELIAEAKLLRQHK  1096
              L+AE +LLRQ K
Sbjct  1519  MLLAELRLLRQRK  1557


>gb|BC049366.1| Homo sapiens dystrobrevin, beta, mRNA (cDNA clone MGC:57126 IMAGE:4817552), 
complete cds
Length=2435

 Score =  163 bits (412),  Expect = 7e-37, Method: Compositional matrix adjust.
 Identities = 138/502 (27%), Positives = 230/502 (45%), Gaps = 80/502 (15%)
 Frame = +3

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  330   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  509

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN++   YD+   G++ V S K  + ++C   
Sbjct  510   SSIYYQLNKRLHSTHQ--ISVEQSISLLLNFMTAAYDSEGRGKLTVFSVKAMLATMCGGK  683

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  684   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  851

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  852   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  1028

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT-----  904
              +  NY +CQ+CF+ G     H   + M E+                   C PT      
Sbjct  1029  QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHP  1208

Query  905   ----SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD--  958
                   E   D A ++  +  T         M    V  +  G  + TP    Q S D  
Sbjct  1209  VFPEQPEKPLDLAHIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDIP  1358

Query  959   ----DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                 D H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  + 
Sbjct  1359  SHLADEHALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NV  1511

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMP  1074
              R P  +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              P
Sbjct  1512  TRPPTDLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QP  1655

Query  1075  TSPQSPRDAELIAEAKLLRQHK  1096
             T  ++ ++  L+AE +LLRQ K
Sbjct  1656  TPEKAQQNPTLLAELRLLRQRK  1721


>gb|U46745.1|HSU46745 Human dystrobrevin-beta mRNA, complete cds
Length=2817

 Score =  163 bits (412),  Expect = 7e-37, Method: Compositional matrix adjust.
 Identities = 150/550 (27%), Positives = 256/550 (46%), Gaps = 83/550 (15%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  347   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  523

Query  694   LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
             L+TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  524   LSTIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  703

Query  752   EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  704   MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  868

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  869   QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  1048

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRD-FAKVLKNKFRTKRYFAK  928
             +  NY +CQ CF+ G     H   + M EY +  +  + + +  +K L      K     
Sbjct  1049  QCHNYQLCQDCFWRGHAGGSHSNQHQMKEYTSWKSPAKKLTNALSKSLSCASSRKPLHPM  1228

Query  929   HP-------RMGYL----PVQTVLE----------GDNMETPASSPQLSHDDTHSRIEHY  967
              P        + ++    PV ++ +          G    T +S P+ S  + +  +   
Sbjct  1229  FPDQPEKPLNLAHIVPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSEVEQNKLLARA  1408

Query  968   ASRLAEMENSNGSYLNDSISPNESIDDEHLLI----------------------------  999
             A    +     G  +  S++  + + DEH+LI                            
Sbjct  1409  APAFLK-----GKGIQYSLNVADRLADEHVLIGLYVNMLRNNPSCMLESSNRLDEEHRLI  1573

Query  1000  QHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQ  1056
               Y   L  +S  SQP   RS   I  ++++ +  +  +++A+LE +NR +  E  RL+ 
Sbjct  1574  ARYAARLAAESSSSQPPQQRSAPDISFTIDANK--QQRQLIAELENKNREILQEIQRLRL  1747

Query  1057  QHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQ  1116
             +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  ++L  Q
Sbjct  1748  EHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRRELMVQ  1897

Query  1117  LHRLRQLLEQ  1126
             L  L +LL++
Sbjct  1898  LEGLMKLLKE  1927


>ref|NM_058459.4| Caenorhabditis elegans DYstroBrevin homolog family member (dyb-1) 
(dyb-1) mRNA, complete cds
Length=1948

 Score =  162 bits (411),  Expect = 8e-37, Method: Compositional matrix adjust.
 Identities = 140/499 (28%), Positives = 220/499 (44%), Gaps = 73/499 (14%)
 Frame = +3

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIIN--  692
             L D +++RF+ YR A KLR +Q+   + L+ +    +A  ++ L  N  P+  +   +  
Sbjct  156   LQDFDSIRFATYRAACKLRFIQQKTKVHLVDIWNMIEAFRENGL--NALPLHTVIKTSRA  329

Query  693   --CLTTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCK  748
                LTT++  L +    +  V+  + + + L +LL  YD   TGR+ V S K  + +LC 
Sbjct  330   ELLLTTVFHNLNKRLVASQHVDTDVSISLLLAFLLGAYDKQNTGRLTVFSIKVALATLCA  509

Query  749   AHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
               L DK RY+F Q+A S G  D  +    L   + +   + E  +FG S  E +V  CF 
Sbjct  510   GKLVDKLRYIFSQIADSNGLMDHIKFTDFLQQILSLTTAVFEAPTFGFS--ENAVNQCF-  680

Query  809   FANNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRY  866
               +   ++   +FLD    +P    ++WLP+LHR+A+     H   C+ C+     GFRY
Sbjct  681   --HKDEKVSLNVFLDTFLSDPCPPCIMWLPLLHRMASVSNVYHPVVCDACQVRSFTGFRY  854

Query  867   RSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYF  926
             +  +  NY +CQSCF+ GR ++ H   + M EY +                 K  TK+  
Sbjct  855   KCQRCANYQLCQSCFWRGRTSQNHSNEHEMKEYSS----------------YKSPTKQLV  986

Query  927   -AKHPRMGYLPVQTVLEGDNMET-------PASSPQ---------LSHDDTHSRIEHYAS  969
              + H  +  +P  + +   N++        P SS           +    T  R +H A+
Sbjct  987   HSIHKSLQCIPATSTVGDANIDIFNAKIGGPVSSKPARPLNLNNIVPATPTTIRRQHAAT  1166

Query  970   RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN--QDSPLSQPRSPAQILISLES  1027
               A+   S    L    S    IDDEH LI  Y   L+   D PLS  R       S+ S
Sbjct  1167  SSADWPTS-PVLLPGQASHGGVIDDEHKLIARYAAKLSGRADYPLSNGR-------SMNS  1322

Query  1028  EERGELERILADLEEENRNLQAEYDRLKQQ-HEHKGLSPLPSPPEMMPTSPQSPRDAELI  1086
                G+   ++A LEEEN  +  E  RL+ Q     GL+ L              RD ++ 
Sbjct  1323  SMVGDERTLIAQLEEENSMMVREMARLESQTTSDDGLAGL--------------RDRKME  1460

Query  1087  AEAKLLRQHKGRLEARMQI  1105
              E K+    + R E  MQ+
Sbjct  1461  LEEKMFEMQQRRRELMMQL  1517


>emb|AJ131742.1| Caenorhabditis elegans mRNA for dystrobrevin
Length=1773

 Score =  162 bits (411),  Expect = 9e-37, Method: Compositional matrix adjust.
 Identities = 140/499 (28%), Positives = 220/499 (44%), Gaps = 73/499 (14%)
 Frame = +1

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIIN--  692
             L D +++RF+ YR A KLR +Q+   + L+ +    +A  ++ L  N  P+  +   +  
Sbjct  133   LQDFDSIRFATYRAACKLRFIQQKTKVHLVDIWNMIEAFRENGL--NALPLHTVIKTSRA  306

Query  693   --CLTTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCK  748
                LTT++  L +    +  V+  + + + L +LL  YD   TGR+ V S K  + +LC 
Sbjct  307   ELLLTTVFHNLNKRLVASQHVDTDVSISLLLAFLLGAYDKQNTGRLTVFSIKVALATLCA  486

Query  749   AHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
               L DK RY+F Q+A S G  D  +    L   + +   + E  +FG S  E +V  CF 
Sbjct  487   GKLVDKLRYIFSQIADSNGLMDHIKFTDFLQQILSLTTAVFEAPTFGFS--ENAVNQCF-  657

Query  809   FANNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRY  866
               +   ++   +FLD    +P    ++WLP+LHR+A+     H   C+ C+     GFRY
Sbjct  658   --HKDEKVSLNVFLDTFLSDPCPPCIMWLPLLHRMASVSNVYHPVVCDACQVRSFTGFRY  831

Query  867   RSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYF  926
             +  +  NY +CQSCF+ GR ++ H   + M EY +                 K  TK+  
Sbjct  832   KCQRCANYQLCQSCFWRGRTSQNHSNEHEMKEYSS----------------YKSPTKQLV  963

Query  927   -AKHPRMGYLPVQTVLEGDNMET-------PASSPQ---------LSHDDTHSRIEHYAS  969
              + H  +  +P  + +   N++        P SS           +    T  R +H A+
Sbjct  964   HSIHKSLQCIPATSTVGDANIDIFNAKIGGPVSSKPARPLNLNNIVPATPTTIRRQHAAT  1143

Query  970   RLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN--QDSPLSQPRSPAQILISLES  1027
               A+   S    L    S    IDDEH LI  Y   L+   D PLS  R       S+ S
Sbjct  1144  SSADWPTS-PVLLPGQASHGGVIDDEHKLIARYAAKLSGRADYPLSNGR-------SMNS  1299

Query  1028  EERGELERILADLEEENRNLQAEYDRLKQQ-HEHKGLSPLPSPPEMMPTSPQSPRDAELI  1086
                G+   ++A LEEEN  +  E  RL+ Q     GL+ L              RD ++ 
Sbjct  1300  SMVGDERTLIAQLEEENSMMVREMARLESQTTSDDGLAGL--------------RDRKME  1437

Query  1087  AEAKLLRQHKGRLEARMQI  1105
              E K+    + R E  MQ+
Sbjct  1438  LEEKMFEMQQRRRELMMQL  1494


>ref|XM_001380100.1| PREDICTED: Monodelphis domestica similar to beta-dystrobrevin 
(LOC100030691), mRNA
Length=2139

 Score =  162 bits (411),  Expect = 9e-37, Method: Compositional matrix adjust.
 Identities = 140/501 (27%), Positives = 232/501 (46%), Gaps = 78/501 (15%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDI----LQIIN  692
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I    L+ I 
Sbjct  76    NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHNTEISVSRLETI-  252

Query  693   CLTTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCK  748
              +++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C 
Sbjct  253   -ISSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCG  423

Query  749   AHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
               + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF 
Sbjct  424   GKMLDKLRYIFSQMSDSNGLMIFNKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP  597

Query  809   FANNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRY  866
                 + +I   +FLD +  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRY
Sbjct  598   ---QQKKIMLNMFLDTLMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRY  768

Query  867   RSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT---  904
             R  +  NY +CQ+CF+ G     H   + M E+                   C PT    
Sbjct  769   RCQQCHNYQLCQNCFWRGHANGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPP  948

Query  905   ------SGEDVRDFAKVLKNKFRTKR--YFAKHPRMGYLPVQTVLEGDNMETPASSPQLS  956
                     E   D A ++  +  T        H   G +P  T     + E P      S
Sbjct  949   HPVFPEQPEKPLDLAHIVPPRPLTNMNDTMVSHMSSG-VPTPTKRLQYSQEIP------S  1107

Query  957   H-DDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQP  1015
             H  D H+ I  Y SRL      + + + DS S    +D+EH LI  Y   L  ++  +  
Sbjct  1108  HLADEHALIASYVSRL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NVT  1260

Query  1016  RSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPT  1075
             R P  +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              PT
Sbjct  1261  RPPTDLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QPT  1404

Query  1076  SPQSPRDAELIAEAKLLRQHK  1096
               ++ ++  L+AE +LLRQ K
Sbjct  1405  PEKAQQNPTLLAELRLLRQRK  1467


>ref|NM_032978.6| Homo sapiens dystrobrevin, alpha (DTNA), transcript variant 4, 
mRNA
Length=4579

 Score =  162 bits (410),  Expect = 1e-36, Method: Compositional matrix adjust.
 Identities = 150/550 (27%), Positives = 249/550 (45%), Gaps = 83/550 (15%)
 Frame = +3

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  291   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  467

Query  694   LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
             L+TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  468   LSTIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  647

Query  752   EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  648   MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  812

Query  812   NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  813   QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  992

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKH  929
             +  NY +CQ CF+ G     H   + M EY   T+     +     L          ++ 
Sbjct  993   QCHNYQLCQDCFWRGHAGGSHSNQHQMKEY---TSWKSPAKKLTNALSKSLSCAS--SRE  1157

Query  930   PRMGYLPVQTVLEGDNMETPASSPQLSHDDT------HSRIEHYASRLAEMENS------  977
             P     P Q     +        P  S +DT       S    + +R +  ++S      
Sbjct  1158  PLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSEVEQNK  1337

Query  978   ----------NGSYLNDSISPNESIDDEHLLI----------------------------  999
                        G  +  S++  + + DEH+LI                            
Sbjct  1338  LLARAAPAFLKGKGIQYSLNVADRLADEHVLIGLYVNMLRNNPSCMLESSNRLDEEHRLI  1517

Query  1000  QHYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQ  1056
               Y   L  +S  SQP   RS   I  ++++ +  +  +++A+LE +NR +  E  RL+ 
Sbjct  1518  ARYAARLAAESSSSQPPQQRSAPDISFTIDANK--QQRQLIAELENKNREILQEIQRLRL  1691

Query  1057  QHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQ  1116
             +HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  ++L  Q
Sbjct  1692  EHEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRRELMVQ  1841

Query  1117  LHRLRQLLEQ  1126
             L  L +LL++
Sbjct  1842  LEGLMKLLKE  1871


>dbj|AK301386.1| Homo sapiens cDNA FLJ58632 complete cds, highly similar to Dystrobrevin 
beta
Length=2330

 Score =  162 bits (410),  Expect = 1e-36, Method: Compositional matrix adjust.
 Identities = 138/502 (27%), Positives = 230/502 (45%), Gaps = 80/502 (15%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  212   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  391

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H    +V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  392   SSIYYQLNKRLPSTHQ--TSVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  565

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  566   MLDKLRYVFSQMSDSNGLMIFSKFDQFLTEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  733

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  734   -QQRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  910

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT-----  904
              +  NY +CQ+CF+ G     H   + M E+                   C PT      
Sbjct  911   QQCHNYQLCQNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHP  1090

Query  905   ----SGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD--  958
                   E   D A ++  +  T         M    V  +  G  + TP    Q S D  
Sbjct  1091  VFPEQPEKPLDLAHIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDIP  1240

Query  959   ----DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQ  1014
                 D H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  + 
Sbjct  1241  SHLADEHALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEAG-NV  1393

Query  1015  PRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMP  1074
              R P  +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              P
Sbjct  1394  TRPPTDLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QP  1537

Query  1075  TSPQSPRDAELIAEAKLLRQHK  1096
             T  ++ ++  L+AE +LLRQ K
Sbjct  1538  TPEKAQQNPTLLAELRLLRQRK  1603


>ref|XM_001667709.1| Caenorhabditis briggsae hypothetical protein CBG22285 partial 
mRNA
Length=1755

 Score =  161 bits (408),  Expect = 2e-36, Method: Compositional matrix adjust.
 Identities = 140/495 (28%), Positives = 217/495 (43%), Gaps = 68/495 (13%)
 Frame = +1

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQIIN--  692
             L D +++RF+ YR A KLR +Q+   + L+ +    +A  ++ L  N  P+  +   +  
Sbjct  127   LQDFDSIRFATYRAACKLRFIQQKTKVHLVDIWNMIEAFRENGL--NALPLHTVIKTSRA  300

Query  693   --CLTTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCK  748
                LTT++  L +    +  V+  + + + L +LL  YD   TGR+ V S K  + +LC 
Sbjct  301   ELLLTTVFHNLNKRLVASQHVDTDVSISLLLAFLLGAYDKQNTGRLTVFSIKVALATLCA  480

Query  749   AHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
               L DK RY+F Q+A S G  D  +    L   + +   + E  +FG S  E +V  CF 
Sbjct  481   GKLVDKLRYIFSQIADSNGLMDHIKFTDFLQQVLSLTTAVFEAPTFGFS--ESAVTQCF-  651

Query  809   FANNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRY  866
               +   ++   +FLD    +P    ++WLP+LHR+AA     H   C+ C+     GFRY
Sbjct  652   --HKDDKVSLNVFLDTFLSDPCPPCIMWLPLLHRMAAVSNVYHPVVCDACQVRSFTGFRY  825

Query  867   RSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYF  926
             +  +  NY +CQSCF+ GR ++ H   + M EY          +  AK L +        
Sbjct  826   KCQRCANYQLCQSCFWRGRTSQNHSNEHEMKEY-------SSYKSPAKQLVHSI------  966

Query  927   AKHPRMGYLPVQTVLEG-----DNMETPASSPQ--------LSHDDTHSRIEHYASRLAE  973
               H  +  +P  +  +      +    P   P         +    T  R +H A+  A+
Sbjct  967   --HKSLQCIPASSSGDANIDILNTTGVPIGKPTRPLNLNNIVPATPTTIRRQHAATSSAD  1140

Query  974   MENSNGSYLNDSISPNESIDDEHLLIQHYCQSLN--QDSPLSQPRSPAQILISLESEERG  1031
                S    L    S    IDDEH LI  Y   L+   D PLS  RS    +I    +ER 
Sbjct  1141  WPTS-PVLLPGQASHGGVIDDEHKLIARYAAKLSGRADYPLSNGRSMNSSMI---EDER-  1305

Query  1032  ELERILADLEEENRNLQAEYDRLKQQ-HEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAK  1090
                 ++A LEEEN  +  E  RL+ Q     GL+ L              RD ++  E K
Sbjct  1306  ---TLIAQLEEENSMMVREMARLESQTTSDDGLAGL--------------RDRKMELEEK  1434

Query  1091  LLRQHKGRLEARMQI  1105
             +    + R E  MQ+
Sbjct  1435  MFEMQQRRRELMMQL  1479


>ref|XM_001054053.1| PREDICTED: Rattus norvegicus similar to dystrobrevin alpha isoform 
1 (predicted), transcript variant 1 (RGD1561985_predicted), 
mRNA
Length=2111

 Score =  161 bits (407),  Expect = 3e-36, Method: Compositional matrix adjust.
 Identities = 145/549 (26%), Positives = 249/549 (45%), Gaps = 81/549 (14%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  409   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  588

Query  695   TTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +T++ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  589   STMFYQLNKRMPSTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  768

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  769   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  933

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  934   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1113

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHP  930
               NY +CQ CF+ G     H   + M EY   T+     +     L          ++ P
Sbjct  1114  CHNYQLCQDCFWRGHAGGSHSNQHQMKEY---TSWKSPAKKLTNALSKSLSCAS--SREP  1278

Query  931   RMGYLPVQTVLEGDNMETPASSPQLSHDDT------HSRIEHYASRLAEMENS-------  977
                  P Q     +        P  S +DT       S    + +R +  ++S       
Sbjct  1279  LHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSEVEQNKI  1458

Query  978   ---------NGSYLNDSISPNESIDDEHLLI----------------------------Q  1000
                       G  ++ S++  + + DEH+LI                             
Sbjct  1459  LARAAPAFLKGKGIHYSLNVADRLADEHVLIGLYVNMLRNNPSCMLESSNRLDEEHRLIA  1638

Query  1001  HYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQ  1057
              Y   L  +S  SQP   RS   +  ++++ +  +  +++A+LE +NR +  E  RL+ +
Sbjct  1639  RYAARLAAESSSSQPTQQRSAPDVSFTIDANK--QQRQLIAELENKNREILQEIQRLRVE  1812

Query  1058  HEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQL  1117
             HE              PT  ++ ++  L+AE +LLRQ K  LE RM  L++  ++L  QL
Sbjct  1813  HEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELEQRMSALQESRRELMVQL  1962

Query  1118  HRLRQLLEQ  1126
               L +LL++
Sbjct  1963  EGLMKLLKE  1989


>ref|XM_001054243.1| PREDICTED: Rattus norvegicus similar to dystrobrevin alpha isoform 
1 (predicted), transcript variant 3 (RGD1561985_predicted), 
mRNA
Length=2080

 Score =  160 bits (406),  Expect = 3e-36, Method: Compositional matrix adjust.
 Identities = 147/549 (26%), Positives = 248/549 (45%), Gaps = 81/549 (14%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  257   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  436

Query  695   TTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +T++ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  437   STMFYQLNKRMPSTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  616

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  617   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  781

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  782   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  961

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHP  930
               NY +CQ CF+ G     H   + M EY   T+     +     L          ++ P
Sbjct  962   CHNYQLCQDCFWRGHAGGSHSNQHQMKEY---TSWKSPAKKLTNALSKSLSCAS--SREP  1126

Query  931   RMGYLPVQTVLEGDNMETPASSPQLSHDDT------HSRIEHYASRLAEMENS-------  977
                  P Q     +        P  S +DT       S    + +R +  ++S       
Sbjct  1127  LHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHSVPSSGSPFITRSSPPKDSEVEQNKI  1306

Query  978   ---------NGSYLNDSISPNESIDDEHLLI----------------------------Q  1000
                       G  ++ S++  + + DEH+LI                             
Sbjct  1307  LARAAPAFLKGKGIHYSLNVADRLADEHVLIGLYVNMLRNNPSCMLESSNRLDEEHRLIA  1486

Query  1001  HYCQSLNQDSPLSQP---RSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQ  1057
              Y   L  +S  SQP   RS   +  ++++ +  +  +++A+LE +NR +  E  RL+ +
Sbjct  1487  RYAARLAAESSSSQPTQQRSAPDVSFTIDANK--QQRQLIAELENKNREILQEIQRLRVE  1660

Query  1058  HEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQL  1117
             HE     P P   +  PT         L+AE +LLRQ K  LE RM  L++  ++L  QL
Sbjct  1661  HEQAS-QPTPEKAQQNPT---------LLAELRLLRQRKDELEQRMSALQESRRELMVQL  1810

Query  1118  HRLRQLLEQ  1126
               L +LL++
Sbjct  1811  EGLMKLLKE  1837


>tpd|BR000175.1| TPA_exp: Ciona intestinalis Ci-ZF(ZZ)-4 mRNA for zinc finger 
protein, complete cds
Length=2253

 Score =  159 bits (403),  Expect = 8e-36, Method: Compositional matrix adjust.
 Identities = 128/431 (29%), Positives = 205/431 (47%), Gaps = 44/431 (10%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDILQI--INCL  694
             + ++++FS YRT++KL R+Q A  L  ++ +     + +  L + +  +D +    +N  
Sbjct  140   EFHDIKFSVYRTSLKLGRIQDAFHLRGITTTTLYSKVKKLILNKTNTSIDNVTTEGMN--  313

Query  695   TTIYDRLEQ-----EHNNLVNVP--LCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLC  747
                Y+ LE       H++L  V   LC  +C   +   +      R+ V++     I L 
Sbjct  314   ---YEELEGLVRSLYHDSLSKVSKKLCECLC-TLVFQTFQDFTENRVSVIAVVLFFIILG  481

Query  748   KAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCF  807
                L  KY+ LF   + S     + R GL+L   +++   +GE  +FG  NI  ++ SCF
Sbjct  482   GEELVKKYKLLFSLYSGSLRMLTRSRCGLMLAHCVRLTDVVGEDINFG--NISSAIASCF  655

Query  808   QFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYR  867
                      E  L L W+  EPQS+VWLP +HR+  A+++ H+ +C  CK  PIIG R++
Sbjct  656   SGVLGASISEQQL-LQWLFKEPQSLVWLPTMHRLNLAKSSVHEVQCAECKIRPIIGLRFQ  832

Query  868   SLKHFNYDICQSCFFS-GRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYF  926
              LK  +YD C  CF +    ++ HK+++P  EYCTP    E V  FA+ ++N   TKRY 
Sbjct  833   CLKCLDYDTCHHCFLTQSNSSRSHKLNHPRQEYCTPAGGREKVNAFARTIRN-IVTKRYK  1009

Query  927   AKHPRMGYLPVQTVLEGDN--METPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLND  984
              K     +LP+      DN  MET     +L+       I H A+  AE E      L  
Sbjct  1010  QKPLSSSFLPIDQSPSSDNVVMET---RDKLNESSDFVEINHLAA--AEREE-----LEK  1159

Query  985   SISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEEN  1044
              +S  +  +D+        +S   D P            S E E+R  L+  L  + ++N
Sbjct  1160  LVSKLKEENDKMSGTVQLLESTKHDVP------------SNEIEDRLILQSHLDTVTQQN  1303

Query  1045  RNLQAEYDRLK  1055
             ++LQ+E D LK
Sbjct  1304  KSLQSELDNLK  1336


>gb|DQ516347.1| Homo sapiens dystrotelin mRNA, complete cds
Length=2051

 Score =  158 bits (400),  Expect = 2e-35, Method: Compositional matrix adjust.
 Identities = 95/291 (32%), Positives = 156/291 (53%), Gaps = 12/291 (4%)
 Frame = +1

Query  638   LNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNL-KQNDQPMDILQIINCLTT  696
             LN++  S YRTA KL+ +Q    LDL+  S     L + +  +     + + Q+   L  
Sbjct  142   LNSIENSIYRTAFKLQSVQTLCQLDLIDSSLIQQVLLRPSFWEARKHSLSVQQLSQALQE  321

Query  697   IYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYR  756
             ++ +  +E+   V+ P   ++ L+ L  +Y++  TG ++++     +I+L       KYR
Sbjct  322   LFQKAREENPGQVH-PRAPELTLSLLTTMYNSKGTGFLQLMPAAAALITLSGDSPLSKYR  498

Query  757   YLFKQVA-SSTGFCD------QRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF  809
              LF+  A +S G  D      +R L  LL D  QIP  +GE  +     +E + RSCFQ 
Sbjct  499   ALFQLYAENSRGGYDSGPRMTRRVLRKLLTDLQQIPTFVGESRAL--CPVESATRSCFQG  672

Query  810   ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
               + P I+   FL W++ EP  ++WLP  HR++AAE   H A+C +C+  PI G RYR L
Sbjct  673   VLS-PAIKEEKFLSWVQSEPPILLWLPTCHRLSAAERVTHPARCTLCRTFPITGLRYRCL  849

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKF  920
             K  N+DICQ CF SG  +K H+  +P++E+C   ++ ++ +   + L+N  
Sbjct  850   KCLNFDICQMCFLSGLHSKSHQKSHPVIEHCIQMSAMQNTKLLFRTLRNNL  1002


>dbj|AK020881.1| Mus musculus adult retina cDNA, RIKEN full-length enriched library, 
clone:A930021A21 product:utrophin, full insert sequence
Length=885

 Score =  158 bits (399),  Expect = 2e-35, Method: Compositional matrix adjust.
 Identities = 73/154 (47%), Positives = 113/154 (73%), Gaps = 4/154 (2%)
 Frame = +1

Query  279  QDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRS  338
            +D+Q EI+AH D++ ++D N QK++++L  S++A +LQ RLD+MN +W++L+ KS +IR+
Sbjct  400  KDIQAEIDAHNDIFKSIDGNRQKMVKALGNSEEATMLQHRLDDMNQRWNDLKAKSASIRA  579

Query  339  HLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTK  398
            HLEAS+++W RL  SL+EL+ WL +KD+EL +Q PIGGD PA+Q Q D  +  +RELK K
Sbjct  580  HLEASAEKWNRLLASLEELIKWLNMKDEELKKQMPIGGDVPALQLQYDHCKVLRRELKEK  759

Query  399  EPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELP  432
            E  +++ ++  R+FL +QP+E  E    EPR  P
Sbjct  760  EYSVLNAVDQARVFLADQPIEAPE----EPRRNP  849


>ref|XM_001787345.1| PREDICTED: Bos taurus similar to Dystrotelin (LOC100137960), 
mRNA
Length=2013

 Score =  154 bits (388),  Expect = 4e-34, Method: Compositional matrix adjust.
 Identities = 94/291 (32%), Positives = 151/291 (51%), Gaps = 12/291 (4%)
 Frame = +1

Query  638   LNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNL-KQNDQPMDILQIINCLTT  696
             LN++  S YRTA KLR +Q    LDL+  S     L   +L +  +  + + Q+   L  
Sbjct  280   LNSIENSTYRTAFKLRSVQTLCQLDLIGSSLIQHVLRHQSLWEAGESTLSVQQLFQALQE  459

Query  697   IYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYR  756
             ++ ++  E    ++ P   ++ L+ L  +YD+  TG I++      +I+L       KY 
Sbjct  460   MFQKVRVEKPGQMH-PRASELTLSLLTTMYDSTGTGFIKLAPAAAALITLSGDSPLTKYT  636

Query  757   YLFKQVA-SSTGFCD------QRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF  809
              LF+  A ++ G  D      +R L  LL D  QIP  +GE  +    ++E + RSCFQ 
Sbjct  637   ALFQLYAENNRGGHDLGARMTRRVLRNLLTDLQQIPTVVGESRAL--CSVESATRSCFQG  810

Query  810   ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
               + P I+   FL W++ EP  ++W+P  +R++A E A H  +C IC+  PI G RYR L
Sbjct  811   VLS-PVIKEEKFLSWLQSEPPILLWIPTCYRLSATEMATHPVRCRICRNFPITGLRYRCL  987

Query  870   KHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKF  920
             K  N+DICQ+CF S    + H+  +P+VE C   ++ +D R   +  +N  
Sbjct  988   KCLNFDICQACFLSSFQGESHQKSHPVVENCIQMSAKDDTRLVLRTPRNNL  1140


>gb|S60973.1| dystrophin {out-of-frame deletion of exon 50} [human, fibroblasts, 
mRNA Mutant, 362 nt]
Length=362

 Score =  154 bits (388),  Expect = 4e-34, Method: Compositional matrix adjust.
 Identities = 75/75 (100%), Positives = 75/75 (100%), Gaps = 0/75 (0%)
 Frame = +3

Query  1    MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
            MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  138  MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  317

Query  61   EQRRPQLEELITAAQ  75
            EQRRPQLEELITAAQ
Sbjct  318  EQRRPQLEELITAAQ  362


>gb|M63072.1|HUMDMDC Human Duchenne muscular dystrophy protein (DMD) mRNA, 3' end
Length=362

 Score =  154 bits (388),  Expect = 4e-34, Method: Compositional matrix adjust.
 Identities = 75/75 (100%), Positives = 75/75 (100%), Gaps = 0/75 (0%)
 Frame = +3

Query  1    MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
            MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL
Sbjct  138  MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  317

Query  61   EQRRPQLEELITAAQ  75
            EQRRPQLEELITAAQ
Sbjct  318  EQRRPQLEELITAAQ  362


>gb|BC046265.1| Xenopus laevis dystrobrevin, alpha, mRNA (cDNA clone MGC:53516 
IMAGE:5572622), complete cds
Length=3736

 Score =  151 bits (382),  Expect = 2e-33, Method: Compositional matrix adjust.
 Identities = 129/477 (27%), Positives = 215/477 (45%), Gaps = 71/477 (14%)
 Frame = +3

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL +++L   D    +++ ++   L
Sbjct  201   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNIIEALRENSLNNVDPNVELNVARLEAVL  380

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + +NV   + + LN+LL  YD+   G+I V + K  + +LC   + 
Sbjct  381   STIFYQLNKRMPTTHQINVEQSISLMLNFLLAAYDSEGHGKITVFAVKMALATLCGGKIM  560

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY++  ++ + G          L + +++P  + E  SFG +  E + RSCF   + 
Sbjct  561   DKLRYIYSMISDANGVMVSGCYDQFLREVLKLPTAIFEGPSFGYT--EQAARSCF---SQ  725

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  726   QKKVTLNSFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  905

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKR------  924
               NY +CQ CF+ G  +  H   + M EY   T+     +  +  L              
Sbjct  906   CHNYQLCQDCFWRGHASGSHSNQHQMKEY---TSWKSPAKKLSTALSKSLSCASSREPLH  1076

Query  925   -YFAKHPRMG-----YLPVQTVLE-GDNM---ETPASSPQLS-----HDDTHSRIEHY--  967
               F   P M       +P + V    DN+     P+S    +     H  T      Y  
Sbjct  1077  PMFPDQPEMPLNLAHIVPPRPVTSMNDNIFSHSVPSSGSPFTNKISPHKSTEVEQSKYLA  1256

Query  968   ------------------ASRLAEMENSNGSYLN----------DSISPNESIDDEHLLI  999
                               A RLA+     G Y N          DS S    +D+EH LI
Sbjct  1257  RAAPTLLKGKGLQYSLGVADRLADEHALIGVYANMLQNNLPRMLDSPS---RLDEEHRLI  1427

Query  1000  QHYCQSL-NQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLK  1055
               Y   L  ++S   Q R  + I  ++++ +  +  +++A+LE +NR +  E  RL+
Sbjct  1428  ARYAARLAAENSSSVQQRGGSDITFTIDANK--QQRQLIAELENKNREILQEIQRLR  1592


>emb|AJ544617.1| Takifugu rubripes dmd gene for putative dystrophin, exons 74-82
Length=17490

 Score =  150 bits (379),  Expect = 4e-33, Method: Compositional matrix adjust.
 Identities = 74/83 (89%), Positives = 78/83 (93%), Gaps = 0/83 (0%)
 Frame = +2

Query  1044  NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  1103
             NR LQ+EYDRLK+ H+ KGLSPLPSPPEM+P SPQS RDAELIAEAKLLRQHKGRLEARM
Sbjct  7343  NRKLQSEYDRLKKAHDRKGLSPLPSPPEMLPVSPQSARDAELIAEAKLLRQHKGRLEARM  7522

Query  1104  QILEDHNKQLESQLHRLRQLLEQ  1126
             QILEDHNKQLESQLHRLRQLLEQ
Sbjct  7523  QILEDHNKQLESQLHRLRQLLEQ  7591


 Score =  106 bits (265),  Expect = 8e-20, Method: Compositional matrix adjust.
 Identities = 45/54 (83%), Positives = 52/54 (96%), Gaps = 0/54 (0%)
 Frame = +2

Query  993   DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRN  1046
             DDEH+LIQHYCQSLNQ SPLSQPRSPAQILIS+E+EE+GELER+L DLE+ENR+
Sbjct  6677  DDEHMLIQHYCQSLNQGSPLSQPRSPAQILISMETEEKGELERVLNDLEQENRS  6838


 Score = 97.8 bits (242),  Expect = 3e-17, Method: Composition-based stats.
 Identities = 49/62 (79%), Positives = 52/62 (83%), Gaps = 9/62 (14%)
 Frame = +1

Query  903  TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDTHS  962
            TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQT+LEGDNMET          DTH+
Sbjct  196  TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTILEGDNMET---------*DTHT  348

Query  963  RI  964
            +I
Sbjct  349  QI  354


 Score = 58.9 bits (141),  Expect = 2e-05, Method: Compositional matrix adjust.
 Identities = 26/32 (81%), Positives = 30/32 (93%), Gaps = 0/32 (0%)
 Frame = +3

Query  1199  GHNVGSLFHMADDLGRAMESLVSVMTDEEGAE  1230
             G ++GSLFHMADDLGRAMESLVS+MTDE+ AE
Sbjct  9453  GRSIGSLFHMADDLGRAMESLVSIMTDEQSAE  9548


 Score = 46.2 bits (108),  Expect(2) = 4e-05, Method: Compositional matrix adjust.
 Identities = 23/32 (71%), Positives = 27/32 (84%), Gaps = 1/32 (3%)
 Frame = +2

Query  1168  GEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
             G+++L SP QD S GLEEVMEQLNNSFP S+G
Sbjct  8168  GDDELSSPSQDAS-GLEEVMEQLNNSFPHSQG  8260


 Score = 31.2 bits (69),  Expect(2) = 4e-05, Method: Compositional matrix adjust.
 Identities = 29/42 (69%), Positives = 35/42 (83%), Gaps = 1/42 (2%)
 Frame = +1

Query  1128  QAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGE  1169
             Q ++KVNGT +SSPSTS QRSDSS P LLRV  SQT+D+MG+
Sbjct  7966  QTDSKVNGTALSSPSTSSQRSDSSLP-LLRVAASQTTDTMGK  8088


 Score = 45.4 bits (106),  Expect = 0.19, Method: Compositional matrix adjust.
 Identities = 21/23 (91%), Positives = 22/23 (95%), Gaps = 0/23 (0%)
 Frame = +2

Query  970   RLAEMENSNGSYLNDSISPNESI  992
             RLAEMEN NGSYLNDSISPNES+
Sbjct  4826  RLAEMENRNGSYLNDSISPNESM  4894


 Score = 45.4 bits (106),  Expect = 0.20, Method: Compositional matrix adjust.
 Identities = 19/22 (86%), Positives = 21/22 (95%), Gaps = 0/22 (0%)
 Frame = +3

Query  949   PASSPQLSHDDTHSRIEHYASR  970
             P SSPQLSHDDTH+RIEHYA+R
Sbjct  1716  PGSSPQLSHDDTHTRIEHYANR  1781


>ref|XM_002245696.1| Branchiostoma floridae hypothetical protein (BRAFLDRAFT_131875) 
mRNA, complete cds
Length=1915

 Score =  150 bits (379),  Expect = 5e-33, Method: Compositional matrix adjust.
 Identities = 127/454 (27%), Positives = 204/454 (44%), Gaps = 81/454 (17%)
 Frame = +1

Query  742   GIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEP  801
              + ++C   L DK RY+F Q++ S G     +    L +++ +P  + E  SFG +  E 
Sbjct  4     ALSTMCAGKLVDKLRYIFSQISDSRGQLVYPKFDQFLQEALALPSAVYEGPSFGYN--ET  177

Query  802   SVRSCFQFANNKPEIEAALFLDWMRLEPQ--SMVWLPVLHRVAAAETAKHQAKCNICKEC  859
             + +SCFQ A     +    FLD M  +P    +VWLP++HR+A  E  +    C  C+  
Sbjct  178   AAKSCFQSAQ---RVTINDFLDVMMADPGPPCLVWLPLMHRMANVENVE----CAYCQRE  336

Query  860   PIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNK  919
              ++GFRY+  + FNY +CQ+CF+ G  +  H   + M EY   ++     + F   LK  
Sbjct  337   SMMGFRYKCQRCFNYQLCQNCFWRGYTSGNHTTDHEMKEY---SSWKSPAKQFGHALKKS  507

Query  920   FRT--KRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDD---THSRIEHYASRLAEM  974
             FR   K     HPR    P QT L+  N+  P+  P L+++    T    EH        
Sbjct  508   FRCVPKHAEPNHPRFPDEPEQT-LDLSNIVPPSPPPALANESALATSISSEHTTP-----  669

Query  975   ENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQD-----------SP-LSQPRSPA-QI  1021
               +  ++  D++     +DDEH LI  Y   L  +           SP L Q RSP  ++
Sbjct  670   --TKRAFPVDTMDSTTRMDDEHRLIARYAARLAAEQNEQNTTPVDVSPLLHQSRSPGTEL  843

Query  1022  LISLESEER-----GELER--------------------ILADLEEENRNLQAEYDRLKQ  1056
              ++L++  +      ELE                     +L++ + +NR +  E  RL+Q
Sbjct  844   ALNLDANRQQRELIAELEHKNSPREVAEKLAQWLREQTDLLSECQHKNREIMREIQRLRQ  1023

Query  1057  QHEH--KGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLE  1114
             +H+   +G+                 R+  L+AE +LLRQ K  LE RM  L++  ++L 
Sbjct  1024  EHDEASRGM--------------DESRNPTLLAELRLLRQRKDELELRMSALQESRRELM  1161

Query  1115  SQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRS  1148
              QL  L +LL+   +      T   SP T   +S
Sbjct  1162  VQLEGLMKLLKSHGSSPTPRSTPGGSPLTGSAKS  1263


>gb|EF120476.1| Schistosoma bovis dystrophin mRNA, partial cds
Length=3107

 Score =  149 bits (377),  Expect = 7e-33, Method: Compositional matrix adjust.
 Identities = 69/162 (42%), Positives = 96/162 (59%), Gaps = 16/162 (9%)
 Frame = +1

Query  711   VPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCD  770
             V +CVD+ LNWLLNVYD  R G IRVLSFK  +  +  A+L++KYRYLF  ++   G  D
Sbjct  721   VNVCVDLILNWLLNVYDRMRCGTIRVLSFKVALALMSMANLDEKYRYLFSLISDRDGCVD  900

Query  771   QRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ----------------FANNKP  814
             ++RLG LL++ + IPR LGE   FG  +    V++CFQ                  ++KP
Sbjct  901   EQRLGALLYECVLIPRNLGETGQFGNEDFNQYVKTCFQQVLEISKHSDKIDGTLTYHSKP  1080

Query  815   EIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNIC  856
                   FL W+RL PQ + WLP+LHR+A +E   H  +C++C
Sbjct  1081  TARIVHFLTWLRLNPQMLTWLPLLHRLALSEPVIHHIRCSVC  1206


>emb|AJ544616.1| Takifugu rubripes dmd gene for putative dystrophin, exons 67-73
Length=14923

 Score =  149 bits (377),  Expect = 8e-33, Method: Compositional matrix adjust.
 Identities = 73/123 (59%), Positives = 85/123 (69%), Gaps = 27/123 (21%)
 Frame = +1

Query  661   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
             +DLLS+  AC+  DQH LKQN+Q +DI Q++ CLT++Y RLEQ H++LVNVPLCVDMCLN
Sbjct  8218  VDLLSMPLACEVFDQHGLKQNEQLLDISQLVTCLTSLYQRLEQSHSHLVNVPLCVDMCLN  8397

Query  721   WLLNVYDT---------------------------GRTGRIRVLSFKTGIISLCKAHLED  753
             WLLNVYDT                           GRTG+IR LSFKTGIISLCKAHLED
Sbjct  8398  WLLNVYDTYDWHTQAFLARLGVLVLIFGFCFVLGSGRTGKIRTLSFKTGIISLCKAHLED  8577

Query  754   KYR  756
             KYR
Sbjct  8578  KYR  8586


 Score =  128 bits (321),  Expect = 2e-26, Method: Compositional matrix adjust.
 Identities = 59/72 (81%), Positives = 63/72 (87%), Gaps = 1/72 (1%)
 Frame = +2

Query  803    VRSCFQF-ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  861
              V  CF   ANNKPE+EAA+FLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI
Sbjct  12350  VVICFCIQANNKPELEAAMFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI  12529

Query  862    IGFRYRSLKHFN  873
              IGFR   L H++
Sbjct  12530  IGFRSVELPHYS  12565


 Score =  112 bits (281),  Expect = 9e-22, Method: Compositional matrix adjust.
 Identities = 51/57 (89%), Positives = 53/57 (92%), Gaps = 0/57 (0%)
 Frame = +2

Query  758    LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKP  814
              LF+QVAS+TGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF    P
Sbjct  9836   LFRQVASATGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFVRRAP  10006


 Score = 93.2 bits (230),  Expect = 8e-16, Method: Composition-based stats.
 Identities = 39/47 (82%), Positives = 40/47 (85%), Gaps = 0/47 (0%)
 Frame = +2

Query  865    RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRD  911
              RYRSLKHFNYDICQSCFFSGRVAKGHKM YPMVEYCTP     DV +
Sbjct  14447  RYRSLKHFNYDICQSCFFSGRVAKGHKMQYPMVEYCTPV*MPPDVSN  14587


 Score = 54.3 bits (129),  Expect(2) = 7e-12, Method: Compositional matrix adjust.
 Identities = 25/26 (96%), Positives = 25/26 (96%), Gaps = 0/26 (0%)
 Frame = +1

Query  636   ADLNNVRFSAYRTAMKLRRLQKALCL  661
             ADLNNVRFSAYRTAMKLRRLQKALC 
Sbjct  7423  ADLNNVRFSAYRTAMKLRRLQKALCC  7500


 Score = 45.8 bits (107),  Expect(2) = 7e-12, Method: Compositional matrix adjust.
 Identities = 18/22 (81%), Positives = 20/22 (90%), Gaps = 0/22 (0%)
 Frame = +3

Query  615   NHETQTTCWDHPKMTELYQSLA  636
             +H+TQTTCWDHPKM ELYQSL 
Sbjct  7257  SHQTQTTCWDHPKMAELYQSLG  7322


>gb|EF120477.1| Schistosoma haematobium dystrophin mRNA, partial cds
Length=3104

 Score =  149 bits (377),  Expect = 8e-33, Method: Compositional matrix adjust.
 Identities = 69/162 (42%), Positives = 96/162 (59%), Gaps = 16/162 (9%)
 Frame = +1

Query  711   VPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCD  770
             V +CVD+ LNWLLNVYD  R G IRVLSFK  +  +  A+L++KYRYLF  ++   G  D
Sbjct  721   VNVCVDLILNWLLNVYDRMRCGTIRVLSFKVALALMSMANLDEKYRYLFSLISDRDGCVD  900

Query  771   QRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ----------------FANNKP  814
             ++RLG LL++ + IPR LGE   FG  +    V++CFQ                  ++KP
Sbjct  901   EQRLGALLYECVLIPRNLGETGQFGNEDFNQYVKTCFQQVLEISKHSDKIDGTLTYHSKP  1080

Query  815   EIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNIC  856
                   FL W+RL PQ + WLP+LHR+A +E   H  +C++C
Sbjct  1081  TARIVHFLTWLRLNPQMLTWLPLLHRLALSEQVIHHIRCSVC  1206


>gb|AC093167.11| Homo sapiens Xp BAC RP11-593P4 (Roswell Park Cancer Institute 
Human BAC Library) complete sequence
Length=75001

 Score =  146 bits (368),  Expect = 9e-32, Method: Compositional matrix adjust.
 Identities = 72/76 (94%), Positives = 73/76 (96%), Gaps = 0/76 (0%)
 Frame = -3

Query  94     IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
              +ERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV
Sbjct  19430  VERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  19251

Query  154    DAIQKKITETKQLAKD  169
              DAIQKKITETK   KD
Sbjct  19250  DAIQKKITETKVSIKD  19203


 Score = 79.3 bits (194),  Expect = 1e-11, Method: Compositional matrix adjust.
 Identities = 39/40 (97%), Positives = 40/40 (100%), Gaps = 0/40 (0%)
 Frame = -2

Query  54     KATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  93
              +ATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR
Sbjct  69594  QATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  69475


>gb|AF213438.1|AF213438 Homo sapiens dystrophin (DMD) gene, exon 53 and partial cds
Length=677

 Score =  146 bits (368),  Expect = 9e-32, Method: Compositional matrix adjust.
 Identities = 72/76 (94%), Positives = 73/76 (96%), Gaps = 0/76 (0%)
 Frame = +1

Query  94   IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
            +ERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV
Sbjct  277  VERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  456

Query  154  DAIQKKITETKQLAKD  169
            DAIQKKITETK   KD
Sbjct  457  DAIQKKITETKVSIKD  504


>gb|AC193238.3| Pan troglodytes BAC clone CH251-308A5 from chromosome x, complete 
sequence
Length=177586

 Score =  145 bits (366),  Expect = 1e-31, Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%), Gaps = 0/76 (0%)
 Frame = -2

Query  94      IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
               +ERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYT+
Sbjct  117393  VERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTI  117214

Query  154     DAIQKKITETKQLAKD  169
               DAIQKKITETK   KD
Sbjct  117213  DAIQKKITETKVSIKD  117166


 Score =  129 bits (323),  Expect = 1e-26, Method: Compositional matrix adjust.
 Identities = 67/74 (90%), Positives = 68/74 (91%), Gaps = 0/74 (0%)
 Frame = -1

Query  206    INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
              I AS   +  RVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL
Sbjct  64156  IIASEHLVLCRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  63977

Query  266    EDSKGVKELMKQWQ  279
              EDSKGVKELMKQWQ
Sbjct  63976  EDSKGVKELMKQWQ  63935


 Score =  104 bits (259),  Expect = 3e-19, Method: Compositional matrix adjust.
 Identities = 50/52 (96%), Positives = 50/52 (96%), Gaps = 0/52 (0%)
 Frame = -2

Query  165    QLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  216
              QLAKDLRQWQ NVDVANDLALKLLRDYSADDTRKVHMITENINASW SIHKR
Sbjct  94374  QLAKDLRQWQINVDVANDLALKLLRDYSADDTRKVHMITENINASWGSIHKR  94219


 Score = 79.3 bits (194),  Expect = 1e-11, Method: Compositional matrix adjust.
 Identities = 39/40 (97%), Positives = 40/40 (100%), Gaps = 0/40 (0%)
 Frame = -2

Query  54      KATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  93
               +ATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR
Sbjct  167313  QATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  167194


>emb|CT476801.2| RP43-004N07, complete sequence
Length=182257

 Score =  145 bits (366),  Expect = 1e-31, Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%), Gaps = 0/76 (0%)
 Frame = -3

Query  94      IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
               +ERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYT+
Sbjct  122201  VERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTI  122022

Query  154     DAIQKKITETKQLAKD  169
               DAIQKKITETK   KD
Sbjct  122021  DAIQKKITETKVSIKD  121974


 Score =  129 bits (323),  Expect = 1e-26, Method: Compositional matrix adjust.
 Identities = 67/74 (90%), Positives = 68/74 (91%), Gaps = 0/74 (0%)
 Frame = -3

Query  206    INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
              I AS   +  RVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL
Sbjct  68960  IIASEHLVLCRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  68781

Query  266    EDSKGVKELMKQWQ  279
              EDSKGVKELMKQWQ
Sbjct  68780  EDSKGVKELMKQWQ  68739


 Score =  104 bits (259),  Expect = 3e-19, Method: Compositional matrix adjust.
 Identities = 50/52 (96%), Positives = 50/52 (96%), Gaps = 0/52 (0%)
 Frame = -1

Query  165    QLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  216
              QLAKDLRQWQ NVDVANDLALKLLRDYSADDTRKVHMITENINASW SIHKR
Sbjct  99178  QLAKDLRQWQINVDVANDLALKLLRDYSADDTRKVHMITENINASWGSIHKR  99023


 Score = 79.3 bits (194),  Expect = 1e-11, Method: Compositional matrix adjust.
 Identities = 39/40 (97%), Positives = 40/40 (100%), Gaps = 0/40 (0%)
 Frame = -2

Query  54      KATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  93
               +ATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR
Sbjct  172137  QATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  172018


>emb|CR972866.3| RP43-009N23, complete sequence
Length=201804

 Score =  145 bits (366),  Expect = 1e-31, Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%), Gaps = 0/76 (0%)
 Frame = -1

Query  94      IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
               +ERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYT+
Sbjct  145938  VERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTI  145759

Query  154     DAIQKKITETKQLAKD  169
               DAIQKKITETK   KD
Sbjct  145758  DAIQKKITETKVSIKD  145711


 Score =  129 bits (323),  Expect = 1e-26, Method: Compositional matrix adjust.
 Identities = 67/74 (90%), Positives = 68/74 (91%), Gaps = 0/74 (0%)
 Frame = -1

Query  206    INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
              I AS   +  RVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL
Sbjct  92697  IIASEHLVLCRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  92518

Query  266    EDSKGVKELMKQWQ  279
              EDSKGVKELMKQWQ
Sbjct  92517  EDSKGVKELMKQWQ  92476


 Score =  104 bits (259),  Expect = 3e-19, Method: Compositional matrix adjust.
 Identities = 50/52 (96%), Positives = 50/52 (96%), Gaps = 0/52 (0%)
 Frame = -2

Query  165     QLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  216
               QLAKDLRQWQ NVDVANDLALKLLRDYSADDTRKVHMITENINASW SIHKR
Sbjct  122915  QLAKDLRQWQINVDVANDLALKLLRDYSADDTRKVHMITENINASWGSIHKR  122760


 Score = 79.3 bits (194),  Expect = 1e-11, Method: Compositional matrix adjust.
 Identities = 39/40 (97%), Positives = 40/40 (100%), Gaps = 0/40 (0%)
 Frame = -3

Query  54      KATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  93
               +ATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR
Sbjct  195874  QATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  195755


>emb|CT485784.2| RP43-026J01, complete sequence
Length=201375

 Score =  145 bits (366),  Expect = 1e-31, Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%), Gaps = 0/76 (0%)
 Frame = -2

Query  94      IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
               +ERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYT+
Sbjct  108317  VERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTI  108138

Query  154     DAIQKKITETKQLAKD  169
               DAIQKKITETK   KD
Sbjct  108137  DAIQKKITETKVSIKD  108090


 Score =  129 bits (323),  Expect = 1e-26, Method: Compositional matrix adjust.
 Identities = 67/74 (90%), Positives = 68/74 (91%), Gaps = 0/74 (0%)
 Frame = -2

Query  206    INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
              I AS   +  RVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL
Sbjct  55076  IIASEHLVLCRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  54897

Query  266    EDSKGVKELMKQWQ  279
              EDSKGVKELMKQWQ
Sbjct  54896  EDSKGVKELMKQWQ  54855


 Score =  104 bits (259),  Expect = 3e-19, Method: Compositional matrix adjust.
 Identities = 50/52 (96%), Positives = 50/52 (96%), Gaps = 0/52 (0%)
 Frame = -3

Query  165    QLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  216
              QLAKDLRQWQ NVDVANDLALKLLRDYSADDTRKVHMITENINASW SIHKR
Sbjct  85294  QLAKDLRQWQINVDVANDLALKLLRDYSADDTRKVHMITENINASWGSIHKR  85139


 Score = 79.3 bits (194),  Expect = 1e-11, Method: Compositional matrix adjust.
 Identities = 39/40 (97%), Positives = 40/40 (100%), Gaps = 0/40 (0%)
 Frame = -1

Query  54      KATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  93
               +ATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR
Sbjct  158253  QATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  158134


>ref|XM_002017724.1| Drosophila persimilis GL17134 (Dper\GL17134), mRNA
Length=2451

 Score =  144 bits (364),  Expect = 2e-31, Method: Compositional matrix adjust.
 Identities = 119/466 (25%), Positives = 209/466 (44%), Gaps = 47/466 (10%)
 Frame = +1

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  43    LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  222

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  223   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  402

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +      A
Sbjct  403   LVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPA  573

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP+LHR+A  ET  H   C++C +    GFRYR  +
Sbjct  574   ENKVTVNDFMATLMSEPGPSCLVWLPLLHRLATVETIVHPTICSVCHKENFTGFRYRCQR  753

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRT--KRYFAK  928
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +      L+  FR   ++    
Sbjct  754   CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQI---GHSLRKSFRCVPEKTTQV  924

Query  929   HPRMGYLPVQTVLEGDNMETPASSPQLSH----DDTHSRIEHYASRLAEMENSNGSYLND  984
              PR    P +T L   ++  P  SP  SH    D T +    +   L        S L D
Sbjct  925   LPRFPDQPEKT-LNLSHIVPP--SPLPSHNGFNDPTLALAGVHHGHLPPGIFDRSSTL-D  1092

Query  985   SISPNESI-------------------------DDEHLLIQHYCQSLNQDSPLSQPRSPA  1019
             S +   SI                         D+EH LI  Y   L Q++    P + +
Sbjct  1093  SRATGRSIDSANCTGGGGGGGTTISRLAAASANDEEHRLIARYAARLAQEN--RAPSNMS  1266

Query  1020  QILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSP  1065
             +    + ++       ++A LE +N+ +  E  RL++Q E + ++P
Sbjct  1267  ESATPIGTDNSRAQRELIAQLESKNKEIMREIARLRRQQETEQMAP  1404


>gb|AC193178.3| Pan troglodytes BAC clone CH251-299A18 from chromosome x, complete 
sequence
Length=168302

 Score =  143 bits (360),  Expect = 7e-31, Method: Compositional matrix adjust.
 Identities = 67/68 (98%), Positives = 68/68 (100%), Gaps = 0/68 (0%)
 Frame = -2

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              +DLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  47995  VDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  47816

Query  721    WLLNVYDT  728
              WLLNVYDT
Sbjct  47815  WLLNVYDT  47792


 Score =  132 bits (331),  Expect = 2e-27, Method: Compositional matrix adjust.
 Identities = 62/74 (83%), Positives = 63/74 (85%), Gaps = 0/74 (0%)
 Frame = -3

Query  793    SFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK  852
              SF  S   PS+      ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK
Sbjct  21408  SFLSSFCPPSLSLLSLQANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK  21229

Query  853    CNICKECPIIGFRY  866
              CNICKECPIIGFRY
Sbjct  21228  CNICKECPIIGFRY  21187


 Score =  115 bits (288),  Expect = 1e-22, Method: Compositional matrix adjust.
 Identities = 53/58 (91%), Positives = 54/58 (93%), Gaps = 0/58 (0%)
 Frame = -1

Query  758    LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPE  815
              LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF +  P 
Sbjct  42425  LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFVSYSPS  42252


 Score =  107 bits (268),  Expect = 3e-20, Method: Compositional matrix adjust.
 Identities = 54/55 (98%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = -3

Query  991   SIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
             S DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR
Sbjct  8157  SRDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  7993


 Score =  102 bits (253),  Expect = 2e-18, Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 53/61 (86%), Gaps = 5/61 (8%)
 Frame = -3

Query  893    HYPMVEYCTP-----TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  947
              ++P++   +P     TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME
Sbjct  17301  NHPVLNLISP*SPF*TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  17122

Query  948    T  948
              T
Sbjct  17121  T  17119


 Score = 92.8 bits (229),  Expect = 1e-15, Method: Compositional matrix adjust.
 Identities = 38/40 (95%), Positives = 39/40 (97%), Gaps = 0/40 (0%)
 Frame = -2

Query  865    RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
              RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTP +
Sbjct  18934  RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPVS  18815


 Score = 63.5 bits (153),  Expect = 6e-07, Method: Compositional matrix adjust.
 Identities = 29/34 (85%), Positives = 32/34 (94%), Gaps = 0/34 (0%)
 Frame = -3

Query  723    LNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYR  756
              L +++ GRTGRIRVLSFKTGIISLCKAHLEDKYR
Sbjct  44982  LILHNRGRTGRIRVLSFKTGIISLCKAHLEDKYR  44881


 Score = 54.3 bits (129),  Expect = 4e-04, Method: Compositional matrix adjust.
 Identities = 25/25 (100%), Positives = 25/25 (100%), Gaps = 0/25 (0%)
 Frame = -2

Query  636    ADLNNVRFSAYRTAMKLRRLQKALC  660
              ADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  61363  ADLNNVRFSAYRTAMKLRRLQKALC  61289


 Score = 52.8 bits (125),  Expect = 0.001, Method: Compositional matrix adjust.
 Identities = 21/24 (87%), Positives = 22/24 (91%), Gaps = 0/24 (0%)
 Frame = -3

Query  613    YINHETQTTCWDHPKMTELYQSLA  636
              Y +HETQTTCWDHPKMTELYQSL 
Sbjct  98385  YFSHETQTTCWDHPKMTELYQSLG  98314


 Score = 52.8 bits (125),  Expect = 0.001, Method: Compositional matrix adjust.
 Identities = 25/32 (78%), Positives = 28/32 (87%), Gaps = 0/32 (0%)
 Frame = -1

Query  970    RLAEMENSNGSYLNDSISPNESIDDEHLLIQH  1001
              RLAEMENSNGSYLNDSISPNES+   HL +Q+
Sbjct  10958  RLAEMENSNGSYLNDSISPNESM*VSHLFLQN  10863


 Score = 50.8 bits (120),  Expect = 0.004, Method: Compositional matrix adjust.
 Identities = 21/23 (91%), Positives = 21/23 (91%), Gaps = 0/23 (0%)
 Frame = -3

Query  592     FLSTSVQGPWERAISPNKVPYYI  614
               F S SVQGPWERAISPNKVPYYI
Sbjct  161502  FFSASVQGPWERAISPNKVPYYI  161434


 Score = 48.9 bits (115),  Expect = 0.019, Method: Compositional matrix adjust.
 Identities = 22/23 (95%), Positives = 22/23 (95%), Gaps = 0/23 (0%)
 Frame = -1

Query  949    PASSPQLSHDDTHSRIEHYASRL  971
              PASSPQLSHDDTHSRIEHYASR 
Sbjct  12143  PASSPQLSHDDTHSRIEHYASRY  12075


>emb|CU302226.2| CH251-299A18, complete sequence
Length=168302

 Score =  143 bits (360),  Expect = 7e-31, Method: Compositional matrix adjust.
 Identities = 67/68 (98%), Positives = 68/68 (100%), Gaps = 0/68 (0%)
 Frame = +2

Query  661     LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
               +DLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  120308  VDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  120487

Query  721     WLLNVYDT  728
               WLLNVYDT
Sbjct  120488  WLLNVYDT  120511


 Score =  132 bits (331),  Expect = 2e-27, Method: Compositional matrix adjust.
 Identities = 62/74 (83%), Positives = 63/74 (85%), Gaps = 0/74 (0%)
 Frame = +3

Query  793     SFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK  852
               SF  S   PS+      ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK
Sbjct  146895  SFLSSFCPPSLSLLSLQANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAK  147074

Query  853     CNICKECPIIGFRY  866
               CNICKECPIIGFRY
Sbjct  147075  CNICKECPIIGFRY  147116


 Score =  115 bits (288),  Expect = 1e-22, Method: Compositional matrix adjust.
 Identities = 53/58 (91%), Positives = 54/58 (93%), Gaps = 0/58 (0%)
 Frame = +1

Query  758     LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPE  815
               LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF +  P 
Sbjct  125878  LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFVSYSPS  126051


 Score =  107 bits (268),  Expect = 3e-20, Method: Compositional matrix adjust.
 Identities = 54/55 (98%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = +3

Query  991     SIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
               S DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR
Sbjct  160146  SRDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  160310


 Score =  102 bits (253),  Expect = 2e-18, Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 53/61 (86%), Gaps = 5/61 (8%)
 Frame = +3

Query  893     HYPMVEYCTP-----TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  947
               ++P++   +P     TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME
Sbjct  151002  NHPVLNLISP*SPF*TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  151181

Query  948     T  948
               T
Sbjct  151182  T  151184


 Score = 92.8 bits (229),  Expect = 1e-15, Method: Compositional matrix adjust.
 Identities = 38/40 (95%), Positives = 39/40 (97%), Gaps = 0/40 (0%)
 Frame = +2

Query  865     RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
               RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTP +
Sbjct  149369  RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPVS  149488


 Score = 63.5 bits (153),  Expect = 6e-07, Method: Compositional matrix adjust.
 Identities = 29/34 (85%), Positives = 32/34 (94%), Gaps = 0/34 (0%)
 Frame = +3

Query  723     LNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYR  756
               L +++ GRTGRIRVLSFKTGIISLCKAHLEDKYR
Sbjct  123321  LILHNRGRTGRIRVLSFKTGIISLCKAHLEDKYR  123422


 Score = 54.3 bits (129),  Expect = 4e-04, Method: Compositional matrix adjust.
 Identities = 25/25 (100%), Positives = 25/25 (100%), Gaps = 0/25 (0%)
 Frame = +2

Query  636     ADLNNVRFSAYRTAMKLRRLQKALC  660
               ADLNNVRFSAYRTAMKLRRLQKALC
Sbjct  106940  ADLNNVRFSAYRTAMKLRRLQKALC  107014


 Score = 52.8 bits (125),  Expect = 0.001, Method: Compositional matrix adjust.
 Identities = 21/24 (87%), Positives = 22/24 (91%), Gaps = 0/24 (0%)
 Frame = +3

Query  613    YINHETQTTCWDHPKMTELYQSLA  636
              Y +HETQTTCWDHPKMTELYQSL 
Sbjct  69918  YFSHETQTTCWDHPKMTELYQSLG  69989


 Score = 52.8 bits (125),  Expect = 0.001, Method: Compositional matrix adjust.
 Identities = 25/32 (78%), Positives = 28/32 (87%), Gaps = 0/32 (0%)
 Frame = +1

Query  970     RLAEMENSNGSYLNDSISPNESIDDEHLLIQH  1001
               RLAEMENSNGSYLNDSISPNES+   HL +Q+
Sbjct  157345  RLAEMENSNGSYLNDSISPNESM*VSHLFLQN  157440


 Score = 50.8 bits (120),  Expect = 0.004, Method: Compositional matrix adjust.
 Identities = 21/23 (91%), Positives = 21/23 (91%), Gaps = 0/23 (0%)
 Frame = +3

Query  592   FLSTSVQGPWERAISPNKVPYYI  614
             F S SVQGPWERAISPNKVPYYI
Sbjct  6801  FFSASVQGPWERAISPNKVPYYI  6869


 Score = 48.9 bits (115),  Expect = 0.019, Method: Compositional matrix adjust.
 Identities = 22/23 (95%), Positives = 22/23 (95%), Gaps = 0/23 (0%)
 Frame = +1

Query  949     PASSPQLSHDDTHSRIEHYASRL  971
               PASSPQLSHDDTHSRIEHYASR 
Sbjct  156160  PASSPQLSHDDTHSRIEHYASRY  156228


>gb|BC150093.1| Bos taurus cDNA clone IMAGE:8324137
Length=2369

 Score =  142 bits (358),  Expect = 1e-30, Method: Compositional matrix adjust.
 Identities = 85/271 (31%), Positives = 144/271 (53%), Gaps = 15/271 (5%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  217   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHSTEISVSRLETVI  396

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  397   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  570

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  571   MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  738

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR 
Sbjct  739   -QQKKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRC  915

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
              +  NY +CQ+CF+ G  +  H   + M E+
Sbjct  916   QQCHNYQLCQNCFWRGHASGPHSNQHQMKEH  1008


>ref|XM_001918076.1| PREDICTED: Equus caballus dystrotelin (DYTN), mRNA
Length=1713

 Score =  142 bits (358),  Expect = 1e-30, Method: Compositional matrix adjust.
 Identities = 97/263 (36%), Positives = 138/263 (52%), Gaps = 12/263 (4%)
 Frame = +1

Query  644  SAYRTAMKLRRLQKALCLDLLSLSAACDAL-DQHNLKQNDQPMDILQIINCLTTIYDRLE  702
            S YRTA KLR +Q    LDL+  S     L  Q   +  + P  + Q++  L  ++ R+ 
Sbjct  43   SIYRTAFKLRSVQTLCQLDLVHSSLIRHVLLRQCFWEARESPFSVQQLLQTLQELFRRVS  222

Query  703  QEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQV  762
             E+   V+ P   ++ L+ L  +YD+ RT  +++      +I+L       KYR LF+  
Sbjct  223  VENPGQVH-PRASELTLSLLTALYDSTRTSFVKLTPAAAALIALSGDSPLTKYRALFQLY  399

Query  763  ASST-GFCD------QRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPE  815
            A S  G  D      +R L  LL D  QIP  +GE  S   S++E +VRSCFQ   + P 
Sbjct  400  AGSYRGANDSGARMTRRVLRNLLVDLQQIPTVVGE--SRVPSSVESAVRSCFQGVLS-PA  570

Query  816  IEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYD  875
            I+   FL W++ EP  + WLP  HR++A ET    A+C IC++ PI G RY  LK  N+D
Sbjct  571  IKEEKFLSWLQAEPPILQWLPTCHRLSATETVTRPARCGICRDFPITGLRYHCLKCLNFD  750

Query  876  ICQSCFFSGRVAKGHKMHYPMVE  898
            ICQ CF SG   K H +  P V+
Sbjct  751  ICQVCFLSGLHTKAHPVTEPRVQ  819


>gb|M86889.1|HUMDYST06 H.sapiens dystrophin gene, exon 65
Length=351

 Score =  142 bits (357),  Expect = 1e-30, Method: Compositional matrix adjust.
 Identities = 67/68 (98%), Positives = 68/68 (100%), Gaps = 0/68 (0%)
 Frame = +3

Query  661  LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
            +DLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN
Sbjct  99   VDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  278

Query  721  WLLNVYDT  728
            WLLNVYDT
Sbjct  279  WLLNVYDT  302


>dbj|AK083752.1| Mus musculus 9 days embryo whole body cDNA, RIKEN full-length 
enriched library, clone:D030074O22 product:dystrobrevin, beta, 
full insert sequence
Length=3768

 Score =  141 bits (356),  Expect = 2e-30, Method: Compositional matrix adjust.
 Identities = 85/271 (31%), Positives = 145/271 (53%), Gaps = 15/271 (5%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  290   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHSTEISVSRLETVI  469

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  470   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMVAAYDSEGRGKLTVFSVKAMLATMCGGK  643

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             + DK RY+F Q++ S G     +L   L +++++P  + E  SFG +  E +VR+CF   
Sbjct  644   MLDKLRYIFSQMSDSNGLMMFGKLDQFLKEALKLPTAVFEGPSFGYT--EHAVRTCFP--  811

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C    ++GFRYR 
Sbjct  812   -QQKKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCHCESMMGFRYRC  988

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
              +  NY +CQ+CF+ G  +  H   + M E+
Sbjct  989   QQCHNYQLCQNCFWRGHASGAHSNQHQMKEH  1081


>gb|BC078203.1| Danio rerio dystrobrevin, gamma, mRNA (cDNA clone IMAGE:7152475), 
partial cds
Length=1275

 Score =  141 bits (356),  Expect = 2e-30, Method: Compositional matrix adjust.
 Identities = 86/271 (31%), Positives = 141/271 (52%), Gaps = 15/271 (5%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDI----LQIIN  692
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I    L+ I 
Sbjct  304   NYDTIRLSTYRTACKLRFVQKKCNLHLVDVWNMIEAFRDNGLNTLDVCTEISVARLETI-  480

Query  693   CLTTIYDRLEQE--HNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              LT IY +L +     + ++V     + LN++   +DT   GR+ V S K  +  LC   
Sbjct  481   -LTCIYQQLNKRLPTTHQISVQHNTSLLLNFMATAHDTDAQGRLTVFSVKMMLSVLCGGK  657

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++ S G  +  +    L +++++P  + E  SFG   ++   RSCF   
Sbjct  658   LVDKLRYIFSQISDSHGAMEMSKFDHFLREALKLPAAVFEGPSFG--YLDHLARSCFP--  825

Query  811   NNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRS  868
               + ++   +FLD +  +P  Q ++WLP++HR+   E   H   C+ C+   + GFRYR 
Sbjct  826   -QQKKVMLNMFLDALMSDPPPQCLIWLPLVHRMGNVENVHHPVSCSFCRSDGMTGFRYRC  1002

Query  869   LKHFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
              + FNY +CQ+CF+ G  +  H  H+ M E+
Sbjct  1003  QQCFNYQLCQNCFWRGHASGNHSNHHDMKEH  1095


>gb|S62620.1| (mdx3Cv)=dystrophin gene {5'region, alternatively spliced} [mice, 
mRNA Partial Mutant, 374 nt]
Length=374

 Score =  140 bits (354),  Expect = 3e-30, Method: Compositional matrix adjust.
 Identities = 66/66 (100%), Positives = 66/66 (100%), Gaps = 0/66 (0%)
 Frame = +3

Query  616  HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQ  675
            HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQ
Sbjct  177  HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQ  356

Query  676  HNLKQN  681
            HNLKQN
Sbjct  357  HNLKQN  374


>ref|XM_002066076.1| Drosophila willistoni GK22187 (Dwil\GK22187), mRNA
Length=2388

 Score =  140 bits (352),  Expect = 7e-30, Method: Compositional matrix adjust.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 7/271 (2%)
 Frame = +1

Query  635  LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIIN  692
            L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +Q   + + ++  
Sbjct  43   LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEQQSEVSVARLET  222

Query  693  CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
             ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  223  LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  402

Query  751  LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
            L DK RY+F Q++   G     +L   L + + +P  + E  +F   + +  +      A
Sbjct  403  LVDKLRYIFSQISDGAGQLVAWKLSEFLREVLALPAAVYESPTF---HYKDGLEEEIFPA  573

Query  811  NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             NK  +   +        P  +VWLP+LHR+A  ET  H   C++C +    GFRYR  +
Sbjct  574  ENKVTVNDFMATLMSEPGPSCLVWLPLLHRLATVETIVHPTICSVCHKENFTGFRYRCQR  753

Query  871  HFNYDICQSCFFSGRVAKGHKMHYPMVEYCT  901
               Y +CQ CF+ G+ +  H+  + + EY +
Sbjct  754  CHAYQLCQECFWHGKTSLNHQNDHEVKEYSS  846


>gb|AF043067.1|AF043067 Gallus gallus dystrophin mRNA, alternatively spliced, partial 
cds
Length=216

 Score =  139 bits (349),  Expect = 1e-29, Method: Composition-based stats.
 Identities = 72/94 (76%), Positives = 72/94 (76%), Gaps = 22/94 (23%)
 Frame = +1

Query  898  EYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSH  957
            EYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET         
Sbjct  1    EYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET---------  153

Query  958  DDTHSRIEHYASRLAEMENSNGSYLNDSISPNES  991
                         LAEMENSNGSYLNDSISPNES
Sbjct  154  -------------LAEMENSNGSYLNDSISPNES  216


>emb|AJ720148.1| Gallus gallus mRNA for hypothetical protein, clone 11i20
Length=4001

 Score =  138 bits (347),  Expect = 2e-29, Method: Compositional matrix adjust.
 Identities = 85/284 (29%), Positives = 147/284 (51%), Gaps = 28/284 (9%)
 Frame = +3

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             + + +R S YRTA KLR +QK   L L+ +    +A   + L   D    +++ ++   +
Sbjct  243   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHNTEINVSRLETII  422

Query  695   TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDT-----GRT--------GRIRVL  737
             ++IY     RL   H   ++V   + + LN+++  YD+     GR         G++ V 
Sbjct  423   SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSTQ*GGGRG*PTVSEGHGKLTVF  596

Query  738   SFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGS  797
             S K  + ++C   + DK RY+F Q++ S G     +    L + +++P  + E  SFG +
Sbjct  597   SVKAMLATMCGGKILDKLRYIFSQISDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT  776

Query  798   NIEPSVRSCFQFANNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNI  855
               E SVR+CF     + +I   +FLD +  +P  Q +VWLP++HR+A  E   H  +C+ 
Sbjct  777   --EHSVRTCFP---QQKKITLNMFLDTLMADPPPQCLVWLPLMHRLAHVENVFHPVECSY  941

Query  856   CKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
             C+   ++GFRYR  +  NY +CQ+CF+ G  +  H   + M E+
Sbjct  942   CRCESMMGFRYRCQQCHNYQLCQNCFWRGHASGPHSNQHQMKEH  1073


>gb|BT011443.1| Drosophila melanogaster RE48865 full insert cDNA
Length=3395

 Score =  137 bits (346),  Expect = 3e-29, Method: Compositional matrix adjust.
 Identities = 80/291 (27%), Positives = 144/291 (49%), Gaps = 10/291 (3%)
 Frame = +3

Query  635   LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
             L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  606   LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  785

Query  693   CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              ++++Y  L +       VP+     + LNWLL  Y +  +G+IRV S K  + ++C   
Sbjct  786   LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAYTSDNSGKIRVFSIKVALATMCSGK  965

Query  751   LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             L DK RY+F Q++   G     +LG  L + + +P  + E  +F   + +  +      A
Sbjct  966   LVDKLRYIFSQISDGAGQLVAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPA  1136

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NK  +   +        P  +VWLP++HR+A  ET  H   C++C +    GFRYR  +
Sbjct  1137  ENKVTVNDFMATLMSEPGPSCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQR  1316

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
                Y +CQ CF+ G+ +  H+  + + EY +  +  + +      L+  FR
Sbjct  1317  CHAYQLCQECFWHGKTSLNHQNDHEVKEYSSYKSPSKQI---GHSLRKSFR  1460


>gb|AF533682.1| Homo sapiens IL1RAPL1/dystrophin fusion protein mRNA, partial 
cds
Length=400

 Score =  137 bits (346),  Expect = 3e-29, Method: Compositional matrix adjust.
 Identities = 68/73 (93%), Positives = 70/73 (95%), Gaps = 0/73 (0%)
 Frame = +2

Query  88   TIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWK  147
            T +T  +ERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWK
Sbjct  182  TELTVTVERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWK  361

Query  148  EGPYTVDAIQKKI  160
            EGPYTVDAIQKKI
Sbjct  362  EGPYTVDAIQKKI  400


>gb|DQ443726.1| Danio rerio dystrotelin mRNA, complete cds
Length=2092

 Score =  137 bits (346),  Expect = 3e-29, Method: Compositional matrix adjust.
 Identities = 102/349 (29%), Positives = 164/349 (46%), Gaps = 46/349 (13%)
 Frame = +2

Query  638   LNNVRFSAYRTAMKLRRLQKALCLDLLSL-------------SAACDALDQHNLKQNDQP  684
             LN VR + YR A+KLR LQK   ++L+ L               +  +L Q +++Q+ + 
Sbjct  62    LNEVRLAVYRAALKLRSLQKLCQMNLVLLQDLRPILNTLWSSGESTISLAQEDVQQHLEE  241

Query  685   MDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGII  744
             +          +I   L  +      V    D     L  ++D G+TG I + S +  +I
Sbjct  242   L--------FRSISPELPDQ-----AVTEATDQTTRLLFKLFDRGQTGVILLRSVEAALI  382

Query  745   SLCKAHLEDKYRYLFKQVASSTGFCDQRR-------LGLLLHDSIQIPRQLGEVASFGGS  797
             +LC   L  K R LF+   S +G  +  R       L +LL D  Q+P  + E   FG  
Sbjct  383   ALCGDTLSAKQRALFRLAESYSGNQESDRGSISRSALRVLLEDLSQVPAVVQENHVFG--  556

Query  798   NIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICK  857
             + E +V SCF    +    E   F+ W++ EP+ ++WL  L+R++ +E  +H+  C+ CK
Sbjct  557   HAETAVSSCFNGVISAGVTEEH-FIWWLQSEPRLLLWLSTLYRISVSEAVQHRVHCHACK  733

Query  858   ECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLK  917
               PI G RYR LK  N  +CQSCF + R ++ HK  + ++EYCT  +  E +   A   +
Sbjct  734   AFPITGLRYRCLKCLNVHLCQSCFLTERRSRKHKPSHSVLEYCTQPSWKESMASLASSAR  913

Query  918   NKFRTKRYFAKHPRMGYLPVQTVLEGDNME--TPASSPQL---SHDDTH  961
             +         +H R      + +  G + E    AS+P L   ++ DTH
Sbjct  914   HAL-----VPRHTRREAERKRALRAGSSAELRYSASNPALQFAAYADTH  1045


>gb|BC118294.1| Bos taurus dystrobrevin, alpha, mRNA (cDNA clone MGC:140020 IMAGE:8286407), 
complete cds
Length=1764

 Score =  137 bits (344),  Expect = 6e-29, Method: Compositional matrix adjust.
 Identities = 89/269 (33%), Positives = 143/269 (53%), Gaps = 11/269 (4%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPM--DILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D  M  ++ ++   L
Sbjct  379   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNVDPNMELNVARLEAVL  558

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + + V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  559   STIFYQLNKRMPTTHQIQVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  738

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  739   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  903

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  904   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMLGFRYRCQQ  1083

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
               NY +CQ CF+ G     H   + M EY
Sbjct  1084  CHNYQLCQDCFWRGHAGGSHSNQHQMKEY  1170


>ref|NM_010087.3| Mus musculus dystrobrevin alpha (Dtna), transcript variant 2, 
mRNA
Length=1708

 Score =  135 bits (340),  Expect = 1e-28, Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 144/269 (53%), Gaps = 11/269 (4%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  415   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  594

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  595   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  774

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  775   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  939

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  940   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1119

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
               NY +CQ CF+ G     H   + M EY
Sbjct  1120  CHNYQLCQDCFWRGHAGGSHSNQHQMKEY  1206


>dbj|AK003829.2| Mus musculus 18-day embryo whole body cDNA, RIKEN full-length 
enriched library, clone:1110019N08 product:dystrobrevin alpha, 
full insert sequence
Length=1609

 Score =  135 bits (340),  Expect = 1e-28, Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 144/269 (53%), Gaps = 11/269 (4%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  341   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  520

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  521   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  700

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  701   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  865

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  866   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1045

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
               NY +CQ CF+ G     H   + M EY
Sbjct  1046  CHNYQLCQDCFWRGHAGGSHSNQHQMKEY  1132


>gb|AF143542.1|AF143542 Mus musculus alpha-dystrobrevin 3 mRNA, complete cds
Length=1593

 Score =  135 bits (340),  Expect = 1e-28, Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 144/269 (53%), Gaps = 11/269 (4%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  320   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVARLEAVL  499

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  500   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  679

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  680   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  844

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  845   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1024

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
               NY +CQ CF+ G     H   + M EY
Sbjct  1025  CHNYQLCQDCFWRGHAGGSHSNQHQMKEY  1111


>gb|BT006937.1| Homo sapiens dystrobrevin, alpha mRNA, complete cds
Length=1116

 Score =  135 bits (340),  Expect = 2e-28, Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 144/269 (53%), Gaps = 11/269 (4%)
 Frame = +1

Query  637  DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND--QPMDILQIINCL  694
            DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  76   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTELNVSRLEAVL  255

Query  695  TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
            +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  256  STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  435

Query  753  DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
            DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  436  DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  600

Query  813  KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
            + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  601  QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  780

Query  871  HFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
              NY +CQ CF+ G     H   + M EY
Sbjct  781  CHNYQLCQDCFWRGHAGGSHSNQHQMKEY  867


>ref|NM_001392.4| Homo sapiens dystrobrevin, alpha (DTNA), transcript variant 7, 
mRNA
Length=1763

 Score =  135 bits (339),  Expect = 2e-28, Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 144/269 (53%), Gaps = 11/269 (4%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND--QPMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  427   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTELNVSRLEAVL  606

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  607   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  786

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  787   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  951

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  952   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1131

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
               NY +CQ CF+ G     H   + M EY
Sbjct  1132  CHNYQLCQDCFWRGHAGGSHSNQHQMKEY  1218


>gb|U26742.1|HSU26742 Human dystrobrevin-delta mRNA, complete cds
Length=1707

 Score =  135 bits (339),  Expect = 2e-28, Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 144/269 (53%), Gaps = 11/269 (4%)
 Frame = +1

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND--QPMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  400   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTELNVSRLEAVL  579

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  580   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  759

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  760   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  924

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  925   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1104

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
               NY +CQ CF+ G     H   + M EY
Sbjct  1105  CHNYQLCQDCFWRGHAGGSHSNQHQMKEY  1191


>gb|EU831619.1| Synthetic construct Homo sapiens clone HAIB:100066648; DKFZo007D0419 
dystrobrevin, alpha protein (DTNA) gene, encodes complete 
protein
Length=1159

 Score =  135 bits (339),  Expect = 2e-28, Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 144/269 (53%), Gaps = 11/269 (4%)
 Frame = +2

Query  637  DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND--QPMDILQIINCL  694
            DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  98   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTELNVSRLEAVL  277

Query  695  TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
            +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  278  STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  457

Query  753  DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
            DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  458  DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  622

Query  813  KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
            + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  623  QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  802

Query  871  HFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
              NY +CQ CF+ G     H   + M EY
Sbjct  803  CHNYQLCQDCFWRGHAGGSHSNQHQMKEY  889


>emb|AJ009668.1| Homo sapiens mRNA for alpha-dystrobrevin-3
Length=1644

 Score =  135 bits (339),  Expect = 2e-28, Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 144/269 (53%), Gaps = 11/269 (4%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND--QPMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  335   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRKNALNNLDPNTELNVSRLEAVL  514

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  515   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  694

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  695   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  859

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  860   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1039

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
               NY +CQ CF+ G     H   + M EY
Sbjct  1040  CHNYQLCQDCFWRGHAGGSHSNQHQMKEY  1126


>ref|NM_001128175.1| Homo sapiens dystrobrevin, alpha (DTNA), transcript variant 9, 
mRNA
Length=1728

 Score =  134 bits (338),  Expect = 2e-28, Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 144/269 (53%), Gaps = 11/269 (4%)
 Frame = +3

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND--QPMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  423   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTELNVSRLEAVL  602

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  603   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  782

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  783   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  947

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  948   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1127

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
               NY +CQ CF+ G     H   + M EY
Sbjct  1128  CHNYQLCQDCFWRGHAGGSHSNQHQMKEY  1214


>gb|BC005300.1| Homo sapiens dystrobrevin, alpha, mRNA (cDNA clone MGC:12368 
IMAGE:3933795), complete cds
Length=1710

 Score =  134 bits (338),  Expect = 2e-28, Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 144/269 (53%), Gaps = 11/269 (4%)
 Frame = +2

Query  637   DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND--QPMDILQIINCL  694
             DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  383   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTELNVSRLEAVL  562

Query  695   TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  563   STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  742

Query  753   DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  743   DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  907

Query  813   KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  908   QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  1087

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
               NY +CQ CF+ G     H   + M EY
Sbjct  1088  CHNYQLCQDCFWRGHAGGSHSNQHQMKEY  1174


>emb|CR611269.1| full-length cDNA clone CS0DN002YF11 of Adult brain of Homo sapiens 
(human)
Length=1481

 Score =  134 bits (337),  Expect = 3e-28, Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 144/269 (53%), Gaps = 11/269 (4%)
 Frame = +2

Query  637  DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND--QPMDILQIINCL  694
            DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  206  DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTELNVSRLEAVL  385

Query  695  TTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
            +TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   + 
Sbjct  386  STIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIM  565

Query  753  DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
            DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   + 
Sbjct  566  DKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---SQ  730

Query  813  KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
            + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  +
Sbjct  731  QKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQ  910

Query  871  HFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
              NY +CQ CF+ G     H   + M EY
Sbjct  911  CHNYQLCQDCFWRGHAGGSHSNQHQMKEY  997


>gb|BT007812.1| Synthetic construct Homo sapiens dystrobrevin, alpha mRNA, partial 
cds
Length=1116

 Score =  134 bits (337),  Expect = 3e-28, Method: Compositional matrix adjust.
 Identities = 89/270 (32%), Positives = 146/270 (54%), Gaps = 13/270 (4%)
 Frame = +1

Query  637  DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
            DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  76   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  252

Query  694  LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
            L+TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  253  LSTIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  432

Query  752  EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  433  MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  597

Query  812  NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  598  QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  777

Query  870  KHFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
            +  NY +CQ CF+ G     H   + M EY
Sbjct  778  QCHNYQLCQDCFWRGHAGGSHSNQHQMKEY  867


>gb|EU831705.1| Synthetic construct Homo sapiens clone HAIB:100066734; DKFZo003D0420 
dystrobrevin, alpha protein (DTNA) gene, encodes complete 
protein
Length=1159

 Score =  134 bits (337),  Expect = 3e-28, Method: Compositional matrix adjust.
 Identities = 89/270 (32%), Positives = 146/270 (54%), Gaps = 13/270 (4%)
 Frame = +2

Query  637  DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQH---NLKQNDQPMDILQIINC  693
            DL+ +R S YRTA KLR +QK   L L+ +    +AL ++   NL  N + +++ ++   
Sbjct  98   DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTE-LNVSRLEAV  274

Query  694  LTTIYDRLEQEH--NNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHL  751
            L+TI+ +L +     + ++V   + + LN+LL  +D    G+I V + K  + +LC   +
Sbjct  275  LSTIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKI  454

Query  752  EDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
             DK RY+F  ++ S+G     R    L + +++P  + E  SFG +  E S RSCF   +
Sbjct  455  MDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYT--EQSARSCF---S  619

Query  812  NKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
             + ++    FLD +  +P  Q +VWLP+LHR+A  E   H  +C+ C    ++GFRYR  
Sbjct  620  QQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQ  799

Query  870  KHFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
            +  NY +CQ CF+ G     H   + M EY
Sbjct  800  QCHNYQLCQDCFWRGHAGGSHSNQHQMKEY  889


>ref|XM_426570.2| PREDICTED: Gallus gallus similar to dystrophin-like protein (LOC429012), 
mRNA
Length=1928

 Score =  134 bits (336),  Expect = 4e-28, Method: Compositional matrix adjust.
 Identities = 118/431 (27%), Positives = 191/431 (44%), Gaps = 44/431 (10%)
 Frame = +1

Query  694   LTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLED  753
             L  +++R   E    V+ P   +  L+ L  +YD   TG I+  S    +I+L +  L  
Sbjct  4     LKELFERARLEKPGQVD-PRAAEFTLSLLEAMYDRSGTGHIKTRSAAAALIALSRDTLLA  180

Query  754   KYRYLFKQVASSTG---FCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
             KYR  F+  A   G      +  L  LL D  QIP  +GE  +   S +E +  SCF   
Sbjct  181   KYRAFFEFYAVPDGKKALITRSALRGLLTDLNQIPAAVGEGCT--SSCVEIATHSCFHGV  354

Query  811   NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
                  +E   FL W+R  P  + WLP  +R++A E   H+ +C +CK  PI G RYR LK
Sbjct  355   LKSGIVEEK-FLSWLRSGPTLLQWLPTCYRLSATEMVSHRVRCRVCKTFPITGLRYRCLK  531

Query  871   HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKF-----RTK--  923
               N+D+CQ CFF+GR +K HK  +P+VE+C   ++  + + F   ++N       R K  
Sbjct  532   CLNFDLCQVCFFTGRHSKPHKSSHPVVEHCVQMSAKANAKHFLCTVRNNLFQDCCRRKEA  711

Query  924   -----------RYFAKHPRM---GYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYAS  969
                        R+F  H  +     L     L  +N+  P ++P L      S+     +
Sbjct  712   QGGKVLEITEERHFPTHKNILPPAELSASPFLRRENLSLPVNNPILESPKFTSK-----N  876

Query  970   RLAEMENSNGSYL----NDSISPNESIDDEHLLIQHYCQSLNQDS-----PLSQPRSPAQ  1020
             R    +N N S +       I    S + + L +    +S++  S      L++ +   Q
Sbjct  877   RTVLHKNDNNSKILEQGKTKIQAISSFEADVLKMHGSIKSIHNKSRYMKKQLNKWKHKMQ  1056

Query  1021  ILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSP  1080
              L + + ++  ++E  L  L   + NLQ E  ++KQ  E K +    + P         P
Sbjct  1057  FLHNCQEDKSFKIEAKLQSLRASHENLQMELCKMKQ--EVKTVLQSTAHPSFSLCQNMIP  1230

Query  1081  RDAELIAEAKL  1091
              D  ++ E+K+
Sbjct  1231  GDQHVLQESKM  1263


>emb|BX004756.7| Zebrafish DNA sequence from clone CH211-59A4 in linkage group 
1, complete sequence
Length=169530

 Score =  133 bits (335),  Expect = 5e-28, Method: Compositional matrix adjust.
 Identities = 70/160 (43%), Positives = 96/160 (60%), Gaps = 28/160 (17%)
 Frame = -1

Query  389   RAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEK------------LYQEPR-------  429
             +AF+REL  KEPVI  TL+  + FL E P EGL++             Y   R       
Sbjct  6495  QAFRRELGAKEPVINGTLDNAKTFLAEMPREGLKQRPGQKGIAFVLPFYTYSRYNHRL*P  6316

Query  430   ---------ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
                      ++ PEER QNV R+LRK+ E+V   W+ L   S DWQ++++  LERL ELQ
Sbjct  6315  VFLPLM*CADVSPEERVQNVGRILRKEVEDVTVRWKNLGAASVDWQQQLELALERLMELQ  6136

Query  481   EATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKA  520
             +A D+LD KLRQ E +K SW+PVG+LL+D LQ+H+++VK 
Sbjct  6135  DAQDQLDYKLRQTESVKNSWKPVGELLVDDLQNHIDRVKV  6016


 Score = 60.8 bits (146),  Expect(2) = 1e-14, Method: Compositional matrix adjust.
 Identities = 29/53 (54%), Positives = 41/53 (77%), Gaps = 0/53 (0%)
 Frame = -2

Query  164    KQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  216
              +QL+KDL+QWQT ++V N+LA KLL  Y+ DDT KV  +TE++N +W +I KR
Sbjct  19460  QQLSKDLQQWQTQMNVTNELANKLLTLYADDDTSKVKQMTESMNLAWANIKKR  19302


 Score = 48.9 bits (115),  Expect(2) = 1e-14, Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 43/71 (60%), Gaps = 0/71 (0%)
 Frame = -3

Query  94     IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
              +E++Q  W++    L  R   L  M KDS+ WLEA++  E ++ +A  KLESWK+  ++V
Sbjct  19744  VEKLQAHWEDSHAKLTARVLTLQNMYKDSSDWLEARKRVEPLIKKANEKLESWKKVSHSV  19565

Query  154    DAIQKKITETK  164
              + ++ +  + K
Sbjct  19564  EDLKGQNADVK  19532


 Score = 80.9 bits (198),  Expect = 4e-12, Method: Compositional matrix adjust.
 Identities = 37/67 (55%), Positives = 51/67 (76%), Gaps = 0/67 (0%)
 Frame = -3

Query  271    VKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELR  330
              V +L   WQDLQ EI+AH + YH+LDEN  +I+ SLEG+D+AV+LQ+RLD+M  +W EL 
Sbjct  11248  VCDLF*SWQDLQAEIDAHRETYHSLDENGHRIVSSLEGTDNAVVLQKRLDDMGQRWHELC  11069

Query  331    KKSLNIR  337
               K ++IR
Sbjct  11068  NKVMSIR  11048


 Score = 76.3 bits (186),  Expect = 9e-11, Method: Compositional matrix adjust.
 Identities = 40/63 (63%), Positives = 47/63 (74%), Gaps = 0/63 (0%)
 Frame = -3

Query  217    VSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMK  276
                ++EA LE   R LQ + LDLEKFL WLTEAETTANVLQDAT KE LLE+   V+ L++
Sbjct  17500  AGDKEADLEAGLRQLQHYYLDLEKFLNWLTEAETTANVLQDATFKEGLLENPTTVRHLLE  17321

Query  277    QWQ  279
              QWQ
Sbjct  17320  QWQ  17312


 Score = 70.1 bits (170),  Expect = 8e-09, Method: Compositional matrix adjust.
 Identities = 32/63 (50%), Positives = 44/63 (69%), Gaps = 0/63 (0%)
 Frame = -1

Query  336   IRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKREL  395
             +R +L+A  DQWK LH+SLQELL WLQLK +EL +Q P+GGD P V +Q   H+    ++
Sbjct  9612  LRPYLDAGVDQWKHLHMSLQELLNWLQLKREELEKQKPVGGDVPTVHQQLLTHKVSPGQI  9433

Query  396   KTK  398
             + K
Sbjct  9432  QFK  9424


 Score = 65.5 bits (158),  Expect = 2e-07, Method: Compositional matrix adjust.
 Identities = 28/46 (60%), Positives = 38/46 (82%), Gaps = 0/46 (0%)
 Frame = -1

Query  10     PALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKA  55
               AL  FN++WTEL DWL+LLD ++++QRVMVGDL++INEM +K K 
Sbjct  23832  AALDKFNKSWTELDDWLALLDHMVQTQRVMVGDLDEINEMTVKLKV  23695


 Score = 61.6 bits (148),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 29/51 (56%), Positives = 38/51 (74%), Gaps = 0/51 (0%)
 Frame = -3

Query  519   KALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV  569
             +A + EIAP+++NV+HVN LA       IQLSP NLS ++DLN RW+LLQV
Sbjct  3907  QAFQEEIAPIQDNVNHVNQLASTFRPSDIQLSPDNLSRIDDLNMRWRLLQV  3755


 Score = 54.7 bits (130),  Expect = 3e-04, Method: Compositional matrix adjust.
 Identities = 26/40 (65%), Positives = 32/40 (80%), Gaps = 0/40 (0%)
 Frame = -2

Query  54     KATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  93
              ++ +QD+EQR PQL + ITAAQNLKNKT+N E R  ITDR
Sbjct  21932  QSALQDMEQRCPQLNKQITAAQNLKNKTNNPETRATITDR  21813


>gb|AC094963.9| Rattus norvegicus X BAC CH230-6L20 (Children's Hospital Oakland 
Research Institute) complete sequence
Length=213440

 Score =  132 bits (331),  Expect = 2e-27, Method: Compositional matrix adjust.
 Identities = 65/75 (86%), Positives = 70/75 (93%), Gaps = 0/75 (0%)
 Frame = +2

Query  94     IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
              +ERIQ QWDEVQE LQNRRQQLNEMLKDSTQWLEAKEEAEQV+GQAR KL+SWKEGP+T+
Sbjct  74708  VERIQIQWDEVQEQLQNRRQQLNEMLKDSTQWLEAKEEAEQVIGQARGKLDSWKEGPHTM  74887

Query  154    DAIQKKITETKQLAK  168
              DAIQKKITETK  AK
Sbjct  74888  DAIQKKITETKVSAK  74932


 Score =  117 bits (292),  Expect = 5e-23, Method: Compositional matrix adjust.
 Identities = 57/64 (89%), Positives = 62/64 (96%), Gaps = 0/64 (0%)
 Frame = +3

Query  216     RVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELM  275
               RVSEREAALEET RLLQQFPLDLEKFLAW+TEAETTANVLQDA+RKE+LLEDS+GV+ELM
Sbjct  129282  RVSEREAALEETQRLLQQFPLDLEKFLAWITEAETTANVLQDASRKEKLLEDSRGVRELM  129461

Query  276     KQWQ  279
               K WQ
Sbjct  129462  KPWQ  129473


 Score = 92.0 bits (227),  Expect = 2e-15, Method: Compositional matrix adjust.
 Identities = 46/52 (88%), Positives = 47/52 (90%), Gaps = 0/52 (0%)
 Frame = +1

Query  165    QLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  216
              QLAKDLRQ Q NVDVANDLALKLLRDYSADDTRKVHMITENIN SW +I KR
Sbjct  89557  QLAKDLRQRQINVDVANDLALKLLRDYSADDTRKVHMITENINTSWGNILKR  89712


 Score = 78.6 bits (192),  Expect = 2e-11, Method: Compositional matrix adjust.
 Identities = 38/40 (95%), Positives = 40/40 (100%), Gaps = 0/40 (0%)
 Frame = +1

Query  54     KATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  93
              +AT+QDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR
Sbjct  29866  QATLQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  29985


>gb|M86892.1|HUMDYST09 H.sapiens dystrophin gene, exon 68
Length=354

 Score =  130 bits (327),  Expect = 5e-27, Method: Composition-based stats.
 Identities = 62/76 (81%), Positives = 65/76 (85%), Gaps = 4/76 (5%)
 Frame = +1

Query  791  VASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQ  850
            ++SFG     PS+      ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQ
Sbjct  46   LSSFG----PPSLSLLSLQANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQ  213

Query  851  AKCNICKECPIIGFRY  866
            AKCNICKECPIIGFRY
Sbjct  214  AKCNICKECPIIGFRY  261


>gb|DQ443727.1| Mus musculus dystrotelin mRNA, complete cds
Length=2427

 Score =  130 bits (327),  Expect = 5e-27, Method: Compositional matrix adjust.
 Identities = 87/297 (29%), Positives = 144/297 (48%), Gaps = 12/297 (4%)
 Frame = +2

Query  636   ADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDAL-DQHNLKQNDQPMDILQIINCL  694
               LN V  S YRTA KLR +Q    LDL+        L    + +  +  + + Q+   L
Sbjct  320   GTLNRVENSVYRTAFKLRSVQTLCQLDLMDSFLIQQVLWRGRSGESTETSISVQQLFQEL  499

Query  695   TTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDK  754
               ++ R    +   V+ P   ++ L+ L+ ++D   +G ++       +++L       K
Sbjct  500   RELFQRTGMGNAAQVH-PRAPELTLSLLMAMFDRTGSGILKRQPVAAALVALSGDSPLTK  676

Query  755   YRYLFKQVA-------SSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCF  807
             YR  F+  A        S     +R L  LL D  QIP  +GE  S+    +E ++ SCF
Sbjct  677   YRAFFQLYAEKNRRGDDSQARMTRRVLRALLTDLQQIPTVVGE--SYTLRPVESAIHSCF  850

Query  808   QFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYR  867
             +   +   I+   FL W + EP  ++WLP  +R++AAET  H  +C++C+  PIIG RY 
Sbjct  851   RGVLSS-GIKEEKFLSWAQSEPLVLLWLPTCYRLSAAETVTHPVRCSVCRTFPIIGLRYH  1027

Query  868   SLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKR  924
              LK  ++DIC+ CF SG     H+  + ++E C   ++ E+ +   + L+N    KR
Sbjct  1028  CLKCLDFDICELCFLSGLHKNSHEKSHTVMEECVQMSATENTKLLFRSLRNNLPQKR  1198


>ref|XM_001606073.1| PREDICTED: Nasonia vitripennis similar to ENSANGP00000002882 
(LOC100122516), mRNA
Length=1842

 Score =  130 bits (326),  Expect = 6e-27, Method: Compositional matrix adjust.
 Identities = 61/171 (35%), Positives = 94/171 (54%), Gaps = 0/171 (0%)
 Frame = +1

Query  751  LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
            LE+KY YLF Q+A       +  L  LL +  +I   LGE  ++G   I  S+ +CF   
Sbjct  211  LEEKYGYLFHQLADHNACLSRVALNTLLTNICKITEMLGENVAYGNHLIRTSIDNCFSVT  390

Query  811  NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
                 +  A F  W+  EP  ++W+  L+R+ +AE   H +KC+ CK  PI G RY  LK
Sbjct  391  QGCLGVSEAEFAAWLMQEPPLLMWITTLNRIKSAEQIVHNSKCSSCKTTPIRGPRYSCLK  570

Query  871  HFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFR  921
               Y+ CQ+CF  G+++  HK+ +P+ EYC  T+S E  +   ++++NK R
Sbjct  571  CTGYNQCQTCFLYGKISGKHKLKHPVREYCIKTSSKEITKLLLELIRNKLR  723


>emb|AL806516.4| Mouse DNA sequence from clone RP23-453N20 on chromosome X Contains 
part of the Dmd gene for dystrophin muscular dystrophy 
and a CpG island, complete sequence
Length=179534

 Score =  130 bits (326),  Expect = 7e-27, Method: Compositional matrix adjust.
 Identities = 63/71 (88%), Positives = 67/71 (94%), Gaps = 0/71 (0%)
 Frame = +1

Query  94      IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
               +ERIQ QWDEVQE LQNRRQQLNEMLKDSTQWLEAKEEAEQV+GQ R KL+SWKEGP+TV
Sbjct  106690  VERIQIQWDEVQEQLQNRRQQLNEMLKDSTQWLEAKEEAEQVIGQVRGKLDSWKEGPHTV  106869

Query  154     DAIQKKITETK  164
               DAIQKKITETK
Sbjct  106870  DAIQKKITETK  106902


 Score =  116 bits (291),  Expect = 6e-23, Method: Compositional matrix adjust.
 Identities = 56/64 (87%), Positives = 63/64 (98%), Gaps = 0/64 (0%)
 Frame = +2

Query  216     RVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELM  275
               RVSE+EAALEETHRLLQQFPLDLEKFL+W+TEAETTANVLQDA+RKE+LLEDS+GV+ELM
Sbjct  178166  RVSEQEAALEETHRLLQQFPLDLEKFLSWITEAETTANVLQDASRKEKLLEDSRGVRELM  178345

Query  276     KQWQ  279
               K WQ
Sbjct  178346  KPWQ  178357


 Score =  112 bits (279),  Expect = 2e-21, Method: Compositional matrix adjust.
 Identities = 52/55 (94%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = +2

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKA  55
             MPSSL+LEVPALADFNRAWTELTDWLSLLD+VIKSQRVMVGDLEDINEMIIKQK 
Sbjct  5336  MPSSLLLEVPALADFNRAWTELTDWLSLLDRVIKSQRVMVGDLEDINEMIIKQKV  5500


 Score = 94.4 bits (233),  Expect = 4e-16, Method: Compositional matrix adjust.
 Identities = 47/56 (83%), Positives = 49/56 (87%), Gaps = 0/56 (0%)
 Frame = +3

Query  161     TETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  216
               T   QLAKDLRQ Q +VDVANDLALKLLRDYSADDTRKVHMITENIN SW +IHKR
Sbjct  130215  THV*QLAKDLRQRQISVDVANDLALKLLRDYSADDTRKVHMITENINTSWGNIHKR  130382


 Score = 77.8 bits (190),  Expect = 3e-11, Method: Compositional matrix adjust.
 Identities = 38/40 (95%), Positives = 40/40 (100%), Gaps = 0/40 (0%)
 Frame = +2

Query  54     KATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  93
              +AT+QDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR
Sbjct  63002  QATLQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  63121


>emb|AJ544612.1| Takifugu rubripes dmd gene for putative dystrophin, exons 57-65
Length=14136

 Score = 78.2 bits (191),  Expect(2) = 9e-27, Method: Compositional matrix adjust.
 Identities = 34/59 (57%), Positives = 51/59 (86%), Gaps = 0/59 (0%)
 Frame = +3

Query  279   QDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIR  337
             QDLQ EI++HT++YH+LDEN Q+I+ SL  ++DA LL+RRLDNM+ +W++LR K+L++R
Sbjct  3903  QDLQAEIDSHTELYHSLDENGQRIVTSLGDTEDAALLRRRLDNMSQRWNDLRTKTLSMR  4079


 Score = 72.0 bits (175),  Expect(2) = 9e-27, Method: Compositional matrix adjust.
 Identities = 33/60 (55%), Positives = 43/60 (71%), Gaps = 0/60 (0%)
 Frame = +2

Query  331   KKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRA  390
             K  L  R+HLE+    WKRLH+SLQELL WL+L++ +L ++ P+GGD PAVQ Q D HR 
Sbjct  4142  KPRLFSRAHLESEMAPWKRLHMSLQELLNWLRLRNQQLEKEPPVGGDVPAVQAQLDTHRV  4321


 Score =  103 bits (258),  Expect = 4e-19, Method: Compositional matrix adjust.
 Identities = 49/91 (53%), Positives = 74/91 (81%), Gaps = 0/91 (0%)
 Frame = +3

Query  430   ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLK  489
             ++ PEERAQNV R++RK+A++V  +W++LN  S +WQ+K++  L+RL ELQEA D LD +
Sbjct  8382  DISPEERAQNVGRVIRKEADDVIMKWDRLNTDSVEWQKKLELALDRLMELQEAEDLLDGQ  8561

Query  490   LRQAEVIKGSWQPVGDLLIDSLQDHLEKVKA  520
             LRQAE++K +W+PVGDLLI+SL ++++K K 
Sbjct  8562  LRQAEMVKEAWEPVGDLLIESLPENIDKAKV  8654


 Score = 76.6 bits (187),  Expect = 7e-11, Method: Compositional matrix adjust.
 Identities = 52/166 (31%), Positives = 76/166 (45%), Gaps = 37/166 (22%)
 Frame = +2

Query  88   TIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWK  147
            T     ++R+Q  W++    L +R +QL+ M +DS  WL+AK+  +  + +A  +LESW 
Sbjct  26   TFFVPVVDRLQAHWEDSHTKLLDRMKQLHNMQQDSIDWLDAKKRVDVHISRASDRLESWL  205

Query  148  EGPYTVDAIQKKITETK-------------------------------------QLAKDL  170
            E  YTVD ++K+  E K                                        K+L
Sbjct  206  EITYTVDELKKQNAELKVGLELLTLRMHQVSAGLNW*ERQLLHIYH*PGFPPLQVFMKEL  385

Query  171  RQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  216
            +QWQ  VD  N LA  LL  Y+ DDT KV  +  N+ A+W  I KR
Sbjct  386  QQWQGQVDETNALADNLLTLYANDDTHKVTQVNNNMMATWTHISKR  523


 Score = 76.3 bits (186),  Expect = 1e-10, Method: Compositional matrix adjust.
 Identities = 44/78 (56%), Positives = 52/78 (66%), Gaps = 4/78 (5%)
 Frame = +1

Query  202   ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
             +T  I+A     H  VS+R+ ALE   +LLQQF LDL+KFL WLTEAETT NVL DAT K
Sbjct  826   VTSVISAK---CHSSVSDRKTALEAALKLLQQFYLDLDKFLNWLTEAETTCNVLIDATNK  996

Query  262   ERLLEDSKGVKELMKQWQ  279
             ERL E     K L+ QW+
Sbjct  997   ERLPEQP-AAKNLLAQWK  1047


 Score = 59.3 bits (142),  Expect = 1e-05, Method: Compositional matrix adjust.
 Identities = 27/52 (51%), Positives = 38/52 (73%), Gaps = 0/52 (0%)
 Frame = +3

Query  518   VKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV  569
             ++  + EIAP+K++V+H+N LA       IQLSP NL  ++DLNTRW+LLQV
Sbjct  9237  MQEFQEEIAPIKDDVTHMNQLASTFGPHDIQLSPANLERIDDLNTRWRLLQV  9392


>gb|AF213440.1|AF213440 Homo sapiens dystrophin (DMD) gene, exon 55 and partial cds
Length=618

 Score =  129 bits (323),  Expect = 1e-26, Method: Compositional matrix adjust.
 Identities = 67/74 (90%), Positives = 68/74 (91%), Gaps = 0/74 (0%)
 Frame = +1

Query  206  INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
            I AS   +  RVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL
Sbjct  70   IIASEHLVLCRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  249

Query  266  EDSKGVKELMKQWQ  279
            EDSKGVKELMKQWQ
Sbjct  250  EDSKGVKELMKQWQ  291


>gb|AC079175.24| Homo sapiens Xp BAC RP11-122N14 (Roswell Park Cancer Institute 
Human BAC Library) complete sequence
Length=163198

 Score =  129 bits (323),  Expect = 1e-26, Method: Compositional matrix adjust.
 Identities = 67/74 (90%), Positives = 68/74 (91%), Gaps = 0/74 (0%)
 Frame = +1

Query  206    INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
              I AS   +  RVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL
Sbjct  34336  IIASEHLVLCRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  34515

Query  266    EDSKGVKELMKQWQ  279
              EDSKGVKELMKQWQ
Sbjct  34516  EDSKGVKELMKQWQ  34557


 Score =  120 bits (300),  Expect = 6e-24, Method: Compositional matrix adjust.
 Identities = 58/58 (100%), Positives = 58/58 (100%), Gaps = 0/58 (0%)
 Frame = +1

Query  280     DLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIR  337
               DLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIR
Sbjct  154777  DLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIR  154950


 Score =  109 bits (272),  Expect = 1e-20, Method: Compositional matrix adjust.
 Identities = 52/52 (100%), Positives = 52/52 (100%), Gaps = 0/52 (0%)
 Frame = +3

Query  165   QLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  216
             QLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR
Sbjct  4086  QLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  4241


>gb|AY525165.1| Gallus gallus clone Dp71shoB putative short dystrophin mRNA, 
partial cds
Length=173

 Score =  128 bits (322),  Expect = 2e-26, Method: Compositional matrix adjust.
 Identities = 57/57 (100%), Positives = 57/57 (100%), Gaps = 0/57 (0%)
 Frame = +3

Query  597  VQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLR  653
            VQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLR
Sbjct  3    VQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLR  173


>ref|XM_001892815.1| Brugia malayi Zinc finger, ZZ type family protein partial mRNA
Length=1644

 Score =  128 bits (321),  Expect = 2e-26, Method: Compositional matrix adjust.
 Identities = 127/504 (25%), Positives = 210/504 (41%), Gaps = 91/504 (18%)
 Frame = +1

Query  725   VYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQI  784
             +Y    TGR+ V + K  + +LC   L DK RY F QV++S+G  +  +    L   + +
Sbjct  16    LYFRQHTGRLTVFAIKIALATLCAGKLMDKLRYAFSQVSNSSGTMEWDKFSGYLQQVLAL  195

Query  785   PRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVA  842
                + E  +FG +  E ++  CFQ       +    FLD M  +P    ++WLP+LHR+A
Sbjct  196   ATAVFEGPTFGYT--ETALGQCFQ---KDQRVNLNAFLDVMLADPCPPCLMWLPLLHRMA  360

Query  843   AAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTP  902
             + E   H   C+ C+     GFRY+  +  NY +C+ CF+ GR +  H   + M EY   
Sbjct  361   SVEHVYHPVVCDACQVRSFTGFRYKCQRCTNYQLCEQCFWRGRTSSAHSNEHEMKEY---  531

Query  903   TTSGEDVRDFAKVLKNKFRTKRY--FAKHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT  960
             ++     +  A  +    R       + HP     P + +   D       +P  S    
Sbjct  532   SSYKSPTKQLAHSIHKSLRCVPVPNRSTHPIFPERPERPL---DLANILPITPTTSRRRL  702

Query  961   HSRIEHYASRL--AEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDS--PLSQPR  1016
                ++ + S++   +   +NGS          ++DDEH LI  Y   L+  +  P   P+
Sbjct  703   SEGLKDWTSQILPGQFPVTNGS----------NMDDEHKLIARYSAKLSGRTQYPFVLPK  852

Query  1017  SPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTS  1076
               A  +     +E    + ++A LEEEN  +  E + LKQQ E +               
Sbjct  853   DRATSM-----DENLNEKTLIARLEEENGEMIREMEMLKQQQELENT-------------  978

Query  1077  PQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGT  1136
                  D +L      LR+ K +LE +M+I++   +QL  QL  L   L Q +      G+
Sbjct  979   -----DEQLNG----LRERKAQLEEKMRIMQQTRRQLMQQLEVLMSELNQSKG-----GS  1116

Query  1137  TVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPS  1196
               + P +            L  +GS+                 ST   +   Q  +S P+
Sbjct  1117  MGAIPES------------LTGIGSR----------------VSTAFRDRAVQRASSVPA  1212

Query  1197  SRGHNVGSLFHMADDLGRAMESLV  1220
             ++    G L H ADD+   M +L+
Sbjct  1213  AQLQ--GDLLHAADDITNNMSTLL  1278


>gb|EF473649.1| Danio rerio utrophin-like mRNA, partial sequence
Length=10542

 Score =  127 bits (318),  Expect = 5e-26, Method: Compositional matrix adjust.
 Identities = 102/234 (43%), Positives = 137/234 (58%), Gaps = 52/234 (22%)
 Frame = +2

Query  993    DDEHLLIQHYCQSLN-QDSPLSQPRSPA---------------------QILISLESEER  1030
              D+EH LI  YCQ+L  + S  SQP+SPA                     QIL ++E EER
Sbjct  9620   DEEHALILQYCQTLGGEGSSFSQPQSPAHINRTPTHNTHSPSYLLQSPAQILQAVEREER  9799

Query  1031   GELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAK  1090
              GELERI+A LE++ R LQ EY+ L+ Q+                 +  +P +A+L+AEAK
Sbjct  9800   GELERIIARLEDDQRVLQREYEELRFQYGQP----------GAAAASGAPDEADLLAEAK  9949

Query  1091   LLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDS  1150
              LLRQHKGRLEARMQILEDHNKQLESQL+RLRQLL QP+    +NGT+ SS   SL +  +
Sbjct  9950   LLRQHKGRLEARMQILEDHNKQLESQLYRLRQLLHQPE----LNGTSSSS---SLHQDAA  10108

Query  1151   SQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGS  1204
               QP +              ++ L    ++++ L EVM+Q+N+SFP+    +V S
Sbjct  10109  GQPEI-------------SDEFLHQCANSNSALAEVMDQINHSFPACSPSSVSS  10231


>dbj|AB171279.1| Macaca fascicularis brain cDNA clone: QorA-13928, similar to 
human dystrobrevin, alpha (DTNA), transcript variant 2, mRNA, 
RefSeq: NM_032975.2
Length=1832

 Score =  113 bits (283),  Expect(2) = 7e-26, Method: Compositional matrix adjust.
 Identities = 62/183 (33%), Positives = 95/183 (51%), Gaps = 7/183 (3%)
 Frame = +3

Query  719   LNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLL  778
             L   L  +D    G+I V + K  + +LC   + DK RY+F  ++ S+G     R    L
Sbjct  579   LTSCLQRFDPEGHGKISVFAVKMALATLCGGKIMDKLRYIFSMISDSSGVMVYGRYDQFL  758

Query  779   HDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEP--QSMVWLP  836
              + +++P  + E  SFG +  E S RSCF   + + ++    FLD +  +P  Q +VWLP
Sbjct  759   REVLKLPTAVFEGPSFGYT--EQSARSCF---SQQKKVTLNGFLDTLMSDPPPQCLVWLP  923

Query  837   VLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPM  896
             +LHR+A  E   H  +C+ C    ++GFRYR  +  NY +CQ CF+ G     H   + M
Sbjct  924   LLHRLANVENVFHPVECSYCHSESMMGFRYRCQQCHNYQLCQDCFWRGHAGGSHSNQHQM  1103

Query  897   VEY  899
              EY
Sbjct  1104  KEY  1112


 Score = 34.3 bits (77),  Expect(2) = 7e-26, Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 40/69 (57%), Gaps = 2/69 (2%)
 Frame = +1

Query  637  DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQ--PMDILQIINCL  694
            DL+ +R S YRTA KLR +QK   L L+ +    +AL ++ L   D    +++ ++   L
Sbjct  319  DLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNIELNVSRLEAVL  498

Query  695  TTIYDRLEQ  703
            +TI+ +L +
Sbjct  499  STIFYQLNK  525


>dbj|AK094494.1| Homo sapiens cDNA FLJ37175 fis, clone BRACE2028410, highly similar 
to Homo sapiens beta-dystrobrevin (BDTN) mRNA
Length=2200

 Score = 79.3 bits (194),  Expect(2) = 4e-25, Method: Compositional matrix adjust.
 Identities = 56/193 (29%), Positives = 98/193 (50%), Gaps = 13/193 (6%)
 Frame = +1

Query  637  DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
            + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  202  NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRNNGLNTLDHTTEISVSRLETVI  381

Query  695  TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
            ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  382  SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  555

Query  751  LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
            + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  556  MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  723

Query  811  NNKPEIEAALFLD  823
              + +I   +FLD
Sbjct  724  -QQRKIMLNMFLD  759


 Score = 65.9 bits (159),  Expect(2) = 4e-25, Method: Compositional matrix adjust.
 Identities = 28/71 (39%), Positives = 43/71 (60%), Gaps = 0/71 (0%)
 Frame = +2

Query  829  PQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAK  888
            PQ +VWLP++HR+A  E   H  +C+ C+   ++GFRYR  +  NY +CQ+CF+ G    
Sbjct  779  PQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRCQQCHNYQLCQNCFWRGHAGG  958

Query  889  GHKMHYPMVEY  899
             H   + M E+
Sbjct  959  PHSNQHQMKEH  991


>emb|AJ544620.1| Takifugu rubripes utrn gene for putative utrophin, exons 55-78
Length=56648

 Score = 95.5 bits (236),  Expect(2) = 9e-25, Method: Compositional matrix adjust.
 Identities = 50/84 (59%), Positives = 56/84 (66%), Gaps = 6/84 (7%)
 Frame = +3

Query  652    LRRLQKALCL------DLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEH  705
              L  L   LCL      DLL L+ A +   QH L  N Q + +  IINCLT+IYD LEQEH
Sbjct  34815  LTPLSSVLCLLPSPAVDLLDLNVAQNTFKQHKLANNSQLLSVPDIINCLTSIYDGLEQEH  34994

Query  706    NNLVNVPLCVDMCLNWLLNVYDTG  729
               +LVNVPLCVDMCLNWLLNVYDT 
Sbjct  34995  KDLVNVPLCVDMCLNWLLNVYDTC  35066


 Score = 48.1 bits (113),  Expect(2) = 9e-25, Method: Compositional matrix adjust.
 Identities = 19/28 (67%), Positives = 25/28 (89%), Gaps = 0/28 (0%)
 Frame = +2

Query  729    GRTGRIRVLSFKTGIISLCKAHLEDKYR  756
              GR+G+IRVLS K G++SLCK HLE+KY+
Sbjct  35183  GRSGKIRVLSMKIGLLSLCKGHLEEKYK  35266


 Score =  108 bits (270),  Expect = 2e-20, Method: Compositional matrix adjust.
 Identities = 49/59 (83%), Positives = 53/59 (89%), Gaps = 0/59 (0%)
 Frame = +1

Query  811    NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSL  869
              NNK E+E   F+DWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI+GFR  +L
Sbjct  38485  NNKVELEPRQFVDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIVGFR*SAL  38661


 Score =  108 bits (269),  Expect = 2e-20, Method: Compositional matrix adjust.
 Identities = 50/89 (56%), Positives = 66/89 (74%), Gaps = 0/89 (0%)
 Frame = +1

Query  430    ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLK  489
              +L PEE+A+ + R +RKQ  EV   WE+L  H   WQ ++D+ LERLQELQ + D+LDL+
Sbjct  25009  DLTPEEKARGLARAIRKQTGEVRERWERLKGHIGGWQSQVDQALERLQELQSSMDQLDLR  25188

Query  490    LRQAEVIKGSWQPVGDLLIDSLQDHLEKV  518
              L QAE  K +WQPVGDLLID+LQDH++K 
Sbjct  25189  LTQAEEAKAAWQPVGDLLIDALQDHIDKT  25275


 Score = 96.7 bits (239),  Expect = 8e-17, Method: Compositional matrix adjust.
 Identities = 55/85 (64%), Positives = 65/85 (76%), Gaps = 8/85 (9%)
 Frame = +1

Query  1045   RNLQAEYDRLKQQHEHKGLSPLPSPPEMM---PTSPQSPRDAELIAEAKLLRQHKGRLEA  1101
              RNLQ EY++L++QH  +G     +PPE      TS   P +A+L+AEAKLLRQHKGRLEA
Sbjct  51496  RNLQREYEQLQEQHGQRG-----APPEGQWESETSFSHPDEADLLAEAKLLRQHKGRLEA  51660

Query  1102   RMQILEDHNKQLESQLHRLRQLLEQ  1126
              RM ILE+HNKQLESQLHRLRQLL Q
Sbjct  51661  RMHILEEHNKQLESQLHRLRQLLHQ  51735


 Score = 94.4 bits (233),  Expect = 3e-16, Method: Compositional matrix adjust.
 Identities = 42/53 (79%), Positives = 48/53 (90%), Gaps = 0/53 (0%)
 Frame = +2

Query  903    TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQL  955
              TTSGED+RDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDNMET  ++  L
Sbjct  41618  TTSGEDMRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNMET*VTTEGL  41776


 Score = 92.0 bits (227),  Expect = 2e-15, Method: Compositional matrix adjust.
 Identities = 42/51 (82%), Positives = 47/51 (92%), Gaps = 0/51 (0%)
 Frame = +1

Query  758    LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
              LF QVAS+   CDQR+LGLLLH++IQIPRQLGEVA+FGGSNIEPSVRSCFQ
Sbjct  36361  LFSQVASAGDTCDQRQLGLLLHEAIQIPRQLGEVAAFGGSNIEPSVRSCFQ  36513


 Score = 88.2 bits (217),  Expect = 3e-14, Method: Compositional matrix adjust.
 Identities = 36/52 (69%), Positives = 44/52 (84%), Gaps = 2/52 (3%)
 Frame = +2

Query  860    PIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRD  911
              P++  RYRSLKHFNYD+CQSCFFSGR AKGHK++YPMVEYCTP ++   + D
Sbjct  40253  PVV--RYRSLKHFNYDVCQSCFFSGRTAKGHKLNYPMVEYCTPVSAPGCLHD  40402


 Score = 70.5 bits (171),  Expect = 6e-09, Method: Compositional matrix adjust.
 Identities = 30/68 (44%), Positives = 49/68 (72%), Gaps = 0/68 (0%)
 Frame = +3

Query  271    VKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELR  330
              +  L   ++D+Q EI+AH D+Y ++D N  K++++L  S++A  LQ RLD+MN +W++L+
Sbjct  18084  ISSLSAVFKDIQAEIDAHNDIYKSVDGNKSKMVKALGSSEEAAFLQHRLDDMNQRWNDLK  18263

Query  331    KKSLNIRS  338
               KS NIRS
Sbjct  18264  AKSANIRS  18287


 Score = 56.2 bits (134),  Expect = 1e-04, Method: Compositional matrix adjust.
 Identities = 25/31 (80%), Positives = 28/31 (90%), Gaps = 0/31 (0%)
 Frame = +3

Query  630    ELYQSLADLNNVRFSAYRTAMKLRRLQKALC  660
               L+  +ADLNNVRFSAYRTAMK+RRLQKALC
Sbjct  32766  SLFLPVADLNNVRFSAYRTAMKIRRLQKALC  32858


 Score = 55.8 bits (133),  Expect = 1e-04, Method: Compositional matrix adjust.
 Identities = 25/50 (50%), Positives = 39/50 (78%), Gaps = 1/50 (2%)
 Frame = +3

Query  337    RSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPA-VQKQN  385
              R+HLEAS+++W RL   L+EL  W+ +KD++L++Q P+GGD P  +Q+QN
Sbjct  19101  RAHLEASAERWSRLLGLLEELWRWICMKDEDLAKQMPVGGDVPTLLQQQN  19250


 Score = 55.5 bits (132),  Expect = 2e-04, Method: Compositional matrix adjust.
 Identities = 29/52 (55%), Positives = 37/52 (71%), Gaps = 0/52 (0%)
 Frame = +1

Query  519    KALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVA  570
              +A R EIAPL+++V  VN+L+ +LT L IQLS      L+ LN RWKLLQVA
Sbjct  26074  QAFREEIAPLRQDVRVVNELSAELTPLDIQLSSTAARQLDQLNMRWKLLQVA  26229


 Score = 51.6 bits (122),  Expect = 0.003, Method: Compositional matrix adjust.
 Identities = 37/54 (68%), Positives = 43/54 (79%), Gaps = 1/54 (1%)
 Frame = +3

Query  993    DDEHLLIQHYCQSLN-QDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
              DDEH LI  YCQ+L  + SP SQP+SPAQIL ++E EERGELERI+A LEEE R
Sbjct  51207  DDEHTLILQYCQTLGGESSPCSQPQSPAQILQAVEREERGELERIIARLEEEQR  51368


 Score = 51.6 bits (122),  Expect = 0.003, Method: Compositional matrix adjust.
 Identities = 22/29 (75%), Positives = 27/29 (93%), Gaps = 0/29 (0%)
 Frame = +3

Query  567    LQVAVEDRVRQLHEAHRDFGPASQHFLST  595
              +QVAVEDR++ L EAHRDFGP+SQHFLS+
Sbjct  27339  VQVAVEDRLKLLQEAHRDFGPSSQHFLSS  27425


 Score = 47.8 bits (112),  Expect = 0.037, Method: Compositional matrix adjust.
 Identities = 18/21 (85%), Positives = 20/21 (95%), Gaps = 0/21 (0%)
 Frame = +2

Query  616    HETQTTCWDHPKMTELYQSLA  636
              H+TQTTCWDHPKMTELYQ+L 
Sbjct  32030  HQTQTTCWDHPKMTELYQTLG  32092


 Score = 40.0 bits (92),  Expect = 7.4, Method: Compositional matrix adjust.
 Identities = 18/19 (94%), Positives = 18/19 (94%), Gaps = 0/19 (0%)
 Frame = +1

Query  952    SPQLSHDDTHSRIEHYASR  970
              SPQLSHDDTHSRIE YASR
Sbjct  44701  SPQLSHDDTHSRIEQYASR  44757


>gb|AC152831.2| Ornithorhynchus anatinus chromosome UNK clone OABb-168A1, complete 
sequence
Length=139370

 Score = 73.6 bits (179),  Expect(2) = 2e-24, Method: Compositional matrix adjust.
 Identities = 32/49 (65%), Positives = 39/49 (79%), Gaps = 0/49 (0%)
 Frame = +1

Query  900    CTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
              C  TTS E++RDFA  LKNKFR+K YF++HP+ GYLPVQ+VLE D  ET
Sbjct  69037  CPQTTSSENMRDFATTLKNKFRSKHYFSRHPQRGYLPVQSVLEADFSET  69183


 Score = 68.9 bits (167),  Expect(2) = 2e-24, Method: Compositional matrix adjust.
 Identities = 29/47 (61%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
 Frame = +2

Query  860    PIIGF-RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTS  905
              P+  F RYRSLK FN DICQ CF +GR +KG+K+HYP++EY TP  S
Sbjct  68780  PVPPFPRYRSLKQFNVDICQMCFLTGRASKGNKLHYPIMEYYTPVRS  68920


 Score = 94.4 bits (233),  Expect = 4e-16, Method: Compositional matrix adjust.
 Identities = 39/57 (68%), Positives = 49/57 (85%), Gaps = 0/57 (0%)
 Frame = +1

Query  758    LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKP  814
              LF QVA   G CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EPS+RSCF+F + +P
Sbjct  66739  LFSQVAHPGGLCDQRHLGILLHEAIQVPRQLGEVAAFGGSNVEPSIRSCFRFVSAEP  66909


 Score = 89.0 bits (219),  Expect = 2e-14, Method: Compositional matrix adjust.
 Identities = 37/57 (64%), Positives = 43/57 (75%), Gaps = 0/57 (0%)
 Frame = +3

Query  810    ANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRY  866
              +  KP +E A FL+W  LEPQSMVWL VLHRVA AE  KHQ KC++C+ CPI GFRY
Sbjct  67434  STGKPVVEVAQFLEWANLEPQSMVWLAVLHRVALAEPVKHQTKCSVCRHCPIKGFRY  67604


 Score = 87.4 bits (215),  Expect = 4e-14, Method: Compositional matrix adjust.
 Identities = 37/67 (55%), Positives = 52/67 (77%), Gaps = 0/67 (0%)
 Frame = +3

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              +DL+ LS A +  ++H L+  +  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LN
Sbjct  64962  VDLVPLSTALEIFNEHELQPGEHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMTLN  65141

Query  721    WLLNVYD  727
              WLLNVYD
Sbjct  65142  WLLNVYD  65162


 Score = 84.0 bits (206),  Expect = 5e-13, Method: Compositional matrix adjust.
 Identities = 41/93 (44%), Positives = 59/93 (63%), Gaps = 0/93 (0%)
 Frame = +3

Query  430    ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLK  489
              ++ P  R QN +RL+ KQA   +  WEKL     D  R I+ TLE+L +++ A +ELD  
Sbjct  60486  DVSPRLRGQNGSRLVWKQATVASELWEKLTARCVDQHRHIERTLEQLLDVRRAMEELDAS  60665

Query  490    LRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALR  522
              L QAE ++ +W+P+GDL IDSL DH++  K  R
Sbjct  60666  LGQAEGVRATWEPIGDLFIDSLPDHIQTTKVGR  60764


 Score = 74.3 bits (181),  Expect = 4e-10, Method: Compositional matrix adjust.
 Identities = 42/71 (59%), Positives = 49/71 (69%), Gaps = 2/71 (2%)
 Frame = +2

Query  1045   RNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ  1104
              R LQ E  RLK QHE  G +P  +     P + Q P + EL+AEA++LRQHK RLE RMQ
Sbjct  71141  RILQGELRRLKWQHEEAGEAPPLA--AGTPEAAQDPHNEELLAEARILRQHKSRLETRMQ  71314

Query  1105   ILEDHNKQLES  1115
              ILEDHNKQLES
Sbjct  71315  ILEDHNKQLES  71347


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 26/62 (41%), Positives = 32/62 (51%), Gaps = 9/62 (14%)
 Frame = +2

Query  588    ASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYR  647
              A Q     SV GP          P   +H+ QTTCWDHPKMTELYQ+L +      + +R
Sbjct  63146  AGQKGHCLSVTGP---------APCVSSHQAQTTCWDHPKMTELYQTLGEKGTTGRAGWR  63298

Query  648    TA  649
               A
Sbjct  63299  RA  63304


 Score = 49.3 bits (116),  Expect = 0.015, Method: Compositional matrix adjust.
 Identities = 22/34 (64%), Positives = 27/34 (79%), Gaps = 0/34 (0%)
 Frame = +2

Query  626    PKMTELYQSLADLNNVRFSAYRTAMKLRRLQKAL  659
              P    L +  A+LNN++FSAYRTAMKLRR+QKAL
Sbjct  63518  PNRVSLCRFPAELNNIKFSAYRTAMKLRRVQKAL  63619


 Score = 48.5 bits (114),  Expect = 0.025, Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 35/57 (61%), Gaps = 0/57 (0%)
 Frame = +3

Query  337    RSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKR  393
              R+ LEA SDQ  +L   LQE++ WL  KD+ELS Q P+ GD   VQ++ + H    R
Sbjct  59226  RARLEAFSDQSGKLQAPLQEIVDWLGHKDEELSAQLPLRGDVALVQQEKETHAVSSR  59396


 Score = 45.1 bits (105),  Expect = 0.25, Method: Compositional matrix adjust.
 Identities = 17/29 (58%), Positives = 25/29 (86%), Gaps = 0/29 (0%)
 Frame = +3

Query  568    QVAVEDRVRQLHEAHRDFGPASQHFLSTS  596
              Q +V +R++QL +AHRDFGP SQHFL+++
Sbjct  61587  QTSVSERLKQLQDAHRDFGPGSQHFLASA  61673


 Score = 44.7 bits (104),  Expect = 0.33, Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 29/47 (61%), Gaps = 0/47 (0%)
 Frame = +2

Query  524    EIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVA  570
              E++P+K+ V  VND A QL    + LS  N   LE +NTRWK LQV 
Sbjct  61142  ELSPMKDGVKLVNDRAHQLAISDVHLSMENSRALEQINTRWKQLQVG  61282


 Score = 43.5 bits (101),  Expect = 0.79, Method: Compositional matrix adjust.
 Identities = 18/22 (81%), Positives = 19/22 (86%), Gaps = 0/22 (0%)
 Frame = +2

Query  594    STSVQGPWERAISPNKVPYYIN  615
              + SVQ PWERAISPNKVPYYI 
Sbjct  62207  TASVQVPWERAISPNKVPYYIK  62272


 Score = 42.7 bits (99),  Expect = 1.4, Method: Compositional matrix adjust.
 Identities = 22/38 (57%), Positives = 27/38 (71%), Gaps = 2/38 (5%)
 Frame = +3

Query  933    GYLPVQTVLEGDNMETPASSPQLSHDDTHSRIEHYASR  970
              G+L  +T+  G +   PASSP L H DTHSRIEH+ASR
Sbjct  69837  GWL-ARTLGRGCSFR-PASSPVLPHADTHSRIEHFASR  69944


>gb|DQ788696.1| Danio rerio utrophin isoform G mRNA, partial cds, alternatively 
spliced
Length=462

 Score =  121 bits (303),  Expect = 3e-24, Method: Compositional matrix adjust.
 Identities = 54/103 (52%), Positives = 82/103 (79%), Gaps = 0/103 (0%)
 Frame = +1

Query  279  QDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRS  338
            +D+Q EIEAH DV+ +++ N  K++++L GS++AV LQ+RLD+MN +WS+L+ KS NIR+
Sbjct  151  KDIQAEIEAHNDVFRSVEGNKLKMVKALGGSEEAVFLQQRLDDMNQRWSDLKAKSANIRA  330

Query  339  HLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAV  381
            HLEAS+++W RL   L++L  W+ LKD+EL++Q PIGGD P +
Sbjct  331  HLEASAERWNRLLSVLEDLSRWIGLKDEELNKQMPIGGDVPTL  459


>dbj|AK240524.1| Sus scrofa mRNA, clone:UTR010089D01, expressed in uterus
Length=1782

 Score =  120 bits (301),  Expect = 5e-24, Method: Compositional matrix adjust.
 Identities = 101/381 (26%), Positives = 168/381 (44%), Gaps = 54/381 (14%)
 Frame = +1

Query  743   IISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPS  802
             + ++C   + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E S
Sbjct  7     LATMCGGKMLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHS  180

Query  803   VRSCFQFANNKPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECP  860
             VR+CF     + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   
Sbjct  181   VRTCFP---QQKKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCGS  351

Query  861   IIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEY-------------------CT  901
             ++GFRYR  +  NY +CQ+CF+ G  +  H   + M E+                   C 
Sbjct  352   MMGFRYRCQQCHNYQLCQNCFWRGHASGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCV  531

Query  902   PTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD---  958
             PT        F +  +            P                 TP    Q S     
Sbjct  532   PTREPPHP-VFPEQPEKPLDLANIVPPRPLANMNDTMVSHMSSGAPTPTKRLQYSQHIPS  708

Query  959   ---DTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQP  1015
                D H+ I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  +  
Sbjct  709   HLADEHALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEA-GNVT  861

Query  1016  RSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPT  1075
             R P  +  + ++ +  +  +++A+LE +NR +  E  RL+ +HE              PT
Sbjct  862   RPPTDLSFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QPT  1005

Query  1076  SPQSPRDAELIAEAKLLRQHK  1096
               ++ ++  L+AE +LLRQ K
Sbjct  1006  PEKAQQNPTLLAELRLLRQRK  1068


>gb|L05647.1|HUMDYSTR13 Homo sapiens dystrophin (DMD) gene, exon 56
Length=360

 Score =  120 bits (300),  Expect = 6e-24, Method: Compositional matrix adjust.
 Identities = 58/58 (100%), Positives = 58/58 (100%), Gaps = 0/58 (0%)
 Frame = +1

Query  280  DLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIR  337
            DLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIR
Sbjct  70   DLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIR  243


>dbj|AK294357.1| Homo sapiens cDNA FLJ57272 complete cds, highly similar to Dystrobrevin 
beta
Length=1495

 Score =  107 bits (266),  Expect(2) = 7e-24, Method: Compositional matrix adjust.
 Identities = 102/375 (27%), Positives = 167/375 (44%), Gaps = 72/375 (19%)
 Frame = +2

Query  758   LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIE  817
             +F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF     + +I 
Sbjct  395   VFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP---QQRKIM  559

Query  818   AALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYD  875
               +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR  +  NY 
Sbjct  560   LNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRCQQCHNYQ  739

Query  876   ICQSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT---------SGE  907
             +CQ+CF+ G     H   + M E+                   C PT            E
Sbjct  740   LCQNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHPVFPEQPE  919

Query  908   DVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD------DTH  961
                D A ++  +  T         M    V  +  G  + TP    Q S D      D H
Sbjct  920   KPLDLAHIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDIPSHLADEH  1069

Query  962   SRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQI  1021
             + I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  +  R P  +
Sbjct  1070  ALIASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEA-GNVTRPPTDL  1222

Query  1022  LISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPR  1081
               + ++ +  +  +++A+LE +NR +  E  RL+ +HE              PT  ++ +
Sbjct  1223  SFNFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------*PTPEKAQQ  1366

Query  1082  DAELIAEAKLLRQHK  1096
             +  L+AE +LLRQ K
Sbjct  1367  NPTLLAELRLLRQRK  1411


 Score = 33.9 bits (76),  Expect(2) = 7e-24, Method: Compositional matrix adjust.
 Identities = 27/97 (27%), Positives = 48/97 (49%), Gaps = 8/97 (8%)
 Frame = +1

Query  637  DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDI--LQIINCL  694
            + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  106  NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  285

Query  695  TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYD  727
            ++IY     RL   H   ++V   + + LN+++  YD
Sbjct  286  SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYD  390


>gb|DQ431251.1| Schistosoma mansoni dystrobrevin mRNA, complete cds
Length=2687

 Score =  118 bits (295),  Expect = 3e-23, Method: Compositional matrix adjust.
 Identities = 81/308 (26%), Positives = 136/308 (44%), Gaps = 28/308 (9%)
 Frame = +3

Query  638   LNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQP---MDILQIINCL  694
              +++RF+AYRTA KLR +Q+    +++ L    +   +  L Q + P   +D       L
Sbjct  300   FDSIRFAAYRTASKLRFIQQRTLFNIMDLWRVVETFREFGLHQLNDPQASLDYGSTFRLL  479

Query  695   TTIYDRLEQEHN------------NLVNVP---LCVDMCLNWLLNVYDTGRTGRIRVLSF  739
             + IY  +   +             N +N P   +  ++ L WL    D   TGR+ V   
Sbjct  480   SRIYSHIPTTNMNVTTTTDETTSTNAINRPAVIIAAEILLGWLGYALDLCATGRLSVTGL  659

Query  740   KTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNI  799
             K  + +L  A   DK+RY F  ++  +G     +    L D +++P     ++ F G+N 
Sbjct  660   KITLSTLTNARPADKFRYHFTLLSDPSGALIFSKFEAYLQDLLKLP-----ISVFEGTNF  824

Query  800   EPSVRSC-FQFANNKPEIEAALFLDWMRLE--PQSMVWLPVLHRVAAAETAKHQAKCNIC  856
               + ++    F      +    FLD M  +  PQ +VWL + HR+ +    +H  +C  C
Sbjct  825   YYTPQASQTMFTGRSKNVVLEEFLDRMLSDQGPQVLVWLTIFHRLISVANVRHNVRCEGC  1004

Query  857   KECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVL  916
             K  PI G RY+  +  +Y++CQ CF+ G     H   + + EY     S    R F   L
Sbjct  1005  KREPICGLRYKCTRCPHYNLCQDCFWIGVTTDQHTNAHDVKEYS--AASKSHSRQFGHSL  1178

Query  917   KNKFRTKR  924
             +  F+  R
Sbjct  1179  RKSFQFGR  1202


>gb|M86891.1|HUMDYST08 H.sapiens dystrophin gene, exon 67
Length=433

 Score =  117 bits (292),  Expect = 5e-23, Method: Composition-based stats.
 Identities = 53/57 (92%), Positives = 54/57 (94%), Gaps = 0/57 (0%)
 Frame = +3

Query  758  LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKP  814
            LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQF +  P
Sbjct  168  LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFVSYSP  338


>emb|AL844151.3| Mouse DNA sequence from clone RP23-73O7 on chromosome X Contains 
part of the Dmd gene for dystrophin muscular dystrophy, 
complete sequence
Length=134513

 Score =  116 bits (291),  Expect = 6e-23, Method: Compositional matrix adjust.
 Identities = 56/64 (87%), Positives = 63/64 (98%), Gaps = 0/64 (0%)
 Frame = +2

Query  216  RVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELM  275
            RVSE+EAALEETHRLLQQFPLDLEKFL+W+TEAETTANVLQDA+RKE+LLEDS+GV+ELM
Sbjct  632  RVSEQEAALEETHRLLQQFPLDLEKFLSWITEAETTANVLQDASRKEKLLEDSRGVRELM  811

Query  276  KQWQ  279
            K WQ
Sbjct  812  KPWQ  823


 Score =  111 bits (277),  Expect = 3e-21, Method: Compositional matrix adjust.
 Identities = 53/60 (88%), Positives = 56/60 (93%), Gaps = 0/60 (0%)
 Frame = +3

Query  278     WQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIR  337
               W DLQGEIE HTD+YHNLDEN QKILRSLEGSD+A LLQRRLDNMNFKWSEL+KKSLNIR
Sbjct  127173  W*DLQGEIETHTDIYHNLDENGQKILRSLEGSDEAPLLQRRLDNMNFKWSELQKKSLNIR  127352


>emb|CR622461.1| full-length cDNA clone CS0DB006YJ19 of Neuroblastoma Cot 10-normalized 
of Homo sapiens (human)
Length=1775

 Score =  116 bits (290),  Expect = 8e-23, Method: Compositional matrix adjust.
 Identities = 107/411 (26%), Positives = 185/411 (45%), Gaps = 62/411 (15%)
 Frame = +1

Query  820   LFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDIC  877
             +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR  +  NY +C
Sbjct  379   MFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRCQQCHNYQLC  558

Query  878   QSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPV  937
             Q+CF+ G     H   + M E+ +        +  AK L +             +G +P 
Sbjct  559   QNCFWRGHAGGPHSNQHQMKEHSS-------WKSPAKKLSHAISKS--------LGCVPT  693

Query  938   QTVLEGDNMETPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSI-SPNESI----  992
             +        E P     L+H             L  M ++  S+++  + +P +S+    
Sbjct  694   REPPHPVFPEQPEKPLDLAHIVP-------PRPLTNMNDTMVSHMSSGVPTPTKSVLDSP  852

Query  993   ---DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQA  1049
                D+EH LI  Y   L  ++  +  R P  +  + ++ +  +  +++A+LE +NR +  
Sbjct  853   SRLDEEHRLIARYAARLAAEA-GNVTRPPTDLSFNFDANK--QQRQLIAELENKNREILQ  1023

Query  1050  EYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDH  1109
             E  RL+ +HE              PT  ++ ++  L+AE +LLRQ K  LE RM  L++ 
Sbjct  1024  EIQRLRLEHEQAS----------QPTPEKAQQNPTLLAELRLLRQRKDELEQRMSALQES  1173

Query  1110  NKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGE  1169
              ++L  QL  L +LL     +A+  G+  +SP+    R     PM +R   + ++ +   
Sbjct  1174  RRELMVQLEELMKLL-----KAQATGSPHTSPTHGGGR---PMPMPVRSTSAGSTPTHCP  1329

Query  1170  EDLLSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGRAMESLV  1220
             +D LS        ++E   Q       +R +    L   AD +   M SLV
Sbjct  1330  QDSLS---GVGGDVQEAFAQ------GTRRNLRNDLLVAADSITNTMSSLV  1455


>gb|AC156952.22| Mus musculus 10 BAC RP24-385D2 (Roswell Park Cancer Institute 
(C57BL/6J Male) Mouse BAC Library) complete sequence
Length=179140

 Score =  115 bits (287),  Expect = 2e-22, Method: Compositional matrix adjust.
 Identities = 60/82 (73%), Positives = 70/82 (85%), Gaps = 1/82 (1%)
 Frame = -2

Query  1045    RNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ  1104
               RNLQ EY++LK+QH  +GL P+ SPP+ + +   +  D+ELIAEAKLLRQHKGRLEARMQ
Sbjct  131475  RNLQVEYEQLKEQHLRRGL-PVGSPPDSIVSPHHTSEDSELIAEAKLLRQHKGRLEARMQ  131299

Query  1105    ILEDHNKQLESQLHRLRQLLEQ  1126
               ILEDHNKQLESQLHRLRQLLEQ
Sbjct  131298  ILEDHNKQLESQLHRLRQLLEQ  131233


 Score =  111 bits (278),  Expect = 2e-21, Method: Compositional matrix adjust.
 Identities = 49/60 (81%), Positives = 53/60 (88%), Gaps = 0/60 (0%)
 Frame = -1

Query  811     NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
               NNKPEI    F+DWM LEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI+GFR  +L+
Sbjct  165169  NNKPEISVKEFIDWMHLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIVGFR*EALR  164990


 Score = 95.5 bits (236),  Expect = 1e-16, Method: Compositional matrix adjust.
 Identities = 43/54 (79%), Positives = 48/54 (88%), Gaps = 0/54 (0%)
 Frame = -1

Query  755     YRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
               +  LFK+VA  T  CDQR+LGLLLHD+IQIPRQLGEVA+FGGSNIEPSVRSCFQ
Sbjct  167479  FVGLFKEVAGPTEMCDQRQLGLLLHDAIQIPRQLGEVAAFGGSNIEPSVRSCFQ  167318


 Score = 94.4 bits (233),  Expect = 4e-16, Method: Compositional matrix adjust.
 Identities = 41/46 (89%), Positives = 45/46 (97%), Gaps = 0/46 (0%)
 Frame = -1

Query  903     TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
               TTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ET
Sbjct  147112  TTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLET  146975


 Score = 87.8 bits (216),  Expect = 4e-14, Method: Compositional matrix adjust.
 Identities = 35/46 (76%), Positives = 39/46 (84%), Gaps = 0/46 (0%)
 Frame = -1

Query  859     CPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
               C  +  RYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC P +
Sbjct  161791  CSFLHHRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYCIPVS  161654


 Score = 62.8 bits (151),  Expect = 1e-06, Method: Compositional matrix adjust.
 Identities = 39/53 (73%), Positives = 46/53 (86%), Gaps = 0/53 (0%)
 Frame = -3

Query  993     DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
               +DEH LIQ YCQ+L  +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE R
Sbjct  131972  EDEHALIQQYCQTLGGESPVSQPQSPAQILKSVEREERGELERIIADLEEEQR  131814


 Score = 44.7 bits (104),  Expect = 0.36, Method: Compositional matrix adjust.
 Identities = 19/29 (65%), Positives = 24/29 (82%), Gaps = 0/29 (0%)
 Frame = -2

Query  1168    GEEDLLSPPQDTSTGLEEVMEQLNNSFPS  1196
                 EDLL+PP DTST L +VMEQ+N++FPS
Sbjct  126783  ASEDLLAPPHDTSTDLTDVMEQINSTFPS  126697


 Score = 40.0 bits (92),  Expect = 7.7, Method: Compositional matrix adjust.
 Identities = 17/23 (73%), Positives = 20/23 (86%), Gaps = 0/23 (0%)
 Frame = -3

Query  948     TPASSPQLSHDDTHSRIEHYASR  970
               +P+ SPQL HDDTHSRIE YA+R
Sbjct  140627  SPSQSPQLFHDDTHSRIEQYATR  140559


>gb|AC153893.3| Mus musculus 10 BAC RP23-124O20 (Roswell Park Cancer Institute 
(C57BL/6J Female) Mouse BAC Library) complete sequence
Length=228194

 Score =  115 bits (287),  Expect = 2e-22, Method: Compositional matrix adjust.
 Identities = 60/82 (73%), Positives = 70/82 (85%), Gaps = 1/82 (1%)
 Frame = -2

Query  1045   RNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ  1104
              RNLQ EY++LK+QH  +GL P+ SPP+ + +   +  D+ELIAEAKLLRQHKGRLEARMQ
Sbjct  14632  RNLQVEYEQLKEQHLRRGL-PVGSPPDSIVSPHHTSEDSELIAEAKLLRQHKGRLEARMQ  14456

Query  1105   ILEDHNKQLESQLHRLRQLLEQ  1126
              ILEDHNKQLESQLHRLRQLLEQ
Sbjct  14455  ILEDHNKQLESQLHRLRQLLEQ  14390


 Score =  111 bits (278),  Expect = 2e-21, Method: Compositional matrix adjust.
 Identities = 49/60 (81%), Positives = 53/60 (88%), Gaps = 0/60 (0%)
 Frame = -1

Query  811    NNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
              NNKPEI    F+DWM LEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI+GFR  +L+
Sbjct  48326  NNKPEISVKEFIDWMHLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIVGFR*EALR  48147


 Score =  104 bits (260),  Expect = 2e-19, Method: Compositional matrix adjust.
 Identities = 45/89 (50%), Positives = 68/89 (76%), Gaps = 0/89 (0%)
 Frame = -2

Query  430    ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLK  489
              EL PEERAQ + + +RKQ+ EV  +WE LN  +++WQ+++ + LE+L++LQ A D+LD  
Sbjct  95191  ELTPEERAQKIAKAMRKQSSEVREKWENLNAVTSNWQKQVGKALEKLRDLQGAMDDLDAD  95012

Query  490    LRQAEVIKGSWQPVGDLLIDSLQDHLEKV  518
              +++ E ++  W+PVGDLLIDSLQDH+EK 
Sbjct  95011  MKEVEAVRNGWKPVGDLLIDSLQDHIEKT  94925


 Score = 95.5 bits (236),  Expect = 1e-16, Method: Compositional matrix adjust.
 Identities = 43/54 (79%), Positives = 48/54 (88%), Gaps = 0/54 (0%)
 Frame = -1

Query  755    YRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
              +  LFK+VA  T  CDQR+LGLLLHD+IQIPRQLGEVA+FGGSNIEPSVRSCFQ
Sbjct  50636  FVGLFKEVAGPTEMCDQRQLGLLLHDAIQIPRQLGEVAAFGGSNIEPSVRSCFQ  50475


 Score = 94.4 bits (233),  Expect = 4e-16, Method: Compositional matrix adjust.
 Identities = 41/46 (89%), Positives = 45/46 (97%), Gaps = 0/46 (0%)
 Frame = -1

Query  903    TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
              TTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ET
Sbjct  30269  TTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLET  30132


 Score = 93.6 bits (231),  Expect = 6e-16, Method: Compositional matrix adjust.
 Identities = 51/90 (56%), Positives = 61/90 (67%), Gaps = 6/90 (6%)
 Frame = -3

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              +DLL L+   +   QH L QNDQ + +  +INCLTT YD LEQ H +LVNVPLCVDMCLN
Sbjct  64101  VDLLELNTTNEVFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQLHKDLVNVPLCVDMCLN  63922

Query  721    WLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
              WLLNVYDT        LSFK  ++S  +AH
Sbjct  63921  WLLNVYDT*VCH----LSFK*SLVS--EAH  63850


 Score = 87.8 bits (216),  Expect = 4e-14, Method: Compositional matrix adjust.
 Identities = 35/46 (76%), Positives = 39/46 (84%), Gaps = 0/46 (0%)
 Frame = -1

Query  859    CPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
              C  +  RYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC P +
Sbjct  44948  CSFLHHRYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYCIPVS  44811


 Score = 68.9 bits (167),  Expect = 2e-08, Method: Compositional matrix adjust.
 Identities = 30/50 (60%), Positives = 40/50 (80%), Gaps = 0/50 (0%)
 Frame = -2

Query  337     RSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQND  386
               R+HLEAS+++W RL  SL+EL+ WL +KD+EL +Q PIGGD PA+Q Q D
Sbjct  134032  RAHLEASAEKWNRLLASLEELIKWLNMKDEELKKQMPIGGDVPALQLQYD  133883


 Score = 67.0 bits (162),  Expect = 7e-08, Method: Compositional matrix adjust.
 Identities = 28/59 (47%), Positives = 47/59 (79%), Gaps = 0/59 (0%)
 Frame = -2

Query  280     DLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRS  338
               D+Q EI+AH D++ ++D N QK++++L  S++A +LQ RLD+MN +W++L+ KS +IRS
Sbjct  146749  DIQAEIDAHNDIFKSIDGNRQKMVKALGNSEEATMLQHRLDDMNQRWNDLKAKSASIRS  146573


 Score = 62.8 bits (151),  Expect = 1e-06, Method: Compositional matrix adjust.
 Identities = 39/53 (73%), Positives = 46/53 (86%), Gaps = 0/53 (0%)
 Frame = -3

Query  993    DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
              +DEH LIQ YCQ+L  +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE R
Sbjct  15129  EDEHALIQQYCQTLGGESPVSQPQSPAQILKSVEREERGELERIIADLEEEQR  14971


 Score = 53.9 bits (128),  Expect = 5e-04, Method: Compositional matrix adjust.
 Identities = 25/33 (75%), Positives = 29/33 (87%), Gaps = 0/33 (0%)
 Frame = -1

Query  631    LYQSLADLNNVRFSAYRTAMKLRRLQKALCLDL  663
              L+   ADLNNVRFSAYRTA+K+RRLQKALC +L
Sbjct  71912  LFSISADLNNVRFSAYRTAIKIRRLQKALCREL  71814


 Score = 53.1 bits (126),  Expect = 9e-04, Method: Compositional matrix adjust.
 Identities = 22/32 (68%), Positives = 29/32 (90%), Gaps = 0/32 (0%)
 Frame = -3

Query  567    LQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQ  598
              +QV+V+DR++QL EAHRDFGP+SQHFLS+  Q
Sbjct  87033  VQVSVDDRLKQLQEAHRDFGPSSQHFLSSKYQ  86938


 Score = 48.1 bits (113),  Expect = 0.034, Method: Compositional matrix adjust.
 Identities = 19/30 (63%), Positives = 24/30 (80%), Gaps = 0/30 (0%)
 Frame = -2

Query  612    YYINHETQTTCWDHPKMTELYQSLADLNNV  641
              +  +H+TQTTCWDHPKMTEL+QSL +   V
Sbjct  73789  FLPSHQTQTTCWDHPKMTELFQSLGECCCV  73700


 Score = 46.6 bits (109),  Expect = 0.097, Method: Compositional matrix adjust.
 Identities = 25/52 (48%), Positives = 33/52 (63%), Gaps = 0/52 (0%)
 Frame = -1

Query  519    KALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVA  570
              +A R EIAP+   V  +NDL+ QL+ L +  S      L+DLN RWKLLQV+
Sbjct  89909  QAFREEIAPINLKVKTMNDLSSQLSPLDLHPSLKMSRQLDDLNMRWKLLQVS  89754


 Score = 44.7 bits (104),  Expect = 0.36, Method: Compositional matrix adjust.
 Identities = 19/29 (65%), Positives = 24/29 (82%), Gaps = 0/29 (0%)
 Frame = -2

Query  1168  GEEDLLSPPQDTSTGLEEVMEQLNNSFPS  1196
               EDLL+PP DTST L +VMEQ+N++FPS
Sbjct  9940  ASEDLLAPPHDTSTDLTDVMEQINSTFPS  9854


 Score = 40.0 bits (92),  Expect = 7.7, Method: Compositional matrix adjust.
 Identities = 17/23 (73%), Positives = 20/23 (86%), Gaps = 0/23 (0%)
 Frame = -3

Query  948    TPASSPQLSHDDTHSRIEHYASR  970
              +P+ SPQL HDDTHSRIE YA+R
Sbjct  23784  SPSQSPQLFHDDTHSRIEQYATR  23716


>gb|L04186.1|HUMDYSDMD Homo sapiens dystrophin (DMD) gene, exon 57
Length=343

 Score =  114 bits (286),  Expect = 2e-22, Method: Compositional matrix adjust.
 Identities = 57/75 (76%), Positives = 63/75 (84%), Gaps = 2/75 (2%)
 Frame = +1

Query  318  RLDNMNFKWSELRKKSL--NIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIG  375
            R+ N   ++S++ +  L    RSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIG
Sbjct  22   RIINYTSRYSDMDRCCLLFFFRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIG  201

Query  376  GDFPAVQKQNDVHRA  390
            GDFPAVQKQNDVHR 
Sbjct  202  GDFPAVQKQNDVHRV  246


>gb|L22094.1|MUSUTROPH Mouse utrophin (Dmd1) gene, one complete exon and two partial 
introns
Length=1286

 Score =  114 bits (286),  Expect = 3e-22, Method: Composition-based stats.
 Identities = 50/64 (78%), Positives = 54/64 (84%), Gaps = 0/64 (0%)
 Frame = +2

Query  807  FQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRY  866
            F   NNKPEI    F+DWM LEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI+GFR 
Sbjct  722  FPQNNNKPEISVKEFIDWMHLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIVGFR*  901

Query  867  RSLK  870
             +L+
Sbjct  902  EALR  913


>gb|AC079864.22| Homo sapiens Xp BAC RP11-662G16 (Roswell Park Cancer Institute 
Human BAC Library) complete sequence
Length=161874

 Score =  114 bits (285),  Expect = 3e-22, Method: Compositional matrix adjust.
 Identities = 54/55 (98%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = -2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKA  55
              MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQK 
Sbjct  40532  MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKV  40368


>gb|AF213436.1|AF213436 Homo sapiens dystrophin (DMD) gene, exon 51 and partial cds
Length=907

 Score =  114 bits (285),  Expect = 3e-22, Method: Compositional matrix adjust.
 Identities = 54/55 (98%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = +1

Query  1    MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKA  55
            MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQK 
Sbjct  502  MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKV  666


>emb|X51934.1| Human dystrophin gene, exon 51 with flanking sequence
Length=3159

 Score =  114 bits (285),  Expect = 3e-22, Method: Compositional matrix adjust.
 Identities = 54/55 (98%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = +2

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKA  55
             MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQK 
Sbjct  1709  MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKV  1873


>gb|M65035.1|HUMDYSGP Human dystrophin gene deletion junction fragment
Length=2202

 Score =  114 bits (285),  Expect = 3e-22, Method: Compositional matrix adjust.
 Identities = 54/55 (98%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = +2

Query  1     MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKA  55
             MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQK 
Sbjct  1046  MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKV  1210


>emb|AL357149.13| Human DNA sequence from clone RP11-352E13 on chromosome 6 Contains 
the 3' end of the UTRN gene for utrophin (homologous to 
dystrophin), complete sequence
Length=201399

 Score =  114 bits (285),  Expect = 3e-22, Method: Compositional matrix adjust.
 Identities = 61/82 (74%), Positives = 69/82 (84%), Gaps = 1/82 (1%)
 Frame = +2

Query  1045   RNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ  1104
              RNLQ EY++LK QH  +GL P+ SPPE + +   +  D+ELIAEAKLLRQHKGRLEARMQ
Sbjct  27986  RNLQVEYEQLKDQHLRRGL-PVGSPPESIISPHHTSEDSELIAEAKLLRQHKGRLEARMQ  28162

Query  1105   ILEDHNKQLESQLHRLRQLLEQ  1126
              ILEDHNKQLESQLHRLRQLLEQ
Sbjct  28163  ILEDHNKQLESQLHRLRQLLEQ  28228


 Score = 94.4 bits (233),  Expect = 4e-16, Method: Compositional matrix adjust.
 Identities = 41/46 (89%), Positives = 45/46 (97%), Gaps = 0/46 (0%)
 Frame = +2

Query  903    TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
              TTSGEDVRDF KVLKNKFR+K+YFAKHPR+GYLPVQTVLEGDN+ET
Sbjct  12569  TTSGEDVRDFTKVLKNKFRSKKYFAKHPRLGYLPVQTVLEGDNLET  12706


 Score = 61.6 bits (148),  Expect = 3e-06, Method: Compositional matrix adjust.
 Identities = 39/53 (73%), Positives = 46/53 (86%), Gaps = 0/53 (0%)
 Frame = +3

Query  993    DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
              +DEH LIQ YCQ+L  +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE R
Sbjct  27468  EDEHALIQQYCQTLGGESPVSQPQSPAQILKSVEREERGELERIIADLEEEQR  27626


 Score = 45.1 bits (105),  Expect = 0.29, Method: Compositional matrix adjust.
 Identities = 19/28 (67%), Positives = 24/28 (85%), Gaps = 0/28 (0%)
 Frame = +2

Query  1170   EDLLSPPQDTSTGLEEVMEQLNNSFPSS  1197
              EDLL+PP DTST L EVMEQ++++FPS 
Sbjct  32432  EDLLAPPHDTSTDLTEVMEQIHSTFPSC  32515


 Score = 40.0 bits (92),  Expect = 7.7, Method: Compositional matrix adjust.
 Identities = 17/23 (73%), Positives = 20/23 (86%), Gaps = 0/23 (0%)
 Frame = +3

Query  948    TPASSPQLSHDDTHSRIEHYASR  970
              +P+ SPQL HDDTHSRIE YA+R
Sbjct  19296  SPSQSPQLFHDDTHSRIEQYATR  19364


>emb|X16089.1| Human Cf56a/Cf23a region DNA for an exon of Duchenne Muscular 
Dystrophy locus
Length=357

 Score =  114 bits (284),  Expect = 4e-22, Method: Compositional matrix adjust.
 Identities = 54/55 (98%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = +1

Query  1    MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKA  55
            MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQK 
Sbjct  61   MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKV  225


>gb|S38776.1| Homo sapiens dystrophin (DMD) mRNA, partial cds, alternatively 
spliced
Length=300

 Score =  112 bits (281),  Expect = 1e-21, Method: Compositional matrix adjust.
 Identities = 52/53 (98%), Positives = 52/53 (98%), Gaps = 0/53 (0%)
 Frame = +1

Query  615  NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLS  667
             HETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLS
Sbjct  142  GHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLS  300


>emb|CR954286.2| Pan troglodytes chromosome X BAC RP43-001A02, complete sequence
Length=186572

 Score =  112 bits (280),  Expect = 1e-21, Method: Compositional matrix adjust.
 Identities = 53/55 (96%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = -2

Query  1      MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKA  55
              MPSSLMLEVPALADFNRAWTELTDWLSLLD+VIKSQRVMVGDLEDINEMIIKQK 
Sbjct  96403  MPSSLMLEVPALADFNRAWTELTDWLSLLDRVIKSQRVMVGDLEDINEMIIKQKV  96239


 Score = 79.3 bits (194),  Expect = 1e-11, Method: Compositional matrix adjust.
 Identities = 39/40 (97%), Positives = 40/40 (100%), Gaps = 0/40 (0%)
 Frame = -1

Query  54     KATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  93
              +ATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR
Sbjct  49949  QATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDR  49830


>emb|AL513184.7| Human DNA sequence from clone RP11-386H19 on chromosome 6 Contains 
part of the UTRN gene for utrophin (homologous to dystrophin), 
complete sequence
Length=81461

 Score =  112 bits (279),  Expect = 2e-21, Method: Compositional matrix adjust.
 Identities = 47/89 (52%), Positives = 71/89 (79%), Gaps = 0/89 (0%)
 Frame = +2

Query  430    ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLK  489
              EL PEERAQ + + +RKQ+ EV  +WE LN  +++WQ+++D+ LE+L++LQ A D+LD  
Sbjct  21293  ELTPEERAQKIAKAMRKQSSEVKEKWESLNAVTSNWQKQVDKALEKLRDLQGAMDDLDAD  21472

Query  490    LRQAEVIKGSWQPVGDLLIDSLQDHLEKV  518
              +++AE ++  W+PVGDLLIDSLQDH+EK+
Sbjct  21473  MKEAESVRNGWKPVGDLLIDSLQDHIEKI  21559


 Score =  110 bits (276),  Expect = 4e-21, Method: Compositional matrix adjust.
 Identities = 49/59 (83%), Positives = 51/59 (86%), Gaps = 0/59 (0%)
 Frame = +3

Query  807    FQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFR  865
              F   NNKPEI    F+DWM LEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPI+GFR
Sbjct  70863  FHQNNNKPEISVKEFIDWMHLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIVGFR  71039


 Score = 97.1 bits (240),  Expect = 5e-17, Method: Compositional matrix adjust.
 Identities = 45/61 (73%), Positives = 51/61 (83%), Gaps = 0/61 (0%)
 Frame = +2

Query  748    KAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCF  807
              K +L   +  LFK+VA  T  CDQR+LGLLLHD+IQIPRQLGEVA+FGGSNIEPSVRSCF
Sbjct  66854  KVNLLPLFADLFKEVAGPTEMCDQRQLGLLLHDAIQIPRQLGEVAAFGGSNIEPSVRSCF  67033

Query  808    Q  808
              Q
Sbjct  67034  Q  67036


 Score = 89.0 bits (219),  Expect = 2e-14, Method: Compositional matrix adjust.
 Identities = 42/63 (66%), Positives = 47/63 (74%), Gaps = 0/63 (0%)
 Frame = +3

Query  666    LSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNV  725
              LS   +   QH L QNDQ + +  +INCLTT YD LEQ H +LVNVPLCVDMCLNWLLNV
Sbjct  54984  LSTTNEIFKQHKLNQNDQLLSVPDVINCLTTTYDGLEQMHKDLVNVPLCVDMCLNWLLNV  55163

Query  726    YDT  728
              YDT
Sbjct  55164  YDT  55172


 Score = 87.0 bits (214),  Expect = 6e-14, Method: Compositional matrix adjust.
 Identities = 34/41 (82%), Positives = 38/41 (92%), Gaps = 0/41 (0%)
 Frame = +2

Query  865    RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTS  905
              RYRSLKHFNYD+CQSCFFSGR AKGHK+HYPMVEYC P ++
Sbjct  76082  RYRSLKHFNYDVCQSCFFSGRTAKGHKLHYPMVEYCIPVST  76204


 Score = 54.3 bits (129),  Expect = 4e-04, Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 27/29 (93%), Gaps = 0/29 (0%)
 Frame = +3

Query  636    ADLNNVRFSAYRTAMKLRRLQKALCLDLL  664
              ADLNNVRFSAYRTA+K+RRLQKALC +L 
Sbjct  47337  ADLNNVRFSAYRTAIKIRRLQKALCCELF  47423


 Score = 52.8 bits (125),  Expect = 0.001, Method: Compositional matrix adjust.
 Identities = 19/27 (70%), Positives = 25/27 (92%), Gaps = 0/27 (0%)
 Frame = +1

Query  610    VPYYINHETQTTCWDHPKMTELYQSLA  636
              +P++ +H+TQTTCWDHPKMTEL+QSL 
Sbjct  44938  LPFFSSHQTQTTCWDHPKMTELFQSLG  45018


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 21/29 (72%), Positives = 28/29 (96%), Gaps = 0/29 (0%)
 Frame = +3

Query  567    LQVAVEDRVRQLHEAHRDFGPASQHFLST  595
              +QV+V+DR++QL EAHRDFGP+SQHFLS+
Sbjct  27762  VQVSVDDRLKQLQEAHRDFGPSSQHFLSS  27848


 Score = 47.8 bits (112),  Expect = 0.038, Method: Compositional matrix adjust.
 Identities = 26/51 (50%), Positives = 32/51 (62%), Gaps = 0/51 (0%)
 Frame = +2

Query  520    ALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVA  570
              A R EIAP+   V  VNDL+ QL+ L +  S      L+DLN RWKLLQV+
Sbjct  24854  AFREEIAPINFKVKTVNDLSSQLSPLDLHPSLKMSRQLDDLNMRWKLLQVS  25006


 Score = 40.0 bits (92),  Expect = 8.5, Method: Compositional matrix adjust.
 Identities = 18/28 (64%), Positives = 22/28 (78%), Gaps = 0/28 (0%)
 Frame = +2

Query  729    GRTGRIRVLSFKTGIISLCKAHLEDKYR  756
              GRTG+IRV S K G++SL K  LE+KYR
Sbjct  62243  GRTGKIRVQSLKIGLMSLSKGLLEEKYR  62326


>gb|AC187490.2| Rhesus macaque BAC clone CH250-77H12 from chromosome unknown, 
complete sequence
Length=176231

 Score =  111 bits (278),  Expect = 2e-21, Method: Compositional matrix adjust.
 Identities = 59/82 (71%), Positives = 67/82 (81%), Gaps = 1/82 (1%)
 Frame = -2

Query  1045    RNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQ  1104
               RNLQ EY++LK QH  +   P+ SPPE + +   +  D+ELIAEAKLLRQHKGRLEARMQ
Sbjct  174148  RNLQVEYEQLKDQHLRRAF-PIGSPPESIVSPHHTSEDSELIAEAKLLRQHKGRLEARMQ  173972

Query  1105    ILEDHNKQLESQLHRLRQLLEQ  1126
               ILEDHNKQLESQLHRLRQLLEQ
Sbjct  173971  ILEDHNKQLESQLHRLRQLLEQ  173906


 Score = 61.6 bits (148),  Expect = 3e-06, Method: Compositional matrix adjust.
 Identities = 39/53 (73%), Positives = 46/53 (86%), Gaps = 0/53 (0%)
 Frame = -1

Query  993     DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
               +DEH LIQ YCQ+L  +SP+SQP+SPAQIL S+E EERGELERI+ADLEEE R
Sbjct  174983  EDEHALIQQYCQTLGGESPVSQPQSPAQILKSVEREERGELERIIADLEEEQR  174825


 Score = 43.9 bits (102),  Expect = 0.52, Method: Compositional matrix adjust.
 Identities = 19/27 (70%), Positives = 24/27 (88%), Gaps = 0/27 (0%)
 Frame = -2

Query  1170    EDLLSPPQDTSTGLEEVMEQLNNSFPS  1196
               EDLL+PP DTST L EVMEQ++++FPS
Sbjct  169708  EDLLAPPHDTSTDLTEVMEQIHSTFPS  169628


>gb|AY390386.1| Rattus norvegicus dystrophin-related mRNA, partial cds
Length=223

 Score =  111 bits (277),  Expect = 3e-21, Method: Composition-based stats.
 Identities = 49/55 (89%), Positives = 51/55 (92%), Gaps = 0/55 (0%)
 Frame = +2

Query  709  VNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVA  763
            +  PLCVDMCLNWLLNV +TGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQV 
Sbjct  56   IACPLCVDMCLNWLLNVCNTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVG  220


>emb|Z81522.1| Caenorhabditis elegans Cosmid F32B4, complete sequence
Length=41212

 Score =  110 bits (276),  Expect = 3e-21, Method: Compositional matrix adjust.
 Identities = 51/92 (55%), Positives = 64/92 (69%), Gaps = 5/92 (5%)
 Frame = -2

Query  851    AKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVR  910
              +KCN+CK  PIIG RYR L  FN D+CQ+CFFS R AK H+ ++PM EYC  TTS +D R
Sbjct  32166  SKCNVCKMFPIIGIRYRCLTCFNCDLCQNCFFSQRTAKSHRTNHPMQEYCEKTTSSDDAR  31987

Query  911    DFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLE  942
              DFAK+++NKFR     A   + GYLP+   LE
Sbjct  31986  DFAKMIRNKFR-----ASKRQKGYLPIDVSLE  31906


 Score = 62.8 bits (151),  Expect(2) = 1e-11, Method: Compositional matrix adjust.
 Identities = 47/153 (30%), Positives = 64/153 (41%), Gaps = 50/153 (32%)
 Frame = -1

Query  723    LNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYR-------------YLFK---QVASST  766
              L  +   R G +RVLSFK  +I      LE+KYR             +L     Q++   
Sbjct  33457  LTYFCRSRDGIMRVLSFKIAMIVFSNIPLEEKYRCTLFF*LPVP*NRFLISRSFQISFPG  33278

Query  767    GFCDQRR------------------LG---------------LLLHDSIQIPRQLGEVAS  793
                CD +                   LG               +   DS QIPR +GE A+
Sbjct  33277  RSCDPKTNCIAFI*SYPRKCFIDLFLGNNSFWFLKKIDFW*IIDFFDS-QIPRLVGESAA  33101

Query  794    FGGSNIEPSVRSCFQFANNKPEIEAALFLDWMR  826
              FGG+N+EPSVRSCF+     P I    F+DW++
Sbjct  33100  FGGTNVEPSVRSCFETVRLAPTISEGAFIDWVK  33002


 Score = 37.0 bits (84),  Expect(2) = 1e-11, Method: Compositional matrix adjust.
 Identities = 13/22 (59%), Positives = 18/22 (81%), Gaps = 0/22 (0%)
 Frame = -3

Query  828    EPQSMVWLPVLHRVAAAETAKH  849
              EPQS+VWL V+HR+  +E+ KH
Sbjct  32954  EPQSIVWLAVMHRLVISESTKH  32889


 Score = 77.8 bits (190),  Expect = 3e-11, Method: Compositional matrix adjust.
 Identities = 43/111 (38%), Positives = 68/111 (61%), Gaps = 1/111 (0%)
 Frame = -3

Query  618    TQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHN  677
              ++ T W+HP   E+ + L+  N V+F AYRTAMKLR LQK LCLDL+ L+    A  +  
Sbjct  34535  SEKTQWEHPVWVEIVKELSQFNRVKFLAYRTAMKLRALQKRLCLDLVDLTLLEKAFVRLK  34356

Query  678    LKQNDQPMDILQIINCLTTIYDRLEQEHNNLV-NVPLCVDMCLNWLLNVYD  727
                  ++   +  ++  L  +Y+ L  ++ N V +V L VD+C+N+LLN++D
Sbjct  34355  GLSAEECPGLEGMVCALLPMYEALHAKYPNQVQSVSLAVDICINFLLNLFD  34203


 Score = 53.5 bits (127),  Expect(2) = 2e-08, Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
 Frame = -2

Query  560    LNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLSTSVQGPWERAIS-PNKVPYYI  614
              L  R+  L+ A+  R   +  A  DFGP S+HFL+ SV  PW+RAIS  N +PYYI
Sbjct  35235  LRFRYSTLKRAIRIRQAAVRNAASDFGPTSEHFLNQSVTLPWQRAISKSNLLPYYI  35068


 Score = 35.0 bits (79),  Expect(2) = 2e-08, Method: Compositional matrix adjust.
 Identities = 29/121 (23%), Positives = 55/121 (45%), Gaps = 0/121 (0%)
 Frame = -3

Query  448    AEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLL  507
               E +   W +L +    W + +   ++RLQEL+    E  L L  +E    + + V  + 
Sbjct  35654  CERLKKNWAELGIEVESWDKLVQHAMQRLQELERNLAECQLHLTSSENEIETMKAVEKIH  35475

Query  508    IDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL  567
              ++ L+   E+   +   I  ++  V  VND A +L    ++L  +    +E +N R  LL
Sbjct  35474  LEDLKIAREETDQISKRIDEVRLFVDDVNDAAARLLAEDLKLDEHAKGQIEHVNKR*VLL  35295

Query  568    Q  568
              +
Sbjct  35294  E  35292


 Score = 52.8 bits (125),  Expect = 0.001, Method: Compositional matrix adjust.
 Identities = 28/90 (31%), Positives = 46/90 (51%), Gaps = 0/90 (0%)
 Frame = -3

Query  329    LRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVH  388
              + KK L  R  LE +  +W++L   L +LL W++ K   +  + P GG   AV +Q    
Sbjct  37415  ISKKKLFFRERLEKAEQEWEKLSDGLADLLSWVEAKKQAIMDEQPTGGSLSAVMQQASFV  37236

Query  389    RAFKRELKTKEPVIMSTLETVRIFLTEQPL  418
              +  +RE+++K     ST+E    FL +  L
Sbjct  37235  KGLQREIESKTANYKSTVEEAHSFLMQHDL  37146


 Score = 51.6 bits (122),  Expect = 0.003, Method: Compositional matrix adjust.
 Identities = 34/125 (27%), Positives = 61/125 (48%), Gaps = 0/125 (0%)
 Frame = -2

Query  212    SIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGV  271
              S H  +  R A LE + R  + F   L +F  WL+  E   + L   T   + ++D+   
Sbjct  38094  STHFSIRIRRAVLEASLRSRRDFHSALSEFEKWLSRQEDNCSKLSADTSNHQAIKDTSKR  37915

Query  272    KELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRK  331
              K   + ++ L  E+ AH DV  ++++  + +  SLE  ++ V L +R+     +W+ LRK
Sbjct  37914  KNWTQSFKTLNAELNAHEDVMKSVEKMGKMLAESLESGNEKVELLKRVGETTRRWTALRK  37735

Query  332    KSLNI  336
               +  I
Sbjct  37734  TTNEI  37720


 Score = 42.4 bits (98),  Expect = 1.7, Method: Compositional matrix adjust.
 Identities = 22/42 (52%), Positives = 32/42 (76%), Gaps = 0/42 (0%)
 Frame = -3

Query  1084   ELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLE  1125
              +++ EAK LR HK RLE R +ILE  N+QLE QL RL+++++
Sbjct  29219  QVMDEAKALRLHKQRLEHRSRILEQQNEQLEMQLQRLKKVID  29094


>gb|AC112800.6| Rattus norvegicus X BAC CH230-275F1 (Children's Hospital Oakland 
Research Institute) complete sequence
Length=147560

 Score =  110 bits (276),  Expect = 4e-21, Method: Compositional matrix adjust.
 Identities = 52/55 (94%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = +3

Query  1       MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKA  55
               MPSSL+LEVPALADFNRAWTELTDWLSLLD+VIKSQRVMVGDLEDINEMIIKQK 
Sbjct  113562  MPSSLLLEVPALADFNRAWTELTDWLSLLDRVIKSQRVMVGDLEDINEMIIKQKV  113726


>gb|DQ788695.1| Danio rerio dystrophin isoform Dp116 mRNA, partial cds, alternatively 
spliced
Length=315

 Score =  110 bits (276),  Expect = 4e-21, Method: Compositional matrix adjust.
 Identities = 52/86 (60%), Positives = 69/86 (80%), Gaps = 0/86 (0%)
 Frame = +3

Query  279  QDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRS  338
            +DLQ EI+AH + YH+LDEN  +I+ SLEG+D+AV+LQ+RLD+M  +W EL  K ++IR 
Sbjct  54   KDLQAEIDAHRETYHSLDENGHRIVSSLEGTDNAVVLQKRLDDMGQRWHELCNKVMSIRP  233

Query  339  HLEASSDQWKRLHLSLQELLVWLQLK  364
            +L+A  DQWK LH+SLQELL WLQLK
Sbjct  234  YLDAGVDQWKHLHMSLQELLNWLQLK  311


>gb|AF213439.1|AF213439 Homo sapiens dystrophin (DMD) gene, exon 54 and partial cds
Length=589

 Score =  109 bits (272),  Expect = 1e-20, Method: Compositional matrix adjust.
 Identities = 52/52 (100%), Positives = 52/52 (100%), Gaps = 0/52 (0%)
 Frame = +2

Query  165  QLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  216
            QLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR
Sbjct  269  QLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  424


>gb|M86898.1|HUMDYST15 H.sapiens dystrophin gene, exon 74
Length=299

 Score =  107 bits (268),  Expect = 3e-20, Method: Compositional matrix adjust.
 Identities = 54/55 (98%), Positives = 54/55 (98%), Gaps = 0/55 (0%)
 Frame = +2

Query  991   SIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  1045
             S DDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR
Sbjct  65    SRDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENR  229


>gb|U01229.1|U01229 Torpedo californica dystrophin mRNA, partial cds
Length=865

 Score =  107 bits (267),  Expect = 4e-20, Method: Compositional matrix adjust.
 Identities = 49/62 (79%), Positives = 59/62 (95%), Gaps = 0/62 (0%)
 Frame = +1

Query  1    MPSSLMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDL  60
            MPSSL+++VPALADFN+AW ELTDWLSLLD+VIKSQ V VGD+E+IN+MIIKQKAT+QDL
Sbjct  679  MPSSLLMDVPALADFNKAWVELTDWLSLLDRVIKSQLVTVGDVEEINDMIIKQKATLQDL  858

Query  61   EQ  62
            +Q
Sbjct  859  DQ  864


>dbj|AK296450.1| Homo sapiens cDNA FLJ56097 complete cds, highly similar to Homo 
sapiens dystrobrevin, alpha (DTNA), transcript variant 2, 
mRNA
Length=1932

 Score =  107 bits (266),  Expect = 6e-20, Method: Compositional matrix adjust.
 Identities = 111/392 (28%), Positives = 172/392 (43%), Gaps = 58/392 (14%)
 Frame = +2

Query  849   HQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGED  908
             H  +C+ C    ++GFRYR  +  NY +CQ CF+ G     H   + M EY +       
Sbjct  209   HPVECSYCHSESMMGFRYRCQQCHNYQLCQDCFWRGHAGGSHSNQHQMKEYTS-------  367

Query  909   VRDFAKVLKNKFRTKRYFA--KHPRMGYLPVQTVLEGDNMETPASSPQLSHDDT---HSR  963
              +  AK L N        A  + P     P Q     +        P  S +DT   HS 
Sbjct  368   WKSPAKKLTNALSKSLSCASSREPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHS-  544

Query  964   IEHYASRLAEMENSNGSYLNDS-ISPNESIDDEHLLIQHYCQSLNQDSPLSQP---RSPA  1019
                       + +S   ++  S +  +  +D+EH LI  Y   L  +S  SQP   RS  
Sbjct  545   ----------VPSSGSPFITRSMLESSNRLDEEHRLIARYAARLAAESSSSQPPQQRSAP  694

Query  1020  QILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQS  1079
              I  ++++ +  +  +++A+LE +NR +  E  RL+ +HE +   P P   +  PT    
Sbjct  695   DISFTIDANK--QQRQLIAELENKNREILQEIQRLRLEHE-QASQPTPEKAQQNPT----  853

Query  1080  PRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVS  1139
                  L+AE +LLRQ K  LE RM  L++  ++L  QL  L +LL+   A     G+  S
Sbjct  854   -----LLAELRLLRQRKDELEQRMSALQESRRELMVQLEGLMKLLKTQGA-----GSPRS  1003

Query  1140  SPSTSLQRSDSSQPMLLRVVGSQTSDSMGEEDLLSPPQDTSTGLEEVMEQLNNSFPSSRG  1199
             SPS ++ R     PM +R   + ++ +         PQD+ TG   V   +  +F  S  
Sbjct  1004  SPSHTISRPI---PMPIRSASACSTPTHT-------PQDSLTG---VGGDVQEAFAQSSR  1144

Query  1200  HNV-GSLFHMADDLGRAMESLVSVMTDEEGAE  1230
              N+   L   AD +   M SLV  +  E G+E
Sbjct  1145  RNLRNDLLVAADSITNTMSSLVKELNSEVGSE  1240


>gb|AC192936.3| Pan troglodytes BAC clone CH251-433G11 from chromosome x, complete 
sequence
Length=189198

 Score =  103 bits (257),  Expect = 5e-19, Method: Compositional matrix adjust.
 Identities = 50/52 (96%), Positives = 52/52 (100%), Gaps = 0/52 (0%)
 Frame = +1

Query  519   KALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVA  570
             +ALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV+
Sbjct  3433  QALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVS  3588


 Score = 60.5 bits (145),  Expect = 6e-06, Method: Compositional matrix adjust.
 Identities = 27/28 (96%), Positives = 28/28 (100%), Gaps = 0/28 (0%)
 Frame = +3

Query  568    QVAVEDRVRQLHEAHRDFGPASQHFLST  595
              QVAVEDRVRQLHEAHRDFGPASQHFLS+
Sbjct  99678  QVAVEDRVRQLHEAHRDFGPASQHFLSS  99761


 Score = 50.8 bits (120),  Expect = 0.004, Method: Compositional matrix adjust.
 Identities = 21/23 (91%), Positives = 21/23 (91%), Gaps = 0/23 (0%)
 Frame = +3

Query  592     FLSTSVQGPWERAISPNKVPYYI  614
               F S SVQGPWERAISPNKVPYYI
Sbjct  129240  FFSASVQGPWERAISPNKVPYYI  129308


>emb|CR955037.3| Pan troglodytes chromosome X BAC RP43-016I09, complete sequence
Length=201964

 Score =  103 bits (257),  Expect = 5e-19, Method: Compositional matrix adjust.
 Identities = 50/52 (96%), Positives = 52/52 (100%), Gaps = 0/52 (0%)
 Frame = +3

Query  519    KALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVA  570
              +ALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV+
Sbjct  26703  QALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVS  26858


 Score = 60.5 bits (145),  Expect = 6e-06, Method: Compositional matrix adjust.
 Identities = 27/28 (96%), Positives = 28/28 (100%), Gaps = 0/28 (0%)
 Frame = +2

Query  568     QVAVEDRVRQLHEAHRDFGPASQHFLST  595
               QVAVEDRVRQLHEAHRDFGPASQHFLS+
Sbjct  122777  QVAVEDRVRQLHEAHRDFGPASQHFLSS  122860


 Score = 50.8 bits (120),  Expect = 0.004, Method: Compositional matrix adjust.
 Identities = 21/23 (91%), Positives = 21/23 (91%), Gaps = 0/23 (0%)
 Frame = +2

Query  592     FLSTSVQGPWERAISPNKVPYYI  614
               F S SVQGPWERAISPNKVPYYI
Sbjct  152294  FFSASVQGPWERAISPNKVPYYI  152362


>gb|M86884.1|HUMDYST01 H.sapiens dystrophin gene, exon 60
Length=332

 Score =  103 bits (257),  Expect = 5e-19, Method: Compositional matrix adjust.
 Identities = 50/52 (96%), Positives = 52/52 (100%), Gaps = 0/52 (0%)
 Frame = +2

Query  519  KALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVA  570
            +ALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV+
Sbjct  143  QALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVS  298


>ref|XM_968674.2| PREDICTED: Tribolium castaneum similar to kakapo (LOC662585), 
mRNA
Length=25598

 Score =  102 bits (255),  Expect = 1e-18, Method: Compositional matrix adjust.
 Identities = 103/474 (21%), Positives = 214/474 (45%), Gaps = 33/474 (6%)
 Frame = +1

Query  59     DLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEM  118
              +++Q +P+++++  + ++L  +   +  +  +   IE + N WD +      R + L + 
Sbjct  20863  EIDQTKPEVDQVRASGKDLM-RLCGEPDKPEVKKHIEDLDNAWDNITALYAKREENLIDA  21039

Query  119    LKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYT--VDAIQKKITETKQLAKDLRQWQTN  176
              ++ + ++ E  +     L +A  K    K GP    +DA++K+I + K    ++      
Sbjct  21040  MEKAMEFHETLQNLLAFLDKAEKKFA--KMGPLGTDIDAVKKQIDQLKNFKAEVDPHMVK  21213

Query  177    VDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPL  236
              V+  N  A +L    SAD    +      +N  W  + + + ER+  LE     L QF  
Sbjct  21214  VEALNRQAQELTERTSADQAAAIKEPLSGVNKRWDDLLRGIVERQRQLENALLRLGQFQH  21393

Query  237    DLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLD  296
               L + L W+++ + T + L+      ++LE      EL K  + L  +I+AH      L+
Sbjct  21394  ALNELLVWISKTDKTLDELKPVQGDPQILE-----IELAK-LKVLVNDIQAHQTSVDTLN  21555

Query  297    ENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQE  356
              +  ++I+ + EGSD+A + Q +L+ +N +W  L +K+ + +  LE S ++ +R +  +Q+
Sbjct  21556  DAGRQIIETGEGSDEASITQDKLNTLNTQWRALMQKAADRQRELEDSLNEAQRFNAEIQD  21735

Query  357    LLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQ  416
              LL WL   D  ++   P+GG      +Q +       E++   P + + L   + +L   
Sbjct  21736  LLSWLCDVDGIITASKPVGGLPETASEQLERFMEIYNEIEDNRPKVETVLAQGQEYL---  21906

Query  417    PLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERL  476
                                 +  N    L+     +   W+ +   + D + K++  L+  
Sbjct  21907  ------------------RKGSNAASNLQHNLRTLKQRWDSVTSRANDKKIKLEIALKEA  22032

Query  477    QELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKE  530
               E  EA +     L  AE I  + +PV  +L +++Q  +E+ K  + +++  +E
Sbjct  22033  TEFHEALENFVEWLTNAEKILSNLKPVSRVL-ETIQGQMEEHKIFQKDVSAHRE  22191


 Score = 91.3 bits (225),  Expect = 3e-15, Method: Compositional matrix adjust.
 Identities = 93/400 (23%), Positives = 187/400 (46%), Gaps = 19/400 (4%)
 Frame = +1

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              FN    +L  WL  +D +I + + + G  E  +E + +      ++E  RP++E ++   
Sbjct  21715  FNAEIQDLLSWLCDVDGIITASKPVGGLPETASEQLERFMEIYNEIEDNRPKVETVLAQG  21894

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              Q    K SN  A + +   +  ++ +WD V     +++ +L   LK++T++ EA E   +
Sbjct  21895  QEYLRKGSN--AASNLQHNLRTLKQRWDSVTSRANDKKIKLEIALKEATEFHEALENFVE  22068

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL--LRDYS  192
               L  A   L + K     ++ IQ ++ E K   KD+     + ++  DL  K   L+ +S
Sbjct  22069  WLTNAEKILSNLKPVSRVLETIQGQMEEHKIFQKDV---SAHREIMLDLDKKGTHLKYFS  22239

Query  193    -ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
                 D   +  +  ++   W  +  + +ER  AL+  ++  ++F       + WL E E +
Sbjct  22240  QKQDVILIKNLLVSVQHRWERVASKSAERTRALDLGYKEAKEFHDGWSGLMTWLNETEDS  22419

Query  252    ANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDD  311
               + L      E +  D + +K  + + Q+ Q  + A    Y ++   + K+L+      D
Sbjct  22420  LDRL----LSESVGNDPEAIKSRLHKHQEFQRNLSAKQGTYDHV-MKTGKVLKEKAPKSD  22584

Query  312    AVLLQRRLDNMNFKWSELRKKSLNIRSHLEAS---SDQWKRLHLSLQELLVWLQLKDDEL  368
                 +++ + ++  KW+ +  KS++ +  LE +   S Q+K    ++  LL WL+  + EL
Sbjct  22585  EPTIRQMMSDLKAKWTAVCNKSVDRQRKLEEALLYSGQFKD---AIAALLQWLKKVEKEL  22755

Query  369    SRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
              S  +P+ GD   V    D+H  F++EL+ +   + S + T
Sbjct  22756  SVDSPVHGDLDTVNHLVDLHNQFEKELERRNEQMESVIRT  22875


 Score = 55.8 bits (133),  Expect = 1e-04, Method: Compositional matrix adjust.
 Identities = 82/390 (21%), Positives = 175/390 (44%), Gaps = 53/390 (13%)
 Frame = +1

Query  205    NINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERL  264
              ++   + ++ K++  ++A +E + R  +QF     K L WL++        +  +  E+L
Sbjct  16732  SVGRQYNALQKKLDHKKAEIEGSLRDGRQFEASCAKTLGWLSD--------ELGSLSEKL  16887

Query  265    LEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL-EGSD--------DAVLL  315
              L     ++++++Q      ++  H  +Y ++     +++  L +G D        D+  L
Sbjct  16888  L--ISAIRDVLEQ------QLAHHEPIYRDVLAREHEVIMLLNKGRDMLARNNRSDSRSL  17043

Query  316    QRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIG  375
              QR LD +  +W +LRK++++ ++ L+   +  ++ +  L+  L WL+  +D+L    P  
Sbjct  17044  QRDLDKIQQQWEKLRKETVDRQTRLQTCKEHCRKYYKVLESFLPWLRQAEDKLDTLRPSS  17223

Query  376    GDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEE  435
                   ++KQ    +AF+ E+  K     +T      F++   ++              +E
Sbjct  17224  FQRKHIEKQLKELQAFRNEVWKKSGEYENTRTLGDTFVSACDID--------------KE  17361

Query  436    RAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEV  495
                +N    L+++ +++N +  +      D  RK+ +  E ++ELQ   +  + KL   + 
Sbjct  17362  VVKNELNDLKERWDKLNNDLIERTQALEDQSRKLADFNENIRELQHGVERCEDKLASHDA  17541

Query  496    IKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLS  555
              + G+ +             LE++KALR E A L++ +  V   A+ L +   Q +  +  
Sbjct  17542  LGGAARDPK---------LLERIKALREETAKLRKPLQTVKQQAQDLASEAAQ-NGIDAH  17691

Query  556    TLED----LNTRWKLLQVAVEDRVRQLHEA  581
               LED    L  R   L   ++DR  +L  A
Sbjct  17692  HLEDEVDSLGDRIDELTSKLDDRCSELQSA  17781


 Score = 54.7 bits (130),  Expect = 3e-04, Method: Compositional matrix adjust.
 Identities = 82/393 (20%), Positives = 167/393 (42%), Gaps = 23/393 (5%)
 Frame = +1

Query  12     LADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELI  71
              LADFN    EL   +   +  + S   + G   D  +++ + KA  ++  + R  L+ + 
Sbjct  17461  LADFNENIRELQHGVERCEDKLASHDALGGAARD-PKLLERIKALREETAKLRKPLQTVK  17637

Query  72     TAAQNLKNKTS-NQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKE  130
                AQ+L ++ + N      + D ++ + ++ DE+   L +R  +L       TQ+ E  +
Sbjct  17638  QQAQDLASEAAQNGIDAHHLEDEVDSLGDRIDELTSKLDDRCSELQSAATAVTQFNEQVK  17817

Query  131    EAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRD  190
                   L     +L+  K     +  ++ +I +  +    + +   +V+ A     +L+  
Sbjct  17818  GLSHDLTGLETELDEMKPPGRDLKTVRGQIDDIGRFLVKINKATDDVNDAIAAGERLVDS  17997

Query  191    YSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAET  250
                A DT +     E +      +  R   RE +LE+ H+ L+QF +             +
Sbjct  17998  GFAPDTAQTRQQVETLRKQLGKLDDRARSREQSLEDIHKKLEQFYM-------------S  18138

Query  251    TANVL---QDATRKERLLED-SKGVKELMKQWQDLQG----EIEAHTDVYHNLDENSQKI  302
               ANVL    DA+ + R L+     V  +  Q QD +      +E       N +   Q +
Sbjct  18139  HANVLDDIHDASEQLRKLKAVGSEVDSIRAQQQDFKKFRAKTVEPVGKAVENCNRVGQGL  18318

Query  303    LRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQ  362
              ++S     +  +L++ L+ MN +W++L+++  +    L+ +  Q  +   +L  L  WL 
Sbjct  18319  IQSAAPGVNTAILEKDLEKMNEQWNDLKERLNDRERRLDVALLQSGKFQEALDGLAKWLT  18498

Query  363    LKDDELSRQAPIGGDFPAVQKQNDVHRAFKREL  395
                ++ ++ Q P   D+  V+ Q    +  K+ L
Sbjct  18499  DTEELVANQKPPSADYKVVKAQLQEQKFLKKML  18597


 Score = 49.3 bits (116),  Expect = 0.014, Method: Compositional matrix adjust.
 Identities = 111/566 (19%), Positives = 225/566 (39%), Gaps = 54/566 (9%)
 Frame = +1

Query  9      VPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLE  68
              +P +  F+     L DW+   + V++S     GD+  +            DL++ RP LE
Sbjct  19423  LPLVKQFHNNHNRLVDWMQGAESVLQSAEPHEGDIARLE----------LDLQELRPVLE  19572

Query  69     ELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLN-------EMLKD  121
               +      L   +  + A T I   + R   ++D + E +Q R ++++       E+  D
Sbjct  19573  HINLLGPQLCQNSPGEGAST-IEGLVTRDNRRFDAIAEQIQRRAERIHLGKQRALEVTGD  19749

Query  122    STQWLEAKEEAEQVLGQARAKLESWKEGPYT-VDAIQKKITETKQLAKDLRQWQTNVDVA  180
                + LE   E E  +  A        E P    D I+ ++ E K L  D+   +  V   
Sbjct  19750  IDELLEWFREVESQIRDA--------EKPSAEPDLIRVQLKEHKALNDDISSQKGRVRDV  19905

Query  181    NDLALKLLRDY-SADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLE  239
                 A K+LR+   ++DT  +    E++  +  ++    S+R   LE+   L + F     
Sbjct  19906  LSTAKKVLRESPPSEDTSLIREKMEDLRETMDTVSALSSDRLGILEQALPLAEHFHDTHN  20085

Query  240    KFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENS  299
                  WL++ E   ++L     +  L+   +   E+  Q       I  H  +   L++  
Sbjct  20086  VLSNWLSDIEEQISMLAMPAMRPDLIAQQQDRNEMFIQ------SINDHKPLVDKLNKTG  20247

Query  300    QKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLV  359
              + ++R L   DD   +Q  LD+ N +++ L+ +    +  LE +  +  +    L+ +L 
Sbjct  20248  EALIR-LCNDDDGSKVQELLDSDNARYAALKLELRERQQALEQALQESSQFSDKLEGMLR  20424

Query  360    WLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLE  419
               L    D+++   PI    P ++ Q + + A   +L  ++    +        + + P  
Sbjct  20425  ALSNTADQVNNLEPISAHVPKIKDQIEDNDALISDLDKRKEAYAAVQRAADDVINKAP--  20598

Query  420    GLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQEL  479
                              R+    + ++++ +++   W+ +   + +  R +D+TL+  Q+ 
Sbjct  20599  ---------------NRSDPAIKDIKRKLDKLKNLWDDVQKATNNRGRSLDDTLDAAQKF  20733

Query  480    QEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLA  539
               +    +   L+  E    S +P   +   ++Q     ++ +R EI   K  V  V    
Sbjct  20734  WKELHAIMATLKDLEDSLVSQEPPA-VEPKAIQQQQVALQEIRHEIDQTKPEVDQVRASG  20910

Query  540    RQLTTL-GIQLSPYNLSTLEDLNTRW  564
              + L  L G    P     +EDL+  W
Sbjct  20911  KDLMRLCGEPDKPEVKKHIEDLDNAW  20988


 Score = 44.7 bits (104),  Expect = 0.35, Method: Compositional matrix adjust.
 Identities = 59/278 (21%), Positives = 117/278 (42%), Gaps = 10/278 (3%)
 Frame = +1

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F  A   L  WL  +++ +     + GDL+ +N ++       ++LE+R  Q+E +I   
Sbjct  22699  FKDAIAALLQWLKKVEKELSVDSPVHGDLDTVNHLVDLHNQFEKELERRNEQMESVIRTG  22878

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
               +L+ K +  +A T I  ++  +   W+ V +  + R  +L+E L ++ +  ++      
Sbjct  22879  TDLERKANRADA-TQIRSQLTELNELWNSVTKLTRIRSGRLDEALHEAERLHKSVHMLLD  23055

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +A  +L      P       +++    +   +L+  +   +   DLA  +L     D
Sbjct  23056  WLSEAERQLRFVGSTPEDEATAYEQLQALDRFRAELKDKEREKNHTLDLAQSVLAKAHPD  23235

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANV  254
                  +    + I + W  + +   +R   L    + L+     LE+ + WL   E T   
Sbjct  23236  AINVIKNWIKVIQSRWEEVSQWAMQRHQKLTAHMQSLRDLDECLEELIQWLLGLENTLIA  23415

Query  255    LQ------DATRKERLLEDSKGVKELMKQWQDLQGEIE  286
              L+      D    E+L+ D    KE M+  Q  QGE++
Sbjct  23416  LKREDLPMDIPATEQLIADH---KEFMENTQKRQGEVD  23520


 Score = 43.5 bits (101),  Expect = 0.75, Method: Compositional matrix adjust.
 Identities = 85/418 (20%), Positives = 171/418 (40%), Gaps = 38/418 (9%)
 Frame = +1

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+ A     +WL+  ++++ + + +   LE I   + + K   +D+   R  + +L   
Sbjct  22036  EFHEALENFVEWLTNAEKILSNLKPVSRVLETIQGQMEEHKIFQKDVSAHREIMLDLDKK  22215

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQ---------  124
                +LK  +  Q+   +I + +  +Q++W+ V      R + L+   K++ +         
Sbjct  22216  GTHLKYFSQKQDV-ILIKNLLVSVQHRWERVASKSAERTRALDLGYKEAKEFHDGWSGLM  22392

Query  125    -WLEAKEEA-EQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVAND  182
               WL   E++ +++L       ES    P   +AI+ ++ + ++  ++L   Q   D    
Sbjct  22393  TWLNETEDSLDRLLS------ESVGNDP---EAIKSRLHKHQEFQRNLSAKQGTYDHVMK  22545

Query  183    LALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFL  242
                  L       D   +  +  ++ A W ++  +  +R+  LEE      QF   +   L
Sbjct  22546  TGKVLKEKAPKSDEPTIRQMMSDLKAKWTAVCNKSVDRQRKLEEALLYSGQFKDAIAALL  22725

Query  243    AWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKI  302
               WL + E   +V         +  D   V  L+      + E+E   +   ++      +
Sbjct  22726  QWLKKVEKELSV------DSPVHGDLDTVNHLVDLHNQFEKELERRNEQMESVIRTGTDL  22887

Query  303    LRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQ  362
               R    +D A  ++ +L  +N  W+ + K +      L+ +  + +RLH S+  LL WL 
Sbjct  22888  ERKANRAD-ATQIRSQLTELNELWNSVTKLTRIRSGRLDEALHEAERLHKSVHMLLDWLS  23064

Query  363    LKDDELSRQAPIGGDFP-----AVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTE  415
                  E  RQ    G  P     A ++   + R F+ ELK KE     TL+  +  L +
Sbjct  23065  ----EAERQLRFVGSTPEDEATAYEQLQALDR-FRAELKDKEREKNHTLDLAQSVLAK  23223


 Score = 43.1 bits (100),  Expect = 1.1, Method: Compositional matrix adjust.
 Identities = 35/175 (20%), Positives = 86/175 (49%), Gaps = 6/175 (3%)
 Frame = +1

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
               L  F    ++   W + + ++I+S+ +    +E   E  ++ +    + + +RP  EE+
Sbjct  15019  GLTAFLAGASQFEQWHASIVEIIESRELAKLSIE---EYAVRMQEIAANRDDKRPLFEEV  15189

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEA-K  129
              I   ++L NK    +   +  DR++ ++NQW E+   L + +Q+L++   +     EA +
Sbjct  15190  IKCGKDLLNKRDTTDTANV-RDRVKSMENQWRELG-SLLDEKQKLSKQRAEQLNAYEALR  15363

Query  130    EEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLA  184
              ++    L +  A++   +     ++ ++K+  E K + K+ + + + +D  ND+ 
Sbjct  15364  QQVCDWLSRFEARIARLEVVAIDIEILKKQNEELKPITKEYKDYSSTIDKVNDIG  15528


>gb|AE013599.4| Drosophila melanogaster chromosome 2R, complete sequence
Length=21146708

 Features in this part of subject sequence:
   Dystrobrevin-like, isoform C
   Dystrobrevin-like, isoform D

 Score = 81.6 bits (200),  Expect(2) = 1e-18, Method: Compositional matrix adjust.
 Identities = 50/190 (26%), Positives = 84/190 (44%), Gaps = 24/190 (12%)
 Frame = +1

Query  731      TGRIRVLSFKTGIISLCKAHLEDKYRY---------------------LFKQVASSTGFC  769
                +G+IRV S K  + ++C   L DK R                      +F Q++   G  
Sbjct  8335675  SGKIRVFSIKVALATMCSGKLVDKLRCE*CTHHLITK*TRLKLFHRTDIFSQISDGAGQL  8335854

Query  770      DQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEP  829
                   +LG  L + + +P  + E  +F   + +  +      A NK  +   +        P
Sbjct  8335855  VAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPAENKVTVNDFMATLMSEPGP  8336025

Query  830      QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKG  889
                  +VWLP++HR+A  ET  H   C++C +    GFRYR  +   Y +CQ CF+ G+ +  
Sbjct  8336026  SCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQRCHAYQLCQECFWHGKTSLN  8336205

Query  890      HKMHYPMVEY  899
                H+  + + EY
Sbjct  8336206  HQNDHEVKEY  8336235


 Features in this part of subject sequence:
   Dystrobrevin-like, isoform C
   Dystrobrevin-like, isoform D

 Score = 41.2 bits (95),  Expect(2) = 1e-18, Method: Compositional matrix adjust.
 Identities = 26/96 (27%), Positives = 50/96 (52%), Gaps = 4/96 (4%)
 Frame = +2

Query  635      LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
                L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  8335313  LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  8335492

Query  693      CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVY  726
                 ++++Y  L +       VP+     + LNWLL  Y
Sbjct  8335493  LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAY  8335600


 Features in this part of subject sequence:
   short stop, isoform H
   short stop, isoform C

 Score = 49.7 bits (117),  Expect = 0.010, Method: Compositional matrix adjust.
 Identities = 51/256 (19%), Positives = 105/256 (41%), Gaps = 28/256 (10%)
 Frame = -3

Query  160      ITETKQLAKDLRQWQTNVDVANDLALKLLR-DYSADDTRKVHMITENINASWRSIHKRVS  218
                + + K LA D++  Q +VD  ND   +L+  +  + +          +N  W+ + ++ S
Sbjct  9761640  LAKLKVLANDIQAHQNSVDTLNDAGRQLIETEKGSVEASTTQEKLRKLNNEWKQLLQKAS  9761461

Query  219      EREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQW  278
                +R+  LEE  R    +  +++  L WL + +      +             G+ E   + 
Sbjct  9761460  DRQHELEEALREAHGYIAEVQDILGWLGDVDAVIGASKPVG----------GLPETATE-  9761314

Query  279      QDLQGEIEAHTDVYHNLDENSQK-----------ILRSLEGSDDAVLLQRRLDNMNFKWS  327
                     ++E   +VY+ LDEN  K           I R  +    +  LQ  L  +  +W 
Sbjct  9761313  -----QLERFMEVYNELDENRPKVETIQAQGQEYIKRQNQMKVSSSNLQHTLRTLKQRWD  9761149

Query  328      ELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDV  387
                 +  ++ + +  LE +  +    H +LQ  + WL   +  LS   P+      +Q Q + 
Sbjct  9761148  AVVSRASDKKIKLEIALKEATEFHDTLQAFVEWLTQAEKLLSNAEPVSRVLETIQAQMEE  9760969

Query  388      HRAFKRELKTKEPVIM  403
                H+  ++++ T    ++
Sbjct  9760968  HKVLQKDVSTHREAML  9760921


 Features in this part of subject sequence:
   short stop, isoform H
   short stop, isoform C

 Score = 48.9 bits (115),  Expect = 0.018, Method: Compositional matrix adjust.
 Identities = 101/495 (20%), Positives = 201/495 (40%), Gaps = 54/495 (10%)
 Frame = -3

Query  5        LMLEVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRR  64
                L + +    +F+       +WL+  ++++ +   +   LE I   + + K   +D+   R
Sbjct  9761112  LEIALKEATEFHDTLQAFVEWLTQAEKLLSNAEPVSRVLETIQAQMEEHKVLQKDVSTHR  9760933

Query  65       PQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQ  124
                  +  L     +LK  +  Q+   +I + +  +Q++W+ V      R + L+   K++ +
Sbjct  9760932  EAMLLLDKKGTHLKYFSQKQDV-ILIKNLLVSVQHRWERVVSKAAERTRALDHGYKEARE  9760756

Query  125      W-------LEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNV  177
                +       ++  +E EQVL Q   +  + KE       I+K I + K+  + L   Q+  
Sbjct  9760755  FNDAWSGMMQYLQETEQVLDQIIEEATASKEPQ----KIKKYIGKLKETHRQLGAKQSVY  9760588

Query  178      DVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLD  237
                D        LL      D   +  +   +   W  +  +  +R+  LEE   L  QF   
Sbjct  9760587  DGTMRTGKNLLERAPKGDRPVLDKMLIELKEQWTRVWSKSIDRQRKLEEALLLSGQFSDA  9760408

Query  238      LEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDE  297
                L + L WL +A            K RL E+     +L    + +QG  E H  +  +L +
Sbjct  9760407  LGELLDWLKKA------------KSRLNENGPVHGDL----ETVQGLCEHHKHIEQDLQK  9760276

Query  298      NS---QKIL---RSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 +   Q +L   R LE S +   + R+LD M   W E++         L+ +    ++L+
Sbjct  9760275  RAAQMQGVLKTGRDLERSGNNPEVGRQLDEMQSIWEEVKSAVAKRGERLQVALVDAEKLN  9760096

Query  352      LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
                  +Q L  WL   + +L        D    ++  D+H  F ++L+ +E     T E    
Sbjct  9760095  ARVQALFDWLDHAEHKLRYAKNAPDDEKVSREMMDIHMDFMKDLRVREREKTETFEYAED  9759916

Query  412      FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +         K Y  P  +P          +++     +   WE++   + + + K+++
Sbjct  9759915  IIN--------KAY--PDAIP----------IIKNWLSIIQQRWEEVRQWAINRESKLEQ  9759796

Query  472      TLERLQELQEATDEL  486
                 L+ L++L +  +EL
Sbjct  9759795  HLQSLKDLDDTIEEL  9759751


 Features in this part of subject sequence:
   short stop, isoform H
   short stop, isoform C

 Score = 47.0 bits (110),  Expect = 0.072, Method: Compositional matrix adjust.
 Identities = 67/363 (18%), Positives = 154/363 (42%), Gaps = 25/363 (6%)
 Frame = -1

Query  26       LSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEE----------------  69
                L  L +    Q   + D++D+++   + K    +L+Q R Q E+                
Sbjct  9765485  LKALREFYDHQSQTLDDIQDVSDEFKRMKPVGSELDQIRRQQEDFRNFRERKVEPLAINV  9765306

Query  70       --LITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
                  +  A ++L     +  + T I   +E++ ++W++++E +  R ++L+  L  S ++ E
Sbjct  9765305  DKVNVAGRDLVRSAGSGVSTTAIEKDLEKLNDRWNDLKERMNERDRRLDVALLQSGKFQE  9765126

Query  128      AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                A     + L      + + K        ++ ++ E K L K L   Q ++    +L  ++
Sbjct  9765125  ALAGLSKWLSDTEEMVANQKPPSSDYKVVKAQLQEQKFLKKMLLDRQNSMGSLANLGKEV  9764946

Query  188      LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
                       +   +     ++   + ++     +RE  LEE   + ++F   +     WL  
Sbjct  9764945  ANHCEPGERASIEKQLNDLMKRFDALTDGAEQRELDLEEAMEVAKRFHDKISPLELWLDN  9764766

Query  248      AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
                 E +   +      E +  D + +++ +++   L  EI      + +L + + +++  L 
Sbjct  9764765  TERSVKAM------ELIPTDEEKIQQRIREHDRLHDEILGKKPDFSDLADVTAQLMH-LV  9764607

Query  308      GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
                  ++AV L  ++  +  +++ L   S NI + L  S    + L LS Q+L+ W++  + E
Sbjct  9764606  SDEEAVNLGEKVRGVTERYTGLVDASDNIGALLAESRQGLRHLVLSYQDLVAWMESMEAE  9764427

Query  368      LSR  370
                L R
Sbjct  9764426  LKR  9764418


 Features in this part of subject sequence:
   short stop, isoform H
   short stop, isoform C

 Score = 42.4 bits (98),  Expect = 1.5, Method: Compositional matrix adjust.
 Identities = 77/364 (21%), Positives = 157/364 (43%), Gaps = 40/364 (10%)
 Frame = -3

Query  14       DFNRAWTELTDWLS----LLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEE  69
                +FN AW+ +  +L     +LDQ+I+ +     + + I + I K K T + L  ++   + 
Sbjct  9760758  EFNDAWSGMMQYLQETEQVLDQIIE-EATASKEPQKIKKYIGKLKETHRQLGAKQSVYDG  9760582

Query  70       LITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAK  129
                 +   +NL  +    + R ++   +  ++ QW  V     +R+++L E L  S Q+ +A 
Sbjct  9760581  TMRTGKNLLERAPKGD-RPVLDKMLIELKEQWTRVWSKSIDRQRKLEEALLLSGQFSDAL  9760405

Query  130      EEAEQVLGQARAKLESWKEGPYTVD--AIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
                 E    L +A+++L   + GP   D   +Q      K + +DL++    +       LK 
Sbjct  9760404  GELLDWLKKAKSRLN--ENGPVHGDLETVQGLCEHHKHIEQDLQKRAAQMQGV----LKT  9760243

Query  188      LRDYS-ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
                 RD   + +  +V    + + + W  +   V++R   L+      ++    ++    WL 
Sbjct  9760242  GRDLERSGNNPEVGRQLDEMQSIWEEVKSAVAKRGERLQVALVDAEKLNARVQALFDWLD  9760063

Query  247      EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL  306
                 AE      ++A       +D K  +E+M          + H D   +L    ++   + 
Sbjct  9760062  HAEHKLRYAKNAP------DDEKVSREMM----------DIHMDFMKDLRVREREKTETF  9759931

Query  307      EGSDDAV---------LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQEL  357
                E ++D +         +++  L  +  +W E+R+ ++N  S LE      K L  +++EL
Sbjct  9759930  EYAEDIINKAYPDAIPIIKNWLSIIQQRWEEVRQWAINRESKLEQHLQSLKDLDDTIEEL  9759751

Query  358      LVWL  361
                L WL
Sbjct  9759750  LAWL  9759739


 Features in this part of subject sequence:
   short stop, isoform H
   short stop, isoform C

 Score = 42.4 bits (98),  Expect = 1.9, Method: Compositional matrix adjust.
 Identities = 52/250 (20%), Positives = 116/250 (46%), Gaps = 19/250 (7%)
 Frame = -3

Query  281      LQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHL  340
                L  +I+AH +    L++  ++++ + +GS +A   Q +L  +N +W +L +K+ + +  L
Sbjct  9761622  LANDIQAHQNSVDTLNDAGRQLIETEKGSVEASTTQEKLRKLNNEWKQLLQKASDRQHEL  9761443

Query  341      EASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEP  400
                E +  +       +Q++L WL   D  +    P+GG      +Q +       EL    P
Sbjct  9761442  EEALREAHGYIAEVQDILGWLGDVDAVIGASKPVGGLPETATEQLERFMEVYNELDENRP  9761263

Query  401      VIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNL  460
                 +    ET++        +G E + ++ +        Q+  R L+++       W+ +  
Sbjct  9761262  KV----ETIQA-------QGQEYIKRQNQMKVSSSNLQHTLRTLKQR-------WDAVVS  9761137

Query  461      HSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKA  520
                 ++D + K++  L+   E  +        L QAE +  + +PV  +L +++Q  +E+ K 
Sbjct  9761136  RASDKKIKLEIALKEATEFHDTLQAFVEWLTQAEKLLSNAEPVSRVL-ETIQAQMEEHKV  9760960

Query  521      LRGEIAPLKE  530
                L+ +++  +E
Sbjct  9760959  LQKDVSTHRE  9760930


>gb|AC007356.8|AC007356 Drosophila melanogaster, chromosome 2R, region 49A-49B, BAC clone 
BACR24H09, complete sequence
Length=189557

 Score = 81.6 bits (200),  Expect(2) = 1e-18, Method: Compositional matrix adjust.
 Identities = 50/190 (26%), Positives = 84/190 (44%), Gaps = 24/190 (12%)
 Frame = +1

Query  731    TGRIRVLSFKTGIISLCKAHLEDKYRY---------------------LFKQVASSTGFC  769
              +G+IRV S K  + ++C   L DK R                      +F Q++   G  
Sbjct  21589  SGKIRVFSIKVALATMCSGKLVDKLRCE*CTHHLITK*TRLKLFHRTDIFSQISDGAGQL  21768

Query  770    DQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEP  829
                 +LG  L + + +P  + E  +F   + +  +      A NK  +   +        P
Sbjct  21769  VAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPAENKVTVNDFMATLMSEPGP  21939

Query  830    QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKG  889
                +VWLP++HR+A  ET  H   C++C +    GFRYR  +   Y +CQ CF+ G+ +  
Sbjct  21940  SCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQRCHAYQLCQECFWHGKTSLN  22119

Query  890    HKMHYPMVEY  899
              H+  + + EY
Sbjct  22120  HQNDHEVKEY  22149


 Score = 41.2 bits (95),  Expect(2) = 1e-18, Method: Compositional matrix adjust.
 Identities = 26/96 (27%), Positives = 50/96 (52%), Gaps = 4/96 (4%)
 Frame = +2

Query  635    LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
              L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  21227  LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  21406

Query  693    CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVY  726
               ++++Y  L +       VP+     + LNWLL  Y
Sbjct  21407  LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAY  21514


>gb|AC007476.5|AC007476 Drosophila melanogaster, chromosome 2R, region 49A-49B, BAC clone 
BACR37P06, complete sequence
Length=171705

 Score = 81.6 bits (200),  Expect(2) = 1e-18, Method: Compositional matrix adjust.
 Identities = 50/190 (26%), Positives = 84/190 (44%), Gaps = 24/190 (12%)
 Frame = +1

Query  731     TGRIRVLSFKTGIISLCKAHLEDKYRY---------------------LFKQVASSTGFC  769
               +G+IRV S K  + ++C   L DK R                      +F Q++   G  
Sbjct  136474  SGKIRVFSIKVALATMCSGKLVDKLRCE*CTHHLITK*TRLKLFHRTDIFSQISDGAGQL  136653

Query  770     DQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEP  829
                  +LG  L + + +P  + E  +F   + +  +      A NK  +   +        P
Sbjct  136654  VAWKLGEFLREVLALPAAVYESPTF---HYKEGLEEEIFPAENKVTVNDFMATLMSEPGP  136824

Query  830     QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKG  889
                 +VWLP++HR+A  ET  H   C++C +    GFRYR  +   Y +CQ CF+ G+ +  
Sbjct  136825  SCLVWLPLVHRLATVETIVHPTVCSVCHKENFTGFRYRCQRCHAYQLCQECFWHGKTSLN  137004

Query  890     HKMHYPMVEY  899
               H+  + + EY
Sbjct  137005  HQNDHEVKEY  137034


 Score = 41.2 bits (95),  Expect(2) = 1e-18, Method: Compositional matrix adjust.
 Identities = 26/96 (27%), Positives = 50/96 (52%), Gaps = 4/96 (4%)
 Frame = +2

Query  635     LADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLK--QNDQPMDILQIIN  692
               L   +++RF++YRTA KLR +QK+  L L+ +    +A  ++ L   +    + + ++  
Sbjct  136112  LQTFDSIRFASYRTASKLRYIQKSTNLHLVDIWNVIEAFRENGLNTLEPQSEVSVARLET  136291

Query  693     CLTTIYDRLEQEHNNLVNVPL--CVDMCLNWLLNVY  726
                ++++Y  L +       VP+     + LNWLL  Y
Sbjct  136292  LVSSLYHNLNKRLPTAQQVPVDSKAGLLLNWLLAAY  136399


>emb|Z11860.1| H.sapiens gene encoding dystrophin, exon 60
Length=989

 Score =  101 bits (252),  Expect = 2e-18, Method: Compositional matrix adjust.
 Identities = 49/52 (94%), Positives = 51/52 (98%), Gaps = 0/52 (0%)
 Frame = +1

Query  519  KALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVA  570
            +ALRGEIAPLKENVSHV DLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV+
Sbjct  643  QALRGEIAPLKENVSHVKDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQVS  798


>ref|XM_001946815.1| PREDICTED: Acyrthosiphon pisum similar to dystrophin CG34157-PC 
(LOC100166731), mRNA
Length=3726

 Score =  101 bits (251),  Expect = 3e-18, Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 125/234 (53%), Gaps = 10/234 (4%)
 Frame = +1

Query  29    LDQVIKSQRVMVGDLEDINEMIIKQKAT------MQDLEQRRPQLEELITAAQNLKNKTS  82
             L +++K+ R     L++INE I+K+ +       +++LEQ++PQL+EL+  A+NLK  ++
Sbjct  2962  LQEIVKNLRDNWNYLKNINENILKKPSVTSIENVLRELEQKKPQLDELVHTAENLKADSN  3141

Query  83    NQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAK  142
              Q+    +  ++ +++  WDE    +  R+ +LN ML DS ++   K E +  L +   +
Sbjct  3142  RQQ----LHGKVTKLREHWDETNNKVMQRKTELNAMLSDSQRYETKKMEIDTWLTRMENR  3309

Query  143   LESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMI  202
             L+       T D +  +  E K    +L Q++ ++D+ N L  KL+  Y  DDT K+  +
Sbjct  3310  LQRMSSVGNTADVLDAQQREQKSFHVELHQYKHHIDLFNQLTQKLIAVYQNDDTSKIKKL  3489

Query  203   TENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQ  256
             TE ++  +++++  +  R   L      LQ      + FL WL+EAE++   ++
Sbjct  3490  TEQVHQRFQNLNTNIISRGKVLHSAINSLQNLDKSFDNFLGWLSEAESSMETIE  3651


>gb|AF213442.1|AF213442 Homo sapiens dystrophin (DMD) gene, exon 70 and partial cds
Length=952

 Score =  101 bits (251),  Expect = 3e-18, Method: Composition-based stats.
 Identities = 48/61 (78%), Positives = 53/61 (86%), Gaps = 5/61 (8%)
 Frame = +1

Query  893  HYPMVEYCTP-----TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  947
            ++P++   +P     TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME
Sbjct  235  NHPVLNLISP*SPF*TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  414

Query  948  T  948
            T
Sbjct  415  T  417


>gb|M86894.1|HUMDYST11 H.sapiens dystrophin gene, exon 70
Length=284

 Score =  101 bits (251),  Expect = 3e-18, Method: Composition-based stats.
 Identities = 48/61 (78%), Positives = 53/61 (86%), Gaps = 5/61 (8%)
 Frame = +3

Query  893  HYPMVEYCTP-----TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  947
            ++P++   +P     TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME
Sbjct  18   NHPVLNLISP*SPF*TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNME  197

Query  948  T  948
            T
Sbjct  198  T  200


>ref|XM_001195605.1| PREDICTED: Strongylocentrotus purpuratus similar to dystonin 
(LOC756550), mRNA
Length=9330

 Score = 98.6 bits (244),  Expect = 2e-17, Method: Compositional matrix adjust.
 Identities = 114/582 (19%), Positives = 251/582 (43%), Gaps = 39/582 (6%)
 Frame = +1

Query  11    ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
             AL     +  EL +W++  ++ +  QR ++GD +     + K K    D+      ++ +
Sbjct  5629  ALGQLESSLDELLNWMNRTEKALSDQRPVMGDTKGAEIELAKHKVLQNDIMAHESSVKSV  5808

Query  71    ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKE  130
               A QN      N++   ++  +++ + N+W  +      R+++L   L ++  + E   
Sbjct  5809  NQAGQNFVASADNRQVANVVRSKLDDVNNKWANLTRMSDGRQRELEGALGETKNFAEEAT  5988

Query  131   EAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRD  190
                + L     +L S +      +  ++++     L K + + +   D       +L R 
Sbjct  5989  RLLRWLHDINGQLSSSQPVGGLPETAREQLDRHNDLRKHMDREKLAFDSLMQAGQQLKRQ  6168

Query  191   YS--ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEA  248
                 AD    V    + + A W + +++ ++R+  LE+     Q F   L+ F++WLT A
Sbjct  6169  SGPEADREGGVGHTLKTLQAQWDAANQKATDRKRKLEDALTQAQNFHDALQAFISWLTTA  6348

Query  249   ETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEG  308
             E T N    +++    + D+  + + + + +D   +I+AH +   +LD    + L+    
Sbjct  6349  EKTMN----SSKPPSTVLDT--INQQITEHKDFLMDIQAHKETMRDLDRAGTQ-LKYFSQ  6507

Query  309   SDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDEL  368
               D +L++  L ++  +W +++ +  +    L++   + K+      +L  WL     +L
Sbjct  6508  KQDVILIKNLLISVQNRWEKVQSRCNDRTRQLDSGFKRAKQFDEQYGKLFGWLTDSQAQL  6687

Query  369   SRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEP  428
              +   IG D   ++ Q   H+ F+R L  K+P+  + + + R                  
Sbjct  6688  DQDKSIGSDPETLKAQLRRHKDFQRALGAKQPLYDNIVRSGRSL--------------RD  6825

Query  429   RELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDL  488
             +  P +      T+ +     ++  EW+ +   S D QRK++E L    + ++A   L  
Sbjct  6826  KSNPAD------TKTINGMLTDLKDEWDLVCGRSVDRQRKLEEALLHSGQFKDALQALLE  6987

Query  489   KLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGI  547
              L Q E       PV GD  ID++ + +E  K  + ++   K +V  VN  A+ L     
Sbjct  6988  WLYQVEPTLSDETPVDGD--IDTVMNLMEAHKGFQRDLGSRKNSVKSVNKSAKDLMDKSS  7161

Query  548   QLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHEAH  582
             + + +  + +++L ++W+ +       Q  +ED +++  + H
Sbjct  7162  EDTSHLRAKIQELASKWETVCEQSVHKQERLEDAMKEAEDFH  7287


 Score = 90.5 bits (223),  Expect = 5e-15, Method: Compositional matrix adjust.
 Identities = 115/554 (20%), Positives = 237/554 (42%), Gaps = 51/554 (9%)
 Frame = +1

Query  40    VGDLEDINEMIIKQ-KATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQ  98
             + D +DI + I +   A  QD+E  +   ++L+T   +  NK   Q+        ++ + 
Sbjct  5080  IKDQQDILQAIKEDIDAVKQDVEMTKQLGQDLMTHCSD-SNKPEVQK-------NVDELN  5235

Query  99    NQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQK  158
             N WD + +  ++R Q+L++  + +  + +  +     + +A  +++           +++
Sbjct  5236  NSWDNLNDAFKDRHQKLDDADEAAQAFQDGLDRMNDYMTKAEEQVDRMPAVGSDPQTVRR  5415

Query  159   KITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVS  218
             ++       K+L +    ++  N L  +LL   + ++   V     ++N  W+++  +  
Sbjct  5416  QLDNLNAFKKELGRNNLELETVNQLGNRLLTKCTPENQELVQAPMSDMNRRWKNLQDKTF  5595

Query  219   EREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQW  278
             +R+  LE     L Q    L++ L W+   E     L D   +  ++ D+KG +  + + 
Sbjct  5596  DRQHKLEAGFLALGQLESSLDELLNWMNRTE---KALSD---QRPVMGDTKGAEIELAKH  5757

Query  279   QDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRS  338
             + LQ +I AH     ++++  Q  + S +    A +++ +LD++N KW+ L + S   + 
Sbjct  5758  KVLQNDIMAHESSVKSVNQAGQNFVASADNRQVANVVRSKLDDVNNKWANLTRMSDGRQR  5937

Query  339   HLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTK  398
              LE +  + K        LL WL   + +LS   P+GG     ++Q D H   ++ +  +
Sbjct  5938  ELEGALGETKNFAEEATRLLRWLHDINGQLSSSQPVGGLPETAREQLDRHNDLRKHM-DR  6114

Query  399   EPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPE-ERAQNVTRLLRKQAEEVNTEWEK  457
             E +   +L              ++   Q  R+  PE +R   V   L+     +  +W+ 
Sbjct  6115  EKLAFDSL--------------MQAGQQLKRQSGPEADREGGVGHTLKT----LQAQWDA  6240

Query  458   LNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEK  517
              N  + D +RK+++ L + Q   +A       L  AE    S +P   +L D++   + +
Sbjct  6241  ANQKATDRKRKLEDALTQAQNFHDALQAFISWLTTAEKTMNSSKPPSTVL-DTINQQITE  6417

Query  518   VKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYN--------LSTLEDLNTRWKLLQV  569
              K    +I   KE +       R L   G QL  ++         + L  +  RW+ +Q 
Sbjct  6418  HKDFLMDIQAHKETM-------RDLDRAGTQLKYFSQKQDVILIKNLLISVQNRWEKVQS  6576

Query  570   AVEDRVRQLHEAHR  583
                DR RQL    +
Sbjct  6577  RCNDRTRQLDSGFK  6618


 Score = 77.8 bits (190),  Expect = 4e-11, Method: Compositional matrix adjust.
 Identities = 101/478 (21%), Positives = 213/478 (44%), Gaps = 39/478 (8%)
 Frame = +1

Query  14    DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
             +F+ A      WL+  ++ + S +     L+ IN+ I + K  + D++  +  + +L  A
Sbjct  6301  NFHDALQAFISWLTTAEKTMNSSKPPSTVLDTINQQITEHKDFLMDIQAHKETMRDLDRA  6480

Query  74    AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE  133
                LK  +  Q+   +I + +  +QN+W++VQ    +R +QL+   K + Q+ E   +  
Sbjct  6481  GTQLKYFSQKQDV-ILIKNLLISVQNRWEKVQSRCNDRTRQLDSGFKRAKQFDEQYGKLF  6657

Query  134   QVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSA  193
               L  ++A+L+  K      + ++ ++   K   + L   Q   D        L    + 
Sbjct  6658  GWLTDSQAQLDQDKSIGSDPETLKAQLRRHKDFQRALGAKQPLYDNIVRSGRSLRDKSNP  6837

Query  194   DDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTAN  253
              DT+ ++ +  ++   W  +  R  +R+  LEE      QF   L+  L WL + E T  
Sbjct  6838  ADTKTINGMLTDLKDEWDLVCGRSVDRQRKLEEALLHSGQFKDALQALLEWLYQVEPT--  7011

Query  254   VLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAV  313
              L D T  +    D   V  LM+  +  Q ++ +  +   +++++++ ++   + S+D  
Sbjct  7012  -LSDETPVD---GDIDTVMNLMEAHKGFQRDLGSRKNSVKSVNKSAKDLMD--KSSEDTS  7173

Query  314   LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAP  373
              L+ ++  +  KW  + ++S++ +  LE +  + +  H  +Q LL WL   +  L  Q P
Sbjct  7174  HLRAKIQELASKWETVCEQSVHKQERLEDAMKEAEDFHDIVQLLLEWLADAEQSLRFQGP  7353

Query  374   IGGDFPAVQKQNDVHRAFK-----RELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEP  428
             +  D   +++Q + H+ FK     +E++  +  +M   +T+           L K +  P
Sbjct  7354  LSNDPEVIREQMETHKDFKDSFGSQEMRMNDACVMG--DTI-----------LSKCH--P  7488

Query  429   RELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDEL  486
               +P          +++     +   WE++   S     ++DETL+ L E  E  ++L
Sbjct  7489  EAVP----------VIKHWITVLQARWEEVMALSDQKSDRLDETLDNLAENAELLEKL  7632


 Score = 53.1 bits (126),  Expect = 9e-04, Method: Compositional matrix adjust.
 Identities = 113/581 (19%), Positives = 233/581 (40%), Gaps = 41/581 (7%)
 Frame = +1

Query  9     VPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLE  68
             +P    FN +  ELT WL  ++  +K+ +    D E+I   +   +   Q + +++  + 
Sbjct  4309  LPQTLQFNESHEELTKWLDEVEGDLKNLKPPGLDAEEIRREVDNNRFMKQTVAEKQQHVN  4488

Query  69    ELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEA  128
             +L   A  L   +    A+ +   + +    +++ V+E +  R +++ ++L+ ++ ++E 
Sbjct  4489  KLNRIAPELAKLSPGAGAQGVQA-KADDDNRRYENVKEDVNKRGEKMFDLLQRTSSFVED  4665

Query  129   KEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLL  188
              +   + L     KL   +      D ++K++ + + L  ++      VDV      +++
Sbjct  4666  LDSTLEQLNITAEKLSRPEPISADPDHLRKQMKKLQALRDNIDSQMDVVDVMRKAGNEMI  4845

Query  189   RDYSADD--TRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
                S  D   R +    + ++  W  I    ++R A L+E     + F         W  
Sbjct  4846  EASSPSDPHVRDLKDKLDQMSNKWDDITATANKRSADLQEALHSAESF---------W-E  4995

Query  247   EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL  306
             E   T+  ++D   + +  E        +K  QD+   I+   D      E ++++ + L
Sbjct  4996  EMNGTSGTIKDLQDQIKSQEPPAVEIPAIKDQQDILQAIKEDIDAVKQDVEMTKQLGQDL  5175

Query  307   E---GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQL  363
                    +   +Q+ +D +N  W  L     +    L+ + +  +     L  +  ++  
Sbjct  5176  MTHCSDSNKPEVQKNVDELNNSWDNLNDAFKDRHQKLDDADEAAQAFQDGLDRMNDYMTK  5355

Query  364   KDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEK  423
              ++++ R   +G D   V++Q D   AFK+EL      + +  +     LT+   E  E 
Sbjct  5356  AEEQVDRMPAVGSDPQTVRRQLDNLNAFKKELGRNNLELETVNQLGNRLLTKCTPENQE-  5532

Query  424   LYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEAT  483
             L Q P                     ++N  W+ L   + D Q K++     L +L+ + 
Sbjct  5533  LVQAP-------------------MSDMNRRWKNLQDKTFDRQHKLEAGFLALGQLESSL  5655

Query  484   DELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQL  542
             DEL   + + E      +PV GD      +  L K K L+ +I   + +V  VN   +  
Sbjct  5656  DELLNWMNRTEKALSDQRPVMGD--TKGAEIELAKHKVLQNDIMAHESSVKSVNQAGQNF  5829

Query  543   TTLGIQLSPYNL--STLEDLNTRWKLLQVAVEDRVRQLHEA  581
                       N+  S L+D+N +W  L    + R R+L  A
Sbjct  5830  VASADNRQVANVVRSKLDDVNNKWANLTRMSDGRQRELEGA  5952


 Score = 52.4 bits (124),  Expect = 0.001, Method: Compositional matrix adjust.
 Identities = 73/397 (18%), Positives = 182/397 (45%), Gaps = 24/397 (6%)
 Frame = +1

Query  9     VPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQR----R  64
             + +L+DF  A   L  WL   +++      ++G +     ++  QK  ++ L++      
Sbjct  379   INSLSDFETAHNRLKTWLGEKERMAS----VLGPIGVEPGILRNQKLQVEVLQEEFAAHE  546

Query  65    PQLEELITAAQNLKNKTSNQEARTIITDRIER----IQNQWDEVQEHLQNRRQQLNEMLK  120
             PQ+E+L+ A Q + +K   Q+ R+  T  I++    ++NQWD ++  L +R  +++++L+
Sbjct  547   PQMEQLLEAGQAIVDK---QDPRSRTTSPIQQQVADLKNQWDALKGQLDDREGKIDDVLR  717

Query  121   DSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA  180
              S  + +  +++   L   R K+ +      + + +++++ ETK L ++  + +   D  
Sbjct  718   KSEHFHDILQDSSDWLIDFRNKISNLAPISNSPEVVRQQMEETKNLQREADRRKPQQDKL  897

Query  181   NDLALKLLRDYSADDTRK--VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDL  238
             ++   +L  + + + T K  V +  E++   +  +  ++ ER+  L+      + F    
Sbjct  898   SETHRELT-ELNPELTAKAEVTLKLESVRTPYNDLCHKLDERQGKLQAALLQSRDFEESY  1074

Query  239   EKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDEN  298
                L WL   +   N ++  + K  +L      +  + + +++  EI      Y  + E 
Sbjct  1075  GSMLRWLDTKDKELNQVKPISAKPEVL------RRQVVEHEEIPKEIVKQVYTYERMLEK  1236

Query  299   SQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELL  358
                +    +   +   LQ + D++  KW+ +  ++      L+ ++++ K     L + L
Sbjct  1237  IDSLKDEADSPAEKNELQGKRDSLQTKWNSVNDRATQRGERLKEANEKAKVYSDELNQFL  1416

Query  359   VWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKREL  395
              WL+  +D +S   P+      V++Q ++ +  + ++
Sbjct  1417  PWLRSAEDRMSSLGPVTAKPNVVRRQYELIKQLQEDI  1527


 Score = 49.3 bits (116),  Expect = 0.015, Method: Compositional matrix adjust.
 Identities = 67/296 (22%), Positives = 126/296 (42%), Gaps = 33/296 (11%)
 Frame = +1

Query  311   DAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSR  370
             D+   + +LDN+N +W  LR+++   +  +E ++ + + L  ++ E+   L   +     
Sbjct  2245  DSDSFREQLDNLNKRWQRLRERANKRQDDVERTTSRMQDLKHTMGEVDELLGKAESAQML  2424

Query  371   QAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQ--EP  428
             Q P+G D   V++Q    + + R     EP++    +  R+          + L Q  EP
Sbjct  2425  QKPVGADVDTVKQQQKEFKTYMRNF--VEPLVPRLRDANRVG---------QSLVQSAEP  2571

Query  429   RELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDL  488
             R           T  L    E +N  W +L+  ++D + K++E L R  + QEA   L  
Sbjct  2572  RV---------NTNQLEGDMEAMNDRWNRLHAKNSDREAKLNEGLLRCGKFQEALQSLMG  2724

Query  489   KLRQAE-VIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGI  547
              + + E ++     P  D  +  ++  L + + L   I   + +V  + ++  QL+ +  
Sbjct  2725  WIGETEDLVSTQKDPSSDYKV--VKAQLAEQQLLDRLITDREPSVDALKEMGEQLSKVSE  2898

Query  548   QLSPYNL-STLEDLNTRWKLLQVAVEDRVRQLHEA-------HRDFGPASQHFLST  595
                   +   L DL  RW+ L  AV DR ++L +        H    P SQ   +T
Sbjct  2899  PQDRMRIQQQLSDLERRWRALVDAVRDRRQKLEQTEKTAKDFHEQIAPLSQWLDAT  3066


 Score = 42.7 bits (99),  Expect = 1.3, Method: Compositional matrix adjust.
 Identities = 55/270 (20%), Positives = 125/270 (46%), Gaps = 10/270 (3%)
 Frame = +1

Query  15    FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
             F  A   L +WL  ++  +  +  + GD++ +  ++   K   +DL  R+  ++ +  +A
Sbjct  6958  FKDALQALLEWLYQVEPTLSDETPVDGDIDTVMNLMEAHKGFQRDLGSRKNSVKSVNKSA  7137

Query  75    QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
             ++L +K+S  E  + +  +I+ + ++W+ V E   +++++L + +K++  + +  +   +
Sbjct  7138  KDLMDKSS--EDTSHLRAKIQELASKWETVCEQSVHKQERLEDAMKEAEDFHDIVQLLLE  7311

Query  135   VLGQARAKLESWKEGPYTVD--AIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS  192
              L  A   L    +GP + D   I++++   K         +  ++ A  +   +L    
Sbjct  7312  WLADAEQSLRF--QGPLSNDPEVIREQMETHKDFKDSFGSQEMRMNDACVMGDTILSKCH  7485

Query  193   ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
              +    +      + A W  +     ++   L+ET   L +    LEK + WL ++E   
Sbjct  7486  PEAVPVIKHWITVLQARWEEVMALSDQKSDRLDETLDNLAENAELLEKLMDWLNKSE---  7656

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQ  282
             +VLQD   K    ED   ++ L+K+ QD +
Sbjct  7657  HVLQDRDSKP-TPEDVDRIQALLKEHQDFE  7743


 Score = 41.6 bits (96),  Expect = 3.1, Method: Compositional matrix adjust.
 Identities = 73/391 (18%), Positives = 162/391 (41%), Gaps = 25/391 (6%)
 Frame = +1

Query  94    IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
             +E + ++W+ +     +R  +LNE L    ++ EA +     +G+    + + K+     
Sbjct  2602  MEAMNDRWNRLHAKNSDREAKLNEGLLRCGKFQEALQSLMGWIGETEDLVSTQKDPSSDY  2781

Query  154   DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
               ++ ++ E + L + +   + +VD   ++  +L +     D  ++     ++   WR++
Sbjct  2782  KVVKAQLAEQQLLDRLITDREPSVDALKEMGEQLSKVSEPQDRMRIQQQLSDLERRWRAL  2961

Query  214   HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKE  273
                V +R   LE+T +  + F   +     WL   E +         +  +  D   +++
Sbjct  2962  VDAVRDRRQKLEQTEKTAKDFHEQIAPLSQWLDATERS------LASQPPVSTDKAQIQK  3123

Query  274   LMKQWQDLQGEIEAHT-DVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKK  332
              ++  Q ++ +++ H  DV   +  ++ + L+ +    +   LQ RLD +  ++  +R K
Sbjct  3124  QIQDQQAMERDVQNHGPDVRETM--SAGRKLQRMVSPSERDSLQTRLDAVQDRYDNIRDK  3297

Query  333   SLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFK  392
             +L  +  L  +    +        LL WL   + +L R  PI      VQKQ D      
Sbjct  3298  TLQKKVDLNRALATSQVFGEDEAALLRWLTDMERKLGRPQPISIHPEVVQKQLDNQTVLH  3477

Query  393   RELKTKEPVIMSTLETVRIFL----------TEQPLEGLEKLYQEPRELPPEERAQNVTR  442
               +  ++P I   L   +  L           +Q L+ ++  Y    +   ++ +Q    
Sbjct  3478  ASVLDRQPEIRKVLSDGQDLLRQCTGKEVSDVQQKLDHIQNRYDNIFQKSEDQLSQ----  3645

Query  443   LLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                +QA  +  E+ +L    ADW +K ++ L
Sbjct  3646  --LQQAVPLANEFNRLQSEFADWLKKAEQDL  3732


 Score = 41.2 bits (95),  Expect = 3.4, Method: Compositional matrix adjust.
 Identities = 125/607 (20%), Positives = 255/607 (42%), Gaps = 83/607 (13%)
 Frame = +1

Query  3     SSLMLEVPALADFNRAWTELTDWLSLLDQ---------VIKSQRVMVGDLEDINEMIIKQ  53
             S L   VP   +FNR  +E  DWL   +Q          +++Q+ +   L+D    I + 
Sbjct  3640  SQLQQAVPLANEFNRLQSEFADWLKKAEQDLRNFDPSASVETQKAVQEKLQD---EIDRH  3810

Query  54    KATMQDLEQRRPQLEELI--TAAQNLKNKTSNQEAR-TIITDRIERIQNQWDEVQEHLQN  110
             +  +Q+L ++  +L EL     A  ++ + ++   R   +  R + I+ +     +  Q 
Sbjct  3811  RPILQELNEKGTRLIELSPGQGAAEIRQQLNDDNQRFNELASRTKDIEYRLSAALDGAQK  3990

Query  111   RRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDL  170
              +Q ++ +LK    WL+  +  +Q   QAR  +          D ++ ++ + K + K++
Sbjct  3991  VQQSMDGLLK----WLDEADRQQQT--QARETIS------VEPDGVRDQLKKAKAIDKEI  4134

Query  171   RQWQTNVDVANDLALKLLRDYSADDTR---KVHMITENINASWRSIHKRVSEREAALEET  227
                Q+ V      A  L+   S  D R   ++     ++   +  +  R ++R   LEE 
Sbjct  4135  TGKQSRVQDTLGAAEALIEQTS--DPRQQARLESQANDLKQRFDDLSARSADRVEVLEEA  4308

Query  228   HRLLQQFPLDLEKFLAWLTEAETTANVLQ----DATRKERLLEDSKGVKELMKQWQDLQG  283
                  QF    E+   WL E E     L+    DA    R +++++ +K+ +        
Sbjct  4309  LPQTLQFNESHEELTKWLDEVEGDLKNLKPPGLDAEEIRREVDNNRFMKQTV-------A  4467

Query  284   EIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEAS  343
             E + H +  + +       L  L     A  +Q + D+ N ++  + K+ +N R   E  
Sbjct  4468  EKQQHVNKLNRIAPE----LAKLSPGAGAQGVQAKADDDNRRYENV-KEDVNKRG--EKM  4626

Query  344   SDQWKRLHLSLQEL---LVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEP  400
              D  +R    +++L   L  L +  ++LSR  PI  D   ++KQ    +A +  + ++  
Sbjct  4627  FDLLQRTSSFVEDLDSTLEQLNITAEKLSRPEPISADPDHLRKQMKKLQALRDNIDSQ--  4800

Query  401   VIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKL--  458
               M  ++ +R    E        + +      P        R L+ + ++++ +W+ +  
Sbjct  4801  --MDVVDVMRKAGNE--------MIEASSPSDPH------VRDLKDKLDQMSNKWDDITA  4932

Query  459   --NLHSADWQRKIDETLERLQELQEATDEL-DLKLRQAEVIKGSWQPVGDLLIDSLQDHL  515
               N  SAD Q  +       +E+   +  + DL+    + IK    P   + I +++D  
Sbjct  4933  TANKRSADLQEALHSAESFWEEMNGTSGTIKDLQ----DQIKSQEPPA--VEIPAIKDQQ  5094

Query  516   EKVKALRGEIAPLKENVSHVNDLARQLTT-LGIQLSPYNLSTLEDLNTRWKLLQVAVEDR  574
             + ++A++ +I  +K++V     L + L T       P     +++LN  W  L  A +DR
Sbjct  5095  DILQAIKEDIDAVKQDVEMTKQLGQDLMTHCSDSNKPEVQKNVDELNNSWDNLNDAFKDR  5274

Query  575   VRQLHEA  581
              ++L +A
Sbjct  5275  HQKLDDA  5295


>emb|CT027835.13| Zebrafish DNA sequence from clone CH211-66E18 in linkage group 
14, complete sequence
Length=83584

 Score = 97.8 bits (242),  Expect = 3e-17, Method: Compositional matrix adjust.
 Identities = 58/138 (42%), Positives = 71/138 (51%), Gaps = 25/138 (18%)
 Frame = -1

Query  750    HLEDKYRYLFK------------QVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFG--  795
              H+ D Y  LF              V  S+ FCD  R  L +    ++    G  + FG  
Sbjct  80986  HVPDFYLILFY*GYSLSSVFHRVVVTRSSFFCDCFRDSLWVE---KVHSTNGYASCFGA*  80816

Query  796    --------GSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETA  847
                      G+N       CF   + K  IE + FL+WM LEPQS+VWLPVLHRV  AETA
Sbjct  80815  LGMHNEQYGANCCCLSLVCFLQVSGKSAIELSHFLEWMSLEPQSVVWLPVLHRVTVAETA  80636

Query  848    KHQAKCNICKECPIIGFR  865
              KHQA+C ICK+CPI GFR
Sbjct  80635  KHQARCYICKQCPIKGFR  80582


 Score = 77.8 bits (190),  Expect = 3e-11, Method: Compositional matrix adjust.
 Identities = 45/73 (61%), Positives = 51/73 (69%), Gaps = 2/73 (2%)
 Frame = -3

Query  1044   NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  1103
              +R LQ EY RLK +HE    SP     E  P SP   +D EL+AEA++LRQHK RLE RM
Sbjct  52226  HRVLQGEYRRLKWKHEEAAASP--QLLESGPGSPPGQQDEELLAEARVLRQHKTRLETRM  52053

Query  1104   QILEDHNKQLESQ  1116
              QILEDHNKQLESQ
Sbjct  52052  QILEDHNKQLESQ  52014


 Score = 75.9 bits (185),  Expect = 1e-10, Method: Compositional matrix adjust.
 Identities = 33/46 (71%), Positives = 41/46 (89%), Gaps = 0/46 (0%)
 Frame = -2

Query  903    TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
              TTSGE +RDFAK LKNKFR+K+YF+KHP+ GYLPVQ+VLE ++ ET
Sbjct  75984  TTSGEKMRDFAKTLKNKFRSKQYFSKHPQRGYLPVQSVLEVESSET  75847


 Score = 67.8 bits (164),  Expect = 3e-08, Method: Compositional matrix adjust.
 Identities = 27/41 (65%), Positives = 33/41 (80%), Gaps = 0/41 (0%)
 Frame = -1

Query  862    IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTP  902
              + FRYRSLK FN DICQ+CF +GR  KG K+HYP++EY TP
Sbjct  76471  MCFRYRSLKQFNVDICQTCFLTGRTTKGKKLHYPIMEYYTP  76349


 Score = 40.8 bits (94),  Expect = 4.6, Method: Compositional matrix adjust.
 Identities = 17/27 (62%), Positives = 20/27 (74%), Gaps = 0/27 (0%)
 Frame = -2

Query  946    METPASSPQLSHDDTHSRIEHYASRLA  972
               + P SSP+L H DTHSRIEH+ASR  
Sbjct  72402  FDRPCSSPRLPHADTHSRIEHFASRYG  72322


>emb|BX510641.9| Zebrafish DNA sequence from clone CH211-106M9 in linkage group 
14, complete sequence
Length=161300

 Score = 97.4 bits (241),  Expect = 4e-17, Method: Compositional matrix adjust.
 Identities = 58/138 (42%), Positives = 71/138 (51%), Gaps = 25/138 (18%)
 Frame = -3

Query  750    HLEDKYRYLFK------------QVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFG--  795
              H+ D Y  LF              V  S+ FCD  R  L +    ++    G  + FG  
Sbjct  88287  HVPDFYLILFY*GYSLSSVFHRVVVIRSSFFCDCFRDSLWVE---KVHSTNGYASCFGA*  88117

Query  796    --------GSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETA  847
                      G+N       CF   + K  IE + FL+WM LEPQS+VWLPVLHRV  AETA
Sbjct  88116  LGMHNEQYGANCCCLSLVCFLQVSGKSAIELSHFLEWMSLEPQSVVWLPVLHRVTVAETA  87937

Query  848    KHQAKCNICKECPIIGFR  865
              KHQA+C ICK+CPI GFR
Sbjct  87936  KHQARCYICKQCPIKGFR  87883


 Score = 82.8 bits (203),  Expect = 1e-12, Method: Compositional matrix adjust.
 Identities = 34/67 (50%), Positives = 51/67 (76%), Gaps = 0/67 (0%)
 Frame = -2

Query  661     LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
               +DL  LS+  D   +  L+  +  MD++++I+ LT++Y+RLE+E + L+N+PLCVDMCLN
Sbjct  111424  VDLFKLSSVVDVFREQELQHGEHVMDVVEVIHALTSLYERLEEERSVLINIPLCVDMCLN  111245

Query  721     WLLNVYD  727
               WLLNVYD
Sbjct  111244  WLLNVYD  111224


 Score = 81.3 bits (199),  Expect = 3e-12, Method: Compositional matrix adjust.
 Identities = 35/51 (68%), Positives = 43/51 (84%), Gaps = 0/51 (0%)
 Frame = -2

Query  758    LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQ  808
              LF+QV    G  DQ+ L LLLH++IQ+PRQLGEVA+FGGSN+EPSVRSCF+
Sbjct  94855  LFRQVCGPGGLTDQKHLSLLLHEAIQVPRQLGEVAAFGGSNVEPSVRSCFR  94703


 Score = 77.8 bits (190),  Expect = 3e-11, Method: Compositional matrix adjust.
 Identities = 45/73 (61%), Positives = 51/73 (69%), Gaps = 2/73 (2%)
 Frame = -3

Query  1044   NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  1103
              +R LQ EY RLK +HE    SP     E  P SP   +D EL+AEA++LRQHK RLE RM
Sbjct  60435  HRVLQGEYRRLKWKHEEAAASP--QLLESGPGSPPGQQDEELLAEARVLRQHKTRLETRM  60262

Query  1104   QILEDHNKQLESQ  1116
              QILEDHNKQLESQ
Sbjct  60261  QILEDHNKQLESQ  60223


 Score = 75.9 bits (185),  Expect = 1e-10, Method: Compositional matrix adjust.
 Identities = 33/46 (71%), Positives = 41/46 (89%), Gaps = 0/46 (0%)
 Frame = -2

Query  903    TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
              TTSGE +RDFAK LKNKFR+K+YF+KHP+ GYLPVQ+VLE ++ ET
Sbjct  83455  TTSGEKMRDFAKTLKNKFRSKQYFSKHPQRGYLPVQSVLEVESSET  83318


 Score = 75.5 bits (184),  Expect = 2e-10, Method: Compositional matrix adjust.
 Identities = 42/91 (46%), Positives = 57/91 (62%), Gaps = 0/91 (0%)
 Frame = -1

Query  430     ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLK  489
               E+ P  R  NV+R + KQA   +  WEKL     D  R ++ TLERL ++Q A +EL   
Sbjct  149516  EVSPRRRMLNVSRSVWKQANVASDLWEKLTARCVDRHRHMERTLERLLQIQAAMEELAAA  149337

Query  490     LRQAEVIKGSWQPVGDLLIDSLQDHLEKVKA  520
               L QAE ++ +W+PVGDL IDSLQDH++  K 
Sbjct  149336  LEQAEGVRDAWEPVGDLFIDSLQDHIDATKV  149244


 Score = 69.3 bits (168),  Expect = 1e-08, Method: Compositional matrix adjust.
 Identities = 33/60 (55%), Positives = 40/60 (66%), Gaps = 3/60 (5%)
 Frame = -1

Query  846    TAKHQAKCNICKE--CPI-IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTP  902
              T K      +CK   C I + FRYRSLK FN DICQ+CF +GR  KG K+HYP++EY TP
Sbjct  83999  TVKMNTSITVCKMHLCFITMCFRYRSLKQFNVDICQTCFLTGRTTKGKKLHYPIMEYYTP  83820


 Score = 48.5 bits (114),  Expect = 0.024, Method: Compositional matrix adjust.
 Identities = 23/49 (46%), Positives = 31/49 (63%), Gaps = 0/49 (0%)
 Frame = -1

Query  521     LRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV  569
                + E++ +KE + H+NDLA +L    + LS  N   LE LN RWKLLQV
Sbjct  138056  FKEELSQVKEGMKHINDLAHELAISDVHLSMDNARALEHLNNRWKLLQV  137910


 Score = 48.1 bits (113),  Expect = 0.027, Method: Compositional matrix adjust.
 Identities = 19/27 (70%), Positives = 24/27 (88%), Gaps = 1/27 (3%)
 Frame = -1

Query  611     PYYINHETQTTCWDHPKMTELYQSLAD  637
               P+Y +H+ QTTCWDHPKMTELYQ+L +
Sbjct  119546  PFY-SHQAQTTCWDHPKMTELYQALGE  119469


 Score = 47.8 bits (112),  Expect = 0.043, Method: Compositional matrix adjust.
 Identities = 33/76 (43%), Positives = 46/76 (60%), Gaps = 13/76 (17%)
 Frame = -1

Query  589     SQHFLSTSVQGPWERAI--SPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAY  646
               + HFLS  ++  +  AI  SP+   Y+++  T       P +  L    ADLNN++FSAY
Sbjct  116027  THHFLSVMLKISYFFAIFFSPHS*-YFLD*MTS------PLLLSL---TADLNNIKFSAY  115878

Query  647     RTAMKLRRLQKAL-CL  661
               RTAMKLR +QKAL C+
Sbjct  115877  RTAMKLRHVQKALRCM  115830


 Score = 46.6 bits (109),  Expect = 0.093, Method: Compositional matrix adjust.
 Identities = 18/28 (64%), Positives = 25/28 (89%), Gaps = 0/28 (0%)
 Frame = -3

Query  568     QVAVEDRVRQLHEAHRDFGPASQHFLST  595
               Q ++E+R++QL +AHRDFGP SQHFLS+
Sbjct  132366  QGSIEERLKQLQDAHRDFGPGSQHFLSS  132283


 Score = 43.9 bits (102),  Expect = 0.63, Method: Compositional matrix adjust.
 Identities = 20/30 (66%), Positives = 21/30 (70%), Gaps = 0/30 (0%)
 Frame = -3

Query  585     FGPASQHFLSTSVQGPWERAISPNKVPYYI  614
               + P S      SVQ PWERAISPNKVPYYI
Sbjct  126792  YCPLSSFVTPGSVQIPWERAISPNKVPYYI  126703


 Score = 43.5 bits (101),  Expect = 0.67, Method: Compositional matrix adjust.
 Identities = 16/39 (41%), Positives = 27/39 (69%), Gaps = 0/39 (0%)
 Frame = -2

Query  718     CLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYR  756
               C   +   + +GR G++RVLSFK G++ LC A +++KY+
Sbjct  108307  CFECVCVSFSSGRNGKMRVLSFKMGLVILCNADIQEKYK  108191


 Score = 40.8 bits (94),  Expect = 4.6, Method: Compositional matrix adjust.
 Identities = 17/27 (62%), Positives = 20/27 (74%), Gaps = 0/27 (0%)
 Frame = -1

Query  946    METPASSPQLSHDDTHSRIEHYASRLA  972
               + P SSP+L H DTHSRIEH+ASR  
Sbjct  80438  FDRPCSSPRLPHADTHSRIEHFASRYG  80358


>emb|BX511121.15| Zebrafish DNA sequence from clone DKEYP-110A12 in linkage group 
17, complete sequence
Length=90921

 Score = 97.4 bits (241),  Expect = 5e-17, Method: Compositional matrix adjust.
 Identities = 42/50 (84%), Positives = 45/50 (90%), Gaps = 0/50 (0%)
 Frame = -2

Query  816    IEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFR  865
              IE   F+DWM LEPQSMVWLPVLHRV AAETAKHQAKCNICKECP++GFR
Sbjct  67766  IELQQFVDWMHLEPQSMVWLPVLHRVTAAETAKHQAKCNICKECPMVGFR  67617


 Score = 89.7 bits (221),  Expect = 1e-14, Method: Compositional matrix adjust.
 Identities = 39/55 (70%), Positives = 46/55 (83%), Gaps = 0/55 (0%)
 Frame = -3

Query  758    LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
              LF QVAS+ G C QR+L LLLH+SIQIP QLGE A+FGGSN+EPSVRSCFQ+  +
Sbjct  75604  LFAQVASAAGVCTQRQLELLLHNSIQIPHQLGEAAAFGGSNMEPSVRSCFQYVGS  75440


 Score = 88.6 bits (218),  Expect = 2e-14, Method: Compositional matrix adjust.
 Identities = 44/67 (65%), Positives = 49/67 (73%), Gaps = 0/67 (0%)
 Frame = -2

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              +DLL LS A    DQHNL  N Q ++I  IINCL TIY  L+Q H +LVNVPLCVDMCLN
Sbjct  83969  VDLLELSIAQSVFDQHNLTHNGQLLEIPGIINCLCTIYCELQQVHPDLVNVPLCVDMCLN  83790

Query  721    WLLNVYD  727
              WLL VYD
Sbjct  83789  WLLKVYD  83769


 Score = 81.6 bits (200),  Expect = 2e-12, Method: Compositional matrix adjust.
 Identities = 35/46 (76%), Positives = 42/46 (91%), Gaps = 0/46 (0%)
 Frame = -1

Query  903    TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
              TTSGEDVRDF KVLKNKFR+K+YF KHPR+GYLPVQT+LE ++ +T
Sbjct  61602  TTSGEDVRDFTKVLKNKFRSKKYFTKHPRLGYLPVQTILEEEHSDT  61465


 Score = 74.3 bits (181),  Expect = 4e-10, Method: Compositional matrix adjust.
 Identities = 29/43 (67%), Positives = 37/43 (86%), Gaps = 0/43 (0%)
 Frame = -3

Query  862    IGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
              + FRYRSLKHFNY++CQ+CFFSGR++K H +  PMVEYCTP +
Sbjct  64438  LCFRYRSLKHFNYNVCQTCFFSGRISKDHHLSDPMVEYCTPVS  64310


 Score = 50.4 bits (119),  Expect = 0.006, Method: Compositional matrix adjust.
 Identities = 23/28 (82%), Positives = 26/28 (92%), Gaps = 0/28 (0%)
 Frame = -2

Query  633    QSLADLNNVRFSAYRTAMKLRRLQKALC  660
              Q +ADL++VRFSAYRTAMK RRLQKALC
Sbjct  87710  QCVADLSHVRFSAYRTAMKSRRLQKALC  87627


 Score = 42.4 bits (98),  Expect = 1.8, Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 28/35 (80%), Gaps = 0/35 (0%)
 Frame = -3

Query  722    LLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYR  756
              LL ++++GR+G+++VLS K G+ SL K  ++DKY+
Sbjct  77416  LLFLFNSGRSGKVQVLSMKIGLFSLSKGPIKDKYK  77312


 Score = 40.4 bits (93),  Expect = 6.4, Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 24/33 (72%), Gaps = 3/33 (9%)
 Frame = -2

Query  612    YY---INHETQTTCWDHPKMTELYQSLADLNNV  641
              YY    +HE Q+T WDHP+MT+L+QS+  L N+
Sbjct  88865  YY*LPFSHEQQSTSWDHPEMTQLFQSMGLLFNL  88767


>gb|M86893.1|HUMDYST10 H.sapiens dystrophin gene, exon 69
Length=247

 Score = 96.3 bits (238),  Expect = 1e-16, Method: Composition-based stats.
 Identities = 38/40 (95%), Positives = 39/40 (97%), Gaps = 0/40 (0%)
 Frame = +1

Query  865  RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTT  904
            RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTP +
Sbjct  94   RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPVS  213


>ref|XM_001365106.1| PREDICTED: Monodelphis domestica similar to microfilament and 
actin filament cross-linker protein (LOC100025003), mRNA
Length=16749

 Score = 95.5 bits (236),  Expect = 2e-16, Method: Compositional matrix adjust.
 Identities = 127/557 (22%), Positives = 251/557 (45%), Gaps = 32/557 (5%)
 Frame = +1

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  ++++ +QR + GD + I   + K      D+   +  ++ +
Sbjct  12787  ALGQFQHALEELMSWLTHTEELLDAQRPINGDPKVIEVELAKHHVLKNDVLAHQATVDTV  12966

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKE  130
                A   L   ++  +  + + +R+E +   W+ V +  + R QQL   L+ +  +    E
Sbjct  12967  NKAGNELLESSAGDDDASSLRNRLETMNQCWESVLQKTEEREQQLQSTLQQAQGFHSEIE  13146

Query  131    EAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLR-QWQTNVDVANDLALKLL-  188
              +    L +   +L S K      +  ++++    +L   L+ Q +T   + +   L LL 
Sbjct  13147  DFLLRLTRMENQLSSSKPTGGLPETAREQLDAHMELYDQLKGQEETYNQLLDKGRLMLLS  13326

Query  189    RDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEA  248
              RD S   ++    +T  +   W  +  ++ ER++ LEE   L  +F   L++F+ WLT A
Sbjct  13327  RDDSGSGSKTEQSVT-LLEQKWHVVSSKMEERKSKLEEVLNLATEFQNSLQEFINWLTLA  13503

Query  249    ETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEG  308
              E + N+    +    L+ ++  ++  + + +    E+ AH D    LD+   + L+ L  
Sbjct  13504  EQSLNIAPPPS----LILNTILLQ--IDEHKVFANEVNAHRDHIIELDQTGNQ-LKFLSQ  13662

Query  309    SDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDEL  368
                D VL++  L ++  +W ++ ++S+     L+ +  + K+ H + ++L+ WL+  ++ L
Sbjct  13663  KQDVVLIKNLLVSVQSRWEKVVQRSVERGRSLDDARKRAKQFHEAWKKLIDWLEDAENHL  13842

Query  369    SRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEP  428
                +  I  D   ++ Q   H+ F++ L  K+PV  +T+ T R               +E 
Sbjct  13843  DSELEISNDPDKIKLQLSRHKEFQKTLGGKQPVYDTTIRTGRAL-------------KEK  13983

Query  429    RELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDL  488
                LP +   Q +   L     EV  +W+ +   S + Q K++E L    +  +A   L  
Sbjct  13984  TSLPDD--VQKLDNCLG----EVRDKWDTVCGKSVERQHKLEEALLFSGQFMDALQALVD  14145

Query  489    KLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGI  547
               L + E      QPV GDL  D + + ++  K  + E+      V  +  L R+L     
Sbjct  14146  WLYKVEPQLAEDQPVHGDL--DLVMNLMDAHKVFQKELGKRTGTVQVLKRLGRELIENSR  14319

Query  548    QLSPYNLSTLEDLNTRW  564
                + +    L++L+TRW
Sbjct  14320  DDTTWVRVQLQELSTRW  14370


 Score = 68.6 bits (166),  Expect = 2e-08, Method: Compositional matrix adjust.
 Identities = 107/479 (22%), Positives = 213/479 (44%), Gaps = 25/479 (5%)
 Frame = +1

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW +L DWL   +  + S+  +  D + I   + + K   + L  ++P  +  I   
Sbjct  13786  FHEAWKKLIDWLEDAENHLDSELEISNDPDKIKLQLSRHKEFQKTLGGKQPVYDTTIRTG  13965

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              + LK KTS  +    + + +  ++++WD V      R+ +L E L  S Q+++A +    
Sbjct  13966  RALKEKTSLPDDVQKLDNCLGEVRDKWDTVCGKSVERQHKLEEALLFSGQFMDALQALVD  14145

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   +   K   K+L +    V V   L  +L+ + S D
Sbjct  14146  WLYKVEPQLAEDQPVHGDLDLVMNLMDAHKVFQKELGKRTGTVQVLKRLGRELIEN-SRD  14322

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA--  252
              DT  V +  + ++  W ++ K    ++  LE   +  ++F   +   L WL+EAE T   
Sbjct  14323  DTTWVRVQLQELSTRWDTVCKLSVSKQTRLEHALKQAEEFRNAVHMLLEWLSEAEQTLRF  14502

Query  253    -NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDD  311
                 L D T   + L D    KE MK+ ++ + ++ A   +  +        + ++   D 
Sbjct  14503  RGALPDDTEALQSLIDVH--KEFMKKVEEKRVDVNASVAMGED--------ILAMCHPDC  14652

Query  312    AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSR-  370
                 ++  +  +  ++ E+   +   +  LEA+  +       L+ELL W+Q  +  L + 
Sbjct  14653  VTTIKHWITIIRARFEEVLTWAKQHQQRLEAALSELIANAELLEELLAWIQWAETTLIQR  14832

Query  371    -QAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVR---IFLTEQPLEGLEKLYQ  426
               Q P   +   V+     H+AF  E+  K+P +    +T +   I  T  P   +EK   
Sbjct  14833  DQEPTPQNIDRVKSLISEHQAFMEEMTRKQPDVDRVTKTYKRKAIEPTHAPF--IEKSRS  15006

Query  427    EPREL----PPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQE  481
                + L    PP     + +     +  +++  W+++ L + + QRK+++ L+RL+EL+E
Sbjct  15007  NRKSLGQTAPPPMPLLSQSEAKNPRIHQLSARWQQVWLLALERQRKLNDMLDRLEELKE  15183


 Score = 60.8 bits (146),  Expect = 5e-06, Method: Compositional matrix adjust.
 Identities = 86/381 (22%), Positives = 176/381 (46%), Gaps = 27/381 (7%)
 Frame = +1

Query  37     RVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL---ITAAQNLK--NKTSNQEARTIIT  91
              R M   L D+++ +   +A  +D++  + Q+E++   ++  Q+LK   K S  E R ++ 
Sbjct  9190   REMFSQLADLDDELDSMRAIGRDIDSLQSQIEDVRLFLSKIQSLKLDIKASEGECRQMLE  9369

Query  92     DR-----------IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWL-EAKEEAEQVLGQA  139
              +            +E +  Q  ++ E  + R++QL   L     +  + KE  +      
Sbjct  9370   EEGSLDLLGLKRELEALSKQCGKLTERGKARQEQLELTLARVGDFYSKMKELNDMTTAAE  9549

Query  140    RAKLESWKEGPYTVDAIQKKITETKQLAKD-LRQWQTNVDVANDLALKLLRDYSAD-DTR  197
                +   W  G   VDAI +++ + K   K+ +   Q  +   N L   L++      D +
Sbjct  9550   EGEALQWVVGT-EVDAINQQLADFKMFQKEQVDPLQMKLQQVNGLGQGLIQSAGKHCDVQ  9726

Query  198    KVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQD  257
               +    E INA W +++K+V++R A L+E      +F   LE  L+WL + E        
Sbjct  9727   GLEHDMEEINARWNTLNKKVAQRIAQLQEALLHCGKFQDALEPLLSWLADTEDLI-----  9891

Query  258    ATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQR  317
              A +K    E  K VK  +++ + LQ  ++        L    ++I +S E +D   ++  
Sbjct  9892   ANQKPPSAE-YKVVKAQIQEQKLLQRLLDDRKATVDMLQAEGERIAQSAELADREKII-S  10065

Query  318    RLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGD  377
              +L+++  +W+EL  K+ + +  LE      K+ H + + +  +L + + +L+   P+G  
Sbjct  10066  QLESLGRRWTELLSKAASRQKQLEDILVLAKQFHETAEPVSDFLSVTEKKLANSEPVGTQ  10245

Query  378    FPAVQKQNDVHRAFKRELKTK  398
                 +Q+Q   H+A + E++++
Sbjct  10246  TAKIQQQIARHKALEEEIESR  10308


 Score = 57.4 bits (137),  Expect = 5e-05, Method: Compositional matrix adjust.
 Identities = 76/360 (21%), Positives = 158/360 (43%), Gaps = 22/360 (6%)
 Frame = +1

Query  12    LADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQ----DLEQRRPQL  67
             LA F  A T+L  WL+  + ++     ++G L     M+  QK  +Q    + E R+PQ 
Sbjct  7525  LASFQAAETQLRPWLTEKELMMS----VLGPLSIDPNMLNAQKQQVQFMLKEFEARKPQH  7692

Query  68    EELITAAQN-LKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWL  126
             E+L  AAQ  L        + + + + ++ I N+W E+ + L +R  Q+++ L  STQ+ 
Sbjct  7693  EQLNQAAQGILTGPGDGSPSASQVQEELQNINNKWIELTDRLNSRSSQIDQTLVKSTQYQ  7872

Query  127   EAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA----ND  182
             E  +   + +     +L           A+++++ ET ++  DL Q    +  A    ++
Sbjct  7873  ELLQNLSERVKAVGQQLNGQSAISTQPAAVKQQLEETSEIRSDLEQLDHEITDAQALCDE  8052

Query  183   LALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFL  242
             L+  +   Y  D+ RK     E +    + +    ++R   L+      QQF    ++  
Sbjct  8053  LSTLIGEQYLKDELRKR---LETVALPLKGLEDLAADRMNKLQTALASTQQFQQMFDELR  8223

Query  243   AWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKI  302
              WL + +      Q  + K   L         +++ ++ Q  +   +  Y  +    + +
Sbjct  8224  TWLDDKQNQQAKAQPISAKLDRLHCQ------LQEQEEFQKSLNQRSGSYEVIIIEGESL  8385

Query  303   LRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQ  362
             L S+   ++   LQ +L  +   W EL KK+ + +S L+    + ++    +++L+ W++
Sbjct  8386  LLSVHPGEEKKTLQSQLIELKSHWEELSKKAADRQSRLKDCLQKAQKYQWHVEDLIPWIE  8565


 Score = 55.1 bits (131),  Expect = 2e-04, Method: Compositional matrix adjust.
 Identities = 120/583 (20%), Positives = 238/583 (40%), Gaps = 56/583 (9%)
 Frame = +1

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F   + EL+ W+     +I        D E + +   + +   + + + +P +++L+   
Sbjct  11470  FWETYEELSPWIEETQTLISQLPPPAIDHEQLKQQQEEMRQLRESIAEHKPHIDKLLKIG  11649

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE-  133
                LK    N+    ++ ++ ++ +  +  ++E ++ R   L+E +  S Q  E  ++ E 
Sbjct  11650  PQLKELNPNE--GEMVQEKYQKAETTYARIKEEVRRRALALDEAVSQSAQISEFHDKMEP  11823

Query  134    --QVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLL-RD  190
                + L    ++L      P  VD I++ +++ K  A +L + Q + +       +L+ R 
Sbjct  11824  MLETLENLSSRLRIPPLIPAEVDKIRECLSDNKSTAMELEKLQPSFEALKRRGEELIGRS  12003

Query  191    YSADDTRKVHMITENINAS---WRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
                AD       I + ++     W  I  +  ERE    +   L ++F  D+   LA + +
Sbjct  12004  QGADKDLAAKEIQDKLDQMVFFWEDIKAQAEEREVKFLDVLELAEKFWYDMAALLATIKD  12183

Query  248    AETTANVLQDATRKERLLEDSKGVK-ELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL  306
                 T +++ D         +S G+   ++KQ  +    I+  TD  H   E     +R L
Sbjct  12184  ---TQDIVHDL--------ESPGIDPSIIKQQVEAAETIKEETDGLHEELE----FIRIL  12318

Query  307    E-------GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLV  359
                      G  +   +++ +D MN  W  L K        LE +     +   +LQ +  
Sbjct  12319  GADLIFACGETEKPEVKKSIDEMNNAWENLNKTWRERLEKLEEAMQAAVQYQDTLQTMFD  12498

Query  360    WLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLE  419
              WL     +L    P+G D   V+ Q +  + FK E                  + +Q +E
Sbjct  12499  WLDNTVIKLCNMPPVGTDLNTVKDQLNEMKEFKME------------------VYQQQIE  12624

Query  420    GLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQEL  479
               +EKL  +   +  +   +    ++R+   E+   WE L    A  Q K++  L  L + 
Sbjct  12625  -MEKLNHQGELMLKKATDETDRDIIREPLTELKHLWENLGEKIAHRQHKLEGALLALGQF  12801

Query  480    QEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDL  538
              Q A +EL   L   E +  + +P+ GD  +  ++  L K   L+ ++   +  V  VN  
Sbjct  12802  QHALEELMSWLTHTEELLDAQRPINGDPKV--IEVELAKHHVLKNDVLAHQATVDTVNKA  12975

Query  539    ARQL--TTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRVRQLH  579
                +L  ++ G   +    + LE +N  W+ +    E+R +QL 
Sbjct  12976  GNELLESSAGDDDASSLRNRLETMNQCWESVLQKTEEREQQLQ  13104


 Score = 50.4 bits (119),  Expect = 0.005, Method: Compositional matrix adjust.
 Identities = 75/304 (24%), Positives = 128/304 (42%), Gaps = 34/304 (11%)
 Frame = +1

Query  97    IQNQWDEVQEHLQNRRQQLNEMLKDST----------QWLEAKEEAEQVLGQARAKLESW  146
             +  Q++++   LQ RR  L  ML              QWLE+KE A +    + +     
Sbjct  7114  VSQQYEKLGGVLQERRDSLLAMLSSMQEVQEEASSLLQWLESKENALKAFDASSS-----  7278

Query  147   KEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDY-SADDTRKVHMITEN  205
                P   + ++ +    K    +L Q    +    +    LL+ Y ++ + +    + E 
Sbjct  7279  ---PTKTETMRAQAECNKAFLAELEQNSPKIHKVKEALAGLLKKYPNSQEAKHWKEMEEE  7449

Query  206   INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
             +++ W   ++  + R+  LEE+   L  F     +   WLTE E   +VL   +    +L
Sbjct  7450  LSSRWERANEVTAARQQKLEESANQLASFQAAETQLRPWLTEKELMMSVLGPLSIDPNML  7629

Query  266   EDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRS-LEGSDDAVLLQRRLDNMNF  324
                K      +Q Q +  E EA    +  L++ +Q IL    +GS  A  +Q  L N+N 
Sbjct  7630  NAQK------QQVQFMLKEFEARKPQHEQLNQAAQGILTGPGDGSPSASQVQEELQNINN  7791

Query  325   KWSELRKKSLNIRS----HLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPA  380
             KW EL  + LN RS         S Q++ L   LQ L   ++    +L+ Q+ I     A
Sbjct  7792  KWIELTDR-LNSRSSQIDQTLVKSTQYQEL---LQNLSERVKAVGQQLNGQSAISTQPAA  7959

Query  381   VQKQ  384
             V++Q
Sbjct  7960  VKQQ  7971


 Score = 41.6 bits (96),  Expect = 2.7, Method: Compositional matrix adjust.
 Identities = 115/557 (20%), Positives = 222/557 (39%), Gaps = 91/557 (16%)
 Frame = +1

Query  50    IIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQ  109
             I++QK++++   +   Q  E           T++    T +  ++  +  Q+ ++ +  Q
Sbjct  6274  IVRQKSSLEATREMVTQFME-----------TADGATATGLQGKLAEVSEQFSQLCQRQQ  6420

Query  110   NRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKD  169
              +   L ++L     +    E+ +Q L      L +  +    +    ++I E   L  +
Sbjct  6421  EKESSLKKLLPQVEMFEHISEKLQQFLDSRARMLATGNQPDRDIAQFSQQIQE---LNLE  6591

Query  170   LRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHR  229
             + + Q N+D    L + L     A DT +     + +   +  + K V ERE        
Sbjct  6592  MGEQQENLDALEHLVIDLSSCGFALDTSQHEERVQKLKKDFMGLQKSVQEREKETSSCQE  6771

Query  230   LLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQW--QDLQ-GEIE  286
              L +F   ++    WL E+E    V++ +     L +  + ++ L+  W  + LQ  EI 
Sbjct  6772  QLDEFRKLVQALQKWLKESEGNMPVMESSMSTRDLQKQIEQLEALLDDWTSKGLQVEEIN  6951

Query  287   AHTDVYHNL---------DENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIR  337
                    NL            +  +L SL GS  +V       N      +L +    I+
Sbjct  6952  RKGLALENLIVEITAPETQSKTGSVLPSLGGSVGSV-------NGYHTCKDLTE----IQ  7098

Query  338   SHLEASSDQWKRLHLSLQE---------------------LLVWLQLKDDEL----SRQA  372
              H+   S Q+++L   LQE                     LL WL+ K++ L    +  +
Sbjct  7099  CHMSDVSQQYEKLGGVLQERRDSLLAMLSSMQEVQEEASSLLQWLESKENALKAFDASSS  7278

Query  373   PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELP  432
             P   +   ++ Q + ++AF  EL+   P         +I   ++ L GL K Y      P
Sbjct  7279  PTKTE--TMRAQAECNKAFLAELEQNSP---------KIHKVKEALAGLLKKY------P  7407

Query  433   PEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQ  492
               + A++     ++  EE+++ WE+ N  +A  Q+K++E+  +L   Q A  +L   L +
Sbjct  7408  NSQEAKH----WKEMEEELSSRWERANEVTAARQQKLEESANQLASFQAAETQLRPWLTE  7575

Query  493   AEVIKGSWQPVGDLLIDS--LQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLS  550
              E++      +G L ID   L    ++V+ +  E    K     +N  A+ + T     S
Sbjct  7576  KELMMS---VLGPLSIDPNMLNAQKQQVQFMLKEFEARKPQHEQLNQAAQGILTGPGDGS  7746

Query  551   PYNLST---LEDLNTRW  564
             P        L+++N +W
Sbjct  7747  PSASQVQEELQNINNKW  7797


>gb|AF070567.1|AF070567 Homo sapiens clone 24544 beta-dystrobrevin mRNA, partial cds
Length=1559

 Score = 92.8 bits (229),  Expect = 1e-15, Method: Compositional matrix adjust.
 Identities = 85/313 (27%), Positives = 137/313 (43%), Gaps = 67/313 (21%)
 Frame = +3

Query  820   LFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDIC  877
             +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR  +  NY +C
Sbjct  27    MFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRCQQCHNYQLC  206

Query  878   QSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT---------SGEDV  909
             Q+CF+ G     H   + M E+                   C PT            E  
Sbjct  207   QNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHPVFPEQPEKP  386

Query  910   RDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD------DTHSR  963
              D A ++  +  T         M    V  +  G  + TP    Q S D      D H+ 
Sbjct  387   LDLAHIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDIPSHLADEHAL  536

Query  964   IEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILI  1023
             I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  +  R P  +  
Sbjct  537   IASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEA-GNVTRPPTDLSF  689

Query  1024  SLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDA  1083
             + ++ +  +  +++A+LE +NR +  E  RL+ +HE              PT  ++ ++ 
Sbjct  690   NFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNP  833

Query  1084  ELIAEAKLLRQHK  1096
              L+AE +LLRQ K
Sbjct  834   TLLAELRLLRQRK  872


>ref|XM_001515580.1| PREDICTED: Ornithorhynchus anatinus similar to macrophin 1 (LOC100085264), 
mRNA
Length=21111

 Score = 92.8 bits (229),  Expect = 1e-15, Method: Compositional matrix adjust.
 Identities = 137/588 (23%), Positives = 259/588 (44%), Gaps = 34/588 (5%)
 Frame = +1

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  ++++ +QR + GD + I   + K      D+   +  +E +
Sbjct  17605  ALGQFQHALEELMGWLTHTEELLDAQRPINGDPKVIEVELAKHHVLKNDVLAHQATVETV  17784

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKE  130
                A   L   ++  +A ++ T R+E +   W+ V +  + R QQL   L+ +  +    E
Sbjct  17785  NKAGNELLESSAGDDASSLRT-RLETMNQCWESVLQKTEEREQQLQSTLQQAQGFHSEIE  17961

Query  131    EAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLR-QWQTNVDVANDLALKLLR  189
              +    L +   +L + K      +  ++++    +L   L+ + +    + +   L LL 
Sbjct  17962  DFLLELTRMENQLSASKPTGGLPETAREQLDAHLELHSQLKAKEELYGQLLDKGRLMLLS  18141

Query  190    DYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE  249
                 +    K       +   W+++  ++ ER++ LEE   L  +F   L++F+ WLT AE
Sbjct  18142  RQDSGTGSKTEQSIALLEQKWQAVSSKMEERKSKLEEVLSLATEFQNSLQEFINWLTLAE  18321

Query  250    TTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGS  309
               + NV   A     +L    G  +  K + +   E+ AH D    LD+   + L+ L   
Sbjct  18322  QSLNV---AASPSLILNTVLGQIDEHKVFAN---EVNAHRDQIIELDQTGNQ-LKFLSQK  18480

Query  310    DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELS  369
               D VL++  L ++  +W ++ ++S+     L+ +  + K+ H + ++L+ WL+  +  L 
Sbjct  18481  QDVVLIKNLLVSVQSRWEKVVQRSVERGRALDDARKRAKQFHEAWKKLIDWLEDAEKLLD  18660

Query  370    RQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPR  429
               +  I  D   ++ Q   H+ F++ L  K+PV  +T+ T R  L E+ L           
Sbjct  18661  SELEISNDPDKIKLQLSKHKEFQKTLGGKQPVYDTTIRTGRA-LKEKAL-----------  18804

Query  430    ELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLK  489
               LP +   Q +  LL     EV  +W+ +   S + Q K++E L    +  +A   L   
Sbjct  18805  -LPDD--TQKLDNLLG----EVRDKWDTVCGKSVERQHKLEEALLFSGQFMDALQALVDW  18963

Query  490    LRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQ  548
              L + E      QPV GDL  D + + ++  K  + E+      V  +    R+L      
Sbjct  18964  LYKVEPQLAEDQPVHGDL--DLVMNLMDAHKVFQKELGKRTGTVQVLKRSGRELIENSRD  19137

Query  549    LSPYNLSTLEDLNTRWKL---LQVAVEDRVRQLHEAHRDFGPASQHFL  593
               + +    L++L+TRW     L V+ + R+ Q  +   +F  A    L
Sbjct  19138  DTTWVKGQLQELSTRWDTVCKLSVSKQTRLEQALKQAEEFRNAVHMLL  19281


 Score = 64.3 bits (155),  Expect = 4e-07, Method: Compositional matrix adjust.
 Identities = 105/478 (21%), Positives = 213/478 (44%), Gaps = 23/478 (4%)
 Frame = +1

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW +L DWL   ++++ S+  +  D + I   + K K   + L  ++P  +  I   
Sbjct  18601  FHEAWKKLIDWLEDAEKLLDSELEISNDPDKIKLQLSKHKEFQKTLGGKQPVYDTTIRTG  18780

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              + LK K    +    + + +  ++++WD V      R+ +L E L  S Q+++A +    
Sbjct  18781  RALKEKALLPDDTQKLDNLLGEVRDKWDTVCGKSVERQHKLEEALLFSGQFMDALQALVD  18960

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   +   K   K+L +    V V      +L+ + S D
Sbjct  18961  WLYKVEPQLAEDQPVHGDLDLVMNLMDAHKVFQKELGKRTGTVQVLKRSGRELIEN-SRD  19137

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT---  251
              DT  V    + ++  W ++ K    ++  LE+  +  ++F   +   L WL+EAE T   
Sbjct  19138  DTTWVKGQLQELSTRWDTVCKLSVSKQTRLEQALKQAEEFRNAVHMLLEWLSEAEQTLRF  19317

Query  252    ANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDD  311
                 L D T   + L D    KE MK+ ++ + ++ A   +         +++ ++   D 
Sbjct  19318  RGALPDDTEALQSLIDIH--KEFMKKVEEKRVDVNAAVGMG--------EVILAVCHPDC  19467

Query  312    AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSR-  370
                 ++  L  +  ++ E+   +   +  LEA+  +       L+ELL W+Q  +  L + 
Sbjct  19468  ITNIKHWLTVIRARFEEVLTWAKQHQQRLEAALSELVANAELLEELLAWIQWAETTLIQR  19647

Query  371    -QAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG--LEKLYQE  427
               Q P   +   V+     H+AF  E+  K+P +    +T +   +E P     +EK    
Sbjct  19648  DQEPTPQNIDQVKALISEHQAFMEEMTRKQPDVDRVTKTYKRKASE-PTHAPFIEKSRSN  19824

Query  428    PREL----PPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQE  481
               + L    PP     + +     +  +++  W+++ L + + QRK+++ L+RL+EL+E
Sbjct  19825  RKSLSQPTPPPMPILSQSEAKNPRINQLSARWQQVWLLALERQRKLNDALDRLEELKE  19998


 Score = 57.8 bits (138),  Expect = 3e-05, Method: Compositional matrix adjust.
 Identities = 83/364 (22%), Positives = 165/364 (45%), Gaps = 30/364 (8%)
 Frame = +1

Query  12     LADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQ----DLEQRRPQL  67
              L  F  A  +L  WL   + ++     ++G L     M+  QK  +Q    + E RR Q 
Sbjct  12343  LDSFQAAEAQLRPWLKEKELMMS----VLGPLSIDPNMLNAQKQQVQFMLKEFEARRQQH  12510

Query  68     EELITAAQNLKNKTSNQEARTI-ITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWL  126
              E+L  AAQ +     +    T    D++E I  +W E+ E L +R  Q+++ +  STQ+ 
Sbjct  12511  EQLNQAAQGIFAGPGDASPSTGQARDQLEGINQKWVELTERLNSRSSQIDQAIVKSTQYQ  12690

Query  127    EA-KEEAEQV--LGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVA---  180
              E  +  AEQV  +GQ  +   +    P   DA+++++ ET ++  DL +    +  A   
Sbjct  12691  ELLRGLAEQVKAVGQQLSGQSAISAQP---DAVKQQLEETSEIRSDLERLDHEIAEAQAL  12861

Query  181    -NDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLE  239
               + L+L +   Y  D+ RK     E +    + +    ++R   L+      QQF    +
Sbjct  12862  CDQLSLLIGEQYLKDELRKR---LETVALPLKGLEDLAADRLNRLQTALASTQQFQQMFD  13032

Query  240    KFLAWLTEAETT-ANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDEN  298
              +  AWL +     A     + + ERL       +  +++ ++ Q  +  H+  Y  +   
Sbjct  13033  ELRAWLDDKRNQQARAGPTSAKLERL-------QAQLQEQEEFQKSLNQHSGSYEVIVAE  13191

Query  299    SQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELL  358
               + +L S++  ++   LQ +L  +   W+EL K + + ++ L+    + ++    +++L+
Sbjct  13192  GETLLLSVQPGEEKAALQGQLAALRSHWAELGKHAADRQARLKDCLQKAQKYRWYVEDLV  13371

Query  359    VWLQ  362
               W++
Sbjct  13372  PWIE  13383


 Score = 57.8 bits (138),  Expect = 4e-05, Method: Compositional matrix adjust.
 Identities = 92/425 (21%), Positives = 172/425 (40%), Gaps = 23/425 (5%)
 Frame = +1

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F  A   L  WL+  + +I +Q+    + + +   I +QK   + L+ R+  +E +I A 
Sbjct  14653  FQDALEPLLSWLTDTEDLIANQKPPSAEYKVVKAQIQEQKLLQRLLDDRKATVE-MIQAE  14829

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
                   + +    +  I  ++E ++ +W  +      R++QL E+L  + ++ E  E    
Sbjct  14830  GGRIAQAAEPADQEKIVGQLESLEGRWAGLLHKAAARQRQLEEILVLAKEFHETTEPISD  15009

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L     KL + +        IQ++I   K L  ++      V +A  +   L       
Sbjct  15010  FLSVTEKKLANSEPVGTQTAKIQQQIVRHKALEDEVESRAAGVQLAVGVGRSLSSLTGPT  15189

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANV  254
              +   +    + + A +R + +R   R A L +     + F       L WL E E     
Sbjct  15190  ERGALAERLDALQARYREVRERCGRRAALLGQALCDARLFGDGEVAVLNWLAEVEDKLGS  15369

Query  255    LQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDE---NSQKILRSLEGSDD  311
              +     K  +L+         KQ  D     E   +   N+D+   N Q +L+   G ++
Sbjct  15370  VSVKDYKRDVLQ---------KQHADQLALNEEIVNRKKNVDQAIKNGQALLKQTTG-EE  15519

Query  312    AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSR-  370
               +L+Q +LD +  +++++   S      LE +     +   + +EL  W+    DEL+  
Sbjct  15520  VLLIQEKLDGIKTRYADITATSSKALRTLEQARQLATKFQATHEELTGWMNTVADELAAS  15699

Query  371    --QAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPL---EGLEKLY  425
                Q+P G   P  Q++    +  K+E+     V+ +  E  R  L   P    EGL+KL 
Sbjct  15700  GGQSPTGEQIPQFQQR---QKELKKEVMEHRLVLDTVNEVSRALLELVPWRAREGLDKLV  15870

Query  426    QEPRE  430
               E  E
Sbjct  15871  SEANE  15885


 Score = 54.7 bits (130),  Expect = 4e-04, Method: Compositional matrix adjust.
 Identities = 82/338 (24%), Positives = 154/338 (45%), Gaps = 38/338 (11%)
 Frame = +1

Query  106    EHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQ  165
              E   NR ++LN M         A EE+E +          W  G   VDAI +++ + K 
Sbjct  14314  EDFYNRLKELNRMTT-------AAEESEAL---------QWVVGT-EVDAINQQLADFKM  14442

Query  166    LAKD-LRQWQTNVDVANDLALKLLRDYSAD-DTRKVHMITENINASWRSIHKRVSEREAA  223
                K+ +   Q  +   N L   L++    + D + +    E INA W +++K+V++R A 
Sbjct  14443  FQKEQVDPLQLKLQQVNGLGQGLIQSAGKNCDVQGLEHDMEAINARWNTLNKKVAQRIAQ  14622

Query  224    LEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQG  283
              L+E      +F   LE  L+WLT+ E        A +K    E  K VK  +++ + LQ 
Sbjct  14623  LQEALLHCGKFQDALEPLLSWLTDTEDLI-----ANQKPPSAE-YKVVKAQIQEQKLLQR  14784

Query  284    EIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEAS  343
               ++        +     +I ++ E +D   ++  +L+++  +W+ L  K+   +  LE  
Sbjct  14785  LLDDRKATVEMIQAEGGRIAQAAEPADQEKIVG-QLESLEGRWAGLLHKAAARQRQLEEI  14961

Query  344    SDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVI-  402
                  K  H + + +  +L + + +L+   P+G     +Q+Q   H+A + E++++   + 
Sbjct  14962  LVLAKEFHETTEPISDFLSVTEKKLANSEPVGTQTAKIQQQIVRHKALEDEVESRAAGVQ  15141

Query  403    --------MSTLE--TVRIFLTEQPLEGLEKLYQEPRE  430
                      +S+L   T R  L E+ L+ L+  Y+E RE
Sbjct  15142  LAVGVGRSLSSLTGPTERGALAER-LDALQARYREVRE  15252


 Score = 47.8 bits (112),  Expect = 0.036, Method: Compositional matrix adjust.
 Identities = 119/551 (21%), Positives = 219/551 (39%), Gaps = 57/551 (10%)
 Frame = +1

Query  42     DLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQW  101
              D+  + E I + K  +  L +  PQL+EL            N E   ++ +R    +  +
Sbjct  16399  DMRQLRESIAEHKPHIDKLLKIGPQLKEL------------NPEEGEMVQERYRAAEAVY  16542

Query  102    DEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE---QVLGQARAKLESWKEGPYTVDAIQK  158
                ++E ++ R   L+E +  S Q  E  ++ E   + L    ++L      P  V+ I++
Sbjct  16543  ARIKEEVRLRALALDEAVSQSAQIAEFHDKIEPMLETLENLSSRLRVPPLIPAEVEKIRE  16722

Query  159    KITETKQLAKDLRQWQTNVDVANDLALKLL-RDYSADDTRKVHMITENINAS---WRSIH  214
               I + K    +L + Q +         +L+ R    D       I + ++     W  I 
Sbjct  16723  CIGDNKNATVELEKLQPSFGALKRRGEELIGRSQGPDKDLAAKEIQDKLDQMVFFWEDIK  16902

Query  215    KRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVK-E  273
               R  ERE    +   L ++F  D+   LA + +   T +++ D         +S G+   
Sbjct  16903  ARAEEREMKFLDVLELAEKFWFDMAALLATIRD---TQDIVHDL--------ESPGIDPS  17049

Query  274    LMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE---GSDDAVLLQRRLDNMNFKWSELR  330
              ++KQ  +    I+  TD  H   E  + +   L    G  +   +++ +D MN  W  L 
Sbjct  17050  IIKQQVEAAETIKEETDGLHEELEFIRILGADLIFACGETEKPEVKKSIDEMNNAWENLS  17229

Query  331    KKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRA  390
              K        LE +     +   +LQ +  WL     +L    P+G D   V++Q +  + 
Sbjct  17230  KMWKERLERLEEAMQAAVQYQDALQSMFDWLDNTVIKLCNMPPVGTDLNTVKEQLNEMKE  17409

Query  391    FKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEE  450
              FK E                  + +Q +E +EKL  +   +  +   +    ++R+   E
Sbjct  17410  FKTE------------------VYQQQIE-MEKLNHQGELMLKKATDETDRDIIREPLTE  17532

Query  451    VNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLID  509
              +   WE L       Q K++  L  L + Q A +EL   L   E +  + +P+ GD  + 
Sbjct  17533  LKHLWENLGEKITRRQHKLEGALLALGQFQHALEELMGWLTHTEELLDAQRPINGDPKV-  17709

Query  510    SLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLST-LEDLNTRWKLLQ  568
               ++  L K   L+ ++   +  V  VN    +L          +L T LE +N  W+ + 
Sbjct  17710  -IEVELAKHHVLKNDVLAHQATVETVNKAGNELLESSAGDDASSLRTRLETMNQCWESVL  17886

Query  569    VAVEDRVRQLH  579
                 E+R +QL 
Sbjct  17887  QKTEEREQQLQ  17919


>ref|XM_001084824.1| PREDICTED: Macaca mulatta similar to dystrobrevin, beta isoform 
1 (LOC696167), mRNA
Length=774

 Score = 92.8 bits (229),  Expect = 1e-15, Method: Compositional matrix adjust.
 Identities = 74/269 (27%), Positives = 121/269 (44%), Gaps = 58/269 (21%)
 Frame = +1

Query  637  DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDI----LQIIN  692
            + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I    L+ + 
Sbjct  28   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETV-  204

Query  693  CLTTIYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLE  752
             +++IY +L +       +P                  T +I V                
Sbjct  205  -ISSIYYQLNKR------LP-----------------STHQINV----------------  264

Query  753  DKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANN  812
                  F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF     
Sbjct  265  ------FSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP---Q  411

Query  813  KPEIEAALFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLK  870
            + +I   +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR  +
Sbjct  412  QRKIMLNMFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRCQQ  591

Query  871  HFNYDICQSCFFSGRVAKGHKMHYPMVEY  899
              NY +CQ+CF+ G     H   + M E+
Sbjct  592  CHNYQLCQNCFWRGHAGGPHSNQHQMKEH  678


>dbj|AK294174.1| Homo sapiens cDNA FLJ60475 complete cds, highly similar to Dystrobrevin 
beta
Length=1857

 Score = 92.4 bits (228),  Expect = 1e-15, Method: Compositional matrix adjust.
 Identities = 85/313 (27%), Positives = 137/313 (43%), Gaps = 67/313 (21%)
 Frame = +3

Query  820   LFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDIC  877
             +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR  +  NY +C
Sbjct  549   MFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRCQQCHNYQLC  728

Query  878   QSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT---------SGEDV  909
             Q+CF+ G     H   + M E+                   C PT            E  
Sbjct  729   QNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHPVFPEQPEKP  908

Query  910   RDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD------DTHSR  963
              D A ++  +  T         M    V  +  G  + TP    Q S D      D H+ 
Sbjct  909   LDLAHIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDIPSHLADEHAL  1058

Query  964   IEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILI  1023
             I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  +  R P  +  
Sbjct  1059  IASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEA-GNVTRPPTDLSF  1211

Query  1024  SLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDA  1083
             + ++ +  +  +++A+LE +NR +  E  RL+ +HE              PT  ++ ++ 
Sbjct  1212  NFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNP  1355

Query  1084  ELIAEAKLLRQHK  1096
              L+AE +LLRQ K
Sbjct  1356  TLLAELRLLRQRK  1394


>dbj|AK225724.1| Homo sapiens mRNA for dystrobrevin, beta isoform 4 variant, clone: 
TST03693
Length=2177

 Score = 92.4 bits (228),  Expect = 1e-15, Method: Compositional matrix adjust.
 Identities = 85/313 (27%), Positives = 137/313 (43%), Gaps = 67/313 (21%)
 Frame = +3

Query  820   LFLDWMRLEP--QSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDIC  877
             +FLD M  +P  Q +VWLP++HR+A  E   H  +C+ C+   ++GFRYR  +  NY +C
Sbjct  633   MFLDTMMADPPPQCLVWLPLMHRLAHVENVFHPVECSYCRCESMMGFRYRCQQCHNYQLC  812

Query  878   QSCFFSGRVAKGHKMHYPMVEY-------------------CTPTT---------SGEDV  909
             Q+CF+ G     H   + M E+                   C PT            E  
Sbjct  813   QNCFWRGHAGGPHSNQHQMKEHSSWKSPAKKLSHAISKSLGCVPTREPPHPVFPEQPEKP  992

Query  910   RDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPASSPQLSHD------DTHSR  963
              D A ++  +  T         M    V  +  G  + TP    Q S D      D H+ 
Sbjct  993   LDLAHIVPPRPLTN--------MNDTMVSHMSSG--VPTPTKRLQYSQDIPSHLADEHAL  1142

Query  964   IEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILI  1023
             I  Y +RL      + + + DS S    +D+EH LI  Y   L  ++  +  R P  +  
Sbjct  1143  IASYVARL-----QHCARVLDSPS---RLDEEHRLIARYAARLAAEA-GNVTRPPTDLSF  1295

Query  1024  SLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDA  1083
             + ++ +  +  +++A+LE +NR +  E  RL+ +HE              PT  ++ ++ 
Sbjct  1296  NFDANK--QQRQLIAELENKNREILQEIQRLRLEHEQAS----------QPTPEKAQQNP  1439

Query  1084  ELIAEAKLLRQHK  1096
              L+AE +LLRQ K
Sbjct  1440  TLLAELRLLRQRK  1478


 Score = 50.1 bits (118),  Expect = 0.008, Method: Compositional matrix adjust.
 Identities = 37/137 (27%), Positives = 67/137 (48%), Gaps = 14/137 (10%)
 Frame = +2

Query  637  DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDI--LQIINCL  694
            + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  242  NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  421

Query  695  TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
            ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  422  SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  595

Query  751  LEDKYR------YLFKQ  761
            + DK R      Y+F+ 
Sbjct  596  MLDKLR*KDNAKYVFRH  646


>ref|XM_002221469.1| Branchiostoma floridae hypothetical protein (BRAFLDRAFT_123563) 
mRNA, complete cds
Length=2976

 Score = 92.0 bits (227),  Expect = 2e-15, Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 113/234 (48%), Gaps = 23/234 (9%)
 Frame = +1

Query  628   MTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQND--QPM  685
             MTE+     D+  +R   YRTA KLR +QK   L L+ +    +A  ++ L   +    +
Sbjct  1069  MTEMRTQNFDV--IRLGTYRTACKLRFVQKKTNLHLVDIWNMIEAFRENGLNTLELTTEL  1242

Query  686   DILQIINCLTTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKT  741
             ++ ++ + +++I      RL   H   +NV   + + LNWL++ YD     ++ V S K 
Sbjct  1243  NVSRVESIVSSIMYQLNKRLPSTHQ--INVDQSISLLLNWLMSAYDPEALAKMSVFSIKM  1416

Query  742   GIISLCKAHLEDKYRY------LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFG  795
              + ++C   L     +      +F Q++ S G     +    L +++ +P  + E  SFG
Sbjct  1417  ALSTMCAGKLHKATSFITSSSDIFSQISDSRGQLVYPKFDQFLQEALALPSAVYEGPSFG  1596

Query  796   GSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQ--SMVWLPVLHRVAAAETA  847
              +  E + +SCFQ A     +    FLD M  +P    +VWLP++HR+A  E A
Sbjct  1597  YN--ETAAKSCFQSAQ---RVTINDFLDVMMADPGPPCLVWLPLMHRMANVENA  1743


 Score = 49.3 bits (116),  Expect = 0.013, Method: Compositional matrix adjust.
 Identities = 55/200 (27%), Positives = 88/200 (44%), Gaps = 27/200 (13%)
 Frame = +1

Query  958   DDTHSRIEHYASRLAEMENSNGS-------YLNDSISPNESIDDEHLLIQHYCQSLNQDS  1010
             DD H  I  YA+RLA  +N   +        L+ S SP   +    L +    Q     +
Sbjct  1780  DDEHRLIARYAARLAAEQNEQNTTPVDVSPLLHQSRSPGTEL---ALNLDANRQQRELIA  1950

Query  1011  PLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEH--KGLSPLPS  1068
              L    SP ++   L    R + + +L++ + +NR +  E  RL+Q+H+   +G+     
Sbjct  1951  ELEHKNSPREVAEKLAQWLREQTD-LLSECQHKNREIMREIQRLRQEHDEASRGM-----  2112

Query  1069  PPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQ  1128
                         R+  L+AE +LLRQ K  LE RM  L++  ++L  QL  L +LL+   
Sbjct  2113  ---------DESRNPTLLAELRLLRQRKDELELRMSALQESRRELMVQLEGLMKLLKSHG  2265

Query  1129  AEAKVNGTTVSSPSTSLQRS  1148
             +      T   SP T   +S
Sbjct  2266  SSPTPRSTPGGSPLTGSAKS  2325


>emb|AL672064.17| Mouse DNA sequence from clone RP23-91G19 on chromosome X Contains 
the Drp2 gene for dystrophin related protein 2, the Taf7l 
gene for TAF7-like RNA polymerase II TATA box binding protein 
(TBP)-associated factor, a novel pseudogene, the Timm8a1 
gene for translocase of inner mitochondrial membrane 8 homolog 
a1 (yeast), the 3' end of the Btk gene for Bruton agammaglobulinemia 
tyrosine kinase and two CpG islands, complete 
sequence
Length=152177

 Score = 90.5 bits (223),  Expect = 5e-15, Method: Compositional matrix adjust.
 Identities = 39/60 (65%), Positives = 46/60 (76%), Gaps = 0/60 (0%)
 Frame = +2

Query  807    FQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRY  866
              F  +  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI GFRY
Sbjct  42443  FL*STGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPIKGFRY  42622


 Score = 87.4 bits (215),  Expect = 4e-14, Method: Compositional matrix adjust.
 Identities = 39/54 (72%), Positives = 47/54 (87%), Gaps = 0/54 (0%)
 Frame = +3

Query  758    LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              LF QVA+S   CDQR LG LLH++IQ+PRQLGEVA+FGGSN+EPSVRSCF+F +
Sbjct  42021  LFSQVANSGSQCDQRHLGALLHEAIQVPRQLGEVAAFGGSNVEPSVRSCFRFVS  42182


 Score = 84.0 bits (206),  Expect = 5e-13, Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 55/67 (82%), Gaps = 0/67 (0%)
 Frame = +2

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              +DL++L+ A +  ++H+L+ ++  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LN
Sbjct  40709  VDLVTLTTALEIFNEHDLQASEHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLN  40888

Query  721    WLLNVYD  727
              WLLNV+D
Sbjct  40889  WLLNVFD  40909


 Score = 81.6 bits (200),  Expect = 2e-12, Method: Compositional matrix adjust.
 Identities = 39/88 (44%), Positives = 56/88 (63%), Gaps = 0/88 (0%)
 Frame = +2

Query  433    PEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQ  492
              P +R QN++R + KQA   +  WEKL     D  R I+ TLE L E+Q A +EL   L Q
Sbjct  34589  PRQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIEHTLEHLLEIQGAMEELSSTLTQ  34768

Query  493    AEVIKGSWQPVGDLLIDSLQDHLEKVKA  520
              AE ++ +W+P+GDL IDSL +H++ +K 
Sbjct  34769  AEGVRATWEPIGDLFIDSLPEHIQAIKV  34852


 Score = 74.7 bits (182),  Expect = 3e-10, Method: Compositional matrix adjust.
 Identities = 32/46 (69%), Positives = 39/46 (84%), Gaps = 0/46 (0%)
 Frame = +1

Query  903    TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
              TTS E++RDFA  LKNKFR+K+YF+KHP+ GYLPVQ+VLE D  ET
Sbjct  47005  TTSSENMRDFATTLKNKFRSKQYFSKHPQRGYLPVQSVLESDCSET  47142


 Score = 68.6 bits (166),  Expect = 2e-08, Method: Compositional matrix adjust.
 Identities = 41/74 (55%), Positives = 47/74 (63%), Gaps = 6/74 (8%)
 Frame = +1

Query  1044   NRNLQAEYDRLKQQHEHKGLSP--LPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEA  1101
               R LQ E  RLK QHE    +P  +    E  P      R+ EL+AEA++LRQHK RLE 
Sbjct  50437  GRILQGELRRLKWQHEEAAEAPTLVEGSAEATPDH----RNEELLAEARILRQHKSRLET  50604

Query  1102   RMQILEDHNKQLES  1115
              RMQILEDHNKQLES
Sbjct  50605  RMQILEDHNKQLES  50646


 Score = 65.9 bits (159),  Expect = 1e-07, Method: Compositional matrix adjust.
 Identities = 26/39 (66%), Positives = 33/39 (84%), Gaps = 0/39 (0%)
 Frame = +1

Query  865    RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT  903
              RYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TP 
Sbjct  44440  RYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPV  44556


 Score = 51.6 bits (122),  Expect = 0.003, Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 30/46 (65%), Gaps = 3/46 (6%)
 Frame = +2

Query  598    QGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRF  643
              +G WE  +      +  +H+ QTTCWDHPKMTELYQ+L +  N RF
Sbjct  38150  KGSWECDVGAIDA-FVCSHQAQTTCWDHPKMTELYQTLGE--NARF  38278


 Score = 48.5 bits (114),  Expect = 0.023, Method: Compositional matrix adjust.
 Identities = 21/24 (87%), Positives = 24/24 (100%), Gaps = 0/24 (0%)
 Frame = +2

Query  636    ADLNNVRFSAYRTAMKLRRLQKAL  659
              ADLNN++FSAYRTAMKLRR+QKAL
Sbjct  39608  ADLNNIKFSAYRTAMKLRRVQKAL  39679


 Score = 47.0 bits (110),  Expect = 0.059, Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 35/56 (62%), Gaps = 0/56 (0%)
 Frame = +3

Query  333    SLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVH  388
              S+   + LEA SD   +L L L+E++ WL  KD+ELS Q P+ GD   VQ++ + H
Sbjct  31251  SVTCSARLEAFSDLSGKLQLPLREIIDWLSQKDEELSAQLPLQGDVALVQQEKETH  31418


 Score = 45.8 bits (107),  Expect = 0.17, Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 28/46 (60%), Gaps = 0/46 (0%)
 Frame = +1

Query  524    EIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV  569
              E +P+K+ V  VNDLA QL    + LS  N   LE +N RWK LQV
Sbjct  35227  EFSPVKDGVKLVNDLAHQLAISDVHLSMENSRALEQINIRWKQLQV  35364


 Score = 45.4 bits (106),  Expect = 0.21, Method: Compositional matrix adjust.
 Identities = 18/27 (66%), Positives = 24/27 (88%), Gaps = 0/27 (0%)
 Frame = +2

Query  569    VAVEDRVRQLHEAHRDFGPASQHFLST  595
              V+V +R++QL +AHRDFGP SQHFLS+
Sbjct  35813  VSVAERLKQLQDAHRDFGPGSQHFLSS  35893


 Score = 42.0 bits (97),  Expect = 2.0, Method: Compositional matrix adjust.
 Identities = 18/20 (90%), Positives = 18/20 (90%), Gaps = 0/20 (0%)
 Frame = +1

Query  595    TSVQGPWERAISPNKVPYYI  614
               SVQ PWERAISPNKVPYYI
Sbjct  37810  ASVQVPWERAISPNKVPYYI  37869


 Score = 41.2 bits (95),  Expect = 3.3, Method: Compositional matrix adjust.
 Identities = 18/22 (81%), Positives = 19/22 (86%), Gaps = 0/22 (0%)
 Frame = +1

Query  949    PASSPQLSHDDTHSRIEHYASR  970
              PASSP L H DTHSRIEH+ASR
Sbjct  47419  PASSPMLPHADTHSRIEHFASR  47484


>ref|XM_002221736.1| Branchiostoma floridae hypothetical protein (BRAFLDRAFT_123699) 
mRNA, complete cds
Length=6462

 Score = 90.1 bits (222),  Expect = 6e-15, Method: Compositional matrix adjust.
 Identities = 120/558 (21%), Positives = 231/558 (41%), Gaps = 39/558 (6%)
 Frame = +1

Query  12    LADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELI  71
             +  F  A  EL  WL   +  +  ++ + GD + I   + K K    D+   +  ++ + 
Sbjct  3289  MGQFTAAIDELLTWLKHTEASLDEEKPVAGDTKLIEIELAKHKVLQNDILAHQSSVDSVH  3468

Query  72    TAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEE  131
              A + +    +  EA+ I  D++  +  +W +V +   +++  L  +L +S  +    EE
Sbjct  3469  QAGKRIIQAENKAEAKAI-QDKLAALDKRWSDVLQKAADKQTNLEALLNESQGFHVVLEE  3645

Query  132   AEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDY  191
                 +G+   KL + K      +  ++++    +L + +      +D A     +L+   
Sbjct  3646  LLHWVGETETKLSTTKPTGGLPETAKEQVDRHMELQQQIDDKAEEIDAALFEGQELVAKC  3825

Query  192   SADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
                    V      +   W  +    +ER++ LE+  +  Q F   L+ F++WLT AE T
Sbjct  3826  DKTAASNVEHGLNKLATQWEGLLAHAAERKSKLEDALKQAQDFHDSLQSFISWLTNAEKT  4005

Query  252   ANVLQDATRKERLLEDSKGVKELMKQWQD----LQGEIEAHTDVYHNLDENSQKILRSLE  307
              N L+ A+           V E + Q  D     +  I  H +    LD+     L+   
Sbjct  4006  LNNLKPASM----------VMETLSQQIDDHKAFEKNIADHRETMLQLDKMGTH-LKYFS  4152

Query  308   GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
                D +L++  L ++  +W  +  +      HLE +  + ++ + S ++L+ WL   ++ 
Sbjct  4153  QKQDVILIKNLLISVQGRWERILSRYGERSRHLEDALKRARQFNDSWKKLMDWLDEAENH  4332

Query  368   LSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQE  427
             L  +APIG D   ++ Q    + F+R L  K+P+  ST++T R    +   +  +KL ++
Sbjct  4333  LDSEAPIGNDPDKIKAQLLKFKEFQRALAAKQPLYDSTMKTGRSLKDKGTPQDGQKLDEK  4512

Query  428   PRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELD  487
               EL                      +W+ +   S D Q  ++E L    +  +A   L 
Sbjct  4513  LTEL--------------------RDKWDLICAKSVDRQHTLEEALLFSGQFADALQALL  4632

Query  488   LKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLG  546
               L + E       PV GD  ID++   +   K  + E+A    +V  V   AR++    
Sbjct  4633  DWLYKTEPNLAEDLPVHGD--IDTVLTLIGNHKVFQRELASRTSSVQTVRKQAREILNSS  4806

Query  547   IQLSPYNLSTLEDLNTRW  564
              + +      LEDLN +W
Sbjct  4807  TEDTSELRRQLEDLNIKW  4860


 Score = 69.3 bits (168),  Expect = 1e-08, Method: Compositional matrix adjust.
 Identities = 112/567 (19%), Positives = 233/567 (41%), Gaps = 47/567 (8%)
 Frame = +1

Query  25    WLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQ  84
             WL   +  + +   +  D   I + I   K    +++ R+  +E +    + L  K S+ 
Sbjct  2998  WLGTAEARLATFPPIGADPSTIKKQIDNLKEFKTEVDPRQVAVEAMNNQGEQLMKKVSSD  3177

Query  85    EARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLE  144
             EAR  I + +  +  +W+ +Q  + +R+ +L   L    Q+  A +E    L    A L+
Sbjct  3178  EARLSIQEPLHDMNKRWEGLQRSIVDRQHKLEAALLKMGQFTAAIDELLTWLKHTEASLD  3357

Query  145   SWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITE  204
               K        I+ ++ + K L  D+   Q++VD  +    ++++  +  + + +     
Sbjct  3358  EEKPVAGDTKLIEIELAKHKVLQNDILAHQSSVDSVHQAGKRIIQAENKAEAKAIQDKLA  3537

Query  205   NINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERL  264
              ++  W  + ++ ++++  LE      Q F + LE+ L W+ E ET  +  +        
Sbjct  3538  ALDKRWSDVLQKAADKQTNLEALLNESQGFHVVLEELLHWVGETETKLSTTK--------  3693

Query  265   LEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL-EGSD--------DAVLL  315
                + G+ E  K+      +++ H ++   +D+ +++I  +L EG +         A  +
Sbjct  3694  --PTGGLPETAKE------QVDRHMELQQQIDDKAEEIDAALFEGQELVAKCDKTAASNV  3849

Query  316   QRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIG  375
             +  L+ +  +W  L   +   +S LE +  Q +  H SLQ  + WL   +  L+   P  
Sbjct  3850  EHGLNKLATQWEGLLAHAAERKSKLEDALKQAQDFHDSLQSFISWLTNAEKTLNNLKPAS  4029

Query  376   GDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEE  435
                  + +Q D H+AF++ +      ++                 L+K+    +      
Sbjct  4030  MVMETLSQQIDDHKAFEKNIADHRETMLQ----------------LDKMGTHLKYFS---  4152

Query  436   RAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEV  495
             + Q+V  L++     V   WE++     +  R +++ L+R ++  ++  +L   L +AE 
Sbjct  4153  QKQDVI-LIKNLLISVQGRWERILSRYGERSRHLEDALKRARQFNDSWKKLMDWLDEAEN  4329

Query  496   IKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLS  555
                S  P+G+   D ++  L K K  +  +A  +          R L   G       L 
Sbjct  4330  HLDSEAPIGN-DPDKIKAQLLKFKEFQRALAAKQPLYDSTMKTGRSLKDKGTPQDGQKLD  4506

Query  556   -TLEDLNTRWKLLQVAVEDRVRQLHEA  581
               L +L  +W L+     DR   L EA
Sbjct  4507  EKLTELRDKWDLICAKSVDRQHTLEEA  4587


 Score = 62.8 bits (151),  Expect = 1e-06, Method: Compositional matrix adjust.
 Identities = 101/556 (18%), Positives = 238/556 (42%), Gaps = 34/556 (6%)
 Frame = +1

Query  46    INEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQE---ARTIITDRIERIQNQWD  102
             I E I + +A   +LE+  P +E L     +L  K++  +   +   I D+++++   W+
Sbjct  2395  IKEQISENEALRSELEKHLPAIETLRGKGDDLIGKSAGVDKDPSAKAIQDKLDQMNFLWE  2574

Query  103   EVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITE  162
             ++    + R Q + E    + ++ E       VL + +  ++  +E     D ++++   
Sbjct  2575  DIVSRSEERDQAMLETHDTAERFWEELGNVLNVLKETQDSIKELEEPAIQPDIVREQQEV  2754

Query  163   TKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREA  222
              + + +++   Q +++    L   L       D   V    E++NA+W +++    ERE 
Sbjct  2755  LQAIKEEMESTQDDIETVRQLGEDLTSLCGEPDKPVVSKNVEDLNATWDTLNASWEEREE  2934

Query  223   ALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQ  282
              LEE  R+  Q+   L+  L WL  AE              +  D   +K+ +   ++ +
Sbjct  2935  VLEEAMRVALQYQDALQALLVWLGTAEARLATFPP------IGADPSTIKKQIDNLKEFK  3096

Query  283   GEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEA  342
              E++        ++   +++++ +   +  + +Q  L +MN +W  L++  ++ +  LEA
Sbjct  3097  TEVDPRQVAVEAMNNQGEQLMKKVSSDEARLSIQEPLHDMNKRWEGLQRSIVDRQHKLEA  3276

Query  343   SSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVI  402
             +  +  +   ++ ELL WL+  +  L  + P+ GD   ++ +   H+  + ++   +  +
Sbjct  3277  ALLKMGQFTAAIDELLTWLKHTEASLDEEKPVAGDTKLIEIELAKHKVLQNDILAHQSSV  3456

Query  403   MSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHS  462
              S  +  +                  R +  E +A+   + ++ +   ++  W  +   +
Sbjct  3457  DSVHQAGK------------------RIIQAENKAE--AKAIQDKLAALDKRWSDVLQKA  3576

Query  463   ADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALR  522
             AD Q  ++  L   Q      +EL   + + E    + +P G  L ++ ++ +++   L+
Sbjct  3577  ADKQTNLEALLNESQGFHVVLEELLHWVGETETKLSTTKPTGG-LPETAKEQVDRHMELQ  3753

Query  523   GEIAPLKENVSHVNDLARQLTTLGIQLSPYNLS-TLEDLNTRWKLLQVAVEDRVRQLHEA  581
              +I    E +       ++L     + +  N+   L  L T+W+ L     +R  +L +A
Sbjct  3754  QQIDDKAEEIDAALFEGQELVAKCDKTAASNVEHGLNKLATQWEGLLAHAAERKSKLEDA  3933

Query  582   HR---DFGPASQHFLS  594
              +   DF  + Q F+S
Sbjct  3934  LKQAQDFHDSLQSFIS  3981


 Score = 59.7 bits (143),  Expect = 1e-05, Method: Compositional matrix adjust.
 Identities = 88/399 (22%), Positives = 170/399 (42%), Gaps = 32/399 (8%)
 Frame = +1

Query  15    FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
             FN +W +L DWL   +  + S+  +  D + I   ++K K   + L  ++P  +  +   
Sbjct  4279  FNDSWKKLMDWLDEAENHLDSEAPIGNDPDKIKAQLLKFKEFQRALAAKQPLYDSTMKTG  4458

Query  75    QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
             ++LK+K + Q+ + +  +++  ++++WD +     +R+  L E L  S Q+ +A +    
Sbjct  4459  RSLKDKGTPQDGQKL-DEKLTELRDKWDLICAKSVDRQHTLEEALLFSGQFADALQALLD  4635

Query  135   VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
              L +    L         +D +   I   K   ++L    ++V      A ++L + S +
Sbjct  4636  WLYKTEPNLAEDLPVHGDIDTVLTLIGNHKVFQRELASRTSSVQTVRKQAREIL-NSSTE  4812

Query  195   DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE-----  249
             DT ++    E++N  W +  +    ++  L++  +  ++F   +   L WL EAE     
Sbjct  4813  DTSELRRQLEDLNIKWENASRLSVVKQQRLDQAMKQAEEFHTSVHCLLEWLAEAEHVLRF  4992

Query  250   -TTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEG  308
              +   V  +    E L +  K  KE+  Q + LQ  +        ++ E   KI      
Sbjct  4993  QSQIPVDDEDMLMESLTQQEKFEKEMADQQRKLQEAM--------DMGEAILKICHP---  5139

Query  309   SDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW-------L  361
              D    ++  L  +  +W E+   +   R+ LE +    K     L  L  W       L
Sbjct  5140  -DAITTVKHWLTIIMARWEEVTSWASQHRARLEDALKVLKANEELLDRLTAWVEGAEHTL  5316

Query  362   QLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEP  400
             Q  DDE     P+  +   VQK  + H+ F+ E+ TK+P
Sbjct  5317  QTLDDE-----PLPDNMEDVQKLMEEHQMFQNEMSTKQP  5418


 Score = 57.8 bits (138),  Expect = 3e-05, Method: Compositional matrix adjust.
 Identities = 76/350 (21%), Positives = 154/350 (44%), Gaps = 13/350 (3%)
 Frame = +1

Query  14    DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
             DF+ +      WL+  ++ + + +     +E +++ I   KA  +++   R  + +L   
Sbjct  3949  DFHDSLQSFISWLTNAEKTLNNLKPASMVMETLSQQIDDHKAFEKNIADHRETMLQLDKM  4128

Query  74    AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE  133
               +LK  +  Q+   +I + +  +Q +W+ +      R + L + LK + Q+ ++ ++  
Sbjct  4129  GTHLKYFSQKQDV-ILIKNLLISVQGRWERILSRYGERSRHLEDALKRARQFNDSWKKLM  4305

Query  134   QVLGQARAKLESWKEGPYT--VDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDY  191
               L +A   L+S  E P     D I+ ++ + K+  + L   Q   D        L    
Sbjct  4306  DWLDEAENHLDS--EAPIGNDPDKIKAQLLKFKEFQRALAAKQPLYDSTMKTGRSLKDKG  4479

Query  192   SADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
             +  D +K+      +   W  I  +  +R+  LEE      QF   L+  L WL + E  
Sbjct  4480  TPQDGQKLDEKLTELRDKWDLICAKSVDRQHTLEEALLFSGQFADALQALLDWLYKTE--  4653

Query  252   ANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDD  311
              N+ +D      +  D   V  L+   +  Q E+ + T     + + +++IL S   ++D
Sbjct  4654  PNLAEDLP----VHGDIDTVLTLIGNHKVFQRELASRTSSVQTVRKQAREILNS--STED  4815

Query  312   AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWL  361
                L+R+L+++N KW    + S+  +  L+ +  Q +  H S+  LL WL
Sbjct  4816  TSELRRQLEDLNIKWENASRLSVVKQQRLDQAMKQAEEFHTSVHCLLEWL  4965


 Score = 45.4 bits (106),  Expect = 0.20, Method: Compositional matrix adjust.
 Identities = 65/308 (21%), Positives = 137/308 (44%), Gaps = 21/308 (6%)
 Frame = +1

Query  15    FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
             F  A   L DWL   +  +     + GD++ +  +I   K   ++L  R   ++ +   A
Sbjct  4606  FADALQALLDWLYKTEPNLAEDLPVHGDIDTVLTLIGNHKVFQRELASRTSSVQTVRKQA  4785

Query  75    QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQW-------LE  127
             + + N  S+ E  + +  ++E +  +W+        ++Q+L++ +K + ++       LE
Sbjct  4786  REILN--SSTEDTSELRRQLEDLNIKWENASRLSVVKQQRLDQAMKQAEEFHTSVHCLLE  4959

Query  128   AKEEAEQVLG-QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALK  186
                EAE VL  Q++  ++         D + + +T+ ++  K++   Q  +  A D+   
Sbjct  4960  WLAEAEHVLRFQSQIPVDD-------EDMLMESLTQQEKFEKEMADQQRKLQEAMDMGEA  5118

Query  187   LLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             +L+    D    V      I A W  +    S+  A LE+  ++L+     L++  AW+ 
Sbjct  5119  ILKICHPDAITTVKHWLTIIMARWEEVTSWASQHRARLEDALKVLKANEELLDRLTAWVE  5298

Query  247   EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL  306
              AE T   L D    E L ++ + V++LM++ Q  Q E+      Y  + +  ++ + ++
Sbjct  5299  GAEHTLQTLDD----EPLPDNMEDVQKLMEEHQMFQNEMSTKQPEYDRITKGHKRRISTV  5466

Query  307   EGSDDAVL  314
             + S    L
Sbjct  5467  DHSPGGFL  5490


>ref|XM_001505526.1| PREDICTED: Ornithorhynchus anatinus similar to dystonin (LOC100073893), 
mRNA
Length=13662

 Score = 89.7 bits (221),  Expect = 9e-15, Method: Compositional matrix adjust.
 Identities = 144/603 (23%), Positives = 261/603 (43%), Gaps = 88/603 (14%)
 Frame = +1

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  10039  ALGQFQHALDELLTWLTHTEDLLNEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  10218

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEML----------K  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L          +
Sbjct  10219  KKAGTDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDTALLQAQGFHGEIE  10395

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKE--GPYTV-DAIQKKITETKQ--LAK  168
              D  QWL   E    A + +G     AR +L S  E    + V + I K++ E  Q  LA+
Sbjct  10396  DLHQWLTDTERHLLASKPVGGLPETAREQLNSHLELCAAFEVKEEIYKRLMEKGQQMLAR  10575

Query  169    DLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETH  228
                   +TNVD          +D +            N+   W S+  ++SER+  LEE  
Sbjct  10576  CPESAETNVD----------QDIN------------NLKEKWESVQTKLSERKTKLEEAL  10689

Query  229    RLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAH  288
               L  +F   L+ F+ WLT+AE T  +   A+R   +L+    V   + + +    E+ +H
Sbjct  10690  NLAMEFHNSLQDFINWLTQAEQTLTI---ASRPSLILD---TVLFQIDEHKVFATEVNSH  10851

Query  289    TDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWK  348
               D    LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K
Sbjct  10852  RDQVIELDKTGTH-LKYFSQKQDVVLIKNLLISVQNRWEKVVQRLVERGRALDDARKRAK  11028

Query  349    RLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
              + H +  +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T
Sbjct  11029  QFHEAWNKLMEWLEESEKSLDSELEIANDPDKIKAQLTQHKEFQKSLGAKHSVYDTTNRT  11208

Query  409    VRIF-----LTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSA  463
               R       LT+  L+ L+ +  E R+                       +W+ +   S 
Sbjct  11209  GRSLKEKASLTDDNLK-LDDMLSELRD-----------------------KWDTICGKSV  11316

Query  464    DWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALR  522
              + Q K++E L    +  +A   L   L + E      QPV GD  ID + + ++  K  +
Sbjct  11317  ERQNKLEEALLFSGQFTDALQALIDWLYKIEPQLAEDQPVHGD--IDLVMNLIDNHKVFQ  11490

Query  523    GEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKL---LQVAVEDRVRQ-L  578
               E+     +V  +   AR+L       S +    +++L+TRW+    L V+ + R+ + L
Sbjct  11491  KELGKRTSSVQALKRSARELVEGSRDDSSWVKVQMQELSTRWETVCALSVSKQTRLEEAL  11670

Query  579    HEA  581
              H+A
Sbjct  11671  HQA  11679


 Score = 63.9 bits (154),  Expect = 6e-07, Method: Compositional matrix adjust.
 Identities = 88/389 (22%), Positives = 175/389 (44%), Gaps = 16/389 (4%)
 Frame = +1

Query  14     DFNRAWTELTDWLSLLDQV--IKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELI  71
              +F+ +  +  +WL+  +Q   I S+  ++  L+ +   I + K    ++   R Q+ EL 
Sbjct  10702  EFHNSLQDFINWLTQAEQTLTIASRPSLI--LDTVLFQIDEHKVFATEVNSHRDQVIELD  10875

Query  72     TAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEE  131
                  +LK  +  Q+   +I + +  +QN+W++V + L  R + L++  K + Q+ EA  +
Sbjct  10876  KTGTHLKYFSQKQDV-VLIKNLLISVQNRWEKVVQRLVERGRALDDARKRAKQFHEAWNK  11052

Query  132    AEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDY  191
                + L ++   L+S  E     D I+ ++T+ K+  K L    +  D  N     L    
Sbjct  11053  LMEWLEESEKSLDSELEIANDPDKIKAQLTQHKEFQKSLGAKHSVYDTTNRTGRSLKEKA  11232

Query  192    S-ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAET  250
              S  DD  K+  +   +   W +I  +  ER+  LEE      QF   L+  + WL + E 
Sbjct  11233  SLTDDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALIDWLYKIEP  11412

Query  251    TANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGS-  309
                         + +  D   V  L+   +  Q E+   T     L  ++++++   EGS 
Sbjct  11413  ------QLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELV---EGSR  11565

Query  310    DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELS  369
              DD+  ++ ++  ++ +W  +   S++ ++ LE +  Q +  H  +  LL WL   +  L 
Sbjct  11566  DDSSWVKVQMQELSTRWETVCALSVSKQTRLEEALHQAEEFHSVVHVLLEWLAEAEQTLR  11745

Query  370    RQAPIGGDFPAVQKQNDVHRAFKRELKTK  398
                  +  D  A++   D H+ F ++L+ K
Sbjct  11746  FHGLLPDDEEALRTLIDQHKEFMKKLEEK  11832


 Score = 62.4 bits (150),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 54/206 (26%), Positives = 100/206 (48%), Gaps = 35/206 (16%)
 Frame = +1

Query  204   ENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAET-TANV--------  254
             E++N  W++++K+V++R A L+E      +F   +E  L+WL + E   AN         
Sbjct  7006  EDVNTRWKTLNKKVAQRAAQLQEALLHCGRFQDAMESLLSWLVDTEDLVANQKPPSAEFK  7185

Query  255   -----LQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGS  309
                  +Q+    +RLL+D K   E++K+    +GE                KI  + E +
Sbjct  7186  VVKAQIQEQKLLQRLLDDRKPTIEVIKR----EGE----------------KIAETAEPA  7305

Query  310   DDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELS  369
             D   +L ++L  ++ +W  L  K+      LEA S   ++ H +L+ L+ WL + + +L+
Sbjct  7306  DKVKIL-KQLSLLDSRWDALLNKAETRNRQLEAISVVAQQFHETLEPLVEWLTITEKKLA  7482

Query  370   RQAPIGGDFPAVQKQNDVHRAFKREL  395
                PIG   P +Q+Q   H+A + ++
Sbjct  7483  NSEPIGTQTPKLQEQIAQHKALEDDI  7560


 Score = 58.9 bits (141),  Expect = 2e-05, Method: Compositional matrix adjust.
 Identities = 119/586 (20%), Positives = 245/586 (41%), Gaps = 84/586 (14%)
 Frame = +1

Query  41     GDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNL---KNKTSNQEARTIITDRIERI  97
               ++E I E I + K  + DLE+ +P  E L    + +      T+   +   + D+++++
Sbjct  9133   AEVEKIKEQISENKNVLVDLEKLQPVYETLKQRGEEMIARSGGTNKDISAKAVQDKLDQM  9312

Query  98     QNQWDEVQEHLQNRRQQLNEMLK-------DSTQWLEAKEEAEQVLGQARAKLESWKEGP  150
                 W+++Q   + R  +L ++++       D    +   ++ +  + +    LES    P
Sbjct  9313   VLAWEDIQNLAEEREAKLLDVMELAEKFWCDHMSLVVTTKDTQDFIRE----LESPGVDP  9480

Query  151    YTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASW  210
                V   Q+     + + +++   Q  +D+  +L  +L+      D   V+   + +N++W
Sbjct  9481   SVVKQQQEA---AEAIREEIDGLQEELDIVINLGSELITACGEPDKPIVNKSIDELNSAW  9651

Query  211    RSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKG  270
               S++K   ER   LEE  +   Q+   L+    W+  A    + +        +  D + 
Sbjct  9652   DSLNKTWKERIDKLEEAMQAAVQYQDGLQAIFDWVDIAGGKLSSMSP------IGTDLET  9813

Query  271    VKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELR  330
              VK+ +++ +  + E          L+  ++ +L+ +    D   +Q  L  +   W  L 
Sbjct  9814   VKQQIEELKQFKAEAYQQQIEMERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLD  9993

Query  331    KKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRA  390
              +K +N +  LE +     +   +L ELL WL   +D L+ Q P+GGD  A++ +   H  
Sbjct  9994   EKIVNRQHKLEGALLALGQFQHALDELLTWLTHTEDLLNEQKPVGGDPKAIEIELAKHHV  10173

Query  391    FKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQA-E  449
               + ++   +    ST+E V+                           +  T L+   A E
Sbjct  10174  LQNDVLAHQ----STVEAVK---------------------------KAGTDLIESSAGE  10260

Query  450    EVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLID  509
              E +    KL + +  WQ  +++T +R Q       +LD  L QA+   G  + +   L D
Sbjct  10261  EASNLQNKLEVLNQRWQNVLEKTEQRKQ-------QLDTALLQAQGFHGEIEDLHQWLTD  10419

Query  510    SLQDHLEKVKALRGEIAPLKENV-SHV---------NDLARQLTTLGIQL---SPYNLST  556
              + + HL   K + G     +E + SH+          ++ ++L   G Q+    P +  T
Sbjct  10420  T-ERHLLASKPVGGLPETAREQLNSHLELCAAFEVKEEIYKRLMEKGQQMLARCPESAET  10596

Query  557    -----LEDLNTRWKLLQVAVEDRVRQLHEA---HRDFGPASQHFLS  594
                   + +L  +W+ +Q  + +R  +L EA     +F  + Q F++
Sbjct  10597  NVDQDINNLKEKWESVQTKLSERKTKLEEALNLAMEFHNSLQDFIN  10734


 Score = 56.2 bits (134),  Expect = 1e-04, Method: Compositional matrix adjust.
 Identities = 124/561 (22%), Positives = 242/561 (43%), Gaps = 71/561 (12%)
 Frame = +1

Query  43    LEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWD  102
             LE +  +I  QK   + L  +    ++++   +NL  KT   E +  +  +I  I+  WD
Sbjct  5542  LECLQSLIKDQKEFQKSLTSQCDSYKKIVAEGENLLLKTQGAE-KADLQVQINTIKTNWD  5718

Query  103   EVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVD--AIQKKI  160
              + + +  R+++L + L+ + ++ E  E  +  + +    L   K     +D    +  I
Sbjct  5719  GLNKQVVERQEELKDCLEKALKYKEHVENLQPWIDKCHNNLAEIK---VCIDPAGTENSI  5889

Query  161   TETKQLAKDLRQWQTNVDVANDLALKLL----------RDYSADDTRKVHMITENINA--  208
              + K L K++ Q    V++ N+ A  LL          R+ +    ++V  +TE + +  
Sbjct  5890  EKVKALQKEMDQHFGMVELLNNAANSLLNASEIDQEAIREGNKSLNQRVDTLTEQLQSKK  6069

Query  209   -SWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLED  267
              S  ++ K++ E + A +ET RLL+     LE + +   +A +  ++    ++++ L   
Sbjct  6070  QSLENMSKKLKEFQEASKETQRLLKGAKEQLEVYDSLGPQACSNKHLTIMQSQQKSL---  6240

Query  268   SKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWS  327
                        Q L+ ++E    V       +Q+++     S+    L  + +++  +  
Sbjct  6241  -----------QTLKHQVEMAKKV-------AQELVVEASDSEGTADLLIQAESLEREHR  6366

Query  328   ELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDV  387
             ++ ++  +  S LEA          S++E+       DDEL   AP+G +   +Q+Q + 
Sbjct  6367  DVSQQVEDKCSFLEAKLQGIGHFQNSIREMFSQFAEFDDELDSMAPVGREGDTLQRQRED  6546

Query  388   HRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQ  447
              + F   LK  + +I+S     +            K+     E  P+         +++ 
Sbjct  6547  IKDF---LKKLQDLIVSNGNANKTC----------KMMLASEEASPDLVG------IKRD  6669

Query  448   AEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLL  507
              E ++ +  KL   +   + +++ T+ RL+E  E   E    L++AE  + S  PVG + 
Sbjct  6670  LEALSKQCNKLLDRAKVREEQVESTVSRLEEFYEKLKEFSGCLQRAEENEESQGPVG-ME  6846

Query  508   IDSLQDHLEKVKAL-RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLST------LEDL  560
              +++   L   K   + EI  L+     VN L + L    IQ +  + ST      LED+
Sbjct  6847  TETINQQLNIFKMFQKEEIDSLQAKQQEVNWLGQGL----IQSAAKSTSTERLEHELEDV  7014

Query  561   NTRWKLLQVAVEDRVRQLHEA  581
             NTRWK L   V  R  QL EA
Sbjct  7015  NTRWKTLNKKVAQRAAQLQEA  7077


 Score = 47.4 bits (111),  Expect = 0.049, Method: Compositional matrix adjust.
 Identities = 105/498 (21%), Positives = 201/498 (40%), Gaps = 59/498 (11%)
 Frame = +1

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW +L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  11032  FHEAWNKLMEWLEESEKSLDSELEIANDPDKIKAQLTQHKEFQKSLGAKHSVYDTTNRTG  11211

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK K S  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  11212  RSLKEKASLTDDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  11391

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  11392  WLYKIEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELV-EGSRD  11568

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA--  252
              D+  V +  + ++  W ++      ++  LEE     ++F   +   L WL EAE T   
Sbjct  11569  DSSWVKVQMQELSTRWETVCALSVSKQTRLEEALHQAEEFHSVVHVLLEWLAEAEQTLRF  11748

Query  253    -NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDD  311
                +L D     R L D    KE MK+ ++ + E+   T                  G  +
Sbjct  11749  HGLLPDDEEALRTLIDQH--KEFMKKLEEKRAELNKAT------------------GMGE  11868

Query  312    AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS---------------LQE  356
              AVL     D++    + ++     IR+  E     W + H                 L+ 
Sbjct  11869  AVLAICHPDSI----TTIKHWITIIRARFEEVL-AWAKQHQQRLAGALAGLIAKQELLEA  12033

Query  357    LLVWLQLKDDELSRQ--APIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETV-RIFL  413
              LL WLQ  +  LS +    I  +   V+     H+ F  E+  K+P +    +T  R   
Sbjct  12034  LLTWLQWAETTLSDKDKETIPQEIEEVKALIAEHQTFMEEMTRKQPDVDKVTKTYKRKAA  12213

Query  414    TEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQ-------  466
                 P++    +  + R     +R+ +          ++ T+  ++NL  + WQ       
Sbjct  12214  DPSPIQSHIPVLDKGR--TGRKRSPSSAVYPSGSQTQIETKNPRVNLLVSKWQQVWLLAL  12387

Query  467    ---RKIDETLERLQELQE  481
                 RK+++ L+RL+EL+E
Sbjct  12388  ERRRKLNDALDRLEELKE  12441


 Score = 40.4 bits (93),  Expect = 6.9, Method: Compositional matrix adjust.
 Identities = 45/172 (26%), Positives = 72/172 (41%), Gaps = 9/172 (5%)
 Frame = +1

Query  134   QVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDY--  191
             Q L Q      SW   P   +A++ +  + K    +L+Q    V    D   +LL     
Sbjct  4492  QWLQQMDKNTTSWDAPPTDNEAVRAQFEQNKTFEAELKQNVNKVQELKDKLSELLEQNPD  4671

Query  192   SADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
             S +  +  HM+ E I++ W+ +++  ++R+  LEE+   L QF     +   WL E E  
Sbjct  4672  SPEAPKWKHML-EEIDSKWKELNQLTADRQQKLEESSNNLTQFQTVEAQLKQWLVEKELM  4848

Query  252   ANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKIL  303
             A+VL   +    +L   K      +Q Q L  E +     Y  L    Q IL
Sbjct  4849  ASVLGPLSIDPNMLNTQK------QQVQILLNEFDTRKPQYEQLKTTGQSIL  4986


>ref|XM_002205053.1| Branchiostoma floridae hypothetical protein (BRAFLDRAFT_118483) 
mRNA, complete cds
Length=4272

 Score = 89.4 bits (220),  Expect = 1e-14, Method: Compositional matrix adjust.
 Identities = 120/559 (21%), Positives = 232/559 (41%), Gaps = 39/559 (6%)
 Frame = +1

Query  12    LADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELI  71
             +  F  A  EL  WL   +  +  ++ + GD + I   + K K    D+   +  ++ + 
Sbjct  976   MGQFTAAIDELLTWLKHTEASLDEEKPVAGDTKLIEIELAKHKVLQNDILAHQSSVDSVH  1155

Query  72    TAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEE  131
              A + +    +  EA+ I  D++  +  +W +V +   +++  L  +L +S  +    EE
Sbjct  1156  QAGKRIIQAENKAEAKAI-QDKLAALDKRWSDVLQKAADKQTNLEALLNESQGFHVVLEE  1332

Query  132   AEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDY  191
                 +G+   KL + K      +  ++++    +L + +      +D A     +L+   
Sbjct  1333  LLHWVGETETKLSTTKPTGGLPETAKEQVDRHMELQQQIDDKAEEIDAALFEGQELVAKC  1512

Query  192   SADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
                    V      +   W  +    +ER++ LE+  +  Q F   L+ F++WLT AE T
Sbjct  1513  DKTAASNVEHGLNKLATQWEGLLAHAAERKSKLEDALKQAQDFHDSLQSFISWLTNAEKT  1692

Query  252   ANVLQDATRKERLLEDSKGVKELMKQWQD----LQGEIEAHTDVYHNLDENSQKILRSLE  307
              N L+ A+           V E + Q  D     +  I  H +    LD+     L+   
Sbjct  1693  LNNLKPASM----------VMETLSQQIDDHKAFEKNIADHRETMLQLDKMGTH-LKYFS  1839

Query  308   GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
                D +L++  L ++  +W  +  +      HLE +  + ++ + S ++L+ WL   ++ 
Sbjct  1840  QKQDVILIKNLLISVQGRWERILSRYGERSRHLEDALKRARQFNDSWKKLMDWLDEAENH  2019

Query  368   LSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQE  427
             L  +APIG D   ++ Q    + F+R L  K+P+  ST++T R    +   +  +KL ++
Sbjct  2020  LDSEAPIGNDPDKIKAQLLKFKEFQRALAAKQPLYDSTMKTGRSLKDKGTPQDGQKLDEK  2199

Query  428   PRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELD  487
               EL                      +W+ +   S D Q  ++E L    +  +A   L 
Sbjct  2200  LTEL--------------------RDKWDLICAKSVDRQHTLEEALLFSGQFADALQALL  2319

Query  488   LKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLG  546
               L + E       PV GD  ID++   +   K  + E+A    +V  V   AR++    
Sbjct  2320  DWLYKTEPNLAEDLPVHGD--IDTVLTLIGNHKVFQRELASRTSSVQTVRKQAREILNSS  2493

Query  547   IQLSPYNLSTLEDLNTRWK  565
              + +      LEDLN +W+
Sbjct  2494  TEDTSELQRQLEDLNIKWE  2550


 Score = 67.4 bits (163),  Expect = 5e-08, Method: Compositional matrix adjust.
 Identities = 112/567 (19%), Positives = 232/567 (40%), Gaps = 47/567 (8%)
 Frame = +1

Query  25    WLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQ  84
             WL   +  + +   +  D   I + I   K    +++ R+  +E +      L  K S+ 
Sbjct  685   WLGTAEARLATFPPIGADPSTIKKQIDNLKEFKTEVDPRQVAVEAMNNQGDQLMKKVSSD  864

Query  85    EARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLE  144
             EAR  I + +  +  +W+ +Q  + +R+ +L   L    Q+  A +E    L    A L+
Sbjct  865   EARLSIQEPLHDMNKRWEGLQRSIVDRQHKLEAALLKMGQFTAAIDELLTWLKHTEASLD  1044

Query  145   SWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITE  204
               K        I+ ++ + K L  D+   Q++VD  +    ++++  +  + + +     
Sbjct  1045  EEKPVAGDTKLIEIELAKHKVLQNDILAHQSSVDSVHQAGKRIIQAENKAEAKAIQDKLA  1224

Query  205   NINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERL  264
              ++  W  + ++ ++++  LE      Q F + LE+ L W+ E ET  +  +        
Sbjct  1225  ALDKRWSDVLQKAADKQTNLEALLNESQGFHVVLEELLHWVGETETKLSTTK--------  1380

Query  265   LEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL-EGSD--------DAVLL  315
                + G+ E  K+      +++ H ++   +D+ +++I  +L EG +         A  +
Sbjct  1381  --PTGGLPETAKE------QVDRHMELQQQIDDKAEEIDAALFEGQELVAKCDKTAASNV  1536

Query  316   QRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIG  375
             +  L+ +  +W  L   +   +S LE +  Q +  H SLQ  + WL   +  L+   P  
Sbjct  1537  EHGLNKLATQWEGLLAHAAERKSKLEDALKQAQDFHDSLQSFISWLTNAEKTLNNLKPAS  1716

Query  376   GDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEE  435
                  + +Q D H+AF++ +      ++                 L+K+    +      
Sbjct  1717  MVMETLSQQIDDHKAFEKNIADHRETMLQ----------------LDKMGTHLKYFS---  1839

Query  436   RAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEV  495
             + Q+V  L++     V   WE++     +  R +++ L+R ++  ++  +L   L +AE 
Sbjct  1840  QKQDVI-LIKNLLISVQGRWERILSRYGERSRHLEDALKRARQFNDSWKKLMDWLDEAEN  2016

Query  496   IKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLS  555
                S  P+G+   D ++  L K K  +  +A  +          R L   G       L 
Sbjct  2017  HLDSEAPIGN-DPDKIKAQLLKFKEFQRALAAKQPLYDSTMKTGRSLKDKGTPQDGQKLD  2193

Query  556   -TLEDLNTRWKLLQVAVEDRVRQLHEA  581
               L +L  +W L+     DR   L EA
Sbjct  2194  EKLTELRDKWDLICAKSVDRQHTLEEA  2274


 Score = 61.6 bits (148),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 101/556 (18%), Positives = 237/556 (42%), Gaps = 34/556 (6%)
 Frame = +1

Query  46    INEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQE---ARTIITDRIERIQNQWD  102
             I E I + +A   +LE+  P +E L     +L  K++  +   +   I D+++++   W+
Sbjct  82    IKEQISENEALRSELEKHLPAIETLRGKGDDLIGKSAGVDKDPSAKAIQDKLDQMNFLWE  261

Query  103   EVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITE  162
             ++    + R Q + E    + ++ E       VL + +  ++  +E     D ++++   
Sbjct  262   DIVSRSEERDQAMLETHDTAERFWEELGNVLNVLKETQDSIKELEEPAIQPDIVREQQEV  441

Query  163   TKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREA  222
              + + +++   Q +++    L   L       D   V    E++NA+W +++    ERE 
Sbjct  442   LQAIKEEMESTQDDIETVRQLGEDLTSLCGEPDKPVVSKNVEDLNATWDTLNASWEEREE  621

Query  223   ALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQ  282
              LEE  R+  Q+   L+  L WL  AE              +  D   +K+ +   ++ +
Sbjct  622   VLEEAMRVALQYQDALQALLVWLGTAEARLATFPP------IGADPSTIKKQIDNLKEFK  783

Query  283   GEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEA  342
              E++        ++    ++++ +   +  + +Q  L +MN +W  L++  ++ +  LEA
Sbjct  784   TEVDPRQVAVEAMNNQGDQLMKKVSSDEARLSIQEPLHDMNKRWEGLQRSIVDRQHKLEA  963

Query  343   SSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVI  402
             +  +  +   ++ ELL WL+  +  L  + P+ GD   ++ +   H+  + ++   +  +
Sbjct  964   ALLKMGQFTAAIDELLTWLKHTEASLDEEKPVAGDTKLIEIELAKHKVLQNDILAHQSSV  1143

Query  403   MSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHS  462
              S  +  +                  R +  E +A+   + ++ +   ++  W  +   +
Sbjct  1144  DSVHQAGK------------------RIIQAENKAE--AKAIQDKLAALDKRWSDVLQKA  1263

Query  463   ADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALR  522
             AD Q  ++  L   Q      +EL   + + E    + +P G  L ++ ++ +++   L+
Sbjct  1264  ADKQTNLEALLNESQGFHVVLEELLHWVGETETKLSTTKPTGG-LPETAKEQVDRHMELQ  1440

Query  523   GEIAPLKENVSHVNDLARQLTTLGIQLSPYNLS-TLEDLNTRWKLLQVAVEDRVRQLHEA  581
              +I    E +       ++L     + +  N+   L  L T+W+ L     +R  +L +A
Sbjct  1441  QQIDDKAEEIDAALFEGQELVAKCDKTAASNVEHGLNKLATQWEGLLAHAAERKSKLEDA  1620

Query  582   HR---DFGPASQHFLS  594
              +   DF  + Q F+S
Sbjct  1621  LKQAQDFHDSLQSFIS  1668


 Score = 59.3 bits (142),  Expect = 1e-05, Method: Compositional matrix adjust.
 Identities = 88/399 (22%), Positives = 170/399 (42%), Gaps = 32/399 (8%)
 Frame = +1

Query  15    FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
             FN +W +L DWL   +  + S+  +  D + I   ++K K   + L  ++P  +  +   
Sbjct  1966  FNDSWKKLMDWLDEAENHLDSEAPIGNDPDKIKAQLLKFKEFQRALAAKQPLYDSTMKTG  2145

Query  75    QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
             ++LK+K + Q+ + +  +++  ++++WD +     +R+  L E L  S Q+ +A +    
Sbjct  2146  RSLKDKGTPQDGQKL-DEKLTELRDKWDLICAKSVDRQHTLEEALLFSGQFADALQALLD  2322

Query  135   VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
              L +    L         +D +   I   K   ++L    ++V      A ++L + S +
Sbjct  2323  WLYKTEPNLAEDLPVHGDIDTVLTLIGNHKVFQRELASRTSSVQTVRKQAREIL-NSSTE  2499

Query  195   DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAE-----  249
             DT ++    E++N  W +  +    ++  L++  +  ++F   +   L WL EAE     
Sbjct  2500  DTSELQRQLEDLNIKWENASRLSVVKQQRLDQAMKQAEEFHTSVHCLLEWLAEAEHVLRF  2679

Query  250   -TTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEG  308
              +   V  +    E L +  K  KE+  Q + LQ  +        ++ E   KI      
Sbjct  2680  QSQIPVDDEDMLMESLTQQEKFEKEMADQQRKLQEAM--------DMGEAILKICHP---  2826

Query  309   SDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW-------L  361
              D    ++  L  +  +W E+   +   R+ LE +    K     L  L  W       L
Sbjct  2827  -DAITTVKHWLTIIMARWEEVTSWASQHRARLEDALKVLKANEELLDRLTAWVEGAEHTL  3003

Query  362   QLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEP  400
             Q  DDE     P+  +   VQK  + H+ F+ E+ TK+P
Sbjct  3004  QTLDDE-----PLPDNMEDVQKLMEEHQMFQNEMSTKQP  3105


 Score = 58.9 bits (141),  Expect = 2e-05, Method: Compositional matrix adjust.
 Identities = 81/366 (22%), Positives = 160/366 (43%), Gaps = 13/366 (3%)
 Frame = +1

Query  14    DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
             DF+ +      WL+  ++ + + +     +E +++ I   KA  +++   R  + +L   
Sbjct  1636  DFHDSLQSFISWLTNAEKTLNNLKPASMVMETLSQQIDDHKAFEKNIADHRETMLQLDKM  1815

Query  74    AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE  133
               +LK  +  Q+   +I + +  +Q +W+ +      R + L + LK + Q+ ++ ++  
Sbjct  1816  GTHLKYFSQKQDV-ILIKNLLISVQGRWERILSRYGERSRHLEDALKRARQFNDSWKKLM  1992

Query  134   QVLGQARAKLESWKEGPYT--VDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDY  191
               L +A   L+S  E P     D I+ ++ + K+  + L   Q   D        L    
Sbjct  1993  DWLDEAENHLDS--EAPIGNDPDKIKAQLLKFKEFQRALAAKQPLYDSTMKTGRSLKDKG  2166

Query  192   SADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
             +  D +K+      +   W  I  +  +R+  LEE      QF   L+  L WL + E  
Sbjct  2167  TPQDGQKLDEKLTELRDKWDLICAKSVDRQHTLEEALLFSGQFADALQALLDWLYKTE--  2340

Query  252   ANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDD  311
              N+ +D      +  D   V  L+   +  Q E+ + T     + + +++IL S   ++D
Sbjct  2341  PNLAEDLP----VHGDIDTVLTLIGNHKVFQRELASRTSSVQTVRKQAREILNS--STED  2502

Query  312   AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQ  371
                LQR+L+++N KW    + S+  +  L+ +  Q +  H S+  LL WL   +  L  Q
Sbjct  2503  TSELQRQLEDLNIKWENASRLSVVKQQRLDQAMKQAEEFHTSVHCLLEWLAEAEHVLRFQ  2682

Query  372   APIGGD  377
             + I  D
Sbjct  2683  SQIPVD  2700


 Score = 45.1 bits (105),  Expect = 0.24, Method: Compositional matrix adjust.
 Identities = 65/308 (21%), Positives = 137/308 (44%), Gaps = 21/308 (6%)
 Frame = +1

Query  15    FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
             F  A   L DWL   +  +     + GD++ +  +I   K   ++L  R   ++ +   A
Sbjct  2293  FADALQALLDWLYKTEPNLAEDLPVHGDIDTVLTLIGNHKVFQRELASRTSSVQTVRKQA  2472

Query  75    QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQW-------LE  127
             + + N  S+ E  + +  ++E +  +W+        ++Q+L++ +K + ++       LE
Sbjct  2473  REILN--SSTEDTSELQRQLEDLNIKWENASRLSVVKQQRLDQAMKQAEEFHTSVHCLLE  2646

Query  128   AKEEAEQVLG-QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALK  186
                EAE VL  Q++  ++         D + + +T+ ++  K++   Q  +  A D+   
Sbjct  2647  WLAEAEHVLRFQSQIPVDD-------EDMLMESLTQQEKFEKEMADQQRKLQEAMDMGEA  2805

Query  187   LLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
             +L+    D    V      I A W  +    S+  A LE+  ++L+     L++  AW+ 
Sbjct  2806  ILKICHPDAITTVKHWLTIIMARWEEVTSWASQHRARLEDALKVLKANEELLDRLTAWVE  2985

Query  247   EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL  306
              AE T   L D    E L ++ + V++LM++ Q  Q E+      Y  + +  ++ + ++
Sbjct  2986  GAEHTLQTLDD----EPLPDNMEDVQKLMEEHQMFQNEMSTKQPEYDRITKGHKRRISTV  3153

Query  307   EGSDDAVL  314
             + S    L
Sbjct  3154  DHSPGGFL  3177


>ref|XM_684808.3| PREDICTED: Danio rerio similar to dystonin (LOC561403), mRNA
Length=25301

 Score = 89.0 bits (219),  Expect = 2e-14, Method: Compositional matrix adjust.
 Identities = 137/591 (23%), Positives = 250/591 (42%), Gaps = 73/591 (12%)
 Frame = +1

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  ++++  QR   GD + I   + K      D+   +  +E +
Sbjct  21616  ALGQFQHALDELLTWLTHTEELLGEQRKACGDPKAIEIELAKHHVLQNDVLAHKSTVEAV  21795

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEML----------K  120
                A  +L   ++ +EAR +  +++E +  +W  + E  + RRQ L+  L          +
Sbjct  21796  NRAGCDLMESSAGEEARGL-QNKLENLNQRWKNILEKTEQRRQLLDSALLQAQGFHGEIE  21972

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDA---IQKKITETKQLAKDL  170
              D  +WL+  E    A + +G     AR +L +  E   T++    I K + E  Q  + L
Sbjct  21973  DMQRWLKDSERQLLASKAVGGLPDTAREQLNTHLELCSTLEVKEEIYKHLLERGQ--QIL  22146

Query  171    RQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRL  230
                     D   +L L+ L+D                   W S+  +V ER+  LEE   +
Sbjct  22147  AMTPEGQDSTTELDLRNLQD------------------KWESVQAKVKERKVKLEEALAM  22272

Query  231    LQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTD  290
                 F   L+ F+ WLT+AE T  ++  A+    +LE    +   + + +    E+ +H D
Sbjct  22273  ATDFHNSLQDFINWLTQAEQTLTMVSPASL---ILE---TIMFQIDEHKVFVTEVNSHRD  22434

Query  291    VYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRL  350
                  LD+     L+      D VL++  L ++  +W ++ ++S+     L+ +  + K+ 
Sbjct  22435  QIMELDKTGTH-LKYFSQKQDVVLIKNLLLSVQSRWEKVVQRSVERGRLLDDARKRAKQF  22611

Query  351    HLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVR  410
              H S  +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L +K  V  +T  T R
Sbjct  22612  HESWSKLMEWLEESERALDTELEIANDPDKIKTQLTQHKEFQKALGSKHSVYDTTSRTGR  22791

Query  411    IFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKID  470
                  +  L                   Q+  + L     E+  +W+ +   S + Q K++
Sbjct  22792  ALKDKTSL-------------------QDDNQKLDHMLSELRDKWDTVCGKSVERQNKLE  22914

Query  471    ETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLK  529
              E L    +  +A   L   L + E      QPV GD  ID + + ++  K  + E+    
Sbjct  22915  EALLFSGQFTDALQALIDWLYKVEPQLAEDQPVHGD--IDLVLNLIDSHKVFQKELGKRT  23088

Query  530    ENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKL---LQVAVEDRVRQ  577
               +V  +   AR L       S +    +++L+TRW+    L V+ + R+ Q
Sbjct  23089  GSVQALKRSARDLIESSHDDSSWVKVQMQELSTRWETVCSLSVSKQTRLEQ  23241


 Score = 52.4 bits (124),  Expect = 0.001, Method: Compositional matrix adjust.
 Identities = 115/588 (19%), Positives = 242/588 (41%), Gaps = 90/588 (15%)
 Frame = +1

Query  42     DLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQE---ARTIITDRIERIQ  98
              ++E I E I + KA   DLE+ +P  E L    + +  ++   +   +   + D+++++ 
Sbjct  20713  EVEKIREQISENKALSVDLEKLQPSYETLKQRGEEMIARSQGADKDLSAKAVQDKLDQMV  20892

Query  99     NQWDEVQEHLQNRRQQLNEML-----------------KDSTQWLEAKEEAE---QVLGQ  138
                W ++Q  L+ R  +L +++                 KD+ + L+  EE      V+ Q
Sbjct  20893  FLWTDIQALLEEREAKLLDVMDLAEKFWCDHCALIVTIKDTQELLKELEEPGVDPSVVKQ  21072

Query  139    ARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRK  198
               +  +E ++E    +D +Q+++                 +V  +L  +L+      D   
Sbjct  21073  QQESVEGFRE---EIDGLQEEL-----------------NVVQNLGAELMTACGEPDKPV  21192

Query  199    VHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDA  258
              +    + +N++W +++K   ER   LEE  +   QF   L+     +   E   + +   
Sbjct  21193  IKKSIDEVNSAWETLNKTWKERVEILEEAMQAAVQFQDSLQNMFDSVDIMEGKLDSMSPV  21372

Query  259    TRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRR  318
                      D + VK+ +++ ++ +G+          L+  +  +L+ +   DD   +   
Sbjct  21373  GT------DLETVKQQIEELKEFKGDAYQLQIEMERLNHQAGLLLKKVMDEDDRTSISEP  21534

Query  319    LDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDF  378
              ++ +   W  L KK +N +  LE +     +   +L ELL WL   ++ L  Q    GD 
Sbjct  21535  MNELKMLWENLDKKIINRQHKLEGALLALGQFQHALDELLTWLTHTEELLGEQRKACGDP  21714

Query  379    PAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQ  438
               A++ +   H   + ++   +    ST+E V          G + +         E  A 
Sbjct  21715  KAIEIELAKHHVLQNDVLAHK----STVEAVN-------RAGCDLM---------ESSAG  21834

Query  439    NVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKG  498
                 R L+ + E +N  W+ +   +   ++ +D  L + Q      +++   L+ +E    
Sbjct  21835  EEARGLQNKLENLNQRWKNILEKTEQRRQLLDSALLQAQGFHGEIEDMQRWLKDSERQLL  22014

Query  499    SWQPVG---DLLIDSLQDHLEKVKALRGEIAPLKENV-SHVNDLARQLTTLGIQLSPYNL  554
              + + VG   D   + L  HLE    L      +KE +  H+ +  +Q+    + ++P   
Sbjct  22015  ASKAVGGLPDTAREQLNTHLELCSTLE-----VKEEIYKHLLERGQQI----LAMTPEGQ  22167

Query  555    ST-----LEDLNTRWKLLQVAVEDRVRQLHEA---HRDFGPASQHFLS  594
               +     L +L  +W+ +Q  V++R  +L EA     DF  + Q F++
Sbjct  22168  DSTTELDLRNLQDKWESVQAKVKERKVKLEEALAMATDFHNSLQDFIN  22311


 Score = 46.6 bits (109),  Expect = 0.087, Method: Compositional matrix adjust.
 Identities = 76/322 (23%), Positives = 133/322 (41%), Gaps = 10/322 (3%)
 Frame = +1

Query  12     LADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQD-LEQRRPQLEEL  70
              L +F     E T  LS  ++  +SQ  +  + E IN+ +   K   +D +E  + QL+EL
Sbjct  18331  LEEFYSKTQEFTSNLSTAERQEESQGSVGLETEVINQQLESFKVFQKDVIESLQSQLQEL  18510

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKE  130
               T  Q L        +   +   +E + ++W+ + + +  R  QL+E L    ++ +A E
Sbjct  18511  NTLGQALIQNAPKGTSTKNLDHDLEEVNSRWNTLNKKVAERSAQLHEALLHCGRFQDALE  18690

Query  131    EAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRD  190
                   L      + + K        ++ +I E K L + L   +  V++      K+   
Sbjct  18691  SLLSWLTDTEELVANQKPPSAEFKVVKAQIQEQKLLQRLLDDRKATVELIKTEGRKVTDL  18870

Query  191    YSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAET  250
                  D  K+    E +   W ++ K+   R   LE    + QQF   LE    WLT  E 
Sbjct  18871  ADTVDKEKIGREIECLGQRWDALLKKAENRHKQLENISVVAQQFHETLEPLTEWLTATEK  19050

Query  251    -TANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGS  309
                AN     T+  +L       +E + Q + L+ E+     V +      Q  LR+L   
Sbjct  19051  RLANSEPIGTQTSKL-------EEQISQHKALEEEVLGRGKVLYQAMSLGQS-LRTLGCV  19206

Query  310    DDAVLLQRRLDNMNFKWSELRK  331
              DD   +Q +L+N    + EL++
Sbjct  19207  DDKETVQVKLENTQRSFLELQE  19272


 Score = 46.6 bits (109),  Expect = 0.099, Method: Compositional matrix adjust.
 Identities = 79/405 (19%), Positives = 169/405 (41%), Gaps = 10/405 (2%)
 Frame = +1

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ +W++L +WL   ++ + ++  +  D + I   + + K   + L  +    +      
Sbjct  22609  FHESWSKLMEWLEESERALDTELEIANDPDKIKTQLTQHKEFQKALGSKHSVYDTTSRTG  22788

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              + LK+KTS Q+    +   +  ++++WD V      R+ +L E L  S Q+ +A +    
Sbjct  22789  RALKDKTSLQDDNQKLDHMLSELRDKWDTVCGKSVERQNKLEEALLFSGQFTDALQALID  22968

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +   +V      A  L+ + S D
Sbjct  22969  WLYKVEPQLAEDQPVHGDIDLVLNLIDSHKVFQKELGKRTGSVQALKRSARDLI-ESSHD  23145

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANV  254
              D+  V +  + ++  W ++      ++  LE+     ++F   +   L WL EAE     
Sbjct  23146  DSSWVKVQMQELSTRWETVCSLSVSKQTRLEQALSQAEEFHSTVHILLEWLAEAE-----  23310

Query  255    LQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVL  314
               Q       L +D + ++ L++Q ++    +E             + IL S+   D    
Sbjct  23311  -QSLRFHGALPDDEEALRALIEQHKEFMKRLEEKRLALSKATSMGEAIL-SICHPDSITT  23484

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSR--QA  372
              ++     +  ++ E+   +   +  L ++ D+ +     L++LL WLQ  +  L    + 
Sbjct  23485  IKHWNTIIKARFEEVTAWARQHQQRLSSALDELQATQELLEKLLNWLQWAETTLGEKDKD  23664

Query  373    PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQP  417
              P+  +   V+     H+ F  E+  K+P +    +T +   T  P
Sbjct  23665  PMPQELEEVKALIAEHQTFLEEMTRKQPDVDKVTKTHKRKATADP  23799


 Score = 40.8 bits (94),  Expect = 4.9, Method: Compositional matrix adjust.
 Identities = 61/271 (22%), Positives = 125/271 (46%), Gaps = 30/271 (11%)
 Frame = +1

Query  21     ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
              E+  W+  +++ ++    +  D   I + + K+ A  QD+  R+  +     +A  LK K
Sbjct  15055  EMLSWMEKVEESLQETPAVALDSRSIADALSKETALEQDMISRQSSV-----SAMQLKVK  15219

Query  81     ----TSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ-V  135
                  +++  A  ++  R+E +  ++ +  E  + + +++ E+     ++ +  EE +Q V
Sbjct  15220  AFVESADPAAAALLQTRMEALSQRFTDASERHKLKLKRMEELKLKVEEFEKTSEELQQFV  15399

Query  136    LGQARAKLESWKEGPYTVDAIQKKITETKQLAKD----LRQWQTNVDVANDLALKLLR--  189
              L  ++A  E+        D  Q+ I E  QL +D    L Q   +V+  + L+ +L +  
Sbjct  15400  LKSSQALTET--------DGAQRNIAELSQLVQDTSAELSQHVKDVETLHKLSEELSKLG  15555

Query  190    -DYSADDTR-KVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
               + SAD  + K+  I++N NA    + + ++E+ A +      LQ+F       + WL E
Sbjct  15556  PEGSADLLQNKMKNISDNFNA----LKETLTEKMAEVSSCQNQLQEFRAAAGVLMKWLEE  15723

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQW  278
               +     LQ    ++ L  D K V +L+  W
Sbjct  15724  TKERVPTLQPNCSEQGLRTDLKTVNDLLDAW  15816


>emb|Z68331.3| Human DNA sequence from clone GHc-521F8 on chromosome X Contains 
the 3' end of the DRP2 gene for dystrophin related protein 
2 and the 3' end of the TAF7L gene for TAF7-like RNA polymerase 
II 50kDa TATA box binding protein (TBP)-associated factor, 
complete sequence
Length=27757

 Score = 88.6 bits (218),  Expect = 2e-14, Method: Compositional matrix adjust.
 Identities = 39/54 (72%), Positives = 48/54 (88%), Gaps = 0/54 (0%)
 Frame = +2

Query  758   LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
             LF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EPSVRSCF+F +
Sbjct  4634  LFSQVANSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEPSVRSCFRFVS  4795


 Score = 87.0 bits (214),  Expect = 5e-14, Method: Compositional matrix adjust.
 Identities = 38/59 (64%), Positives = 45/59 (76%), Gaps = 0/59 (0%)
 Frame = +2

Query  807   FQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFR  865
             F  +  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI GFR
Sbjct  5117  FP*STGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPIKGFR  5293


 Score = 85.1 bits (209),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 40/96 (41%), Positives = 65/96 (67%), Gaps = 6/96 (6%)
 Frame = +2

Query  661   LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
             +DL++L+ A +  ++H+L+ ++  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LN
Sbjct  2297  VDLVTLTTALEIFNEHDLQASEHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLN  2476

Query  721   WLLNVYD-----TGRTGRIRVLSF-KTGIISLCKAH  750
             WLLNV+D          RI+     + G++  C +H
Sbjct  2477  WLLNVFDR*GLSALEASRIKFNGISQVGLVGRCCSH  2584


 Score = 73.6 bits (179),  Expect = 7e-10, Method: Compositional matrix adjust.
 Identities = 32/46 (69%), Positives = 38/46 (82%), Gaps = 0/46 (0%)
 Frame = +3

Query  903   TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
             TTS E++RDFA  LKNKFR+K YF+KHP+ GYLPVQ+VLE D  ET
Sbjct  8634  TTSSENMRDFATTLKNKFRSKHYFSKHPQRGYLPVQSVLEADYSET  8771


 Score = 69.7 bits (169),  Expect = 1e-08, Method: Compositional matrix adjust.
 Identities = 40/72 (55%), Positives = 47/72 (65%), Gaps = 2/72 (2%)
 Frame = +3

Query  1044   NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  1103
               R LQ E  RLK QHE    +  PS  +    +    R+ EL+AEA++LRQHK RLE RM
Sbjct  12513  GRILQGELRRLKWQHEEA--AEAPSLADGSTEAATDHRNEELLAEARILRQHKSRLETRM  12686

Query  1104   QILEDHNKQLES  1115
              QILEDHNKQLES
Sbjct  12687  QILEDHNKQLES  12722


 Score = 65.9 bits (159),  Expect = 1e-07, Method: Compositional matrix adjust.
 Identities = 26/39 (66%), Positives = 33/39 (84%), Gaps = 0/39 (0%)
 Frame = +2

Query  865   RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT  903
             RYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TP 
Sbjct  6812  RYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPV  6928


 Score = 49.3 bits (116),  Expect = 0.015, Method: Compositional matrix adjust.
 Identities = 21/24 (87%), Positives = 24/24 (100%), Gaps = 0/24 (0%)
 Frame = +2

Query  636   ADLNNVRFSAYRTAMKLRRLQKAL  659
             ADLNN++FSAYRTAMKLRR+QKAL
Sbjct  1298  ADLNNIKFSAYRTAMKLRRVQKAL  1369


 Score = 40.4 bits (93),  Expect = 6.2, Method: Compositional matrix adjust.
 Identities = 17/26 (65%), Positives = 20/26 (76%), Gaps = 0/26 (0%)
 Frame = +3

Query  949   PASSPQLSHDDTHSRIEHYASRLAEM  974
             PASSP   H DTHSRIEH+ASR  ++
Sbjct  9069  PASSPMWPHADTHSRIEHFASRYHQV  9146


>gb|AC194760.4| Pan troglodytes BAC clone CH251-694P16 from chromosome x, complete 
sequence
Length=171262

 Score = 88.2 bits (217),  Expect = 2e-14, Method: Compositional matrix adjust.
 Identities = 39/54 (72%), Positives = 48/54 (88%), Gaps = 0/54 (0%)
 Frame = -3

Query  758    LFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFAN  811
              LF QVA+S   CDQR LG+LLH++IQ+PRQLGEVA+FGGSN+EPSVRSCF+F +
Sbjct  23711  LFSQVANSGSQCDQRHLGVLLHEAIQVPRQLGEVAAFGGSNVEPSVRSCFRFVS  23550


 Score = 87.0 bits (214),  Expect = 5e-14, Method: Compositional matrix adjust.
 Identities = 38/59 (64%), Positives = 45/59 (76%), Gaps = 0/59 (0%)
 Frame = -3

Query  807    FQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFR  865
              F  +  KP IEA+ FL+W+ LEPQSMVWL VLHRV  AE  KHQ KC+IC++CPI GFR
Sbjct  23228  FP*STGKPVIEASQFLEWVNLEPQSMVWLAVLHRVTIAEQVKHQTKCSICRQCPIKGFR  23052


 Score = 85.1 bits (209),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 40/96 (41%), Positives = 65/96 (67%), Gaps = 6/96 (6%)
 Frame = -3

Query  661    LDLLSLSAACDALDQHNLKQNDQPMDILQIINCLTTIYDRLEQEHNNLVNVPLCVDMCLN  720
              +DL++L+ A +  ++H+L+ ++  MD++++I+CLT +Y+RLE+E   LVNVPLCVDM LN
Sbjct  26048  VDLVTLTTALEIFNEHDLQASEHVMDVVEVIHCLTALYERLEEERGILVNVPLCVDMSLN  25869

Query  721    WLLNVYD-----TGRTGRIRVLSF-KTGIISLCKAH  750
              WLLNV+D          RI+     + G++  C +H
Sbjct  25868  WLLNVFDR*GLSALEASRIKFNGISQVGLVGRCCSH  25761


 Score = 83.6 bits (205),  Expect = 7e-13, Method: Compositional matrix adjust.
 Identities = 39/90 (43%), Positives = 59/90 (65%), Gaps = 0/90 (0%)
 Frame = -3

Query  433    PEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQ  492
              P++R QN++R + KQA   +  WEKL     D  R I+ TLE+L E+Q A +EL   L Q
Sbjct  32468  PKQRIQNLSRFVWKQATVASELWEKLTARCVDQHRHIERTLEQLLEIQGAMEELSTTLSQ  32289

Query  493    AEVIKGSWQPVGDLLIDSLQDHLEKVKALR  522
              AE ++ +W+P+GDL IDSL +H++ +K  +
Sbjct  32288  AEGVRATWEPIGDLFIDSLPEHIQAIKVCK  32199


 Score = 73.6 bits (179),  Expect = 7e-10, Method: Compositional matrix adjust.
 Identities = 32/46 (69%), Positives = 38/46 (82%), Gaps = 0/46 (0%)
 Frame = -1

Query  903    TTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMET  948
              TTS E++RDFA  LKNKFR+K YF+KHP+ GYLPVQ+VLE D  ET
Sbjct  19723  TTSSENMRDFATTLKNKFRSKHYFSKHPQRGYLPVQSVLEADYSET  19586


 Score = 67.8 bits (164),  Expect = 4e-08, Method: Compositional matrix adjust.
 Identities = 40/72 (55%), Positives = 47/72 (65%), Gaps = 2/72 (2%)
 Frame = -2

Query  1044   NRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARM  1103
               R LQ E  RLK QHE    +P  S  +    +    R+ EL+AEA++LRQHK RLE RM
Sbjct  15843  GRILQGELRRLKWQHEEAAEAP--SLADGSTEAAPDHRNEELLAEARILRQHKSRLETRM  15670

Query  1104   QILEDHNKQLES  1115
              QILEDHNKQLES
Sbjct  15669  QILEDHNKQLES  15634


 Score = 65.9 bits (159),  Expect = 1e-07, Method: Compositional matrix adjust.
 Identities = 26/39 (66%), Positives = 33/39 (84%), Gaps = 0/39 (0%)
 Frame = -3

Query  865    RYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPT  903
              RYRSLK FN DICQ+CF +GR +KG+K+HYP++EY TP 
Sbjct  21533  RYRSLKQFNVDICQTCFLTGRASKGNKLHYPIMEYYTPV  21417


 Score = 49.3 bits (116),  Expect = 0.015, Method: Compositional matrix adjust.
 Identities = 21/24 (87%), Positives = 24/24 (100%), Gaps = 0/24 (0%)
 Frame = -3

Query  636    ADLNNVRFSAYRTAMKLRRLQKAL  659
              ADLNN++FSAYRTAMKLRR+QKAL
Sbjct  27047  ADLNNIKFSAYRTAMKLRRVQKAL  26976


 Score = 47.8 bits (112),  Expect = 0.037, Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 30/51 (58%), Gaps = 4/51 (7%)
 Frame = -3

Query  601    WERAISPNKVPYYI-NHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAM  650
              W   I    +   + +H+ QTTCWDHPKMTELYQ+L    NV F  YR  +
Sbjct  28793  WVGGIDAGTIDAIVCSHQAQTTCWDHPKMTELYQTLG--KNVGF-LYRVGI  28650


 Score = 47.4 bits (111),  Expect = 0.056, Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 33/51 (64%), Gaps = 0/51 (0%)
 Frame = -2

Query  338    SHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVH  388
              + LEA SD   +L L LQE++ WL  KD+ELS Q P+ GD   VQ++ + H
Sbjct  36513  ARLEAFSDHSGKLQLPLQEIIDWLSQKDEELSAQLPLQGDVALVQQEKETH  36361


 Score = 46.6 bits (109),  Expect = 0.087, Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 31/52 (59%), Gaps = 0/52 (0%)
 Frame = -1

Query  518    VKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLLQV  569
              ++  + E +P+K+ V  VNDLA QL    + LS  N   LE +N RWK LQV
Sbjct  31825  LQLFKEEFSPMKDGVKLVNDLAHQLAISDVHLSMENSQALEQINVRWKQLQV  31670


 Score = 44.3 bits (103),  Expect = 0.39, Method: Compositional matrix adjust.
 Identities = 26/53 (49%), Positives = 27/53 (50%), Gaps = 6/53 (11%)
 Frame = -3

Query  593    LSTSVQGPWERAISPNKVPYYINHET------QTTCWDHPKMTELYQSLADLN  639
              L  SVQ PWERAISPNKVPYYI   T        TC   P    L   L  L+
Sbjct  29123  LPASVQVPWERAISPNKVPYYIK*VTI*IRSGSVTCPPPPSPAFLLPVLVTLS  28965


 Score = 43.5 bits (101),  Expect = 0.74, Method: Compositional matrix adjust.
 Identities = 17/28 (60%), Positives = 23/28 (82%), Gaps = 0/28 (0%)
 Frame = -1

Query  569    VAVEDRVRQLHEAHRDFGPASQHFLSTS  596
               +V +R++QL +AHRDFGP SQHFLS +
Sbjct  31240  ASVSERLKQLQDAHRDFGPGSQHFLSCT  31157


 Score = 40.4 bits (93),  Expect = 5.6, Method: Compositional matrix adjust.
 Identities = 17/22 (77%), Positives = 18/22 (81%), Gaps = 0/22 (0%)
 Frame = -1

Query  949    PASSPQLSHDDTHSRIEHYASR  970
              PASSP   H DTHSRIEH+ASR
Sbjct  19288  PASSPMWPHADTHSRIEHFASR  19223


>ref|XR_024528.1| PREDICTED: Pan troglodytes similar to dystonin (LOC462793), mRNA
Length=24172

 Score = 88.2 bits (217),  Expect = 3e-14, Method: Compositional matrix adjust.
 Identities = 137/602 (22%), Positives = 252/602 (41%), Gaps = 81/602 (13%)
 Frame = +1

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  19654  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  19833

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  19834  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  20010

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQ-----LAK  168
              D  QWL   E    A + LG     A+ +L    E     +A ++      Q     LA+
Sbjct  20011  DLQQWLTDTERHLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLAR  20190

Query  169    DLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETH  228
                +  +TN+D          +D +            N+   W S+  +++ER+  LEE  
Sbjct  20191  CPKSAETNID----------QDIN------------NLKEKWESVETKLNERKTKLEEAL  20304

Query  229    RLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAH  288
               L  +F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H
Sbjct  20305  NLAMEFHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSH  20466

Query  289    TDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWK  348
               +    LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K
Sbjct  20467  REQIIELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAK  20643

Query  349    RLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
              + H +  +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T
Sbjct  20644  QFHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT  20823

Query  409    VRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRK  468
                                  R L  +    +    L     E+  +W+ +   S + Q K
Sbjct  20824  -------------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNK  20946

Query  469    IDETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAP  527
              ++E L    +  +A   L   L + E      QPV GD  ID + + ++  KA + E+  
Sbjct  20947  LEEALLFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKAFQKELGK  21120

Query  528    LKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHE  580
                 +V  +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E
Sbjct  21121  RTSSVQALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEE  21300

Query  581    AH  582
               H
Sbjct  21301  FH  21306


 Score = 65.9 bits (159),  Expect = 1e-07, Method: Compositional matrix adjust.
 Identities = 87/387 (22%), Positives = 174/387 (44%), Gaps = 12/387 (3%)
 Frame = +1

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+ +  +  +WL+  +Q +         L+ +   I + K    ++   R Q+ EL   
Sbjct  20317  EFHNSLQDFINWLTQAEQTLNVASRPSLILDTVLFQIDEHKVFANEVNSHREQIIELDKT  20496

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE  133
                +LK  +  Q+   +I + +  +Q++W++V + L  R + L++  K + Q+ EA  +  
Sbjct  20497  GTHLKYFSQKQDV-VLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEAWSKLM  20673

Query  134    QVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-  192
              + L ++   L+S  E     D I+ ++ + K+  K L    +  D  N     L    S 
Sbjct  20674  EWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTGRSLKEKTSL  20853

Query  193    ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
              ADD  K+  +   +   W +I  +  ER+  LEE      QF   L+  + WL   E   
Sbjct  20854  ADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALIDWLYRVE--P  21027

Query  253    NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGS-DD  311
               + +D    + +  D   V  L+   +  Q E+   T     L  ++++++   EGS DD
Sbjct  21028  QLAED----QPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELI---EGSRDD  21186

Query  312    AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQ  371
              +  ++ ++  ++ +W  +   S++ ++ LEA+  Q +  H  +  LL WL   +  L   
Sbjct  21187  SSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRFH  21366

Query  372    APIGGDFPAVQKQNDVHRAFKRELKTK  398
                +  D  A++   D H+ F ++L+ K
Sbjct  21367  GVLPDDEDALRTLIDQHKEFMKKLEEK  21447


 Score = 62.4 bits (150),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 85/387 (21%), Positives = 167/387 (43%), Gaps = 22/387 (5%)
 Frame = +1

Query  24     DWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSN  83
              DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K + 
Sbjct  19363  DWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKVTE  19542

Query  84     QEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKL  143
              +  +  + D +  ++  WD ++E + NR+ +L   L    Q+  A +E    L      L
Sbjct  19543  ESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQHALDELLTWLTHTEGLL  19722

Query  144    ESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMIT  203
                 K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +    
Sbjct  19723  SEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQNKL  19902

Query  204    ENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER  263
              E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              ER
Sbjct  19903  EVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLQQWLTDT-------------ER  20043

Query  264    LLEDSK---GVKELMKQWQDLQGEI----EAHTDVYHNLDENSQKILRSLEGSDDAVLLQ  316
               L  SK   G+ E  K+  ++  E+    EA  + Y +L +  Q++L     S +  + Q
Sbjct  20044  HLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLARCPKSAETNIDQ  20223

Query  317    RRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGG  376
                ++N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +    
Sbjct  20224  -DINNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRPSL  20400

Query  377    DFPAVQKQNDVHRAFKRELKT-KEPVI  402
                  V  Q D H+ F  E+ + +E +I
Sbjct  20401  ILDTVLFQIDEHKVFANEVNSHREQII  20481


 Score = 61.2 bits (147),  Expect = 4e-06, Method: Compositional matrix adjust.
 Identities = 135/560 (24%), Positives = 233/560 (41%), Gaps = 119/560 (21%)
 Frame = +1

Query  68     EELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
              E+ I   +NL  KT   E +  +  ++  I+  WD   + ++ R  +L E L+ + ++ E
Sbjct  15232  EKTIAEGENLLLKTQGSE-KAALQLQLNTIKTNWDTFNKQVKERENKLKESLEKALKYKE  15408

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKK--ITETKQLAKDLRQWQTNVDVANDLAL  185
                E     + + +  LE  K   + +D  + +  I + K L K++ Q    V++ N+ A 
Sbjct  15409  QVETLRPWIDKCQNNLEEIK---FCLDPAEGENSIAKLKSLQKEMDQHFGMVELLNNTAN  15579

Query  186    KLL------RDYSADDTR----KVHMITENINAS---WRSIHKRVSEREAALEETHRLLQ  232
               LL      ++   D+ +    KV M+TE +++      ++ ++  E +   +E+ R LQ
Sbjct  15580  SLLSVCEIDKEVVTDENKSLIQKVDMVTEQLHSKKFCLENMTQKFKEFQEVSKESKRQLQ  15759

Query  233    --QFPLDLEKFLA-------WLTEAETTANVLQDATRK----ERLLED-------SKGVK  272
                +  LD+   L        +LT  +T    LQ    +    +RL +D       SKG  
Sbjct  15760  CAKEQLDIHDSLGSQAYSNKYLTMLQTQQKSLQALKHQVDLAKRLAQDLVVEASDSKGTS  15939

Query  273    ELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKK  332
              +++ Q + +  E   H+ +   +DE    +   L+G       Q  +  M  +++E    
Sbjct  15940  DVLLQVETIAQE---HSTLSQQVDEKCSFLETKLQGIGH---FQNTIREMFSQFAEF---  16092

Query  333    SLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFK  392
                                              DDEL   AP+G D   +QKQ +  +AF 
Sbjct  16093  --------------------------------DDELDSMAPVGRDAETLQKQKETIKAF-  16173

Query  393    RELKTKEPVIMS---TLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLL-RKQA  448
                LK  E +I S     +T ++ L  +  E    L    R+L  E  ++   +LL R QA
Sbjct  16174  --LKKLEALIASNDNANKTCKMMLATE--ETSPDLVGIKRDL--EALSKQCNKLLDRAQA  16335

Query  449    EEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLI  508
               E                 +++ T++RL+E      E  + L++AE  + S  PVG +  
Sbjct  16336  RE----------------EQVEGTIKRLEEFYSKLKEFSILLQKAEEHEESQGPVG-MET  16464

Query  509    DSLQDHLEKVKAL-RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLST------LEDLN  561
              +++   L   K   + EI PL+     VN L + L    IQ +  + ST      L+D+N
Sbjct  16465  ETINQQLNMFKVFQKEEIEPLQGKQQDVNWLGQGL----IQSAAKSTSTQGLEHDLDDVN  16632

Query  562    TRWKLLQVAVEDRVRQLHEA  581
               RWK L   V  R  QL EA
Sbjct  16633  ARWKTLNKKVAQRAAQLQEA  16692


 Score = 52.8 bits (125),  Expect = 0.001, Method: Compositional matrix adjust.
 Identities = 64/278 (23%), Positives = 123/278 (44%), Gaps = 6/278 (2%)
 Frame = +1

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  20647  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  20826

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  20827  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  21006

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  21007  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELI-EGSRD  21183

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA--  252
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T   
Sbjct  21184  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRF  21363

Query  253    -NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHT  289
                VL D     R L D    KE MK+ ++ + E+   T
Sbjct  21364  HGVLPDDEDALRTLIDQH--KEFMKKLEEKRAELNKAT  21471


 Score = 50.8 bits (120),  Expect = 0.004, Method: Compositional matrix adjust.
 Identities = 79/352 (22%), Positives = 141/352 (40%), Gaps = 48/352 (13%)
 Frame = +1

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  19156  QEELDIVINLGSELIAACGEPDKPIVKKSIDELNSAWDSLNKAWKDRIDKLEEAMQAAVQ  19335

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  19336  YQDGLQAVFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  19491

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  19492  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQ  19671

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  19672  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  19803

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  19804  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  19941

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRG  523
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G
Sbjct  19942  TEQRKQ-------QLDGALRQAKGFHGEIEDLQQWLTDT-ERHLLASKPLGG  20073


 Score = 45.1 bits (105),  Expect = 0.26, Method: Compositional matrix adjust.
 Identities = 105/512 (20%), Positives = 219/512 (42%), Gaps = 64/512 (12%)
 Frame = +1

Query  87     RTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLE--  144
              + ++TD  + +  + D V E L +++  L  M +   ++ E  +E+++ L  A+ +L+  
Sbjct  15607  KEVVTDENKSLIQKVDMVTEQLHSKKFCLENMTQKFKEFQEVSKESKRQLQCAKEQLDIH  15786

Query  145    -SWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-ADDTRKVHMI  202
               S     Y+     K +T  +   K L+  +  VD+A  LA  L+ + S +  T  V + 
Sbjct  15787  DSLGSQAYS----NKYLTMLQTQQKSLQALKHQVDLAKRLAQDLVVEASDSKGTSDVLLQ  15954

Query  203    TENINASWRSIHKRVSEREAALEETHRLLQQFPLDL----EKFLAWLTEAETTANVLQDA  258
               E I     ++ ++V E+ + LE   + +  F   +     +F  +  E ++ A V +DA
Sbjct  15955  VETIAQEHSTLSQQVDEKCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDA  16134

Query  259    TRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRR  318
                 E L +  + +K  +K+       +EA      N ++  + +L + E S D V ++R 
Sbjct  16135  ---ETLQKQKETIKAFLKK-------LEALIASNDNANKTCKMMLATEETSPDLVGIKRD  16284

Query  319    LDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDF  378
              L+ ++ + ++L  ++      +E +  + +  +  L+E  + LQ  ++    Q P+G + 
Sbjct  16285  LEALSKQCNKLLDRAQAREEQVEGTIKRLEEFYSKLKEFSILLQKAEEHEESQGPVGMET  16464

Query  379    PAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQ  438
                + +Q ++ + F++E                     +PL+G ++      +   +  A+
Sbjct  16465  ETINQQLNMFKVFQKE-------------------EIEPLQGKQQDVNWLGQGLIQSAAK  16587

Query  439    NV-TRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIK  497
              +  T+ L    ++VN  W+ LN   A    ++ E L      Q+A + L           
Sbjct  16588  STSTQGLEHDLDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESL-----------  16734

Query  498    GSWQPVGDLLIDSLQDHLEKVKALRGEIAP-------LKENVSHVNDLARQLTTLGIQLS  550
               SW    + L+ + +    + K ++ +I         L +  S V  + R+   +     
Sbjct  16735  LSWMVDTEELVANQKPPSAEFKVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIATTAE  16914

Query  551    PYN----LSTLEDLNTRWKLLQVAVEDRVRQL  578
              P +    L  L  L++RW+ L    E R RQL
Sbjct  16915  PADKVKILKQLSLLDSRWEALLNKAETRNRQL  17010


>dbj|AB018271.2| Homo sapiens mRNA for KIAA0728 protein, partial cds
Length=5680

 Score = 88.2 bits (217),  Expect = 3e-14, Method: Compositional matrix adjust.
 Identities = 137/602 (22%), Positives = 251/602 (41%), Gaps = 81/602 (13%)
 Frame = +1

Query  11    ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
             AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  1294  ALGQFQHALDELLAWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  1473

Query  71    ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
               A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  1474  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  1650

Query  121   DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQ-----LAK  168
             D  QWL   E    A + LG     A+ +L    E     +A ++      Q     LA+
Sbjct  1651  DLQQWLTDTERHLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLAR  1830

Query  169   DLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETH  228
               +  +TN+D   D+                     N+   W S+  +++ER+  LEE  
Sbjct  1831  CPKSAETNID--QDI--------------------NNLKEKWESVETKLNERKTKLEEAL  1944

Query  229   RLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAH  288
              L  +F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H
Sbjct  1945  NLAMEFHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSH  2106

Query  289   TDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWK  348
              +    LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K
Sbjct  2107  REQIIELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAK  2283

Query  349   RLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
             + H +  +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T
Sbjct  2284  QFHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT  2463

Query  409   VRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRK  468
                                 R L  +    +    L     E+  +W+ +   S + Q K
Sbjct  2464  -------------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNK  2586

Query  469   IDETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAP  527
             ++E L    +  +A   L   L + E      QPV GD  ID + + ++  KA + E+  
Sbjct  2587  LEEALLFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKAFQKELGK  2760

Query  528   LKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHE  580
                +V  +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E
Sbjct  2761  RTSSVQALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEE  2940

Query  581   AH  582
              H
Sbjct  2941  FH  2946


 Score = 67.0 bits (162),  Expect = 6e-08, Method: Compositional matrix adjust.
 Identities = 86/387 (22%), Positives = 171/387 (44%), Gaps = 12/387 (3%)
 Frame = +1

Query  14    DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
             +F+ +  +  +WL+  +Q +         L+ +   I + K    ++   R Q+ EL   
Sbjct  1957  EFHNSLQDFINWLTQAEQTLNVASRPSLILDTVLFQIDEHKVFANEVNSHREQIIELDKT  2136

Query  74    AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE  133
               +LK  +  Q+   +I + +  +Q++W++V + L  R + L++  K + Q+ EA  +  
Sbjct  2137  GTHLKYFSQKQDV-VLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEAWSKLM  2313

Query  134   QVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-  192
             + L ++   L+S  E     D I+ ++ + K+  K L    +  D  N     L    S 
Sbjct  2314  EWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTGRSLKEKTSL  2493

Query  193   ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
             ADD  K+  +   +   W +I  +  ER+  LEE      QF   L+  + WL   E   
Sbjct  2494  ADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALIDWLYRVEPQL  2673

Query  253   NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGS-DD  311
                      + +  D   V  L+   +  Q E+   T     L  ++++++   EGS DD
Sbjct  2674  ------AEDQPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELI---EGSRDD  2826

Query  312   AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQ  371
             +  ++ ++  ++ +W  +   S++ ++ LEA+  Q +  H  +  LL WL   +  L   
Sbjct  2827  SSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRFH  3006

Query  372   APIGGDFPAVQKQNDVHRAFKRELKTK  398
               +  D  A++   D H+ F ++L+ K
Sbjct  3007  GVLPDDEDALRTLIDQHKEFMKKLEEK  3087


 Score = 62.8 bits (151),  Expect = 1e-06, Method: Compositional matrix adjust.
 Identities = 103/489 (21%), Positives = 209/489 (42%), Gaps = 43/489 (8%)
 Frame = +1

Query  24    DWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSN  83
             DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K + 
Sbjct  1003  DWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKVTE  1182

Query  84    QEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKL  143
             +  +  + D +  ++  WD ++E + NR+ +L   L    Q+  A +E    L      L
Sbjct  1183  ESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQHALDELLAWLTHTEGLL  1362

Query  144   ESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMIT  203
                K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +    
Sbjct  1363  SEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQNKL  1542

Query  204   ENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER  263
             E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              ER
Sbjct  1543  EVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLQQWLTDT-------------ER  1683

Query  264   LLEDSK---GVKELMKQWQDLQGEI----EAHTDVYHNLDENSQKILRSLEGSDDAVLLQ  316
              L  SK   G+ E  K+  ++  E+    EA  + Y +L +  Q++L     S +  + Q
Sbjct  1684  HLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLARCPKSAETNIDQ  1863

Query  317   RRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGG  376
               ++N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +    
Sbjct  1864  -DINNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRPSL  2040

Query  377   DFPAVQKQNDVHRAFKRELKTKEPVIMSTLET---VRIFLTEQPLEGLEKLYQEPRELPP  433
                 V  Q D H+ F  E+ +    I+   +T   ++ F  +Q +  ++ L      +  
Sbjct  2041  ILDTVLFQIDEHKVFANEVNSHREQIIELDKTGTHLKYFSQKQDVVLIKNLL-----ISV  2205

Query  434   EERAQNVTRLL----------RKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEAT  483
             + R + V + L          RK+A++ +  W KL     +W  + +++L+   E+    
Sbjct  2206  QSRWEKVVQRLVERGRSLDDARKRAKQFHEAWSKL----MEWLEESEKSLDSELEIANDP  2373

Query  484   DELDLKLRQ  492
             D++  +L Q
Sbjct  2374  DKIKTQLAQ  2400


 Score = 53.5 bits (127),  Expect = 6e-04, Method: Compositional matrix adjust.
 Identities = 64/278 (23%), Positives = 123/278 (44%), Gaps = 6/278 (2%)
 Frame = +1

Query  15    FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
             F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  2287  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  2466

Query  75    QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
             ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  2467  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  2646

Query  135   VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
              L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  2647  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELI-EGSRD  2823

Query  195   DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA--  252
             D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T   
Sbjct  2824  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRF  3003

Query  253   -NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHT  289
               VL D     R L D    KE MK+ ++ + E+   T
Sbjct  3004  HGVLPDDEDALRTLIDQH--KEFMKKLEEKRAELNKAT  3111


 Score = 50.8 bits (120),  Expect = 0.004, Method: Compositional matrix adjust.
 Identities = 79/352 (22%), Positives = 141/352 (40%), Gaps = 48/352 (13%)
 Frame = +1

Query  174   QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
             Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  796   QEELDIVINLGSELIAACGEPDKPIVKKSIDELNSAWDSLNKAWKDRIDKLEEAMQAAVQ  975

Query  234   FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
             +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  976   YQDGLQAVFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  1131

Query  292   YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  1132  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQ  1311

Query  352   LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
              +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  1312  HALDELLAWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  1443

Query  412   FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  1444  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  1581

Query  472   TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRG  523
             T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G
Sbjct  1582  TEQRKQ-------QLDGALRQAKGFHGEIEDLQQWLTDT-ERHLLASKPLGG  1713


>ref|NM_001144771.1| Homo sapiens dystonin (DST), transcript variant 4, mRNA
Length=17656

 Score = 87.8 bits (216),  Expect = 4e-14, Method: Compositional matrix adjust.
 Identities = 137/602 (22%), Positives = 252/602 (41%), Gaps = 81/602 (13%)
 Frame = +3

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  13002  ALGQFQHALDELLAWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13181

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  13182  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  13358

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQ-----LAK  168
              D  QWL   E    A + LG     A+ +L    E     +A ++      Q     LA+
Sbjct  13359  DLQQWLTDTERHLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLAR  13538

Query  169    DLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETH  228
                +  +TN+D          +D +            N+   W S+  +++ER+  LEE  
Sbjct  13539  CPKSAETNID----------QDIN------------NLKEKWESVETKLNERKTKLEEAL  13652

Query  229    RLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAH  288
               L  +F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H
Sbjct  13653  NLAMEFHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSH  13814

Query  289    TDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWK  348
               +    LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K
Sbjct  13815  REQIIELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAK  13991

Query  349    RLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
              + H +  +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T
Sbjct  13992  QFHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT  14171

Query  409    VRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRK  468
                                  R L  +    +    L     E+  +W+ +   S + Q K
Sbjct  14172  -------------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNK  14294

Query  469    IDETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAP  527
              ++E L    +  +A   L   L + E      QPV GD  ID + + ++  KA + E+  
Sbjct  14295  LEEALLFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKAFQKELGK  14468

Query  528    LKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHE  580
                 +V  +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E
Sbjct  14469  RTSSVQALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEE  14648

Query  581    AH  582
               H
Sbjct  14649  FH  14654


 Score = 65.5 bits (158),  Expect = 2e-07, Method: Compositional matrix adjust.
 Identities = 87/387 (22%), Positives = 174/387 (44%), Gaps = 12/387 (3%)
 Frame = +3

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+ +  +  +WL+  +Q +         L+ +   I + K    ++   R Q+ EL   
Sbjct  13665  EFHNSLQDFINWLTQAEQTLNVASRPSLILDTVLFQIDEHKVFANEVNSHREQIIELDKT  13844

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE  133
                +LK  +  Q+   +I + +  +Q++W++V + L  R + L++  K + Q+ EA  +  
Sbjct  13845  GTHLKYFSQKQDV-VLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEAWSKLM  14021

Query  134    QVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-  192
              + L ++   L+S  E     D I+ ++ + K+  K L    +  D  N     L    S 
Sbjct  14022  EWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTGRSLKEKTSL  14201

Query  193    ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
              ADD  K+  +   +   W +I  +  ER+  LEE      QF   L+  + WL   E   
Sbjct  14202  ADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALIDWLYRVE--P  14375

Query  253    NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGS-DD  311
               + +D    + +  D   V  L+   +  Q E+   T     L  ++++++   EGS DD
Sbjct  14376  QLAED----QPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELI---EGSRDD  14534

Query  312    AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQ  371
              +  ++ ++  ++ +W  +   S++ ++ LEA+  Q +  H  +  LL WL   +  L   
Sbjct  14535  SSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRFH  14714

Query  372    APIGGDFPAVQKQNDVHRAFKRELKTK  398
                +  D  A++   D H+ F ++L+ K
Sbjct  14715  GVLPDDEDALRTLIDQHKEFMKKLEEK  14795


 Score = 62.0 bits (149),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 85/387 (21%), Positives = 167/387 (43%), Gaps = 22/387 (5%)
 Frame = +3

Query  24     DWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSN  83
              DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K + 
Sbjct  12711  DWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKVTE  12890

Query  84     QEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKL  143
              +  +  + D +  ++  WD ++E + NR+ +L   L    Q+  A +E    L      L
Sbjct  12891  ESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQHALDELLAWLTHTEGLL  13070

Query  144    ESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMIT  203
                 K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +    
Sbjct  13071  SEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQNKL  13250

Query  204    ENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER  263
              E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              ER
Sbjct  13251  EVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLQQWLTDT-------------ER  13391

Query  264    LLEDSK---GVKELMKQWQDLQGEI----EAHTDVYHNLDENSQKILRSLEGSDDAVLLQ  316
               L  SK   G+ E  K+  ++  E+    EA  + Y +L +  Q++L     S +  + Q
Sbjct  13392  HLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLARCPKSAETNIDQ  13571

Query  317    RRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGG  376
                ++N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +    
Sbjct  13572  -DINNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRPSL  13748

Query  377    DFPAVQKQNDVHRAFKRELKT-KEPVI  402
                  V  Q D H+ F  E+ + +E +I
Sbjct  13749  ILDTVLFQIDEHKVFANEVNSHREQII  13829


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 64/278 (23%), Positives = 123/278 (44%), Gaps = 6/278 (2%)
 Frame = +3

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  13995  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  14174

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  14175  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  14354

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  14355  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELI-EGSRD  14531

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA--  252
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T   
Sbjct  14532  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRF  14711

Query  253    -NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHT  289
                VL D     R L D    KE MK+ ++ + E+   T
Sbjct  14712  HGVLPDDEDALRTLIDQH--KEFMKKLEEKRAELNKAT  14819


 Score = 50.8 bits (120),  Expect = 0.004, Method: Compositional matrix adjust.
 Identities = 79/352 (22%), Positives = 141/352 (40%), Gaps = 48/352 (13%)
 Frame = +3

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12504  QEELDIVINLGSELIAACGEPDKPIVKKSIDELNSAWDSLNKAWKDRIDKLEEAMQAAVQ  12683

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  12684  YQDGLQAVFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  12839

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  12840  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQ  13019

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  13020  HALDELLAWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  13151

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  13152  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  13289

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRG  523
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G
Sbjct  13290  TEQRKQ-------QLDGALRQAKGFHGEIEDLQQWLTDT-ERHLLASKPLGG  13421


>ref|NM_001144770.1| Homo sapiens dystonin (DST), transcript variant 3, mRNA
Length=17774

 Score = 87.8 bits (216),  Expect = 4e-14, Method: Compositional matrix adjust.
 Identities = 137/602 (22%), Positives = 252/602 (41%), Gaps = 81/602 (13%)
 Frame = +1

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  13120  ALGQFQHALDELLAWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13299

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  13300  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  13476

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQ-----LAK  168
              D  QWL   E    A + LG     A+ +L    E     +A ++      Q     LA+
Sbjct  13477  DLQQWLTDTERHLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLAR  13656

Query  169    DLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETH  228
                +  +TN+D          +D +            N+   W S+  +++ER+  LEE  
Sbjct  13657  CPKSAETNID----------QDIN------------NLKEKWESVETKLNERKTKLEEAL  13770

Query  229    RLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAH  288
               L  +F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H
Sbjct  13771  NLAMEFHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSH  13932

Query  289    TDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWK  348
               +    LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K
Sbjct  13933  REQIIELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAK  14109

Query  349    RLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
              + H +  +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T
Sbjct  14110  QFHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT  14289

Query  409    VRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRK  468
                                  R L  +    +    L     E+  +W+ +   S + Q K
Sbjct  14290  -------------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNK  14412

Query  469    IDETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAP  527
              ++E L    +  +A   L   L + E      QPV GD  ID + + ++  KA + E+  
Sbjct  14413  LEEALLFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKAFQKELGK  14586

Query  528    LKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHE  580
                 +V  +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E
Sbjct  14587  RTSSVQALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEE  14766

Query  581    AH  582
               H
Sbjct  14767  FH  14772


 Score = 65.5 bits (158),  Expect = 2e-07, Method: Compositional matrix adjust.
 Identities = 87/387 (22%), Positives = 174/387 (44%), Gaps = 12/387 (3%)
 Frame = +1

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+ +  +  +WL+  +Q +         L+ +   I + K    ++   R Q+ EL   
Sbjct  13783  EFHNSLQDFINWLTQAEQTLNVASRPSLILDTVLFQIDEHKVFANEVNSHREQIIELDKT  13962

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE  133
                +LK  +  Q+   +I + +  +Q++W++V + L  R + L++  K + Q+ EA  +  
Sbjct  13963  GTHLKYFSQKQDV-VLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEAWSKLM  14139

Query  134    QVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-  192
              + L ++   L+S  E     D I+ ++ + K+  K L    +  D  N     L    S 
Sbjct  14140  EWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTGRSLKEKTSL  14319

Query  193    ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
              ADD  K+  +   +   W +I  +  ER+  LEE      QF   L+  + WL   E   
Sbjct  14320  ADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALIDWLYRVE--P  14493

Query  253    NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGS-DD  311
               + +D    + +  D   V  L+   +  Q E+   T     L  ++++++   EGS DD
Sbjct  14494  QLAED----QPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELI---EGSRDD  14652

Query  312    AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQ  371
              +  ++ ++  ++ +W  +   S++ ++ LEA+  Q +  H  +  LL WL   +  L   
Sbjct  14653  SSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRFH  14832

Query  372    APIGGDFPAVQKQNDVHRAFKRELKTK  398
                +  D  A++   D H+ F ++L+ K
Sbjct  14833  GVLPDDEDALRTLIDQHKEFMKKLEEK  14913


 Score = 62.0 bits (149),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 85/387 (21%), Positives = 167/387 (43%), Gaps = 22/387 (5%)
 Frame = +1

Query  24     DWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSN  83
              DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K + 
Sbjct  12829  DWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKVTE  13008

Query  84     QEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKL  143
              +  +  + D +  ++  WD ++E + NR+ +L   L    Q+  A +E    L      L
Sbjct  13009  ESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQHALDELLAWLTHTEGLL  13188

Query  144    ESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMIT  203
                 K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +    
Sbjct  13189  SEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQNKL  13368

Query  204    ENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER  263
              E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              ER
Sbjct  13369  EVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLQQWLTDT-------------ER  13509

Query  264    LLEDSK---GVKELMKQWQDLQGEI----EAHTDVYHNLDENSQKILRSLEGSDDAVLLQ  316
               L  SK   G+ E  K+  ++  E+    EA  + Y +L +  Q++L     S +  + Q
Sbjct  13510  HLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLARCPKSAETNIDQ  13689

Query  317    RRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGG  376
                ++N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +    
Sbjct  13690  -DINNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRPSL  13866

Query  377    DFPAVQKQNDVHRAFKRELKT-KEPVI  402
                  V  Q D H+ F  E+ + +E +I
Sbjct  13867  ILDTVLFQIDEHKVFANEVNSHREQII  13947


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 64/278 (23%), Positives = 123/278 (44%), Gaps = 6/278 (2%)
 Frame = +1

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  14113  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  14292

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  14293  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  14472

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  14473  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELI-EGSRD  14649

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA--  252
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T   
Sbjct  14650  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRF  14829

Query  253    -NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHT  289
                VL D     R L D    KE MK+ ++ + E+   T
Sbjct  14830  HGVLPDDEDALRTLIDQH--KEFMKKLEEKRAELNKAT  14937


 Score = 50.8 bits (120),  Expect = 0.004, Method: Compositional matrix adjust.
 Identities = 79/352 (22%), Positives = 141/352 (40%), Gaps = 48/352 (13%)
 Frame = +1

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12622  QEELDIVINLGSELIAACGEPDKPIVKKSIDELNSAWDSLNKAWKDRIDKLEEAMQAAVQ  12801

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  12802  YQDGLQAVFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  12957

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  12958  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQ  13137

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  13138  HALDELLAWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  13269

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  13270  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  13407

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRG  523
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G
Sbjct  13408  TEQRKQ-------QLDGALRQAKGFHGEIEDLQQWLTDT-ERHLLASKPLGG  13539


>ref|NM_001144769.1| Homo sapiens dystonin (DST), transcript variant 2, mRNA
Length=18090

 Score = 87.8 bits (216),  Expect = 4e-14, Method: Compositional matrix adjust.
 Identities = 137/602 (22%), Positives = 252/602 (41%), Gaps = 81/602 (13%)
 Frame = +2

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  13436  ALGQFQHALDELLAWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13615

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  13616  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  13792

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQ-----LAK  168
              D  QWL   E    A + LG     A+ +L    E     +A ++      Q     LA+
Sbjct  13793  DLQQWLTDTERHLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLAR  13972

Query  169    DLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETH  228
                +  +TN+D          +D +            N+   W S+  +++ER+  LEE  
Sbjct  13973  CPKSAETNID----------QDIN------------NLKEKWESVETKLNERKTKLEEAL  14086

Query  229    RLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAH  288
               L  +F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H
Sbjct  14087  NLAMEFHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSH  14248

Query  289    TDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWK  348
               +    LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K
Sbjct  14249  REQIIELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAK  14425

Query  349    RLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
              + H +  +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T
Sbjct  14426  QFHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT  14605

Query  409    VRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRK  468
                                  R L  +    +    L     E+  +W+ +   S + Q K
Sbjct  14606  -------------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNK  14728

Query  469    IDETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAP  527
              ++E L    +  +A   L   L + E      QPV GD  ID + + ++  KA + E+  
Sbjct  14729  LEEALLFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKAFQKELGK  14902

Query  528    LKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHE  580
                 +V  +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E
Sbjct  14903  RTSSVQALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEE  15082

Query  581    AH  582
               H
Sbjct  15083  FH  15088


 Score = 65.5 bits (158),  Expect = 2e-07, Method: Compositional matrix adjust.
 Identities = 87/387 (22%), Positives = 174/387 (44%), Gaps = 12/387 (3%)
 Frame = +2

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+ +  +  +WL+  +Q +         L+ +   I + K    ++   R Q+ EL   
Sbjct  14099  EFHNSLQDFINWLTQAEQTLNVASRPSLILDTVLFQIDEHKVFANEVNSHREQIIELDKT  14278

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE  133
                +LK  +  Q+   +I + +  +Q++W++V + L  R + L++  K + Q+ EA  +  
Sbjct  14279  GTHLKYFSQKQDV-VLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEAWSKLM  14455

Query  134    QVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-  192
              + L ++   L+S  E     D I+ ++ + K+  K L    +  D  N     L    S 
Sbjct  14456  EWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTGRSLKEKTSL  14635

Query  193    ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
              ADD  K+  +   +   W +I  +  ER+  LEE      QF   L+  + WL   E   
Sbjct  14636  ADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALIDWLYRVE--P  14809

Query  253    NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGS-DD  311
               + +D    + +  D   V  L+   +  Q E+   T     L  ++++++   EGS DD
Sbjct  14810  QLAED----QPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELI---EGSRDD  14968

Query  312    AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQ  371
              +  ++ ++  ++ +W  +   S++ ++ LEA+  Q +  H  +  LL WL   +  L   
Sbjct  14969  SSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRFH  15148

Query  372    APIGGDFPAVQKQNDVHRAFKRELKTK  398
                +  D  A++   D H+ F ++L+ K
Sbjct  15149  GVLPDDEDALRTLIDQHKEFMKKLEEK  15229


 Score = 62.0 bits (149),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 85/387 (21%), Positives = 167/387 (43%), Gaps = 22/387 (5%)
 Frame = +2

Query  24     DWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSN  83
              DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K + 
Sbjct  13145  DWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKVTE  13324

Query  84     QEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKL  143
              +  +  + D +  ++  WD ++E + NR+ +L   L    Q+  A +E    L      L
Sbjct  13325  ESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQHALDELLAWLTHTEGLL  13504

Query  144    ESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMIT  203
                 K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +    
Sbjct  13505  SEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQNKL  13684

Query  204    ENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER  263
              E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              ER
Sbjct  13685  EVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLQQWLTDT-------------ER  13825

Query  264    LLEDSK---GVKELMKQWQDLQGEI----EAHTDVYHNLDENSQKILRSLEGSDDAVLLQ  316
               L  SK   G+ E  K+  ++  E+    EA  + Y +L +  Q++L     S +  + Q
Sbjct  13826  HLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLARCPKSAETNIDQ  14005

Query  317    RRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGG  376
                ++N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +    
Sbjct  14006  -DINNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRPSL  14182

Query  377    DFPAVQKQNDVHRAFKRELKT-KEPVI  402
                  V  Q D H+ F  E+ + +E +I
Sbjct  14183  ILDTVLFQIDEHKVFANEVNSHREQII  14263


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 64/278 (23%), Positives = 123/278 (44%), Gaps = 6/278 (2%)
 Frame = +2

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  14429  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  14608

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  14609  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  14788

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  14789  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELI-EGSRD  14965

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA--  252
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T   
Sbjct  14966  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRF  15145

Query  253    -NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHT  289
                VL D     R L D    KE MK+ ++ + E+   T
Sbjct  15146  HGVLPDDEDALRTLIDQH--KEFMKKLEEKRAELNKAT  15253


 Score = 50.8 bits (120),  Expect = 0.004, Method: Compositional matrix adjust.
 Identities = 79/352 (22%), Positives = 141/352 (40%), Gaps = 48/352 (13%)
 Frame = +2

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12938  QEELDIVINLGSELIAACGEPDKPIVKKSIDELNSAWDSLNKAWKDRIDKLEEAMQAAVQ  13117

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  13118  YQDGLQAVFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  13273

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  13274  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQ  13453

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  13454  HALDELLAWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  13585

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  13586  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  13723

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRG  523
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G
Sbjct  13724  TEQRKQ-------QLDGALRQAKGFHGEIEDLQQWLTDT-ERHLLASKPLGG  13855


>ref|NM_183380.2| Homo sapiens dystonin (DST), transcript variant 1, mRNA
Length=18035

 Score = 87.8 bits (216),  Expect = 4e-14, Method: Compositional matrix adjust.
 Identities = 137/602 (22%), Positives = 252/602 (41%), Gaps = 81/602 (13%)
 Frame = +2

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  13394  ALGQFQHALDELLAWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13573

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  13574  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  13750

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQ-----LAK  168
              D  QWL   E    A + LG     A+ +L    E     +A ++      Q     LA+
Sbjct  13751  DLQQWLTDTERHLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLAR  13930

Query  169    DLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETH  228
                +  +TN+D          +D +            N+   W S+  +++ER+  LEE  
Sbjct  13931  CPKSAETNID----------QDIN------------NLKEKWESVETKLNERKTKLEEAL  14044

Query  229    RLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAH  288
               L  +F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H
Sbjct  14045  NLAMEFHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSH  14206

Query  289    TDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWK  348
               +    LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K
Sbjct  14207  REQIIELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAK  14383

Query  349    RLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
              + H +  +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T
Sbjct  14384  QFHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT  14563

Query  409    VRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRK  468
                                  R L  +    +    L     E+  +W+ +   S + Q K
Sbjct  14564  -------------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNK  14686

Query  469    IDETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAP  527
              ++E L    +  +A   L   L + E      QPV GD  ID + + ++  KA + E+  
Sbjct  14687  LEEALLFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKAFQKELGK  14860

Query  528    LKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHE  580
                 +V  +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E
Sbjct  14861  RTSSVQALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEE  15040

Query  581    AH  582
               H
Sbjct  15041  FH  15046


 Score = 65.5 bits (158),  Expect = 2e-07, Method: Compositional matrix adjust.
 Identities = 87/387 (22%), Positives = 174/387 (44%), Gaps = 12/387 (3%)
 Frame = +2

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+ +  +  +WL+  +Q +         L+ +   I + K    ++   R Q+ EL   
Sbjct  14057  EFHNSLQDFINWLTQAEQTLNVASRPSLILDTVLFQIDEHKVFANEVNSHREQIIELDKT  14236

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE  133
                +LK  +  Q+   +I + +  +Q++W++V + L  R + L++  K + Q+ EA  +  
Sbjct  14237  GTHLKYFSQKQDV-VLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEAWSKLM  14413

Query  134    QVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-  192
              + L ++   L+S  E     D I+ ++ + K+  K L    +  D  N     L    S 
Sbjct  14414  EWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTGRSLKEKTSL  14593

Query  193    ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
              ADD  K+  +   +   W +I  +  ER+  LEE      QF   L+  + WL   E   
Sbjct  14594  ADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALIDWLYRVE--P  14767

Query  253    NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGS-DD  311
               + +D    + +  D   V  L+   +  Q E+   T     L  ++++++   EGS DD
Sbjct  14768  QLAED----QPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELI---EGSRDD  14926

Query  312    AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQ  371
              +  ++ ++  ++ +W  +   S++ ++ LEA+  Q +  H  +  LL WL   +  L   
Sbjct  14927  SSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRFH  15106

Query  372    APIGGDFPAVQKQNDVHRAFKRELKTK  398
                +  D  A++   D H+ F ++L+ K
Sbjct  15107  GVLPDDEDALRTLIDQHKEFMKKLEEK  15187


 Score = 62.0 bits (149),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 85/387 (21%), Positives = 167/387 (43%), Gaps = 22/387 (5%)
 Frame = +2

Query  24     DWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSN  83
              DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K + 
Sbjct  13103  DWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKVTE  13282

Query  84     QEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKL  143
              +  +  + D +  ++  WD ++E + NR+ +L   L    Q+  A +E    L      L
Sbjct  13283  ESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQHALDELLAWLTHTEGLL  13462

Query  144    ESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMIT  203
                 K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +    
Sbjct  13463  SEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQNKL  13642

Query  204    ENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER  263
              E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              ER
Sbjct  13643  EVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLQQWLTDT-------------ER  13783

Query  264    LLEDSK---GVKELMKQWQDLQGEI----EAHTDVYHNLDENSQKILRSLEGSDDAVLLQ  316
               L  SK   G+ E  K+  ++  E+    EA  + Y +L +  Q++L     S +  + Q
Sbjct  13784  HLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLARCPKSAETNIDQ  13963

Query  317    RRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGG  376
                ++N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +    
Sbjct  13964  -DINNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRPSL  14140

Query  377    DFPAVQKQNDVHRAFKRELKT-KEPVI  402
                  V  Q D H+ F  E+ + +E +I
Sbjct  14141  ILDTVLFQIDEHKVFANEVNSHREQII  14221


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 64/278 (23%), Positives = 123/278 (44%), Gaps = 6/278 (2%)
 Frame = +2

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  14387  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  14566

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  14567  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  14746

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  14747  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELI-EGSRD  14923

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA--  252
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T   
Sbjct  14924  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRF  15103

Query  253    -NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHT  289
                VL D     R L D    KE MK+ ++ + E+   T
Sbjct  15104  HGVLPDDEDALRTLIDQH--KEFMKKLEEKRAELNKAT  15211


 Score = 50.8 bits (120),  Expect = 0.004, Method: Compositional matrix adjust.
 Identities = 79/352 (22%), Positives = 141/352 (40%), Gaps = 48/352 (13%)
 Frame = +2

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12896  QEELDIVINLGSELIAACGEPDKPIVKKSIDELNSAWDSLNKAWKDRIDKLEEAMQAAVQ  13075

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  13076  YQDGLQAVFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  13231

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  13232  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQ  13411

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  13412  HALDELLAWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  13543

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  13544  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  13681

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRG  523
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G
Sbjct  13682  TEQRKQ-------QLDGALRQAKGFHGEIEDLQQWLTDT-ERHLLASKPLGG  13813


>ref|NM_015548.3| Homo sapiens dystonin (DST), transcript variant 1eA, mRNA
Length=16645

 Score = 87.8 bits (216),  Expect = 4e-14, Method: Compositional matrix adjust.
 Identities = 137/602 (22%), Positives = 252/602 (41%), Gaps = 81/602 (13%)
 Frame = +1

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  12004  ALGQFQHALDELLAWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  12183

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  12184  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  12360

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQ-----LAK  168
              D  QWL   E    A + LG     A+ +L    E     +A ++      Q     LA+
Sbjct  12361  DLQQWLTDTERHLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLAR  12540

Query  169    DLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETH  228
                +  +TN+D          +D +            N+   W S+  +++ER+  LEE  
Sbjct  12541  CPKSAETNID----------QDIN------------NLKEKWESVETKLNERKTKLEEAL  12654

Query  229    RLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAH  288
               L  +F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H
Sbjct  12655  NLAMEFHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSH  12816

Query  289    TDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWK  348
               +    LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K
Sbjct  12817  REQIIELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAK  12993

Query  349    RLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
              + H +  +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T
Sbjct  12994  QFHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT  13173

Query  409    VRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRK  468
                                  R L  +    +    L     E+  +W+ +   S + Q K
Sbjct  13174  -------------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNK  13296

Query  469    IDETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAP  527
              ++E L    +  +A   L   L + E      QPV GD  ID + + ++  KA + E+  
Sbjct  13297  LEEALLFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKAFQKELGK  13470

Query  528    LKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHE  580
                 +V  +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E
Sbjct  13471  RTSSVQALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEE  13650

Query  581    AH  582
               H
Sbjct  13651  FH  13656


 Score = 65.5 bits (158),  Expect = 2e-07, Method: Compositional matrix adjust.
 Identities = 87/387 (22%), Positives = 174/387 (44%), Gaps = 12/387 (3%)
 Frame = +1

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+ +  +  +WL+  +Q +         L+ +   I + K    ++   R Q+ EL   
Sbjct  12667  EFHNSLQDFINWLTQAEQTLNVASRPSLILDTVLFQIDEHKVFANEVNSHREQIIELDKT  12846

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE  133
                +LK  +  Q+   +I + +  +Q++W++V + L  R + L++  K + Q+ EA  +  
Sbjct  12847  GTHLKYFSQKQDV-VLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEAWSKLM  13023

Query  134    QVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-  192
              + L ++   L+S  E     D I+ ++ + K+  K L    +  D  N     L    S 
Sbjct  13024  EWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTGRSLKEKTSL  13203

Query  193    ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
              ADD  K+  +   +   W +I  +  ER+  LEE      QF   L+  + WL   E   
Sbjct  13204  ADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALIDWLYRVE--P  13377

Query  253    NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGS-DD  311
               + +D    + +  D   V  L+   +  Q E+   T     L  ++++++   EGS DD
Sbjct  13378  QLAED----QPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELI---EGSRDD  13536

Query  312    AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQ  371
              +  ++ ++  ++ +W  +   S++ ++ LEA+  Q +  H  +  LL WL   +  L   
Sbjct  13537  SSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRFH  13716

Query  372    APIGGDFPAVQKQNDVHRAFKRELKTK  398
                +  D  A++   D H+ F ++L+ K
Sbjct  13717  GVLPDDEDALRTLIDQHKEFMKKLEEK  13797


 Score = 62.0 bits (149),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 85/387 (21%), Positives = 167/387 (43%), Gaps = 22/387 (5%)
 Frame = +1

Query  24     DWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSN  83
              DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K + 
Sbjct  11713  DWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKVTE  11892

Query  84     QEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKL  143
              +  +  + D +  ++  WD ++E + NR+ +L   L    Q+  A +E    L      L
Sbjct  11893  ESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQHALDELLAWLTHTEGLL  12072

Query  144    ESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMIT  203
                 K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +    
Sbjct  12073  SEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQNKL  12252

Query  204    ENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER  263
              E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              ER
Sbjct  12253  EVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLQQWLTDT-------------ER  12393

Query  264    LLEDSK---GVKELMKQWQDLQGEI----EAHTDVYHNLDENSQKILRSLEGSDDAVLLQ  316
               L  SK   G+ E  K+  ++  E+    EA  + Y +L +  Q++L     S +  + Q
Sbjct  12394  HLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLARCPKSAETNIDQ  12573

Query  317    RRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGG  376
                ++N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +    
Sbjct  12574  -DINNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRPSL  12750

Query  377    DFPAVQKQNDVHRAFKRELKT-KEPVI  402
                  V  Q D H+ F  E+ + +E +I
Sbjct  12751  ILDTVLFQIDEHKVFANEVNSHREQII  12831


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 64/278 (23%), Positives = 123/278 (44%), Gaps = 6/278 (2%)
 Frame = +1

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  12997  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  13176

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  13177  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  13356

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  13357  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELI-EGSRD  13533

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA--  252
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T   
Sbjct  13534  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRF  13713

Query  253    -NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHT  289
                VL D     R L D    KE MK+ ++ + E+   T
Sbjct  13714  HGVLPDDEDALRTLIDQH--KEFMKKLEEKRAELNKAT  13821


 Score = 50.8 bits (120),  Expect = 0.004, Method: Compositional matrix adjust.
 Identities = 79/352 (22%), Positives = 141/352 (40%), Gaps = 48/352 (13%)
 Frame = +1

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  11506  QEELDIVINLGSELIAACGEPDKPIVKKSIDELNSAWDSLNKAWKDRIDKLEEAMQAAVQ  11685

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  11686  YQDGLQAVFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  11841

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  11842  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQ  12021

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  12022  HALDELLAWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  12153

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  12154  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  12291

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRG  523
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G
Sbjct  12292  TEQRKQ-------QLDGALRQAKGFHGEIEDLQQWLTDT-ERHLLASKPLGG  12423


>ref|XM_001995054.1| Drosophila grimshawi GH22959 (Dgri\GH22959), mRNA
Length=16200

 Score = 87.4 bits (215),  Expect = 4e-14, Method: Compositional matrix adjust.
 Identities = 104/502 (20%), Positives = 225/502 (44%), Gaps = 26/502 (5%)
 Frame = +1

Query  29     LDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEART  88
              L++ +  Q       +DI +  +  +    +++Q +P++E++     NL N     + + 
Sbjct  11755  LEETLSCQEPPAAQPQDIKKQQVALQEIRHEIDQTKPEVEQVRRHGSNLMNMCGEPD-KP  11931

Query  89     IITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKE  148
               +   IE + N WD +      R + L + ++ + ++ E  +   + L +A  K      
Sbjct  11932  EVKKHIEDLDNAWDNITALYAKREENLIDAMEKAMEFHETLQNLLKFLTKAEDKFAHLGA  12111

Query  149    GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINA  208
                  +DA++++I + K    ++      V+  N  A++L    S +    +      +N 
Sbjct  12112  VGSDIDAVKRQIEQLKAFKDEVDPHMVEVEALNRQAVELTERTSPEQAASIREPLTVVNR  12291

Query  209    SWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDS  268
               W S+ + + +R+  LE     L QF   L + L W+ + ++T + L+      +LLE  
Sbjct  12292  RWESLLRGMVDRQKQLEHALLHLGQFQHALNELLVWINKTDSTLDQLKPIPGDPQLLE--  12465

Query  269    KGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSE  328
                  EL K  + L  +I+AH +    L++  ++++ + +GS +A   Q +L  +N +W +
Sbjct  12466  ---VELAK-LKVLANDIQAHQNSVDTLNDAGRQLIETEKGSVEASTTQEKLRKLNNEWKQ  12633

Query  329    LRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVH  388
              L +K+ + +  LE S  + +     +Q++L WL   D  +    P+GG      +Q +  
Sbjct  12634  LLQKASDRQHELEESLREAQGYIAEVQDILGWLGDVDAVIGASKPVGGLPETATEQLERF  12813

Query  389    RAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQA  448
                   EL    P +    ET++        +G E + ++ +   P    Q+  R L+++ 
Sbjct  12814  MEVYNELDENRPKV----ETIQA-------QGQEYIKRQNQMKVPSSNLQHTLRTLKQR-  12957

Query  449    EEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLI  508
                    W+ +   ++D + K++  L+   E  +        L QAE    + +PV  +L 
Sbjct  12958  ------WDAVVSRASDKKIKLEIALKEATEFHDTLQAFVEWLTQAEKQLSNAEPVSRVL-  13116

Query  509    DSLQDHLEKVKALRGEIAPLKE  530
              +++Q  +E+ K L+ +++  +E
Sbjct  13117  ETIQAQMEEHKVLQKDVSTHRE  13182


 Score = 54.7 bits (130),  Expect = 3e-04, Method: Compositional matrix adjust.
 Identities = 114/586 (19%), Positives = 252/586 (43%), Gaps = 49/586 (8%)
 Frame = +1

Query  21     ELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNK  80
              EL +W   +D  ++   +   + + +   + + ++   D+  ++ ++ ++  A++ +  +
Sbjct  10738  ELLEWFREMDTTLREADLPAMEPKLVRAQLQEHRSINDDISSQKGRVRDVTAASKKVLRE  10917

Query  81     TSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQAR  140
              +   E    + ++++ ++   D V +    R   L + L  S  + ++ +     L +  
Sbjct  10918  SPQSENTATLREKLDDLKEIVDTVAQLCSERLGILEQALPLSEHFADSHQGLTTWLDEME  11097

Query  141    AKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVH  200
               ++          D I  +  + ++L   + + +  +D  N     L    + DD+ K++
Sbjct  11098  QQISRLSMPALRPDQITLQQDKNERLLHSIAEHKPLLDKLNKTGEALGALVADDDSAKIN  11277

Query  201    MITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATR  260
               I +  NA + ++   + ER+ ALE   +   QF   LE  L  L      AN +    +
Sbjct  11278  EILDTDNARYAALRLELRERQQALENALQESSQFSDKLEGMLRAL------ANTVDQVNQ  11439

Query  261    KERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKIL-RSLEGSDDAVL-LQRR  318
               + L    + ++E ++    L  +++   D +  +   +  ++ ++   +D AV  ++ +
Sbjct  11440  LDPLSALPQKIREQIEDNDALMDDLDKRQDAFSAVQRAANDVIAKAGNKADPAVRDIKAK  11619

Query  319    LDNMNFKWSEL----RKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE--LSRQA  372
              L+ +N  W+++    +K+  ++   L  +   WK+L+  ++       LKD E  LS Q 
Sbjct  11620  LEKLNTLWNDVQKATKKRGSSLDDILSVAEPFWKQLNSVMK------TLKDLEETLSCQE  11781

Query  373    PIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELP  432
              P       ++KQ    +  + E+   +P +    E VR   +      L  +  EP +  
Sbjct  11782  PPAAQPQDIKKQQVALQEIRHEIDQTKPEV----EQVRRHGS-----NLMNMCGEPDK--  11928

Query  433    PEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQ  492
              PE         ++K  E+++  W+ +    A  +  + + +E+  E  E    L   L +
Sbjct  11929  PE---------VKKHIEDLDNAWDNITALYAKREENLIDAMEKAMEFHETLQNLLKFLTK  12081

Query  493    AEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLARQLTTLGIQLSPY  552
              AE        VG   ID+++  +E++KA + E+ P   ++  V  L RQ   L  + SP 
Sbjct  12082  AEDKFAHLGAVGS-DIDAVKRQIEQLKAFKDEVDP---HMVEVEALNRQAVELTERTSPE  12249

Query  553    NLSTLED----LNTRWKLLQVAVEDRVRQLHEAHRDFGPASQHFLS  594
                +++ +    +N RW+ L   + DR +QL  A    G   QH L+
Sbjct  12250  QAASIREPLTVVNRRWESLLRGMVDRQKQLEHALLHLG-QFQHALN  12384


 Score = 49.3 bits (116),  Expect = 0.014, Method: Compositional matrix adjust.
 Identities = 88/413 (21%), Positives = 167/413 (40%), Gaps = 34/413 (8%)
 Frame = +1

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+       +WL+  ++ + +   +   LE I   + + K   +D+   R  +  L   
Sbjct  13027  EFHDTLQAFVEWLTQAEKQLSNAEPVSRVLETIQAQMEEHKVLQKDVSTHREAMLLLDKK  13206

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEA-----  128
                +LK  +  Q+   +I + +  +Q++W+ V      R + L+   K++ ++ +A     
Sbjct  13207  GTHLKYFSQKQDV-ILIKNLLVSVQHRWERVVSKAAERTRALDHGYKEAREFNDAWNGMM  13383

Query  129    --KEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALK  186
                 +E EQVL Q   +  + KE P  +     K+ ET    + L   Q+  D        
Sbjct  13384  QYLQETEQVLDQIIEEATASKE-PQKIKKYIIKLKETH---RQLGAKQSVYDATMRTGKN  13551

Query  187    LLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
              L+      D   +  +   +   W  +  +  ER+  LEE   L  QF   L + L WL 
Sbjct  13552  LMERAPKGDRPVLDKMLLELKEQWTRVWSKSIERQRKLEEALLLSGQFSDALGELLEWLK  13731

Query  247    EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENS---QKIL  303
              +A            K RL E+     +L    + +QG  E H  +  +L + +   Q +L
Sbjct  13732  KA------------KSRLNENGPVHGDL----ETVQGLCEHHKHIEQDLQKRAAQMQGVL  13863

Query  304    ---RSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
                 R LE S +   +  +LD +   W E++         LE +    ++L+  +Q L  W
Sbjct  13864  KTGRDLERSGNNPEVGAKLDELQSIWDEVQNAVGKRGERLEVALTDAEKLNARVQALFDW  14043

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFL  413
              L   +++L        D    ++  D+H  F ++L+ +E     T E   + +
Sbjct  14044  LDHAENKLRYAKNAPDDEKVSREMMDIHMEFMKDLRVREREKSETFEYAEVII  14202


 Score = 46.6 bits (109),  Expect = 0.093, Method: Compositional matrix adjust.
 Identities = 66/363 (18%), Positives = 152/363 (41%), Gaps = 25/363 (6%)
 Frame = +1

Query  26     LSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELIT-------------  72
              L  L +    Q   + D++D++E   + K    +L+Q R Q E+                
Sbjct  9091   LKALREFYDMQSQTLDDIQDVSEEFKRMKPVGSELDQIRRQQEDFRNFRERKVEPLAQNV  9270

Query  73     -----AAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
                   + ++L        +  +I   +E++ ++W++++E +  R ++L+  L  S ++ E
Sbjct  9271   DKVNMSGRDLVRSAGTGVSTNVIEKDLEKLNDRWNDLKERMNERDRRLDVALLQSGKFQE  9450

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
              A     + L      + + K        ++ ++ E K L K L   Q ++    +L  ++
Sbjct  9451   ALAGLSKWLSDTEEMVANQKSPSCDYKVVKAQLQEQKFLKKMLLDRQNSMGSLANLGKEV  9630

Query  188    LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
                     +   +     ++   + ++     +RE  LEE   + ++F   +     WL  
Sbjct  9631   ASHCEPAERASIEKQLNDLMKRFDALTNGAEQREQDLEEAMEVAKRFHDKISPLELWLDN  9810

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
               E     +      E +  D + +++ +++   L  EI      + +L + + +++  L 
Sbjct  9811   TERAVKAM------ELIPTDEEKIQQRIREHDRLHDEILGKQPDFTDLADVAGQLMH-LV  9969

Query  308    GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
                ++AV L  ++  +  +++ L   S NI + L  S    + L LS Q+L+ W++  ++E
Sbjct  9970   SDEEAVNLGEKVRTVTERYTGLVDASDNIGALLAESRQGLRHLVLSYQDLVAWMESMENE  10149

Query  368    LSR  370
              L R
Sbjct  10150  LKR  10158


 Score = 45.8 bits (107),  Expect = 0.16, Method: Compositional matrix adjust.
 Identities = 57/251 (22%), Positives = 115/251 (45%), Gaps = 17/251 (6%)
 Frame = +1

Query  156   IQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-ADDTRKVHMITENINASWRSIH  214
             +Q++I E K L  DL+  Q ++D     A  LL   S A  T+KV     ++   +  + 
Sbjct  5791  LQEQIREHKVLLADLQSHQASIDSVQVSAKHLLASASNARITKKVESNLNDVTGKFEKLF  5970

Query  215   KRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDA--TRKERLLEDSKGVK  272
             ++ ++R   L++ H  L        K+L  ++  E     LQ+A  +R+  LL      +
Sbjct  5971  EKANKRGEFLDDVHGRLS-------KYLDDISNMEQRMGSLQEALDSRETSLL----ATE  6117

Query  273   ELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKK  332
             EL ++  DL  E +    ++ +   N + ++  L    D   L+ R+  +  +W  +   
Sbjct  6118  ELARRMLDLAREKDQLAPLFEDCVRNGKDLI-GLRDVTDTGALRDRIKELESQWRNI-NI  6291

Query  333   SLNIRSHLEASSDQWKRLHLSLQE-LLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAF  391
             S++ R+ L     + +  + SL++ +L WL   +  ++  AP+  D   +++QND  +  
Sbjct  6292  SIDERAKLSKQKAERQVAYESLKDDVLSWLTRTEGRVNGLAPVAIDLDKIRQQNDELKPI  6471

Query  392   KRELKTKEPVI  402
              ++ +   P I
Sbjct  6472  CKDYRDYAPTI  6504


 Score = 42.0 bits (97),  Expect = 2.1, Method: Compositional matrix adjust.
 Identities = 109/572 (19%), Positives = 229/572 (40%), Gaps = 84/572 (14%)
 Frame = +1

Query  30    DQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTI  89
             D+ IK  R ++ D+ +   ++   KA ++D+ +R+      +  A+ L+ +  N      
Sbjct  6940  DRCIKQARKILEDMYEKQSLLDTTKAQVKDILRRKSD----VPGAEQLRLENDN------  7089

Query  90    ITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDS-------TQWLEAKEEAEQVLGQARAK  142
                    IQ +W  + +  +NR    +E L+D          WL++KE    VLG     
Sbjct  7090  -------IQEKWKNLNDICKNR-IAFSEKLRDFLDTHGNLKSWLDSKERMLTVLG-----  7230

Query  143   LESWKEGPYTVD--AIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD-DTRKV  199
                    P + D   +Q ++ + + L ++ R  Q  +    +L   ++   +   D + V
Sbjct  7231  -------PISSDPRMVQSQVQQVQVLREEFRTQQPQLKHFQELGHDVVDHLAGTPDAQAV  7389

Query  200   HMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQ-DA  258
              +  +++   W  +  ++ +R  +L       ++F   + +    L       + L  D 
Sbjct  7390  ELKLKDVLTKWDDLMGKLDDRANSLGGAADSSKEFDAAVNRLREALQNISDNLDTLPLDG  7569

Query  259   TRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRR  318
               +E L           ++ ++L+ ++E    +  ++++++  +   L        +  R
Sbjct  7570  DHQENL-----------RKIENLERQLEGQRPLLADVEQSAATLCNILGDPASRADVNSR  7716

Query  319   LDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDF  378
             +  +  ++S L+KK    ++  EAS    +    +  + L WL  +   L+ +  +    
Sbjct  7717  VAALEKQYSALQKKLDTKKAETEASLRDGRHFAENCSKTLGWLSGELSNLTDRLLVSAHK  7896

Query  379   PAVQKQNDVHRAFKRELKTKE-PVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERA  437
             P +Q Q D H    RE+  +E  VIM                    L  + ++L   ER 
Sbjct  7897  PTLQHQIDTHEPIYREVMAREHEVIM--------------------LINKGKDLT--ERQ  8010

Query  438   QNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIK  497
             Q+  R +++  + +  +WEKL   + D   ++   +E  ++  + ++     LR AE   
Sbjct  8011  QD--RGVKRDLDRIQQQWEKLRREAVDRHTRLQTCMEHCKKYSQTSETFLAWLRTAEDKL  8184

Query  498   GSWQPVGDLLIDSLQDHLEKVKALRGEI---APLKENVSHVNDLARQLTTLGIQLSPYNL  554
                 P G L   +L+  L  ++  R E+   +   EN   + D    LT+  I   P   
Sbjct  8185  ADLTP-GVLSKSNLETRLRDLQTFRSEVWKHSGEFENTKGLGDTF--LTSCDIDKEPIK-  8352

Query  555   STLEDLNTRWKLLQVAVEDRVRQLHEAHRDFG  586
             + L+D+  RW+ L   +  R  ++    R  G
Sbjct  8353  AELQDIRDRWERLNNDLIARAHEIENCSRRLG  8448


 Score = 40.8 bits (94),  Expect = 4.6, Method: Compositional matrix adjust.
 Identities = 96/506 (18%), Positives = 204/506 (40%), Gaps = 67/506 (13%)
 Frame = +1

Query  93    RIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESW------  146
             +++ +  +WD++   L +R   L      S ++  A     + L      L++       
Sbjct  7396  KLKDVLTKWDDLMGKLDDRANSLGGAADSSKEFDAAVNRLREALQNISDNLDTLPLDGDH  7575

Query  147   KEGPYTVDAIQKKITETKQLAKDLRQ-WQTNVDVANDLALKLLRDYSADDTRKVHMITEN  205
             +E    ++ +++++   + L  D+ Q   T  ++  D A +      AD   +V  + + 
Sbjct  7576  QENLRKIENLERQLEGQRPLLADVEQSAATLCNILGDPASR------ADVNSRVAALEKQ  7737

Query  206   INASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLL  265
              +A  + +  + +E EA+L +     + F  +  K L WL+        L + T  +RLL
Sbjct  7738  YSALQKKLDTKKAETEASLRDG----RHFAENCSKTLGWLS------GELSNLT--DRLL  7881

Query  266   EDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAV------LLQRRL  319
                     +      LQ +I+ H  +Y  +     +++  +    D         ++R L
Sbjct  7882  --------VSAHKPTLQHQIDTHEPIYREVMAREHEVIMLINKGKDLTERQQDRGVKRDL  8037

Query  320   DNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFP  379
             D +  +W +LR+++++  + L+   +  K+   + +  L WL+  +D+L+   P      
Sbjct  8038  DRIQQQWEKLRREAVDRHTRLQTCMEHCKKYSQTSETFLAWLRTAEDKLADLTPGVLSKS  8217

Query  380   AVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQN  439
              ++ +    + F+ E+        +T      FLT   ++      +EP           
Sbjct  8218  NLETRLRDLQTFRSEVWKHSGEFENTKGLGDTFLTSCDID------KEP-----------  8346

Query  440   VTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGS  499
                 ++ + +++   WE+LN        +I+    RL +  +    LD  LR+ E    +
Sbjct  8347  ----IKAELQDIRDRWERLNNDLIARAHEIENCSRRLGDFNDELRNLDHSLRRCEDRLAA  8514

Query  500   WQPVGDLLIDSLQDHLEKVKALRGEIA----PLKENVSHVNDLARQLTTLGIQLSPYNLS  555
                +G    D     LE+VKA+R E+     PL+       D++ +    G   + +  S
Sbjct  8515  HDALGGAAKDP--KLLERVKAIREELTSLGKPLQSLKGQAKDISAEARATGGD-ADHLTS  8685

Query  556   TLEDLNTRWKLLQVAVEDRVRQLHEA  581
              ++ L  R   LQ  ++DR  +L  A
Sbjct  8686  EVDSLADRMSELQERLDDRCGELQSA  8763


>gb|AF213443.1|AF213443 Homo sapiens dystrophin (DMD) gene, exon 75 and partial cds
Length=603

 Score = 87.4 bits (215),  Expect = 4e-14, Method: Compositional matrix adjust.
 Identities = 48/63 (76%), Positives = 50/63 (79%), Gaps = 0/63 (0%)
 Frame = +1

Query  1083  AELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPS  1142
             AELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQ + E     T +    
Sbjct  1     AELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQVRREMGFLQTFIFPS*  180

Query  1143  TSL  1145
             T L
Sbjct  181   TKL  189


>gb|AF400226.1| Homo sapiens bullous pemphigoid antigen 1 eA (BPAG1) mRNA, complete 
cds
Length=16282

 Score = 86.7 bits (213),  Expect = 7e-14, Method: Compositional matrix adjust.
 Identities = 136/602 (22%), Positives = 251/602 (41%), Gaps = 81/602 (13%)
 Frame = +1

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  11896  ALGQFQHALDELLAWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  12075

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                   +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  12076  NKGGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  12252

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQ-----LAK  168
              D  QWL   E    A + LG     A+ +L    E     +A ++      Q     LA+
Sbjct  12253  DLQQWLTDTERHLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLAR  12432

Query  169    DLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETH  228
                +  +TN+D          +D +            N+   W S+  +++ER+  LEE  
Sbjct  12433  CPKSAETNID----------QDIN------------NLKEKWESVETKLNERKTKLEEAL  12546

Query  229    RLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAH  288
               L  +F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H
Sbjct  12547  NLAMEFHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSH  12708

Query  289    TDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWK  348
               +    LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K
Sbjct  12709  REQIIELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAK  12885

Query  349    RLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
              + H +  +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T
Sbjct  12886  QFHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT  13065

Query  409    VRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRK  468
                                  R L  +    +    L     E+  +W+ +   S + Q K
Sbjct  13066  -------------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNK  13188

Query  469    IDETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAP  527
              ++E L    +  +A   L   L + E      QPV GD  ID + + ++  KA + E+  
Sbjct  13189  LEEALLFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKAFQKELGK  13362

Query  528    LKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHE  580
                 +V  +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E
Sbjct  13363  RTSSVQALKRSARELIXGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEE  13542

Query  581    AH  582
               H
Sbjct  13543  FH  13548


 Score = 63.9 bits (154),  Expect = 5e-07, Method: Compositional matrix adjust.
 Identities = 84/386 (21%), Positives = 171/386 (44%), Gaps = 10/386 (2%)
 Frame = +1

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+ +  +  +WL+  +Q +         L+ +   I + K    ++   R Q+ EL   
Sbjct  12559  EFHNSLQDFINWLTQAEQTLNVASRPSLILDTVLFQIDEHKVFANEVNSHREQIIELDKT  12738

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE  133
                +LK  +  Q+   +I + +  +Q++W++V + L  R + L++  K + Q+ EA  +  
Sbjct  12739  GTHLKYFSQKQDV-VLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEAWSKLM  12915

Query  134    QVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-  192
              + L ++   L+S  E     D I+ ++ + K+  K L    +  D  N     L    S 
Sbjct  12916  EWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTGRSLKEKTSL  13095

Query  193    ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
              ADD  K+  +   +   W +I  +  ER+  LEE      QF   L+  + WL   E   
Sbjct  13096  ADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALIDWLYRVE--P  13269

Query  253    NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDA  312
               + +D    + +  D   V  L+   +  Q E+   T     L  ++++++      DD+
Sbjct  13270  QLAED----QPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELIXG--SRDDS  13431

Query  313    VLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQA  372
                ++ ++  ++ +W  +   S++ ++ LEA+  Q +  H  +  LL WL   +  L    
Sbjct  13432  SWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRFHG  13611

Query  373    PIGGDFPAVQKQNDVHRAFKRELKTK  398
               +  D  A++   D H+ F ++L+ K
Sbjct  13612  VLPDDEDALRTLIDQHKEFMKKLEEK  13689


 Score = 61.6 bits (148),  Expect = 3e-06, Method: Compositional matrix adjust.
 Identities = 85/387 (21%), Positives = 167/387 (43%), Gaps = 22/387 (5%)
 Frame = +1

Query  24     DWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSN  83
              DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K + 
Sbjct  11605  DWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKVTE  11784

Query  84     QEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKL  143
              +  +  + D +  ++  WD ++E + NR+ +L   L    Q+  A +E    L      L
Sbjct  11785  ESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQFQHALDELLAWLTHTEGLL  11964

Query  144    ESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMIT  203
                 K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +    
Sbjct  11965  SEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKGGNDLIESSAGEEASNLQNKL  12144

Query  204    ENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKER  263
              E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              ER
Sbjct  12145  EVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLQQWLTDT-------------ER  12285

Query  264    LLEDSK---GVKELMKQWQDLQGEI----EAHTDVYHNLDENSQKILRSLEGSDDAVLLQ  316
               L  SK   G+ E  K+  ++  E+    EA  + Y +L +  Q++L     S +  + Q
Sbjct  12286  HLLASKPLGGLPETAKEQLNVHMEVCAAFEAKEETYKSLMQKGQQMLARCPKSAETNIDQ  12465

Query  317    RRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGG  376
                ++N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +    
Sbjct  12466  -DINNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRPSL  12642

Query  377    DFPAVQKQNDVHRAFKRELKT-KEPVI  402
                  V  Q D H+ F  E+ + +E +I
Sbjct  12643  ILDTVLFQIDEHKVFANEVNSHREQII  12723


 Score = 52.4 bits (124),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 109/534 (20%), Positives = 216/534 (40%), Gaps = 81/534 (15%)
 Frame = +1

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMV----------GDLEDINEMIIKQKATMQDLEQRR  64
               + A ++ T +   +DQ+++S   +V           ++E I E I + K    D+E+ +
Sbjct  10882  LDEAISQSTQFHDKIDQILESLERIVERLRQPPSISAEVEKIKEQISENKNVSVDMEKLQ  11061

Query  65     PQLEELITAAQNLKNKTSNQE---ARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKD  121
              P  E L    + +  ++   +   +   + D+++++   W+ +   ++ R  +L      
Sbjct  11062  PLYETLKQRGEEMIARSGGTDKDISAKAVQDKLDQMVFIWENIHTLVEEREAKL------  11223

Query  122    STQWLEAKEEAEQVLGQARAKLESWK---------EGPYTVDAIQKKITETKQ-LAKDLR  171
                  L+  E AE+      + + + K         EGP    ++ K+  E  + + +++ 
Sbjct  11224  ----LDVMELAEKFWCDHMSLIVTIKDTQDFIRDLEGPGIDPSVVKQQQEAAETIREEID  11391

Query  172    QWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLL  231
                Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +  
Sbjct  11392  GLQEELDIVINLGSELIAACGEPDKPIVKKSIDELNSAWDSLNKAWKDRIDKLEEAMQAA  11571

Query  232    QQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHT  289
               Q+   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE   
Sbjct  11572  VQYQDGLQAVFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE---  11733

Query  290    DVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKR  349
                   L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +
Sbjct  11734  --MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLEERIINRQHKLEGALLALGQ  11907

Query  350    LHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETV  409
                 +L ELL WL   +  LS Q P+GGD  A++ +   H   + +               
Sbjct  11908  FQHALDELLAWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND---------------  12042

Query  410    RIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKI  469
               +   +  +E + K   +  E    E A N+                KL + +  WQ  +
Sbjct  12043  -VLAHQSTVEAVNKGGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVL  12177

Query  470    DETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRG  523
              ++T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G
Sbjct  12178  EKTEQRKQ-------QLDGALRQAKGFHGEIEDLQQWLTDT-ERHLLASKPLGG  12315


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 64/278 (23%), Positives = 122/278 (43%), Gaps = 6/278 (2%)
 Frame = +1

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  12889  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  13068

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  13069  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  13248

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+   S D
Sbjct  13249  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKAFQKELGKRTSSVQALKRSARELIXG-SRD  13425

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA--  252
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T   
Sbjct  13426  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQTLRF  13605

Query  253    -NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHT  289
                VL D     R L D    KE MK+ ++ + E+   T
Sbjct  13606  HGVLPDDEDALRTLIDQH--KEFMKKLEEKRAELNKAT  13713


>emb|CU677663.1| Synthetic construct Homo sapiens gateway clone IMAGE:100020365 
5' read DTNB mRNA
Length=1208

 Score = 86.7 bits (213),  Expect = 8e-14, Method: Compositional matrix adjust.
 Identities = 60/203 (29%), Positives = 103/203 (50%), Gaps = 13/203 (6%)
 Frame = +2

Query  637  DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
            + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  92   NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHTTEISVSRLETVI  271

Query  695  TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
            ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  272  SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMIAAYDSEGRGKLTVFSVKAMLATMCGGK  445

Query  751  LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
            + DK RY+F Q++ S G     +    L + +++P  + E  SFG +  E SVR+CF   
Sbjct  446  MLDKLRYVFSQMSDSNGLMIFSKFDQFLKEVLKLPTAVFEGPSFGYT--EHSVRTCFP--  613

Query  811  NNKPEIEAALFLDWMRLEPQSMV  833
              + +I   +FLD M  +P S V
Sbjct  614  -QQRKIMLNMFLDTMMADPPSPV  679


>ref|XM_001252266.1| PREDICTED: Bos taurus similar to dystonin, transcript variant 
1 (DST), mRNA
Length=16542

 Score = 86.3 bits (212),  Expect = 1e-13, Method: Compositional matrix adjust.
 Identities = 136/602 (22%), Positives = 250/602 (41%), Gaps = 81/602 (13%)
 Frame = +1

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  11914  ALGQFQHALDELLAWLTHTEGLLGEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  12093

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA ++  +++E +  +W  V E  + R+Q L+  L+          
Sbjct  12094  NKAGNDLIESSAGEEASSL-QNKLEVLNQRWQNVLEKTEQRKQHLDAALRQAKGFHGEIE  12270

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQ-----LAK  168
              D  QWL   E    A + LG     AR +L +  E     D  ++      Q     LA+
Sbjct  12271  DLQQWLTDTERHLLASKPLGGLPETAREQLNAHLEICAAFDVKEETYKNLMQKGQQMLAR  12450

Query  169    DLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETH  228
                +  +TN+D   D+                     N+   W S+  +++ER+  LEE  
Sbjct  12451  CPKSAETNID--QDI--------------------NNLKEKWESVETKLNERKVKLEEAL  12564

Query  229    RLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAH  288
               L  +F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H
Sbjct  12565  TLAMEFHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSH  12726

Query  289    TDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWK  348
               +    LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K
Sbjct  12727  REQIIELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDEARKRAK  12903

Query  349    RLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
              + H +  +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T
Sbjct  12904  QFHDAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTSRT  13083

Query  409    VRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRK  468
                                  R L  +    +    L     E+  +W+ +   S + Q K
Sbjct  13084  -------------------GRSLKEKTTLADDNLKLDDMLSELRDKWDTICGKSVERQNK  13206

Query  469    IDETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAP  527
              ++E L    +  +A   L   L + E      QPV GD  ID + + ++  K  + E+  
Sbjct  13207  LEEALLFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGK  13380

Query  528    LKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHE  580
                 +V  +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E
Sbjct  13381  RTSSVQALKRSARELIEGNQDDSSWVRVQVQELSTRWETVCALSISKQSRLEAALRQAEE  13560

Query  581    AH  582
               H
Sbjct  13561  FH  13566


 Score = 62.0 bits (149),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 85/391 (21%), Positives = 174/391 (44%), Gaps = 12/391 (3%)
 Frame = +1

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+ +  +  +WL+  +Q +         L+ +   I + K    ++   R Q+ EL   
Sbjct  12577  EFHNSLQDFINWLTQAEQTLNVASRPSLILDTVLFQIDEHKVFANEVNSHREQIIELDKT  12756

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE  133
                +LK  +  Q+   +I + +  +Q++W++V + L  R + L+E  K + Q+ +A  +  
Sbjct  12757  GTHLKYFSQKQDV-VLIKNLLISVQSRWEKVVQRLVERGRSLDEARKRAKQFHDAWSKLM  12933

Query  134    QVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-  192
              + L ++   L+S  E     D I+ ++ + K+  K L    +  D  +     L    + 
Sbjct  12934  EWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTSRTGRSLKEKTTL  13113

Query  193    ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
              ADD  K+  +   +   W +I  +  ER+  LEE      QF   L+  + WL   E   
Sbjct  13114  ADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALIDWLYRVE--P  13287

Query  253    NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGS-DD  311
               + +D    + +  D   V  L+   +  Q E+   T     L  ++++++   EG+ DD
Sbjct  13288  QLAED----QPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI---EGNQDD  13446

Query  312    AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQ  371
              +  ++ ++  ++ +W  +   S++ +S LEA+  Q +  H  +  LL WL   +  L   
Sbjct  13447  SSWVRVQVQELSTRWETVCALSISKQSRLEAALRQAEEFHSVVHALLEWLAEAEQTLRFH  13626

Query  372    APIGGDFPAVQKQNDVHRAFKRELKTKEPVI  402
                +  D  A++   D H+ F + L+ K   +
Sbjct  13627  GVLPDDEDALRTLIDQHKEFMKRLEEKRAAL  13719


 Score = 48.1 bits (113),  Expect = 0.033, Method: Compositional matrix adjust.
 Identities = 82/353 (23%), Positives = 144/353 (40%), Gaps = 50/353 (14%)
 Frame = +1

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  11416  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWDSLNKAWKDRVDRLEEAMQTAVQ  11595

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  11596  YQDGLQALFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  11751

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  11752  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  11931

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  L  Q P+GGD  A++ +   H   + ++   +    ST+E V  
Sbjct  11932  HALDELLAWLTHTEGLLGEQKPVGGDPKAIEIELAKHHVLQNDVLAHQ----STVEAVN-  12096

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQA-EEVNTEWEKLNLHSADWQRKID  470
                                      +A N   L+   A EE ++   KL + +  WQ  ++
Sbjct  12097  ------------------------KAGN--DLIESSAGEEASSLQNKLEVLNQRWQNVLE  12198

Query  471    ETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRG  523
              +T +R Q        LD  LRQA+   G  + +   L D+ + HL   K L G
Sbjct  12199  KTEQRKQ-------HLDAALRQAKGFHGEIEDLQQWLTDT-ERHLLASKPLGG  12333


 Score = 47.8 bits (112),  Expect = 0.042, Method: Compositional matrix adjust.
 Identities = 59/282 (20%), Positives = 127/282 (45%), Gaps = 17/282 (6%)
 Frame = +1

Query  57    MQDLEQRRPQLEELITAAQNLKNKTSNQEA-RTIITDRIERIQNQWDEVQEHLQNRRQQL  115
             +Q+ + R+PQ E+L TA + +  +     +    + +++  +  +WD +   L++R  ++
Sbjct  6796  LQEFDTRKPQYEQLTTAGRGILQRPGEHPSLHGTVKEQLAAVTQKWDSLTGQLRDRCDRI  6975

Query  116   NEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQT  175
             ++ +  STQ+        + L     +L S   G    DA+ +++   ++L + + Q   
Sbjct  6976  DQAVGKSTQYQSLLRSLSEKLADLDDQLSSSVAGSPHPDAMSQQLETAQKLKQAVEQEGK  7155

Query  176   NVDVA----NDLALKLLRDY-SADDTRKVHMITENINASWRSIHKRVSEREAALEETHRL  230
              +  A    +DLA  +  +Y  A+ +R++  + ++     +     V   ++A   +H+ 
Sbjct  7156  RISAAQALGDDLAALVREEYLRAELSRQLEGVLKSFKDLEQKAETHVEHLQSACASSHQ-  7332

Query  231   LQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTD  290
              QQ   D   F AWL   +   N     + K  +LE       L+K  +D +  + A + 
Sbjct  7333  FQQMSRD---FQAWLDTKKEEQNKSPLISAKVDVLES------LVKDQKDFRKTLTAQSH  7485

Query  291   VYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKK  332
             +Y       + +L   +GS + V LQ +L+ +   W  L+K+
Sbjct  7486  LYEKTIAEGENLLLKTQGS-EKVALQLQLNTIKTNWDGLQKQ  7608


 Score = 43.5 bits (101),  Expect = 0.78, Method: Compositional matrix adjust.
 Identities = 70/345 (20%), Positives = 160/345 (46%), Gaps = 16/345 (4%)
 Frame = +1

Query  54    KATMQDLEQRRPQLEELITAAQNLKNKTS-NQEARTIITDRIERIQNQWDEVQEHLQNRR  112
             KA  ++++Q    +E+L  AA +L      +QE   ++ +  E +  + D V E +  ++
Sbjct  7774  KALQKEMDQHFGLVEQLSGAAGSLLGVCEVDQE---VVAEERECLLRKVDTVTEQVHRKK  7944

Query  113   QQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLR  171
               L  M +   ++ E   EA++ L  A+ +L      GP    +    + +T+Q  K L+
Sbjct  7945  FSLENMAQKFKEFQEVSREAQRQLQGAKDQLAVHDSLGPQAHSSKSLTVLQTQQ--KALQ  8118

Query  172   QWQTNVDVANDLALKLLRDYS-ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRL  230
               ++ VD+A  LA  L+ + S +  T ++ +  E +     S+ ++V ++ + LE   + 
Sbjct  8119  TLKSQVDLAQGLARDLVAEASDSKGTSEILLQAETLAQEHDSLSQQVDDKCSFLETKLQG  8298

Query  231   LQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSK-GVKELMKQWQDLQGEIEAHT  289
             +  F   + +  +   E +   + +    R    L+  K  ++  +++       ++A  
Sbjct  8299  IGHFQNTIREMFSQFAEFDDELDGMAPVGRDAETLQKQKEAIRAFLEK-------LDALI  8457

Query  290   DVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKR  349
                 N ++  + +L + E S D V ++R L+ ++ + ++L  ++   +  +E +  + + 
Sbjct  8458  ANNANANKTCKMMLATEEASPDLVGIKRDLEALSKQCNKLWDRAQARKEQVEGTIVRLEE  8637

Query  350   LHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRE  394
              +  LQE    LQ  ++    Q P+G +   + +Q DV + F++E
Sbjct  8638  FYSKLQEFSTLLQKAEELEESQGPVGMETETINQQLDVFKVFQKE  8772


>ref|XM_615341.3| PREDICTED: Bos taurus similar to dystonin, transcript variant 
2 (DST), mRNA
Length=17520

 Score = 86.3 bits (212),  Expect = 1e-13, Method: Compositional matrix adjust.
 Identities = 136/602 (22%), Positives = 250/602 (41%), Gaps = 81/602 (13%)
 Frame = +1

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  12892  ALGQFQHALDELLAWLTHTEGLLGEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13071

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA ++  +++E +  +W  V E  + R+Q L+  L+          
Sbjct  13072  NKAGNDLIESSAGEEASSL-QNKLEVLNQRWQNVLEKTEQRKQHLDAALRQAKGFHGEIE  13248

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQ-----LAK  168
              D  QWL   E    A + LG     AR +L +  E     D  ++      Q     LA+
Sbjct  13249  DLQQWLTDTERHLLASKPLGGLPETAREQLNAHLEICAAFDVKEETYKNLMQKGQQMLAR  13428

Query  169    DLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETH  228
                +  +TN+D   D+                     N+   W S+  +++ER+  LEE  
Sbjct  13429  CPKSAETNID--QDI--------------------NNLKEKWESVETKLNERKVKLEEAL  13542

Query  229    RLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAH  288
               L  +F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H
Sbjct  13543  TLAMEFHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSH  13704

Query  289    TDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWK  348
               +    LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K
Sbjct  13705  REQIIELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDEARKRAK  13881

Query  349    RLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
              + H +  +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T
Sbjct  13882  QFHDAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTSRT  14061

Query  409    VRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRK  468
                                  R L  +    +    L     E+  +W+ +   S + Q K
Sbjct  14062  -------------------GRSLKEKTTLADDNLKLDDMLSELRDKWDTICGKSVERQNK  14184

Query  469    IDETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAP  527
              ++E L    +  +A   L   L + E      QPV GD  ID + + ++  K  + E+  
Sbjct  14185  LEEALLFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGK  14358

Query  528    LKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHE  580
                 +V  +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E
Sbjct  14359  RTSSVQALKRSARELIEGNQDDSSWVRVQVQELSTRWETVCALSISKQSRLEAALRQAEE  14538

Query  581    AH  582
               H
Sbjct  14539  FH  14544


 Score = 62.0 bits (149),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 85/391 (21%), Positives = 174/391 (44%), Gaps = 12/391 (3%)
 Frame = +1

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+ +  +  +WL+  +Q +         L+ +   I + K    ++   R Q+ EL   
Sbjct  13555  EFHNSLQDFINWLTQAEQTLNVASRPSLILDTVLFQIDEHKVFANEVNSHREQIIELDKT  13734

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAE  133
                +LK  +  Q+   +I + +  +Q++W++V + L  R + L+E  K + Q+ +A  +  
Sbjct  13735  GTHLKYFSQKQDV-VLIKNLLISVQSRWEKVVQRLVERGRSLDEARKRAKQFHDAWSKLM  13911

Query  134    QVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-  192
              + L ++   L+S  E     D I+ ++ + K+  K L    +  D  +     L    + 
Sbjct  13912  EWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTSRTGRSLKEKTTL  14091

Query  193    ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTA  252
              ADD  K+  +   +   W +I  +  ER+  LEE      QF   L+  + WL   E   
Sbjct  14092  ADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALIDWLYRVE--P  14265

Query  253    NVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGS-DD  311
               + +D    + +  D   V  L+   +  Q E+   T     L  ++++++   EG+ DD
Sbjct  14266  QLAED----QPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI---EGNQDD  14424

Query  312    AVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQ  371
              +  ++ ++  ++ +W  +   S++ +S LEA+  Q +  H  +  LL WL   +  L   
Sbjct  14425  SSWVRVQVQELSTRWETVCALSISKQSRLEAALRQAEEFHSVVHALLEWLAEAEQTLRFH  14604

Query  372    APIGGDFPAVQKQNDVHRAFKRELKTKEPVI  402
                +  D  A++   D H+ F + L+ K   +
Sbjct  14605  GVLPDDEDALRTLIDQHKEFMKRLEEKRAAL  14697


 Score = 48.1 bits (113),  Expect = 0.033, Method: Compositional matrix adjust.
 Identities = 82/353 (23%), Positives = 144/353 (40%), Gaps = 50/353 (14%)
 Frame = +1

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12394  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWDSLNKAWKDRVDRLEEAMQTAVQ  12573

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  12574  YQDGLQALFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  12729

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  12730  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  12909

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  L  Q P+GGD  A++ +   H   + ++   +    ST+E V  
Sbjct  12910  HALDELLAWLTHTEGLLGEQKPVGGDPKAIEIELAKHHVLQNDVLAHQ----STVEAVN-  13074

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQA-EEVNTEWEKLNLHSADWQRKID  470
                                      +A N   L+   A EE ++   KL + +  WQ  ++
Sbjct  13075  ------------------------KAGN--DLIESSAGEEASSLQNKLEVLNQRWQNVLE  13176

Query  471    ETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRG  523
              +T +R Q        LD  LRQA+   G  + +   L D+ + HL   K L G
Sbjct  13177  KTEQRKQ-------HLDAALRQAKGFHGEIEDLQQWLTDT-ERHLLASKPLGG  13311


 Score = 47.8 bits (112),  Expect = 0.042, Method: Compositional matrix adjust.
 Identities = 59/282 (20%), Positives = 127/282 (45%), Gaps = 17/282 (6%)
 Frame = +1

Query  57    MQDLEQRRPQLEELITAAQNLKNKTSNQEA-RTIITDRIERIQNQWDEVQEHLQNRRQQL  115
             +Q+ + R+PQ E+L TA + +  +     +    + +++  +  +WD +   L++R  ++
Sbjct  7774  LQEFDTRKPQYEQLTTAGRGILQRPGEHPSLHGTVKEQLAAVTQKWDSLTGQLRDRCDRI  7953

Query  116   NEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQT  175
             ++ +  STQ+        + L     +L S   G    DA+ +++   ++L + + Q   
Sbjct  7954  DQAVGKSTQYQSLLRSLSEKLADLDDQLSSSVAGSPHPDAMSQQLETAQKLKQAVEQEGK  8133

Query  176   NVDVA----NDLALKLLRDY-SADDTRKVHMITENINASWRSIHKRVSEREAALEETHRL  230
              +  A    +DLA  +  +Y  A+ +R++  + ++     +     V   ++A   +H+ 
Sbjct  8134  RISAAQALGDDLAALVREEYLRAELSRQLEGVLKSFKDLEQKAETHVEHLQSACASSHQ-  8310

Query  231   LQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTD  290
              QQ   D   F AWL   +   N     + K  +LE       L+K  +D +  + A + 
Sbjct  8311  FQQMSRD---FQAWLDTKKEEQNKSPLISAKVDVLES------LVKDQKDFRKTLTAQSH  8463

Query  291   VYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKK  332
             +Y       + +L   +GS + V LQ +L+ +   W  L+K+
Sbjct  8464  LYEKTIAEGENLLLKTQGS-EKVALQLQLNTIKTNWDGLQKQ  8586


 Score = 43.5 bits (101),  Expect = 0.78, Method: Compositional matrix adjust.
 Identities = 70/345 (20%), Positives = 160/345 (46%), Gaps = 16/345 (4%)
 Frame = +1

Query  54    KATMQDLEQRRPQLEELITAAQNLKNKTS-NQEARTIITDRIERIQNQWDEVQEHLQNRR  112
             KA  ++++Q    +E+L  AA +L      +QE   ++ +  E +  + D V E +  ++
Sbjct  8752  KALQKEMDQHFGLVEQLSGAAGSLLGVCEVDQE---VVAEERECLLRKVDTVTEQVHRKK  8922

Query  113   QQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKE-GPYTVDAIQKKITETKQLAKDLR  171
               L  M +   ++ E   EA++ L  A+ +L      GP    +    + +T+Q  K L+
Sbjct  8923  FSLENMAQKFKEFQEVSREAQRQLQGAKDQLAVHDSLGPQAHSSKSLTVLQTQQ--KALQ  9096

Query  172   QWQTNVDVANDLALKLLRDYS-ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRL  230
               ++ VD+A  LA  L+ + S +  T ++ +  E +     S+ ++V ++ + LE   + 
Sbjct  9097  TLKSQVDLAQGLARDLVAEASDSKGTSEILLQAETLAQEHDSLSQQVDDKCSFLETKLQG  9276

Query  231   LQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSK-GVKELMKQWQDLQGEIEAHT  289
             +  F   + +  +   E +   + +    R    L+  K  ++  +++       ++A  
Sbjct  9277  IGHFQNTIREMFSQFAEFDDELDGMAPVGRDAETLQKQKEAIRAFLEK-------LDALI  9435

Query  290   DVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKR  349
                 N ++  + +L + E S D V ++R L+ ++ + ++L  ++   +  +E +  + + 
Sbjct  9436  ANNANANKTCKMMLATEEASPDLVGIKRDLEALSKQCNKLWDRAQARKEQVEGTIVRLEE  9615

Query  350   LHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRE  394
              +  LQE    LQ  ++    Q P+G +   + +Q DV + F++E
Sbjct  9616  FYSKLQEFSTLLQKAEELEESQGPVGMETETINQQLDVFKVFQKE  9750


>ref|XM_861695.1| PREDICTED: Canis familiaris dystonin, transcript variant 14 (DST), 
mRNA
Length=17884

 Score = 86.3 bits (212),  Expect = 1e-13, Method: Compositional matrix adjust.
 Identities = 136/597 (22%), Positives = 249/597 (41%), Gaps = 72/597 (12%)
 Frame = +3

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  13266  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13445

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  13446  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  13622

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
              D  QWL   E    A + LG     AR +L +  E     D         +++ K L Q 
Sbjct  13623  DLHQWLTDTERHLLASKPLGGLPETAREQLNAHMEICAAFDV-------KEEIYKSLMQK  13781

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
                 +         L R   + +T  +     N+   W S+  +++ER+  LEE   L  +
Sbjct  13782  GQQM---------LARCPKSAET--IDQDLNNLKEKWESVETKLNERKTKLEEALNLAME  13928

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYH  293
              F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H +   
Sbjct  13929  FHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSHREQII  14090

Query  294    NLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS  353
               LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K+ H +
Sbjct  14091  ELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEA  14267

Query  354    LQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFL  413
                +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T     
Sbjct  14268  WSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT-----  14432

Query  414    TEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                             R L  +    +    L     E+  +W+ +   S + Q K++E L
Sbjct  14433  --------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEAL  14570

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENV  532
                  +  +A   L   L + E      QPV GD  ID + + ++  K  + E+     +V
Sbjct  14571  LFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGKRTSSV  14744

Query  533    SHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHEAH  582
                +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E H
Sbjct  14745  QALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFH  14915


 Score = 62.0 bits (149),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 87/389 (22%), Positives = 166/389 (42%), Gaps = 23/389 (5%)
 Frame = +3

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              + DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K 
Sbjct  12969  IFDWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKV  13148

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
              + +  +  + D +  ++  WD + E + NR+ +L   L    Q+  A +E    L     
Sbjct  13149  TEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQHALDELLTWLTHTEG  13328

Query  142    KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHM  201
               L   K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +  
Sbjct  13329  LLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQN  13508

Query  202    ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
                E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              
Sbjct  13509  KLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLHQWLTDT-------------  13649

Query  262    ERLLEDSK---GVKELMKQWQDLQGEIEAHTDV----YHNLDENSQKILRSLEGSDDAVL  314
              ER L  SK   G+ E  ++  +   EI A  DV    Y +L +  Q++L     S  A  
Sbjct  13650  ERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKS--AET  13823

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPI  374
              + + L+N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +  
Sbjct  13824  IDQDLNNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRP  14003

Query  375    GGDFPAVQKQNDVHRAFKRELKT-KEPVI  402
                    V  Q D H+ F  E+ + +E +I
Sbjct  14004  SLILDTVLFQIDEHKVFANEVNSHREQII  14090


 Score = 60.8 bits (146),  Expect = 4e-06, Method: Compositional matrix adjust.
 Identities = 140/566 (24%), Positives = 241/566 (42%), Gaps = 84/566 (14%)
 Frame = +3

Query  45     DINEMIIK-QKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDE  103
              D+ E ++K QK   + L  +    E+ I   +NL  KT   E +  +  ++  I+  WD 
Sbjct  8766   DVLESLLKDQKDFSKMLSAQSSIYEKTIAEGENLLLKTQGSE-KAALQSQLNTIKTSWDG  8942

Query  104    VQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKK--IT  161
                + ++ R  ++ + L+ + ++ E  E     + + +  LE  K   + +D  + +    
Sbjct  8943   FNKQVKEREDKVKDSLEKALKYKEHVETLRPWIDKCQNNLEEIK---FCLDPTETENSTA  9113

Query  162    ETKQLAKDLRQWQTNVDVANDLALKLL------RDYSADDTR----KVHMITENINA---  208
                K L K++ Q    V++ N+ A  LL      ++   D+ +    K+ M+TE +++   
Sbjct  9114   RLKSLQKEMNQHLGMVELLNNAANSLLSVCEVDKEVITDENKSLIQKIDMVTEQLHSKKF  9293

Query  209    SWRSIHKRVSEREAALEETHRLLQ--QFPLDLEKFLAWLTEAETTANVLQDATRKERLLE  266
              S  ++ ++  E +   +E  R LQ  +  LD+   L     +    +VLQ          
Sbjct  9294   SLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVHDSLGPQAYSNKYLSVLQT---------  9446

Query  267    DSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKW  326
                KG++ L  Q            D+   L ++        +G+ D VLLQ   +++  + 
Sbjct  9447   QQKGLQTLKHQ-----------VDLVKGLAQDLVVEASDSKGTSD-VLLQS--ESLVQEH  9584

Query  327    SELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQND  386
              S L ++     S LE           +++E+       DDEL   AP+G D   +QKQ +
Sbjct  9585   SALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVETLQKQKE  9764

Query  387    VHRAFKRELKTKEPVIMS---TLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
                +AF   LK  E +I S     +T ++ L  +  E    L    R+L  E  ++   +L
Sbjct  9765   AIKAF---LKKLEALIASNDNANKTCKMMLAME--ETSPDLIGIKRDL--EALSKQCNKL  9923

Query  444    L-RKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQP  502
              L R QA E                 +++ T+ERL+E      E    L++AE  + S  P
Sbjct  9924   LDRAQARE----------------EQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGP  10055

Query  503    VGDLLIDSLQDHLEKVKAL-RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLST-----  556
              VG +  +++   L   KA  + EI PL+     VN L + L    IQ +    ST     
Sbjct  10056  VG-METETINQQLNVFKAFQKEEIEPLQVKQQDVNWLGQGL----IQSAAKGTSTQGLEH  10220

Query  557    -LEDLNTRWKLLQVAVEDRVRQLHEA  581
               L+D+N RWK L   V  R  QL EA
Sbjct  10221  DLDDVNARWKTLNKKVAQRAAQLQEA  10298


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 97/443 (21%), Positives = 181/443 (40%), Gaps = 68/443 (15%)
 Frame = +3

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12768  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWESLNKAWKDRVDKLEEAMQAAVQ  12947

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  12948  YQDGLQAIFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  13103

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  13104  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  13283

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  13284  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  13415

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  13416  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  13553

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G     +E 
Sbjct  13554  TEQRKQ-------QLDGALRQAKGFHGEIEDLHQWLTDT-ERHLLASKPLGGLPETAREQ  13709

Query  532    V-SHV---------NDLARQLTTLGIQL---SPYNLSTL-EDLNT---RWKLLQVAVEDR  574
              + +H+          ++ + L   G Q+    P +  T+ +DLN    +W+ ++  + +R
Sbjct  13710  LNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKSAETIDQDLNNLKEKWESVETKLNER  13889

Query  575    VRQLHEA---HRDFGPASQHFLS  594
                +L EA     +F  + Q F++
Sbjct  13890  KTKLEEALNLAMEFHNSLQDFIN  13958


 Score = 50.1 bits (118),  Expect = 0.007, Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 106/237 (44%), Gaps = 1/237 (0%)
 Frame = +3

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  14256  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  14435

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  14436  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  14615

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  14616  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI-EGSRD  14792

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T
Sbjct  14793  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQT  14963


 Score = 49.7 bits (117),  Expect = 0.011, Method: Compositional matrix adjust.
 Identities = 102/506 (20%), Positives = 211/506 (41%), Gaps = 52/506 (10%)
 Frame = +3

Query  87     RTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESW  146
              + +ITD  + +  + D V E L +++  L  M +   ++ E  +EA++ L  A+ +L+  
Sbjct  9213   KEVITDENKSLIQKIDMVTEQLHSKKFSLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVH  9392

Query  147    KE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-ADDTRKVHMITE  204
                 GP         + +T+Q  K L+  +  VD+   LA  L+ + S +  T  V + +E
Sbjct  9393   DSLGPQAYSNKYLSVLQTQQ--KGLQTLKHQVDLVKGLAQDLVVEASDSKGTSDVLLQSE  9566

Query  205    NINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK-ER  263
              ++     ++ ++V ER + LE   + +  F   + +  +   E +   + +    R  E 
Sbjct  9567   SLVQEHSALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVET  9746

Query  264    LLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMN  323
              L +  + +K  +K+       +EA      N ++  + +L   E S D + ++R L+ ++
Sbjct  9747   LQKQKEAIKAFLKK-------LEALIASNDNANKTCKMMLAMEETSPDLIGIKRDLEALS  9905

Query  324    FKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQK  383
               + ++L  ++      +E + ++ +  +  L+E    LQ  ++    Q P+G +   + +
Sbjct  9906   KQCNKLLDRAQAREEQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGPVGMETETINQ  10085

Query  384    QNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
              Q +V +AF++E      V    +  +   L +   +G                    T+ 
Sbjct  10086  QLNVFKAFQKEEIEPLQVKQQDVNWLGQGLIQSAAKG------------------TSTQG  10211

Query  444    LRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPV  503
              L    ++VN  W+ LN   A    ++ E L      Q+A + L            SW   
Sbjct  10212  LEHDLDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESL-----------LSWMVD  10358

Query  504    GDLLIDSLQDHLEKVKALRGEIAP-------LKENVSHVNDLARQLTTLGIQLSPYN---  553
               + L+ + +    + K ++ +I         L +  S V  + R+   +     P +   
Sbjct  10359  TEELVANQKPPSAEFKVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIAATAEPADKVK  10538

Query  554    -LSTLEDLNTRWKLLQVAVEDRVRQL  578
               L  L  L++RW+ L    E R RQL
Sbjct  10539  ILKQLSLLDSRWEALLNKAETRNRQL  10616


>emb|AJ544618.1| Takifugu rubripes utrn gene for putative utrophin, exons 1-54 
and joined CDS
Length=46600

 Score = 65.1 bits (157),  Expect(2) = 1e-13, Method: Compositional matrix adjust.
 Identities = 43/126 (34%), Positives = 61/126 (48%), Gaps = 40/126 (31%)
 Frame = +3

Query  8      EVPALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDI---------------NEMIIK  52
              +  A  D N+  TEL+DWL L+ Q++KS  V VGD+E+I               N  +++
Sbjct  38802  DTVAPTDLNKTATELSDWLGLITQMLKSNIVTVGDIEEIRTTMGRLQVSILDVVNASLLR  38981

Query  53     Q-------------------------KATMQDLEQRRPQLEELITAAQNLKNKTSNQEAR  87
                                        + T  DLEQR  QLE++ T AQN+KNKTSN + R
Sbjct  38982  L*FCCVM*PAG*DLIPLCLCACPLCWQVTKNDLEQRHHQLEDIFTLAQNIKNKTSNLDVR  39161

Query  88     TIITDR  93
              T IT++
Sbjct  39162  TSITEK  39179


 Score = 41.2 bits (95),  Expect(2) = 1e-13, Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 37/62 (59%), Gaps = 2/62 (3%)
 Frame = +2

Query  86     ARTIIT--DRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKL  143
               R I+T    +ER+++QWD  Q  ++ R QQL+ M+  S++W E ++E + ++G    + 
Sbjct  39269  CRLIVTHLSVVERVRSQWDGTQHGVEARLQQLDNMIGHSSRWEEQRKEVKALIGHHEGRF  39448

Query  144    ES  145
               +
Sbjct  39449  HN  39454


 Score = 53.1 bits (126),  Expect(2) = 3e-11, Method: Compositional matrix adjust.
 Identities = 30/62 (48%), Positives = 41/62 (66%), Gaps = 0/62 (0%)
 Frame = +3

Query  216    RVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELM  275
              R ++R A L+   + LQ    +LE FL WL EAETT NVL DA+++E L +D+  VKEL 
Sbjct  40488  RATDRHAHLDSELKGLQMSLRELETFLKWLQEAETTVNVLADASQREDLSQDTAHVKELR  40667

Query  276    KQ  277
              +Q
Sbjct  40668  RQ  40673


 Score = 45.1 bits (105),  Expect(2) = 3e-11, Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 33/51 (64%), Gaps = 0/51 (0%)
 Frame = +2

Query  166    LAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKR  216
              L +DL + Q  V   N+L+  LL +YSADDTR++  +T+  NA W SI+ R
Sbjct  40217  LLQDLGRGQAAVAGFNELSAHLLHEYSADDTRRIKEVTDKHNAVWSSINNR  40369


>ref|XM_861613.1| PREDICTED: Canis familiaris dystonin, transcript variant 9 (DST), 
mRNA
Length=17755

 Score = 85.9 bits (211),  Expect = 1e-13, Method: Compositional matrix adjust.
 Identities = 136/597 (22%), Positives = 249/597 (41%), Gaps = 72/597 (12%)
 Frame = +3

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  13266  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13445

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  13446  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  13622

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
              D  QWL   E    A + LG     AR +L +  E     D         +++ K L Q 
Sbjct  13623  DLHQWLTDTERHLLASKPLGGLPETAREQLNAHMEICAAFDV-------KEEIYKSLMQK  13781

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
                 +         L R   + +T  +     N+   W S+  +++ER+  LEE   L  +
Sbjct  13782  GQQM---------LARCPKSAET--IDQDLNNLKEKWESVETKLNERKTKLEEALNLAME  13928

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYH  293
              F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H +   
Sbjct  13929  FHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSHREQII  14090

Query  294    NLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS  353
               LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K+ H +
Sbjct  14091  ELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEA  14267

Query  354    LQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFL  413
                +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T     
Sbjct  14268  WSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT-----  14432

Query  414    TEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                             R L  +    +    L     E+  +W+ +   S + Q K++E L
Sbjct  14433  --------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEAL  14570

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENV  532
                  +  +A   L   L + E      QPV GD  ID + + ++  K  + E+     +V
Sbjct  14571  LFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGKRTSSV  14744

Query  533    SHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHEAH  582
                +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E H
Sbjct  14745  QALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFH  14915


 Score = 61.6 bits (148),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 87/389 (22%), Positives = 166/389 (42%), Gaps = 23/389 (5%)
 Frame = +3

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              + DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K 
Sbjct  12969  IFDWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKV  13148

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
              + +  +  + D +  ++  WD + E + NR+ +L   L    Q+  A +E    L     
Sbjct  13149  TEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQHALDELLTWLTHTEG  13328

Query  142    KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHM  201
               L   K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +  
Sbjct  13329  LLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQN  13508

Query  202    ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
                E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              
Sbjct  13509  KLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLHQWLTDT-------------  13649

Query  262    ERLLEDSK---GVKELMKQWQDLQGEIEAHTDV----YHNLDENSQKILRSLEGSDDAVL  314
              ER L  SK   G+ E  ++  +   EI A  DV    Y +L +  Q++L     S  A  
Sbjct  13650  ERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKS--AET  13823

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPI  374
              + + L+N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +  
Sbjct  13824  IDQDLNNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRP  14003

Query  375    GGDFPAVQKQNDVHRAFKRELKT-KEPVI  402
                    V  Q D H+ F  E+ + +E +I
Sbjct  14004  SLILDTVLFQIDEHKVFANEVNSHREQII  14090


 Score = 60.8 bits (146),  Expect = 5e-06, Method: Compositional matrix adjust.
 Identities = 140/566 (24%), Positives = 241/566 (42%), Gaps = 84/566 (14%)
 Frame = +3

Query  45     DINEMIIK-QKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDE  103
              D+ E ++K QK   + L  +    E+ I   +NL  KT   E +  +  ++  I+  WD 
Sbjct  8766   DVLESLLKDQKDFSKMLSAQSSIYEKTIAEGENLLLKTQGSE-KAALQSQLNTIKTSWDG  8942

Query  104    VQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKK--IT  161
                + ++ R  ++ + L+ + ++ E  E     + + +  LE  K   + +D  + +    
Sbjct  8943   FNKQVKEREDKVKDSLEKALKYKEHVETLRPWIDKCQNNLEEIK---FCLDPTETENSTA  9113

Query  162    ETKQLAKDLRQWQTNVDVANDLALKLL------RDYSADDTR----KVHMITENINA---  208
                K L K++ Q    V++ N+ A  LL      ++   D+ +    K+ M+TE +++   
Sbjct  9114   RLKSLQKEMNQHLGMVELLNNAANSLLSVCEVDKEVITDENKSLIQKIDMVTEQLHSKKF  9293

Query  209    SWRSIHKRVSEREAALEETHRLLQ--QFPLDLEKFLAWLTEAETTANVLQDATRKERLLE  266
              S  ++ ++  E +   +E  R LQ  +  LD+   L     +    +VLQ          
Sbjct  9294   SLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVHDSLGPQAYSNKYLSVLQT---------  9446

Query  267    DSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKW  326
                KG++ L  Q            D+   L ++        +G+ D VLLQ   +++  + 
Sbjct  9447   QQKGLQTLKHQ-----------VDLVKGLAQDLVVEASDSKGTSD-VLLQS--ESLVQEH  9584

Query  327    SELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQND  386
              S L ++     S LE           +++E+       DDEL   AP+G D   +QKQ +
Sbjct  9585   SALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVETLQKQKE  9764

Query  387    VHRAFKRELKTKEPVIMS---TLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
                +AF   LK  E +I S     +T ++ L  +  E    L    R+L  E  ++   +L
Sbjct  9765   AIKAF---LKKLEALIASNDNANKTCKMMLAME--ETSPDLIGIKRDL--EALSKQCNKL  9923

Query  444    L-RKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQP  502
              L R QA E                 +++ T+ERL+E      E    L++AE  + S  P
Sbjct  9924   LDRAQARE----------------EQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGP  10055

Query  503    VGDLLIDSLQDHLEKVKAL-RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLST-----  556
              VG +  +++   L   KA  + EI PL+     VN L + L    IQ +    ST     
Sbjct  10056  VG-METETINQQLNVFKAFQKEEIEPLQVKQQDVNWLGQGL----IQSAAKGTSTQGLEH  10220

Query  557    -LEDLNTRWKLLQVAVEDRVRQLHEA  581
               L+D+N RWK L   V  R  QL EA
Sbjct  10221  DLDDVNARWKTLNKKVAQRAAQLQEA  10298


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 97/443 (21%), Positives = 181/443 (40%), Gaps = 68/443 (15%)
 Frame = +3

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12768  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWESLNKAWKDRVDKLEEAMQAAVQ  12947

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  12948  YQDGLQAIFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  13103

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  13104  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  13283

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  13284  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  13415

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  13416  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  13553

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G     +E 
Sbjct  13554  TEQRKQ-------QLDGALRQAKGFHGEIEDLHQWLTDT-ERHLLASKPLGGLPETAREQ  13709

Query  532    V-SHV---------NDLARQLTTLGIQL---SPYNLSTL-EDLNT---RWKLLQVAVEDR  574
              + +H+          ++ + L   G Q+    P +  T+ +DLN    +W+ ++  + +R
Sbjct  13710  LNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKSAETIDQDLNNLKEKWESVETKLNER  13889

Query  575    VRQLHEA---HRDFGPASQHFLS  594
                +L EA     +F  + Q F++
Sbjct  13890  KTKLEEALNLAMEFHNSLQDFIN  13958


 Score = 50.1 bits (118),  Expect = 0.008, Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 106/237 (44%), Gaps = 1/237 (0%)
 Frame = +3

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  14256  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  14435

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  14436  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  14615

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  14616  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI-EGSRD  14792

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T
Sbjct  14793  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQT  14963


 Score = 49.7 bits (117),  Expect = 0.012, Method: Compositional matrix adjust.
 Identities = 102/506 (20%), Positives = 211/506 (41%), Gaps = 52/506 (10%)
 Frame = +3

Query  87     RTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESW  146
              + +ITD  + +  + D V E L +++  L  M +   ++ E  +EA++ L  A+ +L+  
Sbjct  9213   KEVITDENKSLIQKIDMVTEQLHSKKFSLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVH  9392

Query  147    KE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-ADDTRKVHMITE  204
                 GP         + +T+Q  K L+  +  VD+   LA  L+ + S +  T  V + +E
Sbjct  9393   DSLGPQAYSNKYLSVLQTQQ--KGLQTLKHQVDLVKGLAQDLVVEASDSKGTSDVLLQSE  9566

Query  205    NINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK-ER  263
              ++     ++ ++V ER + LE   + +  F   + +  +   E +   + +    R  E 
Sbjct  9567   SLVQEHSALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVET  9746

Query  264    LLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMN  323
              L +  + +K  +K+       +EA      N ++  + +L   E S D + ++R L+ ++
Sbjct  9747   LQKQKEAIKAFLKK-------LEALIASNDNANKTCKMMLAMEETSPDLIGIKRDLEALS  9905

Query  324    FKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQK  383
               + ++L  ++      +E + ++ +  +  L+E    LQ  ++    Q P+G +   + +
Sbjct  9906   KQCNKLLDRAQAREEQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGPVGMETETINQ  10085

Query  384    QNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
              Q +V +AF++E      V    +  +   L +   +G                    T+ 
Sbjct  10086  QLNVFKAFQKEEIEPLQVKQQDVNWLGQGLIQSAAKG------------------TSTQG  10211

Query  444    LRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPV  503
              L    ++VN  W+ LN   A    ++ E L      Q+A + L            SW   
Sbjct  10212  LEHDLDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESL-----------LSWMVD  10358

Query  504    GDLLIDSLQDHLEKVKALRGEIAP-------LKENVSHVNDLARQLTTLGIQLSPYN---  553
               + L+ + +    + K ++ +I         L +  S V  + R+   +     P +   
Sbjct  10359  TEELVANQKPPSAEFKVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIAATAEPADKVK  10538

Query  554    -LSTLEDLNTRWKLLQVAVEDRVRQL  578
               L  L  L++RW+ L    E R RQL
Sbjct  10539  ILKQLSLLDSRWEALLNKAETRNRQL  10616


>ref|XM_861601.1| PREDICTED: Canis familiaris dystonin, transcript variant 8 (DST), 
mRNA
Length=17710

 Score = 85.9 bits (211),  Expect = 1e-13, Method: Compositional matrix adjust.
 Identities = 136/597 (22%), Positives = 249/597 (41%), Gaps = 72/597 (12%)
 Frame = +3

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  13221  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13400

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  13401  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  13577

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
              D  QWL   E    A + LG     AR +L +  E     D         +++ K L Q 
Sbjct  13578  DLHQWLTDTERHLLASKPLGGLPETAREQLNAHMEICAAFDV-------KEEIYKSLMQK  13736

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
                 +         L R   + +T  +     N+   W S+  +++ER+  LEE   L  +
Sbjct  13737  GQQM---------LARCPKSAET--IDQDLNNLKEKWESVETKLNERKTKLEEALNLAME  13883

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYH  293
              F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H +   
Sbjct  13884  FHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSHREQII  14045

Query  294    NLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS  353
               LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K+ H +
Sbjct  14046  ELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEA  14222

Query  354    LQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFL  413
                +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T     
Sbjct  14223  WSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT-----  14387

Query  414    TEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                             R L  +    +    L     E+  +W+ +   S + Q K++E L
Sbjct  14388  --------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEAL  14525

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENV  532
                  +  +A   L   L + E      QPV GD  ID + + ++  K  + E+     +V
Sbjct  14526  LFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGKRTSSV  14699

Query  533    SHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHEAH  582
                +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E H
Sbjct  14700  QALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFH  14870


 Score = 61.6 bits (148),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 87/389 (22%), Positives = 166/389 (42%), Gaps = 23/389 (5%)
 Frame = +3

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              + DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K 
Sbjct  12924  IFDWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKV  13103

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
              + +  +  + D +  ++  WD + E + NR+ +L   L    Q+  A +E    L     
Sbjct  13104  TEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQHALDELLTWLTHTEG  13283

Query  142    KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHM  201
               L   K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +  
Sbjct  13284  LLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQN  13463

Query  202    ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
                E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              
Sbjct  13464  KLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLHQWLTDT-------------  13604

Query  262    ERLLEDSK---GVKELMKQWQDLQGEIEAHTDV----YHNLDENSQKILRSLEGSDDAVL  314
              ER L  SK   G+ E  ++  +   EI A  DV    Y +L +  Q++L     S  A  
Sbjct  13605  ERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKS--AET  13778

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPI  374
              + + L+N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +  
Sbjct  13779  IDQDLNNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRP  13958

Query  375    GGDFPAVQKQNDVHRAFKRELKT-KEPVI  402
                    V  Q D H+ F  E+ + +E +I
Sbjct  13959  SLILDTVLFQIDEHKVFANEVNSHREQII  14045


 Score = 60.8 bits (146),  Expect = 4e-06, Method: Compositional matrix adjust.
 Identities = 140/566 (24%), Positives = 241/566 (42%), Gaps = 84/566 (14%)
 Frame = +3

Query  45     DINEMIIK-QKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDE  103
              D+ E ++K QK   + L  +    E+ I   +NL  KT   E +  +  ++  I+  WD 
Sbjct  8721   DVLESLLKDQKDFSKMLSAQSSIYEKTIAEGENLLLKTQGSE-KAALQSQLNTIKTSWDG  8897

Query  104    VQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKK--IT  161
                + ++ R  ++ + L+ + ++ E  E     + + +  LE  K   + +D  + +    
Sbjct  8898   FNKQVKEREDKVKDSLEKALKYKEHVETLRPWIDKCQNNLEEIK---FCLDPTETENSTA  9068

Query  162    ETKQLAKDLRQWQTNVDVANDLALKLL------RDYSADDTR----KVHMITENINA---  208
                K L K++ Q    V++ N+ A  LL      ++   D+ +    K+ M+TE +++   
Sbjct  9069   RLKSLQKEMNQHLGMVELLNNAANSLLSVCEVDKEVITDENKSLIQKIDMVTEQLHSKKF  9248

Query  209    SWRSIHKRVSEREAALEETHRLLQ--QFPLDLEKFLAWLTEAETTANVLQDATRKERLLE  266
              S  ++ ++  E +   +E  R LQ  +  LD+   L     +    +VLQ          
Sbjct  9249   SLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVHDSLGPQAYSNKYLSVLQT---------  9401

Query  267    DSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKW  326
                KG++ L  Q            D+   L ++        +G+ D VLLQ   +++  + 
Sbjct  9402   QQKGLQTLKHQ-----------VDLVKGLAQDLVVEASDSKGTSD-VLLQS--ESLVQEH  9539

Query  327    SELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQND  386
              S L ++     S LE           +++E+       DDEL   AP+G D   +QKQ +
Sbjct  9540   SALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVETLQKQKE  9719

Query  387    VHRAFKRELKTKEPVIMS---TLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
                +AF   LK  E +I S     +T ++ L  +  E    L    R+L  E  ++   +L
Sbjct  9720   AIKAF---LKKLEALIASNDNANKTCKMMLAME--ETSPDLIGIKRDL--EALSKQCNKL  9878

Query  444    L-RKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQP  502
              L R QA E                 +++ T+ERL+E      E    L++AE  + S  P
Sbjct  9879   LDRAQARE----------------EQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGP  10010

Query  503    VGDLLIDSLQDHLEKVKAL-RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLST-----  556
              VG +  +++   L   KA  + EI PL+     VN L + L    IQ +    ST     
Sbjct  10011  VG-METETINQQLNVFKAFQKEEIEPLQVKQQDVNWLGQGL----IQSAAKGTSTQGLEH  10175

Query  557    -LEDLNTRWKLLQVAVEDRVRQLHEA  581
               L+D+N RWK L   V  R  QL EA
Sbjct  10176  DLDDVNARWKTLNKKVAQRAAQLQEA  10253


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 97/443 (21%), Positives = 181/443 (40%), Gaps = 68/443 (15%)
 Frame = +3

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12723  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWESLNKAWKDRVDKLEEAMQAAVQ  12902

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  12903  YQDGLQAIFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  13058

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  13059  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  13238

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  13239  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  13370

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  13371  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  13508

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G     +E 
Sbjct  13509  TEQRKQ-------QLDGALRQAKGFHGEIEDLHQWLTDT-ERHLLASKPLGGLPETAREQ  13664

Query  532    V-SHV---------NDLARQLTTLGIQL---SPYNLSTL-EDLNT---RWKLLQVAVEDR  574
              + +H+          ++ + L   G Q+    P +  T+ +DLN    +W+ ++  + +R
Sbjct  13665  LNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKSAETIDQDLNNLKEKWESVETKLNER  13844

Query  575    VRQLHEA---HRDFGPASQHFLS  594
                +L EA     +F  + Q F++
Sbjct  13845  KTKLEEALNLAMEFHNSLQDFIN  13913


 Score = 50.1 bits (118),  Expect = 0.009, Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 106/237 (44%), Gaps = 1/237 (0%)
 Frame = +3

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  14211  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  14390

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  14391  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  14570

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  14571  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI-EGSRD  14747

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T
Sbjct  14748  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQT  14918


 Score = 49.3 bits (116),  Expect = 0.012, Method: Compositional matrix adjust.
 Identities = 102/506 (20%), Positives = 211/506 (41%), Gaps = 52/506 (10%)
 Frame = +3

Query  87     RTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESW  146
              + +ITD  + +  + D V E L +++  L  M +   ++ E  +EA++ L  A+ +L+  
Sbjct  9168   KEVITDENKSLIQKIDMVTEQLHSKKFSLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVH  9347

Query  147    KE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-ADDTRKVHMITE  204
                 GP         + +T+Q  K L+  +  VD+   LA  L+ + S +  T  V + +E
Sbjct  9348   DSLGPQAYSNKYLSVLQTQQ--KGLQTLKHQVDLVKGLAQDLVVEASDSKGTSDVLLQSE  9521

Query  205    NINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK-ER  263
              ++     ++ ++V ER + LE   + +  F   + +  +   E +   + +    R  E 
Sbjct  9522   SLVQEHSALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVET  9701

Query  264    LLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMN  323
              L +  + +K  +K+       +EA      N ++  + +L   E S D + ++R L+ ++
Sbjct  9702   LQKQKEAIKAFLKK-------LEALIASNDNANKTCKMMLAMEETSPDLIGIKRDLEALS  9860

Query  324    FKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQK  383
               + ++L  ++      +E + ++ +  +  L+E    LQ  ++    Q P+G +   + +
Sbjct  9861   KQCNKLLDRAQAREEQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGPVGMETETINQ  10040

Query  384    QNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
              Q +V +AF++E      V    +  +   L +   +G                    T+ 
Sbjct  10041  QLNVFKAFQKEEIEPLQVKQQDVNWLGQGLIQSAAKG------------------TSTQG  10166

Query  444    LRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPV  503
              L    ++VN  W+ LN   A    ++ E L      Q+A + L            SW   
Sbjct  10167  LEHDLDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESL-----------LSWMVD  10313

Query  504    GDLLIDSLQDHLEKVKALRGEIAP-------LKENVSHVNDLARQLTTLGIQLSPYN---  553
               + L+ + +    + K ++ +I         L +  S V  + R+   +     P +   
Sbjct  10314  TEELVANQKPPSAEFKVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIAATAEPADKVK  10493

Query  554    -LSTLEDLNTRWKLLQVAVEDRVRQL  578
               L  L  L++RW+ L    E R RQL
Sbjct  10494  ILKQLSLLDSRWEALLNKAETRNRQL  10571


>ref|XM_861627.1| PREDICTED: Canis familiaris dystonin, transcript variant 10 (DST), 
mRNA
Length=17587

 Score = 85.9 bits (211),  Expect = 1e-13, Method: Compositional matrix adjust.
 Identities = 136/597 (22%), Positives = 249/597 (41%), Gaps = 72/597 (12%)
 Frame = +3

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  13098  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13277

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  13278  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  13454

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
              D  QWL   E    A + LG     AR +L +  E     D         +++ K L Q 
Sbjct  13455  DLHQWLTDTERHLLASKPLGGLPETAREQLNAHMEICAAFDV-------KEEIYKSLMQK  13613

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
                 +         L R   + +T  +     N+   W S+  +++ER+  LEE   L  +
Sbjct  13614  GQQM---------LARCPKSAET--IDQDLNNLKEKWESVETKLNERKTKLEEALNLAME  13760

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYH  293
              F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H +   
Sbjct  13761  FHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSHREQII  13922

Query  294    NLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS  353
               LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K+ H +
Sbjct  13923  ELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEA  14099

Query  354    LQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFL  413
                +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T     
Sbjct  14100  WSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT-----  14264

Query  414    TEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                             R L  +    +    L     E+  +W+ +   S + Q K++E L
Sbjct  14265  --------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEAL  14402

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENV  532
                  +  +A   L   L + E      QPV GD  ID + + ++  K  + E+     +V
Sbjct  14403  LFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGKRTSSV  14576

Query  533    SHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHEAH  582
                +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E H
Sbjct  14577  QALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFH  14747


 Score = 61.6 bits (148),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 87/389 (22%), Positives = 166/389 (42%), Gaps = 23/389 (5%)
 Frame = +3

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              + DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K 
Sbjct  12801  IFDWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKV  12980

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
              + +  +  + D +  ++  WD + E + NR+ +L   L    Q+  A +E    L     
Sbjct  12981  TEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQHALDELLTWLTHTEG  13160

Query  142    KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHM  201
               L   K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +  
Sbjct  13161  LLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQN  13340

Query  202    ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
                E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              
Sbjct  13341  KLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLHQWLTDT-------------  13481

Query  262    ERLLEDSK---GVKELMKQWQDLQGEIEAHTDV----YHNLDENSQKILRSLEGSDDAVL  314
              ER L  SK   G+ E  ++  +   EI A  DV    Y +L +  Q++L     S  A  
Sbjct  13482  ERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKS--AET  13655

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPI  374
              + + L+N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +  
Sbjct  13656  IDQDLNNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRP  13835

Query  375    GGDFPAVQKQNDVHRAFKRELKT-KEPVI  402
                    V  Q D H+ F  E+ + +E +I
Sbjct  13836  SLILDTVLFQIDEHKVFANEVNSHREQII  13922


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 97/443 (21%), Positives = 181/443 (40%), Gaps = 68/443 (15%)
 Frame = +3

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12600  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWESLNKAWKDRVDKLEEAMQAAVQ  12779

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  12780  YQDGLQAIFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  12935

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  12936  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  13115

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  13116  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  13247

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  13248  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  13385

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G     +E 
Sbjct  13386  TEQRKQ-------QLDGALRQAKGFHGEIEDLHQWLTDT-ERHLLASKPLGGLPETAREQ  13541

Query  532    V-SHV---------NDLARQLTTLGIQL---SPYNLSTL-EDLNT---RWKLLQVAVEDR  574
              + +H+          ++ + L   G Q+    P +  T+ +DLN    +W+ ++  + +R
Sbjct  13542  LNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKSAETIDQDLNNLKEKWESVETKLNER  13721

Query  575    VRQLHEA---HRDFGPASQHFLS  594
                +L EA     +F  + Q F++
Sbjct  13722  KTKLEEALNLAMEFHNSLQDFIN  13790


 Score = 49.7 bits (117),  Expect = 0.009, Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 106/237 (44%), Gaps = 1/237 (0%)
 Frame = +3

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  14088  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  14267

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  14268  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  14447

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  14448  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI-EGSRD  14624

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T
Sbjct  14625  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQT  14795


 Score = 46.2 bits (108),  Expect = 0.10, Method: Compositional matrix adjust.
 Identities = 82/368 (22%), Positives = 159/368 (43%), Gaps = 25/368 (6%)
 Frame = +3

Query  94     IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
              ++ +  +W  + + +  R  QL E L    ++ +A E     +      + + K      
Sbjct  10383  LDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESLLSWMVDTEELVANQKPPSAEF  10562

Query  154    DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
                ++ +I E K L + L   ++ V+V      K+       D  K+      +++ W ++
Sbjct  10563  KVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIAATAEPADKVKILKQLSLLDSRWEAL  10742

Query  214    HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT-ANVLQDATRKERLLEDSKGVK  272
                +   R   LE    + QQF   LE    WLT  E   AN     T+  +L       +
Sbjct  10743  LNKAETRNRQLEGISVVAQQFHETLEPLNEWLTTIEKKLANCEPIGTQASKL-------E  10901

Query  273    ELMKQWQDLQGEIEAHTDVYHNLDE---NSQKILRSLEGSDDAVLLQRRLDNMNFKWSEL  329
              E + Q + LQ +I        N+D+   N  ++L+   G D+ +++Q +L+ +  ++ ++
Sbjct  10902  EQITQHKVLQEDILLRK---QNVDQALLNGLELLKQTTG-DEVLIIQDKLEAIKARYKDI  11069

Query  330    RKKSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFPAVQKQNDVH  388
               K S ++   LE +    +RLH + +EL  WL +++ + LS +  +     A Q Q    
Sbjct  11070  TKLSTDVAKTLEQALQLARRLHATREELCTWLDKVEVELLSYETQVLTGEAASQAQAR-Q  11246

Query  389    RAFKRELKTKEPVIMSTLETVRIFLTEQPL---EGLEKLYQEPRELPPEERAQNVTRLLR  445
              +  K+E K  + ++ S  E     L   P    EGLEK+  E       +R + V+  + 
Sbjct  11247  KELKKEAKNSKALLDSLNEVSSALLELVPWRAREGLEKMVAEDN-----DRYRLVSDTIT  11411

Query  446    KQAEEVNT  453
              ++ EE++ 
Sbjct  11412  QKVEEIDA  11435


>ref|XM_861585.1| PREDICTED: Canis familiaris dystonin, transcript variant 7 (DST), 
mRNA
Length=17320

 Score = 85.9 bits (211),  Expect = 1e-13, Method: Compositional matrix adjust.
 Identities = 136/597 (22%), Positives = 249/597 (41%), Gaps = 72/597 (12%)
 Frame = +3

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  12831  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13010

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  13011  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  13187

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
              D  QWL   E    A + LG     AR +L +  E     D         +++ K L Q 
Sbjct  13188  DLHQWLTDTERHLLASKPLGGLPETAREQLNAHMEICAAFDV-------KEEIYKSLMQK  13346

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
                 +         L R   + +T  +     N+   W S+  +++ER+  LEE   L  +
Sbjct  13347  GQQM---------LARCPKSAET--IDQDLNNLKEKWESVETKLNERKTKLEEALNLAME  13493

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYH  293
              F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H +   
Sbjct  13494  FHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSHREQII  13655

Query  294    NLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS  353
               LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K+ H +
Sbjct  13656  ELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEA  13832

Query  354    LQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFL  413
                +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T     
Sbjct  13833  WSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT-----  13997

Query  414    TEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                             R L  +    +    L     E+  +W+ +   S + Q K++E L
Sbjct  13998  --------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEAL  14135

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENV  532
                  +  +A   L   L + E      QPV GD  ID + + ++  K  + E+     +V
Sbjct  14136  LFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGKRTSSV  14309

Query  533    SHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHEAH  582
                +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E H
Sbjct  14310  QALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFH  14480


 Score = 61.6 bits (148),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 87/389 (22%), Positives = 166/389 (42%), Gaps = 23/389 (5%)
 Frame = +3

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              + DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K 
Sbjct  12534  IFDWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKV  12713

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
              + +  +  + D +  ++  WD + E + NR+ +L   L    Q+  A +E    L     
Sbjct  12714  TEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQHALDELLTWLTHTEG  12893

Query  142    KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHM  201
               L   K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +  
Sbjct  12894  LLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQN  13073

Query  202    ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
                E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              
Sbjct  13074  KLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLHQWLTDT-------------  13214

Query  262    ERLLEDSK---GVKELMKQWQDLQGEIEAHTDV----YHNLDENSQKILRSLEGSDDAVL  314
              ER L  SK   G+ E  ++  +   EI A  DV    Y +L +  Q++L     S  A  
Sbjct  13215  ERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKS--AET  13388

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPI  374
              + + L+N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +  
Sbjct  13389  IDQDLNNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRP  13568

Query  375    GGDFPAVQKQNDVHRAFKRELKT-KEPVI  402
                    V  Q D H+ F  E+ + +E +I
Sbjct  13569  SLILDTVLFQIDEHKVFANEVNSHREQII  13655


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 97/443 (21%), Positives = 181/443 (40%), Gaps = 68/443 (15%)
 Frame = +3

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12333  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWESLNKAWKDRVDKLEEAMQAAVQ  12512

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  12513  YQDGLQAIFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  12668

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  12669  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  12848

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  12849  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  12980

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  12981  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  13118

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G     +E 
Sbjct  13119  TEQRKQ-------QLDGALRQAKGFHGEIEDLHQWLTDT-ERHLLASKPLGGLPETAREQ  13274

Query  532    V-SHV---------NDLARQLTTLGIQL---SPYNLSTL-EDLNT---RWKLLQVAVEDR  574
              + +H+          ++ + L   G Q+    P +  T+ +DLN    +W+ ++  + +R
Sbjct  13275  LNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKSAETIDQDLNNLKEKWESVETKLNER  13454

Query  575    VRQLHEA---HRDFGPASQHFLS  594
                +L EA     +F  + Q F++
Sbjct  13455  KTKLEEALNLAMEFHNSLQDFIN  13523


 Score = 49.7 bits (117),  Expect = 0.009, Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 106/237 (44%), Gaps = 1/237 (0%)
 Frame = +3

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  13821  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  14000

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  14001  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  14180

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  14181  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI-EGSRD  14357

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T
Sbjct  14358  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQT  14528


 Score = 46.2 bits (108),  Expect = 0.10, Method: Compositional matrix adjust.
 Identities = 82/368 (22%), Positives = 159/368 (43%), Gaps = 25/368 (6%)
 Frame = +3

Query  94     IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
              ++ +  +W  + + +  R  QL E L    ++ +A E     +      + + K      
Sbjct  10116  LDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESLLSWMVDTEELVANQKPPSAEF  10295

Query  154    DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
                ++ +I E K L + L   ++ V+V      K+       D  K+      +++ W ++
Sbjct  10296  KVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIAATAEPADKVKILKQLSLLDSRWEAL  10475

Query  214    HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT-ANVLQDATRKERLLEDSKGVK  272
                +   R   LE    + QQF   LE    WLT  E   AN     T+  +L       +
Sbjct  10476  LNKAETRNRQLEGISVVAQQFHETLEPLNEWLTTIEKKLANCEPIGTQASKL-------E  10634

Query  273    ELMKQWQDLQGEIEAHTDVYHNLDE---NSQKILRSLEGSDDAVLLQRRLDNMNFKWSEL  329
              E + Q + LQ +I        N+D+   N  ++L+   G D+ +++Q +L+ +  ++ ++
Sbjct  10635  EQITQHKVLQEDILLRK---QNVDQALLNGLELLKQTTG-DEVLIIQDKLEAIKARYKDI  10802

Query  330    RKKSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFPAVQKQNDVH  388
               K S ++   LE +    +RLH + +EL  WL +++ + LS +  +     A Q Q    
Sbjct  10803  TKLSTDVAKTLEQALQLARRLHATREELCTWLDKVEVELLSYETQVLTGEAASQAQAR-Q  10979

Query  389    RAFKRELKTKEPVIMSTLETVRIFLTEQPL---EGLEKLYQEPRELPPEERAQNVTRLLR  445
              +  K+E K  + ++ S  E     L   P    EGLEK+  E       +R + V+  + 
Sbjct  10980  KELKKEAKNSKALLDSLNEVSSALLELVPWRAREGLEKMVAEDN-----DRYRLVSDTIT  11144

Query  446    KQAEEVNT  453
              ++ EE++ 
Sbjct  11145  QKVEEIDA  11168


>ref|XM_861669.1| PREDICTED: Canis familiaris dystonin, transcript variant 12 (DST), 
mRNA
Length=23878

 Score = 85.9 bits (211),  Expect = 1e-13, Method: Compositional matrix adjust.
 Identities = 138/602 (22%), Positives = 250/602 (41%), Gaps = 82/602 (13%)
 Frame = +3

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  19299  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  19478

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  19479  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  19655

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDA---IQKKITETKQ--LAK  168
              D  QWL   E    A + LG     AR +L +  E     D    I K + +  Q  LA+
Sbjct  19656  DLHQWLTDTERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLAR  19835

Query  169    DLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETH  228
                +  +T   +  DL                     N+   W S+  +++ER+  LEE  
Sbjct  19836  CPKSAET---IDQDL--------------------NNLKEKWESVETKLNERKTKLEEAL  19946

Query  229    RLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAH  288
               L  +F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H
Sbjct  19947  NLAMEFHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSH  20108

Query  289    TDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWK  348
               +    LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K
Sbjct  20109  REQIIELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAK  20285

Query  349    RLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
              + H +  +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T
Sbjct  20286  QFHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT  20465

Query  409    VRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRK  468
                                  R L  +    +    L     E+  +W+ +   S + Q K
Sbjct  20466  -------------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNK  20588

Query  469    IDETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAP  527
              ++E L    +  +A   L   L + E      QPV GD  ID + + ++  K  + E+  
Sbjct  20589  LEEALLFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGK  20762

Query  528    LKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHE  580
                 +V  +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E
Sbjct  20763  RTSSVQALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEE  20942

Query  581    AH  582
               H
Sbjct  20943  FH  20948


 Score = 62.0 bits (149),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 87/389 (22%), Positives = 166/389 (42%), Gaps = 23/389 (5%)
 Frame = +3

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              + DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K 
Sbjct  19002  IFDWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKV  19181

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
              + +  +  + D +  ++  WD + E + NR+ +L   L    Q+  A +E    L     
Sbjct  19182  TEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQHALDELLTWLTHTEG  19361

Query  142    KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHM  201
               L   K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +  
Sbjct  19362  LLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQN  19541

Query  202    ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
                E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              
Sbjct  19542  KLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLHQWLTDT-------------  19682

Query  262    ERLLEDSK---GVKELMKQWQDLQGEIEAHTDV----YHNLDENSQKILRSLEGSDDAVL  314
              ER L  SK   G+ E  ++  +   EI A  DV    Y +L +  Q++L     S  A  
Sbjct  19683  ERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKS--AET  19856

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPI  374
              + + L+N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +  
Sbjct  19857  IDQDLNNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRP  20036

Query  375    GGDFPAVQKQNDVHRAFKRELKT-KEPVI  402
                    V  Q D H+ F  E+ + +E +I
Sbjct  20037  SLILDTVLFQIDEHKVFANEVNSHREQII  20123


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 97/443 (21%), Positives = 181/443 (40%), Gaps = 68/443 (15%)
 Frame = +3

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  18801  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWESLNKAWKDRVDKLEEAMQAAVQ  18980

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  18981  YQDGLQAIFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  19136

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  19137  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  19316

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  19317  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  19448

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  19449  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  19586

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G     +E 
Sbjct  19587  TEQRKQ-------QLDGALRQAKGFHGEIEDLHQWLTDT-ERHLLASKPLGGLPETAREQ  19742

Query  532    V-SHV---------NDLARQLTTLGIQL---SPYNLSTL-EDLNT---RWKLLQVAVEDR  574
              + +H+          ++ + L   G Q+    P +  T+ +DLN    +W+ ++  + +R
Sbjct  19743  LNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKSAETIDQDLNNLKEKWESVETKLNER  19922

Query  575    VRQLHEA---HRDFGPASQHFLS  594
                +L EA     +F  + Q F++
Sbjct  19923  KTKLEEALNLAMEFHNSLQDFIN  19991


 Score = 50.1 bits (118),  Expect = 0.008, Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 106/237 (44%), Gaps = 1/237 (0%)
 Frame = +3

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  20289  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  20468

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  20469  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  20648

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  20649  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI-EGSRD  20825

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T
Sbjct  20826  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQT  20996


 Score = 46.6 bits (109),  Expect = 0.093, Method: Compositional matrix adjust.
 Identities = 82/368 (22%), Positives = 159/368 (43%), Gaps = 25/368 (6%)
 Frame = +3

Query  94     IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
              ++ +  +W  + + +  R  QL E L    ++ +A E     +      + + K      
Sbjct  16590  LDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESLLSWMVDTEELVANQKPPSAEF  16769

Query  154    DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
                ++ +I E K L + L   ++ V+V      K+       D  K+      +++ W ++
Sbjct  16770  KVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIAATAEPADKVKILKQLSLLDSRWEAL  16949

Query  214    HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT-ANVLQDATRKERLLEDSKGVK  272
                +   R   LE    + QQF   LE    WLT  E   AN     T+  +L       +
Sbjct  16950  LNKAETRNRQLEGISVVAQQFHETLEPLNEWLTTIEKKLANCEPIGTQASKL-------E  17108

Query  273    ELMKQWQDLQGEIEAHTDVYHNLDE---NSQKILRSLEGSDDAVLLQRRLDNMNFKWSEL  329
              E + Q + LQ +I        N+D+   N  ++L+   G D+ +++Q +L+ +  ++ ++
Sbjct  17109  EQITQHKVLQEDILLRK---QNVDQALLNGLELLKQTTG-DEVLIIQDKLEAIKARYKDI  17276

Query  330    RKKSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFPAVQKQNDVH  388
               K S ++   LE +    +RLH + +EL  WL +++ + LS +  +     A Q Q    
Sbjct  17277  TKLSTDVAKTLEQALQLARRLHATREELCTWLDKVEVELLSYETQVLTGEAASQAQAR-Q  17453

Query  389    RAFKRELKTKEPVIMSTLETVRIFLTEQPL---EGLEKLYQEPRELPPEERAQNVTRLLR  445
              +  K+E K  + ++ S  E     L   P    EGLEK+  E       +R + V+  + 
Sbjct  17454  KELKKEAKNSKALLDSLNEVSSALLELVPWRAREGLEKMVAEDN-----DRYRLVSDTIT  17618

Query  446    KQAEEVNT  453
              ++ EE++ 
Sbjct  17619  QKVEEIDA  17642


>ref|XM_861540.1| PREDICTED: Canis familiaris dystonin, transcript variant 3 (DST), 
mRNA
Length=17716

 Score = 85.9 bits (211),  Expect = 1e-13, Method: Compositional matrix adjust.
 Identities = 138/602 (22%), Positives = 250/602 (41%), Gaps = 82/602 (13%)
 Frame = +3

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  13137  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13316

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  13317  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  13493

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDA---IQKKITETKQ--LAK  168
              D  QWL   E    A + LG     AR +L +  E     D    I K + +  Q  LA+
Sbjct  13494  DLHQWLTDTERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLAR  13673

Query  169    DLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETH  228
                +  +T   +  DL                     N+   W S+  +++ER+  LEE  
Sbjct  13674  CPKSAET---IDQDL--------------------NNLKEKWESVETKLNERKTKLEEAL  13784

Query  229    RLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAH  288
               L  +F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H
Sbjct  13785  NLAMEFHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSH  13946

Query  289    TDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWK  348
               +    LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K
Sbjct  13947  REQIIELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAK  14123

Query  349    RLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLET  408
              + H +  +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T
Sbjct  14124  QFHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT  14303

Query  409    VRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRK  468
                                  R L  +    +    L     E+  +W+ +   S + Q K
Sbjct  14304  -------------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNK  14426

Query  469    IDETLERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAP  527
              ++E L    +  +A   L   L + E      QPV GD  ID + + ++  K  + E+  
Sbjct  14427  LEEALLFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGK  14600

Query  528    LKENVSHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHE  580
                 +V  +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E
Sbjct  14601  RTSSVQALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEE  14780

Query  581    AH  582
               H
Sbjct  14781  FH  14786


 Score = 62.0 bits (149),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 87/389 (22%), Positives = 166/389 (42%), Gaps = 23/389 (5%)
 Frame = +3

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              + DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K 
Sbjct  12840  IFDWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKV  13019

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
              + +  +  + D +  ++  WD + E + NR+ +L   L    Q+  A +E    L     
Sbjct  13020  TEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQHALDELLTWLTHTEG  13199

Query  142    KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHM  201
               L   K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +  
Sbjct  13200  LLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQN  13379

Query  202    ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
                E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              
Sbjct  13380  KLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLHQWLTDT-------------  13520

Query  262    ERLLEDSK---GVKELMKQWQDLQGEIEAHTDV----YHNLDENSQKILRSLEGSDDAVL  314
              ER L  SK   G+ E  ++  +   EI A  DV    Y +L +  Q++L     S  A  
Sbjct  13521  ERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKS--AET  13694

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPI  374
              + + L+N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +  
Sbjct  13695  IDQDLNNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRP  13874

Query  375    GGDFPAVQKQNDVHRAFKRELKT-KEPVI  402
                    V  Q D H+ F  E+ + +E +I
Sbjct  13875  SLILDTVLFQIDEHKVFANEVNSHREQII  13961


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 97/443 (21%), Positives = 181/443 (40%), Gaps = 68/443 (15%)
 Frame = +3

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12639  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWESLNKAWKDRVDKLEEAMQAAVQ  12818

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  12819  YQDGLQAIFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  12974

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  12975  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  13154

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  13155  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  13286

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  13287  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  13424

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G     +E 
Sbjct  13425  TEQRKQ-------QLDGALRQAKGFHGEIEDLHQWLTDT-ERHLLASKPLGGLPETAREQ  13580

Query  532    V-SHV---------NDLARQLTTLGIQL---SPYNLSTL-EDLNT---RWKLLQVAVEDR  574
              + +H+          ++ + L   G Q+    P +  T+ +DLN    +W+ ++  + +R
Sbjct  13581  LNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKSAETIDQDLNNLKEKWESVETKLNER  13760

Query  575    VRQLHEA---HRDFGPASQHFLS  594
                +L EA     +F  + Q F++
Sbjct  13761  KTKLEEALNLAMEFHNSLQDFIN  13829


 Score = 50.1 bits (118),  Expect = 0.008, Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 106/237 (44%), Gaps = 1/237 (0%)
 Frame = +3

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  14127  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  14306

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  14307  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  14486

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  14487  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI-EGSRD  14663

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T
Sbjct  14664  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQT  14834


 Score = 46.6 bits (109),  Expect = 0.093, Method: Compositional matrix adjust.
 Identities = 82/368 (22%), Positives = 159/368 (43%), Gaps = 25/368 (6%)
 Frame = +3

Query  94     IERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTV  153
              ++ +  +W  + + +  R  QL E L    ++ +A E     +      + + K      
Sbjct  10428  LDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESLLSWMVDTEELVANQKPPSAEF  10607

Query  154    DAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSI  213
                ++ +I E K L + L   ++ V+V      K+       D  K+      +++ W ++
Sbjct  10608  KVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIAATAEPADKVKILKQLSLLDSRWEAL  10787

Query  214    HKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT-ANVLQDATRKERLLEDSKGVK  272
                +   R   LE    + QQF   LE    WLT  E   AN     T+  +L       +
Sbjct  10788  LNKAETRNRQLEGISVVAQQFHETLEPLNEWLTTIEKKLANCEPIGTQASKL-------E  10946

Query  273    ELMKQWQDLQGEIEAHTDVYHNLDE---NSQKILRSLEGSDDAVLLQRRLDNMNFKWSEL  329
              E + Q + LQ +I        N+D+   N  ++L+   G D+ +++Q +L+ +  ++ ++
Sbjct  10947  EQITQHKVLQEDILLRK---QNVDQALLNGLELLKQTTG-DEVLIIQDKLEAIKARYKDI  11114

Query  330    RKKSLNIRSHLEASSDQWKRLHLSLQELLVWL-QLKDDELSRQAPIGGDFPAVQKQNDVH  388
               K S ++   LE +    +RLH + +EL  WL +++ + LS +  +     A Q Q    
Sbjct  11115  TKLSTDVAKTLEQALQLARRLHATREELCTWLDKVEVELLSYETQVLTGEAASQAQAR-Q  11291

Query  389    RAFKRELKTKEPVIMSTLETVRIFLTEQPL---EGLEKLYQEPRELPPEERAQNVTRLLR  445
              +  K+E K  + ++ S  E     L   P    EGLEK+  E       +R + V+  + 
Sbjct  11292  KELKKEAKNSKALLDSLNEVSSALLELVPWRAREGLEKMVAEDN-----DRYRLVSDTIT  11456

Query  446    KQAEEVNT  453
              ++ EE++ 
Sbjct  11457  QKVEEIDA  11480


>ref|XM_861682.1| PREDICTED: Canis familiaris dystonin, transcript variant 13 (DST), 
mRNA
Length=16499

 Score = 85.9 bits (211),  Expect = 1e-13, Method: Compositional matrix adjust.
 Identities = 136/597 (22%), Positives = 249/597 (41%), Gaps = 72/597 (12%)
 Frame = +1

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  11962  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  12141

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  12142  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  12318

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
              D  QWL   E    A + LG     AR +L +  E     D         +++ K L Q 
Sbjct  12319  DLHQWLTDTERHLLASKPLGGLPETAREQLNAHMEICAAFDV-------KEEIYKSLMQK  12477

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
                 +         L R   + +T  +     N+   W S+  +++ER+  LEE   L  +
Sbjct  12478  GQQM---------LARCPKSAET--IDQDLNNLKEKWESVETKLNERKTKLEEALNLAME  12624

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYH  293
              F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H +   
Sbjct  12625  FHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSHREQII  12786

Query  294    NLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS  353
               LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K+ H +
Sbjct  12787  ELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEA  12963

Query  354    LQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFL  413
                +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T     
Sbjct  12964  WSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT-----  13128

Query  414    TEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                             R L  +    +    L     E+  +W+ +   S + Q K++E L
Sbjct  13129  --------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEAL  13266

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENV  532
                  +  +A   L   L + E      QPV GD  ID + + ++  K  + E+     +V
Sbjct  13267  LFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGKRTSSV  13440

Query  533    SHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHEAH  582
                +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E H
Sbjct  13441  QALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFH  13611


 Score = 61.6 bits (148),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 87/389 (22%), Positives = 166/389 (42%), Gaps = 23/389 (5%)
 Frame = +1

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              + DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K 
Sbjct  11665  IFDWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKV  11844

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
              + +  +  + D +  ++  WD + E + NR+ +L   L    Q+  A +E    L     
Sbjct  11845  TEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQHALDELLTWLTHTEG  12024

Query  142    KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHM  201
               L   K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +  
Sbjct  12025  LLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQN  12204

Query  202    ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
                E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              
Sbjct  12205  KLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLHQWLTDT-------------  12345

Query  262    ERLLEDSK---GVKELMKQWQDLQGEIEAHTDV----YHNLDENSQKILRSLEGSDDAVL  314
              ER L  SK   G+ E  ++  +   EI A  DV    Y +L +  Q++L     S  A  
Sbjct  12346  ERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKS--AET  12519

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPI  374
              + + L+N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +  
Sbjct  12520  IDQDLNNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRP  12699

Query  375    GGDFPAVQKQNDVHRAFKRELKT-KEPVI  402
                    V  Q D H+ F  E+ + +E +I
Sbjct  12700  SLILDTVLFQIDEHKVFANEVNSHREQII  12786


 Score = 60.8 bits (146),  Expect = 5e-06, Method: Compositional matrix adjust.
 Identities = 140/566 (24%), Positives = 241/566 (42%), Gaps = 84/566 (14%)
 Frame = +1

Query  45    DINEMIIK-QKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDE  103
             D+ E ++K QK   + L  +    E+ I   +NL  KT   E +  +  ++  I+  WD 
Sbjct  7468  DVLESLLKDQKDFSKMLSAQSSIYEKTIAEGENLLLKTQGSE-KAALQSQLNTIKTSWDG  7644

Query  104   VQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKK--IT  161
               + ++ R  ++ + L+ + ++ E  E     + + +  LE  K   + +D  + +    
Sbjct  7645  FNKQVKEREDKVKDSLEKALKYKEHVETLRPWIDKCQNNLEEIK---FCLDPTETENSTA  7815

Query  162   ETKQLAKDLRQWQTNVDVANDLALKLL------RDYSADDTR----KVHMITENINA---  208
               K L K++ Q    V++ N+ A  LL      ++   D+ +    K+ M+TE +++   
Sbjct  7816  RLKSLQKEMNQHLGMVELLNNAANSLLSVCEVDKEVITDENKSLIQKIDMVTEQLHSKKF  7995

Query  209   SWRSIHKRVSEREAALEETHRLLQ--QFPLDLEKFLAWLTEAETTANVLQDATRKERLLE  266
             S  ++ ++  E +   +E  R LQ  +  LD+   L     +    +VLQ          
Sbjct  7996  SLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVHDSLGPQAYSNKYLSVLQT---------  8148

Query  267   DSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKW  326
               KG++ L  Q            D+   L ++        +G+ D VLLQ   +++  + 
Sbjct  8149  QQKGLQTLKHQ-----------VDLVKGLAQDLVVEASDSKGTSD-VLLQS--ESLVQEH  8286

Query  327   SELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQND  386
             S L ++     S LE           +++E+       DDEL   AP+G D   +QKQ +
Sbjct  8287  SALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVETLQKQKE  8466

Query  387   VHRAFKRELKTKEPVIMS---TLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
               +AF   LK  E +I S     +T ++ L  +  E    L    R+L  E  ++   +L
Sbjct  8467  AIKAF---LKKLEALIASNDNANKTCKMMLAME--ETSPDLIGIKRDL--EALSKQCNKL  8625

Query  444   L-RKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQP  502
             L R QA E                 +++ T+ERL+E      E    L++AE  + S  P
Sbjct  8626  LDRAQARE----------------EQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGP  8757

Query  503   VGDLLIDSLQDHLEKVKAL-RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLST-----  556
             VG +  +++   L   KA  + EI PL+     VN L + L    IQ +    ST     
Sbjct  8758  VG-METETINQQLNVFKAFQKEEIEPLQVKQQDVNWLGQGL----IQSAAKGTSTQGLEH  8922

Query  557   -LEDLNTRWKLLQVAVEDRVRQLHEA  581
              L+D+N RWK L   V  R  QL EA
Sbjct  8923  DLDDVNARWKTLNKKVAQRAAQLQEA  9000


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 97/443 (21%), Positives = 181/443 (40%), Gaps = 68/443 (15%)
 Frame = +1

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  11464  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWESLNKAWKDRVDKLEEAMQAAVQ  11643

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  11644  YQDGLQAIFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  11799

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  11800  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  11979

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  11980  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  12111

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  12112  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  12249

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G     +E 
Sbjct  12250  TEQRKQ-------QLDGALRQAKGFHGEIEDLHQWLTDT-ERHLLASKPLGGLPETAREQ  12405

Query  532    V-SHV---------NDLARQLTTLGIQL---SPYNLSTL-EDLNT---RWKLLQVAVEDR  574
              + +H+          ++ + L   G Q+    P +  T+ +DLN    +W+ ++  + +R
Sbjct  12406  LNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKSAETIDQDLNNLKEKWESVETKLNER  12585

Query  575    VRQLHEA---HRDFGPASQHFLS  594
                +L EA     +F  + Q F++
Sbjct  12586  KTKLEEALNLAMEFHNSLQDFIN  12654


 Score = 49.7 bits (117),  Expect = 0.009, Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 106/237 (44%), Gaps = 1/237 (0%)
 Frame = +1

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  12952  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  13131

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  13132  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  13311

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  13312  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI-EGSRD  13488

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T
Sbjct  13489  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQT  13659


 Score = 49.3 bits (116),  Expect = 0.012, Method: Compositional matrix adjust.
 Identities = 102/506 (20%), Positives = 211/506 (41%), Gaps = 52/506 (10%)
 Frame = +1

Query  87    RTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESW  146
             + +ITD  + +  + D V E L +++  L  M +   ++ E  +EA++ L  A+ +L+  
Sbjct  7915  KEVITDENKSLIQKIDMVTEQLHSKKFSLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVH  8094

Query  147   KE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-ADDTRKVHMITE  204
                GP         + +T+Q  K L+  +  VD+   LA  L+ + S +  T  V + +E
Sbjct  8095  DSLGPQAYSNKYLSVLQTQQ--KGLQTLKHQVDLVKGLAQDLVVEASDSKGTSDVLLQSE  8268

Query  205   NINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK-ER  263
             ++     ++ ++V ER + LE   + +  F   + +  +   E +   + +    R  E 
Sbjct  8269  SLVQEHSALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVET  8448

Query  264   LLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMN  323
             L +  + +K  +K+       +EA      N ++  + +L   E S D + ++R L+ ++
Sbjct  8449  LQKQKEAIKAFLKK-------LEALIASNDNANKTCKMMLAMEETSPDLIGIKRDLEALS  8607

Query  324   FKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQK  383
              + ++L  ++      +E + ++ +  +  L+E    LQ  ++    Q P+G +   + +
Sbjct  8608  KQCNKLLDRAQAREEQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGPVGMETETINQ  8787

Query  384   QNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
             Q +V +AF++E      V    +  +   L +   +G                    T+ 
Sbjct  8788  QLNVFKAFQKEEIEPLQVKQQDVNWLGQGLIQSAAKG------------------TSTQG  8913

Query  444   LRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPV  503
             L    ++VN  W+ LN   A    ++ E L      Q+A + L            SW   
Sbjct  8914  LEHDLDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESL-----------LSWMVD  9060

Query  504   GDLLIDSLQDHLEKVKALRGEIAP-------LKENVSHVNDLARQLTTLGIQLSPYN---  553
              + L+ + +    + K ++ +I         L +  S V  + R+   +     P +   
Sbjct  9061  TEELVANQKPPSAEFKVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIAATAEPADKVK  9240

Query  554   -LSTLEDLNTRWKLLQVAVEDRVRQL  578
              L  L  L++RW+ L    E R RQL
Sbjct  9241  ILKQLSLLDSRWEALLNKAETRNRQL  9318


>ref|XM_861654.1| PREDICTED: Canis familiaris dystonin, transcript variant 11 (DST), 
mRNA
Length=17962

 Score = 85.9 bits (211),  Expect = 1e-13, Method: Compositional matrix adjust.
 Identities = 136/597 (22%), Positives = 249/597 (41%), Gaps = 72/597 (12%)
 Frame = +3

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  13464  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13643

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  13644  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  13820

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
              D  QWL   E    A + LG     AR +L +  E     D         +++ K L Q 
Sbjct  13821  DLHQWLTDTERHLLASKPLGGLPETAREQLNAHMEICAAFDV-------KEEIYKSLMQK  13979

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
                 +         L R   + +T  +     N+   W S+  +++ER+  LEE   L  +
Sbjct  13980  GQQM---------LARCPKSAET--IDQDLNNLKEKWESVETKLNERKTKLEEALNLAME  14126

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYH  293
              F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H +   
Sbjct  14127  FHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSHREQII  14288

Query  294    NLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS  353
               LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K+ H +
Sbjct  14289  ELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEA  14465

Query  354    LQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFL  413
                +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T     
Sbjct  14466  WSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT-----  14630

Query  414    TEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                             R L  +    +    L     E+  +W+ +   S + Q K++E L
Sbjct  14631  --------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEAL  14768

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENV  532
                  +  +A   L   L + E      QPV GD  ID + + ++  K  + E+     +V
Sbjct  14769  LFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGKRTSSV  14942

Query  533    SHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHEAH  582
                +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E H
Sbjct  14943  QALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFH  15113


 Score = 61.6 bits (148),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 87/389 (22%), Positives = 166/389 (42%), Gaps = 23/389 (5%)
 Frame = +3

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              + DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K 
Sbjct  13167  IFDWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKV  13346

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
              + +  +  + D +  ++  WD + E + NR+ +L   L    Q+  A +E    L     
Sbjct  13347  TEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQHALDELLTWLTHTEG  13526

Query  142    KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHM  201
               L   K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +  
Sbjct  13527  LLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQN  13706

Query  202    ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
                E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              
Sbjct  13707  KLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLHQWLTDT-------------  13847

Query  262    ERLLEDSK---GVKELMKQWQDLQGEIEAHTDV----YHNLDENSQKILRSLEGSDDAVL  314
              ER L  SK   G+ E  ++  +   EI A  DV    Y +L +  Q++L     S  A  
Sbjct  13848  ERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKS--AET  14021

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPI  374
              + + L+N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +  
Sbjct  14022  IDQDLNNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRP  14201

Query  375    GGDFPAVQKQNDVHRAFKRELKT-KEPVI  402
                    V  Q D H+ F  E+ + +E +I
Sbjct  14202  SLILDTVLFQIDEHKVFANEVNSHREQII  14288


 Score = 60.8 bits (146),  Expect = 5e-06, Method: Compositional matrix adjust.
 Identities = 140/566 (24%), Positives = 241/566 (42%), Gaps = 84/566 (14%)
 Frame = +3

Query  45     DINEMIIK-QKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDE  103
              D+ E ++K QK   + L  +    E+ I   +NL  KT   E +  +  ++  I+  WD 
Sbjct  8970   DVLESLLKDQKDFSKMLSAQSSIYEKTIAEGENLLLKTQGSE-KAALQSQLNTIKTSWDG  9146

Query  104    VQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKK--IT  161
                + ++ R  ++ + L+ + ++ E  E     + + +  LE  K   + +D  + +    
Sbjct  9147   FNKQVKEREDKVKDSLEKALKYKEHVETLRPWIDKCQNNLEEIK---FCLDPTETENSTA  9317

Query  162    ETKQLAKDLRQWQTNVDVANDLALKLL------RDYSADDTR----KVHMITENINA---  208
                K L K++ Q    V++ N+ A  LL      ++   D+ +    K+ M+TE +++   
Sbjct  9318   RLKSLQKEMNQHLGMVELLNNAANSLLSVCEVDKEVITDENKSLIQKIDMVTEQLHSKKF  9497

Query  209    SWRSIHKRVSEREAALEETHRLLQ--QFPLDLEKFLAWLTEAETTANVLQDATRKERLLE  266
              S  ++ ++  E +   +E  R LQ  +  LD+   L     +    +VLQ          
Sbjct  9498   SLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVHDSLGPQAYSNKYLSVLQT---------  9650

Query  267    DSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKW  326
                KG++ L  Q            D+   L ++        +G+ D VLLQ   +++  + 
Sbjct  9651   QQKGLQTLKHQ-----------VDLVKGLAQDLVVEASDSKGTSD-VLLQS--ESLVQEH  9788

Query  327    SELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQND  386
              S L ++     S LE           +++E+       DDEL   AP+G D   +QKQ +
Sbjct  9789   SALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVETLQKQKE  9968

Query  387    VHRAFKRELKTKEPVIMS---TLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
                +AF   LK  E +I S     +T ++ L  +  E    L    R+L  E  ++   +L
Sbjct  9969   AIKAF---LKKLEALIASNDNANKTCKMMLAME--ETSPDLIGIKRDL--EALSKQCNKL  10127

Query  444    L-RKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQP  502
              L R QA E                 +++ T+ERL+E      E    L++AE  + S  P
Sbjct  10128  LDRAQARE----------------EQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGP  10259

Query  503    VGDLLIDSLQDHLEKVKAL-RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLST-----  556
              VG +  +++   L   KA  + EI PL+     VN L + L    IQ +    ST     
Sbjct  10260  VG-METETINQQLNVFKAFQKEEIEPLQVKQQDVNWLGQGL----IQSAAKGTSTQGLEH  10424

Query  557    -LEDLNTRWKLLQVAVEDRVRQLHEA  581
               L+D+N RWK L   V  R  QL EA
Sbjct  10425  DLDDVNARWKTLNKKVAQRAAQLQEA  10502


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 97/443 (21%), Positives = 181/443 (40%), Gaps = 68/443 (15%)
 Frame = +3

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12966  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWESLNKAWKDRVDKLEEAMQAAVQ  13145

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  13146  YQDGLQAIFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  13301

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  13302  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  13481

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  13482  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  13613

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  13614  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  13751

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G     +E 
Sbjct  13752  TEQRKQ-------QLDGALRQAKGFHGEIEDLHQWLTDT-ERHLLASKPLGGLPETAREQ  13907

Query  532    V-SHV---------NDLARQLTTLGIQL---SPYNLSTL-EDLNT---RWKLLQVAVEDR  574
              + +H+          ++ + L   G Q+    P +  T+ +DLN    +W+ ++  + +R
Sbjct  13908  LNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKSAETIDQDLNNLKEKWESVETKLNER  14087

Query  575    VRQLHEA---HRDFGPASQHFLS  594
                +L EA     +F  + Q F++
Sbjct  14088  KTKLEEALNLAMEFHNSLQDFIN  14156


 Score = 49.7 bits (117),  Expect = 0.009, Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 106/237 (44%), Gaps = 1/237 (0%)
 Frame = +3

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  14454  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  14633

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  14634  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  14813

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  14814  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI-EGSRD  14990

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T
Sbjct  14991  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQT  15161


 Score = 49.3 bits (116),  Expect = 0.012, Method: Compositional matrix adjust.
 Identities = 102/506 (20%), Positives = 211/506 (41%), Gaps = 52/506 (10%)
 Frame = +3

Query  87     RTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESW  146
              + +ITD  + +  + D V E L +++  L  M +   ++ E  +EA++ L  A+ +L+  
Sbjct  9417   KEVITDENKSLIQKIDMVTEQLHSKKFSLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVH  9596

Query  147    KE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-ADDTRKVHMITE  204
                 GP         + +T+Q  K L+  +  VD+   LA  L+ + S +  T  V + +E
Sbjct  9597   DSLGPQAYSNKYLSVLQTQQ--KGLQTLKHQVDLVKGLAQDLVVEASDSKGTSDVLLQSE  9770

Query  205    NINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK-ER  263
              ++     ++ ++V ER + LE   + +  F   + +  +   E +   + +    R  E 
Sbjct  9771   SLVQEHSALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVET  9950

Query  264    LLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMN  323
              L +  + +K  +K+       +EA      N ++  + +L   E S D + ++R L+ ++
Sbjct  9951   LQKQKEAIKAFLKK-------LEALIASNDNANKTCKMMLAMEETSPDLIGIKRDLEALS  10109

Query  324    FKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQK  383
               + ++L  ++      +E + ++ +  +  L+E    LQ  ++    Q P+G +   + +
Sbjct  10110  KQCNKLLDRAQAREEQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGPVGMETETINQ  10289

Query  384    QNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
              Q +V +AF++E      V    +  +   L +   +G                    T+ 
Sbjct  10290  QLNVFKAFQKEEIEPLQVKQQDVNWLGQGLIQSAAKG------------------TSTQG  10415

Query  444    LRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPV  503
              L    ++VN  W+ LN   A    ++ E L      Q+A + L            SW   
Sbjct  10416  LEHDLDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESL-----------LSWMVD  10562

Query  504    GDLLIDSLQDHLEKVKALRGEIAP-------LKENVSHVNDLARQLTTLGIQLSPYN---  553
               + L+ + +    + K ++ +I         L +  S V  + R+   +     P +   
Sbjct  10563  TEELVANQKPPSAEFKVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIAATAEPADKVK  10742

Query  554    -LSTLEDLNTRWKLLQVAVEDRVRQL  578
               L  L  L++RW+ L    E R RQL
Sbjct  10743  ILKQLSLLDSRWEALLNKAETRNRQL  10820


>ref|XM_532183.2| PREDICTED: Canis familiaris dystonin, transcript variant 1 (DST), 
mRNA
Length=24184

 Score = 85.9 bits (211),  Expect = 1e-13, Method: Compositional matrix adjust.
 Identities = 136/597 (22%), Positives = 249/597 (41%), Gaps = 72/597 (12%)
 Frame = +3

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  19686  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  19865

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  19866  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  20042

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
              D  QWL   E    A + LG     AR +L +  E     D         +++ K L Q 
Sbjct  20043  DLHQWLTDTERHLLASKPLGGLPETAREQLNAHMEICAAFDV-------KEEIYKSLMQK  20201

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
                 +         L R   + +T  +     N+   W S+  +++ER+  LEE   L  +
Sbjct  20202  GQQM---------LARCPKSAET--IDQDLNNLKEKWESVETKLNERKTKLEEALNLAME  20348

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYH  293
              F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H +   
Sbjct  20349  FHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSHREQII  20510

Query  294    NLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS  353
               LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K+ H +
Sbjct  20511  ELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEA  20687

Query  354    LQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFL  413
                +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T     
Sbjct  20688  WSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT-----  20852

Query  414    TEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                             R L  +    +    L     E+  +W+ +   S + Q K++E L
Sbjct  20853  --------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEAL  20990

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENV  532
                  +  +A   L   L + E      QPV GD  ID + + ++  K  + E+     +V
Sbjct  20991  LFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGKRTSSV  21164

Query  533    SHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHEAH  582
                +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E H
Sbjct  21165  QALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFH  21335


 Score = 61.6 bits (148),  Expect = 2e-06, Method: Compositional matrix adjust.
 Identities = 87/389 (22%), Positives = 166/389 (42%), Gaps = 23/389 (5%)
 Frame = +3

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              + DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K 
Sbjct  19389  IFDWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKV  19568

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
              + +  +  + D +  ++  WD + E + NR+ +L   L    Q+  A +E    L     
Sbjct  19569  TEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQHALDELLTWLTHTEG  19748

Query  142    KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHM  201
               L   K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +  
Sbjct  19749  LLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQN  19928

Query  202    ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
                E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              
Sbjct  19929  KLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLHQWLTDT-------------  20069

Query  262    ERLLEDSK---GVKELMKQWQDLQGEIEAHTDV----YHNLDENSQKILRSLEGSDDAVL  314
              ER L  SK   G+ E  ++  +   EI A  DV    Y +L +  Q++L     S  A  
Sbjct  20070  ERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKS--AET  20243

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPI  374
              + + L+N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +  
Sbjct  20244  IDQDLNNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRP  20423

Query  375    GGDFPAVQKQNDVHRAFKRELKT-KEPVI  402
                    V  Q D H+ F  E+ + +E +I
Sbjct  20424  SLILDTVLFQIDEHKVFANEVNSHREQII  20510


 Score = 60.8 bits (146),  Expect = 5e-06, Method: Compositional matrix adjust.
 Identities = 140/566 (24%), Positives = 241/566 (42%), Gaps = 84/566 (14%)
 Frame = +3

Query  45     DINEMIIK-QKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDE  103
              D+ E ++K QK   + L  +    E+ I   +NL  KT   E +  +  ++  I+  WD 
Sbjct  15192  DVLESLLKDQKDFSKMLSAQSSIYEKTIAEGENLLLKTQGSE-KAALQSQLNTIKTSWDG  15368

Query  104    VQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKK--IT  161
                + ++ R  ++ + L+ + ++ E  E     + + +  LE  K   + +D  + +    
Sbjct  15369  FNKQVKEREDKVKDSLEKALKYKEHVETLRPWIDKCQNNLEEIK---FCLDPTETENSTA  15539

Query  162    ETKQLAKDLRQWQTNVDVANDLALKLL------RDYSADDTR----KVHMITENINA---  208
                K L K++ Q    V++ N+ A  LL      ++   D+ +    K+ M+TE +++   
Sbjct  15540  RLKSLQKEMNQHLGMVELLNNAANSLLSVCEVDKEVITDENKSLIQKIDMVTEQLHSKKF  15719

Query  209    SWRSIHKRVSEREAALEETHRLLQ--QFPLDLEKFLAWLTEAETTANVLQDATRKERLLE  266
              S  ++ ++  E +   +E  R LQ  +  LD+   L     +    +VLQ          
Sbjct  15720  SLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVHDSLGPQAYSNKYLSVLQT---------  15872

Query  267    DSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKW  326
                KG++ L  Q            D+   L ++        +G+ D VLLQ   +++  + 
Sbjct  15873  QQKGLQTLKHQ-----------VDLVKGLAQDLVVEASDSKGTSD-VLLQS--ESLVQEH  16010

Query  327    SELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQND  386
              S L ++     S LE           +++E+       DDEL   AP+G D   +QKQ +
Sbjct  16011  SALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVETLQKQKE  16190

Query  387    VHRAFKRELKTKEPVIMS---TLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
                +AF   LK  E +I S     +T ++ L  +  E    L    R+L  E  ++   +L
Sbjct  16191  AIKAF---LKKLEALIASNDNANKTCKMMLAME--ETSPDLIGIKRDL--EALSKQCNKL  16349

Query  444    L-RKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQP  502
              L R QA E                 +++ T+ERL+E      E    L++AE  + S  P
Sbjct  16350  LDRAQARE----------------EQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGP  16481

Query  503    VGDLLIDSLQDHLEKVKAL-RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLST-----  556
              VG +  +++   L   KA  + EI PL+     VN L + L    IQ +    ST     
Sbjct  16482  VG-METETINQQLNVFKAFQKEEIEPLQVKQQDVNWLGQGL----IQSAAKGTSTQGLEH  16646

Query  557    -LEDLNTRWKLLQVAVEDRVRQLHEA  581
               L+D+N RWK L   V  R  QL EA
Sbjct  16647  DLDDVNARWKTLNKKVAQRAAQLQEA  16724


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 97/443 (21%), Positives = 181/443 (40%), Gaps = 68/443 (15%)
 Frame = +3

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  19188  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWESLNKAWKDRVDKLEEAMQAAVQ  19367

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  19368  YQDGLQAIFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  19523

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  19524  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  19703

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  19704  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  19835

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  19836  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  19973

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G     +E 
Sbjct  19974  TEQRKQ-------QLDGALRQAKGFHGEIEDLHQWLTDT-ERHLLASKPLGGLPETAREQ  20129

Query  532    V-SHV---------NDLARQLTTLGIQL---SPYNLSTL-EDLNT---RWKLLQVAVEDR  574
              + +H+          ++ + L   G Q+    P +  T+ +DLN    +W+ ++  + +R
Sbjct  20130  LNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKSAETIDQDLNNLKEKWESVETKLNER  20309

Query  575    VRQLHEA---HRDFGPASQHFLS  594
                +L EA     +F  + Q F++
Sbjct  20310  KTKLEEALNLAMEFHNSLQDFIN  20378


 Score = 49.7 bits (117),  Expect = 0.009, Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 106/237 (44%), Gaps = 1/237 (0%)
 Frame = +3

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  20676  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  20855

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  20856  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  21035

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  21036  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI-EGSRD  21212

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T
Sbjct  21213  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQT  21383


 Score = 49.3 bits (116),  Expect = 0.012, Method: Compositional matrix adjust.
 Identities = 102/506 (20%), Positives = 211/506 (41%), Gaps = 52/506 (10%)
 Frame = +3

Query  87     RTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESW  146
              + +ITD  + +  + D V E L +++  L  M +   ++ E  +EA++ L  A+ +L+  
Sbjct  15639  KEVITDENKSLIQKIDMVTEQLHSKKFSLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVH  15818

Query  147    KE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-ADDTRKVHMITE  204
                 GP         + +T+Q  K L+  +  VD+   LA  L+ + S +  T  V + +E
Sbjct  15819  DSLGPQAYSNKYLSVLQTQQ--KGLQTLKHQVDLVKGLAQDLVVEASDSKGTSDVLLQSE  15992

Query  205    NINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK-ER  263
              ++     ++ ++V ER + LE   + +  F   + +  +   E +   + +    R  E 
Sbjct  15993  SLVQEHSALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVET  16172

Query  264    LLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMN  323
              L +  + +K  +K+       +EA      N ++  + +L   E S D + ++R L+ ++
Sbjct  16173  LQKQKEAIKAFLKK-------LEALIASNDNANKTCKMMLAMEETSPDLIGIKRDLEALS  16331

Query  324    FKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQK  383
               + ++L  ++      +E + ++ +  +  L+E    LQ  ++    Q P+G +   + +
Sbjct  16332  KQCNKLLDRAQAREEQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGPVGMETETINQ  16511

Query  384    QNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
              Q +V +AF++E      V    +  +   L +   +G                    T+ 
Sbjct  16512  QLNVFKAFQKEEIEPLQVKQQDVNWLGQGLIQSAAKG------------------TSTQG  16637

Query  444    LRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPV  503
              L    ++VN  W+ LN   A    ++ E L      Q+A + L            SW   
Sbjct  16638  LEHDLDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESL-----------LSWMVD  16784

Query  504    GDLLIDSLQDHLEKVKALRGEIAP-------LKENVSHVNDLARQLTTLGIQLSPYN---  553
               + L+ + +    + K ++ +I         L +  S V  + R+   +     P +   
Sbjct  16785  TEELVANQKPPSAEFKVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIAATAEPADKVK  16964

Query  554    -LSTLEDLNTRWKLLQVAVEDRVRQL  578
               L  L  L++RW+ L    E R RQL
Sbjct  16965  ILKQLSLLDSRWEALLNKAETRNRQL  17042


>ref|XM_861733.1| PREDICTED: Canis familiaris dystonin, transcript variant 17 (DST), 
mRNA
Length=17644

 Score = 85.5 bits (210),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 136/597 (22%), Positives = 249/597 (41%), Gaps = 72/597 (12%)
 Frame = +3

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  13026  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13205

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  13206  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  13382

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
              D  QWL   E    A + LG     AR +L +  E     D         +++ K L Q 
Sbjct  13383  DLHQWLTDTERHLLASKPLGGLPETAREQLNAHMEICAAFDV-------KEEIYKSLMQK  13541

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
                 +         L R   + +T  +     N+   W S+  +++ER+  LEE   L  +
Sbjct  13542  GQQM---------LARCPKSAET--IDQDLNNLKEKWESVETKLNERKTKLEEALNLAME  13688

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYH  293
              F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H +   
Sbjct  13689  FHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSHREQII  13850

Query  294    NLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS  353
               LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K+ H +
Sbjct  13851  ELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEA  14027

Query  354    LQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFL  413
                +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T     
Sbjct  14028  WSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT-----  14192

Query  414    TEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                             R L  +    +    L     E+  +W+ +   S + Q K++E L
Sbjct  14193  --------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEAL  14330

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENV  532
                  +  +A   L   L + E      QPV GD  ID + + ++  K  + E+     +V
Sbjct  14331  LFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGKRTSSV  14504

Query  533    SHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHEAH  582
                +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E H
Sbjct  14505  QALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFH  14675


 Score = 61.6 bits (148),  Expect = 3e-06, Method: Compositional matrix adjust.
 Identities = 87/389 (22%), Positives = 166/389 (42%), Gaps = 23/389 (5%)
 Frame = +3

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              + DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K 
Sbjct  12729  IFDWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKV  12908

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
              + +  +  + D +  ++  WD + E + NR+ +L   L    Q+  A +E    L     
Sbjct  12909  TEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQHALDELLTWLTHTEG  13088

Query  142    KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHM  201
               L   K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +  
Sbjct  13089  LLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQN  13268

Query  202    ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
                E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              
Sbjct  13269  KLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLHQWLTDT-------------  13409

Query  262    ERLLEDSK---GVKELMKQWQDLQGEIEAHTDV----YHNLDENSQKILRSLEGSDDAVL  314
              ER L  SK   G+ E  ++  +   EI A  DV    Y +L +  Q++L     S  A  
Sbjct  13410  ERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKS--AET  13583

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPI  374
              + + L+N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +  
Sbjct  13584  IDQDLNNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRP  13763

Query  375    GGDFPAVQKQNDVHRAFKRELKT-KEPVI  402
                    V  Q D H+ F  E+ + +E +I
Sbjct  13764  SLILDTVLFQIDEHKVFANEVNSHREQII  13850


 Score = 60.8 bits (146),  Expect = 5e-06, Method: Compositional matrix adjust.
 Identities = 140/566 (24%), Positives = 241/566 (42%), Gaps = 84/566 (14%)
 Frame = +3

Query  45     DINEMIIK-QKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDE  103
              D+ E ++K QK   + L  +    E+ I   +NL  KT   E +  +  ++  I+  WD 
Sbjct  8532   DVLESLLKDQKDFSKMLSAQSSIYEKTIAEGENLLLKTQGSE-KAALQSQLNTIKTSWDG  8708

Query  104    VQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKK--IT  161
                + ++ R  ++ + L+ + ++ E  E     + + +  LE  K   + +D  + +    
Sbjct  8709   FNKQVKEREDKVKDSLEKALKYKEHVETLRPWIDKCQNNLEEIK---FCLDPTETENSTA  8879

Query  162    ETKQLAKDLRQWQTNVDVANDLALKLL------RDYSADDTR----KVHMITENINA---  208
                K L K++ Q    V++ N+ A  LL      ++   D+ +    K+ M+TE +++   
Sbjct  8880   RLKSLQKEMNQHLGMVELLNNAANSLLSVCEVDKEVITDENKSLIQKIDMVTEQLHSKKF  9059

Query  209    SWRSIHKRVSEREAALEETHRLLQ--QFPLDLEKFLAWLTEAETTANVLQDATRKERLLE  266
              S  ++ ++  E +   +E  R LQ  +  LD+   L     +    +VLQ          
Sbjct  9060   SLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVHDSLGPQAYSNKYLSVLQT---------  9212

Query  267    DSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKW  326
                KG++ L  Q            D+   L ++        +G+ D VLLQ   +++  + 
Sbjct  9213   QQKGLQTLKHQ-----------VDLVKGLAQDLVVEASDSKGTSD-VLLQS--ESLVQEH  9350

Query  327    SELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQND  386
              S L ++     S LE           +++E+       DDEL   AP+G D   +QKQ +
Sbjct  9351   SALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVETLQKQKE  9530

Query  387    VHRAFKRELKTKEPVIMS---TLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
                +AF   LK  E +I S     +T ++ L  +  E    L    R+L  E  ++   +L
Sbjct  9531   AIKAF---LKKLEALIASNDNANKTCKMMLAME--ETSPDLIGIKRDL--EALSKQCNKL  9689

Query  444    L-RKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQP  502
              L R QA E                 +++ T+ERL+E      E    L++AE  + S  P
Sbjct  9690   LDRAQARE----------------EQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGP  9821

Query  503    VGDLLIDSLQDHLEKVKAL-RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLST-----  556
              VG +  +++   L   KA  + EI PL+     VN L + L    IQ +    ST     
Sbjct  9822   VG-METETINQQLNVFKAFQKEEIEPLQVKQQDVNWLGQGL----IQSAAKGTSTQGLEH  9986

Query  557    -LEDLNTRWKLLQVAVEDRVRQLHEA  581
               L+D+N RWK L   V  R  QL EA
Sbjct  9987   DLDDVNARWKTLNKKVAQRAAQLQEA  10064


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 97/443 (21%), Positives = 181/443 (40%), Gaps = 68/443 (15%)
 Frame = +3

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12528  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWESLNKAWKDRVDKLEEAMQAAVQ  12707

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  12708  YQDGLQAIFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  12863

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  12864  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  13043

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  13044  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  13175

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  13176  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  13313

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G     +E 
Sbjct  13314  TEQRKQ-------QLDGALRQAKGFHGEIEDLHQWLTDT-ERHLLASKPLGGLPETAREQ  13469

Query  532    V-SHV---------NDLARQLTTLGIQL---SPYNLSTL-EDLNT---RWKLLQVAVEDR  574
              + +H+          ++ + L   G Q+    P +  T+ +DLN    +W+ ++  + +R
Sbjct  13470  LNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKSAETIDQDLNNLKEKWESVETKLNER  13649

Query  575    VRQLHEA---HRDFGPASQHFLS  594
                +L EA     +F  + Q F++
Sbjct  13650  KTKLEEALNLAMEFHNSLQDFIN  13718


 Score = 49.7 bits (117),  Expect = 0.009, Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 106/237 (44%), Gaps = 1/237 (0%)
 Frame = +3

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  14016  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  14195

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  14196  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  14375

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  14376  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI-EGSRD  14552

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T
Sbjct  14553  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQT  14723


 Score = 49.3 bits (116),  Expect = 0.013, Method: Compositional matrix adjust.
 Identities = 102/506 (20%), Positives = 211/506 (41%), Gaps = 52/506 (10%)
 Frame = +3

Query  87     RTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESW  146
              + +ITD  + +  + D V E L +++  L  M +   ++ E  +EA++ L  A+ +L+  
Sbjct  8979   KEVITDENKSLIQKIDMVTEQLHSKKFSLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVH  9158

Query  147    KE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-ADDTRKVHMITE  204
                 GP         + +T+Q  K L+  +  VD+   LA  L+ + S +  T  V + +E
Sbjct  9159   DSLGPQAYSNKYLSVLQTQQ--KGLQTLKHQVDLVKGLAQDLVVEASDSKGTSDVLLQSE  9332

Query  205    NINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK-ER  263
              ++     ++ ++V ER + LE   + +  F   + +  +   E +   + +    R  E 
Sbjct  9333   SLVQEHSALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVET  9512

Query  264    LLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMN  323
              L +  + +K  +K+       +EA      N ++  + +L   E S D + ++R L+ ++
Sbjct  9513   LQKQKEAIKAFLKK-------LEALIASNDNANKTCKMMLAMEETSPDLIGIKRDLEALS  9671

Query  324    FKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQK  383
               + ++L  ++      +E + ++ +  +  L+E    LQ  ++    Q P+G +   + +
Sbjct  9672   KQCNKLLDRAQAREEQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGPVGMETETINQ  9851

Query  384    QNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
              Q +V +AF++E      V    +  +   L +   +G                    T+ 
Sbjct  9852   QLNVFKAFQKEEIEPLQVKQQDVNWLGQGLIQSAAKG------------------TSTQG  9977

Query  444    LRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPV  503
              L    ++VN  W+ LN   A    ++ E L      Q+A + L            SW   
Sbjct  9978   LEHDLDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESL-----------LSWMVD  10124

Query  504    GDLLIDSLQDHLEKVKALRGEIAP-------LKENVSHVNDLARQLTTLGIQLSPYN---  553
               + L+ + +    + K ++ +I         L +  S V  + R+   +     P +   
Sbjct  10125  TEELVANQKPPSAEFKVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIAATAEPADKVK  10304

Query  554    -LSTLEDLNTRWKLLQVAVEDRVRQL  578
               L  L  L++RW+ L    E R RQL
Sbjct  10305  ILKQLSLLDSRWEALLNKAETRNRQL  10382


>ref|XM_861720.1| PREDICTED: Canis familiaris dystonin, transcript variant 16 (DST), 
mRNA
Length=17550

 Score = 85.5 bits (210),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 136/597 (22%), Positives = 249/597 (41%), Gaps = 72/597 (12%)
 Frame = +2

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  12932  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13111

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  13112  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  13288

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
              D  QWL   E    A + LG     AR +L +  E     D         +++ K L Q 
Sbjct  13289  DLHQWLTDTERHLLASKPLGGLPETAREQLNAHMEICAAFDV-------KEEIYKSLMQK  13447

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
                 +         L R   + +T  +     N+   W S+  +++ER+  LEE   L  +
Sbjct  13448  GQQM---------LARCPKSAET--IDQDLNNLKEKWESVETKLNERKTKLEEALNLAME  13594

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYH  293
              F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H +   
Sbjct  13595  FHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSHREQII  13756

Query  294    NLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS  353
               LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K+ H +
Sbjct  13757  ELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEA  13933

Query  354    LQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFL  413
                +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T     
Sbjct  13934  WSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT-----  14098

Query  414    TEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                             R L  +    +    L     E+  +W+ +   S + Q K++E L
Sbjct  14099  --------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEAL  14236

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENV  532
                  +  +A   L   L + E      QPV GD  ID + + ++  K  + E+     +V
Sbjct  14237  LFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGKRTSSV  14410

Query  533    SHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHEAH  582
                +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E H
Sbjct  14411  QALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFH  14581


 Score = 61.6 bits (148),  Expect = 3e-06, Method: Compositional matrix adjust.
 Identities = 87/389 (22%), Positives = 166/389 (42%), Gaps = 23/389 (5%)
 Frame = +2

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              + DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K 
Sbjct  12635  IFDWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKV  12814

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
              + +  +  + D +  ++  WD + E + NR+ +L   L    Q+  A +E    L     
Sbjct  12815  TEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQHALDELLTWLTHTEG  12994

Query  142    KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHM  201
               L   K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +  
Sbjct  12995  LLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQN  13174

Query  202    ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
                E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              
Sbjct  13175  KLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLHQWLTDT-------------  13315

Query  262    ERLLEDSK---GVKELMKQWQDLQGEIEAHTDV----YHNLDENSQKILRSLEGSDDAVL  314
              ER L  SK   G+ E  ++  +   EI A  DV    Y +L +  Q++L     S  A  
Sbjct  13316  ERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKS--AET  13489

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPI  374
              + + L+N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +  
Sbjct  13490  IDQDLNNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRP  13669

Query  375    GGDFPAVQKQNDVHRAFKRELKT-KEPVI  402
                    V  Q D H+ F  E+ + +E +I
Sbjct  13670  SLILDTVLFQIDEHKVFANEVNSHREQII  13756


 Score = 60.8 bits (146),  Expect = 5e-06, Method: Compositional matrix adjust.
 Identities = 140/566 (24%), Positives = 241/566 (42%), Gaps = 84/566 (14%)
 Frame = +2

Query  45    DINEMIIK-QKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDE  103
             D+ E ++K QK   + L  +    E+ I   +NL  KT   E +  +  ++  I+  WD 
Sbjct  8438  DVLESLLKDQKDFSKMLSAQSSIYEKTIAEGENLLLKTQGSE-KAALQSQLNTIKTSWDG  8614

Query  104   VQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKK--IT  161
               + ++ R  ++ + L+ + ++ E  E     + + +  LE  K   + +D  + +    
Sbjct  8615  FNKQVKEREDKVKDSLEKALKYKEHVETLRPWIDKCQNNLEEIK---FCLDPTETENSTA  8785

Query  162   ETKQLAKDLRQWQTNVDVANDLALKLL------RDYSADDTR----KVHMITENINA---  208
               K L K++ Q    V++ N+ A  LL      ++   D+ +    K+ M+TE +++   
Sbjct  8786  RLKSLQKEMNQHLGMVELLNNAANSLLSVCEVDKEVITDENKSLIQKIDMVTEQLHSKKF  8965

Query  209   SWRSIHKRVSEREAALEETHRLLQ--QFPLDLEKFLAWLTEAETTANVLQDATRKERLLE  266
             S  ++ ++  E +   +E  R LQ  +  LD+   L     +    +VLQ          
Sbjct  8966  SLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVHDSLGPQAYSNKYLSVLQT---------  9118

Query  267   DSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKW  326
               KG++ L  Q            D+   L ++        +G+ D VLLQ   +++  + 
Sbjct  9119  QQKGLQTLKHQ-----------VDLVKGLAQDLVVEASDSKGTSD-VLLQS--ESLVQEH  9256

Query  327   SELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQND  386
             S L ++     S LE           +++E+       DDEL   AP+G D   +QKQ +
Sbjct  9257  SALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVETLQKQKE  9436

Query  387   VHRAFKRELKTKEPVIMS---TLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
               +AF   LK  E +I S     +T ++ L  +  E    L    R+L  E  ++   +L
Sbjct  9437  AIKAF---LKKLEALIASNDNANKTCKMMLAME--ETSPDLIGIKRDL--EALSKQCNKL  9595

Query  444   L-RKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQP  502
             L R QA E                 +++ T+ERL+E      E    L++AE  + S  P
Sbjct  9596  LDRAQARE----------------EQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGP  9727

Query  503   VGDLLIDSLQDHLEKVKAL-RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLST-----  556
             VG +  +++   L   KA  + EI PL+     VN L + L    IQ +    ST     
Sbjct  9728  VG-METETINQQLNVFKAFQKEEIEPLQVKQQDVNWLGQGL----IQSAAKGTSTQGLEH  9892

Query  557   -LEDLNTRWKLLQVAVEDRVRQLHEA  581
              L+D+N RWK L   V  R  QL EA
Sbjct  9893  DLDDVNARWKTLNKKVAQRAAQLQEA  9970


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 97/443 (21%), Positives = 181/443 (40%), Gaps = 68/443 (15%)
 Frame = +2

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12434  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWESLNKAWKDRVDKLEEAMQAAVQ  12613

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  12614  YQDGLQAIFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  12769

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  12770  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  12949

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  12950  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  13081

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  13082  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  13219

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G     +E 
Sbjct  13220  TEQRKQ-------QLDGALRQAKGFHGEIEDLHQWLTDT-ERHLLASKPLGGLPETAREQ  13375

Query  532    V-SHV---------NDLARQLTTLGIQL---SPYNLSTL-EDLNT---RWKLLQVAVEDR  574
              + +H+          ++ + L   G Q+    P +  T+ +DLN    +W+ ++  + +R
Sbjct  13376  LNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKSAETIDQDLNNLKEKWESVETKLNER  13555

Query  575    VRQLHEA---HRDFGPASQHFLS  594
                +L EA     +F  + Q F++
Sbjct  13556  KTKLEEALNLAMEFHNSLQDFIN  13624


 Score = 49.7 bits (117),  Expect = 0.009, Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 106/237 (44%), Gaps = 1/237 (0%)
 Frame = +2

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  13922  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  14101

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  14102  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  14281

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  14282  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI-EGSRD  14458

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T
Sbjct  14459  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQT  14629


 Score = 49.3 bits (116),  Expect = 0.013, Method: Compositional matrix adjust.
 Identities = 102/506 (20%), Positives = 211/506 (41%), Gaps = 52/506 (10%)
 Frame = +2

Query  87     RTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESW  146
              + +ITD  + +  + D V E L +++  L  M +   ++ E  +EA++ L  A+ +L+  
Sbjct  8885   KEVITDENKSLIQKIDMVTEQLHSKKFSLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVH  9064

Query  147    KE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-ADDTRKVHMITE  204
                 GP         + +T+Q  K L+  +  VD+   LA  L+ + S +  T  V + +E
Sbjct  9065   DSLGPQAYSNKYLSVLQTQQ--KGLQTLKHQVDLVKGLAQDLVVEASDSKGTSDVLLQSE  9238

Query  205    NINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK-ER  263
              ++     ++ ++V ER + LE   + +  F   + +  +   E +   + +    R  E 
Sbjct  9239   SLVQEHSALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVET  9418

Query  264    LLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMN  323
              L +  + +K  +K+       +EA      N ++  + +L   E S D + ++R L+ ++
Sbjct  9419   LQKQKEAIKAFLKK-------LEALIASNDNANKTCKMMLAMEETSPDLIGIKRDLEALS  9577

Query  324    FKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQK  383
               + ++L  ++      +E + ++ +  +  L+E    LQ  ++    Q P+G +   + +
Sbjct  9578   KQCNKLLDRAQAREEQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGPVGMETETINQ  9757

Query  384    QNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
              Q +V +AF++E      V    +  +   L +   +G                    T+ 
Sbjct  9758   QLNVFKAFQKEEIEPLQVKQQDVNWLGQGLIQSAAKG------------------TSTQG  9883

Query  444    LRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPV  503
              L    ++VN  W+ LN   A    ++ E L      Q+A + L            SW   
Sbjct  9884   LEHDLDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESL-----------LSWMVD  10030

Query  504    GDLLIDSLQDHLEKVKALRGEIAP-------LKENVSHVNDLARQLTTLGIQLSPYN---  553
               + L+ + +    + K ++ +I         L +  S V  + R+   +     P +   
Sbjct  10031  TEELVANQKPPSAEFKVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIAATAEPADKVK  10210

Query  554    -LSTLEDLNTRWKLLQVAVEDRVRQL  578
               L  L  L++RW+ L    E R RQL
Sbjct  10211  ILKQLSLLDSRWEALLNKAETRNRQL  10288


>ref|XM_861709.1| PREDICTED: Canis familiaris dystonin, transcript variant 15 (DST), 
mRNA
Length=16630

 Score = 85.5 bits (210),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 136/597 (22%), Positives = 249/597 (41%), Gaps = 72/597 (12%)
 Frame = +3

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  12012  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  12191

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  12192  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  12368

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
              D  QWL   E    A + LG     AR +L +  E     D         +++ K L Q 
Sbjct  12369  DLHQWLTDTERHLLASKPLGGLPETAREQLNAHMEICAAFDV-------KEEIYKSLMQK  12527

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
                 +         L R   + +T  +     N+   W S+  +++ER+  LEE   L  +
Sbjct  12528  GQQM---------LARCPKSAET--IDQDLNNLKEKWESVETKLNERKTKLEEALNLAME  12674

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYH  293
              F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H +   
Sbjct  12675  FHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSHREQII  12836

Query  294    NLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS  353
               LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K+ H +
Sbjct  12837  ELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEA  13013

Query  354    LQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFL  413
                +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T     
Sbjct  13014  WSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT-----  13178

Query  414    TEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                             R L  +    +    L     E+  +W+ +   S + Q K++E L
Sbjct  13179  --------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEAL  13316

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENV  532
                  +  +A   L   L + E      QPV GD  ID + + ++  K  + E+     +V
Sbjct  13317  LFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGKRTSSV  13490

Query  533    SHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHEAH  582
                +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E H
Sbjct  13491  QALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFH  13661


 Score = 61.6 bits (148),  Expect = 3e-06, Method: Compositional matrix adjust.
 Identities = 87/389 (22%), Positives = 166/389 (42%), Gaps = 23/389 (5%)
 Frame = +3

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              + DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K 
Sbjct  11715  IFDWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKV  11894

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
              + +  +  + D +  ++  WD + E + NR+ +L   L    Q+  A +E    L     
Sbjct  11895  TEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQHALDELLTWLTHTEG  12074

Query  142    KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHM  201
               L   K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +  
Sbjct  12075  LLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQN  12254

Query  202    ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
                E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              
Sbjct  12255  KLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLHQWLTDT-------------  12395

Query  262    ERLLEDSK---GVKELMKQWQDLQGEIEAHTDV----YHNLDENSQKILRSLEGSDDAVL  314
              ER L  SK   G+ E  ++  +   EI A  DV    Y +L +  Q++L     S  A  
Sbjct  12396  ERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKS--AET  12569

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPI  374
              + + L+N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +  
Sbjct  12570  IDQDLNNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRP  12749

Query  375    GGDFPAVQKQNDVHRAFKRELKT-KEPVI  402
                    V  Q D H+ F  E+ + +E +I
Sbjct  12750  SLILDTVLFQIDEHKVFANEVNSHREQII  12836


 Score = 60.8 bits (146),  Expect = 5e-06, Method: Compositional matrix adjust.
 Identities = 140/566 (24%), Positives = 241/566 (42%), Gaps = 84/566 (14%)
 Frame = +3

Query  45    DINEMIIK-QKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDE  103
             D+ E ++K QK   + L  +    E+ I   +NL  KT   E +  +  ++  I+  WD 
Sbjct  7518  DVLESLLKDQKDFSKMLSAQSSIYEKTIAEGENLLLKTQGSE-KAALQSQLNTIKTSWDG  7694

Query  104   VQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKK--IT  161
               + ++ R  ++ + L+ + ++ E  E     + + +  LE  K   + +D  + +    
Sbjct  7695  FNKQVKEREDKVKDSLEKALKYKEHVETLRPWIDKCQNNLEEIK---FCLDPTETENSTA  7865

Query  162   ETKQLAKDLRQWQTNVDVANDLALKLL------RDYSADDTR----KVHMITENINA---  208
               K L K++ Q    V++ N+ A  LL      ++   D+ +    K+ M+TE +++   
Sbjct  7866  RLKSLQKEMNQHLGMVELLNNAANSLLSVCEVDKEVITDENKSLIQKIDMVTEQLHSKKF  8045

Query  209   SWRSIHKRVSEREAALEETHRLLQ--QFPLDLEKFLAWLTEAETTANVLQDATRKERLLE  266
             S  ++ ++  E +   +E  R LQ  +  LD+   L     +    +VLQ          
Sbjct  8046  SLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVHDSLGPQAYSNKYLSVLQT---------  8198

Query  267   DSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKW  326
               KG++ L  Q            D+   L ++        +G+ D VLLQ   +++  + 
Sbjct  8199  QQKGLQTLKHQ-----------VDLVKGLAQDLVVEASDSKGTSD-VLLQS--ESLVQEH  8336

Query  327   SELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQND  386
             S L ++     S LE           +++E+       DDEL   AP+G D   +QKQ +
Sbjct  8337  SALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVETLQKQKE  8516

Query  387   VHRAFKRELKTKEPVIMS---TLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
               +AF   LK  E +I S     +T ++ L  +  E    L    R+L  E  ++   +L
Sbjct  8517  AIKAF---LKKLEALIASNDNANKTCKMMLAME--ETSPDLIGIKRDL--EALSKQCNKL  8675

Query  444   L-RKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQP  502
             L R QA E                 +++ T+ERL+E      E    L++AE  + S  P
Sbjct  8676  LDRAQARE----------------EQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGP  8807

Query  503   VGDLLIDSLQDHLEKVKAL-RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLST-----  556
             VG +  +++   L   KA  + EI PL+     VN L + L    IQ +    ST     
Sbjct  8808  VG-METETINQQLNVFKAFQKEEIEPLQVKQQDVNWLGQGL----IQSAAKGTSTQGLEH  8972

Query  557   -LEDLNTRWKLLQVAVEDRVRQLHEA  581
              L+D+N RWK L   V  R  QL EA
Sbjct  8973  DLDDVNARWKTLNKKVAQRAAQLQEA  9050


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 97/443 (21%), Positives = 181/443 (40%), Gaps = 68/443 (15%)
 Frame = +3

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  11514  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWESLNKAWKDRVDKLEEAMQAAVQ  11693

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  11694  YQDGLQAIFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  11849

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  11850  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  12029

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  12030  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  12161

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  12162  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  12299

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G     +E 
Sbjct  12300  TEQRKQ-------QLDGALRQAKGFHGEIEDLHQWLTDT-ERHLLASKPLGGLPETAREQ  12455

Query  532    V-SHV---------NDLARQLTTLGIQL---SPYNLSTL-EDLNT---RWKLLQVAVEDR  574
              + +H+          ++ + L   G Q+    P +  T+ +DLN    +W+ ++  + +R
Sbjct  12456  LNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKSAETIDQDLNNLKEKWESVETKLNER  12635

Query  575    VRQLHEA---HRDFGPASQHFLS  594
                +L EA     +F  + Q F++
Sbjct  12636  KTKLEEALNLAMEFHNSLQDFIN  12704


 Score = 49.7 bits (117),  Expect = 0.009, Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 106/237 (44%), Gaps = 1/237 (0%)
 Frame = +3

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  13002  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  13181

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  13182  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  13361

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  13362  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI-EGSRD  13538

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T
Sbjct  13539  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQT  13709


 Score = 49.3 bits (116),  Expect = 0.013, Method: Compositional matrix adjust.
 Identities = 102/506 (20%), Positives = 211/506 (41%), Gaps = 52/506 (10%)
 Frame = +3

Query  87    RTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESW  146
             + +ITD  + +  + D V E L +++  L  M +   ++ E  +EA++ L  A+ +L+  
Sbjct  7965  KEVITDENKSLIQKIDMVTEQLHSKKFSLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVH  8144

Query  147   KE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-ADDTRKVHMITE  204
                GP         + +T+Q  K L+  +  VD+   LA  L+ + S +  T  V + +E
Sbjct  8145  DSLGPQAYSNKYLSVLQTQQ--KGLQTLKHQVDLVKGLAQDLVVEASDSKGTSDVLLQSE  8318

Query  205   NINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK-ER  263
             ++     ++ ++V ER + LE   + +  F   + +  +   E +   + +    R  E 
Sbjct  8319  SLVQEHSALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVET  8498

Query  264   LLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMN  323
             L +  + +K  +K+       +EA      N ++  + +L   E S D + ++R L+ ++
Sbjct  8499  LQKQKEAIKAFLKK-------LEALIASNDNANKTCKMMLAMEETSPDLIGIKRDLEALS  8657

Query  324   FKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQK  383
              + ++L  ++      +E + ++ +  +  L+E    LQ  ++    Q P+G +   + +
Sbjct  8658  KQCNKLLDRAQAREEQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGPVGMETETINQ  8837

Query  384   QNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
             Q +V +AF++E      V    +  +   L +   +G                    T+ 
Sbjct  8838  QLNVFKAFQKEEIEPLQVKQQDVNWLGQGLIQSAAKG------------------TSTQG  8963

Query  444   LRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPV  503
             L    ++VN  W+ LN   A    ++ E L      Q+A + L            SW   
Sbjct  8964  LEHDLDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESL-----------LSWMVD  9110

Query  504   GDLLIDSLQDHLEKVKALRGEIAP-------LKENVSHVNDLARQLTTLGIQLSPYN---  553
              + L+ + +    + K ++ +I         L +  S V  + R+   +     P +   
Sbjct  9111  TEELVANQKPPSAEFKVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIAATAEPADKVK  9290

Query  554   -LSTLEDLNTRWKLLQVAVEDRVRQL  578
              L  L  L++RW+ L    E R RQL
Sbjct  9291  ILKQLSLLDSRWEALLNKAETRNRQL  9368


>ref|XM_861528.1| PREDICTED: Canis familiaris dystonin, transcript variant 2 (DST), 
mRNA
Length=18082

 Score = 85.5 bits (210),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 136/597 (22%), Positives = 249/597 (41%), Gaps = 72/597 (12%)
 Frame = +3

Query  11     ALADFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEEL  70
              AL  F  A  EL  WL+  + ++  Q+ + GD + I   + K      D+   +  +E +
Sbjct  13464  ALGQFQHALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAV  13643

Query  71     ITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLK----------  120
                A  +L   ++ +EA  +  +++E +  +W  V E  + R+QQL+  L+          
Sbjct  13644  NKAGNDLIESSAGEEASNL-QNKLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIE  13820

Query  121    DSTQWLEAKEE---AEQVLG----QARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQW  173
              D  QWL   E    A + LG     AR +L +  E     D         +++ K L Q 
Sbjct  13821  DLHQWLTDTERHLLASKPLGGLPETAREQLNAHMEICAAFDV-------KEEIYKSLMQK  13979

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
                 +         L R   + +T  +     N+   W S+  +++ER+  LEE   L  +
Sbjct  13980  GQQM---------LARCPKSAET--IDQDLNNLKEKWESVETKLNERKTKLEEALNLAME  14126

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYH  293
              F   L+ F+ WLT+AE T NV   A+R   +L+    V   + + +    E+ +H +   
Sbjct  14127  FHNSLQDFINWLTQAEQTLNV---ASRPSLILD---TVLFQIDEHKVFANEVNSHREQII  14288

Query  294    NLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLS  353
               LD+     L+      D VL++  L ++  +W ++ ++ +     L+ +  + K+ H +
Sbjct  14289  ELDKTGTH-LKYFSQKQDVVLIKNLLISVQSRWEKVVQRLVERGRSLDDARKRAKQFHEA  14465

Query  354    LQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFL  413
                +L+ WL+  +  L  +  I  D   ++ Q   H+ F++ L  K  V  +T  T     
Sbjct  14466  WSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRT-----  14630

Query  414    TEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETL  473
                             R L  +    +    L     E+  +W+ +   S + Q K++E L
Sbjct  14631  --------------GRSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEAL  14768

Query  474    ERLQELQEATDELDLKLRQAEVIKGSWQPV-GDLLIDSLQDHLEKVKALRGEIAPLKENV  532
                  +  +A   L   L + E      QPV GD  ID + + ++  K  + E+     +V
Sbjct  14769  LFSGQFTDALQALIDWLYRVEPQLAEDQPVHGD--IDLVMNLIDNHKVFQKELGKRTSSV  14942

Query  533    SHVNDLARQLTTLGIQLSPYNLSTLEDLNTRWKLL-------QVAVEDRVRQLHEAH  582
                +   AR+L       S +    +++L+TRW+ +       Q  +E  +RQ  E H
Sbjct  14943  QALKRSARELIEGSRDDSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFH  15113


 Score = 61.6 bits (148),  Expect = 3e-06, Method: Compositional matrix adjust.
 Identities = 87/389 (22%), Positives = 166/389 (42%), Gaps = 23/389 (5%)
 Frame = +3

Query  22     LTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKT  81
              + DW+ +    + S   +  DLE + + I + K    +  Q++ ++E L   A+ L  K 
Sbjct  13167  IFDWVDIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIEMERLNHQAELLLKKV  13346

Query  82     SNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARA  141
              + +  +  + D +  ++  WD + E + NR+ +L   L    Q+  A +E    L     
Sbjct  13347  TEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQHALDELLTWLTHTEG  13526

Query  142    KLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHM  201
               L   K       AI+ ++ +   L  D+   Q+ V+  N     L+   + ++   +  
Sbjct  13527  LLSEQKPVGGDPKAIEIELAKHHVLQNDVLAHQSTVEAVNKAGNDLIESSAGEEASNLQN  13706

Query  202    ITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK  261
                E +N  W+++ ++  +R+  L+   R  + F  ++E    WLT+              
Sbjct  13707  KLEVLNQRWQNVLEKTEQRKQQLDGALRQAKGFHGEIEDLHQWLTDT-------------  13847

Query  262    ERLLEDSK---GVKELMKQWQDLQGEIEAHTDV----YHNLDENSQKILRSLEGSDDAVL  314
              ER L  SK   G+ E  ++  +   EI A  DV    Y +L +  Q++L     S  A  
Sbjct  13848  ERHLLASKPLGGLPETAREQLNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKS--AET  14021

Query  315    LQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPI  374
              + + L+N+  KW  +  K    ++ LE + +     H SLQ+ + WL   +  L+  +  
Sbjct  14022  IDQDLNNLKEKWESVETKLNERKTKLEEALNLAMEFHNSLQDFINWLTQAEQTLNVASRP  14201

Query  375    GGDFPAVQKQNDVHRAFKRELKT-KEPVI  402
                    V  Q D H+ F  E+ + +E +I
Sbjct  14202  SLILDTVLFQIDEHKVFANEVNSHREQII  14288


 Score = 60.8 bits (146),  Expect = 5e-06, Method: Compositional matrix adjust.
 Identities = 140/566 (24%), Positives = 241/566 (42%), Gaps = 84/566 (14%)
 Frame = +3

Query  45     DINEMIIK-QKATMQDLEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDE  103
              D+ E ++K QK   + L  +    E+ I   +NL  KT   E +  +  ++  I+  WD 
Sbjct  8970   DVLESLLKDQKDFSKMLSAQSSIYEKTIAEGENLLLKTQGSE-KAALQSQLNTIKTSWDG  9146

Query  104    VQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTVDAIQKK--IT  161
                + ++ R  ++ + L+ + ++ E  E     + + +  LE  K   + +D  + +    
Sbjct  9147   FNKQVKEREDKVKDSLEKALKYKEHVETLRPWIDKCQNNLEEIK---FCLDPTETENSTA  9317

Query  162    ETKQLAKDLRQWQTNVDVANDLALKLL------RDYSADDTR----KVHMITENINA---  208
                K L K++ Q    V++ N+ A  LL      ++   D+ +    K+ M+TE +++   
Sbjct  9318   RLKSLQKEMNQHLGMVELLNNAANSLLSVCEVDKEVITDENKSLIQKIDMVTEQLHSKKF  9497

Query  209    SWRSIHKRVSEREAALEETHRLLQ--QFPLDLEKFLAWLTEAETTANVLQDATRKERLLE  266
              S  ++ ++  E +   +E  R LQ  +  LD+   L     +    +VLQ          
Sbjct  9498   SLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVHDSLGPQAYSNKYLSVLQT---------  9650

Query  267    DSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKW  326
                KG++ L  Q            D+   L ++        +G+ D VLLQ   +++  + 
Sbjct  9651   QQKGLQTLKHQ-----------VDLVKGLAQDLVVEASDSKGTSD-VLLQS--ESLVQEH  9788

Query  327    SELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQND  386
              S L ++     S LE           +++E+       DDEL   AP+G D   +QKQ +
Sbjct  9789   SALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVETLQKQKE  9968

Query  387    VHRAFKRELKTKEPVIMS---TLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
                +AF   LK  E +I S     +T ++ L  +  E    L    R+L  E  ++   +L
Sbjct  9969   AIKAF---LKKLEALIASNDNANKTCKMMLAME--ETSPDLIGIKRDL--EALSKQCNKL  10127

Query  444    L-RKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQP  502
              L R QA E                 +++ T+ERL+E      E    L++AE  + S  P
Sbjct  10128  LDRAQARE----------------EQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGP  10259

Query  503    VGDLLIDSLQDHLEKVKAL-RGEIAPLKENVSHVNDLARQLTTLGIQLSPYNLST-----  556
              VG +  +++   L   KA  + EI PL+     VN L + L    IQ +    ST     
Sbjct  10260  VG-METETINQQLNVFKAFQKEEIEPLQVKQQDVNWLGQGL----IQSAAKGTSTQGLEH  10424

Query  557    -LEDLNTRWKLLQVAVEDRVRQLHEA  581
               L+D+N RWK L   V  R  QL EA
Sbjct  10425  DLDDVNARWKTLNKKVAQRAAQLQEA  10502


 Score = 52.0 bits (123),  Expect = 0.002, Method: Compositional matrix adjust.
 Identities = 97/443 (21%), Positives = 181/443 (40%), Gaps = 68/443 (15%)
 Frame = +3

Query  174    QTNVDVANDLALKLLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQ  233
              Q  +D+  +L  +L+      D   V    + +N++W S++K   +R   LEE  +   Q
Sbjct  12966  QEELDMVINLGSELIAACGEPDKPIVKKSIDELNSAWESLNKAWKDRVDKLEEAMQAAVQ  13145

Query  234    FPLDLEKFLAWLTEAETTANVLQDATRKERLLEDSKGVKELMKQWQD--LQGEIEAHTDV  291
              +   L+    W+   +     L   +     LE  K   E +KQ++    Q +IE     
Sbjct  13146  YQDGLQAIFDWV---DIAGGKLASMSPIGTDLETVKQQIEELKQFKSEAYQQQIE-----  13301

Query  292    YHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLH  351
                 L+  ++ +L+ +    D   +Q  L  +   W  L ++ +N +  LE +     +  
Sbjct  13302  MERLNHQAELLLKKVTEESDKHTVQDPLMELKLIWDSLDERIINRQHKLEGALLALGQFQ  13481

Query  352    LSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRI  411
               +L ELL WL   +  LS Q P+GGD  A++ +   H   + +                +
Sbjct  13482  HALDELLTWLTHTEGLLSEQKPVGGDPKAIEIELAKHHVLQND----------------V  13613

Query  412    FLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDE  471
                 +  +E + K   +  E    E A N+                KL + +  WQ  +++
Sbjct  13614  LAHQSTVEAVNKAGNDLIESSAGEEASNLQN--------------KLEVLNQRWQNVLEK  13751

Query  472    TLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKEN  531
              T +R Q       +LD  LRQA+   G  + +   L D+ + HL   K L G     +E 
Sbjct  13752  TEQRKQ-------QLDGALRQAKGFHGEIEDLHQWLTDT-ERHLLASKPLGGLPETAREQ  13907

Query  532    V-SHV---------NDLARQLTTLGIQL---SPYNLSTL-EDLNT---RWKLLQVAVEDR  574
              + +H+          ++ + L   G Q+    P +  T+ +DLN    +W+ ++  + +R
Sbjct  13908  LNAHMEICAAFDVKEEIYKSLMQKGQQMLARCPKSAETIDQDLNNLKEKWESVETKLNER  14087

Query  575    VRQLHEA---HRDFGPASQHFLS  594
                +L EA     +F  + Q F++
Sbjct  14088  KTKLEEALNLAMEFHNSLQDFIN  14156


 Score = 49.7 bits (117),  Expect = 0.009, Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 106/237 (44%), Gaps = 1/237 (0%)
 Frame = +3

Query  15     FNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAA  74
              F+ AW++L +WL   ++ + S+  +  D + I   + + K   + L  +    +      
Sbjct  14454  FHEAWSKLMEWLEESEKSLDSELEIANDPDKIKTQLAQHKEFQKSLGAKHSVYDTTNRTG  14633

Query  75     QNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQ  134
              ++LK KTS  +    + D +  ++++WD +      R+ +L E L  S Q+ +A +    
Sbjct  14634  RSLKEKTSLADDNLKLDDMLSELRDKWDTICGKSVERQNKLEEALLFSGQFTDALQALID  14813

Query  135    VLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSAD  194
               L +   +L   +     +D +   I   K   K+L +  ++V      A +L+ + S D
Sbjct  14814  WLYRVEPQLAEDQPVHGDIDLVMNLIDNHKVFQKELGKRTSSVQALKRSARELI-EGSRD  14990

Query  195    DTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETT  251
              D+  V +  + ++  W ++      ++  LE   R  ++F   +   L WL EAE T
Sbjct  14991  DSSWVKVQMQELSTRWETVCALSISKQTRLEAALRQAEEFHSVVHALLEWLAEAEQT  15161


 Score = 49.3 bits (116),  Expect = 0.013, Method: Compositional matrix adjust.
 Identities = 102/506 (20%), Positives = 211/506 (41%), Gaps = 52/506 (10%)
 Frame = +3

Query  87     RTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESW  146
              + +ITD  + +  + D V E L +++  L  M +   ++ E  +EA++ L  A+ +L+  
Sbjct  9417   KEVITDENKSLIQKIDMVTEQLHSKKFSLENMAQKFKEFQEVSKEAKRQLQCAKEQLDVH  9596

Query  147    KE-GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYS-ADDTRKVHMITE  204
                 GP         + +T+Q  K L+  +  VD+   LA  L+ + S +  T  V + +E
Sbjct  9597   DSLGPQAYSNKYLSVLQTQQ--KGLQTLKHQVDLVKGLAQDLVVEASDSKGTSDVLLQSE  9770

Query  205    NINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRK-ER  263
              ++     ++ ++V ER + LE   + +  F   + +  +   E +   + +    R  E 
Sbjct  9771   SLVQEHSALSQQVDERCSFLETKLQGIGHFQNTIREMFSQFAEFDDELDSMAPVGRDVET  9950

Query  264    LLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMN  323
              L +  + +K  +K+       +EA      N ++  + +L   E S D + ++R L+ ++
Sbjct  9951   LQKQKEAIKAFLKK-------LEALIASNDNANKTCKMMLAMEETSPDLIGIKRDLEALS  10109

Query  324    FKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQK  383
               + ++L  ++      +E + ++ +  +  L+E    LQ  ++    Q P+G +   + +
Sbjct  10110  KQCNKLLDRAQAREEQVEGTIERLEEFYSKLKEFSTLLQKAEEHEESQGPVGMETETINQ  10289

Query  384    QNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRL  443
              Q +V +AF++E      V    +  +   L +   +G                    T+ 
Sbjct  10290  QLNVFKAFQKEEIEPLQVKQQDVNWLGQGLIQSAAKG------------------TSTQG  10415

Query  444    LRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPV  503
              L    ++VN  W+ LN   A    ++ E L      Q+A + L            SW   
Sbjct  10416  LEHDLDDVNARWKTLNKKVAQRAAQLQEALLHCGRFQDALESL-----------LSWMVD  10562

Query  504    GDLLIDSLQDHLEKVKALRGEIAP-------LKENVSHVNDLARQLTTLGIQLSPYN---  553
               + L+ + +    + K ++ +I         L +  S V  + R+   +     P +   
Sbjct  10563  TEELVANQKPPSAEFKVVKAQIQEQKLLQRLLDDRKSTVEVIKREGEKIAATAEPADKVK  10742

Query  554    -LSTLEDLNTRWKLLQVAVEDRVRQL  578
               L  L  L++RW+ L    E R RQL
Sbjct  10743  ILKQLSLLDSRWEALLNKAETRNRQL  10820


>ref|NM_001144187.1| Drosophila melanogaster short stop (shot), transcript variant 
K, mRNA
Length=17743

 Score = 85.5 bits (210),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 102/502 (20%), Positives = 224/502 (44%), Gaps = 26/502 (5%)
 Frame = +1

Query  29     LDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEART  88
              L++ +  Q       +DI +  +  +    +++Q +P++E++     NL N     + + 
Sbjct  12238  LEETLSCQEPPAAQPQDIKKQQVALQEIRHEIDQTKPEVEQVRRHGSNLMNMCGEPD-KP  12414

Query  89     IITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKE  148
               +   IE + N WD +      R + L + ++ + ++ E  +   + L +A  K      
Sbjct  12415  EVKKHIEDLDNAWDNITALYAKREENLIDAMEKAMEFHETLQNLLKFLTKAEDKFAHLGA  12594

Query  149    GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINA  208
                  +DA++++I + K    ++      V+  N  A++L    S +    +      +N 
Sbjct  12595  VGSDIDAVKRQIEQLKSFKDEVDPHMVEVEALNRQAVELTERTSPEQAASIREPLSVVNR  12774

Query  209    SWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDS  268
               W ++ + + ER+  LE     L QF   L + L W+ + ++T + L+      +LLE  
Sbjct  12775  RWEALLRGMVERQKQLEHALLHLGQFQHALNELLVWINKTDSTLDQLKPIPGDPQLLE--  12948

Query  269    KGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSE  328
                  EL K  + L  +I+AH +    L++  ++++ + +GS +A   Q +L  +N +W +
Sbjct  12949  ---VELAK-LKVLANDIQAHQNSVDTLNDAGRQLIETEKGSVEASTTQEKLRKLNNEWKQ  13116

Query  329    LRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVH  388
              L +K+ + +  LE +  +       +Q++L WL   D  +    P+GG      +Q +  
Sbjct  13117  LLQKASDRQHELEEALREAHGYIAEVQDILGWLGDVDAVIGASKPVGGLPETATEQLERF  13296

Query  389    RAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQA  448
                   EL    P +    ET++        +G E + ++ +        Q+  R L+++ 
Sbjct  13297  MEVYNELDENRPKV----ETIQA-------QGQEYIKRQNQMKVSSSNLQHTLRTLKQR-  13440

Query  449    EEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLI  508
                    W+ +   ++D + K++  L+   E  +        L QAE +  + +PV  +L 
Sbjct  13441  ------WDAVVSRASDKKIKLEIALKEATEFHDTLQAFVEWLTQAEKLLSNAEPVSRVL-  13599

Query  509    DSLQDHLEKVKALRGEIAPLKE  530
              +++Q  +E+ K L+ +++  +E
Sbjct  13600  ETIQAQMEEHKVLQKDVSTHRE  13665


 Score = 56.2 bits (134),  Expect = 1e-04, Method: Compositional matrix adjust.
 Identities = 101/486 (20%), Positives = 198/486 (40%), Gaps = 54/486 (11%)
 Frame = +1

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+       +WL+  ++++ +   +   LE I   + + K   +D+   R  +  L   
Sbjct  13510  EFHDTLQAFVEWLTQAEKLLSNAEPVSRVLETIQAQMEEHKVLQKDVSTHREAMLLLDKK  13689

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEA-----  128
                +LK  +  Q+   +I + +  +Q++W+ V      R + L+   K++ ++ +A     
Sbjct  13690  GTHLKYFSQKQDV-ILIKNLLVSVQHRWERVVSKAAERTRALDHGYKEAREFNDAWSGMM  13866

Query  129    --KEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALK  186
                 +E EQVL Q   +  + KE       I+K I + K+  + L   Q+  D        
Sbjct  13867  QYLQETEQVLDQIIEEATASKEP----QKIKKYIGKLKETHRQLGAKQSVYDGTMRTGKN  14034

Query  187    LLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
              LL      D   +  +   +   W  +  +  +R+  LEE   L  QF   L + L WL 
Sbjct  14035  LLERAPKGDRPVLDKMLIELKEQWTRVWSKSIDRQRKLEEALLLSGQFSDALGELLDWLK  14214

Query  247    EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENS---QKIL  303
              +A            K RL E+     +L    + +QG  E H  +  +L + +   Q +L
Sbjct  14215  KA------------KSRLNENGPVHGDL----ETVQGLCEHHKHIEQDLQKRAAQMQGVL  14346

Query  304    ---RSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
                 R LE S +   + R+LD M   W E++         L+ +    ++L+  +Q L  W
Sbjct  14347  KTGRDLERSGNNPEVGRQLDEMQSIWEEVKSAVAKRGERLQVALVDAEKLNARVQALFDW  14526

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              L   + +L        D    ++  D+H  F ++L+ +E     T E     +       
Sbjct  14527  LDHAEHKLRYAKNAPDDEKVSREMMDIHMDFMKDLRVREREKTETFEYAEDIIN------  14688

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
                K Y  P  +P          +++     +   WE++   + + + K+++ L+ L++L 
Sbjct  14689  --KAY--PDAIP----------IIKNWLSIIQQRWEEVRQWAINRESKLEQHLQSLKDLD  14826

Query  481    EATDEL  486
              +  +EL
Sbjct  14827  DTIEEL  14844


 Score = 49.3 bits (116),  Expect = 0.015, Method: Compositional matrix adjust.
 Identities = 83/396 (20%), Positives = 170/396 (42%), Gaps = 42/396 (10%)
 Frame = +1

Query  14     DFNRAWTELTDWLS----LLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEE  69
              +FN AW+ +  +L     +LDQ+I+ +     + + I + I K K T + L  ++   + 
Sbjct  13837  EFNDAWSGMMQYLQETEQVLDQIIE-EATASKEPQKIKKYIGKLKETHRQLGAKQSVYDG  14013

Query  70     LITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAK  129
               +   +NL  +    + R ++   +  ++ QW  V     +R+++L E L  S Q+ +A 
Sbjct  14014  TMRTGKNLLERAPKGD-RPVLDKMLIELKEQWTRVWSKSIDRQRKLEEALLLSGQFSDAL  14190

Query  130    EEAEQVLGQARAKLESWKEGPYTVD--AIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
               E    L +A+++L   + GP   D   +Q      K + +DL++    +       LK 
Sbjct  14191  GELLDWLKKAKSRLN--ENGPVHGDLETVQGLCEHHKHIEQDLQKRAAQMQGV----LKT  14352

Query  188    LRDYS-ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
               RD   + +  +V    + + + W  +   V++R   L+      ++    ++    WL 
Sbjct  14353  GRDLERSGNNPEVGRQLDEMQSIWEEVKSAVAKRGERLQVALVDAEKLNARVQALFDWLD  14532

Query  247    EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL  306
               AE      ++A       +D K  +E+M          + H D   +L    ++   + 
Sbjct  14533  HAEHKLRYAKNAP------DDEKVSREMM----------DIHMDFMKDLRVREREKTETF  14664

Query  307    EGSDDAV---------LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQEL  357
              E ++D +         +++  L  +  +W E+R+ ++N  S LE      K L  +++EL
Sbjct  14665  EYAEDIINKAYPDAIPIIKNWLSIIQQRWEEVRQWAINRESKLEQHLQSLKDLDDTIEEL  14844

Query  358    LVWLQLKDDEL--SRQAPIGGDFPAVQKQNDVHRAF  391
              L WL   +  L   +   +  + P V+K  + H+ F
Sbjct  14845  LAWLSGLEGTLLNLKHEQLPDEIPPVEKLIEDHKEF  14952


 Score = 48.1 bits (113),  Expect = 0.033, Method: Compositional matrix adjust.
 Identities = 67/363 (18%), Positives = 154/363 (42%), Gaps = 25/363 (6%)
 Frame = +1

Query  26     LSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEE----------------  69
              L  L +    Q   + D++D+++   + K    +L+Q R Q E+                
Sbjct  9574   LKALREFYDHQSQTLDDIQDVSDEFKRMKPVGSELDQIRRQQEDFRNFRERKVEPLAINV  9753

Query  70     --LITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
                +  A ++L     +  + T I   +E++ ++W++++E +  R ++L+  L  S ++ E
Sbjct  9754   DKVNVAGRDLVRSAGSGVSTTAIEKDLEKLNDRWNDLKERMNERDRRLDVALLQSGKFQE  9933

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
              A     + L      + + K        ++ ++ E K L K L   Q ++    +L  ++
Sbjct  9934   ALAGLSKWLSDTEEMVANQKPPSSDYKVVKAQLQEQKFLKKMLLDRQNSMGSLANLGKEV  10113

Query  188    LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
                     +   +     ++   + ++     +RE  LEE   + ++F   +     WL  
Sbjct  10114  ANHCEPGERASIEKQLNDLMKRFDALTDGAEQRELDLEEAMEVAKRFHDKISPLELWLDN  10293

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
               E +   +      E +  D + +++ +++   L  EI      + +L + + +++  L 
Sbjct  10294  TERSVKAM------ELIPTDEEKIQQRIREHDRLHDEILGKKPDFSDLADVTAQLMH-LV  10452

Query  308    GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
                ++AV L  ++  +  +++ L   S NI + L  S    + L LS Q+L+ W++  + E
Sbjct  10453  SDEEAVNLGEKVRGVTERYTGLVDASDNIGALLAESRQGLRHLVLSYQDLVAWMESMEAE  10632

Query  368    LSR  370
              L R
Sbjct  10633  LKR  10641


>gb|M86900.1|HUMDYST17 H.sapiens dystrophin gene, exon 76
Length=287

 Score = 85.5 bits (210),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 42/43 (97%), Positives = 43/43 (100%), Gaps = 0/43 (0%)
 Frame = +2

Query  1127  PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGE  1169
             PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMG+
Sbjct  86    PQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSDSMGK  214


>dbj|AK157158.1| Mus musculus activated spleen cDNA, RIKEN full-length enriched 
library, clone:F830205H16 product:dystrobrevin, beta, full 
insert sequence
Length=3686

 Score = 85.1 bits (209),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 109/222 (49%), Gaps = 17/222 (7%)
 Frame = +3

Query  637  DLNNVRFSAYRTAMKLRRLQKALCLDLLSLSAACDALDQHNLKQNDQPMDIL--QIINCL  694
            + + +R S YRTA KLR +QK   L L+ +    +A   + L   D   +I   ++   +
Sbjct  291  NFDVIRLSTYRTACKLRFVQKRCNLHLVDIWNMIEAFRDNGLNTLDHSTEISVSRLETVI  470

Query  695  TTIY----DRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAH  750
            ++IY     RL   H   ++V   + + LN+++  YD+   G++ V S K  + ++C   
Sbjct  471  SSIYYQLNKRLPSTHQ--ISVEQSISLLLNFMVAAYDSEGRGKLTVFSVKAMLATMCGGK  644

Query  751  LEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFA  810
            + DK+RY+F Q++ S G     +L   L +++++P  + E A      I    R+C  + 
Sbjct  645  MLDKWRYIFSQMSDSNGLMMLGKLDQFLKEALKLPTAVFEGA------ILCLHRACSPYL  806

Query  811  NNKPEIEAALFLDWMR---LEPQSMVWLPVLHRVAAAETAKH  849
                E + A ++          Q +VWLP++HR+A  E  +H
Sbjct  807  FFAAEEDNAEYVFRHHDG*FSSQCLVWLPLMHRLAHVENGEH  932


>ref|NM_001144188.1| Drosophila melanogaster short stop (shot), transcript variant 
L, mRNA
Length=17981

 Score = 85.1 bits (209),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 102/502 (20%), Positives = 224/502 (44%), Gaps = 26/502 (5%)
 Frame = +2

Query  29     LDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEART  88
              L++ +  Q       +DI +  +  +    +++Q +P++E++     NL N     + + 
Sbjct  12461  LEETLSCQEPPAAQPQDIKKQQVALQEIRHEIDQTKPEVEQVRRHGSNLMNMCGEPD-KP  12637

Query  89     IITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKE  148
               +   IE + N WD +      R + L + ++ + ++ E  +   + L +A  K      
Sbjct  12638  EVKKHIEDLDNAWDNITALYAKREENLIDAMEKAMEFHETLQNLLKFLTKAEDKFAHLGA  12817

Query  149    GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINA  208
                  +DA++++I + K    ++      V+  N  A++L    S +    +      +N 
Sbjct  12818  VGSDIDAVKRQIEQLKSFKDEVDPHMVEVEALNRQAVELTERTSPEQAASIREPLSVVNR  12997

Query  209    SWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDS  268
               W ++ + + ER+  LE     L QF   L + L W+ + ++T + L+      +LLE  
Sbjct  12998  RWEALLRGMVERQKQLEHALLHLGQFQHALNELLVWINKTDSTLDQLKPIPGDPQLLE--  13171

Query  269    KGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSE  328
                  EL K  + L  +I+AH +    L++  ++++ + +GS +A   Q +L  +N +W +
Sbjct  13172  ---VELAK-LKVLANDIQAHQNSVDTLNDAGRQLIETEKGSVEASTTQEKLRKLNNEWKQ  13339

Query  329    LRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVH  388
              L +K+ + +  LE +  +       +Q++L WL   D  +    P+GG      +Q +  
Sbjct  13340  LLQKASDRQHELEEALREAHGYIAEVQDILGWLGDVDAVIGASKPVGGLPETATEQLERF  13519

Query  389    RAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQA  448
                   EL    P +    ET++        +G E + ++ +        Q+  R L+++ 
Sbjct  13520  MEVYNELDENRPKV----ETIQA-------QGQEYIKRQNQMKVSSSNLQHTLRTLKQR-  13663

Query  449    EEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLI  508
                    W+ +   ++D + K++  L+   E  +        L QAE +  + +PV  +L 
Sbjct  13664  ------WDAVVSRASDKKIKLEIALKEATEFHDTLQAFVEWLTQAEKLLSNAEPVSRVL-  13822

Query  509    DSLQDHLEKVKALRGEIAPLKE  530
              +++Q  +E+ K L+ +++  +E
Sbjct  13823  ETIQAQMEEHKVLQKDVSTHRE  13888


 Score = 55.8 bits (133),  Expect = 1e-04, Method: Compositional matrix adjust.
 Identities = 101/486 (20%), Positives = 198/486 (40%), Gaps = 54/486 (11%)
 Frame = +2

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+       +WL+  ++++ +   +   LE I   + + K   +D+   R  +  L   
Sbjct  13733  EFHDTLQAFVEWLTQAEKLLSNAEPVSRVLETIQAQMEEHKVLQKDVSTHREAMLLLDKK  13912

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEA-----  128
                +LK  +  Q+   +I + +  +Q++W+ V      R + L+   K++ ++ +A     
Sbjct  13913  GTHLKYFSQKQDV-ILIKNLLVSVQHRWERVVSKAAERTRALDHGYKEAREFNDAWSGMM  14089

Query  129    --KEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALK  186
                 +E EQVL Q   +  + KE       I+K I + K+  + L   Q+  D        
Sbjct  14090  QYLQETEQVLDQIIEEATASKEP----QKIKKYIGKLKETHRQLGAKQSVYDGTMRTGKN  14257

Query  187    LLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
              LL      D   +  +   +   W  +  +  +R+  LEE   L  QF   L + L WL 
Sbjct  14258  LLERAPKGDRPVLDKMLIELKEQWTRVWSKSIDRQRKLEEALLLSGQFSDALGELLDWLK  14437

Query  247    EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENS---QKIL  303
              +A            K RL E+     +L    + +QG  E H  +  +L + +   Q +L
Sbjct  14438  KA------------KSRLNENGPVHGDL----ETVQGLCEHHKHIEQDLQKRAAQMQGVL  14569

Query  304    ---RSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
                 R LE S +   + R+LD M   W E++         L+ +    ++L+  +Q L  W
Sbjct  14570  KTGRDLERSGNNPEVGRQLDEMQSIWEEVKSAVAKRGERLQVALVDAEKLNARVQALFDW  14749

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              L   + +L        D    ++  D+H  F ++L+ +E     T E     +       
Sbjct  14750  LDHAEHKLRYAKNAPDDEKVSREMMDIHMDFMKDLRVREREKTETFEYAEDIIN------  14911

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
                K Y  P  +P          +++     +   WE++   + + + K+++ L+ L++L 
Sbjct  14912  --KAY--PDAIP----------IIKNWLSIIQQRWEEVRQWAINRESKLEQHLQSLKDLD  15049

Query  481    EATDEL  486
              +  +EL
Sbjct  15050  DTIEEL  15067


 Score = 48.9 bits (115),  Expect = 0.018, Method: Compositional matrix adjust.
 Identities = 83/396 (20%), Positives = 170/396 (42%), Gaps = 42/396 (10%)
 Frame = +2

Query  14     DFNRAWTELTDWLS----LLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEE  69
              +FN AW+ +  +L     +LDQ+I+ +     + + I + I K K T + L  ++   + 
Sbjct  14060  EFNDAWSGMMQYLQETEQVLDQIIE-EATASKEPQKIKKYIGKLKETHRQLGAKQSVYDG  14236

Query  70     LITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAK  129
               +   +NL  +    + R ++   +  ++ QW  V     +R+++L E L  S Q+ +A 
Sbjct  14237  TMRTGKNLLERAPKGD-RPVLDKMLIELKEQWTRVWSKSIDRQRKLEEALLLSGQFSDAL  14413

Query  130    EEAEQVLGQARAKLESWKEGPYTVD--AIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
               E    L +A+++L   + GP   D   +Q      K + +DL++    +       LK 
Sbjct  14414  GELLDWLKKAKSRLN--ENGPVHGDLETVQGLCEHHKHIEQDLQKRAAQMQGV----LKT  14575

Query  188    LRDYS-ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
               RD   + +  +V    + + + W  +   V++R   L+      ++    ++    WL 
Sbjct  14576  GRDLERSGNNPEVGRQLDEMQSIWEEVKSAVAKRGERLQVALVDAEKLNARVQALFDWLD  14755

Query  247    EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL  306
               AE      ++A       +D K  +E+M          + H D   +L    ++   + 
Sbjct  14756  HAEHKLRYAKNAP------DDEKVSREMM----------DIHMDFMKDLRVREREKTETF  14887

Query  307    EGSDDAV---------LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQEL  357
              E ++D +         +++  L  +  +W E+R+ ++N  S LE      K L  +++EL
Sbjct  14888  EYAEDIINKAYPDAIPIIKNWLSIIQQRWEEVRQWAINRESKLEQHLQSLKDLDDTIEEL  15067

Query  358    LVWLQLKDDEL--SRQAPIGGDFPAVQKQNDVHRAF  391
              L WL   +  L   +   +  + P V+K  + H+ F
Sbjct  15068  LAWLSGLEGTLLNLKHEQLPDEIPPVEKLIEDHKEF  15175


 Score = 47.8 bits (112),  Expect = 0.039, Method: Compositional matrix adjust.
 Identities = 67/363 (18%), Positives = 153/363 (42%), Gaps = 25/363 (6%)
 Frame = +2

Query  26     LSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELI--------------  71
              L  L +    Q   + D++D+++   + K    +L+Q R Q E+                
Sbjct  9797   LKALREFYDHQSQTLDDIQDVSDEFKRMKPVGSELDQIRRQQEDFRNFRERKVEPLAINV  9976

Query  72     ----TAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
                   A ++L     +  + T I   +E++ ++W++++E +  R ++L+  L  S ++ E
Sbjct  9977   DKVNVAGRDLVRSAGSGVSTTAIEKDLEKLNDRWNDLKERMNERDRRLDVALLQSGKFQE  10156

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
              A     + L      + + K        ++ ++ E K L K L   Q ++    +L  ++
Sbjct  10157  ALAGLSKWLSDTEEMVANQKPPSSDYKVVKAQLQEQKFLKKMLLDRQNSMGSLANLGKEV  10336

Query  188    LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
                     +   +     ++   + ++     +RE  LEE   + ++F   +     WL  
Sbjct  10337  ANHCEPGERASIEKQLNDLMKRFDALTDGAEQRELDLEEAMEVAKRFHDKISPLELWLDN  10516

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
               E +   +      E +  D + +++ +++   L  EI      + +L + + +++  L 
Sbjct  10517  TERSVKAM------ELIPTDEEKIQQRIREHDRLHDEILGKKPDFSDLADVTAQLMH-LV  10675

Query  308    GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
                ++AV L  ++  +  +++ L   S NI + L  S    + L LS Q+L+ W++  + E
Sbjct  10676  SDEEAVNLGEKVRGVTERYTGLVDASDNIGALLAESRQGLRHLVLSYQDLVAWMESMEAE  10855

Query  368    LSR  370
              L R
Sbjct  10856  LKR  10864


>ref|NM_001144185.1| Drosophila melanogaster short stop (shot), transcript variant 
I, mRNA
Length=17758

 Score = 85.1 bits (209),  Expect = 2e-13, Method: Compositional matrix adjust.
 Identities = 102/502 (20%), Positives = 224/502 (44%), Gaps = 26/502 (5%)
 Frame = +1

Query  29     LDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEART  88
              L++ +  Q       +DI +  +  +    +++Q +P++E++     NL N     + + 
Sbjct  12238  LEETLSCQEPPAAQPQDIKKQQVALQEIRHEIDQTKPEVEQVRRHGSNLMNMCGEPD-KP  12414

Query  89     IITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKE  148
               +   IE + N WD +      R + L + ++ + ++ E  +   + L +A  K      
Sbjct  12415  EVKKHIEDLDNAWDNITALYAKREENLIDAMEKAMEFHETLQNLLKFLTKAEDKFAHLGA  12594

Query  149    GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINA  208
                  +DA++++I + K    ++      V+  N  A++L    S +    +      +N 
Sbjct  12595  VGSDIDAVKRQIEQLKSFKDEVDPHMVEVEALNRQAVELTERTSPEQAASIREPLSVVNR  12774

Query  209    SWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDS  268
               W ++ + + ER+  LE     L QF   L + L W+ + ++T + L+      +LLE  
Sbjct  12775  RWEALLRGMVERQKQLEHALLHLGQFQHALNELLVWINKTDSTLDQLKPIPGDPQLLE--  12948

Query  269    KGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSE  328
                  EL K  + L  +I+AH +    L++  ++++ + +GS +A   Q +L  +N +W +
Sbjct  12949  ---VELAK-LKVLANDIQAHQNSVDTLNDAGRQLIETEKGSVEASTTQEKLRKLNNEWKQ  13116

Query  329    LRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVH  388
              L +K+ + +  LE +  +       +Q++L WL   D  +    P+GG      +Q +  
Sbjct  13117  LLQKASDRQHELEEALREAHGYIAEVQDILGWLGDVDAVIGASKPVGGLPETATEQLERF  13296

Query  389    RAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQA  448
                   EL    P +    ET++        +G E + ++ +        Q+  R L+++ 
Sbjct  13297  MEVYNELDENRPKV----ETIQA-------QGQEYIKRQNQMKVSSSNLQHTLRTLKQR-  13440

Query  449    EEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLI  508
                    W+ +   ++D + K++  L+   E  +        L QAE +  + +PV  +L 
Sbjct  13441  ------WDAVVSRASDKKIKLEIALKEATEFHDTLQAFVEWLTQAEKLLSNAEPVSRVL-  13599

Query  509    DSLQDHLEKVKALRGEIAPLKE  530
              +++Q  +E+ K L+ +++  +E
Sbjct  13600  ETIQAQMEEHKVLQKDVSTHRE  13665


 Score = 55.8 bits (133),  Expect = 1e-04, Method: Compositional matrix adjust.
 Identities = 101/486 (20%), Positives = 198/486 (40%), Gaps = 54/486 (11%)
 Frame = +1

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+       +WL+  ++++ +   +   LE I   + + K   +D+   R  +  L   
Sbjct  13510  EFHDTLQAFVEWLTQAEKLLSNAEPVSRVLETIQAQMEEHKVLQKDVSTHREAMLLLDKK  13689

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEA-----  128
                +LK  +  Q+   +I + +  +Q++W+ V      R + L+   K++ ++ +A     
Sbjct  13690  GTHLKYFSQKQDV-ILIKNLLVSVQHRWERVVSKAAERTRALDHGYKEAREFNDAWSGMM  13866

Query  129    --KEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALK  186
                 +E EQVL Q   +  + KE       I+K I + K+  + L   Q+  D        
Sbjct  13867  QYLQETEQVLDQIIEEATASKEP----QKIKKYIGKLKETHRQLGAKQSVYDGTMRTGKN  14034

Query  187    LLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
              LL      D   +  +   +   W  +  +  +R+  LEE   L  QF   L + L WL 
Sbjct  14035  LLERAPKGDRPVLDKMLIELKEQWTRVWSKSIDRQRKLEEALLLSGQFSDALGELLDWLK  14214

Query  247    EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENS---QKIL  303
              +A            K RL E+     +L    + +QG  E H  +  +L + +   Q +L
Sbjct  14215  KA------------KSRLNENGPVHGDL----ETVQGLCEHHKHIEQDLQKRAAQMQGVL  14346

Query  304    ---RSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
                 R LE S +   + R+LD M   W E++         L+ +    ++L+  +Q L  W
Sbjct  14347  KTGRDLERSGNNPEVGRQLDEMQSIWEEVKSAVAKRGERLQVALVDAEKLNARVQALFDW  14526

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              L   + +L        D    ++  D+H  F ++L+ +E     T E     +       
Sbjct  14527  LDHAEHKLRYAKNAPDDEKVSREMMDIHMDFMKDLRVREREKTETFEYAEDIIN------  14688

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
                K Y  P  +P          +++     +   WE++   + + + K+++ L+ L++L 
Sbjct  14689  --KAY--PDAIP----------IIKNWLSIIQQRWEEVRQWAINRESKLEQHLQSLKDLD  14826

Query  481    EATDEL  486
              +  +EL
Sbjct  14827  DTIEEL  14844


 Score = 48.9 bits (115),  Expect = 0.018, Method: Compositional matrix adjust.
 Identities = 83/396 (20%), Positives = 170/396 (42%), Gaps = 42/396 (10%)
 Frame = +1

Query  14     DFNRAWTELTDWLS----LLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEE  69
              +FN AW+ +  +L     +LDQ+I+ +     + + I + I K K T + L  ++   + 
Sbjct  13837  EFNDAWSGMMQYLQETEQVLDQIIE-EATASKEPQKIKKYIGKLKETHRQLGAKQSVYDG  14013

Query  70     LITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAK  129
               +   +NL  +    + R ++   +  ++ QW  V     +R+++L E L  S Q+ +A 
Sbjct  14014  TMRTGKNLLERAPKGD-RPVLDKMLIELKEQWTRVWSKSIDRQRKLEEALLLSGQFSDAL  14190

Query  130    EEAEQVLGQARAKLESWKEGPYTVD--AIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
               E    L +A+++L   + GP   D   +Q      K + +DL++    +       LK 
Sbjct  14191  GELLDWLKKAKSRLN--ENGPVHGDLETVQGLCEHHKHIEQDLQKRAAQMQGV----LKT  14352

Query  188    LRDYS-ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
               RD   + +  +V    + + + W  +   V++R   L+      ++    ++    WL 
Sbjct  14353  GRDLERSGNNPEVGRQLDEMQSIWEEVKSAVAKRGERLQVALVDAEKLNARVQALFDWLD  14532

Query  247    EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL  306
               AE      ++A       +D K  +E+M          + H D   +L    ++   + 
Sbjct  14533  HAEHKLRYAKNAP------DDEKVSREMM----------DIHMDFMKDLRVREREKTETF  14664

Query  307    EGSDDAV---------LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQEL  357
              E ++D +         +++  L  +  +W E+R+ ++N  S LE      K L  +++EL
Sbjct  14665  EYAEDIINKAYPDAIPIIKNWLSIIQQRWEEVRQWAINRESKLEQHLQSLKDLDDTIEEL  14844

Query  358    LVWLQLKDDEL--SRQAPIGGDFPAVQKQNDVHRAF  391
              L WL   +  L   +   +  + P V+K  + H+ F
Sbjct  14845  LAWLSGLEGTLLNLKHEQLPDEIPPVEKLIEDHKEF  14952


 Score = 47.8 bits (112),  Expect = 0.039, Method: Compositional matrix adjust.
 Identities = 67/363 (18%), Positives = 153/363 (42%), Gaps = 25/363 (6%)
 Frame = +1

Query  26     LSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELI--------------  71
              L  L +    Q   + D++D+++   + K    +L+Q R Q E+                
Sbjct  9574   LKALREFYDHQSQTLDDIQDVSDEFKRMKPVGSELDQIRRQQEDFRNFRERKVEPLAINV  9753

Query  72     ----TAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
                   A ++L     +  + T I   +E++ ++W++++E +  R ++L+  L  S ++ E
Sbjct  9754   DKVNVAGRDLVRSAGSGVSTTAIEKDLEKLNDRWNDLKERMNERDRRLDVALLQSGKFQE  9933

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
              A     + L      + + K        ++ ++ E K L K L   Q ++    +L  ++
Sbjct  9934   ALAGLSKWLSDTEEMVANQKPPSSDYKVVKAQLQEQKFLKKMLLDRQNSMGSLANLGKEV  10113

Query  188    LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
                     +   +     ++   + ++     +RE  LEE   + ++F   +     WL  
Sbjct  10114  ANHCEPGERASIEKQLNDLMKRFDALTDGAEQRELDLEEAMEVAKRFHDKISPLELWLDN  10293

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
               E +   +      E +  D + +++ +++   L  EI      + +L + + +++  L 
Sbjct  10294  TERSVKAM------ELIPTDEEKIQQRIREHDRLHDEILGKKPDFSDLADVTAQLMH-LV  10452

Query  308    GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
                ++AV L  ++  +  +++ L   S NI + L  S    + L LS Q+L+ W++  + E
Sbjct  10453  SDEEAVNLGEKVRGVTERYTGLVDASDNIGALLAESRQGLRHLVLSYQDLVAWMESMEAE  10632

Query  368    LSR  370
              L R
Sbjct  10633  LKR  10641


>ref|NM_166019.1| Drosophila melanogaster short stop (shot), transcript variant 
H, mRNA
Length=27845

 Score = 85.1 bits (209),  Expect = 3e-13, Method: Compositional matrix adjust.
 Identities = 102/502 (20%), Positives = 224/502 (44%), Gaps = 26/502 (5%)
 Frame = +2

Query  29     LDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEART  88
              L++ +  Q       +DI +  +  +    +++Q +P++E++     NL N     + + 
Sbjct  22280  LEETLSCQEPPAAQPQDIKKQQVALQEIRHEIDQTKPEVEQVRRHGSNLMNMCGEPD-KP  22456

Query  89     IITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKE  148
               +   IE + N WD +      R + L + ++ + ++ E  +   + L +A  K      
Sbjct  22457  EVKKHIEDLDNAWDNITALYAKREENLIDAMEKAMEFHETLQNLLKFLTKAEDKFAHLGA  22636

Query  149    GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINA  208
                  +DA++++I + K    ++      V+  N  A++L    S +    +      +N 
Sbjct  22637  VGSDIDAVKRQIEQLKSFKDEVDPHMVEVEALNRQAVELTERTSPEQAASIREPLSVVNR  22816

Query  209    SWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDS  268
               W ++ + + ER+  LE     L QF   L + L W+ + ++T + L+      +LLE  
Sbjct  22817  RWEALLRGMVERQKQLEHALLHLGQFQHALNELLVWINKTDSTLDQLKPIPGDPQLLE--  22990

Query  269    KGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSE  328
                  EL K  + L  +I+AH +    L++  ++++ + +GS +A   Q +L  +N +W +
Sbjct  22991  ---VELAK-LKVLANDIQAHQNSVDTLNDAGRQLIETEKGSVEASTTQEKLRKLNNEWKQ  23158

Query  329    LRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVH  388
              L +K+ + +  LE +  +       +Q++L WL   D  +    P+GG      +Q +  
Sbjct  23159  LLQKASDRQHELEEALREAHGYIAEVQDILGWLGDVDAVIGASKPVGGLPETATEQLERF  23338

Query  389    RAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQA  448
                   EL    P +    ET++        +G E + ++ +        Q+  R L+++ 
Sbjct  23339  MEVYNELDENRPKV----ETIQA-------QGQEYIKRQNQMKVSSSNLQHTLRTLKQR-  23482

Query  449    EEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLI  508
                    W+ +   ++D + K++  L+   E  +        L QAE +  + +PV  +L 
Sbjct  23483  ------WDAVVSRASDKKIKLEIALKEATEFHDTLQAFVEWLTQAEKLLSNAEPVSRVL-  23641

Query  509    DSLQDHLEKVKALRGEIAPLKE  530
              +++Q  +E+ K L+ +++  +E
Sbjct  23642  ETIQAQMEEHKVLQKDVSTHRE  23707


 Score = 55.8 bits (133),  Expect = 2e-04, Method: Compositional matrix adjust.
 Identities = 101/486 (20%), Positives = 198/486 (40%), Gaps = 54/486 (11%)
 Frame = +2

Query  14     DFNRAWTELTDWLSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITA  73
              +F+       +WL+  ++++ +   +   LE I   + + K   +D+   R  +  L   
Sbjct  23552  EFHDTLQAFVEWLTQAEKLLSNAEPVSRVLETIQAQMEEHKVLQKDVSTHREAMLLLDKK  23731

Query  74     AQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEA-----  128
                +LK  +  Q+   +I + +  +Q++W+ V      R + L+   K++ ++ +A     
Sbjct  23732  GTHLKYFSQKQDV-ILIKNLLVSVQHRWERVVSKAAERTRALDHGYKEAREFNDAWSGMM  23908

Query  129    --KEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALK  186
                 +E EQVL Q   +  + KE       I+K I + K+  + L   Q+  D        
Sbjct  23909  QYLQETEQVLDQIIEEATASKEP----QKIKKYIGKLKETHRQLGAKQSVYDGTMRTGKN  24076

Query  187    LLRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
              LL      D   +  +   +   W  +  +  +R+  LEE   L  QF   L + L WL 
Sbjct  24077  LLERAPKGDRPVLDKMLIELKEQWTRVWSKSIDRQRKLEEALLLSGQFSDALGELLDWLK  24256

Query  247    EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENS---QKIL  303
              +A            K RL E+     +L    + +QG  E H  +  +L + +   Q +L
Sbjct  24257  KA------------KSRLNENGPVHGDL----ETVQGLCEHHKHIEQDLQKRAAQMQGVL  24388

Query  304    ---RSLEGSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVW  360
                 R LE S +   + R+LD M   W E++         L+ +    ++L+  +Q L  W
Sbjct  24389  KTGRDLERSGNNPEVGRQLDEMQSIWEEVKSAVAKRGERLQVALVDAEKLNARVQALFDW  24568

Query  361    LQLKDDELSRQAPIGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLEG  420
              L   + +L        D    ++  D+H  F ++L+ +E     T E     +       
Sbjct  24569  LDHAEHKLRYAKNAPDDEKVSREMMDIHMDFMKDLRVREREKTETFEYAEDIIN------  24730

Query  421    LEKLYQEPRELPPEERAQNVTRLLRKQAEEVNTEWEKLNLHSADWQRKIDETLERLQELQ  480
                K Y  P  +P          +++     +   WE++   + + + K+++ L+ L++L 
Sbjct  24731  --KAY--PDAIP----------IIKNWLSIIQQRWEEVRQWAINRESKLEQHLQSLKDLD  24868

Query  481    EATDEL  486
              +  +EL
Sbjct  24869  DTIEEL  24886


 Score = 48.5 bits (114),  Expect = 0.021, Method: Compositional matrix adjust.
 Identities = 83/396 (20%), Positives = 170/396 (42%), Gaps = 42/396 (10%)
 Frame = +2

Query  14     DFNRAWTELTDWLS----LLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEE  69
              +FN AW+ +  +L     +LDQ+I+ +     + + I + I K K T + L  ++   + 
Sbjct  23879  EFNDAWSGMMQYLQETEQVLDQIIE-EATASKEPQKIKKYIGKLKETHRQLGAKQSVYDG  24055

Query  70     LITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAK  129
               +   +NL  +    + R ++   +  ++ QW  V     +R+++L E L  S Q+ +A 
Sbjct  24056  TMRTGKNLLERAPKGD-RPVLDKMLIELKEQWTRVWSKSIDRQRKLEEALLLSGQFSDAL  24232

Query  130    EEAEQVLGQARAKLESWKEGPYTVD--AIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
               E    L +A+++L   + GP   D   +Q      K + +DL++    +       LK 
Sbjct  24233  GELLDWLKKAKSRLN--ENGPVHGDLETVQGLCEHHKHIEQDLQKRAAQMQGV----LKT  24394

Query  188    LRDYS-ADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLT  246
               RD   + +  +V    + + + W  +   V++R   L+      ++    ++    WL 
Sbjct  24395  GRDLERSGNNPEVGRQLDEMQSIWEEVKSAVAKRGERLQVALVDAEKLNARVQALFDWLD  24574

Query  247    EAETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSL  306
               AE      ++A       +D K  +E+M          + H D   +L    ++   + 
Sbjct  24575  HAEHKLRYAKNAP------DDEKVSREMM----------DIHMDFMKDLRVREREKTETF  24706

Query  307    EGSDDAV---------LLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQEL  357
              E ++D +         +++  L  +  +W E+R+ ++N  S LE      K L  +++EL
Sbjct  24707  EYAEDIINKAYPDAIPIIKNWLSIIQQRWEEVRQWAINRESKLEQHLQSLKDLDDTIEEL  24886

Query  358    LVWLQLKDDEL--SRQAPIGGDFPAVQKQNDVHRAF  391
              L WL   +  L   +   +  + P V+K  + H+ F
Sbjct  24887  LAWLSGLEGTLLNLKHEQLPDEIPPVEKLIEDHKEF  24994


 Score = 47.8 bits (112),  Expect = 0.041, Method: Compositional matrix adjust.
 Identities = 67/363 (18%), Positives = 154/363 (42%), Gaps = 25/363 (6%)
 Frame = +2

Query  26     LSLLDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEE----------------  69
              L  L +    Q   + D++D+++   + K    +L+Q R Q E+                
Sbjct  19616  LKALREFYDHQSQTLDDIQDVSDEFKRMKPVGSELDQIRRQQEDFRNFRERKVEPLAINV  19795

Query  70     --LITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLE  127
                +  A ++L     +  + T I   +E++ ++W++++E +  R ++L+  L  S ++ E
Sbjct  19796  DKVNVAGRDLVRSAGSGVSTTAIEKDLEKLNDRWNDLKERMNERDRRLDVALLQSGKFQE  19975

Query  128    AKEEAEQVLGQARAKLESWKEGPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKL  187
              A     + L      + + K        ++ ++ E K L K L   Q ++    +L  ++
Sbjct  19976  ALAGLSKWLSDTEEMVANQKPPSSDYKVVKAQLQEQKFLKKMLLDRQNSMGSLANLGKEV  20155

Query  188    LRDYSADDTRKVHMITENINASWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTE  247
                     +   +     ++   + ++     +RE  LEE   + ++F   +     WL  
Sbjct  20156  ANHCEPGERASIEKQLNDLMKRFDALTDGAEQRELDLEEAMEVAKRFHDKISPLELWLDN  20335

Query  248    AETTANVLQDATRKERLLEDSKGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLE  307
               E +   +      E +  D + +++ +++   L  EI      + +L + + +++  L 
Sbjct  20336  TERSVKAM------ELIPTDEEKIQQRIREHDRLHDEILGKKPDFSDLADVTAQLMH-LV  20494

Query  308    GSDDAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDE  367
                ++AV L  ++  +  +++ L   S NI + L  S    + L LS Q+L+ W++  + E
Sbjct  20495  SDEEAVNLGEKVRGVTERYTGLVDASDNIGALLAESRQGLRHLVLSYQDLVAWMESMEAE  20674

Query  368    LSR  370
              L R
Sbjct  20675  LKR  20683


>ref|XM_002090815.1| Drosophila yakuba GE13333 (Dyak\GE13333), mRNA
Length=26415

 Score = 84.7 bits (208),  Expect = 3e-13, Method: Compositional matrix adjust.
 Identities = 102/502 (20%), Positives = 224/502 (44%), Gaps = 26/502 (5%)
 Frame = +1

Query  29     LDQVIKSQRVMVGDLEDINEMIIKQKATMQDLEQRRPQLEELITAAQNLKNKTSNQEART  88
              L++ +  Q       +DI +  +  +    +++Q +P++E++     NL N     + + 
Sbjct  21979  LEETLSCQEPPAAQPQDIKKQQVALQEIRHEIDQTKPEVEQVRRHGSNLMNMCGEPD-KP  22155

Query  89     IITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKE  148
               +   IE + N WD +      R + L + ++ + ++ E  +   + L +A  K      
Sbjct  22156  EVKKHIEDLDNAWDNITALYAKREENLIDAMEKAMEFHETLQNLLKFLTKAEDKFAHLGA  22335

Query  149    GPYTVDAIQKKITETKQLAKDLRQWQTNVDVANDLALKLLRDYSADDTRKVHMITENINA  208
                  +DA++++I + K    ++      V+  N  A++L    S +    +      +N 
Sbjct  22336  VGSDIDAVKRQIEQLKSFKDEVDPHMVEVEALNRQAVELTERTSPEQAASIREPLSVVNR  22515

Query  209    SWRSIHKRVSEREAALEETHRLLQQFPLDLEKFLAWLTEAETTANVLQDATRKERLLEDS  268
               W ++ + + ER+  LE     L QF   L + L W+ + ++T + L+      +LLE  
Sbjct  22516  RWEALLRGMVERQKQLEHALLHLGQFQHALNELLVWINKTDSTLDQLKPIPGDPQLLE--  22689

Query  269    KGVKELMKQWQDLQGEIEAHTDVYHNLDENSQKILRSLEGSDDAVLLQRRLDNMNFKWSE  328
                  EL K  + L  +I+AH +    L++  ++++ + +GS +A   Q +L  +N +W +
Sbjct  22690  ---VELAK-LKVLANDIQAHQNSVDTLNDAGRQLIETEKGSVEASTTQEKLRKLNNEWKQ  22857

Query  329    LRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELSRQAPIGGDFPAVQKQNDVH  388
              L +K+ + +  LE +  +       +Q++L WL   D  +    P+GG      +Q +  
Sbjct  22858  LLQKASDRQHELEEALREAHGYIAEVQDILGWLGDVDAVIGASKPVGGLPETATEQLERF  23037

Query  389    RAFKRELKTKEPVIMSTLETVRIFLTEQPLEGLEKLYQEPRELPPEERAQNVTRLLRKQA  448
                   EL    P +    ET++        +G E + ++ +        Q+  R L+++ 
Sbjct  23038  MEVYNELDENRPKV----ETIQA-------QGQEYIKRQNQMKVSSSNLQHTLRTLKQR-  23181

Query  449    EEVNTEWEKLNLHSADWQRKIDETLERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLI  508
                    W+ +   ++D + K++  L+   E  +        L QAE +  + +PV  +L 
Sbjct  23182  ------WDAVVSRASDKKIKLEIALKEATEFHDTLQAFVEWLTQAEKLLSNAEPVSRVL-  23340

Query  509    DSLQDHLEKVKALRGEIAPLKE  530
              +++Q  +E+ K L+ +++  +E
Sbjct  23341  ETIQAQMEEHKVLQKDVSTHRE  23406



  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
    Posted date:  May 26, 2009  5:42 PM
  Number of letters in database: 1,583,934,596
  Number of sequences in database:  8,742,655

Lambda     K      H
   0.315    0.130    0.377 
Gapped
Lambda     K      H
   0.267   0.0410    0.140 
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 8742655
Number of Hits to DB: 1847194189
Number of extensions: 27373293
Number of successful extensions: 148679
Number of sequences better than 100: 312
Number of HSP's better than 100 without gapping: 0
Number of HSP's gapped: 147951
Number of HSP's successfully gapped: 535
Length of query: 1230
Length of database: 27353738372
Length adjustment: 158
Effective length of query: 1072
Effective length of database: 7736573300
Effective search space: 8293606577600
Effective search space used: 8293606577600
T: 13
A: 40
X1: 16 (7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (20.4 bits)
S2: 83 (36.6 bits)




BioPerl-1.007002/t/data/2008.blasttable000444000766000024       123613155576321 17322 0ustar00cjfieldsstaff000000000000# BLASTP 2.2.18+
# Iteration: 0
# Query:  gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I, homoserine dehydrogenase I [Escherichia coli]
# RID: 8ZT9P56E015
# Database: swissprot
# Fields: query id, subject ids, % identity, % positives, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 3 hits found
gi|1786183|gb|AAC73113.1|	gi|34395933|sp|P00561.2|AK1H_ECOLI	100.00	100.00	820	0	0	1	820	1	820	0.0	1567
gi|1786183|gb|AAC73113.1|	gi|416596|sp|P00562.3|AK2H_ECOLI	30.09	49.94	821	530	14	5	812	16	805	2e-91	 331
gi|1786183|gb|AAC73113.1|	gi|416597|sp|P08660.2|AK3_ECOLI	30.15	48.41	471	288	10	3	460	6	448	4e-47	 184





BioPerl-1.007002/t/data/27-contig_Newbler.ace000444000766000024      2237213155576321 20557 0ustar00cjfieldsstaff000000000000AS 1 27

CO contig00001 203 27 38 U
gTAGGACttga*CGTC*GgAGCt**GgATTt*AGCTC*C*CTG*AaTGTT
*cGg*ATGGAAATGT*GCT*GA*CcTGg***TtGGGGA*t*Acc**a*Gg
*TCGAa**GAATCtgTT*Attt**CGTGCag*ACg*AA*TTttCCcTTCg
Aa*ct*GGAtGa*G*cA*Ca*TGgA*G*ATGAGg**TtCCCcATt*TTC*
gTG

BQ
8 64 64 64 64 64 64 29 5 29 29 64 64 64 64 64 10 64 64 64 22 64 8 64 64 64 11 64 64 64 64 64 64 64 64 64 64 19 64 64 64 64 0 64 19 64 64 64 64 64 
64 64 64 64 64 64 64 64 64 64 64 14 47 64 16 64 21 64 64 64 64 64 25 47 25 20 25 64 25 64 64 64 64 14 41 64 64 64 64 16 25 64 64 64 39 16 5 64 64 64 
64 64 12 12 64 64 17 64 64 64 58 23 5 64 49 7 64 64 64 21 64 8 21 21 64 64 64 29 64 29 64 35 55 64 20 64 64 19 55 64 64 64 64 64 64 9 64 11 64 64 
64 10 64 64 20 64 64 64 25 64 64 

AF species2703|6185 U 102
AF species2004|3290 U -18
AF species2702|8138 U -3
AF species2788|6026 U 122
AF species3098|4869 U 117
AF species1827|9888 U 171
AF species2742|48 U 28
AF species2011|1996 U -28
AF species3089|7597 U 149
AF species1961|5108 U 84
AF species2011|4145 U 150
AF species1667|4956 U -3
AF species980|9980 U 143
AF species2907|6509 U 170
AF species1973|7670 U 77
AF species2779|6708 U -9
AF species2024|3244 U 101
AF species2216|7882 U 112
AF species1037|7115 U 27
AF species2742|9239 U 23
AF species1961|9433 U 27
AF species158|7890 U 8
AF species2703|5769 U 182
AF species2119|1909 U 113
AF species2739|2104 U 57
AF species1635|5973 U 8
AF species2066|9064 U 25

BS 1 7 species2702|8138
BS 8 24 species1635|5973
BS 25 25 species2702|8138
BS 26 26 species1635|5973
BS 27 27 species2702|8138
BS 28 75 species1635|5973
BS 76 76 species2739|2104
BS 77 78 species1635|5973
BS 79 79 species2739|2104
BS 80 80 species1635|5973
BS 81 81 species2739|2104
BS 82 82 species1635|5973
BS 83 83 species2739|2104
BS 84 89 species1635|5973
BS 90 91 species2739|2104
BS 92 107 species1635|5973
BS 108 109 species2739|2104
BS 110 121 species1635|5973
BS 122 122 species2742|9239
BS 123 129 species1635|5973
BS 130 130 species2739|2104
BS 131 131 species1635|5973
BS 132 132 species2739|2104
BS 133 137 species1635|5973
BS 138 142 species2739|2104
BS 143 143 species3098|4869
BS 144 159 species2739|2104
BS 160 160 species2119|1909
BS 161 164 species1973|7670
BS 165 166 species2119|1909
BS 167 175 species1973|7670
BS 176 181 species2119|1909
BS 182 184 species2703|5769
BS 185 185 species2119|1909
BS 186 191 species2703|5769
BS 192 192 species2119|1909
BS 193 198 species2703|5769
BS 199 203 species2119|1909

RD species2703|6185 108 0 0
TGGGGATACCAAGTCGAAGAATCGCTGATTCTTGCACTGGTATTTTCCCT
CGAACTGGATAAG*CA*C*GTGGA*G*ATGAGGG*TTCCC*ATT*TTGGT
GTAGTTCT

QA 61 97 61 97
DS CHROMAT_FILE: species2703|6185 PHD_FILE: species2703|6185.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2004|3290 122 0 0
TGTCTCCGTCCTTCTCCAGATAGGACTT*AACGTCTG*AGCTT*G*ATTT
*AGCTC*C*CTG*AATGTT*CGG*ATGGAAATGT*GCT*GA*CCTGG***
TTGGGGAC**ACC**A*GG*TC

QA 21 122 21 122
DS CHROMAT_FILE: species2004|3290 PHD_FILE: species2004|3290.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2702|8138 125 0 0
CCAGGTAGGACTTGA*CGTC*GGAGCT**GGATTT*AGCTC*C*CTG*AA
TGTT*CGG*ATGGAAATGT*GCT*GA*CCTGG***TTGGGGA**GACC**
A*GG*TCGAA**GAATCTGTT*ATT

QA 5 125 5 125
DS CHROMAT_FILE: species2702|8138 PHD_FILE: species2702|8138.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2788|6026 114 0 0
TTATTTGTGCATTGGAA*TTTTCC*TTC*AAA*TTGGATGA*G*CA*C*G
TGGA**TATGAGG**TTCCCCATT*TTCA*TGAAGCTCTCTACACACTCT
AATGAATAATTTAG

QA 14 82 14 82
DS CHROMAT_FILE: species2788|6026 PHD_FILE: species2788|6026.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species3098|4869 110 0 0
ATCTGTTATTTTTGCACTGGAA*TTTTCC*TTC*AAA*TTGGATGA*G**
AACA*TGGA**TATGCGGAGACCCATCTTCGTGAAGCTCTCTGCAGATTT
TTATGAATTT

QA 19 65 19 65
DS CHROMAT_FILE: species3098|4869 PHD_FILE: species3098|4869.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species1827|9888 104 0 0
ACGTGGATATGAGGGCT*CCC*AT*CTTC*GTGAAGCTCTCTGCAGATTT
TGATGTATTTTTTGTTGGTTGGGGTTTCTAGGTTTTGAAGTTGGGAGAGT
GCTT

QA 9 33 9 33
DS CHROMAT_FILE: species1827|9888 PHD_FILE: species1827|9888.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2742|48 120 0 0
CTTTTAGCTC*C*CTG*AATGTTT*GG*ATGGAAATGT*GCT*GA*CCTG
G***TTGGGGA*T*A**TGA*G*ATCGAA**GAATCT*TTGATTTTTACA
CTGGAATTTCCCTTCGAATT

QA 2 97 2 97
DS CHROMAT_FILE: species2742|48 PHD_FILE: species2742|48.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2011|1996 116 0 0
CATTCCAGTGTGTCTCCGTCCTTGGTAATGTATGTTTTGA*CGTC*GGAG
CT**GGATTT*AGCTC*C*CTGTA*TGTT*CGG*ATGGAAATGT*GCT*G
A*CCTGG***TTGGGG

QA 37 116 37 116
DS CHROMAT_FILE: species2011|1996 PHD_FILE: species2011|1996.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species3089|7597 112 0 0
CGAA*CT*GGATGA*G*CA*CA*TGGA*G*ATGAGGGCT*CCC*AT*CTT
C*GTGCAGTTCTCTGCAGATCTTGATGAATTTTTTATTTGTTGGTGTTTC
TAGGTTTTGTAA

QA 1 55 1 55
DS CHROMAT_FILE: species3089|7597 PHD_FILE: species3089|7597.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species1961|5108 110 0 0
GG**A*TG***TGA*GG*TC*AAA*GAATCTGTTGTTTTGGCATTTGAAT
TTTCCTTCGAACTGGATGAGAACATGCAAGTGAGGAGTCCCATTTTCATG
AAGCTCTCTG

QA 1 31 1 31
DS CHROMAT_FILE: species1961|5108 PHD_FILE: species1961|5108.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2011|4145 109 0 0
TTCGAATTGGACAAG*CA*C*GTGGA*G*ATGAGG**TTCCCCATT*TTC
A*TGCAACTCTCTGCAGATCTTGATGAATTTCTTGTCTACTGGTGTGTTT
AGGTTTTGT

QA 13 54 13 54
DS CHROMAT_FILE: species2011|4145 PHD_FILE: species2011|4145.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species1667|4956 120 0 0
TTTTTCCATGTATGTTTTAACATCTGTTGAGCTTTTAGCTC*C*CTG*AA
TGTT*CGG*ATGGAAATGT*GCT*GATC**GGG**TTGGGGA*TG***TG
A*G*ATCGAA**GAATCT*T

QA 33 120 33 120
DS CHROMAT_FILE: species1667|4956 PHD_FILE: species1667|4956.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species980|9980 109 0 0
ATTTCCCTTCGAATTGTATAAG*CA*CA*TGGA*G*ATGAGG**TTCCCC
ATT*TTC*GTGTAGCTCTCTAGCTACTTTTATGTATTTTTTATTTGTTGG
TGTTTGTAG

QA 20 61 20 61
DS CHROMAT_FILE: species980|9980 PHD_FILE: species980|9980.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2907|6509 107 0 0
A*TGGA*G*ATGAGGGCT*CCC*AT*CTTC*GTGCAGCTCTCTACAGATT
TTGATATATTTTTTATTTGTTGGGGTTTGTAGAGGTTTTAATTGGGAAAG
TGCTTCT

QA 1 34 1 34
DS CHROMAT_FILE: species2907|6509 PHD_FILE: species2907|6509.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species1973|7670 104 0 0
CGGATGGAAATATGCTGACTGGGAAGGGGACACCAGGTCGAAGAATCTGT
AATTTGTGCATTGGTATTTGCCTTCGAACTGAATGA*GT*A*CA*TGGAT
ATGA

QA 85 99 85 99
DS CHROMAT_FILE: species1973|7670 PHD_FILE: species1973|7670.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2779|6708 124 0 0
CTTTCTCGACGTAGGACTTGA*CGTC*GGAGCT**GGATTT*AGCTC*C*
CTG*AATGTT*CGG*ATGGAAATGTA**TTGA*CCTGG***TTGGGGAC*
*ACC**A*G*ATCGAA**GAATCT

QA 11 124 11 124
DS CHROMAT_FILE: species2779|6708 PHD_FILE: species2779|6708.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2024|3244 112 0 0
GGGATACGAGGTCGAAGAATCTGTTATTTTTGCACTTGTATTTCCCTTCG
AA*CT*GGATGA*G*CA*C*GTG*AAG*ATGAGG**TTCCCCATT*TTCA
*TGAAACTCTCT

QA 49 103 49 103
DS CHROMAT_FILE: species2024|3244 PHD_FILE: species2024|3244.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2216|7882 110 0 0
TCTGTT*ATT***CGTGCAG*ACG*AACTT**CCCTTCGAA*CT*GGATA
AGAACGTGGATATGCGGAGACCCATCTTCGTGCAACTCTCTACAAATTTT
GATAAATTTC

QA 1 49 1 49
DS CHROMAT_FILE: species2216|7882 PHD_FILE: species2216|7882.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species1037|7115 119 0 0
GCTTTTAGCTC*C*CTG*AATGTTT*GG*ATGGAAATGT*GCT*GATC*T
GG***TTGGGGA*T*ACC**AA**ATCGAA**GAATCGTTGATTGTGGCA
TTTGAATTTGCCTTCGAAC

QA 3 87 3 87
DS CHROMAT_FILE: species1037|7115 PHD_FILE: species1037|7115.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2742|9239 120 0 0
ATGAGCTTTTAGCTC*C*CTG*AATGTTT*GG*ATGGAAATGT*GCT*GA
*CCTGG***TTGGGGA*T*A**TGA*G*ATCGAA**GAATCT*TTGATTT
TTACACTGGAATTTCCCTTC

QA 7 102 7 102
DS CHROMAT_FILE: species2742|9239 PHD_FILE: species2742|9239.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species1961|9433 119 0 0
GCTTTTAGCTC*C*CTG*AATGTTT*GG*ATGGAAATGT*GCT*GA*CCT
G**C*TTGGGGA*TG***TGA*GG*TC*AAA*GAATCTGTTGTTTTGGCA
TTTGAATTTTCCTTCGAAC

QA 3 88 3 88
DS CHROMAT_FILE: species1961|9433 PHD_FILE: species1961|9433.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species158|7890 125 0 0
T*GA*CGTC*GGAGCT**GGATTT*AGCTC**TCTG*AATGTTT*GG*AT
GGAAATGT*GCT*GA*CCTGG***TTGGGGA*T*ACC**A*GG*TCGAA*
T*AATCTGATATTTGTGATCTGAAC

QA 1 108 1 108
DS CHROMAT_FILE: species158|7890 PHD_FILE: species158|7890.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2703|5769 103 0 0
AGGG*TTCCC*ATT*TTGGTGTAGTTCTCGACAGATTTTGATGTATTTTT
TGTTTGTTGGTGTATCTAGGGCTTTTATTTTTTCAAGGGTTTCTTCTTTG
GCG

QA 1 17 1 17
DS CHROMAT_FILE: species2703|5769 PHD_FILE: species2703|5769.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2119|1909 110 0 0
AATTAATGGCATTTGCGTATGAATCGTTGGCAGATTGGCAACCTCCTTGA
*G*CA*CA*TGGA*G*ATGAGG**TTCCCCAT*CTTC*GTGTAATTCTCT
GGAAACCCTA

QA 48 91 48 91
DS CHROMAT_FILE: species2119|1909 PHD_FILE: species2119|1909.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2739|2104 124 0 0
TGGAAATGT*GCT*GA*CCTGG***TTGGGGA*T*ACC**A*GG*TCGAA
**GAATCTGTT*ATT***CGTGCAG*ACG*AA*TTT*CCCTTCGAA*CT*
GGAGTAACACGTGGAGATGAGGGC

QA 1 103 1 103
DS CHROMAT_FILE: species2739|2104 PHD_FILE: species2739|2104.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species1635|5973 130 0 0
TTGA*CGTC*GGAGCT*CG*ATTT*AGCTC*C*CTG*AATGTT*CGG*AT
GGAAATGT*GCT*GA*CC*GGG*AT*GGGGA**GACC**A*GG*TCGAA*
T*AATCTGTT*ATT***CGTGC*GGACG*A

QA 1 130 1 130
DS CHROMAT_FILE: species1635|5973 PHD_FILE: species1635|5973.phd.1 TIME: Thu Jul 27 12:33:48 2000

RD species2066|9064 119 0 0
GAGCTTTTAGC*CGC*CTG*AATGTT**GGGATGGAAATGT*GCT*GA*C
CTG**C*TTGGGGA*T*AC*T*A*GG*TCGAA**GAATCGTTGATTTGTG
CAGTTGTATTTCCCCTCGA

QA 5 89 5 89
DS CHROMAT_FILE: species2066|9064 PHD_FILE: species2066|9064.phd.1 TIME: Thu Jul 27 12:33:48 2000
BioPerl-1.007002/t/data/503384.MEGABLAST.0000444000766000024       175213155576321 17022 0ustar00cjfieldsstaff000000000000'Contig634'=='-503384' (1 7941 321 7620) 19
'Contig634'=='-503384' (374 7576 540 7410) 5
'Contig634'=='-503384' (579 7384 783 7180) 23
'Contig1853'=='+503384' (1691 6406 1905 6620) 11
'Contig1853'=='+503384' (1933 6630 2201 6897) 31
'Contig1853'=='+503384' (2277 6963 2312 6998) 0
'Contig3700'=='-503384' (4083 9434 4794 8723) 79
'Contig3700'=='-503384' (2161 11335 2753 10744) 53
'Contig3700'=='-503384' (3198 10310 3753 9759) 47
'Contig3700'=='-503384' (2839 10666 3169 10338) 32
'Contig3700'=='-503384' (5241 8482 5355 8368) 4
'Contig3700'=='-503384' (3622 9890 3753 9759) 9
'Contig3997'=='-503384' (1546 1704 1968 1282) 22
'Contig3997'=='-503384' (2060 1205 2498 767) 28
'Contig3997'=='-503384' (2560 723 2931 351) 22
'Contig3997'=='-503384' (3052 233 3284 4) 20
'Contig3997'=='-503384' (1315 1942 1502 1755) 10
'Contig3997'=='-503384' (1033 2215 1279 1969) 30
'Contig3997'=='-503384' (865 2374 960 2279) 6
'Contig3997'=='-503384' (1 3329 165 3164) 26
'Contig3997'=='-503384' (198 3116 273 3041) 6
BioPerl-1.007002/t/data/503384.MEGABLAST.2000444000766000024     10175313155576321 17066 0ustar00cjfieldsstaff000000000000MEGABLAST 2.2.4 [Aug-26-2002]


Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), 
"A greedy algorithm for aligning DNA sequences", 
J Comput Biol 2000; 7(1-2):203-14.

Database: cneoA.nt 
           4935 sequences; 17,206,226 total letters

Searching.......... done
Query= 503384 11337 bp 2 contigs
         (11,337 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Contig3700                                                            785   0.0  
Contig3997                                                            664   0.0  
Contig634                                                             486   e-136
Contig1853                                                            339   1e-91

>Contig3700
          Length = 5631

 Score =  785 bits (396), Expect = 0.0
 Identities = 639/718 (88%), Gaps = 12/718 (1%)
 Strand = Plus / Minus

                                                                        
Query: 8723 gacggcagcccaccgcgccaatcaggttcatccaaattcgtcatcctcgggccgaacatt 8782
            |||||||||||||| || ||||||||||||||||||||  ||||||||||||||||||||
Sbjct: 4794 gacggcagcccaccacgtcaatcaggttcatccaaatttatcatcctcgggccgaacatt 4735

                                                                        
Query: 8783 ggacagtactttgaagtatcaagctcagaaggatccagctgcagttcttcgccttccact 8842
            ||||||||||||||||||||||||||||||||||||| |||||||||||| |||||||| 
Sbjct: 4734 ggacagtactttgaagtatcaagctcagaaggatccaactgcagttcttctccttccacg 4675

                                                                        
Query: 8843 ccgtcgcattcgcctaaccgtctcaatcatcaacactcatttgacacttctaaaagccgt 8902
            || ||||||||||||||||||||||||||||  |||||||||||| |||| ||  |||||
Sbjct: 4674 ccatcgcattcgcctaaccgtctcaatcatcggcactcatttgacccttccaacggccgt 4615

                                                                        
Query: 8903 tcaccctctccgactgaatgtgacgagattgaccgggtagaatattcatctccagccata 8962
            |||| ||||||||| |||||||||||||||||| |||| ||||||||||||| | |||||
Sbjct: 4614 tcacgctctccgaccgaatgtgacgagattgactgggtggaatattcatctctatccata 4555

                                                                        
Query: 8963 gaaatggaagcatgccaaatgtcgggctgggacagtagtgtctccgagttgtcagagggc 9022
            |  ||||||||||| || ||| || |||||| |||||||||||| || ||||||||||| 
Sbjct: 4554 gggatggaagcatgtcagatgccgagctgggccagtagtgtctctgaattgtcagagggt 4495

                                                                        
Query: 9023 gactcggagacagagacttccgtgattattacccctgatagagatattcgggat-g--gt 9079
            ||||| |||||||||| ||||||||||||||| ||||||||||||||||||||| |  ||
Sbjct: 4494 gactcagagacagagagttccgtgattattactcctgatagagatattcgggatggtcgt 4435

                                                                        
Query: 9080 caaagtcagcgcttggatatccgggatatcgtaaggtggaaatacgctttgataagcctt 9139
            |||||||||||||||||||||| |||||||||||||||| | |||  |||| |||| |||
Sbjct: 4434 caaagtcagcgcttggatatccaggatatcgtaaggtggcagtacaatttggtaagtctt 4375

                                                                        
Query: 9140 gttaaacatatgtttcataggcct-tacttctcaaacagacctccatcaaatctgaacat 9198
            ||||||||||||||||||||| || |||||||||||||||| |||||||||||||||  |
Sbjct: 4374 gttaaacatatgtttcatagg-ctctacttctcaaacagacttccatcaaatctgaatgt 4316

                                                                        
Query: 9199 ccggctttgagaccgaatcgcttattatcttgccgtacaacttcgagccatacggtggta 9258
            | |||||||||||||||||||    |||||| ||| |||||||||||||||||||| || 
Sbjct: 4315 ctggctttgagaccgaatcgc---ctatcttcccgcacaacttcgagccatacggtagtg 4259

                                                                        
Query: 9259 cctcgtgactttaatcgtcgctgtagcgaatcttgctctgttacatc-ggcctcaagctc 9317
            ||| | |||||||||||||||||||||||| || | |||||| |||| || ||| |||||
Sbjct: 4258 ccttgcgactttaatcgtcgctgtagcgaacctcgttctgttgcatcagg-ctctagctc 4200

                                                                        
Query: 9318 tagttttcatgcccctcagccgggagagttgaa-ccaacatggagatactgtggcttgtg 9376
            ||||| | |||||||||||  ||||||    ||  |||||||||||||| ||||||||||
Sbjct: 4199 tagttctaatgcccctcagttgggaga-cccaagtcaacatggagataccgtggcttgtg 4141

                                                                      
Query: 9377 aagcttgcggtagaggcacgacaatcactaacgcaaaaaagattatgccttgtcaagt 9434
            |||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||
Sbjct: 4140 aagcttgcggtagaggcacgaccatcactaacgcaaagaagattatgccttgtcaagt 4083



 Score =  753 bits (380), Expect = 0.0
 Identities = 541/594 (91%), Gaps = 3/594 (0%)
 Strand = Plus / Minus

                                                                         
Query: 10744 taccatatttttctccgttctaccgtattctt-cacatgtatctgcatatcaacgtaaca 10802
             ||||||| |||||||| || ||||||| | || ||||||||||||| |||  | | || |
Sbjct: 2753  taccatacttttctccattttaccgtactattccacatgtatctgcgtatttatgcaata 2694

                                                                         
Query: 10803 tacaatttccaagatacaacaggaattcaaacaagaaaaatcagatcctcaaccccgcac 10862
             ||||||||||||| |||||||||||| ||||||| |||||||||||||||||||||||||
Sbjct: 2693  tacaatttccaagttacaacaggaatgcaaacaacaaaaatcagatcctcaaccccgcac 2634

                                                                         
Query: 10863 caaacttctttacacagataaggtttacctcatctctcatttgtctccatattctccacc 10922
             ||||||||||||||||||||||||| |||||||| |||||||| ||||||||||||||||
Sbjct: 2633  caaacttctttacacagataaggttcacctcatccctcatttgcctccatattctccacc 2574

                                                                         
Query: 10923 attcccttccagcctcactcgcaccctcgtttaacccttcgtcctgtgcccacttt-tct 10981
             |||||||||||||||| ||| ||| ||| ||||| ||||| |||||| |||| ||| |||
Sbjct: 2573  attcccttccagcctcgctcacactctcatttaatccttcatcctgtcccca-tttctct 2515

                                                                         
Query: 10982 tttatgatcattctcatccatcgcaacacctcgacgactttctcaactccatccccaacc 11041
             ||||||||||  |||||||||| |||||||||||||||||||||||||||||| ||||||
Sbjct: 2514  tttatgatcaccctcatccatctcaacacctcgacgactttctcaactccatctccaacc 2455

                                                                         
Query: 11042 ctgccctcgccatcattcaaacattttttgagaaatgcagccactttaatagcatcctta 11101
              ||||||||||||||||||||||||||||||||||||| ||||||||| |||||||||| 
Sbjct: 2454  ttgccctcgccatcattcaaacattttttgagaaatgcggccactttagtagcatccttg 2395

                                                                         
Query: 11102 tctgccggcggactatcttctctggactcgatccataattcaatagtcctgagcacatcg 11161
             ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
Sbjct: 2394  tctgccggcggactatcttctctggactcgatccataattcaatagttctgagcacatcg 2335

                                                                         
Query: 11162 ggaagctcggtcgagttcatgagagcgggtttgggcggcctgatgatcttgacactctgt 11221
             ||||||||||| ||||||||||| ||||||||||| ||| | |||||||||||| | |||
Sbjct: 2334  ggaagctcggttgagttcatgagggcgggtttggggggcttaatgatcttgacattttgt 2275

                                                                         
Query: 11222 ctctgctgcggcgggattgaccgtgatgtggagcggcctctgtacgcgccgacacctccc 11281
             ||||||||||| |||||||||||||||||||| |||||||||||| |||||||| |||||
Sbjct: 2274  ctctgctgcggtgggattgaccgtgatgtggaacggcctctgtacccgccgacaactccc 2215

                                                                   
Query: 11282 aacttgacaggtgagacactggtactcgtccctcttgatctggatctatcccca 11335
             || |||||||| |||||||| |||||||||||||| || ||||||||| |||||
Sbjct: 2214  aatttgacaggagagacactagtactcgtccctctcgacctggatctaccccca 2161



 Score =  726 bits (366), Expect = 0.0
 Identities = 511/558 (91%), Gaps = 8/558 (1%)
 Strand = Plus / Minus

                                                                         
Query: 9759  ctaaagatatcaggacatcactccggccattgttgaggccttccttccgagaaattcgtt 9818
             |||| |||||||||||||||||||||||| |||||||||||| |||||||||||||| ||
Sbjct: 3753  ctaatgatatcaggacatcactccggccactgttgaggcctttcttccgagaaattcatt 3694

                                                                         
Query: 9819  atctcaccgtacccttcaaccaatccatattctccttgacagattcgacgggcgtactaa 9878
             ||||||  ||||||||||||||||||||||||||||||||||||||||||| ||||| ||
Sbjct: 3693  atctcatagtacccttcaaccaatccatattctccttgacagattcgacggacgtacaaa 3634

                                                                         
Query: 9879  ggacta-c--ctg-g-tacgcccccttttaaagtctgctgctgtgctgaatactcgcttc 9933
             |||||| |   || | || ||| || |||| |||||  ||||||||||| ||||| ||||
Sbjct: 3633  ggactatctggtgtgctatgccgcc-tttagagtctattgctgtgctgattactcacttc 3575

                                                                         
Query: 9934  gaaaacagtatatcgaagccgcgacaccgcaagccgcacaaactatactcaagacctgtc 9993
             |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Sbjct: 3574  gaaaacagtatatcgaagccgcgacaccgcaagcggcacaaactatactcaagacctgtc 3515

                                                                         
Query: 9994  agaatactttcttgtccggaggagcgctcacttcgggaaggagacggcctgttaccatca 10053
             |||||| |||| |||||||||||||||||||||||||||||| |||||||||||| ||||
Sbjct: 3514  agaataatttcatgtccggaggagcgctcacttcgggaaggaaacggcctgttactatca 3455

                                                                         
Query: 10054 ctcccgtatcgcattcggagctcatagaagaactgcgtccacattcggctcaggaactcc 10113
             |||||||||| |||||||||||||||||||||||||||||||| ||||| ||||||||||
Sbjct: 3454  ctcccgtatctcattcggagctcatagaagaactgcgtccacactcggcccaggaactcc 3395

                                                                         
Query: 10114 attcgctactcgctctttgtcaagctgctatagactcgaattctggatccaaac-aaagt 10172
             ||||||||||| ||||||||||||||||| | ||||| ||||||||||  |||| ||| |
Sbjct: 3394  attcgctactcactctttgtcaagctgctgtggactcaaattctggatgtaaactaaa-t 3336

                                                                         
Query: 10173 acttcaaagtatatcaagtctcgccatgggccatactacgccttgatgtcaacaatgagc 10232
             ||||||||||||||||||||||||||||| ||||||||||| ||||||||| ||||||||
Sbjct: 3335  acttcaaagtatatcaagtctcgccatggaccatactacgctttgatgtcagcaatgagc 3276

                                                                         
Query: 10233 aaaatgaatggggagcaaagtccctcttactgggacatgttctgtaagtggaatttgagt 10292
             ||| ||||||||||||||||||| ||||||||||||||||||||||||||| ||| ||| 
Sbjct: 3275  aaattgaatggggagcaaagtccttcttactgggacatgttctgtaagtgggattcgagc 3216

                               
Query: 10293 atggtcgtagagctcttg 10310
             ||| ||||||||||||||
Sbjct: 3215  atgatcgtagagctcttg 3198



 Score =  400 bits (202), Expect = e-110
 Identities = 300/332 (90%), Gaps = 4/332 (1%)
 Strand = Plus / Minus

                                                                         
Query: 10338 agacgtcgcctctggtaagaaggactttttggacttttcatcaggtccattatggcattc 10397
             ||||||||||||||||||||| || |||||| ||||| |||||| |||||||||||| ||
Sbjct: 3169  agacgtcgcctctggtaagaa-gaatttttgaactttccatcagttccattatggcagtc 3111

                                                                         
Query: 10398 gctgaccacttgaccgctgttcgtgatggggctaacaggagccatctccgcattaagtaa 10457
             ||||||| | |||||| ||||||||| |||||||| ||||||||||||||||||||||||
Sbjct: 3110  gctgaccgcatgaccgttgttcgtgacggggctaataggagccatctccgcattaagtaa 3051

                                                                         
Query: 10458 agcaataactcgccaggcctactttcgttcctcacaaggctcccctgctcgctcatatcc 10517
             |||||||||||||||| ||||||||| |||||||||| |||| |||||||||||||||||
Sbjct: 3050  agcaataactcgccagacctactttcattcctcacaaagctcgcctgctcgctcatatcc 2991

                                                                         
Query: 10518 c---accgacgccataactcttgtctctgaggaagatctgctcgtacgcaataaattact 10574
             |   |||||||||| |||||  ||||||||||||||| | || |||||||| ||||||||
Sbjct: 2990  cgccaccgacgccacaactcacgtctctgaggaagatatacttgtacgcaacaaattact 2931

                                                                         
Query: 10575 gatgttgttcgagaagtgttttggtatgatgccaagagctaattaactcagaggatcact 10634
             |||||||||||||| |||||| |||||||||||||||||||||||||||||||||| |||
Sbjct: 2930  gatgttgttcgagaggtgtttcggtatgatgccaagagctaattaactcagaggattact 2871

                                             
Query: 10635 atatcatcggggtgtacaggaatttgtacttg 10666
              |||||| ||| |||||||||||| |||||||
Sbjct: 2870  gtatcattgggatgtacaggaattcgtacttg 2839



 Score =  196 bits (99), Expect = 1e-48
 Identities = 112/116 (96%), Gaps = 2/116 (1%)
 Strand = Plus / Minus

                                                                        
Query: 8368 gaccgggaacgtacgagggaatggagacggcctttgagagcctgttgatgtagtcgtcct 8427
            ||||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct: 5355 gaccggg-acgtacgagggaatggacacggcctttgagagcctgttgatgtagtcgtcct 5297

                                                                    
Query: 8428 tgtggtcgtcgac-gtactggaggaacttgggatcggccattgctgtgcttgtggg 8482
            ||||||||||||| |||||||||||||||||||||||||||||||||| |||||||
Sbjct: 5296 tgtggtcgtcgacagtactggaggaacttgggatcggccattgctgtgtttgtggg 5241


>Contig3997
          Length = 12734

 Score =  664 bits (335), Expect = 0.0
 Identities = 401/423 (94%)
 Strand = Plus / Minus

                                                                        
Query: 1282 accttgcgaatgtccaataaacccatcacgacgtcacctctgaccacttccttttcatct 1341
            |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
Sbjct: 1968 accttgcgaatgtccaataaacccatgacgacgtcacctctgaccacttccttttcatct 1909

                                                                        
Query: 1342 gttccaaccaccagcgccctccccacaaaactccttcccggcacatacttgcccacatcc 1401
            || || |||||||||||||| ||||||||||||||||| |||||||||||||||||||||
Sbjct: 1908 gtaccgaccaccagcgccctgcccacaaaactccttccaggcacatacttgcccacatcc 1849

                                                                        
Query: 1402 cctcttcccttttcgtccacggcacgtacatccacttgatccaccgcaacagcataaacc 1461
            ||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||
Sbjct: 1848 cctcttcccttttcgtccacggcacgtacatccacttgatccaccgccacggcataaacc 1789

                                                                        
Query: 1462 tgtacgagcacttggttctttcccgtctttcctgggggttttgagtgagagctaaactct 1521
            ||||||||||||||||||||||||||||| || || |||||||||||||| |||||||||
Sbjct: 1788 tgtacgagcacttggttctttcccgtcttaccaggaggttttgagtgagaactaaactct 1729

                                                                        
Query: 1522 acaaggggcgggagctggtcacggaggtgtgcgggggtagcgttgtggtggtcaaatgtg 1581
            ||||||||||||||||||||||| |||||||||||||||||||| ||||| || ||||||
Sbjct: 1728 acaaggggcgggagctggtcacgaaggtgtgcgggggtagcgttatggtgatcgaatgtg 1669

                                                                        
Query: 1582 gaatggagtgtgatggatgccatggtggcgtgtggaagaccaaggatacgtgcgtctagg 1641
            |||||||||||||||||||||||| ||||||||||||||||||||||||| |||||||||
Sbjct: 1668 gaatggagtgtgatggatgccatgctggcgtgtggaagaccaaggatacgggcgtctagg 1609

                                                                        
Query: 1642 tcgggcgctgatttggccgggtttgactgtttgtaagcgcccagaggtaaaatcaagttg 1701
            || || |||||||| ||||||||||| |||||||||||||||| ||||||||||||||||
Sbjct: 1608 tcaggtgctgatttagccgggtttgattgtttgtaagcgcccaaaggtaaaatcaagttg 1549

               
Query: 1702 cta 1704
            |||
Sbjct: 1548 cta 1546



 Score =  648 bits (327), Expect = 0.0
 Identities = 412/440 (93%), Gaps = 2/440 (0%)
 Strand = Plus / Minus

                                                                        
Query: 767  actcactttccgccactcttcaatgctctttttgcagtgtcatacaccctttgcccaccc 826
            ||||||||||||||||||||||||||||||  ||||||||||||||||| ||||||||| 
Sbjct: 2498 actcactttccgccactcttcaatgctcttcgtgcagtgtcatacacccgttgcccacct 2439

                                                                        
Query: 827  tgggtgtcaaacacaaagtcatacccattttcctccagattgatcatcactgccgccgga 886
            || || ||||||||||||||||| ||||||||||||||||||||||||||||||||||| 
Sbjct: 2438 tgcgtatcaaacacaaagtcatatccattttcctccagattgatcatcactgccgccggc 2379

                                                                        
Query: 887  gaacccatgagcactcccttggccccattctcaatacacttt-tggtgagcctcatgcga 945
            ||||||||||||||||||||||||||||| |||||||| ||| |||||||||||||||||
Sbjct: 2378 gaacccatgagcactcccttggccccattttcaataca-tttctggtgagcctcatgcga 2320

                                                                        
Query: 946  gtcgtccccaccggggacgatagccgtcacgtatacacctgcgcgggacatgacctgaca 1005
            ||||||||| || |||| |||||||||||| || ||||||||||| ||||| ||||| ||
Sbjct: 2319 gtcgtccccgccagggatgatagccgtcacatagacacctgcgcgagacatcacctggca 2260

                                                                        
Query: 1006 gacgagtgcggcgataccagtatgggcgttgatgataatggcgcggaactggcgattgag 1065
            |||||||||||||||||||||||||||||||||||  ||||||||||| |||||||||||
Sbjct: 2259 gacgagtgcggcgataccagtatgggcgttgatgacgatggcgcggaattggcgattgag 2200

                                                                        
Query: 1066 agagccacgaacgcatcgcgctgcagcgatgccttggagagggagaatcgagagttgttc 1125
            ||||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||
Sbjct: 2199 agagccacggacgcatcgcgctgcagcgatgccttggagagggagaatagagagttgttc 2140

                                                                        
Query: 1126 gagtgtgagaagggtagggaatggtgctcgagagacacgtcgacggtcgacaagaatgta 1185
            ||||||||||||||||||||||||||| ||||| ||||||||||| || |||||||||||
Sbjct: 2139 gagtgtgagaagggtagggaatggtgcacgagaaacacgtcgacgatccacaagaatgta 2080

                                
Query: 1186 ctctgccaatgcgccgctct 1205
            ||||||||||||||||||||
Sbjct: 2079 ctctgccaatgcgccgctct 2060



 Score =  563 bits (284), Expect = e-159
 Identities = 351/373 (94%), Gaps = 1/373 (0%)
 Strand = Plus / Minus

                                                                        
Query: 351  aaaaagcagaacactagttgataatcctcacgaccctcacgccacactcatcccatcctt 410
            ||||||||| |||||| |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2931 aaaaagcag-acactaattgataatcctcacgaccctcacgccacactcatcccatcctt 2873

                                                                        
Query: 411  ggcgtttaaagacatctgctcccctttcaaagggcaccactgcgttctcaccttccagca 470
            | ||||||||||| |||||||||||||||||||||||||||||| |||||||||||| ||
Sbjct: 2872 gacgtttaaagacctctgctcccctttcaaagggcaccactgcgctctcaccttccaaca 2813

                                                                        
Query: 471  ctggcctaaaggatgccatacacggttcctccatcacatcgcggcaatccatcccggatg 530
            |||| ||||||| ||||||||||||||||||||||||||| ||||| ||||||||||| |
Sbjct: 2812 ctggtctaaaggttgccatacacggttcctccatcacatcacggcagtccatcccggacg 2753

                                                                        
Query: 531  cgtcaatctctggctcaccagacccgatgggagagacgtattcaaaggcgataaactttg 590
            ||||||||||||||||||||||||| ||||| ||||| |||||||||| |||||||||||
Sbjct: 2752 cgtcaatctctggctcaccagacccaatgggggagacatattcaaaggagataaactttg 2693

                                                                        
Query: 591  agtctttgcgttttgaaccaaacactgttctcagtgtcttgatgcccgacgggcgggaag 650
            | |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||
Sbjct: 2692 aatctttgcgttttgaaccaaacactgttctcagtgtcttgatgccggacgggcgggaag 2633

                                                                        
Query: 651  ccaagtggggcgggacgcggttcagagttgtttcggggcgcttggtcgataccaatctac 710
            |||| ||||||||||||||||||||||||| |||||| ||||||||||||||||||||||
Sbjct: 2632 ccaaatggggcgggacgcggttcagagttgcttcgggccgcttggtcgataccaatctac 2573

                         
Query: 711  agaatgcacattt 723
            | ||| |||||||
Sbjct: 2572 aaaatacacattt 2560



 Score =  299 bits (151), Expect = 1e-79
 Identities = 214/234 (91%), Gaps = 5/234 (2%)
 Strand = Plus / Minus

                                                                        
Query: 4    ttgatagatctccagtcatagggcctctagtccggcgcacaagaagtgcaaggtttttag 63
            |||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||
Sbjct: 3284 ttgatagatctccagtcatagggcctctggtccggcgcacaagaagtgcaaggtttttag 3225

                                                                        
Query: 64   ggcgaagctggggtagttctacagggagagaagttgatggggaagcagagctcgggcaag 123
            |||||||||||| |||||||  |||| ||||||||||||||||||||||||| ||||| |
Sbjct: 3224 ggcgaagctgggatagttctgtagggggagaagttgatggggaagcagagctggggcagg 3165

                                                                        
Query: 124  cgggcagtagtatcggacgagattggtgtacaagagagatggatgaaggg-tatgggacg 182
            ||||| ||||| ||||||||| | |||||||||||||||||||||| ||| |||||||| 
Sbjct: 3164 cgggcggtagtgtcggacgaggtcggtgtacaagagagatggatga-gggatatgggact 3106

                                                                  
Query: 183  tttaatgattgatgac-att-gtatcgattttgtacaagtatcttg-gactgtt 233
            ||||||||||||| |  ||| ||| ||||||||||||||||||||| |||||||
Sbjct: 3105 tttaatgattgattaagatttgtaacgattttgtacaagtatcttgagactgtt 3052



 Score =  293 bits (148), Expect = 7e-78
 Identities = 179/189 (94%), Gaps = 2/189 (1%)
 Strand = Plus / Minus

                                                                        
Query: 1755 actcacgtgtacccaggagcactttcttgatcccttccatgcgattccatcaacatc-cc 1813
            ||||||||||||||||||||||| |||||||||||||||||||| |||||||||| | ||
Sbjct: 1502 actcacgtgtacccaggagcactctcttgatcccttccatgcgactccatcaaca-cacc 1444

                                                                        
Query: 1814 atcaccatacgaactcccttcccactttgacccgcctgtaaatctatacccagcagcgct 1873
            |||||||||||||||||||||||||||||||||||||  ||| |||||||||||||||||
Sbjct: 1443 atcaccatacgaactcccttcccactttgacccgcctccaaacctatacccagcagcgct 1384

                                                                        
Query: 1874 cttcgacctcttgatcatggacggtaaaggcaattcagccaatccatcatctttttcgcc 1933
            ||| ||||||||||||||||||||||||||||||||||||||||||||||||| ||| ||
Sbjct: 1383 ctttgacctcttgatcatggacggtaaaggcaattcagccaatccatcatcttcttcccc 1324

                     
Query: 1934 tgcctcact 1942
            |||||||||
Sbjct: 1323 tgcctcact 1315



 Score =  252 bits (127), Expect = 2e-65
 Identities = 220/250 (88%), Gaps = 6/250 (2%)
 Strand = Plus / Minus

                                                                        
Query: 1969 gaccgtggccgacttcgctcctcgagcctctaaagatgctagactttctcgaatgcgaca 2028
            |||||||||| ||||| ||| |||||||||| || | ||||||| || ||||||||||||
Sbjct: 1279 gaccgtggcccacttcactcttcgagcctctgaatacgctagaccttgtcgaatgcgaca 1220

                                                                        
Query: 2029 aatgtcctcctccattatcgtggtacatggataaccttgagcggctcctctcgggagggg 2088
            | ||  | || ||||||||||| |||| ||||||||| ||||| |||||||||||||| |
Sbjct: 1219 actg--c-ccaccattatcgtgatacacggataacctcgagcgactcctctcgggaggtg 1163

                                                                        
Query: 2089 gtgaaga---gcgatagagacgttcagagtcttggggggtcatctctggaaggatggtga 2145
            |||||||   |||||||||||||||||||||||| || ||||| ||||||||||||||||
Sbjct: 1162 gtgaagaggggcgatagagacgttcagagtcttgcggcgtcatttctggaaggatggtga 1103

                                                                        
Query: 2146 ggatgtcggggtccaggaaggaaggcggttcaaaccctgcccgcggagttgttggacgtg 2205
            |||||||||||||||||||||| || ||||| ||||||||||| || |||||||| ||||
Sbjct: 1102 ggatgtcggggtccaggaaggaggggggttcgaaccctgcccggggggttgttgggcgtg 1043

                      
Query: 2206 tagggatagg 2215
            ||||||||||
Sbjct: 1042 tagggatagg 1033



 Score =  143 bits (72), Expect = 1e-32
 Identities = 90/96 (93%)
 Strand = Plus / Minus

                                                                        
Query: 2279 tgagggagatgtaggacgagagtattgagagagacggccaggtgatgacgatgatggggg 2338
            |||||||||||||||||||||||||||||||||||| | ||| |||||| |||| |||||
Sbjct: 960  tgagggagatgtaggacgagagtattgagagagacgacaaggcgatgacaatgacggggg 901

                                                
Query: 2339 taaaggcgatggggtccttggcggatagacgggagc 2374
            |||||||||||||||||||||||| |||||||||||
Sbjct: 900  taaaggcgatggggtccttggcgggtagacgggagc 865



 Score =  121 bits (61), Expect = 5e-26
 Identities = 142/168 (84%), Gaps = 5/168 (2%)
 Strand = Plus / Minus

                                                                        
Query: 3164 ttcgtcatctgagcctgcttggcctgatgcactctccatatcctcgtcgtcctttgaagg 3223
            |||||| ||||||||||||||||||||||||||||||||||| ||||| ||||| | |||
Sbjct: 165  ttcgtcgtctgagcctgcttggcctgatgcactctccatatcgtcgtcatccttgggagg 106

                                                                        
Query: 3224 aagaggcggcggctgttccg-ccgtgttgcgaggggggttgattactctaggtgcaagag 3282
            |||||| || || | ||||  || |||||||||||||| |||| || ||| |||| || |
Sbjct: 105  aagaggtggaggtt-ttcccaccatgttgcgaggggggatgatcaccctaagtgccag-g 48

                                                            
Query: 3283 -tgggacgagaggtggtatgcggtaggtggtcgggatggagggcggat 3329
             |||| | ||||||||||| |||||| ||||| ||||| |||| ||||
Sbjct: 47   ctggggccagaggtggtat-cggtagatggtctggatgaagggaggat 1



 Score =  103 bits (52), Expect = 1e-20
 Identities = 70/76 (92%)
 Strand = Plus / Minus

                                                                        
Query: 3041 gtgcgaacgccgcgacgaggagcgaatggactgtgctctgctacaaggccgggaagacga 3100
            |||||| |||||||| |||||||||||||||||||||||||||||||||| ||| || ||
Sbjct: 273  gtgcgagcgccgcgatgaggagcgaatggactgtgctctgctacaaggcctggaggaaga 214

                            
Query: 3101 tttgggagtgcgtgag 3116
            ||||||||||| ||||
Sbjct: 213  tttgggagtgcatgag 198


>Contig634
          Length = 858

 Score =  486 bits (245), Expect = e-136
 Identities = 304/323 (94%), Gaps = 3/323 (0%)
 Strand = Plus / Minus

                                                                        
Query: 7620 tatatatatacgtaccagaaatacacatgcagtcaacaccggcgaaaaacttgtcctttt 7679
            ||||||| |||||||||||||| ||||||||||||||||||||||| |||||||||||||
Sbjct: 321  tatatat-tacgtaccagaaatgcacatgcagtcaacaccggcgaagaacttgtcctttt 263

                                                                        
Query: 7680 cagattcaataaacttgtccaggttgacagaaccattctcctccataccctcaaaacaga 7739
            ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||
Sbjct: 262  cagattcaataaacttgtcaaggttgacagaaccattctcctccataccctcaaaacaga 203

                                                                        
Query: 7740 ctttgaggttgacaggaagctcgataccaagcttcttgtgcgcctcgaggacgtttaacc 7799
            ||||||| |||||||||||||| |||||||||||||| ||||||||||| ||||| ||||
Sbjct: 202  ctttgagattgacaggaagctcaataccaagcttcttatgcgcctcgagaacgttcaacc 143

                                                                        
Query: 7800 agcccatgactggacccttgtcatcggttgagccacggccgtaaagtcggccactgccgt 7859
            |||||||||| |||||||||||||| ||||||||||||||||| ||||||||||||||||
Sbjct: 142  agcccatgacaggacccttgtcatccgttgagccacggccgtagagtcggccactgccgt 83

                                                                        
Query: 7860 tgggatcgggggtgagctcaaagggagggtagagccagccgtcttcgagtaga-gcgggt 7918
            ||||||| |||||||||||||| |||||||||||||||||||||||||| | | ||||||
Sbjct: 82   tgggatccggggtgagctcaaacggagggtagagccagccgtcttcgagca-atgcgggt 24

                                   
Query: 7919 tggacatcgtagtggccatagac 7941
            ||||| ||||||||||| |||||
Sbjct: 23   tggacgtcgtagtggccgtagac 1



 Score =  291 bits (147), Expect = 3e-77
 Identities = 162/167 (97%)
 Strand = Plus / Minus

                                                                        
Query: 7410 cttactgagagcgataagatccgtcatcggttcgtggacggtaccgccaaagacaccaga 7469
            |||||||||||||| ||| |||||||||||||||||||||||||||||||||||||||||
Sbjct: 540  cttactgagagcgacaaggtccgtcatcggttcgtggacggtaccgccaaagacaccaga 481

                                                                        
Query: 7470 gtgaagatccctgtcaggcccagaaatcttgatctcgtaatagttgatacctctgagacc 7529
            ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 480  gtggagatccctgtcaggcccagaaatcttgatctcgtaatagttgatacctctgagacc 421

                                                           
Query: 7530 ataagtgagacagggggtcttggtgtcaagccagtaattgtctatat 7576
            |||||||||||| ||||||||||||||||||||||| ||||||||||
Sbjct: 420  ataagtgagacacggggtcttggtgtcaagccagtagttgtctatat 374



 Score =  224 bits (113), Expect = 5e-57
 Identities = 183/206 (88%), Gaps = 2/206 (0%)
 Strand = Plus / Minus

                                                                        
Query: 7180 aaacccacagtcgtaacagtgtcgtcggagatggtgacctcaccaccaacagc-ggcatg 7238
            |||| ||||||| |||| || ||| | || |||||||| |||||||| |||||  |||||
Sbjct: 783  aaactcacagtcttaacggtatcgcccgatatggtgacttcaccaccgacagcatgcatg 724

                                                                        
Query: 7239 aatatcttccatctggaagtggatagcctcaaacttggctcgctcatcgtcggtgacagg 7298
            |||||||| ||||| ||| |||||||| ||||||||||||||||||||||||||||||||
Sbjct: 723  aatatcttgcatctcgaaatggatagcttcaaacttggctcgctcatcgtcggtgacagg 664

                                                                        
Query: 7299 cgcgatgaggtccttgataccggtaacgaggatctggccgtcgggagtgacaagcttgga 7358
             |||||||||||||||| |||| ||||||||||||||||||||||||| |||||| ||||
Sbjct: 663  ggcgatgaggtccttgacaccgctaacgaggatctggccgtcgggagtaacaagcctgga 604

                                      
Query: 7359 cactatatataacactcgtcagctct 7384
            ||||| ||| |||||| |||||||||
Sbjct: 603  cactagata-aacacttgtcagctct 579


>Contig1853
          Length = 2314

 Score =  339 bits (171), Expect = 1e-91
 Identities = 204/215 (94%)
 Strand = Plus / Plus

                                                                        
Query: 6406 aaatactcactcggatgtagttgtcagtgtcaatcttctcgttggtggaatgagctccgt 6465
            |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1691 aaatacgcactcggatgtagttgtcagtgtcaatcttctcgttggtggaatgagctccgt 1750

                                                                        
Query: 6466 catcaccccttccgacaggtaacaaaaggacgttgaggttgagaatgttggcaaagtcga 6525
            ||||||||||||||||||| ||||  ||||| ||||||||||||||||||||||||||||
Sbjct: 1751 catcaccccttccgacaggcaacaggaggacattgaggttgagaatgttggcaaagtcga 1810

                                                                        
Query: 6526 gggtgacagggatagaaccgccttcacgggtgtagtcgggcacttggccgtaaacagact 6585
            | ||||||||||| |||||||||||||||||||| || |||||||||||||||||||| |
Sbjct: 1811 gagtgacagggatggaaccgccttcacgggtgtaatcaggcacttggccgtaaacagatt 1870

                                               
Query: 6586 cggtagccttgtgcgccgctcgataagagtagtgc 6620
            ||||||||||||||||||| |||||||||||||||
Sbjct: 1871 cggtagccttgtgcgccgcacgataagagtagtgc 1905



 Score =  285 bits (144), Expect = 2e-75
 Identities = 243/274 (88%), Gaps = 11/274 (4%)
 Strand = Plus / Plus

                                                                        
Query: 6630 ggtcagtctttatcatccacttgcatt-gttgccaaccgtgctcacattggggtcagcct 6688
            ||||||||||||| || ||||||||||  || |||| | ||||||| |||||||||||||
Sbjct: 1933 ggtcagtctttat-at-cacttgcattattttccaatcatgctcacgttggggtcagcct 1990

                                                                        
Query: 6689 gaaag-aaaacgattgtcagcc---tctttacattcatcaa-cactcgccgggggcataa 6743
            ||||| ||||| ||||||||||   | |||||||||||||| || || || |||| |  |
Sbjct: 1991 gaaagcaaaaccattgtcagccttttttttacattcatcaacca-tc-cc-ggggaacca 2047

                                                                        
Query: 6744 ctcacaatccaaggctcaccaccgtgagtgagatacacctccatcttgttcttggaacca 6803
            |||||||||||||||||||| || ||||| ||||||||||||||||||||||||||||||
Sbjct: 2048 ctcacaatccaaggctcaccgccatgagtaagatacacctccatcttgttcttggaacca 2107

                                                                        
Query: 6804 agttttttgaattcttcctcaacgtacttgacgacgaggtcagtcacactggcaacagtg 6863
            ||||| ||||| ||||||||||||||||||||||| ||||| || || ||||| ||||||
Sbjct: 2108 agtttcttgaactcttcctcaacgtacttgacgacaaggtcggtgacgctggcgacagtg 2167

                                              
Query: 6864 aggttgggtacaagacggatagagaatttgccta 6897
            ||||||||||||||||||||||||||||||||||
Sbjct: 2168 aggttgggtacaagacggatagagaatttgccta 2201



 Score = 71.9 bits (36), Expect = 5e-11
 Identities = 36/36 (100%)
 Strand = Plus / Plus

                                                
Query: 6963 acccttgacacagcagggaatcacagtcttggaacc 6998
            ||||||||||||||||||||||||||||||||||||
Sbjct: 2277 acccttgacacagcagggaatcacagtcttggaacc 2312


  Database: cneoA.nt
    Posted date:  Dec 12, 2002  3:26 PM
  Number of letters in database: 17,206,226
  Number of sequences in database:  4935
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 0, Extension: 0
Number of Hits to DB: 9213
Number of Sequences: 4935
Number of extensions: 21
Number of successful extensions: 21
Number of sequences better than 1.0e-01: 4
length of query: 11337
length of database: 17,206,226
effective HSP length: 19
effective length of query: 11318
effective length of database: 17,112,461
effective search space: 193678833598
effective search space used:        0
S2: 21 (42.1 bits)
BioPerl-1.007002/t/data/5X_1895.FASTXY000444000766000024     22512313155576321 16657 0ustar00cjfieldsstaff000000000000 FASTXY compares a DNA sequence to a protein sequence data bank
 version 3.4t07 Nov 21, 2001
Please cite:
 Pearson et al, Genomics (1997) 46:24-36

 5X_1895.fa, 7972 aa
 vs /home/jason/genomes/S_cerevisea/pep/yeast_nrpep.fasta library

       opt      E()
< 20    53     0:====
  22     0     0:           one = represents 17 library sequences
  24     0     0:
  26     0     0:
  28     0     2:*
  30     4    13:*
  32    11    49:= *
  34    55   132:====   *
  36   202   270:============   *
  38   373   447:======================    *
  40   619   623:====================================*
  42   895   762:============================================*========
  44  1008   840:=================================================*==========
  46  1000   856:==================================================*========
  48   915   819:================================================*=====
  50   820   748:===========================================*=====
  52   694   657:======================================*==
  54   552   562:=================================*
  56   428   469:========================== *
  58   381   385:======================*
  60   279   312:================= *
  62   194   250:============  *
  64   163   199:========== *
  66   117   157:=======  *
  68    62   124:====   *
  70    50    97:===  *
  72    36    76:=== *
  74    26    59:== *
  76    17    46:= *
  78    26    36:==*
  80    18    28:=*
  82    11    21:=*
  84    25    17:*=
  86    19    13:*=
  88    11    10:*          inset = represents 1 library sequences
  90    11     8:*
  92     9     6:*         :=====*===
  94     9     5:*         :====*====
  96    13     4:*         :===*=========
  98     5     3:*         :==*==
 100     6     2:*         :=*====
 102    13     2:*         :=*===========
 104     5     1:*         :*====
 106     5     1:*         :*====
 108     4     1:*         :*===
 110     1     1:*         :*
 112     0     0:          *
 114     4     0:=         *====
 116     1     0:=         *=
 118     5     0:=         *=====
>120    32     0:==        *================================
4215311 residues in  9190 sequences
  Expectation_n fit: rho(ln(x))= 4.0381+/-0.00065; mu= 23.8752+/- 0.039
 mean_var=56.2146+/-11.145, 0's: 53 Z-trim: 75  B-trim: 416 in 2/58
 Lambda= 0.1711
 Kolmogorov-Smirnov  statistic: 0.0414 (N=29) at  52

FASTY (3.42 Sept 2001) function [optimized, BL50 matrix (15:-5)] ktup: 2
 join: 62, opt: 62, gap-pen: -14/ -2 shift: -20, subs: -20 width:  16
The best scores are:                                       opt bits E(9190)
NR_SC:SW-YNN2_YEAST SW:YNN2_YEAST P53914 sacch (1056) [f] 2172  547 1.6e-154
NR_SC:SW-MPCP_YEAST SW:MPCP_YEAST P23641 sacch ( 311) [r]  432  117 1.3e-25
NR_SC:SW-YEO3_YEAST SW:YEO3_YEAST P40035 sacch ( 300) [r]  154   48 5.7e-05
NR_SC:SW-RIM2_YEAST SW:RIM2_YEAST P38127 sacch ( 377) [r]  134   44   0.002
NR_SC:SW-Q05330 SW:Q05330 Q05330 saccharomyces ( 302) [f]  122   41   0.014
NR_SC:SW-AMYH_YEAST SW:AMYH_YEAST P08640 sacch (1367) [f]  128   43   0.014
NR_SC:SW-PET8_YEAST SW:PET8_YEAST P38921 sacch ( 284) [r]  121   40   0.016
NR_SC:SW-AGA1_YEAST SW:AGA1_YEAST P32323 sacch ( 725) [f]  124   41   0.018
NR_SC:SW-PMT_YEAST SW:PMT_YEAST P32332 sacchar ( 324) [r]  120   40    0.02
NR_SC:GP-CAA81388_1 gi|439289|emb|CAA81388.1 ( ( 751) [r]  115   39   0.085
NR_SC:SW-Q07229 SW:Q07229 Q07229 saccharomyces ( 817) [r]  115   39    0.09
NR_SC:SW-VRP1_YEAST SW:VRP1_YEAST P37370 sacch ( 817) [r]  115   39    0.09
NR_SC:SW-Q12215 SW:Q12215 Q12215 saccharomyces ( 556) [f]  112   38    0.12
NR_SC:SW-YH17_YEAST SW:YH17_YEAST P38898 sacch ( 153) [r]  106   36    0.13
NR_SC:GP-CAB58511_1 gi|6064291|emb|CAB58511.1  ( 894) [f]  113   39    0.13
NR_SC:SW-YN23_YEAST SW:YN23_YEAST P53832 sacch ( 503) [f]  110   38    0.15
NR_SC:SW-YHC8_YEAST SW:YHC8_YEAST P38739 sacch ( 605) [f]  110   38    0.17
NR_SC:SW-FLO1_YEAST SW:FLO1_YEAST P32768 sacch (1537) [f]  113   39     0.2
NR_SC:PIR-S53465 PIR:S53465 flocculation prote (1537) [f]  113   39     0.2
NR_SC:SW-Q06143 SW:Q06143 Q06143 saccharomyces ( 298) [r]  105   36    0.25
NR_SC:PIR-S58652 PIR:S58652 hypothetical prote ( 216) [r]  103   36    0.28
NR_SC:SW-YKT9_YEAST SW:YKT9_YEAST P36045 sacch ( 187) [f]  102   35     0.3
NR_SC:SW-YAG3_YEAST SW:YAG3_YEAST P39712 sacch (1322) [f]  109   38    0.35
NR_SC:PIR-S51959 PIR:S51959 hypothetical prote (1367) [f]  109   38    0.36
NR_SC:SW-Q12444 SW:Q12444 Q12444 saccharomyces ( 126) [f]   99   34    0.38
NR_SC:SW-TOA1_YEAST SW:TOA1_YEAST P32773 sacch ( 286) [r]  102   36     0.4
NR_SC:SW-SIM1_YEAST SW:SIM1_YEAST P40472 sacch ( 475) [f]  104   36    0.41
NR_SC:GP-CAA47602_1 gi|4824|emb|CAA47602.1 (X6 ( 307) [r]  102   36    0.42
NR_SC:SW-YMC1_YEAST SW:YMC1_YEAST P32331 sacch ( 307) [r]  102   36    0.42
NR_SC:SW-YG5F_YEAST SW:YG5F_YEAST P53320 sacch ( 366) [r]  102   36    0.48
NR_SC:SW-TIR3_YEAST SW:TIR3_YEAST P40552 sacch ( 269) [f]  100   35    0.54
NR_SC:SW-Q08428 SW:Q08428 Q08428 saccharomyces ( 113) [f]   96   34    0.59
NR_SC:SW-FLO5_YEAST SW:FLO5_YEAST P38894 sacch (1075) [f]  104   37    0.71
NR_SC:SW-YK82_YEAST SW:YK82_YEAST P36170 sacch (1169) [f]  104   37    0.76
NR_SC:SW-YOD0_YEAST SW:YOD0_YEAST Q08193 sacch ( 484) [f]  100   35    0.82
NR_SC:SW-CW14_YEAST SW:CW14_YEAST O13547 sacch ( 238) [f]   97   34    0.84
NR_SC:SW-TIR1_YEAST SW:TIR1_YEAST P10863 sacch ( 254) [r]   97   34    0.87
NR_SC:SW-Q08873 SW:Q08873 Q08873 saccharomyces ( 200) [f]   95   34       1
NR_SC:SW-TIR2_YEAST SW:TIR2_YEAST P33890 sacch ( 251) [f]   95   34     1.2
NR_SC:SW-CBF5_YEAST SW:CBF5_YEAST P33322 sacch ( 483) [f]   97   35     1.4
NR_SC:SW-KRE1_YEAST SW:KRE1_YEAST P17260 sacch ( 313) [f]   95   34     1.4
NR_SC:GP-CAA52447_1 gi|396560|emb|CAA52447.1 ( ( 250) [f]   94   34     1.4
NR_SC:GP-CAA81388_1 gi|439289|emb|CAA81388.1 ( ( 751) [f]   98   35     1.6
NR_SC:SW-VRP1_YEAST SW:VRP1_YEAST P37370 sacch ( 817) [f]   98   35     1.7
NR_SC:SW-Q07229 SW:Q07229 Q07229 saccharomyces ( 817) [f]   98   35     1.7
NR_SC:SW-Q12218 SW:Q12218 Q12218 saccharomyces ( 487) [f]   94   34     2.3
NR_SC:GP-AAA35091_1 gi|295671|gb|AAA35091.1 (L ( 406) [f]   92   33     2.8
NR_SC:SW-SR40_YEAST SW:SR40_YEAST P32583 sacch ( 406) [f]   92   33     2.8
NR_SC:SW-TIP1_YEAST SW:TIP1_YEAST P27654 sacch ( 210) [f]   89   32       3
NR_SC:SW-O94086 SW:O94086 O94086 saccharomyces ( 168) [f]   88   32     3.1
NR_SC:SW-YM8Z_YEAST SW:YM8Z_YEAST Q04951 sacch ( 389) [f]   91   33     3.3
NR_SC:SW-YGC8_YEAST SW:YGC8_YEAST P53189 sacch ( 542) [f]   92   33     3.5
NR_SC:SW-YG1F_YEAST SW:YG1F_YEAST P53214 sacch ( 551) [f]   92   33     3.5
NR_SC:GP-AAA35015_1 gi|172526|gb|AAA35015.1 (M ( 570) [f]   92   33     3.6
NR_SC:SW-HRB1_YEAST SW:HRB1_YEAST P38922 sacch ( 429) [f]   90   33     4.2
NR_SC:SW-MID2_YEAST SW:MID2_YEAST P36027 sacch ( 376) [f]   89   33     4.5
NR_SC:SW-Q08438 SW:Q08438 Q08438 saccharomyces ( 674) [r]   91   33     4.8
NR_SC:SW-CCC1_YEAST SW:CCC1_YEAST P47818 sacch ( 322) [f]   88   32     4.8


>>NR_SC:SW-YNN2_YEAST SW:YNN2_YEAST P53914 saccharomyces  (1056 aa)
 initn: 3325 init1: 1027 opt: 2172  Z-score: 2877.6  bits: 547.0 E(): 1.6e-154
Smith-Waterman score: 3401;  51.588% identity (58.124% ungapped) in 1165 aa overlap (2180-5623:3-1053)

    2180      2210      2240      2270      2300      2330         
5X_189 RKQLDPRIPALINNGVKANHRSFFVMVGDKGRDQVCPGMQAAMRFD*HRCR/LVNLHFLL
       .: .: :::.:: :::....::.::.:::..:.:                  : :::.:.
NR_SC: KKAIDSRIPSLIRNGVQTKQRSIFVIVGDRARNQ------------------LPNLHYLM
             10        20        30                          40    

     2360      2390       2420      2450      2480      2510       
5X_189 SQARVSSRPSVLWCYKKD-LGFTT*VAASENLQQTIYFRPIATSHRKKREAKIKRDVKRG
        .: ..   :::: :::  ::::                    ::::::: :::...:::
NR_SC: MSADLKMNKSVLWAYKKKLLGFT--------------------SHRKKRENKIKKEIKRG
           50        60                            70        80    

      2540      2570      2600      2630      2660      2690       
5X_189 IRDANEQDPFELFVTVTDIRYTYYKDSAKILGQTFGMLVLQDYEAITPNLLARTIETVEG
        :..::.:::: :..  .:::.:::.: ::::.:.:: .:::.::.::::::::::::::
NR_SC: TREVNEMDPFESFISNQNIRYVYYKESEKILGNTYGMCILQDFEALTPNLLARTIETVEG
           90       100       110       120       130       140    

      2720      2750       2780      2810      2840      2870      
5X_189 GGIVVLLLKTMSSLKQLYAMAM/DKL*CRDGVE*SDFS*LLI*DVHSRYRTDAHQFVQPR
       :::::.:::.::::::::.:.: :                    ::.::::.::  :  :
NR_SC: GGIVVILLKSMSSLKQLYTMTM-D--------------------VHARYRTEAHGDVVAR
          150       160                            170       180   

       2900      2930      2960      2990      3020      3050      
5X_189 FNERFILSLGSNPDCLVLDDELNVLPLSKGKDIQIGKAGEEDDRGRKRKAEELKEMKENL
       :::::::::::::.:::.:::::::::: .:...     :.:.   :.   ::.:.::.:
NR_SC: FNERFILSLGSNPNCLVVDDELNVLPLSGAKNVKPLPPKEDDELPPKQL--ELQELKESL
           190       200       210       220       230         240 

       3080      3110      3140      3170      3200      3230      
5X_189 EGVDIVGSLAKLAKTVDQAKAILTFVEAISEKNLSSTVALTAGRGRGKSAALGLAIGAAL
       : :. .:::..:.:::.::.:::.:..:::::.:. :::::::::::::::::..:.::.
NR_SC: EDVQPAGSLVSLSKTVNQAHAILSFIDAISEKTLNFTVALTAGRGRGKSAALGISIAAAV
             250       260       270       280       290       300 

       3260      3290      3320      3350      3380      3410      
5X_189 AHDYSNIFVTSPDPENLKTLFEFVFKALDALGYEEHIDYDVVQSTNPDFKKAIVRVNIFR
       .: :::::::::.::::::::::.::..:::::.::::::..:::::::.::::::.: :
NR_SC: SHGYSNIFVTSPSPENLKTLFEFIFKGFDALGYQEHIDYDIIQSTNPDFNKAIVRVDIKR
             310       320       330       340       350       360 

       3440      3470      3500      3530      3560      3590      
5X_189 GHRQTIQYISPEDSHVLGQAELVIIDEAAAIPLPLVRKLIGPYLVFMASTINGYEGTGRS
        :::::::: :.: .::::::::.::::::::::.:..:.::::::::::::::::::::
NR_SC: DHRQTIQYIVPQDHQVLGQAELVVIDEAAAIPLPIVKNLLGPYLVFMASTINGYEGTGRS
             370       380       390       400       410       420 

       3620      3650      3680      3710      3740      3770      
5X_189 LSIKLIQQLREQTRPSITKDSENAAASSAGSSSKAAAAGRSGAGLVRSLREIKLDEPIRY
       ::.:::::::.:.  :  .....:..:  .. . .   ..:     :.::::.:::::::
NR_SC: LSLKLIQQLRNQNNTSGRESTQTAVVSRDNKEKDSHLHSQS-----RQLREISLDEPIRY
             430       440       450       460            470      

       3800      3830         3860      3890      3920      3950   
5X_189 SPGDNVEKWLNNLLCLDATIVSK---SIQGCPHPSKCELYYVNRDTLFSYHPASEVFLQR
       .::: .:::::.:::::.:....   . .: ::::.:.:. :::::::::::.:: ::..
NR_SC: APGDPIEKWLNKLLCLDVTLIKNPRFATRGTPHPSQCNLFVVNRDTLFSYHPVSENFLEK
        480       490       500       510       520       530      

          3980      4010      4040      4070       4100      4130  
5X_189 MMALYVASHYKNSPNDLQMLSDAPAHHLFVLLPPIDEND-NTLPDPLVVLQVALEGNISR
       ::::::.:::::::::::..::::::.::::::::: .: . .:::: :.:.::::.::.
NR_SC: MMALYVSSHYKNSPNDLQLMSDAPAHKLFVLLPPIDPKDGGRIPDPLCVIQIALEGEISK
        540       550       560       570       580       590      

           4160      4190      4220      4250      4280      4310  
5X_189 EAILKEMAQSGMRSSGDMIPWIISTQFQDNDFATLSGARVVRIATHPDYARMGYGSRAME
       :.. . ... :.:..::.:::.:: ::::..::.:::::.:::::.:.:: :::::::.:
NR_SC: ESVRNSLSR-GQRAGGDLIPWLISQQFQDEEFASLSGARIVRIATNPEYASMGYGSRAIE
        600        610       620       630       640       650     

           4340      4370       4400      4430      4460      4490 
5X_189 ALESFYNGTSYNFDDVPVDMGESFAD\VPRSDL*VTSFIPFPQNRTSTECVSQNANLQND
        :.....:         .::.:   : :  .:  .        .:.: . .... :: .:
NR_SC: LLRDYFEGKF-------TDMSE---D-VRPKDYSI--------KRVSDKELAKT-NLLKD
         660              670                   680       690      

            4520      4550      4580      4610      4640      4670 
5X_189 TIAIRDPSRMPPLLQRLSERKPETLDYLGVSFGLTRDLLRFWKKGGFTPLYASQKENALT
        . .:: . .:::: .:::. :. : :::::.:::..: .:::...:.:.:  :  : ::
NR_SC: DVKLRDAKTLPPLLLKLSEQPPHYLHYLGVSYGLTQSLHKFWKNNSFVPVYLRQTANDLT
         700       710       720       730       740       750     

            4700      4730      4760      4790      4820      4850 
5X_189 GEYTFVMLKVLASAGGGGEWLGAFAQGMSCLLLQDEVHMGND*RL*TDFRQRFMNLLSYE
       ::.: :::.::   :  ..::  ::.                     :::.::..::::.
NR_SC: GEHTCVMLNVLE--GRESNWLVEFAK---------------------DFRKRFLSLLSYD
         760         770                            780       790  

            4880      4910          4940      4970      5000       
5X_189 AFKKFDASIALSILESTVPRNSPSPAP----KLLTNTELSSLLTPFDIKRLESYADSMLD
        :.:: :  :::..::.   .. :       : :: :.:.....:::.:::.::....::
NR_SC: -FHKFTAVQALSVIESSKKAQDLSDDEKHDNKELTRTHLDDIFSPFDLKRLDSYSNNLLD
             800       810       820       830       840       850 

      5030      5060      5090        5120      5150      5180     
5X_189 YHVVLDLVPTIASLFFGKRLETS--LPPAQQAILLALGLQRKNVEALENELGITSTQTLA
       :::. :..: .: :.:: ..  :  :  .:.:::::.::::::.... .::.. :.::.:
NR_SC: YHVIGDMIPMLALLYFGDKMGDSVKLSSVQSAILLAIGLQRKNIDTIAKELNLPSNQTIA
             860       870       880       890       900       910 

        5210      5240      5270           5300      5330      5360
5X_189 LFGKVLRKMTKSLEDIRKASIASELP-----AEPTLAGRSANGSNKFVALQQTIEQDLAD
       .:.:..:::.. .... . ::   ::     :   . :.  .. :   ::.: .:.:: .
NR_SC: MFAKIMRKMSQYFRQLLSQSIEETLPNIKDDAIAEMDGEEIKNYNAAEALDQ-MEEDLEE
             920       930       940       950       960        970

             5390      5420      5450       5480      5510         
5X_189 SAVQLNGEDDDASKKEQRELLNTLNMEEFAI-DQGGDWTEAEKQVERLASGKGGTRLSST
       ..    .:  .: ...:.::.:.::....:: :.. .:.:..:..:  :..:: . :.. 
NR_SC: AG----SEAVQAMREKQKELINSLNLDKYAINDNSEEWAESQKSLEIAAKAKGVVSLKTG
                  980       990      1000      1010      1020      

    5540       5570      5600       
5X_189 VSVKVDKLDD\AKRRRRRARMRVPRMRRR
        .  ..: .:   :.. .: :. ::  ..
NR_SC: KKRTTEKAED-IYRQEMKA-MKKPRKSKK
       1030       1040       1050   

>>NR_SC:SW-MPCP_YEAST SW:MPCP_YEAST P23641 saccharomyces  (311 aa)
rev-comp initn: 1094 init1: 429 opt: 432  Z-score: 563.4  bits: 117.1 E(): 1.3e-25
Smith-Waterman score: 964;  54.242% identity (66.543% ungapped) in 330 aa overlap (7938-6947:19-287)

      7930      7900      7870      7840      7810      7780       
5X_18- RFALAGALGCAVTHGALTPVDVVKTRIQLEPEVYNRVGRFFNSS*GF*EL*GVVLMSQT\
       .::::::.::. ::....:.::::::::::: :::                         
NR_SC: KFALAGAIGCGSTHSSMVPIDVVKTRIQLEPTVYN-------------------------
       20        30        40        50                            

       7750      7720      7690      7660      7630      7600      
5X_18- KGMVASFRQIIAKEGAGALLTGFGPTAVGYAIQGAFKFGG*VMMSLQITA*SRANLPISY
       ::::.::.:::: ::::::::::::: .::.:::::::::                   :
NR_SC: KGMVGSFKQIIAGEGAGALLTGFGPTLLGYSIQGAFKFGG-------------------Y
            60        70        80        90                       

       7570      7540      7510      7480      7450      7420      
5X_18- EFWKKKAIDLVGVDKARENRQAIYLGASAIAEFFADIALCPLEATRIRLVSQPSFANGLS
       : .::  :: .: : : . ....:.:..:.:::.:::::::::::::::::::.::::: 
NR_SC: EVFKKFFIDNLGYDTASRYKNSVYMGSAAMAEFLADIALCPLEATRIRLVSQPQFANGLV
          100       110       120       130       140       150    

       7390      7360      7330      7300       7270      7240     
5X_18- GGFLRILREEGPAAFYAGFGPILFKQVPYTMAKFAV*VDRTA*\YQTFG*YYRSYEVAVE
       ::: :::.::: ..::.:: ::::::.::..::: :    .   :  :.           
NR_SC: GGFSRILKEEGIGSFYSGFTPILFKQIPYNIAKFLVFERASEF-YYGFAG----------
          160       170       180       190        200             

        7210      7180      7150      7120      7090      7060     
5X_18- KILKATGKSKDSLTGGQLTGLNLTSGLIAGLAAAVISQPADTLLSKINKTKGAPGQSTTS
                :..:.. . : ::: ::: ::::::..::::::::::.:::: ::::::..
NR_SC: --------PKEKLSSTSTTLLNLLSGLTAGLAAAIVSQPADTLLSKVNKTKKAPGQSTVG
                   210       220       230       240       250     

        7030      7000      6970       
5X_18- RLVQMAGQLGVSGLFTGMTTRLVMIGTLTAGQ
        :.:.: :::  : :.:. :::::.::::. :
NR_SC: LLAQLAKQLGFFGSFAGLPTRLVMVGTLTSLQ
         260       270       280       

>>NR_SC:SW-YEO3_YEAST SW:YEO3_YEAST P40035 saccharomyces  (300 aa)
rev-comp initn: 412 init1: 136 opt: 154  Z-score: 192.8  bits: 48.5 E(): 5.7e-05
Smith-Waterman score: 469;  33.043% identity (41.455% ungapped) in 345 aa overlap (7943-6915:18-294)

            7920      7890      7860       7830      7800          
5X_18- YAD/CALAGALGCAVTHGALTPVDVVKTRIQLEPEVY\TGLVVFSTVPKDFENCKAWC*C
       ::  :.:.: ..:. ::...::.:.:: :.:..:..: :.                    
NR_SC: YAT-CTLGGIIACGPTHSSITPLDLVKCRLQVNPKLY-TS--------------------
        20         30        40        50                          

   7770      7740      7710      7680      7650      7620          
5X_18- HKQ*GMVASFRQIIAKEGAGALLTGFGPTAVGYAIQGAFKFGG*VMMSLQITA*SRANLP
             . .::.:::.::   . :::: : :::..::: :.::  ...            
NR_SC: -----NLQGFRKIIANEGWKKVYTGFGATFVGYSLQGAGKYGGYEYFKHL----------
               60        70        80        90       100          

   7590      7560      7530      7500      7470      7440          
5X_18- ISYEFWKKKAIDLVGVDKARENRQAIYLGASAIAEFFADIALCPLEATRIR-LVSQPSFA
         :  : . ..             ..:: ::: :::.::: :::.:: ...  ...: : 
NR_SC: --YSSWLSPGV-------------TVYLMASATAEFLADIMLCPFEAIKVKQQTTMPPFC
                             110       120       130       140     

    7410      7380       7350      7320      7290      7260        
5X_18- NGLSGGFLRILREEGP-AAFYAGFGPILFKQVPYTMAKFAV*VDRTA**SNIWLILS\SY
       :..  :. ..  : :   ::: :. :.  .:.:::: ::                 . :.
NR_SC: NNVVDGWKKMYAESGGMKAFYKGIVPLWCRQIPYTMCKF-----------------T-SF
         150       160       170       180                         

      7230      7200      7170      7140      7110      7080       
5X_18- EVAVEKILKATGKSKDSLTGGQLTGLNLTSGLIAGLAAAVISQPADTLLSKINKTKGAPG
       :  :.:: ..  :.:. ... :  ......: .::.  :..:.:::...::::. . : .
NR_SC: EKIVQKIYSVLPKKKEEMNALQQISVSFVGGYLAGILCAAVSHPADVMVSKINSERKA-N
       190       200       210       220       230       240       

      7050      7020      6990      6960       6930     
5X_18- QSTTSRLVQMAGQLGVSGLFTGMTTRLVMIGTLTAGQ/W*VSNAFDAGV
       .: .    ..  ..: .::..:. .:.:::::::. : : . ..: : :
NR_SC: ESMSVASKRIYQKIGFTGLWNGLMVRIVMIGTLTSFQ-WLIYDSFKAYV
        250       260       270       280        290    

>>NR_SC:SW-RIM2_YEAST SW:RIM2_YEAST P38127 saccharomyces  (377 aa)
rev-comp initn:  79 init1:  79 opt: 134  Z-score: 164.9  bits: 43.6 E(): 0.002
Smith-Waterman score: 145;  26.047% identity (30.769% ungapped) in 215 aa overlap (7929-7299:180-366)

   7930      7900      7870      7840      7810       7780         
5X_18- LAGALGCAVTHGALTPVDVVKTRIQLEPEVYNRVGRFFNSS*GF\WNCKAWC*CHKQ*GM
       .:.: .  .:  : .:. ..:::.::.    . : .. ::     :.:            
NR_SC: MAAATAGWATATATNPIWLIKTRVQLDKAGKTSVRQYKNS-----WDC------------
     180       190       200       210            220              

    7750      7720      7690      7660      7630      7600         
5X_18- VASFRQIIAKEGAGALLTGFGPTAVGYAIQGAFKFGG*VMMSLQITA*SRANLPISYEFW
          ....: .::  .:  :.. . .: ...: ...    .:.  :   :  ..  . :  
NR_SC: ---LKSVIRNEGFTGLYKGLSASYLG-SVEGILQWLLYEQMKRLIKERSIEKFGYQAEGT
               230       240        250       260       270        

    7570      7540      7510      7480      7450      7420         
5X_18- KKKAIDLVGVDKARENRQAIYLGASAIAEFFADIALCPLEATRIRLVSQPSFA-----NG
       :. .      .:..:  :    :....:.: :.::  : :..: :: . :.       .:
NR_SC: KSTS------EKVKEWCQ--RSGSAGLAKFVASIATYPHEVVRTRLRQTPKENGKRKYTG
      280             290         300       310       320       330

         7390      7360      7330          
5X_18- LSGGFLRILREEGPAAFYAGFGPILFKQVPYTMAKF
       :  .:  :..:::  ..:.:. : :.. :: ..  :
NR_SC: LVQSFKVIIKEEGLFSMYSGLTPHLMRTVPNSIIMF
              340       350       360      

>>NR_SC:SW-Q05330 SW:Q05330 Q05330 saccharomyces cerevis  (302 aa)
 initn:  76 init1:  76 opt: 122  Z-score: 150.1  bits: 40.6 E(): 0.014
Smith-Waterman score: 123;  24.713% identity (28.667% ungapped) in 174 aa overlap (896-1372:55-219)

             920       950       980      1010      1040      1070 
5X_189 RTHRKRYQRHFHPHHRRHHL*THHRSHLDRNR*RRPLAANLQRLVPVCDRPQPIPNNH*C
       :::..... : : :. :.:   :::.:: ..: ..      ::   . .: . : . :  
NR_SC: RTHQHHHRTHQHHHRTRQH---HHRTHLHHHRIHQRHHHIRQRHHHIRQRRHRILQRHHR
           60        70           80        90       100       110 

            1100      1130                    1160       1190      
5X_189 QRHEKSKEGRRNENTPLRLL--------------TA*PRQGPSSL*FHPVVV-HSALVPH
        :...     : . : ::::              ..  :.  ..  ..:.   :...: :
NR_SC: IRQRRLPTLPRRQATALRLLLILLHLHHTLLRHQVTAQRHQVTAQRLQPIPQHHQVIVLH
             120       130       140       150       160       170 

       1220      1250      1280      1310      1340      1370
5X_189 R*QTHLCPARLLQEHQAWQHSSLGLAPAEGMGTYRPIGNLKDQRGVKKLRALIQ
       : .:      : ..:   ::  : : : . ..  . .   . :  .. :  ..:
NR_SC: RLHT------LQHHHPIPQHHLLTLPPLQTIALLHLLTPQHLQATAQDLLHILQ
                   180       190       200       210         

>>NR_SC:SW-AMYH_YEAST SW:AMYH_YEAST P08640 saccharomyces  (1367 aa)
 initn: 142 init1:  95 opt: 128  Z-score: 150.0  bits: 42.7 E(): 0.014
Smith-Waterman score: 152;  26.792% identity (28.629% ungapped) in 265 aa overlap (3295-4068:302-556)

         3310      3340      3370      3400      3430      3460    
5X_189 TSKLCLNLSSKPLMPWVTRSTLIMMSCKAQTPTSKRLL*GSTSSEVTDKPSNTSPPKILT
       ::: :   ..:   :  : :.    : .: .:: .   . :.:. ::.. ...:   . :
NR_SC: TSKTC---TKKTTTPVPTPSSSTTESSSAPVPTPSSSTTESSSAPVTSSTTESSSAPVPT
                310       320       330       340       350        

         3490      3520      3550      3580      3610      3640    
5X_189 FSAKLSLSSLMKLPPSLFPLFVNSSAPISCLWPPPSTVTRVLAVHCPSSSFSNSVNR/PR
        :.. . ::   .  :      .::::..      .: .    :  :::: ..: .  : 
NR_SC: PSSSTTESSSAPVTSSTTE---SSSAPVTS----STTESSSAPVPTPSSSTTESSSA-PV
      360       370          380           390       400        410

          3670      3700       3730      3760      3790      3820  
5X_189 PSITKDSENAAASSAGSSSKAAA\VVDRALVSCDLFVRSSLMSLSVTPPETMLKSG*TTS
        : : .: .: ..:. . :..:  :.. .  : .  : ::    : .:  :  .: . .:
NR_SC: TSSTTESSSAPVTSSTTESSSAP-VTSSTTESSSAPVTSSTTESSSAPVPTPSSSTTESS
              420       430        440       450       460         

           3850      3880            3910      3940      3970      
5X_189 SASMPPSSPNLSKVALTLPNASFT------MSTATLSSLITPLQKCSCKG*WRSTS-LPT
       :: .  :. . :.. .  :..: :      ....:  :  .:.   : . .  :..  ::
NR_SC: SAPVTSSTTESSSAPVPTPSSSTTESSSAPVTSSTTESSSAPVPTPSSSTTESSSAPAPT
     470       480       490       500       510       520         

        4000      4030      4060  
5X_189 TRTLLTTCRCFPMLPLIIFSFSSPLST
         .  :     :.      : :.:. :
NR_SC: PSSSTTESSSAPVTSSTTESSSAPVPT
     530       540       550      

>>NR_SC:SW-PET8_YEAST SW:PET8_YEAST P38921 saccharomyces  (284 aa)
rev-comp initn:  91 init1:  91 opt: 121  Z-score: 149.1  bits: 40.3 E(): 0.016
Smith-Waterman score: 121;  34.146% identity (35.897% ungapped) in 82 aa overlap (7583-7338:172-249)

           7560      7530      7500      7470      7440      7410  
5X_18- YEFWKKKAIDLVGVDKARENRQAIYLGASAIAEFFADIALCPLEATRIRLVSQPSFANGL
       ::. ::      : ....  . ::    ..::  .:  .  ::.  . ::. . . :. :
NR_SC: YEYLKKTWAKANGQSQVEPWKGAI---CGSIAGGIAAATTTPLDFLKTRLMLNKTTAS-L
             180       190          200       210       220        

           7380      7350    
5X_18- SGGFLRILREEGPAAFYAGFGP
       .. ..:: ::::::.:..: ::
NR_SC: GSVIIRIYREEGPAVFFSGVGP
       230       240         

>>NR_SC:SW-AGA1_YEAST SW:AGA1_YEAST P32323 saccharomyces  (725 aa)
 initn: 156 init1:  88 opt: 124  Z-score: 148.1  bits: 41.4 E(): 0.018
Smith-Waterman score: 144;  23.699% identity (26.032% ungapped) in 346 aa overlap (3286-4232:176-520)

            3310      3340      3370      3400      3430      3460 
5X_189 TPKTSKLCLNLSSKPLMPWVTRSTLIMMSCKAQTPTSKRLL*GSTSSEVTDKPSNTSPPK
       : ...    .:::    :  : ..    : .... ...   ....:: .. .::.::  .
NR_SC: TTSSNPTTTSLSSTSTSPSSTSTSPSSTSTSSSSTSTSSSSTSTSSSSTSTSPSSTSTSS
         180       190       200       210       220       230     

            3490      3520      3550      3580      3610       3640
5X_189 ILTFSAKLSLSSLMKLPPSLFPLFVNSSAPISCLWPPPSTVTRVLAVHCPSSSFSN/YRE
        :: ... : :. ..   .      .: .  :      ::     ..   :.: :. :  
NR_SC: SLTSTSSSSTSTSQSSTSTSSSSTSTSPSSTSTSSSSTSTSPSSKSTSASSTSTSS-YST
         240       250       260       270       280       290     

             3670      3700      3730       3760      3790         
5X_189 QTRPSITKDSENAAASSAGSSSKAAAAGRSGAGL\GDLFVRSSLMSLSVTPPETMLKSG*
       .: ::.:..: . :..: .:.: ...   : ..: :. .. ::  :.:.  : : . :  
NR_SC: STSPSLTSSSPTLASTSPSSTSISSTFTDSTSSL-GSSIASSST-SVSLYSPSTPVYSVP
          300       310       320        330        340       350  

    3820                     3850      3880      3910       3940   
5X_189 TTSSASMPP---------------SSPNLSKVALTLPNASFTMSTA-TLSSLITPLQKCS
       .:::    :               ::  ..: ...    ::.:::  :  : .: .    
NR_SC: STSSNVATPSMTSSTVETTVSSQSSSEYITKSSISTTIPSFSMSTYFTTVSGVTTMYTTW
            360       370       380       390       400       410  

          3970               4000      4030      4060         4090 
5X_189 CKG*WRS---------TSLPTTRTLLTTCRCFPMLPLIIFSFSSPLSTRMIIPSL---TL
       :    .:          .. :  :. :   :.:     ... :  .::. .  :.   :.
NR_SC: CPYSSESETSTLTSMHETVTTDATVCTHESCMPSQTTSLITSSIKMSTKNVATSVSTSTV
            420       430       440       450       460       470  

               4120      4150      4180      4210       
5X_189 LSSFK/CAL--EGNISREAILKEMAQSGMRSSGDMIPWIISTQFQDNDF
        ::.  :.   : . :  ..    ..:  ... .   :. :   .:.::
NR_SC: ESSYA-CSTCAETSHSYSSVQTASSSSVTQQTTSTKSWVSSMTTSDEDF
             480       490       500       510       520

>>NR_SC:SW-PMT_YEAST SW:PMT_YEAST P32332 saccharomyces c  (324 aa)
rev-comp initn:  86 init1:  86 opt: 120  Z-score: 147.1  bits: 40.1 E(): 0.02
Smith-Waterman score: 120;  29.630% identity (29.630% ungapped) in 81 aa overlap (7162-6920:231-311)

    7160      7130      7100      7070      7040      7010         
5X_18- LNLTSGLIAGLAAAVISQPADTLLSKINKTKGAPGQSTTSRLVQMAGQLGVSGLFTGMTT
       :.::.. :.::..::. .: :..:..: . ::   ..  . ::. .   ::..:. :...
NR_SC: LHLTASTISGLGVAVVMNPWDVILTRIYNQKGDLYKGPIDCLVKTVRIEGVTALYKGFAA
              240       250       260       270       280       290

    6980      6950          
5X_18- RLVMIGTLTAGQCKFQMRLMQ
       ..  :.  :     :. . :.
NR_SC: QVFRIAPHTIMCLTFMEQTMK
              300       310 

>>NR_SC:GP-CAA81388_1 gi|439289|emb|CAA81388.1 (Z26645)   (751 aa)
rev-comp initn:  83 init1:  83 opt: 115  Z-score: 135.9  bits: 39.2 E(): 0.085
Smith-Waterman score: 139;  26.996% identity (29.218% ungapped) in 263 aa overlap (7747-6985:222-472)

         7730      7700      7670      7640      7610              
5X_18- PLSDKSLPRRVPVLFSLVSAPPPSVTPSRVPSSSVGK**CLFK*PPRAALTCQ----LVT
       :: . ::: .:    .  .::::  ::.   .:.  : .     :: . .       :. 
NR_SC: PLPSASLPTHVS---NPPQAPPPPPTPTIGLDSKNIKPTDNAVSPPSSEVPAGGLPFLAE
             230          240       250       260       270        

   7580        7550      7520      7490      7460       7430       
5X_18- SFGRR--RPLTSLVSTRPVRTDRPSTLVPLPSPSSSPTLLSVPLRPLESGLS/PQPS\LP
         .::  :  .  ::.  ..:.  ..    : :::.: . .    ::      : :: ::
NR_SC: INARRSERGAVEGVSSTKIQTENHKSPSQRPLPSSAPPIPTSHAPPLPPTAP-PPPS-LP
      280       290       300       310       320       330        

       7400      7370      7340      7310      7280        7250    
5X_18- TVFPVVSLGF*GRKVPLPSTPVSALSSSSRFLIPWPSSPCKSTVL/P**SNIW/PNTIAA
       .:  . . .  . . : :  :..  :.:.  .   :  :  .  : : ....  ::  ..
NR_SC: NVTSAPKKATSAPRPPPPPLPAAMSSASTNSVKATPVPPTLAPPL-PNTTSVP-PNKASS
        340       350       360       370       380         390    

         7220      7190      7160      7130      7100      7070    
5X_18- TRSPSRRSSRPLASPRTLLLVDSSLVLTLLPVLSPVWPPPLSLNPPTPSCLRSTRPRAPP
         .:      :   :   . ..:.:  . .: :.:. :::    ::. .    . :  ::
NR_SC: MPAPPP----PPPPPPGAFSTSSALSASSIP-LAPLPPPP----PPSVATSVPSAPPPPP
          400           410       420            430       440     

           7040      7010         
5X_18- --ASLPPLGSSRWLVSSVFPVSSPV*P
         ..  : .::.    :    :: :.:
NR_SC: TLTTNKPSASSKQSKISSSSSSSAVTP
         450       460       470  

>>NR_SC:SW-Q07229 SW:Q07229 Q07229 saccharomyces cerevis  (817 aa)
rev-comp initn:  83 init1:  83 opt: 115  Z-score: 135.4  bits: 39.3 E(): 0.09
Smith-Waterman score: 134;  26.996% identity (29.218% ungapped) in 263 aa overlap (7747-6985:222-472)

         7730      7700      7670      7640      7610              
5X_18- PLSDKSLPRRVPVLFSLVSAPPPSVTPSRVPSSSVGK**CLFK*PPRAALTCQ----LVT
       :: . ::: .:    .  .::::  ::.   .:.  : .     :: . .       :. 
NR_SC: PLPSASLPTHVS---NPPQAPPPPPTPTIGLDSKNIKPTDNAVSPPSSEVPAGGLPFLAE
             230          240       250       260       270        

   7580        7550      7520      7490      7460       7430       
5X_18- SFGRR--RPLTSLVSTRPVRTDRPSTLVPLPSPSSSPTLLSVPLRPLESGLS/PQPS\LP
         .::  :  .  ::.  ..:.  ..    : :::.: . .    ::      : :: ::
NR_SC: INARRSERGAVEGVSSTKIQTENHKSPSQPPLPSSAPPIPTSHAPPLPPTAP-PPPS-LP
      280       290       300       310       320       330        

       7400      7370      7340      7310      7280        7250    
5X_18- TVFPVVSLGF*GRKVPLPSTPVSALSSSSRFLIPWPSSPCKSTVL/P**SNIW/PNTIAA
       .:  . . .  .   : :  :..  :.:.  .   :  :  .  : : ....  ::  ..
NR_SC: NVTSAPKKATSAPAPPPPPLPAAMSSASTNSVKATPVPPTLAPPL-PNTTSVP-PNKASS
        340       350       360       370       380         390    

         7220      7190      7160      7130      7100      7070    
5X_18- TRSPSRRSSRPLASPRTLLLVDSSLVLTLLPVLSPVWPPPLSLNPPTPSCLRSTRPRAPP
         .:      :   :   . ..:.:  . .: :.:. :::    ::. .    . :  ::
NR_SC: MPAPPP----PPPPPPGAFSTSSALSASSIP-LAPLPPPP----PPSVATSVPSAPPPPP
          400           410       420            430       440     

           7040      7010         
5X_18- --ASLPPLGSSRWLVSSVFPVSSPV*P
         ..  : .::.    :    :: :.:
NR_SC: TLTTNKPSASSKQSKISSSSSSSAVTP
         450       460       470  

>>NR_SC:SW-VRP1_YEAST SW:VRP1_YEAST P37370 saccharomyces  (817 aa)
rev-comp initn:  83 init1:  83 opt: 115  Z-score: 135.4  bits: 39.3 E(): 0.09
Smith-Waterman score: 134;  26.996% identity (29.218% ungapped) in 263 aa overlap (7747-6985:222-472)

         7730      7700      7670      7640      7610              
5X_18- PLSDKSLPRRVPVLFSLVSAPPPSVTPSRVPSSSVGK**CLFK*PPRAALTCQ----LVT
       :: . ::: .:    .  .::::  ::.   .:.  : .     :: . .       :. 
NR_SC: PLPSASLPTHVS---NPPQAPPPPPTPTIGLDSKNIKPTDNAVSPPSSEVPAGGLPFLAE
             230          240       250       260       270        

   7580        7550      7520      7490      7460       7430       
5X_18- SFGRR--RPLTSLVSTRPVRTDRPSTLVPLPSPSSSPTLLSVPLRPLESGLS/PQPS\LP
         .::  :  .  ::.  ..:.  ..    : :::.: . .    ::      : :: ::
NR_SC: INARRSERGAVEGVSSTKIQTENHKSPSQPPLPSSAPPIPTSHAPPLPPTAP-PPPS-LP
      280       290       300       310       320       330        

       7400      7370      7340      7310      7280        7250    
5X_18- TVFPVVSLGF*GRKVPLPSTPVSALSSSSRFLIPWPSSPCKSTVL/P**SNIW/PNTIAA
       .:  . . .  .   : :  :..  :.:.  .   :  :  .  : : ....  ::  ..
NR_SC: NVTSAPKKATSAPAPPPPPLPAAMSSASTNSVKATPVPPTLAPPL-PNTTSVP-PNKASS
        340       350       360       370       380         390    

         7220      7190      7160      7130      7100      7070    
5X_18- TRSPSRRSSRPLASPRTLLLVDSSLVLTLLPVLSPVWPPPLSLNPPTPSCLRSTRPRAPP
         .:      :   :   . ..:.:  . .: :.:. :::    ::. .    . :  ::
NR_SC: MPAPPP----PPPPPPGAFSTSSALSASSIP-LAPLPPPP----PPSVATSVPSAPPPPP
          400           410       420            430       440     

           7040      7010         
5X_18- --ASLPPLGSSRWLVSSVFPVSSPV*P
         ..  : .::.    :    :: :.:
NR_SC: TLTTNKPSASSKQSKISSSSSSSAVTP
         450       460       470  

>>NR_SC:SW-Q12215 SW:Q12215 Q12215 saccharomyces cerevis  (556 aa)
 initn:  89 init1:  89 opt: 112  Z-score: 133.5  bits: 38.4 E(): 0.12
Smith-Waterman score: 115;  27.381% identity (29.677% ungapped) in 168 aa overlap (789-1284:154-311)

            810       840       870        900       930       960 
5X_189 PSSTCSLLFGPISTKTRDQHM*LATEGNDETAT\TLSYTQKTISTSFSSSPPSTSPLNSS
       ::.: ::  . ::. ::     . .  ..  :: :.: :. : :.. :..  .::  .::
NR_SC: PSTTSSLSSAQISSTTRRTSTDMKS--SEMIAT-TVSTTSTTSSSTSSTTSSTTSSTTSS
           160       170         180        190       200       210

             990      1020      1050      1080      1110      1140 
5X_189 SESSRSESITSSPGSKPAAFGSGL*PSSAYTE*SLMSAS*KEQRGPQK*EHTAPPLNRIT
       . :: . : :::  :. ..  .. . ::. . ..  ..:        ..  ..  .  .:
NR_SC: TTSSTTSSSTSSTTSSTTSSTTSSTTSSTTSSTTSSTTS--------STTSSTTSIFSVT
              220       230       240               250       260  

            1170      1200      1230         1260       
5X_189 SSGSIFTLVSPCCCPLGTCTPPLTNPFVP---SAPTPGAPGMAALEPWT
       ::.: .:: :     . . :   .. .::   :. : ..: .... : :
NR_SC: SSSSSITLSSSEHTTVDSRTSSPSSTLVPVSSSSSTLSTPKVTSMTPST
            270       280       290       300       310 

>>NR_SC:SW-YH17_YEAST SW:YH17_YEAST P38898 saccharomyces  (153 aa)
rev-comp initn:  71 init1:  71 opt: 106  Z-score: 132.4  bits: 36.3 E(): 0.13
Smith-Waterman score: 106;  26.897% identity (28.889% ungapped) in 145 aa overlap (5788-5367:6-144)

      5780      5750      5720      5690      5660      5630       
5X_18- CIPFRTMQESYILLNQI*VKE*EP*SQI*I*NQKHPLTPSLPSSFHPSPLHSLSSSSSHP
       :.   .:: : :    : . . .:  .    .. :: ::.     ::   :  .. .  :
NR_SC: CLTPSSMQYSDIY---IHTPHPHPHPHPHTPTHTHPHTPTPTPHPHPHTPHPHTTPTPTP
          10           20        30        40        50        60  

         5600      5570       5540      5510      5480      5450   
5X_18- WH---PHPCPSPPSLCH/PSSLSTFTLTVLDSLAPPLPDASLSTCFSASVQSPP*SIANS
        :   ::   :  ::   ::   :  :..:   . :::    .  .:.    ::  :. .
NR_SC: HHTHTPHTTLSNLSLNL-PSHYPTSPLVTLPHSTIPLPT---TIHLSTYYYHPPPIITVT
             70         80        90       100          110        

          5420       5390        
5X_18- SMLRVFNSSLCS-FFDASSSSPFSCT
        .: . ::.  . ..      :  ::
NR_SC: LQLPISNSTTITLLLPYHPPCPTHCT
      120       130       140    

>>NR_SC:GP-CAB58511_1 gi|6064291|emb|CAB58511.1 (A74265)  (894 aa)
 initn:  70 init1:  70 opt: 113  Z-score: 132.3  bits: 38.8 E(): 0.13
Smith-Waterman score: 113;  27.820% identity (28.244% ungapped) in 133 aa overlap (892-1290:514-644)

           910       940       970      1000      1030      1060   
5X_189 LSYTQKTISTSFSSSPPSTSPLNSSSESSRSESITSSPGSKPAAFGSGL*PSSAYTE*SL
       .: .  : .. :: :  :.   .::: :. ::: ::: ::  ..   .   :.. :  : 
NR_SC: ISSSTTTSTSIFSESSKSSVIPTSSSTSGSSESETSSAGSVSSSSFISSESSKSPTYSSS
           520       530       540       550       560       570   

          1090      1120      1150      1180      1210      1240   
5X_189 MSAS*KEQRGPQK*EHTAPPLNRITSSGSIFTLVSPCCCPLGTCTPPLTNPFVPSAPTPG
                  :..  . :: .   .: .  :::.   :   .::  .. : . :. :  
NR_SC: SLPLVTSATTSQETASSLPPATTTKTSEQT-TLVTVTSCESHVCTESIS-PAIVSTATVT
           580       590       600        610       620        630 

          1270      
5X_189 APGMAALEPWTCP
       . :...     ::
NR_SC: VSGVTTEYTTWCP
             640    

>>NR_SC:SW-YN23_YEAST SW:YN23_YEAST P53832 saccharomyces  (503 aa)
 initn: 117 init1:  72 opt: 110  Z-score: 131.4  bits: 37.8 E(): 0.15
Smith-Waterman score: 110;  29.752% identity (30.252% ungapped) in 121 aa overlap (895-1256:165-283)

          910       940       970      1000      1030      1060    
5X_189 SYTQKTISTSFSSSPPSTSPLNSSSESSRSESITSSPGSKPAAFGSGL*PSSAYTE*SLM
       : ...: ::. :::  .::  .::: :: : . :.:  :. .. .:.  ::.. . .:  
NR_SC: SSSSSTTSTTTSSSETTTSSSSSSSSSSTSTTSTTSTTSSTTSTSSS--PSTTSSSTSAS
          170       180       190       200       210         220  

          1090      1120      1150      1180      1210      1240   
5X_189 SAS*/TRAKRAAEMRTHRSAS*PHNLVRVHLHSSFTLLLSTRHLYPTVDKPICAQRAYSR
       :.:  : . .:.   :  ..:   . . .   :: ..  ::..   .: . . .:   . 
NR_SC: SSSE-TSSTQATSSSTTSTSSSTSTATVTSTPSSTSIGTSTHYTTRVVTQSVVSQANQQA
             230       240       250       260       270       280 

         
5X_189 ST
       ::
NR_SC: ST
         

>>NR_SC:SW-YHC8_YEAST SW:YHC8_YEAST P38739 saccharomyces  (605 aa)
 initn:  90 init1:  90 opt: 110  Z-score: 130.4  bits: 37.9 E(): 0.17
Smith-Waterman score: 110;  29.545% identity (29.545% ungapped) in 88 aa overlap (4832-5095:216-303)

          4850      4880      4910      4940      4970      5000   
5X_189 S*TFSHMRHSKSLTLLSLSPSSNLPSLATLPPPHPNFSPTPSSLRSSLRLTSNVLNRTPT
       . . :    . : ::.: : ::.  :  :     :  . : ::  .:   :: . . .::
NR_SC: TSSTSTTTSTTSSTLISTSTSSSSSSTPTTTSSAPISTSTTSSTSTSTSTTSPTSSSAPT
         220       230       240       250       260       270     

          5030      5060      5090 
5X_189 ACSTITSSSTLFLPSLPYSSARGLKPAY
       . :. : .:: :  . : ..  .   .:
NR_SC: SSSNTTPTSTTFTTTSPSTAPSSTTVTY
         280       290       300   

>>NR_SC:SW-FLO1_YEAST SW:FLO1_YEAST P32768 saccharomyces  (1537 aa)
 initn:  70 init1:  70 opt: 113  Z-score: 129.4  bits: 39.1 E():  0.2
Smith-Waterman score: 113;  27.820% identity (28.244% ungapped) in 133 aa overlap (892-1290:1144-1274)

           910       940       970      1000      1030      1060   
5X_189 LSYTQKTISTSFSSSPPSTSPLNSSSESSRSESITSSPGSKPAAFGSGL*PSSAYTE*SL
       .: .  : .. :: :  :.   .::: :. ::: ::: ::  ..   .   :.. :  : 
NR_SC: ISSSTTTSTSIFSESSKSSVIPTSSSTSGSSESETSSAGSVSSSSFISSESSKSPTYSSS
          1150      1160      1170      1180      1190      1200   

          1090      1120      1150      1180      1210      1240   
5X_189 MSAS*KEQRGPQK*EHTAPPLNRITSSGSIFTLVSPCCCPLGTCTPPLTNPFVPSAPTPG
                  :..  . :: .   .: .  :::.   :   .::  .. : . :. :  
NR_SC: SLPLVTSATTSQETASSLPPATTTKTSEQT-TLVTVTSCESHVCTESIS-PAIVSTATVT
          1210      1220      1230       1240      1250       1260 

          1270      
5X_189 APGMAALEPWTCP
       . :...     ::
NR_SC: VSGVTTEYTTWCP
            1270    

>>NR_SC:PIR-S53465 PIR:S53465 flocculation protein FLO1   (1537 aa)
 initn:  70 init1:  70 opt: 113  Z-score: 129.4  bits: 39.1 E():  0.2
Smith-Waterman score: 113;  27.820% identity (28.244% ungapped) in 133 aa overlap (892-1290:1144-1274)

           910       940       970      1000      1030      1060   
5X_189 LSYTQKTISTSFSSSPPSTSPLNSSSESSRSESITSSPGSKPAAFGSGL*PSSAYTE*SL
       .: .  : .. :: :  :.   .::: :. ::: ::: ::  ..   .   :.. :  : 
NR_SC: ISSSTTTSTSIFSESSKSSVIPTSSSTSGSSESETSSAGSVSSSSFISSESSKSPTYSSS
          1150      1160      1170      1180      1190      1200   

          1090      1120      1150      1180      1210      1240   
5X_189 MSAS*KEQRGPQK*EHTAPPLNRITSSGSIFTLVSPCCCPLGTCTPPLTNPFVPSAPTPG
                  :..  . :: .   .: .  :::.   :   .::  .. : . :. :  
NR_SC: SLPLVTSATTSQETASSLPPATTTKTSEQT-TLVTVTSCESHVCTESIS-PAIVSTATVT
          1210      1220      1230       1240      1250       1260 

          1270      
5X_189 APGMAALEPWTCP
       . :...     ::
NR_SC: VSGVTTEYTTWCP
            1270    

>>NR_SC:SW-Q06143 SW:Q06143 Q06143 saccharomyces cerevis  (298 aa)
rev-comp initn: 153 init1: 102 opt: 105  Z-score: 127.5  bits: 36.4 E(): 0.25
Smith-Waterman score: 105;  30.986% identity (30.986% ungapped) in 71 aa overlap (7509-7299:16-86)

   7510        7480      7450      7420      7390      7360        
5X_18- PW/W/HSAIAEFFADIALCPLEATRIRLVSQPSFANGLSGGFLRILREEGPAAFYAGFGP
       :: : ... : .:: ..  ::. ...:: . :     :   .  :: .:: ...:.:.. 
NR_SC: PW-W-YGGAAGIFATMVTHPLDLAKVRLQAAPMPKPTLFRMLESILANEGVVGLYSGLSA
            20        30        40        50        60        70   

     7330      7300 
5X_18- ILFKQVPYTMAKF
        ...:  :: ..:
NR_SC: AVLRQCTYTTVRF
            80      

>>NR_SC:PIR-S58652 PIR:S58652 hypothetical protein YFR03  (216 aa)
rev-comp initn:  77 init1:  77 opt: 103  Z-score: 126.6  bits: 35.7 E(): 0.28
Smith-Waterman score: 103;  44.444% identity (44.444% ungapped) in 36 aa overlap (5677-5570:44-79)

         5660      5630      5600          
5X_18- TPSLPSSFHPSPLHSLSSSSSHPWHPHPCPSPPSLC
       .::::. : : :.  : ::::  :       : : :
NR_SC: SPSLPTRFTPCPVAVLPSSSSPSWSFSTSCMPESTC
            50        60        70         

>>NR_SC:SW-YKT9_YEAST SW:YKT9_YEAST P36045 saccharomyces  (187 aa)
 initn:  81 init1:  81 opt: 102  Z-score: 126.0  bits: 35.4 E():  0.3
Smith-Waterman score: 102;  28.235% identity (28.571% ungapped) in 85 aa overlap (4862-5116:96-179)

          4880      4910      4940      4970      5000      5030   
5X_189 KSLTLLSLSPSSNLPSLATLPPPHPNFSPTPSSLRSSLRLTSNVLNRTPTACSTITSSST
       .:.. ..  :: .   ::. ::: :  . .:.    .:: :      : :      .. .
NR_SC: RSMVDIAAHPSPTATVLASSPPPPPPATHVPAEALFTLRETPPPQLATLTLSEEPPATPA
         100       110       120       130       140       150     

          5060      5090        
5X_189 LFLPSLPYSSARGLKPAYRLPSRPS
          :: : . .:: .: .:. . ::
NR_SC: PSAPSAPSARVRGHSP-HRVGASPS
         160       170          

>>NR_SC:SW-YAG3_YEAST SW:YAG3_YEAST P39712 saccharomyces  (1322 aa)
 initn:  71 init1:  71 opt: 109  Z-score: 124.8  bits: 38.0 E(): 0.35
Smith-Waterman score: 117;  27.612% identity (28.906% ungapped) in 134 aa overlap (892-1290:933-1061)

           910       940        970      1000      1030      1060  
5X_189 LSYTQKTISTSFSSSPPSTSPLNSS-SESSRSESITSSPGSKPAAFGSGL*PSSAYTE*S
       .: :  . :    ::  :. : .:: : ::.::. ..: .:. ....:   :.:.:.  :
NR_SC: ISSTTTSASILSESSKSSVIPTSSSTSGSSESETGSASSASSSSSISSE-SPKSTYSSSS
            940       950       960       970       980        990 

           1090      1120      1150      1180      1210      1240  
5X_189 LMSAS*KEQRGPQK*EHTAPPLNRITSSGSIFTLVSPCCCPLGTCTPPLTNPFVPSAPTP
       :  ..       :.   . ::..   .: .  :::.   :   .::  ... .: .: . 
NR_SC: LPPVTSATTS--QEITSSLPPVTTTKTSEQT-TLVTVTSCESHVCTESISSAIVSTATVT
            1000        1010      1020       1030      1040        

           1270      
5X_189 GAPGMAALEPWTCP
        . . .    : ::
NR_SC: VSGATTEYTTW-CP
     1050       1060 

>>NR_SC:PIR-S51959 PIR:S51959 hypothetical protein YAL06  (1367 aa)
 initn:  71 init1:  71 opt: 109  Z-score: 124.6  bits: 38.0 E(): 0.36
Smith-Waterman score: 117;  27.612% identity (28.906% ungapped) in 134 aa overlap (892-1290:978-1106)

           910       940        970      1000      1030      1060  
5X_189 LSYTQKTISTSFSSSPPSTSPLNSS-SESSRSESITSSPGSKPAAFGSGL*PSSAYTE*S
       .: :  . :    ::  :. : .:: : ::.::. ..: .:. ....:   :.:.:.  :
NR_SC: ISSTTTSASILSESSKSSVIPTSSSTSGSSESETGSASSASSSSSISSE-SPKSTYSSSS
       980       990      1000      1010      1020       1030      

           1090      1120      1150      1180      1210      1240  
5X_189 LMSAS*KEQRGPQK*EHTAPPLNRITSSGSIFTLVSPCCCPLGTCTPPLTNPFVPSAPTP
       :  ..       :.   . ::..   .: .  :::.   :   .::  ... .: .: . 
NR_SC: LPPVTSATTS--QEITSSLPPVTTTKTSEQT-TLVTVTSCESHVCTESISSAIVSTATVT
       1040        1050      1060       1070      1080      1090   

           1270      
5X_189 GAPGMAALEPWTCP
        . . .    : ::
NR_SC: VSGATTEYTTW-CP
          1100       

>>NR_SC:SW-Q12444 SW:Q12444 Q12444 saccharomyces cerevis  (126 aa)
 initn:  79 init1:  79 opt:  99  Z-score: 124.2  bits: 34.5 E(): 0.38
Smith-Waterman score: 99;  25.472% identity (25.962% ungapped) in 106 aa overlap (5480-5790:19-124)

    5480      5510      5540      5570      5600      5630         
5X_189 LRSKLRDLHLVRAARDCPAQSA*KWTSLTMTKRRRRRARMRVPRMRRRRGERVEGRRVER
       .. : :  .  :  :.   .      .:   .: ::. : :  : ::.: .: . :  ..
NR_SC: MKRKKRKKRKKRRERETMMKIPRILKKLRRKRRTRRKRRKRRKRRRRKRRKRRRKRSPRK
       20        30        40        50        60        70        

    5660      5690       5720        5750      5780   
5X_189 RR*GESKRMFLVSYL-DL*LWLLF-FNSYLV/LVKCMILAWF*MVYN
       ::  ..:  : .  . :    ::: : .. . ...:.    : ....
NR_SC: RRKRRNKDAFYILIISDPSRSLLFGFRKFSI-IIQCLTYFSFHILFH
       80        90       100        110       120    

>>NR_SC:SW-TOA1_YEAST SW:TOA1_YEAST P32773 saccharomyces  (286 aa)
rev-comp initn:  66 init1:  66 opt: 102  Z-score: 123.7  bits: 35.6 E():  0.4
Smith-Waterman score: 124;  34.091% identity (47.619% ungapped) in 88 aa overlap (998-736:216-278)

       990       960       930       900       870       840       
5X_18- DVIDSDLDDSDDEFRGDVDGGEDENDVDIVFCVYDKVCCCLIIPLCG*LHMLIARFCGNR
       : . :.::::::..  . .: ::  : ....:.::::                       
NR_SC: DEVGSELDDSDDDYLIS-EGEEDGPDENLMLCLYDKV-----------------------
         220       230        240       250                        

        810       780       750     
5X_18- S/TRVKNKWKTVFKDGMIHLNGKDYLFAK
         ::.: .::  .:::.. .: .:: : :
NR_SC: --TRTKARWKCSLKDGVVTINRNDYTFQK
               260       270        

>>NR_SC:SW-SIM1_YEAST SW:SIM1_YEAST P40472 saccharomyces  (475 aa)
 initn: 145 init1:  99 opt: 104  Z-score: 123.7  bits: 36.3 E(): 0.41
Smith-Waterman score: 120;  27.632% identity (30.216% ungapped) in 152 aa overlap (916-1359:109-251)

             940       970      1000      1030      1060      1090 
5X_189 STSFSSSPPSTSPLNSSSESSRSESITSSPGSKPAAFGSGL*PSSAYTE*SLMSAS*KEQ
       :.. :.:  ..:  .::: .:  :: . : .:. ::  : .  .:. :. :  ::. .  
NR_SC: SATASTSQGASSSSSSSSATSTLESSSVSSSSEEAAPTSTVVSTSSATQSSASSATKSST
      110       120       130       140       150       160        

            1120      1150      1180      1210      1240      1270 
5X_189 RGPQK*EHTAPPLNRITSSGSIFTLVSPCCCPLGTCTPPLTNPFVPSAPTPGAPGMAALE
        . .    :.   .  .::.:  .  :      :.    :..   ::           ..
NR_SC: SSTSPSTSTSTSTSSTSSSSSSSSSSSSSSSGSGSIYGDLADFSGPSEK---------FQ
      170       180       190       200       210                  

                1300      1330         
5X_189 PWTCPC----RGNGNISADWEFEGPAGGEEAS
         : ::     :.: :: ::  ::  .: : .
NR_SC: DGTIPCDKFPSGQGVISIDWIGEGGWSGVENT
     220       230       240       250 

>>NR_SC:GP-CAA47602_1 gi|4824|emb|CAA47602.1 (X67122) mi  (307 aa)
rev-comp initn:  77 init1:  77 opt: 102  Z-score: 123.4  bits: 35.6 E(): 0.42
Smith-Waterman score: 102;  32.609% identity (32.609% ungapped) in 46 aa overlap (7433-7296:252-297)

           7410      7380      7350      7320        
5X_18- VSQPSFANGLSGGFLRILREEGPAAFYAGFGPILFKQVPYTMAKFA
       ...:.:.:..:.    .  . : .::. :::: ... .: . : ::
NR_SC: LQKPKFGNSISSVAKTLYANGGIGAFFKGFGPTMLRAAPANGATFA
             260       270       280       290       

>>NR_SC:SW-YMC1_YEAST SW:YMC1_YEAST P32331 saccharomyces  (307 aa)
rev-comp initn:  77 init1:  77 opt: 102  Z-score: 123.4  bits: 35.6 E(): 0.42
Smith-Waterman score: 102;  32.609% identity (32.609% ungapped) in 46 aa overlap (7433-7296:252-297)

           7410      7380      7350      7320        
5X_18- VSQPSFANGLSGGFLRILREEGPAAFYAGFGPILFKQVPYTMAKFA
       ...:.:.:..:.    .  . : .::. :::: ... .: . : ::
NR_SC: LQKPKFGNSISSVAKTLYANGGIGAFFKGFGPTMLRAAPANGATFA
             260       270       280       290       

>>NR_SC:SW-YG5F_YEAST SW:YG5F_YEAST P53320 saccharomyces  (366 aa)
rev-comp initn:  64 init1:  64 opt: 102  Z-score: 122.4  bits: 35.7 E(): 0.48
Smith-Waterman score: 103;  19.597% identity (21.935% ungapped) in 347 aa overlap (7944-6968:12-342)

        7930      7900      7870      7840             7810        
5X_18- IRRFALAGALGCAVTHGALTPVDVVKTRIQLEPEVYN-------RVGRFFNSS*GF*EL*
       ...  :... : ..:   :::.:::. :.: .  . .       .:    .:.  .  ..
NR_SC: LKERMLSAGAGSVLTSLILTPMDVVRIRLQQQQMIPDCSCDGAAEVPNAVSSGSKMKTFT
              20        30        40        50        60        70 

     7780      7750        7720       7690          7660      7630 
5X_18- GVVLMSQTIGYGCLFPTNHC--QGGCRCSS\TGFGPTAVGY----AIQGAFKFGG*VMMS
       .:   .:... . .:  . :  .  :. ::   :. :  ..    ...:  ..   . ..
NR_SC: NV--GGQNLNNAKIFWESACFQELHCKNSS-LKFNGTLEAFTKIASVEGITSLWRGISLT
                80        90        100       110       120        

            7600      7570      7540      7510      7480      7450 
5X_18- LQITA*SRANLPISYEFWKKKAIDLVGVDKARENRQAIYLGASAIAEFFADIALCPLEAT
       : ..  .      .::. .    :.  . ..  . . .. ::  ::. ::  .. ::: .
NR_SC: LLMAIPANMVYFSGYEYIR----DVSPIASTYPTLNPLFCGA--IARVFAATSIAPLELV
      130       140           150       160         170       180  

             7420      7390      7360      7330      7300          
5X_18- RIRLVSQPS/SRQRSFRWFP*DFEGGRSRCLLRRFRPYPLQAGSLYHGQVRRVSRPY/WR
       . .: : :  : . .  :.      ...:  ..   :    . .:..:    .     ::
NR_SC: KTKLQSIPR-SSKSTKTWMMVKDLLNETRQEMKMVGP----SRALFKG----LEITL-WR
            190        200       210           220           230   

    7270      7240      7210      7180      7150      7120         
5X_18- NNQTFG*YYRSYEVAVEKILKATGKSKDSLTGGQLTGLNLTSGLIAGLAAAVISQPAD--
       .    . :. :::.  :..   . .  .. ..      ...:: :.:. ::. ..: :  
NR_SC: DVPFSAIYWSSYELCKERLWLDSTRFASKDANWVHFINSFASGCISGMIAAICTHPFDVG
            240       250       260       270       280       290  

            7090      7060      7030      7000      6970 
5X_18- ------TLLSKINKTKGAPGQSTTSRLVQMAGQLGVSGLFTGMTTRLVMI
             ..... .   :  ...  . :  .    :...:.::...:.. :
NR_SC: KTRWQISMMNNSDPKGGNRSRNMFKFLETIWRTEGLAALYTGLAARVIKI
            300       310       320       330       340  

>>NR_SC:SW-TIR3_YEAST SW:TIR3_YEAST P40552 saccharomyces  (269 aa)
 initn:  91 init1:  91 opt: 100  Z-score: 121.4  bits: 35.1 E(): 0.54
Smith-Waterman score: 100;  29.091% identity (29.358% ungapped) in 110 aa overlap (829-1158:112-220)

            850       880       910       940       970      1000  
5X_189 QKRAISICN*PQRGMMRQQHTLSYTQKTISTSFSSSPPSTSPLNSSSESSRSESITSSPG
       :. .::: .  :      ... . .. . :.: :::  :.:  .::: .: : : .:: .
NR_SC: QSAGISITSLGQTVSESGSESATASSDASSASESSSAASSSASESSSAASSSASESSSAA
             120       130       140       150       160       170 

           1030      1060      1090      1120      1150  
5X_189 SKPAAFGSGL*PSSAYTE*SLMSAS*KEQRGPQK*EHTAPPLNRITSSGS
       :. :. .:.   ::: .: .  :.: : . .      ..   .. .:..:
NR_SC: SSSASESSSAASSSA-SEAAKSSSSAKSSGSSAASSAASSASSKASSAAS
             180        190       200       210       220

>>NR_SC:SW-Q08428 SW:Q08428 Q08428 saccharomyces cerevis  (113 aa)
 initn:  95 init1:  95 opt:  96  Z-score: 120.7  bits: 33.7 E(): 0.59
Smith-Waterman score: 121;  54.545% identity (60.000% ungapped) in 33 aa overlap (902-1000:31-60)

           920       950       980      
5X_189 HRKRYQRHFHPHHRRHHL*THHRSHLDRNR*RR
       ::.: .:: . ::::::   ::: .  : : ::
NR_SC: HRRRRRRHHRRHHRRHH---HHRRRRRRRRRRR
               40           50        60

>>NR_SC:SW-FLO5_YEAST SW:FLO5_YEAST P38894 saccharomyces  (1075 aa)
 initn:  72 init1:  72 opt: 104  Z-score: 119.3  bits: 36.7 E(): 0.71
Smith-Waterman score: 121;  28.030% identity (31.624% ungapped) in 132 aa overlap (895-1290:707-823)

          910       940       970      1000      1030      1060    
5X_189 SYTQKTISTSFSSSPPSTSPLNSSSESSRSESITSSPGSKPAAFGSGL*PSSAYTE*SLM
       : :...: :: :.:  : :  .:.: :: : ::.:   ..:.  .:.: : .. :     
NR_SC: SSTSSVIPTSSSTSGSSESKTSSASSSSSSSSISSESPKSPTNSSSSLPPVTSATTG---
        710       720       730       740       750       760      

         1090      1120      1150      1180      1210      1240    
5X_189 SAS*KEQRGPQK*EHTAPPLNRITSSGSIFTLVSPCCCPLGTCTPPLTNPFVPSAPTPGA
                 :..  . :: .   .: .  :::.   :   .::  ... .: .: .  .
NR_SC: ----------QETASSLPPATTTKTSEQT-TLVTVTSCESHVCTESISSAIVSTATVTVS
                     770       780        790       800       810  

         1270      
5X_189 PGMAALEPWTCP
          .    : ::
NR_SC: GVTTEYTTW-CP
            820    

>>NR_SC:SW-YK82_YEAST SW:YK82_YEAST P36170 saccharomyces  (1169 aa)
 initn:  64 init1:  64 opt: 104  Z-score: 118.8  bits: 36.7 E(): 0.76
Smith-Waterman score: 104;  25.532% identity (26.471% ungapped) in 141 aa overlap (880-1290:839-978)

     880       910         940       970      1000      1030       
5X_189 QQHTLSYTQKTISTSF--SSSPPSTSPLNSSSESSRSESITSSPGSKPAAFGSGL*PSSA
       .. . . :.  ::..:   ::: ::    :.. .:..:: .::  .  .  .... :::.
NR_SC: HETSTASTSVQISSQFVTPSSPISTVAPRSTGLNSQTESTNSSKETMSSENSASVMPSSS
      840       850       860       870       880       890        

        1060       1090      1120       1150      1180      1210   
5X_189 YT--E*SLMSAS\EKSKEGRRNENTPLRLLTA*/PSSGSIFTLVSPCCCPLGTCTPPLTN
        :  ... .... : :.   :...:  :. . . ::..   ::..   :  ..:.  ...
NR_SC: ATSPKTGKVTSD-ETSSGFSRDRTTVYRMTSET-PSTNEQTTLITVSSCESNSCSNTVSS
      900       910        920       930        940       950      

          1240      1270      
5X_189 PFVPSAPTPGAPGMAALEPWTCP
         : .: :      .    : ::
NR_SC: AVVSTATTTINGITTEYTTW-CP
        960       970         

>>NR_SC:SW-YOD0_YEAST SW:YOD0_YEAST Q08193 saccharomyces  (484 aa)
 initn: 116 init1:  69 opt: 100  Z-score: 118.2  bits: 35.3 E(): 0.82
Smith-Waterman score: 100;  46.429% identity (48.148% ungapped) in 56 aa overlap (916-1083:405-458)

             940       970      1000      1030      1060       
5X_189 STSFSSSPPSTSPLNSSSESSRSESITSSPGSKPAAFGSGL*PSSAYTE*SLMSAS
       :.: :::  :.:  .:::::: : : .::  :.:.:  ..:  :.: .  : .:.:
NR_SC: SSSSSSSSSSSSSASSSSESSSSTSKASS--SSPSASETSLLKSAASATSSSQSSS
          410       420       430         440       450        

>>NR_SC:SW-CW14_YEAST SW:CW14_YEAST O13547 saccharomyces  (238 aa)
 initn:  77 init1:  77 opt:  97  Z-score: 118.1  bits: 34.3 E(): 0.84
Smith-Waterman score: 97;  24.183% identity (24.667% ungapped) in 153 aa overlap (784-1234:53-205)

       790        820       850       880       910         940    
5X_189 EHRLPLVLYSLD-LFPQKRAISICN*PQRGMMRQQHTLSYTQKTISTSFSSS--PPSTSP
       ::.   :   :: . :.. : .  .  . .  .:. .:. .... :.: :::    :.. 
NR_SC: EHENSAVKKCLDSICPNNDADAAYSAFKSSCSEQNASLGDSSSSASSSASSSSKASSSTK
             60        70        80        90       100       110  

          970      1000      1030      1060      1090      1120    
5X_189 LNSSSESSRSESITSSPGSKPAAFGSGL*PSSAYTE*SLMSAS*KEQRGPQK*EHTAPPL
        .::: :: ... .:: .:.  : .:.  :::. .  .  :.: . .    . :...   
NR_SC: ASSSSASSSTKASSSSASSSTKASSSSAAPSSSKASSTESSSSSSSSTKAPSSEESSSTY
            120       130       140       150       160       170  

          1150      1180      1210       
5X_189 \TA*PRQGPSSL*FHPVVVHSALVPHR*QTHLCP
        ..  .:. :.   :   . :. : ... .   :
NR_SC: -VSSSKQASSTSEAHSSSAASSTVSQETVSSALP
             180       190       200     

>>NR_SC:SW-TIR1_YEAST SW:TIR1_YEAST P10863 saccharomyces  (254 aa)
rev-comp initn:  78 init1:  78 opt:  97  Z-score: 117.7  bits: 34.3 E(): 0.87
Smith-Waterman score: 97;  39.241% identity (41.892% ungapped) in 79 aa overlap (1483-1263:100-178)

           1460      1430           1400       1370      1340      
5X_18- SRLLTC*KTRNGKLSCSKHES----PT/SARAGSSSRSP-SPTLESKPEASSPPAGPSNS
       :::    :. ::  : :   :    :: :. : ::: .: : .  :. ::.:  :.::.:
NR_SC: SRLEPALKSLNGDASSSAAPSSSAAPT-SSAAPSSSAAPTSSAASSSSEAKSSSAAPSSS
     100       110       120        130       140       150        

       1310      1280      
5X_18- QSADMFPFPRQGQVQGSSAA
       .. .    : ......::::
NR_SC: EAKSSSAAPSSSEAKSSSAA
      160       170        

>>NR_SC:SW-Q08873 SW:Q08873 Q08873 saccharomyces cerevis  (200 aa)
 initn:  85 init1:  85 opt:  95  Z-score: 116.3  bits: 33.7 E():    1
Smith-Waterman score: 95;  31.868% identity (32.222% ungapped) in 91 aa overlap (7-275:63-153)

       10        40        70        100        130       160      
5X_189 LVNIIYGVKRGDVNTRYEVIPVLISIQI/DSIS-FLSPTRSYGCLFPSLYYFIDIMNVSA
       :.::.: .  :..:        .  .:. :.:: ::: .:.::     :.  ::... . 
NR_SC: LANILYEADTGEANHISWKSSKMPFVQM-DQISQFLSFSRKYGVPEDELFQTIDLFEKKD
             70        80        90        100       110       120 

        190       220       250        
5X_189 LFT*T*MLSELSVQLSKVHCDEFPNES*EIST
              :. ::   .: : :.::  . ..::
NR_SC: PAIVFQTLKSLSRYANKKHTDRFPVLGPQLST
             130       140       150   

>>NR_SC:SW-TIR2_YEAST SW:TIR2_YEAST P33890 saccharomyces  (251 aa)
 initn:  92 init1:  92 opt:  95  Z-score: 115.1  bits: 33.8 E():  1.2
Smith-Waterman score: 95;  33.846% identity (33.846% ungapped) in 65 aa overlap (889-1083:120-184)

            910       940       970      1000      1030      1060  
5X_189 TLSYTQKTISTSFSSSPPSTSPLNSSSESSRSESITSSPGSKPAAFGSGL*PSSAYTE*S
       : . .  : :.  :::  ..: . ::::.. :   .:: .:. :: .:..  ::  :  .
NR_SC: TEASSAATSSAVASSSETTSSAVASSSEATSSAVASSSEASSSAATSSAVASSSEATSST
     120       130       140       150       160       170         

            
5X_189 LMSAS
       . :..
NR_SC: VASST
     180    

>>NR_SC:SW-CBF5_YEAST SW:CBF5_YEAST P33322 saccharomyces  (483 aa)
 initn:  77 init1:  77 opt:  97  Z-score: 114.2  bits: 34.6 E():  1.4
Smith-Waterman score: 97;  20.635% identity (21.757% ungapped) in 252 aa overlap (4951-5685:225-470)

       4960      4990      5020      5050      5080      5110      
5X_189 TELSSLLTPFDIKRLESYADSMLDYHVVLDLVPTIASLFFGKRLETSLPPAQQAI-----
       .: ....:  :.   .   :.  :   . ...  . .:. : .  .    : .:.     
NR_SC: SENDNMVTLHDVMDAQWVYDNTRDESYLRSIIQPLETLLVGYKRIVVKDSAVNAVCYGAK
          230       240       250       260       270       280    

              5140      5170      5200      5230      5260         
5X_189 LLALGLQR--KNVEALENELGITSTQTLALFGKVLRKMTKSLEDIRKASIAS/VTSC*AD
       :.  :: :  ...: : .:. . .:.  :.   . .  : .: .  .. .:: :  :  .
NR_SC: LMIPGLLRYEEGIE-LYDEIVLITTKGEAIAVAIAQMSTVDLASCDHGVVAS-VKRCIME
          290        300       310       320       330        340  

     5290      5320       5350      5380      5410      5440       
5X_189 PRRPISQRV*QVC\PLQQTIEQDLADSAVQLNGEDDDASKKEQRELLNTLNMEEFAIDQG
         : .  :   .  :. :  .:  ::. ..  :. .. . .. ..    :.  : . ...
NR_SC: --RDLYPRRWGLG-PVAQKKKQMKADGKLDKYGRVNENTPEQWKKEYVPLDNAEQSTSSS
              350        360       370       380       390         

      5470      5500      5530      5560      5590      5620       
5X_189 GDWTEAEKQVERLASGKGGTRLSSTVSVKVDKLDDDKAKAEKGKDAGAKDAKKKRRESGG
        .  :.:.. ..   .:  . .. . . : .  .::. : .: :    .  .::....  
NR_SC: QETKETEEEPKK---AKEDSLIKEVETEKEEVKEDDSKKEKKEKKDKKEKKEKKEKKDKK
     400       410          420       430       440       450      

      5650      5680 
5X_189 EKGGKKKVRRE*ED
       ::  ::. .:. ::
NR_SC: EKKEKKEKKRKSED
        460       470

>>NR_SC:SW-KRE1_YEAST SW:KRE1_YEAST P17260 saccharomyces  (313 aa)
 initn:  88 init1:  88 opt:  95  Z-score: 113.9  bits: 33.9 E():  1.4
Smith-Waterman score: 95;  39.655% identity (40.351% ungapped) in 58 aa overlap (889-1062:139-195)

            910       940       970      1000      1030      1060
5X_189 TLSYTQKTISTSFSSSPPSTSPLNSSSESSRSESITSSPGSKPAAFGSGL*PSSAYTE
       : ..:... :.. ::.  :.:   ::: :: : . :.: ::  :  :.   ::. .::
NR_SC: TQTFTHSSTSAT-SSASSSVSSSVSSSGSSSSVKTTTSTGSAVAETGTRPDPSTDFTE
      140       150        160       170       180       190     

>>NR_SC:GP-CAA52447_1 gi|396560|emb|CAA52447.1 (X74428)   (250 aa)
 initn:  91 init1:  91 opt:  94  Z-score: 113.8  bits: 33.6 E():  1.4
Smith-Waterman score: 94;  33.846% identity (33.846% ungapped) in 65 aa overlap (889-1083:119-183)

            910       940       970      1000      1030      1060  
5X_189 TLSYTQKTISTSFSSSPPSTSPLNSSSESSRSESITSSPGSKPAAFGSGL*PSSAYTE*S
       : . .  : :.  :::  ..: . ::::.. :   .:: .:. :: .:..  ::  :  .
NR_SC: TEASSAATSSAVASSSETTSSAVASSSEATSSAVASSSEASSSAATSSAVASSSEATSSA
      120       130       140       150       160       170        

            
5X_189 LMSAS
       . :..
NR_SC: VASST
      180   

>>NR_SC:GP-CAA81388_1 gi|439289|emb|CAA81388.1 (Z26645)   (751 aa)
 initn:  76 init1:  76 opt:  98  Z-score: 113.2  bits: 35.0 E():  1.6
Smith-Waterman score: 105;  23.759% identity (24.723% ungapped) in 282 aa overlap (3283-4117:140-414)

             3310      3340      3370      3400       3430         
5X_189 LTPKTSKLCLNLSSKPLMPWVTRSTLIMMSCKAQTPTSKRLL*GSTS\PRSPTNHPIHLP
       :.:  .   .  :: : .: .  :.   .    ..:.    : :... :. : :.: :.:
NR_SC: LSPAPAVPSIPSSSAPPIPDIPSSAAPPIPIVPSSPAPPLPLSGASA-PKVPQNRP-HMP
     140       150       160       170       180        190        

    3460       3490      3520      3550          3580       3610   
5X_189 RRFSRSRPS*/RLSSLMKLPPSLFPLFVNSSAPISC----LWPPPSTVTRVLA/DSLSIK
             :    : :: ..::    : . ..: :         :::  .  .   :: .::
NR_SC: SVRPAHRSHQ-RKSSNISLPSVSAPPLPSASLPTHVSNPPQAPPPPPTPTIGL-DSKNIK
       200        210       220       230       240        250     

           3640      3670      3700       3730      3760      3790 
5X_189 \PFSNSVNRHDHRLPRIARMRLPALLVHLPR\RGCW*IGRWSRAISS*DQA**AYPLLPR
        : .:.:.  . ..:  .   :  . ..  . ::       ..  .   ..    ::   
NR_SC: -PTDNAVSPPSSEVPAGGLPFLAEINARRSE-RGAVEGVSSTKIQTENHKSPSQRPLPSS
          260       270       280        290       300       310   

            3820       3850      3880      3910      3940      3970
5X_189 RQC*KVVEQPPLP/PMPPSSPNLSKVALTLPNASFTMSTATLSSLITPLQKCSCKG*WRS
            . . :::: :  :  :.: .:. . :. . .        : . ... : ..   .
NR_SC: APPIPTSHAPPLP-PTAPPPPSLPNVT-SAPKKATSAPRPPPPPLPAAMSSASTNSVKAT
           320        330        340       350       360       370 

             4000       4030      4060      4090        
5X_189 TSLPTTRTLLTTCRCFP\SSRSSSFRSPPPYRRE**YPP*PSCRPSSRA
          ::    : .    :  ...::. .:::       :: :.   .: :
NR_SC: PVPPTLAPPLPNTTSVP-PNKASSMPAPPP-----PPPPPPGAFSTSSA
             380        390       400            410    

>>NR_SC:SW-VRP1_YEAST SW:VRP1_YEAST P37370 saccharomyces  (817 aa)
 initn:  76 init1:  76 opt:  98  Z-score: 112.7  bits: 35.1 E():  1.7
Smith-Waterman score: 110;  25.088% identity (26.296% ungapped) in 283 aa overlap (3283-4117:140-414)

             3310      3340      3370      3400       3430         
5X_189 LTPKTSKLCLNLSSKPLMPWVTRSTLIMMSCKAQTPTSKRLL*GSTS\PRSPTNHPIHLP
       :.:  .   .  :: : .: .  :.   .    ..:.    : :... :. : :.: :.:
NR_SC: LSPAPAVPSIPSSSAPPIPDIPSSAAPPIPIVPSSPAPPLPLSGASA-PKVPQNRP-HMP
     140       150       160       170       180        190        

    3460       3490      3520      3550          3580       3610   
5X_189 RRFSRSRPS*/RLSSLMKLPPSLFPLFVNSSAPISC----LWPPPSTVTRVLA/DSLSIK
             :    : :: ..::    : . ..: :         :::  .  .   :: .::
NR_SC: SVRPAHRSHQ-RKSSNISLPSVSAPPLPSASLPTHVSNPPQAPPPPPTPTIGL-DSKNIK
       200        210       220       230       240        250     

           3640      3670      3700       3730      3760      3790 
5X_189 \PFSNSVNRHDHRLPRIARMRLPALLVHLPR\RGCW*IGRWSRAISS*DQA**AYPLLPR
        : .:.:.  . ..:  .   :  . ..  . ::    :  :  :.. ..   . : :: 
NR_SC: -PTDNAVSPPSSEVPAGGLPFLAEINARRSE-RGAVE-GVSSTKIQTENHKSPSQPPLPS
          260       270       280        290        300       310  

             3820       3850      3880      3910      3940         
5X_189 R-QC*KVVEQPPLP/PMPPSSPNLSKVALTLPNASFTMSTATLSSLITPLQKCSCKG*WR
             . . :::: :  :  :.: .:. . :. . .  .     : . ... : ..   
NR_SC: SAPPIPTSHAPPLP-PTAPPPPSLPNVT-SAPKKATSAPAPPPPPLPAAMSSASTNSVKA
            320        330        340       350       360       370

    3970      4000       4030      4060      4090        
5X_189 STSLPTTRTLLTTCRCFP\SSRSSSFRSPPPYRRE**YPP*PSCRPSSRA
       .   ::    : .    :  ...::. .:::       :: :.   .: :
NR_SC: TPVPPTLAPPLPNTTSVP-PNKASSMPAPPP-----PPPPPPGAFSTSSA
              380        390       400            410    

>>NR_SC:SW-Q07229 SW:Q07229 Q07229 saccharomyces cerevis  (817 aa)
 initn:  76 init1:  76 opt:  98  Z-score: 112.7  bits: 35.1 E():  1.7
Smith-Waterman score: 102;  24.735% identity (25.926% ungapped) in 283 aa overlap (3283-4117:140-414)

             3310      3340      3370      3400       3430         
5X_189 LTPKTSKLCLNLSSKPLMPWVTRSTLIMMSCKAQTPTSKRLL*GSTS\PRSPTNHPIHLP
       :.:  .   .  :: : .: .   .   .    ..:.    : :... :. : :.: :.:
NR_SC: LSPAPAVPSIPSSSAPPIPDIPSFAAPPIPIVPSSPAPPLPLSGASA-PKVPQNRP-HMP
     140       150       160       170       180        190        

    3460       3490      3520      3550          3580       3610   
5X_189 RRFSRSRPS*/RLSSLMKLPPSLFPLFVNSSAPISC----LWPPPSTVTRVLA/DSLSIK
             :    : :: ..::    : . ..: :         :::  .  .   :: .::
NR_SC: SVRPAHRSHQ-RKSSNISLPSVSAPPLPSASLPTHVSNPPQAPPPPPTPTIGL-DSKNIK
       200        210       220       230       240        250     

           3640      3670      3700       3730      3760      3790 
5X_189 \PFSNSVNRHDHRLPRIARMRLPALLVHLPR\RGCW*IGRWSRAISS*DQA**AYPLLPR
        : .:.:.  . ..:  .   :  . ..  . ::    :  :  :.. ..   . : :: 
NR_SC: -PTDNAVSPPSSEVPAGGLPFLAEINARRSE-RGAVE-GVSSTKIQTENHKSPSQPPLPS
          260       270       280        290        300       310  

             3820       3850      3880      3910      3940         
5X_189 R-QC*KVVEQPPLP/PMPPSSPNLSKVALTLPNASFTMSTATLSSLITPLQKCSCKG*WR
             . . :::: :  :  :.: .:. . :. . .  .     : . ... : ..   
NR_SC: SAPPIPTSHAPPLP-PTAPPPPSLPNVT-SAPKKATSAPAPPPPPLPAAMSSASTNSVKA
            320        330        340       350       360       370

    3970      4000       4030      4060      4090        
5X_189 STSLPTTRTLLTTCRCFP\SSRSSSFRSPPPYRRE**YPP*PSCRPSSRA
       .   ::    : .    :  ...::. .:::       :: :.   .: :
NR_SC: TPVPPTLAPPLPNTTSVP-PNKASSMPAPPP-----PPPPPPGAFSTSSA
              380        390       400            410    

>>NR_SC:SW-Q12218 SW:Q12218 Q12218 saccharomyces cerevis  (487 aa)
 initn:  63 init1:  63 opt:  94  Z-score: 110.2  bits: 33.9 E():  2.3
Smith-Waterman score: 97;  27.778% identity (28.302% ungapped) in 108 aa overlap (775-1092:87-194)

          790        820       850       880       910       940   
5X_189 SVFEHRLPLV-LYSLDLFPQKRAISICN*PQRGMMRQQHTLSYTQKTISTSFSSSPPSTS
       :. :: : .:  ::  :.:. .:..   . . .   ..  .. .. . ::: : .: :. 
NR_SC: SAVEHMLTMVPWYSSRLLPELEAMDASLTTSSSAATSSSEVASSSIASSTSSSVAPSSSE
         90       100       110       120       130       140      

           970      1000       1030      1060      1090
5X_189 PLNSSSESSRSESITSS-PGSKPAAFGSGL*PSSAYTE*SLMSAS*KE
        ..::   : :: ..::   :.  . .:..  ::. .  : .. : .:
NR_SC: VVSSSVAPSSSEVVSSSVAPSSSEVVSSSVASSSSEVASSSVAPSSSE
        150       160       170       180       190    

>>NR_SC:GP-AAA35091_1 gi|295671|gb|AAA35091.1 (L11275) s  (406 aa)
 initn:  78 init1:  78 opt:  92  Z-score: 108.5  bits: 33.3 E():  2.8
Smith-Waterman score: 109;  30.682% identity (30.682% ungapped) in 88 aa overlap (895-1158:26-113)

          910       940       970      1000      1030      1060    
5X_189 SYTQKTISTSFSSSPPSTSPLNSSSESSRSESITSSPGSKPAAFGSGL*PSSAYTE*SLM
       : .... :.: :::  :.:  .::.::: : : .:: .:. .. .:    ::. .  :  
NR_SC: SSSSSSSSSSSSSSSSSSSSSSSSGESSSSSSSSSSSSSSDSSDSSDSESSSSSSSSSSS
          30        40        50        60        70        80     

         1090      1120      1150  
5X_189 SAS*KEQRGPQK*EHTAPPLNRITSSGS
       :.: ..... .. . ..   .  .::.:
NR_SC: SSSSSDSESSSESDSSSSGSSSSSSSSS
          90       100       110   

>>NR_SC:SW-SR40_YEAST SW:SR40_YEAST P32583 saccharomyces  (406 aa)
 initn:  78 init1:  78 opt:  92  Z-score: 108.5  bits: 33.3 E():  2.8
Smith-Waterman score: 109;  30.682% identity (30.682% ungapped) in 88 aa overlap (895-1158:26-113)

          910       940       970      1000      1030      1060    
5X_189 SYTQKTISTSFSSSPPSTSPLNSSSESSRSESITSSPGSKPAAFGSGL*PSSAYTE*SLM
       : .... :.: :::  :.:  .::.::: : : .:: .:. .. .:    ::. .  :  
NR_SC: SSSSSSSSSSSSSSSSSSSSSSSSGESSSSSSSSSSSSSSDSSDSSDSESSSSSSSSSSS
          30        40        50        60        70        80     

         1090      1120      1150  
5X_189 SAS*KEQRGPQK*EHTAPPLNRITSSGS
       :.: ..... .. . ..   .  .::.:
NR_SC: SSSSSDSESSSESDSSSSGSSSSSSSSS
          90       100       110   

>>NR_SC:SW-TIP1_YEAST SW:TIP1_YEAST P27654 saccharomyces  (210 aa)
 initn:  77 init1:  77 opt:  89  Z-score: 108.1  bits: 32.3 E():    3
Smith-Waterman score: 89;  35.000% identity (35.593% ungapped) in 60 aa overlap (913-1089:104-163)

              940       970       1000      1030      1060         
5X_189 ISTSFSSSPPSTSPLNSSSE-SSRSESITSSPGSKPAAFGSGL*PSSAYTE*SLMSAS*K
       :.....:  :..:   :::: .: :.. .:: ... :: .:.  :::. .  :   .: :
NR_SC: IAAALASVSPASSEAASSSEAASSSKAASSSEATSSAAPSSSAAPSSSAAPSSSAESSSK
           110       120       130       140       150       160   

>>NR_SC:SW-O94086 SW:O94086 O94086 saccharomyces cerevis  (168 aa)
 initn:  74 init1:  74 opt:  88  Z-score: 107.9  bits: 31.9 E():  3.1
Smith-Waterman score: 88;  29.348% identity (29.348% ungapped) in 92 aa overlap (7217-7491:5-96)

     7220      7250       7280      7310      7340      7370       
5X_189 DLLDGNLVAAIVLAKYSI/TYAVRSTYTANLAMV*GTCLKRIGPKPA*KAAGPSSLKILR
       .. .:.  : .:  . .: :..  ..:. ::..:   ::.  . .:  . . ::  ::: 
NR_SC: NMEQGKRYAMLVNCSRGI-TFSFNKSYAPNLTVVYVHCLNTAALRPEYNPTTPSFAKILS
           10        20         30        40        50        60   

      7400      7430      7460      7490
5X_189 KPPERPLAKDG*ETSLIRVASRGQRAMSAKNSA
       .  .      :   ::  . :::  .: ::  :
NR_SC: NILKSVGLGIGAACSLTLAKSRGCVTMVAKIPA
            70        80        90      

>>NR_SC:SW-YM8Z_YEAST SW:YM8Z_YEAST Q04951 saccharomyces  (389 aa)
 initn:  69 init1:  69 opt:  91  Z-score: 107.4  bits: 33.0 E():  3.3
Smith-Waterman score: 91;  47.222% identity (47.222% ungapped) in 36 aa overlap (895-1002:99-134)

          910       940       970      1000
5X_189 SYTQKTISTSFSSSPPSTSPLNSSSESSRSESITSS
       : . .:...: :::: :.:  .::. :: : ::..:
NR_SC: SEAASTVGSSTSSSPSSSSSTSSSASSSASSSISAS
      100       110       120       130    

>>NR_SC:SW-YGC8_YEAST SW:YGC8_YEAST P53189 saccharomyces  (542 aa)
 initn:  76 init1:  76 opt:  92  Z-score: 107.0  bits: 33.4 E():  3.5
Smith-Waterman score: 93;  27.551% identity (28.125% ungapped) in 98 aa overlap (829-1122:192-287)

            850       880       910       940       970      1000  
5X_189 QKRAISICN*PQRGMMRQQHTLSYTQKTISTSFSSSPPSTSPLNSSSESSRSESITSSPG
       :  : :  :      . .:..   :.   :.: :::  :..  .::. :: : : .:: .
NR_SC: QAAATSTLNQQTSTSIASQESTESTNTPTSSSTSSSTSSST--SSSTSSSTSSSTSSSTS
             200       210       220       230         240         

           1030      1060      1090      1120
5X_189 SKPAAFGSGL*PSSAYTE*SLMSAS*KEQRGPQK*EHT
       :. ..  :.   ..: :  .  :.:     .:.   ..
NR_SC: SSTSSSTSSTQETAATTSEGSSSSSAAITSSPKAIAYS
     250       260       270       280       

>>NR_SC:SW-YG1F_YEAST SW:YG1F_YEAST P53214 saccharomyces  (551 aa)
 initn:  63 init1:  63 opt:  92  Z-score: 106.9  bits: 33.4 E():  3.5
Smith-Waterman score: 123;  27.010% identity (27.815% ungapped) in 311 aa overlap (3034-3951:8-313)

      3040      3070        3100      3130       3160      3190    
5X_189 RQRSSKR*RKTWK-V*TSLVLLP-SWQRLSTRPRLS*LLS/TAISEKNLSSTVALTAGRG
       :..::    . :. .  .:. :: :       :  :.  : :: :  .::.. ..:..  
NR_SC: RKKSSASSLSMWRTILMALTTLPLSVLSQELVPANSTTSS-TAPSITSLSAVESFTSSTD
        10        20        30        40         50        60      

         3220       3250      3280      3310      3340      3370   
5X_189 RGKSAALG\SPSVQLLLMTTLTSLLLLLTPKTSKLCLNLSSKPLMPWVTRSTLIMMSCKA
         .::.:. .::.  . .:.. .   :::  .: :  .:::. ..  :. :.    : ..
NR_SC: ATSSASLS-TPSIASVSFTSFPQSSSLLT-LSSTLSSELSSSSMQ--VSSSSTSSSSSEV
         70         80        90        100         110       120  

          3400      3430      3460      3490      3520      3550   
5X_189 QTPTSKRLL*GSTSSEVTDKPSNTSPPKILTFSAKLSLSSLMKLPPSLFPLFVNSSAPIS
        . .:.  .  :.:: .  . :.. :   .. ...   :: ..   ::     .:.  .:
NR_SC: TSSSSSSSISPSSSSSTIISSSSSLPTFTVASTSSTVASSTLSTSSSLVISTSSSTFTFS
            130       140       150       160       170       180  

            3580      3610      3640      3670      3700      3730 
5X_189 CL/SAST-INGYEGTGRSLSIKLIQQLREQTRPSITKDSENAAASSAGSSSKAAAAGRSG
          :.:. :..  .:. : :   . .   .. :: ...  ... ::..:::   . . : 
NR_SC: SE-SSSSLISSSISTSVSTSSVYVPSSSTSSPPSSSSELTSSSYSSSSSSSTLFSYSSSF
             190       200       210       220       230       240 

              3760      3790      3820      3850       3880        
5X_189 A/ASRAISS/SRSSLMSLSVTPPETMLKSG*TTSSASMPPSS-PNLSKVALTLPNASFTM
       . .: . :: : ::  : : .   ...  ....::. .  :: :..:. . . :..:.: 
NR_SC: S-SSSSSSS-SSSSSSSSSSSSSSSYFTLSTSSSSSIYSSSSYPSFSSSSSSNPTSSITS
               250       260       270       280       290         

     3910      3940    
5X_189 STATLSSLITPLQKCS
       ..:  :: ::: .. :
NR_SC: TSA--SSSITPASEYS
     300         310   

>>NR_SC:GP-AAA35015_1 gi|172526|gb|AAA35015.1 (M16165) S  (570 aa)
 initn:  79 init1:  79 opt:  92  Z-score: 106.7  bits: 33.4 E():  3.6
Smith-Waterman score: 113;  26.923% identity (27.723% ungapped) in 104 aa overlap (916-1227:24-124)

             940       970      1000      1030      1060      1090 
5X_189 STSFSSSPPSTSPLNSSSESSRSESITSSPGSKPAAFGSGL*PSSAYTE*SLMSAS*KEQ
       ::. ::: :  .: .:..::: .   : : .:. .. . . .: :. :: : . . .  .
NR_SC: STTESSSAPVPTPSSSTTESSVAPVPTPSSSSNITSSAPSSTPFSSSTESSSVPVPTPSS
            30        40        50        60        70        80   

            1120      1150      1180      1210     
5X_189 RGPQK*EHTAPPLNRITSSGSIFTLVSPCCCPLGTCTPPLTNPF
          . .: .. :..  :. .:.  . .:      : . : . ::
NR_SC: ---STTESSSAPVSSSTTESSVAPVPTPSSSSNITSSAPSSIPF
               90       100       110       120    

>>NR_SC:SW-HRB1_YEAST SW:HRB1_YEAST P38922 saccharomyces  (429 aa)
 initn:  68 init1:  68 opt:  90  Z-score: 105.5  bits: 32.8 E():  4.2
Smith-Waterman score: 90;  28.947% identity (29.730% ungapped) in 76 aa overlap (6937-7158:28-103)

     6940        6970      7000      7030      7060      7090      
5X_189 ETYTGQQ*--GYRS*QDEWSYR*RDRKHRADQPSGRA*RW*TGRGRPWSC*S*TRGCRRV
       .:: :..    ::. ... .:: :.: .  :.: .:       :::  .    .:     
NR_SC: DTYRGSRDRGEYRGGRERSDYRERERFNNRDNPRSRDRYDDRRRGRDVTGRYGNRRDDYP
        30        40        50        60        70        80       

       7120      7150  
5X_189 ER*RRRPNQR*DRK*G
       .  : : : : : . :
NR_SC: RSFRSRHNTRDDSRRG
        90       100   

>>NR_SC:SW-MID2_YEAST SW:MID2_YEAST P36027 saccharomyces  (376 aa)
 initn:  73 init1:  73 opt:  89  Z-score: 104.9  bits: 32.5 E():  4.5
Smith-Waterman score: 97;  24.742% identity (27.273% ungapped) in 194 aa overlap (3349-3930:11-186)

           3370      3400      3430      3460      3490      3520  
5X_189 RSTLIMMSCKAQTPTSKRLL*GSTSSEVTDKPSNTSPPKILTFSAKLSLSSLMKLPPSLF
       :  :...::  .:  .. .. .:.:.  . . . .:  .. . :. :: :          
NR_SC: RLLLLILSC-ISTIRAQFFVQSSSSNSSAVSTARSSVSRVSSSSSILSSS----------
                20        30        40        50                   

           3550      3580      3610      3640       3670      3700 
5X_189 PLFVNSSAPISCLWPPPSTVTRVLAVHCPSSSFSNSVN/MTRPSITKDSENAAASSAGSS
        .  .:::  : :    :: .: :. :  ::.   :.. .:  :...:: ....:::.:.
NR_SC: -MVSSSSADSSSL--TSSTSSRSLVSHTSSSTSIASIS-FTSFSFSSDSSTSSSSSASSD
       60        70          80        90        100       110     

            3730      3760       3790      3820      3850      3880
5X_189 SKAAAAGRSGAGLVRSLRE\TSLMSLSVTPPETMLKSG*TTSSASMPPSSPNLSKVALTL
       :.....   ..  . :    ::  . :..   .. ..  ..:: :   :.:. :    . 
NR_SC: SSSSSSFSISSTSATSESS-TSSTQTSTSSSSSLSSTPSSSSSPSTITSAPSTS----ST
         120       130        140       150       160           170

             3910      
5X_189 PNASFTMSTATLSSLI
       :...   . .:..:.:
NR_SC: PSTTAYNQGSTITSII
              180      

>>NR_SC:SW-Q08438 SW:Q08438 Q08438 saccharomyces cerevis  (674 aa)
rev-comp initn:  78 init1:  78 opt:  91  Z-score: 104.4  bits: 33.3 E():  4.8
Smith-Waterman score: 103;  35.714% identity (35.714% ungapped) in 56 aa overlap (1082-915:586-641)

    1080      1050      1020       990       960       930     
5X_18- DADINDYSV*AEDGHKPEPNAAGLLPGDDVIDSDLDDSDDEFRGDVDGGEDENDVD
       : : .: .   . : : : :       ::  :.: ::.::.   : :  .:..: :
NR_SC: DNDEEDDNKKNDTGGKDEDNDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
         590       600       610       620       630       640 

>>NR_SC:SW-CCC1_YEAST SW:CCC1_YEAST P47818 saccharomyces  (322 aa)
 initn:  81 init1:  81 opt:  88  Z-score: 104.4  bits: 32.2 E():  4.8
Smith-Waterman score: 88;  23.188% identity (23.188% ungapped) in 69 aa overlap (2052-2258:247-315)

          2070      2100      2130      2160      2190      2220   
5X_189 GIIPLFFFFFVPEFQSVGVLNIIFVYIQLLSFSTTYSKHHKQ*GSNSTHASQRLSTMVSK
       :..::  .::: .  .  . .:: . . :. :. . .:     ::....   .   ::  
NR_SC: GLVPLVPYFFVSDVGTGLIYSIIVMVVTLFWFGYVKTKLSMGSGSSTSKKVTEGVEMVVV
        250       260       270       280       290       300      

          2250  
5X_189 RTTGVSSSW
         ......:
NR_SC: GGVAAGAAW
        310     




7972 residues in 1 query   sequences
4215311 residues in 9190 library sequences
 Scomplib [34t10]
 start: Tue Jan  8 20:41:56 2002 done: Tue Jan  8 20:43:22 2002
 Scan time: 25.790 Display time: 58.770

Function used was FASTXY [version 3.4t07 Nov 21, 2001]
BioPerl-1.007002/t/data/8HVP.pdb000444000766000024     44671013155576321 16160 0ustar00cjfieldsstaff000000000000HEADER    HYDROLASE(ACID PROTEINASE)              26-OCT-90   8HVP      8HVP   2
COMPND    HIV-1 PROTEASE (HIV-1 PR) COMPLEX WITH INHIBITOR              8HVP   3
COMPND   2 VAL-SER-GLN-ASN-LEU-PSI(CH(OH)-CH2)-VAL-ILE-VAL (U-85548E)   8HVP   4
SOURCE    SYNTHETIC, BASED ON SEQUENCE FROM HUMAN (HOMO SAPIENS)        8HVP   5
SOURCE   2 IMMUNODEFICIENCY VIRUS TYPE 1 PROTEASE                       8HVP   6
AUTHOR    M.JASKOLSKI,M.MILLER,A.G.TOMASSELLI,T.K.SAWYER,D.G.STAPLES,   8HVP   7
AUTHOR   2 R.L.HEINRIKSON,J.SCHNEIDER,S.B.H.KENT,A.WLODAWER             8HVP   8
REVDAT   1   31-OCT-93 8HVP    0                                        8HVP   9
JRNL        AUTH   M.JASKOLSKI,A.G.TOMASSELLI,T.K.SAWYER,D.G.STAPLES,   8HVP  10
JRNL        AUTH 2 R.L.HEINRIKSON,J.SCHNEIDER,S.B.H.KENT,A.WLODAWER     8HVP  11
JRNL        TITL   STRUCTURE AT 2.5-*ANGSTROMS RESOLUTION OF            8HVP  12
JRNL        TITL 2 CHEMICALLY SYNTHESIZED HUMAN IMMUNODEFICIENCY VIRUS  8HVP  13
JRNL        TITL 3 TYPE 1 PROTEASE COMPLEXED WITH A                     8HVP  14
JRNL        TITL 4 HYDROXYETHYLENE*-BASED INHIBITOR                     8HVP  15
JRNL        REF    BIOCHEMISTRY                  V.  30  1600 1991      8HVP  16
JRNL        REFN   ASTM BICHAW  US ISSN 0006-2960                  033  8HVP  17
REMARK   1                                                              8HVP  18
REMARK   1 REFERENCE 1                                                  8HVP  19
REMARK   1  AUTH   A.WLODAWER,M.MILLER,M.JASKOLSKI,B.K.SATHYANARAYANA,  8HVP  20
REMARK   1  AUTH 2 E.BALDWIN,I.T.WEBER,L.M.SELK,L.CLAWSON,J.SCHNEIDER,  8HVP  21
REMARK   1  AUTH 3 S.B.H.KENT                                           8HVP  22
REMARK   1  TITL   CONSERVED FOLDING IN RETROVIRAL PROTEASES. CRYSTAL   8HVP  23
REMARK   1  TITL 2 STRUCTURE OF A SYNTHETIC /HIV$-1 PROTEASE            8HVP  24
REMARK   1  REF    SCIENCE                       V. 245   616 1989      8HVP  25
REMARK   1  REFN   ASTM SCIEAS  US ISSN 0036-8075                  038  8HVP  26
REMARK   1 REFERENCE 2                                                  8HVP  27
REMARK   1  AUTH   I.T.WEBER,M.MILLER,M.JASKOLSKI,J.LEIS,A.M.SKALKA,    8HVP  28
REMARK   1  AUTH 2 A.WLODAWER                                           8HVP  29
REMARK   1  TITL   MOLECULAR MODELING OF THE /HIV$-1 PROTEASE AND ITS   8HVP  30
REMARK   1  TITL 2 SUBSTRATE BINDING SITE                               8HVP  31
REMARK   1  REF    SCIENCE                       V. 243   928 1989      8HVP  32
REMARK   1  REFN   ASTM SCIEAS  US ISSN 0036-8075                  038  8HVP  33
REMARK   1 REFERENCE 3                                                  8HVP  34
REMARK   1  AUTH   M.MILLER,M.JASKOLSKI,J.K.M.RAO,J.LEIS,A.WLODAWER     8HVP  35
REMARK   1  TITL   CRYSTAL STRUCTURE OF A RETROVIRAL PROTEASE PROVES    8HVP  36
REMARK   1  TITL 2 RELATIONSHIP TO ASPARTIC PROTEASE FAMILY             8HVP  37
REMARK   1  REF    NATURE                        V. 337   576 1989      8HVP  38
REMARK   1  REFN   ASTM NATUAS  UK ISSN 0028-0836                  006  8HVP  39
REMARK   1 REFERENCE 4                                                  8HVP  40
REMARK   1  AUTH   J.SCHNEIDER,S.B.H.KENT                               8HVP  41
REMARK   1  TITL   ENZYMATIC ACTIVITY OF A SYNTHETIC 99 RESIDUE         8HVP  42
REMARK   1  TITL 2 PROTEIN CORRESPONDING TO THE PUTATIVE /HIV$-1        8HVP  43
REMARK   1  TITL 3 PROTEASE                                             8HVP  44
REMARK   1  REF    CELL(CAMBRIDGE,MASS.)         V.  54   363 1988      8HVP  45
REMARK   1  REFN   ASTM CELLB5  US ISSN 0092-8674                  998  8HVP  46
REMARK   2                                                              8HVP  47
REMARK   2 RESOLUTION. 2.5  ANGSTROMS.                                  8HVP  48
REMARK   3                                                              8HVP  49
REMARK   3 REFINEMENT. REFINEMENT BY THE                                8HVP  50
REMARK   3  RESTRAINED LEAST-SQUARES PROCEDURE OF J. KONNERT AND W.     8HVP  51
REMARK   3  HENDRICKSON (PROGRAM *PROFFT*).  THE R VALUE IS 0.138 FOR   8HVP  52
REMARK   3  4768 REFLECTIONS IN THE RESOLUTION RANGE 10 TO 2.5          8HVP  53
REMARK   3  ANGSTROMS.                                                  8HVP  54
REMARK   3                                                              8HVP  55
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF             8HVP  56
REMARK   3      SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED          8HVP  57
REMARK   3      STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE         8HVP  58
REMARK   3      WEIGHTS OF THE CORRESPONDING RESTRAINTS)                8HVP  59
REMARK   3    DISTANCE RESTRAINTS (ANGSTROMS)                           8HVP  60
REMARK   3      BOND DISTANCE                            0.014(0.018)   8HVP  61
REMARK   3      ANGLE DISTANCE                           0.053(0.035)   8HVP  62
REMARK   3      PLANAR 1-4 DISTANCE                      0.067(0.050)   8HVP  63
REMARK   3    PLANE RESTRAINT (ANGSTROMS)                0.020(0.025)   8HVP  64
REMARK   3    CHIRAL-CENTER RESTRAINT (ANGSTROMS**3)     0.179(0.150)   8HVP  65
REMARK   3    NON-BONDED CONTACT RESTRAINTS (ANGSTROMS)                 8HVP  66
REMARK   3      SINGLE TORSION CONTACT                   0.217(0.300)   8HVP  67
REMARK   3      MULTIPLE TORSION CONTACT                 0.264(0.300)   8HVP  68
REMARK   3      POSSIBLE HYDROGEN BOND                   0.306(0.300)   8HVP  69
REMARK   3    CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES)          8HVP  70
REMARK   3      PLANAR (OMEGA)                             3.7(4.0)     8HVP  71
REMARK   3      STAGGERED                                 20.0(10.0)    8HVP  72
REMARK   3      ORTHONORMAL                               18.2(20.0)    8HVP  73
REMARK   3    ISOTROPIC THERMAL FACTOR RESTRAINTS (ANGSTROMS**2)        8HVP  74
REMARK   3      MAIN-CHAIN BOND                          2.449(3.000)   8HVP  75
REMARK   3      MAIN-CHAIN ANGLE                         3.577(3.500)   8HVP  76
REMARK   3      SIDE-CHAIN BOND                          6.239(5.000)   8HVP  77
REMARK   3      SIDE-CHAIN ANGLE                         8.633(8.000)   8HVP  78
REMARK   3      HYDROGEN BOND                           12.014(25.000)  8HVP  79
REMARK   4                                                              8HVP  80
REMARK   4 THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND     8HVP  81
REMARK   4 C-TERMINI FROM BOTH SUBUNITS FORMING A FOUR-STRANDED         8HVP  82
REMARK   4 ANTIPARALLEL BETA-SHEET.                                     8HVP  83
REMARK   5                                                              8HVP  84
REMARK   5 THE PEPTIDE BOND BETWEEN RESIDUES LEU I 5 AND VAL I 6 HAS    8HVP  85
REMARK   5 BEEN REPLACED BY A HYDROXYETHYLENE GROUP CH(OH)-CH2.  THESE  8HVP  86
REMARK   5 RESIDUES HAVE BEEN RENAMED AS LOV I 5 TO DENOTE THIS         8HVP  87
REMARK   5 MODIFICATION.                                                8HVP  88
SEQRES   1 A   99  PRO GLN ILE THR LEU TRP GLN ARG PRO LEU VAL THR ILE  8HVP  89
SEQRES   2 A   99  ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR  8HVP  90
SEQRES   3 A   99  GLY ALA ASP ASP THR VAL LEU GLU GLU MET ASN LEU PRO  8HVP  91
SEQRES   4 A   99  GLY LYS TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY  8HVP  92
SEQRES   5 A   99  PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO VAL GLU  8HVP  93
SEQRES   6 A   99  ILE ABA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY  8HVP  94
SEQRES   7 A   99  PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR  8HVP  95
SEQRES   8 A   99  GLN ILE GLY ABA THR LEU ASN PHE                      8HVP  96
SEQRES   1 B   99  PRO GLN ILE THR LEU TRP GLN ARG PRO LEU VAL THR ILE  8HVP  97
SEQRES   2 B   99  ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR  8HVP  98
SEQRES   3 B   99  GLY ALA ASP ASP THR VAL LEU GLU GLU MET ASN LEU PRO  8HVP  99
SEQRES   4 B   99  GLY LYS TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY  8HVP 100
SEQRES   5 B   99  PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO VAL GLU  8HVP 101
SEQRES   6 B   99  ILE ABA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY  8HVP 102
SEQRES   7 B   99  PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR  8HVP 103
SEQRES   8 B   99  GLN ILE GLY ABA THR LEU ASN PHE                      8HVP 104
SEQRES   1 I    7  VAL SER GLN ASN LOV ILE VAL                          8HVP 105
FTNOTE   1                                                              8HVP 106
FTNOTE   1 THE INHIBITOR RESIDUE LOV I 5 IS LEU-VAL WITH THE PEPTIDE    8HVP 107
FTNOTE   1 BOND REPLACED BY CHOH-CH2.                                   8HVP 108
HET    ABA  A  67       6     ALPHA-AMINO-N-BUTYRIC ACID                8HVP 109
HET    ABA  A  95       6     ALPHA-AMINO-N-BUTYRIC ACID                8HVP 110
HET    ABA  B  67       6     ALPHA-AMINO-N-BUTYRIC ACID                8HVP 111
HET    ABA  B  95       6     ALPHA-AMINO-N-BUTYRIC ACID                8HVP 112
HET    LOV  I   5      15     LEU-PSI(CHOH-CH2)-VAL                     8HVP 113
FORMUL   1  ABA    2(C4 H9 N1 O2)                                       8HVP 114
FORMUL   2  ABA    2(C4 H9 N1 O2)                                       8HVP 115
FORMUL   3  LOV    C12 H21 N1 O2                                        8HVP 116
FORMUL   4  HOH   *80(H2 O1)                                            8HVP 117
HELIX    1  HA GLY A   86  GLY A   94  1                                8HVP 118
HELIX    2  HB GLY B   86  GLY B   94  1                                8HVP 119
SHEET    1 COA 8 LYS A  43  GLY A  49  0                                8HVP 120
SHEET    2 COA 8 GLY A  52  ILE A  66 -1                                8HVP 121
SHEET    3 COA 8 HIS A  69  GLY A  78 -1                                8HVP 122
SHEET    4 COA 8 THR A  31  GLU A  34  1                                8HVP 123
SHEET    5 COA 8 ASN A  83  ILE A  85 -1                                8HVP 124
SHEET    6 COA 8 GLN A  18  ASP A  25  1                                8HVP 125
SHEET    7 COA 8 PRO A   9  ILE A  15 -1                                8HVP 126
SHEET    8 COA 8 GLU A  65  ILE A  66 -1                                8HVP 127
SHEET    1 COB 8 LYS B  43  GLY B  49  0                                8HVP 128
SHEET    2 COB 8 GLY B  52  ILE B  66 -1                                8HVP 129
SHEET    3 COB 8 HIS B  69  GLY B  78 -1                                8HVP 130
SHEET    4 COB 8 THR B  31  GLU B  34  1                                8HVP 131
SHEET    5 COB 8 ASN B  83  ILE B  85 -1                                8HVP 132
SHEET    6 COB 8 GLN B  18  ASP B  25  1                                8HVP 133
SHEET    7 COB 8 PRO B   9  ILE B  15 -1                                8HVP 134
SHEET    8 COB 8 GLU B  65  ILE B  66 -1                                8HVP 135
SHEET    1 INT 4 PRO A   1  THR A   4  0                                8HVP 136
SHEET    2 INT 4 THR B  96  PHE B  99 -1                                8HVP 137
SHEET    3 INT 4 THR A  96  PHE A  99 -1                                8HVP 138
SHEET    4 INT 4 PRO B   1  THR B   4 -1                                8HVP 139
TURN     1 S1A GLY A  16  GLN A  18     SURFACE                         8HVP 140
TURN     2 FLA ILE A  50  GLY A  52     FLAP                            8HVP 141
TURN     3 S2A ILE A  66  HIS A  69     SURFACE                         8HVP 142
TURN     4 S1B GLY B  16  GLN B  18     SURFACE                         8HVP 143
TURN     5 FLB ILE B  50  GLY B  52     FLAP                            8HVP 144
TURN     6 S2B ILE B  66  HIS B  69     SURFACE                         8HVP 145
SITE     1 DTA  3 ASP A  25  THR A  26  GLY A  27                       8HVP 146
SITE     1 DTB  3 ASP B  25  THR B  26  GLY B  27                       8HVP 147
CRYST1   51.650   58.760   61.620  90.00  90.00  90.00 P 21 21 21    4  8HVP 148
ORIGX1      1.000000  0.000000  0.000000        0.00000                 8HVP 149
ORIGX2      0.000000  1.000000  0.000000        0.00000                 8HVP 150
ORIGX3      0.000000  0.000000  1.000000        0.00000                 8HVP 151
SCALE1      0.019361  0.000000  0.000000        0.00000                 8HVP 152
SCALE2      0.000000  0.017018  0.000000        0.00000                 8HVP 153
SCALE3      0.000000  0.000000  0.016228        0.00000                 8HVP 154
ATOM      1  N   PRO A   1      -2.473   7.901  33.687  1.00  4.25      8HVP 155
ATOM      2  CA  PRO A   1      -1.739   6.714  34.100  1.00  4.33      8HVP 156
ATOM      3  C   PRO A   1      -0.269   6.799  33.769  1.00  9.25      8HVP 157
ATOM      4  O   PRO A   1      -0.005   7.325  32.661  1.00 12.86      8HVP 158
ATOM      5  CB  PRO A   1      -2.443   5.724  33.177  1.00  2.00      8HVP 159
ATOM      6  CG  PRO A   1      -3.860   6.187  32.991  1.00  2.00      8HVP 160
ATOM      7  CD  PRO A   1      -3.897   7.440  33.874  1.00  5.50      8HVP 161
ATOM      8  N   GLN A   2       0.530   6.256  34.695  1.00 10.03      8HVP 162
ATOM      9  CA  GLN A   2       1.979   6.233  34.355  1.00 13.56      8HVP 163
ATOM     10  C   GLN A   2       2.193   4.743  34.046  1.00 13.76      8HVP 164
ATOM     11  O   GLN A   2       1.946   3.952  34.978  1.00 18.02      8HVP 165
ATOM     12  CB  GLN A   2       2.943   6.797  35.362  1.00 16.19      8HVP 166
ATOM     13  CG  GLN A   2       4.417   6.732  34.939  1.00 23.62      8HVP 167
ATOM     14  CD  GLN A   2       5.358   7.151  36.052  1.00 25.05      8HVP 168
ATOM     15  OE1 GLN A   2       5.681   8.310  36.371  1.00 26.46      8HVP 169
ATOM     16  NE2 GLN A   2       5.839   6.106  36.720  1.00  9.24      8HVP 170
ATOM     17  N   ILE A   3       2.514   4.430  32.820  1.00  9.51      8HVP 171
ATOM     18  CA  ILE A   3       2.669   3.034  32.417  1.00  3.63      8HVP 172
ATOM     19  C   ILE A   3       4.120   2.826  31.951  1.00  2.00      8HVP 173
ATOM     20  O   ILE A   3       4.386   3.445  30.877  1.00  2.00      8HVP 174
ATOM     21  CB  ILE A   3       1.767   2.617  31.198  1.00  3.69      8HVP 175
ATOM     22  CG1 ILE A   3       0.258   2.901  31.456  1.00 10.88      8HVP 176
ATOM     23  CG2 ILE A   3       1.934   1.127  30.775  1.00  2.00      8HVP 177
ATOM     24  CD1 ILE A   3      -0.505   2.898  30.060  1.00  2.00      8HVP 178
ATOM     25  N   THR A   4       4.824   1.984  32.617  1.00  2.00      8HVP 179
ATOM     26  CA  THR A   4       6.176   1.497  32.422  1.00  2.00      8HVP 180
ATOM     27  C   THR A   4       6.348   0.565  31.229  1.00  2.00      8HVP 181
ATOM     28  O   THR A   4       5.347  -0.027  30.769  1.00  2.00      8HVP 182
ATOM     29  CB  THR A   4       6.444   0.709  33.777  1.00  8.70      8HVP 183
ATOM     30  OG1 THR A   4       5.107   0.099  33.936  1.00 16.25      8HVP 184
ATOM     31  CG2 THR A   4       6.918   1.568  34.954  1.00 15.09      8HVP 185
ATOM     32  N   LEU A   5       7.603   0.350  30.815  1.00  2.00      8HVP 186
ATOM     33  CA  LEU A   5       7.782  -0.501  29.624  1.00  2.00      8HVP 187
ATOM     34  C   LEU A   5       8.206  -1.934  29.728  1.00  2.00      8HVP 188
ATOM     35  O   LEU A   5       8.198  -2.583  28.652  1.00  2.00      8HVP 189
ATOM     36  CB  LEU A   5       8.554   0.400  28.653  1.00  2.11      8HVP 190
ATOM     37  CG  LEU A   5       7.838   1.671  28.247  1.00 13.00      8HVP 191
ATOM     38  CD1 LEU A   5       8.765   2.681  27.561  1.00 15.68      8HVP 192
ATOM     39  CD2 LEU A   5       6.655   1.336  27.358  1.00  9.29      8HVP 193
ATOM     40  N   TRP A   6       8.464  -2.513  30.877  1.00  2.00      8HVP 194
ATOM     41  CA  TRP A   6       8.824  -3.837  31.313  1.00  2.00      8HVP 195
ATOM     42  C   TRP A   6       7.847  -4.872  30.752  1.00  2.00      8HVP 196
ATOM     43  O   TRP A   6       8.306  -6.024  30.814  1.00  2.00      8HVP 197
ATOM     44  CB  TRP A   6       8.899  -4.179  32.830  1.00 12.98      8HVP 198
ATOM     45  CG  TRP A   6       9.272  -3.021  33.684  1.00 21.96      8HVP 199
ATOM     46  CD1 TRP A   6       8.422  -2.112  34.276  1.00 30.51      8HVP 200
ATOM     47  CD2 TRP A   6      10.596  -2.571  33.963  1.00 18.88      8HVP 201
ATOM     48  NE1 TRP A   6       9.134  -1.114  34.904  1.00 33.17      8HVP 202
ATOM     49  CE2 TRP A   6      10.473  -1.376  34.713  1.00 28.60      8HVP 203
ATOM     50  CE3 TRP A   6      11.850  -3.073  33.668  1.00 17.70      8HVP 204
ATOM     51  CZ2 TRP A   6      11.587  -0.673  35.140  1.00 25.35      8HVP 205
ATOM     52  CZ3 TRP A   6      12.971  -2.388  34.070  1.00 16.22      8HVP 206
ATOM     53  CH2 TRP A   6      12.816  -1.205  34.770  1.00 24.66      8HVP 207
ATOM     54  N   GLN A   7       6.701  -4.474  30.281  1.00  3.35      8HVP 208
ATOM     55  CA  GLN A   7       5.777  -5.391  29.605  1.00  4.83      8HVP 209
ATOM     56  C   GLN A   7       5.131  -4.473  28.544  1.00  6.60      8HVP 210
ATOM     57  O   GLN A   7       5.124  -3.274  28.779  1.00 10.09      8HVP 211
ATOM     58  CB  GLN A   7       4.599  -5.998  30.279  1.00 15.11      8HVP 212
ATOM     59  CG  GLN A   7       4.607  -7.028  31.358  1.00 25.54      8HVP 213
ATOM     60  CD  GLN A   7       3.219  -7.169  31.970  1.00 27.66      8HVP 214
ATOM     61  OE1 GLN A   7       2.758  -6.275  32.677  1.00 34.29      8HVP 215
ATOM     62  NE2 GLN A   7       2.530  -8.274  31.717  1.00 33.00      8HVP 216
ATOM     63  N   ARG A   8       4.599  -5.119  27.534  1.00 10.31      8HVP 217
ATOM     64  CA  ARG A   8       3.859  -4.416  26.470  1.00  7.99      8HVP 218
ATOM     65  C   ARG A   8       2.767  -3.614  27.169  1.00  9.42      8HVP 219
ATOM     66  O   ARG A   8       2.109  -4.182  28.074  1.00 10.32      8HVP 220
ATOM     67  CB  ARG A   8       3.114  -5.384  25.554  1.00  2.44      8HVP 221
ATOM     68  CG  ARG A   8       4.035  -6.115  24.616  1.00  7.69      8HVP 222
ATOM     69  CD  ARG A   8       3.548  -7.457  24.224  1.00 10.72      8HVP 223
ATOM     70  NE  ARG A   8       4.459  -7.893  23.140  1.00 17.94      8HVP 224
ATOM     71  CZ  ARG A   8       4.365  -9.137  22.652  1.00 24.69      8HVP 225
ATOM     72  NH1 ARG A   8       3.648 -10.046  23.327  1.00 28.41      8HVP 226
ATOM     73  NH2 ARG A   8       4.780  -9.377  21.409  1.00 16.19      8HVP 227
ATOM     74  N   PRO A   9       2.644  -2.399  26.655  1.00  8.38      8HVP 228
ATOM     75  CA  PRO A   9       1.582  -1.480  27.170  1.00  4.47      8HVP 229
ATOM     76  C   PRO A   9       0.252  -1.823  26.524  1.00  6.26      8HVP 230
ATOM     77  O   PRO A   9      -0.263  -1.296  25.504  1.00  5.60      8HVP 231
ATOM     78  CB  PRO A   9       2.282  -0.150  26.990  1.00  2.17      8HVP 232
ATOM     79  CG  PRO A   9       3.222  -0.285  25.805  1.00  2.00      8HVP 233
ATOM     80  CD  PRO A   9       3.440  -1.777  25.604  1.00  2.00      8HVP 234
ATOM     81  N   LEU A  10      -0.348  -2.883  27.099  1.00  6.46      8HVP 235
ATOM     82  CA  LEU A  10      -1.701  -3.352  26.712  1.00 10.06      8HVP 236
ATOM     83  C   LEU A  10      -2.741  -2.850  27.746  1.00  6.81      8HVP 237
ATOM     84  O   LEU A  10      -2.726  -3.162  28.930  1.00  8.01      8HVP 238
ATOM     85  CB  LEU A  10      -1.805  -4.859  26.486  1.00 11.47      8HVP 239
ATOM     86  CG  LEU A  10      -1.168  -5.664  25.387  1.00  6.53      8HVP 240
ATOM     87  CD1 LEU A  10      -1.627  -7.116  25.317  1.00  3.53      8HVP 241
ATOM     88  CD2 LEU A  10      -1.448  -5.076  24.022  1.00  3.83      8HVP 242
ATOM     89  N   VAL A  11      -3.704  -2.079  27.315  1.00 10.23      8HVP 243
ATOM     90  CA  VAL A  11      -4.870  -1.494  28.000  1.00 10.17      8HVP 244
ATOM     91  C   VAL A  11      -6.200  -1.883  27.305  1.00 10.78      8HVP 245
ATOM     92  O   VAL A  11      -6.155  -2.128  26.085  1.00  8.04      8HVP 246
ATOM     93  CB  VAL A  11      -4.647   0.027  28.000  1.00  2.00      8HVP 247
ATOM     94  CG1 VAL A  11      -3.356   0.398  28.688  1.00  2.00      8HVP 248
ATOM     95  CG2 VAL A  11      -4.777   0.526  26.562  1.00  2.00      8HVP 249
ATOM     96  N   THR A  12      -7.321  -1.952  28.016  1.00  9.58      8HVP 250
ATOM     97  CA  THR A  12      -8.636  -2.332  27.473  1.00  9.66      8HVP 251
ATOM     98  C   THR A  12      -9.284  -1.117  26.787  1.00  6.66      8HVP 252
ATOM     99  O   THR A  12      -9.279  -0.073  27.455  1.00  7.20      8HVP 253
ATOM    100  CB  THR A  12      -9.705  -2.879  28.514  1.00  4.40      8HVP 254
ATOM    101  OG1 THR A  12      -9.016  -3.028  29.802  1.00  6.88      8HVP 255
ATOM    102  CG2 THR A  12     -10.282  -4.234  28.065  1.00  2.00      8HVP 256
ATOM    103  N   ILE A  13      -9.821  -1.318  25.613  1.00  6.50      8HVP 257
ATOM    104  CA  ILE A  13     -10.428  -0.306  24.756  1.00  5.69      8HVP 258
ATOM    105  C   ILE A  13     -11.897  -0.668  24.616  1.00  6.09      8HVP 259
ATOM    106  O   ILE A  13     -12.166  -1.865  24.447  1.00 11.04      8HVP 260
ATOM    107  CB  ILE A  13      -9.658  -0.150  23.397  1.00  6.87      8HVP 261
ATOM    108  CG1 ILE A  13     -10.082  -0.976  22.187  1.00  2.00      8HVP 262
ATOM    109  CG2 ILE A  13      -8.149  -0.446  23.606  1.00  2.63      8HVP 263
ATOM    110  CD1 ILE A  13      -9.521  -0.698  20.775  1.00  2.00      8HVP 264
ATOM    111  N   ARG A  14     -12.800   0.270  24.732  1.00  4.95      8HVP 265
ATOM    112  CA  ARG A  14     -14.234   0.099  24.650  1.00  2.00      8HVP 266
ATOM    113  C   ARG A  14     -14.585   0.804  23.314  1.00  2.00      8HVP 267
ATOM    114  O   ARG A  14     -14.408   2.018  23.365  1.00  7.49      8HVP 268
ATOM    115  CB  ARG A  14     -15.240   0.751  25.610  1.00  2.00      8HVP 269
ATOM    116  CG  ARG A  14     -16.495  -0.153  25.613  1.00 13.07      8HVP 270
ATOM    117  CD  ARG A  14     -17.390   0.154  26.767  1.00 25.60      8HVP 271
ATOM    118  NE  ARG A  14     -17.828   1.546  26.751  1.00 36.29      8HVP 272
ATOM    119  CZ  ARG A  14     -18.341   2.165  25.680  1.00 36.27      8HVP 273
ATOM    120  NH1 ARG A  14     -18.644   1.522  24.555  1.00 34.49      8HVP 274
ATOM    121  NH2 ARG A  14     -18.324   3.505  25.698  1.00 36.80      8HVP 275
ATOM    122  N   ILE A  15     -14.972  -0.035  22.412  1.00  8.77      8HVP 276
ATOM    123  CA  ILE A  15     -15.300   0.406  21.054  1.00  3.96      8HVP 277
ATOM    124  C   ILE A  15     -16.698  -0.064  20.662  1.00  8.76      8HVP 278
ATOM    125  O   ILE A  15     -16.961  -1.125  20.072  1.00  8.48      8HVP 279
ATOM    126  CB  ILE A  15     -14.189  -0.175  20.117  1.00  4.59      8HVP 280
ATOM    127  CG1 ILE A  15     -14.445   0.353  18.694  1.00  2.67      8HVP 281
ATOM    128  CG2 ILE A  15     -14.116  -1.716  20.057  1.00  8.19      8HVP 282
ATOM    129  CD1 ILE A  15     -13.982   1.820  18.564  1.00 19.57      8HVP 283
ATOM    130  N   GLY A  16     -17.652   0.774  21.052  1.00 11.70      8HVP 284
ATOM    131  CA  GLY A  16     -19.075   0.587  20.773  1.00 12.24      8HVP 285
ATOM    132  C   GLY A  16     -19.543  -0.807  21.211  1.00 11.42      8HVP 286
ATOM    133  O   GLY A  16     -19.625  -1.776  20.426  1.00 13.44      8HVP 287
ATOM    134  N   GLY A  17     -19.839  -0.786  22.503  1.00  7.14      8HVP 288
ATOM    135  CA  GLY A  17     -20.345  -1.959  23.199  1.00  7.99      8HVP 289
ATOM    136  C   GLY A  17     -19.544  -3.205  22.882  1.00  7.25      8HVP 290
ATOM    137  O   GLY A  17     -20.097  -4.287  22.977  1.00  8.85      8HVP 291
ATOM    138  N   GLN A  18     -18.286  -3.052  22.572  1.00  9.70      8HVP 292
ATOM    139  CA  GLN A  18     -17.295  -4.100  22.321  1.00  8.42      8HVP 293
ATOM    140  C   GLN A  18     -16.040  -3.785  23.133  1.00  2.58      8HVP 294
ATOM    141  O   GLN A  18     -15.570  -2.635  23.044  1.00  7.27      8HVP 295
ATOM    142  CB  GLN A  18     -16.983  -4.271  20.825  1.00 15.99      8HVP 296
ATOM    143  CG  GLN A  18     -18.009  -5.084  20.044  1.00 18.33      8HVP 297
ATOM    144  CD  GLN A  18     -18.240  -6.375  20.808  1.00 30.10      8HVP 298
ATOM    145  OE1 GLN A  18     -17.295  -6.798  21.495  1.00 33.38      8HVP 299
ATOM    146  NE2 GLN A  18     -19.461  -6.908  20.792  1.00 30.23      8HVP 300
ATOM    147  N   LEU A  19     -15.525  -4.704  23.914  1.00  2.00      8HVP 301
ATOM    148  CA  LEU A  19     -14.294  -4.432  24.669  1.00  2.00      8HVP 302
ATOM    149  C   LEU A  19     -13.078  -5.133  24.062  1.00  3.47      8HVP 303
ATOM    150  O   LEU A  19     -13.214  -6.341  23.784  1.00  6.90      8HVP 304
ATOM    151  CB  LEU A  19     -14.544  -4.830  26.126  1.00  5.54      8HVP 305
ATOM    152  CG  LEU A  19     -15.446  -3.905  26.934  1.00 12.65      8HVP 306
ATOM    153  CD1 LEU A  19     -15.808  -4.594  28.261  1.00 11.26      8HVP 307
ATOM    154  CD2 LEU A  19     -14.638  -2.638  27.230  1.00 11.67      8HVP 308
ATOM    155  N   LYS A  20     -11.926  -4.503  23.901  1.00  3.26      8HVP 309
ATOM    156  CA  LYS A  20     -10.754  -5.222  23.378  1.00  4.92      8HVP 310
ATOM    157  C   LYS A  20      -9.509  -4.758  24.142  1.00  7.51      8HVP 311
ATOM    158  O   LYS A  20      -9.547  -3.736  24.811  1.00  9.95      8HVP 312
ATOM    159  CB  LYS A  20     -10.492  -5.064  21.911  1.00  2.00      8HVP 313
ATOM    160  CG  LYS A  20     -11.596  -4.904  20.908  1.00  2.81      8HVP 314
ATOM    161  CD  LYS A  20     -12.439  -6.133  20.701  1.00 14.45      8HVP 315
ATOM    162  CE  LYS A  20     -13.681  -5.897  19.858  1.00 20.29      8HVP 316
ATOM    163  NZ  LYS A  20     -14.671  -6.960  20.258  1.00 13.89      8HVP 317
ATOM    164  N   GLU A  21      -8.450  -5.528  24.023  1.00 11.23      8HVP 318
ATOM    165  CA  GLU A  21      -7.121  -5.258  24.584  1.00 11.12      8HVP 319
ATOM    166  C   GLU A  21      -6.306  -4.595  23.490  1.00  7.90      8HVP 320
ATOM    167  O   GLU A  21      -6.198  -5.254  22.433  1.00 14.97      8HVP 321
ATOM    168  CB  GLU A  21      -6.396  -6.524  25.010  1.00 22.94      8HVP 322
ATOM    169  CG  GLU A  21      -6.511  -6.993  26.451  1.00 45.49      8HVP 323
ATOM    170  CD  GLU A  21      -6.037  -6.153  27.597  1.00 59.44      8HVP 324
ATOM    171  OE1 GLU A  21      -5.411  -5.103  27.298  1.00 66.60      8HVP 325
ATOM    172  OE2 GLU A  21      -6.236  -6.426  28.782  1.00 64.09      8HVP 326
ATOM    173  N   ALA A  22      -5.842  -3.384  23.557  1.00  4.69      8HVP 327
ATOM    174  CA  ALA A  22      -5.083  -2.822  22.433  1.00  2.00      8HVP 328
ATOM    175  C   ALA A  22      -3.771  -2.331  23.023  1.00  2.00      8HVP 329
ATOM    176  O   ALA A  22      -3.717  -2.079  24.211  1.00  2.00      8HVP 330
ATOM    177  CB  ALA A  22      -5.778  -1.670  21.762  1.00  2.00      8HVP 331
ATOM    178  N   LEU A  23      -2.856  -2.120  22.138  1.00  2.17      8HVP 332
ATOM    179  CA  LEU A  23      -1.487  -1.667  22.382  1.00  6.32      8HVP 333
ATOM    180  C   LEU A  23      -1.200  -0.210  22.007  1.00  2.87      8HVP 334
ATOM    181  O   LEU A  23      -1.368   0.186  20.853  1.00  2.00      8HVP 335
ATOM    182  CB  LEU A  23      -0.598  -2.622  21.548  1.00  5.69      8HVP 336
ATOM    183  CG  LEU A  23       0.896  -2.607  21.807  1.00 12.05      8HVP 337
ATOM    184  CD1 LEU A  23       1.271  -3.607  22.904  1.00  7.79      8HVP 338
ATOM    185  CD2 LEU A  23       1.656  -2.921  20.509  1.00  2.00      8HVP 339
ATOM    186  N   LEU A  24      -0.718   0.497  23.015  1.00  3.16      8HVP 340
ATOM    187  CA  LEU A  24      -0.279   1.898  22.890  1.00  3.72      8HVP 341
ATOM    188  C   LEU A  24       1.112   1.953  22.222  1.00  3.04      8HVP 342
ATOM    189  O   LEU A  24       2.176   1.939  22.804  1.00  2.00      8HVP 343
ATOM    190  CB  LEU A  24      -0.197   2.459  24.308  1.00  2.00      8HVP 344
ATOM    191  CG  LEU A  24      -1.339   2.182  25.232  1.00  2.07      8HVP 345
ATOM    192  CD1 LEU A  24      -0.927   2.514  26.671  1.00  4.92      8HVP 346
ATOM    193  CD2 LEU A  24      -2.489   2.999  24.687  1.00  2.00      8HVP 347
ATOM    194  N   ASP A  25       1.103   1.961  20.945  1.00  2.09      8HVP 348
ATOM    195  CA  ASP A  25       2.174   1.976  19.989  1.00  2.00      8HVP 349
ATOM    196  C   ASP A  25       2.377   3.416  19.493  1.00  3.53      8HVP 350
ATOM    197  O   ASP A  25       1.640   3.918  18.627  1.00  2.00      8HVP 351
ATOM    198  CB  ASP A  25       1.836   0.942  18.934  1.00  2.00      8HVP 352
ATOM    199  CG  ASP A  25       2.875   0.696  17.889  1.00 15.58      8HVP 353
ATOM    200  OD1 ASP A  25       4.067   1.036  18.055  1.00 20.52      8HVP 354
ATOM    201  OD2 ASP A  25       2.571   0.117  16.827  1.00 21.05      8HVP 355
ATOM    202  N   THR A  26       3.380   4.060  20.113  1.00  2.00      8HVP 356
ATOM    203  CA  THR A  26       3.768   5.394  19.656  1.00  5.15      8HVP 357
ATOM    204  C   THR A  26       4.638   5.366  18.381  1.00  6.87      8HVP 358
ATOM    205  O   THR A  26       5.138   6.438  17.990  1.00  7.76      8HVP 359
ATOM    206  CB  THR A  26       4.647   6.055  20.772  1.00  2.00      8HVP 360
ATOM    207  OG1 THR A  26       5.776   5.124  20.726  1.00 17.12      8HVP 361
ATOM    208  CG2 THR A  26       3.999   6.139  22.139  1.00  3.59      8HVP 362
ATOM    209  N   GLY A  27       4.828   4.213  17.743  1.00  5.41      8HVP 363
ATOM    210  CA  GLY A  27       5.606   4.072  16.516  1.00  2.00      8HVP 364
ATOM    211  C   GLY A  27       4.672   3.955  15.314  1.00  2.00      8HVP 365
ATOM    212  O   GLY A  27       5.098   3.911  14.154  1.00  2.00      8HVP 366
ATOM    213  N   ALA A  28       3.413   3.936  15.597  1.00  2.00      8HVP 367
ATOM    214  CA  ALA A  28       2.284   3.786  14.690  1.00  2.00      8HVP 368
ATOM    215  C   ALA A  28       1.672   5.159  14.463  1.00  2.00      8HVP 369
ATOM    216  O   ALA A  28       1.406   5.901  15.423  1.00  2.25      8HVP 370
ATOM    217  CB  ALA A  28       1.255   2.844  15.307  1.00  2.00      8HVP 371
ATOM    218  N   ASP A  29       1.436   5.455  13.207  1.00  2.00      8HVP 372
ATOM    219  CA  ASP A  29       0.844   6.762  12.826  1.00  2.00      8HVP 373
ATOM    220  C   ASP A  29      -0.661   6.737  13.095  1.00  2.61      8HVP 374
ATOM    221  O   ASP A  29      -1.276   7.740  13.500  1.00  3.70      8HVP 375
ATOM    222  CB  ASP A  29       1.148   6.901  11.319  1.00  2.00      8HVP 376
ATOM    223  CG  ASP A  29       2.630   7.176  11.147  1.00  9.16      8HVP 377
ATOM    224  OD1 ASP A  29       3.604   6.862  11.837  1.00 11.36      8HVP 378
ATOM    225  OD2 ASP A  29       2.799   7.898  10.186  1.00  2.00      8HVP 379
ATOM    226  N   ASP A  30      -1.221   5.573  12.797  1.00  2.00      8HVP 380
ATOM    227  CA  ASP A  30      -2.617   5.259  12.873  1.00  3.29      8HVP 381
ATOM    228  C   ASP A  30      -2.903   4.122  13.882  1.00  3.40      8HVP 382
ATOM    229  O   ASP A  30      -1.955   3.505  14.335  1.00  2.00      8HVP 383
ATOM    230  CB  ASP A  30      -3.141   4.849  11.482  1.00 14.10      8HVP 384
ATOM    231  CG  ASP A  30      -3.037   5.898  10.398  1.00  5.79      8HVP 385
ATOM    232  OD1 ASP A  30      -3.903   6.799  10.369  1.00 15.54      8HVP 386
ATOM    233  OD2 ASP A  30      -2.104   5.769   9.590  1.00  4.06      8HVP 387
ATOM    234  N   THR A  31      -4.207   3.934  14.032  1.00  2.00      8HVP 388
ATOM    235  CA  THR A  31      -4.872   2.952  14.847  1.00  2.00      8HVP 389
ATOM    236  C   THR A  31      -5.409   1.865  13.930  1.00  3.56      8HVP 390
ATOM    237  O   THR A  31      -6.279   2.174  13.098  1.00  2.00      8HVP 391
ATOM    238  CB  THR A  31      -6.027   3.608  15.691  1.00  2.00      8HVP 392
ATOM    239  OG1 THR A  31      -5.350   4.649  16.454  1.00  4.30      8HVP 393
ATOM    240  CG2 THR A  31      -6.747   2.629  16.643  1.00  4.26      8HVP 394
ATOM    241  N   VAL A  32      -4.846   0.678  14.061  1.00  3.84      8HVP 395
ATOM    242  CA  VAL A  32      -5.180  -0.486  13.241  1.00  3.65      8HVP 396
ATOM    243  C   VAL A  32      -5.806  -1.599  14.089  1.00  5.26      8HVP 397
ATOM    244  O   VAL A  32      -5.175  -2.213  14.958  1.00  8.26      8HVP 398
ATOM    245  CB  VAL A  32      -3.978  -1.037  12.451  1.00  2.00      8HVP 399
ATOM    246  CG1 VAL A  32      -4.397  -2.340  11.729  1.00  2.00      8HVP 400
ATOM    247  CG2 VAL A  32      -3.290  -0.152  11.453  1.00  2.00      8HVP 401
ATOM    248  N   LEU A  33      -7.055  -1.927  13.825  1.00  8.12      8HVP 402
ATOM    249  CA  LEU A  33      -7.689  -3.029  14.570  1.00  9.44      8HVP 403
ATOM    250  C   LEU A  33      -7.695  -4.318  13.767  1.00 11.79      8HVP 404
ATOM    251  O   LEU A  33      -7.567  -4.386  12.525  1.00 13.91      8HVP 405
ATOM    252  CB  LEU A  33      -8.986  -2.441  15.102  1.00 13.84      8HVP 406
ATOM    253  CG  LEU A  33      -8.958  -1.273  16.070  1.00 10.78      8HVP 407
ATOM    254  CD1 LEU A  33      -9.958  -1.540  17.202  1.00 14.10      8HVP 408
ATOM    255  CD2 LEU A  33      -7.596  -1.040  16.703  1.00  8.06      8HVP 409
ATOM    256  N   GLU A  34      -7.755  -5.399  14.526  1.00 13.04      8HVP 410
ATOM    257  CA  GLU A  34      -7.818  -6.752  13.935  1.00 20.97      8HVP 411
ATOM    258  C   GLU A  34      -9.196  -6.789  13.246  1.00 26.23      8HVP 412
ATOM    259  O   GLU A  34     -10.068  -6.058  13.775  1.00 26.64      8HVP 413
ATOM    260  CB  GLU A  34      -7.809  -7.851  14.958  1.00 24.11      8HVP 414
ATOM    261  CG  GLU A  34      -6.716  -8.047  15.995  1.00 33.56      8HVP 415
ATOM    262  CD  GLU A  34      -7.117  -8.936  17.145  1.00 39.68      8HVP 416
ATOM    263  OE1 GLU A  34      -8.277  -9.103  17.521  1.00 50.11      8HVP 417
ATOM    264  OE2 GLU A  34      -6.154  -9.480  17.715  1.00 38.53      8HVP 418
ATOM    265  N   GLU A  35      -9.368  -7.573  12.190  1.00 29.97      8HVP 419
ATOM    266  CA  GLU A  35     -10.640  -7.631  11.456  1.00 30.84      8HVP 420
ATOM    267  C   GLU A  35     -11.838  -7.488  12.388  1.00 33.78      8HVP 421
ATOM    268  O   GLU A  35     -11.952  -8.112  13.465  1.00 35.01      8HVP 422
ATOM    269  CB  GLU A  35     -10.787  -8.899  10.639  1.00 37.69      8HVP 423
ATOM    270  CG  GLU A  35     -12.124  -9.032   9.878  1.00 47.54      8HVP 424
ATOM    271  CD  GLU A  35     -12.190  -8.046   8.737  1.00 54.43      8HVP 425
ATOM    272  OE1 GLU A  35     -11.147  -7.728   8.170  1.00 59.79      8HVP 426
ATOM    273  OE2 GLU A  35     -13.347  -7.647   8.490  1.00 51.62      8HVP 427
ATOM    274  N   MET A  36     -12.742  -6.600  11.998  1.00 35.17      8HVP 428
ATOM    275  CA  MET A  36     -13.938  -6.213  12.769  1.00 34.80      8HVP 429
ATOM    276  C   MET A  36     -14.900  -5.424  11.884  1.00 33.96      8HVP 430
ATOM    277  O   MET A  36     -14.593  -4.843  10.834  1.00 35.00      8HVP 431
ATOM    278  CB  MET A  36     -13.557  -5.476  14.052  1.00 39.18      8HVP 432
ATOM    279  CG  MET A  36     -14.633  -4.659  14.686  1.00 43.69      8HVP 433
ATOM    280  SD  MET A  36     -14.210  -4.109  16.366  1.00 42.64      8HVP 434
ATOM    281  CE  MET A  36     -13.318  -2.583  16.030  1.00 43.05      8HVP 435
ATOM    282  N   ASN A  37     -16.139  -5.505  12.341  1.00 33.16      8HVP 436
ATOM    283  CA  ASN A  37     -17.299  -4.872  11.708  1.00 30.97      8HVP 437
ATOM    284  C   ASN A  37     -17.597  -3.625  12.537  1.00 25.69      8HVP 438
ATOM    285  O   ASN A  37     -17.679  -3.665  13.758  1.00 24.78      8HVP 439
ATOM    286  CB  ASN A  37     -18.481  -5.810  11.509  1.00 39.66      8HVP 440
ATOM    287  CG  ASN A  37     -18.341  -6.766  10.331  1.00 47.27      8HVP 441
ATOM    288  OD1 ASN A  37     -18.080  -7.975  10.496  1.00 45.86      8HVP 442
ATOM    289  ND2 ASN A  37     -18.535  -6.233   9.113  1.00 51.14      8HVP 443
ATOM    290  N   LEU A  38     -17.615  -2.544  11.789  1.00 24.97      8HVP 444
ATOM    291  CA  LEU A  38     -17.905  -1.242  12.405  1.00 24.99      8HVP 445
ATOM    292  C   LEU A  38     -19.052  -0.710  11.559  1.00 26.54      8HVP 446
ATOM    293  O   LEU A  38     -19.182  -1.171  10.426  1.00 27.63      8HVP 447
ATOM    294  CB  LEU A  38     -16.654  -0.412  12.533  1.00  9.19      8HVP 448
ATOM    295  CG  LEU A  38     -15.633  -0.869  13.564  1.00  7.97      8HVP 449
ATOM    296  CD1 LEU A  38     -14.307  -0.141  13.325  1.00  3.35      8HVP 450
ATOM    297  CD2 LEU A  38     -16.116  -0.603  14.984  1.00  2.00      8HVP 451
ATOM    298  N   PRO A  39     -19.822   0.125  12.205  1.00 28.28      8HVP 452
ATOM    299  CA  PRO A  39     -20.957   0.755  11.496  1.00 31.06      8HVP 453
ATOM    300  C   PRO A  39     -20.293   1.736  10.537  1.00 31.57      8HVP 454
ATOM    301  O   PRO A  39     -19.269   2.307  10.965  1.00 34.27      8HVP 455
ATOM    302  CB  PRO A  39     -21.788   1.345  12.625  1.00 29.25      8HVP 456
ATOM    303  CG  PRO A  39     -21.118   1.006  13.920  1.00 28.19      8HVP 457
ATOM    304  CD  PRO A  39     -19.672   0.683  13.557  1.00 28.38      8HVP 458
ATOM    305  N   GLY A  40     -20.732   1.877   9.307  1.00 32.44      8HVP 459
ATOM    306  CA  GLY A  40     -20.110   2.849   8.410  1.00 33.97      8HVP 460
ATOM    307  C   GLY A  40     -19.616   2.402   7.052  1.00 34.68      8HVP 461
ATOM    308  O   GLY A  40     -19.398   1.219   6.758  1.00 35.21      8HVP 462
ATOM    309  N   LYS A  41     -19.469   3.412   6.198  1.00 35.81      8HVP 463
ATOM    310  CA  LYS A  41     -18.925   3.262   4.838  1.00 36.30      8HVP 464
ATOM    311  C   LYS A  41     -17.386   3.281   4.987  1.00 33.40      8HVP 465
ATOM    312  O   LYS A  41     -16.797   4.227   5.542  1.00 35.77      8HVP 466
ATOM    313  CB  LYS A  41     -19.254   4.390   3.899  1.00 49.20      8HVP 467
ATOM    314  CG  LYS A  41     -20.408   4.437   2.919  1.00 58.64      8HVP 468
ATOM    315  CD  LYS A  41     -20.336   5.775   2.162  1.00 64.83      8HVP 469
ATOM    316  CE  LYS A  41     -21.688   6.194   1.630  1.00 72.01      8HVP 470
ATOM    317  NZ  LYS A  41     -21.910   7.657   1.792  1.00 73.29      8HVP 471
ATOM    318  N   TRP A  42     -16.732   2.248   4.522  1.00 29.59      8HVP 472
ATOM    319  CA  TRP A  42     -15.253   2.248   4.608  1.00 22.94      8HVP 473
ATOM    320  C   TRP A  42     -14.773   2.518   3.176  1.00 20.11      8HVP 474
ATOM    321  O   TRP A  42     -15.536   2.544   2.183  1.00 14.17      8HVP 475
ATOM    322  CB  TRP A  42     -14.842   0.942   5.282  1.00 28.31      8HVP 476
ATOM    323  CG  TRP A  42     -15.282  -0.273   4.525  1.00 33.50      8HVP 477
ATOM    324  CD1 TRP A  42     -16.362  -1.083   4.754  1.00 32.54      8HVP 478
ATOM    325  CD2 TRP A  42     -14.651  -0.797   3.348  1.00 33.46      8HVP 479
ATOM    326  NE1 TRP A  42     -16.448  -2.076   3.808  1.00 20.81      8HVP 480
ATOM    327  CE2 TRP A  42     -15.404  -1.915   2.937  1.00 33.44      8HVP 481
ATOM    328  CE3 TRP A  42     -13.563  -0.401   2.582  1.00 41.85      8HVP 482
ATOM    329  CZ2 TRP A  42     -15.056  -2.635   1.800  1.00 39.65      8HVP 483
ATOM    330  CZ3 TRP A  42     -13.247  -1.112   1.437  1.00 42.57      8HVP 484
ATOM    331  CH2 TRP A  42     -13.974  -2.224   1.039  1.00 34.13      8HVP 485
ATOM    332  N   LYS A  43     -13.475   2.752   3.099  1.00 15.53      8HVP 486
ATOM    333  CA  LYS A  43     -12.789   2.960   1.779  1.00 12.02      8HVP 487
ATOM    334  C   LYS A  43     -11.555   2.127   2.029  1.00  7.46      8HVP 488
ATOM    335  O   LYS A  43     -11.421   1.942   3.270  1.00  3.03      8HVP 489
ATOM    336  CB  LYS A  43     -12.666   4.432   1.446  1.00 28.19      8HVP 490
ATOM    337  CG  LYS A  43     -14.101   4.997   1.265  1.00 40.71      8HVP 491
ATOM    338  CD  LYS A  43     -14.354   6.419   1.710  1.00 44.03      8HVP 492
ATOM    339  CE  LYS A  43     -15.819   6.760   1.913  1.00 40.79      8HVP 493
ATOM    340  NZ  LYS A  43     -16.296   6.538   3.299  1.00 31.16      8HVP 494
ATOM    341  N   PRO A  44     -10.964   1.530   1.017  1.00  2.00      8HVP 495
ATOM    342  CA  PRO A  44      -9.809   0.651   1.204  1.00  2.00      8HVP 496
ATOM    343  C   PRO A  44      -8.531   1.468   1.232  1.00  2.00      8HVP 497
ATOM    344  O   PRO A  44      -8.449   2.240   0.235  1.00  3.68      8HVP 498
ATOM    345  CB  PRO A  44      -9.677  -0.160  -0.080  1.00  2.00      8HVP 499
ATOM    346  CG  PRO A  44     -10.913   0.196  -0.881  1.00  2.00      8HVP 500
ATOM    347  CD  PRO A  44     -11.263   1.632  -0.429  1.00  5.60      8HVP 501
ATOM    348  N   LYS A  45      -7.634   1.190   2.136  1.00  2.35      8HVP 502
ATOM    349  CA  LYS A  45      -6.334   1.863   2.191  1.00  2.00      8HVP 503
ATOM    350  C   LYS A  45      -5.187   0.879   2.204  1.00  2.00      8HVP 504
ATOM    351  O   LYS A  45      -5.554  -0.283   2.399  1.00  7.09      8HVP 505
ATOM    352  CB  LYS A  45      -6.290   2.747   3.456  1.00  2.00      8HVP 506
ATOM    353  CG  LYS A  45      -7.303   3.866   3.198  1.00 13.15      8HVP 507
ATOM    354  CD  LYS A  45      -6.860   4.811   2.087  1.00 22.65      8HVP 508
ATOM    355  CE  LYS A  45      -6.052   5.987   2.595  1.00 35.40      8HVP 509
ATOM    356  NZ  LYS A  45      -6.802   6.967   3.422  1.00 34.17      8HVP 510
ATOM    357  N   MET A  46      -3.938   1.263   2.040  1.00  2.93      8HVP 511
ATOM    358  CA  MET A  46      -2.761   0.436   2.137  1.00  2.00      8HVP 512
ATOM    359  C   MET A  46      -1.770   1.228   3.060  1.00  4.68      8HVP 513
ATOM    360  O   MET A  46      -1.271   2.308   2.692  1.00  2.00      8HVP 514
ATOM    361  CB  MET A  46      -1.897   0.104   0.967  1.00  2.00      8HVP 515
ATOM    362  CG  MET A  46      -2.491   0.275  -0.400  1.00 15.83      8HVP 516
ATOM    363  SD  MET A  46      -1.717  -1.122  -1.330  1.00 17.98      8HVP 517
ATOM    364  CE  MET A  46      -2.553  -2.456  -0.465  1.00 19.37      8HVP 518
ATOM    365  N   ILE A  47      -1.468   0.467   4.116  1.00  5.17      8HVP 519
ATOM    366  CA  ILE A  47      -0.489   1.037   5.099  1.00  4.11      8HVP 520
ATOM    367  C   ILE A  47       0.681   0.049   5.176  1.00  2.00      8HVP 521
ATOM    368  O   ILE A  47       0.362  -1.114   4.842  1.00  2.00      8HVP 522
ATOM    369  CB  ILE A  47      -1.228   1.212   6.477  1.00  5.25      8HVP 523
ATOM    370  CG1 ILE A  47      -1.328  -0.200   7.109  1.00  2.75      8HVP 524
ATOM    371  CG2 ILE A  47      -2.625   1.852   6.260  1.00  2.00      8HVP 525
ATOM    372  CD1 ILE A  47      -1.695  -0.199   8.619  1.00  2.00      8HVP 526
ATOM    373  N   GLY A  48       1.771   0.502   5.750  1.00  2.00      8HVP 527
ATOM    374  CA  GLY A  48       2.986  -0.256   5.916  1.00  2.00      8HVP 528
ATOM    375  C   GLY A  48       3.429  -0.381   7.358  1.00  2.00      8HVP 529
ATOM    376  O   GLY A  48       3.114   0.432   8.206  1.00  2.00      8HVP 530
ATOM    377  N   GLY A  49       4.183  -1.399   7.611  1.00  2.62      8HVP 531
ATOM    378  CA  GLY A  49       4.834  -2.034   8.737  1.00  5.23      8HVP 532
ATOM    379  C   GLY A  49       6.290  -2.440   8.424  1.00  5.87      8HVP 533
ATOM    380  O   GLY A  49       6.831  -2.026   7.383  1.00  2.00      8HVP 534
ATOM    381  N   ILE A  50       6.948  -3.231   9.277  1.00  7.18      8HVP 535
ATOM    382  CA  ILE A  50       8.337  -3.622   9.004  1.00  8.75      8HVP 536
ATOM    383  C   ILE A  50       8.353  -4.671   7.862  1.00 10.38      8HVP 537
ATOM    384  O   ILE A  50       9.457  -4.857   7.293  1.00 14.18      8HVP 538
ATOM    385  CB  ILE A  50       9.222  -4.290  10.104  1.00  3.20      8HVP 539
ATOM    386  CG1 ILE A  50       8.369  -5.376  10.819  1.00  7.88      8HVP 540
ATOM    387  CG2 ILE A  50      10.011  -3.433  11.122  1.00  2.00      8HVP 541
ATOM    388  CD1 ILE A  50       9.330  -6.431  11.442  1.00  7.33      8HVP 542
ATOM    389  N   GLY A  51       7.241  -5.358   7.718  1.00  5.35      8HVP 543
ATOM    390  CA  GLY A  51       7.196  -6.459   6.747  1.00  7.47      8HVP 544
ATOM    391  C   GLY A  51       6.899  -6.022   5.330  1.00  5.78      8HVP 545
ATOM    392  O   GLY A  51       7.236  -6.807   4.460  1.00  5.82      8HVP 546
ATOM    393  N   GLY A  52       6.242  -4.902   5.158  1.00  9.54      8HVP 547
ATOM    394  CA  GLY A  52       5.832  -4.260   3.901  1.00  9.17      8HVP 548
ATOM    395  C   GLY A  52       4.413  -3.690   4.108  1.00 14.31      8HVP 549
ATOM    396  O   GLY A  52       3.987  -3.499   5.276  1.00 11.31      8HVP 550
ATOM    397  N   PHE A  53       3.704  -3.538   2.983  1.00 13.41      8HVP 551
ATOM    398  CA  PHE A  53       2.331  -3.040   2.907  1.00  7.22      8HVP 552
ATOM    399  C   PHE A  53       1.207  -4.078   2.933  1.00  5.57      8HVP 553
ATOM    400  O   PHE A  53       1.265  -5.145   2.325  1.00  2.00      8HVP 554
ATOM    401  CB  PHE A  53       2.177  -2.160   1.660  1.00 14.11      8HVP 555
ATOM    402  CG  PHE A  53       2.851  -0.839   1.755  1.00 13.69      8HVP 556
ATOM    403  CD1 PHE A  53       4.229  -0.754   1.952  1.00 22.88      8HVP 557
ATOM    404  CD2 PHE A  53       2.103   0.330   1.689  1.00 18.71      8HVP 558
ATOM    405  CE1 PHE A  53       4.887   0.484   2.043  1.00 14.77      8HVP 559
ATOM    406  CE2 PHE A  53       2.697   1.573   1.833  1.00 21.08      8HVP 560
ATOM    407  CZ  PHE A  53       4.082   1.649   1.998  1.00 23.64      8HVP 561
ATOM    408  N   ILE A  54       0.140  -3.688   3.614  1.00  4.36      8HVP 562
ATOM    409  CA  ILE A  54      -1.133  -4.337   3.819  1.00  3.22      8HVP 563
ATOM    410  C   ILE A  54      -2.253  -3.369   3.329  1.00  2.00      8HVP 564
ATOM    411  O   ILE A  54      -2.125  -2.159   3.486  1.00  2.00      8HVP 565
ATOM    412  CB  ILE A  54      -1.614  -4.762   5.245  1.00  5.34      8HVP 566
ATOM    413  CG1 ILE A  54      -1.592  -3.583   6.253  1.00  2.80      8HVP 567
ATOM    414  CG2 ILE A  54      -1.058  -6.054   5.886  1.00  2.77      8HVP 568
ATOM    415  CD1 ILE A  54      -2.307  -3.981   7.605  1.00  2.00      8HVP 569
ATOM    416  N   LYS A  55      -3.275  -3.967   2.753  1.00  2.00      8HVP 570
ATOM    417  CA  LYS A  55      -4.444  -3.221   2.267  1.00  2.00      8HVP 571
ATOM    418  C   LYS A  55      -5.389  -3.178   3.475  1.00  2.00      8HVP 572
ATOM    419  O   LYS A  55      -5.530  -4.334   3.882  1.00  2.00      8HVP 573
ATOM    420  CB  LYS A  55      -5.247  -3.838   1.121  1.00  2.00      8HVP 574
ATOM    421  CG  LYS A  55      -6.371  -2.871   0.727  1.00 19.34      8HVP 575
ATOM    422  CD  LYS A  55      -7.458  -3.479  -0.139  1.00 31.54      8HVP 576
ATOM    423  CE  LYS A  55      -7.086  -3.526  -1.608  1.00 41.63      8HVP 577
ATOM    424  NZ  LYS A  55      -6.541  -2.204  -2.039  1.00 43.89      8HVP 578
ATOM    425  N   VAL A  56      -5.863  -2.045   3.935  1.00  2.00      8HVP 579
ATOM    426  CA  VAL A  56      -6.766  -1.944   5.091  1.00  3.51      8HVP 580
ATOM    427  C   VAL A  56      -8.103  -1.307   4.731  1.00  2.00      8HVP 581
ATOM    428  O   VAL A  56      -8.239  -0.704   3.640  1.00  2.00      8HVP 582
ATOM    429  CB  VAL A  56      -6.058  -1.152   6.206  1.00 13.97      8HVP 583
ATOM    430  CG1 VAL A  56      -4.901  -1.905   6.855  1.00 20.53      8HVP 584
ATOM    431  CG2 VAL A  56      -5.578   0.210   5.724  1.00 20.25      8HVP 585
ATOM    432  N   ARG A  57      -9.117  -1.478   5.563  1.00  2.00      8HVP 586
ATOM    433  CA  ARG A  57     -10.425  -0.817   5.243  1.00  2.00      8HVP 587
ATOM    434  C   ARG A  57     -10.705   0.111   6.440  1.00  2.00      8HVP 588
ATOM    435  O   ARG A  57     -10.834  -0.364   7.571  1.00  2.00      8HVP 589
ATOM    436  CB  ARG A  57     -11.596  -1.712   4.948  1.00 10.35      8HVP 590
ATOM    437  CG  ARG A  57     -12.503  -2.169   6.043  1.00 21.42      8HVP 591
ATOM    438  CD  ARG A  57     -13.604  -3.058   5.659  1.00 33.04      8HVP 592
ATOM    439  NE  ARG A  57     -13.279  -4.410   5.254  1.00 46.89      8HVP 593
ATOM    440  CZ  ARG A  57     -14.189  -5.376   5.028  1.00 58.68      8HVP 594
ATOM    441  NH1 ARG A  57     -15.506  -5.234   5.228  1.00 63.21      8HVP 595
ATOM    442  NH2 ARG A  57     -13.791  -6.553   4.522  1.00 60.66      8HVP 596
ATOM    443  N   GLN A  58     -10.744   1.371   6.167  1.00  2.00      8HVP 597
ATOM    444  CA  GLN A  58     -10.864   2.541   6.987  1.00  6.11      8HVP 598
ATOM    445  C   GLN A  58     -12.217   3.163   7.270  1.00  6.18      8HVP 599
ATOM    446  O   GLN A  58     -13.067   3.354   6.382  1.00  8.69      8HVP 600
ATOM    447  CB  GLN A  58     -10.075   3.622   6.187  1.00  2.00      8HVP 601
ATOM    448  CG  GLN A  58     -10.251   5.006   6.805  1.00  2.00      8HVP 602
ATOM    449  CD  GLN A  58      -9.557   6.086   6.013  1.00  7.49      8HVP 603
ATOM    450  OE1 GLN A  58      -8.836   5.872   5.041  1.00  2.00      8HVP 604
ATOM    451  NE2 GLN A  58      -9.815   7.325   6.445  1.00 13.29      8HVP 605
ATOM    452  N   TYR A  59     -12.355   3.582   8.522  1.00  7.47      8HVP 606
ATOM    453  CA  TYR A  59     -13.547   4.225   9.066  1.00  4.02      8HVP 607
ATOM    454  C   TYR A  59     -13.052   5.500   9.761  1.00  6.05      8HVP 608
ATOM    455  O   TYR A  59     -12.153   5.352  10.594  1.00  7.99      8HVP 609
ATOM    456  CB  TYR A  59     -14.302   3.395  10.112  1.00  3.56      8HVP 610
ATOM    457  CG  TYR A  59     -14.644   1.994   9.688  1.00  3.34      8HVP 611
ATOM    458  CD1 TYR A  59     -15.789   1.814   8.903  1.00  4.20      8HVP 612
ATOM    459  CD2 TYR A  59     -13.841   0.884   9.984  1.00  8.25      8HVP 613
ATOM    460  CE1 TYR A  59     -16.103   0.554   8.425  1.00  2.00      8HVP 614
ATOM    461  CE2 TYR A  59     -14.175  -0.394   9.527  1.00  5.59      8HVP 615
ATOM    462  CZ  TYR A  59     -15.329  -0.548   8.767  1.00  2.59      8HVP 616
ATOM    463  OH  TYR A  59     -15.798  -1.764   8.361  1.00  3.97      8HVP 617
ATOM    464  N   ASP A  60     -13.652   6.572   9.380  1.00  5.89      8HVP 618
ATOM    465  CA  ASP A  60     -13.507   7.951   9.779  1.00  6.71      8HVP 619
ATOM    466  C   ASP A  60     -14.482   8.235  10.951  1.00  7.90      8HVP 620
ATOM    467  O   ASP A  60     -15.503   7.548  11.133  1.00  8.18      8HVP 621
ATOM    468  CB  ASP A  60     -13.742   8.895   8.611  1.00  9.56      8HVP 622
ATOM    469  CG  ASP A  60     -13.156   8.619   7.249  1.00 22.85      8HVP 623
ATOM    470  OD1 ASP A  60     -13.378   7.490   6.734  1.00 32.24      8HVP 624
ATOM    471  OD2 ASP A  60     -12.560   9.477   6.558  1.00 19.65      8HVP 625
ATOM    472  N   GLN A  61     -14.164   9.259  11.713  1.00  5.23      8HVP 626
ATOM    473  CA  GLN A  61     -14.911   9.652  12.914  1.00  8.26      8HVP 627
ATOM    474  C   GLN A  61     -15.543   8.417  13.566  1.00  7.43      8HVP 628
ATOM    475  O   GLN A  61     -16.629   8.040  13.126  1.00 11.00      8HVP 629
ATOM    476  CB  GLN A  61     -15.890  10.784  12.685  1.00 12.02      8HVP 630
ATOM    477  CG  GLN A  61     -15.524  12.023  11.914  1.00 22.18      8HVP 631
ATOM    478  CD  GLN A  61     -16.578  13.116  11.902  1.00 31.81      8HVP 632
ATOM    479  OE1 GLN A  61     -16.590  14.122  11.172  1.00 32.58      8HVP 633
ATOM    480  NE2 GLN A  61     -17.559  12.972  12.808  1.00 33.12      8HVP 634
ATOM    481  N   ILE A  62     -14.984   7.777  14.564  1.00  7.95      8HVP 635
ATOM    482  CA  ILE A  62     -15.452   6.605  15.301  1.00  3.16      8HVP 636
ATOM    483  C   ILE A  62     -14.889   6.781  16.720  1.00  5.26      8HVP 637
ATOM    484  O   ILE A  62     -13.654   6.804  16.818  1.00  6.64      8HVP 638
ATOM    485  CB  ILE A  62     -14.904   5.234  14.757  1.00  2.00      8HVP 639
ATOM    486  CG1 ILE A  62     -15.353   4.874  13.323  1.00  7.65      8HVP 640
ATOM    487  CG2 ILE A  62     -15.263   4.060  15.735  1.00  2.00      8HVP 641
ATOM    488  CD1 ILE A  62     -16.862   4.480  13.149  1.00  2.00      8HVP 642
ATOM    489  N   PRO A  63     -15.727   6.880  17.728  1.00  7.38      8HVP 643
ATOM    490  CA  PRO A  63     -15.324   7.094  19.130  1.00  3.35      8HVP 644
ATOM    491  C   PRO A  63     -14.771   5.819  19.712  1.00  3.57      8HVP 645
ATOM    492  O   PRO A  63     -15.206   4.705  19.380  1.00  2.00      8HVP 646
ATOM    493  CB  PRO A  63     -16.544   7.574  19.883  1.00  3.75      8HVP 647
ATOM    494  CG  PRO A  63     -17.642   7.706  18.862  1.00  7.00      8HVP 648
ATOM    495  CD  PRO A  63     -17.205   6.901  17.626  1.00  8.19      8HVP 649
ATOM    496  N   VAL A  64     -13.778   6.036  20.575  1.00  3.62      8HVP 650
ATOM    497  CA  VAL A  64     -13.112   4.851  21.174  1.00  2.00      8HVP 651
ATOM    498  C   VAL A  64     -12.778   5.200  22.592  1.00  2.00      8HVP 652
ATOM    499  O   VAL A  64     -12.370   6.340  22.771  1.00  2.00      8HVP 653
ATOM    500  CB  VAL A  64     -11.862   4.551  20.328  1.00  4.74      8HVP 654
ATOM    501  CG1 VAL A  64     -11.044   3.381  20.852  1.00  7.63      8HVP 655
ATOM    502  CG2 VAL A  64     -12.216   4.410  18.854  1.00  3.77      8HVP 656
ATOM    503  N   GLU A  65     -12.940   4.276  23.508  1.00  2.00      8HVP 657
ATOM    504  CA  GLU A  65     -12.593   4.737  24.880  1.00  4.11      8HVP 658
ATOM    505  C   GLU A  65     -11.357   4.018  25.366  1.00  2.94      8HVP 659
ATOM    506  O   GLU A  65     -11.406   2.812  25.550  1.00  3.01      8HVP 660
ATOM    507  CB  GLU A  65     -13.809   4.650  25.764  1.00 10.50      8HVP 661
ATOM    508  CG  GLU A  65     -13.607   5.129  27.203  1.00 20.47      8HVP 662
ATOM    509  CD  GLU A  65     -14.912   5.221  27.953  1.00 26.07      8HVP 663
ATOM    510  OE1 GLU A  65     -15.671   6.055  27.394  1.00 24.43      8HVP 664
ATOM    511  OE2 GLU A  65     -15.121   4.544  28.944  1.00 26.09      8HVP 665
ATOM    512  N   ILE A  66     -10.262   4.769  25.350  1.00  4.40      8HVP 666
ATOM    513  CA  ILE A  66      -8.950   4.279  25.736  1.00  2.43      8HVP 667
ATOM    514  C   ILE A  66      -8.793   4.502  27.245  1.00  3.70      8HVP 668
ATOM    515  O   ILE A  66      -8.297   5.504  27.736  1.00  2.15      8HVP 669
ATOM    516  CB  ILE A  66      -7.662   4.768  25.027  1.00  5.92      8HVP 670
ATOM    517  CG1 ILE A  66      -7.599   4.255  23.562  1.00 15.82      8HVP 671
ATOM    518  CG2 ILE A  66      -6.359   4.383  25.791  1.00  2.00      8HVP 672
ATOM    519  CD1 ILE A  66      -8.540   5.033  22.584  1.00 21.51      8HVP 673
HETATM  520  N   ABA A  67      -9.180   3.408  27.866  1.00  2.00      8HVP 674
HETATM  521  CA  ABA A  67      -9.148   3.211  29.308  1.00  2.00      8HVP 675
HETATM  522  C   ABA A  67      -9.795   4.420  29.938  1.00  2.00      8HVP 676
HETATM  523  O   ABA A  67      -9.344   5.181  30.820  1.00  2.00      8HVP 677
HETATM  524  CB  ABA A  67      -7.885   2.703  29.913  1.00  2.00      8HVP 678
HETATM  525  CG  ABA A  67      -6.489   3.137  29.574  1.00  2.00      8HVP 679
ATOM    526  N   GLY A  68     -11.010   4.625  29.439  1.00  2.00      8HVP 680
ATOM    527  CA  GLY A  68     -11.923   5.629  29.949  1.00  2.00      8HVP 681
ATOM    528  C   GLY A  68     -11.592   7.068  29.742  1.00  2.00      8HVP 682
ATOM    529  O   GLY A  68     -11.979   7.847  30.699  1.00  2.00      8HVP 683
ATOM    530  N   HIS A  69     -10.964   7.281  28.598  1.00  2.00      8HVP 684
ATOM    531  CA  HIS A  69     -10.611   8.538  27.948  1.00  2.00      8HVP 685
ATOM    532  C   HIS A  69     -11.134   8.384  26.498  1.00  2.67      8HVP 686
ATOM    533  O   HIS A  69     -10.822   7.471  25.750  1.00  2.00      8HVP 687
ATOM    534  CB  HIS A  69      -9.162   9.000  27.663  1.00  2.00      8HVP 688
ATOM    535  CG  HIS A  69      -8.434   9.125  28.962  1.00  4.09      8HVP 689
ATOM    536  ND1 HIS A  69      -8.028  10.287  29.581  1.00  2.00      8HVP 690
ATOM    537  CD2 HIS A  69      -8.278   8.108  29.849  1.00  2.00      8HVP 691
ATOM    538  CE1 HIS A  69      -7.573  10.005  30.777  1.00  2.00      8HVP 692
ATOM    539  NE2 HIS A  69      -7.627   8.709  30.902  1.00  2.00      8HVP 693
ATOM    540  N   LYS A  70     -11.904   9.346  26.079  1.00  6.44      8HVP 694
ATOM    541  CA  LYS A  70     -12.526   9.291  24.767  1.00  8.83      8HVP 695
ATOM    542  C   LYS A  70     -11.741   9.907  23.623  1.00  7.79      8HVP 696
ATOM    543  O   LYS A  70     -11.516  11.125  23.688  1.00 10.27      8HVP 697
ATOM    544  CB  LYS A  70     -13.843  10.049  24.944  1.00 22.25      8HVP 698
ATOM    545  CG  LYS A  70     -14.883   9.579  25.948  1.00 29.40      8HVP 699
ATOM    546  CD  LYS A  70     -15.966   8.698  25.354  1.00 37.56      8HVP 700
ATOM    547  CE  LYS A  70     -16.817   9.292  24.261  1.00 37.79      8HVP 701
ATOM    548  NZ  LYS A  70     -16.128   9.251  22.942  1.00 41.52      8HVP 702
ATOM    549  N   ALA A  71     -11.503   9.158  22.563  1.00  3.86      8HVP 703
ATOM    550  CA  ALA A  71     -10.970   9.668  21.300  1.00  2.78      8HVP 704
ATOM    551  C   ALA A  71     -12.079   9.535  20.237  1.00  2.59      8HVP 705
ATOM    552  O   ALA A  71     -13.038   8.782  20.491  1.00  4.78      8HVP 706
ATOM    553  CB  ALA A  71      -9.727   8.913  20.899  1.00  4.57      8HVP 707
ATOM    554  N   ILE A  72     -12.030  10.206  19.107  1.00  2.00      8HVP 708
ATOM    555  CA  ILE A  72     -12.956  10.132  17.989  1.00  2.00      8HVP 709
ATOM    556  C   ILE A  72     -12.213  10.270  16.652  1.00  2.52      8HVP 710
ATOM    557  O   ILE A  72     -11.966  11.415  16.204  1.00  5.79      8HVP 711
ATOM    558  CB  ILE A  72     -14.141  11.152  18.026  1.00  6.76      8HVP 712
ATOM    559  CG1 ILE A  72     -15.012  10.896  19.279  1.00  3.79      8HVP 713
ATOM    560  CG2 ILE A  72     -15.063  11.154  16.767  1.00  2.00      8HVP 714
ATOM    561  CD1 ILE A  72     -15.934  12.133  19.516  1.00  8.03      8HVP 715
ATOM    562  N   GLY A  73     -11.986   9.137  15.984  1.00  2.00      8HVP 716
ATOM    563  CA  GLY A  73     -11.254   9.270  14.752  1.00  3.83      8HVP 717
ATOM    564  C   GLY A  73     -11.100   8.060  13.882  1.00  8.34      8HVP 718
ATOM    565  O   GLY A  73     -11.824   7.096  14.087  1.00  9.36      8HVP 719
ATOM    566  N   THR A  74     -10.204   8.214  12.900  1.00 10.69      8HVP 720
ATOM    567  CA  THR A  74      -9.923   7.185  11.888  1.00 12.72      8HVP 721
ATOM    568  C   THR A  74      -9.556   5.963  12.729  1.00 11.88      8HVP 722
ATOM    569  O   THR A  74      -9.029   6.181  13.819  1.00 15.49      8HVP 723
ATOM    570  CB  THR A  74      -8.837   7.541  10.804  1.00  7.19      8HVP 724
ATOM    571  OG1 THR A  74      -9.107   8.917  10.330  1.00  2.00      8HVP 725
ATOM    572  CG2 THR A  74      -8.823   6.625   9.549  1.00  2.00      8HVP 726
ATOM    573  N   VAL A  75      -9.883   4.817  12.264  1.00 12.35      8HVP 727
ATOM    574  CA  VAL A  75      -9.637   3.501  12.863  1.00  9.52      8HVP 728
ATOM    575  C   VAL A  75      -9.761   2.580  11.630  1.00  9.87      8HVP 729
ATOM    576  O   VAL A  75     -10.825   2.592  10.989  1.00 11.30      8HVP 730
ATOM    577  CB  VAL A  75     -10.642   3.268  13.978  1.00  2.00      8HVP 731
ATOM    578  CG1 VAL A  75     -10.584   1.893  14.631  1.00  5.44      8HVP 732
ATOM    579  CG2 VAL A  75     -10.617   4.277  15.098  1.00  2.00      8HVP 733
ATOM    580  N   LEU A  76      -8.698   1.941  11.264  1.00  8.47      8HVP 734
ATOM    581  CA  LEU A  76      -8.485   1.037  10.143  1.00  8.80      8HVP 735
ATOM    582  C   LEU A  76      -8.671  -0.403  10.608  1.00  6.70      8HVP 736
ATOM    583  O   LEU A  76      -8.303  -0.703  11.759  1.00  5.67      8HVP 737
ATOM    584  CB  LEU A  76      -7.063   1.316   9.584  1.00 10.20      8HVP 738
ATOM    585  CG  LEU A  76      -6.536   2.738   9.571  1.00 12.70      8HVP 739
ATOM    586  CD1 LEU A  76      -5.017   2.742   9.427  1.00 20.05      8HVP 740
ATOM    587  CD2 LEU A  76      -7.172   3.539   8.442  1.00 10.50      8HVP 741
ATOM    588  N   VAL A  77      -9.237  -1.283   9.797  1.00  7.51      8HVP 742
ATOM    589  CA  VAL A  77      -9.467  -2.667  10.311  1.00  8.48      8HVP 743
ATOM    590  C   VAL A  77      -8.655  -3.482   9.296  1.00  8.66      8HVP 744
ATOM    591  O   VAL A  77      -8.707  -3.060   8.148  1.00  3.51      8HVP 745
ATOM    592  CB  VAL A  77     -10.848  -3.182  10.711  1.00  2.00      8HVP 746
ATOM    593  CG1 VAL A  77     -11.601  -2.130  11.543  1.00  2.00      8HVP 747
ATOM    594  CG2 VAL A  77     -11.772  -3.758   9.676  1.00  2.00      8HVP 748
ATOM    595  N   GLY A  78      -7.917  -4.370   9.966  1.00  9.07      8HVP 749
ATOM    596  CA  GLY A  78      -7.027  -5.213   9.216  1.00 10.45      8HVP 750
ATOM    597  C   GLY A  78      -6.278  -6.298   9.987  1.00 13.11      8HVP 751
ATOM    598  O   GLY A  78      -6.391  -6.475  11.207  1.00  8.30      8HVP 752
ATOM    599  N   PRO A  79      -5.496  -6.967   9.126  1.00 13.87      8HVP 753
ATOM    600  CA  PRO A  79      -4.648  -8.082   9.501  1.00 16.71      8HVP 754
ATOM    601  C   PRO A  79      -3.373  -7.754  10.248  1.00 16.35      8HVP 755
ATOM    602  O   PRO A  79      -2.271  -8.046   9.729  1.00 21.24      8HVP 756
ATOM    603  CB  PRO A  79      -4.357  -8.828   8.183  1.00 15.48      8HVP 757
ATOM    604  CG  PRO A  79      -4.513  -7.802   7.104  1.00 17.22      8HVP 758
ATOM    605  CD  PRO A  79      -5.426  -6.726   7.664  1.00 15.67      8HVP 759
ATOM    606  N   THR A  80      -3.508  -7.329  11.491  1.00 13.99      8HVP 760
ATOM    607  CA  THR A  80      -2.388  -7.007  12.382  1.00  7.93      8HVP 761
ATOM    608  C   THR A  80      -2.093  -8.073  13.416  1.00  7.15      8HVP 762
ATOM    609  O   THR A  80      -2.972  -8.837  13.836  1.00  7.15      8HVP 763
ATOM    610  CB  THR A  80      -2.810  -5.655  13.104  1.00  3.57      8HVP 764
ATOM    611  OG1 THR A  80      -1.958  -5.424  14.269  1.00  3.18      8HVP 765
ATOM    612  CG2 THR A  80      -4.299  -5.646  13.443  1.00  3.91      8HVP 766
ATOM    613  N   PRO A  81      -0.864  -8.073  13.929  1.00  7.89      8HVP 767
ATOM    614  CA  PRO A  81      -0.489  -8.998  15.016  1.00  5.91      8HVP 768
ATOM    615  C   PRO A  81      -1.384  -8.738  16.238  1.00  4.90      8HVP 769
ATOM    616  O   PRO A  81      -1.567  -9.712  17.002  1.00  2.72      8HVP 770
ATOM    617  CB  PRO A  81       0.999  -8.797  15.310  1.00  2.00      8HVP 771
ATOM    618  CG  PRO A  81       1.464  -7.910  14.202  1.00  5.30      8HVP 772
ATOM    619  CD  PRO A  81       0.284  -7.232  13.546  1.00  4.56      8HVP 773
ATOM    620  N   VAL A  82      -1.821  -7.500  16.368  1.00  2.00      8HVP 774
ATOM    621  CA  VAL A  82      -2.634  -7.088  17.513  1.00  2.23      8HVP 775
ATOM    622  C   VAL A  82      -3.237  -5.715  17.207  1.00  4.19      8HVP 776
ATOM    623  O   VAL A  82      -3.001  -5.045  16.193  1.00  7.31      8HVP 777
ATOM    624  CB  VAL A  82      -1.794  -7.114  18.814  1.00  7.05      8HVP 778
ATOM    625  CG1 VAL A  82      -0.584  -6.170  18.866  1.00  2.42      8HVP 779
ATOM    626  CG2 VAL A  82      -2.637  -6.925  20.078  1.00  2.00      8HVP 780
ATOM    627  N   ASN A  83      -4.043  -5.282  18.137  1.00  2.00      8HVP 781
ATOM    628  CA  ASN A  83      -4.725  -4.010  18.139  1.00  2.00      8HVP 782
ATOM    629  C   ASN A  83      -3.712  -2.932  18.472  1.00  2.00      8HVP 783
ATOM    630  O   ASN A  83      -3.102  -3.058  19.533  1.00  2.00      8HVP 784
ATOM    631  CB  ASN A  83      -5.890  -4.091  19.148  1.00  2.77      8HVP 785
ATOM    632  CG  ASN A  83      -6.999  -5.034  18.701  1.00  3.99      8HVP 786
ATOM    633  OD1 ASN A  83      -7.292  -5.238  17.505  1.00  2.00      8HVP 787
ATOM    634  ND2 ASN A  83      -7.656  -5.622  19.696  1.00  3.16      8HVP 788
ATOM    635  N   ILE A  84      -3.572  -1.899  17.667  1.00  2.00      8HVP 789
ATOM    636  CA  ILE A  84      -2.627  -0.855  18.109  1.00  2.00      8HVP 790
ATOM    637  C   ILE A  84      -3.331   0.495  18.104  1.00  2.00      8HVP 791
ATOM    638  O   ILE A  84      -4.139   0.805  17.202  1.00  3.31      8HVP 792
ATOM    639  CB  ILE A  84      -1.337  -0.942  17.265  1.00  5.68      8HVP 793
ATOM    640  CG1 ILE A  84      -1.582  -0.361  15.856  1.00  2.00      8HVP 794
ATOM    641  CG2 ILE A  84      -0.704  -2.369  17.165  1.00  2.00      8HVP 795
ATOM    642  CD1 ILE A  84      -0.535  -0.914  14.813  1.00 14.28      8HVP 796
ATOM    643  N   ILE A  85      -3.119   1.204  19.200  1.00  2.00      8HVP 797
ATOM    644  CA  ILE A  85      -3.629   2.562  19.300  1.00  2.00      8HVP 798
ATOM    645  C   ILE A  85      -2.456   3.427  18.810  1.00  5.58      8HVP 799
ATOM    646  O   ILE A  85      -1.316   3.339  19.342  1.00  6.20      8HVP 800
ATOM    647  CB  ILE A  85      -4.238   2.871  20.688  1.00  5.40      8HVP 801
ATOM    648  CG1 ILE A  85      -5.468   2.004  21.077  1.00  5.42      8HVP 802
ATOM    649  CG2 ILE A  85      -4.563   4.413  20.787  1.00 10.10      8HVP 803
ATOM    650  CD1 ILE A  85      -6.502   1.744  19.986  1.00  2.00      8HVP 804
ATOM    651  N   GLY A  86      -2.685   4.160  17.715  1.00  5.21      8HVP 805
ATOM    652  CA  GLY A  86      -1.546   4.956  17.199  1.00  3.26      8HVP 806
ATOM    653  C   GLY A  86      -1.677   6.387  17.647  1.00  2.00      8HVP 807
ATOM    654  O   GLY A  86      -2.687   6.774  18.224  1.00  4.46      8HVP 808
ATOM    655  N   ARG A  87      -0.753   7.212  17.229  1.00  4.56      8HVP 809
ATOM    656  CA  ARG A  87      -0.726   8.647  17.515  1.00  4.66      8HVP 810
ATOM    657  C   ARG A  87      -1.927   9.421  17.003  1.00  5.62      8HVP 811
ATOM    658  O   ARG A  87      -1.997  10.624  17.295  1.00  6.22      8HVP 812
ATOM    659  CB  ARG A  87       0.560   9.251  16.954  1.00  3.84      8HVP 813
ATOM    660  CG  ARG A  87       1.799   8.465  17.393  1.00  5.19      8HVP 814
ATOM    661  CD  ARG A  87       3.062   9.249  17.176  1.00  5.47      8HVP 815
ATOM    662  NE  ARG A  87       3.301   9.385  15.743  1.00  2.00      8HVP 816
ATOM    663  CZ  ARG A  87       2.800  10.279  14.915  1.00  7.29      8HVP 817
ATOM    664  NH1 ARG A  87       2.082  11.345  15.275  1.00  2.00      8HVP 818
ATOM    665  NH2 ARG A  87       2.986  10.036  13.612  1.00  2.00      8HVP 819
ATOM    666  N   ASN A  88      -2.856   8.785  16.310  1.00  7.72      8HVP 820
ATOM    667  CA  ASN A  88      -4.072   9.472  15.825  1.00  3.58      8HVP 821
ATOM    668  C   ASN A  88      -5.002   9.692  17.029  1.00  3.98      8HVP 822
ATOM    669  O   ASN A  88      -5.394  10.821  17.322  1.00  2.18      8HVP 823
ATOM    670  CB  ASN A  88      -4.685   8.771  14.638  1.00  2.00      8HVP 824
ATOM    671  CG  ASN A  88      -5.413   7.486  14.820  1.00  2.00      8HVP 825
ATOM    672  OD1 ASN A  88      -4.900   6.432  15.179  1.00  4.63      8HVP 826
ATOM    673  ND2 ASN A  88      -6.741   7.466  14.648  1.00  9.19      8HVP 827
ATOM    674  N   LEU A  89      -5.319   8.597  17.694  1.00  3.27      8HVP 828
ATOM    675  CA  LEU A  89      -6.191   8.594  18.868  1.00  2.44      8HVP 829
ATOM    676  C   LEU A  89      -5.324   8.934  20.075  1.00  2.55      8HVP 830
ATOM    677  O   LEU A  89      -5.871   9.591  20.952  1.00  3.74      8HVP 831
ATOM    678  CB  LEU A  89      -6.970   7.280  19.019  1.00  2.00      8HVP 832
ATOM    679  CG  LEU A  89      -7.632   6.620  17.823  1.00  2.00      8HVP 833
ATOM    680  CD1 LEU A  89      -8.393   5.334  18.111  1.00  2.00      8HVP 834
ATOM    681  CD2 LEU A  89      -8.555   7.677  17.200  1.00  2.00      8HVP 835
ATOM    682  N   LEU A  90      -4.090   8.493  20.116  1.00  4.39      8HVP 836
ATOM    683  CA  LEU A  90      -3.089   8.713  21.163  1.00  3.40      8HVP 837
ATOM    684  C   LEU A  90      -2.852  10.152  21.590  1.00  3.55      8HVP 838
ATOM    685  O   LEU A  90      -2.420  10.305  22.734  1.00  7.46      8HVP 839
ATOM    686  CB  LEU A  90      -1.762   8.046  20.789  1.00  2.00      8HVP 840
ATOM    687  CG  LEU A  90      -1.440   6.613  21.147  1.00  2.96      8HVP 841
ATOM    688  CD1 LEU A  90       0.014   6.252  20.880  1.00  2.00      8HVP 842
ATOM    689  CD2 LEU A  90      -1.605   6.435  22.661  1.00  5.53      8HVP 843
ATOM    690  N   THR A  91      -3.069  11.165  20.783  1.00  2.00      8HVP 844
ATOM    691  CA  THR A  91      -2.847  12.561  21.080  1.00  2.00      8HVP 845
ATOM    692  C   THR A  91      -4.221  13.159  21.410  1.00  2.00      8HVP 846
ATOM    693  O   THR A  91      -4.409  14.271  21.937  1.00  3.25      8HVP 847
ATOM    694  CB  THR A  91      -2.236  13.400  19.903  1.00  4.96      8HVP 848
ATOM    695  OG1 THR A  91      -3.365  13.663  18.960  1.00 17.62      8HVP 849
ATOM    696  CG2 THR A  91      -1.080  12.973  19.042  1.00  2.00      8HVP 850
ATOM    697  N   GLN A  92      -5.294  12.504  21.000  1.00  2.02      8HVP 851
ATOM    698  CA  GLN A  92      -6.596  13.066  21.374  1.00  3.23      8HVP 852
ATOM    699  C   GLN A  92      -6.603  12.983  22.917  1.00  5.73      8HVP 853
ATOM    700  O   GLN A  92      -6.911  13.969  23.600  1.00  5.39      8HVP 854
ATOM    701  CB  GLN A  92      -7.860  12.421  20.850  1.00  7.97      8HVP 855
ATOM    702  CG  GLN A  92      -7.866  11.997  19.398  1.00  4.65      8HVP 856
ATOM    703  CD  GLN A  92      -9.225  12.013  18.760  1.00  5.71      8HVP 857
ATOM    704  OE1 GLN A  92     -10.220  11.988  19.488  1.00 16.81      8HVP 858
ATOM    705  NE2 GLN A  92      -9.287  12.137  17.436  1.00  2.61      8HVP 859
ATOM    706  N   ILE A  93      -6.271  11.804  23.441  1.00  5.24      8HVP 860
ATOM    707  CA  ILE A  93      -6.314  11.492  24.869  1.00  3.10      8HVP 861
ATOM    708  C   ILE A  93      -5.177  12.056  25.735  1.00  4.44      8HVP 862
ATOM    709  O   ILE A  93      -5.169  11.736  26.956  1.00  3.21      8HVP 863
ATOM    710  CB  ILE A  93      -6.503   9.960  25.137  1.00  2.00      8HVP 864
ATOM    711  CG1 ILE A  93      -5.111   9.269  25.304  1.00  2.32      8HVP 865
ATOM    712  CG2 ILE A  93      -7.287   9.152  24.091  1.00  2.00      8HVP 866
ATOM    713  CD1 ILE A  93      -5.310   7.869  25.962  1.00  2.00      8HVP 867
ATOM    714  N   GLY A  94      -4.273  12.804  25.180  1.00  3.49      8HVP 868
ATOM    715  CA  GLY A  94      -3.074  13.462  25.609  1.00  3.23      8HVP 869
ATOM    716  C   GLY A  94      -1.929  12.631  26.127  1.00  5.18      8HVP 870
ATOM    717  O   GLY A  94      -1.345  13.046  27.151  1.00  6.47      8HVP 871
HETATM  718  N   ABA A  95      -1.543  11.513  25.567  1.00  6.81      8HVP 872
HETATM  719  CA  ABA A  95      -0.435  10.616  26.015  1.00  7.01      8HVP 873
HETATM  720  C   ABA A  95       0.920  11.278  25.762  1.00  7.48      8HVP 874
HETATM  721  O   ABA A  95       1.150  11.979  24.750  1.00  8.83      8HVP 875
HETATM  722  CB  ABA A  95      -0.535   9.266  25.311  1.00  4.08      8HVP 876
HETATM  723  CG  ABA A  95       0.190   7.994  25.563  1.00  2.00      8HVP 877
ATOM    724  N   THR A  96       1.891  11.127  26.657  1.00  8.14      8HVP 878
ATOM    725  CA  THR A  96       3.209  11.673  26.385  1.00  6.16      8HVP 879
ATOM    726  C   THR A  96       4.297  10.662  26.760  1.00  8.82      8HVP 880
ATOM    727  O   THR A  96       4.046   9.894  27.710  1.00 10.15      8HVP 881
ATOM    728  CB  THR A  96       3.586  12.991  27.148  1.00  2.00      8HVP 882
ATOM    729  OG1 THR A  96       3.868  12.461  28.475  1.00  2.00      8HVP 883
ATOM    730  CG2 THR A  96       2.600  14.110  27.001  1.00  2.00      8HVP 884
ATOM    731  N   LEU A  97       5.429  10.771  26.063  1.00  4.92      8HVP 885
ATOM    732  CA  LEU A  97       6.537   9.909  26.444  1.00  3.00      8HVP 886
ATOM    733  C   LEU A  97       7.472  10.829  27.262  1.00  4.93      8HVP 887
ATOM    734  O   LEU A  97       8.019  11.760  26.678  1.00  2.00      8HVP 888
ATOM    735  CB  LEU A  97       7.413   9.402  25.337  1.00  5.81      8HVP 889
ATOM    736  CG  LEU A  97       6.810   8.527  24.265  1.00 17.78      8HVP 890
ATOM    737  CD1 LEU A  97       7.531   8.868  22.950  1.00 15.15      8HVP 891
ATOM    738  CD2 LEU A  97       6.989   7.069  24.694  1.00  2.00      8HVP 892
ATOM    739  N   ASN A  98       7.600  10.406  28.472  1.00  2.00      8HVP 893
ATOM    740  CA  ASN A  98       8.451  10.928  29.503  1.00  2.00      8HVP 894
ATOM    741  C   ASN A  98       9.592   9.944  29.781  1.00  2.00      8HVP 895
ATOM    742  O   ASN A  98       9.567   8.718  29.800  1.00  2.00      8HVP 896
ATOM    743  CB  ASN A  98       7.683  11.180  30.790  1.00  2.00      8HVP 897
ATOM    744  CG  ASN A  98       6.342  11.853  30.762  1.00  2.00      8HVP 898
ATOM    745  OD1 ASN A  98       6.256  13.075  30.810  1.00  2.00      8HVP 899
ATOM    746  ND2 ASN A  98       5.257  11.097  30.774  1.00  2.00      8HVP 900
ATOM    747  N   PHE A  99      10.683  10.600  30.112  1.00  2.30      8HVP 901
ATOM    748  CA  PHE A  99      12.018  10.064  30.493  1.00  2.00      8HVP 902
ATOM    749  C   PHE A  99      13.022  11.183  30.820  1.00  2.00      8HVP 903
ATOM    750  O   PHE A  99      14.206  10.802  30.941  1.00  2.00      8HVP 904
ATOM    751  CB  PHE A  99      12.574   9.271  29.336  1.00  5.09      8HVP 905
ATOM    752  CG  PHE A  99      13.135   9.982  28.143  1.00  3.95      8HVP 906
ATOM    753  CD1 PHE A  99      14.475  10.327  28.094  1.00 13.06      8HVP 907
ATOM    754  CD2 PHE A  99      12.355  10.142  26.995  1.00 13.99      8HVP 908
ATOM    755  CE1 PHE A  99      15.075  10.890  26.971  1.00 15.26      8HVP 909
ATOM    756  CE2 PHE A  99      12.936  10.661  25.858  1.00 16.96      8HVP 910
ATOM    757  CZ  PHE A  99      14.267  11.058  25.842  1.00 18.46      8HVP 911
ATOM    758  OXT PHE A  99      12.728  12.395  30.861  1.00  8.17      8HVP 912
TER     759      PHE A  99                                              8HVP 913
ATOM    760  N   PRO B   1      13.362  14.768  29.011  1.00 22.23      8HVP 914
ATOM    761  CA  PRO B   1      12.150  15.030  28.252  1.00 19.96      8HVP 915
ATOM    762  C   PRO B   1      10.839  14.677  28.948  1.00 20.06      8HVP 916
ATOM    763  O   PRO B   1      10.645  14.321  30.108  1.00 17.36      8HVP 917
ATOM    764  CB  PRO B   1      12.333  14.144  27.001  1.00 21.73      8HVP 918
ATOM    765  CG  PRO B   1      13.829  14.070  26.828  1.00 20.36      8HVP 919
ATOM    766  CD  PRO B   1      14.266  13.841  28.287  1.00 22.67      8HVP 920
ATOM    767  N   GLN B   2       9.851  14.769  28.117  1.00 21.74      8HVP 921
ATOM    768  CA  GLN B   2       8.434  14.690  27.889  1.00 20.96      8HVP 922
ATOM    769  C   GLN B   2       8.208  14.858  26.363  1.00 19.81      8HVP 923
ATOM    770  O   GLN B   2       8.087  16.028  25.925  1.00 20.13      8HVP 924
ATOM    771  CB  GLN B   2       7.647  15.813  28.601  1.00 11.77      8HVP 925
ATOM    772  CG  GLN B   2       6.163  15.754  28.480  1.00 21.59      8HVP 926
ATOM    773  CD  GLN B   2       5.211  16.418  29.425  1.00 29.24      8HVP 927
ATOM    774  OE1 GLN B   2       4.849  15.901  30.495  1.00 30.58      8HVP 928
ATOM    775  NE2 GLN B   2       4.626  17.557  29.014  1.00 33.48      8HVP 929
ATOM    776  N   ILE B   3       8.245  13.802  25.569  1.00 18.52      8HVP 930
ATOM    777  CA  ILE B   3       8.062  13.949  24.104  1.00 15.36      8HVP 931
ATOM    778  C   ILE B   3       6.545  13.969  23.859  1.00 15.34      8HVP 932
ATOM    779  O   ILE B   3       5.743  13.463  24.671  1.00 14.19      8HVP 933
ATOM    780  CB  ILE B   3       8.794  12.957  23.149  1.00  4.31      8HVP 934
ATOM    781  CG1 ILE B   3      10.325  13.000  23.437  1.00  2.00      8HVP 935
ATOM    782  CG2 ILE B   3       8.554  13.117  21.635  1.00  7.74      8HVP 936
ATOM    783  CD1 ILE B   3      10.587  12.109  24.687  1.00  2.00      8HVP 937
ATOM    784  N   THR B   4       6.286  14.583  22.716  1.00 13.82      8HVP 938
ATOM    785  CA  THR B   4       4.895  14.834  22.268  1.00 11.46      8HVP 939
ATOM    786  C   THR B   4       4.650  13.952  21.069  1.00  7.87      8HVP 940
ATOM    787  O   THR B   4       5.597  13.673  20.332  1.00  6.67      8HVP 941
ATOM    788  CB  THR B   4       4.683  16.389  22.049  1.00 14.61      8HVP 942
ATOM    789  OG1 THR B   4       3.283  16.733  22.322  1.00  2.27      8HVP 943
ATOM    790  CG2 THR B   4       5.274  16.924  20.736  1.00  9.91      8HVP 944
ATOM    791  N   LEU B   5       3.394  13.552  20.937  1.00  7.96      8HVP 945
ATOM    792  CA  LEU B   5       3.055  12.678  19.798  1.00  8.46      8HVP 946
ATOM    793  C   LEU B   5       2.487  13.354  18.578  1.00  6.62      8HVP 947
ATOM    794  O   LEU B   5       2.051  12.623  17.675  1.00  5.80      8HVP 948
ATOM    795  CB  LEU B   5       2.218  11.576  20.479  1.00 14.06      8HVP 949
ATOM    796  CG  LEU B   5       2.985  10.781  21.553  1.00 13.25      8HVP 950
ATOM    797  CD1 LEU B   5       2.022   9.789  22.194  1.00  2.00      8HVP 951
ATOM    798  CD2 LEU B   5       4.211  10.126  20.907  1.00  2.00      8HVP 952
ATOM    799  N   TRP B   6       2.529  14.670  18.435  1.00  8.33      8HVP 953
ATOM    800  CA  TRP B   6       1.928  15.413  17.312  1.00  6.13      8HVP 954
ATOM    801  C   TRP B   6       2.582  14.965  15.991  1.00  7.83      8HVP 955
ATOM    802  O   TRP B   6       2.001  14.765  14.926  1.00  5.80      8HVP 956
ATOM    803  CB  TRP B   6       1.974  16.899  17.526  1.00  2.70      8HVP 957
ATOM    804  CG  TRP B   6       1.085  17.568  18.496  1.00  8.01      8HVP 958
ATOM    805  CD1 TRP B   6       1.502  18.226  19.617  1.00  4.80      8HVP 959
ATOM    806  CD2 TRP B   6      -0.353  17.645  18.504  1.00 12.18      8HVP 960
ATOM    807  NE1 TRP B   6       0.424  18.693  20.322  1.00 13.10      8HVP 961
ATOM    808  CE2 TRP B   6      -0.728  18.360  19.666  1.00 12.26      8HVP 962
ATOM    809  CE3 TRP B   6      -1.349  17.193  17.640  1.00  9.93      8HVP 963
ATOM    810  CZ2 TRP B   6      -2.052  18.623  20.007  1.00  5.70      8HVP 964
ATOM    811  CZ3 TRP B   6      -2.669  17.461  17.968  1.00 11.20      8HVP 965
ATOM    812  CH2 TRP B   6      -3.007  18.182  19.115  1.00  4.84      8HVP 966
ATOM    813  N   GLN B   7       3.860  14.795  16.175  1.00  9.46      8HVP 967
ATOM    814  CA  GLN B   7       4.910  14.331  15.306  1.00  6.51      8HVP 968
ATOM    815  C   GLN B   7       5.473  13.072  15.957  1.00  6.44      8HVP 969
ATOM    816  O   GLN B   7       5.491  12.888  17.193  1.00 14.42      8HVP 970
ATOM    817  CB  GLN B   7       6.018  15.376  15.205  1.00 10.65      8HVP 971
ATOM    818  CG  GLN B   7       5.548  16.697  14.609  1.00 11.70      8HVP 972
ATOM    819  CD  GLN B   7       4.947  17.582  15.683  1.00 18.36      8HVP 973
ATOM    820  OE1 GLN B   7       5.412  17.694  16.813  1.00 18.82      8HVP 974
ATOM    821  NE2 GLN B   7       3.842  18.206  15.310  1.00 16.66      8HVP 975
ATOM    822  N   ARG B   8       5.926  12.182  15.138  1.00  2.00      8HVP 976
ATOM    823  CA  ARG B   8       6.531  10.933  15.569  1.00  2.47      8HVP 977
ATOM    824  C   ARG B   8       7.555  11.268  16.617  1.00  2.00      8HVP 978
ATOM    825  O   ARG B   8       8.108  12.376  16.572  1.00  4.59      8HVP 979
ATOM    826  CB  ARG B   8       7.357  10.413  14.377  1.00  2.00      8HVP 980
ATOM    827  CG  ARG B   8       6.402  10.086  13.256  1.00  4.99      8HVP 981
ATOM    828  CD  ARG B   8       7.280   9.765  12.065  1.00 11.69      8HVP 982
ATOM    829  NE  ARG B   8       6.366   9.124  11.145  1.00 18.34      8HVP 983
ATOM    830  CZ  ARG B   8       6.534   8.935   9.847  1.00 20.17      8HVP 984
ATOM    831  NH1 ARG B   8       7.634   9.201   9.166  1.00 29.34      8HVP 985
ATOM    832  NH2 ARG B   8       5.440   8.519   9.212  1.00 18.36      8HVP 986
ATOM    833  N   PRO B   9       7.902  10.289  17.418  1.00  4.14      8HVP 987
ATOM    834  CA  PRO B   9       8.905  10.504  18.481  1.00  2.00      8HVP 988
ATOM    835  C   PRO B   9      10.327  10.229  18.002  1.00  3.36      8HVP 989
ATOM    836  O   PRO B   9      11.066   9.312  18.449  1.00  4.57      8HVP 990
ATOM    837  CB  PRO B   9       8.345   9.633  19.605  1.00  2.00      8HVP 991
ATOM    838  CG  PRO B   9       7.101   8.985  19.042  1.00  2.00      8HVP 992
ATOM    839  CD  PRO B   9       7.321   8.943  17.528  1.00  2.00      8HVP 993
ATOM    840  N   LEU B  10      10.819  11.046  17.082  1.00  2.00      8HVP 994
ATOM    841  CA  LEU B  10      12.209  10.938  16.611  1.00  2.00      8HVP 995
ATOM    842  C   LEU B  10      13.190  11.593  17.589  1.00  2.00      8HVP 996
ATOM    843  O   LEU B  10      13.077  12.784  17.952  1.00  2.00      8HVP 997
ATOM    844  CB  LEU B  10      12.381  11.504  15.230  1.00  2.00      8HVP 998
ATOM    845  CG  LEU B  10      12.146  10.576  14.064  1.00  2.00      8HVP 999
ATOM    846  CD1 LEU B  10      12.269  11.376  12.775  1.00  8.81      8HVP1000
ATOM    847  CD2 LEU B  10      13.183   9.464  14.152  1.00 12.85      8HVP1001
ATOM    848  N   VAL B  11      14.234  10.887  17.891  1.00  2.00      8HVP1002
ATOM    849  CA  VAL B  11      15.287  11.363  18.798  1.00  6.05      8HVP1003
ATOM    850  C   VAL B  11      16.641  11.041  18.188  1.00  4.35      8HVP1004
ATOM    851  O   VAL B  11      16.652  10.633  17.020  1.00 10.00      8HVP1005
ATOM    852  CB  VAL B  11      15.046  10.704  20.164  1.00  2.00      8HVP1006
ATOM    853  CG1 VAL B  11      13.763  11.201  20.825  1.00  2.00      8HVP1007
ATOM    854  CG2 VAL B  11      15.103   9.194  20.040  1.00  2.00      8HVP1008
ATOM    855  N   THR B  12      17.661  11.184  18.991  1.00  3.92      8HVP1009
ATOM    856  CA  THR B  12      19.029  10.968  18.446  1.00  6.27      8HVP1010
ATOM    857  C   THR B  12      19.788  10.030  19.346  1.00  7.20      8HVP1011
ATOM    858  O   THR B  12      19.728  10.174  20.565  1.00  2.07      8HVP1012
ATOM    859  CB  THR B  12      19.610  12.432  18.259  1.00  2.00      8HVP1013
ATOM    860  OG1 THR B  12      20.461  12.429  17.101  1.00  5.09      8HVP1014
ATOM    861  CG2 THR B  12      20.265  12.929  19.561  1.00  2.00      8HVP1015
ATOM    862  N   ILE B  13      20.471   9.059  18.789  1.00 11.31      8HVP1016
ATOM    863  CA  ILE B  13      21.235   8.044  19.558  1.00 16.39      8HVP1017
ATOM    864  C   ILE B  13      22.720   8.005  19.256  1.00 17.43      8HVP1018
ATOM    865  O   ILE B  13      23.115   8.508  18.157  1.00 16.05      8HVP1019
ATOM    866  CB  ILE B  13      20.491   6.678  19.202  1.00 17.54      8HVP1020
ATOM    867  CG1 ILE B  13      20.494   6.535  17.660  1.00 18.07      8HVP1021
ATOM    868  CG2 ILE B  13      19.058   6.601  19.789  1.00 11.02      8HVP1022
ATOM    869  CD1 ILE B  13      20.418   5.094  17.098  1.00 19.66      8HVP1023
ATOM    870  N   ARG B  14      23.576   7.463  20.130  1.00 19.20      8HVP1024
ATOM    871  CA  ARG B  14      25.006   7.365  19.723  1.00 25.30      8HVP1025
ATOM    872  C   ARG B  14      25.243   5.828  19.659  1.00 26.26      8HVP1026
ATOM    873  O   ARG B  14      24.886   5.226  20.683  1.00 28.15      8HVP1027
ATOM    874  CB  ARG B  14      26.194   7.762  20.539  1.00 34.20      8HVP1028
ATOM    875  CG  ARG B  14      26.381   8.789  21.594  1.00 46.14      8HVP1029
ATOM    876  CD  ARG B  14      27.682   8.861  22.313  1.00 43.75      8HVP1030
ATOM    877  NE  ARG B  14      28.833   9.135  21.480  1.00 43.33      8HVP1031
ATOM    878  CZ  ARG B  14      29.471   8.225  20.734  1.00 45.45      8HVP1032
ATOM    879  NH1 ARG B  14      29.249   6.920  20.723  1.00 38.71      8HVP1033
ATOM    880  NH2 ARG B  14      30.324   8.673  19.806  1.00 51.01      8HVP1034
ATOM    881  N   ILE B  15      25.820   5.334  18.598  1.00 28.90      8HVP1035
ATOM    882  CA  ILE B  15      26.161   3.902  18.521  1.00 31.28      8HVP1036
ATOM    883  C   ILE B  15      27.548   3.841  17.877  1.00 31.86      8HVP1037
ATOM    884  O   ILE B  15      27.550   4.139  16.675  1.00 34.27      8HVP1038
ATOM    885  CB  ILE B  15      25.242   2.986  17.647  1.00 27.40      8HVP1039
ATOM    886  CG1 ILE B  15      23.801   3.550  17.659  1.00 30.83      8HVP1040
ATOM    887  CG2 ILE B  15      25.353   1.501  18.118  1.00 23.72      8HVP1041
ATOM    888  CD1 ILE B  15      23.181   3.677  16.232  1.00 31.58      8HVP1042
ATOM    889  N   GLY B  16      28.579   3.493  18.599  1.00 33.66      8HVP1043
ATOM    890  CA  GLY B  16      29.920   3.439  17.998  1.00 36.17      8HVP1044
ATOM    891  C   GLY B  16      30.272   4.691  17.191  1.00 38.23      8HVP1045
ATOM    892  O   GLY B  16      30.783   4.588  16.042  1.00 38.72      8HVP1046
ATOM    893  N   GLY B  17      30.023   5.875  17.760  1.00 37.56      8HVP1047
ATOM    894  CA  GLY B  17      30.371   7.125  17.058  1.00 36.56      8HVP1048
ATOM    895  C   GLY B  17      29.469   7.488  15.882  1.00 34.87      8HVP1049
ATOM    896  O   GLY B  17      29.718   8.398  15.074  1.00 32.49      8HVP1050
ATOM    897  N   GLN B  18      28.403   6.723  15.803  1.00 31.88      8HVP1051
ATOM    898  CA  GLN B  18      27.332   7.006  14.853  1.00 32.64      8HVP1052
ATOM    899  C   GLN B  18      26.368   7.826  15.739  1.00 31.59      8HVP1053
ATOM    900  O   GLN B  18      26.015   7.341  16.831  1.00 29.27      8HVP1054
ATOM    901  CB  GLN B  18      26.622   5.781  14.308  1.00 47.57      8HVP1055
ATOM    902  CG  GLN B  18      27.596   4.851  13.567  1.00 57.60      8HVP1056
ATOM    903  CD  GLN B  18      27.932   5.467  12.218  1.00 61.19      8HVP1057
ATOM    904  OE1 GLN B  18      28.763   6.373  12.162  1.00 64.28      8HVP1058
ATOM    905  NE2 GLN B  18      27.207   4.959  11.223  1.00 59.60      8HVP1059
ATOM    906  N   LEU B  19      26.148   9.042  15.302  1.00 29.82      8HVP1060
ATOM    907  CA  LEU B  19      25.149   9.917  15.979  1.00 29.89      8HVP1061
ATOM    908  C   LEU B  19      23.936   9.593  15.112  1.00 27.07      8HVP1062
ATOM    909  O   LEU B  19      24.220   9.604  13.892  1.00 30.34      8HVP1063
ATOM    910  CB  LEU B  19      25.656  11.339  16.015  1.00 29.62      8HVP1064
ATOM    911  CG  LEU B  19      26.168  11.974  17.294  1.00 32.57      8HVP1065
ATOM    912  CD1 LEU B  19      25.019  12.444  18.202  1.00 26.91      8HVP1066
ATOM    913  CD2 LEU B  19      27.095  11.019  18.059  1.00 31.34      8HVP1067
ATOM    914  N   LYS B  20      22.804   9.170  15.621  1.00 26.45      8HVP1068
ATOM    915  CA  LYS B  20      21.700   8.810  14.674  1.00 22.28      8HVP1069
ATOM    916  C   LYS B  20      20.315   9.136  15.205  1.00 20.11      8HVP1070
ATOM    917  O   LYS B  20      20.097   9.503  16.388  1.00 16.11      8HVP1071
ATOM    918  CB  LYS B  20      21.865   7.380  14.163  1.00 19.56      8HVP1072
ATOM    919  CG  LYS B  20      21.341   7.177  12.725  1.00 27.74      8HVP1073
ATOM    920  CD  LYS B  20      22.260   6.479  11.751  1.00 26.62      8HVP1074
ATOM    921  CE  LYS B  20      23.498   5.759  12.178  1.00 18.42      8HVP1075
ATOM    922  NZ  LYS B  20      23.364   4.515  12.946  1.00 16.64      8HVP1076
ATOM    923  N   GLU B  21      19.343   9.036  14.287  1.00 17.43      8HVP1077
ATOM    924  CA  GLU B  21      17.937   9.319  14.635  1.00 13.51      8HVP1078
ATOM    925  C   GLU B  21      17.078   8.089  14.826  1.00  8.57      8HVP1079
ATOM    926  O   GLU B  21      17.075   7.126  14.079  1.00  3.48      8HVP1080
ATOM    927  CB  GLU B  21      17.226  10.239  13.644  1.00 26.89      8HVP1081
ATOM    928  CG  GLU B  21      17.343  11.745  13.974  1.00 33.60      8HVP1082
ATOM    929  CD  GLU B  21      16.331  12.542  13.170  1.00 40.53      8HVP1083
ATOM    930  OE1 GLU B  21      15.879  11.992  12.167  1.00 35.62      8HVP1084
ATOM    931  OE2 GLU B  21      16.073  13.654  13.684  1.00 34.83      8HVP1085
ATOM    932  N   ALA B  22      16.282   8.155  15.875  1.00  8.69      8HVP1086
ATOM    933  CA  ALA B  22      15.408   7.042  16.232  1.00  8.62      8HVP1087
ATOM    934  C   ALA B  22      14.029   7.471  16.690  1.00  7.93      8HVP1088
ATOM    935  O   ALA B  22      13.780   8.599  17.108  1.00  4.79      8HVP1089
ATOM    936  CB  ALA B  22      16.186   6.273  17.291  1.00  2.50      8HVP1090
ATOM    937  N   LEU B  23      13.131   6.527  16.570  1.00  8.97      8HVP1091
ATOM    938  CA  LEU B  23      11.715   6.576  16.855  1.00  6.82      8HVP1092
ATOM    939  C   LEU B  23      11.585   5.806  18.182  1.00 10.95      8HVP1093
ATOM    940  O   LEU B  23      11.945   4.613  18.112  1.00 10.10      8HVP1094
ATOM    941  CB  LEU B  23      11.013   5.782  15.759  1.00  2.00      8HVP1095
ATOM    942  CG  LEU B  23       9.562   5.834  15.401  1.00  2.00      8HVP1096
ATOM    943  CD1 LEU B  23       9.296   7.140  14.617  1.00  2.00      8HVP1097
ATOM    944  CD2 LEU B  23       9.141   4.802  14.364  1.00  2.16      8HVP1098
ATOM    945  N   LEU B  24      11.191   6.493  19.227  1.00 10.43      8HVP1099
ATOM    946  CA  LEU B  24      10.892   5.811  20.501  1.00 12.28      8HVP1100
ATOM    947  C   LEU B  24       9.608   5.010  20.194  1.00  9.36      8HVP1101
ATOM    948  O   LEU B  24       8.578   5.662  19.993  1.00 12.60      8HVP1102
ATOM    949  CB  LEU B  24      10.632   6.813  21.639  1.00  7.17      8HVP1103
ATOM    950  CG  LEU B  24      11.653   7.929  21.812  1.00  5.54      8HVP1104
ATOM    951  CD1 LEU B  24      11.357   8.652  23.109  1.00  9.55      8HVP1105
ATOM    952  CD2 LEU B  24      13.056   7.317  21.731  1.00  2.00      8HVP1106
ATOM    953  N   ASP B  25       9.701   3.708  20.205  1.00  8.50      8HVP1107
ATOM    954  CA  ASP B  25       8.569   2.830  19.890  1.00  5.50      8HVP1108
ATOM    955  C   ASP B  25       7.962   2.057  21.057  1.00  2.68      8HVP1109
ATOM    956  O   ASP B  25       8.249   0.858  21.174  1.00  2.00      8HVP1110
ATOM    957  CB  ASP B  25       9.094   1.887  18.758  1.00  2.00      8HVP1111
ATOM    958  CG  ASP B  25       7.855   1.344  18.064  1.00 12.58      8HVP1112
ATOM    959  OD1 ASP B  25       6.760   1.311  18.713  1.00  2.00      8HVP1113
ATOM    960  OD2 ASP B  25       7.891   1.001  16.863  1.00  2.00      8HVP1114
ATOM    961  N   THR B  26       7.021   2.612  21.812  1.00  2.88      8HVP1115
ATOM    962  CA  THR B  26       6.460   1.826  22.933  1.00  4.04      8HVP1116
ATOM    963  C   THR B  26       5.802   0.529  22.459  1.00  4.48      8HVP1117
ATOM    964  O   THR B  26       5.428  -0.322  23.290  1.00  2.00      8HVP1118
ATOM    965  CB  THR B  26       5.410   2.570  23.847  1.00  2.00      8HVP1119
ATOM    966  OG1 THR B  26       4.403   3.014  22.912  1.00  2.00      8HVP1120
ATOM    967  CG2 THR B  26       6.022   3.695  24.670  1.00  2.00      8HVP1121
ATOM    968  N   GLY B  27       5.722   0.437  21.144  1.00  2.00      8HVP1122
ATOM    969  CA  GLY B  27       5.087  -0.711  20.511  1.00  2.00      8HVP1123
ATOM    970  C   GLY B  27       6.094  -1.684  19.944  1.00  3.33      8HVP1124
ATOM    971  O   GLY B  27       5.613  -2.651  19.311  1.00  7.98      8HVP1125
ATOM    972  N   ALA B  28       7.374  -1.463  20.157  1.00  3.25      8HVP1126
ATOM    973  CA  ALA B  28       8.441  -2.340  19.672  1.00  2.00      8HVP1127
ATOM    974  C   ALA B  28       9.025  -3.158  20.823  1.00  2.00      8HVP1128
ATOM    975  O   ALA B  28       9.481  -2.652  21.845  1.00  2.00      8HVP1129
ATOM    976  CB  ALA B  28       9.618  -1.683  19.001  1.00  2.00      8HVP1130
ATOM    977  N   ASP B  29       8.954  -4.439  20.553  1.00  2.00      8HVP1131
ATOM    978  CA  ASP B  29       9.483  -5.475  21.428  1.00  4.80      8HVP1132
ATOM    979  C   ASP B  29      11.009  -5.367  21.606  1.00  5.96      8HVP1133
ATOM    980  O   ASP B  29      11.496  -5.585  22.727  1.00  5.93      8HVP1134
ATOM    981  CB  ASP B  29       9.022  -6.840  20.899  1.00  7.65      8HVP1135
ATOM    982  CG  ASP B  29       7.845  -7.432  21.624  1.00 16.24      8HVP1136
ATOM    983  OD1 ASP B  29       6.883  -6.685  21.858  1.00 26.97      8HVP1137
ATOM    984  OD2 ASP B  29       7.868  -8.631  21.991  1.00 19.75      8HVP1138
ATOM    985  N   ASP B  30      11.716  -5.174  20.516  1.00  7.34      8HVP1139
ATOM    986  CA  ASP B  30      13.124  -5.121  20.191  1.00  4.67      8HVP1140
ATOM    987  C   ASP B  30      13.557  -3.784  19.597  1.00  2.00      8HVP1141
ATOM    988  O   ASP B  30      12.700  -2.963  19.244  1.00  2.00      8HVP1142
ATOM    989  CB  ASP B  30      13.428  -6.156  19.051  1.00  2.00      8HVP1143
ATOM    990  CG  ASP B  30      12.960  -7.523  19.518  1.00 19.35      8HVP1144
ATOM    991  OD1 ASP B  30      13.301  -7.714  20.722  1.00 28.54      8HVP1145
ATOM    992  OD2 ASP B  30      12.257  -8.296  18.837  1.00 18.48      8HVP1146
ATOM    993  N   THR B  31      14.855  -3.654  19.335  1.00  6.35      8HVP1147
ATOM    994  CA  THR B  31      15.480  -2.459  18.741  1.00  2.45      8HVP1148
ATOM    995  C   THR B  31      16.107  -2.874  17.421  1.00  2.57      8HVP1149
ATOM    996  O   THR B  31      16.989  -3.703  17.343  1.00  2.38      8HVP1150
ATOM    997  CB  THR B  31      16.541  -1.792  19.696  1.00  8.53      8HVP1151
ATOM    998  OG1 THR B  31      15.856  -1.705  20.992  1.00  2.64      8HVP1152
ATOM    999  CG2 THR B  31      17.128  -0.445  19.245  1.00  2.00      8HVP1153
ATOM   1000  N   VAL B  32      15.639  -2.267  16.360  1.00  3.43      8HVP1154
ATOM   1001  CA  VAL B  32      16.019  -2.557  14.989  1.00  2.00      8HVP1155
ATOM   1002  C   VAL B  32      16.527  -1.268  14.365  1.00  3.55      8HVP1156
ATOM   1003  O   VAL B  32      15.737  -0.339  14.189  1.00  5.13      8HVP1157
ATOM   1004  CB  VAL B  32      14.832  -3.093  14.175  1.00  3.44      8HVP1158
ATOM   1005  CG1 VAL B  32      15.292  -3.729  12.866  1.00  2.00      8HVP1159
ATOM   1006  CG2 VAL B  32      13.975  -4.061  15.009  1.00  2.00      8HVP1160
ATOM   1007  N   LEU B  33      17.793  -1.326  14.034  1.00  2.00      8HVP1161
ATOM   1008  CA  LEU B  33      18.476  -0.151  13.433  1.00  4.39      8HVP1162
ATOM   1009  C   LEU B  33      18.702  -0.677  12.018  1.00  2.00      8HVP1163
ATOM   1010  O   LEU B  33      18.716  -1.893  11.949  1.00  2.00      8HVP1164
ATOM   1011  CB  LEU B  33      19.648   0.118  14.374  1.00  2.00      8HVP1165
ATOM   1012  CG  LEU B  33      19.431   0.854  15.671  1.00  2.00      8HVP1166
ATOM   1013  CD1 LEU B  33      19.625  -0.019  16.915  1.00  2.00      8HVP1167
ATOM   1014  CD2 LEU B  33      20.578   1.874  15.710  1.00 13.97      8HVP1168
ATOM   1015  N   GLU B  34      18.668   0.153  11.026  1.00 11.86      8HVP1169
ATOM   1016  CA  GLU B  34      18.921  -0.217   9.609  1.00 19.66      8HVP1170
ATOM   1017  C   GLU B  34      20.269  -0.927   9.455  1.00 21.70      8HVP1171
ATOM   1018  O   GLU B  34      20.770  -1.586  10.388  1.00 23.50      8HVP1172
ATOM   1019  CB  GLU B  34      19.178   1.123   8.828  1.00 24.09      8HVP1173
ATOM   1020  CG  GLU B  34      20.154   1.911   9.701  1.00 41.99      8HVP1174
ATOM   1021  CD  GLU B  34      21.007   3.034   9.293  1.00 54.75      8HVP1175
ATOM   1022  OE1 GLU B  34      20.792   3.376   8.110  1.00 66.31      8HVP1176
ATOM   1023  OE2 GLU B  34      21.836   3.539  10.050  1.00 60.98      8HVP1177
ATOM   1024  N   GLU B  35      20.890  -0.735   8.281  1.00 23.86      8HVP1178
ATOM   1025  CA  GLU B  35      22.198  -1.316   8.006  1.00 25.01      8HVP1179
ATOM   1026  C   GLU B  35      23.404  -0.584   8.615  1.00 24.91      8HVP1180
ATOM   1027  O   GLU B  35      23.690   0.564   8.213  1.00 24.28      8HVP1181
ATOM   1028  CB  GLU B  35      22.593  -1.469   6.535  1.00 30.71      8HVP1182
ATOM   1029  CG  GLU B  35      21.865  -2.546   5.752  1.00 26.17      8HVP1183
ATOM   1030  CD  GLU B  35      21.271  -3.614   6.626  1.00 30.32      8HVP1184
ATOM   1031  OE1 GLU B  35      22.050  -4.030   7.510  1.00 30.03      8HVP1185
ATOM   1032  OE2 GLU B  35      20.109  -3.919   6.410  1.00 30.07      8HVP1186
ATOM   1033  N   MET B  36      24.050  -1.359   9.474  1.00 20.99      8HVP1187
ATOM   1034  CA  MET B  36      25.262  -0.922  10.165  1.00 21.40      8HVP1188
ATOM   1035  C   MET B  36      26.132  -2.128  10.553  1.00 21.96      8HVP1189
ATOM   1036  O   MET B  36      25.723  -3.207  11.032  1.00 18.06      8HVP1190
ATOM   1037  CB  MET B  36      24.977   0.070  11.272  1.00 12.31      8HVP1191
ATOM   1038  CG  MET B  36      24.552  -0.590  12.536  1.00 20.81      8HVP1192
ATOM   1039  SD  MET B  36      24.155   0.798  13.659  1.00 41.04      8HVP1193
ATOM   1040  CE  MET B  36      25.800   1.572  13.710  1.00 21.74      8HVP1194
ATOM   1041  N   ASN B  37      27.413  -1.843  10.318  1.00 22.96      8HVP1195
ATOM   1042  CA  ASN B  37      28.526  -2.803  10.481  1.00 26.45      8HVP1196
ATOM   1043  C   ASN B  37      29.058  -3.002  11.889  1.00 24.22      8HVP1197
ATOM   1044  O   ASN B  37      30.257  -2.750  12.146  1.00 27.66      8HVP1198
ATOM   1045  CB  ASN B  37      29.608  -2.306   9.499  1.00 35.13      8HVP1199
ATOM   1046  CG  ASN B  37      30.495  -3.456   9.064  1.00 43.47      8HVP1200
ATOM   1047  OD1 ASN B  37      30.062  -4.594   9.339  1.00 51.18      8HVP1201
ATOM   1048  ND2 ASN B  37      31.615  -3.120   8.422  1.00 42.91      8HVP1202
ATOM   1049  N   LEU B  38      28.241  -3.500  12.795  1.00 22.53      8HVP1203
ATOM   1050  CA  LEU B  38      28.712  -3.604  14.184  1.00 21.71      8HVP1204
ATOM   1051  C   LEU B  38      29.813  -4.653  14.215  1.00 21.57      8HVP1205
ATOM   1052  O   LEU B  38      29.954  -5.430  13.278  1.00 20.06      8HVP1206
ATOM   1053  CB  LEU B  38      27.544  -3.677  15.174  1.00 22.38      8HVP1207
ATOM   1054  CG  LEU B  38      26.588  -2.485  15.107  1.00 17.47      8HVP1208
ATOM   1055  CD1 LEU B  38      25.171  -2.817  15.535  1.00 18.42      8HVP1209
ATOM   1056  CD2 LEU B  38      27.118  -1.340  15.949  1.00 13.96      8HVP1210
ATOM   1057  N   PRO B  39      30.589  -4.547  15.271  1.00 23.87      8HVP1211
ATOM   1058  CA  PRO B  39      31.705  -5.450  15.533  1.00 24.03      8HVP1212
ATOM   1059  C   PRO B  39      31.177  -6.642  16.331  1.00 22.54      8HVP1213
ATOM   1060  O   PRO B  39      30.523  -6.397  17.364  1.00 18.45      8HVP1214
ATOM   1061  CB  PRO B  39      32.671  -4.638  16.389  1.00 24.63      8HVP1215
ATOM   1062  CG  PRO B  39      31.828  -3.570  17.034  1.00 24.98      8HVP1216
ATOM   1063  CD  PRO B  39      30.461  -3.575  16.383  1.00 24.62      8HVP1217
ATOM   1064  N   GLY B  40      31.474  -7.812  15.802  1.00 20.94      8HVP1218
ATOM   1065  CA  GLY B  40      31.097  -9.019  16.495  1.00 28.11      8HVP1219
ATOM   1066  C   GLY B  40      30.325 -10.166  15.898  1.00 29.39      8HVP1220
ATOM   1067  O   GLY B  40      30.129 -10.333  14.677  1.00 33.81      8HVP1221
ATOM   1068  N   LYS B  41      29.914 -10.980  16.864  1.00 28.89      8HVP1222
ATOM   1069  CA  LYS B  41      29.099 -12.177  16.775  1.00 27.88      8HVP1223
ATOM   1070  C   LYS B  41      27.619 -11.718  16.829  1.00 27.43      8HVP1224
ATOM   1071  O   LYS B  41      27.198 -10.864  17.628  1.00 28.52      8HVP1225
ATOM   1072  CB  LYS B  41      29.182 -13.120  17.945  1.00 36.31      8HVP1226
ATOM   1073  CG  LYS B  41      30.254 -13.963  18.544  1.00 30.73      8HVP1227
ATOM   1074  CD  LYS B  41      30.984 -14.877  17.594  1.00 29.28      8HVP1228
ATOM   1075  CE  LYS B  41      30.202 -15.339  16.383  1.00 31.88      8HVP1229
ATOM   1076  NZ  LYS B  41      30.925 -16.450  15.716  1.00 27.56      8HVP1230
ATOM   1077  N   TRP B  42      26.882 -12.441  16.040  1.00 27.58      8HVP1231
ATOM   1078  CA  TRP B  42      25.433 -12.279  15.901  1.00 28.24      8HVP1232
ATOM   1079  C   TRP B  42      24.929 -13.670  15.533  1.00 27.17      8HVP1233
ATOM   1080  O   TRP B  42      25.696 -14.610  15.362  1.00 25.95      8HVP1234
ATOM   1081  CB  TRP B  42      25.069 -11.149  14.956  1.00 37.00      8HVP1235
ATOM   1082  CG  TRP B  42      25.665 -11.312  13.604  1.00 46.23      8HVP1236
ATOM   1083  CD1 TRP B  42      26.672 -10.578  13.038  1.00 49.04      8HVP1237
ATOM   1084  CD2 TRP B  42      25.321 -12.335  12.655  1.00 49.52      8HVP1238
ATOM   1085  NE1 TRP B  42      26.965 -11.059  11.780  1.00 49.97      8HVP1239
ATOM   1086  CE2 TRP B  42      26.160 -12.136  11.531  1.00 52.47      8HVP1240
ATOM   1087  CE3 TRP B  42      24.387 -13.359  12.630  1.00 47.48      8HVP1241
ATOM   1088  CZ2 TRP B  42      26.077 -12.948  10.410  1.00 56.71      8HVP1242
ATOM   1089  CZ3 TRP B  42      24.320 -14.162  11.521  1.00 51.28      8HVP1243
ATOM   1090  CH2 TRP B  42      25.135 -13.968  10.417  1.00 54.84      8HVP1244
ATOM   1091  N   LYS B  43      23.640 -13.766  15.434  1.00 29.09      8HVP1245
ATOM   1092  CA  LYS B  43      22.759 -14.900  15.205  1.00 26.73      8HVP1246
ATOM   1093  C   LYS B  43      21.470 -14.400  14.572  1.00 26.40      8HVP1247
ATOM   1094  O   LYS B  43      20.741 -13.573  15.156  1.00 25.74      8HVP1248
ATOM   1095  CB  LYS B  43      22.374 -15.506  16.587  1.00 28.42      8HVP1249
ATOM   1096  CG  LYS B  43      22.805 -14.615  17.747  1.00 30.96      8HVP1250
ATOM   1097  CD  LYS B  43      22.046 -14.565  19.021  1.00 33.44      8HVP1251
ATOM   1098  CE  LYS B  43      22.143 -15.700  19.992  1.00 33.13      8HVP1252
ATOM   1099  NZ  LYS B  43      21.336 -15.432  21.218  1.00 27.94      8HVP1253
ATOM   1100  N   PRO B  44      21.198 -14.885  13.376  1.00 27.94      8HVP1254
ATOM   1101  CA  PRO B  44      19.947 -14.533  12.677  1.00 27.06      8HVP1255
ATOM   1102  C   PRO B  44      18.740 -14.831  13.575  1.00 23.74      8HVP1256
ATOM   1103  O   PRO B  44      18.699 -15.616  14.543  1.00 23.37      8HVP1257
ATOM   1104  CB  PRO B  44      19.990 -15.297  11.359  1.00 27.32      8HVP1258
ATOM   1105  CG  PRO B  44      20.901 -16.460  11.652  1.00 28.58      8HVP1259
ATOM   1106  CD  PRO B  44      21.943 -15.906  12.624  1.00 28.32      8HVP1260
ATOM   1107  N   LYS B  45      17.710 -14.060  13.249  1.00 18.28      8HVP1261
ATOM   1108  CA  LYS B  45      16.424 -14.073  13.919  1.00 10.05      8HVP1262
ATOM   1109  C   LYS B  45      15.410 -13.403  12.980  1.00  5.88      8HVP1263
ATOM   1110  O   LYS B  45      15.736 -12.676  12.016  1.00  3.74      8HVP1264
ATOM   1111  CB  LYS B  45      16.469 -13.321  15.250  1.00  5.89      8HVP1265
ATOM   1112  CG  LYS B  45      15.077 -13.238  15.847  1.00  3.10      8HVP1266
ATOM   1113  CD  LYS B  45      14.828 -12.229  16.904  1.00  3.91      8HVP1267
ATOM   1114  CE  LYS B  45      15.080 -12.795  18.299  1.00  3.48      8HVP1268
ATOM   1115  NZ  LYS B  45      14.644 -11.709  19.238  1.00  2.00      8HVP1269
ATOM   1116  N   MET B  46      14.172 -13.713  13.353  1.00  2.04      8HVP1270
ATOM   1117  CA  MET B  46      13.017 -13.163  12.665  1.00  2.00      8HVP1271
ATOM   1118  C   MET B  46      12.014 -12.324  13.423  1.00  2.00      8HVP1272
ATOM   1119  O   MET B  46      11.701 -12.644  14.579  1.00  2.00      8HVP1273
ATOM   1120  CB  MET B  46      12.370 -14.279  11.814  1.00  3.38      8HVP1274
ATOM   1121  CG  MET B  46      13.015 -14.194  10.454  1.00  2.00      8HVP1275
ATOM   1122  SD  MET B  46      12.190 -15.349   9.346  1.00 12.32      8HVP1276
ATOM   1123  CE  MET B  46      13.204 -15.043   7.890  1.00  2.00      8HVP1277
ATOM   1124  N   ILE B  47      11.642 -11.224  12.801  1.00  2.00      8HVP1278
ATOM   1125  CA  ILE B  47      10.647 -10.378  13.456  1.00  4.30      8HVP1279
ATOM   1126  C   ILE B  47       9.698  -9.929  12.362  1.00  4.03      8HVP1280
ATOM   1127  O   ILE B  47      10.103  -9.976  11.206  1.00  3.63      8HVP1281
ATOM   1128  CB  ILE B  47      11.266  -9.238  14.339  1.00  9.07      8HVP1282
ATOM   1129  CG1 ILE B  47      11.967  -8.226  13.478  1.00  2.00      8HVP1283
ATOM   1130  CG2 ILE B  47      12.234  -9.803  15.421  1.00  2.00      8HVP1284
ATOM   1131  CD1 ILE B  47      12.567  -6.882  13.575  1.00  2.00      8HVP1285
ATOM   1132  N   GLY B  48       8.520  -9.579  12.813  1.00  9.14      8HVP1286
ATOM   1133  CA  GLY B  48       7.495  -9.090  11.877  1.00 10.44      8HVP1287
ATOM   1134  C   GLY B  48       6.462  -8.295  12.687  1.00 11.81      8HVP1288
ATOM   1135  O   GLY B  48       6.614  -8.152  13.908  1.00  9.14      8HVP1289
ATOM   1136  N   GLY B  49       5.420  -7.962  11.938  1.00 10.82      8HVP1290
ATOM   1137  CA  GLY B  49       4.259  -7.215  12.439  1.00  9.96      8HVP1291
ATOM   1138  C   GLY B  49       3.348  -6.879  11.271  1.00  8.95      8HVP1292
ATOM   1139  O   GLY B  49       2.977  -7.831  10.575  1.00 10.25      8HVP1293
ATOM   1140  N   ILE B  50       2.977  -5.625  11.070  1.00 10.74      8HVP1294
ATOM   1141  CA  ILE B  50       2.065  -5.320   9.923  1.00  8.35      8HVP1295
ATOM   1142  C   ILE B  50       2.934  -5.730   8.761  1.00 10.18      8HVP1296
ATOM   1143  O   ILE B  50       4.071  -5.215   8.934  1.00 16.59      8HVP1297
ATOM   1144  CB  ILE B  50       1.691  -3.801   9.905  1.00  2.25      8HVP1298
ATOM   1145  CG1 ILE B  50       0.659  -3.526  11.033  1.00  2.00      8HVP1299
ATOM   1146  CG2 ILE B  50       1.104  -3.143   8.635  1.00  2.00      8HVP1300
ATOM   1147  CD1 ILE B  50      -0.606  -4.427  10.901  1.00  3.68      8HVP1301
ATOM   1148  N   GLY B  51       2.549  -6.448   7.743  1.00  9.92      8HVP1302
ATOM   1149  CA  GLY B  51       3.517  -6.626   6.624  1.00  7.18      8HVP1303
ATOM   1150  C   GLY B  51       3.983  -8.042   6.403  1.00  9.03      8HVP1304
ATOM   1151  O   GLY B  51       3.886  -8.678   5.324  1.00  7.91      8HVP1305
ATOM   1152  N   GLY B  52       4.516  -8.536   7.516  1.00 12.04      8HVP1306
ATOM   1153  CA  GLY B  52       5.046  -9.907   7.691  1.00  8.63      8HVP1307
ATOM   1154  C   GLY B  52       6.357  -9.841   8.450  1.00  2.00      8HVP1308
ATOM   1155  O   GLY B  52       6.654  -8.801   9.024  1.00  3.66      8HVP1309
ATOM   1156  N   PHE B  53       7.168 -10.849   8.266  1.00  5.97      8HVP1310
ATOM   1157  CA  PHE B  53       8.486 -11.020   8.918  1.00  2.93      8HVP1311
ATOM   1158  C   PHE B  53       9.600 -10.612   7.988  1.00  6.45      8HVP1312
ATOM   1159  O   PHE B  53       9.330 -10.629   6.780  1.00 10.93      8HVP1313
ATOM   1160  CB  PHE B  53       8.731 -12.469   9.389  1.00  4.32      8HVP1314
ATOM   1161  CG  PHE B  53       7.829 -12.804  10.557  1.00  6.51      8HVP1315
ATOM   1162  CD1 PHE B  53       6.449 -12.738  10.377  1.00 10.36      8HVP1316
ATOM   1163  CD2 PHE B  53       8.304 -13.121  11.813  1.00  8.98      8HVP1317
ATOM   1164  CE1 PHE B  53       5.561 -13.038  11.367  1.00  2.00      8HVP1318
ATOM   1165  CE2 PHE B  53       7.401 -13.420  12.840  1.00 12.75      8HVP1319
ATOM   1166  CZ  PHE B  53       6.017 -13.366  12.645  1.00  2.00      8HVP1320
ATOM   1167  N   ILE B  54      10.745 -10.320   8.523  1.00  7.04      8HVP1321
ATOM   1168  CA  ILE B  54      11.958  -9.948   7.787  1.00  7.76      8HVP1322
ATOM   1169  C   ILE B  54      13.116 -10.492   8.653  1.00  7.51      8HVP1323
ATOM   1170  O   ILE B  54      12.882 -10.557   9.868  1.00  3.94      8HVP1324
ATOM   1171  CB  ILE B  54      12.079  -8.397   7.617  1.00  2.00      8HVP1325
ATOM   1172  CG1 ILE B  54      12.250  -7.836   9.045  1.00  2.00      8HVP1326
ATOM   1173  CG2 ILE B  54      10.884  -7.810   6.871  1.00  2.00      8HVP1327
ATOM   1174  CD1 ILE B  54      13.120  -6.569   9.130  1.00  2.00      8HVP1328
ATOM   1175  N   LYS B  55      14.226 -10.783   8.026  1.00  4.94      8HVP1329
ATOM   1176  CA  LYS B  55      15.310 -11.368   8.834  1.00  9.23      8HVP1330
ATOM   1177  C   LYS B  55      16.257 -10.246   9.271  1.00  9.31      8HVP1331
ATOM   1178  O   LYS B  55      16.554  -9.326   8.485  1.00  6.93      8HVP1332
ATOM   1179  CB  LYS B  55      16.077 -12.445   8.077  1.00 24.98      8HVP1333
ATOM   1180  CG  LYS B  55      17.423 -12.772   8.729  1.00 43.02      8HVP1334
ATOM   1181  CD  LYS B  55      18.300 -13.675   7.872  1.00 53.33      8HVP1335
ATOM   1182  CE  LYS B  55      19.689 -13.826   8.488  1.00 57.93      8HVP1336
ATOM   1183  NZ  LYS B  55      20.300 -15.107   8.046  1.00 57.35      8HVP1337
ATOM   1184  N   VAL B  56      16.739 -10.399  10.488  1.00  2.00      8HVP1338
ATOM   1185  CA  VAL B  56      17.636  -9.397  11.048  1.00  2.00      8HVP1339
ATOM   1186  C   VAL B  56      18.747 -10.115  11.799  1.00  3.32      8HVP1340
ATOM   1187  O   VAL B  56      18.425 -11.224  12.256  1.00  6.46      8HVP1341
ATOM   1188  CB  VAL B  56      16.915  -8.401  11.980  1.00  7.22      8HVP1342
ATOM   1189  CG1 VAL B  56      15.835  -7.629  11.242  1.00  9.44      8HVP1343
ATOM   1190  CG2 VAL B  56      16.426  -9.056  13.283  1.00  2.54      8HVP1344
ATOM   1191  N   ARG B  57      19.878  -9.457  11.914  1.00  2.00      8HVP1345
ATOM   1192  CA  ARG B  57      20.953 -10.051  12.721  1.00  4.67      8HVP1346
ATOM   1193  C   ARG B  57      20.907  -9.356  14.096  1.00  5.22      8HVP1347
ATOM   1194  O   ARG B  57      20.774  -8.130  14.141  1.00  4.28      8HVP1348
ATOM   1195  CB  ARG B  57      22.321  -9.885  12.141  1.00 12.84      8HVP1349
ATOM   1196  CG  ARG B  57      22.619 -10.531  10.797  1.00 12.46      8HVP1350
ATOM   1197  CD  ARG B  57      23.827  -9.835  10.266  1.00 21.00      8HVP1351
ATOM   1198  NE  ARG B  57      23.544  -8.448   9.903  1.00 35.91      8HVP1352
ATOM   1199  CZ  ARG B  57      24.355  -7.415  10.205  1.00 41.63      8HVP1353
ATOM   1200  NH1 ARG B  57      25.344  -7.628  11.082  1.00 36.55      8HVP1354
ATOM   1201  NH2 ARG B  57      24.147  -6.171   9.742  1.00 42.40      8HVP1355
ATOM   1202  N   GLN B  58      20.958 -10.164  15.132  1.00  4.24      8HVP1356
ATOM   1203  CA  GLN B  58      20.929  -9.868  16.548  1.00  2.00      8HVP1357
ATOM   1204  C   GLN B  58      22.342  -9.804  17.176  1.00  2.00      8HVP1358
ATOM   1205  O   GLN B  58      22.962 -10.910  17.183  1.00  2.00      8HVP1359
ATOM   1206  CB  GLN B  58      20.304 -11.052  17.328  1.00  2.00      8HVP1360
ATOM   1207  CG  GLN B  58      20.132 -10.685  18.794  1.00 10.91      8HVP1361
ATOM   1208  CD  GLN B  58      19.611 -11.801  19.668  1.00 14.93      8HVP1362
ATOM   1209  OE1 GLN B  58      20.247 -12.176  20.650  1.00 21.50      8HVP1363
ATOM   1210  NE2 GLN B  58      18.463 -12.419  19.366  1.00  8.34      8HVP1364
ATOM   1211  N   TYR B  59      22.711  -8.672  17.773  1.00  2.46      8HVP1365
ATOM   1212  CA  TYR B  59      23.981  -8.488  18.487  1.00  2.00      8HVP1366
ATOM   1213  C   TYR B  59      23.860  -8.440  20.013  1.00  2.00      8HVP1367
ATOM   1214  O   TYR B  59      22.999  -7.699  20.501  1.00  2.00      8HVP1368
ATOM   1215  CB  TYR B  59      24.663  -7.193  17.998  1.00  2.00      8HVP1369
ATOM   1216  CG  TYR B  59      25.115  -7.295  16.566  1.00  6.62      8HVP1370
ATOM   1217  CD1 TYR B  59      24.334  -6.931  15.475  1.00  2.00      8HVP1371
ATOM   1218  CD2 TYR B  59      26.472  -7.625  16.426  1.00  7.16      8HVP1372
ATOM   1219  CE1 TYR B  59      24.924  -7.013  14.197  1.00 13.21      8HVP1373
ATOM   1220  CE2 TYR B  59      27.053  -7.668  15.184  1.00  2.00      8HVP1374
ATOM   1221  CZ  TYR B  59      26.266  -7.379  14.061  1.00 10.93      8HVP1375
ATOM   1222  OH  TYR B  59      26.862  -7.420  12.834  1.00 18.08      8HVP1376
ATOM   1223  N   ASP B  60      24.633  -9.148  20.812  1.00  2.88      8HVP1377
ATOM   1224  CA  ASP B  60      24.403  -8.973  22.274  1.00 10.69      8HVP1378
ATOM   1225  C   ASP B  60      25.131  -7.704  22.730  1.00 12.02      8HVP1379
ATOM   1226  O   ASP B  60      25.650  -6.906  21.932  1.00 11.21      8HVP1380
ATOM   1227  CB  ASP B  60      24.563 -10.226  23.106  1.00 23.41      8HVP1381
ATOM   1228  CG  ASP B  60      23.408 -11.152  22.704  1.00 35.13      8HVP1382
ATOM   1229  OD1 ASP B  60      22.330 -10.514  22.641  1.00 39.29      8HVP1383
ATOM   1230  OD2 ASP B  60      23.547 -12.357  22.451  1.00 40.70      8HVP1384
ATOM   1231  N   GLN B  61      25.017  -7.501  24.024  1.00  9.58      8HVP1385
ATOM   1232  CA  GLN B  61      25.528  -6.383  24.782  1.00  8.24      8HVP1386
ATOM   1233  C   GLN B  61      26.170  -5.216  24.081  1.00  6.58      8HVP1387
ATOM   1234  O   GLN B  61      27.297  -4.831  24.407  1.00  9.84      8HVP1388
ATOM   1235  CB  GLN B  61      26.343  -6.903  25.975  1.00 16.61      8HVP1389
ATOM   1236  CG  GLN B  61      25.415  -7.298  27.125  1.00 26.01      8HVP1390
ATOM   1237  CD  GLN B  61      26.090  -7.394  28.471  1.00 32.51      8HVP1391
ATOM   1238  OE1 GLN B  61      25.901  -6.537  29.345  1.00 38.87      8HVP1392
ATOM   1239  NE2 GLN B  61      26.890  -8.447  28.635  1.00 31.15      8HVP1393
ATOM   1240  N   ILE B  62      25.451  -4.465  23.264  1.00  4.26      8HVP1394
ATOM   1241  CA  ILE B  62      25.901  -3.266  22.573  1.00  4.05      8HVP1395
ATOM   1242  C   ILE B  62      25.487  -2.015  23.327  1.00  4.67      8HVP1396
ATOM   1243  O   ILE B  62      24.297  -1.891  23.661  1.00  8.81      8HVP1397
ATOM   1244  CB  ILE B  62      25.358  -3.272  21.084  1.00  8.11      8HVP1398
ATOM   1245  CG1 ILE B  62      26.214  -4.274  20.264  1.00  9.08      8HVP1399
ATOM   1246  CG2 ILE B  62      25.307  -1.837  20.493  1.00  2.00      8HVP1400
ATOM   1247  CD1 ILE B  62      25.909  -4.298  18.753  1.00  5.72      8HVP1401
ATOM   1248  N   PRO B  63      26.441  -1.145  23.610  1.00  6.99      8HVP1402
ATOM   1249  CA  PRO B  63      26.257   0.127  24.321  1.00  6.15      8HVP1403
ATOM   1250  C   PRO B  63      25.557   1.142  23.435  1.00 10.75      8HVP1404
ATOM   1251  O   PRO B  63      25.783   1.158  22.192  1.00 18.39      8HVP1405
ATOM   1252  CB  PRO B  63      27.658   0.603  24.697  1.00  4.93      8HVP1406
ATOM   1253  CG  PRO B  63      28.565  -0.542  24.385  1.00  5.11      8HVP1407
ATOM   1254  CD  PRO B  63      27.881  -1.296  23.236  1.00  7.62      8HVP1408
ATOM   1255  N   VAL B  64      24.704   1.984  23.980  1.00  9.55      8HVP1409
ATOM   1256  CA  VAL B  64      24.008   2.929  23.077  1.00 11.32      8HVP1410
ATOM   1257  C   VAL B  64      23.721   4.095  24.018  1.00 16.28      8HVP1411
ATOM   1258  O   VAL B  64      23.720   3.938  25.259  1.00 12.69      8HVP1412
ATOM   1259  CB  VAL B  64      22.849   2.191  22.397  1.00 19.36      8HVP1413
ATOM   1260  CG1 VAL B  64      21.563   3.000  22.225  1.00 23.40      8HVP1414
ATOM   1261  CG2 VAL B  64      23.047   1.598  20.998  1.00  8.04      8HVP1415
ATOM   1262  N   GLU B  65      23.494   5.231  23.349  1.00 17.51      8HVP1416
ATOM   1263  CA  GLU B  65      23.096   6.447  24.099  1.00 16.89      8HVP1417
ATOM   1264  C   GLU B  65      21.817   7.080  23.554  1.00 12.66      8HVP1418
ATOM   1265  O   GLU B  65      21.791   7.691  22.462  1.00  9.45      8HVP1419
ATOM   1266  CB  GLU B  65      24.275   7.407  24.126  1.00 24.37      8HVP1420
ATOM   1267  CG  GLU B  65      24.133   8.725  24.886  1.00 30.75      8HVP1421
ATOM   1268  CD  GLU B  65      25.488   9.323  25.173  1.00 39.91      8HVP1422
ATOM   1269  OE1 GLU B  65      26.063   8.614  26.038  1.00 44.11      8HVP1423
ATOM   1270  OE2 GLU B  65      25.943  10.307  24.621  1.00 37.32      8HVP1424
ATOM   1271  N   ILE B  66      20.735   6.933  24.320  1.00 11.61      8HVP1425
ATOM   1272  CA  ILE B  66      19.445   7.540  23.954  1.00 13.42      8HVP1426
ATOM   1273  C   ILE B  66      19.282   8.909  24.610  1.00 11.36      8HVP1427
ATOM   1274  O   ILE B  66      18.767   9.003  25.728  1.00 15.10      8HVP1428
ATOM   1275  CB  ILE B  66      18.189   6.630  24.167  1.00  9.27      8HVP1429
ATOM   1276  CG1 ILE B  66      18.336   5.338  23.325  1.00  2.00      8HVP1430
ATOM   1277  CG2 ILE B  66      16.862   7.369  23.809  1.00  8.85      8HVP1431
ATOM   1278  CD1 ILE B  66      19.244   4.315  24.056  1.00  7.34      8HVP1432
HETATM 1279  N   ABA B  67      19.675   9.925  23.907  1.00 13.30      8HVP1433
HETATM 1280  CA  ABA B  67      19.686  11.326  24.264  1.00 17.39      8HVP1434
HETATM 1281  C   ABA B  67      20.287  11.692  25.627  1.00 21.03      8HVP1435
HETATM 1282  O   ABA B  67      19.628  12.392  26.429  1.00 22.00      8HVP1436
HETATM 1283  CB  ABA B  67      18.331  12.009  24.095  1.00 17.35      8HVP1437
HETATM 1284  CG  ABA B  67      17.117  11.103  24.237  1.00  2.14      8HVP1438
ATOM   1285  N   GLY B  68      21.561  11.352  25.809  1.00 20.94      8HVP1439
ATOM   1286  CA  GLY B  68      22.410  11.595  26.957  1.00 19.29      8HVP1440
ATOM   1287  C   GLY B  68      22.128  10.707  28.162  1.00 21.25      8HVP1441
ATOM   1288  O   GLY B  68      22.270  11.054  29.350  1.00 19.60      8HVP1442
ATOM   1289  N   HIS B  69      21.648   9.524  27.841  1.00 21.09      8HVP1443
ATOM   1290  CA  HIS B  69      21.241   8.476  28.776  1.00 19.62      8HVP1444
ATOM   1291  C   HIS B  69      21.902   7.215  28.214  1.00 22.76      8HVP1445
ATOM   1292  O   HIS B  69      21.499   6.919  27.070  1.00 26.88      8HVP1446
ATOM   1293  CB  HIS B  69      19.712   8.249  28.887  1.00  6.31      8HVP1447
ATOM   1294  CG  HIS B  69      18.965   9.364  29.578  1.00  6.71      8HVP1448
ATOM   1295  ND1 HIS B  69      18.239   9.336  30.775  1.00  2.00      8HVP1449
ATOM   1296  CD2 HIS B  69      18.872  10.645  29.079  1.00  4.67      8HVP1450
ATOM   1297  CE1 HIS B  69      17.797  10.537  30.965  1.00  2.00      8HVP1451
ATOM   1298  NE2 HIS B  69      18.136  11.362  29.966  1.00  2.00      8HVP1452
ATOM   1299  N   LYS B  70      22.882   6.618  28.881  1.00 21.04      8HVP1453
ATOM   1300  CA  LYS B  70      23.479   5.386  28.360  1.00 15.05      8HVP1454
ATOM   1301  C   LYS B  70      22.499   4.241  28.662  1.00 14.48      8HVP1455
ATOM   1302  O   LYS B  70      21.698   4.282  29.589  1.00 17.68      8HVP1456
ATOM   1303  CB  LYS B  70      24.764   4.931  28.983  1.00 19.55      8HVP1457
ATOM   1304  CG  LYS B  70      26.061   5.280  28.284  1.00 26.69      8HVP1458
ATOM   1305  CD  LYS B  70      27.064   5.766  29.331  1.00 32.24      8HVP1459
ATOM   1306  CE  LYS B  70      26.499   6.941  30.115  1.00 37.76      8HVP1460
ATOM   1307  NZ  LYS B  70      25.683   7.818  29.224  1.00 41.20      8HVP1461
ATOM   1308  N   ALA B  71      22.681   3.244  27.867  1.00 11.10      8HVP1462
ATOM   1309  CA  ALA B  71      21.983   1.964  27.880  1.00  9.54      8HVP1463
ATOM   1310  C   ALA B  71      22.726   1.051  26.855  1.00  7.05      8HVP1464
ATOM   1311  O   ALA B  71      23.279   1.503  25.829  1.00  2.34      8HVP1465
ATOM   1312  CB  ALA B  71      20.501   2.157  27.721  1.00 11.33      8HVP1466
ATOM   1313  N   ILE B  72      22.740  -0.219  27.216  1.00  2.00      8HVP1467
ATOM   1314  CA  ILE B  72      23.436  -1.261  26.493  1.00  5.49      8HVP1468
ATOM   1315  C   ILE B  72      22.535  -2.468  26.329  1.00  6.66      8HVP1469
ATOM   1316  O   ILE B  72      22.105  -2.907  27.440  1.00  8.44      8HVP1470
ATOM   1317  CB  ILE B  72      24.713  -1.760  27.296  1.00 16.05      8HVP1471
ATOM   1318  CG1 ILE B  72      25.370  -2.891  26.447  1.00 22.97      8HVP1472
ATOM   1319  CG2 ILE B  72      24.456  -2.172  28.756  1.00  4.00      8HVP1473
ATOM   1320  CD1 ILE B  72      26.364  -3.766  27.265  1.00 29.98      8HVP1474
ATOM   1321  N   GLY B  73      22.338  -2.923  25.093  1.00  2.00      8HVP1475
ATOM   1322  CA  GLY B  73      21.437  -4.104  25.069  1.00  2.00      8HVP1476
ATOM   1323  C   GLY B  73      21.562  -4.865  23.788  1.00  2.00      8HVP1477
ATOM   1324  O   GLY B  73      22.599  -4.727  23.158  1.00  2.00      8HVP1478
ATOM   1325  N   THR B  74      20.498  -5.596  23.498  1.00  5.86      8HVP1479
ATOM   1326  CA  THR B  74      20.407  -6.405  22.281  1.00  4.20      8HVP1480
ATOM   1327  C   THR B  74      19.924  -5.357  21.268  1.00 10.15      8HVP1481
ATOM   1328  O   THR B  74      19.176  -4.428  21.619  1.00 13.28      8HVP1482
ATOM   1329  CB  THR B  74      19.452  -7.629  22.317  1.00  6.75      8HVP1483
ATOM   1330  OG1 THR B  74      19.460  -8.272  23.630  1.00  6.45      8HVP1484
ATOM   1331  CG2 THR B  74      19.772  -8.692  21.245  1.00  8.22      8HVP1485
ATOM   1332  N   VAL B  75      20.406  -5.565  20.074  1.00 10.13      8HVP1486
ATOM   1333  CA  VAL B  75      20.079  -4.601  18.997  1.00 10.03      8HVP1487
ATOM   1334  C   VAL B  75      20.060  -5.449  17.734  1.00 11.32      8HVP1488
ATOM   1335  O   VAL B  75      21.000  -6.240  17.598  1.00 11.34      8HVP1489
ATOM   1336  CB  VAL B  75      21.142  -3.496  19.106  1.00 13.15      8HVP1490
ATOM   1337  CG1 VAL B  75      21.682  -3.092  17.736  1.00  2.00      8HVP1491
ATOM   1338  CG2 VAL B  75      20.687  -2.271  19.902  1.00  4.38      8HVP1492
ATOM   1339  N   LEU B  76      19.015  -5.307  16.930  1.00 14.07      8HVP1493
ATOM   1340  CA  LEU B  76      18.838  -6.041  15.685  1.00  9.94      8HVP1494
ATOM   1341  C   LEU B  76      19.164  -5.080  14.518  1.00 10.85      8HVP1495
ATOM   1342  O   LEU B  76      18.576  -3.981  14.537  1.00 11.91      8HVP1496
ATOM   1343  CB  LEU B  76      17.392  -6.465  15.439  1.00  2.00      8HVP1497
ATOM   1344  CG  LEU B  76      16.542  -7.066  16.480  1.00  2.00      8HVP1498
ATOM   1345  CD1 LEU B  76      15.141  -7.466  16.026  1.00  9.50      8HVP1499
ATOM   1346  CD2 LEU B  76      17.233  -8.266  17.113  1.00  2.00      8HVP1500
ATOM   1347  N   VAL B  77      19.930  -5.635  13.604  1.00  7.40      8HVP1501
ATOM   1348  CA  VAL B  77      20.229  -4.897  12.378  1.00  7.40      8HVP1502
ATOM   1349  C   VAL B  77      19.442  -5.598  11.245  1.00  8.21      8HVP1503
ATOM   1350  O   VAL B  77      19.282  -6.837  11.310  1.00  7.68      8HVP1504
ATOM   1351  CB  VAL B  77      21.701  -4.837  12.004  1.00 13.92      8HVP1505
ATOM   1352  CG1 VAL B  77      21.869  -4.214  10.605  1.00 11.45      8HVP1506
ATOM   1353  CG2 VAL B  77      22.529  -4.150  13.037  1.00  2.00      8HVP1507
ATOM   1354  N   GLY B  78      19.006  -4.810  10.277  1.00  2.90      8HVP1508
ATOM   1355  CA  GLY B  78      18.214  -5.472   9.211  1.00  4.68      8HVP1509
ATOM   1356  C   GLY B  78      17.538  -4.397   8.411  1.00  6.60      8HVP1510
ATOM   1357  O   GLY B  78      17.738  -3.235   8.784  1.00  7.71      8HVP1511
ATOM   1358  N   PRO B  79      16.748  -4.834   7.447  1.00 10.98      8HVP1512
ATOM   1359  CA  PRO B  79      16.106  -3.946   6.482  1.00 11.80      8HVP1513
ATOM   1360  C   PRO B  79      14.924  -3.116   6.916  1.00 12.03      8HVP1514
ATOM   1361  O   PRO B  79      13.925  -3.134   6.146  1.00 16.48      8HVP1515
ATOM   1362  CB  PRO B  79      15.733  -4.828   5.284  1.00 12.17      8HVP1516
ATOM   1363  CG  PRO B  79      15.721  -6.236   5.798  1.00 13.14      8HVP1517
ATOM   1364  CD  PRO B  79      16.530  -6.238   7.088  1.00 13.32      8HVP1518
ATOM   1365  N   THR B  80      15.064  -2.344   7.971  1.00  7.91      8HVP1519
ATOM   1366  CA  THR B  80      14.035  -1.456   8.479  1.00  2.64      8HVP1520
ATOM   1367  C   THR B  80      14.090  -0.056   7.858  1.00  3.39      8HVP1521
ATOM   1368  O   THR B  80      15.170   0.550   7.674  1.00  3.04      8HVP1522
ATOM   1369  CB  THR B  80      14.154  -1.226  10.073  1.00  2.00      8HVP1523
ATOM   1370  OG1 THR B  80      13.256  -0.108  10.331  1.00  2.00      8HVP1524
ATOM   1371  CG2 THR B  80      15.609  -0.947  10.440  1.00  4.77      8HVP1525
ATOM   1372  N   PRO B  81      12.872   0.473   7.706  1.00  2.00      8HVP1526
ATOM   1373  CA  PRO B  81      12.720   1.836   7.182  1.00  2.97      8HVP1527
ATOM   1374  C   PRO B  81      12.849   2.875   8.255  1.00  5.81      8HVP1528
ATOM   1375  O   PRO B  81      12.603   4.034   7.866  1.00 12.28      8HVP1529
ATOM   1376  CB  PRO B  81      11.315   1.919   6.596  1.00  4.46      8HVP1530
ATOM   1377  CG  PRO B  81      10.562   0.987   7.528  1.00  2.00      8HVP1531
ATOM   1378  CD  PRO B  81      11.549  -0.103   7.918  1.00  2.00      8HVP1532
ATOM   1379  N   VAL B  82      13.092   2.533   9.501  1.00  5.50      8HVP1533
ATOM   1380  CA  VAL B  82      13.253   3.579  10.533  1.00  6.56      8HVP1534
ATOM   1381  C   VAL B  82      14.035   2.859  11.635  1.00  4.46      8HVP1535
ATOM   1382  O   VAL B  82      13.744   1.691  11.882  1.00  5.73      8HVP1536
ATOM   1383  CB  VAL B  82      12.044   4.308  11.099  1.00  2.00      8HVP1537
ATOM   1384  CG1 VAL B  82      12.390   5.643  11.816  1.00  2.00      8HVP1538
ATOM   1385  CG2 VAL B  82      10.922   4.609  10.118  1.00 10.74      8HVP1539
ATOM   1386  N   ASN B  83      15.039   3.560  12.122  1.00  4.25      8HVP1540
ATOM   1387  CA  ASN B  83      15.747   2.886  13.236  1.00  3.60      8HVP1541
ATOM   1388  C   ASN B  83      14.616   3.030  14.285  1.00  5.95      8HVP1542
ATOM   1389  O   ASN B  83      13.973   4.099  14.278  1.00  4.66      8HVP1543
ATOM   1390  CB  ASN B  83      16.995   3.589  13.654  1.00 12.96      8HVP1544
ATOM   1391  CG  ASN B  83      17.932   3.864  12.499  1.00 11.76      8HVP1545
ATOM   1392  OD1 ASN B  83      17.831   3.133  11.507  1.00 27.72      8HVP1546
ATOM   1393  ND2 ASN B  83      18.820   4.811  12.706  1.00  2.00      8HVP1547
ATOM   1394  N   ILE B  84      14.506   2.010  15.091  1.00  2.00      8HVP1548
ATOM   1395  CA  ILE B  84      13.469   1.945  16.101  1.00  2.00      8HVP1549
ATOM   1396  C   ILE B  84      14.169   1.483  17.373  1.00  2.00      8HVP1550
ATOM   1397  O   ILE B  84      14.819   0.450  17.231  1.00  2.00      8HVP1551
ATOM   1398  CB  ILE B  84      12.560   0.805  15.520  1.00  2.00      8HVP1552
ATOM   1399  CG1 ILE B  84      11.828   1.260  14.244  1.00  2.00      8HVP1553
ATOM   1400  CG2 ILE B  84      11.560   0.129  16.485  1.00  9.06      8HVP1554
ATOM   1401  CD1 ILE B  84      11.228  -0.085  13.628  1.00  2.00      8HVP1555
ATOM   1402  N   ILE B  85      13.901   2.146  18.451  1.00  2.34      8HVP1556
ATOM   1403  CA  ILE B  85      14.252   1.917  19.851  1.00  2.00      8HVP1557
ATOM   1404  C   ILE B  85      12.981   1.300  20.488  1.00  2.00      8HVP1558
ATOM   1405  O   ILE B  85      11.935   1.937  20.654  1.00  2.00      8HVP1559
ATOM   1406  CB  ILE B  85      14.685   3.237  20.568  1.00  3.01      8HVP1560
ATOM   1407  CG1 ILE B  85      15.613   3.980  19.566  1.00  2.00      8HVP1561
ATOM   1408  CG2 ILE B  85      15.401   3.184  21.944  1.00  2.00      8HVP1562
ATOM   1409  CD1 ILE B  85      17.057   3.398  19.444  1.00  2.00      8HVP1563
ATOM   1410  N   GLY B  86      12.996   0.016  20.615  1.00  2.00      8HVP1564
ATOM   1411  CA  GLY B  86      12.066  -0.875  21.226  1.00  2.00      8HVP1565
ATOM   1412  C   GLY B  86      12.290  -0.728  22.764  1.00  2.00      8HVP1566
ATOM   1413  O   GLY B  86      13.261  -0.115  23.155  1.00  2.00      8HVP1567
ATOM   1414  N   ARG B  87      11.345  -1.332  23.437  1.00  2.00      8HVP1568
ATOM   1415  CA  ARG B  87      11.186  -1.347  24.865  1.00  2.00      8HVP1569
ATOM   1416  C   ARG B  87      12.359  -1.917  25.601  1.00  2.00      8HVP1570
ATOM   1417  O   ARG B  87      12.493  -1.592  26.770  1.00  4.46      8HVP1571
ATOM   1418  CB  ARG B  87      10.035  -2.294  25.221  1.00  2.00      8HVP1572
ATOM   1419  CG  ARG B  87       8.742  -1.723  24.711  1.00  5.98      8HVP1573
ATOM   1420  CD  ARG B  87       7.604  -2.374  25.417  1.00 11.70      8HVP1574
ATOM   1421  NE  ARG B  87       7.475  -3.756  24.962  1.00 15.15      8HVP1575
ATOM   1422  CZ  ARG B  87       7.955  -4.754  25.720  1.00 20.65      8HVP1576
ATOM   1423  NH1 ARG B  87       8.651  -4.475  26.828  1.00 28.10      8HVP1577
ATOM   1424  NH2 ARG B  87       7.624  -6.024  25.457  1.00 15.02      8HVP1578
ATOM   1425  N   ASN B  88      13.093  -2.801  24.933  1.00  5.56      8HVP1579
ATOM   1426  CA  ASN B  88      14.222  -3.463  25.659  1.00  4.96      8HVP1580
ATOM   1427  C   ASN B  88      15.090  -2.404  26.326  1.00  6.07      8HVP1581
ATOM   1428  O   ASN B  88      15.400  -2.392  27.534  1.00  5.28      8HVP1582
ATOM   1429  CB  ASN B  88      14.893  -4.460  24.738  1.00  2.00      8HVP1583
ATOM   1430  CG  ASN B  88      15.562  -3.844  23.543  1.00  2.00      8HVP1584
ATOM   1431  OD1 ASN B  88      15.159  -2.730  23.191  1.00  5.31      8HVP1585
ATOM   1432  ND2 ASN B  88      16.597  -4.483  23.018  1.00  2.22      8HVP1586
ATOM   1433  N   LEU B  89      15.549  -1.503  25.477  1.00  7.26      8HVP1587
ATOM   1434  CA  LEU B  89      16.385  -0.373  25.908  1.00  7.41      8HVP1588
ATOM   1435  C   LEU B  89      15.470   0.724  26.462  1.00  7.21      8HVP1589
ATOM   1436  O   LEU B  89      15.891   1.509  27.298  1.00  5.18      8HVP1590
ATOM   1437  CB  LEU B  89      17.200   0.132  24.722  1.00 14.09      8HVP1591
ATOM   1438  CG  LEU B  89      18.234  -0.671  23.985  1.00 12.91      8HVP1592
ATOM   1439  CD1 LEU B  89      19.037   0.253  23.055  1.00 15.14      8HVP1593
ATOM   1440  CD2 LEU B  89      19.172  -1.343  24.974  1.00  7.63      8HVP1594
ATOM   1441  N   LEU B  90      14.248   0.749  25.906  1.00 10.04      8HVP1595
ATOM   1442  CA  LEU B  90      13.308   1.791  26.357  1.00 12.16      8HVP1596
ATOM   1443  C   LEU B  90      13.197   1.796  27.879  1.00 10.68      8HVP1597
ATOM   1444  O   LEU B  90      13.085   2.850  28.500  1.00 10.90      8HVP1598
ATOM   1445  CB  LEU B  90      11.996   1.662  25.574  1.00 14.64      8HVP1599
ATOM   1446  CG  LEU B  90      11.977   2.391  24.240  1.00  7.36      8HVP1600
ATOM   1447  CD1 LEU B  90      10.753   2.062  23.390  1.00  3.51      8HVP1601
ATOM   1448  CD2 LEU B  90      12.061   3.867  24.584  1.00  2.00      8HVP1602
ATOM   1449  N   THR B  91      13.183   0.608  28.426  1.00  8.44      8HVP1603
ATOM   1450  CA  THR B  91      13.022   0.350  29.861  1.00  3.22      8HVP1604
ATOM   1451  C   THR B  91      14.275   0.740  30.603  1.00  9.25      8HVP1605
ATOM   1452  O   THR B  91      14.263   0.702  31.862  1.00 14.93      8HVP1606
ATOM   1453  CB  THR B  91      12.746  -1.177  29.952  1.00  2.00      8HVP1607
ATOM   1454  OG1 THR B  91      11.985  -1.448  28.683  1.00  5.45      8HVP1608
ATOM   1455  CG2 THR B  91      11.729  -1.671  30.939  1.00  2.00      8HVP1609
ATOM   1456  N   GLN B  92      15.364   1.062  29.885  1.00  2.00      8HVP1610
ATOM   1457  CA  GLN B  92      16.575   1.395  30.670  1.00  2.00      8HVP1611
ATOM   1458  C   GLN B  92      16.828   2.837  30.989  1.00  2.00      8HVP1612
ATOM   1459  O   GLN B  92      17.685   3.073  31.889  1.00  3.27      8HVP1613
ATOM   1460  CB  GLN B  92      17.800   0.851  29.928  1.00  9.30      8HVP1614
ATOM   1461  CG  GLN B  92      17.766  -0.674  29.945  1.00  9.24      8HVP1615
ATOM   1462  CD  GLN B  92      19.084  -1.220  29.396  1.00 17.32      8HVP1616
ATOM   1463  OE1 GLN B  92      19.908  -0.523  28.794  1.00 18.99      8HVP1617
ATOM   1464  NE2 GLN B  92      19.167  -2.526  29.698  1.00  2.00      8HVP1618
ATOM   1465  N   ILE B  93      16.165   3.783  30.406  1.00  2.00      8HVP1619
ATOM   1466  CA  ILE B  93      16.302   5.224  30.521  1.00  2.00      8HVP1620
ATOM   1467  C   ILE B  93      15.160   5.863  31.278  1.00  2.00      8HVP1621
ATOM   1468  O   ILE B  93      15.193   7.088  31.545  1.00  2.00      8HVP1622
ATOM   1469  CB  ILE B  93      16.471   5.800  29.054  1.00  2.81      8HVP1623
ATOM   1470  CG1 ILE B  93      15.196   5.560  28.201  1.00 10.61      8HVP1624
ATOM   1471  CG2 ILE B  93      17.720   5.198  28.360  1.00  5.18      8HVP1625
ATOM   1472  CD1 ILE B  93      14.935   6.429  26.938  1.00  7.21      8HVP1626
ATOM   1473  N   GLY B  94      14.276   4.993  31.747  1.00  2.00      8HVP1627
ATOM   1474  CA  GLY B  94      13.153   5.380  32.551  1.00  2.98      8HVP1628
ATOM   1475  C   GLY B  94      11.954   5.851  31.761  1.00  4.43      8HVP1629
ATOM   1476  O   GLY B  94      11.159   6.610  32.386  1.00 12.15      8HVP1630
HETATM 1477  N   ABA B  95      11.749   5.424  30.513  1.00  3.99      8HVP1631
HETATM 1478  CA  ABA B  95      10.532   5.892  29.810  1.00  2.00      8HVP1632
HETATM 1479  C   ABA B  95       9.235   5.310  30.389  1.00  2.00      8HVP1633
HETATM 1480  O   ABA B  95       8.950   4.191  30.772  1.00  2.00      8HVP1634
HETATM 1481  CB  ABA B  95      10.573   5.581  28.338  1.00 10.70      8HVP1635
HETATM 1482  CG  ABA B  95       9.913   6.570  27.369  1.00  2.00      8HVP1636
ATOM   1483  N   THR B  96       8.263   6.208  30.504  1.00  2.00      8HVP1637
ATOM   1484  CA  THR B  96       6.873   5.955  30.799  1.00  2.00      8HVP1638
ATOM   1485  C   THR B  96       6.069   6.697  29.685  1.00  2.00      8HVP1639
ATOM   1486  O   THR B  96       6.618   7.581  29.045  1.00  2.00      8HVP1640
ATOM   1487  CB  THR B  96       6.405   6.322  32.261  1.00  2.00      8HVP1641
ATOM   1488  OG1 THR B  96       6.686   7.717  32.450  1.00  2.00      8HVP1642
ATOM   1489  CG2 THR B  96       7.012   5.382  33.287  1.00  2.00      8HVP1643
ATOM   1490  N   LEU B  97       4.837   6.299  29.600  1.00  2.00      8HVP1644
ATOM   1491  CA  LEU B  97       3.747   6.890  28.809  1.00  2.76      8HVP1645
ATOM   1492  C   LEU B  97       2.804   7.571  29.829  1.00  2.00      8HVP1646
ATOM   1493  O   LEU B  97       2.468   6.848  30.824  1.00  2.00      8HVP1647
ATOM   1494  CB  LEU B  97       3.007   5.780  28.010  1.00  7.78      8HVP1648
ATOM   1495  CG  LEU B  97       3.760   5.169  26.836  1.00  9.06      8HVP1649
ATOM   1496  CD1 LEU B  97       2.939   4.176  26.020  1.00  4.90      8HVP1650
ATOM   1497  CD2 LEU B  97       4.171   6.292  25.876  1.00  5.54      8HVP1651
ATOM   1498  N   ASN B  98       2.345   8.784  29.722  1.00  2.00      8HVP1652
ATOM   1499  CA  ASN B  98       1.395   9.239  30.747  1.00  2.00      8HVP1653
ATOM   1500  C   ASN B  98       0.195   9.892  30.048  1.00  2.00      8HVP1654
ATOM   1501  O   ASN B  98       0.433  10.583  29.061  1.00  2.00      8HVP1655
ATOM   1502  CB  ASN B  98       1.901  10.240  31.788  1.00  2.00      8HVP1656
ATOM   1503  CG  ASN B  98       3.196   9.814  32.407  1.00  7.17      8HVP1657
ATOM   1504  OD1 ASN B  98       4.049   9.299  31.687  1.00  2.00      8HVP1658
ATOM   1505  ND2 ASN B  98       3.267  10.027  33.722  1.00 14.16      8HVP1659
ATOM   1506  N   PHE B  99      -0.920   9.629  30.739  1.00  2.00      8HVP1660
ATOM   1507  CA  PHE B  99      -2.145  10.323  30.261  1.00  2.68      8HVP1661
ATOM   1508  C   PHE B  99      -3.092  10.586  31.440  1.00  6.92      8HVP1662
ATOM   1509  O   PHE B  99      -3.744  11.659  31.306  1.00 14.80      8HVP1663
ATOM   1510  CB  PHE B  99      -2.816   9.806  29.052  1.00  2.00      8HVP1664
ATOM   1511  CG  PHE B  99      -3.328   8.440  29.015  1.00  2.45      8HVP1665
ATOM   1512  CD1 PHE B  99      -2.473   7.420  28.560  1.00  2.00      8HVP1666
ATOM   1513  CD2 PHE B  99      -4.636   8.153  29.387  1.00  3.88      8HVP1667
ATOM   1514  CE1 PHE B  99      -2.895   6.105  28.428  1.00  2.00      8HVP1668
ATOM   1515  CE2 PHE B  99      -5.101   6.833  29.243  1.00  7.55      8HVP1669
ATOM   1516  CZ  PHE B  99      -4.222   5.848  28.780  1.00  2.00      8HVP1670
ATOM   1517  OXT PHE B  99      -3.162   9.808  32.396  1.00  2.00      8HVP1671
TER    1518      PHE B  99                                              8HVP1672
ATOM   1519  N   VAL I   1       1.002   5.256   2.453  1.00 33.69      8HVP1673
ATOM   1520  CA  VAL I   1       1.982   6.316   2.835  1.00 33.44      8HVP1674
ATOM   1521  C   VAL I   1       1.924   6.584   4.348  1.00 28.16      8HVP1675
ATOM   1522  O   VAL I   1       2.567   7.494   4.904  1.00 27.53      8HVP1676
ATOM   1523  CB  VAL I   1       1.922   7.494   1.842  1.00 41.97      8HVP1677
ATOM   1524  CG1 VAL I   1       0.853   8.555   2.110  1.00 45.29      8HVP1678
ATOM   1525  CG2 VAL I   1       3.267   8.164   1.591  1.00 41.45      8HVP1679
ATOM   1526  N   SER I   2       1.230   5.717   5.055  1.00 22.94      8HVP1680
ATOM   1527  CA  SER I   2       1.138   5.731   6.519  1.00 18.94      8HVP1681
ATOM   1528  C   SER I   2       1.996   4.575   7.075  1.00 18.27      8HVP1682
ATOM   1529  O   SER I   2       1.709   3.452   6.587  1.00 18.68      8HVP1683
ATOM   1530  CB  SER I   2      -0.342   5.585   6.864  1.00  4.46      8HVP1684
ATOM   1531  OG  SER I   2      -0.461   4.626   7.920  1.00 10.63      8HVP1685
ATOM   1532  N   GLN I   3       2.962   4.735   7.985  1.00 12.32      8HVP1686
ATOM   1533  CA  GLN I   3       3.735   3.601   8.529  1.00 11.88      8HVP1687
ATOM   1534  C   GLN I   3       3.378   3.262   9.996  1.00  7.48      8HVP1688
ATOM   1535  O   GLN I   3       3.068   4.175  10.740  1.00  4.65      8HVP1689
ATOM   1536  CB  GLN I   3       5.258   3.756   8.428  1.00 10.50      8HVP1690
ATOM   1537  CG  GLN I   3       5.755   4.804   9.360  1.00 18.97      8HVP1691
ATOM   1538  CD  GLN I   3       7.152   4.776   9.912  1.00 28.03      8HVP1692
ATOM   1539  OE1 GLN I   3       7.500   5.754  10.608  1.00 22.68      8HVP1693
ATOM   1540  NE2 GLN I   3       7.906   3.701   9.651  1.00 26.36      8HVP1694
ATOM   1541  N   ASN I   4       3.464   1.991  10.356  1.00  6.40      8HVP1695
ATOM   1542  CA  ASN I   4       3.154   1.352  11.620  1.00  5.82      8HVP1696
ATOM   1543  C   ASN I   4       4.079   0.279  12.181  1.00  3.93      8HVP1697
ATOM   1544  O   ASN I   4       3.939  -0.926  11.913  1.00  3.17      8HVP1698
ATOM   1545  CB  ASN I   4       1.783   0.611  11.539  1.00  2.00      8HVP1699
ATOM   1546  CG  ASN I   4       0.795   1.717  11.224  1.00 17.75      8HVP1700
ATOM   1547  OD1 ASN I   4       0.393   1.852  10.076  1.00  2.00      8HVP1701
ATOM   1548  ND2 ASN I   4       0.596   2.492  12.300  1.00 23.43      8HVP1702
HETATM 1549  CD1 LOV I   5       6.990   1.440  11.323  1.00  2.00   1  8HVP1703
HETATM 1550  CD2 LOV I   5       9.002   1.876  12.515  1.00 11.48   1  8HVP1704
HETATM 1551  C1G LOV I   5       7.861   0.862  12.418  1.00  3.76   1  8HVP1705
HETATM 1552  C1B LOV I   5       7.163   0.772  13.787  1.00  4.12   1  8HVP1706
HETATM 1553  C1A LOV I   5       5.904  -0.101  13.814  1.00  2.00   1  8HVP1707
HETATM 1554  CS  LOV I   5       5.465  -0.675  15.137  1.00  2.00   1  8HVP1708
HETATM 1555  N   LOV I   5       4.881   0.722  13.126  1.00  6.07   1  8HVP1709
HETATM 1556  OS  LOV I   5       5.369   0.252  16.190  1.00  2.00   1  8HVP1710
HETATM 1557  CT  LOV I   5       4.310  -1.642  15.109  1.00  2.00   1  8HVP1711
HETATM 1558  CA  LOV I   5       4.567  -2.908  15.940  1.00  5.81   1  8HVP1712
HETATM 1559  CB  LOV I   5       3.269  -3.761  15.889  1.00  5.21   1  8HVP1713
HETATM 1560  CG1 LOV I   5       3.478  -5.277  15.902  1.00  4.64   1  8HVP1714
HETATM 1561  CG2 LOV I   5       2.342  -3.457  17.047  1.00 12.50   1  8HVP1715
HETATM 1562  C   LOV I   5       5.830  -3.684  15.551  1.00  7.18   1  8HVP1716
HETATM 1563  O   LOV I   5       6.281  -3.728  14.374  1.00 10.72   1  8HVP1717
ATOM   1564  N   ILE I   7       6.427  -4.343  16.512  1.00  3.60      8HVP1718
ATOM   1565  CA  ILE I   7       7.551  -5.249  16.261  1.00  6.98      8HVP1719
ATOM   1566  C   ILE I   7       7.249  -6.445  17.181  1.00  7.58      8HVP1720
ATOM   1567  O   ILE I   7       7.022  -6.186  18.373  1.00 10.06      8HVP1721
ATOM   1568  CB  ILE I   7       9.010  -4.748  16.351  1.00  3.23      8HVP1722
ATOM   1569  CG1 ILE I   7      10.003  -5.658  15.565  1.00  2.00      8HVP1723
ATOM   1570  CG2 ILE I   7       9.628  -4.887  17.793  1.00  2.11      8HVP1724
ATOM   1571  CD1 ILE I   7       9.341  -6.707  14.634  1.00 17.88      8HVP1725
ATOM   1572  N   VAL I   8       7.164  -7.651  16.671  1.00  8.36      8HVP1726
ATOM   1573  CA  VAL I   8       6.932  -8.756  17.647  1.00 14.10      8HVP1727
ATOM   1574  C   VAL I   8       8.045  -9.788  17.397  1.00 17.57      8HVP1728
ATOM   1575  O   VAL I   8       8.550  -9.863  16.247  1.00 18.47      8HVP1729
ATOM   1576  CB  VAL I   8       5.477  -9.194  17.710  1.00 21.86      8HVP1730
ATOM   1577  CG1 VAL I   8       4.575  -8.212  18.485  1.00 19.23      8HVP1731
ATOM   1578  CG2 VAL I   8       4.801  -9.569  16.397  1.00 22.28      8HVP1732
ATOM   1579  OXT VAL I   8       8.299 -10.540  18.365  1.00 10.36      8HVP1733
TER    1580      VAL I   8                                              8HVP1734
HETATM 1581  O   HOH A   1       5.216  -3.028  12.131  1.00  2.00      8HVP1735
HETATM 1582  O   HOH A   2      10.614   1.714  32.700  1.00 39.80      8HVP1736
HETATM 1583  O   HOH A   3      12.751  11.193  35.699  1.00 26.47      8HVP1737
HETATM 1584  O   HOH A   4       5.396  -4.251  21.781  1.00  2.00      8HVP1738
HETATM 1585  O   HOH A   5       5.258   7.699  15.004  1.00 40.55      8HVP1739
HETATM 1586  O   HOH A   6      15.785  -6.670  20.952  1.00 20.52      8HVP1740
HETATM 1587  O   HOH A   7      -5.291  -9.959  12.451  1.00  2.62      8HVP1741
HETATM 1588  O   HOH A   8       0.869 -10.774  29.130  1.00 30.76      8HVP1742
HETATM 1589  O   HOH A   9      -7.945 -10.283  10.294  1.00  9.96      8HVP1743
HETATM 1590  O   HOH A  10      12.572   7.951  34.543  1.00  7.75      8HVP1744
HETATM 1591  O   HOH A  11      25.971 -12.456  20.059  1.00  3.45      8HVP1745
HETATM 1592  O   HOH A  12      -4.522  -6.762   2.552  1.00 22.74      8HVP1746
HETATM 1593  O   HOH A  13       4.817  12.754  11.271  1.00 28.72      8HVP1747
HETATM 1594  O   HOH A  14      22.399   1.048   5.265  1.00 18.11      8HVP1748
HETATM 1595  O   HOH A  15       9.276  10.929  33.431  1.00 20.98      8HVP1749
HETATM 1596  O   HOH A  16       5.249  -8.716  27.053  1.00  3.47      8HVP1750
HETATM 1597  O   HOH A  17     -19.140   7.249  24.019  1.00 25.75      8HVP1751
HETATM 1598  O   HOH A  18      11.323  -9.792  22.237  1.00 47.47      8HVP1752
HETATM 1599  O   HOH A  19      12.200  -6.659  25.388  1.00 45.69      8HVP1753
HETATM 1600  O   HOH A  20     -12.130   2.034  28.265  1.00 13.33      8HVP1754
HETATM 1601  O   HOH A  21      19.984  -7.962   8.693  1.00 36.85      8HVP1755
HETATM 1602  O   HOH A  22     -17.280   5.660  23.688  1.00  8.42      8HVP1756
HETATM 1603  O   HOH A  23      18.021 -17.711  15.693  1.00  8.89      8HVP1757
HETATM 1604  O   HOH A  24      -3.849  14.080  15.702  1.00 23.80      8HVP1758
HETATM 1605  O   HOH A  25      -7.116  -7.821  21.203  1.00 31.21      8HVP1759
HETATM 1606  O   HOH A  26      -6.504   5.609  11.945  1.00  2.67      8HVP1760
HETATM 1607  O   HOH A  27      -7.990  10.695  13.759  1.00  2.00      8HVP1761
HETATM 1608  O   HOH A  28     -23.308   0.870  21.029  1.00 32.65      8HVP1762
HETATM 1609  O   HOH A  29      11.743  14.669  35.485  1.00 30.26      8HVP1763
HETATM 1610  O   HOH A  30       9.104  -9.450   4.424  1.00 12.53      8HVP1764
HETATM 1611  O   HOH A  31       5.681   5.771  12.682  1.00 11.19      8HVP1765
HETATM 1612  O   HOH A  32     -12.526  12.035  28.606  1.00 15.53      8HVP1766
HETATM 1613  O   HOH A  33       3.280  -7.615   1.460  1.00 27.88      8HVP1767
HETATM 1614  O   HOH A  34      12.685  15.267  15.689  1.00 21.25      8HVP1768
HETATM 1615  O   HOH A  35     -21.369   4.254  23.436  1.00 21.59      8HVP1769
HETATM 1616  O   HOH A  36     -16.670   6.393   7.864  1.00  8.51      8HVP1770
HETATM 1617  O   HOH A  37      18.486  -6.156  25.609  1.00 17.82      8HVP1771
HETATM 1618  O   HOH A  38      17.557  14.261  29.659  1.00 10.62      8HVP1772
HETATM 1619  O   HOH A  39      -8.192 -12.788  12.929  1.00 16.07      8HVP1773
HETATM 1620  O   HOH A  40      -8.920  -9.751  22.041  1.00 17.34      8HVP1774
HETATM 1621  O   HOH A  41      -4.431   3.460  -1.908  1.00 38.28      8HVP1775
HETATM 1622  O   HOH A  42      -5.066   7.197  37.048  1.00 17.03      8HVP1776
HETATM 1623  O   HOH A  43       9.683 -12.586  18.588  1.00 25.99      8HVP1777
HETATM 1624  O   HOH A  44       0.851  13.123  31.812  1.00  2.00      8HVP1778
HETATM 1625  O   HOH A  45      34.321  -8.096  15.559  1.00  2.00      8HVP1779
HETATM 1626  O   HOH A  46     -13.318   4.972   4.869  1.00  2.00      8HVP1780
HETATM 1627  O   HOH A  47      -5.729  16.438  24.228  1.00  2.00      8HVP1781
HETATM 1628  O   HOH A  48      27.210   9.667  11.528  1.00  2.00      8HVP1782
HETATM 1629  O   HOH A  49     -15.949   0.283   0.917  1.00  2.00      8HVP1783
HETATM 1630  O   HOH A  50      -7.424   8.402  35.088  1.00  6.93      8HVP1784
HETATM 1631  O   HOH A  51       3.081  15.236  11.693  1.00  7.66      8HVP1785
HETATM 1632  O   HOH A  52     -20.129   3.488  21.314  1.00  8.95      8HVP1786
HETATM 1633  O   HOH A  53       2.983  -9.210  35.762  1.00 12.16      8HVP1787
HETATM 1634  O   HOH A  54      22.227  -8.499  25.853  1.00 12.87      8HVP1788
HETATM 1635  O   HOH A  55      10.098   8.441   9.848  1.00 14.24      8HVP1789
HETATM 1636  O   HOH A  56       6.471 -10.064  28.863  1.00 16.97      8HVP1790
HETATM 1637  O   HOH A  57       3.437 -11.087  26.858  1.00 17.91      8HVP1791
HETATM 1638  O   HOH A  58      11.363  14.729  19.108  1.00 19.73      8HVP1792
HETATM 1639  O   HOH A  59      -6.962  11.176  11.506  1.00 20.82      8HVP1793
HETATM 1640  O   HOH A  60       6.623  16.089  10.621  1.00 22.95      8HVP1794
HETATM 1641  O   HOH A  61       6.668 -11.009  25.008  1.00 22.95      8HVP1795
HETATM 1642  O   HOH A  62       9.364  14.464  14.156  1.00 23.28      8HVP1796
HETATM 1643  O   HOH A  63      -2.980   4.497   0.672  1.00 24.40      8HVP1797
HETATM 1644  O   HOH A  64      22.290  10.937  22.020  1.00 24.99      8HVP1798
HETATM 1645  O   HOH A  65      23.350   9.385  11.027  1.00 25.21      8HVP1799
HETATM 1646  O   HOH A  66     -18.687  10.603   9.135  1.00 25.85      8HVP1800
HETATM 1647  O   HOH A  67      25.618   7.811  33.389  1.00 26.92      8HVP1801
HETATM 1648  O   HOH A  68      28.885  -6.845  11.462  1.00 28.02      8HVP1802
HETATM 1649  O   HOH A  69     -23.158   4.537  25.077  1.00 29.77      8HVP1803
HETATM 1650  O   HOH A  70      -2.599  14.244  31.864  1.00 32.04      8HVP1804
HETATM 1651  O   HOH A  71      -0.659   9.877  12.451  1.00 34.04      8HVP1805
HETATM 1652  O   HOH A  72       7.949  12.768  10.878  1.00 34.69      8HVP1806
HETATM 1653  O   HOH A  73      10.081  15.243   9.186  1.00 37.44      8HVP1807
HETATM 1654  O   HOH A  74     -19.436   8.318  11.246  1.00 38.80      8HVP1808
HETATM 1655  O   HOH A  75       2.184  -8.186  27.493  1.00 42.83      8HVP1809
HETATM 1656  O   HOH A  76      22.220 -16.223   7.085  1.00 44.72      8HVP1810
HETATM 1657  O   HOH A  77     -23.272   4.114  21.546  1.00 47.20      8HVP1811
HETATM 1658  O   HOH A  78      22.039 -14.292  24.350  1.00 52.48      8HVP1812
HETATM 1659  O   HOH A  79       0.071  -8.208  34.109  1.00 56.14      8HVP1813
HETATM 1660  O   HOH A  80      11.280  -7.333  31.371  1.00 59.48      8HVP1814
CONECT  514  513  515  520                                              8HVP1815
CONECT  520  514  521                                                   8HVP1816
CONECT  521  520  522  524                                              8HVP1817
CONECT  522  521  523  526                                              8HVP1818
CONECT  523  522                                                        8HVP1819
CONECT  524  521                                                        8HVP1820
CONECT  525  524                                                        8HVP1821
CONECT  526  522  527                                                   8HVP1822
CONECT  716  715  717  718                                              8HVP1823
CONECT  718  716  719                                                   8HVP1824
CONECT  719  718  720  722                                              8HVP1825
CONECT  720  719  721  724                                              8HVP1826
CONECT  721  720                                                        8HVP1827
CONECT  722  719                                                        8HVP1828
CONECT  723  722                                                        8HVP1829
CONECT  724  720  725                                                   8HVP1830
CONECT 1273 1272 1274 1279                                              8HVP1831
CONECT 1279 1273 1280                                                   8HVP1832
CONECT 1280 1279 1281 1283                                              8HVP1833
CONECT 1281 1280 1282 1285                                              8HVP1834
CONECT 1282 1281                                                        8HVP1835
CONECT 1283 1280                                                        8HVP1836
CONECT 1284 1283                                                        8HVP1837
CONECT 1285 1281 1286                                                   8HVP1838
CONECT 1475 1474 1476 1477                                              8HVP1839
CONECT 1477 1475 1478                                                   8HVP1840
CONECT 1478 1477 1479 1481                                              8HVP1841
CONECT 1479 1478 1480 1483                                              8HVP1842
CONECT 1480 1479                                                        8HVP1843
CONECT 1481 1478                                                        8HVP1844
CONECT 1482 1481                                                        8HVP1845
CONECT 1483 1479 1484                                                   8HVP1846
CONECT 1543 1542 1544 1555                                              8HVP1847
CONECT 1549 1551                                                        8HVP1848
CONECT 1550 1551                                                        8HVP1849
CONECT 1551 1549 1550 1552                                              8HVP1850
CONECT 1552 1551 1553                                                   8HVP1851
CONECT 1553 1552 1554 1555                                              8HVP1852
CONECT 1554 1553 1556 1557                                              8HVP1853
CONECT 1555 1543 1553                                                   8HVP1854
CONECT 1556 1554                                                        8HVP1855
CONECT 1557 1554 1558                                                   8HVP1856
CONECT 1558 1557 1559 1562                                              8HVP1857
CONECT 1559 1558 1560 1561                                              8HVP1858
CONECT 1560 1559                                                        8HVP1859
CONECT 1561 1559                                                        8HVP1860
CONECT 1562 1558 1563 1564                                              8HVP1861
CONECT 1563 1562                                                        8HVP1862
CONECT 1564 1562 1565                                                   8HVP1863
MASTER       71    3    5    2   20    6    2    6 1657    3   49   17  8HVP1864
END                                                                     8HVP1865
BioPerl-1.007002/t/data/AAC12660.fa000444000766000024       106113155576321 16161 0ustar00cjfieldsstaff000000000000>AAC12660 TAK1 binding protein [Homo sapiens]. 
MAAQRRSLLQSEQQPSWTDDLPLCHLSGVGSASNRSYSADGKGTESHPPEDSWLKFRSEN
NCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLES
IDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLLNNKLYV
ANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQVGIICGQEST
RRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLMSEGLYKALEAAH
GPGQANQEIAAMIDTEFAKQTSLDAVAQAVVDRVKRIHSDTFASGGERARFCPRHEDMTL
LVRNFGYPLGEMSQPTPSPAPAAGGRVYPVSVPYSSAQSTSKTSVTLSLVMPSQGQMVNG
AHSASTLDEATPTLTNQSPTLTLQSTNTHTQSSSSSSDGGLFRSRPAHSLPPGEDGRVEP
YVDFAEFYRLWSVDHGEQSVVTAP
BioPerl-1.007002/t/data/AB077698.gb000444000766000024      1646113155576321 16221 0ustar00cjfieldsstaff000000000000LOCUS       AB077698                2701 bp    mRNA    linear   PRI 01-MAR-2002
DEFINITION  Homo sapiens mRNA for hCHCR-G, complete cds.
ACCESSION   AB077698
VERSION     AB077698.1  GI:19032344
KEYWORDS    .
SOURCE      Homo sapiens cDNA to mRNA.
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1
  AUTHORS   Squillace,R.M., Chenault,D.M. and Wang,E.H.
  TITLE     Inhibition of myogenesis by the novel Muscleblind-related protein
            CHCR
  JOURNAL   Unpublished
REFERENCE   2
  AUTHORS   Squillace,R.M. and Wang,E.H.
  TITLE     Genomic structure, chromosomal localization, and splicing variation
            of the human CHCR gene, cloning and characterization of mouse CHCR
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 2701)
  AUTHORS   Squillace,R.M., Chenault,D.M. and Wang,E.H.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JAN-2002) Edith H. Wang, University of Washington,
            Pharmacology; 1959 NE Pacific Ave., Box 357280, Seattle, Washington
            98195, USA (E-mail:ehwang@u.washington.edu, Tel:206-616-5376,
            Fax:206-685-3822)
FEATURES             Location/Qualifiers
     source          1..2701
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xq26.1"
     gene            1..2701
                     /gene="CHCR"
     5'UTR           <1..79
                     /gene="CHCR"
     CDS             80..1144
                     /gene="CHCR"
                     /note="Cys3His CCG1-Required
                     Encoded on BAC clone RP5-842K24 (AL050310)
                     The human CHCR (Cys3His CCG1-Required) protein is highly
                     related to EXP/MBNL (Y13829, NM_021038, AF401998) and MBLL
                     (NM_005757,AF061261), which together comprise the human
                     Muscleblind family"
                     /codon_start=1
                     /product="hCHCR-G"
                     /protein_id="BAB85648.1"
                     /db_xref="GI:19032345"
                     /translation="MTAVNVALIRDTKWLTLEVCREFQRGTCSRADADCKFAHPPRVC
                     HVENGRVVACFDSLKGRCTRENCKYLHPPPHLKTQLEINGRNNLIQQKTAAAMFAQQM
                     QLMLQNAQMSSLGSFPMTPSIPANPPMAFNPYIPHPGMGLVPAELVPNTPVLIPGNPP
                     LAMPGAVGPKLMRSDKLEVCREFQRGNCTRGENDCRYAHPTDASMIEASDNTVTICMD
                     YIKGRCSREKCKYFHPPAHLQARLKAAHHQMNHSAASAMALQPGTLQLIPKRSALEKP
                     NGATPVFNPTVFHCQQALTNLQLPQPAFIPAGPILCMAPASNIVPMMHGATPTTVSAA
                     TTPATSVPFAAPTTGNQLKF"
     misc_feature    137..196
                     /gene="CHCR"
                     /note="Cys3His, zinc finger
                     Encoded on BAC clone RP5-842K24 (AL050310)"
     misc_feature    239..292
                     /gene="CHCR"
                     /note="Cys3His, zinc finger
                     Encoded on BAC clone RP5-842K24 (AL050310)"
     misc_feature    617..676
                     /gene="CHCR"
                     /note="Cys3His, zinc finger
                     Encoded on BAC clone RP5-842K24 (AL050310)"
     misc_feature    725..778
                     /gene="CHCR"
                     /note="Cys3His, zinc finger
                     Encoded on BAC clone RP5-842K24 (AL050310)"
     3'UTR           1145..2659
                     /gene="CHCR"
     polyA_site      1606
                     /gene="CHCR"
                     /note="Encoded on BAC clone RP5-842K24 (AL050310);
                     PolyA_site#1 used by CHCR EST clone PLACE1010202
                     (AK002178)"
     polyA_site      2660
                     /gene="CHCR"
                     /note="Encoded on BAC clone RP5-842K24 (AL050310);
                     PolyA_site#2 used by CHCR EST clone DKFZp434G2222
                     (AL133625)"
BASE COUNT      817 a    570 c    525 g    789 t
ORIGIN      
        1 aattcatttt taatccttta atagtccaca gtaatattgt cctaaagagg gtacattgga
       61 ttttaatttt gctttcaata tgacggctgt caatgttgcc ctgattcgtg ataccaagtg
      121 gctgacttta gaagtctgta gagaatttca gagaggaact tgctctcgag ctgatgcaga
      181 ttgcaagttt gcccatccac caagagtttg ccatgtggaa aatggtcgtg tggtggcctg
      241 ttttgattct ctaaagggtc ggtgtacccg agagaactgc aagtaccttc accctcctcc
      301 acacttaaaa acgcagctgg agattaatgg gcggaacaat ctgattcaac agaagactgc
      361 cgcagccatg ttcgcccagc agatgcagct tatgctccaa aacgctcaaa tgtcatcact
      421 tggttctttt cctatgactc catcaattcc agctaatcct cccatggctt tcaatcctta
      481 cataccacat cctgggatgg gcctcgttcc tgcagaactt gtaccaaata cacctgttct
      541 gattcctgga aacccacctc ttgcaatgcc aggagctgtt ggcccaaaac tgatgcgttc
      601 agataaactg gaggtttgcc gagaatttca gcgtggaaat tgtacccgtg gggagaatga
      661 ttgccgctat gctcacccta ctgatgcttc catgattgaa gcgagtgata atactgtgac
      721 aatctgcatg gattacatca aaggtcgatg ctcgcgggag aaatgcaagt actttcatcc
      781 tcctgcacac ttgcaagcca gactcaaggc agctcatcat cagatgaacc attcagctgc
      841 ctctgccatg gccctgcagc ctggtacact gcaactgata ccaaagagat cagcactgga
      901 aaagcccaat ggtgccaccc cggtctttaa tcccactgtt ttccactgcc aacaggctct
      961 gactaacctg cagctcccac agccggcatt tatccctgca gggccaatac tgtgcatggc
     1021 acccgcttca aatattgtgc ccatgatgca cggtgctaca cctaccactg tgtctgcagc
     1081 aacaacacct gccaccagcg ttccgttcgc tgcaccaact acaggcaatc agctgaaatt
     1141 ctgaacagca gagttatgga gtatcagaat ctttccatgg aaacctccat atggcctttc
     1201 tatatatatt ctcgtatgtc ttattctacc aacacaacaa taagcgtgtt gcagtcaatg
     1261 tattaagcaa agcaaacctg ccagccagca aattcaaata aaaaataaag cattaaaaat
     1321 caatggagat gttaaaacaa cacaaataga aaactagtaa ctaccatcca tcctatttga
     1381 attatcaagc agaacatgac cataaaattt ggtaacttgt tacattactc tttgtgattt
     1441 tctaataacc atgctaagtg tatttccaca gtgagctttt ggcttactat atacattctt
     1501 ggtggataaa ttgttcatct gtttttgaag tgttacctta ctattttgtt tacaagatag
     1561 tctattgggt tgattcagga tgtaacaaat atattcagta ccatttcttg tgttgtattg
     1621 tgttgtgctg tgttaggttt ttacatactg tagtgttttg ctgtatatgt gtggtgtttg
     1681 atttcaacta aagtgttatt agtggggaac agaagtatat gtgcttaaga acatgacagg
     1741 ttcatgcaaa tatgctctct ttctttagaa tatttctgta ggtttcttgg gactgacatt
     1801 taaaacgcct cacttttgaa tgtgcacaaa acctgctcat taacatgcat gtgtataatt
     1861 tgtacctgca gatctgatgt tgcataatac aatcaaatta ctagattttt taaagagaga
     1921 aataattacc tgcacaaagc agagaacttc ataaaacatt aacccctaat tcactcttct
     1981 taaatagctt ggcaaataag actttacctt taaatgaatt tctcagcatt tatactaaaa
     2041 attatgtaac gtgctcatta gattttttgt gtgtgtggct tgagaatccc atctcctaaa
     2101 ttgagtgtct aaaactgagc catttgtcat cttcagctga gaaactggta cttgggagct
     2161 taaaaatatg ctaattacaa gttataaatc aaacggagag atgggggcat ggagatagtt
     2221 tttacgtact ggaggaaagt gtgtaaaacc atggcaatgt caccttttac acaaatgcca
     2281 ttttccaaat gcaaatggct catgctcttt agactactct ttgaataaca agtaagatgc
     2341 aatctagcaa aagtcagtca gggtgaaaga gaattggttg caaatgagga cttccctccc
     2401 caaatggaca gtcttctctg ttgatcacag agggagcctg agtacaggct tggagaaatg
     2461 gctaggacag ggaacaggga agcacttaca attattcctt gatttattca aaagaactgg
     2521 gaaagatggt tgtagttgtc tttagcttcg gttcaactga gtttcgtttt gttaaacagt
     2581 tcagtgaagg agaaagcacc tgtgatatat ggcaagtgtc cccctgccca aactttaaca
     2641 tcagaccctc tcacatcata aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa
     2701 a
//
BioPerl-1.007002/t/data/AE003528_ecoli.bls000444000766000024      1760413155576321 17544 0ustar00cjfieldsstaff000000000000BLASTN 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= AE003528 Drosophila melanogaster genomic scaffold
142000013386050 section 40 of 54, complete sequence.
         (283,821 letters)

Database: ecoli.nt
           400 sequences; 4,662,239 total letters

Searching.................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gb|AE000450.1|AE000450 Escherichia coli K-12 MG1655 section 340 ...    60  1e-06
gb|AE000359.1|AE000359 Escherichia coli K-12 MG1655 section 249 ...    48  0.004
gb|AE000281.1|AE000281 Escherichia coli K-12 MG1655 section 171 ...    40  1.1
gb|AE000274.1|AE000274 Escherichia coli K-12 MG1655 section 164 ...    40  1.1
gb|AE000117.1|AE000117 Escherichia coli K-12 MG1655 section 7 of...    40  1.1
gb|AE000502.1|AE000502 Escherichia coli K-12 MG1655 section 392 ...    38  4.3
gb|AE000454.1|AE000454 Escherichia coli K-12 MG1655 section 344 ...    38  4.3
gb|AE000443.1|AE000443 Escherichia coli K-12 MG1655 section 333 ...    38  4.3
gb|AE000404.1|AE000404 Escherichia coli K-12 MG1655 section 294 ...    38  4.3
gb|AE000369.1|AE000369 Escherichia coli K-12 MG1655 section 259 ...    38  4.3
gb|AE000287.1|AE000287 Escherichia coli K-12 MG1655 section 177 ...    38  4.3
gb|AE000283.1|AE000283 Escherichia coli K-12 MG1655 section 173 ...    38  4.3
gb|AE000253.1|AE000253 Escherichia coli K-12 MG1655 section 143 ...    38  4.3
gb|AE000201.1|AE000201 Escherichia coli K-12 MG1655 section 91 o...    38  4.3

>gb|AE000450.1|AE000450 Escherichia coli K-12 MG1655 section 340 of 400 of the complete genome
          Length = 11414

 Score = 60.0 bits (30), Expect = 1e-06
 Identities = 36/38 (94%)
 Strand = Plus / Minus

                                                   
Query: 79116 gacatcatcgccattctgggaatggatgaactgtctga 79153
             |||||||||||||| ||||| |||||||||||||||||
Sbjct: 4712  gacatcatcgccatcctgggtatggatgaactgtctga 4675


 Score = 40.1 bits (20), Expect = 1.1
 Identities = 23/24 (95%)
 Strand = Plus / Minus

                                     
Query: 78617 tggccagatgaacgagcccccggg 78640
             |||||||||||||||||| |||||
Sbjct: 5208  tggccagatgaacgagccgccggg 5185


>gb|AE000359.1|AE000359 Escherichia coli K-12 MG1655 section 249 of 400 of the complete genome
          Length = 11001

 Score = 48.1 bits (24), Expect = 0.004
 Identities = 24/24 (100%)
 Strand = Plus / Minus

                                      
Query: 193000 tgttgctgctgttgcagattgctg 193023
              ||||||||||||||||||||||||
Sbjct: 10696  tgttgctgctgttgcagattgctg 10673


>gb|AE000281.1|AE000281 Escherichia coli K-12 MG1655 section 171 of 400 of the complete genome
          Length = 11855

 Score = 40.1 bits (20), Expect = 1.1
 Identities = 23/24 (95%)
 Strand = Plus / Plus

                                      
Query: 211974 ataaatatgtgcaccattagtaac 211997
              |||||||||||| |||||||||||
Sbjct: 3068   ataaatatgtgcgccattagtaac 3091


>gb|AE000274.1|AE000274 Escherichia coli K-12 MG1655 section 164 of 400 of the complete genome
          Length = 13793

 Score = 40.1 bits (20), Expect = 1.1
 Identities = 23/24 (95%)
 Strand = Plus / Plus

                                      
Query: 227803 ctggagatgctggaaatgctcact 227826
              |||||||||||||||||| |||||
Sbjct: 3532   ctggagatgctggaaatggtcact 3555


>gb|AE000117.1|AE000117 Escherichia coli K-12 MG1655 section 7 of 400 of the complete genome
          Length = 13416

 Score = 40.1 bits (20), Expect = 1.1
 Identities = 20/20 (100%)
 Strand = Plus / Minus

                                
Query: 2754 gctgctgctgttgctgccac 2773
            ||||||||||||||||||||
Sbjct: 3441 gctgctgctgttgctgccac 3422


>gb|AE000502.1|AE000502 Escherichia coli K-12 MG1655 section 392 of 400 of the complete genome
          Length = 11313

 Score = 38.2 bits (19), Expect = 4.3
 Identities = 22/23 (95%)
 Strand = Plus / Plus

                                     
Query: 171913 ttttatgtagattttacttgtta 171935
              |||||||| ||||||||||||||
Sbjct: 428    ttttatgttgattttacttgtta 450


>gb|AE000454.1|AE000454 Escherichia coli K-12 MG1655 section 344 of 400 of the complete genome
          Length = 12175

 Score = 38.2 bits (19), Expect = 4.3
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                                 
Query: 176663 agacaaatttatgagcgtt 176681
              |||||||||||||||||||
Sbjct: 9769   agacaaatttatgagcgtt 9751


>gb|AE000443.1|AE000443 Escherichia coli K-12 MG1655 section 333 of 400 of the complete genome
          Length = 11577

 Score = 38.2 bits (19), Expect = 4.3
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                                 
Query: 160348 gcatttgttgtttgcggac 160366
              |||||||||||||||||||
Sbjct: 8826   gcatttgttgtttgcggac 8844


>gb|AE000404.1|AE000404 Escherichia coli K-12 MG1655 section 294 of 400 of the complete genome
          Length = 14000

 Score = 38.2 bits (19), Expect = 4.3
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                                 
Query: 193629 ttagcgaccaccacgtcgg 193647
              |||||||||||||||||||
Sbjct: 13496  ttagcgaccaccacgtcgg 13478


>gb|AE000369.1|AE000369 Escherichia coli K-12 MG1655 section 259 of 400 of the complete genome
          Length = 9720

 Score = 38.2 bits (19), Expect = 4.3
 Identities = 22/23 (95%)
 Strand = Plus / Minus

                                    
Query: 50797 catcaatattattgaatatttca 50819
             ||||| |||||||||||||||||
Sbjct: 869   catcactattattgaatatttca 847


>gb|AE000287.1|AE000287 Escherichia coli K-12 MG1655 section 177 of 400 of the complete genome
          Length = 10876

 Score = 38.2 bits (19), Expect = 4.3
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                                
Query: 94068 tcaccagccagccgctgcc 94086
             |||||||||||||||||||
Sbjct: 443   tcaccagccagccgctgcc 461


>gb|AE000283.1|AE000283 Escherichia coli K-12 MG1655 section 173 of 400 of the complete genome
          Length = 10857

 Score = 38.2 bits (19), Expect = 4.3
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                                 
Query: 104663 acgttagcggcactgactc 104681
              |||||||||||||||||||
Sbjct: 893    acgttagcggcactgactc 875


>gb|AE000253.1|AE000253 Escherichia coli K-12 MG1655 section 143 of 400 of the complete genome
          Length = 10582

 Score = 38.2 bits (19), Expect = 4.3
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                                 
Query: 191578 cgttgaaaatggaaatctt 191596
              |||||||||||||||||||
Sbjct: 2595   cgttgaaaatggaaatctt 2577


>gb|AE000201.1|AE000201 Escherichia coli K-12 MG1655 section 91 of 400 of the complete genome
          Length = 11275

 Score = 38.2 bits (19), Expect = 4.3
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                                 
Query: 249230 tggctgctgctccagttgt 249248
              |||||||||||||||||||
Sbjct: 2297   tggctgctgctccagttgt 2315


  Database: ecoli.nt
    Posted date:  Jun 14, 2001  3:27 PM
  Number of letters in database: 4,662,239
  Number of sequences in database:  400
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 592338
Number of Sequences: 400
Number of extensions: 592338
Number of successful extensions: 42599
Number of sequences better than 10.0: 14
length of query: 283821
length of database: 4,662,239
effective HSP length: 20
effective length of query: 283801
effective length of database: 4,654,239
effective search space: 1320877682439
effective search space used: 1320877682439
T: 0
A: 0
X1: 6 (11.9 bits)
X2: 10 (19.8 bits)
S1: 12 (24.3 bits)
S2: 19 (38.2 bits)
BioPerl-1.007002/t/data/AE003644_Adh-genomic.gb000444000766000024    130542613155576321 20436 0ustar00cjfieldsstaff000000000000LOCUS       AE003644              263309 bp    DNA     linear   INV 14-FEB-2003
DEFINITION  Drosophila melanogaster chromosome 2L section 53 of 83 of the
            complete sequence.
ACCESSION   AE003644 AE002690 AE014134
VERSION     AE003644.3  GI:22946496
KEYWORDS    .
SOURCE      Drosophila melanogaster (fruit fly)
  ORGANISM  Drosophila melanogaster
            Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota;
            Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha;
            Ephydroidea; Drosophilidae; Drosophila.
REFERENCE   1  (bases 1 to 263309)
  AUTHORS   Adams,M.D., Celniker,S.E., Holt,R.A., Evans,C.A., Gocayne,J.D.,
            Amanatides,P.G., Scherer,S.E., Li,P.W., Hoskins,R.A., Galle,R.F.,
            George,R.A., Lewis,S.E., Richards,S., Ashburner,M., Henderson,S.N.,
            Sutton,G.G., Wortman,J.R., Yandell,M.D., Zhang,Q., Chen,L.X.,
            Brandon,R.C., Rogers,Y.H., Blazej,R.G., Champe,M., Pfeiffer,B.D.,
            Wan,K.H., Doyle,C., Baxter,E.G., Helt,G., Nelson,C.R., Gabor,G.L.,
            Abril,J.F., Agbayani,A., An,H.J., Andrews-Pfannkoch,C., Baldwin,D.,
            Ballew,R.M., Basu,A., Baxendale,J., Bayraktaroglu,L., Beasley,E.M.,
            Beeson,K.Y., Benos,P.V., Berman,B.P., Bhandari,D., Bolshakov,S.,
            Borkova,D., Botchan,M.R., Bouck,J., Brokstein,P., Brottier,P.,
            Burtis,K.C., Busam,D.A., Butler,H., Cadieu,E., Center,A.,
            Chandra,I., Cherry,J.M., Cawley,S., Dahlke,C., Davenport,L.B.,
            Davies,P., de Pablos,B., Delcher,A., Deng,Z., Mays,A.D., Dew,I.,
            Dietz,S.M., Dodson,K., Doup,L.E., Downes,M., Dugan-Rocha,S.,
            Dunkov,B.C., Dunn,P., Durbin,K.J., Evangelista,C.C., Ferraz,C.,
            Ferriera,S., Fleischmann,W., Fosler,C., Gabrielian,A.E., Garg,N.S.,
            Gelbart,W.M., Glasser,K., Glodek,A., Gong,F., Gorrell,J.H., Gu,Z.,
            Guan,P., Harris,M., Harris,N.L., Harvey,D., Heiman,T.J.,
            Hernandez,J.R., Houck,J., Hostin,D., Houston,K.A., Howland,T.J.,
            Wei,M.H., Ibegwam,C., Jalali,M., Kalush,F., Karpen,G.H., Ke,Z.,
            Kennison,J.A., Ketchum,K.A., Kimmel,B.E., Kodira,C.D., Kraft,C.,
            Kravitz,S., Kulp,D., Lai,Z., Lasko,P., Lei,Y., Levitsky,A.A.,
            Li,J., Li,Z., Liang,Y., Lin,X., Liu,X., Mattei,B., McIntosh,T.C.,
            McLeod,M.P., McPherson,D., Merkulov,G., Milshina,N.V., Mobarry,C.,
            Morris,J., Moshrefi,A., Mount,S.M., Moy,M., Murphy,B., Murphy,L.,
            Muzny,D.M., Nelson,D.L., Nelson,D.R., Nelson,K.A., Nixon,K.,
            Nusskern,D.R., Pacleb,J.M., Palazzolo,M., Pittman,G.S., Pan,S.,
            Pollard,J., Puri,V., Reese,M.G., Reinert,K., Remington,K.,
            Saunders,R.D., Scheeler,F., Shen,H., Shue,B.C., Siden-Kiamos,I.,
            Simpson,M., Skupski,M.P., Smith,T., Spier,E., Spradling,A.C.,
            Stapleton,M., Strong,R., Sun,E., Svirskas,R., Tector,C., Turner,R.,
            Venter,E., Wang,A.H., Wang,X., Wang,Z.Y., Wassarman,D.A.,
            Weinstock,G.M., Weissenbach,J., Williams,S.M., WoodageT,
            Worley,K.C., Wu,D., Yang,S., Yao,Q.A., Ye,J., Yeh,R.F.,
            Zaveri,J.S., Zhan,M., Zhang,G., Zhao,Q., Zheng,L., Zheng,X.H.,
            Zhong,F.N., Zhong,W., Zhou,X., Zhu,S., Zhu,X., Smith,H.O.,
            Gibbs,R.A., Myers,E.W., Rubin,G.M. and Venter,J.C.
  TITLE     The genome sequence of Drosophila melanogaster
  JOURNAL   Science 287 (5461), 2185-2195 (2000)
  MEDLINE   20196006
   PUBMED   10731132
REFERENCE   2  (bases 1 to 263309)
  AUTHORS   Celniker,S.E., Adams,M.D., Kronmiller,B., Wan,K.H., Holt,R.A.,
            Evans,C.A., Gocayne,J.D., Amanatides,P.G., Brandon,R.C., Rogers,Y.,
            Banzon,J., An,H., Baldwin,D., Banzon,J., Beeson,K.Y., Busam,D.A.,
            Carlson,J.W., Center,A., Champe,M., Davenport,L.B., Dietz,S.M.,
            Dodson,K., Dorsett,V., Doup,L.E., Doyle,C., Dresnek,D., Farfan,D.,
            Ferriera,S., Frise,E., Galle,R.F., Garg,N.S., George,R.A.,
            Gonzalez,M., Houck,J., Hoskins,R.A., Hostin,D., Howland,T.J.,
            Ibegwam,C., Jalali,M., Kruse,D., Li,P., Mattei,B., Moshrefi,A.,
            McIntosh,T.C., Moy,M., Murphy,B., Nelson,C., Nelson,K.A., Nunoo,J.,
            Pacleb,J., Paragas,V., Park,S., Patel,S., Pfeiffer,B.,
            Phouanenavong,S., Pittman,G.S., Puri,V., Richards,S., Scheeler,F.,
            Stapleton,M., Strong,R., Svirskas,R., Tector,C., Tyler,D.,
            Williams,S.M., Zaveri,J.S., Smith,H.O., Venter,J.C. and Rubin,G.M.
  TITLE     Sequencing of Drosophila melanogaster genome
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 263309)
  AUTHORS   Misra,S., Crosby,M.A., Matthews,B.B., Bayraktaroglu,L.,
            Campbell,K., Hradecky,P., Huang,Y., Kaminker,J.S., Prochnik,S.E.,
            Smith,C.D., Tupy,J.L., Bergman,C.M., Berman,B.P., Carlson,J.W.,
            Celniker,S.E., Clamp,M.E., Drysdale,R.A., Emmert,D., Frise,E., de
            Grey,A.D.N.J., Harris,N.L., Kronmiller,B., Marshall,B.,
            Millburn,G.H., Richter,J., Russo,S., Searle,S.M.J., Smith,E.,
            Shu,S., Smutniak,F., Whitfield,E.J., Ashburner,M., Gelbart,W.M.,
            Rubin,G.M., Mungall,C.J. and Lewis,S.E.
  TITLE     Annotation of Drosophila melanogaster genome
  JOURNAL   Unpublished
REFERENCE   4  (bases 1 to 263309)
  AUTHORS   Adams,M.D., Celniker,S.E., Gibbs,R.A., Rubin,G.M. and Venter,C.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-MAR-2000) Celera Genomics, 45 West Gude Drive,
            Rockville, MD 20850, USA
REFERENCE   5  (bases 1 to 263309)
  AUTHORS   .
  CONSRTM   FlyBase
  TITLE     Direct Submission
  JOURNAL   Submitted (06-SEP-2002) University of California Berkeley, 539 Life
            Sciences Addition, Berkeley, CA 94720, USA
REFERENCE   6  (bases 1 to 263309)
  AUTHORS   .
  CONSRTM   FlyBase
  TITLE     Direct Submission
  JOURNAL   Submitted (23-JAN-2003) University of California Berkeley, 539 Life
            Sciences Addition, Berkeley, CA 94720, USA
COMMENT     On Sep 16, 2002 this sequence version replaced gi:10728786.
FEATURES             Location/Qualifiers
     source          1..263309
                     /organism="Drosophila melanogaster"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:7227"
                     /chromosome="2L"
                     /note="genotype: y[1]; cn[1] bw[1] sp[1]; Rh6[1]"
     gene            20111..23268
                     /gene="noc"
                     /locus_tag="CG4491"
                     /note="last curated on Thu Dec 13 16:51:32 PST 2001"
                     /map="35B2-35B2"
                     /db_xref="FLYBASE:FBgn0005771"
     mRNA            join(20111..20584,20887..23268)
                     /gene="noc"
                     /locus_tag="CG4491"
                     /product="CG4491-RA"
                     /db_xref="FLYBASE:FBgn0005771"
     CDS             join(20495..20584,20887..22410)
                     /gene="noc"
                     /locus_tag="CG4491"
                     /note="noc gene product"
                     /codon_start=1
                     /product="CG4491-PA"
                     /protein_id="AAF53399.1"
                     /db_xref="GI:7298163"
                     /db_xref="FLYBASE:FBgn0005771"
                     /translation="MVVLEGGGGVVTIGNNQYLQPDYLAPLPTTMDAKKSPLALLAQT
                     CSQIGADSSAVKPLLAMDKNKTKPGACSSSSNSSSSSGSAEISAAKSPSGQAKSPKSS
                     TPISSTATSASLSNTSTGEIKLAFKPYETNVLSHQNQNSFKSSSSLDAEPTRPSSKNS
                     SSAQERVPSRSKSNATPTDGGKAEISAHDSSSSRKTVSPSGSSQRGASPIVRSGMEVL
                     NNANGTAQHPKEMSSMAAAAAAAAAAYKAAGPYGLNPLSALCCPPGMEQHANPAFRPP
                     FAGGFSHHHAAMLAVAANGGYPGGAPGGGPAGQPNPYISYQRIKTPAGGEAIVPVCKD
                     PYCQGCPYSAHTQQMLMGAPCPAGCTQCEHQKYGLAMASAAGLPPAHPYSQAAAAAAA
                     NAAAARSAPYVCSWVVGDAYCGKRFQTSDELFSHLRTHTGNLSDPAAAAAALAQSQAQ
                     SLLGTLFPPSALRAGYPTPPLSPMSAAAAAARYHPYAKPPPGALAGGPSPFGAAGAFN
                     PAAAAAAAALGPYYSPYAMYGQRMGAAHQ"
     gene            25127..25198
                     /locus_tag="CR31985"
     tRNA            25127..25198
                     /locus_tag="CR31985"
                     /product="tRNA-Pro"
                     /map="35B2-35B2"
                     /db_xref="FLYBASE:FBgn0051985"
     gene            47340..47390
                     /locus_tag="CR31977"
     tRNA            47340..47390
                     /locus_tag="CR31977"
                     /product="tRNA-Gly"
                     /map="35B2-35B2"
                     /db_xref="FLYBASE:FBgn0051977"
     gene            complement(47556..47626)
                     /locus_tag="CR31978"
     tRNA            complement(47556..47626)
                     /locus_tag="CR31978"
                     /product="tRNA-Gly"
                     /map="35B2-35B2"
                     /db_xref="FLYBASE:FBgn0051978"
     gene            complement(47870..47940)
                     /locus_tag="CR31982"
     tRNA            complement(47870..47940)
                     /locus_tag="CR31982"
                     /product="tRNA-Gly"
                     /map="35B2-35B2"
                     /db_xref="FLYBASE:FBgn0051982"
     gene            complement(59795..59865)
                     /locus_tag="CR31981"
     tRNA            complement(59795..59865)
                     /locus_tag="CR31981"
                     /product="tRNA-Gly"
                     /map="35B2-35B2"
                     /db_xref="FLYBASE:FBgn0051981"
     gene            complement(60103..60173)
                     /locus_tag="CR31980"
     tRNA            complement(60103..60173)
                     /locus_tag="CR31980"
                     /product="tRNA-Gly"
                     /map="35B2-35B2"
                     /db_xref="FLYBASE:FBgn0051980"
     gene            complement(76884..78324)
                     /gene="BG:DS04641.8"
                     /locus_tag="CG4218"
                     /note="last curated on Thu Dec 13 17:04:18 PST 2001"
                     /map="35B2-35B2"
                     /db_xref="FLYBASE:FBgn0028881"
     mRNA            complement(join(76884..77044,77116..77503,77900..78324))
                     /gene="BG:DS04641.8"
                     /locus_tag="CG4218"
                     /product="CG4218-RA"
                     /db_xref="FLYBASE:FBgn0028881"
     CDS             complement(join(76890..77044,77116..77503,77900..78202))
                     /gene="BG:DS04641.8"
                     /locus_tag="CG4218"
                     /note="BG:DS04641.8 gene product"
                     /codon_start=1
                     /product="CG4218-PA"
                     /protein_id="AAF53400.1"
                     /db_xref="GI:7298164"
                     /db_xref="FLYBASE:FBgn0028881"
                     /translation="MATRQPTPRQLAYLDELKMRLQELRDRQASFMEQTAKILSRMSS
                     SSMDGSESETLPTDSIDENVTTNTTAGVGAGITKGSKSSLNIKKLIQRFEDLRKNSQE
                     FGDLPEVPEELINVDVRRILNGYEKLIEEGHVLQQSWFLLKKSTESCARFASANGMKS
                     EDRPPLKTNSGIVEVCNVVPEHSPEVAETPRVKKSKSLLSNMVTSSEIVDKKAEVFST
                     KMAKGKCNFQDYGHARWGAFMQLIIRVLRPFHGGSRKTKKIPAHNANNMRIPSHLPPK
                     RKPIY"
     gene            complement(92321..92975)
                     /gene="BG:DS01486.1"
                     /locus_tag="CG3473"
                     /note="last curated on Thu Dec 13 16:46:20 PST 2001"
                     /map="35B3-35B3"
                     /db_xref="FLYBASE:FBgn0028913"
     mRNA            complement(92321..92975)
                     /gene="BG:DS01486.1"
                     /locus_tag="CG3473"
                     /product="CG3473-RA"
                     /db_xref="FLYBASE:FBgn0028913"
     CDS             complement(92373..92828)
                     /gene="BG:DS01486.1"
                     /locus_tag="CG3473"
                     /note="BG:DS01486.1 gene product"
                     /codon_start=1
                     /product="CG3473-PA"
                     /protein_id="AAF53401.1"
                     /db_xref="GI:7298165"
                     /db_xref="FLYBASE:FBgn0028913"
                     /translation="MAALTPRIIKETQRLLEDPVPGISATPDECNARYFHVLVTGPKD
                     SPFEGGNFKLELFLPEDYPMKAPKVRFLTKIFHPNIDRVGRICLDILKDKWSPALQIR
                     TVLLSIQALLSAPNPDDPLANDVAELWKVNERRAIQLARECTLKHAMQN"
     gene            128108..128179
                     /locus_tag="CR31983"
     tRNA            128108..128179
                     /locus_tag="CR31983"
                     /product="tRNA-Pro"
                     /map="35B3-35B3"
                     /db_xref="FLYBASE:FBgn0051983"
     gene            complement(128645..128716)
                     /locus_tag="CR31979"
     tRNA            complement(128645..128716)
                     /locus_tag="CR31979"
                     /product="tRNA-Pro"
                     /map="35B3-35B3"
                     /db_xref="FLYBASE:FBgn0051979"
     gene            128923..128994
                     /locus_tag="CR31984"
     tRNA            128923..128994
                     /locus_tag="CR31984"
                     /product="tRNA-Pro"
                     /map="35B3-35B3"
                     /db_xref="FLYBASE:FBgn0051984"
     gene            complement(129025..218563)
                     /gene="osp"
                     /locus_tag="CG3479"
                     /note="last curated on Thu Sep 12 16:03:17 PDT 2002"
                     /map="35B3-35B4"
                     /db_xref="FLYBASE:FBgn0003016"
     mRNA            complement(join(129025..130124,130381..130729,
                     130936..131047,131100..131249,131362..131501,
                     131576..131710,131840..134493,139933..140509,
                     141100..141165,165331..165399,217718..218563))
                     /gene="osp"
                     /locus_tag="CG3479"
                     /product="CG3479-RA"
                     /db_xref="FLYBASE:FBgn0003016"
     CDS             complement(join(129928..130124,130381..130729,
                     130936..131047,131100..131249,131362..131501,
                     131576..131710,131840..134493,139933..140509,
                     141100..141165,165331..165399,217718..217930))
                     /gene="osp"
                     /locus_tag="CG3479"
                     /note="osp gene product"
                     /codon_start=1
                     /product="CG3479-PA"
                     /protein_id="AAF53402.3"
                     /db_xref="GI:28380372"
                     /db_xref="FLYBASE:FBgn0003016"
                     /translation="MSTTTITTTVPAAPSKSAPPTPTTTGAAGATTNARTADCRKFTP
                     NIFNKSKCSHCFRQREEHSAAALECNRVSKCGYLFVAPDWDFSNPLYRTKRWQRRWFV
                     LYDDGELTYSVDDYPETIPQACVDMTKVLEVTSAVEVTGHPNSIAITAPERVTFVKGT
                     SSEESQWWLNILAAFPKSKGRHKRSATLPGGQVVGSLRPTSNGDLTLSTKLGNRHSSY
                     HKDTLTSSQSAGNLLSSLDLGPSSTKTAGSPLTTTQSALADDEEDDGVETGEDVDEDE
                     EDETSVPRKSKTVSMGGQDENNRNAGNEITNRVSQPTTCLLIEDIRRDEKTIKDIANT
                     ITNLSQQQNKRWSTAVNNALNNQHHFGHHSQYQVTSRDETDFQMSSNSSSTKSQNPAS
                     ERPKSLPLASNSTPAIVSAIVKKIPTVMEQGDKTKPTARLQLHLKSPKHYQHERGDPD
                     GGCNLDELCVNYMAKTDELRSVGKANSKSSSGQGKPPVKEESLNAKKGWLMKQDNRTC
                     EWSKHWFTLSGAALFYYRDPLCEERGVLDGVLDVNSLTSVIPEPAASKQHAFQLTTWD
                     KQRLVLASLSPSSRNSWLAVLRSAAGLPQLDTPPKQTDIEQDFIKAQLQQPSSSPVTP
                     GTPAGPHFSSDEEYRTASEGGRRDSLDWGSPLSPSPPVLRSCLRNRSLASLHKRSRSS
                     PPSSRRSTVDSVASDELPLLVVPEEMQPTESRELKQQCETLRAEASLREARMSELLAT
                     LQRTEQQLTARLQEQQQQLNSELTQAKQSASDLMHNLGMQLTESQCQIKQLEDRLAQG
                     IEENEGLYKRLRELQAQDHSGGAALSNLQRHKIKRMDSLSDLTTISDIDPYCLQRDSL
                     AEEYNELRSRFEKAVNEIRAMKRELKQSQNQYDALELAQAALQQKLERRQHEDGAQLQ
                     LMAARIQDLTLKYSSSERQVRALKQKLAKSERRRSLSLKGKEQLELKLSELQRETVER
                     KEGTPPESSSSESSSQSPLNAHLLQRLHSLEHVLLGSKERLEQSLTQLQQIRAGQRTR
                     RSVSPMNDRKDGLRQLERALAETCVMVSEQMELTCLQDSCHKCCDLRQRVEKLSALQQ
                     QTETDLQRSEQLLEQRETDLAQALEKCASQEQEQELLLQQRQELSEELGRQQERCRRL
                     EKRLELLEREHGKQLECLREVYHTEHANAADEQSFRKRYQTEIEQLRTLCEKGLSAME
                     TSHKRLTMDLEQKHKMEIERLLAEKETALAEETQATLAALDAMRKAHQSEVQREVARF
                     KQEFLRQVQRGEQMRGDGAKLKEEDLGELRMEILAFSEKYSIKCVENAALEEKLHMAN
                     SKLRHFQQMQQLELRNKQFRAHLASDDPSNDVHFVQGLTSDAREDADCEDSEPAPQIL
                     GATATRTTATTTTTATATTTSAAPSETESNPDSDRETADSSRAPPEKMEQSLFVIPSH
                     MLNSSLVPAANASDQSQRSQLYRDLDGPEDGYEPCYRPFDIFAIYQNRLSYQGLKGSS
                     TFGKSLRKSAAQTSPASSEITTTTTAPTTDPKKPSHKQMFKTAAVINIQQQVAQEEKA
                     Q"
     gene            144804..148151
                     /locus_tag="CG32954"
                     /note="synonyms: Adh, Adhr; last curated on Tue Nov 05
                     07:50:23 PST 2002"
                     /map="35B3-35B3"
                     /db_xref="FLYBASE:FBgn0052954"
     mRNA            join(144804..144892,145552..145686,145752..146156,
                     146227..146892,147319..147723,147775..148151)
                     /locus_tag="CG32954"
                     /product="CG32954-RA"
                     /db_xref="FLYBASE:FBgn0052954"
     mRNA            join(144804..144892,145552..145686,145752..146156,
                     146227..146892,147319..147723,147775..148151)
                     /locus_tag="CG32954"
                     /product="CG32954-RC"
                     /db_xref="FLYBASE:FBgn0052954"
     mRNA            join(144804..145686,145752..146156,146227..146668)
                     /locus_tag="CG32954"
                     /product="CG32954-RH"
                     /db_xref="FLYBASE:FBgn0052954"
     mRNA            join(144804..144892,145378..145686,145752..146156,
                     146227..146668)
                     /locus_tag="CG32954"
                     /product="CG32954-RG"
                     /db_xref="FLYBASE:FBgn0052954"
     mRNA            join(144804..144892,145552..145686,145752..146156,
                     146227..146668)
                     /locus_tag="CG32954"
                     /product="CG32954-RB"
                     /db_xref="FLYBASE:FBgn0052954"
     mRNA            join(145518..145686,145752..146156,146227..146892,
                     147319..147723,147775..148151)
                     /locus_tag="CG32954"
                     /product="CG32954-RD"
                     /db_xref="FLYBASE:FBgn0052954"
     mRNA            join(145518..145686,145752..146156,146227..146892,
                     147319..147723,147775..148151)
                     /locus_tag="CG32954"
                     /product="CG32954-RE"
                     /db_xref="FLYBASE:FBgn0052954"
     mRNA            join(145518..145686,145752..146156,146227..146668)
                     /locus_tag="CG32954"
                     /product="CG32954-RF"
                     /db_xref="FLYBASE:FBgn0052954"
     CDS             join(145588..145686,145752..146156,146227..146493)
                     /locus_tag="CG32954"
                     /note="CG32954 gene product from transcript CG32954-RA"
                     /codon_start=1
                     /product="CG32954-PA"
                     /protein_id="AAF53403.1"
                     /db_xref="GI:7298167"
                     /db_xref="FLYBASE:FBgn0052954"
                     /translation="MSFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENP
                     AAIAELKAINPKVTVTFYPYDVTVPIAETTKLLKTIFAQLKTVDVLINGAGILDDHQI
                     ERTIAVNYTGLVNTTTAILDFWDKRKGGPGGIICNIGSVTGFNAIYQVPVYSGTKAAV
                     VNFTSSLAKLAPITGVTAYTVNPGITRTTLVHTFNSWLDVEPQVAEKLLAHPTQPSLA
                     CAENFVKAIELNQNGAIWKLDLGTLEAIQWTKHWDSGI"
     CDS             join(145588..145686,145752..146156,146227..146493)
                     /locus_tag="CG32954"
                     /note="CG32954 gene product from transcript CG32954-RB"
                     /codon_start=1
                     /product="CG32954-PB"
                     /protein_id="AAO41197.1"
                     /db_xref="GI:28380373"
                     /db_xref="FLYBASE:FBgn0052954"
                     /translation="MSFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENP
                     AAIAELKAINPKVTVTFYPYDVTVPIAETTKLLKTIFAQLKTVDVLINGAGILDDHQI
                     ERTIAVNYTGLVNTTTAILDFWDKRKGGPGGIICNIGSVTGFNAIYQVPVYSGTKAAV
                     VNFTSSLAKLAPITGVTAYTVNPGITRTTLVHTFNSWLDVEPQVAEKLLAHPTQPSLA
                     CAENFVKAIELNQNGAIWKLDLGTLEAIQWTKHWDSGI"
     CDS             join(145588..145686,145752..146156,146227..146493)
                     /locus_tag="CG32954"
                     /note="CG32954 gene product from transcript CG32954-RD"
                     /codon_start=1
                     /product="CG32954-PD"
                     /protein_id="AAO41198.1"
                     /db_xref="GI:28380374"
                     /db_xref="FLYBASE:FBgn0052954"
                     /translation="MSFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENP
                     AAIAELKAINPKVTVTFYPYDVTVPIAETTKLLKTIFAQLKTVDVLINGAGILDDHQI
                     ERTIAVNYTGLVNTTTAILDFWDKRKGGPGGIICNIGSVTGFNAIYQVPVYSGTKAAV
                     VNFTSSLAKLAPITGVTAYTVNPGITRTTLVHTFNSWLDVEPQVAEKLLAHPTQPSLA
                     CAENFVKAIELNQNGAIWKLDLGTLEAIQWTKHWDSGI"
     CDS             join(145588..145686,145752..146156,146227..146493)
                     /locus_tag="CG32954"
                     /note="CG32954 gene product from transcript CG32954-RF"
                     /codon_start=1
                     /product="CG32954-PF"
                     /protein_id="AAO41199.1"
                     /db_xref="GI:28380375"
                     /db_xref="FLYBASE:FBgn0052954"
                     /translation="MSFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENP
                     AAIAELKAINPKVTVTFYPYDVTVPIAETTKLLKTIFAQLKTVDVLINGAGILDDHQI
                     ERTIAVNYTGLVNTTTAILDFWDKRKGGPGGIICNIGSVTGFNAIYQVPVYSGTKAAV
                     VNFTSSLAKLAPITGVTAYTVNPGITRTTLVHTFNSWLDVEPQVAEKLLAHPTQPSLA
                     CAENFVKAIELNQNGAIWKLDLGTLEAIQWTKHWDSGI"
     CDS             join(145588..145686,145752..146156,146227..146493)
                     /locus_tag="CG32954"
                     /note="CG32954 gene product from transcript CG32954-RG"
                     /codon_start=1
                     /product="CG32954-PG"
                     /protein_id="AAO41200.1"
                     /db_xref="GI:28380376"
                     /db_xref="FLYBASE:FBgn0052954"
                     /translation="MSFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENP
                     AAIAELKAINPKVTVTFYPYDVTVPIAETTKLLKTIFAQLKTVDVLINGAGILDDHQI
                     ERTIAVNYTGLVNTTTAILDFWDKRKGGPGGIICNIGSVTGFNAIYQVPVYSGTKAAV
                     VNFTSSLAKLAPITGVTAYTVNPGITRTTLVHTFNSWLDVEPQVAEKLLAHPTQPSLA
                     CAENFVKAIELNQNGAIWKLDLGTLEAIQWTKHWDSGI"
     CDS             join(145588..145686,145752..146156,146227..146493)
                     /locus_tag="CG32954"
                     /note="CG32954 gene product from transcript CG32954-RH"
                     /codon_start=1
                     /product="CG32954-PH"
                     /protein_id="AAO41201.1"
                     /db_xref="GI:28380377"
                     /db_xref="FLYBASE:FBgn0052954"
                     /translation="MSFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENP
                     AAIAELKAINPKVTVTFYPYDVTVPIAETTKLLKTIFAQLKTVDVLINGAGILDDHQI
                     ERTIAVNYTGLVNTTTAILDFWDKRKGGPGGIICNIGSVTGFNAIYQVPVYSGTKAAV
                     VNFTSSLAKLAPITGVTAYTVNPGITRTTLVHTFNSWLDVEPQVAEKLLAHPTQPSLA
                     CAENFVKAIELNQNGAIWKLDLGTLEAIQWTKHWDSGI"
     CDS             join(146797..146892,147319..147723,147775..148092)
                     /locus_tag="CG32954"
                     /note="CG32954 gene product from transcript CG32954-RC"
                     /codon_start=1
                     /product="CG32954-PC"
                     /protein_id="AAF53404.1"
                     /db_xref="GI:7298168"
                     /db_xref="FLYBASE:FBgn0052954"
                     /translation="MFDLTGKHVCYVADCGGIALETSKVLMTKNIAKLAILQSTENPQ
                     AIAQLQSIKPSTQIFFWTYDVTMAREDMKKYFDEVMVQMDYIDVLINGATLCDENNID
                     ATINTNLTGMMNTVATVLPYMDRKMGGTGGLIVNVTSVIGLDPSPVFCAYSASKFGVI
                     GFTRSLADPLYYSQNGVAVMAVCCGPTRVFVDRELKAFLEYGQSFADRLRRAPCQSTS
                     VCGQNIVNAIERSENGQIWIADKGGLELVKLHWYWHMADQFVHYMQSNDEEDQD"
     CDS             join(146797..146892,147319..147723,147775..148092)
                     /locus_tag="CG32954"
                     /note="CG32954 gene product from transcript CG32954-RE"
                     /codon_start=1
                     /product="CG32954-PE"
                     /protein_id="AAO41202.1"
                     /db_xref="GI:28380378"
                     /db_xref="FLYBASE:FBgn0052954"
                     /translation="MFDLTGKHVCYVADCGGIALETSKVLMTKNIAKLAILQSTENPQ
                     AIAQLQSIKPSTQIFFWTYDVTMAREDMKKYFDEVMVQMDYIDVLINGATLCDENNID
                     ATINTNLTGMMNTVATVLPYMDRKMGGTGGLIVNVTSVIGLDPSPVFCAYSASKFGVI
                     GFTRSLADPLYYSQNGVAVMAVCCGPTRVFVDRELKAFLEYGQSFADRLRRAPCQSTS
                     VCGQNIVNAIERSENGQIWIADKGGLELVKLHWYWHMADQFVHYMQSNDEEDQD"
     gene            complement(148188..148550)
                     /locus_tag="TE19174"
     repeat_region   complement(148188..148550)
                     /map="35B3-35B3"
                     /transposon="jockey{}370"
                     /db_xref="FLYBASE:FBti0019174"
     gene            complement(171878..180982)
                     /locus_tag="TE19175"
     repeat_region   complement(171878..180982)
                     /map="35B3-35B4"
                     /transposon="roo{}371"
                     /db_xref="FLYBASE:FBti0019175"
     gene            241917..242519
                     /gene="BG:DS07721.3"
                     /locus_tag="CG15282"
                     /note="last curated on Thu Dec 13 16:55:15 PST 2001"
                     /map="35B4-35B4"
                     /db_xref="FLYBASE:FBgn0028855"
     mRNA            join(241917..242005,242077..242519)
                     /gene="BG:DS07721.3"
                     /locus_tag="CG15282"
                     /product="CG15282-RA"
                     /db_xref="FLYBASE:FBgn0028855"
     CDS             join(241994..242005,242077..242304)
                     /gene="BG:DS07721.3"
                     /locus_tag="CG15282"
                     /note="BG:DS07721.3 gene product"
                     /codon_start=1
                     /product="CG15282-PA"
                     /protein_id="AAF53405.2"
                     /db_xref="GI:22946499"
                     /db_xref="FLYBASE:FBgn0028855"
                     /translation="MKFLVIVFVALIAVASALPQFGYGGFGGFGGFGGQQQQQEGFGG
                     FGGFGEQQQQQESFGGFGGFGGIEQQQQQQQGGFF"
     gene            complement(254058..258098)
                     /gene="BG:DS07721.6"
                     /locus_tag="CG12636"
                     /note="last curated on Thu Dec 13 16:58:13 PST 2001"
                     /map="35B4-35B5"
                     /db_xref="FLYBASE:FBgn0028854"
     mRNA            complement(join(254058..254071,254173..255772,
                     255972..257281,257807..257914,258002..258098))
                     /gene="BG:DS07721.6"
                     /locus_tag="CG12636"
                     /product="CG12636-RA"
                     /db_xref="FLYBASE:FBgn0028854"
     CDS             complement(join(254058..254071,254173..255772,
                     255972..257281,257807..257914,258002..258098))
                     /gene="BG:DS07721.6"
                     /locus_tag="CG12636"
                     /note="BG:DS07721.6 gene product"
                     /codon_start=1
                     /product="CG12636-PA"
                     /protein_id="AAF53406.1"
                     /db_xref="GI:7298170"
                     /db_xref="FLYBASE:FBgn0028854"
                     /translation="MGHLEFFASISDACSTVEYDKITWQLCDITENKIIARLKNATGL
                     VVKLLPYKVHILNEPDRRKVFLLRGPTLRLPPYALKENAVYDFSLTVISRFDPRNRMT
                     TTQTIKGVAKTTFTPQILCRRNCALGVYAPLDSIHLISKCDDCPGTVKRYEWWLLDTE
                     SQPTLESSHKYLILHTLEPLVQIRLRVWVKGQGWADAFYTLRRNNGPQHGSCTIYPFL
                     GVEGFTMFEIDCPGFESPFPPITYRYMVSYGVVASNVPYSRIVLTLPAAETIMISICD
                     AIDMCVEKRVEVKVLSIDKSMLTGQKEVMNYVPNFFKRGHWNRAYIMGIAAITFIETS
                     IDGDEFYSYLTGLVASTGSQMEQITTLSSHMLIRLHPVDFRGATVMAEMFSHLGDSFS
                     AIVQEHEWLHREGYYSLTAMHMFFMSILGKKTESHSNAMCSLHNPACMNLQIIDLEKP
                     FVIKFDPLILVRINSWLMSTWFLYRCIYFLGVIATQRHHPYDDALTIHKSGIAYQINV
                     TEVTENTKDIQVKTIDHIHVIKLSTKLLYELQRRLNHSSILLQIISQQNFHNIYWWYP
                     DPFPSKTSVLIVHAYSPVQFFRSAKEFQLTNPLVYKTNITHFNDASFNQYMTNNSIQN
                     STEVHIYSVMLNHKAMLAVRIVNCSELMYIKMRLHRWPTLGQIRQHACRITPDMQGKR
                     IWIANSCERSPAYVAIHKPGEIRYKTEDKDQLSARGRKKGNRTHDGSETPEVRQKADF
                     IDYDNEDIVEEVLPLNYSILLEIYQCNIWKNRSLDPGWSEDHCTTSFEHSRGSSVQCT
                     CHTLGALSSRIFPISSQLFVEHIPVPIFTFNMILMIFFALLFLLLVFKFLLHLNIISA
                     YLKNPEFRLQCDASVGKSDQSFVSGSEILLVIVTGGQEFAGTTSNVKFYLKSPHRQQT
                     SYQITQDPGHPKLLRNSTIKIMVPRGHIYIPTRLALRLVPNGRYPSWYCRSITVVDLK
                     LKVQQLFLVESWIEGGSHIQFMRSKYFTYGNYSRYPKYTWCKRFRSRAEQLYFSWYLI
                     NAITGPSQTHGI"
BASE COUNT    77534 a  53560 c  53766 g  78449 t
ORIGIN      
        1 acgtgctggc aaatgcaaat aacgaatttt agcacggcac tgactttggc acgactttgg
       61 atcgtctgca ttgactttgg tcccctttcg ctgagttttc cggaagagaa cgccggcata
      121 tagaccatga tatagtggca aagtaatttg aaatgaaaat taatgacatg caatcaattt
      181 tcgtagtcgt cgttatttgt tattttgatg acttgccttg cgcacacaca aacttggctc
      241 gctctcactc tcgcccattt gtcaagggct aaacaattgg gagcatgaaa atgaaatatg
      301 tctgccatgc tggagaggag tagctccagt tcagtgagga ctgtttgctt ttaaccgcaa
      361 tatgcttaag ttgcggttat ttattgtctg gcatttatag tgcggcagaa aggagcagta
      421 ctttgctacc ctctacacgg aggaatatat tgcttgtatg tactagaaga cttgtcaaac
      481 tcgtcagatc ttcgaattac acgtgcttat aagacaaaag tatacaaatt ctatcaaaat
      541 attaacaata tttaatgtgc aactgtgaca tacaaactga aatcactcat acgacatgta
      601 taccagggat aatttattaa cccaagtaca tatatggttt ttttcttatt ttttataata
      661 tttaaaacta atatctttgt gcttgaacta gtcacttgtt ttccgttggt aagttggctt
      721 aaaatattga aagggtattt acctagatta atgttcacct tttcttttga ttttcgcgta
      781 ttaaaccctc gtgcagaatg ttttctgtct gattcgtatc gacatatttc gcccgcattt
      841 tgtattccgg ctgtcaacgc caaaagttca agctgatcag accctctgtt gccctcttca
      901 cctccttcaa tcatttcctt ccccgcagcg ctttgttcct cttttttggg tgactgacat
      961 gagctttcgt ttataccgtc ctccgtgccc cgccatccca atccttctga ttgatgggcg
     1021 acagcaaaaa aagttggcac ttgctttgca gtgtgttgtg ccagagtccc cagaaccacc
     1081 caatcgccca tccatccaaa aatggagcca gttttggtcg ggaaaggtgg tcaaaacacc
     1141 acccgaaata agtcatcgcg tgcagagttg ccatcaagct aaagccaaga ttgattagtt
     1201 attgaaaaga catcagctgg ggaaattggg caactcgtaa aaacacgagg taataccctg
     1261 taattaacgt atatctaagg aatgttactt tattttacac ttaaaagtat taatatgatc
     1321 aataattatt attttttttc agtttgggtc ttatataata taaaggaaga atattatttt
     1381 gattttctca ctgtgtaatc actttggggc cttcgcaaat aagtcataat gatttttgat
     1441 cgatgcgccc cagtccgagg acgtcggtgg atcattaaca aaactgaaac ttgccgaggg
     1501 agacaacctt cccctatcga ttcctcgatt ccctgtgcat aatcattttc aataaataat
     1561 ttttcctccg tccgggactt ccactctttg ttgttggtgt ttttcgacgc tatttttttt
     1621 gtcggttggc ataatgacag catgacagga taaattactg ccaaatgaat ggggcaaaat
     1681 atgtcttaag cgacacactc acacacacac acacacacaa gcacacgcag acagccacgc
     1741 ccacttggcg ctgccaaaag ccaaacatca aaaattgttt tccctctttt ctgttgtgta
     1801 atttaccacc aaacagcgat ggccgaatga aggaaggcaa cgcccgcatg ggtaaaatta
     1861 ataggcataa taattttttg acagcacacc caaggataac gcaggcaact catcagagtc
     1921 ctttgcatgc ggcggtagtg aatttttttt ccaaccccgg cggttgggga attcgttgag
     1981 tgacaggcag gttgatgata aatgatgtcg ctgatgttgg tccgggttgt gccccggcaa
     2041 cttgcctctt gccacgtcac ggaggcaatc gtttggggcg cccccgtcct gtatatcctc
     2101 caaaagtgct ccctgctccc ctccctttct ctgacagaca cagtcgtcgc ctgattactt
     2161 tgatgacgtt gccacatatt tgtgtgttct tcccccatcc aggaattaaa ttcataatat
     2221 tttgtgcact ctcactttgc gtttcaatgg gaagtttagg gtacatcagc tagggtagta
     2281 agttgggcta caaaattttt aatcagtcaa acagaacaat ctgtttgcta agatgaccta
     2341 aatatcattt tctaaagatt tattttaata actttttaca acttttcaca gtttaagatt
     2401 ttattatgtt agttaaccaa tttaaaagaa aaaagtatga cgttagttga atagtatgta
     2461 tatttggtat cttttcttct aatccctcac atttcattag agtccatgac aaaacaacga
     2521 aaagttcgag acttttcttg atcattctat tctatcacat attttggctc ggcaaataaa
     2581 gttgaataat taattgatga aataattcgg agcgtgtgtc gctttgacat tgaataattg
     2641 ctttccattt ggccaaaaac cactcacgtg gccatatcgt ccgtcagctg ttatctactg
     2701 aatagatata aacctacgag cctagaaaaa cataaagacg gcaatctata tgataagtgc
     2761 caagtcatca ggatccaatc tatcacaggc gatgtgtcaa tttaaagtgt gagaaaattg
     2821 ctggaattga tgaatgatga tgacggtacg gatcgcaaag aaaaagtaat tagtgcgact
     2881 caatggtgtg tgtactcttc aaatttaggg aatattctat ttatatatcc ccttattttc
     2941 agatgaaaag atgattttcc taaacaaata gcaaaaatat atattgaagt cattttcggc
     3001 gtcattgtga tcgtgactcg tttacactct gtaattcatc aatttattaa aatacaaagt
     3061 tgtattgctc gtttggaaat ggcaaattac tctacgtttg tggtagtaag cgctaaatgc
     3121 acataaaatg tgtttttaat tgcgaattgc caaatggtaa cgagcagcat tcagtttttg
     3181 ttgataattg agcgatttta aaatcgccag acttgcagat tacgtatacg tactatgtgt
     3241 aattaactaa gctctcaata aaaatcaaat agaatgtact gaatgtagag tggcattgtt
     3301 ggccgtggca tagaaattga aatcaacacc catacaatgg atactgaatc tgaaatggct
     3361 cataaataaa acaattgagt taagccataa atcaaacact taatacaata gtttccgctt
     3421 ttattattat gtgttcgctt tcaacttccc aactacgctg tgcactcgca taaaatagcc
     3481 ataaattaaa ataacagtaa aataaaccac tgagtgcgga ctatttgctg gcaaaggagt
     3541 gctttataac catatagtca tatagccacg gctgctctat gctctataca agtacagtgg
     3601 tgtgtgtgtg tgtgtgtgtg ggccattgtg aagcggccta agctcgcaaa ttagcataca
     3661 aactgtctgg cagaaaattc gccattgaaa gagaccaggt gagtcgcacg ataatattaa
     3721 tatgtacctc acttaatcat aaatgcccgg cgacatgcga gaccccttcc ttgtgccccg
     3781 tcgccatatg aaaagcaatt gatgtatggt agtaggtagg tactggcaac tgccaactgg
     3841 caaccagttg tttgttgttt cagttgcggg ttttgttatt ttccctgaaa gctcagcagg
     3901 cagacatttc ggaattgggt ggctcggtac caacaagttg catgtcgcta actagttaat
     3961 aataatgctt tggacaaaaa gtggcagcct gtgtgacgtg acgcattgca tgacatgcaa
     4021 gtggctattt gggcggtgtg aggtggccta ttgccaccca aacgatacga tccgatccgt
     4081 tacgatacga tgcgatactt agacccagtt cgagacccgg ccaagcaaag tcgaagcgaa
     4141 actaagccaa attagaagct tttcattttc tgtcgtataa tttatgaccg gcacttttcg
     4201 agtcaattca gccaagcgtt aatcgccgtt tgactcgttt cccccgtgcg ttcagcaatg
     4261 tgcataattc agactacact ggacaacaag atagcgaact atagaaatgt ctatcaatat
     4321 gtataattta taaagatttg tttgccatga aagtatactt aatacattta caaaacattt
     4381 aaatacaaaa caacattgta aaatagtaat tttccaaatg tgttctaaat gaatagctaa
     4441 acaaaaataa atatattcgt gtgaaggcaa aatacattac caaaccagca agctcaaagt
     4501 aagccaactt ttctttacga aacatttctt ttgctgggca gtgaaggtgg tagacatcag
     4561 tccaactgca ccgaatggaa atggaacgga gagtcggcac tttgtcgcat tgtcgtccac
     4621 atggactgta gactggccct ccttggccac gtcgccggct accggcttcc acagttatta
     4681 ttattattgt aatttgctgg ctcagacccc acgttgacag cgtgtcattt cgaatcgttt
     4741 tgtttagtca tagtcacagt gggtcccctt ccttgccact gccctgcact ttgtttcccg
     4801 cttcggttta ctggttcggc tgggcttttt acacgaaaat ggtaatatgg catatttcat
     4861 aattaattgt gaaattatac aaagatatgt atgcaaaaat gctcggaaaa gtcataattt
     4921 tcatgtgact tggttttttg ccctgcccta tacccttcaa acaaaaggca tggcgaattg
     4981 attatgactt tggtatcgta aaggtgattt ataaatctga gttatggttt aaaaatcctt
     5041 atattcattg tagtaatatt taatccctta aaaactgcta cctaactgcc tattttaatt
     5101 tttctgtgcc gacattcccc ttcaacgtga acaacacgca ctggtgtaaa actcaggcct
     5161 tgttacatat caaagttggc tgtccaaagt taaaactctt acaattcata ggaattaatt
     5221 ggtttccatg gaggtgccgg tgtccgtgtt gcggaaggaa ctacttgcgg acagggaatg
     5281 ttgatgcgat gacgccagcg acaactacat aaaagtttgt gaaaggtgaa atcatgaccg
     5341 ggccaggcaa tgcaaatcag gaagcgagtt caacacctgc tcgaacggca gaaggacgaa
     5401 acttcactga cgcgcagtag aaaaacccag gggggctgtg ggcaacaccc accccctcac
     5461 ggaaaaccaa ctgtcattgc cttgtaatgg aggttgattt aacgggggag gtggaggtga
     5521 cgtgtcaact gtcaatttgt atttgaaaag ctgtcacttg cgctgcctcc acccagatat
     5581 tcgtactgcc acatacaaat cacaacaaat aaacgccaat tgacagcgac aacccagcga
     5641 agaagaagcc atcgcggtac agtgagcact gacaatatgg gatgatgtaa gaaaatatta
     5701 tttggtatta cattttaccc atatggtttg ttataaaatc cataaattat tatgataata
     5761 tttaaaacaa tctaattaaa ttagaccaaa taaacagagt aggtatatgt atgattttta
     5821 gtcctatttc tccaaatgaa tacttctgcc tttcgagctt cacattttcc ccaactcgga
     5881 ctcctccagg ggtcacaccc atcaattgaa ctttgtcatg ggatacgcat ttctccgttt
     5941 gactgctaaa tgctcgtgtc ttgagagttt atttgtctta cttatttatg tttatgtgct
     6001 cttcttaagc gttgctaaat taggcgcacg tccgtttcgg gttggtattc ggattgaatt
     6061 ggattggatt ggggtggcaa atggtgtggg cgatacggga cctacaacac cacctcttcc
     6121 gaatagcagc tgtgcctaat ttatttcagt ggacgtgccc ccatttcgcc tgtggctgcc
     6181 gcccatcggc tcgaatcaaa ccgaagccca gaacgaatcc cacagtttga agatttattt
     6241 cgttctgaag aacattaaaa ttttacaaat tgctttaatc aaataaattg ccgcgtttat
     6301 ggtgataaat tgtgtttggg gccagcaagt ttttgattca ggacgcgtga acacaactgg
     6361 ggaattagag taaatgaaag agaaagggag tgagttaaat gcagtgtgaa aaaataagtg
     6421 cggccatatg tggggtatgg tgttaagtct gatttaactg atgtaacatt gacaatgaat
     6481 aactttgatg aagactacct accactttag agctgagcct ctcaaatttg gtcttcgtct
     6541 caacccttca gcacgtcgga cttattaaat ataatttatg gttgctttca atttattttc
     6601 aacgccagcc gaactattat agtgtttcca tcttcactta agtttgcttc cgataacgat
     6661 aacgataagt atattgcgtg tatatataac gctgttcacc taagtgactc ttttgcataa
     6721 tgaatggacg aacgggtgag ttaaagaagc cgggcatgga gaacaagaag aaacttaatg
     6781 acttgacatc tgcagacatg gccaccataa tactttgtat gtaaatttcg ccaataaagt
     6841 aatttctttt aatgagccgc gggctagtca gaaagcggcg aaagaaattg ggaatgggaa
     6901 tgagaatggg tgagccatta agtatcgcat aaagtaacaa aatgaattag gccccgacaa
     6961 gatgatgatg atggtgatgg tggcgatggt agtgcggtgg tgcaacgttg atggggccca
     7021 cggcccctat caactcggta gtctcgatgc gcggaagtaa ttgagttaaa tatgcacaag
     7081 atgacagcat aaattatgcg cctcacaaaa aaagagttaa atgtggtctt gtggcaaaca
     7141 aaagggtgga gggttggccg gggaaagaca atgacaagaa ccgccagttc agcgctgcga
     7201 tggcaaacaa aaggcaacaa atgagggaag cctacttatc aacggcatgg gaaccgcgcc
     7261 gaagcccgta cctttgagca ctcaagattc ggtccttgaa aggggttgca atctacctcc
     7321 tcgactgctg acacttgaaa aagtgtgcat aacaaattcg ataatgaact atgaaatttt
     7381 tgccagattg taaccctttt tggcattgtc ggaaatccct gccccacatg tcacagttga
     7441 aatttatttt gctgtcataa attttgaaat aacaattatt gccatttata gccggcaaag
     7501 ggaatccttg aaatgggttt ccatttgcat aataaacgct tgtcccagag gaagacgtat
     7561 ttcatccttg gcattgtcat aatttcaggg aaggacttag tttgagggat gacgtacgac
     7621 ggattgagga aagctagttc ttgcggttgg gaaaatatga cattgtaata atattatttc
     7681 ataagtttgt gcttaaaagc tgaatatata ttcctccatc gatatacatt catggtaaat
     7741 accattattt tcattcattc cttctattat aacattttaa aagaagattg tgtacattac
     7801 ttcgacaaat tcttgctgtt ttgcactgaa ccagataaaa taccattcta tgtagaccga
     7861 aatttcgttc tatatatttt taaaattacc cagttttttg agaatgtttc tcagatattt
     7921 ctctatattt ttcattcttt cacgtgtgtt cgaagtgaag catagaaagt aaatcaactg
     7981 taaaatggtt cgttcctgct cgtaaagtat aaatttgttc cacaatctgc agaaaaatat
     8041 gttggaaata tgcatatttc ccccgttttc tctgcactcc aactactcgt aatttttatc
     8101 ccaaaaattg ttcggctagt gagtgtgtga gaaaagtctc gagatgagaa atctgtgttt
     8161 aggtacgcca ctactcactc ggcttcctca cctcagccgt tttccattta aatgtaaatt
     8221 aatggtcagt taagctgtca gccatggagt tttgggtctc attcagttca gttctgcggc
     8281 tctaacgatt tgggtggttg gttgatggga tgatgggaat gaccatcgca gcacatcaca
     8341 gatttgtggt gttaatttgc tgtgaaatgt tgactgacca gagaccagtg accggtgacc
     8401 ggtgaccggt ggaccagttt accagttgat gccatttgcc tgtaattaat tgtctgtgtt
     8461 taatgtgagt taattttatt tatggccagc tcgttattta catttacgca gcgaatggag
     8521 tccgatcttc acacggcacg caattacaga acaatatttc agatttcatt cacatttttc
     8581 tcttagctgt ttctttttta gtcccagaag tcatcgttgt tgtcaggaat cgttgtctgc
     8641 ccgagacgtg gcaacactga caggacactt ctgacagccc tgagacagcg gggactaagc
     8701 ttctgctaat gtcaacagca aacagttcaa attgtgcaaa atatagcaac gagtggtgga
     8761 aatgggtata tcagatattg taggaagaag tcgcatagct atacaacttt cagggttgcc
     8821 aggctgacta aaattattat ttatgacagc tagtcgaaat atttattttt ctaaaaacaa
     8881 ttctgtaagc gaaataattt catattaaat tttgtacaaa agcggtaaga gaattcaaaa
     8941 attttggttt aattaaggaa ttaaggaaaa aataaaaaag tctgtctttc tcaatttaca
     9001 aaccttatga gcctgcatta catccagcta ttgtagggca tttcaagata taaaattgca
     9061 ttgccagtga acaaagaggg gcgaaggcgg ggaatacgaa caaaagggct ggaaaacaaa
     9121 agccaaacaa taagcaacag tgacagtggc actgttgtct tctgctccac gttcccttct
     9181 gaatctgaca gttgtcaact gctgttggct gccgcctttt tcgttactcg gctgtcatcc
     9241 tccgaccctt tgctgttttt gaaatttttc ttatttcttg tacatatatt ttttcgggac
     9301 tgtggtaatg ggtgtgcacc gctccagtta tgacgttctt catcagtccg gagctcacct
     9361 acgttgtaga accgcccggt aaatcaagtt ctagtcttca cttacctgga ataaactcgc
     9421 agcattgttg tcttcggctg cgatcataaa tttcctttta accagtttag aagtggggga
     9481 aaaatatcat aaaatacgaa atgaagtacg ctcgacatgc ctcggacgct gtagaattta
     9541 tgtgacaatt ttgtccagaa taaatgactg cagactggcc agagaaggat gccccatatg
     9601 tgtatgtgcg cattctggtt tgcggtaggg tatcaagcgg gtctattaat taggcatcaa
     9661 atctaaaaat taataaggca cataaaatat atctagataa attataaaaa aatatttaac
     9721 aaaatctatg atgctcatat acgagacacc ttaaacatga tgtataagaa gcatgatgta
     9781 tagttgttta gcaacacaat aaaaagttaa ttgactattt taaaaatact tcccatttca
     9841 gggtacttca aattccaata ctatttcttt caacagcaat ttccaacttt ctccatgtcg
     9901 tagaaattag ttgggctaaa aggcacgcac accgaggagg aaaccagcca gaggaaggaa
     9961 gagtgatgca agtcctggtc agcgtttggc tccggcgatt gccattccac aatgcccaca
    10021 aaatgggtgc ccactaaaaa ctaagccact ggccagcgga cggaaaaagt gggtgtggat
    10081 gtccatgggg gttgtggaga ttgcggcttg aggatgcagg atgcagggga ggagggttcg
    10141 ccacttcagc acttggtctg ggttcgcttt tgtctgttgt cggtcatgtt gcataaatct
    10201 cattttgggc tttatttact cacaaaatgt tcacgtttcg agctagaccg cctctacact
    10261 tcctgtgcag ctcgtgcgcc ctctctgtcc agcaaataaa ttcatttagt ggcatttagt
    10321 ggcccctttc accttattgt ccgtgggcca tggccatccg atctcacccc caggatgagc
    10381 ttgggtccag gatattgcta gtgtcccatg tgtatgtgtg cattttatgg cagtgcctgc
    10441 gtttttgcgg ccaaacatga agtgaaaatt atgcacacac atatggcaaa tgtatcgcaa
    10501 ttgttttgcc catccccccc attttcaccc aacccttgtt gtggctgctg gatttggctt
    10561 tagtcggcag ttaattttca tattttccag ccgcactcac ataccagaac caccataccg
    10621 tacccaccca ctgccaccac tgtgcggaca tttcgtcgta aataaattta acaatttatt
    10681 tagattgcaa tgacaggcgg atgctattaa aagcgaaatt tatgaggtcc tttggcgcta
    10741 ttcgaagggg aggaagatgg aaacggaaga tgcacaaatg aacttcatga tattgcaatt
    10801 tgcaacagac aagacgtaca aaaacgtagt ggaatgcttc tgaaaaccaa aataacttta
    10861 cttaaaaata tcaatttatt tctgattttc tagaccatac atacagacgc cattttaaaa
    10921 tctcatttaa aatctctctt caaagaacag gaaatgcgtt ttccataagt caagaagatg
    10981 ctgacagctg gcgattaaaa atcccaagtt gggacagtac aaatcaaacc acttgaccca
    11041 acgatgtcat caattagaaa tttgaactct catcctgaca gatttttttt ttaagtatag
    11101 cacttgacta tgttaggtca ccaaaataaa tacacacaaa tttgttttat ttcctttccc
    11161 agccacatgt tggactcgat aacttcaact gcagaaagca gaacattttc atgaatatat
    11221 ttcgtattaa ataatttatt ggcaacgttt aactaacccc aaacgtgaat ggcaaatgaa
    11281 gttggaaaag ggttaaacta tgcactggga aatccacttt tgccatcttt gacaagctgg
    11341 tggagggcaa ccgtgcgtta aacaaacttc ctgcataatc ccaaacccat gaatcttgtc
    11401 aaccaccacc cccttttcaa ttcgaataga ggaagttaac ccccgttcgg ttttggatat
    11461 gcttttgttt gcctgaaatt gactgattac ccacaaaatt accaacattt atttgtccgt
    11521 aatttgagac attaataaaa gttccttttc tgtttgttcc cgccttgggt tctttggtgt
    11581 tgcgttagtt tgccggatgt tacccctttt cataccggca actgacagtt ggcttctaat
    11641 atttcaaaat ttgtaacatt tgttacactc aaatgacatc agctaattag cccaagacgg
    11701 caacgaattt gttgatgtta attaggtttt atgacctcca tgggagatcg ggttcaggtt
    11761 ctgtgggaat tgaggcatag aaaaaatgtt aaaatggaat acaatacttg cttttagaat
    11821 tcaaatgttt tgtaggaaaa ataaaagttt ttaccacata atctgaatct gaattaaatt
    11881 tttaccatag tgaagtttgc gaaatgcaaa ataaattgaa atggacaact taagaatagc
    11941 accataaatt atttaaattt tccctcatct taaaatatca taaatggcac ttgatggcat
    12001 cacataactt tttgggggct tccaggcaat tggctgtagt gcgttattta tgacccctct
    12061 gagcccaagt gttgacggaa gttgtgagaa ccattcaatt ttcttggggt cctcattgtt
    12121 agaaattcgg ggaactaatt gagcgtgtct catgaggttt cggcacttga aacaaacgga
    12181 gacgagcaac cggcatcaca gccaacagac tacaactacc gagaactcaa tttacttttt
    12241 cattagggcg agcgaggatg gctgccaagg attgaggagc ccaagggtgg agggcacttg
    12301 agtgcagctc caattatggg gcgaaactga cgtcagctcg cggctcgact caactcataa
    12361 tgaaaacatt taacctgtcg tcgtcagtga ttcaacatga aaatcattcc gcatccaggc
    12421 ccggcgattt ggttttcctc tgtctatcca ctttttcaat tattcgagag cactgcgatg
    12481 cgatgagatg cgatgagatg cccaacgcca tggttgcgga tcctttcgag gaatcggagc
    12541 ggaggcaagc tggaaaaagc gaagggagaa aaaacgaagc acttgagtgg gaattgacag
    12601 agaggcaggt ttcaagttga gtgcataata cacctttttc ttctgcacgg gctccttgtt
    12661 gtcattaatg agacgtcttc ttcaggccca gcgccgattc tggtccggat cgggggttct
    12721 tttggaccgg gtgcacaatc atttccactc caggttgtca aagactatgg acaaggtccc
    12781 tcgtcatctt ttgtggcagg ccagccgcgt cgcggtacct ggccctcacc gcaccccaag
    12841 aaccccacac ccttttctcg cagtgtgcgt gtgtgtgtgt gttttggaca tttcgggcat
    12901 tatgtcgcgc ctactttttc cgccttgcgc ccttcgttaa atgagcgtcg tccgcgtcta
    12961 gcctttgatc ttacgcttcg cttctaattt gattatgaac gcactctatc gcacgaggaa
    13021 gtagtccggc atgttcttgg gctcacactc tagcactccg ggtcctttga taccctatat
    13081 cgggggtaga tttctgatcg aactagaacc ttatgataat aggaagatct cagatatcgc
    13141 tttaaagaca ggtatatatt tttatgattt gtaataacat caagggaaag taatgcatta
    13201 atgcaataat ggtttttttt aaatggcttt ccattatcat aaacaaattt aaacatgcac
    13261 gctgatgggt atctaagagt gccgatagct atctcagaat tccaccttgc taccattcta
    13321 aacgtcttca ttttcagctc gaatgctctg cggctggggc agcactttca ttccactcac
    13381 ccacttgcaa acacactcca agtccattcc gcttccactg atgttgatgc tgatgagtgc
    13441 gcgccgcggc ttactcaatg acgcgttgaa agtgccataa aaaaggacat gaagacgtcg
    13501 ccgggtctcg gtggcagccg gagatgggga tgtcagggtg gggttaggtg ctgacagcat
    13561 tttaaatgaa atgaaaacga gatgctttca ctttggccca caagtaaatg tctcacttgg
    13621 gtagatacct cctggccgct tctgttcgca tagattgcca aagtaagcag aagtaatgcc
    13681 agcaaccgag aatggagtat ttgtattccg ggcggggtga aaatcctttt ggtaccaaaa
    13741 aaaaaaaagg gttttgtgtg atatcccgtt caaaagacga ttacattcat atcaatgggc
    13801 acagtaaata tacaacttta agtgtcgtat gctaattaaa aataagttta aagcttatca
    13861 cagacgggtg gggtaagttg aactctaacc atttgtaaat tatattttat tattatattt
    13921 ttatcgactt tggtgcttcc ccaaaaagaa cgacgagatt ctaacaaaaa taaagggtga
    13981 tagattcgaa tttatacaga cacgtgacga tacgcaggac catcaataaa gtaacacaga
    14041 aatcgtagag atgcgagcga aattcgaatg agtagttaac tcaaacgcag cgactgagca
    14101 gcaataacag ctccaacaaa atgcccgaca gtcgtaaagg acccttgtaa gaacaaacac
    14161 gccatgcata gctgatgaat cctccgaacg tgaagagtta tacgggaaga tgtgaggcaa
    14221 accccttgcg caataaaaac taaattatat ccttttgagg ttcaagtggc ggcggaaaag
    14281 aacaaaacgc tgcagaagca acatgttggc cagacgtgaa gtcacagacc gaccagaaag
    14341 atccatccga agcacaagag atatatatgc atgtataaac gtataaacca accgaccgac
    14401 agacgtcgcc gacccacaca ctatttaatt tagtacaaaa ttattatgcg caacattagc
    14461 actcgtctcg gtttgcctgg gttttcctct cggcttgggt ttttatcgag tctgggtttt
    14521 gggcatgggt cttttctcga gttcggagcg tgaggtgcct caaatgaggt gtgaatttcg
    14581 ctgtcagccc gtcattctca acggactgag gagaacacac aaaagtgccg acattggtgc
    14641 ttcttctgtg tcggttttga atttatgtta atacagtcgc gctttgaagc cagcgtaacg
    14701 ttgagcatcg caattgtctc aataccctcg gagtattcaa attaatcggc atagtctctt
    14761 ataataaata gcagtgcgca tctgcaagtc tgaaaacata ttaaacaccc aaaagttcat
    14821 tcattattaa taatcttttt cccttttttc cgtaccttgg ctcacatgga tctattataa
    14881 aacaatgcat cataagctgt gctcttacgt tacggtttgt ctaaaaatat gtattcacaa
    14941 cgcttgccat tccatatatc ataatcgaac agaacgagca gaggaaaaca tttgcaaggc
    15001 acccagcgag catcagcaga acaacaaaca aaatatttat ggccaaacat aaaaatcttt
    15061 atgaccttcc cgattcaatc agagcagagc tggagctggg cgagcacaac aactgagcca
    15121 ggtcccaatg cgactacagc tacaacgact ggcgcttcct ggcgaacaca ggatatagcc
    15181 atccataagg tgtttccccc cggccaactc gccctgccgc cctgccgccc atgtgtgttc
    15241 gccttgataa agagaacgta aattatggcc ctatatatca tgggaaatct atcgacaacg
    15301 ttgaattttt atggtctccg aaggaacggc gcagtttaac gagccggcga gagtctggcc
    15361 atgtttattg atttactcgc taatttttca gctccggcaa agacggccga ggagtgcggt
    15421 caatcaagga catccgagga ctggcccggg ctgagatgag agtcgatcgc ggcaggcagg
    15481 ccattgtcct tgatttatgg tccgtcattc attgccagcc accaaagttg acacttctgc
    15541 gtatatcccg gagttcgtcc tgccattgtc atccagtcac tcccctcgat gtcgtcgtcc
    15601 tgcgtccttc gacgtccctc ccgttgcgct catcctgaca ttttgacaaa taattttatt
    15661 gatgctctgt tcctcgccgt ctgtgtttgg tttttaattg tcgctcagct gcgctggacg
    15721 cacgtgataa ttgctcattt tatgacgcat ttatcaaatg ctcggccttg gtctcgtcct
    15781 tggcattggc atcggcatcg gcattcggaa tgtcctttgt tcggtggtga ttttctgcat
    15841 catgctgcgt ctgacagttg gactagcgta ctcctcctgt tcctcttcta ccttcccctt
    15901 caatcctccg cagatgagac agtcacgcgt catttatttg gccgtgacat ttccactccg
    15961 ggttgccatt ttgcattcgc gggaattagg aatggatttg gaaaaactgt ccgaactctt
    16021 cggttcaagt acattcaatt ctgcattcag cagatggtgc tatgagctat caaaatcaat
    16081 aagctgtgaa actagatgga aattgtatgc tttttaaaat attattaatg taaaggttat
    16141 ttgtataaag acaaatattt accattccta gaactttctt catcatccgt acaactttta
    16201 aaatctatat ttccttcgaa taaataatct attctcatag atgaactttt cgtgatttat
    16261 ttgttggatt aaacctttat caataaccgc cgtatatcaa caggacatct ccgccctctg
    16321 gacccacagc cgtcagatcg gatgttgtag gcaattaata cttaataccc aaaatggcaa
    16381 taaaaattga tgccatcaat ttatcatttt agaatcctgc acgtgtcaac tcgtaggtat
    16441 ttccactttt tgtgtgtgtg tccattgttc caatatttgt tttttttttt agaggggagc
    16501 attggcaacg attaatttgc tgtattaatc cagcaagcga tgccgcacgg ggggtgttgc
    16561 aaacacaacc cgcagttggc aaaaagaatc cccttttttt ggtgcattac cgtaaaattt
    16621 caatgtcacc attattcttc ttccttttgg gcaactatta cgagataaat cgttgtcgat
    16681 aaattatcga caggcagcag gcggagctcg gactcgattc agctgggtag tcgcagcggg
    16741 acaccctctg caccccatcc ccttcataga gtacgggata cattttttag ggatcctgct
    16801 tagttcgctt tcatacggtt ctattgaatt tattgcagtt tgtttttcaa ttttttaaat
    16861 ggcattttcg cccttccgcg ttgggaagtg agttatggtc ttgctcgatg gcacgtagat
    16921 gcattcaaat cggaagtaat tatggtgaaa cataagcgat atgagggaaa atagctgaat
    16981 ggcttatcaa gcgtgaacaa ttttgaaatc acttttcaat gagggtgata tttgtaaaaa
    17041 aaaaatatta aaaaaaaaaa aacaaataaa aaagtagcac atcaagtcaa aggcacttga
    17101 actagcagat gagtcacaac gaatgctcag atgaaaacca aatctttaga gtaattaatt
    17161 tcatggtaat ataattcata tattcccatg ccaaacaggg taaaatatgt cggccaagat
    17221 aatagctttt ttaagactac gcacaaggat cttcagcagc aaaataaagc aattatcgtg
    17281 ggtcggtttg ggagttcttc tttgtgcgta agtcaactaa aaatccgcag acagttaaac
    17341 gactttccct taccagtggc aaccacttca cggatatata tataccttca tattgccgga
    17401 gataatgtca aatttattgc attatttttc gctcctttcg cccgccagtt gctctgcatg
    17461 cgtgccaccc actcttgccg caggcaaacc atccaccacc cgccgccacc cactggtgtg
    17521 cataaatcaa aaggtaaatg gctgcatttt tatgactgcg ccgccatcgt cgtcgttcgc
    17581 cttttgcgct gcttcgcttt tatcacacaa acatttctgt gataataaat gccataaaaa
    17641 tgaagaaata tgtggttaat tttatgtgct gcctctgcca ttccgccgct tgttgttctt
    17701 gctcttgttg ttgtagttgt tgttgtggca tccagtatac ttccttttta tattccccat
    17761 ataaatgttt tcgcggctac aaatttttcc cactacattt ggatatctct cggcgctttc
    17821 ctttacaact ttggcgaaga tatcgagagt attcgaattc gaaactcctt atagttgcat
    17881 aaaacgagat ttttagtctt aaaggactct gatgcactat ataactagaa gctcaatata
    17941 gttttttatt tcagatctta ttattgttaa cctaatagaa ctgctgcatc tttaactgcg
    18001 taccttgtaa tttaaattac gctttttttt atatttgtaa tcttcgctac acgacctcct
    18061 tttgaataaa atgaagttat caacgctgaa atgctgcagg gtgagcatta gtctgaaagc
    18121 aaatcgcttt agtcacggta tcaaggtgtt ccgcacttcc gcttggcaat ttcttcggct
    18181 tcgtgtaatt tataatattt ttgtattatt tatatgacac ccccggccac tggtttgaat
    18241 ttaccttcag cccactcccg caatttgcta gtaaataatt cacatacagg agcagcgaat
    18301 ttatgacgct gacaaagtgg ccataaaaaa taacaaataa taagagaaaa tgctatggaa
    18361 cgtgtgcgta aactctccaa ctctgcagca gtatacatgc atatatacac gtatatacat
    18421 tattttggca acactttttt cgctttgttg cacgcaaaac cgcaaattat gtctaagccg
    18481 tatcgtaaag tatcgcagca cgctcttaac taataaatcc atcatttcgc cgaaggccga
    18541 gagtgtttcc tctacctgtt ttagcctcga aggtatttcg ctgccgggtt tcggcttagg
    18601 gattcccaca gaaaaatgtc taaacactct aaatcgggat taaaagtgtc gcttctgggt
    18661 tttcggctta tcgtccatat ttatacagat tttaatttac ttgccagggg ctttgaaggg
    18721 ttcttaaaac tcagcttggt gattaggtaa catatcccaa gggccagata ttccaaaatc
    18781 ccctcggggc ttgagttaaa catcttgata catagtttat ggttagtcca accgatttgg
    18841 ttgggattac gttggagttt taatatcggt taggtaaagt ggctagaatg atctagatca
    18901 acaaaatcta aatgattagt cacataatat tttctaacta cttaaataat agtaatcaat
    18961 tatgtttaga aggagctagc ctattattag ctcttaataa tttaatataa atcagcctcg
    19021 ttttgcaatt aaacattatt agtattcagt aattatcttg aaaccaagca acgtgattaa
    19081 cgcgatttcg tgcgaaacgt aaataagtaa gttaggcaag tgctaactgg aaaattcaat
    19141 ccaattgtag agcgattaaa aatgcagcgg agttaaccaa accattaaac tattaccaac
    19201 tctctgagtg caacatgcca caacacacat tcgcttgttt gatatgtgca gattaattac
    19261 acacacacca aggaaggagg aaaaattgct tggaaaaact tttcgacgcg acaacaaaac
    19321 aacgatttcc acttaaacag caaaacagga gccacgaaaa aaaagaggga aaaccaaccg
    19381 cagaagttaa tcgaaaaacg ctaaacaaag gccacaacaa cagctgtgcg agtgagcggg
    19441 tcagagggag agaggtgaag tgccagagcg ggagagcgac aaacaaatta atttttatat
    19501 gacattaaaa cgagcgaagc gaggcgatgg aaatggttga agagtgtgtt taagtgttga
    19561 gtggtttgct tttccgagca acaaatctcg gtgcgaagac aatgaggcct ctgccgcgcc
    19621 gctgccgcca ccactgcagc gctgctgctg ctgacagccc catcaagaaa aagttccccc
    19681 agagagacac agagagggag agtgagcgtg acatatgtgc caagataaaa ttaatgtgcc
    19741 ccccaaagca gccacaacaa caacaactca ctgagcggcg ctctcagcgc tcaactgttg
    19801 ctctctggac gagtgttgcc gtggtgcagc catattatta tgattttaca ggaagccaaa
    19861 tcggagagcg agagagagaa aacctgtctt ggcttccatt gcaaggcgca tgcgattgtg
    19921 attggacaaa aagtacgcca tatttgaaaa ttacgcacag tgcatctcgc tcgcatgcag
    19981 caggcggtgc tcctctaacg caggcagcaa gccaaagtgt gcagcgctgc tcgccggaga
    20041 gcgctctctc gcgagtgagc gaacgcttcg ctgcgagggc agttacgctc gctgccgcag
    20101 tcgttgaatt caattcgaat tttgacttcg cagcgttcag acgtgttcgg aaaaacctga
    20161 aaaccattcg agtgacaaga gatataacca acaaaaataa gaaacctcag tcaactgtgg
    20221 tcactgatcg agagtgtttc gtttcgagtg aaaaagtgaa atcagagcca aaacacaaat
    20281 cgcttggcca gcaaattgaa atagtgctac agagataaat tctctgctca aaactacaag
    20341 tgtgttaaat cgccgatttt ctttggattt accaacgttt gccgacgcat ttctgtggat
    20401 taacctcatc gtcgccgaag caaagctacg catttgtagc cttgtctcgc aactcacgtg
    20461 gattaccctc gagaaaacac actaagcaac tgatatggtt gtcttggaag gaggcggcgg
    20521 cgttgttacc atcggtaaca accagtacct tcaaccggat tatctggccc cattgccaac
    20581 gacggttagt attgactaag ttaaaagctg taaaattttg ggatggccgt aaaatctatg
    20641 gttttaaatt ttgcgtactt aagaattaaa tttggaaagt tcataacatc aaacaatttt
    20701 tcaaatctaa aaatttatat cgtcattaat actttcacga acaaactttc tttggaagaa
    20761 attgcatttt ctcatagttt taacttctca ccaaattaaa atcaatatta tcttaaaact
    20821 cgtaaaaaac tttaaaatta caaaaaacct aattccaact ccacattttc attttattca
    20881 taacagatgg acgccaaaaa gagtcccttg gctctgctcg cacagacttg ctcccaaatt
    20941 ggagcggatt cgtcggcagt gaaacccctg ctggcaatgg acaagaacaa gacaaagccc
    21001 ggagcatgct cctcgtcgtc gaactcgtcg agttcctcgg gcagtgctga gatctcggca
    21061 gccaagtcac cctccggcca ggccaaatcg cccaagtcga gcactccaat cagctcgacg
    21121 gcaaccagcg caagtctgag taataccagc accggtgaaa tcaaactggc cttcaagccc
    21181 tacgagacca atgtgctgag ccaccagaac cagaactcct tcaagagcag ctcttcgctg
    21241 gatgcggaac ccacgcgtcc cagctctaag aactcctcat ccgcccagga gcgtgtgcca
    21301 tcgcgcagca aatcaaatgc cacgcccaca gatggcggca aggcggagat ttccgcgcac
    21361 gattcctcat ccagccgaaa gactgtctcc ccgtcgggat cgtcgcaacg cggcgccagt
    21421 cccattgtgc gctccggcat ggaggtgctg aacaatgcca acggaaccgc ccagcatccc
    21481 aaggaaatga gcagcatggc tgcggcggca gcagcagcag cagcggctta caaggccgcc
    21541 ggaccctatg ggctgaatcc cctgtccgcc ctgtgctgcc cgcccggaat ggagcagcac
    21601 gccaatcccg ctttccggcc accgtttgcc ggaggattct cacaccatca cgccgccatg
    21661 ttggcagttg ccgccaatgg aggatatcca ggcggagctc ccggcggtgg accagccgga
    21721 cagcccaatc cgtacataag ttatcagcgc atcaagacac cagctggcgg cgaggctata
    21781 gtgccagtct gcaaggatcc gtattgccag ggatgtccct actcggcgca cacgcaacaa
    21841 atgctcatgg gtgccccctg ccccgccgga tgcacccagt gcgagcatca gaaatacggc
    21901 ctggccatgg ccagtgccgc cggactgcca ccagctcatc catactcgca ggcagcggcc
    21961 gctgctgcgg caaacgcggc ggcagcccgt tcggcaccct acgtgtgcag ttgggtggtg
    22021 ggcgatgcct actgcggcaa gcgattccag acctccgacg agctcttctc ccacctgcgc
    22081 acccatacgg gcaatctctc cgatccggcg gctgctgcgg cggccttggc ccaatcgcag
    22141 gctcaatccc tgctgggaac cctatttccg ccatcggctc tccgagctgg ctatccaaca
    22201 ccaccactga gtcccatgtc agcggctgcg gcagcggcga ggtatcatcc atacgccaag
    22261 ccaccaccag gcgccttggc tggaggacct tcgcccttcg gcgccgctgg agcattcaat
    22321 cctgccgcgg cggctgcggc agctgctctg ggaccctact actcgccata cgccatgtac
    22381 ggccagagga tgggagcggc tcatcagtaa agtgacttcc acaagagtta aataccaaaa
    22441 aaaaggggat tacgttgaag agacaaccag agatatagaa tgaaaccatt tccaaaccct
    22501 gtttgagata ctttcatgga aaacaaaaaa gataaaagca caaaacgatt gcaaaggctg
    22561 acacatctct ggcttttgcg ctattctgtg atactaaact gtagtttaaa gagcgctagt
    22621 tacacttaag tttcgcaaac agaaaataat caaccaccta aagaacagta gtagccgcaa
    22681 aaatagcagg atcactctct tctatcatcg taaatgtcta cattgttagg taaaaagaag
    22741 tgcagccaac acgaagttca ctcactctta tttgttctca aagttcaacc aaagtttttt
    22801 aagtcttagc cagaacacat tctacaactt ccaattttgt taatgaagaa cccattgctg
    22861 agatgttcaa acattgtttt agtttaactt cgctttaagt tctattaact attattacga
    22921 ttatctgcaa gcatacaaca aaccaacaat tgaaataatg ttctttaagt caacttatat
    22981 ttaaagtaag tgtaatgaat atttgtaata ccaaccaatc agagataaaa aattaaaaaa
    23041 aaataataat aattacgaaa aataaaaatg aatatttcat ataattatgt actgtgtgta
    23101 aattctataa atataaacta gatttgctat ttactccttg atgtacgcaa accacaatac
    23161 gatctacaca agaagccacg gaatatcaaa caaaaataac ttaaactaca tgcaacacat
    23221 tcgtataaaa ctgagaaata tacaagaaaa aacaattttt agaagcataa accacgaatc
    23281 ttttcttttg aaacaaactc ttttacagct ggaaaacttt ttgttgggcc ataatttcgc
    23341 ttcggttatc tgcgctgttt ggctagctca catatgggtc ataaatattg ctgataatgc
    23401 tccactaggt tttcaattat atttacataa ggctgagtgg caaattccgg aaaccataac
    23461 aaggtctaat tctcttaatt ttatagttct tacttagaaa tgggactaaa ggagttttta
    23521 attctgagaa ttgaactgct tcttataagt atcattgata ttaaatgtaa ggttctaggc
    23581 aaataaataa ataaaatctt ataggttatt ctttaaaaat attttaatta gttttatttt
    23641 agacaaaagg tattttaatg tgctctcaat tttttctgga tgcactcgaa gaaatctggg
    23701 tttccccatc tcacctaaca catttgaaat tcaaattagt actattaatt tgcattgctt
    23761 gttgcatttt aagcgcactc aatttgtatg cagcgattcg tattcagcct aaaaaatcaa
    23821 atcaaaagca aatttcaatt tcacgagggg tggggtaaat aacttgattg ggcaagcctt
    23881 aataaaacag tcgccggcaa cagtcataaa acacccaagc tgaaaattaa aaatcaataa
    23941 aaatcacatt tgtaccaaca atgtgtataa caaaaatcaa ttgccattca atgagcaact
    24001 caaatgcata tataaatgaa tatgtgtgca tatgtacgta tgtatgtaca tataaaaaaa
    24061 tcgctgacaa agcgaaatga ctaacattat tcacaaaaaa tatgcttcag aaatatcaaa
    24121 atctgaaacc aaccagacaa ctcaaactta agcaacaatc agccacagca acaatgaaaa
    24181 tcaatggtga tatttcgagt gtatctcata aataaattaa ttgtgacaat attcaattga
    24241 ttcgatttga aattatcgca ttcaactgtc aagcgatcaa cgacaacgtt ttttcaattg
    24301 tttcaatttc cagcggattc tttcaatgtc tgttttcatt cccccttcaa cccacttgaa
    24361 tgttgtttct gatttgattt tgattcgttg cgaacacagc cgtttggccc caatacaaat
    24421 gtgggaatat gatattccgc agggtcgggg ctgccaaggg gtagacttat caatactcag
    24481 caatcagtgt tgtcaaatga agtggcgaag tgcgagttct tgatttcaga atgctgaggg
    24541 atttcaattt tgtaaagcat ttcaaagaag tgggagtgct ccaatggtat gttttatata
    24601 ttcagcaaaa caataatgca ataaaagagc aggaaatcag aaatcaaata aaataaacca
    24661 tgtatgcaaa aaccatttat tgaaacgcct cagtaggctt agtatagaaa atttaatatc
    24721 ttcctctgtt ttccccgaac tttggatact tttaatcgtg ttttgattcc gttgaaagct
    24781 gcgcttgtag ggcgttttga ttgttgttgc tgtcgttcca aatttaattt atttacatgc
    24841 cacgcatttc tttgttttac cctgctgtcc atgttaaaca atctgttttg gatgtcaaca
    24901 ctcgcgcggc gcctccgaac ggcagccata aaagcaaaat caacttgaaa ggcagcaaaa
    24961 gcagcggaac accgaaacaa aaaccaaatc aacaacaaac tcagcaactt tttgttaaaa
    25021 atagtgtgtt tctgaatggg gagcaaatag ctccaactct atcgttttct cgccaagaga
    25081 tcttgcaatg gactgaagtt ggcggcttgg accccgttgt ccaactggct cgttggtcta
    25141 ggggtatgat ttccgcttag ggtgcgggag gtcccgggtt caaatcccgg acgagcccaa
    25201 gtcaaaacaa ttttttactt taatttttat ttttagttca atagaagagt tgaggtaaca
    25261 cttgtttctt gaaaagttta attcttatgc tggattcgct aaaacgtaga aggtaacgtt
    25321 tgcgacacta taaatggcag aatttgtcgc ttttctttct ttttgtgtta aaatacagag
    25381 attcaaaaag aaaaattaaa tgtttggacc atgttctcca atgaactaat aacctccttt
    25441 aggtactgtt attcaataaa ttcattaaat tattcttctt catacaatgt atggaataca
    25501 atacaatttt aaagcacctc tgtttccatg gacttattgt tgcatttagt accagccatt
    25561 tgaactatca gaagttgagt cataattatt aatactctac attaatgggc ctgtttagag
    25621 ccataaatat aaatatatag acggcagagc ttataccatg gcaaaacctt tatggtatct
    25681 tgtgactttg gggctagccc ctgtctaaat ttatgagctc gtggaaatta agtctaatca
    25741 gtggttgtga tttctttcaa gaggtttaaa tgtgtaaatt tcgtcgatgt atgaaaacca
    25801 ataaagttcc cttgcagtta aatgaagtat tacatttgaa ttaaatacct ctggtttatt
    25861 tatataaata cccacttctg ggtattgttc acccctctag tcagtaagag tatttgaatg
    25921 gctgccttac gaaacccatt gattgaaatc ttcatttgtt ccttttgtga tattggttca
    25981 ttatttattg gcacctcaga actgacaact tgtgggatgg ttattgctac aaagtcgtaa
    26041 aatcgatttt attgtccgag acgtatataa agatgttcaa gattatgcga catgaaaagc
    26101 atgtgtgata atttacgatc aaaatagaaa tgtggaatat gacaaaaata gtaaaaaaaa
    26161 ttatattgtt aggaactaga actagtagaa actattttta tttatttatt aatcgagttt
    26221 cagaataatc aacatgtttg cagccattct gctaaaacgg acaaccaacc gcctataaat
    26281 aatttataat agccgactga gattgcaggt ggattatttg tggccctata caatgtcgac
    26341 agcggttcag tgctgtgatt ttccttggca gattgatata ttattgcact ggcaagttga
    26401 cgtttaagat tcggtgattt attccatgat ttatgaagtg ccgtttgaga ttagccagag
    26461 attagcattc gcgaactttg ccattgtaca actgatagta aataatacac accattcatg
    26521 gctatttatg cttagctttt tgtaatacaa attaatttcg cgttcaagtg attacgtctt
    26581 cgacgaattt gcaacaaagt caagtttaaa aagcgactgt gcagataaat gtcgcagtat
    26641 ccaaaactag gggacttgtt gccacattcc cggcccaaaa agtccggaga cttgttctaa
    26701 taggtggcga gacccactcg catgttggcc ataaattaaa cgcaacagca cagcagctga
    26761 ctgatgtcag tgttgtcgtc gcagctaatt aacagttttg ttataaatta cacccagagc
    26821 cattacaatt tttcgtattc tcggctcaag ttgccggtct ctgagggcgg cacacccatt
    26881 tggggcgtca atcatgcgta aagtgacaca gatgtgacat ccagcggggg cccactgttg
    26941 gtaagtgact agcggataca tttgtatctt taagtctgtg tgcccaatgt caactgtcaa
    27001 ctccttaata attttccgta gtcttatttc ttatttcttt tttttttctg tgaaattcac
    27061 gcccccgctg cgagtcggtc cagggtccct cctcttcgaa tatcccatgc tgtgttgtga
    27121 cattgttgct gctgttagcc tgctttgttt taatatttat ggcttcctcg tgtcattttc
    27181 ataatgttgc gtttgacact ttccctctgg gctccaccaa cagaaatcac acatacacag
    27241 cccttcacgt tccgtattat cttacattat atgggcggtt gcctgggatc gcccatcttg
    27301 ttcatttagc atctcagtct ttttttcaga ttttgtgtaa aatgtttttg tgaaatgaca
    27361 tttgtagctg acacgacgac aactgtcaac gggcactcgg taggcattta tttcggattt
    27421 gttttaggcg tggtaaacaa gatctatgta gtagtagaag taaggtggcg gattggaaat
    27481 ggttgcggtt gaggcagaag ttgaagccgt ggcttattgt catgcatgaa ggttttaaag
    27541 ccacattttt atcaattaaa tattttcatt aattttgtgt tgcgaacaaa agcgtagcca
    27601 ctttgagtta tgtaccccca accccttttg ttttaagcct ataaagatac tacaaagaac
    27661 gcaaagccat aaattacagc cgggaaacag ggaataaaat atgatatggg aatggaaaaa
    27721 taaaatatac gtccattggt atctataaac aaatatatgt aatgaaaaaa aaaatatatt
    27781 aaatctcgct gagaatttat gaccctgcaa ggccttccaa ctgaagccgc ggcataaata
    27841 cttcagctgt gattattatt gcacccagcg agccacccaa aaggaatgcc aggcagaacc
    27901 tggctaaaaa gccagcggaa acaactggaa agcgacaaaa aaaaacgaaa taccttgagc
    27961 caagccgatt ttactgtgcc acacttcaaa ggccaaccgc cgacattgtg tgtttttcgg
    28021 gggagcttgg cgctaatata ttattgatag atatatcagt gatatatgtg acactggtca
    28081 gtggcgggct ttgcttacgt tagatctaga ttgtaaatta cccgtggcaa gaaaatgccg
    28141 actgtccgga agggtttgtt cgcctggcgt gggctgattg gtaaaatcag gtcactggca
    28201 gaaagccgtc agcggcaatc gccatacgca gataacttat ttatcggaaa tggctgttga
    28261 caaatccggt aatgaatttc tacgatctcg cgtttaatcg atgattcgtt aaatttattt
    28321 cgttttcttt gtactttaat attaattatt aatgtcaagc tgtcagatta aagtttgtgc
    28381 gacgaggaaa gtctgcagtc gtagtcgact cagtaacgcc ctatactagc ttttcaaagt
    28441 gaagagatat tgtgtgatca tgggatgtgt tctactaaat tttccataaa gaagaatgaa
    28501 tgggtatata ttccagtgcg cctcaacatt tttaagtgca ttcacatacc ctttaaggct
    28561 ctgaaataag ctttacagcg aagcctcgaa agggaataaa tatttcatgg catgtcaacc
    28621 gataaccgcg attggccaaa gccgcctgtt aagtgtgata tagtcagagt cagaagttgc
    28681 taaatatggg cttgacctgc tgctgtggtt gttgtggctg ctgccgctgt ccgatggcca
    28741 cattattaag ccaattcagc ggcagcagat aaataaataa aatttgaaac attgccgcaa
    28801 caataaaagg cgacagtaca cgatttatta aacggagtgg ctgctgctgg gttgcccggc
    28861 tccaaatgaa gaggcaaaac acaacaccgt cagcagcaac agcaaaagca acaagaaagc
    28921 aaaagcaacc gaaaagcaaa agcaacagaa aagcaaaagc agcagctgcc accgtgttgt
    28981 tgctcacatt actctttttg gcgtggccca ggctggcagg cagacagagg gaaaccgaca
    29041 gcagatacaa agatacagat acattcgcta tatagaaaac acacaatact tgaggttgag
    29101 gccaaaatga ctaatgacca gcgattatca agcgataaaa ggcaaagaga gccaccagca
    29161 acaacaaaga taatttatta ttgttttaaa catttgtgtt ttgcgctcaa acgagataca
    29221 tttgtctcct ccatgccgtt tagaaacctt ttcggctttt gttcattaag ccaatgatga
    29281 aataaaaata ccataaaaat ataaccaaag aaggtttgcc taataaatga atacccctta
    29341 tatataaggg ctcttataca atatattgcc catatgtaaa acgtatttta ttcattctga
    29401 gcggcgcaac tatttagcat atgtttttgg gagcctttgt ggcaacctgt aattagctgg
    29461 ccctctctac agtccgcttt tttcatttct ttttttttta ctaccttttg agtgttaagt
    29521 tttcgttggc taccagaatt ggtggcggca aaggcagaag ctccacagaa ccagacaaca
    29581 ataataaact cgaagattca tgaaagcggc aaaaggaaaa taaacagtca acgcgacgta
    29641 aatttaagac ttttagtatt tcatttcttt tgtttctgcg cttccctaac cagccttctt
    29701 cagactacta tcaagccgaa actatacaaa aaataagcgt gcttttgaat ataggaaagc
    29761 aacataccta ttacctaaaa tatactttta ttaggctgtc ttaaaattac atagggctca
    29821 tacatacagc tgcggttaaa ataatagcac taaattaaac atacataaat aatatgatcc
    29881 aaaaagttgg cacatatcac aatatggtgg ctcattctat tgccgtggtt caatatactt
    29941 catctatagg gtatccacaa aggggtaaaa tgatcttagc ccgattgtta ctggtagcgt
    30001 tgtaaatgtg aagtggtcga aattaaaaat atatttatga cttaagtggc aataaattat
    30061 gtttcttgtt aaaattctat tgtttcagcg tctgctgggc tgttaaaatt tgctgcttct
    30121 ggctttcttt ttcaccctct gaatttattt attcttttgg ttttgcctaa attattcact
    30181 tcgtggtgtg gctacataaa tttgctcaca attgtgcgct tatgacaata tttatgactt
    30241 gctaatgaaa attttattta taattttgta tgctgttgcg gatgcgctaa atatactttt
    30301 taaaaatatt cacggcttat atttctactg ataacaaaat tattatagtt caagcgaaat
    30361 catgttgcac atgaacaaaa aaaaaacaga ttttaaatat gttttcaagt gtcattatct
    30421 gttgtcaaga ctgtttgtcc attggtgtct gaggtcatct tgagtgattt gttgttttta
    30481 cactttaagg ctttttcgtt ttgattttat gagcctatta atttaagaac actcttttcc
    30541 aatgagtaca tatatgaata tatacgtttt attagaggca caaatggaaa acgagaattg
    30601 gagtacataa attcaatatg ttttaattaa gagtattttt cacttcgtta aaatgaaatg
    30661 gtgtgatttc gatttctaga caaaacaaca ctgcacagat tactaagtca gtttccgttg
    30721 gcatttttgt gggcactgga ataaaattga ttttataacg acacaattat gttggtctaa
    30781 tctgaatgaa gagcaattaa aatgaaaatt tatggcccta atgtgccaca tactcagcga
    30841 gttcaagagc cgactcggct gtcatcagct tattatattt tatttgagtt tacgaggtct
    30901 gccagattca agtgattata ttttctgtgg ccaattaaaa atttgtttaa ctaacaatat
    30961 ggacttttac ttaagttttt acttatgtaa acagcacctt cggaatcatt taaaaatagc
    31021 ttgtgctttt ttgtgggcag tcttatgata aacaatggac tgcaacgtct gtgttttctt
    31081 taataacatt actggtatta ggctactaag cttccgagct aagataataa acaaaatttg
    31141 tgaggaattt aaaagacaaa cggcgcagga aaacaagata atagcatcag ttaagtctcg
    31201 tgattgtcgt gccgccccat gacaaggtct ttcgttctcg aattagagag gatcgtctaa
    31261 atttagtagt aactcagtaa gtttgttacc tgtcatttag ataacatacg tctgaaagta
    31321 aatgacgctc atagactctt gaggtctaaa accagatggt tattgcagca ttatatatga
    31381 tctctattta cgtttcattt agttggcaaa tatttgaaat catggctgtc gcctaactga
    31441 cataattatt tacaaaaaaa aaagtatgtt ttttggggct taagcataaa aacctcaaat
    31501 aataataaga cgacttcaaa ttatttaaaa cgaaatctgt agtcaagacg tgtctttaga
    31561 tagctttaag tcttcaccca acccaaatcg gcggtcagtc acagctgtcg ggctttaatg
    31621 ccgcccacca tttggccaac aaggctggat ctgtccgcta ctttggcagt ggcactcttc
    31681 tcgtggccat ttaatcacag tattaactct tttgctgagc cgcctgtcac tcatgtctct
    31741 actggtcgct cagtgggggt tgtgggacag acgtcgatgt tataaacact actgtcttcc
    31801 agctgtcaag ttggtctaag tttttgagcg caaaataaaa gccgacttga cagctgaacg
    31861 gtcgaccaac tcatgttgat gatgatgatt attatgtatt ttgtattttg tatttttgcc
    31921 gtttctcgtt ttactgccca atgacactct tacactgaga aaatagccgt tgaaatatta
    31981 catgatcatg attataacaa atttagttct gaaattgaat gttctctaat caacaaaaat
    32041 gcacacatgc ttaattaagt tgaagttggc gcgtcgtttc tctcagtgtt ttgaggcttg
    32101 gccggtacag gcacacacag tcgcccatgc acattcgttt aggcttttaa acgcttaggt
    32161 cgtcttatgt tggacttaac gcgctgcccg atgccaaaag ccaacagttg gacatctgaa
    32221 gacgcctcaa aaactcgatg gcggcggcgg cggcgaaaca tgaaatgaat ttggacgcgc
    32281 ttcggataat gaaaacgaaa cgaggcgcgc gcgcgctcca caaaacggac agaccaaaaa
    32341 caaaactgta gatggaaata acaccgaaaa aagtcaagta aaatcccagc cgacacaaag
    32401 aataaaaacg tcaaaagtga ttttgcgctt tggtcagcag cagcgacagc ggcgaagcga
    32461 aatcaaaaag tgccgccgcc gtcagcactt cccccctaaa ctaccaaccg ccttttggcc
    32521 aacaaaatgg ccagtgtcca cagttaactg ttttgtacga gccgttgagc ttttgggcgc
    32581 ttgggaattc tgacgtttcg tttttcggtt ctgtagcttt ctacgggggt cttcttattt
    32641 tttaaaccaa tttggttatt tcggcacgta ctcttctcag ttgttactta cagccacgaa
    32701 aacttattcc agggattttg atatagctcg ctacgctaaa aataatattc aatgtgtttc
    32761 cctttttctt cttaaaacaa attgaatttt cttaaggtgg aactcattgc aaccaataga
    32821 aatcgataat tgcgccaaca gagttcacag ctgggaaaat tcaattagtt tcccaggcaa
    32881 tgaattcggg ttagggcctg tcattcccca cgcacacact aactcacgca aaactgcagg
    32941 tcttgttctt cgacctcttc tcgccaaatg cgaacctgta aaaaattgtt tataaattat
    33001 tgattaaatg acaatgcgat gtcagagttt gatttatggc ccggcagaga gacacgcaag
    33061 cggctcagcc agggtgtgtg agagtgggca cgacagcgca cattgaaaaa ttattaagca
    33121 aacaataaaa gatggccgac gtcccccgcc gaacgattta tgacagctaa ttatatacga
    33181 gatggagcca cggagctcca agaaacgctt ggcccaaaag ttacacaacg gccaaaaccg
    33241 aaaacgcaat gcagaggggg agtgtggcca ccctatatat tgccgttttt ctcgtattaa
    33301 tttatcatcg aaaaaaggcg aaacaaaagt gacatcgagt cagtcatcaa tcaaaaatta
    33361 cgaaatgacc aaaagaaaag tatgagaaac tttgcaataa attatcgggt aaaatagggt
    33421 ctcaaatttt cccgtggttg ctttcaatta gcggttttag cactgttaac ctttaattaa
    33481 aacaaataat atgctaatta cggggaatta atacgccact tcagatatca agtttctttt
    33541 tttttagaat aagtttggta cccgtgaaaa cgaaattcat taaagcaatc tcatactcat
    33601 tatggaaatt tttcctctgc accttgtggg gcaatcttat cacacctaat tatgggtctt
    33661 acctcaaaga acttgttgaa tcagatgtgt ttttcggggc ttacaggcaa gatcaatggc
    33721 actaatggaa tatttctagt ttaaaagttc ctatgtgaat tgaaagtaaa tccctcttac
    33781 atcctttaag aaccccaacc gattgcagtt ttcgttatca gttcttcgga gctgtctgat
    33841 ataacagagt gacattatct tgaatgaggg ctctgtgcgc cataagtcgg aaacaaatcc
    33901 tacttaacta aggtctttca agtctttgcg gatttaacta cgttttgtca tttagtacgt
    33961 actcgtagta caagttaaag taaccgattt tcataaacag tcaaaggggt tgtatggcat
    34021 ccaagatgtg actgttattt gtttttactt ggaatacagt acaccttcgt atttactcct
    34081 ataataatca gctccattta tttatgatac gagagacggg cacctcaaaa atctgaagta
    34141 tctgccatat ataaagacga agcggacttc atgacatatg attgtgtcgg tcgcgaggtg
    34201 taaataccgg ggattatgct gctgcgaaag ctactgggtt cttagcaaat aggaatcaga
    34261 ggcagccact tggataacca ctttcgtaac ccttcttttc gtcatcatca tcttctgata
    34321 taacaactgt gctaatattt gccaaacatt caacgctgtc cgggcggtac atttcgtatg
    34381 atataagcca tgttggttgc ttttcaaaaa attctttata atacgtctct gccacggcag
    34441 tgtttatcaa gtgtaacacg ctgtgtctct atttgttttc caacactcgc tgtctgagca
    34501 aagttgatta cacatcccgc tttatggcaa acaacaatcc gagccgtttc tcctcactct
    34561 tgacatacaa taactgaaag agatttacag ccgttgggcc ttgctctatc tcggcgtgta
    34621 cccgtaattt ccagttacca gatttcactt ttttatttgt gtgttttatt taattttttg
    34681 ttggcttgtt taaataaatg gaaataaatc tgcacgtcgg cctggtggca cggaattgat
    34741 ttacaccgta taatgcgcat ttttctcgtg tttaacagac taaatgtctg tttataagac
    34801 cggggcaagc cgactgggta cgacaacggt cgggtgttgt gttgtcgcgc tataaaatat
    34861 atttaacaaa ctgatttatt gcattttgat aacctctcac tgggtcgggc cattgcctca
    34921 actcgccatc cccgcttcat attcgtcgtc taggagctgt cgtcggtcct cggatcccgc
    34981 ggaccagaaa acctaatggc atcgagcaca actgtgcaaa atgtcaagcc acgccagatg
    35041 aagaagaacg cgttttataa ttgcctggta atttatgagg cactttttat atgtgtacac
    35101 ccacacggac atttacagat ttatagaatt ttattacggc agagtgtgcc tttaatgatt
    35161 ttgtttacaa atgaattggg gctttttacg cacttggttt atttaatttt acaaattatt
    35221 gctaaggcgc cagaacttaa tgacgtaaat atatagcatt tcaatctatt tagcatgctt
    35281 gaggtacata aaaattcaat ggctttaaag ttgaaattta tttctgggta aaccccaatg
    35341 acataatcta gagcgtatag ttctcattta attgggacat atgactgtca gacttttctt
    35401 tttttcttgt ccaaagatta gccattttga catttttgtg tcaaaatatt tgcgcattca
    35461 aatgctgcga ctaaaaaaaa aatgaacttt aaggcgactt gagcgatagg taaacgaagc
    35521 cctcgacatt tgacgcaatc tgcaaagttt gttcacgtgt gacaaggtta attttattca
    35581 taaatgaact gataatgctt gaatctagtg tgtacttagg aactagtatt cgtgattgaa
    35641 atgacagaca gctggattga cagtcaaaca gttgtcagag gaagataacg acacacttgt
    35701 tgtgcgctag aatagatact cgtagatatt ttgacaacga gtttttgtta ttggtatggc
    35761 caaatgagga taagtccaat gcaagaacaa gcatttaaaa ttcatgacaa gtataataaa
    35821 tacaaatatt tggttctata aactgtattt attttataaa tgtctgctca ggctaatccc
    35881 ccatctcagc tcttttcggg taataagtga aacagtataa agtggagaat gacatatgca
    35941 gatgtggatg gaagaataaa agagcaccac cttctgctgg ctttcagtca ttaagtcatt
    36001 tacatatttg ccaacaaaat gtcagccata aaatataaac taaagcaact gtgtgaagag
    36061 cagaacccgc acaaagtggg aacccaagcg cccggcaaag gcaaaaagcc gggaagataa
    36121 atgaaggcgc agctgctgcg gctacatcaa cgctaattgc tctgtgcatc ttacagatac
    36181 tcgacgggct gagcagctaa gatacagata cacggtgcgc gaggactggg agatatatac
    36241 atacatatac gtttatatat acaaaatcat aattcatatt tcttcctttc cctcatttct
    36301 tgtcgcttct cgagctgttg tcttcgcgtc tttggcggac ttgcgatctg tttgacgggg
    36361 acggatggcg gccagcgaca gcaaaaatgt caaaatgcat taacatttaa ttgaggctaa
    36421 tttaaggcga aatatttcgc ttggcatata tgaaaattta tgcgtctcat ttcggtcagc
    36481 tcttcgtcag ttctttcgct ttcgttctgc ttttttctca gtctcttgct gtcttcttgt
    36541 ctgacagagc cggatatgtt tgagaaatga gtgcattttg taaaaatgtc acattacatt
    36601 taatttatgc acgccaacgc tgaaagccat ttaggtacat atctgtatct tttcagtgcc
    36661 cttttgcagc tccttgcact ggaagtgtgg catgaaattg tcttgatggc gatgatgata
    36721 ttgcttgttt gtttctcatc gcaatgtttt gtctgcgaaa atgatttaca ttcgagcgaa
    36781 attttttgtg gtttcttttt gttggtctgg ttttgttaag aaacagttgg cacataagta
    36841 aataagtatc tacatttaaa ggtattcata gcccatgaag tattctgcaa tccgtccgaa
    36901 aacaaagtac agctaaatga aagaaagaaa ttaatacaat caacttattt taaagggaat
    36961 atgtgcgtct actctcccac tgcttagaca ttaaacacca aatatgtttt aaatttacat
    37021 agaaatcaat tccaatctgg gaacttgagc tatcaatcat tcagtcggct gaagaaagtc
    37081 ctcaacaaac tctgccccgc ccagtgacaa aatttgacag gaaagctggc aggaggtcgt
    37141 acgccgcccc actcgtcggt aagtgagtgt aaacttgagt ccggacctcg aactcggact
    37201 ttggaccacc agctgccagg aacgagatgc ggctgtcaag ctttttaagc ccaaaacgtt
    37261 gtcgacgaat tgattttgct cctctcagca ggactcttag ccaactgaca ctggcaggcg
    37321 gtccttgcaa gagtgatgag aaaatgaaca ttttgtagcc aaaaaaaaag agatatatac
    37381 aaaaatgtta tgtatgaaaa caagattaga atagtacaca attttttttg gtatataata
    37441 taatatcata cagaaattta tcctaaacgc tgattatagg acttacacat atgcatttga
    37501 ataaatagct aaaatatttt aaggtatttg atccgactta aatcctgaag tcggcaacac
    37561 tgccgtccat gcagacaaag catcaaccac ctcggacttg tcactgatat cagctggatg
    37621 cggaactgga gctaaaagct gggcgaagtg gctacgccca acagctaaac aaagtttgaa
    37681 ttgactttgt taactcgact ggtgggctca agtggtagat actcgtacgt atgtagatac
    37741 ttacgcttgt gcatgccccc cgtgctctga aaggcgtgct gtgaaatctg caaattgccg
    37801 tgtcattatt tgttagcatc aaaccgaaac tcagccagga actaggatga tgtcaacgcc
    37861 ccttgggcaa ccttaacccc aagaagccct cgcctcgcac tcattcacat tgtgctcggc
    37921 gtcaaaaagt gtaattggca gtccgcccga cagtggacag tcgattcctg gggatcggat
    37981 cggtcctgga attgtaaaat tggggtgtaa cccactgtcg gcttacacac tcaagtcaag
    38041 cgaccaacgc catccccatc aaccgaactg aactcaactc aactcagctc agctcaaccc
    38101 aaccgaactg aactgaactg aaccgacgag ctggaaccgg cagacagttg gtaactgtca
    38161 gtgggcatgt tcgacttgac agcataatat tacaaatccc tgccgaaagc agacagtaac
    38221 gatgacagga cggccggcaa cgcaacgggg caaaaggcga aaaggacaac cgcagggcgg
    38281 cctgcaaata gagagagaga gagagagata gagggagagg aggatggaaa aatatcctgc
    38341 cctatgagaa ggcatatttt attcctcagg taaaatgtca gactagggga aatcatttta
    38401 ccccaaaatt gtttgcggtt agccagagaa tgggccgcag ttgccctttt cgggcggaaa
    38461 attgagctgg ccagttcaag ggtctggact gggtactgga ttgaatcaaa agtaaagtgg
    38521 ccatgattac attccatatg acggttcaat caatcaaaaa ttgatttccc attgcaaatt
    38581 tcatgcaaaa atggctgtca aggattgcct ttgttatggc aatatacata agctaaaaga
    38641 ttaacgagcg tgattttatt tattttaaat aaattaaata cgtaatatcc ataaacgttg
    38701 cttatgttgg gggtaccatt tattttcccc ctacttttaa atatttcgaa ataaatttct
    38761 aagaaaatca ggttttacgt tcatctatta aaaatcaaat tcataccttg gggcttccca
    38821 acgagcagcc attcaattaa cagacaaaca gacagatgaa gatttacctc atcgccaact
    38881 tccatttccc ccaatacgcg aacggtaatc aattaatgtt gtgtagggga aatcacataa
    38941 atttgcgtaa cattaaacgg atcgagtcgt cggcttgaaa cggacgcatt cgatatggtc
    39001 acatttcaca aattttacga ggagcctttc aagttgatag aaacatttac gagccactcc
    39061 gtccatggcc gggtctccag acttggtctg gttcgcctgg tagcaattgg taaacaagtt
    39121 tatggccagt ctgcatccaa ctgcaactcc atatccactg cacattttct ctcttgattc
    39181 gccgacgtgg ctataaattt attgcacttc cttttgcata taattttcaa attaagtgtt
    39241 gcttcatgta aattgataca tttactgaat gtatttttcg agctctttgc tgatagtacc
    39301 agccaagact agttggctgt ccggctttta agattctcag cgaacgaagt tagggaccat
    39361 aaaacgctgc ttttcaatga ttcatggggt tctacatatt ttctattgcg gagcggcccg
    39421 gatgtcagaa aatgtaggtg caataaatta cctaaatagt gtgtgattta agtcgttgtt
    39481 agtcaagttt aagagagctg ttcaaaataa tattgctgac acgcagaata atggttatcg
    39541 ttgtatttaa ttgcgaaaat tgtttgcatt aaaatgcgat tttaattaaa ctatgaaaaa
    39601 ctatgttctt attttgaacc acgtcgtata aacacactga agcaaactag tgtgcttagt
    39661 aacaagataa tataatactt agagcaacgt ccttcaatgg tttggctaac tctgctcatc
    39721 tcaccttctc cacttttagt tcttgacggt ttcttcagcc atttcttggc cacttgagcg
    39781 ctcctcgggc aacttcgggg ccttgcgttc ctttcgttca gctgacagtc acttcctgtc
    39841 agcgtggagc agctcgatcc cctggaaccc cctctaagcc ccgcctgtga cggctcatta
    39901 gcatgtgtgc gtggctggtc ctgctactct gcccgtcact cctttggcct gccattaatt
    39961 tcgcaaactc gccctgctcg ttcgtctctt gtgtctcctt ggggcgttta caacttagcc
    40021 aacttgcagt gtaacgcttt gtattgttca cgcaaaattt atttccgcta cgtcatgaac
    40081 atcctgctgt cgtcgttgca gttgtagttg tattgtagtt gtcctcatca acatccttgt
    40141 tgtatttgtt gttaatttac gtaataaata cgcttgaaaa tgttgcacgc acatgcaaaa
    40201 tgaattacgt tgctggggag cagcaacggc agcagcagca acatcaacaa cagcaacaac
    40261 agcagcaaca tcaacttaac tgtcacttgt cacagggacg tttcaggggc ctccctctgg
    40321 atgtcctggc ggtgctgtcg tctctcacat gtcaacgggc gtcgctttgc ttggcatttt
    40381 tgtgatgtga aatgaagcaa cgaggtgaca gcagcagcag caacagcagc ggcagcagca
    40441 acagcaacag cagcagctaa aggggagttg ctgctccttg cagcggcagc ataaaatgaa
    40501 ttactcgcgt gaacaacaaa acctgtcaga aggctgtcag ctgtggaggc gacacgtggg
    40561 tggggcccca tgtcgcattt gcaatcgccc agtctcgctg atgttgctgg tgtgtgctag
    40621 gtgtcagcgc atcgcatttg aaatcctcgc acactgaaaa acagttgaca gtcagcagtc
    40681 agggcagcga caaagtattg ctcccgacat tcaacgccag cggcagcagc aacagcagca
    40741 gcagcagcaa catgttgcca tcgctcgcat ccatggccat gcatatgaaa tgtgagtgtg
    40801 cgaaatcttt tgtgggtccg tggcccatga ttatcttacc tcaaattgct tgtagcaatc
    40861 atggaaaaag caacgttgcg gttgtcaagc tctttgggtt ctccctcgtt tcattccgtt
    40921 ttcttcttct tttttttttt ttttttggcc acagcaattt tcattttcgc actccattat
    40981 aaagtaattt ttttgcatta cttatgcctg tcaacgtctg gcgcttttcg ccgctttctt
    41041 cttcctgttt ccgaggcaac gccccacgaa cgtgtgggta tccttctcgt tggcaaagat
    41101 taatatgttg ccgctgtgcc gcatcctgta ctcactcgct cagtttgcca gcttgccgct
    41161 gtttgaacgc tcgcatgtgt gacagtttgc aaatgtgatt gacaactgac actggcatat
    41221 aaattcaaag ctttcgcaca cactcaaccg ttgacagtgt acacggagag gacagtatcc
    41281 gcagcaacag caactgcctc ctgccttgaa ggcatgacaa actgactgac tgaatgacgg
    41341 acgtgccgga ggtctgaacg gtcgcactga ctcactagct gactgactga ctgatggccc
    41401 gactgtctgc aatgcagttg ggtgttgtct caactcaact cagttagaga actgggcaag
    41461 tagtcgcaat tcatcagcga aagatcttgg gaaagattta gggttgtctt ttgcactcag
    41521 cttaagcaaa taattaatta cagtccattt tgaaattggg ttttataagt tgtaagaaat
    41581 aactagaact aagttatatt aggtttcttg ttggtttttg agtttgttgg attgttgttt
    41641 tattttttgt cattgaagac tgcaagatca tgattaaaag tactcaaaca aatacttttc
    41701 cattaatgca agatatacat ttcccccaat tcgaaagagc tcaagccatt tgatcgttcc
    41761 gcagtaagta cgatcattat ggtggaccga caactctgcg aagtcatttc cccaaagtac
    41821 aggtctccat ctatattttg ttagttgctt cccgtttctt tcaattaccc agccacggcc
    41881 tatagaaact aataccaatt atcatgacaa cttccgtttc tcagctcaaa ttactgcggc
    41941 ctaattgcta tttagggctc ctttcggaac gtcgagccgc gtaatgtcca attattcaaa
    42001 caagagacgg agcccataac cgctgacaca accgtccggc ccgggtttga taatagactc
    42061 atcagacatc ggtcgccatc atcgtcatca tcgccacgca gcaggtagtt ccttcaaaag
    42121 gagggaaaac tcatttggga gagtacacag gaagaaatga aaatgattca aataccggac
    42181 ctccacaaaa cttccgaact taagcttatg atgttagccc attggttgtg taatgtgata
    42241 aggttcaact ttatggacta tatcatacta aacctagtgt attaaagcgt tagatcgact
    42301 gttaatcgga tgctttcagg tctatctatc tcatgtattt ctctctgtgt attagtgatg
    42361 agacgcaaac ctgtcgctcg tgctgacgac aaatgtcttc agcggaagtg acacaacaaa
    42421 aatccctggc aaccgaaagg gaacaaaaaa cgcttgatta taaatgcccg atgccgcgaa
    42481 gaaaataaaa ctaataaatt gatgttgatc tggcgatgct ggctaccgtc tcaaagcaaa
    42541 acaaacgcgc catgacaatg acaaaatcaa gcggcagggc tgacaatgat ggaagtgaca
    42601 acgacaatgg cgctgaatga caggaggatg tggatgtgat ggcactgcag aagcagaagg
    42661 agtggggcgt cggcagaggg ttttctggag gggatccgag gggtcgacca gtggcagctg
    42721 ttcgctaact cgacactctt ggcgtgactt gtcaacgggc atcattcggc tggcgtcgag
    42781 gttggggttg ccgttgatgc tggagcaaga agatcatcat tcatgacgat gatgatgcgg
    42841 tctacgcctt ttgtttatca aatttcaatg agattggacg actgatggag gtagcacatc
    42901 actttgaaac gcatcgtctt tgtgctcagc tgggatcgat ttcactgaaa ctagcatcgg
    42961 tcttgggggg aatatatcaa attttaaact cgtactacaa gtaatgattc taatacaaac
    43021 tttatctaat tttagaaatt ataatattac caaacttggg tctttacttc gttgtcacca
    43081 tttctcgtga tctccatgct tgcggtcagt cttgtataga ttttgccatc ctggccacag
    43141 gaaaagacaa gcaattctcc gtttatccgt cagtcagtcg agtcatcgat ccatcagcca
    43201 ttcaatcatt cactcatttc gactgttgtc actcactcgc actcgagtgg aaggaaaaga
    43261 agggagccgg ggcagacgag gcagacgggg caggagactt caggcaacca cgttgcacga
    43321 ttccgtggtg cgcttcaatg aaaacaaact gatatttgcc tgacacttga gattgattgt
    43381 catccatcaa gggagctgct gctgtcgtct ggctgagtga ttgaatggca aggatgcgct
    43441 gtttgcattt cgaatttaca tgccagcccc gttctcgttc tcgtttccat ctggactatc
    43501 tacctaccaa ccgctcccca ggctggttgc cctgcccctc agtatttcgg cgttggcctg
    43561 aattgatatt caattacgtt ttattttgcc aagccaaaag gcggcaagga gtagtaggtc
    43621 cgagtagtag gtcggcttgt ggctttcaca ctcggtccac aagttgtttt gaccaacgtc
    43681 tccattacgt gacaacctgg atacaagtga tggtccttct tggcaccgtg gatcttgttt
    43741 gcattggcat gttggttggc cggctggaag aaccgcagaa aagcagaaaa tctgccaatt
    43801 cagattggcc ttctcaagag tcatgtggtc aagcagcagc tgttaagttg ccatgtgata
    43861 tccaatttac acgaaagatg cttggaatca gtgaaaggca taattgtgcg actctttttt
    43921 atggcgagca aagcaatatg gcctcgaaaa accgtacacg catttgtaat aaaagtcgcg
    43981 cacatttttt caaattaaat ttcgaagccg tttcaattgc aattgaagct caatttgttt
    44041 taattaaaaa attgtttatg tcggttattc attgaaaaca ttgttttaac atgtaatatc
    44101 aatttgctgc aatttatttc caatcaataa agatctgaaa tttcaattat ttatcaaggc
    44161 atttgagcgg cgctcgcata agcaatctca acatactgta attcaacctt ttcgtatact
    44221 cgaatgacat tttattatgt ttaatagtat atatagtcta ctggatttaa ttctcatgtt
    44281 atataaattt agtgttttct tttatcaaac aagaactccg aactctcagc tccatattca
    44341 actgggagac attcaaagac aaaagacaaa cacacatttt tcatttggtt tgactttcct
    44401 cctcgaggca ccaaccattt tcaaatcgtc caagtagcgc ataaagaaat tgaattcatt
    44461 aaacattagc ttcctgacac gatcgtcgcc aagcctccgc cggcagagac cttaaaacat
    44521 ttagtgtcgc aatatgcaaa tccataaatt ttctgcccca gacaggcggg gagtgtgagg
    44581 ggatccggtg gaggcgatgg agcctcagtc ctcggttgtc ggagacaaga catacacacg
    44641 cgataaagaa attcgattag gcatcaattt taaatgagac gcattcccct gcctccttgc
    44701 cacgacaggc cgcctgctgt ggatgccacg taacctgata tggtgacact cgtccatgtc
    44761 gttcacgtcg tcgtcgcggt tgcaatctaa tttatgactt aattatcagg ccatatttaa
    44821 tgtgtccaat aaactagtct acaaaattat accaacacgt cgttgtttag gctttgccgc
    44881 gatctgcggt gcactgagaa cgctaatcgg atgggaatat ttaattattt ctaagaatac
    44941 ttaaggaatg atatttagga ataaagattt cagataaaat ggaattagtt taaattaata
    45001 atttaatatt aatgtgtttg taaatacatt ttaataggaa atctgttcag ctgaaaaacc
    45061 ttctatgtgg tatttaagat ttaaatgagc cagtggtgta aagattaaac ttgtttcaag
    45121 gttgccactt agatgttcta tggcaatgat tgcaatttct ttcagtgcat tggtcttggc
    45181 tagcctttgc ttaacgcgta atcggagcgc ggggaacttg aatttcagca actcaactcg
    45241 ccaactgtcc gtggtgtggc ctcctttaat tctgcggcca tcaatttgct tttaaatgca
    45301 acaatttggt tgccattgcg gcggcaccac cgacagagtc tgcaccacgt catcgtcacc
    45361 gcagcatgca gcattattat tttttttttt aatacgtatt ttgtttttat tttggcagtg
    45421 gcgacggaac ggtcgatcgg gcttggcttg gttggcttgc tggttcagca ataaaaattt
    45481 cgtgaagtgg caataaaatt ccatttaaaa tggcagcgat tatgtctcaa cagaccatta
    45541 aagtcactca aatgacaact actacttagg cactcacagc caacacaccg caccactttc
    45601 agcatcgcct tggacgcaca gcagcattta ttttgtattt attcttcaat tttttcttta
    45661 tttttttact ccttctgtgt tgatcgtggc tcgcagatcg cgacatttga tgacgggcgc
    45721 cggacttgga agtcaaccgc attcgcacag tggggcacat tttattacct tgggtggtgc
    45781 cgatcccacc agtgatccac ttgcgtgggt gcctccatta gtattgtgga ttgatcggat
    45841 atgaacttgg aaagtttggc ttgccatata acgaatcact gtaagtaata caactatcga
    45901 aagctacatt tcagtcatgt tgtttacaat agttttagat atatattttc tttatttgca
    45961 tacatggccc tgatttcatg ctcttaacat tcaattactt tgggacccca gtggcctcat
    46021 caggacttaa aaactccaac caaattgcat ttttccccca gtttttcttg tgtgctcagc
    46081 tgaaaagtgg acgaaactac cccaatgcga atttcctgct gactttgcat tttattattt
    46141 gacggtagag tctggttgcc accactgccg cgttttttcc ctcagtatga tatgctcatt
    46201 ttagcaaacg actttggctg cttatggtcc gacttcctgg ccattttggc actatgcact
    46261 ctccgaggtt atgacgtctt cgtcggcacc atcatcgttt agataagtga attttttcct
    46321 acgcaggggg ttgtataatt tctgttgata ggcttaggtt ctataatata cttagcagag
    46381 ttttcatgac ccgtgctatg taaactccat ggttgcaaag gatgtgcttg cgaaacccaa
    46441 tacaaaaagg atgtttgccc gtacatctga aatttaatgc caaaatttga ctttcaagtg
    46501 gttcgaaaca aaaaagagcg agtattgtca tcctataggg gtccccattc tcccaactcg
    46561 actccagttg atcctcatta gtggtcacat gtcagcttga cgcgcatttg ctgtataatt
    46621 ttgtcattca tcatttttcg cccatttcat tttgcgctac atgccgaagg actcgtattt
    46681 cacgctcatc cctctgctcc tctggccgtt tcccgcagag tggtgtcatc ttttccagcg
    46741 tcgcatgaca tgtgacaaca atgtggaacc gttgtcattg tcgctggtag ctgttttgct
    46801 gtgacacctc ccagcattcc cctgcagaag ttttcggggc cagtggatct ctgcccagct
    46861 aggtgtgatt ttcaacaagt acgttcattt ttctgcttca gttttcccat tttcctacgc
    46921 atccctgcca ccgtgagccc tgtgatatat tacccaaccg aaaacacgac gctcgagtga
    46981 gtgatgagtg actgaatggg ccacactaat gagggaaccg agtgctggtc agctactgtc
    47041 agtcggcatg aaaatgaatg acattcgctt gggtgtgtgg tttgattagc cagcaaaact
    47101 gaacgacgac tagaatatat ttggtatgtc ttctgtggaa aatagttgcc taattggcgc
    47161 ttttgatatt ttcattataa tacaccaggt aaaataatat gtttattatt ataaagatat
    47221 agattttata aggatgcttt actatctata cgggtatttt aaacgttatc ttctagtaaa
    47281 taagaaaaaa aaactgttta tccaattatg ttcggaattt cagctaaaga atttacgaag
    47341 catcggtggt tcagtggtag aatgctcgcc tgccacgcgg gcggcccggg ttcgattccc
    47401 ggccgatgca taatactttt ttaaactttt tttttgtatt tctaatgaac ttgtttaaat
    47461 tgtatttgta gcatacttat tatagataag atataatcat atcaaaaata tgataacaaa
    47521 ttataatatt caatatcata attaaaatat taaattgcat cggccgggaa tcgaacccgg
    47581 gccgcccgcg tggcaggcga gcattctacc actgaaccac cgatgctgtc gtgaagatgc
    47641 atattttccg acaaaaaatt tttcttttag cgaaaaactt gtctaggatc tccgcaaaaa
    47701 ccatttgttg tgactgtaaa accggatttc gaatgcaacc aaccaacttc aaagacttgg
    47761 gtgagcaggt ttgaagttta tgtttgtaaa gcaatttcgg atgatggtaa atcaaaaata
    47821 aacagaaaaa tgtcataatt aaaataacgc aggtattaaa atacttgttt gcatcggccg
    47881 ggaatcgaac ccgggccgcc cgcgtggcag gcgagcattc taccactgaa ccaccgatgc
    47941 ttcttaattt gatccgccaa aatatacaaa attaagctta tgtcggacgg attgaatggt
    48001 gtttaaaaat agacaagaga ttatgaatga attcataaac taaaactcta agtttctaaa
    48061 tttttttata tttgttatat agtttttgat atggtctaat cgaattcaaa acaacgtcaa
    48121 ggggtacata aatataacat ttcagtttcc agaattccca ggttatccaa acgtgaaaga
    48181 cgagtaccac tgacagccgt ctattaactt ctgtgaactc aaacatctaa gagcctatta
    48241 gcaaccagag ctcaactact catgaacgca aacaaacaaa gctctcagga ctcgcaggca
    48301 tcaggagacc ccataattaa ggtaacctga gctaattttc cgagcacacc acaccgcgac
    48361 agacaacaat tgtcgccaga ttttgaaccg ttcctgccaa acaacccttc caggcaggat
    48421 gtccatcatc tgacaagccc agcccaaccc tttgtgttcc cggccccgtt gacaagcgct
    48481 gaaaaatatc aaatttcatg caatttcaat gtgaagtggt ggcaggagtt gcgaagagca
    48541 aaaccaaaag aaagccaacc aacgctagca aagaaactca agctattgga cttgtaaata
    48601 ccacttaaat aataaattta gttgttttat aaatgtaatg atattaagtt ttgatccact
    48661 gaaagttttt ataccataaa ctctgcaaga aaattcgcct aattaaaaaa taagaagtgt
    48721 ataattcctg cattttcaat ttttttttta agtgatgttc aagtgtcata tactcctttg
    48781 cccactgatt acagggtacg ataaaaaaga ctcggcgcgg gaattgaggg aaatatgacg
    48841 acggtttttg agtgacagca gcgcggcaac acctaattca atttaacaat tcatttatca
    48901 taatcaggca tcaagccgtt gtcactcaca attacgatca agccgtagtg aaggccgagc
    48961 agaaaaggcc aacaaaagga cgccccgatt cctcccctca atcttctcgt atcgcctgat
    49021 tgccccgcgc tactcgtctt actcttcctg ccagcctgcc gccaggatct ccttcctctg
    49081 ccccattgtc ctccgactcc tcggtcttcc tgtctcagtc tcagtcgctt cctgccagcc
    49141 tgcctgggac tcgctatctg tcacttggct gccagcggtg caacgcagca cgaagtccaa
    49201 ccagtcggcg gcgaaacagc caacaactca ttgtcagtta aatgttgaga gctactcaca
    49261 ttttaaatga gacaacagcg aaacagctgc gaaacgcaga agactgtcag atctcggggg
    49321 aatatcgaga aaattcatag cagtcaagac cttggcggtt accaaaaagt taagcgaatc
    49381 aactccccca cgatttcttt caaagtaaag cgatcagttt taaactaatt tctaacccat
    49441 ttcttagttt cctacacaat ataattaatt catagaaatt caaaaaatgg gttataggtt
    49501 aatcatcatt ttatgttttt agaaaggact atattttacg aaatcatttt attcttaggc
    49561 ctaccagctc tgtcatatgt acatatattc tgttccatat tcactaaaaa ctacaagcag
    49621 gagatacatt ctgcagcttc tagttacgtg atactctaga ctatcgagct tccagtaaca
    49681 tttcagataa gacttaatta aaatgaaatt tcaaaaggtg gtcacaattt ggattgctgg
    49741 taaatattcg tcgaaaatat cctcgttgct ttagtgtacg tacacatgtg catattacat
    49801 attccgtgtt gcatttctct ttgctcagct gccacttcca ctggccatta atttaacggc
    49861 caacagcagt gacagaacag agggaacacc catgctgccc cttgtgttac gttgctgcgt
    49921 tacgttacgt tagtgtgccc cctccgcacg ctgtgtggca ctatctgttt ggctcgtagt
    49981 catacaacac acccaccccc ctcttcgagc ccttttcgag ctgtcagcca acaatgcttt
    50041 cgctgtcaga aacagcagag ttgctgctgt tgctgttgct gctgtgcaat ttgttatacg
    50101 ttgcactgtg gatttttata acaatttcta ccatattttt ctagaccaga gtttggggcg
    50161 agggtgtatg gggcatataa ggatggtcac atgtcaacaa caacgatgca ttctgacagc
    50221 ccaatgacat tttctacatt ttcgtaaatt gcttcgattt gtttgggggc ccttggcgtt
    50281 gttggttgtg ttatatgacc gaaggcaaaa tgggtcccca ctgcgttgtg caatggcaac
    50341 atgggaagga tgtgacatcc acgtgaacgt atttatttat atagattttt tatcggctgc
    50401 acatttttgt aaactcggta aagagcttgg tgaaactgaa aggagctttt cgatttcagc
    50461 tccatcgctc taaccgaaac tgcgactgca tttcatactc aatcattttt aggtttctca
    50521 catttttgct gactctttca tcacaattga caccaaacac tgccagcccc tttatgtttt
    50581 tattataccc ataaattttc attatagtag atatgatgta cattagcttg ttcagtttcc
    50641 tttcaagtta atttgatttg atggcttttt cgaatgtgta tttttataaa tatcagctgg
    50701 cgtttataat gatctacacg cgcccaccat tgcaagcatt tgttttggct ataaaatatg
    50761 agccaacacg gcacttaatt ctcaacgaag cattctgtgc cacagcccca tgcactgaaa
    50821 ataaggccgt aaaagtatgt tgaatgcact ctaaaaatac agtttgaaca tcaaatagtt
    50881 ccttagaaag aaataaatat cacacctatg ttaagttggt tcaatgtgta ttgttttttg
    50941 aaactacgct ggattgctag taatttcttc tcagtgcata tatgcaacaa tgtagactgc
    51001 aattgtgttt accacttggt tttgaggcgg tgagtttgtg ccaaaatgaa tggaccataa
    51061 agcaaagaca caataaacgc aactcgcgcg attagcaaaa taactctagg atgaccgagt
    51121 acagtcagta tattgaatac aataccttgc gaaaagctct atttaataat aatatttatg
    51181 catggccagg ccgtcagact aattgactca taaattagcc aaaggacaga cccctcgtcc
    51241 accaccattt tctcttttat aaaatcttga caaattcacc cgcatgtctg tgacacttgg
    51301 acatcaagca cggggtctga gaaatcatga tgggaactgc gacagacgga cagtgacaca
    51361 aagtgcattt gacaaatgac atttcacaga ctgccagaca cacaatcctg gggtggatat
    51421 tcaagggaag gcccacattc tggggcccca tcaaaaccaa agtgttttta agtgaattag
    51481 tttctctgat tttttttttt ttttttgcct taagtactct tcagttgggt atcgtaatta
    51541 ccaagaagtg gacctttaaa taattaaatt tatatctcaa aaattgtaag tagaaaaatt
    51601 gtaagtaaaa atatatcccg ttaaaagtta taagctttaa caaaatacat tttcaaagtc
    51661 attaaatatt cgctgtgcgt tttcagatgg cttattagtg cttagtactt cgcgactgtg
    51721 tggatctcac ccttaacaaa atttatattt atgtcttatt tttaggaagt attcagtttt
    51781 tcgtcattct tttataagct tttcgtcgtt cagcgtttcg cgttgccatc accgtcttct
    51841 tcgcccaaaa gaagatctca atttccactt caatttgtct gctgtcactg gtaattgagt
    51901 tcaatttaca ataatgtgct ctgacgtttg tgcggctgag cgccagctgg gaggctggga
    51961 catccgagca ggcggagtgg caagtgtacg aatgtcttgc gattgcaatt tgtacccgct
    52021 gactctggac tcccgactcc cgactccggt ttccttactc tgatcccaaa cgaagccccc
    52081 gaccgctggg tttctggagt cagcacagca tctctttggg ggtcagtggt ggtcagggag
    52141 ttcaacagtt tccaattgag ggggcgtgac tgccaaaggc gaatggaatg gaaattgtaa
    52201 ttgatgcccc ggatattgat ggcacttact ggatttgaag tggtttgcat ttttagagcc
    52261 attgtgtttc ctatggtggg atattcttca tctatgtctg gacatcaact tacagtttcc
    52321 ttacgccata aataaatcga aaagtgaatc cattatgatc tttatttcgt tgaacaaacg
    52381 taaatttgtg aaatcacttt atatcttata tttttataca tttatcatat agcctaatag
    52441 ccttccattt gctttaatgt ttaacgttat gcttttatca tattcatatc atatatatgc
    52501 ggtcaattac gggcaatcct gttgactaaa tccagcttag taaacttcaa atgtaacgtt
    52561 tcctagacac cgaattataa accttttgtt atctgcgagt ccttgcccac tttactgagg
    52621 tggtacaatt tttgcaaact tttcaaataa agccaaagaa cataggggtt agagaatggg
    52681 atttgctgag ctggtttcgg gttcatacat agggcataat aaatcttttt aacgaaaaca
    52741 ataaatcgca tttcacgcat actctggcac ggcgcaaaca ctctggcagc agaggagggc
    52801 ggccaaaaat aataatggca agacctagta acggctggga agagagaagc caacgtgagt
    52861 ttggcccaga gcagtcaagg taaacccttt gcccgaagaa aattgtagaa tttatgcatt
    52921 gggtggagga attctcgccg aaagacaacg aaaacccatg ggccaagtaa tttctcagcg
    52981 taaagcagtc aacgagtttc ctctttaacg aaagaaaaaa acacttagtg caactctcat
    53041 acccttaaaa agggttcaat caactttttc aaagccttag gcaggacctg gcaaattgaa
    53101 atttaatttt atgattatcc tgaacagagc tttattttta atttaacttg acttaaaagt
    53161 tatttgaatg atttctctga ataattccat tttatttcac gattttattt aagtaaataa
    53221 ttcgagctct aaaaattcga tacaaatttg tatctatcta gaggtatctc ttgttacgat
    53281 acgaggtatt cccaaatgcg tgtatgcctg tcacttaaga ctttatacct atccccccac
    53341 atgtgtgtgg cagttagcca gtgtgagtgt gattacacct acttgaagtc atatatcttt
    53401 cactttgcgc tttcaacagt ttgtgacgtc ctctcccgtc tacacattta tcctccactc
    53461 cactcgaggg ggcggttaac aaaagctctt tgatataccg ccaccaactc gacgcgactc
    53521 gactttcgag acatgctacc aacacttcaa ccctatatat atatatacca aacccatagc
    53581 catagccata cccatactat agcctcgcct catttgctgc tgcctctgcc cgaaaagctc
    53641 agaagtgggc atgtcagcga aaatcaccgt aaattttccg cattgtttaa aatttattac
    53701 actttcagat ttgccagcga actgaaccgc accgcgaacg gggggcaaac gatgcctgaa
    53761 tgttgggggt gttggtgcgg ttgatgagga agtcgtttgg ggcacgccct ttgtttgccg
    53821 gggtttctcc ggggccgcct gctatctctg acatgttgct gtctaataag tgtaaccagt
    53881 aattttctta tcacgtaaac tgactcatgt agctgccacc ttttggcctc atggagccag
    53941 aacgctagtt tgaatatttt aaaatctcga aactgatcgg taatagcgca tttatgggaa
    54001 ttttaaaaac aaatcgttgg atatgaaagc attaactgta attataaatc ttattagata
    54061 gatttatatt taaaaacatt aattactaaa tattatgttc atagagatgt actctgttat
    54121 ggtttgataa ctattagttt tacgggtttt gtgtccaact cactttaata taacatggac
    54181 ctcgatcatt tggcactgat gatagtagtg atcctttatg gcattaacga cgtaagtata
    54241 gttatataaa agtaaaagat actattaatt tttttttagg tcaccccgaa ggttgagttc
    54301 accaacatca aatgttcgtc ttctgacact tcgtacgttt actacgagag ttgccgtatt
    54361 aaatcggtga ataggacgta taagtatatt tctgtgaatt ccagactgtt aatattgccc
    54421 cttacaaatg ccacagttcg tataaaagtg atttttattc ttgtataatt aattaaaagt
    54481 atatcttcta gataaacgtt gccctataca agcgatataa tggctataag ccatttctct
    54541 acaacgtttc tgtggatgcc tgtagatttt tgagaactca aaaatcgaac atagtcgtta
    54601 aatatttatt cgatttaatt ctcttaaaat cgaatataag aagtccgacc tgcccattca
    54661 atgtaagtta accaaaatga gtacttatac gcctatagca aaaatacttt tttagcagtc
    54721 ctttatttct gtggataagc tgactaccaa ctttctgaat aataagctta cgcaagttct
    54781 gccagttccc gaaggcgact atctttttgc atttagatgg ttctcttata atatttatcg
    54841 ttcctctgta aacgtatata taacgatttc ctaaatgtta gttttgaaaa cttggacgcc
    54901 taggtaaatg gatatataca taatgtacat tcttaagatg acacctaatc aatttttatt
    54961 tcagttgata atctgttcaa aagggattct tcatcatttt actaaaccaa acataattat
    55021 tagatgtata acgcttatgt atgtaaatta tatgttgagt acgttagtaa taaatgttgc
    55081 tatgtgtttt ttttataaca tcctggacaa agtaataatt tcgaatcaat tgacaatttc
    55141 atgaacagaa tttgacaatt ttaagcacta aattatcata tcggaaacat aaatattaaa
    55201 ctaaatacta atgctccaat gttatcccat aagcagacaa aatataatgt gtgcataatt
    55261 ttcggctaat ccatatttca tgtccgacaa ctgcattggc ttttggaaaa tctctacgtt
    55321 atcgaaaaca tcctgttttt gcggaaagcc cgtttatgaa atatatacat atatagtgcc
    55381 cctcgctatg agtatctgat agatatgggt aaacaaaaaa aggttaagcc agaaccaaac
    55441 tcgaaattcg aatctaagct cggactgcat ccgcttgtaa atcatattaa aatatttatg
    55501 ctgccgcccg atatcccctg ctgttgcttt attttttgtc gtttggcttt cacattttgt
    55561 ggggccaacg ataaattgtg aacaaatgac attatgcaca tgtgctgcgg tatctgtgtg
    55621 tgtgcggttt atttagtgca tttagataaa gcgagcgaaa atgtcaactc tagcgactat
    55681 ttttcgtgtt cgtaagtttg ttgggactga cactgccact gccacacagc tactgcaact
    55741 ggctgcaatt atcgtgcaac aaatcatggc aacagtgggg attcaattca gttggggatc
    55801 ggttcggttg gactcgcttc ggttgggtta tttatgagat tttaggatgc cagctctctg
    55861 tgacctccgc cggatgttta gtcgcagtaa cttttgtttt gttgttggcc accggaggtt
    55921 gggacttata atatttatta aaattatgca cacggtttgg catttaatat atgtaatgac
    55981 ggttaaagcg gtagctggtt ccattgaatg gatgctcaaa acaggtgtaa ttattcctaa
    56041 aagcggtgac tgaataattg atatcaatag cgatggataa atgaaaaggt atttactcta
    56101 ctagcagatt tttggacatg attagcatat ttaattttaa tccagaaacg tgtttcaaaa
    56161 cgtaatcgca ttccaattga agcatttaat attacgtacg gaaatgtaat aatataatat
    56221 aatatataat ataatataat tgctatttat cgcagtaatt gtagtaaata taatagctaa
    56281 gcctataaat ctgttcatag ggcttattaa ccaaaaattg attacttatt ttattaaata
    56341 tataatatcg gattggatgt tttgacttac atataagagc agttcgaaaa acttattcat
    56401 atattaatat tctagataat aactctttat agtcagtaca taaacgtgtt agttttcata
    56461 tagaaaacac attttcgaat ttttcttccg tcgcaaccta tcaaacattg accgagtcca
    56521 gacgtggcaa gaccagaccc aatgtcacaa caatctccaa tctccaatcg attcccagca
    56581 caattgctgt tgattaagat gctgatggtg ccccctggcc acatcgctct ccatttgttg
    56641 gctgttgtgt aaatgtttgt gttattgatt aattacattt acaacaatca aagttcattg
    56701 agtgatacca atcaaaacaa cgccagcaaa caacatggga tgcagtgcga tgcaatgaat
    56761 cttcgagtgg aagttggagt ggtggggcca aatggacgcg gagcgatcgg aatggctaac
    56821 tgaatgactg agtgactgga tgactgagtg actgaatgac tgactgagtg agtgactgaa
    56881 cgagcaaaga acatgtctaa tgtgcttgtg gtgttgcccc ttgctggctg attgctgcat
    56941 gttcggcttg tcgctgcttg tatggcattt gtctgttttg ggctccgcgt tgctttgatc
    57001 ttatttcttt ctcctttttt tttttttttg atcttcactc gctttgattg atcaattaaa
    57061 ttcatttgta aacaacttct tgccgacgat gatgcggcat aaagagtaca gatgtattcc
    57121 ccaacagagg aagccggcgt cctcaaagag cggagaagat ttatttggtt ttctatattt
    57181 acgcgggagt cggtcgatct gcggtccggt taaagccaca acaaacacat cccgctgata
    57241 ataattacca gatgattggg cctatctgga taaattggtt ttgaggttgc aactagaaac
    57301 aagaatttgt aaatttgatt gatgcttatt ccatttttat ggtagaaaaa gccttaatct
    57361 tatatacaga tgagtgttga tttattttta ttgaattata ttttgagtat tttcggtttt
    57421 gaaatgagca ttttattttt aagttttccc acatttgcac agtaatttca gccatcgtgt
    57481 tggccatgta ctgcaagttt atcgtacatt tttatagctg tcagtgcgtt ggctgtcaag
    57541 tgtcaaaaac atttgcagcg tgcaacgcgc caaatgcaaa atgcaaatgc acttacgaac
    57601 gtctctcgcc aaatgcctga caatgacaag ccaagagaag atatacatat ataaaaagtg
    57661 tacgtacttg ctcgacggat ttgcattgtt cgccagatat gtattacaca agtcacaggc
    57721 agtcagcata acagcagttg ggtttacaat agttcctcgt gttcgagcag gggcacacac
    57781 atgactaacc caccaactga ctgactaact cgccgactga ctgactgcac gtacatacat
    57841 atagcaatga tgataatgac ggtgccatgg ggttgatgat gctctgacat tgcctgacgc
    57901 cttgattaaa ctgtcattta acttcattta ttttgacaca aaactgacaa gagaccccca
    57961 ttctaagtgg cagcttattc aattttgcac acccgtcagc gaacaaagag tattcaataa
    58021 aataaaatta aatactattt attatgtagt tcgtagacgt attccatatg caatcctcga
    58081 tgcggtcatc acactgctga gagattgcat attcagatgg gttacccgat cccaaagtaa
    58141 caaatcaatt ccactcatcc gcaagtcatc atcgagagga ggcaactcat ttatgctaaa
    58201 taacaagtga ttaaagttcg ttttgcgccg atataaagct gtcactaaac ataaattaca
    58261 atatgtcagt ctcgagaacc tttgactttt attaatgtaa acatgaaaag caacacgcac
    58321 gccgaacctc cgaacgagcg cacaacagct acaacatgct gacactgaaa gccgagataa
    58381 gttacccagg cacacagact gggtcttggg acctcgtctc ataccccgac catatagccc
    58441 agacccagac ctaaaaaccc caactcccaa gccgggctcc acttggaacc aacgctgaca
    58501 ggcaaaagtt ttgtccaagc gacgagctgt gtgtttgtta ttaaagaacc cgatgtgcag
    58561 cagtgcaaag aagatgcaac acttgaggct gcctaggatg ggattatggt atatggtata
    58621 aaatacaggc cccaattctg ttgttggctt ggttaatggt aaacttacat attatattaa
    58681 tttatcctac aaaaatgact cgcttttcgg aaacttcctt ctctactcct gtcccaacat
    58741 tatttttcat atcagtatgt ttcactgtac tataacagca ccaccccact agttttgcat
    58801 tcatctggcc atacctccgt ataacgtcct gggcttttgt gtgtttgcgc tcacttagcg
    58861 atcatatcat tttgacatgc tcgtgtgttt aagctgtcaa attgcctgct gtctacggct
    58921 gctgtctgcg atagcttgtg gctccctctc tgtcctcatc tccatctcgc tctggcggag
    58981 tcttaactat cttttcgctt tacatggact agtcgctcac tcctcggggc cccggttgtc
    59041 tatttgtatc tggacaggca cttcggtcgg cctcatgcct ccttaagttg acgtgttacg
    59101 ctgtcagcat ggagaaaacc tcaatttcaa actgtcagtt tatatgtcag ctccaactga
    59161 cagttctcca tgttgtcgct gtctctctct ctctcgccga ttcgtttcgt ttctttcatt
    59221 gggttacgtg gtttggcatg cgctagcttt ggcttttcca cggacttgga tacagataca
    59281 aagccagcga cagcgacaga tacttagatg ggcatttgaa taatgcgcac acaagtctgg
    59341 cttacaagag gggcttgctt ggggatacta tactgcttaa ggctgctcat ttggccatga
    59401 tcctaactct attcatggtg cgcgccttct tcaggggaaa caactcaact cgactcattc
    59461 ggactgctgt ccgcatggtg aatgggcaaa agatacggat gtgagtacga gtccgcagaa
    59521 tccagtgatc gtttcccaac cgatgtttga ttaagtttta caaccacgat ttctagaagt
    59581 gagacgactt tttaagtagc atgaagttgt acggccgatg ctactgtact gattaacttc
    59641 atatgcgtat aataggtaaa cttctttcat gcatgttata ttttatacag taattgacat
    59701 tagtcttgta aaaattttgt acttttccac taagtagtgt taaaaagtta accttgagaa
    59761 aggggttttt cccttaaata tcaaaaagct attttgcatc ggccgggaat cgaacccggg
    59821 ccgcccgcgt ggcaggcgag cattctacca ctgaaccacc gatgctgttg gaaaagttag
    59881 gttttccgca taaaattttc cttttggcaa aaaagttggc aaacatcttt gaatatgaat
    59941 atcaaattat ggttaaaacc ggcttttttt catatgaaga agttacataa gaaaaaatca
    60001 aacttgttca aaataacaga ttaatatgca atatttgtaa gtgaatgtga ctatttttaa
    60061 aaaattaaaa cgtagttaaa ttatggtata aaaaatgtat tttgcatcgg ccgggaatcg
    60121 aacccaggcc gcccgcgtgg caggcgagca ttctaccact gaaccaccga tgcttcttta
    60181 tttcttgcgt cagcattttc caataataat aactggccat ttagtttttc catcgatgcc
    60241 gaatcgtcgt gccaataaaa aattggcaaa cataaacgcc ctccttcctc tacgatcata
    60301 aggatcatta tcatcgttat tataattcct ttatttgata gatgttttgt taaattatat
    60361 cctgagttaa taaaatacta aagtagaatg cctctctctt cacctgaggg acaaacccct
    60421 tctcaggcaa ggacagttac ctggccgtgt tcttaagcga taaataaagt tgtgaacatt
    60481 ggctcgattt gtttgtaggt aggtccgccg ttcggttcgc ttgccaaggt atggtgtggt
    60541 atgggttggt gtttagcagt cgccatcccc atccccacgg tcttatggct gccgcagtgt
    60601 ctccctcccc atcaccatcc accgacccca taaccatgcc cataccatcc atcctgatcc
    60661 gagccttggc tttgtcggcc ctgtcgttcg ttgcactgcg tcggacacaa aagatttacg
    60721 attatggcgc gactattaaa aagtttcgcc tctcgcacac ctccgccacc gctactcctc
    60781 atctctcact caagcccaca tccaaagtca aaatattgtg taaaaaataa aaaataaaag
    60841 gccaacaaac agagtggggg cctggtttgc agccggctct ctggatcgat taattatgtg
    60901 cggaatttgg tttattgagt acgaaccgcc tttaaattgt ctaaaagacc cggagagctg
    60961 tcagggcatg ttcattcgtt tcggggggcg atcgcagatc gctgatcgcc gatcggagaa
    61021 cggagaacgg gtttcaacgg ctgactacgc ctgtaattta tgagtttaac tataattttt
    61081 aacatttacg ctgcgcctgc gtgcgcttgc aatatgacaa ttttactgcg cgacaaggag
    61141 ctctacgaag ggagtaaata tgtacgtatt cagtcaggag tcgaatggac tcgagttcgg
    61201 agagatcggg gaacaggtca tatttggact ctacatggac agctggtcaa ttgagttggc
    61261 ccgaatgccg gcgtgttggc ggggcaacca ttttgttgtt ttcgattaga ctgttaagtt
    61321 gtcaagctga aattgatttg tagccactgg ccggcctctt ttaaattgct caaattaatg
    61381 ttacacaagg tgttgccttc gttgaggtta caaccgctgc accaactctg gctgctcagc
    61441 caactggatg ctgatcgtaa atcgatctgg ctaaccatgt gcccggcctg ccaaggggtg
    61501 ttatgactgc tgttagatgc cggactaatc gcggttttgt acgagtgtcc aagccttaat
    61561 cgatactgat tggcgtgaac tatttgcctg taaaattgta gctggtttat ttggagcttt
    61621 ggcaacactt gtgctgtttt gaagcaagca cttccacagc ttaacttccg atttcgttat
    61681 ttatatccgc ttcagccact gttaatcaac attcttctca cagtaaactt ttatatagtc
    61741 ataattacat ttattagttg gtaaaatata taagtttcga ttatattcga tttattattg
    61801 taatcctagg agatcgggat agtcctgagg cgactgcata taccgagcac tgcgatacag
    61861 tttaagagat gaaggcttat ttacggcatt aaaaagcatt tgaccctgta tgctcagcac
    61921 tccgttaata tagtcattcg atagcttttt gttcaggggg gccttattct ctggcccttc
    61981 tactttcact ggagccttat ccgatttctt ggtgccgaaa ccaaggatgg aaccctccac
    62041 aaccaaagcc aaagctaaaa ttaataccaa agtccaacgt aactgcttcg attgcatttc
    62101 aagagtttaa tgctatgaag ttctccgaag agtctttttt tcccagtttg atatgagtga
    62161 ttgacacata acactcggct ggcaatggat gtaatcgtac tgatcggaca cgaacaagtg
    62221 cttaatcgct ttatagcgtg atttctggac gcgattgcaa cccactaaaa atcccaatta
    62281 actgtcattc tcattatatg ctggttatct gataatccaa atattgcgat tgcgattgcg
    62341 acactcaagg ggacgccatc atggtcggcc tgactaatca ttttcaaaat ccactccgat
    62401 taggcgttat gcacacgtcc actaatccac taacgtttcc agctcactga tctgtggatt
    62461 tcattggggg agcgaaaagg aggttggtgc gtggaaagca gtttccagtt accaaccaac
    62521 taactaactg actgactggc tgactgacag tcagattcgg tctctatcct ccggatctgg
    62581 cttcaaagga gtgtgcgacg cctttgacgg cagtggattt ggattgccct ggccccgccc
    62641 cgcaccgcca cgcctagttc ttgatccggg gttccaagtg gcggggactt gtgagtgtgt
    62701 caggcccgac tataatctga catttaatta ataataaagt tgacagtttg ttttgagtga
    62761 ctgtgacagt tttaattgag atttgttctc caaataccct gcacggttcg cagtaaagct
    62821 tatgcgtttc cgcccgtgca gatgacagtc attttggata gttattaaac ataaaagatt
    62881 atttgctaca gcttatttaa agttggtgac atgggaagat tggaaactaa tgtatgttct
    62941 gaatagagct tatcagcagc cattttattt gtagattaaa aaagttttat attcaccacg
    63001 aaagccctaa acatctgagt agatatagaa tagttgcagc gagctgactg attttcccca
    63061 gcgatctccc tcccactcaa tcttcatttt tagccacttg tagttggaca tcgacaaatg
    63121 accatcgcaa tctgcctttg atcttcaagt gcctcaatct tggccccttc ccgaaccact
    63181 aattactggg ttgtgcaggg cattcgaatg gacatgatat tcgaaacgag cggtgagagt
    63241 cagtgagtga atgagcaccc accagcgtca acgaggtgcc actcagaaaa gtccaaacca
    63301 cttaagtgcc ttgtgggctg agaggggggg aatttccagc caaaaaataa gaaagaaaac
    63361 aaaaaaaaaa aaaaaaacgc ataacgaaat ggtctttcgg cttttgtgag tgtagtcagg
    63421 tcgattgaga ggcgattagc gaacaaaaca gaagtggcat gttttgatga tgatcagccg
    63481 ggcacgtcgg attgccagca atcaaatctg aatggtgtgg gggtttctct tggtctacgg
    63541 gggagctccg taagctagac acgcgtaaaa acgctcccca gatgactttt caattgagtt
    63601 gttaagctgt ctgatgacgg ttgtcaagtt ccctccgttc gctccccatt tgccgctaca
    63661 ttcgctatat ggcaaatgct tgcgcgataa ttgagtttta tgattgacac gacaactttg
    63721 ctttttaaat tgacataaat ttcaatatgt cgcatacaaa agcgaggaac acaactgcga
    63781 gttaagcgaa ccgaaagcga tctatctccg cctgccccct ccaaattcac ccctgccact
    63841 gcccaccagt tctcaatatt ctgccagggc gataaattgt gcaataaatt tcaattactg
    63901 ttatttcgcc cggcaaagcg cccatagaat ccaaaccagc tctcgaccaa aaacccatat
    63961 aaactattta agtgaaccga aaaaaaatgc ggaaaaaatg attgtggaaa aggaaggcga
    64021 aacaagaaat atgcgacaca caaattgtga taaattttat gttaaagtgc atgaaattat
    64081 atggcgacac atttgggcac tcataaattt tatttaaaca atttacaatt gtcattcgag
    64141 aattgcttgt cgcaattgtt gttgcaatag cttttgttgt tgttctcgtt ggctttgcag
    64201 tcagcgagcg actggacagt gactttgttg ttgggctata gtttatgttg ttgcttatgt
    64261 gcggctttgg cctgcgaatt atttatgttt tattgtcagt tggaggttat tatattgcca
    64321 tattgaagca cgttagcgct ataaaaataa aaagccaatg atatgcacgt tttaagtggc
    64381 ttaaaaaaaa taatgctttt acgacggtaa gtgaaggttg ggctgacttc aatgcagacg
    64441 ttgattggat atttgtattg ggcacttttc aatgaggtac tgaaacgatc attacttata
    64501 atcaatttct accttattgt ttataacccc tttaaatata ctcttaatat ccttttaatt
    64561 tcggctttca attattcata tattaataac tttagtgcat ctgcaaactg tctaagaatg
    64621 acagctgggt aagcccgaca gcagttcatt cggttggtta aaccaaccaa aatggttggg
    64681 gaaaattgtt tgcatcccga gtgcgcacaa gtcatttgcc ttcgcctggc actcgtgatg
    64741 tgcgtttgat ttgccagctt aattaaccca gcgagttgct ccgaaacatt tccagtcgaa
    64801 aagcagcggc agccgcaagt caatcaagtg agaacatcaa agcaaatgtc gcctgcactt
    64861 tgcactgccg acaagatgaa ggcgaaccgc tgggaaagtt tcgtagaacc cgaattccgg
    64921 aggacttcac tcaaagttct cgccctcgtt cagtccaact gacagggcca gacattttgg
    64981 ccctgtccat ccactgcgca ccactgcgat ccacttcaga gcatcctgct gccagcagcc
    65041 aaaatccagc ttccaccagc caacattcag cattcagcat tcagtgccag tgacaactta
    65101 ctttggcatt tggctgtcaa catgctgtca gacatttaaa caataaatga ccaaacactt
    65161 ttcattatgt tgctctttgc ggtttcgcct gcaaaggaca ggaaaaccga ctttgacttt
    65221 ggctcgcaat tggaatccga gtttgaatcg gacgtcgatt caaagccccc cttttaaaac
    65281 tgactgattc gcacaaagaa tgttggccat tcatatgaaa atacttttca aattgatgct
    65341 gatgtgggtc aacttgtggg gcggtcagag ttcaacgttt ttactgctgt tactgtcata
    65401 aaaacgttgc caacatgcgc caagacccaa aaaagttata cggccggccg actgaatgtg
    65461 cttttggtcg gcgatacaaa tgcgaaccca tttcaaaaat gttgacaccc aacatagggc
    65521 aattaaattc atttttcatt catctgttac gtgtgtgctg cgctggacac agttggcagc
    65581 cttgttgaaa gtaattgaca tattgcgttg caaagtttga aaggtttttc tcttatggca
    65641 aacgcacacg cttttggccg gaattctgtg gactggtatg tgtgtcgaaa ggctggccag
    65701 aatcaggata tttctacttt ggtaaacgtt tttgccaact gtcaacatgg atcgattatg
    65761 gtggagactg gaaaatcata tttagaatat tagtttcgtt ttgaaattct tgagctagga
    65821 gtttttgtga atgcttaaaa tatcttcttt tgacccataa agcaaatatt atttttctgg
    65881 tagatttgtt gtttcttgaa taatttctca acatctttta tggactcttg aactttttag
    65941 caattatttc ccataaaata tcactcaccg cacccattaa tgcccacaat agattccaaa
    66001 tatccagtgc cagcgattta ttgccttacc ctcacaatct tcttgtcact tccagtgtca
    66061 gttggctatt aagtgcgttt cgaggccatt aatggactct aaacacgttg atggcattct
    66121 ttccttcaag acagaacatt cgaacaaatt gctctgcaca cattaggaag atttcgaatg
    66181 gctttctcct cggtccttgg acaccgctcc tccaccgctc tccacatgcc cacgcacctt
    66241 gggcactaag tcgcctccat cgtcgggcca taaatttcgt tttatttatg agcatttaat
    66301 ttttgtaaca ttaatttaaa cataactgcc aaaacataaa tttgcttccg tttcaactaa
    66361 ttatgtccgc cttcatccct ccggcaccct cgcttcgctt ttcgtggcaa tcgctcaagc
    66421 atgaaaattg ttgactgcac aaaaggcaac atcagaaaca cccccgcaca gtcgaaaacc
    66481 gcataaattt aaatgtatgc ccccggtcgg gatcccccaa gcacccctcc acacactctt
    66541 ttttccgttt agggactgtg cgagcgccac gttttatctt tccgttcgcg gggaaatggg
    66601 attatgggtc cacccatatg gaggggggca aggcggtggg gggggtggag ttctttaagt
    66661 gccgttacac atgcatcggc accgacatcg catgcatata aattttgatc tgttttgccg
    66721 gctgcccttt tgaactgcgt ccaaattagt tgctcatcca ggcaattaaa caaaatgggc
    66781 cttctgcagg gctggataaa atgcatgaga attccttcaa cttaacatac tagcttttgg
    66841 aaaataaaag gagccccaat tgaaattgta ttttttaaag attttcactg ttcctagact
    66901 actataaagt ggtctttaga tttatattga taacttatat gtcactgata ctctaattcg
    66961 ctagatagta aacataatct acataaatta aaagaagcaa attgtttttt aattattatt
    67021 agttttcata attttacttt aatgtttcat agaccaaaat ggtctcaact cctttcacgg
    67081 ttctacttgg ctgcttctgg tgccctggaa gccaaaaaca aaaaccgaat aaagaaatac
    67141 ggccagagac acggcacaaa cataataatc ataaatatat caggcagcta actttcggct
    67201 tggcataata aaatccaatt aaaaaccaaa gaaagcaaat gtttacgacc tgacacagtc
    67261 caagggggcg atggaccgca gaggggaacg gggtggccga aaagggctgt ctgtctgtcg
    67321 acggatacat tgagttatgt taatgggcgg cacaaaatat gtctgcgccc ccacaaagag
    67381 gggcccatgt cgaattggag agtgtttttt ggggtagcaa tttctatggg cagtgcagac
    67441 aaaaatattt tccggaaggg ttgaggcaat aatatttgaa atgatattgc caagatggat
    67501 atattttcat atacatattt gtttaaaaat actttgagtc ttggcaccct gaatttcagc
    67561 attgatttgg taaatatcaa gttaagagca ttcacaagaa gtttcccttg cgatcttcat
    67621 gtatcattta agacccttag cttatacact ctccccagtt ggacatagac aaaacggtag
    67681 tcaacaagcc ctggcagcaa cagcatccat tcgcaactaa caccacataa ttcacaggaa
    67741 atgacaaaca gctgagctcg agccatcagg gcaccctttc tcctgggggc tgctaagccc
    67801 caaaccccca aaatccctgc cccttggcaa gtgtcagcgt aaatcttgaa actcgccgag
    67861 cagaaagtgt tgcctttgtg gaaattgact tggccaaaac cagcagcaga ccagactcgg
    67921 acttgaagtg ggtgtgacga ggtgggccga gacggtggtg ctttgcactt tattatttat
    67981 gactgtcggg ttgagtacga attcatttta tttatgaagc aagtcagcca agcgaccagc
    68041 caaacagcca aaaaagaaag acaacccaaa acgaatggct aacggacaac tgtggtcgtt
    68101 gtggctttct cgactactga aaaacaaaaa gcaactcttt cattctacgc ccagatggga
    68161 aatggtttcg gttcacacag caatggttta tgtggcttac aaccttaacc attaatttca
    68221 tattgaaaat gctctgtttg agcagtaaaa tttccttcat ttcaaaattg acacattaca
    68281 tttaacgcct aaatttaaaa ttaacataag taaatatttt ttaatcgtac actaaatagg
    68341 ttacgattaa gtaatagctg cctttcacaa atgataaatc agattttttt tataccatcc
    68401 caagaaatgt tctatattta agtaaggacc aaaacttttt atttccactg tacttacagt
    68461 gaggactccc caaagaacgt aatcccatcc gcagttggct acacttgaac tgtggctcag
    68521 cgagacaatg aggccatccc ctttcctttt agttcctccc tcaatccacg actttggcca
    68581 cgttcgtagc aattttcgag tcggctaatt agctttgggt gtattgttta taaatttatg
    68641 acgcatgtta aatgggttta atttatttat ggcactttga ccgcccttac aagagccaag
    68701 tccaagacca tggccgagtc gagtgcttaa gctgtggcca attgaatttt cgtttgtgaa
    68761 ttatgtttat gagctgttct gttcagttct gttttggttg ggttgtggtt ctggttctag
    68821 ttgtggcgtg atgggctttc ctggttgggg gacactgctg aggcaatgtt ccacatattt
    68881 gtgcggttaa ttagagacgc ctcatggcgg ggcgccacca gagtaagcgc ccgacaagag
    68941 acccaattaa aacttcaagt tgtcagctat ccagctatca gcaccaccat cctcccccgg
    69001 cgggtcaaat ggctctatta tgcggattcg aagcgaaggt gggcggagaa atcaaccccg
    69061 attatgaaaa tgggaataca aaattctgat gactatcatt atgagtatgg tgattattca
    69121 aaatgtacaa aactctttaa tgtgctcgag ggataagaac gacttaattg aataattttg
    69181 gaaaatgcag ggtatcgggt atattaactt tgaagtagga ttacggattg ttatcaaatg
    69241 ttactttcgg ataagcattt gaggtcctgc ttcattttta tttagctgaa cattggctta
    69301 ctatatgaaa tgataatggt agggtgtaat aaatatcgaa atagtttaca ttatataggg
    69361 atgtttctct tagttattcc ttaaagttag ggtatttttc aagccgatct ctatacggcg
    69421 tggctactcc ttccgaagaa attcggttgt cgcacccagg cgccggggtc gaatgatcaa
    69481 tgggcgctaa ttagtgtgtc ctctgcttcg gaacctttac acatgcttgc tcgattgccg
    69541 catccactcc gctggacgcc tccatgctcc tgacccgggg ggttttcagt tacaagtgct
    69601 gattacggcc atgcctttcc ctagtattat gtatgtgttt tttgtttttc gggtttcccg
    69661 ctgcggccgc aggtcattta ttatgttgct gttgttgggc gagacttgaa tttcaatcat
    69721 gagctgttgt tgctgccgct gctgctgccg ttgggccttc gattagaaat tgcgataatg
    69781 tccgatggcg acaaagtttc cgaggcgccc agaaagaatg gccagttgga gaaccgactt
    69841 tcaccgccac atcccacatt ctacacaccc aatccccgat ccccattccc atatcccaca
    69901 tcctcgccca tcggcgcctg tctgcagttt gtcaatgcga cggcggccag agggcttatc
    69961 tgcacttggc tgccactaaa ttatgtttta tctgcatctg tgggtcatcg tgttactccc
    70021 atgcacaggg agtacattta gcgtatatgt acatatatct ccgacgctgt tgtggtcact
    70081 ttgatcgatg ggccccgagc gctaatgagc agcaattaat aaagccatgg actttgttga
    70141 ccgcaacaat attccagtat atttgtgcgg gcattcggga gaatagagac attccggggg
    70201 ggttggtggc caacccaatg gccagtgact tgtcggtgtc cagctgatta atgccacgcc
    70261 acgataatga ggttttgact tggactcggg ccttggctct ggtatatgtt ttaatgccca
    70321 tttgattgat gcccaaggcg aaggcaaaac cacttgaggc actgccaaaa actaagtttg
    70381 gcaaaagtat tttgtggaca actgagtggc aatagcttga gggttgatgg gttaattctt
    70441 gagaactcga aaagggttgg ccaactcaag ctgagataat tctatatcac aatttaaagt
    70501 cctcagctgt gtagatgggt gtgcatttaa catttaaatc catagaagtt ttgaataaat
    70561 gtttaaaagt gtaaaataaa taccggctgt tattaattaa cttgtcagct agatagacaa
    70621 aacccagcaa atagaacagc atgtttatat aaagtgtgtt gtggccagaa aaagttattt
    70681 tccggcacct gtcagacaaa cctttcaatg ccatttccct ttcgctgtca cgcttttctt
    70741 ttatttataa aacgcccagg gatagggcag ctgcaacgat taccacgaaa aaagcgaata
    70801 taaatatatt taagttatgt aaatgaaatg cgctttgcaa ttgctttttt ggccgaaccc
    70861 ctcccgcaac actgcgcaaa aatacatatt ttttggcgca gtagtttttg gagcgcgtgc
    70921 aaaaataatt tatgggggcc atcaacaatc cttagagctg aaatgataga tggcgtgcca
    70981 ggatgtctgc catccagcga gagtcggact aaaactgaaa ctgaaaccga aactgagtct
    71041 gtaactgagt tggtaaccga gagtcggggc caaagtcgaa ggcaagttaa cccaaaaagc
    71101 cgaaatacgc tgcgggcgca atatttctcg cactcactgt caccgaggga tatggaagtt
    71161 ggggccacgg gtccttcgac tggatggtgt cgagcacttt tcgaattgaa atgtcgtttt
    71221 ggctggcgct agaatttttc attgccaatt gctgccagca gtggcaactc ggggtgaaga
    71281 cgggctttgc caagagctgc catatttctc gagagcccgg cacaaatgtc acatcaatct
    71341 tgtgtccagc gttgcgtaag aagtaaagaa aatattcatt ttgttttttt tgcgccatgt
    71401 cccgcttctt tgccacccca aatgaaggag aaacatgaaa tcaagtcttc ccgctggctg
    71461 cttgcgaaaa tgattaatgg cctggcgtgt tgtgcgaatt ttatatgcaa gacggctagt
    71521 gcacaaaaag gccaagaagg gccagttggc cacgtctttt gattgaatga actgtcttat
    71581 ggcgtccgca agttgttcat aataaactat gaagagactg attgtattag gatattatat
    71641 ttaagttcat taaaaaaaga ccgcaatgat attaaatcta gcattactta gaaggttaat
    71701 tggttgtcca agttaactaa tgccttactt ttgaaccttt gtcttttagc aacttaagca
    71761 tttatcgtgt aaaataaaca ttctattaaa ttgattacac tttgtgttta aaattgaaat
    71821 ttagcgcacc ataacgcaat taaaccagca ccctcagcat aatttgccaa gtaacgttgc
    71881 cacacaagca caagttatca agtcatcaag tgaggttgat accacccccc tttgaggcca
    71941 ccgcatagtt gactacacca gccccctcta gaaagtctcc tcatctccta ctccagtgct
    72001 cacctcgaac atggccacag cgtcatttgc gctgcttaaa agttgattcg aaaagtttta
    72061 catcgcaacc aagtggggaa agtggcggaa aagtgggtga aaaggtggga aatttgcgag
    72121 acaggaagtg agagatgggg acgtggatcc ttgaacatgc cgccgtcgac gccttcgctt
    72181 ttcatcctgg cttctggctc ctggctcctg gctcgcacac acagacacac acttgcacgc
    72241 aattaggcat aatcacctac acacacaatt aaacaggaac ccgccaaaac accaactcac
    72301 acagatactc tcgcacacat gcatcctcgg ccgggttata acctgcttgc agcgccatcg
    72361 tcgccgtaca atttccgcaa gtcgtaaaag tcggtaattt ataccttttg ccccatatgc
    72421 tacggcatgg taatttgtta agtagagtta aaataattgc tcgtatttat aatttacaca
    72481 ttttgccttg gaaatttatc gtcgcgctga aagtgcgcta gtagatacag gtcccaaagg
    72541 ccccaaagga ggatcctgca ctccgaaaac acaactgtaa agtgtaggta aggggttttg
    72601 gggttttggg ctggtcggcc aagttgccaa catgcctccg ctatttttcg gtgtattttc
    72661 cacttttgcg ctgtgcgcaa atttatggcc acaagttgcc cctgctaaac tgaatgaatg
    72721 agtaagtgag cttctgctcc aggcgatgct gcagcagcac ctccctctgg caaagttgaa
    72781 agttttagcc gctattaatt tcccacacca cccccttttt tcggggtaaa gctgggctct
    72841 ctgtggggaa tatgaatttc acttgaagag atttaccgac cattcggggt ccagaatgaa
    72901 agaaaaacaa tttgatttca cttgataaac gctggacata ctaaagtatg gcattcatgt
    72961 actagtcgag tgtatttgtt tggttccaga ttctccattc acccaaaaac cttaatttta
    73021 aaattagtaa ccttaaaaca aaaaatttga attttcaact ttcagccatg ccctgaaaat
    73081 taacttgcca ttctagtatt atgacgaaaa atggtttagt accttccaaa aatagtatat
    73141 tgtggcataa tattcatata gtccttgcat aaatcgtgtg tttaagggca tggggaaata
    73201 ttaagagaca aagtaacatt ttatatgaac ccaaggcttg gtaacattca ttttccgtcc
    73261 aaattaccaa gtaactccat tttgcacgaa aatttcgaaa accataaaac attgtgaacg
    73321 ataaatttca ttttaatggc tggagaatgg ttggggcacg gcttttttcc ctctcagttg
    73381 cactcagtta cattgtgtgc ttgctggaaa cattttataa aacatttatt tgcttgattc
    73441 ctagcctcat ttccgccaga catttcgcac ccgcttcgag cgcaaagccc aaagcccgaa
    73501 gccccttttg gccccggtag aattctaccc caaattcagc agaaaagata tatattttgt
    73561 ctgcactccg cgctcttcct tttcgggcca taatgaggcc ataaaaaggg ttaaataaaa
    73621 tgtgcagcaa ttgctttgct aaagccaacg aggtctagtg taccccattc acctcgtttt
    73681 ccccccctgc cagccattag gttccgacca ctgacagcga aaatttgccc gattttcgcg
    73741 ccgttgctca agaattatcg acgtcttttt tatttggtcg tggaatgtca gaagaagagg
    73801 cgttggctct gggttggaaa agccggggga aaaagtgtgc agcgggtggg acgcagaaat
    73861 tacagcttgt agctacaaat tgcttccgtt gcaggcactt tggggctctt tagctgggag
    73921 gagggcagcc caaaatagac acatcaatga aatttattag tttgcatgtg caagtgcagc
    73981 tggcggtggt cgggattttc catttcccgc cggaccgagg tctaattcgc ttccttaacc
    74041 cctgcccccg cgaacggatg taaattgctg ctaatttgct ttgtacactg aaattaatgg
    74101 aatctcaaat gatagccagc ttgacggagt aatggtagac gtgataaatg ccatttagag
    74161 taacaattat tcataagtag gtaaaaagaa cattcaagtt tctactacta ctactattaa
    74221 atgctggatt aaagcaatac acatagtttt ccaacttaac tttcagaaaa tgtaaaaatt
    74281 ctttgataac agttgaaatt caaattttcc atttcatcca tccatcctaa aacgaacaca
    74341 ttcagatttc cttgaatttt gcagagttga agtctgttag gactttgatc ttgccgccct
    74401 cctttcacac atttatggct ttatgatgcg ccccatatgc acgacaaatg cagcgaaatg
    74461 aaacttgaat ttggcttccc gatccgccca ccaattcacg tgccccccac tttacctttt
    74521 ggccgccacg cctttacgat gcctcaaatg gtgtgataat taggtgaaca gacgtctgcc
    74581 aacgtgtgtc ggcgcaacat caaagagaac actgcgcccc acgaccgctg cctcctacca
    74641 cccccccgcc cacaatcgcc gagtagtatc cgcccctgta aaatgtgcga tgacgaattc
    74701 ccagaactgt ttgctatgtc agtttacaat tgttgggcat tccgcggaac tagatttcta
    74761 gattccgagt ccaatgtttg tctaggcgtc gacattttgg gtgtttatta tctgagaggt
    74821 tggttgttta tttattccaa ccaactgctt gggatacatg tgtactttgg gaccgggcaa
    74881 acaggagcta cgatgcaaca gaatgcaggt aggtaggtta ctagcacttt gctaaacatt
    74941 ttaaaaagcg tttcaacacg agtaaaagac ataaaatgaa tgctttgaaa cttactaaat
    75001 ttacgagaaa taaaaaaatg agtatggcta taacccattg tgtgccaaga tttgagctta
    75061 tgatttatgt actggacaat caagatcaac ccaattaacc atagaaacaa cagaggttaa
    75121 agcttgctgc agaccttgag gccgactggc caaaataata cccatgtgca acgtggactg
    75181 gcatgccata tttggtggct ctgcgtcttt ccacctgcaa aacggcagac aatgttgcag
    75241 gtcaaaacga ttcaagcgcc aacggattgg aaccgcggtg tcagcctaag ccactttgca
    75301 actcgtttgt tgcccctcga tgatccgtgg acatacgttg cggcaacgtt agccgcctcg
    75361 aatatatcta tctatatatc tgtatatatt tttgtatcta gcaggttgca tgcggccgcc
    75421 tgtcgctgat taatatcgcc atcgtcatcg ccactcgtgt ctgttccgca gataaggcgc
    75481 tgcctccaag acacagcccc tctagatcag tccgatggat atatctatat gtatatccac
    75541 gccacagcaa accggcatcg atgccacaaa tcattgccaa acatgatttc ttattatggc
    75601 cagcaaaggt gtcgctggaa ttcgtgtttg ccttccagct tagacttgtt atttctgatt
    75661 taaatgcttg taactttaat tataattaat tagccattta tatatgtgta cagcttgatt
    75721 tatccctcag gatgttagca gatagcaggt gaaacccttt tacgtagata ccatattata
    75781 atgctataca atacagcttg tttaactcgt ctggttaagc ccactcactt ttttgtcatt
    75841 tacttatggg acttcaatta atatttcgaa tggaaagtta atcaaattcg gatgatgcat
    75901 atcccagggc tatcagataa atagccatgc gctcaagtaa atatatcact ttcaatgata
    75961 atccaaacgt gaaagcttcc tgctgagatc cccgccatcc tcctgtccat ctatactata
    76021 tgtatggtat atatagtttt ccgtcgccca catggagtgg gcctccgctc attagctgct
    76081 gcattcggag atgctgaaca agccacttaa tttaaattta aatgtttact tctcgctatg
    76141 cgtgtgtgtt gcgtgttgtg tggggccgag tattttgtct gcgttgcttt tagtgtttct
    76201 acaccctcct caaccaatgt atcactcctt cagtacactg caaaaatata aagcatgtga
    76261 aattaatgtt ttaaattata atgctaacca ctctagcttt atatattaat tttacgaatt
    76321 tcttattgat acctaataac cataagtata acatctaaag ttactttacc aaagttagca
    76381 atacaatgtg tagagtgact gtagtgacag cttatgttct gttctaatat gcagtttaag
    76441 ttattttttt gaacagtgca tcatccgctc tgtgtcacga cagggcaaga tttattttcg
    76501 gtattccatg ggcgactaaa atgcgctgtc agcgcagcag ttgctgccat acgtcgccgt
    76561 cgcccggcta tggtcatgcc ttgggcttgg gccatataga tacattagct gatggtggtc
    76621 cggatccgga ccaaggggac ccacagagcg atcgttcccc ctcattgcac ttgacactcg
    76681 aaattgatgc gccactgcgc ccaagccggg ccacattaat taggcaaaat attgacacgc
    76741 tgacgtgtgg tgttgcctat tgattaacgc gtcttttcaa tgggatcggt tttattggat
    76801 tatttttagt gggattttgg ggggattggt ttggcttagt ttggatcttc acttgtggtt
    76861 ttttgtgtgt ggttggctat tgaaaaggcc tagtagatgg gcttcctctt cggtggcagg
    76921 tggctgggaa tcctcatgtt gttggcgttg tgagctggaa ttttctttgt cttcctgctg
    76981 ccgccgtgga aaggacgaag aacgcgtatg atcaactgca taaatgctcc ccagcgcgca
    77041 tgacctaggg tttagatgag gctttggatt aacctacatg ggactgctct tttcgtggtc
    77101 ttttgatgcc cttaccatag tcctggaaat tgcatttccc ctttgccatc ttggtgctga
    77161 aaacctctgc cttcttatcc actatctccg aactagtaac catattcgag agcagcgatt
    77221 tagatttctt aacccgcggt gtttcagcta cctcaggact atgttctggt accacattgc
    77281 atacctcaac gataccagag ttggtcttca atggaggacg atcctccgat ttcatgccat
    77341 ttgcgctggc gaaccgagca caactctccg tggacttctt gagcagaaac caggattgct
    77401 ggagaacatg accttcttcg atgagtttct cgtagccatt gagaatgcgg cgcacatcca
    77461 cgttgatcag ttcctcggga acctcgggaa gatcgccaaa ctcctgaaat caatacaaaa
    77521 agtaaataca taaaatagtt gcaaagaata tttcaaaatt ttgttgagct gcacttttta
    77581 gttgcaattg tatcaatcga ctgtcatatg aacacaacct ttaaagccct taatcgcttt
    77641 cagcattcca ataaaacatt tttgggttat atacaattta tttaaatatt aagtatttca
    77701 cgctgaaaga caatccaggt ctgaatccaa aaatgttcgt cagtataaat ccaatatatc
    77761 ctcatataaa aggtttgcaa tttttcaaat gacaaaagta acacttaaat gaactacttg
    77821 tcaattaaat tttgctatga acgtagtagt ttagggtaat aagattaagc aataattatt
    77881 gatggtaatg caaacccacc tgcgagttct tccgcagatc ttcaaagcgc tgaattagct
    77941 tcttgatatt aagactgctc ttggaaccct tggtgatccc ggcacccaca cccgctgtag
    78001 tattggttgt cacattttca tcgatcgaat cggttggtaa tgtctcggat tccgacccat
    78061 ccatactgga ggagctcatc ctgctgagta tcttggccgt ttgctccatg aaggacgcct
    78121 ggcgatcgcg tagctcctgc agtcgcatct tcagctcgtc gaggtatgcc agctggcggg
    78181 gtgtgggctg cctggttgcc attgtcaatt ttgctatccc acttttagat tctttcgaac
    78241 atgtgaatgg atccgaaaat gcttaagttt tcggtttttt tttttgggct atggatactt
    78301 gtgttgggct tgtcagacca attgtctcta aataagagtt tcagtgctta atactatgac
    78361 tgcaaagaga ctgactactc ggttaccggt tttatgacaa cgccaccata gtttgtaact
    78421 aagtatgctg tgcattggaa cccaaggaag taagctataa ccattcgaat tatttcttaa
    78481 gagcaaagac ccttttagcg atgtaactat tctatcatat acgtaatttg atgtaaagtg
    78541 gattagggta tttttagagt atcgcttggt cgtatttcat aagtttggct cgctctttgg
    78601 acatggccta ttactcgcta tttttatggg ccccaaattg agatatctcc tgcaattctg
    78661 gctgagctaa ctaagttgta actgcccgct gcctcacgaa accgatccct cccccaactt
    78721 tcattcgcct gtggttgaac aatggagcga tgtggcaagg acagtgggtg cggaggggca
    78781 actcctgata cacctatata tctctggttt agcgtcttgg ctggactcac ctttgcgatg
    78841 ctgcgggtgg ttggggctag tttggaattt cacggaggaa aacgtgccgc tgccatcggc
    78901 tgacgcctac aatgaagaaa agggggcgtg tcggccactc tgtgactccc agactgctgt
    78961 tgatttcccc cggaggtgga taccaacccc tccagcatcc tcctcccatg ccagagagtg
    79021 tgcaattgtt gttttcatat tttaatgcct ttttgagttg gtaggcgtgc cacgacacga
    79081 ttcttcttac cgataagctg ttatttttat gggcccccgc cgaatcggat cgacttgaag
    79141 tggagtcggt ggtgcagggt attgccgggt ggagccgggt ggtgctccgt ggtgtgcggt
    79201 gtgggctggc tgccgactta aagaagttaa aattattaca ccgcaattgt cttgatcgtt
    79261 gatttatgtg cgcttttgtt gtcggctctc ctggctcgcg gctatggttt ttcgcttttt
    79321 attacttttt tgaagttgcc agttggccaa caggcaaatt tgtgtggctg ttgatattta
    79381 ttgggcatgg tccgggcatt ggcatcaatt gtgtatgcaa catgggaagt tgattatgcc
    79441 tctcattagc caccgtattt tttccttgtg cacgaaatgg cgacaattcc attcccatgg
    79501 acatgaaagt ggcccatttg cagtttacta gcacatcggg tttggatagt aggtaattta
    79561 ttttgctagc atgtcttttc gattactaat agttattaaa attactaaaa tagttaagtt
    79621 aaaataatag atttattaaa gatcatattg atcttgacat ttttcttatt tgcgtggaag
    79681 ctaaaaacag aattttcaat gggatagcct tccatttcat ttcgaattag tcaatggctc
    79741 ttttcggcaa ctttaggcat tccctaattg agttcttgat tcggcgactc cacttcctcc
    79801 tcagcgtttt tcggtgaatg tctggccggt gtcataatct catcgcctcc tccggaccaa
    79861 gcccaaccca atgcgatccg atccgagtcc cattgtgcga ctccagcacg attaaagcca
    79921 accgcatttg cagccgcctt caattgcctg aaaacttaat gatttcatct ttcattgaat
    79981 tcaaatttgt ttccccatcg ggcccccacg atgtccgagt gcgatttgca gctgtgcagg
    80041 gagcacgacg ttcgatgttg gggcaccggc aaaatgtgct cgatgtttgg ggctgccgaa
    80101 tgtgggcgtg cccccatcat acgcccctgg agttattgtc gttgctgttc tgcactgttg
    80161 atagccaacg ccgcggactc ggttggccga gcctcgaaaa ataacgaatt tattatttat
    80221 ttcacctgac agccccagca acagactcta taaatttccc tagccaatcc actccggacc
    80281 ggaatcatat ttatggtccc atctgtatct ttctggcgat gcgcatatga aaacgaaatt
    80341 attgataagg catgcatagc tccatatgta catacatata tacgtatgcc ctttattgta
    80401 cagctctgat tgaaatacct ttcgtctggc aatgcaacag cttcatttgg acaaccaatg
    80461 agaaaagaaa atgaaaaaaa tcaaggagaa accgaaaggt ggaaatcagc tgcagcaaca
    80521 aagtttattg gcaacacaca aggaggtaag aataataaaa ccttaaccca atatcctgct
    80581 tatggtcata atttttatgc tgcttccagc gaagaaacca aaaaaaaaaa cagtgcagat
    80641 cgaccgcctg ggctcagcat atagcagttg gtccaggtcc aggtccaagt ccagggaact
    80701 ttccctccaa tcccaatcca caacgtgccg cgtatttcat tatgaattgc tcttaacgat
    80761 gttccatttt tcatgagcgc attcataaac ctttttctta ttttcgactt gaagcggatt
    80821 gttgtttgca tctcgccgtt gccgttggtg gaaaagagga gattctgtct ggcggtttgg
    80881 ctgccgccag cactcctcct ccgcttcggt tagcaagtga atgaataatt gcaccaaggt
    80941 gttgtaagga gagctctgct atccgcagtc ctattctgta cagtggttgt gatatacata
    81001 aaacaagtgc aaaactgtgt attaacactt gggagaaatt aaaactctca atcagattct
    81061 tttctataat tagttgttaa aaatccacta aagtttattt aaaatcaggt tctaaaaaca
    81121 aatagtaaat ataaagcatt gcttaaaatt taactcaata attttggaat caatctgttg
    81181 gacaatgatt accaaactcc ttttttatat ttatgatgga atttcatata tttcgttctt
    81241 taaaatgaat taatttttaa aaggcgaatg ctatctttat ttattaagaa aacctctgca
    81301 cttttttttc gaacattttt gattgacaat acgctgaaaa atattttaac tagctttggt
    81361 aaaagtaatt tttcaaatgc cagttagagg cccctaggga gacttcaagc ccttgcaatg
    81421 ccccctgttt ccgcttcctt cacttctttc cgttttggcg aaaaccaatt cccttttaca
    81481 attccgcggc tctgtggcct cttggtcttg ggctctgagc tgcactgaaa gaaatattta
    81541 tgtgtattta atttttccgc attaaaatcg gcaattttaa gaacacaatg aattcttctt
    81601 taaagttttg tgcagtcaag ttttatgcat ttcaggtaag attcaactta gttaaggaat
    81661 ttcttaagga cttactctaa attgtttgca gtgttaggaa gggtttccgc ggaccatatc
    81721 ggctcgggcc gctgtcaaag gcgcagcggg ccgtcgtaaa atcgcggcaa acacaattga
    81781 aaaacgaccg ggccgtggga gcgagatggg gctaggaggt gcaagtggga tgggaatatg
    81841 ggtgagtgaa ggagtgcggc ggcaaacact ccacacttgt cagcagcggc cttagtcgat
    81901 ccaagcccct ctgccagcct ctccgtgacg gcccagaatc tcgcttatgc ccacaaatca
    81961 taaattgccg ccttaaaatt tatcttcaat tttcgagacc ccatgtggtg cttagcgaat
    82021 ggtgttttga aatttattgc tgcatttgca ataaatattg tcagttgagt cgggccaaca
    82081 gtggaagcga gatgggggag tgctggttgg agcgggatgg ccataatggc ggcgtttgct
    82141 tgctttttgc atgattgccg ctgtaacgcc tttgcccgaa acccgcaagc ccctccttcc
    82201 ttttggccac actccgcctc tgaaaatccc cccattcagt tgtttcctcc tcgccgtccc
    82261 ccggattctt tattgttttc gtgcatatta atgcacgctg attgcgggcc atggttagct
    82321 gaaagagggg tcgttcagcc gcagggggaa tcccccgcgt ggcagttagc agctgccgta
    82381 ctgtgtcctt tccagccaaa aagacctccg ccaccccacc gatgattgtt aatttacagc
    82441 gcgagaaatt gattgccatt ttgttaagat agtatgtgcg aattgagaac tgtgtgtcca
    82501 ttctgtgggg aaatcttacg cagggatgtg ctcttcttta tttgctggtt aattgtggtt
    82561 tcttttatac caacataata tttatcgcct cggatcggga gtgggtctaa ttggagtagc
    82621 gccttaatga aatcatcaag acgagatgat gtgaggtttg gtagaatagc ataccaattt
    82681 tatttagtaa gataaaaatt aggtaacatg ttatttacct ataagttgtt tacctatatg
    82741 ttatttatac atatttatac atttattgtt tgctattctt gtaagccctg ttaccgtagg
    82801 agctcacata agctaagctc aaagtttgag gcattgttct gctcgatccg aatatcattg
    82861 gggctcaaat ttttagcacc aacgtcatag cagatacttt gggttttttt tctgcactct
    82921 tgctgagcct accgagcaca cagtaaatga aagtaagctc gaagagcttc gacgactcgt
    82981 tggacgtcag gcggcattgg cagacccatc aatcaattca cagagaaccc agacacggac
    83041 actcgaatcg taaaccccgt gaaactcgta actcgggcgc tgcctacaaa gtccgaaaga
    83101 atggaataac tttccctacc gcccctgcgc tttctgttgc cacaatttgt ttgcactgct
    83161 gtcaggcgtc gatgactctt cgtcttcctc tgactccttc cctttcggtt accttgtaaa
    83221 aaacggagcg ggacaacacg tacacagaga gaaattttag caactcaact atattgtgaa
    83281 gaattggaaa ggttaaatag gcctattttg gtaatattga acaagatttt gttagtggca
    83341 taaatatttt ttcaagccgg gtccttgaat tttgataaag agatatatac aaaaacgtag
    83401 ttctcagtgg catagcagtc aggccttgca caaaacccat cgattcgagc atgtgacacg
    83461 catcaggcag agctcatcaa tctcctgtcg gcccaaacaa aatatgcaat atgttcacat
    83521 tgcggtaggg agaaacctca acacgaaagg cgagcatcga taccacgggg ttcggttcgg
    83581 gtttgcgagg gagcggccaa agtgagatat aaaaacaaaa attagaactc tgccgaattc
    83641 cgaacccctt catgttactg cggcctaacc gcattcagta aatattgtac gggcgaaaca
    83701 aaacgaagga aaaaaattag agagtatgtg ttgacagcag tcatcaatca agtgacacaa
    83761 cttttgacat gtcaaatgaa cgagtgagcg cataaattac aatggcagca accatttata
    83821 cgaccccgaa agttacagac ccagtgagat agtgattgta ggcctccagt agccgacgaa
    83881 taggtaaaca tgccggcaat tggaaaaccg atttcatcag gagggatggg gctggttacg
    83941 gaaaggggaa tgggaagggg aagtgcggcg tgttaaatgt cattacactt atcgataaga
    84001 ttgataagtg taaacggttt tgcgtgtcgt tgcttcttct gagtcatctg ctgcacaaca
    84061 gaagcgccgc acttaatcac tccgcaactg actcccagac tcggataccc agattcccgt
    84121 actcacacct ctacgtaagc catcagttgc cagccagaca atctgtcaaa cagtcacgct
    84181 gacaggcatt tccacttaaa acaatgccaa acagcaacag ctgcggaaaa actcctcatt
    84241 tcactctcca cactacgctg taatttatcc gtattcgact tcgcgatgtg ggaaagtagt
    84301 tgagccggcg agaaattcaa gattgtgttt atcagccgaa gagtactcaa ctcgttagtt
    84361 tcgaattcat gccaattgag tttattacta cattacgagg agattatgta agagaattga
    84421 ataggtaatg tccacactgt ttttcccggc aaataaacaa taaataaagg ttccatttaa
    84481 catgtgcaag tttcatataa ttcattcctt taaacggttg caaatttata ttgcatcata
    84541 atccttaaaa cttgggcata tgctcatacc acccatcaaa aatataatgt aggcttatag
    84601 acttctttga tcaccgtttt acgaactctg caatctgttc tggataataa aatcaaaagt
    84661 tgccaacagt ttggagtttg cttttcactt ttcgcacagt ttccggcgtg acagatttta
    84721 cttttcgcta gcgagtgtga gcctctcgcc tgggtgtgcg gtgtgtgtgt ggtgtgagtg
    84781 tgcggtgtgt gcgccgctgg cagtgacaaa tcctttagcg ttatttgcgc atgtcgacac
    84841 tttgacaggc gccgacacat gcgagtcgct ccacgtacgc agtcgtccaa agcccctatc
    84901 atatttcttt gggtctcagt ggattctctt tgttgccatc gcttcctgtc tgcccagctt
    84961 gcggcaaagt ttttaataaa tttgcgtcgt tttcgttgtt tttcaatttt ttggttggtt
    85021 ttttgccggc ttgcgggtga acgaaatcca ccgaaaacat ttatttcaat tttcccccca
    85081 tgtcggacag gcagcgcaac atgagaaagg aaaatttctg ctgccacagt actttacaaa
    85141 tttgtttccg tctcaagcgc ggcgacaggc gaggagcgtt gacagctgtc agtggagctg
    85201 gctcttgagt tgaagccaaa aaatattgac agttatcgta cgtcacatgc aaatcaagtc
    85261 ggacgcggtg cagtcgtgcg atatgtttac cgttgcccgc tcaccaaatt ggaaaatgtt
    85321 tgtctttttc ggctctaaaa gttgatttaa ctagacagca atataccttt cagtacacag
    85381 ccacgaattt tacgcagcaa ggtggaaagt gtaataaaac tatttgcaag ctgatttaaa
    85441 atgattttcc attgcttagg tctaccatat accagttcta tcaacggtat ccaagcgtat
    85501 tcttaagtat ttctgaacta cgaagagtaa aaataaaact aaattcgaga aatttccgaa
    85561 aaattcaaag tttgccaaac aaaatgcagc gaaacgaaac gaattgaatt gtgaaaatcc
    85621 tttgcaatta agaactgtca acggtctttt gtagacacaa cattcttgga attgtttgca
    85681 aattccccaa cactcatttg atttacgatt cacttcgccg cgttgaaagt aatttggcgc
    85741 tcgattttct tttccgaatt tccctgccgc tcatgccatt ttgccttgac tgttcttcgc
    85801 ctggctgttt gttggctgtc tggggcctga catgttggca tctctttgta attgattagc
    85861 cagcggggtt attcactgac attgcatgtc gaatccaatg agaacagtct ccgttcctcg
    85921 ggggagatca cctcgagagt tttctgggcg tgagtctgct agtgattgat gggactgatc
    85981 gcaaaaatca attgatcaag caacactttt atgaactcga cgcggtcatg aatcatttag
    86041 aaatcaattt gcaactacgg ttgatgggta aaatatatag tagaagtgta acattgtatg
    86101 ctctataaga tcacataaat aacataatac ctccttgcct ataatcttaa tatctttgta
    86161 gaaacttgtc gaacaacttc ttcatggcaa gcccaagtaa cattctaaat tgttagattg
    86221 tatctggcaa ataagtaaat aagtgaacaa ttgccttgtt tgcattggaa ttatgtggag
    86281 gcttaccgtc atccgtttcc ttatcaccgc caatgttgat gttagattgt cgcattccgt
    86341 tcactaggtg atcgatggga ccataaagct gccaaagtgt aattccagta ggcgccttag
    86401 ttcagagtgt gcgactgcac ttaactatat acagtatcta taaatcccat gcggccatgt
    86461 ttatcttgcg gatatagtgg atggcagata agcggccggt aagccgagtg atttacggtg
    86521 ctttgcagcc cccatcaatc aaaaccggaa acgtcagatc gtcgccttaa attatgatcg
    86581 ctctctctca gtagaaaggc aaccctcttc cgatccttta tgcccccagc atcgattaat
    86641 aatacgccgc ttatcgagaa tgcaatttat aatacaaaat ggcagtcgaa agccgctcga
    86701 gaaaaaaggg atcataatta atatttaaag gatgcaggca cagtactgtg cccccggctc
    86761 cccatttcca gccccatctg gtgtgctctc ctgttgcttc atcggcgatt ccaatcagat
    86821 aacattagca cgtcacatca cacagcgtgc aaaaattatt attcattgaa tttgtgataa
    86881 atgtgacagg cccaacagca ctccgagggg tcttaacaat gccgacgagc cgatcaacca
    86941 accggcctgc ctgcatttcc agaccaatat ggccaatatg ggccaggacc ggaccgaacc
    87001 aggccgcatc gaagctgtca aaaatttgtt gcaaaaagat attatctgat atggattgaa
    87061 aggaccagag atgacgatga cggacccagt ctctgcctct gtgtgcgaat cagtggtggc
    87121 agtttggctt aaaacccatt acctgaaaat aatatatgat tataagtgtg attttaaatg
    87181 ttcaccgcag ctggactttt tttcaagttt attcggaggg gataatataa acgtttttga
    87241 tctctgaaga ctttactatt tttatggcat gtctttggca tcactggcca atgtatctgc
    87301 tccgggctca tcaataatga ggcgacgagg atgcggctcg tcggcaacgt tgctgatgat
    87361 ggcgatgacc atgatcgatg attgacctgt ttttgttgcg cccatcttta gagtgacgat
    87421 tgccggcgag tcttcttctg gccctgacca cacccattga caggcatctg caatgtgcaa
    87481 ttatttgcgg agaatcacaa cagcaggcgg agtagtactc aaatggaatt gccacattga
    87541 ttgatgtgct caataaattg cacgatgagc atcaactgtt tctgcagtct ggcgcttggt
    87601 atttggcatg tgataaggcc gatggaagct gacaacggag tcgagctgcg gagcatttaa
    87661 atgtccaata gatgtctgca caagagcatg aaaaatagtt gaaataagca aaggattttg
    87721 atggacagtt aggaaaaacc atttatcaat taatatacat ttgcacacca tgtctaagaa
    87781 actgattaag tatcattcaa ttatttattc tgtaaacgaa ctgctcaaaa aaatatactg
    87841 acatttcatt tgacacctta tggtcttgtg tttttcgcat atgcttcagg gatcggaatc
    87901 ttaatcccca gcggaatgcc tttcagcgta tgaatcattg gcaaggcccc acagtcttcg
    87961 gggaacattt taattatggt ttttaatttc acggcccata tggcgggctg tcaggtgatt
    88021 tcccctgaaa tatgcgcaga actcacatct atcaagaacg cctggttggt tggaggcact
    88081 gccgagcgaa gattgcgcac tgagcggtga aatatttcac tctatttctg ttttcgtctt
    88141 tcagaatgaa attaagtgtt aatctcattt gatttgtcat tttcacatga cgtgatttgg
    88201 cggccttcgc agctctggca atagaaacga tcgctctggc tcttgatgta tgggaaacaa
    88261 atgtttctct gacacattta tttgtttaat gagacgttga ataattagtt ggatatggca
    88321 caagctcaag aaaatacaac cgatacaaag gcgaaaacac aacttgcata gctgtggata
    88381 cctccatccc tacaactaca cccccgacgc acacacatca gttggcacag caatttataa
    88441 attatgattg acgactctgt gtgcggaatt gtgtgaccca tcgcagttag cccctaccca
    88501 gaccattatt ccccactttg aaactcggct ccaccatgtg agactcgtct gacatttttc
    88561 tatatagttt tttgccctgg cctcggtcat tatggctgac agcgcgcctt caaaatgatg
    88621 agtttagatt gatggccgca catcactcag cgagatggca gccacaccga gtgaagacgc
    88681 aactctgaac aggttgggcg aagtcaaaat accctatcaa aggactctga acaggtcctt
    88741 atatgacttt atctaaggaa gccagtgaag ccattcatat ttgccatata ttcggtaaag
    88801 tactagttta ttatagaaag agagccttta aaaatggttg ttaatgaatc tcaaaaatac
    88861 ataactatta aacttactca aacacactta ttaacgtctt tctaaagatg aacaaaaatg
    88921 gttgttaatg aatctcaaaa atacataact attattcaaa acttattcaa aaacacttat
    88981 taacgtctta ctaaagatga aacaagactt atttggatca gaaaatatac ataattatat
    89041 ttcatataaa ttaaaaatgt aaaaaacttt ttcttaatct cttcatataa aagtttcagc
    89101 acaatccgtt ttatccatgt tgccctctgg agacagagaa ttcaaatcca atacgactgc
    89161 aggctatctg tggtttttgg gcccaaatca ccatgctcca ctgcttcgcc tgttgacatg
    89221 tcactaattt cagaatcgct aagctgattt tgctgaaatc tgattttttg ctgtgaacca
    89281 gcccctggga tagttgctcc accccatctt cctttcgcaa ctccgacgat gattgatgtg
    89341 tttggcatat gaaaaaccga actgaaaaca aaaacccttt ttccgaaaca tattctatgt
    89401 cattttgtgt gccggaggag agcagagtag aaatgtatta atcatccgtg gcgaagccta
    89461 gcgagtcgag gtgataaatt aagtttgaag acgattggga aatgtctgtc gagtaattag
    89521 tgaactgagc tgggtctgga ttggattggg gtctctggtc gggtctttcc agatcccaaa
    89581 ggccggcgaa gccttggagg cggcggcggc ctaagagagc aataatgatg tgcctgacag
    89641 aagaaatgca agagaccgaa attaaatatg ataaaagacc cacacagtct gttggcataa
    89701 ttaagtatga catgcaaaag tatgaattat cactgaaatg tcaaagtgtc acagctgcca
    89761 tcaggcggcg atggagatgg agatggggaa tctggcggaa ggcataaata aaaccagaga
    89821 agagagtgca agaagccatg acaacgaacg ccgcgtgtgg gattaactga cttgaaaatt
    89881 tatgatatga aaaattactt tagctcggcg aacacacaca cacacgcaca cgcacactgc
    89941 atatagcata caaaactgca aactgaaaga tgcaaagtgg cgggcgagat acaaatacac
    90001 aaagagagat gtttattttg tattttattc atcgtcgtct cccattgagc atcagcagca
    90061 tcgcatcgca tcgagaaatt tgtggcccga acaaatttcc caaagtctgt gttgaaaaat
    90121 taatgtgcac aactgtcagt gcagtgacag agatgcgatg tgaatggggt tcatattcgg
    90181 atgcggatcg gatcggaact gaactgaact gaactgaact gagcggggcg tgagggttac
    90241 tgttgtgaaa gctcttgata aatgattttg aaatgtgaca aaatgcttac gagcgggatt
    90301 accggggacg agacgacgac ggcccaagga ttgtttgctc cgggttcgga aaaagagtta
    90361 tttgccagct gagggaccag caaagtttgt tttgtgccag cggaatcaga tgggattata
    90421 gagatttgct caaatgaagt tgtaacagaa gtgaatgctc agatgagtga agggaaggtg
    90481 cgagtcctga gctagacgaa tataagctgt acgcccatga aaatcaaata aaataggatt
    90541 tgttttgttg gcactcggaa caaatcaata ttgaattttt gcgattttag taaagattat
    90601 ttggagaata gaaaaggttt ctataagctg tataatatat aagtgtgcat tgtcattatt
    90661 taagattatt ttttaaatgt gtatgtgaca tttatagaac agaaactaaa gataataaaa
    90721 taatattttg actgaagatt atatggattt atatggccat ctcaataaat cactgccatg
    90781 ctatcttcaa tcgacgtgaa atggttttca ttctcgatat gcctgaccca tgcagttgtg
    90841 tcttatataa tggcctttca taagtcatac tacctttcct tttattttgg ccataaccca
    90901 tcaaggcatc aatcaggcgt tgtcgcgaca ttataaagac tcgaaaccta agacaccatc
    90961 agtttacctc tgcggctgac ccaaggaaat cgagctgcga cgcagacatc aacgatcacc
    91021 ggatcggtaa tcggtgatcg acgccttttg gcgttaccat gccatcgatc ttgttagctt
    91081 tgacgcatct gtaagtggcg gcgacacaag tcggaaagtg aaatgcaaaa gatcccccgc
    91141 cggatcgatg gatggatcgc atcgggccaa gacatcatca gtcaagtggc gcgactgcgt
    91201 ccgtggccgg gtcaattcgc gtgacagctc tcttgattta tgcgcagaca cttgagtaac
    91261 cctcgagata atcaccaaat tccccgccag ggcgcacact atttatcata taattaagcg
    91321 agtcgataat gttattacac tgtctataaa tcggacactg ccagatcgga gctgcgccga
    91381 tagattggtc ccataagtgt gtggcaggtg tcttagcggg tctcttttag aaagtgggaa
    91441 gtacttgggc aacatttgac acgacggtaa acatgcgggt ctaactaggc ttctgatcgg
    91501 aaaatacgac gccattcagt taattgaaaa cccatagcaa tatatttaag taccgtgtat
    91561 tacgaagatt tggggtttga aaaggttacc caaaaagtga aaacaaagtt aataacataa
    91621 ataattcaca aattttatgt aattcatgaa aatatttacg ataaacagta catcaaaatt
    91681 gagtaattaa aaaaaccgaa ctttacacat ttggttttca taacaccatt tcagtactga
    91741 gtatcgggta gtcgataggg gagaccttag gattcctttg ttcgggggcg attaagcgaa
    91801 agcgccactc cctaacctcc gagcagtgtc cactttccca tccagccagt ccatataaat
    91861 caattaattt aaactgtcag gcagctgtca aattgtgttg ctaccgggag cgtttttcgt
    91921 ttcgcttttg actcgctcga cttggccggg gttttgtttt actttgtttt gggttctcga
    91981 gttgcggggg aagccggcaa agagactttg ggtacggcga catgtcgaga tttactactg
    92041 agtgattgac gactttatgt gtcattaaat accgttagca gtcgcctttg tatgccgcac
    92101 actggaccgg actcattttt catgccacta cgcccgcgtt tagtgaaagt cgatgcgatt
    92161 tgtagcttcg gcacttgtgg ctgcacattt caattagaca tcacgccgcg ggggcggtaa
    92221 ttactcgccg acacaaatca gttaggagtg gatactaaag cttaatatgc ggtttaagga
    92281 aaatgcacat aggacaaaac aattccaata tttaataaag ttcacatttt aagcaccctt
    92341 ctaaggatca aatttaattc atttttggga acttaatttt gcatcgcatg tttcaaagtg
    92401 cattccctag caagttgaat ggccctacgc tcgttgacct tccacaattc cgcaacgtcg
    92461 ttggccagtg gatcatctgg gtttggagca ctcaacaggg cctggatcga aagaagaacg
    92521 gtacgaattt gcaaagcagg actccattta tccttcagga tgtccagaca aattcgaccc
    92581 acacggtcga tgtttggatg gaaaatcttt gtcaaaaatc gaacctttgg tgctttcata
    92641 ggatagtctt cgggtaaaaa taattccaat ttaaaatttc caccctcaaa aggggaatct
    92701 ttggggccag taacgaggac gtggaaataa cgcgcattac actcatcagg cgtggcacta
    92761 atcccgggaa ctgggtcctc cagaaggcgc tgtgtctcct tgatgattcg tggagtcagt
    92821 gcggccatcc tctgtctacc acttcttgtg aattgccttt gatccgtttc ctccaaaaaa
    92881 acgctgttaa atttgatgtg tttaagtaga ttttaagtag atttaatttg aataaaattt
    92941 ctgaattaca ctgtcggtta cttggttttt ctagcaagac tgcttgctac aactgatgca
    93001 taacctgtca ataaattaac ttagttgatt tgaatgccca agtcatctca ataagaccga
    93061 atcaaatgct caattcccat acatttgcaa ttatccttca gtgggcattg aaattgaaat
    93121 tgactagagg cacttgcccc tccataccgc tcccaccacc cacaacaata aaagcgaacc
    93181 gcatttccat cctgcaacgc ttgagggtcc ttctgaaatc ccgggtgaac tggcaatgtt
    93241 aactggcact caactagcag cttattagca aactttccca ttggattata tagttgaata
    93301 ttataataat cgagttaggt tcgtgtaagt ggatgctccg ccgcccctgc aatccgcata
    93361 cttttggggg catggttagc agtcagcttt catgcacaat ttccgttttc atggctccgg
    93421 gcatgaaaat aagcccacag tttatgagac gacgtggagg acgacgtctc atgttggtgt
    93481 aacaaaaagt gggcaacttt ttagagcgcc gaggaaatac tttgctaaat tgccagggca
    93541 gtggcagtgg cgccccacat ctcctccaac catcgaactt tgggcctgcc ctcgtggaat
    93601 ggctacaaaa accaataaca ggacgtaata cactcatgtg tgtgcgaatt ggggggattc
    93661 caacttttac aaatcgttag catttcgcac gtttattgag ttgtttttgt atgtaaattg
    93721 gttgcataac ttttgccatg gaaagtgtcg agtggccgga atggcaacac aaacgcaacc
    93781 taaccctttc agtgccctcg cactattcta cactggatta ttgtctgtag attttcagat
    93841 acgcaaacga acattccctg cccgtctgag tgtcctcgtg tgcataaact ttgattccac
    93901 tttgaatgcg ccagcgcatg ctaaacgcgt tggaatccct ggatggggta tttcgatata
    93961 ggagtaccct ggaaatattt aactctttta gccataaatt gtgacagatt caatgtacga
    94021 aatccaatca aaaatgctca caaatatttt aaaatataat ttcccatctg tataaaactt
    94081 attagggaat tatatttttt tttttaatct aaagaacatt gagttctctt aaatgacttt
    94141 tcatttaact tgaattttat taaggggaaa tgtatgtagc tcaacatacc ctcatcatcc
    94201 acgagtgcga agcataaaaa gtttaagcta tttgcgtatc tcgccaacga aggcttttcc
    94261 tagtgggaaa atgatgcggg gaaaggtcgc tctgtctgtg gttgtcggtt tggtttgcat
    94321 tggtttgctt cggtggtgca tatttgtcgt ttgcggtttt cagctgcaaa tattatagca
    94381 aattgaactg taaatagttt ttattgccct ttttgccaca gagccggagt caaacagggt
    94441 cgagtcgaga aaatgccggg atgaagtgca gcatagctct gatttttgtt ttccaactat
    94501 atcgggtctg gccagcccag gccacagttt gttggcagaa attccatttt gcagccaacc
    94561 caggatgggc cacaaaatga agttgtgtca caaagattaa ctcagagaaa taccgaagca
    94621 aacaattgac tggaagcgcg acatctctat aagcgaaaat atttgaaaaa aacgaaacac
    94681 tattattata ataatctata ataatctata gttaaaaaga aaattcgaaa ttaatcgttt
    94741 attagttgtt tcaatttgag tgttttctaa tgaaatttca ttgttttaat aatgaatata
    94801 aggcagcata aattcactta actcaagcac accccctaac gaattgccac ctttggacac
    94861 aagacccaat gaaatcaaac aacacaggcg acacccccac atcggatgat taatggctgg
    94921 caaattaata tgaaattccg tagccggcat cgtcatcctc gcagaacacg aaactaataa
    94981 tttgtgtgcc gtaatttgca tagatatatc attattatta tatttcttta taaatatttc
    95041 gtacacgcct cgcattttca ttaatcaatc ggtgtgcagg gtaggcggag gaaagacatg
    95101 acatgaaaaa tatgtttgcc agtcgatgga aaaattataa tttataaaaa ttttaagagc
    95161 actgcaacgt gcgccactcg cgccatcaat caaaaatctc ggtggacatt gcagacgaat
    95221 ggaaggtgta cagatggacg ggcgcctgtc tgggatccca gattacgacg gtagccatca
    95281 gaggctccgg accaatgacc gaccgtccat tcactttctt aataataaga gtcgaagtgt
    95341 gttaatacct tgagaataag tttttctact tcaaatcata ctcaattgtt gagatatttt
    95401 tcagacttgc agattgtaag ctttccgctg aatagtacca ttattataat aaaatcattc
    95461 ataaaatgta accaaaggct ttaaaaaata tttaattaaa aataaaataa acaatattca
    95521 agcattattg ttattataag aattttcatg attagacggg gtattcgaag ttcgtaaccc
    95581 aaaaccgctt ctattcttca gttataaatg attcaaatta tggaaccgac aatgagatga
    95641 agaccatgac gatgctgccc cgacttctga tgatgatgat gttcggttct cgctttttag
    95701 ctattgtctg cccgcctcgg cggatgttga aaaatgtgaa aattgtgaaa aattctacaa
    95761 caatccaaaa taacaaatgc cccagacgga aatgccggaa aaaagaagta tactatatta
    95821 gttttgttcc aggacgtgac aggccggtca ggcgtccagg ggcatcaatt tgttcgctct
    95881 caagcgagat taatgatgtt gcactctggg gcacaggggg catctaacat taaatgccag
    95941 ctaattaatg atcaaactgt tgcaagaagc gacacgcccc cagcagcata atgtgcccac
    96001 atttcgcacg attggagctg agaaccaagt gacacagtag tcactccata tggatgatga
    96061 ttgctctgct cggacgcact tcccatccgg ttttgtgtgt cccatgatta atgagcttat
    96121 tatgtacttt gccactcgct caatctctcc ttcactcggt tcagatcctg tggacaagtc
    96181 agaatctctt ttctttttgg cacaggcctc attattcttc attgttcatt tgacgtagtg
    96241 tgccagaaag atttattaca agcccactgg cccagggatg aaaaaggttt ccgattattt
    96301 tcaaaaggag tgggaaagtc actcaacaca ttagagtaac acattttatt atagcatggc
    96361 atatggctaa tagcaaggtt tcttattaat aatagcattc tgataatgta ttgagctacc
    96421 cattgctcaa cttacactgc aacctgtatt taattatttg cccaattggt tatatggatt
    96481 tctctctgat ttctgcaatt tacccactca acgcatcatt ccgaaccttc tgaattaaaa
    96541 tgtttatagg cccctgagct cgacaatttg ccgtatttct cagctaaggc agcggcaaca
    96601 ttgcagtggc aacaaaatca gcgaacgaac gcgctgacag ctgtcaacat gtcgtatgat
    96661 taatgttggc caaatgcggt tgcatttttg tgcgtttcgc gctgtaaatg aaatgataaa
    96721 ttgggtgtgc aaacattttt gcctcgttcg ccatccagtg gaccgatttg cagcttaata
    96781 acgaaatgaa aacagagcag gcagcgttga agcgagaagt ccctcaatta aattgccttt
    96841 caccagcaga atgccattca ggaaactttg ccacatatcc gttcgttcgt tccccacttg
    96901 gagttgcaca aacagatgat attcttgttg ttgttatagc tcttacggag ttgttgcagt
    96961 ggcacacctt tgttgacacc tttggccaac acaacctcaa cctcgggcgc tttcgtggcg
    97021 tgtgtgaagt ggcatgtcca catccgtttc gcctcgcgtt tgattgattg aaactgcagt
    97081 tgcaacttgc tggcaccaaa aggcgttgac agctcgcctc tggcagtcgt gtgaatcgag
    97141 gggaagtggg agtacacctt acaaagtgca caaatcaccg ctagtaatgt gcgacctttg
    97201 cactcgtgtc agttaaacgc gacttgggtg aaatcactgc aatcgaaatc aatgaaatgt
    97261 ctgaatagaa aatcgctagt tggaaaaatg atagatattg actcgtgctt tccgttcgta
    97321 gccattgata aaatagctaa tcatccacgt aaataaagat ggttataaaa agtcacgcta
    97381 gtttttattg tgaggataaa catatactat tgcactttta catttattcc aaggaaagga
    97441 tctacttttg ggtaaccaga aattgaaatt aaatattagg tattaggtat taaactaatc
    97501 atctgtctat ttcaggaaat atcgactatc tgatatccgt taccgataaa aattagtcaa
    97561 aaaatgaaaa tgatcaaaat atttttcaag ctgttttaat ttacattttt aaaatcttac
    97621 agacaagata tccgttcctc aatttttccg ctctctaatg caaattaccc acttgcatct
    97681 tcggatgcga aatccgtcca tcattcgaat ggcgctgcat ttggttacaa cttgagtcaa
    97741 tttcctgctg cgacttgaaa tgcacaacta ataaccagaa tgggccggga atttcgccta
    97801 gcaaggcaaa cattataaat gcacccataa atgcgtcata aaccaggcgg caacacggaa
    97861 tcaaggattg cggggtggcg ggatttcaag acgttgatgg cagcgtcgca aaatatgggc
    97921 aaaggctgca agcggcaaca acataataaa ttaattatat gcaacatcag caacagtgcc
    97981 tccccccacc atcccctttt taaccgtact cacttgagtg atgtgtggca taaagtcgtg
    98041 agcgtgagcg tctattagca gtcaacgttg acgacgtaca acagaaccgg caacgatccg
    98101 acccgcccct acagtcccac cgcccccttt tctgcttctt ctccttcgtg acaaggcgca
    98161 cacgagcgcg aacaaacaag gggcgtggca cgggggcaag ggcagggcag tgcagtgcag
    98221 atagtttagc atgtgtggca tctcgggaag gcgagccaag tcaagacaag tcaagacagg
    98281 agtagagtcg agttcagttg agttgcgttg ggttgggttg gattttgcgg gacttggggc
    98341 aagctaaggg gtaaaggaga tagggaacaa cagagccagt caaacgggca atccatccat
    98401 cagccgctgg cagacagcaa ttgcaagctg caagttgtgc tggctatgtg gcacgtttga
    98461 tgttgctgct ttaaccacac cgagccagtt attactgctg caaaactgct ccaatttgct
    98521 gggaatttac aaagcgaaag ggttttgaat tagtccttga aattatgtag aaattgataa
    98581 atgctgcatc ttatataagg cgtgaaaggc agttaaattc gtgtttttct tactattaat
    98641 tgcttttcaa ttgtttattt atttgcatta atttggtgta gtaaaatata ataatagatt
    98701 tatggtatta ggaattcatt aatttccaat ttttaaagta aatatcacat tttaatgcca
    98761 tgtttttaat ttttgtaaac aacttaattt gttcaaatgc ttcatatacc tcttgcctca
    98821 ctttgaaaga gtattcgttg ttcgtcttac gcaaagcaac gttgccttaa taattctcgc
    98881 attgttgctg caaagacgct gccacaaatg ttgctgatgt tgctgactgg ccaacttaag
    98941 gagacgctga ccgtagattg catcgggctt cgaggggatg ggagactgtt ctgattggaa
    99001 aatcaagtgt gtgcatcgga tggggagaac gcttgcagcc ggggcatgtt tgcctgcttt
    99061 taatggcccc aactgacaga gactgcagct ccgctaattg cgaatgcttg acgcatgttg
    99121 cagccactca tgggtagaca tggacgcagg gcttgttgcg tatcgtgagg gggggtgtgg
    99181 ggccatcggg ggcggtgtgg caggtctttt gcttagacag ctccacttcg ctgcgctcct
    99241 cactcaattc gtctcgagtc ctcgcggccc gaagcgcagc gtgattttta attagttttc
    99301 ttagaaatta aattgttaat ttgatcgacg cattttccgc actcgccggc tgcccctcaa
    99361 tcttaatctc cttcgccgag ctgctaagtg gcctgttgct ttgacttcat tatggtggtt
    99421 ggtgctggct gtttgctatt tgctgtttgc tgttcggttg tttgagctct ttgtctgctc
    99481 attaatgcca attctggcgc gccagagttg acgcctgcca ccatatcgcc atatcgccat
    99541 atcgcccctc ctggcccatc tgcccccctc ctttggtcac ggccatcatg caagacaagt
    99601 tgcactcgtg actgagtgcg cgagtgtcgg ttgtttatgg gtcttacggg gaacgagcta
    99661 ttcggaaatt gcggttgcga agggcaaacg ggggtaaagt ggtctagagt caaacatatt
    99721 ttgcagttaa gggaatgcaa cgtaagaaat tgctcgctga catgcgactt ggaaaaagta
    99781 atctaagaac ggattgatgg atgaatcgtt agtcagcatg aggatggtgg tactcaaatg
    99841 gcggaggact gagttatgat acggcagttg ccatctgtat aataaggttt ttgactagaa
    99901 gaagtaaata gtgagatatt aatatataaa gaaaatatac gaaatatatg tggtcacaat
    99961 tatgataagg aattcattct ttgcctaatt gtattaaatt ataattaaat tatcagtcat
   100021 ttgctccgaa aaaaattaga tcacaatttt tatagctgcg aaatgataaa aaaatgtgtt
   100081 aaacaaacta gtgggattga aaaggcttat cctttgttat tacatgcaaa gcgcggtcaa
   100141 agtttatacg gtgtcggaat agaccaaact agtttaccag taaccccgat tgcacacggg
   100201 cttccacccc gaaacatctc aactgattgt tgcccacgac caaacaactt tcgcctccaa
   100261 tcagtcagtc aatcaatcaa tcaatcagtc agcgctcaac tgacaatttg tagccccctc
   100321 ccccctgaag cgggtgccac cacctcggcg actcagtcac gccctttacg gtggtgcaac
   100381 gtctacgttc aggtggttgg ggttgcggtg catgtgcatg tgccactcac tggcaattaa
   100441 ggccgaaata aaataataca ccgaaaatgc caattaacct ttgaatgcca tgcatgacca
   100501 cgtagcccct gcactcgatg cacaggaatg ggctatgtgc tgcactgtgt gtgttcgggc
   100561 ggggggatga ggggcgaaag ataaaataat tacccagacg cataactcga aagtaaaata
   100621 taaatttaat ttatgcatgc acacaacgat ggacaagaaa aaggaccgac cgaaaagcac
   100681 ccggatccgt agccagtgca atttatctca cgcggatcgc agatatacac atccatccat
   100741 ccaaccatcc agccatcccc ccagatcccc attcggccca ccaatgcatc gcctgcattt
   100801 cgatggcgga gccctaaata ggaaataatt tatgatgcga cattttcatc agcaattcgt
   100861 taaaattcat gcatgcatgc atttttaagc agtcgtcgca gccccctcca aacaccactc
   100921 actccgccac agagccaccc cttttggtgt cgtatttata aatttattaa gccctaaaag
   100981 gaggggatca ctccttggcc ctgagttcgg cagacaaagc cgggcgacga caacacgaat
   101041 cgcatgtaaa attcttactt taatcgatgc aaatatgcag cagcagcagc agcagcggca
   101101 acaacaattg ctgatgacgc cgatggtggt gcatgctgca tgacaggcgg tgctgcagag
   101161 tggtaaggtg gtgcgctgca tgtgtgtgtg tcgccgggga ggcctgcagg cctgaaggga
   101221 aacagaaact cggccatcgc gataataaat caattttcac aataaacagt tgtgtgccct
   101281 ggcggcagac gaaggcgacg gttgactgta cagtgggacc tagaaaggag gaattacaaa
   101341 accataacat aagcggcttg taagcttaaa ttcgaatcct gagtcagaga aatccgttgg
   101401 tatctaaaaa catacttata aatcctttcg cacatattct tatagagttc attacgcaat
   101461 gataaatgat cagcattgac agtccaaaac tcatgttttt cagtaaaatg caatgaaatg
   101521 taaaaataac ttcaaaattt ccagtagcat gaaatttaat attaataaga ttttttccta
   101581 ttaccttaat tccactgtgc aactcggcca tatttggtgc gagcggcttg catatctcgc
   101641 accacttcat gtcttggcag cgacataata aattaactgc actgcaatta ttttcacatt
   101701 ttcgcaaagt gaataaaaat tataaaatta tgtggaagcg atgaaagggg cgttgagccc
   101761 tcaagggggc aggtcgatag cgtggccgcg aaagtgagag cttatgtaag ggattagctg
   101821 ggggccgagc atgtgactcc tgacccttgg ccttccccct ttcccagaca agcaccttga
   101881 gtgccggttt cccccagaaa aaccagtcca gtctgcagtt aatcaaaata tcaaattaac
   101941 tgtcgtgtct gtggcaaata aatcaaaata aaagccggtc ccaggcttcg agcccagctg
   102001 aactgaatcg ggctaaaaaa caccgccccc ttcgagaccc ccttagttct cctgccaccc
   102061 ggggcaacct cctcaatcaa gccaactgat gacgctcccc tatgaaaatt tcacatgcag
   102121 agactgcctg atgagtgagc tgaatttatt ataggccatg ttgatggcga tgtacgcgat
   102181 tttatgaatg agcagcgagg tgtgagatgc ggcagagggc aagggaccga attggcgaag
   102241 gggcgagttt ggtgtgtcgt caacgccttt ggcggtgatt attcaatgtc aaaacttaat
   102301 gtccccaaat tgcagttgtt gtcagcggtc agccgtgaaa ttgaatgcat gtcgcccgga
   102361 tgcagaaagc gggttcacaa gtgcccaatg cggcagctgt tgcatagttt taggcgtgac
   102421 acatgtcaac tcttgccacc ctcgatccct caatcttgcc attcggcgat tatcccccaa
   102481 acgcagccgg cgattcgagc aatccaaaaa aaaaaataat aaaatcgaaa ggttggcatt
   102541 cggtagtgaa tgctgaaata ccctcttaag tcgattattt attcttaatt taaattaaat
   102601 tgattttttt ctttagccca tgtgtttagt ttgtttgatt gataagttgt gttaactaat
   102661 acaattaaca aaatattttc tgcacctaaa ccgctcatta aaattcaagc taaaggtgtg
   102721 caactcacag acagggtata aaattcccca atccatggcc agccaaactc aacccgaacg
   102781 ccactcgagt tcaactcatt tggcagcagc tgccatgggg catgtccagt tgcaaggagg
   102841 gattgggagt aatgatcggg aagggggcga gtccgagttg ggagaagctt gttaccataa
   102901 aattggtgta aacgaattgc agtcatcgtc atcgtcgtcg ccgacggtct gtcggcattg
   102961 caaaagtcca aatcgctcgt ggagcggggg gtgcgtcatt gtgaaatgtc tgtaatttgg
   103021 acaatttgat gaatggttat ttgccacgag atggcaaagt ggtcattatt ctttatctcc
   103081 ttcgctcgtt cctttttctc cactctgctg cattttttcg gttacatttt tttcgttcaa
   103141 cgtttactaa ctttttcatt gcacatttgg tgcagctttt tagcattttt tggtcacctc
   103201 tgcagcagca gaactaagtg tattgttgtt cagaggatat cattagttgg ttattaagta
   103261 gccggacagt aatctttgtt aacgaagata tcacgttttg aagtaaccag cttggaatct
   103321 gctatttaga ggaaagtatt tcaaaaatta atgcattagg ctattggttt ttgataagct
   103381 atgcattttt aatgaatttt taaaacaatt ttattgataa ggaacttatt tctaaaaatg
   103441 ggtatcttcg aaacttatta tagcaagcaa acctgacatt taaagcatac caatccaatt
   103501 aggaattatt aataattata ttgaattata tttttaatcc aattaaaaac tttttgaaac
   103561 tggaaattgt ttcttacagg gtatttaaag cgctaggcac ataagctcag ttgcccatgt
   103621 tccgtgcttt gttttaacaa agccgtttca tggaggaata aatggcaatt gctttgcctg
   103681 ctgctcgttt cataattcaa taaattcata aggcgttcac ctggctgctt ggaagcggta
   103741 atattgtcat tagcctcttt tccccacagt taataggctt ttgggtggct atgatcgctg
   103801 ggtggagacg gattcgtgac ctgttatcat ttggccagcc gatcgcagtc cacattttgg
   103861 tcggttggtc gttttgtttg gcctggtctg ctgatgtgct gtgtgtgcgg tcgcggtcag
   103921 ctgaaagcca tctgtttggc caccctcttt agccacaaac cagcaacgct cctgccacgc
   103981 ccccaccccg agaacgccct tgggctggcc agaatgcgtt ccacatggcg gcaggcctaa
   104041 ttacatttct cggcaaatgg caaatggaga atggcgtgat tgcacacgca aatgcgctcc
   104101 gttgtttata tgcgtagcaa atagatttat gcgctcgtat tttacacggt taattcctta
   104161 aggcaaagcc cccacagttg gagcggaaga agcaactgag gcacttgctg cattgcactg
   104221 aaaagaaaat acagtataat aaaaataagt ttcttgaatt ggtattttgt ttatattgta
   104281 ttttcttagc accgctaaaa cataagttta aataagcatg tttcggacaa ttcaaatcta
   104341 gaaccatgtt gagctctgca ttacttcact tatgaaatgt caaattttct ttcagtgccc
   104401 taaccccttc ccagtgtctg gacacttccc actgttcatc tgaatggata tgccatttcc
   104461 tgcctattgc tctgggcctt ttgcacatag ggtccctctc ttttggtctg ggaagtacgc
   104521 taagcatgcg accaacgacc cactcgtgca agtacttaaa ttaccaaatg ggttatgccc
   104581 tcgcaaatat tccagaaatg tctaagaaaa tacaaggggc taaacggacc aacatttaag
   104641 gcaaactgca ttggaattga gtctgcgcag gcagatatat aaaaaatact tgtgacttac
   104701 agttttgtgg caatgataac tctagtaaat atatatgtct ttctctaaat aaacaataaa
   104761 ataatttctt ggcacatatg aaatgttgag ttttggcggt accttaaaat tcaggcccca
   104821 aattcaacgc ccccttgaat gtcgctggca cttggtatgc tatttaattt tccggactgt
   104881 tcattaatca aatgttgcca tatttgcatt ggctcagctt catccatttg gcccctgccc
   104941 cttcggatcg ctcaccaact tggtatgcga atgcccgggt tttataaatg ggatatgaaa
   105001 tggcctaggc atctttccca gccaccacat cccgattccc ctaggtcgct taatttattt
   105061 gtaaatatta acacataaat ttttcagaac gaacgtttcg cgatgttgtt ctggggattt
   105121 gtgtgcagct ccggggcatt tatcaatatt ttattggccc cataagctta ttaattgtcc
   105181 gggttacctt tttgtggggg atttaattag ccgacagtgg cattgtaatt gcattgccaa
   105241 tgctggagca atccattcga ttcatcacca tgaaggtatt ggaccaaaaa ctccccatat
   105301 gcaaagattc gtgtggcgcg tcacttgtgc gcatggtaac actgaccaca aacgaactgc
   105361 aaggacactg atgacgggta atggaataaa atggaatgaa tcggatggag atgggcgaac
   105421 ggaacgaact ggcggctgct cctgacaagt gcacacgaat gagtttcatg agttgcactc
   105481 ctccggacgt actccgggaa tcggggacgt ggagaatact ctgacctcca ttaaaaggta
   105541 taatacgcac aatggcatat taatatgtga atgcagaagt aatcccgaca taaggttgat
   105601 caacttaact tttgttttat atatgaatat tatattttgt aaaaattgtt attttttatt
   105661 cttttttatt ctttttattc ttcaagtcta ttttattgtt atagtttgtg ttatgaatga
   105721 aataatagca aatctgccat ggaggtctac tatccccagc tatgttagtg tatccaggaa
   105781 ttcctcttcc ggcttgactg agtgacagct gcttgccagt cggacattac gtgtggctga
   105841 agctaaccgt actcgtactc ccagtccaga tggctcctcc gcctgcctgg acacatgaag
   105901 atgacatgag tctgcccgcc cctggctgta aactctgatg atggcctctc ctggcaggca
   105961 actcatgctg aaaaatcctg ttgacgagga taaaatgcaa aaacaagccg agtcgagtcg
   106021 agtcgagtag tgtcgagtcg aggaagaggc ggagctaagt gaagtgtaga cacagtgtcg
   106081 ggctttgcat cctgggacgg gacttggctt gggataagtt tattgttgta tgtgccacac
   106141 gaattgtttt ctggtcaaat ctgtcactcg gcctgtccaa ctgtcacagt ctaaaacgaa
   106201 taggaagagt aggagttggg gaaagaaaag accatgacat ggaccctagt accaggacca
   106261 gctagactcc aatcccccat tgcaggattc agattctaga gattgatgat ggcattgcgt
   106321 tgattgtgga aaatgtgtga taacctaatg gcaggggaaa ttgtaaataa aattttcacc
   106381 tgatgaataa aaactgggtt tagaacatgg agaaaaaggt aaactaatct caatctcatt
   106441 ctgaaaggat agtaagttaa gcccactcga taacgacgag gcctacctga tttgaagtct
   106501 accgaacaga ttgcgctgag aaaataagca cccgcggctt ttgcctatgg ccgattacac
   106561 acaaagacct tccgccgacg gctgtctgga atcgatagcc gatttacccg acttcctggg
   106621 ggggcaccat gctgatttca atttctcgca gcgcaacatg aaacgctaca aaataataat
   106681 gatgacgatt ggcccggtcc gggcattact ttacagtcaa gtatctcggt gccttgcgca
   106741 tttcttgact tctcaatgat agagcccggc actcgtcggc ttcctttctt tcggcaattt
   106801 ctttattatt gctcagtgga ttttcgttcg ttttcgaatt cgacgatcca tcgaagcgac
   106861 cgcatgtggt cacaactccc ggacgaaaag aaattaatgg gcttgggata gaaaccgttc
   106921 gttcgattca ttcatgaaac cctcgactaa ttcaagctga aatgtgtgaa caacaatgga
   106981 ggaaggcaac aggcaaccag gcaaccaggc agcctcacag cctcttctgt tgattaatgt
   107041 atgaacgcac atcggtagtc ggttcgtccc catcctctcc agaaatccag tagccacgct
   107101 gctctgtcga tcggactgag tgtcattaag gttgactgga gcgcagctgg aaccgcctac
   107161 ggattcgatt ccggactcct aactagaact cgggcgcgga gaaaatgtca aatcgctttt
   107221 ggcgcaaaat gcgatttggt gcaactcaat acaggcccag tttgccggcc aagtgagttc
   107281 atttgagcga tcatgcatca tgcatgatga tgatcgaaaa tgggaacgaa atggtacgga
   107341 tgcgggtacg agatcgggat cggaatcggc ttcggttact ggggatcatg agcactgaat
   107401 ctcctctgct gacggggcgt aaataaatcc aatttgttgc gcgcgtgagc gttgactgtt
   107461 tttctcggtt atttttatta ttttcttctc cagatcggtc gttgtgcctc ttcctcaagt
   107521 tggccatcca tctgtgaacg tataatgtct tggctttccg gttgccacaa catgtcaatc
   107581 atgctccgtg gcatatcaaa cgcatttccc attgttcgga ttgatatttt cttgttgact
   107641 tcgttttttt atgccataat atattgtgat cggttcgttt tgcagctttg gctgatgatt
   107701 ttataatggg atttgtgttc atgctggccg gttagatgat caggtcgatg acgaggcacg
   107761 gtgcggatga gttatggccg caaagtgtga cgaaactgtc ttgattggaa gtaattgtat
   107821 attaagttta aggagaaaaa cgtatttcta aagatcatta gttaaccaat gtactctcgt
   107881 ctttcacaca cttataaaaa gtaaacacct aatgttattg aaaataaagt gtattgtata
   107941 tatggaaaac tattaggatt tcttgatgca gatgctgaaa ctaagttaat tgtaaataat
   108001 acttcatttt tcgaaagaaa tacagcatgt ggaaagatat atagaaaatc ataaatcgaa
   108061 agccccttta caagcaatct ctaatgagaa tataccaaac caagaaataa acaatagaat
   108121 aaatacggca tttcagatca taaataaccg aacatgtaag aaatggtaga gaatgccttc
   108181 gcataatagc aaagttttcg ttaaacgatt gcgggtatgg ggagcgaata aacgcaatgg
   108241 gaaaaatccg tacccagccc aatcccctcg agaaccactt gttttatggc cagcaatatt
   108301 tttgcatgct gaggcagagg aaaagggtgg gaaaacaccg ccgccgcctg agagcgacaa
   108361 aaagacgtta atcacgttga gttatgtgac attcttatat ctctgcgcca ccaaagtgtc
   108421 acgtacgcat ttgttccaag ccaaccgctt cggcggcgtg tgtgggtggg tggttcagtg
   108481 gtttggtggt tcggtggttc agtgggtagc tgttgctttt tctgctcctg ctgctgctgt
   108541 cagtttgcca ttgttatttg ctgcaatttt gcagttttct tttgcctgct cgccgtctcg
   108601 tttcttttca gccagttcgt ttgggatttt atcgccagga tagcgaacag aaactgaact
   108661 gaacttcact actggcagtt gcttcttctt cttcttctgc agcatatgcc acacactcca
   108721 cagaaaaatg gggtttttat tttccgctcc ttaccctttc tttcatgtcg aaattttctg
   108781 tgattttttc cacacactcg tgttacaaaa cacaacacga gacaaaaggg atttttctta
   108841 tttcgcctcc gtcacgtgag tgtgtgtgtt agtttgtttg ctgagttttg ccgtatttgt
   108901 ttgtttgtca tttcctttgt tctttccctg ctctctgcca ttgtcaacac tctctcctct
   108961 tgtttgcggc tgttttgggt gcaaattgca cttttgttgg aacaaatgcg atggaaacaa
   109021 tgccaccatt gagaggaaac gaaagataga cataggcaga gaggttgggg tctaaaactc
   109081 cttttcattt cgcttaactt ttcacttttt caactcattt caagccatgg aactttaccc
   109141 ctttacccct ttaccactca ttccacagaa tccactggtc ttgtctgatt gtctgcctgc
   109201 cgttgacagt ttgacttatg cgacatatgc aatctggaaa ttactctttg agttggttct
   109261 cccggtaaat gacagttttc cacagatggg ttagattcct ataggaaaca ataaattcta
   109321 aacaataatt ctatatacta ttttgagtta tgtttactat gacgacctac ataatcataa
   109381 gtgaaagtaa atgcattaaa ttaaagtaaa tgcattaatt tatttataag ttataactat
   109441 tatacatatg gatattatga attaacacac gttataaatt cttccgtccc acgaattaaa
   109501 ttccaatcat cgttaatttc cccgtttttc cgcgtcaaag cgtgccgcct atggacgctt
   109561 ttcatatttt ggtaattttg acaaatcgtt tctcatcagc ggcagaaagc gaattgtccc
   109621 aaatggttta gaaaaatgcc cgaggcgcat gaagtaaatt aattacgcct ttcaatcatt
   109681 ttgaaatgta tctttttcct ggtccaaatt gggcgcatca tttgtcagaa ggcaatccgc
   109741 ccccaccccc tcctaattcg gtatccccaa aacatttgcg tgttcatgtc agttggcccg
   109801 gtcgaaatgc gtcgatggcg tcgaaaaaca aaatggtagg aggagtgcct tcaagggagt
   109861 gagttaatcg aaacccatca actcgacggc ggcagaagca ataatcaaaa gctgtaatta
   109921 tgtattattt attttttatt tattgtgcat tactcacggc gagaatcggt accgatatga
   109981 gggaagccga tcgccagctg atttattgtt gataaattta tgaaaaaaat ttccttaccg
   110041 acccttttct ggccagaact tgcgtccgcc agagcgtccc ggcaggctga aactcatcaa
   110101 tatcattaat cataaaatta agtatcattt atattaattt attattgtgc cacagaaatt
   110161 tcaacagagc attcgttgcc attctcggca ccaccgctgg ctccactgat ttatcatata
   110221 atgctcatta tcgtcctcat atttatcatg atgatgttgt gctcattttc gtcagtctca
   110281 cgtctcgctc tggccggcta ctctgtctct gtctcattcg ctggccatca ttaatcagct
   110341 tccaatcccc cctctcgctc gctcgtcatt agccctctct ctcgctcctt tcgtgcccag
   110401 ctcgaagcgg tgtaattaat tatggtcttt tgtattccgc cgacaatttt cagtgcttta
   110461 tggctctcct ctcttctggg cttatgaaat attgtgtata aattggaagc acttaatcat
   110521 ttcgatttac attttaatta aaatattata tatcaaaaac gggtccccga tgatcggatg
   110581 ccggttgccg gccaccaggg ggcgcttaac ccaaaacatg tgtcgatggg taatgccgca
   110641 aagtgtctgg cttttgccgg gattccccat tataaagtaa tttgtaagtt ttataaacag
   110701 gcaaagagag tcaattaaat aacccaaact atgaattcaa ttcccgcaaa cacgttacat
   110761 ccggtgagct cctgttggaa ggacatttta atctacaaca ttgggtgtca aagggcattc
   110821 caatggaaaa taataatgga acaaaaaggg gactcaaagg caggccaaga gtcagacagg
   110881 agtcattgcc gaacaaacaa tgaatggcat gaaaggaccg actctaagcc agaacaggag
   110941 ccaatctaac gactagctaa aaaattaaaa cgaaatgcta tggccaagcg aacacgaatc
   111001 gaagaggcaa aacgtctgcg actccttggc caattcacaa tttaacaaac taataaatat
   111061 tttgctttcg ccttccggcg ctacaggctc tgagcaatgt gctcgctcca aaggacatgg
   111121 attccagtgc ctggaaaaat ggagcaattt ctttggcatc tccaaagtgc tgggtaccca
   111181 ggggcgggga gaaagcactt gggagaatgg taaggagggg caaagcagaa atatataaat
   111241 caaaggttgc actaaacttt agcctgctcg atgtcgttgc caggataaca acaagaacga
   111301 tgagtattgc tggtgaaatg catctagcga tggcaacgtg agtcgtgcag acgaagtaaa
   111361 ataatgtgat ggccctgtta aaatataatt caaactcaaa agcatggaaa gtatcgcgca
   111421 ctaatcaaat atatcgtgca gatcgattga gatcaagtcg gatattttaa tgaaactaca
   111481 agtggtatta aattatttat ttatttttat taatttaaaa gaaaattcac gtaactattt
   111541 ttaatgaaat atcaaaaaag ttgtaatatt caagatttac taagtcactt aataataaag
   111601 tcaatttaat tttttatttt tcggtgctca aaatgtgttt cgtggcacgt tgacatcacc
   111661 aatgggatca gcactgcgga agcctttggc tgcttgataa cttgataggt gctggctgca
   111721 ttgttggtgc caccgttgtt gttatttctc ttgttgttgt tgtgctgctg ccaacaagga
   111781 cacttcggtg ttggcctcaa gaaggagcaa cgcgacggag ggaggggaca ggattgcgac
   111841 tggggctccg ggatccgcac atggcttgca actgccaggc tgtcggatat gcactgacat
   111901 aaattgcttc aactgacaac gccagcggac aagaggagcg tgggggcgag acctgcagga
   111961 tggatactgc cgtgcccagg accttgcccc atgattactg cctctgtctc tgtctcggtc
   112021 tcggcgctgg caataacttt tctgtgtccg gggccccgtc tgctgctttg gggtaaaatt
   112081 aatattaaaa tggaagcatc gccttcgccc aatgtccgac gcattgcaat gccagcaagg
   112141 acccacgatt ggaggtacac actctaaaaa agatactttc caattttttt accaaagttt
   112201 tcgaccatta aatcgctggt taagttttaa ccgaaaagtt gtattttaac ttgatcttta
   112261 atttaatatt attaactgaa attattaaac aggttttcca ttcttcaaga aaaagattct
   112321 cgaagtattt tttagaacac catatcgttt tacgactggt acatttttaa aattaatcct
   112381 tggagtgaat acagttatcc ttattctcag tgcaccttcg aactcccctc ttcgtagctg
   112441 atgggggcac tgccagggca aaggacattt ccaatttatt tacgctcaga ggcactttgt
   112501 ctgctccgct cttcttggcc aaactcctct gatgctcctt gttcggactg ctctctgctc
   112561 ctcgttcact actttctctt ggtcctttcc cgctgtatat gacagtattt gtgtagcttg
   112621 tcagggagaa acagattggt agaaaggggg gatcagaggt cgaatctctt tgcctctttg
   112681 ctggtctgcc ttttattttt gacagcaaaa tgttccttct ggtcgtgtta gcgtgaaaag
   112741 tgttgaaagg tgtgaaaatg aaaatttact acttggccgt caagatttat gctgcccaat
   112801 attttcgttt tcccttcaaa atgggggcac gacggaaata gaaactttta aaccattaga
   112861 agcggagaaa ggatgacatc ataatttgta catcaccttt acaaaataat ctaattggaa
   112921 tatagccttc ataaatatcg tcttctagag ggtgattaca tacatttcga tctgtgtcct
   112981 actcgtctat gttcacttat aaccactcac agtattatga aacgcaatta gttatatttt
   113041 tataagacac ccaaccatgt cattatgctc ttcatcgtag tatatatata tatgatttta
   113101 tatatatttt atgatatata tgtatttttt ccaattatta attcccatgc tgcaacgcct
   113161 ctaatatcaa tttccgcttg tactggggat ccattgggaa tgttctcccc tgattgtctt
   113221 atcgattgcc gacaacctga tccaatactt cactcccgtc tgtcactcgc actgtcgtcg
   113281 attggcatcc cgacttgaca tatcccacag cagcagcaac aaatcttgtg tcaagcatcc
   113341 cgacacgcac ttgataaatt attatctgca gtccgggtga tgaaaggcaa tgaagttagt
   113401 ggaggagaat gggcgaaaag ccaccacaga gttcgcatcg gtgccctcag tgccctgcac
   113461 tttgcacttt ggctcaattt atatttaaaa gacagggggt atttgcagtg cgatctaaag
   113521 gattgcaatg cagagaaaaa aagcggaagg tcggaaattg gaactgacac cagttaattc
   113581 agccatgttt ctccatctct caataattat ctctcaaatt gaagatgacc gattagttaa
   113641 tacttttata tctgttttta aaaatcaata agcaaaaaca caaaagaaaa aatcgatctt
   113701 ttacttttga aatactttac attgcggttg aataatataa tatagcttcg ttttatatag
   113761 aagacagtaa tcattatatt ttttattgca aagcagagtg atatcgcttc cacaaaggag
   113821 tgaatctgag tgcaacattt ttcttcatga aaaacacaaa aacaatttaa aatattttca
   113881 tattttcata gtatggtagc ttttcacgga attgtttgat gatatagttt ccctgaattc
   113941 aggcataatt tgatacttat ttaacgcatt tgtgatactt gttttcagtg catctagaat
   114001 ggacaatctc tggattgtcc attggatctg gatctggaca agggaaaggg aaggagcttc
   114061 tgcaggagtg gccggaaaag tgtccaacag ttctccagag cgacgcgtaa gtggagcggt
   114121 aaacaagtga cccgaccacg cccaccgggc acccacaagg aggccgcagg atgttggcaa
   114181 tcgaaggcag tgaaggcata aggaataagg aagctgggga agccgagagt tgtgggcaaa
   114241 atgttggctg cagtcgctca gcgggcgggc gccatttacc aagtgtcaaa agcaaagcta
   114301 aagctattgt cgacatgact ttggacgaca acaacagcaa gaaatgtgct ttcccaccga
   114361 aaaagtgaaa tgctttgttg gcaattgccg aggagtttcc cggagcaagt cggagaactt
   114421 gcagctgtgc aggatctgcc ggctctgccg gtcttgctgg aaaggatagt ggaaaaggag
   114481 cgatggcggc agcatgtgtc aacttctttt cagaccgaga aagggatttt cctctccggc
   114541 gggtcaagac gaaggcgtac ccgatagaaa agtgggtgac aagtaaccgg aaaatgtatt
   114601 ttattgtttg catccggaca tttcgttttc ccgacctctg ccccctgact gttcgggtgt
   114661 gtttcacccc gcagagtcac caaccgacca atgacttggt cttctggcac taaatttgtc
   114721 gagtaattga tgagattgca ctttttctcc aaactcgttc aagaaggaga gctgcagatg
   114781 ttctgagaga gttgtgggcg ttattgtggt aatgtcctgg ttgagaatag tggcaccgta
   114841 atggatggag atatgtactc aaggaaatgc tggtgctatt ggcataaatg gagtagtggc
   114901 atataatcaa caaaatttgt ggcttggttc aacaaaattt gatggagccc taagcgttta
   114961 gaatttctat tataagatta accaaaatat tttactggtg cattgtcata aacaccgatc
   115021 ctcggtgctc aacgccatgt tctctgtctc tgtccacctc ccactgacca cccatttgaa
   115081 ccagttcgag tcaggctaac ttgatagatt gtctaaatgt gctgcgtatg aatgaatgaa
   115141 tgaatgaatg aatgaataag cgagtgcgag tacagcccct tctgccaagc aaacccccct
   115201 gtccaccagt tgatggccac ctcgaatacg cccgttgggt tcgcctgatg cttctacgag
   115261 attgatggcc aaaatggctg ttgaaacaac ggcaaagcga acaggcagca gtgactgccg
   115321 ctcaatgaag aaaaataatc accaacatca tttattttcc gttttgcctg ccgacgtcgt
   115381 acagcacaca tcaatctttt gcaacagcaa cagccaacta tcgaccatga ccaggcctgg
   115441 actctggctg aaaacagggg gattgagatt ggtaaccggg aactgggaac tgggactttt
   115501 ggccgtgatg tatacttttg tgagcctgac agcttctgac gtggatgtgg acgtggacga
   115561 gaagccaggc ttcagcttga tgtttgatgc ttgatgctag gagcctcctg gaggttggag
   115621 gattggggag tttctggact gacagacgac ttttgacgtt tgcctgcaat taacgatacc
   115681 atcccactgg ctcagtgttg aaaaatgact gcagctgcag gtgaaaatgg cacgccagag
   115741 tgttggttaa tgacacgaca acagttcgag tcagccagcg aagaaaacga cccctccccc
   115801 gcatttaaat cattaatccc aatgacaagg accccacaca cgcagcccca tcactcagcc
   115861 agagtgatgt caaagataga cgagcagccc gaagcagcgg agaacgtttc tagaagtgga
   115921 agttggatgt gtcaggagca gggggagcat cctcggagat ggatctgggg tcggagtcag
   115981 tgtctaggag tcgcgtcctc gtttgctgag actaatttgt ggctctcttc tgagacgccc
   116041 actatgcgag ccattacact ttgagaaaat actgaaataa aatacattca gatttttcag
   116101 atattatttt ttagttttat aataaaaata aataattttc tatttgctta aatttatgga
   116161 gattacattt catattattt cgagctatac aagaaaagat tttccacagt gcagccacga
   116221 ttttttgatc cttgttgagg ctcgttatgt gactggtgac ttggttttgt tgccagtcac
   116281 ttgaaaagtc attaatcatt ttgggggatt tcgctttttg cgccatttgg ggcgtagttg
   116341 tgcgccgagc tgtcggagtc gctggatttc gactcggagt gctgcagaaa tccatcacgc
   116401 acccaaatgg cagccactcg catcagccac caccacccaa cacaggcaac acattcaaag
   116461 aggcaacagc caacagctaa cagccaacat caatgtcaac gtcaggcggc ggagcaggac
   116521 gcggatgtgt tcgcggatgg gagcgcggat gtgtgcgcgg atgtgagcgc ggacaaggcg
   116581 acggcagcga cgtctgacag gcggaagaaa agagtcaccc atcaagtgag cttggcaaaa
   116641 aggacgaggt ggggtagagc agtcactgaa tgaaagtgct ttgtgattag gagtcaaagc
   116701 atatgctttt taatttgcat gtcagctcgc ggtgccagat gatgttctac acgcgcggct
   116761 tagattagga tgcctgtcta ttctaccatg cctgtctatt ctagtcagca ggttactatc
   116821 cgcaatttgt gttcttgcca tgtgagcttt ttgggaaaat tgtagcttaa acggattcgt
   116881 gaaaactgga aagcaaaggg ttcaagtggg catatttgtt gaaccgacgt agatgtaact
   116941 tgcagttgat cgtcaataga ggaaaaggga tgatcatcat caaaacataa tatatcttta
   117001 tacctaaaac aaaaatgaac gctattccta tcaggaagta tttaggtaga gtgagtgcta
   117061 agaagaattt tcaattgtat gcttaaactc aaccttctaa ctctcacagt tcccgagatg
   117121 ttattggttg tcgatttgtg cattcctttc taccatgtgc aaaaaactaa caaatctttt
   117181 ctaaaatgcg ctgctttatt accacttgat gtcaattgta ttcttttcat gatcagttaa
   117241 cctcttcttc caatgttgta atgaacaggt ttgccgtttc gcatcagctc cgtgattgga
   117301 tagctacctc cttgggcggc gtcggcggtg ggttcgcact gtgggacatt accaaaaact
   117361 ggagcggcag tcatcaggac aacggccaaa acggcaaaaa gaacagcctg gtgaagatgg
   117421 ttttaattgt ttaattaact cataatggat tgagaaatct gttaaactca ccaacaactt
   117481 catcttgcga gatttgaatt taaagaatgt gttttctgca gagtgcaatg ctttttatac
   117541 cccagagaag tttcttatcg cttccacagt atgatcatta cacgctaaag ccgcgataat
   117601 tgggagctgg gttatattgt aactcggtgg aagaacataa atatttccaa agaatcgcaa
   117661 taatcaagaa tattgttttt cctggtatta ctgcattgga gaattaccaa tattcatcat
   117721 aggctcttac tatattgggg ctttatatgg gggttctata tatgattaat caacctcttc
   117781 gtgcggtatt gtatttaata ggtttgccct tccggtttgc acattgtggc agattcgcga
   117841 aaactggaac ggtagtcatc aggacaacag ccaaaacggc gaaaagaaca gcttgatgaa
   117901 attgatttag tgttaaataa aattattata atcactcaat ctgtccaact tacgaacaac
   117961 ttcatctgca cagtaacaca tttttattgg gagttttaac tattctagtg tctttgatat
   118021 aactattaat ttctcaaggt catgcttttc caatatgtta cgatttcttt ttttattgaa
   118081 attcactggt caaggcaatg agatatattt tccgtccaac aaaacgaatt gcctaccctt
   118141 aaactgtttt cttattttaa ctaattccac caacgttata attttataaa agtttaacta
   118201 aaaatgcctt cattcaaata tattgctcca tctagcgaca atggacagca atgagataat
   118261 aaagggttat tttacatata ggctacaaat ggttaacgtt attacgcgtg taaatttaca
   118321 tatagctaag tttcgaacta cgatggttgg tgtattgtct acaccaactt aacgaagtag
   118381 cggcgacacc accaaactta tcgaagggtt gacaggactg taaaacttct gttaactaag
   118441 gaactttgca ttctgtaaca agaaaataat ccttttgtat ttaaaataag ttgttaggaa
   118501 ggagaatcct gcgtcgggta ggtctccttt ttaatacttt ctaacttact tagaaatcag
   118561 ccatttaacc aaggcagaaa tgaaaaaaaa atttctaaga actttgattt tttgcagaaa
   118621 gagtggaagg aaatgtataa aatatgtaca ttttccaaga agttcctatt ttcaaaaaag
   118681 tgtttgggat gttggtgaaa catgatttaa tggcaatata gatattaaaa gtgattttag
   118741 taatgcttta aaatgacaaa ttatggcttg tgacttgtgc caaagaaagt caccagaaac
   118801 gtaaaggtac taaaagttcc tgctgcctgt cacctgcctg ccactcggcc atcgagatcg
   118861 tctgctaaaa gccgggcaat taataacgcg cacacccctc gcgaaaccca aagctagtca
   118921 cttaacgcta atactctaga ggcgcggtga ctaattaaaa cagcagttaa attagcaaag
   118981 taaagctggg cgagtagttg acaaattgtc agccagatct ccacacaaac caaaccgatc
   119041 ctattcgaat tgaaacccgc cgcatctatc agcggcgaca gaaacacttt gcctgtcgtc
   119101 tgccggcttg ttggtttctt ggtttgtttg tttggcttta gccatctggc ggacactatg
   119161 agttggccaa ttctgcgcca taagatgccg ttaaatggac acgcagcgcg agccacatct
   119221 ggagaacgag ctaatgccaa atccagagtc agagctagag cctcggactg gcggcgagtt
   119281 ctcgctctgc gtagccagag atgcttcctg tttgataaat ttgaaaatca attgaaaatg
   119341 cctgaaaggc cgacgcatct tggtgggaga cagacggaca cacacacaag ccgagagaga
   119401 ttcgcggaaa agcagctgga agctgttccg actcgaatcg gagatgctgc cccctgggaa
   119461 ctggaagtca actgcttatg taggacagga attaaatcag ccgaatcatt ttaaagtatt
   119521 taggattaat actgagtttt ggatgttcta attatttcgg ctgggctttg acaagttttt
   119581 atttcatagc aatggacatt aggaattttc taggaacaat tgatattcct gaggacagta
   119641 atctcacatt tagtagcact caatatacct gtcactaact gaagtcactc cataagcacg
   119701 cactggcatt cgcatctctg gcactggcca taacctagaa tattttagtt ttttattgat
   119761 attttctagc catctattta ccgcggctgg atcatctgcc cgatgctcgg atccgccagc
   119821 cccgcgccaa tcgatgcaaa taaatcacta tggaaaatgc agtcgatgaa aaaaagcgac
   119881 gcgtaagtgc cgccaaataa atttcgcaat ttatttattg cagagccgcg cgggctgccg
   119941 ttcaatttgg atggcgatgt tgggatggaa gtgtggggat ttccccctgc tgcactccaa
   120001 ctactcggag tggagcgtcc atggtcaggt ttttggctat cggcaacaaa caggcgcgtc
   120061 gcggaagaaa agtattttat ttcattgcca gcaaattggc aataagtgaa atttgttggc
   120121 cccgctcggc aggtgtgcgt gtgtttggcc gagctggcca atggcgattg aaggaaatgg
   120181 aaatttgaat cgcacgcaga ttcccttacc ggggaaaatt gggttagcaa tgccatcttt
   120241 tcgggcgggc gtgttcgggc atttttaaca ggtcctaaag agccacttaa tatatcatcg
   120301 gggcggttta atttgccgat taagtcgctg cagcaggcag caggcacctg cgaaattccc
   120361 gtgaagcgca agcgtaaccg atcgactctg acccatttcg ccattgttaa cattcacttt
   120421 tgtggccgta atttattgtt ttgcctgcac cttcaacggc atgatttctg cataaataaa
   120481 tcagccgaat cagtcgagct ggcggggcaa agtgcaaatg aattagcatt tgtattcacc
   120541 cgattcccat acgcatcatt agcctaagag gcggcatcaa gtgtaattta accgttaaca
   120601 aaagcccatt gtaggctaac aacccattgt gaagagagtg tgtgcgcgtg tgtggaaagc
   120661 cttttacccg ccagtcggag agaaaagaat ccgcgcggac gcaaattgat tgaacgccgc
   120721 gaaggagtcg cactgcaaga tgcactgcag tcggatcttc agctggagtt ggagtctaag
   120781 cggtagattc tggctaatga ccgcaaatta acactggcca aggagccgca agacgagtgt
   120841 cattaacaga agtgtttgcc aggcggtcgc tcgagtggca gccactcact ttggtcttcg
   120901 ggtttggtgc gggcttttag catatcttct aatagatcgc caacttggca tacttaactt
   120961 acgttcgcag ttagtgtttt ccttaactct ttctggccag ttgaccgtgc taagttgggc
   121021 cataaatcgg cagttaactc tggaagatct gcagctaccg tagtcgctgg gggcactcat
   121081 aatttaaaga ttcttaaagt tcggtatggg tggcgagaaa agtttaggag aaagaaaaag
   121141 tccatctctg ttctgaatgc ggtaattggt gctgatatat tttactgtca gaaaatgact
   121201 taccaataaa cgttatgttc cctatttcac tttattatct caacattctg gaaatcaact
   121261 aaactagccc caaaatcaag ataatcctat caatatcctg actttgatgc acttaccatc
   121321 taagccatga cagactttta tgtgggaagt ttcaccaaac taacccaaat cttgtccaat
   121381 tatctaacgc tatgaaaagc tatccggttc accccgctct tcaatttgca attttgaagc
   121441 gaaaacccac cgaaaatgca acatttcgtt tgcaaattgc ttgtgtgtag gttttggaca
   121501 actttttatt tctgttagca tctttctatt cctataatta ccacagaaat cgcataacaa
   121561 gctgctgcaa cgatgataaa aaacgaaaag ttcgcaatgg ggggagtagc cgggaaactg
   121621 ggtcagctgt gtggcattat tggtttagtg gatcaaaccc acagcgacta cgcaaaaggc
   121681 aatttgagtt gcagagcaaa acgacataaa acaaaaagca tggacctcca ccggccacat
   121741 ttattagatc aatgtctcgg caaccagagc accaaccgta gtgcaatagc tacccacaag
   121801 accaagactt ggactgctga ataaattgca gaggctgcgg cctactcgag cagcaaggaa
   121861 aacaaaaaaa aaaaacctgg ggaaaacaca aaatcaaacg aatgactagc atgaggccaa
   121921 tatataataa tggttaaacg cccaggcagc ggtgcactgc accgcagcaa catctaataa
   121981 cagcagcagc agcagcaaca tctgcaacaa cggccacaag aacaagcaaa catccaaaca
   122041 agcagcaagc tagcaactgc ccattaaacg gagctacgga gaatccacct cgattggcac
   122101 tggcgaaaca atttaaatag aattcgccag catcagtggg aaattcgaat tgaatttgtt
   122161 gctgatgcat gtccatgttg ctgctgttca tgttcaattt tccagcacca cccaaccgaa
   122221 aaatcggata gtgaagatta tcattaaaat atattgctgc ctaaatatgt gagagattta
   122281 tacactcttg aagcagcgga atataacggt ttgaagtaga taatatttag aggaaatgac
   122341 aaggttataa agattatagc tttccaactt gttatgatct gttttaaata taattccatt
   122401 ttttatttcc gccaatgcat ggacatagca tacctatacc ccataaatgg cttagttaat
   122461 cttccatgaa attgattcca tattttatcg gctacaattt agtcaaatag gatagatatc
   122521 catagaaacc cttcttcttc tagggtagcg agcagcgatt gtaggaaacg catgggcaca
   122581 cttgccgcaa gatttatatg catgcatgat cggtattaga aaattgtctg agcaaatgtt
   122641 tttggcaagc atgttgcaca tgttgctcat tgctgccgca ctgccacata tactcgtagt
   122701 ttctccagca agatcaataa aacctggccg gctactggcc ttgccttggt cggttccgcc
   122761 tattgccgtt tgttgtctgc cagcctgcat attaatttat gtttcgacat ttgccttggc
   122821 ccggagaatt tccaaaccgc accaaaacca cacccaacca caatttgttg ttttgcctct
   122881 gcctcctgct tttcggctgt ttggtcagtc gcctgacagg cgaagcctaa aattcaatta
   122941 aaaatattaa ggctgaacct gggctactac tgcttattag acttttcggc cgaacatttt
   123001 cttatggatg ttgatttggg gttcttccgc cctgcccccg cccacgggac tagagaacat
   123061 tttcgatcac agatctctga tcgacccctt aagccccttt aaccgatagt ttgctcgatt
   123121 gctttggcta ccgatcaacg accgaaagca atccaaaagt gtgtttatct aagctgaact
   123181 gggaattatc actgctcgta aagaaaaaca gcaaagtttt atgacttaat gatgaaaaat
   123241 cacagtgtcg acgtccaaga acttttcaca ttaaaatcag aacaagcact tccttacgac
   123301 tgctttaaaa ttggagttta attgtactga taaagattca taccataaat gataaacata
   123361 ttaataggca tattaataag ggctttgaaa gataaaagct actagtgtta attcaatttt
   123421 tcttttcaac attttgtctt ttgtgtcagc taaatatcta caaacaattt gagacatttt
   123481 acttaacaca tctcttaata aggctcagta tatctgtaaa gcatagcaag atttgccctc
   123541 ttgttttttt tttcaggccc ccaccctcct tacttctttc cgatcttgat gccttatgat
   123601 tcgcgatgat cttgaccatg ttaattccct cgggggtgtg tgctctgtta cgttaacttt
   123661 ggctacaagc cgaaaaaaag atacgcactg tgcgcgctcc gttaaccggc aaaaaacgag
   123721 aaaatgtcga caaatttatg acttcacagt taaccacggt cggagatgca gatcccagaa
   123781 gggggatctt ttgactgtgt gcccaactac cgcgcaattt acgatcggtt catttaggtg
   123841 gaccattgtc caccgatgca ccgatgttta tgcaatgttt ttgtgatttc atatcggcca
   123901 gctgggaatt tgtagcggca acgcctttgc catcgccatc accatcgcct ttcattgtgg
   123961 gcgttgggat ctgggatcat ttcccttttc ccccaagagt tcgggcattt cagtgccatc
   124021 tccgttgaat ctttctccac tttttgttgg ctgcttattc tgggagaagc gcaccctagc
   124081 caaatatgtg cgagccaaaa acgtgaatcg aacaaattgt tactgcctta aatagtaaac
   124141 agattttgtc gttcattcca gccacggcca aaaacgggct ctgcgtatta cggcagcgac
   124201 aagcaagagg ctgaattcga ttcttcccag ccgattccca gagggttgag ctgggtcaat
   124261 cctcgccaga ggtccccagg agcatttaaa aatcaatttg ggcgcattta tgtttcacac
   124321 gatggcccag agaggaacca aaacagaaac gtcgcaatgt ctgagtcggg taggtcttga
   124381 gtttgatgat tatctcggtt tgtgtgactt tcggtttcca agctcgtgta cgattcgtgt
   124441 agtatatggt gtgtgcctgg aaaatggatg gaaatgtgtg tcaccgggtc tctgtgtctt
   124501 ttcatcctcc tcctcctcct ggctggctgg caatcctcca gctttagatg caactcccat
   124561 tcccaatcca ctggcacagc ctctgccatt tccatttcca ttcccaattc gaaacaatta
   124621 ccaattgttt atttgttctt acaacttgtt gtcgacttcc ccagtggcct gatggtgctg
   124681 gtggccccac cgatctatcg ttttcctctt cgcctccacg aattcatcaa ttgccacaca
   124741 atcttgatct cgagtcggca cacagaagtt tgctctgtcg aaacggtccc aagcctaaac
   124801 tttccttggc cacttcgaca gtcggcactt tatcttcgcc ggcttttaat ttcactaatg
   124861 acaattgatg atcgtaaacg tttatgaaaa tggaaaacct aatgaaaccg aatttcccca
   124921 tgtgagttaa gccaacttaa ataagcctcg cgcagtccga aataaatgaa ataaatcagt
   124981 ggctttaaac cacgtaaaat tactgtttat tggcttggag gaagttttga tatttatatt
   125041 ctttaggtgc aatagatact atgagatttc attgataaat atattctttt tcactttcaa
   125101 tatgaaaaat tgatcagtcg atttaattct ttttataata atgttatcaa aaagaaacaa
   125161 tgaaatttta aaaaatttat ttttcgcagg gtatataaat taaatataaa taaagtttca
   125221 aaattttgca ctggaattct cttaagtgtt cggttggcat ccaattagct cagttattga
   125281 ataaaatgtg gcactgccac acacatttgg tgaatgctcg cggaggcatt tcaagatcgc
   125341 ggcactcgta aatcgccgac cagcccacaa tgcgatccca aagacaatcc gcaacaggga
   125401 tgactagaaa agtatgccag cagccttttg gactcggatt tttgctgttc tgctgctgct
   125461 gctgctgctg ccacttcgac ggcacagaag ttgtcatcgt caattagttt aaaggcagta
   125521 taaatttatg ttaacagcaa ccaaacataa tatcccccga gagtccaagc agcaagcaga
   125581 gcgaaaacga aacgaaacaa ttttcccttt tcaccaacat caacgccagc taccgtttct
   125641 gccactgttg caagtcgctg atattgctgt tgcaagttgc agatgttact gcggctgctg
   125701 ctgctgattt tgttgttgcg gcattgtttt ggggcgcgcg atttcgtggc cgttataaca
   125761 ggcccaaaag aatccgaggc agacgttatg cctcaatgaa gtcagagttg gagttggagc
   125821 tggagctgaa gatatctggg acggggaagc aatccccctg ccctgtgaga agaaggccaa
   125881 ttgggtcgtg gctgggcctt tgatgttgtc gcagtttgtt agaatctgtt gcggcacaat
   125941 gagccacaat aagaaacaaa aagttggcac atgggaccag gcgtagcatt atttaatgta
   126001 atcgatcgtg atgggtttgt tctaatttgc ggtgattttg tttttggcgc ttgttaagaa
   126061 cgtccgaagt gaaagagcca agcgaaatcc tttgaagttg gccaacgatt tagtgtcgta
   126121 tcttttatgg tgtatcataa aagtttactg cccgaatgta attagtcgag gggcataaag
   126181 aagtcatttt tctccgtcta aaattgtggt ttattaactg gattaatgaa aatgataacc
   126241 aaccgagaaa ggtagttgct tcatttccat ttataattat tattacacaa caagattagt
   126301 acttgttcgt acataaattt ttattttgag aacgaatata cgaatttgag tttaatacgt
   126361 aaattcagga ttcttgctac atacattact ggtttcatgg ccatgttctt gtttccagtt
   126421 gcgtatcaca ggctaatcag agtttcgtac ctgcattata tacatatgcg aagacttttc
   126481 tcaatctcaa gctggaaaat tgcatggaca actagatggt aattgcaggt gtgcaacatg
   126541 gtaatgacga ctttggccag cggcctggta ttgggtggaa atggaggccc caattggggg
   126601 atgattggat gggatgggtc ggggccgggg cgcgatcggg aattgcgttg ggaagaggcg
   126661 gacgacatcc acccaatcat ggtcattacc tgggacttgt tatggttgcc aatgatcaga
   126721 tcactgctca taggtgaccc aaattctgtg cctgctactt atacatattc atagccaaaa
   126781 cagttcattt ttgtttaaat atgtgacagt gaatacccta aaaaatggca aatctatctg
   126841 aaacgggaca aaacagggtt caatgaccag cgatggaatc acctgcctgc gcttaacccc
   126901 gcttgattcg atgccactga agtcggcctg ccaatcgctt gaattaagta atttcgattc
   126961 cgtcacgtca gacggcaatc cacgcgacgg cagctgagga gataatcaaa taaatgcatt
   127021 gttagccggg ttttcaagtt gaaagaaaag cgccactcgg gattatttgc tttcccgagt
   127081 gtccccacaa gggtcagggc cagactcaat gaaaagccgg tcagagcgag gggcaaccca
   127141 aacgaattgt atcgatggct tgccaatgaa gtgaaaatcg tgattccaaa ggcaaacagc
   127201 ggcctgtaat tttcactaat ttctacacgt ttttttttcc tttggcttca attggcttgc
   127261 ttttctagtt ttttcgtcgt caacattttg tcgatttgct tcccaagtag ctaaaacaat
   127321 tatgcgaatt aatggcgaac gggggaatga atcgcgcaat ttcaatagtc attccaattg
   127381 ccaaaagttc aaatcaattg caactcattt aaagtgacgt cacaatcgct ctgctgccaa
   127441 aaaaggcaat cgatccacaa ggaaaacaca acccaagtgt ccatagaaga ttttccagag
   127501 ttctcgcgaa aaactccata acagcaaatg cattctgcat tttaaactga ccaaagggtt
   127561 ttttttagtc catctcaagt cgcacgtccc aagggaacgt tatccgacgt ttatggaatg
   127621 agacttcagt cttccatcga ttgaccatgg gcgtagtcag tttgtaaagg tccaccggaa
   127681 gtactatatt ccaagcggct gttatgaaaa aagtattgtt tgtgtggtgt gctctttgta
   127741 aacaacaaag atagttagtt tttaattcct tctttcccct ccggatgaaa atcttgacta
   127801 cgctcttggc cagttgattt tctttctgag ttttctgaaa tccatttgga tgcggcagac
   127861 tgcttggaac catcgacgtc tgaacacgct tatttattca gtagttactg tttttgctgg
   127921 ctgctgcagg aattactcga aatggcatgt aatgagttga gttctcgttg ccctttcgtt
   127981 ttttgccggt gtcttcagtt ttcctggaaa gcttatgcca gatttagaca gcgccaaagc
   128041 tctcttcgca cttgcgtatg aagtgcccgc catagcaaag cggattttta gcgcttgttt
   128101 accaactggc tcgttggtct aggggtatga tttccgctta gggtgcggga ggtcccgggt
   128161 tcaaatcccg gacgagccca agatggagta gtttttttgt gtttattttt tatttccttt
   128221 aacttcccag aaattgagac ataacaattg ctagtacaat tatagaggat gtaagaaaaa
   128281 cagcaagact aaaattcatc ttcggcaatc tcaacccctt tatttaatta aatcaacatc
   128341 attttgcata tataaaaagc taagccaact tgaaaagaaa gactcaacgt ccaacgggtt
   128401 catatacaca caaataaaaa aaaaacaatg tttgaagttt gattacgaaa tatttattat
   128461 cggagcactt aagcgaacaa ttctaattac atttgtatat atatcatatt atctgcaagt
   128521 gcacaaagtt aagcttttag aattaaagac taacgaaggg ctttaaatgt tattgctcta
   128581 cccatccttt ttgtcattta ctatctttta agaccaccat tggaaaaaaa tagataatca
   128641 tcttgggctc gtccgggatt tgaacccggg acctcccgca ccctaagcgg aaatcatacc
   128701 cctagaccaa cgagccaagt gatcgtcgcg actcacataa tcagaccaat tttgcgcagt
   128761 aatagttggt cttgctcaca atttccatca aaatattttt aaaatgtata agaactggtt
   128821 tcatagatac tttcaaggct ggagctttct gttgaccatg aaagaaacct gctcttttcg
   128881 tgctgtgata tgagtaagct ttttgaccaa cgtaagacaa ctggctcgtt ggtctagggg
   128941 tatgatttcc gcttagggtg cgggaggtcc cgggttcaaa tcccggacga gcccaagaga
   129001 aaagaacttt ttgtttcaaa ttataaactt tgcttatact ttttattttt gttgcacaaa
   129061 taacgactta tgggtaaata atattaacat ttgttgtttt gccccgctta tttaataaga
   129121 ttaaaattgc tttaattaag gtagaatata ttgattaata ccaatggtta acaaaacaaa
   129181 aataaaatta gacgatatat tgtttgtatt ttctttatgt ataatgcatt tacatgtatg
   129241 taagctgaaa acaatttcga tttatttaat acaaacgaaa aaagaagcaa ctaagcttga
   129301 atacttgttg ctcgcttgaa agttgaccta tgaactacat aaacataaat aaatgacaca
   129361 ttttgtggac atagagaatt ggataaacgt acagtagaat aacatacaga tacaaagata
   129421 gaatagatga taaatacata aatttggccc aaaattgttg tggtttttct tgctgttgat
   129481 gacgcagtgg atgctgctgt tgttacattt gttggggtta gttttccatt gctcgacgtc
   129541 ccttccactt tttgcattgg aagggggtga acagtcgttg ttagctaaac tccattggaa
   129601 atctgaagct cctcatatat gtatgtatat atttcatttg actgctacat caccaacatc
   129661 atcatcatca tcttagttat gatcttcaac cagttttgcg ctctgttaga gtaatgttat
   129721 tcgttttatg tacatacatc atggatgctg tgccgttcga ttttgttttg catttggttg
   129781 cttggtttaa ttaatatatt ttaaataatt ataattattt agttattatt agcactaatt
   129841 attctttggt tgttccactg gttctgtttg ttgttttctt gctcttggtt attgcatttc
   129901 attttcgtta ttatttgttc gatttgttca ttgtgctttt tcttcctggg ctacctgttg
   129961 ctgaatgtta atgacggcag ccgttttaaa catttgcttg tgactgggct tttttggatc
   130021 ggttgttggt gctgttgttg ttgttgttat ttctgatgat gctggtgatg tctgtgcagc
   130081 ggatttcctt aaactcttgc caaacgtgga actgcccttc agacctgcaa agagtcccaa
   130141 aaaagaagga aatgtatcta aaattagtta tattttaatt tttacagaaa gacaaatata
   130201 caaatgtgtg attataacga caggagcact gggaaaggat ctggagagat tgacggaaag
   130261 actgaagaca aaagcagaga cagccgtgat gataacgatt acgtgtatag agtgtagaga
   130321 gaagagtacg ctgccccagg agggaataga gtggatcgag aatggcgttt ttgcgtttac
   130381 cttggtagct caaacgattc tgatagatgg caaatatatc gaagggcctg tagcatggct
   130441 cgtaaccatc ctcgggccca tcgagatctc gatagagttg cgatctctga ctctgatcag
   130501 aagcgtttgc ggctggcacg agggaactgt ttagcatatg ggagggtatc acgaagagac
   130561 tttgctccat tttctcgggt ggcgcccgcg atgaatcggc ggtttctcta tcggaatcgg
   130621 gattggactc agtttcgctc ggggccgctg atgtggttgt tgctgtggct gtagttgtgg
   130681 ttgtggcagt ggttcttgtt gctgtggcac ccaatatttg tggtgcaggc ttgggaagtt
   130741 ggttgtagtt gtgttgtgtt gtttgtgttg tgtttttata ttttttgtat tttttttttt
   130801 gggatagtgg aagatggtaa caaagtggat tagttgttgt ctgcagttgt agtgattagt
   130861 gttagtcaca atttatacta attgatctag agttaattaa ggggttctaa gtgatataat
   130921 actgcagttt cttacctcgc tatcttcaca atcagcatct tctcgagcgt cggaggtcag
   130981 gccctgcacg aagtgaacat catttgatgg atcatcggag gccaagtgag cacgaaattg
   131041 tttgtttctg caagatgtca ttaaagtaag ggtgtccaat tgaatataaa ttaccgtacc
   131101 tcagctccag ttgctgcatc tgctgaaaat gtcttagctt gctattggcc atatgcagtt
   131161 tttcctccaa ggccgcgttc tccacacact tgatggaata cttttcggaa aatgcgagaa
   131221 tttccattcg cagctctccg agatcctccc taaatagaag ataaggttcg ttttagtttt
   131281 aatcgaattg tgctcaagga tttgatattt gtatgcatgt gttttaggcc atcttccaca
   131341 aaatattcat tctatactta ctctttcagt ttggcgccat cccctcgcat ttgttcgcct
   131401 ctttgaacct gtcgcagaaa ctcctgcttg aatcgagcca cctcccgctg aacttcactc
   131461 tggtgtgctt ttctcatcgc atccagagca gccaaagtgg cctgtaaatg tagtaaataa
   131521 atccaaagaa gttaagaatc caaacaaagg tggattggcg ggctatgagc tgtacctgag
   131581 tttcctcggc cagggcagtt tccttctcgg ccagcaggcg ctctatctcc atcttgtgtt
   131641 tctgctcaag atccatagta agccgcttat gcgaagtttc catggcactc aatcccttct
   131701 cgcagagtgt ctgaaatgta cagtatgaaa gttcgttatt aaaacggatt taacttttat
   131761 ttatttattt atatactata atatatgcca tataaatgat tttttttagc gtacagtggg
   131821 ttgcagtgtt taaactcacc ctcagctgtt cgatctcagt ttggtaccgc tttcggaaac
   131881 tctgctcatc ggctgcgttg gcatgttcgg tgtggtagac ctccctcagg cactccagtt
   131941 gcttgccatg ttcccgctcg aggagctcca gtcgcttttc cagtcgccga caacgctcct
   132001 gctgccttcc taattcctcg ctcagctcct gacgctgctg caggagcagt tcctgctcct
   132061 gctcctggct ggcgcacttt tccagtgctt gggccaggtc agtctcccgc tgctccagca
   132121 gctgctcact ccgttgcaaa tccgtttcgg tttgctgctg caaggcggat agcttttcta
   132181 cacgctgacg cagatcgcaa cacttgtgac acgaatcctg caagcaagtc agctccatct
   132241 gctcactgac catcacacat gtttcggcca gagctcgttc cagctggcgt aggccatctt
   132301 tgcgatcgtt catgggcgaa acggagcgac gagtcctttg gccggcgcga atttgctgca
   132361 attgggtgag actctgctcc agacgctcct tactgccgag gagcacgtgc tccaggctgt
   132421 gcaatcgctg caacaggtgg gcatttagtg gtgactggct actggattcg ctgctggaag
   132481 actcgggtgg cgtaccctcc tttctctcca ccgtttccct ttgcaactcg cttagtttca
   132541 gttccagttg ctctttaccc ttcaaggaca acgaacgtct cctctcggat ttggccaatt
   132601 tctgcttaag agcccgcacc tgacgctccg aactgctgta cttcagggtc agatcctgaa
   132661 tacgggctgc catcagctgc agttgggctc catcctcgtg ctgccgcctc tccagcttct
   132721 gctgcagcgc agcttgtgcc agctccaagg catcgtattg attttgcgac tgcttcagtt
   132781 cccgcttcat ggctcgaatt tcgttaacgg ccttctcgaa gcgggatctc agctcattgt
   132841 actcctcggc cagcgaatcg cgttgcaggc agtagggatc aatgtcgctg atggtggtta
   132901 gatcgctcag tgagtccatg cgtttaattt tgtgacgctg caggttgctg agagcggcac
   132961 caccactgtg atcctgagcc tgtaactctc tcaaacgctt gtagagtcct tcgttctcct
   133021 cgattccctg cgccagacgg tcctccaact gcttgatttg gcactgactc tcggtgagct
   133081 gcattcccaa attgtgcatc agatcggagg cactctgttt ggcctgggta agttcgctat
   133141 tcaactgctg ttgttgctcc tgcagccggg cagtcaactg ttgttccgtt ctttggaggg
   133201 tggccagtag ctccgacatg cgggcctccc gcagtgaagc ctctgcccgc aaggtctcgc
   133261 attgttgctt gagttccctg ctctcggttg gctgcatttc ctcgggaact actaagagag
   133321 gcaattcatc actggccaca ctgtctacag tactgcgccg tgaacttggt ggcgaactgc
   133381 gactcctttt gtgcaagctg gccaagcttc gattgcgcag acaacttctc aaaacaggtg
   133441 gtgatggtga caacggtgat ccccagtcca gactatcccg cctgccgccc tccgatgccg
   133501 tcctgtactc ctcatccgag gagaaatgtg gacctgctgg agtgcctgga gtgacgggac
   133561 tcgacgatgg ctgttgcagt tgagccttga taaagtcctg ctctatatct gtctgtttgg
   133621 gtggtgtgtc tagttggggc aatccggcag cacttctcag gaccgccagc cagctatttc
   133681 gcgaactggg cgacaagctg gccaaaacca agcgctgttt gtcccaagtg gtcagctgaa
   133741 aagcgtgctg tttgcttgcc gcaggttcgg gtattacgct ggttagacta ttaacatcca
   133801 ggacgccgtc gagaacacct cgttcctcgc acaggggatc tctatagtag aaaagcgctg
   133861 caccgctcaa ggtgaaccag tgcttggacc actcacaagt ccgattgtcc tgcttcatga
   133921 gccaaccctt cttggcattc agcgattcct ccttaaccgg aggcttacct tgaccagagg
   133981 atgacttact gttggccttg cccaccgatc gcagctcatc cgttttggcc atgtagttaa
   134041 cacacagctc gtccagattg catccgccat cgggatcgcc cctctcgtgt tggtaatgtt
   134101 tcggtgactt taggtgtaat tgcagcctgg cagtgggttt tgtcttgtca ccctgctcca
   134161 taaccgtggg tatctttttg actatggccg aaacaatcgc aggcgtggag ttagatgcca
   134221 ggggcaggga tttaggtcgc tcgctggctg ggttttggga tttggtgctg ctgctgttgg
   134281 aggacatctg gaagtccgtc tcatccctgg atgtcacttg gtactggctg tgatggccga
   134341 aatgatgctg gttgttcagg gcattgttga ccgccgtgga ccagcgtttg ttctgctgtt
   134401 gactcagatt cgttatggtg ttggcaatgt ccttgatcgt cttttcatca cgtcgaatat
   134461 cctcgattag caagcatgtc gtgggctggg aaactgaaga aatgaaaaaa ttaaattaag
   134521 gaacaagtca aattgtattt agcttagctt ttttttacca aagatcaaag caaagactat
   134581 ttagtataat taattcaatg aacccaaatc accattaacc accatcaaag aataaagaaa
   134641 agatcgttaa aacagataac caggcaatta taagtataca agcttgtcgg tgatcaagga
   134701 tcataaattg tccatcggcc ttagccaaaa acaaagctca accagcaatc tacgcattct
   134761 tttctcataa ttggctcagc atcttcatta aatactttga aatatgagca tgttggtaat
   134821 ttcatttggc tggctggctg gccggtatct ctcttggcta agcaaaccat atcaatgcca
   134881 ttgactgaaa ttaacttaga cacaggatcg tgtggacggt ggattgagga ctgaggattg
   134941 aggactgagg attgaggact gaggattgag gaccgagaat tcggagccac actccacccc
   135001 taacaatatt tatgtccagc atagggccgt aaaacgcgca gagagagcca agttatgtgc
   135061 gggcaaatat aataaaatta ttaaaacggg cacacggtgt attgtaaggg gatccgaggg
   135121 atcgcgataa gccaggccag aaagccctga aagagatccc gagagcgctg cagagtgcca
   135181 taattttatt aacacccaaa caagtcgagg aggacaagcc atcaagtacg aaccagacga
   135241 acgagaggca agcaccgagt tgtcccataa aatatgtgat tacaaaatat atatttagac
   135301 ctgttccagc cagccgccac atttaggttt attatgatta tgatacaaat ttccgactgg
   135361 ccataaagtc gagcgtctga gatgactgga ctgaccgaat ccgaacctcg aacacacagc
   135421 gctctggatg cgcatcaatt cggtcagtcg aacaggttgg tcgcttttcg gctgctccag
   135481 cggcgtttat cttgattatt gagctgttgc gaaaagcgaa aggaggtgga ccagcagcct
   135541 ctgaactcca gcttaagata cggatgccaa agccaaggct ccagcaccga gttcgggatg
   135601 ggtatggtta cgggggatcc agctcaaagc tctgacagaa acagagctgg ccactgactg
   135661 actgactcac cgagcaggtt caaggttact gtgctaacag cgccaagggg aggttacggg
   135721 ttacggtgca atggcgatgg tgatgacgat gggcatgggg tatgccttta attggtcgac
   135781 ttgtcggccc atcgcgttca agcaaaagcc tgaccaaagt ggccctggcg actctacgtc
   135841 gattagggtt tggggccggg actatgtcag caatggaatt tataatgctt atgatattac
   135901 acatatccga agggaaggac aatagtactt taccctttaa aatgcggtta tgcttactac
   135961 tctgctatca gggattctgg ggcatataag aacgaattta cgtatatata ataatataat
   136021 aatacgtata tttacgtctg ataataagat gactcacgtt tcaagcattc gatgctgttc
   136081 tattaaatct aaagccatat taaagaacag atttgaacaa ttgaacaatt agtttgcaat
   136141 aaatcaaatt tacaatctca agaacgcact cgaaactata aagtttattg agggtcccct
   136201 ggggagtaac aaaagctaaa atatttttct tagccttaag aagtaacaat gaggacctct
   136261 ctgctggctt acaggtcatc cttcattcgt ttcttgattc cccgccgaac tggccataaa
   136321 accatcccca cttgctgctt tattatctgt ggctctttgt ttcgctttcg tggcctgccc
   136381 ttgatgtgtt ttgcaccatt taatatttat tgtggctttt actacgcgct ttcaagttca
   136441 agatcaaatc agagaacaca gacttcagtg gggcgaacga aatgaaggcg cgtaaggtgc
   136501 taagtgtaat taagttgata aaaacagtgt tcgcagatac atgggctggc tagtggcttg
   136561 atgccgctgt tgatgcacaa agccctataa ttatggttcc tggcagttga ggaactcggg
   136621 cgatgcgacc atataaacgg ggtggatcgg gtgaggattt tcggaattgt ctctggtggc
   136681 gactctttat tcatttcttt aattaacagc atttgattaa ttatggccac aattaagcgc
   136741 actcagaaca acccactcaa tcatggacgg gcttcctgca aaaaaactcc agaactcccc
   136801 gatttccgag attcccgaca ttgccctcac tttgccaacg aagctcccgc ctcagacgta
   136861 ataaataatc aaattgcaag ttgatttacc tgcccggctc tgccttttgg gcgaacgaaa
   136921 gcgaaaattg cctttggatt ggaatcgctc ccgcccgtcg gaacccagcc cttccgcccg
   136981 agggacccct cacacgatga ctttgaaaaa tttctaactg accgtacagc ccgctgctcc
   137041 ctgtggaaaa aaaaaaacaa caaaaaacca tataccatat acaaaatcct gccagaccgg
   137101 accccagctt gttgcataaa ttttgctttc gagtcgttac acttatgaat attgattggt
   137161 tataggtgat ggtggcttct actgccggac tgccggtggt tctcctttcg agtttcaaag
   137221 tctcccagtt ctggtgctca gcagtctcgt aaatcgcaca acctgcatcg ttagctgccg
   137281 agacgcctcc tggcccatcc agtgctgtca ttttgcattt gcacagaagt tgtccggcct
   137341 caatggagct gggtctgtcc cgcctaacca cgtttgttaa catgcttttt ctgtgtggct
   137401 cataatgggg ctgctcaata gaaagataat gaattcgcgg tagaactaat ggaactcttt
   137461 ttctctctct cccggcatcc acgaatcttt ttacaaagtt gcaaagggct gtaattagcg
   137521 attgatatag tatgaaggtt agccaccgat aacatagctc ggcagatagt tcaaatgcaa
   137581 gttctatgtc agaggcacac tgggaaaatc ggagagaaaa gtttcagaaa caaactttaa
   137641 agtaatgtaa agaccaaatt atacaagaca taaatctttg tttacattaa taagcattct
   137701 ttcagtgcat cagattaatg gaatgcgcag ctactttgtt gcaatcataa gtagttactt
   137761 ctgtacatcc tccggtctct tacaatttgt cattgtaata caatcttgca cttaattctt
   137821 gtgaaatgca aacttcttcg gaaactcgtt tgattgtaat gggccctagg ttgatgattt
   137881 gattgctggc ctgtgttttg tattttttgg ggcgtttaat cgccggttag ctgtgtagct
   137941 gcatttcgtc acctctaccg agagtctgct gaaatttcta aactaatcca cagagcgagg
   138001 cttttccaca ccagagcccg agatttattt gcactgtaat tattcacttt gccgtgaaac
   138061 tttgcccatt acaagtccct acagagagac atacatacgt acatagctag ggacatggct
   138121 agagaagcca catggtggtg cactcatgtc cagaggggct atcatgtagc gctgacttgg
   138181 aaaatatttc aactggcccc gtcctgacat tggcctgccg acggctatta ggtgtagaca
   138241 gtttataatc tttgtcgttg tgcattttaa gagctttttt cttcctccat cctgcatcct
   138301 aacacccatt cagaaagtgc tcgcccagcc aaccgtccaa tgaattgcct catttgccgc
   138361 acaattttgc ttattgatgg aatgtaatta gtctatgtca gcacccaagc tccacgaagc
   138421 gcgagtgagc gaaatgccct agagtcctac ctggtaactg atctcggcct cgccaaatct
   138481 ccagacccat tactagccaa cggtgcatcg ctaatcgaaa aaggtggcaa atgtgagtgt
   138541 gaaaactgac cattagaatg gccccagaag cggtactttc cgcaggtaag tgcaataatg
   138601 aaatgcattc tttagatcta ttattattac ggattgtgtg gataaatgaa atgaatagtc
   138661 ggaagcctag agaattgttc agctgcaatc gtttcatatt cctaagcttc gacaatattt
   138721 cgtttcttcg atattttgtt taaattacaa aaagttataa agcaatgaac acttgaatca
   138781 gtcatgatgc tgggtaaatt ttcgctttcc atttcgtggg ctttgcaatt cgaactggtt
   138841 cacgtcttta actggcgatt tatcaactga ataatgccat ttgatgtgga tgctgagcca
   138901 tgaatttgca accaaggagg ggagttggtc cagtccacaa cgaacaccac taccaccctc
   138961 tttggattca tccgtgatgg cacaacaacg gatctgaggg cagacacact ataatttaag
   139021 cgtgaatatc atttttccat gaacaagtat cctgcagcaa tgtatgtgag aacattcaca
   139081 gtaactgcaa ttaccgaccc accaaccaac cgatcctcac aacggaccaa ctccactcga
   139141 gagtctggct gggatctaaa gaaaatttat gaagcctacc attatacgat cttaagtagt
   139201 ggcgaggatt cctctccagc cagccagccc tgcttcacga ttgtccctgt ctttgtgtgt
   139261 gaattcaagg ttaatttcgt ggctgcggct ttaactagct gcacgcactg ccccccatcg
   139321 ccatcttctt cattcgcttc cttgccccga atatagaata ttcctgcaat ccctcagtgg
   139381 agtctctcgg actcgctgtc cgtctgttcc caagttgata attttgattg ctgcaagcca
   139441 taaatgatca taaaaattat agcagccgat acgagctcaa ccgaacccag tgcttccaca
   139501 tccacgaaaa gtcaagcgga acaaaaatcg cgaaaagggt tcaaaataca gagcaaaaga
   139561 taactaagct tgccagccat tttcattaaa aagtaaaagt cagattcatc aactgtattg
   139621 cgtaaagata aatgccattt tggccctaca accacttatt attcagttga ctgttaaatt
   139681 gcttgagtta tttccacaac ttgatgaagt ttgttattga tagagccaat tttataatac
   139741 taatctaaca cgagattcag ttaatgtttc attaaaataa aagtttagtt agaagaatat
   139801 acttctagat tttaaaattt atactttcta agagcttttt gcaattatat ggtttgtgtt
   139861 tccgctaagt tataaattag ctgatcagct ttttagattt ctctaaagaa aagttagttt
   139921 tattttactt accccgattt gtgatctcgt tgccggcatt acgattgttc tcgtcctggc
   139981 cccccatgct gaccgtcttt gactttctgg gcaccgacgt ctcatcctcc tcgtcctcgt
   140041 cgacatcctc gcccgtttcc acgccgtcgt cctcctcatc atcggcgaga gctgattgcg
   140101 tggtggtcag aggcgaacca gcggtcttcg tggagctggg acccagatca aggctgctca
   140161 acagattgcc tgccgactgg gaagacgtta gggtgtcctt gtgataggag ctgtgccgat
   140221 tgcccagctt agtggatagt gttaggtcgc cgttgctcgt tgggcgtaga ctgcccacca
   140281 cctgaccacc gggcagggtg gcgcttctct tgtggcgacc cttcgacttg ggaaaggcag
   140341 ccaggatgtt gagccaccac tgggattcct ctgaactggt gcccttcaca aaggtcacgc
   140401 gctcgggagc ggttatggcg atggagttgg ggtgacctgt cacctccacg gcgctggtaa
   140461 cctccagcac tttggtcata tcaacgcacg cctgcggtat ggtttcgggc tatagaaaat
   140521 atatgtaaat taaagagtaa acaagttgta ttttaagatt ttaattagga gaattaatta
   140581 atcggtaatc aaatgaactc ggcctatcgc gtaataatat acatttttta atttaatgac
   140641 taataaataa tataaaatct aattaatagt tcagtaagtt agtaaaagta aatcaatctg
   140701 gtggcaattt aagaagccac tttaattctt tcacttcata aataatcggc tggttaagga
   140761 aaggtacatt tattgttgtt tttaccgcca gcacacttat tggttctacc gataacgtcc
   140821 agcaatgcta taataccata attagaagct cttttgggat tgtataatat tttatgagct
   140881 ttgttatctt ataaattcag accaccccat aacagaaagt tttattatct ttttattttt
   140941 ttgttatcac tggagaacca acgagacggt atttaaaaca gaaaaacaca attatgccta
   141001 tggattgatt agctattaca aactcaaaaa ttcgttttaa ttttattatt agctataaaa
   141061 atggaaatgg tttaaaatat gttcaaatga attacttaca taatcatcaa ccgagtacgt
   141121 cagctcgcca tcatcataga gaacaaacca tcttctttgc cagcgctaca attgaaaaag
   141181 aagacaaatt ttattaaaaa tattaaacta ttctcaagtt tctattattt gatctttact
   141241 aagtctaagt ctgtggctat cagtcgatga gagtgatcaa ctctaaaaca aatttacatt
   141301 gtcgcttgca atttgcaaca tgaaaggtgg gacgagaaat ggtgaggaaa gacaagatcg
   141361 gatgtaaata atgttcaacg cccccgacag aaatcataat tcctttataa ttcgttcttt
   141421 cataaatttt caggcgttgt cattcccatg aaaggcaacc aagccccaaa cgccttcgcc
   141481 tttgcattgg cactgattcg ctgtggatct ggatctctat ctgtatctgc atctgtatct
   141541 gtatctgaat atgaatctga atcggaatct ggatctgatt ctcattgtta ttgttggttg
   141601 ccagaatcat aacaaacgtg caacagccac aagggtatag gactcaacgt gtgtctgata
   141661 tttatgcaaa ttgttaaaag tcaaagcaaa ttaagctcaa ccttcagcga agatgacgtt
   141721 gaattctgtt gccccattgc gctgcaagtt gctagttgca agttgcaagt tgcacctttc
   141781 tgcagttgat ttctcctcat ccacctatgc agtcaggtga gagggagtga gtgcgagtgg
   141841 agtgctgagg tgtgtcaagc gaattattta taaggcctag aagaaggcag ctcgcacgcg
   141901 aataatcaag actcagcacc aatttttagt ttatggtcta gttctttata ggttttgtac
   141961 ctcttttttt tgcgttggct attttgcgat tgaattcata aatatggaat caaatctata
   142021 gagtggagag tggaactaac gaggtgagag gtaacaatat agtttttggg caatcagaag
   142081 caacaaacaa atatctgcaa taactcgttg aattcgaaac aaaattaact gcatttatac
   142141 taaatatata attgctatag gatgagttag ccgtcttgcg gtttcccaaa ccccaaaagc
   142201 aaagtcaagc gtgtaggaaa cctgatcaga tcgcgggaaa gattctctgc actcaattac
   142261 gtcaaaccag gttgatttcc tccttttcgc tgtcgagaga ttggcaaatg ggtcaaatgg
   142321 gtcaggcagt ggaatagtaa attagattat gtttgcatcg agatgcaatg caagccgcgc
   142381 cccaaataaa tggaacgtgc gctagtaggg ttcccccttg cccctggtaa cccttccttt
   142441 caccacccgt tttcccgctt ttccgctccc aaacactaga ggtaagctgc ttagaccccg
   142501 gcgtttagaa gccccagttt cgtttcacta ggcagacaca ctcgcagcgg gaagacaatg
   142561 ccaccgccac cgccaccgac ttaatcagcc cgggaaacga catctcaatg ctggcgagtg
   142621 tgtacctaca tatggacatg ggcgtgcgtt ggtgcgggag ctggtgtaaa tcggttttgg
   142681 caggtacgcc gctggcgtca ttaccccccc agaggttgaa tgtcaccggc ggcatgactt
   142741 gggggccaag ccgataaggc gcacactgtc cactgcacgg tgtacactga taaaaatata
   142801 tatcaagacc aaatattgtt aaagataatt gatgtgtaaa ggaaatacac ttgcaagtta
   142861 aaatgttttc accttaatgt gtttttcttt taaatactct attaactaat ataaattatc
   142921 accaaaacaa aacattaatt tgggaaatgt tatcaccaaa agcttttgcc actatagaaa
   142981 atacagataa atctaaaaat aaattccttt gacgcatgca cgaaataaga taaacaaatt
   143041 tgattttatt ttcttattta cacaattcat tttatttgca tgcatttcat tttgttcagt
   143101 gtacctaata aaaacgattt cgtttgcccc aagcagtaag aagatgttag gcacgtctgc
   143161 tgataaggaa aactgtagcc ccagactagg ccagaccata ttaaattaac gtctggaggc
   143221 gcgaaaatca tacgattttt ttttatatta cttcgcggtc agttgccaag gcaggagagc
   143281 aacccgttcg attagtgggt caatttggaa aatgagttat tgactctggg aaattgttga
   143341 gctgaaaatt taatcggagc ccgaaaattt ccaatcatgc attccccaag tgaccatata
   143401 tggattagtg ataacgctcg atgcgacccc caaagattat caaaaatatt taataagaat
   143461 atatgaaaaa aagatttaac ttttatgaat tcctaagcgt cctcaaagct tcgggagaac
   143521 tgggccatat atgacccgaa atacatgttt atactttagc aaatgtattt tccaattagg
   143581 tgatagaact tgtgtgcaca cacacatata gttctatatc aacaaacagg tttaagtttt
   143641 atgcaaattg aaagcttatt tcttccgcat gcttatctct ttccttctca tcatttgtat
   143701 gcaaaaaata catatgaatt tgcagtagcc tcctcccaca tcatatttaa cgccctatat
   143761 tcaaaatttg ctcaagaaaa tatttgaacc aaattgattt ttagtcaatt agtttttaag
   143821 taattaagtg gagtaaacat atacaatttt attcttacca aacacatata ctcatatatt
   143881 ttgaataaat aaataaacaa atatatataa aatctacgaa attggcaaac aaattttaaa
   143941 gcattatagt attgccgatt taattaatat aattaaataa tatgtacatg tattaatctt
   144001 gtgtgcgagc atgggttaaa tctagctgca ttcgaaaccg ctactctggc tcggccacaa
   144061 agtgggcttg gtcgctgttg cggacaagtg agattgctaa tgagctgctt ttagggggcg
   144121 tgttgtgctt gctttccaac ttttctagat tgattctacg ctgcctccag cagccacccc
   144181 tcccatcacc attcccatca ccatccagtc ccgttggctc ccagtcacag tattacacgt
   144241 atgcaaatta agccgaagtt caattgcgac cgcagcaaca acacgatctt tctacacttc
   144301 tccttgctat gcttgacatt cacaaggtca aagctcttaa tattctggct cgtggcccta
   144361 cactgtaaga aattactata gaaataacgg tacacggaat aagatatttt ttttagtcca
   144421 tatgctttta acaaatgtgt tttaagttta tgttatatta ttgttagaaa accggtgttt
   144481 ttttaaaatc ggttaaaaaa ttactacgag agaaaaatac aaattttgta aataagattg
   144541 actctttttc gattttggaa tattttcatt cattttatgt ttttacgttt tcacttattt
   144601 gtttctcagt gcactttctg gtgttccatt ttctattggg cactttaccc cgcatttgtt
   144661 tgcagatcac ttgcttgcgc atttttattg cattttacat attacacatt atttgaacgc
   144721 cgctgctgct gcatccgtcg acgtcgactg cactcgcccc cacgagagaa cagtatttaa
   144781 ggagctgcga aggtccaagt catgcattat tgtctcagtg cagttgtcag ttgcagttca
   144841 gcagacgggc taacgagtac ttgcatctct tcaaatttac ttaattgatc aagtaagtag
   144901 caaaagggca cacaattgaa ggaaattctt gtttaattga atttattatg caagtgcgga
   144961 aataaaatga cagtattaaa tagtaaatat tttgtaaaat catatataat caaatttatt
   145021 caatcagaac taattcaagc tgtcacaagt agtgcgaact caattaattg gcatcgaatt
   145081 aaaatttgga ggcctgttcc gcatattcct cttggaaaat cacctgttag ttaacttcta
   145141 aaaataggaa ttttaacata actcgtccct gttaatcggc gccgtgcctt cgttagctat
   145201 ctcaaaagcg agcgcgtgca gacgagcagt aattttccaa gcatcaggca tataatatac
   145261 taatactaat actaatacta atataagaat actaatatag aaaaagcttt gccggtacaa
   145321 aatcccaaac aaaaacaaac cgtgtgtgcc gaaaaataaa aataaaccat aaactaggca
   145381 gcgctgccgt cgccggctga gcagcctgcg tacatagccg agatcgcgta acggtagata
   145441 atgaaaagct ctacgtaacc gaagcttctg ctgtacggat cttcctataa atacggggcc
   145501 gacacgaact ggaaaccaac aactaacgga gccctcttcc aattgaaaca gatcgaaaga
   145561 gcctgctaaa gcaaaaaaga agtcaccatg tcgtttactt tgaccaacaa gaacgtgatt
   145621 ttcgttgccg gtctgggagg cattggtctg gacaccagca aggagctgct caagcgcgat
   145681 ctgaaggtaa ctatgcgatg cccacaggct ccatgcagcg atggaggtta atctcgtgta
   145741 ttcaatccta gaacctggtg atcctcgacc gcattgagaa cccggctgcc attgccgagc
   145801 tgaaggcaat caatccaaag gtgaccgtca ccttctaccc ctatgatgtg accgtgccca
   145861 ttgccgagac caccaagctg ctgaagacca tcttcgccca gctgaagacc gtcgatgtcc
   145921 tgatcaacgg agctggtatc ctggacgatc accagatcga gcgcaccatt gccgtcaact
   145981 acactggcct ggtcaacacc acgacggcca ttctggactt ctgggacaag cgcaagggcg
   146041 gtcccggtgg tatcatctgc aacattggat ccgtcactgg attcaatgcc atctaccagg
   146101 tgcccgtcta ctccggcacc aaggccgccg tggtcaactt caccagctcc ctggcggtaa
   146161 gttgatcaaa ggaaacgcaa agttttcaag aaaaaacaaa actaatttga tttataacac
   146221 ctttagaaac tggcccccat taccggcgtg acggcttaca ctgtgaaccc cggcatcacc
   146281 cgcaccaccc tggtgcacac gttcaactcc tggttggatg ttgagcctca ggttgccgag
   146341 aagctcctgg ctcatcccac ccagccctcg ttggcctgcg ccgagaactt cgtcaaggct
   146401 atcgagctga accagaacgg agccatctgg aaactggact tgggcaccct ggaggccatc
   146461 cagtggacca agcactggga ctccggcatc taagaagtga tactcccaaa aaaaaaaaaa
   146521 aacataacat tagttcatag ggttctgcga accagaagat attcacgcaa ggcaataagg
   146581 ctgattcgat gcacactcac attcttctcc taatacgata ataaaacttt ccatgaaaaa
   146641 tatggaaaaa tatatgaaaa ttgagaaatc caaaaaactg ataaacgctc tacttaatta
   146701 aaatagataa atgggagcgg caggaatggc ggagcatggc caagttcctc cgccaatcag
   146761 tcgtaaaaca gaagtcgtgg aaagcggata gaaagaatgt tcgatttgac gggcaagcat
   146821 gtctgctatg tggcggattg cggaggaatt gcactggaga ccagcaaggt tctcatgacc
   146881 aagaatatag cggtcagtga gcgggaagct cggtttctgt ccagatcgaa ctcaaaacta
   146941 gtccagccag tcgctgtcga aactaattaa gttaatgagt ttttcatgtt agtttcgcgc
   147001 tgagcaacaa ttaagtttat gtttcagttc ggcttagatt tcgctgaagg acttgccact
   147061 ttcaatcaat actttagaac aaaatcaaaa ctcattctaa tagcttggtg ttcatctttt
   147121 tttttaatga taagcatttt gtcgtttata ctttttatat ttcgatatta aaccacctat
   147181 gaagtctatt ttaatcgcca gataagcaat atattgtgta aatatttgta ttctttatca
   147241 ggaaattcag ggagacgggg aagttactat ctactaaaag ccaaacaatt tcttacagtt
   147301 ttactctctc tactctagaa actggccatt ttacagagta cggaaaatcc ccaggccatc
   147361 gctcagttgc agtcgataaa gccgagtacc caaatatttt tctggaccta cgacgtgacc
   147421 atggcaaggg aagatatgaa gaagtacttc gatgaggtga tggtccaaat ggactacatc
   147481 gatgtcctga tcaatggtgc tacgctgtgc gatgaaaata acattgatgc caccatcaat
   147541 acaaatctaa cgggaatgat gaacactgtg gccacagtgt taccctatat ggacagaaaa
   147601 atgggaggaa ctggtgggct aattgtgaac gtcacttcgg tcattggatt ggacccttcg
   147661 ccggttttct gcgcatatag tgcatccaaa ttcggtgtaa ttggatttac cagaagtcta
   147721 gcggtgagtt gaatacgatc ttatgcggat aaattcataa ttttttggtt tcaggaccct
   147781 ctttactatt cccaaaacgg ggtagctgtg atggcggttt gttgtggtcc tacaagggtc
   147841 tttgtggacc gggaactgaa agcgtttttg gaatacggac aatcctttgc cgatcgcctg
   147901 cggcgagcgc cctgccaatc gacatcggtt tgtggtcaga atattgtcaa tgccatcgag
   147961 agatcggaga atggtcagat atggattgcg gataagggtg gactcgagtt ggtcaaattg
   148021 cattggtact ggcacatggc cgaccagttc gtgcactata tgcagagcaa tgatgaagag
   148081 gatcaagatt gaattcgaat caaataaaat aatgctttac gcaaaaagta ggcaattcat
   148141 tttcctatga taatagatat tttttttttt tttttttttt tttttttttt tttttttttt
   148201 gatgatgttt ttattatttg atcaacgcac tgttacccat gcggcaactt aatttgatct
   148261 gcttaaatta ttttatttta ctatgtgtct tggttactta agactaacag atttttaatc
   148321 ctaaaaatga tagggagaat tataatagtt gatataacat agtattctaa tgaattttaa
   148381 aactaagact ttctaggtca aaaccaggtt agggaggtca tgagggtggt gtcgcttgag
   148441 tcttcttttg actctagtcc gagggtcagc attgaccaca gctgcagttc ctagcttcct
   148501 tgctaggctg ttggggtgta cattaagcct ttccatatat ttttgggcga gcgaatgttg
   148561 atgggagcta taattagatg tgcttaatta tgatggggtt acgttatgca tgttgtggga
   148621 atgtgaacta tactgttttt tttttgacat cagtcgacta tatgttctcc taacaacctt
   148681 tgatctaaat tgtaagtgca aagtcaagtc caactactca aggctttttc aacaacaata
   148741 tacgtagact ttacgtgcaa catttctaga acgtctctag tgcatctcaa ctatgcgaat
   148801 gcatgtcgaa attttgctag agcaatgccg tgcattgaac tttggcacat ttccaaacgc
   148861 acaggcagac ccagtcagcc ataggaaacc caatcggacg accgagaatc gaatgcgaaa
   148921 acaaacaaat ctgccgacac attgcccagg aatattggca ctgagagcct acagatacac
   148981 caggaaaaaa aaaaaataaa tgctgggata gttttggtat tttcggtact aatctaacgc
   149041 aatagccctt ctacggtcga gtaaactgaa aaactcttaa tatttttatg ttgcattcat
   149101 taagtagtat acattttcta cttccaatct tgccttggct ttttctcatc gtgtagctat
   149161 atctcagcta tatggtgggg tgagttgtgg gcacgccgcc ttggcatact tccaattcga
   149221 gtgcgttgtc ttccttctag tcgggggcca ctcggttcgt aaaaaatcaa tagccagcag
   149281 accaaaaaga gccacaatat catcggacat tgaggaccca acgcaacgga atggaaccaa
   149341 cggaatcgca tggagtggaa tctggccagg ccatatcaaa gcatttttcc agagttccca
   149401 ctccctgccg tccgccggcg ttgcaagttt gctttccttt cgatggcgca acttaattcc
   149461 aaaaatcgat tagtcactgt aagcgaacca tgcaattgtc cagcattttt catttataac
   149521 tccttttttt cgtttaattt ttgctggttt cctccccttt tccacttttt ttttttggca
   149581 cacgcttgat taatttggtc agctgccggt tggcaaggag gtggggggga ggacatttaa
   149641 aaatgcagga agtaatcgat tggctagggc acaatagcca aaatgggaga ggcagtgcaa
   149701 tcgcaaaaaa tattggggta tgttcgcctg aaggaaatgc cggaaaatat tgaaaattac
   149761 gataccaaga tacattgcac gaaataataa atattctggg ccggtaattg accaattttg
   149821 tttgtccatt tgattgtagg tgtactcgta aatggtaggt tatattaaat gactaataat
   149881 tatattgaat gcaactattc atactaagag tatctaggct tcgactagtt ctagtatttt
   149941 ccccaacact gtagatcgaa caaaaacatg cgaccgaccg gttgccggca gtaggtggag
   150001 attaatcaac aaaaaaaaat ttgcggaaaa atggaggaaa aaattactga tgctttttaa
   150061 atggcaatac gtgcctggtc accaggtatt tcactaatta acctgacgga tgcacaccac
   150121 agccaaagaa gatagtgatt atgcaactgc atggatcgct gctgttgtct gtgtatgagc
   150181 gttgtgagat aatgaagtac tgatctgatg ggagtttata gccaacactg ataatgcact
   150241 cattatgaaa cctaatagcc attcattaat ggagtgggaa atcaatggta ttatagtaat
   150301 taagcaaagg ttatgagtgt tgaaaccaaa ctgcaggatg tctgattgtt ccttaagagt
   150361 aatgctctaa taattagtgg aatataaaga attgaatttc catttgctat gtatgtaagt
   150421 gtaaattaat ataagactat atatatgata aatgttacaa tgggtcttag aatacattgt
   150481 gatttgctct aaagcttgaa ttctgatgtt ctgatctagt tcccctcggg cagagttcac
   150541 caatctcgac tcgttttata cgacatgcgg caatgtggcg aaaaagaaac agatgaacac
   150601 atgttagata tggaagcaaa taccccttgc ccgccaagac cgctctcaga ctttgaagct
   150661 ctgaaagcca agtcccattt gtatggccga cttgttgtct cgggccagag actatataac
   150721 tctcggcctg cgattcagat tttgactgag acaccgatgt ggagcttgga gcggcgcata
   150781 aagattatct acggccgcac atggcaccag gcggtcagac aagattatat gcgaaatgtg
   150841 aagccaaata acaagtgtta ctcaaggcag caaattaata gccaacattt ttctaaacta
   150901 atcacgacaa gtgctccggg tttgaggctg acacagaaaa tcaaacagcc ggctgaaaag
   150961 gcaaaactcc aacttggcca actggtggcc caaaaacagc aaatagacag atagatctga
   151021 gcgcggctta aatgccaaaa aatgcagtaa gcgaaaaata aacatgaaga aaaatgacag
   151081 gcaaaaacgt tacttgccct ccgggggtcg tcgcatccac cttatccgcc ccactccgaa
   151141 tatagcacca ttgctccccc atggacaacc attccccatt cgggagtgga gcgaacttga
   151201 gccgacgatc tgagattccg acacgtgccg ggcgacaatg ggaatggtcc aaaatgtcca
   151261 taacaatggc gctggagtac aaacagcaaa cattttgtaa atttgcgtcc attgacactc
   151321 cgaatgatac agatctcgct gctctcgatc tcgtttctga tccagagggt caccctgttt
   151381 aaccgggagg gccacatagc cggtagattg gcccacgcaa agttcctacc cctcgccagt
   151441 tcagtcccct acctgaacta cactctcgtg gtacccattt cagccttgag gcagcaacca
   151501 ctttgtatgt acaagagacg aatgtgaaat gatgtcgatg cactgcaaaa atgagctgga
   151561 tattgaatta aatcggtgaa tttagtaggt tgacgaaaat ccaaaacatt tactaaacta
   151621 aaagatacaa tctatacccc cttttccagt tctacgaaaa ttccacgatt tttctaacta
   151681 cccctctcgt tttttttttc agtgtaaaaa taagtaatat tctgagaggg gtaaacgggt
   151741 gaaagggtgc tgactgaaag ggggagctcg ggaccggtcc tgggtgcatg taacacaatc
   151801 aggaagtaat ttttatgcta tgtacccata gcatgtgtcg ccgtcatcgt cgacgtagct
   151861 gatgctgctg ctgtcgctgt tgattttgcc cagtttgttg gtgttgccac agccgaggtg
   151921 gatgtggata tggatgtgga tgcgagtgat ccggccagtc agcggagaca gtcgctcggt
   151981 caggcggcag ccgggaagat ggcaagttga gctgggttct caactctctg ccgagttgtc
   152041 gggggaattg cattcgagcg cccgagctca agcttgagct cccttctccc tttgggaggc
   152101 aaagtcgagg aactgggtgc attggggggc attgattggc aagatgatga cgacgacgat
   152161 gatgtgaggc aatcgctgaa tcaatcttgg ccagtagttc agcgtttact gttattagtt
   152221 gctggaacat tgcattttga tcgttcccaa tatggtttgc tcttcgtttt ttaatagaaa
   152281 aagaaaaacg cctggggcaa taaaatggtt aagcgatggc cagagagtta agatacaatt
   152341 ctgaattaat ataaaaggtg atcagatatt gtttaaaagt ttggtctttt tgaagattag
   152401 tatgagtaat cggagagcaa atttattaaa ttttttatac agttaatatt aacatagaaa
   152461 atgccaagaa aatgttttaa aaatattgca attttataac cagtttcttg tgtatgccct
   152521 ccggttaatt atgacacttt aatgagcaga aaatgaaatc gaaatcactc tggctgaaca
   152581 atccaatcaa caactctatc taaataacaa gtatctcgaa tgcaatttaa gctgccccac
   152641 gaagacctgc gaaatgggaa actaacggaa aaacaacgaa ttgtgaaata attcggcaat
   152701 ttcaaaattg atggcaagcc aaaattgagg caatagaaat cgattagcgc cacgcttcag
   152761 ctgaccagcg aaaagtttaa aaaagcatta aaaacaaagc ggcagagtcg gaaaaaaatt
   152821 aagttatcga cacaaatgaa aatgttcggt agtaaacgga ctcgtgcgga atgcgttttc
   152881 gtctacgcca tattctttgg gttttcctct ccggaaaact cattcagcca ttaaatgccg
   152941 ttatctgctg attacacaat aaaagcacaa ccacaaagca gcagcaacaa atgctactgc
   153001 agcagcgccc agagctaaga gacctaattc gaggcgcatc tgtagaagag ttgcggcaac
   153061 tgcagcaaca acagcaactg caacagcaac agcagcagca gcaaaagcag ccaaagcaac
   153121 aatagcaaca tgcaataata taacgtaaca tttagaacgt ctttgttgtt gctgctgcaa
   153181 cttgtgttgc tgttacccac agaaaggctg accaagagaa aaggctgccg caacaatttc
   153241 tcgcaacatt ttgctgcctt gcatcattta gagctgcacc cagagaaaat acgggccatt
   153301 gagaatgtaa caaaaatatt ttgaataaat ttaacttttt aacaagttaa tgcacgtgaa
   153361 tttaattttt gatgaaatta tctacaagtg ggttgcataa ttttctgaag tgtaagcact
   153421 gctattagtt agatgaatag taaggggagt ggcacatgcg gcatgcagca gtatgtgcag
   153481 ctgactaaga actaaaagcc gcagcaaaaa cgaaaaaaaa aaacagattg gcataaagaa
   153541 cagtggaaag cctttcacca cgcattttga gacgtccaac caaaaatgtt tctgaaaatt
   153601 agcttttagg attaagttac ttaacttcat taggtaactt catcaaaaac aaaatatatc
   153661 aacacacaag tattactatt ttaaagaatt atcagatgta tctttttcgt atctaaaact
   153721 tttgcagtaa atcagtaaat tttatcttta ttaatattaa tttatatatt tattcactgt
   153781 gcaaatgatt aagataattc atcataaatt tttattataa ttatctgata taaattcagt
   153841 tgattaggga taaaaaatca acacagagag ggagctaaag gtcgttttga gtgtgaagac
   153901 ataatattga acaatgtcgt atatgtacaa tataataccc ttgaagaaag ctacaatatt
   153961 aagccaatct agggaatagt gatcaattca ataaaaatta ataattattt ttcccttgaa
   154021 aaaatttctt ttacattttc ttaaggatac cgatgtaaaa taaatgaaga tcactaccga
   154081 cgaaagggta tccatcgttc cttgcagcca gctatccttt ctggtttcgg agctcagaaa
   154141 atgcggtttg tgttcgcctt cctacctggg ctgccttgta tctaggtgca agaaatcgag
   154201 tctcaaattg cgccaaagcc gcaaactggc ccgctccgct cttggccatt agttattaga
   154261 gcttggtcag ctagcaagca gcagcgtgtg gtgtgtgctg tgtggcgatt ttgcctttgt
   154321 attggtgtct tggaattttc aacaagtttt gctaaaatat gatattaccc aagcaggttg
   154381 cagccgaaaa caaaaagagc aacaagcgcg gcaaaaatat ttgtatggat atttggaaat
   154441 ggcgccccgt tcccagtcag cgtggatggg tgaacaaact ccaaaagtga ctttggttgc
   154501 aagactcgaa aaatgcataa atgaaatgca ttcgagggga gcgcggaact atggacatcg
   154561 taagtcagct gaccattgat tgacgttgat tgtgctggcc cgtttggttt gtcgcgcgtt
   154621 cagtgaactc atttacagat tcggtttctt ttcttttttt aatgtttgtt ttagcaatga
   154681 cacgacatta aatgtcagct ggagtacccc caattttttg tcagccaatc tgacagcatt
   154741 gtgtgagttg tgaccatggc agaagcactt gtgaaggaag atgggttgaa ttaagataga
   154801 gtcatagaga tatgcatgca cgtggccatt cggccaggca tttcgcacga taatgaagct
   154861 tatgcaaatt accaaaggtt gaaggtcttt gctcagcatc atttgttgtc gagattttct
   154921 cgtttgattt atgaaaattg catatgtttt tcctgtgtgg aaacaaagtg ggcaatttaa
   154981 agttaggaat tttaggcagt tccactttag caaccatatc caaatgttaa aaactataca
   155041 actgacaggt cgtacatatt aaccatgtta cacacgccaa ttatgttaag tatgtttcgt
   155101 gcattacaaa gcttcttata aaaagctgta ttataaacaa cgcataagat ctgtgggtta
   155161 tctagggtta tttcatcgat tgattgcaca tatatataca atattttttt tgctcgagac
   155221 ttgcgcacta ttgaaatgca aatgccgtgg tcagtgagat tttaaatctc aagttaatag
   155281 gagtaatttt acaatggacc gcaagccgag gagaggaata ttaaaatttc ttattttgct
   155341 ttcgatcttc cttgctactg tatcagtttt ggccgagaaa aatgaaatcg cacttggaaa
   155401 cagatgtcgg cttacacacg tgggacctcg ttgctaaaat ttgttaaagc atttaaagaa
   155461 ttttcttatt ttgtatatat gaaaaatgta cgagcgattt tgaattcatc ttttttcctt
   155521 tgctttggtc aaataaatat aatacatttt taattaaaaa catcaaagat aggttccttt
   155581 tcatatgaat attcgctgaa ctaggctatt caactggagc agccaaagtt tgcgcaaata
   155641 actcccacag ttcagagtgt aatatgccat tatatattga tgcaaatgaa cttttgacta
   155701 acgaaggtca attgtctttt gtcagtgttt ctatatagtt tattatggtc tgttgtcata
   155761 gtcacaacac aaatggatgg atggatggat ggagtggctg aggttccccg aagcacagat
   155821 aagcattggc taattaagag cctccgaccc catgccactc accccccccc ctcccccctt
   155881 ggatacaaaa acaaactaat tgaatcggcc agagtatcga aatatatata accaaaacag
   155941 aaacagagag aaaaaatcga agaaaaatgc cataatgggt tcactaattg cttcaattag
   156001 acatcgactg gggcttttga aggcagcata cagcaacagg tgtgcaaaac gaccgacaaa
   156061 gttgtgcaat acctatggag ctcaattgca gtcggtccct cggttggggc caagtacttg
   156121 aatctctcta ttgtttttaa aaagttcacg atatttctgt tgttttgctt tttgcggtca
   156181 cacctttgtg gatttttcaa ttaaacgatc agctgacctt gatacttctt gactcgcaat
   156241 cgagtttatg cttacacgct tcaatctata tatctcgatt tattctgtta ttcggtctta
   156301 actcacctga aagaaaagaa aatatttgaa aagattcatt agtgaattat taaatgcaag
   156361 aacatggact taaggagaac aaacacactt ccttattgcc aacggggaga tgcctaatct
   156421 ggccagccat taagagccca agaaaccctc acatacacta agagaaaaat atccacaata
   156481 cttatgatct attaaataat tttaagcaag gattgagtat gtgaattaat aatattttct
   156541 aataagagtt gatcaaaaca ctgtctctta aatctttggc atgcacaagt tgtatttaaa
   156601 atagatcagg aactaactgc aaattgtttt gcgtgctatc aactccttga tgcctaaaaa
   156661 gatcccagca aagagctggc tggcataatg aattgtcaat cattatgcaa tcttcgagtg
   156721 aaaaatgatg cagcaggttt ccctgctctg ctctcgctgg gatatctctt agccggcgaa
   156781 tgcgtgggcc gccaacattt agacacactc tgagacagtc ggacgctcgg acggacagac
   156841 ggacagacag acagacagac agacaggcga tcttgtgatg tgcaacatgg tcttagatct
   156901 tttgccgtgg catgtggcgc tagagtaaaa ggcctcggag agaaagaggc ttgaactcga
   156961 gctcgaatct cgacttggag gagttgggac ccatcattta taacacggac agctcgagat
   157021 ggcgttcctt accctttttc ggctcgcttt ttggcatttg ttatgtggcg ttctcgtttg
   157081 cattcagaaa tacgtaaacg catacataca catagcatag tatgcatagc atacagtata
   157141 cagcttccaa aagacacggc ccttttagga gacaagacaa gttgcgcgat gatggatgcc
   157201 acaagctggg ctcataaatt cagcttgttt ttaagtcggg aaacagaaga tggaaagatc
   157261 tgcgggggcg tctattggtt acccttgtca acacacccag tctgaatggc tattgggaaa
   157321 tgcctttgtg ttcgattgaa atgcttacga aagagtttga tatgtttaaa aaatgatagg
   157381 aaattgagtt ggaacaccat tcattcattg aattcataaa atgaataata tgaataatag
   157441 ctaagtgtac gaaaaactta aaattagatt tagttttatg tattaactaa gcgggaaact
   157501 attttttttt gttagttact gtactactac tgctgttacg aaaattacta atgattgaca
   157561 ttcatttaaa catttctttt agtttattat aaaaatagat ggctaataaa tggcaagtgt
   157621 cttgaaactc ggaagcactt gctgtatttg agtccattct taacttgtct ttaattcggt
   157681 ttgactattg ttcaacatgt gagaaaacat aaaaaaaaac tagtcacaaa aacacataat
   157741 atttattgac tgcttgtagc tttaattgac aattaaaagt tgaactaata accaatcaga
   157801 ctcaattctc accgtaaatt acaaaacaaa ctgaaaacta atcaatgcca taatgatcaa
   157861 atccgattgc caaagcaccg caggaagtca attattggtt taatcattac caaaacagct
   157921 cgaagctctc attttcaata tttgtaaatt gattattgca ttgttgttgc tcgcaagtga
   157981 atgcaacttc ctttggggcg acaaaagagc acaggctgtg gtcataaaaa gttaatagag
   158041 ttgactatta acttgtcagt gggccccata gcacacttgt tggccatttt gcaagtggcg
   158101 actattgcaa aatatataca tacacaggta tttcgtacat gtatgtacat acgtatgtaa
   158161 actggggctg ggagaatcca gagagttggc aagtcgtcaa ctcaccaagt cgtcaatcat
   158221 tttcatttcg ttaaacgtgt caaatgacgg tcgcgagcgg aaatcgttca ctagtagtta
   158281 ttttctttta tgggggaatg ggctaactgc cggcgactgg gagagcggca attggcttat
   158341 taaatgcgcc ttaatgcgat acgtgttaaa cggggagtga gcagcaaatg tacaaaaaaa
   158401 taaaaaatac aaagtgaaca taaaaaaaaa aacaattgca acatcgctgg acacgcccac
   158461 aaatctgcag ctgcagaagg cgttttttcg taattagtgc gaacaagaca ctctccaaac
   158521 agagctggaa aaacaatact cgcaaacggg ggggtagcac aaaaaacaaa gtaattacgc
   158581 ggaaatcaaa catctaacat ctccctggtg attttgcaaa agtcgttacc gttatgatga
   158641 aaactttagc gcgaccattt ccaccgcccg tcccctagtt ttcccaacca gccatagtat
   158701 caccatctct tttttgtttg gctgcacaat attgcacatg ggcacagatg acaaaaacaa
   158761 actgcggcag cggataaaaa atgaaaagca caaatgccgg cagaaacgat agacgaactt
   158821 gcataaagca tcagccgcca gccatcaaat gaaaaaagtt aaataatacc ttacagtggg
   158881 tttggaagag gggtgggggg tctcagaaag atgagtagag atctcatacg cgtttggatt
   158941 cctgcatttc gaatgaggag tactctagtt ctagaatata gaaagcttat tgaaataaat
   159001 tatctgcaaa tcaaataaat gtcgtattct tcaccaacac ctaacattta ttattattat
   159061 taaagttaac cttctcttag aaggatttca ttgtttgagc tatttgtatc tttatgtagg
   159121 gtattcactg tccagatata agaagtgcaa tgctttttat tagggctggc ccgctagtcc
   159181 ctggtgagca cagtaaaacc acaccacagt tagaaatata gcgtctcttt ccgccgtcag
   159241 acagttcgtc aatgcaacca cacatgagct gccaccacgc cccccggcgc accactgcac
   159301 caccgccctc cgcccatcgt tcatggcggc tccattcaac gacaatgacg gcgtggaaat
   159361 ccaatacgcg atctctccaa gtcaacgtca tcgccgttag acgctcggtc tacgtaagtc
   159421 tcgccttgtc tcaactcagt gttttatgta atggcagaag caaaaagcga gaaaaactcc
   159481 gaaggcgacc aaagctggac atattccatt gaccacatgg tatcgcgtac tgcactccaa
   159541 atatgaacga ttgataatcc atcaaagttt ttacactgcc tcgaggttca agtaatcgat
   159601 atgagctgcc tattcgaata atgaatttca attaaaaatt agtattgtaa aatgccaaga
   159661 taaactttta aagtgtttca gttagttatg ggattatatt ctttttacaa acacttgaga
   159721 tcttcaaaat aaatcatatt agtttgtaaa accaagagct aagcagttat gtaatttctt
   159781 ttttcttata acgggtatat ataagagcaa tgcttttatg atcattgtca ttgtcatgaa
   159841 atatgacctt aaacaatgtg cacaagtaat tctcttattg tctcgttttt gctgactgat
   159901 aggaaagaat ggaccccaga gatgagtttt cattttcccc gctttggcct tttttgccat
   159961 tgaatctgtg tgacggtgtt ggccacaatc tgcagcattt accgttggca attgtgggcc
   160021 ccttcaagac ccgagcaatc aattaacaca cctttgggtg ggttaaacag agggaggcga
   160081 aggtgggcag gaggagctgg agcacccacg ttgagaactc catccacatc gctccatccg
   160141 ctgcactcca ccgttgacag ttgcaaatgc atcaggcggt cgcgagtcgt gggctaattt
   160201 gcggtttcag cttgcagccc aactaattaa catataaatt tagaggtgtt gcacttttgt
   160261 atttatttat gaatgaaact gacagagaca aagagacggc ctggtcgtgg aggtggagaa
   160321 ggaggctggc agggagtggg aaagtttcaa gtgcactgag aaaaatttta agtaaattaa
   160381 aagcaatatt ttgcgtatac aaattgctca tacatataat cctcaaaaaa tgaattgttt
   160441 tcgttaactc aaaagaatgt tacaatatgt actgcctaac ttatgtttgg cattttgcat
   160501 tttttgtcaa ctttttctgt cagtgtgcaa atctgcaata tgcatctcgt actcatatgc
   160561 aagccaaggt cgatttctgt tccgttcaac tgcagcagca gcagcagcag catcgacaac
   160621 agcggattgc agtttatggg aaagagttta gccagccaag atttattggc atgttattct
   160681 aattgctatt tattagcggt gggagacggc agagcagctg ccccgctgtc tgacagtcag
   160741 tcattcagtt agtcattcca ttcaattgtt catgcagcca ttttcaagtt ggcaggccgt
   160801 caagtgtgca aattagtttg tttggtttgg tttttatgca tgtgcttaac ccacttgtac
   160861 gctgtgtgct caaaattgat caccataaac aaataaatgc atatttgaaa aatgtcaaaa
   160921 tgaaatgtat ttgaatgctt gcaaagggct tggtaaaata gctgttatac aattacaaaa
   160981 gaaaaaaaaa acaagattat gaaatatttt ttagtttttt tttttgttta tcaaacttgt
   161041 tcatcttcaa agcaattaac acctctgaaa tcgaatttgt tatgtccggt tttcgtgatt
   161101 tcttctttta aatctccatc gttaacacac aattaacagc tatataaatt cgtaacaact
   161161 ttttcggtgc aatagcatcg tgatccattc gtttaggggt gatcgatcgt tgtttgcccc
   161221 aactcagact atatactcat tagttctaga ttacagatct ccccgcccat tcatccgcat
   161281 cacccacagt ctcaccggca attcatttcc acttccaacc catttcgatc ggtacgccca
   161341 caatcgagcg actgcaatcc gcagagaact taatcgatag actccatttc tatcatccgt
   161401 taattgcgac taatgaattt gcttacgtgt agacaatttt cagttaatat tctaattttt
   161461 ttttcccctc accccagcct cccccgctgg ccgtaacgta attagtttcg agaggaaatt
   161521 acaaacgact acgcgcactg tgggcgtaaa gtgaaaaaat ctaaatcact aaaccaaata
   161581 gtttcgcatc actctggttc gccagtgaga tgtttaagaa gagaacgggc ccagcgtcgt
   161641 aaaatgttgg atgcttattt ttatagcgga ttctcttggc tatcaaaatg ccataaagcg
   161701 agtctgggtc tctaagcctg accgcaaatc gcagctatta ccgctagaga aactaaatta
   161761 atatgcagca tttcgtgtaa ttcgcccacc aagccaaaac acttccttaa taaagcccag
   161821 ggagaccacc gaccgccggg ccagctaatg cgtgcataat ttttaataaa tatttttcaa
   161881 gatccccagc tgcagcagct gggttggcaa gtaaggccga gactgcgaga ctgagagact
   161941 gggagactgc ctgcggaggc aggccgaaaa tgcttcctgg tttaattaat aaagcccctg
   162001 agagaagaca ccgagtacca gtcagactcc gactcctggc caacttgtca atcaacaaca
   162061 ttcttatttt ccttttaaaa acggtggcca gagccatgac cgtgatgatt gtgattatca
   162121 atttcattat caggcccagg ctcgagatca acccgaggca aacacttccg ttttagaagg
   162181 ggaggccatc tcttcgacga gcaggtccat tgaactcccc ttgtggcgca ctcctcgccc
   162241 caactcaatg cctcctcacg caaaagtcgt cattatgaaa atatttcccc gcaacccagg
   162301 atctctggca aaaagcttat cggctgctgc tcagccagcg cttatgttgc ccacgtgtcc
   162361 gtctgtccaa gtagtctttg gagcaggttt tcctttctgg aaattatgca ctttgtatgc
   162421 agaaaagttg gcgaggcgat aaaaatctgc ataattccaa gccgtaagtt tattgccgtt
   162481 tcctagcatt cggggcgcaa gggaaaatga tgctcgaccg ggcggcagag aatgatagct
   162541 ggagaaaagg agacccctcc gctctgaccc gtctttcata atcgtaatca atattaagtt
   162601 atatgataaa ttatcggata ccaaattgca gcatttaact tgtcaaagga aattatcgga
   162661 aattatgcta aaaagggttt cagcgcggca gacgcggtga aattactttc ggaactccca
   162721 gatgcttaac ttaactgtcg atttgtctta agggctataa gactgatcgg ggtattgggc
   162781 caatctgaga gctacgttga accagttatg gccagcaaat tgatttgttt aacagtgatt
   162841 atgactgtct gctgtatccc atggttttat gtcaattata tcagttacct tgtgtgagta
   162901 tactaagact caattgtctg ctaaagtaaa aaagtttgat ttttcattgg taatgataca
   162961 agtgtaagct ttaattaacg tggatatcta atcgaaatag gatagaaaat catgtctagc
   163021 ccgacacctt caggccacac aatcaagttc aggtgccaga ccaacggacc caaggcaaaa
   163081 gccatcctaa tatcgttcaa aataaaaaag tgcccatgca tagagtcgag acaataagaa
   163141 attgactgca cctgcactgt ttgtggggtc gtaaatctgg ggaggtggta tctgggactg
   163201 cggagcacgt aattgccaca ctggagctac attatggata cattatggcg gcaggaaagg
   163261 gagcaggcag cagcggttct ttgtgggtaa cccagagccc cgagctgtgg atttgctgga
   163321 ggccaggaaa ggggaaccac ttgatgactg ctcaacggag ataaagaact gatggccgat
   163381 ggcgatactt ctcaagaagt tgggaaagtt agacaacatg atacacagga cttgggtgaa
   163441 atggaaattg agtggcgaat tgccactgcc taaataggaa atttttaacg aaacaagatt
   163501 atagcttgcc ttaaaaataa tgttaatttc tagagcccta tttttaaatc ctagatatta
   163561 gacatctaga catctagaca ttaaaaataa ttaataattt gtgtgccagg caatgtctag
   163621 tgaatttcgt tcattaattc aattacagac acacattcgc caaaagaaag tctttgctaa
   163681 acactggcta gtttggttaa atttatttcc ttcccgttcc agcaccacca attagccccg
   163741 ccctcgattc aagacatttg atcgttgaat ctgagtgctt ttccagtgct agcacgacac
   163801 agctcatggc agaaaacaac atccggtttg tgagctggag attgcgactg cttctgcaca
   163861 aatgttaatt aaatacctgt ccatctatta aaaaacatac gtaaatttat gttgttaaca
   163921 aggaagtgcg ctctgcgcat gcgcacactt ttattattat catcagcatc ggagatggcc
   163981 gtcgctcagc acacatcaga ggaggcagtg tggccgccac ttggccattt ctacctgtgg
   164041 agcccacctg cctctttcct ctcaccaaaa cgcccgccaa accacctgta actgtttcgc
   164101 agccatttgc atatgtcgcc gaacgtttgc gttgcggttt taacgatgcg ctgctgtcgc
   164161 cacgtcgcta cgtcattcgc taattggtcg agatacaaat cgccacgaga gagtgaagtg
   164221 acgacgttgc agcccccacc agtcccataa gccaaaccaa gaccaagtcc acatccaagt
   164281 ccaagtccaa acccaggaag aggatgagga tgtggaagag gcgttgccgg tgttggccat
   164341 cagctgatgc aactgcgggt gctgctggca gtacatgcac tgcaaccaaa gtagtactat
   164401 atatgattct tatttaatta ttattaatta ttcttattta atagttataa tgttataata
   164461 tagtcccatc tttatattac aaagtaatac aaactaccaa ccatgagatt gtattcaatt
   164521 cattttttaa agtgtatcaa gtgccaaact gtcatcatta cctaccttac cgtacccacc
   164581 ccgtgtcacc tttctcttgg ccaacaaaca gcggcacttt ctttgccaaa cgtccaaaaa
   164641 caaatcggtg gctctgctgc gtcgcctctg tcccgccaga tgctgtcaaa tatttactca
   164701 agtgtttctg cttttcacac caccccgtca aagccaccaa atcgccaacc atgaccagcg
   164761 tacttcactc cccctaccaa cagccaccac cccacctggg tggacaaggc tggcaatttg
   164821 ctttatggga tttacttgta gtgtggatag gcggtttggc atttttggga aagtggacat
   164881 cggaaatttg gttagcctta atgcattcaa ggtgtgattt ttccgttcgt gtgcccccaa
   164941 acaaactggt tcgccaagtg tggaactctt gggatgagga tctcactaag tcagtttgtt
   165001 ggagaagcca tgaaaattag gtgctacact tgcagcggtc attaggttca caatgtatta
   165061 gatatgaatc tatttcctgt tttaaatggg tatcatattc ggctaaacaa acaaaataag
   165121 caaagactcg caacacctgc gatgaaaacg atttcatata tatgtttaaa caaatttcta
   165181 ttagtctaga ctgttagtta gtctgctttg ttgggtccac attaaattta attcaattta
   165241 ttacaccatt gaatggcata ttagtgatca aatctcgttg tcattttctc gcatatatat
   165301 tttaatatta tcatattcgt tagaactcac ctttgttctg tacaatggat tgctaaagtc
   165361 ccaatctggc gccacaaaca gatatccgca tttggagacc tttcgcgatg cctgcagatg
   165421 ttgaaataga aaaaatggtt atgttaatat ttgtggtaaa caaaagtgtc acataagcct
   165481 aataaaaaca tttcaatgct gattgctttt cgaatataaa ttatataatt ttggctcgaa
   165541 tgtctagtga attatgaaaa tattttctag ctctttgata acaaatgatc aataaattac
   165601 caaaactatt taatcttaat tagcaaaaca aatttattcg gaaatggcat tggcgaaaaa
   165661 taatcgaaaa agaaaatgaa cagagttatc aaatcgcgct tatctcctga ccgtaaaaga
   165721 aatcaaaatt tatatgtatt tttaattaaa aaacgtcaaa ttttcgtagc ctcctttttt
   165781 gtttggcttt aaagttgtct gcttatcgcg cacgtgttat gtttacctat accgcaacca
   165841 ggtatatctg cacacattta tatagttttt tagcaaagct attcgtctaa cccgtgacta
   165901 atgttaatga cgtgcgccaa ttcaactgtt tgcgtggtat ttttggttct cgcttttagt
   165961 tttttttatt tttggagggg ttaaagtaaa taaaataaat tacaagtaga aactactatg
   166021 aaaaccagac cacttggctg ccacacattg gtggggtttc aacgggtctt ggcctttgca
   166081 cacctctggt ctagagctgg aacaataagc gacaattggg ccgcatttaa agtggatttc
   166141 agtcgttagt cgcgcccgcc attaggctgc tgtcggtctc ttgtttggga ttgttttggg
   166201 tctgctttgg gtgggtggtt ggtacataca tattgtgtat tgtgtacata tatattttcg
   166261 atttgacaaa gctgcaaacg agagtgccaa atggggggat agcacaatgc tcccaccaat
   166321 tgaacccagc tgaactggcg tttaatttga gccaactgtg acggtggctt aaggtcgcca
   166381 atcagcttct aattaaagaa agtgagacaa tctttaaatt aaaaacaatg aaacatataa
   166441 acgccaacta agtaaagaaa acagtatgta tttgtagaat ttataacagg cttttaagac
   166501 aatataataa atacattatt ggccacatta tttaaaagtt ttagttgatc aaatcaaacc
   166561 aatattggat tttatcaaat ctacatatca gacgaatttt agcataaaaa ggaatatatc
   166621 ataaaaaaag gaaaatactt taaattccaa attttttagt ggcctcacag tttctattcc
   166681 cacacaacat aactttgaaa acgctcacca attaagccac cttttgccat tggcaacgac
   166741 tttaagcatc gcctaggact cgatcccgac cgaccccgat catgtcttgt aagctgacac
   166801 cataaaatgt ttacaaaaca ataaaatagc aaaaacgaaa atcaaagccc aaaaacgaaa
   166861 tgtgtaatac ggtagttccc ggccactcac tcgcctccaa aactatccaa caacttaaca
   166921 aagttggtca aaagagaaaa aaatgcctcc cactcctctg ccacggaggt ctaatcgggg
   166981 tactctatat acatgttttc ttattttttt ggggtctcca gctgtctggt ttgcaattac
   167041 gctggctaat tttatttatc tgtcttggat tgtttttttt tttttgcatt ttatgatatt
   167101 ttctgtggtt ggtgctgttg tagtcggtgg tgggtcgttt aaatgcgcca ttaacattga
   167161 tttatgtgaa aagtcgcacg tttgtattca aataactggg ggagagagag aatgagtgag
   167221 agacttgcaa ccgttgcagc aacagtagcc gcaattgcaa tcgcaagttg cagttgcagt
   167281 tgcagcttgc agctgctgtc aggctttcat caggctaagt cagtcgacac gttttccaca
   167341 taaatttcaa tgggtccgaa aagttaagtg acagaaatag gttcaggttt agtgggtagc
   167401 taaggtagca ccttctaagt aacgacccgt ttaccgatag ctggctcaca cgatcaccaa
   167461 attgcgatct acttttgtca cattacggcc actgctaaac tgtgcgacgt gtggggactc
   167521 cgatggatgc gatggaaaaa aagagggggt ttcaaaaata ccgttggcta ctcgtaatac
   167581 ccgaccacgt agcccacaag accgactcca ctggcactgg cagacattca gccattcaaa
   167641 cataaattat caatgccagc ctggtcgctg ttttgcttgt ttgggggaaa aaaaaataaa
   167701 aaacttttac gaaaactaca ggcgaaaaaa attggcaaaa ttcgtgacta aatgagtcac
   167761 aattgtcttc taaattgtgc gaactgtttt ccattttcgg tgtccccaaa agaattgatc
   167821 aaacacataa gtaaagactt tgtgtgtatg gatgccagta taccctcagt aaatagtttt
   167881 taataattgt ttggcaattg atagctgtgg gaaaacattt gcctctcata aggtcagtca
   167941 tgcactatga ttaagattgt aggttcacct ttgaaaatac aaaaaatggc aacataattg
   168001 gcagtaagtt attttaatta aaaataacaa taaggctacg agatgagaaa aatatgtgaa
   168061 ctgtgatatg tttggccaaa gtaaagtgaa tgaatatgct tattgtattg ctgtgtgaat
   168121 tgatgtgtta tatttttaag ttgtgtctac atgtttttta gtaatttctt cacttttaag
   168181 atccaggagc caagccaact tcttgtttaa gggtatttca aatcaaaaac aagccaccaa
   168241 gccaggctga atatttatgc atcgcgcatg tcgctgctga cacacaaatg ggagattttc
   168301 aaatgaaatg gggcaaacca cgtggaactg gagggggggg ggcttttggg gctgcgcgtg
   168361 cagaattttg agtgagccgc tggaatggtg ggcgtggcaa cgcccccagg cgctggctaa
   168421 tgaagcaaag tgcgccgtgc aaatgtggac cgacacagac agaaataaaa ccacagccca
   168481 actgattgat cgctccgagt gagtaactca gccacaaata cgaatgctaa tgacaaatca
   168541 aaaggttgtg actgttgaga atcgcgtatg tattcggctt caaggtaatt taagaagttt
   168601 acaaaaaatt tttaattgaa aaccattacc aatctagcgg attttctcaa cctacatatg
   168661 ttcgagcaca ttttaacaaa caaaatttaa gcaatgaaat tctctttata taacctgtga
   168721 tgatttctat ttaaagtatt atatattcaa cattttaaca ggtaactatg tgtaatgtgt
   168781 tttgaaaccc aaagagttat gtaaaacgaa atgcgtgatt aaatacattc ctgtagaact
   168841 caaaaacgtt tttacaaaag aatcacacac tgaaaacact cgatatgaag tcatgcaaac
   168901 gcaattatgt atgagagaca cgggcaagaa aactataggc gatcgatgga tcttagatca
   168961 tacttatccg caataaatgc agtcttatac ttactggttc tgccagattc gacgaggttc
   169021 gctattgcgc aagcgtgcaa gatacgaata gagaatgcat tcggttagtt ggtgaattaa
   169081 atagttatag aaaaagagaa ggggtgaaga cgaacgaaat gactcaatta gcagcgggga
   169141 agatgtctca gatgagaggc tgatggtgat gcattttgac atttagccac atttgagatg
   169201 acattcaaga cgctcgagat gagcccgaac cccatcttac cccttagttg cagcggcagc
   169261 caaatgaatt taaattgcat gagaccgact tgttttcgat ttaatttgat aagaaacccg
   169321 gggcgagacg ggtcgtccgt agtcgtcgca tacttatgac tgtgaaatgt caaatcaaaa
   169381 gtcacgtttt tcactcgccg ccaagctagc tgatttattg gcagcagtcg gggctattaa
   169441 ctgaatcgta ccgctggcca taaatcggct gccggctgag ctccacttgc agagttgtgg
   169501 aaaatttcac ttttgctgcc gcagcggcta ataagccaaa aaccgattga caaataaaca
   169561 atttgtggca tccatcccct ccacatacga gtatcacata catctatcta tctgcacata
   169621 tggtataccg tgtttagtta gtgagtcgca cgcacacgtg gatccacatc caagtccaag
   169681 tcaaagtcaa gccatgccaa gtcaagtccc aaacaaacct ggtccaactt cgagttggag
   169741 tggaaagttg tttgcagctt caatctcttg aatctcgtcg aatctcttgg gcttttaact
   169801 caatttcagc ctgctttagc tgcctagctt tgtttgttta tttattttgt gtttatttat
   169861 acatgtgtat tttcaatctt tgccattgca gttgttgttt cgcttcgagt ttctaagttg
   169921 cggcttaata ggcaagccac aacaaccaac atcctcaacc acagtaacaa caacaaccga
   169981 ctaaatcatc attagccaca tccatccagt tggcaaagag atggcaacag gtttttcaac
   170041 catcccatca tgctataaac agtttctgct aaagttatcg aatagtattt tgaatttgat
   170101 ttcccattca atgaagccat taaattcaaa cacaaaaaac acgcgcatac tacacgcata
   170161 attcattaat agaagtcaaa tgattaatat tctttgatta aaaaattgca aataaacaaa
   170221 aattatattt tgttttgcag cgtttgagca tcatctcacg caatctgtta gagattgctg
   170281 aattttttat tagcattttg gaattttcaa tcatttctgc agaactctga cacaaatgct
   170341 aattaagtgg attccatgaa aacaacacgg cgacaaaaac aaaatattca cagtaagcgc
   170401 tggagaatcc ccaaagttta ttttaaataa ataaatattt aacaataaaa ctattcttca
   170461 gaaagcgaaa ccaaggcggc atttttggca tttcattggc gtaatgctta tatatgggac
   170521 atgaaaatta cagaccatca attcttataa ttgaaccatc aaattgtaaa gtggatgaag
   170581 tccagcaaag tctgggcttt tgtcatacag ttcatacctt cagtaaagtg ggccagcgat
   170641 cgagaaaagc aagatcgagt gagacaattg gtattacttg actggccatc aatgaatgaa
   170701 aacaattttt accagaaacc gtcttttttt ccggttataa atcgtatcaa tcaatcgatg
   170761 gggaggtttc cgaggagcat aattaatgtg tgagaacaac tttcttcgct gaccatgaat
   170821 cgaagcgcct cagtgtttcg gattccgaca cagactgcgc ctgaaacaaa aatgaaagtg
   170881 gccctcgatt tgttggccat aaagggccgt cgccgatctt aggcccgatt aactcaatga
   170941 cggctaatct cttctcattc ataactataa acatatatat atatatatgt gcctttacac
   171001 accacgcatg gaagcgtctc cgacatgaaa tatgattaat aagtttcgca cgattattaa
   171061 gtcccccaga ctctgatcaa aaagcaagag gcaacgaact gggagaagaa agtggtttgc
   171121 gatccgccaa gacacaggtt gattgacttc aagagggttg ggacatgggt taatgccatc
   171181 agcatattta aataaatttc tgtgggtaag ctttactcct agtatcgacg tagtttaaaa
   171241 ataaacagta tgggaaaata tacaatttat acagtttatt aaactaatct ctccatatga
   171301 aacatattgg taaaataagc gattaatctt aataaaccat taacaaacta agaattattt
   171361 aattttaaat gatatatata ttatcctatt ttttagaaca tatctttata tcaaaaataa
   171421 tcttaatatt tattattatc aaaaccaaaa cttctgatgc acctttgaca acttattcaa
   171481 gggtatgaaa aatcgaaagt acaaaagaaa tcgaaagcga aactgcgcaa cacaaacgaa
   171541 acttgaacag aaacagagag gccgaacatc aagtgcaaca aaccgatgaa ccgccgagcc
   171601 gagaaggggc agatcctcgt cggaagggga agggaagggg gaggggcgct gtggcgtgga
   171661 gtgcaacggg tgcagggggg tccgagtggc aagtgcatgg cacggcatgg catgaaaata
   171721 ttgtgtgcta tggcactggg tagcaagtgt gactgaccag cagctgagag gcaactgcat
   171781 ttggaaatga aagcgaatgt cgtcgattta gcggttgtgt gtcgacggtt tagtgcacca
   171841 tgaaaaataa aacaaaaatt tttcaagaga gtataactgt aaaatcccaa ataagaagac
   171901 tttactcgtt gagtttttgt aagaaactga ttttatttgg aaatatcttc ggtttaaata
   171961 ggtgacatga gaatcgcatc ttaaagtaaa tggcctacgc agaggcctaa gtaaatagtc
   172021 cccgccttat cgaggtccca cgctcgggca catctgccta tcttgagcgg cgaggacctt
   172081 atctgtggtc tcccactaag ggactatttt aggaggcggg gaacgatctc aagtgactga
   172141 ctcatgtagt gtgcacttaa attacatgtt tttgagcaat gcacccatgt cgccttagat
   172201 aacaaaatcc taaatataat ttatcgctct cgattcattt acataagata tgaacggagc
   172261 ccaaaattgt aagtctttaa atatattcgt gttcatgtgt gaacattctg ccaaagggcc
   172321 agcaagctga gatgtacatt agtatattag ttgcatttat aacagtagtg gactgtattt
   172381 atttgatata tgttcattta ttttgcaact aagatttcaa tgggcctagt ttttctggct
   172441 tttaatttta ttggattaca attatggttt atattatttt taattcaaca atttgtactc
   172501 aattaactta ttttaaacat tttgcttttt ctatgtagaa gtacattttc tattaaacaa
   172561 cgatatagtg gactgtatat ttttatttgt tatattattt tattgtttat ttactattga
   172621 tatttatagt actggcaacg gacctgcaaa ggttattgct tgcattcttt gttgcacagc
   172681 acatttccgt atgaaatata ttattaatac tatcattagt attaaagcaa taattaatcc
   172741 agcatgtccg gaaatatgat ggaaatgtaa atctttcaat ttttgatggt tctctttcat
   172801 aaatttaatt tcattattca atcgttcaaa ttcctcagta tgatttaata ttgatagttt
   172861 cagcggatcc caaataatct tcggcgcttc actaacttct cctatataag gtgttgataa
   172921 taattcttca ctttcggact gaatgttatg gtgggcaact agaattttat cgtcggttct
   172981 tgccgtacaa tatggcgcaa tgcttaaaac tccttgctga ggcaaatcaa acaattcaat
   173041 ttgagagcca gtacattgca gacggacttt tgaattcgca ggaaccttaa acaaccaact
   173101 acttttcttt tctaactcta cccagtaacc tttagagtcg actactgttt tatagatgca
   173161 gttcgccgct ttatctggct ttagaggctg aatctcacat gcattatcat tcgctgaatt
   173221 ccagggccaa cttcctttgc atattctctt atttagttgc catttctgac attgatttaa
   173281 tgtggcttcc gtcattatgt gataggaatc tatctcaaaa ttataaatta aatattcgga
   173341 cgttgtatgc accattatta tccgatcttc atttcgaatt ggcaccggaa taagcctgaa
   173401 caatttggat ggatgcctgc taaacagagg cacttttgca ctaatgatca atttatcgtc
   173461 gatgaataaa cccctggctg ttaacagtgt atacacctcc ttaagttccg tacctgaccg
   173521 ttttcctgga attactaggt tctccgaaag actctgctga attttggcaa tttctttttt
   173581 aagctgattt ggcctgagaa tatttgtatt tagcctaccg tgattaatat caatcaacag
   173641 gcttataatg cctgcttgaa ttttttcgcc ttcttcaatc aatgagtgta gctgtttcgt
   173701 aatcataaag aattttattg attccttata aacataataa ttttctttaa gaacttctgt
   173761 catgttctca attcttattt gcatacttct aaaattggag ttaacatctt ctgttgttct
   173821 ctttaataga ttagaagttg aatcaaccac agatgtttgt ttttgaatta gtttatcaag
   173881 gttgttctgg ttatctaaca aattcttcat attttcttct aattgctctc tatcatcttc
   173941 atccattata ccaaataaaa tatgatacaa ggaacccata aattcgaaag gagcacgctt
   174001 gcttctagat ctagactgta tcataaacaa tttattgttt tcttcaagtt ccgataactg
   174061 actttgcata ttatctaaga ctagactaca ttgctcttca aagctatgaa gtctttcgca
   174121 aactttcctc atactttgta taagcgcatt accctttgtt aacattttaa aatatggatc
   174181 cattttataa tagataacca aattccaaga agtactcaca atctcaacat ctcctagcgg
   174241 gtctagatat attgctgagg ttttatttat tttgtctata gaatatcttg gtgctatatc
   174301 tttaggtaat gcgctagaaa cttgacaact taacacaaac aacaacattg ccataatgat
   174361 tccgatcttg gacattcccg atgtcgctct agttcgtctt tttggctctt ggtcagcctc
   174421 atttttgtca acagacttta ttccttccaa gggacaaatt ttagtaatgg gtctagtgat
   174481 atatccttcc tgcatcttta ctttagccac tcggacctta tcatcattcc ccttatgcac
   174541 cttttccacc tttcctaaag gccatcttgc aggatgacaa ttctcatcct ttaataaaac
   174601 tatttgccct tcttctatat taggaatttc ctttttccat ttattccttt gctggagcgt
   174661 atgcaaatat tcacttttcc acttaaccca gaaatctttc ttcatttttt ggataagtct
   174721 ccacctatcc aaatttccga ttttttcatc ttccattggt tcgactattt ctaaaggtgg
   174781 tcttccaatt aaaaaatgac ctggtgttaa aacttcttgt tggtccttct cactaactat
   174841 agtgtataat ggccttgaat ttaagcatgc ttctatttga cataaaagag ttgacatttc
   174901 ttcgtaagtc aaaatagtgt cgccgattat acgctttaaa tggtatttca ttgacttaac
   174961 tccagcttcc caaatacctc cgaagtgagg tcctgccggg ggaataaaat gccaatcaat
   175021 cctgtccttt tcaagctgcg ctgcaatcgt tatattttct tgtattgcat taaataactc
   175081 ttgatctaat tttcttgcag ctcctacaaa atttgttccg ttgtctgaat agatattgga
   175141 acattttccc cgtctagcaa taaatcttct gagtgctgct aaaaatgcgt ctgaagttag
   175201 atcgcttacc atttctaagt gtatggcttt ggtggccatg caaacgaata cagcaacgta
   175261 tcctttaaat gttttttggc cacgattttt tgaacattta acataataag gacctgcgta
   175321 atctattcca gtattaagaa acgggaatgt catcgtcact ctatattttg gcaagttacc
   175381 cattatttgc tgagctgtat tttgtttata ccttgcacac gttacacatt ctcttaaata
   175441 ctttttcaac gaatttttca acccgaaaat ccaatacttt ctttggatat agtttcgcat
   175501 taggtttatc cctccatgca atgtttcctt atgagcattt tttattaata agcttgttag
   175561 gtggcatttt tctaaaatga ttggatgttt aacattaaat tctgcattgg aattttgcaa
   175621 tcttcctcca actcttagaa ccccatcctt gtccaaaaat ggattcaatg acaatatttt
   175681 attatttgtc ttgatttcct ttttgatttt aaggcacttt atctcttgcc taaactggta
   175741 ttcttgttgt ttcttaataa caactgtttc cgctattctt atctccttta ctgaaataat
   175801 tgatgaatag gctttatttc ttgttttcat ctgcacgaat ctatttatgt atgctattat
   175861 acgtataagt ttttctatac tggaatacct ttctattaat tcgtaaatag gatcatctat
   175921 tttgtcattt aataccgtat ttattaagac aggttcttct acagactgct gccgaggcca
   175981 aagttctttt gggtctgcta gccatttcgg acctttccac caaaaatcac agttgatcaa
   176041 ctggttagaa tccactcccc tggatgctaa atctgctgga ttatcctctg acttaacatg
   176101 attccattca gtatttttta atttccgaat gtcatccgtt cttcttttta taaatttgat
   176161 cttactttga ccactgttaa tccatgctaa ggtaatcgtg gaatcactcc aagcatagat
   176221 ctccattata ttgtcaattg atccttttag tctttggatt aattcactaa gcaggtgagc
   176281 tgcacacagc tcgagtttgg gaattgtctt cctatttttt atagggttga ctctactttt
   176341 gctagctatt atattaacat gaggtcctac tttagcatag actactgcag catatgcttt
   176401 ttcggaggcg tccgcaaatc cgtgaatctg aatgactgaa gaactgtttg aattaatcca
   176461 ccttgggatt cgaatattct ctaacaataa taaattttct ttatattttt cccaataatt
   176521 tttatcttct atggataatt cctgatccca ttcactttta tttatccaaa gtttttgaat
   176581 aaaaagtttt cctgaaaccg tgactggtgc caaccatcct aacggatcaa atatttttgc
   176641 tagcgttgat aacacaacgc gcttatttat attttttgat tcatcattac aatttacgct
   176701 gaacttaaat aaatcctttt gaggttccca ttttagtcct aaagttttaa cacattcatt
   176761 ttcgataata ttgagaacct tattgtcccc tgtgtcctcc acagtggtta atattttgga
   176821 attgttggaa atccatttcc ttaagttgaa tccaactttc tgcaattcat ggggaattaa
   176881 tgttattaat ttattagctt cttctaccga atcagctcca gtcattaggt catccatata
   176941 gaaatcattc ctaattattg cactaataac ttggttttta catttatctg caatatctac
   177001 cagaaccctg gtagccaaat atggtgcaga tgcagttccg taagtgactg tggttaattt
   177061 atatgtttta attttttctt ttggagaatt tctccataaa atatattgat atttttgatc
   177121 attattatct attttaattt gtcggtacat cttttcaatg tctgccgaaa caacaaattc
   177181 ccattttctc catttaataa taatgtcaaa aatatctttt tgaactcgtg gcccaaccca
   177241 cattatgtcg ttcaaacttt tgttattcgt agtttttgct gaagcatcaa aaactactct
   177301 caatttggtc gtaaggcttg aatctctaat cactgcctgg tgcggtaaaa aatatttgcc
   177361 ttcatcactc acttcaatca tgtgtcctaa atccatgtat tcattcatga atttagtgta
   177421 gtcaacctta agtttttcat ttctttttag ttttttctcc agattcatgt aacgagctat
   177481 cgcttgtttc tttgaatctc ctaaggtgac atcctccttg aatggaattg acacaatgta
   177541 tcgcccatct gaatcttttt ttgtcgtttt gataaattta ttttcacaga tttcagactc
   177601 gatatcatct ttttcttctt cttccacttc ccagtagcga tctaactctt ttatttctat
   177661 tgttgtggct acaatggttt cttttccttt ggatttttta catccagaaa ctatccaccc
   177721 gaaatcagtt ttttgcccaa ggagaccgtc tatttttata actccatttt gcagaatgtg
   177781 agtatatacg tctgctccaa tgattaaatc aatgcgaccc ggtttattaa aatcggggtc
   177841 ggctaattta aagttcttcc attttttctg atcaacatta atcgtgttga ctggaagtgc
   177901 cttcataagt tttgggagaa taattgcttc aatttctaaa tttttcggag aatttcttat
   177961 cgaaataacc gctttgtgct tggagatgca cgttcctgtg gaagatactc cacttatttc
   178021 agtatgagac cgaaattttt tcaattttag aatctgtgca gactcttctg aaataattgt
   178081 gctttgagag ccactatcaa tcaatgctct taattgttca aagcctccat acctcgactt
   178141 tacttgaatc aaggccgtgg ccaacaaggc ttgacctgtt gttctacacg tattcacttt
   178201 ttctggatta tgacctgcaa agtgaagtaa cgtgtggtga ggtttacgac aagtcgaaca
   178261 aagctgctcg cttatacatt ttttaccaaa cggatgcctc agacatctta ggcaaatccc
   178321 attttttctt acccagtcag accgttctgc tggattcatt attttaaatt tatggcattg
   178381 aattaaataa tgccctggta gtttgcaata tgcacaattg tcactataat ttttattctt
   178441 gttattatta atcattttct ttacaggttt tacttcctgt gagaatgatg atatagaatt
   178501 gagcctttgc tctaaaaagt ccatgacatc agaaagtgcc tgtatttctt ttgtcttttt
   178561 aacatggctt tcatataaat tgagtgattc tttattgaat ttccgaagaa ttatgtgagc
   178621 gaaaattgca tccacatctt ctggtaattg tgcctttaat tttataatat aaattgactc
   178681 gttaatcgtg tcaataaatg tctttatttg cttattggat tctaaattta aatttggcat
   178741 atccataagc ctattcatat gatctgagaa tatgtttctt ttattctcat atcgcttggt
   178801 caaaaactcc caagtggctt cataattttc tccagagccg agcagtaaat gagtaaccac
   178861 atttctggct tctcctttta atgctgactt tagataatta aatttgagag aaggactgag
   178921 atcctctctc acatgtatga gctctgtaaa gagttcatta aaaagatccc attctttgga
   178981 atcaccaaag aaggtgggaa tctgtatttt aggcagggtt ggtaactcct ccgccttaac
   179041 aaccgtcgac atttcagctt tatttattgt gccactgagt cgactattaa tggctgtaag
   179101 aatattttgt ttgtcaaatt caagttcgct aatttcttct tcgaatagcg aactctcaaa
   179161 atgactattc acctgttcaa tcaggttatc tattttatgc cataaaaatt caattttatt
   179221 tttccttatt ttaaggaaat ctggactact gtctattagt ttagacgtat cttctagata
   179281 tactcgaaat tggccaacat tattacgaaa tgcctgctct acttttaaag cgttgttttg
   179341 tgctataccc tctttttcag ggtgaccacg catttcaagg tttaatgtag ggggagggtt
   179401 tgatttaggg acagtgtttg atttagggaa agtgttttct accgactcgc ccttaatttt
   179461 ttcattttta tttttaattt tttctaacac catcattatt aaatcatact gcttcgcgtt
   179521 aaaatattca tgatcgacaa cgccgatctt taacaaattg ctatgattag caatgaaaca
   179581 tttttgaagc tcatttaatt ttagaatttc tacatctgtt aatgttggtt ttacttccaa
   179641 ctttctaatt tccaaaataa tttcggactg cttcttaagg aattgaatag tcttttctga
   179701 catcattttg aaaatttttt gtaatttctt aatatatata gtacgtgtat atgtatttta
   179761 tatgtattta tatatatatg tgtgtttgga taaacagaaa attcttgttt tgacttagct
   179821 gatgtcgttg ttgttgctgc tgctgttgct gctgttgttg ctgctgttgc tactgctgtt
   179881 gctgcttctg ctgctgctgt tgttgctgct tctgctgctg gtagaggctc ctttgaattt
   179941 gacttccttc tcttctttaa ggctccgtcg atgtttaaag atgatttttt tttttttttt
   180001 tttggcacgt tttattattt ttgtagtcca gtcagatttt ttgtttttta gccatttatt
   180061 tcggcattta tgctcttttg gcatatacac tgcactctat ttatgagctg atttaatgct
   180121 attagagcat ttataaggca ctgttttcag gcacttttta tttaatttat gctcttatgg
   180181 catatacact gcactctatt tatgagctga tttaatgcta ttagagcatt tataaggcac
   180241 ttttgttatg cactttttaa tttcacaatt gctgatgtat ggcctcaagc acgccttacc
   180301 acaatttata atggtacaca aagcaacctt tagctataga ctataaggtg cttgttttaa
   180361 aacataaaag attcttttgt atcttttgct ttttattttt atactctgtt ccttaccttt
   180421 ggtaggggga aacaagagtc acttattttt gctaccttta gctgtaagat gcttaaagga
   180481 gctggccttt ctctgagttc cttacctttg gtagggggaa actgcagagt cgattaaagg
   180541 ctcgattgac caaatgtaaa atcccaaata agaagacttt actcgttgag tttttgtaag
   180601 aaactgattt tatttggaaa tatcttcggt ttaaataggt gacatgagaa tcgcatctta
   180661 aagtaaatgg cctacgcaga ggcctaagta aatagtcccc gccttatcga ggtcccacgc
   180721 tcgggcacat ctgcctatct tgagcggcga ggaccttatc tgtggtctcc cactaaggga
   180781 ctattttagg aggcggggaa cgatctcaag tgactgactc atgtagtgtg cacttaaatt
   180841 acatgttttt gagcaatgca cccatgtcgc cttagataac aaaatcctaa atataattta
   180901 tcgctctcga ttcatttaca taagatatga acggagccca aaattgtaag tctttaaata
   180961 tattcgtgtt catgtgtgaa caataacaat tccaaaatac tatgaaattt acggattttt
   181021 caacagttct ttgtccaaaa tttgattcga aaaactacag aaaaagaagc tagctatata
   181081 gtagaattac catcttttgt aatttttctc agtgcaatcg ctcgatcatc gcctgcggtg
   181141 cgcggtcgcg cttcaagctc catttacgaa aaaaaaagcg gatcgaagcg agggccaaag
   181201 agatacgacc atcgcattgg cgatactgag gggcaagcag acagtatgtc tgtttgtccg
   181261 cgaaccgatc cgatccgatc cggaaccgct gccagcgatc gaatccgatt cgaggcgagt
   181321 caacgtatcc ccaacatccg accagttctc tgcattgcat gccaagaatt tcgactgcat
   181381 cgcccagcta gagtgggaaa gtttgggtcc caacattgtt gcagtcccat cggcggcctc
   181441 cgagttatta acataacata atattgactt ggatgggcgt tcggctgcat tgtgtaatat
   181501 ttaagaaaga caaaaacaaa aatattggaa atttcagttt cctacacctc gcgtctttct
   181561 ctttccagtt tcactttcgt tgcacgctct gtgggaagtg catgtgtgca tcatgctgtg
   181621 cgggaatggc ttggaatcga cttggatgag atcacctgca tgggtgacat cgtttaggac
   181681 cggtaattag tcttcattat gagtggagaa attgagtatg aaacgcaaca taaggaaatg
   181741 aagatgcttt ataggtttcc tctccatttt attcattttt ctatataaag ctattggcta
   181801 gctatattat ctgatagaag gaaacctttt cccttaaaaa aaaaaaaaaa acaaacataa
   181861 catcaattaa taacaatcaa cggccccttc agatcttttt gtaattgatc caattgcgat
   181921 ttccgtcgat ttacgcatta tggttaccac aattaaagaa taaccgcaaa ttcaaagcaa
   181981 caaacccata aggcaacaat taaagtcaag attacaattg ctcaaaagga aacctcgacc
   182041 agactaaact aattaaaact ccgtgggtaa ctcgtaaaag ccaagccaaa caagtcatag
   182101 tgaagtaaat aaaataaatg atataaaaat ctagtcattc aaccagtggc cacacactaa
   182161 ggcggaaaat gcaatccttt tactattgtg atggctagga aattacaata gaaaaactgt
   182221 cagaaattga tttccaaatg ggaaaacaac gcacggggca gccacgagaa aacaagaaat
   182281 tacaaaacaa tagtttaaag gcaacatttc actttcaatg aatcggtttg cggagatgaa
   182341 gaagggctag gtggaggctt ttattggtag cttcatcatc tttcgcatct ggattcgtag
   182401 agacgtactg cgtggatgga tgtggatgct gctccgtggt ggtggcctct tcatttgaaa
   182461 gctcagcatt tgaaatcgac gtccgatggt ggaaaatcgt gcacatgaat ttcagtaagt
   182521 aaaagtaaaa atcaccttca acgttttcgg cttcttgtgc gccgcagcag cagcggcagc
   182581 agcatatgtt tgcatttgat tgtgtttctt tttcttttcc agctgtacga gtatgtattt
   182641 cttattttta tttttatttt tattgccgca catgagtttg caagttgccg gggactcaaa
   182701 ctcaactcca ctctttttcg acttttgggc gatagacatc gcacatacac tcgctcgcac
   182761 aggtcgtgtc tggcaatctg acttcacgtt ggcaatccga cgaaggggca gacggtatta
   182821 caattcattt agaaatgcat ttaaaaatac ataaaatacc cacagcattg gcggggagtg
   182881 cgcggtgagt gttggcaaat gaaaatgaaa gcgaaaagaa tgccgaaatg aaatggaaag
   182941 ttttcgccaa gttttcgcag tgtgatcata acagctgtat gcatcatatg tgtaggaaaa
   183001 ctggaaagtc ttgctatttt atcaaaagca gtttattact gagattttaa ctttaaaaga
   183061 acaactgtgt atacatgttt tgaaatcaca acaaatttta tgaaactgaa gttaaagacc
   183121 cagcactgca atttaatctc acaccaaaac gccgctaaca gatttcccaa cttttcaaaa
   183181 tatatgcaat tacaagcaat tgcagtgtgg ccagcttatt tagttatgca caggacaatc
   183241 aagatttccc caacacttgc cgctggttac attcccaatc aacagcaatc atcgttattt
   183301 atgagagttg cacaacgatg atctgtaaga aaacatggaa aaaaatcgca gacccaaaat
   183361 aaaggggacc aaaaggacca cctggattga ttgtctttgg gtatccgaaa ttaatcatct
   183421 gtccgatttc aaggaaagtc cgcgatgaag ggcatttcgg gtatgagggg gctgacagat
   183481 gaccaacagc aaatgattcg ttgtcgtgcc cttgtgtgtc aaattcatca ttaaatgtca
   183541 acgcttcggg ggacctcatg cgaaactctc gccagaaaac ctaaaagcca agccaaacca
   183601 aaccgaacca aaccaatcca agatcgaact gagggggtaa atcggagaag gtgcagccaa
   183661 aaaggttaac aactcgatgc caattgagta acttaacaag gagagccaca gggcgcttaa
   183721 acggagcaaa acaaaggcgg aaaacttgac agggctagga taaatagaag gagttcgatt
   183781 tgaggttact ctactcttga taaatacatc attgttatat tgtaatatat caaataaaac
   183841 attattggaa agaagtcctt ttaaaacata ttttattata ttgcttatat aatacaattt
   183901 tgtgtttcgg ttgatacaat tttcctgatt atacattatt acagcatctt tagttcacct
   183961 gcaaaccatt aagccctcat ctgttctcct aaccttgaca acagtattcc gcttccttgc
   184021 atgcagtttc cttaaagata taccctctat aaatatatat atatacttta ctttatatat
   184081 aaaacaggcc cataacaagg cgtcttgcaa cgcgagaaaa cttgcagcag gagaaaaaac
   184141 gaaataattg cgcgactgca taaattttcg caggccaaaa gacggccaga cagaccgact
   184201 cacagctact ttcgttttta atttaaaaaa aaaagaagca aaaacaacaa caaaaaatac
   184261 ggtactgaag gaggaaaagc gctttgtggt tgtgtgtata ttcaagagat cgttgatcgt
   184321 cgatcgccgt caaatggcaa cgaaccttcg acagaccgca gccaagtttt gcctttgcac
   184381 ataaatttcg tgtggccatc gcaactggcg gaggggggga aaaagtgagg aaaaccgagg
   184441 aaaagtgagg gacaaggggc agcatagggt actgccgatg aagatcgatg attgtcatcg
   184501 tcatcggctg ctttgccgct tgttgccgct gctgctgctg ttgacactaa gtgaaagtga
   184561 acttgatggg gccacgtcat gatcgccgtc attcatgatc gactccgttt gatcttaggt
   184621 ttcctttttg gccacaacag ctctgcattt tccccgccat tcatccaatt agaaatgttt
   184681 gacatttaac attgttccgg gatacgcaat atgcggcggg cagctcgcaa ctgggcggct
   184741 tagatgaaaa ccaatgcttt tcgcaatttg actggaattt tcactgtatt ttcctcatgt
   184801 gtgtgtgtga gcccgttgtc cattgccagc aatttgcgtt cgattttggc caagaaaaaa
   184861 aggtgaaaag tgaaatatga caaggggtgg cggtaagggg agtgagtgta atgtcttatc
   184921 tgcagctgca attgaatttc tggttgtatt cgaaccctcc tttttccgcc aaaacgatgt
   184981 tgtattttac aatttggttt cttttttagt tttcggccag ttttgattgc acttggggag
   185041 attagataag caaatgttaa gttatgcgat cgtaaactaa agctgcgggt tttccttttt
   185101 tctcctatgc ggttgtgaat ataaaatcgc cgtaaagtat tgaaatgggg actgaacgac
   185161 ttaaagggga aacttttcga gaaaatgatg cagcctaaat aagccattag tgaattatat
   185221 attgggctta gtttaagccg ggggtcataa gattaggaaa cttacatttt tattgacatt
   185281 tcgtgaaaga agtggtaaat ctttatgaaa agtattgtag attaaaaata atctgtgcaa
   185341 ttaggtcaga atatatttgc ttaacctagc tttaaaaaat ccctgacgag acttttaaat
   185401 ccaaatgata ttattataaa atttttgata atcacccatt aaatgacctc taacgtatat
   185461 ttagaaactg gcacaacgtt tcttaaaccc ttaccaaaca agaattttat ctgaaatttt
   185521 taattatcaa caagcttacg tatgttttca tttttgaccg acatagatta gcattggaaa
   185581 tggctttatc gctcgggtgt actggttgta tttgcttacc tgcaatgaga taaagaacaa
   185641 ggtagaaaaa ttagtttggt tggttaagtt atgataaata ctacgttttg tacggaacca
   185701 cagccaacgt tcattgagtg gtgcattgag gtaaaaacta gcacaaatgt ctttattcga
   185761 gtcagtaatt caacaaaaca atgaacacac acaaaccaaa aaggttgggt tatcttatat
   185821 ggttttgggg ccgatccgga ctccgtgcgg ttgttgtaat tacaaaattg gttcggcaag
   185881 cggtagagag agtttcccgg ttaccccccc gctcaaccca tcagccattc tgatgatttt
   185941 tatgaatgaa aacagaggcc agaaacggtg ttcggcgttt gtctatttat ggataggcgc
   186001 aatgctccgc tctacacgtc tattcctata tagactttgg ccggtttcac atttcattaa
   186061 gtggaaaatc agttgctcaa ttagcgagaa tcgaaaaagt gggacataac agcgtcggcg
   186121 ttgcaacttc ctttttgtct tttttttcac tcctccacct tattgtcaca ttattgttaa
   186181 aggcagagaa accagcgaaa caaacaaccg gcaagcgaac caaattcaac agaagaagtc
   186241 acttaagtgc caacgtaaaa acgtttaaat gccattgcgc atacgccacg ttgagcggtc
   186301 gaggtaggag aagaggtcgt cagtcgctaa gctatttaac ataatttggt catgccattg
   186361 cattgcaagc gttattactt ttacggcaag gtctgcatgg ctagcaaagc tttgagctca
   186421 cttgtaaaag attttccagg tttgcatttg agatattgga aatcttcagt gattaaagtg
   186481 ggtggtgata aaaagtaaat tttaaccgcc acataaataa gaaaacttta gtttaagtgt
   186541 gcatattgta attaaaattt taagaatcat ctcaataaaa taaatagtaa gacaacatgt
   186601 tttgtaggca taactttaaa agagttaagc aacaactttt tctttaaagt taattttaac
   186661 tgtacaatgc aacacgaaaa acaaagtgtt atagcttctt tagtttggct agggcattcc
   186721 tcattctaag tgggaattta ctaccctttt tcgctaggaa tcccaattgg gacttcaggc
   186781 ctcaattcac ttcgctatgt gacacagata ggtttgttag gagtatgtct cattgttgcc
   186841 tgggcagtta tgttttcttt tcggaaattt tgtgtgtcag cggggcaaag tgtaataaaa
   186901 cgcaactgct gcagtttgtg ttacttttat ggacttttgg ttttcggctt gagtcgatgc
   186961 agtaaacccc acgacgacgt ccagttacat aaagacctaa cttattttgg tatgggtatt
   187021 ttttttttgg tgtcgaatgc atcaggccga ggagaaataa aattttggaa tgtgggcgaa
   187081 gtggacttat actttcgctg ttatttacga tccaatacta atttttgaat cttcgatgcc
   187141 ataaagatta gagggagacg gacgccaaag acttgggagc tggtcaagta ccgctagaat
   187201 gaagtttgcg cgcgccaaaa caattccaaa ccgacaagaa gaatcgcaaa aaaaggagcc
   187261 aagacgatgg ggccaggcaa caaattcgca tgacttccgt cattgacata caacatgaca
   187321 gttgatttct gtatttgata tcccagtgaa tttaccactg tctcgtgtgt gagtgtgtct
   187381 cggcaaaaga ctccaaaaaa aaaaaaaaaa aaaccaaaca aagaaccaag gaatctctgg
   187441 aggaaaatgt gtgatgagtg ccagccagtc cgcaagtcag aagacccgga gtcatcttct
   187501 gactacgtgc aacgttaaaa gaacatttcg ctgagccagc agcggcacca gaatcttgga
   187561 gactgggact ccactcccgg catctcgtct cgggcactct tcttcgggaa ccgttaaatg
   187621 gtacaatatt gaaatttatt tttatgctga tgctgatgct gatgatgatg atcatttggc
   187681 gttggaagaa ccggttgcga tggccctgct cctggccatg ccaatgccag tgcggaattg
   187741 cctggttcca aggaacgctg tttttgccgt gtcccaatgc caattggcca aatgtcaaag
   187801 caacgcaaat tcatcatcaa gccagtgaca gcacagacga agtggcagaa aaatactgga
   187861 tgaactttaa atgtgatggg aacataggaa ataaggaatg atgggaattt ttggcaatga
   187921 ctgggcgttg acttcaatgg aattattatt gaaaaatggg aaattttata tttatttaaa
   187981 tatatagtaa taaaagagca ttcatcactc aaaagtaaat gtacatttta atatacatcg
   188041 tttatttttg gtgtattttt aatagttgtg tttttggtat ggtaggaata attgcatttc
   188101 tatgaattct taattttaag aatatggtaa atatatcagt ctatgtttaa atatatgctg
   188161 cagttccatt tcacagttgt ttttttccta tcaagtttcc ttggccagct cagcaagttc
   188221 agtgaaaata tgcacattag ccccgtccca agtgcaatgt gtcccacaac ccgcacagtg
   188281 gctgaaaaac attaccaatc gaggagaatt ggttgttggt gcgctgttgg ctggcactgg
   188341 cactgcgtgc tacttatcgc cgtcacttgg ccaagaagtc gaggtggaag aagaaaattc
   188401 aagtataaat taccaaacca agcaaagaac ctgctaccaa gacttatgac cgtatttgat
   188461 attgcctaat ggtctgcagg ctgctttgcc ggttgctttt tctattaaat gtttttctct
   188521 ttctgcggcg gtttaaggag agaagcagca gcaacttggc tacttttcaa ctagaagtag
   188581 gagttgttga ctggaattgc tcaatttgtg tgtgcagcac agcagcagtc gcacaaacaa
   188641 agccaaacaa gccaagttag atgatgctga cgtacattcg aagctcgtcc gcctcacaga
   188701 ccggcggcgt cttaccaatc gaagtctctt ggctcgttgg tgacggcatt tccagccaac
   188761 attgttgtcc caaacaaacg gcaacaccaa cgtagcgcgt aagcaacaac aaccacggcc
   188821 acaacttggc aattgcaagt tgtataattt atttattttt tctatttctc ttctattgta
   188881 cgtacacttg cttgaaaatc gggttctgcc atctaacaat gcagtttgct tcgattaaaa
   188941 atagggacga tttaaaaaaa ttatacaaaa tcttattaag atacactata atgtcgacgg
   189001 tttcttaaag acaatttcaa cttgtgtatt attgttaata tgtacatcac gataaacgta
   189061 acgcgttctt tcttttaata actaattctt tttttttatg ctgcttaaat tgtaggatta
   189121 atcagattac agtatacaaa tttgcttgag atatatttgc tgtaagtgta atcgatttcc
   189181 gtcaaactag tgtaattagt cagccgccta tcgattccta ctcgattcag caattttttt
   189241 cgttcgacgg attttcaatt ttaaattgta caaaaaaaaa aacgctgggg gctgcctgag
   189301 caaagtgttg tagttgcgct gccgtagatc gattcaatga atttaaaatg catttaactt
   189361 gaaatttagg tcacaagtag tggctgctgt tgaggcagtt gcagttgcac cgcagtagat
   189421 gttgcagcag caaccagtaa agctgctgca gtatccactg cacgttcatc aagtcagaaa
   189481 tattctttgc ctggcatttg gaagacaact tgcgagttag aattgttttt gctagcagtt
   189541 ttgcagctag atgactggtt ttagttgaac attgctttgg gtagtgccgg aaagttggtt
   189601 aagtgcggga atgccctatg ccatctattc cacactcccc acttcgattc taattacgct
   189661 cttagctcgg tcaagctttt agcccgattc tacggacaag ttaactcagg tggaattact
   189721 taaaacaagt ttacacttga ctacttgttg ctattgcaat ttgtggtttg taaatattta
   189781 tgagcttaga ctagccagtg aatacaacat gattggcatc ataaaatacc atggaaatct
   189841 aaggcaagct aatatttcgc tgatttacca gttgaaaatc atctaattag acgagtttcg
   189901 aattctattt gtcttggcca aacttgaatg taatatatca aagctaatta gtcgacatct
   189961 ggctactgtt gatgctgctg catttaccac ggcttctggc aactttcaca ctttccattt
   190021 tcacactcgg aaattaatca aaagaaaaat taagcacaga cgacgcttat ttatttagtt
   190081 tttttttcgt gttgctttta gttggttttg tctttgattc tttggaatgc tttaaatgca
   190141 tttgaaaacc ataacaaata tttttattgt aaattgtttt gggccttaaa tggggtgagc
   190201 gccaagcagc aacaagagta atacaatagg cattgtggaa aattcaagtg gaaaataaaa
   190261 caaaagccat tgaaaccaaa taatacaaaa taaaagggat aggattttac taccaaatga
   190321 attagagatg agctaaatga aaaatgatca gatatgaaga aattgtatgt tagcaaaaat
   190381 ctattttccc ctaaattctc ctaaatctaa actaatatat gagaagctta ttacaacatg
   190441 taaatttttg aaccatttta aattgcattt aaatttattt ttttaaattt tttaacacgt
   190501 gtacaacact ttcatttgtt cacctagtgt attgggatct ggcattttga tctggaatcc
   190561 tagaaataag ttggtcagtt gtgggttgtt gcatagatca ctgcacacat gcatcggtgg
   190621 ggctgtcccc gccacctttt atcccattct caccgccaaa cattagacat cagctaactg
   190681 cggttttcac cagaactctt tgttcaatgg aaacaatgct ttgaactgtt accgagtcca
   190741 acgaaaaaaa aagaggtcgt aaatgggttg agattcgggg gcgttgtcgt gtggacaaat
   190801 gtgttttgtg tcgaatccca aaaggccaac tgggtcagtc acactatcac aaccaaaaaa
   190861 aaaaaaaaaa aaaccgaaaa aatgcagaat ggtgttcaca taaatgaaaa gtattccaga
   190921 aagaagcaga agaaaaactt tctcgcactc gaatctaatg acttcagatg cctggactct
   190981 cgaggaattc taaaccgtca gagcaggaag taaagatgca ggaatcaaac ggagacaaga
   191041 tcacttttct ggactggcat tatcaaaaaa gaaaacaaca aagaatgggg gactggcaat
   191101 ggactgcatc gacttgtcaa tcaagcgatt gacttttgcg caaaatccgc agacaatctg
   191161 gatgccaatg gagtagcgaa gtccacgaag acgactacta cgatgatgat gatgatgata
   191221 tctaagctgg gctcaggctc aagctcagca ctccacagac catcgatgga tcgcagtata
   191281 cagtatccag tgtatcccaa ctaacagttg aagagcttag cgtagttgtg gcattttagc
   191341 ttggccttaa gcgaaaaaat tattcctttg cctaatttgg tttaaatgga aattccgcac
   191401 accatattgt acgaaggact ttaaatgact gaacgacgac gagggccaag aacccaatgg
   191461 cagggcaatg ccaaagactt ctcggattcg tgtcttgttc taagtgaact atttttggta
   191521 tttctcctcg tagcggaaag ttggcgattt ggtttgggct ccccgaccga agggccaaat
   191581 tgtactggag atgcgtccaa tcactgcgaa atgatttacg atcacgataa agagattagt
   191641 gcggccagag ttcgctcaac cgaaactcaa agaaaaagcg aaataaatga gtttggcaat
   191701 caatttaaat caagagcgaa tgccgtgcag attggaaaag tcagctacaa cctattttga
   191761 acttgtaaaa tattctttgg tatattttgc atattaaata aatcggttta catgcaaaac
   191821 tgcaccgata acgcatataa agtagcgaaa tgattttata aactgtatgc cgatataaag
   191881 taaatagttt atttaaaaac ttttcaacat tgtccatatg tgtttaaatt tatataactt
   191941 caatgcattg agtttgtaat cctttctctt ggaactcatc ctccgactta cgataaattc
   192001 gctgcaataa gccggattaa atattgcagg tcgagtcaaa gaccaataaa aatgcattta
   192061 atcccccaac catataattt ataacattcg ccgagccaaa ggcaaaaggc aaacaaaagt
   192121 aaaagtacag aggtccccgc cgcagagcct ataaataccg catacacata ctatatggcg
   192181 catatgggta tggttgcggc ctggaaaacc cgaagagatt gagatacctt cgcgtatata
   192241 aactcgtata tatttaggga cacaacacac cgattgcagc gacgcatgtg gcatggtggc
   192301 atggggcact ggcacatttg aactttaaca cacgaccgag gcacaataaa aatttcaagt
   192361 ttgtccaaga gacatatggc caaagatccg ctgatccgcg gggtcaacgt tataaaatcg
   192421 caagcggcag cagcagccac ggtaacaaca acaaaaaaaa aaaggcagca acaagcaaat
   192481 aatttatgac caacttgatg catggtggcc atttaagtta tggactgact tctccgaagg
   192541 gaaccgtcga cggggtgtga actgcccgat cagcaattgc aattgcaatt gcaccattta
   192601 taccggggta tatatgtatc tatatatata tgcgcacata tgaaaacaga tgacgcatcg
   192661 tctgcgtctg caatgaatgc actttttctg caatttgact tttccgaaga caaagcagac
   192721 gagctgtctt ctcgtctgcg gatcgcagtt tggggatcgg aaatcgggaa tggtgggggg
   192781 tttgtttttg ggctcttttg ttttcagtta gttgtcaaaa gtcagtcgga ggctgaaatg
   192841 ggtcccaaac tgacagacgc agctgactgg gcccctcttc tttcccagct gaaaacgaaa
   192901 aaagaaaaat aaactagtca gccttccaag tgggtgtgcc agactttact tagacgcact
   192961 caaaatttcg taagacaaca atgctgcgag aaaaatatta caaaaacttt tcaacgagat
   193021 actcgtctaa agtttgcatg cagaaagtta aaataatatt gtttgaaaag aaagcatact
   193081 gtgaaaaaaa tgaatattaa atattgaagt acagcacttt aattgataag aggaaactga
   193141 actactaaac tggtaaagtc cgaacatgaa ccgagcattt taaattaact caaataagtt
   193201 tccgccactg atcaagcgaa cttaaatatg attaatggct cgatgtccag gcgatttagt
   193261 aaatgactcg tcatccgcct ctctgcagcc tcattttgca tctttaattt tgggttaatt
   193321 agcatatacg cataaatgca tttcaccgac caaaaatctg aaatctgtgt catccgaaat
   193381 gatggggcta aaaaaatgtt ggcaccagaa tcgtgcgcaa gaaatttacc caactgcaaa
   193441 atgtctgccc aataaaaata aacagctcgt cacacgaaaa accaaacaaa acgcaaaaga
   193501 cgaggaaaaa aatgcacatt gatgttaatt attttggcag ttgaatgcag cagccaggca
   193561 gcaaggcata atgtttattt ttacaattct ccttcttatt gtgaaatggg cgcaaagtgc
   193621 atattaaaat gtcagccggc agacaaagat ggagaggaca aactgaaagc ggcaggttaa
   193681 gaaaataata ataaaaatat acaaaataag atgcgcaact tttcaaaatt acgaacagcc
   193741 agcgttattt ttcgcaaaat ttgccaaatt cggcagaaac aaggcaacag ccaaagaatt
   193801 aaacgacaca aaaaaaaccg gagaacaaat aaataaacaa attcagtgct gcgttgagtg
   193861 cgctcactca gaaaacagtt gattcagcag aaaaaaaata tgaaccaagc aaaatcgaaa
   193921 cggtttttga tgcaagatat caagttgtgt ctggaggtaa cctcctcctc ggctgccgaa
   193981 gcccaaagct ggccaagtca atgcaatggc caatgggttg ggcactggcc aaagtagacc
   194041 cattgtcgac attcatctgt ccgactgtct ttatggtttc cgacgacggc ctccgagcgg
   194101 cccaattaac ccttatgtct ggtggaaaca tcctttaaat ttaattccat ttttgagcag
   194161 gcctcataac atgacaaatg aagtggaaca ttaagattaa tcgctgtagt cagcaaatta
   194221 tattacaaat ataaactcaa tgtcatgcaa aatgcttaat gattaatgca ataaaacaag
   194281 agctatttat cccctcataa ataatgtatt atgtacgatt tttaataatt ttaaaagctt
   194341 aagtttcata tttcactaac tcacttcccc ttaacacaca aattcttaag catcttagaa
   194401 ggtcgcttga cccatatgca ttttaattaa aaatggctga aaatgcattt cggccaacaa
   194461 gttctcgccc agtactgggt taaggcattc cttttggcta gtcaaaagac aatccgacaa
   194521 tgtcgtaact tggcgctaag ttaagcggct atgaaagcca gttactccac ctcctgatcg
   194581 tgtcgctttt gtggccactt ggcccggtgg cagttccagt ttttagctgt tttgtttttt
   194641 ttttcttact tttctgtaag gaaaaataaa acagaaaaaa aaaaacagag agccagagga
   194701 actgtagtct ccgctcatca attgacaggt aaccgctacg ccttggacat tgatatgatt
   194761 agcgactttt aatttaacgc ttctctgaag cgcgttagag cagcaagacc tcggatgcat
   194821 ttgtgcctat gactcctccg ggccagatca gatctgtagc ttgagtttgc atttccgcaa
   194881 ccagatgcaa cacaaagtaa tcgagtatac ggagtcgcgt aaccgaaact ctggccagtt
   194941 cctccacgag tccagccagg ctcgactgga gtcgtaattt gtcagctttt agtaataact
   195001 ttggacattt accgtaagcg acagcgatcg cgataagttt tcaacctgtt gtcttggggc
   195061 agccggagct gagcagagca gagctctttg ctctcctgga gcagataaaa gaccagatag
   195121 ccacgatccg ccattcatcc tcgatccccg gattgtccac cagatacttt ttcgagtccc
   195181 gaactgcgcc taattgattt tcgcatgcga cgtgacggtc tgacggtctc cttgcctgcc
   195241 tttcggtatt ttcgcttggg attttcttat ttggtggcat aattattgtc attcataaat
   195301 tgtgggctcg ttatctatag gccagtgagt gagtggagtg gcgcggactg cagtgaagta
   195361 aagtgaagtg gtttcgtttg ggagataaat gtgcaaatga tttgccaact gcgatttatg
   195421 ccacaacggc tttttctcca caagcctctt tctctcgctt tttatgacta ccataaaaat
   195481 gttccacgaa gcaattcctc ctccactcac caaaactaaa tgacaagatt ttcgaattcg
   195541 ctggcggacc aactccaccc gttgatatat atttgataat ttcataaatg ttcagcagtc
   195601 aaaggaactg gcttcttagt catgaattcg tgcggttact attactaagc aaagaacata
   195661 atgaaatgta taccattaac aatttgtaag cttcttgatc gatacaatat tgaccaatat
   195721 cggttcaact ttgtatataa tgtgttgtaa cacaaatgga ataagcctga ctgacatttt
   195781 cagcaatcga aagtgcagaa gattattctg taatcaattt ccctttcttt cttgctgtca
   195841 gcctataatt tgttccctac gaaatgatta tagcatttgc tgctgtgcga aaaaaaaaca
   195901 accagtttgt attactcccc acttttgaat gtcggttatc gctgaaagct catcgcgatt
   195961 acacaattcg ctgctcagta caaaaaaccg aaattgcaat tgcagcagca actgaaaaac
   196021 tccagactcc gagggttaac attttgtaaa tatttgctgc tgcatgtgag gctttcttat
   196081 ttattgagtt cgcttttttt gtccgctctg gccgtcgttt tgtcttgctg cattttgtat
   196141 tttggccgca actcttgtta atttcaatgt gaaaaagaag tcaagtgagg tcgaatctgg
   196201 gtatgaacat ttagtcgttg gggctaataa caacaacctc gaaaagagtc tgcgacccat
   196261 tgaggtgggt gagatgttgt ggtttttttc aactcgtttt ttcttcttgg ctgaaaactt
   196321 ttgaaattgt tttctgcttg tttttgcggc ttgtaattgt tgttattata caatttgcaa
   196381 aaagtagcaa aaaatgccaa taacaatgta aaccgctaag caacaataaa attttacaag
   196441 ctccaccagt ggcaagtttt ttgttttttt tttttttttt ggtgcacttc ttactgcata
   196501 tttgacattt cacttgtgca gctggtaaag ttgcaagttg caactgagga gtatctagag
   196561 ttttatttat ttactttttt atgtgaattt caatgatatt ttgtctagat ttttcatggc
   196621 aaaatatttc agatttttgc gatagattaa acgaataaaa attgcaacaa taatagcgac
   196681 agactcgagg gtctttgttt tgttgttgtt gttgtagttc cctgatttat tgattttcca
   196741 agcagataat gtgtgatttt tctcatagac tcttgcaatt gcagttgttg ttgttattgt
   196801 tattgtttcc taatgtgaga aacttgtgtg tcaagagagc tttacctatt gttgcataat
   196861 cgggcgccaa aaaagcccgc tgaagccccc accgaaaccc aactgaatcc aaccgaaccg
   196921 aacccagcca acctacgacg atgtcggtgc aacttatatc ttatgtgaac tccaaaaggc
   196981 agtcttggca tgttgaaaag aagaaaaatg gaatgaaaag atacagaaac gttttaaaca
   197041 ggctaatatg acaaaatttt cagacagctt gtctactgag ttaaatagtg gggggcccta
   197101 cagtcgaggg tggtctgaat attttgtgat aatgtgttac caatgtaaat taaaatgcta
   197161 aattcaaatc aggtatttag atgtttataa atacaagttt tggttaagta tcttgattaa
   197221 aacaaaccgt tcaataaaag aaaataagta caaattgaat ccgatacagc caactatcgt
   197281 caaatctatg attttctttt cgtccgaccg ccttgagtga tatatatttc atgacatata
   197341 caagccttaa tttaaaatat tacttaataa ttaacttttc aaatgcacgt acatgcaaac
   197401 tttttaaacg cccctcgcca agggggagta acctaagctg ttggaaacta tcttacccag
   197461 cctgcagcca agtaacttaa gcatcgccaa aagccaccat aaaaggtaat ttgcataatt
   197521 tctaattaaa atatttttaa actcgcaaga caaagcggca aagacgaaga gaaggctggc
   197581 aaagttccat tcggtttcag gttttttttt cctgttcgga aaaactctat tgggcgtcta
   197641 gataaaaatt taaattaatt taaatttgat ttttatagcc attcacctgc aggagaagaa
   197701 aacgagccga caaaagagtg tccaaaaaaa aaaaaaagtt aaagtcaatc tatgcattcg
   197761 taattaatta aatcgctttg agcctgattt tttcgctttt cgatttcaaa ttagaggagt
   197821 ggcatttaaa ggggcggagg ggaaagactt ttctttttgt caattatttg aagtgggaac
   197881 gtgctgtggc aatgaagtga aagttgtttc aatatcgaat caaacagtct tcgctggaag
   197941 tgaaaaaatg aagtaatttt tcagttaaaa atagaaagaa aataataata agaaaataca
   198001 ttacagagtt atgggtttct ctatacattt gaaatataaa aaacttgtta cagtttagtt
   198061 gggtaaaaaa aaatgccggg tttacaatga aaaataataa caaaagctgc ggcccgatca
   198121 tcatcacttc acctgttttt cgtttatttc tcattttcat tttcttattt gttcaatgct
   198181 ataatttcga tttttttttt tttaagcaga tcccattgat aatgatcttg cgccagtcac
   198241 tcatccgaac ttgactcgtc agccggtttt cgtagtgttt tccattgtgt gatcgacttt
   198301 gtccgtttgt ccgtcgctca gttagtcagt cagtcaagtc agaccgtcag tttgtcactc
   198361 tgtcagtctg tcaggtgtat tgaggcattc gaaaattgta tcgaattata gacccaaacg
   198421 tattgtaatc aacttgactg gacttgaaag caaagatcat aaaggaaaat atactatcga
   198481 atgtgtacgg tatcaagaaa aactaattag atatgcaaat ctggataatc tgtgggattt
   198541 tgatttgaaa tgtgtaacat ctcttttagt ttatcttaat gttcgtgttc atactacagg
   198601 tgagtgatgt taacatacac aaagttacca attacttaat aaaactcgaa tttaatatag
   198661 tttaaggctt tcatctctga catctcaatg aacctgtaaa atgttttgta aaaactgacc
   198721 taattagggt atttaacctt cgtcggtaaa acgtttcaac cttttttgct gcccggctcg
   198781 ccataataat aagcgcccct tttttttttg tttgcaatgc aacacaattt agtacttcta
   198841 cctctccgcc tgaaccccaa tctctggctc cgtttataaa tcatttctcc ggtggatcag
   198901 caattacaaa cacatggcag atgtttaaaa ctgggcgagc gagagagaaa acccctgatt
   198961 ttgattacaa tcgtcggata atgggtagat acgtacagat gtacggctac agacatataa
   199021 tttaatagaa ttgttgtaaa aatgtttacc cagtgcggtt tgaggttttc gtttcgattg
   199081 catgagttgc tttgctgcga atgcgatgta agttggcccg atatatagca ttcagttgtc
   199141 agtatactca ggtttttatt acggctaatg ataatgctat atggcatgag tatgaaattc
   199201 cagatacgca tacgacgaag gttgcttcga ctgaggaaaa gtcctacacg atttgcatgt
   199261 ttaacggcgg tttcgccgat ccaaatatgg ccaaaaacgt atctgccgac aatggtgaat
   199321 gttgtttaac atcctacgat tatttattat tgccacttga gacaataaag tcaataattc
   199381 aattgcacat tgtatattgt atgctgtata ttgcacacac gtgaaagtgc agcggcagaa
   199441 acattttggc gaaaggctcg gccacaaaaa tctaattagt aatgcattag tgagtccaaa
   199501 catggtaaat cgggaagtgg aaaattgtaa atggtaactg tatgccttat tattttccta
   199561 ttttcctggc catgtttgtg ccgcattgaa atcaaaagta aaagcttaaa ttccccgaaa
   199621 aaaaaacgaa actcaatctc aaagtttcaa gccgcattta aaagagatca ttgatcagtg
   199681 ggtgttcctc cataaatggg tcatggctat atccctcctc ctacccttta aagccatgtc
   199741 tcttaacaat aattgtacag ttgggggctc ctcattacac ccgccatgac acactttcga
   199801 tcgtgccaag agatcgtgaa atgggagcac acagcttttg tttgataaaa ctcgaattga
   199861 aaacgaaaag aaatgattga ttgatacaat gataattgaa aaagagagta gccagatctg
   199921 tgatagcgga aaagaggctg aacgaagtga attaatgaga tctaaatacg acattgatgt
   199981 gatgttctaa ataattagtt ttgatgggaa agccagctga agcgaatgca tgaaaatggt
   200041 acaaagaaag tgcatttgat tcgttgtttt tgtttatctc ggaaagggag tagggattaa
   200101 gctagatgga tttataatcc aatttctcca gtcgtaatct agtaatgaca tcattccaaa
   200161 ccactaatat gatggcaacc atataatagt tcccatttca attggactag attcgatttt
   200221 tctagattac gtttccttgc ccctctgaga acttctctat cgcgctggac gtgtctgcat
   200281 aatgacaagc cacaaaagtg aaaaaaaaaa agtaggaacc aaaatcatta caatgcccaa
   200341 gacttgggct ttcgaaaatg ccaatggaga cgcaccgggc caggcggtcg ccaacacaat
   200401 gcatttgatt gaataatgaa gcccaagtaa tggcaaagcc aaacaacatc gacagagaga
   200461 cacacacata ccaaataaaa cccgattcca gttgaatcca aggcaaaacg cactcgtaag
   200521 cttggcaaag gcaaacacac gggcaaaagt cgaatgataa acaaatgcag atataaagga
   200581 aaataaagag accaaaagaa aacattcgaa tacaaaatag agtagttaca attttgagga
   200641 aattacataa cattaggcat gagcagttta aagcagccgc gcgattgttg ggcaaggcaa
   200701 aagtcatcgc gcgaattaat gaagtggaaa ataaacaaat tcgtataata cgtacggcaa
   200761 gcgggggaaa aactcgagta aggcagccta gttttccgct gcttgccgac aaggctggcg
   200821 gaaaatgaaa ttagcttcgt aaacatacag agacaaaagg cgatgacaat tttccaaaaa
   200881 ggttacataa ctctacttct tctgtcatta gggcttccga cagattattc cattgttttt
   200941 caccgtggtc actggccccc taatgtggtt ttcggtgggt ggagatgggg ggcaaggttc
   201001 gcctggttgt tctggcaaat tatctaacaa attgccaatg ttacacttgt taactcgttt
   201061 cgatttgctg agcaagaaag tgaactccag cgctgtaaca aagacctttc gtgtactttt
   201121 tgcggtaaac aaaaagactt ttttttcgtt gaaaaatggt gtgaaattaa cattgggatt
   201181 tgaatgagaa atgagcattt gagcatttct ttaataagca aataaaatta acataagtag
   201241 tagtaaaaac gtttagagac catttaaaaa tatatattat aatataataa gtatttagtt
   201301 tatttaggtg attcttcagg cttagcttag aattgttaga tgaaattgtg ttggaattta
   201361 aaagatttga tataataaat agagtctttt ataatattaa agcttcaagt tgggcgacgt
   201421 cttactgatc attcagaacg cgcaatggag tgaggcattt agaaatgagg tagactcttc
   201481 agttctcagc tttcttcaaa cgcttttatt gcttaacgct ttgccacggc gattctaact
   201541 gtcatagtag acaaaccgaa acgggacgga aataggtaaa gaaattgagg gaagagtgct
   201601 tggcgggttc tcaatgagtt ttacagttaa atgtgtttat tttttccatt ataatttctt
   201661 aaaaatacga aaatgggaat gggtcagaaa ctcccgctcc attttgacca cgtgtgctgc
   201721 tggccgggga gaagcgaagg cccctgactc caaaaatcac ttgctacatg atgcccctcc
   201781 tttcgacacg ttttactgat cgtgccaata aatcaccgcc ttttgtcgcc atctctttcg
   201841 catttaggct agccgtccct ctctgttttc gcctgctgcc agccaaagcc aataaatcaa
   201901 attgcaaccg tcaattgctg ttaatttcct tggcgttgca tgaatgtttt gaatttactt
   201961 tttatctttt tcatttcggt tggatatata tattcggaca tacattttcc ccacttttat
   202021 atgtgtcaat atataaaatg cataaattat ttattgctaa aaagcaaaat gtcataagtg
   202081 tctgtccatg tggacactgt gggaaccttt cagttgatat tttctgcatg aattgggttt
   202141 gggtttgttt ttgttttttt tttgttggga ccctctcttt ctgcggcttg tgttgaaata
   202201 tttcgtcgtt ttgttgtgtc aattggcggt ctatagtcca tagcagatag atcgtttggt
   202261 cactggaaac cccaaaagag gccagctggg cggttttgtt agtcatgagg tccaggaccc
   202321 ggagagcttg ttgtaaattt tgatgtattg attagagtag gttcaaaaac ccacttccac
   202381 cgattgacca gggggtgaga ggccagactc tggcaaagac ataaattcaa tagtggccta
   202441 atgcagtgaa cggatataaa aaccatttat tctcgactga ttttattgtg cataacatgt
   202501 cactttgtgt caacaatttt tcgttctttt gttcagctgc aagagataca ttttgtagaa
   202561 ccactaatac atataattta ttttcttccc aaatcaacac tttcttctca ctaaaaaaaa
   202621 aataggaaat tccccacagt tctattctta gagcagctcg tattaaaatt aattgcttca
   202681 catgtacggg aaaaacctgt tagcgccgct ctggccggct ttctgagccc tgaaacggca
   202741 acaaacaaaa aaggtcagca ctttatattg acccaaaaaa aggcaacaaa cgaaaaacga
   202801 aaaaccaaaa caaaaaacac aaacaacttg aacgccaacg ccaagaaaag tcaagcattt
   202861 ctatgtacat acttatatac aagttttata gcgacaacaa acttcgagat tccgttgata
   202921 attctcagat gtctgtggaa aggtcattta atagactagg gatcagctga taagaacacg
   202981 atgtcgtcgt gggtttttag aggtctgccc ggccatttga attcaattga attaatttgg
   203041 attttatggt tcatttagat gggccatttt cgggcgctaa ttgaagagcc agatccgata
   203101 agctcgtccg tccagatgtg ctgggaaaat aaatagagca cacaagtgac ttcaatttga
   203161 agagggaaac aagaaattac tttcttaagt gtcaacacag ataacggggc tttcgtagag
   203221 gatcaattac aacctgtcaa tcagtgatta tgtttgaaat gtttggttga tgcaagttcg
   203281 tgtgcctgaa agttcaaggt tttgataagc atgataaagt gggtaatttc aagagtaatg
   203341 accattgtaa agaaattttc atgtgatcga attcccttac tgttaatttt cctaaccctt
   203401 aattttctga tcgtaaagca agcactaaat tcaatatttt ggccaacacg caacagaaag
   203461 caatcaagac gaattaccag aaaatgcacg tttataaaaa cacctttcaa gtgcagaaca
   203521 caatctggtc ttccatgttc ttcggagcaa tttttcaaga atttcgcata ttttggcatg
   203581 agaaccgaag taggaagaaa ccttatgaac gaacatcatc acctgggagt aatcataaaa
   203641 atttgcataa ggaaaataaa gcctgtgtgt aataacagta aaaatgcctg aaataagaaa
   203701 aacacaagac ccaaagaaaa catgaaaaaa aagcgagtgg agtacataat aataatataa
   203761 ttttctataa tagaactcaa tgtgccgagt gaaagagatg gatagagaac aaacgagcac
   203821 agcagcaact gattgaggga acacaacaat aataataaca acatcagaac acacaagcac
   203881 acgtaacaca cacacacaca cacacgggga ccagttcaac aacctttttc tctgaaggag
   203941 cctctgaaga aaatcagcaa cagagagaca gcacacagaa aaaacaagtt gaataataat
   204001 tattaacaaa atttgtttcg tataaaaata ttacaataaa tactgcgagc actaataact
   204061 aattctagac gaagatttga tttcatatgt taataaaata ctacacttaa atattttttt
   204121 aatttttttc aagtaaatct ttatgatcac tgaccagtta ctatttattc ttctaactgt
   204181 tgttattaat ttaattgaat taatttaaat ttgttattag ccccatcttt tgtatttctg
   204241 tgtagaagaa gagagggaga gagtaagatc aattgggtgg gggagacccg aatggggcga
   204301 ttacttcact cacaccacgc attcggggca tccacatcca catcgatggt gatcatcggg
   204361 aagaatctca agaaactcaa gaagtgcagg aagaagaaga aaaatgatga gaagactggg
   204421 cgaaaattgc ccacaaaagg gcgccaacag aaaccacaat aacaacaacg aaacggtacc
   204481 ttgaagagaa tcttggaaat ttcacaaatc aaatcaatat aattgttttt cccttactca
   204541 ctttccagct ggatattgat atatgaagag gatagatggg ttagatgggc tacaattacc
   204601 tagtaaacat gagaaaaaag attttcgaac ggaagttgat agctgcattg gagttgtttg
   204661 ttcttttatc gatttttttt ttttatattt tagcctttat ttttaccttc agtccgccgc
   204721 gtgcgtactt tctatttgca aagtgcggaa gccgtgctca ctatcagata cacagatatt
   204781 aactcttgga ttgccttgcc ctaggttgtc agtcatttgc atttgacgat gattgcgcca
   204841 tgaaccgttc catgagtact cattcacact cattcgcact cacttcactt cagtcacatt
   204901 tccaatgact ttttgtccgc cgactggcgc gtgcaagaaa tcgaaaatga ctgacaaaat
   204961 atatattcat attcaaatca gttgtccaac tgctccatct cggctgacaa acgggctgca
   205021 cctagacctt gtcaacgggt tcggtttgaa aaagagaccg atcgcaaatt caaaagccaa
   205081 acttctccaa tgcgcggttc aaattgaacg caaaaaaaca atgagaattg atttgaaaaa
   205141 aaaaaatcaa ttcaagctac cattgcgcaa aacttattca acgtgcttta agattgattt
   205201 taaaaggcta agtttaatga tttaggaata aattaaaaaa aaaaatgtat gtacttagga
   205261 taaaatgcgt acataatcct attttatgct tatactagca ctaataaata attaatattt
   205321 tattttgtac gaaatgaatt tgtctagtat tctaagtttc tcgtttacat ttacaatttc
   205381 tagtcattaa tttaggttta acccttttca gtgtatttca agtttccatt taataaaagt
   205441 gctacttttt catcttgtta gtggattttt attttgttgt ttttgctact tctcctattg
   205501 ctcgaacaag ccactcaggc cataatctaa acgaattgaa tggaaataaa gtgggccaca
   205561 cacacacaca ctcacgtcac actgccacat ttgtcaactt aaatgaaaat gaatgaaacg
   205621 caatgaaatg tatcgagtgt gtgagtatat ttgtacaacc gcatcaagtc agaggccaag
   205681 cccacctaac gcctcaaaag tgagttggaa ttggaatttc tgtgtcagac tcaacctcaa
   205741 ttaggtctgt cattgtcgag ccaagaagtg atcatgttaa atgcaaaata atttgattaa
   205801 ttaaattaaa attacttaat ttgtgtgaag aaaaaacata cgtatacgag gtgtgtgtgt
   205861 ggagagcgtc tgactttcac acgaaattca gctcagctga tgaagcgacg acattagccc
   205921 aattcgcttt gatgatttat tagatttttt ctaggttctt taaattattt ttctgctgct
   205981 atttcttcat tttgaccgct ttggcagcag caaaaaatta atttctcttc ttttcttttg
   206041 acggaagtgg gttaataact gataacgctg cgaaaatgta aacatgacta aaaatgaacg
   206101 tgcaactttg cggacaaaat ggttaaacag taaaataaaa aaaaatatcg cgtaaataac
   206161 ttgattttat ttgacattta atttccggcg agagaataaa catattcatt ttactttgcg
   206221 gaaacacaac ttcttatgga ccttttattt atgtattatt tatatatttc ttgctggaac
   206281 atcagctaat taaattattt ctatacgcca gccttatagc tttcattttc ccgtaaaaaa
   206341 aataataaat ccatataata tttttagtat tctcagctga tttataaatt ggtaggagaa
   206401 aaaagaatga ataatagttg atgaatctgt cagcgaaact atttgttcta cttaactgat
   206461 ttattgaaac caatctttta ttgttttacc ttataagata catgtaatcg aacgaagcac
   206521 ggctgaaaaa ttcaaagtca acgtgctaag aaaatttaag cagattttaa agaccaccta
   206581 ggatttgtga cttttgcaaa aacctttaaa atgtttgtct gaacaatggt ttcattcatt
   206641 atccacaggc aattagcata aatctaaaaa tacctttgtt tacaaaatag ggttctcgga
   206701 taagcgtaga atattttatg acttttcgtt ttcgtacata cctgaaacga gaacaagaag
   206761 agaaacgtaa aaataattta gtaagaagat gtgaaaactt agtaaacgtg tttgaaagcc
   206821 ccttggcaaa atatttctgc gggatggaaa gaacgggcta atcaccatat aacgccaaac
   206881 acatcatcag tagcatcatc atcaccaggt aaacccgtag agacaaagca aaaggttctt
   206941 atcttaaatg attcataatt gtgcagaatg aaaacgtgtt gtctcctttt gttttacgtt
   207001 ttttggggtc aaatatttgc tttcgaaaaa tattgttatt taaaacttca acaacaacta
   207061 attatgcccc gaaaatgcct attaatggcc accatgataa atggtttcgg ataaggggta
   207121 aaaagacaaa ttagggccgc aatttgcaag tcaacattta ggcagccaag tgatagttaa
   207181 ttttcattct tttttttttt tgcttctgcg agtttttgtt tgcggcatgc cccacatcac
   207241 aacaatcgca ctcgcaatct agctagccaa atatggccaa acaagaaata tatctaaaat
   207301 atctttaatt aaaagtacaa acgtacaaat tatgcaagac gtgctcaaat atggcaaaca
   207361 cctaaatatt tcatgagttg ataaattgca cgcatattgc cgagccaaaa aatgccacaa
   207421 gccacagaca cccgcaaaca aaacatttcc gtacatacat atgaatagta tctgcgctct
   207481 gttctgtaca tgatatctgc aggcgaagct cgcccattta aagcccaaaa gatacagata
   207541 ccgaaagctt aagccaaatc ggcaattcca caacaaccca cgtactgtgg gaggctagaa
   207601 acaaatcgaa gacaaaacat aaacattgca catggtgggt gactgacttg gtggagcagg
   207661 gcttatcggg gaattgggtg gttcgatgga tttggtggtt tggtggttgg gtagtcccaa
   207721 cacaagtaca cccacccgtt gacatcggca cagcatgcgg aatccaaatc agtttggtaa
   207781 aatgcatttt tctcgagtgc tttgtatttt tctgcctgca gctatgttaa atacttgagc
   207841 tgcgaaaatt ggaaaagagt tttgacaatt tctcgaagcg caaaacaata atctatatat
   207901 caccacagtc tattttgcat atttattatt tatgtgcaga ataggaagtg aacatatggg
   207961 ttcatatatg agttataatt gataaacttg aggggttgat tcatatgtag ttttaggtta
   208021 cttagtcgct tttactacta tgcagtatat atatatatat atatatatat atatatatat
   208081 atattgatat atatatatat caatatattc aatattttat tcccttctac aatattgaat
   208141 ttaagtcagc tttttagctc ttttaatcac attcatattg aataaaaccc ccttcgcttc
   208201 gtattttgaa tccattgttt caatttctcc catcagaaaa cggcatgtat ctttgctcca
   208261 tttaaacgcc ttccttttcg actttaagcc ctctttttac caagtttcga tcactcatca
   208321 tttgcattgt agccgccaca atttacagta attgcagact gaaatcgctc tttttttgag
   208381 cagcaagaca acaaatttat tttatttaaa tgaaattccc ccgagggcaa tggcggcgtt
   208441 gtttgctatt ttttattcat tttttttttt agggcgcggc ttgaagctcg gatttttgct
   208501 tcataggggg ctgtgtgttc agggtgtctg cagcgaagcg aaattatcat gtccacctac
   208561 gtaatttagc atgtgttgtt gccgttgttg caattgctaa aattattggt tataaataaa
   208621 tgcttttggc attgtcgtcg gcaacggagt ctgggccttg ttcattttgc ctattttcgg
   208681 gtatgtaatt gccaatttct tgagcttatt gtttttgccc atgctcccct atatgaaaca
   208741 actctgcgta tcaatttttt tttattttgg gactgtctgg gcaggtctct gaaatcatac
   208801 caaaagatct tcaaacttcc attgttttca aaaacgacgt ttccaagaag ttcacgaaaa
   208861 aaaacccatg ccaaacattt tacgcacaaa aaatcaacga agagaagcca aattctaaac
   208921 tgccaaataa atggaatgta ttttagatga tttatctaga cgcgcggcaa cagcgcacaa
   208981 caagctgaga agagcataaa attgaatctt ctacctggaa gtgttaaagc tcctcagctt
   209041 tataggccgc acccggttcg cttcctcacc tgcccgtgga ttcctattga atttcgactt
   209101 gactcgactt caactcgacg cggctcgatc accttgaccg cacacaaaac acaaacatac
   209161 acaaaaaaaa aaccaaaaca cagatactga gagaccgaga gagagagaaa aaatttacat
   209221 atcgccattt gccacggccc caaaacccga agaatcttaa aaaacgagct gagctcaaag
   209281 aactacggtg atcgaagcaa taaaaagaaa ttggcaaggc gaatttacgc ttggaaaagc
   209341 caaagaaaac ccatgaaagc atcgaagata atcataatca ttaaaggtga aatgggagat
   209401 actaacaata gatttactga tatgcataag catcttagaa ttgaaatgaa aatcaatgca
   209461 tattaatctt ctactcaaag aattattttt ttatggcaag aaacttgcac ttcacactta
   209521 cttccatctt ctaatctcct tattcaaatt acgcttaatc ataaaaaata gcttttgatg
   209581 catcttcatt ttactcgttt gttttacaag attaattaaa aaacatctga ttcgatttta
   209641 gagttttctt aatatcattc cacaataata actcattaat caaaactttg gtcgcaataa
   209701 aaatcttcta gctcatggct gattgctatt tgtacacatt ttgacaggtg agtttttgat
   209761 ttataagatc tgtcttatgt ttattcatga agcgcacagg catttttcac attcagtaac
   209821 cctcaaaaaa cttgactaat gcatacataa atatttattt atttcgtttt aatacgaatt
   209881 ctgtgttagt tatacaggaa attagcattt gatagttaat tacaaacgcc cgaggggcgg
   209941 atattttttt ttttaaatcg gcacatattt tcggttagcc cgtttcggtg ctaaaatatg
   210001 cgcaccaata aatatttggc cagacaattt acaataattg cggcgacggg aggtgtggaa
   210061 atgtggaatt atggcatgca gtttggaccg cgacgggtct aaactaacga tttctaccga
   210121 gctctggcaa agcttccgat atcgtgcaaa ttactttcca attaaacagc aatttcaatg
   210181 gtcgaggaag agaaagagtg gaatggcaaa atacaggttg cagtcgtggc aaaatcataa
   210241 ttataaacta atttgaaatc aagatgccct tctcaacacg tcattatttc aggaaaatgc
   210301 caaggcgcgt taccccatcc ccccaagatc ttatggatcc actgaatctt ccacggcctc
   210361 cgtctttatc gctggcaatc taatggtgtt tgcccggtgt taccccctct ttggttacct
   210421 gggtcttatt attccagctc tatctctttc aaagcaaaga accgtgccca ggggcaggtg
   210481 taaagatgcc ataactcaga agatttcgca gcgcgccatt tgaactggaa cttgggctcc
   210541 agcccggagt tggatagtct agtattgtgt cttgattgag tgagcccggc gaagagaata
   210601 agaattcaat tatgcagcaa aatgtcacat ggaacggctg gcgaagggaa caatggacgg
   210661 aggcagtgca tctgtgcccc ttttcctccg gtcctcccct tcctccagct gacgatgatg
   210721 gctgatgtat gaagtggcaa aatcgctgca gtgaggcagc aacaagtgaa tgtgcaagtt
   210781 ggggatctac ctggacttct ttcttagcca aatgccgaga ctacggggag cagcagtaga
   210841 tggatgactg gatggcatgg cttggaactg cggcggctac tgaacagaat tagctttcaa
   210901 tttgagcagc agcaggaagc agggctacgg cgaatagatt gtgcgtttgt atcttgccac
   210961 agtggttaga attagatttg cgaaaattaa ttaagtgtca gctgcgatga ctaatcaaaa
   211021 ggaaaaaatg tttcactttc gagaaataag aaatttcgta tttataaggt ttaatgcatt
   211081 aaaatgaaga tattgaaaat atcgaaaata gcaaacagtt tacggcgatt tgtttcttac
   211141 catttggttt ttcgatcgat ttctaaataa aacgataaca gagcttttcc ccttatctta
   211201 tcccactgtt ttcgaagact tgaaaagccg acttaattaa ggcatagcgc atagatagaa
   211261 taggtagacg aaaaaaaaag aaataaataa ataaaatgac gccgcagcgg aagatgtcgt
   211321 cgggagttta taaactaaac tcttgagctc aaactcaatc taagggggga ccctcaacta
   211381 aatccgccaa tggggctctc tattccacat cttggtttta gacttttgcc gacttcagct
   211441 tgttttttat gaggaaatct aatagctagg gctagcgatg aagctgaatc taaagcagtc
   211501 gcagagatga agctgttggc gttaagaagt cgatttggtt ttgccgctgc tgtagatgtt
   211561 gctggtggaa tgaaatggaa tgattgatga tttgttggct gtgtatcgcg ataaggttgg
   211621 tgggcccatt tgttgtttgc ccccatagct gaacaaaggc aaaaagagcg ccagagattg
   211681 aagaagaagc agccaacttt ctgggcattg tcttcggtta cctctgctca tgtttttgag
   211741 cgacagagaa gttcgtgctg ataattgtga cacggcccca tgcaaaaaaa aaaaaaaaaa
   211801 agaaagacag cgcagaatcg agatccaaag tgcagagtgg ctgaagaata ttcagacgat
   211861 gccccctgct aattgcaacc acagacaggc aactgcagac agacaataaa gtacaaatag
   211921 cagcaacaaa gttaaaaaga taagctccat cgccaagttg gttgaattct taacctatac
   211981 ggtgatccgt agatgctctt ctgttctatg aatatcttga ataattttgt aggtgctttc
   212041 tcaaatacaa gcagaccaaa tagcgataac ttgttaaatg ttttgaaata catttcgttc
   212101 ggaatgtgtg ttgcaatatc ttataataat taatatatta agataacgac atggaaacat
   212161 ggaaaaacat ggcagagcac atatacaata gattagaacc aataccgctc gaataacaaa
   212221 ctccagtata caatctggtc aaggattttg tcttcacagc aaaagagttg acttctctta
   212281 tctggttgat ggtgcttagt atgcgcaact gccaactact cagtatcttg cagactgtct
   212341 actgcaggtg aatgtatctt cgagatacgt tttagtttcc tttacttatc aggtcttcag
   212401 ccagttcttt tgttttcaca cttgcacaat agtattcctt ggccttatcg ctttgaagtg
   212461 ttaccttgat gtttaacaat gcaactaacc aactatagat ttagatagca acgagatgac
   212521 cccaaaagcg atcgtggatg atgcaggtga gtggtgagtg gacgggttca atgcacttga
   212581 ctcggctggg tggcatatac acaactaatt aacctagaaa aatgcaaatt tctgcaacac
   212641 acccacttca catacctacc tatgtactta gaagggggcc ccgagtgctg ggaacaattt
   212701 ctaagccaaa caatcaatca acgttggttg ttggccactt gagcacgtta agactggaaa
   212761 cgaggataca cgaaggtatg tacacatata tatatgctat aggtgcgggg atgcatgtac
   212821 aggatgggtg tgcaaaagta atatttatta tgtgtatact tctctgacaa acaacacaag
   212881 aacttggccg aggcccaggc ccaggccaag gcacactgtc agaaaccgag aactaactat
   212941 cctcaaaggg ccaaagggga acacgcgaga ccgagaggcc gagtgaatga ggtctatagc
   213001 aactccactg gagacctgga gacggaatac agacggtata caggatggta tgggactccc
   213061 agaacgggcc tcgtctcctc tccgatggca tgctgccaat agctcaataa caccccgggg
   213121 accaattgag atctttttgg tgggataggc aggcacctag gacaccgatg gccaagcgtc
   213181 taagacaaac agtgaaacag agagggtaat acaggcaaaa ataggagaat cacagacaaa
   213241 tgctcaacgg gggcacacag ctcgaaaatg acacacgatg gctaacagtg agtcaatctt
   213301 ggttaattct attgatttta agcacttttg ttatacaatt ttttaaacaa aaaggtgtga
   213361 aatatttttc ttattcacaa actataaaat gttatttctt taactttagt taagttttaa
   213421 atgaaggcat ggacacagct ttaccttcaa gttgttaata acttgttagc aaatttagcg
   213481 tatttgtaaa aaacaatata tttcgaagct tagttgtcaa caatgatgca ataaataaac
   213541 tatttattag tacttaaaaa atatttctta ttatttactt tgcctagtgt ttttattttt
   213601 ctatgtccct tggcccacgg tgtcccatgc caattgtttt gccagacaaa tagacgaccg
   213661 ccaaaagcag caaaaagtcc acaattactg cctataggtt agacctcttg gtggggccgc
   213721 agctttagtt ttagtctaag tcctagtggg gtgcccagtc acgcggccgg tccaaaaatg
   213781 aaaaaacgct agcaagatga gattttctcg gggttatggg ctggctgctt tttggcgttt
   213841 ggggccacca gaaccacgag aaatgctgcc agcctttgac ctgacctgtc aacatggcac
   213901 agcccccaaa aacacgagct tcatcttctc gaatataatg ggttttgaag tggatggtcc
   213961 ctgtgatgat aactacaatg ttccgctcca ttgacttgac aatgcattct gacatccgtt
   214021 ttgcacctcg tcgctttttc ttggcctttg tttttttttt tttttttttt tttttgctgt
   214081 gcgcattttc ctgtctgtgt accgccaact acaaagggaa cccctaacga taggtggtcc
   214141 tatgccatgc catctcgtcc cattcgatcc catggccagg taatccgaga gccgtgttag
   214201 ggacgctttt gccggcttca ttagccttca gatcggcgac agacaatgca acaattatgg
   214261 cccagcattt atgcactagt caaaaccaaa acagaagaca ggcgaacatg gacactcttc
   214321 tggagagcaa gaaacaaaag caaaagtgtt gctaaattta gaacgactgc caagtagaaa
   214381 agaaaatctg tgcgcctagt cggggtgcca agcctgtgag gtctgtcggt tgagtaaccg
   214441 caaaagggga ccgctggagg ggcatcttga ggggtctgag gtggaactga ctgctgccga
   214501 cgccttctaa ttgccgctcg acgagcggaa gccaagagtt gagttctatt tttacataca
   214561 tatacatatt agctgcggag caactgcatc cacaggaagg gggagccaaa tgtggaacac
   214621 acactgaacc gaaggagtgc ggagaacaca cgcttcccag atttgacttt aaaatgtctg
   214681 ccggcggagg ggttccttaa tgacaagcgt aacgatattc caatgattta aaaatagttt
   214741 ctaaggtttt gcattcaagt agctccagct gaagttttat ctttatgcaa cgaatgcgtt
   214801 tacaattatt attgttaata ggcttttgcc gaaacttttc agtaaaataa aaagttagaa
   214861 aaactgcata tatacataac gtattggttt cacaataagc ccacacctga acgtattata
   214921 ggaaacagtc gaatggttta ttagtaaggg tgtttaacct tagatctgcc tacttatgaa
   214981 aaacttaccc ctgctgtgct ccacttcctc atccacttcc cgatacccgc catatccatc
   215041 gacttgttga cacagttgtt ctacccactg gctattgact caaatgactt tcacactcaa
   215101 atagtaaagt ttatttattt tcttctttgt gaacactcag ctccaacgct tcgctcagct
   215161 agggtaattc aatattgtaa ctcgagctat ttataaatta ggaaatgctg ccaggaacag
   215221 ctaagccaac aaatcgatca actagttctc cagtttatgg atcatttaca taccccctgc
   215281 actctgtact atcatttcta gatctattct caccgaaagg cgacattttt cacggctgtc
   215341 aagtgctgtt ggcctccggc cttttcagag ggtatttcaa tatgagttct cgttgttttt
   215401 tttgggtctg tgacttcctc aataaatggt taacaataca ataaagtcgg tcggtgtgtg
   215461 agcgttttgt gctaatttca tgggggtcaa tctggcactg ttttttaaga tcagtcacgc
   215521 agttgaagtt cccccggctc acggacacat ttgaagcatt tggaaaacaa aagtttgatt
   215581 tctacgcgct cttagcctac aaaaagcaat tttcgcctga ggccaagctg cgctagaaat
   215641 ctctcgcgta tccgaatcat ttttgggtga tcaattaaaa aaagagccat tccaatttgg
   215701 caagcggaca agcggcgagc cagaaattgc ttttgacaat cgcataatta attttcgcag
   215761 gcttctcgaa aaaccaggca cttgtggccg tcaatgtaat atatcagaaa aacaactaaa
   215821 cagaataata aaacatttgt cgacctataa aactgcacaa aattgcctgt caactgaatt
   215881 gagaacgaga acagcaataa tagaataatc agatcagaat ttattagggt cagttgtgta
   215941 aaaatatatt ttcacaaaat tattacgaaa cgagaacaaa aattgtaaaa attaaaaaat
   216001 gactttacgg ggcaaacgaa acaaaaagag ggcaggttaa taatagacag agaaatgttg
   216061 cactggtcag ctagctacgt gtaaaatcca tttatttaaa attttatatt gagtttttta
   216121 aatttttaca atattaactt gattgcaaat caaaatcatg tttattttga gtcagcaaaa
   216181 taaatttaaa actttcatat atgtaaccaa gtgcaacagc gctgcttttt gttctctatc
   216241 tcaactcttt cattctaaac actatcttaa tctcctaaag aaataagatt agatattgtc
   216301 ggccaaaatg atgcttaatc ttggatttaa tctttcgaca agtgtttaga agcagttgac
   216361 atatctttcc cgctgttctt caaccacctt catttgcata gttcaacgaa aaatccaact
   216421 ttcccaatgg taaactagtc ttctggtttt atttttcata tagtcgtctc agtttccttc
   216481 gctcttttac gacagcgatt ttatgtttat taaatacaaa ttccaaaact tatcgtgcgg
   216541 cttataagaa agcaggttgg cctttcagct cagacttcaa ggcggtgggc atggtgtttt
   216601 tttttttagt tcggggcgtc cgtatagtat tgtcgtaaat ttttggtaac ccagccccat
   216661 cgcaggtaaa caaaataaac gattttcact tttttcttcg gcttctcgct cggtcagttg
   216721 agtccaggtg ggtttttatg ttttctatgc tttgattagt ttttgttatt ttaattagtt
   216781 ttcagtggca ttttatttcg tatcgtcatt ttctatcccg aattctaaaa ccacaagact
   216841 acagtgaaac gagaaagcga gagttttcct ttgtcgtgcc gcaattttgt ttattgttta
   216901 aatgctggct gtcttctggc gatttttgta acttgattga acgaaagttt caagattaga
   216961 agatgttttt gcccggggca aaccgatgcc ttaggtcata ttaatgaatt aatcttggtc
   217021 aagaacttag tttcttcctt aaaaagtcgt tgtaatcaaa ctaaatgtca gctttgatca
   217081 tgtttaccga tcagattatg ctgtcttctt taaaaatgtt ttaattaaaa ttaatgatga
   217141 aagtccagtc atagctcatt aataagttta aactgatatg tctgcgaacg ttctgcattt
   217201 ctaactttct cactgcccat ctgcaaaatg ttaaagacat aaaaatatct ataaaatgtt
   217261 cacaactaag tttaatccca acaagatata tttcccataa atgtcaccca aaactgcagc
   217321 aagatgcaca agaagcctga gatgagacga agaaccaaat ggaactataa ttttcggaac
   217381 agaggaataa caaagaaaag cccgcacaga attggaaact aaataaagat ttattcagca
   217441 cacacaaaac taaatttatc ctatagtttt tccagggtga cttccctcaa ctccaagtac
   217501 agtgaatgtt ctcattaggc actttatctt aattttgggc aaggtgttag aagttttaac
   217561 agaacatcga actaaaatta ggtagttctt ttgaacttaa aacagttata gatagacatg
   217621 aaataaatat ttataccact gtttcctata agttaacaat atcttctatt cttaggattt
   217681 ataacttgtc caaaaaggtg aaaaatccga gactcaccct attgcattcc aaggcggcgg
   217741 ccgagtgctc ctcccgctgt cgaaaacagt ggctgcactt gctcttgttg aaaatgttcg
   217801 gcgtgaactt gcggcagtcg gcggtgcgag cgtttgttgt tgctcctgcc gcgcctgttg
   217861 ttgttggagt gggtggtgcc gatttcgagg gggcggcagg caccgttgtt gttattgtcg
   217921 tggttgacat ttcgctagtg cgctgctgcg tcggttcaac aaacaaaaag agtggggaaa
   217981 cttgcagagg agaaagagag tgcggaaatg gtggtacttt tagagttttc gcagaaatgg
   218041 catggctatt atttttaact cgatttgttt tgtttttcgt ttactttttg caaggacgcg
   218101 aagttacgtt aaccaaaaca ttggcttgtt tttgttttgg ctctaaaagc cagcctttct
   218161 taactatttc ggcacttcag aatttatcag ctctgataaa cttcttattt tcgggtattt
   218221 ggttacacgc tcagtgagag agcgaaaaag agagatgggg aaattattca atttcgcttt
   218281 gcacttcgct ttcttagctt tggcacacat gcacacaatt acgcacaaaa acacacacgg
   218341 acgcccgcgt aagcccaaca aatacacata cactcgcgca cgcgagaacc agagcagaag
   218401 tttggggctt tttcttcttt ggccttcttc gccgcctttt gttttgtttt ttttttcttt
   218461 cgtattactc gtatttttgt tgttattttt agtggtatat tcgtcgaccc ggtattattt
   218521 gttttatgct cgcgcggaaa acgcgctctt tttttgaagc accgttcgcg cacgctgctc
   218581 aaaacggaat gagcaatcgc accgattcac cgaaaaatac tgaaacatgt tgagacacaa
   218641 aaaatactga aacatgctga aacagggaga aataccgcaa acaagtaact atgggaatta
   218701 attttcgtca agtttgcgta tatataccct ttcgaataat atgtatttaa tattcatatt
   218761 tatttatact tcatatggaa tgtctttcgt actttagaaa ataagtcaaa aatagtttag
   218821 gaactataaa ctatatagct caatctatta atcttcagta aactttctga aagggtataa
   218881 cattccgctc tctctctgca catgttctct tttgtcggca atgttaaccg tttctgtttg
   218941 cagcaacagc ttctgttgag gtaaatgtta agttaacagt ttacgatttt tcttttaaag
   219001 tttgttgaat tgcccaaaaa ctaaagataa aaggataaaa tgctacaaaa ataacttact
   219061 taggtaaagc tgactaatct tgttaatcat gagttacaga atagccaagt tacaaataat
   219121 atgatttttt ggtttattat tgctttttaa agtattattc gtatatttct tctaaatctt
   219181 aatttgttat ccagggatta catacttttg ttaagcaata aaatgcatca acaaatagta
   219241 tgttctattt attcaaacgt taagctacga atctgcaaaa gcaatcgaca gactagttag
   219301 ttgcatccat ttccaactgc catatgaata aacgttaatt taaataaatt aaaaataatt
   219361 taaagtaaag gggtgaactt aaaatagagt attttgaaat tgtgcgaata aatctatgat
   219421 atgcgaacaa tgattaaaat ttttgtattt gtcaacgaga caaaaatttc cttaagtgat
   219481 actcaaagtt tgttgataaa taaaaatccg gcaaacaaaa atatccgaat cggtggatgt
   219541 taaccgattg aatctctaag cgcgcaatgt tagtttcaca gtcgaattcc tctcatagtg
   219601 ttggtagagc ctcatgcact tgttgcttca tgttgcaagg taaagcaata aatgttgctg
   219661 gcgattttaa caacgaataa taaattctat tgtagttata atttctatat atataaaggt
   219721 tcctgaattt acgtcaaggg aatttaatag ttttaaaata aacttatttt aggtgtatgt
   219781 tgttaaaaac tataaaacta gactttcaga agttttcaac attttcttta gcaacatgct
   219841 gctaagcttg ccacacgaat gttgccacac ttccgtcttg taattgatga ggtttttgac
   219901 tctcgaactg gaaaaatgaa ttatgctggt ggaaaaatca aagccggcaa aggcaatcat
   219961 ttcatgccac agacaatttg tttacagatc tcgccagaaa aggccaatgc aacaacaaga
   220021 gcaagcggta cccataacaa taacaattaa ctgcacactt cattaacaac ctcggtcaac
   220081 aaattttcaa gtgcgatgca gaacagaagg agaaggcaat agagataaac ccttttcagg
   220141 caccacaaaa atataaataa aaggcaatgc actgcggaaa aaatgacaca tatttaaagc
   220201 acattatata aaaacaatat gcttttggta aatgtataaa cagtataaca attaataata
   220261 aattggattg aacttaataa aaaaaattag gagtaatgtc aaattacaac atatggaaat
   220321 ttatgtgctt ataccacgtt tttttctctg tgtagaacga aaattgatta attacgcttg
   220381 tcaagggttc tggcatttga tggggcttgc ggggagaggt aaaggccgca gggaacgagg
   220441 taaaaaggag tcggccctcg atcaaatatt ttgactgcca cctaccatat ggggggctct
   220501 gtgtgtaatg aggggtaaag atgggggggg ggggttcggg atctcgcaac ggaaagacta
   220561 atgtctggcg ctgccctcaa agaattaagg aggaggagcc ggtgagaata aaggtgaaat
   220621 gaagaagcga cgtaagtccc aacattattc acttccatac gttttattga gtttggatga
   220681 tcgaagtggt atttataaca tttttatatt atacaaatta atacttatga attttaaaac
   220741 taaaacaaaa cgattatatt gtacatacat acctatgtat attttaaaca agccaaaatt
   220801 aatttagagc taactttgga acactgttat attaaatagt ttccatctga gataaactat
   220861 ttgtatacta aatactagac atttcgaacg atgtgtttat tgagctaaat atttactagt
   220921 gatacgtgat aatcattggc aagcagcgag ttcattgacc atttcgcttc tgggtctggc
   220981 atttacggta attagttgat tttaaatttg attcggattt ggctgactct tgtgcaattg
   221041 ccgaaaatac ctcgattgca ttggcagctg ccttgcaaca aaacattgca tgataatggc
   221101 ttctttttcg ggtccattgt tgcgctctaa gttgttattg ttgttgtggt aatacctgca
   221161 tagccgaaaa atgcattacc gaatattgat ttcgatgtgg aagggggaca cactttgtgt
   221221 gcgagttttt tttttttttg gttttatttt tggtagccac cgaacgccac tcgttttgca
   221281 cattttccac tctcattcaa atgtcaatcg agtcacgagt tgagttgtcc ccttttaacg
   221341 cccccctcca tcaccttctc tcaccaactc cttgcactcc aaatgaattt aaagtaatgt
   221401 ggaagacaaa caatgaagat gaaaaaccta tttccctaaa tatttccata gtccttaccg
   221461 cacgccaggt cgttaaaatt ctgcgccttt caaaattacc caagatgact ttattagctt
   221521 tccgactaaa tctggaatca gttaaactac ttaatacacc atttgaaatc gccttttcaa
   221581 accatattgg ttttatagtc tttcaaaaca ttttgagatt tttgaatgta tctcaagccc
   221641 attaaagtta agttttagct cagacaggct aagcaaatgt ttcccaaaca ttaagtttta
   221701 tgtatcatta actgatccaa cggcaattag ttcgaccgac ttgggactgg caaccaaaaa
   221761 aaaaaaacat gcaacatggg gcaggagcaa caacaagtgc atccgatccc gccttcgggg
   221821 tgtgtgacca aaaacttgga tcacgcttct tgtcggagca cttgggttaa taagtatctc
   221881 gtctagccat gcaaatcgtg taccgaatcg aaaatcaaag cactgaactt gaggcaatct
   221941 aagctgtcag ctccaccgcc cccgttggtt ccgttgttgc tgagtttttc ataatctgcg
   222001 cgtgggctgg cactttccat attttcccaa agaaaaacag cctttaaaat tcgaacaatt
   222061 ttgcgccctt ttgacagcaa gcgagtctcg attcatgggt aattttgtga gaagagggcg
   222121 aggtctaaat gctgcacatg acgtctggtt tggttgttgc tgttgctgct acatataaaa
   222181 ttgcagctgc aacactttca cttttttcta tgctaatttt ctaaaaaaaa aaaattgaaa
   222241 aaaattggtt tcggaatttt gaaaagtgac aatgtatttt ggaaagataa aaagtaagct
   222301 attcaattta acttagtata caagaactgg ccacaatatt aaattcttct tttgtctaac
   222361 taattatgta tttaaagctt gaatgtctta tgcgggtcaa aagaaaagca catatgtagt
   222421 ttcgaaaacg aaccaagcac taagaatact ataaatatct ttagaaaaga caatgattta
   222481 tgttgaactt gccaccaaat tccaatggag ctgcaagtct agacttaatt caaagataag
   222541 ttatgaatag attatgtggg atagcgacga aaatagaact acaaagatat atggcatatt
   222601 tatgaagaca ttcgaactag acattttatg aattttttag tatttctagt tgttattttt
   222661 agatccaaat aaattaggcc tctttcagga cacgattctt tcttactacg attcaaactc
   222721 tttattttaa caatacttgc attttctata tatattcgtt ttcctttcaa agcaatgaaa
   222781 accacttcct atatacaact agtttgcggt tgcaaataag caaatatttt tacatgcagc
   222841 catgtttttg ggcgtcaaaa agactccata actgaccgta gcaagctaaa acctataacg
   222901 aaaccgatcc aaggccccaa ctaacggaaa ccacctgcga acaattttca ttcggcagca
   222961 acaaaacgaa gaaaagccaa cgaaaaatgc cgcaaatcga cgtctgacag tctttggctg
   223021 gtactggtac caatttggca gcgattcgcg gactcacgcc aattccaggg tgtggacccc
   223081 gggggaaaaa aaggggctga aagacacggc tttgggggaa aaattagggg gatggggcag
   223141 cgggggcttc aaacgtccat agaccttttc gtgaaagtga aatttttcgc aaaatccgct
   223201 ccagagtttt gcgagtgtcg gtgtgtctgg caagcctcga ctggcagttg ggtttcctgc
   223261 acttttatta tgctagtcgc actcgtctcg agctgtaaaa actcagcttt tgggagaaaa
   223321 ttaattttat tcaagccaac taatatatat tttaatacga ttttatgctg tttgcttaac
   223381 atgaacttta atatgaacat tcaaaagaca ggaactatac tgccagcgaa tgccttcact
   223441 gtttcttatt ctaataaaaa cccattctaa ttaaaaccca tttaatttcc ttttctttat
   223501 tttttggtca aaaggggtaa tagtttgact tcatgttgga actccatttt aagaacattg
   223561 acgtgtcatt agtagctctt ggaatccata ctccttacct atggccttat atttttccac
   223621 tgctaacttt gtccagtctt acagtcaaag atacaaaaac gcggatatga ctcacattgg
   223681 gtattatatt taaaatatac tatacaaata tcctccaaga gcaccctgtg gtttgataac
   223741 caccgcgttc ggatttgata attggcttaa agcgcgtgaa taataacaac cagcagcggc
   223801 agtagttgca accacagacg tcagtggcag caggctgcta ggaaatcgcg tttcattaac
   223861 atggaagaag gaaaattgaa aattgggaaa aggagaaaag cggcgcaacc atgacatgag
   223921 acgagtggca aggaaaagcg ttgcaggccg gacgtccaac actgcgtata cttgttgcgc
   223981 ttggcaaact tatctattca agttgtttta ttttttctct cattttcctc tcgatataat
   224041 acctttcgtt tgtttgtttt tcggaaaagc agaaggaaat atatatacta tatatttttt
   224101 tcacttttca ttatgtcggt tggttttctt acgggtgacc gcgacaacat aatttaccgt
   224161 taactcttca tcaacgcaac tcggcacgca aagtaacaaa attgtggcgc aaggagtttt
   224221 ccattttccg agtttcccat ttgctcgctc agttttgtcg tgtcatatga tttatttgac
   224281 atgacagcca aacgaacaat gatttatttg tcaatacagc atttttaatg aattttattt
   224341 tcaattattt atttgttgtt tgttttatat ctagttttta gtttttttta agtactcttt
   224401 ttgtgtttgc tgtgcaatcg caaaagtcca gatgcagacc aaacacgcaa tttcgacgcc
   224461 cagttgagtt ccgagtgtga gcacagtttt ctacactatg aatcccacaa acgtgggttt
   224521 cctaccagca ccaattttgt gcacctgctg accagacatc gaataaatac agcaaaaaca
   224581 caaacacaat taaaaataag aatgaacgct tgattatctc gactacttga tacccgttac
   224641 tcaactagta agggtgcgcc gtaattggct ttgaattgga aattagtaag aaaatgagtc
   224701 aaataaaaag aaatgtgtgt tttaggatcg aaaacgcttt cttctacctg tttttttttt
   224761 tttttacagc aaaacagaaa tcaattatgg ctcactgagc gttaacattt tgaataaaaa
   224821 ctcagtttaa ttggcagaac caaaaattaa ggagttttat tacagaaatc tcatgcactc
   224881 agtgaaggga aacatgtaat tagcttagag ctataaaact aatattaatg tttttaccta
   224941 ttataaaact ttccttataa atgaatatgc acaaaattaa tatattgtag tattaaatat
   225001 aaattatata taattttatt aaggcttttg caactaatcc cgcttaaacg atatgtgccc
   225061 aagtgcatct cgctgcagca agggcgagca aatattaatt tcacttttga ctgcacttga
   225121 cccactctct ttttaactca aagtgaagtg catcttggcg aagcaccagc tacggggccc
   225181 agagctttat gcagataaat catataataa acagaacaca gcaggatatc acttcgctgg
   225241 gtaggatgcg gccgcaagag acttgaagat ttgattcgat gacgagtttc ttccacttgc
   225301 tggcgtagag atttcgcgat gtgtttgctt tgctgctgag tcacggatgc taaggaagga
   225361 gctcaaaaca aattgaaagc cgccataaaa ttgcacaaga aatcgataaa cttaaagctg
   225421 caaaacaaat taaattatgc tcttgaggat ttaaaaaacc aaaactgaaa ggcaaagtaa
   225481 aagtctaggc cataaagact cattcgatat gcgtatttaa ttgaaacttt tttcgttcgt
   225541 cgtttcctgt ttgttaaggc gatgttaccc cccccccccc catcataatc ccaacggata
   225601 acaatttcgc cctgtgggct gtcgttcctt ccccttgcca gccaacttat gactacaact
   225661 tttgccattt accaaaccca aatctcctgc tggatatatc tttgtttttt ttttttctat
   225721 cttacataag ccgaatgcaa gttgcatttg aatacaatta gcagtttatg attttcactt
   225781 ttacaacatt ttcaacatga ggcaacccca ctccttccca acggagtcca tcgataaagt
   225841 gcattggcca gcggacaaca cgtgtgttgc tgttgctgtt gcatttgccc gctgttgttg
   225901 gccatggtaa tttcgactcg aacaactcat tttcgattgc gaaacaagtg gcaaaagggc
   225961 aggcatgggc atccagagag atagacaaaa acccaactta ataggacaat tgattgcttt
   226021 gggagtgtta caaaagctgg tggaacaaac accaaatgta accaattaca atcgggaggg
   226081 cagggaagca aagtttttgg tcgaaaatga aaagtcaaaa tgatgcatga gcatgtggaa
   226141 acttctctga ggggtccgat cggacatgct taagttggca aaacgttgct tgtcttttgt
   226201 aattatttag ttatattatt tcgtaaattt tctttaaaga aaacattaat tatgctgcat
   226261 ttacaagcgc agcaaacccg catcaaaaag agacacttaa gcgttcgaaa attgttttat
   226321 ccattagtcc gtcgtcaact tgacccaaac acctcatcaa gtcggaaagt atcactttaa
   226381 agagctttac aaattacgac ttaatcgcgt gccaaccaca aaaaaccaaa agactacaag
   226441 aaaactacag gcagaacaac acgaactctt acgaagtcag cagaaacacc atcaagttca
   226501 aagtaacaaa cacaaaacca caaagtgaag gaaaactctt tttagacctg ggttgtgcat
   226561 gatggggtca ttgaaatttt ctggttttaa acgttaaact taaagagcgg taggaaccta
   226621 aaacttcaaa ttgtcatagt ctgtcagctt cattaagatc attcactttt ataagtgcat
   226681 tttatctaat taaaatgctt ttcaatagat gtgtttcctt tttgacttcg gcgctccaac
   226741 ggcttgacct tgtctctaaa attttaatgc ttttggcagc tgaaaggtga ctttgattac
   226801 ttgatttgat tttaataatt ctaattgctc tacggatgca tttccttctc aggcagactc
   226861 ttggcattga ttgatgaaac gtaactttga ctttgaaatt ggttcttgac gtttttgtcg
   226921 ttggcgtgcc aaaagcatca tggtcaacta atacagaccg caaaaaaacg caggcaacaa
   226981 tttaatatga aaagagaaaa ttcacgcttg attggtagac catttcactt gtctaagaaa
   227041 caaaaagaaa acacaagtgt caggggaaaa cttcacacgc cagcgaatgg caaacggcaa
   227101 tcaaattaga acaccacatg aatatgaata ttcgattaaa tgatgaatgc actgctggcc
   227161 atataccacc gtatttcgcc cccacttaca gtcaaacccc cttgtcgtga ataaaaacgt
   227221 gccaaatgta tgaatgaatg actggttgac tgaatgaggt ggcaaaatat aaacgtcgtg
   227281 cttgcacggt gggtaaataa gttgtttaat acaaatacaa aatacaaaaa tcaaatacat
   227341 taatgcaaca tgatttgtat aattaatatg tagctcctca ctaaaacgaa cttatttttt
   227401 ataggttgaa atcttaactt gttatctaaa atcaaatttg tttcaatttt cttgtaaatt
   227461 tagcataata tgaattttta gccaataaaa agtgatcttg gcccactgta tttccgacag
   227521 ttgctcgagt aggagtcaag tggaagtgga gtagtgtaaa gtgaagaagt gtaagtagca
   227581 gtagcctctg tctttcggtt gcctttggct tcttggtgcc actggatttt cgctggctga
   227641 catacgccaa aaaatgccgg cccctcgaac aaaaagaaaa aaaaaaacac aaaacagaaa
   227701 tcgtattttg ctataattta atcaaaattg gaattgcggc ctgtcccaca tgaatatttc
   227761 aatggggaga gtgctttttt ttctccagcc cgccccgccg caatatttgc attcgttttc
   227821 attcggcgat tcgcttttga cagtgtaacg gccgcaacct gtcataacac atggggtaaa
   227881 ataaaaaata tttacaaaaa atgaaaaaaa aaaattggca aaaagcgcaa gttacaattt
   227941 atgtttgatg gacattcgtc ggattggttg ggtgaaattt tgatggtggc gacgacgttg
   228001 atgacgtcca cagttggaca ttgatgggag tgagtgtgct ctttaattag ctgcacacaa
   228061 caacaaaaaa acacctgggc aaaaaaggaa aacttttcag ctcggcttgt caccgcttga
   228121 atgggaaaac gctgttcgaa atgcatggaa tatggtttac aatctgatcg cagcttgtag
   228181 attagccacg agctcaacac attcagccaa tctgtcgaca cttgtcaggg agtcataaaa
   228241 aggccacacc cagtcgagct taggcactca taagtattca tattccgagc tctaaactct
   228301 atccaaagtt atgttcatgt tttacatcaa gcgctttatg gactttggtt ttacagctaa
   228361 agttattcta atgtgatgtt tatagatatt caaaagttga taacgataaa aaaaaatggc
   228421 tttctttaaa atattccatg tatgtttggg tcgcacaata aacatttgat cagatatttt
   228481 tcaggttctg ttaaatcaag acaacatttt tgaaacaatt atctttttat tgtaaacatt
   228541 caccaagaaa tatgatacat attattaagg ttataaacta aataccttta taaattataa
   228601 tataatattt aatatgatta agccgtgaat tatgtcttga tattactaca aatttcttag
   228661 attaacaaat ggctcagttg aacaaaatat cagaagttcc ttgcttgaaa tgtttgaact
   228721 ttttccccct tattcgtaca attctccacc caccgctaag aactataaat aaatacaata
   228781 tgcacataaa atttattcac ataggcaaat agaaatcttt agcgcggctg catagaatta
   228841 aaaaccgatg aggcaaagat ttgaatgcac gtgtgttaat cataaatttt aaacatgttt
   228901 caaatgcagt cggcggtgga aaagtggaca ggaggacagt gggacagatg gacggactga
   228961 tggctggaaa cgattcggcg gtgtcggcgt ccaaaaaagc gaacgcagct ataataaacg
   229021 catgaaaata tgcctgaggc gtgcgccaag cgatttcacc tacagataca tgtatatata
   229081 gaaatatata tgtatgcact gcagtggtgg cgcaaggggg gattttcggg gcaaaacggg
   229141 ggctggtcgc aaccacgtcg acttgtcact tttttgcata aacgcaccca attttcgatg
   229201 cgtatatgag tgagagcgaa cgagactttg gctttgcctt tggttttgtt tttggtttgg
   229261 tttttggttt ggttttggcc acatgccagt gcgtagtgaa ctttttcgtg gaaagggagg
   229321 cgttaagagc ttgccgcgcc tcagtttcag tctattaaaa gagctgcaag ctgggctcgg
   229381 tggttgtcaa ttttattcca ttattttccc tttcccccca ctgttgtttt tttgtagcct
   229441 taatgctctt gtaatgggcc aacaaattgc cattggggcc gttgttatcc gaggtctttg
   229501 cgcctgatcg tgttgtgaat tggcaattcg atgtgttttt agcccagcta cagtggcaaa
   229561 tgtcacagaa ctctgcaaac gtgatggatc aactgggata gaacacgcca ctagtgattt
   229621 caattagttt tgcgaatatt ttaactcagg cattaactaa tttgtgtgta tttacacgtt
   229681 aaatctcaac aagctaaaat atgtaagagg tcaacaaaca attgtgaaac aattattttt
   229741 taaagcttaa cggcttatta tgattatggt tttcttaggg taaataagta tattaagttc
   229801 cggaaatagt atgtatgagg aagaacggat cgtttccact ctacaatttc tataacttta
   229861 ataaccagaa tttttgaatt tagttaatac taatttgttg atactaatct aaatgtcaaa
   229921 taattcaatc cggacgaaca ataaagaatg atgaactaaa tatgcaactg catctcctga
   229981 taacattata tcagcagtgt atgcagtttt agtcagctta ctaatttaaa tattaataat
   230041 caacttttag tgatatcaaa atcactttta tattgccatg caaataggtt taaccagaaa
   230101 gcaaataatt cttatgtgca ctgcatatga ctctaattaa gtgctttcat ttttttttgg
   230161 aatgaaattc ttctgttttg aagtctacgt acaattaact tttttttttg ccaagccacc
   230221 tataattata aggcaattat tttctgttcg aaagaagccc tagtaatgtc atttttataa
   230281 aagaaatctc aacgctctgt cacagacaat gtgcattttc gcgtgcaacg gttttgccca
   230341 tttcccattg tgaaaatgaa agtaattgta ggtaagtttt tcttgtgatt gcatttttgt
   230401 tgccacagac tgtggacaaa acgattttca actagttttg agagattgca ttggcctgca
   230461 catttccaca cttcaaagtg aacgaaagaa attgaaatta attaaataca taagcaacac
   230521 gaaagcggct tttccccctt cttttttttt ttttttgttt tcttcctatc acctgcgagt
   230581 cactcaatca actgtgacgc atcgtgaaca aaaattgttt gtcaacaaat tggagcgcga
   230641 ccaagcccac aacaaacaac aactaaaaat gcaattaaaa atcgaaatgg gaaaacaata
   230701 aaatcaccag agaaatatgt gcttaaagca taaacatgaa ccaagccaga tggagtaaaa
   230761 aacgaacaaa atattttaca acactttcgc tcgttagaag cgggcgggtg cagcctcagc
   230821 caattcgact acagtgctcc acgaaagtgt acggctaact cttggctgca ctgagaaaaa
   230881 tatttcaaat tgagcagaaa aagagttggt gctttgcaat ggctagcaat ctttacaaaa
   230941 tataaataga ataaaatata gtgtatatat cgataggtat ttgtgaagtt gtgtttatcg
   231001 gacactagtt tttctcagtg tggctatctg tctcccctct atgcactcat tgccgcttta
   231061 attgcccggt gaaaatgtgc agcaactgca gttggggcta caaaacactg caacactaag
   231121 gcgcttacct gccgctctac tctaattacc cgaaaactct tgggagtcga tgcctcttga
   231181 tcatctgtga tccctttctg taagattttt tgaaagatgc cgccgtgctg ggcgagcaag
   231241 tgaaattcaa gtgaaattaa tcaaatttgt tttgaattta ggttgagacg tggatgcgat
   231301 ttgttcgggc gagaggattg tttgtgctgc ttggctaggg tgtaattaga ttgcagttaa
   231361 acaagtgaaa ttttaggtat aattagtgtt ttactattta ttacctaact ttaaaatgtt
   231421 ctttatttgt atatttttta ttgtgttaat agctaataaa ttcctattca gacagcatcg
   231481 cacataaaac actgatagcc aaataaattt ttagcaataa caattcatca aataacgccc
   231541 attcaatgcc gcaattcgcc tttcttctgc cgttggaaac tcaatttcaa tttgctgcca
   231601 actccccctc cgcggccaat tgacagcttc ttgggccagc accttggcga aacttgggtc
   231661 aattggttgc cataaatctt catagaacat tgttgactgc cggcgacagt gcgaaataaa
   231721 aatacgaatt tcattacaat ttgtgtccat accccggcta ttctctctcc cttgctattt
   231781 taaattatag aaatgtaata aatcaaaatc tcgttaactt gctgcgacgt tcaaatttgt
   231841 ttcaggttaa agtcaagacg gtgggaaaag gattccgaat cgaaatcgga atcggaatct
   231901 attctaatta aataggttta ctcgaatgca atcgacggat ggctggctgc agcgagcagg
   231961 tcgctctgat taatgccgtc gagcaagata atgacaagac aacacccaga aagccaccca
   232021 atggttggtg gttgggggtt tggggttttg gggtggttat atgcgaatct cgatcatctt
   232081 tgctcagtcg tgtgtgcaac agcaacagca acaggttgta acttggctgt gttgcatgca
   232141 accgatgatt aaaacggggc aggccccaaa ctcttaattc ttggccattt tcactgaaat
   232201 tgttaaatat aatttcgaaa gaaattcttt ctttcctctg gcttgactgg caattactac
   232261 gtttctcttg tttattttgt ttcctttttg cactacatat atattttttt tcttgctttc
   232321 attatgattt ttttttctat gctggcgcat ttcatgcgcg acttcattta actgtgcttt
   232381 gcatgattat tgctccagtt atcagctgaa cgacaacaac ggctagagca tgagcatgaa
   232441 caacagcttc tgggacggcg gccagacaaa ataatgtgca acaaactgct gcatgctaca
   232501 aatatgggca gtggattggg ctgtgcagaa aagcaaaaaa agaaggtgca gctgggcaga
   232561 tcgcttcggg cttcgtcgag ctgcaaatat gtttgcattc gagtcgtgga tgcattcaaa
   232621 ataacaaata ttcattcata cacgcattag cctcaccagt tattcataaa atattcgcaa
   232681 tcataatact taggtaatac aacaaatatt aaatgcgtaa tggaagccag cagttgttgc
   232741 ggcttataat caaataaaag attaagtaat gctaattatt tggatacaga ccacatttat
   232801 ttatatattt gtataggtat aggtattata aactgctaaa agcattaaac gttcatataa
   232861 acgttctttg attgttagcc actacgaaat taaaaaaagc cataagcaga attgaatgta
   232921 aattgttgtt tggaaaacca atgttctgca gaaacgttaa aacgaatctt gtcttgattt
   232981 tctcagctta tccgcattta tttagaaaat gtgctcgagg tcacttccac acccaagtgc
   233041 aatcaaaatc gtagacgtcc gagcacttaa ttaaatttac attgctgcaa acgtacttca
   233101 accgagccat gcccaacata aaagggggga ccgtttgtga ttttacattt tagatttttt
   233161 cgccaggcca tttgagggat actcgctcgg gctcacctgc tgctcgttat ctttagtatt
   233221 tatgtcatcg ttaaatttgg cttccagctg cttttacctg gactcgaaac aagtgcacac
   233281 acgaagcgtt cctgctttgc ttttttgcta ttcagcctct ctgctcgtgt cgccggcata
   233341 ggtgtggcac aaaatattta aacacagcat aaaaattaaa aactagtcta atcacaggcc
   233401 cgagccagat ccaagtgtct agtgttgggg ctggaaaatg gcctcaaccg agatcattta
   233461 cggtaggcca cgtgatttga tacttaaagg aagatataaa tttaaactta atgacgattt
   233521 aaagccaaga aaggatccat agggagaagt gtcgagatag tgaaaggttg aacgtcgaat
   233581 ccagaggtgt gttctttacg cattgattta tttgcattca tttcgattga cacgtcttaa
   233641 atctttattt tatatcagtc gatttgcaat tatcacttaa cttcgtcgat taaagtaagc
   233701 caggaaaatt ccaaatattt tagcgaaagt cgagagacta aaaattaaat aataaactaa
   233761 ttttatgtaa tctatgtaaa agtatatatt tttattcgat actccaaata taggtcatta
   233821 tttttaaaca tatgtatttg accaaaaccc acttctcacg atagtcaaaa tccgactggc
   233881 aaaggagagt ctggaaaatg gaccatgtgc catttacaga ggggccatgg taatctgatt
   233941 tgtgattaag acttcaaatg aatacaaatc cctgctttgg ggactggaga tcccagtaag
   234001 gtttagccaa cgcttccaac tctcaaacta tcgtactggc aacaggtgta aatgattccg
   234061 ggcctggaac ttgacgtcgt tgcccccttt ccacctgacc agtgcgttct gagcaaattc
   234121 aagtgaattt cctcaagaaa ctggttgctt tgccgagtct tagtacgtcg tattaagttt
   234181 aatttgcatg gcgaactgaa aatggaaaaa aaaaaatgga aatactttta aaagaccccc
   234241 aggcgccagc aacttgacac atttctgcgg gccatgagaa tgaacttttt tacgatgcga
   234301 aatgcttttc caatagttga cccaattgcc ccagaggcag aagaaagggc gaccccgtgg
   234361 attgacatca atcattgcac tatgagacat tattctaaac gtcattctcc tttagccgtc
   234421 ctagctgggt caattagaaa tgacttggca gcttttgggt aagagcacca gtaccaagtg
   234481 caagttactc tgggtgaggg agagcccagc acctctaccc attcgataga aaagaaaatc
   234541 tgcagctaaa cgacaatcga ttagggtcag ccctcgttgg gcctggaaag ttgccccaat
   234601 gaacgcccag caagtggcgc ccatggtgaa aaactgcagt tggtagccaa gcgtagccta
   234661 aaaaatatga cagaaaaaaa ttagaacgaa gttcaaatcg tagcctaaaa ttatggtaag
   234721 atttttgatt tatgttagtg gaatgttcaa gccgtatctc attttgattt agtagtttga
   234781 aataccgcca caaagttaag tgctaatttt taaggtatta taaacatatt tatctaaatt
   234841 ttaacaaaca aagacattac ataattttaa aaacaagaag ttccctcaat ttgttaagat
   234901 ctaaaaaata caaattggaa aacattttcc ggtgcatatt agccagcatg gtcgagttca
   234961 gtgggccaag gagtaaacaa ggcttggtca agtggctagt ggctgcgatt tgcatgacca
   235021 gtcgattgcg ataggtgtgc gtgaggcgat ccccgaatcg aacgtagtgg gtcccgcaaa
   235081 agcggaagat cgaaactgga acacttcaat gtgccagagc aattactgca gcagttccaa
   235141 cttctcagtt tcccagtcat gcaagcgatt tttccggtgg gcatggggta tcaagtgcac
   235201 cagaggatcg gagggaaatg gattttcttt cggttgggtt gcgttgcgtt gtctatgact
   235261 cccatcgctg gttatactgg cttagtagct ggcacagtga gccaattgat catttgacca
   235321 tggaatttac atacagtcca tggtggttag cactttttgt ggttttgcca atgattgcta
   235381 aaggaaaaga aattggtaac cggctgtggg gcgcaattta ggcgcctgct cagtcggtcg
   235441 cctgccaatg taattgttta aaataaaatt actatgcaat aattttttac tacataaaat
   235501 gcattatttc aaacgaaatg aacggaagaa ctgtgacacc acctaccgga aatctagtga
   235561 atataaaagc tttaaaagct ctgtaatccg cgccacctat aggcaaatat atcaaggtgc
   235621 taaagtcgac atctactaaa atgttgcata cttttaggga tacacgataa gcacagtggt
   235681 gtcgctctct agcggacgta ttcttaaacg tgccgcgcta cagcgacacc taggggagca
   235741 tgtcaaaact attttaaatt tagaagaagt cagtttttcc caatactttt taacattaat
   235801 tgggaattta tagatctaaa aaaaattagt gggagcaatg aatgtcttca atgtataaaa
   235861 tgttaggcag gcaaaagaat tgataacacc aaacctccta ttcctcccac tacatacatg
   235921 ctgtatcctg ataggcgagc attgaattgt gccccagaga ttgtaaatca cagattaagt
   235981 gcataatgac tgtattttgc cattcaatgg aatgtaaagt caatctttat tcagcaacat
   236041 ttatgaatat actgttccca gcgcttacat ttatcgattt taatttagta aatttggaac
   236101 tacaataaaa cggttattct atacatatat agtgcctaaa acattttttg ttactaagtc
   236161 tgtgggtgaa ttagggttcg tgaaagaaca ataggtaatt aatatttcat ttgagcttaa
   236221 atggaaacac agtgcctcca ctttaagata cccgttattg agccaaagga tatttattca
   236281 gatagtcagt gttaattaaa atagcagtgc ttgggacctg caagttaaag atattccatg
   236341 aatttcggta tatcatattt tctttttttt tcagtcttgt gctctaccag atgatcaaga
   236401 agataaatgc agtaccattt gctaccctac tattaagccc ttgttaaagc atgtgggatt
   236461 gtgccatcaa aataatgaag tggtttacca actgcaagac aaaattcgcg aacaggagat
   236521 cgaaataatt ttttgacgag attgtcgtcg gcggcgagcc tgaaggttat cggcttaagt
   236581 cgtttggcaa acctaagtcc gacgaattac tctttattaa gagtcaagtt agggccaagt
   236641 ttacgacttg tgatcggaac aatgccggaa ctaaaaccat ttatgctgtt atgaaaaaag
   236701 ccggatggtg ggatcctacc aattaaggta ggagatgatt acacgcttta catttataag
   236761 cattttaatt caacttcttt ttaaaacttc tgaggttgaa gaaattctga tgctaaatcg
   236821 acccctaaaa tgtaacattt cctttcggaa tgacattgta gatatattaa attgagctaa
   236881 gactgaaaac cataaaagaa tacttttcaa aagattgtaa ctttatttta ttatacttaa
   236941 gaaaatggtt gtaaattatt tatactcaaa agcttcagtt ttgagattcg gggaaatttg
   237001 gattttcttt tcatttggcg atatgttgtt gctgttataa gtattctctt cagcaattat
   237061 aaatctaatt taagaagtat atgaaatttt aaaagctaat ttataaagtg ctaccccaac
   237121 aaatagaaat gcctaagaat acttgcaagt gcgtcataga tacttatcaa acatgccccc
   237181 atttgctggg ctaagtgagg cgaataattc atgtcaatat caaaactcat ttacctgcgg
   237241 ttgccccagt ctctctgtct catcaaaaag cttgtgacgc aaaaaccaac taagaagtag
   237301 atcaaacgag gctgtggagc ccaattccat gggttggggg tgcatggcaa ttctaaggcc
   237361 aattgaggca aatgcgttca accgcaatgc ctcttataag ccatcgttga caacccagtt
   237421 tggtgactgc gaaacgaatg tttcgaaatc tcgatttgaa atatggaaaa gtttttgtct
   237481 catcttgcca cagataggcg gcaatgccga caacgaagcg attttaatta ctttctccca
   237541 gtcattcatt catttccact tgttgcccat cagttaaaag tcagaagagg aaactcacca
   237601 aatggtaatt ccatttccat ttcggacatt tcacgctcga aaggatttta tcccacaccg
   237661 accaccgaaa ctgatgtcta tcgtcctgtg gccattacaa cttattgcta ctactgcggc
   237721 tacacttaat acaccaaatt aactttttcg tggggggttt ttctcaacgc cccctttcca
   237781 acaccgccaa gcatgccgcc cactcgaaaa gcaaggacgc gtttatctgc cggttatctc
   237841 gccttttgtt gattaatagc tttgcggtaa ttaatttgcc atgaatgagg tgcatttgta
   237901 tagaacgaga tggattggta tggaaataaa ctcgaacgct gaggtgcgct catggatgtc
   237961 aatgtgatta ttatttaaat caagaggatg gtttgggaaa tatttgatct aatgagatat
   238021 gatttactat gtgttaataa tcttaactct gatatcagaa aatattttgt gacgcaaatt
   238081 aggatgtggc aaaaaagtat tgttatttgc cattgataaa ctgtgatgat tgtgaaatga
   238141 attatatggg taagatataa atacactagt gaggtggagt aatgaattat tcgaagctac
   238201 ctttcgcaaa tcagttattt aaaacaagct tatgataagg atgtttgtac tggaatagat
   238261 ttaaccaata gtccttcatc cttggcagag tccttgcatt acctgaaact tttctcatta
   238321 tatctgcacc ggcacagcaa cgaacagtgg aaaccgaagt actccaacgg cagagccaac
   238381 tttctgcccg cccacagctt caggttttac caatgacttc cgtcatcacc gacacactca
   238441 aagtgtaaat ttgcatttgc ttctaattac gagcgggtac aagaaattgc ccagaactga
   238501 ggccggagaa ggcccgcatt tgcagcattt gcagcatcgg agcatcttgg caactcggaa
   238561 acttggcatc tgcaaatgga ggagcacttg cggcaattgc aatttagaat ttcaattata
   238621 tttatatttt ttatggggtt ttagggtggt gcctaggtgg aaaatgcccg cacacacgga
   238681 agtgctggaa aactacaaat caagtgccac gcacgcaaat ttcctttaat taaaaccaaa
   238741 cttttaagag cccctcgtct gcatcttctt cacgttcctc ggccgcagat gcatcttcac
   238801 ttggttaccc aactgcaaac tactcgggat caacttaagc gaatccaagg cgacataatc
   238861 ttcgagtgag gcccaaagtg cgggccgctt ttgttggtcg cagggcgaag ggattaaagg
   238921 ccaaagtttg ctcaggtgaa gaaatacaat tagcgagtag gacgaggaca ctgtggcaca
   238981 aatgaagtac cgaaattcat tttaaaatgt cttgtcctta tattacaatg aaacttacat
   239041 gctatttttc ccaatttaaa ttgcacggca ttactaatta ttcgaaatta ctgtttaagt
   239101 cacaaattag ctgcaaaata attaagttgc taagttttta atcaattctt accaaggatt
   239161 aagcaaggtt attgcacgac tgtaatgaac tgcatagata aataaaaagt tttacaaggc
   239221 ataattatta gtattattaa ctggttcatt tacggattta atgccctttt tttggggctc
   239281 ttttggtttt aatgtgccta aaattagctg gggtcaggga atgccactcc tgattgggat
   239341 tatgaatatg aagtcaaagc ctacaaaaat ctcttccaag tttggttttg taagtaaaat
   239401 tcagttttct tcgcgttcca gccggaagtg cacttagtat aaaaaaaaaa acgcggtgag
   239461 ggcaaaaagc gggccaaaag gcaataaaga aaacttcgcc gcccttcgaa gcgatgcgag
   239521 tgcagtggga aacttttcta acccatatta aaacatattt gcgcaaaaat atgcagatgc
   239581 ccgcagagtg caaggaagtt ttcacgaata tatgcaggtt cctgccatat ctatatatgg
   239641 acaggtggcg gcggtgcgtt ggcagtcaat tgctcattga cttggctcaa aaattgttga
   239701 gtgtcgagtt ctaagtccta agcccctgct aacatgttgg cgaaagttcc cggcaccaga
   239761 tacggaagag ccgacatctt cctcttcgga ataccatttc tttcgggctt agtttccagt
   239821 tgagtttacg tgagcttgga tttcaagctg tgcgcgcaca taagtttgcg gcttaagcat
   239881 gtgaaattca tatggatgga aatggaacca cccacacgcc accccacata ttcagctcca
   239941 ggaatttgca cccacctgca ggtggggcat aacattctga ctgggctaat gcattgctag
   240001 ccacccaaat aacctaagac attgcgtcgc acgggggtgc caaagaagtc aagccaagtt
   240061 actagtgcca aaagtttaaa attaaacgta gttatatcaa aaaaaaaaca gcttggttgg
   240121 aaacgtaggg tactactgaa ctatatataa cgaagaatgt gtatcttaaa tagtttaaat
   240181 gttttttttt tactatttta tttaaccttt ctttcattcg ccaataccaa cttaacgtaa
   240241 atcaagaaac taacgtagtc aacagtttgt tgtttaccta tcggtgacgc aaatatttaa
   240301 ttataaattc agctcgatta aagtttaaaa gagcaaagaa tgtcccaaaa atgttgcgtt
   240361 gtaagcaaaa ggctaattat gtttatgcaa agtgtttttt ttttgaactt atggaaccta
   240421 atggaatata atttgaacaa aattattgaa aattgacggt aattgaaatg aatttgaaca
   240481 aatttcagtg cacggctttg ggtgtcgtgt tgggccacca tcaaaggagt caaagagcgt
   240541 tgaatgttga atgttgcaac tttgacacgc gacgcagacg ttggcccaga gtgttttccc
   240601 cggagctctg caattttaag ggcctaggcc tcccgaaaag ggttcattag acattttacc
   240661 aaaattactg cacatttcca aaaagcaacg gctatatgat tagttttgaa gcggtggttt
   240721 atttgaagta gagggtttac tttgatttaa gttaagttga gcgagtttgc gttgtaagtt
   240781 acttgaacat taaacggata aagtcactag tacccacact aaacagctta cttgccaacc
   240841 gggaagaggg acttgtggtg cccgactaaa cacaaattcg atgaaataaa aataaattag
   240901 ctgctttaaa tgagccaaat aaattcattt agggttttat gcgctccact gaagtatgcc
   240961 aaaaggcacc gtcttcgtcg tcgcagtctt tcgcatcacc ctcttttcgg atggcagggt
   241021 taagagccaa gttaaaggca acacgtattg ccaaactcga ttgccgctgg cgccgcacac
   241081 caaatgcaat ttcacttcac cctcgtcgag gtacggtaaa atttccaggg tctccggtct
   241141 ccggtcgcca gtattcccca ttcgctgcag gtgattcccc atcgagacac ttatctattg
   241201 agtgagcttg gttcgcttcg tttggaccgc tcttgaagtg aacgccaacg aaataagaaa
   241261 acaacaaagt ttcttttgat tatgtcaatg gaatttgttt atctcaacga aatgtaaccg
   241321 aattgaaaaa aatatgtttt ttttacgctc atttgcattt acttttgccc ggatataaat
   241381 gtggcaattg gaaggggtga tttgttcaaa tgtccagctc agtaagattc aataattata
   241441 tatacacgta acacattaat gtgattctat ggtaaacatt agagtaagga agcaaatttg
   241501 ttttgagaac cccagaaaca aaggcatcat caacaacgtc aagtagcatc aacaacgtct
   241561 agtttgggtt caatatattg attcttggaa acgtgcctct agaaactgaa tagcttagtc
   241621 ataaattcag taaaaatact atttaaatat aaattggcaa actattaaaa ttcatatcaa
   241681 aagccacgca cctggcgcct gttcccctaa aaaaaaatgg aaaccggtca ataaccacaa
   241741 caaattcaaa accggattgg aagagaaacg ctggtcacct gtgaggaaag cccccacgtc
   241801 tggtccagtg tctgggacaa gtttttattt cagtgcgggt aaagaacctc cgaaattcaa
   241861 acattatatg aattcaaaaa aatcgtataa atagagaaag acgtgacaga aagggcacag
   241921 tatcgagtgc aacatcgaag catcctcatc ttctgggata ttagtacaaa ttgaattcat
   241981 tttcaaattc aatatgaaat tcttggtaag tttggccacc agagctacac ctcgcaggga
   242041 ttaaggactt tataaaaata ataaacggcc attcaggtga tcgtttttgt ggcccttatc
   242101 gccgttgctt ccgcgcttcc tcaattcgga tatggaggat tcggtggatt cggaggattc
   242161 ggtggccaac agcagcagca agaaggattc ggcggtttcg gaggcttcgg agaacagcaa
   242221 cagcagcagg aaagcttcgg tggattcggc ggatttggag gaatcgagca gcagcagcag
   242281 cagcaacaag gaggcttctt ctaaggctgt tactttagtt cctcgactaa aaattaaaat
   242341 aaattatttg aacgtattag tataacaaac acaaaacagt ttttgttttt aaatactcat
   242401 ttacatgttt tgacaatggc ttattgtagg cctttagatc gacagagatt ttattaatga
   242461 gtaaccttca tttatttcgc ttgcttataa atacgtttgg gtttattttt ttggacataa
   242521 gcaacatcaa gaaaaatgaa ttattaaatt aaattaaaaa tttgtgtttc aacataaaaa
   242581 attgttttta tttagctaat cgaaaatcac ttaatgggtt aatgacattt ttgtgctata
   242641 acaacattaa ttgcaaacac ttgaataatt cgcaaatgat gttggcataa aaaccaaagg
   242701 cagatactga ctcatgcaaa attgtgaaat aaccaaatgt tctgacagca ataatttaac
   242761 aaaaaaccta atttgattag cgaagagcat acgccaagaa gagctgattg caaacctgta
   242821 tttttagtgg gcccgtcaac cccagatact tgaacgtttt caacaacaga aaaaatcccc
   242881 tataaacaca aacgttcaca atgatttgaa cagggaagtc cgagcggcga tcgcaccgtg
   242941 ctcaaccagt tttgaatggg cataaagcct aacaaaaatt cagataaata ctcatagcca
   243001 gcagccgaaa ctcaaacagt tgattttagc attccggtga aataagattg ttcgcttgag
   243061 gaatattttc aatattcaac atgaaattca cggtattttt cgctaaaaat tggctaatat
   243121 agacatctac gttatttttt agttgaaact aaatgtattg tactgtatgt attatttttt
   243181 tagataatcg tttttgttgc gctcctcgcc tttgcatcgg cccagttcgg tccgtttggt
   243241 caaattatta ggggtattga acgatttgaa ggtggtctgc aacaacaaca gcagcagcag
   243301 caaagcggct ttggcggtgg tcagcagcag caacagcagg aggagggtgt catcttcaga
   243361 ggtcctttcg gcggcggagt ggagttcttc caggagcaac agcagcagca gcaaggcggt
   243421 ggaggtcagc agcaacagca gcaggagaac ctatttaact tcttcggcta aagctcctta
   243481 gtgagggaaa ctagacatag actgaccact atctatagaa ctcaaaagca agccattaac
   243541 taaagccatg atcgtagaga taaacacacg ataaataaat atttttaaaa acacacaatt
   243601 ataaaccaag acataataat gcttttctat aatcctagtt taaatattta atactagttc
   243661 atgcaaaacc aagctaattt tagtttaata aagcaataac gctttgtcat ataaaattac
   243721 acgaaatcaa atacaaacaa tttgtttacg aggccaagga gcagacaatt tgcctgctat
   243781 ttggatgtga attcagcaat gacttcgtgt tttgtgtcaa aatcgcgatg atggccatgg
   243841 ccaattgtta tggccaaagt tttaagccaa aaatcgcaaa actctaatga gtgctatcgt
   243901 tgaaatcaga ggagagcaag tgggtgtgga agggtcggtg gcatttttgg ttcctttatc
   243961 cgaaagcacc gaaacaccat caaagtcatt aagcggaaaa cccttttggc ttcttttcca
   244021 cgcattttca tttcgccttg taatgacttc atcccggctt cagagtcttt ggggttttgg
   244081 ttctggtttt gttattggag acaatttcga agccatcctg tagttgcctg tctgacaaaa
   244141 caacgccagt cagctataca gccagcgcca tccaccaaga aagccaagag caccaacact
   244201 cgtaactaca aaacaacttt ttaattgcaa ttaaatacgt aacaagtttt tagttgtaag
   244261 tgcgactacg gagcacacag ggaacttagc cgtggcaata gtgcccattg gtgccggaat
   244321 attgttgttg tgggttaccc ttatctatcc tttgctatct gctgaatata tatacaaaga
   244381 tatatatata tatagatata tatactatat acgtatctat gagattgcca ttgcagtgtt
   244441 tgcctcactc gcactctgtg tgtattgcaa aattgagttg tgcgctttgg ggttttaatt
   244501 gttaattgtt ggctcagcgg gcagcgcttt tgacgtcgtt gatgacagtc gactgtgggg
   244561 ccagaacgat gtggattggg tcgtaagaaa atcgcacttt ggggattata ttgaagtcgg
   244621 tggagagtgg aaagtgggaa gaggaaagtg gagaaagata aaagattctg ggcccaatcc
   244681 tctgcgagga ggcggaagaa aaggatgttg cggattaggg aattaaattg aaacccctaa
   244741 tgattttcgg gttatgcggg gaaacacaca ttttgcggga acttttaatc aaatcatcaa
   244801 gttcatcgag gcatacgcat gcaatcatta cccgaacggc tttatgactg aacaattaag
   244861 aagaaaaggt tgaaaactgc tggtaaattt gcttaataaa ttactgggaa agtccgattt
   244921 gaaaatagtt tagctaaagc attgcactct gatagacgca atattgtaat ttttttatat
   244981 gttcgtaaag atttatttga ttctctttag atgcaatcgg taatcgtatt atgtccgtgg
   245041 aaagtgaagt atattggaca ttagcatttt ccatacattg ttaatatttg atatgccatt
   245101 taatttgaat gcaaattaaa atttgatggg gccactgatg ttgtcgctta cccacttacc
   245161 ttttgcatct aatggatctt tatgtgcacc cacttgggca gcggttaagt aattcgcccg
   245221 gagtcatttt gtgaggccaa agctgtgcca gtaacctcta agtgtctgtt tttcttcacc
   245281 tgtaccggga ttcggtattc cttgactcac taatttggcc gcaatttaca taaaggacgc
   245341 gcggccccaa atgttgttag ccatggtaat attccgtttc ttcgtcgtta ttttgttgtg
   245401 tattttttga agcacccgcc gaaaaagaaa gcgtaatttc ttttgccatt caacttgatt
   245461 aaattagagt aaagggagca aggcatagcg actgtgtact aatgagaggc agctgcagtt
   245521 tagtgcccgt ccgagaatat tatccaactt cccaggactc caacgccatc tctactctcc
   245581 aaacagtgac agatgtatga cttggcattt atagttttga gccgcaattt tcagtgattt
   245641 atttatgcat gaaatgcaaa caaaatctga ataattacca acaaaagcta actgaactga
   245701 cagttagaca gccagcccaa acaaagcaag aaatgcgata cgaaccaaag cggcggcacc
   245761 gactatgtgc gctaaggata gacaggacta caggcagcga ctcttgagct gtcagaaggc
   245821 atctgtgtgg gaatattata atatttgcaa tctgcaaaat gctactttcc ccatattcat
   245881 atgacgagaa atgagcgggc tcagacaaca aagcggcacc agtgacatgc tcaagtatga
   245941 cggaagctgc aggtctttgt tttgaccatt aaaagtactt gatgtgctta aaaacgtttg
   246001 caaaaataac tattatattc gaagtagtaa taatgtgaaa tcgtttgggt caatctttac
   246061 gtacacaatg gttatgaatc ttcaaccaaa gttgttattc ttcaatcagt ttccaagtta
   246121 tagtccctgt atgtatttca aataatctga taagctttac atatttataa atatatacga
   246181 aaatttgcga cgaaaatgtt actcaaagat aatactgagt acaattataa aaacctttgg
   246241 caaatttaca tataatttag ttagtttcaa ttaagcttaa acactgagaa gtgatttata
   246301 attagtttag tgcgtgacat gaataacagc acacttcatt tccggccaaa gatcattgtg
   246361 ttgaactagt ggccgctggc aatctaataa caaagtttgc gcacttaaac actttggcct
   246421 tttggcttca actggatctg gccacgccca cttagggctc cgccccgaga aggaagtggg
   246481 cggaagagga ggatgtggta gaggagttgg gatccccatt ataccgccga ctttctatgc
   246541 ctttgcagtg cagcagtaaa aatgactgca cacagctgtg cttcatggct gcgatggcga
   246601 atctggagaa ggctggcgct actgcggcag taagatttta ttagcggtgg tattagcagc
   246661 gacagcaagc cagaaaggag cccatcctgc cactcacacc cactttgcca tggacagcca
   246721 tctacagtgg ttggcgttgc atattaatgc aggcataaaa atatttacaa cttttttatg
   246781 cagcaaacaa catttttcgc taccgctgcc gacgggcgtt ttgttttctt ggcaaattta
   246841 atataatttc tggtcgttta atgagggtca ttcaaaagtg ttcgtcgaga aaacttccat
   246901 tttcgccgag tagccggcgg gcacaacaag tgtgccggcc attatgagtg accctcggta
   246961 gggtgtcgta aaaatcgctc aagaacatta tgcaaaataa gagatgcggc cataaagtga
   247021 agagagtcta aaggccccga agcacttgaa gagcaaatcg cgcccactgt gccgatgatt
   247081 ttcggaacgg cattgtgagc agtgaacagt ggaatccgca ttttggagtc gcctacggtt
   247141 tttgtctttc gcttaatccc tgcgccggct cgcaaattcc aatgctggtt tctgtcatcc
   247201 ccaaaagttg ctcggcccct ccacaaaaaa ggatgcgggt gtcgtggccc ataaccgaaa
   247261 ggattataca aataaaaata aaaaatatat ataaagaaga ggccatgggt gggtgaggtg
   247321 ttataaattt gggacagcag gtgaaaacaa tttggtgcat aaagttttcg cttagcagct
   247381 cagcgcgttg gcgacccaag gacctcgtgc caggatatgg ctctgacttc tgttttgcgg
   247441 cccaatgcgg tttgacacaa aacggagaaa acaaaaaggg gcctaaataa cagaaaataa
   247501 aaaatctcaa agaagaaaaa catcaagttc aggaaaaagg gacgagcata cacaaaaatt
   247561 actgacttgg caggcatatt tttgcatttg cagagctacg attgtcaaaa aggaaaaatg
   247621 tggtgtaaaa aggataaagg atgtagcaat tttctgctgg tattagtttt ttttttaaac
   247681 caaaatagtt attgcttagc aatataatga actcatactg attaataatc catatagaga
   247741 gagtagcttg tagtgaataa tgcgttcttg aaatttttaa aaaactttaa aaatggcaag
   247801 agtaacagcc tacacactac agtattctaa tcataggaaa tataaaagaa taatctgcac
   247861 cattacaccg tcatgatagg aataatcttt cctgacaaag cccctaatgc atttcccctt
   247921 ctaggtccat ggtcaatgca gccactttag gtggctgaga agaccaaccg gcaatgacag
   247981 cgatttctca tgttagacgt gcctttttat gtggctcgga aattaaagta atcatttttt
   248041 attgcgcgaa caaacaaagg cattatactt tacagctctg gctaagaggg agagatgaca
   248101 aacacaatgc agaagggaga atggagacga ccacaaaatg cactgaagga caattgagtg
   248161 cagaaatatg gccaaaagcc ggagagaaac tagcaaacgg atacgctggc cgaacaggca
   248221 aaccaaactg aaaccatcta gaaacaacaa cagccactaa cagtgatgtc gaatctttag
   248281 tttaaaaata ataatactca acttgtccaa tatatttagg ctcatgtcaa tgaatttgct
   248341 aggaaggaat tgttttgttt attttatatt ttttatacac gtctaaaaac cgaattaaga
   248401 tgtgaactgc ttttaaaaga taagtttgaa ataataaaaa tctttgccta taaataacta
   248461 caattctatt cgatgtccaa gttcagacta ttcaggcgat gcaaatttta ttttaaaacg
   248521 aaatcacgac atatacaaca atatggaatt ttttttgttg tattattttg actaatgagt
   248581 gtaataaaaa tgattgaaaa catttagcta aagtacaaaa attgtcaaca ctgaccacta
   248641 aacgtaacca gccagcggta gtggatggac ttgggttttg gacgtggacc cggatcgtcc
   248701 aactacccac ttccacctcc cacatcccag atcccagcta accattcgct gctcgatgct
   248761 cgaagctgga aactcggacc tgacaccact cgactcgcac cctcgacggt ccaagaacaa
   248821 aggctttggc agctgcgaca atgacagcag cgaaaataaa aatatgtaca ctcaaacata
   248881 catagagagt ctggggcggc agagccacca acccgccgcc attgagaaaa ttgcattaaa
   248941 atctatggag tgtgcataga aaacggagga ggatgttccg cccgaaaagg actggggact
   249001 ggccgggtgg cgacggagtg ccggagtgtt ggatagtttc agtttttcgg aactgcgaaa
   249061 tggcgaattc gtgaaaaatt aaaggaaaaa ggatatgacg ccacattgca acatgaacgc
   249121 aaaattgcaa ttttattata ttttaacaat gcacttcgtt acgtgattcc cgtcaggaat
   249181 tgtcctcatt cccactgcac tccaagtaaa gccaagagac aaactcttac cttgtacgct
   249241 tcttccctac agatacgctt tatatatacc tagatataca tatatatgta tatagcgttt
   249301 tttttttatt ttggtggttt ccctgatggt tttatgcatg caatctgaat gcaggacaaa
   249361 ttcacagtta acagtcatat tttattgagt ttttgtgaat cgtagtcata aattcattta
   249421 gattgtgcat gaggaaatgc atttcgcatg catttgttgt aacacaaatg tgctttctga
   249481 gatttatttc gtttcgaata aataaagacg tgttgcatag cgaaagtata agggaatgaa
   249541 taaagaacag agaaatccat tgggaaataa ttgaacttga agtattttaa agtatttact
   249601 taaattttga tcagaactaa actgttgaaa ttaggataaa taaaggatat agtttttcaa
   249661 tataagaaag aggctcctgc atttaaacat cactcatgtc tgtttttgcc atgagatggg
   249721 ctttggcaaa tttgtctctt ttattttgaa tgttttgttt accaagtaat ttttcataat
   249781 aggctttgcc aactgattgt tgtgtgtttg ccctttaaat accagaacaa ctaaagccgt
   249841 aaataatacg tattttcttt ttcggcctgt tacgttttcc tatggtgctt gcttttcatt
   249901 tgcgctagaa aaatattatt tacactttat gatttcttta tatagcacta attgctgcct
   249961 ttattttatg tttaacccct aagcttggtc tttgcctttg gcagtaaaat aaaatgctta
   250021 aaatgcgaag acctggaata agaataagca aaacaggcca agatggaaag caagacaaag
   250081 gaaataaaat gaatgagata gaaaactttg acaaaatgaa aaccattttc ttaaggggaa
   250141 tatatacaat tagatttgct cagtaaggcc tcttctttgc gatcatttgg cttgaaatta
   250201 taaatacatt ataatgtagt atataatgtc aatacaaact aagtgggtgc ataaacaggt
   250261 tattaattgt gatgcaaagt tttttatttt ggaagagtta aaagtttgac agccgtcaga
   250321 tgcaaagctc catcgtcgtc cttcgcggcg gatactcaga cattcgagag tgatctgcta
   250381 aactcaaata tacacacaaa acgcacacac acatccatcg cacacacact cacatgaacg
   250441 tagtcagata atataaaaag tttttccctt ctacggattt atttttatgc cttctgcctt
   250501 agcatatgct tgtttatagc ctgtgctgct tatgccacag tgcttccttc gcttttcttt
   250561 gctcgtgctg gttttgctgc ttttcttgag cgtgtaaagt ttatttttgt tacttattat
   250621 tattattctg gctctgttcg ttgctttggt ccttctccat cttattatgc gtcagtatat
   250681 gtgtccgcgt atgtgtgtgt atacatatct gcgtacttat ttttcgtaat taatttcgtg
   250741 cttcgaaaca tctgcagctg gatttttact gcatccgaaa ttacgcatac gccccatgta
   250801 atgcagactt gatggtttgc tttcagctac agccacaatt tcgcgcaaaa cgtagctgca
   250861 aacgacttcg tgtttggctt aaagccccct ttctgtcaca ataaaaatgc caatttgtta
   250921 accaaaattt aaggctgcca aggaatattt gccaacttcg caagtcagcc agcgcagact
   250981 tgaagggagg gagagaaagt ttagggcatg ggtaaacaat tgacacaacg aattcttgca
   251041 aattttatag gcaaaatacc gtcaacggaa ctccactgca ccacacggcg tatgtgcaat
   251101 gcgccgctga gggcgttggt ggattgggaa ttggaagttg aaaaaccgag aataccgcag
   251161 acgacgactt aggcgaagta ccacatgagc agaagaagaa atctactcag ggcatatgac
   251221 ataagtgtac ttgttttgtg acattgttag aaaataattt aaaatggatt aggtggatta
   251281 aaaggcttaa atacatgacc aaaacacaaa taaaaaaata gatagtcagt aaagtttact
   251341 tcaaaataac gtaatcttta gttattagtt agttagttaa atgaagtatg ataaatgttt
   251401 tcctaaaact aatatcatct gacagtcact caatcaaaat ctgcatcgtt ctttttaaat
   251461 tttttccaac tgcatttgcc tatgagccac tgcagtgtcg cgtcgttgct gcgtaaacaa
   251521 accggtggga aaatatgtgg tgggaaagcg aatatcgggc tgaagggaaa atgccaccga
   251581 tatacatata tatttacaga cggttttcct cgagggatag ctaacgttgc tgcagcacct
   251641 tagccaaact ttgccttaaa tggaaatttt tgctgtttgc cccgagcgca aatctttttg
   251701 agcttgagtc cccagctccc aagctgtgag ccataagctg aaatatgtcg gccaaaagcg
   251761 agcgagtgca gcaaatcaga aggaaatttg ccaatgccaa gcggcaacaa ttttcaggat
   251821 aactaatcca ctcacacact tcacacttca atttccgcac ggttttctta cctgtctcat
   251881 ggtggggaga aaattcgaag ttgtttgtta ttgccgctcg ttattgttgc catgttccat
   251941 gtcgttttcc atttcgattg tgtcactaac atgttgcgca tccacgggcc aaagggggcg
   252001 gcaggcggct gggcggttac cgtgggaggg gggcgtggca gcggccaatg atttgaggag
   252061 tgcgcccagg caatttcaca acgggcacgt atgcaaacag tggccaaaaa gtgggcgttg
   252121 ttatgccagg gcctcgaaat gggaatgtgc caaactgtcg gctgcaattt tgtcggctgg
   252181 tggcttcaga aaaacgcata aacagaaaaa agcacgtaag aacgttgcta gatttccccg
   252241 actctggtat acccactaat catattaaaa cctcgaacat accactttca aagctgcctt
   252301 atattagtta gaaagatggc atcaaatctt attggcattt attttacaat ttataattta
   252361 agaggcgctt gttttaagta caaagtagta acaattaaat tgaacacata cgcatactta
   252421 taaataataa ataaatttaa gccctaatat tgaggtaaag gttggaaatt ctttcaagta
   252481 tgaacggtaa cctatcattt acctgtacca agtataccca aattttagaa ttgaagtaga
   252541 gggtacctag gcactaaccc gaaggactac gatatgacaa attcagctgc gtatgtcgtc
   252601 tccttgggct tatggctgag tgaagagaat aatggccgtg ccctcagtac aatttccgtt
   252661 gcatactctg tgcgacattc gaacaaagag gaaaaaatcg ctccgtgcga aatgggaggc
   252721 agatgtgcaa atccatgcct aactacaagg taagcagaaa tcggaactgg ttgcagattg
   252781 agctgttgcc aaaatttccg aaatccaaga ctggcttaca gcctgaaggg tgaatactga
   252841 agtgccagat ggaaatgcat cagaattgcg accagatttg aaacgccgtc aatcatcagg
   252901 ggaattggaa atcatttatg cttagagcta ttcttaagat tctttgtttt agacactgtc
   252961 accaaatgtt atcagttatt aaatacgttt cgcaagtaat tgaataaatc gaataaaact
   253021 tgaacttttg caagaatatt ttatttgggt attgtaaatt attctcatag agacaaacta
   253081 ttcaagaccc aagccaccgc aacttaaaac atttataatg cccagtaacg ttatgaaaat
   253141 gcatttttcg actgtcccca cgacaatgag aaacgagaac aacagaagcg aagaaaaaaa
   253201 ctcccccgac ttctggcata aaatatcaca cgttggaaac gtttttcgca gcatttgtgt
   253261 ggcatttaat taaatgcatt tttattttat tttttttttt taatttcacc caacgtcaca
   253321 taaaatatgc gaacaaaaaa ataggtgtgg accacaagaa acaggtgcga aggagagaca
   253381 gtgcaaaaag gtgttaatgg tgactatgaa attccatttg catacactct caagttacaa
   253441 aaaataataa acgaaaagca tagtttctaa aaaaagcgat aatttttaat gcaattttac
   253501 ctttttatac gtgtgtgtat gtctgtgttt tttgcccctt tcggctaagt aatggtaatt
   253561 aggcgtggaa aaatccatta gcccaagccc ggtcggaaac agttgccaga acataaggcg
   253621 gagcccttcg agtgctaatt tgaattattt aaatttcaaa attgccatca aatgctccac
   253681 acgttatact taaaatgtaa atacagaaat cgaacagaat atatatagtt ttatacccgc
   253741 aagaggcaaa cataatattt taattggagc ttttgataga tattagaaaa tatatacgac
   253801 ttttaaaatt agttcaaagt tccgactgtg tgaatgccta ataatataca atatgtttta
   253861 tttaatttat ttattaatat gaacattcaa taaagtactt gctttcttac tatgtttgtg
   253921 gccataacca acgtaaaatg ataacttcga ataacacatg aatagctaaa ccaattaaaa
   253981 aagcgaaaaa tcccagcata accactaagt gaactttgag ggaattatca acgttttccc
   254041 tagtctcttc ctgaatgcta gataccgtgt gctttccgaa gtacaaggtt acaaacgcca
   254101 atgtaatagc cgttttgcag atccacacgc aagtgcgttc gaactgattc atgatgatgc
   254161 ccccgacctt actttgcgat ggcccggtta ttgcattaat caaataccaa ctgaaataaa
   254221 gctgctctgc tcgactccgg aaccgcttgc accacgtata cttgggatat ctactatagt
   254281 tgccatatgt aaagtacttg gatcgcataa actgtatgtg actcccgcct tcaatccagc
   254341 tctctacgag gaatagctgc tgaactttca acttcagatc caccactgtt atggagcgac
   254401 agtaccacga tggataccgt ccattgggaa cgagacgcaa tgccaaacgg gttggtatat
   254461 agatatgtcc acggggaacc attatcttaa tggtgctatt tctgagtaat ttcggatgtc
   254521 ctggatcctg agtaatttga tacgatgttt gctgacgatg cggcgattta aggtaaaact
   254581 ttacgtttga tgtagttccg gcaaactcct gaccaccagt tacaatcacg agtagaatct
   254641 ccgaaccact cacaaacgat tgatccgact ttccaactga cgcatcgcat tgcaatcgaa
   254701 attccggatt cttcagatag gcagaaataa tgttgaggtg taagagaaac ttgaagacga
   254761 gcagcagaaa aagcagagcg aaaaaaatca ttaggatcat attgaacgta aatatgggta
   254821 cgggtatgtg ctcgacaaac aattgcgatg aaattggaaa aatacgagag gatagggctc
   254881 ctaaggtatg gcaggtgcac tgaacagatg agccacgact gtgctcaaag gaggtggtgc
   254941 aatgatcctc gctccagccg ggatccaatg aacggttctt ccagatgttg cactggtaaa
   255001 tttccaaaag tatcgagtag ttcagaggta gaacctcctc cactatgtcc tcattgtcat
   255061 agtcaataaa gtccgctttt tgtctcacct ctggtgtctc cgagccatcg tgcgtcctgt
   255121 tccccttctt ccttccccgc gcacttaact gatccttgtc ttcggtttta tatcggattt
   255181 cgcccggctt gtgtatggcc acatatgccg ggctccgttc acaggagttg gctatccaaa
   255241 tgcgtttacc ctgcatatca ggtgttatcc gacaagcgtg ctgccttatc tgtccgagcg
   255301 ttggccatct gtgcaatcgc atcttaatat acattagctc cgaacaattt acgattcgca
   255361 ctgccaacat ggccttgtgg tttagcatca cactgtatat gtggacttct gtactattct
   255421 ggatactatt attggtcatg tactgattga aggacgcgtc gttgaaatgc gtgatattcg
   255481 tcttgtatac taaaggatta gtcagctgaa actccttggc ggatctaaaa aattgaacgg
   255541 gactgtaagc gtgaacgata agcacactgg tcttcgaggg gaatggatct ggataccacc
   255601 agtagatatt gtggaagttc tgctgcgaga tgatctgtag cagaatagag ctatggttca
   255661 gtctgcgttg cagttcatag agcagctttg tcgataattt aataacgtgt atgtggtcga
   255721 ttgtcttcac ctggatgtcc ttggtgttct ctgtcacctc agtcacatta atctggttgt
   255781 aaacatgcaa aaaattcaga aaatgttatc aataaagcaa tccaattata tcaataagca
   255841 aagtgaaaat gacgtttcgt attcttaaat atataatgcg aaaatataat ataatagtta
   255901 taaatatata tattgggata tcaaaaatct tgtgatgcat tagattataa atttttcgaa
   255961 tacatgccta cctggtacgc aatgccgctc ttgtggattg ttaatgcgtc atcatacgga
   256021 tgatgtcttt gagtggctat gacgccaaga aagtaaatgc acctgtacaa gaaccatgta
   256081 ctcatcagcc agctattgat ccgcaccaaa atgagtggat caaacttaat gacgaacggc
   256141 ttctccaaat cgattatttg caaattcatg cacgcgggat tatgtagact acacatggcg
   256201 tttgaatggc tttcggtttt ttttcctaaa atggacataa agaacatatg catggccgtc
   256261 aacgaatagt agccctcccg atgaagccat tcatgctcct gaacgatcgc cgagaagctg
   256321 tcgcccaagt ggctaaacat ttctgccatg acggtggctc cacgaaaatc gactggatgc
   256381 agcctaataa gcatgtgcga gctcagcgtg gtaatctgct ccatctgcga ccccgttgag
   256441 gcgaccaagc cagtcagata agagtagaat tcatctccat cgattgacgt ctctataaaa
   256501 gtgatggcag ctattcccat gatataggcc ctattccaat gacctcgctt aaagaaattc
   256561 ggcacatagt tcattacttc tttttgcccc gttagcatgc ttttatctat cgacaatact
   256621 ttcacttcta cacgtttttc gacgcacatg tcaatggcat cacatatcga gatcatgata
   256681 gtctctgcag cgggtagggt gagcacaatc cttgagtatg gcacattcga ggccacaact
   256741 ccatatgaca ccatatagcg ataggttatt ggcgggaaag gcgactcaaa tccggggcaa
   256801 tcgatctcga acattgtgaa gccctcgacg cccaaaaaag gatatattgt gcaactacca
   256861 tgttgagggc cattgttccg gcgcagcgtg tagaacgcat ctgcccaccc ttggcccttc
   256921 acccacactc ttagacggat ctgaacgagg ggctctagag tgtggagaat cagatattta
   256981 tgagaggatt ccagagtggg ctgtgattct gtgtccaaca accaccactc atatctttta
   257041 accgtacccg gacagtcatc gcatttcgag atcaggtgta tgctgtccaa cggcgcataa
   257101 acacctagag cgcaatttcg acggcaaagg atttggggcg tgaaggttgt tttagcgacg
   257161 ccttttattg tttgggttgt ggtcattcga ttccgcggat cgaagcgtga gatgacggtt
   257221 aagctgaagt cgtaaacggc attctcctta agagcatatg ggggtaatct caacgtgggg
   257281 cctaaaaaaa ataattttga tataccctaa agtaggtaat gacttattta tgtaagatgt
   257341 ttcctatttg acagagtaaa atattgcgct tttatcaaga taatttgaaa aaaattctat
   257401 tttacataac attttaatat ctgtcaatag tatttcccca acgcactttt caatatcacc
   257461 gccattacaa atctagtttt gttcatcata ctcactcttg gacatatact ttttgcaata
   257521 attgttaaat ggatcgtcta agctgataca agtccacaag aattgcttcg actttataga
   257581 ttcccttatt ttcaacctgt ccttcgagct ggatccgtcg ataataatgg gttttctgac
   257641 gtcgaccaga cgtcgctcat tgcctttgat aaggggttcg attgggggcg gtttgtactt
   257701 catatagcac tgaaataaag tttaaaccct gaggggttat acatttcttc tagacttggt
   257761 ccactcacac gagctaccgt agttacgccg tttattacag ctttacctcg cagcaaaaag
   257821 actttccgcc tatccggttc gtttaggatg tgcaccttgt agggcagtag cttcaccacc
   257881 agtcctgtgg cattttttag acgagcaata atttctgcgg ttagaatata tcaacattta
   257941 ttcacttgtt tcaccatcga aatttaaaaa aaattaatag aataaagaaa ataaaactta
   258001 ctgttctctg tgatatcaca taattgccat gttattttat catactccac tgtggagcat
   258061 gcatcgctaa tggacgcaaa aaattctaga tgacccatgg gagagaaata tactggcttt
   258121 tcgggatttt tgcaaaattc taactccaaa gctggtaggc acgacacatt tggtggtttg
   258181 cgtactttaa ttttgaaacg cactacatgt gccaatagct ttcttctgtc gttcaaagaa
   258241 ctaactttcg ccacaatgta tttatgtttc gtattgtaga atcgggccgt acatcgatgg
   258301 aaataacaac gattgtatac gattcgctta cttcttatgc cccattttcg cattaacttt
   258361 cgaagatttt tggtgtattt ccaatccgaa tgtatctcat caattaagta atcattggta
   258421 tctacagtca ggttgacagc aaagtttttc tttcccaggc tcggcatagt tgtgaaaact
   258481 gaatactctt ctccataaac tggatttcgg ttcatgaata ggtacacctt caatggacct
   258541 ttttggccaa gcaattgttg gttttttaca gaacttgttc tgccattaac attcggtgca
   258601 aggcaaggta ctgcgaaatt ataatcattg acagtttgat tttgatactc tgtagagctg
   258661 ttatttatgc aggttgagct ttgattatag atgggatact catcaactag ggggaaatca
   258721 gctaagctga atgagacatt tccattttgg gacttgcttc cttcgattcc gttttcatac
   258781 gtttggtttt cgtatccata acttatttcg gtattgactg aactccacga atagtcttca
   258841 tcattaaaga ggtgagttga attctcacct ggtttttgct cggaaatatt cttataagta
   258901 cgtgcagcat cttccaaacc aaacttttca cttggtatag tgggatatgt cttagtagtc
   258961 gtattatatt cctcaaagct agaaaagtcg tagcttttat taagaacggg atcccacaat
   259021 ctctcaattc ttctctcctc ctcttcggga atcgttcgac gtattatttt atgacgctta
   259081 cgacttaaca ttttagtaaa tctagtacgt tctgaaaaag agattttccc agcttcagca
   259141 cttctccacg gatgagaagt aggcccgcct tcagggctct ctgtcgaacg attgtatgcc
   259201 tccagaaatg tgccatccaa taaggacatt aatggggttc cgctgttttc catgatcaag
   259261 actagcgaca tcgatatggt catgaagtac aggaacatat catagtttac acaatcgtat
   259321 cgaaaaatat ttcacttttt gcttaatttc ctccattttc gattaaattt tgactcaaga
   259381 agcaaggtaa ggactgtctg acgtggtttg gcaatttcag cggaccagct ctttcatttt
   259441 tttaattgca taatactcga actgggaatg tgtggttgac aggcgacatg acattttacc
   259501 gcagaaaatg ttcgtatatc ttgttggatt tttaattttt ttcatcacta ccctcttgtt
   259561 tgcctttttc ctgttcctgc tgttgttgtt cttgtcgtgt cgctgcctac ataattgttt
   259621 taattaattg cgaattgtgc atgcaaaaag cataaagtgc acttcaaatg tgtgaaaagg
   259681 aacaaaagcg taaaaggctt ttctgcacag ctggtaattt attgaccaca atagcatcca
   259741 gaatcggcgt catcaacaag agcgattaca gaacacggct taaccccaac ttcaaatcca
   259801 agctcatccg ctttcccatt ccaatttcca tttacacagt ccatataaat caaatgaaat
   259861 taactgagag tgagcgagtg caggaaaagc agcaaataga gtgttgaatt tttataaacc
   259921 acaaaagcaa cgagcattga caatagacaa tcatacttta tttactataa acttcgcaca
   259981 tgcatagtgt tttttatgcc aggaggagtg gccaggaagc tgttccaaga cagggcgaca
   260041 atttcttaaa ttgttcgaac aaatgagaat ggaatagaag taatggaagc caaggagaaa
   260101 cccatttaca ggcgagcgca cgtcgcataa aaaataaggc accgagaaaa agtggaaact
   260161 gatttcactt cctctgaatg ctttagagat actctacccc ataaattgtt ctcatatagt
   260221 cttgggagta attcagtttg tgacttaacc cttcttatct gttgcttttg aaccattaac
   260281 aagtaaatct tataaatact attttgatat aggttagact atctttgagc tttatgattt
   260341 gaaacaatta atatatattt aaaaaattga agtttattaa ataaagtttt tgacttgtct
   260401 caattattgg ccgtgcgtac caaaccccaa aaaaaagagt ataaaaactt taacagtaaa
   260461 gaaaaaaaag caaaaatgaa agaatggagc attttacgat ttagcatgtg cggaccaact
   260521 gtgggtcggg tggtttgggg cctgatgaac cggcggacgg acggattcac atacggacgg
   260581 agcggagcgc cagtggagga ccgccaagtt caggactttg gcgcgtcaag tgcttttcat
   260641 tttccgagca cgtcgccgcg tcataaaaca aaaacgcatg aagcgcaacg gagaagacga
   260701 agcggggcgt tcgggcacgt ttagcatata tattttcaca cttgcaatca tactttaagc
   260761 agaaaagtac gctctcacat acggccaagt ttttacggta gagatggaat cttaaaaaaa
   260821 aaacgcaaga aaacgcatat cttgaaaaca gcataagctc gatgaaataa atacatcgtt
   260881 caattcacac ttctcttaaa cgaagaactt aaatttattt atttcaagtt gatccctaac
   260941 acaataagta tgagtatctc aatcaaaaac cacagattct gcattaatcc gcgaaatagg
   261001 attgagatgc attttatatg atattttttt taggatatcc tgccttgtat aaatcgaagt
   261061 tccctgaacg gaatagttct ttctatgcca tccctaagtg ttacacactc atgactctga
   261121 cacccagttg gtgtcgggtc gggactttcc cgtatcttca ttttcattca cagccaaaag
   261181 ccgtgccata aaagtgcgtc gggattgtcg acaaactttt gctttcttta cttgctcttt
   261241 ttttttaccc ttgtttgcca tcgtgggtgt gatgataata atttcaagag tcacatcgac
   261301 tggcgcgttt atctgttttt ttttttattc gacggcggcg gcttcctacg actgcggctt
   261361 ttgggttggc tttcattaaa atgtcataga ccccgttggc gcatcttaat taccaaaaat
   261421 gataaaattt cataaataat gtgctttgct gataaattaa tattaatgcg agcggtctgg
   261481 caggctggct gaaaagtgtc tcgcagtcgt ctaatagatg tcaactctga tatctgctca
   261541 tttgacggtc tgacattatt aactgaatcg acttatcact tgtcgtcgag aagggttcgg
   261601 taagaagaag gtcctggtgt atttgacatt aaaaggattt cgctagatcc gccatgattt
   261661 ctgacactaa tgacgaataa tgttatctaa attatgtaga ttaaatattc gaaatgcgaa
   261721 atagttgcga cgcgtgtcat tattttgctc agtcaaagtt caaagcgcta tgccactcgt
   261781 catcctcatc gtcccttctt ccccttctcg ttattgccat cgccggcatg gaatgcttaa
   261841 tggatctgaa agcagcgtga aaccattctg caatcctttt tgtgcccatt accctgccag
   261901 cagctcatcc actccatcca tcacttggct gaaaactctt tatgctcaca aactttccag
   261961 ctgaagcatt ttcgatggcc ccggggggat ggagttcggt ttactttgga ccggactggt
   262021 tccggcggtg acgtctgttt cggccacgtt ggcaactttg catgcggttt gtctccggtc
   262081 caaagttctc gggccctgcg ccctttaatg atccatgccg caaatgaatt gcagtccagt
   262141 tgcaattgct gcacttgatt tgcggtgcga cttaatggtt aacaattatc tggtggcctt
   262201 ctgcgggcag gagttccctg ttcctgaagt tgacactaag tgtgcggcag ttagcacatt
   262261 gaccagattt aagtcttcag agttcccaaa tttaaacaaa cttaggtcct aggtctccaa
   262321 tattatttaa agacgtcttt tttaacttat tcctatttag ataaaattca tagaattata
   262381 tatacagcct tttcttataa atgaacttaa cttaggactt aacttgtgat tgacggacat
   262441 tcacccacaa ctaaaccacg aaatgtgtca gcgacaatta caagaatccg aaactgtcgc
   262501 acaccggcac ttggccacgc cccgcacatc cggagccgca tccgtagtcc catccgtttc
   262561 cccatccgta cacccaactc caggctgcac aatatcaatt atcgggcttc aagtgtcgct
   262621 caagtgtcac gtcaaacacc aacacaaaat acgagcaaag agcatcgagc atccagcatt
   262681 gagtatctag catcgggaga cccgcgagca cacatgacaa tccagtttcc gccccgagca
   262741 tcctggctgc actttgcaac ccatccgggc ccccgaaccc atcaggacat gctcctttaa
   262801 cgcctccccc aatacgtgta tgtaagtaac attttgcgct tttgactttg attgattaca
   262861 aaagcaattg agcatatcgt cacgctgggg ggagcaaaaa aaaaaaaaaa tctgaaatcg
   262921 aacaaagcaa ggcaaatgaa ttaacataaa taaaagaggc caaggaacga attttcattg
   262981 acagcttccg acaaaaggaa aagcgtaggg caattagaag tatccatttt ccgttttcca
   263041 cctaccaatt ctaatgagca atgccttcta attttcatca aggcttctga ttttccaaat
   263101 cgcttatggc tgcgagattt cggtgaagct tctcagacag gcttgccatt aattagcaca
   263161 attgaagcgg gcttaacgac accctttgca aggctaatga aaataaaatt tcaattacgt
   263221 ttaattgata aactaatcaa caaaggtcga caggcaatga ttgatggggt tttctcgttc
   263281 tcttctttaa attttcgtag aagtacata
//

BioPerl-1.007002/t/data/AF032047.gbk000444000766000024       475613155576321 16337 0ustar00cjfieldsstaff000000000000LOCUS       ALSEB2MP1                291 bp    DNA     linear   PRI 30-JUN-1998
DEFINITION  Alouatta seniculus beta-2-microglobulin precursor, gene, exon 1.
ACCESSION   AF032047
VERSION     AF032047.1  GI:3264957
KEYWORDS    .
SEGMENT     1 of 2
SOURCE      Alouatta seniculus (howler monkey)
  ORGANISM  Alouatta seniculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Primates; Platyrrhini; Cebidae; Alouattinae;
            Alouatta.
REFERENCE   1  (bases 1 to 291)
  AUTHORS   Canavez,F.C., Ladasky,J.J., Muniz,J.A., Seuanez,H.N., Parham,P. and
            Cavanez,C.
  TITLE     beta2-Microglobulin in neotropical primates (Platyrrhini)
  JOURNAL   Immunogenetics 48 (2), 133-140 (1998)
  MEDLINE   98298008
   PUBMED   9634477
REFERENCE   2  (bases 1 to 291)
  AUTHORS   Canavez,F.C., Ladasky,J.J., Seuanez,H.N. and Parham,P.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-OCT-1997) Structural Biology, Stanford University,
            Fairchild Building, Campus West Dr., Room #D-100, Stanford, CA
            94305-5126, USA
FEATURES             Location/Qualifiers
     source          1..291
                     /organism="Alouatta seniculus"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:9503"
     mRNA            join(<136..202,AF032048.1:67..345,AF032048.1:1162..1189)
                     /product="beta-2-microglobulin precursor"
     sig_peptide     136..195
     CDS             join(136..202,AF032048.1:67..345,AF032048.1:1162..1175)
                     /codon_start=1
                     /product="beta-2-microglobulin precursor"
                     /protein_id="AAC52091.1"
                     /db_xref="GI:3264961"
                     /translation="MARFVVVALLALLSLSGLEAIQHAPKIQVYSRHPAENGKPNFLN
                     CYVSGFHPSDIEVDLLKNGKKIEKVEHSDLSFSKDWSFYLLYYTEFTPNEKDEYACRV
                     SHVTFPTPKTVKWDRTM"
     sig_peptide     136..195
     exon            <136..202
                     /number=1
     intron          203..>291
                     /number=1
BASE COUNT       31 a    103 c     78 g     79 t
ORIGIN      
        1 cggtccccgc gggccttctc ctgattggct gtccccgcgg gccttgtcct tattggctgt
       61 gcccgactcc gtataacata aatagaggcg tcgagttgcg cgggcattac tgcagcggac
      121 cgcacttggg tcgagatggc tcgcttcgtg gtggtagccc tgctcgcgct actctctctg
      181 tctggcctgg aggctatcca gcgtaagtct ctcctcccgt ccggcgctgg tcctttccct
      241 cccgccccaa ctctctgtag ccctctctgt gctctctcgt tccgttacct g
//

BioPerl-1.007002/t/data/AF165282.gb000444000766000024       602013155576321 16156 0ustar00cjfieldsstaff000000000000LOCUS       HSATPCB01     226 bp    DNA             PRI       17-AUG-1999
DEFINITION  Homo sapiens ATP cassette binding transporter 1 (ABC1) gene, exon
            12.
ACCESSION   AF165282
VERSION     AF165282.1  GI:5734104
KEYWORDS    .
SOURCE      human.
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 226)
  AUTHORS   Rust,S., Rosier,M., Funke,H., Real,J., Amoura,Z., Piette,J.C.,
            Deleuze,J.F., Brewer,H.B., Duverger,N., Denefle,P. and Assmann,G.
  TITLE     Tangier disease is caused by mutations in the gene encoding
            ATP-binding cassette transporter 1
  JOURNAL   Nat. Genet. 22 (4), 352-355 (1999)
  MEDLINE   99364413
   PUBMED   10431238
REFERENCE   2  (bases 1 to 226)
  AUTHORS   Rust,S., Rosier,M., Funke,H., Real,J., Amoura,Z., Piette,J.C.,
            Deleuze,J.F., Brewer,H.B., Duverger,N., Denefle,P. and Assmann,G.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUL-1999) Genomics, Rhone-Poulenc Rorer, 2 rue Gaston
            Cremieux, Evry 91006, France
FEATURES             Location/Qualifiers
     source          1..226
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /chromosome="9"
                     /map="9q31"
     gene            join(<1..226,AF165283.1:1..197,AF165284.1:1..243,
                     AF165285.1:1..242,AF165286.1:1..225,AF165287.1:1..152,
                     AF165288.1:1..163,AF165289.1:1..158,AF165290.1:1..241,
                     AF165291.1:1..93,AF165292.1:1..223,AF165293.1:1..69,
                     AF165294.1:1..134,AF165295.1:1..169,AF165296.1:1..145,
                     AF165297.1:1..119,AF165298.1:1..209,AF165299.1:1..115,
                     AF165300.1:1..53,AF165301.1:1..126,AF165302.1:1..95,
                     AF165303.1:1..190,AF165304.1:1..198,AF165305.1:1..136,
                     AF165306.1:1..165,AF165307.1:1..150,AF165308.1:1..141,
                     AF165309.1:1..83,AF165310.1:1..>264)
                     /gene="ABC1"
     mRNA            join(<16..221,AF165283.1:16..192,AF165284.1:16..238,
                     AF165285.1:16..237,AF165286.1:16..>220)
                     /gene="ABC1"
                     /product="ATP cassette binding transporter 1"
     exon            16..221
                     /gene="ABC1"
                     /number=12
     CDS             join(<16..221,AF165283.1:16..192,AF165284.1:16..238,
                     AF165285.1:16..237,AF165286.1:16..>220)
                     /gene="ABC1"
                     /codon_start=1
                     /db_xref="GI:5734134"
BASE COUNT       69 a     46 c     58 g     53 t
ORIGIN      
        1 ctgttcttct atcagtgtgt caacctgaac aagctagaac ccatagcaac agaagtctgg
       61 ctcatcaaca agtccatgga gctgctggat gagaggaagt tctgggctgg tattgtgttc
      121 actggaatta ctccaggcag cattgagctg ccccatcatg tcaagtacaa gatccgaatg
      181 gacattgaca atgtggagag gacaaataaa atcaaggatg ggtaag
//
BioPerl-1.007002/t/data/AF222649-rc.gbk000444000766000024      1225113155576321 16757 0ustar00cjfieldsstaff000000000000LOCUS       AF222649rc              1659 bp    RNA     linear   VRL 10-JAN-2001
DEFINITION  Influenza A virus (A/Quail/Hong Kong/NT28/99(H9N2)) segment 3 PA
            (PA) gene, partial cds.
ACCESSION   AF222649rc
VERSION     AF222649rc.1  
KEYWORDS    .
SOURCE      Influenza A virus (A/Quail/Hong Kong/NT28/99(H9N2))
  ORGANISM  Influenza A virus (A/Quail/Hong Kong/NT28/99(H9N2))
            Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
            Influenzavirus A.
REFERENCE   1  (bases 1 to 1659)
  AUTHORS   Guan,Y., Shortridge,K.F., Krauss,S., Chin,P.S., Dyrting,K.C.,
            Ellis,T.M., Webster,R.G. and Peiris,M.
  TITLE     H9N2 influenza viruses possessing H5N1-like internal genomes
            continue to circulate in poultry in southeastern China
  JOURNAL   J. Virol. 74 (20), 9372-9380 (2000)
   PUBMED   11000205
REFERENCE   2  (bases 1 to 1659)
  AUTHORS   Guan,Y., Krauss,S., Webster,R.G. and Shortridge,K.F.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JAN-2000) Virology and Molecular Biology, St. Jude
            Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105,
            USA
FEATURES             Location/Qualifiers
     source          complement(1..1659)
                     /organism="Influenza A virus (A/Quail/Hong
                     Kong/NT28/99(H9N2))"
                     /mol_type="genomic RNA"
                     /strain="A/Quail/Hong Kong/NT28/99(H9N2)"
                     /db_xref="taxon:109241"
                     /segment="3"
     gene            complement(1..1653)
                     /gene="PA"
     CDS             complement(1..1653)
                     /gene="PA"
                     /codon_start=1
                     /product="PA"
                     /protein_id="AAG48207.1"
                     /db_xref="GI:12060686"
                     /translation="MEDFVRQCFSPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEV
                     CFMYSDFHFIDERGESIIVEFGDPNVLLKHRFEIIEGRDRTMAWTVVNSICNTTGVEK
                     PKYLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSERTHIHIFSFTGEEMATKAD
                     YTLDEESRARIKTRLFTIRQELASRGLWDSFRQSERGEETIEERFEITGTMRRLADQS
                     LPPNFSSLENFRAYVDGFEPNGCIEGKLSQMSKEVTARIEPFLKTTPRPLKLPDGPPC
                     SQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPKIIKPHEKGINPNY
                     LLAWKQVLAELQDIENDEKIPKTKNMKKTSQLKWALGENMAPEKVDFEDCKDVGDLKQ
                     YDSDEPELKSLASWIQSEFNKACELTDSSWVELDEIGEDVAPIEHIASMRRNYFTAEV
                     SHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMVSKCRTKEGRRKTNLYGFIIKGR
                     SHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEVGDMLLR"
     misc_feature    complement(4..1593)
                     /gene="PA"
                     /note="Influenza RNA-dependent RNA polymerase subunit PA;
                     Region: Flu_PA; pfam00603"
                     /db_xref="CDD:144261"
     gene            complement(join(1081..1653,894..1079))
                     /gene="PA-X"
     CDS             complement(join(1081..1653,894..1079))
                     /gene="PA-X"
                     /product="PA-X"
                     /codon_start=1
BASE COUNT      374 a    412 c    312 g    561 t
ORIGIN
        1 tctcaggagc atgtccccta cttcaagaac acagtacttc tcccacttgt gtggctccaa
       61 tctcgggtct gtaagagaaa attccatgct cacaaagttt accacatcag tatcattcct
      121 caaatgggac cttcccttga taatgaaccc atacaggttt gttttccgtc tcccttcttt
      181 tgttctgcat ttgcttacca ttgggatcaa ttggaagtca tccatggctg cacaagatgc
      241 attgagcaac gctgtattga tatacactcc cttcattata tactcagtag cccggcaatg
      301 tgacacttct gctgtgaagt aattccttct catactcgca atgtgctcga ttggggcaac
      361 atcttctcct atttcatcaa gttctaccca gcttgaatcg gtcagttcac atgccttgtt
      421 aaattcactc tggatccaac ttgctagcga tttgagctct ggttcatcac tatcatattg
      481 tttcaggtca ccaacgtctt tgcagtcctc aaagtccact ttctccggtg ccatattctc
      541 acctaatgcc cattttaatt ggcttgtttt cttcatgttc ttcgtttttg ggatcttttc
      601 atcattttca atgtcctgga gctctgccag cacctgcttc caagctaaga gataatttgg
      661 gtttataccc ttctcatgtg gtttgataat tttgggctct ttccagccga aaaatgtttt
      721 catgcatttg atcgcatcat acagcggtat cccctctccc tcatgactcg ggtcctcaat
      781 gcttaatttc aaagcatcca tcagtaagaa ttttgacctt tgggaacagg gaggtccatc
      841 aggcaatttt agaggacgtg gtgttgtttt aagaaagggc tcaattctgg ccgttacctc
      901 ttttgacatc tgagaaagct tgccctcaat gcagccgttc ggttcgaatc catccacata
      961 ggctctaaag ttttcaaggc tggagaaatt cggtgggaga ctttggtcgg caagcctgcg
     1021 cattgttcct gtgatttcaa atctttcttc aattgtctct tcgcctctct cggactgacg
     1081 aaaggaatcc catagacccc tgctagccag ttcctgtctt atggtgaaca gcctagtttt
     1141 gatccttgcc ctgctctctt catcaagggt atagtccgcc ttggtggcca tttcttcccc
     1201 agtaaatgaa aagatgtgaa tgtgtgttct ctcggatttt atcttgttgg ccttttctag
     1261 atagtatatg tgcacttccc tccgtgtcac tccaatctca atgaatcgat tctccttgta
     1321 atcatacaga tctggaaggt atttaggttt ttcgactccc gtagtgttac agatgctatt
     1381 cactactgtc catgccattg ttcggtctct tccttcaatt atttcaaatc ggtgtttcaa
     1441 taacacattt ggatcaccaa attccacaat tattgattcg cctctttcgt caatgaagtg
     1501 gaaatctgaa tacatgaagc agacttccag atgagtgcat attgccgcaa acttgttcgt
     1561 ttcgattttc gggtcttccc cgtactcttt cattgccttt tccgcaagct cgacgatcat
     1621 tgggctgaag cattgtcgca caaagtcttc cattttgaa
//
BioPerl-1.007002/t/data/AF305198.gb000444000766000024       725113155576321 16167 0ustar00cjfieldsstaff000000000000LOCUS       AF305198                1744 bp    DNA     linear   BCT 18-DEC-2000
DEFINITION  Virginia creeper phytoplasma 16S ribosomal RNA gene, partial
            sequence; and tRNA-Ile gene, complete sequence.
ACCESSION   AF305198
VERSION     AF305198.1  GI:11878216
KEYWORDS    .
SOURCE      Virginia creeper phytoplasma
  ORGANISM  Virginia creeper phytoplasma
            Bacteria; Firmicutes; Mollicutes; Acholeplasmatales;
            Acholeplasmataceae; Candidatus Phytoplasma; 16SrV (Elm yellows
            group).
REFERENCE   1  (bases 1 to 1744)
  AUTHORS   Harrison,N.A., Griffiths,H.M., Carpio,M.L. and Richardson,P.A.
  TITLE     Detection of an Elm yellows group (16SrV) phytoplasma associated
            with Virginia creeper plants in southern Florida
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1744)
  AUTHORS   Griffiths,H.M., Harrison,N.A., Carpio,M.L. and Richardson,P.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-SEP-2000) Research and Education Center, University
            of Florida, 3205 College Avenue, Fort Lauderdale, FL 33314-7799,
            USA
FEATURES             Location/Qualifiers
     source          1..1744
                     /organism="Virginia creeper phytoplasma"
                     /mol_type="genomic DNA"
                     /strain="VC-Fl"
                     /db_xref="taxon:145578"
     rRNA            <1..1491
                     /product="16S ribosomal RNA"
     tRNA            1599..1675
                     /product="tRNA-Ile"
ORIGIN      
        1 gcctaataca tgcaagtcga acggagaccc ttcaaaaggt cttagtggcg aacgggtgag
       61 taacacgtaa gtaacctacc tttaagacga ggataacaat cggaaacggt tgctaagact
      121 ggataggaaa cagaaaggca tctttttgtt tttaaaagac cttcttcgga gggtatgctt
      181 aaagaggggc ttgcgccaca ttagttagtt ggtgaggtaa aggcttacca agattatgat
      241 gtgtagctgg actgagaggt tgaacagcca cattgggact gagacacggc ccaaactcct
      301 acgggaggca gcagtaggga attttcggca atggaggaaa ctctgaccga gcgacgccgc
      361 gtgaacgatg aagtatttcg gtatgtaaag ttcttttatt gaagaagaaa aaatagtgga
      421 aaaactatct tgacgttatt caatgaataa gccccggcta actatgtgcc agcagccgcg
      481 gtaagacata gggggcgagc gttatccgga attattgggc gtaaagggtg cgtaggcggt
      541 tagataagtc tataatttaa tttcagtgct taacgctgtc ttgttataga aactgtcttg
      601 actagagtga gatagaggca agcggaattc catgtgtagc ggtaaaatgt gtaaatatat
      661 ggaggaacac cagaagcgta ggcggcttgc tgggtcttta ctgacgctga ggcacgaaag
      721 cgtggggagc aaacaggatt agataccctg gtagtccacg ctgtaaacga tgagtactaa
      781 gtgtcggggg taactcggta ctgaagttaa cacattaagt actccgcctg agtagtacgt
      841 acgcaagtat gaaacttaaa ggaattgacg ggactccgca caagcggtgg atcatgttgt
      901 ttaattcgaa gatacacgaa aaaccttacc aggtcttgac atactctgca aagctataga
      961 aatatagtgg aggttatcag ggatacaggt ggtgcatggt tgtcgtcagt tcgtgtcgtg
     1021 agatgttagg ttaagtccta aaacgaacgc aacccctgtc gctagttgcc agcacgtaat
     1081 ggtggggact ttagcgagac tgccaattaa acattggagg aaggtgggga taacgtcaaa
     1141 tcatcatgcc ccttatgatc tgggctacaa acgtgataca atggctatta caaagagtag
     1201 ctgaaacgcg agtttttagc caatctcaaa aaggtagtct cagtacggat tgaagtctgc
     1261 aactcgactt tatgaagctg gaatcgctag taatcgcgaa tcagcatgtc gcggtgaata
     1321 cgttctcggg gtttgtacac accgcccgtc aaaccacgaa agttagcaat acccgaaagc
     1381 agtggcttaa cttcgcaaga agagggagct gtctaaggta gggttgatga ttggggttaa
     1441 gtcgtaacaa ggtatcctta ccggaaggtg aggatggatc acctcctttc taaggacata
     1501 catataaaaa tcatcatctt cagttttgaa agacttaggt taaaatataa gtttttcttt
     1561 ttataaaaaa aagtgtttct cttatataaa agaccaaagg gcctatagct cagttggtta
     1621 gagcacacgc ctgataagcg tgaggtcggt ggttcgagtc cacttaggcc caccaatttt
     1681 atatcaggaa aatatttact tcgaagaaag ttctttgaaa agtagataaa catgatttgc
     1741 ttaa
//

BioPerl-1.007002/t/data/AHCYL1.kegg000444000766000024       727713155576321 16465 0ustar00cjfieldsstaff000000000000ENTRY       10768             CDS       H.sapiens
NAME        AHCYL1
DEFINITION  S-adenosylhomocysteine hydrolase-like 1 [EC:3.3.1.1]
ORTHOLOG    KO: K01251  adenosylhomocysteinase
CLASS       Metabolism; Amino Acid Metabolism; Methionine metabolism
            [PATH:hsa00271]
            Metabolism; Metabolism of Other Amino Acids; Selenoamino acid
            metabolism [PATH:hsa00450]
POSITION    1:join(26813..26932,50794..50905,52974..53117,54122..54222,54657..
            54759,56523..56617,57185..57291,58104..58220,58427..58490,59255..
            59343,59706..59776,60133..60227,60312..60410,60811..60879,61308..
            61386,62491..62611,63434..63440)
DBLINKS     LocusLink: 10768
            GDB: 9958257
            NCBI: 21361647
            SP: O43865
CODON_USAGE       T               C               A               G
          T   7   8   1  10   8  10   6   2   7  11   1   0  11   8   0   8
          C   3  10   2  16   3   8   4   3   2   6   6  17   3   6   7   3
          A   9  15   3  14   6  11  15   1  11  11  14  24   2   8   2   4
          G  10   9   7  17  18  11  11   3  21  11  10  23   5  11   6  11
AASEQ       530
            MSMPDAMPLPGVGEELKQAKEIEDAEKYSFMATVTKAPKKQIQFADDMQEFTKFPTKTGR
            RSLSRSISQSSTDSYSSAASYTDSSDDEVSPREKQQTNSKGSSNFCVKNIKQAEFGRREI
            EIAEQDMSALISLRKRAQGEKPLAGAKIVGCTHITAQTAVLIETLCALGAQCRWSACNIY
            STQNEVAAALAEAGVAVFAWKGESEDDFWWCIDRCVNMDGWQANMILDDGGDLTHWVYKK
            YPNVFKKIRGIVEESVTGVHRLYQLSKAGKLCVPAMNVNDSVTKQKFDNLYCCRESILDG
            LKRTTDVMFGGKQVVVCGYGEVGKGCCAALKALGAIVYITEIDPICALQACMDGFRVVKL
            NEVIRQVDVVITCTGNKNVVTREHLDRMKNSCIVCNMGHSNTEIDVTSLRTPELTWERVR
            SQVDHVIWPDGKRVVLLAEGRLLNLSCSTVPTFVLSITATTQALALIELYNAPEGRYKQD
            VYLLPKKMDEYVASLHLPSFDAHLTELTDDQAKYLGLNKNGPFKPNYYRY
NTSEQ       1593
            atgtcgatgcctgacgcgatgccgctgcccggggtcggggaggagctgaagcaggccaag
            gagatcgaggacgccgagaagtactccttcatggccaccgtcaccaaggcgcccaagaag
            caaatccagtttgctgatgacatgcaggagttcaccaaattccccaccaaaactggccga
            agatctttgtctcgctcgatctcacagtcctccactgacagctacagttcagctgcatcc
            tacacagatagctctgatgatgaggtttctccccgagagaagcagcaaaccaactccaag
            ggcagcagcaatttctgtgtgaagaacatcaagcaggcagaatttggacgccgggagatt
            gagattgcagagcaagacatgtctgctctgatttcactcaggaaacgtgctcagggggag
            aagcccttggctggtgctaaaatagtgggctgtacacacatcacagcccagacagcggtg
            ttgattgagacactctgtgccctgggggctcagtgccgctggtctgcttgtaacatctac
            tcaactcagaatgaagtagctgcagcactggctgaggctggagttgcagtgttcgcttgg
            aagggcgagtcagaagatgacttctggtggtgtattgaccgctgtgtgaacatggatggg
            tggcaggccaacatgatcctggatgatgggggagacttaacccactgggtttataagaag
            tatccaaacgtgtttaagaagatccgaggcattgtggaagagagcgtgactggtgttcac
            aggctgtatcagctctccaaagctgggaagctctgtgttccggccatgaacgtcaatgat
            tctgttaccaaacagaagtttgataacttgtactgctgccgagaatccattttggatggc
            ctgaagaggaccacagatgtgatgtttggtgggaaacaagtggtggtgtgtggctatggt
            gaggtaggcaagggctgctgtgctgctctcaaagctcttggagcaattgtctacattacc
            gaaatcgaccccatctgtgctctgcaggcctgcatggatgggttcagggtggtaaagcta
            aatgaagtcatccggcaagtcgatgtcgtaataacttgcacaggaaataagaatgtagtg
            acacgggagcacttggatcgcatgaaaaacagttgtatcgtatgcaatatgggccactcc
            aacacagaaatcgatgtgaccagcctccgcactccggagctgacgtgggagcgagtacgt
            tctcaggtggaccatgtcatctggccagatggcaaacgagttgtcctcctggcagagggt
            cgtctactcaatttgagctgctccacagttcccacctttgttctgtccatcacagccaca
            acacaggctttggcactgatagaactctataatgcacccgaggggcgatacaagcaggat
            gtgtacttgcttcctaagaaaatggatgaatacgttgccagcttgcatctgccatcattt
            gatgcccaccttacagagctgacagatgaccaagcaaaatatctgggactcaacaaaaat
            gggccattcaaacctaattattacagatactaa
///
BioPerl-1.007002/t/data/ATF14F8.gbk000444000766000024     54051213155576321 16401 0ustar00cjfieldsstaff000000000000LOCUS       ATF14F8     96892 bp    DNA             PLN       07-AUG-2000
DEFINITION  Arabidopsis thaliana DNA chromosome 5, BAC clone F14F8 (ESSA
            project).
ACCESSION   AL391144
VERSION     AL391144.1  GI:9755607
KEYWORDS    .
SOURCE      thale cress.
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Embryophyta; Tracheophyta; Spermatophyta;
            Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II;
            Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 96892)
  AUTHORS   Sato,S., Nakamura,Y., Kaneko,T., Kato,T., Asamizu,E., Kotani,H.,
            Tabata,S., Mewes,H.W., Rudd,S., Lemcke,K. and Mayer,K.F.X.
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 96892)
  AUTHORS   EU Arabidopsis sequencing,project.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-AUG-2000) MIPS, at the Max-Planck-Institut fuer
            Biochemie, Am Klopferspitz 18a, D-82152 Martinsried, FRG, E-mail:
            lemcke@mips.biochem.mpg.de,mayer@mips.biochem.mpg.de
COMMENT     Information on performance of analysis and a more detailed
            annotation of this entry and other sequences of chromosomes 3, 4
            and 5 can be viewed at: http://www.mips.biochem.mpg.de/proj/thal/.
FEATURES             Location/Qualifiers
     source          1..96892
                     /organism="Arabidopsis thaliana"
                     /variety="Columbia"
                     /db_xref="taxon:3702"
                     /chromosome="5"
     exon            626..652
                     /gene="F14F8_10"
                     /number=1
     gene            626..2147
                     /gene="F14F8_10"
     CDS             join(626..652,743..1199,1277..1424,1504..1781,1870..2147)
                     /gene="F14F8_10"
                     /note="strong similarity to putative phytochelatin
                     synthetase - Arabidopsis thaliana, EMBL:AJ006787"
                     /codon_start=1
                     /product="putative phytochelatin synthetase"
                     /protein_id="CAC01762.1"
                     /db_xref="GI:9755608"
                     /translation="MSWTADGYVATVTMNNFQIYRHIQNPGWTLGWTWAKKEVIWSMV
                     GAQTTEQGDCSKFKGNVPHCCKKTPTVVDLLPGVPYNQQFSNCCKGGVIGAWGQDPSA
                     AVSQFQVSAGLAGTTNKTVKLPKNFTLLGPGPGYTCGPAKIVPSTVFLTTDKRRKTQA
                     LMTWNVTCTYSQFLARKHPSCCVSFSSFYNDTITPCPSCACGCENKKSCVKADSKILT
                     KKGLNTPKKDNTPLLQCTHHMCPVRVHWHVKTNYKDYWRVKIAITNFNYRMNHTLWTL
                     AIQHPNLNNVTQVFSFDYKPVSPYGSINDTGMFYGTKFYNDLLMEAGPSGNVQSEVLL
                     QKDQKTFTFKQGWAFPRKVYFNGDECMLPPPDSYPFLPNSAQGNFASFSLTILLLLFI
                     SIW"
     intron          653..742
                     /gene="F14F8_10"
                     /number=1
     exon            743..1199
                     /gene="F14F8_10"
                     /number=2
     intron          1200..1276
                     /gene="F14F8_10"
                     /number=2
     exon            1277..1424
                     /gene="F14F8_10"
                     /number=3
     intron          1425..1503
                     /gene="F14F8_10"
                     /number=3
     exon            1504..1781
                     /gene="F14F8_10"
                     /number=4
     intron          1782..1869
                     /gene="F14F8_10"
                     /number=4
     exon            1870..2147
                     /gene="F14F8_10"
                     /number=5
     gene            3192..5279
                     /gene="F14F8_20"
     CDS             join(3192..3253,3824..4205,4309..4524,4578..4796,
                     4969..5125,5254..5279)
                     /gene="F14F8_20"
                     /note="similarity to Mitochondrial carrier protein - Ribes
                     nigrum, EMBL:AJ007580
                     Contains Mitochondrial energy transfer proteins signature
                     AA284-293"
                     /codon_start=1
                     /product="putative mitochondrial carrier protein"
                     /protein_id="CAC01763.1"
                     /db_xref="GI:9755609"
                     /translation="MDTPPTSRIASFGQTEINWDKLDKRRFYINGAGLFTGVTVALYP
                     VSVVKTRLQVASKEIAERSAFSVVKGILKNDGVPGLYRGFGTVITGAVPARIIFLTAL
                     ETTKISAFKLVAPLELSEPTQAAIANGIAGMTASLFSQAVFVPIDVVSQKLMVQGYSG
                     HATYTGGIDVATKIIKSYGVRGLYRGFGLSVMTYSPSSAAWWASYGSSQRVIWRLAMN
                     VLSFLEFGFATKATIPLIQYLLLLGRFLGYGGDSDATAAPSKSKIVMVQAAGGIIAGA
                     TASSITTPLDTIKTRLQVMGHQENRPSAKQVVKKLLAEDGWKGFYRGLGPRFFSMSAW
                     GTSMILTYEYLKRLCAIED"
     exon            3192..3253
                     /gene="F14F8_20"
                     /number=1
     intron          3254..3823
                     /gene="F14F8_20"
                     /number=1
     exon            3824..4205
                     /gene="F14F8_20"
                     /number=2
     intron          4206..4308
                     /gene="F14F8_20"
                     /number=2
     exon            4309..4524
                     /gene="F14F8_20"
                     /number=3
     intron          4525..4577
                     /gene="F14F8_20"
                     /number=3
     exon            4578..4796
                     /gene="F14F8_20"
                     /number=4
     intron          4797..4968
                     /gene="F14F8_20"
                     /number=4
     exon            4969..5125
                     /gene="F14F8_20"
                     /number=5
     intron          5126..5253
                     /gene="F14F8_20"
                     /number=5
     exon            5254..5279
                     /gene="F14F8_20"
                     /number=6
     gene            7805..9695
                     /gene="F14F8_30"
     CDS             join(7805..8146,8760..9010,9099..9267,9375..9695)
                     /gene="F14F8_30"
                     /codon_start=1
                     /product="reversibly glycosylated polypeptide-3"
                     /protein_id="CAC01764.1"
                     /db_xref="GI:9755610"
                     /translation="MVEPANTVGLPVNPTPLLKDELDIVIPTIRNLDFLEMWRPFLQP
                     YHLIIVQDGDPSKKIHVPEGYDYELYNRNDINRILGPKASCISFKDSACRCFGYMVSK
                     KKYIFTIDDDCFVAKDPSGKAVNALEQHIKNLLCPSSPFFFNTLYDPYREGADFVRGY
                     PFSLREGVSTAVSHGLWLNIPDYDAPTQLVKPKERNTRYVDAVMTIPKGTLFPMCGMN
                     LAFDRDLIGPAMYFGLMGDGQPIGRYDDMWAGWCIKVICDHLSLGVKTGLPYIYHSKA
                     SNPFVNLKKEYKGIFWQEEIIPFFQNAKLSKEAVTVQQCYIELSKMVKEKLSSLDPYF
                     DKLADAMVTWIEAWDELNPPAASGKA"
     exon            7805..8146
                     /gene="F14F8_30"
                     /number=1
     intron          8147..8759
                     /gene="F14F8_30"
                     /number=1
     exon            8760..9010
                     /gene="F14F8_30"
                     /number=2
     intron          9011..9098
                     /gene="F14F8_30"
                     /number=2
     exon            9099..9267
                     /gene="F14F8_30"
                     /number=3
     intron          9268..9374
                     /gene="F14F8_30"
                     /number=3
     exon            9375..9695
                     /gene="F14F8_30"
                     /number=4
     exon            11254..12399
                     /gene="F14F8_40"
                     /number=1
     gene            11254..12643
                     /gene="F14F8_40"
     CDS             join(11254..12399,12473..12643)
                     /gene="F14F8_40"
                     /note="similarity to several hypothetical proteins -
                     Arabidopsis thaliana"
                     /codon_start=1
                     /product="putative protein"
                     /protein_id="CAC01765.1"
                     /db_xref="GI:9755611"
                     /translation="MRRRSKKIKTENNSNPETSEERNKFDEIPHDLVIEILERLPLKS
                     VARFLTVSKLWATTIRSPDFRKSYRGGSSSEPRTLIVSDLNFKEPNPKLHFFRPSISS
                     PSFLSSLTCPFTYPRHEEYYYHHVNGLISVGYGTDQIVINPTTGKFITLPRPKTRRKL
                     VISFFGYDSVSDQYKVLCMTERLRGHPEEASSQHQVYTLGAKQKSWKMINCSIPHRPW
                     SWNAVCINGVVYYIAKTGEGMFRRCLMRFDLKSDNLDLCTILPEEIQTSLHDYFLINY
                     KGKVAIPNQPNFYTYDVWVMNQEGGKIEWLKNITFTIKPRKGFVRYLFVTGTTHTGEF
                     ILAPTSYTDEFYVFHYNPDMNSFRKIRVQAPGVKFSFAQKASVVFSDHSLLRLDNLHI
                     RGSTHTATGEFILAPRFYSDDLNVIHFNPDTNSFRSTKVEVYEDYE"
     intron          12400..12472
                     /gene="F14F8_40"
                     /number=1
     exon            12473..12643
                     /gene="F14F8_40"
                     /number=2
     CDS             join(15197..15443,15612..16009)
                     /gene="F14F8_50"
                     /note="similarity to several hypothetical proteins -
                     Arabidopsis thaliana"
                     /codon_start=1
                     /product="putative protein"
                     /protein_id="CAC01766.1"
                     /db_xref="GI:9755612"
                     /translation="MMRRRNKKTKTVISNPETLEERNKFDEIPHDLVIEILGRLPAKS
                     VARFLTVSKLWATSIRSLDFIKSYPLGSSSKPRTLVASKQVVANPSTGRTIPLPRVKT
                     RRTIATSFFGYDSVSDQYKVLCMTVKAYGDLRDESSQHQVFTLGAKKKSFRMIDTSII
                     PHRPCSNGVCIDSVVYYVAKTGAGMLHLCIMRFDLSSEILDLFTSLPQEIRPPS"
     exon            15197..15443
                     /gene="F14F8_50"
                     /number=1
     gene            15197..16009
                     /gene="F14F8_50"
     intron          15444..15611
                     /gene="F14F8_50"
                     /number=1
     exon            15612..16009
                     /gene="F14F8_50"
                     /number=2
     gene            16790..26395
                     /gene="F14F8_60"
     exon            complement(16790..19855)
                     /gene="F14F8_60"
                     /number=1
     gene            complement(join(16790..19855,20136..20912,21378..21497,
                     21654..21876,22204..22400,22527..23158,23335..23448,
                     23538..23938,24175..24536,24604..24715,24889..24984,
                     25114..25171,25257..25329,25544..25589,25900..26018,
                     26300..26395))
                     /gene="F14F8_60"
     CDS             complement(join(16790..19855,20136..20912,21378..21497,
                     21654..21876,22204..22400,22527..23158,23335..23448,
                     23538..23938,24175..24536,24604..24715,24889..24984,
                     25114..25171,25257..25329,25544..25589,25900..26018,
                     26300..26395))
                     /gene="F14F8_60"
                     /note="Contains Prokaryotic membrane lipoprotein lipid
                     attachment site AA801-811"
                     /codon_start=1
                     /product="hypothetical protein"
                     /protein_id="CAC01767.1"
                     /db_xref="GI:9755613"
                     /translation="MKSGSAAKLIVEALLQRFLPLARRRIETAQAQDGQYLRPSDPAY
                     EQVLDSLAMIARHTPVPLLEALLRWRESESPKGANDASTFQRKLAVECIFCSACIRFV
                     ECCPQEGLTEKLWSGLENFVFDWLINADRVVSQVEYPSLVDLRGLLLDLVAQLLGALS
                     RISSVTERFFMELNTRRIDTSVARSETLSIINGMRYLKLGVKSEGGLNASASFVAKAN
                     PLIRDIHKRKSELYHALCNMLSNILAPLSDGGKSQWPPSVAEPALTLWYEAVGRIRVQ
                     LIQWMEKQSKHLGVRQSDLVSLLYAYLVITVLNMYNWMNRLAIRFLFLVIIENFAPYM
                     QDKNHRYMALDCLHRVLRFYLSVYASSQPPNRIWDYLDSVTSQLLTVLRKGMLTQDVQ
                     QDKLVEFCVTIAEHNLDFAMNHMLLELLKQDSPSEAKIIGLRALLALVMSPSSQYVGL
                     EIFKGHGIGHYIPKVKAAIESILRSCHRTYSQALLTSSRTTIDAVNKEKSQGSLFQSV
                     LKCIPYLIEEVGRSDKITEIIPQHGISIDPGVRVEAVQVLNRIVRYLPHRRFAVMRGM
                     ANFILKLPDEFPLLIQASLGRLLELMRFWRACLVDDRQDTDAEEENKTAKGNDRFKKL
                     SFHQAADAIEFRASDIDAVGLIFLSSVDSQIRHTALELLRCVRALRNDIRDLMIQEHP
                     DHVMKFEAEPIYMIDVLEEHGDDIVQSCYWDSARPFDLRRDSDAIPSDVTLQSIIFES
                     LDKNKWGRCLSELVKYAAELCPRSVQEAKSEIMHRLAHITPVEFGGKANQSQDTDNKL
                     DQWLLYAMFVCSCPPDGKDAGSIASTRDMYHLIFPYLRFGSETHNHAATMALGRSHLE
                     ACEIMFSELASFMEEISSETETKPKWKIQKGGRREDLRVHVSNIYRTVSENVWPGMLA
                     RKPVFRLHYLRFIEDSTRQISLAPHESFQDMQPLRYALASVLRFLAPEFVESKSEKFD
                     VRSRKRLFDLLLSWSDDTGNTWGQDGVSDYRREVERYKTSQHNRSKDSVDKISFDKEL
                     NEQIEAIQWASLNAMASLLYGPCFDDNARKMSGRVISWINSLFIEPAPRVPFGYSPAD
                     PRTPSYSKYTGEGGRGTTGRDRHRGGHQRVALAKLALKNLLLTNLDLFPACIDQCYYS
                     DAAIADGYFSVLAEVYMRQEIPKCEIQRLLSLILYKVVDPSRQIRDDALQMLETLSMR
                     EWAEDGIEGSGGYRAAVVGNLPDSYQQFQYKLSCKLAKDHPELSQLLCEEIMQRQLDA
                     VDIIAQHQVLTCMAPWIENLNFWKLKDSGWSERLLKSLYYVTWRHGDQFPDEIEKLWS
                     TIASKPRNISPVLDFLITKGIEDCDSNASAEITGAFATYFSVAKRVSLYLARICPQRT
                     IDHLVYQLSQRMLEDSIEPIGYSANRGDSNGNFVLEFSQGPATAPQVVSVADSQPHMS
                     PLLVRGSLDGPLRNTSGSLSWRTAGMTGRSASGPLSPMPPELNIVPVATGRSGQLLPS
                     LVNASGPLMGVRSSTGSLRSRHVSRDSGDYLIDTPNSGEDVLHSGIAMHGVNAKELQS
                     ALQGHQQHSLTHADIALILLAEIAYENDEDFREHLPLLFHVTFVSMDSSEDIVLEHCQ
                     HLLVNLLYSLAGRHLELYEVENSDGENKQQVVSLIKYVQSKRGSMMWENEDPTVVRTD
                     LPSAALLSALVQSMVDAIFFQGDLRETWGTEALKWAMECTSRHLACRSHQIYRALRPS
                     VTSDACVSLLRCLHRCLSNPIPPVLGFIMEILLTLQVMVENMEPEKVILYPQLFWGCV
                     AMMHTDFVHVYCQVLELFSRIIDRLSFRDKTTENVLLSSMPRDEFNTNDLGEFQRSES
                     RGYEMPPSSGTLPKFEGVQPLVLKGLMSTVSHEFSIEVLSRITVPSCDSIFGDAETRL
                     LMHITGLLPWLCLQLTQDQVMVSALPLQQQYQKACSVASNIAVWCRAKSLDELATVFV
                     AYARGEIKRVENLLACVSPLLCNKWFPKHSALAFGHLLRLLKKGPVDYQRVILLMLKA
                     LLQHTPMDASQSPHMYTIVSQLVESTLCWEALSVLEALLQSCSPVQGGTGGSHPQDSS
                     YSENGTDEKTLVPQTSFKARSGPLQYAMMAATMSQPFPLGAAAAESGIPPRDVALQNT
                     RLMLGRVLDNCALGRRDYRRLVPFVTTIANM"
     intron          complement(19856..20135)
                     /gene="F14F8_60"
                     /number=1
     exon            complement(20136..20912)
                     /gene="F14F8_60"
                     /number=2
     intron          complement(20913..21377)
                     /gene="F14F8_60"
                     /number=2
     exon            complement(21378..21497)
                     /gene="F14F8_60"
                     /number=3
     intron          complement(21498..21653)
                     /gene="F14F8_60"
                     /number=3
     exon            complement(21654..21876)
                     /gene="F14F8_60"
                     /number=4
     intron          complement(21877..22203)
                     /gene="F14F8_60"
                     /number=4
     exon            complement(22204..22400)
                     /gene="F14F8_60"
                     /number=5
     intron          complement(22401..22526)
                     /gene="F14F8_60"
                     /number=5
     exon            complement(22527..23158)
                     /gene="F14F8_60"
                     /number=6
     intron          complement(23159..23334)
                     /gene="F14F8_60"
                     /number=6
     exon            complement(23335..23448)
                     /gene="F14F8_60"
                     /number=7
     intron          complement(23449..23537)
                     /gene="F14F8_60"
                     /number=7
     exon            complement(23538..23938)
                     /gene="F14F8_60"
                     /number=8
     intron          complement(23939..24174)
                     /gene="F14F8_60"
                     /number=8
     exon            complement(24175..24536)
                     /gene="F14F8_60"
                     /number=9
     intron          complement(24537..24603)
                     /gene="F14F8_60"
                     /number=9
     exon            complement(24604..24715)
                     /gene="F14F8_60"
                     /number=10
     intron          complement(24716..24888)
                     /gene="F14F8_60"
                     /number=10
     exon            complement(24889..24984)
                     /gene="F14F8_60"
                     /number=11
     intron          complement(24985..25113)
                     /gene="F14F8_60"
                     /number=11
     exon            complement(25114..25171)
                     /gene="F14F8_60"
                     /number=12
     intron          complement(25172..25256)
                     /gene="F14F8_60"
                     /number=12
     exon            complement(25257..25329)
                     /gene="F14F8_60"
                     /number=13
     intron          complement(25330..25543)
                     /gene="F14F8_60"
                     /number=13
     exon            complement(25544..25589)
                     /gene="F14F8_60"
                     /number=14
     intron          complement(25590..25899)
                     /gene="F14F8_60"
                     /number=14
     exon            complement(25900..26018)
                     /gene="F14F8_60"
                     /number=15
     intron          complement(26019..26299)
                     /gene="F14F8_60"
                     /number=15
     exon            complement(26300..26395)
                     /gene="F14F8_60"
                     /number=16
     misc_feature    27422..29058
                     /note="putative Mutator like transposase"
     gene            complement(join(29425..29769,29840..30004))
                     /gene="F14F8_70"
     exon            complement(29425..29769)
                     /gene="F14F8_70"
                     /number=1
     gene            29425..30004
                     /gene="F14F8_70"
     CDS             complement(join(29425..29769,29840..30004))
                     /gene="F14F8_70"
                     /note="similarity to hypothetical protein AT4g04780 -
                     Arabidopsis thaliana, EMBL:AL161501"
                     /codon_start=1
                     /product="putative protein"
                     /protein_id="CAC01768.1"
                     /db_xref="GI:9755614"
                     /translation="MSTNSYYSSASSSGFRVCPPGVPSKCWCGEEIITFTSKTKENPY
                     RRFYRCAIAMKRENEEHLFKWVDEALLDEIKMVNEKCKRVAENISDLRMNVMVNMELL
                     NKNAKQMEEELIKKMEGELLTMKENVEELGRTCHGKVSFEDCRGCCCDCCIYCMALGK
                     SVGVVEVLE"
     intron          complement(29770..29839)
                     /gene="F14F8_70"
                     /number=1
     exon            complement(29840..30004)
                     /gene="F14F8_70"
                     /number=2
     exon            complement(31395..31505)
                     /gene="F14F8_80"
                     /number=1
     gene            complement(join(31395..31505,31597..31700,31806..31920,
                     32027..32074,32167..32256,32333..32407,32602..32754,
                     33036..33120,33210..33280,33373..33423,33563..33979,
                     34057..34188,34338..34451,34537..34654,34956..35014,
                     35276..35342,35433..35563,35663..35872,36327..37211))
                     /gene="F14F8_80"
     gene            31395..37211
                     /gene="F14F8_80"
     CDS             complement(join(31395..31505,31597..31700,31806..31920,
                     32027..32074,32167..32256,32333..32407,32602..32754,
                     33036..33120,33210..33280,33373..33423,33563..33979,
                     34057..34188,34338..34451,34537..34654,34956..35014,
                     35276..35342,35433..35563,35663..35872,36327..37211))
                     /gene="F14F8_80"
                     /note="Contains Prokaryotic membrane lipoprotein lipid
                     attachment site AA922-932;Bacteriophage-type RNA
                     polymerase family active site signatures
                     AA708-719;Bacteriophage-type RNA polymerase family active
                     site signatures AA781-795"
                     /codon_start=1
                     /product="DNA-directed RNA polymerase (mitochondrial)"
                     /protein_id="CAC01769.1"
                     /db_xref="GI:9755615"
                     /translation="MSSAQTPLFLANQTKVFDHLIPLHKPFISSPNPVSQSFPMWRNI
                     AKQAISRSAARLNVSSQTRGLLVSSPESIFSKNLSFRFPVLGSPCHGKGFRCLSGITR
                     REEFSKSERCLSGTLARGYTSVAEEEVLSTDVEEEPEVDELLKEMKKEKKRESHRSWR
                     MKKQDQFGMGRTKFQNLWRRQVKIETEEWERAAAEYMELLTDMCEQKLAPNLPYVKSL
                     FLGWFEPLRDAIAKDQELYRLGKSKATYAHYLDQLPADKISVITMHKLMGHLMTGGDN
                     GCVKVVHAACTVGDAIEQEIRICTFLDKKKKGDDNEESGGVENETSMKEQDKLRKKVN
                     ELIKKQKLSAVRKILQSHDYTKPWIADVRAKVGSRLIELLVRTAYIQSPADQQDNDLP
                     DVRPAFVHTFKVAKGSMNSGRKYGVIECDPLVRKGLEKSGRYAVMPYMPMLVPPLKWS
                     GYDKGAYLFLTSYIMKTHGAKQQREALKSAPKGQLQPVFEALDTLGSTKWRVNKRVLT
                     VVDRIWSSGGCVADMVDRSDVPLPEKPDTEDEGILKKWKWEVKSAKKVNSERHSQRCD
                     TELKLSVARKMKDEEAFYYPHNMDFRGRAYPMPPHLNHLGSDLCRGVLEFAEGRPMGI
                     SGLRWLKIHLANLYAGGVDKLSLDGRLAFTENHLDDIFDSADRPLEGSRWWLQAEDPF
                     QCLAVCISLTEALRSPSPETVLSHIPIHQDGSCNGLQHYAALGRDTLGAEAVNLVAGE
                     KPADVYSGIATRVLDIMRRDADRDPEVFPEALRARKLLNQVDRKLVKQTVMTSVYGVT
                     YIGARDQIKRRLKERSDFGDEKEVFGAACYAAKVTLAAIDEMFQAARAIMRWFGECAK
                     IIASENETVRWTTPLGLPVVQPYHQMGTKLVKTSLQTLSLQHETDQVIVRRQRTAFPP
                     NFIHSLDGSHMMMTAVACKRAGVCFAGVHDSFWTHACDVDKLNIILREKFVELYSQPI
                     LENLLESFEQSFPHLDFPPLPERGDLDLKVVLDSPYFFN"
     intron          complement(31506..31596)
                     /gene="F14F8_80"
                     /number=1
     exon            complement(31597..31700)
                     /gene="F14F8_80"
                     /number=2
     intron          complement(31701..31805)
                     /gene="F14F8_80"
                     /number=2
     exon            complement(31806..31920)
                     /gene="F14F8_80"
                     /number=3
     intron          complement(31921..32026)
                     /gene="F14F8_80"
                     /number=3
     exon            complement(32027..32074)
                     /gene="F14F8_80"
                     /number=4
     intron          complement(32075..32166)
                     /gene="F14F8_80"
                     /number=4
     exon            complement(32167..32256)
                     /gene="F14F8_80"
                     /number=5
     intron          complement(32257..32332)
                     /gene="F14F8_80"
                     /number=5
     exon            complement(32333..32407)
                     /gene="F14F8_80"
                     /number=6
     intron          complement(32408..32601)
                     /gene="F14F8_80"
                     /number=6
     exon            complement(32602..32754)
                     /gene="F14F8_80"
                     /number=7
     intron          complement(32755..33035)
                     /gene="F14F8_80"
                     /number=7
     exon            complement(33036..33120)
                     /gene="F14F8_80"
                     /number=8
     intron          complement(33121..33209)
                     /gene="F14F8_80"
                     /number=8
     exon            complement(33210..33280)
                     /gene="F14F8_80"
                     /number=9
     intron          complement(33281..33372)
                     /gene="F14F8_80"
                     /number=9
     exon            complement(33373..33423)
                     /gene="F14F8_80"
                     /number=10
     intron          complement(33424..33562)
                     /gene="F14F8_80"
                     /number=10
     exon            complement(33563..33979)
                     /gene="F14F8_80"
                     /number=11
     intron          complement(33980..34056)
                     /gene="F14F8_80"
                     /number=11
     exon            complement(34057..34188)
                     /gene="F14F8_80"
                     /number=12
     intron          complement(34189..34337)
                     /gene="F14F8_80"
                     /number=12
     exon            complement(34338..34451)
                     /gene="F14F8_80"
                     /number=13
     intron          complement(34452..34536)
                     /gene="F14F8_80"
                     /number=13
     exon            complement(34537..34654)
                     /gene="F14F8_80"
                     /number=14
     intron          complement(34655..34955)
                     /gene="F14F8_80"
                     /number=14
     exon            complement(34956..35014)
                     /gene="F14F8_80"
                     /number=15
     intron          complement(35015..35275)
                     /gene="F14F8_80"
                     /number=15
     exon            complement(35276..35342)
                     /gene="F14F8_80"
                     /number=16
     intron          complement(35343..35432)
                     /gene="F14F8_80"
                     /number=16
     exon            complement(35433..35563)
                     /gene="F14F8_80"
                     /number=17
     intron          complement(35564..35662)
                     /gene="F14F8_80"
                     /number=17
     exon            complement(35663..35872)
                     /gene="F14F8_80"
                     /number=18
     intron          complement(35873..36326)
                     /gene="F14F8_80"
                     /number=18
     exon            complement(36327..37211)
                     /gene="F14F8_80"
                     /number=19
     exon            38393..39739
                     /gene="F14F8_90"
                     /number=1
     gene            38393..39739
                     /gene="F14F8_90"
     CDS             38393..39739
                     /gene="F14F8_90"
                     /note="similarity to unusual floral organs protein UFO -
                     Arabidopsis thaliana, PIR:S57710
                     Contains Prokaryotic membrane lipoprotein lipid attachment
                     site AA422-432"
                     /codon_start=1
                     /product="putative protein"
                     /protein_id="CAC01770.1"
                     /db_xref="GI:9755616"
                     /translation="MERLGFWGLLMGSVEKSLDSGNSLACSASAKNGDEESSTSSKQV
                     SPLKGSGSRNTSPLGRVGSRNTSPSRQKVVKTKPRGLEEETVASFGKQVVADVQMEDG
                     IWAMLPEDLLNEILARVPPFMIFRIRSVCKKWNLILQDNSFLKFHSNVSSHGPCLLTF
                     WKNSPQIPQCSVFSLPLKTWYKIPFTFLPPWAFWLVGSSGGLVCFSGLDGLTFRTLVC
                     NPLMQSWRTLPSMHYNQQRQLIMVVDRSDKSFKVIATSDIYGDKSLPTEVYDSKTDKW
                     SLHQIMPAVNLCSSKMAYCDSRLYLETLSPLGLMMYRLDSGQWEHIPAKFPRSLLDGY
                     LVAGTQKRLFLVGRIGLYSTLQSMRIWELDHTKVSWVEISRMPPKYFRALLRLSAERF
                     ECFGQDNLICFTSWNQGKGLLYNVDKKIWSWISGCALQSCNSQVCFYEPRFDASVL"
     gene            complement(join(40286..40506,40590..40848,40971..41219,
                     41307..41440,41520..41757))
                     /gene="F14F8_100"
     gene            40286..41757
                     /gene="F14F8_100"
     CDS             complement(join(40286..40506,40590..40848,40971..41219,
                     41307..41440,41520..41757))
                     /gene="F14F8_100"
                     /note="similarity to RXF26 - Arabidopsis thaliana,
                     EMBL:AB008020
                     Contains Protein splicing signature AA340-347"
                     /codon_start=1
                     /product="putative protein"
                     /protein_id="CAC01771.1"
                     /db_xref="GI:9755617"
                     /translation="MKSLLICLVLLELVWLGNGQSRDHQPLAPAFFVFGDSLVDSGNN
                     NYIPTLARANYFPYGIDFGFPTGRFCNGRTVVDYGATYLGLPLVPPYLSPLSIGQNAL
                     RGVNYASAAAGILDETGRHYVRGARTTFNGQISQFEITIELRLRRFFQNPADLRKYLA
                     KSIIGINIGSNDYINNYLMPERYSTSQTYSGEDYADLLIKTLSAQISRLYNLGARKMV
                     LAGSGPLGCIPSQLSMVTGNNTSGCVTKINNMVSMFNSRLKDLANTLNTTLPGSFFVY
                     QNVFDLFHDMVVNPSRYGLVVSNEACCGNGRYGGALTCLPLQQPCLDRNQYVFWDAFH
                     PTETANKIIAHNTFSKSANYSYPISVYELAKL"
     exon            complement(40286..40506)
                     /gene="F14F8_100"
                     /number=1
     intron          complement(40507..40589)
                     /gene="F14F8_100"
                     /number=1
     exon            complement(40590..40848)
                     /gene="F14F8_100"
                     /number=2
     intron          complement(40849..40970)
                     /gene="F14F8_100"
                     /number=2
     exon            complement(40971..41219)
                     /gene="F14F8_100"
                     /number=3
     intron          complement(41220..41306)
                     /gene="F14F8_100"
                     /number=3
     exon            complement(41307..41440)
                     /gene="F14F8_100"
                     /number=4
     intron          complement(41441..41519)
                     /gene="F14F8_100"
                     /number=4
     exon            complement(41520..41757)
                     /gene="F14F8_100"
                     /number=5
     gene            46886..48648
                     /gene="F14F8_110"
     CDS             join(46886..47205,47285..47438,47517..47646,47727..47884,
                     47974..48177,48304..48648)
                     /gene="F14F8_110"
                     /note="strong similarity to serine/threonine-specific
                     protein kinase NPK15 - Nicotiana tabacum
                     Contains Protein kinases signatures and profile AA235-247"
                     /codon_start=1
                     /product="serine/threonine-specific protein kinase-like
                     protein"
                     /protein_id="CAC01772.1"
                     /db_xref="GI:9755618"
                     /translation="MVNRSDLVVIGISVGLALGLLLALLLFFAIKWYYGRSHLRRCAN
                     EQNSPTLPVHTAKRGVVIPDDRANTESSQPPENGAPTQHQPWWNNHTKDLTVSASGIP
                     RYNYKDIQKATQNFTTVLGQGSFGPVYKAVMPNGELAAAKVHGSNSSQGDREFQTEVS
                     LLGRLHHRNLVNLTGYCVDKSHRMLIYEFMSNGSLENLLYGGEGMQVLNWEERLQIAL
                     DISHGIEYLHEGAVPPVIHRDLKSANILLDHSMRAKVADFGLSKEMVLDRMTSGLKGT
                     HGYMDPTYISTNKYTMKSDIYSFGVIILELITAIHPQQNLMEYINLASMSPDGIDEIL
                     DQKLVGNASIEEVRLLAKIANRCVHKTPRKRPSIGEVTQFILKIKQSRSRGRRQDTMS
                     SSFGVGYEEDLSRVMSRIKDQHVELGLLAGVKEENHQERNIATT"
     exon            46886..47205
                     /gene="F14F8_110"
                     /number=1
     intron          47206..47284
                     /gene="F14F8_110"
                     /number=1
     exon            47285..47438
                     /gene="F14F8_110"
                     /number=2
     intron          47439..47516
                     /gene="F14F8_110"
                     /number=2
     exon            47517..47646
                     /gene="F14F8_110"
                     /number=3
     intron          47647..47726
                     /gene="F14F8_110"
                     /number=3
     exon            47727..47884
                     /gene="F14F8_110"
                     /number=4
     intron          47885..47973
                     /gene="F14F8_110"
                     /number=4
     exon            47974..48177
                     /gene="F14F8_110"
                     /number=5
     intron          48178..48303
                     /gene="F14F8_110"
                     /number=5
     exon            48304..48648
                     /gene="F14F8_110"
                     /number=6
     exon            complement(50390..50636)
                     /gene="F14F8_120"
                     /number=1
     gene            complement(join(50390..50636,50709..50866,50944..51148,
                     51230..51519,51628..51793,51886..51974,52074..52141,
                     52255..52549))
                     /gene="F14F8_120"
     gene            50390..52549
                     /gene="F14F8_120"
     CDS             complement(join(50390..50636,50709..50866,50944..51148,
                     51230..51519,51628..51793,51886..51974,52074..52141,
                     52255..52549))
                     /gene="F14F8_120"
                     /note="similarity to auxin-independent growth promoter -
                     Nicotiana tabacum, PIR:A44226
                     Contains Prokaryotic membrane lipoprotein lipid attachment
                     site AA101-111"
                     /codon_start=1
                     /product="putative protein"
                     /protein_id="CAC01773.1"
                     /db_xref="GI:9755619"
                     /translation="MEKFLYHRKLWEMNVKLLGESKVEKLKNSFVSRPRMSLWMIRAV
                     TVLLLWSCFVHLMALGEMWGPRLFKGWPSCFNHHQLSTAAEMTSLPTKIALPPKRVYV
                     NNGYLMVSCNGGLNQMRAAICDMVTVARYMNVTLIVPELDKTSFWNDPSEFKDIFDVD
                     HFISSLRDEVRILKELPPRLKKRVELGVYHEMPPISWSNMSYYQNQILPLVKKHKVLH
                     LNRTDTRLANNGLPVEVQKLRCRVNFNGLKFTPQIEELGRRVVKILREKGPFLVLHLR
                     YEMDMLAFSGCSHGCNPEEEEELTRMRYAYPWWKEKVINSELKRKDGLCPLTPEETAL
                     TLTALGIDRNVQIYIAAGEIYGGQRRMKALTDAFPNVVRKETLLESSDLDFCRNHSSQ
                     MAALDYLVALESDIFVPTNDGNMARVVEGHRRFLGFKKTIQLNRRFLVKLIDEYTEGL
                     LSWDVFSSTVKAFHSTRMGSPKRRLVIPNRPKEEDYFYANPQECLQLLDEPLRVI"
     intron          complement(50637..50708)
                     /gene="F14F8_120"
                     /number=1
     exon            complement(50709..50866)
                     /gene="F14F8_120"
                     /number=2
     intron          complement(50867..50943)
                     /gene="F14F8_120"
                     /number=2
     exon            complement(50944..51148)
                     /gene="F14F8_120"
                     /number=3
     intron          complement(51149..51229)
                     /gene="F14F8_120"
                     /number=3
     exon            complement(51230..51519)
                     /gene="F14F8_120"
                     /number=4
     intron          complement(51520..51627)
                     /gene="F14F8_120"
                     /number=4
     exon            complement(51628..51793)
                     /gene="F14F8_120"
                     /number=5
     intron          complement(51794..51885)
                     /gene="F14F8_120"
                     /number=5
     exon            complement(51886..51974)
                     /gene="F14F8_120"
                     /number=6
     intron          complement(51975..52073)
                     /gene="F14F8_120"
                     /number=6
     exon            complement(52074..52141)
                     /gene="F14F8_120"
                     /number=7
     intron          complement(52142..52254)
                     /gene="F14F8_120"
                     /number=7
     exon            complement(52255..52549)
                     /gene="F14F8_120"
                     /number=8
     exon            57051..57238
                     /gene="F14F8_130"
                     /number=1
     gene            57051..58303
                     /gene="F14F8_130"
     CDS             join(57051..57238,57324..57413,57893..57967,58072..58303)
                     /gene="F14F8_130"
                     /note="strong similarity to 40S RIBOSOMAL PROTEINs -
                     different species"
                     /codon_start=1
                     /product="ribosomal protein-like"
                     /protein_id="CAC01774.1"
                     /db_xref="GI:9755620"
                     /translation="MRKLKYHEKKLIKKVNFLEWKREGNHRENEITYRYHMGSRDDYK
                     KLVPLFALKALFYLFFFFWMVQKLTNIMKQMDPADPFRIQMTDMLLEKLYNMGVIPTR
                     KSLTLTERLSVSSFCRRRLSTVLVHLKFAEHHKEAVTYIEQGHVRVGPETITDPAFLV
                     TRNMEDFITWVDSSKIKRKVLEYNDTLDDYDMLA"
     intron          57239..57323
                     /gene="F14F8_130"
                     /number=1
     exon            57324..57413
                     /gene="F14F8_130"
                     /number=2
     intron          57414..57892
                     /gene="F14F8_130"
                     /number=2
     exon            57893..57967
                     /gene="F14F8_130"
                     /number=3
     intron          57968..58071
                     /gene="F14F8_130"
                     /number=3
     exon            58072..58303
                     /gene="F14F8_130"
                     /number=4
     exon            58702..58968
                     /gene="F14F8_140"
                     /number=1
     gene            58702..59507
                     /gene="F14F8_140"
     CDS             join(58702..58968,59223..59507)
                     /gene="F14F8_140"
                     /note="strong similarity to plastid-specific ribosomal
                     protein 3 precursor - Spinacia oleracea, EMBL:AF239218"
                     /codon_start=1
                     /product="ribosomal protein 3 precursor-like protein"
                     /protein_id="CAC01775.1"
                     /db_xref="GI:9755621"
                     /translation="MAVQANQSASFGFRTASPSQKLSSKPIAHISLSTKLKPSSRPSL
                     SCSTWNQGQIPARHSCINPGIFAYPPSNLTFSHELPESESPPLGKKKMRVLVKPLEKP
                     KVVLKFVWMQKDIGVALDHMIPGFGTIPLSPYYFWPRKDAWEELKTLLESKPWISELH
                     RVFLLNQATDIINLWQSSGGDLS"
     intron          58969..59222
                     /gene="F14F8_140"
                     /number=1
     exon            59223..59507
                     /gene="F14F8_140"
                     /number=2
     exon            complement(59695..60144)
                     /gene="F14F8_150"
                     /number=1
     gene            complement(59695..60144)
                     /gene="F14F8_150"
     gene            59695..60144
                     /gene="F14F8_150"
     CDS             complement(59695..60144)
                     /gene="F14F8_150"
                     /note="similarity to Glucosamine-6-phosphate
                     acetyltransferase EMeg32 protein - Mus musculus,
                     EMBL:AJ001006"
                     /codon_start=1
                     /product="acetyltransferase-like protein"
                     /protein_id="CAC01776.1"
                     /db_xref="GI:9755622"
                     /translation="MAETFKIRKLEISDKRKGFIELLGQLTVTGSVTDEEFDRRFEEI
                     RSYGDDHVICVIEEETSGKIAATGSVMIEKKFLRNCGKAGHIEDVVVDSRFRGKQLGK
                     KVVEFLMDHCKSMGCYKVILDCSVENKVFYEKCGMSNKSIQMSKYFD"
     exon            complement(60500..61509)
                     /gene="F14F8_160"
                     /number=1
     gene            complement(join(60500..61509,61704..61899))
                     /gene="F14F8_160"
     gene            60500..61899
                     /gene="F14F8_160"
     CDS             complement(join(60500..61509,61704..61899))
                     /gene="F14F8_160"
                     /note="similarity to other proline-rich proteins"
                     /codon_start=1
                     /product="proline-rich protein"
                     /protein_id="CAC01777.1"
                     /db_xref="GI:9755623"
                     /translation="MERITTLWFWFSLMIFLGISINGGLSQGQQHVMKKTRSSAVVVG
                     TVYCDTCFNGAFSKSPNHLISGALVAVECIDENSKPSFRQEVKTDKRGEFKVKLPFSV
                     SKHVKKIKRCSVKLLSSSQPYCSIASSATSSSLKRLKSNHHGENTRVFSAGFFTFRPE
                     NQPEICSQKPINLRGSKPLLPDPSFPPPLQDPPNPSPLPNLPIVPPLPNLPVPKLPVP
                     DLPLPLVPPLLPPGPQKSASLHNKKSDSLKDKKTEALKPNFFFPPNPLNPPSIIPPNP
                     LIPSIPTPTLPPNPLIPSPPSLPPIPLIPTPPTLPTIPLLPTPPTPTLPPIPTIPTLP
                     PLPVLPPVPIVNPPSLPPPPPSFPVPLPPVPGLPGIPPVPLIPGIPPAPLIPGIPPLS
                     PSFSSHHQP"
     intron          complement(61510..61703)
                     /gene="F14F8_160"
                     /number=1
     exon            complement(61704..61899)
                     /gene="F14F8_160"
                     /number=2
     gene            65402..66566
                     /gene="F14F8_170"
     exon            65402..65521
                     /gene="F14F8_170"
                     /number=1
     CDS             join(65402..65521,65615..66056,66144..66253,66540..66566)
                     /gene="F14F8_170"
                     /note="similarity to RING-H2 finger protein RHB1a -
                     Arabidopsis thaliana, EMBL:AF079179"
                     /codon_start=1
                     /product="putative protein"
                     /protein_id="CAC01778.1"
                     /db_xref="GI:9755624"
                     /translation="MGCVSSCFGVDDFEDYPNPSSSVNRSCPCPRCLVNNFLNLYISL
                     FRRGETRSLPSSLQATNVSIATSTSYDNFMSNTFHSTPRPLPYDADPRYFRSRRDSLV
                     SRRDKGSSHSHEEAEPLRSDADVDSESFSVEGSKWANKLIISGEDSKEEFSRSSRRIL
                     QSRTMSTSNEGLYITSDDEDVCPTCLEEYISENPKIVTKCSHHFHLSCIYEWMERSEN
                     CPVCGKVMEFHETP"
     intron          65522..65614
                     /gene="F14F8_170"
                     /number=1
     exon            65615..66056
                     /gene="F14F8_170"
                     /number=2
     intron          66057..66143
                     /gene="F14F8_170"
                     /number=2
     exon            66144..66253
                     /gene="F14F8_170"
                     /number=3
     intron          66254..66539
                     /gene="F14F8_170"
                     /number=3
     exon            66540..66566
                     /gene="F14F8_170"
                     /number=4
     exon            complement(67196..67322)
                     /gene="F14F8_180"
                     /number=1
     gene            complement(join(67196..67322,67451..67599,67737..67820,
                     67911..68010,68100..68161,68252..68333,69185..69369))
                     /gene="F14F8_180"
     gene            67196..69369
                     /gene="F14F8_180"
     CDS             complement(join(67196..67322,67451..67599,67737..67820,
                     67911..68010,68100..68161,68252..68333,69185..69369))
                     /gene="F14F8_180"
                     /note="sequence differences to mRNA EMBL:M55551
                     Contains MADS-box domain signature and profile AA3-57"
                     /codon_start=1
                     /product="MADS box protein AGL2"
                     /protein_id="CAC01779.1"
                     /db_xref="GI:9755625"
                     /translation="MGRGRVELKRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVA
                     LIIFSNRGKLYEFCSSSNMLKTLDRYQKCSYGSIEVNNKPAKELENSYREYLKLKGRY
                     ENLQRQQRNLLGEDLGPLNSKELEQLERQLDGSLKQVRSIKTQYMLDQLSDLQNKEQM
                     LLETNRALAMKLDDMIGVRSHHMGGGGGWEGGEQNVTYAHHQAQSQGLYQPLECNPTL
                     QMGCCFGDDDDDDRYDNPVCSEQITATTQAQAQQGNGYIPGWML"
     intron          complement(67323..67450)
                     /gene="F14F8_180"
                     /number=1
     exon            complement(67451..67599)
                     /gene="F14F8_180"
                     /number=2
     intron          complement(67600..67736)
                     /gene="F14F8_180"
                     /number=2
     exon            complement(67737..67820)
                     /gene="F14F8_180"
                     /number=3
     intron          complement(67821..67910)
                     /gene="F14F8_180"
                     /number=3
     exon            complement(67911..68010)
                     /gene="F14F8_180"
                     /number=4
     intron          complement(68011..68099)
                     /gene="F14F8_180"
                     /number=4
     exon            complement(68100..68161)
                     /gene="F14F8_180"
                     /number=5
     intron          complement(68162..68251)
                     /gene="F14F8_180"
                     /number=5
     exon            complement(68252..68333)
                     /gene="F14F8_180"
                     /number=6
     intron          complement(68334..69184)
                     /gene="F14F8_180"
                     /number=6
     exon            complement(69185..69369)
                     /gene="F14F8_180"
                     /number=7
     tRNA            73241..73314
                     /note="tRNA predicted as a tRNA- Ile : anticodon aat"
                     /product="tRNA-Ile"
     exon            73400..73789
                     /gene="F14F8_190"
                     /number=1
     gene            73400..76723
                     /gene="F14F8_190"
     CDS             join(73400..73789,74082..74363,74478..74565,74673..74794,
                     74868..75007,75092..75164,75307..75395,75470..75575,
                     75662..75853,75961..76155,76247..76324,76424..76723)
                     /gene="F14F8_190"
                     /note="strong similarity to several N2, N2-dimethylguanine
                     tRNA methyltransferases"
                     /codon_start=1
                     /product="N2, N2-dimethylguanine tRNA
                     methyltransferase-like protein"
                     /protein_id="CAC01780.1"
                     /db_xref="GI:9755626"
                     /translation="MNFSKRFVGFKQLSILRYSLPNPYGLFRVSPLCLSETATKLEAI
                     GFIQASLKPVAKFRHLYSHIYRFKLCDLPFGFQIRVGNSISESSAPKEKNLRSAMETD
                     LNDYTVIKEGEAEVLMHKKNQVFFNKAQVNNRDMSIAVLRAFIIKRKQEHEAMLSKRA
                     RSSGKVVEKDVSETSKEETPTENGDDNGKTNGEHEVTTQDGPKEAAKTAYESARRELK
                     PPRVLEALSASGLRALRYAREVEGIGQVVALDNDPASVEACQRNIKFNGLMSTSKVES
                     HLTDARVHMLSHPKDFDVVDLDPYGAPSIFLDSAVQSVADGGLLMCTATDMAVLCGAN
                     GEVCYSKYGSYPLKGKYCHEMALRILLASIESHANRYKRYIVPVLSVQMDFYVRVFVR
                     VYTSASAMKNTPLKLSYVYQCIGCDSFHLQSVGRSLPKNNSVRYLPGVGPVVPQDCTH
                     CGKKYNMGGPIWSAPIHDQEWVNSILNGVKSMKDRYPAYDRICAELPDVPLFLSLHSL
                     SATLKCTSPSAALFRSAVINAKYRVSGSHVNPLGIKTDAPMEIIWDIMRCWVKNHPIK
                     PQSPEHPGSVILSKEPSHQADFSRHVGSLSKAQAKKVARFLPNPEKHWGPKIRAGRTI
                     TSKHVSLLGHEAVNGHLNNNHKEAGDEEEEEEEEEPEEDIIEGEPELKRQKTTEDFAS
                     TS"
     intron          73790..74081
                     /gene="F14F8_190"
                     /number=1
     exon            74082..74363
                     /gene="F14F8_190"
                     /number=2
     intron          74364..74477
                     /gene="F14F8_190"
                     /number=2
     exon            74478..74565
                     /gene="F14F8_190"
                     /number=3
     intron          74566..74672
                     /gene="F14F8_190"
                     /number=3
     exon            74673..74794
                     /gene="F14F8_190"
                     /number=4
     intron          74795..74867
                     /gene="F14F8_190"
                     /number=4
     exon            74868..75007
                     /gene="F14F8_190"
                     /number=5
     intron          75008..75091
                     /gene="F14F8_190"
                     /number=5
     exon            75092..75164
                     /gene="F14F8_190"
                     /number=6
     intron          75165..75306
                     /gene="F14F8_190"
                     /number=6
     exon            75307..75395
                     /gene="F14F8_190"
                     /number=7
     intron          75396..75469
                     /gene="F14F8_190"
                     /number=7
     exon            75470..75575
                     /gene="F14F8_190"
                     /number=8
     intron          75576..75661
                     /gene="F14F8_190"
                     /number=8
     exon            75662..75853
                     /gene="F14F8_190"
                     /number=9
     intron          75854..75960
                     /gene="F14F8_190"
                     /number=9
     exon            75961..76155
                     /gene="F14F8_190"
                     /number=10
     intron          76156..76246
                     /gene="F14F8_190"
                     /number=10
     exon            76247..76324
                     /gene="F14F8_190"
                     /number=11
     intron          76325..76423
                     /gene="F14F8_190"
                     /number=11
     exon            76424..76723
                     /gene="F14F8_190"
                     /number=12
     tRNA            77114..77185
                     /note="tRNA predicted as a tRNA- Asp : anticodon gtc"
                     /product="tRNA-Asp"
     exon            77389..78435
                     /gene="F14F8_200"
                     /number=1
     gene            77389..78435
                     /gene="F14F8_200"
     CDS             77389..78435
                     /gene="F14F8_200"
                     /note="similarity to ring finger protein - Cicer
                     arietinum, EMBL:AB026262"
                     /codon_start=1
                     /product="putative protein"
                     /protein_id="CAC01781.1"
                     /db_xref="GI:9755627"
                     /translation="MSSAKLFGCSINVNVEAEEEEGGDGGSSTNVEVSRSGNQPDCEA
                     MSFSNQMEIGVRNTYYQFLESNSDSGSDSMYAEPEFIDFFDRESYEVDTVREVCVSSN
                     QRVSTPGYFNIWDQDVDLGLGIGLGSRSGSGQLPGDSGGVGVEVGRGVTPVEYNLFGE
                     EAMVVDEVLEWENFNNAIHLVQEPAYASMEGEEEEEEDEVVMEFAASIYSDAWEILLY
                     DNMTNSAPMDLDVEVWLDSVDGYAPMDYNAIIGQMFDNETGIKGTPPASKSVVDGLPD
                     VELTIEELSSVSIVCAICKDEVVFKEKVKRLPCKHYYHGECIIPWLGIRNTCPVCRHE
                     LPTDDLEYERKRRA"
     exon            84193..84753
                     /gene="F14F8_210"
                     /number=1
     gene            84193..84753
                     /gene="F14F8_210"
     CDS             84193..84753
                     /gene="F14F8_210"
                     /note="similarity to putative bZIP DNA-binding protein -
                     Capsicum chinense, EMBL:AF127797
                     Contains bZIP transcription factors basic domain signature
                     AA77-92;bZIP transcription factors basic domain signature
                     AA78-92"
                     /codon_start=1
                     /product="bZIP DNA-binding protein-like"
                     /protein_id="CAC01782.1"
                     /db_xref="GI:9755628"
                     /translation="MQPNYDSSSLNNMQQQDYFNLNNYYNNLNPSTNNNNLNILQYPQ
                     IQELNLQSPVSNNSTTSDDATEEIFVINERKQRRMVSNRESARRSRMRKQRHLDELLS
                     QVAWLRSENHQLLDKLNQVSDNNDLVIQENSSLKEENLELRQVITSMKKLGGGIHDKY
                     SSPSSMDELDQDFSSITDDPRTHHPS"
     exon            complement(86945..87304)
                     /gene="F14F8_220"
                     /number=1
     gene            complement(join(86945..87304,87538..88299))
                     /gene="F14F8_220"
     gene            86945..88299
                     /gene="F14F8_220"
     CDS             complement(join(86945..87304,87538..88299))
                     /gene="F14F8_220"
                     /codon_start=1
                     /product="CONSTANS"
                     /protein_id="CAC01783.1"
                     /db_xref="GI:9755629"
                     /translation="MLKQESNDIGSGENNRARPCDTCRSNACTVYCHADSAYLCMSCD
                     AQVHSANRVASRHKRVRVCESCERAPAAFLCEADDASLCTACDSEVHSANPLARRHQR
                     VPILPISGNSFSSMTTTHHQSEKTMTDPEKRLVVDQEEGEEGDKDAKEVASWLFPNSD
                     KNNNNQNNGLLFSDEYLNLVDYNSSMDYKFTGEYSQHQQNCSVPQTSYGGDRVVPLKL
                     EESRGHQCHNQQNFQFNIKYGSSGTHYNDNGSINHNAYISSMETGVVPESTACVTTAS
                     HPRTPKGTVEQQPDPASQMITVTQLSPMDREARVLRYREKRKTRKFEKTIRYASRKAY
                     AEIRPRVNGRFAKREIEAEEQGFNTMLMYNTGYGIVPSF"
     intron          complement(87305..87537)
                     /gene="F14F8_220"
                     /number=1
     exon            complement(87538..88299)
                     /gene="F14F8_220"
                     /number=2
     exon            complement(91899..92249)
                     /gene="F14F8_230"
                     /number=1
     gene            complement(join(91899..92249,92359..93075))
                     /gene="F14F8_230"
     gene            91899..93075
                     /gene="F14F8_230"
     CDS             complement(join(91899..92249,92359..93075))
                     /gene="F14F8_230"
                     /codon_start=1
                     /product="CONSTANS-like 1"
                     /protein_id="CAC01784.1"
                     /db_xref="GI:9755630"
                     /translation="MLKVESNWAQACDTCRSAACTVYCRADSAYLCSSCDAQVHAANR
                     LASRHERVRVCQSCERAPAAFFCKADAASLCTTCDSEIHSANPLARRHQRVPILPISE
                     YSYSSTATNHSCETTVTDPENRLVLGQEEEDEDEAEAASWLLPNSGKNSGNNNGFSIG
                     DEFLNLVDYSSSDKQFTDQSNQYQLDCNVPQRSYGEDGVVPLQIEVSKGMYQEQQNFQ
                     LSINCGSWGALRSSNGSLSHMVNVSSMDLGVVPESTTSDATVSNPRSPKAVTDQPPYP
                     PAQMLSPRDREARVLRYREKKKMRKFEKTIRYASRKAYAEKRPRIKGRFAKKKDVDEE
                     ANQAFSTMITFDTGYGIVPSF"
     intron          complement(92250..92358)
                     /gene="F14F8_230"
                     /number=1
     exon            complement(92359..93075)
                     /gene="F14F8_230"
                     /number=2
     exon            complement(94278..94439)
                     /gene="F14F8_240"
                     /number=1
     gene            complement(join(94278..94439,94541..94631,94708..94851,
                     94920..94985,95075..95212,95305..95406,95503..95628,
                     95837..95917,96250..96321,96588..96865))
                     /gene="F14F8_240"
     gene            94278..96865
                     /gene="F14F8_240"
     CDS             complement(join(94278..94439,94541..94631,94708..94851,
                     94920..94985,95075..95212,95305..95406,95503..95628,
                     95837..95917,96250..96321,96588..96865))
                     /gene="F14F8_240"
                     /note="similarity to sterol esterase - Rattus norvegicus,
                     EMBL:Z22803
                     Contains Carboxylesterases type-B signatures AA214-229"
                     /codon_start=1
                     /product="Carboxylesterase-like protein"
                     /protein_id="CAC01785.1"
                     /db_xref="GI:9755631"
                     /translation="MHSPLQTQQPEQRCWPMTSTVSEIEEVLPDEDSDRTTLLNGEPL
                     RRRVSGKSPVDEGPRRIFRQQSFGRDIGHAAAETYLITGLSFKLLRYLGLSMDDKITC
                     PYMLCYASYAWLSSRLDLYLPSNNDGLKPVVVFVTGGAWIIGWLLVNKFMFANLVLIF
                     RYKAWGSLLGMQLAERDIIVACLDYRNFPQGTISDMVTDASQGISFVCNNISAFGGDP
                     NRIYLMGQSAGAHIAACALLEQATKELKGESISWTVSQIKAYFGLSGGYNLYKLVDHF
                     HNRGLYRSIFLSIMEGEESFEKFSPEVRLKDPVVGKAASLLPPIILFHGSSDYSIPCD
                     ESKTFTDALQAVGAKAELVLYSGKTHTDLFLQDPLRGGKDELFDDIVSVIHAEDNDGL
                     TKDSLAPPRKRLVPELLLKLAREISPF"
     intron          complement(94440..94540)
                     /gene="F14F8_240"
                     /number=1
     exon            complement(94541..94631)
                     /gene="F14F8_240"
                     /number=2
     intron          complement(94632..94707)
                     /gene="F14F8_240"
                     /number=2
     exon            complement(94708..94851)
                     /gene="F14F8_240"
                     /number=3
     intron          complement(94852..94919)
                     /gene="F14F8_240"
                     /number=3
     exon            complement(94920..94985)
                     /gene="F14F8_240"
                     /number=4
     intron          complement(94986..95074)
                     /gene="F14F8_240"
                     /number=4
     exon            complement(95075..95212)
                     /gene="F14F8_240"
                     /number=5
     intron          complement(95213..95304)
                     /gene="F14F8_240"
                     /number=5
     exon            complement(95305..95406)
                     /gene="F14F8_240"
                     /number=6
     intron          complement(95407..95502)
                     /gene="F14F8_240"
                     /number=6
     exon            complement(95503..95628)
                     /gene="F14F8_240"
                     /number=7
     intron          complement(95629..95836)
                     /gene="F14F8_240"
                     /number=7
     exon            complement(95837..95917)
                     /gene="F14F8_240"
                     /number=8
     intron          complement(95918..96249)
                     /gene="F14F8_240"
                     /number=8
     exon            complement(96250..96321)
                     /gene="F14F8_240"
                     /number=9
     intron          complement(96322..96587)
                     /gene="F14F8_240"
                     /number=9
     exon            complement(96588..96865)
                     /gene="F14F8_240"
                     /number=10
BASE COUNT    30580 a  17554 c  17879 g  30879 t
ORIGIN      
        1 aggaagatgg taagctaagt tgggagatat gtttgtgtca gaagttgact catggccagt
       61 ccccactttt tctttatatc ttcaacccca agttactttc tcacttctca tctctgaatc
      121 attagggttt tcgtttcttt accaacaaaa gatagttgag atgttgtatt cggacgagaa
      181 cacgtcagtt tctaaggtgt tctattatca atcactacca taaacattgc ttaaagttat
      241 gggaaacaag aaagaataaa tttggagaat gcaacaacaa gtaggtgaaa gcccatcttc
      301 agaccaaaaa gactcatcaa taatctgtaa aaaacttatg ttttaaatcc cataaacaca
      361 tcaattcaaa ttcctgaaga agaaaaagcc tgaggttaaa cactgcacct gggaatcaat
      421 ttccttaaat ctttactcaa aagatgaggc tcctcttcag cttctgcttc ttcttcttca
      481 tgatcatctt taccgcaagt gagtcctgta tattcatttt tgcccgcaca ttaacttact
      541 tttcttactc tctgattttc tttttttcac agctgcttat gatccattag atcctagtgg
      601 taacattaca atcaaatggg atattatgtc ctggacggca gatggctatg tggtaagaat
      661 cctctgcact tgtgcgtgag tgtatatatg cttgaaactg gcacaaactc tcatcatctc
      721 tatacattct gtgcatttgc aggctacggt aactatgaac aacttccaaa tctaccggca
      781 catacaaaac cctggttgga cattaggttg gacatgggca aagaaagagg tgatttggtc
      841 aatggttggt gcacaaacaa cagaacaagg agactgttcc aagtttaagg gaaatgtacc
      901 tcattgctgt aagaaaaccc ctacagttgt tgatctcttg ccaggtgtgc cttataatca
      961 acagttctca aactgttgca aaggaggtgt aattggagct tggggtcaag atccatcagc
     1021 cgctgtatcc cagtttcagg ttagtgctgg tttagctgga actacaaaca agactgtcaa
     1081 gcttcctaag aacttcactt tgcttggtcc cggccctggt tacacttgcg gtcctgccaa
     1141 aatcgtgccc tctaccgttt ttctcacaac tgacaaacgg cgaaaaacac aagctttgag
     1201 taagcaatca atcaaaaacc ttaacttgtt ccatcatcga aatctaaaca tcaatttcaa
     1261 acttatgttt ctgcagtgac atggaatgtt acctgcacat actcacagtt tttagcaaga
     1321 aagcatccaa gctgttgtgt ctccttctct tctttctaca acgacaccat aactccttgc
     1381 ccgtcttgtg cctgtggctg cgagaacaaa aagagctgcg tcaagtgagt aacaaatcat
     1441 tgaaatccaa actctttctt agatatcctc tgaaaaaata tcaatatgaa tgttttcttg
     1501 cagggctgat tctaagattc taaccaagaa aggtctcaac acaccaaaaa aggacaacac
     1561 tcctttgttg caatgcacac atcacatgtg ccctgttaga gtccactggc acgttaaaac
     1621 taactacaaa gactattggc gagtgaagat agcaatcaca aatttcaatt accggatgaa
     1681 tcatacactc tggactttag caattcagca tccaaatctc aacaatgtga ctcaagtttt
     1741 cagctttgac tacaaaccag tctctcctta cggatccata agtaaataaa tacctccctc
     1801 aaccacaact attcaacttc aaaccaacca ttgaatgact aataacattc ttaaatcttt
     1861 ttgatacaga tgatactgga atgttctatg gaacgaagtt ttacaatgat ttattaatgg
     1921 aagctggacc ttcagggaat gtgcaatcag aggttttgct acagaaagat caaaagactt
     1981 ttactttcaa gcaaggttgg gcttttccta gaaaagttta ctttaatggt gatgaatgta
     2041 tgttacctcc accagattca tacccttttc taccaaactc tgcacaaggg aactttgctt
     2101 cgttctcact caccattctt cttctcctat tcatctcaat atggtgattt gatctgatcc
     2161 ttctgggttt taaaacactg aaccagaact gttttttgta aactcattgc aaagattgta
     2221 aaagaaaaaa aggagttttg tgagaggaaa tgattagaga tgtgcaaggc ttttttacct
     2281 tgatcactgc cattgatcaa tgactctgta cttcttggct ttttgctttg gtactaatgt
     2341 gaaagtgaag catattgatt tgattgagaa agtggcaaaa caacgaaatg tttttaattg
     2401 ggctcaaata aacgcatttt gaatccagcc caataaaggc ctggtttaac attcacgcgt
     2461 ttcaatagat tcgcgtgtgt attattttcg ttggtctgaa aaggcaaaag gtcaaaaacg
     2521 gcgttttgtt tgggagacac tttttgttcg aagatatttt ctcattctct gatctctctg
     2581 tccgaaacgg ctccgttaat tttaaagtaa atattccaaa ataagtttat gtcaaggcta
     2641 gtctttttga aaataagatc agaattttac ctatatatat atatttattt atcaaaaaaa
     2701 gtagacacta cttacaaaga ttagtattat caacgagtaa tacaaaatgg tttgcaagtt
     2761 aatttaatta aaaacaaaaa actaagattg ctaaaataca gtatttgtga acaagttgaa
     2821 ctaaaatcta gaagccagtc ccgcacggtg gcttttaagc ccaaatcaat gcccctttga
     2881 ttgagagatc tgaaatttag gactcaaaaa gtttgttgct gaccaaacgc gaaactttga
     2941 ttaaaaacgc gtttgcgttt taaaattctc ctgtgtttgt gtatgtgtgg aaaattaatt
     3001 tcttctcccg acgaatccca aaagtttgtt gaaatttgcc tccaagaaat ctgcaattag
     3061 aaatttcatt tcgccgtcat cgtcttcttc ttctgattct gattaattcc agatgtcttc
     3121 ctgagtctta cggagattag gtcattttcg cctcgactcg aactctgtct cgcagcttcc
     3181 gtgagagagt catggacacg ccaccgactt ctcgtatcgc atcttttggt cagacggaga
     3241 ttaactggga caagtacgtt cttcattttc ctcctcaatt tccatcgatt gatccgcttg
     3301 ttttctagtt ttgattgatt ctctgtggcg ttgttgttat tagtccgaac tttgtttatt
     3361 gttgtttcga tccagttttt gtgattctgt gattggtttc ttcggtggat ttatcgacat
     3421 gaaatggata tcgctcgttg ttttgacgga atcatttcgt ggaggtaatt gaagatttcc
     3481 gaatttattg gaaagaatct ggttctcggg ctcctgagaa gctcgatttc agaaattgat
     3541 ttggtgcaga agatttgttc gctagtgtta atcaaatctt tgtttaggta aaagatctag
     3601 taggcatttg gatagtttta gtgttcctta ttcttacggt ataatctgag gtcctacgtc
     3661 taaggttttt ggaaatgtgt gatgagtagg gccaaaacaa acttgaaacc attacaaatt
     3721 tggttgtaag atttccgaga ggtacctgaa gaatcataca acaaataata tcttcatact
     3781 agctctaatt atttttgctc tctctccttc ttttatcttg cagacttgac aaaaggaggt
     3841 tctacattaa tggagctggc ctcttcactg gtgttacagt agctctgtat cctgtatccg
     3901 ttgtgaaaac aaggcttcaa gttgcttcta aagagattgc tgagagaagt gccttttctg
     3961 tagttaaagg aattttaaag aatgatggtg ttcctggtct gtaccgaggt tttggtactg
     4021 tcattacagg tgctgtacct gcaagaatca tatttctaac tgctcttgag accactaaga
     4081 tttctgcttt taagttggtt gcacctttgg agttaagtga acctacacaa gccgccattg
     4141 caaatggaat tgctggcatg acagcatctc ttttctcaca ggctgtgttt gtcccaattg
     4201 atgttgtatg tattatatac aacactaccg ctttgtaaga tttgtaaatg ctgtgaatgt
     4261 tctatcacta tgagttgctg aaaaccatat ttctcctatt ttctgcaggt tagccaaaag
     4321 ttgatggtac aaggatactc aggtcatgct acatatactg gtggtatcga tgttgccaca
     4381 aaaatcatta agtcatatgg tgtaagggga ttatacagag ggtttggtct gtctgttatg
     4441 acctattctc cttcaagtgc cgcttggtgg gctagctatg gatcaagcca acgtgttatc
     4501 tggaggttag ccatgaatgt tctagttaat tgatgatagt ttccatttta gtttgattgc
     4561 aagaacttgc atttcagtcg ttcctggaat ttggatttgc taccaaagct acaattccgc
     4621 tgatacaata tctgctactg ttgggcagat tcttaggtta tggtggtgac tcggatgcaa
     4681 ctgctgctcc tagtaagtca aaaattgtta tggtccaggc tgctggagga attattgctg
     4741 gtgcaacagc atcctcaatt acaacaccat tagacacaat caaaacgcga ctgcaggtat
     4801 aaagtgttcc cattcatagt aaaaacttga ttttattttg catttacttt ttttaactct
     4861 aatgaatata gaagagcttc cgtgcctgct gtcctggttc tcaaatagat aacttcgggt
     4921 attgctacat agaaactatg ctaaacaaac ggtaaaatct ctgtgcaggt catgggacat
     4981 caagaaaata gaccttcagc gaaacaagtg gtgaaaaaac tgctagcaga agatggctgg
     5041 aaaggattct ataggggttt gggcccaaga ttctttagca tgtcggcttg gggaacctcg
     5101 atgatattga cttacgaata cttaagtaag agttcttttc ttttataccc aaaatctcac
     5161 tttgagccac tctcaaaacc aaccaagatt cttcttttga aatgctagct gctcctctga
     5221 catgtttcac tctttcatgg tttttttttc cagagcgtct gtgtgcaata gaagattaga
     5281 aagcttcact actgttcgtt ggtttttctc cttctactaa ctcgagtaga cggcatcacc
     5341 ttgattcaaa tctcggctat tgggagcttc catgttgaca attggaccat tctttcaact
     5401 ttgaagtctg agttccgtta ttgtaatcat tctttcaact taatttgcgt attggagtgt
     5461 attcttacag cagaagaaat tctagcttac gttcttctgc tttatgtagc ttctgagatt
     5521 taagaagctt caaaacaatg caatcacttc atgaaatctt atagtcgtac ggatgtacgt
     5581 gttatcgtaa cagtcaaaat ttgagttgtt gcaaatggct tctcatttgc ataactgtct
     5641 tcacaaagta tcctcattct taggatatca gccaaagcta acctctggtc attctcattg
     5701 atagcaatat aatcatcatc aaacctctgg tcattctcat tgatagcgac atatacatca
     5761 tcaagtactt tattataact atgatcattc tcattgatgc tgtgtctctt agcaaaaaaa
     5821 aggccactag ccataggcta acaccaaatc accaagagcg cttactgggt tttattttag
     5881 ctcatatacg taaatctatt actccagttc ctaagattta agagtgttta ttatcctaaa
     5941 caaaaagcca ccgatatatc taattgttat tcaaaatcag ataaaataaa ataaatcgta
     6001 tatatacgaa aagtttcaag ataaacaaga aaagtagtta gtatttgacc ttttttagtt
     6061 tatttcctcg tagcaggctc atttttttcc cctctctgac tcagcagatt aatttctcca
     6121 ttaggataat aacttaaata tttccggaga cttaaatatt cttacaacgt ctttatcaac
     6181 aaaaacaaaa ttcttgaata gcgatctctt ttcttttaat taaaaaaaaa gactttaaaa
     6241 atgaggataa aatcaaatat aataatgcat tattgatagt aacttaaaca tgcatggagc
     6301 tcttaattat ttttgggaga cttttagata tttatgaaat aaaataaagt gtagatgttt
     6361 taaaaataaa aataaaataa agtgtcgatc acctaccgac ctatacgtgc atgtattctc
     6421 gtttatacga tagttacatg atttatgcaa taatcataga cgacgtgcat cgacgagcgg
     6481 cccacgacca cgacgtaagg attacggtcc acgtcgtaag gattacgttt taaatttata
     6541 gtttatcaat tgtatatcgt aaataataaa tttagaatga ctgagaattt gttgagaaat
     6601 gaaaatatta gagaatttat cgaatgattc gaatctaaag cgaataataa tttttttgat
     6661 gatttatgtc cttttgtttc gtcgacattt atgatttaag tcctagcata tactatattg
     6721 tacttattac cttatacaat acgatttgta tatatacgaa ctttaactaa aaataaagtt
     6781 aaatgttgaa gagtttaaga cactaccata gctcccccac atccacatgc actatttctt
     6841 cgtaacatat caaattaaaa ccatgcattt attaagttgt cagttaagga aacaaaaagt
     6901 tgtgaatgta tttgatttta atttattttt tcagtttttt tcttttaggt agaaagaatg
     6961 aaaccttagt tttgtacata ataaaaacct tactatctta cattccagtc aacaaattaa
     7021 atacagtgag tacattttgt tagatatacg ttcatttcat tagcacatac gttatatact
     7081 tatatagtaa tcataatcat aaaactgtac atatgaattt atttggttgc aaaataaagt
     7141 tagcttcaat caattataat aaatgcttca ctattttaga gttttggttt atttaggggt
     7201 atttaaatct aaataaaact gaaaatgaag caaaagcaaa cttaaattaa agtacatctt
     7261 ttattgggtc cgaaaaactg aaattaaatt tcgtagtagt cttaaatgat tttgaccttt
     7321 ttaaataata tattcaaatg tgtttcaaac acgaatcaaa ctataccaaa aaaaaaaaaa
     7381 aagttggata aaaaataaaa cctgactaca cctcaacttt ggatcaaaat ctatgaatat
     7441 attttcaaaa ttatcttagt caaattttaa attaattaat tatttatata aaatttaata
     7501 attatcataa ccttggatta aatttatcta cagtcaaaaa ttaattttaa atcaattaat
     7561 taatagcatt attacaatcc ctaattgtac gggacgaata aaaaagtaga aaactcaagt
     7621 tcctttcttt accatacagc tttttcgatt ggagttgaat aagtcttcat ctgacacgtg
     7681 taaccctggc acatgccgtc cactaaaaca cgtgcgagat ctgtataaat caaacctacg
     7741 cgtttcatct ctcttttcaa aactcaccga cgcgatccga tctcatctct ctcatttcga
     7801 aaccatggtt gagccggcga atactgttgg tcttccggtg aacccgactc cgttgctgaa
     7861 agatgagctc gatatcgtga ttccgactat cagaaacctc gatttcctcg agatgtggag
     7921 gccttttctt cagccttacc atctgatcat cgtccaggac ggagatccat cgaagaagat
     7981 ccatgtccct gaaggttacg actacgagct ctacaacagg aacgacatta accgaatcct
     8041 cggacctaag gcttcttgta tctcgtttaa ggattctgct tgtcgatgct ttgggtacat
     8101 ggtgtctaag aagaagtata tcttcaccat tgatgacgat tgcttcgtaa gttacttgaa
     8161 ttttgagttt tgtattcgtt tttatgcttg atttgagagt tttgtcaatt ttggttctag
     8221 atctgttttt ttgagcttat ttgtttgtgt ttgtgtggat ttttcaagtt cattgcttga
     8281 atttcgtaga tttggtgaga gatcaattat acgattcact aaatttgacg gatcttaggt
     8341 ttgtgagata atccttggtt cgattagcta ggcaattcaa tgttttgtac cagatccata
     8401 gatctgcttg ttgagtctga atatgttttc acttttgtgt aattagccat gatctctaat
     8461 gtttacttgt agattttctg tgagctgatg tctcttttgt tgacgacatt gttgttgagc
     8521 tgatatctct gagtcattat agctaccttt acgatatggt tgcacgtcct tgttcatcac
     8581 ttttttcttt tgttttacct ttttgagatt tgtggggcat atccaaggat gagtctcgat
     8641 gacgcttgtg tttagtttat aattttctga gttttttttg gaggaactct ttgatcaatg
     8701 gcttgatctg gattttaacc gctttttaat tcatgtattt ctttgatgtg tacatgtagg
     8761 ttgccaagga tccatcaggc aaagcagtga acgctcttga gcaacacatc aagaaccttc
     8821 tctgcccatc gtctcccttt ttcttcaaca ccttgtatga tccttaccgt gaaggtgctg
     8881 atttcgtccg tggataccct ttcagtctcc gtgaaggtgt ttccactgct gtttcccatg
     8941 gtctttggct caacatccct gactacgatg ccccgaccca actcgtgaag cctaaggaga
     9001 ggaacaccag gtgacaataa ttatcatcat aacatgttta tgtgtttttt tgtcaggata
     9061 ttcaaatgtc agtttttgct aaacgtttga tatgtcaggt atgtggatgc tgtcatgacc
     9121 atcccaaagg gaacactttt cccaatgtgt ggtatgaact tggcttttga ccgtgatttg
     9181 attggcccgg ctatgtactt tggtctcatg ggtgatggtc agcctattgg tcgttacgac
     9241 gatatgtggg ctggttggtg catcaaggta atttcttctt attcccttgt aagactcata
     9301 attgagtata gctaaatatg aagcacatgc tctgtactaa gcgatacctc catttggggt
     9361 tgaatctttt ataggtgatc tgtgaccact tgagcttggg agtgaagacc ggtttaccgt
     9421 atatctacca cagcaaagcg agcaaccctt ttgttaacct gaagaaggaa tacaagggaa
     9481 tcttctggca ggaggagatc attccgttct tccagaacgc aaagctatcg aaagaagcag
     9541 taactgttca gcaatgctac attgagctct caaagatggt caaggagaag ttgagctcct
     9601 tagacccgta ctttgacaag cttgcagatg ccatggttac atggattgaa gcttgggatg
     9661 agcttaaccc accagcagcc agtggcaaag cttgagagca gtatgagcca aaaagaaaaa
     9721 gccaccaaag ttttggttat ttttagctca aattatcgtt acttttaaat ttctgatttt
     9781 acgaaccttt cttgcttttt ttacacattt gagtagtttt catcatcagt actttctcat
     9841 tgtccggtta tggtttttgc atttggttta aatatcaccg gtttatttat aaacagtggt
     9901 ggattagtag tactattttc tgagtttttt tctttgtttc attaataaaa aggccttttc
     9961 ataggtgttt gcaattagtt tttttccccc attaatcatc gattatcata ggtatgttat
    10021 ggctttaaat ggtataagga aattgcttat agaccaaaaa aaagttgaat tgctattgag
    10081 agagctttta caaaagaaag agcattgttc aataagcttt tcacatttgg tcgatatttt
    10141 gatcaaccta tcataggtat ctcaattaat aaaccggaat gttaatatgt tttgcaagat
    10201 atccctacaa tcaaaccgtg aagacccgac ccggttgcgc aagatccatt ttcctacttg
    10261 gttaaatggt caagcccatt aaccatacta taggcctgtt gccattttcg accgacctct
    10321 ctatttctac ttactactta aagaagcaag aggagacgta gaggttcata cagggtttaa
    10381 aaacaagagc aagtcaccat gatgatagca agaaatcagt ccaagaagtt gaagacggag
    10441 aacaattcac aaactttgca aactcgaagg aagggaacaa atatgtcgtt ccttttgacc
    10501 tagtgatcga gattccgtag ctaggtctgt cctcttatcc aaggtatggg ggaaaatagt
    10561 ccgcagtaga cttttcatga catctttccc gtttacgtca ctgtcgtctc agcctgatcg
    10621 tctcttcgtt gttttcattg atttcattaa tatcttacgt tttttgcggt gattcctctt
    10681 ttgtggaaaa gtattatcac catataaacc agttggattc actttatgtg atgctggcac
    10741 tatattgttt atgcctctca tctcaagttc tcaactattc tttttgcggt ttcctcattt
    10801 cgtgatgaga ttcttagaca ttgcatgtgt attgtgcttt tcttcttctt atcaagaacc
    10861 aactttgttc aaattagatt ctcaaagtgg gctttctttt agcatctacg cgattgtgtg
    10921 gttgactact tttcttttaa gtataatttc atagttttgt tttatttcat tttagtatat
    10981 acagtactac aactgtgtag ttaacttact acagtagcat gtatttcatt tgaccaaaac
    11041 tttggtatat caattaacgt ttttactttt tactttttac tttttacact cctggtttac
    11101 ccaattttgt gcaaaatgat gcttatccat gaagaccgga cccggttatg taagatccac
    11161 gaggtttatt acgttcggat ctgctccttt atctccattt ctcagctggg gtagagagag
    11221 agatctaggg tttcgaaaga agagcgatcg atcatgagaa gacgcagcaa aaagatcaaa
    11281 accgagaaca acagcaatcc agaaacgtcg gaagagagaa acaagtttga tgaaatccct
    11341 catgacctag tgatcgagat acttgaaaga ttgcctttga aatctgtagc caggtttctc
    11401 acagtatcca agttatgggc aacaactata cgcagtccag atttcagaaa atcttaccgg
    11461 ggtggatctt cgtcggagcc tcgtacccta atcgtttccg acctaaattt taaggaacca
    11521 aacccaaagt tgcatttctt caggccgtct atatcatcac cgtcttttct atcaagtctg
    11581 acatgtccgt tcacatatcc tcggcacgaa gagtactatt atcatcatgt taatggattg
    11641 ataagcgttg gatatggtac agaccaaatc gtaattaacc ccacgactgg aaaattcata
    11701 actttaccaa gacccaaaac aaggagaaag ctcgtaataa gttttttcgg gtatgattca
    11761 gtgagtgatc aatacaaagt gttgtgcatg acggaaagac tgcgtggcca tccagaagaa
    11821 gcatcatctc aacatcaagt gtacacattg ggagctaaac agaaatcatg gaaaatgatt
    11881 aattgtagca tccctcaccg tccttggtcg tggaacgccg tgtgcataaa tggtgttgtg
    11941 tattacattg ctaaaacggg ggagggtatg tttcgtcggt gcttaatgag atttgatttg
    12001 aagtctgaca atttggatct ttgcactatt ttacctgaag agattcaaac aagtctacat
    12061 gattactttt tgatcaacta caaggggaaa gtagccatac ccaatcaacc taatttctat
    12121 acatatgatg tgtgggttat gaatcaggaa ggtggaaaaa ttgaatggtt gaagaatata
    12181 actttcacta ttaaacctcg gaagggtttt gttcgttatc tattcgtcac aggcactact
    12241 catacgggtg agtttatttt ggcaccaacg tcctataccg atgagtttta tgtcttccat
    12301 tacaatcccg acatgaatag ttttagaaag ataagggttc aagcacccgg agttaagttt
    12361 agttttgctc agaaagcttc agttgttttt tcggatcacg tagagagtgt ttggttgttg
    12421 taggagagac atggttttga tacccataat catcagtatc gaaccttgga agagtttatt
    12481 gcgtttggat aatttacaca ttagaggctc tactcatacg gctacgggag agtttatttt
    12541 ggcaccacgg ttctattctg atgatcttaa tgttatccat ttcaatcccg acacgaatag
    12601 ttttagaagc actaaggttg aagtatacga agactatgag tgaaagcgtc atggtacaag
    12661 agcaatggtt tttcgggatt acgtagtctt aagtttttct aggagagaca gtttcatgtt
    12721 ttgataccta tcgtatttga aatgtttgca ttgatagacc cttttttagg gaaatttttg
    12781 tcacttcatt gcttaattta gttaaaccag ttggatttgt ctactttctt ttctcctttt
    12841 acaactatta tttatttcat ctgttttagg acatgcttta tatgaatgaa tcatttatca
    12901 tttatcaatc atttagtatc taaaagagtt tatgctcttt gatatatcta cgaagaataa
    12961 tactaaggtg ggagtcaatg tttgaaatat tgataagccg gaagacgtaa gtaagggctt
    13021 gattggttct ccctctgcca cccgcaaacg ctgcgtttgc gggtgatagc ggttattagc
    13081 ggttggcacc aatcatagaa accgctagat accgcttcgg accgctcgaa atcgccagat
    13141 ttcaaaagct ccttcccgca agcatttgcg gttgcgggcg gtagcggtta agttaaaaaa
    13201 aaatattaat taattaaaat aattatgtct tccacccaaa ccttatactt attcttatca
    13261 gaaaacccta atcaatgaaa ccctattctc tcaattatgg catccaccca aactgacaaa
    13321 aatcaaagtc aaaatcaaga atcaaacgta cgtatgatct atcctttcat ccattcatta
    13381 gctagtgtaa ttctcggaat atttcatggc atcgttgttt ttttttattt tgtttttttt
    13441 tgagtttttt gattgaatac atgttttgat ttgttttctc gattagaaaa tcatttggtc
    13501 aaacgagacc acatttgcgt tacttcaacg ggttattgtg gagaaataaa cggaagaatc
    13561 caaagacccc aaaatcagat ttctaagtga tgttcaaaaa gaaaatattc ttaagaatat
    13621 taacgtttgg aaaaaatttg agttggagat gtgttaaaaa tcgtttggat atcttgaaga
    13681 aactttatca tatgtataga ggcaatccgg aaaacccgcg agttcaacgt tatttacagt
    13741 ttatcacact acttgatgca atttttggtg atgtaccaaa tgcataaagt attaaacttt
    13801 ttcttacaaa atttatttat ttttgaattt ttagttttat ttatggtttt aattattaag
    13861 tatgtttaat ttttcaaata ttatcaattt atcataataa tatattgtat tttttttctt
    13921 ttaatagtaa tatattatat ttattttggt tattttttat ttaattacta tcgcacccgc
    13981 tggtttacca gtcataaaac tcccgcaaac gcacccataa ccaaacgctc aaccagtcgt
    14041 tcaaaacact tgataacgct tgaaaccgca accgcccgtt tccgcaaact cccgcaaccg
    14101 caaccgcacc cgctgcgttt aaaccagtca ggccctaagt gatgcatctt gactaaataa
    14161 aatttatgtt aaattacaaa agttgtcgat ataacagccg atttgtctat actactaagg
    14221 ccaggactta gtagttgcgt tgattcctct atatcatgtg tatgtccgtt cccatatcag
    14281 gtaccattct cattatgtta ataacttgat tgtggtcaaa agcaaatcat aattttaatg
    14341 actttattaa agtatgaatc caataactcg agatttatga agattttaaa ttacatttta
    14401 caaatcaaaa tctaataaca ttaaacttta acagagtctt ataaaatctt aattgaataa
    14461 cacaagattt tttaacattt caagtcacta aaaatccata taaatcacaa accaataaca
    14521 ccttttagtt aaaaatacag aaatccaaat ctcatggttt aaggtgagat ttgaattaat
    14581 tttacaaaaa tcatatgaac ttccctaaaa ttatcaaaat catttaaaaa ctcaagaaac
    14641 tcaaatcact ttaaattcta atttgaatac acgccctttc taagtttcaa tataaaagag
    14701 cacttgcttt tccggattac gtagagagtc ttaggtgttt agtaggagag gcagtttcat
    14761 ggcgttgatc tctctttttt aactttggtt gattactcta ttgattactt actcttattt
    14821 cacaaacaat cttacctctt tttataaaat cattcggact ttgtctcctt gcttctgggg
    14881 tattattgac actatagttt ctgtctacca aaacgagttc gtgataacat tattatacat
    14941 atgaaaagag gtcatgattt aatcctcaac ccaatcccac aaaaggtata aagatgcata
    15001 tatatacgtg aagacgggac ccgggtacgt aaatccactt taccagtcgg gtatagatat
    15061 gtaggttcaa aaaaagcgca ttggttatac cttgtctcca tatttataag ttttaaatta
    15121 ttactatata ctcagctgga aaaaaagcat acaaaagaca gagaaatcta gggtttcgaa
    15181 accagagcga tcgatcatga tgagaagacg caacaaaaag accaaaaccg tgatcagcaa
    15241 tccagaaacg ttggaagaga gaaacaagtt tgatgaaatc cctcatgacc tagtgatcga
    15301 gattcttggg agattgcctg ccaaatctgt agctaggttt ctcacagtat ccaagttatg
    15361 ggcaactagt atccgcagtc tagatttcat caaatcttac ccgcttggat cttcgtcgaa
    15421 gcctcgtacc ttagttgctt ctagtgaacc agatctcaat atggaacacc acgaatgata
    15481 cttcttctcg cagtcttcct catcaacgtc tcttgtatca cgtgtgagtg tgacatgtcc
    15541 gctcccatat tactatgatc atcactaata tcatcatgtt aatgggttga taatcattgg
    15601 acatggtcca gagcaagtcg tggctaaccc tagcacaggt cgaaccatac ctttaccaag
    15661 agtcaaaacc aggagaacga tagcaacaag ttttttcggg tatgattctg ttagtgatca
    15721 atacaaagtg ttgtgtatga cggtaaaagc gtatggtgat ctgagggatg agtcatctca
    15781 acatcaagta ttcacattgg gagctaaaaa gaaatcattc agaatgatag atactagtat
    15841 tattcctcac cgtccttgct ctaacggtgt gtgcatagat agtgttgtgt attatgttgc
    15901 taaaacgggg gcgggaatgt tgcatctatg cataatgaga tttgacttga gttctgaaat
    15961 attggatctt tttactagtt tgcctcaaga gattcgacct ccaagttgaa ttattgagaa
    16021 tttgataaac tacgagggga aactagccat accaacggaa actacttcat atacatatgt
    16081 tgtgtgggtt atagatcagg attctgaaaa acatgaatgc ttgaagaaat taactttcag
    16141 tattgaacca gcttggaaga attcatttgt taatctacgc ctcataggct acactactca
    16201 tacgtgtgag tttattttgc atcaccacac tataattatg agatttatgt ctcccattgc
    16261 aatcccgaca cgaatagttt tagacgcact aaggttgaag catccgcagc gttcaagttt
    16321 ccttttataa gagcaatggt ttttccggat tacgtagaga gtgttaggat gttgtaggag
    16381 aggcagtttc atgctgtata atactctctt tataaaactt tagcacttat aaagagagta
    16441 ttcattcgac gactctaatg tacaaaatcg aggatgtaat tgtacattac aattcacgat
    16501 tacaattcac gactatacgt gcacattaca attcacgatt ttggttgact tcactatcta
    16561 ttagttcttt atgttttcac aatttcacag aaaaaaactc tgatcataat aaagtaacaa
    16621 ataaaacttt ccttcttaca tgtctggaat acattggact ctactaaccg cgatcataca
    16681 agttagttgc tacgacacca aactattcac acacagacac attgcttctt taaaacttct
    16741 ggaaagcata caaattacca aaaataaatt caaaacttta ctgaaaatgt tacatgtttg
    16801 cgatcgttgt gacaaaaggt accaatcttc tgtaatctct tcttcctaga gcgcaattat
    16861 caagaacccg acccaacatt agccttgtgt tctgtaaagc cacatctctc ggaggtatcc
    16921 ctgactctgc cgcagctgca ccaagaggga aaggttgcga cattgttgca gccatcattg
    16981 cgtactgaag aggtccgctt cgggctttaa atgaagtctg aggtacaagc gttttctcat
    17041 cagtcccgtt ttcagagtaa ctcgaatcct gagggtggga tccaccggtg cccccttgta
    17101 ccgggctgca gctctgaaga agagcttcga gaacactcaa tgcctcccaa cacagagtgc
    17161 tttcgactag ctgtgaaaca attgtgtaca tgtggggact ctgcgaagca tccatgggag
    17221 tgtgttggag caatgccttg agcataagta atatgactcg ttggtaatcc actggtcctt
    17281 tttttagcag tcttaacaag tgaccgaaag ctaaagctga gtgtttcggg aaccatttgt
    17341 tgcagagcag aggagagaca catgcaagga gattttcaac tcttttaatc tcgccacgag
    17401 catatgcgac aaaaacagtc gctaattcat cgagtgattt tgcccgacac cagacagcaa
    17461 tgttagatgc cacagaacat gccttttgat attgctgctg gagtggtaac gcagaaacca
    17521 tgacttggtc ttgggtcagc tgcaagcaaa gccaaggaag tagacctgtg atatgcataa
    17581 ggagtcttgt ctcagcatcg ccaaatatag agtcacatga aggcactgta atccttgata
    17641 ggacctcaat agagaactcg tggctaacag tagacatcag tcctttgagg acaagaggtt
    17701 gtacaccttc gaactttgga agagttccac ttgacggcgg catctcgtac cctctagatt
    17761 ctgacctttg gaattccccc aaatcattag tgttgaattc atcccgaggc atacttgaca
    17821 agagtacatt ttcagttgtt ttgtcacgaa atgatagccg gtcaataata cgggagaaga
    17881 gctcaagaac ctggcaatag acatggacga agtctgtgtg catcatggcg acacagcccc
    17941 agaagagctg tgggtagagt atgactttct ctggctccat gttctctacc atgacctgta
    18001 gcgtcagaag gatttccata ataaaaccca aaactggagg aatgggattg ctaagacatc
    18061 gatgaagaca gcgtagaagg gagacacatg catcacttgt cacacttggg cgtagcgcac
    18121 ggtatatttg gtgtgaccga catgctagat gtcttgacgt gcattccata gcccatttga
    18181 gagcttcagt tccccaagtt tctcgaagat ctccttggaa gaatatagca tcaaccatac
    18241 tctgaacaag tgcagacaaa agagcggcac taggaagatc tgttctcaca accgttggat
    18301 cttcattctc ccacatcatg cttcctcgtt ttgattgcac atacttaatt aaactcacaa
    18361 cctgttgttt gttctctcca tcgctgtttt ccacctcata tagctccaaa tgccgacccg
    18421 ctagtgagta caataaattc acaagtaaat gttgacaatg ctctagcaca atgtcttcag
    18481 agctatccat cgaaacaaaa gtgacgtgga agagcaaagg cagatgttcc ctaaaatctt
    18541 catcattctc atatgcgatt tctgcaagaa gaatcagagc tatgtcagca tgagtgagtg
    18601 agtgctgttg atgtccctgc aaggctgatt gaagttcctt tgcattgacg ccgtgcattg
    18661 cgatccctga atgcaacaca tcttctccag aatttggtgt atctatgagg taatctccgc
    18721 tatcacgtga gacatggcga ctcctcaaac ttcctgtaga gctacgaact cccattaaag
    18781 gtcctgatgc attcaccaat gatggcagga gctgaccaga acgaccagta gctacaggaa
    18841 caatattcaa ctcaggaggc attggactta aaggcccaga agcacttcgc ccagtcatcc
    18901 ctgctgttct ccagcttagg cttccacttg tattcctaag gggaccatca agggagcctc
    18961 tgacaagaag tggtgacata tgtggttggc tgtctgcaac tgaaacaact tgaggtgctg
    19021 tggcaggtcc ctgagagaac tccagcacaa agtttccatt ggaatcaccc cggtttgcac
    19081 tataaccaat gggttcaata ctgtcttcca gcatccgctg tgacagttgg taaaccaggt
    19141 gatcaatagt acgctgagga catattcgtg cgaggtacaa acttacacgc ttagcaactg
    19201 aaaaatatgt agcaaatgca ccagttattt cggcagatgc atttgaatca cagtcctcaa
    19261 ttccctttgt gatcaagaaa tccaatacag ggctgatgtt tctgggctta ctagcaatgg
    19321 tactccaaag tttttcaatt tcatcaggga attgatcccc gtgtcgccat gtcacatagt
    19381 aaagactttt tagtaatctt tcactccaac ccgaatcctt gagtttccag aaattaaggt
    19441 tctcaatcca tggagccata caggtcaaga cctgatgctg agcaattata tcaacagcat
    19501 caagctgacg ctgcataatt tcttcacaaa gcagctggct taactccgga tgatccttgg
    19561 cgagtttgca ggagagcttg tattggaact gttgatatga atctggaaga ttacctacaa
    19621 ctgctgctct atagcctcct gaaccttcta taccatcctc agcccactca cgcatagaaa
    19681 gtgtctcaag catttgaaga gcatcatcgc gaatttgtct agatggatcg actaccttgt
    19741 agagaattag acttaagagc ctctggattt cacattttgg tatttcttgt cgcatgtaaa
    19801 cctcagccaa cacactgaag tacccatcag ctatagccgc atcagagtag taacactggg
    19861 aaaagtacag atgaattagg tcatgcagtt tagaagagtc taatcaagga tgtagtcaaa
    19921 cagatgagca aagcatagaa gtgaaaaaag cttattaaga gaattcagat gcttaaactg
    19981 gagctaataa aacaaaacta tctgatacgg aaccatcact gcatggataa gttgtcatca
    20041 ttggtcaaga tttatcaaac atctgaccta gtaattacca agacgacagt ataattaaac
    20101 acaacttcca tgcattcagt cagatagaac attacctgat caatgcaggc aggaaagaga
    20161 tccaagtttg taagtagaag attcttcagg gccaattttg ccaacgcaac acgttgatga
    20221 ccacctctat gcctatcacg acctgttgtc cctcgtccac cttctcccgt gtatttggag
    20281 taagatggag ttcttggatc agcaggcgag taaccaaaag ggaccctggg agcaggctca
    20341 atgaacaaac tatttatcca agatatcaca cggccgctca tttttcttgc attgtcatca
    20401 aaacacggtc cataaagaag ggaagccatt gcattcaatg aggcccactg gatggcttca
    20461 atttgctcat tcagttcctt gtcaaaagaa atcttgtcta cagaatcttt ggaccggtta
    20521 tgctgtgagg tcttatagcg ctctacttca cggcgataat cactaacacc atcctgtccc
    20581 cacgtatttc cagtgtcatc ggaccaggaa agaagcagat cgaatagacg tttcctactt
    20641 ctaacatcaa acttctctga ttttgattca acaaattcag gggcaaggaa tcttaaaaca
    20701 gacgcaagtg catatcgcag aggctgcatg tcctgaaagc tttcatgagg tgccaacgat
    20761 atttgtcttg ttgaatcttc aatgaaccgc agataatgga ggcggaaaac tggtttacga
    20821 gcaagcattc caggccagac attctcagac actgttcgat atatattaga gacatgaaca
    20881 cggaggtcct ctcttcgacc tcctttttgg atctgcattc atatcatagg aacacatcgt
    20941 tttagcgtca agtctcaata ttaatcaccc agctgtaaat caatgtaaca aaaatggtga
    21001 agaggaatcc aacggtcatt aatttcatat tcagggaaaa acttagtaat tcgacatccg
    21061 tagcagccca tgtgtgagaa aatactggat acttccgttc cctcaactct aatgattcaa
    21121 aatgaagctc aataaagaca catagaggta caaataatgg caatgacttc tagtactttt
    21181 catccatgag atttccctta cttgttctcc ccttttttta ttcatttgct taggtaagtt
    21241 ttgtaatgaa tctatagtga taatgagtac aaccgtaaat ctgtgcagcc cagcagcata
    21301 gtgaatgctg taggatttcc aggtataatt ctgaaagaaa gtattctaca ttgttttaca
    21361 atttgacaag tatatacctt ccactttggc ttcgtctctg tctctgatga aatctcctcc
    21421 atgaaagatg caagctcgct aaacataatt tcacatgctt ccaaatgaga gcgcccgaga
    21481 gccatagttg cagcatgcta catgcaagga agtataacgt aaagattgta aaaacttatc
    21541 taggagaaaa aattcaacca aaaccacatt aacctaacaa gacaagtagg tttaaaagac
    21601 tgacaaaact accaacttca gactaaaaat gcagagacac aaaaacaact tacgttgtgg
    21661 gtctctgacc caaatctaag ataagggaaa ataaggtggt acatgtctct ggttgatgca
    21721 atgctacccg catctttgcc atcaggtgga cacgaacaca caaacatagc atacagaagc
    21781 cattgatcca gtttgttatc tgtatcttgt gactggtttg cctttccacc aaactcaaca
    21841 ggtgtaatat gggccaggcg gtgcataatt tcagacctgg aaatgaaaag ggcactttag
    21901 tttccttcat gttattaaga atagcaaaag agttatggca ataaaatgag acaaaaaaat
    21961 tcttcctaaa ttttaaaatt cccacagtaa agtgaaattt atttgcacgt tatactaggg
    22021 catgaatttt actgaaggat tgttgatcca taaagcctac tttacttttt taatctttat
    22081 agactggtag gacagcgttg acggtcagag aagactcaag aaaacacacc aaggatgatg
    22141 tagttaggaa aatatacttg gagcaaacac actaaagata atgcagctaa gaaatatact
    22201 tacttggctt cttgaacaga gcgtgggcag agctcagcag catatttaac aagctcgctg
    22261 agacatcgac cccatttgtt tttatcaagg ctctcaaaga taatggattg aagagtcaca
    22321 tcagaaggaa tggcatcgga atctcgtctt aaatcaaaag gacgggcaga atcccaatag
    22381 caactttgaa caatatcatc ctattatgtg aaagaaataa aggatacaaa tcttaatttt
    22441 ctataaagcc agacggtttt aaaccataat caaccaaaag gctaaaaagc ctctgaaatg
    22501 gtgagatcta cacagaagct acttacccca tgttcttcca agacatcgat catgtatatg
    22561 ggttcagctt caaatttcat aacatggtct gggtgctctt gaatcatgag atcccgaata
    22621 tcatttctca aagcacgtac acatcgtaat aattctaggg cagtgtgccg aatctgactg
    22681 tcgactgaac taagaaatat tagcccaaca gcatcaatat cagaagcgcg aaactcaatt
    22741 gcatctgctg cttgatgaaa agataatttc ttgaacctat catttccctt tgctgttttg
    22801 ttttcttctt cagcatcagt atcttgtctg tcatctacta aacaagccct ccagaaacgc
    22861 atgagttcca acagacgtcc tagtgatgct tgaatgagga gtgggaattc atcaggaagc
    22921 tttaagatga agtttgccat tcctctcatg actgcaaaac gacgatgagg aaggtatcta
    22981 acaatccggt tcaggacttg cactgcttcc actcgaactc caggatcaat acttatacca
    23041 tgctgaggta ttatttccgt gatcttatca ctccggccaa cttcctcaat cagataaggt
    23101 atgcacttca gcactgactg gaagagagat ccttgagact tttctttatt cacagcatct
    23161 gcatataaca tgaaggttag cgaaaagtgt tttcggaaag taacagccag gggatcctag
    23221 gtagaaaatc aaaaataata tcacacttaa atacacacaa catataaaga tttcttaacc
    23281 tcctcacaaa accatgtaaa tcagactaag ctttttgcgt aaaactaagt ttaccgattg
    23341 tagtcctcga tgatgttaga agagcttgac tgtaggtcct gtggcaggat cttaaaattg
    23401 actcaattgc tgctttcacc tttggtatgt aatggcctat cccatgacct attaagtgaa
    23461 cactaagaaa agttaagtgt atgaaaggaa aagcttattg agacctacta acaacctaat
    23521 tcaggttaac gggttaccct taaatatctc caacccaaca tactggcttg aaggcgacat
    23581 aacaagggca agtaaagcac ggagaccaat aatctttgct tcgcttggac tatcttgctt
    23641 taacagttct agtaacatgt gattcatagc aaagtcaagg ttatgttcag ctatggtcac
    23701 acagaactca acgagtttat cttgctggac atcctgagtg agcattcctt ttctcagaac
    23761 tgttagcaat tgtgatgtca cactatccaa gtaatcccat atacgatttg gtggctggga
    23821 cgaagcatag acactcaaat aaaacctcaa cacccggtga agacaatcaa gtgccatgta
    23881 gcgatggttc ttatcctgca tataaggcgc aaaattctct ataatgacca agaacaagct
    23941 tgaaaaagaa caatgaagtc acaggtgctc aacatacttg aaaaaaaata agctgctgca
    24001 gttacaactg cacatcaggg tttgggacgt gataattggt tccatgcatt cttacttaat
    24061 ttaaattacg aatacaggca aacttactct cagaagcttg tacagttgtt ccatgtgaga
    24121 gcttaaatta tgatgaaata taagcgggtc accgagacag agaagaagac tcacaagcgg
    24181 atagccaacc tattcatcca attatacatg ttaaggactg taatcacaag gtaggcatac
    24241 aaaagtgata ctaaatcaga ttgacgtaca ccaagatgtt tactctgttt ctccatccac
    24301 tggattagct gcactctgat gcgtccaaca gcctcatacc agagtgtcag tgcaggttct
    24361 gcaactgaag gaggccactg gcttttgcca ccatcggaaa gtggcgccaa gatgttagag
    24421 agcatattgc aaagcgcatg ataaagctca cttttacgtt tgtgtatatc ccggataaga
    24481 gggtttgctt ttgctacaaa ggaggcagac gcattcagcc caccctcact cttaacctgt
    24541 aaataaacat actgtcacgt tcactttctg aagcctgcct tttctaagat atctgagaca
    24601 taccccaagc ttcaagtaac gcatcccatt aatgatgctg agagtttcac ttcttgcaac
    24661 gcttgtatca atccggcgag tattgagttc catgaaaaac ctctccgtga cagagctgaa
    24721 tctgttagtg aaaattaaat aaatggataa gagtggttgt ggcttaaaat agatcatcac
    24781 tttcacaaat tcttttctgc caactaaact tgtgaatgga agtccacata ttcttttcat
    24841 ttatacttta gcatgcttgg aggattgata acttacaaaa tgaattacct aatacgggac
    24901 agtgcaccca ggagttgagc aaccaagtca agaaggagac ccctcaaatc gaccagcgat
    24961 gggtattcca cttggctaac aaccctgtaa cggagaagca cccagaactt agaaattcag
    25021 gtttttacaa ctcgaaaaag gaatgccaaa ggataaaaga agtgtttagc gaatcatata
    25081 aaattcaacc gttccagatt ctgaaatcac tacctgtcag cgttgattag ccaatcaaaa
    25141 acaaagttct caagtccaga ccatagcttc tctgccattc acgagagatg ttcttctttt
    25201 agcaaggcag taaccacatt ttgttgaaaa gaatctaaaa agagagacta acaaaccagt
    25261 gagcccttcc tgcgggcaac actccacaaa gcgaatgcaa gctgagcaga agatgcactc
    25321 aacagccaac tgattccagt aatgtaaaac catattttag aaagttgaaa accaatatcg
    25381 aaaattgatt aaataagcca ttaaaatatt agggttcata aatggaggta agagtactaa
    25441 gaaacagaga agtaagagta aaacagtctg gtcagttgga tctagtgtac atagttacca
    25501 aaaccccgag gaattgttcc tatgaagagt cgaaagaaaa tacctttctc tggaaagtcg
    25561 aggcatcatt tgcaccttta ggtgattcac tgcaagccac aaacaaacac aatattagta
    25621 atggtctaga gaagtggctt cacccaatca tagataacat ctagtcaata aattcaccta
    25681 tacgaagaaa aagtgataat ccacataaga attatgataa tgcaccaaag agtccaaaag
    25741 aaacactgaa acatagaaga tcaatgactc aaacctaaaa ataatgcaag atgtagaaat
    25801 aatagcctcg tgggagacaa ggtcttctag acgtatttca tacagacaag agtcagatac
    25861 catctaattg ttaagagaga gaaataacaa tatacccacc tttccctcca tctaagaaga
    25921 gcttctaaaa gaggaacagg tgtatgacgg gcaatcatag ccaatgaatc caacacctgc
    25981 tcataagcag gatctgatgg acgaaggtac tgtccatcct gcaaacatca taccaagaac
    26041 cacatcacta ccaaagagct atttaagaac aaatacgtat actagtcagt aagctacagt
    26101 cggaacagcg gcatttccaa ttcaatgtaa tacttccagt aaaccgtact caagactaag
    26161 tttcaactac tgagaatgaa actatctaat ttgcagatac caactcctta gagcactgaa
    26221 aacttaaact acctgactct atatggattc aaatgtgtgt taaaaaaaaa aaaaaaggct
    26281 tattgagaag gagaggaacc tgagcctgag ctgtctcgat tcgtcgtctt gcgagaggca
    26341 ggaaacgctg aagaagcgct tctactatca atttcgcagc actcccagac ttcatcacgt
    26401 tcagcaagaa tagatcctca aaagcgaaat gtcctctaaa ttaaattaag aaaaattcaa
    26461 caataagatt tatagacccg aatcgaacag aatacgagac tgaatctcgt gaaattttcc
    26521 cagaaataat gagaaatacc aaaggagagc accacgaatc acgaaatcat tctagggttt
    26581 agttcgtcga tccggcaaga gaatcgctaa gaaatttctt tgatcgacga cgagcttcct
    26641 cgttcctctt ttcttatttg tttttgtttt caatatattt tttttgtttc tttttttttt
    26701 ctgaaaagtg tttaacgtta agatgtttaa taaaaatcat ttgttaacta acaacattta
    26761 aggtagattc aattaaataa aacaaacaaa atacaacaag tagtacagta tagtatcaat
    26821 ctcgggatct tttgtctgaa actaattata tttttgtcaa cgtctcgaaa gtaaattaga
    26881 gaagctatat agattttttg ttttttcatt tcgcataatt gacaaaaaat ttacaagact
    26941 attaattacc atgcttattt tctttggatt ggctgatttt tgaggtataa actatttcga
    27001 ttctcagctt tcactcccag acttttgggc ccttaaattt ccaccatcaa ctttcatatt
    27061 cctcaaaatt acatcatcta ctttcgaatt catgcttaaa catacatttt caattgaacc
    27121 attcatttaa ccgggattaa caacaaatct gcgtttactg taccgcgatt gcgattaacc
    27181 cgactaatac ccagacccat taagaaaacg acgtcgtttt catttcgttt aactcatcaa
    27241 aaagagaaag aaaacgacgt cgttttcatt cttctttaac tctcaaatcg atttggtcgt
    27301 tcttctttaa tctcgacact gtgaaattag ggttcttgag agagaaagac aaaaggggat
    27361 ttggagtttt cttcttcgat tcgaattatt gggtttcgat ttgggtttcg aatagggaga
    27421 aatgaagaat tggtgggagg aaggattgat ttaccaaagc gatccagatg accccgattt
    27481 cgaacctcca gagagtgaca ttgaagccga cgatggaagt gatagtggtg atagcggagt
    27541 cgaggaggac gaagccaccg gagttgaggg agacgacgtt gggatagatg gagacagaga
    27601 atctgatgga gaggagaata gagaagacga tggtgacata gcgtctgatg gagacgtcaa
    27661 tctagaagac gatggagaca gagatgaaag tcaaaagaag aggacgagag aagagaaaag
    27721 aaaggaggaa gaggctgaag aaggtcaaaa gaagaagaga aaacagaaga aggatgagcc
    27781 ggaagaagat ttggccgaga ggtttgagtt cgagatagag gaagcagtag ctatgtggta
    27841 tgatgagtta aagattagaa ggaacgaaat accagaaagt aataatgaag aagaagatca
    27901 tgtgatcact agagataaga agattaggtt agcttcggat gataggttag ctataggcag
    27961 aacattcttc actggttttg aattcaaaga ggttgtcttg cattatgcaa tgaagcatag
    28021 gataaatgct aaacaaaata ggtgggaaaa ggataaaatt agctttagat gtgctcaaag
    28081 gaaggagtgt gaatggtatg tctatgcctc atactctcac gagaggcaat tgtgggtttt
    28141 gaagaccaaa tgtctggatc attcttgtac ttctaatgga aaatgcaagc tgttgaagag
    28201 gaaagtgatt ggtagattgt ttatggataa gctaaggttg cagcctaatt tcatgcctct
    28261 tgacattcag aggcatatca aggagcaatg gaagctagtt agtactattg gacaagtgca
    28321 agatggaaga cttctagctc ttaagtggct gaaagaagaa tatgcccaac agtttgcaca
    28381 ccttcgaggc tatgtggcag aaatcttgag tacaaacaaa ggatcaactg caattgttga
    28441 taccattagg gatgcaaacg agaatgatgt cttcaaccgg atttatgttt gtcttggagc
    28501 aatgaagaat gtgttttact tctgtaggcc tctcattggg atagatggaa cgtttttgaa
    28561 gcatgcggtt aagggatgtc tgttcactgc tatagctcat gatgcgaaca accaaatcta
    28621 tccagtggcg tgggcaactg ttcagtctaa gaatgcagac aattggctct ggtttttgaa
    28681 tcagctgaag catgacttgg aactaaagga tggcagtggc tatgtggtca tatcagatcg
    28741 ttgcaaggtt agtattatct tatgtctaat tgtttaatta tgtatagatg atagtgcttt
    28801 atagatgcta atgtgtttgt atttgacagg ggattattag tgctgtcaag aagaagaatc
    28861 aagagattaa ggtttgtttc tgttttaggc tgctgtttgg ttagccattt tggtgctcat
    28921 gtttgaatgt tgtttctgtt ttaggaggct ggaacatctc agcctacaat ggagctccaa
    28981 gaaacaacac atggagctga tacaatcaca ctcactcaga gaagcagtca atgggatcaa
    29041 tcggaccagt tggactagtt ctagttctca atcctctttt gtctattttg gaacaatctt
    29101 aacaatcttc atcctctttt gtctattttg gatgatgtat tattcggtta atgtttagga
    29161 tgttctttat cctcttgagg ctttgtagga tgatgtatta ttcggttaat gttttggatg
    29221 ttctttatcc ctcttttgta tggattctta tctattctta tgttatgcat cgattcacat
    29281 tagacaaaga cacataagac ataacataga tagattcaca aaccctccat cgtttaatct
    29341 cgacacttac acaatccaaa acaaagacaa acatagccaa acccctacaa gcttcaaaac
    29401 agagactaat ccaatactac aatttcactc caaaacctca acaacaccta cactcttccc
    29461 caaagccata caatagatgc aacaatcaca acagcaaccc ctacagtctt caaagctgac
    29521 tttgccatga catgtcctac ctagctcttc cacattctcc ttcatggtca agagttcacc
    29581 ctccatcttc ttaatcagct cttcctccat ctgcttagcg tttttattaa ggagctccat
    29641 attaaccatc acgttcattc tgaggtcact aatattctct gcaactctct tacacttctc
    29701 atttaccatc ttaatttcgt ccaagagagc ttcatcaacc catttgaaca agtgctcttc
    29761 attttctctc tataaaacag aatttccaat catttactcc ttcaatcaat caaatatatc
    29821 acaaaatcga aaggtgtacc ttcattgcta tcgcacaacg gtagaatctc cggtatggat
    29881 tctcctttgt tttcgatgtg aatgtaatga tctcttctcc acaccaacat ttcgagggga
    29941 caccaggagg acagacacga aatcctgaac tggaagcgga tgagtagtag ctgttggtgc
    30001 tcattttctt ataaaattgt cgaatgaaga accctaatcg actaaatcga ttttgcagaa
    30061 gaagaagaat gaaaacgacg tcgttttctt tctctttttg atgagttaaa cgaaatgaaa
    30121 acgacgtcgt tttcttaaca ggtctgagta ttagtcgggt taatcgcaat cgcggtacag
    30181 taaacgcgga tttgtggtta atctcggtta aatgaatggt tcaattggaa atgtatgttt
    30241 aagcatgaat ccgaaagtag atgatgtaat tttaggaata tgaaagttga tggtggaaat
    30301 ttaaggatcc aaaagtccga aggtgaaaac tgagaatcga aatagtttat ggctcgaaaa
    30361 tcagccaacc cattttcttt taataagtct gtggatgtgt tggcaaaatt ggtttaagcg
    30421 atttgtcgct ttaatgctta tgagccggta cgtttccgtt gagctgatga ttacagattt
    30481 tgattttaga gatttgcaat ttgtgttgaa gaaatgaagt ggtttccgac gtttattacc
    30541 atagccttaa gctgttattt ctttgtggag cttcgattag tttttccagc taaaattcca
    30601 agaaaataca tgtccgattt tattatcggt ggtgatcttt taccggaatt gttgctctga
    30661 cggcgaagga tgttatcgga atactttggt tactcatcta acacgtgtta tgttgttgac
    30721 acgttcttaa ggatggagtc aaattgaagt tttcttcttg catcgacatt tctcttttgg
    30781 gtctgataga tcttgttaac atctgtaatc gggcttttga agtccatttt gtatgtttgg
    30841 tttgtttaat acaatatatt acacttatgg gaaaaaaaac aaaaaaaaaa acagacgtgt
    30901 tacatatata ttttcaatct atattttctg tgaaaaaatg gcttccacca attcagtttc
    30961 tcagttaata gtagtaatcc atttcgtata gtgaacacca gtcaaggctt gtggtacagt
    31021 tcttgctatt ctacagtgta ccgacgggtt tacacatgac atcaaatagt ttctaaccaa
    31081 cttccggtac tcccaaaccg ggatttctct cagatcagaa gctacaactc tcatctcagg
    31141 aggtttcatt aagcttcgtc agcacaagta aattcaaagg atttcttcta ctccttctct
    31201 ctgtctgcgt ctctgtatac aaaacccagc agcttttctt ttgttctggc ccttgcaaga
    31261 agtttgtctt tcttctcgtc catctaacac gtacagctca agccttgggg ttgatactat
    31321 gttctgaaag aatattgttt cttgagagct tcagagatgt ctgagaatct tagtggaaga
    31381 cattactttc tttatcagtt gaagaaataa ggtgaatcta acaccacttt taaatccaaa
    31441 tctcctcgtt ctggcagagg aggaaagtct aaatgaggaa acgattgctc aaagctctcc
    31501 agcaactgtt aaaaagggaa caaaaaacaa actcagttca tgaagcagtc ttctacatgc
    31561 catatatact gaaccatttg aacatatgac acttacattc tctagtatcg gttgtgaata
    31621 cagctcaaca aacttttccc gtagtattat gtttagttta tccacatcac acgcatgcgt
    31681 ccaaaaagag tcatgaactc ctgttagaat aatttttaca tgccatgtgt taattgacac
    31741 aaagaccaag gttaagaaga agatggaggt ccaaaagatt taacttgtga aaaaaaggac
    31801 agaacctgca aaacacacgc ctgctctttt acaggcaacc gcagtcatca tcatatgaga
    31861 cccatccagg gagtgaataa aatttggagg aaaagctgtc ctttgtcgcc tcacaatgac
    31921 ctacaaaagc ccacgaaact cttttaggaa taggcctctg catcgtactc tgtttcctta
    31981 cttatctttt gtttctatgt aaaaccaagg taaagtggaa gcagacctga tcagtttcat
    32041 gctgaagcga tagggtctgg agggatgtct ttacctgcat tcattttgat agaaagtgaa
    32101 aacagtcaca ttcagattca acagacgaga gtaatggtgt cagtgataac ttttaggaag
    32161 acttacgagt tttgttccca tttggtggta aggttgtaca acaggaagac ccaatggggt
    32221 tgtccatcga actgtttcat tttctgaagc aataatctgc tcatgaaaat tattaaggat
    32281 tattaaaagt ccaaaagcat atttaattga cgctggaaaa aagtctacac accttcgcac
    32341 attcaccaaa ccaacgcatg atggcgcgtg cagcttgaaa catctcatct atagcagcta
    32401 atgttacctg ccccaaacat aacaaaacaa aagattatcc cctcatagca tttttacttt
    32461 tgagaagttt ccaacgtaca tgagaactag aaagtagtaa ttaatcattt gttaaagcac
    32521 acgcgttctt tgaagattag atgaaggaaa ttgccaaatt aagattttct agtgccagtg
    32581 ctttatctgt tgctaatata cctttgctgc atagcaagca gccccaaaaa cttctttttc
    32641 atcaccaaaa tcacttcgtt ccttcaacct tctctttatt tgatcccgag cgccaatgta
    32701 ggtgacacca tagactgatg tcataaccgt ctgctttaca agcttacgat ccacctacag
    32761 attttgaaca accgtcaaca agttgtatca gctgaccagt tatgtgaatg agtaaacaat
    32821 gtacccaaac aaaacagata tcaggcaact tgctcacatg ccaatactac tacatataca
    32881 ttagaacggt tcattaaaat ttattggtga tttaacaatg ttttttgagg atgtaatgta
    32941 tgagatttct actccactat gcaagcacgg aagcggaaac cgagaaacac aaggttagga
    33001 caatggaaaa agaatgaaaa gaatttcata cggacctggt taagtaattt tcttgcacgc
    33061 aatgcctctg gaaaaacttc aggatctctg tctgcatctc ggcgcataat atcaagaacc
    33121 ctgcaggtat atgcatatga aattttgaat ggacatttat ttactcgatt aaacttaagt
    33181 tagctttaag cagtagatgc agagcttacc tggtagctat tcctgaataa acatctgccg
    33241 gcttctcacc tgcaactaga ttaacagctt ctgctcctaa ctgataatca tcttataaaa
    33301 ccataatcag taaagaaaga tgacaagcag ccaacaaaaa gaaccataga agattaaaaa
    33361 caagagaatt actgtgtctc tcccaagagc ggcataatgc tgtaaaccat tgcaggaacc
    33421 atcctggcca gaaccaaagt gaaggaaggg aagttcattt gaagaaacac acagattgaa
    33481 cgagaaacta caacgtaaag tcaaaaaaaa attgaagcct tcaggagaag atgccaaagt
    33541 ggcaacttct accagaaagt acctgatgta taggaatatg tgacagaact gtctctgggg
    33601 atgggcttct cagagcttca gtcagactta tgcagacagc caagcactga aatgggtctt
    33661 cagcctgcag ccaccatctg cttccttcaa gtggtctgtc tgccgaatca aatatgtcat
    33721 ccaagtgatt ttcagtgaaa gctagccgtc catcaagtga taacttatct acaccaccag
    33781 catacaagtt tgctaagtgt atcttcagcc agcgtaagcc tgaaattccc ataggccttc
    33841 cctcagcaaa ctccaaaaca ccccgacaca aatcagagcc aagatgattt aagtgtgggg
    33901 gcatgggata tgcacgaccc cggaagtcca tattgtgggg atagtaaaaa gcttcctcat
    33961 ctttcatttt ccgtgctacc tgctcacatt taaacagtta tgaacagaac tctcaaactg
    34021 gcacattact ttaataacaa ggcggataaa gctcaccgaa agcttgagtt ctgtgtcaca
    34081 tcgctgagaa tgtctctcgc tgttcacctt tttagcagat ttgacttccc acttccattt
    34141 cttaagaatg ccctcatctt cagtatccgg cttttctggt aaaggaacct gcagtttgaa
    34201 attaaagaat taaagaggcc tcgtgatgca caagggatag aaaatatgtc tgcgccaaca
    34261 ataactaatg tcaaactgtt gtacagatga aaaacagtag ccattataag atcaaagtaa
    34321 cacatggagt aactcacatc actccgatcc accatatcag caacacatcc gccactgctc
    34381 catatcctat ctacaaccgt taagactcgc ttatttactc tccatttagt acttccaagc
    34441 gtatccaggg cctaaaaatg tccataatat atttacagaa attaaaactg taactgattc
    34501 ccacataacg cacgtgaaga aacattaatc ttctacctca aagactggtt gtagttgtcc
    34561 tttaggtgcg ctcttaagtg cctctctttg ttgcttggct ccatgagttt tcattatata
    34621 agacgtcaag aacaagtaag cacctttgtc atatctgcga aacacaaaat aaaagtgaaa
    34681 tgacttacat aagtttcacc aaaagtaaag tattacaagc atcttatgaa gaaatgttga
    34741 cagttctcga agctatacaa atctaaattt cctttctctt aaacttagat agataagctt
    34801 taaggtttct gtcttctctg agtaactaag ctggccacaa aagaatgtac atttttaatc
    34861 atactgaatt cattttggaa tttatgtttg agataccatg caatgcaatt atttaatcat
    34921 ttggggtaag tatacagcaa agaaagctca tttaccccga ccatttgaga ggaggaacca
    34981 gcattggcat gtatggcatc actgcatatc tcccctgcac cacaaagaaa aaagcgacat
    35041 tcacatttcc aacaatatat agattagatg tctcagttat accttagtct tcaaatccca
    35101 gaaatattta atctaattta caggggctac ccaagtcaaa ccctctttag atataacatt
    35161 cgacaaaatg accataataa atgactccga gctctgaaaa agagtcaaca ctatttttgt
    35221 cgattttggg ttaaatttgt tctgataaca aacaaaacgc gaatagatca cctacacttt
    35281 tttccaagcc tttgcggacc aaagggtcac actcgattac accatatttt ctcccagaat
    35341 tcctgttgta caagaaagac tggaatatga gcctatgaca ttcagggcaa gaagataagc
    35401 ctagttgaaa gtcatagacc gaaatttctc acatgcttcc tttcgctacc ttgaaggtat
    35461 gcacaaatgc aggtcggaca tcaggcagat cattatcctg ctgatcagct ggagactgta
    35521 tataagctgt tcttacgagt aactctatta gacgacttcc aacctggaat atatattaga
    35581 aaatatcaaa atattagcaa cttatgcagc caacataatc tttctacctc tccaacaatt
    35641 ttgcagccaa gcataaacag accttagccc taacatctgc gatccatggt ttcgtatagt
    35701 catgtgactg caagatcttt ctaactgctg acaacttctg tttctttatc aactcattga
    35761 ccttttttct taacttatct tgttccttca tagaagtttc attttcaact cccccactct
    35821 cctcattgtc atcccctttt ttcttcttat ccaagaatgt gcatattctt atctatcaat
    35881 tcacatagag aaaaacaaca ccattagaat acaaaccatc caaaacacca tagagaagat
    35941 caagacaatc aaggaaccct aaaggctaat aatacaagag aaaatattac ttcacacctc
    36001 catataaagg ttgtttttat atgattaatt acaactgtaa catgctaaaa tgaaggagtt
    36061 ccattcacaa atagtgaata ttttatcaat atcatgttcc acatattaaa gcaatcggtt
    36121 ttgctttaag atcaggctaa cagttccagt atccagctat ggtatacata gagtttaatc
    36181 ctcaatggtt taggttcact agtgagggaa acagtttaag agatcaaatt tcccactata
    36241 ccggcaaacc aagaaaatta ccggcagatg atatgatata attatataaa caaagtagaa
    36301 accagatcaa gatgaagcta cccaacctct tgttcaatgg catcgcctac tgtacacgca
    36361 gcatgaacaa ccttaacaca accgttatca ccaccagtca tcaaatgccc catcaacttg
    36421 tgcattgtaa taacagatat cttgtcggca ggcaactgat caaggtaatg tgcataagtt
    36481 gctttgctct tccctaatct atacaactcc tggtctttag caattgcatc tcttaatggt
    36541 tcgaaccaac ccagaaataa agacttcaca taaggcagat taggcgcaag cttttgctca
    36601 cacatatctg tcaaaagctc catgtactct gcagcagctc tttcccattc ttcagtctcg
    36661 atcttaactt gtcttctcca taaattctgg aacttggtac gacccattcc aaattggtct
    36721 tgcttcttca tccgccacga acgatgactt tctctcttct tctctttctt catctccttc
    36781 aacaattcat ctacctcagg ctcttcctca acatctgttg ataagacctc ctcttcggct
    36841 acactcgtgt accctctagc caaagtccca ctaaggcacc tctcgctctt ggaaaactcc
    36901 tctcgcctcg tgatcccact taaacaacga aaaccctttc cgtgacatgg tgatcccaag
    36961 accggaaacc gaaagctcaa atttttcgag aaaatagact ccggagaaga cacaagaagg
    37021 ccacgagttt gggaactgac gtttaatcta gcagctgacc tcgaaattgc ttgtttagca
    37081 atgtttctcc acatggggaa ggattgggaa actgggtttg gagaagaaat aaagggttta
    37141 tgcaatggaa tcaagtgatc gaatacctta gtctgatttg ccaagaacag tggggtttga
    37201 gcactggaca tcaatcgaac ttaaaaattg agtaaaatcg ataaaccaga acaataacca
    37261 actcgagatt gaataaattc gatcgcatga gcaaagaaaa atggcaaatt gggaagagtt
    37321 tcatagacgg aagaaaataa aaacaaatgg tgagtgaagc gtacacgacg aagccgcctt
    37381 aaaccctcgc ttaaaaaccc ttgctttctt aagcctctgt tttttttttc tgggttgtct
    37441 ctgtttctca catgtcaaac aattaaaaaa taaattaaaa atatctaccc taaattcgac
    37501 ccgtatagga ggatcttacc cgacccggga agtatctgat taaggcctct aataacggcc
    37561 caaagtctct ttactatgca aaaaggcttg acgaatttat ggagcccaat tagttaaata
    37621 tatatataca aaatgaattt tattatagtt tcttctatta tttttaccat ttcatacaac
    37681 tttttagtgg aacccaatta atcaacaaca aaaaaaggtg gaacccaatt acaatgccga
    37741 atataattaa aatatttaga tttttgtatg aataattcac ttggatttta tttttttggt
    37801 caacaatatc aatttgtgtt aataataatt attctagtct attatttgta aataaatttg
    37861 gactaaaaat ctatttttct tgggatgtgt cgactagtgg ttgggttgct agttgtgttt
    37921 caccaatgat aactcacacc tgattattcg ctccaaattt gatcgtttcc acctcatagt
    37981 tttaatatat taccatttaa ccccttaact tttgtctgag aagtaacaag cctgatttgt
    38041 ttcctttcct cggaactgaa gctacaaaga aattgtatta ggtctctctc tctatctctc
    38101 tcttcttcgt gttactaaaa aggacgaagc ttgttgcata atatgttgag gtaaattact
    38161 aattactgat ccaaagttcg aatctttgct ccaactccag gctagctgat tgcgtagctt
    38221 ccgattgatt tctacctgag ttttgagttc ctttgtggcc acttcgttgt tcttctgctg
    38281 ggttttttgc tcgaggatct gatacttctg tttggtcgat gatcgagtga tcttcgttgg
    38341 gttttgggga tctaagtcgt ctatatagct aatggtttgg atttgagttt gaatggagcg
    38401 tttaggattt tggggattgc taatgggtag tgtggaaaag tcattggatt ctggaaattc
    38461 gttggcttgc tctgcatctg ctaagaatgg agacgaagag agtagtactt catcgaagca
    38521 agtttcacca ttgaagggtt ctgggtcgag aaatactagt cctttaggtc gagttgggtc
    38581 gagaaacacg agtccttcta ggcagaaagt ggtgaagacg aagcctcgtg gtctagagga
    38641 agaaacagtt gcttcatttg gtaaacaagt tgttgctgat gtgcagatgg aagatggtat
    38701 atgggcaatg cttccagagg atttgctcaa tgagatttta gctagggttc caccgtttat
    38761 gatatttcga atccggtctg tttgtaaaaa atggaacttg attcttcagg ataatagttt
    38821 tctcaagttt cactcaaatg tgtcatctca tgggccttgt cttctcactt tctggaagaa
    38881 ctcgccgcag attccgcaat gctcagtttt tagtttgcca ttgaagacat ggtacaaaat
    38941 tccattcacg tttttgcctc catgggcttt ttggttggtt ggttcttcag gtggtctcgt
    39001 ttgtttttcg ggtcttgatg gtctaacttt cagaacttta gtatgcaatc ctctgatgca
    39061 gagttggagg actctaccga gtatgcacta taaccaacaa aggcaattga ttatggtcgt
    39121 ggatcgctca gacaaatcgt tcaaagtcat agccacaagt gatatatacg gggataagtc
    39181 acttcctact gaagtttatg attccaaaac tgacaaatgg tccttacatc agataatgcc
    39241 tgcggtgaac ttatgctcct cgaaaatggc ttattgtgat tcccggttat atctagaaac
    39301 tctttcgcct cttggtttga tgatgtatcg gcttgattca gggcaatggg aacacattcc
    39361 agctaaattc ccgagatctt tgttggatgg ttacttagtt gctggaactc agaagagatt
    39421 gtttctcgtg ggaaggattg gcctctacag tactctccaa agcatgagaa tatgggagct
    39481 tgatcacaca aaggtctctt gggtagagat aagtagaatg ccaccaaagt acttccgagc
    39541 acttctgaga ctttcggctg agaggttcga gtgttttgga caagataatt tgatctgctt
    39601 tacgtcttgg aatcaaggaa aaggtcttct atacaatgtg gataagaaaa tttggtcttg
    39661 gatttccggt tgtgctcttc agtcatgcaa cagccaagtg tgcttttatg agccaagatt
    39721 tgatgcatct gtcctctgaa caataagtta tcgtctgtct cacatcattc ttgaaaactt
    39781 acaagttcgc cagcaaaaca tgtcagaaat atgaaatcaa agagggtttg atgtgtacct
    39841 tcagtgttaa tgaagacctg gtcagcaatg atatgcttca ccaatggtta acaatatcga
    39901 ggagaaaaac tgtaagataa acttgtttct agctttctgt aaattagcat tcactcgata
    39961 tgaaaacttt ctcaatatcc cctgtctcgt ccgcgtgaaa tatatataca cttaatttta
    40021 gtttcctgtg ctgaattttc cttttctata tcgtaaattt aagcttctct ttgcaaatag
    40081 tgactgctag ttcaagaata tcttgttggc taacacttat gagaatgaga aagttttaag
    40141 ttataacatt ggaatataga tgtgatctta aacatttggg caattggtac atacaaatcc
    40201 catacttaat gtcttctaac tagaaactag aaaaccgagg agactcttga aatggggagg
    40261 taatctagct ttgagataca tttctctaca atttagctaa ttcatagaca ctgatagggt
    40321 aggagtagtt tgcagacttg ctgaaggtat tgtgagctat tattttgttg gcagtttctg
    40381 ttggatgaaa tgcatcccaa aagacatatt gattcctatc caagcaaggt tgctgcaatg
    40441 gaaggcatgt taaggctcct ccatatctcc cgttaccgca gcacgcttcg tttgatacta
    40501 caagacctgc aaaaagaaga actaaaactc agtactgata tatagaaata agagtaaacc
    40561 cttataaata gggattgagg tcattttacc atatctagaa ggattcacaa ccatatcatg
    40621 aaatagatca aagacgtttt gatagacaaa gaaagatcct ggcagagttg tgttgagagt
    40681 atttgctaga tctttcagac ggctattgaa cattgaaacc atattgttga tttttgtcac
    40741 acacccgctg gtgttgttgc cagttaccat agatagctga ctaggtatgc aacctaatgg
    40801 tcctgaccca gctaacacca tttttcttgc acctaagttg tatagtctct gcaaaatgtt
    40861 tgtaaaagaa cacagttttc actttctgag tatgagatga atatctgcat cactattgtc
    40921 aattttgtac taagagatga tgggagagtc ataaaagatc attgacttac ggatatttga
    40981 gctgagagag tcttgatcaa gagatctgca taatcttctc cactgtaggt ttggctggtg
    41041 gagtatctct caggcataag gtagttgttg atatagtcat tgcttcctat attgatccca
    41101 attatcgatt ttgcaagata ctttctcaga tctgcagggt tttgaaagaa acgccggagg
    41161 cgtaactcga tcgtaatctc aaactgcgat atctgtccat taaatgtagt tcttgctccc
    41221 tggaaaaaca gaggtaaatg aacctatatg taagaagaag aaaaggtttt aaaatcttta
    41281 ttatgaaaga gtttaagttg cttgaccctc acataatgtc gaccggtttc atctaaaatc
    41341 ccagctgctg cagatgcgta gttaacccct cgtaaggcat tttgcccaat ggataaagga
    41401 gataagtatg gtggcaccaa tggcaagccg aggtacgttg ctacattacg acaaaattgt
    41461 gagaaagtta agttaaaaat tgtgaaacca atattatgat ctttagtctt tagctgtacc
    41521 tccataatca acaacggtac ggccattgca gaaacgacca gtggggaagc caaaatcaat
    41581 tccataaggg aaataattag ctcgtgcaag agttggaatg taattgttgt ttccactatc
    41641 aactaaagaa tctccaaaga caaagaaagc tggagcaaga ggttgatgat ctctagattg
    41701 gccattgcct aaccagacaa gctctaacaa cacaagacaa atcaacaaac ttttcatgct
    41761 tggttactat ctttatctct ttctctgttt tgagttcttt gagataagct tatgaagaaa
    41821 acaacgctac tacatatctt tatggtgata tagaaagaga catggttacg tgacataaga
    41881 gaccgtgttt ggttcagagg aactggtcgt ggtaaatgat ctcatggagt gtagtggtta
    41941 actgttactg ttctgaaaga tttgtatttt ttctttttct catttactgc ttcttttatt
    42001 ttcttactct attcgtcttc tttttgatag agacagcttt aagaaaaagc caacctctaa
    42061 acctccttat ttcgtaaata tgtttactag tcattgatgg ttttgctcat agcttctgaa
    42121 ttctgattga aatataaaag tgaccactct gttatgtaat gatggttttt cagatgtgtc
    42181 taaaccggct tatagtttat gataaccgga tggatgtagc tagtgtaatg ggcccttatt
    42241 tgagggctga atcttcgggt ttaggtgaat tttcatgatc catctatgtt tcattagtta
    42301 atatcatttg ggattagtat tttgtacttc ctacgaatat taacagctag agtatcattt
    42361 gaaaacgtta gttaaatgca tagtaggatt attttttata acaaaagtat taaatttgtg
    42421 aaggttttca aggaacggac cagaatcgga gaactcgtcc tcgtgtctca aaaagaatat
    42481 atcaatttcg atgtcactac aataataagg tacaatatat ttcattagaa atggtccaac
    42541 aaagcatatc atttagcaaa tcgatggtca agggatcttt cttgggtaaa atacaaaaac
    42601 aaaaaagatc agacttattt agaaacccta agcaaccaat gttattagtt ttcaatcaag
    42661 caactaatca agcttttcat tataaagata gctttgaaat ttatatatca actcggaaat
    42721 atttcaagaa aatatgtgtg actgcaaata atcattccca aatgaaacaa gagttgattc
    42781 gaaataaatg aaaaagcaat ttcctatcgt gaaaaatgtc tccagttttt cgaaacagtt
    42841 atgtggaata tggatgatgt tttagtttct caataaaata cttctttagt taataaacct
    42901 cctttgcaat taccaaggag aagtatcttt ttgtcggaaa accctagcta gcctcttgtt
    42961 tctacaaatt ctataacatc cctatatttg tataatatcg aaatcaaggt caagtattga
    43021 agaactgata aatactttac aaaagcaacg caactacttt tcagtacaaa cgaccaagga
    43081 tataatatga agaagacgag tttgaagtta atgaccctcg ttttagggtt ttgcttcgtc
    43141 atttatcttc ttcaagggcc tcgaggtttg aatctactca ttcttttgat ggtcatatga
    43201 tgttgatgtt gatgatgatg atgatgatga agatgcatat acatatactg tttacttgca
    43261 tggttctaat atccttgaat atgatatatg tttcttctct tcgtacatgc atttatgtaa
    43321 ttgttgcatt ctcacaagat ccatcgtttt agaataaaac tttaaatatg ttagtgagtt
    43381 acaaatttta ttttaagacc tgtagtctta acaattatat ttataaatgt aggcggttcg
    43441 agaaatggag atctcttgat agcacgaaag gtaatgacac atatcgaaag ttttgagtta
    43501 aattaatatt tggttttatg tttgatcatt ttcattttag gattcagtta tttgtcagag
    43561 aatcaacgtt gattcagcta tccatattgg aacaatttta aaaatgaatc atcatcaata
    43621 tcttcttctt agatttggtc tattttccgc agttgatatc tctggaaccg attgaaacaa
    43681 aaaatgcagc gagatcgttg aaagattcaa tatcaacaga tttagaggaa gaggttgatc
    43741 gtctgatgga gcacgaatat ccttcaccag taaagccgag gaaaagaact ccggttcaca
    43801 atggcgtgcg taatcgtcac taattgaccc ttgttctatt gttctttcaa ttagtagttt
    43861 aataagtttg gtaaaatcat aaaatggacg tatcctgtaa tgctgaatat tagtatatta
    43921 cttatacaaa gactttatca actatttgga gtgcttgtat tttttgagat ttaaaaaaaa
    43981 atctcattgt tttggagata tttaaaattt tcgaaattag tatattccac ttacatatac
    44041 ttgtatataa atattgtttt atcattcttt gtacttctta aatagatcgg aaaactagat
    44101 cataacccgt gttatacagc acggacatta atattttgta taaattaaat tgtatacttt
    44161 gtttgaatta cataagaaat agtatagtat aaaagtgatg ccataatatt tttcaatgtt
    44221 ttactattta catataatgc attagattga ctttgtttaa aaatgttatt gttataataa
    44281 atacaacata tgtagtttta agtaaatgtg taaaatttgt atagaagtta ttttggtaag
    44341 aaacatgttt cctttgtatt agaggatcta atttttggtc taatttagaa ttagtttttg
    44401 tatagtattt tggttatatt tgtggaccta attggggcct atattagatt atctttaata
    44461 gggctgacga aaaaacggac ccgataacca actcaatact cgaaccaaaa aatcgggtta
    44521 gggcgggtta aaattttagg aaatttcctt attgggtaga gttttagtaa acccgtggat
    44581 atccgattgg accggaaatt acccgttatc taaaaagagt attcaaaaac ccaaacatta
    44641 atttaatatc caaaatatta attatatgat attattttat ttgattttaa atatatagta
    44701 aaatgcgagt tgtatatgtt ttcttgatat tatttatatt gtttagtgtt taaaattata
    44761 cacttgtatt ttgattgtta attttagagt ttcacctgta atataccatc ttatattaat
    44821 atcgatttaa acccgtcaat tctaggattt tccagcttgt attaaaaatt gaatcacatc
    44881 atacacataa aaaaatctaa tatgttatta attattgttg tatataagat tataaattct
    44941 taaaataata tgcatgaaat tgaatataat atttaaatta tgacccagta cttagtaata
    45001 aattttctta aatctatttt tgacccgtta taatattttt tcatgtattg aacagtttat
    45061 attcgttttt aaaagtttaa attatggcat atgcgaaaaa actctaatta tttttttata
    45121 acgatgatat tattttttcg caaaaataga atcatataaa gatgagaggt gaactataat
    45181 aattaataaa aaattaatat gataatttag atatcaaatc taatttgttg attttaattg
    45241 gttaattttt tggaaattaa taatgtattt cattttttaa tgaaatttaa ttaattaaat
    45301 tagtatttga ctttttaatt tttaaagaga tgaattaatt tactctttaa attttatttc
    45361 taatggcata cctatgtaat tacttaaaaa aataaggtta tatttaaaat gtatttccca
    45421 aataatatag taggataaaa gtgttttgtc atggaagtag tgttaattac tttgaattac
    45481 atttcacacg agaatacgtt aacaaaaaca tagttttatg acatttctct aacttttttg
    45541 gaattaaatg tggacataca ttacttgtat atattttgat gaaaaaaata aagcaaacca
    45601 agttggattt ggtcaagtcg tcagttctga actatatcga ataagaaaac tcaattattt
    45661 attatcattt tgcataccaa cttgaagtac aacttttttc ttcattttta tgtctttggg
    45721 tcatgcttca aaagttcaaa tcattcacct aaacaaataa aaaggtaata taaactccat
    45781 ggtttagcaa taactctcat tttgtatcaa aattagttaa acaactgtgc aagagagctt
    45841 aaaatatcac atgtgaacta aacaaaatag cttaaaggat aaaattatta gaagatacta
    45901 ttttagtaaa gataaaatgt gaataatata tgggctaaat ttataatgct aaaaagtatt
    45961 aagcctacca aaaagtaata gttacaaatt aaatatttca gaataaaatg attttattaa
    46021 acgcgctttt aaagcgaaca aatattcttt cggaccaaaa aaaaaaaagg aggaagaaaa
    46081 aaatgttgga gttagctctg tttctttgtt catcagttta ctttatggac gaggtcctca
    46141 tgtagatttg actttgtttc aaagcggagg aagaaggaga aggcaacact aaaagatcaa
    46201 aaccttagat ctttgcttac gctttcgcct ggttaggtaa gtgtttaaga atgttcaatg
    46261 gctttatgct gctcctagga ttttgatttt gcaattctct tggttggtaa aaaaggcttc
    46321 tgggtgtttt tccttcttat ttcgagattt gatcgaaccc acttgatttc tatcttgatt
    46381 agttggtttt actagtgtta cagaacaatt tgtgattttg ggctttgatt ctctgcgaat
    46441 atagttgcgt gttagctcta gggtatcttc tagcaaacca aaagtgggat ctttggttta
    46501 tcatggagat ctcgatccaa tttcggttag aattcaaaga aggaaaaaat tgaatctttg
    46561 agaagctttt gttattgagt taattcagtg atgatcctat gcttgtgatg tgtgaaaatg
    46621 tttttgttgc ttgtccttgt cttttgtata aatcactgag tagcttcgtt tagtgtctca
    46681 ccaatgattt aaccttggtt tgctagttta ctgaacatgg agtacaatgt ctagatggag
    46741 ttggaattgt atgtctagta ataatgtgtg taatgcttca tgatgcaaaa ccttgctttt
    46801 gaattttttg taggaacggt ttttcagaaa caaaagattc catttttaga ttcaattccc
    46861 ttctggtttg aaaaatgata tcaaaatggt gaatagaagt gatttggtgg tgattggcat
    46921 ctcggttggg cttgcacttg gtctcttgct cgctctgctt ttgttcttcg ccataaaatg
    46981 gtactatggc cgctctcacc tcaggcgatg cgctaatgaa cagaattccc cgactctacc
    47041 tgttcacact gctaaaagag gtgtagtaat ccctgatgat agagcaaaca cagaatcgtc
    47101 acagccacct gagaatggag caccaactca acatcagcca tggtggaaca accacaccaa
    47161 agatctcact gtatctgcat ccggcatacc tagatataac tacaagtgag tattcagtct
    47221 gaagctttag tttgcgtgaa tttgttattg ggttgttgta gcttatggtc tgaaacttct
    47281 ttagggatat tcagaaagca acacaaaatt tcacaaccgt tctaggacaa ggatcttttg
    47341 gtcctgtcta caaagcggtt atgcccaatg gagaattagc tgcagcgaaa gttcatggct
    47401 ctaattcaag tcaaggagac agagagtttc aaaccgaggt aagtgtacag atccactcat
    47461 ttccctggtc catgcacaat ggagataaca gagcagtatt ggtttcttgt ttccaggtat
    47521 ctttacttgg gagactgcat caccggaatc ttgtgaactt gacaggatac tgtgtcgata
    47581 aaagtcaccg gatgttgatc tatgagttca tgagtaatgg aagtttggag aatcttttgt
    47641 atggcggtga gtcgtccttt gttttcttct atcaatataa gacgcagcaa gaaattaatc
    47701 acaagatttt ctactttact tttcaggtga aggaatgcaa gtcttgaatt gggaagagcg
    47761 gcttcaaatc gctcttgaca tctcccacgg cattgaatac cttcacgaag gggccgtacc
    47821 gccagttatt caccgtgatc ttaagtcagc aaacattttg ttagatcatt ccatgagagc
    47881 taaggtaaga gagcaaatat ttaatacgct tactcaaaac tgtttggtta aaccttataa
    47941 aattttggtt tttttttttt cttgttggta taggtcgcgg atttcgggtt gtcgaaagag
    48001 atggttttag atagaatgac ttccggattg aagggtactc acggctacat ggatccaaca
    48061 tacatttcga ctaacaaata cacgatgaag agcgacattt acagtttcgg tgtcatcatt
    48121 cttgagctca ttactgcaat ccatccccaa cagaatctga tggaatacat caacctggta
    48181 agttaaaatc cctggtctat gcaaccaaac cgaataaccc aaaaatctga aattaaaacc
    48241 caaatcgaac caaaactcag tgagtgattg tgagatcaat gattctgttt ttctgatgat
    48301 caggcttcga tgagtccaga tggtatcgac gaaatactcg atcagaaact agtgggaaac
    48361 gcaagcattg aagaagtgag gttactggcg aagattgcaa acaggtgtgt gcataagaca
    48421 ccaagaaaaa gaccatctat tggagaagta acacagttca tactaaagat caaacaaagt
    48481 cggtctcgag gaagaagaca ggacacgatg tcttcatcgt ttggtgttgg ttatgaggaa
    48541 gatctgtcaa gggttatgag caggattaag gatcagcatg ttgagttagg gttattggct
    48601 ggtgttaagg aagagaatca tcaagagagg aacattgcaa caacatagta actctttact
    48661 ttaggagtaa gtctttttgt acatattacc acatgagtct caaaagtaag atttctccct
    48721 cttctgcaaa aagaaaagag tttttgcttg ctgacaacaa caacaaaaat ttgaggttat
    48781 gttataaaga ctcttaacaa aagatatatc tagttcttat ttttgggtta agtttttgtg
    48841 tacttttcaa tccgaaaaat cattaccaac gttatagcat cattcatacc atcatcatca
    48901 taatagtcat aacactaatc taaaaagttt gtaagaagaa ggaattacaa gttcactaag
    48961 tactacttca taaacaatag acacctatat tttgaaacca ttaattaata atggtatctt
    49021 catcaacttt tttgtgtact tgttgtgctg cgaaagctat gtgtctcggt ggatccaaca
    49081 atattaatat tcaatcaata agcaattaaa gggagttgtt gacaaaaaaa caaaacaaag
    49141 aaaaactttg gagacatatc gaaacagcta aaacatcatg tcacataact tgtaatagcg
    49201 atgtaaaatc ctttaaagaa accaataatc atactgaaat attgttgtat ttgcaaggag
    49261 atgattatag tgtcgataag atcaagaacc tctacgaaat ttgatgagta gccgacgaag
    49321 tagaatttct tggatcaccc cttgatatat ttaaacccta ttgaatatat cttggagcac
    49381 ttgtataatt atcataatag ttattttctc tcttggatca ctcgaataca cttgagacta
    49441 catatattca tgctctttaa ataatctgta ttttctcgag atataataat ggtttgatct
    49501 tcttaaaata aatttgaaat gaacatcatg ggttagtgag ttagggtcat tttccacttg
    49561 ctctatcact tctcaaaatg attgcaaaaa tggaagtgtt ttggttggct ttgaactttt
    49621 gaacccaaag tagtttcaac atattaaata ggtgaaaatt tagtgatctt gcactaacca
    49681 atatataaga ggagctgatt ccactctagg tgtttaggta ggtagtggag catattgaat
    49741 aagttggtga aaattagtga tcttatacta aaccaatata ataatagtca caaatttcat
    49801 aactaaaagt tgacaaaaaa taaacataat ttttaaaaag atggatacaa aaagtaataa
    49861 aatttcagtt gaaaatctaa atttaagatt ttgtgtagta ttgtattttc ttttctgttt
    49921 ttgttattta taatgtcttt atctaggcaa aatcgcttga aaatattacg aaatttttat
    49981 ttaaataaaa tactctcaga cacctagctg ctataaccga ttctaagaag tagagcaatg
    50041 ttaattgagc aatctgataa tgccatttta gctatagagt tttttttatc ttttttatgt
    50101 aaaacatatt gggattgatt ttatcaagag agaaaaaaat aatatgaaaa atatatatct
    50161 gtaaccaagg tttaattaca caaaatggca cttattattt agctaacaaa actggcaagg
    50221 ccatggatgc caaactttac agtgtaagct ttaatcaaca ttctaatctc catccatgga
    50281 agctctttca gaaatctcta caccaagaac actaaataac ttcaatctgt aaaactcact
    50341 gtaaattcct ctttcaagct gttctctcgc cagtggtgga gtcacattct caaatgactc
    50401 tcaatggttc atctaacagc tgcagacatt cttgtgggtt ggcgtagaag tagtcttctt
    50461 ccttgggtct attgggaatc actaaccgtc tcttagggct tcccattcga gtagagtgaa
    50521 atgccttcac cgtggatgaa aatacatccc aactcaacaa tccttcagta tactcatcta
    50581 tcagcttaac taggaacctc ctattcagct ggattgtctt cttgaacccc aagaatctgg
    50641 aaaaaatggt gtcagcctcg ggatgataaa tatgggaaga aagaagaaga aagataacgg
    50701 tatttcacct gcgatgacct tcaacaactc ttgccatgtt cccatcattg gttggaacaa
    50761 atatgtcgct ctcaagtgcc actaggtaat caagtgcagc catttgagat gaatggttcc
    50821 ggcaaaaatc cagatcagag gattcgagta gggtttcttt ccggacctga gttagttaag
    50881 ataatggagt caatggaaga tataagtttg aaaaaattgc agaggctgaa atgacctact
    50941 taccacattt ggaaaagcgt ctgttaaagc cttcatccgc ctttgaccac catagatttc
    51001 tccagcagct atgtaaattt gaacatttcg gtcaataccc aacgcggtca gagtgagagc
    51061 ggtttcctca ggagttaaag ggcaaaggcc atctttcctc ttcagctcag agtttatgac
    51121 tttctctttc caccatggat aagcatatct gcaaacaaag agaatttaca tcaatagatc
    51181 catcaaagtc ggaacaaaag caggaagatt tttcggggat tttttatacc tcattcttgt
    51241 tagttcttct tcttcctcgg ggttgcaacc atgtgaacaa ccagaaaatg ctaacatatc
    51301 catctcatat ctgagatgca ggacaagaaa gggacctttc tctctcagaa tcttgactac
    51361 tcgtctacct aattcctcaa tctgaggagt aaacttaagc ccattgaaat ttactcggca
    51421 cctcagcttc tgaacctcca caggcagtcc attattagca agtcgggtat ccgttctgtt
    51481 cagatgtaaa accttatgtt ttttcaccag tggaagaatc tgtatccaga tattatttag
    51541 tttgaaaaga attagcaaac tgatttaggt ataaaaacca tagtgaagac taatctcgaa
    51601 caaaaagacc aaacttggat gactaacctg attttggtag taagacatgt ttgaccaact
    51661 aataggaggc atttcgtggt acactccaag ctcaaccctt ttcttaagcc ttggaggtaa
    51721 ctctttgagt atccgaactt catctcttaa cgaacttatg aagtgatcca catcgaatat
    51781 gtctttaaac tcactgcccc gaagaagaaa acattgtaag agattgttga atcggaaaat
    51841 aaaaaaaaac agagttcaca aagaagcttc aagtgagata cataccttgg atcgttccaa
    51901 aaagaggtct tgtcaagctc cggcacaata agtgtaacat tcatgtatct tgcaacggtt
    51961 accatatcac atatctgtag aaagtagacg aaaaacaaag taagcaaatc tatcactaga
    52021 agatgaaacc ttgtaaagag atgttatttc caatggttta gttatcatct tacagctgct
    52081 cgcatttgat tgagtcctcc attgcaggaa accataagat aaccattgtt cacatatacc
    52141 cctgagaaga aaaaacaaag agcttagttt ccagattcat ctccaagacc aagtaaggta
    52201 cattatccga ttcaaccaca aatttcatca atcaatgttc tcaaaagaac ttacttttag
    52261 gtggaagagc aattttggta ggaagagacg tcatctctgc ggcagtggac agttgatggt
    52321 gattgaaaca agaaggccaa cctttaaaca atcttggtcc ccacatctct cccaaagcca
    52381 tcaaatgaac aaaacagctc caaagcaaca atacagtaac agcacgaatc atccataagc
    52441 tcatacgagg cctcgaaaca aaagagttct tgagtttctc aactttgctc tctcctaaaa
    52501 gcttaacatt catctcccat agtttcctgt ggtaaagaaa cttctccatt ttacacattt
    52561 ttctatatca cccaccaacc ccactctcac agaagattct cacagttccc aaaacccctc
    52621 agaggaattt catcgaacac ttaaagggta agcctggaaa aactaaccac agcttaaaag
    52681 actgcagatt taaaaggaca ggaatgaaac aatataatag gtttggtgct caagctttta
    52741 attatcctct ctaataacac tcagagaaaa tgtaatctcc acacaaatct gtgagcatta
    52801 atcacacctc gaaaaaccca gatttttagt tttaaagtag cccacgatga tctcgactta
    52861 ataatctgac taaaacccag atcttgctct attaaataaa agaagaatct ctctctctct
    52921 ctcaggtttt aattaagagt caactttcaa ctctcaattg atggaagctc acacttccag
    52981 ttacagaaaa aatgacacag agaaggcttt gaaattcagc aatggcgatc gatcaaagta
    53041 gccgtacaaa aaaaaaaatg ggagacgaga gtctccgtgg agaaccggtc ggtgttgacc
    53101 ggagaaggaa gaagaaggac gtcggagaaa tagggagaag atttcggtgt ggagaaaaaa
    53161 agagacaaga atgtgcaaat ttcagaactt ttttctacca aggaggaaaa aaaaaagaag
    53221 cagtctttag gtttcttctt ttttgtcggc aaaaactgga gtgtcattta taaacttttt
    53281 ttttacagag aaatattttt tgtaatattc tttgcaattt aaaatatatt ttttgataca
    53341 gagccaaagt agacctttaa ttaaatttat aaaatacatt gtattatttt gctattagtg
    53401 gatatgtata gttatataca tacacttata tgtattttgg ataacttaaa caaggtacaa
    53461 atttgaattt tggttgacca aatacattca agctattttt taagttttat tttccagagg
    53521 gataaattaa tatatttgga agttaaataa cagagtttca gttatatcta aaccacatta
    53581 gcaggttgcc cctagactaa ctctgtcatt aagcaaaact aatccacaag ttaacttcca
    53641 gaaagtattt gacaagaaaa taaaatcaaa ttacatattt aacatacata aatatgtgtt
    53701 aacccaatca ttttcaagat tggttgaaaa acgaaattaa attttatttg agttaactaa
    53761 taaaataaat ttatcgataa atggaaatta atacggcaag attcattttc tgtcggttct
    53821 ttataaaaat aaaattaaaa aattgttcaa aagggcatat tctagacttg tggatcgctc
    53881 gttttgtgac agcaatgaca aagagagatc caaataaata ttgaatattt ggcaaataaa
    53941 taaaataaaa aagtaggcct acaatatact atataataat taaatatata tggatggacc
    54001 aactctattt attgctcaca gttgtcattt gtcaatctaa aataaaatat agaaaagtat
    54061 gtggaagtgt attatgttta ttgattaaaa agaattaaac gataaaaagg tccaaaacat
    54121 tagatcaaaa cttaagctag ctttgttacc ttgatttcga ctgaagtatg gtataaatct
    54181 ggccccgagc cgactgaact aacattttca gcattatgtt attcgaaatt tcgacagtat
    54241 gataatgagt atatttaaaa gaagcattat gtataatttt gagagaagaa aagattgagc
    54301 attttttagt atgttttttt tttttagggt gaaaattgga tctaaggata tttataggaa
    54361 acaaatggat gaatacataa gaaggaatta atatgtttcg tcatgaacca agtaaccaac
    54421 ataaatagat acattttaaa ctttttataa aagcagccat taatagaaga tggtctttta
    54481 aaattggatt tgttttattt gcttttcaaa ttttatcaca attttgtctt gttcatagtt
    54541 tttaagaaaa atattaacca caactttgtc ttgttcatat tttattttac aaaattggct
    54601 aaaatcacat tctatttatt tatgagtttt aaaatataaa ttagattttg gtgatattca
    54661 atttataata ttttaataaa ttttcagtag tctctctaga aatatacaag tttttttaat
    54721 gtacctctaa atattttaaa atcaagaaaa tcaatctaga tatggttctt tataagaaag
    54781 tacacaagcc aacaaacact cgtagtctcg tagatgtttt tatcaagtat atatatatac
    54841 attcattata ctattttcaa atcgttggta aatcaactga taattttttt ttcctatcca
    54901 ttatatataa aacaaatata aatatgtcgc ctattacatc ataaaatttg aggaagtaaa
    54961 aaaaaaattg aaatttcaaa cctatcaact aaattttctg atttaacaga tttaatttat
    55021 ttttattttt ttagtttaaa aaaactcatt cattaaacat gtgaaagtga ctaaccacga
    55081 tgtctagctg tagcggcagt ttaataaagc tttaagcaat gatctcgctc gccggccaag
    55141 tttagaaaca atgaaagatc aaattgaatg atttgttttc ttttgtcatt cgtgaagaca
    55201 atttaaaaag atacacgtgt agatgtgagg ttatgaacag gttattgttt taaaacacag
    55261 cattatatca gccaatatat atcaatatat agacgatgtt cggtccaaaa atctagatca
    55321 atctccttca tgtttgctat tcgaaaatga ttgttattta tatcaaatcg tgcgtgtaac
    55381 atcgattgat aaatattgga aatttaagta aaggccaatt gtcacgtaat gacttgaaag
    55441 catctccaat gtaattcagt atttatttct tttcacttga cgatagaaga atttgattag
    55501 agatgagtta cttattgagc gaattaatgt acgttatttt ctatgaccat atacattcca
    55561 ccgacatcgg acattacact gctgtcggaa cttaatgatt tatttttcta aatacgaata
    55621 catttctcca atggaaaaaa tctaagagtt ttaagatttt tctataactg taattgtcat
    55681 ttcaacgaag agtttaagaa gaaaacagag agaaaagcgt gtaaatatct gtagttttaa
    55741 tcaaatgggt catttctatt tcagtctata tatttaatca aaattgcaat tcacaaattt
    55801 taatgcttac gtattttaag taacattaaa tgaacatctt cgtcctaaaa gttacttgat
    55861 attaatagaa aggtaaagta acagaacaaa gcattaacga tatatttata tttcaaaact
    55921 tacacacaag tattcagaat taagaaaaga acaaaacaaa taaaggagac gtttctgcga
    55981 ttatgttttt gcttgaaata gaacaaacaa acacgtattg gtaaagaaac caataacttt
    56041 gaagatagct taaacgcaaa atatatagtg aaaaaaggga aatcaacaat tattatatat
    56101 ccccacgaaa ctcggtgtcg gtggctcaat catcttaaca ctctaaactt ttaagcccat
    56161 tcgtgcgcat gcgtgtatgt atatacgtgt gcattggatt tgaaattttg gtcgttatcg
    56221 agagttctag tagattatgc attttgtgta acaagtgtaa tataattggg accctttatt
    56281 actttctata aaacttaatt cttttaacct atagatcacc cgtttgtcaa ttatatcaat
    56341 caagggtccc ttattagctg cattttccga tcgataatag agaagatcat ccaatgcttt
    56401 acaatcactt ccatgcgacc tcacatacaa ttacttccat tgcatagtat gtagtaaaac
    56461 tatatatttt gcttccaatg gatttgatgc ttgtttatgc ttagaacttc caaataatct
    56521 tttttaacgt agcgaattga ttttgcattc aaagcaccct tagtaaatcc gtttcctagt
    56581 ctagtcccat aattaaggta aaatctacat gggcttctca ggcccataat gagaagttta
    56641 aaaggctcaa ctcaacaaga tttagttatg ctaaggcctt acaagttaca atcaaacaga
    56701 ggatagggac cgtcggattt atctgacttc ctctccttcg attagggttt ctgaattact
    56761 actcctctgc caattagggt ttaagcctct ccagcatttt ctttcagctc aaacccaaga
    56821 acctcatcgc cgattatttc ttcatcctta ctctatcccg cgccgattaa tctctctcag
    56881 gtaaactact tcaattttac tcatagacta attgtacaga gattgataaa tcctatgttg
    56941 ttcccattag aatgttcaag ggtttatgat tattcaggat ttcaaatctg aattattgga
    57001 caaataaacc ctaatttcgt ataatttgca tatcatcagt accgtccgag atgagaaagc
    57061 tcaagtatca cgagaagaag cttataaaga aagtaaattt cttagaatgg aaaagagaag
    57121 gtaaccatcg ggaaaacgag attacgtatc gataccacat gggctctcgt gatgattaca
    57181 aaaagttggt acctttattt gctcttaaag ctctgttcta cttattcttc ttcttctggt
    57241 tcgagtgttt tgtgatgaac aatggtcttt ttctgattct tgagaatgtt ttttcttttg
    57301 ggcaggtatt caggattgtg taggatggtg cagaaactga cgaatataat gaaacaaatg
    57361 gatccagcag atccttttcg tattcagatg actgatatgc ttttggagaa gctgtgagtt
    57421 ttttaaatat atataccagt ttgttcaagt atagagctta ttacaagcaa tggttctttg
    57481 ttttctctag atttaggtcg tagaacatga gacttgatca ttttctgcag ttttttacac
    57541 cgatcttatc ttagagacct cctgttgttt ttcttgttaa ccacttttag agataattaa
    57601 aattgggggt ccttatgctt ctatatagat tttaggaccg ttggtttgaa atccattaga
    57661 ggttgaattc atcctggtaa aatgtgtgat ctaatgggtt tctttcagaa tctgtttctt
    57721 gaatagcttc tacatagagc taagttacta tataatatag gcttattgta tagggaaaaa
    57781 gagccatcct actgaaactt gttgattgcg tagttccact ctgcaatgag aaaacttgtt
    57841 ctcttaatgg ctgactgact tgtgtttctt acatgtacgc ttgaaacggc agatataaca
    57901 tgggtgttat accgactagg aaaagcttga ctctaactga gcggttatca gtttcatcct
    57961 tctgtaggta agagtatatg caagagccta tataggcagt tacttaaacc cttgatagcc
    58021 aaatgttctc atttcgtttg cctcatatcg gttctttttt tttatttgca ggcgtaggct
    58081 atctactgtg ctggttcacc tgaagtttgc agagcaccac aaagaagctg tgacatacat
    58141 agagcaagga cacgttcgtg taggaccaga aacaattact gatccagctt tcttagtaac
    58201 tcggaacatg gaagatttca tcacttgggt tgattcatcc aagattaaac gaaaggttct
    58261 tgagtacaat gacacattgg atgattatga catgcttgct tagctttgag gaagttaaaa
    58321 aagactgatg ttttgtaaaa gccaaaaaag gttcactgct actactattg cagggtttgt
    58381 ttggattttt gaatatgcaa atgtgctact attcccttgt ctttaatctt actttcgatc
    58441 tatttgcaag aagaaacttg aaaacaaatg tcatgaaaat attgaatcta actcatatta
    58501 tcgtcaaatt gtataagttg gagccacaga aatggatgaa cataaaatat taaatctaat
    58561 tattatttga cacttcaaat tacaaaaccc gtttgattcg atccgacccg acccgaccag
    58621 aaaatcgcaa aacctgtgtt tttgctttcc ccggtctctc aaaataaaat tgctcgctta
    58681 gaagcttcaa acgcagctga aatggcggtt caagcaaatc agagtgcttc ttttgggttc
    58741 agaacagctt caccttctca gaagctctct tcgaaaccca tagctcatat ctctctatcg
    58801 acgaagctca aaccctcttc tcgaccatcg ctttcgtgct ctacttggaa tcagggtcaa
    58861 attccggcga gacactcctg tatcaatccc ggaatattcg catatccccc ctccaatctt
    58921 accttctctc atgaactacc agaatctgaa tctccgccac ttggaaaggt cagtcatcgt
    58981 caaaaaactt ctcttggaac aaattggggt tataagcttg ttagacaaag ttgcagcctt
    59041 tttttgtcat ttgaacgaaa atgtggtaaa ccaaatgtat tgtctccatc tatttaattg
    59101 tggtagaaga ggcagtgtgt gctagtgtta aacctccctt atgttgcttc attgtgaaaa
    59161 cttttgtgaa aggaagtaga gatgtatgat tcttcccttg ttatcgtcat cttatattgc
    59221 agaagaagat gcgtgtgtta gtgaagccgc tagagaaacc aaaggtggta ctgaagtttg
    59281 tatggatgca aaaggacata ggagttgcat tagaccatat gattccagga tttggaacaa
    59341 tcccacttag tccatactac ttctggccta ggaaagatgc ttgggaagag ctcaaaactt
    59401 tgttagagag caagccttgg atctctgagc ttcatcgtgt cttcctcctt aaccaagcta
    59461 cagacatcat caatctttgg caatcaagcg gtggagattt gtcttgattt ggattcacca
    59521 gatatatctg tttatcatag gtatcattaa cttttcaaag tctaaagctt ttgtgttgtt
    59581 tagtctatca ttagtcctct gtgtaatcat cgaaactcga aaaaacttct atcattaaaa
    59641 tggcgaattc aaaacaagaa aacaaaagat catcatcatc atcatgatga acgtttaatc
    59701 gaagtactta gacatttgaa tcgatttatt actcatccca catttctcat agaacacttt
    59761 gttctccaca ctacaatcta gaatcacctt atagcaaccc attgatttgc aatgatccat
    59821 aagaaactca acaactttct tccccagctg tttcccgcga aaccttgaat ccacaacaac
    59881 gtcttcaatg tgcccagctt taccgcaatt cctcagaaac ttcttctcta tcatcacact
    59941 acccgtagca gcgatttttc ccgaagtttc ttcttcgatc acgcagatca cgtggtcgtc
    60001 accatacgat ctgatttctt cgaatcgccg atcgaattct tcgtctgtta ctgatccggt
    60061 gacggttagt tgacctagaa gctcgatgaa tccttttctc ttatcggaga tctccagttt
    60121 tcggatcttg aatgtctcag ccatagaatc agatcggata attttgaatt tgagtttttt
    60181 tttataagat ccagtcactc actggaactg aatataatca cccatagaaa aacaaatgtg
    60241 ataattacga aaaggtactt attcttttag atagttacaa aaagtttccg aatctcttaa
    60301 tgaagtcaaa atgggccatt tgttttttaa attgactttt gatgtaacaa aagcagcaag
    60361 ataaaaactc catagtaaac aatatttatt gaaatgacaa caagccaaca agtgaaaatg
    60421 cagaggaaaa aagtaacaat ttaaagcgga tgatacatat agattacata attggaaatg
    60481 taaggaaagg attgctaatt tagggttgat ggtgactaga aaaggaaggt gaaagaggag
    60541 ggattcccgg gatgagaggg gccggaggga ttccagggat aagagggacc ggagggatgc
    60601 cagggagtcc agggaccgga gggagcggaa cagggaaaga aggtggtggt ggcggtagtg
    60661 aaggcggatt cacgataggg acaggtggaa gaaccggaag aggtggaaga gtcggaattg
    60721 ttggaatcgg tggcagagta ggagtcgggg gagtaggaag taacggaatt gtagggagag
    60781 ttgggggagt agggattagt gggattggag ggagacttgg gggagaagga ataagcgggt
    60841 ttggagggag agtaggggtt gggatagaag gaatgagcgg gtttggaggg atgatagatg
    60901 gcgggtttaa cgggtttggc ggaaagaaga aattgggttt tagtgcttcg gttttcttgt
    60961 ctttcaagga atcagatttc ttgttatgca aggaagctga tttctgaggt cctggtggaa
    61021 gaagaggagg aactagagga agaggtaagt ccggaacagg taactttgga acaggtaagt
    61081 ttggaagagg aggaacgata gggagatttg ggagagggga aggattagga ggatcttgga
    61141 gcggtggagg aaatgaagga tccggtaaaa gaggcttgga accgcggaga ttgataggtt
    61201 tttggctaca aatctctggt tggttttcgg gtctgaaagt gaagaaccct gcagagaaaa
    61261 ccctagtatt ctctccatga tggtttgatt taaggcgttt gagagaagaa gaagtagcag
    61321 acgaagctat agaacagtaa ggctgtgagc tacttagcaa cttcacagag catctcttga
    61381 tcttcttcac atgtttgctc acagagaatg gtagcttcac tttgaattcg ccgcgcttgt
    61441 ctgttttcac ttcttgtctg aaactcggtt tcgagttctc gtcaatgcat tccactgcaa
    61501 ctaaagcacc tgcaacaaga tccacaaaac ttttcataat tctttctaag attttagacc
    61561 cacaaacaag aaaaaaccct ataagtttcc aaaacagagt gctctgttct agaatccaaa
    61621 aaacattatt ttccaagtag tgttaccaag aaaacacgag caagactgca agaggaaaaa
    61681 aaaacaaaaa tcagaaacca gacctgagat taagtggttg ggtgatttcg agaaggcgcc
    61741 gttaaaacaa gtgtcacagt agacagttcc tactacaact gcagaagaac gtgtcttctt
    61801 cataacatgt tgctgtcctt gagacaaacc tccattgata gagattccta agaaaatcat
    61861 aagactaaac caaaaccata aggtcgttat tctctccata attatcgact ctatctctca
    61921 ctatcggagg aaagaggggg tatatatata ggagtgtggt gtgaagatga gtgagccacg
    61981 aaaaacgaag agattgttaa aagatgagtg aagcttatct ctttttgttt tgccatgtta
    62041 ataagaatca tgggaaaaat acaaaatcga actacaaagc tagctactat aatgtcttgt
    62101 gaccctatct ttctacagct cagtagctga attattgtaa aaaatagtaa gaggtgagaa
    62161 aaaagacaac actaatattt tggattcacg ttcgcgtgtc gattagattt gatcgaacag
    62221 tacacggtaa aaacacgttc aaagtaaaat accaaacctg ttatatcatt gtttcttgaa
    62281 ttgcggggtt gctaaaacta aaaaaattca gacacatatg attttttttt ttttttctga
    62341 gttaaaggtt ccgaagatga acatatctga gatacttttg tgttgaaaat atctgttatc
    62401 atcatctttc ccttatttac attctgaatt ttggatgaga ctaaaacatg acatgatgtt
    62461 ttcatttcca aactgtgaat cactgtctgt catgtttgat gtttatagta tagtctacat
    62521 ccatgttttt ttaaagaatg acatttacaa tcattattgt tagaaggata tcctaattgt
    62581 caatattaca tcgaaatatt tatttttaga acatccgaga atagatgatt agttactgtg
    62641 gtgatgattt tgatagttaa ctaatatcag taacagtcta tcatggacgg atttacatat
    62701 ttctaatcgg taatccaaac tagatgtaag aagaggttac agagattcat taattcgcaa
    62761 tataattgtt ctaagaaact tatacattgc ttattataca tttgtttata gatttggaga
    62821 aacatatagc cagtgaggct aaagttgata actagactta agtaagttat agtttctatt
    62881 ttctttaaca gaggaaacaa tacatgcaat ttaagaaagt gaaggcttat gggaatgaga
    62941 atggggaagg gaatacagtt ggagagtctc tgtcgattca cgagacacta aggatgtcca
    63001 cacaatcata tatacccaat tcttacttct gtcttcttat agagtactac atacatactc
    63061 attcttgata agggacaaaa aattaaataa aatgagttaa agaatgtgaa tgttttttaa
    63121 tggtattaaa gactctgaat gttcttctcg aattttcata ttttaacttt tgatttttgt
    63181 gttttttttt aatcaggaac gccgtatgtg ctaaaaaaaa taccatttca tgagaataaa
    63241 caaattctat tagtcgacga cataaaaaac aacaaacaaa cactatggtg gattatagat
    63301 agactaggga atattgtaac tttataaaaa atattgaaaa aatatgaaaa cattgtaaac
    63361 taaaaatcat taatttctag ataatatagg actaaataat aaaatgggcc aagatcaaat
    63421 taacccaaac tgtagtttac aacttggttg ttcccattcc ttgatatggg ctaagtgaca
    63481 taaaaagccc gactctttat tgtccactaa caattggtct tttaacttct tgatggatta
    63541 attgtgggtg tagaagatta ttttgactat ataaaaacag aaaattaact aaatattttc
    63601 gatatattaa ataactagat gatagatgat ttttttttgc agtaatttca taaatttagt
    63661 ttcataaatt agtttggttg aattcaaatt tagtaaattg tcaaatttga gacatagatg
    63721 atagaactaa gattagtaat tagtagcgct atatatgact caatggatgt gaacaagatg
    63781 ataatttaaa aaaatgtttt ataaaattct ttttgtccaa tgaacaatag gttaaaacgg
    63841 acaaatttac ttttgtgatt taattattgc catgcatttt ggcatatagt cactctgttt
    63901 cataatataa gctgtttaat ttttgtcatt taacaatttt aatacgtgta acatttcgtc
    63961 atgcaatgtt attttatgtg tagatatcta atttattaaa tgtactttta tttcagttat
    64021 aaaagttata cataatctgc gattataaaa ttttatatta atataatgcg ttaaacatta
    64081 agtatctgtt tacgataata ccaaaataaa aaacaaggga aaaattccat cccaaatttt
    64141 tgcttttgtt acttttgaat agcaaatctc taatgtatta tttttctaaa ataaaatctt
    64201 cctatcctaa tgtcatcatc tacaaaatca ttaaaatatg taatgtctga ttaactaaaa
    64261 taattttatc aactagtata aaataagaga atcaaccaaa aaagtttggt ttaaattgta
    64321 tagagagagt cctccattag cgtccagcaa caacgcccac ccactttcac accaacttga
    64381 acacactact cctcctcctt cactttttcc ttcaatctct cttctcgctg acgacttgga
    64441 aataaagtga gggaaaatat tcctccaact tcactttcct gagaatctgc aaataaagca
    64501 attcaacttc cttttctttc tttctaaatg aaatttcgtt ctttgtctca gtctctctct
    64561 ctttcttcgg tcgagtccga tcaaaattga aaacccattg agttcctcgc caaaaggtat
    64621 agtcttcgtt atttcttctg taattggata atggggtttg atcgattctg attagtacaa
    64681 tcccaaagtg ttgttctttg ttttctggta aattttctct gctttttttg tgttctgttt
    64741 taaaacaatt attctgagtt aagcaaagca acttgtggtt ttgttgtgta atgatatcaa
    64801 gtgggttatt ttttttatta taagtttctc tgttttattg cgtttgttag ggattatcta
    64861 cctaaattag gtttcaactt ttaatcggtt agttgcttgc atttcacttt gaccactttt
    64921 gccctttttt gtatatcccc aattgaagcc tcgagttttc tttttgacca aacacaattt
    64981 tgtactgagt ttggtgaatg tttgtttgat gtctcttgtt gggaatctct ctgctttaaa
    65041 gttacttact gtcaatgctg gcaataaatc tttagttttt tactattttc ataatataat
    65101 ggattgtttt gggggttgtg atgagttttg gatagtaatt gaagaggttt aaaactccct
    65161 taaaaaacta cagtccaaac agtgatcaga tcattctaca ggtgaaattt gagagaatga
    65221 atcaacgaga gaagctgatt gttggtgaaa tgtttggaga gtttctgtaa atagacgcct
    65281 cggatttggc attgttagtg aaggttaaag gagtttccta gaagtttcaa agcaatttgc
    65341 ctccaagttc ttgacttata aaacatattg gaactaacat ttcaagaaag aagagaagga
    65401 gatgggctgt gtttcttctt gctttggggt cgatgacttt gaggattacc ccaatccaag
    65461 tagttctgtt aacagaagct gcccatgccc gagatgtctt gttaacaact tccttaacct
    65521 ggtaatgctc tttttgcagt ttttactttt cacctgctac ttatatgaaa taaaggagag
    65581 ttcattgaag cttcggattt gatctcttct gcagtatatc tctttattca gaagaggcga
    65641 aacccgctct ctcccatcct ccttacaggc tactaatgta tcgatagcta catcaacttc
    65701 gtatgataac tttatgtcta atacattcca ttctactcca aggcctctgc cttatgacgc
    65761 tgatccaaga tacttccggt caaggcgtga ttcgcttgtt tctagacgcg ataagggttc
    65821 aagtcattct catgaggaag ctgagccctt aagaagtgat gctgatgtgg attctgagtc
    65881 tttctcagtg gaaggaagca aatgggctaa caagcttatt atctctggtg aagattccaa
    65941 agaagagttc tctagatcct ctcggaggat tcttcagtca aggacaatgt ctactagtaa
    66001 cgaaggcctg tatataacat ctgatgatga agatgtctgt ccaacgtgtc ttgaaggtat
    66061 tcattttcat cttttttttt ctttttcttg gatcaatgca tttcaaagaa gcttagtatc
    66121 agattatttc gtgtgttttg tagaatacat atcagagaac ccgaagattg ttacaaagtg
    66181 ttctcaccat ttccacctca gttgcattta tgaatggatg gagagaagtg aaaactgccc
    66241 tgtttgtgga aaggtaaaca cttttcatgt tcttccaagc cagttttcgg cttctcattt
    66301 actagtgttt cagagtcaga ctcagacacc atcacgcgta aatagacgag tgatccagag
    66361 atcaatagaa tgaaagatgt acaacaaccc tagaagcaca tgcgtaaaat ctttacttgt
    66421 cttgtctatg acaaatatgg ctaatcattc ttcctgaaac tcagaacatt tgaattattt
    66481 ctcattcatg ttgactaaag aatatttttt tctctgctgt gaattcgtct catttgcagg
    66541 tgatggagtt ccacgaaaca ccgtaacttg ttgccattga tcctgtcttg tactgcctag
    66601 accggacctg gggagattga caaggcagca gagagatgtg aatatatttt ttaacaatat
    66661 atgatattgt atatgatggg gaaatgagga aacgtctctc tgcacgtttg gcttatggag
    66721 ttctgaggaa accctcttga gagaaaacaa cagcagcagc agaacagatg cacacaggaa
    66781 tctgacatgt ttcttaggat ttgcctttgg cgcagtgttt tgttcaaggc atgaaacttt
    66841 ttacatcatt ttgtatgatt acttttaacc ttttatgaat ttatgaatat atatgtgatg
    66901 cttgtatttt ggcatatagt ttacattggg tatttgggtc aaggagagat cacattgtaa
    66961 cccaaatgtt tctcattaca tgataataaa ccagtgtcat ggttcagtgt taaaacaagt
    67021 tccacacatt tgaattctta atataagcaa ggattcccaa aagatacaaa tgtcttgaag
    67081 atcctcagga ccattatata tagccactta tgtctacaaa tccaaagtct tgtgtctata
    67141 cttttatata tataaaagat cttttgttgg tgagctttaa cacagcacat gactctcaga
    67201 gcatccaccc cgggatgtaa ccgtttccct gctgcgcctg agcttgggtt gtcgcagtta
    67261 tttgctctga gcataccgga ttatcatacc tgtcatcatc atcatcatca ccaaaacagc
    67321 aacttaaaag gttcacacac attgatgatc ctctttacac caagtaacta aagaacctta
    67381 tataagtaca atcttagtag tgaagtacac aagctgattt gcagatgatt gtttaaggca
    67441 aaggatttac cccatttgca gagttggatt gcattcaaga ggctggtata gtccctgaga
    67501 ctgagcttga tgatgcgcgt aggtaacatt ctgttcacca ccttcccatc ctcctcctcc
    67561 tcccatatga tgacttctca caccaatcat atcatccagc taaacattta catttcacca
    67621 aaagactata atcagaaaca agaaaactag agatgtttcc aaaaatgttt agaaacttaa
    67681 actctgtgaa agagattgat cgcaaggcac caaatgcatt tattctgtaa ttataccttc
    67741 attgccaaag ctctattggt ttcaagcaac atttgctctt tattttgaag atccgagagc
    67801 tggtcaagca tgtactgtgt ctgcaaacaa tcatcatacc accatagtag ttataattaa
    67861 acaacacaaa ttaatctcat ttgaatcatt gattccatgt ataaagatac cttgatggac
    67921 cgaacttgct tgagagagcc gtccagttga cgctcaagct gctctaactc ctttgaattc
    67981 aaaggtccta aatcctcccc aagaagattt ctgcaccaac aaaagccaca cacacctaca
    68041 aatatgaatc tacatggata cagaattgag taaatatacg gaggtagaca gatatgtacc
    68101 tctgttgacg ttgaaggttc tcatatctac ccttaagctt cagatattct ctgtagctgt
    68161 tctgaaatat ttcacgaaaa caaactttta aaaaagatct ttcttgaaat gatatgatag
    68221 gaatctaaaa tagtatttga attaagaaca cctcaagttc tttggcaggt ttgttgttga
    68281 cttcaatgga tccatagctg catttctggt accgatcaag tgtcttgagc atgctgaaaa
    68341 taactcaaaa agagagaata agagtttatt aaaaagatca tacttgactt tggagatcta
    68401 aacctataaa tcaccataaa aaaaaagctc ttcaagtttt aaagtattct tccatcaaaa
    68461 ttgaagattg tttccattat ttatctgatt atatacgagt tgatttggat ttgattgttt
    68521 caactttcaa acgtaaagtt tcgtatttat atttacaaat atcaatagtt caatcctatc
    68581 atttgcaagc aatatcttac gttttcgttt gattcacaaa ttgtgatttg aaaaaaggaa
    68641 ttaatcgcta tattttcttg aatgcatgta agcaaaacta ttttaacata taattaaaaa
    68701 tctattaaac attgttttta agaaaaaaca aacaatcaaa gccttcacag atatacacgc
    68761 gtttgaagtt ttaaccacca taaagtatga tgaactaaca aatggttaat gcatgtaacc
    68821 atatattatc attctacgtt ggatacttgt aattttcata gaaatctgtg aacaactttt
    68881 aagtttccaa tcacacagac atatattaat tatataaaac ttttcagatt gcatatcagg
    68941 atttggaatc tattcgatta caaaattcac agttctaaat cattgacaac aaaaaaacca
    69001 gatcttaaat ttcaagaatt ggaaaaaaac cctagaaaat gaaatcaaga aatctaatta
    69061 actcaacttc gtagaaatca agatcgtgtg atctatatat aacaagtcct tgagacaaag
    69121 atctaagctc agatctagca aaaactcaat caagaaactg ataaagagtg agagagttgt
    69181 ttactttgag gagctgcaaa actcatagag ctttccacgg ttggagaaga tgatgagagc
    69241 aacttcagca tcacagagaa cagacaattc ataagctttc ttcaacaaac cgttcctacg
    69301 ctttgcaaac gttacttgtc tgttgatttt gttctctatc ctcttcagct ctactcttcc
    69361 tcttcccatt tctttttgtt accttaattt ccacttttta tgtctataca caaatatggg
    69421 tatgtaatgt ttatctatat acagacacac aaaaacataa gttgggtatc tctttttcag
    69481 aggaaagatc tgatcttttt gagtttttat ggtctggaga attgatggta tttggaaaaa
    69541 agaaattaac cctaatttca agaacaaaag gtactagctt aaggaagaag aagaggaaac
    69601 ttctgtttgt ctgatttttt atttataggg ttattgattc tttttcctct ctttaattgt
    69661 gtttggaagt gtgtggaggt tgtgaaatct taatgaaaat tttgttttga atcaatggaa
    69721 tctattgaga gcaaaagata agaaatgtgt gagggtgagg ttagggtttg gtgtgttttc
    69781 tcatttctag cccatctctc tgcttcttta ttcttcttta ctttcattcc cacgctctct
    69841 ttaagcacgt gtgatacagt caccaaataa ttggctcttg tgatacaatt accaattaaa
    69901 cttgtatata tatgtttata tgttatttaa aggataaatt tttatttcgt attacttact
    69961 ttagagtttt cattataggg ttattattta atttgaacat ctatgtgttt ctcctcaggt
    70021 agaattcatg tttgtgtata tatgggtgtc tactatttat ggaatattta tacaaaacat
    70081 ctaaacatat cattgcttga aaattctatg tttatatcat aatagcaaat tgtttatgtt
    70141 tagttatata taacacaaca atagtactct aagaaaaaca gcatcatgca cgtttgatgg
    70201 ttgactagta actagacaca cgaggcacaa aggttatcag ttgattaaca tgtgtatgta
    70261 tatacggtct ttcacttatc acattacaaa cttgaaagta aaatttgttt agcgatatta
    70321 agaaagttta tatatagaga cctcgtacta gctggaaatg tatatctaaa atgaaagtac
    70381 actccctctt acatacagtt taatatattt tcaacataaa acatatgtac atagtactag
    70441 cttatttttt aaccaaaact tttgggtttg atagtttaac aactcggtca agaatctcat
    70501 attttcttac ttcaaataat tgccaatata ttctagttct ttttgttttt aaattatacc
    70561 tggtaatttt ctaacgagag tctcataatt gcaagttgta gtagtcttgc agctggatat
    70621 gaagcgcgtg aattaaaact aaataatact tacaataaat gaaagcaacg tatcatatca
    70681 ttttctagtt gttttcagaa gccgcagaaa agcatcttct accttaaaat gggtttccat
    70741 gtgtcgatgc cttattggat catactttct tactttttaa ttcagtttaa aataaattga
    70801 aaaatgagat aaacatttaa gtggttcaat tatcataaaa aacactaaaa ctgataaaat
    70861 agccacataa tataggtcat atcaaataaa tgagaaataa tatttgtatg cctaaatcaa
    70921 gttatccatg tttgaaggtg tttgcagtga ggtatatatg tttttgtcta ataaagatta
    70981 cagttatgat tatgtaacat aaattagata atatttacag ctcgcgatac actacaattg
    71041 aaacgtggtt aattagtgaa actgaaattt gaagaagagg atgaaatatg aatgatattc
    71101 gttaaaatga tctcttagat tgtatagtca ttgtccccca ttgccaaaag atcaaccact
    71161 tacataaagt aaaacgcatc tttagttaaa agctaaccaa aagagtggaa catatttatt
    71221 tttggattgc atttgcgaat ttcatcaata tatggttttg ttcaattggg aaatttaaat
    71281 aactccacta aaatgtacaa agtaattttt tttcgacaaa gaatctatga agctaaaaaa
    71341 tctacccata agtcactttt agcagaaata ccaccatata gacaagggat tattgttgat
    71401 tttgccattt tttatagaga tcttttgaaa ttgccatttt tactaaaatc ttacggataa
    71461 gccattttct aagatttaaa aatatatgga tttcggactt tttttggtaa aaatacgtag
    71521 tttacacaaa atactaaacc ctaagaacaa ccacaaccga gtaaacccaa acataatgaa
    71581 taaaacgtat attcattcac gtaacctgaa aaatggcaaa attcacaaac tattaaaaaa
    71641 agggcaaaat ccacaaatgc catcccaaaa aatggcattt tcataattga ttctatagac
    71701 aattattttt ctgcctatta actttatttg ttttgataaa gataaccaac ctactatcag
    71761 ttatggttga ttttttttat tcatattaaa aaaaacaaga aaacgaagta actttattta
    71821 agttaaacaa aaattcaaga aaaatgtgtg tttgcaccaa ttatggtaca tcaactgcca
    71881 aaaacccacc tatagttgct cactgaaaga aaggtccagc agagcatttg gttactagat
    71941 gaatttctcc ggtttaatga cgataaaacc cggttaaagt taacctactc agtaattcat
    72001 aagcatccgg tacatctaag caaagtgcct tatttgcagt aacagatcaa gaattggaat
    72061 aagagacttc tcgaataaac aagacattct tcaactttaa cattaccatt accaatggac
    72121 cgattacact tatcatagtg tcaagaagat gaaacaacta taaaataccg agaaaatggt
    72181 caagattttg agcattcagg gcaagggaaa caacctttgg cttggcaatt atcgcaagcc
    72241 actgatcttg tgtttgatga gtcactgaaa ccaaagaatc ctcctgattt gattgttcct
    72301 gttcctttgc aacggccaca agctacattc ttaagatctc cacattttcg acacatgcca
    72361 agagatctgc aaaacttgtg tttagaaaca tatgatgatg gcaagttata gattcaaaaa
    72421 caagtctaat gtcattcagc catggacata caacactcta gaacatttct tatagccgtc
    72481 agcaaccaca atgaacagtc ttaagatcat gtctcattac aaaggtcaga ttttcagaat
    72541 ccataatcaa gatcaagaat gattcaatac ctgaatattt caaaaatcaa aagatctttc
    72601 agtgaggaat acagaatttc aggaaaacca ttactttcac atggtgtgaa ctcagaaaaa
    72661 aaatgtaatc cattggagat tgaaactaaa aacataactc aacaatggat tttttttttc
    72721 attcagaatc tatccttcca aactacagat cacaaagaaa ctcttaagga tgaaaaaata
    72781 gtttaaatca aaccctcttg gattaaaatc aagcagctca ttgcaattct aagcagctac
    72841 tacaagcatc atcattatca cataacaaca aaacaaatcc acacggttta aatccaaaac
    72901 aggatataac acgacatggg ttccactcag aacatgaaag attgagcaaa aagttggatt
    72961 ttgtggaatt tcagaaatct tatgtaatga acttgaaaag ctttattacc ttctctgaga
    73021 agcagcgata aaagcatcaa ctttaggagc agcgatggtg gcaccaagaa gcagagcccc
    73081 aactgccaaa cccgcaactt cgtttgacgt taaactctgc atcgtcgtct tcctttttct
    73141 cttctcttct ctcgttcctt cttcttaact tgatgataat gatatcctga atttatttca
    73201 aacgggtaaa tattttacat atctagagct tatcagatat ggcctattag ctcagttggt
    73261 tagagcgtcg tgctaataac gcgaaggtca caggttcgat ccctgtatag gccacttttt
    73321 tgtttttcct tcttttaata atttcaattt tgaccccgta tcttttgatt tcaccaattt
    73381 gtatcccaaa gttaaataaa tgaatttctc caaacgattt gtagggttta aacaacttag
    73441 tatactccgt tactcgcttc caaacccgta cggcctcttt agagtttcac ctttgtgtct
    73501 ctctgaaact gcaacaaagc ttgaagcgat agggtttatt caagcttcac tcaaaccagt
    73561 cgctaaattt cgacatcttt attcacatat ctatagattc aagctttgtg atttgccatt
    73621 cgggtttcag attcgtgttg gtaattcaat ttctgaatcc tctgctccta aagagaagaa
    73681 tctgagatca gcaatggaaa cggatctcaa tgattatact gtcattaagg aaggagaagc
    73741 tgaggttctt atgcacaaga agaaccaagt cttcttcaac aaagctcagg tttgctatat
    73801 gatttgattt tctgcaaagg ttcttcctct ttggtgataa ttgattgaat tatgtcaagg
    73861 gcaatcttag gattgatcaa gtattagttt tgagcatttt atcttggttt aagatttcaa
    73921 atttagtgtt tttttcttgt tatggattag tgtcatgctt gtgttagtga gaaatttgaa
    73981 ggcaactgat cccaaatcct tcttagcaat tatgttctct tgtgtgaatc catatggata
    74041 taagtgtgag ctaaactaat tgcgtgttgt tttatggtta ggttaacaat agggacatgt
    74101 ctattgctgt gctaagggca tttataatca aacgcaagca agagcatgag gctatgttat
    74161 ctaaaagagc tagatcatct gggaaagtgg ttgagaagga tgtctctgaa acttccaagg
    74221 aagaaactcc tactgaaaac ggtgacgata atggaaaaac caatggagaa cacgaagtaa
    74281 caactcagga tggaccaaag gaagctgcta agaccgcata tgaatctgca cgaagggaac
    74341 tcaaaccacc aagagtgctt gaggtttacc tatattcttt cctttatgac tgtaatagct
    74401 gtacttttgt tttcttattt cgttgcttat tatgcgtttc tagttgataa ctttttcttg
    74461 tgttatttat tttataggcc ctgtcagctt cagggctacg ggctttgagg tatgctcgtg
    74521 aagttgaagg aattggtcaa gttgtggctt tagataatga cccaggtatt ttttccttct
    74581 caacgtttgt gcttgtgaag aggttcgaga ctctactttt ctttcgtcct aacatcccag
    74641 aataatatag tatttccatt ttcctattaa agcatcggtt gaagcctgcc agagaaacat
    74701 taagttcaat ggtttgatgt ctacttcaaa ggtggagtca catcttactg atgctcgtgt
    74761 tcacatgctc agccacccaa aagattttga tgtggtaagt atccaatttt tgcaaaatct
    74821 tttcatctta ttgatcacat aactaacttg gttcagtgat gtcttaggtt gatcttgacc
    74881 catatggtgc gccgtctatt ttccttgact cagctgttca atcagttgcc gatggtggtt
    74941 tgctgatgtg tacagcaact gacatggcag tgttatgtgg agctaacggc gaggtctgct
    75001 attccaagtg agattttact ccttcattac cttattctga aaacaaatat ctttgatttt
    75061 gtctgaatgt cttaaatctg tctgttgtta gatatggctc ttatccactg aaagggaaat
    75121 attgtcatga gatggctttg aggatcctcc tcgccagcat cgaggtaatt ttttgctacc
    75181 gttgaattga ttcactctcg ccaaatcttc caggctttga ttgttttaaa gatgctcgac
    75241 tggtatttct tttctaaaaa gcttttgttt ttgatatatt gactttggtc atatttttat
    75301 ttgcagagcc atgcaaatcg ctacaagcgg tatattgttc ctgttctatc ggtccaaatg
    75361 gatttctacg ttcgtgtttt tgtccgcgtc tacacgtgag ttttcctttc ttttcaaact
    75421 gttcctctca attaaaggga agtaaagatt gaagctttat gaaatgcagt tcggcgagtg
    75481 caatgaagaa tactccacta aagctctcat atgtctacca atgcattggt tgtgattcct
    75541 ttcatcttca gtctgttgga agatctctcc ctaaggtttt gtggctgtct cgttgcaatg
    75601 ttagtttagt agtttttgaa agctgccttt tctgataatc ctcttctata atttcttaca
    75661 gaataacagt gtgagatatc tacctggagt tggtcctgtt gttcctcagg attgcactca
    75721 ttgtggaaag aaatataata tgggtggacc aatatggtct gctccaatcc acgatcaaga
    75781 atgggtgaat tcgatactaa acggtgttaa atccatgaaa gacagatatc ctgcttacga
    75841 ccgaatttgc gctgttctta ccacaatctc agaggcaaaa ctctcctcca cactctgata
    75901 gctttagttt ttggttttga tcaatttctc taaatcccta aatgtttggc ttgtctccag
    75961 gaattgccag atgttcctct ctttttgagc ctgcatagtc tctctgcaac gctaaaatgt
    76021 acttcaccat cagctgcttt gtttcgatca gcggtaatca atgcaaagta ccgtgtctct
    76081 gggtcccatg tgaacccgct tgggattaaa actgatgctc caatggagat tatctgggac
    76141 atcatgcggt gctgggtaaa ccaaccattt aagtctaaag gcacaagctt tgaatgtcat
    76201 ttcttttcct cattgataat gaatgaactc gtttgtttga ttgtaggtga aaaatcatcc
    76261 cataaagccg caatcacctg aacatcctgg aagtgtgatt ctatctaaag aaccatctca
    76321 tcaggtctct ctttcactaa gccattgttg taatgcttca ttcattgttt atatatttaa
    76381 agttccaaac ttgaatcttt aaacaccgct ttctttcgga caggctgact tttcgcgcca
    76441 cgtcggttcg cttagtaaag cacaggcgaa gaaagtagcc cggtttctac caaacccaga
    76501 gaagcattgg ggtcccaaga taagggcagg tcgtacaatc acaagcaaac atgtatcgct
    76561 tcttggtcat gaagcagtaa acggtcatct caataacaat cataaagaag caggagacga
    76621 agaagaagaa gaagaagaag aagagcccga agaagatatc atcgagggtg agccagagct
    76681 caaacgccaa aagacaacag aagattttgc ctcaacatca tagggcgaat gtttacacaa
    76741 gaattttata tttttgtttg caaaagattt tctcttttct tttcttaaac atttgttatc
    76801 acagttctgc gtttttgatc ctagcacttc accatttttg cagacttcta caacaaacaa
    76861 cttataagtc tctattggat tcttcagatc tgttagagac tatttaaaaa aaccttgtaa
    76921 tgtgtaagtt ttcatcagta acacttttct atgaatcttt catcattatt tccagttttt
    76981 attggcaata tgattgatac ataaacgagg aaaacaataa tcatggagta tcattaactt
    77041 ttgatcctaa gcagcaaaca aattgtataa caaacaagtt cattaacgat aaaacagaaa
    77101 gaagagcaaa taagtcgttg tagtatagtg gtaagtattc ccgcctgtca cgcgggtgac
    77161 ccgggttcga tccccggcaa cggcgttact tttttctttt tccttttttc cttttcaaag
    77221 ttttccacgg cataatcgta aagcccagcc cacgagtgaa agtaacagag acgatacacg
    77281 tcataatgtg atcatcttaa aatctttttt tatgtataga gagatacgaa tcttttaacc
    77341 ttgtcaaatt ttgtttttct tttctctctg aacccgaaaa ctccagcaat gtcgtcggcg
    77401 aaacttttcg gttgttctat taacgttaac gttgaggcag aggaagaaga aggcggtgac
    77461 ggtggtagct caaccaacgt ggaggtttct cgatctggta accaaccgga ttgtgaagct
    77521 atgagtttct ccaatcagat ggaaatcggc gttcgcaata catattacca gtttctagag
    77581 tcgaattcag attctggatc ggattctatg tatgcagaac ctgaattcat cgatttcttc
    77641 gatcgagagt cgtacgaggt cgacacggtc cgtgaggttt gtgtaagttc gaatcagagg
    77701 gttagtactc caggttattt caatatttgg gatcaggatg tagatttagg gcttggaatc
    77761 gggttaggtt caaggtcggg ttcgggtcag ttacctggtg attcaggtgg ggttggggtc
    77821 gaagttggta ggggtgttac tcctgttgag tataatctct ttggagagga agctatggtg
    77881 gttgatgaag tattggaatg ggagaatttc aataacgcta tccacttggt tcaagaacct
    77941 gcctatgcta gtatggaggg agaagaagaa gaagaagaag acgaagtagt aatggaattt
    78001 gcagcatcca tttatagtga tgcttgggaa atattattgt acgataacat gacaaactct
    78061 gctcctatgg atttggatgt tgaagtttgg ctagatagtg tagatggata tgctcctatg
    78121 gattacaatg ctatcatagg acaaatgttt gataacgaga ctggaatcaa aggaactcct
    78181 cctgcatcca aaagtgtagt agatggtctt cctgatgtgg agcttaccat tgaagaattg
    78241 agcagtgtga gcattgtttg cgcgatatgc aaagatgagg ttgtgtttaa ggagaaagtt
    78301 aagaggcttc cttgtaagca ttactatcat ggagagtgta taataccttg gttggggata
    78361 aggaatactt gcccggtttg tcggcatgag cttcctactg atgatctgga gtatgaaagg
    78421 aagaggagag catgaaggcg tggtagtggc gggttggaaa gggagtcgat gctcgggtag
    78481 agaaggagta actgtgcgtt atatcttcga taattgtcta atcagtaacg atctgttcct
    78541 cgttgatatg atgtacatat tggttctaga taataggaag catacatttt ttagccatat
    78601 ctttttgcaa gttatttagg ttcattaatc ttattagact ttgcaggtaa ttgcagtcag
    78661 aggttatatt taattgttga tccgactttg attagttcta aatatgattt ttttcggatg
    78721 tggttttgtt gctttaacag cgcaagattc tactgtaaaa cgtgaaagaa agtgaaaagc
    78781 tcaatcatgt tatttttacc gtttgtgtta tctaggattt gaatcaatta gagatgagat
    78841 gttgttgcca tggggctaat ccattgtctg atgtgatgaa tccggcggat ccagagtcaa
    78901 gtcatgtgag tctgtgacca ccttgtggtt aaccaaaaac atattaaaac gatggatttg
    78961 gtccggttaa acgtggtctt ctgggaatgg gtctcatatg gacctgatct aatccaaagt
    79021 acgggccttt tagtccacta aagaatctct agtttaaatt ggtgtaattt ggttttattt
    79081 ggaagctaca aatactaaga atttccacat gaacgtgtat ttgggtatcc acacgaccat
    79141 actctataca caattttttt tgttcgcatg cgtttgaatt ttgccaatta ggtcaatttt
    79201 taattagttg tttaaaagct tttgaattat ttatttatat tttcatgttt cattttcact
    79261 aactacttga aatatgaacc gaaagtccat tagcaataag attgttaaac aaaactaaag
    79321 ttaaaagtca ttttcactgg cagtggctcc ctcttttctc ttatagtgac tctacatttc
    79381 taaagagcca aacttcaaac attgagtgtc gatttttttt aataaaaatt ctttttaata
    79441 atcttagatt ttttttaatt tttttttctg gctcttggat acccatttgg ctcaacacta
    79501 tttgcttatc ctctcatatg cgataatcat gtctcttgtc tcattcgatg taacaaatac
    79561 tccacacaga aaatttctta acttctaaaa ctataagctc ctctatgaaa tcttaatttt
    79621 aaaccttgtg cgtcatttac gttgttcaca tcaaccatag agagttgcaa ttaactactt
    79681 gcaaatgatc tagtatatgg aatttggcaa gaatttccat gttcctcagt ttagactcat
    79741 cttaccaaag ctatatacag tatatcttta aatgactaaa catttgtgac gttttaaaac
    79801 tttatttgtg tggatatgtt tcgaagtaca aacggattaa ataagtgaac tgcaatgaaa
    79861 aaagtataag aaaatcaaaa taaaacgtaa tgtagttgga gtgggtgaat aacatcacat
    79921 caaaacaaat tcatcacacc atttgaaatg ttttcattag ataattatta cctcaatcat
    79981 tttgggattg acatttgcgc tcgagtcttc agtgacgttc tcccactttg tcttcttgtc
    80041 tcttaggatt ctctctcttc tccttaaggg acattaagct ttctagacca aaatgcacat
    80101 caactacgta ctctcaacca ataataacta gacaagatta tcaagttaaa aattcaacgt
    80161 aaatcatatt ttagactaat aatttcatgg ggtaaacttg tgattgtgtt gtgtgattaa
    80221 atttgcatgg gtaaaatttg ttatcttata gttcgttttc ctactcaaat tgtaaaatct
    80281 ggctttgata tatacaaaac ataagcacac taattctttt taaaaactaa aaagaactaa
    80341 aataaacaaa ggaaaacaca gttaggcaat gataagtggg ttatttgaga attcgtaaaa
    80401 ttattagcat aatcataact attatgatta ggactggcaa tatatagttg taaaaattgg
    80461 cagtaatagt ggttagtgga gcaagacctt agtaaagttt acaagtatct tagcatattt
    80521 gttttggcct ttctccatat ctttctatta aattagagaa atgatggact acggtcgtgc
    80581 ctaagataca ataatttaat agatcatgta gttttgtaat atttgattat ctgataaaga
    80641 ttatttaaac aagagatcaa atttacaccg caaatattaa taaaaagtta ggtatatata
    80701 tatatatata tagttaaaac atatttataa gtattcttaa tttggcaaat tggatagaat
    80761 tatttaaagg tacgaaaaca aaataccata gtataaaatg gatatacaat tataatattt
    80821 tcataaaaac aaaaggtgta gaattataaa aattatcgta aaaggtgtga tgatacaata
    80881 gactttgatt tggtgattgg cttatcctta atccaccaat caggtgtacc atcatgacat
    80941 catccatttt tcattaaaaa aacattataa caataaatta atatgttgat gatttttgga
    81001 gtttgcttaa caaagaagat cgtggaattt cgaattctca tatggtatta aagattaaga
    81061 ggccgatgaa tataatctga ccaaaaaaga gtttcaagaa caattaccaa cgagtcaaaa
    81121 tataatatat atgttagaaa aatgtgacaa aagttatatg tttttgtttt agttagaata
    81181 gcatgtttag atacgacaac atttacatgg catgtactat ttagattaaa ttacagttac
    81241 acaaaattat aaatttctta acagaataga agatctaagg gaattctttg gtaaaaaaaa
    81301 tgaaaaatca aggtaggcca atttcaggtg gtagtgtcat tgatgggacc aaaacaatga
    81361 aacattcaaa aacactttat agtttatgat ccagtgaaaa ataatactaa aagaatatca
    81421 gaaaaggaaa cactaagaaa aagcaaattg gaaaaaagta gaaaatgata aaataagaaa
    81481 aagaacttga ggctgtggaa gaagaacaaa ccgtgcaaag gacatgagac tgaaataaag
    81541 atgaaataga ctttgtctaa atgatatgac ttgatggtgt gtatttgcct ttcgtttgac
    81601 taacacagtg atatgcacac tctattttat tctaatttgc catattatgc atcaacaggg
    81661 aatttcaaag tttaagtcag tcaaatattt ttaggtgttg tgaatttcac attacaaagt
    81721 tataaagtag ttttaaagtc accagatgag aatctatgag atcaacaagt acagccaaat
    81781 gaatatccag tctgatgaat taaaaaaaac tatactacac atgttcaaca taaactatag
    81841 tgtttcttga atatatgtgg tttcctcaaa tagtaaggtg catcagtaaa acccgaaatt
    81901 agttattgaa ataaacaagc tccattattg tataactttc agtcgacacc caaaaagtct
    81961 atctaaagag gaccaatatc aatatgcaca tatttttaat taacattgcc tttctatgga
    82021 tggattatta taaacccatg catgcctaag tttttggtta tatttatctt aaagaaagat
    82081 atgtttttaa tagtagaata gtagcaagaa agaaaagagg agaccaaaaa aacgattttt
    82141 tcaattctcc aatcattaat tgtacaaaac tcaaaaacga ttttcctaaa gtttgatatc
    82201 gttatataaa aatccagaca tctattctct taatcttgac caactaagag ataacactcg
    82261 ctcattttat aacttagtta gttagttaaa tcaatgaatt ttcttttggt tttagtttgt
    82321 aatcactaat caatgatcat tatacaagtg tgtgtggttt taaactaaat aaaaggtatt
    82381 gttttaagtg gttgttgagt catcggctcc tcaattgtat tatagcctct gccttagcct
    82441 ttgtaatgaa catcataaaa cgacaaggca agcctgccta acacatcttg ctttcctagt
    82501 gcaagtaagg agtttgtttt tgtaaatagt ggtctttgac catatatcta tatataataa
    82561 aagaagagtt gaattaataa ttctgttctt gtatcaatat gatcttcttt gtattgattc
    82621 tataagtata aaaacatacc acttgagaca aacaaaaaac cataaatagg gttaaaggat
    82681 gaatcatgtg aatagaccat gcatggttcg agtatttcca ttgcgctaag gactgaagac
    82741 tggaaatgtt ttcaatgaca agaataaaca agtatttcac atatctctaa gattaattag
    82801 tactatatat gatatgggat gattggttaa gagatcatgc ataatcaatg ggttactaag
    82861 tactgtagat ttgggttttg tatacaatgt atattgaaac ttcggtatgc catgtttgtg
    82921 tgtggaaaaa ataggaaaag attgtcattt tttcggtaaa attctaattt attaattatt
    82981 gtattactaa catttatata ttaattatta agtctttagg tttgctttat ttttgtttac
    83041 gtctgtctgt gtgatattag tattatagta gaagaccaca tttttttata gtttatctag
    83101 gacctaatat atgcagaaat caatataata attaattaaa gaagagaagc aaatcttaaa
    83161 ggtcctatag atatataatc ttcttctttt ttctaaagag gaagaagaag agaaattggt
    83221 gattaatttt acgtagatgt tagaactaat tcatttagaa aaagatatat actttataaa
    83281 ttgacttatt tggcatcatc gccactttat atattggcta acaaaagcat cgtgtttcga
    83341 aactaaaata attttgaaaa ccccacaact aaaaactaca atttttttta tctctgatgt
    83401 aagcacataa cattgatcta aagcttgatt ttatccacaa tatatatgta catatggtac
    83461 ccaagtcctt atgtgtcatt atcatcataa tgcatgaaca tgatatagaa accttttcca
    83521 gttcatgtcc tgcatgaaca tcatgatcat gtttcttgta tgtgtatcgt ttagagatac
    83581 cactagatgg ccatggccct gttagtctgc tactcacatg tacacgacaa gatgccacca
    83641 cttggttgtt aaactaatcc tataatgaag tagcaccttc acgtgtcatc atatatacac
    83701 atccatatat aatttatgtg aatatgatac actatgatct atgcatacaa gccatgaagc
    83761 caaggttact ataaaattca agcattcaat tccttcccaa gtctcattct catgcatgga
    83821 caaccaatga atatacaata tatgtatggg gacttctaac caacatgttt atcgatcttt
    83881 acaacagcaa agtagccata gcagatttac acagcaacgt gtaaatactt ttttaaactt
    83941 ctctcagtaa gtcatttaca agaaaaaaaa ttatgtccat agccaatggg ttatgtctta
    84001 tatcgacata atctaaatta ttttttaaaa agcaaaaccc tcttaagcca atgtcacgaa
    84061 agccaccaat ttgcaaaaaa agttgtggtc cacttgtatg cctttctcag ctgtataaac
    84121 actccttctc atccaatctc caccattaaa ctcaccctct ttgagttcta aagagagaga
    84181 gagaaattga ccatgcagcc aaattatgat agctcaagtc ttaacaacat gcaacaacaa
    84241 gactacttca acttgaacaa ctactacaac aacttaaacc cttcaaccaa taacaacaac
    84301 ctcaatatcc tccaataccc tcaaattcaa gaactcaacc tacaatctcc ggtaagcaac
    84361 aactccacaa cttccgatga cgcaactgaa gaaatcttcg tcatcaacga gaggaagcaa
    84421 agacgtatgg tatctaacag agagtcagca agaagatcaa gaatgagaaa gcaaagacac
    84481 ttagatgagc ttctctcaca ggttgcttgg cttcgaagcg agaaccacca gcttttagat
    84541 aagcttaacc aagtctccga caacaatgat cttgttattc aagagaactc gagtcttaaa
    84601 gaagaaaact tggagcttcg tcaggttatc acatccatga agaagcttgg aggaggcata
    84661 catgacaaat attcttctcc gtcgtctatg gatgaattgg atcaagactt ttcttctatc
    84721 acagatgatc caagaactca tcatccatca tgagttgttc tgatcgagaa aaacattact
    84781 tcaagtttct gcctctaatc ttatctattt tctttctttg gtatcacttt ttaaaccgtt
    84841 taactacgta ccaaagtttg ggttttattt gtttttctgt tgttttgtca gaagataatt
    84901 aaatgatgga tatttgaaga tgatgctgta aacaaagatt tataattata tacataaatt
    84961 tggaaaagaa gagtataatt ttataataat tatacgtaga gaaataaaaa gaagacaaac
    85021 aactaccacc aaaccctctt cacccaatag agaagccaag tttgatatac ttgaagaaaa
    85081 gtaaattatt caaaaggccg cggatcttgt taattattct gcattctcag tgaggatagt
    85141 tcgaggagga tctttctgaa atcaatgaga tgattaaaaa tatcattcat ttacttaaaa
    85201 ctatccgttg tgcaattatg aagttcgttg tcgaaatgct tagaataact catcgtgaat
    85261 gataagatta ttatcttttg ataagataaa gatagaaaat gatcatgcaa caacaaaaaa
    85321 ggaaacttcc tgaaagaaga taagcttagt tcggaagact acttgggccg tcccctgaaa
    85381 cagaagttta tcgcgcaaga ataattgggc cttatatcag atcctttggc ccagcccgtt
    85441 agtattagac aagaccagtt gcgtgcgtca ttgttgaata tttcgaagtt tgatgatcga
    85501 tcgtcgctca aaatttaggg cttttcactt cacaatcccg atttggggtt ttctggtaaa
    85561 ctcctttaat ctcagctcgt cagacaaaat cgatctggga tgaatttgga tctaattgag
    85621 caaaaaattg tgttttttca atctattgaa tttcacatcc ttaaaccctt gcatattcaa
    85681 tctattgaat ttcgcatatt tttcctcaaa tttatccaaa atcatcccaa atctattgtg
    85741 acgggttgaa agtaagtttc tttatcgaaa atcagtttga atgaatgtta gggtttatat
    85801 tttgatggtg actgattccg atttgtataa atgttagggt ttatactggt ttctgactct
    85861 ctggtaagta tagagatgat tatatattaa atggtgtttt aaggcgtgtt cagatatagc
    85921 tgtgcttgtg ttgttctgtt ttggcatttt tcatttgttc tgtctttact tcttcttagt
    85981 cagtctgtgg atttcctttg taatggttat tggttagtta ggaactactc tcaggccttc
    86041 ttcacatgac accaaagttt tttgtggatt atgtggagga aattgctatt ttagtatatg
    86101 gtcattgaag caagataaga accttagaaa gcagagtgtt ataatttttc tgtcaaactc
    86161 atgctgtagt tgcagacttt ttcctacttc agattaagga gaatggtttt ttttttgtaa
    86221 gcaagaagtt aaaagagtga gaatctatga aggcccaggg accatgtaaa gtttgggaat
    86281 ggttttaaaa tttgatggct ttgagaatcg atctgaacta tccttagatt tttggaaaag
    86341 tgcaaaaaag tgcaaagtgc agcatcctta tatcacttta tgaacttttc acgtgaggtc
    86401 tcgaatccat cacttaacat taacacatag tataagctat acacttggtt gttattactt
    86461 atttcttctt acagttcttg aagccgagaa catatatggc tgatggtttc tacaattagg
    86521 aacgtgatat gactcatttt agtaagaagt tgtgatttac agctgaggag tctgtgttat
    86581 caacttgaat tgtagaatct ttttgttgtc agggaggcgt gaaagtgtca catgttcagg
    86641 ttatcgggaa gttattggct ttgaaccttg gcttccctct tagtagttag caaggtgaaa
    86701 tctgcgtttt cacttcttga tgatccatat ttcacaaatg gggatctgta ccaattagac
    86761 tggttttgtt taactaatgc agagaaagaa gaatactata gttttaatta gccaaaacta
    86821 caaacccatt tgcacaacag tagtaatact tcttgaagct aagaatttca ccaaacctaa
    86881 cataatctca aactaaaagt aatttacagc ttgcaatcta gtttttcttt ttgccacagg
    86941 agtatcagaa tgaaggaaca atcccatatc ctgtgttgta cattagcatc gtgttgaacc
    87001 cttgctcctc ggcttcgatt tctctctttg cgaaccggcc attgacccgc ggtcttatct
    87061 ctgcatatgc cttcctcgaa gcatacctta ttgtcttctc aaatttcctt gtcttcctct
    87121 tctctctgta tctcaggacc ctggcttctc tgtccattgg actgagttgt gttactgtta
    87181 tcatctggct tgcagggtca ggttgttgct ctactgtccc tttgggcgtt cttgggtgtg
    87241 aagctgttgt gacacatgct gttgactccg gcacaacacc agtttccatg gatgaaatgt
    87301 atgcctaatg acagaaacaa agacattctc aatccccctg gtaagaggac taaagagagt
    87361 cgatgcaaaa ggaagcatat attgttttta ttatagactt ctggtgaaat ttctatgtgc
    87421 tatagatcaa ctgttggcag tggatcagtg gatttgtgtg tatgatgaaa gaattcaccc
    87481 tgctgcgtta tgggaagatg ctaaattgaa ggggtaacaa atatacaaaa gccttacgtt
    87541 atggttaatg gaaccattgt cgttgtagtg agtccctgag gagccatatt tgatattgaa
    87601 ctgaaaattc tgttggttat ggcactggtg gccccttgat tcttcaagtt taagcggaac
    87661 aactctatct cccccgtagc tcgtctgtgg tacgctgcag ttttgttggt gttgactgta
    87721 ttcacctgtg aatttgtagt ccatactcga gttgtaatcc acaaggttta gatactcatc
    87781 actaaacaat aacccattgt tttggttatt gttatttttg tctgaattag ggaacagcca
    87841 cgaagcaacc tccttggcat ccttatcacc ttcttcacct tcctcttgat ccaccaccag
    87901 tctcttctct ggatcggtca ttgttttctc gctttggtgg tgagtagtgg tcatggagct
    87961 gaaagagttt ccagaaattg gtagaattgg aactcgctga tggcgtctag caagtgggtt
    88021 tgcagaatga acctctgaat cacaggctgt gcatagagag gcatcatctg cctcacacaa
    88081 aaaagcagcc ggagcacgct cacatgactc gcagacccgg acacgtttat ggcgggaagc
    88141 aacgcgattg gcagagtgaa cttgagcatc acagctcatg cacaagtagg cagaatctgc
    88201 atggcaatac acggtgcagg cgtttgaccg gcatgtgtca cagggtcgtg ccctgttgtt
    88261 ctctccacta cctatgtcgt tactctcttg tttcaacata ataactcaga tgtagtaagt
    88321 ttgatggtgt gggagctggt atctgaaaga aggggctaat aaagcttata tctggtgtga
    88381 gagaataagt agaggggaga tcgaatcctg agtgcctaca cgtggcacag cgttagtggc
    88441 tcttacatgt tattggatcc tcttgcagct agttgagctt ttgggaaggc ctatgtgtaa
    88501 agtgtaaagt gtaaagtgta aagtgtaaac atctcctcct atgcacttct tcgttgggac
    88561 ccgttcacaa gttgcttagg ttttgccact tgccatactg agattctcaa gaggaagtgg
    88621 tccggataat gccatggtgt tgcaggcaaa ttgttactat tttttcgtat caccttttac
    88681 tattttcata tgcattttat ttaaagtaaa gctagattcg ttttatctct ttggctttat
    88741 acaaagttta agtggttgaa tattcatcct gaaccttgtg attactgttc aggtatctct
    88801 ccgagtaagg cttcgagtgt cagagccatc accaactgtt atgggttgac tacctataca
    88861 aaggttagac aaactcgtga atatggtata gttgttgttc cattatttgt gaatgcatct
    88921 gcatcattta gaaagatttg caattgaaac tttcgaagga ttttctgatg aaaagtgtta
    88981 taatgtttaa tctggttcat aaagtcatgg taatgagaat catatcggaa aagtgacatg
    89041 aaaaacatag agacggtgga ttttctagga tcaaactcga atccgccaag tagtcttgag
    89101 actacaaatt agaatttacc tgacgcacaa gttaaaactt aaaaggcatt ttggagtcca
    89161 catgagcaat aattagattt atcatatata gtatgtagaa atttgcactt ggtaaccatt
    89221 atagtaagta gttacaaaac atgactcatg agtgttgtca catctctgta atttgggttt
    89281 atgatgatac tctatactat ttattgtagc tttattagat ctcaacctgt ggaagtaatc
    89341 taatacaaac gacacttgta tggaattttc aggacatgtt tctaagatca cagaggtaat
    89401 tgtgaagttt tctgctacac tcatttacta gtccacatga tccatagatg caatttaacc
    89461 atcttcactc tatttggtga cccattcatg tgtttagcat cgtgggtttt cctgtactaa
    89521 taaccattag tacttggagt tgccttgttg gtgttatgct cataatgttt actatgtgga
    89581 agctacagga tacgatactc tctaggtttg aggactagct ccagttacgc ttttgggtcc
    89641 agtgaatgta tgatacccat tatgtggtcc aaaaagaatg agatttgacg gacgctctag
    89701 tggccaaatt catatggcta ccttcactct atgccttaag agctgaaaag tgagtgtttt
    89761 ttttttgtat aaaatgctgg tcctaggata cacttttcgc atctcttcct ctttcatatt
    89821 tgcttacacc gcacttctct ttcccatttt gaactttaaa ctttgaaaag tttttttttg
    89881 cttggtaatt ggaacttaac atacaagttc ttgttattta ctggttttac gatgaatgta
    89941 atggcattta gaattgttat gaaatggtta tatgatcatt gaattctaaa gaaaagattc
    90001 taggttcttt agtaagcatt tttggagatc tttatcctgc caagttggat aagttgaggc
    90061 atctttggct tttagtgctt tggtgatgaa attttttgga gattgtaacg tggttcgagt
    90121 tcatgaagag taaattgtgt attggccttt tcacttgtag ctcaagaaaa aagtagtttt
    90181 gcttattatt gctcgttgac agtctctaat taagtttatt gttgtagcgg tttggaactt
    90241 ctctcacatg tgtaggcctt cggataactg ttacgagtaa tagatcatat gtaacaatat
    90301 cctcaaagtt gcatcgagat tttcaagaaa acactattgc ttatttgttt tcattcttta
    90361 tcaggtttcc gtggtttcga atactttgct tctttcagat taacgaaaac cctatttagt
    90421 tgcaaagact gagaagagaa taagagtcga gggaccatat aaagcttgta attgtacgtt
    90481 tatgcggatt ctccactttc catggctgtg agaaactatc tgaggaaaag tgcagtgacc
    90541 tttggcaaaa ggtaatcact tttatgcact ttcacgtgct agctcgaatc cacaccaaat
    90601 agtaacattc tattggctct gaaactcata gtgctccaag tggttgtcat tgcattttaa
    90661 aaattcctga caagaaattt agtagaaact ttgctacttc aagtttcctt ctttatgata
    90721 tgctagctcg tattatatgc aacatgggat atctttgttt tgcttgtgtg gcttataagt
    90781 ttatgttgca tgatcaaaac agatcactga ataaattttc tggtggtctg agaactcgct
    90841 gcagtgaatg aatgagatcc atgtaagtgg ccccaaaaga acataattta caacactctg
    90901 gtaggtaaat tcatgtggat actaaaactg actcatttat ggctaaaaag tattgatttg
    90961 gtacatgaat tcatcagctt aaccgttgaa gtgggaagct atcctagtgg taaataagtt
    91021 gatctctggc cctttccagg tggcaaaaag tgaaggcttt acagtgtcac cctttttctt
    91081 ttggttgcgt cgttattctt tagtgccagt atataccttg gaaaaagtga gctattattc
    91141 taaaagatag accaagaaat agatttctca cactgaatat ctttgttcat ttggatggtc
    91201 cataggcatt gacatattct gctagtagtg gttgtgagtg atagaatctt gttatccgag
    91261 acaacctcgt gggaatggat ttagcaccaa tgctaatcac taatcagtac aagaatatgc
    91321 gttgatgtaa ttgtacctat tagcattgtt cactcaggat tcttggttat ttgttacctg
    91381 actattcagt gtgtgatttt attggagttt tacatgttta cacttgtctc tgtaatctac
    91441 ttttggtata aaatcatatt gagtacaact ttcttttctc agggatgtgc gaaattgtct
    91501 ttggggcggc ataagtggaa tcatttatct tctacgtgat aaagtgatgt ggaaagtgtc
    91561 accaagaaag gaatcattaa ctttgaactt aggcaaggtg agttacgtgt tgactgttct
    91621 tggtacagct agctatacta atgcatatct ctttgtagca tcagtttgaa tttagactgt
    91681 agggcagtat ttcatagata agaggacttc taccaagtgg gcaaaatttg tattaactta
    91741 cagcagctaa gtatgagtgt atatctaatt aactcgtact agttaggcaa aactagtaaa
    91801 ctacagaccc tatatgcata aaaccgtggt aataacttgc aggaatttca aaccagaagt
    91861 aatttacaag catgcagtct agttttgcca tagcagcatc agaatgatgg aacaattcca
    91921 tatccggtgt caaatgttat cattgtggag aaagcttggt ttgcctcttc atcgacatct
    91981 ttcttctttg caaaccggcc cttgatccgt ggtcttttct ctgcatacgc tttccttgaa
    92041 gcatatctta tcgtcttctc aaatttcctc atcttcttct tctctctgta tctcaggact
    92101 ctagcttctc tgtcccttgg actgagcatc tgagctggag ggtaaggtgg ttggtctgtt
    92161 accgctttgg gcgatcttgg gtttgatact gttgcgtcac tcgttgttga ctccggcaca
    92221 actcccaggt ccatagatga aacattcacc taatgacagt aacaaagaca ttcttagaaa
    92281 tttacttcat ggatttgtgt gaaagaagca gcatgctggt catagtaacg gatctgaatt
    92341 aaatatatga aagcttacca tatgactgag ggaaccattg gagcttcgaa gagctcccca
    92401 ggagccacag ttgatactca gctgaaagtt ctgttgctct tggtacatgc cctttgatac
    92461 ttcaatttga agtggaacaa ctccatcttc cccatagctc ctctgaggta cgttgcagtc
    92521 tagttgatac tgattggatt gatctgtgaa ttgcttatca ctcgaactat aatcaacaag
    92581 gttcagaaac tcatccccaa tcgagaagcc attgttgtta ccactgtttt tccctgaatt
    92641 aggcaacaac catgaagccg cctctgcttc atcttcatcc tcttcttctt gaccaagcac
    92701 aagtctgttc tctggatctg tcactgttgt ctcacatgaa tggttagtgg ccgtggaact
    92761 gtaagagtac tcagaaatgg gcagaattgg aactcgttga tggcgtctag caagtgggtt
    92821 tgcggaatga atctctgaat cacaggttgt gcatagagat gcagcatctg ccttgcagaa
    92881 aaaggcagcc ggggctcgct cacatgattg acagactcga acacgttcat ggcgggaagc
    92941 aagacgattg gcagcatgaa cttgagcatc acaactggag cacaagtagg cagaatcagc
    93001 ccggcagtac acggtgcagg cggctgatcg gcatgtatca caggcttgtg cccagttact
    93061 ctctactttc aacatactaa ccgcagatgt tgtagttgtt tgatggtgag tgagatcgta
    93121 tgtaaaggca gcaggggact aagaaggcta tattagttgt tgaatggaaa tggaaaggaa
    93181 ggatagaatt ctgagggctg gacacgtggc gagaagtttg tgggtttgat gttgagtgat
    93241 catcttgtgg ctggctgagt ttttgagaag gggtccagtg cagagatgct tacagctttg
    93301 gaatcatcaa ccagcacgaa atgtgaaaga aagaaaaaaa ctaattgtct tcttatatct
    93361 ttgcaatggc accaatagtt actacttttt ctctctttct tcctcaataa gtgtaaacac
    93421 ctcttcctat gtaatcttct ataggaccca tccacatgtt acctaggttc tgaaacgtgc
    93481 aacttctaac tatttttgta tcatctacta ctattttggt aaagctggaa actttagtag
    93541 ctctttggct tgaccattag cctaatgttt atcttgattc ttaacttttg ccatgttcta
    93601 actgttcagg tttctctcat cgtctcatga tttcaattat aaaaattaaa tgatcactgt
    93661 ttagcattgt taaaaagatt atgactctta accatttgtt atcttcgaat gatgctaggt
    93721 gtcttttttg gtgatatgtt ggagataata gatatggcat gtcctaactt tgtttccttc
    93781 cacatcaagt cggtcaagct gatttggcca acggtggaga tccaaggagc caattggaat
    93841 ctgccaagtc gctacgagtc tctagagatt aggagccaca agttgaagca aatggtgggt
    93901 ccaaattaag gtgaataacg atagttatat caacatcacc tgtggtctgt ttatacaagt
    93961 ccaatttgct tatgatcacc atcatatttc atagttacaa aacatgtata agtctatcaa
    94021 gtgtttgtca catctcaatc acctttttga gaatatgata aaactcgata ttatctttac
    94081 tagcttttat tagatttcaa acttgtggaa gtaatcatat tcatgtgttc aaatctacat
    94141 gggtcaaata aatttggtgg agcaacaaag tttgttttta tttacatgat gttctactga
    94201 tgcaattaaa aacacagcaa ctaacaaagg taaaaactga ggatcaacaa acaaagcttg
    94261 ttttcctttc ttggcagtca gaaagggcta atctcacgag ccagtttcag taacaactct
    94321 ggtacaagac gctttctggg aggagccaac gagtctttgg tcagcccatc attgtcctcc
    94381 gcatgtatca cagagactat gtcatcaaag agttcgtctt tacctcctcg taagggatcc
    94441 tataaacaat actctcatga gttttattgt actcacactg agctaagtgt ttgtgtgtgt
    94501 gacacaatgt aaggtaagtt gactgattta tgtggcttac ctgaagaaat aagtcagtat
    94561 gtgtctttcc gctgtataaa acaagctcgg cttttgctcc aacagcttgc agagcgtctg
    94621 taaaagtttt gctgcaaacg aggtggtttt agtatcccaa aaggtttcat cagtaatgta
    94681 tcacttcaag aagatgatca tatatacctt tcatcgcatg gtatggaata atctgaggat
    94741 ccgtggaaaa gtataatagg aggtaaaaga gaagcagctt ttccaacaac tgggtctttc
    94801 agtcttactt ccggagagaa tttctcaaag gactcttctc cttccattat gctgcaagtt
    94861 ggagttgaac attagatctg atcagactgc gtttaggatt tggttaacca agcatttacc
    94921 ttaggaaaat cgagcgatac agaccccgat tatggaagtg atcaaccaac ttgtatagat
    94981 tgtacctatt gaagttcaaa atgataagca gatcaattgc tgtagaccaa aaagcacata
    95041 gaagccaacg ggaatccaaa agcttagaag ataccctcca gataatccaa aataagcttt
    95101 tatctgggac actgtccagg agatgctctc tccttttaat tctttagtag cttgttccaa
    95161 tagagcacaa gcggctatat gggcaccagc tgattgcccc atcaggtaga tcctagagag
    95221 acaagcagat acatgcagtt taatagccga gagaccaatt ggaagatcaa atggtaaata
    95281 aaaacaaagc caatgagatg aaacctgttg gggtcacctc caaatgcaga gatgttattg
    95341 cagacaaatg agattccttg agaagcatca gtcaccatat cactaattgt tccctgagga
    95401 aagttcctat accataaaga acggattgct tggtaaatgc atgaaagttc ttcctatatt
    95461 cataaaagac gactagtttt ttgaattgtg taatttgttt acctgtagtc aaggcatgct
    95521 acaatgatat ctctttctgc tagctgcatt cccaagagcg agccccaagc tttgtaccta
    95581 aatatcagta caagattagc aaacatgaac ttattaacaa gcaaccagct agtacaagaa
    95641 gatgaaactt gagtgagtca gtgagataag aatacagagc ccatcatgat ctttactttt
    95701 ttctttttgt aactcaaaca tcaacaaaag aacagtgaag gggaaaactt ctataagtgg
    95761 gacacgagaa attgtaaaac aaacaaattt caacattatg cagaagagaa tgctgtaaat
    95821 ctgatgtgca acccacccaa taatccaagc tccacccgtc acaaaaacca caaccggctt
    95881 caagccatcg ttgttgcttg gcaagtacag atccagccta tcaaatcacc gttcatacat
    95941 caataatctc aagacaaagg tgatgtgata aaagcaggca ttcaacatac cacttaaggc
    96001 cgatgtgaaa ggagaaggta agattctatt cagttcacac acaaacctgt tccttggttg
    96061 atctccatac actatactcc tccggacttg ctttgagaaa aaataactat atgcaactgc
    96121 acaagataat acaaacttga gacgaggaat caaagactaa ttttccaatt aaaacaacat
    96181 cttaatcaaa aggaaaaatc ctttctatga atttatttat cagcaaagaa aaaaaaaaaa
    96241 aaatcaaacc ttgaagaaag ccaggcataa gaagcatagc ataacatgta agggcaagta
    96301 attttgtcat ccatcgatag cctaccctga acaaaactta acaattagat caatccttgc
    96361 tcaactggaa atataaaaag aagaagttaa acaagagcaa aacaacagca catggagtaa
    96421 ctttcataat tagagtaaag ttccaaaata aaagacagag aacttttata tatcattgga
    96481 ttctttgcag agcaaggcaa agccagctaa tatctacacg aattacctcc ctaagcgtaa
    96541 tcatcaatat acctaaatcc aaaaacaggg acaatcgaga tcagtacccg aggtatcgaa
    96601 gaagcttgaa gctaagtcca gtaattagat acgtttcagc tgccgcgtgg ccgatatcgc
    96661 gaccgaacga ttgctgccgg aaaatccgac gaggtccttc gtcaaccggc gacttcccgg
    96721 aaactcgacg acgtaacggt tcaccgttaa gaagagtcgt tctatcggag tcctcatcgg
    96781 gtagaacttc ctcgatctcc gataccgtcg aggtcatcgg ccagcatcgc tgctccggct
    96841 gctgagtctg aagaggcgaa tgcatctttt ccgccgtgaa atagtggatc tc
//


BioPerl-1.007002/t/data/AY095303S1.gbk000444000766000024      1573413155576321 16610 0ustar00cjfieldsstaff000000000000LOCUS       AY095303S1              2375 bp    DNA     linear   PLN 21-JAN-2003
DEFINITION  Chlamydomonas reinhardtii c-type cytochrome synthesis 1 (CCS1)
            gene, ccs1-ac206 allele, 5'UTR and exons 1 through 6.
ACCESSION   AY095303
VERSION     AY095303.1  GI:25986619
KEYWORDS    .
SEGMENT     1 of 2
SOURCE      Chlamydomonas reinhardtii
  ORGANISM  Chlamydomonas reinhardtii
            Eukaryota; Viridiplantae; Chlorophyta; Chlorophyceae; Volvocales;
            Chlamydomonadaceae; Chlamydomonas.
REFERENCE   1  (bases 1 to 2375)
  AUTHORS   Dreyfuss,B.W., Hamel,P.P., Nakamoto,S.S. and Merchant,S.
  TITLE     Functional Analysis of a Divergent System II Protein, Ccs1,
            Involved in c-Type Cytochrome Biogenesis
  JOURNAL   J. Biol. Chem. 278 (4), 2604-2613 (2003)
   PUBMED   12427747
REFERENCE   2  (bases 1 to 2375)
  AUTHORS   Dreyfuss,B.W., Hamel,P., Nakamoto,S.S. and Merchant,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-APR-2002) Department of Chemistry & Biochemistry,
            University of California, Los Angeles, P.O. Box 951569, 405 Hilgard
            Avenue, Los Angeles, CA 90095-1569, USA
FEATURES             Location/Qualifiers
     source          1..2375
                     /organism="Chlamydomonas reinhardtii"
                     /mol_type="genomic DNA"
                     /strain="ccs1-ac206"
                     /db_xref="taxon:3055"
     gene            order(124..2375,AY095304.1:1..1465)
                     /gene="CCS1"
                     /allele="ccs1-ac206"
     mRNA            join(124..330,512..825,1045..1233,1418..1798,2000..2131,
                     2253..2345,AY095304.1:6..303,AY095304.1:495..677,
                     AY095304.1:863..1465)
                     /gene="CCS1"
                     /product="c-type cytochrome synthesis 1"
     exon            124..330
                     /gene="CCS1"
                     /number=1
     5'UTR           124..206
                     /gene="CCS1"
     CDS             join(207..330,512..825,1045..1233,1418..1798,2000..2131,
                     2253..2345,AY095304.1:6..303,AY095304.1:495..677,
                     AY095304.1:863..1098)
                     /gene="CCS1"
                     /codon_start=1
                     /product="c-type cytochrome synthesis 1"
                     /protein_id="AAM44130.1"
                     /db_xref="GI:25986621"
                     /translation="MQPYASVSGRCLSRPDALHVIPFGRPLQAIAGRRFVRCFAKGGQ
                     PGDKKKLNVTDKLRLGNTPPTLDVLKAPRPTDAPSAIDDAPSTSGLGLGGGVASPRTL
                     VQSNAVQVAWRRLMKELSSLPRAIAIMALIAVLSGLGTFIPQNKSIEYYLVNYPDGAE
                     KVLGFLTGDLILTLQLDHIYTADYFYLSMGLLAASLAACTYTRQWPAVKVAQRWRFLT
                     QPKSLLKQGRTEVLPNARVSDLGAILLQRGYQVRESCACQRTAAALLLRFHSVAADPS
                     PLLSFVLVAQVFVKDGSLYGFKGLAGKLGPIGVHAALLLCLFGTAWSGFGTLKGNVMC
                     PEGQDFQVASFLQPSSPIASMPASASNVIHVNKFTIDYRPDGSVAQFYSDLSLLDPAQ
                     GGKEMMRKTISVNDPFRFNGVTMYQTDWSLSAVTLRVLGQDAPLARAAQAAEAQAAAS
                     TSGPTSSASSTSDALPQQRTAFNLPMASLEGKPGVAGRLWATFLPLAEPGQDGSAPKG
                     ISILARDPQSVVFYDAKGQFVGVRRPGSGKPIEVEGLALVVEDVTGATGLELKSDPGV
                     PAVYAGFGGLMVTTLISYLSHSQVWALQQGSSLFVSGRTNRAKLAFDRELDDILNAVP
                     ELPPTAATTVASSASTAAPAPTAKQ"
     exon            512..825
                     /gene="CCS1"
                     /number=2
     exon            1045..1233
                     /gene="CCS1"
                     /number=3
     exon            1418..1798
                     /gene="CCS1"
                     /number=4
     variation       1648
                     /gene="CCS1"
                     /note="results in readthrough of typical intron 4 and
                     addition of 36 amino acids within stromal loop"
                     /replace="g"
     exon            2000..2131
                     /gene="CCS1"
                     /number=5
     exon            2253..2345
                     /gene="CCS1"
                     /number=6
BASE COUNT      474 a    718 c    697 g    486 t
ORIGIN      
        1 cacatacgac cccaagcagg gccctgcgtg ggtgaaatgc cacacgcggc acgaatccgt
       61 cggccactcc atgaattgcc cacaaggcca caattgagcc tacaaggatg tggaagtgat
      121 aactacctag ctccactacc agctgcgact gcccagttct cgagctttct ttctgtccgg
      181 ccccgcgctt gcacgcgtgc acaaaaatgc agccatacgc ttccgtgagc gggcgatgtc
      241 tatctagacc agatgcattg catgtgatac cgtttgggcg accgctgcaa gcaattgccg
      301 ggcggcggtt cgttcgctgt tttgcgaaag gtgcgcagcc ggggaaagaa cacacgaatg
      361 ggtgtgcagg caattgatgg tttcactatc aattaattat cagggctggg ttgtacgcac
      421 ttggcagtgg acttgcatgc gtggaagcga tgtcgccacg ctgctattca aatattaagt
      481 tggagcctgc tctgctggac ccaaaacata ggaggacaac ctggtgacaa gaagaagctc
      541 aacgtgacgg acaagctgcg cctcgggaac actcctccca cgctggacgt gcttaaagcg
      601 ccacggccaa ccgacgctcc ctcagccatc gatgacgccc ccagcacttc gggcctgggg
      661 ctgggcggag gagtggcgag ccccaggact ttggtgcagt ccaatgccgt gcaggtggcg
      721 tggcgccggc tcatgaagga gctgtcgtcg ctcccacgcg ccatcgccat catggccctc
      781 atcgccgtgc tgtcgggcct gggcaccttc atcccccaaa acaaggtgcg ggggaatgcg
      841 acacatgaag ttaatgcaat tctgccaacc aagctgaagc acttgcattg gagccgcgcg
      901 ggatgagcca gcacaccagc tttgacctgc gcgtaccgca accaggcacc tacgccctcc
      961 cgcgcagtgc ctccctttcg gtctctccga ctcttccaac ctgtctgacc ctcatctcca
     1021 ccccccaatg tatccatcca acagtccatc gagtactacc tggtcaacta cccagacggc
     1081 gcggagaagg tgctggggtt cctgactggc gacctcattc tgaccctaca gctggaccac
     1141 atctacaccg ctgactattt ctacctgtcc atggggctgc tggccgcctc cctggctgcc
     1201 tgcacctaca cccgccagtg gcccgccgta aaggtgcgtg cgtaaagggt ttgggagtcg
     1261 taggaggaag gcagggtaga tggcgggaag gggcggacag agaggaagga ttggggcgta
     1321 ggttgtggtg acggagaagg cccggttgga gcctgcacgg gggttaggta aaggtgaaag
     1381 gcaggcaaat accgcccact cgtcgtgttc ctgacaggtg gctcagcgct ggcgcttcct
     1441 gacgcagccg aagtcgctgc ttaagcaggg gcgcacggag gtgttgccca acgcgcgtgt
     1501 gtccgacctg ggcgctatcc tgctgcagcg gggctaccag gtgagggaga gctgtgcgtg
     1561 tcagcgtacg gctgctgcat tacttcttag gtttcactcc gtcgctgctg acccttcacc
     1621 tctgctttcc tttgttcttg tggctcaagt gtttgtgaag gacggctcct tatacggctt
     1681 caagggcctg gccggcaaac tggggcccat cggcgtgcac gcggcgctgc tgctgtgcct
     1741 gttcggtacg gcgtggagcg ggttcggcac cctcaagggc aacgtcatgt gcccggaggt
     1801 gagggagcag aggacgcaca tggttgtctg gtggcggcac ggagacacgg tagtgacaag
     1861 ccggctcagg gcagtttggg aaggtggtga tgcaagttgc tggccaggga agtacgctca
     1921 cccatgttct ccgagtgctt gctatgttcc aacacgatcc cagaaatcgc acgaggacca
     1981 atcaacgttg cgcctgcagg gtcaagactt ccaggtggct tccttcctgc agccgtcctc
     2041 gccaattgcc agcatgcccg cctccgcctc caacgtcatc cacgtcaaca agttcaccat
     2101 tgactaccgc ccagatggct cagtggcgca ggtgcgtgcg ctacaggttg gccggaacca
     2161 tgccacactt tgcaccctca ccattcctgc gatagtgttg gttctcatca gtactgacgt
     2221 attcatctcc ctccatctgc cctatcccgc agttctactc ggacttgtcg ctgcttgatc
     2281 ccgcccaggg cggcaaggaa atgatgcgca agaccatcag cgtgaacgac cccttccgct
     2341 tcaacgtgag aatacaacgc atgacggtac ctgct
//

BioPerl-1.007002/t/data/AY763288.gb000444000766000024       646113155576321 16224 0ustar00cjfieldsstaff000000000000
LOCUS       AY763288                 723 bp    DNA     linear   INV 18-JAN-2006
DEFINITION  Leishmania guyanensis putative elongation factor 1 beta gene,
            complete cds.
ACCESSION   AY763288
VERSION     AY763288.1  GI:54300415
KEYWORDS    .
SOURCE      Leishmania guyanensis
  ORGANISM  Leishmania guyanensis
            Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae;
            Leishmania; Leishmania guyanensis species complex.
REFERENCE   1  (bases 1 to 723)
  AUTHORS   Walker,J., Acestor,N., Gongora,R., Quadroni,M., Segura,I., Fasel,N.
            and Saravia,N.G.
  TITLE     Comparative protein profiling identifies elongation factor-1beta
            and tryparedoxin peroxidase as factors associated with metastasis
            in Leishmania guyanensis
  JOURNAL   Mol. Biochem. Parasitol. 145 (2), 254-264 (2006)
   PUBMED   16325936
REFERENCE   2  (bases 1 to 723)
  AUTHORS   Vergel,C., Gongora,R.E., Saravia,N. and Walker,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-SEP-2004) Biochemistry and Molecular Biology, Centro
            Internacional de Entrenamiento e Investigaciones Medicas, Av 1a
            Norte No. 3-03, Cali, Valle, Colombia
FEATURES             Location/Qualifiers
     source          1..723
                     /organism="Leishmania guyanensis"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:5670"
                     /clone="WHI/BT/78/M5313"
                     /dev_stage="promastigote"
                     /note="subgenus Viannia"
     mRNA            <1..>723
                     /product="putative elongation factor 1 beta"
     CDS             1..723
                     /note="similar to elongation factor 1 beta of Leishmania
                     major (Friedlin)"
                     /codon_start=1
                     /product="putative elongation factor 1 beta"
                     /protein_id="AAV32818.1"
                     /db_xref="GI:54300416"
                     /translation="MSVKDVSKKAAELEARLGGKLFLGGAKPTAEDVRMLNDLLGANH
                     ASLYRWVKNMATYTEGERKAWGAPVRTAAPELRMPAPAAAAPAAAKKPVPAAAAPAAA
                     KKPAPAPKAVAPAEDDDIGLFGETTEEEQAALEAKRAKDAEKKKAKKDVIAKSPILFD
                     IKAWDDTVDLEALAQKLHAIQRDGLVWGDHKLAPVAFGVKKLQQLVVIEDDKVSGDDL
                     EEMIMGFEDEVQSIDIVAWNKI"
     misc_feature    379..381
                     /note="putative; phosphorylation site"
ORIGIN      
        1 atgtctgtga aggacgtgag caagaaggcc gccgagctgg aggcgaggct gggcggcaag
       61 ctgttcctgg gcggcgcgaa gccgacggcg gaggacgtga ggatgctcaa cgacctgctc
      121 ggcgcgaacc acgcgagcct gtaccggtgg gtgaagaaca tggcgaccta cacggagggc
      181 gagcgcaagg cgtggggcgc accggtgcgc actgctgcgc cggagctgcg catgcccgcg
      241 cctgccgcgg cggcgcctgc tgccgctaag aagcccgtgc ctgccgcggc ggcgcctgct
      301 gccgctaaga agcccgcgcc tgcgccgaag gctgttgccc ctgcagagga cgacgacatc
      361 ggcctgttcg gcgagacgac ggaggaggag caggcggcgc tggaggcgaa gagggcaaag
      421 gacgcggaga agaagaaggc gaagaaggac gtgattgcga agtcgcccat cctgttcgac
      481 atcaaggcgt gggacgacac ggtggacctg gaggcgctcg cgcagaagct gcacgcgatt
      541 cagcgcgacg gcctggtgtg gggtgaccac aagctggcgc ccgttgcgtt cggcgtgaag
      601 aagctgcagc agctggtcgt gatcgaggat gacaaagtgt ctggcgacga cctggaggag
      661 atgatcatgg gcttcgagga tgaggtgcag tcgattgata tcgtcgcctg gaacaagatc
      721 tga
//
BioPerl-1.007002/t/data/AnnIX-v003.gbk000444000766000024      5775013155576321 17056 0ustar00cjfieldsstaff000000000000LOCUS       DMSOS       14000 bp    DNA             INV       21-Aug-2001
DEFINITION  D.melanogaster FlyBase-curated sequence: AnnIX.v003
ACCESSION   AnnIX.v003
SOURCE      fruit fly.
  ORGANISM  Drosophila melanogaster
            Eukaryotae; mitochondrial eukaryotes; Metazoa; Arthropoda;
            Tracheata; Insecta; Pterygota; Diptera; Brachycera; Muscomorpha;
            Ephydroidea; Drosophilidae; Drosophila.
REFERENCE   1
  AUTHORS   FBrf0104946 == FlyBase, 1996-, other
COMMENT     Reference sequence of AnnIX == FBgn0000083
COMMENT     This record is derived from the following:
            AC009344 AC009344.8 17-FEB-2001
            AY007377 AY007377.1 14-SEP-2000
            AF261718 AF261718.1 28-AUG-2000
            M34068 M34068.1 26-APR-1993
            AA390914 AA390914.1 23-APR-2001
            AW942105 AW942105.1 23-APR-2001
COMMENT     The following contributed to reference sequence development:
            bases 1..14000 == AC009344 14575..28574
COMMENT     Reference sequence based on BDGP genomic sequence.
FEATURES             Location/Qualifiers
     gene            1..14000
                     /gene="AnnIX"
                     /organism="Drosophila melanogaster"
     exon            4191..4247
                     /comment="exon boundaries inferred from FlyBase alignment
                     of cDNA to reference sequence"
                     /evidence="experimental"
                     /gene="AnnIX"
                     /label="AnnIX|exon|1"
                     /number="1"
                     /primary="AF261718:1..57"
                     /primary="AY007377:1..57"
     mRNA            join(4191..4247,6408..6461,7031..7739,7800..7981,
                     9240..9499)
                     /gene="AnnIX"
                     /comment="mRNA structure inferred from FlyBase alignment of
                     cDNA to reference sequence"
                     /evidence="experimental"
                     /label="AnnIX-RA|mRNA"
                     /primary="AY007377:1..1263"
                     /primary="M34068:<1..1095"
                     /symbol="AnnIX-RA"
     mRNA            join(4191..4247,6408..6461,7031..7739,7800..7981,
                     9686..9879)
                     /gene="AnnIX"
                     /comment="mRNA structure inferred from FlyBase alignment of
                     EST and cDNA to reference sequence"
                     /evidence="experimental"
                     /label="AnnIX-RB|mRNA"
                     /primary="AF261718:1..1197"
                     /primary="AW942105:complement(>512..1)"
                     /symbol="AnnIX-RB"
     intron          4248..6407
                     /label="AnnIX|intron|1-2"
     exon            6408..6461
                     /comment="exon boundaries inferred from FlyBase alignment
                     of cDNA to reference sequence"
                     /evidence="experimental"
                     /gene="AnnIX"
                     /label="AnnIX|exon|2"
                     /number="2"
                     /primary="AF261718:58..111"
                     /primary="AY007377:58..111"
     CDS             join(6432..6461,7031..7739,7800..7981,9686..9739)
                     /gene="AnnIX"
                     /aa_size="324"
                     /derived_from="AnnIX-RB"
                     /evidence="predicted"
                     /label="AnnIX-P2|CDS"
                     /symbol="AnnIX-P2"
                     /translation="MSSAEYYPFKCTPTVYPADPFDPVEDAAILRKAMKGFGTDEKAII
                     EILARRGIVQRLEIAEAFKTSYGKDLISDLKSELGGKFEDVILALMTPLPQFYAQELHD
                     AISGLGTDEEAIIEILCTLSNYGIKTIAQFYEQSFGKSLESDLKGDTSGHFKRLCVSLV
                     QGNRDENQGVDEAAAIADAQALHDAGEGQWGTDESTFNSILITRSYQQLRQIFLEYENL
                     SGNDIEKAIKREFSGSVEKGFLAIVKCCKSKIDYFSERLHDSMAGMGTKDKTLIRIIVS
                     RSEIDLGDIKEAFQNKYGKSLESWIKDDLSGDYSYVLQCLASY"
     CDS             join(6432..6461,7031..7739,7800..7981,9240..9293)
                     /gene="AnnIX"
                     /aa_size="324"
                     /derived_from="AnnIX-RA"
                     /evidence="predicted"
                     /label="AnnIX-P1|CDS"
                     /symbol="AnnIX-P1"
                     /translation="MSSAEYYPFKCTPTVYPADPFDPVEDAAILRKAMKGFGTDEKAII
                     EILARRGIVQRLEIAEAFKTSYGKDLISDLKSELGGKFEDVILALMTPLPQFYAQELHD
                     AISGLGTDEEAIIEILCTLSNYGIKTIAQFYEQSFGKSLESDLKGDTSGHFKRLCVSLV
                     QGNRDENQGVDEAAAIADAQALHDAGEGQWGTDESTFNSILITRSYQQLRQIFLEYENL
                     SGNDIEKAIKREFSGSVEKGFLAIVKCCKSKIDYFSERLHDSMAGMGTKDKTLIRIIVS
                     RSEIDLGDIKEAFQNKYGKSLESWIKEDAETDIGYVLVTLTAW"
     intron          6462..7030
                     /label="AnnIX|intron|2-3"
     exon            7031..7739
                     /comment="exon boundaries inferred from FlyBase alignment
                     of cDNA to reference sequence"
                     /evidence="experimental"
                     /gene="AnnIX"
                     /label="AnnIX|exon|3"
                     /number="3"
                     /primary="AW942105:complement(512..376)"
                     /primary="AF261718:112..820"
                     /primary="AY007377:112..820"
                     /primary="M34068:1..655"
     intron          7740..7799
                     /label="AnnIX|intron|3-4"
     exon            7800..7981
                     /comment="exon boundaries inferred from FlyBase alignment
                     of cDNA to reference sequence"
                     /evidence="experimental"
                     /gene="AnnIX"
                     /label="AnnIX|exon|4"
                     /number="4"
                     /primary="M34068:656..837"
                     /primary="AF261718:821..1002"
                     /primary="AW942105:complement(375..193)"
                     /primary="AY007377:821..1002"
     intron          7982..9239
                     /label="AnnIX|intron|4-5"
     intron          7982..9685
                     /label="AnnIX|intron|4-6"
     exon            9240..9499
                     /comment="exon boundaries inferred from FlyBase alignment
                     of cDNA to reference sequence"
                     /evidence="experimental"
                     /gene="AnnIX"
                     /label="AnnIX|exon|5"
                     /number="5"
                     /primary="AY007377:1003..1263"
                     /primary="M34068:838..1095"
     exon            9686..9879
                     /comment="exon boundaries inferred from FlyBase alignment
                     of cDNA to reference sequence"
                     /evidence="experimental"
                     /gene="AnnIX"
                     /label="AnnIX|exon|6"
                     /number="6"
                     /primary="AF261718:1003..1197"
                     /primary="AW942105:complement(>193..1)"
BASE COUNT     3803 a   3178 c   2983 g   4036 t
ORIGIN
        1 accgttagaa atgttatgcg ggatacatag ttaagttgca taccctttga gttacaatca
       61 ctagttaata atatctacgt tattaccaac acgcacactt tatcgtaata cctccttgaa
      121 gtttaattta tacatcaact ttatcagtca aaactttgat ttcgtctgac acttttttcg
      181 attacgatcc gtcgccaata attgcgataa atcttatcaa gtctttttgg gattggcgct
      241 caaatttaca atatggccgt acatcctact tatgtatgtt ttttaactaa ttaatcacca
      301 caatgcaaag tactctttct ttgttgagcc catatgcact cacatttgca ccatgaatca
      361 tgtcagtagc tcgtttcatg taacaatttc tactttgcca gattacgatg cgttcggaac
      421 aggcagataa gaattcggcc catccaagaa aggccttgac agttctaccc caaaatagag
      481 atatcctcgt gatattagaa ggaacccaac aatatgctcg ttcttatctt cttatagaaa
      541 tttgtgaatt cccgtatcca atgaaatcat tttacttagt aaaatgattt gttaggcctt
      601 aaaaaaaaac aaaaacaccc gaactatcag taccacaatt taagagagaa ctcgttatta
      661 tttaacttta ttaattatgt atttctttat caaaagagca gactttttgt ttgtgactgt
      721 cttcaacatt agatccgtct ttaacattag atcagatcac ctgacacggg aaactctcgt
      781 agactttata caattcaaaa aaaccaaaat cgttacttga cacaaatatc ataactaatg
      841 cataaaatat gaaatgagag atatctaaaa tagcttggca tattttcttg gtaaaataaa
      901 tgtgttaaat acaaagaatg taaaatgcaa taaatgatac atatatcaaa aatggaatac
      961 cacggttact ttaagtgcta gcataacaaa ttacaataat aattcaatat ctagccattc
     1021 gttgcacata atttggaggg ttaagagggt aaacaatgga tgggaaatgg gctgggttag
     1081 ttgcgaattg gtttatatgg tttataatcc aacatcagta ttatcgtttt cgttagtatg
     1141 taaatacaat ttgattttgt tctatcgtga atttcaattg gaagctttta tgagttctgt
     1201 cccaccacct gcacgtagtt ggctggaaag agtccgtagc ggttcttgca caatcccctc
     1261 caccacccat cgtcgatctt ctcgatgtgg gtgatcacgt catctggatc aaaggatatc
     1321 tcgtcgtcat ccgccgcctg gtagtcgtac agggcaatgg cgtggattcc ggtgtcctcc
     1381 agatagtcgg ccaaattgtc tgagttcgcg tagattgcct cctcgggaac ggttgcggtg
     1441 ccactcggag caacagcctc tgaaacggtt ccattcgttg gtggcaaggg cgaggcagcc
     1501 ttaatctcgg cctggttctg gtacagtggc tcttcttcaa ctactggctc aggatcggct
     1561 tgaggttgcg gctcaggttg gacttggact tgggcgtgga cttcgggttg aggcgtcggc
     1621 acatacactg gtgattgcgg ctcacttctg ggaggcgtgt ccacggtctc aacctcaatt
     1681 tggggcacca catctggtgg tggagctgca gccttggcca ctggagctgt ttccggctct
     1741 cgagcgggga ccactgtcgg agtaggagca accgcagctg atgttgtact tgccgttggc
     1801 tcctcctttg cttctaattc tattttaaca ggctgcgcct tgggaatgat aatgggttcc
     1861 tttcgtgctg gaggggtttc agaaacaggc gactgcatct ggttaaatgc actgatagca
     1921 ttgccaatgc caccggtccg acctgtctgg atggccgccc tgctgccctt tggaggcggt
     1981 gcttccgtcg aggtacgagg agtgttctcg gccacagtct tcttggcggc ttcctcccga
     2041 tcccgcttgt ccttggcctc acggagacgt ttctgttcct cggcccgctt acgtgactcc
     2101 tcctcggagt ttttagccag attctcgaac ttggcacgca aattggaagg cttggcacct
     2161 tcgatgactg gcttgacctt gtggtccacc tggctggcgt gcttctgcgg agcctctttg
     2221 tggtcccatc ccaccgcgga cttgtccttt cggtcctcct gaacgccaaa cttgccgcca
     2281 aagcccttgg agtaatctta tgttgggaga agatataaat aaaataatca gacatgaaca
     2341 tactaagaaa aaatcaatga gaaattcatt tccgttaggt aacttaccct tctgagactc
     2401 gtgcttctcc accttctcga tgtgatccca gcccacggcg gatttatcca cccgatcgga
     2461 ctgcactcca aatttgcctc cgaagccggt ggcgtaatcc ttctgggagg cgtgcttctc
     2521 gaccttttcg acgtggtccc agcccacggc agacttgtcc ttgcgatcct cttgcactcc
     2581 gaactttccc ccaaaaccat cgctgtagtc cttctgcgag gcgtgctttc ccaccttgcc
     2641 ctggtagtca tgacccacag ccgacttgtc catgcggtcc ttctcaacgc caaacttgcc
     2701 cccgtatccg tatcctgcgt tctgatcctt cagcagctgc ttcttcttgt ccagatcggc
     2761 ctgctccgtc tcctcgcgca gcttgtccat gctaaaaaga ataaagaaag ggaacaatga
     2821 acccgatacc cagtgtttcg agaatttcgg atgactcact cgatggtgcc tgctgtgcga
     2881 ccgctgccgt cgatcgtctt tgatccccag cgctgctcct gctcactgac atcgttcacg
     2941 aagtccggat ccgtctccca gtcgtcgtcc tccgcggagg ctgcactggt ggcctgaatc
     3001 tggtgaccgg cacttgcctt ccacattctt tttaccggtt tctggtcgct ggttactcgc
     3061 ttatccttat ctgctgggta gatagataaa caccatgacg agtgtgagta gtcggggcag
     3121 gttttcagtt gcaggggctc cgcttccgat tcgtggccca gataacaagt cacaaaacac
     3181 cgaagaaggg aggggccgac aaagccggat cgggaacaag atgccactgg cgctctatgt
     3241 tcatatgtat actcacatcc cgatgactaa ctcctactgc aagaggaact tatgatctga
     3301 tgccgctagg gatgtctgca aatttctggg aggagaaggg ttaaacaatt gattcataaa
     3361 gagaccaaca aacgggaaac taactgaact aaatttcatt cgatacaatg gatgcatcga
     3421 tatgctacga aaagccgata aattattgtg atgagcttga caaaaggtag ttgctgcagt
     3481 tttaggggcg cccaatttaa atgattaaga gatacagtcg tggttctttt actttattcg
     3541 ataagtcaat gcaccgatat atactgcagt accaatatat gtgatcgtga tcaatagaac
     3601 tgagtgctcg ggcaaaaggt atttgatgtt ataccaagtg gcgccatagt aatttgtata
     3661 attaataaga ttctgccaga acggtaatta acaggtataa gagttgactt ttttcatata
     3721 accgcaaaca tatcatcgat atatcgatag ttttggattt gaatttgctt cgatgtcggc
     3781 tgacaattaa cgtaattggt ttttatatat agttataaaa atacaaataa aaatagttat
     3841 aaaacggctt aggaaggaac aggatattta tttaactgta ttgccctaac ggctgaatat
     3901 tgaagtcaaa ggttacattt tgaaattcaa tgcgtaatca gatcttattt tcccaatgtc
     3961 gtcattatca caacggaaat atcatgaatg tctcaacagc ttccaatgcc gatgattcat
     4021 ccatctcgga acactttaga ttctacggtg tatactatga cgacgcagaa gataccagct
     4081 tccagttagg cgctaccacc gaatatttcc tagcaacaac aacctatcgc cggttggttc
     4141 atctctaatc gacttccagc gagagagcgc gagtataaaa gccaaagacg gagcgcaaac
     4201 agctatggta tttattcaca tcgcttgcag ttcgcatcgt ctgacttgta cgttgaaaat
     4261 cgaatatcat tggtaaatca aaaggaattt gtagataaaa ctcattgttt actctcgctg
     4321 tgccagaaat cgcaaaaaat caagcggaaa atcagtcgga aaagtgagaa aagaaagtgt
     4381 gtgctaaaca ctcaaagata attttcattt gtgccattcc aaaatgggca ttttgtagaa
     4441 ttctagttgt gggtgcggta tcgcgagaat tctccagaat cttgtttctc tatttacttt
     4501 atatttcaat aataaaagcc tcgggtggga gaaaaattca aaaccgaaag atgacatcat
     4561 caaactcaaa agcaaaagcc ccactctttt ggcgttttct ctcgcgacgc gtgtgacttt
     4621 tctcatctcc gacgaaatct aagtaaactt ttctgttcct ttcttgcttt cccattttac
     4681 gtaggaatga gaagcggaat ttttcgaaat atctctatcc cccagtgccc tgcttaattt
     4741 agtaattcaa tcaacttcaa ttgcccgaca ggcacttcaa actacagtaa gcactgtgta
     4801 tgagcgcctg tgccttgctc agcattactc accggaatcg gatgtggcca cattccaccg
     4861 tccacaaaat atagtagtag tgtactcgag gccgtgcaat tatagtagaa taggtgtgtc
     4921 atcaaggttt attactaagt gaattgctca gtgcatttgc aaaacatttt tgaaacattt
     4981 cgaggtacag tccatcgagg tctccaaaag aagttggcaa aagcttttgt ttatggagtt
     5041 tttcacacat ggtcacgagc tattccagtt tttacaccta tattataata tctctttttt
     5101 aaagtcgtgc tcagagctta aaattgacgt cacaaatctg gtgaatcact gagtgctgta
     5161 atttcaatgt atcatcagtc tatttcaaga acaacattac cagatacgct atgctaaagc
     5221 atatctatca atcttgtttt ttccagaccc caaccacttt ttataatgaa acaaaagaat
     5281 tgtaattaag ggtgttttca aacacaaatg tgttttctac attgaggtca aactattacg
     5341 gagaactcca atcaatattt agagagtcta accaattatt attgattaca ttattctcaa
     5401 cttgcattat aatttattta aaaagaaatc atatattaac taaagtagtc tataaacact
     5461 agaatcttga gtttaattgt acgccatacg taaaagaacc ggtttcaacg ttggccaaaa
     5521 cattttgttt gtttatagct cgactgcaga ggcgtttgta gttgtatctt tttgttaact
     5581 tttttgtttt tttggatggc gtcgccacgt caagtctttt ataatgcttt tttcggctgc
     5641 cttttgttga ctttctactt tggcggcagc atagaaaggc aaacatgtat tttcagcact
     5701 gtcgcactgt gattactaat ttggggaagc tatcaaaaat ctcaatccat ttatcattag
     5761 gtaatttggc cctattgatt ttagggatta tgtggactag tccctcgaga tagtgttcca
     5821 cttgacaact gaagtggagt ggtagatcta gaacgcaaac gggtgacgag tcagacattt
     5881 ccctgaagct ttctcttggc cacaaccaag ccgtgcccga tgttttccaa gccagaacgc
     5941 aatgagctca tccgtttatg aggccacttc gtgtgggttt ggtctggcct atcacgaaac
     6001 tgccgcgcca tgccatttgg ctatcagacg cacccggttc caaggttcgt tcctccgcaa
     6061 actgcgtact gaaaagtgga aactttcact tttccccggc agtacgttga acttcgattt
     6121 gggcaccggt cggcaaggaa aactaaaaaa aaaaacatct cggtaaataa actaggaaaa
     6181 aaaatcaatg ggtaaaaatg ctctcagacc agcgccaggc tggctacggg gcgtatgcgt
     6241 aatgtgaggc ttttacgagt tgatgatgtc accaggcagg aattaaccga aggccgggct
     6301 tattgggtct gggaaacata acgtatccaa cattgctggg ggttcagttt tcatcacgat
     6361 ttcggcgtag ccattattca ttatgatttc tcacttccta cttacagatt tttcacaaca
     6421 aaccaatcaa aatgagttcc gctgagtact acccattcaa ggtgagttta caatggattg
     6481 tactttatga gtctggtata aatcaattat ttcatgcgat tagcgccgtt aatgtaaaaa
     6541 atcagatcaa attagattca acagatagat gagaatatct taatattatt ttttctaaaa
     6601 cgtgtgttgt tgtcaagtaa gcaagatttt tctcgatgca atctataaat tattacaacg
     6661 accagatgct acgaaattat ctataattgg gctattaaat tatcatcaga ggtgtatact
     6721 agacaatcgt tgacaaacaa gtaccgattg gtgggagaag agagtgataa gagggtttca
     6781 gttatgagtt ccttagataa gagtcacaac gaaaaaaaaa gtcaatttag aaagctaact
     6841 ttattgcaga ggaattcatg caatactgag ataatacatg tagggaataa ccacatatgt
     6901 atttgtattt agaacaagtg ccactgagta gtgttgagtc atttctttgg gattacgtgc
     6961 cctgcattaa aatacaccca attcttcttt gttgttactc atttgctgat tgcctatatt
     7021 cgatttgcag tgcacaccca ctgtctaccc ggcggatccc ttcgatcccg tcgaggatgc
     7081 ggctattctg cgcaaggcga tgaaaggctt cggcaccgac gagaaggcca tcatcgagat
     7141 cctggccagg cgtggcatcg tccagcgttt ggagatcgct gaggcgttca agacctcgta
     7201 cggcaaggac ctgatctcgg acctcaagtc cgaactgggc ggcaaattcg aggatgttat
     7261 cctggctctg atgacgccgc tgccccagtt ctatgcccag gagctgcacg acgccatctc
     7321 gggactggga accgacgagg aggccatcat cgagatcctc tgcacgctgt ccaactacgg
     7381 catcaagacc attgcccagt tctacgagca gagcttcggc aagtccctag agtccgacct
     7441 gaagggcgac accagtggcc acttcaagcg gctgtgtgtc tcgctcgtcc agggcaaccg
     7501 ggatgagaac cagggcgtgg acgaggccgc ggccatcgcc gatgcccagg ctctgcacga
     7561 cgccggcgag ggacagtggg gcacagatga gtccaccttc aactcgatcc tgatcacccg
     7621 ctcctaccag cagctgcgcc agatcttcct cgaatacgag aatctgtcgg gcaacgacat
     7681 cgagaaggcc atcaagcggg agtttagcgg ctccgtggag aagggtttcc tggccatcgg
     7741 tacgttctta tagcatccta ttctttaggg tcccttctaa ctgatgcatt gctctgcagt
     7801 caagtgctgc aagtccaaga tcgactactt ttcggagcgc ctgcacgact caatggccgg
     7861 catgggcacc aaggacaaga cgctgatccg catcattgtc agccggtcgg agatcgatct
     7921 gggtgacatc aaggaggcat tccagaacaa gtacggcaag agcttggagt cctggatcaa
     7981 ggtaaatacc gatttcaatt acattcatat ctgcgtgtgc ttgccagaac tttcgattct
     8041 gcaccctgtt caatgtgcca ctaactcgca ttcgattgca cctgcaacaa atcccattaa
     8101 ttgtggctcc atcaaagttt aataatcgtt catccaagct ggcttctcct gttgttgtta
     8161 ctgctccttt gcccaacact ttcttgccga tttctgaagc cattatccct tcccgcccga
     8221 ttgcttcatt tgtgtgcata aaacattaaa acttggcata ttctatattt ttagggcgat
     8281 acatccggcg attataagcg tgccctattg gctattgttg gcttctaaaa agaaccccat
     8341 ccaacaataa tttatctctt tcgtctgttc cacgctctaa actatatgca aacagaatgt
     8401 acaaacaaaa ttccgatatc aaatagttga caatgtatag tttttgaatt ggaacacgtt
     8461 ttaacgaaga cgcagtgcat ttaagtcgta gaatcagaac cccagtctcg catcctgttg
     8521 attattataa ccattgtgac ttttattatt atgactatgc acgccacatg cacataattg
     8581 tatctctata attactacac ctcaggctac ttgcattgct gtgtaggtat actttcagtt
     8641 ttgttttgag tctcatttgc aagatatttt aacttttaaa aaatacgaaa ataaaaaata
     8701 cgaaaaaatg aaatacaaaa ttcaaatcga gtttctgtta cctttagcag aggtctctgc
     8761 actgcttgtc atgtaaataa cagcgctaca ttgggtcgcc taacatcaaa acattaaaca
     8821 ttaaaaaggg cgtggattaa accaacttaa aaatcgattt aaatggggct aaatgagtat
     8881 attagccctc tttaattgtc tatataaact agatcagcaa gtgtataagg tatacaaact
     8941 gttaaatata gttcaattta gatctaaata tacttgcact gcttgctaaa agtacatgtc
     9001 aattacatgt aaatataatg tacatacaat ttcaagatgt aaaactttaa atgttatgtt
     9061 aaatttgaaa gacattcatt tgctgatcag gtagatatat agttgattac cccttggagg
     9121 agtagcttcc ggcaattaac caaaccataa gccatgtata caaagtaaaa ggcgtttaat
     9181 gctctgaccc tctgctcttt tcacgctttt ctctacccgt ttaaacgaac caacaacagg
     9241 aggatgccga gaccgatatt ggatacgtcc tggtcactct tacggcttgg tagacggaag
     9301 cagccggaat atccgaatat ctatgagcaa taccccactg ttcaagtaga aaatgccaaa
     9361 aacaaaaaaa cgttgcattt ccccaaaaaa aagtataaca aaagcgaaga acaaatggag
     9421 ttggtctata tacagtagtt gtgatgtgtt ctaaaaatcc aatctacaaa acgcttagta
     9481 ttttccctct gtgcaataac gtctaacgtt caacgattat ttaacatttt tacgtatttt
     9541 tattttgtat acatgtcttt ttttattgta aattatggcg catcaaagtc gtatgcgtag
     9601 tttgtgcttg tattaactaa taaagttggc ttacactcaa cggcaaagct gggtcacatt
     9661 caccatccac tgatctcctt tccaggacga cctctccgga gactacagct acgtcttgca
     9721 gtgcctggcc tcctactaag gatttcctcg ttggatcgat tgttaaccat tctatttgtt
     9781 gtaactctta ctttaaggca agcatcgttt gccaactgtt ttgcggaaga ttcatagcct
     9841 atgttcaatt cataaatgca ctgtaaaatc gcggtaaata attggaagat tttttcactt
     9901 atctagggta accgaaacca agggggaatg ggtattgggg aatattcgtt aagggggaat
     9961 gctgtttggg ttttctactt ggcaactcga tcctggtagg ctgcccacag gcggtcgcgg
    10021 tacgtctgag ccgcctgctt cgggctgctg gccttcagaa tgcccctgcc caccactccg
    10081 atgtcggcac cccgctcctt gaccacatgc tccggactct ggtactgctg gcccaattgg
    10141 tccacgccct cgtctatctt cacaccgggc gtcagttgca gaagtccggg gaaggcaaag
    10201 gcatcggagg attggcatac cacaccggca acgaaatcta catcggctcc ctcggttgcg
    10261 atcttgttgc tgttctcctt gtacttggcg tcgatcaggt tgccgctggc agacatctcc
    10321 gccagcagga agacgccgcg ttccttgccg gctcctcctt cgccaaggcc cgccttcaga
    10381 ccctgcagaa tactacgtcc aggtaaggtg tgggccgtga ccagatctgc ccaactggaa
    10441 atcttataga tgcccttgcc gtactgcagg gacaccgtgt tgccgatgtc tgcaaacttg
    10501 cgatcctcca tcagcaggaa attgtgccgc tgggccagag cttgcaggtc agcgatgaat
    10561 ttatcactga aatcctccac aatgtctacg tgcgtcttca gcaggcaaat gtacggaccg
    10621 cacttgtcgg ccacgtccag gatctcatcg gcgtgtgtca ggtcggcggc caagcagagg
    10681 ttcgtctgtt tgctggctat caggttgaag aggcgcttgg ccaccgcgct cttagccaga
    10741 ttggcgcgat tctcgtaggt cagtttagtg cgctgcaagt cgttggctgc ggggaaagtg
    10801 atggtgatta gttaacactt caattttgaa acgtgcacgt agacctatct tatcgcctct
    10861 tcttatcgct atatggttgt tttgtaccta tgccaatttt cttcaatagc ttcacacttt
    10921 ggcgatccca aagtacataa ctcttttcaa ctgggaatca attttggcta ttgtttatac
    10981 agtatcttaa gagtatatac aaaagttact ccccaaaggc aaagacgatg attatgatga
    11041 gattagaata ctgtgacttt acaggtggaa acaaaaagca aaccggttcc catacatctc
    11101 atcaaagcgc cataaacgaa atgtgattat ttatagaaga tgggcttgat tgaaggagca
    11161 ggctggctct cgagtgggct gataagcgtg gtggcataat tgagtgcgga ccggacactg
    11221 ccctgaatca gaatcacgtg ccgcattccc gggaatgatc cggtccgata gtggaatcca
    11281 gatcggccta ccgccgttta tggcggttgt ataactttat agtagcgcga ctggagcgct
    11341 ccctaattga atttgttcga ggccatgtgc tggccgagtg tcatgtactt attatctatc
    11401 tatgcatcta tctatctggc agatatcacg gggatctgga gcatacgcac ctctgacaac
    11461 gtcgccctta tcgccgccga cgaaggtacc atcgctgttg atttgcacgg cggcgatgta
    11521 cttggccacc gcctccactg tggacttctc gatgcgcccg gcctcgtgaa gtgtgttcag
    11581 cagaaaggag agcgtgaaga gcgagtgcat ccgcacgccg tgcttggcga tgttggccac
    11641 tccgccctgc tcacggtcta cgacgaccac ggcgtcggtg accacaatgc cctcgccttg
    11701 cagatcccgc accgtgtcca ggatgctgga gccggaggtg accacgtcct cgacaatcag
    11761 acaggtgtcg ccagcattga agatgccctc gaccagcttc ttggtgccgt acgccttggc
    11821 ctccttgcgc cgcaccagca tgggagttcc ctgctgcacg gacacaatgg tggccagcgg
    11881 gagcgccgtg tagggaacac cgcacacgtg tttggcgctc agctgcttgt ccttgatgtg
    11941 ttccaccagc aggtcggata cggtttgctg cgggaagacc aagttagcta ctgccattga
    12001 catggagcac taatcccaaa tactgaccat cacatccgga taactgacga tcactcggag
    12061 gtcgaagtag accggcgaat ttatgcccac tttcatcttg aagtcgccga acttgaaggc
    12121 attgatctcg aagagcttca gggccagggc ccgcattttg tcggagttct gggcaaccat
    12181 gctggcaatt ctaaatctcg atcttaattc ttcacacacg tgctagctag gctccaataa
    12241 gaaccgtcca attgggagtc tacgcttttt aaacatgctg ccagtgtgca cgtatctgct
    12301 gtgacattgg ggcacatttc gaacacccta attaaggtac aagttctggt tgcgccgcct
    12361 gggtggttaa cttcgctatg ccgccaaact tatcgaagtt caaattatta taaatgtcgt
    12421 agattttatc aacattggct tcgaattaat aaacgtttat tattagttat agggtaacaa
    12481 agtagcataa gtgttaaggt tttgaaataa actattttgc atgtgaaata tttcccaaat
    12541 tcataaaata tataaccttt agtttctgag aagtcttaag aaatttcaag gaaatgaatg
    12601 gatggattat atacaatatt ttgtccgctg cattgctgta ttgttcacta cttagcattt
    12661 gtaatctgaa agctttggct ccgcccacaa acccttgact gcaacttcaa ggggaggagt
    12721 ctagtcattt tgcaaccacc aatgacagtc ctgtaagctc atattgcaaa atgaaagcca
    12781 aagcgcctgc gtaagtcaac aaagtttgcg ccattcattg aaacaattcc agatcctttg
    12841 gcgcgtgttt ccaaaattta gtttcttttc gctggtctcc aaataagtcg caaatttgtg
    12901 ctccaaaagc ggcaacttct tagtcgaaaa atcggttttc tctcaatcca tttctcgcct
    12961 gcgttgcgat ggccagttca agtggtgaac ctgctgatga agtggctaat aagcgtcctc
    13021 gtcttgtggc taatcccaag gccaccaaaa tagttgaacc cacaccggcc aaggtcacca
    13081 atcgggtgcc caagtgcgcc cgctgccgga accatgggat catttcagag ctgcggggtc
    13141 acaagaagct ctgcacctac aagaactgca agtgcgccaa gtgtgtcctg atctttgaga
    13201 ggcagcggat catggccgct caggtaagtt aggatttata tgcacgatga caagcaatcc
    13261 tttctgctta attggcaatc attgacatta ctatcctcat tttatgatta ctgcccactt
    13321 gctaacttta atgtcatcta tcctggatgg taaaatcgct atcccaaaaa tagcttttta
    13381 aaaattcggt gcattcgaat acagaaaatt gcctggttag atccatccat agacatccaa
    13441 accatccaga ccagatatat tgctctaaca ttcggagact ttattcccag tcctttagaa
    13501 aatttcttct tgtaaaaaca tattcccttt attagcattt acttaaaatg acatatcaaa
    13561 tattctcaaa agccaaaagt tttctaaaat aacttcagga tattaatgta taaatgtata
    13621 agcataaacg taattgtgtt tcatgttgta ttgttcgcaa tggattccgt gatcgatttt
    13681 tactaggtat aactttgaaa cccaatttaa gcctttcgat tataatttaa cttgattaat
    13741 gtcactgtta tatttataat ttactaacct gggacgacaa acaaaaacac ctattagcaa
    13801 ggggagctta aattaacaat agcaccgaaa actccgacat tttcttatat cgtgttttgt
    13861 gaBioPerl-1.007002/t/data/BAB68554.gb000444000766000024       342513155576321 16206 0ustar00cjfieldsstaff000000000000LOCUS       BAB68554                 141 aa            linear   VRT 11-APR-2002
DEFINITION  alpha D-globin [Aldabrachelys elephantina].
ACCESSION   BAB68554
PID         g15824047
VERSION     BAB68554.1  GI:15824047
DBSOURCE    accession AB072353.1
KEYWORDS    .
SOURCE      Aldabra giant tortoise.
  ORGANISM  Aldabrachelys elephantina
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Testudines; Cryptodira; Testudinoidea; Testudinidae; Aldabrachelys.
REFERENCE   1
  AUTHORS   Shishikura,F.
  TITLE     The primary structure of hemoglobin D from the Aldabra giant
            tortoise, Geochelone gigantea
  JOURNAL   Zoolog. Sci. 19, 197-206 (2002)
REFERENCE   2  (residues 1 to 141)
  AUTHORS   Shishikura,F.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-SEP-2001) Fumio Shishikura, Nihon University School
            of Medicine, Biology; Oyaguchi-kamimachi, 30-1, Itabashi-ku, Tokyo
            173-8610, Japan (E-mail:fshishi@med.nihon-u.ac.jp,
            Tel:81-3-3972-8111(ex.2291), Fax:81-3-3972-0027)
FEATURES             Location/Qualifiers
     source          1..141
                     /organism="Aldabrachelys elephantina"
                     /db_xref="taxon:167804"
                     /note="synonym:Dipsochelys dussumieri~synonym:Geochelone
                     gigantea"
     Protein         1..141
                     /product="alpha D-globin"
     CDS             1..141
                     /coded_by="join(AB072353.1:1..92,AB072353.1:307..511,
                     AB072353.1:739..>864)"
                     /note="hemoglobin D"
ORIGIN      
        1 mlteddkqli qhvwekvleh qedfgaeale rmfivypstk tyfphfdlhh dseqirhhgk
       61 kvvgalgdav khidnlsatl selsnlhayn lrvdpvnfkl lshcfqvvlg ahlgreytpq
      121 vqvaydkfla avsavlaeky r
//
BioPerl-1.007002/t/data/BC000007.gbk000444000766000024      1563413155576321 16341 0ustar00cjfieldsstaff000000000000LOCUS       BC000007                 981 bp    mRNA    linear   PRI 09-DEC-2005
DEFINITION  Homo sapiens px19-like protein, mRNA (cDNA clone MGC:1082
            IMAGE:3505068), complete cds.
ACCESSION   BC000007
VERSION     BC000007.2  GI:33875090
KEYWORDS    MGC.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 981)
  AUTHORS   Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G.,
            Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D.,
            Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K.,
            Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F.,
            Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L.,
            Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L.,
            Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S.,
            Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J.,
            Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J.,
            McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S.,
            Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W.,
            Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A.,
            Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S.,
            Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y.,
            Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D.,
            Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M.,
            Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E.,
            Schnerch,A., Schein,J.E., Jones,S.J. and Marra,M.A.
  CONSRTM   Mammalian Gene Collection Program Team
  TITLE     Generation and initial analysis of more than 15,000 full-length
            human and mouse cDNA sequences
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 99 (26), 16899-16903 (2002)
   PUBMED   12477932
REFERENCE   2  (bases 1 to 981)
  CONSRTM   NIH MGC Project
  TITLE     Direct Submission
  JOURNAL   Submitted (03-NOV-2000) National Institutes of Health, Mammalian
            Gene Collection (MGC), Bethesda, MD 20892-2590, USA
  REMARK    NIH-MGC Project URL: http://mgc.nci.nih.gov
COMMENT     On Aug 19, 2003 this sequence version replaced gi:12652536.
            Contact: MGC help desk
            Email: cgapbs-r@mail.nih.gov
            Tissue Procurement: ATCC
            cDNA Library Preparation: Rubin Laboratory
            cDNA Library Arrayed by: The I.M.A.G.E. Consortium (LLNL)
            DNA Sequencing by: Institute for Systems Biology
            http://www.systemsbiology.org
            contact: amadan@systemsbiology.org
            Anup Madan, Jessica Fahey, Erin Helton, Mark Ketteman, Anuradha
            Madan, Stephanie Rodrigues, Amy Sanchez and Michelle Whiting
            
            Clone distribution: MGC clone distribution information can be found
            through the I.M.A.G.E. Consortium/LLNL at: http://image.llnl.gov
            Series: IRAL Plate: 7 Row: f Column: 3
            This clone was selected for full length sequencing because it
            passed the following selection criteria: matched mRNA gi: 31543450.
            
            Differences found between this sequence and the human reference
            genome (build 36) are described in misc_difference features below
            and these differences were also compared to chimpanzee genomic
            sequences available as of 09/15/2004.
FEATURES             Location/Qualifiers
     source          1..981
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /clone="MGC:1082 IMAGE:3505068"
                     /tissue_type="Placenta, choriocarcinoma"
                     /clone_lib="NIH_MGC_21"
                     /lab_host="DH10B-R"
                     /note="Vector: pOTB7"
     gene            1..981
                     /gene="PX19"
                     /note="synonyms: CGI-106, PRELI"
                     /db_xref="GeneID:27166"
                     /db_xref="MIM:605733"
     CDS             174..833
                     /gene="PX19"
                     /codon_start=1
                     /product="PX19 protein"
                     /protein_id="AAH00007.1"
                     /db_xref="GI:12652537"
                     /db_xref="GeneID:27166"
                     /db_xref="MIM:605733"
                     /translation="MVKYFLGQSVLRSSWDQVFAAFWQRYPNPYSKHVLTEDIVHREV
                     TPDQKLLSRRLLTKTNRMPRWAERLFPANVAHSVYVLEDSIVDPQNQTMTTFTWNINH
                     ARLMVVEERCVYCVNSDNSGWTEIRREAWVSSSLFGVSRAVQEFGLARFKSNVTKTMK
                     GFEYILAKLQGEAPSKTLVETAKEAKEKAKETALAATEKAKDLASKAATKKQQQQQQF
                     V"
     misc_difference 623
                     /gene="PX19"
                     /note="'G' in cDNA is 'A' in the human genome; no amino
                     acid change.  The chimpanzee genome agrees with the cDNA
                     sequence, suggesting that this difference is unlikely to
                     be due to an artifact."
     misc_difference 878
                     /gene="PX19"
                     /note="'C' in cDNA is 'T' in the human genome.  The
                     chimpanzee genome agrees with the cDNA sequence,
                     suggesting that this difference is unlikely to be due to
                     an artifact."
     misc_difference 925..981
                     /gene="PX19"
                     /note="polyA tail: 57 bases do not align to the human
                     genome."
ORIGIN      
        1 ctcatggcgg cggcggcggc ggcggcagct gcttgggcgc ggtgcggtgg tgactgagct
       61 acgagcctgg cggcgggtgt gcgccgagcc ccggcccggc ccggccctcg cgtgcctccc
      121 aggctccgca cccctgatgc tgcgcgggtg ctgagcccgc ttcggccggg acgatggtga
      181 agtatttcct gggccagagc gtgctccgga gttcctggga ccaagtgttc gccgccttct
      241 ggcagcggta cccgaatccc tatagcaaac atgtcttgac ggaagacata gtacaccggg
      301 aggtgacccc tgaccagaaa ctgctgtccc ggcgactcct gaccaagacc aacaggatgc
      361 cacgctgggc cgagcgacta tttcctgcca atgttgctca ctcggtgtac gtcctggagg
      421 actctattgt ggacccacag aatcagacca tgactacctt cacctggaac atcaaccacg
      481 cccggctgat ggtggtggag gaacgatgtg tttactgtgt gaactctgac aacagtggct
      541 ggactgaaat ccgccgggaa gcctgggtct cctctagctt atttggtgtc tccagagctg
      601 tccaggaatt tggtcttgcc cggttcaaaa gcaacgtgac caagactatg aagggttttg
      661 aatatatctt ggctaagctg caaggcgagg ccccttccaa aacacttgtt gagacagcca
      721 aggaagccaa ggagaaggca aaggagacgg cactggcagc tacagagaag gccaaggacc
      781 tcgccagcaa ggcggccacc aagaagcagc agcagcagca acagtttgtg tagccagtct
      841 accaccacca cagcacccca gacagctagg cttagcccct ctgccctccc ttcattgtac
      901 tttatcatta aaaatcaact tccaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa
      961 aaaaaaaaaa aaaaaaaaat a
//

BioPerl-1.007002/t/data/BEL16-LTR_AG.embl000444000766000024       260313155576321 17311 0ustar00cjfieldsstaff000000000000ID   BEL16-LTR_AG repbase; DNA   ; ANG   ; 287 BP.
XX
AC   .
XX
DT   03-APR-2003 (Rel. 8.03, Created)
DT   03-APR-2003 (Rel. 8.03, Last updated, Version 1)
XX
DE   BEL16-LTR_AG is a long terminal repeat of the BEL16_AG LTR
DE   retrotransposon - a consensus sequence.
XX
KW   5-bp TSD; BEL16-I_AG; BEL16-LTR_AG; BEL16_AG; Bel clade;
KW   LTR retrotransposon; reverse transcriptase.
XX
OS   Anopheles gambiae str. PEST
OC   Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera;
OC   Endopterygota; Diptera; Nematocera; Culicoidea; Culicidae; Anophelinae;
OC   Anopheles; Anopheles gambiae.
XX
RN   [1]
RP   1-287
RA   Kapitonov V.V., Pavlicek A., Jurka J.;
RT   "BEL16_AG, a nonautonomous family of Bel/Pao-like LTR retrotransposons
RT   from African malaria mosquito.";
RL   Repbase Reports 3(3), 40-40 (2003).
XX
CC   [1] (Consensus)
XX
CC   BEL16-LTR_AG flank an internal portion of BEL16_AG (deposited as
CC   BEL16-I_AG).
XX
SQ   Sequence 287 BP; 85 A; 51 C; 75 G; 76 T; 0 others;
     tgttggaatg taagggttat gaaacggtca ttttgaattg tttgcggttg ttttgtcagt        60
     tgggaattaa aagttaaatg tattttctgg cagcactgcc gatcgacaat ttgtgattaa       120
     gtatgtgtgc gaataaagcg gcactagcgc atgaaactcg atacgagccg gacgtgttct       180
     ttactttgtc tcctttggcg atcgaagacg acacaacaaa acacaacgta gggcgtagag       240
     gcgtcaaggg ggaaaggaac caacaaacca tgttccagaa cgcaaca                     287
//
BioPerl-1.007002/t/data/BK000016-tpa.gbk000444000766000024       764113155576321 17112 0ustar00cjfieldsstaff000000000000LOCUS       BK000016                1162 bp    mRNA    linear   ROD 17-MAY-2002
DEFINITION  TPA: Mus musculus pantothenate kinase 4 mRNA, partial cds.
ACCESSION   BK000016
VERSION     BK000016.1  GI:20043254
KEYWORDS    Third Party Annotation; TPA.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus.
REFERENCE   1  (bases 1 to 1162)
  AUTHORS   Zhou,B., Westaway,S.K., Levinson,B., Johnson,M.A., Gitschier,J. and
            Hayflick,S.J.
  TITLE     A novel pantothenate kinase gene (PANK2) is defective in
            Hallervorden-Spatz syndrome
  JOURNAL   Nat. Genet. 28 (4), 345-349 (2001)
  MEDLINE   21372465
   PUBMED   11479594
REFERENCE   2  (bases 1 to 1162)
  AUTHORS   Zhou,B., Westaway,S.K., Levinson,B., Johnson,M.A., Gitschier,J. and
            Hayflick,S.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-JUL-2001) Medicine and HHMI, University of
            California, San Francisco, 3rd and Parnassus Avenues, San
            Francisco, CA 94143, USA
PRIMARY     TPA_SPAN            PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-455               BE554781.1         1-455
            177-687             BG146074.1         1-511
            608-956             AA671765.1         45-393
            656-1162            BE982078.1         1-507               c
FEATURES             Location/Qualifiers
     source          1..1162
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /db_xref="taxon:10090"
     CDS             <1..1119
                     /note="PANK4"
                     /codon_start=1
                     /product="pantothenate kinase 4"
                     /protein_id="DAA00010.1"
                     /db_xref="GI:20043255"
                     /translation="ERGASGGGSGGDSLDKSITLPPDEIFRNLENAKRFAIDIGGSLT
                     KLAYYSTVQHKVAKVRSFDHPGKDVEQDHEPPYEISVQEEITARLHFIKFENTYMEAC
                     LDFIRDHLVNTETKVIQATGGGAYKFKDLIEEKLRLKVDKEDVMTCLIKGCNFVLKNI
                     PHEAFMYQKDADPEFRFQTNHPNIFPYLLVNIGSGVSIVKVETEDRFEWIGGSSIGGG
                     TFWGLGALLTKTKKFDELLQLASRGRHANVDMLVQDIYGGAHQTLGLSGNLIASSFGK
                     SATADREFSKEDMAKSLLHMISNDIGQLACLYAKLHGLDRVYFGGFFIRGHPVTMRTI
                     TYSINFFSKGEVQALFLRHEGYLGAIGAFLKGAEQDSE"
BASE COUNT      290 a    308 c    332 g    232 t
ORIGIN      
        1 gagcgtggag cgagtggcgg cgggagcggc ggggacagtc tggacaagag catcacgctg
       61 ccccccgacg agatcttccg caacctggag aacgccaagc gcttcgccat tgatataggt
      121 ggatcattga ccaagttggc atactattcc accgtacagc acaaagtggc caaagtgaga
      181 tcttttgacc acccgggaaa ggacgtggag caggatcatg agccacccta tgagatctca
      241 gtccaggagg agatcacagc tcgcctgcat ttcatcaagt ttgagaatac ctacatggaa
      301 gcctgcctgg acttcatcag agaccaccta gtcaacactg agaccaaggt catccaggcc
      361 actgggggtg gagcctataa gttcaaggac ctcatcgagg aaaagctgcg tctgaaggtg
      421 gacaaagagg atgtaatgac ctgcttgata aaggggtgca acttcgtgct gaagaacatc
      481 ccgcatgagg ccttcatgta ccagaaagac gcagacccag agtttcgatt tcagacaaat
      541 caccccaaca tcttccccta cctcctagtc aacattggct ctggcgtctc catcgtgaag
      601 gtggagacag aggaccggtt tgagtggatt ggtggaagct ccattggagg aggcaccttc
      661 tggggcctcg gggctctgct caccaaaaca aagaagtttg atgagctgct gcagctggct
      721 tccagaggcc ggcatgccaa cgttgacatg ctggtccagg acatctatgg tggggcccac
      781 cagaccctgg gcctgagtgg caatctcatc gcaagcagtt ttgggaagtc agccactgct
      841 gacagagagt tctccaaaga agacatggcc aagagcctgc tgcacatgat cagcaatgac
      901 atcgggcagc tcgcctgtct gtacgccaag ctccacggct tggacagggt ctactttggg
      961 ggcttcttca tccggggtca ccccgtgacc atgcgcacaa tcacctacag cattaacttc
     1021 ttctccaagg gtgaagtcca ggcactcttc ctgagacatg aaggctacct gggagccatc
     1081 ggggcatttt taaaaggagc cgagcaagac agtgagtaga gtcactgctg tgagcagtgg
     1141 ctggctgtgc aggacgcggc cg
//
BioPerl-1.007002/t/data/BLOSUM50000444000766000024       411213155576321 15757 0ustar00cjfieldsstaff000000000000#  Matrix made by matblas from blosum50.iij
#  * column uses minimum score
#  BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 50
#  Entropy =   0.4808, Expected =  -0.3573
   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
A  5 -2 -1 -2 -1 -1 -1  0 -2 -1 -2 -1 -1 -3 -1  1  0 -3 -2  0 -2 -1 -1 -5 
R -2  7 -1 -2 -4  1  0 -3  0 -4 -3  3 -2 -3 -3 -1 -1 -3 -1 -3 -1  0 -1 -5 
N -1 -1  7  2 -2  0  0  0  1 -3 -4  0 -2 -4 -2  1  0 -4 -2 -3  4  0 -1 -5 
D -2 -2  2  8 -4  0  2 -1 -1 -4 -4 -1 -4 -5 -1  0 -1 -5 -3 -4  5  1 -1 -5 
C -1 -4 -2 -4 13 -3 -3 -3 -3 -2 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -3 -3 -2 -5 
Q -1  1  0  0 -3  7  2 -2  1 -3 -2  2  0 -4 -1  0 -1 -1 -1 -3  0  4 -1 -5 
E -1  0  0  2 -3  2  6 -3  0 -4 -3  1 -2 -3 -1 -1 -1 -3 -2 -3  1  5 -1 -5 
G  0 -3  0 -1 -3 -2 -3  8 -2 -4 -4 -2 -3 -4 -2  0 -2 -3 -3 -4 -1 -2 -2 -5 
H -2  0  1 -1 -3  1  0 -2 10 -4 -3  0 -1 -1 -2 -1 -2 -3  2 -4  0  0 -1 -5 
I -1 -4 -3 -4 -2 -3 -4 -4 -4  5  2 -3  2  0 -3 -3 -1 -3 -1  4 -4 -3 -1 -5 
L -2 -3 -4 -4 -2 -2 -3 -4 -3  2  5 -3  3  1 -4 -3 -1 -2 -1  1 -4 -3 -1 -5 
K -1  3  0 -1 -3  2  1 -2  0 -3 -3  6 -2 -4 -1  0 -1 -3 -2 -3  0  1 -1 -5 
M -1 -2 -2 -4 -2  0 -2 -3 -1  2  3 -2  7  0 -3 -2 -1 -1  0  1 -3 -1 -1 -5 
F -3 -3 -4 -5 -2 -4 -3 -4 -1  0  1 -4  0  8 -4 -3 -2  1  4 -1 -4 -4 -2 -5 
P -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3 -2 -1 -2 -5 
S  1 -1  1  0 -1  0 -1  0 -1 -3 -3  0 -2 -3 -1  5  2 -4 -2 -2  0  0 -1 -5 
T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  2  5 -3 -2  0  0 -1  0 -5 
W -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1  1 -4 -4 -3 15  2 -3 -5 -2 -3 -5 
Y -2 -1 -2 -3 -3 -1 -2 -3  2 -1 -1 -2  0  4 -3 -2 -2  2  8 -1 -3 -2 -1 -5 
V  0 -3 -3 -4 -1 -3 -3 -4 -4  4  1 -3  1 -1 -3 -2  0 -3 -1  5 -4 -3 -1 -5 
B -2 -1  4  5 -3  0  1 -1  0 -4 -4  0 -3 -4 -2  0  0 -5 -3 -4  5  2 -1 -5 
Z -1  0  0  1 -3  4  5 -2  0 -3 -3  1 -1 -4 -1  0 -1 -2 -2 -3  2  5 -1 -5 
X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1  0 -3 -1 -1 -1 -1 -1 -5 
* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5  1 
BioPerl-1.007002/t/data/BN000066-tpa.embl000444000766000024      3632413155576321 17316 0ustar00cjfieldsstaff000000000000
ID   AGA000066  standard; DNA; INV; 5195 BP.
XX
AC   BN000066;
XX
SV   BN000066.1
XX
DT   07-OCT-2002 (Rel. 73, Created)
DT   21-NOV-2002 (Rel. 73, Last updated, Version 11)
XX
DE   TPA: Anopheles gambiae achE1 gene for acetylcholinesterase, exons 1-6
XX
KW   acetylcholinesterase; achE1 gene; Third Party Annotation; TPA.
XX
OS   Anopheles gambiae (African malaria mosquito)
OC   Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera;
OC   Endopterygota; Diptera; Nematocera; Culicoidea; Anopheles.
XX
RN   [1]
RP   1-5195
RA   Fort P.P.;
RT   ;
RL   Submitted (30-NOV-2001) to the EMBL/GenBank/DDBJ databases.
RL   Fort P.P., CRBM-UPR1086, Cnrs, 1919 route de Mende, 34293 MONTPELLIER CEDEX
RL   5, FRANCE.
XX
RN   [3]
RA   Weill M., Fort P., Berthomi eu A., Dubois M.P., Pasteur N., Raymond M.;
RT   "A novel acetylcholinesterase gene in mosquitoes codes for the insecticide
RT   target and is non-homologous to the ace gene in Drosophila";
RL   Proc. R. Soc. Lond., B, Biol. Sci. 269:2007-2016(2002).
XX
CC   see also AJ488492 for achE-1 from Kisumu strain
CC   Third Party Annotation Database: This TPA record uses Anopheles gambiae
CC   trace archive data (http://trace.ensembl.org)
XX
AH   TPA_SPAN        PRIMARY_IDENTIFIER   PRIMARY_SPAN   COMP
AS   1-685           TI55475028           11-685             
AS   1-747           TI47553499           11-747             
AS   1-800           TI55407518           11-800             
AS   188-895         TI57630934           11-707             
AS   223-845         TI57283198           11-622             
AS   251-895         TI47098900           11-644             
AS   272-999         TI56725015           11-727             
AS   387-1193        TI57310066           11-806             
AS   431-1195        TI56845856           11-764             
AS   522-1220        TI55215818           11-698             
AS   546-1208        TI57401582           11-661             
AS   566-1208        TI56169014           11-642             
AS   584-1306        TI59761948           11-722             
AS   738-1306        TI55852606           11-568             
AS   827-1634        TI57602219           11-807             
AS   1064-1769       TI44966390           11-705             
AS   1065-1822       TI60742945           11-757             
AS   1129-1954       TI56042882           11-825             
AS   1223-1979       TI60461178           11-756             
AS   1226-1868       TI56472916           11-642             
AS   1296-1989       TI44952509           11-693             
AS   1364-2170       TI56006358           11-806             
AS   1561-2341       TI58704241           11-780             
AS   1582-2385       TI44875600           11-803             
AS   1740-2415       TI55894404           11-675             
AS   1794-2585       TI56056818           11-791             
AS   1834-2644       TI47256770           11-809             
AS   1848-2729       TI56446066           11-879             
AS   1849-2515       TI44984669           11-665             
AS   2216-3002       TI57417259           11-786             
AS   2224-3029       TI56867244           11-805             
AS   2226-3057       TI59803037           11-831             
AS   2299-3083       TI60503347           11-784             
AS   2614-3351       TI44891398           11-736             
AS   2654-3419       TI55336738           11-765             
AS   2663-3304       TI60709914           11-641             
AS   2672-3417       TI56453591           11-745             
AS   2691-3260       TI55690247           11-569             
AS   2697-3494       TI55745954           11-797             
AS   2885-3706       TI58733608           11-821             
AS   2896-3700       TI58130218           11-803             
AS   2946-3741       TI56432498           11-795             
AS   2992-3702       TI47561255           11-710             
AS   2992-3702       TI55208429           11-710             
AS   3029-3807       TI47256418           11-778             
AS   3030-3831       TI47233061           11-801             
AS   3123-3892       TI55870944           11-769             
AS   3255-4043       TI47465031           11-787             
AS   3325-4045       TI55382589           11-720             
AS   3535-4255       TI46993841           11-720             
AS   3574-4244       TI56607077           11-670             
AS   3596-4394       TI56526265           11-798             
AS   3704-4484       TI56050293           11-780             
AS   3724-4560       TI59807029           11-836             
AS   3745-4549       TI55159438           11-804             
AS   3753-4596       TI56586965           11-842             
AS   3800-4577       TI56592754           11-777             
AS   3833-4635       TI47243257           11-801             
AS   3837-4272       TI59628661           11-435             
AS   3899-4728       TI56895999           11-829             
AS   3938-4704       TI59830483           11-766             
AS   3942-4704       TI55700050           11-762             
AS   4116-4912       TI56961976           11-796             
AS   4137-4761       TI46929238           11-623             
AS   4148-4961       TI59909853           11-813             
AS   4285-5046       TI47085450           11-759             
AS   4315-5069       TI58096045           11-754             
AS   4387-5177       TI58084392           11-790             
AS   4455-5175       TI55094688           11-720             
AS   4455-5195       TI55297322           11-740             
AS   4491-5195       TI56990277           11-704             
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..5195
FT                   /db_xref="taxon:7165"
FT                   /organism="Anopheles gambiae"
FT   CDS             join(<1780..1914,2001..2538,2618..2815,2902..3609,
FT                   3676..3848,3956..4077)
FT                   /codon_start=3
FT                   /gene="achE1"
FT                   /product="acetylcholinesterase"
FT                   /EC_number="3.1.1.7"
FT                   /function="hydrolyzes acetylcholine at cholinergic
FT                   synapses"
FT                   /protein_id="CAD29865.2"
FT                   /translation="AFFTPYIGHGESVRIIDAELGTLEHVHSGATPRRRGLTRRESNSD
FT                   ANDNDPLVVNTDKGRIRGITVDAPSGKKVDVWLGIPYAQPPVGPLRFRHPRPAEKWTGV
FT                   LNTTTPPNSCVQIVDTVFGDFPGATMWNPNTPLSEDCLYINVVAPRPRPKNAAVMLWIF
FT                   GGGFYSGTATLDVYDHRALASEENVIVVSLQYRVASLGFLFLGTPEAPGNAGLFDQNLA
FT                   LRWVRDNIHRFGGDPSRVTLFGESAGAVSVSLHLLSALSRDLFQRAILQSGSPTAPWAL
FT                   VSREEATLRALRLAEAVGCPHEPSKLSDAVECLRGKDPHVLVNNEWGTLGICEFPFVPV
FT                   VDGAFLDETPQRSLASGRFKKTEILTGSNTEEGYYFIIYYLTELLRKEEGVTVTREEFL
FT                   QAVRELNPYVNGAARQAIVFEYTDWTEPDNPNSNRDALDKMVGDYHFTCNVNEFAQRYA
FT                   EEGNNVYMYLYTHRSKGNPWPRWTGVMHGDEINYVFGEPLNPTLGYTEDEKDFSRKIMR
FT                   YWSNFAKTGNPNPNTASSEFPEWPKHTAHGRHYLELGLNTSFVGRGPRLRQCAFWKKYL
FT                   PQLVAATSNLPGPAPPSEPCESSAFFYRPDLIVLLVSLLTATVRFIQ"
FT   mRNA            join(<1780..1914,2001..2538,2618..2815,2902..3609,
FT                   3676..3848,3956..>4596)
FT                   /gene="achE1"
FT   exon            <1780..1914
FT                   /number=1
FT                   /gene="achE1"
FT   intron          1915..2000
FT                   /number=1
FT                   /gene="achE1"
FT   exon            2001..2538
FT                   /number=2
FT                   /gene="achE1"
FT   intron          2539..2617
FT                   /number=2
FT                   /gene="achE1"
FT   exon            2618..2815
FT                   /number=3
FT                   /gene="achE1"
FT   intron          2816..2901
FT                   /number=3
FT                   /gene="achE1"
FT   exon            2902..3609
FT                   /number=4
FT                   /gene="achE1"
FT   intron          3610..3675
FT                   /number=4
FT                   /gene="achE1"
FT   exon            3676..3848
FT                   /number=5
FT                   /gene="achE1"
FT   intron          3849..3955
FT                   /number=5
FT                   /gene="achE1"
FT   exon            3956..>4596
FT                   /number=6
FT                   /gene="achE1"
FT   polyA_signal    4628..4633
FT                   /gene="achE1"
XX
SQ   Sequence 5195 BP; 1326 A; 1468 C; 1183 G; 1218 T; 0 other;
     gaggtggatt ggtacggatt ggtcatttcc gttcttcttc atgtgcgttt cttactctcc        60
     tgccttctca aacgaacttc agaacgaaaa aaaacacgcg acggagagta agaagctgta       120
     cagacactct agtcctcaca cacacaactt gcttactttg tccgtccgtt tgattccgct       180
     ctttctatgt gtgactttct ggcacccttt acttcgtcac tattcatttc atttccaata       240
     aacttttaat gtgtctttct tttttattct aaatatctat agtaaatgtt ctgtagcaag       300
     tatcttgtag tagaattgta tagaagtaga tttttgtatg agtttgcatc atcccttccc       360
     aatggggttg actccgtttc aaccaacgcc aaaagctatc ggcataaagt atggttcctt       420
     gcaaaggctt ttatgaaaca cgaatgtgtt gaaagctttt gcaaatggaa atgttaaagc       480
     ctttaagttc caatcgcttt ttgtatccat ttagtttgca tgaacaacag gaaatcaaaa       540
     tattggtaac gacaatcgct ggcgggcgtt cctttcttgt ctaatcaaat catctacgat       600
     tgtaattaca aacttccaag tttgcgtatg acaatgttaa atgtctaaga cgctcaaatg       660
     caaccaatag agtataatta ctaaggcggg cagtagaaac caaaatatct taaataatgt       720
     caagcaaaac aaaaagaaca attccgttca ctgctcaaag aaagccctaa ctaactacct       780
     aaccttttca tcgatgaccc tgtactgaca tggtaagata ttctttatcc tttaactctt       840
     ctgcacccta cgcactcaat gcaacacacg cactactatt actgctacta ctctcgcact       900
     cacgagcacc tacttgcact caagccggca ctcaatgtac tagcgaaaca cgtcgcatct       960
     aagcactcac aaggaagcac acatttgcaa atagcaccta ccggaacagc tttgaatgtg      1020
     ccagcacagc attgaacagg ttcgcgcctt tactcctgtg ctctgttttc tcgatcggaa      1080
     tgttcgaaag ttgaaaagcg cattttttca tctctctttt tctattcttc ttcgtatttt      1140
     tatccctctc tcgtcgtgtt ttttctaaac attaccatac ttcttccgct acgaactcgc      1200
     caagaaccag aacgcagcgt gcgtgcggtg cttgcggtgt gtgtgtgtgt gtgtgtattc      1260
     cacggctgcg agaagcaaga tcggagaaca ggcatcattc ccctttcaca gacaattgca      1320
     cttttgtact agaacagaaa acgagacagc ataatttcca acagcctcat tcactcatac      1380
     caggctcaca ccgactttta accgaaacat gtactacaga aacaaaaaca aacaatatgg      1440
     agagtgctcg cgctgatact aagttaatat gaagagatta ctggcgaggt catcgatccc      1500
     atcccgacat catcgctcca ggctccagac ctaccaagtc gcctaccatt acctacccac      1560
     caccgaccac tactcacaca gcattatcac ttccgccgcc gtcgccgccg ccgccgacgc      1620
     cgccgacgcc accaccttca caccgccctg ccaaaatgaa tgcgcattgt tgcgatagat      1680
     tgaatttcct tggttgttgt tgttgttggt tttcttttga catgtttgtg tgttgttttt      1740
     tctttctctc tctctctttc tgtggttcca acatttcaga cgcatttttt acaccatata      1800
     taggtcacgg tgagtccgta cgaattatag atgccgagtt gggcacgctc gagcatgtcc      1860
     acagtggagc aacgccgcgg cgacgcggcc tgacgaggcg cgagtcaaac tcgggtaagt      1920
     acgcgattgg aagtgggggg acgtttaccc taccgtgtac tactacaacg cactttaccc      1980
     ccacgcacac gcaccggcag acgcgaacga caacgatccg ctggtggtca acacggataa      2040
     ggggcgcatc cgcggcatta cggtcgatgc gcccagcggc aagaaggtgg acgtgtggct      2100
     cggcattccc tacgcccagc cgccggtcgg gccgctacgg ttccgtcatc cgcggccggc      2160
     cgaaaagtgg accggcgtgc tgaacacgac cacaccgccc aacagctgcg tgcagatcgt      2220
     ggacaccgtg ttcggcgact tcccgggcgc gaccatgtgg aacccgaaca cgcccctgtc      2280
     cgaggactgt ctgtacatta acgtggtggc accgcgaccc cggcccaaga atgcggccgt      2340
     catgctgtgg atcttcggcg gcggcttcta ctccggcacc gccaccctgg acgtgtacga      2400
     ccaccgggcg cttgcgtcgg aggagaacgt gatcgtggtg tcgctgcagt accgcgtggc      2460
     cagtctgggc ttcctgtttc tcggcacccc ggaagcgccg ggcaatgcgg gactgttcga      2520
     tcagaacctt gcgctacggt aggtgtcttt gcatgtgtga atgagggtat agtattctaa      2580
     cgaggtgctc ttcttcccat cacttcttgg gagtcagctg ggtgcgggac aacattcacc      2640
     ggttcggtgg cgatccgtcg cgtgtgacac tgttcggcga gagtgccggt gccgtctcgg      2700
     tgtcgctgca tctgctgtcc gccctttccc gcgatctgtt ccagcgggcc atcctgcaga      2760
     gcggctcgcc gacggcaccg tgggcattgg tatcgcgcga ggaagccaca ctaaggtacg      2820
     tgccagctgc tgctttcccc aaaccaccaa cccgcaacag ctcacacaac cctcttttcc      2880
     gtcgctcttt tctcgctcca gagcactgcg gttggccgag gcggtcggct gcccgcacga      2940
     accgagcaag ctgagcgatg cggtcgagtg cctgcgcggc aaggacccgc acgtgctggt      3000
     caacaacgag tggggcacgc tcggcatttg cgagttcccg ttcgtgccgg tggtcgacgg      3060
     tgcgttcctg gacgagacgc cgcagcgttc gctcgccagc gggcgcttca agaagacgga      3120
     gatcctcacc ggcagcaaca cggaggaggg ctactacttc atcatctact acctgaccga      3180
     gctgctgcgc aaggaggagg gcgtgaccgt gacgcgcgag gagttcctgc aggcggtgcg      3240
     cgagctcaac ccgtacgtga acggggcggc ccggcaggcg atcgtgttcg agtacaccga      3300
     ctggaccgag ccggacaacc cgaacagcaa ccgggacgcg ctggacaaga tggtgggcga      3360
     ctatcacttc acctgcaacg tgaacgagtt cgcgcagcgg tacgccgagg agggcaacaa      3420
     cgtctacatg tatctgtaca cgcaccgcag caaaggcaac ccgtggccgc gctggacggg      3480
     cgtgatgcac ggcgacgaga tcaactacgt gttcggcgaa ccgctcaacc ccaccctcgg      3540
     ctacaccgag gacgagaaag actttagccg gaagatcatg cgatactggt ccaactttgc      3600
     caaaaccggg taagtgtgtg tgtcaaacag cagagtgtcg atcgctctaa caccagcgtc      3660
     ttctctcttc tacagcaatc caaatcccaa cacggccagc agcgaattcc ccgagtggcc      3720
     caagcacacc gcccacggac ggcactatct ggagctgggc ctcaacacgt ccttcgtcgg      3780
     tcggggccca cggttgaggc agtgtgcctt ctggaagaag taccttcccc agctagttgc      3840
     agctacctgt aagtctcgtg cagcacttga aaccccctcc cacatcccca tcagggtcca      3900
     ggttgcaata ataaatttca ctttctctct ctcacgtctc ttttccccaa aacagcgaac      3960
     ctaccagggc cagcaccgcc tagtgaaccg tgcgaaagca gcgcattttt ttaccgacct      4020
     gatctgatcg tgctgctggt gtcgctgctt acggcgaccg tcagattcat acaataatta      4080
     ctaccccatc catggcctag ttcgtttaag ctttaagata gtgaggaaca aatttttccc      4140
     aaacaatttt ccccccttta gagcagaacc gagggagaga taggactaca tagcgaaaag      4200
     ggaaaacaag tggtggcgga cgaggagaga agaagcaaat cgaataatcg aagcaacaac      4260
     aacaacaaca aaaaaactgc aaccgggttc actaaaccca gggggcagct cagtagcaaa      4320
     ctactactta aataactact ttcttatggc aaattatggc aagagcagtc gtgatgggtt      4380
     cgatcagtat ccatctgacc ggagcagctg aaccgtttca tgggcagttg ctgcaataca      4440
     ccacgacccg tacacacagt aacacacttt ttatagcttt acactaacaa ccactctccc      4500
     cacgctcctc ttccccttcc cctccacaca gacagcagcg ccgtttgtag caggatctac      4560
     taccgtgcgg tttggtatgg cggccaacaa cactaaacac cacacatcta ctaaaacaca      4620
     ccggaacaat aaacaaatgt taaacttact atatgaatat acatctagac gcatatatac      4680
     gcatgaacta ctacttccct cgtgttctga caaaacacat taccttgtcc cccctccccc      4740
     tccggtttgc ttaccaccac tgcaccacca gtatgaattt gttccataat aacgcttcgt      4800
     aactcgttac caggagcaca actgggtcgt tggcggagtg ctgcgcgttt cgtgctgaag      4860
     atgtaaacta gcaccgcgca cactttcgac acgcaaccac agctacacat cacgaaagca      4920
     acatcctggc cctatccgtt ttctcattct taaaacttct ttccttagac caaaaccaac      4980
     gcaaactagc aaaaggtact tgagtaaccg gtccagtaca cactgtgcta caattgagcg      5040
     tagggaggag gtataatttc tgcaaaatgt ataaaacaaa actaaaacaa actaattact      5100
     tgcaatccat tctaaagcac gaaaactcct caaaataaaa acgggaagta aacaaaaaaa      5160
     tcagaacgaa caaatttacc taaaaaaaag taaac                                 5195
//

BioPerl-1.007002/t/data/BOSS_DROME.FASTP_v35_04000444000766000024      1370713155576321 20213 0ustar00cjfieldsstaff000000000000# fasta35 -E 1 -H BOSS_DROME.fa wormpep190
FASTA searches a protein or DNA sequence data bank
 version 35.04 Aug. 28, 2008
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query: BOSS_DROME.fa
  1>>>BOSS_DROME Protein bride of sevenless precursor. - 896 aa
Library: wormpep190 10449259 residues in 23771 sequences

10449259 residues in 23771 sequences
Statistics:  Expectation_n fit: rho(ln(x))= 5.6522+/-0.000443; mu= 12.7762+/- 0.026
 mean_var=109.3856+/-23.016, 0's: 1 Z-trim: 2  B-trim: 0 in 0/59
 Lambda= 0.122629
Algorithm: FASTA (3.5 Sept 2006) [optimized]
Parameters: BL50 matrix (15:-5) ktup: 2
 join: 38, opt: 26, open/ext: -10/-2, width:  16
 Scan time:  2.980

The best scores are:                                      opt bits E(23771)
F35H10.10 CE24945 WBGene00018073 status:Confirmed  (1404)  207 48.2 9.2e-05

>>F35H10.10 CE24945 WBGene00018073 status:Confirmed UniP  (1404 aa)
 initn:  94 init1:  94 opt: 207  Z-score: 196.5  bits: 48.2 E(): 9.2e-05
Smith-Waterman score: 275; 22.7% identity (52.3% similar) in 728 aa overlap (207-847:640-1330)

        180       190       200       210       220          230   
BOSS_D RAISIDNASLAENLLIQEVQFLQQCTTYSMGIFVDWELYKQLESVIKD---LEYNIWPIP
                                     : : . .   .: :: ..   :. ..  .:
F35H10 NQAGRNITIVPKSVFGYASALHGDSQESLKGYFSSGDTDASLVSVDSEHSALQRSFTALP
     610       620       630       640       650       660         

           240       250        260       270       280            
BOSS_D GTRAHLFPKVAHLLHQMPWGEKIASV-EIATETLEMYNEFMEAARQEHMCLM--------
       ..: . .  . .::..: :    :.. :   :.: ..  : . : .. .::         
F35H10 SSRNQALA-LLKLLNRMQWQFVTAALSEQDPESLSLFRAFERLALDRGVCLAEVLNIGGS
     670        680       690       700       710       720        

             290        300           310       320             330
BOSS_D ---HFKSDDNVYIMFGN-KLASHF----KENGTLFSVPTDRTDDEFLAD------LPNRA
          ...:  :: :.:.. . :. .    :  :.  .:   .. : .:        .:. .
F35H10 RLDNIRSTTNVTIVFSTARDAADYLIASKIRGNHVNVMMGEAHDWYLHAPNNKELFPGTV
      730       740       750       760       770       780        

                340       350       360          370               
BOSS_D FVLMENEI--DLSTAVELDATPTALDEILIGKSVLPSR---VLSFAGSII--------DL
        :  .: .  :.   .:  .:: .: : :   : . ::   .::  ...:        .:
F35H10 SVQPRNILYGDFREWLET-TTPLTLPE-LWYWSYIESRYGCALSQKSKVIYGKMCTGDEL
      790       800        810        820       830       840      

       380          390       400       410       420       430    
BOSS_D MNWLR-GSLSK--HCKRGEEHDLYVLESCFNFLNFIEDWRTSEYRQAHDTAEILSLLLMR
       .:    : ..:  . .:: :. :....: .. :   ..    :. . .   .::. :  .
F35H10 LNIESLGRMTKAGYLSRGVERFLFAMDSVYKSLCPAQNGLCLEFYE-QGRRQILTQL--K
        850       860       870       880       890        900     

          440       450       460       470       480       490    
BOSS_D KLGTAMNFQMYQKKVLTLDKITGESRTELREIASQNFVTNVTTYYHYNRDNHTSLELKTK
       : .:  . ..:.     :  :...   .:  ::. ...:..    .:   : .  : : .
F35H10 KTSTEDDVEIYE----FLPDINNHFTYHL--IANWTLTTGLRMTNQYRNGNGVPTESKCQ
           910           920         930       940       950       

                           500            510       520            
BOSS_D -----------FGQ------VFNCQYSAGDN-----RRYPFLFDGESV----MFWRIKMD
                  : :      ::  .   :..     .: :  : .:..    .: .:   
F35H10 PPMCKCFLDGDFFQRPLDSFVFRPDEPEGSDQSSYIKRQP-AFGSEKIEYQSVFEHITTG
       960       970       980       990       1000      1010      

      530       540            550       560       570       580   
BOSS_D TWVATGLTAAILGLIATL-----AILVFIVVRISLGDVFEGNPTTSILLLLSLILVFCSF
        :     . ..:.::..:     :.::...:.. :  : .:: . .: ::...:..    
F35H10 HWRDHPHNYVLLALITVLVVVAIAVLVLVLVKLYL-RVVKGNQSLGISLLIGIIIL----
       1020      1030      1040      1050       1060      1070     

           590       600       610       620       630       640   
BOSS_D VPYSIEYVGEQRNSHVTFEDAQTLNTLCAVRVFIMTLVYCFVFSLLLCRAVMLASIGSEG
         ::  .         .:. .   ...: .::..  : : . :.... .:..: .  . :
F35H10 --YSTAFF-------FVFDPT---DSVCRLRVILHGLGYTICFGVMIAKATQLRNAETLG
                     1080         1090      1100      1110         

            650       660       670       680            690       
BOSS_D -GFLSHVNGYIQAVICAFSVVAQVGMSVQLLVVMHVASETVSCENIY-----YGRWLWGL
        :   :.. .   ..  : : .:...:.. ..   ...  :   :.      .:.  . .
F35H10 FGTAIHISFWNYWLLLFFIVGVQIALSISWFLEPFMSTIGVIDTNVQRMMCTMGKVEFVV
    1120      1130      1140      1150      1160      1170         

       700       710        720       730       740       750      
BOSS_D LAYDFALLCCVGALIPSIYRS-QRNYREGILIVIGSVLIMVIWVAWIALSLFGD-EWRDA
         .   .:  .. .:  . :. .:::.:   .. ..:: .  :::::.: :  : :.::.
F35H10 SNFYVMILIFMALFISMLNRNIKRNYKETKWLLYSTVLCFFTWVAWITLYLVLDHEFRDT
    1180      1190      1200      1210      1220      1230         

         760       770        780       790          800       810 
BOSS_D AIPLGLQASGWAVLVGILI-PRTFLIVRGIERSDIA---QALPSLTSLAFAQNNQYSSEQ
       .: . : : . ..:.:.:. :. .... . :   .:   . .:. :.: : ....  :..
F35H10 VIVVELVACA-TILLGFLFGPKIYILL-SYEPVVVAFKRDPFPNHTDL-FEKDDDLPSQR
    1240       1250      1260       1270      1280       1290      

             820       830       840         850       860         
BOSS_D SVYECVNPAMRHCSQDEVNHQSPSEIPTL--PLRGGGPRRQQFFANLRQANANINPQRPP
       .    :.::    :... . .. :   .   :. . ::                      
F35H10 A----VSPASSTSSSSNRSSSGSSYTSSSKRPVNAVGPLPLNKNVEDQSPIFHTVMRKKT
           1300      1310      1320      1330      1340      1350  

     870       880       890                               
BOSS_D PRPQQSPSRSSVSSLPPSPDHNKITRF                         
                                                           
F35H10 KVRRSNSEHDTIMNVGIPMTSVPIIRSPSARDEKVHRVAISPPIRDYNSINH
           1360      1370      1380      1390      1400    



896 residues in 1 query   sequences
10449259 residues in 23771 library sequences
 Scomplib [35.04]
 start: Wed Oct 22 20:59:06 2008 done: Wed Oct 22 20:59:09 2008
 Total Scan time:  2.980 Total Display time:  0.030

Function used was FASTA [version 35.04 Aug. 28, 2008]
BioPerl-1.007002/t/data/Bird_Ovomucoids.nex000444000766000024      3545113155576321 20523 0ustar00cjfieldsstaff000000000000#NEXUS 


BEGIN DATA;
DIMENSIONS  NTAX=89 NCHAR=88;

[!Data from:

Laskowski, M., Jr., and W.M. Fitch.  1989.  Evolution of avian ovomucoids and of birds.  Pp. 371-387 in B.  Fernholm, K. Bremer, and H. Jšrnvall (eds.),  The Hierarchy of Life.  Elsevier Press, Amsterdam. 

Thanks to Walter Fitch for supplying the data matrix,   March 1990.]
FORMAT DATATYPE=PROTEIN  SYMBOLS = " 1 2 3 4"  MISSING=? GAP=-  MATCHCHAR=. ;
MATRIX
[                                        10        20        30        40        50        60        70        80       ]
[                                        .         .         .         .         .         .         .         .        ]

Struthio_camelus                VKYPNTNEEGKEVVLPKILSPIGSDGVYSNELANIEYTNVSK??????FAT--VDDYKPVPLDYMLDSKTSNKNNVVESSGTLRHFGK   [86]
Rhea_americana                  .............L..E..N.V.T................?.D?????...--...H...S.E..........D.....N...S....   [86]
Pterocnemia_pennata             .............L..E..N.V.A..................DHD?EV...--...H...S.E..........D.....N...S....   [86]
Casuarius_casuarius             ........D....L.....N.........DD......A....DHDKEV...--..E....SPE.......N..DS....N...G....   [86]
Dromaius_novaehollandiae        ........D....L.....N..........D......A..??D?????...--.......S.E.......N..D.....N...G....   [86]
Nothoprocta_cinerascens         .....A.D.....P...TP...A.NA.FGS....V....I..DHDK?????T-..G...AT.E.F..NQ.A..A....KNV....L..   [87]
Eudromia_elegans                .R.....D.....P...TP..V.AN....S....V....I?.?????????S-I.G...AT.EFF..NQ....A.A..KNV..N.I.E   [87]
Pygoscelis_adeliae_f            .TF..........LVT.......T..................DHDKEVI..--.......S.E..............D.N...S....   [86]
Pygoscelis_adeliae_y            .T...........LVT.......T..................DHDKEVI..--.......S.E..............D.N...S....   [86]
Spheniscus_humboldti            .T.S.........LIT.......T..................D?DKEVI..--I......S.E..............D.N.I.S....   [86]
Phalacrocorax_sulcirostris      .S.SK.......ALVT.......T..............KI..DHDKEVI..--.......S.E.............AD.N...S....   [86]
Anhinga_novaehollandeae         .L.S.........LVT.......T................T.DHDKEVI.S--.......S.E..............D.N...S....   [86]
Nycticorax_nycticorax           .T.S.A....R..LVT.......A..........M....I..DHDGEVIV.--.......SPEN.V.......D..AD.N...S....   [86]
Chauna_chavaria                 .R...........L.T.T.....T..................DRDKEAV..--......AT.E....NQ....S...D.N...S....   [86]
Anseranas_semipalmata           .R...S.......L.T.D...................A....DHDKEAV..--..E...AT.E....NQ........D.N...S....   [86]
Dendrocygna_arcuata             .RF..........L.T.E...V.................I..D?DKEAV..--......AT.E....N..G......D.N...S....   [86]
Dendrocygna_autumnalis          .RF..........L.T.D.....................I..DHDKEAV..--......AT.E....N..G......D.N...S....   [86]
Dendrocygna_eytoni_d            .RF..........L.T.DVI.V............L....I..DHDKEAV..--....R.DT.E....N..G......D.N...S....   [86]
Dendrocygna_eytoni_e            .RF..........L.T.DVI.V............L....I..DHDKEAV..--..E.R.DT.E....N..G......D.N...S....   [86]
Dendrocygna_viduata             .RFS.........L.T.E...V.................I..D?D?EAV..--......AT.E....N..G.R....D.N...S....   [86]
Coscoroba_coscoroba             ..F..........L.T.D.I...T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S....   [86]
Cygnus_atratus                  .RF..........L.T.D.....T...............I..DHDKEAV..--......ATME....N..G......D.N...S....   [86]
Goose                           .RF..........L.T.D.....T...............I..DHDKEAV..--......ATVE....N..D......D.N...S....   [86]
Anser_indicus                   .RF..........L.T.D.A...T...............I..DHDKEAV..--......ATVE....N..D......D.N...S....   [86]
Branta_canadensis               .RF.......R..L.T.D.....T...............I..DHD???V..--......ATVE....N..G......D.N...S....   [86]
Cereopsis_novaehollandiae       ..F..........L...DVI.T.T...............I..D?D??AV..--......ARME....N..G......D.N...S....   [86]
Chloephaga_picta                .RF..........L.T.E.....T...............I..D??KEAV..--..G...ATME....N..G......D.N...S...E   [86]
Duck                            .RF..........L.T.E...V.T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S...E   [86]
Anas_platyrhynchos              .RF........D.L.T.E...V.T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S...E   [86]
Megapodius_freycinet            .R...........LVTQDV?...T....?....G...??I????????LV.--......ST.EDK..NQ....S...D.N...S....   [86]
Leipoa_ocellata                 IRH..........LVTEDS....T...............I..E?DK??VV.--..G.THAT.ELK..NQ....G..AQ.N...S....   [86]
Ortalis_vetula                  ...........D.LA.EDPNL.......T-.......???????????..PN-...H..ALQEQKI.N..D..S...D.N...S....   [86]
Penelope_jacquacu               ...........D.LA.EDP.........T-.........I..ERDKEA..PN-...H..ALQEQK..N..D..S...D.N...S....   [86]
Penelope_superciliaris          ...........D.LVAEDP....................I..E?DKEA..PN-...H..ALQEQK..N..D..S...D.N...S....   [87]
Bonasa_umbellus                 .RF........V.LV.EDPR...T.A.....M.......I..EHD???L.AS-..E...ATME.R..N..G........N.N.S...T   [87]
Tympanuchus_cupido              .RF........D.LVTED.H...T...............I..EHD???L.AS-..E...ATME.R..N..G........N...S....   [87]
Oreortyx_pictus                 .RF........D.LAT.E.H...T........S......I..EHDTEA..AS-..E...AT.E.R.....A........N...S....   [87]
Callipepla_squamata_n           .RF........D.LAT.E.H...T........Y......I..EHD??A..AS-..E...DT.E.R..N..A........N...S....   [87]
Callipepla_squamata_s           .RF........D.LAT.E.H...T........Y......I..EHD??A..AS-..E...DT.E.R..N..AS.......N...S....   [87]
Lophortyx_californicus          .RF........D.LVT.E.Q...T........Y......I..EHD?EA..AS-..E...AT.E.R..N..A........N...S....   [87]
Colinus_virginianus             .RF........D.LATEE.H...T....MS.MF......T..EHDTEA..AS-..E...AMSE.R..N..V........N...S....   [87]
Cyrtonyx_montezumae_l           .RF........D.LVTEEV....T........S..A.?.I.?E?D???..AS-..E...AT.E.VI.N..G........N...S....   [87]
Cyrtonyx_montezumae_s           .RF........D.LVTEEV....T........S..A.?.I.?E?D???..AS-..E...ATSE.VI.N..G........N...S....   [87]
Alectoris_chukar                ARF..A.....D..VTED.R...T....T-.........I..EHDGETL.A--..E...AT.E.R.....G........N...S....   [85]
Alectoris_rufa                  ARF..A.....D..VTED.H...T....T-.........I..EHD???L.A--..E...AT.E.R.....G........N...S....   [85]
Francolinus_afer                .RF..A....RD..VSEN.R...TH........SM....I..EHDREAP.AS-..E...ATME.RV.NI.G......K.N...S....   [87]
Francolinus_erckelii            .RF..A.....D.AVSEN.R...T...N-.....M....I??EHD?EAP.AS-..E...ATME.RV.NI.G......K.N...S.K..   [86]
Francolinus_coqui_v             .RF..A....RD..VSEN.R...T.........SMN...I..E?D?EA???S-..E...GTME.RV.NI.G......K.N...S....   [87]
Francolinus_coqui_a             .RF..A....RD.AVSEN.R...T.........SMN...I..E?D?EA???S-..E...GTME.RV.NI.G......K.N...S....   [87]
Francolinus_francolinus_a       ARF........V.LDS.D.I...T..LHDS..S...H.KIK.EHDRE????S-..G...ETAEET..N..R........N........   [87]
Francolinus_francolinus_v       .RF........V.LDS.D.I...T..LHDS..S...H.KIK.EHDRE????S-..G...ETAEET..N..R........N........   [87]
Francolinus_pondicerianus       ARFS.A.....D.LVIDDPR.M.T....DS..F.M....I..EHD???LPAS-..E...DTTEER..N..G........N...S....   [87]
Perdix_perdix                   .RF........D.LVTED.Q...T...............I..EHT???L.AS-..E...ATME.R..N..G..D.....N...N....   [87]
Coturnix_delegorguei            .RF........DE.V.DE.RF..T....NH.MF.K....I..EQDGET???S-..E...A.K..RV.N..G........N...NR...   [87]
Coturnix_coturnix_japonica_1    .RF........DE.V.DE.RL..T....NH.MF.K....I..EQDGETL.AS-..E...A.K..RV.N...........N...N....   [87]
Coturnix_coturnix_japonica_2    .RF........DE.V.DE.RL..T....NH.MF.K....I..EQDGETL.AS-..E...A.K..RV.N..G........N...N....   [87]
Arborophilia_torqueola          .RF..S.....V..VKEDPR...T.........H..T??I?.?????????S-....M.ATME.RV.N..G........N...S....   [87]
Bambusicola_thoracica           ARF..A.....V.LDTQE.R...T.......MS......I.IK?DKE?L.AS-..E...ETAEERI.N..G........N....N...   [87]
Tragopan_satyra                 .RF........D.LVTED.H...T...............I..GHDREAL.AS-..E...ATME.R..N..G........N...S....   [87]
Tragopan_temmincki              .RF........D.LVTED.R...T...............I..GHD???L.AS-..E...ATME.R..N..G........N...S....   [87]
Lophophorus_impejanus           .RF..A.....D.LVTED.R...T...............I..EHDREAL.AS-..E...ATME.R..N..G........N...S....   [87]
Crossoptilon_auritum            .RF........D.LVAED.R...T...............I..ERDGEAL.AS-..E...ATME.R..N..G........N...S....   [87]
Lophura_edwardsi                .RF........D.LVAED.R...T.......M.......I..ERDGEAL.AS-..E...ATME.R..N..G........N...S....   [87]
Lophura_ignita                  .RF........D.LVGEDIR...T.......M.......N..ERDGEAL.AS-..E...ATME.R..N.SD........N...S....   [87]
Gallus_gallus                   ARF..ADK...D.LVN.D.R...T....T.D..S..F..I..EHDKETL.AS-..E...DTAEDR..N..G........N...S....   [87]
Grey_jungle_fowl                ARF..ADK...D.LVN.D.R...T....T.D..S..F..I..EHDKETL.AS-..E...DTVEDR..N..G........N...S....   [87]
Phasianus_colchicus             .RF..........LVAED.R.V.T.....S.........I..EHEGEAL.AS-..E...ATME.R..N..G........N...NR..Q   [87]
Syrmaticus_ellioti              .RF..K.....D.LVAED.H...T...............I..ER?G??L.AS-..E...ATME.R..N..G........N...S....   [87]
Syrmaticus_reevesii             .RF..K.......LVAED.H...T.....S.........I..ERNGEAL.AS-..E...ATME.R..N..G........N...SR..E   [87]
Chrysolophus_amherstiae         .RFL.....S.D-LVAED.H...T...............I..EHDG?AL.AS-..E...ATME.R..N..G........N...N....   [86]
Polyplectron_bicalcaratum       .RF....K...D.LA.EEVR...T.....D.S..RD...I..EHDR?????S-..E.Q.TTTEHRVNNE.G......K.N..VS....   [87]
Argusianus_argus_argus          .RF........D.LVSEDRH...T.....H..T......I..EHD?EAL.A--..EH..AT.EDR..N.I...D..L..N...S....   [86]
Pavo_cristatus                  .RF..A.....D.LVSED.H...T.....H.........I..EHDREAL.AS-..E...AT.EHR..N..G........N...S....   [87]
Afropavo_congensis              .RF........D.SAS.D.R...T.....H.........I..EHDGEAL.AS-..E...ATMEQR..N..G........N...S....   [87]
Numida_meleagris                .RF..A.....D.LVTED.R...T......D........I.?????EAL.A--..E...ATME.R..N..D........N...S....   [86]
Acryllium_vulturinum            .RF..A.....D.LVIED.R...T......D........I..EHD???L.A--..E...ATME.R..N..D........N...S....   [86]
Meleagris_gallopavo             .RF........D.LVTED.R...T...H.-.........I..EHDREAL.AS-..E...AT.E.R..N..G........N...S....   [86]
Grus_carunculatus               .T...........LVT.......T..................DHDKEAT..--......AT.E..F...........D.N...S....   [86]
Anthropoides_virgo              .T...........LVT.......T..................DHDKEVT..--......AT.E..F...........D.N...S....   [86]
Grus_vipio                      IT...........LVT.......T..................DHDKEAT..--......AT.E..F...........D.N...S....   [86]
Fulica_atra                     .T...........LVT.....V.TN......S..........DYDKEVT..--..G.Q.AS.E.VF.N.....D..AD.N...S....   [86]
Vanellus_spinosus               .T...........LVT.......T..........L.......DYDKEVI..--......AS................D.N...S..E.   [86]
Larus_rudibundus                .T...........LAT.A...V....................DYDKEDI..--......AS................D.N...S..E.   [86]
Turnix_sylvatica                .RF........DT.AD.D.P.........-.M.......I..EHD??T???S-..E...GMMERL..N..ND.......N...N...E   [86]
Gallirallus_australis           .T.........V.LVT.NI..V.TN...T..S.I...S....DYD???T..??..G.QSA.Q..VF.N........AD.N...S....   [88]
Geococcyx_californianus         .A...A......ALVTTARLH..T....G.....L.H..I..DYNKEVI.S--.N.....S.L....N..G.....AD.N...S....   [86]
Dacelo_novaeguineae             .......D.....LVTE......T.R................EHDKEAI..-Q..EH..AT...RI.......D..MD.N...S....   [87]
Carpococcyx_renauldi            .R...S......GLATT.R....T....G.....L....I..DYD???I..--.......T.ED...NI.H..Y..AH.N..FS....   [86]
Podargus_strigoides             .T.......S...LVDEV.....T..........L.-..I..DRDK??I..--....Q..MG...............D.N...N....   [85]
;
END;
BEGIN GENETICCode;
StandardNUCLEAR;
END;

BEGIN CODONS;
CODESET * UNTITLED = Universal: all ;
END;

BEGIN ASSUMPTIONS;
	OPTIONS  DEFTYPE=unord PolyTcount=MINSTEPS ;
END; 

BEGIN TREES; 

	TRANSLATE
		1	Struthio_camelus,
		2	Rhea_americana,
		3	Pterocnemia_pennata,
		4	Casuarius_casuarius,
		5	Dromaius_novaehollandiae,
		6	Nothoprocta_cinerascens,
		7	Eudromia_elegans,
		8	Pygoscelis_adeliae_f,
		9	Pygoscelis_adeliae_y,
		10	Spheniscus_humboldti,
		11	Phalacrocorax_sulcirostris,
		12	Anhinga_novaehollandeae,
		13	Nycticorax_nycticorax,
		14	Chauna_chavaria,
		15	Anseranas_semipalmata,
		16	Dendrocygna_arcuata,
		17	Dendrocygna_autumnalis,
		18	Dendrocygna_eytoni_d,
		19	Dendrocygna_eytoni_e,
		20	Dendrocygna_viduata,
		21	Coscoroba_coscoroba,
		22	Cygnus_atratus,
		23	Goose,
		24	Anser_indicus,
		25	Branta_canadensis,
		26	Cereopsis_novaehollandiae,
		27	Chloephaga_picta,
		28	Duck,
		29	Anas_platyrhynchos,
		30	Megapodius_freycinet,
		31	Leipoa_ocellata,
		32	Ortalis_vetula,
		33	Penelope_jacquacu,
		34	Penelope_superciliaris,
		35	Bonasa_umbellus,
		36	Tympanuchus_cupido,
		37	Oreortyx_pictus,
		38	Callipepla_squamata_n,
		39	Callipepla_squamata_s,
		40	Lophortyx_californicus,
		41	Colinus_virginianus,
		42	Cyrtonyx_montezumae_l,
		43	Cyrtonyx_montezumae_s,
		44	Alectoris_chukar,
		45	Alectoris_rufa,
		46	Francolinus_afer,
		47	Francolinus_erckelii,
		48	Francolinus_coqui_v,
		49	Francolinus_coqui_a,
		50	Francolinus_francolinus_a,
		51	Francolinus_francolinus_v,
		52	Francolinus_pondicerianus,
		53	Perdix_perdix,
		54	Coturnix_delegorguei,
		55	Coturnix_coturnix_japonica_1,
		56	Coturnix_coturnix_japonica_2,
		57	Arborophilia_torqueola,
		58	Bambusicola_thoracica,
		59	Tragopan_satyra,
		60	Tragopan_temmincki,
		61	Lophophorus_impejanus,
		62	Crossoptilon_auritum,
		63	Lophura_edwardsi,
		64	Lophura_ignita,
		65	Gallus_gallus,
		66	Grey_jungle_fowl,
		67	Phasianus_colchicus,
		68	Syrmaticus_ellioti,
		69	Syrmaticus_reevesii,
		70	Chrysolophus_amherstiae,
		71	Polyplectron_bicalcaratum,
		72	Argusianus_argus_argus,
		73	Pavo_cristatus,
		74	Afropavo_congensis,
		75	Numida_meleagris,
		76	Acryllium_vulturinum,
		77	Meleagris_gallopavo,
		78	Grus_carunculatus,
		79	Anthropoides_virgo,
		80	Grus_vipio,
		81	Fulica_atra,
		82	Vanellus_spinosus,
		83	Larus_rudibundus,
		84	Turnix_sylvatica,
		85	Gallirallus_australis,
		86	Geococcyx_californianus,
		87	Dacelo_novaeguineae,
		88	Carpococcyx_renauldi,
		89	Podargus_strigoides
	;
	TREE  * PAUP_1 =  [&R] (1,(((2,3),(4,5)),((((((((((6,7),((30,31),(((32,33),34),(((((((35,57),((((53,67),70),(62,(63,64),(68,69))),(((54,(55,56)),84),74))),(((46,(48,49)),47),71)),((36,59),60),(61,(75,76))),(72,73),77),((44,45),((((50,51),58),52),(65,66)))),(((37,((38,39),40)),41),(42,43)))))),14),15),((((16,20),(18,19)),17),((((21,26),(27,(28,29))),22),((23,24),25)))),(78,79,80)),87),((81,85),(82,83))),(8,9,(10,((11,(86,88)),13),12))),89)));

END;


BEGIN NOTES;
	TEXT  TAXON=26 TEXT= G_removed_from_end_of_sequence;
END;

BEGIN MACCLADE;
Version 3.05;
LastModified -1425155265;
Singles 1000&/0;
END;
BioPerl-1.007002/t/data/CG11099.fasaln000444000766000024      1757713155576321 17014 0ustar00cjfieldsstaff000000000000>mel;CG11099-PA_2R_EXON_15751501-15753284
ATGAACAAAACGATTCTGCACTGGAGCTACCTGAATTTCAAGGATGTCCCGATGGATCTGTTCCTCTACGAGGATCTCGAGGAAGTCTACCTCAAGGAGAACTTCATCTCGGTGATACCCAAATGGCTGCTGAACATCACCACACTGAAGTTTATTCATTTGGCTGGCAATAATCTGAGTGAACTGCCGGTGGACATCTATATGCTGGAGAATCTGGAGTTCCTGGACGTATCCAACAATGAGCTCAAGGAGCTGCCCCCCACACTGGGTCTCCTGTTGAATCTCCAGCAGCTGAATGTGTCGGGGAATCAGCTCACCGAACTACCAGTGGAGCTAAGTGGTTTGCGCAATCTGGAGCACCTGAACATTGGCAAGAACCAATTTCGACGCCTGCCGGTTCAGCTGAGCGAGTGCGTCCGCCTCAACGAGCTGAATGTGAGCGACAACGAGGCGCTTGTCCACATCCCCGAGCGCATCTCCAACCTGCCCATGCTGCAGTCCCTCGCCGCAGATCGTTGTGCGCTCGTCTACTTGCCGGCAGCTCTCTCCAAGTTCATGAACCATGTGCGCATCTTCCACAACACCGCTATCAACTACATACCCATGGTCTATGAGAGGTTCTATCAAAACTTTTACGACAACCGCCAGAGGAATACTCCCGTCGCCGTGCATCGCAAGGGTTTGTTTTGGGTCCGCGAGCTGGAGACCAGCACCAGGTTGCTTCTTCCGGTTGGCACCCGCACAGTATTTCCGGTTCCGTCGGTGGAGAACCGCGTTTCGCTCTACGATGACTGTCTGCACGCTCTGCAGACGCTGAACCGCTTCACGCCCGTATATGAGAATGTAGCCATGCATCGTCTGCTCCCAGAACCGTACATCAGTTCCCACATCAACAATGGACCCATCGCCCGCTGCACGAACTCCACCTGCTCCAGATGTCTCTATACCTCGTACTACTTCATGGTTGTGAAAAGGCGTGGCAGTACATC
 CAAACAGCTCTTCACCTGCAACTTCTGCACCAACCGATGTGGTCTCCTTTGGTTGACTAGCAATGATAAGAAGTACTACCAATTGGCTTGGCGAGTCTCAGATGATGACGACGATGATGAGGAAGAACACATGGCCAGCAACAAA
>sim;w501+f
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCCCCCACACNNNNNNNNNNNNNNNNNNTCCAGCAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAACATNNNNNNNNNCCAATTTCGCCNNNTGCCGGTGCAGCTGAGCGAGTGCNNNNNNNTCAACGAGCTGAATGTGAGCGACAACGAGGCGCTGGTCCACATCCCCGAGCGCATCTCCAACCTGCCCATGCTGCAGTCCCTCGCCGCCGATCGTTGTGCGCTCGTCTACTTGCCGGCAGCTCTCTCCAAGTTCATGAACCATGTGCGCATCTTCCACAACACCGCTATCAACTACATACCCATGGTCTATGAGAGGTTCTATCAAAACTTTTACGACAACCGCCAGAGGAATACTCCCGTCGCCGTTCATCGCAAGGGTTTGTTTTGGGTCCGAGAGCTGGAGACCGGCACCAGGTTGCTGCTTCCGGTGGGCACCCGCACAGTATTTCCGGTTCCGTCGGTGGAGAACCGGGTCTCACTCTACGACGACTGTCTGCACGCTCTGCAGACGCTGAACCGCTTCACGCCCGTTTATGAGAATGTAGCCATGCATCGCCTGCTCCCAGAACCGTACATCAGTTCCCACATCAACAATGGACCCATCGCCCGCTGCACGAACTCCACCTGCTCCAGATGTCTGTATACCTCGTACTACTTCATGGTTGTGAAAAGNNNNNNNNNNNNNNN
 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGACGATGATGAGGAAGAACACATGGCCNNNNNNNNN
>sim;sim
ATGAACAAAACGATTCTGCACTGGAGCTATCTGAATTTCAAGGATGTGCCGATGGATCTGTTCCTCTACGAGGATCTCGAGGAGGTCTACCTCAAGGAGAACTTCATCTCGGTAATACCCAAATGGTTGCTGAACATCACCACACTGAAGTTTATTCATTTGGCTGGCAATAATNTGAGTGAGCTGCCGGTGGACATCTATATGCTGGAGAACCTGGAGTTCCTGGACGTATCCAACAATGAGCTCAAGGAGCTGCCCCCCNNNNTGGGTCTCCTGTTGAATCTCCAGCAGCTGAATGTGTCTGGCAATCAGCTCACCGAACTTCCAGTGGAGCTCAGTGGTTTGCGCAATCTGGAGCACCTGAACATCGGCAAGAACCAATTTCGCCGCCTGCCGGTGCAGCTGAGCGAGTGTGTCCGCCTCAACGAGCTGAATGTGAGCGACAACGAGGCGCTGGTCCACATCCCCGAGCGCATCTCCAACCTGCCCATGCTGCAGTCCCTCGCCGCCGATCGTTGTGCGCTCGTCTACTTGCCGGCTGCTCTCTCCAAGTTCATGAACCATGTGCGCATCTTCCACAACACCGCTATCAACTACATACCCATGGTCTATGAGAGGTTCTATCAAAACTTTTACGACAACCGCCAGAGGAATACTCCCGTCGCCGTTCATCGCAAGGGTTTGTTTTGGGTCCGAGAGCTGGAGACCGGCACCAGGTTGCTGCTTCCGGTGGGCACCCGCACAGTATTTCCGGTTCCGTCAGCGGAGAACCGGGTATCGCTCTATGACGACTGTCTGCACGCTCTGCAGACGCTGAACCGCTTCACGCCCGTTTATGAGAATGTAGCCATGCATCGTCTGCTCCCAGAACCGTACATCAGTTCCCACATCAACAATGGACCCATCGCCCGCTGCACGAACTCCACATGCTCCAGATGTCTGTATACCTCGTACTACTTCATGGTTGTGAAAAGGCGTGGCAGTACATC
 CAAGCAGCTCTTCACCTGCAACTTCTGCACCAACCGATGTGGTCTCCTTTGGTTGACCAGCAATGATAAGAAGTACTACCAATTGGCTTGGCGAGTCTCAGATGATGACGACGATGATGAGGAAGAACACATGGCCAGCAGCAAA
>sim;md199
ATGAACAAAACGATTCTGCACTGGAGCTATCTGAATTTCAAGGATGTGCCGATGGATCTGTTCCTCTACGAGGATCTCGAGGAGGTCTACCTCAAGGAGAACTTCATCTCGGTGATACCCAAATGGTTGCTGAACATCACTACACTGAAGTTTATTCATTTGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGCCGTTCATCGCAAGGGTTTGTTTTGGGTCCGCGAGCTGGAGACCCGCACCAGGTTGCTGCTTCCGGTGGGCACCCGCACAGTATTTCCGGTTCCGTCGGTGGAGAACCGGGTCTCGCTCTACGACGACTGTCTGCACGCTCTGCAGACGCTGAACCGCTTCACGCCCGTTTATGAGAATGTAGCCATGCATCGCCTGCTCCCAGAACCGTACATCAGTTCCCACATCAACAATGGACCCATCGCCCGCTGCACGAACTCCACCTGCTCCAGATGTCTGTATACCTCGTACTACTTCATGGTTGTGAAAAGGCGTGGCAGTACGTC
 CAAGCAGCTCTTCACCTGCAACTTCTGCACCAACCGATGTGGTCTCCTTTGGTTGACCAGCAATGATAAGAAATACTACCAACTGGCTTGGCGAGTCTCAGATGATGACGACGATGATGAGGAAGAACACATGGCCAGCAGCAAA
>sim;md106
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGNTCAACGGTTTGNNNNNNNNGGAGCACNTGAACATNGGCAAGAACNNNNNNNNNNNNNNNCCGGTGCAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGACAACGAGGNNNNNNNNCACATCCCCGAGNNNNNNTCCAACCTGCCCATGNTGCAGTCCCTNNCCGCCGATNGTTGTGCGCTNNNNTACTTGCCGGNNNNNNNNTCCAAGTTCATGAACCATGTGNNNNNNNNNCACAACACCGCTATCAANTACATACCCATGGTNTATGAGAGGTTCTATCAAAACTTTTACGACAACCGCCAGAGGAATACTCCCGTCGCCGTTCANCGCAAGGGTTTGTTTTGGGTCCGCNAGCTGGAGACNNNNNNNNNNNNNNNGCTTCCGGTGGGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCGTGGCAGTACATC
 CAAGCAGCTCTTCACCTGCAACTTCTGCACCAACCGATGTGGTCTCCTTTGGTTGACCAGCAATGATAAGAAGTACTACCAATTGGCTTGGCGAGTGTCAGATGATGACGACGATGAGGAGGCAGAACACATGGTCAGCAGCAAA
>sim;newc
ATGAACAAAACGATTCTGCACTGGAGCTATCTGAATTTCAAGGATGTGCCGATGGATCTGTTCCTCTACGAGGATCTCGAGGAGGTCTACCTCAAGGANAACTTCATCTCGGTGATACCCAAATGGCTGCTGAACATCACCACACTGAAGTTTATTCATTTGGCTGGCAACAATCTGAGTGANCTGCCGGTGGACATCTATATGCTGGAGAATCTAGAGTTCCTGGACGTGTCCAACAACGAGCTCAAGGAGCTGCCCCCCACACTGGGTCTCCTGTTGAATCTCCAGCAGCTGANNGTGTCGGGNNNNNNNNNNNNNNAACTACCAGTGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGCCGTTCATCGCAAGGGTTTGTTTTGGGTCCGCGAGCTNGAGACCAGCACCAGGTTGCTGCTTCCGGTGGGCACCCGCACAGTATTTCCGGTTCCGTCGGCGGAGAACCGGGTCTCACTCTACGACGACTGTGTGCACGCTCTGCAGACGCTGAACCGCTTCACGCCCGTTTATGAGAATATAGCCATGCACCGTCTGCTCCCAGAACCGTACATCAGTTCCCACATCAACAATGGACCCATCGCCCGCTGCACGAACTCCACCTGCTCTAGATGTCTGTATACCTCGTACTACTTCATGGTTGNGAAAAGNNNNNNNNNNNNNNN
 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>yak;yak
ATGAACAAAACGATTCTGCACTGGAGCTACCTGAATTTCAAGGATGTGCCAATGGATCTCTTTCTCTACGAGGATCTCGAGGAGGTCTATCTCAAGGAGAACTTCATCTCGGTGATACCCAAATGGCTGCTGAACATCACCACACTGAAGTTCATCCACCTGGCGGGCAACAATCTGAGTGAATTGCCTGCGGACATCTATATGCTGGAGAACCTTGAGTTCCTGGACGTATCCAACAATGAGCTCAAGGAGCTGCCCCCCACACTGGGTCTCCTCTTGAGTCTCCAGCAGCTGAATGTGTCGGGCAATCAGCTCACCGAACTTCCAGTGGAACTCAGTGGTTTGCGCAATCTGGAGCACCTGAACATCGGCAAGAACCAATTTCGCCGCCTGCCGGTGCAGCTGAGCGAGTGCGTCCGCCTCAACGAGCTGAATGTGAGCGACAACGAGGCGCTGGTCCACATCCCCGAGCGCATCTCCAACCTCCCCATGCTGCAGTCCCTCGCCGCCGATCGTTGTGCGCTCGTCTACTTGCCGGCAGCTCTCTCCAAGTTCATGAACCATGTGCGCATCTTCCACAACACTGCTATCAACTACATACCCATGGTCTATGAGAGGTTCTATCAAAACTTTTACGACAACCGCCAGCGAAATACTCCCGTCGCCGTTCATCGCAAGGGTCTGTTTTGGGTCCGCGATCTGGAGACCAGCACCCGATTGCTGCTTCCGGTGGGCACTCGCACAGTATTTCCGGTTCCGTCGGCTGAGAATAGGGTATCGCTCTACGACGACTGTCTGCATGCTCTGCAGACGCTGAACCGCTTCACGCCCGTCTACGAGAATGGCGCCATGCATCGACTGCTGCCAGAACCGTACATCAGTTCCCACATCAACAATGGACCCATCGCCCGCTGCACGAACTCCACCTGCTCCAGATGTCTGTACACCTCGTACTACTTCATGGTCGTGAAAAGGCGTGGCAGTACGTC
 CAAGCAGCTCTTCACCTGCAACTTCTGCACCAACCGATGCGGAGTCCTCTGGTTGACCAGCAATGACAAGAAGTACTACCAGCTGGCTTGGCGACTGTCGGATGATGACGACGACGATGAGGCGGATCAGACGGCCAGTGGCAAA
BioPerl-1.007002/t/data/CG2865.fasaln000444000766000024      1746713155576321 16733 0ustar00cjfieldsstaff000000000000>mel;CG2865-PA_X_EXON_2137737-2148845
ATGACCTTGCCCACAAACACACACGCATCTGCAAACGACGGCGGCAGCGGCAACAACAACCACAGCAATATCAGCAGTAACAACAGCAGCAGCAGCGACGAAGACTCAGACATGTTTGGACCACCCCGCTGCTCCCCGCCCATCGGCTATCACCATCACCGTTCCCGTGTGCCCATGATCTCGCCAAAGCTGCGGCAGCGCGAGGAGCGCAAGCGGATCCTCCAGCTCTGCGCCCACAAGATGGAGAGGATCAAGGACTCGGAGGCGAACCTGCGGCGCAGCGTCTGCATCAACAACACCTACTGCCGCCTGAATGACGAACTGCGGCGCGAGAAGCAGATGCGCTACCTCCAGAATCTGCCCAGAACCAGCGACAGCGGCGCAAGCACCGAACTGGCGCGTGAGAATCTCTTCCAGCCGAACATGGACGACGCCAAGCCGGCCGGCAATAGCACTAGCAATAATATCAACGCCAACGGCAAGCCTTCATCCTCTTTTGGCGATGCCTTTGGCTCCTCAAACGGATCATCGTCGGGTCGCGGCGGAATTTGCTCCCTGGAGAATCAACCGCCCGAGCGTCAGCAGTTGGGGACGCCCGCTGGTGCCTCCGCTCCCGAGGCGGCCAATTCGGCGCCCCTTTCCGTTTCGGGCTCGGCATCGGAACGCGTGAATAACCGAAAACGCCACCTGTCCAGCTGCAACTTGGTCAACGATCTGGAAATACTGGACAGGGAGCTGAGCGCCATCAATGCACCCATGCTGCTAATCGATCCAGAGATTACCCAAGGAGCCGAACAGCTGGAGAAGGCCGCCTTGTCCGCCAGCAGGAAGAGATTGAGGAGCAATAGCGGCAGCGAGGACGAAAGTGATCGCCTGGTGCGCGAGGCTCTGTCCCAGTTCTACATACCGCCACAGCGCCTCATCTCCGCCATTGAGGAGTGTCCCCTGGATGTGGTTGGCTTGGGTATGGGAATGAATGTGAATGTGAA
 TGTGGGAGGAATTAGTGGAATCGGTGGCATCGGAGGAGCTGCAGGCGCTGGCGTCGAAATGCCCGGAGGCAAACGGATGAAGCTGAATGACCATCACCATCTCAATCACCATCACCATTTGCACCATCATCTGGAGCTGGTCGATTTCGACATGAACCAAAACCAAAAGGATTTCGAGGTGATCATGGACGCCTTGAGGCTGGGAACGGCGACACCGCCGAGCGGCGCCAGCAGCGATTCTTGCGGACAGGCGGCGATGATGAGCGAGTCGGCCAGCGTGTTCCACAATCTGGTGGTCACCTCGTTGGAGACA
>sim;c1674_CG2865-PA_EXON
ATGACCTTGCCCACAAACACACACGCNTCTGCAAANNNNNNNNNNNGCGGCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCCCACAAGANNNNGAGGATCAANNNNNNGGAGGCGAANNNNNGGCGCAGNNNNNGCATCAACAACACNTACTGCCGCCTGAACGACGAGNTGCGGCGCGAGAAGCAGATGCGCTACCTCCAGAATCTGCCCAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>sim;md199_CG2865-PA_EXON
ATGACCTTGCCCACAAACACACACGCATCTGCAAACGACGGCGGCAGCGGCAACAACAACCACAGCAATATTAGCAGCAACAACAACAGCAGCAGCGACGAAGACTCGGACATGTTTGGACCACCCCGCTGCTCCCCGCCCATCGGCTATCACCATCACCGATCCCGTGTGCCCATGATCTCGCCAAAGCTGCGGCAGCGCGAGGAGCGCAAGCGGATCCTCCAGCTGTGCGCCCACAAGATGGAGAGGATCAAGGACTCGGAGGCGAACCTGCGGCGCAGCGTCTGCATCAACAACACCTACTGCCGCCTGAACGACGAGCTGCGGCGCGAGAAGCAGATGCGCTACCTCCAGAATCTGCCCAGNNNNNNNNACAGCGGCNNNNGCACCGAANTGGCGCGTGANAATCTCTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAGCAATANNNNNNNNNNNNNNGGCAAGCCTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>sim;w501+f_CG2865-PA_EXON
ATGACCTTGCCCACAAACACACACGCATCTGCAAACGACGGCGGCAGCGGCAACAACAACCATAGCAATATTAGCAGCAACAACAACAGCAGCAGCGACGAAGACTCGGACATGTTTGGACCACCCCGCTGCTCCCCGCCCATCGGCTATCACCATCACCGTTCCCGTGTGCCCATGATCTCGCCAAAGCTGCGGCAGCGCGAGGAGCGCAAGCGGATCCTCCAGCTGTGCGCCCACAAGATGGAGAGGATCAAGGACTCGGAGGCGAACCTGCGGCGCAGCGTCTGCATCAACAACACCTACTGCCGCCTGAACGACGAGCTGCGGCGCGAGAAGCAGATGCGCTACCTCCAGAATCTGCCCAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCCGCNNNNNNNNNNNNNNNNNNNNNATTGAGGAGCNNNNNNNNNNNNNAGGACGANNNNNNNNNCCTGGTGCGCNNGGCTCTGTCNNNNNNNNNNNNNNNNNNNNNNNNNNTGATCTCCGCCATNGAGGAGTGTCCCCNNNATGTGGTTGGCTTGGGTATGGGAANNNNNNNNNNNNNGAA
 TGTGGGAGGAATCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCGCTGGCGTCNNNNNNNNNGGAGGCAAANNNNNNAAGCTGANNGACCATCNNNNNNNNNNNNNNNATCACCATTTGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAAACCAAAANNNNNNNNAGGTGATCNTGGACGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACA
>sim;sim_CG2865-PA_EXON
ATGACCTTGCCCACAAACACACACGCATCTGCAAACGACGGCGGCAGCGGCAACAACAACCATAGCAATATTAGCAGCAACAACAACAGCAGCAGCGACGAAGACTCGGACATGTTTGGACCACCCCGCTGCTCCCCGCCCATCGGCTATCACCATCACCGTTCCCGTGTGCCCATGATCTCGCCAAAGCTGCGGCAGCGCGAGGAGCGCAAGCGGATCCTCCAGCTGTGCGCCCACAAGATGGAGAGGATCAAGGACTCGGAGGCGAACCTGCGGCGCAGCGTCTGCATCAACAACACCTACTGCCGCCTGAACGACGAGCTGCGGCGCGAGAAGCAGATGCGCTACCTCCAGAATCTGCCCAGAACCAGCGACAGCGGTGCAAGCACCGAACTGGCGCGTGAGAATCTCTTCCAGCCGAACATGGACGACGCCAAGCCGGCCGGCAATAGCACTAGCAATAATATCAACGCCAACGGCAAGCCTTCATCCTCCTTTGTCGATGCCTTTGGCTCCTCAAACGGATCGTCGTCGGGTCGCGGCGGAATTTGCTCCCTGGAGAATCAACCGCCCGAGCGTCAGCAGCTGGGGACACCCGCTGGAGCCTCCGCTCCCGAGGCGGCCAATTCGGCGCCCCTTTCCGTTTCGGGCTCGGCATCGGAACGCGTGAATAACCGGAAGCGCCACCTGTCCAGCTGCAACTTGGTCAACGATCTGGAAATACTGGACAGGGAGCTGAGCGCCATCAATGCACCCATGCTGCTAATCGATCCGGAGATTACCCAGGGAGCCGAGCAGCTGGAGAAGGCCGCCTTGTCCGCCAGCAGGAAGAGATTGAGGAGCAATAGCAGCAGCGAGGACGAAAGTGATCGCCTGGTGCGCGAGGCTCTGTCCCAGTTCTACATACCGCCACAGCGCCTGATCTCCGCCATTGAGGAGTGTCCCCTGGATGTGGTTGGCTTGGGTATGGGAANNNNNNTGAATGTGAA
 TGTGGGAGGAATCGGTGGAATCGGTAGCATCGGAGGAGCTGCAGGCGCTGGCGTCGAAATGCCCGGAGGCAAACGGATGAAGCTGAATGACCATCACCATCTCAACCACCATCACCATTTGCACCACCATCTGGAGCTGGTCGATTTCGACATGAACCAAAACCAAAAGGATTTCGAGGTGATCATGGACGCCTTGAGACTGGGAACGGCGACGCCGCCGAGCGGCGCCAGCAGCGATTCTTGCGGACAGGCGGCGATGATGAGCGAGTCGGCCAGCGTGTTCCACAATCTGGTGGTCACCTCGTTGGAGACA
>yak;CG2865-PA_EXON
ATGACCTTGCCCACAAACACACACGCATCTGCAAACGACGGCGGCAGCGGCAACAACAACCACAGCAACATTAACAATAACAACAGCAGCAGCAGCGACGAAGACTCGGACATGTTTGGACCACCCCGCTGCTCGCCGCCCATCGGCTACCACCATCACCGTTCCCGGGTGCCCATGATCTCCCCCAAGCTGCGACAGCGCGAGGAGCGCAAGCGGATCCTCCAGCTCTGCGCCCACAAGCTGGAGCGGATCAAGGACTCGGAGGCGAACCTGCGCCGCAGCGTCTGCATCAACAACACCTACTGCCGCCTCACCGACGAGCTGCGGCGCGAGAAGCAGATGCGCTACCTCCAGAATCTGCCCAGAACCAGCGACAGCGGCACAACCACCGAACTGGCGCGTGAGAATCTCTTCCAGCCGAACATGGACGATGCCAAGCCGGCCAGCAATAGTACTAGCAATAATATCAATGCCAACGGCAAGCCTTCAACCGCCTTCGCCGATGCCTTTGGCTCCTCAAACGGATCGTCGTCGGGTCGCGGTGGCATTTGCTCCCTGGAGAATCAGCCGCCCGATCGTCAGCAGCTGGGAACGCCCGCTGGAGCCTCCGCGCCCGAGGCGGCCAATTCGGCGCCACTTTCCGTTTCCGGTTCGGCATCGGAACGCGTGAATAACCGGAAACGTCACCTGTCCAGCTGCAATTTGGTCAACGATCTGGAGATACTGGACAGAGAACTGAGCGCCATCAATGCACCCATGCTGCTAATCGATCCGGAGATTACCCAAGGTGCCGAGCAGCTGGAGAAGGCGGCCTTGTCCGCCAGCAGGAAGAGATTGAGGAGCAATAGCAGCAGCGAGGACGAAAGTGATCGCTTGGTCCGCGAGGCTCTGTCCCAGTTCTACATACCGCCTCAGCGCCTGATCTCCGCCATCGAGGAGTGTCCCCTGGATGTGGTCGGCTTGGGTATGGGAATGAATGTGNNNNNNAA
 TGTGGGAGGAATCGGTGGCATCAGTGGCATCGGAGGAGCTGCAGGCGCTGGCGTCGAAGTGTCCGGAAGCAAACGGATGAAGCTGAACGACCATCACCATCTCAACCACCATCACCATTTGCACCATCATCTGGAGCTGGTCGATTTCGATATGAACCAAAACCAAAAGGATTTCGAGGTGATCATGGACGCCTTGAGGCTGGGAACGCCGACGCCGCCGAGCGGCGCAAGCAGCGATTCTTGCGGACAGGCGGCAATGATGAGCGAGTCGGCCAGCGTTTTCCACAATCTGGTGGTCACCTCGTTGGAGACA
BioPerl-1.007002/t/data/D10483.gbk000444000766000024     75560013155576321 16215 0ustar00cjfieldsstaff000000000000LOCUS       ECO110K               111408 bp    DNA     linear   BCT 29-MAY-2002
DEFINITION  Escherichia coli genomic DNA. (0.0 - 2.4 min).
ACCESSION   D10483 J01597 J01683 J01706 K01298 K01990 M10420 M10611 M12544
            V00259 X04711 X54847 X54945 X55034 X56742
VERSION     D10483.2  GI:21321891
KEYWORDS    Complete and shotgun sequencing; thrA; thrA1; thrA2; thrB; thrC;
            yaaA; yaaJ; talB; mog; chlG; dnaK; dnaJ; groP; gef; nhaA; ant;
            rpsT; yaaC; ileS; lspA; yaaD; lytB; yaaF; dapB; carA; pyrA; carB;
            yaaV; caiE; caiD; caiC; caiB; caiA; caiT; fixA; fixC; yaaT; yabE;
            yabF; kefC; trkC; folA; tmrA; apaH; apaG; pdxA; surA; imp; ostA;
            yabH; yabP; yabQ; hepA; polB; dinA; araD; araA; araB; araC; yabI;
            yabJ; yabK; tbpA; yabN; yabM; leuD; leuC; leuB; leuA; leuLP; lueO;
            ilvI; ilvH; brnP; shl; fruR; yabB; yabC; ftsL; pbpB; ftsI; murE;
            murF; mra; mraY; murX; murD; ftsW; murG; murC; ddl; ddlB; ftsQ;
            ftsA; divA; ftsZ; sfiB; sulB; lpxC; envA; asmB; yacA; secA; prlD;
            azi; pea; mutT; yacG; htgA; htpY; yaaI; nhaR; antO; caiF; fixB;
            yaaU; yabO.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Ohtsubo,H. and Ohtsubo,E.
  TITLE     Nucleotide sequence of an insertion element, IS1
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 75 (2), 615-619 (1978)
  MEDLINE   78137003
   PUBMED   273224
REFERENCE   2
  AUTHORS   Smith,B.R. and Schleif,R.
  TITLE     Nucleotide sequence of the L-arabinose regulatory region of
            Escherichia coli K12
  JOURNAL   J. Biol. Chem. 253 (19), 6931-6933 (1978)
  MEDLINE   79005683
   PUBMED   357433
REFERENCE   3
  AUTHORS   Greenfield,L., Boone,T. and Wilcox,G.
  TITLE     DNA sequence of the araBAD promoter in Escherichia coli B/r
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 75 (10), 4724-4728 (1978)
  MEDLINE   79116194
   PUBMED   368797
REFERENCE   4
  AUTHORS   Johnsrud,L.
  TITLE     DNA sequence of the transposable element IS1
  JOURNAL   Mol. Gen. Genet. 169 (2), 213-218 (1979)
  MEDLINE   79177885
   PUBMED   375010
REFERENCE   5
  AUTHORS   Smith,D.R. and Calvo,J.M.
  TITLE     Nucleotide sequence of the E coli gene coding for dihydrofolate
            reductase
  JOURNAL   Nucleic Acids Res. 8 (10), 2255-2274 (1980)
  MEDLINE   81053692
   PUBMED   6159575
REFERENCE   6
  AUTHORS   Ogden,S., Haggerty,D., Stoner,C.M., Kolodrubetz,D. and Schleif,R.
  TITLE     The Escherichia coli L-arabinose operon: binding sites of the
            regulatory proteins and a mechanism of positive and negative
            regulation
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 77 (6), 3346-3350 (1980)
  MEDLINE   81013881
   PUBMED   6251457
REFERENCE   7
  AUTHORS   Katinka,M., Cossart,P., Sibilli,L., Saint-Girons,I.,
            Chalvignac,M.A., Le Bras,G., Cohen,G.N. and Yaniv,M.
  TITLE     Nucleotide sequence of the thrA gene of Escherichia coli
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 77 (10), 5730-5733 (1980)
  MEDLINE   81077247
   PUBMED   7003595
REFERENCE   8
  AUTHORS   Miyada,C.G., Horwitz,A.H., Cass,L.G., Timko,J. and Wilcox,G.
  TITLE     DNA sequence of the araC regulatory gene from Escherichia coli B/r
  JOURNAL   Nucleic Acids Res. 8 (22), 5267-5274 (1980)
  MEDLINE   81124262
   PUBMED   7008027
REFERENCE   9
  AUTHORS   Cossart,P., Katinka,M. and Yaniv,M.
  TITLE     Nucleotide sequence of the thrB gene of E. coli, and its two
            adjacent regions; the thrAB and thrBC junctions
  JOURNAL   Nucleic Acids Res. 9 (2), 339-347 (1981)
  MEDLINE   81150470
   PUBMED   6259626
REFERENCE   10
  AUTHORS   Lee,N.L., Gielow,W.O. and Wallace,R.G.
  TITLE     Mechanism of araC autoregulation and the domains of two overlapping
            promoters, Pc and PBAD, in the L-arabinose regulatory region of
            Escherichia coli
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 78 (2), 752-756 (1981)
  MEDLINE   81199399
   PUBMED   6262769
REFERENCE   11
  AUTHORS   Mackie,G.A.
  TITLE     Nucleotide sequence of the gene for ribosomal protein S20 and its
            flanking regions
  JOURNAL   J. Biol. Chem. 256 (15), 8177-8182 (1981)
  MEDLINE   81264207
   PUBMED   6267039
REFERENCE   12
  AUTHORS   Stoner,C.M. and Schleif,R.
  TITLE     Is the amino acid but not the nucleotide sequence of the
            Escherichia coli araC gene conserved?
  JOURNAL   J. Mol. Biol. 154 (4), 649-652 (1982)
  MEDLINE   82216830
   PUBMED   6283093
REFERENCE   13
  AUTHORS   Gilson,E., Nikaido,H. and Hofnung,M.
  TITLE     Sequence of the malK gene in E.coli K12
  JOURNAL   Nucleic Acids Res. 10 (22), 7449-7458 (1982)
  MEDLINE   83116968
   PUBMED   6296778
REFERENCE   14
  AUTHORS   Parsot,C., Cossart,P., Saint-Girons,I. and Cohen,G.N.
  TITLE     Nucleotide sequence of thrC and of the transcription termination
            region of the threonine operon in Escherichia coli K12
  JOURNAL   Nucleic Acids Res. 11 (21), 7331-7345 (1983)
  MEDLINE   84069770
   PUBMED   6316258
REFERENCE   15
  AUTHORS   Bardwell,J.C. and Craig,E.A.
  TITLE     Major heat shock gene of Drosophila and the Escherichia coli
            heat-inducible dnaK gene are homologous
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 81 (3), 848-852 (1984)
  MEDLINE   84144800
   PUBMED   6322174
REFERENCE   16
  AUTHORS   Innis,M.A., Tokunaga,M., Williams,M.E., Loranger,J.M., Chang,S.Y.,
            Chang,S. and Wu,H.C.
  TITLE     Nucleotide sequence of the Escherichia coli prolipoprotein signal
            peptidase (lsp) gene
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 81 (12), 3708-3712 (1984)
  MEDLINE   84222028
   PUBMED   6374664
REFERENCE   17
  AUTHORS   Bouvier,J., Patte,J.C. and Stragier,P.
  TITLE     Multiple regulatory signals in the control region of the
            Escherichia coli carAB operon
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 81 (13), 4139-4143 (1984)
  MEDLINE   84248073
   PUBMED   6377309
REFERENCE   18
  AUTHORS   Bouvier,J., Richaud,C., Richaud,F., Patte,J.C. and Stragier,P.
  TITLE     Nucleotide sequence and expression of the Escherichia coli dapB
            gene
  JOURNAL   J. Biol. Chem. 259 (23), 14829-14834 (1984)
  MEDLINE   85054974
   PUBMED   6094578
REFERENCE   19
  AUTHORS   Kamio,Y., Lin,C.K., Regue,M. and Wu,H.C.
  TITLE     Characterization of the ileS-lsp operon in Escherichia coli.
            Identification of an open reading frame upstream of the ileS gene
            and potential promoter(s) for the ileS-lsp operon
  JOURNAL   J. Biol. Chem. 260 (9), 5616-5620 (1985)
  MEDLINE   85182715
   PUBMED   2985604
REFERENCE   20
  AUTHORS   Friedberg,D., Rosenthal,E.R., Jones,J.W. and Calvo,J.M.
  TITLE     Characterization of the 3' end of the leucine operon of Salmonella
            typhimurium
  JOURNAL   Mol. Gen. Genet. 199 (3), 486-494 (1985)
  MEDLINE   85295470
   PUBMED   2993799
REFERENCE   21
  AUTHORS   Cowing,D.W., Bardwell,J.C., Craig,E.A., Woolford,C., Hendrix,R.W.
            and Gross,C.A.
  TITLE     Consensus sequence for Escherichia coli heat shock gene promoters
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 82 (9), 2679-2683 (1985)
  MEDLINE   85190560
   PUBMED   3887408
REFERENCE   22
  AUTHORS   Chong,P., Hui,I., Loo,T. and Gillam,S.
  TITLE     Structural analysis of a new GC-specific insertion element IS186
  JOURNAL   FEBS Lett. 192 (1), 47-52 (1985)
  MEDLINE   86030702
   PUBMED   2996940
REFERENCE   23
  AUTHORS   Birnbaum,M.J., Haspel,H.C. and Rosen,O.M.
  TITLE     Cloning and characterization of a cDNA encoding the rat brain
            glucose-transporter protein
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 83 (16), 5784-5788 (1986)
  MEDLINE   86287338
   PUBMED   3016720
REFERENCE   24
  AUTHORS   Sekiguchi,T., Ortega-Cesena,J., Nosoh,Y., Ohashi,S., Tsuda,K. and
            Kanaya,S.
  TITLE     DNA and amino-acid sequences of 3-isopropylmalate dehydrogenase of
            Bacillus coagulans. Comparison with the enzymes of Saccharomyces
            cerevisiae and Thermus thermophilus
  JOURNAL   Biochim. Biophys. Acta 867, 36-44 (1986)
REFERENCE   25
  AUTHORS   Ohki,M., Tamura,F., Nishimura,S. and Uchida,H.
  TITLE     Nucleotide sequence of the Escherichia coli dnaJ gene and
            purification of the gene product
  JOURNAL   J. Biol. Chem. 261 (4), 1778-1781 (1986)
  MEDLINE   86111849
   PUBMED   3003084
REFERENCE   26
  AUTHORS   Mackie,G.A.
  TITLE     Structure of the DNA distal to the gene for ribosomal protein S20
            in Escherichia coli K12: presence of a strong terminator and an IS1
            element
  JOURNAL   Nucleic Acids Res. 14 (17), 6965-6981 (1986)
  MEDLINE   87016337
   PUBMED   2429258
REFERENCE   27
  AUTHORS   Blanchin-Roland,S., Blanquet,S., Schmitter,J.M. and Fayat,G.
  TITLE     The gene for Escherichia coli diadenosine tetraphosphatase is
            located immediately clockwise to folA and forms an operon with ksgA
  JOURNAL   Mol. Gen. Genet. 205 (3), 515-522 (1986)
  MEDLINE   87172305
   PUBMED   3031429
REFERENCE   28
  AUTHORS   Lee,N., Gielow,W., Martin,R., Hamilton,E. and Fowler,A.
  TITLE     The organization of the araBAD operon of Escherichia coli
  JOURNAL   Gene 47 (2-3), 231-244 (1986)
  MEDLINE   87163495
   PUBMED   3549454
REFERENCE   29
  AUTHORS   Gronger,P., Manian,S.S., Reilander,H., O'Connell,M., Priefer,U.B.
            and Puhler,A.
  TITLE     Organization and partial sequence of a DNA region of the Rhizobium
            leguminosarum symbiotic plasmid pRL6JI containing the genes fixABC,
            nifA, nifB and a novel open reading frame
  JOURNAL   Nucleic Acids Res. 15 (1), 31-49 (1987)
  MEDLINE   87146339
   PUBMED   3029674
REFERENCE   30
  AUTHORS   Nonet,M.L., Marvel,C.C. and Tolan,D.R.
  TITLE     The hisT-purF region of the Escherichia coli K-12 chromosome.
            Identification of additional genes of the hisT and purF operons
  JOURNAL   J. Biol. Chem. 262 (25), 12209-12217 (1987)
  MEDLINE   87308226
   PUBMED   3040734
REFERENCE   31
  AUTHORS   Karpel,R., Olami,Y., Taglicht,D., Schuldiner,S. and Padan,E.
  TITLE     Sequencing of the gene ant which affects the Na+/H+ antiporter
            activity in Escherichia coli
  JOURNAL   J. Biol. Chem. 263 (21), 10408-10414 (1988)
  MEDLINE   88273145
   PUBMED   2839489
REFERENCE   32
  AUTHORS   Jaiswal,A.K., McBride,O.W., Adesnik,M. and Nebert,D.W.
  TITLE     Human dioxin-inducible cytosolic NAD(P)H:menadione oxidoreductase.
            cDNA sequence and localization of gene to chromosome 16
  JOURNAL   J. Biol. Chem. 263 (27), 13572-13578 (1988)
  MEDLINE   88330879
   PUBMED   2843525
REFERENCE   33
  AUTHORS   Lozoya,E., Hoffmann,H., Douglas,C., Schulz,W., Scheel,D. and
            Hahlbrock,K.
  TITLE     Primary structures and catalytic properties of isoenzymes encoded
            by the two 4-coumarate: CoA ligase genes in parsley
  JOURNAL   Eur. J. Biochem. 176 (3), 661-667 (1988)
  MEDLINE   89005119
   PUBMED   3169018
REFERENCE   34
  AUTHORS   Sato,S., Nakada,Y. and Shiratsuchi,A.
  TITLE     IS421, a new insertion sequence in Escherichia coli
  JOURNAL   FEBS Lett. 249 (1), 21-26 (1989)
  MEDLINE   89252065
   PUBMED   2542093
REFERENCE   35
  AUTHORS   Roa,B.B., Connolly,D.M. and Winkler,M.E.
  TITLE     Overlap between pdxA and ksgA in the complex pdxA-ksgA-apaG-apaH
            operon of Escherichia coli K-12
  JOURNAL   J. Bacteriol. 171 (9), 4767-4777 (1989)
  MEDLINE   89359108
   PUBMED   2670894
REFERENCE   36
  AUTHORS   Matsubara,Y., Indo,Y., Naito,E., Ozasa,H., Glassberg,R.,
            Vockley,J., Ikeda,Y., Kraus,J. and Tanaka,K.
  TITLE     Molecular cloning and nucleotide sequence of cDNAs encoding the
            precursors of rat long chain acyl-coenzyme A, short chain
            acyl-coenzyme A, and isovaleryl-coenzyme A dehydrogenases. Sequence
            homology of four enzymes of the acyl-CoA dehydrogenase family
  JOURNAL   J. Biol. Chem. 264 (27), 16321-16331 (1989)
  MEDLINE   89380240
   PUBMED   2777793
REFERENCE   37
  AUTHORS   Minami-Ishii,N., Taketani,S., Osumi,T. and Hashimoto,T.
  TITLE     Molecular cloning and sequence analysis of the cDNA for rat
            mitochondrial enoyl-CoA hydratase. Structural and evolutionary
            relationships linked to the bifunctional enzyme of the peroxisomal
            beta-oxidation system
  JOURNAL   Eur. J. Biochem. 185 (1), 73-78 (1989)
  MEDLINE   90032688
   PUBMED   2806264
REFERENCE   38
  AUTHORS   Chen,H., Sun,Y., Stark,T., Beattie,W. and Moses,R.E.
  TITLE     Nucleotide sequence and deletion analysis of the polB gene of E.
            coli
  JOURNAL   DNA Cell Biol. 9, 613-635 (1990)
REFERENCE   39
  AUTHORS   Angerer,A., Gaisser,S. and Braun,V.
  TITLE     Nucleotide sequences of the sfuA, sfuB, and sfuC genes of Serratia
            marcescens suggest a periplasmic-binding-protein-dependent iron
            transport mechanism
  JOURNAL   J. Bacteriol. 172 (2), 572-578 (1990)
  MEDLINE   90130288
   PUBMED   2404942
REFERENCE   40
  AUTHORS   Ricca,E. and Calvo,J.M.
  TITLE     The nucleotide sequence of leuA from Salmonella typhimurium
  JOURNAL   Nucleic Acids Res. 18 (5), 1290 (1990)
  MEDLINE   90206796
   PUBMED   2181403
REFERENCE   41
  AUTHORS   Schaaff,I., Hohmann,S. and Zimmermann,F.K.
  TITLE     Molecular analysis of the structural gene for yeast transaldolase
  JOURNAL   Eur. J. Biochem. 188 (3), 597-603 (1990)
  MEDLINE   90235831
   PUBMED   2185015
REFERENCE   42
  AUTHORS   Rosenthal,E.R. and Calvo,J.M.
  TITLE     The nucleotide sequence of leuC from Salmonella typhimurium
  JOURNAL   Nucleic Acids Res. 18 (10), 3072 (1990)
  MEDLINE   90272436
   PUBMED   2190189
REFERENCE   43
  AUTHORS   Chen,H., Lawrence,C.B., Bryan,S.K. and Moses,R.E.
  TITLE     Aphidicolin inhibits DNA polymerase II of Escherichia coli, an
            alpha-like DNA polymerase
  JOURNAL   Nucleic Acids Res. 18 (23), 7185-7186 (1990)
  MEDLINE   91088346
   PUBMED   2124684
REFERENCE   44
  AUTHORS   Mallonee,D.H., White,W.B. and Hylemon,P.B.
  TITLE     Cloning and sequencing of a bile acid-inducible operon from
            Eubacterium sp. strain VPI 12708
  JOURNAL   J. Bacteriol. 172 (12), 7011-7019 (1990)
  MEDLINE   91072253
   PUBMED   2254270
REFERENCE   45
  AUTHORS   Bouvier,J. and Stragier,P.
  TITLE     Nucleotide sequence of the lsp-dapB interval in Escherichia coli
  JOURNAL   Nucleic Acids Res. 19 (1), 180 (1991)
  MEDLINE   91187617
   PUBMED   2011499
REFERENCE   46
  AUTHORS   Umeda,M. and Ohtsubo,E.
  TITLE     Four types of IS1 with differences in nucleotide sequence reside in
            the Escherichia coli K-12 chromosome
  JOURNAL   Gene 98 (1), 1-5 (1991)
  MEDLINE   91192599
   PUBMED   1849492
REFERENCE   47
  AUTHORS   Arigoni,F., Kaminski,P.A., Hennecke,H. and Elmerich,C.
  TITLE     Nucleotide sequence of the fixABC region of Azorhizobium
            caulinodans ORS571: similarity of the fixB product with eukaryotic
            flavoproteins, characterization of fixX, and identification of nifW
  JOURNAL   Mol. Gen. Genet. 225 (3), 514-520 (1991)
  MEDLINE   91203829
   PUBMED   1850088
REFERENCE   48
  AUTHORS   Munro,A.W., Ritchie,G.Y., Lamb,A.J., Douglas,R.M. and Booth,I.R.
  TITLE     The cloning and DNA sequence of the gene for the
            glutathione-regulated potassium-efflux system KefC of Escherichia
            coli
  JOURNAL   Mol. Microbiol. 5 (3), 607-616 (1991)
  MEDLINE   91260444
   PUBMED   2046548
REFERENCE   49
  AUTHORS   Poulsen,L.K., Refn,A., Molin,S. and Andersson,P.
  TITLE     Topographic analysis of the toxic Gef protein from Escherichia coli
  JOURNAL   Mol. Microbiol. 5 (7), 1627-1637 (1991)
  MEDLINE   92048480
   PUBMED   1943700
REFERENCE   50
  AUTHORS   Poulsen,L.K., Refn,A., Molin,S. and Andersson,P.
  TITLE     The gef gene from Escherichia coli is regulated at the level of
            translation
  JOURNAL   Mol. Microbiol. 5 (7), 1639-1648 (1991)
  MEDLINE   92048481
   PUBMED   1943701
REFERENCE   51 (bases 1 to 111401)
  AUTHORS   Yura,T., Mori,H., Nagai,H., Nagata,T., Ishihama,A., Fujita,N.,
            Isono,K., Mizobuchi,K. and Nakata,A.
  TITLE     Systematic sequencing of the Escherichia coli genome: analysis of
            the 0-2.4 min region
  JOURNAL   Nucleic Acids Res. 20 (13), 3305-3308 (1992)
  MEDLINE   92334977
   PUBMED   1630901
REFERENCE   52
  AUTHORS   Fujita,N., Mori,H., Yura,T. and Ishihama,A.
  TITLE     Systematic sequencing of the Escherichia coli genome: analysis of
            the 2.4-4.1 min (110,917-193,643 bp) region
  JOURNAL   Nucleic Acids Res. 22 (9), 1637-1639 (1994)
  MEDLINE   94261430
   PUBMED   8202364
REFERENCE   53
  AUTHORS   Stragier,P.
  JOURNAL   Unpublished
REFERENCE   54
  AUTHORS   Ishino,Y.
  JOURNAL   Unpublished
REFERENCE   55
  AUTHORS   Ayala,J.A.
  TITLE     Regulation of transcription at 2-minute region of the genetic map
            of Escherichia coli
  JOURNAL   Unpublished
REFERENCE   56 (bases 1 to 111408)
  AUTHORS   Mori,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-FEB-1992) Hirotada Mori, Institute for Virus
            Research, Kyoto University, Genetics and Molecular Biology; 53
            Shogoin Kawara-Machi, Sakyo-ku, Kyoto 606, Japan
            (E-mail:e52985@sakura.kudpc.kyoto-u.ac.jp, Tel:075-751-4042,
            Fax:075-761-5626)
COMMENT     On or before Jun 4, 2002 this sequence version replaced gi:145461,
            gi:147757, gi:147977, gi:145773, gi:146668, gi:145775, gi:145709,
            gi:145770, gi:40949, gi:40916, gi:42462, gi:41931, gi:40841,
            gi:41874, gi:216434.
            Submitted (18-FEB-1992) to DDBJ by:
            Hirotada Mori
            Institute for Virus Research
            Kyoto University
            Kawahara-cho Shogoin Sakyo-ku
            Kyoto 606
            Phone:  075-751-4042
            Fax:    075-761-5626
            Sequence updated (21-DEC-1992) by:
            Hirotada Mori.
FEATURES             Location/Qualifiers
     source          1..111408
                     /organism="Escherichia coli"
                     /strain="K-12"
                     /db_xref="taxon:562"
                     /map="0-2.4 min"
                     /note="Nucleotide position 1-111408 from the initiation
                     site of ThrA (0 min.)."
     gene            1..2463
                     /gene="thrA"
                     /note="synonyms: thrA1, thrA2"
     CDS             1..2463
                     /gene="thrA"
                     /note="ORF_ID:o101#1
                     similar to PIR Accession Number A00671"
                     /codon_start=1
                     /transl_table=11
                     /product="ThrA bifunctional enzyme"
                     /protein_id="BAB96579.1"
                     /db_xref="GI:21321892"
                     /translation="MRVLKFGGTSLANAERFLRVADILESNARQGQVATVLSAPAKIT
                     NHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIK
                     HVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHY
                     LESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACL
                     RADCCEIWTDVNGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQF
                     QIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAAR
                     VFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMLEEFYLELKEGLLEPLAV
                     AERLAIISVVGDGLRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATT
                     GVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKA
                     LLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVNCTSSQAVADQYAD
                     FLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDINVGAGLPVIENLQNLLN
                     AGDELMKFSGILSGSLSYIFGKLDEGMSFSEATRLAREMGYTEPDPRDDLSGMDVARK
                     LLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEG
                     KVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAG
                     NDVTAAGVFADLLRTLSWKLGV"
     gene            2465..3394
                     /gene="thrB"
     CDS             2465..3394
                     /gene="thrB"
                     /note="ORF_ID:o101#2
                     similar to PIR Accession Number A00658"
                     /codon_start=1
                     /transl_table=11
                     /product="Homoserine kinase (EC 2.7.1.39)"
                     /protein_id="BAB96580.1"
                     /db_xref="GI:21321893"
                     /translation="MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAQTF
                     SLNNLGRFADKLPSEPRENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACS
                     VVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDI
                     ISQQVQGLMSGCGCSRIRGLKSRRQKQGYLPAQYRRQDCIAHGRHLAGFIHACYSRQP
                     ELAAKLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQ
                     RVADWLGKNYLQNQEGFVHICRLDTAGARVLEN"
     gene            3395..4681
                     /gene="thrC"
     CDS             3395..4681
                     /gene="thrC"
                     /note="ORF_ID:o101#3
                     similar to PIR Accession Number A01157"
                     /codon_start=1
                     /transl_table=11
                     /product="Threonine synthase (EC 4.2.99.2)"
                     /protein_id="BAB96581.1"
                     /db_xref="GI:21321894"
                     /translation="MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEID
                     EMLKLDFVTRSAKILSAFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGP
                     TLAFKDFGGRFMAQMLTHIAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRG
                     KISPLQEKLFCTLGGNIETVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISR
                     LLAQICYYFEAVAQLPQETRNQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVN
                     DTVPRFLHDGQWSPKATQATLSNAMDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDE
                     TTQQTMRELKELGYTSEPHAAVAYRALRDQLNPGEYGLFLGTAHPAKFKESVEAILGE
                     TLDLPKELAERADLPLLSHNLPADFAALRKLMMNHQ"
     CDS             4895..5191
                     /note="ORF_ID:o101#4"
                     /codon_start=1
                     /transl_table=11
                     /protein_id="BAB96582.1"
                     /db_xref="GI:21321895"
                     /translation="MKKMQSIVLALSLVLVAPMAAQAAEITLVPSVKLQIGDRDNRGY
                     YWDGGHWRDHGWWKQHYEWRGNRWHLHGPPPPPRHHKKAPHDHHGGHGPGKHHR"
     CDS             complement(4971..5402)
                     /note="ORF_ID:o101#5"
                     /codon_start=1
                     /transl_table=11
                     /protein_id="BAB96583.1"
                     /db_xref="GI:21321896"
                     /translation="MMKIPPAMANWCLNATSSVKFAVNAGCGVNALSCLQKHADSIYC
                     RINVGLIRRASVASGAECRIVTRHLSFSGDVCQDHDRRDDHEELSYGGAAVAAVRVGA
                     SDCLAIHNVVSTSRGRASDLHPSNSHDYHDRLSVILLTGLT"
     gene            complement(5344..6120)
                     /gene="yaaA"
     CDS             complement(5344..6120)
                     /gene="yaaA"
                     /note="ORF_ID:o101#6
                     similar to PIR Accession Number S40534"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein"
                     /protein_id="BAB96584.1"
                     /db_xref="GI:21321897"
                     /translation="MLILISPAKTLDYQSPLTTTRYTLPELLDNSQQLIHEARKLTPP
                     QISTLMRISDKLAGINAARFHDWQPDFTPANARQAILAFKGDVYTGLQAETFSEDDFD
                     FAQQHLRMLSGLYGVLRPLDLMQPYRLEMGIRLENARGKDLYQFWGDIITNKLNEALA
                     AQGDNVVINLASDEYFKSVKPKKLNAEIIKPVFLDEKNGKFKIISFYAKKARGLMSRF
                     IIENRLTKPEQLTGFNSEGYFFDEDSSSNGELVFKRYEQR"
     gene            complement(6190..7620)
                     /gene="yaaJ"
     CDS             complement(6190..7620)
                     /gene="yaaJ"
                     /note="ORF_ID:o101#7
                     similar to SwissProt Accession Number P30143"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical 51.7 kd protein in thrC-talB
                     intergenic region (ORF8)."
                     /protein_id="BAB96585.1"
                     /db_xref="GI:21321898"
                     /translation="MPDFFSFINSVLWGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFG
                     KSLKNSIHPQPGGLTSFQSLCTSLAARVGSGNLAGVALAITAGGPGAVFWMWVAAFIG
                     MATSFAECSLAQLYKERDVNGQFRGGPAWYMARGLGMRWMGVLFAVFLLIAYGIIFSG
                     VQANAVARALSFSFDFPPLVTGIILAVFTLLAITRGLHGVARLMQGFVPLMAIIWVLT
                     SLVICVMNIGQLPHVIWSIFESAFGWQEAAGGAAGYTLSQAITNGFQRSMFSNEAGMG
                     STPNAAAAAASWPPHPAAQGIVQMIGIFIDTLVICTASAMLILLAGNGTTYMPLEGIQ
                     LIQKAMRVLMGSWGAEFVTLVVILFAFSSIVANYIYAENNLFFLRLNNPKAIWCLRIC
                     TFATVIGGTLLSLPLMWQLADIIMACMAITNLTAILLLSPVVHTIASDYLRQRKLGVR
                     PVFDPLRYPDIGRQLSPDAWDDVSQE"
     gene            7899..8852
                     /gene="talB"
     CDS             7899..8852
                     /gene="talB"
                     /note="ORF_ID:o101#8
                     similar to PIR Accession Number S40535"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein"
                     /protein_id="BAB96586.1"
                     /db_xref="GI:21321899"
                     /translation="MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILNAAQ
                     IPEYRKLIDDAVAWAKQQSNDRAQQIVDATDKLAVNIGLEILKLVPGRISTEVDARLS
                     YDTEASIAKAKRLIKLYNDAGISNDRILIKLASTWQGIRAAEQLEKEGINCNLTLLFS
                     FAQARACAEAGVFLISPFVGRILDWYKANTDKKEYAPAEDPGVVSVSEIYQYYKEHGY
                     ETVVMGASFRNIGEILELAGCDRLTIAPALLKELAESEGAIERKLSYTGEVKARPARI
                     TESEFLWQHNQDPMAVDKLAEGIRKFAIDQEKLEKMIGDLL"
     gene            9136..9552
                     /gene="chlG"
                     /note="synonym: mog"
     CDS             9136..9552
                     /gene="chlG"
                     /note="ORF_ID:o102#1
                     similar to PIR Accession Number B56688"
                     /codon_start=1
                     /transl_table=11
                     /product="Molybdopterin biosynthesis Mog protein."
                     /protein_id="BAB96587.1"
                     /db_xref="GI:21321900"
                     /translation="MCELVDEMSCHLVLTTGGTGPARRDVTPDATLAVADREMPGFGE
                     QMRQISLHFVPTAILSRQVGVIRKQALILNLPGQPKSIKETLEGVKDAEGNVVVHGIF
                     ASVPYCIQLLEGPYVETAPEVVAAFRPKSARRDVSE"
     CDS             complement(9584..10150)
                     /note="ORF_ID:o102#2
                     similar to PIR Accession Number E56688"
                     /codon_start=1
                     /transl_table=11
                     /product="hgtA 5'-region hypothetical protein 1"
                     /protein_id="BAB96588.1"
                     /db_xref="GI:21321901"
                     /translation="MGNTKLANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIF
                     YGGIAQIFAGLLEYKKGNTFGLTAFTSYGSFWLTLVAILLMPKLGLTDAPNAQFLGVY
                     LGLWGVFTVFMFFGTLKGARVLQFVFFSLTVLFALLAIGNIAGNAAIIHFAGWIGLIC
                     GASAIYLAMGEVLNEQFGRTVLPIGESH"
     gene            10479..10963
                     /gene="htgA"
                     /note="synonym: htpY"
     misc_feature    10479..10963
                     /gene="htgA"
                     /product="Heat shock protein Y"
                     /note="ORF is interrupted by frame-shifting
                     ORF_ID:o102#3
                     similar to PIR Accession Number A40623"
     gene            complement(11030..11435)
                     /gene="yaaI"
     misc_feature    complement(11030..11435)
                     /gene="yaaI"
                     /product="dnaK 5'-region hypothetical protein 1"
                     /note="ORF is interrupted by frame-shifting
                     ORF_ID:o102#4
                     similar to PIR Accession Number C56688"
     gene            11812..13728
                     /gene="dnaK"
     CDS             11812..13728
                     /gene="dnaK"
                     /note="ORF_ID:o102#5
                     similar to PIR Accession Number A03311"
                     /codon_start=1
                     /transl_table=11
                     /product="DnaK protein"
                     /protein_id="BAB96589.1"
                     /db_xref="GI:21321902"
                     /translation="MGKIIGIDLGTTNSCVAIMDGTTPRVLENAEGDRTTPSIIAYTQ
                     DGETLVGQPAKRQAVTNPQNTLFAIKRLIGRRFQDEEVQRDVSIMPFKIIAADNGDAW
                     VEVKGQKMAPPQISAEVLKKMKKTAEDYLGEPVTEAVITVPAYFNDAQRQATKDAGRI
                     AGLEVKRIINEPTAAALAYGLDKGTGNRTIAVYDLGGGTFDISIIEIDEVDGEKTFEV
                     LATNGDTHLGGEDFDSRLINYLVEEFKKDQGIDLRNDPLAMQRLKEAAEKAKIELSSA
                     QQTDVNLPYITADATGPKHMNIKVTRAKLESLVEDLVNRSIEPLKVALQDAGLSVSDI
                     DDVILVGGQTRMPMVQKKVAEFFGKEPRKDVNPDEAVAIGAAVQGGVLTGDVKDVLLL
                     DVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAAD
                     NKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLN
                     EDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIE
                     SALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHAQQQTAGADASANNAKDD
                     DVVDAEFEEVKDKK"
     gene            13817..14947
                     /gene="dnaJ"
                     /note="synonym: groP"
     CDS             13817..14947
                     /gene="dnaJ"
                     /note="ORF_ID:o102#6
                     similar to SwissProt Accession Number P08622"
                     /codon_start=1
                     /transl_table=11
                     /product="DnaJ protein."
                     /protein_id="BAB96590.1"
                     /db_xref="GI:21321903"
                     /translation="MAKQDYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAE
                     AKFKEIKEAYEVLTDSQKRAAYDQYGHAAFEQGGMGGGGFGGGADFSDIFGDVFGDIF
                     GGGRGRQRAARGADLRYNMELTLEEAVRGVTKEIRIPTLEECDVCHGSGAKPGTQPQT
                     CPTCHGSGQVQMRQGFFAVQQTCPHCQGRGTLIKDPCNKCHGHGRVERSKTLSVKIPA
                     GVDTGDRIRLAGEGEAGEHGAPAGDLYVQVQVKQHPIFEREGNNLYCEVPINFAMAAL
                     GGEIEVPTLDGRVKLKVPGETQTGKLFRMRGKGVKSVRGGAQGDLLCRVVVETPVGLN
                     ERQKQLLQELQESFGGPTGEHNSPRSKSFFDGVKKFFDDLTR"
     gene            complement(16400..16609)
                     /gene="gef"
     CDS             complement(16400..16609)
                     /gene="gef"
                     /note="ORF_ID:o102#7
                     similar to PIR Accession Number S16473"
                     /codon_start=1
                     /transl_table=11
                     /product="Gef protein"
                     /protein_id="BAB96591.1"
                     /db_xref="GI:21321904"
                     /translation="MLNTCRVPLTDRKVKEKRAMKQHKAMIVALIVICITAVVAALVT
                     RKDLCEVHIRTGQTEVAVFTAYESE"
     gene            17138..18304
                     /gene="ant"
                     /note="synonym: nhaA"
     CDS             17138..18304
                     /gene="ant"
                     /note="ORF_ID:o102#8
                     similar to SwissProt Accession Number P13738"
                     /codon_start=1
                     /transl_table=11
                     /product="Na(+)/H(+) antiporter 1."
                     /protein_id="BAB96592.1"
                     /db_xref="GI:21321905"
                     /translation="MKHLHRFFSSDASGGIILIIAAILAMIMANSGATSGWYHDFLET
                     PVQLRVGSLEINKNMLLWINDALMAVFFLLVGLEVKRELMQGSLASLRQAAFPVIAAI
                     GGMIVPALLYLAFNYADPITREGWAIPAATDIAFALGVLALLGSRVPLALKIFLMALA
                     IIDDLGAIIIIALFYTNDLSMASLGVAAVAIAVLAVLNLCGARRTGVYILVGVVLWTA
                     VLKSGVHATLAGVIVGFFIPLKEKHGRSPAKRLEHVLHPWVAYLILPLFAFANAGVSL
                     QGVTLDGLTSILPLGIIAGLLIGKPLGISLFCWLALRLKLAHLPEGTTYQQIMVVGIL
                     CGIGFTMSIFIASLAFGSVDPELINWAKLGILVGSISSAVIGYSWLRVRLRPSV"
     gene            18364..19283
                     /gene="antO"
                     /note="synonym: nhaR"
     misc_feature    18364..19283
                     /gene="antO"
                     /product="Transcriptional activator protein NhaR."
                     /note="ORF is interrupted by frame-shifting
                     ORF_ID:o103#1
                     similar to SwissProt Accession Number P10087"
     gene            complement(20478..20741)
                     /gene="rpsT"
     CDS             complement(20478..20741)
                     /gene="rpsT"
                     /note="ORF_ID:o103#2
                     similar to PIR Accession Number A30425"
                     /codon_start=1
                     /transl_table=11
                     /product="Ribosomal protein S20"
                     /protein_id="BAB96593.1"
                     /db_xref="GI:21321906"
                     /translation="MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDK
                     AAAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLTAQINKLA"
     gene            21070..22008
                     /gene="yaaC"
     CDS             21070..22008
                     /gene="yaaC"
                     /note="ORF_ID:o103#3
                     similar to PIR Accession Number A22609"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical 35k protein (ileS-lsp operon)"
                     /protein_id="BAB96594.1"
                     /db_xref="GI:21321907"
                     /translation="MKLIRGIHNLSQAPQEGCVLTIGNFDGVHRGHRALLQGLQEEGR
                     KRNLPVMVMLFEPQPLELFATDKAPARLTRLREKLRYLAECGVDYVLCVRFDRRFAAL
                     TAQNFVSDLLVKHLRVKFLAVGDDFPLALVVKAISCYYRKLAWNTASISPVRKLFAEV
                     ACASAARLRQALADDNLALAESLLGHPFAISGRVVHGDELGRTIGFPTANVPPRRQVS
                     PVKGVYAVEVLGLGEKPLPGVANIGTRPTVAGIRQQLEVHLLDVAMDLYGRHIQVVLR
                     KKIRNEQRFASLDELKAQIARDELTAREFFGLTKPA"
     gene            22051..24861
                     /gene="ileS"
     CDS             22051..24861
                     /gene="ileS"
                     /note="ORF_ID:o103#4
                     similar to PIR Accession Number S40549"
                     /codon_start=1
                     /transl_table=11
                     /product="Isoleucine--tRNA ligase (EC 6.1.1.5)"
                     /protein_id="BAB96595.1"
                     /db_xref="GI:21321908"
                     /translation="MSDYKSTLNLPETGFPMRGDLAKREPGMLARWTDDDLYGIIRAA
                     KKGKKTFILHDGPPYANGSIHIGHSVNKILKDIIVKSKGLSGYDSPYVPGWDCHGLPI
                     ELKVEQEYGKPGEKFTAAEFRAKCREYAATQVDGQRKDFIRLGVLGDWSHPYLTMGLQ
                     NWKANIIRALGKIIGNGHLHKGAKPVHWCVDCRSALAKRKLSITTKLLRPSTLLSRAV
                     DQDALKAKFAVSNVNGPISLVIWTTTPWTLPANRAISIAPDFDYALVQIDGQAVILAK
                     DLVESVMQRIGVTDSRHGKRCGAGAAAFTHPFMGFDVPAILGDHVTLDAGTGAVHTAP
                     GHGPDDYVIGQKYGLETANPVGPDGTYLPGTYPTLDGVNVFKANDIVAALLQEKGALL
                     HVEKMQHSYPCCWRHKTPIIFRATPQWFVSMDQKGLRAQSLKEIKGVQWIPDWGQARI
                     ESMVANRPDWCISRQRTWGVPMSLFVHKDTEELHPRTLELMEEVAKRVEVDGIQAWWD
                     LDAKEILGDEADQYVKVPDTLDVWFDSGSTHSSVVDVRPEFAGHAADMYLEGSDQHRG
                     WFMSSLMISTAMKGKAPYRQVLTHGFTVDGQGRKMSKSIGNTVSPQDVMNKLGADILR
                     LWVASTDYTGEMAVSDEILKRAADTYRRIRNTARFLLANLNGFDPAKDMVKRREMVVL
                     DRWAVVVRKRHRKTSSRRTKHTISTKWYKRLMRFCSVEMGSFYLDIIKDRQYYAKGHS
                     VARRSCQTALYHIAEALVRWMAPILSFTADEVWGYLPGEREKYVFTGEWYEGLFGLAD
                     SEAMNDAFWDELLKVRGEVNKVIEQARADKKVGGSLEAAVTLYAEPELSAKLTALGDE
                     LRFVLLTSGATVADYNDAPADAQQSEVLKGLKVALSKAEGEKCPRCWHYTQDVGKVAE
                     HAEICGRCVSNVAGDGEKRKFA"
     gene            24861..25355
                     /gene="lspA"
     CDS             24861..25355
                     /gene="lspA"
                     /note="ORF_ID:o103#5
                     similar to SwissProt Accession Number P00804"
                     /codon_start=1
                     /transl_table=11
                     /product="Lipoprotein signal peptidase (EC 3.4.23.36)
                     (Prolipoprotein signal peptidase) (Signal peptidase II)
                     (Spase II)."
                     /protein_id="BAB96596.1"
                     /db_xref="GI:21321909"
                     /translation="MSQSICSTGLRWLWLVVVVLIIDLGSKYLILQNFALGDTVPLFP
                     SLNLHYARNYGAAFSFLADSGGWQRWFFAGIAIGISVILAVMMYRSKATQKLNNIAYA
                     LIIGGALGNLFDRLWHGFVVDMIDFYVGDWHFATFNLADTAICVGAALIVLEGFLPSR
                     AKKQ"
     gene            25480..25929
                     /gene="yaaD"
     CDS             25480..25929
                     /gene="yaaD"
                     /note="ORF_ID:o103#6
                     similar to PIR Accession Number JE0402"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical 16.4K protein (lsp-dapB intergenic
                     region)"
                     /protein_id="BAB96597.1"
                     /db_xref="GI:21321910"
                     /translation="MSESVQSNSAVLVHFTLKLDDGTTAESTRNNGKPALFRLGDASL
                     SEGLEQHLLGLKVGDKTTFSLEPDAAFGVPSPDLIQYFSRREFMDAGEPEIGAIMLFT
                     AMDGSEMPGVIREINGDSITVDFNHPLAGQTVHFDIEVLEIDPALEA"
     gene            25931..26881
                     /gene="lytB"
     CDS             25931..26881
                     /gene="lytB"
                     /note="ORF_ID:o103#7
                     similar to PIR Accession Number JE0403"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical 34.8k protein (lsp-dapB intergenic
                     region)"
                     /protein_id="BAB96598.1"
                     /db_xref="GI:21321911"
                     /translation="MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRY
                     VVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKV
                     HMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEK
                     LSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVL
                     VVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQ
                     NVVARLQQLGGGEAIPLEGREENIVFEVPKELRVDIREVD"
     gene            26947..27861
                     /gene="yaaF"
     CDS             26947..27861
                     /gene="yaaF"
                     /note="ORF_ID:o103#8
                     similar to PIR Accession Number JE0404"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical 32.6k protein (lsp-dapB intergenic
                     region)"
                     /protein_id="BAB96599.1"
                     /db_xref="GI:21321912"
                     /translation="MRLPIFLDTDPGIDDAVAIAAAIFAPELDLQLMTTVAGNVSVEK
                     TTRNALQLLHFWNAEIPLAQGAAVPLVRAPRDAASVHGESGMAGYDFVEHNRKPLGIP
                     AFLAIRDALMRAPEPVTLVAIGPLTNIALLLSQCPECKPYIRRLVIMGGSAGRGNCTP
                     NAEFNIAADPEAAACVFRSGIEIVMCGLDVTNQAILTPDYLSTLPQLNRTGKMLHALF
                     SHYRSGSMQSGLRMHDLCAIAWLVRPDLFTLKPCFVAVETQGEFTSGTTVVDIDGCLG
                     KPANVQVALDLDVKGFQQWVAEVLALAS"
     gene            28028..28849
                     /gene="dapB"
     CDS             28028..28849
                     /gene="dapB"
                     /note="ORF_ID:o103#9
                     similar to SwissProt Accession Number P04036"
                     /codon_start=1
                     /transl_table=11
                     /product="Dihydrodipicolinate reductase (EC 1.3.1.26)."
                     /protein_id="BAB96600.1"
                     /db_xref="GI:21321913"
                     /translation="MHDANIRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSL
                     LGSDAGELAGAGKTGVTVQSSLDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIG
                     TTGFDEAGKQAIRDAAADIAIVFAANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHH
                     RHKVDAPSGTALAMGEAIAHALDKDLKDCAVYSREGHTGERVPGTIGFATVRAGDIVG
                     EHTAMFADIGERLEITHKASSRMTFANGAVRSALWLSGKESGLFDMRDVLDLNNL"
     gene            29305..30453
                     /gene="carA"
                     /note="synonym: pyrA"
     CDS             29305..30453
                     /gene="carA"
                     /note="ORF_ID:o103#10
                     similar to SwissProt Accession Number P00907"
                     /codon_start=1
                     /transl_table=11
                     /product="Carbamoyl-phosphate synthase small chain (EC
                     6.3.5.5) (carbamoyl- phosphate synthetase glutamine
                     chain)."
                     /protein_id="BAB96601.1"
                     /db_xref="GI:21321914"
                     /translation="MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILT
                     DPSYSRQIVTLTYPHIGNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYL
                     KRHNIVAIADIDTRKLTRLLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAK
                     EVTTAEAYSWTQGSWTLTGGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTI
                     VPAQTSAEDVLKMNPDGIFLSNGPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLA
                     LASGAKTVKMKFGHHGGNHPVKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFD
                     GTLQGIHRTDKPAFSFQGHPEASPGPHDAAPLFDHFIELIEQYRKTAK"
     gene            30471..33692
                     /gene="carB"
     CDS             30471..33692
                     /gene="carB"
                     /note="ORF_ID:o103#11
                     similar to PIR Accession Number A01198"
                     /codon_start=1
                     /transl_table=11
                     /product="Carbamoyl-phosphate synthase
                     (glutamine-hydrolyzing) (EC 6.3.5.5) large chain"
                     /protein_id="BAB96602.1"
                     /db_xref="GI:21321915"
                     /translation="MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRV
                     ILVNSNPATIMTDPEMADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALEL
                     ERQGVLEEFGVTMIGATADAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAA
                     DVGFPCIIRPSFTMGGSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEM
                     EVVRDKNDNCIIVCSIENFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIG
                     VETGGSNVQFAVNPKNGRLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDE
                     LMNDITGGRTPASFEPSIDYVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQ
                     ESLQKALRGLEVGATGFDPKVSLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVD
                     GVFNLTNIDRWFLVQIEELVRLEEKVAEVGITGLNADFLRQLKRKGFADARLAKLAGV
                     REAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEECEANPSTDREKIMVLG
                     GGPNRIGQGIEFDYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLE
                     DVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAV
                     ERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQT
                     AVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPA
                     YTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKA
                     TGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRST
                     GEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELD
                     ATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIR
                     RSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK"
     gene            complement(33740..33919)
                     /gene="yaaV"
     CDS             complement(33740..33919)
                     /gene="yaaV"
                     /note="ORF_ID:o103#12
                     similar to SwissProt Accession Number P46145"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical 6.8 kd protein in carB-caiE
                     intergenic region."
                     /protein_id="BAB96603.1"
                     /db_xref="GI:21321916"
                     /translation="MTRFEAIKQGHIKIVDISIVCNFTVDKCELNPAYVIKNIDSPKD
                     LLNGQKKTVLIREPY"
     gene            33849..34351
                     /gene="caiF"
     misc_feature    33849..34351
                     /gene="caiF"
                     /product="Transcription activator caiF"
                     /note="ORF is interrupted by frame-shifting
                     ORF_ID:o103#13
                     similar to PIR Accession Number JC6025"
     gene            complement(34438..35049)
                     /gene="caiE"
     CDS             complement(34438..35049)
                     /gene="caiE"
                     /note="ORF_ID:o103#14
                     similar to SwissProt Accession Number P39206"
                     /codon_start=1
                     /transl_table=11
                     /product="Carnitine operon protein caiE."
                     /protein_id="BAB96604.1"
                     /db_xref="GI:21321917"
                     /translation="MERTLTTVSYYAFEGLIPVVHPTAFVHPSAVLIGDVIVGAGVYI
                     GPLASLRGDYGRLIVQAGANIQDGCIMHGYCDTDTIVGENGHIGHGAILHGCLIGRDA
                     LVGMNSVIMDGAVIGEESIVAAMSFVKAGFRGEKRQLLMGTPARAVRNVSDDELHWKR
                     LNTKEYQDLVGRCHVSLHETQPLRQMEENRPRLQGTTDVTPKR"
     gene            complement(35034..35927)
                     /gene="caiD"
     CDS             complement(35034..35927)
                     /gene="caiD"
                     /note="ORF_ID:o103#15
                     similar to PIR Accession Number S40557"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein."
                     /protein_id="BAB96605.1"
                     /db_xref="GI:21321918"
                     /translation="MKQQGTTLPANNHTLKQYAFFAGMLSSLKKQKWRKGMSESLHLT
                     RNGSILEITLDRPKANAIDAKTSFEMGEVFLNFRDDPQLRVAIITGAGEKFFSAGWDL
                     KAAAEGEAPDADFGPGGFAGLTEIFNLDKPVIAAVNGYAFGGAFELALAADFIVCADN
                     ASFALPEAKLGIVPDSGGVLRLPKILPPAIVNEMVMTGRRMGAEEALRWGIVNRVVSQ
                     AELMDNARELAQQLVNSAPLAIAALKEIYRTTSEMPVEEAYRYIRSGVLKHYPSVLHS
                     EDAIEGPLAFAEKRDPVWKGR"
     gene            complement(35928..37496)
                     /gene="caiC"
     CDS             complement(35928..37496)
                     /gene="caiC"
                     /note="ORF_ID:o104#1
                     similar to PIR Accession Number S40558"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein."
                     /protein_id="BAB96606.1"
                     /db_xref="GI:21321919"
                     /translation="MDRGAMDIIGGQHLRQMWDDLADVYGHKTALICESSGGVVNRYS
                     YLELNQEINRTANLFYTLGIRKGDKVALHLDNCPEFIFCWFGLAKIGAIMVPINARLL
                     CEESAWILQNSQACLLVTSAQFYPMYQQIQQEDATQLRHICLTDVALPADDGVSSFTQ
                     LKNQQPATLCYAPPLSTDDTAEILFTSGTTSRPKGVVITHYNLRFAGYYSAWQCALRD
                     DDVYLTVMPAFHIDCQCTAAMAAFSAGATFVLVEKYSARAFWGQVQKYRATVTECIPM
                     MIRTLMVQPPSANDQQHRLREVMFYLNLSEQEKDAFCERFGVRLLTSYGMTETIVGII
                     GDRPGDKRRWPSIGRVGFCYEAEIRDDHNRPLPAGEIGEICIKGIPGKTIFKEYFLNP
                     QATAKVLEADGWLHTGDTGYRDEEDFFYFVDRRCNMIKRGGENVSCVELENIIAAHPK
                     IQDIVVVGIKDSIRDEAIKAFVVLNEGETLSEEEFFRFCEQNMAKFKVPSYLEIRKDL
                     PRNCSGKIIRKNLK"
     gene            complement(37555..38772)
                     /gene="caiB"
     CDS             complement(37555..38772)
                     /gene="caiB"
                     /note="ORF_ID:o104#2
                     similar to PIR Accession Number S40559"
                     /codon_start=1
                     /transl_table=11
                     /product="L-carnitine dehydratase (EC 4.-.-.-)."
                     /protein_id="BAB96607.1"
                     /db_xref="GI:21321920"
                     /translation="MDHLPMPKFGPLAGLRVVFSGIEIAGPFAGQMFAEWGAEVIWIE
                     NVAWADTIRVQPNYPQLSRRNLHALSLNIFKDEGREAFLKLMETTDIFIEASKGPAFA
                     RRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQP
                     MPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAMYEVMLRMGQYFMMDYFNG
                     GEMCPRMSKGKDPYYAGCGLYKCADGYIVMELVGITQIEECFKDIGLAHLLGTPEIPE
                     GTQLIHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQY
                     VARESITQWQTMDGRTCKGPNIMPKFKNNPGQIWRGMPSHGMDTAAILKNIGYSENDI
                     QELVSKGLAKVED"
     gene            complement(38901..40043)
                     /gene="caiA"
     CDS             complement(38901..40043)
                     /gene="caiA"
                     /note="ORF_ID:o105#1
                     similar to PIR Accession Number S40560"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein."
                     /protein_id="BAB96608.1"
                     /db_xref="GI:21321921"
                     /translation="MDFNLNDEQELFVAGIRELMASENWEAYFAECDRDSVYPERFVK
                     ALADMGIDSLLIPEEHGGLDAGFVTLAAVWMELGRLGAPTYVLYQLPGGFNTFLREGT
                     QEQIDKIMAFRGTGKQMWNSAITEPGAGSDVGSLKTTYTRKNGKIYLNGSKCFITSSA
                     YTPYIVVMARDGASPDKPVYTGWFVDMSKPGIKVTKLEKLGLRMDSCCEITFDDVELD
                     EKDMFGREGNGFNRVKEEFDHERFLVALTNYGTAMCAFEDAARYANQRVQFGEAIGRF
                     QLIQEKFAHMAIKLNSMKNMLYEAAWKADNGTITSGDAAMCKYFCANAAFEVVDSAMQ
                     VLGGVGIAGNHRISRFWRDLRVDRVSGGSDEMQILTLGRAVLKQYR"
     gene            complement(40075..41589)
                     /gene="caiT"
     CDS             complement(40075..41589)
                     /gene="caiT"
                     /note="ORF_ID:o105#2
                     similar to PIR Accession Number S40561"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein."
                     /protein_id="BAB96609.1"
                     /db_xref="GI:21321922"
                     /translation="MKNEKRKTGIEPKVFFPPLIIVGILCWLTVRDLDAANVVINAVF
                     SYVTNVWGWAFEWYMVVMLFGWFWLVFGPYAKKRLGNEPPEFSTASWIFMMFASCTSA
                     AVLFWGSIEIYYYISTPPFGLEPNSTGAKELGLAYSLFHWGPLPWATYSFLSVAFAYF
                     FFVRKMEVIRPSSTLVPLVGEKHAKGLFGTIVDNFYLVALIFTMGTSLGLATPLVTEC
                     MQWLFGIPHTLQLDAIIITCWIILNAICVACGLQKGVRIASDVRSYLSFLMLGWVFIV
                     SGASFIMNYFTDSVGMLLMYLPRMLFYTDPIAKGGFPQGWTVFYWAWWVIYAIQMSIF
                     LARISRGRTVRELCFGMVLGLTASTWILWTVLGSNTLLLIDKNIINIPNLIEQYGVAR
                     AIIETWAALPLSTATMWGFFILCFIATVTLVNACSYTLAMSTCREVRDGEEPPLLVRI
                     GWSILVGIIGIVLLALGGLKPIQTAIIAGGCPLFFVNIMVTLSFIKDAKQNWKD"
     gene            42025..42831
                     /gene="fixA"
     CDS             42025..42831
                     /gene="fixA"
                     /note="ORF_ID:o105#3
                     similar to PIR Accession Number S40562"
                     /codon_start=1
                     /transl_table=11
                     /product="FixA homolog."
                     /protein_id="BAB96610.1"
                     /db_xref="GI:21321923"
                     /translation="MNDVSFMISGDAMKIITCYKCVPDEQDIAVNNADGSLDFSKADA
                     KISQYDLNAIEAACQLKQQAAEAQVTALSVGGKALTNAKGRKDVLSRDPDELIVVIDD
                     QFEQALPQQTASALAAAAQKAGFDLILCGDGSSDLYAQQVGLLVGEILNIPAVNGVSK
                     IISLTADTLTVERELEDETETLSIPLPAVVAVSTDINSPQIPSMKAILGAAKKPVQVW
                     SAADIGFNAEAAWSEQQVAAPKQRERQRIVIEGDGEEQIAAFAENLRKVI"
     gene            42810..43787
                     /gene="fixB"
     misc_feature    42810..43787
                     /gene="fixB"
                     /product="FixB protein."
                     /note="ORF is interrupted by frame-shifting
                     ORF_ID:o105#4
                     similar to SwissProt Accession Number P31574"
     gene            43838..45124
                     /gene="fixC"
     CDS             43838..45124
                     /gene="fixC"
                     /note="ORF_ID:o105#5
                     similar to PIR Accession Number S40564"
                     /codon_start=1
                     /transl_table=11
                     /product="FixC protein"
                     /protein_id="BAB96611.1"
                     /db_xref="GI:21321924"
                     /translation="MSEDIFDAIIVGAGLAGSVAALVLAREGAQVLVIERGNSAGAKN
                     VTGGRLYAHSLEHIIPGFADSAPVERLITHEKLAFMTEKSAMTMDYCNGDETSPSQRS
                     YSVLRSKFDAWLMEQAEEAGAQLITGIRVDNLVQRDGKVVGVEADGDVIEAKTVILAD
                     GVNSILAEKLGMAKRVKPTDVAVGVKELIELPKSVIEDRFQLQGNQGAACLFAGSPTD
                     GLMGGGFLYTNENTLSLGLVCGLHHLHDAKKSVPQMLEDFKQHPAVAPLIAGGKLVEY
                     SAHIMPEAGINMLPELVGDGVLIAGDAAGMCMNFGFTIRGMDLAIAAGEAAAKTVLSA
                     MKSDDFSKQKLAEYRQHLESGPLRDMRMYQKLPAFLDNPRMFSGYPELAVGVARDLFT
                     IDGSAPELMRKKILRHGKKVGFINLIKDGMKGVTVL"
     gene            45121..45408
                     /gene="yaaT"
     CDS             45121..45408
                     /gene="yaaT"
                     /note="ORF_ID:o105#6
                     similar to PIR Accession Number S40565"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein"
                     /protein_id="BAB96612.1"
                     /db_xref="GI:21321925"
                     /translation="MTSPVNVDVKLGVNKFNVDEEHPHIVVKADADKQVLELLVKACP
                     AGLYKKQDDGSVRFDYAGCLECGTCRILGLGSALEQWEYPRGTFGVEFRYS"
     gene            45465..46050
                     /gene="yaaU"
     misc_feature    45465..46050
                     /gene="yaaU"
                     /product="Hypothetical 18.4 kd protein in fixC-kefC
                     intergenic region (orf65)."
                     /note="ORF is interrupted by frame-shifting
                     ORF_ID:o105#7
                     similar to SwissProt Accession Number P31679"
     gene            46137..46799
                     /gene="yabE"
     CDS             46137..46799
                     /gene="yabE"
                     /note="ORF_ID:o105#8
                     similar to PIR Accession Number S40566"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein"
                     /protein_id="BAB96613.1"
                     /db_xref="GI:21321926"
                     /translation="MKSSRSKPGFRDLFNRCHFPFVLFVAAIWTCQVIPMFAIYTFGP
                     QIVGLLGLGVGKNAALGNVVISLFFMLGCIPPMLWLSTAGRRPLLIGSFAMMTLALAV
                     LGLIPDMGIWLVVMAFAVYAFFSGGPGNLQWLYPNELFPTDIRASAVGVIMSLSRIGT
                     IVSTWALPIFIDNYGISNTMLMGAGISLFGLLISVAFAPETRGMSLAQTSNMTIRGQR
                     MG"
     gene            46907..47437
                     /gene="yabF"
     CDS             46907..47437
                     /gene="yabF"
                     /note="ORF_ID:o105#9
                     similar to PIR Accession Number S40567"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein"
                     /protein_id="BAB96614.1"
                     /db_xref="GI:21321927"
                     /translation="MILIIYAHPYPHHSHANKRMLEQARTLEGVEIRSLYQLYPDFNI
                     DIAAEQEALSRADLIVWQHPMQWYSIPPLLKLWINKVFSHGWAYGHGGTALHGKHLLW
                     AVTTGGGESHFEIGAHPGFDGLSQPLQATAIYCGLNWLPPFAMHCTFICDDETLEGQA
                     RHYKQRLLEWQEAHHG"
     gene            47430..49292
                     /gene="kefC"
                     /note="synonym: trkC"
     CDS             47430..49292
                     /gene="kefC"
                     /note="ORF_ID:o105#10
                     similar to SwissProt Accession Number P03819"
                     /codon_start=1
                     /transl_table=11
                     /product="Glutathione-regulated potassium-efflux system
                     protein KefC (K(+)/H(+) antiporter)."
                     /protein_id="BAB96615.1"
                     /db_xref="GI:21321928"
                     /translation="MDSHTLIQALIYLGSAALIVPIAVRLGLGSVLGYLIAGCIIGPW
                     GLRLVTDAESILHFAEIGVVLMLFIIGLELDPQRLWKLRAAVFGCGALQMVICGGLLG
                     LFCMLLGLRWQVAELIGMTLALSSTAIAMQAMNERNLMVTQMGRSAFAVLLFQDIAAI
                     PLVAMIPLLATSSASTTMGAFALSALKVAGALVLVVLLGRYVTRPALRFVARSGLREV
                     FSAVALFLVFGFGLLLEEVGLSMAMGAFLAGVLLASSEYRHALESDIEPFKGLLLGLF
                     FIGVGMSIDFGTLLENPLRIVILLLGFLIIKIAMLWLIARPLQVPNKQRRWFAVLLGQ
                     GSEFAFVVFGAAQMANVLEPEWAKSLTLAVALSMAATPILLVILNRLEQSSTEEAREA
                     DEIDEEQPRVIIAGFGRFGQITGRLLLSSGVKMVVLDHDPDHIETLRKFGMKVFYGDA
                     TRMDLLESAGAAKAEVLINAIDDPQTNLQLTEMVKEHFPHLQIIARARDVDHYIRLRQ
                     AGVEKPERETFEGALKTGRLALESLGLGPYEARERADVFRRFNIQMVEEMAMVENDTK
                     ARAAVYKRTSAMLSEIITEDREHLSLIQRHGWQGTEEGKHTGNMADEPETKPSS"
     gene            49482..49961
                     /gene="folA"
                     /note="synonym: tmrA"
     CDS             49482..49961
                     /gene="folA"
                     /note="ORF_ID:o105#11
                     similar to SwissProt Accession Number P00379"
                     /codon_start=1
                     /transl_table=11
                     /product="Dihydrofolate reductase type I (EC 1.5.1.3)."
                     /protein_id="BAB96616.1"
                     /db_xref="GI:21321929"
                     /translation="MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGR
                     HTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQ
                     FLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR"
     gene            complement(50039..50881)
                     /gene="apaH"
     CDS             complement(50039..50881)
                     /gene="apaH"
                     /note="ORF_ID:o105#12
                     similar to PIR Accession Number A26221"
                     /codon_start=1
                     /transl_table=11
                     /product="Bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
                     (EC 3.6.1.41)"
                     /protein_id="BAB96617.1"
                     /db_xref="GI:21321930"
                     /translation="MATYLIGDVHGCYDELIALLHKVEFTPGKDTLWLTGDLVARGPG
                     SLDVLRYVKSLGDSVRLVLGNHDLHLLAVFAGISRNKPLDRLTPLLEAPDADELLNWL
                     RRQPLLQIDEEKKLVMAHAGITPQWDLQTAKECARDVEAVLSSDSYPFFLDAMYGDMP
                     NNWSPELRGLGRLRFITNAFTRMRFCFPNGQLDMYSKESPEEAPAPLKPWFAIPGPVA
                     EEYSIAFGHWASLEGKGTPEGIYALDTGCCWGGTLTCLRWEDKQYFVQPSNRHKDLAE
                     AAAS"
     gene            complement(50888..51265)
                     /gene="apaG"
     CDS             complement(50888..51265)
                     /gene="apaG"
                     /note="ORF_ID:o106#1
                     similar to PIR Accession Number A30273"
                     /codon_start=1
                     /transl_table=11
                     /product="ApaG protein"
                     /protein_id="BAB96618.1"
                     /db_xref="GI:21321931"
                     /translation="MINSPRVCIQVQSVYIEAQSSPDNERYVFAYTVTIRNLGRAPVQ
                     LLGRYWLITNGNGRETEVQGEGVVGVQPLIAPGEEYQYTSGAIIETPLGTMQGHYEMI
                     DENGVPFSIDIPVFRLAVPTLIH"
     gene            complement(52087..53076)
                     /gene="pdxA"
     CDS             complement(52087..53076)
                     /gene="pdxA"
                     /note="ORF_ID:o106#2
                     similar to PIR Accession Number JV0026"
                     /codon_start=1
                     /transl_table=11
                     /product="PdxA protein"
                     /protein_id="BAB96619.1"
                     /db_xref="GI:21321932"
                     /translation="MVKTQRVVITPGEPAGIGPDLVVQLAQREWPVELVVCADATLLT
                     NRAAMLGLPLTLRPYSPNSPAQPQTAGTLTLLPVALRAPVTAGQLAVENGHYVVETLA
                     RACDGCLNGEFAALITGPVHKGVINDAGIPFTGHTEFFEERSQAKKVVMMLATEELRV
                     ALATTHLPLRDIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHM
                     GTEEIDTIIPVLNELRAQGMKLNGPLPADTLFQPKYLDNADAVLAMYHDQGLPVLKYQ
                     GFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLAIKMIVNTQ"
     CDS             complement(53076..53873)
                     /note="ORF_ID:o106#3
                     similar to PIR Accession Number PV0009"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein 98 (pdx 5' region)"
                     /protein_id="BAB96620.1"
                     /db_xref="GI:21321933"
                     /translation="MGNQNDASTELNLSHILIPLPENPTSDQVNEAESQARAIVDQAR
                     NGADFGKLAIAHSADQQALNGGQMGWGRIQELPGIFAQALSTAKKGDIVGPIRSGVGF
                     HILKVNDLRGESKNISVTEVHARHILLKPSPIMTDEQARVKLEQIAADIKSGKTTFAA
                     AAKEFSQDPGSANQGGDLGWATPDIFDPAFRDALTRLNKGQMSAPVHSSFGWHLIELL
                     DTRNVDKTDAAQKDRAYRMLMNRKFSEEAASWMQEQRASAYVKILSN"
     gene            complement(53840..54361)
                     /gene="surA"
     CDS             complement(53840..54361)
                     /gene="surA"
                     /note="ORF_ID:o106#4
                     similar to PIR Accession Number S40574"
                     /codon_start=1
                     /transl_table=11
                     /product="Survival protein SurA precursor (peptidyl-prolyl
                     cis-trans isomerase SurA) (EC 5.2.1.8) (PPiase) (rotamase
                     C)."
                     /protein_id="BAB96621.1"
                     /db_xref="GI:21321934"
                     /translation="MKNWKTLLLGIAMIANTSFAAPQVVDKVAAVVNNGVVLESDVDG
                     LMQSVKLNAAQARQQLPDDATLRHQIMERLIMDQIILQMGQKMGVKISDEQLDQAIAN
                     IAKQNNMTLDQMRSRLAYDGLNYNTYRNQIRKEMIISEVRNNEVRRRITILPQKSNPW
                     RSRWVTKTTPALS"
     gene            complement(54414..56768)
                     /gene="imp"
                     /note="synonym: ostA"
     CDS             complement(54414..56768)
                     /gene="imp"
                     /note="ORF_ID:o106#5
                     similar to SwissProt Accession Number P31554"
                     /codon_start=1
                     /transl_table=11
                     /product="Organic solvent tolerance protein precursor."
                     /protein_id="BAB96622.1"
                     /db_xref="GI:21321935"
                     /translation="MKKRIPTLLATMIATALYSQQGLAADLASQCMLGVPSYDRPLVQ
                     GDTNDLPVTINADHAKGDYPDDAVFTGSVDIMQGNSRLQADEVQLHQKEAPGQPEPVR
                     TVDALGNVHYDDNQVILKGPKGWANLNTKDTNVWEGDYQMVGRQGRGKADLMKQRGEN
                     RYTILDNGSFTSCLPGSDTWSVVGSEIIHDREEQVAEIWNARFKVGPVPIFYSPYLQL
                     PVGDKRRSGFLIPNAKYTTTNYFEFYLPYYWNIAPNMDATITPHYMHRRGNIMWENEF
                     RYLSQAGAGLMELDYLPSDKVYEDEHPNDDSSRRWLFYWNHSGVMDQVWRFNVDYTKV
                     SDPSYFNDFDNKYGSSTDGYATQKFSVGYAVQNFNATVSTKQFQVFSEQNTSSYSAEP
                     QLDVNYYQNDVGPFDTRIYGQAVHFVNTRDDMPEATRVHLEPTINLPLSNNWGSINTE
                     AKLLATHYQQTNLDWYNSRNTTKLDESVNRVMPQFKVDGKMVFERDMEMLAPGYTQTL
                     EPRAQYLYVPYRDQSDIYNYDSSLLQSDYSGLFRDRTYGGLDRIASANQVTTGVTSRI
                     YDDAAVERFNISVGQIYYFTESRTGDDNITWENDDKTGSLVWAGDTYWRISERWGLRG
                     GIQYDTRLDNVATSNSSIEYRRDEDRLVQLNYRYASPEYIQATLPKYYSTAEQYKNGI
                     SQVGAVASWPIADRWSIVGAYYYDTNANKQADSMLGVQYSSCCYAIRVGYERKLNGWD
                     NDKQHAVYDNAIGFNIELRGLSSNYGLGTQEMLRSNILPYQNTL"
     gene            57023..57838
                     /gene="yabH"
     CDS             57023..57838
                     /gene="yabH"
                     /note="ORF_ID:o106#6
                     similar to SwissProt Accession Number P31680"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical 30.6 kd protein in folA-hepA
                     intergenic region (orf81)."
                     /protein_id="BAB96623.1"
                     /db_xref="GI:21321936"
                     /translation="MQYWGKIIGVAVALLMGGGFWGVVLGLLIGHMFDKARSRKMAWF
                     ANQRERQALFFATTFEVMGHLTKSKGRVTEADIHIASQLMDRMNLHGASRTAAQNAFR
                     VGKSDNYPLREKMRQFRSVCFGRFDLIRMFLEIQIQAAFADGSLHPNERAVLYVIAEE
                     LGISRAQFDQFLRMMQGGAQFGGGYQQQTGGGNWQQAQRGPTLEDACNVLGVKPTDDA
                     TTIKRAYRKLMSEHHPDKLVAKGLPPEMMEMAKQKAQEIQQAYELIKQQKGFK"
     gene            58625..58783
                     /gene="yabP"
     CDS             58625..58783
                     /gene="yabP"
                     /note="ORF_ID:o106#7
                     similar to SwissProt Accession Number P39220"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical 5.9 kd protein in surA-hepA
                     intergenic region."
                     /protein_id="BAB96624.1"
                     /db_xref="GI:21321937"
                     /translation="MRDCYLGKKTMKGSNDILYERPGWNANLGVLPRTVLPRTVLTRT
                     VLTWTVLP"
     gene            58780..58938
                     /gene="yabQ"
     CDS             58780..58938
                     /gene="yabQ"
                     /note="ORF_ID:o106#8
                     similar to SwissProt Accession Number P39221"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical 5.7 kd protein in surA-hepA
                     intergenic region."
                     /protein_id="BAB96625.1"
                     /db_xref="GI:21321938"
                     /translation="MNGATSLYDEVIIINKIPPKKIDTKGVATEEVATKKVLLNKLLT
                     TQLLNEPE"
     gene            complement(59346..60009)
                     /gene="yabO"
     misc_feature    complement(59346..60009)
                     /gene="yabO"
                     /product="Hypothetical 24.9 kd protein in surA-hepA
                     intergenic region."
                     /note="ORF is interrupted by frame-shifting
                     ORF_ID:o106#9
                     similar to SwissProt Accession Number P39219"
     CDS             59985..60518
                     /note="ORF_ID:o106#10"
                     /codon_start=1
                     /transl_table=11
                     /protein_id="BAB96626.1"
                     /db_xref="GI:21321939"
                     /translation="MDCSFPSPFSAPLLMRYNDQTQGIQTPTCLIQAFHYLLTVALNG
                     GQFVVTNVRVHCTQSFQTRQLGRQFFVGFVTRCINQCTGRFLDLRFTQLKDSVNILLH
                     GVNQFAAGVTVNRVKLAVKGFKLYLRRQVVAVFIQQHTYRRRWQEAVELQLLRSLGFN
                     HINQFHQQRTYRQRFVF"
     gene            complement(60021..62927)
                     /gene="hepA"
     CDS             complement(60021..62927)
                     /gene="hepA"
                     /note="ORF_ID:o106#11
                     similar to SwissProt Accession Number P23852"
                     /codon_start=1
                     /transl_table=11
                     /product="Probable ATP-dependent helicase HepA."
                     /protein_id="BAB96627.1"
                     /db_xref="GI:21321940"
                     /translation="MPFTLGQRWISDTESELGLGTVVAVDARTVTLLFPSTGENRLYA
                     RSDSPVTRVMFNPGDTITSHDGWQMQVEEVKEENGLLTYIGTRLDTEESGVALREVFL
                     DSKLVFSKPQDRLFAGQIDRMDRFALRYRARKYSSEQFRMPYSGLRGQRTSLIPHQLN
                     IAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVE
                     MLRRFNLRFALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDL
                     LVVDEAHHLVWSEDAPSREYQAIEQLAEHVPGVLLLTATPEQLGMESHFARLRLLDPN
                     RFHDFAQFVEEQKNYRPVADAVAMLLAGNKLSNDELNMLGEMIGEQDIEPLLQAANSD
                     SEDAQSARQELVSMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIKLPLPTQYQTAIKV
                     SGIMGARKSAEDRARDMLYPERIYQEFEGDNATWWNFDPRVEWLMGYLTSHRSQKVLV
                     ICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIG
                     SEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRW
                     YHEGLDAFEHTCPTGRTIYDSVYNDLINYLASPDQTEGFDDLIKNCREQHEALKAQLE
                     QGRDRLLEIHSNGGEKAQALAESIEEQDDDTNLIAFAMNLFDIIGINQDDRGDNMIVL
                     TPSDHMLVPDFPGLSEDGITITFDREVALAREDAQFITWEHPLIRNGLDLILSGDTGS
                     STISLLKNKALPVGTLLVELIYVVEAQAPKQLQLNRFLPPTPVRMLLDKNGNNLAAQV
                     EFETFNRQLNAVNRHTGSKLVNAVQQDVHAILQLGEAQIEKSARALIDAARNEADEKL
                     SAELSRLEALRAVNPNIRDDELTAIESNRQQVMESLDQAGWRLDALRLIVVTHQ"
     CDS             complement(63092..64741)
                     /note="ORF_ID:o107#1
                     dinA; polB
                     similar to E. coli DNA polymerase II (EC 2.7.7.7) (Pol
                     II): PIR Accession Number S15943"
                     /codon_start=1
                     /transl_table=11
                     /protein_id="BAB96628.1"
                     /db_xref="GI:21321941"
                     /translation="MPSRYRLPLRLGRDNSELEWREHGPAKTASFLPQAKGRLIIDGI
                     EALKSAFWDFSSFSLETVAQELLGEGKSIDNPWDRMDEIDRRFAEDKPALATYNLKDC
                     ELVTQIFHKTEIMPFLLERATVNGLPVDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEV
                     PPHASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTE
                     GFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKPLSQALKIIMNAFYGVLGTTACRF
                     FDPRLASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRA
                     LVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGLIQEGDK
                     QRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQEYVRETIDKLMAGELDARLVY
                     RKRLRRPLSEYQRNVPPHVRAARLADEENQKRGRPLQYQNRGTIKYVWTTNGPEPLDY
                     QRSPLDYEHYLTRQLQPVAEGILPFIEDNFATLMTGQLGLF"
     CDS             complement(64698..65447)
                     /note="ORF_ID:o107#2
                     polB
                     similar to E. coli DNA-directed DNA polymerase (EC
                     2.7.7.7) II: PIR Accession Number S15943"
                     /codon_start=1
                     /transl_table=11
                     /protein_id="BAB96629.1"
                     /db_xref="GI:21321942"
                     /translation="MAQAGFILTRHWRDTPQGTEVSFWLATDNGPLQVTLAPQESVAF
                     IPADQVPRAQHILQGEQGFRLTPLALKDFHRQPVYGLYCRAHRQLMNYEKRLREGGVT
                     VYEADVRPPERYLMERFITSPVWVEGDMHNGTIVNARLKPHPDYRPPLKWVSIDIETT
                     RHGELYCIGLEGCGQRIVYMLGPENGDASSLDFELEYVASRPQLLEKLNAWFANYDPD
                     VIIGWNVVQFDLRMLQKHAEPLPSSAASWAR"
     gene            complement(65522..66217)
                     /gene="araD"
     CDS             complement(65522..66217)
                     /gene="araD"
                     /note="ORF_ID:o107#3
                     similar to SwissProt Accession Number P08203"
                     /codon_start=1
                     /transl_table=11
                     /product="L-ribulose-5-phosphate 4-epimerase (EC
                     5.1.3.4)."
                     /protein_id="BAB96630.1"
                     /db_xref="GI:21321943"
                     /translation="MLEDLKRQVLEANLALPKHNLVTLTWGNVSAVDRERGVFVIKPS
                     GVDYSVMTADDMVVVSIETGEVVEGTKKPSSDTPTHRLLYQAFPSIGGIVHTHSRHAT
                     IWAQAGQSIPATGTTHADYFYGTIPCTRKMTDAEINGEYEWETGNVIVETFEKQGIDA
                     AQMPGVLVHSHGPFAWGKNAEDAVHNAIVLEEVAYMGIFCRQLAPQLPDMQQTLLDKH
                     YLRKHGAKAYYGQ"
     gene            complement(66502..68004)
                     /gene="araA"
     CDS             complement(66502..68004)
                     /gene="araA"
                     /note="ORF_ID:o107#4
                     similar to SwissProt Accession Number P08202"
                     /codon_start=1
                     /transl_table=11
                     /product="L-arabinose isomerase (EC 5.3.1.4)."
                     /protein_id="BAB96631.1"
                     /db_xref="GI:21321944"
                     /translation="MTIFDNYEVWFVIGSQHLYGPETLRQVTQHAEHVVNALNTEAKL
                     PCKLVLKPLGTTPDEITAICRDANYDDPCAGLVVWLHTFSPAKMWINGLTMLNKPLLQ
                     FHTQFNAALPWDSIDMDFMNLNQTAHGGREFGFIGARMRQQHAVVTGHWQDKQAHERI
                     GSWMRQAVSKQDTRHLKVCRFGDNMREVAVTDGDKVAAQIKFGFSVNTWAVGDLVQVV
                     NSISDGDVNALVDEYESCYTMTPATQIHGEKRQNVLEAARIELGMKRFLEQGGFHAFT
                     TTFEDLHGLKQLPGLAVQRLMQQGYGFAGEGDWKTAALLRIMKVMSTGLQGGTSFMED
                     YTYHFEKGNDLVLGSHMLEVCPSIAVEEKPILDVQHLGIGGKDDPARLIFNTQTGPAI
                     VASLIDLGDRYRLLVNCIDTVKTPHSLPKLPVANALWKAQPDLPTASEAWILAGGAHH
                     TVFSHALNLNDMRQFAEMHDIEITVIDNDTRLPAFKDALRWNEVYYGFRR"
     gene            complement(68015..69715)
                     /gene="araB"
     CDS             complement(68015..69715)
                     /gene="araB"
                     /note="ORF_ID:o108#1
                     similar to PIR Accession Number B29022"
                     /codon_start=1
                     /transl_table=11
                     /product="Ribulokinase (EC 2.7.1.16)"
                     /protein_id="BAB96632.1"
                     /db_xref="GI:21321945"
                     /translation="MAIAIGLDFGSDSVRALAVDCASGEEIATSVEWYPRWQKGQFCD
                     APNNQFRHHPRDYIESMEAALKTVLAELSVEQRAAVVGIGVDSTGSTPAPIDADGNVL
                     ALRPEFAENPNAMFVLWKDHTAVERSEEITRLCHAPGNVDYSRYIGGIYSSEWFWAKI
                     LHVTRQDSAVAQSAASWIELCDWVPALLSGTTRPQDIRRGRCSAGHKSLWHESWGGLP
                     PASFFDELDPILNRHLPSPLFTDTWTADIPVGTLCPEWAQRLGLPESVVISGGAFDCH
                     MGAVGAGAQPNALVKVIGTSTCDILIADKQSVGERAVKGICGQVDGSVVPGFIGLEAG
                     QSAFGDIYAWFGRVLSWPLEQLAAQHPELKAQINASQKQLLPALTEAWAKNPSLDHLP
                     VVLDWFNGRRSPNANQRLKGVITDLNLATDAPLLFGGLIAATAFGARAIMECFTDQGI
                     AVNNVMALGGIARKNQVIMQACCDVLNRPLQIVASDQCCALGAAIFAAVAAKVHADIP
                     SAQQKMASAVEKTLQPRSEQAQRFEQLYRRYQQWAMSAEQHYLPTSAPAQAAQAVATL
                     "
     gene            70054..70932
                     /gene="araC"
     CDS             70054..70932
                     /gene="araC"
                     /note="ORF_ID:o108#2
                     similar to PIR Accession Number A91473"
                     /codon_start=1
                     /transl_table=11
                     /product="Arabinose operon regulatory protein"
                     /protein_id="BAB96633.1"
                     /db_xref="GI:21321946"
                     /translation="MAEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKG
                     YILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRA
                     YWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLL
                     LRRMEAINESLHPPMDNRVREACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQQ
                     LGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEF
                     RAGCEEKVNDVAVKLS"
     gene            71066..71779
                     /gene="yabI"
     CDS             71066..71779
                     /gene="yabI"
                     /note="ORF_ID:o108#3
                     similar to PIR Accession Number S40581"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein"
                     /protein_id="BAB96634.1"
                     /db_xref="GI:21321947"
                     /translation="MAVVLVAFLESLALVGLILPGTVLMAGLGALIGSGELSFWHAWL
                     AGIIGCLMGDWISFWLGWRFKKPLHRWSFLKKNKALLDKTEHALHQHSMFTILVGRFV
                     GPTRPLVPMVAGMLDLPVAKFITPNIIGCLLWPPFYFLPGILAGAAIDIPAGMQSGEF
                     KWLLLATAVFLWVGGWLCWRLWRSGKATDRLSHYLSRGRLLWLTPLISAIGVVALVVL
                     IRHPLMPVYIDILRKVVGV"
     gene            complement(71894..72592)
                     /gene="yabJ"
     CDS             complement(71894..72592)
                     /gene="yabJ"
                     /note="ORF_ID:o108#4
                     similar to PIR Accession Number S40582"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein"
                     /protein_id="BAB96635.1"
                     /db_xref="GI:21321948"
                     /translation="MLKLTDITWLYHHLPMRFSLTVERGEQVAILGPSGAGKSTLLNL
                     IAGFLTPASGSLTIDGVDHTTMPPSRRPVSMLFQENNLFSHLTVAQNIGLGLNPGLKL
                     NAVQQGKMHAIARQMGIDNLMARLPGELSGGQRQRVALARCLVREQPILLLDELFSAL
                     DPALRQEMLTLVSTSCQQQKMTLLMVSHSVEDAARIATRSVVVADGRIAWQGMTNELL
                     SGKASASALLGITG"
     gene            complement(72576..74186)
                     /gene="yabK"
     CDS             complement(72576..74186)
                     /gene="yabK"
                     /note="ORF_ID:o108#5
                     similar to PIR Accession Number S40583"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein"
                     /protein_id="BAB96636.1"
                     /db_xref="GI:21321949"
                     /translation="MATRRQPLIPGWLIPGVSATTLVVAVALAAFLALWWNAPQDDWV
                     AVWQDSYLWHVVRFSFWQAFLSALLSVIPAIFLARALYRRRFPGRLALLRLCAMTLIL
                     PVLVAVFGILSVYGRQGWLATLCQSLGLEWTFSPYGLQGILLAHVFFNLPMASRLLLQ
                     ALENIPGEQRQLAAQLGMRSWHFFRFVEWPWLRRQIPPVAALIFMLCFASFATVLSLG
                     GGPQATTIELAIYQALSYDYDPARAAMLALLQMVCCLGLVLLSQRLSKAIAPGTTLLQ
                     GWRDPDDRLHSRICDTVLIVLALLLLLPPLLAVIVDGVNRQLPEVLAQPVLWQALWTS
                     LRIALAAGVLCVVLTMMLLWSSRELRARQKMLAGQVLEMSGMLILAMPGIVLATGFFL
                     LLNNTIGLPQSADGIVIFTNALMAIPYALKVLENPMRDITARYSMLCQSLGIEGWSRL
                     KVVELRALKRPLAQALAFACVLSIGDFGVVALFGNDDFRTLPFYLYQQIGSYRSQDGA
                     VTTLILLLLCFLLFTVIEKLPGRNVKTD"
     gene            complement(74162..75133)
                     /gene="tbpA"
     CDS             complement(74162..75133)
                     /gene="tbpA"
                     /note="ORF_ID:o108#6
                     similar to PIR Accession Number S40584"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein."
                     /protein_id="BAB96637.1"
                     /db_xref="GI:21321950"
                     /translation="MSAPAVAVTAPVFAKPVLTVYTYDSFAADWGPGPVVKKAFEADC
                     NCELKLVALEDGVSLLNRLRMEGKNSKADVVLGLDNNLLDAASKTGLFAKSGVAADAV
                     NVPGGWNNDTFVPFDYGYFAFVYDKNKLKNPPQSLKELVESDQNWRVIYQDPRTSTPG
                     LGLLLWMQKVYGDDAPQAWQKLAKKTVTVTKGWSEAYGLFLKGESDLVLSYTTSPAYH
                     ILEEKKDNYAAANFSEGHYLQVEVAARTAASKQPELAQKFLQFMVSPAFQNAIPTGNW
                     MYPVANVTLPAGFEKLTKPATTLEFTPAEVAAQRQAWISEWQRAVSR"
     gene            complement(75308..76963)
                     /gene="yabN"
     CDS             complement(75308..76963)
                     /gene="yabN"
                     /note="ORF_ID:o108#7
                     similar to SwissProt Accession Number P33595"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical 63.9 kd protein in tbpA-leuD
                     intergenic region (orf103)."
                     /protein_id="BAB96638.1"
                     /db_xref="GI:21321951"
                     /translation="MPSARLQQQFIRLWQCCEGKSQDTTLNELAALLSCSRRHMRTLL
                     NTMQDRGWLTWEAEVGRGKRSRLTFLYTGLALQQQRAEDLLEQDRIDQLVQLVGDKAT
                     VRQMLVSHLGRSFRQGRHILRVLYYRPLRNLLPGSALRRSETHIARQIFSSLTRINEE
                     NGELEADIAHHWQQISPLHWRFFLRPGVHFHHGRELEMDDVIASLKRINTLPLYSHIA
                     DIVSPTPWTLDIHLTQPDRWLPLLLGQVPAMILPREWETLSNFASHPIGTGPYAVIRN
                     STNQLKIQAFDDFFGYRALIDEVNVWVLPEIADEPAGGLMLKGPQGEEKEIESRLEEG
                     CYYLLFDSRTHRGANQQVRDWASYVLSPTNLVYFAEEQYQQLWFPAYGLFPRWHHART
                     IKSEKPAGLESLTLTFCQDHSEHRVIAGIMQQILASHQVTLKIKEIDYDQWHTGEIES
                     DIWLNSANFTLPLDFSVFAHLCEVPLLQHCIPIDWQADAARWRNGEMNLANWCQQLVA
                     SKAMVPLLHHWLIIQGQRSMRGLRMNTLGWFDFKSAWFAPPDP"
     gene            77285..78463
                     /gene="yabM"
     CDS             77285..78463
                     /gene="yabM"
                     /note="ORF_ID:o108#8
                     similar to SwissProt Accession Number P31675"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical 42.7 kd protein in tbpA-leuD
                     intergenic region (orf104)."
                     /protein_id="BAB96639.1"
                     /db_xref="GI:21321952"
                     /translation="MIWIMTMARRMNGVYAAFMLVAFMMGVAGALQAPTLSLFLSREV
                     GAQPFWIGLFYAVNAIAGIGVSLWLAKRSDSQGDRRKLIIFCCLMAIGNALLFAFNRH
                     YLTLITCGVLLASLANTAMPQLFALAREYADNSAREVVMFSSVMRAQLSLAWVIGPPL
                     AFMLALNYGFTVMFSIAAGIFTLSLVLIAFMLPSVARVELPSENALSMQGGWQDSNVR
                     MLFVASTLMWTCNTMYIIDMPLWISSELGLPDKLAGFLMGTAAGLEIPAMILAGYYVK
                     RYGKRRMMVIAVAAGVLFYTGLIFFNSRMALMTLQLFNAVFIGIVAGIGMLWFQDLMP
                     GRAGAATTLFTNSISTGVILAGVIQGAIAQSWGHFAVYWVIAVISVVALFLTAKVKDV
                     "
     gene            complement(78512..79117)
                     /gene="leuD"
     CDS             complement(78512..79117)
                     /gene="leuD"
                     /note="ORF_ID:o108#9
                     similar to PIR Accession Number S40585"
                     /codon_start=1
                     /transl_table=11
                     /product="Isopropylmalate isomerase subunit"
                     /protein_id="BAB96640.1"
                     /db_xref="GI:21321953"
                     /translation="MAEKFIKHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLF
                     NDWRFLDEKGQQPNPDFVLNFPQYQGASILLARENFGCGSSREHAPWALTDYGFKVVI
                     APSFADIFYGNSFNNQLLPVKLSDAEVDELFALVKANPGIHFDVDLEAQEVKAGEKTY
                     RFTIDAFRRHCMMNGLDSIGLTLQHDDAIAAYEAKQPAFMN"
     gene            complement(79128..80528)
                     /gene="leuC"
     CDS             complement(79128..80528)
                     /gene="leuC"
                     /note="ORF_ID:o109#1
                     similar to PIR Accession Number S40586"
                     /codon_start=1
                     /transl_table=11
                     /product="3-isopropylmalate dehydratase (EC 4.2.1.33)
                     alpha chain"
                     /protein_id="BAB96641.1"
                     /db_xref="GI:21321954"
                     /translation="MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGL
                     RAHGRPVRQPGKTFATMDHNVSTQTKGINACGEMARIQMQELIKNCKEFGVELYDLNH
                     PYQGIVHVMGPEQGVTLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQ
                     GRAKTMKIEVQGKAAPGITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMT
                     LCNMAIEMGAKAGLVAPDETTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTV
                     VTLQAEEISPQVTWGTNPGQVISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPL
                     TEVAIDKVFIGSCTNSRIEDLRAAAEIVKGRKVAPGVQALVVPGSGPVKAQAEAEGLD
                     KIFIEAGFEWRLPGCSMCLAMNNDRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMA
                     AAAAVTGHFADIRNIK"
     gene            complement(80531..81622)
                     /gene="leuB"
     CDS             complement(80531..81622)
                     /gene="leuB"
                     /note="ORF_ID:o109#2
                     similar to SwissProt Accession Number P30125"
                     /codon_start=1
                     /transl_table=11
                     /product="3-isopropylmalate dehydrogenase (EC 1.1.1.85)
                     (beta-ipm dehydrogenase) (imdH) (3-ipm-dh)."
                     /protein_id="BAB96642.1"
                     /db_xref="GI:21321955"
                     /translation="MSKNYHIAVLPGDGIGPEVMTQALKVLDAVRNRFAMRITTSHYD
                     VGGAAIDNHGQPLPPATVEGCEQADAVLFGSVGGPKWEHLPPDQQPERGALLPLRKHF
                     KLFSNLRPAKLYQGLEAFCPLRADIAANGFDILCVRELTGGIYFGQPKGREGSGQYEK
                     AFDTEVYHRFEIERIARIAFESARKRRHKVTSIDKANVLQSSILWREIVNEIATEYPD
                     VELAHMYIDNATMQLIKDPSQFDVLLCSNLFGDILSDECAMITGSMGMLPSASLNEQG
                     FGLYEPAGGSAPDIAGKNIANPIAQILSLALLLRYSLDADDAACAIERAINRALEEGI
                     RTGDLARGAAAVSTDEMGDIIARYVAEGV"
     gene            complement(81622..83193)
                     /gene="leuA"
     CDS             complement(81622..83193)
                     /gene="leuA"
                     /note="ORF_ID:o109#3
                     similar to PIR Accession Number S40588"
                     /codon_start=1
                     /transl_table=11
                     /product="2-Isopropylmalate synthase"
                     /protein_id="BAB96643.1"
                     /db_xref="GI:21321956"
                     /translation="MSQQVIIFDTTLRDGEQALQASLSVKEKLQIALALERMGVDVME
                     VGFPVSSPGDFESVQTIARQVKNSRVCALARCVEKDIDVAAESLKVAEAFRIHTFIAT
                     SPMHIATKLRSTLDEVIERAIYMVKRARNYTDDVEFSCEDAGRTPIADLARVVEAAIN
                     AGATTINIPDTVGYTMPFEFAGIISGLYERVPSIGKAIISVHTHDDLGLAVGNSLAAV
                     HAGARQVEGAMNGIGERAGNCSLEEVIMAIKVRKDILNVHTAINHQEIWRTSQLVSQI
                     CNMPIPANKAIVGSGAFAHSSGIHQDGVLKNRENYEIMTPESIGLNQIQLNLTSRSGR
                     AAVKHRMDEMGYKESEYNLDNLYDAFLKLADKKGQVFDYDLEALAFIGKQQEEPEHFR
                     LDYFSVQSGSNDIATAAVKLACGEEVKAEAANGNGPVDAVYQAINRITEYNVELVKYS
                     LTAKGHGKDALGQVDIVANYNGRRFHGVGLATDIVESSAKAMVHVLNNIWRAAEVEKE
                     LQRKAQHNENNKETV"
     gene            complement(83286..83372)
                     /gene="leuLP"
     CDS             complement(83286..83372)
                     /gene="leuLP"
                     /note="ORF_ID:o109#4
                     similar to PIR Accession Number A30376"
                     /codon_start=1
                     /transl_table=11
                     /product="LeuABCD leader peptide."
                     /protein_id="BAB96644.1"
                     /db_xref="GI:21321957"
                     /translation="MTHIVRFIGLLLLNASSLRGRRVSGIQH"
     gene            83855..84904
                     /gene="lueO"
     CDS             83855..84904
                     /gene="lueO"
                     /note="ORF_ID:o109#5
                     similar to PIR Accession Number S40589"
                     /codon_start=1
                     /transl_table=11
                     /product="LeuO protein."
                     /protein_id="BAB96645.1"
                     /db_xref="GI:21321958"
                     /translation="MTHSTAMDSVFIRTRIFMFSEFYSFCFFLFYMHDKSYSSGLFLC
                     IPIRERELSVTVELSMPEVQTDHPETAELSKPQLRMVDLNLLTVFDAVMQEQNITRAA
                     HVLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARAFQLFGSVRQALQLVQNELP
                     GSGFEPASSERVFHLCVCSPLDSILTSQIYNHIEQIAPNIHVMFKSSLNQNTEHQLRY
                     QETEFVISYEDFHRPEFTSVPLFKDEMVLVASKNHPTIKGPLLKHDVYNEQHAAVSLD
                     RFASFSQPWYDTVDKQASIAYQGMAMMSVLSVVSQTHLVAIAPRWLAEEFAESLELQV
                     LPLPLKQNSRTCYLS"
     gene            85294..86994
                     /gene="ilvI"
     CDS             85294..86994
                     /gene="ilvI"
                     /note="ORF_ID:o109#6
                     similar to PIR Accession Number S14385"
                     /codon_start=1
                     /transl_table=11
                     /product="Acetolactate synthase (EC 4.1.3.18) III large
                     chain."
                     /protein_id="BAB96646.1"
                     /db_xref="GI:21321959"
                     /translation="MEMLSGGEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGID
                     HVLVRHEQAAVHMADGLARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQ
                     VATSLIGYDAFQECDMVGISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVD
                     LPKDILNPANKLPYVWPESVSMRSYNPTTTGHKGQIKRALQSVVAVKKPVVYVGGGAI
                     TAGCHQQLKETVEALNLPVVCSLMGLGAFPATHRQVLGMLGMHGTYEANMTMHNADVI
                     FAVGVRFDDRTTNNLAKYCPNATVLHIDIDPTSISKTVTADIPIVGDARQVLEQMLEL
                     LSQESAHQPLDEIRDWWQQIEQWRARQCLKYDTHSEKIKPQAVIETLWRLTKGDAYVT
                     SDVGQHQMFAALYYPFDKPRRWINSGGLGSMGFGLPAALGVKMAFPEETVVCVTGDGS
                     IQMNIQELSTALQYELPVLVVNLNNRYLGMVKQWQDMIYSGRHSQSYMQSLPDFVRRG
                     AYGHVGIQISHPHGWKANLARRWNRCAIIAWCLLMLPSMAASTSTRCRFAGAEWMKCG
                     "
     gene            87017..87508
                     /gene="brnP"
                     /note="synonym: ilvH"
     CDS             87017..87508
                     /gene="brnP"
                     /note="ORF_ID:o109#7
                     similar to SwissProt Accession Number P00894"
                     /codon_start=1
                     /transl_table=11
                     /product="Acetolactate synthase isozyme III small subunit
                     (EC 4.1.3.18) (ahas- III) (acetohydroxy-acid synthase III
                     small subunit) (als-III)."
                     /protein_id="BAB96647.1"
                     /db_xref="GI:21321960"
                     /translation="MRRILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLS
                     RMTIQTVGDEKVLEQIEKQLHKLVDVLRVSELGQGAHVEREIMLVKIQASGYGRDEVK
                     RNTEIFRGQIIDVTPSLYTVQLAGTSGKLSAFLASIRDVAKIVEVARSGVVGLSRGDK
                     IMR"
     gene            87688..88692
                     /gene="fruR"
                     /note="synonym: shl"
     CDS             87688..88692
                     /gene="fruR"
                     /note="ORF_ID:o109#8
                     similar to PIR Accession Number JU0298"
                     /codon_start=1
                     /transl_table=11
                     /product="Pep-fructosephosphotransferase system
                     repressor."
                     /protein_id="BAB96648.1"
                     /db_xref="GI:21321961"
                     /translation="MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVRE
                     HNYHPNAVAAGLRAGRTRSIGLVIPDLENTSYTRIANYLERQARQRGYQLLIACSEDQ
                     PDNEMRCIEHLLQRQVDAIIVSTSLPPEHPFYQRWANDPFPIVALDRALDREHFTSVV
                     GADQDDAEMLAEELRKFPAETVLYLGALPELSVSFLREQGFRTAWKDDPREVHFLYAN
                     SYEREAAAQLFEKWLETHPMPQALFTTSFALLQGVMDVTLRRDGKLPSDLAIATFGDN
                     ELLDFLQCPVLAVAQRHRDVAERVLEIVLASLDEPRKPKPGLTRIKRNLYRRGVLSRS
                     "
     gene            89294..89752
                     /gene="yabB"
     CDS             89294..89752
                     /gene="yabB"
                     /note="ORF_ID:o109#9
                     similar to PIR Accession Number S14388"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical protein C."
                     /protein_id="BAB96649.1"
                     /db_xref="GI:21321962"
                     /translation="MFRGATLVNLDSKGRLSVPTRYREQLLENAAGQMVCTIDIYHPC
                     LLLYPLPEWEIIEQKLSRLSSMNPVERRVQRLLLGHASECQMDGAGRLLIAPVLRQHA
                     GLTKEVMLVGQFNKFELWDETTWHQQVKEDIDAEQLATGDLSERLQDLSL"
     gene            89754..90695
                     /gene="yabC"
     CDS             89754..90695
                     /gene="yabC"
                     /note="ORF_ID:o109#10
                     similar to SwissProt Accession Number P18595"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical 34.9 kd protein in fruR-ftsL
                     intergenic region (orfB)."
                     /protein_id="BAB96650.1"
                     /db_xref="GI:21321963"
                     /translation="MMENYKHTTVLLDEAVNGLNIRPDGIYIDGTFGRGGHSRLILSQ
                     LGEEGRLLAIDRDPQAIAVAKTIDDPRFSIIHGPFSALGEYVAERDLIGKIDGILLDL
                     GVSSPQLDDAERGFSFMRDGPLDMRMDPTRGQSAAEWLQTAEEADIAWVLKTYGEERF
                     AKRIARAIVERNREQPMTRTKELAEVVAAATPVKDKFKHPATRTFQAVRIWVNSELEE
                     IEQALKSSLNVLAPGGRLSIISFHSLEDRIVKRFMRENSRGPQVPAGLPMTEEQLKKL
                     GGRQLRALGKLMPGEEEVAENPRARSSVLRIAERTNA"
     gene            90692..91024
                     /gene="ftsL"
     CDS             90692..91024
                     /gene="ftsL"
                     /note="ORF_ID:o110#1
                     similar to PIR Accession Number S14387"
                     /codon_start=1
                     /transl_table=11
                     /product="Cell division protein FtsL"
                     /protein_id="BAB96651.1"
                     /db_xref="GI:21321964"
                     /translation="MISRVTEALSKVKGSMGSHERHALPGVIGDDLLRFGKLPLCLFI
                     CIILTAVTVVTTAHHTRLLTAQREQLVLERDALDIEWRNLILEENALGDHSRVERIAT
                     EKLQMQTC"
     gene            91074..92840
                     /gene="ftsI"
                     /note="synonym: pbpB"
     CDS             91074..92840
                     /gene="ftsI"
                     /note="ORF_ID:o110#2
                     similar to PIR Accession Number A93123"
                     /codon_start=1
                     /transl_table=11
                     /product="Penicillin-binding protein 3 precursor."
                     /protein_id="BAB96652.1"
                     /db_xref="GI:21321965"
                     /translation="MKAAAKTQKPKRQEEHANFISWRFALLCGCILLALAFLLGRVAW
                     LQVISPDMLVKEGDMRSLRVQQVSTSRGMITDRSGRPLAVSVPVKAIWADPKEVHDAG
                     GISVGDRWKALANALNIPLDQLSARINANPKGRFIYLARQVNPDMADYIKKLKLPGIH
                     LREESRRYYPSGEVTAHLIGFTNVDSQGIEGVEKSFDKWLTGQPGERIVRKDRYGRVI
                     EDISSTDSQAAHNLALSIDERLQALVYRELNNAVAFNKAESGSAVLVDVNTGEVLAMA
                     NSPSYNPNNLSGTPKEAMRNRTITDVFEPGSTVKPMVVMTALQRGVVRENSVLNTIPY
                     RINGHEIKDVARYSELTLTGVLQKSSNVGVSKLALAMPSSALVDTYSRFGLGKATNLG
                     LVGERSGLYPQKQRWSDIERATFSFGYGLMVTPLQLARVYATIGSYGIYRPLSITKVD
                     PPVPGERVFPESIVRTVVHMMESVALPGGGGVKAAIKGYRIAIKTGTAKKVGPDGRYI
                     NKYIAYTAGVAPASQPRFALVVVINDPQAGKYYGGAVSAPVFGAIMGGVLRTMNIEPD
                     ALTTGDKNEFVINQGEGTGGRS"
     gene            92827..94314
                     /gene="murE"
     CDS             92827..94314
                     /gene="murE"
                     /note="ORF_ID:o110#3
                     similar to PIR Accession Number S40595"
                     /codon_start=1
                     /transl_table=11
                     /product="UDP-N-acetylmuramoylalanyl-D-glutamate--2,
                     6-diaminopimelate ligase (EC 6.3.2.13) murE"
                     /protein_id="BAB96653.1"
                     /db_xref="GI:21321966"
                     /translation="MADRNLRDLLAPWVPDAPSRALREMTLDSRVAAAGDLFVAVVGH
                     QADGRRYIPQAIAQGVAAIIAEAKDEATDGEIREMHGVPVIYLSQLNERLSALAGRFY
                     HEPSDNLRLVGVTGTNGKTTTTQLLAQWSQLLGEISAVMGTVGNGLLGKVIPTENTTG
                     SAVDVQHELAGLVDQGATFCAMEVSSHGLVQHRVAALKFAASVFTNLSRDHLDYHGDM
                     EHYEAAKWLLYSEHHCGQAIINADDEVGRRWLAKLPDAVAVSMEDHINPNCHGRWLKA
                     TEVNYHDSGATIRFSSSWGDGEIESHLMGAFNVSNLLLALATLLALGYPLADLLKTAA
                     RLQPVCGRMEVFTAPGKPTVVVDYAHTPDALEKALQAARLHCAGKLWCVFGCGGDRDK
                     GKRPLMGAIAEEFADVAVVTDDNPRTEEPRAIINDILAGMLDAGHAKVMEGRAEAVTC
                     AVMQAKENDVVLVAGKGHEDYQIVGNQRLDYSDRVTVARLLGVIA"
     gene            94311..95669
                     /gene="mra"
                     /note="synonym: murF"
     CDS             94311..95669
                     /gene="mra"
                     /note="ORF_ID:o110#4
                     similar to SwissProt Accession Number P11880"
                     /codon_start=1
                     /transl_table=11
                     /product="UDP-n-acetylmuramoylalanyl-d-glutamyl-2,
                     6-diaminopimelate-d-alanyl -d- alanyl ligase (EC 6.3.2.15)
                     (UDP-murnac-pentapeptide synthetase)
                     (d-alanyl-d-alanine-adding enzyme)."
                     /protein_id="BAB96654.1"
                     /db_xref="GI:21321967"
                     /translation="MISVTLSQLTDILNGELQGADITLDAVTTDTRKLTPGCLFVALK
                     GERFDAHDFADQAKAGAAGALLVSRPLDIDLPQLIVKDTRLAFGELAAWVRQQVPARV
                     VALTGSSGKTSVKEMTAAILSQCGNTLYTAGNLNNDIGVPMTLLRLTPEYDYAVIELG
                     ANHQGEIAWTVSLTRPERALVNNLAAAHLEGFGSLAGVAKAKGEIFSGLPENGIAIMN
                     ADNNDWLNWQSVIGSRKVWRFSPNAANSDFTATNIHVTSHGTEFTLQTPTGSVDVLLP
                     LPGRHNIANALAAAALSMSVGATLDAIKAGLANLKAVPGRLFPIQLAENQLLLDDSYN
                     ANVGSMTAAVQVLAEMPGYRVLVVGDMAELGAESEACHVQVGEAAKAAGIDRVLSVGK
                     QSHAISTASGVGEHFADKTALITRLKLLIAEQQVITILVKGSRSAAMEEVVRALQENG
                     TC"
     gene            95663..96745
                     /gene="mraY"
                     /note="synonym: murX"
     CDS             95663..96745
                     /gene="mraY"
                     /note="ORF_ID:o110#5
                     similar to SwissProt Accession Number P15876"
                     /codon_start=1
                     /transl_table=11
                     /product="Phospho-n-acetylmuramoyl-pentapeptide-transferas
                     e (EC 2.7.8.13)."
                     /protein_id="BAB96655.1"
                     /db_xref="GI:21321968"
                     /translation="MLVWLAEHLVKYYSGFNVFSYLTFRAIVSLLTALFISLWMGPRM
                     IAHLQKLSFGQVVRNDGPESHFSKRGTPTMGGIMILTAIVISVLLWAYPSNPYVWCVL
                     VVLVGYGVIGFVDDYRKVVRKDTKGLIARWKYFWMSVIALGVAFALYLAGKDTPATQL
                     VVPFFKDVMPQLGLFYILLAYFVIVGTGNAVNLTDGLDGLAIMPTVFVAGGFALVAWA
                     TGNMNFASYLHIPYLRHAGELVIVCTAIVGAGLGFLWFNTYPAQVFMGDVGSLALGGA
                     LGIIAVLLRQEFLLVIMGGVFVVETLSVILQVGSFKLRGQRIFRMAPIHHHYELKGWP
                     EPRVIVRFWIISLMLVLIGLATLKVR"
     gene            96748..98064
                     /gene="murD"
     CDS             96748..98064
                     /gene="murD"
                     /note="ORF_ID:o110#6
                     similar to PIR Accession Number S08396"
                     /codon_start=1
                     /transl_table=11
                     /product="UDP-n-acetylmuramoylalanine-d-glutamate ligase
                     (EC 6.3.2.9)."
                     /protein_id="BAB96656.1"
                     /db_xref="GI:21321969"
                     /translation="MADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGL
                     DKLPEAVERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCRE
                     AQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDECELYVLELS
                     SFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAKLRIYENAKVCVVNADDALT
                     MPIRGADERCVSFGVNMGDYHLNHQQGETWLRVKGEKVLNVKEMKLSGQHNYTNALAA
                     LALADAAGLPRASSLKALTTFTGLPHRFEVVLEHNGVRWINDSKATNVGSTEAALNGL
                     HVDGTLHLLLGGDGKSADFSPLARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETME
                     QAMRLLAPRVQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELG"
     gene            98064..99308
                     /gene="ftsW"
     CDS             98064..99308
                     /gene="ftsW"
                     /note="ORF_ID:o111#1
                     similar to PIR Accession Number A32581"
                     /codon_start=1
                     /transl_table=11
                     /product="Cell division protein FtsW."
                     /protein_id="BAB96657.1"
                     /db_xref="GI:21321970"
                     /translation="MRLSLPRLKMPRLPGFSILVWISTALKGWVMGSREKDTDSLIMY
                     DRTLLWLTFGLAAIGFIMVTSASMPIGQRLTNDPFFFAKRDGVYLILAFILAIITLRL
                     PMEFWQRYSATMLLGSIILLMIVLVVGSSVKGASRWIDLGLLRIQPAELTKLSLFCYI
                     ANYLVRKGDEVRNNLRGFLKPMGVILVLAVLLLAQPDLGTVVVLFVTTLAMLFLAGAK
                     LWQFIAIIGMGISAVVLLILAEPYRIRRVTAFWNPWEDPFGSGYQLTQSLMAFGRGEL
                     WGQGLGNSVQKLEYLPEAHTDFIFAIIGEELGYVGVVLALLMVFFVAFRAMSIGRKAL
                     EIDHRFSGFLACSIGIWFSFQALVNVGAAAGMLPTKGLTLPLISYGGSSLLIMSTAIM
                     MLLRIDYETRLEKAQAFVRGSR"
     gene            99305..100372
                     /gene="murG"
     CDS             99305..100372
                     /gene="murG"
                     /note="ORF_ID:o111#2
                     similar to PIR Accession Number JQ0544"
                     /codon_start=1
                     /transl_table=11
                     /product="MurG protein."
                     /protein_id="BAB96658.1"
                     /db_xref="GI:21321971"
                     /translation="MSGQGKRLMVMAGGTGGHVFPGLAVAHHLMAQGWQVRWLGTADR
                     MEADLVPKHGIEIDFIRISGLRGKGIKALIAAPLRIFNAWRQARAIMKAYKPDVVLGM
                     GGYVSGPGGLAAWSLGIPVVLHEQNGIAGLTNKWLAKIATKVMQAFPGAFPNAEVVGN
                     PVRTDVLALPLPQQRLAGREGPVRVLVVGGSQGARILNQTMPQVAAKLGDSVTIWHQS
                     GKGSQQSVEQAYAEAGQPQHKVTEFIDDMAAAYAWADVVVCRSGALTVSEIAAAGLPA
                     LFVPFQHKDRQQYWNALPLEKAGAAKIIEQPQLSVDAVANTLAGWSRETLLTMAERAR
                     AASIPDATERVANEVSRVARA"
     gene            100426..101901
                     /gene="murC"
     CDS             100426..101901
                     /gene="murC"
                     /note="ORF_ID:o111#3
                     similar to PIR Accession Number JQ0545"
                     /codon_start=1
                     /transl_table=11
                     /product="UDP-n-acetylmuramate-alanine ligase (EC
                     6.3.2.8)."
                     /protein_id="BAB96659.1"
                     /db_xref="GI:21321972"
                     /translation="MNTQQLAKLRSIVPEMRRVRHIHFVGIGGAGMGGIAEVLANEGY
                     QISGSDLAPNPVTQQLMNLGATIYFNHRPENVRDASVVVVSSAISADNPEIVAAHEAR
                     IPVIRRAEMLAELMRFRHGIAIAGTHGKTTTTAMVSSIYAEAGLDPTFVNGGLVKAAG
                     VHARLGHGRYLIAEADESDASFLHLQPMVAIVTNIEADHMDTYQGDFENLKQTFINFL
                     HNLPFYGRAVMCVDDPVIRELLPRVGRQTTTYGFSEDADVRVEDYQQIGPQGHFTLLR
                     QDKEPMRVTLNAPGRHNALNAAAAVAVATEEGIDDEAILRALESFQGTGRRFDFLGEF
                     PLEPVNGKSGTAMLVDDYGHHPTEVDATIKAARAGWPDKNLVMLFQPHRFTRTRDLYD
                     DFANVLTQVDTLLMLEVYPAGEAPIPGADSRSLCRTIRGRGKIDPILVPDPARVAEML
                     APVLTGNDLILVQGAGNIGKIARSLAEIKLKPQTPEEEQHD"
     gene            101894..102814
                     /gene="ddl"
                     /note="synonym: ddlB"
     CDS             101894..102814
                     /gene="ddl"
                     /note="ORF_ID:o111#4
                     similar to PIR Accession Number A30289"
                     /codon_start=1
                     /transl_table=11
                     /product="D-alanine-d-alanine ligase (EC 6.3.2.4) B."
                     /protein_id="BAB96660.1"
                     /db_xref="GI:21321973"
                     /translation="MTDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKE
                     VDVTQLKSMGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKL
                     LWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAE
                     NALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKYLS
                     DETQYFCPAGLEASQEANLQALVLKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPG
                     MTSHSLVPMAARQAGMSFSQLVVRILELAD"
     gene            102816..103646
                     /gene="ftsQ"
     CDS             102816..103646
                     /gene="ftsQ"
                     /note="ORF_ID:o111#5
                     similar to PIR Accession Number S10852"
                     /codon_start=1
                     /transl_table=11
                     /product="Cell division protein FtsQ."
                     /protein_id="BAB96661.1"
                     /db_xref="GI:21321974"
                     /translation="MSQAALNTRNSEEEVSSRRNNGTRLAGILFLLTVLTTVLVSGWV
                     VLGWMEDAQRLPLSKLVLTGERHYTRNDDIRQSILALGEPGTFMTQDVNIIQTQIEQR
                     LPWIKQVSVRKQWPDELKIHLVEYVPIARWNDQHMVDAEGNTFSVPPERTSKQVLPML
                     YGPEGSANEVLQGYREMGQMLAKDRFTLKEAAMTARRSWQLTLNNDIKLNLGRGDTMK
                     RLARFVELYPVLQQQAQTDGKRISYVDLRYDSGAAVGWAPLPPEESTQQQNQAQAEQQ
                     "
     gene            103643..104905
                     /gene="divA"
                     /note="synonym: ftsA"
     CDS             103643..104905
                     /gene="divA"
                     /note="ORF_ID:o111#6
                     similar to SwissProt Accession Number P06137"
                     /codon_start=1
                     /transl_table=11
                     /product="Cell division protein FtsA."
                     /protein_id="BAB96662.1"
                     /db_xref="GI:21321975"
                     /translation="MIKATDRKLVVGLEIGTAKVAALVGEVLPDGMVNIIGVGSCPSR
                     GMDKGGVNDLESVVKCVQRAIDQAELMADCQISSVYLALSGKHISCQNEIGMVPISEE
                     EVTQEDVENVVHTAKSVRVRDEHRVLHVIPQEYAIDYQEGIKNPVGLSGVRMQAKVHL
                     ITCHNDMAKNIVKAVERCGLKVDQLIFAGLASSYSVLTEDERELGVCVVDIGGGTMDI
                     AVYTGGALRHTKVIPYAGNVVTSDIAYAFGTPPSDAEAIKVRHGCALGSIVGKDESVE
                     VPSVGGRPPRSLQRQTLAEVIEPRYTELLNLVNEEILQLQEKLRQQGVKHHLAAGIVL
                     TGGAAQIEGLAACAQRVFHTQVRIGAPLNITGLTDYAQEPYYSTAVGLLHYGKESHLN
                     GEAEVEKRVTASVGSWIKRLNSWLRKEF"
     gene            104966..106117
                     /gene="ftsZ"
                     /note="synonyms: sfiB, sulB"
     CDS             104966..106117
                     /gene="ftsZ"
                     /note="ORF_ID:o111#7
                     similar to SwissProt Accession Number P06138"
                     /codon_start=1
                     /transl_table=11
                     /product="Cell division protein FtsZ."
                     /protein_id="BAB96663.1"
                     /db_xref="GI:21321976"
                     /translation="MFEPMELTNDAVIKVIGVGGGGGNAVEHMVRERIEGVEFFAVNT
                     DAQALRKTAVGQTIQIGSGITKGLGAGANPEVGRNAADEDRDALRAALEGADMVFIAA
                     GMGGGTGTGAAPVVAEVAKDLGILTVAVVTKPFNFEGKKRMAFAEQGITELSKHVNSL
                     ITIPNDKLLKVLGRGISLLDAFGAANDVLKGAVQGIAELITRPGLMNVDFADVRTVMS
                     EMGHAMMGSGVASGEDRAEEAAEMAISSPLLEDIDLSGARGVLVNITAGFDLRLDEFE
                     TVGNTIRAFASDNATVVIGTSLDPDMNDELRVTVVATGIGMDKRPEITLVTNKQVQQP
                     VMDRYQQHGMAPLTQEQKPVAKVVNDNAPQTAKEPDYLDIPAFLRKQAD"
     gene            106218..107135
                     /gene="asmB"
                     /note="synonyms: envA, lpxC"
     CDS             106218..107135
                     /gene="asmB"
                     /note="ORF_ID:o111#8
                     similar to SwissProt Accession Number P07652"
                     /codon_start=1
                     /transl_table=11
                     /product="Udp-3-o-[3-hydroxymyristoyl] n-acetylglucosamine
                     deacetylase (EC 3.5.1.-) (EnvA protein)."
                     /protein_id="BAB96664.1"
                     /db_xref="GI:21321977"
                     /translation="MIKQRTLKRIVQATGVGLHTGKKVTLTLRPAPANTGVIYRRTDL
                     NPPVDFPADAKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIVIEVNAPEIP
                     IMDGSAAPFVYLLLDAGIDELNCAKKFVRIKETVRVEDGDKWAEFKPYNGFSLDFTID
                     FNHPAIDSSNQRYAMNFSADAFMRQISRARTFGFMRDIEYLQSRGLCLGGSFDCAIVV
                     DDYRVLNEDGLRFEDEFVRHKMLDAIGDLFMCGHNIIGAFTAYKSGHALNNKLLQAVL
                     AKQEAWEYVTFQDDAELPLAFKAPSAVLA"
     gene            107435..107878
                     /gene="yacA"
     CDS             107435..107878
                     /gene="yacA"
                     /note="ORF_ID:o111#9
                     similar to PIR Accession Number B28381"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical 16k protein (eneA-secA intergenic
                     region)."
                     /protein_id="BAB96665.1"
                     /db_xref="GI:21321978"
                     /translation="MVAASLGLPALSNAAEPNAPAKATTRNHEPSAKVNFGQLALLEA
                     NTRRPNSNYSVDYWHQHAIRTVIRHLSFAMAPQTLPVAEESLPLQAQHLALLDTLSAL
                     LTQEGTPSEKGYRIDYAHFTPQAKFSTPVWISQAQGIRAGPQRLT"
     gene            107940..110645
                     /gene="azi"
                     /note="synonyms: pea, prlD, secA"
     CDS             107940..110645
                     /gene="azi"
                     /note="ORF_ID:o111#10
                     similar to SwissProt Accession Number P10408"
                     /codon_start=1
                     /transl_table=11
                     /product="Preprotein translocase SecA subunit."
                     /protein_id="BAB96666.1"
                     /db_xref="GI:21321979"
                     /translation="MLIKLLTKVFGSRNDRTLRRMRKVVNIINAMEPEMEKLSDEELK
                     GKTAEFRARLEKGEVLENLIPEAFAVVREASKRVFGMRHFDVQLLGGMVLNERCIAEM
                     RTGEGKTLTATLPAYLNALTGKGVHVVTVNDYLAQRDAENNRPLFEFLGLTVGINLPG
                     MPAPAKREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDE
                     ARTPLIISGPAEDSSEMYKRVNKIIPHLIRQEKEDSETFQGEGHFSVDEKSRQVNLTE
                     RGLVLIEELLVKEGIMDEGESLYSPANIMLMHHVTAALRAHALFTRDVDYIVKDGEVI
                     IVDEHTGRTMQGRRWSDGLHQAVEAKEGVQIQNENQTLASITFQNYFRLYEKLAGMTG
                     TADTEAFEFSSIYKLDTVVVPTNRPMIRKDLPDLVYMTEAEKIQAIIEDIKERTAKGQ
                     PVLVGTISIEKSELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPAAVTIATNMAG
                     RGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRR
                     IDNQLRGRSGRQGDAGSSRFYLSMEDALMRIFASDRVSGMMRKLGMKPGEAIEHPWVT
                     KAIANAQRKVESRNFDIRKQLLEYDDVANDQRRAIYSQRNELLDVSDVSETINSIRED
                     VFKATIDAYIPPQSLEEMWDIPGLQERLKNDFDLDLPIAEWLDKEPELHEETLRDGIL
                     AQSIEVYQRKEEVVGAEMMRHFEKGVMLQTLDSLWKEHLAAMDYLRQGIHLRGYAQKD
                     PKQEYKRESFSMFAAMLESLKYEVISTLSKVQVRMPEEVEELEQQRRMEAERLAQMQQ
                     LSHQDDDSAAAAALAAQTGERKVGRNDPCPCGSGKKYKQCHGRLQ"
     gene            110705..111094
                     /gene="mutT"
     CDS             110705..111094
                     /gene="mutT"
                     /note="ORF_ID:o111#11
                     similar to PIR Accession Number A27890"
                     /codon_start=1
                     /transl_table=11
                     /product="Mutator MutT (AT-GC transversion)."
                     /protein_id="BAB96667.1"
                     /db_xref="GI:21321980"
                     /translation="MKKLQIAVGIIRNENNEIFITRRAADAHMANKLEFPGGKIEMGE
                     TPEQAVVRELQEEVGITPQHFSLFEKLEYEFPDRHITLWFWLVERWEGEPWGKEGQPG
                     EWMSLVGLNADDFPPANEPVIAKLKRL"
     gene            complement(111310..111408)
                     /gene="yacG"
     CDS             complement(111310..>111408)
                     /gene="yacG"
                     /note="ORF_ID:o111#12
                     similar to SwissProt Accession Number P36681"
                     /codon_start=1
                     /transl_table=11
                     /product="Hypothetical 5.8 kd protein in mutT-guaC
                     intergenic region."
                     /protein_id="BAB96668.1"
                     /db_xref="GI:21321981"
                     /translation="LIDLGEWAAEEKRIPSSGDLSESDDWSEEPKQ"
BASE COUNT    26083 a  28055 c  30531 g  26739 t
ORIGIN      
        1 atgcgagtgt tgaagttcgg cggtacatca ttggcaaatg cagaacgttt tctgcgtgtt
       61 gccgatattc tggaaagcaa tgccaggcag gggcaggtgg ccaccgtcct ctctgcccct
      121 gccaaaatca ccaaccacct ggtggcgatg attgaaaaaa ccattagcgg ccaggatgct
      181 ttacccaata tcagcgatgc cgaacgtatt tttgccgaac ttttgacggg actcgccgcc
      241 gcccagccgg ggttcccgtt ggcgcaattg aaaacattcg tcgatcagga atttgcccaa
      301 ataaaacatg tcctgcatgg cattagtttg ttggggcagt gcccggatag catcaacgct
      361 gcgctgattt gccgtggcga gaagatgtcg atcgccatta tggccggcgt attagaagcg
      421 cgcggtcaca acgttactgt tatcgatccg gtcgaaaaac tgctggcagt ggggcattac
      481 ctcgaatcca ccgtcgatat tgccgagtcc acccgccgta tagcggcaag ccgcattccg
      541 gctgatcaca tggtgctgat ggcaggtttc accgccggta atgagaaagg cgaactggtg
      601 gtgcttggac gcaacggttc cgactactct gctgcggtgc tggctgcctg tttacgcgcc
      661 gattgttgcg agatttggac ggacgttaac ggggtctata cctgcgaccc gcgtcaggtg
      721 cccgacgcga ggttgttgaa gtcgatgtcc taccaggaag cgatggagct ttcctacttc
      781 ggcgctaaag ttcttcaccc ccgcaccatt acccccatcg cccagttcca gatcccttgc
      841 ctgattaaaa ataccggaaa tcctcaagca ccaggtacgc tcattggtgc aagccgtgat
      901 gaagacgaat taccggtcaa gggcatttcc aatctgaata acatggcaat gttcagcgtt
      961 tctggtccgg ggatgaaagg gatggtcggc atggcggcgc gcgtctttgc agcgatgtca
     1021 cgcgcccgta tttccgtggt gctgattacg caatcatctt ccgaatacag catcagtttc
     1081 tgcgttccac aaagcgactg tgtgcgagct gaacgggcaa tgctggaaga gttctaccta
     1141 gaactgaaag aaggcttact ggagccgctg gcagtggcgg aacggctggc cattatctcg
     1201 gtggtaggtg atggtttgcg caccttgcgt gggatctcgg cgaaattctt tgccgcactg
     1261 gcccgcgcca atatcaacat tgtcgccatt gctcagggat cttctgaacg ctcaatctct
     1321 gtcgtggtaa ataacgatga tgcgaccact ggcgtgcgcg ttactcatca gatgctgttc
     1381 aataccgatc aggttatcga agtgtttgtg attggcgtcg gtggcgttgg cggtgcgctg
     1441 ctggagcaac tgaagcgtca gcaaagctgg ctgaagaata aacatatcga cttacgtgtc
     1501 tgcggtgttg ccaactcgaa ggctctgctc accaatgtac atggccttaa tctggaaaac
     1561 tggcaggagg aactggcgca agccaaagag ccgtttaatc tcgggcgctt aattcgcctc
     1621 gtgaaagaat atcatctgct gaacccggtc attgttaact gcacttccag ccaggcagtg
     1681 gcggatcaat atgccgactt cctgcgcgaa ggtttccacg ttgtcacgcc gaacaaaaag
     1741 gccaacacct cgtcgatgga ttactaccat cagttgcgtt atgcggcgga aaaatcgcgg
     1801 cgtaaattcc tctatgacat caacgttggg gctggattac cggttattga gaacctgcaa
     1861 aatctgctca atgcaggtga tgaattgatg aaattctccg gcattctttc tggttcgctt
     1921 tcttatatct tcggcaagtt agacgaaggc atgagtttct ccgaggcgac ccggctggcg
     1981 cgggaaatgg gttataccga accggacccg cgagatgatc tttctggtat ggatgtggcg
     2041 cgtaaactat tgattctcgc tcgtgaaacg ggacgtgaac tggagctggc ggatattgaa
     2101 attgaacctg tgctgcccgc agagtttaac gccgagggtg atgttgccgc ttttatggcg
     2161 aatctgtcac aactcgacga tctctttgcc gcgcgcgtgg cgaaggcccg tgatgaagga
     2221 aaagttttgc gctatgttgg caatattgat gaagatggcg tctgccgcgt gaagattgcc
     2281 gaagtggatg gtaatgatcc gctgttcaaa gtgaaaaatg gcgaaaacgc cctggccttc
     2341 tatagccact attatcagcc gctgccgttg gtactgcgcg gatatggtgc gggcaatgac
     2401 gttacagctg ccggtgtctt tgctgatctg ctacgtaccc tctcatggaa gttaggagtc
     2461 tgacatggtt aaagtttatg ccccggcttc cagtgccaat atgagcgtcg ggtttgatgt
     2521 gctcggggcg gcggtgacac ctgttgatgg tgcattgctc ggagatgtag tcacggttga
     2581 ggcggcacag acattcagtc tcaacaacct cggacgcttt gccgataagc tgccgtcaga
     2641 accacgggaa aatatcgttt atcagtgctg ggagcgtttt tgccaggaac tgggtaagca
     2701 aattccagtg gcgatgaccc tggaaaagaa tatgccgatc ggttcgggct taggctccag
     2761 tgcctgttcg gtggtcgcgg cgctgatggc gatgaatgaa cactgcggca agccgcttaa
     2821 tgacactcgt ttgctggctt tgatgggcga gctggaaggc cgtatctccg gcagcattca
     2881 ttacgacaac gtggcaccgt gttttctcgg tggtatgcag ttgatgatcg aagaaaacga
     2941 catcatcagc cagcaagtgc agggtttgat gagtggctgt gggtgctcgc gtatccgggg
     3001 attaaagtct cgacggcaga agcagggcta tttaccggcg cagtatcgcc gccaggattg
     3061 cattgcgcac gggcgacatc tggcaggctt cattcacgcc tgctattccc gtcagcctga
     3121 gcttgccgcg aagctgatga aagatgttat cgctgaaccc taccgtgaac ggttactgcc
     3181 aggcttccgg caggcgcggc aggcggtcgc ggaaatcggc gcggtagcga gcggtatctc
     3241 cggctccggc ccgaccttgt tcgctctgtg tgacaagccg gaaaccgccc agcgcgttgc
     3301 cgactggttg ggtaagaact acctgcaaaa tcaggaaggt tttgttcata tttgccggct
     3361 ggatacggcg ggcgcacgag tactggaaaa ctaaatgaaa ctctacaatc tgaaagatca
     3421 caacgagcag gtcagctttg cgcaagccgt aacccagggg ttgggcaaaa atcaggggct
     3481 gttttttccg cacgacctgc cggaattcag cctgactgaa attgatgaga tgctgaagct
     3541 ggattttgtc acccgcagtg cgaagatcct ctcggcgttt attggtgatg aaatcccaca
     3601 ggaaatcctg gaagagcgcg tgcgcgcggc gtttgccttc ccggctccgg tcgccaatgt
     3661 tgaaagcgat gtcggttgtc tggaattgtt ccacgggcca acgctggcat ttaaagattt
     3721 cggcggtcgc tttatggcac aaatgctgac ccatattgcg ggtgataagc cagtgaccat
     3781 tctgaccgcg acctccggtg ataccggagc ggcagtggct catgctttct acggtttacc
     3841 gaatgtgaaa gtggttatcc tctatccacg aggcaaaatc agtccactgc aagaaaaact
     3901 gttctgtaca ttgggcggca atatcgaaac tgttgccatc gacggcgatt tcgatgcctg
     3961 tcaggcgctg gtgaagcagg cgtttgatga tgaagaactg aaagtggcgc tagggttaaa
     4021 ctcggctaac tcgattaaca tcagccgttt gctggcgcag atttgctact actttgaagc
     4081 tgttgcgcag ctgccgcagg agacgcgcaa ccagctggtt gtctcggtgc caagcggaaa
     4141 cttcggcgat ttgacggcgg gtctgctggc gaagtcactc ggtctgccgg tgaaacgttt
     4201 tattgctgcg accaacgtga acgataccgt gccacgtttc ctgcacgacg gtcagtggtc
     4261 acccaaagcg actcaggcga cgttatccaa cgcgatggac gtgagtcagc cgaacaactg
     4321 gccgcgtgtg gaagagttgt tccgccgcaa aatctggcaa ctgaaagagc tgggttatgc
     4381 agccgtggat gatgaaacca cgcaacagac aatgcgtgag ttaaaagaac tgggctacac
     4441 ttcggagccg cacgctgccg tagcttatcg tgcgctgcgt gatcagttga atccaggcga
     4501 atatggcttg ttcctcggca ccgcgcatcc ggcgaaattt aaagagagcg tggaagcgat
     4561 tctcggtgaa acgttggatc tgccaaaaga gctggcagaa cgtgctgatt tacccttgct
     4621 ttcacataat ctgcccgccg attttgctgc gttgcgtaaa ttgatgatga atcatcagta
     4681 aaatctattc attatctcaa tcaggccggg tttgctttta tgcagcccgg cttttttatg
     4741 aagaaattat ggagaaaaat gacagggaaa aaggagaaat tctcaataaa tgcggtaact
     4801 tagagattag gattgcggag aataacaacc gccgttctca tcgagtaatc tccggatatc
     4861 gacccataac gggcaatgat aaaaggagta acctgtgaaa aagatgcaat ctatcgtact
     4921 cgcactttcc ctggttctgg tcgctcccat ggcagcacag gctgcggaaa ttacgttagt
     4981 cccgtcagta aaattacaga taggcgatcg tgataatcgt ggctattact gggatggagg
     5041 tcactggcgc gaccacggct ggtggaaaca acattatgaa tggcgaggca atcgctggca
     5101 cctacacgga ccgccgccac cgccgcgcca ccataagaaa gctcctcatg atcatcacgg
     5161 cggtcatggt cctggcaaac atcaccgcta aatgacaaat gccgggtaac aatccggcat
     5221 tcagcgcctg atgcgacgct ggcgcgtctt atcaggccta cgttaattct gcaatatatt
     5281 gaatctgcat gcttttgtag gcaggataag gcgttcacgc cgcatccggc attgactgca
     5341 aacttaacgc tgctcgtagc gtttaaacac cagttcgcca ttgctggagg aatcttcatc
     5401 aaagaagtaa ccttcgctat taaaaccagt cagttgctct ggtttggtca gccgattttc
     5461 aataatgaaa cgactcatca gaccgcgtgc tttcttagcg tagaagctga tgatcttaaa
     5521 tttgccgttc ttctcatcga ggaacaccgg cttgataatc tcggcattca atttcttcgg
     5581 cttcaccgat ttaaaatact catctgacgc cagattaatc accacattat cgccttgtgc
     5641 tgcgagcgcc tcgttcagct tgttggtgat gatatctccc cagaattgat acagatcttt
     5701 ccctcgggca ttctcaagac ggatccccat ttccagacga taaggctgca ttaaatcgag
     5761 cgggcggagt acgccataca agccggaaag cattcgcaaa tgctgttggg caaaatcgaa
     5821 atcgtcttcg ctgaaggttt cggcctgcaa gccggtgtag acatcacctt taaacgccag
     5881 aatcgcctgg cgggcattcg ccggcgtgaa atctggctgc cagtcatgaa agcgagcggc
     5941 gttgataccc gccagtttgt cgctgatgcg catcagcgtg ctaatctgcg gaggcgtcag
     6001 tttccgcgcc tcatggatca actgctggga attgtctaac agctccggca gcgtatagcg
     6061 cgtggtggtc aacgggcttt ggtaatcaag cgttttcgca ggtgaaataa gaatcagcat
     6121 atccagtcct tgcaggaaat ttatgccgac tttagcaaaa aatgagaatg agttgatcga
     6181 tagttgtgat tactcctgcg aaacatcatc ccacgcgtcc ggagaaagct ggcgaccgat
     6241 atccggataa cgcaatggat caaacaccgg gcgcacgccg agtttacgct ggcgtagata
     6301 atcactggca atggtatgaa ccacaggcga gagcagtaaa atggcggtca aattggtaat
     6361 agccatgcag gccattatga tatctgccag ttgccacatc agcggaaggc ttagcaaggt
     6421 gccgccgatg accgttgcga aggtgcagat ccgcaaacac cagatcgctt tagggttgtt
     6481 caggcgtaaa aagaagagat tgttttcggc ataaatgtag ttggcaacga tggagctgaa
     6541 ggcaaacaga ataaccacaa gggtaacaaa ctcagcaccc caggaaccca ttagcacccg
     6601 catcgccttc tggataagct gaataccttc cagcggcatg taggttgtgc cgttacccgc
     6661 cagtaatatc agcatggcgc ttgccgtaca gatgaccagg gtgtcgataa aaatgccaat
     6721 catctggaca atcccttgcg ctgccggatg cggaggccag gacgccgctg ccgctgccgc
     6781 gtttggcgtc gaacccattc ccgcctcatt ggaaaacata ctgcgctgaa aaccgttagt
     6841 aatcgcctgg cttaaggtat atcccgccgc gccgcctgcc gcttcctgcc agccaaaagc
     6901 actctcaaaa atagaccaaa tgacgtgggg aagttgcccg atattcatta cgcaaattac
     6961 caggctggtc agtacccaga ttatcgccat caacgggaca aagccctgca tgagccgggc
     7021 gacgccatga agaccgcgag tgattgccag cagagtaaag acagcgagaa taatgcctgt
     7081 caccagcggg ggaaaatcaa aagaaaaact cagggcgcgg gcaacggcgt tcgcttgaac
     7141 tccgctgaaa attatgccat aggcgatgag caaaaagacg gcgaacagaa cgcccatcca
     7201 gcgcatcccc agcccgcgcg ccatatacca tgccggtccg ccacgaaact gcccattgac
     7261 gtcacgttct ttataaagtt gtgccagaga acattcggca aacgaggtcg ccatgccgat
     7321 aaacgcggca acccacatcc aaaagacggc tccaggtcca ccggcggtaa tagccagcgc
     7381 aacgccggcc aggttgccgc tacccacgcg cgccgcaaga ctggtacaca atgactgaaa
     7441 tgaggttaaa ccgcctggct gtggatgaat gctattttta agacttttgc caaactggcg
     7501 gatgtagcga aactgcacaa atccggtgcg aaaagtgaac caacaacctg cgccgaagag
     7561 caggtaaatc attaccgatc cccaaaggac gctgttaatg aaggagaaaa aatctggcat
     7621 gcatatccct cttattgccg gtcgcgatga ctttcctgtg taaacgttac caattgttta
     7681 agaagtatat acgctacgag gtacttgata acttctgcgt agcatacatg aggttttgta
     7741 taaaaatggc gggcgatatc aacgcagtgt cagaaatccg aaacagtctc gcctggcgat
     7801 aaccgtcttg tcggcggttg cgctgacgtt gcgtcgtgat atcatcaggg cagaccggtt
     7861 acatccccct aacaagctgt ttaaagagaa atactatcat gacggacaaa ttgacctccc
     7921 ttcgtcagta caccaccgta gtggccgaca ctggggacat cgcggcaatg aagctgtatc
     7981 aaccgcagga tgccacaacc aacccttctc tcattcttaa cgcagcgcag attccggaat
     8041 accgtaagtt gattgatgat gctgtcgcct gggcgaaaca gcagagcaac gatcgcgcgc
     8101 agcagatcgt ggacgcgacc gacaaactgg cagtaaatat tggtctggaa atcctgaaac
     8161 tggttccggg ccgtatctca actgaagttg atgcgcgtct ttcctatgac accgaagcgt
     8221 caattgcgaa agcaaaacgc ctgatcaaac tctacaacga tgctggtatt agcaacgatc
     8281 gtattctgat caaactggct tctacctggc agggtatccg tgctgcagaa cagctggaaa
     8341 aagaaggcat caactgtaac ctgaccctgc tgttctcctt cgctcaggct cgtgcttgtg
     8401 cggaagcggg cgtgttcctg atctcgccgt ttgttggccg tattcttgac tggtacaaag
     8461 cgaataccga taagaaagag tacgctccgg cagaagatcc gggcgtggtt tctgtatctg
     8521 aaatctacca gtactacaaa gagcacggtt atgaaaccgt ggttatgggc gcaagcttcc
     8581 gtaacatcgg cgaaattctg gaactggcag gctgcgaccg tctgaccatc gcaccggcac
     8641 tgctgaaaga gctggcggag agcgaagggg ctatcgaacg taaactgtct tacaccggcg
     8701 aagtgaaagc gcgtccggcg cgtatcactg agtccgagtt cctgtggcag cacaaccagg
     8761 atccaatggc agtagataaa ctggcggaag gtatccgtaa gtttgctatt gaccaggaaa
     8821 aactggaaaa aatgatcggc gatctgctgt aatcattctt agcgtgaccg ggaagtcggt
     8881 cacgctacct cttctgaagc ctgtctgtca ctcccttcgc agtgtatcat tctgtttaac
     8941 gagactgttt aaacggaaaa atcttgatga atactttacg tattggctta gtttccatct
     9001 ctgatcgcgc atccagcggc gtttatcagg ataaaggcat ccctgcgctg gaagaatggc
     9061 tgacatgcgc taaccacgcc gtttgaactg gaaacccgct taatccccga tgagcaggcg
     9121 atcatcgagc aaacgttgtg tgagctggtg gatgaaatga gttgccatct ggtgctcacc
     9181 acgggcggaa ctggcccggc gcgtcgtgac gtaacgcccg atgcgacgct ggcagtagcg
     9241 gaccgcgaga tgcctggctt tggtgaacag atgcgccaga tcagcctgca ttttgtacca
     9301 actgcgatcc tttcgcgtca ggtgggcgtg attcgcaaac aggcgctgat ccttaactta
     9361 cccggtcagc cgaagtctat taaagagacg ctggaaggtg tgaaggacgc tgagggtaac
     9421 gttgtggtac acggtatttt tgccagcgta ccgtactgca ttcagttgct ggaagggcca
     9481 tacgttgaaa cggcaccgga agtggttgca gcattcagac cgaagagtgc aagacgcgac
     9541 gttagcgaat aaaaaatacc cgagcggggg gatctcaaaa caattagtgg gattcaccaa
     9601 tcggcagaac ggtgcgacca aactgctcgt tcagtacttc acccatcgcc agatagattg
     9661 cgctggcacc gcagatcagc ccaatccagc cggcaaagtg gatgattgcg gcgttaccgg
     9721 caatgttacc gatcgccagc agggcaaaca gcacggtcag gctaaagaaa acgaattgca
     9781 gaacgcgtgc gcctttcagc gtgccgaaga acataaacac ggtaaatacg ccccacagac
     9841 ccaggtagac accaaggaac tgtgcatttg gcgcatcggt cagacccagt ttcggcatca
     9901 gcagaatcgc aaccagcgtc agccagaaag aaccgtaaga ggtgaatgcg gttaaaccga
     9961 aagtgttgcc ttttttgtac tccagcagac cagcaaaaat ttgcgcgatg ccgccgtaga
    10021 aaatgcccat ggcaagaata ataccgtcca gagcgaaata acccacgttg tgcaggttaa
    10081 gcagaatggt ggtcatgccg aagcccatca ggcccagcgg tgccggatta gccaacttag
    10141 tgttgcccat aattcctcaa aaatcatcat cgaatgaatg gtgaaataat ttccctgaat
    10201 aactgtagtg ttttcagggc gcggcataat aatcagccag tggggcagtg tctacgatct
    10261 tttgagggga aaatgaaaat tttcccggtt tccggtatca gacctgagtg gcgctaacca
    10321 tccggcgcag gcaggcgatt tgcagtacgg ctggaatcgt cacgcgatag cgtgcgtgac
    10381 cgctttaacc ccatttagtg ccgcacctac aggcctccca gcccgcgccg cgcagcaaac
    10441 catgcccaag tacgctcatt gctgcgtggg tgcgtaaaat gcgggtcagt tggctggaaa
    10501 gcaaatgcga cacacctttt gccaataatt tgtctttcat cagcagcggc agcagctctt
    10561 ccagctcatt caccctggca tcgaccgcgt gcagaaactc ctgcttatgt tcctcgtcca
    10621 ttttcttcca ggtattacgc agaaattgtt ccagtaactg ttgctcaatt tcaaacgtag
    10681 acatctcttt gtcggctttc agcttcaatc gctttgaaac atcgagcaaa atggcccgat
    10741 acaatttacc gtgtccgcgc agtttgttgc gatactatcg ccaccaaaat gctgtaattc
    10801 tccggcaatc agctgccagt tgcggcgatg ttgctcggga tgcccttcca tcgatttaaa
    10861 cagttcgttg cgcatcagta cgctggagag gcgagttttg cctttttcat tatgggtgag
    10921 caatcgggcg aaatttgcca actgttcctc actacaatgc tgaagaaaat ccagatctga
    10981 atcattcagg taattaacat tcattttttg tggcttctat attctggcgt tagtcgtcgc
    11041 cgataatttt cagcgtggcc atatccgatg agttcaccgt atgacccgaa aaggtgattt
    11101 ttgagacgca gcgtttattg tcgttatcgc tcttaatgtt gatccagtca gtggtttgcc
    11161 cttcttttat ttctgaagga atattcaggc tctgacctgg cgctgacggg cggctgtgaa
    11221 ataaaccgat gcaccgctta actgtaaatc gccatggtcg gcagagagtt gtatgcgttt
    11281 cacaatgcga caaacaggaa gtttcagcgc cagatcgttg gtttcgttac gcggcattgc
    11341 aatgcgccga ggagtttatg gtcgtttgcc tgcgccgtgc agcacagcat caggctaatc
    11401 gccaggctgg cggaaatcgt aaaaacggat ttcataagga ttctcttagt gggaagaggt
    11461 agggggatga atacccacta gtttactgct gataaagaga agattcaggc acgtaatctt
    11521 ttctttttat tacaattttt tgatgaatgc cttggctgcg attcattctt tatatgaata
    11581 aaattgctgt caattttacg tcttgtcctg ccatatcgcg aaatttctgc gcaaaagcac
    11641 aaaaaatttt tgcatctccc ccttgatgac gtggtttacg accccattta gtagtcaacc
    11701 gcagtgagtg agtctgcaaa aaaatgaaat tgggcagttg aaaccagacg tttcgcccct
    11761 attacagact cacaaccaca tgatgaccga atatatagtg gagacgttta gatgggtaaa
    11821 ataattggta tcgacctggg tactaccaac tcttgtgtag cgattatgga tggcaccact
    11881 cctcgcgtgc tggagaacgc cgaaggcgat cgcaccacgc cttctatcat tgcctatacc
    11941 caggatggtg aaactctagt tggtcagccg gctaaacgtc aggcagtgac gaacccgcaa
    12001 aacactctgt ttgcgattaa acgcctgatt ggtcgccgct tccaggacga agaagtacag
    12061 cgtgatgttt ccatcatgcc gttcaaaatt attgctgctg ataacggcga cgcatgggtc
    12121 gaagttaaag gccagaaaat ggcaccgccg cagatttctg ctgaagtgct gaaaaaaatg
    12181 aagaaaaccg ctgaagatta cctgggtgaa ccggtaactg aagctgttat caccgtaccg
    12241 gcatacttta acgatgctca gcgtcaggca accaaagacg caggccgtat cgctggtctg
    12301 gaagtaaaac gtatcatcaa cgaaccgacc gcagctgcgc tggcttacgg tctggacaaa
    12361 ggcactggca accgtactat cgcggtttat gacctgggtg gtggtacttt cgatatttct
    12421 attatcgaaa tcgacgaagt tgacggcgaa aaaaccttcg aagttctggc aaccaacggt
    12481 gatacccacc tggggggtga agacttcgac agccgtctga tcaactatct ggttgaagaa
    12541 ttcaagaaag atcagggcat tgacctgcgc aacgatccgc tggcaatgca gcgcctgaaa
    12601 gaagcggcag aaaaagcgaa aatcgaactg tcttccgctc agcagaccga cgttaacctg
    12661 ccatacatca ctgcagacgc gaccggtccg aaacacatga acatcaaagt gactcgtgcg
    12721 aaactggaaa gcctggttga agatctggta aaccgttcca ttgagccgct gaaagttgca
    12781 ctgcaggacg ctggcctgtc cgtatctgat atcgacgacg ttatcctcgt tggtggtcag
    12841 actcgtatgc caatggttca gaagaaagtt gctgagttct ttggtaaaga gccgcgtaaa
    12901 gacgttaacc cggacgaagc tgtagcaatc ggtgctgctg ttcagggtgg tgttctgact
    12961 ggtgacgtaa aagacgtact gctgctggac gttaccccgc tgtctctggg tatcgaaacc
    13021 atgggcggtg tgatgacgac gctgatcgcg aaaaacacca ctatcccgac caagcacagc
    13081 caggtgttct ctaccgctga agacaaccag tctgcggtaa ccatccatgt gctgcagggt
    13141 gaacgtaaac gtgcggctga taacaaatct ctgggtcagt tcaacctaga tggtatcaac
    13201 ccggcaccgc gcggcatgcc gcagatcgaa gttaccttcg atatcgatgc tgacggtatc
    13261 ctgcacgttt ccgcgaaaga taaaaacagc ggtaaagagc agaagatcac catcaaggct
    13321 tcttctggtc tgaacgaaga tgaaatccag aaaatggtac gcgacgcaga agctaacgcc
    13381 gaagctgacc gtaagtttga agagctggta cagactcgca accagggcga ccatctgctg
    13441 cacagcaccc gtaagcaggt tgaagaagca ggcgacaaac tgccggctga cgacaaaact
    13501 gctatcgagt ctgcgctgac tgcactggaa actgctctga aaggtgaaga caaagccgct
    13561 atcgaagcga aaatgcagga actggcacag gtttcccaga aactgatgga aatcgcccag
    13621 cagcaacatg cccagcagca gactgccggt gctgatgctt ctgcaaacaa cgcgaaagat
    13681 gacgatgttg tcgacgctga atttgaagaa gtcaaagaca aaaaataatc gccctataaa
    13741 cgggtaatta tactgacacg ggcgaagggg aatttcctct ccgcccgtgc attcatctag
    13801 gggcaattta aaaaagatgg ctaagcaaga ttattacgag attttaggcg tttccaaaac
    13861 agcggaagag cgtgaaatca gaaaggccta caaacgcctg gccatgaaat accacccgga
    13921 ccgtaaccag ggtgacaaag aggccgaggc gaaatttaaa gagatcaagg aagcttatga
    13981 agttctgacc gactcgcaaa aacgtgcggc atacgatcag tatggtcatg ctgcgtttga
    14041 gcaaggtggc atgggcggcg gcggttttgg cggcggcgca gacttcagcg atatttttgg
    14101 tgacgttttc ggcgatattt ttggcggcgg acgtggtcgt caacgtgcgg cgcgcggtgc
    14161 tgatttacgc tataacatgg agctcaccct cgaagaagct gtacgtggcg tgaccaaaga
    14221 gatccgcatt ccgactctgg aagagtgtga cgtttgccac ggtagcggtg caaaaccagg
    14281 tacacagccg cagacttgtc cgacctgtca tggttctggt caggtgcaga tgcgccaggg
    14341 attcttcgct gtacagcaga cctgtccaca ctgtcagggc cgcggtacgc tgatcaaaga
    14401 tccgtgcaac aaatgtcatg gtcatggtcg tgttgagcgc agcaaaacgc tgtccgttaa
    14461 aatcccggca ggggtggaca ctggagaccg catccgtctt gcgggcgaag gtgaagcggg
    14521 cgagcatggc gcaccggcag gcgatctgta cgttcaggtt caggttaaac agcacccgat
    14581 tttcgagcgt gaaggcaaca acctgtattg cgaagtcccg atcaacttcg ctatggcggc
    14641 gctgggtggc gaaatcgaag taccgaccct tgatggtcgc gtcaaactga aagtgcctgg
    14701 cgaaacccag accggtaagc tattccgtat gcgcggtaaa ggcgtcaagt ctgtccgcgg
    14761 tggcgcacag ggtgatttgc tgtgccgcgt tgtcgtcgaa acaccggtag gcctgaacga
    14821 aaggcagaaa cagctgctgc aagagctgca agaaagcttc ggtggcccaa ccggcgagca
    14881 caacagcccg cgctcaaaga gcttctttga tggtgtgaag aagttttttg acgacctgac
    14941 ccgctaacct ccccaaaagc ctgcccgtgg gcaggcctgg gtaaaaatag ggtgcgttga
    15001 agatatgcga gcacctgtaa agtggcgggg atcactccca taagcgctaa cttaagggtt
    15061 gtggtattac gcctgatatg atttaacgtg ccgatgaatt actctcacga taactggtca
    15121 gcaattctgg cccatattgg taagcccgaa gaactggata cttcggcacg taatgccggg
    15181 gctctaaccc gccgccgcga aattcgtgat gctgcaactc tgctacgtct ggggctggct
    15241 tacggccccg gggggatgtc attacgtgaa gtcactgcat gggctcagct ccatgacgtt
    15301 gcaacattat ctgacgtggc tctcctgaag cggctgcgga atgccgccga ctggtttggc
    15361 atacttgccg cacaaacact tgctgtacgc gccgcagtta cgggttgtac aagcggaaag
    15421 agattgcgtc ttgtcgatgg aacagcaatc agtgcgcccg ggggcggcag cgctgaatgg
    15481 cgactacata tgggatatga tcctcatacc tgtcagttca ctgattttga gctaaccgac
    15541 agcagagacg ctgaacggct ggaccgattt gcgcaaacgg cagacgagat acgcattgct
    15601 gaccggggat tcggttcgcg tcccgaatgt atccgctcac ttgcttttgg agaagctgat
    15661 tatatcgtcc gggttcactg gcgaggattg cgctggttaa ctgcagaagg aatgcgcttt
    15721 gacatgatgg gttttctgcg cgggctggat tgcggtaaga acggtgaaac cactgtaatg
    15781 ataggcaatt caggtaataa aaaagccgga gctccctttc cggcacgtct cattgccgta
    15841 tcacttcctc ccgaaaaagc attaatcagt aaaacccgac tgctcagcga gaatcgtcga
    15901 aaaggacgag tagttcaggc ggaaacgctg gaagcagcgg gccatgtgct attgctaaca
    15961 tcattaccgg aagatgaata ttcagcagag caagtggctg attgttaccg tctgcgatgg
    16021 caaattgaac tggcttttaa gcggctcaaa agtttgctgc acctggatgc tttgcgtgca
    16081 aaggaacctg aactcgcgaa agcgtggata tttgctaatc tactcgccgc atttttaatt
    16141 gacgacataa tccagccatc gctggatttc ccccccagaa gtgccggatc cgaaaagaag
    16201 aactaactcg ttgtggagaa taacaaaaat ggtcatctgg agcttacagg tggccattcg
    16261 tgggacagta tccctgacag cctacaaaac gcaattgaag aacgcgaggc atcgtcttaa
    16321 cgaggcaccg aggcgtcgca ttcttcagat ggttcaaccc ttaagttagc gcttatggga
    16381 tcactccccg ccgttgctct tactcggatt cgtaagccgt gaaaacagca acctccgtct
    16441 ggccagttcg gatgtgaacc tcacagaggt cttttctcgt taccagcgcc gccactacgg
    16501 cggtgataca gatgacgatc agggcgacaa tcatcgcctt atgctgcttc attgctctct
    16561 tctccttgac cttacggtca gtaagaggca ctctacatgt gttcagcata taggaggcct
    16621 cgggttgatg gtaaaatatc actcggggct tttctctatc tgccgttcag ctaatgcctg
    16681 agacagacag cctcaagcac ccgccgctat tatatcgctc tctttaaccc attttgtttt
    16741 atcgattcta atcctgaaga cgcctcgcat ttttgtggcg taatttttta atgatttaat
    16801 tatttaactt taatttatct cttcatcgca attattgacg acaagctgga ttatttttga
    16861 aatattggcc taacaagcat cgccgactga caacaaatta attattactt ttcctaatta
    16921 atccctcagg aatcctcacc ttaagctatg attatctagg cttagggtca ctcgtgagcg
    16981 cttacagccg tcaaaaacgc atctcaccgc tgatggcgca aattcttcaa tagctcgtaa
    17041 aaaacgaatt attcctacac tataatctga ttttaacgat gattcgtgcg gggtaaaata
    17101 gtaaaaacga tctattcacc tgaaagagaa ataaaaagtg aaacatctgc atcgattctt
    17161 tagcagtgat gcctcgggag gcattattct tatcattgcc gctatcctgg cgatgattat
    17221 ggccaacagc ggcgcaacca gtggatggta tcacgacttt ctggagacgc cggttcagct
    17281 ccgggttggt tcactcgaaa tcaacaaaaa catgctgtta tggataaatg acgcgctgat
    17341 ggcggtattt ttcctgttag tcggtctgga agttaaacgt gaactgatgc aaggatcgct
    17401 agccagctta cgccaggccg catttccagt tatcgccgct attggtggga tgattgtgcc
    17461 ggcattactc tatctggctt ttaactatgc cgatccgatt acccgcgaag ggtgggcgat
    17521 cccggcggct actgacattg cttttgcact tggtgtactg gcgctgttgg gaagtcgtgt
    17581 tccgttagcg ctgaagatct ttttgatggc tctggctatt atcgacgatc ttggggccat
    17641 cattatcatc gcattgttct acactaatga cttatcgatg gcctctcttg gcgtcgcggc
    17701 tgtagcaatt gcggtactcg cggtattgaa tctgtgtggt gcacgccgca cgggcgtcta
    17761 tattcttgtt ggcgtggtgt tgtggactgc ggtgttgaaa tcgggggttc acgcaactct
    17821 ggcgggggta attgtcggct tctttattcc tttgaaagag aagcatgggc gttctccagc
    17881 gaagcgactg gagcatgtgt tgcacccgtg ggtggcgtat ctgattttgc cgctgtttgc
    17941 atttgctaat gctggcgttt cactgcaagg cgtcacgctg gatggcttga cctccattct
    18001 gccattgggg atcatcgctg gcttgctgat tggcaaaccg ctggggatta gtctgttctg
    18061 ctggttggcg ctgcgtttga aactggcgca tctgcctgag ggaacgactt atcagcaaat
    18121 tatggtggtg gggatcctgt gcggtatcgg ttttactatg tctatcttta ttgccagcct
    18181 ggcctttggt agcgtagatc cagaactgat taactgggcg aaactcggta tcctggtcgg
    18241 ttctatctct tcggcggtaa ttggatacag ctggttacgc gttcgtttgc gtccatcagt
    18301 ttgacaggac ggtttaccgg ggagccataa acggctccct tttcattgtt atcagggaga
    18361 gaaatgagca tgtctcatat caattacaac cacttgtatt acttctggca tgtctataaa
    18421 gaaggttccg tggttggcgc agcggaggcg ctttatttaa ctccacaaac cattaccgga
    18481 cagattcgag cgctggaaga cgccctgcaa gcgaaattat ttaaacgcaa ggggacgtgg
    18541 tctcgaaccc agcgagctgg agaactggtc tatcgctatg ccgataaaat gttcacctta
    18601 agccaggaaa tgctggatat tgtgaactat cgcaaagaat ccaatttatt gtttgacgtt
    18661 ggcgtggctg atgcactttc caaacgcctg gtcagtagcg tacttaacgc cgcagtggta
    18721 gaaggcgagc ccattcatct tcgctgcttc gaatccaccc acgaaatgct gctggagcaa
    18781 ttaagtcagc ataaactgga gatgatcatt tctgactgtc cgatagactc tacgcagcag
    18841 gaaggcctgt tctccgtgag aattggcgaa tgtggcgtga gtttctggtg tacaaatcca
    18901 ccaccagaaa aaccgttccc ggcttgtctg gaagaacggc gacttttgat tcctgggcga
    18961 cgttcaatgt tagggcgcaa attgcttaac tggtttaact cccagggatt aaacgtagaa
    19021 atcctcggcg agtttgatga tgccgctttg atgaaagctt ggctgcaggt ccttttggtg
    19081 gcgatgcaaa tgcaatcttc gttgccccaa cgctttatgc atatgacttt tatgccgata
    19141 aaactgtcgt agaaattggt cgcgtcgaga atgtgatgga agagtaccat gctatttttg
    19201 ctgagcggat gattcagcac ccggcggtac agcgaatctg caatacggat tattctgcgc
    19261 tttttagtcc agcggtgcgt taatcggcag ctcccccaaa gttaaggtgg gggagataga
    19321 ttagttgtac attaccacga ttttgactcg gctcattatt tgcccgcttg agacattgtt
    19381 tccatatgta cgcgggcgaa taaatagagg aatctgatta cttccttcat ggggatgctg
    19441 aaaagagtag taattgctgg taatgactcc aacttattga tagtgtttta tgttcagata
    19501 atgcccgatg actttgtcat gcagctccac cgattttgag aacgacagcg acttccgtcc
    19561 cagccgtgcc aggtgctgcc tcagattcag gttatgccgc tcaattcgct gcgtatatcg
    19621 cttgctgatt acgtgcagct ttcccttcag gcgggattca tacagcggcc agccatccgt
    19681 catccatatc accacgtcaa agggtgacag caggctcata agacgcccca gcgtcgccat
    19741 agtgcgttca ccgaatacgt gcgcaacaac cgtcttccgg agactgtcat acgcgtaaaa
    19801 cagccagcgc tggcgcgatt tagccccgac atagccccac tgttcgtcca tttccgcgca
    19861 gacgatgacg tcactgcccg gctgtatgcg cgaggttacc gactgcggcc tgagtttttt
    19921 aagtgacgta aaatcgtgtt gaggccaacg cccataatgc gggctgttgc ccggcatcca
    19981 acgccattca tggccatatc aatgattttc tggtgcgtac cgggttgaga agcggtgtaa
    20041 gtgaactgca gttgccatgt tttacggcag tgagagcaga gatagcgctg atgtccggcg
    20101 gtgcttttgc cgttacgcac caccccgtca gtagctgaac aggagggaca gctgatagaa
    20161 acagaagcca ctggagcacc tcaaaaacac catcatacac taaatcagta agttggcagc
    20221 atcacctacc tcaatgtgta tcacaatatc catattcttt gtgggggagt ctggagattg
    20281 agtagatatt cttgttcaga atgtatcagc cgatggttct acgattctta agccacgaag
    20341 agttcagata gtacaacggc atgtctcttt tgactatctg gcaaccggca gtgtgttctc
    20401 tcacgcatca caaaagcagc aggcataaaa aaacccgctt gcgcgggctt tttcacaaag
    20461 cttcagcaaa ttggcgatta agccagtttg ttgatctgtg cagtcaggtt agccttatga
    20521 cgtgcagctt tgtttttgtg gatcagacct ttagcagcct gacggtccac gatcggttgc
    20581 atttcgttaa atgctttctg tgcagcagct ttgtcgccag cttcgatagc tgcgtatact
    20641 ttcttgatga aagtacgcat catagagcga cggcttgcgt tgtgcttacg agccttttca
    20701 gactgaatgg cgcgcttctt agctgatttg atattagcca aggtccaact cccaaatgtg
    20761 ttctatatgg acaattcaaa ggccgaggaa tatgcccttt tagccttctt ttgtcaatgg
    20821 atttgtgcaa ataagcgccg ttaatgtgcc ggcactcgtt acgtagtgat ggcgcaggat
    20881 tctaccagct tgcggggtgt gaatacagct tttccgcgat aaaaattgca gcaggcggtc
    20941 agtttcttcc cgtgatttgc gccatggcaa tgaaaagcca cttctttctg atttcggtac
    21001 tcaatcgccg gttaaccttg accgctgtac aaggtctact cggacgattt tcactgtttt
    21061 gagccagaca tgaagctgat acgcggcata cataatctca gccaggcccc gcaagaaggg
    21121 tgtgtgctga ctattggtaa tttcgacggc gtgcatcgcg gtcatcgcgc gctgttacag
    21181 ggcttgcagg aagaagggcg caagcgcaac ttaccggtga tggtgatgct ttttgaacct
    21241 caaccactgg aactgtttgc taccgataaa gccccggcaa gactgacccg gctgcgggaa
    21301 aaactgcgtt accttgcaga gtgtggcgtt gattacgtgc tgtgcgtgcg tttcgacagg
    21361 cgtttcgcgg cgttaaccgc gcaaaatttc gtcagcgatc ttctggtgaa gcatttgcgc
    21421 gtaaaatttc ttgccgtagg tgatgatttc cctttggcgc tggtcgtgaa ggcgatttct
    21481 tgttattaca gaaagctggc atggaatacg gcttcgatat caccagtacg caaacttttt
    21541 gcagaggtgg cgtgcgcatc agcagcacgg ctgcgtcagg cccttgcgga tgacaatctg
    21601 gctctggcag agagtttact ggggcacccg tttgccatct ccgggcgtgt agtccacggt
    21661 gatgaattag ggcgcactat aggtttcccg acggcgaatg taccgccgcg ccgtcaggtt
    21721 tccccggtga aaggggttta tgcggtagaa gtgctgggcc tcggtgaaaa gccgttaccc
    21781 ggcgtggcaa acatcggaac acgcccaacg gttgccggta ttcgccagca gctggaagtg
    21841 catttgttag atgttgcaat ggacctttac ggtcgccata tacaagtagt gctgcgtaaa
    21901 aaaatacgca atgagcagcg atttgcgtcg ctggacgaac tgaaagcgca gattgcgcgt
    21961 gatgaattaa ccgcccgcga attttttggg ctaacaaaac cggcttaagc ctgttatgta
    22021 atcaaaccga aatacggaac cgagaatctg atgagtgact ataaatcaac cctgaatttg
    22081 ccggaaacag ggttcccgat gcgtggcgat ctcgccaagc gcgaacccgg aatgctggcg
    22141 cgttggactg atgatgatct gtacggcatc atccgtgcgg ctaaaaaagg caaaaaaacc
    22201 ttcattctgc atgatggccc tccttatgcg aatggcagca ttcatattgg tcactcggtt
    22261 aacaagattc tgaaagacat tatcgtgaag tccaaagggc tttccggtta tgactcgccg
    22321 tatgtgcctg gctgggactg ccacggtctg ccgatcgagc tgaaagtcga gcaagaatac
    22381 ggtaagccgg gtgagaaatt caccgccgcc gagttccgcg ccaagtgccg cgaatacgcg
    22441 gcgacccagg ttgacggtca acgcaaagac tttatccgtc tgggcgtgct gggcgactgg
    22501 tcgcacccgt acctgaccat gggacttcaa aactggaagg ccaacatcat ccgcgcgctg
    22561 ggcaaaatca tcggcaacgg tcacctgcac aaaggcgcga agccagttca ctggtgcgtt
    22621 gactgccgtt ctgcgctggc gaagcggaag ttgagtatta cgacaaaact tctccgtcca
    22681 tcgacgttgc tttccagggc agtcgatcag gatgcactga aagcaaaatt tgccgtaagc
    22741 aacgttaacg gcccaatctc gctggtaatc tggaccacca cgccgtggac tctgcctgcc
    22801 aaccgcgcaa tctctattgc accagatttc gactatgcgc tggtgcagat cgacggtcag
    22861 gccgtgattc tggcgaaaga tctggttgaa agcgtaatgc agcgtatcgg cgtgaccgat
    22921 tctcggcacg gtaaaaggtg cggagctgga gccgctgcgt ttacccatcc gtttatgggc
    22981 ttcgacgttc cggcaatcct cggcgatcac gttaccctgg atgccggtac cggtgccgtt
    23041 cacaccgcgc ctggccacgg cccggacgac tatgtgatcg gtcagaaata cggcctggaa
    23101 accgctaacc cggttggccc ggacggcact tatctgccgg gcacttatcc gacgctggat
    23161 ggcgtgaacg tcttcaaagc gaacgacatc gtcgctgcgc tgctgcagga aaaaggcgcg
    23221 ctgctgcacg ttgagaaaat gcagcacagc tatccgtgct gctggcgtca caaaacgccg
    23281 atcatcttcc gcgcgacgcc gcagtggttc gtcagcatgg atcagaaagg tctgcgtgcg
    23341 cagtcactga aagagatcaa aggcgtgcag tggatcccgg actggggcca ggcgcgtatc
    23401 gagtcgatgg ttgctaaccg tcctgactgg tgtatctccc gtcagcgcac ctggggtgta
    23461 ccgatgtcac tgttcgtgca caaagacacg gaagagctgc atccgcgtac ccttgaactg
    23521 atggaagaag tggcaaaacg cgttgaagtc gatggcatcc aggcgtggtg ggatctcgat
    23581 gcgaaagaga tcctcggcga cgaagctgat cagtacgtga aagtgccgga cacattggat
    23641 gtatggtttg actccggatc tacccactct tctgttgttg acgtgcgtcc ggaatttgcc
    23701 ggtcacgcag cggacatgta tctggaaggt tctgaccaac accgcggctg gttcatgtct
    23761 tccctaatga tctccaccgc gatgaagggt aaagcgccgt atcgtcaggt actcacccac
    23821 ggctttaccg tggatggtca gggccgcaag atgtctaaat ccatcggcaa taccgtttcg
    23881 ccgcaggatg tgatgaacaa actgggcgcg gatattctgc gtctgtgggt ggcatcaacc
    23941 gactacaccg gtgaaatggc cgtttctgac gagatcctga aacgtgctgc cgatacgtat
    24001 cgtcgtatcc gtaacaccgc gcgcttcctg ctggcaaacc tgaacggttt tgatccagca
    24061 aaagatatgg tgaaacggag agagatggtg gtactggatc gctgggccgt agttgtgcga
    24121 aagcggcaca ggaagacatc ctcaaggcgt acgaagcata cgatttccac gaagtggtac
    24181 aagcgtctga tgcgcttctg ctccgttgag atgggttcct tctacctcga catcatcaaa
    24241 gaccgtcagt actacgccaa aggacacagt gtggcgcgtc gtagctgcca gactgcgcta
    24301 tatcacatcg cagaagcgct ggtgcgctgg atggcaccaa tcctctcctt caccgctgat
    24361 gaagtgtggg gctacctgcc gggcgaacgt gaaaaatacg tcttcaccgg tgagtggtac
    24421 gaaggcctgt ttggcctggc agacagtgaa gcgatgaacg atgcgttctg ggacgagctg
    24481 ttgaaagtgc gtggcgaagt gaacaaagtc attgagcaag cgcgtgccga caagaaagtg
    24541 ggtggctcgc tggaagcggc agtaaccttg tatgcagaac cggaactgtc ggcgaaactg
    24601 accgcgctgg gcgatgaatt acgatttgtc ctgttgacct ccggcgctac cgttgcagac
    24661 tataacgacg cacctgctga tgctcagcag agcgaagtac tcaaagggct gaaagtcgcg
    24721 ttgagtaaag ccgaaggtga gaagtgccca cgctgctggc actacaccca ggatgtcggc
    24781 aaggtggcgg aacacgcaga aatctgcggc cgctgtgtca gcaacgtcgc cggtgacggt
    24841 gaaaaacgta agtttgcctg atgagtcaat cgatctgttc aacagggcta cgctggctgt
    24901 ggctggtggt agtcgtgctg attatcgatc tgggcagcaa atacctgatc ctccagaact
    24961 ttgctctggg ggatacggtc ccgctgttcc cgtcgcttaa tctgcattat gcgcgtaact
    25021 atggcgcggc gtttagtttc cttgccgata gcggcggctg gcagcgttgg ttctttgccg
    25081 gtattgcgat tggtattagc gtgatcctgg cagtgatgat gtatcgctcg aaggccacgc
    25141 agaagctaaa caatatcgct tacgcgctga ttattggcgg cgcgctgggc aacctgttcg
    25201 accgcctgtg gcacggcttc gttgtcgata tgatcgactt ctacgtcggc gactggcact
    25261 tcgccacctt caaccttgcc gatactgcca tctgtgtcgg tgcggcactg attgtgctgg
    25321 aaggtttttt gccttctaga gcgaaaaaac aataataaac cctgccggat gcgatgctga
    25381 cgcatcttat ccggcctaca gattgctgcg aaatcgtagg ccggataagg cgtttacgcc
    25441 gcatccggca aaaatcctta aatataagag caaacctgca tgtctgaatc tgtacagagc
    25501 aatagcgccg tcctggtgca cttcacgcta aaactcgacg atggcaccac cgccgagtct
    25561 acccgcaaca acggtaaacc ggcgctgttc cgcctgggtg atgcttctct ttctgaaggg
    25621 ctggagcaac acctgttggg gctgaaagtg ggcgataaaa ccaccttctc gttggagcca
    25681 gatgcggcgt ttggcgtgcc gtcaccggac ctgattcagt acttctcccg ccgtgaattt
    25741 atggatgcag gcgagccaga aattggcgca atcatgcttt ttaccgcaat ggatggcagt
    25801 gagatgcctg gcgtgatccg cgaaattaac ggcgactcca ttaccgttga tttcaaccat
    25861 ccgctggccg ggcagaccgt tcattttgat attgaagtgc tggaaatcga tccggcactg
    25921 gaggcgtaac atgcagatcc tgttggccaa cccgcgtggt ttttgtgccg gggtagaccg
    25981 cgctatcagc attgttgaaa acgcgctggc catttacggc gcaccgatat atgtccgtca
    26041 cgaagtggta cataaccgct atgtggtcga tagcttgcgt gagcgtgggg ctatctttat
    26101 tgagcagatt agcgaagtac cggacggcgc gatcctgatt ttctccgcac acggtgtttc
    26161 tcaggcggta cgtaacgaag caaaaagtcg cgatttgacg gtgtttgatg ccacctgtcc
    26221 gctggtgacc aaagtgcata tggaagtcgc ccgcgccagt cgccgtggcg aagaatctat
    26281 tctcatcggt cacgccgggc acccggaagt ggaagggaca atgggccagt acagtaaccc
    26341 ggaaggggga atgtatctgg tcgaatcgcc ggacgatgtg tggaaactga cggtcaaaaa
    26401 cgaagagaag ctctccttta tgacccagac cacgctgtcg gtggatgaca cgtctgatgt
    26461 gatcgacgcg ctgcgtaaac gcttcccgaa aattgtcggt ccgcgcaaag atgacatctg
    26521 ctacgccacg actaaccgtc aggaagcggt acgcgccctg gcagaacagg cggaagttgt
    26581 gttggtggtc ggttcgaaaa actcctccaa ctccaaccgt ctggcggagc tggcccagcg
    26641 tatgggcaaa cgcgcgtttt tgattgacga tgcgaaagac atccaggaag agtgggtgaa
    26701 agaggttaaa tgcgtcggcg tgactgcggg cgcatcggct ccggatattc tggtgcagaa
    26761 tgtggtggca cgtttgcagc agctgggcgg tggtgaagcc attccgctgg aaggccgtga
    26821 agaaaacatt gttttcgaag tgccgaaaga gctgcgtgtc gatattcgtg aagtcgatta
    26881 agtcattagc agcctaagtt atgcgaaaat gccggtcttg ttaccggcat tttttatgga
    26941 gaaaacatgc gtttacctat cttcctcgat actgaccccg gcattgacga tgccgtcgcc
    27001 attgccgccg cgatttttgc acccgaactc gacctgcaac tgatgaccac cgtcgcgggt
    27061 aatgtctcgg ttgagaaaac tacccgcaat gccctgcaac tgctgcattt ctggaatgcg
    27121 gagattccgc tcgcccaagg ggccgctgtg ccactggtac gcgcaccgcg tgatgcggca
    27181 tctgtgcacg gcgaatcggg aatggctggc tacgactttg ttgagcacaa ccgaaagccg
    27241 ctcgggatac cggcgtttct ggcgattcgg gatgccctga tgcgtgcacc agagcctgtt
    27301 accctggtgg ccatcggccc gttaaccaat attgcgctgt tactttcaca atgcccggaa
    27361 tgcaagccgt atattcgccg tctggtgatc atgggtggtt ctgccggacg cggcaactgt
    27421 acgccaaacg ccgagtttaa tattgctgcc gatccagaag ctgctgcctg tgtcttccgc
    27481 agtggtattg aaatcgtcat gtgcggtttg gatgtcacca atcaggcaat attaactcct
    27541 gactatctct ctacactgcc gcagttaaac cgtaccggga aaatgcttca cgccctgttt
    27601 agccactacc gtagcggcag tatgcaaagc ggcttgcgaa tgcacgatct ctgcgccatc
    27661 gcctggctgg tgcgcccgga cctgttcact ctcaaaccct gttttgtggc agtggaaact
    27721 cagggcgaat ttacctcagg cacgacggtg gttgatatcg acggttgcct gggcaagcca
    27781 gccaatgtac aggtggcatt ggatctggat gtgaaaggct tccagcagtg ggtggctgag
    27841 gtgctggctc tggcgtcgta acctgtcaca tgttattggc atgcagtcat tcatcgactc
    27901 atgcctttca ctgatatccc tccctgttta tcattaattt ctaattatca gcgtttttgg
    27961 ctggcggcgt agcgatgcgc tggttactct gaaaacggtc tatgcaaatt aacaaaagag
    28021 aatagctatg catgatgcaa acatccgcgt tgccatcgcg ggagccgggg ggcgtatggg
    28081 ccgccagttg attcaggcgg cgctggcatt agagggcgtg cagttgggcg ctgcgctgga
    28141 gcgtgaagga tcttctttac tgggcagcga cgccggtgag ctggccggag ccgggaaaac
    28201 aggcgttacc gtgcaaagca gcctcgatgc ggtaaaagat gattttgatg tgtttatcga
    28261 ttttacccgt ccggaaggta cgctgaacca tctcgctttt tgtcgccagc atggcaaagg
    28321 gatggtgatc ggcactacgg ggtttgacga agccggtaaa caagcaattc gtgacgccgc
    28381 tgccgatatt gcgattgtct ttgcggccaa ttttagcgtt ggcgttaacg tcatgcttaa
    28441 gctgctggag aaagcagcca aagtgatggg tgactacacc gatatcgaaa ttattgaagc
    28501 acatcataga cataaagttg atgcgccgtc aggcaccgca ctggcaatgg gagaggcgat
    28561 cgcccacgcc cttgataaag atctgaaaga ttgcgcggtc tacagtcgtg aaggccacac
    28621 cggtgaacgt gtgcctggca ccattggttt tgccaccgtg cgtgcaggtg acatcgttgg
    28681 tgaacatacc gcgatgtttg ccgatattgg cgagcgtctg gagatcaccc ataaggcgtc
    28741 cagccgtatg acatttgcta acggcgcggt aagatcggct ttgtggttga gtggtaagga
    28801 aagcggtctt tttgatatgc gagatgtact tgatctcaat aatttgtaac cacaaaatat
    28861 ttgttatggt gcaaaaataa cacatttaat ttattgatta taaagggctt taatttttgg
    28921 cccttttatt tttggtgtta tgtttttaaa ttgtctataa gtgccaaaaa ttacatgttt
    28981 tgtcttctgt ttttgttgtt ttaatgtaaa ttttgaccat ttggtccact tttttctgct
    29041 cgtttttatt tcatgcaatc ttcttgctgc gcaagcgttt tccagaacag gttagatgat
    29101 ctttttgtcg cttaatgcct gtaaaacatg catgagccac aaaataatat aaaaaatccc
    29161 gccattaagt tgacttttag cgcccatatc tccagaatgc cgccgtttgc cagaaattcg
    29221 tcggtaagca gatttgcatt gatttacgtc atcattgtga attaatatgc aaataaagtg
    29281 agtgaatatt ctctggaggg tgttttgatt aagtcagcgc tattggttct ggaagacgga
    29341 acccagtttc acggtcgggc cataggggca acaggttcgg cggttgggga agtcgttttc
    29401 aatacttcaa tgaccggtta tcaagaaatc ctcactgatc cttcctattc tcgtcaaatc
    29461 gttactctta cttatcccca tattggcaat gtcggcacca atgacgccga tgaagaatct
    29521 tctcaggtac atgcacaagg tctggtgatt cgcgacctgc cgctgattgc cagcaacttc
    29581 cgtaataccg aagacctctc ttcttacctg aaacgccata acatcgtggc gattgccgat
    29641 atcgataccc gtaagctgac gcgtttactg cgcgagaaag gcgcacagaa tggctgcatt
    29701 atcgcgggcg ataacccgga tgcggcgctg gcgttagaaa aagcccgcgc gttcccaggt
    29761 ctgaatggca tggatctggc aaaagaagtg accaccgcag aagcctatag ctggacacaa
    29821 gggagctgga cgttgaccgg tggcctgcca gaagcgaaaa aagaagacga gctgccgttc
    29881 cacgtcgtgg cttatgattt tggtgccaag cgcaacatcc tgcggatgct ggtggataga
    29941 ggctgtcgcc tgaccatcgt tccggcgcaa acttctgcgg aagatgtgct gaaaatgaat
    30001 ccagacggca tcttcctctc caacggtcct ggcgacccgg ccccgtgcga ttacgccatt
    30061 accgccatcc agaaattcct cgaaaccgat attccggtat tcggcatctg tctcggtcat
    30121 cagctgctgg cgctggcgag cggtgcgaag actgtcaaaa tgaaatttgg tcaccacggc
    30181 ggcaaccatc cggttaaaga tgtggagaaa aacgtggtaa tgatcaccgc ccagaaccac
    30241 ggttttgcgg tggacgaagc aacattacct gcaaacctgc gtgtcacgca taaatccctg
    30301 ttcgacggta cgttacaggg cattcatcgc accgataaac cggcattcag cttccagggg
    30361 caccctgaag ccagccctgg tccacacgac gccgcgccgt tgttcgacca ctttatcgag
    30421 ttaattgagc agtaccgtaa aaccgctaag taatcaggag taaaagagcc atgccaaaac
    30481 gtacagatat aaaaagtatc ctgattctgg gtgcgggccc gattgttatc ggtcaggcgt
    30541 gtgagtttga ctactctggc gcgcaagcgt gtaaagccct gcgtgaagag ggttaccgcg
    30601 tcattctggt gaactccaac ccggcgacca tcatgaccga cccggaaatg gctgatgcaa
    30661 cctacatcga gccgattcac tgggaagttg tacgcaagat tattgaaaaa gagcgcccgg
    30721 acgcggtgct gccaacgatg ggcggtcaga cggcgctgaa ctgcgcgctg gagctggaac
    30781 gtcagggcgt gttggaagag ttcggtgtca ccatgattgg tgccactgcc gatgcgattg
    30841 ataaagcaga agaccgccgt cgtttcgacg tagcgatgaa gaaaattggt ctggaaaccg
    30901 cgcgttccgg tatcgcacac acgatggaag aagcgctggc ggttgccgct gacgtgggct
    30961 tcccgtgcat tattcgccca tcctttacca tgggcggtag cggcggcggt atcgcttata
    31021 accgtgaaga gtttgaagaa atttgcgccc gcggtctgga tctctctccg accaaagagt
    31081 tgctgattga tgagtcgctg atcggctgga aagagtacga gatggaagtg gtgcgtgata
    31141 aaaacgacaa ctgcatcatc gtctgctcta tcgaaaactt cgatgcgatg ggcatccaca
    31201 ccggtgactc catcactgtc gcgccagccc aaacgctgac cgacaaagaa tatcaaatca
    31261 tgcgtaacgc ctcgatggcg gtgctgcgtg aaatcggcgt tgaaaccggt ggttccaacg
    31321 ttcagtttgc ggtgaacccg aaaaacggtc gtctgattgt tatcgaaatg aacccacgcg
    31381 tgtcccgttc ttcggcgctg gcgtcgaaag cgaccggttt cccgattgct aaagtggcgg
    31441 cgaaactggc ggtgggttac accctcgacg aactgatgaa cgacatcact ggcggacgta
    31501 ctccggcctc cttcgagccg tccatcgact atgtggttac taaaattcct cgcttcaact
    31561 tcgaaaaatt cgccggtgct aacgaccgtc tgaccactca gatgaaatcg gttggcgaag
    31621 tgatggcgat tggtcgcacg cagcaggaat ccctgcaaaa agcgctgcgc ggcctggaag
    31681 tcggtgcgac tggattcgac ccgaaagtga gcctggatga cccggaagcg ttaaccaaaa
    31741 tccgtcgcga actgaaagac gcaggcgcag atcgtatctg gtacatcgcc gatgcgttcc
    31801 gtgcgggcct gtctgtggac ggcgtcttca acctgaccaa cattgaccgc tggttcctgg
    31861 tacagattga agagctggtg cgtctggaag agaaagtggc ggaagtgggc atcactggcc
    31921 tgaacgctga cttcctgcgc cagctgaaac gcaaaggctt tgccgatgcg cgcttggcaa
    31981 aactggcggg cgtacgcgaa gcggaaatcc gtaagctgcg tgaccagtat gacctgcacc
    32041 cggtttataa gcgcgtggat acctgtgcgg cagagttcgc caccgacacc gcttacatgt
    32101 actccactta tgaagaagag tgcgaagcga atccgtctac cgaccgtgaa aaaatcatgg
    32161 tgcttggcgg cggcccgaac cgtatcggtc agggtatcga attcgactac tgttgcgtac
    32221 acgcctcgct ggcgctgcgc gaagacggtt acgaaaccat tatggttaac tgtaacccgg
    32281 aaaccgtctc caccgactac gacacttccg accgcctcta cttcgagccg gtaactctgg
    32341 aagatgtgct ggaaatcgtg cgtatcgaga agccgaaagg cgttatcgtc cagtacggcg
    32401 gtcagacccc gctgaaactg gcgcgcgcgc tggaagctgc tggcgtaccg gttatcggca
    32461 ccagcccgga tgctatcgac cgtgcagaag accgtgaacg cttccagcat gcggttgagc
    32521 gtctgaaact gaaacaaccg gcgaacgcca ccgttaccgc tattgaaatg gcggtagaga
    32581 aggcgaaaga gattggctac ccgctggtgg tacgtccgtc ttacgttctc ggcggtcggg
    32641 cgatggaaat cgtctatgac gaagctgacc tgcgtcgcta cttccagacg gcggtcagcg
    32701 tgtctaacga tgcgccagtg ttgctggacc acttcctcga tgacgcggta gaagttgacg
    32761 tggatgccat ctgcgacggc gaaatggtgc tgattggcgg catcatggag catattgagc
    32821 aggcgggcgt gcactccggt gactccgcat gttctctgcc agcctacacc ttaagtcagg
    32881 aaattcagga tgtgatgcgc cagcaggtgc agaaactggc cttcgaattg caggtgcgcg
    32941 gcctgatgaa cgtgcagttt gcggtgaaaa acaacgaagt ctacctgatt gaagttaacc
    33001 cgcgtgcggc gcgtaccgtt ccgttcgtct ccaaagccac cggcgtaccg ctggcaaaag
    33061 tggcggcgcg cgtgatggct ggcaaatcgc tggctgagca gggcgtaacc aaagaagtta
    33121 tcccgccgta ctactcggtg aaagaagtgg tgctgccgtt caataaattc ccgggcgttg
    33181 acccgctgtt agggccagaa atgcgctcta ccggggaagt catgggcgtg ggccgcacct
    33241 tcgctgaagc gtttgccaaa gcgcagctgg gcagcaactc caccatgaag aaacacggtc
    33301 gtgcgctgct ttccgtgcgc gaaggcgata aagaacgcgt ggtggacctg gcggcaaaac
    33361 tgctgaaaca gggcttcgag ctggatgcga cccacggcac ggcgattgtg ctgggcgaag
    33421 caggtatcaa cccgcgtctg gtaaacaagg tgcatgaagg ccgtccgcac attcaggacc
    33481 gtatcaagaa tggcgaatat acctacatca tcaacaccac ctcaggccgt cgtgcgattg
    33541 aagactcccg cgtgattcgt cgcagtgcgc tgcaatataa agtgcattac gacaccaccc
    33601 tgaacggcgg ctttgccacc gcgatggcgc tgaatgccga tgcgactgaa aaagtaattt
    33661 cggtgcagga aatgcacgca cagatcaaat aatagcgtgt catggcagat atttttcatc
    33721 cgctaatttg atcgaataac taatacggtt ctctgatgag gaccgttttt ttttgcccat
    33781 taagtaaatc ttttggggaa tcgatatttt tgatgacata agcaggattt agctcacact
    33841 tatcgacggt gaagttgcat actatcgata tatccacaat tttaatatgg ccttgtttaa
    33901 ttgcttcaaa acgagtcata gccagacttt taatttgtga aactggagtt cgtatgtgtg
    33961 aaggatatgt tgaaaaacca ctctacttgt taatcgccga atggatgatg gctgaaaatc
    34021 ggtgggtgat agcaatagag agatctctat tcatttcgat attgaacaca gcaaggcggt
    34081 taataccctg acttatattc tgtcggaagt cacagaaata agctgcgaag ttaagatgat
    34141 ccctaataag ctggaagggc ggggatgcca gtgtcagcga ctggttaaag tggtcgatat
    34201 ccatgagcaa atttacgcgc gcctgcgcaa taacagtcgg gaaaaattag tcggtgtaag
    34261 aaagacgccg cgtattcctg ccgttccgct cacggaactt aaccgcgagc agaagtggca
    34321 gatgatgttg tcaaagagat tgcgtcgtta attttatctc gttgataccg ggcgtcctgc
    34381 ttgaccagat gcgatgttgt agcatcttat ccagcaacca ggtcgcatcc ggcaagatca
    34441 ccgtttaggc gtcacatccg tcgtcccctg caaacggggg cgattttcct ccatttgcct
    34501 cagtggctgc gtttcatgta acgatacatg acagcgcccg acaagatcct gatactcttt
    34561 ggtattcaac cgtttccagt gtaactcgtc gtcactaaca ttgcgtacag cgcgggctgg
    34621 cgtacccatc aacaactggc gtttctcgcc gcgaaagccc gctttgacaa agctcatggc
    34681 ggcaacaatg ctctcttcgc caatgaccgc gccatccata atcacgctgt tcatcccgac
    34741 caatgcatcg cgaccaatca aacaaccatg caggatcgct ccgtgcccga tatggccgtt
    34801 ttccccaacg atagtgtcag tgtcgcagta gccatgcata atgcagccat cctgaatatt
    34861 ggctcccgct tgcacgatca accgcccgta gtcaccacgc agtgaggcga gtgggccgat
    34921 gtagacaccg gctcccacaa tcacatcgcc aatcaagacg gcactgggat ggacaaacgc
    34981 cgtcgggtga accaccggaa ttaacccctc aaaggcgtaa tagctcacgg ttgttaacgt
    35041 cctttccaca ccggatcgcg cttctcggca aacgccagcg gcccttcaat ggcatcttcc
    35101 gaatgcagaa ccgatggata gtgtttcaac acgccgctgc gaatatagcg atacgcttct
    35161 tctaccggca tttcgctggt ggtgcggtag atctctttca gcgccgcaat cgccagcggg
    35221 gcgctgttaa ccagctgctg agccagttcg cgggcgttat ccatcagttc cgcctggcta
    35281 accacgcggt tgactatccc ccaacgcagc gcctcttctg cgcccattcg tctgccggtc
    35341 atcaccattt cattgacgat ggcaggcggc aggatcttcg gcagacgcag cacaccgccg
    35401 ctgtcaggaa cgatgcccag tttggcttcc ggcagggcga agctggcgtt atcggcacaa
    35461 acaataaaat ctgccgccag cgccagttca aaggcgccgc caaaggcata gccgttcaca
    35521 gctgcgataa ccggtttgtc gagattgaaa atttcggtta atcccgcaaa accacccgga
    35581 ccaaagtcag catccggtgc ttcgccttct gctgccgctt ttaaatccca gcccgcggaa
    35641 aagaacttct ctccggcacc ggtaataatg gcgacacgta attgcggatc gtcacggaaa
    35701 tttagaaata cttcgcccat ttcaaagctg gtttttgcat caatagcatt cgcttttgga
    35761 cgatcaaggg taatttccag aattgatcca ttgcgggtca gatgtaatga ttcactcatt
    35821 ccttttctcc atttttgctt tttcagggac gacaacatcc ctgcaaaaaa tgcatattgt
    35881 tttagagtgt gattattagc tggcagggta gttccctgct gtttcattta tttcagattc
    35941 tttctaatta ttttccccga gcaattacgt ggcagatctt ttctgatctc cagataagag
    36001 ggcactttaa atttcgccat attttgttcg cagaagcgga aaaattcctc ttcgctcaat
    36061 gtttcacctt cattcagcac cacaaatgct ttgatggctt catcgcgaat cgaatcttta
    36121 atacccacaa ccacgatgtc ctgaattttc gggtgcgcgg cgataatatt ttccagctcc
    36181 acgcaggaga cattctcgcc gccacgttta atcatattgc agcggcgatc gacgaaataa
    36241 aaaaagtcct cttcgtcgcg gtatccggta tcgccggtat gcagccagcc atcggcttcc
    36301 agcactttcg cagtggcttg tgggttgaga aagtactctt tgaagatggt tttcccaggt
    36361 atgcctttaa tgcagatttc accgatctca ccagccggga gcgggcgatt gtgatcgtcg
    36421 cggatctccg cttcgtagca aaaccccacc cgaccaatcg acggccagcg tcgtttatcg
    36481 ccaggacgat caccgataat gcccacaatg gtttccgtca tcccataaga cgtcagcaag
    36541 cgaacgccga agcgttcaca aaacgcatct ttttcctgct ccgacaagtt gagataaaac
    36601 atcacttccc gcaggcggtg ttgctgatcg ttcgctgaag gcggctgtac catcaacgta
    36661 cggatcatca tcggaataca ttcggtaacg gtggcgcggt acttctgtac ctgtccccag
    36721 aaggcgcggg cgctgtattt ctcgaccagc acaaaggtgg ccccggcaga aaacgccgcc
    36781 atcgccgcag tacactggca atcgatatga aacgcaggca ttaccgtcag gtagacgtca
    36841 tcgtcacgca gtgcacactg ccaggcggag taatatccag cgaagcgcag gttgtaatgg
    36901 gtaatcacca cacctttcgg tcgggaggtg gtgccggagg tgaagagaat ttccgccgta
    36961 tcgtcagtcg atagcggcgg tgcatagcac aaggtggcag gttgttgatt tttcagttga
    37021 gtaaacgaac tcacgccatc atcagcggga agtgccacat ctgtcaggca aatgtgccgc
    37081 aattgagtgg catcttcctg ctgaatctgt tgatacatag gatagaattg cgcactggtc
    37141 accagcaggc acgcctggct attttgcagg atccacgcgc tttcctcgca caacaggcgg
    37201 gcgttaatcg gcaccataat cgcgccaatt tttgccagcc cgaaccagca aaagataaat
    37261 tccgggcagt tgtcgagatg tagtgcaacc ttgtcgcctt tgcgaatccc cagcgtataa
    37321 aacaggtttg ccgtgcggtt aatctcctga tttaactcaa gataactata ccggttaacg
    37381 actccgccgc tggattcaca aatcagcgcc gttttatgac cgtaaacgtc cgcaagatcg
    37441 tcccacattt gacgtagatg ttgtccgcca atgatatcca ttgcacctct atccattttt
    37501 gttcgtttgt tattgggcgg gcgctagtca ggcaagccga ctgacgccac gcgtttagtc
    37561 ctcaactttg gccagacctt tgctgaccaa ctcctgaatg tcgttttcgc tgtagccgat
    37621 atttttcaaa atggcagccg tgtccatgcc atgtgagggc attccgcgcc agatttgtcc
    37681 ggggttattt ttgaatttcg gcatgatgtt cggccctttg caggtgcgac catccatcgt
    37741 ttgccactga gtgattgatt cgcgagccac atactgtgga ttgctttcca gttccggtac
    37801 ggtcagcact ttggcgcagg cgatattcag ttcagcaaag cgttctttta cttccgcgat
    37861 ggtatgtgtc gccagccagg catcgagttt ctcttcaacc agtgggccgt aagggcattc
    37921 gatacggtgg ataagctgag tgccttccgg gatttctggc gtgccaagca gatgtgcgag
    37981 gccaatatct ttaaagcact cttcaatttg ggtaatgccc accagttcca tcacgatgta
    38041 gccgtcggca catttataca gaccgcaacc ggcgtagtag ggatctttac ctttgctcat
    38101 gcgcgggcac atttcgccgc cgttgaagta atccatcatg aagtactggc ccatacgcag
    38161 catcacttca tacatggcga tgtcgatact ttcgccttta ccggtttcac gcactttatg
    38221 cagtgctgcc agcgccgccg tggtggcggt caggccagaa aagtaatcgg cggtatacgg
    38281 gaaggcaggc attggctggt caacatcacc gttctgaatc aggtaaccac taaaggcctg
    38341 ggcgatagtg ttataggccg gaagattggt gtactcctcg gtgccgtact gaccaaaacc
    38401 ggacaggtga gcgataacca gtttcgggtt gtgctgccac agtacttcat cggtaatgcc
    38461 acgacgggca aaggccggac ctttactggc ttcgatgaag atatcggtgg tttccattaa
    38521 tttcagaaac gcttcgcggc cttcatcttt gaaaatattt aacgacagcg cgtgcaaatt
    38581 gcggcgggag agttgcgggt agttcggttg aacgcgaatg gtgtcggccc aggcgacgtt
    38641 ctcgatccag ataacttccg cgccccattc tgcgaacatt tgcccggcaa acggtccggc
    38701 gatttcgata ccggagaaga caacgcgcaa tccggccaac ggcccgaatt tcggcatggg
    38761 tagatgatcc attatttgct cctgaaaaat ttatgtagcg catgactgcc ggatgcggcg
    38821 taaacgcttt atccggccta cattcgtgct cccgtaggcc tgataagacg catcagcgcg
    38881 gcatcaggca gcgcacggac ttagcggtat tgcttcagca ccgcacgacc cagcgtcagg
    38941 atctgcattt cgtcagatcc cccggagacg cggtctacac gcagatcacg ccagaagcgg
    39001 ctgatgcggt ggttgcccgc aatcccgaca ccgcccagca cctgcattgc gctatccaca
    39061 acttcaaatg ccgcattggc gcagaagtat ttgcacatcg ctgcatcgcc agaggtgatg
    39121 gtgccgttgt ctgctttcca cgctgcttca tacagcatgt ttttcatgga gtttaatttg
    39181 atcgccatgt gggcgaattt ttcctgaatc aactggaaac gaccaatagc ctcgccaaac
    39241 tgcacgcgct gattggcgta gcgcgccgca tcttcaaagg cgcacatcgc cgtaccgtag
    39301 ttggtgaggg ctaccaggaa acgttcatgg tcgaactctt ctttgacgcg gttaaagccg
    39361 ttaccttccc gaccgaacat gtctttctcg tccagttcca cgtcgtcaaa ggtgatttca
    39421 cagcagctat ccatacgcag accgagcttt tcaagtttgg tcactttgat gcccggtttg
    39481 ctcatatcaa caaaccatcc ggtgtagaca ggtttgtccg gagaagcccc gtcgcgcgcc
    39541 atcaccacga tgtacggggt gtaggcgctg ctggtaataa aacacttact accattaaga
    39601 taaatcttac catttttacg ggtataagtc gttttcaggc tacccacgtc ggagcccgcg
    39661 cccggttcgg taatcgctga gttccacatc tgcttaccgg tgccgcggaa agccataatt
    39721 ttgtcgatct gctcttgtgt gccttcgcgc aggaaggtgt tgaacccgcc cggcaactgg
    39781 tacagcacat aggttggtgc ccccagacgt cccagctcca tccacacggc ggcgagagta
    39841 acaaaccccg cgtccagacc accgtgctct tcagggatca gcagactgtc gatacccata
    39901 tccgccagtg ctttgacaaa acgttccggg tagacgctgt cacggtcgca ctcggcaaaa
    39961 taggcctccc agttttcgct ggccatcagt tcgcggatac cggcgacaaa cagttcctgc
    40021 tcatcattta aattaaaatc catctttcaa cctcttgata ttttgggggg ttaattaatc
    40081 tttccagttc tgtttcgcgt ctttaataaa ggagagcgtc accataatgt tgacgaagaa
    40141 cagcgggcat cctccggcga taatggcggt ttgaatcggt ttcaggccgc cgagcgccag
    40201 cagaacaata ccgataatgc caaccagaat tgaccaaccg atacgcacca gcagaggtgg
    40261 ttcttcacca tcgcgtactt cgcggcaagt ggacatcgcc agggtataag agcaggcgtt
    40321 aaccagcgta acggtggcaa taaagcagag gatgaagaag ccccacatgg tggcggtgct
    40381 gagtggcaga gcggcccagg tttcaatgat ggcgcgcgcc acaccgtact gttcgatcag
    40441 atttggaatg ttgatgatgt ttttatctat caacagcaga gtgttactac cgagtacagt
    40501 ccacaggatc caggttgacg ctgtcagccc cagcaccatg ccgaagcaca gttcacgcac
    40561 agtacgacca cgggagatgc gggcgaggaa gatactcatc tggatagcat aaatcaccca
    40621 ccatgcccag tagaacacgg tccagccctg cgggaagccg cctttagcga tgggatcggt
    40681 atagaacaac atgcgcggca gatacatcag caacatcccc accgaatcgg tgaagtagtt
    40741 catgatgaag ctggcaccgc tgacaatgaa cacccaaccc agcatcagga agctcaggta
    40801 actacgcacg tcactggcga tacgtacccc tttttgcaga ccgcaagcga cgcaaatggc
    40861 gttgaggata atccagcagg taatgatgat agcgtccagt tgcagggtat gcggaatgcc
    40921 aaacaaccat tgcatacact cggtcaccag cggcgtggca aggcccagac tggtacccat
    40981 cgtgaagatc aaggcgacga gatagaagtt gtcgacgata gtgccgaaca accctttggc
    41041 gtgtttttca cctaccagcg gcaccagtgt cgagctgggg cgaatcactt ccattttgcg
    41101 gacaaagaag aagtaagcga aggcgactga aaggaagctg taagtggccc acggcagagg
    41161 tccccagtgg aacaagctgt aagccagccc caactctttc gcccctgtcg agttcggttc
    41221 taagccaaac ggcggggtgg agatgtagta gtagatctca atcgatcccc agaacagtac
    41281 ggcagcagac gtacaggagg cgaacatcat aaagatccaa ctggcggtgc taaattctgg
    41341 cggttcgtta cctaaacgct ttttggcata cgggccaaac accagccaga accaaccgaa
    41401 aagcatcacc accatatacc attcaaatgc ccatccccat acattggtga cgtaactgaa
    41461 tacagcatta ataacgacat tcgctgcatc cagatctctg actgtaagcc aacaaagtat
    41521 gccgacgatt attaacggcg gaaagaaaac cttcggttct attcccgttt ttctcttttc
    41581 attcttcatg agttaattcc actgtgaaaa cgaatattta ttttgcgttc ccgtttgttt
    41641 tatttttgtt aacatttaat ataattatta ttaacctcgt ggacgcgtta atggctaact
    41701 cataatgggt attcaataag ctgtattctg tgattggtat cacatttttg tttcgggtga
    41761 atagagggcg ttttttcgtt aattttgatt aataatcagt ttgttatgct ctgttgtgag
    41821 taaaaaataa catctgactt tcaatattgg tgatccataa aacaatattg aaaatttctt
    41881 tttgctacgc cgtgttttca atattggtga ggaacttaac aatattgaaa gttggattta
    41941 tctgcgtgtg acattttcaa tattggtgat taaagtttta tttcaaaatt aaagggcgtg
    42001 atatctgtaa ttaacaccac cgatatgaac gacgtttcct tcatgatttc tggagatgca
    42061 atgaagatta ttacttgcta taagtgcgtg cctgatgaac aggatattgc ggtcaataat
    42121 gctgatggtt cattagactt cagcaaagcc gatgccaaaa taagccaata cgatctcaac
    42181 gctattgaag cggcttgcca gctaaagcaa caggcagcag aggcgcaggt gacagcctta
    42241 agtgtgggcg gtaaagccct gaccaacgcc aaagggcgta aagatgtgct atcgcgcgac
    42301 ccggatgaac tgattgtggt gattgatgac cagttcgagc aggcactgcc gcaacaaacg
    42361 gcgagcgcac tggctgcagc cgcccagaaa gcaggctttg atctgatcct ctgtggcgat
    42421 ggttcttccg acctttatgc ccagcaggtt ggtctgctgg tgggcgaaat cctcaatatt
    42481 ccggcagtta acggcgtcag caaaattatc tccctgacgg cagataccct caccgttgag
    42541 cgcgaactgg aagatgaaac cgaaacctta agcattccgc tgcctgcggt tgttgctgtt
    42601 tccactgata tcaactcccc acaaattcct tcgatgaaag ccattctcgg cgcggcgaaa
    42661 aagcccgtcc aggtatggtc ggcggcggat attggtttta acgcagaggc agcctggtca
    42721 gaacaacagg ttgccgcgcc gaaacagcgc gaacgtcagc gcatcgtgat tgaaggcgac
    42781 ggcgaagaac agatcgccgc atttgctgaa aatcttcgca aagtcattta accacagggg
    42841 atgctacgaa cacattttct caagtctggg tattcagcga taccccttct cgtctgccgg
    42901 aactgatgaa cggtgcgcag gctttagcta atcaaatcaa cacctttgtc ctcgatgatc
    42961 ggcgacggtg tacaggcaat ccagctcggc gctaatcatg tctggaaatt aaacggcaaa
    43021 ccggacgatc ggatgatcga agattacgcc ggtgtcatgg ctgacactat tcgccagcac
    43081 ggcgcagacg gcctggtgct gctgccaaac acccgtcgcg gcaaattact ggcggcaaaa
    43141 ctgggttatc gccttaaagc ggcggtgtct aacgatgcca gcaccgtcag cgtacaggac
    43201 ggtaaagcga cagtgaaaca catggtttac ggtggtctgg cgattggcga agaacgcatt
    43261 gccacgccgt atgcggtact gaccatcagc agcggcacgt tcgatgcggc tcagccagac
    43321 gcgtcacgca ctgtgaaacg cacaccgtgg agtggcaggc tccggctgtg gcgattaccc
    43381 gcacggcaac ccaggcgcgc cagagcaaca gcgtcgatct cgacaaagcc cgtctggtgg
    43441 tcagcgtcgg tcgcggtatt ggcagcaaag agaacattgc gctggcagaa cagctttgca
    43501 aggcgatagg tgcggagttg gcctgttctc gtccggtggc ggaaaacgaa aaatggatgg
    43561 agcacgaacg ctatgtcggt atctccaacc tgatgctgaa acctgaactg tacctggcgg
    43621 tggggatctc cgggcagatc cagcacatgg ttggcgctaa cgcgtcgcaa accattttcg
    43681 ccatcaataa agataaaaat gcgccgatct tccagtacgc ggattacggc attgttggcg
    43741 acgccgtgaa gatccttccg gcgctgaccg cagctttagc gcgttgatcc actctggcag
    43801 ggctgcattt tggccctgcc gctgacaggg agctcttatg tccgaagata tctttgacgc
    43861 catcatcgtc ggtgcagggc ttgctggttc ggttgccgca ctggtgctcg cccgcgaagg
    43921 tgcgcaagtg ttagttatcg agcgtggcaa ttccgcaggt gccaagaacg tcaccggcgg
    43981 gcgtctctat gcccacagtc tggaacacat tattcctggt ttcgccgact ccgcccccgt
    44041 agaacgcctg atcacccatg aaaaactcgc gtttatgacg gaaaagtcag cgatgactat
    44101 ggactactgc aatggtgacg aaacctcgcc atcccagcgt tcttactccg ttttgcgcag
    44161 taaatttgat gcctggctga tggagcaggc cgaagaagcg ggcgcgcagt taattaccgg
    44221 gatccgcgtc gataacctcg tacagcgcga tggcaaagtc gtcggtgtag aagccgatgg
    44281 cgatgtgatt gaagcgaaaa cggtgatcct tgctgatggg gtgaactcca tccttgccga
    44341 aaaattgggg atggcaaaac gcgtcaaacc gacggatgtg gcggttggcg tgaaggaact
    44401 gatcgagtta ccgaagtcgg ttattgaaga ccgttttcag ttgcagggta atcagggggc
    44461 ggcttgcctg tttgcgggat cacccaccga tggcctgatg ggcggcggct tcctttatac
    44521 caatgaaaac accctgtcgc tggggctggt ttgtggtttg catcatctgc atgacgcgaa
    44581 aaaatcggtg ccgcaaatgc tggaagattt caaacagcat ccggccgttg caccgctgat
    44641 cgcgggcggc aagctggtgg aatattccgc tcacataatg ccggaagcag gcatcaacat
    44701 gctgccggag ttggttggtg acggcgtatt gattgccggt gatgccgccg gaatgtgtat
    44761 gaacttcggt tttaccattc gcggtatgga tctggcgatt gccgccgggg aagccgcagc
    44821 aaaaaccgtg ctttcagcga tgaaaagcga cgatttcagt aagcaaaaac tggcggaata
    44881 tcgtcagcat cttgagagtg gtccgctgcg cgatatgcgt atgtaccaga aactaccggc
    44941 gttccttgat aacccacgca tgtttagcgg ctacccggag ctggcggtgg gtgtggcgcg
    45001 tgacctgttc accattgatg gcagcgcgcc ggaactgatg cgcaagaaaa tcctccgcca
    45061 cggcaagaaa gtgggcttca tcaatctaat caaggatggc atgaaaggag tgaccgtttt
    45121 atgacttctc ccgtcaatgt ggacgtcaaa ctgggcgtca ataaattcaa tgtcgatgaa
    45181 gagcatccgc acattgttgt gaaggccgat gctgataaac aggtgctgga gctgctggtg
    45241 aaagcgtgcc ccgcaggtct gtacaagaag caggatgacg gcagtgtgcg cttcgattac
    45301 gccggatgtc tggagtgcgg cacctgtcgc attctggggc tggggtcggc gctggaacag
    45361 tgggaatacc cgcgcggcac ctttggtgtg gagttccgtt acagctaatg ttgctttgat
    45421 acgtaacgcc gcactgactc tcattgcaaa aaacatgaat agctatgcaa ccgtccagaa
    45481 accttgacga tctcaaatgc ttgtcccact accgccgcat tttgctgtgg ggaagcggtg
    45541 gtccgtttct gtatggttat gtactggtaa tgattggcgt ggcgctggag caactgacgc
    45601 cggcgctgaa actggacgct gactggattg gcttgctggg cgcgggaacg ctcgccgggc
    45661 tgttcgttgg cacatcgctg tttggttata tttccgataa agtcggacgg cgcaaaatgt
    45721 tcctcattga tatcatcgcc atcggcgtga tatcggtggc gacgatgttt gtttcatccc
    45781 ccgtcgaact gttggtgatg cgggtattta tcggcattgt catcggtgca gattatccca
    45841 tcgccacctc aatgatcaac gagttctcca gtacccgtca gcgggcggtt ttccatcagc
    45901 tttattgccg cgatgtggta tgttggcgcg acctgtgccg atctggtcgg ctactggctt
    45961 tatgatgtgg aaggcggctg gcgctggatg ctgggtagcg cggcgatccc ctgtctgttg
    46021 attttgattg gtcagattcg aactgcctga atctccccgc tggttattat gcaaagggcg
    46081 agtaaaagag tgcgaggaga tgatgatcaa actgtttgga gaaccggtgg ctttcgatga
    46141 agagcagccg cagcaaaccc ggttttcgcg atctgtttaa tcgctgccat tttccttttg
    46201 ttctgtttgt tgccgccatc tggacctgcc aggtgatccc aatgttcgcc atttacacct
    46261 ttggcccgca aattgttggt ttgttgggat tgggggttgg caaaaacgcg gcactaggaa
    46321 atgtggtgat tagcctgttc tttatgctcg gctgtattcc gccgatgctg tggttaagca
    46381 ctgccggacg gcgtccattg ttgattggca gctttgccat gatgacgctg gcgctggcgg
    46441 ttttggggct aatcccggat atggggatct ggctggtagt gatggccttt gcggtgtatg
    46501 cctttttctc tggcgggccg ggtaatttgc agtggctcta tcctaatgaa ctcttcccga
    46561 cagatatccg cgcctctgcc gtgggcgtga ttatgtcctt aagtcgtatt ggcaccattg
    46621 tttcgacctg ggcactaccg atctttatcg ataattacgg tatcagtaac acgatgctaa
    46681 tgggggcggg tatctcgctg tttggcttgt tgatttccgt agcgtttgcc ccggagactc
    46741 gagggatgtc actggcgcag accagcaata tgacgatccg cgggcagaga atggggtaaa
    46801 ttgttcagat ttctctcttt tctgaatcaa tattattgac tataagccgc gtgaatatat
    46861 gactacactt tgtgggaaaa caaaggcgta atcacgcggg ctacctatga ttcttataat
    46921 ttatgcgcat ccgtatccgc atcattccca tgcgaataaa cggatgcttg aacaggcaag
    46981 gacgctggaa ggcgtcgaaa ttcgctctct ttatcaactc tatcctgact tcaatatcga
    47041 tattgccgcc gagcaggagg cgctgtctcg cgccgatctg atcgtctggc agcatccgat
    47101 gcagtggtac agcattcctc cgctcctcaa actttggatc aataaagttt tctcccacgg
    47161 ctgggcttac ggacatggcg gcacggcgct gcatggcaaa catttgctgt gggcggtgac
    47221 gaccggcggc ggggaaagcc attttgaaat tggtgcgcat ccgggctttg atggtctgtc
    47281 gcagccgcta caggcgacgg caatctactg cgggctgaac tggctgccac cgtttgccat
    47341 gcactgcacc tttatttgtg acgacgaaac cctcgaaggg caggcgcgtc actataagca
    47401 acgtctgctg gaatggcagg aggcccatca tggatagcca tacgctgatt caggcgctga
    47461 tttatctcgg ttcggcagcg ctgattgtac ccattgcggt acgtcttggt ctgggatcgg
    47521 tacttggcta cctgatcgcc ggctgcatta ttggcccgtg ggggctgcga ctggtgaccg
    47581 atgccgaatc tattctgcac tttgccgaga ttggggtggt gctgatgctg tttattatcg
    47641 gcctcgaact cgatccacaa aggctgtgga agctgcgtgc ggcagtgttc ggctgtggcg
    47701 cattgcagat ggtgatttgc ggcggcctgc tggggctgtt ctgcatgtta cttgggctgc
    47761 gctggcaggt cgcggaattg atcggcatga cgctggcgct ctcctctacg gcgattgcca
    47821 tgcaggcgat gaatgaacgc aatctgatgg tgacgcaaat gggtcgcagt gcctttgcgg
    47881 tgctgctgtt ccaggatatc gcggcgatcc cgctggtggc gatgattccg ctactggcaa
    47941 cgagcagtgc ctcgacgacg atgggcgcat ttgctctctc ggcgttaaaa gtggcgggtg
    48001 cgctggtgct ggtggtattg ctggggcgct atgtcacgcg tccggcgctg cgttttgtag
    48061 cccgctctgg cttgcgggaa gtgtttagtg ccgtggcgtt attcctcgtg tttggctttg
    48121 gtttgctgct ggaagaggtc ggcttgtcga tggcgatggg cgcgtttctg gcgggcgtac
    48181 tgctggcaag ctcggaatac cgtcatgcgc tggagagcga tatcgaacca tttaaaggtt
    48241 tgctgttggg gctgtttttc atcggtgttg gcatgtcgat agactttggc acgctgcttg
    48301 aaaacccatt gcgcattgtc attttgctgc tcggtttcct catcatcaaa atcgccatgc
    48361 tgtggctgat tgcccgaccg ttgcaagtgc caaataaaca gcgtcgttgg tttgcggtgt
    48421 tgttagggca gggcagtgag tttgcctttg tggtatttgg cgcggcgcag atggcgaatg
    48481 tgctggagcc ggagtgggcg aaatcgctga ccctggcggt ggcgctgtcg atggcagcaa
    48541 cgccgattct gctggtgatc ctcaatcgcc ttgagcaatc ttctactgag gaagcgcgtg
    48601 aagccgatga gatcgacgaa gaacagccgc gcgtgattat cgccggattc ggtcgttttg
    48661 ggcagattac cggacgttta ctgctctcca gcggggtgaa aatggtggta ctcgatcacg
    48721 atccggacca tatcgaaacc ttgcgtaaat ttggtatgaa agtgttttat ggcgatgcca
    48781 cgcggatgga tttactggaa tctgccggag cggcgaaagc ggaagtgctg attaacgcca
    48841 tcgacgatcc gcaaaccaac ctgcaactga cagagatggt gaaagaacat ttcccgcatt
    48901 tgcagattat tgcccgcgcc cgcgatgtcg accactacat tcgtttgcgt caggcaggcg
    48961 ttgaaaagcc ggagcgtgaa accttcgaag gtgcgctgaa aaccgggcgt ctggcactgg
    49021 aaagtttagg tctggggccg tatgaagcgc gagaacgtgc cgatgtgttc cgccgcttta
    49081 atattcagat ggtggaagag atggcaatgg ttgagaacga caccaaagcc cgcgcggcgg
    49141 tctataaacg caccagcgcg atgttaagtg agatcattac cgaggaccgc gaacatctgt
    49201 cattaattca acgacatggc tggcagggaa ccgaagaagg taaacatacc ggcaacatgg
    49261 cggatgaacc ggaaacgaaa ccctcatcct aataaagagt gacgtaaatc acacttacag
    49321 ctaactgttt gttttgtttc attgtaatgc ggcgagtcca gggagagagc gtggactcgc
    49381 cagcagaata taaaattttc ctcaacatca tcctcgcacc agtcgacgac ggtttacgct
    49441 ttacgtatag tggcgacaat tttttttatc gggaaatctc aatgatcagt ctgattgcgg
    49501 cgttagcggt agatcgcgtt atcggcatgg aaaacgccat gccgtggaac ctgcctgccg
    49561 atctcgcctg gtttaaacgc aacaccttaa ataaacccgt gattatgggc cgccatacct
    49621 gggaatcaat cggtcgtccg ttgccaggac gcaaaaatat tatcctcagc agtcaaccgg
    49681 gtacggacga tcgcgtaacg tgggtgaagt cggtggatga agccatcgcg gcgtgtggtg
    49741 acgtaccaga aatcatggtg attggcggcg gtcgcgttta tgaacagttc ttgccaaaag
    49801 cgcaaaaact gtatctgacg catatcgacg cagaagtgga aggcgacacc catttcccgg
    49861 attacgagcc ggatgactgg gaatcggtat tcagcgaatt ccacgatgct gatgcgcaga
    49921 actctcacag ctattgcttt gagattctgg agcggcggta attttgtata gaatttacgg
    49981 ctagcgccgg atgcgacgcc ggtcgcgtct tatccggcct tcctatatca ggctgtgttt
    50041 aagacgccgc cgcttcggcc aaatccttat gccggttcga cggctggaca aaatactgtt
    50101 tatcttccca gcgcaggcag gttaatgtac caccccagca gcagccggta tccagcgcgt
    50161 atataccttc cggcgtacct ttgccctcca gcgatgccca gtgaccaaag gcgatgctgt
    50221 attcttcagc gacagggcca ggaatcgcaa accacggttt cagtggggca ggggcctctt
    50281 ccggcgattc tttgctgtac atatccagtt gaccgttcgg gaagcaaaaa cgcatacggg
    50341 taaaagcgtt ggtgataaaa cgcagtcttc ccagcccccg caattccggt gaccagttat
    50401 ttggcatatc gccgtacatg gcatcaagaa agaagggata ggagtcactc gatagcaccg
    50461 cttctacatc gcgtgcgcac tctttggcgg tctgcagatc ccactgcggc gtgatccctg
    50521 cgtgggccat caccagcttt ttctcttcgt cgatttgcag cagaggctgg cgccgcagcc
    50581 agttaagcag ctcgtcggca tccggcgctt ccagcagcgg tgtcaggcga tctaacggtt
    50641 tattgcggct gatcccggca aataccgcca gcagatgcag atcgtgattg cccagcacca
    50701 gacgtacgct gtcgcctaag gatttcacat agcgcagaac atccagcgaa cccggcccgc
    50761 gcgcgaccag atcgcccgtc agccagaggg tatctttccc aggggtaaat tctactttat
    50821 gcagcaatgc gatcagttca tcgtaacaac catgaacgtc gccaataagg tatgtcgcca
    50881 tattctttta atgaatgagt gtgggaacgg cgagtcggaa tacgggaatg tcgatgctga
    50941 aagggacgcc attttcatcg atcatttcgt agtgaccctg catggtgccc agcggggttt
    51001 caatgattgc accgctggtg tactggtact cttcgccagg cgcgataagt ggctggacgc
    51061 caaccactcc ttcgccctgg acttcggttt cacggccatt gccattggtg atcagccagt
    51121 aacgccccaa caactgcact ggcgctcgcc ccagattgcg tatggttacg gtataagcaa
    51181 aaacgtaacg ttcattatca ggtgaagatt gagcctcaat gtagacgctt tgaacctgaa
    51241 tacacactcg gggcgaattg atcatcgtta actctcctgc aaaggcgcgt tctccgccca
    51301 gatagttcgc catctggcaa tattgcgcga cagagatatt ttccgctcgc atcgccgggt
    51361 cgatccccat tcccgttaac acctcgacgc taaacaggtt gccgaggctg ttacgaatgg
    51421 ttttacgacg ctggttaaag gcttcggtgg tgatgcggct caacacacga acatctttaa
    51481 ccgggtgagg catcgttgca tgaggaacca ggcgcacgac ggcggaatcc actttgggtg
    51541 gtggtgtaaa ggctgacggc ggtacttcca gtaccgggat cacattgcaa tagtattgcg
    51601 ccatgacgct taatcgacca tacgctttgc tgttcggtcc tgcaaccaga cgattcacca
    51661 cctctttttg caacataaag tgcatgtcgg caatggcatc agtatagcta aacagatgga
    51721 acatcaacgg cgtggagatg ttataaggca ggttgccgaa aacacgcagc ggctgaccca
    51781 ttttctcggc cagttcacca aagttaaagg tcatcgcatc ctgctgataa atcgtcagtt
    51841 tcgggcctaa gaatggatgc gtttgcagac gtgccgccag atcgcggtca agttcgatga
    51901 ccgtcagctg gtccagacgt tcgccgaccg gttcggtcaa tgccgccaga ccggggccga
    51961 tttcgaccat cgcctggccc ttttgcgggt taatggcaga cacaatactg tcgatcacga
    52021 actgatcgtt gagaaagttt tgcccgaagc gtttacgggc taagtggccc tggtggactc
    52081 gattattcat tgggtgttaa caatcatttt gatggcgaga ttaagcgccg taataaaact
    52141 gccgacatcg gctttgccac gtcccgccag ttcaagcgcg gtgccgtggt ccactgatgt
    52201 gcgaataaag ggcaggccca gcgtaatgtt cacaccgcgc ccgaagccct ggtattttag
    52261 cacgggaaga ccctgatcgt ggtacatcgc cagcacggcg tcggcgttat caagatattt
    52321 cggctgaaac agggtatcgg caggcagcgg cccgttgagt ttcatcccct gcgcccgcag
    52381 ctcattgagc accggaataa tggtgtctat ctcttccgta cccatatgac cgccttcgcc
    52441 cgcgtgcgga ttcagcccgc agaccagaat gcgcggttcg gcaataccaa atttggtccg
    52501 caaatcgtga tgcaaaatag caatcacttc gtgcaaaagt gcaggggtga tagcgtctgc
    52561 gatatcgcgc agcggtaaat gcgtcgttgc cagcgccacg cgaagttctt cggtcgccag
    52621 catcatcacc acctttttcg cctgcgaacg ctcttcgaaa aactcggtat gaccggtaaa
    52681 aggaatgcca gcgtcgttaa taacgccttt atgcaccgga cctgtgatca gcgcggcaaa
    52741 ttcgccgttc agacaaccat cgcacgctcg cgccagcgtt tccaccacat aatgcccatt
    52801 ttcaaccgct aactgccccg cagtgacagg tgcacgtagc gcgacaggaa gtagcgttaa
    52861 tgtgcccgca gtttgcggtt gtgcagggga gttgggggaa taagggcgga gggtgagcgg
    52921 caaaccgagc atcgctgccc ggttggtaag gagagtggca tcggcacaaa caaccagttc
    52981 gaccggccac tcacgctgtg caagctggac aactaagtcc gggccaatcc cggcgggctc
    53041 gccgggagtg atcacaacac gttgggtttt aaccattagt tgctcaggat tttaacgtag
    53101 gcgctggcac gttgttcctg catccagctt gctgcttctt ccgagaactt acggttcatc
    53161 agcatgcggt atgcacgatc tttctgcgca gcgtcggttt tatcgacatt acgggtatcc
    53221 agcagttcga ttaaatgcca gccgaatgaa gagtgaaccg gtgcactcat ttgacctttg
    53281 ttcaggcgag tcagggcgtc acggaaggcc ggatcgaaaa tatctggtgt agcccagccg
    53341 agatcgccgc cctggttagc agagcctgga tcctgagaga actctttcgc tgcggcagca
    53401 aaagtcgttt taccactctt gatatcagca gcaatctgtt ccagtttcac acgggcctgt
    53461 tcgtcagtca tgatcggcga cggtttcagc agaatatggc gagcatgaac ttcggtcacc
    53521 gagatatttt tgctttcgcc gcgcaggtcg ttaactttca gaatatggaa gccaacgccg
    53581 gaacgaatcg ggccaacaat gtcgcctttc ttcgcggtgc ttaatgcctg ggcgaagatc
    53641 ccgggcaact cctgaatacg gccccagccc atctggccgc cgttcagcgc ctgctggtcg
    53701 gcagaatgag caatcgccag cttaccgaaa tcagcgccgt tacgcgcctg atcgacaatg
    53761 gcgcgcgcct ggctttccgc ttcgttcacc tgatcagagg tcgggttttc cggcagcggg
    53821 atcaggatgt ggctcaggtt cagctcagtg ctggcgtcgt tttggttacc cacctgctgc
    53881 gccagggatt cgacttctgc ggcaggatgg tgatgcgacg acgcacctcg ttgttacgca
    53941 cttcagagat aatcatctct ttgcggatct ggttacgata ggtgttgtag ttcagtccat
    54001 cgtaagccag acggctgcgc atctgatcca gcgtcatgtt gttctgtttc gcgatgttag
    54061 caatcgcctg atccagctgc tcatcggaga ttttcactcc cattttctgc cccatctgca
    54121 ggatgatttg atccatgatc aaacgttcca tgatttggtg gcgcagcgtc gcgtcatcag
    54181 gaagttgctg ccttgcctga gcagcgttca gttttaccga ctgcattaat ccatcaacgt
    54241 cgctttccag cacgacgccg ttattgacga cggctgcgac tttatcgact acctgggggg
    54301 cagcgaaact ggtattcgcg atcatggcga taccgagaag cagcgttttc cagttcttca
    54361 tactttttcc atttcaatta accgcactgc ggattacgtg gtaaatcaac aaatcacaaa
    54421 gtgttttgat acggcagaat gttcgaacgc agcatctctt gcgtacccag accgtagttg
    54481 gagctcaggc cgcgaagttc gatgttaaag ccgattgcgt tgtcatatac cgcatgttgt
    54541 ttatcgttat cccaaccgtt cagcttccgc tcgtaaccga cgcgaattgc atagcagcag
    54601 gagctgtatt gcacacctaa catagagtcg gcttgcttgt tagcattggt gtcgtagtag
    54661 taggccccaa caatggacca acgatcggca attggccagc tggcgacagc acctacctgc
    54721 gaaataccat tcttatattg ctcagcagtg gaatagtact taggcagcgt agcctgaata
    54781 tattccgggc tggcgtaacg gtaattcagc tgtaccagac ggtcttcatc ccgacggtat
    54841 tcaatgctgg agttactggt cgctacgtta tccagacgtg tatcgtactg aatcccgcca
    54901 cgcaatcccc aacgctcgga gatacgccag taagtatcgc ctgcccacac cagtgaaccc
    54961 gttttgtcgt cattctccca tgttatgttg tcatcgccag tgcgagactc cgtgaaatag
    55021 tagatttgac caacggaaat attaaaacgt tcaacggcag catcatcata tatgcgagat
    55081 gtgacaccgg tcgtcacctg gttagcggag gcaatacggt caagaccgcc gtaagtccgg
    55141 tcccggaaca ggccagagta gtcagattgc agcagagacg agtcgtagtt atagatgtcg
    55201 ctctgatcgc gatacggcac gtacaaatac tgcgcgcgcg gttccagcgt ttgggtataa
    55261 cccggagcca gcatttccat atcgcgttca aagaccattt tgccgtcaac tttgaattgc
    55321 ggcattacgc ggttaacgga ttcgtccagc ttggtcgtgt ttctggagtt ataccagtca
    55381 agattggttt gctgataatg ggttgccagc aacttcgctt cggtattgat gctgccccag
    55441 ttattagaga gcggcaaatt gatggtcggt tccaggtgaa cacgggttgc ttcaggcatg
    55501 tcgtctctgg tgttaacaaa gtgcactgcc tggccgtaaa tacgcgtatc aaacggacca
    55561 acatcattct ggtagtaatt aacgtctaac tgcggctctg ccgagtagct actggtgttc
    55621 tgttcgctga aaacctggaa ctgcttggtt gaaacggtgg cattgaagtt ttgcaccgca
    55681 tagccaacgc tgaatttttg cgttgcgtag ccgtcagtac tggaaccgta cttgttatcg
    55741 aaatcattga agtagctagg atcgctgacc ttggtgtagt cgacgttgaa acgccacacc
    55801 tgatccatga ccccggagtg gttccagtag aataaccaac gacgtgaact gtcatcgttc
    55861 gggtgttcat cttcatagac tttatctgaa ggcagatagt ccagttccat caagccagcg
    55921 cccgcctggg agaggtagcg gaattcgttc tcccacatga tgttgccacg acgatgcata
    55981 taatgcggcg tgatggtggc atccatattt ggcgcgatgt tccagtaata tggcaggtag
    56041 aactcaaagt agttggtggt ggtgtacttg gcgttcggga tcaagaaacc agagcgacgt
    56101 ttgtcaccca ccggcaactg caaatagggg ctataaaaga tcggtaccgg acccacctta
    56161 aagcgggcgt tccagatctc cgcaacttgt tcttcgcggt catgaataat ttcgctacct
    56221 accacgctcc aggtgtcaga acccggcaga caggaggtaa agctaccgtt atccagaatg
    56281 gtatagcggt tttcgccacg ttgtttcatc aggtccgctt taccgcgacc ctggcgaccc
    56341 accatctggt aatcaccttc ccagacgttg gtatctttgg tgttcagatt cgcccagcct
    56401 ttcggccctt tgaggatcac ctggttatcg tcgtaatgga cattaccgag cgcatcaacg
    56461 gtacgtaccg gctccggttg tcctggtgcc tctttttgat ggagctgcac ttcgtcggcc
    56521 tgcagacggc tgttaccctg catgatatcc acgctgccag taaacacggc gtcatccggg
    56581 tagtcccctt tcgcgtggtc agcattgata gtcacgggta agtcattggt atcgccctgt
    56641 accagaggac ggtcatagct tggcacgccc aacatgcact gtgaggcgag gtcggctgcc
    56701 agtccctgtt gactataaag ggcggtggca atcatggtgg ccaggagagt ggggatacgt
    56761 tttttcatac gttgatttta ttgttccatc atcggtaacg ttgcgcgtga caaacggtca
    56821 gagactaacg tactcgtcat ctctacgcta gtgttaatcc tgtccgaata gcgtcagtgg
    56881 tgttaggcac ggcattgaat gacaggtatg ataatgcaaa ttataggcga tgtcccacaa
    56941 ttgaccgcag ccggaaaacg gtaaaagcac ctttatattg tgggagatag ccctgatatc
    57001 cgtgtgtcga tttggggaat atatgcagta ttggggaaaa atcattggcg tggccgtggc
    57061 cttactgatg ggcggcggct tttggggcgt agtgttaggc ctgttaattg gccatatgtt
    57121 tgataaagcc cgtagccgta aaatggcgtg gttcgccaac cagcgtgagc gtcaggcgct
    57181 gttttttgcc accacttttg aagtgatggg gcatttaacc aaatccaaag gtcgcgtcac
    57241 ggaggctgat attcatatcg ccagccagtt gatggaccga atgaatcttc atggcgcttc
    57301 ccgtactgcg gcgcaaaatg cgttccgggt gggaaaatca gacaattacc cgctgcgcga
    57361 aaagatgcgc cagtttcgca gtgtctgctt tggtcgtttt gacttaattc gtatgtttct
    57421 ggagatccag attcaggcgg cgtttgctga tggttcactg cacccgaatg aacgggcggt
    57481 gctgtatgtc attgcagaag aattagggat ctcccgcgct cagtttgacc agtttttgcg
    57541 catgatgcag ggcggtgcac agtttggcgg cggttatcag cagcaaactg gcggtggtaa
    57601 ctggcagcaa gcgcagcgtg gcccaacgct ggaagatgcc tgtaatgtgc tgggcgtgaa
    57661 gccgacggat gatgcgacca ccatcaaacg tgcctaccgt aagctgatga gtgaacacca
    57721 tcccgataag ctggtggcga aaggtttgcc gcctgagatg atggagatgg cgaagcagaa
    57781 agcgcaggaa attcagcagg catatgagct gataaagcag cagaaagggt ttaaatgacc
    57841 ctgtaaatga tgctgagtaa ctgcccacga ttaaaggtgg ccgccctggc ggtcacttct
    57901 ttgagaaaag gcgtttactc agaatggtgg acaggctcaa tgcacggttt acgggagggg
    57961 ttctgtaggt tttatcgcgt tgaccctgct taaggttgag agctttacga cgagcggaat
    58021 tatattttta cgtcttaaaa ataaaaaaca catacctgaa tgagcgattt ttgaaagtat
    58081 atttattcag aacgcgcatc atgagttttt aactcaatgc gaggctatta ccatgaaagt
    58141 atcagttcca ggcatgccgg ttacactttt aaatatgagc aagaacgata tttataagat
    58201 ggtgagcggg gacaagatgg acgtgaagat gaatatcttt caacgcttgt gggagacgtt
    58261 acgccatctg ttctggtcag ataaacagac tgaggcttat aaacttctgt tcaatttcgt
    58321 gaataaccag actggcaaca tcaacgcctc agaatacttt actggggcta tcaacgagaa
    58381 tgagagagaa aagtttatca atagcctgga attattcaat aaacttaaaa catgcgcaaa
    58441 aaatccggat gagttggtcg caaagggcaa tatgcgctgg gtcgcccaga ccttcgggga
    58501 tatcgagtta agtgtcactt ttttcattga aaagaataag atatgtactc agacgttgca
    58561 gctgcataag ggccaaggta acttgggcgt tgatcttaga aaggcttacc ttcccggcgt
    58621 tgacatgagg gattgttacc ttggtaaaaa aacaatgaaa ggtagcaatg atatccttta
    58681 tgagagacct gggtggaatg ctaacctggg cgtgctaccc cggacggtgc taccccggac
    58741 ggtgctaacc cggacggtgc taacctggac ggtgctaccg tgaacggtgc tacctcctta
    58801 tatgatgagg taattattat taataaaatc ccccccaaaa aaattgatac taaaggagtt
    58861 gctactgaag aagttgctac taaaaaagta ctgctgaaca aattactgac aacgcaatta
    58921 ttgaatgagc cagaataagc taaggttgaa ggggctggaa cgccccttca accttagcag
    58981 tagcgtggga tgatttcaca attagaaaga cctgcatgat gagctagaga agaggctagt
    59041 gacgcaaggc gtcgtgcagg acacggatca ccgagatggg catcgccaac cagactgcta
    59101 attagcccat gaataacaat cagaaaggac cataacagac ccgttaaaat gaaatataag
    59161 agacggtcaa cgggtgaaga aaaagttcaa aaattcgctg tggagcagga agggaattac
    59221 cgaatggaaa gcgtagccac acgcaacaac tgaaagcagt ttggcagaaa caaaaaatcc
    59281 ccggactcgg ggatttatgt acaagaggca gcccttagga tgagggtata aacgtacagg
    59341 aaaggttaaa aatccgctgg cgctttaaac gtcatactat tgccatacgc cggatgggta
    59401 atcgtcaaca tctctgcatg tagcaacaaa cgtggtgcca tcgctctcgc ttctggtgat
    59461 gcataaaaac gatcgccgag aatcggatga cccagcgcca gcatatgcac acgcaattga
    59521 tgcgaacgcc cggtaatcgg ttttaacacc actcttgccg tgttatccgc cgcatactcc
    59581 accacttcat attccgtctg cgccaggttt acccgttttc gtaacagcac tttctgtttc
    59641 gggcggtttg gccagtcgca aatcagcggc agatccacca gaccttctgc gggggatgga
    59701 tgcccccaga cgcgggccac atactgcttt ttcggctcgc gctcgcgaga actggcgttt
    59761 taactcccgc tccgcggctt tggtcagcgc cactacaatc acgccgctgg tagccatatc
    59821 cagacgatgc accgattctg cctgcggata atcacgctga atgcgcgtca tcacgctgtc
    59881 tttgtgctct tccagacgac ccggcactga caacaaaccg ctcggcttgt tgaccaccat
    59941 aatatggtca tcctgataca ggataaccaa ccagggttcc tgcggtggat tgtagttttc
    60001 catccccatt ttcggctccg ttactgatgc gttacaacga tcaaacgcag ggcatccaga
    60061 cgccaacctg cctgatccag gctttccatt acctgctgac ggttgctctc aatggcggtc
    60121 agttcgtcgt cacgaatgtt cgggttcact gcacgcagag cttccagacg agacagctcg
    60181 gcagacagtt tttcgtcggc ttcgttacgc gctgcatcaa tcaatgcacg ggcagatttc
    60241 tcgatctgcg cttcacccag ttgaaggata gcgtgaacat cctgctgcac ggcgttaacc
    60301 agtttgctgc cggtgtgacg gttaaccgcg ttaagctggc ggttaaaggt ttcaaactct
    60361 acctgcgccg ccaggttgtt gccgttttta tccagcagca tacgtaccgg cgtcggtggc
    60421 aggaagcggt tgagctgcaa ctgcttcgga gcctgggctt caaccacata aatcagttcc
    60481 accaacagcg tacctaccgg caacgctttg ttttttaaca gtgaaatcgt gctgctaccg
    60541 gtatcgccag aaaggatcag atccagaccg ttgcggatca gcggatgctc ccaggtaata
    60601 aactgtgcat cttcacgcgc cagcgccact tcacgatcaa aggtgatggt gatgccatct
    60661 tccgacaggc cagggaagtc cggcaccagc atatgatcgg acggcgtcag cacgatcatg
    60721 ttgtcgccgc gatcgtcctg attgataccg ataatatcga acaggttcat ggcgaaggcg
    60781 atcaggttgg tatcgtcatc ctgctcttca atgctttctg ccagtgcctg ggctttttcg
    60841 ccaccgttgg agtggatttc cagcaggcgg tcacgaccct gttccagctg tgctttcagc
    60901 gcttcatgtt gctcgcggca gtttttgatc agatcgtcaa agccttcggt ttgatccggt
    60961 gaagccagat agttaatcag atcgttgtat acgctatcgt aaatagtgcg tccggtcggg
    61021 caggtgtgct caaatgcatc cagaccttcg tgataccagc gcaccagcac cgactgagcg
    61081 gttttctcca gataaggcac atggatctga atatcgtgcg cctggccgat acgatccaga
    61141 cgaccaatac gctgctccag tagatccggg ttgaatggca ggtcaaacat caccatgtgg
    61201 ctggcgaact ggaagttacg tccttcagaa ccgatttctg agcacagcag tacctgtgcg
    61261 ccggtgtctt cttcggcaaa ccaggcggca gcgcggtcac gttcgataat cgacatacct
    61321 tcgtggaaca ccgcagcgcg aataccttca cgttcgcgca gtacctgctc cagttgcagc
    61381 gcagtggcag ctttggcgca gatcaccagc actttctgag agcgatggct ggtcaggtag
    61441 cccatcagcc actcaacgcg cggatcgaag ttccaccagg tggcgttatc accttcaaat
    61501 tcctgataaa tacgctccgg gtagagcata tcgcgagcac gatcttccgc acttttacgt
    61561 gcgcccataa tgccggagac tttaatagcc gtctgatact gcgtcggtag cggcagctta
    61621 atggtgtgca gctcgcgttt cgggaatcct ttcacaccgt tacgcgtgtt acggaacagc
    61681 acgcggctgg tgccgtggcg atccatcagc atcgaaacca gctcctgacg ggcgctctgg
    61741 gcatcttcgc tgtcgctgtt tgctgcctgc aacagcggct cgatatcctg ctcgccgatc
    61801 atctcgccga gcatgttcag ttcgtcattg ctcagtttgt tacctgccag cagcatggca
    61861 acggcgtccg caaccggacg ataatttttc tgctcttcaa cgaactgcgc aaaatcgtgg
    61921 aaacggttcg ggtccagcag acgcagacgg gcgaagtggc tttccatccc cagctgttcc
    61981 ggggtcgcgg tcagcagcag aacgcccggc acgtgctctg ccagttgttc aatggcctga
    62041 tattcacggc ttggcgcatc ttcgctccac accaggtgat gcgcttcatc gaccaccagc
    62101 aggtcccatt cggcttcaca gagatgttcc aggcgctgtt tgctacgacg ggcaaaatcc
    62161 agcgagcaaa tcaccagctg ttcggtgtca aacgggttgt aagcatcgtg ctgagcttcg
    62221 gcataacgct catcatcaaa tagcgcaaag cgcaggttga aacggcgcag catttctacc
    62281 agccactgat gctgtaaggt ttccgggacg ataattagca cacgttcagc agcgccagag
    62341 agcagttgct gatgcaggat catcccggct tcaatggttt tccctaaacc cacttcgtca
    62401 gccagcagga cgcgcggcgc gtggcggcga ccaacatcat gagcgatgtt gagctgatgc
    62461 gggatcaggc tggtacgctg accgcgcagg ccgctgtacg gcatacggaa ctgttcgctg
    62521 gaatatttac gcgcgcgata acgcagcgca aagcggtcca tacggtcaat ctgcccggca
    62581 aacagacggt cctgcggttt gctgaacacc agtttgctat caaggaaaac ttcacgcagg
    62641 gctacgccgg actcttcagt atccaggcga gtaccgatat aggtcagcaa gccattttct
    62701 tcttttactt cttcgacttg catctgccag ccgtcatggc tggtaatggt atcaccaggg
    62761 ttgaacatca cgcgggtcac gggggaatca ctgcgtgcgt acagacggtt ttcaccagta
    62821 gatgggaaaa gtaaagtgac agttcgcgca tccaccgcga caacggttcc aagtcccaat
    62881 tcgctttctg tatcgctgat ccagcgttga ccaagtgtaa aaggcatatg tgttcggctc
    62941 tatatcttta attgcaggca ataaccaccc gctaccgtgc ttatgaggta gtggtgttat
    63001 tcaggtccag gaatggaaag ggcgctatgg tactggatgg caaagcattc gtcacgcatc
    63061 aaaatggtat ctggcgaact cttttttttg ctcaaaatag cccaagttgc ccggtcataa
    63121 gtgtagcaaa attatcctca ataaaaggga gtattccctc cgccacgggt tgtagctggc
    63181 gggtcagata gtgttcgtaa tccagtggtg aacgttggta gtccagcggc tccgggccgt
    63241 tggtggtcca tacgtactta atggtgccgc gattctgata ttgcaagggg cgaccacgct
    63301 tttggttttc ttcatcggca aggcgagcgg cgcgtacatg aggcggcaca ttacgctgat
    63361 actcgctcag cggacggcga aggcgtttac ggtaaaccag tcgcgcatcc agttcacccg
    63421 ccatcagttt gtcgatggtt tcgcgtacat attcctgata tggctcgttg cggaagatgc
    63481 gcaggtatag ctcctgctga aactgctggg ccagcggcgt ccagtcggtg cgcacggttt
    63541 ccagcccttt aaacaccatc cgctgcttgt cgccctcctg aatcagtccg gcataacgct
    63601 ttttactgcc ggtatcggct ccgcgaatgg ttggcatcag aaaacggcag aaatgggttt
    63661 catactccag ttctaatgcg ctggtcagcc gttgtttttg cagcgtttcc gcccaccagg
    63721 cgttaacgtg ctgcaccagt gcacgaccga ttttcgccgc ttcttcttcc gaatgtgcgc
    63781 ctttcagcca gacaaacgtt gagtcggtat cgccgtagat aacgtcgtag ccctgtgctt
    63841 caatcaacgc tttggtttgc cgcatgatct gatgaccacg catggtgatc gacgatgcca
    63901 gccgcggatc gaagaagcgg caggcggtgg tgccgagcac gccataaaag gcattcatga
    63961 tgattttcag cgcctgcgac agcggtttgt taccctggcg tttggcttca tcgcgcccgt
    64021 gccagatgtt agtcacaatc tccggcaggc aatgtttttc tcgcgagaac caggcatcga
    64081 gaaaaccttc ggtactgtgc tctggatcag gctgcgccat gccttccacc agcccgacgg
    64141 gatcaatcag aaaggtgcgg atgatcgacg ggtacaggct tttatagtcc agcaccagca
    64201 ctgaatcata aagccctggc cgtgaatcca tcacgtagcc gccagggctg gcgtgcggcg
    64261 gcacttcgcc gagattaggc gcgacataac cagcgcgatg cattcgcgga aaatagagat
    64321 gaccaaatgc cgccaccgaa ccgccgtgtc ggtccaccgg caggccgttc accgttgccc
    64381 gttcgagtaa aaatggcatg atttcagttt tgtggaagat ctgcgtcacc agctcgcaat
    64441 ctttcaggtt ataagttgcc agcgcaggtt tatcttcggc gaaacggcgg tcaatttcgt
    64501 ccattcgatc ccacgggtta tcgatagatt ttccttcgcc taatagctcc tgagcgacag
    64561 tttccagcga gaatgaagag aaatcccaga acgcggattt cagcgcctcg ataccgtcga
    64621 taattagccg acctttagcc tggggcaaaa aagacgccgt ttttgcgggg ccgtgctcgc
    64681 gccactccag ctcgctatta tcgcgcccaa gacgcagcgg aagacggtaa cggctcggca
    64741 tgtttttgca gcattcgcag atcgaactgc accacgttcc aaccgatgat cacatcagga
    64801 tcgtagttgg caaaccaggc gttgagtttt tccagcaact gcgggcggct ggcgacgtat
    64861 tccagttcga aatcaagcga ggaggcgtcg ccattctccg gccccagcat ataaacgatg
    64921 cgctgcccgc agccttccag gccgatgcag tacagctcac cgtggcgggt ggtttcaata
    64981 tctatagaaa cccacttgag cggcggacga tagtcgggat gcggtttcag acgggcatta
    65041 acgatagtgc cattgtgcat atcaccctcg acccacaccg gtgaggtgat aaaccgctcc
    65101 atcagatagc gttctggcgg acgcacatcg gcctcgtaga cggtaacgcc accttcacgc
    65161 aggcgctttt cgtaattcat caattggcga tgggcgcgac agtaaaggcc atacaccggc
    65221 tggcggtgaa aatcctttaa cgccagcggt gtcaggcgaa agccttgttc accctgcaaa
    65281 atatgctgag cgcggggaac ctgatcggcg ggaataaacg ccacggactc ttgcggtgca
    65341 agcgtaacct gcaacggccc gttgtccgtc gccagccaga aggagacttc tgtcccttgc
    65401 ggggtgtccc gccagtgtcg ggttaagata aaacctgcct gcgccacgct gaaaatccat
    65461 caaaaaacca ggcttgagta tagcctggtt tcgtttgatt ggctgtggtt ttatacagtc
    65521 attactgccc gtaatatgcc ttcgcgccat gcttacgcag atagtgttta tccagcagcg
    65581 tttgctgcat atccggtaac tgcggcgcta actgacggca gaatatcccc atataagcga
    65641 cctcttccag cacgatggcg ttatgcaccg catcttcggc atttttgccc catgcaaacg
    65701 ggccgtggga atggaccaga acgccgggca tttgcgctgc atcgataccc tgtttttcaa
    65761 aggtttctac gatgacgtta ccggtttccc actcatattc gccgttgatt tctgcgtcgg
    65821 tcattttgcg ggtgcaggga atggtgccgt agaaatagtc ggcgtgggtg gtgccggttg
    65881 ctggaatcga ctgacccgcc tgcgcccaga tggtggcgtg gcgcgagtgc gtatgcacaa
    65941 tgccgccaat ggaggggaat gcctgataga gcagccggtg agttggcgtg tcggaggagg
    66001 gctttttcgt accttcaacc acttcaccgg tttcgatgct aaccacgacc atatcgtcag
    66061 cggtcatgac gctgtaatcg acgccggaag gtttgatcac aaagacgccg cgctcgcgat
    66121 caacggcgct gacgttgccc catgtgagcg tgaccaggtt gtgttttggc agcgccaggt
    66181 tggcttctaa tacctggcgt ttgagatctt ctaacatgtt gactccttcg tgccggatgc
    66241 gctttgctta tccggcctac aaaatcgcag cgtgtaggcc tgataagacg cgccagcgtc
    66301 gcatcaggcg ttgaatgccg gatgcgcttt gcttatccgg cctacaaaat cgcagcgcgt
    66361 aggcctgata agacgcgcca gcgtcgcatc aggcgttgaa tgccggatgc gctttgctta
    66421 tccggcctac aaaatcgcag cgtgtaggcc agataagacg cgtcagcgtc gcatcaggcg
    66481 ttacataccg gatgcggcta cttagcgacg aaacccgtaa tacacttcgt tccagcgcag
    66541 cgcgtcttta aacgctggca ggcgtgtgtc gttatcaatc accgtgattt caatgtcgtg
    66601 catctcggcg aattggcgca tatcgttgag gttcagtgca tggctgaaga cggtatggtg
    66661 cgcgccacca gcgaggatcc acgcttcgga agcagttggc agatccggtt gcgctttcca
    66721 cagcgcattc gccaccggca gtttcggcag ggagtgcggt gttttcaccg tgtcgataca
    66781 gttaaccagc agacggtaac gatcgccgag atcaatcagg ctggcgacaa tcgctggacc
    66841 ggtttgggta ttgaagatca gtcgggcagg atcgtcctta ccaccaatac cgagatgctg
    66901 aacgtcgagg atcggtttct cttctacggc aatcgacggg cagacttcca gcatatggga
    66961 gccgagcacc aagtcattac ctttctcgaa gtgataggtg tagtcctcca taaaggaggt
    67021 gccgccctgc agaccggttg acatcacctt catgatgcga agcagggcgg cggttttcca
    67081 gtcgccttcg cccgcaaagc cgtaaccctg ctgcatcaga cgctgtacgg ccagacctgg
    67141 aagctgtttc agaccgtgca aatcttcaaa ggtggtggtg aacgcgtgga agccaccttg
    67201 ttccaggaaa cgcttcatcc ccagctcaat acgcgccgct tccagcacgt tctgtcgttt
    67261 ttcgccgtgg atttgtgttg caggcgtcat ggtgtagcag ctttcgtact catcgaccag
    67321 cgcgttaaca tcgccgtcgc tgatggagtt caccacctgc accagatcgc caaccgccca
    67381 ggtattgacg gagaaaccga acttgatctg tgcggcaact ttatcaccat cggtgaccgc
    67441 cacttcacgc atgttatcgc caaaacggca gactttcaga tgacgggtat cctgtttaga
    67501 aaccgcctga cgcatccagg agccgatacg ctcatgggct tgtttatcct gccagtgacc
    67561 ggtaacgacg gcatgttgct gacgcatacg cgcgccaatg aagccgaact cgcgaccgcc
    67621 atgtgcagtc tggttcaggt tcataaagtc catatcgata ctgtcccacg gcagcgccgc
    67681 gttgaactgg gtgtggaatt gcagcaacgg tttgttgagc atggtcaggc cgttgatcca
    67741 cattttggcc ggggagaagg tgtgcagcca caccaccaga ccagcgcacg gatcgtcgta
    67801 attcgcgtcg cggcaaatag cggtgatttc atccggcgtg gtgcccagcg gtttcaacac
    67861 cagtttgcag ggcagtttcg cttccgtatt cagcgcatta acaacgtgct cggcatgttg
    67921 ggtgacctga cgcagggttt ccgggccata cagatgctgg ctgccaatga caaaccacac
    67981 ttcataatta tcaaaaatcg tcattatcgt gtccttatag agtcgcaacg gcctgggcag
    68041 cctgtgccgg ggcggaagtt ggaagatagt gttgttcggc gctcatcgcc cattgctgat
    68101 agcggcgata aagctgttca aagcgttgtg cctgttcgct gcgcggttgc agggttttct
    68161 ctaccgcact ggccattttt tgctgggctg atgggatgtc tgcgtgcact ttcgcggcga
    68221 cggcagcaaa aatcgccgca ccgagcgcac agcactggtc agaggcaaca atttgcagcg
    68281 ggcgattcag cacgtcgcag caggcctgca taatgacttg gtttttccgc gcgatgccgc
    68341 ccagcgccat cacgttattg acggcgatcc cctgatcggt aaagcactcc atgattgcgc
    68401 gtgcgccaaa ggcggtggca gcaatcaaac cgccgaacag cagcggagcg tcggtagcga
    68461 ggttaagatc ggtaatcacc cctttcaggc gttggttagc gtttggcgag cgacgaccgt
    68521 taaaccagtc gagcaccacc ggcaggtgat ccagagacgg atttttggcc catgcttcgg
    68581 tcagcgccgg aagcagttgt ttctggctgg cgttgatttg cgctttcagt tccggatgct
    68641 gggcggcaag ctgttccagc ggccagctga gtacgcgacc gaaccaggcg tagatatcac
    68701 caaacgccga ttggcctgct tccagaccga taaatccagg caccacgctg ccatcaacct
    68761 gaccgcaaat acctttaact gcccgctcgc caacgctctg tttgtcggca atcagaatgt
    68821 cgcaggtgga agtaccgata acttttacca gtgcgttagg ctgtgcgcct gcgccaactg
    68881 cgcccatatg gcagtcaaac gcgccgccgg aaatcaccac gctttcaggc aggccgagac
    68941 gctgcgccca ttccgggcat aaggtgccca ccggaatatc ggcagtccag gtgtcagtga
    69001 acagcgggga aggcaaatgg cgattgagga tcgggtccag ctcatcaaag aaactggctg
    69061 gcggcaagcc gccccagctt tcgtgccaca gagatttatg cccggcgctg caacgtccgc
    69121 gacgaatatc ctgcgggcgg gtggtaccgg aaagcagagc tggcacccag tcgcacagct
    69181 caatccacga tgcggcagat tgcgccacgg cgctgtcctg gcgagtcaca tgcaggattt
    69241 ttgcccagaa ccattcgctg gaataaatac cgccaatata gcgggagtag tcaacattgc
    69301 ccggcgcgtg gcacaaacgg gtaatctctt cgcttctttc aaccgcagtg tggtctttcc
    69361 acaatacgaa catcgcgttc gggttttcgg caaactccgg gcgcagcgcc agcacgttac
    69421 cgtcggcatc aatcggtgcg ggcgtcgagc cggtactgtc aacgccaatc ccgaccacag
    69481 ctgcgcgctg ttcgacgcta agctctgcaa gcacggtttt cagtgccgct tccattgact
    69541 caatgtagtc acgcggatga tgacggaact ggttattcgg ggcatcacaa aattgccctt
    69601 tttgccaacg gggataccac tctacgctgg tggcgatctc ttcaccgctg gcgcagtcca
    69661 ccgccaaagc tcgcacagaa tcactgccaa aatcgaggcc aattgcaatc gccatcgttt
    69721 cactccatcc aaaaaaacgg gtatggagaa acagtagaga gttgcgataa aaagcgtcag
    69781 gtaggatccg ctaatcttat ggataaaaat gctatggcat agcaaagtgt gacgccgtgc
    69841 aaataatcaa tgtggacttt tctgccgtga ttatagacac ttttgttacg cgtttttgtc
    69901 atggctttgg tcccgctttg ttacagaatg cttttaataa gcggggttac cggttgggtt
    69961 agcgagaaga gccagtaaaa gacgcagtga cggcaatgtc tgatgcaata tggacaattg
    70021 gtttcttctc tgaatggtgg gagtatgaaa agtatggctg aagcgcaaaa tgatcccctg
    70081 ctgccgggat actcgtttaa cgcccatctg gtggcgggtt taacgccgat tgaggccaac
    70141 ggttatctcg atttttttat cgaccgaccg ctgggaatga aaggttatat tctcaatctc
    70201 accattcgcg gtcagggggt ggtgaaaaat cagggacgag aatttgtctg ccgaccgggt
    70261 gatattttgc tgttcccgcc aggagagatt catcactacg gtcgtcatcc ggaggctcgc
    70321 gaatggtatc accagtgggt ttactttcgt ccgcgcgcct actggcatga atggcttaac
    70381 tggccgtcaa tatttgccaa tacgggtttc tttcgcccgg atgaagcgca ccagccgcat
    70441 ttcagcgacc tgtttgggca aatcattaac gccgggcaag gggaagggcg ctattcggag
    70501 ctgctggcga taaatctgct tgagcaattg ttactgcggc gcatggaagc gattaacgag
    70561 tcgctccatc cgccgatgga taatcgggta cgcgaggctt gtcagtacat cagcgatcac
    70621 ctggcagaca gcaattttga tatcgccagc gtcgcacagc atgtttgctt gtcgccgtcg
    70681 cgtctgtcac atcttttccg ccagcagtta gggattagcg tcttaagctg gcgcgaggac
    70741 caacgtatca gccaggcgaa gctgcttttg agcactaccc ggatgcctat cgccaccgtc
    70801 ggtcgcaatg ttggttttga cgatcaactc tatttctcgc gagtatttaa aaaatgcacc
    70861 ggggccagcc cgagcgagtt tcgtgccggt tgtgaagaaa aagtgaatga tgtagccgtc
    70921 aagttgtcat aattggtaac gaatcagaca attgacggct tgacggagta gcatagggtt
    70981 tgcagaatcc ctgcttcgtc catttgacag gccacattat gcaagcattg cggaacactt
    71041 tattacccaa ccaccgtgtt cattgatggc ggtggtgttg gtggcctttc tggagtcgct
    71101 ggcgctggtc ggtttgattc tacccggtac ggtgctgatg gcggggctgg gagcgctgat
    71161 tggcagcggc gagttaagtt tctggcacgc ctggctggca gggattattg gctgcttgat
    71221 gggcgactgg atttctttct ggctgggttg gcgttttaaa aagccgttgc atcgctggtc
    71281 atttctgaag aaaaacaaag cactacttga taaaactgaa catgcgttgc atcaacacag
    71341 catgttcacc attctggtcg gtcgttttgt tggcccgacg cgtccgctgg tgccaatggt
    71401 ggcgggaatg ctggatctgc cggtggctaa atttattacg ccgaatatta tcggctgcct
    71461 gctgtggccg ccgttttact tcctgccagg gattctggcg ggcgcggcga tcgatattcc
    71521 tgccggaatg cagagcggtg agtttaaatg gttgctgctg gcaacagcgg tgtttttgtg
    71581 ggttggtggc tggctgtgct ggcggttatg gcgcagcggt aaagcgactg accgtttgag
    71641 tcattatttg tcccgcggtc gtttgttgtg gctgacgccg ttgatttctg ccatcggcgt
    71701 ggtggcgctg gtggtgttaa ttcgccaccc gttgatgccg gtgtatatcg atattttgcg
    71761 taaagtggtt ggggtttagg agatagtctt gtgcgggttg cctgagcgcg acgcttgccg
    71821 cgtcttatca ggcctacaaa acgcactacc cgtaggtcgg ataaggcgtt cacgccgcat
    71881 ccgacagtgc atactaaccc gtaatcccca atagtgccga agcactcgcc ttaccgctca
    71941 acaactcatt ggtcataccc tgccaggcga tgcgcccgtc ggcgactact accgagcgcg
    72001 tggcgatccg cgccgcatct tccacgctgt gcgacaccat caatagcgtc attttttgct
    72061 gctggcagct cgtgctcacc agcgtcaaca tctcctgacg taacgccgga tcgagcgcag
    72121 agaacagttc atcgagcaat aaaatcggct gttcgcgtac cagacaacgc gctaacgcca
    72181 ctcgctgtcg ctgaccgccg gaaagctcgc ccggtaaccg cgccattaaa ttatcaatcc
    72241 ccatctggcg ggcgatagcg tgcattttcc cctgctgtac cgcgttcagt ttcaatcccg
    72301 gatttagccc cagcccgatg ttctgtgcga ccgtcaggtg gctgaacagg ttgttctcct
    72361 gaaacagcat cgacaccgga cggcgtgacg gcggcatagt tgtgtgatct acgccatcga
    72421 tagtcagcga accgctggct ggcgtcagaa aaccggcgat caaattcagc agggtacttt
    72481 tacccgcgcc gcttggcccg aggatcgcca cctgctcgcc gcgttccacc gttaagctaa
    72541 aacgcatcgg caaatggtgg taaagccagg tgatatcagt cagttttaac atttcgcccc
    72601 ggtagttttt caatcacggt aaacagcaga aaacagagca gcagcagaat taacgtggtg
    72661 accgcaccgt cctggctgcg ataggagcca atttgctggt agagataaaa cggcagggtg
    72721 cggaaatcat cgttaccgaa caacgccacc acgccaaaat caccaatcga cagcacgcat
    72781 gcaaaggcca gcgcctgcgc cagtggacgt ttcagggcgc gcagctccac cacttttaag
    72841 cgtgaccagc cttcaatccc cagcgactga cataacatgc tgtagcgggc ggtgatatcg
    72901 cgcatcgggt tttccagcac tttcagcgca taagggatcg ccattaacgc attggtgaaa
    72961 atcacaatgc cgtcagcaga ttgtggcagg ccgatagtgt tgttgagcag taaaaagaag
    73021 ccggtagcca gcacaatccc cggcatggcg aggatcaaca tgccgctcat ctccagcacc
    73081 tgacccgcca gcattttctg ccgcgcccgc agttcgcgac tgctccatag cagcatcatg
    73141 gtcagcacta cgcacaatac acctgccgcc agcgcaatac gcaacgaggt ccacagcgcc
    73201 tgccacagca ccggttgtgc cagcacttcc ggcaactggc gatttacccc atcgacgatc
    73261 accgccagta acggtggcag caacagcagc agcgccagca caattaacac cgtgtcgcaa
    73321 atgcggctat gcagacgatc gtccgggtcg cgccagcctt gcagcagcgt ggtgccgggc
    73381 gcaatggcct tactcaatcg ctgactcaac agcaccagcc cgaggcagca caccatctgg
    73441 agcagcgcca gcattgccgc gcgggcagga tcgtagtcgt aactcagcgc ctgatagatt
    73501 gccagctcga tagtggtcgc ctgcggaccg ccccccagcg atagcacggt ggcgaagctg
    73561 gcgaaacaga gcataaagat aagcgcagca accggcggga tttgtcgccg taaccacggc
    73621 cattcgacga agcggaaaaa atgccagcta cgcatcccaa gctgggcggc aagttgacgc
    73681 tgttcgccgg ggatgttttc cagtgcctgg agtaataagc ggctcgccat cggcagatta
    73741 aaaaacacat gggccagcaa aataccttgc aggccgtagg gcgaaaaggt ccactccaga
    73801 ccgagcgatt ggcagagtgt tgccagccag ccctggcgac catagacgct aagaatgccg
    73861 aaaacagcga ccaacaccgg gaggatcaag gtcattgcac acagacgcaa cagcgccagc
    73921 cgacccggaa agcgcctgcg atagagcgcg cgggcgagga atatcgcggg tatgacagag
    73981 agcagtgccg agagaaacgc ctgccagaag gagaagcgca ccacatgcca cagatagctg
    74041 tcctgccaga ctgccaccca gtcatcctgc ggcgcgttcc accacagggc gagaaacgcc
    74101 gccagcgcaa ccgctaccac cagcgtggtg gcgcttacac ctggaattaa ccagccggga
    74161 attaacggct gacggcgcgt tgccattcgc taatccatgc ctgacgttgt gccgccactt
    74221 cggctggcgt gaactccaac gtggttgcgg gtttggtcaa tttttcaaaa ccggcaggca
    74281 gcgtgacgtt tgccaccgga tacatccagt tgccggttgg gatcgcattc tggaaagccg
    74341 gagaaaccat aaactggagg aatttttgcg ccagctccgg ctgcttgctg gcagcggtgc
    74401 gggcggcgac ttccacttgc agatagtgac cttcgctgaa gttcgcggcg gcgtagttat
    74461 ctttcttctc ttcgagaatg tgataagccg gagaggtggt gtaactcagt accagatcgc
    74521 tttcaccttt taaaaacagg ccgtaggctt cgctccagcc tttggtgacc gtgaccgttt
    74581 tcttcgccag tttctgccag gcttgtgggg cgtcatcgcc atagactttt tgcatccata
    74641 gcaacagacc cagccccggt gtactggtgc gcggatcctg ataaatcacc cgccagtttt
    74701 gatcgctctc aaccagttct ttcaggcttt gtggcgggtt tttcagtttg ttcttgtcat
    74761 aaacgaaggc gaagtagcca taatcaaacg gtacgaaagt gtcattattc cagccgccgg
    74821 gaacgttaac ggcatccgct gccacaccgc ttttggcaaa cagtccggtt ttactggcgg
    74881 cgtctaacag gttgttatcc agccccagca ccacatcggc tttactgttt ttgccttcca
    74941 tccgtagacg gttgagaagc gaaacgccat cttccagcgc caccagtttc agttcgcaat
    75001 tacagtcggc ttcaaaggct tttttaacca ccggaccagg cccccagtcg gcggcgaagg
    75061 aatcgtaggt ataaacagtc agaacgggtt tagcgaaaac gggcgctgtc acagcaacag
    75121 caggggcaga cattttttta acactttgca cctcaaaaaa gagtggcaaa ggacttgaga
    75181 aggagcctca aatcccttcg ccggcgttat ccggatcagg ttcgacgggt attttctcag
    75241 cgcacgcgta cgcgtggcac cccgttgaga acggcgttag tgtagtgatt ttgttatcaa
    75301 ccagcaatca tggatccggt ggcgcaaacc acgctgattt aaaatcgaac cagccgaggg
    75361 tattcatgcg caggccgcgc atactgcgtt gcccctgaat gatcagccag tggtgcaata
    75421 atggcaccat cgctttgctg gcgaccagtt gctggcacca gttcgccaga ttcatctcgc
    75481 cattgcgcca gcgagcagcg tcggcttgcc agtcaatggg aatgcaatgt tgtagcagtg
    75541 gcacttcgca taaatgtgcg aaaacagaga agtccagcgg cagggtaaag ttggcgctgt
    75601 ttagccagat atcactttcg atctctcctg tatgccactg atcgtagtcg atctctttga
    75661 ttttcagcgt cacctggtga cttgccagaa tctgctgcat gatcccggca atcacccgat
    75721 gctcactgtg atcctgacaa aaggttaggg tgaggctttc caggccagcc ggtttttcgc
    75781 tctttatggt gcgggcatgg tgccaacggg ggaacagtcc ataagccggg aaccacagtt
    75841 gctggtactg ttcctcagcg aaatagacca agttagttgg agaaagcaca tagcttgccc
    75901 agtccctgac ttgctgattc gccccgcgat gggtgcggct gtcgaacagt aaatagtagc
    75961 aaccttcctc caggcggctt tcaatctctt tttcctcgcc ctgtggacct tttagcatca
    76021 gccctccggc tggctcgtcg gcaatttccg gcagaaccca gacgttaact tcgtcgatta
    76081 atgcccggta accgaagaag tcatcgaatg cctgaatttt cagttgattg gtgctgttgc
    76141 gaatcaccgc atacggaccg gtgccgatgg gatggctggc aaagttactg agggtttccc
    76201 attcgcgcgg caggatcatc gccggaactt gccccagcag taacggtaac cagcggtccg
    76261 gttgcgtgag atggatatcc agcgtccagg gcgtcggcga cacaatgtca gcaatatgcg
    76321 aatagagcgg cagcgtattg attcgtttta aagaggcgat cacatcgtcc atttccagtt
    76381 cacgaccatg gtgaaaatgg actcctggac gcaaaaagaa acgccagtga agcggtgaaa
    76441 tttgctgcca gtggtgggcg atgtctgctt ccagttcccc attttcctca tttatgcgcg
    76501 ttagcgaact gaagatttgc cgggcgatat gggtttcgga acggcgcaat gcgctgccag
    76561 gtagcagatt acgcaacgga cgatagtaga gcacgcgcag gatgtgccgc ccctggcgga
    76621 agctgcggcc cagatgagaa accagcattt gccgcacagt cgctttgtcg ccaaccaact
    76681 gcaccagttg atcgatacga tcctgctcca gcaggtcttc cgcccgctgt tgctgaagcg
    76741 ccagcccggt atagaggaat gtcagacgcg agcgtttacc gcgcccgact tccgcttccc
    76801 acgtcagcca gccgcgatcc tgcatggtgt tgagcagggt gcgcatatga cgacgcgagc
    76861 agctcaataa cgctgccagt tcgttgagcg ttgtgtcctg cgatttaccc tcgcagcatt
    76921 gccacaggcg gatgaactgt tgttgcagac gagcagatgg cataaaaggg gaactcctgt
    76981 gcaaaagaca gcaattttat tgtccctata ttaagtcaat aattcctaac gatgaagcaa
    77041 gggggtgccc catgcgtcag ttttatcagc actattttac cgcgacagcg aagttgtgct
    77101 ggttgcgttg gttaagcgtc ccacaacgat taaccatgct tgaaggactg atgcagtggg
    77161 atgaccgcaa ttctgaaagt tgacttgcct gcatcatgtg tgactgagta ttggtgtaaa
    77221 atcacccgcc agcagattat acctgctggt tttttttatt ctcgccgcgc taaaaaggga
    77281 acgtatgatc tggataatga cgatggctcg ccgtatgaac ggtgtttacg cggcatttat
    77341 gctggtcgct tttatgatgg gggtggccgg ggcgctacag gctcctacat tgagcttatt
    77401 tctgagtcgt gaggttggcg cgcaaccttt ctggatcggc ctcttttatg cggtgaatgc
    77461 tattgctggg atcggcgtaa gcctctggtt ggcaaaacgt tctgacagtc agggcgatcg
    77521 gcgaaaactg attatatttt gctgtttgat ggctatcggc aatgcgctat tgtttgcatt
    77581 taatcgtcat tatctgacgc ttatcacctg tggtgtgctt ctggcatctc tggccaatac
    77641 ggcaatgcca cagttatttg ctctggcgcg ggaatatgcg gataactcgg cgcgagaagt
    77701 ggtgatgttt agctcggtga tgcgtgcgca gctttctctg gcatgggtta tcggtccacc
    77761 gttggccttt atgctggcgt tgaattacgg ctttacggtg atgttttcga ttgccgccgg
    77821 gatattcaca ctcagtctgg tattgattgc atttatgctt ccgtctgtgg cgcgggtaga
    77881 actgccgtcg gaaaatgctt tatcaatgca aggtggctgg caggatagta acgtacggat
    77941 gttatttgtc gcctcgacgt taatgtggac ctgcaacacc atgtacatta ttgatatgcc
    78001 gttgtggatc agtagcgagt taggattgcc agacaaactg gcgggtttcc tgatggggac
    78061 ggcagctgga ctggaaatac cagcaatgat tctggctggc tactatgtca aacgttatgg
    78121 taagcggcga atgatggtca tagcagtggc ggcaggagta ctgttttaca ccggattgat
    78181 tttctttaat agccgtatgg cgttgatgac gctgcaactt tttaacgctg tatttatcgg
    78241 cattgttgcg ggtattggga tgctatggtt tcaggattta atgcctggaa gagcgggggc
    78301 agctaccacc ttatttacta acagtatttc taccggggta attctggctg gcgttattca
    78361 gggagcaatt gcacaaagtt gggggcactt tgctgtctac tgggtaattg cggttatttc
    78421 tgttgtcgca ttatttttaa ccgcaaaggt taaagacgtt tgatgacgtg gacgatagcg
    78481 gaaagcccgg tcatttgacc gggcaagggg attaattcat aaacgcaggt tgttttgctt
    78541 cataagcggc aatggcgtcg tcgtgctgca aggtaagccc aatactgtcc agaccgttca
    78601 tcatgcagtg gcggcggaag gcatcgatgg taaagcgata ggttttctct cccgctttca
    78661 cctcttgcgc ttccagatcc acgtcgaaat ggatccccgg attagctttc accagcgcaa
    78721 acagttcgtc cacttctgca tcgcttaatt tcaccggcag cagctggttg ttaaagctat
    78781 tgccgtagaa gatgtcagca aaactcggcg caatcaccac tttaaaaccg tagtcggtca
    78841 atgcccaggg cgcgtgctca cgcgaagagc cacagccgaa gttttctcgt gccagcaaaa
    78901 tggaagcgcc ctgatactgc gggaagttca gcacgaagtc cgggtttggc tgttggcctt
    78961 tttcatccag aaaacgccag tcgttaaaca gatgcgcgcc aaaacccgta cgggtcactt
    79021 tctgcaaaaa ctgtttcggg atgattgcat cggtatcgac attggcggca tccagcggaa
    79081 ccaccaggcc tgtgtgtttg ataaatttct ctgccatggt gtgctcctta tttaatgttg
    79141 cgaatgtcgg cgaaatgtcc ggtcacagca gcagcggcag ccattgccgg gctgaccaga
    79201 tgcgtgcgcc cgccgcgccc ctggcggcct tcaaagttac ggttgctggt ggaggcacaa
    79261 cgttcgcccg gattcagacg gtcgttgttc atcgccagac acattgagca gccaggcaag
    79321 cgccattcaa aaccggcttc aataaagatt ttatccagac cttccgcttc cgcctgggct
    79381 tttaccgggc cagagccggg aaccaccagt gcctgcacgc ctggcgcgac ttttcgccct
    79441 ttgacgatct ccgctgccgc gcgtaaatct tcaatgcgcg agttggtaca ggaaccgata
    79501 aacactttgt cgatagccac ttcggtcagc ggaatacccg gtttcagccc catataggcc
    79561 agcgcttttt ctgccgacgc gcgttcaacc ggatcggcaa acgaagccgg atcgggaata
    79621 ttgtcgttca cggaaatcac ctggccggga ttggtgcccc aggtgacctg cggtgaaatt
    79681 tcttctgctt gcagagtgac aacggtatcg aaagttgcgc cttcgtcggt ttgcagggtt
    79741 ttccagtagg caacggcgtc gtcgaaatct ttgcctttcg gcgcatgcag acggcctttg
    79801 acatagttaa aggtggtttc gtccggtgca accagaccgg cttttgcgcc catttcgatt
    79861 gccatattgc acagggtcat acgaccttcc atgcttaaat cacggattgc ttcgccgcaa
    79921 aactccacca catgcccggt gccgcctgcg ctaccggttt taccgataat tgccagcacg
    79981 atatcttttg cggtaatgcc cggcgcggct ttgccctgga cttcaatttt catggttttt
    80041 gcgcggccct gtttcagggt ttgcgttgcc agtacgtgtt caacttcgga agtgccgata
    80101 ccaaaggcca gtgcgccaaa cgcgccgtgg gtggcggtat gcgagtcgcc gcagacaatg
    80161 gtcatccccg gcaaggtgac gccctgttcc ggccccatta cgtggacgat cccctgatac
    80221 gggtgattca ggtcatacag ttcgacgcca aattctttgc agtttttgat cagttcctgc
    80281 atctggatac gcgccatttc accgcaggca ttaatgcctt tggtctgggt agagacgttg
    80341 tgatccatgg tagcgaaggt tttgcccggc tgacgtaccg ggcgaccgtg ggcgcgcaga
    80401 ccatcgaacg cctgcggtga ggtcacttca tgcaccaggt ggcggtcgat atataacagt
    80461 ggggtttcgt tttcggcttc gtacacaacg tgagcgtcga acaatttttc gtataacgtc
    80521 ttagccatga ttacacccct tctgctacat agcgggcaat gatatcgccc atttcatcgg
    80581 tactaacggc ggcagcgcca cgggctaaat ccccggtgcg aatgccttct tctaatgcgc
    80641 ggttaatggc gcgttcaatg gcgcaagccg catcatcggc atccaggctg taacgcagca
    80701 gcagtgccag cgaaaggatt tgtgcaatcg ggttggcgat gtttttgcct gcgatatctg
    80761 gtgccgagcc gcccgccggt tcatacagtc caaaaccttg ctcgttcagg ctggcggaag
    80821 gcaacatccc catcgagcca gtgatcattg cgcactcgtc agacagaatg tcgccaaaca
    80881 ggttggagca cagcagaacg tcaaactgtg atggatcttt aatcagctgc atggtggcgt
    80941 tgtcgatgta catatgcgcc agttcgacat ccgggtattc cgtggcgatc tcgttaacga
    81001 tctcccgcca taaaatagag gattgcagca cgttggcttt atcgatcgac gtcactttgt
    81061 ggcgacgctt gcgagcagat tcaaacgcga tgcgggcgat acgttcgatc tcaaaacggt
    81121 gatacacctc ggtatcaaag gctttttcat attgtccgct accttcgcgg ccttttggct
    81181 gaccgaaata gatgccgccg gtcagttcgc gcacacacag gatgtcgaag ccgtttgcgg
    81241 caatgtctgc acgcagcgga cagaatgctt ccagcccctg atacagtttt gccgggcgca
    81301 ggttgctgaa taatttgaag tgcttacgca gaggcagcag cgcgccgcgt tctggttgct
    81361 ggtctggtgg taaatgttcc cacttcgggc cgcctaccga gccaaacagc acggcatcgg
    81421 cttgctcaca accttcaacc gtcgcaggcg gcagtggttg cccgtggtta tcaatggctg
    81481 cgccgcctac atcgtaatgg ctggtggtga tgcgcatcgc aaagcggttg cgcacggcat
    81541 ccagcacttt cagcgcctgg gtcatcactt ccggaccaat accgtccccc ggcaatacgg
    81601 caatatggta attcttcgac atcacacggt ttccttgttg ttttcgttgt gttgagcttt
    81661 gcgttgcaac tctttttcga cttctgcggc acgccagata ttgttcagaa cgtgcaccat
    81721 ggctttggca gatgactcga caatatcggt agccaggccg acgccgtgga agcggcgacc
    81781 gttgtagtta gcgacgatat ccacctgacc cagcgcatct ttaccgtggc ctttggcggt
    81841 caggctgtat ttcaccagtt cgacgttata ttcagtgatg cggttaattg cctgatagac
    81901 ggcatcgacc ggaccgttac cgttggcggc ttctgctttg acttcttcgc cacaggccag
    81961 tttgacggcg gcggtggcga tatcgttaga gccagactgc acgctgaagt aatccagacg
    82021 gaaatgctcc ggctcttctt gctgcttacc gatgaaggcc agcgcctcca gatcgtaatc
    82081 aaacacctga ccttttttgt ccgccagctt caggaaagca tcgtacaaat tgtctaaatt
    82141 atattcactt tctttatacc ccatctcatc catgcgatgt ttcaccgccg cacgccccga
    82201 acgagaggtc agattcagct ggatttggtt cagaccaata gattctggtg tcatgatttc
    82261 gtagttttcg cggtttttca gcacgccatc ctggtgtata ccggaggagt gtgcgaatgc
    82321 gccgctgcca acaatggctt tgtttgccgg gatcggcata ttacaaatct ggctaactaa
    82381 ctggctggtg cgccatatct cctggtgatt aatggcggtg tggacgttga gaatatcctt
    82441 acgaactttg atcgccatga tgacttcttc cagggaacag tttccggcac gctcgccgat
    82501 cccgttcatt gcgccttcca cctggcgtgc accggcatgt accgccgcca gtgagtttcc
    82561 gaccgccagg cccaaatcgt cgtgggtatg tacggagata atggctttgc cgatgctagg
    82621 cacgcgttca tacaggccgc tgatgattcc ggcgaactca aacggcatgg tgtagcccac
    82681 ggtgtccgga atgttgatgg tggtggcacc ggcattaatc gccgcttcga ccactcgcgc
    82741 cagatcggca atgggtgtac gcccggcatc ttcgcaagaa aattcaacat catcggtgta
    82801 attacgggcg cgtttcacca tatagatagc gcgttcgatc acctcgtcca gcgtgctgcg
    82861 cagcttggtg gcgatgtgca ttggcgaagt ggcaataaag gtatgaatac ggaaggcttc
    82921 ggcgactttc agggattcgg ccgccacgtc gatatctttt tccacgcagc gagctaacgc
    82981 acatacgcgg ctgtttttaa cctggcgggc gatggtttgc accgattcaa aatcgcccgg
    83041 cgaagagacg gggaaaccga cttccatcac gtcaacaccc atacgctcaa gggccagcgc
    83101 aatttgcagt ttttctttca cactcaagct tgcctgtaac gcctgttcac cgtcgcgcaa
    83161 tgtggtatcg aaaataatga cttgctggct catggtttgg gtccttgtct cttttagagc
    83221 gcctcgcttc gggcataaaa aaacccgcgc aatggcgcgg gttttttgtt tgactgcgtg
    83281 ctggcttaat gctggatgcc gctcactcgt ctaccgcgca aagaagatgc gtttagtagt
    83341 agtagaccga taaagcgaac gatgtgagtc attaaatcag ctccagatga atgcgatatg
    83401 cttttagagt tactggatac aaaaacggat gtcaaccctg acgcaataaa aacgtcccgc
    83461 cagcgtgagt tctgcatccg taaaattagc taattgtgct gcggtggtta aagtaagcga
    83521 tattaatttc tgcttaacta ccgacgcttt tcatcggttg acatatttca gcataaattt
    83581 ttgcatctaa tcaacgagga aaaaggggac aaaatgcacg cgttgcaaaa cctatcctga
    83641 tgatttgtat tgaattatat gttttgcgat tttttttgat attgatttgg tgaatattat
    83701 tgatcaatta atgttaagaa ttaatgcatt aaatatataa attaattatt aaataagcac
    83761 atttaatcca ttttgtagat gattgagtat tcgcggtagt tatgattaga ttgttttcgc
    83821 aacaaaaaca ttatggatta ttatgctgtg gtaaatgact cattccacgg caatggattc
    83881 tgtttttatc agaacccgta tctttatgtt ttccgaattt tactcatttt gctttttctt
    83941 attttatatg catgataaat catattcttc aggattattt ctctgcattc caataaggga
    84001 aagggagtta agtgtgacag tggagttaag tatgccagag gtacaaacag atcatccaga
    84061 gacggcggag ttaagcaaac cacagctacg catggtcgat ctcaacttat taaccgtttt
    84121 cgatgccgtg atgcaggagc aaaacattac tcgtgccgct catgttctgg gaatgtcgca
    84181 acctgcggtc agtaacgctg ttgcacgcct gaaggtgatg tttaatgacg agctttttgt
    84241 tcgttatggc cgtggtattc aaccgactgc tcgcgcattt caactttttg gttcagttcg
    84301 tcaggcattg caactagtac aaaatgaatt gcctggttca ggttttgaac ccgcgagcag
    84361 tgaacgtgta tttcatcttt gtgtttgcag cccgttagac agcattctga cctcgcagat
    84421 ttataatcac attgagcaga ttgcgccaaa tatacatgtt atgttcaagt cttcattaaa
    84481 tcagaacact gaacatcagc tgcgttatca ggaaacggag tttgtgatta gttatgaaga
    84541 cttccatcgt cctgaattta ccagcgtacc attatttaaa gatgaaatgg tgctggtagc
    84601 cagcaaaaat catccaacaa ttaagggccc gttactgaaa catgatgttt ataacgaaca
    84661 acatgcggcg gtttcgctcg atcgtttcgc gtcatttagt caaccttggt atgacacggt
    84721 agataagcaa gccagtatcg cgtatcaggg catggcaatg atgagcgtac ttagcgtggt
    84781 gtcgcaaacg catttggtcg ctattgcgcc gcgttggctg gctgaagagt tcgctgaatc
    84841 cttagaatta caggtattac cgctgccgtt aaaacaaaac agcagaacct gttatctctc
    84901 ctagcatgaa gctgccgggc gcgataaagg ccatcagtgg atggaagagc aattagtctc
    84961 aatttgcaaa cgctaactga ttgcagaata ggtcagacat gaatgtctgg tttattctgc
    85021 attttttatt gaatgtagaa ttttattctg aatgtgtggg ctctctattt taggattaat
    85081 taaaaaaata gagaaattgc tgtaagttgt gggattcagc cgatttatta tcaatttaat
    85141 cctctgtaat ggaggatttt atcgtttctt ttcacctttc ctcctgttta ttcttattac
    85201 cccgtgttta tgtctctggc tgccaattgc ttaagcaaga tcggacggtt aatgtgtttt
    85261 acacattttt tccgtcaaac agtgaggcag gccatggaga tgttgtctgg aggcgagatg
    85321 gtcgtccgat cgcttatcga tcagggcgtt aaacaagtat tcggttatcc cggaggcgca
    85381 gtccttgata tttatgatgc attgcatacc gtgggtggta ttgatcatgt attagttcgt
    85441 catgagcagg cggcggtgca tatggccgat ggcttggcgc gcgcgaccgg ggaagtcggc
    85501 gtcgtgctgg taacgtcggg tccaggggcg accaatgcga ttactggcat cgccaccgct
    85561 tatatggatt ccattccatt agttgtcctt tccgggcagg tagcgacctc gttgataggt
    85621 tacgatgcct ttcaggagtg cgacatggtg gggatttcgc gacccgtggt taaacacagt
    85681 tttctggtta agcaaacgga agacattccg caggtgctga aaaaggcttt ctggctggcg
    85741 gcaagcggtc gcccaggacc agtagtcgtt gatttaccga aagatattct taatccggcg
    85801 aacaaattac cctatgtctg gccggagtcg gtcagtatgc gttcttacaa tcccactact
    85861 accggacata aagggcaaat taagcgtgct ctgcaaagcg tggtagcggt aaaaaaaccg
    85921 gttgtctacg taggcggtgg ggcaatcacg gcgggctgcc atcagcagtt gaaagaaacg
    85981 gtggaggcgt tgaatctgcc cgttgtttgc tcattgatgg ggctgggggc gtttccggca
    86041 acgcatcgtc aggtactggg tatgctggga atgcacggta cctacgaagc caatatgacg
    86101 atgcataacg cggatgtgat tttcgccgtc ggggtacgat ttgatgaccg aacgacgaac
    86161 aatctggcaa agtactgccc aaatgccact gttctgcata tcgatattga tcctacttcc
    86221 atttctaaaa ccgtgactgc ggatatcccg attgtggggg atgctcgcca agtcctcgaa
    86281 caaatgcttg aactcttgtc gcaagaatcc gcccatcaac cactggatga gatccgcgac
    86341 tggtggcagc aaattgaaca gtggcgcgct cgtcagtgcc tgaaatatga cactcacagt
    86401 gaaaagatta aaccgcaggc ggtgatcgag actctttggc ggttgacgaa gggagacgct
    86461 tacgtgacgt ccgatgtcgg gcagcaccag atgtttgctg cactttatta tccattcgac
    86521 aaaccgcgtc gctggatcaa ttccggtggc ctcggcagca tgggttttgg tttacctgcg
    86581 gcactgggcg tcaaaatggc gttcccagaa gaaaccgtgg tttgcgtcac tggcgacggc
    86641 agtattcaga tgaacatcca ggaactgtct accgcgttgc aatacgagtt gcccgtactg
    86701 gtggtgaatc tcaataaccg ctatctgggg atggtgaagc agtggcagga catgatctat
    86761 tccggccgtc attcacaatc ttatatgcaa tcgctacccg atttcgtccg tcgcggagcc
    86821 tatgggcatg tcgggatcca gatttctcat ccgcatggct ggaaagcaaa cttagcgagg
    86881 cgctggaaca ggtgcgcaat aatcgcctgg tgtttgttga tgttaccgtc gatggcagcg
    86941 agcacgtcta cccgatgcag attcgcgggg gcggaatgga tgaaatgtgg ttaagcaaaa
    87001 cggagagaac ctgattatgc gccggatatt atcagtctta ctcgaaaatg aatcaggcgc
    87061 gttatcccgc gtgattggcc ttttttccca gcgtggctac aacattgaaa gcctgaccgt
    87121 tgcgccaacc gacgatccga cattatcgcg tatgaccatc cagaccgtgg gcgatgaaaa
    87181 agtacttgag cagatcgaaa agcaattaca caaactggtc gatgtcttgc gcgtgagtga
    87241 gttggggcag ggcgcgcatg ttgagcggga aatcatgctg gtgaaaattc aggccagcgg
    87301 ttacgggcgt gacgaagtga aacgtaatac ggaaatattc cgtgggcaaa ttatcgatgt
    87361 cacaccctcg ctttataccg ttcaattagc aggcaccagc ggtaagctta gtgcattttt
    87421 agcatcgatt cgcgatgtgg cgaaaattgt ggaggttgct cgctctggtg tggtcggact
    87481 ttcgcgcggc gataaaataa tgcgttgaga atgatctcaa tgcgcaattt acagcccaac
    87541 atgtcacgtt gggctttttt tgcgaaatca gtgggaacct ggaataaaag cagttgccgc
    87601 agttaatttt ctgcgcttag atgttaatga atttaaccca taccagtaca atggctatgg
    87661 tttttacatt ttacgcaagg ggcaattgtg aaactggatg aaatcgctcg gctggcggga
    87721 gtgtcgcgga ccactgcaag ctatgttatt aacggcaaag cgaagcaata ccgtgtgagc
    87781 gacaaaaccg ttgaaaaagt catggctgtg gtgcgtgagc acaattacca cccgaacgcc
    87841 gtggcagctg ggcttcgtgc tggacgcaca cgttctattg gtcttgtgat ccccgatctg
    87901 gagaacacca gctatacccg catcgctaac tatcttgaac gccaggcgcg gcaacggggt
    87961 tatcaactgc tgattgcctg ctcagaagat cagccagaca acgaaatgcg gtgcattgag
    88021 caccttttac agcgtcaggt tgatgccatt attgtttcga cgtcgttgcc tcctgagcat
    88081 cctttttatc aacgctgggc taacgacccg ttcccgattg tcgcgctgga ccgcgccctc
    88141 gatcgtgaac acttcaccag cgtggttggt gccgatcagg atgatgccga aatgctggcg
    88201 gaagagttac gtaagtttcc cgccgagacg gtgctttatc ttggtgcgct accggagctt
    88261 tctgtcagct tcctgcgtga acaaggtttc cgtactgcct ggaaagatga tccgcgcgaa
    88321 gtgcatttcc tgtatgccaa cagctatgag cgggaggcgg ctgcccagtt attcgaaaaa
    88381 tggctggaaa cgcatccgat gccgcaggcg ctgttcacaa cgtcgtttgc gttgttgcaa
    88441 ggagtgatgg atgtcacgct gcgtcgcgac ggcaaactgc cttctgacct ggcaattgcc
    88501 acctttggcg ataacgaact gctcgacttc ttacagtgtc cggtgctggc agtggctcaa
    88561 cgtcaccgcg atgtcgcaga gcgtgtgctg gagattgtcc tggcaagcct ggacgaaccg
    88621 cgtaagccaa aacctggttt aacgcgcatt aaacgtaatc tctatcgccg cggcgtgctc
    88681 agccgtagct aagccgcgaa caaaaatacg cgccaggtga atttccctct ggcgcgtaga
    88741 gtacgggact ggacatcaat atgcttaaag taaataagac tattcctgac tattattgat
    88801 aaatgctttt aaacccgccc gttaattaac tcaccagctg aaattcacaa taattaagtg
    88861 atatcgacag cgcgtttttg cattattttg ttacatgcgg cgatgaattg ccgatttaac
    88921 aaacactttt ctttgctttt gcgcaaaccc gctggcatca agcgccacac agacgtaaca
    88981 aggactgtta accggggaag atatgtccta aaatgccgct cgcgtcgcaa actgacactt
    89041 tatatttgct gtggaaaata gtgagtcatt ttaaaacggt gatgacgatg agggattttt
    89101 tcttacagct attcataacg ttaatttgct tcgcacgttg gacgtaaaat aaacaacgct
    89161 gatattagcc gtaaacatcg ggttttttac ctcggtatgc cttgtgactg gcttgacaag
    89221 cttttcctca gctccgtaaa ctcctttcag tgggaaattg tggggcaaag tgggaataag
    89281 gggtgaggct ggcatgttcc ggggagcaac gttagtcaat ctcgacagca aagggcgctt
    89341 atcagtgcct acccgttatc gggaacagct gcttgagaac gctgccggtc aaatggtttg
    89401 caccattgac atttatcacc cgtgcctgct gctttacccc ctgcctgaat gggaaattat
    89461 cgagcaaaaa ttatcgcgtc tgtcgagcat gaacccggtt gagcgccgtg tgcagcgcct
    89521 actgttaggt catgccagcg aatgtcagat ggatggcgca ggtcgattgt taatcgcgcc
    89581 agtactgcgg caacatgccg ggctgacaaa agaagtgatg ctggttggac agttcaacaa
    89641 gtttgagctg tgggatgaaa caacctggca tcaacaggtc aaggaagata tcgacgcaga
    89701 gcagttggct accggagact tatcggagcg actgcaggac ttgtctctat aaaatgatgg
    89761 aaaactataa acatactacg gtgctgctgg atgaagccgt taatggcctc aatatccgtc
    89821 ctgatggcat ctacattgat gggacttttg gtcgcggtgg tcactcacgt ctgatcctct
    89881 cgcagcttgg cgaagagggg cgtttgctgg cgatcgatcg cgacccgcag gctatcgccg
    89941 ttgcgaagac tattgatgat ccgcgcttct ccatcatcca cggacctttc tccgcgctgg
    90001 gcgaatacgt tgccgagcgc gatcttatcg gcaagatcga cggcattctc ctcgatcttg
    90061 gcgtctcttc accgcaactt gatgatgctg aacgtggctt ttcctttatg cgcgatggtc
    90121 cgctggacat gcgtatggac ccaacccgtg ggcagtcagc cgctgaatgg ctacaaaccg
    90181 cagaagaagc cgatatcgcc tgggtattga aaacctatgg tgaagagcgt tttgccaaac
    90241 gcattgcccg cgccattgtc gagcgtaacc gcgaacagcc gatgacccgc accaaagaac
    90301 tggcggaagt cgtggctgct gcaacgccgg tgaaagataa gtttaaacat cccgcgaccc
    90361 gtaccttcca ggcggtgcgc atttgggtaa acagtgaact ggaggagata gagcaggcgc
    90421 taaaaagctc gctcaacgtg ctggccccgg gtgggcggct ttcgatcatc agcttccact
    90481 cgctggaaga ccgtattgtg aaacgtttta tgcgtgaaaa cagccgcggt ccgcaagttc
    90541 cggcagggtt accgatgact gaagagcagc tcaaaaaact gggtggccgt cagctgcgag
    90601 cactaggcaa gttaatgccg ggcgaagaag aggtggctga gaaccctcgt gcccgtagtt
    90661 cagttctgcg tattgcagag aggacgaatg catgatcagc agagtgacag aagctctaag
    90721 caaagttaaa ggatcgatgg gaagccacga gcgccatgca ttgcctggtg ttatcggtga
    90781 cgatcttttg cgatttggga agctgccact ctgcctgttc atttgcatta ttttgacggc
    90841 ggtgactgtg gtaaccacgg cgcaccatac ccgtttactg accgctcagc gcgaacaact
    90901 ggtgctggag cgagatgctt tagacattga atggcgcaac ctgatccttg aagagaatgc
    90961 gctcggcgac catagccggg tggaaaggat cgccacggaa aagctgcaaa tgcagacatg
    91021 ttgatccgtc acaagaaaat atcgtagtgc aaaaataagg ataaacgcga cgcatgaaag
    91081 cagcggcgaa aacgcagaaa ccaaaacgtc aggaagaaca tgccaacttt atcagttggc
    91141 gttttgcgtt gttatgcggc tgtattctcc tggcgctggc ttttctgctc ggacgcgtag
    91201 cgtggttaca agttatctcc ccggatatgc tggtgaaaga gggcgacatg cgttctcttc
    91261 gcgttcagca agtttccacc tcccgcggca tgattactga ccgttctggt cgcccgttag
    91321 cggtgagcgt gccggtaaaa gcgatttggg ctgacccgaa agaagtgcat gacgctggcg
    91381 gtatcagcgt cggtgaccgc tggaaggcgc tggctaacgc gctcaatatt ccgctggatc
    91441 agctttcagc ccgcattaac gccaacccga aagggcgctt tatttatctg gcgcgtcagg
    91501 tgaaccctga catggcggac tacatcaaaa aactgaaact gccggggatt catctgcgtg
    91561 aagagtctcg ccgttactat ccgtccggcg aagtgactgc tcacctcatc ggctttacta
    91621 acgtcgatag tcaagggatt gagggcgttg agaagagttt cgataaatgg cttaccgggc
    91681 agccgggtga gcgcattgtg cgtaaagacc gctatggtcg cgtaattgaa gatatttctt
    91741 ctactgacag ccaggcagcg cacaacctgg cgctgagtat tgatgaacgc ctgcaggcgc
    91801 tggtttatcg cgaactgaac aacgcggtgg cctttaacaa ggctgaatct ggtagcgccg
    91861 tgctggtgga tgtcaacacc ggtgaagtgc tggcgatggc taacagcccg tcatacaacc
    91921 ctaacaatct gagcggcacg ccgaaagagg cgatgcgtaa ccgtaccatc accgacgtgt
    91981 ttgaaccggg ctcaacggtt aaaccgatgg tggtaatgac cgcgttgcaa cgtggcgtgg
    92041 tgcgggaaaa ctcggtactc aataccattc cttatcgaat taacggccac gaaatcaaag
    92101 acgtggcacg ctacagcgaa ttaaccctga ccggggtatt acagaagtcg agtaacgtcg
    92161 gtgtttccaa gctggcgtta gcgatgccgt cctcagcgtt agtagatact tactcacgtt
    92221 ttggactggg aaaagcgacc aatttggggt tggtcggaga acgcagtggc ttatatcctc
    92281 aaaaacaacg gtggtctgac atagagaggg ccaccttctc tttcggctac gggctaatgg
    92341 taacaccatt acagttagcg cgagtctacg caactatcgg cagctacggc atttatcgcc
    92401 cactgtcgat taccaaagtt gaccccccgg ttcccggtga acgtgtcttc ccggaatcca
    92461 ttgtccgcac tgtggtgcat atgatggaaa gcgtggcgct accaggcggc ggcggcgtga
    92521 aggcggcgat taaaggctat cgtatcgcca ttaaaaccgg taccgcgaaa aaggtcgggc
    92581 cggacggtcg ctacatcaat aaatatattg cttataccgc aggcgttgcg cctgcgagtc
    92641 agccgcgctt cgcgctggtt gttgttatca acgatccgca ggcgggtaaa tactacggcg
    92701 gcgccgtttc cgcgccggtc tttggtgcca tcatgggcgg cgtattgcgt accatgaaca
    92761 tcgagccgga tgcgctgaca acgggcgata aaaatgaatt tgtgattaat caaggcgagg
    92821 ggacaggtgg cagatcgtaa tttgcgcgac cttcttgctc cgtgggtgcc agacgcacct
    92881 tcgcgagcac tgcgagagat gacactcgac agccgtgtgg ctgcggcggg cgatctcttt
    92941 gtagctgtag taggtcatca ggcggacggg cgtcgatata tcccgcaggc gatagcgcaa
    93001 ggtgtcgctg ccattattgc agaggcgaaa gatgaggcga ccgatggtga aatccgtgaa
    93061 atgcacggcg taccggtcat ctatctcagc cagctcaacg agcgtttatc tgcactggcg
    93121 ggccgctttt accatgaacc ctctgacaat ttacgtctcg tgggcgtaac gggcaccaac
    93181 ggcaaaacca cgactaccca gctgttggcg cagtggagcc aactgcttgg cgaaatcagc
    93241 gcggtaatgg gcaccgttgg taacggcctg ctggggaaag tgatcccgac agaaaataca
    93301 accggttcgg cagtcgatgt tcagcatgag ctggcggggc tggtggatca gggcgcgacg
    93361 ttttgcgcaa tggaagtttc ctcccacggg ctggtacagc accgtgtggc ggcattgaaa
    93421 tttgcggcgt cggtctttac caacttaagc cgcgatcacc ttgattatca tggtgatatg
    93481 gaacactacg aagccgcgaa atggctgctt tattctgagc atcattgcgg tcaggcgatt
    93541 attaacgccg acgatgaagt gggccgccgc tggctggcaa aactgccgga cgcggttgcg
    93601 gtatcaatgg aagatcatat taatccgaac tgtcacggac gctggttgaa agcgaccgaa
    93661 gtgaactatc acgacagcgg tgcgacgatt cgctttagct caagttgggg cgatggcgaa
    93721 attgaaagcc atctgatggg cgcttttaac gtcagcaacc tgctgctcgc gctggcgaca
    93781 ctgttggcac tcggctatcc actggctgat ctgctgaaaa ccgccgcgcg tctgcaaccg
    93841 gtttgcggac gtatggaagt gttcactgcg ccaggcaaac cgacggtggt ggtggattac
    93901 gcgcatacgc cggatgcact ggaaaaagcc ttacaggcgg cgcgtctgca ctgtgcgggc
    93961 aagctgtggt gtgtctttgg ctgtggtggc gatcgcgata aaggtaagcg tccactgatg
    94021 ggcgcaattg ccgaagagtt tgctgacgtg gcggtggtga cggacgataa cccgcgtacc
    94081 gaagaaccgc gtgccatcat caacgatatt ctggcgggaa tgttagatgc cggacatgcc
    94141 aaagtgatgg aaggccgtgc tgaagcggtg acttgcgccg ttatgcaggc taaagagaat
    94201 gatgtggtac tggtcgcggg caaaggccat gaagattacc agattgttgg caatcagcgt
    94261 ctggactact ccgatcgcgt cacggtggcg cgtctgctgg gggtgattgc atgattagcg
    94321 taacccttag ccaacttacc gacattctca acggtgaact gcaaggtgca gatatcaccc
    94381 ttgatgctgt aaccactgat acccgaaaac tgacgccggg ctgcctgttt gttgccctga
    94441 aaggcgaacg ttttgatgcc cacgattttg ccgaccaggc gaaagctggc gcggcaggcg
    94501 cactactggt tagccgtccg ctggacatcg acctgccgca gttaatcgtc aaggatacgc
    94561 gtctggcgtt tggtgaactg gctgcatggg ttcgccagca agttccggcg cgcgtggttg
    94621 ctctgacggg gtcctccggc aaaacctccg ttaaagagat gacggcggcg attttaagcc
    94681 agtgcggcaa cacgctttat acggcaggca atctcaacaa cgacatcggt gtaccgatga
    94741 cgctgttgcg cttaacgccg gaatacgatt acgcagttat tgaacttggc gcgaaccatc
    94801 agggcgaaat agcctggact gtgagtctga ctcgcccgga acgtgcgctg gtcaacaacc
    94861 tggcagcggc gcatctggaa ggttttggct cgcttgcggg tgtcgcgaaa gcgaaaggtg
    94921 aaatctttag cggcctgccg gaaaacggta tcgccattat gaacgccgac aacaacgact
    94981 ggctgaactg gcagagcgta attggctcac gcaaagtgtg gcgtttctca cccaatgccg
    95041 ccaacagcga tttcaccgcc accaatatcc atgtgacctc gcacggtacg gaatttaccc
    95101 tacaaacccc aaccggtagc gtcgatgttc tgctgccgtt gccggggcgt cacaatattg
    95161 cgaatgcgct ggcagccgct gcgctctcca tgtccgtggg cgcaacgctt gatgctatca
    95221 aagcggggct ggcaaatctg aaagctgttc caggccgtct gttccccatc caactggcag
    95281 aaaaccagtt gctgctcgac gactcctaca acgccaatgt cggttcaatg actgcagcag
    95341 tccaggtact ggctgaaatg ccgggctacc gcgtgctggt ggtgggcgat atggcggaac
    95401 tgggcgctga aagcgaagcc tgccatgtac aggtgggcga ggcggcaaaa gctgctggta
    95461 ttgaccgcgt gttaagcgtg ggtaaacaaa gccatgctat cagcaccgcc agcggcgttg
    95521 gcgaacattt tgctgataaa actgcgttaa ttacgcgtct taaattactg attgctgagc
    95581 aacaggtaat tacgatttta gttaagggtt cacgtagtgc cgccatggaa gaggtagtac
    95641 gcgctttaca ggagaatggg acatgttagt ttggctggcc gaacatttgg tcaaatatta
    95701 ttccggcttt aacgtctttt cctatctgac gtttcgcgcc atcgtcagcc tgctgaccgc
    95761 gctgttcatc tcattgtgga tgggcccgcg tatgattgct catttgcaaa aactttcctt
    95821 tggtcaggtg gtgcgtaacg acggtcctga atcacacttc agcaagcgcg gtacgccgac
    95881 catgggcggg attatgatcc tgacggcgat tgtgatctcc gtactgctgt gggcttaccc
    95941 gtccaatccg tacgtctggt gcgtgttggt ggtgctggta ggttacggtg ttattggctt
    96001 tgttgatgat tatcgcaaag tggtgcgtaa agacaccaaa gggttgatcg ctcgttggaa
    96061 gtatttctgg atgtcggtca ttgcgctggg tgtcgccttc gccctgtacc ttgccggcaa
    96121 agacacgccc gcaacgcagc tggtggtccc attctttaaa gatgtgatgc cgcagctggg
    96181 gctgttctac attctgctgg cttacttcgt cattgtgggt actggcaacg cggtaaacct
    96241 gaccgatggt ctcgacggcc tggcaattat gccgaccgta tttgtcgccg gtggttttgc
    96301 gctggtggcg tgggcgaccg gcaatatgaa ctttgccagc tacttgcata taccgtatct
    96361 gcgacacgcc ggggaactgg ttattgtctg taccgcgata gtcggggcag gactgggctt
    96421 cctgtggttt aacacctatc cggcgcaggt ctttatgggc gatgtaggtt cgctggcgtt
    96481 aggtggtgcg ttaggcatta tcgccgtact gctacgtcag gaattcctgc tggtgattat
    96541 ggggggcgtg ttcgtggtag aaacgctttc tgtcatcctg caggtcggct cctttaaact
    96601 gcgcggacaa cgtattttcc gcatggcacc gattcatcac cactatgaac tgaaaggctg
    96661 gccggaaccg cgcgtcattg tgcgtttctg gattatttcg ctgatgctgg ttctgattgg
    96721 tctggcaacg ctgaaggtac gttaatcatg gctgattatc agggtaaaaa tgtcgtcatt
    96781 atcggcctgg gcctcaccgg gctttcctgc gtggactttt tcctcgctcg cggtgtgacg
    96841 ccgcgcgtta tggatacgcg tatgacaccg cctggcctgg ataaattacc cgaagccgta
    96901 gaacgccaca cgggcagtct gaatgatgaa tggctgatgg cggcagatct gattgtcgcc
    96961 agtcccggta ttgcactggc gcatccatcc ttaagcgctg ccgctgatgc cggaatcgaa
    97021 atcgttggcg atatcgagct gttctgtcgc gaagcacaag caccgattgt ggcgattacc
    97081 ggttctaacg gcaaaagcac ggtcaccacg ctagtgggtg aaatggcgaa agcggcgggg
    97141 gttaacgttg gtgtgggtgg caatattggc ctgcctgcgt tgatgctact ggatgatgag
    97201 tgtgaactgt acgtgctgga actgtcgagc ttccagctgg aaaccacctc cagcttacag
    97261 gcggtagcag cgaccattct gaacgtgact gaagatcata tggatcgcta tccgtttggt
    97321 ttacaacagt atcgtgcagc aaaactgcgc atttacgaaa acgcgaaagt ttgcgtggtt
    97381 aatgctgatg atgccttaac aatgccgatt cgcggtgcgg atgaacgctg cgtcagcttt
    97441 ggcgtcaaca tgggtgacta tcacctgaat catcagcagg gcgaaacctg gctgcgggtt
    97501 aaaggcgaga aagtgctgaa tgtgaaagag atgaaacttt ccgggcagca taactacacc
    97561 aatgcgctgg cggcgctggc gctggcagat gctgcagggt taccgcgtgc cagcagcctg
    97621 aaagcgttaa ccacattcac tggtctgccg catcgctttg aagttgtgct ggagcataac
    97681 ggcgtacgtt ggattaacga ttcgaaagcg accaacgtcg gcagtacgga agcggcgctg
    97741 aatggcctgc acgtagacgg cacactgcat ttgttgctgg gtggcgatgg taaatcggcg
    97801 gactttagcc cactggcgcg ttacctgaat ggcgataacg tacgtctgta ttgtttcggt
    97861 cgtgacggcg cgcagctggc ggcgctacgc ccggaagtgg cagaacaaac cgaaactatg
    97921 gaacaggcga tgcgcttgct ggctccgcgt gttcagccgg gcgatatggt tctgctctcc
    97981 ccagcctgtg ccagccttga tcagttcaag aactttgaac aacgaggcaa tgagtttgcc
    98041 cgtctggcga aggagttagg ttgatgcgtt tatctctccc tcgcctgaaa atgccgcgcc
    98101 tgccaggatt cagtatcctg gtctggatct ccacggcgct aaagggctgg gtgatgggct
    98161 cgcgggaaaa agataccgac agcctgatca tgtacgatcg caccttactg tggctgacct
    98221 tcggcctcgc ggcgattggc tttatcatgg tgacctcggc gtcaatgccc atagggcaac
    98281 gcttaaccaa cgatccgttc ttcttcgcga agcgtgatgg tgtctatctg attttggcgt
    98341 ttattctggc gatcattacg ctgcgtctgc cgatggagtt ctggcaacgc tacagtgcca
    98401 cgatgctgct cggatctatc atcctgctga tgatcgtcct ggtagtgggt agctcggtta
    98461 aaggggcatc gcgttggatc gatctcggtt tgctgcgtat ccagcctgcg gagctgacaa
    98521 aactgtcgct gttttgctat atcgccaact atctggtgcg taaaggcgac gaagtacgta
    98581 ataacctgcg cggcttcctg aaaccgatgg gcgtgattct ggtgttggca gtgttactgc
    98641 tggcacagcc agaccttggt acggtggtgg tgttgtttgt gactacgctg gcgatgttgt
    98701 tcctggcggg agcgaaattg tggcagttca ttgccattat cggtatgggc atttcagcgg
    98761 ttgtgttgct gatactcgcc gaaccgtacc gtatccgccg tgttaccgca ttctggaacc
    98821 cgtgggaaga tccctttggc agcggctatc agttaacgca atcgctgatg gcgtttggtc
    98881 gcggcgaact ttgggggcaa ggtttaggta actcggtaca aaaactggag tatctgccgg
    98941 aagcgcacac tgactttatt ttcgccatta tcggcgaaga actggggtat gtcggtgtgg
    99001 tgctggcact tttaatggta ttcttcgtcg cttttcgcgc gatgtcgatt ggccgtaaag
    99061 cattagaaat tgaccaccgt ttttccggtt ttctcgcctg ttctattggc atctggttta
    99121 gcttccaggc gctggttaac gtaggcgcgg cggcggggat gttaccgacc aaaggtctga
    99181 cattgccgct gatcagttac ggtggttcga gcttactgat tatgtcgaca gccatcatga
    99241 tgctgttgcg tattgattat gaaacgcgtc tggagaaagc gcaggcgttt gtacgaggtt
    99301 cacgatgagt ggtcaaggaa agcgattaat ggtgatggca ggcggaaccg gtggacatgt
    99361 attcccggga ctggcggttg cgcaccatct aatggctcag ggttggcaag ttcgctggct
    99421 ggggactgcc gaccgtatgg aagcggactt agtgccaaaa catggcatcg aaattgattt
    99481 cattcgtatc tctggtctgc gtggaaaagg tataaaagca ctgatagctg ccccgctgcg
    99541 tatcttcaac gcctggcgtc aggcgcgggc gattatgaaa gcgtacaaac ctgacgtggt
    99601 gctcggtatg ggaggctacg tgtcaggtcc aggtggtctg gccgcgtggt cgttaggcat
    99661 tccggttgta cttcatgaac aaaacggtat tgcgggctta accaataaat ggctggcgaa
    99721 gattgccacc aaagtgatgc aggcgtttcc aggtgctttc cctaatgcgg aagtagtggg
    99781 taacccggtg cgtaccgatg tgttggcgct gccgttgccg cagcaacgtt tggctggacg
    99841 tgaaggtccg gttcgtgtgc tggtagtggg tggttctcag ggcgcacgca ttcttaacca
    99901 gacaatgccg caggttgctg cgaaactggg tgattcagtc actatctggc atcagagcgg
    99961 caaaggttcg caacaatccg ttgaacaggc gtatgccgaa gcggggcaac cgcagcataa
   100021 agtgacggaa tttattgatg atatggcggc ggcgtatgcg tgggcggatg tcgtcgtttg
   100081 ccgctccggt gcgttaacgg tgagtgaaat cgccgcggca ggactaccgg cgttgtttgt
   100141 gccgtttcaa cataaagacc gccagcaata ctggaatgcg ctaccgctgg aaaaagcggg
   100201 cgcagccaaa attatcgagc agccacagct tagcgtggat gctgtcgcca acaccctggc
   100261 cgggtggtcg cgagaaacct tattaaccat ggcagaacgc gcccgcgctg catccattcc
   100321 ggatgccacc gagcgagtgg caaatgaagt gagccgggtt gcccgggcgt aattgtagcg
   100381 atgccttttg catcgtatga atttaagaag ttaatggcgt aaagaatgaa tacacaacaa
   100441 ttggcaaaac tgcgttccat cgtgcccgaa atgcgtcgcg ttcggcacat acattttgtc
   100501 ggcattggtg gtgccggtat gggcggtatt gccgaagttc tggccaatga aggttatcag
   100561 atcagtggtt ccgatttagc gccaaatccg gtcacgcagc agttaatgaa tctgggtgcg
   100621 acgatttatt tcaaccatcg cccggaaaac gtacgtgatg ccagcgtggt cgttgtttcc
   100681 agcgcgattt ctgccgataa cccggaaatt gtcgccgctc atgaagcgcg tattccggtg
   100741 atccgtcgtg ccgaaatgct ggctgagtta atgcgttttc gtcatggcat cgccattgcc
   100801 ggaacgcacg gcaaaacgac aaccaccgcg atggtttcca gcatctacgc agaagcgggg
   100861 ctcgacccaa ccttcgttaa cggcgggctg gtaaaagcgg cgggggttca tgcgcgtttg
   100921 gggcatggtc ggtacctgat tgccgaagca gatgagagtg atgcatcgtt cctgcatctg
   100981 caaccgatgg tggcgattgt caccaatatc gaagccgacc acatggatac ctaccagggc
   101041 gactttgaga atttaaaaca gacttttatt aattttctgc acaacctgcc gttttacggt
   101101 cgtgcggtga tgtgtgttga tgatccggtg atccgcgaat tgttaccgcg agtggggcgt
   101161 cagaccacga cttacggctt cagcgaagat gccgacgtgc gtgtagaaga ttatcagcag
   101221 attggcccgc aggggcactt tacgctgctg cgccaggaca aagagccgat gcgcgtcacc
   101281 ctgaatgcgc caggtcgtca taacgcgctg aacgccgcag ctgcggttgc ggttgctacg
   101341 gaagagggca ttgacgacga ggctattttg cgggcgcttg aaagcttcca ggggactggt
   101401 cgccgttttg atttcctcgg tgaattcccg ctggagccag tgaatggtaa aagcggtacg
   101461 gcaatgctgg tcgatgacta cggccaccac ccgacggaag tggacgccac cattaaagcg
   101521 gcgcgcgcag gctggccgga taaaaacctg gtaatgctgt ttcagccgca ccgttttacc
   101581 cgtacgcgcg acctgtatga tgatttcgcc aatgtgctga cgcaggttga taccctgttg
   101641 atgctggaag tgtatccggc tggcgaagcg ccaattccgg gagcggacag ccgttcgctg
   101701 tgtcgcacaa ttcgtggacg tgggaaaatt gatcccattc tggtgccgga tccggcgcgg
   101761 gtagccgaga tgctggcacc ggtattaacc ggtaacgacc tgattctcgt tcagggggct
   101821 ggtaatattg gaaaaattgc ccgttcttta gctgaaatca aactgaagcc gcaaactccg
   101881 gaggaagaac aacatgactg ataaaatcgc ggtcctgttg ggtgggacct ccgctgagcg
   101941 ggaagtttct ctgaattctg gcgcagcggt gttagccgga ctgcgtgaag gcggtattga
   102001 cgcgtatcct gtcgacccga aagaagtcga cgtgacgcaa ctgaagtcga tgggctttca
   102061 gaaagtgttt atcgcgctac acggtcgcgg cggtgaagat ggtacgctgc aggggatgct
   102121 cgagctgatg ggcttgcctt ataccggaag cggagtgatg gcatctgcgc tttcaatgga
   102181 taaactacgc agcaaacttc tatggcaagg tgccggttta ccggtcgcgc cgtgggtagc
   102241 gttaacccgc gcagagtttg aaaaaggcct gagcgataag cagttagcag aaatttctgc
   102301 tctgggtttg ccggttatcg ttaagccgag ccgcgaaggt tccagtgtgg gaatgtcaaa
   102361 agtagtagca gaaaatgctc tacaagatgc attaagattg gcatttcagc acgatgaaga
   102421 agtattgatt gaaaaatggc taagtgggcc ggagttcacg gttgcgatac tcggtgaaga
   102481 aattttaccg tcaatacgta ttcaaccgtc cggaaccttc tatgattatg aggcgaagta
   102541 tctctctgat gagacacagt atttctgccc cgcaggtctg gaagcgtcac aagaggccaa
   102601 tttgcaggca ttagtgctga aagcatggac gacgttaggt tgcaaaggat ggggacgtat
   102661 tgacgttatg ctggacagcg atggacagtt ttatctgctg gaagccaata cctcaccggg
   102721 tatgaccagc cacagcctgg tgccgatggc ggcacgtcag gcaggtatga gcttctcgca
   102781 gttggtagta cgaattctgg aactggcgga ctaatatgtc gcaggctgct ctgaacacgc
   102841 gaaacagcga agaagaggtt tcttctcgcc gcaataatgg aacgcgtctg gcggggatcc
   102901 ttttcctgct gaccgtttta acgacagtgt tggtgagcgg ctgggtcgtg ttgggctgga
   102961 tggaagatgc gcaacgcctg ccgctctcaa agctggtgtt gaccggtgaa cgccattaca
   103021 cacgtaatga cgatatccgg cagtcgatcc tggcattggg tgagccgggt acctttatga
   103081 cccaggatgt caacatcatc cagacgcaaa tagaacaacg cctgccgtgg attaagcagg
   103141 tgagcgtcag aaagcagtgg cctgatgaat tgaagattca tctggttgaa tatgtgccga
   103201 ttgcgcggtg gaatgatcaa catatggtag acgcggaagg aaataccttc agcgtgccgc
   103261 cagaacgcac cagcaagcag gtgcttccaa tgctgtatgg cccggaaggc agcgccaatg
   103321 aagtgttgca gggctatcgc gaaatggggc agatgctggc aaaggacaga tttactctga
   103381 aggaagcggc gatgaccgcg cggcgttcct ggcagttgac gctgaataac gatattaagc
   103441 tcaatcttgg ccggggcgat acgatgaaac gtttggctcg ctttgtagaa ctttatccgg
   103501 ttttacagca gcaggcgcaa accgatggca aacggattag ctacgttgat ttgcgttatg
   103561 actctggagc ggcagtaggc tgggcgccct tgccgccaga ggaatctact cagcaacaaa
   103621 atcaggcaca ggcagaacaa caatgatcaa ggcgacggac agaaaactgg tagtaggact
   103681 ggagattggt accgcgaagg ttgccgcttt agtaggggaa gttctgcccg acggtatggt
   103741 caatatcatt ggcgtgggca gctgcccgtc gcgtggtatg gataaaggcg gggtgaacga
   103801 cctcgaatcc gtggtcaagt gcgtacaacg cgccattgac caggcagaat tgatggcaga
   103861 ttgtcagatc tcttcggtat atctggcgct ttctggtaag cacatcagct gccagaatga
   103921 aattggtatg gtgcctattt ctgaagaaga agtgacgcaa gaagatgtgg aaaacgtcgt
   103981 ccataccgcg aaatcggtgc gtgtgcgcga tgagcatcgt gtgctgcatg tgatcccgca
   104041 agagtatgcg attgactatc aggaagggat caagaatccg gtaggacttt cgggcgtgcg
   104101 gatgcaggca aaagtgcacc tgatcacatg tcacaacgat atggcgaaaa acatcgtcaa
   104161 agcggttgaa cgttgtgggc tgaaagttga ccaactgata tttgccggac tggcatcaag
   104221 ttattcggta ttgacggaag atgaacgtga actgggtgtc tgcgtcgtcg atatcggtgg
   104281 tggtacaatg gatatcgccg tttataccgg tggggcattg cgccacacta aggtaattcc
   104341 ttatgctggc aatgtcgtga ccagtgatat cgcttacgcc tttggcacgc cgccaagcga
   104401 cgccgaagcg attaaagttc gccacggttg tgcgctgggt tccatcgttg gaaaagatga
   104461 gagcgtggaa gtgccgagcg taggtggtcg tccgccacgg agtctgcaac gtcagacact
   104521 ggcagaggtg atcgagccgc gctataccga gctgctcaac ctggtcaacg aagagatatt
   104581 gcagttgcag gaaaagcttc gccaacaagg ggttaaacat cacctggcgg caggcattgt
   104641 attaaccggt ggcgcagcgc agatcgaagg tcttgcagcc tgtgctcagc gcgtgtttca
   104701 tacgcaagtg cgtatcggcg cgccgctgaa cattaccggt ttaacggatt atgctcagga
   104761 gccgtattat tcgacggcgg tgggattgct tcactatggg aaagagtcac atcttaacgg
   104821 tgaagctgaa gtagaaaaac gtgttacagc atcagttggc tcgtggatca agcgactcaa
   104881 tagttggctg cgaaaagagt tttaattttt atgaggccga cgatgattac ggcctcaggc
   104941 gacaggcaca aatcggagag aaactatgtt tgaaccaatg gaacttacca atgacgcggt
   105001 gattaaagtc atcggcgtcg gcggcggcgg cggtaatgct gttgaacaca tggtgcgcga
   105061 gcgcattgaa ggtgttgaat tcttcgcggt aaataccgat gcacaagcgc tgcgtaaaac
   105121 agcggttgga cagacgattc aaatcggtag cggtatcacc aaaggactgg gcgctggcgc
   105181 taatccagaa gttggccgca atgcggctga tgaggatcgc gatgcattgc gtgcggcgct
   105241 ggaaggtgca gacatggtct ttattgctgc gggtatgggt ggtggtaccg gtacaggtgc
   105301 ggcaccagtc gtcgctgaag tggcaaaaga tttgggtatc ctgaccgttg ctgtcgtcac
   105361 taagcctttc aactttgaag gcaagaagcg tatggcattc gcggagcagg ggatcactga
   105421 actgtccaag catgtgaact ctctgatcac tatcccgaac gacaaactgc tgaaagttct
   105481 gggccgcggt atctccctgc tggatgcgtt tggcgcagcg aacgatgtac tgaaaggcgc
   105541 tgtgcaaggt atcgctgaac tgattactcg tccgggtttg atgaacgtgg actttgcaga
   105601 cgtacgcacc gtaatgtctg agatgggcca cgcaatgatg ggttctggcg tggcgagcgg
   105661 tgaagaccgt gcggaagaag ctgctgaaat ggctatctct tctccgctgc tggaagatat
   105721 cgacctgtct ggcgcgcgcg gcgtgctggt taacatcacg gcgggcttcg acctgcgtct
   105781 ggatgagttc gaaacggtag gtaacaccat ccgtgcattt gcttccgaca acgcgactgt
   105841 ggttatcggt acttctcttg acccggatat gaatgacgag ctgcgcgtaa ccgttgttgc
   105901 gacaggtatc ggcatggaca aacgtcctga aatcactctg gtgaccaata agcaggttca
   105961 gcagccagtg atggatcgct accagcagca tgggatggct ccgctgaccc aagagcagaa
   106021 gccggttgct aaagtcgtga atgacaatgc gccgcaaact gcgaaagagc cggattatct
   106081 ggatatccca gcattcctgc gtaagcaagc tgattaagaa ttgactggaa tttgggtttc
   106141 gattctcttt gtgctaaact ggcccgccga atgtatagta cacttcggtt ggataggtaa
   106201 tttggcgaga taatacgatg atcaaacaaa ggacacttaa acgtatcgtt caggcgacgg
   106261 gtgtcggttt acataccggc aagaaagtca ccctgacgtt acgccctgcg ccggccaaca
   106321 ccggggtcat ctatcgtcgc accgacttga atccaccggt agatttcccg gccgatgcca
   106381 aatctgtgcg tgataccatg ctctgtacgt gtctggtcaa cgagcatgat gtacggattt
   106441 caaccgtaga gcacctcaat gctgctctcg cgggcttggg catcgataac attgttatcg
   106501 aagttaacgc gccggaaatc ccgatcatgg acggcagcgc cgctccgttt gtatacctgc
   106561 tgcttgacgc cggtatcgac gagttgaact gcgccaaaaa atttgttcgc atcaaagaga
   106621 ctgttcgtgt cgaagatggc gataagtggg ctgaatttaa gccgtacaat ggtttttcgc
   106681 tggatttcac catcgatttt aaccatccgg ctattgattc cagcaaccag cgctatgcga
   106741 tgaacttctc cgctgatgcg tttatgcgcc agatcagccg tgcgcgtacg ttcggtttca
   106801 tgcgtgatat cgaatatctg cagtcccgtg gtttgtgcct gggcggcagc ttcgattgtg
   106861 ccatcgttgt tgacgattat cgcgtactga acgaagacgg cctgcgtttt gaagacgaat
   106921 ttgtgcgtca caaaatgctc gatgcgatcg gtgacttgtt catgtgtggt cacaatatta
   106981 ttggtgcatt taccgcttat aaatccggtc atgcactgaa taacaaactg ctgcaggctg
   107041 tcctggcgaa acaggaagcc tgggaatatg tgaccttcca ggacgacgca gaactgccgt
   107101 tggccttcaa agcgccttca gctgtactgg cataacgaca tttatactgt cgtataaaat
   107161 tcgactggca aatctggcac tctctccggc caggtgaacc agtcgttttt ttttgaattt
   107221 tataagagct ataaaaaacg gtgcgaacgc tgttttctta agcacttttc cgcacaactt
   107281 atcttcattc gtgctgtgga ctgcaggctt taatgataag atttgtgcgc taaatacgtt
   107341 tgaatatgat cgggatggca ataacgtgag tggaatactg acgcgctggc gacagtttgg
   107401 taaacgctac ttctggccgc atctcttatt agggatggtt gcggcgagtt taggtttgcc
   107461 tgcgctcagc aacgccgccg aaccaaacgc gcccgcaaaa gcgacaaccc gcaaccacga
   107521 gccttcagcc aaagttaact ttggtcaatt ggccttgctg gaagcgaaca cacgccgccc
   107581 gaattcgaac tattccgttg attactggca tcaacatgcc attcgcacgg taatccgtca
   107641 tctttctttc gcaatggcac cgcaaacact gcccgttgct gaagaatctt tgcctcttca
   107701 ggcgcaacat cttgcattac tggatacgct cagcgcgctg ctgacccagg aaggcacgcc
   107761 gtctgaaaag ggttatcgca ttgattatgc gcattttacc ccacaagcaa aattcagcac
   107821 gcccgtctgg ataagccagg cgcaaggcat ccgtgctggc cctcaacgcc tcacctaaca
   107881 acaataaacc tttacttcat tttattaact ccgcaacgcg gggcgtttga gattttatta
   107941 tgctaatcaa attgttaact aaagttttcg gtagtcgtaa cgatcgcacc ctgcgccgga
   108001 tgcgcaaagt ggtcaacatc atcaatgcca tggaaccgga gatggaaaaa ctctccgacg
   108061 aagaactgaa agggaaaacc gcagagtttc gtgcacgtct ggaaaaaggc gaagtgctgg
   108121 aaaatctgat cccggaagct ttcgccgtgg tacgtgaggc aagtaagcgc gtctttggta
   108181 tgcgtcactt cgacgttcag ttactcggcg gtatggttct taacgaacgc tgcatcgccg
   108241 aaatgcgtac cggtgaagga aaaaccctga ccgcaacgct gcctgcttac ctgaacgcac
   108301 taaccggtaa aggcgtgcac gtagttaccg tcaacgacta cctggcgcaa cgtgacgccg
   108361 aaaacaaccg tccgctgttt gaattccttg gcctgactgt cggtatcaac ctgccgggca
   108421 tgccagcacc ggcaaagcgc gaagcttacg cagctgacat cacttacggt acgaacaacg
   108481 aatacggctt tgactacctg cgcgacaaca tggcgttcag ccctgaagaa cgtgtacagc
   108541 gtaaactgca ctatgcgctg gtggacgaag tggactccat cctgatcgat gaagcgcgta
   108601 caccgctgat catttccggc ccggcagaag acagctcgga aatgtataaa cgcgtgaata
   108661 aaattattcc gcacctgatc cgtcaggaaa aagaagactc cgaaaccttc cagggcgaag
   108721 gccacttctc ggtggacgaa aaatctcgcc aggtgaacct gaccgaacgt ggtctggtgc
   108781 tgattgaaga actgctggtg aaagagggca tcatggatga aggggagtct ctgtactctc
   108841 cggccaacat catgctgatg caccacgtaa cggcggcgct gcgcgctcat gcgctgttta
   108901 cccgtgacgt cgactacatc gttaaagatg gtgaagttat catcgttgac gaacacaccg
   108961 gtcgtaccat gcagggccgt cgctggtccg atggtctgca ccaggctgtg gaagcgaaag
   109021 aaggtgtgca gatccagaac gaaaaccaaa cgctggcttc gatcaccttc cagaactact
   109081 tccgtctgta tgaaaaactg gcggggatga ccggtactgc tgataccgaa gctttcgaat
   109141 ttagctcaat ctacaagctg gataccgtcg ttgttccgac caaccgtcca atgattcgta
   109201 aagatctgcc ggacctggtc tacatgactg aagcggaaaa aattcaggcg atcattgaag
   109261 atatcaaaga acgtactgcg aaaggccagc cggtgctggt gggtactatc tccatcgaaa
   109321 aatcggagct ggtgtcaaac gaactgacca aagccggtat taagcacaac gtcctgaacg
   109381 ccaaattcca cgccaacgaa gcggcgattg ttgctcaggc aggttatccg gctgcggtga
   109441 ctatcgcgac caatatggcg ggtcgtggta cagatattgt gctcggtggt agctggcagg
   109501 cagaagttgc cgcgctggaa aatccgaccg cagagcaaat tgaaaaaatt aaagccgact
   109561 ggcaggtacg tcacgatgcg gtactggaag caggtggcct gcatatcatc ggtaccgagc
   109621 gtcacgaatc ccgtcgtatc gataaccagt tgcgcggtcg ttctggtcgt cagggggatg
   109681 ctggttcttc ccgtttctac ctgtcgatgg aagatgcgct gatgcgtatt tttgcttccg
   109741 accgagtatc cggcatgatg cgtaaactgg gtatgaagcc aggcgaagcc attgaacacc
   109801 cgtgggtgac taaagcgatt gccaacgccc agcgtaaagt tgaaagccgt aacttcgaca
   109861 ttcgtaagca actgctggaa tatgatgacg tggctaacga tcagcgtcgc gccatttact
   109921 cccagcgtaa cgaactgttg gatgtcagcg atgtgagcga aaccattaac agcattcgtg
   109981 aagatgtgtt caaagcgacc attgatgcct acattccacc acagtcgctg gaagaaatgt
   110041 gggatattcc ggggctgcag gaacgtctga agaacgattt cgacctcgat ttgccaattg
   110101 ccgagtggct ggataaagaa ccagaactgc atgaagagac gctgcgtgac ggcattctgg
   110161 cgcagtccat cgaagtgtat cagcgtaaag aagaagtggt tggtgctgag atgatgcgtc
   110221 acttcgagaa aggcgtcatg ctgcaaacgc ttgactccct gtggaaagag cacctggcag
   110281 cgatggacta tctgcgtcag ggtatccacc tgcgtggcta cgcacagaaa gatccgaagc
   110341 aggaatacaa acgtgaatcg ttctccatgt ttgcagcgat gctggagtcg ttgaaatatg
   110401 aagttatcag tacgctgagc aaagttcagg tacgtatgcc tgaagaggtt gaggagctgg
   110461 aacaacagcg tcgtatggaa gccgagcgtt tagcgcaaat gcagcagctt agccatcagg
   110521 atgacgactc tgcagccgca gctgcactgg cggcgcaaac cggagagcgc aaagtaggac
   110581 gtaacgatcc ttgcccgtgc ggttctggta aaaaatacaa gcagtgccat ggccgcctgc
   110641 aataaaagct aactgttgaa gtaaaaggcg caggattctg cgcctttttt ataggtttaa
   110701 gacaatgaaa aagctgcaaa ttgcggtagg tattattcgc aacgagaaca atgaaatctt
   110761 tataacgcgt cgcgcagcag atgcgcacat ggcgaataaa ctggagtttc ccggcggtaa
   110821 aattgaaatg ggtgaaacgc cggaacaggc ggtggtgcgt gaacttcagg aagaagtcgg
   110881 gattaccccc caacattttt cgctatttga aaaactggaa tatgaattcc cggacaggca
   110941 tataacactg tggttttggc tggtcgaacg ctgggaaggg gagccgtggg gtaaagaagg
   111001 gcaacccggt gagtggatgt cgctggtcgg tcttaatgcc gatgattttc cgccagccaa
   111061 tgaaccggta attgcgaagc ttaaacgtct gtaggtcaga taaggcgttt tcgccgcatc
   111121 cgacattcgc acacgatgcc tgatgcgacg ctggcgcgtc ttatcaggcc taaagggatt
   111181 tctaactcat tgataaattt gtttttgtag gtcggataag gcgttcacgc cgcatccgac
   111241 atttgcacaa gatgcctgat gcgacgctgt ccgcgtctta tcaggcctac gtgcggcatc
   111301 agacaaatgt cactgctttg gttcttcgct ccagtcatcg ctttcggaaa gatcgccact
   111361 gctggggatt cgtttttctt cagcagccca ttctccgagg tcgatcag
//

BioPerl-1.007002/t/data/D12555.gbk000444000766000024       357613155576321 16155 0ustar00cjfieldsstaff000000000000LOCUS       MUSBC05                  105 bp    DNA     linear   ROD 12-APR-2002
DEFINITION  Mus spretus gene for beta-casein, 3'UTR.
ACCESSION   D12555
VERSION     D12555.1  GI:303649
KEYWORDS    .
SOURCE      Mus spretus (western wild mouse)
  ORGANISM  Mus spretus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus.
REFERENCE   1  (bases 1 to 105)
  AUTHORS   Takahashi,N. and Ko,M.S.
  TITLE     The short 3'-end region of complementary DNAs as PCR-based
            polymorphic markers for an expression map of the mouse genome
  JOURNAL   Genomics 16 (1), 161-168 (1993)
  MEDLINE   93252372
   PUBMED   8486351
COMMENT     Submitted (06-JUL-1993) to DDBJ by:
            Minoru S.H. Ko
            ERATO Research Development Corporation of Japan
            (JRDC)
            5-9-6 Tohkohdai, Tsukuba
            Ibaraki 300-26
            Japan
            Phone:  0298-47-5531
            Fax:    0298-47-5421.
FEATURES             Location/Qualifiers
     source          1..105
                     /organism="Mus spretus"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:10096"
     3'UTR           <1..>105
                     /note="beta-casein
                     genomic DNA sequence corresponding to a part of the 3'UTR
                     of beta-caseine gene, MMBCASE (bases 7015 - 7121)"
     variation       69^70
                     /note="A in MMBCASE"
                     /replace="a"
     variation       103^102
                     /note="T in MMBCASE
                     deleted in CAST/Ei (M. m. castaneus)"
                     /replace="t"
BASE COUNT       37 a      7 c     17 g     44 t
ORIGIN      
        1 agttatatta caggaatttt ataagtgttc aatatggagt tgaaaatgca agtcaataat
       61 gtatacaaat agtttgtgaa aaattggatt ttctattttt ttctt
//

BioPerl-1.007002/t/data/DQ018368.gb000444000766000024       571313155576321 16206 0ustar00cjfieldsstaff000000000000LOCUS       DQ018368                 523 bp    DNA     linear   PLN 23-MAY-2005
DEFINITION  (Populus tomentosa x P. bolleana) x P. tomentosa var. truncata
            BS-LRR type disease resistance protein (RGA6) gene, partial cds.
ACCESSION   DQ018368
VERSION     DQ018368.1  GI:66271013
KEYWORDS    .
SOURCE      (Populus tomentosa x P. bolleana) x P. tomentosa var. truncata
  ORGANISM  (Populus tomentosa x P. bolleana) x P. tomentosa var. truncata
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus.
REFERENCE   1  (bases 1 to 523)
  AUTHORS   Zhang,Q., Lin,S.Z., Lin,Y.Z., Zhou,Y.L., Zhang,Z.Y., Zheng,H.Q.,
            Chen,J.B., Wang,Z.L., Qiao,M.J., Wang,X. and Zhu,B.Q.
  TITLE     Characterization and cloning of disease resistance gene from poplar
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 523)
  AUTHORS   Zhang,Q., Lin,S.Z., Lin,Y.Z., Zhou,Y.L. and Zhang,Z.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-APR-2005) Key Laboratory for Genetics and Breeding in
            Forest Trees and Ornamental Plants, MOE, Beijing Forestry
            University, Box 118, Qinghuadong Road, Beijing 100083, P.R.China
FEATURES             Location/Qualifiers
     source          1..523
                     /organism="(Populus tomentosa x P. bolleana) x P.
                     tomentosa var. truncata"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:328805"
     gene            <1..>523
                     /gene="RGA6"
     mRNA            <1..>523
                     /gene="RGA6"
                     /product="BS-LRR type disease resistance protein"
     CDS             <1..>523
                     /gene="RGA6"
                     /codon_start=1
                     /product="BS-LRR type disease resistance protein"
                     /protein_id="AAY43785.1"
                     /db_xref="GI:66271014"
                     /translation="GMGGIGKTTVARVVYDRIRWQFEGSCFLANVREDLAKKGGQRRL
                     QEQLLSEILMERANICDSSRGIEMIKRRLQRKKILVVLDDVDDRKQLESLAAESKWFG
                     PESRIIITSRDKQVLTRNGVTRIYEAEKLNDDDALMLFSQKAFKKDQPVEDFVKLSKQ
                     VVGYANGPSTCPQS"
ORIGIN      
        1 gggatggggg gtataggtaa gactactgtt gcaagggtag tatatgatag gattcgttgg
       61 caatttgaag gtagctgttt cttagcaaat gtcagagaag atcttgctaa gaaaggtgga
      121 caacgccgtt tacaggagca acttctttct gaaatcttaa tggaacgtgc taatatatgt
      181 gattcttcta gaggaattga aatgataaag cggaggttac aacgtaaaaa gattcttgtt
      241 gttcttgatg atgtagatga ccgtaaacaa ctagaatccc tggctgcgga gagtaaatgg
      301 tttggtccag agagtagaat tatcataaca agcagagata aacaagtgtt gactagaaat
      361 ggtgttacta gaatttatga ggctgagaaa ttgaatgatg atgatgctct tatgttgttt
      421 agccagaaag ctttcaaaaa agaccaacct gttgaggatt ttgtgaaact atccaagcaa
      481 gttgtgggtt atgctaatgg gccttccact tgccctcaaa gtc
//

BioPerl-1.007002/t/data/ECAPAH02.embl000444000766000024     74137413155576321 16674 0ustar00cjfieldsstaff000000000000ID   ECAPAH02   standard; DNA; PRO; 111408 BP.
XX
AC   D10483; J01597; J01683; J01706; K01298; K01990; M10420; M10611; M12544;
AC   V00259; X04711; X54847; X54945; X55034; X56742;
XX
SV   D10483.2
XX
DT   06-AUG-1992 (Rel. 33, Created)
DT   03-JUN-2002 (Rel. 72, Last updated, Version 62)
XX
DE   Escherichia coli genomic DNA. (0.0 - 2.4 min).
XX
KW   ant; antO; apaG; apaH; araA; araB; araC; araD; asmB; azi; brnP; caiA; caiB;
KW   caiC; caiD; caiE; caiF; caiT; carA; carB; chlG;
KW   Complete and shotgun sequencing; dapB; ddl; ddlB; dinA; divA; dnaJ; dnaK;
KW   envA; fixA; fixB; fixC; folA; fruR; ftsA; ftsI; ftsL; ftsQ; ftsW; ftsZ;
KW   gef; groP; hepA; htgA; htpY; ileS; ilvH; ilvI; imp; kefC; leuA; leuB; leuC;
KW   leuD; leuLP; lpxC; lspA; lueO; lytB; mog; mra; mraY; murC; murD; murE;
KW   murF; murG; murX; mutT; nhaA; nhaR; ostA; pbpB; pdxA; pea; polB; prlD;
KW   pyrA; rpsT; secA; sfiB; shl; sulB; surA; talB; tbpA; thrA; thrA1; thrA2;
KW   thrB; thrC; tmrA; trkC; yaaA; yaaC; yaaD; yaaF; yaaI; yaaJ; yaaT; yaaU;
KW   yaaV; yabB; yabC; yabE; yabF; yabH; yabI; yabJ; yabK; yabM; yabN; yabO;
KW   yabP; yabQ; yacA; yacG.
XX
OS   Escherichia coli
OC   Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
OC   Escherichia.
XX
RN   [1]
RP   1-111408
RA   Mori H.;
RT   ;
RL   Submitted (18-FEB-1992) to the EMBL/GenBank/DDBJ databases.
RL   Hirotada Mori, Institute for Virus Research, Kyoto University, Genetics and
RL   Molecular Biology; 53 Shogoin Kawara-Machi, Sakyo-ku, Kyoto 606, Japan
RL   (E-mail:e52985@sakura.kudpc.kyoto-u.ac.jp, Tel:075-751-4042,
RL   Fax:075-761-5626)
XX
RN   [2]
RX   MEDLINE; 79005683.
RA   Smith B.R., Schleif R.;
RT   "Nucleotide sequence of the L-arabinose regulatory region of Escherichia
RT   coli K12";
RL   J. Biol. Chem. 253:6931-6933(1978).
XX
RN   [3]
RX   MEDLINE; 78137003.
RA   Ohtsubo H., Ohtsubo E.;
RT   "Nucleotide sequence of an insertion element, IS1";
RL   Proc. Natl. Acad. Sci. U.S.A. 75:615-619(1978).
XX
RN   [4]
RX   MEDLINE; 79116194.
RA   Greenfield L., Boone T., Wilcox G.;
RT   "DNA sequence of the araBAD promoter in Escherichia coli B/r";
RL   Proc. Natl. Acad. Sci. U.S.A. 75:4724-4728(1978).
XX
RN   [5]
RX   MEDLINE; 79177885.
RA   Johnsrud L.;
RT   "DNA sequence of the transposable element IS1";
RL   Mol. Gen. Genet. 169:213-218(1979).
XX
RN   [6]
RX   MEDLINE; 81053692.
RA   Calvo J.M., Smith D.R.;
RT   "Nucleotide sequence of the E. coli gene coding for dihydrofolate
RT   reductase";
RL   Nucleic Acids Res. 8:2255-2274(1980).
XX
RN   [7]
RX   MEDLINE; 81124262.
RA   Miyada C.G., Horwitz A.H., Cass L.G., Timko J., Wilcox G.;
RT   "DNA sequence of the araC regulatory gene from Escherichia coli B/r";
RL   Nucleic Acids Res. 8:5267-5274(1980).
XX
RN   [8]
RX   MEDLINE; 81013881.
RA   Ogden S., Haggerty D., Stoner C.M., Kolodrubetz D., Schleif R.;
RT   "The Escherichia coli L-arabinose operon: binding sites of the regulatory
RT   proteins and a mechanism of positive and negative regulation";
RL   Proc. Natl. Acad. Sci. U.S.A. 77:3346-3350(1980).
XX
RN   [9]
RX   MEDLINE; 81077247.
RA   Katina M., Cossart P., Sibilli L., Saint-Girons I.;
RT   "Nucleotide sequence of the thrA gene of Escherichia coli";
RL   Proc. Natl. Acad. Sci. U.S.A. 77:5730-5733(1980).
XX
RN   [10]
RX   MEDLINE; 81264207.
RA   Mackie G.A.;
RT   "Nucleotide sequence of the gene for ribosomal protein S20 and its flanking
RT   regions";
RL   J. Biol. Chem. 256:8177-8182(1981).
XX
RN   [11]
RX   MEDLINE; 81150470.
RA   Cossart P., Katinka M., Yaniv M.;
RT   "Nucleotide sequence of the thrB gene of E. coli, and its two adjacent
RT   regions; the thrAB and thrBC junctions";
RL   Nucleic Acids Res. 9:339-347(1981).
XX
RN   [12]
RX   MEDLINE; 81199399.
RA   Lee N.L., Gielow W.O., Wallace R.G.;
RT   "Mechanism of araC autoregulation and the domains of two overlapping
RT   promoters, pC and pBAD, in the L-arabinose regulatory region of Escherichia
RT   coli";
RL   Proc. Natl. Acad. Sci. U.S.A. 78:752-756(1981).
XX
RN   [13]
RX   MEDLINE; 82216830.
RA   Stoner C.M., Schleif R.;
RT   "Is the amino acid but not nucleotide sequence of the Escherichia coli araC
RT   gene conserved?";
RL   J. Mol. Biol. 154:649-652(1982).
XX
RN   [14]
RX   MEDLINE; 83116968.
RA   Gilson E., Nikaido H., Hofnung M.;
RT   "Sequence of the malK gene in E.coli K12";
RL   Nucleic Acids Res. 10:7449-7458(1982).
XX
RN   [15]
RX   MEDLINE; 84069770.
RA   Parsot C., Cossart P., Saint-Girons I., Cohen G.N.;
RT   "Nucleotide sequence of thrC and of the transcription termination region of
RT   the threonine operon in Escherichia coli K12";
RL   Nucleic Acids Res. 11:7331-7345(1983).
XX
RN   [16]
RX   MEDLINE; 85054974.
RA   Bouvier J., Richaud C., Richaud F., Patte J., Stragier P.;
RT   "Nucleotide sequence and expression of the Escherichia coli dapB gene";
RL   J. Biol. Chem. 259:14829-14834(1984).
XX
RN   [17]
RX   MEDLINE; 84144800.
RA   Bardwell J.C., Craig E.A.;
RT   "Major heat shock gene of drosophila and the Escherichia coli heatinducible
RT   dnaK gene are homologous";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:848-852(1984).
XX
RN   [18]
RX   MEDLINE; 84222028.
RA   Innis M.A., Tokunaga M., Williams M.E., Loranger J.M., Chang S., Chang S.,
RA   Wu H.C.;
RT   "Nucleotide sequence of the Escherichia coli prolipoprotein signal
RT   peptidase (lsp) gene";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:3708-3712(1984).
XX
RN   [19]
RX   MEDLINE; 84248073.
RA   Bouvier J., Patte J., Stragier P.;
RT   "Multiple regulatory signals in the control region of the Escherichia coli
RT   carAB operon";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:4139-4143(1984).
XX
RN   [20]
RX   MEDLINE; 86030702.
RA   Chong P., Hui I., Loo T., Gillam S.;
RT   "Structural analysis of a new GC-specific insertion element IS186";
RL   FEBS Lett. 192:47-52(1985).
XX
RN   [21]
RX   MEDLINE; 85182715.
RA   Kamio Y., Lin C., Regue M., Wu H.C.;
RT   "Characterization of the ileX-lsp operon in Escherichia coli:
RT   Identification of an open reading frame upstream of the ileX gene and
RT   potential promoter(s) for the ileS-lsp operon";
RL   J. Biol. Chem. 260:5616-5620(1985).
XX
RN   [22]
RX   MEDLINE; 85295470.
RA   Friedberg D., Rosenthal E.R., Jones J.W., Calvo J.M.;
RT   "Characterization of the 3' end of the leucine operon of Salmonella
RT   typhimurium";
RL   Mol. Gen. Genet. 199:486-494(1985).
XX
RN   [23]
RX   MEDLINE; 85190560.
RA   Cowing D.W.;
RT   "Consensus sequence for Escherichia coli heatshock gene promoters";
RL   Proc. Natl. Acad. Sci. U.S.A. 82:2679-2683(1985).
XX
RN   [24]
RA   Sekiguchi T., Ortega-Cesena J., Nosoh Y., Ohashi S., Tsuda K., Kanaya S.;
RT   "DNA and amino-acid sequences of 3-isopropylmalate dehydrogenase of
RT   Bacillus coagulans. Comparison with the enzymes of Saccharomyces cerevisiae
RT   and Thermus thermophilus";
RL   Biochim. Biophys. Acta 867:36-44(1986).
XX
RN   [25]
RX   MEDLINE; 87163495.
RA   Lee N., Gielow W., Martin R., Hamilton E., Fowler A.;
RT   "The organization of the araBAD operaon of Escherichia coli";
RL   Gene 47:231-244(1986).
XX
RN   [26]
RX   MEDLINE; 86111849.
RA   Ohki M., Tamura F., Nishimura S., Uchida H.;
RT   "Nucleotide sequence of the Escherichia coli dnaJ gene and purification of
RT   the gene product";
RL   J. Biol. Chem. 261:1778-1781(1986).
XX
RN   [27]
RX   MEDLINE; 87172305.
RA   Blanchin-Roland S., Blanquet S., Schmitter J., Fayat G.;
RT   "The gene for Escherichia coli diadenosine tetraphosphatase is located
RT   immediately clockwise to folA and forms an operon with ksgA";
RL   Mol. Gen. Genet. 205:515-522(1986).
XX
RN   [28]
RX   MEDLINE; 87016337.
RA   Mackie G.A.;
RT   "Structure of the DNA distal to the gene for ribosomal protein S20 in
RT   Escherichia coli K12: Presence of a strong terminator and an IS1 element";
RL   Nucleic Acids Res. 14:6965-6981(1986).
XX
RN   [29]
RX   MEDLINE; 86287338.
RA   Birnbaum M.J., Haspel H.C., Rosen O.M.;
RT   "Cloning and characterization of a cDNA encoding the rat brain
RT   glucose-transporter protein";
RL   Proc. Natl. Acad. Sci. U.S.A. 83:5784-5788(1986).
XX
RN   [30]
RX   MEDLINE; 87308226.
RA   Nonet M.L., Marvel C.C., Tolan D.R.;
RT   "The hisT-purF region of the Escherichia coli K-12 chromosome.
RT   Identification of additional genes of the hisT and purF operons";
RL   J. Biol. Chem. 262:12209-12217(1987).
XX
RN   [31]
RX   MEDLINE; 87146339.
RA   Gronger P., Manian S.S., Reilander H., O'Connell M., Priefer U.B.,
RA   Puhler A.;
RT   "Organization and partial sequence of a DNA region of the Rhizobium
RT   leguminosarum symbiotic plasmid pRL6JI containing the genes fixABC, nifA,
RT   nifB and a novel operon reading frame";
RL   Nucleic Acids Res. 15:31-49(1987).
XX
RN   [32]
RX   MEDLINE; 89005119.
RA   Lozoya E., Hoffmann H., Douglas C., Schulz W., Scheel D., Hahlbrock K.;
RT   "Primary structures and catalytic properties of isoenzymes encoded by the
RT   two 4-coumarate:CoA ligase genes in parsley";
RL   Eur. J. Biochem. 176:661-667(1988).
XX
RN   [33]
RX   MEDLINE; 88273145.
RA   Karpel R., Olami Y., Taglicht D., Schuldiner S., Padan E.;
RT   "Sequencing of the gene ant which affects the Na+/H+ antiporter activity in
RT   Escherichia coli";
RL   J. Biol. Chem. 263:10408-10414(1988).
XX
RN   [34]
RX   MEDLINE; 88330879.
RA   Jaiswal A.K., McBride O.W., Adesnik M., Nebert D.W.;
RT   "Human dioxin-inducible cytosolic NAD(P)H:menadione oxidoreductase. cDNA
RT   sequence and localization of gene to chromosome 16";
RL   J. Biol. Chem. 263:13572-13578(1988).
XX
RN   [35]
RX   MEDLINE; 90032688.
RA   Minami-Ishii N., Taketani S., Osumi T., Hashimoto T.;
RT   "Molecular cloning and sequence analysis of the cDNA for rat mitochondrial
RT   enoyl-CoA hydratase. Structural and evolutionary relationships linked to
RT   the bifunctional enzyme of the peroxisomal beta-oxidation system";
RL   Eur. J. Biochem. 185:73-78(1989).
XX
RN   [36]
RX   MEDLINE; 89252065.
RA   Sato S., Nakada Y., Shiratsuchi A.;
RT   "IS421, a new insetion sequence in Escherichia coli";
RL   FEBS Lett. 249:21-26(1989).
XX
RN   [37]
RX   MEDLINE; 89359108.
RA   Roa B.B., Connolly D.M., Winkler M.E.;
RT   "Overlap between pdxA and ksgA in the complex pdxA-ksgA-apaG-apaH operon of
RT   Escherichia coli K-12";
RL   J. Bacteriol. 171:4767-4777(1989).
XX
RN   [38]
RX   MEDLINE; 89380240.
RA   Matsubara Y., Indo Y., Naito E., Ozasa H., Glassberg R., Vockley J.,
RA   Ikeda Y., Kraus J., Tanaka K.;
RT   "Molecular cloning and nucleotide sequence of cDNAs encoding the precursors
RT   of rat long chain acyl-coenzyme A, short chain acyl-coenzyme A, and
RT   isovaleryl-coenzyme A dehydrogenases. Sequence homology of four enzymes of
RT   the acyl-CoA dehydrogenase famil";
RL   J. Biol. Chem. 264:16321-16331(1989).
XX
RN   [39]
RA   Stragier P.;
RT   ;
RL   Unpublished.
XX
RN   [40]
RA   Ishino Y.;
RT   ;
RL   Unpublished.
XX
RN   [41]
RA   Chen H., Sun Y., Stark T., Beattie W., Moses R.E.;
RT   "Nucleotide sequence and deletion analysis of the polB gene of E. coli";
RL   DNA Cell Biol. 9:613-635(1990).
XX
RN   [42]
RX   MEDLINE; 90235831.
RA   Schaaff I., Hohmann S., Zimmermann F.K.;
RT   "Molecular analysis of the structural gene for yeast transaldolase";
RL   Eur. J. Biochem. 188:597-603(1990).
XX
RN   [43]
RX   MEDLINE; 90130288.
RA   Angerer A., Gaisser S., Braun V.;
RT   "Nucleotide sequences of the sfuA, sfuB, and sfuC genes of Serratia
RT   marcescens suggest a periplasmic-binding-protein-dependent iron transport
RT   mechanism";
RL   J. Bacteriol. 172:572-578(1990).
XX
RN   [44]
RX   MEDLINE; 91072253.
RA   Mallonee D.H., White W.B., Hylemon P.B.;
RT   "Cloning and sequencing of a bile acid-inducible operon from Eubacterium
RT   sp. strain VPI 12708";
RL   J. Bacteriol. 172:7011-7019(1990).
XX
RN   [45]
RX   MEDLINE; 90206796.
RA   Ricca E., Calvo J.M.;
RT   "The nucleotide sequence of leuA from Salmonella typhimurium";
RL   Nucleic Acids Res. 18:1290-1290(1990).
XX
RN   [46]
RX   MEDLINE; 90272436.
RA   Rosenthal E.R., Calvo J.M.;
RT   "The nucleotide sequence of leuC from Salmonella typhimurium";
RL   Nucleic Acids Res. 18:3072-3072(1990).
XX
RN   [47]
RX   MEDLINE; 91088346.
RA   Chen H., Lawrence C.B., Bryan S.K., Moses R.E.;
RT   "Aphidicolin inhibits DNA polymerase II of Escherichia coli, an alpha-like
RT   DNA polymerase";
RL   Nucleic Acids Res. 18:7185-7186(1990).
XX
RN   [48]
RA   Ayala J.A.;
RT   "Regulation of transcription at 2-minute region of the genetic map of
RT   Escherichia coli";
RL   Unpublished.
XX
RN   [49]
RX   MEDLINE; 91192599.
RA   Umeda M., Ohtsubo E.;
RT   "Four types of IS1 with differences in nucleotide sequence reside in the
RT   Escherichia coli K-12 chromosome";
RL   Gene 98:1-5(1991).
XX
RN   [50]
RX   MEDLINE; 91203829.
RA   Arigoni F., Kaminski P.A., Hennecke H., Elmerich C.;
RT   "Nucleotide sequence of the fixABC region of Azorhizobium caulinodans
RT   ORS571: similarity of the fixB product with eukaryotic flavoproteins,
RT   characterization of fixX, and identification of nifW";
RL   Mol. Gen. Genet. 225:514-520(1991).
XX
RN   [51]
RX   MEDLINE; 91260444.
RA   Munro A.W., Ritchie G.Y., Lamb A.J., Douglas R.M., Booth I.R.;
RT   "The cloning and DNA sequence of the gene for the glutathione-regulated
RT   potassium-efflux system KefC of Escherichia coli";
RL   Mol. Microbiol. 5:607-616(1991).
XX
RN   [52]
RX   MEDLINE; 92048480.
RA   Poulsen L.K., Refn A., Molin S., Andersson P.;
RT   "Topographic analysis of the toxic Gef protein from Escherichia coli";
RL   Mol. Microbiol. 5:1627-1637(1991).
XX
RN   [53]
RX   MEDLINE; 92048481.
RA   Poulsen L.K., Refn A., Molin S., Andersson P.;
RT   "The gef gene from Escherichia coli is regulated at the level of
RT   translation";
RL   Mol. Microbiol. 5:1639-1648(1991).
XX
RN   [54]
RX   MEDLINE; 91187617.
RA   Bouvier J., Stragier P.;
RT   "Nucleotide sequence of the lsp-dapB interval in Escherichia coli";
RL   Nucleic Acids Res. 19:180-180(1991).
XX
RN   [55]
RP   1-111401
RX   MEDLINE; 92334977.
RA   Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K.,
RA   Mizobuchi K., Nakata A.;
RT   "Systematic sequencing of the Escherichia coli genome: analysis of the
RT   0-2.4min region";
RL   Nucleic Acids Res. 20:3305-3308(1992).
XX
RN   [56]
RX   MEDLINE; 94261430.
RA   Fujita N., Mori H., Yura T., Ishihama A.;
RT   "Systematic sequencing of the Escherichia coli genome: analysis of the
RT   2.4-4.1 min (110,917-193,643 bp) region";
RL   Nucleic Acids Res. 22:1637-1639(1994).
XX
DR   SWISS-PROT; P00907; CARA_ECOLI.
DR   SWISS-PROT; P00968; CARB_ECOLI.
DR   SWISS-PROT; P09151; LEU1_ECOLI.
DR   SWISS-PROT; P28694; MOG_ECOLI.
DR   SWISS-PROT; P28695; YAAH_ECOLI.
DR   SWISS-PROT; P28696; YAAI_ECOLI.
DR   SWISS-PROT; P28697; HTGA_ECOLI.
DR   SWISS-PROT; P30127; LEU2_ECOLI.
DR   SWISS-PROT; P30143; YAAJ_ECOLI.
DR   SWISS-PROT; P31554; OSTA_ECOLI.
DR   SWISS-PROT; P31675; SETA_ECOLI.
DR   SWISS-PROT; P31680; DJLA_ECOLI.
DR   SWISS-PROT; P33595; YABN_ECOLI.
DR   SWISS-PROT; P39206; CAIE_ECOLI.
DR   SWISS-PROT; P39219; RLUA_ECOLI.
DR   SWISS-PROT; P39220; YABP_ECOLI.
DR   SWISS-PROT; P39221; YABQ_ECOLI.
DR   SWISS-PROT; P46145; YAAV_ECOLI.
XX
CC   Submitted (18-FEB-1992) to DDBJ by:
CC   Hirotada Mori
CC   Institute for Virus Research
CC   Kyoto University
CC   Kawahara-cho Shogoin Sakyo-ku
CC   Kyoto 606
CC   Phone:  075-751-4042
CC   Fax:    075-761-5626
CC   Sequence updated (21-DEC-1992) by:
CC   Hirotada Mori
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..111408
FT                   /db_xref="taxon:562"
FT                   /note="Nucleotide position 1-111408 from the initiation
FT                   site of ThrA (0 min.)."
FT                   /sequenced_mol="DNA"
FT                   /organism="Escherichia coli"
FT                   /map="0-2.4 min"
FT                   /strain="K-12"
FT   CDS             1..2463
FT                   /note="ORF_ID:o101#1"
FT                   /note="similar to PIR Accession Number A00671"
FT                   /transl_table=11
FT                   /gene="thrA"
FT                   /gene="thrA1"
FT                   /gene="thrA2"
FT                   /product="ThrA bifunctional enzyme"
FT                   /protein_id="BAB96579.1"
FT                   /translation="MRVLKFGGTSLANAERFLRVADILESNARQGQVATVLSAPAKITN
FT                   HLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHV
FT                   LHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLES
FT                   TVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADC
FT                   CEIWTDVNGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCL
FT                   IKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMS
FT                   RARISVVLITQSSSEYSISFCVPQSDCVRAERAMLEEFYLELKEGLLEPLAVAERLAII
FT                   SVVGDGLRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQM
FT                   LFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLN
FT                   LENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVNCTSSQAVADQYADFLREGFHVVT
FT                   PNKKANTSSMDYYHQLRYAAEKSRRKFLYDINVGAGLPVIENLQNLLNAGDELMKFSGI
FT                   LSGSLSYIFGKLDEGMSFSEATRLAREMGYTEPDPRDDLSGMDVARKLLILARETGREL
FT                   ELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDG
FT                   VCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLR
FT                   TLSWKLGV"
FT   CDS             2465..3394
FT                   /note="ORF_ID:o101#2"
FT                   /note="similar to PIR Accession Number A00658"
FT                   /transl_table=11
FT                   /gene="thrB"
FT                   /product="Homoserine kinase (EC  2.7.1.39)"
FT                   /protein_id="BAB96580.1"
FT                   /translation="MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAQTFS
FT                   LNNLGRFADKLPSEPRENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACSVV
FT                   AALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDIISQ
FT                   QVQGLMSGCGCSRIRGLKSRRQKQGYLPAQYRRQDCIAHGRHLAGFIHACYSRQPELAA
FT                   KLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADW
FT                   LGKNYLQNQEGFVHICRLDTAGARVLEN"
FT   CDS             3395..4681
FT                   /note="ORF_ID:o101#3"
FT                   /note="similar to PIR Accession Number A01157"
FT                   /transl_table=11
FT                   /gene="thrC"
FT                   /product="Threonine synthase (EC  4.2.99.2)"
FT                   /protein_id="BAB96581.1"
FT                   /translation="MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDE
FT                   MLKLDFVTRSAKILSAFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTL
FT                   AFKDFGGRFMAQMLTHIAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKIS
FT                   PLQEKLFCTLGGNIETVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQ
FT                   ICYYFEAVAQLPQETRNQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPR
FT                   FLHDGQWSPKATQATLSNAMDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTM
FT                   RELKELGYTSEPHAAVAYRALRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKE
FT                   LAERADLPLLSHNLPADFAALRKLMMNHQ"
FT   CDS             4895..5191
FT                   /note="ORF_ID:o101#4"
FT                   /transl_table=11
FT                   /protein_id="BAB96582.1"
FT                   /translation="MKKMQSIVLALSLVLVAPMAAQAAEITLVPSVKLQIGDRDNRGYY
FT                   WDGGHWRDHGWWKQHYEWRGNRWHLHGPPPPPRHHKKAPHDHHGGHGPGKHHR"
FT   CDS             complement(4971..5402)
FT                   /note="ORF_ID:o101#5"
FT                   /transl_table=11
FT                   /protein_id="BAB96583.1"
FT                   /translation="MMKIPPAMANWCLNATSSVKFAVNAGCGVNALSCLQKHADSIYCR
FT                   INVGLIRRASVASGAECRIVTRHLSFSGDVCQDHDRRDDHEELSYGGAAVAAVRVGASD
FT                   CLAIHNVVSTSRGRASDLHPSNSHDYHDRLSVILLTGLT"
FT   CDS             complement(5344..6120)
FT                   /note="ORF_ID:o101#6"
FT                   /note="similar to PIR Accession Number S40534"
FT                   /transl_table=11
FT                   /gene="yaaA"
FT                   /product="Hypothetical protein"
FT                   /protein_id="BAB96584.1"
FT                   /translation="MLILISPAKTLDYQSPLTTTRYTLPELLDNSQQLIHEARKLTPPQ
FT                   ISTLMRISDKLAGINAARFHDWQPDFTPANARQAILAFKGDVYTGLQAETFSEDDFDFA
FT                   QQHLRMLSGLYGVLRPLDLMQPYRLEMGIRLENARGKDLYQFWGDIITNKLNEALAAQG
FT                   DNVVINLASDEYFKSVKPKKLNAEIIKPVFLDEKNGKFKIISFYAKKARGLMSRFIIEN
FT                   RLTKPEQLTGFNSEGYFFDEDSSSNGELVFKRYEQR"
FT   CDS             complement(6190..7620)
FT                   /note="ORF_ID:o101#7"
FT                   /note="similar to SwissProt Accession Number P30143"
FT                   /transl_table=11
FT                   /gene="yaaJ"
FT                   /product="Hypothetical 51.7 kd protein in thrC-talB
FT                   intergenic region (ORF8)."
FT                   /protein_id="BAB96585.1"
FT                   /translation="MPDFFSFINSVLWGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFGK
FT                   SLKNSIHPQPGGLTSFQSLCTSLAARVGSGNLAGVALAITAGGPGAVFWMWVAAFIGMA
FT                   TSFAECSLAQLYKERDVNGQFRGGPAWYMARGLGMRWMGVLFAVFLLIAYGIIFSGVQA
FT                   NAVARALSFSFDFPPLVTGIILAVFTLLAITRGLHGVARLMQGFVPLMAIIWVLTSLVI
FT                   CVMNIGQLPHVIWSIFESAFGWQEAAGGAAGYTLSQAITNGFQRSMFSNEAGMGSTPNA
FT                   AAAAASWPPHPAAQGIVQMIGIFIDTLVICTASAMLILLAGNGTTYMPLEGIQLIQKAM
FT                   RVLMGSWGAEFVTLVVILFAFSSIVANYIYAENNLFFLRLNNPKAIWCLRICTFATVIG
FT                   GTLLSLPLMWQLADIIMACMAITNLTAILLLSPVVHTIASDYLRQRKLGVRPVFDPLRY
FT                   PDIGRQLSPDAWDDVSQE"
FT   CDS             7899..8852
FT                   /note="ORF_ID:o101#8"
FT                   /note="similar to PIR Accession Number S40535"
FT                   /transl_table=11
FT                   /gene="talB"
FT                   /product="Hypothetical protein"
FT                   /protein_id="BAB96586.1"
FT                   /translation="MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILNAAQI
FT                   PEYRKLIDDAVAWAKQQSNDRAQQIVDATDKLAVNIGLEILKLVPGRISTEVDARLSYD
FT                   TEASIAKAKRLIKLYNDAGISNDRILIKLASTWQGIRAAEQLEKEGINCNLTLLFSFAQ
FT                   ARACAEAGVFLISPFVGRILDWYKANTDKKEYAPAEDPGVVSVSEIYQYYKEHGYETVV
FT                   MGASFRNIGEILELAGCDRLTIAPALLKELAESEGAIERKLSYTGEVKARPARITESEF
FT                   LWQHNQDPMAVDKLAEGIRKFAIDQEKLEKMIGDLL"
FT   CDS             9136..9552
FT                   /note="ORF_ID:o102#1"
FT                   /note="similar to PIR Accession Number B56688"
FT                   /transl_table=11
FT                   /gene="chlG"
FT                   /gene="mog"
FT                   /product="Molybdopterin biosynthesis Mog protein."
FT                   /protein_id="BAB96587.1"
FT                   /translation="MCELVDEMSCHLVLTTGGTGPARRDVTPDATLAVADREMPGFGEQ
FT                   MRQISLHFVPTAILSRQVGVIRKQALILNLPGQPKSIKETLEGVKDAEGNVVVHGIFAS
FT                   VPYCIQLLEGPYVETAPEVVAAFRPKSARRDVSE"
FT   CDS             complement(9584..10150)
FT                   /note="ORF_ID:o102#2"
FT                   /note="similar to PIR Accession Number E56688"
FT                   /transl_table=11
FT                   /product="hgtA 5'-region hypothetical protein 1"
FT                   /protein_id="BAB96588.1"
FT                   /translation="MGNTKLANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIFY
FT                   GGIAQIFAGLLEYKKGNTFGLTAFTSYGSFWLTLVAILLMPKLGLTDAPNAQFLGVYLG
FT                   LWGVFTVFMFFGTLKGARVLQFVFFSLTVLFALLAIGNIAGNAAIIHFAGWIGLICGAS
FT                   AIYLAMGEVLNEQFGRTVLPIGESH"
FT   misc_feature    10479..10963
FT                   /note="ORF is interrupted by frame-shifting"
FT                   /note="ORF_ID:o102#3"
FT                   /note="similar to PIR Accession Number A40623"
FT                   /gene="htgA"
FT                   /gene="htpY"
FT                   /product="Heat shock protein Y"
FT   misc_feature    complement(11030..11435)
FT                   /note="ORF is interrupted by frame-shifting"
FT                   /note="ORF_ID:o102#4"
FT                   /note="similar to PIR Accession Number C56688"
FT                   /gene="yaaI"
FT                   /product="dnaK 5'-region hypothetical protein 1"
FT   CDS             11812..13728
FT                   /note="ORF_ID:o102#5"
FT                   /note="similar to PIR Accession Number A03311"
FT                   /transl_table=11
FT                   /gene="dnaK"
FT                   /product="DnaK protein"
FT                   /protein_id="BAB96589.1"
FT                   /translation="MGKIIGIDLGTTNSCVAIMDGTTPRVLENAEGDRTTPSIIAYTQD
FT                   GETLVGQPAKRQAVTNPQNTLFAIKRLIGRRFQDEEVQRDVSIMPFKIIAADNGDAWVE
FT                   VKGQKMAPPQISAEVLKKMKKTAEDYLGEPVTEAVITVPAYFNDAQRQATKDAGRIAGL
FT                   EVKRIINEPTAAALAYGLDKGTGNRTIAVYDLGGGTFDISIIEIDEVDGEKTFEVLATN
FT                   GDTHLGGEDFDSRLINYLVEEFKKDQGIDLRNDPLAMQRLKEAAEKAKIELSSAQQTDV
FT                   NLPYITADATGPKHMNIKVTRAKLESLVEDLVNRSIEPLKVALQDAGLSVSDIDDVILV
FT                   GGQTRMPMVQKKVAEFFGKEPRKDVNPDEAVAIGAAVQGGVLTGDVKDVLLLDVTPLSL
FT                   GIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFN
FT                   LDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVR
FT                   DAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETAL
FT                   KGEDKAAIEAKMQELAQVSQKLMEIAQQQHAQQQTAGADASANNAKDDDVVDAEFEEVK
FT                   DKK"
FT   CDS             13817..14947
FT                   /note="ORF_ID:o102#6"
FT                   /note="similar to SwissProt Accession Number P08622"
FT                   /transl_table=11
FT                   /gene="dnaJ"
FT                   /gene="groP"
FT                   /product="DnaJ protein."
FT                   /protein_id="BAB96590.1"
FT                   /translation="MAKQDYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAEA
FT                   KFKEIKEAYEVLTDSQKRAAYDQYGHAAFEQGGMGGGGFGGGADFSDIFGDVFGDIFGG
FT                   GRGRQRAARGADLRYNMELTLEEAVRGVTKEIRIPTLEECDVCHGSGAKPGTQPQTCPT
FT                   CHGSGQVQMRQGFFAVQQTCPHCQGRGTLIKDPCNKCHGHGRVERSKTLSVKIPAGVDT
FT                   GDRIRLAGEGEAGEHGAPAGDLYVQVQVKQHPIFEREGNNLYCEVPINFAMAALGGEIE
FT                   VPTLDGRVKLKVPGETQTGKLFRMRGKGVKSVRGGAQGDLLCRVVVETPVGLNERQKQL
FT                   LQELQESFGGPTGEHNSPRSKSFFDGVKKFFDDLTR"
FT   CDS             complement(16400..16609)
FT                   /note="ORF_ID:o102#7"
FT                   /note="similar to PIR Accession Number S16473"
FT                   /transl_table=11
FT                   /gene="gef"
FT                   /product="Gef protein"
FT                   /protein_id="BAB96591.1"
FT                   /translation="MLNTCRVPLTDRKVKEKRAMKQHKAMIVALIVICITAVVAALVTR
FT                   KDLCEVHIRTGQTEVAVFTAYESE"
FT   CDS             17138..18304
FT                   /note="ORF_ID:o102#8"
FT                   /note="similar to SwissProt Accession Number P13738"
FT                   /transl_table=11
FT                   /gene="ant"
FT                   /gene="nhaA"
FT                   /product="Na(+)/H(+) antiporter 1."
FT                   /protein_id="BAB96592.1"
FT                   /translation="MKHLHRFFSSDASGGIILIIAAILAMIMANSGATSGWYHDFLETP
FT                   VQLRVGSLEINKNMLLWINDALMAVFFLLVGLEVKRELMQGSLASLRQAAFPVIAAIGG
FT                   MIVPALLYLAFNYADPITREGWAIPAATDIAFALGVLALLGSRVPLALKIFLMALAIID
FT                   DLGAIIIIALFYTNDLSMASLGVAAVAIAVLAVLNLCGARRTGVYILVGVVLWTAVLKS
FT                   GVHATLAGVIVGFFIPLKEKHGRSPAKRLEHVLHPWVAYLILPLFAFANAGVSLQGVTL
FT                   DGLTSILPLGIIAGLLIGKPLGISLFCWLALRLKLAHLPEGTTYQQIMVVGILCGIGFT
FT                   MSIFIASLAFGSVDPELINWAKLGILVGSISSAVIGYSWLRVRLRPSV"
FT   misc_feature    18364..19283
FT                   /note="ORF is interrupted by frame-shifting"
FT                   /note="ORF_ID:o103#1"
FT                   /note="similar to SwissProt Accession Number P10087"
FT                   /gene="antO"
FT                   /gene="nhaR"
FT                   /product="Transcriptional activator protein NhaR."
FT   CDS             complement(20478..20741)
FT                   /note="ORF_ID:o103#2"
FT                   /note="similar to PIR Accession Number A30425"
FT                   /transl_table=11
FT                   /gene="rpsT"
FT                   /product="Ribosomal protein S20"
FT                   /protein_id="BAB96593.1"
FT                   /translation="MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKA
FT                   AAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLTAQINKLA"
FT   CDS             21070..22008
FT                   /note="ORF_ID:o103#3"
FT                   /note="similar to PIR Accession Number A22609"
FT                   /transl_table=11
FT                   /gene="yaaC"
FT                   /product="Hypothetical 35k protein (ileS-lsp operon)"
FT                   /protein_id="BAB96594.1"
FT                   /translation="MKLIRGIHNLSQAPQEGCVLTIGNFDGVHRGHRALLQGLQEEGRK
FT                   RNLPVMVMLFEPQPLELFATDKAPARLTRLREKLRYLAECGVDYVLCVRFDRRFAALTA
FT                   QNFVSDLLVKHLRVKFLAVGDDFPLALVVKAISCYYRKLAWNTASISPVRKLFAEVACA
FT                   SAARLRQALADDNLALAESLLGHPFAISGRVVHGDELGRTIGFPTANVPPRRQVSPVKG
FT                   VYAVEVLGLGEKPLPGVANIGTRPTVAGIRQQLEVHLLDVAMDLYGRHIQVVLRKKIRN
FT                   EQRFASLDELKAQIARDELTAREFFGLTKPA"
FT   CDS             22051..24861
FT                   /note="ORF_ID:o103#4"
FT                   /note="similar to PIR Accession Number S40549"
FT                   /transl_table=11
FT                   /gene="ileS"
FT                   /product="Isoleucine--tRNA ligase (EC 6.1.1.5)"
FT                   /protein_id="BAB96595.1"
FT                   /translation="MSDYKSTLNLPETGFPMRGDLAKREPGMLARWTDDDLYGIIRAAK
FT                   KGKKTFILHDGPPYANGSIHIGHSVNKILKDIIVKSKGLSGYDSPYVPGWDCHGLPIEL
FT                   KVEQEYGKPGEKFTAAEFRAKCREYAATQVDGQRKDFIRLGVLGDWSHPYLTMGLQNWK
FT                   ANIIRALGKIIGNGHLHKGAKPVHWCVDCRSALAKRKLSITTKLLRPSTLLSRAVDQDA
FT                   LKAKFAVSNVNGPISLVIWTTTPWTLPANRAISIAPDFDYALVQIDGQAVILAKDLVES
FT                   VMQRIGVTDSRHGKRCGAGAAAFTHPFMGFDVPAILGDHVTLDAGTGAVHTAPGHGPDD
FT                   YVIGQKYGLETANPVGPDGTYLPGTYPTLDGVNVFKANDIVAALLQEKGALLHVEKMQH
FT                   SYPCCWRHKTPIIFRATPQWFVSMDQKGLRAQSLKEIKGVQWIPDWGQARIESMVANRP
FT                   DWCISRQRTWGVPMSLFVHKDTEELHPRTLELMEEVAKRVEVDGIQAWWDLDAKEILGD
FT                   EADQYVKVPDTLDVWFDSGSTHSSVVDVRPEFAGHAADMYLEGSDQHRGWFMSSLMIST
FT                   AMKGKAPYRQVLTHGFTVDGQGRKMSKSIGNTVSPQDVMNKLGADILRLWVASTDYTGE
FT                   MAVSDEILKRAADTYRRIRNTARFLLANLNGFDPAKDMVKRREMVVLDRWAVVVRKRHR
FT                   KTSSRRTKHTISTKWYKRLMRFCSVEMGSFYLDIIKDRQYYAKGHSVARRSCQTALYHI
FT                   AEALVRWMAPILSFTADEVWGYLPGEREKYVFTGEWYEGLFGLADSEAMNDAFWDELLK
FT                   VRGEVNKVIEQARADKKVGGSLEAAVTLYAEPELSAKLTALGDELRFVLLTSGATVADY
FT                   NDAPADAQQSEVLKGLKVALSKAEGEKCPRCWHYTQDVGKVAEHAEICGRCVSNVAGDG
FT                   EKRKFA"
FT   CDS             24861..25355
FT                   /note="ORF_ID:o103#5"
FT                   /note="similar to SwissProt Accession Number P00804"
FT                   /transl_table=11
FT                   /gene="lspA"
FT                   /product="Lipoprotein signal peptidase (EC 3.4.23.36)
FT                   (Prolipoprotein signal peptidase) (Signal peptidase II)
FT                   (Spase II)."
FT                   /protein_id="BAB96596.1"
FT                   /translation="MSQSICSTGLRWLWLVVVVLIIDLGSKYLILQNFALGDTVPLFPS
FT                   LNLHYARNYGAAFSFLADSGGWQRWFFAGIAIGISVILAVMMYRSKATQKLNNIAYALI
FT                   IGGALGNLFDRLWHGFVVDMIDFYVGDWHFATFNLADTAICVGAALIVLEGFLPSRAKK
FT                   Q"
FT   CDS             25480..25929
FT                   /note="ORF_ID:o103#6"
FT                   /note="similar to PIR Accession Number JE0402"
FT                   /transl_table=11
FT                   /gene="yaaD"
FT                   /product="Hypothetical 16.4K protein (lsp-dapB intergenic
FT                   region)"
FT                   /protein_id="BAB96597.1"
FT                   /translation="MSESVQSNSAVLVHFTLKLDDGTTAESTRNNGKPALFRLGDASLS
FT                   EGLEQHLLGLKVGDKTTFSLEPDAAFGVPSPDLIQYFSRREFMDAGEPEIGAIMLFTAM
FT                   DGSEMPGVIREINGDSITVDFNHPLAGQTVHFDIEVLEIDPALEA"
FT   CDS             25931..26881
FT                   /note="ORF_ID:o103#7"
FT                   /note="similar to PIR Accession Number JE0403"
FT                   /transl_table=11
FT                   /gene="lytB"
FT                   /product="Hypothetical 34.8k protein (lsp-dapB intergenic
FT                   region)"
FT                   /protein_id="BAB96598.1"
FT                   /translation="MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYV
FT                   VDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHM
FT                   EVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSF
FT                   MTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGS
FT                   KNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVAR
FT                   LQQLGGGEAIPLEGREENIVFEVPKELRVDIREVD"
FT   CDS             26947..27861
FT                   /note="ORF_ID:o103#8"
FT                   /note="similar to PIR Accession Number JE0404"
FT                   /transl_table=11
FT                   /gene="yaaF"
FT                   /product="Hypothetical 32.6k protein (lsp-dapB intergenic
FT                   region)"
FT                   /protein_id="BAB96599.1"
FT                   /translation="MRLPIFLDTDPGIDDAVAIAAAIFAPELDLQLMTTVAGNVSVEKT
FT                   TRNALQLLHFWNAEIPLAQGAAVPLVRAPRDAASVHGESGMAGYDFVEHNRKPLGIPAF
FT                   LAIRDALMRAPEPVTLVAIGPLTNIALLLSQCPECKPYIRRLVIMGGSAGRGNCTPNAE
FT                   FNIAADPEAAACVFRSGIEIVMCGLDVTNQAILTPDYLSTLPQLNRTGKMLHALFSHYR
FT                   SGSMQSGLRMHDLCAIAWLVRPDLFTLKPCFVAVETQGEFTSGTTVVDIDGCLGKPANV
FT                   QVALDLDVKGFQQWVAEVLALAS"
FT   CDS             28028..28849
FT                   /note="ORF_ID:o103#9"
FT                   /note="similar to SwissProt Accession Number P04036"
FT                   /transl_table=11
FT                   /gene="dapB"
FT                   /product="Dihydrodipicolinate reductase (EC   1.3.1.26)."
FT                   /protein_id="BAB96600.1"
FT                   /translation="MHDANIRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLL
FT                   GSDAGELAGAGKTGVTVQSSLDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTT
FT                   GFDEAGKQAIRDAAADIAIVFAANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHK
FT                   VDAPSGTALAMGEAIAHALDKDLKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTA
FT                   MFADIGERLEITHKASSRMTFANGAVRSALWLSGKESGLFDMRDVLDLNNL"
FT   CDS             29305..30453
FT                   /db_xref="SWISS-PROT:P00907"
FT                   /note="ORF_ID:o103#10"
FT                   /note="similar to SwissProt Accession Number P00907"
FT                   /transl_table=11
FT                   /gene="carA"
FT                   /gene="pyrA"
FT                   /product="Carbamoyl-phosphate synthase small chain (EC
FT                   6.3.5.5) (carbamoyl-phosphate synthetase glutamine chain)."
FT                   /protein_id="BAB96601.1"
FT                   /translation="MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTD
FT                   PSYSRQIVTLTYPHIGNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKR
FT                   HNIVAIADIDTRKLTRLLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVT
FT                   TAEAYSWTQGSWTLTGGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQ
FT                   TSAEDVLKMNPDGIFLSNGPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGA
FT                   KTVKMKFGHHGGNHPVKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGI
FT                   HRTDKPAFSFQGHPEASPGPHDAAPLFDHFIELIEQYRKTAK"
FT   CDS             30471..33692
FT                   /db_xref="SWISS-PROT:P00968"
FT                   /note="ORF_ID:o103#11"
FT                   /note="similar to PIR Accession Number A01198"
FT                   /transl_table=11
FT                   /gene="carB"
FT                   /product="Carbamoyl-phosphate synthase
FT                   (glutamine-hydrolyzing) (EC   6.3.5.5) large chain"
FT                   /protein_id="BAB96602.1"
FT                   /translation="MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVI
FT                   LVNSNPATIMTDPEMADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELER
FT                   QGVLEEFGVTMIGATADAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVG
FT                   FPCIIRPSFTMGGSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVR
FT                   DKNDNCIIVCSIENFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGG
FT                   SNVQFAVNPKNGRLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDIT
FT                   GGRTPASFEPSIDYVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKAL
FT                   RGLEVGATGFDPKVSLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNI
FT                   DRWFLVQIEELVRLEEKVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLR
FT                   DQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGI
FT                   EFDYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKP
FT                   KGVIVQYGGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANAT
FT                   VTAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLD
FT                   HFLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQ
FT                   VQKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAG
FT                   KSLAEQGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAK
FT                   AQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPR
FT                   LVNKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGF
FT                   ATAMALNADATEKVISVQEMHAQIK"
FT   CDS             complement(33740..33919)
FT                   /note="ORF_ID:o103#12"
FT                   /note="similar to SwissProt Accession Number P46145"
FT                   /transl_table=11
FT                   /gene="yaaV"
FT                   /product="Hypothetical 6.8 kd protein in carB-caiE
FT                   intergenic region."
FT                   /protein_id="BAB96603.1"
FT                   /translation="MTRFEAIKQGHIKIVDISIVCNFTVDKCELNPAYVIKNIDSPKDL
FT                   LNGQKKTVLIREPY"
FT   misc_feature    33849..34351
FT                   /note="ORF is interrupted by frame-shifting"
FT                   /note="ORF_ID:o103#13"
FT                   /note="similar to PIR Accession Number JC6025"
FT                   /gene="caiF"
FT                   /product="Transcription activator caiF"
FT   CDS             complement(34438..35049)
FT                   /note="ORF_ID:o103#14"
FT                   /note="similar to SwissProt Accession Number P39206"
FT                   /transl_table=11
FT                   /gene="caiE"
FT                   /product="Carnitine operon protein caiE."
FT                   /protein_id="BAB96604.1"
FT                   /translation="MERTLTTVSYYAFEGLIPVVHPTAFVHPSAVLIGDVIVGAGVYIG
FT                   PLASLRGDYGRLIVQAGANIQDGCIMHGYCDTDTIVGENGHIGHGAILHGCLIGRDALV
FT                   GMNSVIMDGAVIGEESIVAAMSFVKAGFRGEKRQLLMGTPARAVRNVSDDELHWKRLNT
FT                   KEYQDLVGRCHVSLHETQPLRQMEENRPRLQGTTDVTPKR"
FT   CDS             complement(35034..35927)
FT                   /note="ORF_ID:o103#15"
FT                   /note="similar to PIR Accession Number S40557"
FT                   /transl_table=11
FT                   /gene="caiD"
FT                   /product="Hypothetical protein."
FT                   /protein_id="BAB96605.1"
FT                   /translation="MKQQGTTLPANNHTLKQYAFFAGMLSSLKKQKWRKGMSESLHLTR
FT                   NGSILEITLDRPKANAIDAKTSFEMGEVFLNFRDDPQLRVAIITGAGEKFFSAGWDLKA
FT                   AAEGEAPDADFGPGGFAGLTEIFNLDKPVIAAVNGYAFGGAFELALAADFIVCADNASF
FT                   ALPEAKLGIVPDSGGVLRLPKILPPAIVNEMVMTGRRMGAEEALRWGIVNRVVSQAELM
FT                   DNARELAQQLVNSAPLAIAALKEIYRTTSEMPVEEAYRYIRSGVLKHYPSVLHSEDAIE
FT                   GPLAFAEKRDPVWKGR"
FT   CDS             complement(35928..37496)
FT                   /note="ORF_ID:o104#1"
FT                   /note="similar to PIR Accession Number S40558"
FT                   /transl_table=11
FT                   /gene="caiC"
FT                   /product="Hypothetical protein."
FT                   /protein_id="BAB96606.1"
FT                   /translation="MDRGAMDIIGGQHLRQMWDDLADVYGHKTALICESSGGVVNRYSY
FT                   LELNQEINRTANLFYTLGIRKGDKVALHLDNCPEFIFCWFGLAKIGAIMVPINARLLCE
FT                   ESAWILQNSQACLLVTSAQFYPMYQQIQQEDATQLRHICLTDVALPADDGVSSFTQLKN
FT                   QQPATLCYAPPLSTDDTAEILFTSGTTSRPKGVVITHYNLRFAGYYSAWQCALRDDDVY
FT                   LTVMPAFHIDCQCTAAMAAFSAGATFVLVEKYSARAFWGQVQKYRATVTECIPMMIRTL
FT                   MVQPPSANDQQHRLREVMFYLNLSEQEKDAFCERFGVRLLTSYGMTETIVGIIGDRPGD
FT                   KRRWPSIGRVGFCYEAEIRDDHNRPLPAGEIGEICIKGIPGKTIFKEYFLNPQATAKVL
FT                   EADGWLHTGDTGYRDEEDFFYFVDRRCNMIKRGGENVSCVELENIIAAHPKIQDIVVVG
FT                   IKDSIRDEAIKAFVVLNEGETLSEEEFFRFCEQNMAKFKVPSYLEIRKDLPRNCSGKII
FT                   RKNLK"
FT   CDS             complement(37555..38772)
FT                   /note="ORF_ID:o104#2"
FT                   /note="similar to PIR Accession Number S40559"
FT                   /transl_table=11
FT                   /gene="caiB"
FT                   /product="L-carnitine dehydratase (EC   4.-.-.-)."
FT                   /protein_id="BAB96607.1"
FT                   /translation="MDHLPMPKFGPLAGLRVVFSGIEIAGPFAGQMFAEWGAEVIWIEN
FT                   VAWADTIRVQPNYPQLSRRNLHALSLNIFKDEGREAFLKLMETTDIFIEASKGPAFARR
FT                   GITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQPMPA
FT                   FPYTADYFSGLTATTAALAALHKVRETGKGESIDIAMYEVMLRMGQYFMMDYFNGGEMC
FT                   PRMSKGKDPYYAGCGLYKCADGYIVMELVGITQIEECFKDIGLAHLLGTPEIPEGTQLI
FT                   HRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESI
FT                   TQWQTMDGRTCKGPNIMPKFKNNPGQIWRGMPSHGMDTAAILKNIGYSENDIQELVSKG
FT                   LAKVED"
FT   CDS             complement(38901..40043)
FT                   /note="ORF_ID:o105#1"
FT                   /note="similar to PIR Accession Number S40560"
FT                   /transl_table=11
FT                   /gene="caiA"
FT                   /product="Hypothetical protein."
FT                   /protein_id="BAB96608.1"
FT                   /translation="MDFNLNDEQELFVAGIRELMASENWEAYFAECDRDSVYPERFVKA
FT                   LADMGIDSLLIPEEHGGLDAGFVTLAAVWMELGRLGAPTYVLYQLPGGFNTFLREGTQE
FT                   QIDKIMAFRGTGKQMWNSAITEPGAGSDVGSLKTTYTRKNGKIYLNGSKCFITSSAYTP
FT                   YIVVMARDGASPDKPVYTGWFVDMSKPGIKVTKLEKLGLRMDSCCEITFDDVELDEKDM
FT                   FGREGNGFNRVKEEFDHERFLVALTNYGTAMCAFEDAARYANQRVQFGEAIGRFQLIQE
FT                   KFAHMAIKLNSMKNMLYEAAWKADNGTITSGDAAMCKYFCANAAFEVVDSAMQVLGGVG
FT                   IAGNHRISRFWRDLRVDRVSGGSDEMQILTLGRAVLKQYR"
FT   CDS             complement(40075..41589)
FT                   /note="ORF_ID:o105#2"
FT                   /note="similar to PIR Accession Number S40561"
FT                   /transl_table=11
FT                   /gene="caiT"
FT                   /product="Hypothetical protein."
FT                   /protein_id="BAB96609.1"
FT                   /translation="MKNEKRKTGIEPKVFFPPLIIVGILCWLTVRDLDAANVVINAVFS
FT                   YVTNVWGWAFEWYMVVMLFGWFWLVFGPYAKKRLGNEPPEFSTASWIFMMFASCTSAAV
FT                   LFWGSIEIYYYISTPPFGLEPNSTGAKELGLAYSLFHWGPLPWATYSFLSVAFAYFFFV
FT                   RKMEVIRPSSTLVPLVGEKHAKGLFGTIVDNFYLVALIFTMGTSLGLATPLVTECMQWL
FT                   FGIPHTLQLDAIIITCWIILNAICVACGLQKGVRIASDVRSYLSFLMLGWVFIVSGASF
FT                   IMNYFTDSVGMLLMYLPRMLFYTDPIAKGGFPQGWTVFYWAWWVIYAIQMSIFLARISR
FT                   GRTVRELCFGMVLGLTASTWILWTVLGSNTLLLIDKNIINIPNLIEQYGVARAIIETWA
FT                   ALPLSTATMWGFFILCFIATVTLVNACSYTLAMSTCREVRDGEEPPLLVRIGWSILVGI
FT                   IGIVLLALGGLKPIQTAIIAGGCPLFFVNIMVTLSFIKDAKQNWKD"
FT   CDS             42025..42831
FT                   /note="ORF_ID:o105#3"
FT                   /note="similar to PIR Accession Number S40562"
FT                   /transl_table=11
FT                   /gene="fixA"
FT                   /product="FixA homolog."
FT                   /protein_id="BAB96610.1"
FT                   /translation="MNDVSFMISGDAMKIITCYKCVPDEQDIAVNNADGSLDFSKADAK
FT                   ISQYDLNAIEAACQLKQQAAEAQVTALSVGGKALTNAKGRKDVLSRDPDELIVVIDDQF
FT                   EQALPQQTASALAAAAQKAGFDLILCGDGSSDLYAQQVGLLVGEILNIPAVNGVSKIIS
FT                   LTADTLTVERELEDETETLSIPLPAVVAVSTDINSPQIPSMKAILGAAKKPVQVWSAAD
FT                   IGFNAEAAWSEQQVAAPKQRERQRIVIEGDGEEQIAAFAENLRKVI"
FT   misc_feature    42810..43787
FT                   /note="ORF is interrupted by frame-shifting"
FT                   /note="ORF_ID:o105#4"
FT                   /note="similar to SwissProt Accession Number P31574"
FT                   /gene="fixB"
FT                   /product="FixB protein."
FT   CDS             43838..45124
FT                   /note="ORF_ID:o105#5"
FT                   /note="similar to PIR Accession Number S40564"
FT                   /transl_table=11
FT                   /gene="fixC"
FT                   /product="FixC protein"
FT                   /protein_id="BAB96611.1"
FT                   /translation="MSEDIFDAIIVGAGLAGSVAALVLAREGAQVLVIERGNSAGAKNV
FT                   TGGRLYAHSLEHIIPGFADSAPVERLITHEKLAFMTEKSAMTMDYCNGDETSPSQRSYS
FT                   VLRSKFDAWLMEQAEEAGAQLITGIRVDNLVQRDGKVVGVEADGDVIEAKTVILADGVN
FT                   SILAEKLGMAKRVKPTDVAVGVKELIELPKSVIEDRFQLQGNQGAACLFAGSPTDGLMG
FT                   GGFLYTNENTLSLGLVCGLHHLHDAKKSVPQMLEDFKQHPAVAPLIAGGKLVEYSAHIM
FT                   PEAGINMLPELVGDGVLIAGDAAGMCMNFGFTIRGMDLAIAAGEAAAKTVLSAMKSDDF
FT                   SKQKLAEYRQHLESGPLRDMRMYQKLPAFLDNPRMFSGYPELAVGVARDLFTIDGSAPE
FT                   LMRKKILRHGKKVGFINLIKDGMKGVTVL"
FT   CDS             45121..45408
FT                   /note="ORF_ID:o105#6"
FT                   /note="similar to PIR Accession Number S40565"
FT                   /transl_table=11
FT                   /gene="yaaT"
FT                   /product="Hypothetical protein"
FT                   /protein_id="BAB96612.1"
FT                   /translation="MTSPVNVDVKLGVNKFNVDEEHPHIVVKADADKQVLELLVKACPA
FT                   GLYKKQDDGSVRFDYAGCLECGTCRILGLGSALEQWEYPRGTFGVEFRYS"
FT   misc_feature    45465..46050
FT                   /note="ORF is interrupted by frame-shifting"
FT                   /note="ORF_ID:o105#7"
FT                   /note="similar to SwissProt Accession Number P31679"
FT                   /gene="yaaU"
FT                   /product="Hypothetical 18.4 kd protein in fixC-kefC
FT                   intergenic region (orf65)."
FT   CDS             46137..46799
FT                   /note="ORF_ID:o105#8"
FT                   /note="similar to PIR Accession Number S40566"
FT                   /transl_table=11
FT                   /gene="yabE"
FT                   /product="Hypothetical protein"
FT                   /protein_id="BAB96613.1"
FT                   /translation="MKSSRSKPGFRDLFNRCHFPFVLFVAAIWTCQVIPMFAIYTFGPQ
FT                   IVGLLGLGVGKNAALGNVVISLFFMLGCIPPMLWLSTAGRRPLLIGSFAMMTLALAVLG
FT                   LIPDMGIWLVVMAFAVYAFFSGGPGNLQWLYPNELFPTDIRASAVGVIMSLSRIGTIVS
FT                   TWALPIFIDNYGISNTMLMGAGISLFGLLISVAFAPETRGMSLAQTSNMTIRGQRMG"
FT   CDS             46907..47437
FT                   /note="ORF_ID:o105#9"
FT                   /note="similar to PIR Accession Number S40567"
FT                   /transl_table=11
FT                   /gene="yabF"
FT                   /product="Hypothetical protein"
FT                   /protein_id="BAB96614.1"
FT                   /translation="MILIIYAHPYPHHSHANKRMLEQARTLEGVEIRSLYQLYPDFNID
FT                   IAAEQEALSRADLIVWQHPMQWYSIPPLLKLWINKVFSHGWAYGHGGTALHGKHLLWAV
FT                   TTGGGESHFEIGAHPGFDGLSQPLQATAIYCGLNWLPPFAMHCTFICDDETLEGQARHY
FT                   KQRLLEWQEAHHG"
FT   CDS             47430..49292
FT                   /note="ORF_ID:o105#10"
FT                   /note="similar to SwissProt Accession Number P03819"
FT                   /transl_table=11
FT                   /gene="kefC"
FT                   /gene="trkC"
FT                   /product="Glutathione-regulated potassium-efflux system
FT                   protein KefC (K(+)/H(+) antiporter)."
FT                   /protein_id="BAB96615.1"
FT                   /translation="MDSHTLIQALIYLGSAALIVPIAVRLGLGSVLGYLIAGCIIGPWG
FT                   LRLVTDAESILHFAEIGVVLMLFIIGLELDPQRLWKLRAAVFGCGALQMVICGGLLGLF
FT                   CMLLGLRWQVAELIGMTLALSSTAIAMQAMNERNLMVTQMGRSAFAVLLFQDIAAIPLV
FT                   AMIPLLATSSASTTMGAFALSALKVAGALVLVVLLGRYVTRPALRFVARSGLREVFSAV
FT                   ALFLVFGFGLLLEEVGLSMAMGAFLAGVLLASSEYRHALESDIEPFKGLLLGLFFIGVG
FT                   MSIDFGTLLENPLRIVILLLGFLIIKIAMLWLIARPLQVPNKQRRWFAVLLGQGSEFAF
FT                   VVFGAAQMANVLEPEWAKSLTLAVALSMAATPILLVILNRLEQSSTEEAREADEIDEEQ
FT                   PRVIIAGFGRFGQITGRLLLSSGVKMVVLDHDPDHIETLRKFGMKVFYGDATRMDLLES
FT                   AGAAKAEVLINAIDDPQTNLQLTEMVKEHFPHLQIIARARDVDHYIRLRQAGVEKPERE
FT                   TFEGALKTGRLALESLGLGPYEARERADVFRRFNIQMVEEMAMVENDTKARAAVYKRTS
FT                   AMLSEIITEDREHLSLIQRHGWQGTEEGKHTGNMADEPETKPSS"
FT   CDS             49482..49961
FT                   /note="ORF_ID:o105#11"
FT                   /note="similar to SwissProt Accession Number P00379"
FT                   /transl_table=11
FT                   /gene="folA"
FT                   /gene="tmrA"
FT                   /product="Dihydrofolate reductase type I (EC   1.5.1.3)."
FT                   /protein_id="BAB96616.1"
FT                   /translation="MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRH
FT                   TWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFL
FT                   PKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR"
FT   CDS             complement(50039..50881)
FT                   /note="ORF_ID:o105#12"
FT                   /note="similar to PIR Accession Number A26221"
FT                   /transl_table=11
FT                   /gene="apaH"
FT                   /product="Bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
FT                   (EC  3.6.1.41)"
FT                   /protein_id="BAB96617.1"
FT                   /translation="MATYLIGDVHGCYDELIALLHKVEFTPGKDTLWLTGDLVARGPGS
FT                   LDVLRYVKSLGDSVRLVLGNHDLHLLAVFAGISRNKPLDRLTPLLEAPDADELLNWLRR
FT                   QPLLQIDEEKKLVMAHAGITPQWDLQTAKECARDVEAVLSSDSYPFFLDAMYGDMPNNW
FT                   SPELRGLGRLRFITNAFTRMRFCFPNGQLDMYSKESPEEAPAPLKPWFAIPGPVAEEYS
FT                   IAFGHWASLEGKGTPEGIYALDTGCCWGGTLTCLRWEDKQYFVQPSNRHKDLAEAAAS"
FT   CDS             complement(50888..51265)
FT                   /note="ORF_ID:o106#1"
FT                   /note="similar to PIR Accession Number A30273"
FT                   /transl_table=11
FT                   /gene="apaG"
FT                   /product="ApaG protein"
FT                   /protein_id="BAB96618.1"
FT                   /translation="MINSPRVCIQVQSVYIEAQSSPDNERYVFAYTVTIRNLGRAPVQL
FT                   LGRYWLITNGNGRETEVQGEGVVGVQPLIAPGEEYQYTSGAIIETPLGTMQGHYEMIDE
FT                   NGVPFSIDIPVFRLAVPTLIH"
FT   CDS             complement(52087..53076)
FT                   /note="ORF_ID:o106#2"
FT                   /note="similar to PIR Accession Number JV0026"
FT                   /transl_table=11
FT                   /gene="pdxA"
FT                   /product="PdxA protein"
FT                   /protein_id="BAB96619.1"
FT                   /translation="MVKTQRVVITPGEPAGIGPDLVVQLAQREWPVELVVCADATLLTN
FT                   RAAMLGLPLTLRPYSPNSPAQPQTAGTLTLLPVALRAPVTAGQLAVENGHYVVETLARA
FT                   CDGCLNGEFAALITGPVHKGVINDAGIPFTGHTEFFEERSQAKKVVMMLATEELRVALA
FT                   TTHLPLRDIADAITPALLHEVIAILHHDLRTKFGIAEPRILVCGLNPHAGEGGHMGTEE
FT                   IDTIIPVLNELRAQGMKLNGPLPADTLFQPKYLDNADAVLAMYHDQGLPVLKYQGFGRG
FT                   VNITLGLPFIRTSVDHGTALELAGRGKADVGSFITALNLAIKMIVNTQ"
FT   CDS             complement(53076..53873)
FT                   /note="ORF_ID:o106#3"
FT                   /note="similar to PIR Accession Number PV0009"
FT                   /transl_table=11
FT                   /product="Hypothetical protein 98 (pdx 5' region)"
FT                   /protein_id="BAB96620.1"
FT                   /translation="MGNQNDASTELNLSHILIPLPENPTSDQVNEAESQARAIVDQARN
FT                   GADFGKLAIAHSADQQALNGGQMGWGRIQELPGIFAQALSTAKKGDIVGPIRSGVGFHI
FT                   LKVNDLRGESKNISVTEVHARHILLKPSPIMTDEQARVKLEQIAADIKSGKTTFAAAAK
FT                   EFSQDPGSANQGGDLGWATPDIFDPAFRDALTRLNKGQMSAPVHSSFGWHLIELLDTRN
FT                   VDKTDAAQKDRAYRMLMNRKFSEEAASWMQEQRASAYVKILSN"
FT   CDS             complement(53840..54361)
FT                   /note="ORF_ID:o106#4"
FT                   /note="similar to PIR Accession Number S40574"
FT                   /transl_table=11
FT                   /gene="surA"
FT                   /product="Survival protein SurA precursor (peptidyl-prolyl
FT                   cis-trans isomerase SurA) (EC  5.2.1.8) (PPiase) (rotamase
FT                   C)."
FT                   /protein_id="BAB96621.1"
FT                   /translation="MKNWKTLLLGIAMIANTSFAAPQVVDKVAAVVNNGVVLESDVDGL
FT                   MQSVKLNAAQARQQLPDDATLRHQIMERLIMDQIILQMGQKMGVKISDEQLDQAIANIA
FT                   KQNNMTLDQMRSRLAYDGLNYNTYRNQIRKEMIISEVRNNEVRRRITILPQKSNPWRSR
FT                   WVTKTTPALS"
FT   CDS             complement(54414..56768)
FT                   /note="ORF_ID:o106#5"
FT                   /note="similar to SwissProt Accession Number P31554"
FT                   /transl_table=11
FT                   /gene="imp"
FT                   /gene="ostA"
FT                   /product="Organic solvent tolerance protein precursor."
FT                   /protein_id="BAB96622.1"
FT                   /translation="MKKRIPTLLATMIATALYSQQGLAADLASQCMLGVPSYDRPLVQG
FT                   DTNDLPVTINADHAKGDYPDDAVFTGSVDIMQGNSRLQADEVQLHQKEAPGQPEPVRTV
FT                   DALGNVHYDDNQVILKGPKGWANLNTKDTNVWEGDYQMVGRQGRGKADLMKQRGENRYT
FT                   ILDNGSFTSCLPGSDTWSVVGSEIIHDREEQVAEIWNARFKVGPVPIFYSPYLQLPVGD
FT                   KRRSGFLIPNAKYTTTNYFEFYLPYYWNIAPNMDATITPHYMHRRGNIMWENEFRYLSQ
FT                   AGAGLMELDYLPSDKVYEDEHPNDDSSRRWLFYWNHSGVMDQVWRFNVDYTKVSDPSYF
FT                   NDFDNKYGSSTDGYATQKFSVGYAVQNFNATVSTKQFQVFSEQNTSSYSAEPQLDVNYY
FT                   QNDVGPFDTRIYGQAVHFVNTRDDMPEATRVHLEPTINLPLSNNWGSINTEAKLLATHY
FT                   QQTNLDWYNSRNTTKLDESVNRVMPQFKVDGKMVFERDMEMLAPGYTQTLEPRAQYLYV
FT                   PYRDQSDIYNYDSSLLQSDYSGLFRDRTYGGLDRIASANQVTTGVTSRIYDDAAVERFN
FT                   ISVGQIYYFTESRTGDDNITWENDDKTGSLVWAGDTYWRISERWGLRGGIQYDTRLDNV
FT                   ATSNSSIEYRRDEDRLVQLNYRYASPEYIQATLPKYYSTAEQYKNGISQVGAVASWPIA
FT                   DRWSIVGAYYYDTNANKQADSMLGVQYSSCCYAIRVGYERKLNGWDNDKQHAVYDNAIG
FT                   FNIELRGLSSNYGLGTQEMLRSNILPYQNTL"
FT   CDS             57023..57838
FT                   /note="ORF_ID:o106#6"
FT                   /note="similar to SwissProt Accession Number P31680"
FT                   /transl_table=11
FT                   /gene="yabH"
FT                   /product="Hypothetical 30.6 kd protein in folA-hepA
FT                   intergenic region (orf81)."
FT                   /protein_id="BAB96623.1"
FT                   /translation="MQYWGKIIGVAVALLMGGGFWGVVLGLLIGHMFDKARSRKMAWFA
FT                   NQRERQALFFATTFEVMGHLTKSKGRVTEADIHIASQLMDRMNLHGASRTAAQNAFRVG
FT                   KSDNYPLREKMRQFRSVCFGRFDLIRMFLEIQIQAAFADGSLHPNERAVLYVIAEELGI
FT                   SRAQFDQFLRMMQGGAQFGGGYQQQTGGGNWQQAQRGPTLEDACNVLGVKPTDDATTIK
FT                   RAYRKLMSEHHPDKLVAKGLPPEMMEMAKQKAQEIQQAYELIKQQKGFK"
FT   CDS             58625..58783
FT                   /note="ORF_ID:o106#7"
FT                   /note="similar to SwissProt Accession Number P39220"
FT                   /transl_table=11
FT                   /gene="yabP"
FT                   /product="Hypothetical 5.9 kd protein in surA-hepA
FT                   intergenic region."
FT                   /protein_id="BAB96624.1"
FT                   /translation="MRDCYLGKKTMKGSNDILYERPGWNANLGVLPRTVLPRTVLTRTV
FT                   LTWTVLP"
FT   CDS             58780..58938
FT                   /note="ORF_ID:o106#8"
FT                   /note="similar to SwissProt Accession Number P39221"
FT                   /transl_table=11
FT                   /gene="yabQ"
FT                   /product="Hypothetical 5.7 kd protein in surA-hepA
FT                   intergenic region."
FT                   /protein_id="BAB96625.1"
FT                   /translation="MNGATSLYDEVIIINKIPPKKIDTKGVATEEVATKKVLLNKLLTT
FT                   QLLNEPE"
FT   misc_feature    complement(59346..60009)
FT                   /note="ORF is interrupted by frame-shifting"
FT                   /note="ORF_ID:o106#9"
FT                   /note="similar to SwissProt Accession Number P39219"
FT                   /gene="yabO"
FT                   /product="Hypothetical 24.9 kd protein in surA-hepA
FT                   intergenic region."
FT   CDS             59985..60518
FT                   /note="ORF_ID:o106#10"
FT                   /transl_table=11
FT                   /protein_id="BAB96626.1"
FT                   /translation="MDCSFPSPFSAPLLMRYNDQTQGIQTPTCLIQAFHYLLTVALNGG
FT                   QFVVTNVRVHCTQSFQTRQLGRQFFVGFVTRCINQCTGRFLDLRFTQLKDSVNILLHGV
FT                   NQFAAGVTVNRVKLAVKGFKLYLRRQVVAVFIQQHTYRRRWQEAVELQLLRSLGFNHIN
FT                   QFHQQRTYRQRFVF"
FT   CDS             complement(60021..62927)
FT                   /note="ORF_ID:o106#11"
FT                   /note="similar to SwissProt Accession Number P23852"
FT                   /transl_table=11
FT                   /gene="hepA"
FT                   /product="Probable ATP-dependent helicase HepA."
FT                   /protein_id="BAB96627.1"
FT                   /translation="MPFTLGQRWISDTESELGLGTVVAVDARTVTLLFPSTGENRLYAR
FT                   SDSPVTRVMFNPGDTITSHDGWQMQVEEVKEENGLLTYIGTRLDTEESGVALREVFLDS
FT                   KLVFSKPQDRLFAGQIDRMDRFALRYRARKYSSEQFRMPYSGLRGQRTSLIPHQLNIAH
FT                   DVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMLRR
FT                   FNLRFALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDE
FT                   AHHLVWSEDAPSREYQAIEQLAEHVPGVLLLTATPEQLGMESHFARLRLLDPNRFHDFA
FT                   QFVEEQKNYRPVADAVAMLLAGNKLSNDELNMLGEMIGEQDIEPLLQAANSDSEDAQSA
FT                   RQELVSMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIKLPLPTQYQTAIKVSGIMGARK
FT                   SAEDRARDMLYPERIYQEFEGDNATWWNFDPRVEWLMGYLTSHRSQKVLVICAKAATAL
FT                   QLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFAS
FT                   HMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWYHEGLDAFEHT
FT                   CPTGRTIYDSVYNDLINYLASPDQTEGFDDLIKNCREQHEALKAQLEQGRDRLLEIHSN
FT                   GGEKAQALAESIEEQDDDTNLIAFAMNLFDIIGINQDDRGDNMIVLTPSDHMLVPDFPG
FT                   LSEDGITITFDREVALAREDAQFITWEHPLIRNGLDLILSGDTGSSTISLLKNKALPVG
FT                   TLLVELIYVVEAQAPKQLQLNRFLPPTPVRMLLDKNGNNLAAQVEFETFNRQLNAVNRH
FT                   TGSKLVNAVQQDVHAILQLGEAQIEKSARALIDAARNEADEKLSAELSRLEALRAVNPN
FT                   IRDDELTAIESNRQQVMESLDQAGWRLDALRLIVVTHQ"
FT   CDS             complement(63092..64741)
FT                   /note="ORF_ID:o107#1"
FT                   /note="dinA; polB"
FT                   /note="similar to E. coli DNA polymerase II (EC  2.7.7.7)
FT                   (Pol II): PIR Accession Number S15943"
FT                   /transl_table=11
FT                   /protein_id="BAB96628.1"
FT                   /translation="MPSRYRLPLRLGRDNSELEWREHGPAKTASFLPQAKGRLIIDGIE
FT                   ALKSAFWDFSSFSLETVAQELLGEGKSIDNPWDRMDEIDRRFAEDKPALATYNLKDCEL
FT                   VTQIFHKTEIMPFLLERATVNGLPVDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPH
FT                   ASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTEGFLD
FT                   AWFSREKHCLPEIVTNIWHGRDEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRL
FT                   ASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVN
FT                   AWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGLIQEGDKQRMVFKG
FT                   LETVRTDWTPLAQQFQQELYLRIFRNEPYQEYVRETIDKLMAGELDARLVYRKRLRRPL
FT                   SEYQRNVPPHVRAARLADEENQKRGRPLQYQNRGTIKYVWTTNGPEPLDYQRSPLDYEH
FT                   YLTRQLQPVAEGILPFIEDNFATLMTGQLGLF"
FT   CDS             complement(64698..65447)
FT                   /note="ORF_ID:o107#2"
FT                   /note="polB"
FT                   /note="similar to E. coli DNA-directed DNA polymerase (EC
FT                   2.7.7.7) II: PIR Accession Number S15943"
FT                   /transl_table=11
FT                   /protein_id="BAB96629.1"
FT                   /translation="MAQAGFILTRHWRDTPQGTEVSFWLATDNGPLQVTLAPQESVAFI
FT                   PADQVPRAQHILQGEQGFRLTPLALKDFHRQPVYGLYCRAHRQLMNYEKRLREGGVTVY
FT                   EADVRPPERYLMERFITSPVWVEGDMHNGTIVNARLKPHPDYRPPLKWVSIDIETTRHG
FT                   ELYCIGLEGCGQRIVYMLGPENGDASSLDFELEYVASRPQLLEKLNAWFANYDPDVIIG
FT                   WNVVQFDLRMLQKHAEPLPSSAASWAR"
FT   CDS             complement(65522..66217)
FT                   /note="ORF_ID:o107#3"
FT                   /note="similar to SwissProt Accession Number P08203"
FT                   /transl_table=11
FT                   /gene="araD"
FT                   /product="L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4)."
FT                   /protein_id="BAB96630.1"
FT                   /translation="MLEDLKRQVLEANLALPKHNLVTLTWGNVSAVDRERGVFVIKPSG
FT                   VDYSVMTADDMVVVSIETGEVVEGTKKPSSDTPTHRLLYQAFPSIGGIVHTHSRHATIW
FT                   AQAGQSIPATGTTHADYFYGTIPCTRKMTDAEINGEYEWETGNVIVETFEKQGIDAAQM
FT                   PGVLVHSHGPFAWGKNAEDAVHNAIVLEEVAYMGIFCRQLAPQLPDMQQTLLDKHYLRK
FT                   HGAKAYYGQ"
FT   CDS             complement(66502..68004)
FT                   /note="ORF_ID:o107#4"
FT                   /note="similar to SwissProt Accession Number P08202"
FT                   /transl_table=11
FT                   /gene="araA"
FT                   /product="L-arabinose isomerase (EC  5.3.1.4)."
FT                   /protein_id="BAB96631.1"
FT                   /translation="MTIFDNYEVWFVIGSQHLYGPETLRQVTQHAEHVVNALNTEAKLP
FT                   CKLVLKPLGTTPDEITAICRDANYDDPCAGLVVWLHTFSPAKMWINGLTMLNKPLLQFH
FT                   TQFNAALPWDSIDMDFMNLNQTAHGGREFGFIGARMRQQHAVVTGHWQDKQAHERIGSW
FT                   MRQAVSKQDTRHLKVCRFGDNMREVAVTDGDKVAAQIKFGFSVNTWAVGDLVQVVNSIS
FT                   DGDVNALVDEYESCYTMTPATQIHGEKRQNVLEAARIELGMKRFLEQGGFHAFTTTFED
FT                   LHGLKQLPGLAVQRLMQQGYGFAGEGDWKTAALLRIMKVMSTGLQGGTSFMEDYTYHFE
FT                   KGNDLVLGSHMLEVCPSIAVEEKPILDVQHLGIGGKDDPARLIFNTQTGPAIVASLIDL
FT                   GDRYRLLVNCIDTVKTPHSLPKLPVANALWKAQPDLPTASEAWILAGGAHHTVFSHALN
FT                   LNDMRQFAEMHDIEITVIDNDTRLPAFKDALRWNEVYYGFRR"
FT   CDS             complement(68015..69715)
FT                   /note="ORF_ID:o108#1"
FT                   /note="similar to PIR Accession Number B29022"
FT                   /transl_table=11
FT                   /gene="araB"
FT                   /product="Ribulokinase (EC  2.7.1.16)"
FT                   /protein_id="BAB96632.1"
FT                   /translation="MAIAIGLDFGSDSVRALAVDCASGEEIATSVEWYPRWQKGQFCDA
FT                   PNNQFRHHPRDYIESMEAALKTVLAELSVEQRAAVVGIGVDSTGSTPAPIDADGNVLAL
FT                   RPEFAENPNAMFVLWKDHTAVERSEEITRLCHAPGNVDYSRYIGGIYSSEWFWAKILHV
FT                   TRQDSAVAQSAASWIELCDWVPALLSGTTRPQDIRRGRCSAGHKSLWHESWGGLPPASF
FT                   FDELDPILNRHLPSPLFTDTWTADIPVGTLCPEWAQRLGLPESVVISGGAFDCHMGAVG
FT                   AGAQPNALVKVIGTSTCDILIADKQSVGERAVKGICGQVDGSVVPGFIGLEAGQSAFGD
FT                   IYAWFGRVLSWPLEQLAAQHPELKAQINASQKQLLPALTEAWAKNPSLDHLPVVLDWFN
FT                   GRRSPNANQRLKGVITDLNLATDAPLLFGGLIAATAFGARAIMECFTDQGIAVNNVMAL
FT                   GGIARKNQVIMQACCDVLNRPLQIVASDQCCALGAAIFAAVAAKVHADIPSAQQKMASA
FT                   VEKTLQPRSEQAQRFEQLYRRYQQWAMSAEQHYLPTSAPAQAAQAVATL"
FT   CDS             70054..70932
FT                   /note="ORF_ID:o108#2"
FT                   /note="similar to PIR Accession Number A91473"
FT                   /transl_table=11
FT                   /gene="araC"
FT                   /product="Arabinose operon regulatory protein"
FT                   /protein_id="BAB96633.1"
FT                   /translation="MAEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGY
FT                   ILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYW
FT                   HEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRR
FT                   MEAINESLHPPMDNRVREACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQQLGIS
FT                   VLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRAGCE
FT                   EKVNDVAVKLS"
FT   CDS             71066..71779
FT                   /note="ORF_ID:o108#3"
FT                   /note="similar to PIR Accession Number S40581"
FT                   /transl_table=11
FT                   /gene="yabI"
FT                   /product="Hypothetical protein"
FT                   /protein_id="BAB96634.1"
FT                   /translation="MAVVLVAFLESLALVGLILPGTVLMAGLGALIGSGELSFWHAWLA
FT                   GIIGCLMGDWISFWLGWRFKKPLHRWSFLKKNKALLDKTEHALHQHSMFTILVGRFVGP
FT                   TRPLVPMVAGMLDLPVAKFITPNIIGCLLWPPFYFLPGILAGAAIDIPAGMQSGEFKWL
FT                   LLATAVFLWVGGWLCWRLWRSGKATDRLSHYLSRGRLLWLTPLISAIGVVALVVLIRHP
FT                   LMPVYIDILRKVVGV"
FT   CDS             complement(71894..72592)
FT                   /note="ORF_ID:o108#4"
FT                   /note="similar to PIR Accession Number S40582"
FT                   /transl_table=11
FT                   /gene="yabJ"
FT                   /product="Hypothetical protein"
FT                   /protein_id="BAB96635.1"
FT                   /translation="MLKLTDITWLYHHLPMRFSLTVERGEQVAILGPSGAGKSTLLNLI
FT                   AGFLTPASGSLTIDGVDHTTMPPSRRPVSMLFQENNLFSHLTVAQNIGLGLNPGLKLNA
FT                   VQQGKMHAIARQMGIDNLMARLPGELSGGQRQRVALARCLVREQPILLLDELFSALDPA
FT                   LRQEMLTLVSTSCQQQKMTLLMVSHSVEDAARIATRSVVVADGRIAWQGMTNELLSGKA
FT                   SASALLGITG"
FT   CDS             complement(72576..74186)
FT                   /note="ORF_ID:o108#5"
FT                   /note="similar to PIR Accession Number S40583"
FT                   /transl_table=11
FT                   /gene="yabK"
FT                   /product="Hypothetical protein"
FT                   /protein_id="BAB96636.1"
FT                   /translation="MATRRQPLIPGWLIPGVSATTLVVAVALAAFLALWWNAPQDDWVA
FT                   VWQDSYLWHVVRFSFWQAFLSALLSVIPAIFLARALYRRRFPGRLALLRLCAMTLILPV
FT                   LVAVFGILSVYGRQGWLATLCQSLGLEWTFSPYGLQGILLAHVFFNLPMASRLLLQALE
FT                   NIPGEQRQLAAQLGMRSWHFFRFVEWPWLRRQIPPVAALIFMLCFASFATVLSLGGGPQ
FT                   ATTIELAIYQALSYDYDPARAAMLALLQMVCCLGLVLLSQRLSKAIAPGTTLLQGWRDP
FT                   DDRLHSRICDTVLIVLALLLLLPPLLAVIVDGVNRQLPEVLAQPVLWQALWTSLRIALA
FT                   AGVLCVVLTMMLLWSSRELRARQKMLAGQVLEMSGMLILAMPGIVLATGFFLLLNNTIG
FT                   LPQSADGIVIFTNALMAIPYALKVLENPMRDITARYSMLCQSLGIEGWSRLKVVELRAL
FT                   KRPLAQALAFACVLSIGDFGVVALFGNDDFRTLPFYLYQQIGSYRSQDGAVTTLILLLL
FT                   CFLLFTVIEKLPGRNVKTD"
FT   CDS             complement(74162..75133)
FT                   /note="ORF_ID:o108#6"
FT                   /note="similar to PIR Accession Number S40584"
FT                   /transl_table=11
FT                   /gene="tbpA"
FT                   /product="Hypothetical protein."
FT                   /protein_id="BAB96637.1"
FT                   /translation="MSAPAVAVTAPVFAKPVLTVYTYDSFAADWGPGPVVKKAFEADCN
FT                   CELKLVALEDGVSLLNRLRMEGKNSKADVVLGLDNNLLDAASKTGLFAKSGVAADAVNV
FT                   PGGWNNDTFVPFDYGYFAFVYDKNKLKNPPQSLKELVESDQNWRVIYQDPRTSTPGLGL
FT                   LLWMQKVYGDDAPQAWQKLAKKTVTVTKGWSEAYGLFLKGESDLVLSYTTSPAYHILEE
FT                   KKDNYAAANFSEGHYLQVEVAARTAASKQPELAQKFLQFMVSPAFQNAIPTGNWMYPVA
FT                   NVTLPAGFEKLTKPATTLEFTPAEVAAQRQAWISEWQRAVSR"
FT   CDS             complement(75308..76963)
FT                   /note="ORF_ID:o108#7"
FT                   /note="similar to SwissProt Accession Number P33595"
FT                   /transl_table=11
FT                   /gene="yabN"
FT                   /product="Hypothetical 63.9 kd protein in tbpA-leuD
FT                   intergenic region (orf103)."
FT                   /protein_id="BAB96638.1"
FT                   /translation="MPSARLQQQFIRLWQCCEGKSQDTTLNELAALLSCSRRHMRTLLN
FT                   TMQDRGWLTWEAEVGRGKRSRLTFLYTGLALQQQRAEDLLEQDRIDQLVQLVGDKATVR
FT                   QMLVSHLGRSFRQGRHILRVLYYRPLRNLLPGSALRRSETHIARQIFSSLTRINEENGE
FT                   LEADIAHHWQQISPLHWRFFLRPGVHFHHGRELEMDDVIASLKRINTLPLYSHIADIVS
FT                   PTPWTLDIHLTQPDRWLPLLLGQVPAMILPREWETLSNFASHPIGTGPYAVIRNSTNQL
FT                   KIQAFDDFFGYRALIDEVNVWVLPEIADEPAGGLMLKGPQGEEKEIESRLEEGCYYLLF
FT                   DSRTHRGANQQVRDWASYVLSPTNLVYFAEEQYQQLWFPAYGLFPRWHHARTIKSEKPA
FT                   GLESLTLTFCQDHSEHRVIAGIMQQILASHQVTLKIKEIDYDQWHTGEIESDIWLNSAN
FT                   FTLPLDFSVFAHLCEVPLLQHCIPIDWQADAARWRNGEMNLANWCQQLVASKAMVPLLH
FT                   HWLIIQGQRSMRGLRMNTLGWFDFKSAWFAPPDP"
FT   CDS             77285..78463
FT                   /note="ORF_ID:o108#8"
FT                   /note="similar to SwissProt Accession Number P31675"
FT                   /transl_table=11
FT                   /gene="yabM"
FT                   /product="Hypothetical 42.7 kd protein in tbpA-leuD
FT                   intergenic region (orf104)."
FT                   /protein_id="BAB96639.1"
FT                   /translation="MIWIMTMARRMNGVYAAFMLVAFMMGVAGALQAPTLSLFLSREVG
FT                   AQPFWIGLFYAVNAIAGIGVSLWLAKRSDSQGDRRKLIIFCCLMAIGNALLFAFNRHYL
FT                   TLITCGVLLASLANTAMPQLFALAREYADNSAREVVMFSSVMRAQLSLAWVIGPPLAFM
FT                   LALNYGFTVMFSIAAGIFTLSLVLIAFMLPSVARVELPSENALSMQGGWQDSNVRMLFV
FT                   ASTLMWTCNTMYIIDMPLWISSELGLPDKLAGFLMGTAAGLEIPAMILAGYYVKRYGKR
FT                   RMMVIAVAAGVLFYTGLIFFNSRMALMTLQLFNAVFIGIVAGIGMLWFQDLMPGRAGAA
FT                   TTLFTNSISTGVILAGVIQGAIAQSWGHFAVYWVIAVISVVALFLTAKVKDV"
FT   CDS             complement(78512..79117)
FT                   /note="ORF_ID:o108#9"
FT                   /note="similar to PIR Accession Number S40585"
FT                   /transl_table=11
FT                   /gene="leuD"
FT                   /product="Isopropylmalate isomerase subunit"
FT                   /protein_id="BAB96640.1"
FT                   /translation="MAEKFIKHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFN
FT                   DWRFLDEKGQQPNPDFVLNFPQYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAP
FT                   SFADIFYGNSFNNQLLPVKLSDAEVDELFALVKANPGIHFDVDLEAQEVKAGEKTYRFT
FT                   IDAFRRHCMMNGLDSIGLTLQHDDAIAAYEAKQPAFMN"
FT   CDS             complement(79128..80528)
FT                   /db_xref="SWISS-PROT:P30127"
FT                   /note="ORF_ID:o109#1"
FT                   /note="similar to PIR Accession Number S40586"
FT                   /transl_table=11
FT                   /gene="leuC"
FT                   /product="3-isopropylmalate dehydratase (EC 4.2.1.33) alpha
FT                   chain"
FT                   /protein_id="BAB96641.1"
FT                   /translation="MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLR
FT                   AHGRPVRQPGKTFATMDHNVSTQTKGINACGEMARIQMQELIKNCKEFGVELYDLNHPY
FT                   QGIVHVMGPEQGVTLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRA
FT                   KTMKIEVQGKAAPGITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNM
FT                   AIEMGAKAGLVAPDETTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQA
FT                   EEISPQVTWGTNPGQVISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAID
FT                   KVFIGSCTNSRIEDLRAAAEIVKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAG
FT                   FEWRLPGCSMCLAMNNDRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGH
FT                   FADIRNIK"
FT   CDS             complement(80531..81622)
FT                   /note="ORF_ID:o109#2"
FT                   /note="similar to SwissProt Accession Number P30125"
FT                   /transl_table=11
FT                   /gene="leuB"
FT                   /product="3-isopropylmalate dehydrogenase (EC  1.1.1.85)
FT                   (beta-ipm dehydrogenase) (imdH) (3-ipm-dh)."
FT                   /protein_id="BAB96642.1"
FT                   /translation="MSKNYHIAVLPGDGIGPEVMTQALKVLDAVRNRFAMRITTSHYDV
FT                   GGAAIDNHGQPLPPATVEGCEQADAVLFGSVGGPKWEHLPPDQQPERGALLPLRKHFKL
FT                   FSNLRPAKLYQGLEAFCPLRADIAANGFDILCVRELTGGIYFGQPKGREGSGQYEKAFD
FT                   TEVYHRFEIERIARIAFESARKRRHKVTSIDKANVLQSSILWREIVNEIATEYPDVELA
FT                   HMYIDNATMQLIKDPSQFDVLLCSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYE
FT                   PAGGSAPDIAGKNIANPIAQILSLALLLRYSLDADDAACAIERAINRALEEGIRTGDLA
FT                   RGAAAVSTDEMGDIIARYVAEGV"
FT   CDS             complement(81622..83193)
FT                   /db_xref="SWISS-PROT:P09151"
FT                   /note="ORF_ID:o109#3"
FT                   /note="similar to PIR Accession Number S40588"
FT                   /transl_table=11
FT                   /gene="leuA"
FT                   /product="2-Isopropylmalate synthase"
FT                   /protein_id="BAB96643.1"
FT                   /translation="MSQQVIIFDTTLRDGEQALQASLSVKEKLQIALALERMGVDVMEV
FT                   GFPVSSPGDFESVQTIARQVKNSRVCALARCVEKDIDVAAESLKVAEAFRIHTFIATSP
FT                   MHIATKLRSTLDEVIERAIYMVKRARNYTDDVEFSCEDAGRTPIADLARVVEAAINAGA
FT                   TTINIPDTVGYTMPFEFAGIISGLYERVPSIGKAIISVHTHDDLGLAVGNSLAAVHAGA
FT                   RQVEGAMNGIGERAGNCSLEEVIMAIKVRKDILNVHTAINHQEIWRTSQLVSQICNMPI
FT                   PANKAIVGSGAFAHSSGIHQDGVLKNRENYEIMTPESIGLNQIQLNLTSRSGRAAVKHR
FT                   MDEMGYKESEYNLDNLYDAFLKLADKKGQVFDYDLEALAFIGKQQEEPEHFRLDYFSVQ
FT                   SGSNDIATAAVKLACGEEVKAEAANGNGPVDAVYQAINRITEYNVELVKYSLTAKGHGK
FT                   DALGQVDIVANYNGRRFHGVGLATDIVESSAKAMVHVLNNIWRAAEVEKELQRKAQHNE
FT                   NNKETV"
FT   CDS             complement(83286..83372)
FT                   /note="ORF_ID:o109#4"
FT                   /note="similar to PIR Accession Number A30376"
FT                   /transl_table=11
FT                   /gene="leuLP"
FT                   /product="LeuABCD leader peptide."
FT                   /protein_id="BAB96644.1"
FT                   /translation="MTHIVRFIGLLLLNASSLRGRRVSGIQH"
FT   CDS             83855..84904
FT                   /note="ORF_ID:o109#5"
FT                   /note="similar to PIR Accession Number S40589"
FT                   /transl_table=11
FT                   /gene="lueO"
FT                   /product="LeuO protein."
FT                   /protein_id="BAB96645.1"
FT                   /translation="MTHSTAMDSVFIRTRIFMFSEFYSFCFFLFYMHDKSYSSGLFLCI
FT                   PIRERELSVTVELSMPEVQTDHPETAELSKPQLRMVDLNLLTVFDAVMQEQNITRAAHV
FT                   LGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARAFQLFGSVRQALQLVQNELPGSG
FT                   FEPASSERVFHLCVCSPLDSILTSQIYNHIEQIAPNIHVMFKSSLNQNTEHQLRYQETE
FT                   FVISYEDFHRPEFTSVPLFKDEMVLVASKNHPTIKGPLLKHDVYNEQHAAVSLDRFASF
FT                   SQPWYDTVDKQASIAYQGMAMMSVLSVVSQTHLVAIAPRWLAEEFAESLELQVLPLPLK
FT                   QNSRTCYLS"
FT   CDS             85294..86994
FT                   /note="ORF_ID:o109#6"
FT                   /note="similar to PIR Accession Number S14385"
FT                   /transl_table=11
FT                   /gene="ilvI"
FT                   /product="Acetolactate synthase (EC  4.1.3.18) III large
FT                   chain."
FT                   /protein_id="BAB96646.1"
FT                   /translation="MEMLSGGEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDH
FT                   VLVRHEQAAVHMADGLARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVA
FT                   TSLIGYDAFQECDMVGISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPK
FT                   DILNPANKLPYVWPESVSMRSYNPTTTGHKGQIKRALQSVVAVKKPVVYVGGGAITAGC
FT                   HQQLKETVEALNLPVVCSLMGLGAFPATHRQVLGMLGMHGTYEANMTMHNADVIFAVGV
FT                   RFDDRTTNNLAKYCPNATVLHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESA
FT                   HQPLDEIRDWWQQIEQWRARQCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQ
FT                   MFAALYYPFDKPRRWINSGGLGSMGFGLPAALGVKMAFPEETVVCVTGDGSIQMNIQEL
FT                   STALQYELPVLVVNLNNRYLGMVKQWQDMIYSGRHSQSYMQSLPDFVRRGAYGHVGIQI
FT                   SHPHGWKANLARRWNRCAIIAWCLLMLPSMAASTSTRCRFAGAEWMKCG"
FT   CDS             87017..87508
FT                   /note="ORF_ID:o109#7"
FT                   /note="similar to SwissProt Accession Number P00894"
FT                   /transl_table=11
FT                   /gene="ilvH"
FT                   /gene="brnP"
FT                   /product="Acetolactate synthase isozyme III small subunit
FT                   (EC  4.1.3.18) (ahas-III) (acetohydroxy-acid synthase III
FT                   small subunit) (als-III)."
FT                   /protein_id="BAB96647.1"
FT                   /translation="MRRILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSR
FT                   MTIQTVGDEKVLEQIEKQLHKLVDVLRVSELGQGAHVEREIMLVKIQASGYGRDEVKRN
FT                   TEIFRGQIIDVTPSLYTVQLAGTSGKLSAFLASIRDVAKIVEVARSGVVGLSRGDKIMR
FT                   "
FT   CDS             87688..88692
FT                   /note="ORF_ID:o109#8"
FT                   /note="similar to PIR Accession Number JU0298"
FT                   /transl_table=11
FT                   /gene="shl"
FT                   /gene="fruR"
FT                   /product="Pep-fructosephosphotransferase system repressor."
FT                   /protein_id="BAB96648.1"
FT                   /translation="MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREH
FT                   NYHPNAVAAGLRAGRTRSIGLVIPDLENTSYTRIANYLERQARQRGYQLLIACSEDQPD
FT                   NEMRCIEHLLQRQVDAIIVSTSLPPEHPFYQRWANDPFPIVALDRALDREHFTSVVGAD
FT                   QDDAEMLAEELRKFPAETVLYLGALPELSVSFLREQGFRTAWKDDPREVHFLYANSYER
FT                   EAAAQLFEKWLETHPMPQALFTTSFALLQGVMDVTLRRDGKLPSDLAIATFGDNELLDF
FT                   LQCPVLAVAQRHRDVAERVLEIVLASLDEPRKPKPGLTRIKRNLYRRGVLSRS"
FT   CDS             89294..89752
FT                   /note="ORF_ID:o109#9"
FT                   /note="similar to PIR Accession Number S14388"
FT                   /transl_table=11
FT                   /gene="yabB"
FT                   /product="Hypothetical protein C."
FT                   /protein_id="BAB96649.1"
FT                   /translation="MFRGATLVNLDSKGRLSVPTRYREQLLENAAGQMVCTIDIYHPCL
FT                   LLYPLPEWEIIEQKLSRLSSMNPVERRVQRLLLGHASECQMDGAGRLLIAPVLRQHAGL
FT                   TKEVMLVGQFNKFELWDETTWHQQVKEDIDAEQLATGDLSERLQDLSL"
FT   CDS             89754..90695
FT                   /note="ORF_ID:o109#10"
FT                   /note="similar to SwissProt Accession Number P18595"
FT                   /transl_table=11
FT                   /gene="yabC"
FT                   /product="Hypothetical 34.9 kd protein in fruR-ftsL
FT                   intergenic region (orfB)."
FT                   /protein_id="BAB96650.1"
FT                   /translation="MMENYKHTTVLLDEAVNGLNIRPDGIYIDGTFGRGGHSRLILSQL
FT                   GEEGRLLAIDRDPQAIAVAKTIDDPRFSIIHGPFSALGEYVAERDLIGKIDGILLDLGV
FT                   SSPQLDDAERGFSFMRDGPLDMRMDPTRGQSAAEWLQTAEEADIAWVLKTYGEERFAKR
FT                   IARAIVERNREQPMTRTKELAEVVAAATPVKDKFKHPATRTFQAVRIWVNSELEEIEQA
FT                   LKSSLNVLAPGGRLSIISFHSLEDRIVKRFMRENSRGPQVPAGLPMTEEQLKKLGGRQL
FT                   RALGKLMPGEEEVAENPRARSSVLRIAERTNA"
FT   CDS             90692..91024
FT                   /note="ORF_ID:o110#1"
FT                   /note="similar to PIR Accession Number S14387"
FT                   /transl_table=11
FT                   /gene="ftsL"
FT                   /product="Cell division protein FtsL"
FT                   /protein_id="BAB96651.1"
FT                   /translation="MISRVTEALSKVKGSMGSHERHALPGVIGDDLLRFGKLPLCLFIC
FT                   IILTAVTVVTTAHHTRLLTAQREQLVLERDALDIEWRNLILEENALGDHSRVERIATEK
FT                   LQMQTC"
FT   CDS             91074..92840
FT                   /note="ORF_ID:o110#2"
FT                   /note="similar to PIR Accession Number A93123"
FT                   /transl_table=11
FT                   /gene="ftsI"
FT                   /gene="pbpB"
FT                   /product="Penicillin-binding protein 3 precursor."
FT                   /protein_id="BAB96652.1"
FT                   /translation="MKAAAKTQKPKRQEEHANFISWRFALLCGCILLALAFLLGRVAWL
FT                   QVISPDMLVKEGDMRSLRVQQVSTSRGMITDRSGRPLAVSVPVKAIWADPKEVHDAGGI
FT                   SVGDRWKALANALNIPLDQLSARINANPKGRFIYLARQVNPDMADYIKKLKLPGIHLRE
FT                   ESRRYYPSGEVTAHLIGFTNVDSQGIEGVEKSFDKWLTGQPGERIVRKDRYGRVIEDIS
FT                   STDSQAAHNLALSIDERLQALVYRELNNAVAFNKAESGSAVLVDVNTGEVLAMANSPSY
FT                   NPNNLSGTPKEAMRNRTITDVFEPGSTVKPMVVMTALQRGVVRENSVLNTIPYRINGHE
FT                   IKDVARYSELTLTGVLQKSSNVGVSKLALAMPSSALVDTYSRFGLGKATNLGLVGERSG
FT                   LYPQKQRWSDIERATFSFGYGLMVTPLQLARVYATIGSYGIYRPLSITKVDPPVPGERV
FT                   FPESIVRTVVHMMESVALPGGGGVKAAIKGYRIAIKTGTAKKVGPDGRYINKYIAYTAG
FT                   VAPASQPRFALVVVINDPQAGKYYGGAVSAPVFGAIMGGVLRTMNIEPDALTTGDKNEF
FT                   VINQGEGTGGRS"
FT   CDS             92827..94314
FT                   /note="ORF_ID:o110#3"
FT                   /note="similar to PIR Accession Number S40595"
FT                   /transl_table=11
FT                   /gene="murE"
FT                   /product="UDP-N-acetylmuramoylalanyl-D-glutamate--2,
FT                   6-diaminopimelate ligase (EC 6.3.2.13) murE"
FT                   /protein_id="BAB96653.1"
FT                   /translation="MADRNLRDLLAPWVPDAPSRALREMTLDSRVAAAGDLFVAVVGHQ
FT                   ADGRRYIPQAIAQGVAAIIAEAKDEATDGEIREMHGVPVIYLSQLNERLSALAGRFYHE
FT                   PSDNLRLVGVTGTNGKTTTTQLLAQWSQLLGEISAVMGTVGNGLLGKVIPTENTTGSAV
FT                   DVQHELAGLVDQGATFCAMEVSSHGLVQHRVAALKFAASVFTNLSRDHLDYHGDMEHYE
FT                   AAKWLLYSEHHCGQAIINADDEVGRRWLAKLPDAVAVSMEDHINPNCHGRWLKATEVNY
FT                   HDSGATIRFSSSWGDGEIESHLMGAFNVSNLLLALATLLALGYPLADLLKTAARLQPVC
FT                   GRMEVFTAPGKPTVVVDYAHTPDALEKALQAARLHCAGKLWCVFGCGGDRDKGKRPLMG
FT                   AIAEEFADVAVVTDDNPRTEEPRAIINDILAGMLDAGHAKVMEGRAEAVTCAVMQAKEN
FT                   DVVLVAGKGHEDYQIVGNQRLDYSDRVTVARLLGVIA"
FT   CDS             94311..95669
FT                   /note="ORF_ID:o110#4"
FT                   /note="similar to SwissProt Accession Number P11880"
FT                   /transl_table=11
FT                   /gene="murF"
FT                   /gene="mra"
FT                   /product="UDP-n-acetylmuramoylalanyl-d-glutamyl-2,
FT                   6-diaminopimelate-d-alanyl-d-alanyl ligase (EC 6.3.2.15)
FT                   (UDP-murnac-pentapeptide synthetase)
FT                   (d-alanyl-d-alanine-adding enzyme)."
FT                   /protein_id="BAB96654.1"
FT                   /translation="MISVTLSQLTDILNGELQGADITLDAVTTDTRKLTPGCLFVALKG
FT                   ERFDAHDFADQAKAGAAGALLVSRPLDIDLPQLIVKDTRLAFGELAAWVRQQVPARVVA
FT                   LTGSSGKTSVKEMTAAILSQCGNTLYTAGNLNNDIGVPMTLLRLTPEYDYAVIELGANH
FT                   QGEIAWTVSLTRPERALVNNLAAAHLEGFGSLAGVAKAKGEIFSGLPENGIAIMNADNN
FT                   DWLNWQSVIGSRKVWRFSPNAANSDFTATNIHVTSHGTEFTLQTPTGSVDVLLPLPGRH
FT                   NIANALAAAALSMSVGATLDAIKAGLANLKAVPGRLFPIQLAENQLLLDDSYNANVGSM
FT                   TAAVQVLAEMPGYRVLVVGDMAELGAESEACHVQVGEAAKAAGIDRVLSVGKQSHAIST
FT                   ASGVGEHFADKTALITRLKLLIAEQQVITILVKGSRSAAMEEVVRALQENGTC"
FT   CDS             95663..96745
FT                   /note="ORF_ID:o110#5"
FT                   /note="similar to SwissProt Accession Number P15876"
FT                   /transl_table=11
FT                   /gene="mraY"
FT                   /gene="murX"
FT                   /product="Phospho-n-acetylmuramoyl-pentapeptide-transferas
FT                   e (EC  2.7.8.13)."
FT                   /protein_id="BAB96655.1"
FT                   /translation="MLVWLAEHLVKYYSGFNVFSYLTFRAIVSLLTALFISLWMGPRMI
FT                   AHLQKLSFGQVVRNDGPESHFSKRGTPTMGGIMILTAIVISVLLWAYPSNPYVWCVLVV
FT                   LVGYGVIGFVDDYRKVVRKDTKGLIARWKYFWMSVIALGVAFALYLAGKDTPATQLVVP
FT                   FFKDVMPQLGLFYILLAYFVIVGTGNAVNLTDGLDGLAIMPTVFVAGGFALVAWATGNM
FT                   NFASYLHIPYLRHAGELVIVCTAIVGAGLGFLWFNTYPAQVFMGDVGSLALGGALGIIA
FT                   VLLRQEFLLVIMGGVFVVETLSVILQVGSFKLRGQRIFRMAPIHHHYELKGWPEPRVIV
FT                   RFWIISLMLVLIGLATLKVR"
FT   CDS             96748..98064
FT                   /note="ORF_ID:o110#6"
FT                   /note="similar to PIR Accession Number S08396"
FT                   /transl_table=11
FT                   /gene="murD"
FT                   /product="UDP-n-acetylmuramoylalanine-d-glutamate ligase
FT                   (EC  6.3.2.9)."
FT                   /protein_id="BAB96656.1"
FT                   /translation="MADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLD
FT                   KLPEAVERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCREAQ
FT                   APIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDECELYVLELSSFQ
FT                   LETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAKLRIYENAKVCVVNADDALTMPIR
FT                   GADERCVSFGVNMGDYHLNHQQGETWLRVKGEKVLNVKEMKLSGQHNYTNALAALALAD
FT                   AAGLPRASSLKALTTFTGLPHRFEVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTL
FT                   HLLLGGDGKSADFSPLARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLA
FT                   PRVQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELG"
FT   CDS             98064..99308
FT                   /note="ORF_ID:o111#1"
FT                   /note="similar to PIR Accession Number A32581"
FT                   /transl_table=11
FT                   /gene="ftsW"
FT                   /product="Cell division protein FtsW."
FT                   /protein_id="BAB96657.1"
FT                   /translation="MRLSLPRLKMPRLPGFSILVWISTALKGWVMGSREKDTDSLIMYD
FT                   RTLLWLTFGLAAIGFIMVTSASMPIGQRLTNDPFFFAKRDGVYLILAFILAIITLRLPM
FT                   EFWQRYSATMLLGSIILLMIVLVVGSSVKGASRWIDLGLLRIQPAELTKLSLFCYIANY
FT                   LVRKGDEVRNNLRGFLKPMGVILVLAVLLLAQPDLGTVVVLFVTTLAMLFLAGAKLWQF
FT                   IAIIGMGISAVVLLILAEPYRIRRVTAFWNPWEDPFGSGYQLTQSLMAFGRGELWGQGL
FT                   GNSVQKLEYLPEAHTDFIFAIIGEELGYVGVVLALLMVFFVAFRAMSIGRKALEIDHRF
FT                   SGFLACSIGIWFSFQALVNVGAAAGMLPTKGLTLPLISYGGSSLLIMSTAIMMLLRIDY
FT                   ETRLEKAQAFVRGSR"
FT   CDS             99305..100372
FT                   /note="ORF_ID:o111#2"
FT                   /note="similar to PIR Accession Number JQ0544"
FT                   /transl_table=11
FT                   /gene="murG"
FT                   /product="MurG protein."
FT                   /protein_id="BAB96658.1"
FT                   /translation="MSGQGKRLMVMAGGTGGHVFPGLAVAHHLMAQGWQVRWLGTADRM
FT                   EADLVPKHGIEIDFIRISGLRGKGIKALIAAPLRIFNAWRQARAIMKAYKPDVVLGMGG
FT                   YVSGPGGLAAWSLGIPVVLHEQNGIAGLTNKWLAKIATKVMQAFPGAFPNAEVVGNPVR
FT                   TDVLALPLPQQRLAGREGPVRVLVVGGSQGARILNQTMPQVAAKLGDSVTIWHQSGKGS
FT                   QQSVEQAYAEAGQPQHKVTEFIDDMAAAYAWADVVVCRSGALTVSEIAAAGLPALFVPF
FT                   QHKDRQQYWNALPLEKAGAAKIIEQPQLSVDAVANTLAGWSRETLLTMAERARAASIPD
FT                   ATERVANEVSRVARA"
FT   CDS             100426..101901
FT                   /note="ORF_ID:o111#3"
FT                   /note="similar to PIR Accession Number JQ0545"
FT                   /transl_table=11
FT                   /gene="murC"
FT                   /product="UDP-n-acetylmuramate-alanine ligase (EC
FT                   6.3.2.8)."
FT                   /protein_id="BAB96659.1"
FT                   /translation="MNTQQLAKLRSIVPEMRRVRHIHFVGIGGAGMGGIAEVLANEGYQ
FT                   ISGSDLAPNPVTQQLMNLGATIYFNHRPENVRDASVVVVSSAISADNPEIVAAHEARIP
FT                   VIRRAEMLAELMRFRHGIAIAGTHGKTTTTAMVSSIYAEAGLDPTFVNGGLVKAAGVHA
FT                   RLGHGRYLIAEADESDASFLHLQPMVAIVTNIEADHMDTYQGDFENLKQTFINFLHNLP
FT                   FYGRAVMCVDDPVIRELLPRVGRQTTTYGFSEDADVRVEDYQQIGPQGHFTLLRQDKEP
FT                   MRVTLNAPGRHNALNAAAAVAVATEEGIDDEAILRALESFQGTGRRFDFLGEFPLEPVN
FT                   GKSGTAMLVDDYGHHPTEVDATIKAARAGWPDKNLVMLFQPHRFTRTRDLYDDFANVLT
FT                   QVDTLLMLEVYPAGEAPIPGADSRSLCRTIRGRGKIDPILVPDPARVAEMLAPVLTGND
FT                   LILVQGAGNIGKIARSLAEIKLKPQTPEEEQHD"
FT   CDS             101894..102814
FT                   /note="ORF_ID:o111#4"
FT                   /note="similar to PIR Accession Number A30289"
FT                   /transl_table=11
FT                   /gene="ddl"
FT                   /gene="ddlB"
FT                   /product="D-alanine-d-alanine ligase (EC  6.3.2.4) B."
FT                   /protein_id="BAB96660.1"
FT                   /translation="MTDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEV
FT                   DVTQLKSMGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKLLW
FT                   QGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAENAL
FT                   QDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKYLSDETQ
FT                   YFCPAGLEASQEANLQALVLKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHS
FT                   LVPMAARQAGMSFSQLVVRILELAD"
FT   CDS             102816..103646
FT                   /note="ORF_ID:o111#5"
FT                   /note="similar to PIR Accession Number S10852"
FT                   /transl_table=11
FT                   /gene="ftsQ"
FT                   /product="Cell division protein FtsQ."
FT                   /protein_id="BAB96661.1"
FT                   /translation="MSQAALNTRNSEEEVSSRRNNGTRLAGILFLLTVLTTVLVSGWVV
FT                   LGWMEDAQRLPLSKLVLTGERHYTRNDDIRQSILALGEPGTFMTQDVNIIQTQIEQRLP
FT                   WIKQVSVRKQWPDELKIHLVEYVPIARWNDQHMVDAEGNTFSVPPERTSKQVLPMLYGP
FT                   EGSANEVLQGYREMGQMLAKDRFTLKEAAMTARRSWQLTLNNDIKLNLGRGDTMKRLAR
FT                   FVELYPVLQQQAQTDGKRISYVDLRYDSGAAVGWAPLPPEESTQQQNQAQAEQQ"
FT   CDS             103643..104905
FT                   /note="ORF_ID:o111#6"
FT                   /note="similar to SwissProt Accession Number P06137"
FT                   /transl_table=11
FT                   /gene="ftsA"
FT                   /gene="divA"
FT                   /product="Cell division protein FtsA."
FT                   /protein_id="BAB96662.1"
FT                   /translation="MIKATDRKLVVGLEIGTAKVAALVGEVLPDGMVNIIGVGSCPSRG
FT                   MDKGGVNDLESVVKCVQRAIDQAELMADCQISSVYLALSGKHISCQNEIGMVPISEEEV
FT                   TQEDVENVVHTAKSVRVRDEHRVLHVIPQEYAIDYQEGIKNPVGLSGVRMQAKVHLITC
FT                   HNDMAKNIVKAVERCGLKVDQLIFAGLASSYSVLTEDERELGVCVVDIGGGTMDIAVYT
FT                   GGALRHTKVIPYAGNVVTSDIAYAFGTPPSDAEAIKVRHGCALGSIVGKDESVEVPSVG
FT                   GRPPRSLQRQTLAEVIEPRYTELLNLVNEEILQLQEKLRQQGVKHHLAAGIVLTGGAAQ
FT                   IEGLAACAQRVFHTQVRIGAPLNITGLTDYAQEPYYSTAVGLLHYGKESHLNGEAEVEK
FT                   RVTASVGSWIKRLNSWLRKEF"
FT   CDS             104966..106117
FT                   /note="ORF_ID:o111#7"
FT                   /note="similar to SwissProt Accession Number P06138"
FT                   /transl_table=11
FT                   /gene="ftsZ"
FT                   /gene="sfiB"
FT                   /gene="sulB"
FT                   /product="Cell division protein FtsZ."
FT                   /protein_id="BAB96663.1"
FT                   /translation="MFEPMELTNDAVIKVIGVGGGGGNAVEHMVRERIEGVEFFAVNTD
FT                   AQALRKTAVGQTIQIGSGITKGLGAGANPEVGRNAADEDRDALRAALEGADMVFIAAGM
FT                   GGGTGTGAAPVVAEVAKDLGILTVAVVTKPFNFEGKKRMAFAEQGITELSKHVNSLITI
FT                   PNDKLLKVLGRGISLLDAFGAANDVLKGAVQGIAELITRPGLMNVDFADVRTVMSEMGH
FT                   AMMGSGVASGEDRAEEAAEMAISSPLLEDIDLSGARGVLVNITAGFDLRLDEFETVGNT
FT                   IRAFASDNATVVIGTSLDPDMNDELRVTVVATGIGMDKRPEITLVTNKQVQQPVMDRYQ
FT                   QHGMAPLTQEQKPVAKVVNDNAPQTAKEPDYLDIPAFLRKQAD"
FT   CDS             106218..107135
FT                   /note="ORF_ID:o111#8"
FT                   /note="similar to SwissProt Accession Number P07652"
FT                   /transl_table=11
FT                   /gene="envA"
FT                   /gene="asmB"
FT                   /gene="lpxC"
FT                   /product="Udp-3-o-[3-hydroxymyristoyl] n-acetylglucosamine
FT                   deacetylase (EC  3.5.1.-) (EnvA protein)."
FT                   /protein_id="BAB96664.1"
FT                   /translation="MIKQRTLKRIVQATGVGLHTGKKVTLTLRPAPANTGVIYRRTDLN
FT                   PPVDFPADAKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIVIEVNAPEIPIM
FT                   DGSAAPFVYLLLDAGIDELNCAKKFVRIKETVRVEDGDKWAEFKPYNGFSLDFTIDFNH
FT                   PAIDSSNQRYAMNFSADAFMRQISRARTFGFMRDIEYLQSRGLCLGGSFDCAIVVDDYR
FT                   VLNEDGLRFEDEFVRHKMLDAIGDLFMCGHNIIGAFTAYKSGHALNNKLLQAVLAKQEA
FT                   WEYVTFQDDAELPLAFKAPSAVLA"
FT   CDS             107435..107878
FT                   /note="ORF_ID:o111#9"
FT                   /note="similar to PIR Accession Number B28381"
FT                   /transl_table=11
FT                   /gene="yacA"
FT                   /product="Hypothetical 16k protein (eneA-secA intergenic
FT                   region)."
FT                   /protein_id="BAB96665.1"
FT                   /translation="MVAASLGLPALSNAAEPNAPAKATTRNHEPSAKVNFGQLALLEAN
FT                   TRRPNSNYSVDYWHQHAIRTVIRHLSFAMAPQTLPVAEESLPLQAQHLALLDTLSALLT
FT                   QEGTPSEKGYRIDYAHFTPQAKFSTPVWISQAQGIRAGPQRLT"
FT   CDS             107940..110645
FT                   /note="ORF_ID:o111#10"
FT                   /note="similar to SwissProt Accession Number P10408"
FT                   /transl_table=11
FT                   /gene="secA"
FT                   /gene="azi"
FT                   /gene="pea"
FT                   /gene="prlD"
FT                   /product="Preprotein translocase SecA subunit."
FT                   /protein_id="BAB96666.1"
FT                   /translation="MLIKLLTKVFGSRNDRTLRRMRKVVNIINAMEPEMEKLSDEELKG
FT                   KTAEFRARLEKGEVLENLIPEAFAVVREASKRVFGMRHFDVQLLGGMVLNERCIAEMRT
FT                   GEGKTLTATLPAYLNALTGKGVHVVTVNDYLAQRDAENNRPLFEFLGLTVGINLPGMPA
FT                   PAKREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEARTP
FT                   LIISGPAEDSSEMYKRVNKIIPHLIRQEKEDSETFQGEGHFSVDEKSRQVNLTERGLVL
FT                   IEELLVKEGIMDEGESLYSPANIMLMHHVTAALRAHALFTRDVDYIVKDGEVIIVDEHT
FT                   GRTMQGRRWSDGLHQAVEAKEGVQIQNENQTLASITFQNYFRLYEKLAGMTGTADTEAF
FT                   EFSSIYKLDTVVVPTNRPMIRKDLPDLVYMTEAEKIQAIIEDIKERTAKGQPVLVGTIS
FT                   IEKSELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPAAVTIATNMAGRGTDIVLGG
FT                   SWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSG
FT                   RQGDAGSSRFYLSMEDALMRIFASDRVSGMMRKLGMKPGEAIEHPWVTKAIANAQRKVE
FT                   SRNFDIRKQLLEYDDVANDQRRAIYSQRNELLDVSDVSETINSIREDVFKATIDAYIPP
FT                   QSLEEMWDIPGLQERLKNDFDLDLPIAEWLDKEPELHEETLRDGILAQSIEVYQRKEEV
FT                   VGAEMMRHFEKGVMLQTLDSLWKEHLAAMDYLRQGIHLRGYAQKDPKQEYKRESFSMFA
FT                   AMLESLKYEVISTLSKVQVRMPEEVEELEQQRRMEAERLAQMQQLSHQDDDSAAAAALA
FT                   AQTGERKVGRNDPCPCGSGKKYKQCHGRLQ"
FT   CDS             110705..111094
FT                   /note="ORF_ID:o111#11"
FT                   /note="similar to PIR Accession Number A27890"
FT                   /transl_table=11
FT                   /gene="mutT"
FT                   /product="Mutator MutT (AT-GC transversion)."
FT                   /protein_id="BAB96667.1"
FT                   /translation="MKKLQIAVGIIRNENNEIFITRRAADAHMANKLEFPGGKIEMGET
FT                   PEQAVVRELQEEVGITPQHFSLFEKLEYEFPDRHITLWFWLVERWEGEPWGKEGQPGEW
FT                   MSLVGLNADDFPPANEPVIAKLKRL"
FT   CDS             complement(111310..>111408)
FT                   /note="ORF_ID:o111#12"
FT                   /note="similar to SwissProt Accession Number P36681"
FT                   /transl_table=11
FT                   /gene="yacG"
FT                   /product="Hypothetical 5.8 kd protein in mutT-guaC
FT                   intergenic region."
FT                   /protein_id="BAB96668.1"
FT                   /translation="LIDLGEWAAEEKRIPSSGDLSESDDWSEEPKQ"
XX
SQ   Sequence 111408 BP; 26083 A; 28055 C; 30531 G; 26739 T; 0 other;
     atgcgagtgt tgaagttcgg cggtacatca ttggcaaatg cagaacgttt tctgcgtgtt        60
     gccgatattc tggaaagcaa tgccaggcag gggcaggtgg ccaccgtcct ctctgcccct       120
     gccaaaatca ccaaccacct ggtggcgatg attgaaaaaa ccattagcgg ccaggatgct       180
     ttacccaata tcagcgatgc cgaacgtatt tttgccgaac ttttgacggg actcgccgcc       240
     gcccagccgg ggttcccgtt ggcgcaattg aaaacattcg tcgatcagga atttgcccaa       300
     ataaaacatg tcctgcatgg cattagtttg ttggggcagt gcccggatag catcaacgct       360
     gcgctgattt gccgtggcga gaagatgtcg atcgccatta tggccggcgt attagaagcg       420
     cgcggtcaca acgttactgt tatcgatccg gtcgaaaaac tgctggcagt ggggcattac       480
     ctcgaatcca ccgtcgatat tgccgagtcc acccgccgta tagcggcaag ccgcattccg       540
     gctgatcaca tggtgctgat ggcaggtttc accgccggta atgagaaagg cgaactggtg       600
     gtgcttggac gcaacggttc cgactactct gctgcggtgc tggctgcctg tttacgcgcc       660
     gattgttgcg agatttggac ggacgttaac ggggtctata cctgcgaccc gcgtcaggtg       720
     cccgacgcga ggttgttgaa gtcgatgtcc taccaggaag cgatggagct ttcctacttc       780
     ggcgctaaag ttcttcaccc ccgcaccatt acccccatcg cccagttcca gatcccttgc       840
     ctgattaaaa ataccggaaa tcctcaagca ccaggtacgc tcattggtgc aagccgtgat       900
     gaagacgaat taccggtcaa gggcatttcc aatctgaata acatggcaat gttcagcgtt       960
     tctggtccgg ggatgaaagg gatggtcggc atggcggcgc gcgtctttgc agcgatgtca      1020
     cgcgcccgta tttccgtggt gctgattacg caatcatctt ccgaatacag catcagtttc      1080
     tgcgttccac aaagcgactg tgtgcgagct gaacgggcaa tgctggaaga gttctaccta      1140
     gaactgaaag aaggcttact ggagccgctg gcagtggcgg aacggctggc cattatctcg      1200
     gtggtaggtg atggtttgcg caccttgcgt gggatctcgg cgaaattctt tgccgcactg      1260
     gcccgcgcca atatcaacat tgtcgccatt gctcagggat cttctgaacg ctcaatctct      1320
     gtcgtggtaa ataacgatga tgcgaccact ggcgtgcgcg ttactcatca gatgctgttc      1380
     aataccgatc aggttatcga agtgtttgtg attggcgtcg gtggcgttgg cggtgcgctg      1440
     ctggagcaac tgaagcgtca gcaaagctgg ctgaagaata aacatatcga cttacgtgtc      1500
     tgcggtgttg ccaactcgaa ggctctgctc accaatgtac atggccttaa tctggaaaac      1560
     tggcaggagg aactggcgca agccaaagag ccgtttaatc tcgggcgctt aattcgcctc      1620
     gtgaaagaat atcatctgct gaacccggtc attgttaact gcacttccag ccaggcagtg      1680
     gcggatcaat atgccgactt cctgcgcgaa ggtttccacg ttgtcacgcc gaacaaaaag      1740
     gccaacacct cgtcgatgga ttactaccat cagttgcgtt atgcggcgga aaaatcgcgg      1800
     cgtaaattcc tctatgacat caacgttggg gctggattac cggttattga gaacctgcaa      1860
     aatctgctca atgcaggtga tgaattgatg aaattctccg gcattctttc tggttcgctt      1920
     tcttatatct tcggcaagtt agacgaaggc atgagtttct ccgaggcgac ccggctggcg      1980
     cgggaaatgg gttataccga accggacccg cgagatgatc tttctggtat ggatgtggcg      2040
     cgtaaactat tgattctcgc tcgtgaaacg ggacgtgaac tggagctggc ggatattgaa      2100
     attgaacctg tgctgcccgc agagtttaac gccgagggtg atgttgccgc ttttatggcg      2160
     aatctgtcac aactcgacga tctctttgcc gcgcgcgtgg cgaaggcccg tgatgaagga      2220
     aaagttttgc gctatgttgg caatattgat gaagatggcg tctgccgcgt gaagattgcc      2280
     gaagtggatg gtaatgatcc gctgttcaaa gtgaaaaatg gcgaaaacgc cctggccttc      2340
     tatagccact attatcagcc gctgccgttg gtactgcgcg gatatggtgc gggcaatgac      2400
     gttacagctg ccggtgtctt tgctgatctg ctacgtaccc tctcatggaa gttaggagtc      2460
     tgacatggtt aaagtttatg ccccggcttc cagtgccaat atgagcgtcg ggtttgatgt      2520
     gctcggggcg gcggtgacac ctgttgatgg tgcattgctc ggagatgtag tcacggttga      2580
     ggcggcacag acattcagtc tcaacaacct cggacgcttt gccgataagc tgccgtcaga      2640
     accacgggaa aatatcgttt atcagtgctg ggagcgtttt tgccaggaac tgggtaagca      2700
     aattccagtg gcgatgaccc tggaaaagaa tatgccgatc ggttcgggct taggctccag      2760
     tgcctgttcg gtggtcgcgg cgctgatggc gatgaatgaa cactgcggca agccgcttaa      2820
     tgacactcgt ttgctggctt tgatgggcga gctggaaggc cgtatctccg gcagcattca      2880
     ttacgacaac gtggcaccgt gttttctcgg tggtatgcag ttgatgatcg aagaaaacga      2940
     catcatcagc cagcaagtgc agggtttgat gagtggctgt gggtgctcgc gtatccgggg      3000
     attaaagtct cgacggcaga agcagggcta tttaccggcg cagtatcgcc gccaggattg      3060
     cattgcgcac gggcgacatc tggcaggctt cattcacgcc tgctattccc gtcagcctga      3120
     gcttgccgcg aagctgatga aagatgttat cgctgaaccc taccgtgaac ggttactgcc      3180
     aggcttccgg caggcgcggc aggcggtcgc ggaaatcggc gcggtagcga gcggtatctc      3240
     cggctccggc ccgaccttgt tcgctctgtg tgacaagccg gaaaccgccc agcgcgttgc      3300
     cgactggttg ggtaagaact acctgcaaaa tcaggaaggt tttgttcata tttgccggct      3360
     ggatacggcg ggcgcacgag tactggaaaa ctaaatgaaa ctctacaatc tgaaagatca      3420
     caacgagcag gtcagctttg cgcaagccgt aacccagggg ttgggcaaaa atcaggggct      3480
     gttttttccg cacgacctgc cggaattcag cctgactgaa attgatgaga tgctgaagct      3540
     ggattttgtc acccgcagtg cgaagatcct ctcggcgttt attggtgatg aaatcccaca      3600
     ggaaatcctg gaagagcgcg tgcgcgcggc gtttgccttc ccggctccgg tcgccaatgt      3660
     tgaaagcgat gtcggttgtc tggaattgtt ccacgggcca acgctggcat ttaaagattt      3720
     cggcggtcgc tttatggcac aaatgctgac ccatattgcg ggtgataagc cagtgaccat      3780
     tctgaccgcg acctccggtg ataccggagc ggcagtggct catgctttct acggtttacc      3840
     gaatgtgaaa gtggttatcc tctatccacg aggcaaaatc agtccactgc aagaaaaact      3900
     gttctgtaca ttgggcggca atatcgaaac tgttgccatc gacggcgatt tcgatgcctg      3960
     tcaggcgctg gtgaagcagg cgtttgatga tgaagaactg aaagtggcgc tagggttaaa      4020
     ctcggctaac tcgattaaca tcagccgttt gctggcgcag atttgctact actttgaagc      4080
     tgttgcgcag ctgccgcagg agacgcgcaa ccagctggtt gtctcggtgc caagcggaaa      4140
     cttcggcgat ttgacggcgg gtctgctggc gaagtcactc ggtctgccgg tgaaacgttt      4200
     tattgctgcg accaacgtga acgataccgt gccacgtttc ctgcacgacg gtcagtggtc      4260
     acccaaagcg actcaggcga cgttatccaa cgcgatggac gtgagtcagc cgaacaactg      4320
     gccgcgtgtg gaagagttgt tccgccgcaa aatctggcaa ctgaaagagc tgggttatgc      4380
     agccgtggat gatgaaacca cgcaacagac aatgcgtgag ttaaaagaac tgggctacac      4440
     ttcggagccg cacgctgccg tagcttatcg tgcgctgcgt gatcagttga atccaggcga      4500
     atatggcttg ttcctcggca ccgcgcatcc ggcgaaattt aaagagagcg tggaagcgat      4560
     tctcggtgaa acgttggatc tgccaaaaga gctggcagaa cgtgctgatt tacccttgct      4620
     ttcacataat ctgcccgccg attttgctgc gttgcgtaaa ttgatgatga atcatcagta      4680
     aaatctattc attatctcaa tcaggccggg tttgctttta tgcagcccgg cttttttatg      4740
     aagaaattat ggagaaaaat gacagggaaa aaggagaaat tctcaataaa tgcggtaact      4800
     tagagattag gattgcggag aataacaacc gccgttctca tcgagtaatc tccggatatc      4860
     gacccataac gggcaatgat aaaaggagta acctgtgaaa aagatgcaat ctatcgtact      4920
     cgcactttcc ctggttctgg tcgctcccat ggcagcacag gctgcggaaa ttacgttagt      4980
     cccgtcagta aaattacaga taggcgatcg tgataatcgt ggctattact gggatggagg      5040
     tcactggcgc gaccacggct ggtggaaaca acattatgaa tggcgaggca atcgctggca      5100
     cctacacgga ccgccgccac cgccgcgcca ccataagaaa gctcctcatg atcatcacgg      5160
     cggtcatggt cctggcaaac atcaccgcta aatgacaaat gccgggtaac aatccggcat      5220
     tcagcgcctg atgcgacgct ggcgcgtctt atcaggccta cgttaattct gcaatatatt      5280
     gaatctgcat gcttttgtag gcaggataag gcgttcacgc cgcatccggc attgactgca      5340
     aacttaacgc tgctcgtagc gtttaaacac cagttcgcca ttgctggagg aatcttcatc      5400
     aaagaagtaa ccttcgctat taaaaccagt cagttgctct ggtttggtca gccgattttc      5460
     aataatgaaa cgactcatca gaccgcgtgc tttcttagcg tagaagctga tgatcttaaa      5520
     tttgccgttc ttctcatcga ggaacaccgg cttgataatc tcggcattca atttcttcgg      5580
     cttcaccgat ttaaaatact catctgacgc cagattaatc accacattat cgccttgtgc      5640
     tgcgagcgcc tcgttcagct tgttggtgat gatatctccc cagaattgat acagatcttt      5700
     ccctcgggca ttctcaagac ggatccccat ttccagacga taaggctgca ttaaatcgag      5760
     cgggcggagt acgccataca agccggaaag cattcgcaaa tgctgttggg caaaatcgaa      5820
     atcgtcttcg ctgaaggttt cggcctgcaa gccggtgtag acatcacctt taaacgccag      5880
     aatcgcctgg cgggcattcg ccggcgtgaa atctggctgc cagtcatgaa agcgagcggc      5940
     gttgataccc gccagtttgt cgctgatgcg catcagcgtg ctaatctgcg gaggcgtcag      6000
     tttccgcgcc tcatggatca actgctggga attgtctaac agctccggca gcgtatagcg      6060
     cgtggtggtc aacgggcttt ggtaatcaag cgttttcgca ggtgaaataa gaatcagcat      6120
     atccagtcct tgcaggaaat ttatgccgac tttagcaaaa aatgagaatg agttgatcga      6180
     tagttgtgat tactcctgcg aaacatcatc ccacgcgtcc ggagaaagct ggcgaccgat      6240
     atccggataa cgcaatggat caaacaccgg gcgcacgccg agtttacgct ggcgtagata      6300
     atcactggca atggtatgaa ccacaggcga gagcagtaaa atggcggtca aattggtaat      6360
     agccatgcag gccattatga tatctgccag ttgccacatc agcggaaggc ttagcaaggt      6420
     gccgccgatg accgttgcga aggtgcagat ccgcaaacac cagatcgctt tagggttgtt      6480
     caggcgtaaa aagaagagat tgttttcggc ataaatgtag ttggcaacga tggagctgaa      6540
     ggcaaacaga ataaccacaa gggtaacaaa ctcagcaccc caggaaccca ttagcacccg      6600
     catcgccttc tggataagct gaataccttc cagcggcatg taggttgtgc cgttacccgc      6660
     cagtaatatc agcatggcgc ttgccgtaca gatgaccagg gtgtcgataa aaatgccaat      6720
     catctggaca atcccttgcg ctgccggatg cggaggccag gacgccgctg ccgctgccgc      6780
     gtttggcgtc gaacccattc ccgcctcatt ggaaaacata ctgcgctgaa aaccgttagt      6840
     aatcgcctgg cttaaggtat atcccgccgc gccgcctgcc gcttcctgcc agccaaaagc      6900
     actctcaaaa atagaccaaa tgacgtgggg aagttgcccg atattcatta cgcaaattac      6960
     caggctggtc agtacccaga ttatcgccat caacgggaca aagccctgca tgagccgggc      7020
     gacgccatga agaccgcgag tgattgccag cagagtaaag acagcgagaa taatgcctgt      7080
     caccagcggg ggaaaatcaa aagaaaaact cagggcgcgg gcaacggcgt tcgcttgaac      7140
     tccgctgaaa attatgccat aggcgatgag caaaaagacg gcgaacagaa cgcccatcca      7200
     gcgcatcccc agcccgcgcg ccatatacca tgccggtccg ccacgaaact gcccattgac      7260
     gtcacgttct ttataaagtt gtgccagaga acattcggca aacgaggtcg ccatgccgat      7320
     aaacgcggca acccacatcc aaaagacggc tccaggtcca ccggcggtaa tagccagcgc      7380
     aacgccggcc aggttgccgc tacccacgcg cgccgcaaga ctggtacaca atgactgaaa      7440
     tgaggttaaa ccgcctggct gtggatgaat gctattttta agacttttgc caaactggcg      7500
     gatgtagcga aactgcacaa atccggtgcg aaaagtgaac caacaacctg cgccgaagag      7560
     caggtaaatc attaccgatc cccaaaggac gctgttaatg aaggagaaaa aatctggcat      7620
     gcatatccct cttattgccg gtcgcgatga ctttcctgtg taaacgttac caattgttta      7680
     agaagtatat acgctacgag gtacttgata acttctgcgt agcatacatg aggttttgta      7740
     taaaaatggc gggcgatatc aacgcagtgt cagaaatccg aaacagtctc gcctggcgat      7800
     aaccgtcttg tcggcggttg cgctgacgtt gcgtcgtgat atcatcaggg cagaccggtt      7860
     acatccccct aacaagctgt ttaaagagaa atactatcat gacggacaaa ttgacctccc      7920
     ttcgtcagta caccaccgta gtggccgaca ctggggacat cgcggcaatg aagctgtatc      7980
     aaccgcagga tgccacaacc aacccttctc tcattcttaa cgcagcgcag attccggaat      8040
     accgtaagtt gattgatgat gctgtcgcct gggcgaaaca gcagagcaac gatcgcgcgc      8100
     agcagatcgt ggacgcgacc gacaaactgg cagtaaatat tggtctggaa atcctgaaac      8160
     tggttccggg ccgtatctca actgaagttg atgcgcgtct ttcctatgac accgaagcgt      8220
     caattgcgaa agcaaaacgc ctgatcaaac tctacaacga tgctggtatt agcaacgatc      8280
     gtattctgat caaactggct tctacctggc agggtatccg tgctgcagaa cagctggaaa      8340
     aagaaggcat caactgtaac ctgaccctgc tgttctcctt cgctcaggct cgtgcttgtg      8400
     cggaagcggg cgtgttcctg atctcgccgt ttgttggccg tattcttgac tggtacaaag      8460
     cgaataccga taagaaagag tacgctccgg cagaagatcc gggcgtggtt tctgtatctg      8520
     aaatctacca gtactacaaa gagcacggtt atgaaaccgt ggttatgggc gcaagcttcc      8580
     gtaacatcgg cgaaattctg gaactggcag gctgcgaccg tctgaccatc gcaccggcac      8640
     tgctgaaaga gctggcggag agcgaagggg ctatcgaacg taaactgtct tacaccggcg      8700
     aagtgaaagc gcgtccggcg cgtatcactg agtccgagtt cctgtggcag cacaaccagg      8760
     atccaatggc agtagataaa ctggcggaag gtatccgtaa gtttgctatt gaccaggaaa      8820
     aactggaaaa aatgatcggc gatctgctgt aatcattctt agcgtgaccg ggaagtcggt      8880
     cacgctacct cttctgaagc ctgtctgtca ctcccttcgc agtgtatcat tctgtttaac      8940
     gagactgttt aaacggaaaa atcttgatga atactttacg tattggctta gtttccatct      9000
     ctgatcgcgc atccagcggc gtttatcagg ataaaggcat ccctgcgctg gaagaatggc      9060
     tgacatgcgc taaccacgcc gtttgaactg gaaacccgct taatccccga tgagcaggcg      9120
     atcatcgagc aaacgttgtg tgagctggtg gatgaaatga gttgccatct ggtgctcacc      9180
     acgggcggaa ctggcccggc gcgtcgtgac gtaacgcccg atgcgacgct ggcagtagcg      9240
     gaccgcgaga tgcctggctt tggtgaacag atgcgccaga tcagcctgca ttttgtacca      9300
     actgcgatcc tttcgcgtca ggtgggcgtg attcgcaaac aggcgctgat ccttaactta      9360
     cccggtcagc cgaagtctat taaagagacg ctggaaggtg tgaaggacgc tgagggtaac      9420
     gttgtggtac acggtatttt tgccagcgta ccgtactgca ttcagttgct ggaagggcca      9480
     tacgttgaaa cggcaccgga agtggttgca gcattcagac cgaagagtgc aagacgcgac      9540
     gttagcgaat aaaaaatacc cgagcggggg gatctcaaaa caattagtgg gattcaccaa      9600
     tcggcagaac ggtgcgacca aactgctcgt tcagtacttc acccatcgcc agatagattg      9660
     cgctggcacc gcagatcagc ccaatccagc cggcaaagtg gatgattgcg gcgttaccgg      9720
     caatgttacc gatcgccagc agggcaaaca gcacggtcag gctaaagaaa acgaattgca      9780
     gaacgcgtgc gcctttcagc gtgccgaaga acataaacac ggtaaatacg ccccacagac      9840
     ccaggtagac accaaggaac tgtgcatttg gcgcatcggt cagacccagt ttcggcatca      9900
     gcagaatcgc aaccagcgtc agccagaaag aaccgtaaga ggtgaatgcg gttaaaccga      9960
     aagtgttgcc ttttttgtac tccagcagac cagcaaaaat ttgcgcgatg ccgccgtaga     10020
     aaatgcccat ggcaagaata ataccgtcca gagcgaaata acccacgttg tgcaggttaa     10080
     gcagaatggt ggtcatgccg aagcccatca ggcccagcgg tgccggatta gccaacttag     10140
     tgttgcccat aattcctcaa aaatcatcat cgaatgaatg gtgaaataat ttccctgaat     10200
     aactgtagtg ttttcagggc gcggcataat aatcagccag tggggcagtg tctacgatct     10260
     tttgagggga aaatgaaaat tttcccggtt tccggtatca gacctgagtg gcgctaacca     10320
     tccggcgcag gcaggcgatt tgcagtacgg ctggaatcgt cacgcgatag cgtgcgtgac     10380
     cgctttaacc ccatttagtg ccgcacctac aggcctccca gcccgcgccg cgcagcaaac     10440
     catgcccaag tacgctcatt gctgcgtggg tgcgtaaaat gcgggtcagt tggctggaaa     10500
     gcaaatgcga cacacctttt gccaataatt tgtctttcat cagcagcggc agcagctctt     10560
     ccagctcatt caccctggca tcgaccgcgt gcagaaactc ctgcttatgt tcctcgtcca     10620
     ttttcttcca ggtattacgc agaaattgtt ccagtaactg ttgctcaatt tcaaacgtag     10680
     acatctcttt gtcggctttc agcttcaatc gctttgaaac atcgagcaaa atggcccgat     10740
     acaatttacc gtgtccgcgc agtttgttgc gatactatcg ccaccaaaat gctgtaattc     10800
     tccggcaatc agctgccagt tgcggcgatg ttgctcggga tgcccttcca tcgatttaaa     10860
     cagttcgttg cgcatcagta cgctggagag gcgagttttg cctttttcat tatgggtgag     10920
     caatcgggcg aaatttgcca actgttcctc actacaatgc tgaagaaaat ccagatctga     10980
     atcattcagg taattaacat tcattttttg tggcttctat attctggcgt tagtcgtcgc     11040
     cgataatttt cagcgtggcc atatccgatg agttcaccgt atgacccgaa aaggtgattt     11100
     ttgagacgca gcgtttattg tcgttatcgc tcttaatgtt gatccagtca gtggtttgcc     11160
     cttcttttat ttctgaagga atattcaggc tctgacctgg cgctgacggg cggctgtgaa     11220
     ataaaccgat gcaccgctta actgtaaatc gccatggtcg gcagagagtt gtatgcgttt     11280
     cacaatgcga caaacaggaa gtttcagcgc cagatcgttg gtttcgttac gcggcattgc     11340
     aatgcgccga ggagtttatg gtcgtttgcc tgcgccgtgc agcacagcat caggctaatc     11400
     gccaggctgg cggaaatcgt aaaaacggat ttcataagga ttctcttagt gggaagaggt     11460
     agggggatga atacccacta gtttactgct gataaagaga agattcaggc acgtaatctt     11520
     ttctttttat tacaattttt tgatgaatgc cttggctgcg attcattctt tatatgaata     11580
     aaattgctgt caattttacg tcttgtcctg ccatatcgcg aaatttctgc gcaaaagcac     11640
     aaaaaatttt tgcatctccc ccttgatgac gtggtttacg accccattta gtagtcaacc     11700
     gcagtgagtg agtctgcaaa aaaatgaaat tgggcagttg aaaccagacg tttcgcccct     11760
     attacagact cacaaccaca tgatgaccga atatatagtg gagacgttta gatgggtaaa     11820
     ataattggta tcgacctggg tactaccaac tcttgtgtag cgattatgga tggcaccact     11880
     cctcgcgtgc tggagaacgc cgaaggcgat cgcaccacgc cttctatcat tgcctatacc     11940
     caggatggtg aaactctagt tggtcagccg gctaaacgtc aggcagtgac gaacccgcaa     12000
     aacactctgt ttgcgattaa acgcctgatt ggtcgccgct tccaggacga agaagtacag     12060
     cgtgatgttt ccatcatgcc gttcaaaatt attgctgctg ataacggcga cgcatgggtc     12120
     gaagttaaag gccagaaaat ggcaccgccg cagatttctg ctgaagtgct gaaaaaaatg     12180
     aagaaaaccg ctgaagatta cctgggtgaa ccggtaactg aagctgttat caccgtaccg     12240
     gcatacttta acgatgctca gcgtcaggca accaaagacg caggccgtat cgctggtctg     12300
     gaagtaaaac gtatcatcaa cgaaccgacc gcagctgcgc tggcttacgg tctggacaaa     12360
     ggcactggca accgtactat cgcggtttat gacctgggtg gtggtacttt cgatatttct     12420
     attatcgaaa tcgacgaagt tgacggcgaa aaaaccttcg aagttctggc aaccaacggt     12480
     gatacccacc tggggggtga agacttcgac agccgtctga tcaactatct ggttgaagaa     12540
     ttcaagaaag atcagggcat tgacctgcgc aacgatccgc tggcaatgca gcgcctgaaa     12600
     gaagcggcag aaaaagcgaa aatcgaactg tcttccgctc agcagaccga cgttaacctg     12660
     ccatacatca ctgcagacgc gaccggtccg aaacacatga acatcaaagt gactcgtgcg     12720
     aaactggaaa gcctggttga agatctggta aaccgttcca ttgagccgct gaaagttgca     12780
     ctgcaggacg ctggcctgtc cgtatctgat atcgacgacg ttatcctcgt tggtggtcag     12840
     actcgtatgc caatggttca gaagaaagtt gctgagttct ttggtaaaga gccgcgtaaa     12900
     gacgttaacc cggacgaagc tgtagcaatc ggtgctgctg ttcagggtgg tgttctgact     12960
     ggtgacgtaa aagacgtact gctgctggac gttaccccgc tgtctctggg tatcgaaacc     13020
     atgggcggtg tgatgacgac gctgatcgcg aaaaacacca ctatcccgac caagcacagc     13080
     caggtgttct ctaccgctga agacaaccag tctgcggtaa ccatccatgt gctgcagggt     13140
     gaacgtaaac gtgcggctga taacaaatct ctgggtcagt tcaacctaga tggtatcaac     13200
     ccggcaccgc gcggcatgcc gcagatcgaa gttaccttcg atatcgatgc tgacggtatc     13260
     ctgcacgttt ccgcgaaaga taaaaacagc ggtaaagagc agaagatcac catcaaggct     13320
     tcttctggtc tgaacgaaga tgaaatccag aaaatggtac gcgacgcaga agctaacgcc     13380
     gaagctgacc gtaagtttga agagctggta cagactcgca accagggcga ccatctgctg     13440
     cacagcaccc gtaagcaggt tgaagaagca ggcgacaaac tgccggctga cgacaaaact     13500
     gctatcgagt ctgcgctgac tgcactggaa actgctctga aaggtgaaga caaagccgct     13560
     atcgaagcga aaatgcagga actggcacag gtttcccaga aactgatgga aatcgcccag     13620
     cagcaacatg cccagcagca gactgccggt gctgatgctt ctgcaaacaa cgcgaaagat     13680
     gacgatgttg tcgacgctga atttgaagaa gtcaaagaca aaaaataatc gccctataaa     13740
     cgggtaatta tactgacacg ggcgaagggg aatttcctct ccgcccgtgc attcatctag     13800
     gggcaattta aaaaagatgg ctaagcaaga ttattacgag attttaggcg tttccaaaac     13860
     agcggaagag cgtgaaatca gaaaggccta caaacgcctg gccatgaaat accacccgga     13920
     ccgtaaccag ggtgacaaag aggccgaggc gaaatttaaa gagatcaagg aagcttatga     13980
     agttctgacc gactcgcaaa aacgtgcggc atacgatcag tatggtcatg ctgcgtttga     14040
     gcaaggtggc atgggcggcg gcggttttgg cggcggcgca gacttcagcg atatttttgg     14100
     tgacgttttc ggcgatattt ttggcggcgg acgtggtcgt caacgtgcgg cgcgcggtgc     14160
     tgatttacgc tataacatgg agctcaccct cgaagaagct gtacgtggcg tgaccaaaga     14220
     gatccgcatt ccgactctgg aagagtgtga cgtttgccac ggtagcggtg caaaaccagg     14280
     tacacagccg cagacttgtc cgacctgtca tggttctggt caggtgcaga tgcgccaggg     14340
     attcttcgct gtacagcaga cctgtccaca ctgtcagggc cgcggtacgc tgatcaaaga     14400
     tccgtgcaac aaatgtcatg gtcatggtcg tgttgagcgc agcaaaacgc tgtccgttaa     14460
     aatcccggca ggggtggaca ctggagaccg catccgtctt gcgggcgaag gtgaagcggg     14520
     cgagcatggc gcaccggcag gcgatctgta cgttcaggtt caggttaaac agcacccgat     14580
     tttcgagcgt gaaggcaaca acctgtattg cgaagtcccg atcaacttcg ctatggcggc     14640
     gctgggtggc gaaatcgaag taccgaccct tgatggtcgc gtcaaactga aagtgcctgg     14700
     cgaaacccag accggtaagc tattccgtat gcgcggtaaa ggcgtcaagt ctgtccgcgg     14760
     tggcgcacag ggtgatttgc tgtgccgcgt tgtcgtcgaa acaccggtag gcctgaacga     14820
     aaggcagaaa cagctgctgc aagagctgca agaaagcttc ggtggcccaa ccggcgagca     14880
     caacagcccg cgctcaaaga gcttctttga tggtgtgaag aagttttttg acgacctgac     14940
     ccgctaacct ccccaaaagc ctgcccgtgg gcaggcctgg gtaaaaatag ggtgcgttga     15000
     agatatgcga gcacctgtaa agtggcgggg atcactccca taagcgctaa cttaagggtt     15060
     gtggtattac gcctgatatg atttaacgtg ccgatgaatt actctcacga taactggtca     15120
     gcaattctgg cccatattgg taagcccgaa gaactggata cttcggcacg taatgccggg     15180
     gctctaaccc gccgccgcga aattcgtgat gctgcaactc tgctacgtct ggggctggct     15240
     tacggccccg gggggatgtc attacgtgaa gtcactgcat gggctcagct ccatgacgtt     15300
     gcaacattat ctgacgtggc tctcctgaag cggctgcgga atgccgccga ctggtttggc     15360
     atacttgccg cacaaacact tgctgtacgc gccgcagtta cgggttgtac aagcggaaag     15420
     agattgcgtc ttgtcgatgg aacagcaatc agtgcgcccg ggggcggcag cgctgaatgg     15480
     cgactacata tgggatatga tcctcatacc tgtcagttca ctgattttga gctaaccgac     15540
     agcagagacg ctgaacggct ggaccgattt gcgcaaacgg cagacgagat acgcattgct     15600
     gaccggggat tcggttcgcg tcccgaatgt atccgctcac ttgcttttgg agaagctgat     15660
     tatatcgtcc gggttcactg gcgaggattg cgctggttaa ctgcagaagg aatgcgcttt     15720
     gacatgatgg gttttctgcg cgggctggat tgcggtaaga acggtgaaac cactgtaatg     15780
     ataggcaatt caggtaataa aaaagccgga gctccctttc cggcacgtct cattgccgta     15840
     tcacttcctc ccgaaaaagc attaatcagt aaaacccgac tgctcagcga gaatcgtcga     15900
     aaaggacgag tagttcaggc ggaaacgctg gaagcagcgg gccatgtgct attgctaaca     15960
     tcattaccgg aagatgaata ttcagcagag caagtggctg attgttaccg tctgcgatgg     16020
     caaattgaac tggcttttaa gcggctcaaa agtttgctgc acctggatgc tttgcgtgca     16080
     aaggaacctg aactcgcgaa agcgtggata tttgctaatc tactcgccgc atttttaatt     16140
     gacgacataa tccagccatc gctggatttc ccccccagaa gtgccggatc cgaaaagaag     16200
     aactaactcg ttgtggagaa taacaaaaat ggtcatctgg agcttacagg tggccattcg     16260
     tgggacagta tccctgacag cctacaaaac gcaattgaag aacgcgaggc atcgtcttaa     16320
     cgaggcaccg aggcgtcgca ttcttcagat ggttcaaccc ttaagttagc gcttatggga     16380
     tcactccccg ccgttgctct tactcggatt cgtaagccgt gaaaacagca acctccgtct     16440
     ggccagttcg gatgtgaacc tcacagaggt cttttctcgt taccagcgcc gccactacgg     16500
     cggtgataca gatgacgatc agggcgacaa tcatcgcctt atgctgcttc attgctctct     16560
     tctccttgac cttacggtca gtaagaggca ctctacatgt gttcagcata taggaggcct     16620
     cgggttgatg gtaaaatatc actcggggct tttctctatc tgccgttcag ctaatgcctg     16680
     agacagacag cctcaagcac ccgccgctat tatatcgctc tctttaaccc attttgtttt     16740
     atcgattcta atcctgaaga cgcctcgcat ttttgtggcg taatttttta atgatttaat     16800
     tatttaactt taatttatct cttcatcgca attattgacg acaagctgga ttatttttga     16860
     aatattggcc taacaagcat cgccgactga caacaaatta attattactt ttcctaatta     16920
     atccctcagg aatcctcacc ttaagctatg attatctagg cttagggtca ctcgtgagcg     16980
     cttacagccg tcaaaaacgc atctcaccgc tgatggcgca aattcttcaa tagctcgtaa     17040
     aaaacgaatt attcctacac tataatctga ttttaacgat gattcgtgcg gggtaaaata     17100
     gtaaaaacga tctattcacc tgaaagagaa ataaaaagtg aaacatctgc atcgattctt     17160
     tagcagtgat gcctcgggag gcattattct tatcattgcc gctatcctgg cgatgattat     17220
     ggccaacagc ggcgcaacca gtggatggta tcacgacttt ctggagacgc cggttcagct     17280
     ccgggttggt tcactcgaaa tcaacaaaaa catgctgtta tggataaatg acgcgctgat     17340
     ggcggtattt ttcctgttag tcggtctgga agttaaacgt gaactgatgc aaggatcgct     17400
     agccagctta cgccaggccg catttccagt tatcgccgct attggtggga tgattgtgcc     17460
     ggcattactc tatctggctt ttaactatgc cgatccgatt acccgcgaag ggtgggcgat     17520
     cccggcggct actgacattg cttttgcact tggtgtactg gcgctgttgg gaagtcgtgt     17580
     tccgttagcg ctgaagatct ttttgatggc tctggctatt atcgacgatc ttggggccat     17640
     cattatcatc gcattgttct acactaatga cttatcgatg gcctctcttg gcgtcgcggc     17700
     tgtagcaatt gcggtactcg cggtattgaa tctgtgtggt gcacgccgca cgggcgtcta     17760
     tattcttgtt ggcgtggtgt tgtggactgc ggtgttgaaa tcgggggttc acgcaactct     17820
     ggcgggggta attgtcggct tctttattcc tttgaaagag aagcatgggc gttctccagc     17880
     gaagcgactg gagcatgtgt tgcacccgtg ggtggcgtat ctgattttgc cgctgtttgc     17940
     atttgctaat gctggcgttt cactgcaagg cgtcacgctg gatggcttga cctccattct     18000
     gccattgggg atcatcgctg gcttgctgat tggcaaaccg ctggggatta gtctgttctg     18060
     ctggttggcg ctgcgtttga aactggcgca tctgcctgag ggaacgactt atcagcaaat     18120
     tatggtggtg gggatcctgt gcggtatcgg ttttactatg tctatcttta ttgccagcct     18180
     ggcctttggt agcgtagatc cagaactgat taactgggcg aaactcggta tcctggtcgg     18240
     ttctatctct tcggcggtaa ttggatacag ctggttacgc gttcgtttgc gtccatcagt     18300
     ttgacaggac ggtttaccgg ggagccataa acggctccct tttcattgtt atcagggaga     18360
     gaaatgagca tgtctcatat caattacaac cacttgtatt acttctggca tgtctataaa     18420
     gaaggttccg tggttggcgc agcggaggcg ctttatttaa ctccacaaac cattaccgga     18480
     cagattcgag cgctggaaga cgccctgcaa gcgaaattat ttaaacgcaa ggggacgtgg     18540
     tctcgaaccc agcgagctgg agaactggtc tatcgctatg ccgataaaat gttcacctta     18600
     agccaggaaa tgctggatat tgtgaactat cgcaaagaat ccaatttatt gtttgacgtt     18660
     ggcgtggctg atgcactttc caaacgcctg gtcagtagcg tacttaacgc cgcagtggta     18720
     gaaggcgagc ccattcatct tcgctgcttc gaatccaccc acgaaatgct gctggagcaa     18780
     ttaagtcagc ataaactgga gatgatcatt tctgactgtc cgatagactc tacgcagcag     18840
     gaaggcctgt tctccgtgag aattggcgaa tgtggcgtga gtttctggtg tacaaatcca     18900
     ccaccagaaa aaccgttccc ggcttgtctg gaagaacggc gacttttgat tcctgggcga     18960
     cgttcaatgt tagggcgcaa attgcttaac tggtttaact cccagggatt aaacgtagaa     19020
     atcctcggcg agtttgatga tgccgctttg atgaaagctt ggctgcaggt ccttttggtg     19080
     gcgatgcaaa tgcaatcttc gttgccccaa cgctttatgc atatgacttt tatgccgata     19140
     aaactgtcgt agaaattggt cgcgtcgaga atgtgatgga agagtaccat gctatttttg     19200
     ctgagcggat gattcagcac ccggcggtac agcgaatctg caatacggat tattctgcgc     19260
     tttttagtcc agcggtgcgt taatcggcag ctcccccaaa gttaaggtgg gggagataga     19320
     ttagttgtac attaccacga ttttgactcg gctcattatt tgcccgcttg agacattgtt     19380
     tccatatgta cgcgggcgaa taaatagagg aatctgatta cttccttcat ggggatgctg     19440
     aaaagagtag taattgctgg taatgactcc aacttattga tagtgtttta tgttcagata     19500
     atgcccgatg actttgtcat gcagctccac cgattttgag aacgacagcg acttccgtcc     19560
     cagccgtgcc aggtgctgcc tcagattcag gttatgccgc tcaattcgct gcgtatatcg     19620
     cttgctgatt acgtgcagct ttcccttcag gcgggattca tacagcggcc agccatccgt     19680
     catccatatc accacgtcaa agggtgacag caggctcata agacgcccca gcgtcgccat     19740
     agtgcgttca ccgaatacgt gcgcaacaac cgtcttccgg agactgtcat acgcgtaaaa     19800
     cagccagcgc tggcgcgatt tagccccgac atagccccac tgttcgtcca tttccgcgca     19860
     gacgatgacg tcactgcccg gctgtatgcg cgaggttacc gactgcggcc tgagtttttt     19920
     aagtgacgta aaatcgtgtt gaggccaacg cccataatgc gggctgttgc ccggcatcca     19980
     acgccattca tggccatatc aatgattttc tggtgcgtac cgggttgaga agcggtgtaa     20040
     gtgaactgca gttgccatgt tttacggcag tgagagcaga gatagcgctg atgtccggcg     20100
     gtgcttttgc cgttacgcac caccccgtca gtagctgaac aggagggaca gctgatagaa     20160
     acagaagcca ctggagcacc tcaaaaacac catcatacac taaatcagta agttggcagc     20220
     atcacctacc tcaatgtgta tcacaatatc catattcttt gtgggggagt ctggagattg     20280
     agtagatatt cttgttcaga atgtatcagc cgatggttct acgattctta agccacgaag     20340
     agttcagata gtacaacggc atgtctcttt tgactatctg gcaaccggca gtgtgttctc     20400
     tcacgcatca caaaagcagc aggcataaaa aaacccgctt gcgcgggctt tttcacaaag     20460
     cttcagcaaa ttggcgatta agccagtttg ttgatctgtg cagtcaggtt agccttatga     20520
     cgtgcagctt tgtttttgtg gatcagacct ttagcagcct gacggtccac gatcggttgc     20580
     atttcgttaa atgctttctg tgcagcagct ttgtcgccag cttcgatagc tgcgtatact     20640
     ttcttgatga aagtacgcat catagagcga cggcttgcgt tgtgcttacg agccttttca     20700
     gactgaatgg cgcgcttctt agctgatttg atattagcca aggtccaact cccaaatgtg     20760
     ttctatatgg acaattcaaa ggccgaggaa tatgcccttt tagccttctt ttgtcaatgg     20820
     atttgtgcaa ataagcgccg ttaatgtgcc ggcactcgtt acgtagtgat ggcgcaggat     20880
     tctaccagct tgcggggtgt gaatacagct tttccgcgat aaaaattgca gcaggcggtc     20940
     agtttcttcc cgtgatttgc gccatggcaa tgaaaagcca cttctttctg atttcggtac     21000
     tcaatcgccg gttaaccttg accgctgtac aaggtctact cggacgattt tcactgtttt     21060
     gagccagaca tgaagctgat acgcggcata cataatctca gccaggcccc gcaagaaggg     21120
     tgtgtgctga ctattggtaa tttcgacggc gtgcatcgcg gtcatcgcgc gctgttacag     21180
     ggcttgcagg aagaagggcg caagcgcaac ttaccggtga tggtgatgct ttttgaacct     21240
     caaccactgg aactgtttgc taccgataaa gccccggcaa gactgacccg gctgcgggaa     21300
     aaactgcgtt accttgcaga gtgtggcgtt gattacgtgc tgtgcgtgcg tttcgacagg     21360
     cgtttcgcgg cgttaaccgc gcaaaatttc gtcagcgatc ttctggtgaa gcatttgcgc     21420
     gtaaaatttc ttgccgtagg tgatgatttc cctttggcgc tggtcgtgaa ggcgatttct     21480
     tgttattaca gaaagctggc atggaatacg gcttcgatat caccagtacg caaacttttt     21540
     gcagaggtgg cgtgcgcatc agcagcacgg ctgcgtcagg cccttgcgga tgacaatctg     21600
     gctctggcag agagtttact ggggcacccg tttgccatct ccgggcgtgt agtccacggt     21660
     gatgaattag ggcgcactat aggtttcccg acggcgaatg taccgccgcg ccgtcaggtt     21720
     tccccggtga aaggggttta tgcggtagaa gtgctgggcc tcggtgaaaa gccgttaccc     21780
     ggcgtggcaa acatcggaac acgcccaacg gttgccggta ttcgccagca gctggaagtg     21840
     catttgttag atgttgcaat ggacctttac ggtcgccata tacaagtagt gctgcgtaaa     21900
     aaaatacgca atgagcagcg atttgcgtcg ctggacgaac tgaaagcgca gattgcgcgt     21960
     gatgaattaa ccgcccgcga attttttggg ctaacaaaac cggcttaagc ctgttatgta     22020
     atcaaaccga aatacggaac cgagaatctg atgagtgact ataaatcaac cctgaatttg     22080
     ccggaaacag ggttcccgat gcgtggcgat ctcgccaagc gcgaacccgg aatgctggcg     22140
     cgttggactg atgatgatct gtacggcatc atccgtgcgg ctaaaaaagg caaaaaaacc     22200
     ttcattctgc atgatggccc tccttatgcg aatggcagca ttcatattgg tcactcggtt     22260
     aacaagattc tgaaagacat tatcgtgaag tccaaagggc tttccggtta tgactcgccg     22320
     tatgtgcctg gctgggactg ccacggtctg ccgatcgagc tgaaagtcga gcaagaatac     22380
     ggtaagccgg gtgagaaatt caccgccgcc gagttccgcg ccaagtgccg cgaatacgcg     22440
     gcgacccagg ttgacggtca acgcaaagac tttatccgtc tgggcgtgct gggcgactgg     22500
     tcgcacccgt acctgaccat gggacttcaa aactggaagg ccaacatcat ccgcgcgctg     22560
     ggcaaaatca tcggcaacgg tcacctgcac aaaggcgcga agccagttca ctggtgcgtt     22620
     gactgccgtt ctgcgctggc gaagcggaag ttgagtatta cgacaaaact tctccgtcca     22680
     tcgacgttgc tttccagggc agtcgatcag gatgcactga aagcaaaatt tgccgtaagc     22740
     aacgttaacg gcccaatctc gctggtaatc tggaccacca cgccgtggac tctgcctgcc     22800
     aaccgcgcaa tctctattgc accagatttc gactatgcgc tggtgcagat cgacggtcag     22860
     gccgtgattc tggcgaaaga tctggttgaa agcgtaatgc agcgtatcgg cgtgaccgat     22920
     tctcggcacg gtaaaaggtg cggagctgga gccgctgcgt ttacccatcc gtttatgggc     22980
     ttcgacgttc cggcaatcct cggcgatcac gttaccctgg atgccggtac cggtgccgtt     23040
     cacaccgcgc ctggccacgg cccggacgac tatgtgatcg gtcagaaata cggcctggaa     23100
     accgctaacc cggttggccc ggacggcact tatctgccgg gcacttatcc gacgctggat     23160
     ggcgtgaacg tcttcaaagc gaacgacatc gtcgctgcgc tgctgcagga aaaaggcgcg     23220
     ctgctgcacg ttgagaaaat gcagcacagc tatccgtgct gctggcgtca caaaacgccg     23280
     atcatcttcc gcgcgacgcc gcagtggttc gtcagcatgg atcagaaagg tctgcgtgcg     23340
     cagtcactga aagagatcaa aggcgtgcag tggatcccgg actggggcca ggcgcgtatc     23400
     gagtcgatgg ttgctaaccg tcctgactgg tgtatctccc gtcagcgcac ctggggtgta     23460
     ccgatgtcac tgttcgtgca caaagacacg gaagagctgc atccgcgtac ccttgaactg     23520
     atggaagaag tggcaaaacg cgttgaagtc gatggcatcc aggcgtggtg ggatctcgat     23580
     gcgaaagaga tcctcggcga cgaagctgat cagtacgtga aagtgccgga cacattggat     23640
     gtatggtttg actccggatc tacccactct tctgttgttg acgtgcgtcc ggaatttgcc     23700
     ggtcacgcag cggacatgta tctggaaggt tctgaccaac accgcggctg gttcatgtct     23760
     tccctaatga tctccaccgc gatgaagggt aaagcgccgt atcgtcaggt actcacccac     23820
     ggctttaccg tggatggtca gggccgcaag atgtctaaat ccatcggcaa taccgtttcg     23880
     ccgcaggatg tgatgaacaa actgggcgcg gatattctgc gtctgtgggt ggcatcaacc     23940
     gactacaccg gtgaaatggc cgtttctgac gagatcctga aacgtgctgc cgatacgtat     24000
     cgtcgtatcc gtaacaccgc gcgcttcctg ctggcaaacc tgaacggttt tgatccagca     24060
     aaagatatgg tgaaacggag agagatggtg gtactggatc gctgggccgt agttgtgcga     24120
     aagcggcaca ggaagacatc ctcaaggcgt acgaagcata cgatttccac gaagtggtac     24180
     aagcgtctga tgcgcttctg ctccgttgag atgggttcct tctacctcga catcatcaaa     24240
     gaccgtcagt actacgccaa aggacacagt gtggcgcgtc gtagctgcca gactgcgcta     24300
     tatcacatcg cagaagcgct ggtgcgctgg atggcaccaa tcctctcctt caccgctgat     24360
     gaagtgtggg gctacctgcc gggcgaacgt gaaaaatacg tcttcaccgg tgagtggtac     24420
     gaaggcctgt ttggcctggc agacagtgaa gcgatgaacg atgcgttctg ggacgagctg     24480
     ttgaaagtgc gtggcgaagt gaacaaagtc attgagcaag cgcgtgccga caagaaagtg     24540
     ggtggctcgc tggaagcggc agtaaccttg tatgcagaac cggaactgtc ggcgaaactg     24600
     accgcgctgg gcgatgaatt acgatttgtc ctgttgacct ccggcgctac cgttgcagac     24660
     tataacgacg cacctgctga tgctcagcag agcgaagtac tcaaagggct gaaagtcgcg     24720
     ttgagtaaag ccgaaggtga gaagtgccca cgctgctggc actacaccca ggatgtcggc     24780
     aaggtggcgg aacacgcaga aatctgcggc cgctgtgtca gcaacgtcgc cggtgacggt     24840
     gaaaaacgta agtttgcctg atgagtcaat cgatctgttc aacagggcta cgctggctgt     24900
     ggctggtggt agtcgtgctg attatcgatc tgggcagcaa atacctgatc ctccagaact     24960
     ttgctctggg ggatacggtc ccgctgttcc cgtcgcttaa tctgcattat gcgcgtaact     25020
     atggcgcggc gtttagtttc cttgccgata gcggcggctg gcagcgttgg ttctttgccg     25080
     gtattgcgat tggtattagc gtgatcctgg cagtgatgat gtatcgctcg aaggccacgc     25140
     agaagctaaa caatatcgct tacgcgctga ttattggcgg cgcgctgggc aacctgttcg     25200
     accgcctgtg gcacggcttc gttgtcgata tgatcgactt ctacgtcggc gactggcact     25260
     tcgccacctt caaccttgcc gatactgcca tctgtgtcgg tgcggcactg attgtgctgg     25320
     aaggtttttt gccttctaga gcgaaaaaac aataataaac cctgccggat gcgatgctga     25380
     cgcatcttat ccggcctaca gattgctgcg aaatcgtagg ccggataagg cgtttacgcc     25440
     gcatccggca aaaatcctta aatataagag caaacctgca tgtctgaatc tgtacagagc     25500
     aatagcgccg tcctggtgca cttcacgcta aaactcgacg atggcaccac cgccgagtct     25560
     acccgcaaca acggtaaacc ggcgctgttc cgcctgggtg atgcttctct ttctgaaggg     25620
     ctggagcaac acctgttggg gctgaaagtg ggcgataaaa ccaccttctc gttggagcca     25680
     gatgcggcgt ttggcgtgcc gtcaccggac ctgattcagt acttctcccg ccgtgaattt     25740
     atggatgcag gcgagccaga aattggcgca atcatgcttt ttaccgcaat ggatggcagt     25800
     gagatgcctg gcgtgatccg cgaaattaac ggcgactcca ttaccgttga tttcaaccat     25860
     ccgctggccg ggcagaccgt tcattttgat attgaagtgc tggaaatcga tccggcactg     25920
     gaggcgtaac atgcagatcc tgttggccaa cccgcgtggt ttttgtgccg gggtagaccg     25980
     cgctatcagc attgttgaaa acgcgctggc catttacggc gcaccgatat atgtccgtca     26040
     cgaagtggta cataaccgct atgtggtcga tagcttgcgt gagcgtgggg ctatctttat     26100
     tgagcagatt agcgaagtac cggacggcgc gatcctgatt ttctccgcac acggtgtttc     26160
     tcaggcggta cgtaacgaag caaaaagtcg cgatttgacg gtgtttgatg ccacctgtcc     26220
     gctggtgacc aaagtgcata tggaagtcgc ccgcgccagt cgccgtggcg aagaatctat     26280
     tctcatcggt cacgccgggc acccggaagt ggaagggaca atgggccagt acagtaaccc     26340
     ggaaggggga atgtatctgg tcgaatcgcc ggacgatgtg tggaaactga cggtcaaaaa     26400
     cgaagagaag ctctccttta tgacccagac cacgctgtcg gtggatgaca cgtctgatgt     26460
     gatcgacgcg ctgcgtaaac gcttcccgaa aattgtcggt ccgcgcaaag atgacatctg     26520
     ctacgccacg actaaccgtc aggaagcggt acgcgccctg gcagaacagg cggaagttgt     26580
     gttggtggtc ggttcgaaaa actcctccaa ctccaaccgt ctggcggagc tggcccagcg     26640
     tatgggcaaa cgcgcgtttt tgattgacga tgcgaaagac atccaggaag agtgggtgaa     26700
     agaggttaaa tgcgtcggcg tgactgcggg cgcatcggct ccggatattc tggtgcagaa     26760
     tgtggtggca cgtttgcagc agctgggcgg tggtgaagcc attccgctgg aaggccgtga     26820
     agaaaacatt gttttcgaag tgccgaaaga gctgcgtgtc gatattcgtg aagtcgatta     26880
     agtcattagc agcctaagtt atgcgaaaat gccggtcttg ttaccggcat tttttatgga     26940
     gaaaacatgc gtttacctat cttcctcgat actgaccccg gcattgacga tgccgtcgcc     27000
     attgccgccg cgatttttgc acccgaactc gacctgcaac tgatgaccac cgtcgcgggt     27060
     aatgtctcgg ttgagaaaac tacccgcaat gccctgcaac tgctgcattt ctggaatgcg     27120
     gagattccgc tcgcccaagg ggccgctgtg ccactggtac gcgcaccgcg tgatgcggca     27180
     tctgtgcacg gcgaatcggg aatggctggc tacgactttg ttgagcacaa ccgaaagccg     27240
     ctcgggatac cggcgtttct ggcgattcgg gatgccctga tgcgtgcacc agagcctgtt     27300
     accctggtgg ccatcggccc gttaaccaat attgcgctgt tactttcaca atgcccggaa     27360
     tgcaagccgt atattcgccg tctggtgatc atgggtggtt ctgccggacg cggcaactgt     27420
     acgccaaacg ccgagtttaa tattgctgcc gatccagaag ctgctgcctg tgtcttccgc     27480
     agtggtattg aaatcgtcat gtgcggtttg gatgtcacca atcaggcaat attaactcct     27540
     gactatctct ctacactgcc gcagttaaac cgtaccggga aaatgcttca cgccctgttt     27600
     agccactacc gtagcggcag tatgcaaagc ggcttgcgaa tgcacgatct ctgcgccatc     27660
     gcctggctgg tgcgcccgga cctgttcact ctcaaaccct gttttgtggc agtggaaact     27720
     cagggcgaat ttacctcagg cacgacggtg gttgatatcg acggttgcct gggcaagcca     27780
     gccaatgtac aggtggcatt ggatctggat gtgaaaggct tccagcagtg ggtggctgag     27840
     gtgctggctc tggcgtcgta acctgtcaca tgttattggc atgcagtcat tcatcgactc     27900
     atgcctttca ctgatatccc tccctgttta tcattaattt ctaattatca gcgtttttgg     27960
     ctggcggcgt agcgatgcgc tggttactct gaaaacggtc tatgcaaatt aacaaaagag     28020
     aatagctatg catgatgcaa acatccgcgt tgccatcgcg ggagccgggg ggcgtatggg     28080
     ccgccagttg attcaggcgg cgctggcatt agagggcgtg cagttgggcg ctgcgctgga     28140
     gcgtgaagga tcttctttac tgggcagcga cgccggtgag ctggccggag ccgggaaaac     28200
     aggcgttacc gtgcaaagca gcctcgatgc ggtaaaagat gattttgatg tgtttatcga     28260
     ttttacccgt ccggaaggta cgctgaacca tctcgctttt tgtcgccagc atggcaaagg     28320
     gatggtgatc ggcactacgg ggtttgacga agccggtaaa caagcaattc gtgacgccgc     28380
     tgccgatatt gcgattgtct ttgcggccaa ttttagcgtt ggcgttaacg tcatgcttaa     28440
     gctgctggag aaagcagcca aagtgatggg tgactacacc gatatcgaaa ttattgaagc     28500
     acatcataga cataaagttg atgcgccgtc aggcaccgca ctggcaatgg gagaggcgat     28560
     cgcccacgcc cttgataaag atctgaaaga ttgcgcggtc tacagtcgtg aaggccacac     28620
     cggtgaacgt gtgcctggca ccattggttt tgccaccgtg cgtgcaggtg acatcgttgg     28680
     tgaacatacc gcgatgtttg ccgatattgg cgagcgtctg gagatcaccc ataaggcgtc     28740
     cagccgtatg acatttgcta acggcgcggt aagatcggct ttgtggttga gtggtaagga     28800
     aagcggtctt tttgatatgc gagatgtact tgatctcaat aatttgtaac cacaaaatat     28860
     ttgttatggt gcaaaaataa cacatttaat ttattgatta taaagggctt taatttttgg     28920
     cccttttatt tttggtgtta tgtttttaaa ttgtctataa gtgccaaaaa ttacatgttt     28980
     tgtcttctgt ttttgttgtt ttaatgtaaa ttttgaccat ttggtccact tttttctgct     29040
     cgtttttatt tcatgcaatc ttcttgctgc gcaagcgttt tccagaacag gttagatgat     29100
     ctttttgtcg cttaatgcct gtaaaacatg catgagccac aaaataatat aaaaaatccc     29160
     gccattaagt tgacttttag cgcccatatc tccagaatgc cgccgtttgc cagaaattcg     29220
     tcggtaagca gatttgcatt gatttacgtc atcattgtga attaatatgc aaataaagtg     29280
     agtgaatatt ctctggaggg tgttttgatt aagtcagcgc tattggttct ggaagacgga     29340
     acccagtttc acggtcgggc cataggggca acaggttcgg cggttgggga agtcgttttc     29400
     aatacttcaa tgaccggtta tcaagaaatc ctcactgatc cttcctattc tcgtcaaatc     29460
     gttactctta cttatcccca tattggcaat gtcggcacca atgacgccga tgaagaatct     29520
     tctcaggtac atgcacaagg tctggtgatt cgcgacctgc cgctgattgc cagcaacttc     29580
     cgtaataccg aagacctctc ttcttacctg aaacgccata acatcgtggc gattgccgat     29640
     atcgataccc gtaagctgac gcgtttactg cgcgagaaag gcgcacagaa tggctgcatt     29700
     atcgcgggcg ataacccgga tgcggcgctg gcgttagaaa aagcccgcgc gttcccaggt     29760
     ctgaatggca tggatctggc aaaagaagtg accaccgcag aagcctatag ctggacacaa     29820
     gggagctgga cgttgaccgg tggcctgcca gaagcgaaaa aagaagacga gctgccgttc     29880
     cacgtcgtgg cttatgattt tggtgccaag cgcaacatcc tgcggatgct ggtggataga     29940
     ggctgtcgcc tgaccatcgt tccggcgcaa acttctgcgg aagatgtgct gaaaatgaat     30000
     ccagacggca tcttcctctc caacggtcct ggcgacccgg ccccgtgcga ttacgccatt     30060
     accgccatcc agaaattcct cgaaaccgat attccggtat tcggcatctg tctcggtcat     30120
     cagctgctgg cgctggcgag cggtgcgaag actgtcaaaa tgaaatttgg tcaccacggc     30180
     ggcaaccatc cggttaaaga tgtggagaaa aacgtggtaa tgatcaccgc ccagaaccac     30240
     ggttttgcgg tggacgaagc aacattacct gcaaacctgc gtgtcacgca taaatccctg     30300
     ttcgacggta cgttacaggg cattcatcgc accgataaac cggcattcag cttccagggg     30360
     caccctgaag ccagccctgg tccacacgac gccgcgccgt tgttcgacca ctttatcgag     30420
     ttaattgagc agtaccgtaa aaccgctaag taatcaggag taaaagagcc atgccaaaac     30480
     gtacagatat aaaaagtatc ctgattctgg gtgcgggccc gattgttatc ggtcaggcgt     30540
     gtgagtttga ctactctggc gcgcaagcgt gtaaagccct gcgtgaagag ggttaccgcg     30600
     tcattctggt gaactccaac ccggcgacca tcatgaccga cccggaaatg gctgatgcaa     30660
     cctacatcga gccgattcac tgggaagttg tacgcaagat tattgaaaaa gagcgcccgg     30720
     acgcggtgct gccaacgatg ggcggtcaga cggcgctgaa ctgcgcgctg gagctggaac     30780
     gtcagggcgt gttggaagag ttcggtgtca ccatgattgg tgccactgcc gatgcgattg     30840
     ataaagcaga agaccgccgt cgtttcgacg tagcgatgaa gaaaattggt ctggaaaccg     30900
     cgcgttccgg tatcgcacac acgatggaag aagcgctggc ggttgccgct gacgtgggct     30960
     tcccgtgcat tattcgccca tcctttacca tgggcggtag cggcggcggt atcgcttata     31020
     accgtgaaga gtttgaagaa atttgcgccc gcggtctgga tctctctccg accaaagagt     31080
     tgctgattga tgagtcgctg atcggctgga aagagtacga gatggaagtg gtgcgtgata     31140
     aaaacgacaa ctgcatcatc gtctgctcta tcgaaaactt cgatgcgatg ggcatccaca     31200
     ccggtgactc catcactgtc gcgccagccc aaacgctgac cgacaaagaa tatcaaatca     31260
     tgcgtaacgc ctcgatggcg gtgctgcgtg aaatcggcgt tgaaaccggt ggttccaacg     31320
     ttcagtttgc ggtgaacccg aaaaacggtc gtctgattgt tatcgaaatg aacccacgcg     31380
     tgtcccgttc ttcggcgctg gcgtcgaaag cgaccggttt cccgattgct aaagtggcgg     31440
     cgaaactggc ggtgggttac accctcgacg aactgatgaa cgacatcact ggcggacgta     31500
     ctccggcctc cttcgagccg tccatcgact atgtggttac taaaattcct cgcttcaact     31560
     tcgaaaaatt cgccggtgct aacgaccgtc tgaccactca gatgaaatcg gttggcgaag     31620
     tgatggcgat tggtcgcacg cagcaggaat ccctgcaaaa agcgctgcgc ggcctggaag     31680
     tcggtgcgac tggattcgac ccgaaagtga gcctggatga cccggaagcg ttaaccaaaa     31740
     tccgtcgcga actgaaagac gcaggcgcag atcgtatctg gtacatcgcc gatgcgttcc     31800
     gtgcgggcct gtctgtggac ggcgtcttca acctgaccaa cattgaccgc tggttcctgg     31860
     tacagattga agagctggtg cgtctggaag agaaagtggc ggaagtgggc atcactggcc     31920
     tgaacgctga cttcctgcgc cagctgaaac gcaaaggctt tgccgatgcg cgcttggcaa     31980
     aactggcggg cgtacgcgaa gcggaaatcc gtaagctgcg tgaccagtat gacctgcacc     32040
     cggtttataa gcgcgtggat acctgtgcgg cagagttcgc caccgacacc gcttacatgt     32100
     actccactta tgaagaagag tgcgaagcga atccgtctac cgaccgtgaa aaaatcatgg     32160
     tgcttggcgg cggcccgaac cgtatcggtc agggtatcga attcgactac tgttgcgtac     32220
     acgcctcgct ggcgctgcgc gaagacggtt acgaaaccat tatggttaac tgtaacccgg     32280
     aaaccgtctc caccgactac gacacttccg accgcctcta cttcgagccg gtaactctgg     32340
     aagatgtgct ggaaatcgtg cgtatcgaga agccgaaagg cgttatcgtc cagtacggcg     32400
     gtcagacccc gctgaaactg gcgcgcgcgc tggaagctgc tggcgtaccg gttatcggca     32460
     ccagcccgga tgctatcgac cgtgcagaag accgtgaacg cttccagcat gcggttgagc     32520
     gtctgaaact gaaacaaccg gcgaacgcca ccgttaccgc tattgaaatg gcggtagaga     32580
     aggcgaaaga gattggctac ccgctggtgg tacgtccgtc ttacgttctc ggcggtcggg     32640
     cgatggaaat cgtctatgac gaagctgacc tgcgtcgcta cttccagacg gcggtcagcg     32700
     tgtctaacga tgcgccagtg ttgctggacc acttcctcga tgacgcggta gaagttgacg     32760
     tggatgccat ctgcgacggc gaaatggtgc tgattggcgg catcatggag catattgagc     32820
     aggcgggcgt gcactccggt gactccgcat gttctctgcc agcctacacc ttaagtcagg     32880
     aaattcagga tgtgatgcgc cagcaggtgc agaaactggc cttcgaattg caggtgcgcg     32940
     gcctgatgaa cgtgcagttt gcggtgaaaa acaacgaagt ctacctgatt gaagttaacc     33000
     cgcgtgcggc gcgtaccgtt ccgttcgtct ccaaagccac cggcgtaccg ctggcaaaag     33060
     tggcggcgcg cgtgatggct ggcaaatcgc tggctgagca gggcgtaacc aaagaagtta     33120
     tcccgccgta ctactcggtg aaagaagtgg tgctgccgtt caataaattc ccgggcgttg     33180
     acccgctgtt agggccagaa atgcgctcta ccggggaagt catgggcgtg ggccgcacct     33240
     tcgctgaagc gtttgccaaa gcgcagctgg gcagcaactc caccatgaag aaacacggtc     33300
     gtgcgctgct ttccgtgcgc gaaggcgata aagaacgcgt ggtggacctg gcggcaaaac     33360
     tgctgaaaca gggcttcgag ctggatgcga cccacggcac ggcgattgtg ctgggcgaag     33420
     caggtatcaa cccgcgtctg gtaaacaagg tgcatgaagg ccgtccgcac attcaggacc     33480
     gtatcaagaa tggcgaatat acctacatca tcaacaccac ctcaggccgt cgtgcgattg     33540
     aagactcccg cgtgattcgt cgcagtgcgc tgcaatataa agtgcattac gacaccaccc     33600
     tgaacggcgg ctttgccacc gcgatggcgc tgaatgccga tgcgactgaa aaagtaattt     33660
     cggtgcagga aatgcacgca cagatcaaat aatagcgtgt catggcagat atttttcatc     33720
     cgctaatttg atcgaataac taatacggtt ctctgatgag gaccgttttt ttttgcccat     33780
     taagtaaatc ttttggggaa tcgatatttt tgatgacata agcaggattt agctcacact     33840
     tatcgacggt gaagttgcat actatcgata tatccacaat tttaatatgg ccttgtttaa     33900
     ttgcttcaaa acgagtcata gccagacttt taatttgtga aactggagtt cgtatgtgtg     33960
     aaggatatgt tgaaaaacca ctctacttgt taatcgccga atggatgatg gctgaaaatc     34020
     ggtgggtgat agcaatagag agatctctat tcatttcgat attgaacaca gcaaggcggt     34080
     taataccctg acttatattc tgtcggaagt cacagaaata agctgcgaag ttaagatgat     34140
     ccctaataag ctggaagggc ggggatgcca gtgtcagcga ctggttaaag tggtcgatat     34200
     ccatgagcaa atttacgcgc gcctgcgcaa taacagtcgg gaaaaattag tcggtgtaag     34260
     aaagacgccg cgtattcctg ccgttccgct cacggaactt aaccgcgagc agaagtggca     34320
     gatgatgttg tcaaagagat tgcgtcgtta attttatctc gttgataccg ggcgtcctgc     34380
     ttgaccagat gcgatgttgt agcatcttat ccagcaacca ggtcgcatcc ggcaagatca     34440
     ccgtttaggc gtcacatccg tcgtcccctg caaacggggg cgattttcct ccatttgcct     34500
     cagtggctgc gtttcatgta acgatacatg acagcgcccg acaagatcct gatactcttt     34560
     ggtattcaac cgtttccagt gtaactcgtc gtcactaaca ttgcgtacag cgcgggctgg     34620
     cgtacccatc aacaactggc gtttctcgcc gcgaaagccc gctttgacaa agctcatggc     34680
     ggcaacaatg ctctcttcgc caatgaccgc gccatccata atcacgctgt tcatcccgac     34740
     caatgcatcg cgaccaatca aacaaccatg caggatcgct ccgtgcccga tatggccgtt     34800
     ttccccaacg atagtgtcag tgtcgcagta gccatgcata atgcagccat cctgaatatt     34860
     ggctcccgct tgcacgatca accgcccgta gtcaccacgc agtgaggcga gtgggccgat     34920
     gtagacaccg gctcccacaa tcacatcgcc aatcaagacg gcactgggat ggacaaacgc     34980
     cgtcgggtga accaccggaa ttaacccctc aaaggcgtaa tagctcacgg ttgttaacgt     35040
     cctttccaca ccggatcgcg cttctcggca aacgccagcg gcccttcaat ggcatcttcc     35100
     gaatgcagaa ccgatggata gtgtttcaac acgccgctgc gaatatagcg atacgcttct     35160
     tctaccggca tttcgctggt ggtgcggtag atctctttca gcgccgcaat cgccagcggg     35220
     gcgctgttaa ccagctgctg agccagttcg cgggcgttat ccatcagttc cgcctggcta     35280
     accacgcggt tgactatccc ccaacgcagc gcctcttctg cgcccattcg tctgccggtc     35340
     atcaccattt cattgacgat ggcaggcggc aggatcttcg gcagacgcag cacaccgccg     35400
     ctgtcaggaa cgatgcccag tttggcttcc ggcagggcga agctggcgtt atcggcacaa     35460
     acaataaaat ctgccgccag cgccagttca aaggcgccgc caaaggcata gccgttcaca     35520
     gctgcgataa ccggtttgtc gagattgaaa atttcggtta atcccgcaaa accacccgga     35580
     ccaaagtcag catccggtgc ttcgccttct gctgccgctt ttaaatccca gcccgcggaa     35640
     aagaacttct ctccggcacc ggtaataatg gcgacacgta attgcggatc gtcacggaaa     35700
     tttagaaata cttcgcccat ttcaaagctg gtttttgcat caatagcatt cgcttttgga     35760
     cgatcaaggg taatttccag aattgatcca ttgcgggtca gatgtaatga ttcactcatt     35820
     ccttttctcc atttttgctt tttcagggac gacaacatcc ctgcaaaaaa tgcatattgt     35880
     tttagagtgt gattattagc tggcagggta gttccctgct gtttcattta tttcagattc     35940
     tttctaatta ttttccccga gcaattacgt ggcagatctt ttctgatctc cagataagag     36000
     ggcactttaa atttcgccat attttgttcg cagaagcgga aaaattcctc ttcgctcaat     36060
     gtttcacctt cattcagcac cacaaatgct ttgatggctt catcgcgaat cgaatcttta     36120
     atacccacaa ccacgatgtc ctgaattttc gggtgcgcgg cgataatatt ttccagctcc     36180
     acgcaggaga cattctcgcc gccacgttta atcatattgc agcggcgatc gacgaaataa     36240
     aaaaagtcct cttcgtcgcg gtatccggta tcgccggtat gcagccagcc atcggcttcc     36300
     agcactttcg cagtggcttg tgggttgaga aagtactctt tgaagatggt tttcccaggt     36360
     atgcctttaa tgcagatttc accgatctca ccagccggga gcgggcgatt gtgatcgtcg     36420
     cggatctccg cttcgtagca aaaccccacc cgaccaatcg acggccagcg tcgtttatcg     36480
     ccaggacgat caccgataat gcccacaatg gtttccgtca tcccataaga cgtcagcaag     36540
     cgaacgccga agcgttcaca aaacgcatct ttttcctgct ccgacaagtt gagataaaac     36600
     atcacttccc gcaggcggtg ttgctgatcg ttcgctgaag gcggctgtac catcaacgta     36660
     cggatcatca tcggaataca ttcggtaacg gtggcgcggt acttctgtac ctgtccccag     36720
     aaggcgcggg cgctgtattt ctcgaccagc acaaaggtgg ccccggcaga aaacgccgcc     36780
     atcgccgcag tacactggca atcgatatga aacgcaggca ttaccgtcag gtagacgtca     36840
     tcgtcacgca gtgcacactg ccaggcggag taatatccag cgaagcgcag gttgtaatgg     36900
     gtaatcacca cacctttcgg tcgggaggtg gtgccggagg tgaagagaat ttccgccgta     36960
     tcgtcagtcg atagcggcgg tgcatagcac aaggtggcag gttgttgatt tttcagttga     37020
     gtaaacgaac tcacgccatc atcagcggga agtgccacat ctgtcaggca aatgtgccgc     37080
     aattgagtgg catcttcctg ctgaatctgt tgatacatag gatagaattg cgcactggtc     37140
     accagcaggc acgcctggct attttgcagg atccacgcgc tttcctcgca caacaggcgg     37200
     gcgttaatcg gcaccataat cgcgccaatt tttgccagcc cgaaccagca aaagataaat     37260
     tccgggcagt tgtcgagatg tagtgcaacc ttgtcgcctt tgcgaatccc cagcgtataa     37320
     aacaggtttg ccgtgcggtt aatctcctga tttaactcaa gataactata ccggttaacg     37380
     actccgccgc tggattcaca aatcagcgcc gttttatgac cgtaaacgtc cgcaagatcg     37440
     tcccacattt gacgtagatg ttgtccgcca atgatatcca ttgcacctct atccattttt     37500
     gttcgtttgt tattgggcgg gcgctagtca ggcaagccga ctgacgccac gcgtttagtc     37560
     ctcaactttg gccagacctt tgctgaccaa ctcctgaatg tcgttttcgc tgtagccgat     37620
     atttttcaaa atggcagccg tgtccatgcc atgtgagggc attccgcgcc agatttgtcc     37680
     ggggttattt ttgaatttcg gcatgatgtt cggccctttg caggtgcgac catccatcgt     37740
     ttgccactga gtgattgatt cgcgagccac atactgtgga ttgctttcca gttccggtac     37800
     ggtcagcact ttggcgcagg cgatattcag ttcagcaaag cgttctttta cttccgcgat     37860
     ggtatgtgtc gccagccagg catcgagttt ctcttcaacc agtgggccgt aagggcattc     37920
     gatacggtgg ataagctgag tgccttccgg gatttctggc gtgccaagca gatgtgcgag     37980
     gccaatatct ttaaagcact cttcaatttg ggtaatgccc accagttcca tcacgatgta     38040
     gccgtcggca catttataca gaccgcaacc ggcgtagtag ggatctttac ctttgctcat     38100
     gcgcgggcac atttcgccgc cgttgaagta atccatcatg aagtactggc ccatacgcag     38160
     catcacttca tacatggcga tgtcgatact ttcgccttta ccggtttcac gcactttatg     38220
     cagtgctgcc agcgccgccg tggtggcggt caggccagaa aagtaatcgg cggtatacgg     38280
     gaaggcaggc attggctggt caacatcacc gttctgaatc aggtaaccac taaaggcctg     38340
     ggcgatagtg ttataggccg gaagattggt gtactcctcg gtgccgtact gaccaaaacc     38400
     ggacaggtga gcgataacca gtttcgggtt gtgctgccac agtacttcat cggtaatgcc     38460
     acgacgggca aaggccggac ctttactggc ttcgatgaag atatcggtgg tttccattaa     38520
     tttcagaaac gcttcgcggc cttcatcttt gaaaatattt aacgacagcg cgtgcaaatt     38580
     gcggcgggag agttgcgggt agttcggttg aacgcgaatg gtgtcggccc aggcgacgtt     38640
     ctcgatccag ataacttccg cgccccattc tgcgaacatt tgcccggcaa acggtccggc     38700
     gatttcgata ccggagaaga caacgcgcaa tccggccaac ggcccgaatt tcggcatggg     38760
     tagatgatcc attatttgct cctgaaaaat ttatgtagcg catgactgcc ggatgcggcg     38820
     taaacgcttt atccggccta cattcgtgct cccgtaggcc tgataagacg catcagcgcg     38880
     gcatcaggca gcgcacggac ttagcggtat tgcttcagca ccgcacgacc cagcgtcagg     38940
     atctgcattt cgtcagatcc cccggagacg cggtctacac gcagatcacg ccagaagcgg     39000
     ctgatgcggt ggttgcccgc aatcccgaca ccgcccagca cctgcattgc gctatccaca     39060
     acttcaaatg ccgcattggc gcagaagtat ttgcacatcg ctgcatcgcc agaggtgatg     39120
     gtgccgttgt ctgctttcca cgctgcttca tacagcatgt ttttcatgga gtttaatttg     39180
     atcgccatgt gggcgaattt ttcctgaatc aactggaaac gaccaatagc ctcgccaaac     39240
     tgcacgcgct gattggcgta gcgcgccgca tcttcaaagg cgcacatcgc cgtaccgtag     39300
     ttggtgaggg ctaccaggaa acgttcatgg tcgaactctt ctttgacgcg gttaaagccg     39360
     ttaccttccc gaccgaacat gtctttctcg tccagttcca cgtcgtcaaa ggtgatttca     39420
     cagcagctat ccatacgcag accgagcttt tcaagtttgg tcactttgat gcccggtttg     39480
     ctcatatcaa caaaccatcc ggtgtagaca ggtttgtccg gagaagcccc gtcgcgcgcc     39540
     atcaccacga tgtacggggt gtaggcgctg ctggtaataa aacacttact accattaaga     39600
     taaatcttac catttttacg ggtataagtc gttttcaggc tacccacgtc ggagcccgcg     39660
     cccggttcgg taatcgctga gttccacatc tgcttaccgg tgccgcggaa agccataatt     39720
     ttgtcgatct gctcttgtgt gccttcgcgc aggaaggtgt tgaacccgcc cggcaactgg     39780
     tacagcacat aggttggtgc ccccagacgt cccagctcca tccacacggc ggcgagagta     39840
     acaaaccccg cgtccagacc accgtgctct tcagggatca gcagactgtc gatacccata     39900
     tccgccagtg ctttgacaaa acgttccggg tagacgctgt cacggtcgca ctcggcaaaa     39960
     taggcctccc agttttcgct ggccatcagt tcgcggatac cggcgacaaa cagttcctgc     40020
     tcatcattta aattaaaatc catctttcaa cctcttgata ttttgggggg ttaattaatc     40080
     tttccagttc tgtttcgcgt ctttaataaa ggagagcgtc accataatgt tgacgaagaa     40140
     cagcgggcat cctccggcga taatggcggt ttgaatcggt ttcaggccgc cgagcgccag     40200
     cagaacaata ccgataatgc caaccagaat tgaccaaccg atacgcacca gcagaggtgg     40260
     ttcttcacca tcgcgtactt cgcggcaagt ggacatcgcc agggtataag agcaggcgtt     40320
     aaccagcgta acggtggcaa taaagcagag gatgaagaag ccccacatgg tggcggtgct     40380
     gagtggcaga gcggcccagg tttcaatgat ggcgcgcgcc acaccgtact gttcgatcag     40440
     atttggaatg ttgatgatgt ttttatctat caacagcaga gtgttactac cgagtacagt     40500
     ccacaggatc caggttgacg ctgtcagccc cagcaccatg ccgaagcaca gttcacgcac     40560
     agtacgacca cgggagatgc gggcgaggaa gatactcatc tggatagcat aaatcaccca     40620
     ccatgcccag tagaacacgg tccagccctg cgggaagccg cctttagcga tgggatcggt     40680
     atagaacaac atgcgcggca gatacatcag caacatcccc accgaatcgg tgaagtagtt     40740
     catgatgaag ctggcaccgc tgacaatgaa cacccaaccc agcatcagga agctcaggta     40800
     actacgcacg tcactggcga tacgtacccc tttttgcaga ccgcaagcga cgcaaatggc     40860
     gttgaggata atccagcagg taatgatgat agcgtccagt tgcagggtat gcggaatgcc     40920
     aaacaaccat tgcatacact cggtcaccag cggcgtggca aggcccagac tggtacccat     40980
     cgtgaagatc aaggcgacga gatagaagtt gtcgacgata gtgccgaaca accctttggc     41040
     gtgtttttca cctaccagcg gcaccagtgt cgagctgggg cgaatcactt ccattttgcg     41100
     gacaaagaag aagtaagcga aggcgactga aaggaagctg taagtggccc acggcagagg     41160
     tccccagtgg aacaagctgt aagccagccc caactctttc gcccctgtcg agttcggttc     41220
     taagccaaac ggcggggtgg agatgtagta gtagatctca atcgatcccc agaacagtac     41280
     ggcagcagac gtacaggagg cgaacatcat aaagatccaa ctggcggtgc taaattctgg     41340
     cggttcgtta cctaaacgct ttttggcata cgggccaaac accagccaga accaaccgaa     41400
     aagcatcacc accatatacc attcaaatgc ccatccccat acattggtga cgtaactgaa     41460
     tacagcatta ataacgacat tcgctgcatc cagatctctg actgtaagcc aacaaagtat     41520
     gccgacgatt attaacggcg gaaagaaaac cttcggttct attcccgttt ttctcttttc     41580
     attcttcatg agttaattcc actgtgaaaa cgaatattta ttttgcgttc ccgtttgttt     41640
     tatttttgtt aacatttaat ataattatta ttaacctcgt ggacgcgtta atggctaact     41700
     cataatgggt attcaataag ctgtattctg tgattggtat cacatttttg tttcgggtga     41760
     atagagggcg ttttttcgtt aattttgatt aataatcagt ttgttatgct ctgttgtgag     41820
     taaaaaataa catctgactt tcaatattgg tgatccataa aacaatattg aaaatttctt     41880
     tttgctacgc cgtgttttca atattggtga ggaacttaac aatattgaaa gttggattta     41940
     tctgcgtgtg acattttcaa tattggtgat taaagtttta tttcaaaatt aaagggcgtg     42000
     atatctgtaa ttaacaccac cgatatgaac gacgtttcct tcatgatttc tggagatgca     42060
     atgaagatta ttacttgcta taagtgcgtg cctgatgaac aggatattgc ggtcaataat     42120
     gctgatggtt cattagactt cagcaaagcc gatgccaaaa taagccaata cgatctcaac     42180
     gctattgaag cggcttgcca gctaaagcaa caggcagcag aggcgcaggt gacagcctta     42240
     agtgtgggcg gtaaagccct gaccaacgcc aaagggcgta aagatgtgct atcgcgcgac     42300
     ccggatgaac tgattgtggt gattgatgac cagttcgagc aggcactgcc gcaacaaacg     42360
     gcgagcgcac tggctgcagc cgcccagaaa gcaggctttg atctgatcct ctgtggcgat     42420
     ggttcttccg acctttatgc ccagcaggtt ggtctgctgg tgggcgaaat cctcaatatt     42480
     ccggcagtta acggcgtcag caaaattatc tccctgacgg cagataccct caccgttgag     42540
     cgcgaactgg aagatgaaac cgaaacctta agcattccgc tgcctgcggt tgttgctgtt     42600
     tccactgata tcaactcccc acaaattcct tcgatgaaag ccattctcgg cgcggcgaaa     42660
     aagcccgtcc aggtatggtc ggcggcggat attggtttta acgcagaggc agcctggtca     42720
     gaacaacagg ttgccgcgcc gaaacagcgc gaacgtcagc gcatcgtgat tgaaggcgac     42780
     ggcgaagaac agatcgccgc atttgctgaa aatcttcgca aagtcattta accacagggg     42840
     atgctacgaa cacattttct caagtctggg tattcagcga taccccttct cgtctgccgg     42900
     aactgatgaa cggtgcgcag gctttagcta atcaaatcaa cacctttgtc ctcgatgatc     42960
     ggcgacggtg tacaggcaat ccagctcggc gctaatcatg tctggaaatt aaacggcaaa     43020
     ccggacgatc ggatgatcga agattacgcc ggtgtcatgg ctgacactat tcgccagcac     43080
     ggcgcagacg gcctggtgct gctgccaaac acccgtcgcg gcaaattact ggcggcaaaa     43140
     ctgggttatc gccttaaagc ggcggtgtct aacgatgcca gcaccgtcag cgtacaggac     43200
     ggtaaagcga cagtgaaaca catggtttac ggtggtctgg cgattggcga agaacgcatt     43260
     gccacgccgt atgcggtact gaccatcagc agcggcacgt tcgatgcggc tcagccagac     43320
     gcgtcacgca ctgtgaaacg cacaccgtgg agtggcaggc tccggctgtg gcgattaccc     43380
     gcacggcaac ccaggcgcgc cagagcaaca gcgtcgatct cgacaaagcc cgtctggtgg     43440
     tcagcgtcgg tcgcggtatt ggcagcaaag agaacattgc gctggcagaa cagctttgca     43500
     aggcgatagg tgcggagttg gcctgttctc gtccggtggc ggaaaacgaa aaatggatgg     43560
     agcacgaacg ctatgtcggt atctccaacc tgatgctgaa acctgaactg tacctggcgg     43620
     tggggatctc cgggcagatc cagcacatgg ttggcgctaa cgcgtcgcaa accattttcg     43680
     ccatcaataa agataaaaat gcgccgatct tccagtacgc ggattacggc attgttggcg     43740
     acgccgtgaa gatccttccg gcgctgaccg cagctttagc gcgttgatcc actctggcag     43800
     ggctgcattt tggccctgcc gctgacaggg agctcttatg tccgaagata tctttgacgc     43860
     catcatcgtc ggtgcagggc ttgctggttc ggttgccgca ctggtgctcg cccgcgaagg     43920
     tgcgcaagtg ttagttatcg agcgtggcaa ttccgcaggt gccaagaacg tcaccggcgg     43980
     gcgtctctat gcccacagtc tggaacacat tattcctggt ttcgccgact ccgcccccgt     44040
     agaacgcctg atcacccatg aaaaactcgc gtttatgacg gaaaagtcag cgatgactat     44100
     ggactactgc aatggtgacg aaacctcgcc atcccagcgt tcttactccg ttttgcgcag     44160
     taaatttgat gcctggctga tggagcaggc cgaagaagcg ggcgcgcagt taattaccgg     44220
     gatccgcgtc gataacctcg tacagcgcga tggcaaagtc gtcggtgtag aagccgatgg     44280
     cgatgtgatt gaagcgaaaa cggtgatcct tgctgatggg gtgaactcca tccttgccga     44340
     aaaattgggg atggcaaaac gcgtcaaacc gacggatgtg gcggttggcg tgaaggaact     44400
     gatcgagtta ccgaagtcgg ttattgaaga ccgttttcag ttgcagggta atcagggggc     44460
     ggcttgcctg tttgcgggat cacccaccga tggcctgatg ggcggcggct tcctttatac     44520
     caatgaaaac accctgtcgc tggggctggt ttgtggtttg catcatctgc atgacgcgaa     44580
     aaaatcggtg ccgcaaatgc tggaagattt caaacagcat ccggccgttg caccgctgat     44640
     cgcgggcggc aagctggtgg aatattccgc tcacataatg ccggaagcag gcatcaacat     44700
     gctgccggag ttggttggtg acggcgtatt gattgccggt gatgccgccg gaatgtgtat     44760
     gaacttcggt tttaccattc gcggtatgga tctggcgatt gccgccgggg aagccgcagc     44820
     aaaaaccgtg ctttcagcga tgaaaagcga cgatttcagt aagcaaaaac tggcggaata     44880
     tcgtcagcat cttgagagtg gtccgctgcg cgatatgcgt atgtaccaga aactaccggc     44940
     gttccttgat aacccacgca tgtttagcgg ctacccggag ctggcggtgg gtgtggcgcg     45000
     tgacctgttc accattgatg gcagcgcgcc ggaactgatg cgcaagaaaa tcctccgcca     45060
     cggcaagaaa gtgggcttca tcaatctaat caaggatggc atgaaaggag tgaccgtttt     45120
     atgacttctc ccgtcaatgt ggacgtcaaa ctgggcgtca ataaattcaa tgtcgatgaa     45180
     gagcatccgc acattgttgt gaaggccgat gctgataaac aggtgctgga gctgctggtg     45240
     aaagcgtgcc ccgcaggtct gtacaagaag caggatgacg gcagtgtgcg cttcgattac     45300
     gccggatgtc tggagtgcgg cacctgtcgc attctggggc tggggtcggc gctggaacag     45360
     tgggaatacc cgcgcggcac ctttggtgtg gagttccgtt acagctaatg ttgctttgat     45420
     acgtaacgcc gcactgactc tcattgcaaa aaacatgaat agctatgcaa ccgtccagaa     45480
     accttgacga tctcaaatgc ttgtcccact accgccgcat tttgctgtgg ggaagcggtg     45540
     gtccgtttct gtatggttat gtactggtaa tgattggcgt ggcgctggag caactgacgc     45600
     cggcgctgaa actggacgct gactggattg gcttgctggg cgcgggaacg ctcgccgggc     45660
     tgttcgttgg cacatcgctg tttggttata tttccgataa agtcggacgg cgcaaaatgt     45720
     tcctcattga tatcatcgcc atcggcgtga tatcggtggc gacgatgttt gtttcatccc     45780
     ccgtcgaact gttggtgatg cgggtattta tcggcattgt catcggtgca gattatccca     45840
     tcgccacctc aatgatcaac gagttctcca gtacccgtca gcgggcggtt ttccatcagc     45900
     tttattgccg cgatgtggta tgttggcgcg acctgtgccg atctggtcgg ctactggctt     45960
     tatgatgtgg aaggcggctg gcgctggatg ctgggtagcg cggcgatccc ctgtctgttg     46020
     attttgattg gtcagattcg aactgcctga atctccccgc tggttattat gcaaagggcg     46080
     agtaaaagag tgcgaggaga tgatgatcaa actgtttgga gaaccggtgg ctttcgatga     46140
     agagcagccg cagcaaaccc ggttttcgcg atctgtttaa tcgctgccat tttccttttg     46200
     ttctgtttgt tgccgccatc tggacctgcc aggtgatccc aatgttcgcc atttacacct     46260
     ttggcccgca aattgttggt ttgttgggat tgggggttgg caaaaacgcg gcactaggaa     46320
     atgtggtgat tagcctgttc tttatgctcg gctgtattcc gccgatgctg tggttaagca     46380
     ctgccggacg gcgtccattg ttgattggca gctttgccat gatgacgctg gcgctggcgg     46440
     ttttggggct aatcccggat atggggatct ggctggtagt gatggccttt gcggtgtatg     46500
     cctttttctc tggcgggccg ggtaatttgc agtggctcta tcctaatgaa ctcttcccga     46560
     cagatatccg cgcctctgcc gtgggcgtga ttatgtcctt aagtcgtatt ggcaccattg     46620
     tttcgacctg ggcactaccg atctttatcg ataattacgg tatcagtaac acgatgctaa     46680
     tgggggcggg tatctcgctg tttggcttgt tgatttccgt agcgtttgcc ccggagactc     46740
     gagggatgtc actggcgcag accagcaata tgacgatccg cgggcagaga atggggtaaa     46800
     ttgttcagat ttctctcttt tctgaatcaa tattattgac tataagccgc gtgaatatat     46860
     gactacactt tgtgggaaaa caaaggcgta atcacgcggg ctacctatga ttcttataat     46920
     ttatgcgcat ccgtatccgc atcattccca tgcgaataaa cggatgcttg aacaggcaag     46980
     gacgctggaa ggcgtcgaaa ttcgctctct ttatcaactc tatcctgact tcaatatcga     47040
     tattgccgcc gagcaggagg cgctgtctcg cgccgatctg atcgtctggc agcatccgat     47100
     gcagtggtac agcattcctc cgctcctcaa actttggatc aataaagttt tctcccacgg     47160
     ctgggcttac ggacatggcg gcacggcgct gcatggcaaa catttgctgt gggcggtgac     47220
     gaccggcggc ggggaaagcc attttgaaat tggtgcgcat ccgggctttg atggtctgtc     47280
     gcagccgcta caggcgacgg caatctactg cgggctgaac tggctgccac cgtttgccat     47340
     gcactgcacc tttatttgtg acgacgaaac cctcgaaggg caggcgcgtc actataagca     47400
     acgtctgctg gaatggcagg aggcccatca tggatagcca tacgctgatt caggcgctga     47460
     tttatctcgg ttcggcagcg ctgattgtac ccattgcggt acgtcttggt ctgggatcgg     47520
     tacttggcta cctgatcgcc ggctgcatta ttggcccgtg ggggctgcga ctggtgaccg     47580
     atgccgaatc tattctgcac tttgccgaga ttggggtggt gctgatgctg tttattatcg     47640
     gcctcgaact cgatccacaa aggctgtgga agctgcgtgc ggcagtgttc ggctgtggcg     47700
     cattgcagat ggtgatttgc ggcggcctgc tggggctgtt ctgcatgtta cttgggctgc     47760
     gctggcaggt cgcggaattg atcggcatga cgctggcgct ctcctctacg gcgattgcca     47820
     tgcaggcgat gaatgaacgc aatctgatgg tgacgcaaat gggtcgcagt gcctttgcgg     47880
     tgctgctgtt ccaggatatc gcggcgatcc cgctggtggc gatgattccg ctactggcaa     47940
     cgagcagtgc ctcgacgacg atgggcgcat ttgctctctc ggcgttaaaa gtggcgggtg     48000
     cgctggtgct ggtggtattg ctggggcgct atgtcacgcg tccggcgctg cgttttgtag     48060
     cccgctctgg cttgcgggaa gtgtttagtg ccgtggcgtt attcctcgtg tttggctttg     48120
     gtttgctgct ggaagaggtc ggcttgtcga tggcgatggg cgcgtttctg gcgggcgtac     48180
     tgctggcaag ctcggaatac cgtcatgcgc tggagagcga tatcgaacca tttaaaggtt     48240
     tgctgttggg gctgtttttc atcggtgttg gcatgtcgat agactttggc acgctgcttg     48300
     aaaacccatt gcgcattgtc attttgctgc tcggtttcct catcatcaaa atcgccatgc     48360
     tgtggctgat tgcccgaccg ttgcaagtgc caaataaaca gcgtcgttgg tttgcggtgt     48420
     tgttagggca gggcagtgag tttgcctttg tggtatttgg cgcggcgcag atggcgaatg     48480
     tgctggagcc ggagtgggcg aaatcgctga ccctggcggt ggcgctgtcg atggcagcaa     48540
     cgccgattct gctggtgatc ctcaatcgcc ttgagcaatc ttctactgag gaagcgcgtg     48600
     aagccgatga gatcgacgaa gaacagccgc gcgtgattat cgccggattc ggtcgttttg     48660
     ggcagattac cggacgttta ctgctctcca gcggggtgaa aatggtggta ctcgatcacg     48720
     atccggacca tatcgaaacc ttgcgtaaat ttggtatgaa agtgttttat ggcgatgcca     48780
     cgcggatgga tttactggaa tctgccggag cggcgaaagc ggaagtgctg attaacgcca     48840
     tcgacgatcc gcaaaccaac ctgcaactga cagagatggt gaaagaacat ttcccgcatt     48900
     tgcagattat tgcccgcgcc cgcgatgtcg accactacat tcgtttgcgt caggcaggcg     48960
     ttgaaaagcc ggagcgtgaa accttcgaag gtgcgctgaa aaccgggcgt ctggcactgg     49020
     aaagtttagg tctggggccg tatgaagcgc gagaacgtgc cgatgtgttc cgccgcttta     49080
     atattcagat ggtggaagag atggcaatgg ttgagaacga caccaaagcc cgcgcggcgg     49140
     tctataaacg caccagcgcg atgttaagtg agatcattac cgaggaccgc gaacatctgt     49200
     cattaattca acgacatggc tggcagggaa ccgaagaagg taaacatacc ggcaacatgg     49260
     cggatgaacc ggaaacgaaa ccctcatcct aataaagagt gacgtaaatc acacttacag     49320
     ctaactgttt gttttgtttc attgtaatgc ggcgagtcca gggagagagc gtggactcgc     49380
     cagcagaata taaaattttc ctcaacatca tcctcgcacc agtcgacgac ggtttacgct     49440
     ttacgtatag tggcgacaat tttttttatc gggaaatctc aatgatcagt ctgattgcgg     49500
     cgttagcggt agatcgcgtt atcggcatgg aaaacgccat gccgtggaac ctgcctgccg     49560
     atctcgcctg gtttaaacgc aacaccttaa ataaacccgt gattatgggc cgccatacct     49620
     gggaatcaat cggtcgtccg ttgccaggac gcaaaaatat tatcctcagc agtcaaccgg     49680
     gtacggacga tcgcgtaacg tgggtgaagt cggtggatga agccatcgcg gcgtgtggtg     49740
     acgtaccaga aatcatggtg attggcggcg gtcgcgttta tgaacagttc ttgccaaaag     49800
     cgcaaaaact gtatctgacg catatcgacg cagaagtgga aggcgacacc catttcccgg     49860
     attacgagcc ggatgactgg gaatcggtat tcagcgaatt ccacgatgct gatgcgcaga     49920
     actctcacag ctattgcttt gagattctgg agcggcggta attttgtata gaatttacgg     49980
     ctagcgccgg atgcgacgcc ggtcgcgtct tatccggcct tcctatatca ggctgtgttt     50040
     aagacgccgc cgcttcggcc aaatccttat gccggttcga cggctggaca aaatactgtt     50100
     tatcttccca gcgcaggcag gttaatgtac caccccagca gcagccggta tccagcgcgt     50160
     atataccttc cggcgtacct ttgccctcca gcgatgccca gtgaccaaag gcgatgctgt     50220
     attcttcagc gacagggcca ggaatcgcaa accacggttt cagtggggca ggggcctctt     50280
     ccggcgattc tttgctgtac atatccagtt gaccgttcgg gaagcaaaaa cgcatacggg     50340
     taaaagcgtt ggtgataaaa cgcagtcttc ccagcccccg caattccggt gaccagttat     50400
     ttggcatatc gccgtacatg gcatcaagaa agaagggata ggagtcactc gatagcaccg     50460
     cttctacatc gcgtgcgcac tctttggcgg tctgcagatc ccactgcggc gtgatccctg     50520
     cgtgggccat caccagcttt ttctcttcgt cgatttgcag cagaggctgg cgccgcagcc     50580
     agttaagcag ctcgtcggca tccggcgctt ccagcagcgg tgtcaggcga tctaacggtt     50640
     tattgcggct gatcccggca aataccgcca gcagatgcag atcgtgattg cccagcacca     50700
     gacgtacgct gtcgcctaag gatttcacat agcgcagaac atccagcgaa cccggcccgc     50760
     gcgcgaccag atcgcccgtc agccagaggg tatctttccc aggggtaaat tctactttat     50820
     gcagcaatgc gatcagttca tcgtaacaac catgaacgtc gccaataagg tatgtcgcca     50880
     tattctttta atgaatgagt gtgggaacgg cgagtcggaa tacgggaatg tcgatgctga     50940
     aagggacgcc attttcatcg atcatttcgt agtgaccctg catggtgccc agcggggttt     51000
     caatgattgc accgctggtg tactggtact cttcgccagg cgcgataagt ggctggacgc     51060
     caaccactcc ttcgccctgg acttcggttt cacggccatt gccattggtg atcagccagt     51120
     aacgccccaa caactgcact ggcgctcgcc ccagattgcg tatggttacg gtataagcaa     51180
     aaacgtaacg ttcattatca ggtgaagatt gagcctcaat gtagacgctt tgaacctgaa     51240
     tacacactcg gggcgaattg atcatcgtta actctcctgc aaaggcgcgt tctccgccca     51300
     gatagttcgc catctggcaa tattgcgcga cagagatatt ttccgctcgc atcgccgggt     51360
     cgatccccat tcccgttaac acctcgacgc taaacaggtt gccgaggctg ttacgaatgg     51420
     ttttacgacg ctggttaaag gcttcggtgg tgatgcggct caacacacga acatctttaa     51480
     ccgggtgagg catcgttgca tgaggaacca ggcgcacgac ggcggaatcc actttgggtg     51540
     gtggtgtaaa ggctgacggc ggtacttcca gtaccgggat cacattgcaa tagtattgcg     51600
     ccatgacgct taatcgacca tacgctttgc tgttcggtcc tgcaaccaga cgattcacca     51660
     cctctttttg caacataaag tgcatgtcgg caatggcatc agtatagcta aacagatgga     51720
     acatcaacgg cgtggagatg ttataaggca ggttgccgaa aacacgcagc ggctgaccca     51780
     ttttctcggc cagttcacca aagttaaagg tcatcgcatc ctgctgataa atcgtcagtt     51840
     tcgggcctaa gaatggatgc gtttgcagac gtgccgccag atcgcggtca agttcgatga     51900
     ccgtcagctg gtccagacgt tcgccgaccg gttcggtcaa tgccgccaga ccggggccga     51960
     tttcgaccat cgcctggccc ttttgcgggt taatggcaga cacaatactg tcgatcacga     52020
     actgatcgtt gagaaagttt tgcccgaagc gtttacgggc taagtggccc tggtggactc     52080
     gattattcat tgggtgttaa caatcatttt gatggcgaga ttaagcgccg taataaaact     52140
     gccgacatcg gctttgccac gtcccgccag ttcaagcgcg gtgccgtggt ccactgatgt     52200
     gcgaataaag ggcaggccca gcgtaatgtt cacaccgcgc ccgaagccct ggtattttag     52260
     cacgggaaga ccctgatcgt ggtacatcgc cagcacggcg tcggcgttat caagatattt     52320
     cggctgaaac agggtatcgg caggcagcgg cccgttgagt ttcatcccct gcgcccgcag     52380
     ctcattgagc accggaataa tggtgtctat ctcttccgta cccatatgac cgccttcgcc     52440
     cgcgtgcgga ttcagcccgc agaccagaat gcgcggttcg gcaataccaa atttggtccg     52500
     caaatcgtga tgcaaaatag caatcacttc gtgcaaaagt gcaggggtga tagcgtctgc     52560
     gatatcgcgc agcggtaaat gcgtcgttgc cagcgccacg cgaagttctt cggtcgccag     52620
     catcatcacc acctttttcg cctgcgaacg ctcttcgaaa aactcggtat gaccggtaaa     52680
     aggaatgcca gcgtcgttaa taacgccttt atgcaccgga cctgtgatca gcgcggcaaa     52740
     ttcgccgttc agacaaccat cgcacgctcg cgccagcgtt tccaccacat aatgcccatt     52800
     ttcaaccgct aactgccccg cagtgacagg tgcacgtagc gcgacaggaa gtagcgttaa     52860
     tgtgcccgca gtttgcggtt gtgcagggga gttgggggaa taagggcgga gggtgagcgg     52920
     caaaccgagc atcgctgccc ggttggtaag gagagtggca tcggcacaaa caaccagttc     52980
     gaccggccac tcacgctgtg caagctggac aactaagtcc gggccaatcc cggcgggctc     53040
     gccgggagtg atcacaacac gttgggtttt aaccattagt tgctcaggat tttaacgtag     53100
     gcgctggcac gttgttcctg catccagctt gctgcttctt ccgagaactt acggttcatc     53160
     agcatgcggt atgcacgatc tttctgcgca gcgtcggttt tatcgacatt acgggtatcc     53220
     agcagttcga ttaaatgcca gccgaatgaa gagtgaaccg gtgcactcat ttgacctttg     53280
     ttcaggcgag tcagggcgtc acggaaggcc ggatcgaaaa tatctggtgt agcccagccg     53340
     agatcgccgc cctggttagc agagcctgga tcctgagaga actctttcgc tgcggcagca     53400
     aaagtcgttt taccactctt gatatcagca gcaatctgtt ccagtttcac acgggcctgt     53460
     tcgtcagtca tgatcggcga cggtttcagc agaatatggc gagcatgaac ttcggtcacc     53520
     gagatatttt tgctttcgcc gcgcaggtcg ttaactttca gaatatggaa gccaacgccg     53580
     gaacgaatcg ggccaacaat gtcgcctttc ttcgcggtgc ttaatgcctg ggcgaagatc     53640
     ccgggcaact cctgaatacg gccccagccc atctggccgc cgttcagcgc ctgctggtcg     53700
     gcagaatgag caatcgccag cttaccgaaa tcagcgccgt tacgcgcctg atcgacaatg     53760
     gcgcgcgcct ggctttccgc ttcgttcacc tgatcagagg tcgggttttc cggcagcggg     53820
     atcaggatgt ggctcaggtt cagctcagtg ctggcgtcgt tttggttacc cacctgctgc     53880
     gccagggatt cgacttctgc ggcaggatgg tgatgcgacg acgcacctcg ttgttacgca     53940
     cttcagagat aatcatctct ttgcggatct ggttacgata ggtgttgtag ttcagtccat     54000
     cgtaagccag acggctgcgc atctgatcca gcgtcatgtt gttctgtttc gcgatgttag     54060
     caatcgcctg atccagctgc tcatcggaga ttttcactcc cattttctgc cccatctgca     54120
     ggatgatttg atccatgatc aaacgttcca tgatttggtg gcgcagcgtc gcgtcatcag     54180
     gaagttgctg ccttgcctga gcagcgttca gttttaccga ctgcattaat ccatcaacgt     54240
     cgctttccag cacgacgccg ttattgacga cggctgcgac tttatcgact acctgggggg     54300
     cagcgaaact ggtattcgcg atcatggcga taccgagaag cagcgttttc cagttcttca     54360
     tactttttcc atttcaatta accgcactgc ggattacgtg gtaaatcaac aaatcacaaa     54420
     gtgttttgat acggcagaat gttcgaacgc agcatctctt gcgtacccag accgtagttg     54480
     gagctcaggc cgcgaagttc gatgttaaag ccgattgcgt tgtcatatac cgcatgttgt     54540
     ttatcgttat cccaaccgtt cagcttccgc tcgtaaccga cgcgaattgc atagcagcag     54600
     gagctgtatt gcacacctaa catagagtcg gcttgcttgt tagcattggt gtcgtagtag     54660
     taggccccaa caatggacca acgatcggca attggccagc tggcgacagc acctacctgc     54720
     gaaataccat tcttatattg ctcagcagtg gaatagtact taggcagcgt agcctgaata     54780
     tattccgggc tggcgtaacg gtaattcagc tgtaccagac ggtcttcatc ccgacggtat     54840
     tcaatgctgg agttactggt cgctacgtta tccagacgtg tatcgtactg aatcccgcca     54900
     cgcaatcccc aacgctcgga gatacgccag taagtatcgc ctgcccacac cagtgaaccc     54960
     gttttgtcgt cattctccca tgttatgttg tcatcgccag tgcgagactc cgtgaaatag     55020
     tagatttgac caacggaaat attaaaacgt tcaacggcag catcatcata tatgcgagat     55080
     gtgacaccgg tcgtcacctg gttagcggag gcaatacggt caagaccgcc gtaagtccgg     55140
     tcccggaaca ggccagagta gtcagattgc agcagagacg agtcgtagtt atagatgtcg     55200
     ctctgatcgc gatacggcac gtacaaatac tgcgcgcgcg gttccagcgt ttgggtataa     55260
     cccggagcca gcatttccat atcgcgttca aagaccattt tgccgtcaac tttgaattgc     55320
     ggcattacgc ggttaacgga ttcgtccagc ttggtcgtgt ttctggagtt ataccagtca     55380
     agattggttt gctgataatg ggttgccagc aacttcgctt cggtattgat gctgccccag     55440
     ttattagaga gcggcaaatt gatggtcggt tccaggtgaa cacgggttgc ttcaggcatg     55500
     tcgtctctgg tgttaacaaa gtgcactgcc tggccgtaaa tacgcgtatc aaacggacca     55560
     acatcattct ggtagtaatt aacgtctaac tgcggctctg ccgagtagct actggtgttc     55620
     tgttcgctga aaacctggaa ctgcttggtt gaaacggtgg cattgaagtt ttgcaccgca     55680
     tagccaacgc tgaatttttg cgttgcgtag ccgtcagtac tggaaccgta cttgttatcg     55740
     aaatcattga agtagctagg atcgctgacc ttggtgtagt cgacgttgaa acgccacacc     55800
     tgatccatga ccccggagtg gttccagtag aataaccaac gacgtgaact gtcatcgttc     55860
     gggtgttcat cttcatagac tttatctgaa ggcagatagt ccagttccat caagccagcg     55920
     cccgcctggg agaggtagcg gaattcgttc tcccacatga tgttgccacg acgatgcata     55980
     taatgcggcg tgatggtggc atccatattt ggcgcgatgt tccagtaata tggcaggtag     56040
     aactcaaagt agttggtggt ggtgtacttg gcgttcggga tcaagaaacc agagcgacgt     56100
     ttgtcaccca ccggcaactg caaatagggg ctataaaaga tcggtaccgg acccacctta     56160
     aagcgggcgt tccagatctc cgcaacttgt tcttcgcggt catgaataat ttcgctacct     56220
     accacgctcc aggtgtcaga acccggcaga caggaggtaa agctaccgtt atccagaatg     56280
     gtatagcggt tttcgccacg ttgtttcatc aggtccgctt taccgcgacc ctggcgaccc     56340
     accatctggt aatcaccttc ccagacgttg gtatctttgg tgttcagatt cgcccagcct     56400
     ttcggccctt tgaggatcac ctggttatcg tcgtaatgga cattaccgag cgcatcaacg     56460
     gtacgtaccg gctccggttg tcctggtgcc tctttttgat ggagctgcac ttcgtcggcc     56520
     tgcagacggc tgttaccctg catgatatcc acgctgccag taaacacggc gtcatccggg     56580
     tagtcccctt tcgcgtggtc agcattgata gtcacgggta agtcattggt atcgccctgt     56640
     accagaggac ggtcatagct tggcacgccc aacatgcact gtgaggcgag gtcggctgcc     56700
     agtccctgtt gactataaag ggcggtggca atcatggtgg ccaggagagt ggggatacgt     56760
     tttttcatac gttgatttta ttgttccatc atcggtaacg ttgcgcgtga caaacggtca     56820
     gagactaacg tactcgtcat ctctacgcta gtgttaatcc tgtccgaata gcgtcagtgg     56880
     tgttaggcac ggcattgaat gacaggtatg ataatgcaaa ttataggcga tgtcccacaa     56940
     ttgaccgcag ccggaaaacg gtaaaagcac ctttatattg tgggagatag ccctgatatc     57000
     cgtgtgtcga tttggggaat atatgcagta ttggggaaaa atcattggcg tggccgtggc     57060
     cttactgatg ggcggcggct tttggggcgt agtgttaggc ctgttaattg gccatatgtt     57120
     tgataaagcc cgtagccgta aaatggcgtg gttcgccaac cagcgtgagc gtcaggcgct     57180
     gttttttgcc accacttttg aagtgatggg gcatttaacc aaatccaaag gtcgcgtcac     57240
     ggaggctgat attcatatcg ccagccagtt gatggaccga atgaatcttc atggcgcttc     57300
     ccgtactgcg gcgcaaaatg cgttccgggt gggaaaatca gacaattacc cgctgcgcga     57360
     aaagatgcgc cagtttcgca gtgtctgctt tggtcgtttt gacttaattc gtatgtttct     57420
     ggagatccag attcaggcgg cgtttgctga tggttcactg cacccgaatg aacgggcggt     57480
     gctgtatgtc attgcagaag aattagggat ctcccgcgct cagtttgacc agtttttgcg     57540
     catgatgcag ggcggtgcac agtttggcgg cggttatcag cagcaaactg gcggtggtaa     57600
     ctggcagcaa gcgcagcgtg gcccaacgct ggaagatgcc tgtaatgtgc tgggcgtgaa     57660
     gccgacggat gatgcgacca ccatcaaacg tgcctaccgt aagctgatga gtgaacacca     57720
     tcccgataag ctggtggcga aaggtttgcc gcctgagatg atggagatgg cgaagcagaa     57780
     agcgcaggaa attcagcagg catatgagct gataaagcag cagaaagggt ttaaatgacc     57840
     ctgtaaatga tgctgagtaa ctgcccacga ttaaaggtgg ccgccctggc ggtcacttct     57900
     ttgagaaaag gcgtttactc agaatggtgg acaggctcaa tgcacggttt acgggagggg     57960
     ttctgtaggt tttatcgcgt tgaccctgct taaggttgag agctttacga cgagcggaat     58020
     tatattttta cgtcttaaaa ataaaaaaca catacctgaa tgagcgattt ttgaaagtat     58080
     atttattcag aacgcgcatc atgagttttt aactcaatgc gaggctatta ccatgaaagt     58140
     atcagttcca ggcatgccgg ttacactttt aaatatgagc aagaacgata tttataagat     58200
     ggtgagcggg gacaagatgg acgtgaagat gaatatcttt caacgcttgt gggagacgtt     58260
     acgccatctg ttctggtcag ataaacagac tgaggcttat aaacttctgt tcaatttcgt     58320
     gaataaccag actggcaaca tcaacgcctc agaatacttt actggggcta tcaacgagaa     58380
     tgagagagaa aagtttatca atagcctgga attattcaat aaacttaaaa catgcgcaaa     58440
     aaatccggat gagttggtcg caaagggcaa tatgcgctgg gtcgcccaga ccttcgggga     58500
     tatcgagtta agtgtcactt ttttcattga aaagaataag atatgtactc agacgttgca     58560
     gctgcataag ggccaaggta acttgggcgt tgatcttaga aaggcttacc ttcccggcgt     58620
     tgacatgagg gattgttacc ttggtaaaaa aacaatgaaa ggtagcaatg atatccttta     58680
     tgagagacct gggtggaatg ctaacctggg cgtgctaccc cggacggtgc taccccggac     58740
     ggtgctaacc cggacggtgc taacctggac ggtgctaccg tgaacggtgc tacctcctta     58800
     tatgatgagg taattattat taataaaatc ccccccaaaa aaattgatac taaaggagtt     58860
     gctactgaag aagttgctac taaaaaagta ctgctgaaca aattactgac aacgcaatta     58920
     ttgaatgagc cagaataagc taaggttgaa ggggctggaa cgccccttca accttagcag     58980
     tagcgtggga tgatttcaca attagaaaga cctgcatgat gagctagaga agaggctagt     59040
     gacgcaaggc gtcgtgcagg acacggatca ccgagatggg catcgccaac cagactgcta     59100
     attagcccat gaataacaat cagaaaggac cataacagac ccgttaaaat gaaatataag     59160
     agacggtcaa cgggtgaaga aaaagttcaa aaattcgctg tggagcagga agggaattac     59220
     cgaatggaaa gcgtagccac acgcaacaac tgaaagcagt ttggcagaaa caaaaaatcc     59280
     ccggactcgg ggatttatgt acaagaggca gcccttagga tgagggtata aacgtacagg     59340
     aaaggttaaa aatccgctgg cgctttaaac gtcatactat tgccatacgc cggatgggta     59400
     atcgtcaaca tctctgcatg tagcaacaaa cgtggtgcca tcgctctcgc ttctggtgat     59460
     gcataaaaac gatcgccgag aatcggatga cccagcgcca gcatatgcac acgcaattga     59520
     tgcgaacgcc cggtaatcgg ttttaacacc actcttgccg tgttatccgc cgcatactcc     59580
     accacttcat attccgtctg cgccaggttt acccgttttc gtaacagcac tttctgtttc     59640
     gggcggtttg gccagtcgca aatcagcggc agatccacca gaccttctgc gggggatgga     59700
     tgcccccaga cgcgggccac atactgcttt ttcggctcgc gctcgcgaga actggcgttt     59760
     taactcccgc tccgcggctt tggtcagcgc cactacaatc acgccgctgg tagccatatc     59820
     cagacgatgc accgattctg cctgcggata atcacgctga atgcgcgtca tcacgctgtc     59880
     tttgtgctct tccagacgac ccggcactga caacaaaccg ctcggcttgt tgaccaccat     59940
     aatatggtca tcctgataca ggataaccaa ccagggttcc tgcggtggat tgtagttttc     60000
     catccccatt ttcggctccg ttactgatgc gttacaacga tcaaacgcag ggcatccaga     60060
     cgccaacctg cctgatccag gctttccatt acctgctgac ggttgctctc aatggcggtc     60120
     agttcgtcgt cacgaatgtt cgggttcact gcacgcagag cttccagacg agacagctcg     60180
     gcagacagtt tttcgtcggc ttcgttacgc gctgcatcaa tcaatgcacg ggcagatttc     60240
     tcgatctgcg cttcacccag ttgaaggata gcgtgaacat cctgctgcac ggcgttaacc     60300
     agtttgctgc cggtgtgacg gttaaccgcg ttaagctggc ggttaaaggt ttcaaactct     60360
     acctgcgccg ccaggttgtt gccgttttta tccagcagca tacgtaccgg cgtcggtggc     60420
     aggaagcggt tgagctgcaa ctgcttcgga gcctgggctt caaccacata aatcagttcc     60480
     accaacagcg tacctaccgg caacgctttg ttttttaaca gtgaaatcgt gctgctaccg     60540
     gtatcgccag aaaggatcag atccagaccg ttgcggatca gcggatgctc ccaggtaata     60600
     aactgtgcat cttcacgcgc cagcgccact tcacgatcaa aggtgatggt gatgccatct     60660
     tccgacaggc cagggaagtc cggcaccagc atatgatcgg acggcgtcag cacgatcatg     60720
     ttgtcgccgc gatcgtcctg attgataccg ataatatcga acaggttcat ggcgaaggcg     60780
     atcaggttgg tatcgtcatc ctgctcttca atgctttctg ccagtgcctg ggctttttcg     60840
     ccaccgttgg agtggatttc cagcaggcgg tcacgaccct gttccagctg tgctttcagc     60900
     gcttcatgtt gctcgcggca gtttttgatc agatcgtcaa agccttcggt ttgatccggt     60960
     gaagccagat agttaatcag atcgttgtat acgctatcgt aaatagtgcg tccggtcggg     61020
     caggtgtgct caaatgcatc cagaccttcg tgataccagc gcaccagcac cgactgagcg     61080
     gttttctcca gataaggcac atggatctga atatcgtgcg cctggccgat acgatccaga     61140
     cgaccaatac gctgctccag tagatccggg ttgaatggca ggtcaaacat caccatgtgg     61200
     ctggcgaact ggaagttacg tccttcagaa ccgatttctg agcacagcag tacctgtgcg     61260
     ccggtgtctt cttcggcaaa ccaggcggca gcgcggtcac gttcgataat cgacatacct     61320
     tcgtggaaca ccgcagcgcg aataccttca cgttcgcgca gtacctgctc cagttgcagc     61380
     gcagtggcag ctttggcgca gatcaccagc actttctgag agcgatggct ggtcaggtag     61440
     cccatcagcc actcaacgcg cggatcgaag ttccaccagg tggcgttatc accttcaaat     61500
     tcctgataaa tacgctccgg gtagagcata tcgcgagcac gatcttccgc acttttacgt     61560
     gcgcccataa tgccggagac tttaatagcc gtctgatact gcgtcggtag cggcagctta     61620
     atggtgtgca gctcgcgttt cgggaatcct ttcacaccgt tacgcgtgtt acggaacagc     61680
     acgcggctgg tgccgtggcg atccatcagc atcgaaacca gctcctgacg ggcgctctgg     61740
     gcatcttcgc tgtcgctgtt tgctgcctgc aacagcggct cgatatcctg ctcgccgatc     61800
     atctcgccga gcatgttcag ttcgtcattg ctcagtttgt tacctgccag cagcatggca     61860
     acggcgtccg caaccggacg ataatttttc tgctcttcaa cgaactgcgc aaaatcgtgg     61920
     aaacggttcg ggtccagcag acgcagacgg gcgaagtggc tttccatccc cagctgttcc     61980
     ggggtcgcgg tcagcagcag aacgcccggc acgtgctctg ccagttgttc aatggcctga     62040
     tattcacggc ttggcgcatc ttcgctccac accaggtgat gcgcttcatc gaccaccagc     62100
     aggtcccatt cggcttcaca gagatgttcc aggcgctgtt tgctacgacg ggcaaaatcc     62160
     agcgagcaaa tcaccagctg ttcggtgtca aacgggttgt aagcatcgtg ctgagcttcg     62220
     gcataacgct catcatcaaa tagcgcaaag cgcaggttga aacggcgcag catttctacc     62280
     agccactgat gctgtaaggt ttccgggacg ataattagca cacgttcagc agcgccagag     62340
     agcagttgct gatgcaggat catcccggct tcaatggttt tccctaaacc cacttcgtca     62400
     gccagcagga cgcgcggcgc gtggcggcga ccaacatcat gagcgatgtt gagctgatgc     62460
     gggatcaggc tggtacgctg accgcgcagg ccgctgtacg gcatacggaa ctgttcgctg     62520
     gaatatttac gcgcgcgata acgcagcgca aagcggtcca tacggtcaat ctgcccggca     62580
     aacagacggt cctgcggttt gctgaacacc agtttgctat caaggaaaac ttcacgcagg     62640
     gctacgccgg actcttcagt atccaggcga gtaccgatat aggtcagcaa gccattttct     62700
     tcttttactt cttcgacttg catctgccag ccgtcatggc tggtaatggt atcaccaggg     62760
     ttgaacatca cgcgggtcac gggggaatca ctgcgtgcgt acagacggtt ttcaccagta     62820
     gatgggaaaa gtaaagtgac agttcgcgca tccaccgcga caacggttcc aagtcccaat     62880
     tcgctttctg tatcgctgat ccagcgttga ccaagtgtaa aaggcatatg tgttcggctc     62940
     tatatcttta attgcaggca ataaccaccc gctaccgtgc ttatgaggta gtggtgttat     63000
     tcaggtccag gaatggaaag ggcgctatgg tactggatgg caaagcattc gtcacgcatc     63060
     aaaatggtat ctggcgaact cttttttttg ctcaaaatag cccaagttgc ccggtcataa     63120
     gtgtagcaaa attatcctca ataaaaggga gtattccctc cgccacgggt tgtagctggc     63180
     gggtcagata gtgttcgtaa tccagtggtg aacgttggta gtccagcggc tccgggccgt     63240
     tggtggtcca tacgtactta atggtgccgc gattctgata ttgcaagggg cgaccacgct     63300
     tttggttttc ttcatcggca aggcgagcgg cgcgtacatg aggcggcaca ttacgctgat     63360
     actcgctcag cggacggcga aggcgtttac ggtaaaccag tcgcgcatcc agttcacccg     63420
     ccatcagttt gtcgatggtt tcgcgtacat attcctgata tggctcgttg cggaagatgc     63480
     gcaggtatag ctcctgctga aactgctggg ccagcggcgt ccagtcggtg cgcacggttt     63540
     ccagcccttt aaacaccatc cgctgcttgt cgccctcctg aatcagtccg gcataacgct     63600
     ttttactgcc ggtatcggct ccgcgaatgg ttggcatcag aaaacggcag aaatgggttt     63660
     catactccag ttctaatgcg ctggtcagcc gttgtttttg cagcgtttcc gcccaccagg     63720
     cgttaacgtg ctgcaccagt gcacgaccga ttttcgccgc ttcttcttcc gaatgtgcgc     63780
     ctttcagcca gacaaacgtt gagtcggtat cgccgtagat aacgtcgtag ccctgtgctt     63840
     caatcaacgc tttggtttgc cgcatgatct gatgaccacg catggtgatc gacgatgcca     63900
     gccgcggatc gaagaagcgg caggcggtgg tgccgagcac gccataaaag gcattcatga     63960
     tgattttcag cgcctgcgac agcggtttgt taccctggcg tttggcttca tcgcgcccgt     64020
     gccagatgtt agtcacaatc tccggcaggc aatgtttttc tcgcgagaac caggcatcga     64080
     gaaaaccttc ggtactgtgc tctggatcag gctgcgccat gccttccacc agcccgacgg     64140
     gatcaatcag aaaggtgcgg atgatcgacg ggtacaggct tttatagtcc agcaccagca     64200
     ctgaatcata aagccctggc cgtgaatcca tcacgtagcc gccagggctg gcgtgcggcg     64260
     gcacttcgcc gagattaggc gcgacataac cagcgcgatg cattcgcgga aaatagagat     64320
     gaccaaatgc cgccaccgaa ccgccgtgtc ggtccaccgg caggccgttc accgttgccc     64380
     gttcgagtaa aaatggcatg atttcagttt tgtggaagat ctgcgtcacc agctcgcaat     64440
     ctttcaggtt ataagttgcc agcgcaggtt tatcttcggc gaaacggcgg tcaatttcgt     64500
     ccattcgatc ccacgggtta tcgatagatt ttccttcgcc taatagctcc tgagcgacag     64560
     tttccagcga gaatgaagag aaatcccaga acgcggattt cagcgcctcg ataccgtcga     64620
     taattagccg acctttagcc tggggcaaaa aagacgccgt ttttgcgggg ccgtgctcgc     64680
     gccactccag ctcgctatta tcgcgcccaa gacgcagcgg aagacggtaa cggctcggca     64740
     tgtttttgca gcattcgcag atcgaactgc accacgttcc aaccgatgat cacatcagga     64800
     tcgtagttgg caaaccaggc gttgagtttt tccagcaact gcgggcggct ggcgacgtat     64860
     tccagttcga aatcaagcga ggaggcgtcg ccattctccg gccccagcat ataaacgatg     64920
     cgctgcccgc agccttccag gccgatgcag tacagctcac cgtggcgggt ggtttcaata     64980
     tctatagaaa cccacttgag cggcggacga tagtcgggat gcggtttcag acgggcatta     65040
     acgatagtgc cattgtgcat atcaccctcg acccacaccg gtgaggtgat aaaccgctcc     65100
     atcagatagc gttctggcgg acgcacatcg gcctcgtaga cggtaacgcc accttcacgc     65160
     aggcgctttt cgtaattcat caattggcga tgggcgcgac agtaaaggcc atacaccggc     65220
     tggcggtgaa aatcctttaa cgccagcggt gtcaggcgaa agccttgttc accctgcaaa     65280
     atatgctgag cgcggggaac ctgatcggcg ggaataaacg ccacggactc ttgcggtgca     65340
     agcgtaacct gcaacggccc gttgtccgtc gccagccaga aggagacttc tgtcccttgc     65400
     ggggtgtccc gccagtgtcg ggttaagata aaacctgcct gcgccacgct gaaaatccat     65460
     caaaaaacca ggcttgagta tagcctggtt tcgtttgatt ggctgtggtt ttatacagtc     65520
     attactgccc gtaatatgcc ttcgcgccat gcttacgcag atagtgttta tccagcagcg     65580
     tttgctgcat atccggtaac tgcggcgcta actgacggca gaatatcccc atataagcga     65640
     cctcttccag cacgatggcg ttatgcaccg catcttcggc atttttgccc catgcaaacg     65700
     ggccgtggga atggaccaga acgccgggca tttgcgctgc atcgataccc tgtttttcaa     65760
     aggtttctac gatgacgtta ccggtttccc actcatattc gccgttgatt tctgcgtcgg     65820
     tcattttgcg ggtgcaggga atggtgccgt agaaatagtc ggcgtgggtg gtgccggttg     65880
     ctggaatcga ctgacccgcc tgcgcccaga tggtggcgtg gcgcgagtgc gtatgcacaa     65940
     tgccgccaat ggaggggaat gcctgataga gcagccggtg agttggcgtg tcggaggagg     66000
     gctttttcgt accttcaacc acttcaccgg tttcgatgct aaccacgacc atatcgtcag     66060
     cggtcatgac gctgtaatcg acgccggaag gtttgatcac aaagacgccg cgctcgcgat     66120
     caacggcgct gacgttgccc catgtgagcg tgaccaggtt gtgttttggc agcgccaggt     66180
     tggcttctaa tacctggcgt ttgagatctt ctaacatgtt gactccttcg tgccggatgc     66240
     gctttgctta tccggcctac aaaatcgcag cgtgtaggcc tgataagacg cgccagcgtc     66300
     gcatcaggcg ttgaatgccg gatgcgcttt gcttatccgg cctacaaaat cgcagcgcgt     66360
     aggcctgata agacgcgcca gcgtcgcatc aggcgttgaa tgccggatgc gctttgctta     66420
     tccggcctac aaaatcgcag cgtgtaggcc agataagacg cgtcagcgtc gcatcaggcg     66480
     ttacataccg gatgcggcta cttagcgacg aaacccgtaa tacacttcgt tccagcgcag     66540
     cgcgtcttta aacgctggca ggcgtgtgtc gttatcaatc accgtgattt caatgtcgtg     66600
     catctcggcg aattggcgca tatcgttgag gttcagtgca tggctgaaga cggtatggtg     66660
     cgcgccacca gcgaggatcc acgcttcgga agcagttggc agatccggtt gcgctttcca     66720
     cagcgcattc gccaccggca gtttcggcag ggagtgcggt gttttcaccg tgtcgataca     66780
     gttaaccagc agacggtaac gatcgccgag atcaatcagg ctggcgacaa tcgctggacc     66840
     ggtttgggta ttgaagatca gtcgggcagg atcgtcctta ccaccaatac cgagatgctg     66900
     aacgtcgagg atcggtttct cttctacggc aatcgacggg cagacttcca gcatatggga     66960
     gccgagcacc aagtcattac ctttctcgaa gtgataggtg tagtcctcca taaaggaggt     67020
     gccgccctgc agaccggttg acatcacctt catgatgcga agcagggcgg cggttttcca     67080
     gtcgccttcg cccgcaaagc cgtaaccctg ctgcatcaga cgctgtacgg ccagacctgg     67140
     aagctgtttc agaccgtgca aatcttcaaa ggtggtggtg aacgcgtgga agccaccttg     67200
     ttccaggaaa cgcttcatcc ccagctcaat acgcgccgct tccagcacgt tctgtcgttt     67260
     ttcgccgtgg atttgtgttg caggcgtcat ggtgtagcag ctttcgtact catcgaccag     67320
     cgcgttaaca tcgccgtcgc tgatggagtt caccacctgc accagatcgc caaccgccca     67380
     ggtattgacg gagaaaccga acttgatctg tgcggcaact ttatcaccat cggtgaccgc     67440
     cacttcacgc atgttatcgc caaaacggca gactttcaga tgacgggtat cctgtttaga     67500
     aaccgcctga cgcatccagg agccgatacg ctcatgggct tgtttatcct gccagtgacc     67560
     ggtaacgacg gcatgttgct gacgcatacg cgcgccaatg aagccgaact cgcgaccgcc     67620
     atgtgcagtc tggttcaggt tcataaagtc catatcgata ctgtcccacg gcagcgccgc     67680
     gttgaactgg gtgtggaatt gcagcaacgg tttgttgagc atggtcaggc cgttgatcca     67740
     cattttggcc ggggagaagg tgtgcagcca caccaccaga ccagcgcacg gatcgtcgta     67800
     attcgcgtcg cggcaaatag cggtgatttc atccggcgtg gtgcccagcg gtttcaacac     67860
     cagtttgcag ggcagtttcg cttccgtatt cagcgcatta acaacgtgct cggcatgttg     67920
     ggtgacctga cgcagggttt ccgggccata cagatgctgg ctgccaatga caaaccacac     67980
     ttcataatta tcaaaaatcg tcattatcgt gtccttatag agtcgcaacg gcctgggcag     68040
     cctgtgccgg ggcggaagtt ggaagatagt gttgttcggc gctcatcgcc cattgctgat     68100
     agcggcgata aagctgttca aagcgttgtg cctgttcgct gcgcggttgc agggttttct     68160
     ctaccgcact ggccattttt tgctgggctg atgggatgtc tgcgtgcact ttcgcggcga     68220
     cggcagcaaa aatcgccgca ccgagcgcac agcactggtc agaggcaaca atttgcagcg     68280
     ggcgattcag cacgtcgcag caggcctgca taatgacttg gtttttccgc gcgatgccgc     68340
     ccagcgccat cacgttattg acggcgatcc cctgatcggt aaagcactcc atgattgcgc     68400
     gtgcgccaaa ggcggtggca gcaatcaaac cgccgaacag cagcggagcg tcggtagcga     68460
     ggttaagatc ggtaatcacc cctttcaggc gttggttagc gtttggcgag cgacgaccgt     68520
     taaaccagtc gagcaccacc ggcaggtgat ccagagacgg atttttggcc catgcttcgg     68580
     tcagcgccgg aagcagttgt ttctggctgg cgttgatttg cgctttcagt tccggatgct     68640
     gggcggcaag ctgttccagc ggccagctga gtacgcgacc gaaccaggcg tagatatcac     68700
     caaacgccga ttggcctgct tccagaccga taaatccagg caccacgctg ccatcaacct     68760
     gaccgcaaat acctttaact gcccgctcgc caacgctctg tttgtcggca atcagaatgt     68820
     cgcaggtgga agtaccgata acttttacca gtgcgttagg ctgtgcgcct gcgccaactg     68880
     cgcccatatg gcagtcaaac gcgccgccgg aaatcaccac gctttcaggc aggccgagac     68940
     gctgcgccca ttccgggcat aaggtgccca ccggaatatc ggcagtccag gtgtcagtga     69000
     acagcgggga aggcaaatgg cgattgagga tcgggtccag ctcatcaaag aaactggctg     69060
     gcggcaagcc gccccagctt tcgtgccaca gagatttatg cccggcgctg caacgtccgc     69120
     gacgaatatc ctgcgggcgg gtggtaccgg aaagcagagc tggcacccag tcgcacagct     69180
     caatccacga tgcggcagat tgcgccacgg cgctgtcctg gcgagtcaca tgcaggattt     69240
     ttgcccagaa ccattcgctg gaataaatac cgccaatata gcgggagtag tcaacattgc     69300
     ccggcgcgtg gcacaaacgg gtaatctctt cgcttctttc aaccgcagtg tggtctttcc     69360
     acaatacgaa catcgcgttc gggttttcgg caaactccgg gcgcagcgcc agcacgttac     69420
     cgtcggcatc aatcggtgcg ggcgtcgagc cggtactgtc aacgccaatc ccgaccacag     69480
     ctgcgcgctg ttcgacgcta agctctgcaa gcacggtttt cagtgccgct tccattgact     69540
     caatgtagtc acgcggatga tgacggaact ggttattcgg ggcatcacaa aattgccctt     69600
     tttgccaacg gggataccac tctacgctgg tggcgatctc ttcaccgctg gcgcagtcca     69660
     ccgccaaagc tcgcacagaa tcactgccaa aatcgaggcc aattgcaatc gccatcgttt     69720
     cactccatcc aaaaaaacgg gtatggagaa acagtagaga gttgcgataa aaagcgtcag     69780
     gtaggatccg ctaatcttat ggataaaaat gctatggcat agcaaagtgt gacgccgtgc     69840
     aaataatcaa tgtggacttt tctgccgtga ttatagacac ttttgttacg cgtttttgtc     69900
     atggctttgg tcccgctttg ttacagaatg cttttaataa gcggggttac cggttgggtt     69960
     agcgagaaga gccagtaaaa gacgcagtga cggcaatgtc tgatgcaata tggacaattg     70020
     gtttcttctc tgaatggtgg gagtatgaaa agtatggctg aagcgcaaaa tgatcccctg     70080
     ctgccgggat actcgtttaa cgcccatctg gtggcgggtt taacgccgat tgaggccaac     70140
     ggttatctcg atttttttat cgaccgaccg ctgggaatga aaggttatat tctcaatctc     70200
     accattcgcg gtcagggggt ggtgaaaaat cagggacgag aatttgtctg ccgaccgggt     70260
     gatattttgc tgttcccgcc aggagagatt catcactacg gtcgtcatcc ggaggctcgc     70320
     gaatggtatc accagtgggt ttactttcgt ccgcgcgcct actggcatga atggcttaac     70380
     tggccgtcaa tatttgccaa tacgggtttc tttcgcccgg atgaagcgca ccagccgcat     70440
     ttcagcgacc tgtttgggca aatcattaac gccgggcaag gggaagggcg ctattcggag     70500
     ctgctggcga taaatctgct tgagcaattg ttactgcggc gcatggaagc gattaacgag     70560
     tcgctccatc cgccgatgga taatcgggta cgcgaggctt gtcagtacat cagcgatcac     70620
     ctggcagaca gcaattttga tatcgccagc gtcgcacagc atgtttgctt gtcgccgtcg     70680
     cgtctgtcac atcttttccg ccagcagtta gggattagcg tcttaagctg gcgcgaggac     70740
     caacgtatca gccaggcgaa gctgcttttg agcactaccc ggatgcctat cgccaccgtc     70800
     ggtcgcaatg ttggttttga cgatcaactc tatttctcgc gagtatttaa aaaatgcacc     70860
     ggggccagcc cgagcgagtt tcgtgccggt tgtgaagaaa aagtgaatga tgtagccgtc     70920
     aagttgtcat aattggtaac gaatcagaca attgacggct tgacggagta gcatagggtt     70980
     tgcagaatcc ctgcttcgtc catttgacag gccacattat gcaagcattg cggaacactt     71040
     tattacccaa ccaccgtgtt cattgatggc ggtggtgttg gtggcctttc tggagtcgct     71100
     ggcgctggtc ggtttgattc tacccggtac ggtgctgatg gcggggctgg gagcgctgat     71160
     tggcagcggc gagttaagtt tctggcacgc ctggctggca gggattattg gctgcttgat     71220
     gggcgactgg atttctttct ggctgggttg gcgttttaaa aagccgttgc atcgctggtc     71280
     atttctgaag aaaaacaaag cactacttga taaaactgaa catgcgttgc atcaacacag     71340
     catgttcacc attctggtcg gtcgttttgt tggcccgacg cgtccgctgg tgccaatggt     71400
     ggcgggaatg ctggatctgc cggtggctaa atttattacg ccgaatatta tcggctgcct     71460
     gctgtggccg ccgttttact tcctgccagg gattctggcg ggcgcggcga tcgatattcc     71520
     tgccggaatg cagagcggtg agtttaaatg gttgctgctg gcaacagcgg tgtttttgtg     71580
     ggttggtggc tggctgtgct ggcggttatg gcgcagcggt aaagcgactg accgtttgag     71640
     tcattatttg tcccgcggtc gtttgttgtg gctgacgccg ttgatttctg ccatcggcgt     71700
     ggtggcgctg gtggtgttaa ttcgccaccc gttgatgccg gtgtatatcg atattttgcg     71760
     taaagtggtt ggggtttagg agatagtctt gtgcgggttg cctgagcgcg acgcttgccg     71820
     cgtcttatca ggcctacaaa acgcactacc cgtaggtcgg ataaggcgtt cacgccgcat     71880
     ccgacagtgc atactaaccc gtaatcccca atagtgccga agcactcgcc ttaccgctca     71940
     acaactcatt ggtcataccc tgccaggcga tgcgcccgtc ggcgactact accgagcgcg     72000
     tggcgatccg cgccgcatct tccacgctgt gcgacaccat caatagcgtc attttttgct     72060
     gctggcagct cgtgctcacc agcgtcaaca tctcctgacg taacgccgga tcgagcgcag     72120
     agaacagttc atcgagcaat aaaatcggct gttcgcgtac cagacaacgc gctaacgcca     72180
     ctcgctgtcg ctgaccgccg gaaagctcgc ccggtaaccg cgccattaaa ttatcaatcc     72240
     ccatctggcg ggcgatagcg tgcattttcc cctgctgtac cgcgttcagt ttcaatcccg     72300
     gatttagccc cagcccgatg ttctgtgcga ccgtcaggtg gctgaacagg ttgttctcct     72360
     gaaacagcat cgacaccgga cggcgtgacg gcggcatagt tgtgtgatct acgccatcga     72420
     tagtcagcga accgctggct ggcgtcagaa aaccggcgat caaattcagc agggtacttt     72480
     tacccgcgcc gcttggcccg aggatcgcca cctgctcgcc gcgttccacc gttaagctaa     72540
     aacgcatcgg caaatggtgg taaagccagg tgatatcagt cagttttaac atttcgcccc     72600
     ggtagttttt caatcacggt aaacagcaga aaacagagca gcagcagaat taacgtggtg     72660
     accgcaccgt cctggctgcg ataggagcca atttgctggt agagataaaa cggcagggtg     72720
     cggaaatcat cgttaccgaa caacgccacc acgccaaaat caccaatcga cagcacgcat     72780
     gcaaaggcca gcgcctgcgc cagtggacgt ttcagggcgc gcagctccac cacttttaag     72840
     cgtgaccagc cttcaatccc cagcgactga cataacatgc tgtagcgggc ggtgatatcg     72900
     cgcatcgggt tttccagcac tttcagcgca taagggatcg ccattaacgc attggtgaaa     72960
     atcacaatgc cgtcagcaga ttgtggcagg ccgatagtgt tgttgagcag taaaaagaag     73020
     ccggtagcca gcacaatccc cggcatggcg aggatcaaca tgccgctcat ctccagcacc     73080
     tgacccgcca gcattttctg ccgcgcccgc agttcgcgac tgctccatag cagcatcatg     73140
     gtcagcacta cgcacaatac acctgccgcc agcgcaatac gcaacgaggt ccacagcgcc     73200
     tgccacagca ccggttgtgc cagcacttcc ggcaactggc gatttacccc atcgacgatc     73260
     accgccagta acggtggcag caacagcagc agcgccagca caattaacac cgtgtcgcaa     73320
     atgcggctat gcagacgatc gtccgggtcg cgccagcctt gcagcagcgt ggtgccgggc     73380
     gcaatggcct tactcaatcg ctgactcaac agcaccagcc cgaggcagca caccatctgg     73440
     agcagcgcca gcattgccgc gcgggcagga tcgtagtcgt aactcagcgc ctgatagatt     73500
     gccagctcga tagtggtcgc ctgcggaccg ccccccagcg atagcacggt ggcgaagctg     73560
     gcgaaacaga gcataaagat aagcgcagca accggcggga tttgtcgccg taaccacggc     73620
     cattcgacga agcggaaaaa atgccagcta cgcatcccaa gctgggcggc aagttgacgc     73680
     tgttcgccgg ggatgttttc cagtgcctgg agtaataagc ggctcgccat cggcagatta     73740
     aaaaacacat gggccagcaa aataccttgc aggccgtagg gcgaaaaggt ccactccaga     73800
     ccgagcgatt ggcagagtgt tgccagccag ccctggcgac catagacgct aagaatgccg     73860
     aaaacagcga ccaacaccgg gaggatcaag gtcattgcac acagacgcaa cagcgccagc     73920
     cgacccggaa agcgcctgcg atagagcgcg cgggcgagga atatcgcggg tatgacagag     73980
     agcagtgccg agagaaacgc ctgccagaag gagaagcgca ccacatgcca cagatagctg     74040
     tcctgccaga ctgccaccca gtcatcctgc ggcgcgttcc accacagggc gagaaacgcc     74100
     gccagcgcaa ccgctaccac cagcgtggtg gcgcttacac ctggaattaa ccagccggga     74160
     attaacggct gacggcgcgt tgccattcgc taatccatgc ctgacgttgt gccgccactt     74220
     cggctggcgt gaactccaac gtggttgcgg gtttggtcaa tttttcaaaa ccggcaggca     74280
     gcgtgacgtt tgccaccgga tacatccagt tgccggttgg gatcgcattc tggaaagccg     74340
     gagaaaccat aaactggagg aatttttgcg ccagctccgg ctgcttgctg gcagcggtgc     74400
     gggcggcgac ttccacttgc agatagtgac cttcgctgaa gttcgcggcg gcgtagttat     74460
     ctttcttctc ttcgagaatg tgataagccg gagaggtggt gtaactcagt accagatcgc     74520
     tttcaccttt taaaaacagg ccgtaggctt cgctccagcc tttggtgacc gtgaccgttt     74580
     tcttcgccag tttctgccag gcttgtgggg cgtcatcgcc atagactttt tgcatccata     74640
     gcaacagacc cagccccggt gtactggtgc gcggatcctg ataaatcacc cgccagtttt     74700
     gatcgctctc aaccagttct ttcaggcttt gtggcgggtt tttcagtttg ttcttgtcat     74760
     aaacgaaggc gaagtagcca taatcaaacg gtacgaaagt gtcattattc cagccgccgg     74820
     gaacgttaac ggcatccgct gccacaccgc ttttggcaaa cagtccggtt ttactggcgg     74880
     cgtctaacag gttgttatcc agccccagca ccacatcggc tttactgttt ttgccttcca     74940
     tccgtagacg gttgagaagc gaaacgccat cttccagcgc caccagtttc agttcgcaat     75000
     tacagtcggc ttcaaaggct tttttaacca ccggaccagg cccccagtcg gcggcgaagg     75060
     aatcgtaggt ataaacagtc agaacgggtt tagcgaaaac gggcgctgtc acagcaacag     75120
     caggggcaga cattttttta acactttgca cctcaaaaaa gagtggcaaa ggacttgaga     75180
     aggagcctca aatcccttcg ccggcgttat ccggatcagg ttcgacgggt attttctcag     75240
     cgcacgcgta cgcgtggcac cccgttgaga acggcgttag tgtagtgatt ttgttatcaa     75300
     ccagcaatca tggatccggt ggcgcaaacc acgctgattt aaaatcgaac cagccgaggg     75360
     tattcatgcg caggccgcgc atactgcgtt gcccctgaat gatcagccag tggtgcaata     75420
     atggcaccat cgctttgctg gcgaccagtt gctggcacca gttcgccaga ttcatctcgc     75480
     cattgcgcca gcgagcagcg tcggcttgcc agtcaatggg aatgcaatgt tgtagcagtg     75540
     gcacttcgca taaatgtgcg aaaacagaga agtccagcgg cagggtaaag ttggcgctgt     75600
     ttagccagat atcactttcg atctctcctg tatgccactg atcgtagtcg atctctttga     75660
     ttttcagcgt cacctggtga cttgccagaa tctgctgcat gatcccggca atcacccgat     75720
     gctcactgtg atcctgacaa aaggttaggg tgaggctttc caggccagcc ggtttttcgc     75780
     tctttatggt gcgggcatgg tgccaacggg ggaacagtcc ataagccggg aaccacagtt     75840
     gctggtactg ttcctcagcg aaatagacca agttagttgg agaaagcaca tagcttgccc     75900
     agtccctgac ttgctgattc gccccgcgat gggtgcggct gtcgaacagt aaatagtagc     75960
     aaccttcctc caggcggctt tcaatctctt tttcctcgcc ctgtggacct tttagcatca     76020
     gccctccggc tggctcgtcg gcaatttccg gcagaaccca gacgttaact tcgtcgatta     76080
     atgcccggta accgaagaag tcatcgaatg cctgaatttt cagttgattg gtgctgttgc     76140
     gaatcaccgc atacggaccg gtgccgatgg gatggctggc aaagttactg agggtttccc     76200
     attcgcgcgg caggatcatc gccggaactt gccccagcag taacggtaac cagcggtccg     76260
     gttgcgtgag atggatatcc agcgtccagg gcgtcggcga cacaatgtca gcaatatgcg     76320
     aatagagcgg cagcgtattg attcgtttta aagaggcgat cacatcgtcc atttccagtt     76380
     cacgaccatg gtgaaaatgg actcctggac gcaaaaagaa acgccagtga agcggtgaaa     76440
     tttgctgcca gtggtgggcg atgtctgctt ccagttcccc attttcctca tttatgcgcg     76500
     ttagcgaact gaagatttgc cgggcgatat gggtttcgga acggcgcaat gcgctgccag     76560
     gtagcagatt acgcaacgga cgatagtaga gcacgcgcag gatgtgccgc ccctggcgga     76620
     agctgcggcc cagatgagaa accagcattt gccgcacagt cgctttgtcg ccaaccaact     76680
     gcaccagttg atcgatacga tcctgctcca gcaggtcttc cgcccgctgt tgctgaagcg     76740
     ccagcccggt atagaggaat gtcagacgcg agcgtttacc gcgcccgact tccgcttccc     76800
     acgtcagcca gccgcgatcc tgcatggtgt tgagcagggt gcgcatatga cgacgcgagc     76860
     agctcaataa cgctgccagt tcgttgagcg ttgtgtcctg cgatttaccc tcgcagcatt     76920
     gccacaggcg gatgaactgt tgttgcagac gagcagatgg cataaaaggg gaactcctgt     76980
     gcaaaagaca gcaattttat tgtccctata ttaagtcaat aattcctaac gatgaagcaa     77040
     gggggtgccc catgcgtcag ttttatcagc actattttac cgcgacagcg aagttgtgct     77100
     ggttgcgttg gttaagcgtc ccacaacgat taaccatgct tgaaggactg atgcagtggg     77160
     atgaccgcaa ttctgaaagt tgacttgcct gcatcatgtg tgactgagta ttggtgtaaa     77220
     atcacccgcc agcagattat acctgctggt tttttttatt ctcgccgcgc taaaaaggga     77280
     acgtatgatc tggataatga cgatggctcg ccgtatgaac ggtgtttacg cggcatttat     77340
     gctggtcgct tttatgatgg gggtggccgg ggcgctacag gctcctacat tgagcttatt     77400
     tctgagtcgt gaggttggcg cgcaaccttt ctggatcggc ctcttttatg cggtgaatgc     77460
     tattgctggg atcggcgtaa gcctctggtt ggcaaaacgt tctgacagtc agggcgatcg     77520
     gcgaaaactg attatatttt gctgtttgat ggctatcggc aatgcgctat tgtttgcatt     77580
     taatcgtcat tatctgacgc ttatcacctg tggtgtgctt ctggcatctc tggccaatac     77640
     ggcaatgcca cagttatttg ctctggcgcg ggaatatgcg gataactcgg cgcgagaagt     77700
     ggtgatgttt agctcggtga tgcgtgcgca gctttctctg gcatgggtta tcggtccacc     77760
     gttggccttt atgctggcgt tgaattacgg ctttacggtg atgttttcga ttgccgccgg     77820
     gatattcaca ctcagtctgg tattgattgc atttatgctt ccgtctgtgg cgcgggtaga     77880
     actgccgtcg gaaaatgctt tatcaatgca aggtggctgg caggatagta acgtacggat     77940
     gttatttgtc gcctcgacgt taatgtggac ctgcaacacc atgtacatta ttgatatgcc     78000
     gttgtggatc agtagcgagt taggattgcc agacaaactg gcgggtttcc tgatggggac     78060
     ggcagctgga ctggaaatac cagcaatgat tctggctggc tactatgtca aacgttatgg     78120
     taagcggcga atgatggtca tagcagtggc ggcaggagta ctgttttaca ccggattgat     78180
     tttctttaat agccgtatgg cgttgatgac gctgcaactt tttaacgctg tatttatcgg     78240
     cattgttgcg ggtattggga tgctatggtt tcaggattta atgcctggaa gagcgggggc     78300
     agctaccacc ttatttacta acagtatttc taccggggta attctggctg gcgttattca     78360
     gggagcaatt gcacaaagtt gggggcactt tgctgtctac tgggtaattg cggttatttc     78420
     tgttgtcgca ttatttttaa ccgcaaaggt taaagacgtt tgatgacgtg gacgatagcg     78480
     gaaagcccgg tcatttgacc gggcaagggg attaattcat aaacgcaggt tgttttgctt     78540
     cataagcggc aatggcgtcg tcgtgctgca aggtaagccc aatactgtcc agaccgttca     78600
     tcatgcagtg gcggcggaag gcatcgatgg taaagcgata ggttttctct cccgctttca     78660
     cctcttgcgc ttccagatcc acgtcgaaat ggatccccgg attagctttc accagcgcaa     78720
     acagttcgtc cacttctgca tcgcttaatt tcaccggcag cagctggttg ttaaagctat     78780
     tgccgtagaa gatgtcagca aaactcggcg caatcaccac tttaaaaccg tagtcggtca     78840
     atgcccaggg cgcgtgctca cgcgaagagc cacagccgaa gttttctcgt gccagcaaaa     78900
     tggaagcgcc ctgatactgc gggaagttca gcacgaagtc cgggtttggc tgttggcctt     78960
     tttcatccag aaaacgccag tcgttaaaca gatgcgcgcc aaaacccgta cgggtcactt     79020
     tctgcaaaaa ctgtttcggg atgattgcat cggtatcgac attggcggca tccagcggaa     79080
     ccaccaggcc tgtgtgtttg ataaatttct ctgccatggt gtgctcctta tttaatgttg     79140
     cgaatgtcgg cgaaatgtcc ggtcacagca gcagcggcag ccattgccgg gctgaccaga     79200
     tgcgtgcgcc cgccgcgccc ctggcggcct tcaaagttac ggttgctggt ggaggcacaa     79260
     cgttcgcccg gattcagacg gtcgttgttc atcgccagac acattgagca gccaggcaag     79320
     cgccattcaa aaccggcttc aataaagatt ttatccagac cttccgcttc cgcctgggct     79380
     tttaccgggc cagagccggg aaccaccagt gcctgcacgc ctggcgcgac ttttcgccct     79440
     ttgacgatct ccgctgccgc gcgtaaatct tcaatgcgcg agttggtaca ggaaccgata     79500
     aacactttgt cgatagccac ttcggtcagc ggaatacccg gtttcagccc catataggcc     79560
     agcgcttttt ctgccgacgc gcgttcaacc ggatcggcaa acgaagccgg atcgggaata     79620
     ttgtcgttca cggaaatcac ctggccggga ttggtgcccc aggtgacctg cggtgaaatt     79680
     tcttctgctt gcagagtgac aacggtatcg aaagttgcgc cttcgtcggt ttgcagggtt     79740
     ttccagtagg caacggcgtc gtcgaaatct ttgcctttcg gcgcatgcag acggcctttg     79800
     acatagttaa aggtggtttc gtccggtgca accagaccgg cttttgcgcc catttcgatt     79860
     gccatattgc acagggtcat acgaccttcc atgcttaaat cacggattgc ttcgccgcaa     79920
     aactccacca catgcccggt gccgcctgcg ctaccggttt taccgataat tgccagcacg     79980
     atatcttttg cggtaatgcc cggcgcggct ttgccctgga cttcaatttt catggttttt     80040
     gcgcggccct gtttcagggt ttgcgttgcc agtacgtgtt caacttcgga agtgccgata     80100
     ccaaaggcca gtgcgccaaa cgcgccgtgg gtggcggtat gcgagtcgcc gcagacaatg     80160
     gtcatccccg gcaaggtgac gccctgttcc ggccccatta cgtggacgat cccctgatac     80220
     gggtgattca ggtcatacag ttcgacgcca aattctttgc agtttttgat cagttcctgc     80280
     atctggatac gcgccatttc accgcaggca ttaatgcctt tggtctgggt agagacgttg     80340
     tgatccatgg tagcgaaggt tttgcccggc tgacgtaccg ggcgaccgtg ggcgcgcaga     80400
     ccatcgaacg cctgcggtga ggtcacttca tgcaccaggt ggcggtcgat atataacagt     80460
     ggggtttcgt tttcggcttc gtacacaacg tgagcgtcga acaatttttc gtataacgtc     80520
     ttagccatga ttacacccct tctgctacat agcgggcaat gatatcgccc atttcatcgg     80580
     tactaacggc ggcagcgcca cgggctaaat ccccggtgcg aatgccttct tctaatgcgc     80640
     ggttaatggc gcgttcaatg gcgcaagccg catcatcggc atccaggctg taacgcagca     80700
     gcagtgccag cgaaaggatt tgtgcaatcg ggttggcgat gtttttgcct gcgatatctg     80760
     gtgccgagcc gcccgccggt tcatacagtc caaaaccttg ctcgttcagg ctggcggaag     80820
     gcaacatccc catcgagcca gtgatcattg cgcactcgtc agacagaatg tcgccaaaca     80880
     ggttggagca cagcagaacg tcaaactgtg atggatcttt aatcagctgc atggtggcgt     80940
     tgtcgatgta catatgcgcc agttcgacat ccgggtattc cgtggcgatc tcgttaacga     81000
     tctcccgcca taaaatagag gattgcagca cgttggcttt atcgatcgac gtcactttgt     81060
     ggcgacgctt gcgagcagat tcaaacgcga tgcgggcgat acgttcgatc tcaaaacggt     81120
     gatacacctc ggtatcaaag gctttttcat attgtccgct accttcgcgg ccttttggct     81180
     gaccgaaata gatgccgccg gtcagttcgc gcacacacag gatgtcgaag ccgtttgcgg     81240
     caatgtctgc acgcagcgga cagaatgctt ccagcccctg atacagtttt gccgggcgca     81300
     ggttgctgaa taatttgaag tgcttacgca gaggcagcag cgcgccgcgt tctggttgct     81360
     ggtctggtgg taaatgttcc cacttcgggc cgcctaccga gccaaacagc acggcatcgg     81420
     cttgctcaca accttcaacc gtcgcaggcg gcagtggttg cccgtggtta tcaatggctg     81480
     cgccgcctac atcgtaatgg ctggtggtga tgcgcatcgc aaagcggttg cgcacggcat     81540
     ccagcacttt cagcgcctgg gtcatcactt ccggaccaat accgtccccc ggcaatacgg     81600
     caatatggta attcttcgac atcacacggt ttccttgttg ttttcgttgt gttgagcttt     81660
     gcgttgcaac tctttttcga cttctgcggc acgccagata ttgttcagaa cgtgcaccat     81720
     ggctttggca gatgactcga caatatcggt agccaggccg acgccgtgga agcggcgacc     81780
     gttgtagtta gcgacgatat ccacctgacc cagcgcatct ttaccgtggc ctttggcggt     81840
     caggctgtat ttcaccagtt cgacgttata ttcagtgatg cggttaattg cctgatagac     81900
     ggcatcgacc ggaccgttac cgttggcggc ttctgctttg acttcttcgc cacaggccag     81960
     tttgacggcg gcggtggcga tatcgttaga gccagactgc acgctgaagt aatccagacg     82020
     gaaatgctcc ggctcttctt gctgcttacc gatgaaggcc agcgcctcca gatcgtaatc     82080
     aaacacctga ccttttttgt ccgccagctt caggaaagca tcgtacaaat tgtctaaatt     82140
     atattcactt tctttatacc ccatctcatc catgcgatgt ttcaccgccg cacgccccga     82200
     acgagaggtc agattcagct ggatttggtt cagaccaata gattctggtg tcatgatttc     82260
     gtagttttcg cggtttttca gcacgccatc ctggtgtata ccggaggagt gtgcgaatgc     82320
     gccgctgcca acaatggctt tgtttgccgg gatcggcata ttacaaatct ggctaactaa     82380
     ctggctggtg cgccatatct cctggtgatt aatggcggtg tggacgttga gaatatcctt     82440
     acgaactttg atcgccatga tgacttcttc cagggaacag tttccggcac gctcgccgat     82500
     cccgttcatt gcgccttcca cctggcgtgc accggcatgt accgccgcca gtgagtttcc     82560
     gaccgccagg cccaaatcgt cgtgggtatg tacggagata atggctttgc cgatgctagg     82620
     cacgcgttca tacaggccgc tgatgattcc ggcgaactca aacggcatgg tgtagcccac     82680
     ggtgtccgga atgttgatgg tggtggcacc ggcattaatc gccgcttcga ccactcgcgc     82740
     cagatcggca atgggtgtac gcccggcatc ttcgcaagaa aattcaacat catcggtgta     82800
     attacgggcg cgtttcacca tatagatagc gcgttcgatc acctcgtcca gcgtgctgcg     82860
     cagcttggtg gcgatgtgca ttggcgaagt ggcaataaag gtatgaatac ggaaggcttc     82920
     ggcgactttc agggattcgg ccgccacgtc gatatctttt tccacgcagc gagctaacgc     82980
     acatacgcgg ctgtttttaa cctggcgggc gatggtttgc accgattcaa aatcgcccgg     83040
     cgaagagacg gggaaaccga cttccatcac gtcaacaccc atacgctcaa gggccagcgc     83100
     aatttgcagt ttttctttca cactcaagct tgcctgtaac gcctgttcac cgtcgcgcaa     83160
     tgtggtatcg aaaataatga cttgctggct catggtttgg gtccttgtct cttttagagc     83220
     gcctcgcttc gggcataaaa aaacccgcgc aatggcgcgg gttttttgtt tgactgcgtg     83280
     ctggcttaat gctggatgcc gctcactcgt ctaccgcgca aagaagatgc gtttagtagt     83340
     agtagaccga taaagcgaac gatgtgagtc attaaatcag ctccagatga atgcgatatg     83400
     cttttagagt tactggatac aaaaacggat gtcaaccctg acgcaataaa aacgtcccgc     83460
     cagcgtgagt tctgcatccg taaaattagc taattgtgct gcggtggtta aagtaagcga     83520
     tattaatttc tgcttaacta ccgacgcttt tcatcggttg acatatttca gcataaattt     83580
     ttgcatctaa tcaacgagga aaaaggggac aaaatgcacg cgttgcaaaa cctatcctga     83640
     tgatttgtat tgaattatat gttttgcgat tttttttgat attgatttgg tgaatattat     83700
     tgatcaatta atgttaagaa ttaatgcatt aaatatataa attaattatt aaataagcac     83760
     atttaatcca ttttgtagat gattgagtat tcgcggtagt tatgattaga ttgttttcgc     83820
     aacaaaaaca ttatggatta ttatgctgtg gtaaatgact cattccacgg caatggattc     83880
     tgtttttatc agaacccgta tctttatgtt ttccgaattt tactcatttt gctttttctt     83940
     attttatatg catgataaat catattcttc aggattattt ctctgcattc caataaggga     84000
     aagggagtta agtgtgacag tggagttaag tatgccagag gtacaaacag atcatccaga     84060
     gacggcggag ttaagcaaac cacagctacg catggtcgat ctcaacttat taaccgtttt     84120
     cgatgccgtg atgcaggagc aaaacattac tcgtgccgct catgttctgg gaatgtcgca     84180
     acctgcggtc agtaacgctg ttgcacgcct gaaggtgatg tttaatgacg agctttttgt     84240
     tcgttatggc cgtggtattc aaccgactgc tcgcgcattt caactttttg gttcagttcg     84300
     tcaggcattg caactagtac aaaatgaatt gcctggttca ggttttgaac ccgcgagcag     84360
     tgaacgtgta tttcatcttt gtgtttgcag cccgttagac agcattctga cctcgcagat     84420
     ttataatcac attgagcaga ttgcgccaaa tatacatgtt atgttcaagt cttcattaaa     84480
     tcagaacact gaacatcagc tgcgttatca ggaaacggag tttgtgatta gttatgaaga     84540
     cttccatcgt cctgaattta ccagcgtacc attatttaaa gatgaaatgg tgctggtagc     84600
     cagcaaaaat catccaacaa ttaagggccc gttactgaaa catgatgttt ataacgaaca     84660
     acatgcggcg gtttcgctcg atcgtttcgc gtcatttagt caaccttggt atgacacggt     84720
     agataagcaa gccagtatcg cgtatcaggg catggcaatg atgagcgtac ttagcgtggt     84780
     gtcgcaaacg catttggtcg ctattgcgcc gcgttggctg gctgaagagt tcgctgaatc     84840
     cttagaatta caggtattac cgctgccgtt aaaacaaaac agcagaacct gttatctctc     84900
     ctagcatgaa gctgccgggc gcgataaagg ccatcagtgg atggaagagc aattagtctc     84960
     aatttgcaaa cgctaactga ttgcagaata ggtcagacat gaatgtctgg tttattctgc     85020
     attttttatt gaatgtagaa ttttattctg aatgtgtggg ctctctattt taggattaat     85080
     taaaaaaata gagaaattgc tgtaagttgt gggattcagc cgatttatta tcaatttaat     85140
     cctctgtaat ggaggatttt atcgtttctt ttcacctttc ctcctgttta ttcttattac     85200
     cccgtgttta tgtctctggc tgccaattgc ttaagcaaga tcggacggtt aatgtgtttt     85260
     acacattttt tccgtcaaac agtgaggcag gccatggaga tgttgtctgg aggcgagatg     85320
     gtcgtccgat cgcttatcga tcagggcgtt aaacaagtat tcggttatcc cggaggcgca     85380
     gtccttgata tttatgatgc attgcatacc gtgggtggta ttgatcatgt attagttcgt     85440
     catgagcagg cggcggtgca tatggccgat ggcttggcgc gcgcgaccgg ggaagtcggc     85500
     gtcgtgctgg taacgtcggg tccaggggcg accaatgcga ttactggcat cgccaccgct     85560
     tatatggatt ccattccatt agttgtcctt tccgggcagg tagcgacctc gttgataggt     85620
     tacgatgcct ttcaggagtg cgacatggtg gggatttcgc gacccgtggt taaacacagt     85680
     tttctggtta agcaaacgga agacattccg caggtgctga aaaaggcttt ctggctggcg     85740
     gcaagcggtc gcccaggacc agtagtcgtt gatttaccga aagatattct taatccggcg     85800
     aacaaattac cctatgtctg gccggagtcg gtcagtatgc gttcttacaa tcccactact     85860
     accggacata aagggcaaat taagcgtgct ctgcaaagcg tggtagcggt aaaaaaaccg     85920
     gttgtctacg taggcggtgg ggcaatcacg gcgggctgcc atcagcagtt gaaagaaacg     85980
     gtggaggcgt tgaatctgcc cgttgtttgc tcattgatgg ggctgggggc gtttccggca     86040
     acgcatcgtc aggtactggg tatgctggga atgcacggta cctacgaagc caatatgacg     86100
     atgcataacg cggatgtgat tttcgccgtc ggggtacgat ttgatgaccg aacgacgaac     86160
     aatctggcaa agtactgccc aaatgccact gttctgcata tcgatattga tcctacttcc     86220
     atttctaaaa ccgtgactgc ggatatcccg attgtggggg atgctcgcca agtcctcgaa     86280
     caaatgcttg aactcttgtc gcaagaatcc gcccatcaac cactggatga gatccgcgac     86340
     tggtggcagc aaattgaaca gtggcgcgct cgtcagtgcc tgaaatatga cactcacagt     86400
     gaaaagatta aaccgcaggc ggtgatcgag actctttggc ggttgacgaa gggagacgct     86460
     tacgtgacgt ccgatgtcgg gcagcaccag atgtttgctg cactttatta tccattcgac     86520
     aaaccgcgtc gctggatcaa ttccggtggc ctcggcagca tgggttttgg tttacctgcg     86580
     gcactgggcg tcaaaatggc gttcccagaa gaaaccgtgg tttgcgtcac tggcgacggc     86640
     agtattcaga tgaacatcca ggaactgtct accgcgttgc aatacgagtt gcccgtactg     86700
     gtggtgaatc tcaataaccg ctatctgggg atggtgaagc agtggcagga catgatctat     86760
     tccggccgtc attcacaatc ttatatgcaa tcgctacccg atttcgtccg tcgcggagcc     86820
     tatgggcatg tcgggatcca gatttctcat ccgcatggct ggaaagcaaa cttagcgagg     86880
     cgctggaaca ggtgcgcaat aatcgcctgg tgtttgttga tgttaccgtc gatggcagcg     86940
     agcacgtcta cccgatgcag attcgcgggg gcggaatgga tgaaatgtgg ttaagcaaaa     87000
     cggagagaac ctgattatgc gccggatatt atcagtctta ctcgaaaatg aatcaggcgc     87060
     gttatcccgc gtgattggcc ttttttccca gcgtggctac aacattgaaa gcctgaccgt     87120
     tgcgccaacc gacgatccga cattatcgcg tatgaccatc cagaccgtgg gcgatgaaaa     87180
     agtacttgag cagatcgaaa agcaattaca caaactggtc gatgtcttgc gcgtgagtga     87240
     gttggggcag ggcgcgcatg ttgagcggga aatcatgctg gtgaaaattc aggccagcgg     87300
     ttacgggcgt gacgaagtga aacgtaatac ggaaatattc cgtgggcaaa ttatcgatgt     87360
     cacaccctcg ctttataccg ttcaattagc aggcaccagc ggtaagctta gtgcattttt     87420
     agcatcgatt cgcgatgtgg cgaaaattgt ggaggttgct cgctctggtg tggtcggact     87480
     ttcgcgcggc gataaaataa tgcgttgaga atgatctcaa tgcgcaattt acagcccaac     87540
     atgtcacgtt gggctttttt tgcgaaatca gtgggaacct ggaataaaag cagttgccgc     87600
     agttaatttt ctgcgcttag atgttaatga atttaaccca taccagtaca atggctatgg     87660
     tttttacatt ttacgcaagg ggcaattgtg aaactggatg aaatcgctcg gctggcggga     87720
     gtgtcgcgga ccactgcaag ctatgttatt aacggcaaag cgaagcaata ccgtgtgagc     87780
     gacaaaaccg ttgaaaaagt catggctgtg gtgcgtgagc acaattacca cccgaacgcc     87840
     gtggcagctg ggcttcgtgc tggacgcaca cgttctattg gtcttgtgat ccccgatctg     87900
     gagaacacca gctatacccg catcgctaac tatcttgaac gccaggcgcg gcaacggggt     87960
     tatcaactgc tgattgcctg ctcagaagat cagccagaca acgaaatgcg gtgcattgag     88020
     caccttttac agcgtcaggt tgatgccatt attgtttcga cgtcgttgcc tcctgagcat     88080
     cctttttatc aacgctgggc taacgacccg ttcccgattg tcgcgctgga ccgcgccctc     88140
     gatcgtgaac acttcaccag cgtggttggt gccgatcagg atgatgccga aatgctggcg     88200
     gaagagttac gtaagtttcc cgccgagacg gtgctttatc ttggtgcgct accggagctt     88260
     tctgtcagct tcctgcgtga acaaggtttc cgtactgcct ggaaagatga tccgcgcgaa     88320
     gtgcatttcc tgtatgccaa cagctatgag cgggaggcgg ctgcccagtt attcgaaaaa     88380
     tggctggaaa cgcatccgat gccgcaggcg ctgttcacaa cgtcgtttgc gttgttgcaa     88440
     ggagtgatgg atgtcacgct gcgtcgcgac ggcaaactgc cttctgacct ggcaattgcc     88500
     acctttggcg ataacgaact gctcgacttc ttacagtgtc cggtgctggc agtggctcaa     88560
     cgtcaccgcg atgtcgcaga gcgtgtgctg gagattgtcc tggcaagcct ggacgaaccg     88620
     cgtaagccaa aacctggttt aacgcgcatt aaacgtaatc tctatcgccg cggcgtgctc     88680
     agccgtagct aagccgcgaa caaaaatacg cgccaggtga atttccctct ggcgcgtaga     88740
     gtacgggact ggacatcaat atgcttaaag taaataagac tattcctgac tattattgat     88800
     aaatgctttt aaacccgccc gttaattaac tcaccagctg aaattcacaa taattaagtg     88860
     atatcgacag cgcgtttttg cattattttg ttacatgcgg cgatgaattg ccgatttaac     88920
     aaacactttt ctttgctttt gcgcaaaccc gctggcatca agcgccacac agacgtaaca     88980
     aggactgtta accggggaag atatgtccta aaatgccgct cgcgtcgcaa actgacactt     89040
     tatatttgct gtggaaaata gtgagtcatt ttaaaacggt gatgacgatg agggattttt     89100
     tcttacagct attcataacg ttaatttgct tcgcacgttg gacgtaaaat aaacaacgct     89160
     gatattagcc gtaaacatcg ggttttttac ctcggtatgc cttgtgactg gcttgacaag     89220
     cttttcctca gctccgtaaa ctcctttcag tgggaaattg tggggcaaag tgggaataag     89280
     gggtgaggct ggcatgttcc ggggagcaac gttagtcaat ctcgacagca aagggcgctt     89340
     atcagtgcct acccgttatc gggaacagct gcttgagaac gctgccggtc aaatggtttg     89400
     caccattgac atttatcacc cgtgcctgct gctttacccc ctgcctgaat gggaaattat     89460
     cgagcaaaaa ttatcgcgtc tgtcgagcat gaacccggtt gagcgccgtg tgcagcgcct     89520
     actgttaggt catgccagcg aatgtcagat ggatggcgca ggtcgattgt taatcgcgcc     89580
     agtactgcgg caacatgccg ggctgacaaa agaagtgatg ctggttggac agttcaacaa     89640
     gtttgagctg tgggatgaaa caacctggca tcaacaggtc aaggaagata tcgacgcaga     89700
     gcagttggct accggagact tatcggagcg actgcaggac ttgtctctat aaaatgatgg     89760
     aaaactataa acatactacg gtgctgctgg atgaagccgt taatggcctc aatatccgtc     89820
     ctgatggcat ctacattgat gggacttttg gtcgcggtgg tcactcacgt ctgatcctct     89880
     cgcagcttgg cgaagagggg cgtttgctgg cgatcgatcg cgacccgcag gctatcgccg     89940
     ttgcgaagac tattgatgat ccgcgcttct ccatcatcca cggacctttc tccgcgctgg     90000
     gcgaatacgt tgccgagcgc gatcttatcg gcaagatcga cggcattctc ctcgatcttg     90060
     gcgtctcttc accgcaactt gatgatgctg aacgtggctt ttcctttatg cgcgatggtc     90120
     cgctggacat gcgtatggac ccaacccgtg ggcagtcagc cgctgaatgg ctacaaaccg     90180
     cagaagaagc cgatatcgcc tgggtattga aaacctatgg tgaagagcgt tttgccaaac     90240
     gcattgcccg cgccattgtc gagcgtaacc gcgaacagcc gatgacccgc accaaagaac     90300
     tggcggaagt cgtggctgct gcaacgccgg tgaaagataa gtttaaacat cccgcgaccc     90360
     gtaccttcca ggcggtgcgc atttgggtaa acagtgaact ggaggagata gagcaggcgc     90420
     taaaaagctc gctcaacgtg ctggccccgg gtgggcggct ttcgatcatc agcttccact     90480
     cgctggaaga ccgtattgtg aaacgtttta tgcgtgaaaa cagccgcggt ccgcaagttc     90540
     cggcagggtt accgatgact gaagagcagc tcaaaaaact gggtggccgt cagctgcgag     90600
     cactaggcaa gttaatgccg ggcgaagaag aggtggctga gaaccctcgt gcccgtagtt     90660
     cagttctgcg tattgcagag aggacgaatg catgatcagc agagtgacag aagctctaag     90720
     caaagttaaa ggatcgatgg gaagccacga gcgccatgca ttgcctggtg ttatcggtga     90780
     cgatcttttg cgatttggga agctgccact ctgcctgttc atttgcatta ttttgacggc     90840
     ggtgactgtg gtaaccacgg cgcaccatac ccgtttactg accgctcagc gcgaacaact     90900
     ggtgctggag cgagatgctt tagacattga atggcgcaac ctgatccttg aagagaatgc     90960
     gctcggcgac catagccggg tggaaaggat cgccacggaa aagctgcaaa tgcagacatg     91020
     ttgatccgtc acaagaaaat atcgtagtgc aaaaataagg ataaacgcga cgcatgaaag     91080
     cagcggcgaa aacgcagaaa ccaaaacgtc aggaagaaca tgccaacttt atcagttggc     91140
     gttttgcgtt gttatgcggc tgtattctcc tggcgctggc ttttctgctc ggacgcgtag     91200
     cgtggttaca agttatctcc ccggatatgc tggtgaaaga gggcgacatg cgttctcttc     91260
     gcgttcagca agtttccacc tcccgcggca tgattactga ccgttctggt cgcccgttag     91320
     cggtgagcgt gccggtaaaa gcgatttggg ctgacccgaa agaagtgcat gacgctggcg     91380
     gtatcagcgt cggtgaccgc tggaaggcgc tggctaacgc gctcaatatt ccgctggatc     91440
     agctttcagc ccgcattaac gccaacccga aagggcgctt tatttatctg gcgcgtcagg     91500
     tgaaccctga catggcggac tacatcaaaa aactgaaact gccggggatt catctgcgtg     91560
     aagagtctcg ccgttactat ccgtccggcg aagtgactgc tcacctcatc ggctttacta     91620
     acgtcgatag tcaagggatt gagggcgttg agaagagttt cgataaatgg cttaccgggc     91680
     agccgggtga gcgcattgtg cgtaaagacc gctatggtcg cgtaattgaa gatatttctt     91740
     ctactgacag ccaggcagcg cacaacctgg cgctgagtat tgatgaacgc ctgcaggcgc     91800
     tggtttatcg cgaactgaac aacgcggtgg cctttaacaa ggctgaatct ggtagcgccg     91860
     tgctggtgga tgtcaacacc ggtgaagtgc tggcgatggc taacagcccg tcatacaacc     91920
     ctaacaatct gagcggcacg ccgaaagagg cgatgcgtaa ccgtaccatc accgacgtgt     91980
     ttgaaccggg ctcaacggtt aaaccgatgg tggtaatgac cgcgttgcaa cgtggcgtgg     92040
     tgcgggaaaa ctcggtactc aataccattc cttatcgaat taacggccac gaaatcaaag     92100
     acgtggcacg ctacagcgaa ttaaccctga ccggggtatt acagaagtcg agtaacgtcg     92160
     gtgtttccaa gctggcgtta gcgatgccgt cctcagcgtt agtagatact tactcacgtt     92220
     ttggactggg aaaagcgacc aatttggggt tggtcggaga acgcagtggc ttatatcctc     92280
     aaaaacaacg gtggtctgac atagagaggg ccaccttctc tttcggctac gggctaatgg     92340
     taacaccatt acagttagcg cgagtctacg caactatcgg cagctacggc atttatcgcc     92400
     cactgtcgat taccaaagtt gaccccccgg ttcccggtga acgtgtcttc ccggaatcca     92460
     ttgtccgcac tgtggtgcat atgatggaaa gcgtggcgct accaggcggc ggcggcgtga     92520
     aggcggcgat taaaggctat cgtatcgcca ttaaaaccgg taccgcgaaa aaggtcgggc     92580
     cggacggtcg ctacatcaat aaatatattg cttataccgc aggcgttgcg cctgcgagtc     92640
     agccgcgctt cgcgctggtt gttgttatca acgatccgca ggcgggtaaa tactacggcg     92700
     gcgccgtttc cgcgccggtc tttggtgcca tcatgggcgg cgtattgcgt accatgaaca     92760
     tcgagccgga tgcgctgaca acgggcgata aaaatgaatt tgtgattaat caaggcgagg     92820
     ggacaggtgg cagatcgtaa tttgcgcgac cttcttgctc cgtgggtgcc agacgcacct     92880
     tcgcgagcac tgcgagagat gacactcgac agccgtgtgg ctgcggcggg cgatctcttt     92940
     gtagctgtag taggtcatca ggcggacggg cgtcgatata tcccgcaggc gatagcgcaa     93000
     ggtgtcgctg ccattattgc agaggcgaaa gatgaggcga ccgatggtga aatccgtgaa     93060
     atgcacggcg taccggtcat ctatctcagc cagctcaacg agcgtttatc tgcactggcg     93120
     ggccgctttt accatgaacc ctctgacaat ttacgtctcg tgggcgtaac gggcaccaac     93180
     ggcaaaacca cgactaccca gctgttggcg cagtggagcc aactgcttgg cgaaatcagc     93240
     gcggtaatgg gcaccgttgg taacggcctg ctggggaaag tgatcccgac agaaaataca     93300
     accggttcgg cagtcgatgt tcagcatgag ctggcggggc tggtggatca gggcgcgacg     93360
     ttttgcgcaa tggaagtttc ctcccacggg ctggtacagc accgtgtggc ggcattgaaa     93420
     tttgcggcgt cggtctttac caacttaagc cgcgatcacc ttgattatca tggtgatatg     93480
     gaacactacg aagccgcgaa atggctgctt tattctgagc atcattgcgg tcaggcgatt     93540
     attaacgccg acgatgaagt gggccgccgc tggctggcaa aactgccgga cgcggttgcg     93600
     gtatcaatgg aagatcatat taatccgaac tgtcacggac gctggttgaa agcgaccgaa     93660
     gtgaactatc acgacagcgg tgcgacgatt cgctttagct caagttgggg cgatggcgaa     93720
     attgaaagcc atctgatggg cgcttttaac gtcagcaacc tgctgctcgc gctggcgaca     93780
     ctgttggcac tcggctatcc actggctgat ctgctgaaaa ccgccgcgcg tctgcaaccg     93840
     gtttgcggac gtatggaagt gttcactgcg ccaggcaaac cgacggtggt ggtggattac     93900
     gcgcatacgc cggatgcact ggaaaaagcc ttacaggcgg cgcgtctgca ctgtgcgggc     93960
     aagctgtggt gtgtctttgg ctgtggtggc gatcgcgata aaggtaagcg tccactgatg     94020
     ggcgcaattg ccgaagagtt tgctgacgtg gcggtggtga cggacgataa cccgcgtacc     94080
     gaagaaccgc gtgccatcat caacgatatt ctggcgggaa tgttagatgc cggacatgcc     94140
     aaagtgatgg aaggccgtgc tgaagcggtg acttgcgccg ttatgcaggc taaagagaat     94200
     gatgtggtac tggtcgcggg caaaggccat gaagattacc agattgttgg caatcagcgt     94260
     ctggactact ccgatcgcgt cacggtggcg cgtctgctgg gggtgattgc atgattagcg     94320
     taacccttag ccaacttacc gacattctca acggtgaact gcaaggtgca gatatcaccc     94380
     ttgatgctgt aaccactgat acccgaaaac tgacgccggg ctgcctgttt gttgccctga     94440
     aaggcgaacg ttttgatgcc cacgattttg ccgaccaggc gaaagctggc gcggcaggcg     94500
     cactactggt tagccgtccg ctggacatcg acctgccgca gttaatcgtc aaggatacgc     94560
     gtctggcgtt tggtgaactg gctgcatggg ttcgccagca agttccggcg cgcgtggttg     94620
     ctctgacggg gtcctccggc aaaacctccg ttaaagagat gacggcggcg attttaagcc     94680
     agtgcggcaa cacgctttat acggcaggca atctcaacaa cgacatcggt gtaccgatga     94740
     cgctgttgcg cttaacgccg gaatacgatt acgcagttat tgaacttggc gcgaaccatc     94800
     agggcgaaat agcctggact gtgagtctga ctcgcccgga acgtgcgctg gtcaacaacc     94860
     tggcagcggc gcatctggaa ggttttggct cgcttgcggg tgtcgcgaaa gcgaaaggtg     94920
     aaatctttag cggcctgccg gaaaacggta tcgccattat gaacgccgac aacaacgact     94980
     ggctgaactg gcagagcgta attggctcac gcaaagtgtg gcgtttctca cccaatgccg     95040
     ccaacagcga tttcaccgcc accaatatcc atgtgacctc gcacggtacg gaatttaccc     95100
     tacaaacccc aaccggtagc gtcgatgttc tgctgccgtt gccggggcgt cacaatattg     95160
     cgaatgcgct ggcagccgct gcgctctcca tgtccgtggg cgcaacgctt gatgctatca     95220
     aagcggggct ggcaaatctg aaagctgttc caggccgtct gttccccatc caactggcag     95280
     aaaaccagtt gctgctcgac gactcctaca acgccaatgt cggttcaatg actgcagcag     95340
     tccaggtact ggctgaaatg ccgggctacc gcgtgctggt ggtgggcgat atggcggaac     95400
     tgggcgctga aagcgaagcc tgccatgtac aggtgggcga ggcggcaaaa gctgctggta     95460
     ttgaccgcgt gttaagcgtg ggtaaacaaa gccatgctat cagcaccgcc agcggcgttg     95520
     gcgaacattt tgctgataaa actgcgttaa ttacgcgtct taaattactg attgctgagc     95580
     aacaggtaat tacgatttta gttaagggtt cacgtagtgc cgccatggaa gaggtagtac     95640
     gcgctttaca ggagaatggg acatgttagt ttggctggcc gaacatttgg tcaaatatta     95700
     ttccggcttt aacgtctttt cctatctgac gtttcgcgcc atcgtcagcc tgctgaccgc     95760
     gctgttcatc tcattgtgga tgggcccgcg tatgattgct catttgcaaa aactttcctt     95820
     tggtcaggtg gtgcgtaacg acggtcctga atcacacttc agcaagcgcg gtacgccgac     95880
     catgggcggg attatgatcc tgacggcgat tgtgatctcc gtactgctgt gggcttaccc     95940
     gtccaatccg tacgtctggt gcgtgttggt ggtgctggta ggttacggtg ttattggctt     96000
     tgttgatgat tatcgcaaag tggtgcgtaa agacaccaaa gggttgatcg ctcgttggaa     96060
     gtatttctgg atgtcggtca ttgcgctggg tgtcgccttc gccctgtacc ttgccggcaa     96120
     agacacgccc gcaacgcagc tggtggtccc attctttaaa gatgtgatgc cgcagctggg     96180
     gctgttctac attctgctgg cttacttcgt cattgtgggt actggcaacg cggtaaacct     96240
     gaccgatggt ctcgacggcc tggcaattat gccgaccgta tttgtcgccg gtggttttgc     96300
     gctggtggcg tgggcgaccg gcaatatgaa ctttgccagc tacttgcata taccgtatct     96360
     gcgacacgcc ggggaactgg ttattgtctg taccgcgata gtcggggcag gactgggctt     96420
     cctgtggttt aacacctatc cggcgcaggt ctttatgggc gatgtaggtt cgctggcgtt     96480
     aggtggtgcg ttaggcatta tcgccgtact gctacgtcag gaattcctgc tggtgattat     96540
     ggggggcgtg ttcgtggtag aaacgctttc tgtcatcctg caggtcggct cctttaaact     96600
     gcgcggacaa cgtattttcc gcatggcacc gattcatcac cactatgaac tgaaaggctg     96660
     gccggaaccg cgcgtcattg tgcgtttctg gattatttcg ctgatgctgg ttctgattgg     96720
     tctggcaacg ctgaaggtac gttaatcatg gctgattatc agggtaaaaa tgtcgtcatt     96780
     atcggcctgg gcctcaccgg gctttcctgc gtggactttt tcctcgctcg cggtgtgacg     96840
     ccgcgcgtta tggatacgcg tatgacaccg cctggcctgg ataaattacc cgaagccgta     96900
     gaacgccaca cgggcagtct gaatgatgaa tggctgatgg cggcagatct gattgtcgcc     96960
     agtcccggta ttgcactggc gcatccatcc ttaagcgctg ccgctgatgc cggaatcgaa     97020
     atcgttggcg atatcgagct gttctgtcgc gaagcacaag caccgattgt ggcgattacc     97080
     ggttctaacg gcaaaagcac ggtcaccacg ctagtgggtg aaatggcgaa agcggcgggg     97140
     gttaacgttg gtgtgggtgg caatattggc ctgcctgcgt tgatgctact ggatgatgag     97200
     tgtgaactgt acgtgctgga actgtcgagc ttccagctgg aaaccacctc cagcttacag     97260
     gcggtagcag cgaccattct gaacgtgact gaagatcata tggatcgcta tccgtttggt     97320
     ttacaacagt atcgtgcagc aaaactgcgc atttacgaaa acgcgaaagt ttgcgtggtt     97380
     aatgctgatg atgccttaac aatgccgatt cgcggtgcgg atgaacgctg cgtcagcttt     97440
     ggcgtcaaca tgggtgacta tcacctgaat catcagcagg gcgaaacctg gctgcgggtt     97500
     aaaggcgaga aagtgctgaa tgtgaaagag atgaaacttt ccgggcagca taactacacc     97560
     aatgcgctgg cggcgctggc gctggcagat gctgcagggt taccgcgtgc cagcagcctg     97620
     aaagcgttaa ccacattcac tggtctgccg catcgctttg aagttgtgct ggagcataac     97680
     ggcgtacgtt ggattaacga ttcgaaagcg accaacgtcg gcagtacgga agcggcgctg     97740
     aatggcctgc acgtagacgg cacactgcat ttgttgctgg gtggcgatgg taaatcggcg     97800
     gactttagcc cactggcgcg ttacctgaat ggcgataacg tacgtctgta ttgtttcggt     97860
     cgtgacggcg cgcagctggc ggcgctacgc ccggaagtgg cagaacaaac cgaaactatg     97920
     gaacaggcga tgcgcttgct ggctccgcgt gttcagccgg gcgatatggt tctgctctcc     97980
     ccagcctgtg ccagccttga tcagttcaag aactttgaac aacgaggcaa tgagtttgcc     98040
     cgtctggcga aggagttagg ttgatgcgtt tatctctccc tcgcctgaaa atgccgcgcc     98100
     tgccaggatt cagtatcctg gtctggatct ccacggcgct aaagggctgg gtgatgggct     98160
     cgcgggaaaa agataccgac agcctgatca tgtacgatcg caccttactg tggctgacct     98220
     tcggcctcgc ggcgattggc tttatcatgg tgacctcggc gtcaatgccc atagggcaac     98280
     gcttaaccaa cgatccgttc ttcttcgcga agcgtgatgg tgtctatctg attttggcgt     98340
     ttattctggc gatcattacg ctgcgtctgc cgatggagtt ctggcaacgc tacagtgcca     98400
     cgatgctgct cggatctatc atcctgctga tgatcgtcct ggtagtgggt agctcggtta     98460
     aaggggcatc gcgttggatc gatctcggtt tgctgcgtat ccagcctgcg gagctgacaa     98520
     aactgtcgct gttttgctat atcgccaact atctggtgcg taaaggcgac gaagtacgta     98580
     ataacctgcg cggcttcctg aaaccgatgg gcgtgattct ggtgttggca gtgttactgc     98640
     tggcacagcc agaccttggt acggtggtgg tgttgtttgt gactacgctg gcgatgttgt     98700
     tcctggcggg agcgaaattg tggcagttca ttgccattat cggtatgggc atttcagcgg     98760
     ttgtgttgct gatactcgcc gaaccgtacc gtatccgccg tgttaccgca ttctggaacc     98820
     cgtgggaaga tccctttggc agcggctatc agttaacgca atcgctgatg gcgtttggtc     98880
     gcggcgaact ttgggggcaa ggtttaggta actcggtaca aaaactggag tatctgccgg     98940
     aagcgcacac tgactttatt ttcgccatta tcggcgaaga actggggtat gtcggtgtgg     99000
     tgctggcact tttaatggta ttcttcgtcg cttttcgcgc gatgtcgatt ggccgtaaag     99060
     cattagaaat tgaccaccgt ttttccggtt ttctcgcctg ttctattggc atctggttta     99120
     gcttccaggc gctggttaac gtaggcgcgg cggcggggat gttaccgacc aaaggtctga     99180
     cattgccgct gatcagttac ggtggttcga gcttactgat tatgtcgaca gccatcatga     99240
     tgctgttgcg tattgattat gaaacgcgtc tggagaaagc gcaggcgttt gtacgaggtt     99300
     cacgatgagt ggtcaaggaa agcgattaat ggtgatggca ggcggaaccg gtggacatgt     99360
     attcccggga ctggcggttg cgcaccatct aatggctcag ggttggcaag ttcgctggct     99420
     ggggactgcc gaccgtatgg aagcggactt agtgccaaaa catggcatcg aaattgattt     99480
     cattcgtatc tctggtctgc gtggaaaagg tataaaagca ctgatagctg ccccgctgcg     99540
     tatcttcaac gcctggcgtc aggcgcgggc gattatgaaa gcgtacaaac ctgacgtggt     99600
     gctcggtatg ggaggctacg tgtcaggtcc aggtggtctg gccgcgtggt cgttaggcat     99660
     tccggttgta cttcatgaac aaaacggtat tgcgggctta accaataaat ggctggcgaa     99720
     gattgccacc aaagtgatgc aggcgtttcc aggtgctttc cctaatgcgg aagtagtggg     99780
     taacccggtg cgtaccgatg tgttggcgct gccgttgccg cagcaacgtt tggctggacg     99840
     tgaaggtccg gttcgtgtgc tggtagtggg tggttctcag ggcgcacgca ttcttaacca     99900
     gacaatgccg caggttgctg cgaaactggg tgattcagtc actatctggc atcagagcgg     99960
     caaaggttcg caacaatccg ttgaacaggc gtatgccgaa gcggggcaac cgcagcataa    100020
     agtgacggaa tttattgatg atatggcggc ggcgtatgcg tgggcggatg tcgtcgtttg    100080
     ccgctccggt gcgttaacgg tgagtgaaat cgccgcggca ggactaccgg cgttgtttgt    100140
     gccgtttcaa cataaagacc gccagcaata ctggaatgcg ctaccgctgg aaaaagcggg    100200
     cgcagccaaa attatcgagc agccacagct tagcgtggat gctgtcgcca acaccctggc    100260
     cgggtggtcg cgagaaacct tattaaccat ggcagaacgc gcccgcgctg catccattcc    100320
     ggatgccacc gagcgagtgg caaatgaagt gagccgggtt gcccgggcgt aattgtagcg    100380
     atgccttttg catcgtatga atttaagaag ttaatggcgt aaagaatgaa tacacaacaa    100440
     ttggcaaaac tgcgttccat cgtgcccgaa atgcgtcgcg ttcggcacat acattttgtc    100500
     ggcattggtg gtgccggtat gggcggtatt gccgaagttc tggccaatga aggttatcag    100560
     atcagtggtt ccgatttagc gccaaatccg gtcacgcagc agttaatgaa tctgggtgcg    100620
     acgatttatt tcaaccatcg cccggaaaac gtacgtgatg ccagcgtggt cgttgtttcc    100680
     agcgcgattt ctgccgataa cccggaaatt gtcgccgctc atgaagcgcg tattccggtg    100740
     atccgtcgtg ccgaaatgct ggctgagtta atgcgttttc gtcatggcat cgccattgcc    100800
     ggaacgcacg gcaaaacgac aaccaccgcg atggtttcca gcatctacgc agaagcgggg    100860
     ctcgacccaa ccttcgttaa cggcgggctg gtaaaagcgg cgggggttca tgcgcgtttg    100920
     gggcatggtc ggtacctgat tgccgaagca gatgagagtg atgcatcgtt cctgcatctg    100980
     caaccgatgg tggcgattgt caccaatatc gaagccgacc acatggatac ctaccagggc    101040
     gactttgaga atttaaaaca gacttttatt aattttctgc acaacctgcc gttttacggt    101100
     cgtgcggtga tgtgtgttga tgatccggtg atccgcgaat tgttaccgcg agtggggcgt    101160
     cagaccacga cttacggctt cagcgaagat gccgacgtgc gtgtagaaga ttatcagcag    101220
     attggcccgc aggggcactt tacgctgctg cgccaggaca aagagccgat gcgcgtcacc    101280
     ctgaatgcgc caggtcgtca taacgcgctg aacgccgcag ctgcggttgc ggttgctacg    101340
     gaagagggca ttgacgacga ggctattttg cgggcgcttg aaagcttcca ggggactggt    101400
     cgccgttttg atttcctcgg tgaattcccg ctggagccag tgaatggtaa aagcggtacg    101460
     gcaatgctgg tcgatgacta cggccaccac ccgacggaag tggacgccac cattaaagcg    101520
     gcgcgcgcag gctggccgga taaaaacctg gtaatgctgt ttcagccgca ccgttttacc    101580
     cgtacgcgcg acctgtatga tgatttcgcc aatgtgctga cgcaggttga taccctgttg    101640
     atgctggaag tgtatccggc tggcgaagcg ccaattccgg gagcggacag ccgttcgctg    101700
     tgtcgcacaa ttcgtggacg tgggaaaatt gatcccattc tggtgccgga tccggcgcgg    101760
     gtagccgaga tgctggcacc ggtattaacc ggtaacgacc tgattctcgt tcagggggct    101820
     ggtaatattg gaaaaattgc ccgttcttta gctgaaatca aactgaagcc gcaaactccg    101880
     gaggaagaac aacatgactg ataaaatcgc ggtcctgttg ggtgggacct ccgctgagcg    101940
     ggaagtttct ctgaattctg gcgcagcggt gttagccgga ctgcgtgaag gcggtattga    102000
     cgcgtatcct gtcgacccga aagaagtcga cgtgacgcaa ctgaagtcga tgggctttca    102060
     gaaagtgttt atcgcgctac acggtcgcgg cggtgaagat ggtacgctgc aggggatgct    102120
     cgagctgatg ggcttgcctt ataccggaag cggagtgatg gcatctgcgc tttcaatgga    102180
     taaactacgc agcaaacttc tatggcaagg tgccggttta ccggtcgcgc cgtgggtagc    102240
     gttaacccgc gcagagtttg aaaaaggcct gagcgataag cagttagcag aaatttctgc    102300
     tctgggtttg ccggttatcg ttaagccgag ccgcgaaggt tccagtgtgg gaatgtcaaa    102360
     agtagtagca gaaaatgctc tacaagatgc attaagattg gcatttcagc acgatgaaga    102420
     agtattgatt gaaaaatggc taagtgggcc ggagttcacg gttgcgatac tcggtgaaga    102480
     aattttaccg tcaatacgta ttcaaccgtc cggaaccttc tatgattatg aggcgaagta    102540
     tctctctgat gagacacagt atttctgccc cgcaggtctg gaagcgtcac aagaggccaa    102600
     tttgcaggca ttagtgctga aagcatggac gacgttaggt tgcaaaggat ggggacgtat    102660
     tgacgttatg ctggacagcg atggacagtt ttatctgctg gaagccaata cctcaccggg    102720
     tatgaccagc cacagcctgg tgccgatggc ggcacgtcag gcaggtatga gcttctcgca    102780
     gttggtagta cgaattctgg aactggcgga ctaatatgtc gcaggctgct ctgaacacgc    102840
     gaaacagcga agaagaggtt tcttctcgcc gcaataatgg aacgcgtctg gcggggatcc    102900
     ttttcctgct gaccgtttta acgacagtgt tggtgagcgg ctgggtcgtg ttgggctgga    102960
     tggaagatgc gcaacgcctg ccgctctcaa agctggtgtt gaccggtgaa cgccattaca    103020
     cacgtaatga cgatatccgg cagtcgatcc tggcattggg tgagccgggt acctttatga    103080
     cccaggatgt caacatcatc cagacgcaaa tagaacaacg cctgccgtgg attaagcagg    103140
     tgagcgtcag aaagcagtgg cctgatgaat tgaagattca tctggttgaa tatgtgccga    103200
     ttgcgcggtg gaatgatcaa catatggtag acgcggaagg aaataccttc agcgtgccgc    103260
     cagaacgcac cagcaagcag gtgcttccaa tgctgtatgg cccggaaggc agcgccaatg    103320
     aagtgttgca gggctatcgc gaaatggggc agatgctggc aaaggacaga tttactctga    103380
     aggaagcggc gatgaccgcg cggcgttcct ggcagttgac gctgaataac gatattaagc    103440
     tcaatcttgg ccggggcgat acgatgaaac gtttggctcg ctttgtagaa ctttatccgg    103500
     ttttacagca gcaggcgcaa accgatggca aacggattag ctacgttgat ttgcgttatg    103560
     actctggagc ggcagtaggc tgggcgccct tgccgccaga ggaatctact cagcaacaaa    103620
     atcaggcaca ggcagaacaa caatgatcaa ggcgacggac agaaaactgg tagtaggact    103680
     ggagattggt accgcgaagg ttgccgcttt agtaggggaa gttctgcccg acggtatggt    103740
     caatatcatt ggcgtgggca gctgcccgtc gcgtggtatg gataaaggcg gggtgaacga    103800
     cctcgaatcc gtggtcaagt gcgtacaacg cgccattgac caggcagaat tgatggcaga    103860
     ttgtcagatc tcttcggtat atctggcgct ttctggtaag cacatcagct gccagaatga    103920
     aattggtatg gtgcctattt ctgaagaaga agtgacgcaa gaagatgtgg aaaacgtcgt    103980
     ccataccgcg aaatcggtgc gtgtgcgcga tgagcatcgt gtgctgcatg tgatcccgca    104040
     agagtatgcg attgactatc aggaagggat caagaatccg gtaggacttt cgggcgtgcg    104100
     gatgcaggca aaagtgcacc tgatcacatg tcacaacgat atggcgaaaa acatcgtcaa    104160
     agcggttgaa cgttgtgggc tgaaagttga ccaactgata tttgccggac tggcatcaag    104220
     ttattcggta ttgacggaag atgaacgtga actgggtgtc tgcgtcgtcg atatcggtgg    104280
     tggtacaatg gatatcgccg tttataccgg tggggcattg cgccacacta aggtaattcc    104340
     ttatgctggc aatgtcgtga ccagtgatat cgcttacgcc tttggcacgc cgccaagcga    104400
     cgccgaagcg attaaagttc gccacggttg tgcgctgggt tccatcgttg gaaaagatga    104460
     gagcgtggaa gtgccgagcg taggtggtcg tccgccacgg agtctgcaac gtcagacact    104520
     ggcagaggtg atcgagccgc gctataccga gctgctcaac ctggtcaacg aagagatatt    104580
     gcagttgcag gaaaagcttc gccaacaagg ggttaaacat cacctggcgg caggcattgt    104640
     attaaccggt ggcgcagcgc agatcgaagg tcttgcagcc tgtgctcagc gcgtgtttca    104700
     tacgcaagtg cgtatcggcg cgccgctgaa cattaccggt ttaacggatt atgctcagga    104760
     gccgtattat tcgacggcgg tgggattgct tcactatggg aaagagtcac atcttaacgg    104820
     tgaagctgaa gtagaaaaac gtgttacagc atcagttggc tcgtggatca agcgactcaa    104880
     tagttggctg cgaaaagagt tttaattttt atgaggccga cgatgattac ggcctcaggc    104940
     gacaggcaca aatcggagag aaactatgtt tgaaccaatg gaacttacca atgacgcggt    105000
     gattaaagtc atcggcgtcg gcggcggcgg cggtaatgct gttgaacaca tggtgcgcga    105060
     gcgcattgaa ggtgttgaat tcttcgcggt aaataccgat gcacaagcgc tgcgtaaaac    105120
     agcggttgga cagacgattc aaatcggtag cggtatcacc aaaggactgg gcgctggcgc    105180
     taatccagaa gttggccgca atgcggctga tgaggatcgc gatgcattgc gtgcggcgct    105240
     ggaaggtgca gacatggtct ttattgctgc gggtatgggt ggtggtaccg gtacaggtgc    105300
     ggcaccagtc gtcgctgaag tggcaaaaga tttgggtatc ctgaccgttg ctgtcgtcac    105360
     taagcctttc aactttgaag gcaagaagcg tatggcattc gcggagcagg ggatcactga    105420
     actgtccaag catgtgaact ctctgatcac tatcccgaac gacaaactgc tgaaagttct    105480
     gggccgcggt atctccctgc tggatgcgtt tggcgcagcg aacgatgtac tgaaaggcgc    105540
     tgtgcaaggt atcgctgaac tgattactcg tccgggtttg atgaacgtgg actttgcaga    105600
     cgtacgcacc gtaatgtctg agatgggcca cgcaatgatg ggttctggcg tggcgagcgg    105660
     tgaagaccgt gcggaagaag ctgctgaaat ggctatctct tctccgctgc tggaagatat    105720
     cgacctgtct ggcgcgcgcg gcgtgctggt taacatcacg gcgggcttcg acctgcgtct    105780
     ggatgagttc gaaacggtag gtaacaccat ccgtgcattt gcttccgaca acgcgactgt    105840
     ggttatcggt acttctcttg acccggatat gaatgacgag ctgcgcgtaa ccgttgttgc    105900
     gacaggtatc ggcatggaca aacgtcctga aatcactctg gtgaccaata agcaggttca    105960
     gcagccagtg atggatcgct accagcagca tgggatggct ccgctgaccc aagagcagaa    106020
     gccggttgct aaagtcgtga atgacaatgc gccgcaaact gcgaaagagc cggattatct    106080
     ggatatccca gcattcctgc gtaagcaagc tgattaagaa ttgactggaa tttgggtttc    106140
     gattctcttt gtgctaaact ggcccgccga atgtatagta cacttcggtt ggataggtaa    106200
     tttggcgaga taatacgatg atcaaacaaa ggacacttaa acgtatcgtt caggcgacgg    106260
     gtgtcggttt acataccggc aagaaagtca ccctgacgtt acgccctgcg ccggccaaca    106320
     ccggggtcat ctatcgtcgc accgacttga atccaccggt agatttcccg gccgatgcca    106380
     aatctgtgcg tgataccatg ctctgtacgt gtctggtcaa cgagcatgat gtacggattt    106440
     caaccgtaga gcacctcaat gctgctctcg cgggcttggg catcgataac attgttatcg    106500
     aagttaacgc gccggaaatc ccgatcatgg acggcagcgc cgctccgttt gtatacctgc    106560
     tgcttgacgc cggtatcgac gagttgaact gcgccaaaaa atttgttcgc atcaaagaga    106620
     ctgttcgtgt cgaagatggc gataagtggg ctgaatttaa gccgtacaat ggtttttcgc    106680
     tggatttcac catcgatttt aaccatccgg ctattgattc cagcaaccag cgctatgcga    106740
     tgaacttctc cgctgatgcg tttatgcgcc agatcagccg tgcgcgtacg ttcggtttca    106800
     tgcgtgatat cgaatatctg cagtcccgtg gtttgtgcct gggcggcagc ttcgattgtg    106860
     ccatcgttgt tgacgattat cgcgtactga acgaagacgg cctgcgtttt gaagacgaat    106920
     ttgtgcgtca caaaatgctc gatgcgatcg gtgacttgtt catgtgtggt cacaatatta    106980
     ttggtgcatt taccgcttat aaatccggtc atgcactgaa taacaaactg ctgcaggctg    107040
     tcctggcgaa acaggaagcc tgggaatatg tgaccttcca ggacgacgca gaactgccgt    107100
     tggccttcaa agcgccttca gctgtactgg cataacgaca tttatactgt cgtataaaat    107160
     tcgactggca aatctggcac tctctccggc caggtgaacc agtcgttttt ttttgaattt    107220
     tataagagct ataaaaaacg gtgcgaacgc tgttttctta agcacttttc cgcacaactt    107280
     atcttcattc gtgctgtgga ctgcaggctt taatgataag atttgtgcgc taaatacgtt    107340
     tgaatatgat cgggatggca ataacgtgag tggaatactg acgcgctggc gacagtttgg    107400
     taaacgctac ttctggccgc atctcttatt agggatggtt gcggcgagtt taggtttgcc    107460
     tgcgctcagc aacgccgccg aaccaaacgc gcccgcaaaa gcgacaaccc gcaaccacga    107520
     gccttcagcc aaagttaact ttggtcaatt ggccttgctg gaagcgaaca cacgccgccc    107580
     gaattcgaac tattccgttg attactggca tcaacatgcc attcgcacgg taatccgtca    107640
     tctttctttc gcaatggcac cgcaaacact gcccgttgct gaagaatctt tgcctcttca    107700
     ggcgcaacat cttgcattac tggatacgct cagcgcgctg ctgacccagg aaggcacgcc    107760
     gtctgaaaag ggttatcgca ttgattatgc gcattttacc ccacaagcaa aattcagcac    107820
     gcccgtctgg ataagccagg cgcaaggcat ccgtgctggc cctcaacgcc tcacctaaca    107880
     acaataaacc tttacttcat tttattaact ccgcaacgcg gggcgtttga gattttatta    107940
     tgctaatcaa attgttaact aaagttttcg gtagtcgtaa cgatcgcacc ctgcgccgga    108000
     tgcgcaaagt ggtcaacatc atcaatgcca tggaaccgga gatggaaaaa ctctccgacg    108060
     aagaactgaa agggaaaacc gcagagtttc gtgcacgtct ggaaaaaggc gaagtgctgg    108120
     aaaatctgat cccggaagct ttcgccgtgg tacgtgaggc aagtaagcgc gtctttggta    108180
     tgcgtcactt cgacgttcag ttactcggcg gtatggttct taacgaacgc tgcatcgccg    108240
     aaatgcgtac cggtgaagga aaaaccctga ccgcaacgct gcctgcttac ctgaacgcac    108300
     taaccggtaa aggcgtgcac gtagttaccg tcaacgacta cctggcgcaa cgtgacgccg    108360
     aaaacaaccg tccgctgttt gaattccttg gcctgactgt cggtatcaac ctgccgggca    108420
     tgccagcacc ggcaaagcgc gaagcttacg cagctgacat cacttacggt acgaacaacg    108480
     aatacggctt tgactacctg cgcgacaaca tggcgttcag ccctgaagaa cgtgtacagc    108540
     gtaaactgca ctatgcgctg gtggacgaag tggactccat cctgatcgat gaagcgcgta    108600
     caccgctgat catttccggc ccggcagaag acagctcgga aatgtataaa cgcgtgaata    108660
     aaattattcc gcacctgatc cgtcaggaaa aagaagactc cgaaaccttc cagggcgaag    108720
     gccacttctc ggtggacgaa aaatctcgcc aggtgaacct gaccgaacgt ggtctggtgc    108780
     tgattgaaga actgctggtg aaagagggca tcatggatga aggggagtct ctgtactctc    108840
     cggccaacat catgctgatg caccacgtaa cggcggcgct gcgcgctcat gcgctgttta    108900
     cccgtgacgt cgactacatc gttaaagatg gtgaagttat catcgttgac gaacacaccg    108960
     gtcgtaccat gcagggccgt cgctggtccg atggtctgca ccaggctgtg gaagcgaaag    109020
     aaggtgtgca gatccagaac gaaaaccaaa cgctggcttc gatcaccttc cagaactact    109080
     tccgtctgta tgaaaaactg gcggggatga ccggtactgc tgataccgaa gctttcgaat    109140
     ttagctcaat ctacaagctg gataccgtcg ttgttccgac caaccgtcca atgattcgta    109200
     aagatctgcc ggacctggtc tacatgactg aagcggaaaa aattcaggcg atcattgaag    109260
     atatcaaaga acgtactgcg aaaggccagc cggtgctggt gggtactatc tccatcgaaa    109320
     aatcggagct ggtgtcaaac gaactgacca aagccggtat taagcacaac gtcctgaacg    109380
     ccaaattcca cgccaacgaa gcggcgattg ttgctcaggc aggttatccg gctgcggtga    109440
     ctatcgcgac caatatggcg ggtcgtggta cagatattgt gctcggtggt agctggcagg    109500
     cagaagttgc cgcgctggaa aatccgaccg cagagcaaat tgaaaaaatt aaagccgact    109560
     ggcaggtacg tcacgatgcg gtactggaag caggtggcct gcatatcatc ggtaccgagc    109620
     gtcacgaatc ccgtcgtatc gataaccagt tgcgcggtcg ttctggtcgt cagggggatg    109680
     ctggttcttc ccgtttctac ctgtcgatgg aagatgcgct gatgcgtatt tttgcttccg    109740
     accgagtatc cggcatgatg cgtaaactgg gtatgaagcc aggcgaagcc attgaacacc    109800
     cgtgggtgac taaagcgatt gccaacgccc agcgtaaagt tgaaagccgt aacttcgaca    109860
     ttcgtaagca actgctggaa tatgatgacg tggctaacga tcagcgtcgc gccatttact    109920
     cccagcgtaa cgaactgttg gatgtcagcg atgtgagcga aaccattaac agcattcgtg    109980
     aagatgtgtt caaagcgacc attgatgcct acattccacc acagtcgctg gaagaaatgt    110040
     gggatattcc ggggctgcag gaacgtctga agaacgattt cgacctcgat ttgccaattg    110100
     ccgagtggct ggataaagaa ccagaactgc atgaagagac gctgcgtgac ggcattctgg    110160
     cgcagtccat cgaagtgtat cagcgtaaag aagaagtggt tggtgctgag atgatgcgtc    110220
     acttcgagaa aggcgtcatg ctgcaaacgc ttgactccct gtggaaagag cacctggcag    110280
     cgatggacta tctgcgtcag ggtatccacc tgcgtggcta cgcacagaaa gatccgaagc    110340
     aggaatacaa acgtgaatcg ttctccatgt ttgcagcgat gctggagtcg ttgaaatatg    110400
     aagttatcag tacgctgagc aaagttcagg tacgtatgcc tgaagaggtt gaggagctgg    110460
     aacaacagcg tcgtatggaa gccgagcgtt tagcgcaaat gcagcagctt agccatcagg    110520
     atgacgactc tgcagccgca gctgcactgg cggcgcaaac cggagagcgc aaagtaggac    110580
     gtaacgatcc ttgcccgtgc ggttctggta aaaaatacaa gcagtgccat ggccgcctgc    110640
     aataaaagct aactgttgaa gtaaaaggcg caggattctg cgcctttttt ataggtttaa    110700
     gacaatgaaa aagctgcaaa ttgcggtagg tattattcgc aacgagaaca atgaaatctt    110760
     tataacgcgt cgcgcagcag atgcgcacat ggcgaataaa ctggagtttc ccggcggtaa    110820
     aattgaaatg ggtgaaacgc cggaacaggc ggtggtgcgt gaacttcagg aagaagtcgg    110880
     gattaccccc caacattttt cgctatttga aaaactggaa tatgaattcc cggacaggca    110940
     tataacactg tggttttggc tggtcgaacg ctgggaaggg gagccgtggg gtaaagaagg    111000
     gcaacccggt gagtggatgt cgctggtcgg tcttaatgcc gatgattttc cgccagccaa    111060
     tgaaccggta attgcgaagc ttaaacgtct gtaggtcaga taaggcgttt tcgccgcatc    111120
     cgacattcgc acacgatgcc tgatgcgacg ctggcgcgtc ttatcaggcc taaagggatt    111180
     tctaactcat tgataaattt gtttttgtag gtcggataag gcgttcacgc cgcatccgac    111240
     atttgcacaa gatgcctgat gcgacgctgt ccgcgtctta tcaggcctac gtgcggcatc    111300
     agacaaatgt cactgctttg gttcttcgct ccagtcatcg ctttcggaaa gatcgccact    111360
     gctggggatt cgtttttctt cagcagccca ttctccgagg tcgatcag                 111408
//
BioPerl-1.007002/t/data/EG352462.gbxml000444000766000024      1036613155576321 16732 0ustar00cjfieldsstaff000000000000



  EG352462
  437
  single
  mRNA
  linear
  EST
  11-OCT-2006
  11-OCT-2006
  SAAH-aad23f02.g1 Agen 0058 Schmidtea mediterranea cDNA 5' similar to sp|P35779|VA3_SOLRI Venom allergen III (Allergen Sol r 3) (Sol r III) pir|B58853 venom allergen Sol r 3 - black imported fire ant, mRNA sequence
  EG352462
  EG352462.1
  
    gnl|dbEST|42340791
    gb|EG352462.1|
    gi|116038450
  
  
    EST
  
  Schmidtea mediterranea
  Schmidtea mediterranea
  Eukaryota; Metazoa; Platyhelminthes; Turbellaria; Seriata; Tricladida; Paludicola; Dugesiidae; Schmidtea
  
    
      1
      1..437
      
        Wilson,R.
      
      WashU Planaria EST project
      Unpublished (2006)
    
  
  Contact: Wilson, R.~WashU Planaria EST project~Washington University School of Medicine~4444 Forest Park Parkway, Box 8501, St. Louis, MO 63108, USA~Tel: 314 286 1800~Fax: 314 286 1810~Email: submissions@watson.wustl.edu~Library material provided by Dr. Peter Reddien Library constructed by Agencourt Bioscience Corporation Library sequenced by Washington University Genome Sequencing Center ~This trace has been recalled with phred ~original value before phred recall for SR was 516~Seq primer: -28RPpOT
  
    
      source
      1..437
      
        
          1
          437
          EG352462.1
        
      
      
        
          organism
          Schmidtea mediterranea
        
        
          mol_type
          mRNA
        
        
          db_xref
          taxon:79327
        
        
          clone_lib
          Agen 0058
        
        
          lab_host
          DH10B cells
        
        
          note
          Vector: pAGEN-1; Site_1: NotI; Site_2: EcoRV; Total RNA isolated from S.mediterranea
        
      
    
  
  aataaaattacatttgttttccttttactagatttctgttctggagatctttctgatgaagatttttatctaatcttggaaatccatgacaaattccgaaaatctgtggccaatggagaagtttcgaaccaacccaaagcagcgaacatgcaacaaatggtatggagtgaagaagcggcatccagagcgcaggcaaccgcggataaatgctcatttaatcacgacacaataaatgaccgtaaatatggaaattatgaatgggttggacagaatattgccatgttcacaggaggaaatattgccaaaggcgtacaattgtggtttaacgaggtttccggatacacattttcagataatagttgttcagaaaatacttgcggacattatacacaaattgtatgggccaaatctaaagagctgggctgtggactggccaa


BioPerl-1.007002/t/data/ENr111.mfa.example.elems000444000766000024       103713155576321 21023 0ustar00cjfieldsstaff000000000000## Note that element detection relies on computing a false positive rate that uses random permutations of the original data.  
## Due to the stochastic nature of the permutations, you may see subtle differences from run to run.  
## Do not expect these test results to be precisely what you will get when you do your own run on the test dataset. 

500000 3.85
334180 334352 173 449 1.03744e-165
337735 337915 181 458.2 5.02405e-164
262604 262861 258 473.1 3.64789e-117
285427 285608 182 386.1 8.42494e-113
309563 309744 182 383.6 2.88895e-111
BioPerl-1.007002/t/data/Fang_2003.xml000444000766000024     34460513155576321 17005 0ustar00cjfieldsstaff000000000000

  
    phenex-metadata
    
      Jeff Engeman 1st pass (11Dec08)
      Fang, 1993
      doi:10.1643/IA03-131.1
Fang sent matrix; PM merged;
    
  
  
    
      
        OBO_ID
        TTO:1003636
      
      
        OBO_specimens
        
          
          
          
          
          
          
          
          
          
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:1003061
      
      
        OBO_specimens
        
          
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:10000019
      
      
        OBO_specimens
        
          
          
          
        
      
      
        phenex_comment
        Fang used quotes 'Danio erythromicron' in her matrix - ID OK?
      
    
    
      
        OBO_ID
        TTO:1067725
      
      
        OBO_specimens
        
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:1049804
      
      
        OBO_specimens
        
          
          
          
          
          
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:1001979
      
      
        OBO_specimens
        
          
          
          
          
          
          
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:1061537
      
      
        OBO_specimens
        
          
          
          
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:1061538
      
      
        OBO_specimens
        
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:1003080
      
      
        OBO_specimens
        
          
          
          
          
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:1048166
      
      
        OBO_specimens
        
          
          
          
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:1003470
      
      
        OBO_specimens
        
          
          
          
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:1063985
      
      
        OBO_specimens
        
          
          
        
      
    
    
      
        OBO_ID
        TTO:1002069
      
      
        OBO_specimens
        
          
          
          
          
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:10000060
      
      
        OBO_specimens
        
          
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:1003508
      
      
        OBO_specimens
        
          
          
          
          
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:1003220
      
      
        OBO_specimens
        
          
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:1006168
      
      
        OBO_specimens
        
          
          
          
          
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:1003600
      
      
        OBO_specimens
        
          
          
          
          
          
        
      
    
    
      
        OBO_ID
        TTO:10000019
      
      
        OBO_specimens
        
          
          
          
        
      
    
    
      
        OBO_specimens
        
          
          
          
          
        
      
      
        phenex_comment
        Need to add to TTO
      
      
        OBO_ID
        TTO:10000059
      
    
    
      
        OBO_specimens
        
          
          
          
          
        
      
      
        phenex_comment
        Need to add to TTO
      
      
        OBO_ID
        TTO:10000058
      
    
  
  
    
      
        
        
        
      
      
        
        
        
      
      
        
        
      
      
        
        
        
      
      
        
        
        
      
      
        
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                
              
            
          
        
        
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
        
      
      
        
        
      
      
        
        
      
      
        
        
      
      
        
        
        
      
      
        
        
      
      
        
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
        
      
      
        
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
        
      
      
        
        
      
      
        
        
      
      
        
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
          
            OBO_phenotype
            
              
                
                  
                    
                      
                        
                          
                        
                      
                    
                  
                  
                    
                  
                
              
            
          
        
        
          
            OBO_phenotype
            
              
                
                  
                    
                      
                        
                          
                        
                      
                    
                  
                  
                    
                  
                
              
            
          
        
      
      
        
        
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
    
    
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
      
      
      
      
      
    
  

BioPerl-1.007002/t/data/GO.defs.test000444000766000024       310713155576321 17017 0ustar00cjfieldsstaff000000000000!version: $Revision: 1.1 $
!date:                 Fri Sep 20 14:08:27 GMT 2002
!saved-by: gwg
!autogenerated-by: DAG-Edit version 1.311
!
!Gene Ontology definitions
!

term: cellular_component
goid: GO:0005575
definition: The part of a cell of which a gene product is a component; for purpose of GO includes the extracellular environment of cells; a gene product may be a component of one or more parts of a cell; this term includes gene products that are parts of macromolecular complexes, by the definition that all members of a complex normally co-purify under all except extreme conditions.
definition_reference: GO:curators

term: ascus
goid: GO:0005627
definition: A sac-like fruiting body (ascomycete fungi); contains ascospores (typically eight in number).
definition_reference: ISBN:0198547684

term: lipid particle
goid: GO:0005811
definition: Any particle of coalesced lipids in the cytoplasm of a cell.
definition_reference: GO:mah

term: spore wall (sensu Fungi)
goid: GO:0005619
definition: The specialized cell wall of the ascospore (spore), as described in Saccharomyces.
definition_reference: ISBN:0879693568

term: membrane fraction
goid: GO:0005624
definition: That fraction of cells, prepared by disruptive biochemical methods, that includes the plasma and other membranes.
definition_reference: FB:ma

term: microsome
goid: GO:0005792
definition: Any of the small, heterogeneous, artifactual, vesicular particles, 50-150 nm in diameter, that are formed when some eukaryotic cells are homogenized and that sediment on centrifugation at 100000 g.
definition_reference: ISBN:0198506732



BioPerl-1.007002/t/data/GO.defs.test2000444000766000024       166013155576321 17103 0ustar00cjfieldsstaff000000000000!version: $Revision: 1.1 $
!date:                 Fri Sep 20 14:08:27 GMT 2002
!saved-by: gwg
!autogenerated-by: DAG-Edit version 1.311
!
!Gene Ontology definitions
!

term: cellular_component
goid: GO:0003673
definition: The part of a cell of which a gene product is a component; for purpose of GO includes the extracellular environment of cells; a gene product may be a component of one or more parts of a cell; this term includes gene products that are parts of macromolecular complexes, by the definition that all members of a complex normally co-purify under all except extreme conditions.
definition_reference: GO:curators

term: ascus
goid: GO:0005575
definition: A sac-like fruiting body (ascomycete fungi); contains ascospores (typically eight in number).
definition_reference: ISBN:0198547684

term: lipid particle
goid: GO:0018895
definition: Any particle of coalesced lipids in the cytoplasm of a cell.
definition_reference: GO:mah
BioPerl-1.007002/t/data/Genscan.FastA000444000766000024       213513155576321 17167 0ustar00cjfieldsstaff000000000000>description
GTATTGCGTCACTTCCTGTCTTCTCAATCGTTCGTTGGTTGCACTGTGCATGGGGTGTTGTATTCACTTAATATTGAACACTTGGTGTGTTGTATTCACTTAATATTGAACACTTGGTGTGTTGTATTCACTTTACTTAAAATTTTGAACACTTGGGACATTCTAGTCACCTGATAACAACAGTGAGAAACAACCCATATTAAACAAATACAGGGCTCCACCGATTATCAGCGTTAGCATGGCCTCACCGTCTGTTTCACCCGGTGTCTTTGTCTGTTCAGCGTGTGAAATGTTTAGTTACTCCTCTGCCTCCTTTAGTGAAGGGAATAGGTGCAGAAAGTGTAGTTTATTTATGGCTATGGAGGCGAGACTTAGCGAGCTTGAGACGCGGTTCCGCAGCTTGGAGTTAGCTGGAGTTGCGTCAGGTAGCCAGGAGAAGCTAGCTGCTGCGGAGCCGCCTAGCGTAGCTACAGCTAGCGGTCCCCCGGCAGCAGCCGAGCAGCCGGCTAGCCAGGGCGGCTGGGTGACGGTTCGTAGGAAGCGTAGCCCAAAACAAAGGCCCACGGTGCACCACCAACCGCTTCCCGTGGCTAACCGCTTTTCCCCACTCGGCGACACACCCGCTGAGAAACCGACCCTGGTAATTGGCGACTCTGTTTTGCGCTACGTGAAGCCGACTCCAGCGACCATAGTTAAGTGCATTCCGGGGGCCAGAGCGGGCGACATAGAAGCAAATTTACGGCTGCTGGCGAGACGTAATCGTAAATTTGGTAAAGTTATTATTCACGTCGGAGCCAACGACACCCGGCTTCGTCAGTCGGAGGTCACCAAAATTAACTTGGAGTCGGTGTGTAACTACGCAAAAACGATGTCGGACTCCGTAGCATTCTCTGGTCCCCTCCCCAATCTGGCCAGCGAGGAGATGTTTAGCCGCATGTCGTCGCTTCGTCGCTGGCTGTCACGGTGGTGCCCCGAAAACCAGGTGGCCTTTATAGACAATTGGAGCACTTTTTGGGGAAAACCTGGTCTGATTAGGAGAGACGGTGTCCATCCCACACGGGATGGTGCTTCTCTCATTTCTAGTAATTTGGCTAATTTTATT 
BioPerl-1.007002/t/data/Glimmer2.out000444000766000024      5370613155576321 17132 0ustar00cjfieldsstaff000000000000GC Proportion = 33.3%
Minimum gene length = 90
Minimum overlap length = 30
Minimum overlap percent = 10.0%
Threshold score = 90
Use independent scores = True
Ignore independent score on orfs longer than 481
Use strict independent model = True
Use first start codon = True

              Orf     Gene                 Lengths     Gene    -- Frame Scores -  Indep
  ID#  Fr    Start    Start      End      Orf  Gene    Score   F1 F2 F3 R1 R2 R3  Score
       F3      654      681      779      126    99       0    99  _  0  _  _  _    0     0  -1.452     
       R1      984      957      772      213   186       0    99  _  _  0  _  _    0     0  -1.383     
       F2      917      917     1009       93    93       0    99  0  _  _  _  _    0     0  -1.335     
    1  F1      292      292     1620     1329  1329      99    99  _  _  _  _  _    0   396  -1.219     
       R2     1631     1607     1515      117    93       0    99  _  _  _  0  _    0     0  -1.331     
       F2     1592     1706     1837      246   132       0     _  0  _  _  _  _   99     0  -1.346     
       R2     1844     1829     1737      108    93       0     _  0  _  _  0  _   99     0  -1.351     
       F3     1860     1881     2000      141   120       2     _  7  2  _  _ 21   68     2  -1.372     
       F2     1841     1856     2095      255   240       0     _  0  _  _  _  _   99     7  -1.373     
       R3     2152     2017     1865      288   153       0     _  8  _  _  _  0   90    21  -1.397     
       F3     2004     2028     2174      171   147       0     _  _  0  _  _  _   99     0  -1.385     
    2  R1     2385     2349     2233      153   117      99     _  _  _ 99  _  _    0    99  -1.208     
       R1     3039     3033     2944       96    90      14     _  _  _ 14  _  _   85    14  -1.262     
       R3     3253     3235     3098      156   138       0     _  _  0  _  _  0   99     0  -1.356     
       F3     3087     3105     3254      168   150       0     _  _  0  _  _  0   99     0  -1.336     
       R3     3463     3439     3323      141   117       1     _  _ 98  _  _  1    0     1  -1.235     
       F1     3550     3589     3699      150   111       0     0  _ 99  _  _  _    0     0  -1.281     
       R3     3727     3712     3611      117   102       0     _  _ 99  _  _  0    0     0  -1.247     
       R1     4038     4026     3916      123   111       0     _  _ 99  0  _  _    0     0  -1.376     
       R2     4097     4091     3999       99    93       0     _  _ 99  _  0  _    0     0  -1.296     
       F1     4009     4009     4110      102   102       0     0  _ 99  _  _  _    0     0  -1.341     
       F1     4171     4189     4311      141   123       0     0  _ 99  _  0  0    0     0  -1.416     
    3  F3     3258     3279     4397     1140  1119      99     _  _ 99  _  _  _    0   791  -1.201     
       R3     4405     4300     4184      222   117       0     0  _ 99  _  0  0    0     0  -1.360     
       R2     4481     4436     4323      159   114       0     _  _  _  _  0  _   99     0  -1.359     
       F2     4454     4460     4549       96    90       0     _  0  _  _  _  _   99     0  -1.348     
       R1     5025     4962     4801      225   162       0     _  0  _  0  _  _   99     0  -1.394     
       F2     4790     4811     5026      237   216       0     _  0  _  0  _  _   99     0  -1.350     
    4  F1     5038     5062     6156     1119  1095      99    99  _  _  _  _  _    0    99  -1.184     
       R2     6386     6383     6216      171   168       0     0  _ 99  _  0  _    0     0  -1.345     
       F1     6217     6292     6432      216   141       0     0  _ 99  _  _  _    0     0  -1.391     
       R3     6487     6469     6338      150   132       1     _  _ 98  _  _  1    0     1  -1.268     
    5  F3     6105     6156     6617      513   462      99     _  _ 99  _  _  _    0   395  -1.205     
       R2     6722     6704     6600      123   105       0     0  _  _  _  0  _   99     0  -1.380     
       F1     6601     6628     6723      123    96       0     0  _  _  _  0  0   99     0  -1.504     
       R3     6880     6856     6743      138   114       0     _ 99  0  _  _  0    0     0  -1.541     
       R3     7033     6988     6884      150   105       0     _ 99  _  _  _  0    0     0  -1.423     
       F3     7062     7062     7187      126   126       0     _ 99  0  _  0  0    0     0  -1.379     
       R2     7196     7067     6975      222    93       0     _ 99  _  _  0  _    0     0  -1.504     
       R3     7267     7237     7037      231   201       0     _ 99  _  _  _  0    0     0  -1.426     
       F3     7299     7299     7415      117   117       0     _ 99  0  _  _  _    0     0  -1.388     
       R2     7502     7481     7389      114    93       0     _ 99  _  _  0  0    0     0  -1.329     
       F3     7419     7425     7514       96    90       0     _ 98  0  1  _  0    0     0  -1.341     
       R3     7525     7468     7337      189   132       0     _ 99  _  _  _  0    0     0  -1.333     
       R1     7683     7524     7423      261   102       0     _ 96  _  0  _  0    2     1  -1.288     
       F3     7896     7899     8036      141   138       0     _ 99  0  _  0  0    0     0  -1.479     
       R3     8050     8002     7895      156   108       0     _ 99  0  _  0  0    0     0  -1.540     
       R2     8147     8069     7875      273   195       0     _ 99  _  _  0  _    0     0  -1.384     
       R3     8305     8293     8123      183   171       0     _ 99  _  _  _  0    0     0  -1.399     
    6  F2     6674     6686     8602     1929  1917      99     _ 99  _  _  _  _    0  1481  -1.218     
       R3     8986     8935     8819      168   117       0     _ 99  _  _  _  0    0     0  -1.463     
       F3     9003     9003     9197      195   195       0     _ 99  0  _  _  _    0     0  -1.421     
       R1     9246     9240     9142      105    99       0     _ 99  _  0  _  _    0     0  -1.309     
       R3    10417    10360    10199      219   162       0     _ 99  _  _  _  0    0     0  -1.428     
       R3    10576    10576    10421      156   156       0     _ 99  _  _  _  0    0     0  -1.380     
       R1    10851    10809    10576      276   234       0     _ 99  _  0  _  _    0     0  -1.340     
       R1    11097    11088    10999       99    90       0     _ 99  _  0  _  _    0     0  -1.362     
    7  F2     8606     8624    11125     2520  2502      99     _ 99  _  _  _  _    0   792  -1.206     
       R2    11399    11345    11205      195   141       0     _  _ 99  _  0  _    0     0  -1.459     
       R3    11584    11536    11396      189   141       0     _  _ 99  _  _  0    0     0  -1.375     
       R1    11742    11724    11635      108    90       0     _  0 99  0  0  _    0     0  -1.396     
    8  F3    11118    11133    12119     1002   987      99     _  _ 99  _  _  _    0   396  -1.229     
       F1    11974    11974    12129      156   156       0     0  _  _  _  _ 81   18     0  -1.379     
    9  R3    12142    12130    11921      222   210      94     _  _  _  _  _ 94    5   175  -1.287     
       R2    12149    12146    12012      138   135       0     _  _  _  _  0  _   99     0  -1.381     
       R3    12469    12355    12167      303   189       0     _  _  0  _  _  0   99     0  -1.466     
       F3    12123    12129    12470      348   342       6     _  _  6  _  _  _   93     6  -1.391     
       R2    12494    12494    12309      186   186       0     _  _  _  _  0  _   99     0  -1.454     
       F2    12422    12473    12565      144    93       6     _  6  _  _  _  _   93     6  -1.318     
       R1    12651    12636    12541      111    96       0     _  _  1  0  _  _   98     0  -1.441     
       F3    12477    12489    12662      186   174       0     _  _  0  _  _  _   99     1  -1.389     
       R3    13084    13069    12977      108    93       0    99  _  _  _  0  0    0     0  -1.347     
       R2    13169    13166    12972      198   195       0    99  _  _  _  0  _    0     0  -1.282     
       F3    13176    13218    13313      138    96       0    99  _  0  _  _  _    0     0  -1.296     
   10  F1    12670    12715    13449      780   735      99    99  _  _  _  _  _    0   396  -1.211     
       R1    13470    13449    13294      177   156       0    99  _  _  0  _  _    0     0  -1.444     
       R3    13627    13624    13535       93    90       0     _  _  _  _  _  0   99     0  -1.409     
       R2    13691    13688    13593       99    96       0     _  _  _  _  0  _   99     0  -1.364     
   11  F3    13656    13671    13838      183   168      99     _  _ 99  _  _  _    0    99  -1.293     
       R2    13889    13871    13740      150   132       4     _  _  _  _  4  _   95     4  -1.327     
       F1    13762    13774    13917      156   144       0     0  _  _  _  _  _   99     0  -1.376     
       F2    13928    13949    14074      147   126       1     0  1  _ 98  _  _    0     1  -1.301     
       F1    13921    13963    14088      168   126       0     0  _  _ 99  _  _    0     0  -1.425     
       R2    14222    14192    14091      132   102       0     _  _  _ 84  0  _   15     0  -1.473     
       F1    14128    14128    14223       96    96       0     0  _  0 98  0  _    1     0  -1.481     
       F3    14103    14133    14330      228   198       0     _  _  0 99  _  _    0     0  -1.405     
       F2    14216    14270    14362      147    93      38     0 38  _ 50  _  _   11    38  -1.336     
       F1    14248    14296    14397      150   102       0     0  _  _ 96  _  _    3     0  -1.454     
       R2    14603    14594    14439      165   156       0     _  _  _ 99  0  _    0     0  -1.305     
   12  R1    14847    14805    13807     1041   999      99     _  _  _ 99  _  _    0   822  -1.279     
       F2    15419    15440    15544      126   105       0     _  0  0  _ 94  _    5     0  -1.496     
       R3    15682    15682    15530      153   153       0     _  _  0  _ 99  0    0     0  -1.381     
       F2    15584    15599    15688      105    90       0     0  0  0  _ 99  _    0     0  -1.518     
       F3    15210    15219    15746      537   528       0     _  _  0  _ 99  _    0     0  -1.512     
   13  R2    15791    15776    15219      573   558      99     _  _  _  _ 99  _    0   490  -1.295     
       F1    16213    16219    16326      114   108       0     0  _ 99  _  _  _    0     0  -1.297     
       F2    16253    16268    16369      117   102       0     _  0 99  _  _  _    0     0  -1.351     
       R3    17203    17101    17006      198    96       0     _  _ 98  _  _  0    0     0  -1.297     
       F2    17198    17207    17335      138   129       0     _  0 99  0  _  _    0     0  -1.393     
       R1    17370    17349    17158      213   192       0     _  _ 99  0  _  _    0     0  -1.339     
   14  F3    15849    15855    17459     1611  1605      99     _  _ 99  _  _  _    0   593  -1.232     
       R3    17677    17623    17483      195   141       0     _  _ 99  _  _  0    0     0  -1.339     
       R2    18242    18137    18045      198    93       0     _  _ 99  _  0  _    0     0  -1.320     
   15  F3    17463    17484    18374      912   891      99     _  _ 99  _  _  _    0   297  -1.206     
       R2    18620    18554    18438      183   117       0     0  _  _ 99  0  _    0     0  -1.344     
       F1    18439    18535    18633      195    99       0     0  _  _ 99  _  _    0     0  -1.318     
       F2    18677    18719    18811      135    93       4     _  4  _ 95  _  0    0     4  -1.188     
       F1    18808    18835    18927      120    93       0     0  _  _ 99  _  _    0     0  -1.497     
       R2    19040    18995    18885      156   111       0     _  _  _ 99  0  _    0     0  -1.367     
       F3    18978    18981    19124      147   144       0     _  _  0 99  _  _    0     0  -1.309     
       R2    19235    19232    19044      192   189       0     _  _  _ 99  0  _    0     0  -1.301     
       R3    19357    19357    19211      147   147       0     _  _  0 99  _  0    0     0  -1.360     
       F3    19188    19269    19391      204   123       0     _  _  0 99  _  _    0     0  -1.269     
   16  R1    19449    19407    18322     1128  1086      99     _  _  _ 99  _  _    0   986  -1.187     
       F3    19443    19473    19571      129    99       0     _  _  0  _  _  _   99     0  -1.312     
       R2    19631    19628    19527      105   102      23     _  _  _  _ 23  _   76    23  -1.268     
       F2    19610    19616    19720      111   105      42     _ 42  _  _  _  _   57    42  -1.247     
       R3    19873    19843    19718      156   126       0     _  _  0  _  _  0   99     0  -1.478     
       F3    19719    19740    19895      177   156       0     _  _  0  _  _  _   99     0  -1.482     
       F1    20041    20068    20175      135   108       0     0  _ 70  _  _ 28    1     0  -1.444     
       R3    20185    20110    19976      210   135       0     _  _ 99  _  _  0    0    28  -1.372     
   17  F3    19977    19980    20192      216   213      99     _  _ 99  _  _  _    0   268  -1.320     
       F1    20179    20266    20364      186    99       0     0  0  _  _  _ 99    0     0  -1.365     
       R1    20445    20418    20305      141   114       0     _  0  _  0  _ 99    0     0  -1.318     
       F2    20261    20288    20446      186   159       0     _  0  _  _  _ 99    0     0  -1.376     
       F1    20404    20413    20601      198   189       0     0  _  _  _  _ 99    0     0  -1.361     
       F3    20469    20583    20756      288   174       0     _  _  0  _  _ 99    0     0  -1.274     
   18  R3    20824    20749    20189      636   561      99     _  _  _  _  _ 99    0   594  -1.215     
       F1    20752    20773    20910      159   138       4     4  2  _  _  _  _   92     4  -1.340     
       R1    21078    21039    20842      237   198       0     _ 99  _  0  _  _    0     0  -1.243     
       F3    21063    21069    21212      150   144       0     _ 99  0  _  _  _    0     0  -1.350     
       R1    21597    21585    21496      102    90       0     _ 99  _  0  0  _    0     0  -1.313     
       F1    21508    21520    21624      117   105       0     0 99  _  _  0  _    0     0  -1.361     
   19  F2    20765    20801    21703      939   903      99     _ 99  _  _  _  _    0   497  -1.192     
       R3    22108    22078    21914      195   165       0     _ 99  _  _  _  0    0     0  -1.325     
       F3    21918    21945    22109      192   165       0     _ 99  0  _  _  0    0     0  -1.374     
       F3    22113    22116    22238      126   123       0     _ 99  0  0  0  _    0     0  -1.273     
       R2    22277    22232    22020      258   213       0     _ 99  _  _  0  _    0     0  -1.294     
       R1    22320    22194    22081      240   114       0     _ 99  _  0  0  _    0     0  -1.237     
   20  F2    21845    21851    22351      507   501      99     _ 99  _  _  _  _    0   594  -1.193     
       R3    22465    22462    22241      225   222       0     _  _  _  _  _  0   99     0  -1.358     
       R2    22490    22487    22398       93    90       0     _  _ 99  _  0  _    0     0  -1.415     
       F1    22402    22420    22554      153   135       0     0  _ 99  _  _  _    0     0  -1.354     
       R2    22598    22592    22494      105    99       0     _  _ 99  _  0  _    0     0  -1.425     
       R3    22720    22681    22547      174   135       0     _  _ 99  _  _  0    0     0  -1.269     
       F1    22657    22663    22776      120   114       0     0  _ 99  _  0  _    0     0  -1.353     
   21  F3    22332    22359    23099      768   741      99     _  _ 99  _  _  _    0   594  -1.221     
       R2    23501    23471    23271      231   201       0     _  _ 99  _  0  _    0     0  -1.351     
   22  F3    23112    23118    23723      612   606      99     _  _ 99  _  _  _    0   198  -1.186     
       R2    24008    24008    23910       99    99       0     _  _  _  _  0  _   99     0  -1.382     
       F1    23920    23920    24033      114   114       0     0  _  _  _  _  _   99     0  -1.364     
       F1    24220    24241    24330      111    90       0     0  _ 16  _  _  _   83     0  -1.424     
       F2    24320    24365    24454      135    90       0     _  0 19  _  _  _   79     0  -1.403     
       R1    24507    24507    24412       96    96       0     _  _ 99  0  _  _    0     0  -1.387     
       F2    24467    24536    24637      171   102       0     0  0 99  _  _  _    0     0  -1.483     
       R3    24673    24670    24548      126   123       5     0  _ 94  _  _  5    0     5  -1.270     
       F1    24496    24562    24723      228   162       0     0  _ 99  _  _  _    0     0  -1.385     
       R1    25095    25089    24967      129   123       0     _  _ 99  0  _  _    0     0  -1.450     
       R2    25343    25304    25185      159   120       0     _  _ 99  _  0  _    0     0  -1.591     
       F1    25225    25267    25362      138    96       0     0  0 99  _  _  _    0     0  -1.484     
       F2    25208    25331    25444      237   114       0     _  0 99  _  _  _    0     0  -1.501     
       F1    25774    25774    25863       90    90       0     0  0 99  0  _  _    0     0  -1.385     
   23  F3    24150    24216    25895     1746  1680      99     _  _ 99  _  _  _    0  1020  -1.261     
       R3    26158    26125    25970      189   156       0     _  _  _  _  _  0   99     0  -1.368     
       F3    26055    26064    26216      162   153      83     _  _ 83  _  _  _   16    83  -1.262     
       R2    26309    26285    26133      177   153       1     _  _  _  _  1  _   98     1  -1.294     
       R1    26370    26328    26212      159   117       0     _  _  _  0  _  _   99     0  -1.327     
       F3    26463    26592    26684      222    93      19     _  _ 19 14  _  7   59    19  -1.301     
       R3    26698    26647    26477      222   171      84     _  _  0  _  _ 84   14    91  -1.290     
       R1    26703    26697    26557      147   141       0     _  _  _  0  _ 92    7    14  -1.342     
       F2    26672    26684    26890      219   207       0     _  0  _  _  _  _   99     0  -1.325     
       F2    26945    26954    27067      123   114       2     _  2  _ 97  _  _    0     2  -1.253     
   24  R1    27117    27090    26731      387   360      99     _  _  _ 99  _  _    0   196  -1.219     
       R1    27276    27231    27142      135    90       0     _  _  _  0  _  _   99     0  -1.239     
       R1    27405    27375    27280      126    96       4     _  _  _  4  _  _   95     4  -1.307     
       R2    27743    27743    27654       90    90       0     _  _  _  _  0  _   99     0  -1.310     
       F2    27833    27836    27934      102    99       0     _  0  _  _  _  _   99     0  -1.427     
       F1    27904    27952    28092      189   141       7     7  _  _  _  _  _   92     7  -1.317     
   25  F2    28001    28025    28141      141   117      95     _ 95  _  _  _  _    4    95  -1.284     
       R1    28272    28203    28081      192   123      70     _  _  _ 70  _  _   29    70  -1.319     
       F1    28240    28240    28362      123   123       0     0  _ 99  _  _  0    0     0  -1.434     
       R3    28390    28375    28154      237   222       0     _  _ 99  _  _  0    0     0  -1.331     
       R2    28544    28544    28383      162   162       0     _  _ 99  _  0  _    0     0  -1.403     
       F1    28387    28417    28548      162   132       0     0  _ 99  _  _  _    0     0  -1.393     
       F1    28591    28663    28791      201   129       0     0  _ 99  _  0  _    0     0  -1.460     
       R2    28988    28940    28812      177   129       0     _  _ 99  _  0  0    0     0  -1.442     
       R3    29005    28885    28766      240   120       0     _  _ 99  _  _  0    0     0  -1.343     
       R1    29019    28977    28885      135    93       0     _  _ 99  0  0  0    0     0  -1.354     
   26  F3    28155    28185    29195     1041  1011      99     _  _ 99  _  _  _    0   891  -1.249     
       F1    28987    28993    29244      258   252       0     0  _  _  _  _  _   99     0  -1.434     
       R2    29579    29561    29430      150   132       0    99  _  _  _  0  _    0     0  -1.207     
       R1    29622    29616    29521      102    96       0    98  _  _  0  _  _    1     0  -1.321     
       R3    29866    29836    29702      165   135       0    99  _  0  _  0  0    0     0  -1.290     
   27  F1    29263    29263    29946      684   684      99    99  _  _  _  _  _    0   395  -1.187     
End = 29940

   Original Genes =    27
  Potential Genes =    27
        Avg Olaps =   0.1
Potential Changes =     2
Potential Rejects =     2
     Sure Rejects =     2

   Original Genes =    27
  Potential Genes =    25
        Avg Olaps =   0.0
Potential Changes =     0
Potential Rejects =     0
     Sure Rejects =     0

   Original Genes =    27
  Potential Genes =    25
        Avg Olaps =   0.0
Potential Changes =     0
Potential Rejects =     0
     Sure Rejects =     0


Putative Genes:
    1      292     1620  [+1 L=1329 r=-1.219]
    2     2349     2233  [-1 L= 117 r=-1.208]
    3     3279     4397  [+3 L=1119 r=-1.201]
    4     5062     6156  [+1 L=1095 r=-1.184]
    5     6156     6617  [+3 L= 462 r=-1.205]
    6     6686     8602  [+2 L=1917 r=-1.218]
    7     8624    11125  [+2 L=2502 r=-1.206]
    8    11133    12119  [+3 L= 987 r=-1.229]
   10    12715    13449  [+1 L= 735 r=-1.211]
   12    14805    13807  [-1 L= 999 r=-1.279]
   13    15776    15219  [-3 L= 558 r=-1.295]
   14    15855    17459  [+3 L=1605 r=-1.232]
   15    17484    18374  [+3 L= 891 r=-1.206]
   16    19407    18322  [-1 L=1086 r=-1.187]
   17    19980    20192  [+3 L= 213 r=-1.320]
   18    20749    20189  [-2 L= 561 r=-1.215]
   19    20801    21703  [+2 L= 903 r=-1.192]
   20    21851    22351  [+2 L= 501 r=-1.193]
   21    22359    23099  [+3 L= 741 r=-1.221]
   22    23118    23723  [+3 L= 606 r=-1.186]
   23    24216    25895  [+3 L=1680 r=-1.261]
   24    27090    26731  [-1 L= 360 r=-1.219]
   25    28025    28141  [+2 L= 117 r=-1.284]
   26    28185    29195  [+3 L=1011 r=-1.249]
   27    29263        6  [+1 L= 684 r=-1.187]
BioPerl-1.007002/t/data/Glimmer3.detail000444000766000024      3216313155576321 17560 0ustar00cjfieldsstaff000000000000Command:  /bio/sw/glimmer3/bin/glimmer3 -o 50 -g 110 -t 30 ../BCTDNA Glimmer3.icm Glimmer3

Sequence file = ../BCTDNA
ICM model file = Glimmer3.icm
Excluded regions file = none
List of orfs file = none
Truncated orfs = false
Circular genome = true
Minimum gene length = 110 bp
Maximum overlap bases = 50
Input is NOT separate orfs
Threshold score = 30
Use first start codon = false
Start codons = atg,gtg,ttg
Start probs = 0.600,0.300,0.100
Stop codons = taa,tag,tga


>BCTDNA
Sequence length = 29940
GC percentage = 33.3%
Ignore independent score on orfs longer than 482

           ----- Start -----           --- Length ----  ------------- Scores -------------
 ID  Frame   of Orf  of Gene     Stop   of Orf of Gene      Raw InFrm F1 F2 F3 R1 R2 R3 NC
0001    +1    29263    29263        9      684     684     9.68    99 99  -  -  -  -  -  0 1.00
        -1      984      894      769      213     123    -9.85     0 99  -  -  0  -  -  0 1.00
0002    +1      292      298     1623     1329    1323     8.26    99 99  -  -  -  -  -  0 1.00
        +2     1592     1706     1840      246     132    -5.10     0  -  0  -  -  -  - 99 1.00
        +3     1860     1881     2003      141     120    -2.68     0  - 75  0  -  0  - 23 1.00
0003    +2     1841     1949     2098      255     147     6.59    99  - 99  -  -  0  -  0 1.00
        -2     2152     1993     1862      288     129    -3.37     0  - 44  0  -  0  - 55 1.00
        +3     2004     2040     2177      171     135    -1.77     0  -  -  0  -  -  - 99 1.00
0004    -1     2385     2349     2230      153     117     4.69    97  -  -  - 97  -  -  2 1.00
        -2     3253     3235     3095      156     138    -9.03     0  -  -  0  -  0  - 99 1.00
        +3     3087     3126     3257      168     129    -9.09     0  -  -  0  -  0  - 99 1.00
        -2     3463     3439     3320      141     117     7.18     1  -  - 98  -  1  -  0 1.00
        +1     3550     3589     3702      150     111    -0.25     0  0  - 99  -  -  -  0 1.00
        -1     4038     4026     3913      123     111   -10.13     0  -  - 99  0  -  -  0 1.00
        +1     4171     4192     4314      141     120    -8.48     0  0  - 99  -  0  0  0 1.00
0005    +3     3258     3279     4400     1140    1119    10.20    99  -  - 99  -  -  -  0 1.00
        -2     4405     4300     4181      222     117    -0.45     0  0  - 99  -  0  0  0 1.00
        -3     4481     4436     4320      159     114   -12.02     0  -  -  -  -  -  0 99 1.00
        -1     5025     4962     4798      225     162    -6.25     0  -  0  -  0  -  - 99 1.00
        +2     4790     4913     5029      237     114    -7.57     0  -  0  -  0  -  - 99 1.00
0006    +1     5038     5062     6159     1119    1095     9.92    99 99  -  -  -  -  -  0 1.00
        -3     6386     6368     6213      171     153    -1.23     0  0  - 99  -  -  0  0 1.00
        +1     6217     6295     6435      216     138    -7.86     0  0  - 99  -  -  -  0 1.00
        -2     6487     6469     6335      150     132     2.90     0  -  - 99  -  0  -  0 1.00
0007    +3     6105     6156     6620      513     462    12.86    99  -  - 99  -  -  -  0 1.00
        -2     6880     6856     6740      138     114    -9.49     0  - 99  0  -  0  -  0 1.00
        +3     7062     7062     7190      126     126    -3.41     0  - 99  0  -  0  0  0 1.00
        -2     7267     7162     7034      231     126    -8.57     0  - 99  -  -  0  0  0 1.00
        +3     7299     7299     7418      117     117    -2.08     0  - 99  0  -  -  -  0 1.00
        -2     7525     7468     7334      189     132    -0.14     0  - 99  -  -  0  -  0 1.00
        +3     7896     7920     8039      141     117    -7.88     0  - 99  0  -  0  0  0 1.00
        -3     8147     8069     7872      273     195    -0.71     0  - 99  -  -  -  0  0 1.00
        -2     8305     8293     8120      183     171   -10.93     0  - 99  -  -  0  -  0 1.00
0008    +2     6674     6686     8605     1929    1917    12.34    99  - 99  -  -  -  -  0 1.00
        -2     8986     8929     8816      168     111    -9.33     0  - 99  -  -  0  -  0 1.00
        +3     9003     9084     9200      195     114   -11.31     0  - 99  0  -  -  -  0 1.00
        -2    10417    10315    10196      219     117    -9.22     0  - 99  -  -  0  -  0 1.00
        -2    10576    10576    10418      156     156    -7.32     0  - 99  -  -  0  -  0 1.00
        -1    10851    10728    10573      276     153     1.00     0  - 99  -  0  -  -  0 1.00
0009    +2     8606     8624    11128     2520    2502    12.77    99  - 99  -  -  -  -  0 1.00
        -3    11399    11345    11202      195     141    -9.23     0  -  - 99  -  -  0  0 1.00
        -2    11584    11536    11393      189     141    -3.32     0  -  - 99  -  0  -  0 1.00
0010    +3    11118    11133    12122     1002     987    11.55    99  -  - 99  -  -  -  0 1.00
        +1    11974    11974    12132      156     156    -4.16     0  0  -  -  - 54  - 45 1.00
0011    -2    12142    12130    11918      222     210     2.27    92  -  -  -  - 92  -  7 1.00
        -3    12149    12143    12009      138     132    -5.42     0  -  -  -  - 56  0 43 1.00
        -2    12469    12355    12164      303     189    -7.16     0  -  - 20  -  0  - 79 1.00
0012    +3    12123    12273    12473      348     198    10.08    99  -  - 99  -  0  -  0 1.00
        -3    12494    12470    12306      186     162    -4.46     0  -  - 99  -  0  0  0 1.00
        +3    12477    12507    12665      186     156    -5.68     0  -  -  0  -  -  - 99 1.00
        -3    13169    13166    12969      198     195     2.54     0 99  -  -  -  -  0  0 1.00
0013    +1    12670    12715    13452      780     735    11.22    99 99  -  -  -  -  -  0 1.00
        -1    13470    13449    13291      177     156    -7.69     0 99  -  -  0  -  -  0 1.00
0014    +3    13656    13722    13841      183     117     4.01    92  -  - 92  -  -  -  7 1.00
        -3    13889    13871    13737      150     132    -1.62     1  -  -  -  -  -  1 98 1.00
        +1    13762    13774    13920      156     144    -3.79     0  0  -  -  -  -  - 99 1.00
        +2    13928    13949    14077      147     126     3.00     0  0  0  - 99  -  -  0 1.00
        +1    13921    13963    14091      168     126   -10.74     0  0  -  - 99  -  -  0 1.00
        +3    14103    14142    14333      228     189    -3.47     0  -  -  0 99  -  -  0 1.00
        -3    14603    14594    14436      165     156    -3.77     0  -  -  - 99  -  0  0 1.00
0015    -1    14847    14805    13804     1041     999     5.49    99  -  -  - 99  -  -  0 1.00
        -2    15682    15676    15527      153     147    -1.39     0  -  -  0  -  0 99  0 1.00
0016    +3    15210    15219    15749      537     528   -12.48     0  0  -  0  -  - 99  0 1.00
0017    -3    15791    15776    15216      573     558    11.35    99  -  -  -  -  - 99  0 1.00
        +2    17198    17207    17338      138     129    -3.68     0  -  0 99  0  -  -  0 1.00
        -1    17370    17271    17155      213     114     3.30     0  -  - 99  0  -  -  0 1.00
0018    +3    15849    15948    17462     1611    1512     9.36    99  -  - 99  -  -  -  0 1.00
        -2    17677    17623    17480      195     141    -1.26     1  -  - 34  -  1  - 64 1.00
0019    +3    17463    17484    18377      912     891     6.43    99  -  - 99  -  -  -  0 1.00
        -3    18620    18554    18435      183     117    -5.09     0  0  -  - 99  -  0  0 1.00
        -3    19040    18995    18882      156     111    -2.90     0  -  -  - 99  -  0  0 1.00
        +3    18978    19014    19127      147     111     1.67     0  -  -  0 99  -  -  0 1.00
        -3    19235    19211    19041      192     168     1.29     0  -  -  - 99  -  0  0 1.00
        -2    19357    19357    19208      147     147    -3.27     0  -  -  0 99  0  -  0 1.00
        +3    19188    19269    19394      204     123    -2.25     0  -  -  0 98  -  -  1 1.00
0020    -1    19449    19407    18319     1128    1086     7.49    99  -  -  - 99  -  -  0 1.00
        -2    19873    19843    19715      156     126    -8.77     0  -  -  0  -  0  - 99 1.00
        +3    19719    19740    19898      177     156    -7.39     0  -  -  0  -  -  - 99 1.00
        -2    20185    20110    19973      210     135    -0.77     0  -  - 98  -  0  -  1 1.00
0021    +3    19977    19980    20195      216     213     3.39    99  -  - 99  -  -  -  0 1.00
        -1    20445    20418    20302      141     114    -3.04     0  -  0  -  0 99  -  0 1.00
        +2    20261    20309    20449      186     138    -4.98     0  -  0  -  0 99  -  0 1.00
        +1    20404    20413    20604      198     189    -5.81     0  0  -  -  - 99  -  0 1.00
        +3    20469    20583    20759      288     174     2.71     0  -  -  0  - 99  -  0 1.00
0022    -2    20824    20749    20186      636     561     9.10    99  -  -  -  - 99  -  0 1.00
        +1    20752    20773    20913      159     138    -3.20     0  0  0  -  -  -  - 99 1.00
        -1    21078    21039    20839      237     198     4.53     0  - 99  -  0  -  -  0 1.00
        +3    21063    21069    21215      150     144    -2.93     0  - 99  0  -  -  -  0 1.00
0023    +2    20765    20810    21706      939     894    11.73    99  - 99  -  -  -  -  0 1.00
        -2    22108    22051    21911      195     138    -4.96     0  - 99  -  -  0  -  0 1.00
        +3    21918    21945    22112      192     165    -9.58     0  - 99  0  -  0  -  0 1.00
        +3    22113    22116    22241      126     123    -1.18     0  - 99  0  0  -  0  0 1.00
        -3    22277    22187    22017      258     168     3.69     0  - 99  -  -  -  0  0 1.00
        -1    22320    22194    22078      240     114     8.28     0  - 99  -  0  -  0  0 1.00
0024    +2    21845    21851    22354      507     501    10.64    99  - 99  -  -  -  -  0 1.00
        -2    22465    22462    22238      225     222    -1.02     1  -  -  -  -  1  - 98 1.00
        +1    22402    22420    22557      153     135     0.60     0  0  - 99  -  -  -  0 1.00
        -2    22720    22681    22544      174     135     5.32     0  -  - 99  -  0  -  0 1.00
        +1    22657    22663    22779      120     114    -5.87     0  0  - 99  -  -  0  0 1.00
0025    +3    22332    22359    23102      768     741    14.02    99  -  - 99  -  -  -  0 1.00
        -3    23501    23432    23268      231     162    -6.68     0  -  - 99  -  -  0  0 1.00
0026    +3    23112    23118    23726      612     606    11.58    99  -  - 99  -  -  -  0 1.00
        +1    23920    23920    24036      114     114    -9.23     0  0  -  -  -  -  - 99 1.00
0027    -2    24673    24670    24545      126     123     9.42    38  0  - 61  - 38  -  0 1.00
        +1    24496    24586    24726      228     138    -4.39     0  0  - 99  -  -  -  0 1.00
        -1    25095    25089    24964      129     123   -11.50     0  -  - 99  0  -  -  0 1.00
        -3    25343    25304    25182      159     120   -19.97     0  -  - 99  -  -  0  0 1.00
        +2    25208    25331    25447      237     114   -11.98     0  -  0 99  -  -  -  0 1.00
0028    +3    24150    24216    25898     1746    1680    11.26    99  -  - 99  -  -  -  0 1.00
        -2    26158    26125    25967      189     156    -6.07     0  -  -  -  -  0  - 99 1.00
0029    +3    26055    26103    26219      162     114     2.53    65  -  - 65  -  -  - 34 1.00
        -3    26309    26249    26130      177     117    -1.20     3  -  -  -  -  -  3 96 1.00
        -1    26370    26328    26209      159     117    -2.70     0  -  -  -  0  -  - 99 1.00
0030    -2    26698    26593    26474      222     117     4.01    91  -  -  0  - 91  -  8 1.00
        -1    26703    26697    26554      147     141    -3.06     0  -  -  -  0  6  - 93 1.00
        +2    26672    26684    26893      219     207    -1.12     1  -  1  -  -  -  - 98 1.00
        +2    26945    26954    27070      123     114     6.59     0  -  0  - 99  -  -  0 1.00
0031    -1    27117    27090    26728      387     360    10.98    99  -  -  - 99  -  -  0 1.00
        +1    27904    27952    28095      189     141    -0.69     4  4  -  -  -  -  - 95 1.00
0032    +2    28001    28025    28144      141     117     1.77    53  - 53  -  -  -  - 46 1.00
0033    -1    28272    28203    28078      192     123     1.32    35  -  -  - 35  -  - 64 1.00
        +1    28240    28240    28365      123     123    -9.11     0  0  - 99  -  0  -  0 1.00
0034    -2    28390    28276    28151      237     123     6.20    93  -  -  5  - 93  -  0 1.00
        -3    28544    28502    28380      162     120    -5.88     0  -  - 99  -  -  0  0 1.00
        +1    28387    28417    28551      162     132    -3.22     0  0  - 71  -  -  - 28 1.00
        +1    28591    28663    28794      201     129    -6.01     0  0  - 99  -  -  0  0 1.00
        -3    28988    28940    28809      177     129    -9.43     0  -  - 99  -  0  0  0 1.00
        -2    29005    28885    28763      240     120     4.66     0  -  - 99  -  0  -  0 1.00
0035    +3    28155    28188    29198     1041    1008     7.00    99  -  - 99  -  -  -  0 1.00
        +1    28987    29119    29247      258     126    -7.99     0  0  -  -  -  -  - 99 1.00
        -3    29579    29561    29427      150     132     3.22     0 99  -  -  -  -  0  0 1.00
        -2    29866    29836    29699      165     135     0.42     0 99  -  0  -  0  0  0 1.00
BioPerl-1.007002/t/data/Glimmer3.predict000444000766000024       210013155576321 17714 0ustar00cjfieldsstaff000000000000>BCTDNA
orf00001    29263        9  +1     9.60
orf00002      298     1623  +1     8.09
orf00003     1856     2098  +2     3.34
orf00004     2349     2230  -1     2.72
orf00005     3279     4400  +3     9.99
orf00006     5062     6159  +1     9.87
orf00007     6156     6620  +3    12.71
orf00008     6686     8605  +2    12.31
orf00009     8624    11128  +2    12.75
orf00010    11133    12122  +3    11.50
orf00012    12273    12473  +3     8.92
orf00013    12715    13452  +1    11.15
orf00015    14781    13804  -1     5.51
orf00017    15776    15216  -3    11.26
orf00018    15948    17462  +3     9.28
orf00020    19407    18319  -1     7.45
orf00021    19980    20195  +3     3.15
orf00022    20749    20186  -2     9.01
orf00023    20810    21706  +2    11.68
orf00024    21851    22354  +2    10.53
orf00025    22359    23102  +3    13.70
orf00026    23118    23726  +3    11.50
orf00028    24216    25898  +3    11.23
orf00029    26103    26219  +3     2.08
orf00030    26593    26474  -2     3.57
orf00031    27090    26728  -1    10.84
orf00035    28185    29198  +3     6.81
BioPerl-1.007002/t/data/GlimmerHMM.out000444000766000024      2601513155576321 17403 0ustar00cjfieldsstaff000000000000GlimmerHMM
Sequence name: gi|23613028|ref|NC_004326.1|
Sequence length: 69930 bp

Predicted genes/exons

Gene Exon Strand  Exon            Exon Range      Exon
   #    #         Type                           Length


   1    1  +  Terminal       2235       2284       50

   2    1  -  Terminal       2324       2340       17
   2    2  -  Initial        2413       2434       22

   3    1  +  Initial        2461       2667      207
   3    2  +  Internal       2937       2989       53
   3    3  +  Internal       4203       4216       14
   3    4  +  Terminal       4587       4627       41

   4    1  +  Initial        4628       4669       42
   4    2  +  Terminal       5063       5083       21

   5    1  -  Terminal       5095       5102        8
   5    2  -  Initial        5108       5129       22

   6    1  -  Single         5138       5152       15

   7    1  -  Single         5158       5205       48

   8    1  +  Single         5214       5252       39

   9    1  +  Initial        5262       5469      208
   9    2  +  Terminal       5538       5647      110

  10    1  +  Initial        5663       5665        3
  10    2  +  Terminal       5712       5942      231

  11    1  +  Initial        5952       6159      208
  11    2  +  Terminal       6228       6337      110

  12    1  +  Initial        6353       6355        3
  12    2  +  Internal       6402       6431       30
  12    3  +  Internal       6463       6489       27
  12    4  +  Internal       6563       6707      145
  12    5  +  Internal       6911       6960       50
  12    6  +  Internal       7252       7399      148
  12    7  +  Internal       7672       7860      189
  12    8  +  Internal       7915       7967       53
  12    9  +  Internal       8030       8198      169
  12   10  +  Terminal       8204       8322      119

  13    1  +  Initial        8329       8385       57
  13    2  +  Internal       8721       8748       28
  13    3  +  Internal       8820       8976      157
  13    4  +  Terminal      11310      11361       52

  14    1  -  Single        11364      11375       12

  15    1  -  Single        11378      11386        9

  16    1  -  Terminal      11411      11413        3
  16    2  -  Initial       11522      11533       12

  17    1  +  Initial       11541      11595       55
  17    2  +  Internal      11926      11967       42
  17    3  +  Internal      12472      12483       12
  17    4  +  Terminal      12641      12921      281

  18    1  +  Initial       12928      13035      108
  18    2  +  Internal      13334      13350       17
  18    3  +  Internal      13376      13383        8
  18    4  +  Internal      13397      13455       59
  18    5  +  Internal      13481      13497       17
  18    6  +  Internal      13502      13530       29
  18    7  +  Internal      13603      13615       13
  18    8  +  Internal      13649      13656        8
  18    9  +  Internal      13776      13960      185
  18   10  +  Internal      13965      13972        8
  18   11  +  Internal      14173      14189       17
  18   12  +  Internal      14236      14252       17
  18   13  +  Internal      14277      14293       17
  18   14  +  Internal      14487      14515       29
  18   15  +  Internal      14844      14860       17
  18   16  +  Internal      15281      15309       29
  18   17  +  Internal      15470      15477        8
  18   18  +  Internal      15743      15750        8
  18   19  +  Internal      15764      15771        8
  18   20  +  Internal      15785      15792        8
  18   21  +  Internal      16122      16128        7
  18   22  +  Internal      16478      16506       29
  18   23  +  Terminal      17424      17662      239

  19    1  +  Initial       17669      17741       73
  19    2  +  Internal      17907      18091      185
  19    3  +  Internal      18139      18146        8
  19    4  +  Internal      18159      18237       79
  19    5  +  Internal      18275      18292       18
  19    6  +  Internal      18431      18532      102
  19    7  +  Internal      18813      18839       27
  19    8  +  Internal      18933      18943       11
  19    9  +  Internal      19248      19269       22
  19   10  +  Internal      19423      19486       64
  19   11  +  Internal      19520      19551       32
  19   12  +  Internal      19671      19744       74
  19   13  +  Internal      19799      19944      146
  19   14  +  Internal      20356      20421       66
  19   15  +  Internal      20912      26376     5465
  19   16  +  Internal      27215      28172      958
  19   17  +  Internal      28378      28381        4
  19   18  +  Internal      28440      28617      178
  19   19  +  Internal      28980      29244      265
  19   20  +  Internal      29259      29330       72
  19   21  +  Internal      30135      30187       53
  19   22  +  Terminal      30442      30486       45

  20    1  -  Terminal      30483      30503       21
  20    2  -  Initial       30573      30587       15

  21    1  +  Single        30600      30701      102

  22    1  -  Single        30707      30715        9

  23    1  +  Initial       30723      30768       46
  23    2  +  Internal      30950      30951        2
  23    3  +  Internal      31436      31516       81
  23    4  +  Internal      31862      31887       26
  23    5  +  Internal      31902      31915       14
  23    6  +  Internal      32005      32075       71
  23    7  +  Terminal      32357      32401       45

  24    1  -  Single        32408      32413        6

  25    1  -  Single        32450      32470       21

  26    1  +  Initial       32485      32526       42
  26    2  +  Internal      32809      32817        9
  26    3  +  Internal      33416      33470       55
  26    4  +  Terminal      33601      33956      356

  27    1  +  Initial       33967      34133      167
  27    2  +  Internal      34240      34252       13
  27    3  +  Internal      34368      34389       22
  27    4  +  Internal      34917      34929       13
  27    5  +  Internal      35211      35289       79
  27    6  +  Internal      35408      35416        9
  27    7  +  Internal      35421      35516       96
  27    8  +  Internal      35827      35964      138
  27    9  +  Internal      36797      36800        4
  27   10  +  Internal      36871      36886       16
  27   11  +  Internal      37250      37352      103
  27   12  +  Internal      38015      38087       73
  27   13  +  Internal      38193      38242       50
  27   14  +  Internal      38538      38540        3
  27   15  +  Internal      38865      38911       47
  27   16  +  Internal      38966      38992       27
  27   17  +  Internal      39553      39567       15
  27   18  +  Internal      39607      39728      122
  27   19  +  Internal      39785      39797       13
  27   20  +  Internal      40060      40090       31
  27   21  +  Internal      40686      40694        9
  27   22  +  Internal      41048      41114       67
  27   23  +  Terminal      41274      41317       44

  28    1  +  Initial       41321      41383       63
  28    2  +  Internal      41895      41924       30
  28    3  +  Internal      42145      42158       14
  28    4  +  Terminal      42273      42366       94

  29    1  +  Initial       42378      42407       30
  29    2  +  Terminal      43154      43186       33

  30    1  -  Single        43188      43208       21

  31    1  -  Terminal      43211      43217        7
  31    2  -  Initial       43239      43255       17

  32    1  -  Terminal      43260      43358       99
  32    2  -  Initial       43372      43650      279

  33    1  +  Initial       43659      43669       11
  33    2  +  Internal      43827      44543      717
  33    3  +  Internal      45352      45895      544
  33    4  +  Internal      47453      47470       18
  33    5  +  Internal      47477      47501       25
  33    6  +  Internal      47897      47903        7
  33    7  +  Internal      48413      48433       21
  33    8  +  Internal      48698      48711       14
  33    9  +  Internal      49405      49430       26
  33   10  +  Internal      49635      49678       44
  33   11  +  Internal      50184      50212       29
  33   12  +  Internal      50480      50504       25
  33   13  +  Internal      50871      50875        5
  33   14  +  Internal      51003      51079       77
  33   15  +  Internal      51396      51416       21
  33   16  +  Internal      51762      51808       47
  33   17  +  Internal      52597      52652       56
  33   18  +  Internal      52671      52672        2
  33   19  +  Internal      53093      53095        3
  33   20  +  Internal      53262      53308       47
  33   21  +  Internal      53469      53531       63
  33   22  +  Internal      55819      56055      237
  33   23  +  Internal      57050      57132       83
  33   24  +  Terminal      57138      57181       44

  34    1  +  Single        57193      57207       15

  35    1  +  Single        57208      57216        9

  36    1  +  Initial       57240      57338       99
  36    2  +  Internal      57510      57543       34
  36    3  +  Internal      57950      58055      106
  36    4  +  Terminal      58384      58390        7

  37    1  +  Initial       58406      58463       58
  37    2  +  Internal      58550      58656      107
  37    3  +  Internal      59051      59123       73
  37    4  +  Internal      59168      59226       59
  37    5  +  Internal      59407      59451       45
  37    6  +  Internal      59627      59649       23
  37    7  +  Internal      59680      59705       26
  37    8  +  Internal      59968      59977       10
  37    9  +  Internal      60747      60750        4
  37   10  +  Internal      60942      60947        6
  37   11  +  Internal      61442      61464       23
  37   12  +  Internal      61991      62137      147
  37   13  +  Internal      62413      62425       13
  37   14  +  Internal      62508      62522       15
  37   15  +  Terminal      62830      62838        9

  38    1  +  Initial       62839      62850       12
  38    2  +  Internal      63403      63410        8
  38    3  +  Internal      63916      63931       16
  38    4  +  Terminal      63992      64009       18

  39    1  -  Single        64040      64066       27

  40    1  +  Single        64123      64137       15

  41    1  +  Initial       64145      64179       35
  41    2  +  Internal      64194      64266       73
  41    3  +  Internal      64332      65390     1059
  41    4  +  Internal      65945      65955       11
  41    5  +  Internal      66065      66070        6
  41    6  +  Internal      66469      66485       17
  41    7  +  Terminal      66697      66704        8

  42    1  +  Initial       66704      66716       13
  42    2  +  Internal      66964      67005       42
  42    3  +  Internal      68146      68190       45
  42    4  +  Internal      68458      68600      143
  42    5  +  Terminal      68895      68924       30

  43    1  +  Initial       68930      69670      741
  43    2  +  Terminal      69839      69868       30

  44    1  -  Terminal      69866      69929       64
BioPerl-1.007002/t/data/GlimmerM.out000444000766000024       403313155576321 17132 0ustar00cjfieldsstaff000000000000GlimmerM (Version 3.0)
Sequence name: gi|23613028|ref|NC_004326.1|
Sequence length: 69930 bp

Predicted genes/exons

Gene Exon Strand  Exon            Exon Range      Exon
   #    #         Type                           Length

   1    1  -  Single          461        523       63

   2    1  +  Initial        1095       1103        9
   2    2  +  Internal       1167       1208       42
   2    3  +  Terminal       1404       1445       42

   3    1  -  Single         7055       7162      108

   4    1  +  Initial        7273       7356       84
   4    2  +  Internal       7434       7598      165
   4    3  +  Internal       7861       7898       38
   4    4  +  Terminal       7957       7975       19

   5    1  +  Initial       20929      23815     2887
   5    2  +  Terminal      23910      23956       47

   6    1  +  Initial       24046      26310     2265
   6    2  +  Internal      27215      28399     1185
   6    3  +  Internal      28848      28855        8
   6    4  +  Internal      29246      29309       64
   6    5  +  Terminal      29502      29516       15

   7    2  -  Terminal      29593      29600        8
   7    1  -  Initial       29919      30636      718

   8    8  -  Terminal      30737      30744        8
   8    7  -  Internal      31124      31150       27
   8    6  -  Internal      31814      31883       70
   8    5  -  Internal      32469      32515       47
   8    4  -  Internal      33199      34126      928
   8    3  -  Internal      34647      34688       42
   8    2  -  Internal      35216      35334      119
   8    1  -  Initial       36613      36853      241

   9    1  +  Initial       36912      37101      190
   9    2  +  Internal      37285      37300       16
   9    3  +  Terminal      37999      38005        7

  10    5  -  Terminal      42047      42104       58
  10    4  -  Internal      42781      42795       15
  10    3  -  Internal      42864      42888       25
  10    2  -  Internal      43211      43217        7
  10    1  -  Initial       43372      46329     2958

BioPerl-1.007002/t/data/HM138502.gbk000444000766000024      1043713155576321 16371 0ustar00cjfieldsstaff000000000000LOCUS       HM138502                1410 bp    cRNA    linear   VRL 22-APR-2010
DEFINITION  Influenza A virus (A/California/07/2009(H1N1)) segment 6
            neuraminidase (NA) gene, complete cds.
ACCESSION   HM138502
VERSION     HM138502.1  GI:295002854
DBLINK      BioProject: PRJNA37813
KEYWORDS    .
SOURCE      Influenza A virus (A/California/07/2009(H1N1))
  ORGANISM  Influenza A virus (A/California/07/2009(H1N1))
            Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
            Influenzavirus A.
REFERENCE   1  (bases 1 to 1410)
  AUTHORS   Starick,E.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-APR-2010) Friedrich-Loeffler-Institut, Suedufer 10,
            Greifswald-Insel Riems 17493, Germany
COMMENT     Swine influenza A (H1N1) virus isolated during human swine flu
            outbreak of 2009.
            
            ##GISAID_EpiFlu(TM)Data-START##
            Isolate         :: A/California/07/09
            Subtype         :: H1N1
            Lineage         :: swl
            ##GISAID_EpiFlu(TM)Data-END##
FEATURES             Location/Qualifiers
     source          1..1410
                     /organism="Influenza A virus (A/California/07/2009(H1N1))"
                     /mol_type="viral cRNA"
                     /strain="A/California/07/2009"
                     /serotype="H1N1"
                     /host="Homo sapiens"
                     /db_xref="taxon:641809"
                     /segment="6"
                     /country="USA"
                     /collection_date="09-Apr-2009"
                     /note="lineage: swl"
     gene            1..1410
                     /gene="NA"
     CDS             1..1410
                     /gene="NA"
                     /codon_start=1
                     /product="neuraminidase"
                     /protein_id="ADF58339.1"
                     /db_xref="GI:295002855"
                     /translation="MNPNQKIITIGSVCMTIGMANLILQIGNIISIWISHSIQLGNQN
                     QIETCNQSVITYENNTWVNQTYVNISNTNFAAGQSVVSVKLAGNSSLCPVSGWAIYSK
                     DNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMS
                     CPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKS
                     WRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFRIEKGKIVKSVEMNAPNYHY
                     EECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGS
                     CGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQD
                     IVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNS
                     DTVGWSWPDGAELPFTIDK"
ORIGIN      
        1 atgaatccaa accaaaagat aataaccatt ggttcggtct gtatgacaat tggaatggct
       61 aacttaatat tacaaattgg aaacataatc tcaatatgga ttagccactc aattcaactt
      121 gggaatcaaa atcagattga aacatgcaat caaagcgtca ttacttatga aaacaacact
      181 tgggtaaatc agacatatgt taacatcagc aacaccaact ttgctgctgg acagtcagtg
      241 gtttccgtga aattagcagg caattcctct ctctgccctg ttagtggatg ggctatatac
      301 agtaaagaca acagtgtaag aatcggttcc aagggggatg tgtttgtcat aagggaacca
      361 ttcatatcat gctccccctt ggaatgcaga accttcttct tgactcaagg ggccttgcta
      421 aatgacaaac attccaatgg aaccattaaa gacaggagcc catatcgaac cctaatgagc
      481 tgtcctattg gtgaagttcc ctctccatac aactcaagat ttgagtcagt cgcttggtca
      541 gcaagtgctt gtcatgatgg catcaattgg ctaacaattg gaatttctgg cccagacaat
      601 ggggcagtgg ctgtgttaaa gtacaacggc ataataacag acactatcaa gagttggaga
      661 aacaatatat tgagaacaca agagtctgaa tgtgcatgtg taaatggttc ttgctttact
      721 gtaatgaccg atggaccaag taatggacag gcctcataca agatcttcag aatagaaaag
      781 ggaaagatag tcaaatcagt cgaaatgaat gcccctaatt atcactatga ggaatgctcc
      841 tgttatcctg attctagtga aatcacatgt gtgtgcaggg ataactggca tggctcgaat
      901 cgaccgtggg tgtctttcaa ccagaatctg gaatatcaga taggatacat atgcagtggg
      961 attttcggag acaatccacg ccctaatgat aagacaggca gttgtggtcc agtatcgtct
     1021 aatggagcaa atggagtaaa agggttttca ttcaaatacg gcaatggtgt ttggataggg
     1081 agaactaaaa gcattagttc aagaaacggt tttgagatga tttgggatcc gaacggatgg
     1141 actgggacag acaataactt ctcaataaag caagatatcg taggaataaa tgagtggtca
     1201 ggatatagcg ggagttttgt tcagcatcca gaactaacag ggctggattg tataagacct
     1261 tgcttctggg ttgaactaat cagagggcga cccaaagaga acacaatctg gactagcggg
     1321 agcagcatat ccttttgtgg tgtaaacagt gacactgtgg gttggtcttg gccagacggt
     1381 gctgagttgc catttaccat tgacaagtaa
//
BioPerl-1.007002/t/data/HUMBETGLOA.FASTA000444000766000024     43244313155576321 17151 0ustar00cjfieldsstaff000000000000 FASTA searches a protein or DNA sequence data bank
 version 3.3t08 Jan. 17, 2001
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

t/data/HUMBETGLOA.fasta: 3002 nt
 >HUMBETGLOA Human haplotype C4 beta-globin gene, complete cds. 
 vs  /data_2/jason/blastdb/dros_clones.2.5 library
searching /data_2/jason/blastdb/dros_clones.2.5 library

       opt      E()
< 20     4     0:==
  22     4     0:==         one = represents 2 library sequences
  24    11     0:======
  26     9     0:=====
  28    37     0:===================
  30    48     3:=*======================
  32    43    10:====*=================
  34    56    27:=============*==============
  36    53    56:===========================*
  38    67    93:==================================            *
  40    81   130:=========================================                  *
  42    81   159:=========================================                  *
  44    98   175:=================================================          *
  46    86   178:===========================================                *
  48    77   171:=======================================                    *
  50    94   156:===============================================            *
  52    93   137:===============================================            *
  54    70   117:===================================                       *
  56   108    98:================================================*=====
  58    84    80:=======================================*==
  60    70    65:================================*==
  62    79    52:=========================*==============
  64    51    41:====================*=====
  66    38    33:================*==
  68    51    26:============*=============
  70    48    20:=========*==============
  72    41    16:=======*=============
  74    30    12:=====*=========
  76    45    10:====*==================
  78    42     7:===*=================
  80    30     6:==*============
  82    30     4:=*=============
  84    21     4:=*=========
  86    15     3:=*======
  88    14     2:*======
  90    12     2:*=====
  92    23     1:*===========
  94    16     1:*=======
  96    13     1:*======
  98     7     1:*===
 100     7     0:====
 102     7     0:====
 104    11     0:======
 106    10     0:=====
 108     8     0:====
 110     4     0:==
 112     8     0:====
 114     2     0:=
 116     0     0:
 118     5     0:===
>120     9     0:=====
112936249 residues in   657 sequences
  Expectation_n fit: rho(ln(x))= 10.8578+/-0.0125; mu= 7.5547+/- 1.409
 mean_var=242.9513+/-133.277, 0's: 0 Z-trim: 52  B-trim: 0 in 0/23
 Lambda= 0.0823
 Kolmogorov-Smirnov  statistic: 0.2080 (N=29) at  54

FASTA (3.36 June 2000) function [optimized, +5/-4 matrix (5:-4)] ktup: 6
 join: 82, opt: 67, gap-pen: -16/ -4, width:  16
 Scan time: 78.670
The best scores are:                                       opt bits E(1899)
BACR21I23 : AC009391, 189254 bases, from 3R:10 (73982) [r]  261   44   0.017
BACR40P19 : AC010667, 159570 bases, from 4:101 (73982) [f]  261   44   0.017
BACR30L17 : AC012390, 174441 bases, from 4:101 (32481) [f]  261   44   0.018
BACR44L03 : 172190 bases, from 4:101.          (73982) [r]  256   44   0.026
BACH57F14 : 103809 bases, from 4:101.          (32829) [r]  254   43   0.033
BACR19J06 : AC010581, 175053 bases, from 3R:85 (73982) [r]  251   43   0.039
BACR19J06 : AC010581, 175053 bases, from 3R:85 (73982) [f]  242   42   0.081
BACR44L03 : 172190 bases, from 4:101.          (73982) [f]  241   42   0.088
BACR42I20 : AC008195, 164944 bases, from 3R:93 (73982) [f]  238   41    0.11
BACR32K23BACR03G18 : 350380 bases, from X:14.  (73982) [f]  237   41    0.12
BACR12J05 : AC011697, 203853 bases, from X:12. (61893) [r]  237   41    0.12
BACR30J04 : AC008338, 177277 bases, from X:19. (73982) [r]  235   41    0.14
BACR10C18 : AC011705, 170975 bases, from X:19. (73982) [r]  235   41    0.14
BACR32M04 : AC008234, 148847 bases, from 3R:85 (73982) [f]  229   40    0.24
BACR43K14 : AC008356, 162593 bases, from 3R:85 (20633) [f]  229   40    0.27
BACR39E09 : AC009255, 163990 bases, from 2R:42 (73982) [r]  227   40    0.28
BACR13P06 : AC008339, 180296 bases, from 2R:42 (73982) [r]  227   40    0.28
BACR18C01 : AC007808, 167195 bases, from 3R:88 (73982) [f]  226   40     0.3
BACH59K20 : AC010840, 29516 bases, from 4:101. (29516) [r]  227   40    0.31
BACR20B21 : AC099010, 166512 bases, from 2L:27 (73982) [r]  225   40    0.33
BACR13A13 : AC018484, 172748 bases, from 2L:40 (73982) [f]  225   40    0.33
BACR48D17 : AC008255, 183316 bases, from X:13. (73982) [r]  225   40    0.33
BACR06H06 : 186935 bases, from 2L:40.          (44975) [f]  225   40    0.35
BACR22N03 : AC092397, 167201 bases, from 2L:26 (25241) [f]  225   40    0.37
BACR37K05 : AC011253, 197597 bases, from 3R:84 (55637) [f]  223   40     0.4
BACR30L17 : AC012390, 174441 bases, from 4:101 (73982) [r]  221   39    0.46
BACR01O16 : AC093045, 189904 bases, from 2L:29 (73982) [f]  221   39    0.46
BACR14D22 : AC012164, 169384 bases, from X:17. (73982) [f]  221   39    0.46
BACR08A11 : 170075 bases, from 2R:42.          (73982) [f]  221   39    0.46
BACR25O02 : AC018490, 165098 bases, from X:17. (73982) [r]  221   39    0.46
BACR02B16 : AC008331, 186938 bases, from 2L:29 (44978) [f]  221   39    0.48
BACR13P06 : AC008339, 180296 bases, from 2R:42 (38336) [f]  221   39    0.49
BACR11M14 : AC099308, 173101 bases, from X:19. (73982) [f]  219   39    0.54
BACR15O02 : AC009735, 159478 bases, from 3R:82 (73982) [r]  219   39    0.54
BACR21E16 : AC009905, 170662 bases, from 2L:36 (73982) [r]  218   39    0.58
BACR48D17 : AC008255, 183316 bases, from X:13. (73982) [f]  218   39    0.58
BACR15O02 : AC009735, 159478 bases, from 3R:82 (73982) [f]  217   39    0.63
BACR30G03 : AC008355, 151500 bases, from 3R:82 (73982) [f]  217   39    0.63
BACR13P06 : AC008339, 180296 bases, from 2R:42 (73982) [r]  216   39    0.69
BACR22H11 : AC013431, 191558 bases, from X:13. (73982) [r]  216   39    0.69
BACR25C18 : AC092401, 185200 bases, from X:13. (73982) [r]  216   39    0.69
BACR25O02 : AC018490, 165098 bases, from X:17. (73982) [f]  216   39    0.69
BACR11C03 : AC008220, 186549 bases, from 3R:10 (73982) [f]  216   39    0.69
BACR06P08 : AC007975, 180630 bases, from 3R:10 (38670) [f]  216   39    0.74
BACR29F06 : AC008203, 174728 bases, from 3R:95 (73982) [r]  215   39    0.75
BACR48E23 : AC005721, 203183 bases, from 3R:88 (73982) [r]  215   39    0.75
BACR22N03 : AC092397, 167201 bases, from 2L:26 (73982) [r]  215   39    0.75
BACR08H11 : AC008136, 154890 bases, from 3R:88 (73982) [r]  215   39    0.75
BACR15J11 : AC008202, 186159 bases, from 3R:95 (44199) [r]  215   39    0.79
BACR14N05 : AC099033, 170299 bases, from 2R:55 (73982) [f]  214   39    0.81
BACR48A20 : AC011072, 166158 bases, from 2R:55 (73982) [f]  214   39    0.81
BACR19D23 : AC095014, 170801 bases, from 3R:84 (73982) [r]  214   39    0.81
BACR19J06 : AC010581, 175053 bases, from 3R:85 (73982) [f]  214   39    0.81
BACR11B14 : 174999 bases, from 2R:41.          (73982) [r]  213   38    0.88
BACR06P07 : 187793 bases, from 2R:41.          (45833) [f]  213   38    0.93
BACR19J06 : AC010581, 175053 bases, from 3R:85 (73982) [r]  212   38    0.96
BACR25C18 : AC092401, 185200 bases, from X:13. (73982) [f]  210   38     1.1
BACR22N03 : AC092397, 167201 bases, from 2L:26 (73982) [f]  210   38     1.1
BACR03L12 : AC008357, 190672 bases, from 3R:86 (73982) [r]  210   38     1.1
BACR10E07 : AC012675, 176818 bases, from 2L:27 (73982) [f]  210   38     1.1
BACR22H11 : AC013431, 191558 bases, from X:13. (73982) [f]  210   38     1.1
BACR19I14 : AC095013, 175648 bases, from 3R:83 (73982) [f]  210   38     1.1
BACR11C03 : AC008220, 186549 bases, from 3R:10 (73982) [r]  210   38     1.1
BACR23O04 : AC008316, 160817 bases, from 3R:85 (73982) [r]  210   38     1.1
BACR28B01 : AC008139, 170675 bases, from 3R:85 (73982) [r]  210   38     1.1
BACR30F01 : AC008315, 177028 bases, from 3R:85 (73982) [r]  210   38     1.1
BACR06P08 : AC007975, 180630 bases, from 3R:10 (38670) [r]  210   38     1.2
BACR30F01 : AC008315, 177028 bases, from 3R:85 (35068) [r]  210   38     1.2
BACR30G03 : AC008355, 151500 bases, from 3R:82 (73982) [r]  209   38     1.2
BACR15O02 : AC009735, 159478 bases, from 3R:82 (73982) [r]  209   38     1.2
BACR21B19 : AC011250, 161692 bases, from 4:101 (73982) [r]  209   38     1.2
BACR28B01 : AC008139, 170675 bases, from 3R:85 (28715) [r]  210   38     1.2
BACR10P11 : AC007888, 164035 bases, from 2R:57 (73982) [f]  208   38     1.3
BACR48E23 : AC005721, 203183 bases, from 3R:88 (73982) [f]  208   38     1.3
BACR08H11 : AC008136, 154890 bases, from 3R:88 (73982) [f]  208   38     1.3
BACR28F21 : AC010705, 163958 bases, from X:11. (21998) [f]  209   38     1.4
BACR02C24 : 234783 bases, from X:12.           (21843) [r]  209   38     1.4
BACR36J03 : AC091634, 159065 bases, from 2R:50 (73982) [r]  207   38     1.4
BACR40P19 : AC010667, 159570 bases, from 4:101 (73982) [r]  207   38     1.4
BACR14P04 : AC007329, 126140 bases, from 2R:50 (73982) [f]  207   38     1.4
BACR30L17 : AC012390, 174441 bases, from 4:101 (32481) [r]  207   38     1.6
BACR34M23 : AC008190, 158012 bases, from 3R:83 (73982) [f]  205   38     1.7
BACR02C19 : AC008189, 188359 bases, from 3R:82 (73982) [r]  205   38     1.7
BACR24O24 : AC009538, 173927 bases, from 3R:83 (73982) [f]  205   38     1.7
BACR28F21 : AC010705, 163958 bases, from X:11. (21998) [r]  206   37     1.8
BACR02C24 : 234783 bases, from X:12.           (21843) [f]  206   37     1.8
BACR14D22 : AC012164, 169384 bases, from X:17. (73982) [r]  204   37     1.8
BACR11A04 : AC010916, 165307 bases, from 4:101 (73982) [r]  204   37     1.8
BACR01N17 : AC009911, 170184 bases, from 2L:38 (73982) [f]  204   37     1.8

>>BACR21I23 : AC009391, 189254 bases, from 3R:100.        (73982 nt)
rev-comp initn: 188 init1: 188 opt: 261  Z-score: 134.5  bits: 44.2 E(): 0.017
 57.303% identity (59.302% ungapped) in 267 nt overlap (289-31:64902-65167)

    320       310       300       290       280       270          
HUMBE- GATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATATGTAC
                                     :::::::::::::::::: : ::::: :: 
BACR21 GATGTCCTTGGTGGATTATGGTGTTAGGGTATATATATATATATATATATATATATATAT
           64880     64890     64900     64910     64920     64930 

    260       250       240       230       220       210          
HUMBE- ACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTCATGC
       : : ::: ::::: ::::::::  ::  :: : :   : : : : :  ::    : :: :
BACR21 ATATATATATATATATATATATATATATATATATATATATATATATATATAATATAATAC
           64940     64950     64960     64970     64980     64990 

    200           190       180          170       160       150   
HUMBE- ATGCTA----ATAAATTATGTCTAAAAATAGAAT---AAATACAAATCAATGTGCTCTGT
       :   ::    : ::: :::     :::::: :::   ::::: ::  :::  :    :  
BACR21 AAAATATAATACAAAATATAATACAAAATATAATACAAAATATAATACAAAATATAATAC
           65000     65010     65020     65030     65040     65050 

            140       130       120       110       100        90  
HUMBE- GCATTA-GTTACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGAGACCTCTTAAT
         : ::   :::  : ::   : :   : : :: :   :: : : :: : :       ::
BACR21 AAAATATAATACAAAATATAATATAAAATATAATATAAAATATAATATAAAATAAAATAT
           65060     65070     65080     65090     65100     65110 

             80        70        60        50        40        30  
HUMBE- GCAGTCAAAAATACAAATAAATAAAAAGTCACTTACAACCCAAAGTGTGACTATCAATGG
         : : ::: ::: ::  ::::: ::: : :  :: ::   ::: : : : ::: ::   
BACR21 AAAATAAAATATAAAATAAAATATAAAATAAAATATAAAATAAAATAT-AATATAAAATA
           65120     65130     65140     65150      65160     65170

             20        10                                          
HUMBE- GGTAATCAGTGGTGTCAAATAGGAGGT                                 
                                                                   
BACR21 TAAAATAAAATATAATATAAAATATAATATAAAATATAATATAAAATATAATATAAAATA
            65180     65190     65200     65210     65220     65230

>>BACR40P19 : AC010667, 159570 bases, from 4:101.         (73982 nt)
 initn: 190 init1: 190 opt: 261  Z-score: 134.5  bits: 44.2 E(): 0.017
 58.750% identity (60.256% ungapped) in 240 nt overlap (158-392:96540-96778)

       130       140       150       160       170       180       
HUMBE- CCTAATAAGTAACTAATGCACAGAGCACATTGATTTGTATTTATTCTATTTTTAGACATA
                                     :::::: :::  : : :::   : : ::: 
BACR40 ATTACTATATTTACTTTAGCAAACTATTTCTGATTT-TATACACTGTATACATTGCCATT
   96510     96520     96530     96540      96550     96560        

         190       200       210       220       230       240     
HUMBE- A--TTTATTAGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATAT
       :  : ::: :  ::  :: :  : ::  : : ::: :   : :: :  ::  ::::::::
BACR40 AGTTATATAAATATATATAACTATATATATATAAATATATATAACTATATATATATATAT
    96570     96580     96590     96600     96610     96620        

         250       260         270       280       290       300   
HUMBE- GTATATGTATGTGTGTACATA--TACACATATATATATATATATATTTTTTCTTTTCTTA
        ::::: ::: : : :: :::  :: : :::::::::::::::::: : :: :: : :  
BACR40 ATATATATATATATATATATAACTATATATATATATATATATATATATATTTTTATATAT
    96630     96640     96650     96660     96670     96680        

           310       320       330       340       350       360   
HUMBE- CCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCAT
         :       : :::: :::::   ::  :  :: :::    : : :::    :: :  :
BACR40 ATATCCTAGCTCAATCTAAATATAAAGTTGGAATACTTTTGCCAGGGGTTTCTTTCTTTT
    96690     96700     96710     96720     96730     96740        

            370       380       390       400       410       420  
HUMBE- CCATTC-TGTCCTGTAAGTATTTTGCATATTCTGGAGACGCAGGAAGAGATCCATCTACA
       :  : : : :  :    :::: :: :::::                              
BACR40 CTTTCCTTATAATACTGGTATCTTTCATATGACTATATTCCGTAATCTATAAGTCTCTTG
    96750     96760     96770     96780     96790     96800        

>>BACR30L17 : AC012390, 174441 bases, from 4:101.         (32481 nt)
 initn: 190 init1: 190 opt: 261  Z-score: 140.2  bits: 44.1 E(): 0.018
 58.750% identity (60.256% ungapped) in 240 nt overlap (158-392:157679-157917)

       130       140       150       160       170       180       
HUMBE- CCTAATAAGTAACTAATGCACAGAGCACATTGATTTGTATTTATTCTATTTTTAGACATA
                                     :::::: :::  : : :::   : : ::: 
BACR30 ATTACTATATTTACTTTAGCAAACTATTTCTGATTT-TATACACTGTATACATTGCCATT
   157650    157660    157670    157680     157690    157700       

         190       200       210       220       230       240     
HUMBE- A--TTTATTAGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATAT
       :  : ::: :  ::  :: :  : ::  : : ::: :   : :: :  ::  ::::::::
BACR30 AGTTATATAAATATATATAACTATATATATATAAATATATATAACTATATATATATATAT
    157710    157720    157730    157740    157750    157760       

         250       260         270       280       290       300   
HUMBE- GTATATGTATGTGTGTACATA--TACACATATATATATATATATATTTTTTCTTTTCTTA
        ::::: ::: : : :: :::  :: : :::::::::::::::::: : :: :: : :  
BACR30 ATATATATATATATATATATAACTATATATATATATATATATATATATATTTTTATATAT
    157770    157780    157790    157800    157810    157820       

           310       320       330       340       350       360   
HUMBE- CCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCAT
         :       : :::: :::::   ::  :  :: :::    : : :::    :: :  :
BACR30 ATATCCTAGCTCAATCTAAATATAAAGTTGGAATACTTTTGCCAGGGGTTTCTTTCTTTT
    157830    157840    157850    157860    157870    157880       

            370       380       390       400       410       420  
HUMBE- CCATTC-TGTCCTGTAAGTATTTTGCATATTCTGGAGACGCAGGAAGAGATCCATCTACA
       :  : : : :  :    :::: :: :::::                              
BACR30 CTTTCCTTATAATACTGGTATCTTTCATATGACTATATTCCGTAATCTATAAGTCTCTTG
    157890    157900    157910    157920    157930    157940       

>>BACR44L03 : 172190 bases, from 4:101.                   (73982 nt)
rev-comp initn: 206 init1: 206 opt: 256  Z-score: 131.3  bits: 43.6 E(): 0.026
 63.054% identity (68.085% ungapped) in 203 nt overlap (325-132:64216-64412)

          350       340       330       320       310       300    
HUMBE- TCTACCTCAGTTCTAAGCATATCTTCTCCTTATTTGGATTAAAACCTTCTGGTAAGAAAA
                                     ::: : :: :::::  ::::  ::    ::
BACR44 ATGATTAGCGAATGATTTGATAATGAAAAATATATTGAATAAAAAATTCTTATACTGCAA
       64190     64200     64210     64220     64230     64240     

          290       280       270       260       250       240    
HUMBE- GAAAAAATATATATATATATATATGTGTATATGTACACACATACATATACATATATATG-
         : : :::::::::::::::::: : :::::  ::: : ::: ::::: ::::::::: 
BACR44 CCATATATATATATATATATATATATATATATACACATATATATATATATATATATATGT
       64250     64260     64270     64280     64290     64300     

            230       220       210       200       190            
HUMBE- -CATTCATTTGTTGTTGTTTTTCTTAATTTGCTCATGCATGCTAATAAATTATGT----C
         :: ::: : ::   :  :     :::  :  :::  :::  :: ::: : :::     
BACR44 ATATACATATATTAAGGAGT---AAAATAAGTGCAT--ATGAAAAAAAACTGTGTGAGCA
       64310     64320        64330       64340     64350     64360

      180        170         160       150       140       130     
HUMBE- TAA-AAATAGAATAAATACAAAT--CAATGTGCTCTGTGCATTAGTTACTTATTAGGTTT
       ::: ::::::   : :::  :::  : :::::    :   :: : ::: ::::       
BACR44 TAACAAATAGCCAAGATAATAATGACGATGTGGCAAGCAGATCA-TTAATTATATTAATA
            64370     64380     64390     64400      64410         

         120       110       100        90        80        70     
HUMBE- TGGGAAACAAGAGGTAAAAAACTAGAGACCTCTTAATGCAGTCAAAAATACAAATAAATA
                                                                   
BACR44 AAAATAAAAAATTTTGAATCAACGTACATACATATAGTTTACAATACCACAAATTTGGTC
   64420     64430     64440     64450     64460     64470         

>>BACH57F14 : 103809 bases, from 4:101.                   (32829 nt)
rev-comp initn: 170 init1: 170 opt: 254  Z-score: 135.7  bits: 43.2 E(): 0.033
 60.000% identity (63.559% ungapped) in 250 nt overlap (401-165:84585-84833)

      430       420       410       400       390       380        
HUMBE- TTTGGGATATGTAGATGGATCTCTTCCTGCGTCTCCAGAATATGCAAAATACTTACA---
                                     : :: :: :::   ::: : ::  : :   
BACH57 TTGAAATCCCATTTAAATACATGTACTTAAGCCTTCACAATTGCCAACAAACACAGATAT
        84560     84570     84580     84590     84600     84610    

         370          360         350        340        330        
HUMBE- GGACAGAAT---GGATGAAAACTC--TACCTCAGTTCTA-AGCATATCTT-CTCCTTATT
       :::::::::     :  :: :: :  ::  : : :: :: :  :::: :: : : :::: 
BACH57 GGACAGAATACCATACTAACACCCCATATATTATTTATATAATATATTTTACACATTATA
        84620     84630     84640     84650     84660     84670    

      320       310        300       290       280         270     
HUMBE- TGGATTAAAACCTTCT-GGTAAGAAAAGAAAAAATATATATATATATAT--ATGTGTATA
       :: ::: : :  :: :   : :   :   : : ::::::::::::::::  :: : ::::
BACH57 TGTATTTATATTTTATATATTATCTATTTATATATATATATATATATATTAATATATATA
        84680     84690     84700     84710     84720     84730    

         260       250       240       230       220       210     
HUMBE- TGTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCT
       : :: : : ::  ::::: ::::::::  : : :: :::   : : : : :   : : : 
BACH57 TATATATATATTAATATATATATATAT-AAATAATATGTATATATATATATATTTATACA
        84740     84750     84760      84770     84780     84790   

         200       190       180       170       160       150     
HUMBE- CATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGC
        ::  ::  : ::: : ::: : :: : ::: : :: :::                    
BACH57 TATATATATTTATATAATATATTTATACATATATTATATAATATATATAATATATATATA
         84800     84810     84820     84830     84840     84850   

         140       130       120       110       100        90     
HUMBE- ATTAGTTACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGAGACCTCTTAATGCA
                                                                   
BACH57 TATATATATATATATATAATATATTTATACATATATTTGTTTTCTAAAATTATGACTTCG
         84860     84870     84880     84890     84900     84910   

>>BACR19J06 : AC010581, 175053 bases, from 3R:85.         (73982 nt)
rev-comp initn: 195 init1: 195 opt: 251  Z-score: 128.1  bits: 43.0 E(): 0.039
 66.901% identity (70.896% ungapped) in 142 nt overlap (289-154:98989-99128)

    320       310       300       290       280       270          
HUMBE- GATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATATGTAC
                                     :: :::: :::::::::::: :::::::: 
BACR19 TGCACTGGTGTACACGAAGGTGTACGGACTATGTATACATATATATATGTATATATGTAT
    98960     98970     98980     98990     99000     99010        

    260       250       240       230            220       210     
HUMBE- ACACATACATATACATATATATGCATTCATTTGTTGT-----TGTTTTTCTTAATTTGCT
       : : ::: ::::: ::::::::  :::  :::::: :     ::: : :::  ::: : :
BACR19 ATATATATATATATATATATATATATTTGTTTGTTTTTTAAATGTATCTCTCGATTCGTT
    99020     99030     99040     99050     99060     99070        

         200       190       180        170       160       150    
HUMBE- CATGCATGCTAATAAATTATGTCTAA-AAATAGAATAAATACAAATCAATGTGCTCTGTG
         :  ::   : : :  ::::::::: :  ::  :: :::     ::::: :        
BACR19 TTTAAATAAAATTGA--TATGTCTAATAGCTATTATCAATCGTTTTCAATTTCAAAAAGT
    99080     99090       99100     99110     99120     99130      

          140       130       120       110       100        90    
HUMBE- CATTAGTTACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGAGACCTCTTAATGC
                                                                   
BACR19 TTTGTATTGTATTTCGAAGTAATTCTGTTGCGTTTTCTAATTATAATATTCGGTTTTCCC
      99140     99150     99160     99170     99180     99190      

>>BACR19J06 : AC010581, 175053 bases, from 3R:85.         (73982 nt)
 initn: 180 init1: 180 opt: 242  Z-score: 122.3  bits: 41.9 E(): 0.081
 82.857% identity (82.857% ungapped) in 70 nt overlap (234-303:98989-99058)

           210       220       230       240       250       260   
HUMBE- GAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTATGTGTGTAC
                                     ::: ::: :::: ::::::::: : :::: 
BACR19 TGCACTGGTGTACACGAAGGTGTACGGACTATGTATACATATATATATGTATATATGTAT
    98960     98970     98980     98990     99000     99010        

           270       280       290       300       310       320   
HUMBE- ATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAA
       ::::: : :::::::::::::::::::: ::  ::: :::                    
BACR19 ATATATATATATATATATATATATATTTGTTTGTTTTTTAAATGTATCTCTCGATTCGTT
    99020     99030     99040     99050     99060     99070        

           330       340       350       360       370       380   
HUMBE- TAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCCTGTAAGTAT
                                                                   
BACR19 TTTAAATAAAATTGATATGTCTAATAGCTATTATCAATCGTTTTCAATTTCAAAAAGTTT
    99080     99090     99100     99110     99120     99130        

>>BACR44L03 : 172190 bases, from 4:101.                   (73982 nt)
 initn: 211 init1: 211 opt: 241  Z-score: 121.7  bits: 41.8 E(): 0.088
 66.418% identity (67.939% ungapped) in 134 nt overlap (185-317:64197-64328)

          160       170       180       190       200       210    
HUMBE- CATTGATTTGTATTTATTCTATTTTTAGACATAATTTATTAGCATGCATGAGCAAATTAA
                                     :: ::::  ::  ::: :  :   : : ::
BACR44 TTAAAACCATACATGCCGAATGATTAGCGAATGATTTGATA--ATGAAAAATATATTGAA
      64170     64180     64190     64200       64210     64220    

          220       230       240       250       260       270    
HUMBE- GAAAAACAACAACAAATGAATGCATATATATGTATATGTATGTGTGTACATATACACATA
        :::::   :    : :: :  ::::::::: ::::: ::: : : :: :::::::::::
BACR44 TAAAAAATTCTTATACTGCAACCATATATATATATATATATATATATATATATACACATA
        64230     64240     64250     64260     64270     64280    

          280        290       300       310       320       330   
HUMBE- TATATATATATATAT-TTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAG
       ::::::::::::::: : : : : : : ::    ::::  : ::                
BACR44 TATATATATATATATATATGTATATACATATATTAAGGAGTAAAATAAGTGCATATGAAA
        64290     64300     64310     64320     64330     64340    

           340       350       360       370       380       390   
HUMBE- ATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCCTGTAAGTATTTTGCATATT
                                                                   
BACR44 AAAAACTGTGTGAGCATAACAAATAGCCAAGATAATAATGACGATGTGGCAAGCAGATCA
        64350     64360     64370     64380     64390     64400    

>>BACR42I20 : AC008195, 164944 bases, from 3R:93.         (73982 nt)
 initn: 118 init1: 118 opt: 238  Z-score: 119.7  bits: 41.5 E(): 0.11
 68.908% identity (70.690% ungapped) in 119 nt overlap (197-315:52925-53040)

        170       180       190       200       210       220      
HUMBE- TTTATTCTATTTTTAGACATAATTTATTAGCATGCATGAGCAAATTAAGAAAAACAACAA
                                     ::  ::: :   :::: :     ::  : :
BACR42 ATCAACCAAACAATGGCAGCGACATCCTCCCACTCATCATTCAATTTACCGCCACGCCGA
        52900     52910     52920     52930     52940     52950    

        230       240       250       260       270       280      
HUMBE- CAAATGAATGCATATATATGTATATGTATGTGTGTACATATACACATATATATATATATA
        ::::  :: :: : : :  ::::: :::::::::: ::::: : :::::::::: ::: 
BACR42 AAAATCCATACAAAAACA--TATATATATGTGTGTATATATATATATATATATATGTATT
        52960     52970       52980     52990     53000     53010  

        290       300       310       320       330       340      
HUMBE- TATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAAC
       :: ::  : ::::: :: :: ::::::::                               
BACR42 TA-TTGATATTTTCATAACAAAAGGTTTTTCGTTGTCGGTTTTTGGTGTCGTGTTTTGGT
           53020     53030     53040     53050     53060     53070 

>>BACR32K23BACR03G18 : 350380 bases, from X:14.           (73982 nt)
 initn: 194 init1: 194 opt: 237  Z-score: 119.1  bits: 41.3 E(): 0.12
 64.667% identity (68.794% ungapped) in 150 nt overlap (189-333:115618-115763)

      160       170       180       190       200       210        
HUMBE- GATTTGTATTTATTCTATTTTTAGACATAATTTATTAGCATGCATGAGCAAATTAAGAAA
                                     ::: :  : :: :::  : : : : : : :
BACR32 TCGCCGTGGTAGGTATTCAGCTATTCTATTTTTTTCCGAATTCATATGAATAATTATATA
    115590    115600    115610    115620    115630    115640       

      220       230       240       250       260       270        
HUMBE- AACAACAACAAATGAATGCATATATATGTATATGTATGTGTGTACATATACACATATATA
        ::    : : ::  :: ::::::::: ::::: ::: : :::: :: :: : :::::::
BACR32 TAC----ATATATATATACATATATATCTATATATATATTTGTATATTTATATATATATA
    115650        115660    115670    115680    115690    115700   

      280       290        300       310           320       330   
HUMBE- TATATATATATTT-TTTCTTTTCTTACCAGAAGGTTTTAA----TCCAAATAAGGAGAAG
        :::::::::::: ::: : :: : :    :    :::::    :  ::: : :::::::
BACR32 CATATATATATTTATTTATATTGTAAATTTACCAGTTTAAGTCTTTAAAAAATGGAGAAG
        115710    115720    115730    115740    115750    115760   

           340       350       360       370       380       390   
HUMBE- ATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCCTGTAAGTATTTTGCATATT
                                                                   
BACR32 GAGCAGGCTCATGTGTACCTGAATGGCTGTAACTTCCGATGTCTGTTACTCGAAGTCCTG
        115770    115780    115790    115800    115810    115820   

>>BACR12J05 : AC011697, 203853 bases, from X:12.          (61893 nt)
rev-comp initn: 173 init1: 173 opt: 237  Z-score: 120.3  bits: 41.3 E(): 0.12
 62.083% identity (68.664% ungapped) in 240 nt overlap (289-60:202512-202738)

    320       310       300       290       280       270          
HUMBE- GATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATATGTAC
                                     :::::::::::::::::: : ::::: :: 
BACR12 TTCAGATGTATTTGCTGTTACTCATATCGTATATATATATATATATATATATATATATAT
          202490    202500    202510    202520    202530    202540 

    260       250        240        230       220       210        
HUMBE- ACACATACATATACATA-TATA-TGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTCAT
       : : ::: ::::: ::: :::: ::::: :: :: ::::  :  : :: ::  :  :   
BACR12 ATATATATATATATATATTATATTGCATACAATT-TTGT--TCGTCCTAAACATTGTGTA
          202550    202560    202570       202580    202590        

      200       190        180       170       160       150       
HUMBE- GCATGCTAATAAATT-ATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCAT
       ::::  :: : ::::  :: :   :: ::  :: ::::      : ::::::: ::: : 
BACR12 GCATTTTATTCAATTGGTGGC---AACTATGATGAATA------ATTGTGCTCAGTGTAG
   202600    202610       202620    202630          202640         

       140       130         120        110       100        90    
HUMBE- TAGTTACTTATTAGGTTTTGG--GAAAC-AAGAGGTAAAAAACTAGAGACCTCTTAAT-G
       : :  ::      :   : ::  ::::: :::: ::   :::   : ::: :   : : :
BACR12 TCG-AACAAGCCGGCAGTGGGACGAAACGAAGATGTTGCAAATGCGGGACTTGGGACTCG
  202650     202660    202670    202680    202690    202700        

               80        70        60        50        40          
HUMBE- CAG---TCAAAAATACAAATAAATAAAAAGTCACTTACAACCCAAAGTGTGACTATCAAT
       :::   ::  :::: ::::  : :: :: :                              
BACR12 CAGGATTCTGAAATGCAAAGGACTAGAAGGGAGGGTAAGTGGTGGGGAGGCTAGAAGGAC
   202710    202720    202730    202740    202750    202760        

>>BACR30J04 : AC008338, 177277 bases, from X:19.          (73982 nt)
rev-comp initn: 231 init1: 162 opt: 235  Z-score: 117.8  bits: 41.1 E(): 0.14
 60.311% identity (64.583% ungapped) in 257 nt overlap (293-49:8894-9145)

        320       310       300       290       280       270      
HUMBE- TTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATAT
                                     : : :::::: ::::::::::: : :::::
BACR30 TTGCGCCTCTGCCGCTGTTTATTTTCCCACACATATATATGTATATATATATATTTATAT
          8870      8880      8890      8900      8910      8920   

        260       250       240       230       220       210      
HUMBE- GTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTC
        :: :   ::: ::::: ::::: :::  :  ::  ::::   : ::: :::::: ::  
BACR30 ATATATGTATATATATATATATACATGTTTGTATAGGTTG-CATCTTTATTAATTGGCCA
          8930      8940      8950      8960       8970      8980  

          200       190         180        170       160           
HUMBE- AT--GCATGCTAATAAATTATG-TCTA-AAAATA-GAATAAATACAAATCAATGTGC-TC
       ::    :: : : : : :::::  :::  :: :: ::  ::: : :::     :: : ::
BACR30 ATAAATATCCCAGTTATTTATGAACTATCAACTATGATCAAAAAAAAAATTGCGTACATC
           8990      9000      9010      9020      9030      9040  

    150        140       130       120       110        100        
HUMBE- TGTGCAT-TAGTTACTTATTAGGTTTTGGGAAACAAGAGGTA-AAAAACTAGAGACCTCT
        :  :::  :: ::  : :::  : :    ::     :  :: : ::: :  ::   :  
BACR30 CGCACATACAGCTAGGT-TTATATATATTTAACTTTCACATATACAAATTCAAG---TAC
           9050       9060      9070      9080      9090           

       90        80        70            60        50        40    
HUMBE- TAATGCAGTCAAAAATACAAATAAATA----AAAAGTCACTTACAACCCAAAGTGTGACT
        ::: ::   : ::::::::::: :::     :::  : :::::: :             
BACR30 AAATTCAAATACAAATACAAATACATATGCTTAAATACGCTTACATCGGATTTTGTCTAT
     9100      9110      9120      9130      9140      9150        

           30        20        10                                  
HUMBE- ATCAATGGGGTAATCAGTGGTGTCAAATAGGAGGT                         
                                                                   
BACR30 GCCGTCGTCCATATGAGTTCACTTTATGATTTACACACATTTGACTCGAAATTTGATATA
     9160      9170      9180      9190      9200      9210        

>>BACR10C18 : AC011705, 170975 bases, from X:19.          (73982 nt)
rev-comp initn: 162 init1: 162 opt: 235  Z-score: 117.8  bits: 41.1 E(): 0.14
 60.311% identity (64.583% ungapped) in 257 nt overlap (293-49:96960-97211)

        320       310       300       290       280       270      
HUMBE- TTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATAT
                                     : : :::::: ::::::::::: : :::::
BACR10 TTGCGCCTCTGCCGCTGTTTATTTTCCCACACATATATATGTATATATATATATTTATAT
   96930     96940     96950     96960     96970     96980         

        260       250       240       230       220       210      
HUMBE- GTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTC
        :: :   ::: ::::: ::::: :::  :  ::  ::::   : ::: :::::: ::  
BACR10 ATATATGTATATATATATATATACATGTTTGTATAGGTTG-CATCTTTATTAATTGGCCA
   96990     97000     97010     97020      97030     97040        

          200       190         180        170       160           
HUMBE- AT--GCATGCTAATAAATTATG-TCTA-AAAATA-GAATAAATACAAATCAATGTGC-TC
       ::    :: : : : : :::::  :::  :: :: ::  ::: : :::     :: : ::
BACR10 ATAAATATCCCAGTTATTTATGAACTATCAACTATGATCAAAAAAAAAATTGCGTACATC
    97050     97060     97070     97080     97090     97100        

    150        140       130       120       110        100        
HUMBE- TGTGCAT-TAGTTACTTATTAGGTTTTGGGAAACAAGAGGTA-AAAAACTAGAGACCTCT
        :  :::  :: ::  : :::  : :    ::     :  :: : ::: :  ::   :  
BACR10 CGCACATACAGCTAGGT-TTATATATATTTAACTTTCACATATACAAATTCAAG---TAC
    97110     97120      97130     97140     97150     97160       

       90        80        70            60        50        40    
HUMBE- TAATGCAGTCAAAAATACAAATAAATA----AAAAGTCACTTACAACCCAAAGTGTGACT
        ::: ::   : ::::::::::: :::     :::  : :::::: :             
BACR10 AAATTCAAATACAAATACAAATACATATGCTTAAATACGCTTACATCGGATTTTGTCTAT
        97170     97180     97190     97200     97210     97220    

           30        20        10                                  
HUMBE- ATCAATGGGGTAATCAGTGGTGTCAAATAGGAGGT                         
                                                                   
BACR10 GCCGTCGTCCATATGAGTTCACTTTATGATTTACACACATTTGACTCGAAATTTGATATA
        97230     97240     97250     97260     97270     97280    

>>BACR32M04 : AC008234, 148847 bases, from 3R:85.         (73982 nt)
 initn: 223 init1: 223 opt: 229  Z-score: 114.0  bits: 40.4 E(): 0.24
 73.034% identity (73.034% ungapped) in 89 nt overlap (199-287:46334-46422)

      170       180       190       200       210       220        
HUMBE- TATTCTATTTTTAGACATAATTTATTAGCATGCATGAGCAAATTAAGAAAAACAACAACA
                                     :: :::::::    :::  :  : :: :: 
BACR32 GCTCCTGCTTTCTCGCTTCACTTGCCACATTGAATGAGCACGAAAAGTTACTCTACTACC
         46310     46320     46330     46340     46350     46360   

      230       240       250       260       270       280        
HUMBE- AATGAATGCATATATATGTATATGTATGTGTGTACATATACACATATATATATATATATA
       :    :: : :::: :: ::::::::::: : :::::::: : :::::::::::::::: 
BACR32 ATACTATACGTATACATATATATGTATGTATATACATATATATATATATATATATATATG
         46370     46380     46390     46400     46410     46420   

      290       300       310       320       330       340        
HUMBE- TTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTG
                                                                   
BACR32 GCCGAATGCAGCCTCGCTGCCTCTGCTCCATTATCAAAATGCAATTTCATCAATGCTGGC
         46430     46440     46450     46460     46470     46480   

>>BACR43K14 : AC008356, 162593 bases, from 3R:85.         (20633 nt)
 initn: 223 init1: 223 opt: 229  Z-score: 122.9  bits: 40.2 E(): 0.27
 73.034% identity (73.034% ungapped) in 89 nt overlap (199-287:161695-161783)

      170       180       190       200       210       220        
HUMBE- TATTCTATTTTTAGACATAATTTATTAGCATGCATGAGCAAATTAAGAAAAACAACAACA
                                     :: :::::::    :::  :  : :: :: 
BACR43 GCTCCTGCTTTCTCGCTTCACTTGCCACATTGAATGAGCACGAAAAGTTACTCTACTACC
       161670    161680    161690    161700    161710    161720    

      230       240       250       260       270       280        
HUMBE- AATGAATGCATATATATGTATATGTATGTGTGTACATATACACATATATATATATATATA
       :    :: : :::: :: ::::::::::: : :::::::: : :::::::::::::::: 
BACR43 ATACTATACGTATACATATATATGTATGTATATACATATATATATATATATATATATATG
       161730    161740    161750    161760    161770    161780    

      290       300       310       320       330       340        
HUMBE- TTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTG
                                                                   
BACR43 GCCGAATGCAGCCTCGCTGCCTCTGCTCCATTATCAAAATGCAATTTCATCAATGCTGGC
       161790    161800    161810    161820    161830    161840    

>>BACR39E09 : AC009255, 163990 bases, from 2R:42.         (73982 nt)
rev-comp initn: 142 init1: 142 opt: 227  Z-score: 112.7  bits: 40.2 E(): 0.28
 68.421% identity (73.984% ungapped) in 133 nt overlap (345-216:62541-62666)

          370       360       350       340       330       320    
HUMBE- AGGACAGAATGGATGAAAACTCTACCTCAGTTCTAAGCATATCTTCTCCTTATTTGGATT
                                     ::: ::::: :: ::     :: :   :: 
BACR39 TTGAAGTCAATGTCAAGTCCAATGCGGTCATTCCAAGCA-ATTTT----ATAATATAATA
            62520     62530     62540      62550         62560     

          310       300       290         280       270       260  
HUMBE- AAAACCTTCTGGTAAGAAAAGAAAAAATATATATAT--ATATATATGTGTATATGTACAC
         ::: :  :  ::: : :: : ::::::::: :::  :::::: ::::::::: ::   
BACR39 TTAACATAATATTAATATAATATAAAATATATGTATGCATATATTTGTGTATATATATTT
       62570     62580     62590     62600     62610     62620     

            250        240       230       220       210       200 
HUMBE- ACATACATATACATATAT-ATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTCATGCA
       ::::: ::::: :::::: :::  ::::: : :::::   :::                 
BACR39 ACATATATATAAATATATAATG--TTCATATATTGTTAAGTTTGCTGTGCTGCAAAGTTT
       62630     62640       62650     62660     62670     62680   

             190       180       170       160       150       140 
HUMBE- TGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCATTAGT
                                                                   
BACR39 TGGCACTGACCACGAAAGCAGAATCGCCATGAAGGCGATGCTGGAGGCACACGTCGGGTA
         62690     62700     62710     62720     62730     62740   

>>BACR13P06 : AC008339, 180296 bases, from 2R:42.         (73982 nt)
rev-comp initn: 142 init1: 142 opt: 227  Z-score: 112.7  bits: 40.2 E(): 0.28
 68.421% identity (73.984% ungapped) in 133 nt overlap (345-216:18716-18841)

          370       360       350       340       330       320    
HUMBE- AGGACAGAATGGATGAAAACTCTACCTCAGTTCTAAGCATATCTTCTCCTTATTTGGATT
                                     ::: ::::: :: ::     :: :   :: 
BACR13 TTGAAGTCAATGTCAAGTCCAATGCGGTCATTCCAAGCA-ATTTT----ATAATATAATA
       18690     18700     18710     18720          18730     18740

          310       300       290         280       270       260  
HUMBE- AAAACCTTCTGGTAAGAAAAGAAAAAATATATATAT--ATATATATGTGTATATGTACAC
         ::: :  :  ::: : :: : ::::::::: :::  :::::: ::::::::: ::   
BACR13 TTAACATAATATTAATATAATATAAAATATATGTATGCATATATTTGTGTATATATATTT
            18750     18760     18770     18780     18790     18800

            250        240       230       220       210       200 
HUMBE- ACATACATATACATATAT-ATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTCATGCA
       ::::: ::::: :::::: :::  ::::: : :::::   :::                 
BACR13 ACATATATATAAATATATAATG--TTCATATATTGTTAAGTTTGCTGTGCTGCAAAGTTT
            18810     18820       18830     18840     18850        

             190       180       170       160       150       140 
HUMBE- TGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCATTAGT
                                                                   
BACR13 TGGCACTGACCACGAAAGCAGAATCGCCATGAAGGCGATGCTGGAGGCACACGTCGGGTA
    18860     18870     18880     18890     18900     18910        

>>BACR18C01 : AC007808, 167195 bases, from 3R:88.         (73982 nt)
 initn: 100 init1: 100 opt: 226  Z-score: 112.0  bits: 40.0 E():  0.3
 65.693% identity (67.164% ungapped) in 137 nt overlap (170-304:93850-93985)

     140       150       160       170        180       190        
HUMBE- CTAATGCACAGAGCACATTGATTTGTATTTATTCTATTTT-TAGACATAATT-TATTAGC
                                     :::  ::::: : :   :: :: ::   : 
BACR18 AACGGTTGTCCAAGCTCAACTACAAGGAGCATTAAATTTTATGGGTTTAGTTGTAGATGG
   93820     93830     93840     93850     93860     93870         

       200       210       220       230       240       250       
HUMBE- ATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTATGT
       :   : : ::::::: ::: ::   :  : :::  : : :: ::: :: ::::: ::: :
BACR18 AAATAAGTGCAAATTTAGATAACTGATCA-AAACCATTTCAGATAAATATATATATATAT
   93880     93890     93900      93910     93920     93930        

       260       270       280       290       300       310       
HUMBE- GTGTACATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTTAA
        : :: ::::: : :::::::::::::::::: :::   ::  : ::             
BACR18 ATATATATATATATATATATATATATATATATATTTAAGTTCATCACACTTTTTTTTTTT
    93940     93950     93960     93970     93980     93990        

       320       330       340       350       360       370       
HUMBE- TCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCCTGT
                                                                   
BACR18 TTGCATTTATATACCCTTTTGTGGGCCAGGGTAATCAGAAGACTTACACATTTTATTGGG
    94000     94010     94020     94030     94040     94050        

>>BACH59K20 : AC010840, 29516 bases, from 4:101.          (29516 nt)
rev-comp initn: 179 init1: 179 opt: 227  Z-score: 119.1  bits: 40.0 E(): 0.31
 64.189% identity (65.517% ungapped) in 148 nt overlap (300-154:10680-10825)

     330       320       310       300        290       280        
HUMBE- CTCCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGA-AAAAATATATATATATATATAT
                                     ::: : : : : ::::::::::::::::::
BACH59 CCTCGTCAGATCGACTCGGCTATTGATCCTGAATATATATATATATATATATATATATAT
   10650     10660     10670     10680     10690     10700         

      270       260       250       240       230       220        
HUMBE- GTGTATATGTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTA
        : ::::: :: : : ::  ::::: ::::::::  ::  :: : :   : : ::: :  
BACH59 TTATATATATATATATATTTATATATATATATATTTATATATATATATATATATTTATAT
   10710     10720     10730     10740     10750     10760         

      210       200       190       180       170       160        
HUMBE- ATTTGCTCATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGC
       :::   : ::  ::  ::   : :::: : :  : ::  :: ::::: : ::  :: :  
BACH59 ATTATAT-ATTTAT-ATATATATTTATTTATTTATATTTAACAAATATATATACATATAT
   10770      10780      10790     10800     10810     10820       

      150       140       130       120       110       100        
HUMBE- TCTGTGCATTAGTTACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGAGACCTCT
                                                                   
BACH59 ATAATAACGAATCCACGGTAATTTATTAGATAAAAAATATAACCTTTATTCAAAATAAAA
     10830     10840     10850     10860     10870     10880       

>>BACR20B21 : AC099010, 166512 bases, from 2L:27.         (73982 nt)
rev-comp initn: 228 init1: 145 opt: 225  Z-score: 111.4  bits: 39.9 E(): 0.33
 67.361% identity (71.324% ungapped) in 144 nt overlap (303-165:133938-134078)

        330       320       310       300       290       280      
HUMBE- CTTCTCCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATAT
                                     ::: :  : :: : ::::::::::::::::
BACR20 TAATATTACATACATTAGTTTGTTGAACATTAAAATGAAAATATATATATATATATATAT
    133910    133920    133930    133940    133950    133960       

        270         260       250       240       230       220    
HUMBE- ATGTGTATA--TGTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTT
       :: ::: ::   ::    ::::::::: ::::: ::::: ::  ::  :::      :::
BACR20 ATTTGTTTAGCGGTTTTTACATACATACACATA-ATATGTATAAATAAGTTAAAAAATTT
    133970    133980    133990    134000     134010    134020      

          210         200        190       180       170       160 
HUMBE- CTTAATTTG-CT-CATGCATGCTAAT-AAATTATGTCTAAAAATAGAATAAATACAAATC
        :::::: : ::  :: :::   ::: : :: :: ::  :::::::  :  :::      
BACR20 ATTAATTAGACTAAATTCATTGGAATGATATAATATC--AAAATAGTTTGCATAATACAG
     134030    134040    134050    134060      134070    134080    

             150       140       130       120       110       100 
HUMBE- AATGTGCTCTGTGCATTAGTTACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGA
                                                                   
BACR20 CGATTTAGTTAAAATTTCACAACTATCTAGAAGCGAAAACTTGGAACATTTTAGTTTTGC
       134090    134100    134110    134120    134130    134140    

>>BACR13A13 : AC018484, 172748 bases, from 2L:40.         (73982 nt)
 initn: 160 init1: 160 opt: 225  Z-score: 111.4  bits: 39.9 E(): 0.33
 64.493% identity (65.926% ungapped) in 138 nt overlap (167-303:102083-102218)

        140       150       160       170       180       190      
HUMBE- TAACTAATGCACAGAGCACATTGATTTGTATTTATTCTATTTTTAGACATAATTTATTAG
                                     ::: :: ::  :  ::: :   :::: :: 
BACR13 CCGCAACTTTCCGCAAAAATCTTTAACAGTTTTTTTTTACCTCAAGAAACTCTTTAATAC
         102060    102070    102080    102090    102100    102110  

        200        210       220       230       240       250     
HUMBE- CATG-CATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTAT
        ::: ::: : :: ::  : : : :::  :::: :   :  ::::::::  :: :: :::
BACR13 AATGACATAAACATAT--ATATATACATAAACATACATAAACATATATACATACATATAT
         102120      102130    102140    102150    102160    102170

         260       270       280       290       300       310     
HUMBE- GTGTGTACATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTT
        : : :: ::::: : ::::::::::::::: : :    : :: : ::            
BACR13 ATATATATATATATATATATATATATATATAAACTAAAACCTTACGTAAACATAAAAAAG
           102180    102190    102200    102210    102220    102230

         320       330       340       350       360       370     
HUMBE- AATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCCT
                                                                   
BACR13 ATGTTCACAAAATACACAAAAAAGGTTAAATCAAATATAATTACACAAAAAATATTAAAT
           102240    102250    102260    102270    102280    102290

>>BACR48D17 : AC008255, 183316 bases, from X:13.          (73982 nt)
rev-comp initn: 171 init1: 171 opt: 225  Z-score: 111.4  bits: 39.9 E(): 0.33
 67.424% identity (71.774% ungapped) in 132 nt overlap (291-160:52531-52654)

      320       310       300       290       280       270        
HUMBE- TGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATATGT
                                     ::::::::::::::::::::   ::::: :
BACR48 ATTGTATAATTTTCGTTTGCTTTTGCTATTAAATATATATATATATATATAGATATATAT
            52510     52520     52530     52540     52550     52560

      260       250       240       230       220       210        
HUMBE- ACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTCAT
       : :::  :: :: :  ::::::::  ::  :: : :   : : : : ::  : ::   ::
BACR48 ATACATCTATATTTTTATATATAT--ATATATATCTATATATATATATT--TATGTAAAT
            52570     52580       52590     52600       52610      

      200       190       180       170       160       150        
HUMBE- GCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCATT
       : ::: :: :: ::::    :::::::   ::: : ::::::                  
BACR48 GTATG-TATTATATTAAAAATAAAAAT---ATATACACAAATATTATTATATACATAAAT
      52620      52630     52640        52650     52660     52670  

      140       130       120       110       100        90        
HUMBE- AGTTACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGAGACCTCTTAATGCAGTC
                                                                   
BACR48 ATAAATATATATATGTATATATGTTTTATATGTAAAATTATGAAGTATAAGGGTATCTTG
          52680     52690     52700     52710     52720     52730  

>>BACR06H06 : 186935 bases, from 2L:40.                   (44975 nt)
 initn: 160 init1: 160 opt: 225  Z-score: 114.9  bits: 39.8 E(): 0.35
 64.493% identity (65.926% ungapped) in 138 nt overlap (167-303:175937-176072)

        140       150       160       170       180       190      
HUMBE- TAACTAATGCACAGAGCACATTGATTTGTATTTATTCTATTTTTAGACATAATTTATTAG
                                     ::: :: ::  :  ::: :   :::: :: 
BACR06 CCGCAACTTTCCGCAAAAATCTTTAACAGTTTTTTTTTACCTCAAGAAACTCTTTAATAC
     175910    175920    175930    175940    175950    175960      

        200        210       220       230       240       250     
HUMBE- CATG-CATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTAT
        ::: ::: : :: ::  : : : :::  :::: :   :  ::::::::  :: :: :::
BACR06 AATGACATAAACATAT--ATATATACATAAACATACATAAACATATATACATACATATAT
     175970    175980      175990    176000    176010    176020    

         260       270       280       290       300       310     
HUMBE- GTGTGTACATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTT
        : : :: ::::: : ::::::::::::::: : :    : :: : ::            
BACR06 ATATATATATATATATATATATATATATATAAACTAAAACCTTACGTAAACATAAAAAAG
       176030    176040    176050    176060    176070    176080    

         320       330       340       350       360       370     
HUMBE- AATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCCT
                                                                   
BACR06 ATGTTCACAAAATACACAAAAAAGGTTAAATCAAATATAATTACACAAAAAATATTAAAT
       176090    176100    176110    176120    176130    176140    

>>BACR22N03 : AC092397, 167201 bases, from 2L:26.         (25241 nt)
 initn: 153 init1: 124 opt: 225  Z-score: 118.9  bits: 39.8 E(): 0.37
 67.361% identity (71.324% ungapped) in 144 nt overlap (165-303:166819-166959)

          140       150       160       170       180        190   
HUMBE- AGTAACTAATGCACAGAGCACATTGATTTGTATTTATTCTATTTTTAGACATAAT-TTAT
                                     :::  :  :::::::  :: :: :: : ::
BACR22 AGTTGTGAAATTTTAACTAAATCGCTGTATTATGCAAACTATTTT--GATATTATATCAT
   166790    166800    166810    166820    166830      166840      

           200         210       220       230       240       250 
HUMBE- TAGCATGCA-TGAG-CAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATAT
       :   ::: : : :: : :::::: :::      :::  ::  :: ::::: ::::: :::
BACR22 TCCAATGAATTTAGTCTAATTAATAAATTTTTTAACTTATTTATACATAT-TATGTGTAT
     166850    166860    166870    166880    166890     166900     

             260         270       280       290       300         
HUMBE- GTATGTGTGTAC--ATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAA
       ::::::    ::   :: ::: :::::::::::::::::: : :: :  : :::      
BACR22 GTATGTAAAAACCGCTAAACAAATATATATATATATATATATATTTTCATTTTAATGTTC
      166910    166920    166930    166940    166950    166960     

     310       320       330       340       350       360         
HUMBE- GGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTC
                                                                   
BACR22 AACAAACTAATGTATGTAATATTAAAACAACAATTATGAAGACAAACATTAATCTACATT
      166970    166980    166990    167000    167010    167020     

>>BACR37K05 : AC011253, 197597 bases, from 3R:84.         (55637 nt)
 initn: 184 init1: 184 opt: 223  Z-score: 112.1  bits: 39.6 E():  0.4
 63.636% identity (65.468% ungapped) in 143 nt overlap (156-294:158456-158598)

         130       140       150       160       170          180  
HUMBE- AACCTAATAAGTAACTAATGCACAGAGCACATTGATTTGTATTTATTCTAT---TTTTAG
                                     :::  ::: :  ::::: :::     ::: 
BACR37 CTCTACTCTCCATTATTACACGTTTTATTAATTTTTTTTTTCTTATTTTATCAAGATTAA
      158430    158440    158450    158460    158470    158480     

             190       200       210       220       230       240 
HUMBE- ACATAAT-TTATTAGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATAT
       :  :: : ::: ::  ::  ::    : ::  : : : : :   : : ::  :: ::: :
BACR37 ATCTAGTATTAATATAATATATATATATATATATATATATACATATATATATATACATTT
      158490    158500    158510    158520    158530    158540     

             250       260       270       280       290       300 
HUMBE- ATATGTATATGTATGTGTGTACATATACACATATATATATATATATATTTTTTCTTTTCT
       :::: ::::: ::: : : :: ::::: : ::::::::::: :::::: : ::       
BACR37 ATATATATATATATATATATATATATATATATATATATATAAATATATATATTGCTGGAG
      158550    158560    158570    158580    158590    158600     

             310       320       330       340       350       360 
HUMBE- TACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTC
                                                                   
BACR37 CCTTCGACTCATTACAAGATTATTTTATAACATTCTATGGTCTCTATTTCAATTTTTTTT
      158610    158620    158630    158640    158650    158660     

>>BACR30L17 : AC012390, 174441 bases, from 4:101.         (73982 nt)
rev-comp initn: 132 init1: 132 opt: 221  Z-score: 108.8  bits: 39.4 E(): 0.46
 68.382% identity (75.610% ungapped) in 136 nt overlap (323-199:139648-139781)

        350       340       330       320       310       300      
HUMBE- TACCTCAGTTCTAAGCATATCTTCTCCTTATTTGGATTAAAACCTTCTGGTAAGAA-AAG
                                     ::: :: : ::   :: ::::  ::: : :
BACR30 GTCGGAAATAATGTTTACTTTGACGATCATTTTCGAATTAATATTTGTGGTGCGAATATG
    139620    139630    139640    139650    139660    139670       

             290        280       270       260       250          
HUMBE- AA--AAA--ATATATATAT-ATATATATGTGTATATGTACACACATACATATACATATAT
       ::  :::  ::::::: :: ::::: ::   :::::::: : ::::::::::::::::::
BACR30 AATCAAATCATATATAAATGATATACATACATATATGTATATACATACATATACATATAT
    139680    139690    139700    139710    139720    139730       

    240       230            220       210       200       190     
HUMBE- ATGCATTCATTTGT-----TGTTGTTTTTCTTAATTTGCTCATGCATGCTAATAAATTAT
       :  :: : :::: :      :: ::: ::  :: : : :: :: ::              
BACR30 A--CAATAATTTCTGGACAGGTCGTTGTTTGTACTCTTCTAATTCAATCGATGCAAAGTG
      139740    139750    139760    139770    139780    139790     

         180       170       160       150       140       130     
HUMBE- GTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCATTAGTTACTTATTAGGTTT
                                                                   
BACR30 CAAAAGCGAAACAAGGACATGCTGGTTCTCAAAATTAATGGTCCGTAGGGTATTGAAAAG
      139800    139810    139820    139830    139840    139850     

>>BACR01O16 : AC093045, 189904 bases, from 2L:29.         (73982 nt)
 initn: 174 init1: 174 opt: 221  Z-score: 108.8  bits: 39.4 E(): 0.46
 71.134% identity (71.875% ungapped) in 97 nt overlap (197-293:5687-5782)

        170       180       190       200       210       220      
HUMBE- TTTATTCTATTTTTAGACATAATTTATTAGCATGCATGAGCAAATTAAGAAAAACAACAA
                                     ::  ::: ::::   : :::  ::::::::
BACR01 GGTATTGGGCGCAAATCTTTTTTCGAGTGCCAGACATTAGCAGCATTAGACCAACAACAA
       5660      5670      5680      5690      5700      5710      

        230       240       250       260       270       280      
HUMBE- CAAATGAATGCATATATATGTATATGTATGTGTGTACATATACACATATATATATATATA
       :: :: :   : : ::  ::::::: ::: : : :: ::::: : :::::::: ::::::
BACR01 CAGAT-ATCACTTCTACTTGTATATATATATATATATATATATATATATATATGTATATA
       5720       5730      5740      5750      5760      5770     

        290       300       310       320       330       340      
HUMBE- TATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAAC
       ::  :::                                                     
BACR01 TACATTTATATGGAGATATAAGAGCGAGGCATTGCACAACACCGAAAACCCACAGGCAAA
        5780      5790      5800      5810      5820      5830     

>>BACR14D22 : AC012164, 169384 bases, from X:17.          (73982 nt)
 initn: 196 init1: 196 opt: 221  Z-score: 108.8  bits: 39.4 E(): 0.46
 64.029% identity (65.441% ungapped) in 139 nt overlap (158-293:2977-3115)

       130       140       150       160       170        180      
HUMBE- CCTAATAAGTAACTAATGCACAGAGCACATTGATTTGTATTTAT-TCTATTTTTAGACAT
                                     :: : : :::: :: :: :: :: :    :
BACR14 CTGGCCTGCCTAACTTTATAATACAATTTATGGTCTATATTCATCTCGATCTTGATTACT
       2950      2960      2970      2980      2990      3000      

        190         200       210       220       230       240    
HUMBE- AATTTATTAGCAT--GCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATA
         ::: : :   :  :   ::: : ::  : : : : :   : : ::  ::  :::::::
BACR14 GCTTTTTGACTTTGAGGGGGAGTATATATATATATATATATATATATATATATATATATA
       3010      3020      3030      3040      3050      3060      

          250       260       270       280       290       300    
HUMBE- TGTATATGTATGTGTGTACATATACACATATATATATATATATATTTTTTCTTTTCTTAC
       : ::::: ::: :::::: ::::::: ::::: :::::::::: : : :           
BACR14 TATATATATATATGTGTATATATACATATATACATATATATATGTGTATGTGTAGCTTCG
       3070      3080      3090      3100      3110      3120      

          310       320       330       340       350       360    
HUMBE- CAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATC
                                                                   
BACR14 ATTTAACTATGGAAAATTGTTTCTTATGCGCAGAAAGATCATATACATTGTATACATTAA
       3130      3140      3150      3160      3170      3180      

>>BACR08A11 : 170075 bases, from 2R:42.                   (73982 nt)
 initn: 183 init1: 183 opt: 221  Z-score: 108.8  bits: 39.4 E(): 0.46
 74.390% identity (74.390% ungapped) in 82 nt overlap (238-319:63815-63896)

       210       220       230       240       250       260       
HUMBE- AAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTATGTGTGTACATAT
                                     :: :::::: :::: ::: : : :: ::::
BACR08 AACACCTTATGACGATATTTCCATACACATATGTATATGAATATATATATATATATATAT
        63790     63800     63810     63820     63830     63840    

       270       280       290       300       310       320       
HUMBE- ACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAG
       : : :::::::::::::::::::: ::      :: :::::   :::: :::        
BACR08 ATATATATATATATATATATATTTCTTGGCCGTTTTCCAGATTATTTTGATCGGGGATTT
        63850     63860     63870     63880     63890     63900    

       330       340       350       360       370       380       
HUMBE- GAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCCTGTAAGTATTTTG
                                                                   
BACR08 TCGATCCGCGCCCCACTTTCTGTTGCTCAGGTGTGTGTTGCTTTAATTGCACGCTGTAAT
        63910     63920     63930     63940     63950     63960    

>>BACR25O02 : AC018490, 165098 bases, from X:17.          (73982 nt)
rev-comp initn: 196 init1: 196 opt: 221  Z-score: 108.8  bits: 39.4 E(): 0.46
 64.029% identity (65.441% ungapped) in 139 nt overlap (293-158:33829-33967)

        320       310       300       290       280       270      
HUMBE- TTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATAT
                                     : : : :::::::::: ::::: :::::::
BACR25 CAATTTTCCATAGTTAAATCGAAGCTACACATACACATATATATATGTATATATGTATAT
    33800     33810     33820     33830     33840     33850        

        260       250       240       230       220       210      
HUMBE- GTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCT-
        :::::: ::: ::::: ::::::::  ::  :: : :   : : : : :  :: : :: 
BACR25 ATACACATATATATATATATATATATATATATATATATATATATATATATATATATACTC
    33860     33870     33880     33890     33900     33910        

          200       190       180        170       160       150   
HUMBE- -CATGCATGCTAATAAATTATGTCTAAAAATAGA-ATAAATACAAATCAATGTGCTCTGT
        :   ::   : : :::  :    : :: :: :: :: :::: : : ::           
BACR25 CCCCTCAAAGTCAAAAAGCAGTAATCAAGATCGAGATGAATATAGACCATAAATTGTATT
    33920     33930     33940     33950     33960     33970        

           140       130       120       110       100        90   
HUMBE- GCATTAGTTACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGAGACCTCTTAATG
                                                                   
BACR25 ATAAAGTTAGGCAGGCCAGCCAGTGGGCACACTTTTCACAATCCATTTGCGATCAACTAT
    33980     33990     34000     34010     34020     34030        

>>BACR02B16 : AC008331, 186938 bases, from 2L:29.         (44978 nt)
 initn: 174 init1: 174 opt: 221  Z-score: 112.3  bits: 39.4 E(): 0.48
 71.134% identity (71.875% ungapped) in 97 nt overlap (197-293:183604-183699)

        170       180       190       200       210       220      
HUMBE- TTTATTCTATTTTTAGACATAATTTATTAGCATGCATGAGCAAATTAAGAAAAACAACAA
                                     ::  ::: ::::   : :::  ::::::::
BACR02 GGTATTGGGCGCAAATCTTTTTTCGAGTGCCAGACATTAGCAGCATTAGACCAACAACAA
        183580    183590    183600    183610    183620    183630   

        230       240       250       260       270       280      
HUMBE- CAAATGAATGCATATATATGTATATGTATGTGTGTACATATACACATATATATATATATA
       :: :: :   : : ::  ::::::: ::: : : :: ::::: : :::::::: ::::::
BACR02 CAGAT-ATCACTTCTACTTGTATATATATATATATATATATATATATATATATGTATATA
         183640    183650    183660    183670    183680    183690  

        290       300       310       320       330       340      
HUMBE- TATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAAC
       ::  :::                                                     
BACR02 TACATTTATATGGAGATATAAGAGCGAGGCATTGCACAACACCGAAAACCCACAGGCAAA
         183700    183710    183720    183730    183740    183750  

>>BACR13P06 : AC008339, 180296 bases, from 2R:42.         (38336 nt)
 initn: 183 init1: 183 opt: 221  Z-score: 113.4  bits: 39.3 E(): 0.49
 74.390% identity (74.390% ungapped) in 82 nt overlap (238-319:177941-178022)

       210       220       230       240       250       260       
HUMBE- AAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTATGTGTGTACATAT
                                     :: :::::: :::: ::: : : :: ::::
BACR13 AACACCTTATGACGATATTTCCATACACATATGTATATGAATATATATATATATATATAT
           177920    177930    177940    177950    177960    177970

       270       280       290       300       310       320       
HUMBE- ACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAG
       : : :::::::::::::::::::: ::      :: :::::   :::: :::        
BACR13 ATATATATATATATATATATATTTCTTGGCCGTTTTCCAGATTATTTTGATCGGGGATTT
           177980    177990    178000    178010    178020    178030

       330       340       350       360       370       380       
HUMBE- GAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCCTGTAAGTATTTTG
                                                                   
BACR13 TCGATCCGCGCCCCACTTTCTGTTGCTCAGGTGTGTGTTGCTTTAATTGCACGCTGTAAT
           178040    178050    178060    178070    178080    178090

>>BACR11M14 : AC099308, 173101 bases, from X:19.          (73982 nt)
 initn: 166 init1: 166 opt: 219  Z-score: 107.6  bits: 39.2 E(): 0.54
 59.624% identity (62.871% ungapped) in 213 nt overlap (94-301:38069-38275)

            70        80        90       100       110       120   
HUMBE- TTATTTATTTGTATTTTTGACTGCATTAAGAGGTCTCTAGTTTTTTACCTCTTGTTTCCC
                                     :: :::: : : : :::  : :: :::   
BACR11 TCGTGATTAATAAACTCGGAAGTGAAAACTAGCTCTCGACTGTCTTAATTTTTTTTTTTT
    38040     38050     38060     38070     38080     38090        

           130       140       150       160       170       180   
HUMBE- AAAACCTAATAAGTAACTAATGCACAGAGCACATTGATTTGTATTTATTCTATTTTTAGA
          :   ::::: :  :   : : :   : : :::   :  ::  : ::: : :   :  
BACR11 GGGA---AATAATTTTCACGTACGCGTCGTAAATTTGGTGCTACGT-TTCGAGTGCCATC
    38100        38110     38120     38130     38140      38150    

           190        200           210       220       230        
HUMBE- CATAATTTATT-AGCATGCATG-AGCA---AATTAAGAAAAACAACAACAAATGAATGCA
       : :::   ::: : :::::: :  :::   :::  : : : :::   : : ::: :: ::
BACR11 CCTAACACATTCAACATGCACGCTGCATACAATACATATATACATAGATATATGCATACA
        38160     38170     38180     38190     38200     38210    

      240       250       260       270       280       290        
HUMBE- TATATATGTATATGTATGTGTGTACATATACACATATATATATATATATATTTTTTCTTT
       ::::::  ::::: ::: :   :::::::: :::::::::: ::: ::::: : : : : 
BACR11 TATATA--TATATATATATACATACATATATACATATATATTTATGTATATATGTACGTA
        38220       38230     38240     38250     38260     38270  

      300       310       320       330       340       350        
HUMBE- TCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTT
       : :                                                         
BACR11 TATGTAGGATATATAGAGCTCTCCTTCTGGAATTGGGACATGGGGTTTTTGGGTTTGAGT
          38280     38290     38300     38310     38320     38330  

>>BACR15O02 : AC009735, 159478 bases, from 3R:82.         (73982 nt)
rev-comp initn: 162 init1: 162 opt: 219  Z-score: 107.6  bits: 39.2 E(): 0.54
 67.480% identity (69.167% ungapped) in 123 nt overlap (326-207:43412-43534)

           350       340       330       320       310       300   
HUMBE- CTCTACCTCAGTTCTAAGCATATCTTCTCCTTATTTGGATTAAAACCTTCTGGTAAGAAA
                                     :: : ::::   :::: : :   :::   :
BACR15 CGTCAATTAATAAATAAATATGAAGCAAAGTTGTATGGAACTAAACATGCGTTTAACTTA
           43390     43400     43410     43420     43430     43440 

            290       280       270       260       250        240 
HUMBE- AGA-AAAAATATATATATATATATATGTGTATATGTACACACATACATATA-CATATATA
        :: :   :::::::::::::::::: : ::::: :: : : :::::::::  :::::::
BACR15 GGATATGTATATATATATATATATATATATATATATATATATATACATATATTATATATA
           43450     43460     43470     43480     43490     43500 

             230        220       210       200       190          
HUMBE- TGCATTCATTTGT-TGTTGTTTTTCTTAATTTGCTCATGCATGCTAATAAATTATGTCTA
       :  ::  ::   : : ::  : :  ::::::::                           
BACR15 TAAATATATAAATATATTTATATATTTAATTTGAATCGGTTCGTGGTGCGTTTCCGTGAG
           43510     43520     43530     43540     43550     43560 

    180       170       160       150       140       130          
HUMBE- AAAATAGAATAAATACAAATCAATGTGCTCTGTGCATTAGTTACTTATTAGGTTTTGGGA
                                                                   
BACR15 CTTAAATATTCAATTATTAAGTACAACATTTTTACCAAGAAACATTAACATTTAGATTTG
           43570     43580     43590     43600     43610     43620 

>>BACR21E16 : AC009905, 170662 bases, from 2L:36.         (73982 nt)
rev-comp initn: 219 init1: 196 opt: 218  Z-score: 106.9  bits: 39.1 E(): 0.58
 69.492% identity (73.214% ungapped) in 118 nt overlap (341-230:86996-87113)

      370       360       350       340       330       320        
HUMBE- CAGAATGGATGAAAACTCTACCTCAGTTCTAAGCATATCTTCTCCTTATTTGGAT-TAAA
                                     ::: ::: ::: :   ::: :  :: ::::
BACR21 ACTAGATCGACTCGGCTATTGATATTGATCAAGAATACCTTTTATATATATATATATAAA
       86970     86980     86990     87000     87010     87020     

       310           300       290       280       270       260   
HUMBE- ACCT---TCT-GGTAAGAAAAGAAAAAATATATATATATATATATGTGTATATGTACACA
       :  :   : :   ::   : : : :: :::::::::::::::::: : ::::: ::::  
BACR21 ATATATATATATATATATATATATAACATATATATATATATATATATATATATATACAAT
       87030     87040     87050     87060     87070     87080     

           250        240       230       220       210       200  
HUMBE- CATACATATACATATA-TATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTCATGCAT
        ::::::::::::::: :::: ::  ::                                
BACR21 TATACATATACATATATTATGTATATATACATATATATGTACTTTAAAAAATCGGAAACG
       87090     87100     87110     87120     87130     87140     

>>BACR48D17 : AC008255, 183316 bases, from X:13.          (73982 nt)
 initn: 177 init1: 177 opt: 218  Z-score: 106.9  bits: 39.1 E(): 0.58
 60.748% identity (69.149% ungapped) in 214 nt overlap (94-293:86512-86713)

            70        80        90       100         110           
HUMBE- TTATTTATTTGTATTTTTGACTGCATTAAGAGGTCTCTAGTTTTTT--ACCTCTT----G
                                     : ::::: : :::: :  :::: ::    :
BACR48 TAAATTAGAAATATCAGCAGAGCTTCGGGTAAGTCTCCACTTTTGTAGACCTTTTAGCGG
           86490     86500     86510     86520     86530     86540 

       120       130       140       150       160       170       
HUMBE- TTTCCCAAAACCTAATAAGTAACTAATGCACAGAGCACATTGATTTGTATTTAT-TCTAT
       : ::   :: : :  : ::     :::: :::    :::  : :::: :::: :    ::
BACR48 TGTCAGCAACCGTTTTCAG-----AATGTACA----ACAAGGTTTTGAATTTTTGGGCAT
           86550     86560              86570     86580     86590  

        180       190        200       210       220       230     
HUMBE- TTTTAGACATAATTTATTAGCA-TGCATGAGCAAATTAAGAAAAACAACAACAAATGA--
         ::: ::   : :::  :: : : :  :  ::    :: : :::   ::: : : ::  
BACR48 GATTAAAC---ACTTAAAAGGATTTCCCGCCCATCCAAAAATAAAACTCAAGATACGAAG
          86600        86610     86620     86630     86640         

               240       250       260       270       280         
HUMBE- ----ATGCATATATATGTATATGTATGTGTGTACATATACACATATATATATATATATAT
           :::::::::::: ::::: ::: : : :: ::::: :::::::::::: ::::: :
BACR48 CTTCATGCATATATATATATATATATTTATATATATATATACATATATATATGTATATTT
   86650     86660     86670     86680     86690     86700         

     290       300       310       320       330       340         
HUMBE- TTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGA
        : :                                                        
BACR48 CTATAGATGGGCGAATAGCACCAAAGACGAAGTTTTACGAAAAGCACCGAATTTACGTTG
   86710     86720     86730     86740     86750     86760         

>>BACR15O02 : AC009735, 159478 bases, from 3R:82.         (73982 nt)
 initn: 179 init1: 179 opt: 217  Z-score: 106.3  bits: 39.0 E(): 0.63
 64.800% identity (66.393% ungapped) in 125 nt overlap (168-289:126836-126960)

       140       150       160       170       180          190    
HUMBE- AACTAATGCACAGAGCACATTGATTTGTATTTATTCTATTTTTAGACATA---ATTTATT
                                     :::::  :: :: : :  ::   :: ::: 
BACR15 TGTATATCAGAAAGTTCACGAAACCACAGATTATTAAATATTAATATCTATCTATATATA
      126810    126820    126830    126840    126850    126860     

          200       210       220       230       240       250    
HUMBE- AGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTA
        : ::  ::    : ::  : : : :::   :   ::  ::: :::::: : ::::::::
BACR15 TGTATATATATATACATGTATATATACATATATGTATATATGTATATATGTATATATGTA
      126870    126880    126890    126900    126910    126920     

          260       270       280       290       300       310    
HUMBE- TGTGTGTACATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTT
       : : :::: ::::  : :::: :::::::::::::                         
BACR15 TATATGTATATATGTATATATGTATATATATATATACATATACATATATACATATGTATA
      126930    126940    126950    126960    126970    126980     

          320       330       340       350       360       370    
HUMBE- TAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCC
                                                                   
BACR15 TTTATATATATGTGTGAATATGTGTAACTTAATAGGAAAATGAATTTAATAGAGAAACAA
      126990    127000    127010    127020    127030    127040     

>>BACR30G03 : AC008355, 151500 bases, from 3R:82.         (73982 nt)
 initn: 179 init1: 179 opt: 217  Z-score: 106.3  bits: 39.0 E(): 0.63
 64.800% identity (66.393% ungapped) in 125 nt overlap (168-289:39251-39375)

       140       150       160       170       180          190    
HUMBE- AACTAATGCACAGAGCACATTGATTTGTATTTATTCTATTTTTAGACATA---ATTTATT
                                     :::::  :: :: : :  ::   :: ::: 
BACR30 TGTATATCAGAAAGTTCACGAAACCACAGATTATTAAATATTAATATCTATCTATATATA
            39230     39240     39250     39260     39270     39280

          200       210       220       230       240       250    
HUMBE- AGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTA
        : ::  ::    : ::  : : : :::   :   ::  ::: :::::: : ::::::::
BACR30 TGTATATATATATACATGTATATATACATATATGTATATATGTATATATGTATATATGTA
            39290     39300     39310     39320     39330     39340

          260       270       280       290       300       310    
HUMBE- TGTGTGTACATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTT
       : : :::: ::::  : :::: :::::::::::::                         
BACR30 TATATGTATATATGTATATATGTATATATATATATACATATACATATATACATATGTATA
            39350     39360     39370     39380     39390     39400

          320       330       340       350       360       370    
HUMBE- TAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCC
                                                                   
BACR30 TTTATATATATGTGTGAATATGTGTAACTTAATAGGAAAATGAATTTAATAGAGAAACAA
            39410     39420     39430     39440     39450     39460

>>BACR13P06 : AC008339, 180296 bases, from 2R:42.         (73982 nt)
rev-comp initn:  90 init1:  90 opt: 216  Z-score: 105.6  bits: 38.9 E(): 0.69
 63.030% identity (65.409% ungapped) in 165 nt overlap (333-170:71421-71580)

        360       350       340       330       320        310     
HUMBE- ATGAAAACTCTACCTCAGTTCTAAGCATATCTTCTCCTTATTTGGAT-TAAAACCTTCTG
                                     ::: :: :   : : :: :: :  ::::: 
BACR13 ATTTAAATATATCGTTTTTATTTTATTACACTTTTCATATATCGTATATATAGACTTCT-
            71400     71410     71420     71430     71440          

         300       290       280       270       260       250     
HUMBE- GTAAGAAAAGAAAAAATATATATATATATATATGTGTATATGTACACACATACATATACA
       :: :::         :::::::::::::::::: : ::::: :::: :: ::  ::::::
BACR13 GTTAGATTTATGTTTATATATATATATATATATATATATATTTACA-ACTTAATTATACA
   71450     71460     71470     71480     71490      71500        

         240       230       220       210       200       190     
HUMBE- TATATATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTCATGCATGCTAATAAATTAT
         :::    :::  : :::   : :  :::: ::::     ::  ::  ::: :::::: 
BACR13 ACTATGCAAATT-GTATGTGTATCTAGTTCTAAATTAATGTATTGAT--TAAGAAATTAG
    71510     71520      71530     71540     71550       71560     

         180       170       160       150       140       130     
HUMBE- GTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCATTAGTTACTTATTAGGTTT
          :::::::  :::                                             
BACR13 TATTAAAAATGTAATCTTTGCGCCCTTACTTTTAGATTAAACTTTTGACAATTGGCCTGA
       71570     71580     71590     71600     71610     71620     

>>BACR22H11 : AC013431, 191558 bases, from X:13.          (73982 nt)
rev-comp initn: 188 init1: 188 opt: 216  Z-score: 105.6  bits: 38.9 E(): 0.69
 65.185% identity (67.176% ungapped) in 135 nt overlap (293-160:117009-117140)

        320       310       300       290       280       270      
HUMBE- TTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATAT
                                     : : :::::::::::::::::: : :::::
BACR22 TAATTAGTAATAATACGATTACACACACACACACATATATATATATATATATATATATAT
   116980    116990    117000    117010    117020    117030        

        260       250       240       230       220        210     
HUMBE- GTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAAT-TTGCT
        :: : : ::: ::::: ::::::::  ::  :: : :   : :      :::: :  : 
BACR22 ATATATATATATATATATATATATATTAATATATATATATATTTACCAAATAATATAACA
   117040    117050    117060    117070    117080    117090        

         200       190       180       170       160       150     
HUMBE- CATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGC
        ::  :::::  :::: ::  : ::  : :: :  ::::::  ::               
BACR22 TATTTATGCT-CTAAAGTA--TATATGACTACAGCAAATACGCATTTTTTGATTTTTTGT
   117100     117110      117120    117130    117140    117150     

         140       130       120       110       100        90     
HUMBE- ATTAGTTACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGAGACCTCTTAATGCA
                                                                   
BACR22 TCGTAGATAAGATAAGTTAATGTGAAAAGAATAACATGATTGCATACTAAAAAGTTCCAC
      117160    117170    117180    117190    117200    117210     

>>BACR25C18 : AC092401, 185200 bases, from X:13.          (73982 nt)
rev-comp initn: 188 init1: 188 opt: 216  Z-score: 105.6  bits: 38.9 E(): 0.69
 65.185% identity (67.176% ungapped) in 135 nt overlap (293-160:138279-138410)

        320       310       300       290       280       270      
HUMBE- TTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATAT
                                     : : :::::::::::::::::: : :::::
BACR25 TAATTAGTAATAATACGATTACACACACACACACATATATATATATATATATATATATAT
   138250    138260    138270    138280    138290    138300        

        260       250       240       230       220        210     
HUMBE- GTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAAT-TTGCT
        :: : : ::: ::::: ::::::::  ::  :: : :   : :      :::: :  : 
BACR25 ATATATATATATATATATATATATATTAATATATATATATATTTACCAAATAATATAACA
   138310    138320    138330    138340    138350    138360        

         200       190       180       170       160       150     
HUMBE- CATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGC
        ::  :::::  :::: ::  : ::  : :: :  ::::::  ::               
BACR25 TATTTATGCT-CTAAAGTA--TATATGACTACAGCAAATACGCATTTTTTGATTTTTTGT
   138370     138380      138390    138400    138410    138420     

         140       130       120       110       100        90     
HUMBE- ATTAGTTACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGAGACCTCTTAATGCA
                                                                   
BACR25 TCGTAGATAAGATAAGTTAATGTGAAAAGAATAACATGATTGCATACTAAAAAGTTCCAC
      138430    138440    138450    138460    138470    138480     

>>BACR25O02 : AC018490, 165098 bases, from X:17.          (73982 nt)
 initn: 188 init1: 188 opt: 216  Z-score: 105.6  bits: 38.9 E(): 0.69
 62.585% identity (65.248% ungapped) in 147 nt overlap (153-293:33754-33900)

            130       140       150       160            170       
HUMBE- CAAAACCTAATAAGTAACTAATGCACAGAGCACATTGATTTGTA-----TTTATTCTATT
                                     ::: :: :: : ::     : :::  : ::
BACR25 CGGAGCTTAGATTTGGCGCAGCAGACGACACACTTTAATGTATACAATGTATATGATCTT
         33730     33740     33750     33760     33770     33780   

       180       190       200       210        220       230      
HUMBE- TTTAGACATAATTTATTAGCATGCATGAGCAAAT-TAAGAAAAACAACAACAAATGAATG
       : :   :::::   :  :   : :::    ::::  :::  : :::   ::: ::  :: 
BACR25 TCTGCGCATAAGAAACAATTTTCCATAGTTAAATCGAAGCTACACATACACATATATATA
         33790     33800     33810     33820     33830     33840   

        240       250       260       270       280       290      
HUMBE- CATATATATGTATATGTATGTGTGTACATATACACATATATATATATATATATTTTTTCT
         ::::::::::::: ::    : :: ::::: : :::::::::::::::::: : :   
BACR25 TGTATATATGTATATATACACATATATATATATATATATATATATATATATATATATATA
         33850     33860     33870     33880     33890     33900   

        300       310       320       330       340       350      
HUMBE- TTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAG
                                                                   
BACR25 TATATATATATACTCCCCCTCAAAGTCAAAAAGCAGTAATCAAGATCGAGATGAATATAG
         33910     33920     33930     33940     33950     33960   

>>BACR11C03 : AC008220, 186549 bases, from 3R:100.        (73982 nt)
 initn: 209 init1: 209 opt: 216  Z-score: 105.6  bits: 38.9 E(): 0.69
 68.571% identity (69.231% ungapped) in 105 nt overlap (188-291:32153-32257)

       160       170       180       190       200        210      
HUMBE- TGATTTGTATTTATTCTATTTTTAGACATAATTTATTAGCATGCATG-AGCAAATTAAGA
                                     :: :::  : :  :: : :::::: :    
BACR11 TGCGCGCTTAAGTGTTTAAAAATCGGAAAGATATATATGAACACAGGCAGCAAAGTGCAG
          32130     32140     32150     32160     32170     32180  

        220       230       240       250       260       270      
HUMBE- AAAACAACAACAAATGAATGCATATATATGTATATGTATGTGTGTACATATACACATATA
       :  :: : :  : ::  ::  :::::::: ::::: ::: : : :: ::::: : :::::
BACR11 ACCACGAAAGTATATATATATATATATATATATATATATATATATATATATATATATATA
          32190     32200     32210     32220     32230     32240  

        280       290       300       310       320       330      
HUMBE- TATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATA
       ::::::::::::: :                                             
BACR11 TATATATATATATATAAATATATATATATAGATAGGGGAGTAGGCGGTACAGAAGGTTAC
          32250     32260     32270     32280     32290     32300  

>>BACR06P08 : AC007975, 180630 bases, from 3R:100.        (38670 nt)
 initn: 209 init1: 209 opt: 216  Z-score: 110.2  bits: 38.8 E(): 0.74
 68.571% identity (69.231% ungapped) in 105 nt overlap (188-291:154200-154304)

       160       170       180       190       200        210      
HUMBE- TGATTTGTATTTATTCTATTTTTAGACATAATTTATTAGCATGCATG-AGCAAATTAAGA
                                     :: :::  : :  :: : :::::: :    
BACR06 TGCGCGCTTAAGTGTTTAAAAATCGGAAAGATATATATGAACACAGGCAGCAAAGTGCAG
  154170    154180    154190    154200    154210    154220         

        220       230       240       250       260       270      
HUMBE- AAAACAACAACAAATGAATGCATATATATGTATATGTATGTGTGTACATATACACATATA
       :  :: : :  : ::  ::  :::::::: ::::: ::: : : :: ::::: : :::::
BACR06 ACCACGAAAGTATATATATATATATATATATATATATATATATATATATATATATATATA
  154230    154240    154250    154260    154270    154280         

        280       290       300       310       320       330      
HUMBE- TATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATA
       ::::::::::::: :                                             
BACR06 TATATATATATATATAAATATATATATATAGATAGGGGAGTAGGCGGTACAGAAGGTTAC
  154290    154300    154310    154320    154330    154340         

>>BACR29F06 : AC008203, 174728 bases, from 3R:95.         (73982 nt)
rev-comp initn: 198 init1: 198 opt: 215  Z-score: 105.0  bits: 38.7 E(): 0.75
 68.807% identity (70.093% ungapped) in 109 nt overlap (299-192:13760-13867)

    330       320       310       300       290       280          
HUMBE- TCCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGT
                                     ::::  : : :::::::::::::::::: :
BACR29 AAACAAAAAAAAAGAAATAGTATAGAATGCAAAAATATATATATATATATATATATATAT
   13730     13740     13750     13760     13770     13780         

    270       260       250       240        230       220         
HUMBE- GTATATGTACACACATACATATACATATATATGC-ATTCATTTGTTGTTGTTTTTCTTAA
        ::::: :: : : ::: :: ::::::::::::: ::  :  : :   : : :: : : :
BACR29 ATATATATATATATATATATGTACATATATATGCTATATAGATTTCTATATATTCCATTA
   13790     13800     13810     13820     13830     13840         

     210       200       190       180       170       160         
HUMBE- TTTGCTCATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCT
        ::: :::  :    ::::                                         
BACR29 -TTGATCAGTCTGTGTAATCTCTCTCGCTAAAGAAACGCCTGATGCTGGATGCTAGAGGC
    13850     13860     13870     13880     13890     13900        

>>BACR48E23 : AC005721, 203183 bases, from 3R:88.         (73982 nt)
rev-comp initn: 189 init1: 189 opt: 215  Z-score: 105.0  bits: 38.7 E(): 0.75
 64.085% identity (67.407% ungapped) in 142 nt overlap (325-187:64593-64730)

          350       340       330       320       310        300   
HUMBE- TCTACCTCAGTTCTAAGCATATCTTCTCCTTATTTGGATTAAAACCTTCTGGTA-AGAAA
                                     ::::::  ::::    :::   :: : : :
BACR48 TTCGAAAATTTGCTTTAATTCATATATTTATATTTGCTTTAA----TTCATATATATATA
          64570     64580     64590     64600         64610        

           290       280       270       260       250       240   
HUMBE- AGAAAAAATATATATATATATATATGTGTATATGTACACACATACATATACATATATATG
          : : :::::::::::::::::: : ::::: :  : : ::: ::::: :::  ::: 
BACR48 TATATATATATATATATATATATATATATATATATGTATATATATATATATATAATTATC
    64620     64630     64640     64650     64660     64670        

           230       220         210       200       190       180 
HUMBE- CATTCATTTGTTGTTGTTTTTC--TTAATTTGCTCATGCATGCTAATAAATTATGTCTAA
        :     : ::: : :::::::  ::  :::    ::   ::::::::  ::        
BACR48 AAAGTTATAGTTTTAGTTTTTCAGTTTTTTTCAATATAGTTGCTAATAGTTTTGCCGATA
    64680     64690     64700     64710     64720     64730        

             170       160       150       140       130       120 
HUMBE- AAATAGAATAAATACAAATCAATGTGCTCTGTGCATTAGTTACTTATTAGGTTTTGGGAA
                                                                   
BACR48 GTGCTACCTGTAGTTTCCACTTGCCATCTCTAAAAACGTGATAAACACGCTTGTTTTGTT
    64740     64750     64760     64770     64780     64790        

>>BACR22N03 : AC092397, 167201 bases, from 2L:26.         (73982 nt)
rev-comp initn: 206 init1: 206 opt: 215  Z-score: 105.0  bits: 38.7 E(): 0.75
 74.684% identity (74.684% ungapped) in 79 nt overlap (311-233:100674-100752)

      340       330       320       310       300       290        
HUMBE- AAGCATATCTTCTCCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATAT
                                     ::  ::::::  : : ::: : ::::::::
BACR22 CGCGTCTTGCCGCACTCAAAACTGCCACTGCCAGCTGGTAGCACATGAATATATATATAT
        100650    100660    100670    100680    100690    100700   

      280       270       260       250       240       230        
HUMBE- ATATATATATGTGTATATGTACACACATACATATACATATATATGCATTCATTTGTTGTT
       :::::::::: : ::::: :: : : ::: :::::   ::::::  :::           
BACR22 ATATATATATATATATATATATATATATATATATAGGGATATATATATTTTCCTGATATC
        100710    100720    100730    100740    100750    100760   

      220       210       200       190       180       170        
HUMBE- GTTTTTCTTAATTTGCTCATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAA
                                                                   
BACR22 TAGCCACAGCGCGACATGAAAATTCAGCTACGGTCTCGTTCGACGATCGTCTCCCAGCGA
        100770    100780    100790    100800    100810    100820   

>>BACR08H11 : AC008136, 154890 bases, from 3R:88.         (73982 nt)
rev-comp initn: 189 init1: 189 opt: 215  Z-score: 105.0  bits: 38.7 E(): 0.75
 64.085% identity (67.407% ungapped) in 142 nt overlap (325-187:86974-87111)

          350       340       330       320       310        300   
HUMBE- TCTACCTCAGTTCTAAGCATATCTTCTCCTTATTTGGATTAAAACCTTCTGGTA-AGAAA
                                     ::::::  ::::    :::   :: : : :
BACR08 TTCGAAAATTTGCTTTAATTCATATATTTATATTTGCTTTAA----TTCATATATATATA
         86950     86960     86970     86980         86990         

           290       280       270       260       250       240   
HUMBE- AGAAAAAATATATATATATATATATGTGTATATGTACACACATACATATACATATATATG
          : : :::::::::::::::::: : ::::: :  : : ::: ::::: :::  ::: 
BACR08 TATATATATATATATATATATATATATATATATATGTATATATATATATATATAATTATC
   87000     87010     87020     87030     87040     87050         

           230       220         210       200       190       180 
HUMBE- CATTCATTTGTTGTTGTTTTTC--TTAATTTGCTCATGCATGCTAATAAATTATGTCTAA
        :     : ::: : :::::::  ::  :::    ::   ::::::::  ::        
BACR08 AAAGTTATAGTTTTAGTTTTTCAGTTTTTTTCAATATAGTTGCTAATAGTTTTGCCGATA
   87060     87070     87080     87090     87100     87110         

             170       160       150       140       130       120 
HUMBE- AAATAGAATAAATACAAATCAATGTGCTCTGTGCATTAGTTACTTATTAGGTTTTGGGAA
                                                                   
BACR08 GTGCTACCTGTAGTTTCCACTTGCCATCTCTAAAAACGTGATAAACACGCTTGTTTTGTT
   87120     87130     87140     87150     87160     87170         

>>BACR15J11 : AC008202, 186159 bases, from 3R:95.         (44199 nt)
rev-comp initn: 198 init1: 198 opt: 215  Z-score: 108.6  bits: 38.7 E(): 0.79
 68.807% identity (70.093% ungapped) in 109 nt overlap (299-192:182666-182773)

    330       320       310       300       290       280          
HUMBE- TCCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGT
                                     ::::  : : :::::::::::::::::: :
BACR15 AAACAAAAAAAAAGAAATAGTATAGAATGCAAAAATATATATATATATATATATATATAT
      182640    182650    182660    182670    182680    182690     

    270       260       250       240        230       220         
HUMBE- GTATATGTACACACATACATATACATATATATGC-ATTCATTTGTTGTTGTTTTTCTTAA
        ::::: :: : : ::: :: ::::::::::::: ::  :  : :   : : :: : : :
BACR15 ATATATATATATATATATATGTACATATATATGCTATATAGATTTCTATATATTCCATTA
      182700    182710    182720    182730    182740    182750     

     210       200       190       180       170       160         
HUMBE- TTTGCTCATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCT
        ::: :::  :    ::::                                         
BACR15 -TTGATCAGTCTGTGTAATCTCTCTCGCTAAAGAAACGCCTGATGCTGGATGCTAGAGGC
       182760    182770    182780    182790    182800    182810    

>>BACR14N05 : AC099033, 170299 bases, from 2R:55.         (73982 nt)
 initn: 265 init1: 193 opt: 214  Z-score: 104.3  bits: 38.6 E(): 0.81
 79.412% identity (79.412% ungapped) in 68 nt overlap (234-301:116424-116491)

           210       220       230       240       250       260   
HUMBE- GAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTATGTGTGTAC
                                     :: ::::::: : ::::::::: : : :: 
BACR14 AGGTAAAGGGGGTACAGAACTTATATGCACATCCATATATTTATATATGTATATATATAT
        116400    116410    116420    116430    116440    116450   

           270       280       290       300       310       320   
HUMBE- ATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAA
       ::::: : :::::::::::::::::: : :  :::: :                      
BACR14 ATATATATATATATATATATATATATATGTGTTTTTGTGGAAGGACTAAGGCGCGGTTCA
        116460    116470    116480    116490    116500    116510   

           330       340       350       360       370       380   
HUMBE- TAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCCTGTAAGTAT
                                                                   
BACR14 CCGATTGCGATGAACTATGGCATGGAAAGCTGCTCCTCTTTCTCTATTCATAAAACCATT
        116520    116530    116540    116550    116560    116570   

>>BACR48A20 : AC011072, 166158 bases, from 2R:55.         (73982 nt)
 initn: 265 init1: 193 opt: 214  Z-score: 104.3  bits: 38.6 E(): 0.81
 79.412% identity (79.412% ungapped) in 68 nt overlap (234-301:26695-26762)

           210       220       230       240       250       260   
HUMBE- GAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTATGTGTGTAC
                                     :: ::::::: : ::::::::: : : :: 
BACR48 AGGTAAAGGGGGTACAGAACTTATATGCACATCCATATATTTATATATGTATATATATAT
        26670     26680     26690     26700     26710     26720    

           270       280       290       300       310       320   
HUMBE- ATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAA
       ::::: : :::::::::::::::::: : :  :::: :                      
BACR48 ATATATATATATATATATATATATATATGTGTTTTTGTGGAAGGACTAAGGCGCGGTTCA
        26730     26740     26750     26760     26770     26780    

           330       340       350       360       370       380   
HUMBE- TAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCCTGTAAGTAT
                                                                   
BACR48 CCGATTGCGATGAACTATGGCATGGAAAGCTGCTCCTCTTTCTCTATTCATAAAACCATT
        26790     26800     26810     26820     26830     26840    

>>BACR19D23 : AC095014, 170801 bases, from 3R:84.         (73982 nt)
rev-comp initn: 131 init1: 131 opt: 214  Z-score: 104.3  bits: 38.6 E(): 0.81
 64.773% identity (69.091% ungapped) in 176 nt overlap (324-154:100627-100796)

         350       340       330       320       310       300     
HUMBE- CTACCTCAGTTCTAAGCATATCTTCTCCTTATTTGGATTAAAACCTTCTGGTAAGAAAAG
                                     :: : :: :::::  :  : :: : ::  :
BACR19 GGCATCCTCTGACCTTAAAATACTATAAAGATATTGA-TAAAATATAAT-GTTATAAGCG
     100600    100610    100620    100630     100640     100650    

         290       280       270       260       250       240     
HUMBE- AAAAAATATATATATATATATATGTGTATATGTACACACATACATATACATATATATGCA
       ::: :: :::::: :::: :::: : ::::: :: : : ::::::::: ::::::    :
BACR19 AAATAAAATATAT-TATA-ATATATATATATATATATATATACATATATATATATTCTAA
       100660     100670     100680    100690    100700    100710  

         230         220       210       200         190           
HUMBE- TTCATTTGT--TGTTGTTTTTCTTAATTTGCTCATGCATGCTAATAA--ATTAT-GTCTA
       :  : :: :  : :: :: :  :  :: :  : ::  ::  : ::::  :: ::  : ::
BACR19 TATAATTATAATATTATTATAATATATATAATAAT-TATTATTATAATTATAATAATATA
         100720    100730    100740     100750    100760    100770 

    180       170       160       150       140       130          
HUMBE- AAAATAGAATAAATACAAATCAATGTGCTCTGTGCATTAGTTACTTATTAGGTTTTGGGA
       : :::: ::::: :: ::: :  :::                                  
BACR19 ATAATA-AATAATTAGAAAACCTTGTTAGAAAGAAACCATTTATTAAAAATGTTGTCGAA
           100780    100790    100800    100810    100820    100830

>>BACR19J06 : AC010581, 175053 bases, from 3R:85.         (73982 nt)
 initn: 188 init1: 188 opt: 214  Z-score: 104.3  bits: 38.6 E(): 0.81
 72.093% identity (72.093% ungapped) in 86 nt overlap (208-293:63609-63694)

       180       190       200       210       220       230       
HUMBE- TTTAGACATAATTTATTAGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGC
                                     :::: :  :: :: :   : : :  :::  
BACR19 TCGTGCTTATGAAAATAGTCGAATCTATATAAATAATTAATAATATATATATAAAAATAT
    63580     63590     63600     63610     63620     63630        

       240       250       260       270       280       290       
HUMBE- ATATATATGTATATGTATGTGTGTACATATACACATATATATATATATATATTTTTTCTT
       :::::::: ::::: ::: : : :: ::::: : :::::::::::::::: ::: :    
BACR19 ATATATATATATATATATATATATATATATATATATATATATATATATATGTTTATAAAC
    63640     63650     63660     63670     63680     63690        

       300       310       320       330       340       350       
HUMBE- TTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGT
                                                                   
BACR19 TTCCTCAACATGTAATTCTTGGAATACTTTATCAGTTAGCGGATTCATTTTTTGATAAGT
    63700     63710     63720     63730     63740     63750        

>>BACR11B14 : 174999 bases, from 2R:41.                   (73982 nt)
rev-comp initn: 103 init1: 103 opt: 213  Z-score: 103.7  bits: 38.5 E(): 0.88
 62.500% identity (65.217% ungapped) in 168 nt overlap (303-141:116881-117046)

        330       320       310       300       290         280    
HUMBE- CTTCTCCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATAT--ATATATATAT
                                     :: : : : : :: ::::  ::::::  ::
BACR11 GGCGGACGAGTTGACTCAGCTGTTGATACTTATGTATATATAATATATTAATATATTAAT
           116860    116870    116880    116890    116900    116910

          270       260       250       240       230       220    
HUMBE- ATATGTGTATATGTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTT
       : :::: ::::: :  : ::::: :::::  :::: ::  ::   : : :: :: : : :
BACR11 ACATGTATATATATTAATACATATATATATCTATACATAAAT--GTATATTTTTATATAT
           116920    116930    116940    116950      116960        

          210       200       190         180        170       160 
HUMBE- CTTAATTTGCTCATGCATGCTAATAAAT-TATGTCTA-AAAATAGA-ATAAATACAAATC
        : ::: :    :  ::   ::::: :: ::: : :: :: ::: : ::  ::: : :: 
BACR11 TTAAATGTATATAAACAAATTAATATATATATTTATATAATATATATATGCATATATATA
   116970    116980    116990    117000    117010    117020        

             150       140       130       120       110       100 
HUMBE- AATGTGCTCTGTGCATTAGTTACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGA
       :   ::   ::: :::::                                          
BACR11 ATACTGAAATGTACATTAAATCTCAATCCCTAAGTTGCTCCCTCTGCAAGGCTAAACAAA
   117030    117040    117050    117060    117070    117080        

>>BACR06P07 : 187793 bases, from 2R:41.                   (45833 nt)
 initn: 103 init1: 103 opt: 213  Z-score: 107.0  bits: 38.4 E(): 0.93
 62.500% identity (65.217% ungapped) in 168 nt overlap (141-303:178570-178735)

              120       130       140       150       160       170
HUMBE- CCTCTTGTTTCCCAAAACCTAATAAGTAACTAATGCACAGAGCACATTGATTTGTATTTA
                                     ::::: :::   ::   : :: : :::  :
BACR06 TGCAGAGGGAGCAACTTAGGGATTGAGATTTAATGTACATTTCAGTATTATATATATGCA
  178540    178550    178560    178570    178580    178590         

                180        190       200         210       220     
HUMBE- T-TCTAT-TTTTAGACATA-ATTTATTAGCATG--CATGAGCAAATTAAGAAAAACAACA
       : : ::: :: :: : ::: :: :::::   ::   ::   ::  : :: : : : ::  
BACR06 TATATATATTATATAAATATATATATTAATTTGTTTATATACATTTAAATATATAAAAAT
  178600    178610    178620    178630    178640    178650         

         230       240       250       260       270       280     
HUMBE- ACAAATGAATGCATATATATGTATATGTATGTGTGTACATATACACATATATATATATAT
       : : ::  ::: ::: :::: ::::::::  :   :: :::::::  :::  ::::::  
BACR06 ATACATTTATGTATAGATATATATATGTA--TTAATATATATACATGTATTAATATATTA
  178660    178670    178680      178690    178700    178710       

         290       300       310       320       330       340     
HUMBE- ATATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAA
       :::: :: : : : : ::                                          
BACR06 ATATATTATATATACATAAGTATCAACAGCTGAGTCAACTCGTCCGCCTGTTTTTACCTA
    178720    178730    178740    178750    178760    178770       

>>BACR19J06 : AC010581, 175053 bases, from 3R:85.         (73982 nt)
rev-comp initn: 208 init1: 208 opt: 212  Z-score: 103.1  bits: 38.4 E(): 0.96
 81.250% identity (81.250% ungapped) in 64 nt overlap (293-230:63631-63694)

        320       310       300       290       280       270      
HUMBE- TTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATAT
                                     :::::::::::::::::::::: : :::::
BACR19 ATCTATATAAATAATTAATAATATATATATAAAAATATATATATATATATATATATATAT
            63610     63620     63630     63640     63650     63660

        260       250       240       230       220       210      
HUMBE- GTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTC
        :: : : ::: ::::: ::::::::   :: ::                          
BACR19 ATATATATATATATATATATATATATATGTTTATAAACTTCCTCAACATGTAATTCTTGG
            63670     63680     63690     63700     63710     63720

        200       190       180       170       160       150      
HUMBE- ATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCA
                                                                   
BACR19 AATACTTTATCAGTTAGCGGATTCATTTTTTGATAAGTGCACTTAGGACCCGAAACTGGG
            63730     63740     63750     63760     63770     63780

>>BACR25C18 : AC092401, 185200 bases, from X:13.          (73982 nt)
 initn: 198 init1: 198 opt: 210  Z-score: 101.8  bits: 38.1 E():  1.1
 70.968% identity (74.157% ungapped) in 93 nt overlap (202-290:138243-138335)

             180       190       200       210       220           
HUMBE- TCTATTTTTAGACATAATTTATTAGCATGCATGAGCAAATTAAGAAAAACAACA----AC
                                     :: : : :::::  :: :: :  :    ::
BACR25 GTATTCTGAATGTAAAACAGCCTAATTAAAATTATCTAATTAGTAATAATACGATTACAC
         138220    138230    138240    138250    138260    138270  

       230       240       250       260       270       280       
HUMBE- AAATGAATGCATATATATGTATATGTATGTGTGTACATATACACATATATATATATATAT
       : :   :  ::::::::: ::::: ::: : : :: ::::: : ::::::::::::::::
BACR25 ACACACACACATATATATATATATATATATATATATATATATATATATATATATATATAT
         138280    138290    138300    138310    138320    138330  

       290       300       310       320       330       340       
HUMBE- ATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACT
       :::                                                         
BACR25 ATTAATATATATATATATTTACCAAATAATATAACATATTTATGCTCTAAAGTATATATG
         138340    138350    138360    138370    138380    138390  

>>BACR22N03 : AC092397, 167201 bases, from 2L:26.         (73982 nt)
 initn: 183 init1: 183 opt: 210  Z-score: 101.8  bits: 38.1 E():  1.1
 77.333% identity (79.452% ungapped) in 75 nt overlap (225-297:100683-100757)

          200       210       220       230       240       250    
HUMBE- AGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTA
                                     : :: ::::::  :::::::: ::::: ::
BACR22 CCGCACTCAAAACTGCCACTGCCAGCTGGTAGCACATGAATATATATATATATATATATA
         100660    100670    100680    100690    100700    100710  

          260       270       280         290       300       310  
HUMBE- TGTGTGTACATATACACATATATATA--TATATATATTTTTTCTTTTCTTACCAGAAGGT
       : : : :: ::::: : :::::::::   :::::::: ::::: :               
BACR22 TATATATATATATATATATATATATAGGGATATATATATTTTCCTGATATCTAGCCACAG
         100720    100730    100740    100750    100760    100770  

            320       330       340       350       360       370  
HUMBE- TTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGT
                                                                   
BACR22 CGCGACATGAAAATTCAGCTACGGTCTCGTTCGACGATCGTCTCCCAGCGAACTGAAATC
         100780    100790    100800    100810    100820    100830  

>>BACR03L12 : AC008357, 190672 bases, from 3R:86.         (73982 nt)
rev-comp initn: 147 init1: 147 opt: 210  Z-score: 101.8  bits: 38.1 E():  1.1
 65.217% identity (67.669% ungapped) in 138 nt overlap (302-165:5957-6089)

       330       320       310       300       290       280       
HUMBE- TTCTCCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATA
                                     :: :::   : :::::::::::::::::::
BACR03 ATATGTGTGCCAGCCCAACCAGCACACATAAATAAATATATAAATATATATATATATATA
       5930      5940      5950      5960      5970      5980      

       270       260       250       240       230       220       
HUMBE- TGTGTATATGTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTT
       : : ::::::::::   :::  :: : :::::: : :::  :: : : : :  : :: : 
BACR03 TATATATATGTACATGTATAGGTA-AAATATATGTACAT--ATGTATGGGTTATATTGTG
       5990      6000      6010       6020        6030      6040   

       210       200       190       180       170       160       
HUMBE- AATTTGCTCATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTG
         ::: :    ::  ::  : ::: :::   : ::::::   :::: :            
BACR03 GCTTTCCCGGCGC-GGCATAAAAAGTATAAAT-AAAATAATTTAAAAAGGGCCAACGATT
          6050       6060      6070       6080      6090      6100 

       150       140       130       120       110       100       
HUMBE- CTCTGTGCATTAGTTACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGAGACCTC
                                                                   
BACR03 CGAAGGGGGTTAAAACTTTTCCCGAGCCCTGCTCCTCCACTTACCCTTTCTCACGATTTT
            6110      6120      6130      6140      6150      6160 

>>BACR10E07 : AC012675, 176818 bases, from 2L:27.         (73982 nt)
 initn: 202 init1: 202 opt: 210  Z-score: 101.8  bits: 38.1 E():  1.1
 65.000% identity (65.546% ungapped) in 120 nt overlap (169-288:46142-46260)

      140       150       160       170       180       190        
HUMBE- ACTAATGCACAGAGCACATTGATTTGTATTTATTCTATTTTTAGACATAATTTATTAGCA
                                     :::::  :::  ::    ::::::  : : 
BACR10 CGATGAACTTCAGTCAATGCAAATGGAACCTATTC-GTTTCAAGGTGGAATTTAAAAACT
           46120     46130     46140      46150     46160     46170

      200       210       220       230       240       250        
HUMBE- TGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTATGTG
           : : :::  :  :::::::::::   :  ::::    :::: : ::: :::: :::
BACR10 AAGGTAAACAAGATGGGAAAAACAACACAGATCGAATAATCATATTTATATCTGTAGGTG
            46180     46190     46200     46210     46220     46230

      260       270       280       290       300       310        
HUMBE- TGTACATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTTAAT
       ::::::::::    ::: :::::::: : :                              
BACR10 TGTACATATATGTGTATGTATATATAAACAAGCCCTGATGAAAACGTATTGACGATGCAA
            46240     46250     46260     46270     46280     46290

>>BACR22H11 : AC013431, 191558 bases, from X:13.          (73982 nt)
 initn: 198 init1: 198 opt: 210  Z-score: 101.8  bits: 38.1 E():  1.1
 70.968% identity (74.157% ungapped) in 93 nt overlap (202-290:116973-117065)

             180       190       200       210       220           
HUMBE- TCTATTTTTAGACATAATTTATTAGCATGCATGAGCAAATTAAGAAAAACAACA----AC
                                     :: : : :::::  :: :: :  :    ::
BACR22 GTATTCTGAATGTAAAACAGCCTAATTAAAATTATCTAATTAGTAATAATACGATTACAC
         116950    116960    116970    116980    116990    117000  

       230       240       250       260       270       280       
HUMBE- AAATGAATGCATATATATGTATATGTATGTGTGTACATATACACATATATATATATATAT
       : :   :  ::::::::: ::::: ::: : : :: ::::: : ::::::::::::::::
BACR22 ACACACACACATATATATATATATATATATATATATATATATATATATATATATATATAT
         117010    117020    117030    117040    117050    117060  

       290       300       310       320       330       340       
HUMBE- ATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACT
       :::                                                         
BACR22 ATTAATATATATATATATTTACCAAATAATATAACATATTTATGCTCTAAAGTATATATG
         117070    117080    117090    117100    117110    117120  

>>BACR19I14 : AC095013, 175648 bases, from 3R:83.         (73982 nt)
 initn: 251 init1: 188 opt: 210  Z-score: 101.8  bits: 38.1 E():  1.1
 71.930% identity (79.612% ungapped) in 114 nt overlap (187-293:87497-87606)

        160       170       180       190       200       210      
HUMBE- TTGATTTGTATTTATTCTATTTTTAGACATAATTTATTAGCATGCATGAGCAAATTAAGA
                                     :: ::::  ::::   ::::    ::  : 
BACR19 CAAGTCCCCCATGAAAATGGAGAAAAAATGAAATTATGCGCAT---TGAG-TTGTTCGGC
      87470     87480     87490     87500        87510      87520  

        220       230            240         250       260         
HUMBE- AAAACAACAACAAA--TGAA---TGCATATATAT-GT-ATATGTATGTGTGTACATATAC
       ::: : : ::::::  ::::    : :::::::: :: :::::::::: : :: ::::: 
BACR19 AAACCCAAAACAAAGGTGAAGCCAGGATATATATAGTCATATGTATGTATATATATATAT
          87530     87540     87550     87560     87570     87580  

     270       280       290       300       310       320         
HUMBE- ACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGA
       : :::::::::::::::::: : :                                    
BACR19 ATATATATATATATATATATATATAGAGCTGCTTGTTTGGGTCCTACCAGATTTTTTTAT
          87590     87600     87610     87620     87630     87640  

>>BACR11C03 : AC008220, 186549 bases, from 3R:100.        (73982 nt)
rev-comp initn: 188 init1: 188 opt: 210  Z-score: 101.8  bits: 38.1 E():  1.1
 78.261% identity (78.261% ungapped) in 69 nt overlap (298-230:32189-32257)

             320       310       300       290       280       270 
HUMBE- CCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTG
                                     :::: : : :::::::::::::::::: : 
BACR11 ATGAACACAGGCAGCAAAGTGCAGACCACGAAAGTATATATATATATATATATATATATA
    32160     32170     32180     32190     32200     32210        

             260       250       240       230       220       210 
HUMBE- TATATGTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATT
       ::::: :: : : ::: ::::: ::::::::  ::  ::                     
BACR11 TATATATATATATATATATATATATATATATATATATATAAATATATATATATAGATAGG
    32220     32230     32240     32250     32260     32270        

             200       190       180       170       160       150 
HUMBE- TGCTCATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCT
                                                                   
BACR11 GGAGTAGGCGGTACAGAAGGTTACATAATATAACATAGGAGGGCCTTATAAGTCAGAGCG
    32280     32290     32300     32310     32320     32330        

>>BACR23O04 : AC008316, 160817 bases, from 3R:85.         (73982 nt)
rev-comp initn: 188 init1: 188 opt: 210  Z-score: 101.8  bits: 38.1 E():  1.1
 70.968% identity (71.739% ungapped) in 93 nt overlap (291-200:36477-36569)

      320       310       300       290       280       270        
HUMBE- TGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATATGT
                                     : :::::::::::::::::: : ::::: :
BACR23 AGTAGTTAGTATGTTGGTTCGCATATATGTATATATATATATATATATATATATATATAT
      36450     36460     36470     36480     36490     36500      

      260       250       240        230       220       210       
HUMBE- ACACACATACATATACATATATATGCATTCAT-TTGTTGTTGTTTTTCTTAATTTGCTCA
       : : : ::: ::::: ::::::::  ::  :: : ::: : :    :  :: :: : :::
BACR23 ATATATATATATATATATATATATATATATATATAGTTTTAGAAAGTAGTAGTTAGTTCA
      36510     36520     36530     36540     36550     36560      

       200       190       180       170       160       150       
HUMBE- TGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCAT
       : :                                                         
BACR23 TCCGGCTCGGCGGCTTAAAGTTCTTGTAAGTAGATGGGTTTGTTACGCTTGCGTTTGCCA
      36570     36580     36590     36600     36610     36620      

>>BACR28B01 : AC008139, 170675 bases, from 3R:85.         (73982 nt)
rev-comp initn: 219 init1: 147 opt: 210  Z-score: 101.8  bits: 38.1 E():  1.1
 65.217% identity (67.669% ungapped) in 138 nt overlap (302-165:142757-142889)

       330       320       310       300       290       280       
HUMBE- TTCTCCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATA
                                     :: :::   : :::::::::::::::::::
BACR28 ATATGTGTGCCAGCCCAACCAGCACACATAAATAAATATATAAATATATATATATATATA
     142730    142740    142750    142760    142770    142780      

       270       260       250       240       230       220       
HUMBE- TGTGTATATGTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTT
       : : ::::::::::   :::  :: : :::::: : :::  :: : : : :  : :: : 
BACR28 TATATATATGTACATGTATAGGTA-AAATATATGTACAT--ATGTATGGGTTATATTGTG
     142790    142800    142810     142820      142830    142840   

       210       200       190       180       170       160       
HUMBE- AATTTGCTCATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTG
         ::: :    ::  ::  : ::: :::   : ::::::   :::: :            
BACR28 GCTTTCCCGGCGC-GGCATAAAAAGTATAAAT-AAAATAATTTAAAAAGGGCCAACGATT
        142850     142860    142870     142880    142890    142900 

       150       140       130       120       110       100       
HUMBE- CTCTGTGCATTAGTTACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGAGACCTC
                                                                   
BACR28 CGAAGGGGGTTAAAACTTTTCCCGAGCCCTGCTCCTCCACTTACCCTTTCTCACGATTTT
          142910    142920    142930    142940    142950    142960 

>>BACR30F01 : AC008315, 177028 bases, from 3R:85.         (73982 nt)
rev-comp initn: 188 init1: 188 opt: 210  Z-score: 101.8  bits: 38.1 E():  1.1
 70.968% identity (71.739% ungapped) in 93 nt overlap (291-200:143630-143722)

      320       310       300       290       280       270        
HUMBE- TGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATATGT
                                     : :::::::::::::::::: : ::::: :
BACR30 AGTAGTTAGTATGTTGGTTCGCATATATGTATATATATATATATATATATATATATATAT
  143600    143610    143620    143630    143640    143650         

      260       250       240        230       220       210       
HUMBE- ACACACATACATATACATATATATGCATTCAT-TTGTTGTTGTTTTTCTTAATTTGCTCA
       : : : ::: ::::: ::::::::  ::  :: : ::: : :    :  :: :: : :::
BACR30 ATATATATATATATATATATATATATATATATATAGTTTTAGAAAGTAGTAGTTAGTTCA
  143660    143670    143680    143690    143700    143710         

       200       190       180       170       160       150       
HUMBE- TGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCAT
       : :                                                         
BACR30 TCCGGCTCGGCGGCTTAAAGTTCTTGTAAGTAGATGGGTTTGTTACGCTTGCGTTTGCCA
  143720    143730    143740    143750    143760    143770         

>>BACR06P08 : AC007975, 180630 bases, from 3R:100.        (38670 nt)
rev-comp initn: 188 init1: 188 opt: 210  Z-score: 106.3  bits: 38.0 E():  1.2
 78.261% identity (78.261% ungapped) in 69 nt overlap (298-230:154236-154304)

             320       310       300       290       280       270 
HUMBE- CCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTG
                                     :::: : : :::::::::::::::::: : 
BACR06 ATGAACACAGGCAGCAAAGTGCAGACCACGAAAGTATATATATATATATATATATATATA
      154210    154220    154230    154240    154250    154260     

             260       250       240       230       220       210 
HUMBE- TATATGTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATT
       ::::: :: : : ::: ::::: ::::::::  ::  ::                     
BACR06 TATATATATATATATATATATATATATATATATATATATAAATATATATATATAGATAGG
      154270    154280    154290    154300    154310    154320     

             200       190       180       170       160       150 
HUMBE- TGCTCATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCT
                                                                   
BACR06 GGAGTAGGCGGTACAGAAGGTTACATAATATAACATAGGAGGGCCTTATAAGTCAGAGCG
      154330    154340    154350    154360    154370    154380     

>>BACR30F01 : AC008315, 177028 bases, from 3R:85.         (35068 nt)
rev-comp initn: 188 init1: 188 opt: 210  Z-score: 107.0  bits: 38.0 E():  1.2
 70.968% identity (71.739% ungapped) in 93 nt overlap (291-200:143630-143722)

      320       310       300       290       280       270        
HUMBE- TGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATATGT
                                     : :::::::::::::::::: : ::::: :
BACR30 AGTAGTTAGTATGTTGGTTCGCATATATGTATATATATATATATATATATATATATATAT
  143600    143610    143620    143630    143640    143650         

      260       250       240        230       220       210       
HUMBE- ACACACATACATATACATATATATGCATTCAT-TTGTTGTTGTTTTTCTTAATTTGCTCA
       : : : ::: ::::: ::::::::  ::  :: : ::: : :    :  :: :: : :::
BACR30 ATATATATATATATATATATATATATATATATATAGTTTTAGAAAGTAGTAGTTAGTTCA
  143660    143670    143680    143690    143700    143710         

       200       190       180       170       160       150       
HUMBE- TGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCAT
       : :                                                         
BACR30 TCCGGCTCGGCGGCTTAAAGTTCTTGTAAGTAGATGGGTTTGTTACGCTTGCGTTTGCCA
  143720    143730    143740    143750    143760    143770         

>>BACR30G03 : AC008355, 151500 bases, from 3R:82.         (73982 nt)
rev-comp initn: 174 init1: 174 opt: 209  Z-score: 101.1  bits: 38.0 E():  1.2
 59.242% identity (61.275% ungapped) in 211 nt overlap (396-188:39228-39433)

           420       410       400       390       380       370   
HUMBE- GATATGTAGATGGATCTCTTCCTGCGTCTCCAGAATATGCAAAATACTTACAGGACAGAA
                                     :::::  : ::  : ::  ::::   :  :
BACR30 ATAGTATTGAAAATGTAATCATATGTATATCAGAAAGTTCACGAAAC-CACAGATTATTA
     39200     39210     39220     39230     39240      39250      

           360       350       340        330       320       310  
HUMBE- TGGATGAAAACTCTACCTCAGTTCTAAGCATATCT-TCTCCTTATTTGGATTAAAACCTT
          :: :: : :::: :: :  : :: : :::: : : : : : : :  ::  : :  : 
BACR30 AATATTAATA-TCTATCT-ATATATATGTATATATATATACATGTATATATACATATATG
      39260      39270      39280     39290     39300     39310    

            300        290       280       270       260       250 
HUMBE- CTGGTAAGAAAAGA-AAAAATATATATATATATATATGTGTATATGTACACACATACATA
           :: : : : :   : :::: ::::::: ::::: ::::::: :  : : ::: :::
BACR30 TATATATGTATATATGTATATATGTATATATGTATATATGTATATATGTATATATATATA
        39320     39330     39340     39350     39360     39370    

             240       230       220       210       200       190 
HUMBE- TACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTCATGCATGCTAATAAA
       :::::::: ::  :: ::: :::   : ::: : :  :: ::   ::   ::  : : ::
BACR30 TACATATACATATATACATATGT--ATATTTATATATATGTGTGAATATGTGTAACTTAA
        39380     39390       39400     39410     39420     39430  

             180       170       160       150       140       130 
HUMBE- TTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCATTAGTTACTTATTAG
       :                                                           
BACR30 TAGGAAAATGAATTTAATAGAGAAACAACAGACAAAAATTATAAATAATGTTGAAAAGAA
          39440     39450     39460     39470     39480     39490  

>>BACR15O02 : AC009735, 159478 bases, from 3R:82.         (73982 nt)
rev-comp initn: 174 init1: 174 opt: 209  Z-score: 101.1  bits: 38.0 E():  1.2
 59.242% identity (61.275% ungapped) in 211 nt overlap (396-188:126813-127018)

           420       410       400       390       380       370   
HUMBE- GATATGTAGATGGATCTCTTCCTGCGTCTCCAGAATATGCAAAATACTTACAGGACAGAA
                                     :::::  : ::  : ::  ::::   :  :
BACR15 ATAGTATTGAAAATGTAATCATATGTATATCAGAAAGTTCACGAAAC-CACAGATTATTA
         126790    126800    126810    126820     126830    126840 

           360       350       340        330       320       310  
HUMBE- TGGATGAAAACTCTACCTCAGTTCTAAGCATATCT-TCTCCTTATTTGGATTAAAACCTT
          :: :: : :::: :: :  : :: : :::: : : : : : : :  ::  : :  : 
BACR15 AATATTAATA-TCTATCT-ATATATATGTATATATATATACATGTATATATACATATATG
          126850      126860    126870    126880    126890         

            300        290       280       270       260       250 
HUMBE- CTGGTAAGAAAAGA-AAAAATATATATATATATATATGTGTATATGTACACACATACATA
           :: : : : :   : :::: ::::::: ::::: ::::::: :  : : ::: :::
BACR15 TATATATGTATATATGTATATATGTATATATGTATATATGTATATATGTATATATATATA
  126900    126910    126920    126930    126940    126950         

             240       230       220       210       200       190 
HUMBE- TACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTCATGCATGCTAATAAA
       :::::::: ::  :: ::: :::   : ::: : :  :: ::   ::   ::  : : ::
BACR15 TACATATACATATATACATATGT--ATATTTATATATATGTGTGAATATGTGTAACTTAA
  126960    126970    126980      126990    127000    127010       

             180       170       160       150       140       130 
HUMBE- TTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCATTAGTTACTTATTAG
       :                                                           
BACR15 TAGGAAAATGAATTTAATAGAGAAACAACAGACAAAAATTATAAATAATGTTGAAAAGAA
    127020    127030    127040    127050    127060    127070       

>>BACR21B19 : AC011250, 161692 bases, from 4:101.         (73982 nt)
rev-comp initn: 172 init1: 172 opt: 209  Z-score: 101.1  bits: 38.0 E():  1.2
 59.641% identity (63.333% ungapped) in 223 nt overlap (393-180:53098-53316)

        420       410       400       390       380       370      
HUMBE- ATGTAGATGGATCTCTTCCTGCGTCTCCAGAATATGCAAAATACTTACAGGACAGAATGG
                                     :::::  : ::   : :::  : ::::   
BACR21 AGTTTAAATGCAGCCAGAAATGATCAATTAAATATAAATAAAGGTCACATAAAAGAAAAA
     53070     53080     53090     53100     53110     53120       

        360       350          340       330         320       310 
HUMBE- ATGAAAACTCTACCT---CAGTTCTAAGCATATCTTCTCCTT--ATTTGGATTAAAACCT
           :::::  :  :   :: :: : ::: : :    :: ::  : ::: : ::: :  :
BACR21 TAATAAACTTCATTTATACATTTAT-AGCTTTTTAAATCTTTACAATTGCA-TAATATAT
     53130     53140     53150      53160     53170      53180     

             300        290       280       270       260          
HUMBE- TCTGGTAAGAAAAGA-AAAAATATATATATATATATATGTGTATATGTACACACATACAT
            ::: :: : : : : :::::::::::::::::: : ::::: :: : : ::: ::
BACR21 ATATATAATAACATATATATATATATATATATATATATATATATATATATATATATATAT
       53190     53200     53210     53220     53230     53240     

    250       240       230       220          210       200       
HUMBE- ATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAAT---TTGCTCATGCATGCTAA
       ::::::: ::::  :  ::  :::   : ::: : :  ::   ::  : ::  ::  :::
BACR21 ATACATAAATATATA-GCAGATGTATATATTTGTATACATCTATTATTTATTTAT-ATAA
       53250     53260      53270     53280     53290      53300   

       190       180       170       160       150       140       
HUMBE- TAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCATTAGTTACTTA
       : : : :: : ::                                               
BACR21 TCATTCATATATATTATATGTTCACTGATACATAAGCCATTCAGATCGGAATAAAATTGT
         53310     53320     53330     53340     53350     53360   

>>BACR28B01 : AC008139, 170675 bases, from 3R:85.         (28715 nt)
rev-comp initn: 147 init1: 147 opt: 210  Z-score: 108.4  bits: 38.0 E():  1.2
 65.217% identity (67.669% ungapped) in 138 nt overlap (302-165:142757-142889)

       330       320       310       300       290       280       
HUMBE- TTCTCCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATA
                                     :: :::   : :::::::::::::::::::
BACR28 ATATGTGTGCCAGCCCAACCAGCACACATAAATAAATATATAAATATATATATATATATA
     142730    142740    142750    142760    142770    142780      

       270       260       250       240       230       220       
HUMBE- TGTGTATATGTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTT
       : : ::::::::::   :::  :: : :::::: : :::  :: : : : :  : :: : 
BACR28 TATATATATGTACATGTATAGGTA-AAATATATGTACAT--ATGTATGGGTTATATTGTG
     142790    142800    142810     142820      142830    142840   

       210       200       190       180       170       160       
HUMBE- AATTTGCTCATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTG
         ::: :    ::  ::  : ::: :::   : ::::::   :::: :            
BACR28 GCTTTCCCGGCGC-GGCATAAAAAGTATAAAT-AAAATAATTTAAAAAGGGCCAACGATT
        142850     142860    142870     142880    142890    142900 

       150       140       130       120       110       100       
HUMBE- CTCTGTGCATTAGTTACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGAGACCTC
                                                                   
BACR28 CGAAGGGGGTTAAAACTTTTCCCGAGCCCTGCTCCTCCACTTACCCTTTCTCACGATTTT
          142910    142920    142930    142940    142950    142960 

>>BACR10P11 : AC007888, 164035 bases, from 2R:57.         (73982 nt)
 initn: 139 init1: 139 opt: 208  Z-score: 100.5  bits: 37.9 E():  1.3
 62.570% identity (67.879% ungapped) in 179 nt overlap (166-337:41478-41649)

         140       150       160       170        180       190    
HUMBE- GTAACTAATGCACAGAGCACATTGATTTGTATTTATTCT-ATTTTTAGACATAATTTAT-
                                     :::::   : :::  :: : : ::: ::: 
BACR10 GAAAAATTGTATCCTTACTTCATAGCAAAAATTTAAAATAATTCATATATAAAATATATA
     41450     41460     41470     41480     41490     41500       

             200       210       220       230       240       250 
HUMBE- --TAGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATAT
         ::  ::  :  :: :: :::  : : : :   : : ::  ::  :::::::: :::::
BACR10 TATATAAT-AAACAGAAATTTATTATATATA--TATATATATATATATATATAT-TATAT
     41510      41520     41530       41540     41550      41560   

             260       270       280       290       300       310 
HUMBE- GTATGTGTGTACATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGG
        :::   : :: ::::: : ::::::::::::::::::: : : : :: :    : :   
BACR10 ATAT---TATATATATATATATATATATATATATATATTATATATATTATATATATATAT
            41570     41580     41590     41600     41610     41620

             320          330       340       350       360        
HUMBE- TTTTAATCCAAATA---AGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATT
        :::::   :::::   : ::: : ::::                               
BACR10 ATTTAACAGAAATAGATAAGAGTAAATATTTCATGAAATCGTTGATAGGAAATCAGGAAT
            41630     41640     41650     41660     41670     41680

>>BACR48E23 : AC005721, 203183 bases, from 3R:88.         (73982 nt)
 initn: 179 init1: 179 opt: 208  Z-score: 100.5  bits: 37.9 E():  1.3
 61.364% identity (64.671% ungapped) in 176 nt overlap (130-300:64507-64678)

     100       110       120       130        140       150        
HUMBE- CTAGTTTTTTACCTCTTGTTTCCCAAAACCTAATAAGTAA-CTAATGCACAGAGCACATT
                                     ::: ::: ::  :::::   : :  : :: 
BACR48 GCAAGCAATTCCTAGTGTTGTATAATAGATTAACAAGGAATTTAATG--AATATGAAATA
      64480     64490     64500     64510     64520       64530    

      160        170       180          190       200       210    
HUMBE- GATTT-GTATTTATTCTATTTTTAGACATAAT---TTATTAGCATGCATGAGCAAATTAA
        ::::  ::::  ::: :  :: :  :::: :     ::: :: :  ::    : ::: :
BACR48 AATTTAATATTATTTCCA--TTAAAGCATATTCGAAAATTTGCTTTAATTCATATATTTA
        64540     64550       64560     64570     64580     64590  

          220       230       240       250       260       270    
HUMBE- GAAAAACAACAACAAATGAATGCATATATATGTATATGTATGTGTGTACATATACACATA
        :    :   ::   ::  ::  :::::::: ::::: ::: : : :: ::::: : :::
BACR48 TATTTGCTTTAATTCATATATATATATATATATATATATATATATATATATATATATATA
          64600     64610     64620     64630     64640     64650  

          280       290       300       310       320       330    
HUMBE- TATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGA
       : ::::::::::::: : :  :: ::                                  
BACR48 TGTATATATATATATATATAATTATCAAAGTTATAGTTTTAGTTTTTCAGTTTTTTTCAA
          64660     64670     64680     64690     64700     64710  

>>BACR08H11 : AC008136, 154890 bases, from 3R:88.         (73982 nt)
 initn: 179 init1: 179 opt: 208  Z-score: 100.5  bits: 37.9 E():  1.3
 61.364% identity (64.671% ungapped) in 176 nt overlap (130-300:86888-87059)

     100       110       120       130        140       150        
HUMBE- CTAGTTTTTTACCTCTTGTTTCCCAAAACCTAATAAGTAA-CTAATGCACAGAGCACATT
                                     ::: ::: ::  :::::   : :  : :: 
BACR08 GCAAGCAATTCCTAGTGTTGTATAATAGATTAACAAGGAATTTAATG--AATATGAAATA
     86860     86870     86880     86890     86900       86910     

      160        170       180          190       200       210    
HUMBE- GATTT-GTATTTATTCTATTTTTAGACATAAT---TTATTAGCATGCATGAGCAAATTAA
        ::::  ::::  ::: :  :: :  :::: :     ::: :: :  ::    : ::: :
BACR08 AATTTAATATTATTTCCA--TTAAAGCATATTCGAAAATTTGCTTTAATTCATATATTTA
       86920     86930       86940     86950     86960     86970   

          220       230       240       250       260       270    
HUMBE- GAAAAACAACAACAAATGAATGCATATATATGTATATGTATGTGTGTACATATACACATA
        :    :   ::   ::  ::  :::::::: ::::: ::: : : :: ::::: : :::
BACR08 TATTTGCTTTAATTCATATATATATATATATATATATATATATATATATATATATATATA
         86980     86990     87000     87010     87020     87030   

          280       290       300       310       320       330    
HUMBE- TATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGA
       : ::::::::::::: : :  :: ::                                  
BACR08 TGTATATATATATATATATAATTATCAAAGTTATAGTTTTAGTTTTTCAGTTTTTTTCAA
         87040     87050     87060     87070     87080     87090   

>>BACR28F21 : AC010705, 163958 bases, from X:11.          (21998 nt)
 initn: 172 init1: 172 opt: 209  Z-score: 109.6  bits: 37.8 E():  1.4
 75.000% identity (75.000% ungapped) in 76 nt overlap (226-301:149520-149595)

         200       210       220       230       240       250     
HUMBE- GCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTAT
                                     ::: ::  ::  :::::::: ::::: :::
BACR28 GTCGCCTCATCCCCTTTTTTGGATATATACACACATATATATATATATATATATATATAT
  149490    149500    149510    149520    149530    149540         

         260       270       280       290       300       310     
HUMBE- GTGTGTACATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGGTTTT
        : : :: ::::::: ::::::::::::: :::: : : : : : :              
BACR28 ATATTTATATATACATATATATATATATAAATATATGTACATATATGTGCCCCCTTTTCG
  149550    149560    149570    149580    149590    149600         

         320       330       340       350       360       370     
HUMBE- AATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCCT
                                                                   
BACR28 GCACTGCCATGTTGTCCTCGGTTATGTCCGATGGACGCGATAACGGCAAAAACGACGCCG
  149610    149620    149630    149640    149650    149660         

>>BACR02C24 : 234783 bases, from X:12.                    (21843 nt)
rev-comp initn: 172 init1: 172 opt: 209  Z-score: 109.6  bits: 37.8 E():  1.4
 75.000% identity (75.000% ungapped) in 76 nt overlap (301-226:219922-219997)

      330       320       310       300       290       280        
HUMBE- TCTCCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATAT
                                     : : : : : : :::: :::::::::::::
BACR02 GACAACATGGCAGTGCCGAAAAGGGGGCACATATATGTACATATATTTATATATATATAT
          219900    219910    219920    219930    219940    219950 

      270       260       250       240       230       220        
HUMBE- GTGTATATGTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTA
        ::::::: :: : : ::: ::::: ::::::::  ::  :: :::              
BACR02 ATGTATATATAAATATATATATATATATATATATATATATATGTGTGTATATATCCAAAA
          219960    219970    219980    219990    220000    220010 

      210       200       190       180       170       160        
HUMBE- ATTTGCTCATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGC
                                                                   
BACR02 AAGGGGATGAGGCGACACATGTTCTGTCCGTTTTTCGTTGCGTTTTCGGGACTTTTTCGC
          220020    220030    220040    220050    220060    220070 

>>BACR36J03 : AC091634, 159065 bases, from 2R:50.         (73982 nt)
rev-comp initn: 168 init1: 168 opt: 207  Z-score: 99.9  bits: 37.8 E():  1.4
 72.043% identity (73.626% ungapped) in 93 nt overlap (301-209:2749-2839)

      330       320       310       300       290       280        
HUMBE- TCTCCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATAT
                                     : : : : : : : ::::::::::::::::
BACR36 ATGCTTAATCTATATAATACTACTATATGTACATATGTATATACATATATATATATATAT
     2720      2730      2740      2750      2760      2770        

      270       260       250       240       230       220        
HUMBE- GTGTATATGTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTA
        : ::::: :::: : ::: ::::::::  :::: :  : ::::  :  :::::: ::  
BACR36 ATATATATATACATATATATATATACATTAATAT-CTCTGATTTAAT-ATGTTTTCCTGT
     2780      2790      2800      2810       2820       2830      

      210       200       190       180       170       160        
HUMBE- ATTTGCTCATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGC
       :::                                                         
BACR36 ATTCCTGTTCTATATTTGGTATACCTTATCAACTCAACGTCCAACGGTACTTTAAACTGA
       2840      2850      2860      2870      2880      2890      

>>BACR40P19 : AC010667, 159570 bases, from 4:101.         (73982 nt)
rev-comp initn: 179 init1: 179 opt: 207  Z-score: 99.9  bits: 37.8 E():  1.4
 70.000% identity (70.000% ungapped) in 90 nt overlap (301-212:96607-96696)

      330       320       310       300       290       280        
HUMBE- TCTCCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATAT
                                     : : ::  : : ::::::::::::::::::
BACR40 AAATATATATAACTATATATATATAAATATATATAACTATATATATATATATATATATAT
      96580     96590     96600     96610     96620     96630      

      270       260       250       240       230       220        
HUMBE- GTGTATATGTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTA
        : ::::: :: :   ::: ::::: ::::::::  ::  :::: :   : : : :: ::
BACR40 ATATATATATATAACTATATATATATATATATATATATATATTTTTATATATATATCCTA
      96640     96650     96660     96670     96680     96690      

      210       200       190       180       170       160        
HUMBE- ATTTGCTCATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGC
                                                                   
BACR40 GCTCAATCTAAATATAAAGTTGGAATACTTTTGCCAGGGGTTTCTTTCTTTTCTTTCCTT
      96700     96710     96720     96730     96740     96750      

>>BACR14P04 : AC007329, 126140 bases, from 2R:50.         (73982 nt)
 initn: 168 init1: 168 opt: 207  Z-score: 99.9  bits: 37.8 E():  1.4
 72.043% identity (73.626% ungapped) in 93 nt overlap (209-301:68803-68893)

      180       190       200       210       220       230        
HUMBE- TTAGACATAATTTATTAGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCA
                                     :::  :: ::::: : :  :::: :  : :
BACR14 GTTGATAAGGTATACCAAATATAGAACAGGAATACAGGAAAAC-ATATTAAATCAGAG-A
          68780     68790     68800     68810      68820      68830

      240       250       260       270       280       290        
HUMBE- TATATATGTATATGTATGTGTGTACATATACACATATATATATATATATATTTTTTCTTT
       :::  :::::::: ::: : :::: ::::: : :::::::::::::::: : : : : : 
BACR14 TATTAATGTATATATATATATGTATATATATATATATATATATATATATGTATATACATA
            68840     68850     68860     68870     68880     68890

      300       310       320       330       340       350        
HUMBE- TCTTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTT
       : :                                                         
BACR14 TGTACATATAGTAGTATTATATAGATTAAGCATTTTAAGAAGCTCTCTCGTGAAATATTC
            68900     68910     68920     68930     68940     68950

>>BACR30L17 : AC012390, 174441 bases, from 4:101.         (32481 nt)
rev-comp initn: 179 init1: 179 opt: 207  Z-score: 105.6  bits: 37.7 E():  1.6
 70.000% identity (70.000% ungapped) in 90 nt overlap (301-212:157746-157835)

      330       320       310       300       290       280        
HUMBE- TCTCCTTATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATAT
                                     : : ::  : : ::::::::::::::::::
BACR30 AAATATATATAACTATATATATATAAATATATATAACTATATATATATATATATATATAT
      157720    157730    157740    157750    157760    157770     

      270       260       250       240       230       220        
HUMBE- GTGTATATGTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTA
        : ::::: :: :   ::: ::::: ::::::::  ::  :::: :   : : : :: ::
BACR30 ATATATATATATAACTATATATATATATATATATATATATATTTTTATATATATATCCTA
      157780    157790    157800    157810    157820    157830     

      210       200       190       180       170       160        
HUMBE- ATTTGCTCATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGC
                                                                   
BACR30 GCTCAATCTAAATATAAAGTTGGAATACTTTTGCCAGGGGTTTCTTTCTTTTCTTTCCTT
      157840    157850    157860    157870    157880    157890     

>>BACR34M23 : AC008190, 158012 bases, from 3R:83.         (73982 nt)
 initn: 195 init1: 195 opt: 205  Z-score: 98.6  bits: 37.5 E():  1.7
 73.494% identity (74.390% ungapped) in 83 nt overlap (223-304:108588-108670)

            200       210       220       230        240       250 
HUMBE- TTAGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGC-ATATATATGTATAT
                                     :::: : ::   :::  ::::::  : :::
BACR34 TATATTTAATTTAACACTAGTCCGTCATATACAATACATTGCTGCTGTATATACATGTAT
    108560    108570    108580    108590    108600    108610       

             260       270       280       290       300       310 
HUMBE- GTATGTGTGTACATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGG
        ::: : : :: ::::: : :::::::::::::::::: : :  :: ::::::       
BACR34 ATATATATATATATATATATATATATATATATATATATATATAGTTCTCTTACACATAAT
    108620    108630    108640    108650    108660    108670       

             320       330       340       350       360       370 
HUMBE- TTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTG
                                                                   
BACR34 TAACAATTTAGAAATTGCTCACCTGATTAACGTTTACATTTATGTTTGCCACAGTGCTTG
    108680    108690    108700    108710    108720    108730       

>>BACR02C19 : AC008189, 188359 bases, from 3R:82.         (73982 nt)
rev-comp initn: 198 init1: 198 opt: 205  Z-score: 98.6  bits: 37.5 E():  1.7
 77.941% identity (77.941% ungapped) in 68 nt overlap (293-226:131184-131251)

        320       310       300       290       280       270      
HUMBE- TTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATAT
                                     ::: :::::::::::::::::: : :::::
BACR02 TACAATAGAAGTTATACAATGTTACAGTTTAAATATATATATATATATATATATATATAT
        131160    131170    131180    131190    131200    131210   

        260       250       240       230       220       210      
HUMBE- GTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTC
        :: : : ::: ::::: ::::::::  :  ::: : :                      
BACR02 ATATATATATATATATATATATATATAAAAGCATATATAAGCATAGATTATGTAAAGGGG
        131220    131230    131240    131250    131260    131270   

        200       190       180       170       160       150      
HUMBE- ATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCA
                                                                   
BACR02 ATGTGTACTAAACACAAACTTCGTTTTGTCCGCTTTCCCTTAATCCATTTCTCATCCTTT
        131280    131290    131300    131310    131320    131330   

>>BACR24O24 : AC009538, 173927 bases, from 3R:83.         (73982 nt)
 initn: 195 init1: 195 opt: 205  Z-score: 98.6  bits: 37.5 E():  1.7
 73.494% identity (74.390% ungapped) in 83 nt overlap (223-304:24568-24650)

            200       210       220       230        240       250 
HUMBE- TTAGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGC-ATATATATGTATAT
                                     :::: : ::   :::  ::::::  : :::
BACR24 TATATTTAATTTAACACTAGTCCGTCATATACAATACATTGCTGCTGTATATACATGTAT
     24540     24550     24560     24570     24580     24590       

             260       270       280       290       300       310 
HUMBE- GTATGTGTGTACATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGG
        ::: : : :: ::::: : :::::::::::::::::: : :  :: ::::::       
BACR24 ATATATATATATATATATATATATATATATATATATATATATAGTTCTCTTACACATAAT
     24600     24610     24620     24630     24640     24650       

             320       330       340       350       360       370 
HUMBE- TTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTG
                                                                   
BACR24 TAACAATTTAGAAATTGCTCACCTGATTAACGTTTACATTTATGTTTGCCACAGTGCTTG
     24660     24670     24680     24690     24700     24710       

>>BACR28F21 : AC010705, 163958 bases, from X:11.          (21998 nt)
rev-comp initn: 188 init1: 188 opt: 206  Z-score: 107.7  bits: 37.5 E():  1.8
 73.418% identity (73.418% ungapped) in 79 nt overlap (293-215:149530-149608)

        320       310       300       290       280       270      
HUMBE- TTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATAT
                                     : : :::::::::::::::::: : :::::
BACR28 CCCCTTTTTTGGATATATACACACATATATATATATATATATATATATATATATTTATAT
  149500    149510    149520    149530    149540    149550         

        260       250       240       230       220       210      
HUMBE- GTACACACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTC
        :::: : ::: ::::: : ::::::: :   :: :::      :::::           
BACR28 ATACATATATATATATATAAATATATGTACATATATGTGCCCCCTTTTCGGCACTGCCAT
  149560    149570    149580    149590    149600    149610         

        200       190       180       170       160       150      
HUMBE- ATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAATCAATGTGCTCTGTGCA
                                                                   
BACR28 GTTGTCCTCGGTTATGTCCGATGGACGCGATAACGGCAAAAACGACGCCGGCTGCTCTCC
  149620    149630    149640    149650    149660    149670         

>>BACR02C24 : 234783 bases, from X:12.                    (21843 nt)
 initn: 188 init1: 188 opt: 206  Z-score: 107.7  bits: 37.5 E():  1.8
 73.418% identity (73.418% ungapped) in 79 nt overlap (215-293:219909-219987)

          190       200       210       220       230       240    
HUMBE- ATAATTTATTAGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATATATA
                                     :::::      ::: ::   : ::::::: 
BACR02 GGACATAACCGAGGACAACATGGCAGTGCCGAAAAGGGGGCACATATATGTACATATATT
   219880    219890    219900    219910    219920    219930        

          250       260       270       280       290       300    
HUMBE- TGTATATGTATGTGTGTACATATACACATATATATATATATATATTTTTTCTTTTCTTAC
       : ::::: ::: : :::: ::::: : :::::::::::::::::: : :           
BACR02 TATATATATATATATGTATATATAAATATATATATATATATATATATATATATATGTGTG
   219940    219950    219960    219970    219980    219990        

          310       320       330       340       350       360    
HUMBE- CAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATC
                                                                   
BACR02 TATATATCCAAAAAAGGGGATGAGGCGACACATGTTCTGTCCGTTTTTCGTTGCGTTTTC
   220000    220010    220020    220030    220040    220050        

>>BACR14D22 : AC012164, 169384 bases, from X:17.          (73982 nt)
rev-comp initn: 188 init1: 188 opt: 204  Z-score: 97.9  bits: 37.4 E():  1.8
 66.667% identity (67.290% ungapped) in 108 nt overlap (336-230:2982-3089)

           360       350       340        330       320       310  
HUMBE- TGGATGAAAACTCTACCTCAGTTCTAAGCATATCTTC-TCCTTATTTGGATTAAAACCTT
                                     ::: ::: ::   :: : :::::   : ::
BACR14 CTGCCTAACTTTATAATACAATTTATGGTCTATATTCATCTCGATCTTGATTACTGCTTT
            2960      2970      2980      2990      3000      3010 

            300       290       280       270       260       250  
HUMBE- CTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATATGTACACACATACATAT
        ::      :  :  :  :::::::::::::::::: : ::::: :: : : ::: ::::
BACR14 TTGACTTTGAGGGGGAGTATATATATATATATATATATATATATATATATATATATATAT
            3020      3030      3040      3050      3060      3070 

            240       230       220       210       200       190  
HUMBE- ACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATTTGCTCATGCATGCTAATAAAT
       : :::::: :: ::  ::                                          
BACR14 ATATATATGTGTATATATACATATATACATATATATATGTGTATGTGTAGCTTCGATTTA
            3080      3090      3100      3110      3120      3130 

>>BACR11A04 : AC010916, 165307 bases, from 4:101.         (73982 nt)
rev-comp initn: 165 init1: 165 opt: 204  Z-score: 97.9  bits: 37.4 E():  1.8
 56.738% identity (62.016% ungapped) in 282 nt overlap (294-21:75765-76030)

         320       310       300       290       280       270     
HUMBE- ATTTGGATTAAAACCTTCTGGTAAGAAAAGAAAAAATATATATATATATATATGTGTATA
                                     ::::  ::::::::::::::::  : ::::
BACR11 AAACGGTTATGAAAATAATGTAACCATATTAAAATTTATATATATATATATAAATATATA
        75740     75750     75760     75770     75780     75790    

         260           250       240       230       220       210 
HUMBE- TGTACAC----ACATACATATACATATATATGCATTCATTTGTTGTTGTTTTTCTTAATT
       : : :::    : ::: ::::: ::::::::  ::: :  : :     ::: : :: :: 
BACR11 TATCCACTACTATATATATATATATATATATATATTTAAATATATACATTTGTATTTATA
        75800     75810     75820     75830     75840     75850    

             200       190       180       170         160         
HUMBE- TGCTCATGCATGCTAATAAATTATGTCTAAAAATAGAATAAATACAAAT--CAATGTGCT
       :  : :: ::    :::::: ::     : : :: :  ::  ::::  :  : :: :   
BACR11 TATTTATTCA---AAATAAACTA-----ATACATCGTTTACTTACACTTTACTATTTCTA
        75860        75870          75880     75890     75900      

     150       140         130       120       110       100       
HUMBE- CTGTGCATTAGT--TACTTATTAGGTTTTGGGAAACAAGAGGTAAAAAACTAGAGACCTC
       ::::    :  :  :::: :  :  ::      :::  ::  : :::: : :  : : : 
BACR11 CTGTTATGTTATAATACTGAAAAACTT-----GAACTTGAAATGAAAATCGACTG-CTTG
      75910     75920     75930          75940     75950      75960

        90        80        70        60        50        40       
HUMBE- TTAATGCAGTCAAAAATACAAATAAATAAAAAGTCACTTACAACCCAAAGTGTGACTATC
       ::::       :  : ::  :::    ::: : : : :: :::  :::::  : :: : :
BACR11 TTAAATATAAAATTATTAACAATTCCGAAAGACTAAGTTTCAATACAAAG-CTAAC-AAC
            75970     75980     75990     76000     76010          

        30        20        10                                     
HUMBE- AATGGGGTAATCAGTGGTGTCAAATAGGAGGT                            
       :: :  : ::::                                                
BACR11 AAGGTAGGAATCTAGCTTTGGCAGTGATAATAATTAAATAATAATATTAAAGCAAGAATT
    76020     76030     76040     76050     76060     76070        

>>BACR01N17 : AC009911, 170184 bases, from 2L:38.         (73982 nt)
 initn:  93 init1:  93 opt: 204  Z-score: 97.9  bits: 37.4 E():  1.8
 58.238% identity (63.071% ungapped) in 261 nt overlap (54-303:7216-7467)

            30        40        50        60        70        80   
HUMBE- TACCCCATTGATAGTCACACTTTGGGTTGTAAGTGACTTTTTATTTATTTGTATTTTTGA
                                     :::: :  : ::::  :    :::::::::
BACR01 TGTTCATCTTATAGTAAGCAAGAATTGGACAAGTCAAGTATTATGGAAACATATTTTTGA
        7190      7200      7210      7220      7230      7240     

            90          100       110       120       130       140
HUMBE- CTGCATTA---AGAGGTCTCTAGTTTTTTACCTCTTGTTTCCCAAAACCTAATAAGTAAC
        :   :::   :   :     :: ::  ::    :   ::::  :: : : :  : ::::
BACR01 GTTGTTTAGGTACCAGCGAAGAGATTACTATACATCCATTCC--AATCGTGA-GATTAAC
        7250      7260      7270      7280        7290       7300  

              150             160       170       180       190    
HUMBE- TAATGCACAGA---GC---ACATTGATTTGTATTTATTCTATTTTTAGACATAATTTATT
        :::  : :::   ::   ::::  ::   ::: :: : : :  ::: : :  :: ::: 
BACR01 GAATTAAAAGAATGGCTTAACATATATACATATGTAATATGTACTTATATAACATATATA
           7310      7320      7330      7340      7350      7360  

          200       210        220       230       240       250   
HUMBE- AGCATGCATGAGCAAATTAA-GAAAAACAACAACAAATGAATGCATATATATGTATAT-G
          :::  : ::   ::::: :::  : :: ::    : ::  ::::::::  ::: :  
BACR01 TATATGTTTAAG---ATTAACGAATTAAAAGAATGGCTTAA--CATATATACATATGTAA
           7370         7380      7390      7400        7410       

            260       270       280       290       300       310  
HUMBE- TATGTGTGTACATATACACATATATATATATATATATTTTTTCTTTTCTTACCAGAAGGT
       ::: :   :: ::: ::: :::::::: ::::::::: : :: : :: :::         
BACR01 TATATACTTATATA-ACATATATATATCTATATATATATGTTATATTATTATATCTTAAA
      7420      7430       7440      7450      7460      7470      

            320       330       340       350       360       370  
HUMBE- TTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGT
                                                                   
BACR01 CAAGCTGTTCATTTCATTTAAATTATAAATTTAATTATGTCAGACTACGCATAAATTCAA
       7480      7490      7500      7510      7520      7530      



3002 residues in 1 query   sequences
112936249 residues in 657 library sequences
 Scomplib [33t08]
 start: Sat Dec  8 11:42:13 2001 done: Sat Dec  8 11:43:35 2001
 Scan time: 78.670 Display time:  2.420

Function used was FASTA [version 3.3t08 Jan. 17, 2001]
BioPerl-1.007002/t/data/HUMBETGLOA.fa000444000766000024       605513155576321 16635 0ustar00cjfieldsstaff000000000000>HUMBETGLOA Human haplotype C4 beta-globin gene, complete cds. 
ACCTCCTATTTGACACCACTGATTACCCCATTGATAGTCACACTTTGGGTTGTAAGTGAC
TTTTTATTTATTTGTATTTTTGACTGCATTAAGAGGTCTCTAGTTTTTTACCTCTTGTTT
CCCAAAACCTAATAAGTAACTAATGCACAGAGCACATTGATTTGTATTTATTCTATTTTT
AGACATAATTTATTAGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATA
TATATGTATATGTATGTGTGTACATATACACATATATATATATATATATTTTTTCTTTTC
TTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTT
CATCCATTCTGTCCTGTAAGTATTTTGCATATTCTGGAGACGCAGGAAGAGATCCATCTA
CATATCCCAAAGCTGAATTATGGTAGACAAAACTCTTCCACTTTTAGTGCATCAACTTCT
TATTTGTGTAATAAGAAAATTGGGAAAACGATCTTCAATATGCTTACCAAGCTGTGATTC
CAAATATTACGTAAATACACTTGCAAAGGAGGATGTTTTTAGTAGCAATTTGTACTGATG
GTATGGGGCCAAGAGATATATCTTAGAGGGAGGGCTGAGGGTTTGAAGTCCAACTCCTAA
GCCAGTGCCAGAAGAGCCAAGGACAGGTACGGCTGTCATCACTTAGACCTCACCCTGTGG
AGCCACACCCTAGGGTTGGCCAATCTACTCCCAGGAGCAGGGAGGGCAGGAGCCAGGGCT
GGGCATAAAAGTCAGGGCAGAGCCATCTATTGCTTACATTTGCTTCTGACACAACTGTGT
TCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGT
TACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGTT
GGTATCAAGGTTACAAGACAGGTTTAAGGAGACCAATAGAAACTGGGCATGTGGAGACAG
AGAAGACTCTTGGGTTTCTGATAGGCACTGACTCTCTCTGCCTATTGGTCTATTTTCCCA
CCCTTAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATC
TGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGC
TCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACAC
TGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGGTGAGTCTAT
GGGACCCTTGATGTTTTCTTTCCCCTTCTTTTCTATGGTTAAGTTCATGTCATAGGAAGG
GGATAAGTAACAGGGTACAGTTTAGAATGGGAAACAGACGAATGATTGCATCAGTGTGGA
AGTCTCAGGATCGTTTTAGTTTCTTTTATTTGCTGTTCATAACAATTGTTTTCTTTTGTT
TAATTCTTGCTTTCTTTTTTTTTCTTCTCCGCAATTTTTACTATTATACTTAATGCCTTA
ACATTGTGTATAACAAAAGGAAATATCTCTGAGATACATTAAGTAACTTAAAAAAAAACT
TTACACAGTCTGCCTAGTACATTACTATTTGGAATATATGTGTGCTTATTTGCATATTCA
TAATCTCCCTACTTTATTTTCTTTTATTTTTAATTGATACATAATCATTATACATATTTA
TGGGTTAAAGTGTAATGTTTTAATATGTGTACACATATTGACCAAATCAGGGTAATTTTG
CATTTGTAATTTTAAAAAATGCTTTCTTCTTTTAATATACTTTTTTGTTTATCTTATTTC
TAATACTTTCCCTAATCTCTTTCTTTCAGGGCAATAATGATACAATGTATCATGCCTCTT
TGCACCATTCTAAAGAATAACAGTGATAATTTCTGGGTTAAGGCAATAGCAATATCTCTG
CATATAAATATTTCTGCATATAAATTGTAACTGATGTAAGAGGTTTCATATTGCTAATAG
CAGCTACAATCCAGCTACCATTCTGCTTTTATTTTATGGTTGGGATAAGGCTGGATTATT
CTGAGTCCAAGCTAGGCCCTTTTGCTAATCATGTTCATACCTCTTATCTTCCTCCCACAG
CTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCA
CCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAG
TATCACTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAG
TCCAACTACTAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATA
AAAAACATTTATTTTCATTGCAATGATGTATTTAAATTATTTCTGAATATTTTACTAAAA
AGGGAATGTGGGAGGTCAGTGCATTTAAAACATAAAGAAATGAAGAGCTAGTTCAAACCT
TGGGAAAATACACTATATCTTAAACTCCATGAAAGAAGGTGAGGCTGCAAACAGCTAATG
CACATTGGCAACAGCCCTGATGCATATGCCTTATTCATCCCTCAGAAAAGGATTCAAGTA
GAGGCTTGATTTGGAGGTTAAAGTTTTGCTATGCTGTATTTTACATTACTTATTGTTTTA
GCTGTCCTCATGAATGTCTTTTCACTACCCATTTGCTTATCCTGCATCTCTCAGCCTTGA
CTCCACTCAGTTCTCTTGCTTAGAGATACCACCTTTCCCCTGAAGTGTTCCTTCCATGTT
TTACGGCGAGATGGTTTCTCCTCGCCTGGCCACTCAGCCTTAGTTGTCTCTGTTGTCTTA
TAGAGGTCTACTTGAAGAAGGAAAAACAGGGGTCATGGTTTGACTGTCCTGTGAGCCCTT
CTTCCCTGCCTCCCCCACTCACAGTGACCCGGAATCTGCAGTGCTAGTCTCCCGGAACTA
TC
BioPerl-1.007002/t/data/HUMBETGLOA.gff000444000766000024        57413155576321 16771 0ustar00cjfieldsstaff000000000000##gff-version 2
##date 2000-07-31
##sequence-region test
test.fasta	RepeatMasker	similarity	238	289	15.4	+	.	Target "Motif:(TA)n" 2 53
test.fasta	RepeatMasker	similarity	444	537	37.2	+	.	Target "Motif:MIR3" 93 187
test.fasta	RepeatMasker	similarity	1454	1529	23.7	+	.	Target "Motif:T-rich" 1 75
test.fasta	RepeatMasker	similarity	1702	1797	14.6	-	.	Target "Motif:L1MA6" 6200 6300
BioPerl-1.007002/t/data/HUMBETGLOA.grail000444000766000024      1161013155576321 17356 0ustar00cjfieldsstaff000000000000
[Start grail2exons_human_1.3] [Seqlen= 3002]

[Start exons]
[Num= 3]

f 1    866     941     848    1051    96.000    excellent
f 2   1088    1314     924    1331   100.000    excellent
f 0   2161    2279    2116    2289    94.000    excellent

[End exons]

[Start exon_translations]
[Num= 3]

[Start translation]

[trans_start= 866]
MVHLTPEEKSAVTALWGKVNVDEVG

[End translation]

[Start translation]

[trans_start= 1086]
RLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLD
NLKGTFATLSELHCDKLHVDPENFRV

[End translation]

[Start translation]

[trans_start= 2161]
LLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAH

[End translation]

[End exon_translations]

[Start clusters forward]
[Num= 3]

[Start cluster] [Num= 7]
 1    848    941     87
 1    848    957     84
 1    866    941     96
 1    866    957     88
 1    866    919     71
 1    866    934     60
 1    866   1051     47
[End cluster]

[Start cluster] [Num= 17]
 2    930   1331     63
 2    930   1310     61
 2    930   1275     42
 2   1088   1314    100
 2   1088   1310    100
 2   1088   1289    100
 2   1088   1275     96
 2   1088   1331     87
 2   1088   1263     68
 2   1088   1203     60
 2   1088   1212     59
 2   1088   1196     59
 2   1088   1175     52
 2   1116   1310     94
 2   1161   1310     75
 2   1161   1275     53
 2   1161   1331     41
[End cluster]

[Start cluster] [Num= 7]
 0   2131   2254     80
 0   2131   2289     75
 0   2161   2279     94
 0   2161   2289     93
 0   2161   2254     72
 0   2161   2247     65
 0   2161   2244     62
[End cluster]

[End clusters forward]

[Start clusters reverse]
[Num= 1]

[Start cluster] [Num= 6]
 0   1707   1941     79
 0   1707   1891     79
 0   1707   1921     75
 0   1707   1899     74
 0   1707   1833     59
 0   1707   1855     53
[End cluster]

[End clusters reverse]

[End grail2exons_human_1.3]

[Start DNASequence]
>HUMBETGLOA Human haplotype C4 beta-globin gene, complete cds. 
ACCTCCTATTTGACACCACTGATTACCCCATTGATAGTCACACTTTGGGTTGTAAGTGAC
TTTTTATTTATTTGTATTTTTGACTGCATTAAGAGGTCTCTAGTTTTTTACCTCTTGTTT
CCCAAAACCTAATAAGTAACTAATGCACAGAGCACATTGATTTGTATTTATTCTATTTTT
AGACATAATTTATTAGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATA
TATATGTATATGTATGTGTGTACATATACACATATATATATATATATATTTTTTCTTTTC
TTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTT
CATCCATTCTGTCCTGTAAGTATTTTGCATATTCTGGAGACGCAGGAAGAGATCCATCTA
CATATCCCAAAGCTGAATTATGGTAGACAAAACTCTTCCACTTTTAGTGCATCAACTTCT
TATTTGTGTAATAAGAAAATTGGGAAAACGATCTTCAATATGCTTACCAAGCTGTGATTC
CAAATATTACGTAAATACACTTGCAAAGGAGGATGTTTTTAGTAGCAATTTGTACTGATG
GTATGGGGCCAAGAGATATATCTTAGAGGGAGGGCTGAGGGTTTGAAGTCCAACTCCTAA
GCCAGTGCCAGAAGAGCCAAGGACAGGTACGGCTGTCATCACTTAGACCTCACCCTGTGG
AGCCACACCCTAGGGTTGGCCAATCTACTCCCAGGAGCAGGGAGGGCAGGAGCCAGGGCT
GGGCATAAAAGTCAGGGCAGAGCCATCTATTGCTTACATTTGCTTCTGACACAACTGTGT
TCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGT
TACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGTT
GGTATCAAGGTTACAAGACAGGTTTAAGGAGACCAATAGAAACTGGGCATGTGGAGACAG
AGAAGACTCTTGGGTTTCTGATAGGCACTGACTCTCTCTGCCTATTGGTCTATTTTCCCA
CCCTTAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATC
TGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGC
TCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACAC
TGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGGTGAGTCTAT
GGGACCCTTGATGTTTTCTTTCCCCTTCTTTTCTATGGTTAAGTTCATGTCATAGGAAGG
GGATAAGTAACAGGGTACAGTTTAGAATGGGAAACAGACGAATGATTGCATCAGTGTGGA
AGTCTCAGGATCGTTTTAGTTTCTTTTATTTGCTGTTCATAACAATTGTTTTCTTTTGTT
TAATTCTTGCTTTCTTTTTTTTTCTTCTCCGCAATTTTTACTATTATACTTAATGCCTTA
ACATTGTGTATAACAAAAGGAAATATCTCTGAGATACATTAAGTAACTTAAAAAAAAACT
TTACACAGTCTGCCTAGTACATTACTATTTGGAATATATGTGTGCTTATTTGCATATTCA
TAATCTCCCTACTTTATTTTCTTTTATTTTTAATTGATACATAATCATTATACATATTTA
TGGGTTAAAGTGTAATGTTTTAATATGTGTACACATATTGACCAAATCAGGGTAATTTTG
CATTTGTAATTTTAAAAAATGCTTTCTTCTTTTAATATACTTTTTTGTTTATCTTATTTC
TAATACTTTCCCTAATCTCTTTCTTTCAGGGCAATAATGATACAATGTATCATGCCTCTT
TGCACCATTCTAAAGAATAACAGTGATAATTTCTGGGTTAAGGCAATAGCAATATCTCTG
CATATAAATATTTCTGCATATAAATTGTAACTGATGTAAGAGGTTTCATATTGCTAATAG
CAGCTACAATCCAGCTACCATTCTGCTTTTATTTTATGGTTGGGATAAGGCTGGATTATT
CTGAGTCCAAGCTAGGCCCTTTTGCTAATCATGTTCATACCTCTTATCTTCCTCCCACAG
CTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCA
CCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAG
TATCACTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAG
TCCAACTACTAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATA
AAAAACATTTATTTTCATTGCAATGATGTATTTAAATTATTTCTGAATATTTTACTAAAA
AGGGAATGTGGGAGGTCAGTGCATTTAAAACATAAAGAAATGAAGAGCTAGTTCAAACCT
TGGGAAAATACACTATATCTTAAACTCCATGAAAGAAGGTGAGGCTGCAAACAGCTAATG
CACATTGGCAACAGCCCTGATGCATATGCCTTATTCATCCCTCAGAAAAGGATTCAAGTA
GAGGCTTGATTTGGAGGTTAAAGTTTTGCTATGCTGTATTTTACATTACTTATTGTTTTA
GCTGTCCTCATGAATGTCTTTTCACTACCCATTTGCTTATCCTGCATCTCTCAGCCTTGA
CTCCACTCAGTTCTCTTGCTTAGAGATACCACCTTTCCCCTGAAGTGTTCCTTCCATGTT
TTACGGCGAGATGGTTTCTCCTCGCCTGGCCACTCAGCCTTAGTTGTCTCTGTTGTCTTA
TAGAGGTCTACTTGAAGAAGGAAAAACAGGGGTCATGGTTTGACTGTCCTGTGAGCCCTT
CTTCCCTGCCTCCCCCACTCACAGTGACCCGGAATCTGCAGTGCTAGTCTCCCGGAACTA
TC

[End DNASequence]


BioPerl-1.007002/t/data/HUMBETGLOA.grailexp000444000766000024       404013155576321 20052 0ustar00cjfieldsstaff000000000000begin genes
 1 1 summary f 3 866 2289 866 2289 -1 -1
 1 1 exon 866 957 0 1 96
 1 1 exon 1088 1310 2 2 100
 1 1 exon 2161 2289 0 0 94
 1 1 mrna atggtgcatctgactcctgaggagaagtctgccgttactgccctgtggggcaaggtgaacgtggatgaagttggtggtgaggccctgggcaggctgctggtggtctacccttggacccagaggttctttgagtcctttggggatctgtccactcctgatgctgttatgggcaaccctaaggtgaaggctcatggcaagaaagtgctcggtgcctttagtgatggcctggctcacctggacaacctcaagggcacctttgccacactgagtgagctgcactgtgacaagctgcacgtggatcctgagaacttcaggctcctgggcaacgtgctggtctgtgtgctggcccatcactttggcaaagaattcaccccaccagtgcaggctgcctatcagaaagtggtggctggtgtggctaatgccctggcccacaagtatcactaa
 1 1 translation MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH*
end genes
begin exons
 f 1 848 941 1 0 77 0 848 1051 0
 f 1 848 957 1 0 93 0 848 1051 0
 f 1 866 919 0 0 85 0 848 1051 0
 f 1 866 934 0 0 79 0 848 1051 0
 f 1 866 941 0 0 82 0 848 1051 0
 f 1 866 957 0 0 96 0 848 1051 1
 f 1 866 1051 3 0 24 0 848 1051 0
 f 2 930 1275 0 0 28 0 924 1331 0
 f 2 930 1310 0 0 56 0 924 1331 0
 f 2 930 1331 3 0 33 0 924 1331 0
 f 2 1088 1175 1 2 74 0 924 1331 0
 f 2 1088 1196 1 2 78 0 924 1331 0
 f 2 1088 1203 1 2 60 0 924 1331 0
 f 2 1088 1212 1 2 60 0 924 1331 0
 f 2 1088 1263 1 2 64 0 924 1331 0
 f 2 1088 1275 1 2 79 0 924 1331 0
 f 2 1088 1289 1 2 100 0 924 1331 0
 f 2 1088 1310 1 2 100 0 924 1331 1
 f 2 1088 1314 1 2 82 0 924 1331 0
 f 2 1088 1331 2 2 68 0 924 1331 0
 f 2 1116 1310 1 0 92 0 924 1331 0
 f 2 1161 1275 0 0 33 0 924 1331 0
 f 2 1161 1310 0 0 63 0 924 1331 0
 f 2 1161 1331 3 0 21 0 924 1331 0
 f 3 2131 2254 0 0 34 0 2116 2289 0
 f 3 2131 2289 3 0 37 0 2116 2289 0
 f 3 2161 2244 1 0 60 0 2116 2289 0
 f 3 2161 2247 1 0 62 0 2116 2289 0
 f 3 2161 2254 1 0 65 0 2116 2289 0
 f 3 2161 2279 1 0 77 0 2116 2289 0
 f 3 2161 2289 2 0 94 0 2116 2289 1
 r 1 1062 1296 2 2 79 1 1062 1316 0
 r 1 1082 1296 1 2 75 1 1062 1316 0
 r 1 1104 1296 1 2 74 1 1062 1316 0
 r 1 1112 1296 1 2 79 1 1062 1316 1
 r 1 1148 1296 1 2 53 1 1062 1316 0
 r 1 1170 1296 1 2 59 1 1062 1316 0
end exons
BioPerl-1.007002/t/data/HUMBETGLOA.mzef000444000766000024        65513155576321 17170 0ustar00cjfieldsstaff000000000000 ENTER NAME OF THE SEQUENCE FILE (in single quotes)
HUMBETGLOA.fasta
 ENTER 1 FOR FORWARD, 2 FOR REVERSE
1
 ENTER PRIOR PROBABILITY (suggesting .04)
.04
 ENTER OVER LAPPING NUMBER (suggesting 0)
0
 Internal coding exons predicted by MZEF
 File_Name: HUMBETGLOA  Sequence_length:   3002  G+C_content:  0.400
  Coordinates    P    Fr1   Fr2   Fr3  Orf   3ss   Cds   5ss
  1088 -  1310 0.986 0.510 0.468 0.651 221 0.478 0.594 0.571
BioPerl-1.007002/t/data/HUMBETGLOA.tblastx000444000766000024      2610513155576321 17746 0ustar00cjfieldsstaff000000000000TBLASTX 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= HUMBETGLOA Human haplotype C4 beta-globin gene, complete cds. 
         (3002 letters)

Database: ecoli.nt
           400 sequences; 4,662,239 total letters

Searching.................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gb|AE000479.1|AE000479 Escherichia coli K-12 MG1655 section 369 ...    34  0.13
gb|AE000302.1|AE000302 Escherichia coli K-12 MG1655 section 192 ...    31  0.61
gb|AE000277.1|AE000277 Escherichia coli K-12 MG1655 section 167 ...    31  0.84
gb|AE000168.1|AE000168 Escherichia coli K-12 MG1655 section 58 o...    29  2.2
gb|AE000400.1|AE000400 Escherichia coli K-12 MG1655 section 290 ...    29  3.0
gb|AE000408.1|AE000408 Escherichia coli K-12 MG1655 section 298 ...    29  3.0
gb|AE000438.1|AE000438 Escherichia coli K-12 MG1655 section 328 ...    29  3.0
gb|AE000396.1|AE000396 Escherichia coli K-12 MG1655 section 286 ...    29  3.0
gb|AE000466.1|AE000466 Escherichia coli K-12 MG1655 section 356 ...    26  3.4
gb|AE000482.1|AE000482 Escherichia coli K-12 MG1655 section 372 ...    29  4.1
gb|AE000341.1|AE000341 Escherichia coli K-12 MG1655 section 231 ...    29  4.1
gb|AE000198.1|AE000198 Escherichia coli K-12 MG1655 section 88 o...    29  4.1
gb|AE000367.1|AE000367 Escherichia coli K-12 MG1655 section 257 ...    29  4.1
gb|AE000136.1|AE000136 Escherichia coli K-12 MG1655 section 26 o...    29  4.1
gb|AE000327.1|AE000327 Escherichia coli K-12 MG1655 section 217 ...    28  5.7
gb|AE000498.1|AE000498 Escherichia coli K-12 MG1655 section 388 ...    28  7.8
gb|AE000509.1|AE000509 Escherichia coli K-12 MG1655 section 399 ...    28  7.8
gb|AE000306.1|AE000306 Escherichia coli K-12 MG1655 section 196 ...    28  7.8
gb|AE000203.1|AE000203 Escherichia coli K-12 MG1655 section 93 o...    28  7.8
gb|AE000208.1|AE000208 Escherichia coli K-12 MG1655 section 98 o...    28  7.8

>gb|AE000479.1|AE000479 Escherichia coli K-12 MG1655 section 369 of 400 of the complete
            genome
          Length = 10934

 Score = 33.6 bits (67), Expect = 0.13
 Identities = 11/26 (42%), Positives = 16/26 (61%)
 Frame = +1 / -2

                                      
Query: 1057 SAYWSIFPPLGCWWSTLGPRGSLSPL 1134
            +A W++FPP+G  W  L  +   SPL
Sbjct: 5893 AAVWALFPPVGSQWGCLASQWRTSPL 5816


>gb|AE000302.1|AE000302 Escherichia coli K-12 MG1655 section 192 of 400 of the complete
            genome
          Length = 10264

 Score = 31.3 bits (62), Expect = 0.61
 Identities = 8/17 (47%), Positives = 13/17 (76%)
 Frame = +2 / +2

                             
Query: 2177 WSVCWPITLAKNSPHQC 2227
            +  CWP+ L ++SP+QC
Sbjct: 1157 YPACWPLPLRRSSPYQC 1207


>gb|AE000277.1|AE000277 Escherichia coli K-12 MG1655 section 167 of 400 of the complete
            genome
          Length = 11653

 Score = 30.8 bits (61), Expect = 0.84
 Identities = 9/25 (36%), Positives = 14/25 (56%)
 Frame = +2 / -3

                                     
Query: 2174 CWSVCWPITLAKNSPHQCRLPIRKW 2248
            CW     + L K+ P QCR+ + +W
Sbjct: 4931 CWLTASVLRLQKSLPRQCRITVVRW 4857


>gb|AE000168.1|AE000168 Escherichia coli K-12 MG1655 section 58 of 400 of the complete genome
          Length = 12663

 Score = 29.5 bits (58), Expect = 2.2
 Identities = 12/41 (29%), Positives = 24/41 (58%)
 Frame = -1 / +1

                                                     
Query: 2813 KEHFRGKVVSLSKRTEWSQG*EMQDKQMGSEKTFMRTAKTI 2691
            K H RG+ V + ++   ++  E+ D++ G+ +   RT +TI
Sbjct: 13   KRHLRGE*VKVGEKYITARRGELPDQEPGNGEASYRTMRTI 135


>gb|AE000400.1|AE000400 Escherichia coli K-12 MG1655 section 290 of 400 of the complete
            genome
          Length = 14295

 Score = 29.0 bits (57), Expect = 3.0
 Identities = 7/18 (38%), Positives = 10/18 (54%)
 Frame = +2 / +3

                              
Query: 2165 WATCWSVCWPITLAKNSP 2218
            W TCW+ CW      ++P
Sbjct: 9096 WITCWNCCWQAGWISSAP 9149


>gb|AE000408.1|AE000408 Escherichia coli K-12 MG1655 section 298 of 400 of the complete
            genome
          Length = 10944

 Score = 29.0 bits (57), Expect = 3.0
 Identities = 17/39 (43%), Positives = 20/39 (50%)
 Frame = -3 / +1

                                                   
Query: 1020 LSPHAQFLLVSLNLSCNLDTNLPRASPPTSSTFTLPHRA 904
            L+  A FLLV + +S   DT LPR    T  TF    RA
Sbjct: 7618 LTSTAAFLLV*VKISRACDTFLPRIRSATRRTF*AEERA 7734


>gb|AE000438.1|AE000438 Escherichia coli K-12 MG1655 section 328 of 400 of the complete
            genome
          Length = 10426

 Score = 29.0 bits (57), Expect = 3.0
 Identities = 10/28 (35%), Positives = 12/28 (42%)
 Frame = +2 / +3

                                        
Query: 2165 WATCWSVCWPITLAKNSPHQCRLPIRKW 2248
            WA CW  C  + +A NS    R     W
Sbjct: 750  WACCWRTCSLVVVALNSLRAVRQSSTSW 833


>gb|AE000396.1|AE000396 Escherichia coli K-12 MG1655 section 286 of 400 of the complete
           genome
          Length = 10098

 Score = 29.0 bits (57), Expect = 3.0
 Identities = 9/27 (33%), Positives = 18/27 (66%)
 Frame = -3 / -1

                                      
Query: 633 PPSKIYLLAPYHQYKLLLKTSSFASVF 553
           PP++ YLL+P H+++++   S +   F
Sbjct: 309 PPARFYLLSPVHEWRVIAS*SWYHQSF 229


>gb|AE000466.1|AE000466 Escherichia coli K-12 MG1655 section 356 of 400 of the complete
            genome
          Length = 10208

 Score = 26.3 bits (51), Expect(2) = 3.4
 Identities = 11/26 (42%), Positives = 14/26 (53%)
 Frame = +3 / +2

                                      
Query: 2796 SPEVFLPCFTARWFLLAWPLSLSCLC 2873
            S  V L C T  ++L  W L+LS  C
Sbjct: 5579 SSAVVLRCLTTVFWLPVWALTLSICC 5656


 Score = 20.3 bits (38), Expect(2) = 3.4
 Identities = 4/11 (36%), Positives = 7/11 (63%)
 Frame = +3 / +1

                       
Query: 2892 LKKEKQGSWFD 2924
            +K+  +G W D
Sbjct: 5737 MKRPFKGDWLD 5769


>gb|AE000482.1|AE000482 Escherichia coli K-12 MG1655 section 372 of 400 of the complete genome
          Length = 20906

 Score = 28.6 bits (56), Expect = 4.1
 Identities = 14/48 (29%), Positives = 19/48 (39%)
 Frame = +3 / +1

                                                             
Query: 660   SQCQKSQGQVRLSSLRPHPVEPHPRVGQSTPRSREGRSQGWA*KSGQS 803
             S+C    G  R    RP  + P       +P    GR +GW    GQ+
Sbjct: 20239 SRCALILGPARRWVHRPESLSPAASAHGQSPHVAAGRRRGWKRADGQN 20382


>gb|AE000341.1|AE000341 Escherichia coli K-12 MG1655 section 231 of 400 of the complete
            genome
          Length = 10231

 Score = 28.6 bits (56), Expect = 4.1
 Identities = 12/20 (60%), Positives = 13/20 (65%)
 Frame = -2 / +2

                                
Query: 2995 PGD*HCRFRVTVSGGGREEG 2936
            PG  H  +R TVSG GRE G
Sbjct: 7538 PGWLHAVYRETVSGSGREAG 7597


>gb|AE000198.1|AE000198 Escherichia coli K-12 MG1655 section 88 of 400 of the complete genome
          Length = 11639

 Score = 28.6 bits (56), Expect = 4.1
 Identities = 11/22 (50%), Positives = 15/22 (68%)
 Frame = +1 / +3

                                   
Query: 2332  FPKSNY*TGGYYEGP*ASGFCL 2397
             F +S  * GGY+ GP +S FC+
Sbjct: 10947 FQRSGG*PGGYHAGPGSSPFCV 11012


>gb|AE000367.1|AE000367 Escherichia coli K-12 MG1655 section 257 of 400 of the complete
            genome
          Length = 11438

 Score = 28.6 bits (56), Expect = 4.1
 Identities = 8/27 (29%), Positives = 13/27 (47%)
 Frame = +3 / -2

                                       
Query: 1332 CFLSPSFLWLSSCHRKGISNRVQFRMG 1412
            C  + +F+W + CH+  I     F  G
Sbjct: 7990 CLFAAAFVWFAKCHQPVIGRNTTFSKG 7910


>gb|AE000136.1|AE000136 Escherichia coli K-12 MG1655 section 26 of 400 of the complete genome
          Length = 16823

 Score = 28.6 bits (56), Expect = 4.1
 Identities = 11/23 (47%), Positives = 12/23 (51%)
 Frame = -2 / +1

                                    
Query: 2860  RLSGQARRNHLAVKHGRNTSGER 2792
             RLSG+ RR   A  H    SG R
Sbjct: 13873 RLSGKVRRRGSAASHFLYLSGSR 13941


>gb|AE000327.1|AE000327 Escherichia coli K-12 MG1655 section 217 of 400 of the complete
            genome
          Length = 10048

 Score = 28.1 bits (55), Expect = 5.7
 Identities = 9/19 (47%), Positives = 12/19 (62%)
 Frame = +1 / +2

                               
Query: 1231 WTTSRAPLPH*VSCTVTSC 1287
            W  S  P+PH   C+V+SC
Sbjct: 2426 WRQSLYPIPHCYRCSVSSC 2482


>gb|AE000498.1|AE000498 Escherichia coli K-12 MG1655 section 388 of 400 of the complete
            genome
          Length = 10264

 Score = 27.6 bits (54), Expect = 7.8
 Identities = 8/18 (44%), Positives = 10/18 (55%)
 Frame = +3 / +3

                              
Query: 2670 YAVFYITYCFSCPHECLF 2723
            +   + T C SCPH C F
Sbjct: 4278 FITLHFT*CVSCPHNCSF 4331


>gb|AE000509.1|AE000509 Escherichia coli K-12 MG1655 section 399 of 400 of the complete
           genome
          Length = 10589

 Score = 27.6 bits (54), Expect = 7.8
 Identities = 8/17 (47%), Positives = 12/17 (70%)
 Frame = -2 / -3

                            
Query: 682 PWLFWHWLRSWTSNPQP 632
           P L W+W+R   S+P+P
Sbjct: 261 PSLLWYWVRRCLSSPRP 211


>gb|AE000306.1|AE000306 Escherichia coli K-12 MG1655 section 196 of 400 of the complete
            genome
          Length = 10446

 Score = 27.6 bits (54), Expect = 7.8
 Identities = 7/18 (38%), Positives = 12/18 (65%)
 Frame = +3 / +1

                              
Query: 1341 SPSFLWLSSCHRKGISNR 1394
            +P+  W+S CHR+ +  R
Sbjct: 136  TPAGCWISGCHRRSVQQR 189


>gb|AE000203.1|AE000203 Escherichia coli K-12 MG1655 section 93 of 400 of the complete genome
          Length = 10751

 Score = 27.6 bits (54), Expect = 7.8
 Identities = 13/47 (27%), Positives = 23/47 (48%)
 Frame = +1 / +3

                                                           
Query: 1156 LLWATLR*RLMARKCSVPLVMAWLTWTTSRAPLPH*VSCTVTSCTWI 1296
            +L  T R    A   +  +V +   WT S  P P  + C+++S +W+
Sbjct: 1554 ILRLTYRLPTWAEPVTWAMVSSMRVWTPSVRP*PEALICSISSGSWL 1694


>gb|AE000208.1|AE000208 Escherichia coli K-12 MG1655 section 98 of 400 of the complete genome
          Length = 10619

 Score = 27.6 bits (54), Expect = 7.8
 Identities = 10/25 (40%), Positives = 15/25 (60%)
 Frame = -3 / +3

                                     
Query: 981  LSCNLDTNLPRASPPTSSTFTLPHR 907
            ++C L      + P  ++TFTLPHR
Sbjct: 2829 VACTLTCKYRLSLPQRANTFTLPHR 2903


  Database: ecoli.nt
    Posted date:  Jun 14, 2001  3:27 PM
  Number of letters in database: 4,662,239
  Number of sequences in database:  400
  
Lambda     K      H
   0.318    0.135    0.401 


Matrix: BLOSUM62
Number of Hits to DB: 31907970
Number of Sequences: 400
Number of extensions: 491769
Number of successful extensions: 23184
Number of sequences better than 10.0: 20
length of query: 1000
length of database: 1,554,079
effective HSP length: 47
effective length of query: 953
effective length of database: 1,535,279
effective search space: 1463120887
effective search space used: 1463120887
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 16 ( 7.3 bits)
X2: 0 ( 0.0 bits)
S1: 41 (21.7 bits)
S2: 53 (27.2 bits)
BioPerl-1.007002/t/data/KF527485.gbk000444000766000024      1110313155576321 16370 0ustar00cjfieldsstaff000000000000LOCUS       KF527485                1444 bp    cRNA    linear   VRL 02-OCT-2013
DEFINITION  Influenza A virus (A/California/07/2009(H1N1)) segment 5
            nucleocapsid protein (NP) gene, partial cds.
ACCESSION   KF527485
VERSION     KF527485.1  GI:537446968
KEYWORDS    .
SOURCE      Influenza A virus (A/California/07/2009(H1N1))
  ORGANISM  Influenza A virus (A/California/07/2009(H1N1))
            Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
            Influenzavirus A.
REFERENCE   1  (bases 1 to 1444)
  AUTHORS   Le,V.L., Courtney,C.L., Steel,J. and Compans,R.W.
  TITLE     Closely Related Influenza Viruses Induce Contrasting Respiratory
            Tract Immunopathology
  JOURNAL   PLoS ONE 8 (9), E76708 (2013)
   PUBMED   24086762
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1444)
  AUTHORS   Le,V.L., Courtney,C.L., Steel,J. and Compans,R.W.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-AUG-2013) Microbiology and Immunology, Emory
            University, 1518 Clifton Rd Suite 5000, Atlanta, GA 30322, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: Lasergene v. 10
            Sequencing Technology :: ABI37XL; Sanger dideoxy sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..1444
                     /organism="Influenza A virus (A/California/07/2009(H1N1))"
                     /mol_type="viral cRNA"
                     /strain="A/California/07/2009"
                     /serotype="H1N1"
                     /host="Homo sapiens"
                     /db_xref="taxon:641809"
                     /segment="5"
                     /country="USA"
                     /collection_date="09-Apr-2009"
                     /note="passage details: MDCK 6"
     gene            <1..>1444
                     /gene="NP"
     CDS             <1..>1444
                     /gene="NP"
                     /codon_start=2
                     /product="nucleocapsid protein"
                     /protein_id="AGU69828.1"
                     /db_xref="GI:537446969"
                     /translation="ASQGTKRSYEQMETGGERQDATEIRASVGRMIGGIGRFYIQMCT
                     ELKLSDYDGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVGGK
                     WMRELILYDKEEIRRVWRQANNGEDATAGLTHIMIWHSNLNDATYQRTRALVRTGMDP
                     RMCSLMQGSTLPRRSGAAGAAVKGVGTIAMELIRMIKRGINDRNFWRGENGRRTRVAY
                     ERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCLP
                     ACVYGLAVASGHDFEREGYSLVGIDPFKLLQNSQVVSLMRPNENPAHKSQLVWMACHS
                     AAFEDLRVSSFIRGKKVIPRGKLSTRGVQIASNENVETMDSNTLELRSRYWAIRTRSG
                     GNTNQQKASAGQISVQPTFSVQRNLPFERATVMAAFSGNNEGRTSDMRTEVIRMMESA
                     KPEDLSFQGRGVFELSDEKATNPIVPSFDMS"
ORIGIN      
        1 ggcgtctcaa ggcaccaaac gatcatatga acaaatggag actggtgggg agcgccagga
       61 tgccacagaa atcagagcat ctgtcggaag aatgattggt ggaatcggga gattctacat
      121 ccaaatgtgc actgaactca aactcagtga ttatgatgga cgactaatcc agaatagcat
      181 aacaatagag aggatggtgc tttctgcttt tgatgagaga agaaataaat acctagaaga
      241 gcatcccagt gctgggaagg accctaagaa aacaggagga cccatatata gaagagtagg
      301 cggaaagtgg atgagagaac tcatccttta tgacaaagaa gaaataagga gagtttggcg
      361 ccaagcaaac aatggcgaag atgcaacagc aggtcttact catatcatga tttggcattc
      421 caacctgaat gatgccacat atcagagaac aagagcgctt gttcgcaccg gaatggatcc
      481 cagaatgtgc tctctaatgc aaggttcaac acttcccaga aggtctggtg ccgcaggtgc
      541 tgcggtgaaa ggagttggaa caatagcaat ggagttaatc agaatgatca aacgtggaat
      601 caatgaccga aatttctgga ggggtgaaaa tggacgaagg acaagggttg cttatgaaag
      661 aatgtgcaat atcctcaaag gaaaatttca aacagctgcc cagagggcaa tgatggatca
      721 agtaagagaa agtcgaaacc caggaaacgc tgagattgaa gacctcattt tcctggcacg
      781 gtcagcactc attctgaggg gatcagttgc acataaatcc tgcctgcctg cttgtgtgta
      841 tgggcttgca gtagcaagtg ggcatgactt tgaaagggaa gggtactcac tggtcgggat
      901 agacccattc aaattactcc aaaacagcca agtggtcagc ctgatgagac caaatgaaaa
      961 cccagctcac aagagtcaat tggtgtggat ggcatgccac tctgctgcat ttgaagattt
     1021 aagagtatca agtttcataa gaggaaagaa agtgattcca agaggaaagc tttccacaag
     1081 aggggtccag attgcttcaa atgagaatgt ggaaaccatg gactccaata ccctggaact
     1141 gagaagcaga tactgggcca taaggaccag gagtggagga aataccaatc aacaaaaggc
     1201 atccgcaggc cagatcagtg tgcagcctac attctcagtg cagcggaatc tcccttttga
     1261 aagagcaacc gttatggcag cattcagcgg gaacaatgaa ggacggacat ccgacatgcg
     1321 aacagaagtt ataagaatga tggaaagtgc aaagccagaa gatttgtcct tccaggggcg
     1381 gggagtcttc gagctctcgg acgaaaaggc aacgaacccg atcgtgcctt cctttgacat
     1441 gagt
//BioPerl-1.007002/t/data/Kingdoms_DNA.nex000444000766000024     30767113155576321 17717 0ustar00cjfieldsstaff000000000000#NEXUS 


BEGIN DATA;
DIMENSIONS  NTAX=32 NCHAR=2147;

[!These ribosomal sequences are those used in:

Lake, J.A.  1988.  Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences.  Nature, 331:184-186.

Thanks to James Lake for supplying these data, March 1990. 

The two trees in the file are the most parsimonious trees found.

]
FORMAT DATATYPE=DNA  MISSING=? GAP=-  INTERLEAVE ;OPTIONS  MSTAXA=UNCERTAIN  IGNORE=UNINFORM ;

MATRIX

[                                    10        20        30        40        50        60        70        80        90        100]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                --------TAC-----CTGGTTGATCCTGCC---AGTAG-CATATGCTTGTCTCAAAGATACCCACTCCC-----GACC-CGGGGAGGTAGTGACGAAAA   [77]
Rattus_norvegicus           --------TAC-----CTGGTTGATCCTGCC---AGTAG-CATATGCTTGTCTCAAAGATACCCACTCCC-----GACC-CGGGGAGGTAGTGACGAAAA   [77]
Xenopus_laevis              --------TAC-----CTGGTTGATCCTGCC---AGTAG-CATATGCTTGTCTCAAAGATACCCACTCCC-----GACG-CGGGGAGGTAGTGACGAAAA   [77]
A._salina                   --------TAC-----CTGGTTGATCCTGCC---AGTAG-CATATGCTTGTCTCAAAGATACCCACTCCC-----AGCA-CGGGGAGGTAGTGACGAAAA   [77]
S._cerevisiae               --------TAT-----CTGGTTGATCCTGCC---AGTAGTCATATGCTTGTCTCAAAGATACCCAATCCT-----AATT-CAGGGAGGTAGTGACAATAA   [78]
P.MICA                      ---------AT-----CTGGTTGATCCTGCC---AGTAGTCATATGCTTGTCTCAAAGATACCCAATCCT-----GACA-CAGGGAGGTAGTGACAAGAA   [77]
D.DISC                      --------TAA-----CTGGTTGATCCTGCC---AGTAGTCATATGCTTGTCTCAAAGATACTCAATCCC-----AATA-CGGGGAAGTAGTGACAATAA   [78]
T.BRUC                      --------GAT-----CTGGTTGATTCTGCC---AGTAGTCATATGCTTGTTTCAAGGATGCCCAATGTCGAAAAAATA-CGATGAGGCAGCGAAAAGAA   [83]
E.GRAC                      --------AAT-----CTGGTTGATCCTGCC---AGCAGTCATATGCTTTGTTCAAGGGTGCCCCATGCA-AAGACACT-CTGTGAGGCAGCGACGAACA   [82]
Zea_mays                    --------TAC-----CTGGTTGATCCTGCC---AGTAGTCATATGCTTGTCTCAAAGATACCCAATCCT-----GACA-CGGGGAGGTAGTGACAATAA   [78]
D._mobilis                  ------TAACT-----CCGGTTGATCCTGCC---GGTCCCGACCGCTATCGGGGTGGGGTCCGCAATGCG-----GGAAACCGTGACGGGGCCACCCCGA   [81]
S._solfataricus             --------ATT-----CCGGTTGATCCTGCC---GGACCCGACCGCTATCGGGGTAGGGTCCCCAATGCG-----CGAAAGCGTGAGGGCGCTACCCCGA   [79]
T._tenax                    --------AAA-----CCGGTTGATCCTGCC---GGACCTGACCGCTATCGGGGTGGGGTCCGCAATGCG-----GGCAACCGCGACGGGGCCACCCCGA   [79]
M._vannielii                --------ATT-----CCGGTTGATCCCGCC---GGAGGCTACTGCTATTGGGGTTCGATCCGCAATGCA-----CGAAAGTGCGACGGGGGGACCCCAA   [79]
MB._formicicum              --------AGT-----CCGTTTGATCCTGGC---GGAGGCCACTGCTATTGGGTTTCGATCCGCAATGCA-----CGAAAGTGCGACGGGGGAAACCCAA   [79]
MS._hungatei                --------ATT-----CTGGTTGATCCTGCC---AGAGGCCACTGCTATCGGGGTTTGATTTACCATGCG-----GGCAACCGTGATAAGGAAACCCCGA   [79]
H._volacanii                --------ATT-----CCGGTTGATCCTGCC---GGAGGTCATTGCTATTGGGGTCCGATTTACACTGCA-----CGCAAGTGCGATAAGGGGACCCCAA   [79]
HC._morrhuae                --------ATT-----CCGGTTGATCCTGCC---GGAGGCTATTGCTATCGGGGTCCGATTTACACTGCA-----CGCCAGTGCGATAAGGGGACCCCGA   [79]
H.HALO                      --------ATT-----CCGGTTGATCCTGCC---GGAGGCCATTGCTATCGGAGTCCGATTTACACTGTA-----CGAAAGTGCGATAAGGGGACTCCGA   [79]
H._cutirubrum               --------ATT-----CCGGTTGATCCTGCC---GGAGGCCATTGCTATCGGAGTCCGATTTACACTGTA-----CGAAAGTGCGATAAGGGGACTCCGA   [79]
AN._nidulans                --CAAAATGGA-----GAGTTTGATCCTGGCTCAGGAT--GAACGCTGGCGGCGTGC--TCCGCAATGGG-----CGCAAGCCTGACGGAGCAACGCCGC   [84]
HE.CHL                      ----------------------GATCCTGGCTCAGGAC--GAACGCTGGCGGCATGC--TCCGCAATGGG-----CGAAAGCCTGACGGAGCAATGCCGC   [69]
Bc._subtilis                --TTTATCGGA-----GAGTTTGATCCTGGCTCAGGAC--GAACGCTGGCGGCATGC--TCCGCAATGGA-----CGAAAGTCTGACGGAGCAACGCCGC   [84]
MY.CAP                      ----AAAATGA-----GAGTTTGATCCTGGCTCAGGAT--AAACGCTGGCGGCTGGC--TTCACAATGGA-----CGAAAGTCTGATGAAGCAATGCCGC   [82]
E._coli                     ---AAATTGAA-----GAGTTTGATCATGGCTCAGATT--GAACGCTGGCGGCAGGC--TGCACAATGGG-----CGCAAGCCTGATGCAGCCATGCCGC   [83]
MYX.XA                      ---CAATTGGA-----GAGTTTGATCCTGGCTCAGAAC--GAACGCTGGCGGCGTGC--TGCGCAATGGG-----CGAAAGCCTGACGCAGCAACGCCGC   [83]
P.TEST                      --CGAACTATA-----GAGTTTGATCCTGGCTCAGATT--GAACGCTGGCGGCATGC--TGGACAATGGG-----CGAAAGCCTGATCCAGCAATGCCGC   [84]
AG.TUM                      -CTCAACTTGA-----GAGTTTGATCCTGGCTCAGAAC--GAACGCTGGCGGCAGGC--TGGACAATGGG-----CGCAAGCCTGATCCAGCCATGCCGC   [85]
DV.DES                      --TGAACTGGA-----GAGTTTGATTCTGGCTCAGATT--GAACGCTGGCGGCGTGC--TGCGCAATGGG-----CGAAAGCCTGACGCAGCGACGCCGC   [84]
BA.FRG                      -TTACAACGAA-----GAGTTTGATCCTGGCTCAGGAT--GAACGCTAGCTACAGGC--TGGTCAATGGG-----CGCTAGCCTGAACCAGCCAAGTAGC   [85]
'Zea_mays_(chloroplast)'    --CTCAT-GGA-----GAGTTCGATCCTGGCTCAGGAT--GAACGCTGGCGGCATGC--TCCGCAATGGG-----CGAAAGCCTGACGGAGCAATGCCGC   [83]
T.AMIT                      ATCATAGTCAAAATCTGAGTTTGATCCTGGCTCAGAAG--GAACGCTAGCTATATGC--TGGACAATGGG-----CGAAAGCCCGATCCAGCAATATCGC   [91]

[                                    110       120       130       140       150       160       170       180       190       200]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                ATAACA-AT-AC-AGG-------------------ACTCTTTCGAGGCC--CTGTAATTGGAATGAGTCCACTTT-AA---ATCCTTTAACGAGGA-TCC   [148]
Rattus_norvegicus           ATAACA-AT-AC-AGG-------------------ACTCTTTCGAGGCC--CTGTAATTGGAATGAGTCCACTTT-AA---ATCCTTTAACGAGGA-TCC   [148]
Xenopus_laevis              ATAACA-AT-AC-AGG-------------------ACTCTTTCGAGGCC--CTGTAATTGGAATGAGTACACTTT-AA---ATCCTTTAACGAGGA-TCT   [148]
A._salina                   ATAACG-AT-GC-AGG-------------------ACTCATCCGAGGCC--CTGTGATTGGAATGAGTACACTTT-AA---ATCCTTTAACGAGGA-TCC   [148]
S._cerevisiae               ATAACG-AT-AC-AGG-------------------GCCCATTCG-GGTC--TTGTAATTGGAATGAGTACAATGT-AA---ATACCTTAACGAGGA-ACA   [148]
P.MICA                      ATAACA-AT-AC-AGG-------------------GCATATCTG---TC--TTGTAATTGGAATGAGTAGAATTT-AA---ATCCCTTTACGAGTA-CCA   [145]
D.DISC                      ATATCA-AT-AC-CTA-------------------TCCTTTTTG-GAGG----GCAATTGAAATGAACACAAATT-AA---AACTCTTAATTAACA--CA   [145]
T.BRUC                      ATAGAG-CCGAC-CGT-------------------GCCCTAGTG-CATG--GTTGTTTTCAATGGGGGATACTCA-AACCCATCCAATATCGAGTA-ACA   [157]
E.GRAC                      GTAGCA-AC-CC-CGTC------------------GGCCTTACG-TGCCGATGGGGCTTGGAATGGACGCTATCC-AA---AGACAGCCGTGAGTA-TCA   [155]
Zea_mays                    ATAACA-AT-AC-CGG-------------------GCGCGTTAG-TGTC--TGGTAATTGGAATGAGTACAATCT-AA---ATCCCTTAACGAGGA-TCC   [148]
D._mobilis                  GTGCCC-CC-TT-ACG-------------------GG------G-GCTT--TTCCC-------------CGCTGT-AG---GAAGGCGGGG---GA-ATA   [129]
S._solfataricus             GTGCCT-CC-GC-AAG-------------------GA------G-GCTT--TTCCC-------------CGCTCT-AA---AAAGGCGGGG---GA-ATA   [127]
T._tenax                    GTGCCG-GG-CG-AAG-------------------AGCC---CG-GCTT--TTGCC-------------CGGTGT-AA---GGAGCCGGGC---GA-ATA   [130]
M._vannielii                GTGC-T-CA-TGCACA-------------------GCAT---GG-GCTT--TTATC-------------AAGTGT-AA---ACAGCTTGAG---GA-ATA   [130]
MB._formicicum              GTGCCA-CT-CTTAAC-------------------GGGG---TG-GCTT--TTCTT-------------AAGTGT-AA---AAAGCTTTTG---GA-ATA   [131]
MS._hungatei                GTGC----C-AGCACA-------------------GGCT---GG-CTGT--CCACC--------------AGTGT-AA---ATAACT-GGT---GA-AGA   [126]
H._volacanii                GTGCGAGGG-CA-TAT-------------------AGTC---CTCGCTT--TTCTC-------------GACCGT-AA---GGCGGTCGAG---GA-ATA   [132]
HC._morrhuae                GTGCGAGGG-CA-TAC-------------------AGTC---CTCGCTT--TTCGT-------------GACCGT-AA---GAAGGTCTCA---GA-ATA   [132]
H.HALO                      GTGTGAAGG-CA-TAG-------------------AGCC---TTCACTT--TTGTA-------------CACCGT-AA---GGTGGTGCAC---GA-ATA   [132]
H._cutirubrum               GTGTGAAGG-CA-TAG-------------------AGCC---TTCACTT--TTGTA-------------CACCGT-AA---GGTGGTGCAC---GA-ATA   [132]
AN._nidulans                GTGGGG-GA-GG-AAGGTT--TT-T-GGACTGTAAACCC---CT-TTTC--TCAGG-------------GAAGAA-GA---AAG----------------   [138]
HE.CHL                      GTGGGG-GA-TG-AAGGTC--TT-C-GGATTGTAAACCC---TT-GTCT--TCGGG-------------GAAGAA------------GTT----------   [121]
Bc._subtilis                GTGAGT-GA-TG-AAGGTT--TT-C-GGATCGTAAAGCT---CT-GTTG--TTAGG-------------GAAGAA-CA---AGTACCGTTC---GA-ATA   [150]
MY.CAP                      GTGAGT-GA-TG-ACGGCC--TT-C-GGGTTGTAAAGCT---CT-GTTG--TAAGG-------------GAAGAA-AA---AATAGAGTAG---GA-A-A   [147]
E._coli                     GTGTAT-GA-AG-AAGGCC--TT-C-GGGTTGTAAAGTA---CT-TTCA--GCGGG-------------GAGGAAGGG---AGTAAAGTT-----A-ATA   [148]
MYX.XA                      GTGTGT-GA-TG-AAGGTC--TT-T-GGATTGTAAAGCA---CT-TTCG--ACCGG-------------GAAGAA-AA---CCCGTTGGCT---AACATC   [150]
P.TEST                      GTGCAG-GA-TG-AAGGCC--CT-C-GGGTTGTAAACTG---CT-TTTG--TACGG-------------AACGAA--A---AGCCTGGGGC---TA-ATA   [149]
AG.TUM                      GTGAGT-GA-TG-AAGGCC--TT-A-GGGTTGTAAAGCT---CT-TTCA--CCGGA-------------GAAGAT-AA----------------------   [136]
DV.DES                      GTGAGG-GA-TG-AAGGTT--TT-C-GGATCGTAAACCT---CT-GTCA--GAAGG-------------GAAGAA-AC---TACGTTGTGC---TA-ATC   [150]
BA.FRG                      GTGAAG-GA-TG-AAGGCT--CTATGGGTCGTAAACTT---CT-TTTA-?-TATAA-------------GAATAA------AGTGCAGTAT---GT-ATA   [151]
'Zea_mays_(chloroplast)'    GTGGAG-GT-GG-AAGGCC--TA-C-GGGTCGTCAACTT---CT-TTTC--TCGGA-------------GAAGAA-------------------------   [132]
T.AMIT                      GTGAGT-GA-AG-AAGGGCAATG-C-CGCTTGTAAAGCT---CT-TTCG--TCGAG-------------TGCG---------------------------   [140]

[                                    210       220       230       240       250       260       270       280       290       300]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                ATTGGAG-----------------------------GGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCA   [219]
Rattus_norvegicus           ATTGGAG-----------------------------GGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCA   [219]
Xenopus_laevis              ATTGGAG-----------------------------GGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCA   [219]
A._salina                   ATTGGAG-----------------------------GGCAAGTCTGGTGCCAGCAGCCGCGGTAACTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCG   [219]
S._cerevisiae               ATTGGAG-----------------------------GGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCA   [219]
P.MICA                      ATTGGAG-----------------------------GGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCG   [216]
D.DISC                      ATTG?AG-----------------------------GGCAAGTCTGGTGCCAGCRGCCGCGGTAATTCCAGCTCCAATAGCATATACTAAAGTTGTTGCA   [216]
T.BRUC                      ATTGGAG-----------------------------GACAAGTCTGGTGCCAGCACCCGCGGTAATTCCAGCTCCAAAAGCGTATATTAATGCTGTTGCT   [228]
E.GRAC                      ACCGGAG-----------------------------GGCAAGTCTGGTGCCAGCAGCTGCGGTAATTCCAGCTCCGAGGGCGTATACTAACATTGCTGCT   [226]
Zea_mays                    ATTGGAG-----------------------------GGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCA   [219]
D._mobilis                  AGCGGGG-----------------------------GGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCCCCGCGAGTGGTCGGGACGATTATTGGG   [200]
S._solfataricus             AGCGGGG-----------------------------GGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCTCCGCGAGTGGTCGGGGTGATTACTGGG   [198]
T._tenax                    AGCGGGG-----------------------------GGTAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCCCCGCGAGTGGTCAGGGTGATTACTGGG   [201]
M._vannielii                AGGGCTG-----------------------------GGCAAGTTCGGTGCCAGCAGCCGCGGTAATACCGACGGCCCGAGTGGTAGCCACTCTTATTGGG   [201]
MB._formicicum              AGAGCTG-----------------------------GGCAAGACCGGTGCCAGCCGCCGCGGTAACACCGGCAGCTCAAGTGGTGGCCGTTTTTATTGGG   [202]
MS._hungatei                AGGGC?G-----------------------------GGCAAG?????--------------GTAATACCG-------GAGTGGTGGCCGCTATTACTGGG   [176]
H._volacanii                AGAGCTG-----------------------------GGCAAGACCGGTGCCAGCCGCCGCGGTAATACCGGCAGCTCAAGTGATGACCGATATTATTGGG   [203]
HC._morrhuae                AGAGCTG-----------------------------GGCAAGACCGGTGCCAGCCGCCGCGGTAATACCGGCAGCTCGAGTGATAGCCACTATTATTGGG   [203]
H.HALO                      AGGACTG-----------------------------GGCAAGACCGGTGCCAGCCGCCGCGGTAATACCGGCAGTCCGAGTGATGGCCGATCTTATTGGG   [203]
H._cutirubrum               AGGACTG-----------------------------GGCAAGACCGGTGCCAGCCGCCGCGGTAATACCGGCAGTCCGAGTGATGGCCGATCTTATTGGG   [203]
AN._nidulans                -----------TGACGGTACCTGAGGAATAAGCCTCGGCTAATTCCGTGCCAGCAGCCGCGGTAATACGGGAGAGGCAAGCGTTATCCGGAATTATTGGG   [227]
HE.CHL                      ----------TTGACGGTACCCGAGGAGGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTGTCCGGAATGACTGGG   [211]
Bc._subtilis                GGGCGGTACCTTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGG   [250]
MY.CAP                      TGACTTTATCTTGACAGTACCTTACCAGAAAGCCACGGCTAACTATGTGCCAGCAGCCGCGGTAATACATAGGTGGCAAGCGTTATCCGGATTTATTGGG   [247]
E._coli                     CCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGG   [248]
MYX.XA                      CAACGG---CTTGACGGTACCGGGAGAAGAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTGTTCGGAATTATTGGG   [247]
P.TEST                      TCCCCGGGTCATGACGGTACCGTAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACTGGG   [249]
AG.TUM                      -----------TGACGGTATCCGGAGAAGAAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGGCTAGCGTTGTTCGGAATTACTGGG   [225]
DV.DES                      AG-CAGCGTACTGACGGTACCTTCAAAGGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGG   [249]
BA.FRG                      C-----TGTTTTGTATGTATTATATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGG   [246]
'Zea_mays_(chloroplast)'    -------ACAATGACGGTATCTGAGGAATAAGCATCGGCTAACTCTGTGCCAGCAGCCGCGGTAAGACAGAGGATGCAAGCGTTATCCGGAATGATTGGG   [225]
T.AMIT                      ----CGATCAT-GACAGGACTCGAGGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAAGACGGGGGGGGCAAGTGTTCTTCGGAATGACTGGG   [235]

[                                    310       320       330       340       350       360       370       380       390       400]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                GTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCC-----------------------------------------------------   [266]
Rattus_norvegicus           GTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCC-----------------------------------------------------   [266]
Xenopus_laevis              GTTAAAAAGCTCGTAGTTGGATCTTGGGATCGAGCTGGCGGTCCGCCGCGAGGC----------------------------------------------   [273]
A._salina                   GTTAAAAAGCTCGTAGTTGGATATGGGTCTCGGTCGGGTGGTGCCGCCTCAC------------------------------------------------   [271]
S._cerevisiae               GTTAAAAAGCTCGTAGTTGAACTTTGGGCCCGGTTGGCCGGTCCGATTTTTT------------------------------------------------   [271]
P.MICA                      GTTAAAAAGCTCGTAGTTGGATTTCTGCCGAGGACGACCGGTCCGCCTCT--------------------------------------------------   [266]
D.DISC                      GTTAAAAAGCTCGTAGTTGAAGTTTAAGGTTTACCGGGTTTATGTCATTTACCACTT-------------------------------------------   [273]
T.BRUC                      GTTAAAGGGTTCGTAGTTGAACTGTGGGCCACGTAGTTTTGTGCCGTGCCAGTC----------CCGTCCA--------CCTCGGAC-------GTGTT-   [302]
E.GRAC                      GTTAAAACACTTGTAGTCTGCCTACGGGCTGCA-GGTCTGCTGGGTGGCCGGTTTGTTGTTTCTCTGGCCAGGGAAGGACCTCGGTTCGACCCTGTGTTG   [325]
Zea_mays                    GTTAAAAAGCTCGTAGTTGGACCTTGGGCCGGGCCGGGTGCCGCCGCC----------------------------------------------------   [267]
D._mobilis                  CCTAAAGCGCCCGTAGCCG--------GCCCGGCAAGTCCCCTC--------------------------------------------------------   [236]
S._solfataricus             CCTAAAGCGCCTGTAGCCG--------GCCCACCAAGTCGCCCC--------------------------------------------------------   [234]
T._tenax                    CTTAAAGCGCCCGTAGCCG--------GCCCGGCAAGTCGCTCC--------------------------------------------------------   [237]
M._vannielii                CCTAAAGCGTCCGTAGCCG--------GTCCAGTAAGTCCCTGT--------------------------------------------------------   [237]
MB._formicicum              CCTAAAGCGTTCGTAGCCG--------GCTTGATAAGTCTCTGG--------------------------------------------------------   [238]
MS._hungatei                CTTAAAGGGTCCGTAGCTG--------GATATACAAGTCCCTTG--------------------------------------------------------   [212]
H._volacanii                CCTAAAGCGTCCGTAGCCG--------GCCACGAAGGTTCATCG--------------------------------------------------------   [239]
HC._morrhuae                CCTAAAGCGTCCGTAGCCG--------GCCGAACAGGTCCGTCG--------------------------------------------------------   [239]
H.HALO                      CCTAAAGCGTCCGTAGCTG--------GCTGAACAAGTCCGTTG--------------------------------------------------------   [239]
H._cutirubrum               CCTAAAGCGTCCGTAGCTG--------GCTGAACAAGTCCGTTG--------------------------------------------------------   [239]
AN._nidulans                CGTAAAGCGCCTGCAGGCG--------GTTAATCAAGTCTGTTG--------------------------------------------------------   [263]
HE.CHL                      CGTAAAGCGCGTGCAGGCG--------GACATGTAAGTCTGAGG--------------------------------------------------------   [247]
Bc._subtilis                CGTAAAGCGCTCGCAGGCG--------GTTTCTTAAGTCTGATG--------------------------------------------------------   [286]
MY.CAP                      CGTATAGGGTGCGTAGGCG--------GTTTTGCAAGTTTGAGG--------------------------------------------------------   [283]
E._coli                     CGTAAAGCGCACGCAGGCG--------GTTTGTTAAGTCAGATG--------------------------------------------------------   [284]
MYX.XA                      CGTAAAGCGCGTGTAGGCG--------GCGTGACAAGTCGGGTG--------------------------------------------------------   [283]
P.TEST                      CGTAAAGCGTGCGCAGGCG--------GTTTTGTAAGACAGTGG--------------------------------------------------------   [285]
AG.TUM                      CGTAAAGCGCACGTAGGCG--------GATATTTAAGTCAGGGG--------------------------------------------------------   [261]
DV.DES                      CGTAAAGCGCACGTAGGCT--------GTAGTGTAAGTCAGGGG--------------------------------------------------------   [285]
BA.FRG                      TTTAAAGGGAGCGTAGGTG--------GACTGGTAAGTCAGTTG--------------------------------------------------------   [282]
'Zea_mays_(chloroplast)'    CGTAAAGCGTCTGTAGGTG--------GCTTTTCAAGTCCGCCG--------------------------------------------------------   [261]
T.AMIT                      CGTAAAGGGCACGTAGGCG--------GTGAATCGGGTTGAAAG--------------------------------------------------------   [271]

[                                    410       420       430       440       450       460       470       480       490       500]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                ---------GCGAGGCGAGCCACCGCCC-GTCCCC---GCCCCTTGCCTCTCGG-CG-CCCC--------------------------------------   [313]
Rattus_norvegicus           ---------GCGAGGCGGCTCAGCGCCCTGTCCCC---AGCCCCTGCCTCTCGG-CG-CCCC--------------------------------------   [314]
Xenopus_laevis              --------GGCTAC-CGCCTGTCCCAGCCCCTGCCTCTCGGCGCCTCCCCGATG-CT-CTTG--------------------------------------   [324]
A._salina                   --------GGTGGTCACTGCCTCGATCGGACAATTCATTGGATCGTTCGGGGTG-CT-CTTA--------------------------------------   [323]
S._cerevisiae               --------CGTGTACTGGATTTCCAACGGGGCCTT---TCCTTCTGGCTAACCT-TG-AGTC--------------------------------------   [320]
P.MICA                      ---------GGGTGAGTATCTGCTCGCCTGGCATC---TTCTT--GGAGAACGT-AG-CTGG--------------------------------------   [312]
D.DISC                      --------CGTGGT-TAAATCGACACCGGTATCTCT-TTCTTAATAGTTCAGCT-TG-TATT--------------------------------------   [323]
T.BRUC                      ------------TTGACCCACGCCCTCGTGGCCCG---TGAACACACTCAGATA-CA-AG--AAACACGGGAGCGGTTCCT------------CCTCACT   [371]
E.GRAC                      GGCTGCAACGGCTGGACTCAACCCCCAGTGGTACG---TCCCTGCGCCCACCTC-TC-AGTCGATGGTGAGATCTGCTCCTGCCAAAAGTCTGCTTCACT   [420]
Zea_mays                    ---------GTACG-GGCAGAACCGACCGGCTCGA---CCCTTCTGCCGGCGAT-GC-GCTC--------------------------------------   [314]
D._mobilis                  ---------------CTAAATTCCCG-------------------GGCTCAACC-CG-GG----------------------------------------   [260]
S._solfataricus             ---------------TTAAAGTCCCC-------------------GGCTCAACC-GG-GG----------------------------------------   [258]
T._tenax                    ---------------TGAAATCCCCA-------------------GGCTCAACC-TG-GG----------------------------------------   [261]
M._vannielii                ---------------TTAAATTCTCT-------------------GGCTTAACCA-G-AG----------------------------------------   [261]
MB._formicicum              ---------------TGAAATCTCAC-------------------GGCTTAACCGTG-AG----------------------------------------   [263]
MS._hungatei                ---------------AGAAATCCGCC-------------------GGCTTAACCG-G-TG----------------------------------------   [236]
H._volacanii                ---------------GGAAATCCGCC-------------------AGCTCAACT-GG-CG----------------------------------------   [263]
HC._morrhuae                ---------------GGAAATCCACC-------------------CGCTCAACG-GGTGG----------------------------------------   [264]
H.HALO                      ---------------GGAAATCTGTC-------------------CGCTTAACG-GG-CA----------------------------------------   [263]
H._cutirubrum               ---------------GGAAATCTGTC-------------------CGCTTAACG-GG-CA----------------------------------------   [263]
AN._nidulans                ---------------TCAAAGCGTGG-------------------GGCTCAACC-TC-AT----------------------------------------   [287]
HE.CHL                      ---------------TGAAAGCTTGG-------------------AGCTCAACT-CC-GA----------------------------------------   [271]
Bc._subtilis                ---------------TGAAAGCCCCC-------------------GGCTCAACC-GG-GG----------------------------------------   [310]
MY.CAP                      ---------------TTAAAGTCCGG-------------------AGCTCAACT-CC-GG----------------------------------------   [307]
E._coli                     ---------------TGAAATCCCCG-------------------GGCTCAACC-TG-GG----------------------------------------   [308]
MYX.XA                      ---------------TGAAAGCCCTC-------------------AGCTCAACT-GA-GG----------------------------------------   [307]
P.TEST                      ---------------TGAAATCCCCG-------------------GGCTCAACC-TG-GG----------------------------------------   [309]
AG.TUM                      ---------------TGAAATCCCAG-------------------AGCTCAACT-CT-GG----------------------------------------   [285]
DV.DES                      ---------------TGAAATCCCAC-------------------GGCTCAACC-GT-GG----------------------------------------   [309]
BA.FRG                      ---------------TGAAAGTTTGC-------------------GGCTCAACC-GT-AA----------------------------------------   [306]
'Zea_mays_(chloroplast)'    ---------------TCAAATCCCAG-------------------GGCTCAACC-CT-GG----------------------------------------   [285]
T.AMIT                      ---------------TGAAAGTCGCC-------------------AAA--AAGT-GG-CG----------------------------------------   [293]

[                                    510       520       530       540       550       560       570       580       590       600]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                --------------CTCGATGCTCT-TAG-----------------------------------CT-GAGTGTCCCGCGGGGCCCGAAGCGTTTACTT--   [360]
Rattus_norvegicus           --------------CTCGATGCTCT-TAG-----------------------------------CT-GAGTGTCCCGCGGGGCCCGAAGCGTTTACTT--   [361]
Xenopus_laevis              --------------ACTGAGTGTCC-CGG-----------------------------------GG-GC--------------CCGAAGCGTTTACTT--   [357]
A._salina                   --------------ACCGAGTGTCC-TGG-----------------------------------GT-GG--------------CCGATACGTTTACTT--   [356]
S._cerevisiae               --------------CTTGTGGCTCT-TGG-----------------------------------CG-AA--------------CCAGGACTTTTACTT--   [353]
P.MICA                      --------------CACTTGACTGTGTGG-------------------------------TGCGGT-AT--------------CCAGGACTTTTACTT--   [350]
D.DISC                      --------------ATCTTTGATAG-TGC-----------------------------------TT-GT--------------TTGGACATTTCACTG--   [356]
T.BRUC                      --------------TTCACGCATGT-CATGCATGCGAGGGG------------------------G-CG--------------TCCGTGAATTTTACTGT   [417]
E.GRAC                      GCAGGCCAAAGCGGTTTATGCCTCC-CGCACTGGCAACGGACACCAACAGGGGACCCAGC--CTCG-AG--------------CTGGGTAGTCTACCTCT   [502]
Zea_mays                    --------------CTGGCCTTAAC-TGG-----------------------------------CC-GGGT------CGTGCCTCCGGGCCGTTACTT--   [355]
D._mobilis                  -------------------GACTGG-AGG-----------------------------------GG-A--------------------------------   [272]
S._solfataricus             -------------------AACTGG-GGG-----------------------------------CG-A--------------------------------   [270]
T._tenax                    -------------------GGCAGG-GGG-----------------------------------CG-A--------------------------------   [273]
M._vannielii                -------------------GACTGG-CAG-----------------------------------GG-A--------------------------------   [273]
MB._formicicum              -------------------AATTGC-TGG-----------------------------------AG-A--------------------------------   [275]
MS._hungatei                -------------------GCGTTC-AGG-----------------------------------GG-A--------------------------------   [248]
H._volacanii                -------------------GGCGTC-CGG-----------------------------------TGAA--------------------------------   [276]
HC._morrhuae                -------------------GACGTC-CGG-----------------------------------CGGA--------------------------------   [277]
H.HALO                      -------------------GGCGTC-CAG-----------------------------------CGGA--------------------------------   [276]
H._cutirubrum               -------------------GGCGTC-CAG-----------------------------------CGGA--------------------------------   [276]
AN._nidulans                -------------------ACAGGC-AAT-----------------------------------GG-A--------------------------------   [299]
HE.CHL                      -------------------AACGGC-CTT-----------------------------------GG-A--------------------------------   [283]
Bc._subtilis                -------------------AGGGTC-ATT-----------------------------------GG-A--------------------------------   [322]
MY.CAP                      -------------------TTCGCC--TT-----------------------------------GA-A--------------------------------   [318]
E._coli                     -------------------AACTGC-ATC-----------------------------------TG-A--------------------------------   [320]
MYX.XA                      -------------------AAGTGC-GCC-----------------------------------CG-A--------------------------------   [319]
P.TEST                      -------------------AACTGC-CAT-----------------------------------TG-T--------------------------------   [321]
AG.TUM                      -------------------AACTGC-CTT-----------------------------------TG-A--------------------------------   [297]
DV.DES                      -------------------AACTGC-CTT-----------------------------------TG-A--------------------------------   [321]
BA.FRG                      -------------------AATTGC-AGC-----------------------------------TG-A--------------------------------   [318]
'Zea_mays_(chloroplast)'    -------------------ACAGGC-GGT-----------------------------------GG-A--------------------------------   [297]
T.AMIT                      -------------------GAATGC-TCT-----------------------------------CG-A--------------------------------   [305]

[                                    610       620       630       640       650       660       670       680       690       700]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                ----------------------------------TGAAAAAATTAGAGTGTTCAAAGCA----------GGCCCGAGCCGCCT-------GGATACCG-C   [408]
Rattus_norvegicus           ----------------------------------TGAAAAAATTAGAGTGTTCAAAGCA----------GGCCCGAGCCGCCT-------GGATACCG-C   [409]
Xenopus_laevis              ----------------------------------TGAAAAAATTAGAGTGTTCCAAGCA----------GGC-CGCGTCGCCT-------GGATACTT-C   [404]
A._salina                   ----------------------------------TGAACAAATTAGAGTGCTTAAAGCA----------GGTGCACCGCGCCT-------GAATATCA-C   [404]
S._cerevisiae               ----------------------------------TGAAAAAATTAGAGTGTTCAAAGCA----------GGC--GTATTGCTC-------GAATATAT-T   [399]
P.MICA                      ----------------------------------TGAGGAAATTAGAGTGTTTCAAGCC----------AGT---TACGCCTT-------GAATACAT-T   [395]
D.DISC                      ----------------------------------TGAGAAAATTGTGGTGTTTAAAGCA----------GGC--GTCTCGCCT-------GATCTTTTGC   [403]
T.BRUC                      GACC--------------------------------AAAAA----AGTGCGACCAAAGCAGTCTGCCGAC-T--TGAATTACAAAGCATGGGATAACG-A   [477]
E.GRAC                      GGTCCACCACCGGAGCCCACCGTCTTCGACACCCTGGAAAACTCAGTGTGCTCAAAGCATCCCCGCGACGGC--TGAATGTCCATCCATGGAATGTCA-A   [599]
Zea_mays                    ----------------------------------TGAAGAAATTAGAGTGCTCAAAGCA----------AGC---CATCGCTCT------GGATACAT-T   [401]
D._mobilis                  ---------------------------------------------------------------------------TACTGCCG-------GGCTA-----   [285]
S._solfataricus             ---------------------------------------------------------------------------TACTGGTG-------GGCTA-----   [283]
T._tenax                    ---------------------------------------------------------------------------TACTGCCG-------GGCTA-----   [286]
M._vannielii                ---------------------------------------------------------------------------TACTGCTG-------GACTT-----   [286]
MB._formicicum              ---------------------------------------------------------------------------TACTATTA-------GCCTT-----   [288]
MS._hungatei                ---------------------------------------------------------------------------AACTGTAT-------TTCTA-----   [261]
H._volacanii                ---------------------------------------------------------------------------AACCACGT-------GGCTT-----   [289]
HC._morrhuae                ---------------------------------------------------------------------------AACCAGTC-------GGCTT-----   [290]
H.HALO                      ---------------------------------------------------------------------------AACTGTTC-------AGCTT-----   [289]
H._cutirubrum               ---------------------------------------------------------------------------AACTGTTC-------AGCTT-----   [289]
AN._nidulans                ---------------------------------------------------------------------------AACTGATT-------GACTA-----   [312]
HE.CHL                      ---------------------------------------------------------------------------AACTGGAT-------GTCTT-----   [296]
Bc._subtilis                ---------------------------------------------------------------------------AACTGGGG-------AACTT-----   [335]
MY.CAP                      ---------------------------------------------------------------------------GACTGTTT-------TACTA-----   [331]
E._coli                     ---------------------------------------------------------------------------TACTGGCA-------AGCTT-----   [333]
MYX.XA                      ---------------------------------------------------------------------------AACTGTTG-------TGCTT-----   [332]
P.TEST                      ---------------------------------------------------------------------------GACTGCAA-------GGCTA-----   [334]
AG.TUM                      ---------------------------------------------------------------------------TACTGGGT-------ATCTT-----   [310]
DV.DES                      ---------------------------------------------------------------------------TACTGCAC-------AACTT-----   [334]
BA.FRG                      ---------------------------------------------------------------------------TACTGTCA-------GTCTT-----   [331]
'Zea_mays_(chloroplast)'    ---------------------------------------------------------------------------AACTACCA-------AGCTG-----   [310]
T.AMIT                      ---------------------------------------------------------------------------AACCAATT-------CACTT-----   [318]

[                                    710       720       730       740       750       760       770       780       790       800]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                AGCTAGGAATAA---TGGAATAGGA-------------C-CGCGGTTCTATTTTG-------------TTGGTTTTC------GGAACT-G---------   [462]
Rattus_norvegicus           AGCTAGGAATAA---TGGAATAGGA-------------C-CGCGGTTCTATTTTG-------------TTGGTTTTC------GGAACT-G---------   [463]
Xenopus_laevis              AGCTAGGAATAA---TGGAATAGGA-------------C-TCCGGTTCTATTTTG-------------TTGGTTTTC------GGAACT-G---------   [458]
A._salina                   AGCATGGAATGA---TGGAATAGGA-------------C-CTCGGTCTTATTATG-------------TTGGTTTTC------TGGACTTG---------   [459]
S._cerevisiae               AGCATGGAATAA---TAGAATAGGA-------------CGTTTGGTTCTATTTTG-------------TTGGTTTCT------AGGACC-A---------   [454]
P.MICA                      AGCATGGAATAA---TAAGATAGGA-------------C-CTCGGTTCTATTTTG-------------TTGGTTTCT------AGAGCT-G---------   [449]
D.DISC                      AGCATGGTATGA---TGAAACATGA-------------CATTTTACGCTATTGGT-------------TTGCGTTTA------AAG--------------   [454]
T.BRUC                      AGCATCAGCCCTGGG-GCCACCGTTTCGGCTTTTGTTGGTTTTAGAAGTCCTTGGGAGATTATGGGGCCGCGTGCCTTGGGTCGGTGTT-TCGTGTCTCA   [575]
E.GRAC                      GGCATCGACCAAGTGTGGCA----TTGGAGTTGTGCTGCCTTGGGGCCCACTCTGGACAACCTGGTGGTGTGTTCCTG----CAGGATC-AACAGGATCG   [690]
Zea_mays                    AGCATGGGATAA---CATCATAGGA-------------T-TCCGGTCCTATTGTG-------------TTGGCCTTC------GGGATC-G---------   [455]
D._mobilis                  ----------------------------------------------------------------------------------------------------   [285]
S._solfataricus             ----------------------------------------------------------------------------------------------------   [283]
T._tenax                    ----------------------------------------------------------------------------------------------------   [286]
M._vannielii                ----------------------------------------------------------------------------------------------------   [286]
MB._formicicum              ----------------------------------------------------------------------------------------------------   [288]
MS._hungatei                ----------------------------------------------------------------------------------------------------   [261]
H._volacanii                ----------------------------------------------------------------------------------------------------   [289]
HC._morrhuae                ----------------------------------------------------------------------------------------------------   [290]
H.HALO                      ----------------------------------------------------------------------------------------------------   [289]
H._cutirubrum               ----------------------------------------------------------------------------------------------------   [289]
AN._nidulans                ----------------------------------------------------------------------------------------------------   [312]
HE.CHL                      ----------------------------------------------------------------------------------------------------   [296]
Bc._subtilis                ----------------------------------------------------------------------------------------------------   [335]
MY.CAP                      ----------------------------------------------------------------------------------------------------   [331]
E._coli                     ----------------------------------------------------------------------------------------------------   [333]
MYX.XA                      ----------------------------------------------------------------------------------------------------   [332]
P.TEST                      ----------------------------------------------------------------------------------------------------   [334]
AG.TUM                      ----------------------------------------------------------------------------------------------------   [310]
DV.DES                      ----------------------------------------------------------------------------------------------------   [334]
BA.FRG                      ----------------------------------------------------------------------------------------------------   [331]
'Zea_mays_(chloroplast)'    ----------------------------------------------------------------------------------------------------   [310]
T.AMIT                      ----------------------------------------------------------------------------------------------------   [318]

[                                    810       820       830       840       850       860       870       880       890       900]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                -------------------------AGGCCATGATT----------------------------------------AAGAGGGACGGCCGGGGGCATTCG   [497]
Rattus_norvegicus           -------------------------AGGCCATGATT----------------------------------------AAGAGGGACGGCCGGGGGCATTCG   [498]
Xenopus_laevis              -------------------------GGGCCATGATT----------------------------------------AAGAGGGACGGCCGGGGGCATTCG   [493]
A._salina                   -------------------------AGGTAATGGTT----------------------------------------AACAGAGACAGACGGGGGCATTCG   [494]
S._cerevisiae               -------------------------TCGTAATGATT----------------------------------------AATAGGGACGGTCGGGGGCATCGG   [489]
P.MICA                      -------------------------AGGTAATGATT----------------------------------------AATAGGGATAGTTGGGGGCATTCG   [484]
D.DISC                      --------------------------TGTAATGATT----------------------------------------AATAGGGATGGATGGGGGTGTTCA   [488]
T.BRUC                      TTTTTGTGGCGCGCACATTCGGCTCTTCGTGATGTTTTTTTACATTCATTGCGACGCGCGGCTTCCAGGAAT--GAAGGAGGGTAGTTCGGGGGAGAACG   [673]
E.GRAC                      TTGCCCTGCCTGGCC--TTCGGGTCTCGTCAGGCTTCGTCCCCTGTCCCTGCAGCTTGCACCCATCGATCGTAAGTGATGGGACTGTTCGGGGTGAAAGA   [788]
Zea_mays                    -------------------------GAGTAATGATT----------------------------------------AATAGGGACAGTCGGGGGCATTCG   [490]
D._mobilis                  -------------------------------------------------------------------------------GGGGGTGGGAGAGGCCGAGGG   [306]
S._solfataricus             -------------------------------------------------------------------------------GGGGGCGGGAGAGGCGGGGGG   [304]
T._tenax                    -------------------------------------------------------------------------------GGGGGCGGGAGAGGCCGCCGG   [307]
M._vannielii                -------------------------------------------------------------------------------GGGACCGGGAGAGGACAAGGG   [307]
MB._formicicum              -------------------------------------------------------------------------------GAGGCCGGGAGAGGTTAGCGG   [309]
MS._hungatei                -------------------------------------------------------------------------------GGGACCGGGAGAGGTGAGAGG   [282]
H._volacanii                -------------------------------------------------------------------------------GGGACCGGAAGGCTCGAGGGG   [310]
HC._morrhuae                -------------------------------------------------------------------------------GGGGCCGGGAGACCAGAGAGG   [311]
H.HALO                      -------------------------------------------------------------------------------GGGACCGGAAGACCTGAGGGG   [310]
H._cutirubrum               -------------------------------------------------------------------------------GGGACCGGAAGACCTGAGGGG   [310]
AN._nidulans                -------------------------------------------------------------------------------GAGTATGGTAGGGGTAGCGGG   [333]
HE.CHL                      -------------------------------------------------------------------------------GAGAGATGGAGAGGATAGCGG   [317]
Bc._subtilis                -------------------------------------------------------------------------------GAGTGCAGAAGAGGAGAGTGG   [356]
MY.CAP                      -------------------------------------------------------------------------------GAATGCAAGAGAGGTAAGCGG   [352]
E._coli                     -------------------------------------------------------------------------------GAGTCTCGTAGAGGGGGGTAG   [354]
MYX.XA                      -------------------------------------------------------------------------------GAGTGCCGGA?AGGGTGGCGG   [353]
P.TEST                      -------------------------------------------------------------------------------GAGTGCGGCAGAGGGGGATGG   [355]
AG.TUM                      -------------------------------------------------------------------------------GAGTATGGAAGAGGTAAGTGG   [331]
DV.DES                      -------------------------------------------------------------------------------GAATCCGGGAGAGGGTGGCGG   [355]
BA.FRG                      -------------------------------------------------------------------------------GAGTACAGTAGAGGTGGGCGG   [352]
'Zea_mays_(chloroplast)'    -------------------------------------------------------------------------------GAGTACGGTAGGGGCAGAGGG   [331]
T.AMIT                      -------------------------------------------------------------------------------GAGTGAGACAGAGGAGAGTGG   [339]

[                                    910       920       930       940       950       960       970       980       990       1000]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                TATTGCGCCGCTA--GAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCG   [595]
Rattus_norvegicus           TATTGCGCCGCTA--GAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCG   [596]
Xenopus_laevis              TATTGTGCCGCTA--GAGGTGAAATTCTTGGACCGGCGCAAGACGAACCAAAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCG   [591]
A._salina                   TACTGCGACGCTA--GAGGTGAAATTCTTGGACCGTCGCAAGACGAACAACTGCGAACAAGTTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTTA   [592]
S._cerevisiae               TATT-CAATTGTC--GAGGTGAAATTCTTGGATTTATTGAAGACTAACTACTGCGAAAGCGTTTGCCAAGGACGTTTTCGTTAATCAAGAACGAAAGTTG   [586]
P.MICA                      TATT-TAACTGGTCAGAGGTGAAATTCTCGGATTTGTTAAAGACGGACTACTGCGAAAGCATTTGCCAAGGATGTTTTCATTGATCAAGAACGAAAGTTA   [583]
D.DISC                      TATTGGTGGGCGA--GAGGTGAAATTCGTTGACCCTATCAAGATGAACTTCTGCGAAAGCATTCACCAAATACTTCCCCATTAATCAAGAACGAAAGTTT   [586]
T.BRUC                      TACT-GGTGCGTCA-GAGGTGAAATTCTTAGACCGCACCAAGACGAACTACAGCGAAGGCATTCTTCAAGGATACCTTCCTCAATCAAGAACCAAAGTGT   [771]
E.GRAC                      TACG-GGAGCGCCA-GAGGTGAAATTCTTAGATCGCTGCCAGATCCACTGCAGCGAAGGCGTTCTGCAAGTGCACGTCCGTCGATCAAGAATGAGAGTTC   [886]
Zea_mays                    TATTTCATAGTCA--GAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTG   [588]
D._mobilis                  TACTCCCGGGGTA--GGGGCGAAATCCTATAATCCCGGGAGGACCACCAGTGGCGAAGGCGCTCGGCTGGAACACGCCCGACGGTGAGGGGCGAAAGCCG   [404]
S._solfataricus             TACTCCCGGAGTA--GGGGCGAAATCCTTAGATACCGGGAGGACCACCAGTGGCGGAAGCGCCCCGCTAGAACGCGCCCGACGGTGAGAGGCGAAAGCCG   [402]
T._tenax                    TACTCCGGGGGTA--GGGGCGAAATCCTATAATCCCCGGAGGACCACCAGTGGCGAAAGCGGGCGGCCAGAACGCGCCCGACGGTGAGGGGCGAAAGCCG   [405]
M._vannielii                TACTCCAGGGGTA--GCGGTGAAATGTGTTGATCCTTGGAGGACCACCTATGGCGAAGGCACTTGTCTGGAACGGGTCCGACGGTGAGGGACGAAAGCCA   [405]
MB._formicicum              TACTCCCGGGGTA--GGGGTGAAATCCTATAATCCCGGGAGGACCACCTGTGGCGAAGGCGGCTAACTGGAACGGGCCTGACGGTGAGTAACGAAAGCCA   [407]
MS._hungatei                TACTGCCGGGGTA--GGAGTGAAATCCTGTAATCCCGGTGGGACCACCTATGGCGAAGGCATCTCACCAGAACGGGTCCGACAGTGAGGGACGAAAGCTG   [380]
H._volacanii                TACGTCCGGGGTA--GGAGTGAAATCCCGTAATCCTGGACGGACCACCGATGGCGAAAGCACCTCGAGAAGACGGATCCGACGGTGAGGGACGAAAGCTA   [408]
HC._morrhuae                TACGTCCGGGGTA--GGAGTGAAATCCTGTAATCCTGGACGGACCACCGGTAGCGAAAGCGTCTCTGGAGAACGGACCCGACGGTGAGGGACGAAAGCTT   [409]
H.HALO                      TACGTCTGGGGTA--GGAGTGAAATCCTGTAATCCTGGACGGACCGCCGGTGGCGAAAGCGCCTCAGGAGAACGGATCCGACAGTGAGGGACGAAAGCTA   [408]
H._cutirubrum               TACGTCTGGGGTA--GGAGTGAAATCCTGTAATCCTGGACGGACCGCCGGTGGCGAAAGCGCCTCAGGAGAACGGATCCGACAGTGAGGGACGAAAGCTA   [408]
AN._nidulans                AATTCCAGGTGTA--GCGGTGAAATGCGTAGATATCTGGAAGAACACCAGCGGCGAAAGCGCGCTACTGGGCCATAACTGACGCTCATGGACGAAAGCTA   [431]
HE.CHL                      AATTCCCGGTGTA--GCGGTGAAATGCGTAGATATCGGGAGGAACACCCGTGGCGAAGGCGGCTATCTGGACATTATCTGACGCTGAGGCGCGAAAGCGT   [415]
Bc._subtilis                AATTCCACGTGTA--GCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGAGCGAAAGCGT   [454]
MY.CAP                      AATTCCATGTGTA--GCGGTGAAATGCGTAGATATATGGAAGAACACCTGTGGCGAAAGCGGCTTACTGGCTTGTTATTGACGCTGAGGCACGAAAGCGT   [450]
E._coli                     AATTCCAGGTGTA--GCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGT   [452]
MYX.XA                      AATTCCCCAAGTA--GAGGTGAAATTCGTAGATATGGGGAGGAACACCGGTGGCGAAGGCGGCCACCTGGACGGTAACTGACGCTGAGACGCGAAAGCGT   [451]
P.TEST                      AATTCCGCGTGTA--GCAGTGAAATGCGTAGATATGCGGAGGAACACCGATGGCGAAGGCAATCCCCTGGGCCTGCACTGACGCTCATGCACGAAAGCGT   [453]
AG.TUM                      AATTCCGAGTGTA--GAGGTGAAATTCGTAGATATTCGGAGGAACGCCAGTGGCGAAGGCGGCTTACTGGTCCATTACTGACGCTGAGGTGCGAAAGCGT   [429]
DV.DES                      AATTCCAGGTGTA--GGAGTGAAATCCGTAGATATCTGGAGGAACATCAGTGGCGAAGGCGGCCACCTGGACCGGTATTGACGCTGAGGTGCGAAAGCGT   [453]
BA.FRG                      AATTCGTGGTGTA--GCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGT   [450]
'Zea_mays_(chloroplast)'    AATTTCCGGTGGA--GCGGTGAAATGCATTGAGATCGGAAAGAACACCAACGGCGAAAGCACTCTGCTGGGCCGACACTGACACTGAGAGACGAAAGCTA   [429]
T.AMIT                      AATTTCGTGTGTA--GGGGTGAAATCCGTAGATCTACGAAGGAACGCCAAAAGCGAAGGCAGCTCTCTGGGTCCCTACCGACGCTGGGGTGCGAAAGCAT   [437]

[                                    1010      1020      1030      1040      1050      1060      1070      1080      1090      1100]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                GAGGTTCGAAGACGATCAGATACCGTCGTAGTTCCG--ACCATAAACGATGCCGACCGGCG-------------ATGCGGCG------------------   [662]
Rattus_norvegicus           GAGGTTCGAAGACGATCAGATACCGTCGTAGTTCCG--ACCATAAACGATGCCGACTGGCG-------------ATGCGGCG------------------   [663]
Xenopus_laevis              GAGGTTCGAAGACGATCAGATACCGTCGTAGTTCCG--ACCATAAACGATGCCGACTAGCG-------------ATCCGGCG------------------   [658]
A._salina                   GAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTA--ACCATAAACGATGCCAACCAGCG-------------ATCCGCGG------------------   [659]
S._cerevisiae               AGGGATCGAAGACGATCTGATACCGTCGTAGTCTTA--ACCATAAACTATGCCGACTAG---------------ATCGGGTG------------------   [651]
P.MICA                      GGGGATCGAAGACGATCAGATACCGTCCTAGTCTTA--ACCATAAACCATGCCGACTAG-------------AGATTGGAGG------------------   [650]
D.DISC                      GGGGATCGAAGACGATCAGATACCGTCGTAGTCCAA--ACTATAAACTATGTCGACCAGGG-------------ATCGGTTA------------------   [653]
T.BRUC                      GGGGATCAAAGATGATTAGAGACCATTGTAGTCCAC--ACTGCAAACCATGACACCCATGAATTGGGGAACATCATTGGGTGCCCGTGTGGCGGCCTTTT   [869]
E.GRAC                      GGGGAGCAAAGATGATCAGACACCGTCGTAGTCCGGCCACTGTAAACGATGCCGGCCAGGCCTTGGCAGA-GCAA--GAATC------------------   [965]
Zea_mays                    GGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCA--ACCATAAACGATGCCGACCAGGG-------------AT-CAGCG------------------   [654]
D._mobilis                  GGGGAGCGAACCGGATTAGATACCCGGGTAGTCCCG--GCTGTAAACGATGCGGGCTAGGT-------------GTTGGGTG------------------   [471]
S._solfataricus             GGGCAGCAAACGGGATTAGATACCCCGGTAGTCCCG--GCTGTAAACGATGCGGGCTAGGT-------------GTCGAGTA------------------   [469]
T._tenax                    GGGGAGCAAAGGGGATTAGATACCCCTGTAGTCCCG--GCCGTAAACGATGCGGGCTAGCT-------------GTCGGCCG------------------   [472]
M._vannielii                GGGGCGCGAACCGGATTAGATACCCGGGTAGTCCTG--GCCGTAAACTCTGCGAACTAGGT-------------GTCACCTG------------------   [472]
MB._formicicum              GGGGCGCGAACCGGATTAGATACCCGGGTAGTCCTG--GCCGTAAACGATGTGGACTTGGT-------------GTTGGGAT------------------   [474]
MS._hungatei                GGGGAGCAAACCGGATTAGATACCCGGGTAGTCCCA--GCTGTAAACGATGCGCGTTAGGT-------------GTGTCAGT------------------   [447]
H._volacanii                GGGTCTCGAACCGGATTAGATACCCGGGTAGTCCTA--GCTGTAAACGATGCTCGCTAGGT-------------GTGACACA------------------   [475]
HC._morrhuae                GGGTCTCGAACCGGATTAGATACCCGGGTAGTCCAA--GCTGTAAACGATGCTCGCTAGGT-------------GTGGCGTT------------------   [476]
H.HALO                      GGGTCTCGAACCGGATTAGATACCCGGGTAGTCCTA--GCTGTAAACGATGTCCGCTAGGT-------------GTGGCGCA------------------   [475]
H._cutirubrum               GGGTCTCGAACCGGATTAGATACCCGGGTAGTCCTA--GCTGTAAACGATGTCCGCTAGGT-------------GTGGCGCA------------------   [475]
AN._nidulans                GGGGAGCGAAAGGGATTAGATACCCCTGTAGTCCTA--GCCGTAAACGATGAACACTAGGT-------------GTTGCG-T------------------   [497]
HE.CHL                      GGGGAGCAAACAGGATTAGATACCCTGGTAGTCCAC--GCCGTAAACGATGAGTGCTAGGT-------------GTTGGG-G------------------   [481]
Bc._subtilis                GGGGAGCGAACAGGATTAGATACCCTGGTAGTCCAC--GCCGTAAACGATGAGTGCTAAGT-------------GTTAGG-G------------------   [520]
MY.CAP                      GGGGAGCAAATAGGATTAGATACCCTAGTAGTCCAC--GCCGTAAACGATGAGTACTAAGT-------------GTTGGG-G------------------   [516]
E._coli                     GGGGAGCAAACAGGATTAGATACCCTGGTAGTCCAC--GCCGTAAACGATGTCGACTTGGA-------------GGTTGT-G------------------   [518]
MYX.XA                      GGGGAGCAAACAGGATTAGATACCCTGGTAGTCCAC--GCCGTAAACGATGAGAACTAGGT-------------GTCGTG-G------------------   [517]
P.TEST                      GGGGAGCAAACAGGATTAGATACCCTGGTAGTCCAC--GCCCTAAACGATGTCAACTGGTT-------------GTTGGG-T------------------   [519]
AG.TUM                      GGGGAGCAAACAGGATTAGATACCCTGGTAGTCCAC--GCCGTAAACGATGAATGTTAGCC-------------GTCGGG-C------------------   [495]
DV.DES                      GGGGAGCAAACAGGATTAGATACCCTGGTAGTCCAC--GCTGTAAACGATGGATGCTAGAT-------------GTCGGG-G------------------   [519]
BA.FRG                      GGGTATCAAACAGGATTAGATACCCTGGTAGTCCAC--ACAGTAAACGATGAATACTCGCT-------------GTTTGC-G------------------   [516]
'Zea_mays_(chloroplast)'    GGGGAGCAAATGGGATTAGAGACCCCAGTAGTCCTA--GCCGTAAACGATGGATACTAGGT-------------GCTGTG-C------------------   [495]
T.AMIT                      GGGGAGCGAACAGGATTAGATACCCTGGTAGTCCAT--GCCGTAAACGATG---------A-------------GTGTTC-G------------------   [494]

[                                    1110      1120      1130      1140      1150      1160      1170      1180      1190      1200]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                -----------------------------------------------------------------------------------------------GCGTT   [667]
Rattus_norvegicus           -----------------------------------------------------------------------------------------------GCGTT   [668]
Xenopus_laevis              -----------------------------------------------------------------------------------------------GCGTT   [663]
A._salina                   -----------------------------------------------------------------------------------------------ACGTT   [664]
S._cerevisiae               -----------------------------------------------------------------------------------------------GTGTT   [656]
P.MICA                      -----------------------------------------------------------------------------------------------TCGTT   [655]
D.DISC                      -----------------------------------------------------------------------------------------------AAATT   [658]
T.BRUC                      GTGCCGACCCTCGGCCCCAATTTATTTATCAATTTACGTGCCTATTCTATCACCCCCGGTTCCCTCTTTTGAGGTTCTTCCGGGGTTTTTTACGGGAATA   [969]
E.GRAC                      -----------------------------------------------------------------------------------------------CTAGA   [970]
Zea_mays                    -----------------------------------------------------------------------------------------------GTGTT   [659]
D._mobilis                  -----------------------------------------------------------------------------------------------GGCTT   [476]
S._solfataricus             -----------------------------------------------------------------------------------------------GGCTT   [474]
T._tenax                    -----------------------------------------------------------------------------------------------GGCTT   [477]
M._vannielii                -----------------------------------------------------------------------------------------------GGCCT   [477]
MB._formicicum              -----------------------------------------------------------------------------------------------GGCTC   [479]
MS._hungatei                -----------------------------------------------------------------------------------------------GACCA   [452]
H._volacanii                -----------------------------------------------------------------------------------------------GGCTA   [480]
HC._morrhuae                -----------------------------------------------------------------------------------------------GGCTA   [481]
H.HALO                      -----------------------------------------------------------------------------------------------GGCTA   [480]
H._cutirubrum               -----------------------------------------------------------------------------------------------GGCTA   [480]
AN._nidulans                -----------------------------------------------------------------------------------------------GAATC   [502]
HE.CHL                      -----------------------------------------------------------------------------------------------GTATC   [486]
Bc._subtilis                -----------------------------------------------------------------------------------------------GGTTT   [525]
MY.CAP                      -----------------------------------------------------------------------------------------------TAACT   [521]
E._coli                     -----------------------------------------------------------------------------------------------CCCTT   [523]
MYX.XA                      -----------------------------------------------------------------------------------------------GAGTT   [522]
P.TEST                      -----------------------------------------------------------------------------------------------CTTAA   [524]
AG.TUM                      -----------------------------------------------------------------------------------------------AGTAT   [500]
DV.DES                      -----------------------------------------------------------------------------------------------AGTAT   [524]
BA.FRG                      -----------------------------------------------------------------------------------------------ATATA   [521]
'Zea_mays_(chloroplast)'    -----------------------------------------------------------------------------------------------GACTC   [500]
T.AMIT                      -----------------------------------------------------------------------------------------------CCCTT   [499]

[                                    1210      1220      1230      1240      1250      1260      1270      1280      1290      1300]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                ATTCCCATG--ACCC-GCCGGGCAGCTT----CCGGGAAA--CCA--AAGTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAAT   [756]
Rattus_norvegicus           ATTCCCATG--ACCC-GCCGGGCAGCTT----CCGGGAAA--CCA--AAGTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAAT   [757]
Xenopus_laevis              ATTCCCATG--ACCC-GCCGAGCAGCTT----CCGGGAAA--CCA--AAGTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAAT   [752]
A._salina                   ACTTGAATG--ACTC-CGCGGGCAGCTT----CCGGGAAA--CCA--AAGTGTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAAT   [753]
S._cerevisiae               TTTTTAATG--ACCC-ACTCGGTACCTT----ACGAGAAA--TCA--AAGTCTTTGGGTTCTGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAAT   [745]
P.MICA                      ATCTATACG--ACTC-CTTCAGCACCTT----ATGAGAAA--TCA--AAGTCTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAAT   [744]
D.DISC                      TTTTCAA-A--ATTT-AATCGGCACCTT----GTGAGAAA--TCAT-GAGTGTTTAGATTCCGGGGGGAGTATGGTCGCAAGTCTGAAACTTAAAGGAAT   [747]
T.BRUC                      TCCTCAGCA--CGTT-TCTTACTTCTTC----ACGCGAAAGCTTG--GAGGTTACAGTCTCAGGGGGGAGTACGTTCGCAAGAGTGAAACTTAAAGAAAT   [1060]
E.GRAC                      CTCTGTCAG--GGCC-ACTCCTCCCACA----ACGAGAAA-TCCA--CAGCCTGTGGGTTCAGGGGGGAGTACTGTCGCAAGGCTGAAACTTAAAGGAAT   [1060]
Zea_mays                    ACTAATAGG--ACCCCGCTGGCCACCTT----ATGAGAAA--TCA--AAGTCTTTGGGTTCCGGGGGGAGTATGGTCGCAGGGCTAAAACTTAAAGGAAT   [749]
D._mobilis                  ------AGA--GCCC-ACCCAGTGCCGC----A-GGGAAG--CCGTTAAGCCCGCCGCCT----GGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGAAT   [556]
S._solfataricus             ------AGA--GCCT-ACTCGGTGCCGC----A-GGGAAG--CCGTTAAGCCCGCCGCCT----GGGGAGTACGGTCGCAAGACTGAAACTTAAAGGAAT   [554]
T._tenax                    ------AGG--GCCC-GGCCGGTGGCGT----A-GGGAAA--CCGTTAAGCCCGCCGCCT----GGGGAGTACGGCCGCAAGGCTGAAACTTAAAGGAAT   [557]
M._vannielii                ------CGA--GCCC-AGGTGGTGCCGA----A-GGGAAG--CCGTTAAGTTCGCCGCCT----GGGGAGTACGGTCGCAAGACTGAAACTTAAAGGAAT   [557]
MB._formicicum              ------CGA--GCTG-CCCCAGTGCCGA----A-GGGAAG--CTGTTAAGTCCACCGCCT----GGGAAGTACGGTCGCAAGACTGAAACTTAAAGGAAT   [559]
MS._hungatei                ------CGT--GTCA-CTGAGGTGCCGA----A-GGGAAA--CCGTGAAACGCGCCGCCT----GGGGAGTACGGTCGCAAGGCTGAAACTTAAAGGAAT   [532]
H._volacanii                ------CGA--GCCT-GTGTTGTGCCGT----A-GGGAAG--CCGAGAAGCGAGCCGCCT----GGGAAGTACGTCCGCAAGGATGAAACTTAAAGGAAT   [560]
HC._morrhuae                ------CGA--GCCA-GCGCTGTGCCGT----A-GGGAAG--CCGAGAAGCGAGCCGCCT----GGGAAGTACGTCCGCAAGGATGAAACTTAAAGGAAT   [561]
H.HALO                      ------CGA--GCCT-GCGCTGTGCCGT----A-GGGAAG--CCGAGAAGCGGACCGCCT----GGGAAGTACGTCTGCAAGGATGAAACTTAAAGGAAT   [560]
H._cutirubrum               ------CGA--GCCT-GCGCTGTGCCGT----A-GGGAAG--CCGAGAAGCGGACCGCCT----GGGAAGTACGTCTGCAAGGATGAAACTTAAAGGAAT   [560]
AN._nidulans                ------GAC--CCGC---GCAGTGCCGT----A-GCCAAC--GCGTTAAGTGTTCCGCCT----GGGGAGTACGCACGCAAGTTGGAAACTCAAAGGAAT   [580]
HE.CHL                      ------GAC--CCCC---CCGGTGCCGC----A-GTTCAC--GCAATAAGCACTCCGCCT----GGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAAT   [564]
Bc._subtilis                ------CCG--CCCC---TTAGTGCTGC----A-GCTAAC--GCATTAAGCACTCCGCCT----GGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAAT   [603]
MY.CAP                      ------C-------------AGCGCTGC----A-GCTAAC--GCATTAAGTACTCCGCCT----GAGTAGTATGCTCGCAAGAGTGAAACTCAAAGGAAT   [591]
E._coli                     ------GAG--GCG----TGGCTTCCGG----A-GCTAAC--GCGTTAAGTCGACCGCCT----GGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAAT   [600]
MYX.XA                      ------GAC--CCCC---GCGGTGCCGA----A-GCTAAC--GCATTAAGTTCTCCGCCT----GGGAAGTACGGTCGCAAGACTAAAACTCAAAGGAAT   [600]
P.TEST                      ------CTG--ACTC-----AGTAACGA----A-GCTAAC--GCGTGAAGTTGACCGCCT----GGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAAT   [600]
AG.TUM                      --------A--CTGT---TCGGTGGCGC----A-GCTAAC--GCATTAAACATTCCGCCT----GGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAAT   [576]
DV.DES                      ------TC------T---TCGGTGTCGT----A-GTTAAC--GCGTTAAGCATCCCGCCT----GGGGAGTACGGTCGCAAGGCTGAAACTCAAAGAAAT   [598]
BA.FRG                      ------CAG---------TAAGCGGCCA----A-GCGAAA--GCATTAAGTATTCCACCT----GGGGAGTACGCCGGCAACGGTGAAACTCAAAGGAAT   [595]
'Zea_mays_(chloroplast)'    ------GAC--CCGT---GCAGTGCTGT----A-GCTAAC--GCGTTAAGTATCCCGCCT----GGGGAGTACGTTCGCAAGAATGAAACTCAAAGGAAT   [578]
T.AMIT                      ------GGTCTACG----CGGATCAGGGGCCCA-GCTAAC--GCGTGAAACACTCCGCCT----GGGGAGTACGGTCGCAAGACCGAAACTCAAAGGAAT   [582]

[                                    1310      1320      1330      1340      1350      1360      1370      1380      1390      1400]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                TGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCCGGCCCGGACA----------------CGG-A-C   [838]
Rattus_norvegicus           TGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCCGGCCCGGACA----------------CGG-A-C   [839]
Xenopus_laevis              TGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCCGGCCCGGACA----------------CGG-A-A   [834]
A._salina                   TGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCAGGCCCGGACA----------------CTG-G-A   [835]
S._cerevisiae               TGACGGAAGGGCACCACTAGGAGTGGAGCCTGCGGCT-AATTTGACTCAACACGGGGAAACTCACCAGGTCCAGACA----------------CAA-T-A   [826]
P.MICA                      TGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACA----------------TAG-T-A   [826]
D.DISC                      TGACGGAAGGGCACACAATGGAGTGGAGCCTGCGGCTTAATTTGACTCAACTCGGGAAAACTTACCAAGCTAAGATA----------------TAG-T-A   [829]
T.BRUC                      TGACGGAATGGCACCACAAGACGTGGAGCGTGCGGTTTAATTTGACTCAACACGGGGAACTTTACCAGATCCGGACA----------------GGG-T-G   [1142]
E.GRAC                      TGACGGAATGGCACCACAAGGCGTGGAGTATGCGGCTTAATTTGACTCAACGCGGGGAATGTTACCAGGTCAGGACG----------------CAA-C-T   [1142]
Zea_mays                    TGACGGAAGGGCACCACCAGGCGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACA----------------TAG-C-A   [831]
D._mobilis                  TGGCGGGGGAGCACCACAAGGGGTGGAGCCTGCGGTTCAATTGGAGTCAACGCCGGGAATCTCACCGGGGGA-GACA----------------GCA-G-G   [637]
S._solfataricus             TGGCGGGGGAGCACCACAAGGGGTGGAACCTGCGGCTCAATTGGAGTCAACGCCTGGAATCTTACCGGGGGA-GACC----------------GCA-G-T   [635]
T._tenax                    TGGCGGGGGGGCACCACAAGGGGTGAAGCTTGCGGCTTAATTGGAGTCAACGCCGGAAACCTTACCCGGGGC-GACA----------------GCA-G-G   [638]
M._vannielii                TGGCGGGGGAGCACCACAACGGGTGGAGCCTGCGGTTTAATTGGATTCAACGCCGGGCATCTCACCAGGAGC-GACA----------------GCA-T-G   [638]
MB._formicicum              TGGCGGGGGAGCACCACAACGCGTGGAGCCTGCGGTTTAATTGGATTCAACGCCGGACATCTCACCAGGGGC-GACA----------------GCA-G-A   [640]
MS._hungatei                TGGCGGGGGAGCACCACAACGGGTGGAGCCTGCGGTTTAATCGGACTCAACGCCGGAAATCTCACCGGATAA-GACA----------------GCT-G-A   [613]
H._volacanii                TGGCGGGGGAGCACTACAACCGGAGGAGCCTGCGGTTTAATTGGACTCAACGCCGGACATCTCACCAGCTCC-GACT----------------ACA-GTG   [642]
HC._morrhuae                TGGCGGGGGAGCACTACAACCGGAGGAGCCTGCGGTTTAATTGGACTCAACGCCGGACATCTCTCCGGCACC-GACA----------------GTGTGCA   [644]
H.HALO                      TGGCGGGGGAGCACTACAACCGGAGGAGCCTGCGGTTTAATTGGACTCAACGCCGGACATCTCACCAGCCCC-GACA----------------GTA-GTA   [642]
H._cutirubrum               TGGCGGGGGAGCACTACAACCGGAGGAGCCTGCGGTTTAATTGGACTCAACGCCGGACATCTCACCAGCCCC-GACA----------------GTA-GTA   [642]
AN._nidulans                TGACGGGGGCCCGC-ACAAGCGGTGGAGTATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCAGGGTTTGACAT-----CC----CCCGAAT-C-T   [668]
HE.CHL                      TGACGGGGGCCCGC-ACAAGCGTTGGAGCATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACCAAGGCTTGACAT-----CC----TCTGAAT-C-C   [652]
Bc._subtilis                TGACGGGGGCCCGC-ACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACAT-----CC----TCTGACA-A-T   [691]
MY.CAP                      TGACGGGGACCCGC-ACAAGTGGTGGAGCATGTGGTTTAATTCGAAGCAACACGAAGAACCTTACCAGGGCTTGACAT-----CC----AGTGTAA-A-G   [679]
E._coli                     TGACGGGGGCCCGC-ACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACAT-----CC----ACGGAAG-T-T   [688]
MYX.XA                      TGACGGGGGCCCGC-ACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGCAGAACCTTACCTGGTCTTGACAT-----CC----TCAGAAT-C-C   [688]
P.TEST                      TGACGGGGACCCGC-ACAAGCGGTGGATGATGTGGTTTAATTCGATGCAACGCGAAAAACCTTACCCACCTTTGACAT-----GG----CAGGAAC-T-T   [688]
AG.TUM                      TGACGGGGGCCCGC-ACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGCAGAACCTTACCAGCTCTTGACAT-----TCGGGGTTTGGGC-A-G   [668]
DV.DES                      TGACGGGGGCCCGC-ACAAGCGGTGGAGTATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTAGGTTTGACAT-----CC---ACGGAACC-C-T   [687]
BA.FRG                      TGACGGGGGCCCGC-ACAAGCGGAGGAACATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCCGGGCTTAAATT-----GC----AGTGGAA-T-G   [683]
'Zea_mays_(chloroplast)'    TGACGGGGGCCCGC-ACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAAGGCGAAGAACCTTACCAGGGCTTGACAT-----GC----CGCGAAT-C-C   [666]
T.AMIT                      TGACGGGGGCCTGC-ACAAGCGGTGGAGCATGTGGTTTAATTCGATACAACGCGCAAAACCTTACCAGCCCTTGACATATGAACA----ACAAAAC-C-T   [675]

[                                    1410      1420      1430      1440      1450      1460      1470      1480      1490      1500]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                AG-GATTGACA--G-ATTGA--TAGCTCTTTCTC-GATTC--CGTGGGTGGTGGTGCATGGCCGTT-CTTAGTTGGTGGAGCGATTTGTCTGGTTAATTC   [928]
Rattus_norvegicus           AG-GATTGACA--G-GTTGA--TAGCTCTTTCTC-GATTC--CGTGGGTGGTGGTGCATGGCCGTT-CTTAGTTGGTGGAGCGATTTGTCTGGTTAATTC   [929]
Xenopus_laevis              AG-GATTGACA--G-ATTGA--TAGCTCTTTCTC-GATTC--TGTGGGTGGTGGTGCATGGCCGTT-CTTAGTTGGTGGAGCGATTTGTCTGGTTAATTC   [924]
A._salina                   AG-GATTGACA--G-ATTGA--GAGCTCTTTCTT-GATTC--AGTGGGTGGTGGTGCATGGCCGTT-CTTAGTTGGTGGAGCGATTTGTCTGGTTAATTC   [925]
S._cerevisiae               AG-GATTGACA--G-ATTGA--GAGCTCTTTCTT-GATTT--TGTGGGTGGTGGTGCATGGCCGTTTCTCAGTTGGTGGAGTGATTTGTCTGCTTAATTG   [917]
P.MICA                      AG-GATTGACA--G-ATTGA--TAGCTCTTTCTT-GATTC--TATGGGTGGTGGTGCATGGCCGTT-CTTAGTTGGTGGAGTGATTTGTCTGGTTAATTC   [916]
D.DISC                      AG-GATTGACA--G-ACTAA--AAGATCTTTCAT-GATTC--TATAAGTGGTGGTGCATGGTCGTT-CTTAGTTGGTGGAGCGATTTGTCTGGTCAATTC   [919]
T.BRUC                      AG-GATTGACA--G-ATGGA--GTGTTCTTTCTC-GATCC--CCTGAATGGTGGTGCATGGCCGCTTTT-GGTCGGTGGAGTGATTTGTTTGGTTGATTC   [1232]
E.GRAC                      GG-GATTGACA--G-ATTGA--GAGCTCTTTCTT-GATCT--TGTGGACGGTGGTGCATGGCCGCTCCTGA-TTGGTGGAGTGATTTGTCTGGTTGATTC   [1232]
Zea_mays                    AG-GATTGACA--G-ACTGA--GAGCTCTTTCTT-GATTC--TATGGGTGGTGGTGCATGGTCGTT-CTTAGTTGGTGGAGCGATTTGTCTGGTTAATTC   [921]
D._mobilis                  AT-GACGGCCA--G-GTTAA--AG-C-CTTGCCT-GACGC--GCTGAGAGGAGGTGCATGGCCGTC-GCCAGCTCGTGCTGTGAAGTGTCCGGTTAAGTC   [725]
S._solfataricus             AT-GACGGCCA--G-GCTAA--CGAC-CTTGCCT-GACTC--GCGGAGAGGAGGTGCATGGCCGTC-GCCAGCTCGTGTTGTGAAATGTCCGGTTAAGTC   [724]
T._tenax                    AT-GAAGGCCA--G-GCTAA--CGAC-CTTGCCG-GACGA--GCTGAGAGGAGGTGCATGGCCGTC-GTCAGCTCGTGCCGTGAGGTGTCCGGTTAAGTC   [727]
M._vannielii                AT-GACGGCCA--G-GTTGA--CGAC-CTTGCCT-GAAGC--GCTGAGAGGTGGTGCATGGCCATC-GTCAGCTCGTACCGCGAGGCGTCCTGTTAAGTC   [727]
MB._formicicum              AT-GATAGCCA--G-GTTGA--TGAC-CTTGCTT-GACAA--GCTGAGAGGAGGTGCATGGCCGCC-GTCAGCTCGTACCGTGAGGCGTCCTGTTAAGTC   [729]
MS._hungatei                AT-GATAGTCG--G-GATGA--AGAC-TCTACTT-GACTA--GCTGAGAGGAGGTGCATGGCCGTC-GTCAGTTCGTACTGTGAAGCATCCTGTTTAGTC   [702]
H._volacanii                AT-GACGATCA--G-GTTGA--TGAC-CTTATCA-CGACGCTGTAGAGAGGAGGTGCATGGCCGCC-GTCAGCTCGTACCGTGAGGCGTCCTGTTAAGTC   [733]
HC._morrhuae                GT-GACAGTCA--G-TCCGA--TGGG-CTTACTT-GA--GCCACTGAGAGGAGGTGCATGGCCGCC-GTCAGCTCGTACCGTGAGGCGTCCTGTTAAGTC   [733]
H.HALO                      AT-GACGGTCA--G-GTTGA--TGAC-CTTACCC-G-AGGCTACTGAGAGGAGGTGCATGGCCGCC-GTCAGCTCGTACCGTGAGGCGTCCTGTTAAGTC   [732]
H._cutirubrum               AT-GACGGTCA--G-GTTGA--TGAC-CTTACCC-GGAGGCTACTGAGAGGAGGTGCATGGCCGCC-GTCAGCTCGTACCGTGAGGCGTCCTGTTAAGTC   [733]
AN._nidulans                CT-TGGAAACG--A-GAGAG--TGCC-TTCGGGA-GCGGG--G-AGACAGGTGGTGCATGGCTGTC-GTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTC   [756]
HE.CHL                      GA-TAGAGATA--GCGGAGT--GCCC-TTCGGGGAGCAGA--G-AGACAGGTGGTGCATGGTTGTC-GTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTC   [742]
Bc._subtilis                CC-TAGAGATA--G-GACGT--CCCC-TTCGGGG-GCAGA--G-TGACAGGTGGTGCATGGTTGTC-GTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTC   [779]
MY.CAP                      CTATAGAGATA--T-AGTAG--AGGT-T-----A-ACATT--G-AGACAGGTGGTGCATGGTTGTC-GTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTC   [763]
E._coli                     TT-CAGAGATG--A-GAATG--TGCC-TTCGGGA-ACCGT--G-AGACAGGTGCTGCATGGCTGTC-GTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTC   [776]
MYX.XA                      TT-CAGAGATGAGG-GAGTG--CCCG-CAAGGGA-ACTGA--G-AGACAGGTGCTGCATGGCTGTC-GTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTC   [778]
P.TEST                      AC-CAGAGATG--G-TTTGGTGCTCG-AAAGAGA-ACCTG--C-ACACAGGTGCTGCATGGCTGTC-GTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTC   [778]
AG.TUM                      TG-GAGACATT--G-TCCTT--CAGT-TAGGCTG-GCCCC--A-GAACAGGTGCTGCATGGCTGTC-GTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTC   [756]
DV.DES                      CC-CGAAAAGG--A-GGGGT--GCCC-TTCGGGGAGCCGT--G-AGACAGGTGCTGCATGGCTGTC-GTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTC   [776]
BA.FRG                      ATGTGGAAACA--T-GTCAG--TGAG-CAATCAC--CGCT--G-TGA-AGGTGCTGCATGGTTGTC-GTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTG   [770]
'Zea_mays_(chloroplast)'    TC-TTGAAAGA--G-AGGGG--TGCC-CTCGGGA-ACGCG--G-ACACAGGTGGTGCATGGCTGTC-GTCAGCTCGTGCCGTAAGGTGTTGGGTTAAGTC   [754]
T.AMIT                      GT-CCTTAACA--G-GATGG--TACT-------G-ACTTT--C-ATACAGGTGCTGCATGGCTGTC-GTCAGCTCGTGTCGTGAGATGTTTGGTCAAGTC   [757]

[                                    1510      1520      1530      1540      1550      1560      1570      1580      1590      1600]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                CGATAACGAACGAGACTCTGGCATGCTAA-CTAGTT-AC--G--------------------------------------C-GACC----------CCCG   [975]
Rattus_norvegicus           CGATAACGAACGAGACTCTGGCATGCTAA-CTAGTT-AC--G--------------------------------------C-GACC----------CC-G   [975]
Xenopus_laevis              CGATAACGAACGAGACTCCTCCATGCTAA-CTAGTT-AC--G--------------------------------------C-GACC----------CC-C   [970]
A._salina                   CGATAACGAACGAGACTCTAGCCTGCTAA-ATAG-A-CG--ATGGATC--------------------------------C-TAGT----------GG-T   [976]
S._cerevisiae               CGATAACGAACGAGACCTTAACCTACTAA-ATAGTG-GT--G--------------------------------------C-TAGC----------AT-T   [963]
P.MICA                      CGTTAACGAACGAGACCTTAACCTGCTAA-ATAGTT-AC--A--------------------------------------CGTAAC----------TC-C   [963]
D.DISC                      CGATAACGGACGAGACCTCGACCTGCTAA-CTAGTA-GT--ATTTATTAGTCGATATAGACGATAGCTTTTCTGGGGTTTG-GAAT----------GA-T   [1003]
T.BRUC                      CGTCAACGGACGAGATCC-AAGCTGCCCA-GTAG---GT--G--------------------------------------C-CGGG----------AT-T   [1275]
E.GRAC                      CGATAACGAGTGAGACATCTGCCTCCCACTAGCCTG-AG--G--------------------------------------C-TCGC----------AT-T   [1279]
Zea_mays                    CGTTAACGAACGAGACCTCAGCCTGCTAA-CTAGCT-AT--G--------------------------------------C-GGAG----------CC-A   [967]
D._mobilis                  CGGAAACGAGCGAGACCCCCACCC-CTAG-TTGCTA-CC--C-----------------------------------------GGG----------GC-T   [768]
S._solfataricus             CGGCAACGAGCGAGACCCCCACCC-CTAG-TTGGTA-TT--C-----------------------------------------TGG----------AC-T   [767]
T._tenax                    CGGCAACGAGCGAGACCCCCACCC-CTAG-TTGCTA-CC--C-----------------------------------------CGC----------TC-T   [770]
M._vannielii                AGGTAACGAGCGAGACCCGTGCCC-TATG-TTGCGA-CT--A-----------------------------------------CTT----------TC-T   [770]
MB._formicicum              AGGCAACGAGCGAGACCCACGCCC-TTAG-TTACCA-GC--G-----------------------------------------GAT----------CC-T   [772]
MS._hungatei                AGGCAACGAGCGAGACCCACGCGA-GCAG-TTGCCAGCT--T-----------------------------------------GAC----------CT-T   [746]
H._volacanii                AGGCAACGAGCGAGACCCGCACTT-CTAA-TTGCCA-GCAGC-----------------------------------------CAG----------T--T   [777]
HC._morrhuae                AGGCAACGAGCGAGACCCGCGTCC-CTAA-TTGCCA-GCAGC-----------------------------------------CAG----------CC-T   [778]
H.HALO                      AGGCAACGAGCGAGACCCGCACTC-CTAA-TTGCCA-GCGGT-----------------------------------------TAC----------CC-T   [777]
H._cutirubrum               AGGCAACGAGCGAGACCCGCACTC-CTAA-TTGCCA-GCAGT-----------------------------------------TAC----------CC-T   [778]
AN._nidulans                CCGCAACGAGCGCAACCCACGTTT-TTAG-TTGCCA-TC--A-----------------------------------------TTC----------AG-T   [799]
HE.CHL                      CCGCAACGAGCGCAACCCTTATCC-CTAG-TTGCCA-GCG-A-----------------------------------------GAG----------AG-T   [786]
Bc._subtilis                CCGCAACGAGCGCAACCCTTGATC-TTAG-TTGCCA-GC--A-----------------------------------------TTC----------AG-T   [822]
MY.CAP                      CCGCAACGAACGCAACCCTTGTCG-TTAG-TTACTA-AC--A-----------------------------------------TTA----------AG-T   [806]
E._coli                     CCGCAACGAGCGCAACCCTTATCC-TTTG-TTGCCA-GC--G-G---------------------------------------TCC----------GG-C   [820]
MYX.XA                      CCGCAACGAGCGCAACCCTCGCCT-TTAG-TTGCCA-----------------------------------------------CGC----------AA-G   [818]
P.TEST                      CCGCAACGAGCGCAACCCTTGCCA-TTAG-TTGCTA--C--A-----------------------------------------TTC----------AG-T   [820]
AG.TUM                      CCGCAACGAGCGCAACCCTCGCCC-TTAG-TTGCCA-GC--A-----------------------------------------TTT----------AG-T   [799]
DV.DES                      CCGCAACGAGCGCAACCCCTATGG-ATAG-TTGCCA-GC--AAG---------------------------------------TAA----------TG-T   [821]
BA.FRG                      CCATAACGAGCGCAACCCTTATCT-TTAG-TTACTA-AC--AGG---------------------------------------TTA----------TG-C   [815]
'Zea_mays_(chloroplast)'    TCGCAACGAGCGCAACCCTCGTGT-TTAG-TTGCCA-CT--A------------------------------------------TG----------AG-T   [796]
T.AMIT                      CTATAACGAGCGAAACCCTCGTTT-TGTG-TTGCTG-AG--A-C---------------------------------------ATGCGC????GTGCG-T   [811]

[                                    1610      1620      1630      1640      1650      1660      1670      1680      1690      1700]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                AGCGGTCGGCGT---------------------------------------------------------------------------CCCCC--------   [992]
Rattus_norvegicus           AGCGCTCGGCGT---------------------------------------------------------------------------CCCCC--------   [992]
Xenopus_laevis              GGCGGTCGGCGT---------------------------------------------------------------------------CCA----------   [985]
A._salina                   GG-----ATCGC---------------------------------------------------------------------------T------------   [984]
S._cerevisiae               TG---CTGGTTA---------------------------------------------------------------------------TCC----------   [975]
P.MICA                      GG---TTACGTG---------------------------------------------------------------------------GGC----------   [975]
D.DISC                      TTCGGTCATCTC---------------------------------------------------------------------------CTGCTTCAAGGAG   [1028]
T.BRUC                      GT---CCACACA----------GGACAGCAGTCCCTCCGGC-----GGGGATTTTTTCCCCAACG-GTGGTCGTCATCCTTCTTTTTACA----------   [1346]
E.GRAC                      TG---GTAGGGTTCGGCTGCTCGG-TGGCAGCCCC-CTGGCAACAGGGGGAGATGTACCGGTGCATGCTCCCGAGAGCCTCCAGT--TCA----------   [1362]
Zea_mays                    TC---CCGCTAG---------------------------------------------------------------------------TTA----------   [979]
D._mobilis                  AC---GGCTCCG---------------------------------------------------------------------------GGG----------   [780]
S._solfataricus             CC---CGGTCCA---------------------------------------------------------------------------GAA----------   [779]
T._tenax                    TC---GGGGCGG---------------------------------------------------------------------------GGG----------   [782]
M._vannielii                CC---GGAA-GG---------------------------------------------------------------------------TAA----------   [781]
MB._formicicum              TC---GGGATGC---------------------------------------------------------------------------CGG----------   [784]
MS._hungatei                CG---GGTT-GA---------------------------------------------------------------------------TGG----------   [757]
H._volacanii                TC---GACTGGC---------------------------------------------------------------------------TGG----------   [789]
HC._morrhuae                TG---TGCTGGC---------------------------------------------------------------------------TGG----------   [790]
H.HALO                      TT---GGGTAGC---------------------------------------------------------------------------TGG----------   [789]
H._cutirubrum               TT---GGGTAGC---------------------------------------------------------------------------TGG----------   [790]
AN._nidulans                T---------------------------------------------------------------------------------------GG----------   [802]
HE.CHL                      C---------------------------------------------------------------------------------------GG----------   [789]
Bc._subtilis                T---------------------------------------------------------------------------------------GG----------   [825]
MY.CAP                      T---------------------------------------------------------------------------------------GA----------   [809]
E._coli                     C---------------------------------------------------------------------------------------GG----------   [823]
MYX.XA                      T---------------------------------------------------------------------------------------GG----------   [821]
P.TEST                      T---------------------------------------------------------------------------------------GA----------   [823]
AG.TUM                      T---------------------------------------------------------------------------------------GG----------   [802]
DV.DES                      T---------------------------------------------------------------------------------------GG----------   [824]
BA.FRG                      T---------------------------------------------------------------------------------------GA----------   [818]
'Zea_mays_(chloroplast)'    T---------------------------------------------------------------------------------------TG----------   [799]
T.AMIT                      G---------------------------------------------------------------------------------------CC----------   [814]

[                                    1710      1720      1730      1740      1750      1760      1770      1780      1790      1800]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                -------------------------------AA----CTTCTTAGAGGGACAAG---TGG--CG-TT-CAGCCA---CCCGAGATTGA-GCAATAACAGG   [1046]
Rattus_norvegicus           -------------------------------AA----CTTCTTAGAGGGACAAG---TGG--CG-TT-CAGCCA---CC-GAGATTGA-GCAATAACAGG   [1045]
Xenopus_laevis              --------------------------------A----CTTCTTAGAGGGACAAG---TGG--CG-TT-CAGCCA--CAC-GAGATCGA-GCAATAACAGG   [1038]
A._salina                   -------------------------------------CTTCTTAGAGGGACAAG---TGG--CG-TC-TAGCCA--TAT-GAGAGTGA-GCAATAACAGG   [1036]
S._cerevisiae               --------------------------------A----CTTCTTAGAGGGACTAT---CGG--TT-TC-AAGCCG-ATGG-AAGTTTGAGGCAATAACAGG   [1030]
P.MICA                      --------------------------------A----ACTTTTAGAGGGACTTT---GCG--TG-TC-TAACGC-AAGG-AAGTTTGAGGCAATAACAGG   [1030]
D.DISC                      TGTGTAGTCTGACTCGATAGGTACGAATTAAAA----CTTCTTAGAGGGACTAC---CTG--CC-TC-AAGCAG-GCGG-AAGTCCGAGGCAATAACAGG   [1115]
T.BRUC                      --------------------------------GGCCCCTTCTCTGCGGGATTCC---TTGCTTT-TC-GCGCAA-GGTG-AGATTTTGGGCAACAGCAGG   [1407]
E.GRAC                      --------------------------------G----CTTCTCTGAGGTGCTGTGTCCGC--CA-CA-AAGGGC-ATGC-ATGCTAGAGCCAACAGCAGG   [1420]
Zea_mays                    --------------------------------G----CTTCTTAGAGGGACTAT---GGC--CG-TT-TAGGCC-G-CG-AAGTTTGAGGCAATAACAGG   [1033]
D._mobilis                  -------------------------------------CACACTAGGGGGACTGC---CGC--CG-TTTAAGGCG-GAGG-AAGGAGGGGGCCACGGCAGG   [835]
S._solfataricus             --------------------------------C----CACACTAGGGGGACTGC---CGG--CG-T--AAGCCG-GAGG-AAGGAGGGGGCCACGGCAGG   [833]
T._tenax                    --------------------------------G----CACACTAGGGGGACTGC---CGG--CG-T--AAGCCG-GAGG-AAGGAGGGGGCGACGGCAGG   [836]
M._vannielii                --------------------------------G----CACTCATAGGGGACCGC---TAG--CGCT--AAGCTA-GAGG-AAGGAGCGGGCAACGATAGG   [836]
MB._formicicum              --------------------------------G----CACACTAAGGGGACCGC---CAG--TGAT--AAACTG-GAGG-AAGGAGTGGACGACGGTAGG   [839]
MS._hungatei                --------------------------------G----GACACTGCTCGGACCGC---CTC--TGCT--AAAGGG-GAGG-AAGGAATGGGCAACGGTAGG   [812]
H._volacanii                --------------------------------G----TACATTAGAAGGACTGC---CGC--TG-CT-AAAGCG-GAGG-AAGGAACGGGCAACGGTAGG   [844]
HC._morrhuae                --------------------------------G----TACATTAGGGAGACTGC---CGT--CG-CT-AAGACG-GAGG-AAGGAACGGGCAACGGTAGG   [845]
H.HALO                      --------------------------------G----TACATTAGGTGGACTGC---CGC--TG-CC-AAAGCG-GAGG-AAGGAACGGGCAACGGTAGG   [844]
H._cutirubrum               --------------------------------G----TACATTAGGTGGACTGC---CGC--TG-CC-AAAGCG-GAGG-AAGGAACGGGCAACGGTAGG   [845]
AN._nidulans                --------------------------------G----CACTCTAGAGAAACTGC---CGG--TGAC--AAACCG-GAGG-AAGGTGTGGACGACGTCAAG   [857]
HE.CHL                      --------------------------------G----GACTCTAGGGAGACTGC---CCG--GGAC--GACCGG-GAGG-AAGGCGGGGATGACGTCAAA   [844]
Bc._subtilis                --------------------------------G----CACTCTAAGGTGACTGC---CGG--TGAC--AAACCG-GAGG-AAGGTGGGGATGACGTCAAA   [880]
MY.CAP                      --------------------------------G----AACTCTAACGAGACTGC---TAG--TG-T--AAGCTA-GAGG-AAGGTGGGGATGACGTCAAA   [863]
E._coli                     --------------------------------G----AACTCAAAGGAGACTGC---CAG--TGAT--AAACTG-GAGG-AAGGTGGGGATGACGTCAAG   [878]
MYX.XA                      --------------------------------A----T-CTCTAGAGGGACTGC---CGG--TGTT--AAACCG-GAGG-AAGGTGGGGATGACGTCAAG   [875]
P.TEST                      --------------------------------G----CACTCTAATGGGACTGC---CGG--TGAC--AAACCG-GAGG-AAGGTGGGGATGACGTCAAG   [878]
AG.TUM                      --------------------------------G----CACTCTAAGGGGACTGC---CGG--TGAT--AAGCCGAGAGG-AAGGTGGGGATGACGTCAAG   [858]
DV.DES                      --------------------------------G----CACTCTATTCAGACTGC---CCG--GGTT--AACCGG-GAGG-AAGGTGGGGACGACGTCAAG   [879]
BA.FRG                      --------------------------------G----GACTCTAGAGAGACTGC---CGT--CGTA--AGATGT-GAGG-AAGGTGGGGATGACGTCAAA   [873]
'Zea_mays_(chloroplast)'    --------------------------------G----AACCCTGAACAGACCGC---CGG--TGTT--AAGCCG-GAGG-AAGGAGAGGATGAGGCCAAG   [854]
T.AMIT                      --------------------------------G----CACTCACGAGGGACTGC---CAG--TGAG--ATACTG-GAGG-AAGGTGGGGATGACGTCAAG   [869]

[                                    1810      1820      1830      1840      1850      1860      1870      1880      1890      1900]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                TCTGTGATGCCCTTAGA-TGTCCGGGGCTGCACGCGCGCTACACTGACTGGCTCAGCGTG-TGCCTA------------------------CCCTACGCC   [1120]
Rattus_norvegicus           TCTGTGATGCCCTTAGA-TGTCCGGGGCTGCACGCGCGCTACACTGACTGGCTCAGCGTG-TGCCTA------------------------CCCTACGCC   [1119]
Xenopus_laevis              TCTGTGATGCCCTTAGA-TGTCCGGGGCTGCACGCGCGCTACACTGAACGGATCAGCGTG-TGTCTA------------------------CCCTGCGCC   [1112]
A._salina                   TCTGTGATGCCCTTAGA-TGTCCTGGGCCGCACGCGCGCTACACTGGAAGAATCAGCGCG-T--CC-------------------------TCCCTGTCC   [1107]
S._cerevisiae               TCTGTGATGCCCTTAGAACGTTCTGGGCCGCACGCGCGCTACACTGACGGAGCCAGCGAG-T--CTA------------------------ACCTTGGCC   [1103]
P.MICA                      TCTGTGATGCCCTTAGA-TGTTCTGGGCTGCACGCGCGCTACACTGATGCGTTCAACGAG-T--TTA----------------------TGCACTTGCCC   [1104]
D.DISC                      TCTGTGATGCCCTTAGA-TACCTTGGGCCGCACGCGCGCTACAATGTAGGAAACAAAAAG-G--CT--------------------------CCTGGTCC   [1185]
T.BRUC                      TCTGTGATGCTCCTCAA-TGTTCTGGGCGACACGCGCACTACAATGTCAGTGAGAACAAG-AGTCCGAGCGGCACTTCACAATGTCGCTCCCGCTTGATC   [1505]
E.GRAC                      TCTGTGATGCTCCCAGA-TGTCCTGGGCCGCACGCGCACTACATTGTCACAGTGAAGGTG-T--CGA-------CATGCCCACTCCGGTGGGCCCTGGCC   [1509]
Zea_mays                    TCTGTGATGCCCTTAGA-TGTTCTGGGCCGCACGCGCGCTACACTGATGTATCCAACGAG-TATATA------------------------GCCTTGGCC   [1107]
D._mobilis                  TCAGC-ATGCCCCGAAC--CCCCCGGGCTACACGCGGGCTACAATGGCGGGGACAGCGGGAT--CCG------------------------ACC----CC   [902]
S._solfataricus             TCAGC-ATGCCCCGAAA--CTCCCGGGCCGCACGCGGGTTACAATGGCAGGGACAACGGGAT--GCT------------------------ACC----TC   [900]
T._tenax                    TCAGT-ATGCCCCGAAA--CCCCGGGGCTGCACGCGAGCTGCAATGGCGGGGACAGCGGGAT--CCG------------------------ACC----CC   [903]
M._vannielii                TCCGC-ATGCCCCGAAT--CTCCTGGGCTACACGCGGGCTACAATGGCTAGGACAATGGGCT--GCT------------------------ACC----CT   [903]
MB._formicicum              TCCGT-ATGCCCCGAAT--CCCCTGGGCTACACGCGGGCTACAATGGTTAGGACAATGGGTT--CCG------------------------ACA----CT   [906]
MS._hungatei                TCAGC-ATGCCCCGAAT--TATCCGGGCTACACGCGGGCTACAATGGACAGGACAATGGGTT--TCG------------------------ACA----CC   [879]
H._volacanii                TCAGT-ATGCCCCGAAT--GAGCTGGGCTACACGCGGGCTACAATGGTCGAGACAATGGGTT--GCT------------------------ATC----TC   [911]
HC._morrhuae                TCAGT-ATGCCCCGAAT--GTGCCGGGCGACACGCGGGCTACAATGGCCGAGACAGTGGGAC--GCT------------------------ACC----CC   [912]
H.HALO                      TCAGT-ATGCCCCGAAT--GGGCTGGGCAACACGCGGGCTACAATGGTCGAGACAATGGGAA--GCC------------------------ACT----CC   [911]
H._cutirubrum               TCAGT-ATGCCCCGAAT--GGGCTGGGCAACACGCGGGCTACAATGGTCGAGACAATGGGAA--GCC------------------------ACT----CC   [912]
AN._nidulans                TCATC-ATGCCCCTTAC--ATCCTGGGCTACACACGTACTACAATGCTCCGGACAGCGAGAC--GCG------------------------AAG----CC   [924]
HE.CHL                      TCATC-ATGCCCCTTAT--GTCTTGGGCTACACACGTGCTACAATGGGCGGTACAAACCGAA--GCG------------------------AAG----CC   [911]
Bc._subtilis                TCATC-ATGCCCCTTAT--GACCTGGGCTACACACGTGCTACAATGGACAGAACAAAGGGCA--GCG------------------------AAA----CC   [947]
MY.CAP                      TCATC-ATGCCCCTTAT--GTCCTGGGCTACACACGTGCTACAATGGCTGGTACAAAGAGTT--GCA------------------------ATC----CT   [930]
E._coli                     TCATC-ATGGCCCTTAC--GACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAA--GCG------------------------ACC----TC   [945]
MYX.XA                      TCCTC-ATGGCCTTTAT--GACCAGGGCTACACACGTGCTACAATGGCCGGTACAGAGCGTT--GCC------------------------AAC----CC   [942]
P.TEST                      TCCTC-ATGGCCCTTAT--AGGTGGGGCTACACACGTCATACAATGGCTGGTACAAAGGGTT--GCC------------------------AAC----CC   [945]
AG.TUM                      TCCTC-ATGGCCCTTAC--GGGCTGGGCTACACACGTGCTACAATGGTGGTGACAGTGGGCA--GCG------------------------AGA----CA   [925]
DV.DES                      TCATC-ATGGCCCTTAC--GCCTAGGGCTACACACGTACTACAATGGCGCGCACAAAGGGGA--GCG------------------------AGA----CC   [946]
BA.FRG                      TCAGC-ACGGCCCTTAC--GTCCGGGGCTACACACGTGTTACAATGGGGGGTACAGAAGGCA--GCT------------------------AGC----GG   [940]
'Zea_mays_(chloroplast)'    TCATC-ATGCCCCTTAT--GCCCTGGGCGACACACGTGCTACAATGGGCGGGACAAAGGGTC--GCG------------------------ATC----TC   [921]
T.AMIT                      TCCGC-ATGGCCCTTAT--GGGCTGGGCCACACACGTGCTACAATGGCAATGACAATGGGAA--GCA------------------------AGG----CT   [936]

[                                    1910      1920      1930      1940      1950      1960      1970      1980      1990      2000]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                -GGCAGGCGCGGG-TAACCCGTTGAA-CCCCATTCGTGATGGGGATCGGGGATTGCAATTATTCCCCAT-GAACGAGGAATTCCCAGTAAGTGCGGGTCA   [1216]
Rattus_norvegicus           -GGCAGGCGCGGG-TAACCCGTTGAA-CCCCATTCGTGATGGGGATCGGGGATTGCAATTATTCCCCAT-GAACGAGGAATTCCCAGTAAGTGCGGGTCA   [1215]
Xenopus_laevis              -GACAGGTGCGGG-TAACCCGCTGAA-CCCCGTTCGTGATAGGGATCGGGGATTGCAATTATTTCCCAT-GAACGAGGAATTCCCAGTAAGTGCGGGTCA   [1208]
A._salina                   -GAGAGGACCGGG-TAACC-GCTGAA-CCTCTTCCGTGGTTGGGATTGGGGACTGCAAGGATC-CCCAT-GAACCAGGAATCCCTAGTAGGCGCAAGTCA   [1201]
S._cerevisiae               -GAGAGGTCTTGG-TAATCTTGTGAA-ACTCCGTCGTGCTGGGGATAGAGCATTGTAATTATTGCTCTT-CAACGAGGAATTCCTAGTAAGCGCAAGTCA   [1199]
P.MICA                      -GATAGGGTTTGGGTAATCTTTTTAA-ATCGCATCGTGATGGGGATAGATTATTGCAATTATTAATCTT-CAACGAGGAATTCCTAGTAAGCGCGAGTCA   [1201]
D.DISC                      -GGAAGGATTGGG-TAATCATTTGAA-TTTCCTACGTAACTGGGCTTGATCTTTGTAATTATTGATCAT-AAACGAGGAATTCCTTGTAAGCGTAAGTCA   [1281]
T.BRUC                      -AAAAGAGCGGGG-AAACCACGGAATCACGTAGACCCACTTGGGACCGAGTATTGCAATTATTGGTCGCGCAACGAGGAATGTCTCGTAGGCGCAGCTCA   [1603]
E.GRAC                      TGAAGAGGCTGGG-AAATCCTGCAAG-CCTGTGACGTACTGGGGATAGATGGTTGCAACTGTCTGCCTT-GAACGTGGAATGCCTAGTATGCCTGGGTCA   [1606]
Zea_mays                    -GACAGGC-CGGT-AATCTTGGGAAA-TTTCATGCGTGATGGGGATAGATCATTGCAATTGTTGGTCTT-CAACGAGGAATGCCTAGTAAGCGCGAGTCA   [1202]
D._mobilis                  -GAAAGGGGAGGC-GAATCCCTC-AA-ACCCCGCCGTGGTTGGGATCGAGGGCTGCAACTCGCCCTCGT-GAACGAGGAATCCCTAGTAACCGCGCGTCA   [997]
S._solfataricus             -GAAAGGGGGAGC-CAATCCTT--AA-ACCCTGCCGCAGTTGGGATCGAGGGCTGAAACCCGCCCTCGT-GAACGAGGAATCCCTAGTAACCGCGGGTCA   [994]
T._tenax                    -GAAAGGGGGAGG-CAATCCCGT-AA-ACCCCGCCCCAGTAGGGATCGAGGGCTGCAACTCGCCCTCGT-GAACGTGGAATCCCTAGTAACCGCGTGTCA   [998]
M._vannielii                -GAAAAGGGACGC-GAATCTCCG-AA-ACCTAGTCGTAGTTCGGATCGTGGGCTGTAACTCGCCCACGT-GAAGCTGGAATCCGTAGTAATCGCAGTTCA   [998]
MB._formicicum              -GAAAGGTGGAGG-TAATCTCCT-AA-ACCTGGCCTTAGTTCGGATTGAGGGCTGTAACTCGCCCTCAT-GAAGCTGGAATGCGTAGTAATCGCGTGTCA   [1001]
MS._hungatei                -GAGAGGTGAGGA-TAATCTCCT-AA-ACCTGTCCGAAGTTCGGATTGCGGGTTGTAACTCACCCGCAT-GAAGCTGGAATCCGTAGTAATCGCGTTTCA   [974]
H._volacanii                -GAAAGAGAACGC-TAATCTCCT-AA-ACTCGATCGTAGTTCGGATTGAGGGCTGAAACTCGCCCTCAT-GAAGCTGGATTCGGTAGTAATCGCATTTCA   [1006]
HC._morrhuae                -GAGAGGGGACGC-TAATCTCCT-AA-CCTCGGTCGTAGTTCGGATTGCGGGTTGAAACCCACCCGCAT-GAAGCTGGATTCGGTAGTAATCGCATTTCA   [1007]
H.HALO                      -GAGAGGAGGCGC-TAATCTCCT-AA-ACTCGATCGTAGTTCGGATTGAGGGCTGAAACTCGCCCTCAT-GAAGCTGGATTCGGTAGTAATCGCGTGTCA   [1006]
H._cutirubrum               -GAGAGGAGGCGC-TAATCTCCT-AA-ACTCGATCGTAGTTCGGATTGAGGGCTGAAACTCGCCCTCAT-GAAGCTGGATTCGGTAGTAATCGCGTGTCA   [1007]
AN._nidulans                -GCGAGGTGAAGC-AAATCTCCC-AA-ACCGGGGCTCAGTTCAGATTGCAGGCTGCAACTCGCCTGCAT-GAAGGCGGAATCGCTAGTAATCGCAGGTCA   [1019]
HE.CHL                      -GAGAGGTGGAGC-GAACCGGAG-AA-AGCCGTTCCCAGTTCGGATTGCTCTCTGCAACTCGAGAGCAT-GAAGGCGGAATCGCTAGTAATCGCGGGTCA   [1006]
Bc._subtilis                -GCGAGGTTAAGC-CAATCCCAC-AA-ATCTGTTCTCAGTTCGGATCGCAGTCTGCAACTCGACTGCGT-GAAGCTGGAATCGCTAGTAATCGCGGATCA   [1042]
MY.CAP                      -GTGAAGGGGAGC-TAATCTCAA-AA-AACCAGTCTCAGTTCGGATTGAAGTCTGCAACTCGACTTCAT-GAAGCCGGAATCACTAGTAATCGCGAATCA   [1025]
E._coli                     -GCGAGAGCAAGC-GGACCTCAT-AA-AGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCAT-GAAGTCGGAATCGCTAGTAATCGTGGATCA   [1040]
MYX.XA                      -GCGAGGGGGAGC-TAATCGCAT-AA-AACCGGTCTCAGTTCAGATTGGAGTCTGCAACTCGACTCCAT-GAAGGAGGAATCGCTAGTAATCGCAGATCA   [1037]
P.TEST                      -GCGAGGGGGAGC-TAATCCCAT-AA-AGCCAGTCGTAGTCCGGATCGCAGTCTGCAACTCGACTGCGT-GAAGTCGGAATCGCTAGTAATCGTGGATCA   [1040]
AG.TUM                      -GCGATGTCGAGC-TAATCTCCA-AA-AGCCAT-CTCAGTTCGGATTGCACTCTGCAACTCGAGTGCAT-GAAGTTGGAATCGCTAGTAATCGCAGATCA   [1019]
DV.DES                      -GCGAGGTGGAGC-CAATCCCAA-AA-AACGCGTCCCAGTCCGGATTGCAGTCTGCAACTCGACTGCAT-GAAGTTGGAATCGCTAGTAATTCGAGATCA   [1041]
BA.FRG                      -GTGACCGTATGC-TAATCCCA--AA-ATCCTCTCTCAGTTCGGATCGAAGTCTGCAACCCGACTTCGT-GAAGCTGGATTCGCTAGTAATCGCGCATCA   [1034]
'Zea_mays_(chloroplast)'    -GCGAGGGTGAGC-TAACTCCAA-AA-ACCCGTCCTCAGTTCGGATTGCAGGCTGCAACTCGCCTGCAT-GAAGCAGGAATCGCTAGTAATCGCCGGTCA   [1016]
T.AMIT                      -GTAAGGCGGAGC-GAATC-CGG-AA-AGATTGCCTCAGTTCGGATTGTTCTCTGCAACTCGGGAACAT-GAAGTTGAAATCGCTAGTAATCGCGGATCA   [1030]

[                                    2010      2020      2030      2040      2050      2060      2070      2080      2090      2100]
[                                    .         .         .         .         .         .         .         .         .         .]

Homo_sapiens                TA-AGCTTGCGTTGATTAAGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGGATGGTTTAGCTTGACTATCTAGAGGAAGTAAAAGTCG   [1315]
Rattus_norvegicus           TA-AGCTTGCGTTGATTAAGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGGATGGTTTAGCTTGACTATCTAGAGGAAGTAAAAGTCG   [1314]
Xenopus_laevis              TA-AGCTCGCGTTGATTAAGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGGATGGTTTAGCTTGACTATCTAGAGGAAGTAAAAGTCG   [1307]
A._salina                   TT-AGCTTGCGTCGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGCTTGATCCTTTAGAGGAAGTAAAAGTCG   [1300]
S._cerevisiae               TC-AGCTTGCGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTAGTACCGATTGAATGGCTTAGCTTGGTCATTTGGAGGAACTAAAAGTCG   [1298]
P.MICA                      TC-AGCTCGTGCTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGATTGAGTG-----ACCTTATCACTTAGAGGAAGGAGAAGTCG   [1295]
D.DISC                      TT-ACCTTATGCTGAATATGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGATCGAATGATACGGTCTCATTGTTTAGAGGAAGGAGAAGTCG   [1380]
T.BRUC                      TC-AAACTGTGCCGATTACGTCCCTGCCATTTGTACACACCGCCCGTCGTTGTTTCCGAT--GATGGTGCAAATTGCTTCAATAGAGGAAGCAAAAGTCG   [1700]
E.GRAC                      TC-AGCCCAGACCGATTGTGTCCCTGCCATTTGTACACACCGCCCGTCGTTGCTACCGATGG--TGGCTGGAGTCCAGCCACTAGAGGAAGCAAAAGTCG   [1703]
Zea_mays                    TC-AGCTCGCGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGATTGAATGGTCCGGCCTTATCATTTAGAGGAAGGAGAAGTCG   [1301]
D._mobilis                  AC-ATCGCGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCGCTCCACCCGAGGGGAGG-GGGAGCTCCCCCTCCCTGAGGGGGGAGAAGTCG   [1095]
S._solfataricus             AC-AACCCGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCGCTCCACCCGAGCGCGAA-AGGGGCTCCTTTCCCGCGAGGGGGGAGAAGTCG   [1092]
T._tenax                    CC-AACGCGCGGTGAATACGTCCCTGCCCCTTGCACACACCGCCCGTCGCACCACCCGAGGGAGTT-CTCTGCAGAGAACTCCCGAGGGGGGTGAAGTCG   [1096]
M._vannielii                TA-ATACTGCGGTGAATGTGTCCCTGCTCCTTGCACACACCGCCCGTCACACCACCCGAGTTGGGT-TCAGGCCTGGGCTCAGCGAGGGGGGTGAAGTCG   [1096]
MB._formicicum              TA-ACCGCGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCACGCCACCCAAAAAGGGT-TTGGATCTAGGTTCTTTGAGGAGGGCGAAGTCG   [1099]
MS._hungatei                AC-ATAGCGCGGTGAATATGTCCCTGCTCCTTGCACACACCGCCCGTCAAACCACCCGAGTGAGGT-CTTGATCTGGGTTTTGCAAGGGGGGTTAAGTCG   [1072]
H._volacanii                AT-AGAGTGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCAAAGCACCCGAGTGAGGT-CCGGA-------TTCGCAAGGGGGCTTAAGTCG   [1097]
HC._morrhuae                GA-AGAGTGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCAAATCACCCGAGTGAGGT-CCGGA-------TTCGCAAGGGGGATTAAGTCG   [1098]
H.HALO                      GC-AGCGCGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCAAATCACCCGAGTGGGGT-TCGGA-------TCCGCAAGGGGGATTAAGTCG   [1097]
H._cutirubrum               GC-AGCGCGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCAAATCACCCGAGTGGGGT-TCGGA-------TCCGCAAGGGGGATTAAGTCG   [1098]
AN._nidulans                GC-ATACTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGAAGTTGGCC-ATGCCGGTAGGGCTGATGACTGGGGTGAAGTCG   [1117]
HE.CHL                      GC-ATACCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAAAGTCGGCA-ACACCGGTGGGGTCGATGATTGGGGTGAAGTCG   [1104]
Bc._subtilis                GC-ATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTA-ACACCGGTGGGACAGATGATTGGGGTGAAGTCG   [1140]
MY.CAP                      GCTATGTCGCGGTGAATACGTTCTCGGGTCTTGTACACACCGCCCGTCACACCATGAGAGTTGGTA-ATACCGGTAGGACTAGCGATTGGGGTGAAGTCG   [1124]
E._coli                     GA-ATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTT-GCAAATTTGTGATTCATGACTGGGGTGAAGTCG   [1138]
MYX.XA                      GC-ACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTCGATT-GCTCCGGAGTGGTCGGTAACTGGGGTGAAGTCG   [1135]
P.TEST                      GA-ATGTCACGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGCGGGTC-TCGCCGGCGGGGTTCGTGACTGGGGTGAAGTCG   [1138]
AG.TUM                      GC-ATGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTTGGTT-TTACCGGTAGGGTCAGCGACTGGGGTGAAGTCG   [1117]
DV.DES                      GC-ATGCTCGGGTGAATGCGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAAAGTCGGTT-TTACCGGTAGGGCCGATGATTGGGGTGAAGTCG   [1139]
BA.FRG                      GCCACGGCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCAAGCCATGGGAGCCGGGG-GTACCGGTAAAACTGGTGACTGGGGCTAAGTCG   [1133]
'Zea_mays_(chloroplast)'    GCCATACGGCGGCGAATCCGTTCCCGGGCCTTGTACACACCGCCCGTCACACTATAGGAGCTGGCC-AGGTTGGCTAGGCTTGCGACTGGAGTGAAGTCG   [1115]
T.AMIT                      GC-ATGCCGCGGTGAATATGTACCCGGGCCCTGTACACACCGCCCGTCACACCCTGGGAATTGGTT-TCGCCGGTGGGGTCTTCGACTGGGGTGAAGTCG   [1128]

[                                    2110      2120      2130      2140    ]
[                                    .         .         .         .       ]

Homo_sapiens                TAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTA-------   [1355]
Rattus_norvegicus           TAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTA-------   [1354]
Xenopus_laevis              TAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTA-------   [1347]
A._salina                   TAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTA-------   [1340]
S._cerevisiae               TAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTA-------   [1338]
P.MICA                      TAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTC-------   [1335]
D.DISC                      TAACAAGGTATCCGTAGGTGAACCTGCGGATGGATCATTTT------   [1421]
T.BRUC                      TAACAAGGTAGCTGTAGGTGAACCTGCAGCTGGATCATTT-------   [1740]
E.GRAC                      TAACAAGGTTGCTGTAGGTGAACCTGCAGCAGGATCATTG-------   [1743]
Zea_mays                    TAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTG-------   [1341]
D._mobilis                  TAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCT----   [1138]
S._solfataricus             TAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCA-----   [1134]
T._tenax                    TAACAAGGTAGCCGTAGGGGAACCTGCTTCTGGATCACCTCC-----   [1138]
M._vannielii                TAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCC-----   [1138]
MB._formicicum              TAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCT----   [1142]
MS._hungatei                TAACAAGGTAGCCGTAGGGGAATCTGCGGCTGGATCACCTCCT----   [1115]
H._volacanii                TAACAAGGTAGCCGTAGGGGAATCTGCGGCTGGATCACCTCCT----   [1140]
HC._morrhuae                TAACAAGGTAGCCGTAGGGGAATCTGCGGCTGGATCACCTCCT----   [1141]
H.HALO                      TAACAAGGTAGCCGTAGGGGAATCTGCGGCTGGATCACCTCCT----   [1140]
H._cutirubrum               TAACAAGGTAGCCGTAGGGGAATCTGCGGCTGGATCACCTCCT----   [1141]
AN._nidulans                TAACAAGGTAGCCGTACCGGAAGGTGTGGCTGGATCACCTCCTTT--   [1162]
HE.CHL                      TAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCT   [1151]
Bc._subtilis                TAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCT   [1187]
MY.CAP                      TAACAAGGTATCCGTACGGGAACGTGCGGATGGATCACCTCCTTTCT   [1171]
E._coli                     TAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA--   [1183]
MYX.XA                      TAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCTTTCT   [1182]
P.TEST                      TAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCT   [1185]
AG.TUM                      TAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCTTTCT   [1164]
DV.DES                      TAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCTTT--   [1184]
BA.FRG                      TAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGAACACCTCCTTTCT   [1180]
'Zea_mays_(chloroplast)'    TAACAAGGTAGCCGTACTGGAAGGTGCGGCTGGATCACCTCCTTT--   [1160]
T.AMIT                      TAACAAGGTAGCCGTAGGGGAACCTGTGGCTGGATTGAATCC-----   [1170]
;
END;


BEGIN CODONS;
CODESET * UNTITLED = Universal: all ;
END;

BEGIN ASSUMPTIONS;
	OPTIONS  DEFTYPE=unord PolyTcount=MINSTEPS ;
END; 

BEGIN TREES; 

	TRANSLATE
		1	Homo_sapiens,
		2	Rattus_norvegicus,
		3	Xenopus_laevis,
		4	A._salina,
		5	S._cerevisiae,
		6	P.MICA,
		7	D.DISC,
		8	T.BRUC,
		9	E.GRAC,
		10	Zea_mays,
		11	D._mobilis,
		12	S._solfataricus,
		13	T._tenax,
		14	M._vannielii,
		15	MB._formicicum,
		16	MS._hungatei,
		17	H._volacanii,
		18	HC._morrhuae,
		19	H.HALO,
		20	H._cutirubrum,
		21	AN._nidulans,
		22	HE.CHL,
		23	Bc._subtilis,
		24	MY.CAP,
		25	E._coli,
		26	MYX.XA,
		27	P.TEST,
		28	AG.TUM,
		29	DV.DES,
		30	BA.FRG,
		31	'Zea_mays_(chloroplast)',
		32	T.AMIT
	;
	TREE mp_tree_1 =  [&R] ((14,(15,(16,(18,(17,(19,20)))))),((13,(11,12)),(((8,9),(7,(5,(6,(10,(4,(3,(1,2)))))))),(30,(((21,31),(24,(22,23))),((25,27),(26,(29,(28,32)))))))));
	TREE mp_tree_2 =  [&R] ((14,(15,(16,(18,(17,(19,20)))))),((13,(11,12)),(((8,9),(7,(5,(6,(10,(4,(3,(1,2)))))))),(30,(((21,31),(24,(22,23))),((26,(25,27)),(29,(28,32))))))));
	TREE  * UNTITLED =  [&R] ((14,(15,(16,(18,(17,(19,20)))))),((13,(11,12)),(((8,9),(7,(5,(6,(10,(4,(3,(1,2)))))))),(30,(((21,31),(24,(22,23))),((25,27),(26,(29,(28,32)))))))));

END;



BEGIN MACCLADE;
Version 3.05;
LastModified -1425155107;
Singles 1000&/0;
END;
BioPerl-1.007002/t/data/L77119.hmmer000444000766000024       464713155576321 16541 0ustar00cjfieldsstaff000000000000hmmpfam - search one or more sequences against HMM database
HMMER 2.2g (August 2001)
Copyright (C) 1992-2001 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:                 Pfam
Sequence file:            L77119.faa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query sequence: gi|1522636|gb|AAC37060.1|
Accession:      [none]
Description:    M. jannaschii predicted coding region MJECS02 [Methanococcus jannaschii]

Scores for sequence family classification (score includes all domains):
Model       Description                                 Score    E-value  N 
--------    -----------                                 -----    ------- ---
Methylase_M Type I restriction modification system, M  -105.2     0.0022   1

Parsed for domains:
Model       Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------    ------- ----- -----    ----- -----      -----  -------
Methylase_M   1/1     280   481 ..     1   279 []  -105.2   0.0022

Alignments of top-scoring domains:
Methylase_M: domain 1 of 1, from 280 to 481: score -105.2, E = 0.0022
                   *->lrnELentLWavADkLRGsmDaseYKdyVLGLlFlKYiSdkFlerri
                       ++EL+++  av+   R              L+F K++ dk      
  gi|1522636   280    NTSELDKKKFAVLLMNR--------------LIFIKFLEDK------ 306  

                   eieerktdtesepsldyakledqyeqlededlekedfyqkkGvFilPsql
                   +i+         p +   + +++y   ++   ++ ++y ++      + l
  gi|1522636   307 GIV---------PRDLLRRTYEDY---KKSNVLI-NYYDAY-L----KPL 338  

                   FwdfikeaeknkldedigtdldkifseledqialgypaSeedfkGlfpdl
                   F++++   e ++  ++++ + +    ++      + +       Glf ++
  gi|1522636   339 FYEVLNTPEDER--KENIRT-NPYYKDIPYL---N-G-------GLFRSN 374  

                   dfnsnkLgskaqarnetLtelidlfselelgtPmHNG.dfeelgikDlfG
                   ++  ++ +s+   +ne ++e+i+ +++ +++     G++ +el   D++G
  gi|1522636   375 NV--PNELSFTIKDNEIIGEVINFLERYKFTLSTSEGsEEVELNP-DILG 421  

                   DaYEYLLgkFAeneGKsGGeFYTPqeVSkLiaeiLtigqpsegdfsIYDP
                    +YE L+   Ae   K+ G +YTP e++  ia+ + i+  ++        
  gi|1522636   422 YVYEKLINILAEKGQKGLGAYYTPDEITSYIAKNT-IEPIVVE------- 463  

                   AcGSGSLllqaskflgehdgkrnaisyYGQEsn<-*
                             +++ ++    k+n+i +    s+   
  gi|1522636   464 ---------RFKEIIK--NWKINDINF----ST    481  

//
BioPerl-1.007002/t/data/LOAD_Ccd1.dnd000444000766000024       145113155576321 16731 0ustar00cjfieldsstaff000000000000(
(
(
A_aeolicus:0.27435,
S_aureus:0.30536)
:0.01589,
(
M_leprae:0.08606,
M_tubercul:0.06545)
:0.32304)
:0.02937,
(
(
(
(
(
A_fulgidus:0.26385,
T_maritima:0.22186)
:0.04261,
Synechocys:0.37630)
:0.05068,
C_jejuni:0.34050)
:0.00557,
(
M_jannasch:0.35330,
M_thermoau:0.41813)
:0.03001)
:0.04323,
(
(
A_tumefaci:0.19429,
S_meliloti:0.17884)
:0.13366,
(
(
B_sp:0.23437,
(
(
(
E_coli_A:0.10440,
Y_pestis:0.10989)
:0.04376,
V_cholerae:0.16338)
:0.01631,
(
H_influenz:0.11186,
P_multocid:0.10553)
:0.07654)
:0.02011)
:0.09091,
P_aerugino:0.26019)
:0.04366)
:0.02890)
:0.00030,
(
(
(
B_subtilis:0.27453,
H_sp:0.29690)
:0.01772,
N_meningit:0.29801)
:0.02281,
(
C_crescent:0.33036,
(
(
S_solfatar:0.06649,
S_tokodaii:0.06208)
:0.19814,
(
T_acidophi:0.01448,
T_volcaniu:0.01451)
:0.31728)
:0.01669)
:0.01921)
:0.00981);
BioPerl-1.007002/t/data/LittleChrY.dbsnp.xml000444000766000024      4055413155576321 20572 0ustar00cjfieldsstaff000000000000


 



  Homo sapiens
  9606
  12345
  
  
  
  
    
    0
    0
  
  
  
    52
    2000-09-19 17:02
  
  
    120
    2004-10-04 13:37
  
  
    14616
   
GGGTGGGCACTAGTTGGCGGGGTGGAAGGCACCACATTGGTCGCCTGCATGTCGTGGATGCA
GCGCACGGACTGTACCTGAGGGTGACGGGCCCCAAAGT
    C/T
   
GCTGCTGTCCTTGTAGTCTCCCTTCTCCAGCAGGTACTGCAGCCCACGGTAGCCAGGGTACT
AGTAGCCAACCCACGTGCCACTCCGCACCCACACAGAT
  
  
    
      14616
      CGAP-GAI
      607
      59089
      
      
      
      
      52
      
     
http://lpgws.nci.nih.gov:82/perl/gettrace.pl?type=7&trace=
      
       
GGGTGGGCACTAGTTGGCGGGGTGGAAGGCACCACATTGGTCGCCTGCATGTCGTGGATGCA
GCGCACGGACTGTACCTGAGGGTGACGGGCCCCAAAGT
        C/T
       
GCTGCTGTCCTTGTAGTCTCCCTTCTCCAGCAGGTACTGCAGCCCACGGTAGCCAGGGTACT
AGTAGCCAACCCACGTGCCACTCCGCACCCACACAGAT
      
    
    
      1539216
      LEE
      3129
      750160
      
      
      
      
      92
      
     
http://www.bioinformatics.ucla.edu/snp/snp/snp_report.php3?db_ver
sion=db_april_00&allele_id=
      
       
ACCGTGGGCTGCAGTACCTGCTGGAGAAGGGAGACTACAAGGACAGCAGC
        A/G
       
ACTTTGGGGCCCGTCACCCTCAGGTACAGTCCGTGCGCTGCATCCACGAC
      
    
    
      4398532
      LEE
      5288
      ge750160
      
      
      
      
      106
      
       
      
       
ACCGTGGGCTGCAGTACCTGCTGGAGAAGGGAGACTACAAGGACAGCAGC
        A/G
       
ACTTTGGGGCCCGTCACCCTCAGGTACAGTCCGTGCGCTGCATCCACGAC
      
    
    
      4426703
      LEE
      5293
      e750160
      
      
      
      
      106
      
       
      
       
ACCGTGGGCTGCAGTACCTGCTGGAGAAGGGAGACTACAAGGACAGCAGC
        A/G
       
ACTTTGGGGCCCGTCACCCTCAGGTACAGTCCGTGCGCTGCATCCACGAC
      
    
    
      16250752
      CGAP-GAI
      8532
      1500705
      
      
      
      
      120
      
     
http://lpgws.nci.nih.gov/perl/gettrace.pl?type=7&trace=
      
       
GTCGTGGATGCAGCGCACGGACTGTACCTGAGGGTGACGGGCCCCAAAGT
        C/T
       
GCTGCTGTCCTTGTAGTCTCCCTTCTCCAGCAGGTACTGCAGCCCACGGT
      
    
  
  
    
      125
      34_3
      reference
      
        
          
          960600311
          NT_011520.9
          Hs22_11677_34
          22
          18933985
          42112197
          
          29807292
          ref_haplotype
          reference
          
            
              5246027
              5246027
              
              0.913983
              
              24180013
              24180012
              99
              101
             
5246026
             
5246028
              3
              0
              1
            
          
        
      
      
        
        1
       
1
       
0
        1
        1
      
    
    
      125
      35_1
      Celera
      
      
        
          
          960600397
          NT_086921.1
          Hs22_86581_35
          22
          18936537
          48069707
          
          51477137
          alt_assembly_2
          Celera
          
            
              3888702
              3888702
              
              0.919897
              
              22825240
              22825239
              99
              101
             
3888701
             
3888703
              3
              0
              1
              
                
                  1415
                  CRYBB2
                  NM_000496
                  1
                  NP_000487
                  1
                  
                
              
            
          
        
      
      
        
        1
       
1
       
0
        1
        0
      
    
    
      125
      35_1
      reference
      
      
        
          
          960600396
          NT_011520.10
          Hs22_11677_35
          22
          18933985
          42210286
          
          51476066
          ref_haplotype
          reference
          
            
              5246027
              5246027
              
              0.919897
              
              24180013
              24180012
              99
              101
             
5246026
             
5246028
              3
              0
              1
              
                
                  1416
                  CRYBB2P1
                  
                
              
            
          
        
      
      
        
        1
       
1
       
0
        1
        1
      
    
  
  
    
      125
      3171883
      
      
        
          24363
          24363
          
          0.913983
          
          99
          101
          24362
          24364
          3
          0
          1
        
      
    
    
      125
      9863690
      
      
        
          52075
          52075
          
          0.913983
          
          99
          101
          52074
          52076
          3
          0
          1
        
      
    
    
      125
      51511751
      
      
        
          24180012
          24180012
          
          0.913983
          
          99
          101
          24180011
         
24180013
          3
          0
          1
        
      
    
  
  
    
      1
      12345
    
  





BioPerl-1.007002/t/data/M12730.gb000444000766000024      1472613155576321 16025 0ustar00cjfieldsstaff000000000000LOCUS       PNECG                   2355 bp    DNA     circular BCT 21-APR-1996
DEFINITION  Plasmid pNE131 (from S.epidermidis), complete genome.
ACCESSION   M12730
VERSION     M12730.1  GI:150829
KEYWORDS    MLS antibiotics resistance; complete genome;
            macrolide-lincosamide-streptogramin B resistance; plasmid;
            replication and maintenance protein.
SOURCE      Plasmid pNE131
  ORGANISM  Plasmid pNE131
            other sequences; plasmids; Plasmid.
REFERENCE   1  (bases 696 to 1586)
  AUTHORS   Lampson,B.C. and Parisi,J.T.
  TITLE     Naturally occurring Staphylococcus epidermidis plasmid expressing
            constitutive macrolide-lincosamide-streptogramin B resistance
            contains a deleted attenuator
  JOURNAL   J. Bacteriol. 166 (2), 479-483 (1986)
   PUBMED   3084450
REFERENCE   2  (bases 1 to 2355)
  AUTHORS   Lampson,B.C. and Parisi,J.T.
  TITLE     Nucleotide sequence of the constitutive
            macrolide-lincosamide-streptogramin B resistance plasmid pNE131
            from Staphylococcus epidermidis and homologies with Staphylococcus
            aureus plasmids pE194 and pSN2
  JOURNAL   J. Bacteriol. 167 (3), 888-892 (1986)
   PUBMED   3091582
COMMENT     Original source text: Plasmid pNE131 (clone: pNE131.) DNA. Draft
            entry and clean copy sequence for [2] kindly provided by
            J.T.Parisi, 04-AUG-1986. Ribosome binding sites are located at
            positions 754-759, 769-773, and 1944-1948; a -35 region at
            1889-1899, and -10 regions at 733-738, and 1927-1932.
FEATURES             Location/Qualifiers
     source          1..2355
                     /db_xref="taxon:2608"
                     /mol_type="genomic DNA"
                     /clone="pNE131."
                     /specific_host="Staphylococcus epidermidis"
                     /plasmid="Plasmid pNE131"
                     /organism="Plasmid pNE131"
     CDS             join(1959..2355,1..92)
                     /db_xref="GI:150830"
                     /codon_start=1
                     /protein_id="AAA98295.1"
                     /translation="MKERYGTVYKGSQRLIDEESGEVIEVDKLYRKQTSGNFVKAYIV
                     QLISMLDMIGGKKLKIVNYILDNVHLSNNTMIATTREIAKATGTSLQTVITTLKILEE
                     GNIIKRKTGVLMLNPELLMRGDDQKQKYLLLEFGNFEQEANEKQENALYLIIILSRTS
                     IT"
                     /product="replication and maintenance protein"
                     /transl_table=11
     gene            706..1550
                     /gene="ermM"
     -35_signal      706..715
                     /gene="ermM"
     -10_signal      733..738
                     /gene="ermM"
     mRNA            746..1550
                     /gene="ermM"
     CDS             780..1514
                     /protein_id="AAA98296.1"
                     /gene="ermM"
                     /transl_table=11
                     /db_xref="GI:150831"
                     /codon_start=1
                     /product="macrolide-lincosamide-streptogramin
                     B-resistance protein"
                     /translation="MNEKNIKHSQNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHF
                     TLELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNI
                     PYNISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSFALFLMAEVDISILSMVPR
                     EYFHPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKH
                     AGIDDLNNISFEQFLSLFNSYKLFNK"
     terminator      1513..1546
                     /gene="ermM"
                     /note="putative"
BASE COUNT      911 a    359 c    371 g    714 t
ORIGIN      1 bp upstream of TaqI site.
        1 tcgaatttgg gaactttgag caagaggcaa atgaaaaaca agaaaatgca ctttatctga
       61 ttattattct ttcaaggact agtataacat aaatcgtcta caaatagaca aaaaacctgc
      121 acgcttaatg tagatcaaaa gcttaacgca aatgaaatag attgacctcc caataacacc
      181 acgttagtta ttgggagtca atctatgaaa tgcgattaag ctttttctaa ttcacataag
      241 cgtgcaggtt taaagtacat aaaaaatata atgaaaaaaa gcatcattat actaacgtta
      301 taccaacatt atactaattg cttattccaa tttcctattg gttggaacca acaggcgtta
      361 gtgtgttgtt gagttggtac tttcatggga ttaatcccat gaaaccccca accaactcgc
      421 caaagctttg gctaacacac acgccattcc aaccaatagt tttctcggca ttaaagccat
      481 gctctgacgc ttaaatgcac taatgcctta aaaaaacatt aaagtctaac acactagact
      541 tattttcatt cgtaattaag tcgttaaacc gtgtgctcta cgaccaaaag tataaaacct
      601 ttaagaactt tcttttttct tgtaaaaaaa gaaactagat aaatctctca tatcttttat
      661 tcaataatcg catcagattg cagtataaat ttaacgatca ctcatcatgt tcatatttat
      721 cagagctcgt gctataatta tactaatttt ataaggagga aaaaataaag agggttataa
      781 tgaacgagaa aaatataaaa cacagtcaaa actttattac ttcaaaacat aatatagata
      841 aaataatgac aaatataaga ttaaatgaac atgataatat ctttgaaatc ggctcaggaa
      901 aagggcattt tacccttgaa ttagtacaga ggtgtaattt cgtaactgcc attgaaatag
      961 accataaatt atgcaaaact acagaaaata aacttgttga tcacgataat ttccaagttt
     1021 taaacaagga tatattgcag tttaaatttc ctaaaaacca atcctataaa atatttggta
     1081 atatacctta taacataagt acggatataa tacgcaaaat tgtttttgat agtatagctg
     1141 atgagattta tttaatcgtg gaatacgggt ttgctaaaag attattaaat acaaaacgct
     1201 cattcgcatt atttttaatg gcagaagttg atatttctat attaagtatg gttccaagag
     1261 aatattttca tcctaaacct aaagtgaata gctcacttat cagattaaat agaaaaaaat
     1321 caagaatatc acacaaagat aaacagaagt ataattattt cgttatgaaa tgggttaaca
     1381 aagaatacaa gaaaatattt acaaaaaatc aatttaacaa ttccttaaaa catgcaggaa
     1441 ttgacgattt aaacaatatt agctttgaac aattcttatc tcttttcaat agctataaat
     1501 tatttaataa gtaagttaag ggatgcataa actgcatcct taacttgttt ttcgtgtacc
     1561 tattttttgt gaatcgatta tgtcttttgc gcattcactt cttttctata taaatatgag
     1621 cgacagataa gcgtcggaaa agcagcaaaa agtttccttt ttgctgttgg agcatggggg
     1681 ttcagggggt gcagtatctg acgtcaatgc cgagcgaaag cgagccgaag ggtagcattt
     1741 acgttagata accccctgat atgctccgac gctttatata gaaaagaaga ttcaactagg
     1801 taaaatctta atataggttg agatgataag gtttataagg aatttgtttg ttctaatttt
     1861 tcactcattt tgttctaatt tcttttaaca aatgttcttt tttttttaga acagttatga
     1921 tatagttaga atagtttaaa ataaggagtg agaaaaagat gaaagaaaga tatggaacag
     1981 tctataaagg ctctcagagg ctcatagacg aagaaagtgg agaagtcata gaggtagaca
     2041 agttataccg taaacaaacg tctggtaact tcgtaaaggc atatatagtg caattaataa
     2101 gtatgttaga tatgattggc ggaaaaaaac ttaaaatcgt taactatatc ctagataatg
     2161 tccacttaag taacaataca atgatagcta caacaagaga aatagcaaaa gctacaggaa
     2221 caagtctaca aacagtaata acaacactta aaatcttaga agaaggaaat attataaaaa
     2281 gaaaaactgg agtattaatg ttaaaccctg aactactaat gagaggcgac gaccaaaaac
     2341 aaaaatacct cttac
//
BioPerl-1.007002/t/data/MSGEFTUA.gb000555000766000024      1225313155576321 16443 0ustar00cjfieldsstaff000000000000LOCUS       MSGEFTUA                1500 bp    DNA     linear   BCT 18-JUN-1999
DEFINITION  Mycobacterium leprae Tuf gene for elongation factor Tu, complete
            cds.
ACCESSION   D13869
VERSION     D13869.1  GI:434782
KEYWORDS    EF-Tu; elongation factor Tu.
SOURCE      Mycobacterium leprae
  ORGANISM  Mycobacterium leprae
            Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales;
            Corynebacterineae; Mycobacteriaceae; Mycobacterium.
REFERENCE   1  (bases 1 to 1500)
  AUTHORS   Dhandayuthapani,S., Banu,M.J. and Kashiwabara,Y.
  TITLE     Cloning and sequence determination of the gene coding for the
            elongation factor Tu of Mycobacterium leprae
  JOURNAL   J. Biochem. 115 (4), 664-669 (1994)
   PUBMED   8089081
COMMENT     Submitted (07-DEC-1992) to DDBJ by:
            Subranamian Dhandayuthapani
            National Institute for Leprosy Research
            4-2-1 Aobacho, Higashimurayama-shi
            Tokyo 189
            Japan
            Phone:  0423-91-8211
            Fax:    0423-94-9092.
FEATURES             Location/Qualifiers
     source          1..1500
                     /organism="Mycobacterium leprae"
                     /mol_type="genomic DNA"
                     /isolate="Thai 53"
                     /db_xref="taxon:1769"
                     /clone_lib="lambda gt11"
     repeat_region   20..71
                     /rpt_type=direct
                     /rpt_unit="20..29"
                     /rpt_unit="62..71"
     repeat_region   90..231
                     /rpt_type=direct
                     /rpt_unit="90..99"
                     /rpt_unit="222..231"
     RBS             205..210
                     /standard_name="Shine-Dalgarno sequence"
     gene            219..1409
                     /gene="Tuf"
     CDS             219..1409
                     /gene="Tuf"
                     /function="peptide chain elongtion during protein
                     synthesis"
                     /standard_name="EF-Tu"
                     /note="start codon gtg"
                     /codon_start=1
                     /evidence=not_experimental
                     /transl_table=11
                     /product="elongation factor Tu"
                     /protein_id="BAA02982.2"
                     /db_xref="GI:5103687"
                     /translation="MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAITKVLHDKFPNLN
                     ESRAFDQIDNAPEERQRGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMD
                     GAILVVAATDGPMPQTREHVLLARQVGVPYILVALNKSDAVDDEELLELVEMEVRELL
                     AAQEFDEDAPVVRVSALKALEGDAKWVESVTQLMDAVDESIPAPVRETDKPFLMPVED
                     VFTITGRGTVVTGRVERGVVNVNEEVEIVGIRQTTTKTTVTGVEMFRKLLDQGQAGDN
                     VGLLLRGIKREDVERGQVVIKPGTTTPHTEFEGQVYILSKDEGGRHTPFFNNYRPQFY
                     FRTTDVTGVVTLPEGTEMVMPGDNTNISVTLIQPVAMDEGLRFAIREGGPTVGAGRVV
                     KIIK"
     repeat_region   465..729
                     /rpt_type=direct
                     /rpt_unit="465..474"
                     /rpt_unit="720..729"
     repeat_region   883..913
                     /rpt_type=direct
                     /rpt_unit="883..892"
                     /rpt_unit="904..913"
     repeat_region   1169..1369
                     /rpt_type=direct
                     /rpt_unit="1169..1180"
                     /rpt_unit="1358..1369"
ORIGIN      
        1 gctcggtcca agacgcaagg ccggcgaact actccatggt gttcaactcg tactccgaag
       61 tgccggcgaa cgtgtcgaag gagatcatcg cgaaggcgac gggcgagtag gagttgagtg
      121 gtcggaaaag cctacgagtt atgctgacgc ggtcactacc gcggataaat tactaacatt
      181 gctttttaca agcaccaata gtccaggagg acacagaagt ggcgaaggcg aagttcgagc
      241 ggacgaagcc gcacgtcaac atcgggacca tcggtcacgt tgaccacggc aagaccacat
      301 tgaccgcggc tattaccaag gtcctgcatg acaagttccc caacctgaat gagtcgcgcg
      361 cctttgacca gattgacaac gcgcccgagg agcgtcagcg cggtatcacc atcaacattt
      421 cccacgtgga gtatcagacc gagaagcgtc actatgctca cgtcgacgcc ccggggcacg
      481 ccgactacat taagaacatg atcaccggtg cggcccagat ggatggtgcg attctggtgg
      541 tcgctgctac agacggcccg atgccgcaga ctcgcgagca cgtgctgctc gctcgtcagg
      601 tgggtgtacc ttacatcctg gtcgcactta acaagtccga cgccgtggac gacgaggaac
      661 tactcgagct tgtcgagatg gaagtccgtg agttgctggc tgcccaggaa ttcgacgagg
      721 acgccccggt tgtgcgtgtc tcggcattga aggcgctcga gggtgacgcc aagtgggtcg
      781 agtctgtcac acagttgatg gacgctgtcg acgagtcgat cccggctcca gtccgcgaga
      841 ctgacaagcc gttcctgatg cccgttgagg acgtcttcac tatcaccggt cgtggcaccg
      901 tggtcaccgg tcgggtggag cgcggcgtgg tcaacgtgaa cgaggaagtt gagatcgtcg
      961 gcattcgtca gacgaccacc aagaccaccg tcacgggtgt ggaaatgttt cgtaagctgc
     1021 tcgaccaagg tcaggccggt gataacgttg gtctgttgtt gcgtggcatc aagcgcgagg
     1081 acgtcgagcg tggtcaggtg gtcatcaaac ccggcaccac caccccgcat accgagttcg
     1141 aaggccaagt atacatcctg tccaaggacg aaggtggtcg gcacacaccg ttcttcaaca
     1201 actaccgtcc gcagttctac ttccgtacca ctgatgtgac cggtgtggtg actttgccgg
     1261 agggcaccga gatggtgatg ccaggtgaca acaccaacat ctcggtgacg ttgattcagc
     1321 ccgttgccat ggacgagggt ttgcgcttcg cgatccgcga aggtggtccg actgttggtg
     1381 ccggccgggt cgtcaagatc atcaagtaag tcgcatcaac gggccaggtg gttacaacgg
     1441 tccacatttg cgaaacggcg ctcatccgaa aggataggcg cgtttctttt gagtttatgc
//

BioPerl-1.007002/t/data/Mcjanrna_rdbII.gbk000444000766000024       571513155576321 20167 0ustar00cjfieldsstaff000000000000LOCUS       Mc.janrrnA   1475 bp    RNA             RNA       09-NOV-1998
DEFINITION  Methanococcus jannaschii [gene=rrnA gene].
REFERENCE   1
  AUTHORS   Bult,C.J., White,O., Olsen,G.J., Zhou,L., Fleischmann,R.D.,
            Sutton,G.G., Blake,J.A., FitzGerald,L.M., Clayton,R.A.,
            Gocayne,J.D., Kerlavage,A.R., Dougherty,B.A., Tomb,J., Adams,M.D.,
            Reich,C.I., Overbeek,R., Kirkness,E.F., Weinstock,K.G.,
            Merrick,J.M., Glodek,A., Scott,J.D., Geoghagen,N.S., Weidman,J.F.,
            Fuhrmann,J.L., Nguyen,D.T., Utterback,T., Kelley,J.M.,
            Peterson,J.D., Sadow,P.W., Hanna,M.C., Cotton,M.D., Hurst,M.A.,
            Roberts,K.M., Kaine,B.P., Borodovsky,M., Klenk,H.P., Fraser,C.M.,
            Smith,H.O., Woese,C.R. and Venter,J.C.
  TITLE     Complete genome sequence of the methanogenic archaeon,
            Methanococcus jannaschii
  JOURNAL   Science 273 (5278), 1058-1073 (1996)
COMMENT     
            Corresponding GenBank entry: L77117 (bases 157985 to 159459)
              complement
            operon= rrnA gene
BASE COUNT      295 a    422 c    527 g    231 u   2746 others
ORIGIN
        1 AUUCCGGUUG AUCCUGCCGG AGGCCACUGC UAUCGGGGUC CGACUAAGCC AUGCGAGUCA
       61 AGGGGCUCCC UUCGGGGAGC ACCGGCGCAC GGCUCAGUAA CACGUGGCUA ACCUACCCUC
      121 GGGUGGGGGA UAACCUCGGG AAACUGAGGC UAAUCCCCCA UAGGGGAGGA GGUCUGGAAU
      181 GAUCCCUCCC CGAAAGGCGU AAGCUGCCCG AGGAUGGGGC UGCGGCGGAU UAGGUAGUUG
      241 GUGGGGUAAC GGCCCACCAA GCCUACGAUC CGUACGGGCC CUGAGAGGGG GAGCCCGGAG
      301 AUGGACACUG AGACACGGGU CCAGGCCUAC GGGGCGCAGC AGGCGCGAAA CCUCCGCAAU
      361 GCGCGAAAGC GCGACGGGGG GACCCCGAGU GCCCACGCCC UGCGUGGGCU UUUCCGGAGU
      421 GUAAACAGCU CCGGGAAUAA GGGCUGGGCA AGUCCGGUGC CAGCAGCCGC GGUAAUACCG
      481 GCGGCCCAAG UGGUGGCCAC UGUUAUUGGG CCUAAAGCGU CCGUAGCCGG CCCGGUAAGU
      541 CUCUGCUUAA AUCUGCGGCU CAACCGCAGG GCUGGCAGAG AUACUGCCGG GCUUGGGACC
      601 GGGAGAGGCC GGGGGUACCC CAGGGGUAGC GGUGAAAUGC GUUGAUCCCU GGGGGACCAC
      661 CUGUGGCGAA GGCGCCCGGC UGGAACGGGU CCGACGGUGA GGGACGAAGG CCAGGGGAGC
      721 AAACCGGAUU AGAUACCCGG GUAGUCCUGG CUGUAAACUC UGCGGACUAG GUGUCGCGUC
      781 GGCUUCGGGC CGACGCGGUG CCGAAGGGAA GCCGUUAAGU CCGCCGCCUG GGGAGUACGG
      841 UCGCAAGACU GAAACUUAAA GGAAUUGGCG GGGGAGCACU ACAACGGGUG GAGCCUGCGG
      901 UUUAAUUGGA UUCAACGCCG GGCAUCUUAC CAGGGGCGAC GGCAGGAUGA AGGCCAGGUU
      961 GACGACCUUG CCAGACGCGC CGAGAGGUGG UGCAUGGCCG UCGUCAGCUC GUACCGUGAG
     1021 GCGUCCUGUU AAGUCAGGUA ACGAGCGAGA CCCGUGCCCC AUGUUGCUAC CUCCUCCUCC
     1081 GGGAGGAGGG CACUCAUGGG GGACCGCCGG CGCUAAGCCG GAGGAAGGUG CGGGCAACGA
     1141 CAGGUCCGCA UGCCCCGAAU CCCCUGGGCU ACACGCGGGC UACAAUGGCC GGGACAAUGG
     1201 GACGCGACCC CGAAAGGGGG AGCGAAUCCC CUAAACCCGG UCGUAGUCCG GAUCGAGGGC
     1261 UGUAACUCGC CCUCGUGAAG CCGGAAUCCG UAGUAAUCGC GCCUCACCAU GGCGCGGUGA
     1321 AUGCGUCCCU GCUCCUUGCA CACACCGCCC GUCACGCCAC CCGAGUUGAG CCCAAGUGAG
     1381 GCCCUGUCCG CAAGGGCAGG GUCGAACUUG GGUUCAGCGA GGGGGGCGAA GUCGUAACAA
     1441 GGUAGCCGUA GGGGAACUGC GGCUGGAUCA CCUCC
//
BioPerl-1.007002/t/data/MmCT000444000766000024       754413155576321 15425 0ustar00cjfieldsstaff000000000000Codon usage table

Pan troglodytes [gbpri]  325  CDS's

AmAcid   Codon             Number       /1000    Fraction

Pro      CCC              2351.00       22.55        0.41
Pro      CCT              1234.00       11.84        0.22
Pro      CCA              1158.00       11.11        0.20
Pro      CCG               923.00        8.85        0.16

Leu      CTC              2553.00       24.49        0.24
Leu      CTT               985.00        9.45        0.09
Leu      CTA               802.00        7.69        0.08
Leu      CTG              4997.00       47.93        0.48

His      CAC              1745.00       16.74        0.63
His      CAT              1041.00        9.99        0.37
Gln      CAA               925.00        8.87        0.17
Gln      CAG              4576.00       43.90        0.83

Arg      CGC              1580.00       15.16        0.24
Arg      CGT               397.00        3.81        0.06
Arg      CGA               592.00        5.68        0.09
Arg      CGG              1208.00       11.59        0.19

Ser      TCC              2158.00       20.70        0.27
Ser      TCT              1651.00       15.84        0.21
Ser      TCA               923.00        8.85        0.12
Ser      TCG               417.00        4.00        0.05

Phe      TTC              2447.00       23.47        0.70
Phe      TTT              1025.00        9.83        0.30
Leu      TTA               423.00        4.06        0.04
Leu      TTG               733.00        7.03        0.07

Tyr      TAC              2585.00       24.80        0.69
Tyr      TAT              1153.00       11.06        0.31
Ter      TAA                68.00        0.65        0.17
Ter      TAG                69.00        0.66        0.17

Cys      TGC              1448.00       13.89        0.63
Cys      TGT               851.00        8.16        0.37
Ter      TGA               275.00        2.64        0.67
Trp      TGG              2178.00       20.89        1.00

Thr      ACC              3341.00       32.05        0.50
Thr      ACT              1121.00       10.75        0.17
Thr      ACA              1452.00       13.93        0.22
Thr      ACG               821.00        7.88        0.12

Ile      ATC              2742.00       26.30        0.62
Ile      ATT              1065.00       10.22        0.24
Ile      ATA               643.00        6.17        0.14
Met      ATG              2152.00       20.64        1.00

Asn      AAC              1941.00       18.62        0.67
Asn      AAT               949.00        9.10        0.33
Lys      AAA              1276.00       12.24        0.32
Lys      AAG              2707.00       25.97        0.68

Ser      AGC              1872.00       17.96        0.24
Ser      AGT               828.00        7.94        0.11
Arg      AGA              1250.00       11.99        0.19
Arg      AGG              1467.00       14.07        0.23

Ala      GCC              3337.00       32.01        0.39
Ala      GCT              2211.00       21.21        0.26
Ala      GCA              1374.00       13.18        0.16
Ala      GCG              1671.00       16.03        0.19

Val      GTC              1610.00       15.44        0.24
Val      GTT               774.00        7.42        0.12
Val      GTA               397.00        3.81        0.06
Val      GTG              3873.00       37.15        0.58

Asp      GAC              3294.00       31.60        0.70
Asp      GAT              1427.00       13.69        0.30
Glu      GAA              1326.00       12.72        0.22
Glu      GAG              4666.00       44.76        0.78

Gly      GGC              2639.00       25.31        0.37
Gly      GGT               782.00        7.50        0.11
Gly      GGA              1562.00       14.98        0.22
Gly      GGG              2206.00       21.16        0.31



Coding GC 57.49%
1st letter GC 57.76%
2nd letter GC 45.35%
3rd letter GC 45.35%
Genetic code 1
BioPerl-1.007002/t/data/NC_000007-ribosomal-slippage.gb000444000766000024   1744511713155576321 22223 0ustar00cjfieldsstaff000000000000LOCUS       NC_000007          159138663 bp    DNA     linear   CON 29-JUL-2011
DEFINITION  Homo sapiens chromosome 7, GRCh37.p5 Primary Assembly.
ACCESSION   NC_000007 GPC_000000031
VERSION     NC_000007.13  GI:224589819
DBLINK      Project: 168
KEYWORDS    .
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (sites)
  AUTHORS   Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A and Enright
            AJ.
  TITLE     miRBase: microRNA sequences, targets and gene nomenclature
  JOURNAL   Nucleic Acids Res. 34 (DATABASE ISSUE), D140-D144 (2006)
   PUBMED   16381832
REFERENCE   2  (bases 1 to 159138663)
  CONSRTM   International Human Genome Sequencing Consortium
  TITLE     Finishing the euchromatic sequence of the human genome
  JOURNAL   Nature 431 (7011), 931-945 (2004)
   PUBMED   15496913
REFERENCE   3  (sites)
  AUTHORS   Griffiths-Jones S.
  TITLE     The microRNA Registry
  JOURNAL   Nucleic Acids Res. 32 (DATABASE ISSUE), D109-D111 (2004)
   PUBMED   14681370
REFERENCE   4  (bases 1 to 159138663)
  AUTHORS   Hillier,L.W., Fulton,R.S., Fulton,L.A., Graves,T.A., Pepin,K.H.,
            Wagner-McPherson,C., Layman,D., Maas,J., Jaeger,S., Walker,R.,
            Wylie,K., Sekhon,M., Becker,M.C., O'Laughlin,M.D., Schaller,M.E.,
            Fewell,G.A., Delehaunty,K.D., Miner,T.L., Nash,W.E., Cordes,M.,
            Du,H., Sun,H., Edwards,J., Bradshaw-Cordum,H., Ali,J., Andrews,S.,
            Isak,A., Vanbrunt,A., Nguyen,C., Du,F., Lamar,B., Courtney,L.,
            Kalicki,J., Ozersky,P., Bielicki,L., Scott,K., Holmes,A.,
            Harkins,R., Harris,A., Strong,C.M., Hou,S., Tomlinson,C.,
            Dauphin-Kohlberg,S., Kozlowicz-Reilly,A., Leonard,S., Rohlfing,T.,
            Rock,S.M., Tin-Wollam,A.M., Abbott,A., Minx,P., Maupin,R.,
            Strowmatt,C., Latreille,P., Miller,N., Johnson,D., Murray,J.,
            Woessner,J.P., Wendl,M.C., Yang,S.P., Schultz,B.R., Wallis,J.W.,
            Spieth,J., Bieri,T.A., Nelson,J.O., Berkowicz,N., Wohldmann,P.E.,
            Cook,L.L., Hickenbotham,M.T., Eldred,J., Williams,D., Bedell,J.A.,
            Mardis,E.R., Clifton,S.W., Chissoe,S.L., Marra,M.A., Raymond,C.,
            Haugen,E., Gillett,W., Zhou,Y., James,R., Phelps,K., Iadanoto,S.,
            Bubb,K., Simms,E., Levy,R., Clendenning,J., Kaul,R., Kent,W.J.,
            Furey,T.S., Baertsch,R.A., Brent,M.R., Keibler,E., Flicek,P.,
            Bork,P., Suyama,M., Bailey,J.A., Portnoy,M.E., Torrents,D.,
            Chinwalla,A.T., Gish,W.R., Eddy,S.R., McPherson,J.D., Olson,M.V.,
            Eichler,E.E., Green,E.D., Waterston,R.H. and Wilson,R.K.
  TITLE     The DNA sequence of human chromosome 7
  JOURNAL   Nature 424 (6945), 157-164 (2003)
   PUBMED   12853948
REFERENCE   5  (bases 1 to 159138663)
  AUTHORS   Lander,E.S., Linton,L.M., Birren,B., Nusbaum,C., Zody,M.C.,
            Baldwin,J., Devon,K., Dewar,K., Doyle,M., FitzHugh,W., Funke,R.,
            Gage,D., Harris,K., Heaford,A., Howland,J., Kann,L., Lehoczky,J.,
            LeVine,R., McEwan,P., McKernan,K., Meldrim,J., Mesirov,J.P.,
            Miranda,C., Morris,W., Naylor,J., Raymond,C., Rosetti,M.,
            Santos,R., Sheridan,A., Sougnez,C., Stange-Thomann,N.,
            Stojanovic,N., Subramanian,A., Wyman,D., Rogers,J., Sulston,J.,
            Ainscough,R., Beck,S., Bentley,D., Burton,J., Clee,C., Carter,N.,
            Coulson,A., Deadman,R., Deloukas,P., Dunham,A., Dunham,I.,
            Durbin,R., French,L., Grafham,D., Gregory,S., Hubbard,T.,
            Humphray,S., Hunt,A., Jones,M., Lloyd,C., McMurray,A., Matthews,L.,
            Mercer,S., Milne,S., Mullikin,J.C., Mungall,A., Plumb,R., Ross,M.,
            Shownkeen,R., Sims,S., Waterston,R.H., Wilson,R.K., Hillier,L.W.,
            McPherson,J.D., Marra,M.A., Mardis,E.R., Fulton,L.A.,
            Chinwalla,A.T., Pepin,K.H., Gish,W.R., Chissoe,S.L., Wendl,M.C.,
            Delehaunty,K.D., Miner,T.L., Delehaunty,A., Kramer,J.B., Cook,L.L.,
            Fulton,R.S., Johnson,D.L., Minx,P.J., Clifton,S.W., Hawkins,T.,
            Branscomb,E., Predki,P., Richardson,P., Wenning,S., Slezak,T.,
            Doggett,N., Cheng,J.F., Olsen,A., Lucas,S., Elkin,C.,
            Uberbacher,E., Frazier,M., Gibbs,R.A., Muzny,D.M., Scherer,S.E.,
            Bouck,J.B., Sodergren,E.J., Worley,K.C., Rives,C.M., Gorrell,J.H.,
            Metzker,M.L., Naylor,S.L., Kucherlapati,R.S., Nelson,D.L.,
            Weinstock,G.M., Sakaki,Y., Fujiyama,A., Hattori,M., Yada,T.,
            Toyoda,A., Itoh,T., Kawagoe,C., Watanabe,H., Totoki,Y., Taylor,T.,
            Weissenbach,J., Heilig,R., Saurin,W., Artiguenave,F., Brottier,P.,
            Bruls,T., Pelletier,E., Robert,C., Wincker,P., Smith,D.R.,
            Doucette-Stamm,L., Rubenfield,M., Weinstock,K., Lee,H.M.,
            Dubois,J., Rosenthal,A., Platzer,M., Nyakatura,G., Taudien,S.,
            Rump,A., Yang,H., Yu,J., Wang,J., Huang,G., Gu,J., Hood,L.,
            Rowen,L., Madan,A., Qin,S., Davis,R.W., Federspiel,N.A.,
            Abola,A.P., Proctor,M.J., Myers,R.M., Schmutz,J., Dickson,M.,
            Grimwood,J., Cox,D.R., Olson,M.V., Kaul,R., Raymond,C., Shimizu,N.,
            Kawasaki,K., Minoshima,S., Evans,G.A., Athanasiou,M., Schultz,R.,
            Roe,B.A., Chen,F., Pan,H., Ramser,J., Lehrach,H., Reinhardt,R.,
            McCombie,W.R., de la Bastide,M., Dedhia,N., Blocker,H.,
            Hornischer,K., Nordsiek,G., Agarwala,R., Aravind,L., Bailey,J.A.,
            Bateman,A., Batzoglou,S., Birney,E., Bork,P., Brown,D.G.,
            Burge,C.B., Cerutti,L., Chen,H.C., Church,D., Clamp,M.,
            Copley,R.R., Doerks,T., Eddy,S.R., Eichler,E.E., Furey,T.S.,
            Galagan,J., Gilbert,J.G., Harmon,C., Hayashizaki,Y., Haussler,D.,
            Hermjakob,H., Hokamp,K., Jang,W., Johnson,L.S., Jones,T.A.,
            Kasif,S., Kaspryzk,A., Kennedy,S., Kent,W.J., Kitts,P.,
            Koonin,E.V., Korf,I., Kulp,D., Lancet,D., Lowe,T.M., McLysaght,A.,
            Mikkelsen,T., Moran,J.V., Mulder,N., Pollara,V.J., Ponting,C.P.,
            Schuler,G., Schultz,J., Slater,G., Smit,A.F., Stupka,E.,
            Szustakowski,J., Thierry-Mieg,D., Thierry-Mieg,J., Wagner,L.,
            Wallis,J., Wheeler,R., Williams,A., Wolf,Y.I., Wolfe,K.H.,
            Yang,S.P., Yeh,R.F., Collins,F., Guyer,M.S., Peterson,J.,
            Felsenfeld,A., Wetterstrand,K.A., Patrinos,A., Morgan,M.J., de
            Jong,P., Catanese,J.J., Osoegawa,K., Shizuya,H., Choi,S. and
            Chen,Y.J.
  CONSRTM   International Human Genome Sequencing Consortium
  TITLE     Initial sequencing and analysis of the human genome
  JOURNAL   Nature 409 (6822), 860-921 (2001)
   PUBMED   11237011
  REMARK    Erratum:[Nature 2001 Aug 2;412(6846):565]
REFERENCE   6  (sites)
  AUTHORS   Lowe,T.M. and Eddy,S.R.
  TITLE     tRNAscan-SE: a program for improved detection of transfer RNA genes
            in genomic sequence
  JOURNAL   Nucleic Acids Res. 25 (5), 955-964 (1997)
   PUBMED   9023104
  REMARK    This is the methods paper for tRNAscan-SE.
COMMENT     REFSEQ INFORMATION: Features on this sequence have been produced
            for build 37 version 3 of the NCBI's genome annotation [see
            documentation]. The reference sequence is identical to CM000669.1.
            On Jun 10, 2009 this sequence version replaced gi:89161213.
            Assembly Name: GRCh37.p5 Primary Assembly
            The DNA sequence is composed of genomic sequence, primarily
            finished clones that were sequenced as part of the Human Genome
            Project. PCR products and WGS shotgun sequence have been added
            where necessary to fill gaps or correct errors. All such additions
            are manually curated by GRC staff. For more information see:
            http://genomereference.org.
FEATURES             Location/Qualifiers
     source          1..159138663
                     /organism="Homo sapiens"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:9606"
                     /chromosome="7"
     gap             1..10000
                     /estimated_length=10000
     gene            complement(19828..36378)
                     /gene="LOC100132858"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /db_xref="GeneID:100132858"
     mRNA            complement(join(19828..19895,20834..21029,31060..31437,
                     32957..33107,35335..35541,36224..36378))
                     /gene="LOC100132858"
                     /product="putative protein FAM157B-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /transcript_id="XM_001715131.2"
                     /db_xref="GI:239743046"
                     /db_xref="GeneID:100132858"
     CDS             complement(join(19828..19895,20834..21029,31060..31437,
                     32957..33107,35335..35541,36224..36378))
                     /gene="LOC100132858"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="putative protein FAM157B-like"
                     /protein_id="XP_001715183.2"
                     /db_xref="GI:239743047"
                     /db_xref="GeneID:100132858"
     gene            149597..154956
                     /gene="LOC100507642"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 12 ESTs"
                     /db_xref="GeneID:100507642"
     misc_RNA        join(149597..152547,153409..154956)
                     /gene="LOC100507642"
                     /product="hypothetical LOC100507642"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 12 ESTs"
                     /transcript_id="XR_108720.2"
                     /db_xref="GI:341915377"
                     /db_xref="GeneID:100507642"
     gene            192969..300711
                     /gene="FAM20C"
                     /gene_synonym="DKFZp547C074; DMP4; RNS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:56975"
                     /db_xref="HGNC:22140"
                     /db_xref="HPRD:13298"
                     /db_xref="MIM:611061"
     mRNA            join(192969..193804,195554..195732,208898..208976,
                     286381..286473,288281..288396,295815..295995,
                     296620..296729,296971..297052,298612..298671,
                     299697..300711)
                     /gene="FAM20C"
                     /gene_synonym="DKFZp547C074; DMP4; RNS"
                     /product="family with sequence similarity 20, member C"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020223.2"
                     /db_xref="GI:116174741"
                     /db_xref="GeneID:56975"
                     /db_xref="HGNC:22140"
                     /db_xref="HPRD:13298"
                     /db_xref="MIM:611061"
     CDS             join(193200..193804,195554..195732,208898..208976,
                     286381..286473,288281..288396,295815..295995,
                     296620..296729,296971..297052,298612..298671,
                     299697..299946)
                     /gene="FAM20C"
                     /gene_synonym="DKFZp547C074; DMP4; RNS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="dentin matrix protein 4"
                     /protein_id="NP_064608.2"
                     /db_xref="GI:116174742"
                     /db_xref="CCDS:CCDS47522.1"
                     /db_xref="GeneID:56975"
                     /db_xref="HGNC:22140"
                     /db_xref="HPRD:13298"
                     /db_xref="MIM:611061"
     gene            301855..304070
                     /gene="LOC100288496"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100288496"
     exon            301855..302417
                     /gene="LOC100288496"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100288496"
     exon            302908..303160
                     /gene="LOC100288496"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100288496"
     exon            303266..303361
                     /gene="LOC100288496"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:100288496"
     exon            303416..304070
                     /gene="LOC100288496"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=4
                     /pseudo
                     /db_xref="GeneID:100288496"
     gene            330136..331454
                     /gene="LOC100288524"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100288524"
     mRNA            join(330136..330242,330619..330787,331029..331454)
                     /gene="LOC100288524"
                     /product="forkhead box L1-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001195127.1"
                     /db_xref="GI:304376260"
                     /db_xref="GeneID:100288524"
     CDS             join(330136..330242,330619..330787,331029..331454)
                     /gene="LOC100288524"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="forkhead box L1-like"
                     /protein_id="NP_001182056.1"
                     /db_xref="GI:304376261"
                     /db_xref="GeneID:100288524"
     gene            419391..422845
                     /gene="LOC442497"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:442497"
     misc_RNA        join(419391..419509,420384..420480,420815..422845)
                     /gene="LOC442497"
                     /product="hypothetical LOC442497"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033960.1"
                     /db_xref="GI:300069007"
                     /db_xref="GeneID:442497"
     gene            complement(467033..471673)
                     /gene="LOC100131372"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 2 ESTs, 1 Protein"
                     /db_xref="GeneID:100131372"
     misc_RNA        complement(467033..471673)
                     /gene="LOC100131372"
                     /product="hypothetical LOC100131372"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 2 ESTs, 1 Protein"
                     /transcript_id="XR_108721.1"
                     /db_xref="GI:310119890"
                     /db_xref="GeneID:100131372"
     gene            complement(536895..559481)
                     /gene="PDGFA"
                     /gene_synonym="PDGF-A; PDGF1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5154"
                     /db_xref="HGNC:8799"
                     /db_xref="HPRD:01424"
                     /db_xref="MIM:173430"
     mRNA            complement(join(536895..538211,540068..540136,
                     540753..540879,550446..550633,551988..552092,
                     557031..557127,558576..559481))
                     /gene="PDGFA"
                     /gene_synonym="PDGF-A; PDGF1"
                     /product="platelet-derived growth factor alpha
                     polypeptide, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002607.5"
                     /db_xref="GI:197333758"
                     /db_xref="GeneID:5154"
                     /db_xref="HGNC:8799"
                     /db_xref="HPRD:01424"
                     /db_xref="MIM:173430"
     mRNA            complement(join(536895..538211,540753..540879,
                     550446..550633,551988..552092,557031..557127,
                     558576..559481))
                     /gene="PDGFA"
                     /gene_synonym="PDGF-A; PDGF1"
                     /product="platelet-derived growth factor alpha
                     polypeptide, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033023.4"
                     /db_xref="GI:197333759"
                     /db_xref="GeneID:5154"
                     /db_xref="HGNC:8799"
                     /db_xref="HPRD:01424"
                     /db_xref="MIM:173430"
     CDS             complement(join(538201..538211,540753..540879,
                     550446..550633,551988..552092,557031..557127,
                     558576..558638))
                     /gene="PDGFA"
                     /gene_synonym="PDGF-A; PDGF1"
                     /note="isoform 2 preproprotein is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="platelet-derived growth factor subunit A isoform
                     2 preproprotein"
                     /protein_id="NP_148983.1"
                     /db_xref="GI:15208656"
                     /db_xref="CCDS:CCDS47524.1"
                     /db_xref="GeneID:5154"
                     /db_xref="HGNC:8799"
                     /db_xref="HPRD:01424"
                     /db_xref="MIM:173430"
     gene            539717..540130
                     /gene="LOC100132080"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 EST, 1 Protein"
                     /db_xref="GeneID:100132080"
     misc_RNA        539717..540130
                     /gene="LOC100132080"
                     /product="hypothetical LOC100132080"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 EST, 1 Protein"
                     /transcript_id="XR_132526.1"
                     /db_xref="GI:341915378"
                     /db_xref="GeneID:100132080"
     CDS             complement(join(540081..540136,540753..540879,
                     550446..550633,551988..552092,557031..557127,
                     558576..558638))
                     /gene="PDGFA"
                     /gene_synonym="PDGF-A; PDGF1"
                     /note="isoform 1 preproprotein is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="platelet-derived growth factor subunit A isoform
                     1 preproprotein"
                     /protein_id="NP_002598.4"
                     /db_xref="GI:77695917"
                     /db_xref="CCDS:CCDS34578.1"
                     /db_xref="GeneID:5154"
                     /db_xref="HGNC:8799"
                     /db_xref="HPRD:01424"
                     /db_xref="MIM:173430"
     gene            560028..564869
                     /gene="FLJ44511"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:441307"
     misc_RNA        join(560028..562953,563717..563917,564491..564869)
                     /gene="FLJ44511"
                     /product="hypothetical LOC441307"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033963.1"
                     /db_xref="GI:300069028"
                     /db_xref="GeneID:441307"
     gene            complement(588834..767313)
                     /gene="PRKAR1B"
                     /gene_synonym="PRKAR1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5575"
                     /db_xref="HGNC:9390"
                     /db_xref="HPRD:01485"
                     /db_xref="MIM:176911"
     mRNA            complement(join(588834..590239,591026..591107,
                     618893..619014,624145..624205,635783..635941,
                     645830..645876,647028..647089,716866..716957,
                     720193..720363,750966..751164,767227..767313))
                     /gene="PRKAR1B"
                     /gene_synonym="PRKAR1"
                     /product="protein kinase, cAMP-dependent, regulatory, type
                     I, beta, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001164758.1"
                     /db_xref="GI:258613968"
                     /db_xref="GeneID:5575"
                     /db_xref="HGNC:9390"
                     /db_xref="MIM:176911"
                     /db_xref="HPRD:01485"
     mRNA            complement(join(588834..590239,591026..591107,
                     618893..619014,624145..624205,635783..635941,
                     645830..645876,647028..647089,716866..716957,
                     720193..720363,750966..751164,767292..767313))
                     /gene="PRKAR1B"
                     /gene_synonym="PRKAR1"
                     /product="protein kinase, cAMP-dependent, regulatory, type
                     I, beta, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001164759.1"
                     /db_xref="GI:258613970"
                     /db_xref="GeneID:5575"
                     /db_xref="HGNC:9390"
                     /db_xref="MIM:176911"
                     /db_xref="HPRD:01485"
     mRNA            complement(join(588834..590239,591026..591107,
                     618893..619014,624145..624205,635783..635941,
                     645830..645876,647028..647089,716866..716957,
                     720193..720363,750966..751164,766847..766978))
                     /gene="PRKAR1B"
                     /gene_synonym="PRKAR1"
                     /product="protein kinase, cAMP-dependent, regulatory, type
                     I, beta, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001164760.1"
                     /db_xref="GI:258613972"
                     /db_xref="GeneID:5575"
                     /db_xref="HGNC:9390"
                     /db_xref="MIM:176911"
                     /db_xref="HPRD:01485"
     mRNA            complement(join(588834..590239,591026..591107,
                     618893..619014,624145..624205,635783..635941,
                     645830..645876,647028..647089,716866..716957,
                     720193..720363,750966..751164,752692..752844))
                     /gene="PRKAR1B"
                     /gene_synonym="PRKAR1"
                     /product="protein kinase, cAMP-dependent, regulatory, type
                     I, beta, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001164761.1"
                     /db_xref="GI:258613976"
                     /db_xref="GeneID:5575"
                     /db_xref="HGNC:9390"
                     /db_xref="MIM:176911"
                     /db_xref="HPRD:01485"
     mRNA            complement(join(588834..590239,591026..591107,
                     618893..619014,624145..624205,635783..635941,
                     645830..645876,647028..647089,716866..716957,
                     720193..720363,750966..751164,752485..752577))
                     /gene="PRKAR1B"
                     /gene_synonym="PRKAR1"
                     /product="protein kinase, cAMP-dependent, regulatory, type
                     I, beta, transcript variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001164762.1"
                     /db_xref="GI:258613974"
                     /db_xref="GeneID:5575"
                     /db_xref="HGNC:9390"
                     /db_xref="MIM:176911"
                     /db_xref="HPRD:01485"
     mRNA            complement(join(588834..590239,591026..591107,
                     618893..619014,624145..624205,635783..635941,
                     645830..645876,647028..647089,716866..716957,
                     720193..720363,750966..751164,752051..752161))
                     /gene="PRKAR1B"
                     /gene_synonym="PRKAR1"
                     /product="protein kinase, cAMP-dependent, regulatory, type
                     I, beta, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002735.2"
                     /db_xref="GI:258613967"
                     /db_xref="GeneID:5575"
                     /db_xref="HGNC:9390"
                     /db_xref="HPRD:01485"
                     /db_xref="MIM:176911"
     CDS             complement(join(590067..590239,591026..591107,
                     618893..619014,624145..624205,635783..635941,
                     645830..645876,647028..647089,716866..716957,
                     720193..720363,750966..751142))
                     /gene="PRKAR1B"
                     /gene_synonym="PRKAR1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cAMP-dependent protein kinase type I-beta
                     regulatory subunit"
                     /protein_id="NP_002726.1"
                     /db_xref="GI:38257139"
                     /db_xref="CCDS:CCDS34579.1"
                     /db_xref="GeneID:5575"
                     /db_xref="HGNC:9390"
                     /db_xref="HPRD:01485"
                     /db_xref="MIM:176911"
     CDS             complement(join(590067..590239,591026..591107,
                     618893..619014,624145..624205,635783..635941,
                     645830..645876,647028..647089,716866..716957,
                     720193..720363,750966..751142))
                     /gene="PRKAR1B"
                     /gene_synonym="PRKAR1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cAMP-dependent protein kinase type I-beta
                     regulatory subunit"
                     /protein_id="NP_001158230.1"
                     /db_xref="GI:258613969"
                     /db_xref="CCDS:CCDS34579.1"
                     /db_xref="GeneID:5575"
                     /db_xref="HGNC:9390"
                     /db_xref="HPRD:01485"
                     /db_xref="MIM:176911"
     CDS             complement(join(590067..590239,591026..591107,
                     618893..619014,624145..624205,635783..635941,
                     645830..645876,647028..647089,716866..716957,
                     720193..720363,750966..751142))
                     /gene="PRKAR1B"
                     /gene_synonym="PRKAR1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cAMP-dependent protein kinase type I-beta
                     regulatory subunit"
                     /protein_id="NP_001158231.1"
                     /db_xref="GI:258613971"
                     /db_xref="CCDS:CCDS34579.1"
                     /db_xref="GeneID:5575"
                     /db_xref="HGNC:9390"
                     /db_xref="HPRD:01485"
                     /db_xref="MIM:176911"
     CDS             complement(join(590067..590239,591026..591107,
                     618893..619014,624145..624205,635783..635941,
                     645830..645876,647028..647089,716866..716957,
                     720193..720363,750966..751142))
                     /gene="PRKAR1B"
                     /gene_synonym="PRKAR1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cAMP-dependent protein kinase type I-beta
                     regulatory subunit"
                     /protein_id="NP_001158232.1"
                     /db_xref="GI:258613973"
                     /db_xref="CCDS:CCDS34579.1"
                     /db_xref="GeneID:5575"
                     /db_xref="HGNC:9390"
                     /db_xref="HPRD:01485"
                     /db_xref="MIM:176911"
     CDS             complement(join(590067..590239,591026..591107,
                     618893..619014,624145..624205,635783..635941,
                     645830..645876,647028..647089,716866..716957,
                     720193..720363,750966..751142))
                     /gene="PRKAR1B"
                     /gene_synonym="PRKAR1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cAMP-dependent protein kinase type I-beta
                     regulatory subunit"
                     /protein_id="NP_001158234.1"
                     /db_xref="GI:258613975"
                     /db_xref="CCDS:CCDS34579.1"
                     /db_xref="GeneID:5575"
                     /db_xref="HGNC:9390"
                     /db_xref="HPRD:01485"
                     /db_xref="MIM:176911"
     CDS             complement(join(590067..590239,591026..591107,
                     618893..619014,624145..624205,635783..635941,
                     645830..645876,647028..647089,716866..716957,
                     720193..720363,750966..751142))
                     /gene="PRKAR1B"
                     /gene_synonym="PRKAR1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cAMP-dependent protein kinase type I-beta
                     regulatory subunit"
                     /protein_id="NP_001158233.1"
                     /db_xref="GI:258613977"
                     /db_xref="CCDS:CCDS34579.1"
                     /db_xref="GeneID:5575"
                     /db_xref="HGNC:9390"
                     /db_xref="HPRD:01485"
                     /db_xref="MIM:176911"
     gene            642482..648139
                     /gene="LOC100505500"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 19 ESTs"
                     /db_xref="GeneID:100505500"
     misc_RNA        join(642482..642934,647502..648139)
                     /gene="LOC100505500"
                     /product="hypothetical LOC100505500, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 18 ESTs"
                     /transcript_id="XR_108722.1"
                     /db_xref="GI:310119893"
                     /db_xref="GeneID:100505500"
     misc_RNA        join(643035..643253,647502..648139)
                     /gene="LOC100505500"
                     /product="hypothetical LOC100505500, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 17 ESTs"
                     /transcript_id="XR_108723.1"
                     /db_xref="GI:310119894"
                     /db_xref="GeneID:100505500"
     gene            766338..826116
                     /gene="HEATR2"
                     /gene_synonym="FLJ20397; FLJ25564; FLJ31671; FLJ39381"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54919"
                     /db_xref="HGNC:26013"
                     /db_xref="HPRD:07903"
     mRNA            join(766338..766952,769300..769484,780456..780580,
                     780984..781102,794226..794458,796419..796631,
                     801390..801533,803443..803611,810108..810255,
                     813685..813835,814643..814799,819590..819781,
                     825154..826116)
                     /gene="HEATR2"
                     /gene_synonym="FLJ20397; FLJ25564; FLJ31671; FLJ39381"
                     /product="HEAT repeat containing 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017802.3"
                     /db_xref="GI:157388903"
                     /db_xref="GeneID:54919"
                     /db_xref="HGNC:26013"
                     /db_xref="HPRD:07903"
     CDS             join(766358..766952,769300..769484,780456..780580,
                     780984..781102,794226..794458,796419..796631,
                     801390..801533,803443..803611,810108..810255,
                     813685..813835,814643..814799,819590..819781,
                     825154..825290)
                     /gene="HEATR2"
                     /gene_synonym="FLJ20397; FLJ25564; FLJ31671; FLJ39381"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="HEAT repeat-containing protein 2"
                     /protein_id="NP_060272.3"
                     /db_xref="GI:157388904"
                     /db_xref="CCDS:CCDS34580.1"
                     /db_xref="GeneID:54919"
                     /db_xref="HGNC:26013"
                     /db_xref="HPRD:07903"
     gene            855194..914557
                     /gene="SUN1"
                     /gene_synonym="FLJ12407; KIAA0810; MGC176649; UNC84A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23353"
                     /db_xref="HGNC:18587"
                     /db_xref="MIM:607723"
     mRNA            join(855194..855240,872142..872238,878435..878623,
                     881583..881767,882843..882869,882978..883509)
                     /gene="SUN1"
                     /gene_synonym="FLJ12407; KIAA0810; MGC176649; UNC84A"
                     /product="Sad1 and UNC84 domain containing 1, transcript
                     variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001171946.1"
                     /db_xref="GI:284925168"
                     /db_xref="GeneID:23353"
                     /db_xref="HGNC:18587"
                     /db_xref="MIM:607723"
     mRNA            join(856252..856310,878435..878623,881583..881767,
                     882843..882869,882978..883157,891587..891680,
                     892246..892304,892447..892589,893046..893255,
                     894557..894643,895995..896038,897465..897594,
                     899765..900019,901017..901101,905589..905704,
                     908986..909153,912107..912199,912852..914557)
                     /gene="SUN1"
                     /gene_synonym="FLJ12407; KIAA0810; MGC176649; UNC84A"
                     /product="Sad1 and UNC84 domain containing 1, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_025154.5"
                     /db_xref="GI:284925163"
                     /db_xref="GeneID:23353"
                     /db_xref="HGNC:18587"
                     /db_xref="HPRD:16257"
                     /db_xref="MIM:607723"
     mRNA            join(856252..856310,872142..872238,878435..878623,
                     881583..881767,891587..891680,892246..892304,
                     892450..892589,893046..893255,894557..894643,
                     895995..896038,897465..897594,899765..900019,
                     901017..901101,905589..905704,908986..909153,
                     912107..912199,912852..914557)
                     /gene="SUN1"
                     /gene_synonym="FLJ12407; KIAA0810; MGC176649; UNC84A"
                     /product="Sad1 and UNC84 domain containing 1, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001171944.1"
                     /db_xref="GI:284925164"
                     /db_xref="GeneID:23353"
                     /db_xref="HGNC:18587"
                     /db_xref="MIM:607723"
     mRNA            join(856252..856310,856917..857136,872142..872238,
                     878435..878623,881583..881767,882843..882869,
                     882978..883509)
                     /gene="SUN1"
                     /gene_synonym="FLJ12407; KIAA0810; MGC176649; UNC84A"
                     /product="Sad1 and UNC84 domain containing 1, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001171945.1"
                     /db_xref="GI:284925166"
                     /db_xref="GeneID:23353"
                     /db_xref="HGNC:18587"
                     /db_xref="MIM:607723"
     CDS             join(857094..857136,872142..872238,878435..878623,
                     881583..881767,882843..882869,882978..883273)
                     /gene="SUN1"
                     /gene_synonym="FLJ12407; KIAA0810; MGC176649; UNC84A"
                     /note="isoform d is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="SUN domain-containing protein 1 isoform d"
                     /protein_id="NP_001165416.1"
                     /db_xref="GI:284925167"
                     /db_xref="CCDS:CCDS55078.1"
                     /db_xref="GeneID:23353"
                     /db_xref="HGNC:18587"
                     /db_xref="MIM:607723"
     mRNA            join(872142..872238,878435..878623,881583..881767,
                     882843..882869,882978..883157,891021..891119,
                     891587..891680,892246..892304,892447..892589,
                     893046..893255,894557..894643,895995..896038,
                     897465..897594,899765..900019,901017..901101,
                     905589..905704,908986..909153,912107..912199,
                     912852..914557)
                     /gene="SUN1"
                     /gene_synonym="FLJ12407; KIAA0810; MGC176649; UNC84A"
                     /product="Sad1 and UNC84 domain containing 1, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130965.2"
                     /db_xref="GI:284925162"
                     /db_xref="GeneID:23353"
                     /db_xref="HGNC:18587"
                     /db_xref="MIM:607723"
     CDS             join(872162..872238,878435..878623,881583..881767,
                     882843..882869,882978..883157,891021..891119,
                     891587..891680,892246..892304,892447..892589,
                     893046..893255,894557..894643,895995..896038,
                     897465..897594,899765..900019,901017..901101,
                     905589..905704,908986..909153,912107..912199,
                     912852..912968)
                     /gene="SUN1"
                     /gene_synonym="FLJ12407; KIAA0810; MGC176649; UNC84A"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="SUN domain-containing protein 1 isoform a"
                     /protein_id="NP_001124437.1"
                     /db_xref="GI:195972890"
                     /db_xref="CCDS:CCDS47525.1"
                     /db_xref="GeneID:23353"
                     /db_xref="HGNC:18587"
                     /db_xref="MIM:607723"
     CDS             join(872162..872238,878435..878623,881583..881767,
                     891587..891680,892246..892304,892450..892589,
                     893046..893255,894557..894643,895995..896038,
                     897465..897594,899765..900019,901017..901101,
                     905589..905704,908986..909153,912107..912199,
                     912852..912968)
                     /gene="SUN1"
                     /gene_synonym="FLJ12407; KIAA0810; MGC176649; UNC84A"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="SUN domain-containing protein 1 isoform c"
                     /protein_id="NP_001165415.1"
                     /db_xref="GI:284925165"
                     /db_xref="CCDS:CCDS55080.1"
                     /db_xref="GeneID:23353"
                     /db_xref="HGNC:18587"
                     /db_xref="MIM:607723"
     CDS             join(872162..872238,878435..878623,881583..881767,
                     882843..882869,882978..883273)
                     /gene="SUN1"
                     /gene_synonym="FLJ12407; KIAA0810; MGC176649; UNC84A"
                     /note="isoform e is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="SUN domain-containing protein 1 isoform e"
                     /protein_id="NP_001165417.1"
                     /db_xref="GI:284925169"
                     /db_xref="CCDS:CCDS55079.1"
                     /db_xref="GeneID:23353"
                     /db_xref="HGNC:18587"
                     /db_xref="MIM:607723"
     CDS             join(878508..878623,881583..881767,882843..882869,
                     882978..883157,891587..891680,892246..892304,
                     892447..892589,893046..893255,894557..894643,
                     895995..896038,897465..897594,899765..900019,
                     901017..901101,905589..905704,908986..909153,
                     912107..912199,912852..912968)
                     /gene="SUN1"
                     /gene_synonym="FLJ12407; KIAA0810; MGC176649; UNC84A"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="SUN domain-containing protein 1 isoform b"
                     /protein_id="NP_079430.3"
                     /db_xref="GI:110227866"
                     /db_xref="CCDS:CCDS43533.1"
                     /db_xref="GeneID:23353"
                     /db_xref="HGNC:18587"
                     /db_xref="MIM:607723"
     gene            916191..936071
                     /gene="GET4"
                     /gene_synonym="C7orf20; CEE; CGI-20; TRC35"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51608"
                     /db_xref="HGNC:21690"
                     /db_xref="HPRD:12909"
                     /db_xref="MIM:612056"
     mRNA            join(916191..916437,925693..925771,926206..926287,
                     927007..927156,930565..930703,931915..932055,
                     933377..933452,933536..933608,934971..936071)
                     /gene="GET4"
                     /gene_synonym="C7orf20; CEE; CGI-20; TRC35"
                     /product="golgi to ER traffic protein 4 homolog (S.
                     cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015949.2"
                     /db_xref="GI:38570061"
                     /db_xref="GeneID:51608"
                     /db_xref="HGNC:21690"
                     /db_xref="HPRD:12909"
                     /db_xref="MIM:612056"
     CDS             join(916283..916437,925693..925771,926206..926287,
                     927007..927156,930565..930703,931915..932055,
                     933377..933452,933536..933608,934971..935059)
                     /gene="GET4"
                     /gene_synonym="C7orf20; CEE; CGI-20; TRC35"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="Golgi to ER traffic protein 4 homolog"
                     /protein_id="NP_057033.2"
                     /db_xref="GI:38570062"
                     /db_xref="CCDS:CCDS5317.1"
                     /db_xref="GeneID:51608"
                     /db_xref="HGNC:21690"
                     /db_xref="HPRD:12909"
                     /db_xref="MIM:612056"
     gene            919586..921830
                     /gene="LOC100505531"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /db_xref="GeneID:100505531"
     misc_RNA        join(919586..919720,920756..921830)
                     /gene="LOC100505531"
                     /product="hypothetical LOC100505531"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /transcript_id="XR_108724.1"
                     /db_xref="GI:310119895"
                     /db_xref="GeneID:100505531"
     gene            complement(937537..994289)
                     /gene="ADAP1"
                     /gene_synonym="CENTA1; GCS1L; p42IP4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:11033"
                     /db_xref="HGNC:16486"
                     /db_xref="HPRD:09733"
                     /db_xref="MIM:608114"
     mRNA            complement(join(937537..938586,938670..938898,
                     939056..939127,939739..939801,940170..940253,
                     943763..943909,944697..944809,959605..959687,
                     966189..966280,975011..975141,994032..994289))
                     /gene="ADAP1"
                     /gene_synonym="CENTA1; GCS1L; p42IP4"
                     /product="ArfGAP with dual PH domains 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006869.2"
                     /db_xref="GI:187960101"
                     /db_xref="GeneID:11033"
                     /db_xref="HGNC:16486"
                     /db_xref="HPRD:09733"
                     /db_xref="MIM:608114"
     CDS             complement(join(938558..938586,938670..938898,
                     939056..939127,939739..939801,940170..940253,
                     943763..943909,944697..944809,959605..959687,
                     966189..966280,975011..975141,994032..994113))
                     /gene="ADAP1"
                     /gene_synonym="CENTA1; GCS1L; p42IP4"
                     /exception="mismatches in translation"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="arf-GAP with dual PH domain-containing protein
                     1"
                     /protein_id="NP_006860.1"
                     /db_xref="GI:6806913"
                     /db_xref="CCDS:CCDS5318.1"
                     /db_xref="GeneID:11033"
                     /db_xref="HGNC:16486"
                     /db_xref="HPRD:09733"
                     /db_xref="MIM:608114"
     gene            complement(1004486..1015235)
                     /gene="COX19"
                     /gene_synonym="MGC104475"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:90639"
                     /db_xref="HGNC:28074"
                     /db_xref="MIM:610429"
     mRNA            complement(join(1004486..1009092,1012817..1012928,
                     1015064..1015235))
                     /gene="COX19"
                     /gene_synonym="MGC104475"
                     /product="COX19 cytochrome c oxidase assembly homolog (S.
                     cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001031617.2"
                     /db_xref="GI:110349770"
                     /db_xref="GeneID:90639"
                     /db_xref="HGNC:28074"
                     /db_xref="MIM:610429"
     CDS             complement(join(1009014..1009092,1012817..1012928,
                     1015064..1015145))
                     /gene="COX19"
                     /gene_synonym="MGC104475"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytochrome c oxidase assembly protein COX19"
                     /protein_id="NP_001026788.1"
                     /db_xref="GI:71979925"
                     /db_xref="CCDS:CCDS34582.1"
                     /db_xref="GeneID:90639"
                     /db_xref="HGNC:28074"
                     /db_xref="MIM:610429"
     gene            1022835..1029276
                     /gene="CYP2W1"
                     /gene_synonym="MGC34287"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54905"
                     /db_xref="HGNC:20243"
                     /db_xref="HPRD:07901"
     mRNA            join(1022835..1023021,1024048..1024210,1024586..1024735,
                     1024802..1024959,1026260..1026433,1026743..1026881,
                     1026983..1027167,1027913..1028054,1028271..1029276)
                     /gene="CYP2W1"
                     /gene_synonym="MGC34287"
                     /product="cytochrome P450, family 2, subfamily W,
                     polypeptide 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017781.2"
                     /db_xref="GI:64368471"
                     /db_xref="GeneID:54905"
                     /db_xref="HGNC:20243"
                     /db_xref="HPRD:07901"
     CDS             join(1022848..1023021,1024048..1024210,1024586..1024735,
                     1024802..1024959,1026260..1026433,1026743..1026881,
                     1026983..1027167,1027913..1028054,1028271..1028458)
                     /gene="CYP2W1"
                     /gene_synonym="MGC34287"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytochrome P450 2W1"
                     /protein_id="NP_060251.2"
                     /db_xref="GI:64368472"
                     /db_xref="CCDS:CCDS5319.2"
                     /db_xref="GeneID:54905"
                     /db_xref="HGNC:20243"
                     /db_xref="HPRD:07901"
     gene            complement(1036623..1177893)
                     /gene="C7orf50"
                     /gene_synonym="MGC11257; YCR016W"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84310"
                     /db_xref="HGNC:22421"
                     /db_xref="HPRD:14413"
     mRNA            complement(join(1036623..1037440,1040106..1040187,
                     1049586..1049779,1166893..1167022,1177825..1177893))
                     /gene="C7orf50"
                     /gene_synonym="MGC11257; YCR016W"
                     /product="chromosome 7 open reading frame 50, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032350.5"
                     /db_xref="GI:197304706"
                     /db_xref="GeneID:84310"
                     /db_xref="HGNC:22421"
                     /db_xref="HPRD:14413"
     mRNA            complement(join(1036623..1037440,1040106..1040187,
                     1049586..1049779,1166893..1167022,1177835..1177893))
                     /gene="C7orf50"
                     /gene_synonym="MGC11257; YCR016W"
                     /product="chromosome 7 open reading frame 50, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134395.1"
                     /db_xref="GI:197304707"
                     /db_xref="GeneID:84310"
                     /db_xref="HGNC:22421"
                     /db_xref="HPRD:14413"
     mRNA            complement(join(1036623..1037440,1040106..1040187,
                     1049586..1049779,1166893..1167022,1177854..1177893))
                     /gene="C7orf50"
                     /gene_synonym="MGC11257; YCR016W"
                     /product="chromosome 7 open reading frame 50, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134396.1"
                     /db_xref="GI:197304709"
                     /db_xref="GeneID:84310"
                     /db_xref="HGNC:22421"
                     /db_xref="HPRD:14413"
     CDS             complement(join(1037261..1037440,1040106..1040187,
                     1049586..1049779,1166893..1167021))
                     /gene="C7orf50"
                     /gene_synonym="MGC11257; YCR016W"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC84310"
                     /protein_id="NP_115726.1"
                     /db_xref="GI:14150149"
                     /db_xref="CCDS:CCDS5320.1"
                     /db_xref="GeneID:84310"
                     /db_xref="HGNC:22421"
                     /db_xref="HPRD:14413"
     CDS             complement(join(1037261..1037440,1040106..1040187,
                     1049586..1049779,1166893..1167021))
                     /gene="C7orf50"
                     /gene_synonym="MGC11257; YCR016W"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC84310"
                     /protein_id="NP_001127867.1"
                     /db_xref="GI:197304708"
                     /db_xref="CCDS:CCDS5320.1"
                     /db_xref="GeneID:84310"
                     /db_xref="HGNC:22421"
                     /db_xref="HPRD:14413"
     CDS             complement(join(1037261..1037440,1040106..1040187,
                     1049586..1049779,1166893..1167021))
                     /gene="C7orf50"
                     /gene_synonym="MGC11257; YCR016W"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC84310"
                     /protein_id="NP_001127868.1"
                     /db_xref="GI:197304710"
                     /db_xref="CCDS:CCDS5320.1"
                     /db_xref="GeneID:84310"
                     /db_xref="HGNC:22421"
                     /db_xref="HPRD:14413"
     gene            complement(1062569..1062662)
                     /gene="MIR339"
                     /gene_synonym="hsa-mir-339; MIRN339"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:442907"
                     /db_xref="HGNC:31776"
                     /db_xref="miRBase:MI0000815"
     ncRNA           complement(1062569..1062662)
                     /gene="MIR339"
                     /gene_synonym="hsa-mir-339; MIRN339"
                     /ncRNA_class="miRNA"
                     /product="microRNA 339"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029898.1"
                     /db_xref="GI:262206373"
                     /db_xref="GeneID:442907"
                     /db_xref="HGNC:31776"
                     /db_xref="miRBase:MI0000815"
     ncRNA           complement(1062569..1062662)
                     /gene="MIR339"
                     /gene_synonym="hsa-mir-339; MIRN339"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-339"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:442907"
                     /db_xref="miRBase:MI0000815"
                     /db_xref="HGNC:31776"
     gene            1084218..1098903
                     /gene="LOC100505551"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 7 ESTs"
                     /db_xref="GeneID:100505551"
     misc_RNA        join(1084241..1084294,1084973..1086520)
                     /gene="LOC100505551"
                     /product="hypothetical LOC100505551"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 7 ESTs"
                     /transcript_id="XR_108725.1"
                     /db_xref="GI:310119896"
                     /db_xref="GeneID:100505551"
     gene            1094915..1096188
                     /gene="LOC100505568"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /db_xref="GeneID:100505568"
     misc_RNA        join(1094915..1095119,1095740..1096188)
                     /gene="LOC100505568"
                     /product="hypothetical LOC100505568"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_108726.1"
                     /db_xref="GI:310119897"
                     /db_xref="GeneID:100505568"
     gene            1097141..1098897
                     /gene="GPR146"
                     /gene_synonym="PGR8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:115330"
                     /db_xref="HGNC:21718"
                     /db_xref="HPRD:17064"
     mRNA            1097141..1098897
                     /gene="GPR146"
                     /gene_synonym="PGR8"
                     /product="G protein-coupled receptor 146"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138445.2"
                     /db_xref="GI:41349503"
                     /db_xref="GeneID:115330"
                     /db_xref="HGNC:21718"
                     /db_xref="HPRD:17064"
     CDS             1097152..1098153
                     /gene="GPR146"
                     /gene_synonym="PGR8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable G-protein coupled receptor 146"
                     /protein_id="NP_612454.1"
                     /db_xref="GI:19923975"
                     /db_xref="CCDS:CCDS5321.1"
                     /db_xref="GeneID:115330"
                     /db_xref="HGNC:21718"
                     /db_xref="HPRD:17064"
     gene            1126443..1133451
                     /gene="GPER"
                     /gene_synonym="CEPR; CMKRL2; DRY12; FEG-1; GPCR-Br; GPR30;
                     LERGU; LERGU2; LyGPR; MGC99678"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2852"
                     /db_xref="HGNC:4485"
                     /db_xref="MIM:601805"
     mRNA            join(1126443..1126880,1131043..1133451)
                     /gene="GPER"
                     /gene_synonym="CEPR; CMKRL2; DRY12; FEG-1; GPCR-Br; GPR30;
                     LERGU; LERGU2; LyGPR; MGC99678"
                     /product="G protein-coupled estrogen receptor 1,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001505.2"
                     /db_xref="GI:91106388"
                     /db_xref="GeneID:2852"
                     /db_xref="HGNC:4485"
                     /db_xref="HPRD:03484"
                     /db_xref="MIM:601805"
     mRNA            join(1126443..1126880,1127834..1127957,1131043..1133451)
                     /gene="GPER"
                     /gene_synonym="CEPR; CMKRL2; DRY12; FEG-1; GPCR-Br; GPR30;
                     LERGU; LERGU2; LyGPR; MGC99678"
                     /product="G protein-coupled estrogen receptor 1,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001039966.1"
                     /db_xref="GI:91106713"
                     /db_xref="GeneID:2852"
                     /db_xref="HGNC:4485"
                     /db_xref="MIM:601805"
     mRNA            join(1127723..1127957,1131043..1133451)
                     /gene="GPER"
                     /gene_synonym="CEPR; CMKRL2; DRY12; FEG-1; GPCR-Br; GPR30;
                     LERGU; LERGU2; LyGPR; MGC99678"
                     /product="G protein-coupled estrogen receptor 1,
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001098201.1"
                     /db_xref="GI:148228790"
                     /db_xref="GeneID:2852"
                     /db_xref="HGNC:4485"
                     /db_xref="MIM:601805"
     CDS             1131365..1132492
                     /gene="GPER"
                     /gene_synonym="CEPR; CMKRL2; DRY12; FEG-1; GPCR-Br; GPR30;
                     LERGU; LERGU2; LyGPR; MGC99678"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="G-protein coupled estrogen receptor 1"
                     /protein_id="NP_001091671.1"
                     /db_xref="GI:148228791"
                     /db_xref="CCDS:CCDS5322.1"
                     /db_xref="GeneID:2852"
                     /db_xref="HGNC:4485"
                     /db_xref="MIM:601805"
     CDS             1131365..1132492
                     /gene="GPER"
                     /gene_synonym="CEPR; CMKRL2; DRY12; FEG-1; GPCR-Br; GPR30;
                     LERGU; LERGU2; LyGPR; MGC99678"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="G-protein coupled estrogen receptor 1"
                     /protein_id="NP_001496.1"
                     /db_xref="GI:4504091"
                     /db_xref="CCDS:CCDS5322.1"
                     /db_xref="GeneID:2852"
                     /db_xref="HGNC:4485"
                     /db_xref="MIM:601805"
     CDS             1131365..1132492
                     /gene="GPER"
                     /gene_synonym="CEPR; CMKRL2; DRY12; FEG-1; GPCR-Br; GPR30;
                     LERGU; LERGU2; LyGPR; MGC99678"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="G-protein coupled estrogen receptor 1"
                     /protein_id="NP_001035055.1"
                     /db_xref="GI:91106714"
                     /db_xref="CCDS:CCDS5322.1"
                     /db_xref="GeneID:2852"
                     /db_xref="HGNC:4485"
                     /db_xref="MIM:601805"
     gene            complement(1192543..1199855)
                     /gene="ZFAND2A"
                     /gene_synonym="AIRAP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:90637"
                     /db_xref="HGNC:28073"
                     /db_xref="HPRD:14277"
                     /db_xref="MIM:610699"
     mRNA            complement(join(1192543..1192860,1195089..1195220,
                     1197292..1197386,1197794..1197893,1199600..1199855))
                     /gene="ZFAND2A"
                     /gene_synonym="AIRAP"
                     /product="zinc finger, AN1-type domain 2A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182491.2"
                     /db_xref="GI:226532847"
                     /db_xref="GeneID:90637"
                     /db_xref="HGNC:28073"
                     /db_xref="HPRD:14277"
                     /db_xref="MIM:610699"
     CDS             complement(join(1192705..1192860,1195089..1195220,
                     1197292..1197386,1197794..1197848))
                     /gene="ZFAND2A"
                     /gene_synonym="AIRAP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="AN1-type zinc finger protein 2A"
                     /protein_id="NP_872297.2"
                     /db_xref="GI:226532848"
                     /db_xref="CCDS:CCDS5323.1"
                     /db_xref="GeneID:90637"
                     /db_xref="HGNC:28073"
                     /db_xref="HPRD:14277"
                     /db_xref="MIM:610699"
     gene            1272654..1276613
                     /gene="UNCX"
                     /gene_synonym="UNCX4.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:340260"
                     /db_xref="HGNC:33194"
     mRNA            join(1272654..1272927,1273156..1273331,1275468..1276613)
                     /gene="UNCX"
                     /gene_synonym="UNCX4.1"
                     /product="UNC homeobox"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001080461.1"
                     /db_xref="GI:122937320"
                     /db_xref="GeneID:340260"
                     /db_xref="HGNC:33194"
     CDS             join(1272654..1272927,1273156..1273331,1275468..1276613)
                     /gene="UNCX"
                     /gene_synonym="UNCX4.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein unc-4 homolog"
                     /protein_id="NP_001073930.1"
                     /db_xref="GI:122937321"
                     /db_xref="CCDS:CCDS34583.1"
                     /db_xref="GeneID:340260"
                     /db_xref="HGNC:33194"
     gene            complement(1473995..1499109)
                     /gene="MICALL2"
                     /gene_synonym="FLJ23471; FLJ41996; FLJ44858; FLJ45410;
                     JRAB; MGC46023; MICAL-L2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79778"
                     /db_xref="HGNC:29672"
                     /db_xref="HPRD:11364"
     mRNA            complement(join(1473995..1474308,1474737..1474783,
                     1476378..1476492,1477171..1477244,1477526..1477616,
                     1477733..1477856,1477925..1477989,1478476..1478631,
                     1479561..1479721,1480227..1480320,1481828..1482120,
                     1484288..1485064,1486349..1486464,1487211..1487401,
                     1488256..1488397,1489876..1489924,1498820..1499109))
                     /gene="MICALL2"
                     /gene_synonym="FLJ23471; FLJ41996; FLJ44858; FLJ45410;
                     JRAB; MGC46023; MICAL-L2"
                     /product="MICAL-like 2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182924.3"
                     /db_xref="GI:157694514"
                     /db_xref="GeneID:79778"
                     /db_xref="HGNC:29672"
                     /db_xref="HPRD:11364"
     CDS             complement(join(1474232..1474308,1474737..1474783,
                     1476378..1476492,1477171..1477244,1477526..1477616,
                     1477733..1477856,1477925..1477989,1478476..1478631,
                     1479561..1479721,1480227..1480320,1481828..1482120,
                     1484288..1485064,1486349..1486464,1487211..1487401,
                     1488256..1488397,1489876..1489924,1498820..1498962))
                     /gene="MICALL2"
                     /gene_synonym="FLJ23471; FLJ41996; FLJ44858; FLJ45410;
                     JRAB; MGC46023; MICAL-L2"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="MICAL-like protein 2 isoform 1"
                     /protein_id="NP_891554.1"
                     /db_xref="GI:33667117"
                     /db_xref="CCDS:CCDS5324.1"
                     /db_xref="GeneID:79778"
                     /db_xref="HGNC:29672"
                     /db_xref="HPRD:11364"
     gene            complement(1509913..1544018)
                     /gene="INTS1"
                     /gene_synonym="DKFZp586J0619; FLJ46624; INT1; KIAA1440;
                     NET28"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26173"
                     /db_xref="HGNC:24555"
                     /db_xref="MIM:611345"
     mRNA            complement(join(1509913..1510328,1510482..1510591,
                     1510769..1510860,1511207..1511277,1511909..1512022,
                     1512708..1512820,1513202..1513329,1513804..1513996,
                     1514341..1514474,1515584..1515707,1515865..1516091,
                     1516206..1516293,1516430..1516554,1517186..1517309,
                     1517389..1517572,1518002..1518142,1518362..1518521,
                     1519066..1519320,1519953..1520077,1520471..1520569,
                     1520978..1521124,1522182..1522343,1523378..1523489,
                     1523639..1523806,1524734..1524838,1524926..1525105,
                     1526261..1526410,1526558..1526737,1526956..1527085,
                     1527396..1527593,1528980..1529040,1529227..1529318,
                     1532646..1532742,1533390..1533547,1534452..1534529,
                     1535069..1535189,1535792..1535900,1536774..1536950,
                     1538048..1538189,1538343..1538488,1538611..1538797,
                     1538891..1538996,1539109..1539268,1539520..1539657,
                     1539806..1540002,1542537..1542827,1543539..1543637,
                     1543959..1544018))
                     /gene="INTS1"
                     /gene_synonym="DKFZp586J0619; FLJ46624; INT1; KIAA1440;
                     NET28"
                     /product="integrator complex subunit 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001080453.2"
                     /db_xref="GI:160948598"
                     /db_xref="GeneID:26173"
                     /db_xref="HGNC:24555"
                     /db_xref="MIM:611345"
     CDS             complement(join(1510213..1510328,1510482..1510591,
                     1510769..1510860,1511207..1511277,1511909..1512022,
                     1512708..1512820,1513202..1513329,1513804..1513996,
                     1514341..1514474,1515584..1515707,1515865..1516091,
                     1516206..1516293,1516430..1516554,1517186..1517309,
                     1517389..1517572,1518002..1518142,1518362..1518521,
                     1519066..1519320,1519953..1520077,1520471..1520569,
                     1520978..1521124,1522182..1522343,1523378..1523489,
                     1523639..1523806,1524734..1524838,1524926..1525105,
                     1526261..1526410,1526558..1526737,1526956..1527085,
                     1527396..1527593,1528980..1529040,1529227..1529318,
                     1532646..1532742,1533390..1533547,1534452..1534529,
                     1535069..1535189,1535792..1535900,1536774..1536950,
                     1538048..1538189,1538343..1538488,1538611..1538797,
                     1538891..1538996,1539109..1539268,1539520..1539657,
                     1539806..1540002,1542537..1542827,1543539..1543596))
                     /gene="INTS1"
                     /gene_synonym="DKFZp586J0619; FLJ46624; INT1; KIAA1440;
                     NET28"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="integrator complex subunit 1"
                     /protein_id="NP_001073922.2"
                     /db_xref="GI:160948599"
                     /db_xref="CCDS:CCDS47526.1"
                     /db_xref="GeneID:26173"
                     /db_xref="HGNC:24555"
                     /db_xref="MIM:611345"
     gene            1570368..1582679
                     /gene="MAFK"
                     /gene_synonym="FLJ32205; MGC71717; NFE2U; P18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7975"
                     /db_xref="HGNC:6782"
                     /db_xref="HPRD:02561"
                     /db_xref="MIM:600197"
     mRNA            join(1570368..1570534,1578785..1578864,1579577..1582679)
                     /gene="MAFK"
                     /gene_synonym="FLJ32205; MGC71717; NFE2U; P18"
                     /product="v-maf musculoaponeurotic fibrosarcoma oncogene
                     homolog K (avian)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002360.3"
                     /db_xref="GI:82617644"
                     /db_xref="GeneID:7975"
                     /db_xref="HGNC:6782"
                     /db_xref="HPRD:02561"
                     /db_xref="MIM:600197"
     gene            complement(1572090..1574516)
                     /gene="LOC100128653"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 10 ESTs, 1 Protein"
                     /db_xref="GeneID:100128653"
     misc_RNA        complement(1572090..1574516)
                     /gene="LOC100128653"
                     /product="hypothetical LOC100128653"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 10 ESTs, 1 Protein"
                     /transcript_id="XR_108727.1"
                     /db_xref="GI:310119898"
                     /db_xref="GeneID:100128653"
     CDS             join(1578829..1578864,1579577..1580011)
                     /gene="MAFK"
                     /gene_synonym="FLJ32205; MGC71717; NFE2U; P18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transcription factor MafK"
                     /protein_id="NP_002351.1"
                     /db_xref="GI:4505075"
                     /db_xref="CCDS:CCDS5325.1"
                     /db_xref="GeneID:7975"
                     /db_xref="HGNC:6782"
                     /db_xref="HPRD:02561"
                     /db_xref="MIM:600197"
     gene            complement(1581871..1596066)
                     /gene="TMEM184A"
                     /gene_synonym="FLJ24011; MGC9712"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:202915"
                     /db_xref="HGNC:28797"
     mRNA            complement(join(1581871..1586817,1587378..1587575,
                     1588155..1588324,1589490..1589581,1589759..1589834,
                     1589941..1590031,1590453..1590618,1594902..1595120,
                     1595750..1596066))
                     /gene="TMEM184A"
                     /gene_synonym="FLJ24011; MGC9712"
                     /product="transmembrane protein 184A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001097620.1"
                     /db_xref="GI:148276980"
                     /db_xref="GeneID:202915"
                     /db_xref="HGNC:28797"
     CDS             complement(join(1586588..1586817,1587378..1587575,
                     1588155..1588324,1589490..1589581,1589759..1589834,
                     1589941..1590031,1590453..1590618,1594902..1595120))
                     /gene="TMEM184A"
                     /gene_synonym="FLJ24011; MGC9712"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 184A"
                     /protein_id="NP_001091089.1"
                     /db_xref="GI:148276981"
                     /db_xref="CCDS:CCDS43537.1"
                     /db_xref="GeneID:202915"
                     /db_xref="HGNC:28797"
     gene            complement(1606968..1609668)
                     /gene="PSMG3"
                     /gene_synonym="C7orf48; MGC10911; PAC3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84262"
                     /db_xref="HGNC:22420"
                     /db_xref="HPRD:14404"
     mRNA            complement(join(1606968..1607486,1608760..1608996,
                     1609645..1609668))
                     /gene="PSMG3"
                     /gene_synonym="C7orf48; MGC10911; PAC3"
                     /product="proteasome (prosome, macropain) assembly
                     chaperone 3, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134340.1"
                     /db_xref="GI:197245457"
                     /db_xref="GeneID:84262"
                     /db_xref="HGNC:22420"
                     /db_xref="HPRD:14404"
     mRNA            complement(join(1606968..1607486,1608760..1609629))
                     /gene="PSMG3"
                     /gene_synonym="C7orf48; MGC10911; PAC3"
                     /product="proteasome (prosome, macropain) assembly
                     chaperone 3, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032302.3"
                     /db_xref="GI:197245456"
                     /db_xref="GeneID:84262"
                     /db_xref="HGNC:22420"
                     /db_xref="HPRD:14404"
     CDS             complement(join(1607334..1607486,1608760..1608975))
                     /gene="PSMG3"
                     /gene_synonym="C7orf48; MGC10911; PAC3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="proteasome assembly chaperone 3"
                     /protein_id="NP_115678.1"
                     /db_xref="GI:14150060"
                     /db_xref="CCDS:CCDS5327.1"
                     /db_xref="GeneID:84262"
                     /db_xref="HGNC:22420"
                     /db_xref="HPRD:14404"
     CDS             complement(join(1607334..1607486,1608760..1608975))
                     /gene="PSMG3"
                     /gene_synonym="C7orf48; MGC10911; PAC3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="proteasome assembly chaperone 3"
                     /protein_id="NP_001127812.1"
                     /db_xref="GI:197245458"
                     /db_xref="CCDS:CCDS5327.1"
                     /db_xref="GeneID:84262"
                     /db_xref="HGNC:22420"
                     /db_xref="HPRD:14404"
     gene            1609709..1629262
                     /gene="KIAA1908"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:114796"
     misc_RNA        join(1609709..1609915,1614351..1614499,1615423..1615524,
                     1622798..1622905,1624020..1629262)
                     /gene="KIAA1908"
                     /product="hypothetical LOC114796, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027329.1"
                     /db_xref="GI:224967046"
                     /db_xref="GeneID:114796"
     misc_RNA        join(1609709..1609915,1614351..1614499,1615423..1615524,
                     1624020..1629262)
                     /gene="KIAA1908"
                     /product="hypothetical LOC114796, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027328.1"
                     /db_xref="GI:224967045"
                     /db_xref="GeneID:114796"
     misc_RNA        join(1609709..1610169,1614351..1614499,1615423..1615524,
                     1622798..1622905,1624020..1625253,1627457..1629262)
                     /gene="KIAA1908"
                     /product="hypothetical LOC114796, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_021487.2"
                     /db_xref="GI:224967135"
                     /db_xref="GeneID:114796"
     gene            1654106..1656328
                     /gene="TFAMP1"
                     /gene_synonym="MTTF1; TCF6L1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:260341"
                     /db_xref="HGNC:11636"
     misc_RNA        1654106..1656328
                     /gene="TFAMP1"
                     /gene_synonym="MTTF1; TCF6L1"
                     /product="transcription factor A, mitochondrial pseudogene
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_001288.1"
                     /db_xref="GI:29171303"
                     /db_xref="GeneID:260341"
                     /db_xref="HGNC:11636"
     gene            complement(1732446..1733961)
                     /gene="LOC401296"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 3 mRNAs, 3 ESTs, 2 Proteins"
                     /db_xref="GeneID:401296"
     misc_RNA        complement(join(1732446..1733721,1733815..1733961))
                     /gene="LOC401296"
                     /product="hypothetical LOC401296"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 3 mRNAs, 3 ESTs, 2 Proteins"
                     /transcript_id="XR_108728.1"
                     /db_xref="GI:310119899"
                     /db_xref="GeneID:401296"
     gene            1748798..1787590
                     /gene="ELFN1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:392617"
                     /db_xref="HGNC:33154"
     mRNA            join(1748798..1748888,1783940..1787590)
                     /gene="ELFN1"
                     /product="extracellular leucine-rich repeat and
                     fibronectin type III domain containing 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001128636.2"
                     /db_xref="GI:253970413"
                     /db_xref="GeneID:392617"
                     /db_xref="HGNC:33154"
     gene            complement(1778266..1781940)
                     /gene="LOC100505644"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 15 ESTs"
                     /db_xref="GeneID:100505644"
     misc_RNA        complement(join(1778266..1778838,1781845..1781940))
                     /gene="LOC100505644"
                     /product="hypothetical LOC100505644, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 13 ESTs"
                     /transcript_id="XR_108729.1"
                     /db_xref="GI:310119900"
                     /db_xref="GeneID:100505644"
     misc_RNA        complement(join(1778266..1778974,1781845..1781929))
                     /gene="LOC100505644"
                     /product="hypothetical LOC100505644, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 11 ESTs"
                     /transcript_id="XR_132527.1"
                     /db_xref="GI:341915379"
                     /db_xref="GeneID:100505644"
     CDS             1784233..1786719
                     /gene="ELFN1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="extracellular leucine-rich repeat and
                     fibronectin type-III domain-containing protein 1"
                     /protein_id="NP_001122108.1"
                     /db_xref="GI:191252816"
                     /db_xref="GeneID:392617"
                     /db_xref="HGNC:33154"
     gene            complement(1855428..2272583)
                     /gene="MAD1L1"
                     /gene_synonym="MAD1; PIG9; TP53I9; TXBP181"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8379"
                     /db_xref="HGNC:6762"
                     /db_xref="HPRD:04065"
                     /db_xref="MIM:602686"
     mRNA            complement(join(1855428..1855864,1937836..1938026,
                     1976323..1976533,1997264..1997354,2020088..2020176,
                     2041700..2041756,2054137..2054277,2108829..2108973,
                     2188787..2188873,2252847..2252908,2255520..2255634,
                     2255792..2255922,2257597..2257678,2258967..2259091,
                     2262210..2262389,2265045..2265185,2269619..2269778,
                     2270184..2270399,2272507..2272583))
                     /gene="MAD1L1"
                     /gene_synonym="MAD1; PIG9; TP53I9; TXBP181"
                     /product="MAD1 mitotic arrest deficient-like 1 (yeast),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003550.2"
                     /db_xref="GI:62243331"
                     /db_xref="GeneID:8379"
                     /db_xref="HGNC:6762"
                     /db_xref="HPRD:04065"
                     /db_xref="MIM:602686"
     mRNA            complement(join(1855428..1855864,1937836..1938026,
                     1976323..1976533,1997264..1997354,2020088..2020176,
                     2041700..2041756,2054137..2054277,2108829..2108973,
                     2188787..2188873,2252847..2252908,2255520..2255634,
                     2255792..2255922,2257597..2257678,2258967..2259091,
                     2262210..2262389,2265045..2265185,2269619..2269778,
                     2270184..2270362,2272507..2272583))
                     /gene="MAD1L1"
                     /gene_synonym="MAD1; PIG9; TP53I9; TXBP181"
                     /product="MAD1 mitotic arrest deficient-like 1 (yeast),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001013836.1"
                     /db_xref="GI:62243368"
                     /db_xref="GeneID:8379"
                     /db_xref="HGNC:6762"
                     /db_xref="HPRD:04065"
                     /db_xref="MIM:602686"
     mRNA            complement(join(1855428..1855864,1937836..1938026,
                     1976323..1976533,1997264..1997354,2020088..2020176,
                     2041700..2041756,2054137..2054277,2108829..2108973,
                     2188787..2188873,2252847..2252908,2255520..2255634,
                     2255792..2255922,2257597..2257678,2258967..2259091,
                     2262210..2262389,2265045..2265185,2269619..2269778,
                     2270184..2270359,2272507..2272583))
                     /gene="MAD1L1"
                     /gene_synonym="MAD1; PIG9; TP53I9; TXBP181"
                     /product="MAD1 mitotic arrest deficient-like 1 (yeast),
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001013837.1"
                     /db_xref="GI:62243373"
                     /db_xref="GeneID:8379"
                     /db_xref="HGNC:6762"
                     /db_xref="HPRD:04065"
                     /db_xref="MIM:602686"
     CDS             complement(join(1855706..1855864,1937836..1938026,
                     1976323..1976533,1997264..1997354,2020088..2020176,
                     2041700..2041756,2054137..2054277,2108829..2108973,
                     2188787..2188873,2252847..2252908,2255520..2255634,
                     2255792..2255922,2257597..2257678,2258967..2259091,
                     2262210..2262389,2265045..2265185,2269619..2269768))
                     /gene="MAD1L1"
                     /gene_synonym="MAD1; PIG9; TP53I9; TXBP181"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="mitotic spindle assembly checkpoint protein
                     MAD1"
                     /protein_id="NP_003541.2"
                     /db_xref="GI:62243332"
                     /db_xref="CCDS:CCDS43539.1"
                     /db_xref="GeneID:8379"
                     /db_xref="HGNC:6762"
                     /db_xref="HPRD:04065"
                     /db_xref="MIM:602686"
     CDS             complement(join(1855706..1855864,1937836..1938026,
                     1976323..1976533,1997264..1997354,2020088..2020176,
                     2041700..2041756,2054137..2054277,2108829..2108973,
                     2188787..2188873,2252847..2252908,2255520..2255634,
                     2255792..2255922,2257597..2257678,2258967..2259091,
                     2262210..2262389,2265045..2265185,2269619..2269768))
                     /gene="MAD1L1"
                     /gene_synonym="MAD1; PIG9; TP53I9; TXBP181"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="mitotic spindle assembly checkpoint protein
                     MAD1"
                     /protein_id="NP_001013858.1"
                     /db_xref="GI:62243369"
                     /db_xref="CCDS:CCDS43539.1"
                     /db_xref="GeneID:8379"
                     /db_xref="HGNC:6762"
                     /db_xref="HPRD:04065"
                     /db_xref="MIM:602686"
     CDS             complement(join(1855706..1855864,1937836..1938026,
                     1976323..1976533,1997264..1997354,2020088..2020176,
                     2041700..2041756,2054137..2054277,2108829..2108973,
                     2188787..2188873,2252847..2252908,2255520..2255634,
                     2255792..2255922,2257597..2257678,2258967..2259091,
                     2262210..2262389,2265045..2265185,2269619..2269768))
                     /gene="MAD1L1"
                     /gene_synonym="MAD1; PIG9; TP53I9; TXBP181"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="mitotic spindle assembly checkpoint protein
                     MAD1"
                     /protein_id="NP_001013859.1"
                     /db_xref="GI:62243374"
                     /db_xref="CCDS:CCDS43539.1"
                     /db_xref="GeneID:8379"
                     /db_xref="HGNC:6762"
                     /db_xref="HPRD:04065"
                     /db_xref="MIM:602686"
     gene            1878222..1889567
                     /gene="LOC100128374"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 3 ESTs, 1 Protein"
                     /db_xref="GeneID:100128374"
     misc_RNA        join(1878222..1878504,1886884..1889567)
                     /gene="LOC100128374"
                     /product="hypothetical LOC100128374"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 3 ESTs, 1 Protein"
                     /transcript_id="XR_108730.1"
                     /db_xref="GI:310119901"
                     /db_xref="GeneID:100128374"
     gene            complement(1883816..1883889)
                     /gene="MIR4655"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100616160"
                     /db_xref="HGNC:41754"
                     /db_xref="miRBase:MI0017283"
     ncRNA           complement(1883816..1883889)
                     /gene="MIR4655"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4655"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039799.1"
                     /db_xref="GI:337756599"
                     /db_xref="GeneID:100616160"
                     /db_xref="HGNC:41754"
                     /db_xref="miRBase:MI0017283"
     gene            complement(2273926..2281833)
                     /gene="FTSJ2"
                     /gene_synonym="DKFZp686J14194; FJH1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:29960"
                     /db_xref="HGNC:16352"
                     /db_xref="HPRD:06067"
                     /db_xref="MIM:606906"
     mRNA            complement(join(2273926..2275199,2279053..2279342,
                     2281797..2281833))
                     /gene="FTSJ2"
                     /gene_synonym="DKFZp686J14194; FJH1"
                     /product="FtsJ homolog 2 (E. coli)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013393.1"
                     /db_xref="GI:7019376"
                     /db_xref="GeneID:29960"
                     /db_xref="HGNC:16352"
                     /db_xref="HPRD:06067"
                     /db_xref="MIM:606906"
     CDS             complement(join(2274757..2275199,2279053..2279342,
                     2281797..2281804))
                     /gene="FTSJ2"
                     /gene_synonym="DKFZp686J14194; FJH1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative ribosomal RNA methyltransferase 2"
                     /protein_id="NP_037525.1"
                     /db_xref="GI:7019377"
                     /db_xref="CCDS:CCDS5328.1"
                     /db_xref="GeneID:29960"
                     /db_xref="HGNC:16352"
                     /db_xref="HPRD:06067"
                     /db_xref="MIM:606906"
     gene            2281857..2290780
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="HPRD:02634"
                     /db_xref="MIM:600312"
     mRNA            join(2281857..2281891,2284198..2284361,2289492..2289637,
                     2290464..2290780)
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /product="nudix (nucleoside diphosphate linked moiety
                     X)-type motif 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002452.3"
                     /db_xref="GI:40288273"
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="HPRD:02634"
                     /db_xref="MIM:600312"
     mRNA            join(2281857..2281891,2282560..2282610,2284198..2284361,
                     2289492..2289637,2290464..2290780)
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /product="nudix (nucleoside diphosphate linked moiety
                     X)-type motif 1, transcript variant 2A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198948.1"
                     /db_xref="GI:40288275"
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="MIM:600312"
                     /db_xref="HPRD:02634"
     mRNA            join(2281857..2281891,2282560..2282683,2284198..2284361,
                     2289492..2289637,2290464..2290780)
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /product="nudix (nucleoside diphosphate linked moiety
                     X)-type motif 1, transcript variant 2B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198949.1"
                     /db_xref="GI:40288277"
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="HPRD:02634"
                     /db_xref="MIM:600312"
     mRNA            join(2281896..2281927,2282560..2282610,2284198..2284361,
                     2289492..2289637,2290464..2290780)
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /product="nudix (nucleoside diphosphate linked moiety
                     X)-type motif 1, transcript variant 3A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198950.1"
                     /db_xref="GI:40288279"
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="MIM:600312"
                     /db_xref="HPRD:02634"
     mRNA            join(2281896..2281927,2282560..2282683,2284198..2284361,
                     2289492..2289637,2290464..2290780)
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /product="nudix (nucleoside diphosphate linked moiety
                     X)-type motif 1, transcript variant 3B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198952.1"
                     /db_xref="GI:40288281"
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="HPRD:02634"
                     /db_xref="MIM:600312"
     mRNA            join(2282540..2282610,2284198..2284361,2289492..2289637,
                     2290464..2290780)
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /product="nudix (nucleoside diphosphate linked moiety
                     X)-type motif 1, transcript variant 4A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198953.1"
                     /db_xref="GI:40288283"
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="HPRD:02634"
                     /db_xref="MIM:600312"
     mRNA            join(2282540..2282683,2284198..2284361,2289492..2289637,
                     2290464..2290780)
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /product="nudix (nucleoside diphosphate linked moiety
                     X)-type motif 1, transcript variant 4B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198954.1"
                     /db_xref="GI:40288285"
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="MIM:600312"
                     /db_xref="HPRD:02634"
     CDS             join(2282627..2282683,2284198..2284361,2289492..2289637,
                     2290464..2290636)
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /note="isoform p22 is encoded by transcript variant 2B;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="7,8-dihydro-8-oxoguanine triphosphatase isoform
                     p22"
                     /protein_id="NP_945187.1"
                     /db_xref="GI:40288278"
                     /db_xref="CCDS:CCDS5329.1"
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="HPRD:02634"
                     /db_xref="MIM:600312"
     CDS             join(2282627..2282683,2284198..2284361,2289492..2289637,
                     2290464..2290636)
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /note="isoform p22 is encoded by transcript variant 3B;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="7,8-dihydro-8-oxoguanine triphosphatase isoform
                     p22"
                     /protein_id="NP_945190.1"
                     /db_xref="GI:40288282"
                     /db_xref="CCDS:CCDS5329.1"
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="HPRD:02634"
                     /db_xref="MIM:600312"
     CDS             join(2282627..2282683,2284198..2284361,2289492..2289637,
                     2290464..2290636)
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /note="isoform p22 is encoded by transcript variant 4B;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="7,8-dihydro-8-oxoguanine triphosphatase isoform
                     p22"
                     /protein_id="NP_945192.1"
                     /db_xref="GI:40288286"
                     /db_xref="CCDS:CCDS5329.1"
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="HPRD:02634"
                     /db_xref="MIM:600312"
     CDS             join(2284210..2284361,2289492..2289637,2290464..2290636)
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /note="isoform p18 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="7,8-dihydro-8-oxoguanine triphosphatase isoform
                     p18"
                     /protein_id="NP_002443.3"
                     /db_xref="GI:40288274"
                     /db_xref="CCDS:CCDS5330.1"
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="HPRD:02634"
                     /db_xref="MIM:600312"
     CDS             join(2284210..2284361,2289492..2289637,2290464..2290636)
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /note="isoform p18 is encoded by transcript variant 2A;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="7,8-dihydro-8-oxoguanine triphosphatase isoform
                     p18"
                     /protein_id="NP_945186.1"
                     /db_xref="GI:40288276"
                     /db_xref="CCDS:CCDS5330.1"
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="HPRD:02634"
                     /db_xref="MIM:600312"
     CDS             join(2284210..2284361,2289492..2289637,2290464..2290636)
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /note="isoform p18 is encoded by transcript variant 3A;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="7,8-dihydro-8-oxoguanine triphosphatase isoform
                     p18"
                     /protein_id="NP_945188.1"
                     /db_xref="GI:40288280"
                     /db_xref="CCDS:CCDS5330.1"
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="HPRD:02634"
                     /db_xref="MIM:600312"
     CDS             join(2284210..2284361,2289492..2289637,2290464..2290636)
                     /gene="NUDT1"
                     /gene_synonym="MTH1"
                     /note="isoform p18 is encoded by transcript variant 4A;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="7,8-dihydro-8-oxoguanine triphosphatase isoform
                     p18"
                     /protein_id="NP_945191.1"
                     /db_xref="GI:40288284"
                     /db_xref="CCDS:CCDS5330.1"
                     /db_xref="GeneID:4521"
                     /db_xref="HGNC:8048"
                     /db_xref="HPRD:02634"
                     /db_xref="MIM:600312"
     gene            complement(2291405..2354099)
                     /gene="SNX8"
                     /gene_synonym="DKFZp761E1721; Mvp1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:29886"
                     /db_xref="HGNC:14972"
                     /db_xref="HPRD:11592"
     mRNA            complement(join(2291405..2294804,2296509..2296658,
                     2297000..2297149,2297370..2297438,2302865..2302997,
                     2303933..2304093,2309194..2309274,2311485..2311606,
                     2314747..2314864,2317735..2317940,2353963..2354099))
                     /gene="SNX8"
                     /gene_synonym="DKFZp761E1721; Mvp1"
                     /product="sorting nexin 8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013321.2"
                     /db_xref="GI:309747082"
                     /db_xref="GeneID:29886"
                     /db_xref="HGNC:14972"
                     /db_xref="HPRD:11592"
     CDS             complement(join(2294691..2294804,2296509..2296658,
                     2297000..2297149,2297370..2297438,2302865..2302997,
                     2303933..2304093,2309194..2309274,2311485..2311606,
                     2314747..2314864,2317735..2317940,2353963..2354056))
                     /gene="SNX8"
                     /gene_synonym="DKFZp761E1721; Mvp1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="sorting nexin-8"
                     /protein_id="NP_037453.1"
                     /db_xref="GI:23943858"
                     /db_xref="CCDS:CCDS5331.1"
                     /db_xref="GeneID:29886"
                     /db_xref="HGNC:14972"
                     /db_xref="HPRD:11592"
     gene            2394474..2420380
                     /gene="EIF3B"
                     /gene_synonym="EIF3-ETA; EIF3-P110; EIF3-P116; EIF3S9;
                     MGC104664; MGC131875; PRT1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8662"
                     /db_xref="HGNC:3280"
                     /db_xref="MIM:603917"
     mRNA            join(2394474..2395055,2400345..2400537,2402280..2402399,
                     2402705..2402762,2403267..2403395,2404007..2404164,
                     2405952..2406083,2406160..2406226,2406634..2406680,
                     2409107..2409317,2411412..2411484,2412308..2412430,
                     2414163..2414241,2415024..2415162,2416585..2416710,
                     2418324..2418401,2418769..2418877,2419029..2419146,
                     2419914..2420380)
                     /gene="EIF3B"
                     /gene_synonym="EIF3-ETA; EIF3-P110; EIF3-P116; EIF3S9;
                     MGC104664; MGC131875; PRT1"
                     /product="eukaryotic translation initiation factor 3,
                     subunit B, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003751.3"
                     /db_xref="GI:83367073"
                     /db_xref="GeneID:8662"
                     /db_xref="HGNC:3280"
                     /db_xref="HPRD:06795"
                     /db_xref="MIM:603917"
     mRNA            join(2394474..2395055,2400345..2400537,2402280..2402399,
                     2402705..2402762,2403267..2403395,2404007..2404164,
                     2405952..2406083,2406160..2406226,2406634..2406680,
                     2409107..2409317,2411412..2411484,2412308..2412430,
                     2414163..2414241,2415024..2415162,2416585..2416710,
                     2418324..2418401,2418769..2418877,2419029..2419146,
                     2419839..2420380)
                     /gene="EIF3B"
                     /gene_synonym="EIF3-ETA; EIF3-P110; EIF3-P116; EIF3S9;
                     MGC104664; MGC131875; PRT1"
                     /product="eukaryotic translation initiation factor 3,
                     subunit B, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001037283.1"
                     /db_xref="GI:83367071"
                     /db_xref="GeneID:8662"
                     /db_xref="HGNC:3280"
                     /db_xref="MIM:603917"
     CDS             join(2394557..2395055,2400345..2400537,2402280..2402399,
                     2402705..2402762,2403267..2403395,2404007..2404164,
                     2405952..2406083,2406160..2406226,2406634..2406680,
                     2409107..2409317,2411412..2411484,2412308..2412430,
                     2414163..2414241,2415024..2415162,2416585..2416710,
                     2418324..2418401,2418769..2418877,2419029..2419132)
                     /gene="EIF3B"
                     /gene_synonym="EIF3-ETA; EIF3-P110; EIF3-P116; EIF3S9;
                     MGC104664; MGC131875; PRT1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="eukaryotic translation initiation factor 3
                     subunit B"
                     /protein_id="NP_001032360.1"
                     /db_xref="GI:83367072"
                     /db_xref="CCDS:CCDS5332.1"
                     /db_xref="GeneID:8662"
                     /db_xref="HGNC:3280"
                     /db_xref="MIM:603917"
     CDS             join(2394557..2395055,2400345..2400537,2402280..2402399,
                     2402705..2402762,2403267..2403395,2404007..2404164,
                     2405952..2406083,2406160..2406226,2406634..2406680,
                     2409107..2409317,2411412..2411484,2412308..2412430,
                     2414163..2414241,2415024..2415162,2416585..2416710,
                     2418324..2418401,2418769..2418877,2419029..2419132)
                     /gene="EIF3B"
                     /gene_synonym="EIF3-ETA; EIF3-P110; EIF3-P116; EIF3S9;
                     MGC104664; MGC131875; PRT1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="eukaryotic translation initiation factor 3
                     subunit B"
                     /protein_id="NP_003742.2"
                     /db_xref="GI:33239445"
                     /db_xref="CCDS:CCDS5332.1"
                     /db_xref="GeneID:8662"
                     /db_xref="HGNC:3280"
                     /db_xref="MIM:603917"
     gene            2421617..2431910
                     /gene="LOC645357"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:645357"
     gene            complement(2432729..2433770)
                     /gene="LOC402634"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402634"
     gene            2443259..2474240
                     /gene="CHST12"
                     /gene_synonym="C4S-2; C4ST-2; C4ST2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55501"
                     /db_xref="HGNC:17423"
                     /db_xref="HPRD:13056"
                     /db_xref="MIM:610129"
     mRNA            join(2443259..2443308,2472198..2474240)
                     /gene="CHST12"
                     /gene_synonym="C4S-2; C4ST-2; C4ST2"
                     /product="carbohydrate (chondroitin 4) sulfotransferase
                     12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018641.3"
                     /db_xref="GI:105554462"
                     /db_xref="GeneID:55501"
                     /db_xref="HGNC:17423"
                     /db_xref="HPRD:13056"
                     /db_xref="MIM:610129"
     CDS             2472275..2473519
                     /gene="CHST12"
                     /gene_synonym="C4S-2; C4ST-2; C4ST2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="carbohydrate sulfotransferase 12"
                     /protein_id="NP_061111.1"
                     /db_xref="GI:8922112"
                     /db_xref="CCDS:CCDS5333.1"
                     /db_xref="GeneID:55501"
                     /db_xref="HGNC:17423"
                     /db_xref="HPRD:13056"
                     /db_xref="MIM:610129"
     gene            2480699..2486315
                     /gene="LOC100288594"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /db_xref="GeneID:100288594"
     misc_RNA        join(2480699..2480830,2485914..2486315)
                     /gene="LOC100288594"
                     /product="hypothetical LOC100288594"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /transcript_id="XR_108779.1"
                     /db_xref="GI:310119902"
                     /db_xref="GeneID:100288594"
     gene            complement(2514772..2516489)
                     /gene="GRIFIN"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:402635"
                     /db_xref="HGNC:4577"
     exon            complement(2514772..2514942)
                     /gene="GRIFIN"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=4
                     /pseudo
                     /db_xref="GeneID:402635"
     exon            complement(2515304..2515462)
                     /gene="GRIFIN"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:402635"
     exon            complement(2515554..2515633)
                     /gene="GRIFIN"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:402635"
     exon            complement(2516406..2516489)
                     /gene="GRIFIN"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:402635"
     gene            2552163..2568811
                     /gene="LFNG"
                     /gene_synonym="SCDO3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3955"
                     /db_xref="HGNC:6560"
                     /db_xref="MIM:602576"
     mRNA            join(2552163..2552335,2552791..2552962,2564329..2564377,
                     2564853..2564952,2565048..2565201,2565319..2565404,
                     2565878..2566043,2566470..2566555,2566780..2568063)
                     /gene="LFNG"
                     /gene_synonym="SCDO3"
                     /product="LFNG O-fucosylpeptide
                     3-beta-N-acetylglucosaminyltransferase, transcript variant
                     3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001166355.1"
                     /db_xref="GI:261878555"
                     /db_xref="GeneID:3955"
                     /db_xref="HGNC:6560"
                     /db_xref="MIM:602576"
     CDS             join(2552289..2552335,2552791..2552962,2564329..2564377,
                     2564853..2564952,2565048..2565201,2565319..2565404,
                     2565878..2566043,2566470..2566555,2566780..2566846)
                     /gene="LFNG"
                     /gene_synonym="SCDO3"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="beta-1,3-N-acetylglucosaminyltransferase lunatic
                     fringe isoform c"
                     /protein_id="NP_001159827.1"
                     /db_xref="GI:261878556"
                     /db_xref="CCDS:CCDS55081.1"
                     /db_xref="GeneID:3955"
                     /db_xref="HGNC:6560"
                     /db_xref="MIM:602576"
     mRNA            join(2557497..2557578,2558182..2558232,2564329..2564377,
                     2564853..2564952,2565048..2565201,2565319..2565404,
                     2565878..2566043,2566470..2566555,2566780..2568063)
                     /gene="LFNG"
                     /gene_synonym="SCDO3"
                     /product="LFNG O-fucosylpeptide
                     3-beta-N-acetylglucosaminyltransferase, transcript variant
                     4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002304.2"
                     /db_xref="GI:261878561"
                     /db_xref="GeneID:3955"
                     /db_xref="HGNC:6560"
                     /db_xref="MIM:602576"
     CDS             join(2558188..2558232,2564329..2564377,2564853..2564952,
                     2565048..2565201,2565319..2565404,2565878..2566043,
                     2566470..2566555,2566780..2566846)
                     /gene="LFNG"
                     /gene_synonym="SCDO3"
                     /note="isoform d is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="beta-1,3-N-acetylglucosaminyltransferase lunatic
                     fringe isoform d"
                     /protein_id="NP_002295.1"
                     /db_xref="GI:58696422"
                     /db_xref="CCDS:CCDS55082.1"
                     /db_xref="GeneID:3955"
                     /db_xref="HGNC:6560"
                     /db_xref="MIM:602576"
     mRNA            join(2559479..2559927,2564329..2564377,2564853..2564952,
                     2565048..2565201,2565319..2565404,2565878..2566043,
                     2566470..2566555,2568508..2568811)
                     /gene="LFNG"
                     /gene_synonym="SCDO3"
                     /product="LFNG O-fucosylpeptide
                     3-beta-N-acetylglucosaminyltransferase, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040168.1"
                     /db_xref="GI:93141004"
                     /db_xref="GeneID:3955"
                     /db_xref="HGNC:6560"
                     /db_xref="MIM:602576"
     mRNA            join(2559479..2559927,2564329..2564377,2564853..2564952,
                     2565048..2565201,2565319..2565404,2565878..2566043,
                     2566470..2566555,2566780..2568063)
                     /gene="LFNG"
                     /gene_synonym="SCDO3"
                     /product="LFNG O-fucosylpeptide
                     3-beta-N-acetylglucosaminyltransferase, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040167.1"
                     /db_xref="GI:93140998"
                     /db_xref="GeneID:3955"
                     /db_xref="HGNC:6560"
                     /db_xref="MIM:602576"
     CDS             join(2559496..2559927,2564329..2564377,2564853..2564952,
                     2565048..2565201,2565319..2565404,2565878..2566043,
                     2566470..2566555,2568508..2568520)
                     /gene="LFNG"
                     /gene_synonym="SCDO3"
                     /note="isoform b preproprotein is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="beta-1,3-N-acetylglucosaminyltransferase lunatic
                     fringe isoform b preproprotein"
                     /protein_id="NP_001035258.1"
                     /db_xref="GI:93141005"
                     /db_xref="CCDS:CCDS34586.1"
                     /db_xref="GeneID:3955"
                     /db_xref="HGNC:6560"
                     /db_xref="MIM:602576"
     CDS             join(2559496..2559927,2564329..2564377,2564853..2564952,
                     2565048..2565201,2565319..2565404,2565878..2566043,
                     2566470..2566555,2566780..2566846)
                     /gene="LFNG"
                     /gene_synonym="SCDO3"
                     /note="isoform a preproprotein is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="beta-1,3-N-acetylglucosaminyltransferase lunatic
                     fringe isoform a preproprotein"
                     /protein_id="NP_001035257.1"
                     /db_xref="GI:93140999"
                     /db_xref="CCDS:CCDS34587.1"
                     /db_xref="GeneID:3955"
                     /db_xref="HGNC:6560"
                     /db_xref="MIM:602576"
     gene            2566708..2566786
                     /gene="MIR4648"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100616116"
                     /db_xref="HGNC:41560"
                     /db_xref="miRBase:MI0017275"
     ncRNA           2566708..2566786
                     /gene="MIR4648"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4648"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039791.1"
                     /db_xref="GI:337756577"
                     /db_xref="GeneID:100616116"
                     /db_xref="HGNC:41560"
                     /db_xref="miRBase:MI0017275"
     gene            complement(2577444..2595392)
                     /gene="BRAT1"
                     /gene_synonym="BAAT1; C7orf27; MGC22916"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221927"
                     /db_xref="HGNC:21701"
                     /db_xref="HPRD:12914"
     mRNA            complement(join(2577444..2578398,2578813..2578985,
                     2579178..2579276,2579420..2579522,2580613..2580686,
                     2580932..2581118,2581352..2581470,2581754..2581845,
                     2582838..2582957,2583224..2583596,2584543..2584690,
                     2586958..2587112,2593939..2594081,2595121..2595392))
                     /gene="BRAT1"
                     /gene_synonym="BAAT1; C7orf27; MGC22916"
                     /product="BRCA1-associated ATM activator 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152743.3"
                     /db_xref="GI:304555613"
                     /db_xref="GeneID:221927"
                     /db_xref="HGNC:21701"
                     /db_xref="HPRD:12914"
     CDS             complement(join(2577703..2578398,2578813..2578985,
                     2579178..2579276,2579420..2579522,2580613..2580686,
                     2580932..2581118,2581352..2581470,2581754..2581845,
                     2582838..2582957,2583224..2583596,2584543..2584690,
                     2586958..2587112,2593939..2594065))
                     /gene="BRAT1"
                     /gene_synonym="BAAT1; C7orf27; MGC22916"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="BRCA1-associated ATM activator 1"
                     /protein_id="NP_689956.2"
                     /db_xref="GI:304555614"
                     /db_xref="CCDS:CCDS5334.1"
                     /db_xref="GeneID:221927"
                     /db_xref="HGNC:21701"
                     /db_xref="HPRD:12914"
     gene            2598632..2654368
                     /gene="IQCE"
                     /gene_synonym="1700028P05Rik; KIAA1023; MGC41907"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23288"
                     /db_xref="HGNC:29171"
                     /db_xref="HPRD:11050"
     mRNA            join(2598632..2598851,2606750..2606797,2608588..2608633,
                     2611160..2611288,2611826..2611960,2613052..2613122,
                     2617876..2617989,2618110..2618160,2622214..2622284,
                     2623271..2623343,2623870..2623919,2625842..2626005,
                     2627456..2627511,2629541..2629740,2632656..2632760,
                     2634520..2634610,2638099..2638266,2641075..2641098,
                     2644515..2644625,2645510..2645631,2646758..2646861,
                     2649678..2654368)
                     /gene="IQCE"
                     /gene_synonym="1700028P05Rik; KIAA1023; MGC41907"
                     /product="IQ motif containing E, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152558.3"
                     /db_xref="GI:154813190"
                     /db_xref="GeneID:23288"
                     /db_xref="HGNC:29171"
                     /db_xref="HPRD:11050"
     mRNA            join(2598632..2598851,2608588..2608633,2611160..2611288,
                     2611826..2611960,2613052..2613122,2617876..2617989,
                     2618110..2618160,2622214..2622284,2623271..2623343,
                     2623870..2623919,2625842..2626005,2627456..2627511,
                     2629541..2629740,2632656..2632760,2634520..2634610,
                     2638099..2638266,2641075..2641098,2644515..2644625,
                     2645510..2645631,2646758..2646861,2649678..2654368)
                     /gene="IQCE"
                     /gene_synonym="1700028P05Rik; KIAA1023; MGC41907"
                     /product="IQ motif containing E, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001100390.1"
                     /db_xref="GI:154813192"
                     /db_xref="GeneID:23288"
                     /db_xref="HGNC:29171"
                     /db_xref="HPRD:11050"
     CDS             join(2598816..2598851,2606750..2606797,2608588..2608633,
                     2611160..2611288,2611826..2611960,2613052..2613122,
                     2617876..2617989,2618110..2618160,2622214..2622284,
                     2623271..2623343,2623870..2623919,2625842..2626005,
                     2627456..2627511,2629541..2629740,2632656..2632760,
                     2634520..2634610,2638099..2638266,2641075..2641098,
                     2644515..2644625,2645510..2645631,2646758..2646861,
                     2649678..2649796)
                     /gene="IQCE"
                     /gene_synonym="1700028P05Rik; KIAA1023; MGC41907"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="IQ domain-containing protein E isoform 1"
                     /protein_id="NP_689771.3"
                     /db_xref="GI:154813191"
                     /db_xref="CCDS:CCDS43542.1"
                     /db_xref="GeneID:23288"
                     /db_xref="HGNC:29171"
                     /db_xref="HPRD:11050"
     CDS             join(2598816..2598851,2608588..2608633,2611160..2611288,
                     2611826..2611960,2613052..2613122,2617876..2617989,
                     2618110..2618160,2622214..2622284,2623271..2623343,
                     2623870..2623919,2625842..2626005,2627456..2627511,
                     2629541..2629740,2632656..2632760,2634520..2634610,
                     2638099..2638266,2641075..2641098,2644515..2644625,
                     2645510..2645631,2646758..2646861,2649678..2649796)
                     /gene="IQCE"
                     /gene_synonym="1700028P05Rik; KIAA1023; MGC41907"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="IQ domain-containing protein E isoform 2"
                     /protein_id="NP_001093860.1"
                     /db_xref="GI:154813193"
                     /db_xref="CCDS:CCDS47527.1"
                     /db_xref="GeneID:23288"
                     /db_xref="HGNC:29171"
                     /db_xref="HPRD:11050"
     gene            2671603..2704436
                     /gene="TTYH3"
                     /gene_synonym="KIAA1691"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:80727"
                     /db_xref="HGNC:22222"
                     /db_xref="HPRD:12333"
                     /db_xref="MIM:608919"
     mRNA            join(2671603..2671912,2686487..2686656,2686776..2686887,
                     2687052..2687272,2687593..2687688,2689201..2689273,
                     2689547..2689622,2691821..2691876,2692552..2692644,
                     2695726..2695818,2696032..2696168,2697920..2698093,
                     2698574..2698649,2701302..2704436)
                     /gene="TTYH3"
                     /gene_synonym="KIAA1691"
                     /product="tweety homolog 3 (Drosophila)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_025250.2"
                     /db_xref="GI:53831992"
                     /db_xref="GeneID:80727"
                     /db_xref="HGNC:22222"
                     /db_xref="HPRD:12333"
                     /db_xref="MIM:608919"
     CDS             join(2671790..2671912,2686487..2686656,2686776..2686887,
                     2687052..2687272,2687593..2687688,2689201..2689273,
                     2689547..2689622,2691821..2691876,2692552..2692644,
                     2695726..2695818,2696032..2696168,2697920..2698093,
                     2698574..2698649,2701302..2701373)
                     /gene="TTYH3"
                     /gene_synonym="KIAA1691"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein tweety homolog 3"
                     /protein_id="NP_079526.1"
                     /db_xref="GI:51100978"
                     /db_xref="CCDS:CCDS34588.1"
                     /db_xref="GeneID:80727"
                     /db_xref="HGNC:22222"
                     /db_xref="HPRD:12333"
                     /db_xref="MIM:608919"
     gene            2719163..2755069
                     /gene="AMZ1"
                     /gene_synonym="KIAA1950"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:155185"
                     /db_xref="HGNC:22231"
                     /db_xref="HPRD:17232"
     mRNA            join(2719163..2719305,2739868..2740389,2742356..2742523,
                     2748222..2748350,2748709..2748878,2749274..2749450,
                     2751964..2755069)
                     /gene="AMZ1"
                     /gene_synonym="KIAA1950"
                     /product="archaelysin family metallopeptidase 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_133463.1"
                     /db_xref="GI:55741644"
                     /db_xref="GeneID:155185"
                     /db_xref="HGNC:22231"
                     /db_xref="HPRD:17232"
     CDS             join(2740086..2740389,2742356..2742523,2748222..2748350,
                     2748709..2748878,2749274..2749450,2751964..2752512)
                     /gene="AMZ1"
                     /gene_synonym="KIAA1950"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="archaemetzincin-1"
                     /protein_id="NP_597720.1"
                     /db_xref="GI:55741645"
                     /db_xref="CCDS:CCDS34589.1"
                     /db_xref="GeneID:155185"
                     /db_xref="HGNC:22231"
                     /db_xref="HPRD:17232"
     gene            complement(2767739..2883959)
                     /gene="GNA12"
                     /gene_synonym="gep; MGC104623; MGC99644; NNX3; RMP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2768"
                     /db_xref="HGNC:4380"
                     /db_xref="HPRD:05093"
                     /db_xref="MIM:604394"
     mRNA            complement(join(2767739..2771384,2773085..2773135,
                     2834562..2834777,2883487..2883959))
                     /gene="GNA12"
                     /gene_synonym="gep; MGC104623; MGC99644; NNX3; RMP"
                     /product="guanine nucleotide binding protein (G protein)
                     alpha 12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_007353.2"
                     /db_xref="GI:42476110"
                     /db_xref="GeneID:2768"
                     /db_xref="HGNC:4380"
                     /db_xref="HPRD:05093"
                     /db_xref="MIM:604394"
     CDS             complement(join(2770815..2771384,2773085..2773135,
                     2834562..2834777,2883487..2883795))
                     /gene="GNA12"
                     /gene_synonym="gep; MGC104623; MGC99644; NNX3; RMP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="guanine nucleotide-binding protein subunit
                     alpha-12"
                     /protein_id="NP_031379.2"
                     /db_xref="GI:42476111"
                     /db_xref="CCDS:CCDS5335.1"
                     /db_xref="GeneID:2768"
                     /db_xref="HGNC:4380"
                     /db_xref="HPRD:05093"
                     /db_xref="MIM:604394"
     gene            2875255..2875659
                     /gene="LOC100131264"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 3 Proteins"
                     /pseudo
                     /db_xref="GeneID:100131264"
     exon            2875255..2875659
                     /gene="LOC100131264"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 3 Proteins"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100131264"
     gene            complement(2945709..3083509)
                     /gene="CARD11"
                     /gene_synonym="BIMP3; CARMA1; MGC133069"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84433"
                     /db_xref="HGNC:16393"
                     /db_xref="HPRD:06234"
                     /db_xref="MIM:607210"
     mRNA            complement(join(2945709..2946476,2949684..2949799,
                     2951806..2951930,2952921..2953100,2954871..2955006,
                     2956924..2957019,2958125..2958221,2959006..2959246,
                     2962268..2962394,2962766..2962967,2963867..2963999,
                     2966373..2966425,2968232..2968332,2969626..2969708,
                     2972169..2972220,2974087..2974263,2976671..2976868,
                     2977541..2977666,2978313..2978465,2979383..2979562,
                     2983846..2984171,2985453..2985590,2987209..2987421,
                     2998134..2998265,3083301..3083509))
                     /gene="CARD11"
                     /gene_synonym="BIMP3; CARMA1; MGC133069"
                     /product="caspase recruitment domain family, member 11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032415.4"
                     /db_xref="GI:307548883"
                     /db_xref="GeneID:84433"
                     /db_xref="HGNC:16393"
                     /db_xref="HPRD:06234"
                     /db_xref="MIM:607210"
     CDS             complement(join(2946272..2946476,2949684..2949799,
                     2951806..2951930,2952921..2953100,2954871..2955006,
                     2956924..2957019,2958125..2958221,2959006..2959246,
                     2962268..2962394,2962766..2962967,2963867..2963999,
                     2966373..2966425,2968232..2968332,2969626..2969708,
                     2972169..2972220,2974087..2974263,2976671..2976868,
                     2977541..2977666,2978313..2978465,2979383..2979562,
                     2983846..2984171,2985453..2985590,2987209..2987421,
                     2998134..2998140))
                     /gene="CARD11"
                     /gene_synonym="BIMP3; CARMA1; MGC133069"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="caspase recruitment domain-containing protein
                     11"
                     /protein_id="NP_115791.3"
                     /db_xref="GI:157743265"
                     /db_xref="CCDS:CCDS5336.2"
                     /db_xref="GeneID:84433"
                     /db_xref="HGNC:16393"
                     /db_xref="HPRD:06234"
                     /db_xref="MIM:607210"
     gene            3341080..4308632
                     /gene="SDK1"
                     /gene_synonym="FLJ31425"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221935"
                     /db_xref="HGNC:19307"
                     /db_xref="HPRD:07388"
                     /db_xref="MIM:607216"
     mRNA            join(3341080..3341516,3658712..3658871,3678636..3678742,
                     3681590..3681737,3861082..3861215,3990555..3990666,
                     3991362..3991552,3998563..3998646,4002289..4002483,
                     4006950..4007066,4008889..4009056,4011098..4011200,
                     4014001..4014177,4026818..4026954,4050598..4050745,
                     4051727..4051867,4056803..4056984,4088980..4089095,
                     4091270..4091462,4107470..4107568,4116630..4116821,
                     4119095..4119216,4150295..4150404,4152921..4153071,
                     4153669..4153906,4167013..4167128,4169540..4169729,
                     4171957..4172055,4185354..4185548,4188894..4189095,
                     4198080..4198183,4201418..4201488,4213854..4213989,
                     4215407..4215466,4218117..4218218,4245511..4245626,
                     4247731..4247917,4249657..4249794,4259741..4259902,
                     4260871..4260996,4272887..4273051,4277279..4277416,
                     4281425..4281545,4285308..4285437,4304756..4308632)
                     /gene="SDK1"
                     /gene_synonym="FLJ31425"
                     /product="sidekick homolog 1, cell adhesion molecule
                     (chicken), transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152744.3"
                     /db_xref="GI:119220551"
                     /db_xref="GeneID:221935"
                     /db_xref="HGNC:19307"
                     /db_xref="HPRD:07388"
                     /db_xref="MIM:607216"
     CDS             join(3341219..3341516,3658712..3658871,3678636..3678742,
                     3681590..3681737,3861082..3861215,3990555..3990666,
                     3991362..3991552,3998563..3998646,4002289..4002483,
                     4006950..4007066,4008889..4009056,4011098..4011200,
                     4014001..4014177,4026818..4026954,4050598..4050745,
                     4051727..4051867,4056803..4056984,4088980..4089095,
                     4091270..4091462,4107470..4107568,4116630..4116821,
                     4119095..4119216,4150295..4150404,4152921..4153071,
                     4153669..4153906,4167013..4167128,4169540..4169729,
                     4171957..4172055,4185354..4185548,4188894..4189095,
                     4198080..4198183,4201418..4201488,4213854..4213989,
                     4215407..4215466,4218117..4218218,4245511..4245626,
                     4247731..4247917,4249657..4249794,4259741..4259902,
                     4260871..4260996,4272887..4273051,4277279..4277416,
                     4281425..4281545,4285308..4285437,4304756..4305016)
                     /gene="SDK1"
                     /gene_synonym="FLJ31425"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein sidekick-1 precursor"
                     /protein_id="NP_689957.3"
                     /db_xref="GI:119220552"
                     /db_xref="CCDS:CCDS34590.1"
                     /db_xref="GeneID:221935"
                     /db_xref="HGNC:19307"
                     /db_xref="HPRD:07388"
                     /db_xref="MIM:607216"
     gene            3377717..3378258
                     /gene="RPL21P72"
                     /gene_synonym="RPL21_28_779"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271181"
                     /db_xref="HGNC:37043"
     gene            3505147..3506074
                     /gene="LOC100421742"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421742"
     misc_RNA        join(4169317..4169729,4171957..4172055,4185354..4185548,
                     4188894..4189095,4198080..4198183,4201418..4201488,
                     4213854..4213989,4215407..4215466,4218117..4218218,
                     4245511..4245626,4247731..4247917,4249657..4249794,
                     4259741..4259902,4260871..4260996,4272887..4273051,
                     4277279..4277416,4281425..4281545,4285308..4285437,
                     4304756..4304880,4308310..4308632)
                     /gene="SDK1"
                     /gene_synonym="FLJ31425"
                     /product="sidekick homolog 1, cell adhesion molecule
                     (chicken), transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027816.1"
                     /db_xref="GI:240120067"
                     /db_xref="GeneID:221935"
                     /db_xref="HGNC:19307"
                     /db_xref="MIM:607216"
                     /db_xref="HPRD:07388"
     gene            4721930..4811074
                     /gene="FOXK1"
                     /gene_synonym="FLJ14977; FOXK1L"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221937"
                     /db_xref="HGNC:23480"
                     /db_xref="HPRD:18750"
     mRNA            join(4721930..4722499,4780469..4780654,4794090..4794246,
                     4794868..4795014,4796625..4796818,4798682..4798848,
                     4798942..4799226,4800695..4800919,4801815..4811074)
                     /gene="FOXK1"
                     /gene_synonym="FLJ14977; FOXK1L"
                     /product="forkhead box K1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001037165.1"
                     /db_xref="GI:82546823"
                     /db_xref="GeneID:221937"
                     /db_xref="HGNC:23480"
                     /db_xref="HPRD:18750"
     CDS             join(4721940..4722499,4780469..4780654,4794090..4794246,
                     4794868..4795014,4796625..4796818,4798682..4798848,
                     4798942..4799226,4800695..4800919,4801815..4802095)
                     /gene="FOXK1"
                     /gene_synonym="FLJ14977; FOXK1L"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="forkhead box protein K1"
                     /protein_id="NP_001032242.1"
                     /db_xref="GI:82546824"
                     /db_xref="CCDS:CCDS34591.1"
                     /db_xref="GeneID:221937"
                     /db_xref="HGNC:23480"
                     /db_xref="HPRD:18750"
     gene            4729060..4729264
                     /gene="SNORD13P2"
                     /gene_synonym="RNU13P2; U13; U13.12A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6077"
                     /db_xref="HGNC:10111"
     gene            4815262..4834026
                     /gene="KIAA0415"
                     /gene_synonym="SPG48"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9907"
                     /db_xref="HGNC:22197"
                     /db_xref="MIM:613653"
     mRNA            join(4815262..4815387,4820806..4820943,4821199..4821385,
                     4822947..4823091,4823320..4823429,4823834..4824002,
                     4824539..4824679,4825046..4825083,4825153..4825315,
                     4825881..4826059,4827265..4827407,4827785..4827925,
                     4828471..4828582,4829463..4829560,4830090..4830222,
                     4830304..4830518,4830746..4834026)
                     /gene="KIAA0415"
                     /gene_synonym="SPG48"
                     /product="KIAA0415"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014855.2"
                     /db_xref="GI:319996625"
                     /db_xref="GeneID:9907"
                     /db_xref="HGNC:22197"
                     /db_xref="MIM:613653"
     CDS             join(4815347..4815387,4820806..4820943,4821199..4821385,
                     4822947..4823091,4823320..4823429,4823834..4824002,
                     4824539..4824679,4825046..4825083,4825153..4825315,
                     4825881..4826059,4827265..4827407,4827785..4827925,
                     4828471..4828582,4829463..4829560,4830090..4830222,
                     4830304..4830518,4830746..4831016)
                     /gene="KIAA0415"
                     /gene_synonym="SPG48"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC9907"
                     /protein_id="NP_055670.1"
                     /db_xref="GI:82546847"
                     /db_xref="CCDS:CCDS47528.1"
                     /db_xref="GeneID:9907"
                     /db_xref="HGNC:22197"
                     /db_xref="MIM:613653"
     gene            complement(4828196..4828270)
                     /gene="MIR4656"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100616465"
                     /db_xref="HGNC:41749"
                     /db_xref="miRBase:MI0017284"
     ncRNA           complement(4828196..4828270)
                     /gene="MIR4656"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4656"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039800.1"
                     /db_xref="GI:337756601"
                     /db_xref="GeneID:100616465"
                     /db_xref="HGNC:41749"
                     /db_xref="miRBase:MI0017284"
     gene            complement(4838740..4923335)
                     /gene="RADIL"
                     /gene_synonym="FLJ10324; FLJ60975; KIAA1849; MGC161589;
                     RASIP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55698"
                     /db_xref="HGNC:22226"
                     /db_xref="HPRD:07663"
                     /db_xref="MIM:611491"
     mRNA            complement(join(4838740..4839114,4839261..4839400,
                     4839802..4839941,4841284..4841626,4843177..4843385,
                     4845197..4845347,4854909..4855081,4855859..4856096,
                     4856870..4856982,4862025..4862185,4871772..4871809,
                     4874238..4874870,4875989..4876236,4917236..4917834,
                     4923227..4923335))
                     /gene="RADIL"
                     /gene_synonym="FLJ10324; FLJ60975; KIAA1849; MGC161589;
                     RASIP2"
                     /product="Ras association and DIL domains"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018059.4"
                     /db_xref="GI:148612824"
                     /db_xref="GeneID:55698"
                     /db_xref="HGNC:22226"
                     /db_xref="HPRD:07663"
                     /db_xref="MIM:611491"
     CDS             complement(join(4839009..4839114,4839261..4839400,
                     4839802..4839941,4841284..4841626,4843177..4843385,
                     4845197..4845347,4854909..4855081,4855859..4856096,
                     4856870..4856982,4862025..4862185,4871772..4871809,
                     4874238..4874870,4875989..4876236,4917236..4917770))
                     /gene="RADIL"
                     /gene_synonym="FLJ10324; FLJ60975; KIAA1849; MGC161589;
                     RASIP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ras-associating and dilute domain-containing
                     protein"
                     /protein_id="NP_060529.4"
                     /db_xref="GI:148612825"
                     /db_xref="CCDS:CCDS43544.1"
                     /db_xref="GeneID:55698"
                     /db_xref="HGNC:22226"
                     /db_xref="HPRD:07663"
                     /db_xref="MIM:611491"
     gene            complement(4897369..4901625)
                     /gene="PAPOLB"
                     /gene_synonym="PAPT; TPAP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:56903"
                     /db_xref="HGNC:15970"
                     /db_xref="HPRD:08467"
                     /db_xref="MIM:607436"
     mRNA            complement(4897369..4901625)
                     /gene="PAPOLB"
                     /gene_synonym="PAPT; TPAP"
                     /product="poly(A) polymerase beta (testis specific)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020144.4"
                     /db_xref="GI:77874205"
                     /db_xref="GeneID:56903"
                     /db_xref="HGNC:15970"
                     /db_xref="HPRD:08467"
                     /db_xref="MIM:607436"
     CDS             complement(4899528..4901441)
                     /gene="PAPOLB"
                     /gene_synonym="PAPT; TPAP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="poly(A) polymerase beta"
                     /protein_id="NP_064529.4"
                     /db_xref="GI:77874206"
                     /db_xref="GeneID:56903"
                     /db_xref="HGNC:15970"
                     /db_xref="HPRD:08467"
                     /db_xref="MIM:607436"
     gene            complement(4905061..4905433)
                     /gene="RPL22P16"
                     /gene_synonym="RPL22_6_780"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100270959"
                     /db_xref="HGNC:36536"
     gene            complement(4945620..4998844)
                     /gene="MMD2"
                     /gene_synonym="FLJ37205; PAQR10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221938"
                     /db_xref="HGNC:30133"
                     /db_xref="HPRD:17578"
     mRNA            complement(join(4945620..4947230,4949512..4949653,
                     4950776..4950877,4955636..4955710,4959802..4959962,
                     4965082..4965163,4998602..4998844))
                     /gene="MMD2"
                     /gene_synonym="FLJ37205; PAQR10"
                     /product="monocyte to macrophage
                     differentiation-associated 2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001100600.1"
                     /db_xref="GI:154759276"
                     /db_xref="GeneID:221938"
                     /db_xref="HGNC:30133"
                     /db_xref="HPRD:17578"
     mRNA            complement(join(4945620..4947230,4949512..4949581,
                     4950776..4950877,4955636..4955710,4959802..4959962,
                     4965082..4965163,4998602..4998844))
                     /gene="MMD2"
                     /gene_synonym="FLJ37205; PAQR10"
                     /product="monocyte to macrophage
                     differentiation-associated 2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198403.3"
                     /db_xref="GI:154759274"
                     /db_xref="GeneID:221938"
                     /db_xref="HGNC:30133"
                     /db_xref="HPRD:17578"
     CDS             complement(join(4947027..4947230,4949512..4949653,
                     4950776..4950877,4955636..4955710,4959802..4959962,
                     4965082..4965163,4998602..4998648))
                     /gene="MMD2"
                     /gene_synonym="FLJ37205; PAQR10"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="monocyte to macrophage differentiation factor 2
                     isoform 1"
                     /protein_id="NP_001094070.1"
                     /db_xref="GI:154759277"
                     /db_xref="CCDS:CCDS47529.1"
                     /db_xref="GeneID:221938"
                     /db_xref="HGNC:30133"
                     /db_xref="HPRD:17578"
     CDS             complement(join(4947027..4947230,4949512..4949581,
                     4950776..4950877,4955636..4955710,4959802..4959962,
                     4965082..4965163,4998602..4998648))
                     /gene="MMD2"
                     /gene_synonym="FLJ37205; PAQR10"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="monocyte to macrophage differentiation factor 2
                     isoform 2"
                     /protein_id="NP_940685.3"
                     /db_xref="GI:154759275"
                     /db_xref="CCDS:CCDS47530.1"
                     /db_xref="GeneID:221938"
                     /db_xref="HGNC:30133"
                     /db_xref="HPRD:17578"
     gene            5013616..5037800
                     /gene="RNF216L"
                     /gene_synonym="FLJ18559; FLJ98567; FLJ99839; hCG2040556"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:441191"
                     /db_xref="HGNC:33610"
     misc_RNA        join(5013616..5013792,5015932..5016067,5023302..5023404,
                     5024541..5024706,5026198..5026262,5028694..5028808,
                     5035106..5035213,5036241..5037800)
                     /gene="RNF216L"
                     /gene_synonym="FLJ18559; FLJ98567; FLJ99839; hCG2040556"
                     /product="ring finger protein 216-like, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_023384.1"
                     /db_xref="GI:190194404"
                     /db_xref="GeneID:441191"
                     /db_xref="HGNC:33610"
     misc_RNA        join(5013616..5013792,5015932..5016067,5023302..5023404,
                     5024541..5024706,5028694..5028808,5036241..5037800)
                     /gene="RNF216L"
                     /gene_synonym="FLJ18559; FLJ98567; FLJ99839; hCG2040556"
                     /product="ring finger protein 216-like, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_015449.1"
                     /db_xref="GI:190194405"
                     /db_xref="GeneID:441191"
                     /db_xref="HGNC:33610"
     misc_RNA        join(5013616..5013792,5015932..5016067,5023302..5023404,
                     5024541..5024706,5036241..5037800)
                     /gene="RNF216L"
                     /gene_synonym="FLJ18559; FLJ98567; FLJ99839; hCG2040556"
                     /product="ring finger protein 216-like, transcript variant
                     3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_023385.1"
                     /db_xref="GI:190194406"
                     /db_xref="GeneID:441191"
                     /db_xref="HGNC:33610"
     gene            5073611..5074381
                     /gene="LOC100505757"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100505757"
     exon            5073611..5074381
                     /gene="LOC100505757"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100505757"
     gene            complement(5076116..5077516)
                     /gene="LOC100130307"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100130307"
     gene            5085452..5112854
                     /gene="RBAK-LOC389458"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100533952"
     mRNA            join(5085452..5085589,5087664..5087722,5096926..5097052,
                     5097315..5097410,5111993..5112128,5112553..5112854)
                     /gene="RBAK-LOC389458"
                     /product="RBAK-LOC389458 readthrough"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001204513.1"
                     /db_xref="GI:325168188"
                     /db_xref="GeneID:100533952"
     gene            5085452..5109119
                     /gene="RBAK"
                     /gene_synonym="ZNF769"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57786"
                     /db_xref="HGNC:17680"
                     /db_xref="HPRD:16296"
                     /db_xref="MIM:608191"
     mRNA            join(5085452..5085589,5085886..5086027,5087664..5087722,
                     5096926..5097052,5097315..5097410,5103326..5109119)
                     /gene="RBAK"
                     /gene_synonym="ZNF769"
                     /product="RB-associated KRAB zinc finger, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001204456.1"
                     /db_xref="GI:325053657"
                     /db_xref="GeneID:57786"
                     /db_xref="HGNC:17680"
                     /db_xref="MIM:608191"
                     /db_xref="HPRD:16296"
     mRNA            join(5085553..5086027,5087664..5087722,5096926..5097052,
                     5097315..5097410,5103326..5109119)
                     /gene="RBAK"
                     /gene_synonym="ZNF769"
                     /product="RB-associated KRAB zinc finger, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021163.3"
                     /db_xref="GI:113204605"
                     /db_xref="GeneID:57786"
                     /db_xref="HGNC:17680"
                     /db_xref="HPRD:16296"
                     /db_xref="MIM:608191"
     CDS             join(5087708..5087722,5096926..5097052,5097315..5097410,
                     5111993..5112096)
                     /gene="RBAK-LOC389458"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC100533952"
                     /protein_id="NP_001191442.1"
                     /db_xref="GI:325168189"
                     /db_xref="GeneID:100533952"
     CDS             join(5087708..5087722,5096926..5097052,5097315..5097410,
                     5103326..5105232)
                     /gene="RBAK"
                     /gene_synonym="ZNF769"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="RB-associated KRAB zinc finger protein"
                     /protein_id="NP_066986.1"
                     /db_xref="GI:13430850"
                     /db_xref="CCDS:CCDS5337.1"
                     /db_xref="GeneID:57786"
                     /db_xref="HGNC:17680"
                     /db_xref="HPRD:16296"
                     /db_xref="MIM:608191"
     CDS             join(5087708..5087722,5096926..5097052,5097315..5097410,
                     5103326..5105232)
                     /gene="RBAK"
                     /gene_synonym="ZNF769"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="RB-associated KRAB zinc finger protein"
                     /protein_id="NP_001191385.1"
                     /db_xref="GI:325053658"
                     /db_xref="GeneID:57786"
                     /db_xref="HGNC:17680"
                     /db_xref="MIM:608191"
                     /db_xref="HPRD:16296"
     gene            5111691..5112854
                     /gene="LOC389458"
                     /gene_synonym="MGC35170"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:389458"
     misc_RNA        join(5111691..5111831,5111993..5112128,5112553..5112854)
                     /gene="LOC389458"
                     /gene_synonym="MGC35170"
                     /product="hypothetical LOC389458"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_015343.2"
                     /db_xref="GI:325152858"
                     /db_xref="GeneID:389458"
     gene            5156721..5157719
                     /gene="OR10AH1P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402246"
                     /db_xref="HGNC:19647"
     gene            complement(5160941..5184177)
                     /gene="ZNF890P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:645700"
                     /db_xref="HGNC:38691"
     misc_RNA        complement(join(5160941..5161854,5166461..5166556,
                     5167248..5167374,5172079..5172120,5176186..5176320,
                     5183878..5184177))
                     /gene="ZNF890P"
                     /product="zinc finger protein 890, pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_034163.1"
                     /db_xref="GI:301069417"
                     /db_xref="GeneID:645700"
                     /db_xref="HGNC:38691"
     gene            5229835..5273486
                     /gene="WIPI2"
                     /gene_synonym="ATG18B; Atg21; CGI-50; DKFZp434J154;
                     DKFZp686P02188; FLJ12979; FLJ14217; FLJ42984; WIPI-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26100"
                     /db_xref="HGNC:32225"
                     /db_xref="HPRD:15679"
                     /db_xref="MIM:609225"
     mRNA            join(5229835..5230124,5232749..5232802,5239207..5239289,
                     5254166..5254335,5256194..5256290,5256721..5256818,
                     5257553..5257645,5262233..5262303,5265454..5265561,
                     5266811..5266975,5267735..5267842,5269239..5269369,
                     5270466..5273486)
                     /gene="WIPI2"
                     /gene_synonym="ATG18B; Atg21; CGI-50; DKFZp434J154;
                     DKFZp686P02188; FLJ12979; FLJ14217; FLJ42984; WIPI-2"
                     /product="WD repeat domain, phosphoinositide interacting
                     2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015610.3"
                     /db_xref="GI:75677333"
                     /db_xref="GeneID:26100"
                     /db_xref="HGNC:32225"
                     /db_xref="HPRD:15679"
                     /db_xref="MIM:609225"
     mRNA            join(5229835..5230124,5239207..5239289,5254166..5254335,
                     5256194..5256290,5256721..5256818,5257553..5257645,
                     5262233..5262303,5265454..5265561,5266811..5266975,
                     5267735..5267842,5269239..5269369,5270466..5273486)
                     /gene="WIPI2"
                     /gene_synonym="ATG18B; Atg21; CGI-50; DKFZp434J154;
                     DKFZp686P02188; FLJ12979; FLJ14217; FLJ42984; WIPI-2"
                     /product="WD repeat domain, phosphoinositide interacting
                     2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016003.3"
                     /db_xref="GI:75677338"
                     /db_xref="GeneID:26100"
                     /db_xref="HGNC:32225"
                     /db_xref="HPRD:15679"
                     /db_xref="MIM:609225"
     mRNA            join(5229835..5230124,5232749..5232802,5239207..5239289,
                     5254166..5254335,5256194..5256290,5256721..5256818,
                     5257553..5257645,5262233..5262303,5265454..5265561,
                     5266811..5266975,5267735..5267842,5269239..5269336,
                     5270466..5273486)
                     /gene="WIPI2"
                     /gene_synonym="ATG18B; Atg21; CGI-50; DKFZp434J154;
                     DKFZp686P02188; FLJ12979; FLJ14217; FLJ42984; WIPI-2"
                     /product="WD repeat domain, phosphoinositide interacting
                     2, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001033518.1"
                     /db_xref="GI:75677328"
                     /db_xref="GeneID:26100"
                     /db_xref="HGNC:32225"
                     /db_xref="HPRD:15679"
                     /db_xref="MIM:609225"
     mRNA            join(5229835..5230124,5239207..5239289,5254166..5254335,
                     5256194..5256290,5256721..5256818,5257553..5257645,
                     5262233..5262303,5265454..5265561,5266811..5266975,
                     5267735..5267842,5269239..5269336,5270466..5273486)
                     /gene="WIPI2"
                     /gene_synonym="ATG18B; Atg21; CGI-50; DKFZp434J154;
                     DKFZp686P02188; FLJ12979; FLJ14217; FLJ42984; WIPI-2"
                     /product="WD repeat domain, phosphoinositide interacting
                     2, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001033519.1"
                     /db_xref="GI:75677330"
                     /db_xref="GeneID:26100"
                     /db_xref="HGNC:32225"
                     /db_xref="HPRD:15679"
                     /db_xref="MIM:609225"
     CDS             join(5230051..5230124,5232749..5232802,5239207..5239289,
                     5254166..5254335,5256194..5256290,5256721..5256818,
                     5257553..5257645,5262233..5262303,5265454..5265561,
                     5266811..5266975,5267735..5267842,5269239..5269369,
                     5270466..5270578)
                     /gene="WIPI2"
                     /gene_synonym="ATG18B; Atg21; CGI-50; DKFZp434J154;
                     DKFZp686P02188; FLJ12979; FLJ14217; FLJ42984; WIPI-2"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="WD repeat domain phosphoinositide-interacting
                     protein 2 isoform a"
                     /protein_id="NP_056425.1"
                     /db_xref="GI:7661580"
                     /db_xref="CCDS:CCDS5339.1"
                     /db_xref="GeneID:26100"
                     /db_xref="HGNC:32225"
                     /db_xref="HPRD:15679"
                     /db_xref="MIM:609225"
     CDS             join(5230051..5230124,5239207..5239289,5254166..5254335,
                     5256194..5256290,5256721..5256818,5257553..5257645,
                     5262233..5262303,5265454..5265561,5266811..5266975,
                     5267735..5267842,5269239..5269369,5270466..5270578)
                     /gene="WIPI2"
                     /gene_synonym="ATG18B; Atg21; CGI-50; DKFZp434J154;
                     DKFZp686P02188; FLJ12979; FLJ14217; FLJ42984; WIPI-2"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="WD repeat domain phosphoinositide-interacting
                     protein 2 isoform b"
                     /protein_id="NP_057087.2"
                     /db_xref="GI:54111428"
                     /db_xref="CCDS:CCDS34593.1"
                     /db_xref="GeneID:26100"
                     /db_xref="HGNC:32225"
                     /db_xref="HPRD:15679"
                     /db_xref="MIM:609225"
     CDS             join(5230051..5230124,5232749..5232802,5239207..5239289,
                     5254166..5254335,5256194..5256290,5256721..5256818,
                     5257553..5257645,5262233..5262303,5265454..5265561,
                     5266811..5266975,5267735..5267842,5269239..5269336,
                     5270466..5270578)
                     /gene="WIPI2"
                     /gene_synonym="ATG18B; Atg21; CGI-50; DKFZp434J154;
                     DKFZp686P02188; FLJ12979; FLJ14217; FLJ42984; WIPI-2"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="WD repeat domain phosphoinositide-interacting
                     protein 2 isoform c"
                     /protein_id="NP_001028690.1"
                     /db_xref="GI:75677329"
                     /db_xref="CCDS:CCDS47531.1"
                     /db_xref="GeneID:26100"
                     /db_xref="HGNC:32225"
                     /db_xref="HPRD:15679"
                     /db_xref="MIM:609225"
     CDS             join(5230051..5230124,5239207..5239289,5254166..5254335,
                     5256194..5256290,5256721..5256818,5257553..5257645,
                     5262233..5262303,5265454..5265561,5266811..5266975,
                     5267735..5267842,5269239..5269336,5270466..5270578)
                     /gene="WIPI2"
                     /gene_synonym="ATG18B; Atg21; CGI-50; DKFZp434J154;
                     DKFZp686P02188; FLJ12979; FLJ14217; FLJ42984; WIPI-2"
                     /note="isoform d is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="WD repeat domain phosphoinositide-interacting
                     protein 2 isoform d"
                     /protein_id="NP_001028691.1"
                     /db_xref="GI:75677331"
                     /db_xref="CCDS:CCDS47532.1"
                     /db_xref="GeneID:26100"
                     /db_xref="HGNC:32225"
                     /db_xref="HPRD:15679"
                     /db_xref="MIM:609225"
     mRNA            join(5253900..5254335,5256194..5256290,5256721..5256818,
                     5257553..5257645,5262233..5262303,5265454..5265561,
                     5266811..5266975,5267735..5267842,5269239..5269336,
                     5270466..5273486)
                     /gene="WIPI2"
                     /gene_synonym="ATG18B; Atg21; CGI-50; DKFZp434J154;
                     DKFZp686P02188; FLJ12979; FLJ14217; FLJ42984; WIPI-2"
                     /product="WD repeat domain, phosphoinositide interacting
                     2, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001033520.1"
                     /db_xref="GI:75677339"
                     /db_xref="GeneID:26100"
                     /db_xref="HGNC:32225"
                     /db_xref="HPRD:15679"
                     /db_xref="MIM:609225"
     CDS             join(5254132..5254335,5256194..5256290,5256721..5256818,
                     5257553..5257645,5262233..5262303,5265454..5265561,
                     5266811..5266975,5267735..5267842,5269239..5269336,
                     5270466..5270578)
                     /gene="WIPI2"
                     /gene_synonym="ATG18B; Atg21; CGI-50; DKFZp434J154;
                     DKFZp686P02188; FLJ12979; FLJ14217; FLJ42984; WIPI-2"
                     /note="isoform e is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="WD repeat domain phosphoinositide-interacting
                     protein 2 isoform e"
                     /protein_id="NP_001028692.1"
                     /db_xref="GI:75677340"
                     /db_xref="CCDS:CCDS47533.1"
                     /db_xref="GeneID:26100"
                     /db_xref="HGNC:32225"
                     /db_xref="HPRD:15679"
                     /db_xref="MIM:609225"
     gene            5322561..5343704
                     /gene="SLC29A4"
                     /gene_synonym="ENT4; FLJ34923; PMAT"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222962"
                     /db_xref="HGNC:23097"
                     /db_xref="HPRD:15362"
                     /db_xref="MIM:609149"
     mRNA            join(5322561..5322713,5327437..5327616,5330363..5330494,
                     5330755..5330868,5331324..5331452,5334491..5334565,
                     5336567..5336829,5338619..5338757,5338871..5339058,
                     5340053..5340293,5342428..5343704)
                     /gene="SLC29A4"
                     /gene_synonym="ENT4; FLJ34923; PMAT"
                     /product="solute carrier family 29 (nucleoside
                     transporters), member 4, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040661.1"
                     /db_xref="GI:100913033"
                     /db_xref="GeneID:222962"
                     /db_xref="HGNC:23097"
                     /db_xref="MIM:609149"
                     /db_xref="HPRD:15362"
     mRNA            join(5322561..5322713,5327440..5327616,5330363..5330494,
                     5330755..5330868,5331324..5331452,5334491..5334565,
                     5336567..5336829,5338619..5338757,5338871..5339058,
                     5340053..5340293,5342428..5343704)
                     /gene="SLC29A4"
                     /gene_synonym="ENT4; FLJ34923; PMAT"
                     /product="solute carrier family 29 (nucleoside
                     transporters), member 4, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_153247.2"
                     /db_xref="GI:100913031"
                     /db_xref="GeneID:222962"
                     /db_xref="HGNC:23097"
                     /db_xref="HPRD:15362"
                     /db_xref="MIM:609149"
     CDS             join(5327448..5327616,5330363..5330494,5330755..5330868,
                     5331324..5331452,5334491..5334565,5336567..5336829,
                     5338619..5338757,5338871..5339058,5340053..5340293,
                     5342428..5342570)
                     /gene="SLC29A4"
                     /gene_synonym="ENT4; FLJ34923; PMAT"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="equilibrative nucleoside transporter 4"
                     /protein_id="NP_694979.2"
                     /db_xref="GI:100913032"
                     /db_xref="CCDS:CCDS5340.1"
                     /db_xref="GeneID:222962"
                     /db_xref="HGNC:23097"
                     /db_xref="HPRD:15362"
                     /db_xref="MIM:609149"
     CDS             join(5327448..5327616,5330363..5330494,5330755..5330868,
                     5331324..5331452,5334491..5334565,5336567..5336829,
                     5338619..5338757,5338871..5339058,5340053..5340293,
                     5342428..5342570)
                     /gene="SLC29A4"
                     /gene_synonym="ENT4; FLJ34923; PMAT"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="equilibrative nucleoside transporter 4"
                     /protein_id="NP_001035751.1"
                     /db_xref="GI:100913034"
                     /db_xref="CCDS:CCDS5340.1"
                     /db_xref="GeneID:222962"
                     /db_xref="HGNC:23097"
                     /db_xref="HPRD:15362"
                     /db_xref="MIM:609149"
     gene            complement(5346421..5463177)
                     /gene="TNRC18"
                     /gene_synonym="CAGL79; KIAA1856; TNRC18A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84629"
                     /db_xref="HGNC:11962"
     mRNA            complement(join(5346421..5347943,5348506..5348580,
                     5348763..5348999,5352134..5353494,5354615..5354779,
                     5355587..5355703,5359949..5360057,5360163..5360238,
                     5360704..5360821,5363845..5363986,5364727..5364879,
                     5372253..5372680,5385193..5385441,5391450..5391725,
                     5396547..5396907,5399029..5399200,5401225..5401353,
                     5401528..5401664,5402281..5402456,5410006..5410995,
                     5413686..5414115,5415665..5415855,5416478..5416624,
                     5417002..5417207,5417553..5417655,5427303..5428967,
                     5430116..5430259,5434071..5434226,5460691..5461120,
                     5463072..5463177))
                     /gene="TNRC18"
                     /gene_synonym="CAGL79; KIAA1856; TNRC18A"
                     /product="trinucleotide repeat containing 18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001080495.2"
                     /db_xref="GI:169658377"
                     /db_xref="GeneID:84629"
                     /db_xref="HGNC:11962"
     CDS             complement(join(5347737..5347943,5348506..5348580,
                     5348763..5348999,5352134..5353494,5354615..5354779,
                     5355587..5355703,5359949..5360057,5360163..5360238,
                     5360704..5360821,5363845..5363986,5364727..5364879,
                     5372253..5372680,5385193..5385441,5391450..5391725,
                     5396547..5396907,5399029..5399200,5401225..5401353,
                     5401528..5401664,5402281..5402456,5410006..5410995,
                     5413686..5414115,5415665..5415855,5416478..5416624,
                     5417002..5417207,5417553..5417655,5427303..5428967,
                     5430116..5430259,5434071..5434226,5460691..5460877))
                     /gene="TNRC18"
                     /gene_synonym="CAGL79; KIAA1856; TNRC18A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="trinucleotide repeat-containing gene 18 protein"
                     /protein_id="NP_001073964.2"
                     /db_xref="GI:169658378"
                     /db_xref="CCDS:CCDS47534.1"
                     /db_xref="GeneID:84629"
                     /db_xref="HGNC:11962"
     gene            complement(5465587..5468950)
                     /gene="LOC100129484"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 13 ESTs, 1 Protein"
                     /db_xref="GeneID:100129484"
     misc_RNA        complement(5465587..5468950)
                     /gene="LOC100129484"
                     /product="hypothetical LOC100129484"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 13 ESTs, 1 Protein"
                     /transcript_id="XR_108734.1"
                     /db_xref="GI:310119906"
                     /db_xref="GeneID:100129484"
     gene            complement(5515428..5553399)
                     /gene="FBXL18"
                     /gene_synonym="Fbl18; FLJ10776; FLJ11467; FLJ26934;
                     FLJ38075; FLJ41541"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:80028"
                     /db_xref="HGNC:21874"
                     /db_xref="HPRD:07753"
                     /db_xref="MIM:609084"
     mRNA            complement(join(5515428..5521562,5530862..5531080,
                     5540119..5541662,5545043..5545261,5553288..5553399))
                     /gene="FBXL18"
                     /gene_synonym="Fbl18; FLJ10776; FLJ11467; FLJ26934;
                     FLJ38075; FLJ41541"
                     /product="F-box and leucine-rich repeat protein 18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024963.4"
                     /db_xref="GI:157426874"
                     /db_xref="GeneID:80028"
                     /db_xref="HGNC:21874"
                     /db_xref="HPRD:07753"
                     /db_xref="MIM:609084"
     CDS             complement(join(5521406..5521562,5530862..5531080,
                     5540119..5541662,5545043..5545261,5553288..5553305))
                     /gene="FBXL18"
                     /gene_synonym="Fbl18; FLJ10776; FLJ11467; FLJ26934;
                     FLJ38075; FLJ41541"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="F-box/LRR-repeat protein 18"
                     /protein_id="NP_079239.3"
                     /db_xref="GI:157426875"
                     /db_xref="CCDS:CCDS43546.1"
                     /db_xref="GeneID:80028"
                     /db_xref="HGNC:21874"
                     /db_xref="HPRD:07753"
                     /db_xref="MIM:609084"
     gene            complement(5535450..5535548)
                     /gene="MIR589"
                     /gene_synonym="hsa-mir-589; MIRN589"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:693174"
                     /db_xref="HGNC:32845"
                     /db_xref="miRBase:MI0003599"
     ncRNA           complement(5535450..5535548)
                     /gene="MIR589"
                     /gene_synonym="hsa-mir-589; MIRN589"
                     /ncRNA_class="miRNA"
                     /product="microRNA 589"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_030318.1"
                     /db_xref="GI:262205932"
                     /db_xref="GeneID:693174"
                     /db_xref="HGNC:32845"
                     /db_xref="miRBase:MI0003599"
     ncRNA           complement(5535450..5535548)
                     /gene="MIR589"
                     /gene_synonym="hsa-mir-589; MIRN589"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-589"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:693174"
                     /db_xref="miRBase:MI0003599"
                     /db_xref="HGNC:32845"
     gene            complement(5566779..5570232)
                     /gene="ACTB"
                     /gene_synonym="PS1TP5BP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:60"
                     /db_xref="HGNC:132"
                     /db_xref="HPRD:00032"
                     /db_xref="MIM:102630"
     mRNA            complement(join(5566779..5567522,5567635..5567816,
                     5567912..5568350,5568792..5569031,5569166..5569294,
                     5570155..5570232))
                     /gene="ACTB"
                     /gene_synonym="PS1TP5BP1"
                     /product="actin, beta"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001101.3"
                     /db_xref="GI:168480144"
                     /db_xref="GeneID:60"
                     /db_xref="HGNC:132"
                     /db_xref="HPRD:00032"
                     /db_xref="MIM:102630"
     gene            5566786..5573677
                     /gene="LOC100505829"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 41 ESTs"
                     /db_xref="GeneID:100505829"
     misc_RNA        join(5566786..5567353,5573666..5573677)
                     /gene="LOC100505829"
                     /product="hypothetical LOC100505829"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 41 ESTs"
                     /transcript_id="XR_108735.2"
                     /db_xref="GI:341915380"
                     /db_xref="GeneID:100505829"
     CDS             complement(join(5567379..5567522,5567635..5567816,
                     5567912..5568350,5568792..5569031,5569166..5569288))
                     /gene="ACTB"
                     /gene_synonym="PS1TP5BP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="actin, cytoplasmic 1"
                     /protein_id="NP_001092.1"
                     /db_xref="GI:4501885"
                     /db_xref="CCDS:CCDS5341.1"
                     /db_xref="GeneID:60"
                     /db_xref="HGNC:132"
                     /db_xref="HPRD:00032"
                     /db_xref="MIM:102630"
     gene            5595533..5600688
                     /gene="LOC100288712"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100288712"
     misc_RNA        join(5595533..5595610,5596085..5596247,5599449..5599563,
                     5600369..5600688)
                     /gene="LOC100288712"
                     /product="hypothetical LOC100288712"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /transcript_id="XR_132525.1"
                     /db_xref="GI:341915376"
                     /db_xref="GeneID:100288712"
     gene            complement(5632442..5633244)
                     /gene="LOC100652839"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 9 ESTs"
                     /db_xref="GeneID:100652839"
     misc_RNA        complement(join(5632442..5632896,5633117..5633244))
                     /gene="LOC100652839"
                     /product="hypothetical LOC100652839"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 9 ESTs"
                     /transcript_id="XR_132529.1"
                     /db_xref="GI:341915382"
                     /db_xref="GeneID:100652839"
     gene            5632454..5646286
                     /gene="FSCN1"
                     /gene_synonym="FLJ38511; p55; SNL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6624"
                     /db_xref="HGNC:11148"
                     /db_xref="HPRD:04068"
                     /db_xref="MIM:602689"
     mRNA            join(5632454..5633399,5642888..5643044,5643127..5643248,
                     5643494..5643661,5644903..5646286)
                     /gene="FSCN1"
                     /gene_synonym="FLJ38511; p55; SNL"
                     /product="fascin homolog 1, actin-bundling protein
                     (Strongylocentrotus purpuratus)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003088.2"
                     /db_xref="GI:49472815"
                     /db_xref="GeneID:6624"
                     /db_xref="HGNC:11148"
                     /db_xref="HPRD:04068"
                     /db_xref="MIM:602689"
     CDS             join(5632568..5633399,5642888..5643044,5643127..5643248,
                     5643494..5643661,5644903..5645105)
                     /gene="FSCN1"
                     /gene_synonym="FLJ38511; p55; SNL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="fascin"
                     /protein_id="NP_003079.1"
                     /db_xref="GI:4507115"
                     /db_xref="CCDS:CCDS5342.1"
                     /db_xref="GeneID:6624"
                     /db_xref="HGNC:11148"
                     /db_xref="HPRD:04068"
                     /db_xref="MIM:602689"
     gene            complement(5643492..5645489)
                     /gene="LOC100652832"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 10 ESTs"
                     /db_xref="GeneID:100652832"
     misc_RNA        complement(join(5643492..5643668,5644905..5645489))
                     /gene="LOC100652832"
                     /product="hypothetical LOC100652832"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 10 ESTs"
                     /transcript_id="XR_132528.1"
                     /db_xref="GI:341915381"
                     /db_xref="GeneID:100652832"
     gene            complement(5659672..5821361)
                     /gene="RNF216"
                     /gene_synonym="TRIAD3; U7I1; UBCE7IP1; ZIN"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54476"
                     /db_xref="HGNC:21698"
                     /db_xref="HPRD:15550"
                     /db_xref="MIM:609948"
     mRNA            complement(join(5659672..5662810,5663687..5663756,
                     5680785..5681007,5692044..5692141,5751392..5751470,
                     5752346..5752494,5754684..5754821,5756347..5756397,
                     5760664..5760803,5764955..5765069,5769063..5769227,
                     5770346..5770448,5778907..5778983,5780604..5781446,
                     5792477..5792610,5800634..5800769,5821172..5821361))
                     /gene="RNF216"
                     /gene_synonym="TRIAD3; U7I1; UBCE7IP1; ZIN"
                     /product="ring finger protein 216, transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_207111.3"
                     /db_xref="GI:319803088"
                     /db_xref="GeneID:54476"
                     /db_xref="HGNC:21698"
                     /db_xref="HPRD:15550"
                     /db_xref="MIM:609948"
     mRNA            complement(join(5659672..5662810,5663687..5663756,
                     5680785..5681007,5692044..5692141,5751392..5751470,
                     5752346..5752494,5754684..5754821,5756347..5756397,
                     5760664..5760803,5764955..5765069,5769063..5769227,
                     5770346..5770448,5778907..5778983,5780604..5781275,
                     5792477..5792610,5800634..5800769,5821172..5821361))
                     /gene="RNF216"
                     /gene_synonym="TRIAD3; U7I1; UBCE7IP1; ZIN"
                     /product="ring finger protein 216, transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_207116.2"
                     /db_xref="GI:319803089"
                     /db_xref="GeneID:54476"
                     /db_xref="HGNC:21698"
                     /db_xref="MIM:609948"
                     /db_xref="HPRD:15550"
     CDS             complement(join(5662491..5662810,5663687..5663756,
                     5680785..5681007,5692044..5692141,5751392..5751470,
                     5752346..5752494,5754684..5754821,5756347..5756397,
                     5760664..5760803,5764955..5765069,5769063..5769227,
                     5770346..5770448,5778907..5778983,5780604..5781446,
                     5792477..5792610,5800634..5800700))
                     /gene="RNF216"
                     /gene_synonym="TRIAD3; U7I1; UBCE7IP1; ZIN"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase RNF216 isoform a"
                     /protein_id="NP_996994.1"
                     /db_xref="GI:46358403"
                     /db_xref="CCDS:CCDS34594.1"
                     /db_xref="GeneID:54476"
                     /db_xref="HGNC:21698"
                     /db_xref="HPRD:15550"
                     /db_xref="MIM:609948"
     CDS             complement(join(5662491..5662810,5663687..5663756,
                     5680785..5681007,5692044..5692141,5751392..5751470,
                     5752346..5752494,5754684..5754821,5756347..5756397,
                     5760664..5760803,5764955..5765069,5769063..5769227,
                     5770346..5770448,5778907..5778983,5780604..5781275,
                     5792477..5792610,5800634..5800700))
                     /gene="RNF216"
                     /gene_synonym="TRIAD3; U7I1; UBCE7IP1; ZIN"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase RNF216 isoform b"
                     /protein_id="NP_996999.1"
                     /db_xref="GI:46370057"
                     /db_xref="CCDS:CCDS34595.1"
                     /db_xref="GeneID:54476"
                     /db_xref="HGNC:21698"
                     /db_xref="HPRD:15550"
                     /db_xref="MIM:609948"
     gene            5862791..5894066
                     /gene="ZNF815"
                     /gene_synonym="FLJ38969"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:401303"
                     /db_xref="HGNC:22029"
     misc_RNA        join(5862791..5863157,5873158..5873199,5879580..5879706,
                     5880321..5880487,5886397..5887232,5888195..5889147,
                     5893738..5894066)
                     /gene="ZNF815"
                     /gene_synonym="FLJ38969"
                     /product="zinc finger protein 815"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_023382.1"
                     /db_xref="GI:190014639"
                     /db_xref="GeneID:401303"
                     /db_xref="HGNC:22029"
     gene            5920429..5925994
                     /gene="OCM"
                     /gene_synonym="MGC142264; MGC142266; MGC97453; MGC97465;
                     MGC97477; OCM1; OM; ONCM"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:654231"
                     /db_xref="HGNC:8105"
                     /db_xref="MIM:164795"
     mRNA            join(5920429..5920581,5922124..5922256,5923521..5923630,
                     5925695..5925994)
                     /gene="OCM"
                     /gene_synonym="MGC142264; MGC142266; MGC97453; MGC97465;
                     MGC97477; OCM1; OM; ONCM"
                     /product="oncomodulin"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001097622.1"
                     /db_xref="GI:147906121"
                     /db_xref="GeneID:654231"
                     /db_xref="HGNC:8105"
                     /db_xref="MIM:164795"
     CDS             join(5920521..5920581,5922124..5922256,5923521..5923630,
                     5925695..5925720)
                     /gene="OCM"
                     /gene_synonym="MGC142264; MGC142266; MGC97453; MGC97465;
                     MGC97477; OCM1; OM; ONCM"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="oncomodulin-1"
                     /protein_id="NP_001091091.1"
                     /db_xref="GI:147906122"
                     /db_xref="CCDS:CCDS43548.1"
                     /db_xref="GeneID:654231"
                     /db_xref="HGNC:8105"
                     /db_xref="MIM:164795"
     gene            5938341..5965605
                     /gene="CCZ1"
                     /gene_synonym="C7orf28A; CGI-43; H_DJ1163J12.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51622"
                     /db_xref="HGNC:21691"
                     /db_xref="HPRD:12915"
     mRNA            join(5938341..5938550,5939915..5940012,5940104..5940197,
                     5940486..5940563,5941288..5941335,5942292..5942375,
                     5944725..5944900,5949666..5949747,5951492..5951553,
                     5952474..5952585,5958498..5958531,5959480..5959597,
                     5963018..5963176,5963466..5963593,5965263..5965605)
                     /gene="CCZ1"
                     /gene_synonym="C7orf28A; CGI-43; H_DJ1163J12.2"
                     /product="CCZ1 vacuolar protein trafficking and biogenesis
                     associated homolog (S. cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015622.5"
                     /db_xref="GI:56699479"
                     /db_xref="GeneID:51622"
                     /db_xref="HGNC:21691"
                     /db_xref="HPRD:12915"
     CDS             join(5938431..5938550,5939915..5940012,5940104..5940197,
                     5940486..5940563,5941288..5941335,5942292..5942375,
                     5944725..5944900,5949666..5949747,5951492..5951553,
                     5952474..5952585,5958498..5958531,5959480..5959597,
                     5963018..5963176,5963466..5963593,5965263..5965318)
                     /gene="CCZ1"
                     /gene_synonym="C7orf28A; CGI-43; H_DJ1163J12.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="vacuolar fusion protein CCZ1 homolog"
                     /protein_id="NP_056437.4"
                     /db_xref="GI:56699480"
                     /db_xref="CCDS:CCDS34597.1"
                     /db_xref="GeneID:51622"
                     /db_xref="HGNC:21691"
                     /db_xref="HPRD:12915"
     gene            complement(5965777..6010314)
                     /gene="RSPH10B"
                     /gene_synonym="MGC50833; RSPH10B2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222967"
                     /db_xref="HGNC:27362"
                     /db_xref="HPRD:11249"
     mRNA            complement(join(5965777..5966179,5967827..5968025,
                     5972413..5972506,5974651..5974779,5977389..5977532,
                     5978353..5978460,5982955..5983103,5983542..5983621,
                     5984695..5984809,5987851..5988040,5990926..5991047,
                     5992706..5992850,5995636..5995812,5997538..5997658,
                     5998624..5998709,6000322..6000495,6004133..6004201,
                     6005268..6005343,6006494..6006832,6006949..6007068,
                     6010249..6010314))
                     /gene="RSPH10B"
                     /gene_synonym="MGC50833; RSPH10B2"
                     /product="radial spoke head 10 homolog B (Chlamydomonas)"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_173565.3"
                     /db_xref="GI:157502186"
                     /db_xref="GeneID:222967"
                     /db_xref="HGNC:27362"
                     /db_xref="HPRD:11249"
     CDS             complement(join(5965999..5966179,5967827..5968025,
                     5972413..5972506,5974651..5974779,5977389..5977532,
                     5978353..5978460,5982955..5983103,5983542..5983621,
                     5984695..5984809,5987851..5988040,5990926..5991047,
                     5992706..5992850,5995636..5995812,5997538..5997658,
                     5998624..5998709,6000322..6000495,6004133..6004201,
                     6005268..6005343,6006494..6006747))
                     /gene="RSPH10B"
                     /gene_synonym="MGC50833; RSPH10B2"
                     /exception="mismatches in translation"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="radial spoke head 10 homolog B"
                     /protein_id="NP_775836.3"
                     /db_xref="GI:157502187"
                     /db_xref="CCDS:CCDS34598.1"
                     /db_xref="GeneID:222967"
                     /db_xref="HGNC:27362"
                     /db_xref="HPRD:11249"
     gene            complement(6012870..6048737)
                     /gene="PMS2"
                     /gene_synonym="HNPCC4; PMS2CL; PMSL2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5395"
                     /db_xref="HGNC:9122"
                     /db_xref="HPRD:02598"
                     /db_xref="MIM:600259"
     mRNA            complement(join(6012870..6013173,6017219..6017388,
                     6018227..6018327,6022455..6022622,6026390..6027251,
                     6029431..6029586,6031604..6031688,6035165..6035264,
                     6036957..6037054,6038739..6038906,6042084..6042267,
                     6043321..6043423,6043603..6043689,6045523..6045662,
                     6048628..6048737))
                     /gene="PMS2"
                     /gene_synonym="HNPCC4; PMS2CL; PMSL2"
                     /product="PMS2 postmeiotic segregation increased 2 (S.
                     cerevisiae), transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000535.5"
                     /db_xref="GI:190014589"
                     /db_xref="GeneID:5395"
                     /db_xref="HGNC:9122"
                     /db_xref="HPRD:02598"
                     /db_xref="MIM:600259"
     misc_RNA        complement(join(6012870..6013173,6017219..6017388,
                     6018227..6018327,6022455..6022622,6026390..6027251,
                     6029431..6029586,6031604..6031688,6035165..6035264,
                     6036957..6037054,6038739..6038906,6042084..6042267,
                     6043321..6043423,6043603..6043689,6045523..6045657,
                     6048628..6048737))
                     /gene="PMS2"
                     /gene_synonym="HNPCC4; PMS2CL; PMSL2"
                     /product="PMS2 postmeiotic segregation increased 2 (S.
                     cerevisiae), transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_003085.2"
                     /db_xref="GI:190014608"
                     /db_xref="GeneID:5395"
                     /db_xref="HGNC:9122"
                     /db_xref="MIM:600259"
                     /db_xref="HPRD:02598"
     CDS             complement(join(6013030..6013173,6017219..6017388,
                     6018227..6018327,6022455..6022622,6026390..6027251,
                     6029431..6029586,6031604..6031688,6035165..6035264,
                     6036957..6037054,6038739..6038906,6042084..6042267,
                     6043321..6043423,6043603..6043689,6045523..6045662,
                     6048628..6048650))
                     /gene="PMS2"
                     /gene_synonym="HNPCC4; PMS2CL; PMSL2"
                     /exception="mismatches in translation"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="mismatch repair endonuclease PMS2 isoform a"
                     /protein_id="NP_000526.1"
                     /db_xref="GI:4505913"
                     /db_xref="CCDS:CCDS5343.1"
                     /db_xref="GeneID:5395"
                     /db_xref="HGNC:9122"
                     /db_xref="HPRD:02598"
                     /db_xref="MIM:600259"
     gene            6048882..6063465
                     /gene="AIMP2"
                     /gene_synonym="JTV-1; JTV1; P38; PRO0992"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7965"
                     /db_xref="HGNC:20609"
                     /db_xref="HPRD:02915"
                     /db_xref="MIM:600859"
     mRNA            join(6048882..6049129,6054777..6054983,6057445..6057676,
                     6062934..6063465)
                     /gene="AIMP2"
                     /gene_synonym="JTV-1; JTV1; P38; PRO0992"
                     /product="aminoacyl tRNA synthetase complex-interacting
                     multifunctional protein 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006303.3"
                     /db_xref="GI:100814397"
                     /db_xref="GeneID:7965"
                     /db_xref="HGNC:20609"
                     /db_xref="HPRD:02915"
                     /db_xref="MIM:600859"
     CDS             join(6048995..6049129,6054777..6054983,6057445..6057676,
                     6062934..6063322)
                     /gene="AIMP2"
                     /gene_synonym="JTV-1; JTV1; P38; PRO0992"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="aminoacyl tRNA synthase complex-interacting
                     multifunctional protein 2"
                     /protein_id="NP_006294.2"
                     /db_xref="GI:11125770"
                     /db_xref="CCDS:CCDS5344.1"
                     /db_xref="GeneID:7965"
                     /db_xref="HGNC:20609"
                     /db_xref="HPRD:02915"
                     /db_xref="MIM:600859"
     gene            complement(6061878..6098860)
                     /gene="EIF2AK1"
                     /gene_synonym="HCR; HRI; KIAA1369"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:27102"
                     /db_xref="HGNC:24921"
                     /db_xref="HPRD:10684"
                     /db_xref="MIM:613635"
     mRNA            complement(join(6061878..6064432,6066359..6066592,
                     6068246..6068328,6068549..6068663,6077055..6077155,
                     6078191..6078302,6080523..6080850,6082564..6082624,
                     6084193..6084292,6085702..6085782,6086623..6086722,
                     6088438..6088475,6089543..6089676,6094177..6094335,
                     6098597..6098860))
                     /gene="EIF2AK1"
                     /gene_synonym="HCR; HRI; KIAA1369"
                     /product="eukaryotic translation initiation factor 2-alpha
                     kinase 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014413.3"
                     /db_xref="GI:197245434"
                     /db_xref="GeneID:27102"
                     /db_xref="HGNC:24921"
                     /db_xref="HPRD:10684"
                     /db_xref="MIM:613635"
     mRNA            complement(join(6061878..6064432,6066359..6066592,
                     6068246..6068328,6068549..6068663,6077055..6077155,
                     6078191..6078302,6080523..6080850,6082564..6082621,
                     6084193..6084292,6085702..6085782,6086623..6086722,
                     6088438..6088475,6089543..6089676,6094177..6094335,
                     6098597..6098860))
                     /gene="EIF2AK1"
                     /gene_synonym="HCR; HRI; KIAA1369"
                     /product="eukaryotic translation initiation factor 2-alpha
                     kinase 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134335.1"
                     /db_xref="GI:197245436"
                     /db_xref="GeneID:27102"
                     /db_xref="HGNC:24921"
                     /db_xref="MIM:613635"
                     /db_xref="HPRD:10684"
     CDS             complement(join(6064304..6064432,6066359..6066592,
                     6068246..6068328,6068549..6068663,6077055..6077155,
                     6078191..6078302,6080523..6080850,6082564..6082624,
                     6084193..6084292,6085702..6085782,6086623..6086722,
                     6088438..6088475,6089543..6089676,6094177..6094335,
                     6098597..6098714))
                     /gene="EIF2AK1"
                     /gene_synonym="HCR; HRI; KIAA1369"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="eukaryotic translation initiation factor 2-alpha
                     kinase 1 isoform a"
                     /protein_id="NP_055228.2"
                     /db_xref="GI:11125768"
                     /db_xref="CCDS:CCDS5345.1"
                     /db_xref="GeneID:27102"
                     /db_xref="HGNC:24921"
                     /db_xref="HPRD:10684"
                     /db_xref="MIM:613635"
     CDS             complement(join(6064304..6064432,6066359..6066592,
                     6068246..6068328,6068549..6068663,6077055..6077155,
                     6078191..6078302,6080523..6080850,6082564..6082621,
                     6084193..6084292,6085702..6085782,6086623..6086722,
                     6088438..6088475,6089543..6089676,6094177..6094335,
                     6098597..6098714))
                     /gene="EIF2AK1"
                     /gene_synonym="HCR; HRI; KIAA1369"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="eukaryotic translation initiation factor 2-alpha
                     kinase 1 isoform b"
                     /protein_id="NP_001127807.1"
                     /db_xref="GI:197245437"
                     /db_xref="GeneID:27102"
                     /db_xref="HGNC:24921"
                     /db_xref="MIM:613635"
                     /db_xref="HPRD:10684"
     gene            6144550..6201195
                     /gene="USP42"
                     /gene_synonym="FLJ12697"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84132"
                     /db_xref="HGNC:20068"
     mRNA            join(6144550..6144663,6150756..6151005,6154954..6155154,
                     6175472..6175582,6178723..6178825,6179759..6179826,
                     6180545..6180615,6182563..6182645,6183716..6183827,
                     6185147..6185287,6185779..6185879,6187370..6187523,
                     6189214..6189933,6190043..6190137,6193387..6194826,
                     6196385..6196686,6199081..6199124,6200186..6201195)
                     /gene="USP42"
                     /gene_synonym="FLJ12697"
                     /product="ubiquitin specific peptidase 42"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032172.2"
                     /db_xref="GI:134948692"
                     /db_xref="GeneID:84132"
                     /db_xref="HGNC:20068"
     CDS             join(6150765..6151005,6154954..6155154,6175472..6175582,
                     6178723..6178825,6179759..6179826,6180545..6180615,
                     6182563..6182645,6183716..6183827,6185147..6185287,
                     6185779..6185879,6187370..6187523,6189214..6189933,
                     6190043..6190137,6193387..6194826,6196385..6196686,
                     6199081..6199088)
                     /gene="USP42"
                     /gene_synonym="FLJ12697"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ubiquitin carboxyl-terminal hydrolase 42"
                     /protein_id="NP_115548.1"
                     /db_xref="GI:79750944"
                     /db_xref="CCDS:CCDS47535.1"
                     /db_xref="GeneID:84132"
                     /db_xref="HGNC:20068"
     gene            complement(6201410..6312242)
                     /gene="CYTH3"
                     /gene_synonym="ARNO3; GRP1; PSCD3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9265"
                     /db_xref="HGNC:9504"
                     /db_xref="HPRD:05469"
                     /db_xref="MIM:605081"
     mRNA            complement(join(6201410..6204647,6204904..6205058,
                     6205176..6205247,6205365..6205441,6210166..6210277,
                     6210461..6210609,6210833..6210945,6213284..6213364,
                     6217454..6217572,6226681..6226747,6227288..6227352,
                     6230080..6230162,6312105..6312242))
                     /gene="CYTH3"
                     /gene_synonym="ARNO3; GRP1; PSCD3"
                     /product="cytohesin 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004227.3"
                     /db_xref="GI:33946275"
                     /db_xref="GeneID:9265"
                     /db_xref="HGNC:9504"
                     /db_xref="HPRD:05469"
                     /db_xref="MIM:605081"
     CDS             complement(join(6204575..6204647,6204904..6205058,
                     6205176..6205247,6205365..6205441,6210166..6210277,
                     6210461..6210609,6210833..6210945,6213284..6213364,
                     6217454..6217572,6226681..6226747,6227288..6227352,
                     6230080..6230162,6312105..6312138))
                     /gene="CYTH3"
                     /gene_synonym="ARNO3; GRP1; PSCD3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytohesin-3"
                     /protein_id="NP_004218.1"
                     /db_xref="GI:4758968"
                     /db_xref="CCDS:CCDS5346.1"
                     /db_xref="GeneID:9265"
                     /db_xref="HGNC:9504"
                     /db_xref="HPRD:05469"
                     /db_xref="MIM:605081"
     gene            complement(6369040..6388590)
                     /gene="C7orf70"
                     /gene_synonym="MGC12966; SIPAR"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84792"
                     /db_xref="HGNC:22422"
                     /db_xref="HPRD:14427"
     mRNA            complement(join(6369040..6370866,6388204..6388590))
                     /gene="C7orf70"
                     /gene_synonym="MGC12966; SIPAR"
                     /product="chromosome 7 open reading frame 70"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001037163.1"
                     /db_xref="GI:81174548"
                     /db_xref="GeneID:84792"
                     /db_xref="HGNC:22422"
                     /db_xref="HPRD:14427"
     CDS             complement(6370006..6370785)
                     /gene="C7orf70"
                     /gene_synonym="MGC12966; SIPAR"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="STAT3-interacting protein as a repressor"
                     /protein_id="NP_001032240.1"
                     /db_xref="GI:81174549"
                     /db_xref="CCDS:CCDS34599.1"
                     /db_xref="GeneID:84792"
                     /db_xref="HGNC:22422"
                     /db_xref="HPRD:14427"
     gene            6414126..6443598
                     /gene="RAC1"
                     /gene_synonym="MGC111543; MIG5; p21-Rac1; Rac-1; TC-25"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5879"
                     /db_xref="HGNC:9801"
                     /db_xref="HPRD:03627"
                     /db_xref="MIM:602048"
     mRNA            join(6414126..6414401,6426843..6426914,6431555..6431672,
                     6439757..6439819,6441499..6441658,6441947..6443598)
                     /gene="RAC1"
                     /gene_synonym="MGC111543; MIG5; p21-Rac1; Rac-1; TC-25"
                     /product="ras-related C3 botulinum toxin substrate 1 (rho
                     family, small GTP binding protein Rac1), transcript
                     variant Rac1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006908.4"
                     /db_xref="GI:156071503"
                     /db_xref="GeneID:5879"
                     /db_xref="HGNC:9801"
                     /db_xref="HPRD:03627"
                     /db_xref="MIM:602048"
     mRNA            join(6414126..6414401,6426843..6426914,6431555..6431672,
                     6438293..6438349,6439757..6439819,6441499..6441658,
                     6441947..6443598)
                     /gene="RAC1"
                     /gene_synonym="MGC111543; MIG5; p21-Rac1; Rac-1; TC-25"
                     /product="ras-related C3 botulinum toxin substrate 1 (rho
                     family, small GTP binding protein Rac1), transcript
                     variant Rac1b"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018890.3"
                     /db_xref="GI:156071511"
                     /db_xref="GeneID:5879"
                     /db_xref="HGNC:9801"
                     /db_xref="HPRD:03627"
                     /db_xref="MIM:602048"
     CDS             join(6414367..6414401,6426843..6426914,6431555..6431672,
                     6439757..6439819,6441499..6441658,6441947..6442077)
                     /gene="RAC1"
                     /gene_synonym="MGC111543; MIG5; p21-Rac1; Rac-1; TC-25"
                     /note="isoform Rac1 is encoded by transcript variant Rac1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ras-related C3 botulinum toxin substrate 1
                     isoform Rac1"
                     /protein_id="NP_008839.2"
                     /db_xref="GI:9845511"
                     /db_xref="CCDS:CCDS5348.1"
                     /db_xref="GeneID:5879"
                     /db_xref="HGNC:9801"
                     /db_xref="HPRD:03627"
                     /db_xref="MIM:602048"
     CDS             join(6414367..6414401,6426843..6426914,6431555..6431672,
                     6438293..6438349,6439757..6439819,6441499..6441658,
                     6441947..6442077)
                     /gene="RAC1"
                     /gene_synonym="MGC111543; MIG5; p21-Rac1; Rac-1; TC-25"
                     /note="isoform Rac1b is encoded by transcript variant
                     Rac1b; Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ras-related C3 botulinum toxin substrate 1
                     isoform Rac1b"
                     /protein_id="NP_061485.1"
                     /db_xref="GI:9845509"
                     /db_xref="CCDS:CCDS5349.1"
                     /db_xref="GeneID:5879"
                     /db_xref="HGNC:9801"
                     /db_xref="HPRD:03627"
                     /db_xref="MIM:602048"
     gene            complement(6448747..6487643)
                     /gene="DAGLB"
                     /gene_synonym="DAGLBETA; FLJ33624; FLJ33909; FLJ45532;
                     KCCR13L"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221955"
                     /db_xref="HGNC:28923"
                     /db_xref="HPRD:17324"
                     /db_xref="MIM:614016"
     mRNA            complement(join(6448747..6449666,6449761..6450011,
                     6452442..6452514,6452597..6452665,6456258..6456385,
                     6456472..6456552,6461358..6461435,6464383..6464466,
                     6465619..6465745,6470111..6470238,6472468..6472590,
                     6474393..6474651,6475993..6476164,6485584..6485735,
                     6487379..6487643))
                     /gene="DAGLB"
                     /gene_synonym="DAGLBETA; FLJ33624; FLJ33909; FLJ45532;
                     KCCR13L"
                     /product="diacylglycerol lipase, beta, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_139179.3"
                     /db_xref="GI:218931250"
                     /db_xref="GeneID:221955"
                     /db_xref="HGNC:28923"
                     /db_xref="HPRD:17324"
                     /db_xref="MIM:614016"
     mRNA            complement(join(6448747..6449666,6449761..6450011,
                     6452442..6452514,6452597..6452665,6456258..6456385,
                     6456472..6456552,6461358..6461435,6464383..6464466,
                     6465619..6465745,6472468..6472590,6475993..6476164,
                     6485584..6485735,6487379..6487643))
                     /gene="DAGLB"
                     /gene_synonym="DAGLBETA; FLJ33624; FLJ33909; FLJ45532;
                     KCCR13L"
                     /product="diacylglycerol lipase, beta, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001142936.1"
                     /db_xref="GI:218931252"
                     /db_xref="GeneID:221955"
                     /db_xref="HGNC:28923"
                     /db_xref="MIM:614016"
                     /db_xref="HPRD:17324"
     CDS             complement(join(6449468..6449666,6449761..6450011,
                     6452442..6452514,6452597..6452665,6456258..6456385,
                     6456472..6456552,6461358..6461435,6464383..6464466,
                     6465619..6465745,6470111..6470238,6472468..6472590,
                     6474393..6474651,6475993..6476164,6485584..6485735,
                     6487379..6487473))
                     /gene="DAGLB"
                     /gene_synonym="DAGLBETA; FLJ33624; FLJ33909; FLJ45532;
                     KCCR13L"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="sn1-specific diacylglycerol lipase beta isoform
                     1"
                     /protein_id="NP_631918.3"
                     /db_xref="GI:218931251"
                     /db_xref="CCDS:CCDS5350.1"
                     /db_xref="GeneID:221955"
                     /db_xref="HGNC:28923"
                     /db_xref="HPRD:17324"
                     /db_xref="MIM:614016"
     CDS             complement(join(6449468..6449666,6449761..6450011,
                     6452442..6452514,6452597..6452665,6456258..6456385,
                     6456472..6456552,6461358..6461435,6464383..6464466,
                     6465619..6465745,6472468..6472590,6475993..6476164,
                     6485584..6485735,6487379..6487473))
                     /gene="DAGLB"
                     /gene_synonym="DAGLBETA; FLJ33624; FLJ33909; FLJ45532;
                     KCCR13L"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="sn1-specific diacylglycerol lipase beta isoform
                     2"
                     /protein_id="NP_001136408.1"
                     /db_xref="GI:218931253"
                     /db_xref="CCDS:CCDS47536.1"
                     /db_xref="GeneID:221955"
                     /db_xref="HGNC:28923"
                     /db_xref="HPRD:17324"
                     /db_xref="MIM:614016"
     gene            complement(6500712..6523849)
                     /gene="KDELR2"
                     /gene_synonym="ELP-1; ERD2.2; FLJ45532"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:11014"
                     /db_xref="HGNC:6305"
                     /db_xref="HPRD:06598"
                     /db_xref="MIM:609024"
     mRNA            complement(join(6500712..6502806,6505702..6505954,
                     6509227..6509385,6513815..6513915,6523598..6523849))
                     /gene="KDELR2"
                     /gene_synonym="ELP-1; ERD2.2; FLJ45532"
                     /product="KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum
                     protein retention receptor 2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006854.3"
                     /db_xref="GI:154736711"
                     /db_xref="GeneID:11014"
                     /db_xref="HGNC:6305"
                     /db_xref="HPRD:06598"
                     /db_xref="MIM:609024"
     mRNA            complement(join(6500712..6502806,6509227..6509385,
                     6513815..6513915,6523598..6523849))
                     /gene="KDELR2"
                     /gene_synonym="ELP-1; ERD2.2; FLJ45532"
                     /product="KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum
                     protein retention receptor 2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001100603.1"
                     /db_xref="GI:154736712"
                     /db_xref="GeneID:11014"
                     /db_xref="HGNC:6305"
                     /db_xref="MIM:609024"
                     /db_xref="HPRD:06598"
     CDS             complement(join(6502597..6502806,6509227..6509385,
                     6513815..6513915,6523598..6523688))
                     /gene="KDELR2"
                     /gene_synonym="ELP-1; ERD2.2; FLJ45532"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ER lumen protein retaining receptor 2 isoform 2"
                     /protein_id="NP_001094073.1"
                     /db_xref="GI:154736713"
                     /db_xref="CCDS:CCDS43550.1"
                     /db_xref="GeneID:11014"
                     /db_xref="HGNC:6305"
                     /db_xref="HPRD:06598"
                     /db_xref="MIM:609024"
     CDS             complement(join(6502772..6502806,6505702..6505954,
                     6509227..6509385,6513815..6513915,6523598..6523688))
                     /gene="KDELR2"
                     /gene_synonym="ELP-1; ERD2.2; FLJ45532"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ER lumen protein retaining receptor 2 isoform 1"
                     /protein_id="NP_006845.1"
                     /db_xref="GI:5803050"
                     /db_xref="CCDS:CCDS5351.1"
                     /db_xref="GeneID:11014"
                     /db_xref="HGNC:6305"
                     /db_xref="HPRD:06598"
                     /db_xref="MIM:609024"
     gene            complement(6530372..6530732)
                     /gene="RPL31P34"
                     /gene_synonym="RPL31_10_781"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271193"
                     /db_xref="HGNC:35853"
     gene            complement(6536409..6591067)
                     /gene="GRID2IP"
                     /gene_synonym="DELPHILIN"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:392862"
                     /db_xref="HGNC:18464"
                     /db_xref="MIM:610639"
     mRNA            complement(join(6536409..6537476,6537695..6537859,
                     6541412..6541530,6541620..6541749,6542417..6542503,
                     6542639..6542794,6543122..6543318,6544424..6544501,
                     6545451..6545538,6547616..6548032,6548589..6548944,
                     6549914..6550031,6550240..6550337,6550539..6550670,
                     6554006..6554160,6560209..6560392,6561060..6561154,
                     6561519..6561588,6565855..6565940,6566152..6566400,
                     6579349..6579503,6590639..6591067))
                     /gene="GRID2IP"
                     /gene_synonym="DELPHILIN"
                     /product="glutamate receptor, ionotropic, delta 2 (Grid2)
                     interacting protein"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145118.1"
                     /db_xref="GI:223278402"
                     /db_xref="GeneID:392862"
                     /db_xref="HGNC:18464"
                     /db_xref="MIM:610639"
     CDS             complement(join(6537405..6537476,6537695..6537859,
                     6541412..6541530,6541620..6541749,6542417..6542503,
                     6542639..6542794,6543122..6543318,6544424..6544501,
                     6545451..6545538,6547616..6548032,6548589..6548944,
                     6549914..6550031,6550240..6550337,6550539..6550670,
                     6554006..6554160,6560209..6560392,6561060..6561154,
                     6561519..6561588,6565855..6565940,6566152..6566400,
                     6579349..6579503,6590639..6591067))
                     /gene="GRID2IP"
                     /gene_synonym="DELPHILIN"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="delphilin"
                     /protein_id="NP_001138590.1"
                     /db_xref="GI:223278403"
                     /db_xref="CCDS:CCDS47537.1"
                     /db_xref="GeneID:392862"
                     /db_xref="HGNC:18464"
                     /db_xref="MIM:610639"
     gene            6617065..6628610
                     /gene="ZDHHC4"
                     /gene_synonym="FLJ10479; ZNF374"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55146"
                     /db_xref="HGNC:18471"
                     /db_xref="HPRD:15719"
     mRNA            join(6617065..6617351,6618197..6618351,6620186..6620309,
                     6621238..6621311,6621704..6621882,6622937..6623062,
                     6624647..6624891,6628248..6628610)
                     /gene="ZDHHC4"
                     /gene_synonym="FLJ10479; ZNF374"
                     /product="zinc finger, DHHC-type containing 4, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134387.1"
                     /db_xref="GI:197304685"
                     /db_xref="GeneID:55146"
                     /db_xref="HGNC:18471"
                     /db_xref="HPRD:15719"
     mRNA            join(6617065..6617129,6617221..6617351,6618197..6618351,
                     6620186..6620309,6621238..6621311,6621704..6621882,
                     6622937..6623062,6624647..6624891,6628248..6628610)
                     /gene="ZDHHC4"
                     /gene_synonym="FLJ10479; ZNF374"
                     /product="zinc finger, DHHC-type containing 4, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134388.1"
                     /db_xref="GI:197304687"
                     /db_xref="GeneID:55146"
                     /db_xref="HGNC:18471"
                     /db_xref="HPRD:15719"
     mRNA            join(6617065..6617129,6618132..6618351,6620186..6620309,
                     6621238..6621311,6621704..6621882,6622937..6623062,
                     6624647..6624891,6628248..6628610)
                     /gene="ZDHHC4"
                     /gene_synonym="FLJ10479; ZNF374"
                     /product="zinc finger, DHHC-type containing 4, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018106.3"
                     /db_xref="GI:197304684"
                     /db_xref="GeneID:55146"
                     /db_xref="HGNC:18471"
                     /db_xref="HPRD:15719"
     mRNA            join(6617065..6617129,6618197..6618351,6620186..6620309,
                     6621238..6621311,6621704..6621882,6622937..6623062,
                     6624647..6624891,6628248..6628610)
                     /gene="ZDHHC4"
                     /gene_synonym="FLJ10479; ZNF374"
                     /product="zinc finger, DHHC-type containing 4, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134389.1"
                     /db_xref="GI:197304689"
                     /db_xref="GeneID:55146"
                     /db_xref="HGNC:18471"
                     /db_xref="HPRD:15719"
     CDS             join(6620193..6620309,6621238..6621311,6621704..6621882,
                     6622937..6623062,6624647..6624891,6628248..6628541)
                     /gene="ZDHHC4"
                     /gene_synonym="FLJ10479; ZNF374"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable palmitoyltransferase ZDHHC4"
                     /protein_id="NP_060576.1"
                     /db_xref="GI:8922448"
                     /db_xref="CCDS:CCDS5352.1"
                     /db_xref="GeneID:55146"
                     /db_xref="HGNC:18471"
                     /db_xref="HPRD:15719"
     CDS             join(6620193..6620309,6621238..6621311,6621704..6621882,
                     6622937..6623062,6624647..6624891,6628248..6628541)
                     /gene="ZDHHC4"
                     /gene_synonym="FLJ10479; ZNF374"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable palmitoyltransferase ZDHHC4"
                     /protein_id="NP_001127859.1"
                     /db_xref="GI:197304686"
                     /db_xref="CCDS:CCDS5352.1"
                     /db_xref="GeneID:55146"
                     /db_xref="HGNC:18471"
                     /db_xref="HPRD:15719"
     CDS             join(6620193..6620309,6621238..6621311,6621704..6621882,
                     6622937..6623062,6624647..6624891,6628248..6628541)
                     /gene="ZDHHC4"
                     /gene_synonym="FLJ10479; ZNF374"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable palmitoyltransferase ZDHHC4"
                     /protein_id="NP_001127860.1"
                     /db_xref="GI:197304688"
                     /db_xref="CCDS:CCDS5352.1"
                     /db_xref="GeneID:55146"
                     /db_xref="HGNC:18471"
                     /db_xref="HPRD:15719"
     CDS             join(6620193..6620309,6621238..6621311,6621704..6621882,
                     6622937..6623062,6624647..6624891,6628248..6628541)
                     /gene="ZDHHC4"
                     /gene_synonym="FLJ10479; ZNF374"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable palmitoyltransferase ZDHHC4"
                     /protein_id="NP_001127861.1"
                     /db_xref="GI:197304690"
                     /db_xref="CCDS:CCDS5352.1"
                     /db_xref="GeneID:55146"
                     /db_xref="HGNC:18471"
                     /db_xref="HPRD:15719"
     gene            6629915..6648355
                     /gene="C7orf26"
                     /gene_synonym="MGC2718"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79034"
                     /db_xref="HGNC:21702"
                     /db_xref="HPRD:12913"
     mRNA            join(6629915..6630106,6631277..6631498,6634066..6634231,
                     6639460..6639987,6641732..6641771,6647591..6648355)
                     /gene="C7orf26"
                     /gene_synonym="MGC2718"
                     /product="chromosome 7 open reading frame 26"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024067.2"
                     /db_xref="GI:21362069"
                     /db_xref="GeneID:79034"
                     /db_xref="HGNC:21702"
                     /db_xref="HPRD:12913"
     CDS             join(6629915..6630106,6631277..6631498,6634066..6634231,
                     6639460..6639987,6641732..6641771,6647591..6647792)
                     /gene="C7orf26"
                     /gene_synonym="MGC2718"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC79034"
                     /protein_id="NP_076972.2"
                     /db_xref="GI:21362070"
                     /db_xref="CCDS:CCDS5353.1"
                     /db_xref="GeneID:79034"
                     /db_xref="HGNC:21702"
                     /db_xref="HPRD:12913"
     gene            6655527..6663921
                     /gene="ZNF853"
                     /gene_synonym="DKFZp434J1015; DKFZp547K054"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54753"
                     /db_xref="HGNC:21767"
     mRNA            join(6655527..6655817,6656821..6656938,6660753..6663921)
                     /gene="ZNF853"
                     /gene_synonym="DKFZp434J1015; DKFZp547K054"
                     /product="zinc finger protein 853"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017560.1"
                     /db_xref="GI:221139760"
                     /db_xref="GeneID:54753"
                     /db_xref="HGNC:21767"
     CDS             join(6655806..6655817,6656821..6656938,6660753..6662602)
                     /gene="ZNF853"
                     /gene_synonym="DKFZp434J1015; DKFZp547K054"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 853"
                     /protein_id="NP_060030.1"
                     /db_xref="GI:221139761"
                     /db_xref="GeneID:54753"
                     /db_xref="HGNC:21767"
     gene            6712856..6714924
                     /gene="LOC100419773"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419773"
     gene            complement(6728064..6746566)
                     /gene="ZNF12"
                     /gene_synonym="GIOT-3; HZF11; KOX3; ZNF325"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7559"
                     /db_xref="HGNC:12902"
                     /db_xref="HPRD:15773"
                     /db_xref="MIM:194536"
     mRNA            complement(join(6728064..6732334,6736970..6737065,
                     6737316..6737442,6744790..6744854,6746063..6746566))
                     /gene="ZNF12"
                     /gene_synonym="GIOT-3; HZF11; KOX3; ZNF325"
                     /product="zinc finger protein 12, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016265.3"
                     /db_xref="GI:110349773"
                     /db_xref="GeneID:7559"
                     /db_xref="HGNC:12902"
                     /db_xref="HPRD:15773"
                     /db_xref="MIM:194536"
     mRNA            complement(join(6728064..6732118,6732233..6732334,
                     6736970..6737065,6737316..6737442,6744790..6744854,
                     6746063..6746566))
                     /gene="ZNF12"
                     /gene_synonym="GIOT-3; HZF11; KOX3; ZNF325"
                     /product="zinc finger protein 12, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006956.2"
                     /db_xref="GI:110349774"
                     /db_xref="GeneID:7559"
                     /db_xref="HGNC:12902"
                     /db_xref="HPRD:11835"
                     /db_xref="MIM:194536"
                     /db_xref="HPRD:15773"
     CDS             complement(join(6730479..6732334,6736970..6737065,
                     6737316..6737442,6744790..6744804))
                     /gene="ZNF12"
                     /gene_synonym="GIOT-3; HZF11; KOX3; ZNF325"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 12 isoform a"
                     /protein_id="NP_057349.2"
                     /db_xref="GI:66348108"
                     /db_xref="CCDS:CCDS47538.1"
                     /db_xref="GeneID:7559"
                     /db_xref="HGNC:12902"
                     /db_xref="HPRD:15773"
                     /db_xref="MIM:194536"
     CDS             complement(join(6730479..6732118,6732233..6732334,
                     6736970..6737065,6737316..6737442,6744790..6744804))
                     /gene="ZNF12"
                     /gene_synonym="GIOT-3; HZF11; KOX3; ZNF325"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 12 isoform b"
                     /protein_id="NP_008887.2"
                     /db_xref="GI:110349775"
                     /db_xref="CCDS:CCDS47539.1"
                     /db_xref="GeneID:7559"
                     /db_xref="HGNC:12902"
                     /db_xref="HPRD:15773"
                     /db_xref="MIM:194536"
     gene            6746644..6751133
                     /gene="LOC100505863"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 7 ESTs"
                     /db_xref="GeneID:100505863"
     misc_RNA        join(6746644..6748670,6751010..6751133)
                     /gene="LOC100505863"
                     /product="hypothetical LOC100505863"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 7 ESTs"
                     /transcript_id="XR_108737.1"
                     /db_xref="GI:310119909"
                     /db_xref="GeneID:100505863"
     gene            6756941..6758753
                     /gene="LOC100507151"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100507151"
     exon            6756941..6757060
                     /gene="LOC100507151"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100507151"
     exon            6757957..6758753
                     /gene="LOC100507151"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100507151"
     gene            6774936..6791232
                     /gene="PMS2CL"
                     /gene_synonym="PMS2P13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:441194"
                     /db_xref="HGNC:30061"
     misc_RNA        join(6774936..6775020,6776707..6777567,6781316..6781483,
                     6785719..6785819,6786667..6786836,6790880..6791232)
                     /gene="PMS2CL"
                     /gene_synonym="PMS2P13"
                     /product="PMS2 C-terminal like pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002217.1"
                     /db_xref="GI:58652123"
                     /db_xref="GeneID:441194"
                     /db_xref="HGNC:30061"
     gene            6793740..6838396
                     /gene="RSPH10B2"
                     /gene_synonym="FLJ36092; FLJ54347; FLJ95901; RSPH10B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:728194"
                     /db_xref="HGNC:34385"
     mRNA            join(6793740..6793805,6796988..6797107,6797224..6797562,
                     6798715..6798790,6799857..6799925,6803559..6803732,
                     6805337..6805422,6806388..6806508,6808221..6808397,
                     6811178..6811322,6812981..6813102,6815988..6816177,
                     6819241..6819355,6820440..6820519,6820959..6821107,
                     6825580..6825687,6826509..6826652,6829262..6829390,
                     6831535..6831628,6836199..6836397,6837994..6838396)
                     /gene="RSPH10B2"
                     /gene_synonym="FLJ36092; FLJ54347; FLJ95901; RSPH10B"
                     /product="radial spoke head 10 homolog B2 (Chlamydomonas)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001099697.1"
                     /db_xref="GI:153792460"
                     /db_xref="GeneID:728194"
                     /db_xref="HGNC:34385"
     CDS             join(6797309..6797562,6798715..6798790,6799857..6799925,
                     6803559..6803732,6805337..6805422,6806388..6806508,
                     6808221..6808397,6811178..6811322,6812981..6813102,
                     6815988..6816177,6819241..6819355,6820440..6820519,
                     6820959..6821107,6825580..6825687,6826509..6826652,
                     6829262..6829390,6831535..6831628,6836199..6836397,
                     6837994..6838174)
                     /gene="RSPH10B2"
                     /gene_synonym="FLJ36092; FLJ54347; FLJ95901; RSPH10B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="radial spoke head 10 homolog B2"
                     /protein_id="NP_001093167.1"
                     /db_xref="GI:153792461"
                     /db_xref="CCDS:CCDS43552.1"
                     /db_xref="GeneID:728194"
                     /db_xref="HGNC:34385"
     gene            complement(6838566..6865926)
                     /gene="C7orf28B"
                     /gene_synonym="DKFZp586I1023; FLJ60592; H_NH0577018.2;
                     MGC19819"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221960"
                     /db_xref="HGNC:21717"
                     /db_xref="HPRD:12916"
     mRNA            complement(join(6838566..6838910,6840579..6840706,
                     6840996..6841154,6844569..6844686,6845635..6845668,
                     6851583..6851694,6852607..6852668,6854395..6854476,
                     6859397..6859572,6861912..6861995,6862944..6862991,
                     6863720..6863797,6864086..6864179,6864271..6864368,
                     6865709..6865926))
                     /gene="C7orf28B"
                     /gene_synonym="DKFZp586I1023; FLJ60592; H_NH0577018.2;
                     MGC19819"
                     /product="chromosome 7 open reading frame 28B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198097.3"
                     /db_xref="GI:301601640"
                     /db_xref="GeneID:221960"
                     /db_xref="HGNC:21717"
                     /db_xref="HPRD:12916"
     CDS             complement(join(6838855..6838910,6840579..6840706,
                     6840996..6841154,6844569..6844686,6845635..6845668,
                     6851583..6851694,6852607..6852668,6854395..6854476,
                     6859397..6859572,6861912..6861995,6862944..6862991,
                     6863720..6863797,6864086..6864179,6864271..6864368,
                     6865709..6865828))
                     /gene="C7orf28B"
                     /gene_synonym="DKFZp586I1023; FLJ60592; H_NH0577018.2;
                     MGC19819"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="vacuolar fusion protein CCZ1 homolog-like"
                     /protein_id="NP_932765.1"
                     /db_xref="GI:37674289"
                     /db_xref="CCDS:CCDS5354.1"
                     /db_xref="GeneID:221960"
                     /db_xref="HGNC:21717"
                     /db_xref="HPRD:12916"
     gene            complement(6874454..6875425)
                     /gene="OR7E39P"
                     /gene_synonym="hg611; OR7E138P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:253933"
                     /db_xref="HGNC:8412"
     gene            complement(6894674..6899461)
                     /gene="UNC93B2"
                     /gene_synonym="UNC93B2P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:641922"
                     /db_xref="HGNC:13482"
     gene            complement(6906287..6907253)
                     /gene="OR7E136P"
                     /gene_synonym="OR7E139P; OR7E147P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:155340"
                     /db_xref="HGNC:19557"
     gene            complement(6919253..6920211)
                     /gene="OR7E59P"
                     /gene_synonym="OR7E137P; OR7E59; OST119"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402249"
                     /db_xref="HGNC:8434"
     gene            6928031..6928357
                     /gene="LOC100130527"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100130527"
     exon            6928031..6928357
                     /gene="LOC100130527"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100130527"
     gene            complement(6935226..6940255)
                     /gene="LOC100420863"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420863"
     gene            6963443..6971462
                     /gene="LOC647415"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:647415"
     gene            complement(6970611..6979244)
                     /gene="LOC641924"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:641924"
     gene            complement(7106595..7106676)
                     /gene="MIR3683"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100500886"
                     /db_xref="HGNC:38999"
                     /db_xref="miRBase:MI0016084"
     ncRNA           complement(7106595..7106676)
                     /gene="MIR3683"
                     /ncRNA_class="miRNA"
                     /product="microRNA 3683"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037454.1"
                     /db_xref="GI:312147052"
                     /db_xref="GeneID:100500886"
                     /db_xref="HGNC:38999"
                     /db_xref="miRBase:MI0016084"
     gene            complement(7115401..7136417)
                     /gene="LOC100131257"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:100131257"
     misc_RNA        complement(7115401..7136417)
                     /gene="LOC100131257"
                     /product="zinc finger protein 655 pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_034022.1"
                     /db_xref="GI:300360491"
                     /db_xref="GeneID:100131257"
     gene            7222246..7288251
                     /gene="C1GALT1"
                     /gene_synonym="C1GALT; T-synthase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:56913"
                     /db_xref="HGNC:24337"
                     /db_xref="HPRD:16631"
                     /db_xref="MIM:610555"
     mRNA            join(7222246..7222451,7273934..7274170,7277886..7278553,
                     7283155..7288251)
                     /gene="C1GALT1"
                     /gene_synonym="C1GALT; T-synthase"
                     /product="core 1 synthase,
                     glycoprotein-N-acetylgalactosamine
                     3-beta-galactosyltransferase, 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020156.3"
                     /db_xref="GI:305855082"
                     /db_xref="GeneID:56913"
                     /db_xref="HGNC:24337"
                     /db_xref="HPRD:16631"
                     /db_xref="MIM:610555"
     CDS             join(7273951..7274170,7277886..7278553,7283155..7283358)
                     /gene="C1GALT1"
                     /gene_synonym="C1GALT; T-synthase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="glycoprotein-N-acetylgalactosamine
                     3-beta-galactosyltransferase 1"
                     /protein_id="NP_064541.1"
                     /db_xref="GI:9910144"
                     /db_xref="CCDS:CCDS5355.1"
                     /db_xref="GeneID:56913"
                     /db_xref="HGNC:24337"
                     /db_xref="HPRD:16631"
                     /db_xref="MIM:610555"
     gene            7316875..7319295
                     /gene="LOC100505904"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 6 ESTs"
                     /db_xref="GeneID:100505904"
     misc_RNA        join(7316875..7318401,7318538..7319295)
                     /gene="LOC100505904"
                     /product="hypothetical LOC100505904"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 6 ESTs"
                     /transcript_id="XR_108738.2"
                     /db_xref="GI:341915383"
                     /db_xref="GeneID:100505904"
     gene            complement(7398244..7575460)
                     /gene="COL28A1"
                     /gene_synonym="COL28"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:340267"
                     /db_xref="HGNC:22442"
                     /db_xref="MIM:609996"
     mRNA            complement(join(7398244..7398436,7400021..7400159,
                     7410356..7410513,7412629..7413177,7415092..7415128,
                     7420291..7420326,7420413..7420493,7421175..7421243,
                     7457490..7457558,7459516..7459584,7472104..7472172,
                     7472263..7472331,7476026..7476094,7477025..7477093,
                     7480421..7480492,7483216..7483284,7484049..7484120,
                     7491950..7492018,7493071..7493139,7495675..7495743,
                     7514232..7514300,7516743..7516811,7529020..7529088,
                     7530209..7530277,7545645..7545698,7546748..7546792,
                     7550722..7550766,7555445..7555471,7557427..7557468,
                     7559693..7559746,7561536..7561592,7563860..7563880,
                     7570979..7571535,7572383..7572543,7575381..7575460))
                     /gene="COL28A1"
                     /gene_synonym="COL28"
                     /product="collagen, type XXVIII, alpha 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001037763.2"
                     /db_xref="GI:154759254"
                     /db_xref="GeneID:340267"
                     /db_xref="HGNC:22442"
                     /db_xref="MIM:609996"
     CDS             complement(join(7398264..7398436,7400021..7400159,
                     7410356..7410513,7412629..7413177,7415092..7415128,
                     7420291..7420326,7420413..7420493,7421175..7421243,
                     7457490..7457558,7459516..7459584,7472104..7472172,
                     7472263..7472331,7476026..7476094,7477025..7477093,
                     7480421..7480492,7483216..7483284,7484049..7484120,
                     7491950..7492018,7493071..7493139,7495675..7495743,
                     7514232..7514300,7516743..7516811,7529020..7529088,
                     7530209..7530277,7545645..7545698,7546748..7546792,
                     7550722..7550766,7555445..7555471,7557427..7557468,
                     7559693..7559746,7561536..7561592,7563860..7563880,
                     7570979..7571535,7572383..7572506))
                     /gene="COL28A1"
                     /gene_synonym="COL28"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="collagen alpha-1(XXVIII) chain precursor"
                     /protein_id="NP_001032852.2"
                     /db_xref="GI:154759255"
                     /db_xref="CCDS:CCDS43553.1"
                     /db_xref="GeneID:340267"
                     /db_xref="HGNC:22442"
                     /db_xref="MIM:609996"
     gene            7606616..7647112
                     /gene="MIOS"
                     /gene_synonym="FLJ20323"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54468"
                     /db_xref="HGNC:21905"
                     /db_xref="HPRD:07898"
     mRNA            join(7606616..7606703,7607238..7607319,7607657..7607754,
                     7612067..7613400,7613729..7613827,7622749..7623003,
                     7625267..7625436,7628129..7628194,7629036..7629194,
                     7634611..7634763,7635888..7636092,7645573..7645702,
                     7646627..7647112)
                     /gene="MIOS"
                     /gene_synonym="FLJ20323"
                     /product="missing oocyte, meiosis regulator, homolog
                     (Drosophila)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_019005.3"
                     /db_xref="GI:109150418"
                     /db_xref="GeneID:54468"
                     /db_xref="HGNC:21905"
                     /db_xref="HPRD:07898"
     CDS             join(7612107..7613400,7613729..7613827,7622749..7623003,
                     7625267..7625436,7628129..7628194,7629036..7629194,
                     7634611..7634763,7635888..7636092,7645573..7645702,
                     7646627..7646723)
                     /gene="MIOS"
                     /gene_synonym="FLJ20323"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="WD repeat-containing protein mio"
                     /protein_id="NP_061878.3"
                     /db_xref="GI:109150419"
                     /db_xref="CCDS:CCDS43554.1"
                     /db_xref="GeneID:54468"
                     /db_xref="HGNC:21905"
                     /db_xref="HPRD:07898"
     gene            complement(7676575..7758238)
                     /gene="RPA3"
                     /gene_synonym="REPA3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6119"
                     /db_xref="HGNC:10291"
                     /db_xref="HPRD:01567"
                     /db_xref="MIM:179837"
     mRNA            complement(join(7676575..7676713,7677495..7677603,
                     7678701..7678775,7679951..7680806,7725461..7725629,
                     7726859..7726959,7754806..7754857,7758146..7758238))
                     /gene="RPA3"
                     /gene_synonym="REPA3"
                     /product="replication protein A3, 14kDa"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002947.3"
                     /db_xref="GI:52851430"
                     /db_xref="GeneID:6119"
                     /db_xref="HGNC:10291"
                     /db_xref="HPRD:01567"
                     /db_xref="MIM:179837"
     CDS             complement(join(7676631..7676713,7677495..7677603,
                     7678701..7678775,7679951..7680049))
                     /gene="RPA3"
                     /gene_synonym="REPA3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="replication protein A 14 kDa subunit"
                     /protein_id="NP_002938.1"
                     /db_xref="GI:4506587"
                     /db_xref="CCDS:CCDS5356.1"
                     /db_xref="GeneID:6119"
                     /db_xref="HGNC:10291"
                     /db_xref="HPRD:01567"
                     /db_xref="MIM:179837"
     gene            7680342..7918854
                     /gene="LOC729852"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:729852"
     misc_RNA        join(7680342..7680452,7712940..7713084,7841301..7841374,
                     7916912..7918854)
                     /gene="LOC729852"
                     /product="hypothetical LOC729852"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_034084.1"
                     /db_xref="GI:300796247"
                     /db_xref="GeneID:729852"
     gene            complement(7775405..7776459)
                     /gene="LOC100533631"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533631"
     gene            complement(7781737..7782193)
                     /gene="RPL23AP51"
                     /gene_synonym="RPL23A_18_782"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271464"
                     /db_xref="HGNC:36040"
     gene            complement(7948744..7950086)
                     /gene="LOC100132073"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100132073"
     gene            complement(7989470..7998211)
                     /gene="LOC100505921"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /db_xref="GeneID:100505921"
     misc_RNA        complement(join(7989470..7990137,7990303..7990340,
                     7998151..7998211))
                     /gene="LOC100505921"
                     /product="hypothetical LOC100505921"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /transcript_id="XR_108739.1"
                     /db_xref="GI:310119911"
                     /db_xref="GeneID:100505921"
     gene            8008423..8128710
                     /gene="GLCCI1"
                     /gene_synonym="FAM117C; GIG18; TSSN1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:113263"
                     /db_xref="HGNC:18713"
                     /db_xref="HPRD:17043"
     mRNA            join(8008423..8009438,8043538..8043689,8062113..8062199,
                     8095063..8095179,8099726..8099878,8110551..8110761,
                     8124527..8124647,8125823..8128710)
                     /gene="GLCCI1"
                     /gene_synonym="FAM117C; GIG18; TSSN1"
                     /product="glucocorticoid induced transcript 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138426.2"
                     /db_xref="GI:109134328"
                     /db_xref="GeneID:113263"
                     /db_xref="HGNC:18713"
                     /db_xref="HPRD:17043"
     CDS             join(8008982..8009438,8043538..8043689,8062113..8062199,
                     8095063..8095179,8099726..8099878,8110551..8110761,
                     8124527..8124647,8125823..8126168)
                     /gene="GLCCI1"
                     /gene_synonym="FAM117C; GIG18; TSSN1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="glucocorticoid-induced transcript 1 protein"
                     /protein_id="NP_612435.1"
                     /db_xref="GI:55742678"
                     /db_xref="CCDS:CCDS34601.1"
                     /db_xref="GeneID:113263"
                     /db_xref="HGNC:18713"
                     /db_xref="HPRD:17043"
     gene            8019945..8021860
                     /gene="LOC100421597"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421597"
     gene            complement(8152814..8302185)
                     /gene="ICA1"
                     /gene_synonym="ICA69; ICAp69"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3382"
                     /db_xref="HGNC:5343"
                     /db_xref="MIM:147625"
     mRNA            complement(join(8152814..8153674,8167503..8167772,
                     8178470..8178511,8178615..8178677,8181395..8181447,
                     8183505..8183602,8196746..8196844,8198157..8198282,
                     8257935..8258133,8260905..8261028,8268231..8268303,
                     8272220..8272385,8275540..8275635,8302070..8302185))
                     /gene="ICA1"
                     /gene_synonym="ICA69; ICAp69"
                     /product="islet cell autoantigen 1, 69kDa, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004968.2"
                     /db_xref="GI:94721349"
                     /db_xref="GeneID:3382"
                     /db_xref="HGNC:5343"
                     /db_xref="MIM:147625"
     mRNA            complement(join(8152814..8153674,8167503..8167772,
                     8178470..8178511,8178615..8178677,8181395..8181447,
                     8183505..8183602,8196746..8196844,8198157..8198282,
                     8257935..8258133,8260905..8261028,8268231..8268303,
                     8272220..8272385,8275540..8275570,8301630..8301682))
                     /gene="ICA1"
                     /gene_synonym="ICA69; ICAp69"
                     /product="islet cell autoantigen 1, 69kDa, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022307.2"
                     /db_xref="GI:94721348"
                     /db_xref="GeneID:3382"
                     /db_xref="HGNC:5343"
                     /db_xref="HPRD:00971"
                     /db_xref="MIM:147625"
     mRNA            complement(join(8153404..8153674,8167503..8167772,
                     8178470..8178511,8178615..8178677,8181395..8181447,
                     8183505..8183602,8196746..8196844,8198157..8198282,
                     8257935..8258133,8260905..8261028,8268231..8268303,
                     8272220..8272385,8275540..8275635,8301724..8301780))
                     /gene="ICA1"
                     /gene_synonym="ICA69; ICAp69"
                     /product="islet cell autoantigen 1, 69kDa"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001136020.1"
                     /db_xref="GI:209862840"
                     /db_xref="GeneID:3382"
                     /db_xref="HGNC:5343"
                     /db_xref="MIM:147625"
     CDS             complement(join(8153553..8153674,8167503..8167772,
                     8178470..8178511,8178615..8178677,8181395..8181447,
                     8183505..8183602,8196746..8196844,8198157..8198282,
                     8257935..8258133,8260905..8261028,8268231..8268303,
                     8272220..8272385,8275540..8275556))
                     /gene="ICA1"
                     /gene_synonym="ICA69; ICAp69"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="islet cell autoantigen 1"
                     /protein_id="NP_001129492.1"
                     /db_xref="GI:209862841"
                     /db_xref="CCDS:CCDS34602.1"
                     /db_xref="GeneID:3382"
                     /db_xref="HGNC:5343"
                     /db_xref="MIM:147625"
     CDS             complement(join(8153553..8153674,8167503..8167772,
                     8178470..8178511,8178615..8178677,8181395..8181447,
                     8183505..8183602,8196746..8196844,8198157..8198282,
                     8257935..8258133,8260905..8261028,8268231..8268303,
                     8272220..8272385,8275540..8275556))
                     /gene="ICA1"
                     /gene_synonym="ICA69; ICAp69"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="islet cell autoantigen 1"
                     /protein_id="NP_071682.1"
                     /db_xref="GI:12545395"
                     /db_xref="CCDS:CCDS34602.1"
                     /db_xref="GeneID:3382"
                     /db_xref="HGNC:5343"
                     /db_xref="MIM:147625"
     CDS             complement(join(8153553..8153674,8167503..8167772,
                     8178470..8178511,8178615..8178677,8181395..8181447,
                     8183505..8183602,8196746..8196844,8198157..8198282,
                     8257935..8258133,8260905..8261028,8268231..8268303,
                     8272220..8272385,8275540..8275556))
                     /gene="ICA1"
                     /gene_synonym="ICA69; ICAp69"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="islet cell autoantigen 1"
                     /protein_id="NP_004959.2"
                     /db_xref="GI:94721350"
                     /db_xref="CCDS:CCDS34602.1"
                     /db_xref="GeneID:3382"
                     /db_xref="HGNC:5343"
                     /db_xref="MIM:147625"
     gene            8301855..8384146
                     /gene="LOC100505938"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 29 ESTs"
                     /db_xref="GeneID:100505938"
     misc_RNA        join(8301855..8302049,8302210..8302456,8304221..8304310,
                     8380013..8380186,8380647..8380856,8382755..8382920,
                     8383337..8384146)
                     /gene="LOC100505938"
                     /product="hypothetical LOC100505938"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 29 ESTs"
                     /transcript_id="XR_108740.1"
                     /db_xref="GI:310119912"
                     /db_xref="GeneID:100505938"
     gene            8473585..8792593
                     /gene="NXPH1"
                     /gene_synonym="Nbla00697; NPH1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:30010"
                     /db_xref="HGNC:20693"
                     /db_xref="HPRD:06867"
                     /db_xref="MIM:604639"
     mRNA            join(8473585..8474385,8475234..8475397,8790638..8792593)
                     /gene="NXPH1"
                     /gene_synonym="Nbla00697; NPH1"
                     /product="neurexophilin 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152745.2"
                     /db_xref="GI:93141040"
                     /db_xref="GeneID:30010"
                     /db_xref="HGNC:20693"
                     /db_xref="HPRD:06867"
                     /db_xref="MIM:604639"
     CDS             join(8475344..8475397,8790638..8791399)
                     /gene="NXPH1"
                     /gene_synonym="Nbla00697; NPH1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="neurexophilin-1 precursor"
                     /protein_id="NP_689958.1"
                     /db_xref="GI:23097338"
                     /db_xref="CCDS:CCDS47540.1"
                     /db_xref="GeneID:30010"
                     /db_xref="HGNC:20693"
                     /db_xref="HPRD:06867"
                     /db_xref="MIM:604639"
     gene            8978401..8979084
                     /gene="RPL9P19"
                     /gene_synonym="RPL9_4_783"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129634"
                     /db_xref="HGNC:36688"
     gene            9654538..9655816
                     /gene="GAPDHP68"
                     /gene_synonym="GAPDHL13; GAPDL13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100132601"
                     /db_xref="HGNC:4146"
     gene            9673900..9675447
                     /gene="PER4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:168741"
     misc_RNA        9673900..9675447
                     /gene="PER4"
                     /product="period homolog 3 (Drosophila) pseudogene"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002790.2"
                     /db_xref="GI:142358069"
                     /db_xref="GeneID:168741"
     gene            9765729..9767903
                     /gene="LOC340268"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:340268"
     gene            10490863..10493127
                     /gene="LOC100287551"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100287551"
     gene            complement(10971580..10979813)
                     /gene="NDUFA4"
                     /gene_synonym="CI-9k; CI-MLRQ; FLJ27440; MGC104422;
                     MGC126843; MGC126845; MLRQ"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4697"
                     /db_xref="HGNC:7687"
                     /db_xref="HPRD:04831"
                     /db_xref="MIM:603833"
     mRNA            complement(join(10971580..10973319,10977717..10977774,
                     10978435..10978523,10979643..10979813))
                     /gene="NDUFA4"
                     /gene_synonym="CI-9k; CI-MLRQ; FLJ27440; MGC104422;
                     MGC126843; MGC126845; MLRQ"
                     /product="NADH dehydrogenase (ubiquinone) 1 alpha
                     subcomplex, 4, 9kDa"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002489.3"
                     /db_xref="GI:316659406"
                     /db_xref="GeneID:4697"
                     /db_xref="HGNC:7687"
                     /db_xref="HPRD:04831"
                     /db_xref="MIM:603833"
     CDS             complement(join(10973263..10973319,10977717..10977774,
                     10978435..10978523,10979643..10979684))
                     /gene="NDUFA4"
                     /gene_synonym="CI-9k; CI-MLRQ; FLJ27440; MGC104422;
                     MGC126843; MGC126845; MLRQ"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="NADH dehydrogenase [ubiquinone] 1 alpha
                     subcomplex subunit 4"
                     /protein_id="NP_002480.1"
                     /db_xref="GI:4505357"
                     /db_xref="CCDS:CCDS5357.1"
                     /db_xref="GeneID:4697"
                     /db_xref="HGNC:7687"
                     /db_xref="HPRD:04831"
                     /db_xref="MIM:603833"
     gene            11013499..11209250
                     /gene="PHF14"
                     /gene_synonym="MGC176640"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9678"
                     /db_xref="HGNC:22203"
                     /db_xref="HPRD:17845"
     misc_RNA        join(11013499..11013951,11014462..11014572,
                     11030330..11030474,11053374..11053533,11062495..11062606,
                     11068308..11068445,11075267..11075413,11076045..11076315,
                     11076612..11076718,11078387..11078482,11080299..11080402,
                     11082310..11082441,11091239..11091407,11101418..11101468,
                     11101591..11101712,11150977..11151094,11209043..11209250)
                     /gene="PHF14"
                     /gene_synonym="MGC176640"
                     /product="PHD finger protein 14, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033436.1"
                     /db_xref="GI:292781191"
                     /db_xref="GeneID:9678"
                     /db_xref="HGNC:22203"
                     /db_xref="HPRD:17845"
     mRNA            join(11013499..11013951,11014462..11014572,
                     11021999..11022786,11030330..11030474,11053374..11053533,
                     11062495..11062606,11068308..11068445,11075267..11075413,
                     11076045..11076315,11076612..11076718,11078387..11078482,
                     11080299..11080402,11082310..11082441,11091239..11091407,
                     11101418..11101468,11101591..11101712,11142113..11147376)
                     /gene="PHF14"
                     /gene_synonym="MGC176640"
                     /product="PHD finger protein 14, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014660.3"
                     /db_xref="GI:292781135"
                     /db_xref="GeneID:9678"
                     /db_xref="HGNC:22203"
                     /db_xref="HPRD:17845"
     misc_RNA        join(11013499..11013951,11014462..11014572,
                     11030330..11030474,11053374..11053533,11062495..11062606,
                     11068308..11068445,11075267..11075413,11076045..11076315,
                     11076612..11076718,11078387..11078482,11080299..11080402,
                     11082310..11082441,11091239..11091407,11101418..11101468,
                     11101591..11101712,11142113..11147376)
                     /gene="PHF14"
                     /gene_synonym="MGC176640"
                     /product="PHD finger protein 14, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033435.1"
                     /db_xref="GI:292781137"
                     /db_xref="GeneID:9678"
                     /db_xref="HGNC:22203"
                     /db_xref="HPRD:17845"
     CDS             join(11013951,11014462..11014572,11021999..11022786,
                     11030330..11030474,11053374..11053533,11062495..11062606,
                     11068308..11068445,11075267..11075413,11076045..11076315,
                     11076612..11076718,11078387..11078482,11080299..11080402,
                     11082310..11082441,11091239..11091407,11101418..11101468,
                     11101591..11101712,11142113..11142125)
                     /gene="PHF14"
                     /gene_synonym="MGC176640"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="PHD finger protein 14"
                     /protein_id="NP_055475.2"
                     /db_xref="GI:55769548"
                     /db_xref="CCDS:CCDS47542.1"
                     /db_xref="GeneID:9678"
                     /db_xref="HGNC:22203"
                     /db_xref="HPRD:17845"
     gene            complement(11046026..11046479)
                     /gene="RPL23AP52"
                     /gene_synonym="RPL23A_19_784"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271465"
                     /db_xref="HGNC:36723"
     gene            complement(11186492..11204585)
                     /gene="LOC100505960"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 4 ESTs"
                     /db_xref="GeneID:100505960"
     misc_RNA        complement(join(11186492..11186555,11202395..11204585))
                     /gene="LOC100505960"
                     /product="hypothetical LOC100505960"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 4 ESTs"
                     /transcript_id="XR_108741.1"
                     /db_xref="GI:310119913"
                     /db_xref="GeneID:100505960"
     gene            complement(11297002..11298267)
                     /gene="NPM1P11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:10836"
                     /db_xref="HGNC:7913"
     gene            complement(11410062..11871824)
                     /gene="THSD7A"
                     /gene_synonym="KIAA0960"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221981"
                     /db_xref="HGNC:22207"
                     /db_xref="MIM:612249"
     mRNA            complement(join(11410062..11415505,11416197..11416284,
                     11418697..11418907,11419257..11419339,11422148..11422243,
                     11441422..11441595,11445927..11446101,11446537..11446682,
                     11446933..11447050,11450834..11450949,11452283..11452427,
                     11457077..11457230,11464323..11464456,11466293..11466298,
                     11468574..11468752,11485688..11485951,11486857..11487051,
                     11500289..11500392,11501638..11501770,11509506..11509621,
                     11513961..11514195,11521415..11521609,11581046..11581258,
                     11582589..11582744,11630087..11630268,11632881..11633129,
                     11675757..11676588,11871383..11871824))
                     /gene="THSD7A"
                     /gene_synonym="KIAA0960"
                     /product="thrombospondin, type I, domain containing 7A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015204.2"
                     /db_xref="GI:259013332"
                     /db_xref="GeneID:221981"
                     /db_xref="HGNC:22207"
                     /db_xref="MIM:612249"
     CDS             complement(join(11415421..11415505,11416197..11416284,
                     11418697..11418907,11419257..11419339,11422148..11422243,
                     11441422..11441595,11445927..11446101,11446537..11446682,
                     11446933..11447050,11450834..11450949,11452283..11452427,
                     11457077..11457230,11464323..11464456,11466293..11466298,
                     11468574..11468752,11485688..11485951,11486857..11487051,
                     11500289..11500392,11501638..11501770,11509506..11509621,
                     11513961..11514195,11521415..11521609,11581046..11581258,
                     11582589..11582744,11630087..11630268,11632881..11633129,
                     11675757..11676588,11871383..11871572))
                     /gene="THSD7A"
                     /gene_synonym="KIAA0960"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="thrombospondin type-1 domain-containing protein
                     7A precursor"
                     /protein_id="NP_056019.1"
                     /db_xref="GI:150170672"
                     /db_xref="CCDS:CCDS47543.1"
                     /db_xref="GeneID:221981"
                     /db_xref="HGNC:22207"
                     /db_xref="MIM:612249"
     gene            complement(11859946..11860926)
                     /gene="LOC100421595"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421595"
     gene            12250848..12276890
                     /gene="TMEM106B"
                     /gene_synonym="FLJ11273; MGC33727"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54664"
                     /db_xref="HGNC:22407"
                     /db_xref="HPRD:07745"
                     /db_xref="MIM:613413"
     mRNA            join(12250848..12251051,12253827..12254020,
                     12254435..12254653,12258084..12258147,12263852..12264011,
                     12269305..12269445,12270015..12270064,12270688..12270741,
                     12271463..12276890)
                     /gene="TMEM106B"
                     /gene_synonym="FLJ11273; MGC33727"
                     /product="transmembrane protein 106B, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018374.3"
                     /db_xref="GI:197116387"
                     /db_xref="GeneID:54664"
                     /db_xref="HGNC:22407"
                     /db_xref="HPRD:07745"
                     /db_xref="MIM:613413"
     mRNA            join(12250848..12251051,12254435..12254653,
                     12258084..12258147,12263852..12264011,12269305..12269445,
                     12270015..12270064,12270688..12270741,12271463..12276890)
                     /gene="TMEM106B"
                     /gene_synonym="FLJ11273; MGC33727"
                     /product="transmembrane protein 106B, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134232.1"
                     /db_xref="GI:197116388"
                     /db_xref="GeneID:54664"
                     /db_xref="HGNC:22407"
                     /db_xref="MIM:613413"
                     /db_xref="HPRD:07745"
     CDS             join(12254437..12254653,12258084..12258147,
                     12263852..12264011,12269305..12269445,12270015..12270064,
                     12270688..12270741,12271463..12271601)
                     /gene="TMEM106B"
                     /gene_synonym="FLJ11273; MGC33727"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 106B"
                     /protein_id="NP_060844.2"
                     /db_xref="GI:40254893"
                     /db_xref="CCDS:CCDS5358.1"
                     /db_xref="GeneID:54664"
                     /db_xref="HGNC:22407"
                     /db_xref="HPRD:07745"
                     /db_xref="MIM:613413"
     CDS             join(12254437..12254653,12258084..12258147,
                     12263852..12264011,12269305..12269445,12270015..12270064,
                     12270688..12270741,12271463..12271601)
                     /gene="TMEM106B"
                     /gene_synonym="FLJ11273; MGC33727"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 106B"
                     /protein_id="NP_001127704.1"
                     /db_xref="GI:197116389"
                     /db_xref="CCDS:CCDS5358.1"
                     /db_xref="GeneID:54664"
                     /db_xref="HGNC:22407"
                     /db_xref="HPRD:07745"
                     /db_xref="MIM:613413"
     gene            complement(12370509..12443852)
                     /gene="VWDE"
                     /gene_synonym="FLJ14712"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221806"
                     /db_xref="HGNC:21897"
     mRNA            complement(join(12370509..12370823,12373091..12373194,
                     12375767..12375862,12376614..12376709,12376803..12376898,
                     12379948..12380043,12381685..12381780,12382709..12382804,
                     12383821..12383916,12384000..12384095,12391199..12391339,
                     12395737..12395956,12396891..12397141,12399204..12399318,
                     12400773..12400877,12400992..12401147,12406983..12407119,
                     12409171..12410135,12410282..12410490,12412603..12412873,
                     12414315..12414388,12414636..12414853,12417402..12417546,
                     12419103..12419192,12420112..12420359,12423162..12423227,
                     12428753..12428984,12433220..12433404,12443285..12443852))
                     /gene="VWDE"
                     /gene_synonym="FLJ14712"
                     /product="von Willebrand factor D and EGF domains"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001135924.1"
                     /db_xref="GI:209571554"
                     /db_xref="GeneID:221806"
                     /db_xref="HGNC:21897"
     CDS             complement(join(12370809..12370823,12373091..12373194,
                     12375767..12375862,12376614..12376709,12376803..12376898,
                     12379948..12380043,12381685..12381780,12382709..12382804,
                     12383821..12383916,12384000..12384095,12391199..12391339,
                     12395737..12395956,12396891..12397141,12399204..12399318,
                     12400773..12400877,12400992..12401147,12406983..12407119,
                     12409171..12410135,12410282..12410490,12412603..12412873,
                     12414315..12414388,12414636..12414853,12417402..12417546,
                     12419103..12419192,12420112..12420359,12423162..12423227,
                     12428753..12428984,12433220..12433404,12443285..12443342))
                     /gene="VWDE"
                     /gene_synonym="FLJ14712"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="von Willebrand factor D and EGF
                     domain-containing protein precursor"
                     /protein_id="NP_001129396.1"
                     /db_xref="GI:209571555"
                     /db_xref="CCDS:CCDS47544.1"
                     /db_xref="GeneID:221806"
                     /db_xref="HGNC:21897"
     gene            complement(12479045..12480036)
                     /gene="LOC100419641"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419641"
     gene            12510968..12512452
                     /gene="LOC389465"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:389465"
     gene            12530721..12531630
                     /gene="TAS2R2"
                     /gene_synonym="PS9; T2R02; T2R2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:338396"
                     /db_xref="HGNC:20615"
     gene            12610203..12693228
                     /gene="SCIN"
                     /gene_synonym="KIAA1905"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:85477"
                     /db_xref="HGNC:21695"
                     /db_xref="HPRD:11539"
                     /db_xref="MIM:613416"
     mRNA            join(12610203..12610611,12617689..12617843,
                     12620685..12620846,12644139..12644288,12662426..12662518,
                     12664635..12664767,12665387..12665475,12666209..12666424,
                     12668726..12668847,12675670..12675760,12679972..12680142,
                     12683763..12683940,12684209..12684330,12689092..12689169,
                     12691466..12691526,12692213..12693228)
                     /gene="SCIN"
                     /gene_synonym="KIAA1905"
                     /product="scinderin, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001112706.2"
                     /db_xref="GI:194018527"
                     /db_xref="GeneID:85477"
                     /db_xref="HGNC:21695"
                     /db_xref="MIM:613416"
                     /db_xref="HPRD:11539"
     CDS             join(12610413..12610611,12617689..12617843,
                     12620685..12620846,12644139..12644288,12662426..12662518,
                     12664635..12664767,12665387..12665475,12666209..12666424,
                     12668726..12668847,12675670..12675760,12679972..12680142,
                     12683763..12683940,12684209..12684330,12689092..12689169,
                     12691466..12691526,12692213..12692340)
                     /gene="SCIN"
                     /gene_synonym="KIAA1905"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="adseverin isoform 1"
                     /protein_id="NP_001106177.1"
                     /db_xref="GI:162951877"
                     /db_xref="CCDS:CCDS47545.1"
                     /db_xref="GeneID:85477"
                     /db_xref="HGNC:21695"
                     /db_xref="HPRD:11539"
                     /db_xref="MIM:613416"
     mRNA            join(12629148..12629198,12644139..12644288,
                     12662426..12662518,12664635..12664767,12665387..12665475,
                     12666209..12666424,12668726..12668847,12675670..12675760,
                     12679972..12680142,12683763..12683940,12684209..12684330,
                     12689092..12689169,12691466..12691526,12692213..12693228)
                     /gene="SCIN"
                     /gene_synonym="KIAA1905"
                     /product="scinderin, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033128.3"
                     /db_xref="GI:194018526"
                     /db_xref="GeneID:85477"
                     /db_xref="HGNC:21695"
                     /db_xref="HPRD:11539"
                     /db_xref="MIM:613416"
     CDS             join(12662501..12662518,12664635..12664767,
                     12665387..12665475,12666209..12666424,12668726..12668847,
                     12675670..12675760,12679972..12680142,12683763..12683940,
                     12684209..12684330,12689092..12689169,12691466..12691526,
                     12692213..12692340)
                     /gene="SCIN"
                     /gene_synonym="KIAA1905"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="adseverin isoform 2"
                     /protein_id="NP_149119.1"
                     /db_xref="GI:14916473"
                     /db_xref="CCDS:CCDS47546.1"
                     /db_xref="GeneID:85477"
                     /db_xref="HGNC:21695"
                     /db_xref="HPRD:11539"
                     /db_xref="MIM:613416"
     gene            12725170..12725941
                     /gene="LOC100505995"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100505995"
     gene            12726452..12730559
                     /gene="ARL4A"
                     /gene_synonym="ARL4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10124"
                     /db_xref="HGNC:695"
                     /db_xref="MIM:604786"
     mRNA            join(12726452..12726668,12727794..12730559)
                     /gene="ARL4A"
                     /gene_synonym="ARL4"
                     /product="ADP-ribosylation factor-like 4A, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_212460.3"
                     /db_xref="GI:306482558"
                     /db_xref="GeneID:10124"
                     /db_xref="HGNC:695"
                     /db_xref="MIM:604786"
     mRNA            join(12726452..12726668,12727791..12730559)
                     /gene="ARL4A"
                     /gene_synonym="ARL4"
                     /product="ADP-ribosylation factor-like 4A, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001037164.2"
                     /db_xref="GI:306482559"
                     /db_xref="GeneID:10124"
                     /db_xref="HGNC:695"
                     /db_xref="HPRD:11987"
                     /db_xref="MIM:604786"
     mRNA            join(12726911..12727353,12727791..12730559)
                     /gene="ARL4A"
                     /gene_synonym="ARL4"
                     /product="ADP-ribosylation factor-like 4A, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005738.4"
                     /db_xref="GI:306482560"
                     /db_xref="GeneID:10124"
                     /db_xref="HGNC:695"
                     /db_xref="HPRD:11987"
                     /db_xref="MIM:604786"
     mRNA            join(12726911..12727353,12727794..12730559)
                     /gene="ARL4A"
                     /gene_synonym="ARL4"
                     /product="ADP-ribosylation factor-like 4A, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001195396.1"
                     /db_xref="GI:306482561"
                     /db_xref="GeneID:10124"
                     /db_xref="HGNC:695"
                     /db_xref="MIM:604786"
     CDS             12727880..12728482
                     /gene="ARL4A"
                     /gene_synonym="ARL4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ADP-ribosylation factor-like protein 4A"
                     /protein_id="NP_997625.1"
                     /db_xref="GI:47078227"
                     /db_xref="CCDS:CCDS5359.1"
                     /db_xref="GeneID:10124"
                     /db_xref="HGNC:695"
                     /db_xref="MIM:604786"
     CDS             12727880..12728482
                     /gene="ARL4A"
                     /gene_synonym="ARL4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ADP-ribosylation factor-like protein 4A"
                     /protein_id="NP_001032241.1"
                     /db_xref="GI:81295813"
                     /db_xref="CCDS:CCDS5359.1"
                     /db_xref="GeneID:10124"
                     /db_xref="HGNC:695"
                     /db_xref="MIM:604786"
     CDS             12727880..12728482
                     /gene="ARL4A"
                     /gene_synonym="ARL4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ADP-ribosylation factor-like protein 4A"
                     /protein_id="NP_005729.1"
                     /db_xref="GI:5031603"
                     /db_xref="CCDS:CCDS5359.1"
                     /db_xref="GeneID:10124"
                     /db_xref="HGNC:695"
                     /db_xref="MIM:604786"
     CDS             12727880..12728482
                     /gene="ARL4A"
                     /gene_synonym="ARL4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ADP-ribosylation factor-like protein 4A"
                     /protein_id="NP_001182325.1"
                     /db_xref="GI:306482562"
                     /db_xref="GeneID:10124"
                     /db_xref="HGNC:695"
                     /db_xref="MIM:604786"
     gene            13911409..13912181
                     /gene="RPL26P21"
                     /gene_synonym="RPL26_11_785"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:646161"
                     /db_xref="HGNC:35497"
     gene            complement(13930854..14031050)
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="HPRD:02765"
                     /db_xref="MIM:600541"
     mRNA            complement(join(13930854..13935712,13940363..13940464,
                     13946055..13946224,13949257..13949325,13950864..13950932,
                     13971127..13971374,13975333..13975521,13978742..13978871,
                     14026263..14026310,14027711..14027798,14028633..14028764,
                     14030178..14030327,14030953..14031050))
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /product="ets variant 1, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001163148.1"
                     /db_xref="GI:253683428"
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="MIM:600541"
                     /db_xref="HPRD:02765"
     mRNA            complement(join(13930854..13935712,13940363..13940464,
                     13946055..13946224,13949257..13949325,13950864..13950932,
                     13971127..13971374,13975333..13975521,13978742..13978871,
                     14026263..14026310,14027711..14027798,14028633..14028764,
                     14030747..14030865))
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /product="ets variant 1, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001163149.1"
                     /db_xref="GI:253683430"
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="MIM:600541"
                     /db_xref="HPRD:02765"
     mRNA            complement(join(13930854..13935712,13940363..13940464,
                     13946055..13946224,13949257..13949325,13950864..13950932,
                     13971127..13971374,13975333..13975521,13978742..13978871,
                     14017052..14017105,14026263..14026310,14027711..14027798,
                     14028633..14028764,14028893..14029089,14029188..14029642))
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /product="ets variant 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004956.4"
                     /db_xref="GI:253683425"
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="HPRD:02765"
                     /db_xref="MIM:600541"
     mRNA            complement(join(13930854..13935712,13940363..13940464,
                     13946055..13946224,13949257..13949325,13971127..13971374,
                     13975333..13975521,13978742..13978871,14017052..14017105,
                     14026263..14026310,14027711..14027798,14028633..14028764,
                     14029188..14029642))
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /product="ets variant 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001163147.1"
                     /db_xref="GI:253683426"
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="MIM:600541"
                     /db_xref="HPRD:02765"
     mRNA            complement(join(13930854..13935712,13940363..13940464,
                     13946055..13946224,13949257..13949325,13950864..13950932,
                     13971127..13971374,13975333..13975521,13978742..13978871,
                     14017052..14017105,14025741..14026139))
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /product="ets variant 1, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001163150.1"
                     /db_xref="GI:253683432"
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="MIM:600541"
                     /db_xref="HPRD:02765"
     mRNA            complement(join(13930854..13935712,13940363..13940464,
                     13946055..13946224,13949257..13949325,13950864..13950932,
                     13971127..13971374,13975333..13975521,13978742..13978871,
                     14025741..14026139))
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /product="ets variant 1, transcript variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001163151.1"
                     /db_xref="GI:253683434"
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="MIM:600541"
                     /db_xref="HPRD:02765"
     mRNA            complement(join(13930854..13935712,13940363..13940464,
                     13946055..13946224,13949257..13949325,13950864..13950932,
                     13971127..13971374,13978742..13978871,14017052..14017105,
                     14025741..14026139))
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /product="ets variant 1, transcript variant 7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001163152.1"
                     /db_xref="GI:253683436"
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="MIM:600541"
                     /db_xref="HPRD:02765"
     CDS             complement(join(13935491..13935712,13940363..13940464,
                     13946055..13946224,13949257..13949325,13950864..13950932,
                     13971127..13971374,13975333..13975521,13978742..13978871,
                     14017052..14017105,14026263..14026310,14027711..14027798,
                     14028633..14028677))
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ETS translocation variant 1 isoform a"
                     /protein_id="NP_004947.2"
                     /db_xref="GI:31742534"
                     /db_xref="CCDS:CCDS55088.1"
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="HPRD:02765"
                     /db_xref="MIM:600541"
     CDS             complement(join(13935491..13935712,13940363..13940464,
                     13946055..13946224,13949257..13949325,13971127..13971374,
                     13975333..13975521,13978742..13978871,14017052..14017105,
                     14026263..14026310,14027711..14027798,14028633..14028677))
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ETS translocation variant 1 isoform b"
                     /protein_id="NP_001156619.1"
                     /db_xref="GI:253683427"
                     /db_xref="CCDS:CCDS55087.1"
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="HPRD:02765"
                     /db_xref="MIM:600541"
     CDS             complement(join(13935491..13935712,13940363..13940464,
                     13946055..13946224,13949257..13949325,13950864..13950932,
                     13971127..13971374,13975333..13975521,13978742..13978871,
                     14026263..14026310,14027711..14027798,14028633..14028677))
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ETS translocation variant 1 isoform c"
                     /protein_id="NP_001156620.1"
                     /db_xref="GI:253683429"
                     /db_xref="CCDS:CCDS55086.1"
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="HPRD:02765"
                     /db_xref="MIM:600541"
     CDS             complement(join(13935491..13935712,13940363..13940464,
                     13946055..13946224,13949257..13949325,13950864..13950932,
                     13971127..13971374,13975333..13975521,13978742..13978871,
                     14026263..14026310,14027711..14027798,14028633..14028677))
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /note="isoform c is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ETS translocation variant 1 isoform c"
                     /protein_id="NP_001156621.1"
                     /db_xref="GI:253683431"
                     /db_xref="CCDS:CCDS55086.1"
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="HPRD:02765"
                     /db_xref="MIM:600541"
     CDS             complement(join(13935491..13935712,13940363..13940464,
                     13946055..13946224,13949257..13949325,13950864..13950932,
                     13971127..13971374,13975333..13975521,13978742..13978871,
                     14017052..14017105,14025741..14025801))
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /note="isoform d is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ETS translocation variant 1 isoform d"
                     /protein_id="NP_001156622.1"
                     /db_xref="GI:253683433"
                     /db_xref="CCDS:CCDS55085.1"
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="HPRD:02765"
                     /db_xref="MIM:600541"
     CDS             complement(join(13935491..13935712,13940363..13940464,
                     13946055..13946224,13949257..13949325,13950864..13950932,
                     13971127..13971374,13975333..13975521,13978742..13978871,
                     14025741..14025801))
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /note="isoform e is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ETS translocation variant 1 isoform e"
                     /protein_id="NP_001156623.1"
                     /db_xref="GI:253683435"
                     /db_xref="CCDS:CCDS55083.1"
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="HPRD:02765"
                     /db_xref="MIM:600541"
     CDS             complement(join(13935491..13935712,13940363..13940464,
                     13946055..13946224,13949257..13949325,13950864..13950932,
                     13971127..13971374,13978742..13978871,14017052..14017105,
                     14025741..14025801))
                     /gene="ETV1"
                     /gene_synonym="DKFZp781L0674; ER81; MGC104699; MGC120533;
                     MGC120534"
                     /note="isoform f is encoded by transcript variant 7;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ETS translocation variant 1 isoform f"
                     /protein_id="NP_001156624.1"
                     /db_xref="GI:253683437"
                     /db_xref="CCDS:CCDS55084.1"
                     /db_xref="GeneID:2115"
                     /db_xref="HGNC:3490"
                     /db_xref="HPRD:02765"
                     /db_xref="MIM:600541"
     gene            14092633..14093664
                     /gene="LOC100423044"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100423044"
     gene            complement(14110131..14111024)
                     /gene="RPL6P21"
                     /gene_synonym="RPL6_5_786"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100270846"
                     /db_xref="HGNC:35994"
     gene            complement(14184674..14881075)
                     /gene="DGKB"
                     /gene_synonym="DAGK2; DGK; DGK-BETA; KIAA0718"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1607"
                     /db_xref="HGNC:2850"
                     /db_xref="HPRD:06819"
                     /db_xref="MIM:604070"
     mRNA            complement(join(14184674..14188863,14216464..14216524,
                     14217656..14217776,14378140..14378335,14384926..14385016,
                     14517786..14517850,14613837..14613997,14620487..14620576,
                     14622677..14622762,14647059..14647133,14652965..14653038,
                     14661003..14661119,14669861..14669896,14712554..14712652,
                     14722178..14722294,14722378..14722466,14724870..14724987,
                     14733700..14733819,14737720..14737794,14741306..14741355,
                     14758167..14758310,14775666..14775819,14793553..14793573,
                     14797280..14797356,14880819..14881075))
                     /gene="DGKB"
                     /gene_synonym="DAGK2; DGK; DGK-BETA; KIAA0718"
                     /product="diacylglycerol kinase, beta 90kDa, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004080.2"
                     /db_xref="GI:194097336"
                     /db_xref="GeneID:1607"
                     /db_xref="HGNC:2850"
                     /db_xref="HPRD:06819"
                     /db_xref="MIM:604070"
     CDS             complement(join(14188756..14188863,14216464..14216524,
                     14217656..14217776,14378140..14378335,14384926..14385016,
                     14517786..14517850,14613837..14613997,14620487..14620576,
                     14622677..14622762,14647059..14647133,14652965..14653038,
                     14661003..14661119,14669861..14669896,14712554..14712652,
                     14722178..14722294,14722378..14722466,14724870..14724987,
                     14733700..14733819,14737720..14737794,14741306..14741355,
                     14758167..14758310,14775666..14775819,14793553..14793573,
                     14797280..14797356,14880819..14880888))
                     /gene="DGKB"
                     /gene_synonym="DAGK2; DGK; DGK-BETA; KIAA0718"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="diacylglycerol kinase beta isoform 1"
                     /protein_id="NP_004071.1"
                     /db_xref="GI:22027632"
                     /db_xref="CCDS:CCDS47547.1"
                     /db_xref="GeneID:1607"
                     /db_xref="HGNC:2850"
                     /db_xref="HPRD:06819"
                     /db_xref="MIM:604070"
     mRNA            complement(join(14215598..14216524,14217656..14217776,
                     14378140..14378335,14384926..14385016,14517786..14517850,
                     14613837..14613997,14620487..14620576,14622677..14622762,
                     14647059..14647133,14652965..14653038,14661003..14661119,
                     14669861..14669896,14712554..14712652,14722178..14722294,
                     14722378..14722466,14724870..14724987,14733700..14733819,
                     14737720..14737794,14741306..14741355,14758167..14758310,
                     14775666..14775819,14793553..14793573,14797280..14797356,
                     14880819..14881075))
                     /gene="DGKB"
                     /gene_synonym="DAGK2; DGK; DGK-BETA; KIAA0718"
                     /product="diacylglycerol kinase, beta 90kDa, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145695.2"
                     /db_xref="GI:194097337"
                     /db_xref="GeneID:1607"
                     /db_xref="HGNC:2850"
                     /db_xref="HPRD:06819"
                     /db_xref="MIM:604070"
     CDS             complement(join(14216449..14216524,14217656..14217776,
                     14378140..14378335,14384926..14385016,14517786..14517850,
                     14613837..14613997,14620487..14620576,14622677..14622762,
                     14647059..14647133,14652965..14653038,14661003..14661119,
                     14669861..14669896,14712554..14712652,14722178..14722294,
                     14722378..14722466,14724870..14724987,14733700..14733819,
                     14737720..14737794,14741306..14741355,14758167..14758310,
                     14775666..14775819,14793553..14793573,14797280..14797356,
                     14880819..14880888))
                     /gene="DGKB"
                     /gene_synonym="DAGK2; DGK; DGK-BETA; KIAA0718"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="diacylglycerol kinase beta isoform 2"
                     /protein_id="NP_663733.1"
                     /db_xref="GI:22027634"
                     /db_xref="CCDS:CCDS47548.1"
                     /db_xref="GeneID:1607"
                     /db_xref="HGNC:2850"
                     /db_xref="HPRD:06819"
                     /db_xref="MIM:604070"
     gene            14230431..14231750
                     /gene="EEF1A1P26"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100128637"
                     /db_xref="HGNC:37899"
     gene            complement(15024923..15025750)
                     /gene="LOC100128217"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100128217"
     gene            complement(15239943..15601640)
                     /gene="AGMO"
                     /gene_synonym="FLJ16237; MGC131748; TMEM195"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:392636"
                     /db_xref="HGNC:33784"
                     /db_xref="HPRD:13362"
                     /db_xref="MIM:613738"
     mRNA            complement(join(15239943..15240984,15405139..15405244,
                     15405765..15405847,15425071..15425187,15427031..15427165,
                     15430296..15430375,15430465..15430530,15433738..15433804,
                     15458183..15458278,15470630..15470733,15584397..15584548,
                     15599766..15599896,15601345..15601640))
                     /gene="AGMO"
                     /gene_synonym="FLJ16237; MGC131748; TMEM195"
                     /product="alkylglycerol monooxygenase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001004320.1"
                     /db_xref="GI:51972211"
                     /db_xref="GeneID:392636"
                     /db_xref="HGNC:33784"
                     /db_xref="HPRD:13362"
                     /db_xref="MIM:613738"
     CDS             complement(join(15240910..15240984,15405139..15405244,
                     15405765..15405847,15425071..15425187,15427031..15427165,
                     15430296..15430375,15430465..15430530,15433738..15433804,
                     15458183..15458278,15470630..15470733,15584397..15584548,
                     15599766..15599896,15601345..15601470))
                     /gene="AGMO"
                     /gene_synonym="FLJ16237; MGC131748; TMEM195"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="alkylglycerol monooxygenase"
                     /protein_id="NP_001004320.1"
                     /db_xref="GI:51972212"
                     /db_xref="CCDS:CCDS34604.1"
                     /db_xref="GeneID:392636"
                     /db_xref="HGNC:33784"
                     /db_xref="HPRD:13362"
                     /db_xref="MIM:613738"
     gene            complement(15650837..15726308)
                     /gene="MEOX2"
                     /gene_synonym="GAX; MOX2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4223"
                     /db_xref="HGNC:7014"
                     /db_xref="HPRD:02760"
                     /db_xref="MIM:600535"
     mRNA            complement(join(15650837..15652236,15666371..15666543,
                     15725511..15726308))
                     /gene="MEOX2"
                     /gene_synonym="GAX; MOX2"
                     /product="mesenchyme homeobox 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005924.4"
                     /db_xref="GI:84105334"
                     /db_xref="GeneID:4223"
                     /db_xref="HGNC:7014"
                     /db_xref="HPRD:02760"
                     /db_xref="MIM:600535"
     CDS             complement(join(15652012..15652236,15666371..15666543,
                     15725511..15726027))
                     /gene="MEOX2"
                     /gene_synonym="GAX; MOX2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein MOX-2"
                     /protein_id="NP_005915.2"
                     /db_xref="GI:84105335"
                     /db_xref="CCDS:CCDS34605.1"
                     /db_xref="GeneID:4223"
                     /db_xref="HGNC:7014"
                     /db_xref="HPRD:02760"
                     /db_xref="MIM:600535"
     gene            complement(15741003..15741406)
                     /gene="RPL36AP26"
                     /gene_synonym="RPL36A_8_787"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:729909"
                     /db_xref="HGNC:36758"
     gene            complement(16127152..16460947)
                     /gene="ISPD"
                     /gene_synonym="FLJ42815; hCG_1745121; Nip"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:729920"
                     /db_xref="HGNC:37276"
     mRNA            complement(join(16127152..16131424,16255691..16255822,
                     16298015..16298107,16298545..16298637,16317754..16317851,
                     16341046..16341091,16348148..16348252,16415717..16415866,
                     16445686..16445962,16460691..16460947))
                     /gene="ISPD"
                     /gene_synonym="FLJ42815; hCG_1745121; Nip"
                     /product="isoprenoid synthase domain containing,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001101426.3"
                     /db_xref="GI:226246625"
                     /db_xref="GeneID:729920"
                     /db_xref="HGNC:37276"
     mRNA            complement(join(16127152..16131424,16255691..16255822,
                     16298015..16298107,16298545..16298637,16317754..16317851,
                     16341046..16341091,16348148..16348252,16445686..16445962,
                     16460691..16460947))
                     /gene="ISPD"
                     /gene_synonym="FLJ42815; hCG_1745121; Nip"
                     /product="isoprenoid synthase domain containing,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001101417.3"
                     /db_xref="GI:226246624"
                     /db_xref="GeneID:729920"
                     /db_xref="HGNC:37276"
     CDS             complement(join(16131320..16131424,16255691..16255822,
                     16298015..16298107,16298545..16298637,16317754..16317851,
                     16341046..16341091,16348148..16348252,16415717..16415866,
                     16445686..16445962,16460691..16460947))
                     /gene="ISPD"
                     /gene_synonym="FLJ42815; hCG_1745121; Nip"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="2-C-methyl-D-erythritol 4-phosphate
                     cytidylyltransferase-like protein isoform a"
                     /protein_id="NP_001094896.1"
                     /db_xref="GI:157412259"
                     /db_xref="CCDS:CCDS47550.1"
                     /db_xref="GeneID:729920"
                     /db_xref="HGNC:37276"
     CDS             complement(join(16131320..16131424,16255691..16255822,
                     16298015..16298107,16298545..16298637,16317754..16317851,
                     16341046..16341091,16348148..16348252,16445686..16445962,
                     16460691..16460947))
                     /gene="ISPD"
                     /gene_synonym="FLJ42815; hCG_1745121; Nip"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="2-C-methyl-D-erythritol 4-phosphate
                     cytidylyltransferase-like protein isoform b"
                     /protein_id="NP_001094887.1"
                     /db_xref="GI:157671913"
                     /db_xref="CCDS:CCDS47549.1"
                     /db_xref="GeneID:729920"
                     /db_xref="HGNC:37276"
     gene            16248573..16248893
                     /gene="RPL36AP29"
                     /gene_synonym="RPL36A_11_788"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271510"
                     /db_xref="HGNC:36897"
     gene            <16275516..16310229
                     /gene="LOC100506025"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100506025"
     misc_RNA        join(<16275516..16275604,16276934..16276977,
                     16305852..16305936,16308482..16310229)
                     /gene="LOC100506025"
                     /product="hypothetical LOC100506025, transcript variant 2"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038947.1"
                     /db_xref="GI:336595213"
                     /db_xref="GeneID:100506025"
     misc_RNA        join(<16276919..16277038,16301524..16301721,
                     16305852..16305936,16308482..16310229)
                     /gene="LOC100506025"
                     /product="hypothetical LOC100506025, transcript variant 1"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038946.1"
                     /db_xref="GI:336595192"
                     /db_xref="GeneID:100506025"
     gene            complement(16501106..16505474)
                     /gene="SOSTDC1"
                     /gene_synonym="CDA019; DKFZp564D206; ECTODIN; USAG1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:25928"
                     /db_xref="HGNC:21748"
                     /db_xref="HPRD:15417"
                     /db_xref="MIM:609675"
     mRNA            complement(join(16501106..16502588,16505089..16505474))
                     /gene="SOSTDC1"
                     /gene_synonym="CDA019; DKFZp564D206; ECTODIN; USAG1"
                     /product="sclerostin domain containing 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015464.2"
                     /db_xref="GI:100913216"
                     /db_xref="GeneID:25928"
                     /db_xref="HGNC:21748"
                     /db_xref="HPRD:15417"
                     /db_xref="MIM:609675"
     CDS             complement(join(16502173..16502588,16505089..16505293))
                     /gene="SOSTDC1"
                     /gene_synonym="CDA019; DKFZp564D206; ECTODIN; USAG1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="sclerostin domain-containing protein 1
                     precursor"
                     /protein_id="NP_056279.1"
                     /db_xref="GI:23943785"
                     /db_xref="CCDS:CCDS5360.1"
                     /db_xref="GeneID:25928"
                     /db_xref="HGNC:21748"
                     /db_xref="HPRD:15417"
                     /db_xref="MIM:609675"
     gene            16566505..16621114
                     /gene="LOC100506049"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100506049"
     mRNA            join(16566505..16566667,16572120..16572193,
                     16577252..16577321,16596985..16597066,16598514..16598624,
                     16605938..16606027,16607016..16607168,16619699..16619726,
                     16620949..16621114)
                     /gene="LOC100506049"
                     /product="leucine-rich repeat-containing protein
                     ENSP00000371558"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001195280.1"
                     /db_xref="GI:305632813"
                     /db_xref="GeneID:100506049"
     CDS             join(16566578..16566667,16572120..16572193,
                     16577252..16577321,16596985..16597066,16598514..16598624,
                     16605938..16606027,16607016..16607168,16619699..16619726,
                     16620949..16621114)
                     /gene="LOC100506049"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="leucine-rich repeat-containing protein
                     ENSP00000371558"
                     /protein_id="NP_001182209.1"
                     /db_xref="GI:305632814"
                     /db_xref="GeneID:100506049"
     gene            complement(16622873..16626541)
                     /gene="LOC317727"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:317727"
     gene            complement(16639401..16685442)
                     /gene="ANKMY2"
                     /gene_synonym="DKFZp564O043; ZMYND20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57037"
                     /db_xref="HGNC:25370"
                     /db_xref="HPRD:12454"
     mRNA            complement(join(16639401..16640570,16642005..16642134,
                     16644346..16644474,16649255..16649390,16650174..16650388,
                     16655369..16655529,16664608..16664706,16666665..16666803,
                     16676016..16676080,16685132..16685442))
                     /gene="ANKMY2"
                     /gene_synonym="DKFZp564O043; ZMYND20"
                     /product="ankyrin repeat and MYND domain containing 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020319.2"
                     /db_xref="GI:296434288"
                     /db_xref="GeneID:57037"
                     /db_xref="HGNC:25370"
                     /db_xref="HPRD:12454"
     CDS             complement(join(16640386..16640570,16642005..16642134,
                     16644346..16644474,16649255..16649390,16650174..16650388,
                     16655369..16655529,16664608..16664706,16666665..16666803,
                     16676016..16676080,16685132..16685198))
                     /gene="ANKMY2"
                     /gene_synonym="DKFZp564O043; ZMYND20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ankyrin repeat and MYND domain-containing
                     protein 2"
                     /protein_id="NP_064715.1"
                     /db_xref="GI:28461129"
                     /db_xref="CCDS:CCDS5361.1"
                     /db_xref="GeneID:57037"
                     /db_xref="HGNC:25370"
                     /db_xref="HPRD:12454"
     gene            16685759..16746148
                     /gene="BZW2"
                     /gene_synonym="HSPC028; MST017; MSTP017"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:28969"
                     /db_xref="HGNC:18808"
     mRNA            join(16685759..16685929,16705062..16705126,
                     16714037..16714213,16720926..16721029,16722405..16722470,
                     16725530..16725665,16729422..16729531,16734459..16734629,
                     16736540..16736686,16737673..16737811,16744172..16744294,
                     16745685..16746148)
                     /gene="BZW2"
                     /gene_synonym="HSPC028; MST017; MSTP017"
                     /product="basic leucine zipper and W2 domains 2,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001159767.1"
                     /db_xref="GI:229577397"
                     /db_xref="GeneID:28969"
                     /db_xref="HGNC:18808"
     mRNA            join(16685759..16685913,16705062..16705126,
                     16714037..16714213,16720926..16721029,16722405..16722470,
                     16725530..16725665,16729422..16729531,16734459..16734629,
                     16736540..16736686,16737673..16737811,16744172..16744294,
                     16745685..16746148)
                     /gene="BZW2"
                     /gene_synonym="HSPC028; MST017; MSTP017"
                     /product="basic leucine zipper and W2 domains 2,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014038.2"
                     /db_xref="GI:229577400"
                     /db_xref="GeneID:28969"
                     /db_xref="HGNC:18808"
                     /db_xref="HPRD:16571"
     misc_RNA        join(16685759..16685929,16705062..16705126,
                     16714037..16714213,16720926..16721029,16722405..16722470,
                     16729422..16729531,16734459..16734629,16736540..16736686,
                     16737673..16737811,16744172..16744294,16745685..16746148)
                     /gene="BZW2"
                     /gene_synonym="HSPC028; MST017; MSTP017"
                     /product="basic leucine zipper and W2 domains 2,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027624.1"
                     /db_xref="GI:229577404"
                     /db_xref="GeneID:28969"
                     /db_xref="HGNC:18808"
     CDS             join(16705069..16705126,16714037..16714213,
                     16720926..16721029,16722405..16722470,16725530..16725665,
                     16729422..16729531,16734459..16734629,16736540..16736686,
                     16737673..16737811,16744172..16744294,16745685..16745713)
                     /gene="BZW2"
                     /gene_synonym="HSPC028; MST017; MSTP017"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="basic leucine zipper and W2 domain-containing
                     protein 2"
                     /protein_id="NP_001153239.1"
                     /db_xref="GI:229577398"
                     /db_xref="CCDS:CCDS5362.1"
                     /db_xref="GeneID:28969"
                     /db_xref="HGNC:18808"
     CDS             join(16705069..16705126,16714037..16714213,
                     16720926..16721029,16722405..16722470,16725530..16725665,
                     16729422..16729531,16734459..16734629,16736540..16736686,
                     16737673..16737811,16744172..16744294,16745685..16745713)
                     /gene="BZW2"
                     /gene_synonym="HSPC028; MST017; MSTP017"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="basic leucine zipper and W2 domain-containing
                     protein 2"
                     /protein_id="NP_054757.1"
                     /db_xref="GI:7661744"
                     /db_xref="CCDS:CCDS5362.1"
                     /db_xref="GeneID:28969"
                     /db_xref="HGNC:18808"
     gene            16793351..16824161
                     /gene="TSPAN13"
                     /gene_synonym="FLJ22934; NET-6; NET6; TM4SF13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:27075"
                     /db_xref="HGNC:21643"
                     /db_xref="HPRD:15510"
                     /db_xref="MIM:613139"
     mRNA            join(16793351..16793655,16815836..16816003,
                     16816667..16816747,16817423..16817536,16818628..16818741,
                     16823042..16824161)
                     /gene="TSPAN13"
                     /gene_synonym="FLJ22934; NET-6; NET6; TM4SF13"
                     /product="tetraspanin 13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014399.3"
                     /db_xref="GI:62422581"
                     /db_xref="GeneID:27075"
                     /db_xref="HGNC:21643"
                     /db_xref="HPRD:15510"
                     /db_xref="MIM:613139"
     CDS             join(16793593..16793655,16815836..16816003,
                     16816667..16816747,16817423..16817536,16818628..16818741,
                     16823042..16823116)
                     /gene="TSPAN13"
                     /gene_synonym="FLJ22934; NET-6; NET6; TM4SF13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="tetraspanin-13"
                     /protein_id="NP_055214.1"
                     /db_xref="GI:7657373"
                     /db_xref="CCDS:CCDS5363.1"
                     /db_xref="GeneID:27075"
                     /db_xref="HGNC:21643"
                     /db_xref="HPRD:15510"
                     /db_xref="MIM:613139"
     gene            complement(16832264..16844738)
                     /gene="AGR2"
                     /gene_synonym="AG2; GOB-4; HAG-2; PDIA17; XAG-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10551"
                     /db_xref="HGNC:328"
                     /db_xref="HPRD:05896"
                     /db_xref="MIM:606358"
     mRNA            complement(join(16832264..16832581,16834560..16834643,
                     16837255..16837318,16839368..16839441,16840775..16840827,
                     16840944..16841007,16841282..16841427,16844559..16844738))
                     /gene="AGR2"
                     /gene_synonym="AG2; GOB-4; HAG-2; PDIA17; XAG-2"
                     /product="anterior gradient homolog 2 (Xenopus laevis)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006408.3"
                     /db_xref="GI:219521822"
                     /db_xref="GeneID:10551"
                     /db_xref="HGNC:328"
                     /db_xref="HPRD:05896"
                     /db_xref="MIM:606358"
     CDS             complement(join(16832532..16832581,16834560..16834643,
                     16837255..16837318,16839368..16839441,16840775..16840827,
                     16840944..16841007,16841282..16841420))
                     /gene="AGR2"
                     /gene_synonym="AG2; GOB-4; HAG-2; PDIA17; XAG-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="anterior gradient protein 2 homolog precursor"
                     /protein_id="NP_006399.1"
                     /db_xref="GI:5453541"
                     /db_xref="CCDS:CCDS5364.1"
                     /db_xref="GeneID:10551"
                     /db_xref="HGNC:328"
                     /db_xref="HPRD:05896"
                     /db_xref="MIM:606358"
     gene            complement(16889636..16890425)
                     /gene="LOC100287613"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100287613"
     gene            complement(16899030..16921613)
                     /gene="AGR3"
                     /gene_synonym="AG3; BCMP11; hAG-3; HAG3; PDIA18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:155465"
                     /db_xref="HGNC:24167"
                     /db_xref="HPRD:16545"
                     /db_xref="MIM:609482"
     mRNA            complement(join(16899030..16899255,16900124..16900207,
                     16901008..16901071,16901608..16901684,16902234..16902286,
                     16913404..16913467,16918134..16918269,16921568..16921613))
                     /gene="AGR3"
                     /gene_synonym="AG3; BCMP11; hAG-3; HAG3; PDIA18"
                     /product="anterior gradient homolog 3 (Xenopus laevis)"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_176813.3"
                     /db_xref="GI:38455428"
                     /db_xref="GeneID:155465"
                     /db_xref="HGNC:24167"
                     /db_xref="HPRD:16545"
                     /db_xref="MIM:609482"
     CDS             complement(join(16899206..16899255,16900124..16900207,
                     16901008..16901071,16901608..16901684,16902234..16902286,
                     16913404..16913467,16918134..16918242))
                     /gene="AGR3"
                     /gene_synonym="AG3; BCMP11; hAG-3; HAG3; PDIA18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="anterior gradient protein 3 homolog precursor"
                     /protein_id="NP_789783.1"
                     /db_xref="GI:28827801"
                     /db_xref="CCDS:CCDS5365.1"
                     /db_xref="GeneID:155465"
                     /db_xref="HGNC:24167"
                     /db_xref="HPRD:16545"
                     /db_xref="MIM:609482"
     gene            complement(16903489..16906014)
                     /gene="RAD17P1"
                     /gene_synonym="HRAD17P1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:9207"
                     /db_xref="HGNC:9808"
     gene            16928245..16928515
                     /gene="LOC100131425"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 3 Proteins"
                     /pseudo
                     /db_xref="GeneID:100131425"
     exon            16928245..16928515
                     /gene="LOC100131425"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 3 Proteins"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100131425"
     gene            17338276..17385775
                     /gene="AHR"
                     /gene_synonym="bHLHe76"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:196"
                     /db_xref="HGNC:348"
                     /db_xref="HPRD:02596"
                     /db_xref="MIM:600253"
     mRNA            join(17338276..17338953,17349560..17349747,
                     17362125..17362231,17367383..17367472,17369576..17369699,
                     17370380..17370510,17373536..17373738,17374511..17374620,
                     17375269..17375410,17378610..17379852,17382545..17385775)
                     /gene="AHR"
                     /gene_synonym="bHLHe76"
                     /product="aryl hydrocarbon receptor"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001621.4"
                     /db_xref="GI:229577137"
                     /db_xref="GeneID:196"
                     /db_xref="HGNC:348"
                     /db_xref="HPRD:02596"
                     /db_xref="MIM:600253"
     CDS             join(17338889..17338953,17349560..17349747,
                     17362125..17362231,17367383..17367472,17369576..17369699,
                     17370380..17370510,17373536..17373738,17374511..17374620,
                     17375269..17375410,17378610..17379852,17382545..17382688)
                     /gene="AHR"
                     /gene_synonym="bHLHe76"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="aryl hydrocarbon receptor precursor"
                     /protein_id="NP_001612.1"
                     /db_xref="GI:4502003"
                     /db_xref="CCDS:CCDS5366.1"
                     /db_xref="GeneID:196"
                     /db_xref="HGNC:348"
                     /db_xref="HPRD:02596"
                     /db_xref="MIM:600253"
     gene            complement(17830385..17980131)
                     /gene="SNX13"
                     /gene_synonym="KIAA0713; RGS-PX1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23161"
                     /db_xref="HGNC:21335"
                     /db_xref="HPRD:09418"
                     /db_xref="MIM:606589"
     mRNA            complement(join(17830385..17833916,17836450..17836562,
                     17838313..17838381,17838632..17838777,17841211..17841282,
                     17843042..17843203,17854457..17854567,17855805..17855912,
                     17861132..17861271,17865645..17865714,17869633..17869670,
                     17873675..17873807,17874384..17874488,17879430..17879623,
                     17885218..17885317,17889970..17890058,17890449..17890587,
                     17908030..17908113,17913151..17913239,17915103..17915204,
                     17915292..17915413,17929986..17930107,17931169..17931258,
                     17932955..17933057,17936957..17937069,17979907..17980131))
                     /gene="SNX13"
                     /gene_synonym="KIAA0713; RGS-PX1"
                     /product="sorting nexin 13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015132.4"
                     /db_xref="GI:197245415"
                     /db_xref="GeneID:23161"
                     /db_xref="HGNC:21335"
                     /db_xref="HPRD:09418"
                     /db_xref="MIM:606589"
     CDS             complement(join(17833669..17833916,17836450..17836562,
                     17838313..17838381,17838632..17838777,17841211..17841282,
                     17843042..17843203,17854457..17854567,17855805..17855912,
                     17861132..17861271,17865645..17865714,17869633..17869670,
                     17873675..17873807,17874384..17874488,17879430..17879623,
                     17885218..17885317,17889970..17890058,17890449..17890587,
                     17908030..17908113,17913151..17913239,17915103..17915204,
                     17915292..17915413,17929986..17930107,17931169..17931258,
                     17932955..17933057,17936957..17937069,17979907..17979918))
                     /gene="SNX13"
                     /gene_synonym="KIAA0713; RGS-PX1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="sorting nexin-13"
                     /protein_id="NP_055947.1"
                     /db_xref="GI:17864088"
                     /db_xref="CCDS:CCDS47551.1"
                     /db_xref="GeneID:23161"
                     /db_xref="HGNC:21335"
                     /db_xref="HPRD:09418"
                     /db_xref="MIM:606589"
     gene            18001702..18002656
                     /gene="LOC100420223"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420223"
     gene            complement(18066397..18067486)
                     /gene="PRPS1L1"
                     /gene_synonym="PRPS1; PRPS3; PRPSL; PRS-III"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221823"
                     /db_xref="HGNC:9463"
                     /db_xref="HPRD:17914"
                     /db_xref="MIM:611566"
     mRNA            complement(18066397..18067486)
                     /gene="PRPS1L1"
                     /gene_synonym="PRPS1; PRPS3; PRPSL; PRS-III"
                     /product="phosphoribosyl pyrophosphate synthetase 1-like
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_175886.2"
                     /db_xref="GI:31343499"
                     /db_xref="GeneID:221823"
                     /db_xref="HGNC:9463"
                     /db_xref="HPRD:17914"
                     /db_xref="MIM:611566"
     CDS             complement(18066449..18067405)
                     /gene="PRPS1L1"
                     /gene_synonym="PRPS1; PRPS3; PRPSL; PRS-III"
                     /exception="alternative start codon"
                     /note=";
                     non-AUG (ACG) translation initiation codon; Derived by
                     automated computational analysis using gene prediction
                     method: BestRefseq."
                     /codon_start=1
                     /transl_except=(pos:complement(18067403..18067405),aa:Met)
                     /product="ribose-phosphate pyrophosphokinase 3"
                     /protein_id="NP_787082.1"
                     /db_xref="GI:28557709"
                     /db_xref="CCDS:CCDS47552.1"
                     /db_xref="GeneID:221823"
                     /db_xref="HGNC:9463"
                     /db_xref="HPRD:17914"
                     /db_xref="MIM:611566"
     gene            18126572..19036993
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="HPRD:05944"
                     /db_xref="MIM:606543"
     mRNA            join(18126572..18126836,18201852..18201972,
                     18498465..18498524,18535885..18535947,18624904..18625145,
                     18629968..18630109,18631139..18631265,18633531..18633652,
                     18674250..18674365,18684294..18684416,18687408..18687621,
                     18688089..18688306,18705836..18708466)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /product="histone deacetylase 9, transcript variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001204144.1"
                     /db_xref="GI:323423043"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="MIM:606543"
                     /db_xref="HPRD:05944"
     gene            complement(18166843..18166932)
                     /gene="MIR1302-6"
                     /gene_synonym="hsa-mir-1302-6; MIRN1302-6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100302140"
                     /db_xref="HGNC:35298"
                     /db_xref="miRBase:MI0006367"
     ncRNA           complement(18166843..18166932)
                     /gene="MIR1302-6"
                     /gene_synonym="hsa-mir-1302-6; MIRN1302-6"
                     /ncRNA_class="miRNA"
                     /product="microRNA 1302-6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_031635.1"
                     /db_xref="GI:269847213"
                     /db_xref="GeneID:100302140"
                     /db_xref="HGNC:35298"
                     /db_xref="miRBase:MI0006367"
     ncRNA           complement(18166843..18166932)
                     /gene="MIR1302-6"
                     /gene_synonym="hsa-mir-1302-6; MIRN1302-6"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-1302-6"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:100302140"
                     /db_xref="miRBase:MI0006367"
                     /db_xref="HGNC:35298"
     CDS             join(18201948..18201972,18498465..18498524,
                     18535885..18535947,18624904..18625145,18629968..18630109,
                     18631139..18631265,18633531..18633652,18674250..18674365,
                     18684294..18684416,18687408..18687621,18688089..18688306,
                     18705836..18706150)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /note="isoform 6 is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone deacetylase 9 isoform 6"
                     /protein_id="NP_001191073.1"
                     /db_xref="GI:323423044"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="MIM:606543"
                     /db_xref="HPRD:05944"
     mRNA            join(18535369..18535477,18535885..18535947,
                     18624904..18625145,18629968..18630109,18631139..18631265,
                     18633531..18633652,18668973..18669104,18674250..18674365,
                     18684294..18684416,18687408..18687621,18688089..18688306,
                     18705836..18706099,18767203..18767380,18788628..18788761,
                     18801780..18801900,18806729..18806778,18832968..18833075,
                     18868784..18868839,18869084..18869171,18875090..18875209,
                     18875523..18875620,18914101..18914219,18975432..18975565,
                     18993769..18993853,19015429..19015576,19035646..19036993)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /product="histone deacetylase 9, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178423.1"
                     /db_xref="GI:30795201"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="MIM:606543"
                     /db_xref="HPRD:05944"
     mRNA            join(18535369..18535477,18535885..18535947,
                     18624904..18625145,18629968..18630109,18631139..18631265,
                     18633531..18633652,18674250..18674365,18684294..18684416,
                     18687408..18687621,18688089..18688306,18705836..18708466)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /product="histone deacetylase 9, transcript variant 7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001204145.1"
                     /db_xref="GI:323423048"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="MIM:606543"
                     /db_xref="HPRD:05944"
     mRNA            join(18535369..18535646,18535885..18535947,
                     18624904..18625145,18629959..18630109,18631139..18631265,
                     18633531..18633652,18674250..18674365,18684294..18684416,
                     18687408..18687621,18688089..18688306,18705836..18708466)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /product="histone deacetylase 9, transcript variant 8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001204146.1"
                     /db_xref="GI:323423056"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="MIM:606543"
                     /db_xref="HPRD:05944"
     mRNA            join(18535369..18535477,18535885..18535947,
                     18624904..18625145,18629968..18630109,18631139..18631265,
                     18633531..18633652,18668973..18669104,18674250..18674365,
                     18684294..18684416,18687408..18687621,18688089..18688306,
                     18705836..18708465)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /product="histone deacetylase 9, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014707.1"
                     /db_xref="GI:7662279"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="MIM:606543"
                     /db_xref="HPRD:05944"
     mRNA            join(18535885..18535947,18624904..18625145,
                     18629959..18630109,18631139..18631265,18633531..18633652,
                     18668973..18669104,18674250..18674365,18684294..18684416,
                     18687408..18687621,18688089..18688306,18705836..18706099,
                     18767203..18767380,18788628..18788761,18801780..18801900,
                     18806729..18806778,18832968..18833075,18868784..18868839,
                     18869084..18869171,18875090..18875209,18875523..18875620,
                     18914101..18914219,18975432..18975565,18993769..18993853,
                     19015429..19015576,19035646..19036993)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /product="histone deacetylase 9, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178425.2"
                     /db_xref="GI:116284377"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="HPRD:05944"
                     /db_xref="MIM:606543"
     mRNA            join(18535885..18535947,18624904..18625145,
                     18629968..18630109,18631139..18631265,18633531..18633652,
                     18668973..18669104,18674250..18674365,18684294..18684416,
                     18687408..18687621,18688089..18688306,18705836..18706099,
                     18767203..18767380,18788628..18788761,18801780..18801900,
                     18806729..18806778,18832968..18833075,18868784..18868839,
                     18869084..18869171,18875090..18875209,18875523..18875620,
                     18914101..18914219,18975432..18975565,18993769..18993939)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /product="histone deacetylase 9, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_058176.2"
                     /db_xref="GI:116284378"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="MIM:606543"
                     /db_xref="HPRD:05944"
     CDS             join(18535926..18535947,18624904..18625145,
                     18629968..18630109,18631139..18631265,18633531..18633652,
                     18668973..18669104,18674250..18674365,18684294..18684416,
                     18687408..18687621,18688089..18688306,18705836..18706099,
                     18767203..18767380,18788628..18788761,18801780..18801900,
                     18806729..18806778,18832968..18833075,18868784..18868839,
                     18869084..18869171,18875090..18875209,18875523..18875620,
                     18914101..18914219,18975432..18975565,18993769..18993853,
                     19015429..19015576,19035646..19035685)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone deacetylase 9 isoform 4"
                     /protein_id="NP_848510.1"
                     /db_xref="GI:30795202"
                     /db_xref="CCDS:CCDS47554.1"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="HPRD:05944"
                     /db_xref="MIM:606543"
     CDS             join(18535926..18535947,18624904..18625145,
                     18629959..18630109,18631139..18631265,18633531..18633652,
                     18668973..18669104,18674250..18674365,18684294..18684416,
                     18687408..18687621,18688089..18688306,18705836..18706099,
                     18767203..18767380,18788628..18788761,18801780..18801900,
                     18806729..18806778,18832968..18833075,18868784..18868839,
                     18869084..18869171,18875090..18875209,18875523..18875620,
                     18914101..18914219,18975432..18975565,18993769..18993853,
                     19015429..19015576,19035646..19035685)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /note="isoform 5 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone deacetylase 9 isoform 5"
                     /protein_id="NP_848512.1"
                     /db_xref="GI:30795204"
                     /db_xref="CCDS:CCDS47553.1"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="HPRD:05944"
                     /db_xref="MIM:606543"
     CDS             join(18535926..18535947,18624904..18625145,
                     18629968..18630109,18631139..18631265,18633531..18633652,
                     18668973..18669104,18674250..18674365,18684294..18684416,
                     18687408..18687621,18688089..18688306,18705836..18706099,
                     18767203..18767380,18788628..18788761,18801780..18801900,
                     18806729..18806778,18832968..18833075,18868784..18868839,
                     18869084..18869171,18875090..18875209,18875523..18875620,
                     18914101..18914219,18975432..18975565,18993769..18993876)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone deacetylase 9 isoform 1"
                     /protein_id="NP_478056.1"
                     /db_xref="GI:17158039"
                     /db_xref="CCDS:CCDS47555.1"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="HPRD:05944"
                     /db_xref="MIM:606543"
     CDS             join(18535926..18535947,18624904..18625145,
                     18629968..18630109,18631139..18631265,18633531..18633652,
                     18668973..18669104,18674250..18674365,18684294..18684416,
                     18687408..18687621,18688089..18688306,18705836..18706150)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone deacetylase 9 isoform 3"
                     /protein_id="NP_055522.1"
                     /db_xref="GI:7662280"
                     /db_xref="CCDS:CCDS47557.1"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="HPRD:05944"
                     /db_xref="MIM:606543"
     CDS             join(18535926..18535947,18624904..18625145,
                     18629968..18630109,18631139..18631265,18633531..18633652,
                     18674250..18674365,18684294..18684416,18687408..18687621,
                     18688089..18688306,18705836..18706150)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /note="isoform 7 is encoded by transcript variant 7;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone deacetylase 9 isoform 7"
                     /protein_id="NP_001191074.1"
                     /db_xref="GI:323423049"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="MIM:606543"
                     /db_xref="HPRD:05944"
     CDS             join(18535926..18535947,18624904..18625145,
                     18629959..18630109,18631139..18631265,18633531..18633652,
                     18674250..18674365,18684294..18684416,18687408..18687621,
                     18688089..18688306,18705836..18706150)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /note="isoform 8 is encoded by transcript variant 8;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone deacetylase 9 isoform 8"
                     /protein_id="NP_001191075.1"
                     /db_xref="GI:323423057"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="MIM:606543"
                     /db_xref="HPRD:05944"
     mRNA            join(18548900..18549069,18624904..18625145,
                     18629959..18630109,18631139..18631265,18633531..18633652,
                     18668973..18669104,18674250..18674365,18684294..18684416,
                     18687408..18687621,18688089..18688306,18705836..18708466)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /product="histone deacetylase 9, transcript variant 10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001204148.1"
                     /db_xref="GI:323423070"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="MIM:606543"
                     /db_xref="HPRD:05944"
     mRNA            join(18548900..18549069,18624904..18625145,
                     18629968..18630109,18631139..18631259,18633531..18633652,
                     18674250..18674365,18684294..18684416,18687408..18687621,
                     18688089..18688306,18705836..18708466)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /product="histone deacetylase 9, transcript variant 9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001204147.1"
                     /db_xref="GI:323423062"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="MIM:606543"
                     /db_xref="HPRD:05944"
     gene            18618284..18618939
                     /gene="LOC100419901"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419901"
     CDS             join(18624975..18625145,18629959..18630109,
                     18631139..18631265,18633531..18633652,18668973..18669104,
                     18674250..18674365,18684294..18684416,18687408..18687621,
                     18688089..18688306,18705836..18706150)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /note="isoform 10 is encoded by transcript variant 10;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone deacetylase 9 isoform 10"
                     /protein_id="NP_001191077.1"
                     /db_xref="GI:323423071"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="MIM:606543"
                     /db_xref="HPRD:05944"
     CDS             join(18624975..18625145,18629968..18630109,
                     18631139..18631259,18633531..18633652,18674250..18674365,
                     18684294..18684416,18687408..18687621,18688089..18688306,
                     18705836..18706150)
                     /gene="HDAC9"
                     /gene_synonym="DKFZp779K1053; HD7; HD7b; HD9; HDAC; HDAC7;
                     HDAC7B; HDAC9B; HDAC9FL; HDRP; KIAA0744; MITR"
                     /note="isoform 9 is encoded by transcript variant 9;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone deacetylase 9 isoform 9"
                     /protein_id="NP_001191076.1"
                     /db_xref="GI:323423063"
                     /db_xref="GeneID:9734"
                     /db_xref="HGNC:14065"
                     /db_xref="MIM:606543"
                     /db_xref="HPRD:05944"
     gene            complement(18988214..18989485)
                     /gene="NPM1P13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:10834"
                     /db_xref="HGNC:7915"
     gene            complement(19155091..19157295)
                     /gene="TWIST1"
                     /gene_synonym="ACS3; bHLHa38; BPES2; BPES3; CRS1; SCS;
                     TWIST"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7291"
                     /db_xref="HGNC:12428"
                     /db_xref="HPRD:03374"
                     /db_xref="MIM:601622"
     mRNA            complement(join(19155091..19155754,19156294..19157295))
                     /gene="TWIST1"
                     /gene_synonym="ACS3; bHLHa38; BPES2; BPES3; CRS1; SCS;
                     TWIST"
                     /product="twist homolog 1 (Drosophila)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000474.3"
                     /db_xref="GI:68160957"
                     /db_xref="GeneID:7291"
                     /db_xref="HGNC:12428"
                     /db_xref="HPRD:03374"
                     /db_xref="MIM:601622"
     CDS             complement(19156336..19156944)
                     /gene="TWIST1"
                     /gene_synonym="ACS3; bHLHa38; BPES2; BPES3; CRS1; SCS;
                     TWIST"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="twist-related protein 1"
                     /protein_id="NP_000465.1"
                     /db_xref="GI:4507741"
                     /db_xref="CCDS:CCDS5367.1"
                     /db_xref="GeneID:7291"
                     /db_xref="HGNC:12428"
                     /db_xref="HPRD:03374"
                     /db_xref="MIM:601622"
     gene            complement(19184405..19185044)
                     /gene="FERD3L"
                     /gene_synonym="bHLHa31; MGC119861; N-TWIST; NATO3; NTWIST"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222894"
                     /db_xref="HGNC:16660"
                     /db_xref="HPRD:16890"
     mRNA            complement(19184405..19185044)
                     /gene="FERD3L"
                     /gene_synonym="bHLHa31; MGC119861; N-TWIST; NATO3; NTWIST"
                     /product="Fer3-like (Drosophila)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152898.2"
                     /db_xref="GI:40217806"
                     /db_xref="GeneID:222894"
                     /db_xref="HGNC:16660"
                     /db_xref="HPRD:16890"
     CDS             complement(19184485..19184985)
                     /gene="FERD3L"
                     /gene_synonym="bHLHa31; MGC119861; N-TWIST; NATO3; NTWIST"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="fer3-like protein"
                     /protein_id="NP_690862.1"
                     /db_xref="GI:23097242"
                     /db_xref="CCDS:CCDS5368.1"
                     /db_xref="GeneID:222894"
                     /db_xref="HGNC:16660"
                     /db_xref="HPRD:16890"
     gene            complement(19735085..19748660)
                     /gene="TWISTNB"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221830"
                     /db_xref="HGNC:18027"
                     /db_xref="HPRD:16311"
                     /db_xref="MIM:608312"
     mRNA            complement(join(19735085..19738350,19739695..19739903,
                     19744402..19744543,19748386..19748660))
                     /gene="TWISTNB"
                     /product="TWIST neighbor"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001002926.1"
                     /db_xref="GI:50962816"
                     /db_xref="GeneID:221830"
                     /db_xref="HGNC:18027"
                     /db_xref="HPRD:16311"
                     /db_xref="MIM:608312"
     CDS             complement(join(19737939..19738350,19739695..19739903,
                     19744402..19744543,19748386..19748639))
                     /gene="TWISTNB"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-directed RNA polymerase I subunit RPA43"
                     /protein_id="NP_001002926.1"
                     /db_xref="GI:50962817"
                     /db_xref="CCDS:CCDS34606.1"
                     /db_xref="GeneID:221830"
                     /db_xref="HGNC:18027"
                     /db_xref="HPRD:16311"
                     /db_xref="MIM:608312"
     gene            complement(19744981..19745059)
                     /gene="MIR3146"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100422967"
                     /db_xref="HGNC:38368"
                     /db_xref="miRBase:MI0014172"
     ncRNA           complement(19744981..19745059)
                     /gene="MIR3146"
                     /ncRNA_class="miRNA"
                     /product="microRNA 3146"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_036101.1"
                     /db_xref="GI:301171249"
                     /db_xref="GeneID:100422967"
                     /db_xref="HGNC:38368"
                     /db_xref="miRBase:MI0014172"
     gene            complement(19758938..19812404)
                     /gene="TMEM196"
                     /gene_synonym="DKFZp686H19205; DKFZp686K0753; MGC42090"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:256130"
                     /db_xref="HGNC:22431"
                     /db_xref="HPRD:14617"
     mRNA            complement(join(19758938..19761757,19765137..19765391,
                     19769005..19769061,19812173..19812404))
                     /gene="TMEM196"
                     /gene_synonym="DKFZp686H19205; DKFZp686K0753; MGC42090"
                     /product="transmembrane protein 196"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152774.3"
                     /db_xref="GI:197333841"
                     /db_xref="GeneID:256130"
                     /db_xref="HGNC:22431"
                     /db_xref="HPRD:14617"
     CDS             complement(join(19761698..19761757,19765137..19765391,
                     19769005..19769061,19812173..19812319))
                     /gene="TMEM196"
                     /gene_synonym="DKFZp686H19205; DKFZp686K0753; MGC42090"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 196"
                     /protein_id="NP_689987.3"
                     /db_xref="GI:197333842"
                     /db_xref="CCDS:CCDS34607.2"
                     /db_xref="GeneID:256130"
                     /db_xref="HGNC:22431"
                     /db_xref="HPRD:14617"
     gene            20042348..20042915
                     /gene="RPL21P75"
                     /gene_synonym="RPL21_29_789"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:728501"
                     /db_xref="HGNC:36460"
     gene            complement(20174278..20257013)
                     /gene="MACC1"
                     /gene_synonym="7A5; SH3BP4L"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:346389"
                     /db_xref="HGNC:30215"
                     /db_xref="HPRD:12381"
                     /db_xref="MIM:612646"
     mRNA            complement(join(20174278..20180781,20193816..20194004,
                     20197827..20199868,20201371..20201493,20203879..20204022,
                     20210337..20210401,20256922..20257013))
                     /gene="MACC1"
                     /gene_synonym="7A5; SH3BP4L"
                     /product="metastasis associated in colon cancer 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182762.3"
                     /db_xref="GI:157502190"
                     /db_xref="GeneID:346389"
                     /db_xref="HGNC:30215"
                     /db_xref="HPRD:12381"
                     /db_xref="MIM:612646"
     CDS             complement(join(20180569..20180781,20193816..20194004,
                     20197827..20199868,20201371..20201485))
                     /gene="MACC1"
                     /gene_synonym="7A5; SH3BP4L"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="metastasis-associated in colon cancer protein 1"
                     /protein_id="NP_877439.3"
                     /db_xref="GI:157502191"
                     /db_xref="CCDS:CCDS5369.1"
                     /db_xref="GeneID:346389"
                     /db_xref="HGNC:30215"
                     /db_xref="HPRD:12381"
                     /db_xref="MIM:612646"
     gene            20257200..20261328
                     /gene="LOC100506098"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 79 ESTs"
                     /db_xref="GeneID:100506098"
     misc_RNA        join(20257200..20257245,20257879..20257986,
                     20259206..20259379,20260966..20261328)
                     /gene="LOC100506098"
                     /product="hypothetical LOC100506098, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 72 ESTs"
                     /transcript_id="XR_108745.1"
                     /db_xref="GI:310119918"
                     /db_xref="GeneID:100506098"
     misc_RNA        join(20257209..20257245,20257411..20257481,
                     20257879..20257986,20259206..20259379,20260966..20261328)
                     /gene="LOC100506098"
                     /product="hypothetical LOC100506098, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 74 ESTs"
                     /transcript_id="XR_108744.1"
                     /db_xref="GI:310119919"
                     /db_xref="GeneID:100506098"
     misc_RNA        join(20257216..20257245,20257411..20257481,
                     20257879..20257986,20259115..20259379,20260966..20261328)
                     /gene="LOC100506098"
                     /product="hypothetical LOC100506098, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 71 ESTs"
                     /transcript_id="XR_108746.1"
                     /db_xref="GI:310119920"
                     /db_xref="GeneID:100506098"
     gene            complement(20367924..20371370)
                     /gene="LOC100506130"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 15 ESTs"
                     /db_xref="GeneID:100506130"
     misc_RNA        complement(join(20367924..20368479,20368990..20369136,
                     20369313..20369405,20371273..20371370))
                     /gene="LOC100506130"
                     /product="hypothetical LOC100506130, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 14 ESTs"
                     /transcript_id="XR_108747.1"
                     /db_xref="GI:310119921"
                     /db_xref="GeneID:100506130"
     misc_RNA        complement(join(20367924..20368479,20368990..20369136,
                     20371273..20371304))
                     /gene="LOC100506130"
                     /product="hypothetical LOC100506130, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 12 ESTs"
                     /transcript_id="XR_108748.1"
                     /db_xref="GI:310119922"
                     /db_xref="GeneID:100506130"
     gene            20370725..20455382
                     /gene="ITGB8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3696"
                     /db_xref="HGNC:6163"
                     /db_xref="HPRD:05001"
                     /db_xref="MIM:604160"
     mRNA            join(20370725..20371556,20403260..20403345,
                     20406635..20406809,20418674..20418920,20420289..20420454,
                     20421350..20421508,20431026..20431121,20434519..20434608,
                     20438483..20438617,20441344..20441749,20444251..20444476,
                     20445685..20445794,20449238..20449401,20449498..20455382)
                     /gene="ITGB8"
                     /product="integrin, beta 8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002214.2"
                     /db_xref="GI:91984778"
                     /db_xref="GeneID:3696"
                     /db_xref="HGNC:6163"
                     /db_xref="HPRD:05001"
                     /db_xref="MIM:604160"
     CDS             join(20371430..20371556,20403260..20403345,
                     20406635..20406809,20418674..20418920,20420289..20420454,
                     20421350..20421508,20431026..20431121,20434519..20434608,
                     20438483..20438617,20441344..20441749,20444251..20444476,
                     20445685..20445794,20449238..20449401,20449498..20449620)
                     /gene="ITGB8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="integrin beta-8 precursor"
                     /protein_id="NP_002205.1"
                     /db_xref="GI:4504779"
                     /db_xref="CCDS:CCDS5370.1"
                     /db_xref="GeneID:3696"
                     /db_xref="HGNC:6163"
                     /db_xref="HPRD:05001"
                     /db_xref="MIM:604160"
     gene            20621702..20622833
                     /gene="EEF1A1P27"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100130234"
                     /db_xref="HGNC:37900"
     gene            20628618..20629712
                     /gene="LOC402641"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402641"
     gene            20655245..20796637
                     /gene="ABCB5"
                     /gene_synonym="ABCB5alpha; ABCB5beta; EST422562"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:340273"
                     /db_xref="HGNC:46"
                     /db_xref="MIM:611785"
     mRNA            join(20655245..20655460,20662888..20662961,
                     20666180..20666234,20668311..20668461,20671682..20671736,
                     20682807..20682998,20683084..20683255,20685379..20685503,
                     20685584..20685761,20687158..20687271,20687591..20687701,
                     20689645..20689770,20691043..20691246,20698129..20698299,
                     20721128..20721289,20725319..20725459,20738030..20738173,
                     20739448..20739552,20739681..20739758,20744347..20744430,
                     20762639..20762842,20766663..20766763,20767938..20768078,
                     20778606..20778762,20782500..20782697,20784855..20785061,
                     20792983..20793129,20795050..20796637)
                     /gene="ABCB5"
                     /gene_synonym="ABCB5alpha; ABCB5beta; EST422562"
                     /product="ATP-binding cassette, sub-family B (MDR/TAP),
                     member 5, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001163941.1"
                     /db_xref="GI:255708476"
                     /db_xref="GeneID:340273"
                     /db_xref="HGNC:46"
                     /db_xref="MIM:611785"
     CDS             join(20662909..20662961,20666180..20666234,
                     20668311..20668461,20671682..20671736,20682807..20682998,
                     20683084..20683255,20685379..20685503,20685584..20685761,
                     20687158..20687271,20687591..20687701,20689645..20689770,
                     20691043..20691246,20698129..20698299,20721128..20721289,
                     20725319..20725459,20738030..20738173,20739448..20739552,
                     20739681..20739758,20744347..20744430,20762639..20762842,
                     20766663..20766763,20767938..20768078,20778606..20778762,
                     20782500..20782697,20784855..20785061,20792983..20793129,
                     20795050..20795247)
                     /gene="ABCB5"
                     /gene_synonym="ABCB5alpha; ABCB5beta; EST422562"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ATP-binding cassette sub-family B member 5
                     isoform 1"
                     /protein_id="NP_001157413.1"
                     /db_xref="GI:255708477"
                     /db_xref="CCDS:CCDS55090.1"
                     /db_xref="GeneID:340273"
                     /db_xref="HGNC:46"
                     /db_xref="MIM:611785"
     mRNA            join(20686966..20687271,20687591..20687701,
                     20689645..20689770,20691043..20691246,20698129..20698299,
                     20721128..20721289,20725319..20725459,20738030..20738173,
                     20739448..20739552,20739681..20739758,20744347..20744430,
                     20762639..20762842,20766663..20766763,20767938..20768078,
                     20778606..20778762,20782500..20782697,20784855..20785061,
                     20792983..20793129,20795050..20796637)
                     /gene="ABCB5"
                     /gene_synonym="ABCB5alpha; ABCB5beta; EST422562"
                     /product="ATP-binding cassette, sub-family B (MDR/TAP),
                     member 5, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178559.5"
                     /db_xref="GI:255708475"
                     /db_xref="GeneID:340273"
                     /db_xref="HGNC:46"
                     /db_xref="MIM:611785"
     mRNA            join(20686966..20687271,20687591..20687701,
                     20689645..20689770,20691043..20691246,20698129..20698299,
                     20706382..20707187)
                     /gene="ABCB5"
                     /gene_synonym="ABCB5alpha; ABCB5beta; EST422562"
                     /product="ATP-binding cassette, sub-family B (MDR/TAP),
                     member 5, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001163993.1"
                     /db_xref="GI:255708372"
                     /db_xref="GeneID:340273"
                     /db_xref="HGNC:46"
                     /db_xref="MIM:611785"
     mRNA            join(20686966..20687271,20687591..20687701,
                     20689645..20689770,20691043..20691246,20698129..20698299,
                     20698689..20700017)
                     /gene="ABCB5"
                     /gene_synonym="ABCB5alpha; ABCB5beta; EST422562"
                     /product="ATP-binding cassette, sub-family B (MDR/TAP),
                     member 5, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001163942.1"
                     /db_xref="GI:255708370"
                     /db_xref="GeneID:340273"
                     /db_xref="HGNC:46"
                     /db_xref="MIM:611785"
     CDS             join(20691046..20691246,20698129..20698299,
                     20721128..20721289,20725319..20725459,20738030..20738173,
                     20739448..20739552,20739681..20739758,20744347..20744430,
                     20762639..20762842,20766663..20766763,20767938..20768078,
                     20778606..20778762,20782500..20782697,20784855..20785061,
                     20792983..20793129,20795050..20795247)
                     /gene="ABCB5"
                     /gene_synonym="ABCB5alpha; ABCB5beta; EST422562"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ATP-binding cassette sub-family B member 5
                     isoform 2"
                     /protein_id="NP_848654.3"
                     /db_xref="GI:148612844"
                     /db_xref="CCDS:CCDS5371.1"
                     /db_xref="GeneID:340273"
                     /db_xref="HGNC:46"
                     /db_xref="MIM:611785"
     CDS             join(20691046..20691246,20698129..20698299,
                     20706382..20706390)
                     /gene="ABCB5"
                     /gene_synonym="ABCB5alpha; ABCB5beta; EST422562"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ATP-binding cassette sub-family B member 5
                     isoform 4"
                     /protein_id="NP_001157465.1"
                     /db_xref="GI:255708373"
                     /db_xref="CCDS:CCDS55092.1"
                     /db_xref="GeneID:340273"
                     /db_xref="HGNC:46"
                     /db_xref="MIM:611785"
     CDS             join(20691046..20691246,20698129..20698299,
                     20698689..20698712)
                     /gene="ABCB5"
                     /gene_synonym="ABCB5alpha; ABCB5beta; EST422562"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ATP-binding cassette sub-family B member 5
                     isoform 3"
                     /protein_id="NP_001157414.1"
                     /db_xref="GI:255708371"
                     /db_xref="CCDS:CCDS55091.1"
                     /db_xref="GeneID:340273"
                     /db_xref="HGNC:46"
                     /db_xref="MIM:611785"
     gene            complement(20821894..20826508)
                     /gene="SP8"
                     /gene_synonym="BTD"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221833"
                     /db_xref="HGNC:19196"
                     /db_xref="MIM:608306"
     mRNA            complement(join(20821894..20825414,20826397..20826508))
                     /gene="SP8"
                     /gene_synonym="BTD"
                     /product="Sp8 transcription factor, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182700.4"
                     /db_xref="GI:223278385"
                     /db_xref="GeneID:221833"
                     /db_xref="HGNC:19196"
                     /db_xref="HPRD:12208"
                     /db_xref="MIM:608306"
     mRNA            complement(join(20821894..20825414,20825567..20825662,
                     20826397..20826508))
                     /gene="SP8"
                     /gene_synonym="BTD"
                     /product="Sp8 transcription factor, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198956.2"
                     /db_xref="GI:223278384"
                     /db_xref="GeneID:221833"
                     /db_xref="HGNC:19196"
                     /db_xref="MIM:608306"
     CDS             complement(join(20823909..20825414,20826397..20826417))
                     /gene="SP8"
                     /gene_synonym="BTD"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transcription factor Sp8 isoform 1"
                     /protein_id="NP_874359.2"
                     /db_xref="GI:39812496"
                     /db_xref="CCDS:CCDS43555.1"
                     /db_xref="GeneID:221833"
                     /db_xref="HGNC:19196"
                     /db_xref="MIM:608306"
     CDS             complement(20823909..20825381)
                     /gene="SP8"
                     /gene_synonym="BTD"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transcription factor Sp8 isoform 2"
                     /protein_id="NP_945194.1"
                     /db_xref="GI:39812501"
                     /db_xref="CCDS:CCDS5372.1"
                     /db_xref="GeneID:221833"
                     /db_xref="HGNC:19196"
                     /db_xref="MIM:608306"
     gene            20866917..20867439
                     /gene="RPL23P8"
                     /gene_synonym="RPL23_4_790"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:222901"
                     /db_xref="HGNC:36225"
     misc_RNA        20866917..20867439
                     /gene="RPL23P8"
                     /gene_synonym="RPL23_4_790"
                     /product="ribosomal protein L23 pseudogene 8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_026673.1"
                     /db_xref="GI:221307585"
                     /db_xref="GeneID:222901"
                     /db_xref="HGNC:36225"
     gene            20883249..20883586
                     /gene="RPS26P30"
                     /gene_synonym="RPS26_7_791"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271111"
                     /db_xref="HGNC:35574"
     gene            complement(21259597..21261152)
                     /gene="ASS1P11"
                     /gene_synonym="ASSP11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:340274"
                     /db_xref="HGNC:761"
     gene            21420981..21421112
                     /gene="RNU1-15P"
                     /gene_synonym="RNU1P8; U1P11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:26858"
                     /db_xref="HGNC:10140"
     gene            21467689..21554162
                     /gene="SP4"
                     /gene_synonym="HF1B; MGC130008; MGC130009; SPR-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6671"
                     /db_xref="HGNC:11209"
                     /db_xref="HPRD:02764"
                     /db_xref="MIM:600540"
     mRNA            join(21467689..21467876,21468295..21468410,
                     21468907..21470461,21516697..21516925,21521542..21521741,
                     21550640..21554162)
                     /gene="SP4"
                     /gene_synonym="HF1B; MGC130008; MGC130009; SPR-1"
                     /product="Sp4 transcription factor"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003112.3"
                     /db_xref="GI:67010024"
                     /db_xref="GeneID:6671"
                     /db_xref="HGNC:11209"
                     /db_xref="HPRD:02764"
                     /db_xref="MIM:600540"
     CDS             join(21467870..21467876,21468295..21468410,
                     21468907..21470461,21516697..21516925,21521542..21521741,
                     21550640..21550887)
                     /gene="SP4"
                     /gene_synonym="HF1B; MGC130008; MGC130009; SPR-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transcription factor Sp4"
                     /protein_id="NP_003103.2"
                     /db_xref="GI:67010025"
                     /db_xref="CCDS:CCDS5373.1"
                     /db_xref="GeneID:6671"
                     /db_xref="HGNC:11209"
                     /db_xref="HPRD:02764"
                     /db_xref="MIM:600540"
     gene            21510676..21510764
                     /gene="MIR1183"
                     /gene_synonym="hsa-mir-1183; MIRN1183"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100302122"
                     /db_xref="HGNC:35264"
                     /db_xref="miRBase:MI0006276"
     ncRNA           21510676..21510764
                     /gene="MIR1183"
                     /gene_synonym="hsa-mir-1183; MIRN1183"
                     /ncRNA_class="miRNA"
                     /product="microRNA 1183"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_031594.1"
                     /db_xref="GI:269847034"
                     /db_xref="GeneID:100302122"
                     /db_xref="HGNC:35264"
                     /db_xref="miRBase:MI0006276"
     ncRNA           21510676..21510764
                     /gene="MIR1183"
                     /gene_synonym="hsa-mir-1183; MIRN1183"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-1183"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:100302122"
                     /db_xref="miRBase:MI0006276"
                     /db_xref="HGNC:35264"
     gene            21582833..21941457
                     /gene="DNAH11"
                     /gene_synonym="CILD7; DNAHBL; DNAHC11; DNHBL; DPL11;
                     FLJ30095; FLJ37699"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8701"
                     /db_xref="HGNC:2942"
                     /db_xref="HPRD:09134"
                     /db_xref="MIM:603339"
     mRNA            join(21582833..21583214,21584624..21584767,
                     21598420..21598616,21599221..21599410,21600689..21600788,
                     21603804..21604015,21609687..21609917,21611424..21611591,
                     21621523..21621639,21627682..21627819,21628130..21628254,
                     21628826..21629021,21630536..21630640,21630803..21631195,
                     21639405..21639737,21640294..21640548,21640628..21640797,
                     21641014..21641236,21646044..21646160,21646265..21646351,
                     21654732..21654890,21655827..21655925,21657237..21657395,
                     21658718..21658840,21659574..21659696,21675489..21675713,
                     21677229..21677320,21678557..21678683,21695450..21695599,
                     21698416..21698649,21721164..21721302,21723402..21723562,
                     21726717..21726873,21727000..21727145,21730383..21730499,
                     21737693..21737831,21742328..21742420,21744052..21744246,
                     21745078..21745155,21747317..21747453,21750171..21750321,
                     21751330..21751478,21757393..21757543,21760343..21760474,
                     21765429..21765602,21775258..21775462,21778319..21778484,
                     21779189..21779291,21781545..21781784,21784056..21784217,
                     21784488..21784681,21788198..21788360,21789296..21789419,
                     21789840..21789982,21805046..21805207,21813384..21813617,
                     21818576..21818722,21824045..21824158,21826242..21826385,
                     21827019..21827201,21828859..21828960,21840755..21840893,
                     21847501..21847667,21856085..21856320,21857835..21857957,
                     21882162..21882366,21892085..21892249,21893933..21894073,
                     21901471..21901641,21904153..21904275,21906088..21906281,
                     21907477..21907625,21908482..21908609,21912892..21913119,
                     21920320..21920511,21923909..21924028,21932043..21932285,
                     21934241..21934423,21934502..21934617,21938954..21939066,
                     21939598..21939738,21940625..21941457)
                     /gene="DNAH11"
                     /gene_synonym="CILD7; DNAHBL; DNAHC11; DNHBL; DPL11;
                     FLJ30095; FLJ37699"
                     /product="dynein, axonemal, heavy chain 11"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003777.3"
                     /db_xref="GI:114155131"
                     /db_xref="GeneID:8701"
                     /db_xref="HGNC:2942"
                     /db_xref="HPRD:09134"
                     /db_xref="MIM:603339"
     CDS             join(21582864..21583214,21584624..21584767,
                     21598420..21598616,21599221..21599410,21600689..21600788,
                     21603804..21604015,21609687..21609917,21611424..21611591,
                     21621523..21621639,21627682..21627819,21628130..21628254,
                     21628826..21629021,21630536..21630640,21630803..21631195,
                     21639405..21639737,21640294..21640548,21640628..21640797,
                     21641014..21641236,21646044..21646160,21646265..21646351,
                     21654732..21654890,21655827..21655925,21657237..21657395,
                     21658718..21658840,21659574..21659696,21675489..21675713,
                     21677229..21677320,21678557..21678683,21695450..21695599,
                     21698416..21698649,21721164..21721302,21723402..21723562,
                     21726717..21726873,21727000..21727145,21730383..21730499,
                     21737693..21737831,21742328..21742420,21744052..21744246,
                     21745078..21745155,21747317..21747453,21750171..21750321,
                     21751330..21751478,21757393..21757543,21760343..21760474,
                     21765429..21765602,21775258..21775462,21778319..21778484,
                     21779189..21779291,21781545..21781784,21784056..21784217,
                     21784488..21784681,21788198..21788360,21789296..21789419,
                     21789840..21789982,21805046..21805207,21813384..21813617,
                     21818576..21818722,21824045..21824158,21826242..21826385,
                     21827019..21827201,21828859..21828960,21840755..21840893,
                     21847501..21847667,21856085..21856320,21857835..21857957,
                     21882162..21882366,21892085..21892249,21893933..21894073,
                     21901471..21901641,21904153..21904275,21906088..21906281,
                     21907477..21907625,21908482..21908609,21912892..21913119,
                     21920320..21920511,21923909..21924028,21932043..21932285,
                     21934241..21934423,21934502..21934617,21938954..21939066,
                     21939598..21939738,21940625..21940872)
                     /gene="DNAH11"
                     /gene_synonym="CILD7; DNAHBL; DNAHC11; DNHBL; DPL11;
                     FLJ30095; FLJ37699"
                     /exception="unclassified translation discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="dynein heavy chain 11, axonemal"
                     /protein_id="NP_003768.2"
                     /db_xref="GI:51479173"
                     /db_xref="GeneID:8701"
                     /db_xref="HGNC:2942"
                     /db_xref="HPRD:09134"
                     /db_xref="MIM:603339"
     gene            complement(21940517..21985542)
                     /gene="CDCA7L"
                     /gene_synonym="DKFZp762L0311; JPO2; R1; RAM2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55536"
                     /db_xref="HGNC:30777"
                     /db_xref="HPRD:11481"
                     /db_xref="MIM:609685"
     mRNA            complement(join(21940517..21941970,21942596..21942732,
                     21943728..21943877,21945124..21945249,21945907..21946074,
                     21946186..21946257,21947748..21948125,21951235..21951372,
                     21956372..21956512,21985399..21985542))
                     /gene="CDCA7L"
                     /gene_synonym="DKFZp762L0311; JPO2; R1; RAM2"
                     /product="cell division cycle associated 7-like,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018719.4"
                     /db_xref="GI:226371671"
                     /db_xref="GeneID:55536"
                     /db_xref="HGNC:30777"
                     /db_xref="HPRD:11481"
                     /db_xref="MIM:609685"
     mRNA            complement(join(21940517..21941970,21942596..21942732,
                     21943728..21943877,21945124..21945249,21945907..21946074,
                     21946186..21946257,21947748..21948125,21951235..21951372,
                     21956372..21956512,21979880..21979933,21985399..21985542))
                     /gene="CDCA7L"
                     /gene_synonym="DKFZp762L0311; JPO2; R1; RAM2"
                     /product="cell division cycle associated 7-like,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127370.2"
                     /db_xref="GI:226371672"
                     /db_xref="GeneID:55536"
                     /db_xref="HGNC:30777"
                     /db_xref="MIM:609685"
                     /db_xref="HPRD:11481"
     mRNA            complement(join(21940517..21941970,21942596..21942732,
                     21943728..21943877,21945124..21945249,21945907..21946074,
                     21946186..21946257,21947748..21948125,21956372..21956512,
                     21985399..21985542))
                     /gene="CDCA7L"
                     /gene_synonym="DKFZp762L0311; JPO2; R1; RAM2"
                     /product="cell division cycle associated 7-like,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127371.2"
                     /db_xref="GI:226371673"
                     /db_xref="GeneID:55536"
                     /db_xref="HGNC:30777"
                     /db_xref="MIM:609685"
                     /db_xref="HPRD:11481"
     CDS             complement(join(21941940..21941970,21942596..21942732,
                     21943728..21943877,21945124..21945249,21945907..21946074,
                     21946186..21946257,21947748..21948125,21951235..21951372,
                     21956372..21956512,21985399..21985422))
                     /gene="CDCA7L"
                     /gene_synonym="DKFZp762L0311; JPO2; R1; RAM2"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cell division cycle-associated 7-like protein
                     isoform 1"
                     /protein_id="NP_061189.2"
                     /db_xref="GI:31542537"
                     /db_xref="CCDS:CCDS5374.1"
                     /db_xref="GeneID:55536"
                     /db_xref="HGNC:30777"
                     /db_xref="HPRD:11481"
                     /db_xref="MIM:609685"
     CDS             complement(join(21941940..21941970,21942596..21942732,
                     21943728..21943877,21945124..21945249,21945907..21946074,
                     21946186..21946257,21947748..21948125,21956372..21956512,
                     21985399..21985422))
                     /gene="CDCA7L"
                     /gene_synonym="DKFZp762L0311; JPO2; R1; RAM2"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cell division cycle-associated 7-like protein
                     isoform 3"
                     /protein_id="NP_001120843.1"
                     /db_xref="GI:188497637"
                     /db_xref="CCDS:CCDS47558.1"
                     /db_xref="GeneID:55536"
                     /db_xref="HGNC:30777"
                     /db_xref="HPRD:11481"
                     /db_xref="MIM:609685"
     CDS             complement(join(21941940..21941970,21942596..21942732,
                     21943728..21943877,21945124..21945249,21945907..21946074,
                     21946186..21946257,21947748..21948125,21951235..21951372,
                     21956372..21956434))
                     /gene="CDCA7L"
                     /gene_synonym="DKFZp762L0311; JPO2; R1; RAM2"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cell division cycle-associated 7-like protein
                     isoform 2"
                     /protein_id="NP_001120842.1"
                     /db_xref="GI:188497635"
                     /db_xref="CCDS:CCDS47559.1"
                     /db_xref="GeneID:55536"
                     /db_xref="HGNC:30777"
                     /db_xref="HPRD:11481"
                     /db_xref="MIM:609685"
     gene            complement(22157908..22396533)
                     /gene="RAPGEF5"
                     /gene_synonym="GFR; KIAA0277; MR-GEF; REPAC"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9771"
                     /db_xref="HGNC:16862"
                     /db_xref="HPRD:15208"
                     /db_xref="MIM:609527"
     mRNA            complement(join(22157908..22162139,22165222..22165276,
                     22170655..22170719,22175656..22175743,22176551..22176601,
                     22179643..22179733,22184662..22184840,22186515..22186637,
                     22190025..22190122,22194073..22194222,22196428..22196506,
                     22197473..22197503,22200136..22200233,22202015..22202159,
                     22206688..22206766,22232985..22233073,22233533..22233651,
                     22259485..22259610,22270465..22270538,22306583..22306631,
                     22330794..22330860,22347958..22348126,22349588..22349709,
                     22354989..22355095,22357606..22357656,22396449..22396533))
                     /gene="RAPGEF5"
                     /gene_synonym="GFR; KIAA0277; MR-GEF; REPAC"
                     /product="Rap guanine nucleotide exchange factor (GEF) 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012294.3"
                     /db_xref="GI:119392076"
                     /db_xref="GeneID:9771"
                     /db_xref="HGNC:16862"
                     /db_xref="HPRD:15208"
                     /db_xref="MIM:609527"
     CDS             complement(join(22162024..22162139,22165222..22165276,
                     22170655..22170719,22175656..22175743,22176551..22176601,
                     22179643..22179733,22184662..22184840,22186515..22186637,
                     22190025..22190122,22194073..22194222,22196428..22196506,
                     22197473..22197503,22200136..22200233,22202015..22202159,
                     22206688..22206766,22232985..22233073,22233533..22233651,
                     22259485..22259610,22270465..22270538,22306583..22306631,
                     22330794..22330860,22347958..22348126,22349588..22349639))
                     /gene="RAPGEF5"
                     /gene_synonym="GFR; KIAA0277; MR-GEF; REPAC"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="rap guanine nucleotide exchange factor 5"
                     /protein_id="NP_036426.3"
                     /db_xref="GI:119392077"
                     /db_xref="CCDS:CCDS55093.1"
                     /db_xref="GeneID:9771"
                     /db_xref="HGNC:16862"
                     /db_xref="HPRD:15208"
                     /db_xref="MIM:609527"
     gene            complement(22459063..22539901)
                     /gene="STEAP1B"
                     /gene_synonym="MGC87042"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:256227"
                     /db_xref="HGNC:41907"
     mRNA            complement(join(22459063..22459455,22532184..22532348,
                     22532943..22533398,22534391..22534505,22539733..22539901))
                     /gene="STEAP1B"
                     /gene_synonym="MGC87042"
                     /product="STEAP family member 1B, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_207342.2"
                     /db_xref="GI:256600248"
                     /db_xref="GeneID:256227"
                     /db_xref="HGNC:41907"
     CDS             complement(join(22459423..22459455,22532184..22532348,
                     22532943..22533398,22534391..22534474))
                     /gene="STEAP1B"
                     /gene_synonym="MGC87042"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="STEAP family protein MGC87042 isoform 2"
                     /protein_id="NP_997225.1"
                     /db_xref="GI:46409320"
                     /db_xref="CCDS:CCDS55094.1"
                     /db_xref="GeneID:256227"
                     /db_xref="HGNC:41907"
     mRNA            complement(join(22478038..22478374,22532184..22532348,
                     22532943..22533455,22534391..22534505,22539733..22539901))
                     /gene="STEAP1B"
                     /gene_synonym="MGC87042"
                     /product="STEAP family member 1B, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001164460.1"
                     /db_xref="GI:256600249"
                     /db_xref="GeneID:256227"
                     /db_xref="HGNC:41907"
     CDS             complement(join(22478108..22478374,22532184..22532348,
                     22532943..22533455,22534391..22534474))
                     /gene="STEAP1B"
                     /gene_synonym="MGC87042"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="STEAP family protein MGC87042 isoform 1"
                     /protein_id="NP_001157932.1"
                     /db_xref="GI:256600250"
                     /db_xref="GeneID:256227"
                     /db_xref="HGNC:41907"
     gene            complement(22549936..22551681)
                     /gene="EEF1A1P6"
                     /gene_synonym="EEF1AL4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:221838"
                     /db_xref="HGNC:3201"
     gene            22602956..22613617
                     /gene="LOC100506178"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100506178"
     misc_RNA        join(22602956..22603049,22604585..22604771,
                     22611394..22611632,22611704..22613617)
                     /gene="LOC100506178"
                     /product="hypothetical LOC100506178"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038393.1"
                     /db_xref="GI:336088614"
                     /db_xref="GeneID:100506178"
     gene            complement(22765014..22767235)
                     /gene="LOC541472"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 3 ESTs, 1 Protein"
                     /db_xref="GeneID:541472"
     misc_RNA        complement(join(22765014..22766324,22767187..22767235))
                     /gene="LOC541472"
                     /product="hypothetical LOC541472"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 3 ESTs, 1 Protein"
                     /transcript_id="XR_108749.1"
                     /db_xref="GI:310119924"
                     /db_xref="GeneID:541472"
     gene            22766766..22771621
                     /gene="IL6"
                     /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3569"
                     /db_xref="HGNC:6018"
                     /db_xref="HPRD:00970"
                     /db_xref="MIM:147620"
     mRNA            join(22766766..22766900,22767063..22767253,
                     22768312..22768425,22769133..22769279,22771025..22771621)
                     /gene="IL6"
                     /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6"
                     /product="interleukin 6 (interferon, beta 2)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000600.3"
                     /db_xref="GI:224831235"
                     /db_xref="GeneID:3569"
                     /db_xref="HGNC:6018"
                     /db_xref="HPRD:00970"
                     /db_xref="MIM:147620"
     CDS             join(22766882..22766900,22767063..22767253,
                     22768312..22768425,22769133..22769279,22771025..22771192)
                     /gene="IL6"
                     /gene_synonym="BSF2; HGF; HSF; IFNB2; IL-6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="interleukin-6 precursor"
                     /protein_id="NP_000591.1"
                     /db_xref="GI:10834984"
                     /db_xref="CCDS:CCDS5375.1"
                     /db_xref="GeneID:3569"
                     /db_xref="HGNC:6018"
                     /db_xref="HPRD:00970"
                     /db_xref="MIM:147620"
     gene            complement(22813189..22813638)
                     /gene="RPS26P32"
                     /gene_synonym="RPS26; RPS26_13_792"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:389472"
                     /db_xref="HGNC:35753"
     gene            complement(22852251..22862421)
                     /gene="TOMM7"
                     /gene_synonym="TOM7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54543"
                     /db_xref="HGNC:21648"
                     /db_xref="HPRD:16266"
                     /db_xref="MIM:607980"
     mRNA            complement(join(22852251..22852804,22857619..22857667,
                     22862296..22862421))
                     /gene="TOMM7"
                     /gene_synonym="TOM7"
                     /product="translocase of outer mitochondrial membrane 7
                     homolog (yeast)"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_019059.2"
                     /db_xref="GI:48976049"
                     /db_xref="GeneID:54543"
                     /db_xref="HGNC:21648"
                     /db_xref="HPRD:16266"
                     /db_xref="MIM:607980"
     CDS             complement(join(22852789..22852804,22857619..22857667,
                     22862296..22862398))
                     /gene="TOMM7"
                     /gene_synonym="TOM7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="mitochondrial import receptor subunit TOM7
                     homolog"
                     /protein_id="NP_061932.1"
                     /db_xref="GI:9506859"
                     /db_xref="CCDS:CCDS5376.1"
                     /db_xref="GeneID:54543"
                     /db_xref="HGNC:21648"
                     /db_xref="HPRD:16266"
                     /db_xref="MIM:607980"
     gene            22896232..22896305
                     /gene="SNORD93"
                     /gene_synonym="HBII-336"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:692210"
                     /db_xref="HGNC:32755"
     ncRNA           22896232..22896305
                     /gene="SNORD93"
                     /gene_synonym="HBII-336"
                     /ncRNA_class="snoRNA"
                     /product="small nucleolar RNA, C/D box 93"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_003075.1"
                     /db_xref="GI:96974962"
                     /db_xref="GeneID:692210"
                     /db_xref="HGNC:32755"
     gene            22921440..22922051
                     /gene="RPL12P10"
                     /gene_synonym="RPL12_8_793"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392872"
                     /db_xref="HGNC:22583"
     gene            complement(22980878..23053770)
                     /gene="FAM126A"
                     /gene_synonym="DRCTNNB1A; HCC; HLD5; HYCC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84668"
                     /db_xref="HGNC:24587"
                     /db_xref="HPRD:16837"
                     /db_xref="MIM:610531"
     mRNA            complement(join(22980878..22985782,22999875..23000034,
                     23000854..23000941,23004034..23004150,23015829..23015924,
                     23016312..23016427,23016960..23017040,23017888..23018067,
                     23023563..23023664,23030680..23030758,23053544..23053770))
                     /gene="FAM126A"
                     /gene_synonym="DRCTNNB1A; HCC; HLD5; HYCC1"
                     /product="family with sequence similarity 126, member A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032581.3"
                     /db_xref="GI:189571607"
                     /db_xref="GeneID:84668"
                     /db_xref="HGNC:24587"
                     /db_xref="HPRD:16837"
                     /db_xref="MIM:610531"
     CDS             complement(join(22985208..22985782,22999875..23000034,
                     23000854..23000941,23004034..23004150,23015829..23015924,
                     23016312..23016427,23016960..23017040,23017888..23018067,
                     23023563..23023664,23030680..23030730))
                     /gene="FAM126A"
                     /gene_synonym="DRCTNNB1A; HCC; HLD5; HYCC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hyccin"
                     /protein_id="NP_115970.2"
                     /db_xref="GI:19923646"
                     /db_xref="CCDS:CCDS5377.1"
                     /db_xref="GeneID:84668"
                     /db_xref="HGNC:24587"
                     /db_xref="HPRD:16837"
                     /db_xref="MIM:610531"
     gene            23145353..23215040
                     /gene="KLHL7"
                     /gene_synonym="KLHL6; SBBI26"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55975"
                     /db_xref="HGNC:15646"
                     /db_xref="HPRD:13927"
                     /db_xref="MIM:611119"
     mRNA            join(23145353..23145765,23163396..23163498,
                     23164307..23164400,23164667..23164791,23180388..23180563,
                     23183470..23183644,23191686..23191828,23205317..23205557,
                     23207455..23207656,23212567..23212664,23213634..23215040)
                     /gene="KLHL7"
                     /gene_synonym="KLHL6; SBBI26"
                     /product="kelch-like 7 (Drosophila), transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001031710.2"
                     /db_xref="GI:170784845"
                     /db_xref="GeneID:55975"
                     /db_xref="HGNC:15646"
                     /db_xref="HPRD:13927"
                     /db_xref="MIM:611119"
     misc_RNA        join(23145353..23145765,23157453..23157583,
                     23163396..23163498,23164307..23164400,23164667..23164791,
                     23180388..23180563,23183470..23183644,23191686..23191828,
                     23205317..23205557,23207455..23207656,23212567..23212664,
                     23213634..23215040)
                     /gene="KLHL7"
                     /gene_synonym="KLHL6; SBBI26"
                     /product="kelch-like 7 (Drosophila), transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033328.1"
                     /db_xref="GI:289063410"
                     /db_xref="GeneID:55975"
                     /db_xref="HGNC:15646"
                     /db_xref="MIM:611119"
                     /db_xref="HPRD:13927"
     mRNA            join(23145353..23145765,23163396..23163498,
                     23164307..23164400,23164667..23164791,23165380..23165669)
                     /gene="KLHL7"
                     /gene_synonym="KLHL6; SBBI26"
                     /product="kelch-like 7 (Drosophila), transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001172428.1"
                     /db_xref="GI:289063418"
                     /db_xref="GeneID:55975"
                     /db_xref="HGNC:15646"
                     /db_xref="MIM:611119"
                     /db_xref="HPRD:13927"
     misc_RNA        join(23145353..23145765,23157453..23157583,
                     23163396..23163498,23164307..23164400,23164667..23164791,
                     23165380..23165669)
                     /gene="KLHL7"
                     /gene_synonym="KLHL6; SBBI26"
                     /product="kelch-like 7 (Drosophila), transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033329.1"
                     /db_xref="GI:289063411"
                     /db_xref="GeneID:55975"
                     /db_xref="HGNC:15646"
                     /db_xref="MIM:611119"
                     /db_xref="HPRD:13927"
     CDS             join(23145646..23145765,23163396..23163498,
                     23164307..23164400,23164667..23164791,23180388..23180563,
                     23183470..23183644,23191686..23191828,23205317..23205557,
                     23207455..23207656,23212567..23212664,23213634..23213917)
                     /gene="KLHL7"
                     /gene_synonym="KLHL6; SBBI26"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="kelch-like protein 7 isoform 1"
                     /protein_id="NP_001026880.2"
                     /db_xref="GI:170784846"
                     /db_xref="CCDS:CCDS34609.1"
                     /db_xref="GeneID:55975"
                     /db_xref="HGNC:15646"
                     /db_xref="HPRD:13927"
                     /db_xref="MIM:611119"
     CDS             join(23145646..23145765,23163396..23163498,
                     23164307..23164400,23164667..23164791,23165380..23165438)
                     /gene="KLHL7"
                     /gene_synonym="KLHL6; SBBI26"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="kelch-like protein 7 isoform 3"
                     /protein_id="NP_001165899.1"
                     /db_xref="GI:289063419"
                     /db_xref="CCDS:CCDS55095.1"
                     /db_xref="GeneID:55975"
                     /db_xref="HGNC:15646"
                     /db_xref="HPRD:13927"
                     /db_xref="MIM:611119"
     mRNA            join(23145917..23146413,23163396..23163498,
                     23164307..23164400,23164667..23164791,23180388..23180563,
                     23183470..23183644,23191686..23191828,23205317..23205557,
                     23207455..23207656,23212567..23212664,23213634..23215040)
                     /gene="KLHL7"
                     /gene_synonym="KLHL6; SBBI26"
                     /product="kelch-like 7 (Drosophila), transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018846.4"
                     /db_xref="GI:289063408"
                     /db_xref="GeneID:55975"
                     /db_xref="HGNC:15646"
                     /db_xref="HPRD:13927"
                     /db_xref="MIM:611119"
     CDS             join(23163420..23163498,23164307..23164400,
                     23164667..23164791,23180388..23180563,23183470..23183644,
                     23191686..23191828,23205317..23205557,23207455..23207656,
                     23212567..23212664,23213634..23213917)
                     /gene="KLHL7"
                     /gene_synonym="KLHL6; SBBI26"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="kelch-like protein 7 isoform 2"
                     /protein_id="NP_061334.4"
                     /db_xref="GI:289063409"
                     /db_xref="CCDS:CCDS5378.2"
                     /db_xref="GeneID:55975"
                     /db_xref="HGNC:15646"
                     /db_xref="HPRD:13927"
                     /db_xref="MIM:611119"
     gene            23168797..23169457
                     /gene="LOC100419075"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419075"
     gene            23221446..23240630
                     /gene="NUPL2"
                     /gene_synonym="CG1; hCG1; NLP-1; NLP_1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:11097"
                     /db_xref="HGNC:17010"
                     /db_xref="HPRD:14855"
     mRNA            join(23221446..23221825,23224689..23224917,
                     23226671..23226765,23235458..23235534,23236299..23236385,
                     23239077..23239161,23239787..23240630)
                     /gene="NUPL2"
                     /gene_synonym="CG1; hCG1; NLP-1; NLP_1"
                     /product="nucleoporin like 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_007342.2"
                     /db_xref="GI:197245407"
                     /db_xref="GeneID:11097"
                     /db_xref="HGNC:17010"
                     /db_xref="HPRD:14855"
     CDS             join(23221705..23221825,23224689..23224917,
                     23226671..23226765,23235458..23235534,23236299..23236385,
                     23239077..23239161,23239787..23240364)
                     /gene="NUPL2"
                     /gene_synonym="CG1; hCG1; NLP-1; NLP_1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="nucleoporin-like protein 2"
                     /protein_id="NP_031368.1"
                     /db_xref="GI:6679074"
                     /db_xref="CCDS:CCDS5379.1"
                     /db_xref="GeneID:11097"
                     /db_xref="HGNC:17010"
                     /db_xref="HPRD:14855"
     gene            23286316..23314729
                     /gene="GPNMB"
                     /gene_synonym="HGFIN; NMB"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10457"
                     /db_xref="HGNC:4462"
                     /db_xref="HPRD:05081"
                     /db_xref="MIM:604368"
     mRNA            join(23286316..23286546,23292926..23293078,
                     23293788..23293931,23296511..23296684,23299599..23299757,
                     23300075..23300392,23306100..23306234,23307505..23307607,
                     23309586..23309794,23313140..23313233,23313684..23314729)
                     /gene="GPNMB"
                     /gene_synonym="HGFIN; NMB"
                     /product="glycoprotein (transmembrane) nmb, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001005340.1"
                     /db_xref="GI:52694751"
                     /db_xref="GeneID:10457"
                     /db_xref="HGNC:4462"
                     /db_xref="MIM:604368"
                     /db_xref="HPRD:05081"
     mRNA            join(23286316..23286546,23292926..23293078,
                     23293788..23293931,23296511..23296684,23299599..23299757,
                     23300075..23300392,23306136..23306234,23307505..23307607,
                     23309586..23309794,23313140..23313233,23313684..23314729)
                     /gene="GPNMB"
                     /gene_synonym="HGFIN; NMB"
                     /product="glycoprotein (transmembrane) nmb, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002510.2"
                     /db_xref="GI:52694750"
                     /db_xref="GeneID:10457"
                     /db_xref="HGNC:4462"
                     /db_xref="HPRD:05081"
                     /db_xref="MIM:604368"
     CDS             join(23286477..23286546,23292926..23293078,
                     23293788..23293931,23296511..23296684,23299599..23299757,
                     23300075..23300392,23306100..23306234,23307505..23307607,
                     23309586..23309794,23313140..23313233,23313684..23313843)
                     /gene="GPNMB"
                     /gene_synonym="HGFIN; NMB"
                     /note="isoform a precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane glycoprotein NMB isoform a
                     precursor"
                     /protein_id="NP_001005340.1"
                     /db_xref="GI:52694752"
                     /db_xref="CCDS:CCDS34610.1"
                     /db_xref="GeneID:10457"
                     /db_xref="HGNC:4462"
                     /db_xref="HPRD:05081"
                     /db_xref="MIM:604368"
     CDS             join(23286477..23286546,23292926..23293078,
                     23293788..23293931,23296511..23296684,23299599..23299757,
                     23300075..23300392,23306136..23306234,23307505..23307607,
                     23309586..23309794,23313140..23313233,23313684..23313843)
                     /gene="GPNMB"
                     /gene_synonym="HGFIN; NMB"
                     /note="isoform b precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane glycoprotein NMB isoform b
                     precursor"
                     /protein_id="NP_002501.1"
                     /db_xref="GI:4505405"
                     /db_xref="CCDS:CCDS5380.1"
                     /db_xref="GeneID:10457"
                     /db_xref="HGNC:4462"
                     /db_xref="HPRD:05081"
                     /db_xref="MIM:604368"
     gene            23338940..23349180
                     /gene="C7orf30"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:115416"
                     /db_xref="HGNC:21721"
                     /db_xref="HPRD:12918"
     mRNA            join(23338940..23339227,23340458..23340636,
                     23347487..23347568,23348975..23349180)
                     /gene="C7orf30"
                     /product="chromosome 7 open reading frame 30"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138446.1"
                     /db_xref="GI:19923976"
                     /db_xref="GeneID:115416"
                     /db_xref="HGNC:21721"
                     /db_xref="HPRD:12918"
     CDS             join(23338972..23339227,23340458..23340636,
                     23347487..23347568,23348975..23349162)
                     /gene="C7orf30"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC115416"
                     /protein_id="NP_612455.1"
                     /db_xref="GI:19923977"
                     /db_xref="CCDS:CCDS5381.1"
                     /db_xref="GeneID:115416"
                     /db_xref="HGNC:21721"
                     /db_xref="HPRD:12918"
     gene            complement(23349828..23509995)
                     /gene="IGF2BP3"
                     /gene_synonym="CT98; DKFZp686F1078; IMP-3; IMP3; KOC1;
                     VICKZ3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10643"
                     /db_xref="HGNC:28868"
                     /db_xref="HPRD:16306"
                     /db_xref="MIM:608259"
     mRNA            complement(join(23349828..23352079,23352354..23352467,
                     23353141..23353272,23357258..23357332,23358757..23358873,
                     23381683..23381808,23383337..23383472,23385559..23385681,
                     23387219..23387353,23390924..23391205,23401153..23401216,
                     23401309..23401360,23458395..23458443,23508101..23508161,
                     23509555..23509995))
                     /gene="IGF2BP3"
                     /gene_synonym="CT98; DKFZp686F1078; IMP-3; IMP3; KOC1;
                     VICKZ3"
                     /product="insulin-like growth factor 2 mRNA binding
                     protein 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006547.2"
                     /db_xref="GI:30795211"
                     /db_xref="GeneID:10643"
                     /db_xref="HGNC:28868"
                     /db_xref="HPRD:16306"
                     /db_xref="MIM:608259"
     CDS             complement(join(23351981..23352079,23352354..23352467,
                     23353141..23353272,23357258..23357332,23358757..23358873,
                     23381683..23381808,23383337..23383472,23385559..23385681,
                     23387219..23387353,23390924..23391205,23401153..23401216,
                     23401309..23401360,23458395..23458443,23508101..23508161,
                     23509555..23509729))
                     /gene="IGF2BP3"
                     /gene_synonym="CT98; DKFZp686F1078; IMP-3; IMP3; KOC1;
                     VICKZ3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="insulin-like growth factor 2 mRNA-binding
                     protein 3"
                     /protein_id="NP_006538.2"
                     /db_xref="GI:30795212"
                     /db_xref="CCDS:CCDS5382.1"
                     /db_xref="GeneID:10643"
                     /db_xref="HGNC:28868"
                     /db_xref="HPRD:16306"
                     /db_xref="MIM:608259"
     gene            23520202..23522188
                     /gene="LOC389473"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:389473"
     gene            23530007..23531047
                     /gene="RPS2P32"
                     /gene_synonym="RPS2_14_794"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:256355"
                     /db_xref="HGNC:30518"
     misc_RNA        23530007..23531047
                     /gene="RPS2P32"
                     /gene_synonym="RPS2_14_794"
                     /product="ribosomal protein S2 pseudogene 32"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_026676.1"
                     /db_xref="GI:221307604"
                     /db_xref="GeneID:256355"
                     /db_xref="HGNC:30518"
     gene            complement(23544399..23571656)
                     /gene="TRA2A"
                     /gene_synonym="HSU53209"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:29896"
                     /db_xref="HGNC:16645"
                     /db_xref="HPRD:04096"
                     /db_xref="MIM:602718"
     mRNA            complement(join(23544399..23545188,23545365..23545432,
                     23545757..23545885,23547039..23547154,23552513..23552701,
                     23555982..23556147,23561326..23561459,23571408..23571656))
                     /gene="TRA2A"
                     /gene_synonym="HSU53209"
                     /product="transformer 2 alpha homolog (Drosophila)"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013293.3"
                     /db_xref="GI:110227858"
                     /db_xref="GeneID:29896"
                     /db_xref="HGNC:16645"
                     /db_xref="HPRD:04096"
                     /db_xref="MIM:602718"
     CDS             complement(join(23545178..23545188,23545365..23545432,
                     23545757..23545885,23547039..23547154,23552513..23552701,
                     23555982..23556147,23561326..23561459,23571408..23571443))
                     /gene="TRA2A"
                     /gene_synonym="HSU53209"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transformer-2 protein homolog alpha"
                     /protein_id="NP_037425.1"
                     /db_xref="GI:9558733"
                     /db_xref="CCDS:CCDS5383.1"
                     /db_xref="GeneID:29896"
                     /db_xref="HGNC:16645"
                     /db_xref="HPRD:04096"
                     /db_xref="MIM:602718"
     gene            complement(23602083..23603879)
                     /gene="LOC442517"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442517"
     gene            complement(23624335..23626146)
                     /gene="CLK2P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:1197"
                     /db_xref="HGNC:2070"
     misc_RNA        complement(23624335..23626146)
                     /gene="CLK2P"
                     /product="CDC-like kinase 2, pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002711.3"
                     /db_xref="GI:197382428"
                     /db_xref="GeneID:1197"
                     /db_xref="HGNC:2070"
     gene            23636998..23684327
                     /gene="CCDC126"
                     /gene_synonym="FLJ23031; MGC104248"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:90693"
                     /db_xref="HGNC:22398"
                     /db_xref="HPRD:14278"
     mRNA            join(23636998..23637224,23637586..23637670,
                     23650790..23651172,23682550..23684327)
                     /gene="CCDC126"
                     /gene_synonym="FLJ23031; MGC104248"
                     /product="coiled-coil domain containing 126"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138771.3"
                     /db_xref="GI:93277090"
                     /db_xref="GeneID:90693"
                     /db_xref="HGNC:22398"
                     /db_xref="HPRD:14278"
     CDS             join(23650935..23651172,23682550..23682734)
                     /gene="CCDC126"
                     /gene_synonym="FLJ23031; MGC104248"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="coiled-coil domain-containing protein 126
                     precursor"
                     /protein_id="NP_620126.2"
                     /db_xref="GI:40255029"
                     /db_xref="CCDS:CCDS5384.1"
                     /db_xref="GeneID:90693"
                     /db_xref="HGNC:22398"
                     /db_xref="HPRD:14278"
     gene            23658952..23662442
                     /gene="LOC100422533"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100422533"
     gene            23719749..23742269
                     /gene="C7orf46"
                     /gene_synonym="DKFZp686F0810; FLJ45875; MGC72075"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:340277"
                     /db_xref="HGNC:27977"
                     /db_xref="HPRD:14706"
     mRNA            join(23719749..23719902,23724118..23724291,
                     23728888..23729078,23731009..23731215,23737811..23737918,
                     23740405..23740487,23741715..23742269)
                     /gene="C7orf46"
                     /gene_synonym="DKFZp686F0810; FLJ45875; MGC72075"
                     /product="chromosome 7 open reading frame 46, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_199136.3"
                     /db_xref="GI:188219617"
                     /db_xref="GeneID:340277"
                     /db_xref="HGNC:27977"
                     /db_xref="HPRD:14706"
     mRNA            join(23719749..23719902,23724118..23724291,
                     23728888..23729078,23731009..23731215,23740405..23740487,
                     23741715..23742269)
                     /gene="C7orf46"
                     /gene_synonym="DKFZp686F0810; FLJ45875; MGC72075"
                     /product="chromosome 7 open reading frame 46, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127364.1"
                     /db_xref="GI:188219619"
                     /db_xref="GeneID:340277"
                     /db_xref="HGNC:27977"
                     /db_xref="HPRD:14706"
     mRNA            join(23719749..23719902,23728888..23729078,
                     23731009..23731215,23740405..23740487,23741715..23742269)
                     /gene="C7orf46"
                     /gene_synonym="DKFZp686F0810; FLJ45875; MGC72075"
                     /product="chromosome 7 open reading frame 46, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127365.1"
                     /db_xref="GI:188219621"
                     /db_xref="GeneID:340277"
                     /db_xref="HGNC:27977"
                     /db_xref="HPRD:14706"
     CDS             join(23719838..23719902,23724118..23724291,
                     23728888..23729078,23731009..23731215,23737811..23737918,
                     23740405..23740487,23741715..23741783)
                     /gene="C7orf46"
                     /gene_synonym="DKFZp686F0810; FLJ45875; MGC72075"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC340277 isoform 1"
                     /protein_id="NP_954587.2"
                     /db_xref="GI:188219618"
                     /db_xref="CCDS:CCDS5385.1"
                     /db_xref="GeneID:340277"
                     /db_xref="HGNC:27977"
                     /db_xref="HPRD:14706"
     CDS             join(23719838..23719902,23724118..23724291,
                     23728888..23729078,23731009..23731215,23740405..23740487,
                     23741715..23741783)
                     /gene="C7orf46"
                     /gene_synonym="DKFZp686F0810; FLJ45875; MGC72075"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC340277 isoform 2"
                     /protein_id="NP_001120836.1"
                     /db_xref="GI:188219620"
                     /db_xref="CCDS:CCDS47561.1"
                     /db_xref="GeneID:340277"
                     /db_xref="HGNC:27977"
                     /db_xref="HPRD:14706"
     CDS             join(23719838..23719902,23728888..23729078,
                     23731009..23731215,23740405..23740487,23741715..23741783)
                     /gene="C7orf46"
                     /gene_synonym="DKFZp686F0810; FLJ45875; MGC72075"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC340277 isoform 3"
                     /protein_id="NP_001120837.1"
                     /db_xref="GI:188219622"
                     /db_xref="CCDS:CCDS47562.1"
                     /db_xref="GeneID:340277"
                     /db_xref="HGNC:27977"
                     /db_xref="HPRD:14706"
     gene            23749838..23872127
                     /gene="STK31"
                     /gene_synonym="FLJ16102; SGK396; TDRD8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:56164"
                     /db_xref="HGNC:11407"
                     /db_xref="HPRD:10427"
                     /db_xref="MIM:605790"
     mRNA            join(23749838..23749954,23751718..23751764,
                     23751853..23751905,23757100..23757198,23766860..23766934,
                     23768710..23768868,23775157..23775515,23776523..23776697,
                     23792336..23792451,23793934..23794093,23802420..23802542,
                     23808614..23808793,23809259..23809375,23810624..23810743,
                     23811766..23811897,23821038..23821139,23823202..23823282,
                     23825097..23825222,23826127..23826252,23826457..23826543,
                     23827599..23827748,23830443..23830565,23854763..23854831,
                     23871755..23872127)
                     /gene="STK31"
                     /gene_synonym="FLJ16102; SGK396; TDRD8"
                     /product="serine/threonine kinase 31, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_031414.3"
                     /db_xref="GI:170784857"
                     /db_xref="GeneID:56164"
                     /db_xref="HGNC:11407"
                     /db_xref="HPRD:10427"
                     /db_xref="MIM:605790"
     mRNA            join(23749838..23749954,23751726..23751764,
                     23751853..23751905,23757100..23757198,23766860..23766934,
                     23768710..23768868,23775157..23775515,23776523..23776697,
                     23792336..23792451,23793934..23794093,23802420..23802542,
                     23808614..23808793,23809259..23809375,23810624..23810743,
                     23811766..23811897,23821038..23821139,23823202..23823282,
                     23825097..23825222,23826127..23826252,23826457..23826543,
                     23827599..23827748,23830443..23830565,23854763..23854831,
                     23871755..23872127)
                     /gene="STK31"
                     /gene_synonym="FLJ16102; SGK396; TDRD8"
                     /product="serine/threonine kinase 31, transcript variant
                     3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001122833.1"
                     /db_xref="GI:170784858"
                     /db_xref="GeneID:56164"
                     /db_xref="HGNC:11407"
                     /db_xref="MIM:605790"
                     /db_xref="HPRD:10427"
     CDS             join(23749905..23749954,23751718..23751764,
                     23751853..23751905,23757100..23757198,23766860..23766934,
                     23768710..23768868,23775157..23775515,23776523..23776697,
                     23792336..23792451,23793934..23794093,23802420..23802542,
                     23808614..23808793,23809259..23809375,23810624..23810743,
                     23811766..23811897,23821038..23821139,23823202..23823282,
                     23825097..23825222,23826127..23826252,23826457..23826543,
                     23827599..23827748,23830443..23830565,23854763..23854831,
                     23871755..23871985)
                     /gene="STK31"
                     /gene_synonym="FLJ16102; SGK396; TDRD8"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="serine/threonine-protein kinase 31 isoform a"
                     /protein_id="NP_113602.2"
                     /db_xref="GI:14602443"
                     /db_xref="CCDS:CCDS5386.1"
                     /db_xref="GeneID:56164"
                     /db_xref="HGNC:11407"
                     /db_xref="HPRD:10427"
                     /db_xref="MIM:605790"
     mRNA            join(23749997..23750357,23751718..23751764,
                     23751853..23751905,23757100..23757198,23766860..23766934,
                     23768710..23768868,23775157..23775515,23776523..23776697,
                     23792336..23792451,23793934..23794093,23802420..23802542,
                     23808614..23808793,23809259..23809375,23810624..23810743,
                     23811766..23811897,23821038..23821139,23823202..23823282,
                     23825097..23825222,23826127..23826252,23826457..23826543,
                     23827599..23827748,23830443..23830565,23854763..23854831,
                     23871755..23872127)
                     /gene="STK31"
                     /gene_synonym="FLJ16102; SGK396; TDRD8"
                     /product="serine/threonine kinase 31, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032944.2"
                     /db_xref="GI:170784855"
                     /db_xref="GeneID:56164"
                     /db_xref="HGNC:11407"
                     /db_xref="HPRD:10427"
                     /db_xref="MIM:605790"
     CDS             join(23751737..23751764,23751853..23751905,
                     23757100..23757198,23766860..23766934,23768710..23768868,
                     23775157..23775515,23776523..23776697,23792336..23792451,
                     23793934..23794093,23802420..23802542,23808614..23808793,
                     23809259..23809375,23810624..23810743,23811766..23811897,
                     23821038..23821139,23823202..23823282,23825097..23825222,
                     23826127..23826252,23826457..23826543,23827599..23827748,
                     23830443..23830565,23854763..23854831,23871755..23871985)
                     /gene="STK31"
                     /gene_synonym="FLJ16102; SGK396; TDRD8"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="serine/threonine-protein kinase 31 isoform b"
                     /protein_id="NP_116562.2"
                     /db_xref="GI:170784856"
                     /db_xref="CCDS:CCDS43556.1"
                     /db_xref="GeneID:56164"
                     /db_xref="HGNC:11407"
                     /db_xref="HPRD:10427"
                     /db_xref="MIM:605790"
     CDS             join(23751737..23751764,23751853..23751905,
                     23757100..23757198,23766860..23766934,23768710..23768868,
                     23775157..23775515,23776523..23776697,23792336..23792451,
                     23793934..23794093,23802420..23802542,23808614..23808793,
                     23809259..23809375,23810624..23810743,23811766..23811897,
                     23821038..23821139,23823202..23823282,23825097..23825222,
                     23826127..23826252,23826457..23826543,23827599..23827748,
                     23830443..23830565,23854763..23854831,23871755..23871985)
                     /gene="STK31"
                     /gene_synonym="FLJ16102; SGK396; TDRD8"
                     /note="isoform b is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="serine/threonine-protein kinase 31 isoform b"
                     /protein_id="NP_001116305.1"
                     /db_xref="GI:170784859"
                     /db_xref="CCDS:CCDS43556.1"
                     /db_xref="GeneID:56164"
                     /db_xref="HGNC:11407"
                     /db_xref="HPRD:10427"
                     /db_xref="MIM:605790"
     gene            complement(23760929..23761429)
                     /gene="PCMTD1P3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100422595"
                     /db_xref="HGNC:38806"
     gene            24323807..24331484
                     /gene="NPY"
                     /gene_synonym="PYY4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4852"
                     /db_xref="HGNC:7955"
                     /db_xref="HPRD:01214"
                     /db_xref="MIM:162640"
     mRNA            join(24323807..24323894,24324860..24325047,
                     24329118..24329198,24331282..24331484)
                     /gene="NPY"
                     /gene_synonym="PYY4"
                     /product="neuropeptide Y"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000905.3"
                     /db_xref="GI:268834883"
                     /db_xref="GeneID:4852"
                     /db_xref="HGNC:7955"
                     /db_xref="HPRD:01214"
                     /db_xref="MIM:162640"
     CDS             join(24324860..24325047,24329118..24329198,
                     24331282..24331306)
                     /gene="NPY"
                     /gene_synonym="PYY4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="pro-neuropeptide Y preproprotein preproprotein"
                     /protein_id="NP_000896.1"
                     /db_xref="GI:4505449"
                     /db_xref="CCDS:CCDS5387.1"
                     /db_xref="GeneID:4852"
                     /db_xref="HGNC:7955"
                     /db_xref="HPRD:01214"
                     /db_xref="MIM:162640"
     gene            24613085..24727498
                     /gene="MPP6"
                     /gene_synonym="p55T; PALS2; VAM-1; VAM1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51678"
                     /db_xref="HGNC:18167"
                     /db_xref="HPRD:09509"
                     /db_xref="MIM:606959"
     mRNA            join(24613085..24613212,24659671..24659839,
                     24663285..24663403,24681335..24681487,24689231..24689383,
                     24690104..24690331,24703209..24703340,24705207..24705306,
                     24705640..24705708,24708118..24708279,24718750..24718952,
                     24720011..24720139,24727057..24727498)
                     /gene="MPP6"
                     /gene_synonym="p55T; PALS2; VAM-1; VAM1"
                     /product="membrane protein, palmitoylated 6 (MAGUK p55
                     subfamily member 6)"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016447.2"
                     /db_xref="GI:21361597"
                     /db_xref="GeneID:51678"
                     /db_xref="HGNC:18167"
                     /db_xref="HPRD:09509"
                     /db_xref="MIM:606959"
     CDS             join(24663287..24663403,24681335..24681487,
                     24689231..24689383,24690104..24690331,24703209..24703340,
                     24705207..24705306,24705640..24705708,24708118..24708279,
                     24718750..24718952,24720011..24720139,24727057..24727233)
                     /gene="MPP6"
                     /gene_synonym="p55T; PALS2; VAM-1; VAM1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="MAGUK p55 subfamily member 6"
                     /protein_id="NP_057531.2"
                     /db_xref="GI:21361598"
                     /db_xref="CCDS:CCDS5388.1"
                     /db_xref="GeneID:51678"
                     /db_xref="HGNC:18167"
                     /db_xref="HPRD:09509"
                     /db_xref="MIM:606959"
     gene            complement(24737974..24797639)
                     /gene="DFNA5"
                     /gene_synonym="ICERE-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1687"
                     /db_xref="HGNC:2810"
                     /db_xref="HPRD:02996"
                     /db_xref="MIM:608798"
     mRNA            complement(join(24737974..24738878,24742379..24742452,
                     24745803..24745995,24747746..24747873,24749843..24750007,
                     24756873..24756993,24758666..24758837,24784181..24784373,
                     24789183..24789412,24797326..24797639))
                     /gene="DFNA5"
                     /gene_synonym="ICERE-1"
                     /product="deafness, autosomal dominant 5, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004403.2"
                     /db_xref="GI:116734721"
                     /db_xref="GeneID:1687"
                     /db_xref="HGNC:2810"
                     /db_xref="HPRD:02996"
                     /db_xref="MIM:608798"
     mRNA            complement(join(24737974..24738878,24742379..24742452,
                     24745803..24745995,24747746..24747873,24749843..24750007,
                     24756873..24756993,24758666..24758837,24784181..24784373,
                     24797326..24797639))
                     /gene="DFNA5"
                     /gene_synonym="ICERE-1"
                     /product="deafness, autosomal dominant 5, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127454.1"
                     /db_xref="GI:188536093"
                     /db_xref="GeneID:1687"
                     /db_xref="HGNC:2810"
                     /db_xref="MIM:608798"
                     /db_xref="HPRD:02996"
     mRNA            complement(join(24737974..24738878,24742379..24742452,
                     24745803..24745995,24747746..24747873,24749843..24750007,
                     24756873..24756993,24758666..24758837,24784181..24784373,
                     24789183..24789412,24797015..24797083))
                     /gene="DFNA5"
                     /gene_synonym="ICERE-1"
                     /product="deafness, autosomal dominant 5, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127453.1"
                     /db_xref="GI:188536091"
                     /db_xref="GeneID:1687"
                     /db_xref="HGNC:2810"
                     /db_xref="MIM:608798"
                     /db_xref="HPRD:02996"
     CDS             complement(join(24738645..24738878,24742379..24742452,
                     24745803..24745995,24747746..24747873,24749843..24750007,
                     24756873..24756993,24758666..24758837,24784181..24784373,
                     24789183..24789393))
                     /gene="DFNA5"
                     /gene_synonym="ICERE-1"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="non-syndromic hearing impairment protein 5
                     isoform a"
                     /protein_id="NP_004394.1"
                     /db_xref="GI:4758154"
                     /db_xref="CCDS:CCDS5389.1"
                     /db_xref="GeneID:1687"
                     /db_xref="HGNC:2810"
                     /db_xref="HPRD:02996"
                     /db_xref="MIM:608798"
     CDS             complement(join(24738645..24738878,24742379..24742452,
                     24745803..24745995,24747746..24747873,24749843..24750007,
                     24756873..24756993,24758666..24758837,24784181..24784373,
                     24789183..24789393))
                     /gene="DFNA5"
                     /gene_synonym="ICERE-1"
                     /note="isoform a is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="non-syndromic hearing impairment protein 5
                     isoform a"
                     /protein_id="NP_001120925.1"
                     /db_xref="GI:188536092"
                     /db_xref="CCDS:CCDS5389.1"
                     /db_xref="GeneID:1687"
                     /db_xref="HGNC:2810"
                     /db_xref="HPRD:02996"
                     /db_xref="MIM:608798"
     CDS             complement(join(24738645..24738878,24742379..24742452,
                     24745803..24745995,24747746..24747873,24749843..24750007,
                     24756873..24756993,24758666..24758749))
                     /gene="DFNA5"
                     /gene_synonym="ICERE-1"
                     /note="isoform b is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="non-syndromic hearing impairment protein 5
                     isoform b"
                     /protein_id="NP_001120926.1"
                     /db_xref="GI:188536094"
                     /db_xref="CCDS:CCDS47563.1"
                     /db_xref="GeneID:1687"
                     /db_xref="HGNC:2810"
                     /db_xref="HPRD:02996"
                     /db_xref="MIM:608798"
     gene            complement(24836159..25019760)
                     /gene="OSBPL3"
                     /gene_synonym="DKFZp667P1518; KIAA0704; MGC21526; ORP-3;
                     ORP3; OSBP3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26031"
                     /db_xref="HGNC:16370"
                     /db_xref="HPRD:09474"
                     /db_xref="MIM:606732"
     mRNA            complement(join(24836159..24839898,24843934..24844056,
                     24846395..24846521,24849426..24849570,24854678..24854822,
                     24856229..24856307,24859794..24859857,24870387..24870524,
                     24874105..24874355,24880309..24880402,24881898..24882032,
                     24888688..24888795,24892123..24892253,24901232..24901388,
                     24902819..24902911,24903115..24903218,24904961..24905084,
                     24905689..24905856,24910351..24910464,24911361..24911414,
                     24911572..24911688,24931996..24932240,25019505..25019760))
                     /gene="OSBPL3"
                     /gene_synonym="DKFZp667P1518; KIAA0704; MGC21526; ORP-3;
                     ORP3; OSBP3"
                     /product="oxysterol binding protein-like 3, transcript
                     variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015550.2"
                     /db_xref="GI:21735578"
                     /db_xref="GeneID:26031"
                     /db_xref="HGNC:16370"
                     /db_xref="HPRD:09474"
                     /db_xref="MIM:606732"
     mRNA            complement(join(24836159..24839898,24843934..24844056,
                     24846395..24846521,24849426..24849570,24854678..24854822,
                     24856229..24856307,24859794..24859857,24870387..24870524,
                     24874105..24874355,24880309..24880402,24881898..24882032,
                     24888688..24888795,24892123..24892253,24901232..24901388,
                     24903115..24903218,24904961..24905084,24905689..24905856,
                     24910351..24910464,24911361..24911414,24911572..24911688,
                     24931996..24932240,25019505..25019760))
                     /gene="OSBPL3"
                     /gene_synonym="DKFZp667P1518; KIAA0704; MGC21526; ORP-3;
                     ORP3; OSBP3"
                     /product="oxysterol binding protein-like 3, transcript
                     variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145320.1"
                     /db_xref="GI:21735579"
                     /db_xref="GeneID:26031"
                     /db_xref="HGNC:16370"
                     /db_xref="MIM:606732"
                     /db_xref="HPRD:09474"
     mRNA            complement(join(24836159..24839898,24843934..24844056,
                     24846395..24846521,24849426..24849570,24854678..24854822,
                     24856229..24856307,24859794..24859857,24870387..24870524,
                     24874105..24874355,24880309..24880402,24881898..24882032,
                     24892123..24892253,24901232..24901388,24902819..24902911,
                     24903115..24903218,24904961..24905084,24905689..24905856,
                     24910351..24910464,24911361..24911414,24911572..24911688,
                     24931996..24932240,25019505..25019760))
                     /gene="OSBPL3"
                     /gene_synonym="DKFZp667P1518; KIAA0704; MGC21526; ORP-3;
                     ORP3; OSBP3"
                     /product="oxysterol binding protein-like 3, transcript
                     variant 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145321.1"
                     /db_xref="GI:21735581"
                     /db_xref="GeneID:26031"
                     /db_xref="HGNC:16370"
                     /db_xref="MIM:606732"
                     /db_xref="HPRD:09474"
     mRNA            complement(join(24836159..24839898,24843934..24844056,
                     24846395..24846521,24849426..24849570,24854678..24854822,
                     24856229..24856307,24859794..24859857,24870387..24870524,
                     24874105..24874355,24880309..24880402,24881898..24882032,
                     24892123..24892253,24901232..24901388,24903115..24903218,
                     24904961..24905084,24905689..24905856,24910351..24910464,
                     24911361..24911414,24911572..24911688,24931996..24932240,
                     25019505..25019760))
                     /gene="OSBPL3"
                     /gene_synonym="DKFZp667P1518; KIAA0704; MGC21526; ORP-3;
                     ORP3; OSBP3"
                     /product="oxysterol binding protein-like 3, transcript
                     variant 4"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145322.1"
                     /db_xref="GI:21735583"
                     /db_xref="GeneID:26031"
                     /db_xref="HGNC:16370"
                     /db_xref="MIM:606732"
                     /db_xref="HPRD:09474"
     CDS             complement(join(24839802..24839898,24843934..24844056,
                     24846395..24846521,24849426..24849570,24854678..24854822,
                     24856229..24856307,24859794..24859857,24870387..24870524,
                     24874105..24874355,24880309..24880402,24881898..24882032,
                     24888688..24888795,24892123..24892253,24901232..24901388,
                     24902819..24902911,24903115..24903218,24904961..24905084,
                     24905689..24905856,24910351..24910464,24911361..24911414,
                     24911572..24911688,24931996..24932091))
                     /gene="OSBPL3"
                     /gene_synonym="DKFZp667P1518; KIAA0704; MGC21526; ORP-3;
                     ORP3; OSBP3"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="oxysterol-binding protein-related protein 3
                     isoform a"
                     /protein_id="NP_056365.1"
                     /db_xref="GI:14149704"
                     /db_xref="CCDS:CCDS5390.1"
                     /db_xref="GeneID:26031"
                     /db_xref="HGNC:16370"
                     /db_xref="HPRD:09474"
                     /db_xref="MIM:606732"
     CDS             complement(join(24839802..24839898,24843934..24844056,
                     24846395..24846521,24849426..24849570,24854678..24854822,
                     24856229..24856307,24859794..24859857,24870387..24870524,
                     24874105..24874355,24880309..24880402,24881898..24882032,
                     24888688..24888795,24892123..24892253,24901232..24901388,
                     24903115..24903218,24904961..24905084,24905689..24905856,
                     24910351..24910464,24911361..24911414,24911572..24911688,
                     24931996..24932091))
                     /gene="OSBPL3"
                     /gene_synonym="DKFZp667P1518; KIAA0704; MGC21526; ORP-3;
                     ORP3; OSBP3"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="oxysterol-binding protein-related protein 3
                     isoform b"
                     /protein_id="NP_663160.1"
                     /db_xref="GI:21735580"
                     /db_xref="CCDS:CCDS5391.1"
                     /db_xref="GeneID:26031"
                     /db_xref="HGNC:16370"
                     /db_xref="HPRD:09474"
                     /db_xref="MIM:606732"
     CDS             complement(join(24839802..24839898,24843934..24844056,
                     24846395..24846521,24849426..24849570,24854678..24854822,
                     24856229..24856307,24859794..24859857,24870387..24870524,
                     24874105..24874355,24880309..24880402,24881898..24882032,
                     24892123..24892253,24901232..24901388,24902819..24902911,
                     24903115..24903218,24904961..24905084,24905689..24905856,
                     24910351..24910464,24911361..24911414,24911572..24911688,
                     24931996..24932091))
                     /gene="OSBPL3"
                     /gene_synonym="DKFZp667P1518; KIAA0704; MGC21526; ORP-3;
                     ORP3; OSBP3"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="oxysterol-binding protein-related protein 3
                     isoform c"
                     /protein_id="NP_663161.1"
                     /db_xref="GI:21735582"
                     /db_xref="CCDS:CCDS5392.1"
                     /db_xref="GeneID:26031"
                     /db_xref="HGNC:16370"
                     /db_xref="HPRD:09474"
                     /db_xref="MIM:606732"
     CDS             complement(join(24839802..24839898,24843934..24844056,
                     24846395..24846521,24849426..24849570,24854678..24854822,
                     24856229..24856307,24859794..24859857,24870387..24870524,
                     24874105..24874355,24880309..24880402,24881898..24882032,
                     24892123..24892253,24901232..24901388,24903115..24903218,
                     24904961..24905084,24905689..24905856,24910351..24910464,
                     24911361..24911414,24911572..24911688,24931996..24932091))
                     /gene="OSBPL3"
                     /gene_synonym="DKFZp667P1518; KIAA0704; MGC21526; ORP-3;
                     ORP3; OSBP3"
                     /note="isoform d is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="oxysterol-binding protein-related protein 3
                     isoform d"
                     /protein_id="NP_663162.1"
                     /db_xref="GI:21735584"
                     /db_xref="CCDS:CCDS47564.1"
                     /db_xref="GeneID:26031"
                     /db_xref="HGNC:16370"
                     /db_xref="HPRD:09474"
                     /db_xref="MIM:606732"
     gene            complement(24945661..24946221)
                     /gene="LOC100310849"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100310849"
     gene            complement(25158270..25164980)
                     /gene="CYCS"
                     /gene_synonym="CYC; HCS; THC4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54205"
                     /db_xref="HGNC:19986"
                     /db_xref="HPRD:00479"
                     /db_xref="MIM:123970"
     mRNA            complement(join(25158270..25163468,25163570..25163746,
                     25164819..25164980))
                     /gene="CYCS"
                     /gene_synonym="CYC; HCS; THC4"
                     /product="cytochrome c, somatic"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018947.5"
                     /db_xref="GI:300863084"
                     /db_xref="GeneID:54205"
                     /db_xref="HGNC:19986"
                     /db_xref="HPRD:00479"
                     /db_xref="MIM:123970"
     CDS             complement(join(25163320..25163468,25163570..25163738))
                     /gene="CYCS"
                     /gene_synonym="CYC; HCS; THC4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytochrome c"
                     /protein_id="NP_061820.1"
                     /db_xref="GI:11128019"
                     /db_xref="CCDS:CCDS5393.1"
                     /db_xref="GeneID:54205"
                     /db_xref="HGNC:19986"
                     /db_xref="HPRD:00479"
                     /db_xref="MIM:123970"
     gene            complement(25174316..25219817)
                     /gene="C7orf31"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:136895"
                     /db_xref="HGNC:21722"
                     /db_xref="HPRD:12919"
     mRNA            complement(join(25174316..25176412,25181860..25181951,
                     25182259..25182433,25191215..25191303,25194630..25194811,
                     25198120..25198149,25200808..25200879,25207908..25208084,
                     25218794..25218951,25219281..25219817))
                     /gene="C7orf31"
                     /product="chromosome 7 open reading frame 31"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138811.3"
                     /db_xref="GI:38570063"
                     /db_xref="GeneID:136895"
                     /db_xref="HGNC:21722"
                     /db_xref="HPRD:12919"
     CDS             complement(join(25175591..25176412,25181860..25181951,
                     25182259..25182433,25191215..25191303,25194630..25194811,
                     25198120..25198149,25200808..25200879,25207908..25208084,
                     25218794..25218927))
                     /gene="C7orf31"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC136895"
                     /protein_id="NP_620166.3"
                     /db_xref="GI:38570064"
                     /db_xref="CCDS:CCDS5394.1"
                     /db_xref="GeneID:136895"
                     /db_xref="HGNC:21722"
                     /db_xref="HPRD:12919"
     gene            complement(25251783..25252604)
                     /gene="RPL7AP41"
                     /gene_synonym="RPL7A_16_795"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271213"
                     /db_xref="HGNC:36403"
     gene            complement(25264189..25268105)
                     /gene="NPVF"
                     /gene_synonym="C7orf9; RFRP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64111"
                     /db_xref="HGNC:13782"
     mRNA            complement(join(25264189..25264792,25266245..25266645,
                     25267921..25268105))
                     /gene="NPVF"
                     /gene_synonym="C7orf9; RFRP"
                     /product="neuropeptide VF precursor"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022150.3"
                     /db_xref="GI:93204874"
                     /db_xref="GeneID:64111"
                     /db_xref="HGNC:13782"
     CDS             complement(join(25264741..25264792,25266245..25266645,
                     25267921..25268058))
                     /gene="NPVF"
                     /gene_synonym="C7orf9; RFRP"
                     /exception="mismatches in translation"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="FMRFamide-related peptides"
                     /protein_id="NP_071433.3"
                     /db_xref="GI:93204875"
                     /db_xref="CCDS:CCDS5395.1"
                     /db_xref="GeneID:64111"
                     /db_xref="HGNC:13782"
     gene            complement(25729016..25729690)
                     /gene="UBA52P1"
                     /gene_synonym="RPL40_1_796"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:7312"
                     /db_xref="HGNC:12459"
     gene            complement(25870911..25871467)
                     /gene="LOC100506236"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /db_xref="GeneID:100506236"
     misc_RNA        complement(join(25870911..25871179,25871386..25871467))
                     /gene="LOC100506236"
                     /product="hypothetical LOC100506236"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_108752.1"
                     /db_xref="GI:310119926"
                     /db_xref="GeneID:100506236"
     gene            complement(25989539..25989606)
                     /gene="MIR148A"
                     /gene_synonym="hsa-mir-148; MIRN148; MIRN148A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:406940"
                     /db_xref="HGNC:31535"
                     /db_xref="MIM:613786"
                     /db_xref="miRBase:MI0000253"
     ncRNA           complement(25989539..25989606)
                     /gene="MIR148A"
                     /gene_synonym="hsa-mir-148; MIRN148; MIRN148A"
                     /ncRNA_class="miRNA"
                     /product="microRNA 148a"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029597.1"
                     /db_xref="GI:262206160"
                     /db_xref="GeneID:406940"
                     /db_xref="HGNC:31535"
                     /db_xref="MIM:613786"
                     /db_xref="miRBase:MI0000253"
     ncRNA           complement(25989539..25989606)
                     /gene="MIR148A"
                     /gene_synonym="hsa-mir-148; MIRN148; MIRN148A"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-148a"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:406940"
                     /db_xref="miRBase:MI0000253"
                     /db_xref="HGNC:31535"
                     /db_xref="MIM:613786"
     gene            26191847..26226757
                     /gene="NFE2L3"
                     /gene_synonym="NRF3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9603"
                     /db_xref="HGNC:7783"
                     /db_xref="HPRD:09162"
                     /db_xref="MIM:604135"
     mRNA            join(26191847..26192688,26217563..26217742,
                     26223321..26223404,26224153..26226757)
                     /gene="NFE2L3"
                     /gene_synonym="NRF3"
                     /product="nuclear factor (erythroid-derived 2)-like 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004289.6"
                     /db_xref="GI:225735556"
                     /db_xref="GeneID:9603"
                     /db_xref="HGNC:7783"
                     /db_xref="HPRD:09162"
                     /db_xref="MIM:604135"
     CDS             join(26192119..26192688,26217563..26217742,
                     26223321..26223404,26224153..26225403)
                     /gene="NFE2L3"
                     /gene_synonym="NRF3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="nuclear factor erythroid 2-related factor 3"
                     /protein_id="NP_004280.5"
                     /db_xref="GI:225735557"
                     /db_xref="CCDS:CCDS5396.1"
                     /db_xref="GeneID:9603"
                     /db_xref="HGNC:7783"
                     /db_xref="HPRD:09162"
                     /db_xref="MIM:604135"
     gene            complement(26229556..26240413)
                     /gene="HNRNPA2B1"
                     /gene_synonym="DKFZp779B0244; FLJ22720; HNRNPA2; HNRNPB1;
                     HNRPA2; HNRPA2B1; HNRPB1; RNPA2; SNRPB1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3181"
                     /db_xref="HGNC:5033"
                     /db_xref="HPRD:02526"
                     /db_xref="MIM:600124"
     mRNA            complement(join(26229556..26231958,26232115..26232197,
                     26232871..26232993,26233195..26233314,26235467..26235529,
                     26236021..26236101,26236177..26236278,26236427..26236637,
                     26236935..26237081,26237242..26237352,26240192..26240413))
                     /gene="HNRNPA2B1"
                     /gene_synonym="DKFZp779B0244; FLJ22720; HNRNPA2; HNRNPB1;
                     HNRPA2; HNRPA2B1; HNRPB1; RNPA2; SNRPB1"
                     /product="heterogeneous nuclear ribonucleoprotein A2/B1,
                     transcript variant A2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002137.3"
                     /db_xref="GI:156151373"
                     /db_xref="GeneID:3181"
                     /db_xref="HGNC:5033"
                     /db_xref="HPRD:02526"
                     /db_xref="MIM:600124"
     mRNA            complement(join(26229556..26231958,26232115..26232197,
                     26232871..26232993,26233195..26233314,26235467..26235529,
                     26236021..26236101,26236177..26236278,26236427..26236637,
                     26236935..26237081,26237242..26237352,26237451..26237486,
                     26240192..26240413))
                     /gene="HNRNPA2B1"
                     /gene_synonym="DKFZp779B0244; FLJ22720; HNRNPA2; HNRNPB1;
                     HNRPA2; HNRPA2B1; HNRPB1; RNPA2; SNRPB1"
                     /product="heterogeneous nuclear ribonucleoprotein A2/B1,
                     transcript variant B1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_031243.2"
                     /db_xref="GI:156151374"
                     /db_xref="GeneID:3181"
                     /db_xref="HGNC:5033"
                     /db_xref="HPRD:02526"
                     /db_xref="MIM:600124"
     CDS             complement(join(26232136..26232197,26232871..26232993,
                     26233195..26233314,26235467..26235529,26236021..26236101,
                     26236177..26236278,26236427..26236637,26236935..26237081,
                     26237242..26237352,26240192..26240197))
                     /gene="HNRNPA2B1"
                     /gene_synonym="DKFZp779B0244; FLJ22720; HNRNPA2; HNRNPB1;
                     HNRPA2; HNRPA2B1; HNRPB1; RNPA2; SNRPB1"
                     /note="isoform A2 is encoded by transcript variant A2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="heterogeneous nuclear ribonucleoproteins A2/B1
                     isoform A2"
                     /protein_id="NP_002128.1"
                     /db_xref="GI:4504447"
                     /db_xref="CCDS:CCDS5397.1"
                     /db_xref="GeneID:3181"
                     /db_xref="HGNC:5033"
                     /db_xref="HPRD:02526"
                     /db_xref="MIM:600124"
     CDS             complement(join(26232136..26232197,26232871..26232993,
                     26233195..26233314,26235467..26235529,26236021..26236101,
                     26236177..26236278,26236427..26236637,26236935..26237081,
                     26237242..26237352,26237451..26237486,26240192..26240197))
                     /gene="HNRNPA2B1"
                     /gene_synonym="DKFZp779B0244; FLJ22720; HNRNPA2; HNRNPB1;
                     HNRPA2; HNRPA2B1; HNRPB1; RNPA2; SNRPB1"
                     /note="isoform B1 is encoded by transcript variant B1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="heterogeneous nuclear ribonucleoproteins A2/B1
                     isoform B1"
                     /protein_id="NP_112533.1"
                     /db_xref="GI:14043072"
                     /db_xref="CCDS:CCDS43557.1"
                     /db_xref="GeneID:3181"
                     /db_xref="HGNC:5033"
                     /db_xref="HPRD:02526"
                     /db_xref="MIM:600124"
     gene            26240831..26253227
                     /gene="CBX3"
                     /gene_synonym="HECH; HP1-GAMMA; HP1Hs-gamma"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:11335"
                     /db_xref="HGNC:1553"
                     /db_xref="HPRD:05130"
                     /db_xref="MIM:604477"
     mRNA            join(26240831..26241181,26242591..26242642,
                     26245988..26246130,26248013..26248175,26251282..26251376,
                     26251702..26253227)
                     /gene="CBX3"
                     /gene_synonym="HECH; HP1-GAMMA; HP1Hs-gamma"
                     /product="chromobox homolog 3, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_007276.4"
                     /db_xref="GI:325197149"
                     /db_xref="GeneID:11335"
                     /db_xref="HGNC:1553"
                     /db_xref="MIM:604477"
                     /db_xref="HPRD:05130"
     mRNA            join(26241324..26241446,26242591..26242642,
                     26245988..26246130,26248013..26248175,26251282..26251376,
                     26251702..26253227)
                     /gene="CBX3"
                     /gene_synonym="HECH; HP1-GAMMA; HP1Hs-gamma"
                     /product="chromobox homolog 3, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016587.3"
                     /db_xref="GI:325197147"
                     /db_xref="GeneID:11335"
                     /db_xref="HGNC:1553"
                     /db_xref="HPRD:05130"
                     /db_xref="MIM:604477"
     CDS             join(26242619..26242642,26245988..26246130,
                     26248013..26248175,26251282..26251376,26251702..26251828)
                     /gene="CBX3"
                     /gene_synonym="HECH; HP1-GAMMA; HP1Hs-gamma"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="chromobox protein homolog 3"
                     /protein_id="NP_057671.2"
                     /db_xref="GI:20544151"
                     /db_xref="CCDS:CCDS5398.1"
                     /db_xref="GeneID:11335"
                     /db_xref="HGNC:1553"
                     /db_xref="HPRD:05130"
                     /db_xref="MIM:604477"
     CDS             join(26242619..26242642,26245988..26246130,
                     26248013..26248175,26251282..26251376,26251702..26251828)
                     /gene="CBX3"
                     /gene_synonym="HECH; HP1-GAMMA; HP1Hs-gamma"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="chromobox protein homolog 3"
                     /protein_id="NP_009207.2"
                     /db_xref="GI:15082258"
                     /db_xref="CCDS:CCDS5398.1"
                     /db_xref="GeneID:11335"
                     /db_xref="HGNC:1553"
                     /db_xref="HPRD:05130"
                     /db_xref="MIM:604477"
     gene            26315781..26316286
                     /gene="RPL23P7"
                     /gene_synonym="RPL23_5_797"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442659"
                     /db_xref="HGNC:36215"
     gene            26331515..26413949
                     /gene="SNX10"
                     /gene_synonym="MGC33054"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:29887"
                     /db_xref="HGNC:14974"
                     /db_xref="HPRD:15409"
     mRNA            join(26331515..26331753,26386040..26386086,
                     26400595..26400681,26404155..26404255,26404667..26404765,
                     26411441..26411653,26412111..26413949)
                     /gene="SNX10"
                     /gene_synonym="MGC33054"
                     /product="sorting nexin 10, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199835.1"
                     /db_xref="GI:315360659"
                     /db_xref="GeneID:29887"
                     /db_xref="HGNC:14974"
                     /db_xref="HPRD:15409"
     mRNA            join(26331515..26331706,26386040..26386086,
                     26400595..26400681,26404155..26404255,26404667..26404765,
                     26411441..26411653,26412111..26413949)
                     /gene="SNX10"
                     /gene_synonym="MGC33054"
                     /product="sorting nexin 10, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013322.2"
                     /db_xref="GI:23111022"
                     /db_xref="GeneID:29887"
                     /db_xref="HGNC:14974"
                     /db_xref="HPRD:15409"
     misc_RNA        join(26331515..26331706,26386040..26386086,
                     26396627..26396747,26400595..26400681,26404155..26404255,
                     26404667..26404765,26411441..26411653,26412111..26413949)
                     /gene="SNX10"
                     /gene_synonym="MGC33054"
                     /product="sorting nexin 10, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037670.1"
                     /db_xref="GI:315360665"
                     /db_xref="GeneID:29887"
                     /db_xref="HGNC:14974"
                     /db_xref="HPRD:15409"
     CDS             join(26386063..26386086,26400595..26400681,
                     26404155..26404255,26404667..26404765,26411441..26411653,
                     26412111..26412192)
                     /gene="SNX10"
                     /gene_synonym="MGC33054"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="sorting nexin-10 isoform 1"
                     /protein_id="NP_001186764.1"
                     /db_xref="GI:315360660"
                     /db_xref="GeneID:29887"
                     /db_xref="HGNC:14974"
                     /db_xref="HPRD:15409"
     CDS             join(26386063..26386086,26400595..26400681,
                     26404155..26404255,26404667..26404765,26411441..26411653,
                     26412111..26412192)
                     /gene="SNX10"
                     /gene_synonym="MGC33054"
                     /note="isoform 1 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="sorting nexin-10 isoform 1"
                     /protein_id="NP_037454.2"
                     /db_xref="GI:23111023"
                     /db_xref="CCDS:CCDS5399.1"
                     /db_xref="GeneID:29887"
                     /db_xref="HGNC:14974"
                     /db_xref="HPRD:15409"
     mRNA            join(26400504..26400681,26404155..26404255,
                     26404667..26404765,26411441..26411653,26412111..26413949)
                     /gene="SNX10"
                     /gene_synonym="MGC33054"
                     /product="sorting nexin 10, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199837.1"
                     /db_xref="GI:315360661"
                     /db_xref="GeneID:29887"
                     /db_xref="HGNC:14974"
                     /db_xref="HPRD:15409"
     CDS             join(26400580..26400681,26404155..26404255,
                     26404667..26404765,26411441..26411653,26412111..26412192)
                     /gene="SNX10"
                     /gene_synonym="MGC33054"
                     /note="isoform 2 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="sorting nexin-10 isoform 2"
                     /protein_id="NP_001186766.1"
                     /db_xref="GI:315360662"
                     /db_xref="GeneID:29887"
                     /db_xref="HGNC:14974"
                     /db_xref="HPRD:15409"
     mRNA            join(26403945..26404122,26404667..26404765,
                     26411441..26411653,26412111..26413949)
                     /gene="SNX10"
                     /gene_synonym="MGC33054"
                     /product="sorting nexin 10, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199838.1"
                     /db_xref="GI:315360663"
                     /db_xref="GeneID:29887"
                     /db_xref="HGNC:14974"
                     /db_xref="HPRD:15409"
     CDS             join(26404707..26404765,26411441..26411653,
                     26412111..26412192)
                     /gene="SNX10"
                     /gene_synonym="MGC33054"
                     /note="isoform 3 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="sorting nexin-10 isoform 3"
                     /protein_id="NP_001186767.1"
                     /db_xref="GI:315360664"
                     /db_xref="GeneID:29887"
                     /db_xref="HGNC:14974"
                     /db_xref="HPRD:15409"
     gene            26526288..26535987
                     /gene="LOC441204"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:441204"
     misc_RNA        join(26526288..26526317,26533415..26534508,
                     26534639..26534819,26535429..26535501,26535734..26535987)
                     /gene="LOC441204"
                     /product="hypothetical locus LOC441204"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_015364.1"
                     /db_xref="GI:168693610"
                     /db_xref="GeneID:441204"
     gene            complement(26572740..26578444)
                     /gene="KIAA0087"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9808"
                     /db_xref="HGNC:22191"
     misc_RNA        complement(join(26572740..26576639,26578025..26578444))
                     /gene="KIAA0087"
                     /product="KIAA0087"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_022006.1"
                     /db_xref="GI:182765458"
                     /db_xref="GeneID:9808"
                     /db_xref="HGNC:22191"
     gene            26591441..26596826
                     /gene="LOC100506289"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 5 ESTs"
                     /db_xref="GeneID:100506289"
     misc_RNA        join(26591441..26591829,26594428..26596826)
                     /gene="LOC100506289"
                     /product="hypothetical LOC100506289"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 5 ESTs"
                     /transcript_id="XR_108753.1"
                     /db_xref="GI:310119929"
                     /db_xref="GeneID:100506289"
     gene            26677490..26686924
                     /gene="C7orf71"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285941"
                     /db_xref="HGNC:22364"
     mRNA            join(26677490..26677555,26678114..26678963,
                     26680315..26680383,26685919..26686924)
                     /gene="C7orf71"
                     /product="chromosome 7 open reading frame 71"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145531.1"
                     /db_xref="GI:224465157"
                     /db_xref="GeneID:285941"
                     /db_xref="HGNC:22364"
     CDS             join(26678764..26678963,26680315..26680383,
                     26685919..26686159)
                     /gene="C7orf71"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC285941"
                     /protein_id="NP_001139003.1"
                     /db_xref="GI:224465158"
                     /db_xref="CCDS:CCDS47565.1"
                     /db_xref="GeneID:285941"
                     /db_xref="HGNC:22364"
     gene            complement(26706687..26904341)
                     /gene="SKAP2"
                     /gene_synonym="MGC10411; MGC33304; PRAP; RA70; SAPS;
                     SCAP2; SKAP-HOM; SKAP55R"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8935"
                     /db_xref="HGNC:15687"
                     /db_xref="HPRD:05558"
                     /db_xref="MIM:605215"
     mRNA            complement(join(26706687..26709275,26709710..26709811,
                     26724355..26724467,26729904..26729981,26765047..26765184,
                     26765542..26765605,26766501..26766625,26778414..26778497,
                     26779506..26779583,26883649..26883756,26893756..26893781,
                     26894404..26894509,26903982..26904341))
                     /gene="SKAP2"
                     /gene_synonym="MGC10411; MGC33304; PRAP; RA70; SAPS;
                     SCAP2; SKAP-HOM; SKAP55R"
                     /product="src kinase associated phosphoprotein 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003930.3"
                     /db_xref="GI:38202227"
                     /db_xref="GeneID:8935"
                     /db_xref="HGNC:15687"
                     /db_xref="HPRD:05558"
                     /db_xref="MIM:605215"
     CDS             complement(join(26709719..26709811,26724355..26724467,
                     26729904..26729981,26765047..26765184,26765542..26765605,
                     26766501..26766625,26778414..26778497,26779506..26779583,
                     26883649..26883756,26893756..26893781,26894404..26894509,
                     26903982..26904048))
                     /gene="SKAP2"
                     /gene_synonym="MGC10411; MGC33304; PRAP; RA70; SAPS;
                     SCAP2; SKAP-HOM; SKAP55R"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="src kinase-associated phosphoprotein 2"
                     /protein_id="NP_003921.2"
                     /db_xref="GI:16753212"
                     /db_xref="CCDS:CCDS5400.1"
                     /db_xref="GeneID:8935"
                     /db_xref="HGNC:15687"
                     /db_xref="HPRD:05558"
                     /db_xref="MIM:605215"
     gene            26961723..26962585
                     /gene="RPL7AP38"
                     /gene_synonym="RPL7A_11_798"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442660"
                     /db_xref="HGNC:36161"
     gene            complement(27022423..27022986)
                     /gene="HMGB3P20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442661"
                     /db_xref="HGNC:39312"
     gene            27063289..27066099
                     /gene="TPM3P4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402643"
                     /db_xref="HGNC:39167"
     gene            27087754..27088508
                     /gene="NHP2P2"
                     /gene_synonym="TCAG_30283"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442290"
                     /db_xref="HGNC:22797"
     gene            complement(27132612..27135625)
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F; MGC45232"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3198"
                     /db_xref="HGNC:5099"
                     /db_xref="MIM:142955"
     mRNA            complement(join(27132612..27134414,27134880..27135625))
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F; MGC45232"
                     /product="homeobox A1, transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005522.4"
                     /db_xref="GI:84697023"
                     /db_xref="GeneID:3198"
                     /db_xref="HGNC:5099"
                     /db_xref="HPRD:00843"
                     /db_xref="MIM:142955"
     mRNA            complement(join(27132612..27134414,27134880..27134974,
                     27135178..27135625))
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F; MGC45232"
                     /product="homeobox A1, transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_153620.2"
                     /db_xref="GI:84697021"
                     /db_xref="GeneID:3198"
                     /db_xref="HGNC:5099"
                     /db_xref="MIM:142955"
     CDS             complement(join(27134059..27134414,27134880..27135531))
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F; MGC45232"
                     /exception="mismatches in translation"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein Hox-A1 isoform a"
                     /protein_id="NP_005513.1"
                     /db_xref="GI:5031761"
                     /db_xref="CCDS:CCDS5401.1"
                     /db_xref="GeneID:3198"
                     /db_xref="HGNC:5099"
                     /db_xref="MIM:142955"
     CDS             complement(join(27134915..27134974,27135178..27135531))
                     /gene="HOXA1"
                     /gene_synonym="BSAS; HOX1; HOX1F; MGC45232"
                     /exception="mismatches in translation"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein Hox-A1 isoform b"
                     /protein_id="NP_705873.2"
                     /db_xref="GI:84697022"
                     /db_xref="CCDS:CCDS5402.2"
                     /db_xref="GeneID:3198"
                     /db_xref="HGNC:5099"
                     /db_xref="MIM:142955"
     gene            27135713..27139877
                     /gene="HOTAIRM1"
                     /gene_synonym="HOXA1-AS1; NCRNA00179"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100506311"
                     /db_xref="HGNC:37117"
     misc_RNA        join(27135713..27136007,27138717..27138985,
                     27139398..27139877)
                     /gene="HOTAIRM1"
                     /gene_synonym="HOXA1-AS1; NCRNA00179"
                     /product="HOXA transcript antisense RNA, myeloid-specific
                     1 (non-protein coding), transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038366.1"
                     /db_xref="GI:335353771"
                     /db_xref="GeneID:100506311"
                     /db_xref="HGNC:37117"
     misc_RNA        join(27135713..27136007,27139398..27139877)
                     /gene="HOTAIRM1"
                     /gene_synonym="HOXA1-AS1; NCRNA00179"
                     /product="HOXA transcript antisense RNA, myeloid-specific
                     1 (non-protein coding), transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038367.1"
                     /db_xref="GI:335353772"
                     /db_xref="GeneID:100506311"
                     /db_xref="HGNC:37117"
     gene            complement(27139973..27142394)
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3199"
                     /db_xref="HGNC:5103"
                     /db_xref="HPRD:05252"
                     /db_xref="MIM:604685"
     mRNA            complement(join(27139973..27141084,27141729..27142394))
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /product="homeobox A2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006735.3"
                     /db_xref="GI:37596298"
                     /db_xref="GeneID:3199"
                     /db_xref="HGNC:5103"
                     /db_xref="HPRD:05252"
                     /db_xref="MIM:604685"
     CDS             complement(join(27140345..27141084,27141729..27142119))
                     /gene="HOXA2"
                     /gene_synonym="HOX1K"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein Hox-A2"
                     /protein_id="NP_006726.1"
                     /db_xref="GI:10140847"
                     /db_xref="CCDS:CCDS5403.1"
                     /db_xref="GeneID:3199"
                     /db_xref="HGNC:5103"
                     /db_xref="HPRD:05252"
                     /db_xref="MIM:604685"
     gene            complement(27145809..27166639)
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E; MGC10155"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3200"
                     /db_xref="HGNC:5104"
                     /db_xref="HPRD:00842"
                     /db_xref="MIM:142954"
     mRNA            complement(join(27145809..27148339,27149734..27150379,
                     27162178..27162261,27166505..27166639))
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E; MGC10155"
                     /product="homeobox A3, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_153631.2"
                     /db_xref="GI:84043947"
                     /db_xref="GeneID:3200"
                     /db_xref="HGNC:5104"
                     /db_xref="HPRD:00842"
                     /db_xref="MIM:142954"
     mRNA            complement(join(27145809..27148339,27149734..27150379,
                     27159135..27159214))
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E; MGC10155"
                     /product="homeobox A3, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_030661.4"
                     /db_xref="GI:84043946"
                     /db_xref="GeneID:3200"
                     /db_xref="HGNC:5104"
                     /db_xref="HPRD:00842"
                     /db_xref="MIM:142954"
     CDS             complement(join(27147534..27148339,27149734..27150259))
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E; MGC10155"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein Hox-A3 isoform a"
                     /protein_id="NP_109377.1"
                     /db_xref="GI:13562112"
                     /db_xref="CCDS:CCDS5404.1"
                     /db_xref="GeneID:3200"
                     /db_xref="HGNC:5104"
                     /db_xref="HPRD:00842"
                     /db_xref="MIM:142954"
     CDS             complement(join(27147534..27148339,27149734..27150259))
                     /gene="HOXA3"
                     /gene_synonym="HOX1; HOX1E; MGC10155"
                     /note="isoform a is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein Hox-A3 isoform a"
                     /protein_id="NP_705895.1"
                     /db_xref="GI:24497513"
                     /db_xref="CCDS:CCDS5404.1"
                     /db_xref="GeneID:3200"
                     /db_xref="HGNC:5104"
                     /db_xref="HPRD:00842"
                     /db_xref="MIM:142954"
     gene            27154967..27163437
                     /gene="LOC285943"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 mRNAs, 30 ESTs, 1 Protein"
                     /db_xref="GeneID:285943"
     misc_RNA        join(27154967..27155962,27161538..27162504)
                     /gene="LOC285943"
                     /product="hypothetical LOC285943"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 26 ESTs, 1 Protein"
                     /transcript_id="XR_108755.1"
                     /db_xref="GI:310119931"
                     /db_xref="GeneID:285943"
     gene            complement(27168126..27170399)
                     /gene="HOXA4"
                     /gene_synonym="HOX1; HOX1D"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3201"
                     /db_xref="HGNC:5105"
                     /db_xref="HPRD:00841"
                     /db_xref="MIM:142953"
     mRNA            complement(join(27168126..27169190,27169737..27170399))
                     /gene="HOXA4"
                     /gene_synonym="HOX1; HOX1D"
                     /product="homeobox A4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002141.4"
                     /db_xref="GI:148613881"
                     /db_xref="GeneID:3201"
                     /db_xref="HGNC:5105"
                     /db_xref="HPRD:00841"
                     /db_xref="MIM:142953"
     CDS             complement(join(27168844..27169190,27169737..27170352))
                     /gene="HOXA4"
                     /gene_synonym="HOX1; HOX1D"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein Hox-A4"
                     /protein_id="NP_002132.3"
                     /db_xref="GI:148613882"
                     /db_xref="CCDS:CCDS5405.1"
                     /db_xref="GeneID:3201"
                     /db_xref="HGNC:5105"
                     /db_xref="HPRD:00841"
                     /db_xref="MIM:142953"
     gene            27179983..27195547
                     /gene="LOC100133311"
                     /gene_synonym="FLJ34614; FLJ34835; FLJ39015"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100133311"
     misc_RNA        join(27179983..27180158,27191194..27191300,
                     27191913..27195547)
                     /gene="LOC100133311"
                     /gene_synonym="FLJ34614; FLJ34835; FLJ39015"
                     /product="hypothetical LOC100133311, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038832.1"
                     /db_xref="GI:336285459"
                     /db_xref="GeneID:100133311"
     gene            complement(27180671..27183287)
                     /gene="HOXA5"
                     /gene_synonym="HOX1; HOX1.3; HOX1C; MGC9376"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3202"
                     /db_xref="HGNC:5106"
                     /db_xref="HPRD:00840"
                     /db_xref="MIM:142952"
     mRNA            complement(join(27180671..27181704,27182665..27183287))
                     /gene="HOXA5"
                     /gene_synonym="HOX1; HOX1.3; HOX1C; MGC9376"
                     /product="homeobox A5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_019102.3"
                     /db_xref="GI:324073512"
                     /db_xref="GeneID:3202"
                     /db_xref="HGNC:5106"
                     /db_xref="HPRD:00840"
                     /db_xref="MIM:142952"
     CDS             complement(join(27181454..27181704,27182665..27183226))
                     /gene="HOXA5"
                     /gene_synonym="HOX1; HOX1.3; HOX1C; MGC9376"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein Hox-A5"
                     /protein_id="NP_061975.2"
                     /db_xref="GI:24497517"
                     /db_xref="CCDS:CCDS5406.1"
                     /db_xref="GeneID:3202"
                     /db_xref="HGNC:5106"
                     /db_xref="HPRD:00840"
                     /db_xref="MIM:142952"
     gene            complement(27185202..27187393)
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3203"
                     /db_xref="HGNC:5107"
                     /db_xref="HPRD:00839"
                     /db_xref="MIM:142951"
     mRNA            complement(join(27185202..27185536,27186927..27187393))
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /product="homeobox A6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024014.3"
                     /db_xref="GI:334724446"
                     /db_xref="GeneID:3203"
                     /db_xref="HGNC:5107"
                     /db_xref="HPRD:00839"
                     /db_xref="MIM:142951"
     CDS             complement(join(27185277..27185536,27186927..27187368))
                     /gene="HOXA6"
                     /gene_synonym="HOX1; HOX1.2; HOX1B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein Hox-A6"
                     /protein_id="NP_076919.1"
                     /db_xref="GI:13489077"
                     /db_xref="CCDS:CCDS5407.1"
                     /db_xref="GeneID:3203"
                     /db_xref="HGNC:5107"
                     /db_xref="HPRD:00839"
                     /db_xref="MIM:142951"
     misc_RNA        join(27186782..27187031,27191194..27191300,
                     27191913..27195547)
                     /gene="LOC100133311"
                     /gene_synonym="FLJ34614; FLJ34835; FLJ39015"
                     /product="hypothetical LOC100133311, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038831.1"
                     /db_xref="GI:336285458"
                     /db_xref="GeneID:100133311"
     gene            complement(27193335..27196296)
                     /gene="HOXA7"
                     /gene_synonym="ANTP; HOX1; HOX1.1; HOX1A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3204"
                     /db_xref="HGNC:5108"
                     /db_xref="HPRD:00838"
                     /db_xref="MIM:142950"
     mRNA            complement(join(27193335..27194841,27195786..27196296))
                     /gene="HOXA7"
                     /gene_synonym="ANTP; HOX1; HOX1.1; HOX1A"
                     /product="homeobox A7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006896.3"
                     /db_xref="GI:84105267"
                     /db_xref="GeneID:3204"
                     /db_xref="HGNC:5108"
                     /db_xref="HPRD:00838"
                     /db_xref="MIM:142950"
     CDS             complement(join(27194528..27194841,27195786..27196164))
                     /gene="HOXA7"
                     /gene_synonym="ANTP; HOX1; HOX1.1; HOX1A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein Hox-A7"
                     /protein_id="NP_008827.2"
                     /db_xref="GI:24497556"
                     /db_xref="CCDS:CCDS5408.1"
                     /db_xref="GeneID:3204"
                     /db_xref="HGNC:5108"
                     /db_xref="HPRD:00838"
                     /db_xref="MIM:142950"
     gene            complement(27202057..27219880)
                     /gene="HOXA10-HOXA9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100534589"
     misc_RNA        complement(join(27202057..27203460,27204497..27204586,
                     27219265..27219880))
                     /gene="HOXA10-HOXA9"
                     /product="HOXA10-HOXA9 readthrough"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037940.1"
                     /db_xref="GI:325652057"
                     /db_xref="GeneID:100534589"
     gene            complement(27202057..27205149)
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G; MGC1934"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3205"
                     /db_xref="HGNC:5109"
                     /db_xref="HPRD:00844"
                     /db_xref="MIM:142956"
     mRNA            complement(join(27202057..27203460,27204497..27205149))
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G; MGC1934"
                     /product="homeobox A9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152739.3"
                     /db_xref="GI:84043950"
                     /db_xref="GeneID:3205"
                     /db_xref="HGNC:5109"
                     /db_xref="HPRD:00844"
                     /db_xref="MIM:142956"
     CDS             complement(join(27203222..27203460,27204497..27205076))
                     /gene="HOXA9"
                     /gene_synonym="ABD-B; HOX1; HOX1.7; HOX1G; MGC1934"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein Hox-A9"
                     /protein_id="NP_689952.1"
                     /db_xref="GI:23097236"
                     /db_xref="CCDS:CCDS5409.1"
                     /db_xref="GeneID:3205"
                     /db_xref="HGNC:5109"
                     /db_xref="HPRD:00844"
                     /db_xref="MIM:142956"
     gene            complement(27209099..27209182)
                     /gene="MIR196B"
                     /gene_synonym="miR-196b; MIRN196B; miRNA196B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:442920"
                     /db_xref="HGNC:31790"
                     /db_xref="MIM:609688"
                     /db_xref="miRBase:MI0001150"
     ncRNA           complement(27209099..27209182)
                     /gene="MIR196B"
                     /gene_synonym="miR-196b; MIRN196B; miRNA196B"
                     /ncRNA_class="miRNA"
                     /product="microRNA 196b"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029911.1"
                     /db_xref="GI:262205181"
                     /db_xref="GeneID:442920"
                     /db_xref="HGNC:31790"
                     /db_xref="MIM:609688"
                     /db_xref="miRBase:MI0001150"
     ncRNA           complement(27209099..27209182)
                     /gene="MIR196B"
                     /gene_synonym="miR-196b; MIRN196B; miRNA196B"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-196b"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:442920"
                     /db_xref="miRBase:MI0001150"
                     /db_xref="HGNC:31790"
                     /db_xref="MIM:609688"
     gene            complement(27210210..27219880)
                     /gene="HOXA10"
                     /gene_synonym="HOX1; HOX1.8; HOX1H; MGC12859; PL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3206"
                     /db_xref="HGNC:5100"
                     /db_xref="MIM:142957"
     misc_RNA        complement(join(27210210..27211792,27219265..27219880))
                     /gene="HOXA10"
                     /gene_synonym="HOX1; HOX1.8; HOX1H; MGC12859; PL"
                     /product="homeobox A10, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037939.1"
                     /db_xref="GI:325652049"
                     /db_xref="GeneID:3206"
                     /db_xref="HGNC:5100"
                     /db_xref="MIM:142957"
     mRNA            complement(join(27210210..27211792,27212968..27213955))
                     /gene="HOXA10"
                     /gene_synonym="HOX1; HOX1.8; HOX1H; MGC12859; PL"
                     /product="homeobox A10, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018951.3"
                     /db_xref="GI:83977447"
                     /db_xref="GeneID:3206"
                     /db_xref="HGNC:5100"
                     /db_xref="HPRD:00845"
                     /db_xref="MIM:142957"
     CDS             complement(join(27211518..27211792,27212968..27213925))
                     /gene="HOXA10"
                     /gene_synonym="HOX1; HOX1.8; HOX1H; MGC12859; PL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein Hox-A10"
                     /protein_id="NP_061824.3"
                     /db_xref="GI:182765442"
                     /db_xref="CCDS:CCDS5410.2"
                     /db_xref="GeneID:3206"
                     /db_xref="HGNC:5100"
                     /db_xref="MIM:142957"
     gene            complement(27220776..27224835)
                     /gene="HOXA11"
                     /gene_synonym="HOX1; HOX1I"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3207"
                     /db_xref="HGNC:5101"
                     /db_xref="HPRD:00846"
                     /db_xref="MIM:142958"
     mRNA            complement(join(27220776..27222647,27224055..27224835))
                     /gene="HOXA11"
                     /gene_synonym="HOX1; HOX1I"
                     /product="homeobox A11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005523.5"
                     /db_xref="GI:84105266"
                     /db_xref="GeneID:3207"
                     /db_xref="HGNC:5101"
                     /db_xref="HPRD:00846"
                     /db_xref="MIM:142958"
     CDS             complement(join(27222415..27222647,27224055..27224763))
                     /gene="HOXA11"
                     /gene_synonym="HOX1; HOX1I"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein Hox-A11"
                     /protein_id="NP_005514.1"
                     /db_xref="GI:5031759"
                     /db_xref="CCDS:CCDS5411.1"
                     /db_xref="GeneID:3207"
                     /db_xref="HGNC:5101"
                     /db_xref="HPRD:00846"
                     /db_xref="MIM:142958"
     gene            27225027..27228912
                     /gene="HOXA11-AS1"
                     /gene_synonym="HOXA11-AS; HOXA11AS; HOXA11S; NCRNA00076"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221883"
                     /db_xref="HGNC:24957"
                     /db_xref="MIM:607530"
     ncRNA           join(27225027..27225882,27228220..27228912)
                     /gene="HOXA11-AS1"
                     /gene_synonym="HOXA11-AS; HOXA11AS; HOXA11S; NCRNA00076"
                     /ncRNA_class="antisense_RNA"
                     /product="HOXA11 antisense RNA 1 (non-protein coding)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_002795.2"
                     /db_xref="GI:197313738"
                     /db_xref="GeneID:221883"
                     /db_xref="HGNC:24957"
                     /db_xref="MIM:607530"
     gene            complement(27236499..27239725)
                     /gene="HOXA13"
                     /gene_synonym="HOX1; HOX1J"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3209"
                     /db_xref="HGNC:5102"
                     /db_xref="HPRD:00847"
                     /db_xref="MIM:142959"
     mRNA            complement(join(27236499..27238061,27238775..27239725))
                     /gene="HOXA13"
                     /gene_synonym="HOX1; HOX1J"
                     /product="homeobox A13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000522.4"
                     /db_xref="GI:171906561"
                     /db_xref="GeneID:3209"
                     /db_xref="HGNC:5102"
                     /db_xref="HPRD:00847"
                     /db_xref="MIM:142959"
     CDS             complement(join(27237817..27238061,27238775..27239696))
                     /gene="HOXA13"
                     /gene_synonym="HOX1; HOX1J"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein Hox-A13"
                     /protein_id="NP_000513.2"
                     /db_xref="GI:24497554"
                     /db_xref="CCDS:CCDS5412.1"
                     /db_xref="GeneID:3209"
                     /db_xref="HGNC:5102"
                     /db_xref="HPRD:00847"
                     /db_xref="MIM:142959"
     gene            27240040..27246139
                     /gene="HOTTIP"
                     /gene_synonym="FLJ36668; HOXA13-AS1; NCRNA00213"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100316868"
                     /db_xref="HGNC:37461"
                     /db_xref="MIM:614060"
     misc_RNA        join(27240040..27240140,27240242..27241300,
                     27241455..27242257,27244331..27246139)
                     /gene="HOTTIP"
                     /gene_synonym="FLJ36668; HOXA13-AS1; NCRNA00213"
                     /product="HOXA distal transcript antisense RNA
                     (non-protein coding)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037843.2"
                     /db_xref="GI:331284131"
                     /db_xref="GeneID:100316868"
                     /db_xref="HGNC:37461"
                     /db_xref="MIM:614060"
     gene            complement(27278862..27280847)
                     /gene="LOC100129463"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /db_xref="GeneID:100129463"
     misc_RNA        complement(join(27278862..27279594,27280824..27280847))
                     /gene="LOC100129463"
                     /product="hypothetical LOC100129463"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_108760.1"
                     /db_xref="GI:310119936"
                     /db_xref="GeneID:100129463"
     gene            27282164..27286192
                     /gene="EVX1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2128"
                     /db_xref="HGNC:3506"
                     /db_xref="HPRD:00876"
                     /db_xref="MIM:142996"
     mRNA            join(27282164..27283076,27284667..27284923,
                     27285505..27286192)
                     /gene="EVX1"
                     /product="even-skipped homeobox 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001989.3"
                     /db_xref="GI:84043964"
                     /db_xref="GeneID:2128"
                     /db_xref="HGNC:3506"
                     /db_xref="HPRD:00876"
                     /db_xref="MIM:142996"
     CDS             join(27282650..27283076,27284667..27284923,
                     27285505..27286044)
                     /gene="EVX1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox even-skipped homolog protein 1"
                     /protein_id="NP_001980.1"
                     /db_xref="GI:4503615"
                     /db_xref="CCDS:CCDS5413.1"
                     /db_xref="GeneID:2128"
                     /db_xref="HGNC:3506"
                     /db_xref="HPRD:00876"
                     /db_xref="MIM:142996"
     gene            complement(27308934..27309372)
                     /gene="RPL35P4"
                     /gene_synonym="RPL35_3_799"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271006"
                     /db_xref="HGNC:36285"
     gene            complement(27495991..27498476)
                     /gene="LOC401316"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:401316"
     gene            27501304..27502808
                     /gene="PSMC1P2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442291"
                     /db_xref="HGNC:39777"
     gene            complement(27531301..27532382)
                     /gene="LOC442292"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442292"
     gene            complement(27565059..27702620)
                     /gene="HIBADH"
                     /gene_synonym="MGC40361; NS5ATP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:11112"
                     /db_xref="HGNC:4907"
                     /db_xref="HPRD:12238"
                     /db_xref="MIM:608475"
     mRNA            complement(join(27565059..27565991,27570811..27570967,
                     27577960..27578036,27582586..27582719,27668990..27669111,
                     27671955..27672064,27689092..27689252,27702317..27702620))
                     /gene="HIBADH"
                     /gene_synonym="MGC40361; NS5ATP1"
                     /product="3-hydroxyisobutyrate dehydrogenase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152740.3"
                     /db_xref="GI:301601628"
                     /db_xref="GeneID:11112"
                     /db_xref="HGNC:4907"
                     /db_xref="HPRD:12238"
                     /db_xref="MIM:608475"
     CDS             complement(join(27565833..27565991,27570811..27570967,
                     27577960..27578036,27582586..27582719,27668990..27669111,
                     27671955..27672064,27689092..27689252,27702317..27702407))
                     /gene="HIBADH"
                     /gene_synonym="MGC40361; NS5ATP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="3-hydroxyisobutyrate dehydrogenase,
                     mitochondrial precursor"
                     /protein_id="NP_689953.1"
                     /db_xref="GI:23308751"
                     /db_xref="CCDS:CCDS5414.1"
                     /db_xref="GeneID:11112"
                     /db_xref="HGNC:4907"
                     /db_xref="HPRD:12238"
                     /db_xref="MIM:608475"
     gene            27778992..27869386
                     /gene="TAX1BP1"
                     /gene_synonym="CALCOCO3; T6BP; TXBP151"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8887"
                     /db_xref="HGNC:11575"
                     /db_xref="HPRD:05618"
                     /db_xref="MIM:605326"
     mRNA            join(27778992..27779169,27788137..27788305,
                     27797650..27797752,27805453..27805640,27809295..27809453,
                     27824782..27824930,27825018..27825108,27827037..27827222,
                     27831625..27831849,27832685..27832831,27833942..27834065,
                     27835735..27835838,27839584..27839709,27855968..27856013,
                     27856509..27856657,27867357..27867439,27868247..27869386)
                     /gene="TAX1BP1"
                     /gene_synonym="CALCOCO3; T6BP; TXBP151"
                     /product="Tax1 (human T-cell leukemia virus type I)
                     binding protein 1, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001206901.1"
                     /db_xref="GI:332634739"
                     /db_xref="GeneID:8887"
                     /db_xref="HGNC:11575"
                     /db_xref="MIM:605326"
                     /db_xref="HPRD:05618"
     mRNA            join(27779714..27779888,27788137..27788305,
                     27797650..27797752,27805453..27805640,27809295..27809453,
                     27824782..27824930,27825018..27825108,27827037..27827222,
                     27831625..27831849,27832685..27832831,27833942..27834065,
                     27835735..27835838,27839584..27839709,27855968..27856139,
                     27856509..27856657,27867357..27867439,27868247..27869386)
                     /gene="TAX1BP1"
                     /gene_synonym="CALCOCO3; T6BP; TXBP151"
                     /product="Tax1 (human T-cell leukemia virus type I)
                     binding protein 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006024.6"
                     /db_xref="GI:332634733"
                     /db_xref="GeneID:8887"
                     /db_xref="HGNC:11575"
                     /db_xref="HPRD:05618"
                     /db_xref="MIM:605326"
     mRNA            join(27779714..27779888,27788137..27788305,
                     27797650..27797752,27805453..27805640,27809295..27809453,
                     27824782..27824930,27825018..27825108,27827037..27827222,
                     27831625..27831849,27832685..27832831,27833942..27834065,
                     27835735..27835838,27839584..27839709,27855968..27856013,
                     27856509..27856657,27867357..27867439,27868247..27869386)
                     /gene="TAX1BP1"
                     /gene_synonym="CALCOCO3; T6BP; TXBP151"
                     /product="Tax1 (human T-cell leukemia virus type I)
                     binding protein 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001079864.2"
                     /db_xref="GI:332634737"
                     /db_xref="GeneID:8887"
                     /db_xref="HGNC:11575"
                     /db_xref="MIM:605326"
                     /db_xref="HPRD:05618"
     mRNA            join(27779714..27779888,27788137..27788305,
                     27797650..27797752,27809295..27809453,27824782..27824930,
                     27825018..27825108,27827037..27827222,27831625..27831849,
                     27832685..27832831,27833942..27834065,27835735..27835838,
                     27839584..27839709,27855968..27856013,27856509..27856657,
                     27867357..27867439,27868247..27869386)
                     /gene="TAX1BP1"
                     /gene_synonym="CALCOCO3; T6BP; TXBP151"
                     /product="Tax1 (human T-cell leukemia virus type I)
                     binding protein 1, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001206902.1"
                     /db_xref="GI:332634743"
                     /db_xref="GeneID:8887"
                     /db_xref="HGNC:11575"
                     /db_xref="MIM:605326"
                     /db_xref="HPRD:05618"
     CDS             join(27788144..27788305,27797650..27797752,
                     27805453..27805640,27809295..27809453,27824782..27824930,
                     27825018..27825108,27827037..27827222,27831625..27831849,
                     27832685..27832831,27833942..27834065,27835735..27835838,
                     27839584..27839709,27855968..27856139,27856509..27856657,
                     27867357..27867439,27868247..27868448)
                     /gene="TAX1BP1"
                     /gene_synonym="CALCOCO3; T6BP; TXBP151"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="tax1-binding protein 1 isoform 1"
                     /protein_id="NP_006015.4"
                     /db_xref="GI:21361682"
                     /db_xref="CCDS:CCDS5415.1"
                     /db_xref="GeneID:8887"
                     /db_xref="HGNC:11575"
                     /db_xref="HPRD:05618"
                     /db_xref="MIM:605326"
     CDS             join(27788144..27788305,27797650..27797752,
                     27805453..27805640,27809295..27809453,27824782..27824930,
                     27825018..27825108,27827037..27827222,27831625..27831849,
                     27832685..27832831,27833942..27834065,27835735..27835838,
                     27839584..27839709,27855968..27856013,27856509..27856657,
                     27867357..27867439,27868247..27868448)
                     /gene="TAX1BP1"
                     /gene_synonym="CALCOCO3; T6BP; TXBP151"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="tax1-binding protein 1 isoform 2"
                     /protein_id="NP_001073333.1"
                     /db_xref="GI:119943086"
                     /db_xref="CCDS:CCDS43561.1"
                     /db_xref="GeneID:8887"
                     /db_xref="HGNC:11575"
                     /db_xref="HPRD:05618"
                     /db_xref="MIM:605326"
     CDS             join(27788144..27788305,27797650..27797752,
                     27805453..27805640,27809295..27809453,27824782..27824930,
                     27825018..27825108,27827037..27827222,27831625..27831849,
                     27832685..27832831,27833942..27834065,27835735..27835838,
                     27839584..27839709,27855968..27856013,27856509..27856657,
                     27867357..27867439,27868247..27868448)
                     /gene="TAX1BP1"
                     /gene_synonym="CALCOCO3; T6BP; TXBP151"
                     /note="isoform 2 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="tax1-binding protein 1 isoform 2"
                     /protein_id="NP_001193830.1"
                     /db_xref="GI:332634740"
                     /db_xref="GeneID:8887"
                     /db_xref="HGNC:11575"
                     /db_xref="MIM:605326"
                     /db_xref="HPRD:05618"
     CDS             join(27809313..27809453,27824782..27824930,
                     27825018..27825108,27827037..27827222,27831625..27831849,
                     27832685..27832831,27833942..27834065,27835735..27835838,
                     27839584..27839709,27855968..27856013,27856509..27856657,
                     27867357..27867439,27868247..27868448)
                     /gene="TAX1BP1"
                     /gene_synonym="CALCOCO3; T6BP; TXBP151"
                     /note="isoform 3 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="tax1-binding protein 1 isoform 3"
                     /protein_id="NP_001193831.1"
                     /db_xref="GI:332634744"
                     /db_xref="GeneID:8887"
                     /db_xref="HGNC:11575"
                     /db_xref="MIM:605326"
                     /db_xref="HPRD:05618"
     gene            complement(27870192..28220437)
                     /gene="JAZF1"
                     /gene_synonym="DKFZp761K2222; TIP27; ZNF802"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221895"
                     /db_xref="HGNC:28917"
                     /db_xref="HPRD:09373"
                     /db_xref="MIM:606246"
     mRNA            complement(join(27870192..27872595,27880317..27880486,
                     27934839..27935035,28031528..28031600,28220082..28220437))
                     /gene="JAZF1"
                     /gene_synonym="DKFZp761K2222; TIP27; ZNF802"
                     /product="JAZF zinc finger 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_175061.3"
                     /db_xref="GI:91822910"
                     /db_xref="GeneID:221895"
                     /db_xref="HGNC:28917"
                     /db_xref="HPRD:09373"
                     /db_xref="MIM:606246"
     CDS             complement(join(27872419..27872595,27880317..27880486,
                     27934839..27935035,28031528..28031600,28220082..28220196))
                     /gene="JAZF1"
                     /gene_synonym="DKFZp761K2222; TIP27; ZNF802"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="juxtaposed with another zinc finger protein 1"
                     /protein_id="NP_778231.2"
                     /db_xref="GI:91822911"
                     /db_xref="CCDS:CCDS5416.1"
                     /db_xref="GeneID:221895"
                     /db_xref="HGNC:28917"
                     /db_xref="HPRD:09373"
                     /db_xref="MIM:606246"
     gene            28220076..28280996
                     /gene="LOC100128081"
                     /gene_synonym="FLJ59585"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100128081"
     misc_RNA        join(28220076..28220158,28225289..28225371,
                     28256862..28256968,28280076..28280996)
                     /gene="LOC100128081"
                     /gene_synonym="FLJ59585"
                     /product="hypothetical LOC100128081"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_034097.1"
                     /db_xref="GI:300795525"
                     /db_xref="GeneID:100128081"
     gene            complement(28318823..28319318)
                     /gene="LOC402644"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402644"
     gene            28338940..28865511
                     /gene="CREB5"
                     /gene_synonym="CRE-BPA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9586"
                     /db_xref="HGNC:16844"
                     /db_xref="HPRD:09896"
     mRNA            join(28338940..28339060,28534524..28534617,
                     28547234..28547355,28609983..28610155,28758370..28758496,
                     28763839..28763949,28843816..28844139,28848804..28849031,
                     28857688..28857796,28858733..28865511)
                     /gene="CREB5"
                     /gene_synonym="CRE-BPA"
                     /product="cAMP responsive element binding protein 5,
                     transcript variant 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182899.3"
                     /db_xref="GI:59938771"
                     /db_xref="GeneID:9586"
                     /db_xref="HGNC:16844"
                     /db_xref="HPRD:09896"
     gene            28448995..28450377
                     /gene="LOC401317"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 7 ESTs"
                     /db_xref="GeneID:401317"
     misc_RNA        join(28448995..28449042,28449277..28450377)
                     /gene="LOC401317"
                     /product="hypothetical LOC401317"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 7 ESTs"
                     /transcript_id="XR_108761.2"
                     /db_xref="GI:341915384"
                     /db_xref="GeneID:401317"
     mRNA            join(28452144..28452536,28527793..28527864,
                     28534524..28534617,28547234..28547355,28609983..28610155,
                     28758370..28758496,28763839..28763949,28843816..28844139,
                     28848804..28849031,28857688..28857796,28858733..28865511)
                     /gene="CREB5"
                     /gene_synonym="CRE-BPA"
                     /product="cAMP responsive element binding protein 5,
                     transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182898.2"
                     /db_xref="GI:59938769"
                     /db_xref="GeneID:9586"
                     /db_xref="HGNC:16844"
                     /db_xref="HPRD:09896"
     CDS             join(28452534..28452536,28527793..28527864,
                     28534524..28534617,28547234..28547355,28609983..28610155,
                     28758370..28758496,28763839..28763949,28843816..28844139,
                     28848804..28849031,28857688..28857796,28858733..28858896)
                     /gene="CREB5"
                     /gene_synonym="CRE-BPA"
                     /note="isoform alpha is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclic AMP-responsive element-binding protein 5
                     isoform alpha"
                     /protein_id="NP_878901.2"
                     /db_xref="GI:59938770"
                     /db_xref="CCDS:CCDS5417.1"
                     /db_xref="GeneID:9586"
                     /db_xref="HGNC:16844"
                     /db_xref="HPRD:09896"
     mRNA            join(28475234..28475307,28527793..28527864,
                     28534524..28534617,28547234..28547355,28609983..28610155,
                     28758370..28758496,28763839..28763949,28843816..28844139,
                     28848804..28849031,28857688..28857796,28858733..28865511)
                     /gene="CREB5"
                     /gene_synonym="CRE-BPA"
                     /product="cAMP responsive element binding protein 5,
                     transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004904.2"
                     /db_xref="GI:59938773"
                     /db_xref="GeneID:9586"
                     /db_xref="HGNC:16844"
                     /db_xref="HPRD:09896"
     CDS             join(28527811..28527864,28534524..28534617,
                     28547234..28547355,28609983..28610155,28758370..28758496,
                     28763839..28763949,28843816..28844139,28848804..28849031,
                     28857688..28857796,28858733..28858896)
                     /gene="CREB5"
                     /gene_synonym="CRE-BPA"
                     /note="isoform beta is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclic AMP-responsive element-binding protein 5
                     isoform beta"
                     /protein_id="NP_004895.2"
                     /db_xref="GI:59938774"
                     /db_xref="CCDS:CCDS5418.1"
                     /db_xref="GeneID:9586"
                     /db_xref="HGNC:16844"
                     /db_xref="HPRD:09896"
     CDS             join(28534548..28534617,28547234..28547355,
                     28609983..28610155,28758370..28758496,28763839..28763949,
                     28843816..28844139,28848804..28849031,28857688..28857796,
                     28858733..28858896)
                     /gene="CREB5"
                     /gene_synonym="CRE-BPA"
                     /note="isoform gamma is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclic AMP-responsive element-binding protein 5
                     isoform gamma"
                     /protein_id="NP_878902.2"
                     /db_xref="GI:59938772"
                     /db_xref="CCDS:CCDS43562.1"
                     /db_xref="GeneID:9586"
                     /db_xref="HGNC:16844"
                     /db_xref="HPRD:09896"
     gene            complement(28654714..28655481)
                     /gene="RPS2P30"
                     /gene_synonym="RPS2_10_800"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100270911"
                     /db_xref="HGNC:36987"
     mRNA            join(28725721..28725814,28758370..28758496,
                     28763839..28763949,28843816..28844139,28848804..28849031,
                     28857688..28857796,28858733..28865511)
                     /gene="CREB5"
                     /gene_synonym="CRE-BPA"
                     /product="cAMP responsive element binding protein 5,
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001011666.1"
                     /db_xref="GI:59938775"
                     /db_xref="GeneID:9586"
                     /db_xref="HGNC:16844"
                     /db_xref="HPRD:09896"
     CDS             join(28725768..28725814,28758370..28758496,
                     28763839..28763949,28843816..28844139,28848804..28849031,
                     28857688..28857796,28858733..28858896)
                     /gene="CREB5"
                     /gene_synonym="CRE-BPA"
                     /note="isoform delta is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclic AMP-responsive element-binding protein 5
                     isoform delta"
                     /protein_id="NP_001011666.1"
                     /db_xref="GI:59938776"
                     /db_xref="CCDS:CCDS43563.1"
                     /db_xref="GeneID:9586"
                     /db_xref="HGNC:16844"
                     /db_xref="HPRD:09896"
     gene            complement(28992974..28998029)
                     /gene="TRIL"
                     /gene_synonym="KIAA0644"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9865"
                     /db_xref="HGNC:22200"
                     /db_xref="MIM:613356"
     mRNA            complement(28992974..28998029)
                     /gene="TRIL"
                     /gene_synonym="KIAA0644"
                     /product="TLR4 interactor with leucine-rich repeats"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014817.3"
                     /db_xref="GI:116875827"
                     /db_xref="GeneID:9865"
                     /db_xref="HGNC:22200"
                     /db_xref="MIM:613356"
     CDS             complement(28995227..28997662)
                     /gene="TRIL"
                     /gene_synonym="KIAA0644"
                     /exception="unclassified translation discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="TLR4 interactor with leucine rich repeats
                     precursor"
                     /protein_id="NP_055632.2"
                     /db_xref="GI:76880480"
                     /db_xref="GeneID:9865"
                     /db_xref="HGNC:22200"
                     /db_xref="MIM:613356"
     gene            29019583..29052985
                     /gene="LOC100506497"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100506497"
     misc_RNA        join(29019583..29019714,29035781..29035867,
                     29040585..29040671,29040945..29041000,29049639..29052985)
                     /gene="LOC100506497"
                     /product="hypothetical LOC100506497"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038965.1"
                     /db_xref="GI:337298381"
                     /db_xref="GeneID:100506497"
     gene            complement(29035247..29186153)
                     /gene="CPVL"
                     /gene_synonym="HVLP; MGC10029"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54504"
                     /db_xref="HGNC:14399"
                     /db_xref="MIM:609780"
     mRNA            complement(join(29035247..29035498,29070193..29070375,
                     29103677..29103850,29105639..29105737,29111389..29111520,
                     29111917..29112039,29126100..29126166,29132239..29132318,
                     29134700..29134758,29135719..29135833,29152320..29152438,
                     29160509..29160687,29186045..29186153))
                     /gene="CPVL"
                     /gene_synonym="HVLP; MGC10029"
                     /product="carboxypeptidase, vitellogenic-like, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_031311.3"
                     /db_xref="GI:83641873"
                     /db_xref="GeneID:54504"
                     /db_xref="HGNC:14399"
                     /db_xref="MIM:609780"
     mRNA            complement(join(29035247..29035498,29070193..29070375,
                     29103677..29103850,29105639..29105737,29111389..29111520,
                     29111917..29112039,29126100..29126166,29132239..29132318,
                     29134700..29134758,29135719..29135833,29152320..29152438,
                     29160509..29160687,29185957..29186153))
                     /gene="CPVL"
                     /gene_synonym="HVLP; MGC10029"
                     /product="carboxypeptidase, vitellogenic-like, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_019029.2"
                     /db_xref="GI:83641875"
                     /db_xref="GeneID:54504"
                     /db_xref="HGNC:14399"
                     /db_xref="HPRD:07479"
                     /db_xref="MIM:609780"
     CDS             complement(join(29035388..29035498,29070193..29070375,
                     29103677..29103850,29105639..29105737,29111389..29111520,
                     29111917..29112039,29126100..29126166,29132239..29132318,
                     29134700..29134758,29135719..29135833,29152320..29152438,
                     29160509..29160677))
                     /gene="CPVL"
                     /gene_synonym="HVLP; MGC10029"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable serine carboxypeptidase CPVL precursor"
                     /protein_id="NP_112601.3"
                     /db_xref="GI:83641874"
                     /db_xref="CCDS:CCDS5419.1"
                     /db_xref="GeneID:54504"
                     /db_xref="HGNC:14399"
                     /db_xref="MIM:609780"
     CDS             complement(join(29035388..29035498,29070193..29070375,
                     29103677..29103850,29105639..29105737,29111389..29111520,
                     29111917..29112039,29126100..29126166,29132239..29132318,
                     29134700..29134758,29135719..29135833,29152320..29152438,
                     29160509..29160677))
                     /gene="CPVL"
                     /gene_synonym="HVLP; MGC10029"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable serine carboxypeptidase CPVL precursor"
                     /protein_id="NP_061902.2"
                     /db_xref="GI:83641876"
                     /db_xref="CCDS:CCDS5419.1"
                     /db_xref="GeneID:54504"
                     /db_xref="HGNC:14399"
                     /db_xref="MIM:609780"
     gene            29234121..29553944
                     /gene="CHN2"
                     /gene_synonym="ARHGAP3; BCH; MGC138360; RHOGAP3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1124"
                     /db_xref="HGNC:1944"
                     /db_xref="MIM:602857"
     mRNA            join(29234121..29234606,29394241..29394279,
                     29407548..29407603,29433295..29433326,29437989..29438102,
                     29440159..29440444,29519895..29519972,29535568..29535652,
                     29539483..29539656,29544360..29544437,29546844..29546981,
                     29548917..29549022,29552180..29553944)
                     /gene="CHN2"
                     /gene_synonym="ARHGAP3; BCH; MGC138360; RHOGAP3"
                     /product="chimerin (chimaerin) 2, transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004067.2"
                     /db_xref="GI:91106934"
                     /db_xref="GeneID:1124"
                     /db_xref="HGNC:1944"
                     /db_xref="HPRD:04173"
                     /db_xref="MIM:602857"
     CDS             join(29234558..29234606,29394241..29394279,
                     29407548..29407603,29433295..29433326,29437989..29438102,
                     29440159..29440444,29519895..29519972,29535568..29535652,
                     29539483..29539656,29544360..29544437,29546844..29546981,
                     29548917..29549022,29552180..29552351)
                     /gene="CHN2"
                     /gene_synonym="ARHGAP3; BCH; MGC138360; RHOGAP3"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="beta-chimaerin isoform 2"
                     /protein_id="NP_004058.1"
                     /db_xref="GI:4757980"
                     /db_xref="CCDS:CCDS5420.1"
                     /db_xref="GeneID:1124"
                     /db_xref="HGNC:1944"
                     /db_xref="MIM:602857"
     gene            29251729..29253503
                     /gene="NANOGP4"
                     /gene_synonym="NANOGP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:414132"
                     /db_xref="HGNC:23102"
     mRNA            join(29519486..29519972,29535568..29535652,
                     29539483..29539656,29544360..29544437,29546844..29546981,
                     29548917..29549022,29552180..29553944)
                     /gene="CHN2"
                     /gene_synonym="ARHGAP3; BCH; MGC138360; RHOGAP3"
                     /product="chimerin (chimaerin) 2, transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001039936.1"
                     /db_xref="GI:91106927"
                     /db_xref="GeneID:1124"
                     /db_xref="HGNC:1944"
                     /db_xref="MIM:602857"
     CDS             join(29519727..29519972,29535568..29535652,
                     29539483..29539656,29544360..29544437,29546844..29546981,
                     29548917..29549022,29552180..29552351)
                     /gene="CHN2"
                     /gene_synonym="ARHGAP3; BCH; MGC138360; RHOGAP3"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="beta-chimaerin isoform 1"
                     /protein_id="NP_001035025.1"
                     /db_xref="GI:91106928"
                     /db_xref="CCDS:CCDS47566.1"
                     /db_xref="GeneID:1124"
                     /db_xref="HGNC:1944"
                     /db_xref="MIM:602857"
     gene            29591140..29591767
                     /gene="LOC646745"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:646745"
     gene            29603427..29606911
                     /gene="PRR15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222171"
                     /db_xref="HGNC:22310"
                     /db_xref="HPRD:14136"
     mRNA            join(29603427..29603993,29605801..29606911)
                     /gene="PRR15"
                     /product="proline rich 15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_175887.2"
                     /db_xref="GI:31343480"
                     /db_xref="GeneID:222171"
                     /db_xref="HGNC:22310"
                     /db_xref="HPRD:14136"
     CDS             29605946..29606335
                     /gene="PRR15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="proline-rich protein 15"
                     /protein_id="NP_787083.1"
                     /db_xref="GI:28557711"
                     /db_xref="CCDS:CCDS5421.1"
                     /db_xref="GeneID:222171"
                     /db_xref="HGNC:22310"
                     /db_xref="HPRD:14136"
     gene            complement(29685538..29724754)
                     /gene="LOC646762"
                     /gene_synonym="FLJ35551"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:646762"
     misc_RNA        complement(join(29685538..29690955,29724389..29724754))
                     /gene="LOC646762"
                     /gene_synonym="FLJ35551"
                     /product="hypothetical LOC646762"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024278.1"
                     /db_xref="GI:210147393"
                     /db_xref="GeneID:646762"
     gene            complement(29720350..29720444)
                     /gene="MIR550A3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100616354"
                     /db_xref="HGNC:41870"
                     /db_xref="miRBase:MI0003762"
     ncRNA           complement(29720350..29720444)
                     /gene="MIR550A3"
                     /ncRNA_class="miRNA"
                     /product="microRNA 550a-3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039600.1"
                     /db_xref="GI:337756643"
                     /db_xref="GeneID:100616354"
                     /db_xref="HGNC:41870"
                     /db_xref="miRBase:MI0003762"
     gene            complement(29724388..29725437)
                     /gene="LOC100271874"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:100271874"
     misc_RNA        complement(29724388..29725437)
                     /gene="LOC100271874"
                     /product="zinc and ring finger 2 pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_027347.1"
                     /db_xref="GI:298566328"
                     /db_xref="GeneID:100271874"
     gene            29724770..29782022
                     /gene="DPY19L2P3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:442524"
                     /db_xref="HGNC:22367"
     misc_RNA        join(29724770..29725481,29726895..29727859)
                     /gene="DPY19L2P3"
                     /product="dpy-19-like 2 pseudogene 3 (C. elegans),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_036482.1"
                     /db_xref="GI:302318958"
                     /db_xref="GeneID:442524"
                     /db_xref="HGNC:22367"
     misc_RNA        join(29725688..29725784,29726895..29727015,
                     29730534..29730644,29734184..29734241,29736569..29736660,
                     29749630..29749688,29757622..29757675,29763888..29763934,
                     29771564..29771662,29773069..29773194,29781763..29782022)
                     /gene="DPY19L2P3"
                     /product="dpy-19-like 2 pseudogene 3 (C. elegans),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_036554.1"
                     /db_xref="GI:304361752"
                     /db_xref="GeneID:442524"
                     /db_xref="HGNC:22367"
     gene            29846170..29956682
                     /gene="WIPF3"
                     /gene_synonym="CR16; FLJ36931"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:644150"
                     /db_xref="HGNC:22004"
                     /db_xref="MIM:612432"
     mRNA            join(29846170..29846294,29874284..29874430,
                     29915446..29915578,29918625..29918756,29923466..29924209,
                     29927684..29927833,29928922..29929023,29943902..29943978,
                     29954109..29956682)
                     /gene="WIPF3"
                     /gene_synonym="CR16; FLJ36931"
                     /product="WAS/WASL interacting protein family, member 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001080529.2"
                     /db_xref="GI:336455071"
                     /db_xref="GeneID:644150"
                     /db_xref="HGNC:22004"
                     /db_xref="MIM:612432"
     CDS             join(29874341..29874430,29915446..29915578,
                     29918625..29918756,29923466..29924209,29927684..29927833,
                     29928922..29929023,29943902..29943978,29954109..29954132)
                     /gene="WIPF3"
                     /gene_synonym="CR16; FLJ36931"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="WAS/WASL-interacting protein family member 3"
                     /protein_id="NP_001073998.2"
                     /db_xref="GI:336455072"
                     /db_xref="GeneID:644150"
                     /db_xref="HGNC:22004"
                     /db_xref="MIM:612432"
     gene            complement(29959719..30029905)
                     /gene="SCRN1"
                     /gene_synonym="KIAA0193; SES1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9805"
                     /db_xref="HGNC:22192"
                     /db_xref="HPRD:15304"
     mRNA            complement(join(29959719..29963731,29966068..29966248,
                     29976172..29976337,29980298..29980492,29983593..29983795,
                     29994795..29994976,30008525..30008684,30029798..30029905))
                     /gene="SCRN1"
                     /gene_synonym="KIAA0193; SES1"
                     /product="secernin 1, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145514.1"
                     /db_xref="GI:224465189"
                     /db_xref="GeneID:9805"
                     /db_xref="HGNC:22192"
                     /db_xref="HPRD:15304"
     mRNA            complement(join(29959719..29963731,29966068..29966248,
                     29976172..29976337,29980298..29980492,29983593..29983795,
                     29994795..29994976,30008525..30008684,30029559..30029734))
                     /gene="SCRN1"
                     /gene_synonym="KIAA0193; SES1"
                     /product="secernin 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145513.1"
                     /db_xref="GI:224465193"
                     /db_xref="GeneID:9805"
                     /db_xref="HGNC:22192"
                     /db_xref="HPRD:15304"
     mRNA            complement(join(29959719..29963731,29966068..29966248,
                     29976172..29976337,29980298..29980492,29983593..29983795,
                     29994795..29994976,30008525..30008684,30029258..30029425))
                     /gene="SCRN1"
                     /gene_synonym="KIAA0193; SES1"
                     /product="secernin 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014766.4"
                     /db_xref="GI:224465186"
                     /db_xref="GeneID:9805"
                     /db_xref="HGNC:22192"
                     /db_xref="HPRD:15304"
     mRNA            complement(join(29959719..29963731,29966068..29966248,
                     29976172..29976337,29980298..29980492,29983593..29983795,
                     29994795..29994976,30029258..30029425))
                     /gene="SCRN1"
                     /gene_synonym="KIAA0193; SES1"
                     /product="secernin 1, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145515.1"
                     /db_xref="GI:224465191"
                     /db_xref="GeneID:9805"
                     /db_xref="HGNC:22192"
                     /db_xref="HPRD:15304"
     CDS             complement(join(29963573..29963731,29966068..29966248,
                     29976172..29976337,29980298..29980492,29983593..29983795,
                     29994795..29994976,30008525..30008684,30029798..30029856))
                     /gene="SCRN1"
                     /gene_synonym="KIAA0193; SES1"
                     /note="isoform b is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="secernin-1 isoform b"
                     /protein_id="NP_001138986.1"
                     /db_xref="GI:224465190"
                     /db_xref="CCDS:CCDS47567.1"
                     /db_xref="GeneID:9805"
                     /db_xref="HGNC:22192"
                     /db_xref="HPRD:15304"
     CDS             complement(join(29963573..29963731,29966068..29966248,
                     29976172..29976337,29980298..29980492,29983593..29983795,
                     29994795..29994976,30008525..30008683))
                     /gene="SCRN1"
                     /gene_synonym="KIAA0193; SES1"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="secernin-1 isoform a"
                     /protein_id="NP_001138985.1"
                     /db_xref="GI:224465194"
                     /db_xref="CCDS:CCDS5422.1"
                     /db_xref="GeneID:9805"
                     /db_xref="HGNC:22192"
                     /db_xref="HPRD:15304"
     CDS             complement(join(29963573..29963731,29966068..29966248,
                     29976172..29976337,29980298..29980492,29983593..29983795,
                     29994795..29994976,30008525..30008683))
                     /gene="SCRN1"
                     /gene_synonym="KIAA0193; SES1"
                     /note="isoform a is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="secernin-1 isoform a"
                     /protein_id="NP_055581.3"
                     /db_xref="GI:224465187"
                     /db_xref="CCDS:CCDS5422.1"
                     /db_xref="GeneID:9805"
                     /db_xref="HGNC:22192"
                     /db_xref="HPRD:15304"
     CDS             complement(join(29963573..29963731,29966068..29966248,
                     29976172..29976337,29980298..29980492,29983593..29983795,
                     29994795..29994931))
                     /gene="SCRN1"
                     /gene_synonym="KIAA0193; SES1"
                     /note="isoform c is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="secernin-1 isoform c"
                     /protein_id="NP_001138987.1"
                     /db_xref="GI:224465192"
                     /db_xref="CCDS:CCDS47568.1"
                     /db_xref="GeneID:9805"
                     /db_xref="HGNC:22192"
                     /db_xref="HPRD:15304"
     gene            complement(30052884..30066268)
                     /gene="FKBP14"
                     /gene_synonym="FKBP22; FLJ20731"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55033"
                     /db_xref="HGNC:18625"
                     /db_xref="HPRD:16898"
     mRNA            complement(join(30052884..30054509,30058612..30058739,
                     30062281..30062432,30065928..30066268))
                     /gene="FKBP14"
                     /gene_synonym="FKBP22; FLJ20731"
                     /product="FK506 binding protein 14, 22 kDa"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017946.2"
                     /db_xref="GI:51593093"
                     /db_xref="GeneID:55033"
                     /db_xref="HGNC:18625"
                     /db_xref="HPRD:16898"
     CDS             complement(join(30054351..30054509,30058612..30058739,
                     30062281..30062432,30065928..30066124))
                     /gene="FKBP14"
                     /gene_synonym="FKBP22; FLJ20731"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="peptidyl-prolyl cis-trans isomerase FKBP14
                     precursor"
                     /protein_id="NP_060416.1"
                     /db_xref="GI:8923659"
                     /db_xref="CCDS:CCDS5423.1"
                     /db_xref="GeneID:55033"
                     /db_xref="HGNC:18625"
                     /db_xref="HPRD:16898"
     gene            30067977..30157961
                     /gene="PLEKHA8"
                     /gene_synonym="DKFZp313M1034; DKFZp686J09164; FAPP2;
                     MGC3358"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84725"
                     /db_xref="HGNC:30037"
                     /db_xref="MIM:608639"
     mRNA            join(30067977..30068418,30084701..30084817,
                     30085826..30085981,30087448..30087572,30088840..30088998,
                     30090050..30090090,30092325..30092482,30094325..30094481,
                     30094873..30094958,30100500..30100558,30101513..30101643,
                     30102288..30102358,30113687..30113748,30157586..30157961)
                     /gene="PLEKHA8"
                     /gene_synonym="DKFZp313M1034; DKFZp686J09164; FAPP2;
                     MGC3358"
                     /product="pleckstrin homology domain containing, family A
                     (phosphoinositide binding specific) member 8, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001197027.1"
                     /db_xref="GI:308153324"
                     /db_xref="GeneID:84725"
                     /db_xref="HGNC:30037"
                     /db_xref="MIM:608639"
     mRNA            join(30067977..30068418,30084701..30084817,
                     30085826..30085981,30087448..30087572,30088840..30088998,
                     30090050..30090090,30092325..30092482,30094325..30094481,
                     30094873..30094958,30100500..30100558,30101513..30101643,
                     30102288..30102358,30129769..30130360)
                     /gene="PLEKHA8"
                     /gene_synonym="DKFZp313M1034; DKFZp686J09164; FAPP2;
                     MGC3358"
                     /product="pleckstrin homology domain containing, family A
                     (phosphoinositide binding specific) member 8, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032639.3"
                     /db_xref="GI:308153328"
                     /db_xref="GeneID:84725"
                     /db_xref="HGNC:30037"
                     /db_xref="HPRD:10555"
                     /db_xref="MIM:608639"
     mRNA            join(30067977..30068418,30084701..30084817,
                     30085826..30085981,30087448..30087572,30088840..30088998,
                     30090050..30090090,30092325..30092482,30094325..30094481,
                     30094873..30094958,30100500..30100558,30101513..30101643,
                     30102288..30102358,30113687..30113748,30118206..30124279)
                     /gene="PLEKHA8"
                     /gene_synonym="DKFZp313M1034; DKFZp686J09164; FAPP2;
                     MGC3358"
                     /product="pleckstrin homology domain containing, family A
                     (phosphoinositide binding specific) member 8, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001197026.1"
                     /db_xref="GI:308153326"
                     /db_xref="GeneID:84725"
                     /db_xref="HGNC:30037"
                     /db_xref="MIM:608639"
     CDS             join(30068379..30068418,30084701..30084817,
                     30085826..30085981,30087448..30087572,30088840..30088998,
                     30090050..30090090,30092325..30092482,30094325..30094481,
                     30094873..30094958,30100500..30100558,30101513..30101643,
                     30102288..30102358,30113687..30113748,30157586..30157603)
                     /gene="PLEKHA8"
                     /gene_synonym="DKFZp313M1034; DKFZp686J09164; FAPP2;
                     MGC3358"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="pleckstrin homology domain-containing family A
                     member 8 isoform 2"
                     /protein_id="NP_001183956.1"
                     /db_xref="GI:308153325"
                     /db_xref="GeneID:84725"
                     /db_xref="HGNC:30037"
                     /db_xref="MIM:608639"
     CDS             join(30068379..30068418,30084701..30084817,
                     30085826..30085981,30087448..30087572,30088840..30088998,
                     30090050..30090090,30092325..30092482,30094325..30094481,
                     30094873..30094958,30100500..30100558,30101513..30101643,
                     30102288..30102358,30129769..30129791)
                     /gene="PLEKHA8"
                     /gene_synonym="DKFZp313M1034; DKFZp686J09164; FAPP2;
                     MGC3358"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="pleckstrin homology domain-containing family A
                     member 8 isoform 3"
                     /protein_id="NP_116028.1"
                     /db_xref="GI:14249174"
                     /db_xref="CCDS:CCDS5424.1"
                     /db_xref="GeneID:84725"
                     /db_xref="HGNC:30037"
                     /db_xref="MIM:608639"
     CDS             join(30068379..30068418,30084701..30084817,
                     30085826..30085981,30087448..30087572,30088840..30088998,
                     30090050..30090090,30092325..30092482,30094325..30094481,
                     30094873..30094958,30100500..30100558,30101513..30101643,
                     30102288..30102358,30113687..30113748,30118206..30118403)
                     /gene="PLEKHA8"
                     /gene_synonym="DKFZp313M1034; DKFZp686J09164; FAPP2;
                     MGC3358"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="pleckstrin homology domain-containing family A
                     member 8 isoform 1"
                     /protein_id="NP_001183955.1"
                     /db_xref="GI:308153327"
                     /db_xref="GeneID:84725"
                     /db_xref="HGNC:30037"
                     /db_xref="MIM:608639"
     gene            30174552..30202381
                     /gene="C7orf41"
                     /gene_synonym="Ells1; FLJ25903"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222166"
                     /db_xref="HGNC:25457"
                     /db_xref="HPRD:07635"
     mRNA            join(30174552..30174914,30185793..30185915,
                     30197054..30202381)
                     /gene="C7orf41"
                     /gene_synonym="Ells1; FLJ25903"
                     /product="chromosome 7 open reading frame 41"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152793.2"
                     /db_xref="GI:116008439"
                     /db_xref="GeneID:222166"
                     /db_xref="HGNC:25457"
                     /db_xref="HPRD:07635"
     CDS             join(30174753..30174914,30185793..30185915,
                     30197054..30197164)
                     /gene="C7orf41"
                     /gene_synonym="Ells1; FLJ25903"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC222166"
                     /protein_id="NP_690006.2"
                     /db_xref="GI:116008440"
                     /db_xref="CCDS:CCDS5425.2"
                     /db_xref="GeneID:222166"
                     /db_xref="HGNC:25457"
                     /db_xref="HPRD:07635"
     gene            30207444..30207620
                     /gene="RPS27P16"
                     /gene_synonym="RPS27_9_801"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271119"
                     /db_xref="HGNC:36560"
     gene            30323923..30407308
                     /gene="ZNRF2"
                     /gene_synonym="RNF202"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:223082"
                     /db_xref="HGNC:22316"
                     /db_xref="HPRD:15894"
                     /db_xref="MIM:612061"
     mRNA            join(30323923..30325442,30363258..30363353,
                     30395344..30395449,30401993..30402072,30405651..30407308)
                     /gene="ZNRF2"
                     /gene_synonym="RNF202"
                     /product="zinc and ring finger 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_147128.3"
                     /db_xref="GI:40316919"
                     /db_xref="GeneID:223082"
                     /db_xref="HGNC:22316"
                     /db_xref="HPRD:15894"
                     /db_xref="MIM:612061"
     CDS             join(30324974..30325442,30363258..30363353,
                     30395344..30395449,30401993..30402050)
                     /gene="ZNRF2"
                     /gene_synonym="RNF202"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase ZNRF2"
                     /protein_id="NP_667339.1"
                     /db_xref="GI:23821044"
                     /db_xref="CCDS:CCDS5426.1"
                     /db_xref="GeneID:223082"
                     /db_xref="HGNC:22316"
                     /db_xref="HPRD:15894"
                     /db_xref="MIM:612061"
     gene            30329410..30329506
                     /gene="MIR550A1"
                     /gene_synonym="hsa-mir-550a-1; MIR550-1; MIRN550-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:693133"
                     /db_xref="HGNC:32804"
                     /db_xref="miRBase:MI0003600"
     gene            complement(30329410..30329506)
                     /gene="MIR550B1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100500883"
                     /db_xref="HGNC:38992"
                     /db_xref="miRBase:MI0016686"
     ncRNA           30329410..30329506
                     /gene="MIR550A1"
                     /gene_synonym="hsa-mir-550a-1; MIR550-1; MIRN550-1"
                     /ncRNA_class="miRNA"
                     /product="microRNA 550a-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_030319.1"
                     /db_xref="GI:262205937"
                     /db_xref="GeneID:693133"
                     /db_xref="HGNC:32804"
                     /db_xref="miRBase:MI0003600"
     ncRNA           30329410..30329506
                     /gene="MIR550A1"
                     /gene_synonym="hsa-mir-550a-1; MIR550-1; MIRN550-1"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-550-1"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:693133"
                     /db_xref="miRBase:MI0003600"
                     /db_xref="HGNC:32804"
     ncRNA           complement(30329410..30329506)
                     /gene="MIR550B1"
                     /ncRNA_class="miRNA"
                     /product="microRNA 550b-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037513.1"
                     /db_xref="GI:312147126"
                     /db_xref="GeneID:100500883"
                     /db_xref="HGNC:38992"
                     /db_xref="miRBase:MI0016686"
     gene            30409666..30412425
                     /gene="DKFZP586I1420"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:222161"
     misc_RNA        30409666..30412425
                     /gene="DKFZP586I1420"
                     /product="hypothetical protein DKFZp586I1420"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002186.1"
                     /db_xref="GI:54400743"
                     /db_xref="GeneID:222161"
     gene            30430501..30443671
                     /gene="LOC100506516"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 8 ESTs"
                     /db_xref="GeneID:100506516"
     misc_RNA        join(30430501..30430651,30442528..30442638,
                     30443218..30443671)
                     /gene="LOC100506516"
                     /product="hypothetical LOC100506516"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 8 ESTs"
                     /transcript_id="XR_108763.1"
                     /db_xref="GI:310119939"
                     /db_xref="GeneID:100506516"
     gene            complement(30464143..30518393)
                     /gene="NOD1"
                     /gene_synonym="CARD4; CLR7.1; NLRC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10392"
                     /db_xref="HGNC:16390"
                     /db_xref="HPRD:05815"
                     /db_xref="MIM:605980"
     mRNA            complement(join(30464143..30465326,30468990..30469073,
                     30472712..30472795,30475614..30475697,30477189..30477272,
                     30485757..30485840,30486583..30486666,30487914..30487997,
                     30490832..30492656,30494753..30494927,30496337..30496658,
                     30498768..30498856,30499517..30499657,30518222..30518393))
                     /gene="NOD1"
                     /gene_synonym="CARD4; CLR7.1; NLRC1"
                     /product="nucleotide-binding oligomerization domain
                     containing 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006092.2"
                     /db_xref="GI:194733754"
                     /db_xref="GeneID:10392"
                     /db_xref="HGNC:16390"
                     /db_xref="HPRD:05815"
                     /db_xref="MIM:605980"
     CDS             complement(join(30465254..30465326,30468990..30469073,
                     30472712..30472795,30475614..30475697,30477189..30477272,
                     30485757..30485840,30486583..30486666,30487914..30487997,
                     30490832..30492656,30494753..30494927,30496337..30496537))
                     /gene="NOD1"
                     /gene_synonym="CARD4; CLR7.1; NLRC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="nucleotide-binding oligomerization
                     domain-containing protein 1"
                     /protein_id="NP_006083.1"
                     /db_xref="GI:5174617"
                     /db_xref="CCDS:CCDS5427.1"
                     /db_xref="GeneID:10392"
                     /db_xref="HGNC:16390"
                     /db_xref="HPRD:05815"
                     /db_xref="MIM:605980"
     gene            complement(30536237..30544457)
                     /gene="GGCT"
                     /gene_synonym="C7orf24; CRF21; FLJ11717; GCTG; GGC;
                     MGC3077"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79017"
                     /db_xref="HGNC:21705"
                     /db_xref="HPRD:12912"
                     /db_xref="MIM:137170"
     mRNA            complement(join(30536237..30536851,30538419..30538554,
                     30540152..30540297,30544185..30544457))
                     /gene="GGCT"
                     /gene_synonym="C7orf24; CRF21; FLJ11717; GCTG; GGC;
                     MGC3077"
                     /product="gamma-glutamylcyclotransferase, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024051.3"
                     /db_xref="GI:315360615"
                     /db_xref="GeneID:79017"
                     /db_xref="HGNC:21705"
                     /db_xref="HPRD:12912"
                     /db_xref="MIM:137170"
     mRNA            complement(join(30536237..30536851,30537357..30537512,
                     30540152..30540297,30544185..30544457))
                     /gene="GGCT"
                     /gene_synonym="C7orf24; CRF21; FLJ11717; GCTG; GGC;
                     MGC3077"
                     /product="gamma-glutamylcyclotransferase, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199815.1"
                     /db_xref="GI:315360617"
                     /db_xref="GeneID:79017"
                     /db_xref="HGNC:21705"
                     /db_xref="MIM:137170"
                     /db_xref="HPRD:12912"
     mRNA            complement(join(30536237..30536851,30540152..30540297,
                     30544185..30544457))
                     /gene="GGCT"
                     /gene_synonym="C7orf24; CRF21; FLJ11717; GCTG; GGC;
                     MGC3077"
                     /product="gamma-glutamylcyclotransferase, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199816.1"
                     /db_xref="GI:315360619"
                     /db_xref="GeneID:79017"
                     /db_xref="HGNC:21705"
                     /db_xref="MIM:137170"
                     /db_xref="HPRD:12912"
     mRNA            complement(join(30536237..30536851,30544185..30544457))
                     /gene="GGCT"
                     /gene_synonym="C7orf24; CRF21; FLJ11717; GCTG; GGC;
                     MGC3077"
                     /product="gamma-glutamylcyclotransferase, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199817.1"
                     /db_xref="GI:315360621"
                     /db_xref="GeneID:79017"
                     /db_xref="HGNC:21705"
                     /db_xref="MIM:137170"
                     /db_xref="HPRD:12912"
     misc_RNA        complement(join(30536237..30536851,30538419..30538554,
                     30544185..30544457))
                     /gene="GGCT"
                     /gene_synonym="C7orf24; CRF21; FLJ11717; GCTG; GGC;
                     MGC3077"
                     /product="gamma-glutamylcyclotransferase, transcript
                     variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037669.1"
                     /db_xref="GI:315360616"
                     /db_xref="GeneID:79017"
                     /db_xref="HGNC:21705"
                     /db_xref="MIM:137170"
                     /db_xref="HPRD:12912"
     CDS             complement(join(30536708..30536851,30538419..30538554,
                     30540152..30540297,30544185..30544325))
                     /gene="GGCT"
                     /gene_synonym="C7orf24; CRF21; FLJ11717; GCTG; GGC;
                     MGC3077"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="gamma-glutamylcyclotransferase isoform 1"
                     /protein_id="NP_076956.1"
                     /db_xref="GI:13129018"
                     /db_xref="CCDS:CCDS5428.1"
                     /db_xref="GeneID:79017"
                     /db_xref="HGNC:21705"
                     /db_xref="HPRD:12912"
                     /db_xref="MIM:137170"
     CDS             complement(join(30536708..30536851,30544185..30544325))
                     /gene="GGCT"
                     /gene_synonym="C7orf24; CRF21; FLJ11717; GCTG; GGC;
                     MGC3077"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="gamma-glutamylcyclotransferase isoform 4"
                     /protein_id="NP_001186746.1"
                     /db_xref="GI:315360622"
                     /db_xref="GeneID:79017"
                     /db_xref="HGNC:21705"
                     /db_xref="MIM:137170"
                     /db_xref="HPRD:12912"
     CDS             complement(join(30536794..30536851,30537357..30537512,
                     30540152..30540297,30544185..30544325))
                     /gene="GGCT"
                     /gene_synonym="C7orf24; CRF21; FLJ11717; GCTG; GGC;
                     MGC3077"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="gamma-glutamylcyclotransferase isoform 2"
                     /protein_id="NP_001186744.1"
                     /db_xref="GI:315360618"
                     /db_xref="GeneID:79017"
                     /db_xref="HGNC:21705"
                     /db_xref="MIM:137170"
                     /db_xref="HPRD:12912"
     CDS             complement(join(30536794..30536851,30540152..30540297,
                     30544185..30544325))
                     /gene="GGCT"
                     /gene_synonym="C7orf24; CRF21; FLJ11717; GCTG; GGC;
                     MGC3077"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="gamma-glutamylcyclotransferase isoform 3"
                     /protein_id="NP_001186745.1"
                     /db_xref="GI:315360620"
                     /db_xref="GeneID:79017"
                     /db_xref="HGNC:21705"
                     /db_xref="MIM:137170"
                     /db_xref="HPRD:12912"
     gene            complement(30562760..30571836)
                     /gene="LOC100287825"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100287825"
     gene            complement(30587973..30617395)
                     /gene="LOC401320"
                     /gene_synonym="FLJ14434; FLJ37533; FLJ38737; FLJ39368;
                     FLJ39921"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:401320"
     misc_RNA        complement(join(30587973..30590397,30591716..30591795,
                     30601082..30601744,30603347..30603614,30608449..30608605,
                     30616180..30616326,30617265..30617395))
                     /gene="LOC401320"
                     /gene_synonym="FLJ14434; FLJ37533; FLJ38737; FLJ39368;
                     FLJ39921"
                     /product="hypothetical LOC401320"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038889.1"
                     /db_xref="GI:336455107"
                     /db_xref="GeneID:401320"
     gene            30634181..30673649
                     /gene="GARS"
                     /gene_synonym="CMT2D; DSMAV; GlyRS; HMN5; SMAD1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2617"
                     /db_xref="HGNC:4162"
                     /db_xref="HPRD:02617"
                     /db_xref="MIM:600287"
     mRNA            join(30634181..30634759,30638412..30638513,
                     30639563..30639665,30640675..30640816,30642650..30642738,
                     30643112..30643188,30649201..30649346,30651712..30651861,
                     30655512..30655674,30656730..30656894,30661009..30661116,
                     30661933..30662078,30665850..30665935,30668176..30668285,
                     30671064..30671157,30671863..30672053,30673351..30673649)
                     /gene="GARS"
                     /gene_synonym="CMT2D; DSMAV; GlyRS; HMN5; SMAD1"
                     /product="glycyl-tRNA synthetase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002047.2"
                     /db_xref="GI:116805339"
                     /db_xref="GeneID:2617"
                     /db_xref="HGNC:4162"
                     /db_xref="HPRD:02617"
                     /db_xref="MIM:600287"
     CDS             join(30634538..30634759,30638412..30638513,
                     30639563..30639665,30640675..30640816,30642650..30642738,
                     30643112..30643188,30649201..30649346,30651712..30651861,
                     30655512..30655674,30656730..30656894,30661009..30661116,
                     30661933..30662078,30665850..30665935,30668176..30668285,
                     30671064..30671157,30671863..30672053,30673351..30673476)
                     /gene="GARS"
                     /gene_synonym="CMT2D; DSMAV; GlyRS; HMN5; SMAD1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="glycyl-tRNA synthetase"
                     /protein_id="NP_002038.2"
                     /db_xref="GI:116805340"
                     /db_xref="CCDS:CCDS43564.1"
                     /db_xref="GeneID:2617"
                     /db_xref="HGNC:4162"
                     /db_xref="HPRD:02617"
                     /db_xref="MIM:600287"
     gene            complement(30691559..30739719)
                     /gene="CRHR2"
                     /gene_synonym="CRF2; CRFR2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1395"
                     /db_xref="HGNC:2358"
                     /db_xref="HPRD:03614"
                     /db_xref="MIM:602034"
     mRNA            complement(join(30691559..30693216,30694655..30694696,
                     30695196..30695331,30695543..30695628,30700189..30700261,
                     30701772..30701832,30702310..30702463,30704686..30704803,
                     30705146..30705255,30706844..30706929,30721531..30721656,
                     30728807..30728900,30739560..30739719))
                     /gene="CRHR2"
                     /gene_synonym="CRF2; CRFR2"
                     /product="corticotropin releasing hormone receptor 2,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001202475.1"
                     /db_xref="GI:321117172"
                     /db_xref="GeneID:1395"
                     /db_xref="HGNC:2358"
                     /db_xref="MIM:602034"
                     /db_xref="HPRD:03614"
     mRNA            complement(join(30691559..30693216,30694655..30694696,
                     30695196..30695331,30695543..30695628,30700189..30700261,
                     30701772..30701832,30702310..30702463,30704686..30704803,
                     30705146..30705255,30706844..30706929,30721531..30721656,
                     30726005..30726231,30728807..30728900,30739560..30739719))
                     /gene="CRHR2"
                     /gene_synonym="CRF2; CRFR2"
                     /product="corticotropin releasing hormone receptor 2,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001202481.1"
                     /db_xref="GI:321117238"
                     /db_xref="GeneID:1395"
                     /db_xref="HGNC:2358"
                     /db_xref="MIM:602034"
                     /db_xref="HPRD:03614"
     mRNA            complement(join(30691559..30693216,30694655..30694696,
                     30695196..30695331,30695543..30695628,30700189..30700261,
                     30701772..30701832,30702310..30702463,30704686..30704803,
                     30705146..30705255,30706844..30706929,30721531..30721656,
                     30721794..30722141))
                     /gene="CRHR2"
                     /gene_synonym="CRF2; CRFR2"
                     /product="corticotropin releasing hormone receptor 2,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001883.4"
                     /db_xref="GI:321117159"
                     /db_xref="GeneID:1395"
                     /db_xref="HGNC:2358"
                     /db_xref="HPRD:03614"
                     /db_xref="MIM:602034"
     mRNA            complement(join(30691559..30693216,30694655..30694696,
                     30695196..30695331,30695543..30695628,30700189..30700261,
                     30701772..30701832,30702310..30702463,30704686..30704803,
                     30705146..30705252,30706844..30706929,30721531..30721656,
                     30721794..30722141))
                     /gene="CRHR2"
                     /gene_synonym="CRF2; CRFR2"
                     /product="corticotropin releasing hormone receptor 2,
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001202482.1"
                     /db_xref="GI:321117246"
                     /db_xref="GeneID:1395"
                     /db_xref="HGNC:2358"
                     /db_xref="MIM:602034"
                     /db_xref="HPRD:03614"
     mRNA            complement(join(30691559..30693216,30694314..30694424,
                     30694655..30694696,30695196..30695331,30695543..30695628,
                     30700189..30700261,30701772..30701832,30702310..30702463,
                     30704686..30704803,30705146..30705255,30706844..30706929,
                     30721531..30721656,30721794..30722141))
                     /gene="CRHR2"
                     /gene_synonym="CRF2; CRFR2"
                     /product="corticotropin releasing hormone receptor 2,
                     transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001202483.1"
                     /db_xref="GI:321117256"
                     /db_xref="GeneID:1395"
                     /db_xref="HGNC:2358"
                     /db_xref="MIM:602034"
                     /db_xref="HPRD:03614"
     CDS             complement(join(30693076..30693216,30694655..30694696,
                     30695196..30695331,30695543..30695628,30700189..30700261,
                     30701772..30701832,30702310..30702463,30704686..30704803,
                     30705146..30705255,30706844..30706929,30721531..30721656,
                     30728807..30728900,30739560..30739649))
                     /gene="CRHR2"
                     /gene_synonym="CRF2; CRFR2"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="corticotropin-releasing factor receptor 2
                     isoform 2 precursor"
                     /protein_id="NP_001189404.1"
                     /db_xref="GI:321117173"
                     /db_xref="GeneID:1395"
                     /db_xref="HGNC:2358"
                     /db_xref="MIM:602034"
                     /db_xref="HPRD:03614"
     CDS             complement(join(30693076..30693216,30694655..30694696,
                     30695196..30695331,30695543..30695628,30700189..30700261,
                     30701772..30701832,30702310..30702463,30704686..30704803,
                     30705146..30705255,30706844..30706929,30721531..30721656,
                     30726005..30726065))
                     /gene="CRHR2"
                     /gene_synonym="CRF2; CRFR2"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="corticotropin-releasing factor receptor 2
                     isoform 3"
                     /protein_id="NP_001189410.1"
                     /db_xref="GI:321117239"
                     /db_xref="GeneID:1395"
                     /db_xref="HGNC:2358"
                     /db_xref="MIM:602034"
                     /db_xref="HPRD:03614"
     CDS             complement(join(30693076..30693216,30694655..30694696,
                     30695196..30695331,30695543..30695628,30700189..30700261,
                     30701772..30701832,30702310..30702463,30704686..30704803,
                     30705146..30705255,30706844..30706929,30721531..30721656,
                     30721794..30721896))
                     /gene="CRHR2"
                     /gene_synonym="CRF2; CRFR2"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="corticotropin-releasing factor receptor 2
                     isoform 1 precursor"
                     /protein_id="NP_001874.2"
                     /db_xref="GI:32307159"
                     /db_xref="CCDS:CCDS5429.1"
                     /db_xref="GeneID:1395"
                     /db_xref="HGNC:2358"
                     /db_xref="HPRD:03614"
                     /db_xref="MIM:602034"
     CDS             complement(join(30693076..30693216,30694655..30694696,
                     30695196..30695331,30695543..30695628,30700189..30700261,
                     30701772..30701832,30702310..30702463,30704686..30704803,
                     30705146..30705252,30706844..30706929,30721531..30721656,
                     30721794..30721896))
                     /gene="CRHR2"
                     /gene_synonym="CRF2; CRFR2"
                     /note="isoform 4 precursor is encoded by transcript
                     variant 4; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="corticotropin-releasing factor receptor 2
                     isoform 4 precursor"
                     /protein_id="NP_001189411.1"
                     /db_xref="GI:321117247"
                     /db_xref="GeneID:1395"
                     /db_xref="HGNC:2358"
                     /db_xref="MIM:602034"
                     /db_xref="HPRD:03614"
     CDS             complement(join(30694356..30694424,30694655..30694696,
                     30695196..30695331,30695543..30695628,30700189..30700261,
                     30701772..30701832,30702310..30702463,30704686..30704803,
                     30705146..30705255,30706844..30706929,30721531..30721656,
                     30721794..30721896))
                     /gene="CRHR2"
                     /gene_synonym="CRF2; CRFR2"
                     /note="isoform 5 precursor is encoded by transcript
                     variant 5; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="corticotropin-releasing factor receptor 2
                     isoform 5 precursor"
                     /protein_id="NP_001189412.1"
                     /db_xref="GI:321117257"
                     /db_xref="GeneID:1395"
                     /db_xref="HGNC:2358"
                     /db_xref="MIM:602034"
                     /db_xref="HPRD:03614"
     gene            30791751..30932002
                     /gene="INMT-FAM188B"
                     /gene_synonym="FLJ98803"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100526825"
                     /db_xref="HGNC:41995"
     misc_RNA        join(30791751..30791920,30793350..30793554,
                     30805961..30806177,30818048..30818167,30821593..30821828,
                     30825365..30825608,30830781..30831190,30868295..30868353,
                     30876274..30876380,30878816..30878932,30880376..30880464,
                     30890070..30890171,30891832..30891895,30893010..30893075,
                     30898873..30898940,30911858..30911921,30915110..30915271,
                     30921796..30921976,30922536..30922608,30931572..30932002)
                     /gene="INMT-FAM188B"
                     /gene_synonym="FLJ98803"
                     /product="INMT-FAM188B readthrough (non-protein coding)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037598.1"
                     /db_xref="GI:312839847"
                     /db_xref="GeneID:100526825"
                     /db_xref="HGNC:41995"
     gene            30791751..30797218
                     /gene="INMT"
                     /gene_synonym="MGC125940; MGC125941"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:11185"
                     /db_xref="HGNC:6069"
                     /db_xref="MIM:604854"
     mRNA            join(30791751..30791920,30793347..30793554,
                     30795038..30797218)
                     /gene="INMT"
                     /gene_synonym="MGC125940; MGC125941"
                     /product="indolethylamine N-methyltransferase, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006774.4"
                     /db_xref="GI:66933017"
                     /db_xref="GeneID:11185"
                     /db_xref="HGNC:6069"
                     /db_xref="HPRD:06890"
                     /db_xref="MIM:604854"
     mRNA            join(30791751..30791920,30793350..30793554,
                     30795038..30797218)
                     /gene="INMT"
                     /gene_synonym="MGC125940; MGC125941"
                     /product="indolethylamine N-methyltransferase, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199219.1"
                     /db_xref="GI:312836855"
                     /db_xref="GeneID:11185"
                     /db_xref="HGNC:6069"
                     /db_xref="MIM:604854"
     CDS             join(30791767..30791920,30793347..30793554,
                     30795038..30795467)
                     /gene="INMT"
                     /gene_synonym="MGC125940; MGC125941"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="indolethylamine N-methyltransferase isoform 1"
                     /protein_id="NP_006765.4"
                     /db_xref="GI:66933018"
                     /db_xref="CCDS:CCDS5430.1"
                     /db_xref="GeneID:11185"
                     /db_xref="HGNC:6069"
                     /db_xref="MIM:604854"
     CDS             join(30791767..30791920,30793350..30793554,
                     30795038..30795467)
                     /gene="INMT"
                     /gene_synonym="MGC125940; MGC125941"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="indolethylamine N-methyltransferase isoform 2"
                     /protein_id="NP_001186148.1"
                     /db_xref="GI:312836856"
                     /db_xref="GeneID:11185"
                     /db_xref="HGNC:6069"
                     /db_xref="MIM:604854"
     gene            30811033..30932002
                     /gene="FAM188B"
                     /gene_synonym="C7orf67; FLJ22374; FLJ51453; MGC44277"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84182"
                     /db_xref="HGNC:21916"
                     /db_xref="HPRD:13387"
     mRNA            join(30811033..30811172,30818048..30818167,
                     30821593..30821828,30825365..30825608,30830781..30831190,
                     30868295..30868353,30876274..30876380,30878816..30878932,
                     30880376..30880464,30890070..30890171,30891832..30891895,
                     30893010..30893075,30898873..30898940,30911858..30911921,
                     30915110..30915271,30921796..30921976,30922536..30922608,
                     30931572..30932002)
                     /gene="FAM188B"
                     /gene_synonym="C7orf67; FLJ22374; FLJ51453; MGC44277"
                     /product="family with sequence similarity 188, member B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032222.2"
                     /db_xref="GI:93102404"
                     /db_xref="GeneID:84182"
                     /db_xref="HGNC:21916"
                     /db_xref="HPRD:13387"
     CDS             join(30811110..30811172,30818048..30818167,
                     30821593..30821828,30825365..30825608,30830781..30831190,
                     30868295..30868353,30876274..30876380,30878816..30878932,
                     30880376..30880464,30890070..30890171,30891832..30891895,
                     30893010..30893075,30898873..30898940,30911858..30911921,
                     30915110..30915271,30921796..30921976,30922536..30922608,
                     30931572..30931620)
                     /gene="FAM188B"
                     /gene_synonym="C7orf67; FLJ22374; FLJ51453; MGC44277"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC84182"
                     /protein_id="NP_115598.2"
                     /db_xref="GI:93102405"
                     /db_xref="CCDS:CCDS43565.1"
                     /db_xref="GeneID:84182"
                     /db_xref="HGNC:21916"
                     /db_xref="HPRD:13387"
     gene            30928865..30930462
                     /gene="LOC100533673"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533673"
     gene            30951415..30965131
                     /gene="AQP1"
                     /gene_synonym="AQP-CHIP; CHIP28; CO; MGC26324"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:358"
                     /db_xref="HGNC:633"
                     /db_xref="HPRD:00140"
                     /db_xref="MIM:107776"
     mRNA            join(30951415..30951908,30961681..30961845,
                     30962179..30962259,30963065..30965131)
                     /gene="AQP1"
                     /gene_synonym="AQP-CHIP; CHIP28; CO; MGC26324"
                     /product="aquaporin 1 (Colton blood group), transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198098.2"
                     /db_xref="GI:297307114"
                     /db_xref="GeneID:358"
                     /db_xref="HGNC:633"
                     /db_xref="HPRD:00140"
                     /db_xref="MIM:107776"
     CDS             join(30951525..30951908,30961681..30961845,
                     30962179..30962259,30963065..30963244)
                     /gene="AQP1"
                     /gene_synonym="AQP-CHIP; CHIP28; CO; MGC26324"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="aquaporin-1 isoform 1"
                     /protein_id="NP_932766.1"
                     /db_xref="GI:37694062"
                     /db_xref="CCDS:CCDS5431.1"
                     /db_xref="GeneID:358"
                     /db_xref="HGNC:633"
                     /db_xref="HPRD:00140"
                     /db_xref="MIM:107776"
     mRNA            join(30960915..30960930,30961296..30961453,
                     30961681..30961845,30962179..30962259,30963065..30965131)
                     /gene="AQP1"
                     /gene_synonym="AQP-CHIP; CHIP28; CO; MGC26324"
                     /product="aquaporin 1 (Colton blood group), transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001185060.1"
                     /db_xref="GI:297307115"
                     /db_xref="GeneID:358"
                     /db_xref="HGNC:633"
                     /db_xref="MIM:107776"
                     /db_xref="HPRD:00140"
     mRNA            join(30961105..30961453,30961681..30961845,
                     30962179..30962259,30963065..30965131)
                     /gene="AQP1"
                     /gene_synonym="AQP-CHIP; CHIP28; CO; MGC26324"
                     /product="aquaporin 1 (Colton blood group), transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001185061.1"
                     /db_xref="GI:297307117"
                     /db_xref="GeneID:358"
                     /db_xref="HGNC:633"
                     /db_xref="MIM:107776"
                     /db_xref="HPRD:00140"
     mRNA            join(30961119..30961239,30961681..30961845,
                     30962179..30962259,30963065..30965131)
                     /gene="AQP1"
                     /gene_synonym="AQP-CHIP; CHIP28; CO; MGC26324"
                     /product="aquaporin 1 (Colton blood group), transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001185062.1"
                     /db_xref="GI:297307119"
                     /db_xref="GeneID:358"
                     /db_xref="HGNC:633"
                     /db_xref="MIM:107776"
                     /db_xref="HPRD:00140"
     CDS             join(30961201..30961239,30961681..30961845,
                     30962179..30962259,30963065..30963244)
                     /gene="AQP1"
                     /gene_synonym="AQP-CHIP; CHIP28; CO; MGC26324"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="aquaporin-1 isoform 4"
                     /protein_id="NP_001171991.1"
                     /db_xref="GI:297307120"
                     /db_xref="CCDS:CCDS55096.1"
                     /db_xref="GeneID:358"
                     /db_xref="HGNC:633"
                     /db_xref="HPRD:00140"
                     /db_xref="MIM:107776"
     CDS             join(30961223..30961453,30961681..30961845,
                     30962179..30962259,30963065..30963244)
                     /gene="AQP1"
                     /gene_synonym="AQP-CHIP; CHIP28; CO; MGC26324"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="aquaporin-1 isoform 3"
                     /protein_id="NP_001171990.1"
                     /db_xref="GI:297307118"
                     /db_xref="CCDS:CCDS55097.1"
                     /db_xref="GeneID:358"
                     /db_xref="HGNC:633"
                     /db_xref="HPRD:00140"
                     /db_xref="MIM:107776"
     CDS             join(30961319..30961453,30961681..30961845,
                     30962179..30962259,30963065..30963244)
                     /gene="AQP1"
                     /gene_synonym="AQP-CHIP; CHIP28; CO; MGC26324"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="aquaporin-1 isoform 2"
                     /protein_id="NP_001171989.1"
                     /db_xref="GI:297307116"
                     /db_xref="CCDS:CCDS55098.1"
                     /db_xref="GeneID:358"
                     /db_xref="HGNC:633"
                     /db_xref="HPRD:00140"
                     /db_xref="MIM:107776"
     gene            31003636..31019146
                     /gene="GHRHR"
                     /gene_synonym="GHRFR; GRFR; IGHD1B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2692"
                     /db_xref="HGNC:4266"
                     /db_xref="HPRD:00748"
                     /db_xref="MIM:139191"
     mRNA            join(31003636..31003740,31008449..31008551,
                     31008678..31008785,31009482..31009579,31010734..31010831,
                     31011578..31011710,31013600..31013753,31014044..31014104,
                     31014586..31014655,31015392..31015483,31016044..31016173,
                     31016896..31016937,31018734..31019146)
                     /gene="GHRHR"
                     /gene_synonym="GHRFR; GRFR; IGHD1B"
                     /product="growth hormone releasing hormone receptor"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000823.3"
                     /db_xref="GI:297307106"
                     /db_xref="GeneID:2692"
                     /db_xref="HGNC:4266"
                     /db_xref="HPRD:00748"
                     /db_xref="MIM:139191"
     CDS             join(31003684..31003740,31008449..31008551,
                     31008678..31008785,31009482..31009579,31010734..31010831,
                     31011578..31011710,31013600..31013753,31014044..31014104,
                     31014586..31014655,31015392..31015483,31016044..31016173,
                     31016896..31016937,31018734..31018859)
                     /gene="GHRHR"
                     /gene_synonym="GHRFR; GRFR; IGHD1B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="growth hormone-releasing hormone receptor
                     precursor"
                     /protein_id="NP_000814.2"
                     /db_xref="GI:58530851"
                     /db_xref="CCDS:CCDS5432.1"
                     /db_xref="GeneID:2692"
                     /db_xref="HGNC:4266"
                     /db_xref="HPRD:00748"
                     /db_xref="MIM:139191"
     gene            31092076..31151093
                     /gene="ADCYAP1R1"
                     /gene_synonym="PAC1; PACAPR; PACAPRI"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:117"
                     /db_xref="HGNC:242"
                     /db_xref="MIM:102981"
     mRNA            join(31092076..31092293,31102810..31102931,
                     31104447..31104552,31117606..31117713,31120228..31120248,
                     31121328..31121369,31123756..31123865,31124352..31124449,
                     31124925..31125057,31125998..31126151,31126557..31126617,
                     31127241..31127310,31132258..31132349,31139741..31139824,
                     31142851..31142980,31144482..31144523,31146110..31151093)
                     /gene="ADCYAP1R1"
                     /gene_synonym="PAC1; PACAPR; PACAPRI"
                     /product="adenylate cyclase activating polypeptide 1
                     (pituitary) receptor type I, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199635.1"
                     /db_xref="GI:313851017"
                     /db_xref="GeneID:117"
                     /db_xref="HGNC:242"
                     /db_xref="MIM:102981"
     mRNA            join(31092076..31092293,31102810..31102931,
                     31104447..31104552,31117606..31117713,31120228..31120248,
                     31121328..31121369,31123756..31123865,31124352..31124449,
                     31124925..31125057,31125998..31126151,31126557..31126617,
                     31127241..31127310,31132258..31132349,31139744..31139824,
                     31142851..31142980,31144482..31144523,31146110..31151093)
                     /gene="ADCYAP1R1"
                     /gene_synonym="PAC1; PACAPR; PACAPRI"
                     /product="adenylate cyclase activating polypeptide 1
                     (pituitary) receptor type I, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199636.1"
                     /db_xref="GI:313851019"
                     /db_xref="GeneID:117"
                     /db_xref="HGNC:242"
                     /db_xref="MIM:102981"
     mRNA            join(31092076..31092293,31102810..31102931,
                     31104447..31104552,31117606..31117713,31120228..31120248,
                     31121328..31121369,31123756..31123865,31124352..31124449,
                     31124925..31125057,31125998..31126151,31126557..31126617,
                     31127241..31127310,31132258..31132349,31142851..31142980,
                     31144482..31144523,31146110..31151093)
                     /gene="ADCYAP1R1"
                     /gene_synonym="PAC1; PACAPR; PACAPRI"
                     /product="adenylate cyclase activating polypeptide 1
                     (pituitary) receptor type I, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001118.4"
                     /db_xref="GI:313851021"
                     /db_xref="GeneID:117"
                     /db_xref="HGNC:242"
                     /db_xref="HPRD:00045"
                     /db_xref="MIM:102981"
     mRNA            join(31092076..31092293,31102810..31102931,
                     31104447..31104552,31117606..31117713,31123756..31123865,
                     31124352..31124449,31124925..31125057,31125998..31126151,
                     31126557..31126617,31127241..31127310,31132258..31132349,
                     31142851..31142980,31144482..31144523,31146110..31151093)
                     /gene="ADCYAP1R1"
                     /gene_synonym="PAC1; PACAPR; PACAPRI"
                     /product="adenylate cyclase activating polypeptide 1
                     (pituitary) receptor type I, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199637.1"
                     /db_xref="GI:313851022"
                     /db_xref="GeneID:117"
                     /db_xref="HGNC:242"
                     /db_xref="MIM:102981"
     CDS             join(31102881..31102931,31104447..31104552,
                     31117606..31117713,31120228..31120248,31121328..31121369,
                     31123756..31123865,31124352..31124449,31124925..31125057,
                     31125998..31126151,31126557..31126617,31127241..31127310,
                     31132258..31132349,31139741..31139824,31142851..31142980,
                     31144482..31144523,31146110..31146298)
                     /gene="ADCYAP1R1"
                     /gene_synonym="PAC1; PACAPR; PACAPRI"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="pituitary adenylate cyclase-activating
                     polypeptide type I receptor isoform 1 precursor"
                     /protein_id="NP_001186564.1"
                     /db_xref="GI:313851018"
                     /db_xref="GeneID:117"
                     /db_xref="HGNC:242"
                     /db_xref="MIM:102981"
     CDS             join(31102881..31102931,31104447..31104552,
                     31117606..31117713,31120228..31120248,31121328..31121369,
                     31123756..31123865,31124352..31124449,31124925..31125057,
                     31125998..31126151,31126557..31126617,31127241..31127310,
                     31132258..31132349,31139744..31139824,31142851..31142980,
                     31144482..31144523,31146110..31146298)
                     /gene="ADCYAP1R1"
                     /gene_synonym="PAC1; PACAPR; PACAPRI"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="pituitary adenylate cyclase-activating
                     polypeptide type I receptor isoform 2 precursor"
                     /protein_id="NP_001186565.1"
                     /db_xref="GI:313851020"
                     /db_xref="GeneID:117"
                     /db_xref="HGNC:242"
                     /db_xref="MIM:102981"
     CDS             join(31102881..31102931,31104447..31104552,
                     31117606..31117713,31120228..31120248,31121328..31121369,
                     31123756..31123865,31124352..31124449,31124925..31125057,
                     31125998..31126151,31126557..31126617,31127241..31127310,
                     31132258..31132349,31142851..31142980,31144482..31144523,
                     31146110..31146298)
                     /gene="ADCYAP1R1"
                     /gene_synonym="PAC1; PACAPR; PACAPRI"
                     /note="isoform 3 precursor is encoded by transcript
                     variant 3; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="pituitary adenylate cyclase-activating
                     polypeptide type I receptor isoform 3 precursor"
                     /protein_id="NP_001109.2"
                     /db_xref="GI:29171759"
                     /db_xref="CCDS:CCDS5433.1"
                     /db_xref="GeneID:117"
                     /db_xref="HGNC:242"
                     /db_xref="MIM:102981"
     CDS             join(31102881..31102931,31104447..31104552,
                     31117606..31117713,31123756..31123865,31124352..31124449,
                     31124925..31125057,31125998..31126151,31126557..31126617,
                     31127241..31127310,31132258..31132349,31142851..31142980,
                     31144482..31144523,31146110..31146298)
                     /gene="ADCYAP1R1"
                     /gene_synonym="PAC1; PACAPR; PACAPRI"
                     /note="isoform 4 precursor is encoded by transcript
                     variant 4; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="pituitary adenylate cyclase-activating
                     polypeptide type I receptor isoform 4 precursor"
                     /protein_id="NP_001186566.1"
                     /db_xref="GI:313851023"
                     /db_xref="GeneID:117"
                     /db_xref="HGNC:242"
                     /db_xref="MIM:102981"
     gene            complement(31377079..31380538)
                     /gene="NEUROD6"
                     /gene_synonym="Atoh2; bHLHa2; Math-2; MATH2; NEX1M"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:63974"
                     /db_xref="HGNC:13804"
                     /db_xref="HPRD:11387"
                     /db_xref="MIM:611513"
     mRNA            complement(join(31377079..31378903,31380207..31380538))
                     /gene="NEUROD6"
                     /gene_synonym="Atoh2; bHLHa2; Math-2; MATH2; NEX1M"
                     /product="neurogenic differentiation 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022728.2"
                     /db_xref="GI:27475984"
                     /db_xref="GeneID:63974"
                     /db_xref="HGNC:13804"
                     /db_xref="HPRD:11387"
                     /db_xref="MIM:611513"
     CDS             complement(31377869..31378882)
                     /gene="NEUROD6"
                     /gene_synonym="Atoh2; bHLHa2; Math-2; MATH2; NEX1M"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="neurogenic differentiation factor 6"
                     /protein_id="NP_073565.2"
                     /db_xref="GI:27475985"
                     /db_xref="CCDS:CCDS5434.1"
                     /db_xref="GeneID:63974"
                     /db_xref="HGNC:13804"
                     /db_xref="HPRD:11387"
                     /db_xref="MIM:611513"
     gene            31556978..31693303
                     /gene="CCDC129"
                     /gene_synonym="FLJ38344"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:223075"
                     /db_xref="HGNC:27363"
                     /db_xref="HPRD:14137"
     mRNA            join(31556978..31557951,31592620..31592801,
                     31594089..31594137,31594472..31594515,31609372..31609423,
                     31611716..31611802,31614154..31614356,31617477..31618048,
                     31622748..31622805,31681790..31681872,31682296..31683567,
                     31690756..31690883,31691553..31691664,31692132..31693303)
                     /gene="CCDC129"
                     /gene_synonym="FLJ38344"
                     /product="coiled-coil domain containing 129"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_194300.2"
                     /db_xref="GI:154937345"
                     /db_xref="GeneID:223075"
                     /db_xref="HGNC:27363"
                     /db_xref="HPRD:14137"
     CDS             join(31592639..31592801,31594089..31594137,
                     31594472..31594515,31609372..31609423,31611716..31611802,
                     31614154..31614356,31617477..31618048,31622748..31622805,
                     31681790..31681872,31682296..31683567,31690756..31690883,
                     31691553..31691664,31692132..31692443)
                     /gene="CCDC129"
                     /gene_synonym="FLJ38344"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="coiled-coil domain-containing protein 129"
                     /protein_id="NP_919276.2"
                     /db_xref="GI:154937346"
                     /db_xref="CCDS:CCDS5435.2"
                     /db_xref="GeneID:223075"
                     /db_xref="HGNC:27363"
                     /db_xref="HPRD:14137"
     gene            31726631..31748069
                     /gene="C7orf16"
                     /gene_synonym="GSBS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10842"
                     /db_xref="HGNC:16973"
                     /db_xref="HPRD:06820"
                     /db_xref="MIM:604088"
     mRNA            join(31726631..31726920,31732020..31732137,
                     31735083..31735235,31736579..31736731,31746818..31748069)
                     /gene="C7orf16"
                     /gene_synonym="GSBS"
                     /product="chromosome 7 open reading frame 16, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006658.4"
                     /db_xref="GI:300863143"
                     /db_xref="GeneID:10842"
                     /db_xref="HGNC:16973"
                     /db_xref="HPRD:06820"
                     /db_xref="MIM:604088"
     mRNA            join(31726631..31726920,31732020..31732137,
                     31736579..31736731,31746818..31748069)
                     /gene="C7orf16"
                     /gene_synonym="GSBS"
                     /product="chromosome 7 open reading frame 16, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145123.2"
                     /db_xref="GI:300863144"
                     /db_xref="GeneID:10842"
                     /db_xref="HGNC:16973"
                     /db_xref="MIM:604088"
                     /db_xref="HPRD:06820"
     CDS             join(31732056..31732137,31735083..31735235,
                     31736579..31736731,31746818..31746897)
                     /gene="C7orf16"
                     /gene_synonym="GSBS"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="G-substrate isoform 1"
                     /protein_id="NP_006649.2"
                     /db_xref="GI:223468610"
                     /db_xref="CCDS:CCDS5436.1"
                     /db_xref="GeneID:10842"
                     /db_xref="HGNC:16973"
                     /db_xref="HPRD:06820"
                     /db_xref="MIM:604088"
     CDS             join(31732056..31732137,31736579..31736731,
                     31746818..31746897)
                     /gene="C7orf16"
                     /gene_synonym="GSBS"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="G-substrate isoform 2"
                     /protein_id="NP_001138595.1"
                     /db_xref="GI:223468612"
                     /db_xref="CCDS:CCDS47570.1"
                     /db_xref="GeneID:10842"
                     /db_xref="HGNC:16973"
                     /db_xref="HPRD:06820"
                     /db_xref="MIM:604088"
     gene            complement(31792632..32338383)
                     /gene="PDE1C"
                     /gene_synonym="Hcam3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5137"
                     /db_xref="HGNC:8776"
                     /db_xref="HPRD:04287"
                     /db_xref="MIM:602987"
     mRNA            complement(join(31792632..31793167,31815278..31815346,
                     31848645..31848722,31855538..31855768,31862687..31862862,
                     31864481..31864601,31867906..31867987,31876794..31876914,
                     31877484..31877585,31887582..31887710,31890255..31890355,
                     31904556..31904696,31912905..31913021,31917583..31917649,
                     31918609..31918791,31920360..31920473,32209397..32209568,
                     32249101..32249151,32338263..32338383))
                     /gene="PDE1C"
                     /gene_synonym="Hcam3"
                     /product="phosphodiesterase 1C, calmodulin-dependent
                     70kDa, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001191058.1"
                     /db_xref="GI:300796870"
                     /db_xref="GeneID:5137"
                     /db_xref="HGNC:8776"
                     /db_xref="MIM:602987"
                     /db_xref="HPRD:04287"
     mRNA            complement(join(31792632..31793167,31815278..31815346,
                     31848645..31848722,31855538..31855768,31862687..31862862,
                     31864481..31864601,31867906..31867987,31876794..31876914,
                     31877484..31877585,31887582..31887710,31890255..31890355,
                     31904556..31904696,31912905..31913021,31917583..31917649,
                     31918609..31918791,31920360..31920473,32091166..32091192,
                     32109905..32110007,32110591..32110980))
                     /gene="PDE1C"
                     /gene_synonym="Hcam3"
                     /product="phosphodiesterase 1C, calmodulin-dependent
                     70kDa, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001191059.1"
                     /db_xref="GI:300796892"
                     /db_xref="GeneID:5137"
                     /db_xref="HGNC:8776"
                     /db_xref="MIM:602987"
                     /db_xref="HPRD:04287"
     mRNA            complement(join(31792632..31793167,31815278..31815346,
                     31848645..31848722,31855538..31855768,31862687..31862862,
                     31864481..31864601,31867906..31867987,31876794..31876914,
                     31877484..31877585,31887582..31887710,31890255..31890355,
                     31904556..31904696,31912905..31913021,31917583..31917649,
                     31918609..31918791,31920360..31920473,32091166..32091192,
                     32109905..32110466))
                     /gene="PDE1C"
                     /gene_synonym="Hcam3"
                     /product="phosphodiesterase 1C, calmodulin-dependent
                     70kDa, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001191057.1"
                     /db_xref="GI:300796848"
                     /db_xref="GeneID:5137"
                     /db_xref="HGNC:8776"
                     /db_xref="MIM:602987"
                     /db_xref="HPRD:04287"
     CDS             complement(join(31792998..31793167,31815278..31815346,
                     31848645..31848722,31855538..31855768,31862687..31862862,
                     31864481..31864601,31867906..31867987,31876794..31876914,
                     31877484..31877585,31887582..31887710,31890255..31890355,
                     31904556..31904696,31912905..31913021,31917583..31917649,
                     31918609..31918791,31920360..31920473,32209397..32209568,
                     32249101..32249151,32338263..32338347))
                     /gene="PDE1C"
                     /gene_synonym="Hcam3"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium/calmodulin-dependent 3',5'-cyclic
                     nucleotide phosphodiesterase 1C isoform 3"
                     /protein_id="NP_001177987.1"
                     /db_xref="GI:300796871"
                     /db_xref="CCDS:CCDS55100.1"
                     /db_xref="GeneID:5137"
                     /db_xref="HGNC:8776"
                     /db_xref="HPRD:04287"
                     /db_xref="MIM:602987"
     CDS             complement(join(31792998..31793167,31815278..31815346,
                     31848645..31848722,31855538..31855768,31862687..31862862,
                     31864481..31864601,31867906..31867987,31876794..31876914,
                     31877484..31877585,31887582..31887710,31890255..31890355,
                     31904556..31904696,31912905..31913021,31917583..31917649,
                     31918609..31918791,31920360..31920473,32091166..32091192,
                     32109905..32110005))
                     /gene="PDE1C"
                     /gene_synonym="Hcam3"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium/calmodulin-dependent 3',5'-cyclic
                     nucleotide phosphodiesterase 1C isoform 2"
                     /protein_id="NP_001177986.1"
                     /db_xref="GI:300796849"
                     /db_xref="CCDS:CCDS55099.1"
                     /db_xref="GeneID:5137"
                     /db_xref="HGNC:8776"
                     /db_xref="HPRD:04287"
                     /db_xref="MIM:602987"
     CDS             complement(join(31792998..31793167,31815278..31815346,
                     31848645..31848722,31855538..31855768,31862687..31862862,
                     31864481..31864601,31867906..31867987,31876794..31876914,
                     31877484..31877585,31887582..31887710,31890255..31890355,
                     31904556..31904696,31912905..31913021,31917583..31917649,
                     31918609..31918791,31920360..31920473,32091166..32091192,
                     32109905..32110005))
                     /gene="PDE1C"
                     /gene_synonym="Hcam3"
                     /note="isoform 2 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium/calmodulin-dependent 3',5'-cyclic
                     nucleotide phosphodiesterase 1C isoform 2"
                     /protein_id="NP_001177988.1"
                     /db_xref="GI:300796893"
                     /db_xref="CCDS:CCDS55099.1"
                     /db_xref="GeneID:5137"
                     /db_xref="HGNC:8776"
                     /db_xref="HPRD:04287"
                     /db_xref="MIM:602987"
     mRNA            complement(join(31829247..31829873,31848645..31848722,
                     31855538..31855768,31862687..31862862,31864481..31864601,
                     31867906..31867987,31876794..31876914,31877484..31877585,
                     31887582..31887710,31890255..31890355,31904556..31904696,
                     31912905..31913021,31917583..31917649,31918609..31918791,
                     31920360..31920473,32091166..32091192,32109905..32110007,
                     32110818..32111045))
                     /gene="PDE1C"
                     /gene_synonym="Hcam3"
                     /product="phosphodiesterase 1C, calmodulin-dependent
                     70kDa, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005020.2"
                     /db_xref="GI:300796806"
                     /db_xref="GeneID:5137"
                     /db_xref="HGNC:8776"
                     /db_xref="HPRD:04287"
                     /db_xref="MIM:602987"
     mRNA            complement(join(31829247..31829873,31848645..31848722,
                     31855538..31855768,31862687..31862862,31864481..31864601,
                     31867906..31867987,31876794..31876914,31877484..31877585,
                     31887582..31887710,31890255..31890355,31904556..31904696,
                     31912905..31913021,31917583..31917649,31918609..31918791,
                     31920360..31920473,32091166..32091192,32109905..32110466))
                     /gene="PDE1C"
                     /gene_synonym="Hcam3"
                     /product="phosphodiesterase 1C, calmodulin-dependent
                     70kDa, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001191056.1"
                     /db_xref="GI:300796826"
                     /db_xref="GeneID:5137"
                     /db_xref="HGNC:8776"
                     /db_xref="MIM:602987"
                     /db_xref="HPRD:04287"
     CDS             complement(join(31829860..31829873,31848645..31848722,
                     31855538..31855768,31862687..31862862,31864481..31864601,
                     31867906..31867987,31876794..31876914,31877484..31877585,
                     31887582..31887710,31890255..31890355,31904556..31904696,
                     31912905..31913021,31917583..31917649,31918609..31918791,
                     31920360..31920473,32091166..32091192,32109905..32110005))
                     /gene="PDE1C"
                     /gene_synonym="Hcam3"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium/calmodulin-dependent 3',5'-cyclic
                     nucleotide phosphodiesterase 1C isoform 1"
                     /protein_id="NP_001177985.1"
                     /db_xref="GI:300796827"
                     /db_xref="CCDS:CCDS5437.1"
                     /db_xref="GeneID:5137"
                     /db_xref="HGNC:8776"
                     /db_xref="HPRD:04287"
                     /db_xref="MIM:602987"
     CDS             complement(join(31829860..31829873,31848645..31848722,
                     31855538..31855768,31862687..31862862,31864481..31864601,
                     31867906..31867987,31876794..31876914,31877484..31877585,
                     31887582..31887710,31890255..31890355,31904556..31904696,
                     31912905..31913021,31917583..31917649,31918609..31918791,
                     31920360..31920473,32091166..32091192,32109905..32110005))
                     /gene="PDE1C"
                     /gene_synonym="Hcam3"
                     /note="isoform 1 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium/calmodulin-dependent 3',5'-cyclic
                     nucleotide phosphodiesterase 1C isoform 1"
                     /protein_id="NP_005011.1"
                     /db_xref="GI:4826894"
                     /db_xref="CCDS:CCDS5437.1"
                     /db_xref="GeneID:5137"
                     /db_xref="HGNC:8776"
                     /db_xref="HPRD:04287"
                     /db_xref="MIM:602987"
     gene            complement(32496509..32498106)
                     /gene="LOC100130673"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:100130673"
     misc_RNA        complement(32496509..32498106)
                     /gene="LOC100130673"
                     /product="phosphoribosyl pyrophosphate synthetase 2
                     pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_038454.1"
                     /db_xref="GI:336285246"
                     /db_xref="GeneID:100130673"
     gene            32511041..32512613
                     /gene="SLC25A5P5"
                     /gene_synonym="ANTP5; TCAG_29001"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442525"
                     /db_xref="HGNC:511"
     gene            complement(32524945..32534870)
                     /gene="LSM5"
                     /gene_synonym="FLJ12710; YER146W"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23658"
                     /db_xref="HGNC:17162"
                     /db_xref="MIM:607285"
     mRNA            complement(join(32524945..32526905,32527297..32527369,
                     32528237..32528264,32528861..32528956,32534842..32534870))
                     /gene="LSM5"
                     /gene_synonym="FLJ12710; YER146W"
                     /product="LSM5 homolog, U6 small nuclear RNA associated
                     (S. cerevisiae), transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130710.1"
                     /db_xref="GI:195222721"
                     /db_xref="GeneID:23658"
                     /db_xref="HGNC:17162"
                     /db_xref="MIM:607285"
     mRNA            complement(join(32524945..32526905,32527297..32527369,
                     32528237..32528264,32528861..32528956,32534603..32534870))
                     /gene="LSM5"
                     /gene_synonym="FLJ12710; YER146W"
                     /product="LSM5 homolog, U6 small nuclear RNA associated
                     (S. cerevisiae), transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001139499.1"
                     /db_xref="GI:213385304"
                     /db_xref="GeneID:23658"
                     /db_xref="HGNC:17162"
                     /db_xref="MIM:607285"
     misc_RNA        complement(join(32524945..32526905,32527297..32527369,
                     32528237..32528264,32528861..32528956,32529637..32530475))
                     /gene="LSM5"
                     /gene_synonym="FLJ12710; YER146W"
                     /product="LSM5 homolog, U6 small nuclear RNA associated
                     (S. cerevisiae), transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024466.1"
                     /db_xref="GI:213385306"
                     /db_xref="GeneID:23658"
                     /db_xref="HGNC:17162"
                     /db_xref="MIM:607285"
     mRNA            complement(join(32524945..32526905,32527297..32527369,
                     32528237..32528264,32528861..32528956,32529932..32530023))
                     /gene="LSM5"
                     /gene_synonym="FLJ12710; YER146W"
                     /product="LSM5 homolog, U6 small nuclear RNA associated
                     (S. cerevisiae), transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012322.2"
                     /db_xref="GI:195539322"
                     /db_xref="GeneID:23658"
                     /db_xref="HGNC:17162"
                     /db_xref="HPRD:06285"
                     /db_xref="MIM:607285"
     CDS             complement(join(32526873..32526905,32527297..32527369,
                     32528237..32528264,32528861..32528956,32529932..32529977))
                     /gene="LSM5"
                     /gene_synonym="FLJ12710; YER146W"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="U6 snRNA-associated Sm-like protein LSm5 isoform
                     a"
                     /protein_id="NP_036454.1"
                     /db_xref="GI:6912488"
                     /db_xref="CCDS:CCDS5438.1"
                     /db_xref="GeneID:23658"
                     /db_xref="HGNC:17162"
                     /db_xref="MIM:607285"
     CDS             complement(join(32526873..32526905,32527297..32527369,
                     32528237..32528264,32528861..32528915))
                     /gene="LSM5"
                     /gene_synonym="FLJ12710; YER146W"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="U6 snRNA-associated Sm-like protein LSm5 isoform
                     b"
                     /protein_id="NP_001124182.1"
                     /db_xref="GI:195222722"
                     /db_xref="CCDS:CCDS47571.1"
                     /db_xref="GeneID:23658"
                     /db_xref="HGNC:17162"
                     /db_xref="MIM:607285"
     CDS             complement(join(32526873..32526905,32527297..32527369,
                     32528237..32528264,32528861..32528915))
                     /gene="LSM5"
                     /gene_synonym="FLJ12710; YER146W"
                     /note="isoform b is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="U6 snRNA-associated Sm-like protein LSm5 isoform
                     b"
                     /protein_id="NP_001132971.1"
                     /db_xref="GI:213385305"
                     /db_xref="CCDS:CCDS47571.1"
                     /db_xref="GeneID:23658"
                     /db_xref="HGNC:17162"
                     /db_xref="MIM:607285"
     gene            32535176..32623779
                     /gene="AVL9"
                     /gene_synonym="DKFZp686G0344; KIAA0241"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23080"
                     /db_xref="HGNC:28994"
                     /db_xref="HPRD:13788"
                     /db_xref="MIM:612927"
     mRNA            join(32535176..32535414,32582753..32582873,
                     32584306..32584391,32588459..32588530,32590946..32591035,
                     32591841..32591907,32593339..32593379,32594170..32594208,
                     32598171..32598240,32598541..32599076,32609632..32609766,
                     32612811..32613030,32615567..32615684,32619831..32619884,
                     32620414..32620502,32623404..32623779)
                     /gene="AVL9"
                     /gene_synonym="DKFZp686G0344; KIAA0241"
                     /product="AVL9 homolog (S. cerevisiase)"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015060.1"
                     /db_xref="GI:57529130"
                     /db_xref="GeneID:23080"
                     /db_xref="HGNC:28994"
                     /db_xref="HPRD:13788"
                     /db_xref="MIM:612927"
     CDS             join(32535322..32535414,32582753..32582873,
                     32584306..32584391,32588459..32588530,32590946..32591035,
                     32591841..32591907,32593339..32593379,32594170..32594208,
                     32598171..32598240,32598541..32599076,32609632..32609766,
                     32612811..32613030,32615567..32615684,32619831..32619884,
                     32620414..32620502,32623404..32623519)
                     /gene="AVL9"
                     /gene_synonym="DKFZp686G0344; KIAA0241"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="late secretory pathway protein AVL9 homolog"
                     /protein_id="NP_055875.1"
                     /db_xref="GI:57529131"
                     /db_xref="CCDS:CCDS34613.1"
                     /db_xref="GeneID:23080"
                     /db_xref="HGNC:28994"
                     /db_xref="HPRD:13788"
                     /db_xref="MIM:612927"
     gene            complement(32620551..32758780)
                     /gene="DPY19L1P1"
                     /gene_synonym="FLJ23115"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:100129460"
                     /db_xref="HGNC:22395"
     misc_RNA        complement(join(32620551..32620925,32621184..32621276,
                     32625589..32625748,32630491..32630616,32632796..32632918,
                     32660016..32660096,32660625..32660684,32662973..32663051,
                     32672155..32672232,32674864..32674963,32678886..32678977,
                     32695599..32695656,32715544..32715637,32716400..32716520,
                     32718605..32718742,32756330..32756421,32758748..32758780))
                     /gene="DPY19L1P1"
                     /gene_synonym="FLJ23115"
                     /product="dpy-19-like 1 pseudogene 1 (C. elegans)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_036680.1"
                     /db_xref="GI:308522771"
                     /db_xref="GeneID:100129460"
                     /db_xref="HGNC:22395"
     gene            32767562..32769595
                     /gene="LOC441208"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:441208"
     misc_RNA        32767562..32769595
                     /gene="LOC441208"
                     /product="zinc and ring finger 2 pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003502.2"
                     /db_xref="GI:225007645"
                     /db_xref="GeneID:441208"
     gene            32772593..32772689
                     /gene="MIR550A2"
                     /gene_synonym="hsa-mir-550a-2; MIR550-2; MIRN550-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:693134"
                     /db_xref="HGNC:32805"
                     /db_xref="miRBase:MI0003601"
     gene            complement(32772593..32772689)
                     /gene="MIR550B2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100500830"
                     /db_xref="HGNC:38910"
                     /db_xref="miRBase:MI0016687"
     ncRNA           32772593..32772689
                     /gene="MIR550A2"
                     /gene_synonym="hsa-mir-550a-2; MIR550-2; MIRN550-2"
                     /ncRNA_class="miRNA"
                     /product="microRNA 550a-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_030320.1"
                     /db_xref="GI:262205942"
                     /db_xref="GeneID:693134"
                     /db_xref="HGNC:32805"
                     /db_xref="miRBase:MI0003601"
     ncRNA           32772593..32772689
                     /gene="MIR550A2"
                     /gene_synonym="hsa-mir-550a-2; MIR550-2; MIRN550-2"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-550-2"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:693134"
                     /db_xref="miRBase:MI0003601"
                     /db_xref="HGNC:32805"
     ncRNA           complement(32772593..32772689)
                     /gene="MIR550B2"
                     /ncRNA_class="miRNA"
                     /product="microRNA 550b-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037514.1"
                     /db_xref="GI:338797694"
                     /db_xref="GeneID:100500830"
                     /db_xref="HGNC:38910"
                     /db_xref="miRBase:MI0016687"
     gene            32797898..32802536
                     /gene="LOC401321"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:401321"
     misc_RNA        32797898..32802536
                     /gene="LOC401321"
                     /product="hypothetical LOC401321"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_036501.1"
                     /db_xref="GI:302393535"
                     /db_xref="GeneID:401321"
     gene            32861140..32878182
                     /gene="LOC100133317"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /pseudo
                     /db_xref="GeneID:100133317"
     exon            32861140..32861205
                     /gene="LOC100133317"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100133317"
     exon            32862662..32862833
                     /gene="LOC100133317"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100133317"
     exon            32865773..32865873
                     /gene="LOC100133317"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:100133317"
     exon            32867007..32867129
                     /gene="LOC100133317"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=4
                     /pseudo
                     /db_xref="GeneID:100133317"
     exon            32878026..32878182
                     /gene="LOC100133317"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=5
                     /pseudo
                     /db_xref="GeneID:100133317"
     gene            complement(32907778..32931468)
                     /gene="KBTBD2"
                     /gene_synonym="BKLHD1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:25948"
                     /db_xref="HGNC:21751"
                     /db_xref="HPRD:13756"
     mRNA            complement(join(32907778..32910492,32914604..32914769,
                     32919047..32919554,32931148..32931468))
                     /gene="KBTBD2"
                     /gene_synonym="BKLHD1"
                     /product="kelch repeat and BTB (POZ) domain containing 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015483.2"
                     /db_xref="GI:223468658"
                     /db_xref="GeneID:25948"
                     /db_xref="HGNC:21751"
                     /db_xref="HPRD:13756"
     CDS             complement(join(32908957..32910492,32914604..32914769,
                     32919047..32919216))
                     /gene="KBTBD2"
                     /gene_synonym="BKLHD1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="kelch repeat and BTB domain-containing protein
                     2"
                     /protein_id="NP_056298.2"
                     /db_xref="GI:223468659"
                     /db_xref="CCDS:CCDS34614.1"
                     /db_xref="GeneID:25948"
                     /db_xref="HGNC:21751"
                     /db_xref="HPRD:13756"
     gene            complement(32956427..32982782)
                     /gene="RP9P"
                     /gene_synonym="FLJ33904"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:441212"
                     /db_xref="HGNC:33969"
     misc_RNA        complement(join(32956427..32957154,32957923..32957984,
                     32960951..32961042,32969690..32969720,32973426..32973508,
                     32982482..32982782))
                     /gene="RP9P"
                     /gene_synonym="FLJ33904"
                     /product="retinitis pigmentosa 9 pseudogene"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003500.1"
                     /db_xref="GI:134254460"
                     /db_xref="GeneID:441212"
                     /db_xref="HGNC:33969"
     gene            32997005..33046543
                     /gene="FKBP9"
                     /gene_synonym="DKFZp586B1723; FKBP60; FKBP63; MGC126772;
                     MGC138258; PPIase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:11328"
                     /db_xref="HGNC:3725"
                     /db_xref="HPRD:06510"
     mRNA            join(32997005..32997406,33014229..33014374,
                     33014794..33014983,33015966..33016111,33019976..33020165,
                     33028119..33028264,33035775..33035961,33039727..33039872,
                     33042288..33042451,33044787..33046543)
                     /gene="FKBP9"
                     /gene_synonym="DKFZp586B1723; FKBP60; FKBP63; MGC126772;
                     MGC138258; PPIase"
                     /product="FK506 binding protein 9, 63 kDa"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_007270.3"
                     /db_xref="GI:195234780"
                     /db_xref="GeneID:11328"
                     /db_xref="HGNC:3725"
                     /db_xref="HPRD:06510"
     CDS             join(32997186..32997406,33014229..33014374,
                     33014794..33014983,33015966..33016111,33019976..33020165,
                     33028119..33028264,33035775..33035961,33039727..33039872,
                     33042288..33042451,33044787..33044963)
                     /gene="FKBP9"
                     /gene_synonym="DKFZp586B1723; FKBP60; FKBP63; MGC126772;
                     MGC138258; PPIase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="peptidyl-prolyl cis-trans isomerase FKBP9
                     precursor"
                     /protein_id="NP_009201.2"
                     /db_xref="GI:33469985"
                     /db_xref="CCDS:CCDS5439.1"
                     /db_xref="GeneID:11328"
                     /db_xref="HGNC:3725"
                     /db_xref="HPRD:06510"
     gene            complement(33053742..33102409)
                     /gene="NT5C3"
                     /gene_synonym="cN-III; MGC27337; MGC87109; MGC87828;
                     P5'N-1; PN-I; PSN1; UMPH; UMPH1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51251"
                     /db_xref="HGNC:17820"
                     /db_xref="MIM:606224"
     mRNA            complement(join(33053742..33054443,33055282..33055482,
                     33057051..33057213,33059247..33059336,33060884..33060969,
                     33061665..33061711,33063651..33063720,33066429..33066527,
                     33102180..33102409))
                     /gene="NT5C3"
                     /gene_synonym="cN-III; MGC27337; MGC87109; MGC87828;
                     P5'N-1; PN-I; PSN1; UMPH; UMPH1"
                     /product="5'-nucleotidase, cytosolic III, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001002010.1"
                     /db_xref="GI:70608081"
                     /db_xref="GeneID:51251"
                     /db_xref="HGNC:17820"
                     /db_xref="HPRD:05871"
                     /db_xref="MIM:606224"
     misc_RNA        complement(join(33053742..33054443,33055282..33055482,
                     33057051..33057213,33059247..33059336,33060884..33060969,
                     33061665..33061711,33063651..33063720,33066429..33066527,
                     33075546..33075600,33102180..33102409))
                     /gene="NT5C3"
                     /gene_synonym="cN-III; MGC27337; MGC87109; MGC87828;
                     P5'N-1; PN-I; PSN1; UMPH; UMPH1"
                     /product="5'-nucleotidase, cytosolic III, transcript
                     variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029372.1"
                     /db_xref="GI:260763923"
                     /db_xref="GeneID:51251"
                     /db_xref="HGNC:17820"
                     /db_xref="MIM:606224"
     mRNA            complement(join(33053742..33054443,33055282..33055482,
                     33057051..33057213,33059247..33059336,33060884..33060969,
                     33061665..33061711,33063651..33063720,33066429..33066527,
                     33075546..33075600,33080484..33080522))
                     /gene="NT5C3"
                     /gene_synonym="cN-III; MGC27337; MGC87109; MGC87828;
                     P5'N-1; PN-I; PSN1; UMPH; UMPH1"
                     /product="5'-nucleotidase, cytosolic III, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016489.11"
                     /db_xref="GI:70608210"
                     /db_xref="GeneID:51251"
                     /db_xref="HGNC:17820"
                     /db_xref="HPRD:05871"
                     /db_xref="MIM:606224"
     mRNA            complement(join(33053742..33054443,33055282..33055482,
                     33057051..33057213,33059247..33059336,33060884..33060969,
                     33061665..33061711,33063651..33063720,33066429..33066527,
                     33069241..33069326,33075546..33075600,33080484..33080521))
                     /gene="NT5C3"
                     /gene_synonym="cN-III; MGC27337; MGC87109; MGC87828;
                     P5'N-1; PN-I; PSN1; UMPH; UMPH1"
                     /product="5'-nucleotidase, cytosolic III, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001166118.1"
                     /db_xref="GI:260763925"
                     /db_xref="GeneID:51251"
                     /db_xref="HGNC:17820"
                     /db_xref="MIM:606224"
     CDS             complement(join(33054342..33054443,33055282..33055482,
                     33057051..33057213,33059247..33059336,33060884..33060969,
                     33061665..33061711,33063651..33063720,33066429..33066527,
                     33102180..33102332))
                     /gene="NT5C3"
                     /gene_synonym="cN-III; MGC27337; MGC87109; MGC87828;
                     P5'N-1; PN-I; PSN1; UMPH; UMPH1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytosolic 5'-nucleotidase 3 isoform 1"
                     /protein_id="NP_001002010.1"
                     /db_xref="GI:70608082"
                     /db_xref="CCDS:CCDS34616.1"
                     /db_xref="GeneID:51251"
                     /db_xref="HGNC:17820"
                     /db_xref="MIM:606224"
     CDS             complement(join(33054342..33054443,33055282..33055482,
                     33057051..33057213,33059247..33059336,33060884..33060969,
                     33061665..33061711,33063651..33063720,33066429..33066527,
                     33075546..33075581))
                     /gene="NT5C3"
                     /gene_synonym="cN-III; MGC27337; MGC87109; MGC87828;
                     P5'N-1; PN-I; PSN1; UMPH; UMPH1"
                     /note="isoform 2 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytosolic 5'-nucleotidase 3 isoform 2"
                     /protein_id="NP_057573.2"
                     /db_xref="GI:70608211"
                     /db_xref="CCDS:CCDS34617.1"
                     /db_xref="GeneID:51251"
                     /db_xref="HGNC:17820"
                     /db_xref="MIM:606224"
     CDS             complement(join(33054342..33054443,33055282..33055482,
                     33057051..33057213,33059247..33059336,33060884..33060969,
                     33061665..33061711,33063651..33063720,33066429..33066527))
                     /gene="NT5C3"
                     /gene_synonym="cN-III; MGC27337; MGC87109; MGC87828;
                     P5'N-1; PN-I; PSN1; UMPH; UMPH1"
                     /note="isoform 3 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytosolic 5'-nucleotidase 3 isoform 3"
                     /protein_id="NP_001159590.1"
                     /db_xref="GI:260763926"
                     /db_xref="CCDS:CCDS55101.1"
                     /db_xref="GeneID:51251"
                     /db_xref="HGNC:17820"
                     /db_xref="MIM:606224"
     gene            complement(33075824..33075994)
                     /gene="RPS29P14"
                     /gene_synonym="RPS29_3_802"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129599"
                     /db_xref="HGNC:36471"
     gene            complement(33134409..33149002)
                     /gene="RP9"
                     /gene_synonym="PAP-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6100"
                     /db_xref="HGNC:10288"
                     /db_xref="HPRD:08457"
                     /db_xref="MIM:607331"
     mRNA            complement(join(33134409..33135044,33136105..33136166,
                     33136883..33136974,33138919..33139048,33140143..33140173,
                     33148833..33149002))
                     /gene="RP9"
                     /gene_synonym="PAP-1"
                     /product="retinitis pigmentosa 9 (autosomal dominant)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_203288.1"
                     /db_xref="GI:42718019"
                     /db_xref="GeneID:6100"
                     /db_xref="HGNC:10288"
                     /db_xref="HPRD:08457"
                     /db_xref="MIM:607331"
     CDS             complement(join(33134846..33135044,33136105..33136166,
                     33136883..33136974,33138919..33139048,33140143..33140173,
                     33148833..33148984))
                     /gene="RP9"
                     /gene_synonym="PAP-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="retinitis pigmentosa 9 protein"
                     /protein_id="NP_976033.1"
                     /db_xref="GI:42718020"
                     /db_xref="CCDS:CCDS5440.1"
                     /db_xref="GeneID:6100"
                     /db_xref="HGNC:10288"
                     /db_xref="HPRD:08457"
                     /db_xref="MIM:607331"
     gene            33169152..33645680
                     /gene="BBS9"
                     /gene_synonym="B1; C18; D1; MGC118917; PTHB1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:27241"
                     /db_xref="HGNC:30000"
                     /db_xref="HPRD:16262"
                     /db_xref="MIM:607968"
     mRNA            join(33169152..33169653,33185854..33185976,
                     33192313..33192463,33195250..33195314,33217090..33217203,
                     33296848..33297022,33303902..33303986,33312624..33312807,
                     33313439..33313568,33376053..33376234,33380509..33380585,
                     33384193..33384246,33388680..33388782,33397467..33397607,
                     33407379..33407474,33423278..33423450,33427604..33427756,
                     33545075..33545257,33573566..33573788,33644477..33644587,
                     33644807..33645680)
                     /gene="BBS9"
                     /gene_synonym="B1; C18; D1; MGC118917; PTHB1"
                     /product="Bardet-Biedl syndrome 9, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014451.3"
                     /db_xref="GI:75905798"
                     /db_xref="GeneID:27241"
                     /db_xref="HGNC:30000"
                     /db_xref="HPRD:16262"
                     /db_xref="MIM:607968"
     mRNA            join(33169152..33169653,33185854..33185976,
                     33192313..33192463,33195250..33195314,33217090..33217203,
                     33296848..33297022,33303902..33303986,33312624..33312807,
                     33313439..33313568,33376053..33376234,33380509..33380585,
                     33384193..33384246,33388680..33388782,33390831..33390935,
                     33392471..33392485,33397467..33397607,33407379..33407474,
                     33423278..33423450,33427604..33427756,33545075..33545257,
                     33573566..33573788,33644477..33644587,33644807..33645680)
                     /gene="BBS9"
                     /gene_synonym="B1; C18; D1; MGC118917; PTHB1"
                     /product="Bardet-Biedl syndrome 9, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198428.2"
                     /db_xref="GI:75905799"
                     /db_xref="GeneID:27241"
                     /db_xref="HGNC:30000"
                     /db_xref="HPRD:16262"
                     /db_xref="MIM:607968"
     mRNA            join(33169152..33169653,33185854..33185976,
                     33192313..33192463,33195250..33195314,33217090..33217203,
                     33296848..33297022,33303902..33303986,33312624..33312807,
                     33313439..33313568,33376053..33376234,33380509..33380585,
                     33384193..33384246,33388680..33388782,33392471..33392485,
                     33397467..33397607,33407379..33407474,33423278..33423450,
                     33427604..33427756,33545075..33545257,33573566..33573788,
                     33644477..33644587,33644807..33645680)
                     /gene="BBS9"
                     /gene_synonym="B1; C18; D1; MGC118917; PTHB1"
                     /product="Bardet-Biedl syndrome 9, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001033604.1"
                     /db_xref="GI:75905800"
                     /db_xref="GeneID:27241"
                     /db_xref="HGNC:30000"
                     /db_xref="HPRD:16262"
                     /db_xref="MIM:607968"
     mRNA            join(33169152..33169653,33185854..33185976,
                     33192313..33192463,33195250..33195314,33217090..33217203,
                     33296848..33297022,33303902..33303986,33312624..33312807,
                     33313439..33313568,33376053..33376234,33380509..33380585,
                     33384193..33384246,33388680..33388782,33390831..33390935,
                     33397467..33397607,33407379..33407474,33423278..33423450,
                     33427604..33427756,33545075..33545257,33573566..33573788,
                     33644477..33644587,33644807..33645680)
                     /gene="BBS9"
                     /gene_synonym="B1; C18; D1; MGC118917; PTHB1"
                     /product="Bardet-Biedl syndrome 9, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001033605.1"
                     /db_xref="GI:75905802"
                     /db_xref="GeneID:27241"
                     /db_xref="HGNC:30000"
                     /db_xref="HPRD:16262"
                     /db_xref="MIM:607968"
     CDS             join(33185865..33185976,33192313..33192463,
                     33195250..33195314,33217090..33217203,33296848..33297022,
                     33303902..33303986,33312624..33312807,33313439..33313568,
                     33376053..33376234,33380509..33380585,33384193..33384246,
                     33388680..33388782,33397467..33397607,33407379..33407474,
                     33423278..33423450,33427604..33427756,33545075..33545257,
                     33573566..33573788,33644477..33644587,33644807..33644838)
                     /gene="BBS9"
                     /gene_synonym="B1; C18; D1; MGC118917; PTHB1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein PTHB1 isoform 1"
                     /protein_id="NP_055266.2"
                     /db_xref="GI:38569432"
                     /db_xref="CCDS:CCDS5441.1"
                     /db_xref="GeneID:27241"
                     /db_xref="HGNC:30000"
                     /db_xref="HPRD:16262"
                     /db_xref="MIM:607968"
     CDS             join(33185865..33185976,33192313..33192463,
                     33195250..33195314,33217090..33217203,33296848..33297022,
                     33303902..33303986,33312624..33312807,33313439..33313568,
                     33376053..33376234,33380509..33380585,33384193..33384246,
                     33388680..33388782,33390831..33390935,33392471..33392485,
                     33397467..33397607,33407379..33407474,33423278..33423450,
                     33427604..33427756,33545075..33545257,33573566..33573788,
                     33644477..33644587,33644807..33644838)
                     /gene="BBS9"
                     /gene_synonym="B1; C18; D1; MGC118917; PTHB1"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein PTHB1 isoform 2"
                     /protein_id="NP_940820.1"
                     /db_xref="GI:38569434"
                     /db_xref="CCDS:CCDS43566.1"
                     /db_xref="GeneID:27241"
                     /db_xref="HGNC:30000"
                     /db_xref="HPRD:16262"
                     /db_xref="MIM:607968"
     CDS             join(33185865..33185976,33192313..33192463,
                     33195250..33195314,33217090..33217203,33296848..33297022,
                     33303902..33303986,33312624..33312807,33313439..33313568,
                     33376053..33376234,33380509..33380585,33384193..33384246,
                     33388680..33388782,33392471..33392485,33397467..33397607,
                     33407379..33407474,33423278..33423450,33427604..33427756,
                     33545075..33545257,33573566..33573788,33644477..33644587,
                     33644807..33644838)
                     /gene="BBS9"
                     /gene_synonym="B1; C18; D1; MGC118917; PTHB1"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein PTHB1 isoform 3"
                     /protein_id="NP_001028776.1"
                     /db_xref="GI:75905801"
                     /db_xref="CCDS:CCDS47572.1"
                     /db_xref="GeneID:27241"
                     /db_xref="HGNC:30000"
                     /db_xref="HPRD:16262"
                     /db_xref="MIM:607968"
     CDS             join(33185865..33185976,33192313..33192463,
                     33195250..33195314,33217090..33217203,33296848..33297022,
                     33303902..33303986,33312624..33312807,33313439..33313568,
                     33376053..33376234,33380509..33380585,33384193..33384246,
                     33388680..33388782,33390831..33390935,33397467..33397607,
                     33407379..33407474,33423278..33423450,33427604..33427756,
                     33545075..33545257,33573566..33573788,33644477..33644587,
                     33644807..33644838)
                     /gene="BBS9"
                     /gene_synonym="B1; C18; D1; MGC118917; PTHB1"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein PTHB1 isoform 4"
                     /protein_id="NP_001028777.1"
                     /db_xref="GI:75905803"
                     /db_xref="CCDS:CCDS34618.1"
                     /db_xref="GeneID:27241"
                     /db_xref="HGNC:30000"
                     /db_xref="HPRD:16262"
                     /db_xref="MIM:607968"
     gene            33419561..33420478
                     /gene="LOC100421336"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421336"
     gene            33765593..33768068
                     /gene="FLJ20712"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 mRNAs, 2 ESTs, 1 Protein"
                     /db_xref="GeneID:55025"
     misc_RNA        join(33765593..33765721,33767140..33768068)
                     /gene="FLJ20712"
                     /product="hypothetical FLJ20712"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 mRNAs, 2 ESTs, 1 Protein"
                     /transcript_id="XR_108766.1"
                     /db_xref="GI:310119947"
                     /db_xref="GeneID:55025"
     gene            33945112..34194112
                     /gene="BMPER"
                     /gene_synonym="CRIM3; CV-2; CV2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:168667"
                     /db_xref="HGNC:24154"
                     /db_xref="HPRD:16368"
                     /db_xref="MIM:608699"
     mRNA            join(33945112..33945358,33946430..33946515,
                     33976901..33977000,34006091..34006173,34009941..34010031,
                     34014314..34014396,34085918..34086017,34091473..34091582,
                     34094775..34094915,34097671..34097775,34101614..34101659,
                     34118469..34118798,34125368..34125704,34182842..34182972,
                     34192704..34194112)
                     /gene="BMPER"
                     /gene_synonym="CRIM3; CV-2; CV2"
                     /product="BMP binding endothelial regulator"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_133468.3"
                     /db_xref="GI:197304753"
                     /db_xref="GeneID:168667"
                     /db_xref="HGNC:24154"
                     /db_xref="HPRD:16368"
                     /db_xref="MIM:608699"
     CDS             join(33945226..33945358,33946430..33946515,
                     33976901..33977000,34006091..34006173,34009941..34010031,
                     34014314..34014396,34085918..34086017,34091473..34091582,
                     34094775..34094915,34097671..34097775,34101614..34101659,
                     34118469..34118798,34125368..34125704,34182842..34182972,
                     34192704..34192885)
                     /gene="BMPER"
                     /gene_synonym="CRIM3; CV-2; CV2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="BMP-binding endothelial regulator protein
                     precursor"
                     /protein_id="NP_597725.1"
                     /db_xref="GI:37693519"
                     /db_xref="CCDS:CCDS5442.1"
                     /db_xref="GeneID:168667"
                     /db_xref="HGNC:24154"
                     /db_xref="HPRD:16368"
                     /db_xref="MIM:608699"
     gene            complement(34386124..34873943)
                     /gene="AAA1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:404744"
                     /db_xref="MIM:608596"
     misc_RNA        complement(join(34386124..34390459,34457191..34457284,
                     34609324..34609473,34768349..34768428,34797686..34797884))
                     /gene="AAA1"
                     /product="asthma-associated alternatively spliced gene 1,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033664.1"
                     /db_xref="GI:296040456"
                     /db_xref="GeneID:404744"
                     /db_xref="MIM:608596"
     misc_RNA        complement(join(34386124..34390459,34457191..34457284,
                     34768349..34768428,34797686..34797884))
                     /gene="AAA1"
                     /product="asthma-associated alternatively spliced gene 1,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033665.1"
                     /db_xref="GI:296040457"
                     /db_xref="GeneID:404744"
                     /db_xref="MIM:608596"
     gene            34697897..34917944
                     /gene="NPSR1"
                     /gene_synonym="ASRT2; GPR154; GPRA; NPSR; PGR14; VRR1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:387129"
                     /db_xref="HGNC:23631"
                     /db_xref="HPRD:10547"
                     /db_xref="MIM:608595"
     mRNA            join(34697897..34698171,34724164..34724296,
                     34818074..34818177,34851382..34851475,34867013..34867214,
                     34873996..34874072,34884508..34884594,34888095..34888275,
                     34917688..34917944)
                     /gene="NPSR1"
                     /gene_synonym="ASRT2; GPR154; GPRA; NPSR; PGR14; VRR1"
                     /product="neuropeptide S receptor 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_207173.1"
                     /db_xref="GI:46391084"
                     /db_xref="GeneID:387129"
                     /db_xref="HGNC:23631"
                     /db_xref="HPRD:10547"
                     /db_xref="MIM:608595"
     mRNA            join(34697897..34698171,34724164..34724296,
                     34818074..34818177,34851382..34851475,34867013..34867214,
                     34873996..34874072,34884508..34884594,34888095..34888275,
                     34889177..34889590)
                     /gene="NPSR1"
                     /gene_synonym="ASRT2; GPR154; GPRA; NPSR; PGR14; VRR1"
                     /product="neuropeptide S receptor 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_207172.1"
                     /db_xref="GI:46395495"
                     /db_xref="GeneID:387129"
                     /db_xref="HGNC:23631"
                     /db_xref="HPRD:10547"
                     /db_xref="MIM:608595"
     CDS             join(34698025..34698171,34724164..34724296,
                     34818074..34818177,34851382..34851475,34867013..34867214,
                     34873996..34874072,34884508..34884594,34888095..34888275,
                     34917688..34917796)
                     /gene="NPSR1"
                     /gene_synonym="ASRT2; GPR154; GPRA; NPSR; PGR14; VRR1"
                     /note="isoform B is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="neuropeptide S receptor isoform B"
                     /protein_id="NP_997056.1"
                     /db_xref="GI:46391085"
                     /db_xref="CCDS:CCDS5443.1"
                     /db_xref="GeneID:387129"
                     /db_xref="HGNC:23631"
                     /db_xref="HPRD:10547"
                     /db_xref="MIM:608595"
     CDS             join(34698025..34698171,34724164..34724296,
                     34818074..34818177,34851382..34851475,34867013..34867214,
                     34873996..34874072,34884508..34884594,34888095..34888275,
                     34889177..34889267)
                     /gene="NPSR1"
                     /gene_synonym="ASRT2; GPR154; GPRA; NPSR; PGR14; VRR1"
                     /note="isoform A is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="neuropeptide S receptor isoform A"
                     /protein_id="NP_997055.1"
                     /db_xref="GI:46395496"
                     /db_xref="CCDS:CCDS5444.1"
                     /db_xref="GeneID:387129"
                     /db_xref="HGNC:23631"
                     /db_xref="HPRD:10547"
                     /db_xref="MIM:608595"
     gene            34750715..34751094
                     /gene="RPL7P31"
                     /gene_synonym="RPL7_14_803"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100270909"
                     /db_xref="HGNC:36988"
     misc_RNA        complement(join(34758474..34759420,34762896..34763007,
                     34768349..34768428,34807954..34808052,34873773..34873943))
                     /gene="AAA1"
                     /product="asthma-associated alternatively spliced gene 1,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_015356.2"
                     /db_xref="GI:296040436"
                     /db_xref="GeneID:404744"
                     /db_xref="MIM:608596"
     gene            complement(34789865..34791656)
                     /gene="LOC100421175"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421175"
     gene            complement(34968493..35077653)
                     /gene="DPY19L1"
                     /gene_synonym="KIAA0877"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23333"
                     /db_xref="HGNC:22205"
                     /db_xref="MIM:613892"
     mRNA            complement(join(34968493..34971341,34977606..34977731,
                     34978888..34978987,34979765..34979939,34981377..34981496,
                     34982227..34982251,34985279..34985328,34987242..34987313,
                     34989409..34989510,34994310..34994390,34994920..34994979,
                     34997596..34997682,35006506..35006583,35009045..35009144,
                     35013126..35013217,35029496..35029553,35050080..35050173,
                     35050942..35051062,35053180..35053317,35057494..35057581,
                     35058184..35058208,35077430..35077653))
                     /gene="DPY19L1"
                     /gene_synonym="KIAA0877"
                     /product="dpy-19-like 1 (C. elegans)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015283.1"
                     /db_xref="GI:148839334"
                     /db_xref="GeneID:23333"
                     /db_xref="HGNC:22205"
                     /db_xref="MIM:613892"
     CDS             complement(join(34971185..34971341,34977606..34977731,
                     34978888..34978987,34979765..34979939,34981377..34981496,
                     34982227..34982251,34985279..34985328,34987242..34987313,
                     34989409..34989510,34994310..34994390,34994920..34994979,
                     34997596..34997682,35006506..35006583,35009045..35009144,
                     35013126..35013217,35029496..35029553,35050080..35050173,
                     35050942..35051062,35053180..35053317,35057494..35057581,
                     35058184..35058208,35077430..35077508))
                     /gene="DPY19L1"
                     /gene_synonym="KIAA0877"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein dpy-19 homolog 1"
                     /protein_id="NP_056098.1"
                     /db_xref="GI:148839335"
                     /db_xref="CCDS:CCDS43567.1"
                     /db_xref="GeneID:23333"
                     /db_xref="HGNC:22205"
                     /db_xref="MIM:613892"
     gene            complement(35129456..35147346)
                     /gene="DPY19L2P1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:554236"
                     /db_xref="HGNC:22305"
     misc_RNA        complement(join(35129456..35131558,35144256..35144375,
                     35145656..35147346))
                     /gene="DPY19L2P1"
                     /product="dpy-19-like 2 pseudogene 1 (C. elegans)"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002833.1"
                     /db_xref="GI:84872123"
                     /db_xref="GeneID:554236"
                     /db_xref="HGNC:22305"
     gene            complement(35160119..35225653)
                     /gene="LOC100420070"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420070"
     gene            35208787..35209317
                     /gene="S100A11P2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:347701"
                     /db_xref="HGNC:37840"
     gene            complement(35242042..35293711)
                     /gene="TBX20"
                     /gene_synonym="ASD4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57057"
                     /db_xref="HGNC:11598"
                     /db_xref="MIM:606061"
     mRNA            complement(join(35242042..35242382,35244082..35244194,
                     35271116..35271192,35280491..35280649,35284561..35284669,
                     35288289..35288453,35289563..35289815,35293105..35293711))
                     /gene="TBX20"
                     /gene_synonym="ASD4"
                     /product="T-box 20, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001077653.2"
                     /db_xref="GI:261337144"
                     /db_xref="GeneID:57057"
                     /db_xref="HGNC:11598"
                     /db_xref="MIM:606061"
     CDS             complement(join(35242042..35242382,35244082..35244194,
                     35271116..35271192,35280491..35280649,35284561..35284669,
                     35288289..35288453,35289563..35289815,35293105..35293231))
                     /gene="TBX20"
                     /gene_synonym="ASD4"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="T-box transcription factor TBX20 isoform 1"
                     /protein_id="NP_001071121.1"
                     /db_xref="GI:117676399"
                     /db_xref="CCDS:CCDS43568.1"
                     /db_xref="GeneID:57057"
                     /db_xref="HGNC:11598"
                     /db_xref="MIM:606061"
     mRNA            complement(join(35271112..35271192,35280491..35280649,
                     35284561..35284669,35288289..35288453,35289563..35289815,
                     35293105..35293711))
                     /gene="TBX20"
                     /gene_synonym="ASD4"
                     /product="T-box 20, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001166220.1"
                     /db_xref="GI:261337145"
                     /db_xref="GeneID:57057"
                     /db_xref="HGNC:11598"
                     /db_xref="MIM:606061"
     CDS             complement(join(35271112..35271192,35280491..35280649,
                     35284561..35284669,35288289..35288453,35289563..35289815,
                     35293105..35293231))
                     /gene="TBX20"
                     /gene_synonym="ASD4"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="T-box transcription factor TBX20 isoform 2"
                     /protein_id="NP_001159692.1"
                     /db_xref="GI:261337146"
                     /db_xref="GeneID:57057"
                     /db_xref="HGNC:11598"
                     /db_xref="MIM:606061"
     gene            35353466..35416086
                     /gene="LOC401324"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:401324"
     misc_RNA        join(35353466..35353551,35391901..35392001,
                     35412645..35416086)
                     /gene="LOC401324"
                     /product="hypothetical LOC401324"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038864.1"
                     /db_xref="GI:336391120"
                     /db_xref="GeneID:401324"
     gene            complement(35672269..35734772)
                     /gene="HERPUD2"
                     /gene_synonym="FLJ22313; FLJ31032"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64224"
                     /db_xref="HGNC:21915"
                     /db_xref="HPRD:07984"
     mRNA            complement(join(35672269..35673461,35673922..35674039,
                     35674745..35675068,35677960..35678082,35707044..35707198,
                     35709825..35709938,35712811..35712888,35733794..35734237,
                     35734411..35734772))
                     /gene="HERPUD2"
                     /gene_synonym="FLJ22313; FLJ31032"
                     /product="HERPUD family member 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022373.4"
                     /db_xref="GI:188497631"
                     /db_xref="GeneID:64224"
                     /db_xref="HGNC:21915"
                     /db_xref="HPRD:07984"
     CDS             complement(join(35673300..35673461,35673922..35674039,
                     35674745..35675068,35677960..35678082,35707044..35707198,
                     35709825..35709938,35712811..35712888,35733794..35733940))
                     /gene="HERPUD2"
                     /gene_synonym="FLJ22313; FLJ31032"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homocysteine-responsive endoplasmic
                     reticulum-resident ubiquitin-like domain member 2 protein"
                     /protein_id="NP_071768.3"
                     /db_xref="GI:188497632"
                     /db_xref="CCDS:CCDS5446.1"
                     /db_xref="GeneID:64224"
                     /db_xref="HGNC:21915"
                     /db_xref="HPRD:07984"
     gene            35756102..35759322
                     /gene="LOC100506725"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 27 ESTs"
                     /db_xref="GeneID:100506725"
     misc_RNA        join(35756102..35756738,35758680..35759322)
                     /gene="LOC100506725"
                     /product="hypothetical LOC100506725, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 24 ESTs"
                     /transcript_id="XR_108767.1"
                     /db_xref="GI:310119950"
                     /db_xref="GeneID:100506725"
     misc_RNA        join(35756202..35756478,35758680..35759316)
                     /gene="LOC100506725"
                     /product="hypothetical LOC100506725, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 23 ESTs"
                     /transcript_id="XR_108768.1"
                     /db_xref="GI:310119951"
                     /db_xref="GeneID:100506725"
     gene            complement(35805268..35808259)
                     /gene="LOC442293"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442293"
     gene            35840627..35944917
                     /gene="SEPT7"
                     /gene_synonym="CDC10; CDC3; Nbla02942; SEPT7A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:989"
                     /db_xref="HGNC:1717"
                     /db_xref="HPRD:04398"
                     /db_xref="MIM:603151"
     mRNA            join(35840627..35840880,35871102..35871106,
                     35872408..35872510,35903162..35903268,35912276..35912376,
                     35913251..35913385,35919433..35919550,35922094..35922186,
                     35923501..35923597,35925438..35925489,35930278..35930403,
                     35937858..35937993,35942686..35942825,35943864..35944917)
                     /gene="SEPT7"
                     /gene_synonym="CDC10; CDC3; Nbla02942; SEPT7A"
                     /product="septin 7, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001788.4"
                     /db_xref="GI:148352330"
                     /db_xref="GeneID:989"
                     /db_xref="HGNC:1717"
                     /db_xref="HPRD:04398"
                     /db_xref="MIM:603151"
     mRNA            join(35840627..35840880,35841873..35841874,
                     35872408..35872510,35903162..35903268,35912276..35912376,
                     35913251..35913385,35919433..35919550,35922094..35922186,
                     35923501..35923597,35925438..35925489,35930278..35930403,
                     35937858..35937993,35942686..35942825,35943864..35944917)
                     /gene="SEPT7"
                     /gene_synonym="CDC10; CDC3; Nbla02942; SEPT7A"
                     /product="septin 7, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001011553.2"
                     /db_xref="GI:148352328"
                     /db_xref="GeneID:989"
                     /db_xref="HGNC:1717"
                     /db_xref="HPRD:04398"
                     /db_xref="MIM:603151"
     CDS             join(35840820..35840880,35871102..35871106,
                     35872408..35872510,35903162..35903268,35912276..35912376,
                     35913251..35913385,35919433..35919550,35922094..35922186,
                     35923501..35923597,35925438..35925489,35930278..35930403,
                     35937858..35937993,35942686..35942825,35943864..35943903)
                     /gene="SEPT7"
                     /gene_synonym="CDC10; CDC3; Nbla02942; SEPT7A"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="septin-7 isoform 1"
                     /protein_id="NP_001779.3"
                     /db_xref="GI:148352331"
                     /db_xref="GeneID:989"
                     /db_xref="HGNC:1717"
                     /db_xref="HPRD:04398"
                     /db_xref="MIM:603151"
     CDS             join(35840820..35840880,35841873..35841874,
                     35872408..35872510,35903162..35903268,35912276..35912376,
                     35913251..35913385,35919433..35919550,35922094..35922186,
                     35923501..35923597,35925438..35925489,35930278..35930403,
                     35937858..35937993,35942686..35942825,35943864..35943903)
                     /gene="SEPT7"
                     /gene_synonym="CDC10; CDC3; Nbla02942; SEPT7A"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="septin-7 isoform 2"
                     /protein_id="NP_001011553.2"
                     /db_xref="GI:148352329"
                     /db_xref="GeneID:989"
                     /db_xref="HGNC:1717"
                     /db_xref="HPRD:04398"
                     /db_xref="MIM:603151"
     gene            35973498..35974179
                     /gene="LOC100419774"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419774"
     gene            35985900..36014302
                     /gene="SEPT7P3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:646913"
                     /db_xref="HGNC:38038"
     gene            complement(36010757..36034241)
                     /gene="LOC100652753"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100652753"
     exon            complement(36010757..36011413)
                     /gene="LOC100652753"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=6
                     /pseudo
                     /db_xref="GeneID:100652753"
     exon            complement(36013087..36013237)
                     /gene="LOC100652753"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=5
                     /pseudo
                     /db_xref="GeneID:100652753"
     exon            complement(36019564..36019662)
                     /gene="LOC100652753"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=4
                     /pseudo
                     /db_xref="GeneID:100652753"
     exon            complement(36022321..36022638)
                     /gene="LOC100652753"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:100652753"
     exon            complement(36028759..36028815)
                     /gene="LOC100652753"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100652753"
     exon            complement(36034230..36034241)
                     /gene="LOC100652753"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100652753"
     gene            36118694..36125338
                     /gene="PP13004"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA"
                     /db_xref="GeneID:402481"
     misc_RNA        join(36118694..36118925,36124082..36125338)
                     /gene="PP13004"
                     /product="hypothetical LOC402481"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA"
                     /transcript_id="XR_108769.1"
                     /db_xref="GI:310119952"
                     /db_xref="GeneID:402481"
     gene            complement(36148634..36150482)
                     /gene="LOC100631260"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100631260"
     gene            36186443..36187634
                     /gene="MARK2P7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421531"
                     /db_xref="HGNC:39798"
     gene            36192836..36341152
                     /gene="EEPD1"
                     /gene_synonym="HSPC107; KIAA1706"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:80820"
                     /db_xref="HGNC:22223"
                     /db_xref="HPRD:13884"
     mRNA            join(36192836..36193283,36193742..36194811,
                     36278594..36278645,36320724..36320834,36324295..36324429,
                     36327248..36327386,36336602..36336796,36338616..36341152)
                     /gene="EEPD1"
                     /gene_synonym="HSPC107; KIAA1706"
                     /product="endonuclease/exonuclease/phosphatase family
                     domain containing 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_030636.2"
                     /db_xref="GI:71043965"
                     /db_xref="GeneID:80820"
                     /db_xref="HGNC:22223"
                     /db_xref="HPRD:13884"
     CDS             join(36193934..36194811,36278594..36278645,
                     36320724..36320834,36324295..36324429,36327248..36327386,
                     36336602..36336796,36338616..36338815)
                     /gene="EEPD1"
                     /gene_synonym="HSPC107; KIAA1706"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="endonuclease/exonuclease/phosphatase family
                     domain-containing protein 1"
                     /protein_id="NP_085139.2"
                     /db_xref="GI:71043966"
                     /db_xref="CCDS:CCDS34619.1"
                     /db_xref="GeneID:80820"
                     /db_xref="HGNC:22223"
                     /db_xref="HPRD:13884"
     gene            complement(36363759..36429734)
                     /gene="KIAA0895"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23366"
                     /db_xref="HGNC:22206"
                     /db_xref="HPRD:17197"
     mRNA            complement(join(36363759..36366527,36370591..36370688,
                     36373465..36373770,36374655..36374787,36396511..36397199,
                     36423468..36423537,36429576..36429734))
                     /gene="KIAA0895"
                     /product="KIAA0895, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001100425.1"
                     /db_xref="GI:154426319"
                     /db_xref="GeneID:23366"
                     /db_xref="HGNC:22206"
                     /db_xref="HPRD:17197"
     mRNA            complement(join(36363759..36366527,36370591..36370688,
                     36373465..36373770,36374655..36374787,36375763..36375906,
                     36396511..36397199,36406720..36406878))
                     /gene="KIAA0895"
                     /product="KIAA0895, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199708.1"
                     /db_xref="GI:314122245"
                     /db_xref="GeneID:23366"
                     /db_xref="HGNC:22206"
                     /db_xref="HPRD:17197"
     mRNA            complement(join(36363759..36366527,36370591..36370688,
                     36373465..36373770,36374655..36374787,36396511..36397199,
                     36406525..36406850))
                     /gene="KIAA0895"
                     /product="KIAA0895, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015314.2"
                     /db_xref="GI:154426293"
                     /db_xref="GeneID:23366"
                     /db_xref="HGNC:22206"
                     /db_xref="HPRD:17197"
     mRNA            complement(join(36363759..36366527,36370591..36370688,
                     36373465..36373770,36374655..36374787,36375763..36375906,
                     36396511..36397199,36406525..36406842))
                     /gene="KIAA0895"
                     /product="KIAA0895, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199706.1"
                     /db_xref="GI:314122243"
                     /db_xref="GeneID:23366"
                     /db_xref="HGNC:22206"
                     /db_xref="HPRD:17197"
     mRNA            complement(join(36363759..36366527,36370591..36370688,
                     36373465..36373770,36374655..36374787,36396511..36397199,
                     36406313..36406782))
                     /gene="KIAA0895"
                     /product="KIAA0895, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199707.1"
                     /db_xref="GI:314122357"
                     /db_xref="GeneID:23366"
                     /db_xref="HGNC:22206"
                     /db_xref="HPRD:17197"
     CDS             complement(join(36366369..36366527,36370591..36370688,
                     36373465..36373770,36374655..36374787,36396511..36397199,
                     36423468..36423537,36429576..36429683))
                     /gene="KIAA0895"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC23366 isoform 1"
                     /protein_id="NP_001093895.1"
                     /db_xref="GI:154426320"
                     /db_xref="CCDS:CCDS43570.1"
                     /db_xref="GeneID:23366"
                     /db_xref="HGNC:22206"
                     /db_xref="HPRD:17197"
     CDS             complement(join(36366369..36366527,36370591..36370688,
                     36373465..36373770,36374655..36374787,36396511..36397199,
                     36406525..36406549))
                     /gene="KIAA0895"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC23366 isoform 2"
                     /protein_id="NP_056129.2"
                     /db_xref="GI:154426294"
                     /db_xref="CCDS:CCDS47573.1"
                     /db_xref="GeneID:23366"
                     /db_xref="HGNC:22206"
                     /db_xref="HPRD:17197"
     CDS             complement(join(36366369..36366527,36370591..36370688,
                     36373465..36373770,36374655..36374787,36375763..36375906,
                     36396511..36397199,36406525..36406549))
                     /gene="KIAA0895"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC23366 isoform 3"
                     /protein_id="NP_001186635.1"
                     /db_xref="GI:314122244"
                     /db_xref="GeneID:23366"
                     /db_xref="HGNC:22206"
                     /db_xref="HPRD:17197"
     CDS             complement(join(36366369..36366527,36370591..36370688,
                     36373465..36373770,36374655..36374787,36396511..36397199,
                     36406313..36406451))
                     /gene="KIAA0895"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC23366 isoform 4"
                     /protein_id="NP_001186636.1"
                     /db_xref="GI:314122358"
                     /db_xref="GeneID:23366"
                     /db_xref="HGNC:22206"
                     /db_xref="HPRD:17197"
     CDS             complement(join(36366369..36366527,36370591..36370688,
                     36373465..36373770,36374655..36374787,36375763..36375906,
                     36396511..36396924))
                     /gene="KIAA0895"
                     /note="isoform 5 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC23366 isoform 5"
                     /protein_id="NP_001186637.1"
                     /db_xref="GI:314122246"
                     /db_xref="GeneID:23366"
                     /db_xref="HGNC:22206"
                     /db_xref="HPRD:17197"
     gene            36429432..36493400
                     /gene="ANLN"
                     /gene_synonym="DKFZp779A055; scra; Scraps"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54443"
                     /db_xref="HGNC:14082"
                     /db_xref="HPRD:09799"
     mRNA            join(36429432..36429653,36435875..36436028,
                     36438688..36439002,36445790..36446175,36447343..36447565,
                     36450123..36450313,36450668..36450775,36455367..36455493,
                     36456689..36456799,36458853..36459088,36459778..36459923,
                     36460206..36460353,36461466..36461601,36462242..36462418,
                     36463426..36463552,36464154..36464202,36464295..36464351,
                     36465311..36465349,36465624..36465645,36466525..36466637,
                     36478813..36478899,36483364..36483471,36489274..36489446,
                     36492086..36493400)
                     /gene="ANLN"
                     /gene_synonym="DKFZp779A055; scra; Scraps"
                     /product="anillin, actin binding protein"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018685.2"
                     /db_xref="GI:31657093"
                     /db_xref="GeneID:54443"
                     /db_xref="HGNC:14082"
                     /db_xref="HPRD:09799"
     CDS             join(36429636..36429653,36435875..36436028,
                     36438688..36439002,36445790..36446175,36447343..36447565,
                     36450123..36450313,36450668..36450775,36455367..36455493,
                     36456689..36456799,36458853..36459088,36459778..36459923,
                     36460206..36460353,36461466..36461601,36462242..36462418,
                     36463426..36463552,36464154..36464202,36464295..36464351,
                     36465311..36465349,36465624..36465645,36466525..36466637,
                     36478813..36478899,36483364..36483471,36489274..36489446,
                     36492086..36492209)
                     /gene="ANLN"
                     /gene_synonym="DKFZp779A055; scra; Scraps"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="actin-binding protein anillin"
                     /protein_id="NP_061155.2"
                     /db_xref="GI:31657094"
                     /db_xref="CCDS:CCDS5447.1"
                     /db_xref="GeneID:54443"
                     /db_xref="HGNC:14082"
                     /db_xref="HPRD:09799"
     gene            complement(36552549..36764154)
                     /gene="AOAH"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:313"
                     /db_xref="HGNC:548"
                     /db_xref="HPRD:00027"
                     /db_xref="MIM:102593"
     mRNA            complement(join(36552549..36552986,36561645..36561721,
                     36570024..36570120,36571753..36571812,36571892..36571950,
                     36579925..36580097,36588218..36588292,36589045..36589081,
                     36616180..36616262,36633945..36634036,36655986..36656080,
                     36657903..36657951,36660387..36660435,36661316..36661386,
                     36662796..36662856,36671642..36671712,36677457..36677516,
                     36698771..36698870,36713548..36713614,36726304..36726399,
                     36763627..36764154))
                     /gene="AOAH"
                     /product="acyloxyacyl hydrolase (neutrophil), transcript
                     variant 1"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001637.3"
                     /db_xref="GI:294610663"
                     /db_xref="GeneID:313"
                     /db_xref="HGNC:548"
                     /db_xref="HPRD:00027"
                     /db_xref="MIM:102593"
     mRNA            complement(join(36552549..36552986,36554078..36554196,
                     36561645..36561721,36570024..36570120,36571753..36571812,
                     36571892..36571950,36579925..36580097,36588218..36588292,
                     36589045..36589081,36616180..36616262,36633945..36634036,
                     36655986..36656080,36657903..36657951,36660387..36660435,
                     36661316..36661386,36662796..36662856,36671642..36671712,
                     36677457..36677516,36698771..36698870,36713548..36713614,
                     36726304..36726399,36763627..36764154))
                     /gene="AOAH"
                     /product="acyloxyacyl hydrolase (neutrophil), transcript
                     variant 2"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001177506.1"
                     /db_xref="GI:294610664"
                     /db_xref="GeneID:313"
                     /db_xref="HGNC:548"
                     /db_xref="MIM:102593"
                     /db_xref="HPRD:00027"
     mRNA            complement(join(36552549..36552986,36561645..36561721,
                     36570024..36570120,36571753..36571812,36571892..36571950,
                     36579925..36580097,36588218..36588292,36589045..36589081,
                     36616180..36616262,36633945..36634036,36655986..36656080,
                     36657903..36657951,36660387..36660435,36661316..36661386,
                     36662796..36662856,36671642..36671712,36677457..36677516,
                     36698771..36698870,36713548..36713614,36763627..36764154))
                     /gene="AOAH"
                     /product="acyloxyacyl hydrolase (neutrophil), transcript
                     variant 3"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001177507.1"
                     /db_xref="GI:294610666"
                     /db_xref="GeneID:313"
                     /db_xref="HGNC:548"
                     /db_xref="MIM:102593"
                     /db_xref="HPRD:00027"
     CDS             complement(join(36552640..36552986,36554078..36554196,
                     36561645..36561721,36570024..36570120,36571753..36571812,
                     36571892..36571950,36579925..36580097,36588218..36588292,
                     36589045..36589081,36616180..36616262,36633945..36634036,
                     36655986..36656080,36657903..36657951,36660387..36660435,
                     36661316..36661386,36662796..36662856,36671642..36671712,
                     36677457..36677516,36698771..36698870,36713548..36713614,
                     36726304..36726399,36763627..36763753))
                     /gene="AOAH"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 2 preproprotein is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="acyloxyacyl hydrolase isoform 2 preproprotein"
                     /protein_id="NP_001170977.1"
                     /db_xref="GI:294610665"
                     /db_xref="GeneID:313"
                     /db_xref="HGNC:548"
                     /db_xref="MIM:102593"
                     /db_xref="HPRD:00027"
     CDS             complement(join(36552858..36552986,36561645..36561721,
                     36570024..36570120,36571753..36571812,36571892..36571950,
                     36579925..36580097,36588218..36588292,36589045..36589081,
                     36616180..36616262,36633945..36634036,36655986..36656080,
                     36657903..36657951,36660387..36660435,36661316..36661386,
                     36662796..36662856,36671642..36671712,36677457..36677516,
                     36698771..36698870,36713548..36713614,36726304..36726399,
                     36763627..36763753))
                     /gene="AOAH"
                     /note="isoform 1 preproprotein is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="acyloxyacyl hydrolase isoform 1 preproprotein"
                     /protein_id="NP_001628.1"
                     /db_xref="GI:4502115"
                     /db_xref="CCDS:CCDS5448.1"
                     /db_xref="GeneID:313"
                     /db_xref="HGNC:548"
                     /db_xref="HPRD:00027"
                     /db_xref="MIM:102593"
     CDS             complement(join(36552858..36552986,36561645..36561721,
                     36570024..36570120,36571753..36571812,36571892..36571950,
                     36579925..36580097,36588218..36588292,36589045..36589081,
                     36616180..36616262,36633945..36634036,36655986..36656080,
                     36657903..36657951,36660387..36660435,36661316..36661386,
                     36662796..36662856,36671642..36671712,36677457..36677516,
                     36698771..36698870,36713548..36713614,36763627..36763753))
                     /gene="AOAH"
                     /note="isoform 3 preproprotein is encoded by transcript
                     variant 3; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="acyloxyacyl hydrolase isoform 3 preproprotein"
                     /protein_id="NP_001170978.1"
                     /db_xref="GI:294610667"
                     /db_xref="CCDS:CCDS55102.1"
                     /db_xref="GeneID:313"
                     /db_xref="HGNC:548"
                     /db_xref="HPRD:00027"
                     /db_xref="MIM:102593"
     gene            36858468..36859621
                     /gene="NPM1P18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:10829"
                     /db_xref="HGNC:7920"
     gene            complement(36892511..37488895)
                     /gene="ELMO1"
                     /gene_synonym="CED-12; CED12; ELMO-1; KIAA0281; MGC126406"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9844"
                     /db_xref="HGNC:16286"
                     /db_xref="MIM:606420"
     mRNA            complement(join(36892511..36895356,36901264..36901341,
                     36909998..36910080,36917615..36917722,36927165..36927277,
                     36934459..36934622,37052904..37053040,37136224..37136332,
                     37172735..37172839,37250991..37251122,37252940..37253062,
                     37256250..37256300,37262220..37262298,37264484..37264635,
                     37272700..37272799,37283961..37283996,37298786..37298955,
                     37311437..37311487,37354454..37354526,37355524..37355564,
                     37382217..37382367,37488463..37488895))
                     /gene="ELMO1"
                     /gene_synonym="CED-12; CED12; ELMO-1; KIAA0281; MGC126406"
                     /product="engulfment and cell motility 1, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001206480.1"
                     /db_xref="GI:330688433"
                     /db_xref="GeneID:9844"
                     /db_xref="HGNC:16286"
                     /db_xref="MIM:606420"
     mRNA            complement(join(36892511..36895356,36901264..36901341,
                     36909998..36910080,36917615..36917722,36927165..36927277,
                     36934459..36934622,37052904..37053040,37136224..37136332,
                     37172735..37172839,37250991..37251122,37252940..37253062,
                     37256250..37256300,37262220..37262298,37264484..37264635,
                     37272700..37272799,37283961..37283996,37298786..37298955,
                     37311437..37311487,37354454..37354526,37355524..37355564,
                     37382217..37382367,37488278..37488555))
                     /gene="ELMO1"
                     /gene_synonym="CED-12; CED12; ELMO-1; KIAA0281; MGC126406"
                     /product="engulfment and cell motility 1, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014800.10"
                     /db_xref="GI:330688432"
                     /db_xref="GeneID:9844"
                     /db_xref="HGNC:16286"
                     /db_xref="HPRD:12102"
                     /db_xref="MIM:606420"
     mRNA            complement(join(36892511..36895356,36901264..36901341,
                     36909998..36910080,36917615..36917722,36927165..36927277,
                     36934459..36934622,37052904..37053040,37136224..37136332,
                     37172735..37172839,37250991..37251122,37252940..37253062,
                     37256250..37256300,37262220..37262298,37264484..37264635,
                     37272700..37272799,37283961..37283996,37298786..37298955,
                     37311437..37311487,37354454..37354526,37355524..37355564,
                     37382217..37382367,37392636..37393272))
                     /gene="ELMO1"
                     /gene_synonym="CED-12; CED12; ELMO-1; KIAA0281; MGC126406"
                     /product="engulfment and cell motility 1, transcript
                     variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001206482.1"
                     /db_xref="GI:330688435"
                     /db_xref="GeneID:9844"
                     /db_xref="HGNC:16286"
                     /db_xref="MIM:606420"
     misc_RNA        complement(join(36892511..36895356,36901264..36901341,
                     36909998..36910080,36917615..36917722,36927165..36927277,
                     36934459..36934622,37025528..37025871))
                     /gene="ELMO1"
                     /gene_synonym="CED-12; CED12; ELMO-1; KIAA0281; MGC126406"
                     /product="engulfment and cell motility 1, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038121.1"
                     /db_xref="GI:330688438"
                     /db_xref="GeneID:9844"
                     /db_xref="HGNC:16286"
                     /db_xref="MIM:606420"
     misc_RNA        complement(join(36892511..36895356,36901264..36901341,
                     36909998..36910080,36917615..36917722,36934459..36934622,
                     37025528..37025871))
                     /gene="ELMO1"
                     /gene_synonym="CED-12; CED12; ELMO-1; KIAA0281; MGC126406"
                     /product="engulfment and cell motility 1, transcript
                     variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038120.1"
                     /db_xref="GI:330688437"
                     /db_xref="GeneID:9844"
                     /db_xref="HGNC:16286"
                     /db_xref="MIM:606420"
     mRNA            complement(join(36892511..36895356,36901264..36901341,
                     36909998..36910080,36917615..36917722,36927165..36927277,
                     36934459..36934622,37024520..37024717))
                     /gene="ELMO1"
                     /gene_synonym="CED-12; CED12; ELMO-1; KIAA0281; MGC126406"
                     /product="engulfment and cell motility 1, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001039459.2"
                     /db_xref="GI:330417910"
                     /db_xref="GeneID:9844"
                     /db_xref="HGNC:16286"
                     /db_xref="MIM:606420"
     CDS             complement(join(36895156..36895356,36901264..36901341,
                     36909998..36910080,36917615..36917722,36927165..36927277,
                     36934459..36934622,37052904..37053040,37136224..37136332,
                     37172735..37172839,37250991..37251122,37252940..37253062,
                     37256250..37256300,37262220..37262298,37264484..37264635,
                     37272700..37272799,37283961..37283996,37298786..37298955,
                     37311437..37311487,37354454..37354526,37355524..37355564,
                     37382217..37382294))
                     /gene="ELMO1"
                     /gene_synonym="CED-12; CED12; ELMO-1; KIAA0281; MGC126406"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="engulfment and cell motility protein 1 isoform
                     1"
                     /protein_id="NP_055615.8"
                     /db_xref="GI:18765700"
                     /db_xref="CCDS:CCDS5449.1"
                     /db_xref="GeneID:9844"
                     /db_xref="HGNC:16286"
                     /db_xref="MIM:606420"
     CDS             complement(join(36895156..36895356,36901264..36901341,
                     36909998..36910080,36917615..36917722,36927165..36927277,
                     36934459..36934622,37052904..37053040,37136224..37136332,
                     37172735..37172839,37250991..37251122,37252940..37253062,
                     37256250..37256300,37262220..37262298,37264484..37264635,
                     37272700..37272799,37283961..37283996,37298786..37298955,
                     37311437..37311487,37354454..37354526,37355524..37355564,
                     37382217..37382294))
                     /gene="ELMO1"
                     /gene_synonym="CED-12; CED12; ELMO-1; KIAA0281; MGC126406"
                     /note="isoform 1 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="engulfment and cell motility protein 1 isoform
                     1"
                     /protein_id="NP_001193409.1"
                     /db_xref="GI:330688434"
                     /db_xref="GeneID:9844"
                     /db_xref="HGNC:16286"
                     /db_xref="MIM:606420"
     CDS             complement(join(36895156..36895356,36901264..36901341,
                     36909998..36910080,36917615..36917722,36927165..36927277,
                     36934459..36934622,37052904..37053040,37136224..37136332,
                     37172735..37172839,37250991..37251122,37252940..37253062,
                     37256250..37256300,37262220..37262298,37264484..37264635,
                     37272700..37272799,37283961..37283996,37298786..37298955,
                     37311437..37311487,37354454..37354526,37355524..37355564,
                     37382217..37382294))
                     /gene="ELMO1"
                     /gene_synonym="CED-12; CED12; ELMO-1; KIAA0281; MGC126406"
                     /note="isoform 1 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="engulfment and cell motility protein 1 isoform
                     1"
                     /protein_id="NP_001193411.1"
                     /db_xref="GI:330688436"
                     /db_xref="GeneID:9844"
                     /db_xref="HGNC:16286"
                     /db_xref="MIM:606420"
     CDS             complement(join(36895156..36895356,36901264..36901341,
                     36909998..36910080,36917615..36917722,36927165..36927277,
                     36934459..36934619))
                     /gene="ELMO1"
                     /gene_synonym="CED-12; CED12; ELMO-1; KIAA0281; MGC126406"
                     /note="isoform 2 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="engulfment and cell motility protein 1 isoform
                     2"
                     /protein_id="NP_001034548.1"
                     /db_xref="GI:86788140"
                     /db_xref="CCDS:CCDS5450.1"
                     /db_xref="GeneID:9844"
                     /db_xref="HGNC:16286"
                     /db_xref="MIM:606420"
     gene            complement(36958962..36959037)
                     /gene="MIR1200"
                     /gene_synonym="hsa-mir-1200; MIRN1200"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100302113"
                     /db_xref="HGNC:35266"
                     /db_xref="miRBase:MI0006332"
     ncRNA           complement(36958962..36959037)
                     /gene="MIR1200"
                     /gene_synonym="hsa-mir-1200; MIRN1200"
                     /ncRNA_class="miRNA"
                     /product="microRNA 1200"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_031604.1"
                     /db_xref="GI:269847076"
                     /db_xref="GeneID:100302113"
                     /db_xref="HGNC:35266"
                     /db_xref="miRBase:MI0006332"
     ncRNA           complement(36958962..36959037)
                     /gene="MIR1200"
                     /gene_synonym="hsa-mir-1200; MIRN1200"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-1200"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:100302113"
                     /db_xref="miRBase:MI0006332"
                     /db_xref="HGNC:35266"
     gene            37156413..37156790
                     /gene="RPS17P13"
                     /gene_synonym="RPS17_6_804"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271073"
                     /db_xref="HGNC:36664"
     gene            37415096..37415676
                     /gene="RPS10P14"
                     /gene_synonym="RPS10_9_805"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:646942"
                     /db_xref="HGNC:35880"
     gene            complement(37624717..37625937)
                     /gene="LOC442668"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442668"
     gene            37779996..37780913
                     /gene="GPR141"
                     /gene_synonym="PGR13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:353345"
                     /db_xref="HGNC:19997"
                     /db_xref="HPRD:16423"
                     /db_xref="MIM:609045"
     mRNA            37779996..37780913
                     /gene="GPR141"
                     /gene_synonym="PGR13"
                     /product="G protein-coupled receptor 141"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_181791.1"
                     /db_xref="GI:32401434"
                     /db_xref="GeneID:353345"
                     /db_xref="HGNC:19997"
                     /db_xref="HPRD:16423"
                     /db_xref="MIM:609045"
     CDS             37779996..37780913
                     /gene="GPR141"
                     /gene_synonym="PGR13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable G-protein coupled receptor 141"
                     /protein_id="NP_861456.1"
                     /db_xref="GI:32401435"
                     /db_xref="CCDS:CCDS5451.1"
                     /db_xref="GeneID:353345"
                     /db_xref="HGNC:19997"
                     /db_xref="HPRD:16423"
                     /db_xref="MIM:609045"
     gene            37835795..37836478
                     /gene="LOC100420413"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420413"
     gene            37888199..37940003
                     /gene="TXNDC3"
                     /gene_synonym="CILD6; NM23-H8; NME8; sptrx-2; SPTRX2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51314"
                     /db_xref="HGNC:16473"
                     /db_xref="HPRD:16243"
                     /db_xref="MIM:607421"
     mRNA            join(37888199..37888330,37888426..37888658,
                     37889862..37889901,37889980..37890037,37890231..37890337,
                     37896876..37896947,37901630..37901746,37902998..37903064,
                     37903950..37904023,37905127..37905219,37907304..37907500,
                     37916434..37916609,37923905..37924049,37924747..37924854,
                     37927879..37928030,37934068..37934212,37936472..37936709,
                     37939846..37940003)
                     /gene="TXNDC3"
                     /gene_synonym="CILD6; NM23-H8; NME8; sptrx-2; SPTRX2"
                     /product="thioredoxin domain containing 3 (spermatozoa)"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016616.4"
                     /db_xref="GI:254911059"
                     /db_xref="GeneID:51314"
                     /db_xref="HGNC:16473"
                     /db_xref="HPRD:16243"
                     /db_xref="MIM:607421"
     CDS             join(37889869..37889901,37889980..37890037,
                     37890231..37890337,37896876..37896947,37901630..37901746,
                     37902998..37903064,37903950..37904023,37905127..37905219,
                     37907304..37907500,37916434..37916609,37923905..37924049,
                     37924747..37924854,37927879..37928030,37934068..37934212,
                     37936472..37936694)
                     /gene="TXNDC3"
                     /gene_synonym="CILD6; NM23-H8; NME8; sptrx-2; SPTRX2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="thioredoxin domain-containing protein 3"
                     /protein_id="NP_057700.3"
                     /db_xref="GI:148839372"
                     /db_xref="CCDS:CCDS5452.1"
                     /db_xref="GeneID:51314"
                     /db_xref="HGNC:16473"
                     /db_xref="HPRD:16243"
                     /db_xref="MIM:607421"
     gene            complement(37945534..37956525)
                     /gene="SFRP4"
                     /gene_synonym="FRP-4; FRPHE; MGC26498"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6424"
                     /db_xref="HGNC:10778"
                     /db_xref="HPRD:07357"
                     /db_xref="MIM:606570"
     mRNA            complement(join(37945534..37947266,37949219..37949282,
                     37951721..37951919,37953815..37953880,37953975..37954055,
                     37955695..37956525))
                     /gene="SFRP4"
                     /gene_synonym="FRP-4; FRPHE; MGC26498"
                     /product="secreted frizzled-related protein 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003014.3"
                     /db_xref="GI:170784837"
                     /db_xref="GeneID:6424"
                     /db_xref="HGNC:10778"
                     /db_xref="HPRD:07357"
                     /db_xref="MIM:606570"
     CDS             complement(join(37947081..37947266,37949219..37949282,
                     37951721..37951919,37953815..37953880,37953975..37954055,
                     37955695..37956139))
                     /gene="SFRP4"
                     /gene_synonym="FRP-4; FRPHE; MGC26498"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="secreted frizzled-related protein 4 precursor"
                     /protein_id="NP_003005.2"
                     /db_xref="GI:170784838"
                     /db_xref="CCDS:CCDS5453.1"
                     /db_xref="GeneID:6424"
                     /db_xref="HGNC:10778"
                     /db_xref="HPRD:07357"
                     /db_xref="MIM:606570"
     gene            37960163..37991543
                     /gene="EPDR1"
                     /gene_synonym="EPDR; MERP-1; MERP1; UCC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54749"
                     /db_xref="HGNC:17572"
                     /db_xref="HPRD:16865"
     mRNA            join(37960163..37960810,37988442..37988650,
                     37989802..37991543)
                     /gene="EPDR1"
                     /gene_synonym="EPDR; MERP-1; MERP1; UCC1"
                     /product="ependymin related protein 1 (zebrafish),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017549.3"
                     /db_xref="GI:116008437"
                     /db_xref="GeneID:54749"
                     /db_xref="HGNC:17572"
                     /db_xref="HPRD:16865"
     CDS             join(37960182..37960810,37988442..37988650,
                     37989802..37989998)
                     /gene="EPDR1"
                     /gene_synonym="EPDR; MERP-1; MERP1; UCC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="mammalian ependymin-related protein 1 isoform 1
                     precursor"
                     /protein_id="NP_060019.1"
                     /db_xref="GI:24475586"
                     /db_xref="CCDS:CCDS5454.1"
                     /db_xref="GeneID:54749"
                     /db_xref="HGNC:17572"
                     /db_xref="HPRD:16865"
     gene            38217933..38270270
                     /gene="STARD3NL"
                     /gene_synonym="MENTHO; MGC3251"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:83930"
                     /db_xref="HGNC:19169"
                     /db_xref="HPRD:18117"
                     /db_xref="MIM:611759"
     mRNA            join(38217933..38218022,38247048..38247330,
                     38253958..38254035,38254629..38254706,38256626..38256679,
                     38256789..38256906,38259166..38259261,38268400..38268472,
                     38269524..38270270)
                     /gene="STARD3NL"
                     /gene_synonym="MENTHO; MGC3251"
                     /product="STARD3 N-terminal like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032016.2"
                     /db_xref="GI:31543655"
                     /db_xref="GeneID:83930"
                     /db_xref="HGNC:19169"
                     /db_xref="HPRD:18117"
                     /db_xref="MIM:611759"
     CDS             join(38247106..38247330,38253958..38254035,
                     38254629..38254706,38256626..38256679,38256789..38256906,
                     38259166..38259261,38268400..38268455)
                     /gene="STARD3NL"
                     /gene_synonym="MENTHO; MGC3251"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="MLN64 N-terminal domain homolog"
                     /protein_id="NP_114405.1"
                     /db_xref="GI:14042927"
                     /db_xref="CCDS:CCDS5455.1"
                     /db_xref="GeneID:83930"
                     /db_xref="HGNC:19169"
                     /db_xref="HPRD:18117"
                     /db_xref="MIM:611759"
     gene            complement(38279625..38407656)
                     /gene="TRG@"
                     /gene_synonym="TCRG; TRG"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6965"
                     /db_xref="HGNC:12271"
                     /db_xref="MIM:186970"
     gene            complement(38279625..38289173)
                     /gene="TRGC2"
                     /gene_synonym="TCRGC2; TRGC2(2X); TRGC2(3X)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6967"
                     /db_xref="HGNC:12276"
                     /db_xref="IMGT/GENE-DB:TRGC2"
     CDS             complement(join(38279625..38279767,38282029..38282076,
                     38284784..38284831,38288844..>38289173))
                     /gene="TRGC2"
                     /gene_synonym="TCRGC2; TRGC2(2X); TRGC2(3X)"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=3
                     /db_xref="GeneID:6967"
                     /db_xref="HGNC:12276"
                     /db_xref="IMGT/GENE-DB:TRGC2"
     C_region        complement(join(38279625..38279767,38282029..38282076,
                     38284784..38284831,38288844..38289173))
                     /gene="TRGC2"
                     /gene_synonym="TCRGC2; TRGC2(2X); TRGC2(3X)"
                     /standard_name="TRGC2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6967"
     gene            complement(<38292981..>38293030)
                     /gene="TRGJ2"
                     /gene_synonym="J2; TCRGJ2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6969"
                     /db_xref="HGNC:12278"
                     /db_xref="IMGT/GENE-DB:TRGJ2"
     CDS             complement(<38292981..>38293030)
                     /gene="TRGJ2"
                     /gene_synonym="J2; TCRGJ2"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=2
                     /db_xref="GeneID:6969"
                     /db_xref="HGNC:12278"
                     /db_xref="IMGT/GENE-DB:TRGJ2"
     J_segment       complement(38292981..38293030)
                     /gene="TRGJ2"
                     /gene_synonym="J2; TCRGJ2"
                     /standard_name="TRGJ2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6969"
     gene            complement(<38295938..>38295997)
                     /gene="TRGJP2"
                     /gene_synonym="JP2; TCRGJP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6972"
                     /db_xref="HGNC:12281"
                     /db_xref="IMGT/GENE-DB:TRGJP2"
     CDS             complement(<38295938..>38295997)
                     /gene="TRGJP2"
                     /gene_synonym="JP2; TCRGJP2"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=3
                     /db_xref="GeneID:6972"
                     /db_xref="HGNC:12281"
                     /db_xref="IMGT/GENE-DB:TRGJP2"
     J_segment       complement(38295938..38295997)
                     /gene="TRGJP2"
                     /gene_synonym="JP2; TCRGJP2"
                     /standard_name="TRGJP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6972"
     gene            complement(38299244..38313248)
                     /gene="TARP"
                     /gene_synonym="CD3G; TCRG; TCRGC1; TCRGC2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:445347"
                     /db_xref="MIM:609642"
     mRNA            complement(join(38299244..38299831,38301772..38301819,
                     38304950..38305279,38313188..38313248))
                     /gene="TARP"
                     /gene_synonym="CD3G; TCRG; TCRGC1; TCRGC2"
                     /product="TCR gamma alternate reading frame protein,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /transcript_id="NM_001003799.1"
                     /db_xref="GI:51702235"
                     /db_xref="GeneID:445347"
                     /db_xref="MIM:609642"
     mRNA            complement(join(38299244..38299831,38301772..38301819,
                     38304950..38305279,38313188..38313248))
                     /gene="TARP"
                     /gene_synonym="CD3G; TCRG; TCRGC1; TCRGC2"
                     /product="TCR gamma alternate reading frame protein,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /transcript_id="NM_001003806.1"
                     /db_xref="GI:51702237"
                     /db_xref="GeneID:445347"
                     /db_xref="MIM:609642"
     gene            complement(38299689..38305279)
                     /gene="TRGC1"
                     /gene_synonym="C1; TCRGC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6966"
                     /db_xref="HGNC:12275"
                     /db_xref="IMGT/GENE-DB:TRGC1"
     CDS             complement(join(38299689..38299831,38301772..38301819,
                     38304950..>38305279))
                     /gene="TRGC1"
                     /gene_synonym="C1; TCRGC1"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=3
                     /db_xref="GeneID:6966"
                     /db_xref="HGNC:12275"
                     /db_xref="IMGT/GENE-DB:TRGC1"
     C_region        complement(join(38299689..38299831,38301772..38301819,
                     38304950..38305279))
                     /gene="TRGC1"
                     /gene_synonym="C1; TCRGC1"
                     /standard_name="TRGC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6966"
     CDS             complement(join(38299689..38299831,38301772..38301819,
                     38304950..38305094))
                     /gene="TARP"
                     /gene_synonym="CD3G; TCRG; TCRGC1; TCRGC2"
                     /note="T-cell receptor gamma-chain constant region;
                     Derived by automated computational analysis using gene
                     prediction method: Curated Genomic."
                     /codon_start=1
                     /product="TCR gamma alternate reading frame protein
                     isoform 2"
                     /protein_id="NP_001003806.1"
                     /db_xref="GI:51702238"
                     /db_xref="GeneID:445347"
                     /db_xref="MIM:609642"
     CDS             complement(38305091..38305267)
                     /gene="TARP"
                     /gene_synonym="CD3G; TCRG; TCRGC1; TCRGC2"
                     /note="T-cell receptor gamma-chain constant region;
                     Derived by automated computational analysis using gene
                     prediction method: Curated Genomic."
                     /codon_start=1
                     /product="TCR gamma alternate reading frame protein
                     isoform 1"
                     /protein_id="NP_001003799.1"
                     /db_xref="GI:51702236"
                     /db_xref="GeneID:445347"
                     /db_xref="MIM:609642"
     gene            complement(<38309092..>38309141)
                     /gene="TRGJ1"
                     /gene_synonym="J1; TCRGJ1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6968"
                     /db_xref="HGNC:12277"
                     /db_xref="IMGT/GENE-DB:TRGJ1"
     CDS             complement(<38309092..>38309141)
                     /gene="TRGJ1"
                     /gene_synonym="J1; TCRGJ1"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=2
                     /db_xref="GeneID:6968"
                     /db_xref="HGNC:12277"
                     /db_xref="IMGT/GENE-DB:TRGJ1"
     J_segment       complement(38309092..38309141)
                     /gene="TRGJ1"
                     /gene_synonym="J1; TCRGJ1"
                     /standard_name="TRGJ1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6968"
     gene            complement(<38313188..>38313249)
                     /gene="TRGJP"
                     /gene_synonym="JP; TCRGJP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6970"
                     /db_xref="HGNC:12279"
                     /db_xref="IMGT/GENE-DB:TRGJP"
     CDS             complement(<38313188..>38313249)
                     /gene="TRGJP"
                     /gene_synonym="JP; TCRGJP"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=2
                     /db_xref="GeneID:6970"
                     /db_xref="HGNC:12279"
                     /db_xref="IMGT/GENE-DB:TRGJP"
     J_segment       complement(38313188..38313249)
                     /gene="TRGJP"
                     /gene_synonym="JP; TCRGJP"
                     /standard_name="TRGJP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6970"
     gene            complement(<38315860..>38315919)
                     /gene="TRGJP1"
                     /gene_synonym="JP1; TCRGJP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6971"
                     /db_xref="HGNC:12280"
                     /db_xref="IMGT/GENE-DB:TRGJP1"
     CDS             complement(<38315860..>38315919)
                     /gene="TRGJP1"
                     /gene_synonym="JP1; TCRGJP1"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=3
                     /db_xref="GeneID:6971"
                     /db_xref="HGNC:12280"
                     /db_xref="IMGT/GENE-DB:TRGJP1"
     J_segment       complement(38315860..38315919)
                     /gene="TRGJP1"
                     /gene_synonym="JP1; TCRGJP1"
                     /standard_name="TRGJP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6971"
     gene            complement(38331217..38331679)
                     /gene="TRGV11"
                     /gene_synonym="TCRGV11; V4P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6985"
                     /db_xref="HGNC:12286"
                     /db_xref="IMGT/GENE-DB:TRGV11"
     CDS             complement(join(38331217..38331530,38331637..38331679))
                     /gene="TRGV11"
                     /gene_synonym="TCRGV11; V4P"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:6985"
                     /db_xref="IMGT/LIGM:TRGV11"
                     /db_xref="HGNC:12286"
                     /db_xref="IMGT/GENE-DB:TRGV11"
     V_segment       complement(join(38331217..38331530,38331637..38331679))
                     /gene="TRGV11"
                     /gene_synonym="TCRGV11; V4P"
                     /standard_name="TRGV11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6985"
     gene            complement(38335364..38335834)
                     /gene="TRGVB"
                     /gene_synonym="TCRGVB; V6P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6987"
                     /db_xref="HGNC:12297"
                     /db_xref="IMGT/GENE-DB:TRGVB"
     CDS             complement(join(38335364..38335680,38335792..38335834))
                     /gene="TRGVB"
                     /gene_synonym="TCRGVB; V6P"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:6987"
                     /db_xref="HGNC:12297"
                     /db_xref="IMGT/GENE-DB:TRGVB"
     V_segment       complement(join(38335364..38335680,38335792..38335834))
                     /gene="TRGVB"
                     /gene_synonym="TCRGVB; V6P"
                     /standard_name="TRGVB"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6987"
     gene            complement(38339411..38339881)
                     /gene="TRGV10"
                     /gene_synonym="TCRGV10; V3P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6984"
                     /db_xref="HGNC:12285"
                     /db_xref="IMGT/GENE-DB:TRGV10"
     CDS             complement(join(38339411..38339730,38339842..38339881))
                     /gene="TRGV10"
                     /gene_synonym="TCRGV10; V3P"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:6984"
                     /db_xref="HGNC:12285"
                     /db_xref="IMGT/GENE-DB:TRGV10"
     V_segment       complement(join(38339411..38339730,38339842..38339881))
                     /gene="TRGV10"
                     /gene_synonym="TCRGV10; V3P"
                     /standard_name="TRGV10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6984"
     gene            complement(38356618..38357093)
                     /gene="TRGV9"
                     /gene_synonym="MGC47828; TCRGV9; TRGC1; V2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6983"
                     /db_xref="HGNC:12295"
                     /db_xref="IMGT/GENE-DB:TRGV9"
     CDS             complement(join(<38356618..38356937,38357048..38357093))
                     /gene="TRGV9"
                     /gene_synonym="MGC47828; TCRGV9; TRGC1; V2"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:6983"
                     /db_xref="HGNC:12295"
                     /db_xref="IMGT/GENE-DB:TRGV9"
     V_segment       complement(join(38356618..38356937,38357048..38357093))
                     /gene="TRGV9"
                     /gene_synonym="MGC47828; TCRGV9; TRGC1; V2"
                     /standard_name="TRGV9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6983"
     gene            complement(38362047..38362464)
                     /gene="TRGVA"
                     /gene_synonym="TCRGVA; V5P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6986"
                     /db_xref="HGNC:12296"
                     /db_xref="IMGT/GENE-DB:TRGVA"
     CDS             complement(join(38362047..38362342,38362422..38362464))
                     /gene="TRGVA"
                     /gene_synonym="TCRGVA; V5P"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:6986"
                     /db_xref="HGNC:12296"
                     /db_xref="IMGT/GENE-DB:TRGVA"
     V_segment       complement(join(38362047..38362342,38362422..38362464))
                     /gene="TRGVA"
                     /gene_synonym="TCRGVA; V5P"
                     /standard_name="TRGVA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6986"
     gene            complement(38369944..38370422)
                     /gene="TRGV8"
                     /gene_synonym="TCRGV8; V1S8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6982"
                     /db_xref="HGNC:12294"
                     /db_xref="IMGT/GENE-DB:TRGV8"
     CDS             complement(join(<38369944..38370254,38370380..38370422))
                     /gene="TRGV8"
                     /gene_synonym="TCRGV8; V1S8"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:6982"
                     /db_xref="HGNC:12294"
                     /db_xref="IMGT/GENE-DB:TRGV8"
     V_segment       complement(join(38369944..38370254,38370380..38370422))
                     /gene="TRGV8"
                     /gene_synonym="TCRGV8; V1S8"
                     /standard_name="TRGV8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6982"
     gene            complement(38374642..38375115)
                     /gene="TRGV7"
                     /gene_synonym="TCRGV7; V1S7P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6981"
                     /db_xref="HGNC:12293"
                     /db_xref="IMGT/GENE-DB:TRGV7"
     CDS             complement(join(38374642..38374951,38375073..38375115))
                     /gene="TRGV7"
                     /gene_synonym="TCRGV7; V1S7P"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:6981"
                     /db_xref="HGNC:12293"
                     /db_xref="IMGT/GENE-DB:TRGV7"
     V_segment       complement(join(38374642..38374951,38375073..38375115))
                     /gene="TRGV7"
                     /gene_synonym="TCRGV7; V1S7P"
                     /standard_name="TRGV7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6981"
     gene            complement(38380301..38380772)
                     /gene="TRGV6"
                     /gene_synonym="TCRGV5P; TCRGV6; V1S5P; V1S6P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6980"
                     /db_xref="HGNC:12292"
                     /db_xref="IMGT/GENE-DB:TRGV6"
     CDS             complement(join(38380301..38380610,38380730..38380772))
                     /gene="TRGV6"
                     /gene_synonym="TCRGV5P; TCRGV6; V1S5P; V1S6P"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:6980"
                     /db_xref="HGNC:12292"
                     /db_xref="IMGT/GENE-DB:TRGV6"
     V_segment       complement(join(38380301..38380610,38380730..38380772))
                     /gene="TRGV6"
                     /gene_synonym="TCRGV5P; TCRGV6; V1S5P; V1S6P"
                     /standard_name="TRGV6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6980"
     gene            38381178..38418238
                     /gene="LOC100506776"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100506776"
     misc_RNA        join(38381178..38381400,38385622..38385728,
                     38389947..38390051,38415158..38418238)
                     /gene="LOC100506776"
                     /product="hypothetical LOC100506776"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_040085.1"
                     /db_xref="GI:338827734"
                     /db_xref="GeneID:100506776"
     gene            complement(38384631..38385100)
                     /gene="TRGV5P"
                     /gene_synonym="TCRGV5P; V1S5P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6979"
                     /db_xref="HGNC:12291"
                     /db_xref="IMGT/GENE-DB:TRGV5P"
     CDS             complement(join(38384631..38384943,38385058..38385100))
                     /gene="TRGV5P"
                     /gene_synonym="TCRGV5P; V1S5P"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:6979"
                     /db_xref="IMGT/LIGM:TRGV5P"
                     /db_xref="HGNC:12291"
                     /db_xref="IMGT/GENE-DB:TRGV5P"
     V_segment       complement(join(38384631..38384943,38385058..38385100))
                     /gene="TRGV5P"
                     /gene_synonym="TCRGV5P; V1S5P"
                     /standard_name="TRGV5P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6979"
     gene            complement(38388956..38389425)
                     /gene="TRGV5"
                     /gene_synonym="TCRGV5; V1S5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6978"
                     /db_xref="HGNC:12290"
                     /db_xref="IMGT/GENE-DB:TRGV5"
     CDS             complement(join(<38388956..38389266,38389383..38389425))
                     /gene="TRGV5"
                     /gene_synonym="TCRGV5; V1S5"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:6978"
                     /db_xref="HGNC:12290"
                     /db_xref="IMGT/GENE-DB:TRGV5"
     V_segment       complement(join(38388956..38389266,38389383..38389425))
                     /gene="TRGV5"
                     /gene_synonym="TCRGV5; V1S5"
                     /standard_name="TRGV5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6978"
     gene            complement(38393316..38393784)
                     /gene="TRGV4"
                     /gene_synonym="TCRGV4; V1S4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6977"
                     /db_xref="HGNC:12289"
                     /db_xref="IMGT/GENE-DB:TRGV4"
     CDS             complement(join(<38393316..38393626,38393742..38393784))
                     /gene="TRGV4"
                     /gene_synonym="TCRGV4; V1S4"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:6977"
                     /db_xref="IMGT/LIGM:TRGV4"
                     /db_xref="HGNC:12289"
                     /db_xref="IMGT/GENE-DB:TRGV4"
     V_segment       complement(join(38393316..38393626,38393742..38393784))
                     /gene="TRGV4"
                     /gene_synonym="TCRGV4; V1S4"
                     /standard_name="TRGV4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6977"
     gene            complement(38398113..38398580)
                     /gene="TRGV3"
                     /gene_synonym="TCRGV3; V1S3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6976"
                     /db_xref="HGNC:12288"
                     /db_xref="IMGT/GENE-DB:TRGV3"
     CDS             complement(join(<38398113..38398423,38398538..38398580))
                     /gene="TRGV3"
                     /gene_synonym="TCRGV3; V1S3"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:6976"
                     /db_xref="HGNC:12288"
                     /db_xref="IMGT/GENE-DB:TRGV3"
     V_segment       complement(join(38398113..38398423,38398538..38398580))
                     /gene="TRGV3"
                     /gene_synonym="TCRGV3; V1S3"
                     /standard_name="TRGV3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6976"
     gene            complement(<38402465..38402929)
                     /gene="TRGV2"
                     /gene_synonym="MGC42817; TCRGV2; VIS2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6974"
                     /db_xref="HGNC:12287"
                     /db_xref="IMGT/GENE-DB:TRGV2"
     CDS             complement(join(<38402465..38402775,38402887..38402929))
                     /gene="TRGV2"
                     /gene_synonym="MGC42817; TCRGV2; VIS2"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:6974"
                     /db_xref="HGNC:12287"
                     /db_xref="IMGT/GENE-DB:TRGV2"
     V_segment       complement(join(38402465..38402775,38402887..38402929))
                     /gene="TRGV2"
                     /gene_synonym="MGC42817; TCRGV2; VIS2"
                     /standard_name="TRGV2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6974"
     gene            complement(38407187..38407656)
                     /gene="TRGV1"
                     /gene_synonym="TCRGV1; V1S1P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6973"
                     /db_xref="HGNC:12284"
                     /db_xref="IMGT/GENE-DB:TRGV1"
     CDS             complement(join(38407187..38407494,38407614..38407656))
                     /gene="TRGV1"
                     /gene_synonym="TCRGV1; V1S1P"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:6973"
                     /db_xref="HGNC:12284"
                     /db_xref="IMGT/GENE-DB:TRGV1"
     V_segment       complement(join(38407187..38407494,38407614..38407656))
                     /gene="TRGV1"
                     /gene_synonym="TCRGV1; V1S1P"
                     /standard_name="TRGV1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6973"
     gene            complement(38423297..38671167)
                     /gene="AMPH"
                     /gene_synonym="AMPH1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:273"
                     /db_xref="HGNC:471"
                     /db_xref="HPRD:02687"
                     /db_xref="MIM:600418"
     mRNA            complement(join(38423297..38424526,38429405..38429506,
                     38431349..38431618,38433605..38433814,38457425..38457550,
                     38462021..38462077,38466554..38466586,38469442..38469465,
                     38471789..38471812,38475872..38475988,38500883..38501011,
                     38502575..38502713,38505067..38505149,38505773..38505848,
                     38514931..38515016,38516462..38516569,38530650..38530745,
                     38534033..38534127,38543250..38543304,38574531..38574611,
                     38670883..38671167))
                     /gene="AMPH"
                     /gene_synonym="AMPH1"
                     /product="amphiphysin, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001635.3"
                     /db_xref="GI:312922370"
                     /db_xref="GeneID:273"
                     /db_xref="HGNC:471"
                     /db_xref="HPRD:02687"
                     /db_xref="MIM:600418"
     mRNA            complement(join(38423297..38424526,38429405..38429506,
                     38431349..38431618,38433605..38433814,38462021..38462077,
                     38466554..38466586,38469442..38469465,38471789..38471812,
                     38475872..38475988,38500883..38501011,38502575..38502713,
                     38505067..38505149,38505773..38505848,38514931..38515016,
                     38516462..38516569,38530650..38530745,38534033..38534127,
                     38543250..38543304,38574531..38574611,38670883..38671167))
                     /gene="AMPH"
                     /gene_synonym="AMPH1"
                     /product="amphiphysin, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_139316.2"
                     /db_xref="GI:312836840"
                     /db_xref="GeneID:273"
                     /db_xref="HGNC:471"
                     /db_xref="HPRD:02687"
                     /db_xref="MIM:600418"
     CDS             complement(join(38424419..38424526,38429405..38429506,
                     38431349..38431618,38433605..38433814,38457425..38457550,
                     38462021..38462077,38466554..38466586,38469442..38469465,
                     38471789..38471812,38475872..38475988,38500883..38501011,
                     38502575..38502713,38505067..38505149,38505773..38505848,
                     38514931..38515016,38516462..38516569,38530650..38530745,
                     38534033..38534127,38543250..38543304,38574531..38574611,
                     38670883..38670951))
                     /gene="AMPH"
                     /gene_synonym="AMPH1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="amphiphysin isoform 1"
                     /protein_id="NP_001626.1"
                     /db_xref="GI:4502081"
                     /db_xref="CCDS:CCDS5456.1"
                     /db_xref="GeneID:273"
                     /db_xref="HGNC:471"
                     /db_xref="HPRD:02687"
                     /db_xref="MIM:600418"
     CDS             complement(join(38424419..38424526,38429405..38429506,
                     38431349..38431618,38433605..38433814,38462021..38462077,
                     38466554..38466586,38469442..38469465,38471789..38471812,
                     38475872..38475988,38500883..38501011,38502575..38502713,
                     38505067..38505149,38505773..38505848,38514931..38515016,
                     38516462..38516569,38530650..38530745,38534033..38534127,
                     38543250..38543304,38574531..38574611,38670883..38670951))
                     /gene="AMPH"
                     /gene_synonym="AMPH1"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="amphiphysin isoform 2"
                     /protein_id="NP_647477.1"
                     /db_xref="GI:21536423"
                     /db_xref="CCDS:CCDS47574.1"
                     /db_xref="GeneID:273"
                     /db_xref="HGNC:471"
                     /db_xref="HPRD:02687"
                     /db_xref="MIM:600418"
     gene            38694744..38696462
                     /gene="KRT8P20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:441218"
                     /db_xref="HGNC:33372"
     gene            complement(38724946..38726689)
                     /gene="FAM183B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:340286"
                     /db_xref="HGNC:34511"
     misc_RNA        complement(join(38724946..38725812,38725910..38726689))
                     /gene="FAM183B"
                     /product="family with sequence similarity 183, member B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_028347.1"
                     /db_xref="GI:256355156"
                     /db_xref="GeneID:340286"
                     /db_xref="HGNC:34511"
     gene            complement(38763543..38948800)
                     /gene="VPS41"
                     /gene_synonym="HVPS41; hVps41p; HVSP41"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:27072"
                     /db_xref="HGNC:12713"
                     /db_xref="HPRD:10402"
                     /db_xref="MIM:605485"
     mRNA            complement(join(38763543..38765926,38766509..38766588,
                     38768142..38768186,38768292..38768391,38781585..38781721,
                     38783002..38783142,38785159..38785213,38791776..38791913,
                     38794302..38794352,38794495..38794536,38796438..38796582,
                     38797954..38798081,38803055..38803147,38805180..38805261,
                     38807137..38807198,38810798..38810854,38812122..38812237,
                     38813715..38813844,38816279..38816376,38829401..38829467,
                     38835065..38835211,38836345..38836464,38857417..38857482,
                     38860803..38860865,38869854..38869928,38902145..38902222,
                     38908746..38908853,38937691..38937729,38948754..38948800))
                     /gene="VPS41"
                     /gene_synonym="HVPS41; hVps41p; HVSP41"
                     /product="vacuolar protein sorting 41 homolog (S.
                     cerevisiae), transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014396.3"
                     /db_xref="GI:114199474"
                     /db_xref="GeneID:27072"
                     /db_xref="HGNC:12713"
                     /db_xref="HPRD:10402"
                     /db_xref="MIM:605485"
     mRNA            complement(join(38763543..38765926,38766509..38766588,
                     38768142..38768186,38768292..38768391,38781585..38781721,
                     38783002..38783142,38785159..38785213,38791776..38791913,
                     38794302..38794352,38794495..38794536,38796438..38796582,
                     38797954..38798081,38803055..38803147,38805180..38805261,
                     38807137..38807198,38810798..38810854,38812122..38812237,
                     38813715..38813844,38816279..38816376,38829401..38829467,
                     38835065..38835211,38836345..38836464,38857417..38857482,
                     38860803..38860865,38902145..38902222,38908746..38908853,
                     38937691..38937729,38948754..38948800))
                     /gene="VPS41"
                     /gene_synonym="HVPS41; hVps41p; HVSP41"
                     /product="vacuolar protein sorting 41 homolog (S.
                     cerevisiae), transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_080631.3"
                     /db_xref="GI:114199472"
                     /db_xref="GeneID:27072"
                     /db_xref="HGNC:12713"
                     /db_xref="HPRD:10402"
                     /db_xref="MIM:605485"
     CDS             complement(join(38765846..38765926,38766509..38766588,
                     38768142..38768186,38768292..38768391,38781585..38781721,
                     38783002..38783142,38785159..38785213,38791776..38791913,
                     38794302..38794352,38794495..38794536,38796438..38796582,
                     38797954..38798081,38803055..38803147,38805180..38805261,
                     38807137..38807198,38810798..38810854,38812122..38812237,
                     38813715..38813844,38816279..38816376,38829401..38829467,
                     38835065..38835211,38836345..38836464,38857417..38857482,
                     38860803..38860865,38869854..38869928,38902145..38902222,
                     38908746..38908853,38937691..38937729,38948754..38948774))
                     /gene="VPS41"
                     /gene_synonym="HVPS41; hVps41p; HVSP41"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="vacuolar protein sorting-associated protein 41
                     homolog isoform 1"
                     /protein_id="NP_055211.2"
                     /db_xref="GI:114199475"
                     /db_xref="CCDS:CCDS5457.1"
                     /db_xref="GeneID:27072"
                     /db_xref="HGNC:12713"
                     /db_xref="HPRD:10402"
                     /db_xref="MIM:605485"
     CDS             complement(join(38765846..38765926,38766509..38766588,
                     38768142..38768186,38768292..38768391,38781585..38781721,
                     38783002..38783142,38785159..38785213,38791776..38791913,
                     38794302..38794352,38794495..38794536,38796438..38796582,
                     38797954..38798081,38803055..38803147,38805180..38805261,
                     38807137..38807198,38810798..38810854,38812122..38812237,
                     38813715..38813844,38816279..38816376,38829401..38829467,
                     38835065..38835211,38836345..38836464,38857417..38857482,
                     38860803..38860865,38902145..38902222,38908746..38908853,
                     38937691..38937729,38948754..38948774))
                     /gene="VPS41"
                     /gene_synonym="HVPS41; hVps41p; HVSP41"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="vacuolar protein sorting-associated protein 41
                     homolog isoform 2"
                     /protein_id="NP_542198.2"
                     /db_xref="GI:114199473"
                     /db_xref="CCDS:CCDS5458.2"
                     /db_xref="GeneID:27072"
                     /db_xref="HGNC:12713"
                     /db_xref="HPRD:10402"
                     /db_xref="MIM:605485"
     gene            39017609..39504390
                     /gene="POU6F2"
                     /gene_synonym="RPF-1; WT5; WTSL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:11281"
                     /db_xref="HGNC:21694"
                     /db_xref="HPRD:10162"
                     /db_xref="MIM:609062"
     mRNA            join(39017609..39017658,39046357..39046467,
                     39125460..39125631,39243834..39243925,39246991..39247219,
                     39379241..39379614,39446199..39446339,39472676..39472882,
                     39491132..39491300,39500146..39500314,39503781..39504390)
                     /gene="POU6F2"
                     /gene_synonym="RPF-1; WT5; WTSL"
                     /product="POU class 6 homeobox 2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_007252.3"
                     /db_xref="GI:260436856"
                     /db_xref="GeneID:11281"
                     /db_xref="HGNC:21694"
                     /db_xref="HPRD:10162"
                     /db_xref="MIM:609062"
     mRNA            join(39017609..39017658,39046357..39046467,
                     39125460..39125631,39243834..39243925,39246991..39247219,
                     39379241..39379614,39446199..39446339,39472676..39472882,
                     39491132..39491300,39500146..39500314,39503889..39504390)
                     /gene="POU6F2"
                     /gene_synonym="RPF-1; WT5; WTSL"
                     /product="POU class 6 homeobox 2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001166018.1"
                     /db_xref="GI:260436857"
                     /db_xref="GeneID:11281"
                     /db_xref="HGNC:21694"
                     /db_xref="MIM:609062"
                     /db_xref="HPRD:10162"
     CDS             join(39046450..39046467,39125460..39125631,
                     39243834..39243925,39246991..39247219,39379241..39379614,
                     39446199..39446339,39472676..39472882,39491132..39491300,
                     39500146..39500314,39503781..39504285)
                     /gene="POU6F2"
                     /gene_synonym="RPF-1; WT5; WTSL"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="POU domain, class 6, transcription factor 2
                     isoform 1"
                     /protein_id="NP_009183.3"
                     /db_xref="GI:157743257"
                     /db_xref="CCDS:CCDS34620.2"
                     /db_xref="GeneID:11281"
                     /db_xref="HGNC:21694"
                     /db_xref="HPRD:10162"
                     /db_xref="MIM:609062"
     CDS             join(39046450..39046467,39125460..39125631,
                     39243834..39243925,39246991..39247219,39379241..39379614,
                     39446199..39446339,39472676..39472882,39491132..39491300,
                     39500146..39500314,39503889..39504285)
                     /gene="POU6F2"
                     /gene_synonym="RPF-1; WT5; WTSL"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="POU domain, class 6, transcription factor 2
                     isoform 2"
                     /protein_id="NP_001159490.1"
                     /db_xref="GI:260436858"
                     /db_xref="CCDS:CCDS55103.1"
                     /db_xref="GeneID:11281"
                     /db_xref="HGNC:21694"
                     /db_xref="HPRD:10162"
                     /db_xref="MIM:609062"
     gene            39606003..39612480
                     /gene="C7orf36"
                     /gene_synonym="GK003"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57002"
                     /db_xref="HGNC:24857"
                     /db_xref="HPRD:16669"
     mRNA            join(39606003..39606146,39610105..39610226,
                     39611876..39612480)
                     /gene="C7orf36"
                     /gene_synonym="GK003"
                     /product="chromosome 7 open reading frame 36"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020192.3"
                     /db_xref="GI:282721107"
                     /db_xref="GeneID:57002"
                     /db_xref="HGNC:24857"
                     /db_xref="HPRD:16669"
     CDS             join(39606018..39606146,39610105..39610226,
                     39611876..39612305)
                     /gene="C7orf36"
                     /gene_synonym="GK003"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC57002"
                     /protein_id="NP_064577.1"
                     /db_xref="GI:21281667"
                     /db_xref="CCDS:CCDS5459.1"
                     /db_xref="GeneID:57002"
                     /db_xref="HGNC:24857"
                     /db_xref="HPRD:16669"
     gene            complement(39607217..39609830)
                     /gene="LOC100101126"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100101126"
     gene            39649086..39651687
                     /gene="LOC646999"
                     /gene_synonym="FLJ57706"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:646999"
     misc_RNA        39649086..39651687
                     /gene="LOC646999"
                     /gene_synonym="FLJ57706"
                     /product="akirin 1 pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_024390.1"
                     /db_xref="GI:211971078"
                     /db_xref="GeneID:646999"
     gene            39663152..39747723
                     /gene="RALA"
                     /gene_synonym="MGC48949; RAL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5898"
                     /db_xref="HGNC:9839"
                     /db_xref="HPRD:01549"
                     /db_xref="MIM:179550"
     mRNA            join(39663152..39663424,39726230..39726380,
                     39729981..39730189,39736284..39736458,39745722..39747723)
                     /gene="RALA"
                     /gene_synonym="MGC48949; RAL"
                     /product="v-ral simian leukemia viral oncogene homolog A
                     (ras related)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005402.3"
                     /db_xref="GI:324072795"
                     /db_xref="GeneID:5898"
                     /db_xref="HGNC:9839"
                     /db_xref="HPRD:01549"
                     /db_xref="MIM:179550"
     CDS             join(39726267..39726380,39729981..39730189,
                     39736284..39736458,39745722..39745844)
                     /gene="RALA"
                     /gene_synonym="MGC48949; RAL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ras-related protein Ral-A precursor"
                     /protein_id="NP_005393.2"
                     /db_xref="GI:33946329"
                     /db_xref="CCDS:CCDS5460.1"
                     /db_xref="GeneID:5898"
                     /db_xref="HGNC:9839"
                     /db_xref="HPRD:01549"
                     /db_xref="MIM:179550"
     gene            39773167..39834222
                     /gene="NCRNA00265"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:349114"
                     /db_xref="HGNC:28019"
     misc_RNA        join(39773167..39773643,39807003..39807269,
                     39810604..39810690,39818870..39818984,39820102..39820223,
                     39820834..39820950,39821343..39821484,39822334..39822398,
                     39828081..39828203,39828953..39829143,39831193..39831250,
                     39831343..39834222)
                     /gene="NCRNA00265"
                     /product="non-protein coding RNA 265"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_026999.1"
                     /db_xref="GI:224177506"
                     /db_xref="GeneID:349114"
                     /db_xref="HGNC:28019"
     gene            complement(39835086..39837997)
                     /gene="LOC100288083"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100288083"
     gene            complement(39872885..39873392)
                     /gene="LOC100422519"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100422519"
     gene            39873170..39874314
                     /gene="LOC100129321"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129321"
     gene            complement(39892296..39894859)
                     /gene="RWDD4P2"
                     /gene_synonym="FAM28CP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:647009"
                     /db_xref="HGNC:23754"
     gene            39989959..40136733
                     /gene="CDK13"
                     /gene_synonym="CDC2L; CDC2L5; CHED; FLJ35215; hCDK13;
                     KIAA1791"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8621"
                     /db_xref="HGNC:1733"
                     /db_xref="HPRD:04496"
                     /db_xref="MIM:603309"
     mRNA            join(39989959..39991451,40027198..40027857,
                     40037093..40037263,40038960..40039099,40041460..40041630,
                     40085435..40085624,40087420..40087476,40102425..40102526,
                     40102622..40102699,40117604..40117720,40118319..40118450,
                     40127725..40127930,40132384..40132836,40133729..40136733)
                     /gene="CDK13"
                     /gene_synonym="CDC2L; CDC2L5; CHED; FLJ35215; hCDK13;
                     KIAA1791"
                     /product="cyclin-dependent kinase 13, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003718.4"
                     /db_xref="GI:281427100"
                     /db_xref="GeneID:8621"
                     /db_xref="HGNC:1733"
                     /db_xref="HPRD:04496"
                     /db_xref="MIM:603309"
     mRNA            join(39989959..39991451,40027198..40027857,
                     40037093..40037263,40038960..40039099,40041460..40041630,
                     40085435..40085624,40087420..40087476,40102425..40102526,
                     40102622..40102699,40117604..40117720,40118319..40118450,
                     40127725..40127930,40132564..40132836,40133729..40136733)
                     /gene="CDK13"
                     /gene_synonym="CDC2L; CDC2L5; CHED; FLJ35215; hCDK13;
                     KIAA1791"
                     /product="cyclin-dependent kinase 13, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_031267.3"
                     /db_xref="GI:281427101"
                     /db_xref="GeneID:8621"
                     /db_xref="HGNC:1733"
                     /db_xref="MIM:603309"
                     /db_xref="HPRD:04496"
     CDS             join(39990241..39991451,40027198..40027857,
                     40037093..40037263,40038960..40039099,40041460..40041630,
                     40085435..40085624,40087420..40087476,40102425..40102526,
                     40102622..40102699,40117604..40117720,40118319..40118450,
                     40127725..40127930,40132384..40132836,40133729..40134579)
                     /gene="CDK13"
                     /gene_synonym="CDC2L; CDC2L5; CHED; FLJ35215; hCDK13;
                     KIAA1791"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclin-dependent kinase 13 isoform 1"
                     /protein_id="NP_003709.3"
                     /db_xref="GI:145309302"
                     /db_xref="CCDS:CCDS5461.1"
                     /db_xref="GeneID:8621"
                     /db_xref="HGNC:1733"
                     /db_xref="HPRD:04496"
                     /db_xref="MIM:603309"
     CDS             join(39990241..39991451,40027198..40027857,
                     40037093..40037263,40038960..40039099,40041460..40041630,
                     40085435..40085624,40087420..40087476,40102425..40102526,
                     40102622..40102699,40117604..40117720,40118319..40118450,
                     40127725..40127930,40132564..40132836,40133729..40134579)
                     /gene="CDK13"
                     /gene_synonym="CDC2L; CDC2L5; CHED; FLJ35215; hCDK13;
                     KIAA1791"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclin-dependent kinase 13 isoform 2"
                     /protein_id="NP_112557.2"
                     /db_xref="GI:145309300"
                     /db_xref="CCDS:CCDS5462.1"
                     /db_xref="GeneID:8621"
                     /db_xref="HGNC:1733"
                     /db_xref="HPRD:04496"
                     /db_xref="MIM:603309"
     gene            complement(40172342..40174251)
                     /gene="C7orf11"
                     /gene_synonym="ABHS; ORF20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:136647"
                     /db_xref="HGNC:16002"
                     /db_xref="HPRD:12907"
                     /db_xref="MIM:609188"
     mRNA            complement(join(40172342..40172858,40173828..40174251))
                     /gene="C7orf11"
                     /gene_synonym="ABHS; ORF20"
                     /product="chromosome 7 open reading frame 11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138701.3"
                     /db_xref="GI:289063427"
                     /db_xref="GeneID:136647"
                     /db_xref="HGNC:16002"
                     /db_xref="HPRD:12907"
                     /db_xref="MIM:609188"
     CDS             complement(join(40172658..40172858,40173828..40174166))
                     /gene="C7orf11"
                     /gene_synonym="ABHS; ORF20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="TTD non-photosensitive 1 protein"
                     /protein_id="NP_619646.1"
                     /db_xref="GI:20162566"
                     /db_xref="CCDS:CCDS5463.1"
                     /db_xref="GeneID:136647"
                     /db_xref="HGNC:16002"
                     /db_xref="HPRD:12907"
                     /db_xref="MIM:609188"
     gene            40174575..40900366
                     /gene="C7orf10"
                     /gene_synonym="DERP13; FLJ11808; FLJ53872; ORF19"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79783"
                     /db_xref="HGNC:16001"
                     /db_xref="HPRD:09859"
                     /db_xref="MIM:609187"
     mRNA            join(40174575..40174719,40220546..40220597,
                     40221554..40221627,40228094..40228179,40229143..40229193,
                     40234539..40234659,40277234..40277325,40314112..40314255,
                     40356359..40356454,40488886..40488957,40498700..40498797,
                     40535883..40535985,40723655..40723732,40789033..40789096,
                     40899915..40900366)
                     /gene="C7orf10"
                     /gene_synonym="DERP13; FLJ11808; FLJ53872; ORF19"
                     /product="chromosome 7 open reading frame 10, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001193311.1"
                     /db_xref="GI:300863123"
                     /db_xref="GeneID:79783"
                     /db_xref="HGNC:16001"
                     /db_xref="MIM:609187"
                     /db_xref="HPRD:09859"
     mRNA            join(40174575..40174719,40220546..40220597,
                     40221554..40221627,40228094..40228179,40229143..40229193,
                     40234539..40234659,40277234..40277325,40356359..40356454,
                     40488886..40488957,40498700..40498797,40535883..40535985,
                     40789033..40789096,40899915..40900366)
                     /gene="C7orf10"
                     /gene_synonym="DERP13; FLJ11808; FLJ53872; ORF19"
                     /product="chromosome 7 open reading frame 10, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001193312.1"
                     /db_xref="GI:300863125"
                     /db_xref="GeneID:79783"
                     /db_xref="HGNC:16001"
                     /db_xref="MIM:609187"
                     /db_xref="HPRD:09859"
     mRNA            join(40174575..40174719,40220546..40220597,
                     40221554..40221627,40228094..40228179,40229143..40229193,
                     40234539..40234659,40277234..40277325,40314112..40314255,
                     40356359..40356454,40488886..40488957,40498700..40498797,
                     40535883..40535985,40789033..40789096,40899915..40900366)
                     /gene="C7orf10"
                     /gene_synonym="DERP13; FLJ11808; FLJ53872; ORF19"
                     /product="chromosome 7 open reading frame 10, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001193313.1"
                     /db_xref="GI:300863127"
                     /db_xref="GeneID:79783"
                     /db_xref="HGNC:16001"
                     /db_xref="MIM:609187"
                     /db_xref="HPRD:09859"
     mRNA            join(40174575..40174719,40220546..40220597,
                     40221554..40221627,40228094..40228179,40229143..40229181,
                     40234638..40234659,40277234..40277325,40314112..40314255,
                     40356359..40356454,40488886..40488957,40498700..40498797,
                     40535883..40535985,40723655..40723732,40789033..40789096,
                     40899915..40900366)
                     /gene="C7orf10"
                     /gene_synonym="DERP13; FLJ11808; FLJ53872; ORF19"
                     /product="chromosome 7 open reading frame 10, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024728.2"
                     /db_xref="GI:300863122"
                     /db_xref="GeneID:79783"
                     /db_xref="HGNC:16001"
                     /db_xref="HPRD:09859"
                     /db_xref="MIM:609187"
     CDS             join(40174599..40174719,40220546..40220597,
                     40221554..40221627,40228094..40228179,40229143..40229193,
                     40234539..40234659,40277234..40277325,40314112..40314255,
                     40356359..40356454,40488886..40488957,40498700..40498797,
                     40535883..40535985,40723655..40723732,40789033..40789096,
                     40899915..40900078)
                     /gene="C7orf10"
                     /gene_synonym="DERP13; FLJ11808; FLJ53872; ORF19"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="CaiB/baiF CoA-transferase family protein C7orf10
                     isoform 1"
                     /protein_id="NP_001180240.1"
                     /db_xref="GI:300863124"
                     /db_xref="CCDS:CCDS55104.1"
                     /db_xref="GeneID:79783"
                     /db_xref="HGNC:16001"
                     /db_xref="HPRD:09859"
                     /db_xref="MIM:609187"
     CDS             join(40174599..40174719,40220546..40220597,
                     40221554..40221627,40228094..40228179,40229143..40229193,
                     40234539..40234659,40277234..40277325,40356359..40356454,
                     40488886..40488957,40498700..40498797,40535883..40535985,
                     40789033..40789096,40899915..40900078)
                     /gene="C7orf10"
                     /gene_synonym="DERP13; FLJ11808; FLJ53872; ORF19"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="CaiB/baiF CoA-transferase family protein C7orf10
                     isoform 2"
                     /protein_id="NP_001180241.1"
                     /db_xref="GI:300863126"
                     /db_xref="CCDS:CCDS55106.1"
                     /db_xref="GeneID:79783"
                     /db_xref="HGNC:16001"
                     /db_xref="HPRD:09859"
                     /db_xref="MIM:609187"
     CDS             join(40174599..40174719,40220546..40220597,
                     40221554..40221627,40228094..40228179,40229143..40229193,
                     40234539..40234659,40277234..40277325,40314112..40314255,
                     40356359..40356454,40488886..40488957,40498700..40498797,
                     40535883..40535985,40789033..40789096,40899915..40900078)
                     /gene="C7orf10"
                     /gene_synonym="DERP13; FLJ11808; FLJ53872; ORF19"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="CaiB/baiF CoA-transferase family protein C7orf10
                     isoform 3"
                     /protein_id="NP_001180242.1"
                     /db_xref="GI:300863128"
                     /db_xref="CCDS:CCDS55105.1"
                     /db_xref="GeneID:79783"
                     /db_xref="HGNC:16001"
                     /db_xref="HPRD:09859"
                     /db_xref="MIM:609187"
     CDS             join(40174599..40174719,40220546..40220597,
                     40221554..40221627,40228094..40228179,40229143..40229181,
                     40234638..40234659,40277234..40277325,40314112..40314255,
                     40356359..40356454,40488886..40488957,40498700..40498797,
                     40535883..40535985,40723655..40723732,40789033..40789096,
                     40899915..40900078)
                     /gene="C7orf10"
                     /gene_synonym="DERP13; FLJ11808; FLJ53872; ORF19"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="CaiB/baiF CoA-transferase family protein C7orf10
                     isoform 4"
                     /protein_id="NP_079004.1"
                     /db_xref="GI:13376042"
                     /db_xref="GeneID:79783"
                     /db_xref="HGNC:16001"
                     /db_xref="HPRD:09859"
                     /db_xref="MIM:609187"
     gene            40192031..40193766
                     /gene="LOC100419989"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419989"
     gene            complement(41728601..41742706)
                     /gene="INHBA"
                     /gene_synonym="EDF; FRP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3624"
                     /db_xref="HGNC:6066"
                     /db_xref="HPRD:00929"
                     /db_xref="MIM:147290"
     mRNA            complement(join(41728601..41730140,41739585..41740115,
                     41742603..41742706))
                     /gene="INHBA"
                     /gene_synonym="EDF; FRP"
                     /product="inhibin, beta A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002192.2"
                     /db_xref="GI:62953137"
                     /db_xref="GeneID:3624"
                     /db_xref="HGNC:6066"
                     /db_xref="HPRD:00929"
                     /db_xref="MIM:147290"
     CDS             complement(join(41729248..41730140,41739585..41739972))
                     /gene="INHBA"
                     /gene_synonym="EDF; FRP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="inhibin beta A chain precursor"
                     /protein_id="NP_002183.1"
                     /db_xref="GI:4504699"
                     /db_xref="CCDS:CCDS5464.1"
                     /db_xref="GeneID:3624"
                     /db_xref="HGNC:6066"
                     /db_xref="HPRD:00929"
                     /db_xref="MIM:147290"
     gene            41733514..41818976
                     /gene="LOC285954"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285954"
     misc_RNA        join(41733514..41733686,41750196..41750380,
                     41812494..41812592,41816439..41818976)
                     /gene="LOC285954"
                     /product="hypothetical LOC285954, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027118.1"
                     /db_xref="GI:224465159"
                     /db_xref="GeneID:285954"
     misc_RNA        join(41733546..41733686,41750196..41750380,
                     41751261..41752792)
                     /gene="LOC285954"
                     /product="hypothetical LOC285954, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027119.1"
                     /db_xref="GI:224465160"
                     /db_xref="GeneID:285954"
     gene            complement(42000547..42276618)
                     /gene="GLI3"
                     /gene_synonym="ACLS; GCPS; GLI3-190; GLI3FL; PAP-A; PAPA;
                     PAPA1; PAPB; PHS; PPDIV"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2737"
                     /db_xref="HGNC:4319"
                     /db_xref="HPRD:01313"
                     /db_xref="MIM:165240"
     mRNA            complement(join(42000547..42006239,42007194..42007521,
                     42011936..42012226,42017157..42017321,42018198..42018347,
                     42063067..42063207,42064863..42064976,42065798..42066011,
                     42079637..42079838,42084983..42085129,42088090..42088295,
                     42116351..42116456,42187825..42188067,42262729..42262894,
                     42276570..42276618))
                     /gene="GLI3"
                     /gene_synonym="ACLS; GCPS; GLI3-190; GLI3FL; PAP-A; PAPA;
                     PAPA1; PAPB; PHS; PPDIV"
                     /product="GLI family zinc finger 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000168.5"
                     /db_xref="GI:195947346"
                     /db_xref="GeneID:2737"
                     /db_xref="HGNC:4319"
                     /db_xref="HPRD:01313"
                     /db_xref="MIM:165240"
     CDS             complement(join(42003928..42006239,42007194..42007521,
                     42011936..42012226,42017157..42017321,42018198..42018347,
                     42063067..42063207,42064863..42064976,42065798..42066011,
                     42079637..42079838,42084983..42085129,42088090..42088295,
                     42116351..42116456,42187825..42188067,42262729..42262852))
                     /gene="GLI3"
                     /gene_synonym="ACLS; GCPS; GLI3-190; GLI3FL; PAP-A; PAPA;
                     PAPA1; PAPB; PHS; PPDIV"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transcriptional activator GLI3"
                     /protein_id="NP_000159.3"
                     /db_xref="GI:119393899"
                     /db_xref="CCDS:CCDS5465.1"
                     /db_xref="GeneID:2737"
                     /db_xref="HGNC:4319"
                     /db_xref="HPRD:01313"
                     /db_xref="MIM:165240"
     gene            42152850..42154050
                     /gene="HMGN2P30"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100131183"
                     /db_xref="HGNC:39397"
     gene            42834504..42840607
                     /gene="TCP1P1"
                     /gene_synonym="CCT1-3P; TCP1L1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:647047"
                     /db_xref="HGNC:11659"
     gene            complement(42948872..42951689)
                     /gene="C7orf25"
                     /gene_synonym="FLJ21167; MGC2821"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79020"
                     /db_xref="HGNC:21703"
                     /db_xref="HPRD:09861"
     mRNA            complement(join(42948872..42950520,42951514..42951689))
                     /gene="C7orf25"
                     /gene_synonym="FLJ21167; MGC2821"
                     /product="chromosome 7 open reading frame 25, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001099858.1"
                     /db_xref="GI:153792790"
                     /db_xref="GeneID:79020"
                     /db_xref="HGNC:21703"
                     /db_xref="HPRD:09861"
     mRNA            complement(join(42948872..42950515,42951514..42951689))
                     /gene="C7orf25"
                     /gene_synonym="FLJ21167; MGC2821"
                     /product="chromosome 7 open reading frame 25, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024054.2"
                     /db_xref="GI:153791784"
                     /db_xref="GeneID:79020"
                     /db_xref="HGNC:21703"
                     /db_xref="HPRD:09861"
     CDS             complement(join(42949234..42950520,42951514..42951666))
                     /gene="C7orf25"
                     /gene_synonym="FLJ21167; MGC2821"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC79020 isoform a"
                     /protein_id="NP_001093328.1"
                     /db_xref="GI:153792791"
                     /db_xref="CCDS:CCDS47576.1"
                     /db_xref="GeneID:79020"
                     /db_xref="HGNC:21703"
                     /db_xref="HPRD:09861"
     CDS             complement(42949234..42950499)
                     /gene="C7orf25"
                     /gene_synonym="FLJ21167; MGC2821"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC79020 isoform b"
                     /protein_id="NP_076959.2"
                     /db_xref="GI:153791785"
                     /db_xref="CCDS:CCDS5466.1"
                     /db_xref="GeneID:79020"
                     /db_xref="HGNC:21703"
                     /db_xref="HPRD:09861"
     gene            complement(42956460..42971805)
                     /gene="PSMA2"
                     /gene_synonym="HC3; MU; PMSA2; PSC2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5683"
                     /db_xref="HGNC:9531"
                     /db_xref="HPRD:08907"
                     /db_xref="MIM:176842"
     mRNA            complement(join(42956460..42957289,42957377..42957434,
                     42961457..42961530,42962924..42963005,42964274..42964396,
                     42966135..42966267,42966982..42967058,42971717..42971805))
                     /gene="PSMA2"
                     /gene_synonym="HC3; MU; PMSA2; PSC2"
                     /product="proteasome (prosome, macropain) subunit, alpha
                     type, 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002787.4"
                     /db_xref="GI:156071494"
                     /db_xref="GeneID:5683"
                     /db_xref="HGNC:9531"
                     /db_xref="HPRD:08907"
                     /db_xref="MIM:176842"
     CDS             complement(join(42957173..42957289,42957377..42957434,
                     42961457..42961530,42962924..42963005,42964274..42964396,
                     42966135..42966267,42966982..42967058,42971717..42971757))
                     /gene="PSMA2"
                     /gene_synonym="HC3; MU; PMSA2; PSC2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="proteasome subunit alpha type-2"
                     /protein_id="NP_002778.1"
                     /db_xref="GI:4506181"
                     /db_xref="CCDS:CCDS5467.1"
                     /db_xref="GeneID:5683"
                     /db_xref="HGNC:9531"
                     /db_xref="HPRD:08907"
                     /db_xref="MIM:176842"
     gene            42971939..42977456
                     /gene="MRPL32"
                     /gene_synonym="bMRP-59b; HSPC283; L32mt; MRP-L32"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64983"
                     /db_xref="HGNC:14035"
                     /db_xref="HPRD:14752"
                     /db_xref="MIM:611839"
     mRNA            join(42971939..42972115,42974554..42974735,
                     42976921..42977456)
                     /gene="MRPL32"
                     /gene_synonym="bMRP-59b; HSPC283; L32mt; MRP-L32"
                     /product="mitochondrial ribosomal protein L32"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_031903.2"
                     /db_xref="GI:157743250"
                     /db_xref="GeneID:64983"
                     /db_xref="HGNC:14035"
                     /db_xref="HPRD:14752"
                     /db_xref="MIM:611839"
     CDS             join(42971986..42972115,42974554..42974735,
                     42976921..42977175)
                     /gene="MRPL32"
                     /gene_synonym="bMRP-59b; HSPC283; L32mt; MRP-L32"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="39S ribosomal protein L32, mitochondrial
                     precursor"
                     /protein_id="NP_114109.1"
                     /db_xref="GI:13994261"
                     /db_xref="CCDS:CCDS5468.1"
                     /db_xref="GeneID:64983"
                     /db_xref="HGNC:14035"
                     /db_xref="HPRD:14752"
                     /db_xref="MIM:611839"
     gene            43152198..43602938
                     /gene="HECW1"
                     /gene_synonym="KIAA0322; NEDL1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23072"
                     /db_xref="HGNC:22195"
                     /db_xref="HPRD:11385"
                     /db_xref="MIM:610384"
     mRNA            join(43152198..43152536,43153756..43153990,
                     43283474..43283531,43351362..43351686,43360234..43360341,
                     43400485..43400579,43436413..43436488,43447161..43447330,
                     43477602..43477744,43482128..43482228,43483817..43485169,
                     43490427..43490528,43495896..43496046,43503259..43503398,
                     43506046..43506167,43508519..43508704,43519209..43519343,
                     43531674..43531779,43532683..43532779,43540298..43540381,
                     43540812..43540921,43546736..43546856,43547617..43547730,
                     43548568..43548720,43580762..43580860,43581468..43581597,
                     43590044..43590190,43591821..43591935,43594191..43594389,
                     43601414..43602938)
                     /gene="HECW1"
                     /gene_synonym="KIAA0322; NEDL1"
                     /product="HECT, C2 and WW domain containing E3 ubiquitin
                     protein ligase 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015052.3"
                     /db_xref="GI:94536810"
                     /db_xref="GeneID:23072"
                     /db_xref="HGNC:22195"
                     /db_xref="HPRD:11385"
                     /db_xref="MIM:610384"
     gene            43157495..43202786
                     /gene="HECW1-IT1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 4 ESTs, 1 Protein"
                     /db_xref="GeneID:100127950"
                     /db_xref="HGNC:41465"
     misc_RNA        join(43157495..43158174,43158546..43158794,
                     43161402..43161618,43187047..43187184,43188240..43188426,
                     43201209..43201314,43202525..43202786)
                     /gene="HECW1-IT1"
                     /product="HECW1 intronic transcript 1 (non-protein
                     coding)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 4 ESTs, 1 Protein"
                     /transcript_id="XR_108772.1"
                     /db_xref="GI:310119957"
                     /db_xref="GeneID:100127950"
                     /db_xref="HGNC:41465"
     gene            43190494..43190593
                     /gene="MIR3943"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100500829"
                     /db_xref="HGNC:38888"
                     /db_xref="miRBase:MI0016600"
     ncRNA           43190494..43190593
                     /gene="MIR3943"
                     /ncRNA_class="miRNA"
                     /product="microRNA 3943"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037508.1"
                     /db_xref="GI:312147115"
                     /db_xref="GeneID:100500829"
                     /db_xref="HGNC:38888"
                     /db_xref="miRBase:MI0016600"
     gene            43234021..43234081
                     /gene="RNU7-35P"
                     /gene_synonym="U7.35"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100147822"
                     /db_xref="HGNC:34131"
     CDS             join(43283505..43283531,43351362..43351686,
                     43360234..43360341,43400485..43400579,43436413..43436488,
                     43447161..43447330,43477602..43477744,43482128..43482228,
                     43483817..43485169,43490427..43490528,43495896..43496046,
                     43503259..43503398,43506046..43506167,43508519..43508704,
                     43519209..43519343,43531674..43531779,43532683..43532779,
                     43540298..43540381,43540812..43540921,43546736..43546856,
                     43547617..43547730,43548568..43548720,43580762..43580860,
                     43581468..43581597,43590044..43590190,43591821..43591935,
                     43594191..43594389,43601414..43601525)
                     /gene="HECW1"
                     /gene_synonym="KIAA0322; NEDL1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase HECW1"
                     /protein_id="NP_055867.3"
                     /db_xref="GI:94536811"
                     /db_xref="CCDS:CCDS5469.2"
                     /db_xref="GeneID:23072"
                     /db_xref="HGNC:22195"
                     /db_xref="HPRD:11385"
                     /db_xref="MIM:610384"
     gene            43313758..43314181
                     /gene="RPL18AP10"
                     /gene_synonym="RPL18A_4_806"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271285"
                     /db_xref="HGNC:35885"
     gene            complement(43548327..43562141)
                     /gene="LOC100506895"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100506895"
     misc_RNA        complement(join(43548327..43549846,43550582..43551722,
                     43561887..43562141))
                     /gene="LOC100506895"
                     /product="hypothetical LOC100506895"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038276.1"
                     /db_xref="GI:333805654"
                     /db_xref="GeneID:100506895"
     gene            43622692..43666978
                     /gene="STK17A"
                     /gene_synonym="DRAK1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9263"
                     /db_xref="HGNC:11395"
                     /db_xref="HPRD:05288"
                     /db_xref="MIM:604726"
     mRNA            join(43622692..43623048,43635500..43635712,
                     43647855..43647999,43659196..43659322,43663171..43663219,
                     43663308..43663487,43664117..43666978)
                     /gene="STK17A"
                     /gene_synonym="DRAK1"
                     /product="serine/threonine kinase 17a"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004760.2"
                     /db_xref="GI:109255244"
                     /db_xref="GeneID:9263"
                     /db_xref="HGNC:11395"
                     /db_xref="HPRD:05288"
                     /db_xref="MIM:604726"
     CDS             join(43622843..43623048,43635500..43635712,
                     43647855..43647999,43659196..43659322,43663171..43663219,
                     43663308..43663487,43664117..43664441)
                     /gene="STK17A"
                     /gene_synonym="DRAK1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="serine/threonine-protein kinase 17A"
                     /protein_id="NP_004751.2"
                     /db_xref="GI:109255245"
                     /db_xref="CCDS:CCDS5470.1"
                     /db_xref="GeneID:9263"
                     /db_xref="HGNC:11395"
                     /db_xref="HPRD:05288"
                     /db_xref="MIM:604726"
     gene            complement(43678859..43769083)
                     /gene="C7orf44"
                     /gene_synonym="FLJ10803"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55744"
                     /db_xref="HGNC:21868"
                     /db_xref="HPRD:07700"
     mRNA            complement(join(43678859..43679280,43680172..43680248,
                     43684850..43684998,43687134..43687233,43688199..43688251,
                     43769028..43769083))
                     /gene="C7orf44"
                     /gene_synonym="FLJ10803"
                     /product="chromosome 7 open reading frame 44"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018224.2"
                     /db_xref="GI:90855770"
                     /db_xref="GeneID:55744"
                     /db_xref="HGNC:21868"
                     /db_xref="HPRD:07700"
     CDS             complement(join(43679181..43679280,43680172..43680248,
                     43684850..43684998,43687134..43687233,43688199..43688213))
                     /gene="C7orf44"
                     /gene_synonym="FLJ10803"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC55744"
                     /protein_id="NP_060694.2"
                     /db_xref="GI:90855771"
                     /db_xref="CCDS:CCDS5471.1"
                     /db_xref="GeneID:55744"
                     /db_xref="HGNC:21868"
                     /db_xref="HPRD:07700"
     gene            43798272..43846941
                     /gene="BLVRA"
                     /gene_synonym="BLVR; BVR; BVRA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:644"
                     /db_xref="HGNC:1062"
                     /db_xref="HPRD:11229"
                     /db_xref="MIM:109750"
     mRNA            join(43798272..43798333,43810737..43810769,
                     43827503..43827624,43830848..43830967,43832314..43832411,
                     43840064..43840171,43843275..43843446,43846576..43846941)
                     /gene="BLVRA"
                     /gene_synonym="BLVR; BVR; BVRA"
                     /product="biliverdin reductase A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000712.3"
                     /db_xref="GI:40353771"
                     /db_xref="GeneID:644"
                     /db_xref="HGNC:1062"
                     /db_xref="HPRD:11229"
                     /db_xref="MIM:109750"
     CDS             join(43810758..43810769,43827503..43827624,
                     43830848..43830967,43832314..43832411,43840064..43840171,
                     43843275..43843446,43846576..43846834)
                     /gene="BLVRA"
                     /gene_synonym="BLVR; BVR; BVRA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="biliverdin reductase A precursor"
                     /protein_id="NP_000703.2"
                     /db_xref="GI:33589854"
                     /db_xref="CCDS:CCDS5472.1"
                     /db_xref="GeneID:644"
                     /db_xref="HGNC:1062"
                     /db_xref="HPRD:11229"
                     /db_xref="MIM:109750"
     gene            complement(43906157..43946231)
                     /gene="URGCP-MRPS24"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100534592"
     mRNA            complement(join(43906157..43906581,43908562..43908673,
                     43908907..43908975,43921258..43921296,43921506..43921556,
                     43927014..43927084,43946161..43946231))
                     /gene="URGCP-MRPS24"
                     /product="URGCP-MRPS24 readthrough"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001204871.1"
                     /db_xref="GI:325652090"
                     /db_xref="GeneID:100534592"
     gene            complement(43906157..43909145)
                     /gene="MRPS24"
                     /gene_synonym="bMRP-47; bMRP47; HSPC335; MRP-S24; S24mt"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64951"
                     /db_xref="HGNC:14510"
                     /db_xref="HPRD:17593"
                     /db_xref="MIM:611986"
     mRNA            complement(join(43906157..43906581,43908562..43908673,
                     43908907..43908975,43909056..43909145))
                     /gene="MRPS24"
                     /gene_synonym="bMRP-47; bMRP47; HSPC335; MRP-S24; S24mt"
                     /product="mitochondrial ribosomal protein S24"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032014.2"
                     /db_xref="GI:117940051"
                     /db_xref="GeneID:64951"
                     /db_xref="HGNC:14510"
                     /db_xref="HPRD:17593"
                     /db_xref="MIM:611986"
     CDS             complement(join(43906298..43906581,43908562..43908673,
                     43908907..43908975,43909056..43909094))
                     /gene="MRPS24"
                     /gene_synonym="bMRP-47; bMRP47; HSPC335; MRP-S24; S24mt"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="28S ribosomal protein S24, mitochondrial
                     precursor"
                     /protein_id="NP_114403.1"
                     /db_xref="GI:15721937"
                     /db_xref="CCDS:CCDS5473.1"
                     /db_xref="GeneID:64951"
                     /db_xref="HGNC:14510"
                     /db_xref="HPRD:17593"
                     /db_xref="MIM:611986"
     CDS             complement(join(43908585..43908673,43908907..43908975,
                     43921258..43921296,43921506..43921556,43927014..43927084,
                     43946161..43946174))
                     /gene="URGCP-MRPS24"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC100534592"
                     /protein_id="NP_001191800.1"
                     /db_xref="GI:325652091"
                     /db_xref="GeneID:100534592"
     gene            complement(43915501..43965996)
                     /gene="URGCP"
                     /gene_synonym="DKFZp666G166; DKFZp686O0457; URG4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55665"
                     /db_xref="HGNC:30890"
                     /db_xref="MIM:610337"
     mRNA            complement(join(43915501..43918859,43921258..43921296,
                     43921506..43921556,43927014..43927084,43927389..43927415,
                     43965731..43965996))
                     /gene="URGCP"
                     /gene_synonym="DKFZp666G166; DKFZp686O0457; URG4"
                     /product="upregulator of cell proliferation, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001077664.1"
                     /db_xref="GI:117968344"
                     /db_xref="GeneID:55665"
                     /db_xref="HGNC:30890"
                     /db_xref="MIM:610337"
     mRNA            complement(join(43915501..43918859,43921258..43921296,
                     43921506..43921556,43927014..43927084,43946161..43946231))
                     /gene="URGCP"
                     /gene_synonym="DKFZp666G166; DKFZp686O0457; URG4"
                     /product="upregulator of cell proliferation, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017920.3"
                     /db_xref="GI:117968346"
                     /db_xref="GeneID:55665"
                     /db_xref="HGNC:30890"
                     /db_xref="HPRD:11663"
                     /db_xref="MIM:610337"
     mRNA            complement(join(43915501..43918859,43921258..43921296,
                     43921506..43921556,43927014..43927084,43927389..43927415,
                     43946161..43946231))
                     /gene="URGCP"
                     /gene_synonym="DKFZp666G166; DKFZp686O0457; URG4"
                     /product="upregulator of cell proliferation, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001077663.1"
                     /db_xref="GI:117968327"
                     /db_xref="GeneID:55665"
                     /db_xref="HGNC:30890"
                     /db_xref="MIM:610337"
     CDS             complement(join(43916266..43918859,43921258..43921296,
                     43921506..43921556,43927014..43927084,43946161..43946174))
                     /gene="URGCP"
                     /gene_synonym="DKFZp666G166; DKFZp686O0457; URG4"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="up-regulated gene 4 isoform 1"
                     /protein_id="NP_060390.3"
                     /db_xref="GI:117968347"
                     /db_xref="CCDS:CCDS47577.1"
                     /db_xref="GeneID:55665"
                     /db_xref="HGNC:30890"
                     /db_xref="MIM:610337"
     CDS             complement(join(43916266..43918859,43921258..43921296,
                     43921506..43921556,43927014..43927084,43927389..43927415,
                     43946161..43946174))
                     /gene="URGCP"
                     /gene_synonym="DKFZp666G166; DKFZp686O0457; URG4"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="up-regulated gene 4 isoform 3"
                     /protein_id="NP_001071131.1"
                     /db_xref="GI:117968328"
                     /db_xref="CCDS:CCDS47578.1"
                     /db_xref="GeneID:55665"
                     /db_xref="HGNC:30890"
                     /db_xref="MIM:610337"
     CDS             complement(join(43916266..43918859,43921258..43921296,
                     43921506..43921539))
                     /gene="URGCP"
                     /gene_synonym="DKFZp666G166; DKFZp686O0457; URG4"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="up-regulated gene 4 isoform 2"
                     /protein_id="NP_001071132.1"
                     /db_xref="GI:117968345"
                     /db_xref="CCDS:CCDS43572.1"
                     /db_xref="GeneID:55665"
                     /db_xref="HGNC:30890"
                     /db_xref="MIM:610337"
     gene            43958236..43959851
                     /gene="TUBG1P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442673"
                     /db_xref="HGNC:12418"
     gene            43966035..43995735
                     /gene="UBE2D4"
                     /gene_synonym="FLJ32004; HBUCE1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51619"
                     /db_xref="HGNC:21647"
                     /db_xref="HPRD:14242"
     mRNA            join(43966035..43966155,43978030..43978093,
                     43982425..43982456,43982553..43982630,43988231..43988336,
                     43990198..43990291,43992249..43995735)
                     /gene="UBE2D4"
                     /gene_synonym="FLJ32004; HBUCE1"
                     /product="ubiquitin-conjugating enzyme E2D 4 (putative)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015983.3"
                     /db_xref="GI:303228325"
                     /db_xref="GeneID:51619"
                     /db_xref="HGNC:21647"
                     /db_xref="HPRD:14242"
     CDS             join(43966132..43966155,43978030..43978093,
                     43982425..43982456,43982553..43982630,43988231..43988336,
                     43990198..43990291,43992249..43992294)
                     /gene="UBE2D4"
                     /gene_synonym="FLJ32004; HBUCE1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ubiquitin-conjugating enzyme E2 D4"
                     /protein_id="NP_057067.1"
                     /db_xref="GI:8393719"
                     /db_xref="CCDS:CCDS5474.1"
                     /db_xref="GeneID:51619"
                     /db_xref="HGNC:21647"
                     /db_xref="HPRD:14242"
     gene            complement(43980494..44058748)
                     /gene="POLR2J4"
                     /gene_synonym="MGC13098; RPB11-phi"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:84820"
                     /db_xref="HGNC:28195"
     misc_RNA        complement(join(43980494..43984547,43985733..43985923,
                     43992120..43992795,44001572..44001689,44005466..44005560,
                     44005863..44005994,44009331..44009460,44012229..44012290,
                     44012809..44012922,44026200..44026276,44027277..44027487,
                     44027685..44027846,44053192..44053278,44054205..44054382,
                     44056033..44056122,44058660..44058748))
                     /gene="POLR2J4"
                     /gene_synonym="MGC13098; RPB11-phi"
                     /product="polymerase (RNA) II (DNA directed) polypeptide
                     J4, pseudogene"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003655.2"
                     /db_xref="GI:195539386"
                     /db_xref="GeneID:84820"
                     /db_xref="HGNC:28195"
     gene            44040489..44049723
                     /gene="SPDYE1"
                     /gene_synonym="DKFZp434A1014; Ringo1; SPDYE; WBSCR19"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285955"
                     /db_xref="HGNC:16408"
                     /db_xref="HPRD:11677"
     mRNA            join(44040489..44040883,44042189..44042416,
                     44043452..44043510,44044741..44044826,44046867..44047185,
                     44047308..44047412,44048266..44049723)
                     /gene="SPDYE1"
                     /gene_synonym="DKFZp434A1014; Ringo1; SPDYE; WBSCR19"
                     /product="speedy homolog E1 (Xenopus laevis)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_175064.2"
                     /db_xref="GI:30795187"
                     /db_xref="GeneID:285955"
                     /db_xref="HGNC:16408"
                     /db_xref="HPRD:11677"
     CDS             join(44040625..44040883,44042189..44042416,
                     44043452..44043510,44044741..44044826,44046867..44047185,
                     44047308..44047367)
                     /gene="SPDYE1"
                     /gene_synonym="DKFZp434A1014; Ringo1; SPDYE; WBSCR19"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative WBSCR19-like protein 6"
                     /protein_id="NP_778234.2"
                     /db_xref="GI:30795188"
                     /db_xref="CCDS:CCDS5475.1"
                     /db_xref="GeneID:285955"
                     /db_xref="HGNC:16408"
                     /db_xref="HPRD:11677"
     gene            complement(44068486..44080222)
                     /gene="RASA4P"
                     /gene_synonym="DKFZp781H1351; FLJ21767; FLJ99771"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:401331"
     misc_RNA        complement(join(44068486..44069054,44069166..44069230,
                     44070380..44070500,44073775..44073910,44076271..44076408,
                     44078406..44078575,44079118..44079262,44079831..44079968,
                     44080178..44080222))
                     /gene="RASA4P"
                     /gene_synonym="DKFZp781H1351; FLJ21767; FLJ99771"
                     /product="RAS p21 protein activator 4 pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_024116.2"
                     /db_xref="GI:212286157"
                     /db_xref="GeneID:401331"
     gene            44078698..44082082
                     /gene="FLJ35390"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:255031"
     misc_RNA        join(44078698..44078882,44079493..44080701,
                     44081814..44082082)
                     /gene="FLJ35390"
                     /product="hypothetical LOC255031, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_015401.1"
                     /db_xref="GI:212286151"
                     /db_xref="GeneID:255031"
     misc_RNA        join(44079067..44079298,44079493..44081114,
                     44081790..44082082)
                     /gene="FLJ35390"
                     /product="hypothetical LOC255031, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024416.1"
                     /db_xref="GI:212286152"
                     /db_xref="GeneID:255031"
     gene            44084239..44101315
                     /gene="DBNL"
                     /gene_synonym="ABP1; HIP-55; SH3P7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:28988"
                     /db_xref="HGNC:2696"
                     /db_xref="HPRD:06588"
                     /db_xref="MIM:610106"
     mRNA            join(44084239..44084419,44089824..44089879,
                     44091429..44091541,44092466..44092540,44096356..44096502,
                     44097381..44097458,44097728..44097879,44098028..44098079,
                     44098501..44098582,44098953..44099048,44099142..44099257,
                     44099647..44099752,44100376..44101315)
                     /gene="DBNL"
                     /gene_synonym="ABP1; HIP-55; SH3P7"
                     /product="drebrin-like, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014063.6"
                     /db_xref="GI:171906572"
                     /db_xref="GeneID:28988"
                     /db_xref="HGNC:2696"
                     /db_xref="HPRD:06588"
                     /db_xref="MIM:610106"
     mRNA            join(44084239..44084419,44089824..44089879,
                     44091429..44091541,44092466..44092540,44096356..44096502,
                     44097381..44097458,44097728..44097879,44098031..44098079,
                     44098501..44098582,44098953..44099048,44099142..44099257,
                     44099647..44099752,44100376..44101315)
                     /gene="DBNL"
                     /gene_synonym="ABP1; HIP-55; SH3P7"
                     /product="drebrin-like, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001014436.2"
                     /db_xref="GI:171906573"
                     /db_xref="GeneID:28988"
                     /db_xref="HGNC:2696"
                     /db_xref="MIM:610106"
                     /db_xref="HPRD:06588"
     mRNA            join(44084239..44084419,44089824..44089879,
                     44091429..44091541,44092466..44092540,44096356..44096502,
                     44097381..44097458,44097728..44097879,44098028..44098079,
                     44098477..44098582,44098953..44099048,44099142..44099257,
                     44099647..44099752,44100376..44101315)
                     /gene="DBNL"
                     /gene_synonym="ABP1; HIP-55; SH3P7"
                     /product="drebrin-like, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001122956.1"
                     /db_xref="GI:171906574"
                     /db_xref="GeneID:28988"
                     /db_xref="HGNC:2696"
                     /db_xref="MIM:610106"
                     /db_xref="HPRD:06588"
     CDS             join(44084337..44084419,44089824..44089879,
                     44091429..44091541,44092466..44092540,44096356..44096502,
                     44097381..44097458,44097728..44097879,44098028..44098079,
                     44098501..44098582,44098953..44099048,44099142..44099257,
                     44099647..44099752,44100376..44100515)
                     /gene="DBNL"
                     /gene_synonym="ABP1; HIP-55; SH3P7"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="drebrin-like protein isoform a"
                     /protein_id="NP_054782.2"
                     /db_xref="GI:21361670"
                     /db_xref="CCDS:CCDS34622.1"
                     /db_xref="GeneID:28988"
                     /db_xref="HGNC:2696"
                     /db_xref="HPRD:06588"
                     /db_xref="MIM:610106"
     CDS             join(44084337..44084419,44089824..44089879,
                     44091429..44091541,44092466..44092540,44096356..44096502,
                     44097381..44097458,44097728..44097879,44098031..44098079,
                     44098501..44098582,44098953..44099048,44099142..44099257,
                     44099647..44099752,44100376..44100515)
                     /gene="DBNL"
                     /gene_synonym="ABP1; HIP-55; SH3P7"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="drebrin-like protein isoform b"
                     /protein_id="NP_001014436.1"
                     /db_xref="GI:62198235"
                     /db_xref="CCDS:CCDS34623.1"
                     /db_xref="GeneID:28988"
                     /db_xref="HGNC:2696"
                     /db_xref="HPRD:06588"
                     /db_xref="MIM:610106"
     CDS             join(44084337..44084419,44089824..44089879,
                     44091429..44091541,44092466..44092540,44096356..44096502,
                     44097381..44097458,44097728..44097879,44098028..44098079,
                     44098477..44098582,44098953..44099048,44099142..44099257,
                     44099647..44099752,44100376..44100515)
                     /gene="DBNL"
                     /gene_synonym="ABP1; HIP-55; SH3P7"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="drebrin-like protein isoform c"
                     /protein_id="NP_001116428.1"
                     /db_xref="GI:171906575"
                     /db_xref="CCDS:CCDS47579.1"
                     /db_xref="GeneID:28988"
                     /db_xref="HGNC:2696"
                     /db_xref="HPRD:06588"
                     /db_xref="MIM:610106"
     gene            complement(44102326..44105186)
                     /gene="PGAM2"
                     /gene_synonym="GSD10; MGC88743; PGAM-M; PGAMM"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5224"
                     /db_xref="HGNC:8889"
                     /db_xref="HPRD:02027"
                     /db_xref="MIM:612931"
     mRNA            complement(join(44102326..44102529,44104431..44104611,
                     44104715..44105186))
                     /gene="PGAM2"
                     /gene_synonym="GSD10; MGC88743; PGAM-M; PGAMM"
                     /product="phosphoglycerate mutase 2 (muscle)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000290.3"
                     /db_xref="GI:259490363"
                     /db_xref="GeneID:5224"
                     /db_xref="HGNC:8889"
                     /db_xref="HPRD:02027"
                     /db_xref="MIM:612931"
     CDS             complement(join(44102363..44102529,44104431..44104611,
                     44104715..44105128))
                     /gene="PGAM2"
                     /gene_synonym="GSD10; MGC88743; PGAM-M; PGAMM"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="phosphoglycerate mutase 2"
                     /protein_id="NP_000281.2"
                     /db_xref="GI:50593010"
                     /db_xref="CCDS:CCDS34624.1"
                     /db_xref="GeneID:5224"
                     /db_xref="HGNC:8889"
                     /db_xref="HPRD:02027"
                     /db_xref="MIM:612931"
     gene            44104415..44108692
                     /gene="LOC100506936"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 7 ESTs"
                     /db_xref="GeneID:100506936"
     misc_RNA        join(44104415..44105116,44105581..44105676,
                     44108146..44108692)
                     /gene="LOC100506936"
                     /product="hypothetical LOC100506936, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 7 ESTs"
                     /transcript_id="XR_108774.1"
                     /db_xref="GI:310119961"
                     /db_xref="GeneID:100506936"
     gene            complement(44111846..44122129)
                     /gene="POLM"
                     /gene_synonym="FLJ35482; Pol Mu; Tdt-N"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:27434"
                     /db_xref="HGNC:9185"
                     /db_xref="HPRD:16208"
                     /db_xref="MIM:606344"
     mRNA            complement(join(44111846..44112976,44113224..44113307,
                     44113382..44113624,44113730..44113832,44113997..44114129,
                     44116108..44116228,44118339..44118410,44119170..44119340,
                     44119460..44119558,44120332..44120515,44121850..44122129))
                     /gene="POLM"
                     /gene_synonym="FLJ35482; Pol Mu; Tdt-N"
                     /product="polymerase (DNA directed), mu"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013284.2"
                     /db_xref="GI:194018740"
                     /db_xref="GeneID:27434"
                     /db_xref="HGNC:9185"
                     /db_xref="HPRD:16208"
                     /db_xref="MIM:606344"
     CDS             complement(join(44112890..44112976,44113224..44113307,
                     44113382..44113624,44113730..44113832,44113997..44114129,
                     44116108..44116228,44118339..44118410,44119170..44119340,
                     44119460..44119558,44120332..44120515,44121850..44122037))
                     /gene="POLM"
                     /gene_synonym="FLJ35482; Pol Mu; Tdt-N"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-directed DNA/RNA polymerase mu"
                     /protein_id="NP_037416.1"
                     /db_xref="GI:7019493"
                     /db_xref="CCDS:CCDS34625.1"
                     /db_xref="GeneID:27434"
                     /db_xref="HGNC:9185"
                     /db_xref="HPRD:16208"
                     /db_xref="MIM:606344"
     gene            44143960..44154159
                     /gene="AEBP1"
                     /gene_synonym="ACLP; FLJ33612"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:165"
                     /db_xref="HGNC:303"
                     /db_xref="HPRD:04281"
                     /db_xref="MIM:602981"
     mRNA            join(44143960..44144517,44146145..44146486,
                     44147038..44147109,44147228..44147299,44147408..44147530,
                     44147606..44147683,44148498..44148575,44148706..44148783,
                     44148887..44148940,44149614..44149723,44149806..44149945,
                     44150324..44150408,44150512..44150656,44150753..44150838,
                     44151106..44151229,44151453..44151649,44151741..44151920,
                     44152157..44152508,44152590..44152729,44152851..44152950,
                     44153193..44154159)
                     /gene="AEBP1"
                     /gene_synonym="ACLP; FLJ33612"
                     /product="AE binding protein 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001129.3"
                     /db_xref="GI:53692188"
                     /db_xref="GeneID:165"
                     /db_xref="HGNC:303"
                     /db_xref="HPRD:04281"
                     /db_xref="MIM:602981"
     CDS             join(44144265..44144517,44146145..44146486,
                     44147038..44147109,44147228..44147299,44147408..44147530,
                     44147606..44147683,44148498..44148575,44148706..44148783,
                     44148887..44148940,44149614..44149723,44149806..44149945,
                     44150324..44150408,44150512..44150656,44150753..44150838,
                     44151106..44151229,44151453..44151649,44151741..44151920,
                     44152157..44152508,44152590..44152729,44152851..44152950,
                     44153193..44153860)
                     /gene="AEBP1"
                     /gene_synonym="ACLP; FLJ33612"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="adipocyte enhancer-binding protein 1 precursor"
                     /protein_id="NP_001120.3"
                     /db_xref="GI:53692189"
                     /db_xref="CCDS:CCDS5476.1"
                     /db_xref="GeneID:165"
                     /db_xref="HGNC:303"
                     /db_xref="HPRD:04281"
                     /db_xref="MIM:602981"
     gene            44150441..44150523
                     /gene="MIR4649"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100616346"
                     /db_xref="HGNC:41852"
                     /db_xref="miRBase:MI0017276"
     ncRNA           44150441..44150523
                     /gene="MIR4649"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4649"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039792.1"
                     /db_xref="GI:337756579"
                     /db_xref="GeneID:100616346"
                     /db_xref="HGNC:41852"
                     /db_xref="miRBase:MI0017276"
     gene            complement(44154286..44163147)
                     /gene="POLD2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5425"
                     /db_xref="HGNC:9176"
                     /db_xref="MIM:600815"
     mRNA            complement(join(44154286..44154544,44154894..44154995,
                     44155365..44155492,44155714..44155871,44156029..44156109,
                     44156416..44156614,44156732..44156846,44157218..44157341,
                     44157542..44157663,44161433..44161881,44163110..44163147))
                     /gene="POLD2"
                     /product="polymerase (DNA directed), delta 2, regulatory
                     subunit 50kDa, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127218.1"
                     /db_xref="GI:187828567"
                     /db_xref="GeneID:5425"
                     /db_xref="HGNC:9176"
                     /db_xref="MIM:600815"
     mRNA            complement(join(44154286..44154544,44154894..44154995,
                     44155365..44155492,44155714..44155871,44156029..44156109,
                     44156416..44156614,44156732..44156846,44157218..44157341,
                     44157542..44157663,44161433..44161708,44163110..44163147))
                     /gene="POLD2"
                     /product="polymerase (DNA directed), delta 2, regulatory
                     subunit 50kDa, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006230.2"
                     /db_xref="GI:187936922"
                     /db_xref="GeneID:5425"
                     /db_xref="HGNC:9176"
                     /db_xref="HPRD:15982"
                     /db_xref="MIM:600815"
     CDS             complement(join(44154384..44154544,44154894..44154995,
                     44155365..44155492,44155714..44155871,44156029..44156109,
                     44156416..44156614,44156732..44156846,44157218..44157341,
                     44157542..44157663,44161433..44161652))
                     /gene="POLD2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA polymerase delta subunit 2"
                     /protein_id="NP_001120690.1"
                     /db_xref="GI:187828568"
                     /db_xref="CCDS:CCDS5477.1"
                     /db_xref="GeneID:5425"
                     /db_xref="HGNC:9176"
                     /db_xref="MIM:600815"
     CDS             complement(join(44154384..44154544,44154894..44154995,
                     44155365..44155492,44155714..44155871,44156029..44156109,
                     44156416..44156614,44156732..44156846,44157218..44157341,
                     44157542..44157663,44161433..44161652))
                     /gene="POLD2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA polymerase delta subunit 2"
                     /protein_id="NP_006221.1"
                     /db_xref="GI:5453924"
                     /db_xref="CCDS:CCDS5477.1"
                     /db_xref="GeneID:5425"
                     /db_xref="HGNC:9176"
                     /db_xref="MIM:600815"
     gene            complement(44178463..44180916)
                     /gene="MYL7"
                     /gene_synonym="MYL2A; MYLC2A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:58498"
                     /db_xref="HGNC:21719"
                     /db_xref="HPRD:10105"
                     /db_xref="MIM:613993"
     mRNA            complement(join(44178463..44178621,44179120..44179168,
                     44179381..44179459,44179922..44180026,44180311..44180386,
                     44180560..44180673,44180902..44180916))
                     /gene="MYL7"
                     /gene_synonym="MYL2A; MYLC2A"
                     /product="myosin, light chain 7, regulatory"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021223.2"
                     /db_xref="GI:50593014"
                     /db_xref="GeneID:58498"
                     /db_xref="HGNC:21719"
                     /db_xref="HPRD:10105"
                     /db_xref="MIM:613993"
     CDS             complement(join(44178520..44178621,44179120..44179168,
                     44179381..44179459,44179922..44180026,44180311..44180386,
                     44180560..44180673,44180902..44180904))
                     /gene="MYL7"
                     /gene_synonym="MYL2A; MYLC2A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="myosin regulatory light chain 2, atrial isoform"
                     /protein_id="NP_067046.1"
                     /db_xref="GI:10864037"
                     /db_xref="CCDS:CCDS5478.1"
                     /db_xref="GeneID:58498"
                     /db_xref="HGNC:21719"
                     /db_xref="HPRD:10105"
                     /db_xref="MIM:613993"
     gene            complement(44183870..44229022)
                     /gene="GCK"
                     /gene_synonym="FGQTL3; GK; GLK; HHF3; HK4; HKIV; HXKP;
                     LGLK; MODY2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2645"
                     /db_xref="HGNC:4195"
                     /db_xref="HPRD:00680"
                     /db_xref="MIM:138079"
     mRNA            complement(join(44183870..44184879,44185096..44185329,
                     44186062..44186217,44187249..44187432,44189359..44189458,
                     44189568..44189663,44190555..44190674,44191870..44192024,
                     44192900..44193062,44228508..44229022))
                     /gene="GCK"
                     /gene_synonym="FGQTL3; GK; GLK; HHF3; HK4; HKIV; HXKP;
                     LGLK; MODY2"
                     /product="glucokinase (hexokinase 4), transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000162.3"
                     /db_xref="GI:167621407"
                     /db_xref="GeneID:2645"
                     /db_xref="HGNC:4195"
                     /db_xref="HPRD:00680"
                     /db_xref="MIM:138079"
     mRNA            complement(join(44183870..44184879,44185096..44185329,
                     44186062..44186217,44187249..44187432,44189359..44189458,
                     44189568..44189663,44190555..44190674,44191870..44192024,
                     44192900..44193062,44198672..44198887))
                     /gene="GCK"
                     /gene_synonym="FGQTL3; GK; GLK; HHF3; HK4; HKIV; HXKP;
                     LGLK; MODY2"
                     /product="glucokinase (hexokinase 4), transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033507.1"
                     /db_xref="GI:15967158"
                     /db_xref="GeneID:2645"
                     /db_xref="HGNC:4195"
                     /db_xref="HPRD:00680"
                     /db_xref="MIM:138079"
     mRNA            complement(join(44183870..44184879,44185096..44185329,
                     44186062..44186217,44187249..44187432,44189359..44189458,
                     44189568..44189663,44190555..44190674,44191870..44192024,
                     44192900..44193062,44197672..44197795,44198672..44198887))
                     /gene="GCK"
                     /gene_synonym="FGQTL3; GK; GLK; HHF3; HK4; HKIV; HXKP;
                     LGLK; MODY2"
                     /product="glucokinase (hexokinase 4), transcript variant
                     3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033508.1"
                     /db_xref="GI:15967160"
                     /db_xref="GeneID:2645"
                     /db_xref="HGNC:4195"
                     /db_xref="HPRD:00680"
                     /db_xref="MIM:138079"
     CDS             complement(join(44184735..44184879,44185096..44185329,
                     44186062..44186217,44187249..44187432,44189359..44189458,
                     44189568..44189663,44190555..44190674,44191870..44192024,
                     44192900..44193062,44228508..44228552))
                     /gene="GCK"
                     /gene_synonym="FGQTL3; GK; GLK; HHF3; HK4; HKIV; HXKP;
                     LGLK; MODY2"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="glucokinase isoform 1"
                     /protein_id="NP_000153.1"
                     /db_xref="GI:4503951"
                     /db_xref="CCDS:CCDS5479.1"
                     /db_xref="GeneID:2645"
                     /db_xref="HGNC:4195"
                     /db_xref="HPRD:00680"
                     /db_xref="MIM:138079"
     CDS             complement(join(44184735..44184879,44185096..44185329,
                     44186062..44186217,44187249..44187432,44189359..44189458,
                     44189568..44189663,44190555..44190674,44191870..44192024,
                     44192900..44193062,44198672..44198719))
                     /gene="GCK"
                     /gene_synonym="FGQTL3; GK; GLK; HHF3; HK4; HKIV; HXKP;
                     LGLK; MODY2"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="glucokinase isoform 2"
                     /protein_id="NP_277042.1"
                     /db_xref="GI:15967159"
                     /db_xref="CCDS:CCDS5480.1"
                     /db_xref="GeneID:2645"
                     /db_xref="HGNC:4195"
                     /db_xref="HPRD:00680"
                     /db_xref="MIM:138079"
     CDS             complement(join(44184735..44184879,44185096..44185329,
                     44186062..44186217,44187249..44187432,44189359..44189458,
                     44189568..44189663,44190555..44190674,44191870..44192024,
                     44192900..44193062,44197672..44197713))
                     /gene="GCK"
                     /gene_synonym="FGQTL3; GK; GLK; HHF3; HK4; HKIV; HXKP;
                     LGLK; MODY2"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="glucokinase isoform 3"
                     /protein_id="NP_277043.1"
                     /db_xref="GI:15967161"
                     /db_xref="CCDS:CCDS5481.1"
                     /db_xref="GeneID:2645"
                     /db_xref="HGNC:4195"
                     /db_xref="HPRD:00680"
                     /db_xref="MIM:138079"
     gene            44240578..44253893
                     /gene="YKT6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10652"
                     /db_xref="HGNC:16959"
                     /db_xref="HPRD:16205"
                     /db_xref="MIM:606209"
     mRNA            join(44240578..44240838,44244167..44244249,
                     44245984..44246084,44246987..44247091,44247732..44247797,
                     44250622..44250723,44251846..44253893)
                     /gene="YKT6"
                     /product="YKT6 v-SNARE homolog (S. cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006555.3"
                     /db_xref="GI:34304384"
                     /db_xref="GeneID:10652"
                     /db_xref="HGNC:16959"
                     /db_xref="HPRD:16205"
                     /db_xref="MIM:606209"
     CDS             join(44240735..44240838,44244167..44244249,
                     44245984..44246084,44246987..44247091,44247732..44247797,
                     44250622..44250723,44251846..44251881)
                     /gene="YKT6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="synaptobrevin homolog YKT6"
                     /protein_id="NP_006546.1"
                     /db_xref="GI:5730120"
                     /db_xref="CCDS:CCDS5482.1"
                     /db_xref="GeneID:10652"
                     /db_xref="HGNC:16959"
                     /db_xref="HPRD:16205"
                     /db_xref="MIM:606209"
     gene            complement(44256749..44365230)
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     mRNA            complement(join(44256749..44259121,44259659..44259893,
                     44260215..44260309,44260425..44260500,44266115..44266243,
                     44268395..44268523,44268987..44269100,44270605..44270653,
                     44272421..44272465,44273989..44274060,44274238..44274275,
                     44279188..44279262,44280306..44280348,44281299..44281382,
                     44281817..44281939,44282159..44282253,44282849..44282932,
                     44283024..44283126,44286719..44286791,44294141..44294206,
                     44298471..44298525,44302604..44302663,44323730..44323824,
                     44364956..44365230))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /product="calcium/calmodulin-dependent protein kinase II
                     beta, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220.4"
                     /db_xref="GI:212549591"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     mRNA            complement(join(44256749..44259121,44259659..44259893,
                     44260215..44260309,44260425..44260500,44270605..44270653,
                     44272421..44272465,44273989..44274060,44274238..44274275,
                     44279188..44279262,44280306..44280348,44281299..44281382,
                     44281817..44281939,44282159..44282253,44282849..44282932,
                     44283024..44283126,44286719..44286791,44294141..44294206,
                     44298471..44298525,44302604..44302663,44323730..44323824,
                     44364956..44365230))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /product="calcium/calmodulin-dependent protein kinase II
                     beta, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_172078.2"
                     /db_xref="GI:212549588"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     mRNA            complement(join(44256749..44259121,44259659..44259893,
                     44260215..44260309,44260425..44260500,44270605..44270653,
                     44272421..44272465,44273989..44274060,44274238..44274278,
                     44280306..44280348,44281299..44281382,44281817..44281939,
                     44282159..44282253,44282849..44282932,44283024..44283126,
                     44286719..44286791,44294141..44294206,44298471..44298525,
                     44302604..44302663,44323730..44323824,44364956..44365230))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /product="calcium/calmodulin-dependent protein kinase II
                     beta, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_172079.2"
                     /db_xref="GI:212549583"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     mRNA            complement(join(44256749..44259121,44259659..44259893,
                     44260215..44260309,44260425..44260500,44270605..44270653,
                     44272421..44272465,44273989..44274060,44274238..44274275,
                     44280306..44280348,44281299..44281382,44281817..44281939,
                     44282159..44282253,44282849..44282932,44283024..44283126,
                     44286719..44286791,44294141..44294206,44298471..44298525,
                     44302604..44302663,44323730..44323824,44364956..44365230))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /product="calcium/calmodulin-dependent protein kinase II
                     beta, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_172080.2"
                     /db_xref="GI:212549590"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     mRNA            complement(join(44256749..44259121,44259659..44259893,
                     44260215..44260309,44260425..44260500,44270605..44270653,
                     44273989..44274060,44274238..44274278,44280306..44280348,
                     44281299..44281382,44281817..44281939,44282159..44282253,
                     44282849..44282932,44283024..44283126,44286719..44286791,
                     44294141..44294206,44298471..44298525,44302604..44302663,
                     44323730..44323824,44364956..44365230))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /product="calcium/calmodulin-dependent protein kinase II
                     beta, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_172081.2"
                     /db_xref="GI:212549585"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     mRNA            complement(join(44256749..44259121,44259659..44259893,
                     44260215..44260231,44260425..44260500,44270605..44270653,
                     44272421..44272465,44274238..44274275,44279188..44279262,
                     44280306..44280348,44281299..44281382,44281817..44281939,
                     44282159..44282253,44282849..44282932,44283024..44283126,
                     44286719..44286791,44294141..44294206,44298471..44298525,
                     44302604..44302663,44323730..44323824,44364956..44365230))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /product="calcium/calmodulin-dependent protein kinase II
                     beta, transcript variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_172082.2"
                     /db_xref="GI:212549589"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     mRNA            complement(join(44256749..44259121,44259659..44259893,
                     44260215..44260309,44260425..44260500,44270605..44270653,
                     44274238..44274278,44280306..44280348,44281299..44281382,
                     44281817..44281939,44282159..44282253,44282849..44282932,
                     44283024..44283126,44286719..44286791,44294141..44294206,
                     44298471..44298525,44302604..44302663,44323730..44323824,
                     44364956..44365230))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /product="calcium/calmodulin-dependent protein kinase II
                     beta, transcript variant 7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_172083.2"
                     /db_xref="GI:212549587"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     mRNA            complement(join(44256749..44259121,44259659..44259893,
                     44260215..44260309,44260425..44260500,44280306..44280348,
                     44281299..44281382,44281817..44281939,44282159..44282253,
                     44282849..44282932,44283024..44283126,44286719..44286791,
                     44294141..44294206,44298471..44298525,44302604..44302663,
                     44323730..44323824,44364956..44365230))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /product="calcium/calmodulin-dependent protein kinase II
                     beta, transcript variant 8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_172084.2"
                     /db_xref="GI:212549586"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     CDS             complement(join(44259661..44259893,44260215..44260309,
                     44260425..44260500,44266115..44266243,44268395..44268523,
                     44268987..44269100,44270605..44270653,44272421..44272465,
                     44273989..44274060,44274238..44274275,44279188..44279262,
                     44280306..44280348,44281299..44281382,44281817..44281939,
                     44282159..44282253,44282849..44282932,44283024..44283126,
                     44286719..44286791,44294141..44294206,44298471..44298525,
                     44302604..44302663,44323730..44323824,44364956..44365020))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium/calmodulin-dependent protein kinase type
                     II subunit beta isoform 1"
                     /protein_id="NP_001211.3"
                     /db_xref="GI:26051204"
                     /db_xref="CCDS:CCDS5483.1"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     CDS             complement(join(44259661..44259893,44260215..44260309,
                     44260425..44260500,44270605..44270653,44272421..44272465,
                     44273989..44274060,44274238..44274275,44279188..44279262,
                     44280306..44280348,44281299..44281382,44281817..44281939,
                     44282159..44282253,44282849..44282932,44283024..44283126,
                     44286719..44286791,44294141..44294206,44298471..44298525,
                     44302604..44302663,44323730..44323824,44364956..44365020))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium/calmodulin-dependent protein kinase type
                     II subunit beta isoform 2"
                     /protein_id="NP_742075.1"
                     /db_xref="GI:26051206"
                     /db_xref="CCDS:CCDS5484.1"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     CDS             complement(join(44259661..44259893,44260215..44260309,
                     44260425..44260500,44270605..44270653,44272421..44272465,
                     44273989..44274060,44274238..44274278,44280306..44280348,
                     44281299..44281382,44281817..44281939,44282159..44282253,
                     44282849..44282932,44283024..44283126,44286719..44286791,
                     44294141..44294206,44298471..44298525,44302604..44302663,
                     44323730..44323824,44364956..44365020))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium/calmodulin-dependent protein kinase type
                     II subunit beta isoform 3"
                     /protein_id="NP_742076.1"
                     /db_xref="GI:26051208"
                     /db_xref="CCDS:CCDS5485.1"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     CDS             complement(join(44259661..44259893,44260215..44260309,
                     44260425..44260500,44270605..44270653,44272421..44272465,
                     44273989..44274060,44274238..44274275,44280306..44280348,
                     44281299..44281382,44281817..44281939,44282159..44282253,
                     44282849..44282932,44283024..44283126,44286719..44286791,
                     44294141..44294206,44298471..44298525,44302604..44302663,
                     44323730..44323824,44364956..44365020))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium/calmodulin-dependent protein kinase type
                     II subunit beta isoform 4"
                     /protein_id="NP_742077.1"
                     /db_xref="GI:26051210"
                     /db_xref="CCDS:CCDS43573.1"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     CDS             complement(join(44259661..44259893,44260215..44260309,
                     44260425..44260500,44270605..44270653,44273989..44274060,
                     44274238..44274278,44280306..44280348,44281299..44281382,
                     44281817..44281939,44282159..44282253,44282849..44282932,
                     44283024..44283126,44286719..44286791,44294141..44294206,
                     44298471..44298525,44302604..44302663,44323730..44323824,
                     44364956..44365020))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /note="isoform 5 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium/calmodulin-dependent protein kinase type
                     II subunit beta isoform 5"
                     /protein_id="NP_742078.1"
                     /db_xref="GI:26051212"
                     /db_xref="CCDS:CCDS5486.1"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     CDS             complement(join(44259661..44259893,44260215..44260231,
                     44260425..44260500,44270605..44270653,44272421..44272465,
                     44274238..44274275,44279188..44279262,44280306..44280348,
                     44281299..44281382,44281817..44281939,44282159..44282253,
                     44282849..44282932,44283024..44283126,44286719..44286791,
                     44294141..44294206,44298471..44298525,44302604..44302663,
                     44323730..44323824,44364956..44365020))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /note="isoform 6 is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium/calmodulin-dependent protein kinase type
                     II subunit beta isoform 6"
                     /protein_id="NP_742079.1"
                     /db_xref="GI:26051214"
                     /db_xref="CCDS:CCDS5487.1"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     CDS             complement(join(44259661..44259893,44260215..44260309,
                     44260425..44260500,44270605..44270653,44274238..44274278,
                     44280306..44280348,44281299..44281382,44281817..44281939,
                     44282159..44282253,44282849..44282932,44283024..44283126,
                     44286719..44286791,44294141..44294206,44298471..44298525,
                     44302604..44302663,44323730..44323824,44364956..44365020))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /note="isoform 7 is encoded by transcript variant 7;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium/calmodulin-dependent protein kinase type
                     II subunit beta isoform 7"
                     /protein_id="NP_742080.1"
                     /db_xref="GI:26051216"
                     /db_xref="CCDS:CCDS5488.1"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     CDS             complement(join(44259661..44259893,44260215..44260309,
                     44260425..44260500,44280306..44280348,44281299..44281382,
                     44281817..44281939,44282159..44282253,44282849..44282932,
                     44283024..44283126,44286719..44286791,44294141..44294206,
                     44298471..44298525,44302604..44302663,44323730..44323824,
                     44364956..44365020))
                     /gene="CAMK2B"
                     /gene_synonym="CAM2; CAMK2; CAMKB; MGC29528"
                     /note="isoform 8 is encoded by transcript variant 8;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium/calmodulin-dependent protein kinase type
                     II subunit beta isoform 8"
                     /protein_id="NP_742081.1"
                     /db_xref="GI:26051218"
                     /db_xref="CCDS:CCDS5489.1"
                     /db_xref="GeneID:816"
                     /db_xref="HGNC:1461"
                     /db_xref="HPRD:12127"
                     /db_xref="MIM:607707"
     gene            complement(44421965..44530385)
                     /gene="NUDCD3"
                     /gene_synonym="KIAA1068; NudCL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23386"
                     /db_xref="HGNC:22208"
                     /db_xref="HPRD:13831"
                     /db_xref="MIM:610296"
     mRNA            complement(join(44421965..44425720,44431896..44432084,
                     44444039..44444182,44467170..44467302,44524567..44524883,
                     44530008..44530385))
                     /gene="NUDCD3"
                     /gene_synonym="KIAA1068; NudCL"
                     /product="NudC domain containing 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015332.3"
                     /db_xref="GI:122939164"
                     /db_xref="GeneID:23386"
                     /db_xref="HGNC:22208"
                     /db_xref="HPRD:13831"
                     /db_xref="MIM:610296"
     CDS             complement(join(44425610..44425720,44431896..44432084,
                     44444039..44444182,44467170..44467302,44524567..44524883,
                     44530008..44530199))
                     /gene="NUDCD3"
                     /gene_synonym="KIAA1068; NudCL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="nudC domain-containing protein 3"
                     /protein_id="NP_056147.2"
                     /db_xref="GI:122939165"
                     /db_xref="CCDS:CCDS5490.2"
                     /db_xref="GeneID:23386"
                     /db_xref="HGNC:22208"
                     /db_xref="HPRD:13831"
                     /db_xref="MIM:610296"
     gene            44507442..44508580
                     /gene="RPL32P18"
                     /gene_synonym="RPL32_8_807"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:644907"
                     /db_xref="HGNC:36301"
     gene            complement(44550571..44550952)
                     /gene="RPL36AP27"
                     /gene_synonym="RPL36A_9_808"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100128072"
                     /db_xref="HGNC:35650"
     gene            complement(44552134..44580914)
                     /gene="NPC1L1"
                     /gene_synonym="NPC11L1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:29881"
                     /db_xref="HGNC:7898"
                     /db_xref="HPRD:09725"
                     /db_xref="MIM:608010"
     mRNA            complement(join(44552134..44553248,44555402..44555564,
                     44555683..44555796,44556302..44556533,44556806..44556956,
                     44558185..44558265,44560364..44560419,44560591..44560717,
                     44561311..44561435,44561651..44561841,44571354..44571443,
                     44571679..44571816,44573030..44573157,44573338..44573452,
                     44574046..44574228,44575439..44575567,44575855..44576027,
                     44576441..44576541,44578416..44579941,44580805..44580914))
                     /gene="NPC1L1"
                     /gene_synonym="NPC11L1"
                     /product="NPC1 (Niemann-Pick disease, type C1, gene)-like
                     1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013389.2"
                     /db_xref="GI:156231350"
                     /db_xref="GeneID:29881"
                     /db_xref="HGNC:7898"
                     /db_xref="HPRD:09725"
                     /db_xref="MIM:608010"
     mRNA            complement(join(44552134..44553248,44555402..44555564,
                     44555683..44555796,44556302..44556533,44556806..44556956,
                     44560364..44560419,44560591..44560717,44561311..44561435,
                     44561651..44561841,44571354..44571443,44571679..44571816,
                     44573030..44573157,44573338..44573452,44574046..44574228,
                     44575439..44575567,44575855..44576027,44576441..44576541,
                     44578416..44579941,44580805..44580914))
                     /gene="NPC1L1"
                     /gene_synonym="NPC11L1"
                     /product="NPC1 (Niemann-Pick disease, type C1, gene)-like
                     1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001101648.1"
                     /db_xref="GI:156231352"
                     /db_xref="GeneID:29881"
                     /db_xref="HGNC:7898"
                     /db_xref="MIM:608010"
                     /db_xref="HPRD:09725"
     CDS             complement(join(44553046..44553248,44555402..44555564,
                     44555683..44555796,44556302..44556533,44556806..44556956,
                     44558185..44558265,44560364..44560419,44560591..44560717,
                     44561311..44561435,44561651..44561841,44571354..44571443,
                     44571679..44571816,44573030..44573157,44573338..44573452,
                     44574046..44574228,44575439..44575567,44575855..44576027,
                     44576441..44576541,44578416..44579941,44580805..44580858))
                     /gene="NPC1L1"
                     /gene_synonym="NPC11L1"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="Niemann-Pick C1-like protein 1 isoform 1
                     precursor"
                     /protein_id="NP_037521.2"
                     /db_xref="GI:156231351"
                     /db_xref="CCDS:CCDS5491.1"
                     /db_xref="GeneID:29881"
                     /db_xref="HGNC:7898"
                     /db_xref="HPRD:09725"
                     /db_xref="MIM:608010"
     CDS             complement(join(44553046..44553248,44555402..44555564,
                     44555683..44555796,44556302..44556533,44556806..44556956,
                     44560364..44560419,44560591..44560717,44561311..44561435,
                     44561651..44561841,44571354..44571443,44571679..44571816,
                     44573030..44573157,44573338..44573452,44574046..44574228,
                     44575439..44575567,44575855..44576027,44576441..44576541,
                     44578416..44579941,44580805..44580858))
                     /gene="NPC1L1"
                     /gene_synonym="NPC11L1"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="Niemann-Pick C1-like protein 1 isoform 2
                     precursor"
                     /protein_id="NP_001095118.1"
                     /db_xref="GI:156231353"
                     /db_xref="CCDS:CCDS43575.1"
                     /db_xref="GeneID:29881"
                     /db_xref="HGNC:7898"
                     /db_xref="HPRD:09725"
                     /db_xref="MIM:608010"
     gene            complement(44605403..44614137)
                     /gene="DDX56"
                     /gene_synonym="DDX21; DDX26; NOH61"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54606"
                     /db_xref="HGNC:18193"
                     /db_xref="HPRD:12154"
                     /db_xref="MIM:608023"
     mRNA            complement(join(44605403..44605678,44606047..44606123,
                     44607717..44607822,44608502..44608591,44608729..44608802,
                     44609408..44609502,44609614..44609727,44610357..44610476,
                     44611091..44611335,44611946..44612036,44612173..44612343,
                     44612489..44612649,44613182..44613343,44613435..44614137))
                     /gene="DDX56"
                     /gene_synonym="DDX21; DDX26; NOH61"
                     /product="DEAD (Asp-Glu-Ala-Asp) box polypeptide 56"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_019082.2"
                     /db_xref="GI:51094102"
                     /db_xref="GeneID:54606"
                     /db_xref="HGNC:18193"
                     /db_xref="HPRD:12154"
                     /db_xref="MIM:608023"
     CDS             complement(join(44605601..44605678,44606047..44606123,
                     44607717..44607822,44608502..44608591,44608729..44608802,
                     44609408..44609502,44609614..44609727,44610357..44610476,
                     44611091..44611335,44611946..44612036,44612173..44612343,
                     44612489..44612649,44613182..44613343,44613435..44613494))
                     /gene="DDX56"
                     /gene_synonym="DDX21; DDX26; NOH61"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable ATP-dependent RNA helicase DDX56"
                     /protein_id="NP_061955.1"
                     /db_xref="GI:9506931"
                     /db_xref="CCDS:CCDS5492.1"
                     /db_xref="GeneID:54606"
                     /db_xref="HGNC:18193"
                     /db_xref="HPRD:12154"
                     /db_xref="MIM:608023"
     gene            complement(44618762..44621827)
                     /gene="TMED4"
                     /gene_synonym="ERS25; HNLF"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222068"
                     /db_xref="HGNC:22301"
                     /db_xref="HPRD:13666"
                     /db_xref="MIM:612038"
     mRNA            complement(join(44618762..44619227,44620692..44620838,
                     44621048..44621173,44621322..44621422,44621646..44621827))
                     /gene="TMED4"
                     /gene_synonym="ERS25; HNLF"
                     /product="transmembrane emp24 protein transport domain
                     containing 4"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182547.2"
                     /db_xref="GI:33457307"
                     /db_xref="GeneID:222068"
                     /db_xref="HGNC:22301"
                     /db_xref="HPRD:13666"
                     /db_xref="MIM:612038"
     CDS             complement(join(44619078..44619227,44620692..44620838,
                     44621048..44621173,44621322..44621422,44621646..44621805))
                     /gene="TMED4"
                     /gene_synonym="ERS25; HNLF"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane emp24 domain-containing protein 4
                     precursor"
                     /protein_id="NP_872353.2"
                     /db_xref="GI:33457308"
                     /db_xref="CCDS:CCDS5493.1"
                     /db_xref="GeneID:222068"
                     /db_xref="HGNC:22301"
                     /db_xref="HPRD:13666"
                     /db_xref="MIM:612038"
     gene            44646121..44748669
                     /gene="OGDH"
                     /gene_synonym="AKGDH; E1k; OGDC"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4967"
                     /db_xref="HGNC:8124"
                     /db_xref="HPRD:08938"
                     /db_xref="MIM:613022"
     mRNA            join(44646121..44646252,44663916..44664164,
                     44684926..44685117,44687256..44687358,44706335..44706450,
                     44713386..44713540,44714010..44714156,44714777..44714867,
                     44715569..44715748,44721319..44721447,44733424..44733603,
                     44734023..44734175,44735624..44735726,44736028..44736156,
                     44736513..44736663,44736969..44737096,44737203..44737381,
                     44737791..44737862,44739740..44739868,44741142..44741214,
                     44746824..44746987,44747181..44747335,44747478..44748669)
                     /gene="OGDH"
                     /gene_synonym="AKGDH; E1k; OGDC"
                     /product="oxoglutarate (alpha-ketoglutarate) dehydrogenase
                     (lipoamide), transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002541.3"
                     /db_xref="GI:259013550"
                     /db_xref="GeneID:4967"
                     /db_xref="HGNC:8124"
                     /db_xref="HPRD:08938"
                     /db_xref="MIM:613022"
     mRNA            join(44646121..44646252,44663916..44664164,
                     44684926..44685117,44687043..44687133,44706335..44706450,
                     44713386..44713540,44714010..44714156,44714777..44714867,
                     44715569..44715748,44721319..44721447,44733424..44733603,
                     44734023..44734175,44735624..44735726,44736028..44736156,
                     44736513..44736663,44736969..44737096,44737203..44737381,
                     44737791..44737862,44739740..44739868,44741142..44741214,
                     44746824..44746987,44747181..44747335,44747478..44748669)
                     /gene="OGDH"
                     /gene_synonym="AKGDH; E1k; OGDC"
                     /product="oxoglutarate (alpha-ketoglutarate) dehydrogenase
                     (lipoamide), transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001165036.1"
                     /db_xref="GI:259013552"
                     /db_xref="GeneID:4967"
                     /db_xref="HGNC:8124"
                     /db_xref="MIM:613022"
                     /db_xref="HPRD:08938"
     mRNA            join(44646121..44646252,44663916..44664164,
                     44684926..44685117,44687256..44687358,44706335..44706450,
                     44713386..44713540,44714010..44714156,44714777..44714867,
                     44715569..44716195)
                     /gene="OGDH"
                     /gene_synonym="AKGDH; E1k; OGDC"
                     /product="oxoglutarate (alpha-ketoglutarate) dehydrogenase
                     (lipoamide), transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001003941.2"
                     /db_xref="GI:259013551"
                     /db_xref="GeneID:4967"
                     /db_xref="HGNC:8124"
                     /db_xref="MIM:613022"
                     /db_xref="HPRD:08938"
     CDS             join(44663943..44664164,44684926..44685117,
                     44687256..44687358,44706335..44706450,44713386..44713540,
                     44714010..44714156,44714777..44714867,44715569..44715748,
                     44721319..44721447,44733424..44733603,44734023..44734175,
                     44735624..44735726,44736028..44736156,44736513..44736663,
                     44736969..44737096,44737203..44737381,44737791..44737862,
                     44739740..44739868,44741142..44741214,44746824..44746987,
                     44747181..44747335,44747478..44747598)
                     /gene="OGDH"
                     /gene_synonym="AKGDH; E1k; OGDC"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="2-oxoglutarate dehydrogenase, mitochondrial
                     isoform 1 precursor"
                     /protein_id="NP_002532.2"
                     /db_xref="GI:51873036"
                     /db_xref="CCDS:CCDS34627.1"
                     /db_xref="GeneID:4967"
                     /db_xref="HGNC:8124"
                     /db_xref="HPRD:08938"
                     /db_xref="MIM:613022"
     CDS             join(44663943..44664164,44684926..44685117,
                     44687043..44687133,44706335..44706450,44713386..44713540,
                     44714010..44714156,44714777..44714867,44715569..44715748,
                     44721319..44721447,44733424..44733603,44734023..44734175,
                     44735624..44735726,44736028..44736156,44736513..44736663,
                     44736969..44737096,44737203..44737381,44737791..44737862,
                     44739740..44739868,44741142..44741214,44746824..44746987,
                     44747181..44747335,44747478..44747598)
                     /gene="OGDH"
                     /gene_synonym="AKGDH; E1k; OGDC"
                     /note="isoform 3 precursor is encoded by transcript
                     variant 3; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="2-oxoglutarate dehydrogenase, mitochondrial
                     isoform 3 precursor"
                     /protein_id="NP_001158508.1"
                     /db_xref="GI:259013553"
                     /db_xref="CCDS:CCDS55107.1"
                     /db_xref="GeneID:4967"
                     /db_xref="HGNC:8124"
                     /db_xref="HPRD:08938"
                     /db_xref="MIM:613022"
     CDS             join(44663943..44664164,44684926..44685117,
                     44687256..44687358,44706335..44706450,44713386..44713540,
                     44714010..44714156,44714777..44714867,44715569..44715826)
                     /gene="OGDH"
                     /gene_synonym="AKGDH; E1k; OGDC"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="2-oxoglutarate dehydrogenase, mitochondrial
                     isoform 2 precursor"
                     /protein_id="NP_001003941.1"
                     /db_xref="GI:51873038"
                     /db_xref="CCDS:CCDS47580.1"
                     /db_xref="GeneID:4967"
                     /db_xref="HGNC:8124"
                     /db_xref="HPRD:08938"
                     /db_xref="MIM:613022"
     gene            44788530..44809480
                     /gene="ZMIZ2"
                     /gene_synonym="DKFZp761I2123; hZIMP7; KIAA1886; NET27;
                     TRAFIP20; ZIMP7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:83637"
                     /db_xref="HGNC:22229"
                     /db_xref="HPRD:13225"
                     /db_xref="MIM:611196"
     mRNA            join(44788530..44788590,44795787..44795898,
                     44796024..44796138,44796546..44796748,44796977..44797160,
                     44797447..44797707,44798880..44799059,44799750..44799827,
                     44800024..44800192,44801048..44801192,44801294..44801504,
                     44802480..44802585,44802855..44803012,44804018..44804085,
                     44804540..44804608,44804934..44805178,44805763..44805932,
                     44806020..44806262,44807115..44809480)
                     /gene="ZMIZ2"
                     /gene_synonym="DKFZp761I2123; hZIMP7; KIAA1886; NET27;
                     TRAFIP20; ZIMP7"
                     /product="zinc finger, MIZ-type containing 2, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_031449.3"
                     /db_xref="GI:54607107"
                     /db_xref="GeneID:83637"
                     /db_xref="HGNC:22229"
                     /db_xref="HPRD:13225"
                     /db_xref="MIM:611196"
     mRNA            join(44795787..44795898,44796024..44796138,
                     44796546..44796748,44796977..44797160,44797447..44797707,
                     44798880..44799059,44800024..44800192,44801048..44801192,
                     44801294..44801504,44802480..44802585,44802855..44803012,
                     44804018..44804085,44804540..44804608,44804934..44805178,
                     44805763..44805932,44806020..44806262,44807115..44809480)
                     /gene="ZMIZ2"
                     /gene_synonym="DKFZp761I2123; hZIMP7; KIAA1886; NET27;
                     TRAFIP20; ZIMP7"
                     /product="zinc finger, MIZ-type containing 2, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_174929.2"
                     /db_xref="GI:54607109"
                     /db_xref="GeneID:83637"
                     /db_xref="HGNC:22229"
                     /db_xref="MIM:611196"
                     /db_xref="HPRD:13225"
     CDS             join(44795849..44795898,44796024..44796138,
                     44796546..44796748,44796977..44797160,44797447..44797707,
                     44798880..44799059,44799750..44799827,44800024..44800192,
                     44801048..44801192,44801294..44801504,44802480..44802585,
                     44802855..44803012,44804018..44804085,44804540..44804608,
                     44804934..44805178,44805763..44805932,44806020..44806262,
                     44807115..44807222)
                     /gene="ZMIZ2"
                     /gene_synonym="DKFZp761I2123; hZIMP7; KIAA1886; NET27;
                     TRAFIP20; ZIMP7"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger MIZ domain-containing protein 2
                     isoform 1"
                     /protein_id="NP_113637.3"
                     /db_xref="GI:54607108"
                     /db_xref="CCDS:CCDS43576.1"
                     /db_xref="GeneID:83637"
                     /db_xref="HGNC:22229"
                     /db_xref="HPRD:13225"
                     /db_xref="MIM:611196"
     CDS             join(44795849..44795898,44796024..44796138,
                     44796546..44796748,44796977..44797160,44797447..44797707,
                     44798880..44799059,44800024..44800192,44801048..44801192,
                     44801294..44801504,44802480..44802585,44802855..44803012,
                     44804018..44804085,44804540..44804608,44804934..44805178,
                     44805763..44805932,44806020..44806262,44807115..44807222)
                     /gene="ZMIZ2"
                     /gene_synonym="DKFZp761I2123; hZIMP7; KIAA1886; NET27;
                     TRAFIP20; ZIMP7"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger MIZ domain-containing protein 2
                     isoform 2"
                     /protein_id="NP_777589.2"
                     /db_xref="GI:54607110"
                     /db_xref="CCDS:CCDS43577.1"
                     /db_xref="GeneID:83637"
                     /db_xref="HGNC:22229"
                     /db_xref="HPRD:13225"
                     /db_xref="MIM:611196"
     gene            44836241..44842716
                     /gene="PPIA"
                     /gene_synonym="CYPA; CYPH; MGC117158; MGC12404; MGC23397"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5478"
                     /db_xref="HGNC:9253"
                     /db_xref="HPRD:00457"
                     /db_xref="MIM:123840"
     mRNA            join(44836241..44836392,44838846..44838876,
                     44838991..44839079,44839301..44839473,44840886..44842716)
                     /gene="PPIA"
                     /gene_synonym="CYPA; CYPH; MGC117158; MGC12404; MGC23397"
                     /product="peptidylprolyl isomerase A (cyclophilin A)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021130.3"
                     /db_xref="GI:114520617"
                     /db_xref="GeneID:5478"
                     /db_xref="HGNC:9253"
                     /db_xref="HPRD:00457"
                     /db_xref="MIM:123840"
     CDS             join(44836324..44836392,44838846..44838876,
                     44838991..44839079,44839301..44839473,44840886..44841021)
                     /gene="PPIA"
                     /gene_synonym="CYPA; CYPH; MGC117158; MGC12404; MGC23397"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="peptidyl-prolyl cis-trans isomerase A"
                     /protein_id="NP_066953.1"
                     /db_xref="GI:10863927"
                     /db_xref="CCDS:CCDS5494.1"
                     /db_xref="GeneID:5478"
                     /db_xref="HGNC:9253"
                     /db_xref="HPRD:00457"
                     /db_xref="MIM:123840"
     gene            complement(44866488..44887725)
                     /gene="H2AFV"
                     /gene_synonym="FLJ26479; H2AV; MGC10170; MGC10831;
                     MGC1947"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:94239"
                     /db_xref="HGNC:20664"
                     /db_xref="HPRD:13623"
     mRNA            complement(join(44866488..44869762,44875128..44875257,
                     44880498..44880611,44882876..44882953,44887568..44887725))
                     /gene="H2AFV"
                     /gene_synonym="FLJ26479; H2AV; MGC10170; MGC10831;
                     MGC1947"
                     /product="H2A histone family, member V, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138635.3"
                     /db_xref="GI:149999597"
                     /db_xref="GeneID:94239"
                     /db_xref="HGNC:20664"
                     /db_xref="HPRD:13623"
     CDS             complement(join(44869743..44869762,44875128..44875257,
                     44880498..44880611,44882876..44882953,44887568..44887570))
                     /gene="H2AFV"
                     /gene_synonym="FLJ26479; H2AV; MGC10170; MGC10831;
                     MGC1947"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone H2A.V isoform 2"
                     /protein_id="NP_619541.1"
                     /db_xref="GI:20357599"
                     /db_xref="CCDS:CCDS5495.1"
                     /db_xref="GeneID:94239"
                     /db_xref="HGNC:20664"
                     /db_xref="HPRD:13623"
     mRNA            complement(join(44873213..44874161,44875128..44875257,
                     44880498..44880611,44882876..44882953,44887568..44887725))
                     /gene="H2AFV"
                     /gene_synonym="FLJ26479; H2AV; MGC10170; MGC10831;
                     MGC1947"
                     /product="H2A histone family, member V, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012412.4"
                     /db_xref="GI:149999596"
                     /db_xref="GeneID:94239"
                     /db_xref="HGNC:20664"
                     /db_xref="HPRD:13623"
     mRNA            complement(join(44873213..44874161,44875128..44875257,
                     44880498..44880611,44887568..44887725))
                     /gene="H2AFV"
                     /gene_synonym="FLJ26479; H2AV; MGC10170; MGC10831;
                     MGC1947"
                     /product="H2A histone family, member V, transcript variant
                     3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_201436.2"
                     /db_xref="GI:149999599"
                     /db_xref="GeneID:94239"
                     /db_xref="HGNC:20664"
                     /db_xref="HPRD:13623"
     mRNA            complement(join(44873213..44874161,44880498..44880611,
                     44882876..44882953,44887568..44887725))
                     /gene="H2AFV"
                     /gene_synonym="FLJ26479; H2AV; MGC10170; MGC10831;
                     MGC1947"
                     /product="H2A histone family, member V, transcript variant
                     4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_201516.2"
                     /db_xref="GI:149999600"
                     /db_xref="GeneID:94239"
                     /db_xref="HGNC:20664"
                     /db_xref="HPRD:13623"
     mRNA            complement(join(44873213..44874161,44875128..44875257,
                     44882876..44882953,44887568..44887725))
                     /gene="H2AFV"
                     /gene_synonym="FLJ26479; H2AV; MGC10170; MGC10831;
                     MGC1947"
                     /product="H2A histone family, member V, transcript variant
                     5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_201517.2"
                     /db_xref="GI:149999598"
                     /db_xref="GeneID:94239"
                     /db_xref="HGNC:20664"
                     /db_xref="HPRD:13623"
     CDS             complement(join(44874100..44874161,44875128..44875257,
                     44880498..44880611,44882876..44882953,44887568..44887570))
                     /gene="H2AFV"
                     /gene_synonym="FLJ26479; H2AV; MGC10170; MGC10831;
                     MGC1947"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone H2A.V isoform 1"
                     /protein_id="NP_036544.1"
                     /db_xref="GI:6912616"
                     /db_xref="CCDS:CCDS5496.1"
                     /db_xref="GeneID:94239"
                     /db_xref="HGNC:20664"
                     /db_xref="HPRD:13623"
     CDS             complement(join(44874100..44874161,44875128..44875257,
                     44880498..44880611,44887568..44887570))
                     /gene="H2AFV"
                     /gene_synonym="FLJ26479; H2AV; MGC10170; MGC10831;
                     MGC1947"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone H2A.V isoform 3"
                     /protein_id="NP_958844.1"
                     /db_xref="GI:41406067"
                     /db_xref="CCDS:CCDS5497.1"
                     /db_xref="GeneID:94239"
                     /db_xref="HGNC:20664"
                     /db_xref="HPRD:13623"
     CDS             complement(join(44874100..44874161,44875128..44875257,
                     44882876..44882953,44887568..44887570))
                     /gene="H2AFV"
                     /gene_synonym="FLJ26479; H2AV; MGC10170; MGC10831;
                     MGC1947"
                     /note="isoform 5 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone H2A.V isoform 5"
                     /protein_id="NP_958925.1"
                     /db_xref="GI:41406071"
                     /db_xref="CCDS:CCDS5498.1"
                     /db_xref="GeneID:94239"
                     /db_xref="HGNC:20664"
                     /db_xref="HPRD:13623"
     CDS             complement(join(44874156..44874161,44880498..44880611,
                     44882876..44882953,44887568..44887570))
                     /gene="H2AFV"
                     /gene_synonym="FLJ26479; H2AV; MGC10170; MGC10831;
                     MGC1947"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone H2A.V isoform 4"
                     /protein_id="NP_958924.1"
                     /db_xref="GI:41406069"
                     /db_xref="CCDS:CCDS47581.1"
                     /db_xref="GeneID:94239"
                     /db_xref="HGNC:20664"
                     /db_xref="HPRD:13623"
     gene            complement(44915892..44924960)
                     /gene="PURB"
                     /gene_synonym="MGC126784; MGC126786; PURBETA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5814"
                     /db_xref="HGNC:9702"
                     /db_xref="HPRD:12325"
                     /db_xref="MIM:608887"
     mRNA            complement(44915892..44924960)
                     /gene="PURB"
                     /gene_synonym="MGC126784; MGC126786; PURBETA"
                     /product="purine-rich element binding protein B"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033224.3"
                     /db_xref="GI:44680157"
                     /db_xref="GeneID:5814"
                     /db_xref="HGNC:9702"
                     /db_xref="HPRD:12325"
                     /db_xref="MIM:608887"
     gene            complement(44921347..44921399)
                     /gene="MIR4657"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100616393"
                     /db_xref="HGNC:41706"
                     /db_xref="miRBase:MI0017285"
     ncRNA           complement(44921347..44921399)
                     /gene="MIR4657"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4657"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039801.1"
                     /db_xref="GI:337756603"
                     /db_xref="GeneID:100616393"
                     /db_xref="HGNC:41706"
                     /db_xref="miRBase:MI0017285"
     CDS             complement(44924009..44924947)
                     /gene="PURB"
                     /gene_synonym="MGC126784; MGC126786; PURBETA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transcriptional activator protein Pur-beta"
                     /protein_id="NP_150093.1"
                     /db_xref="GI:15147219"
                     /db_xref="CCDS:CCDS5499.1"
                     /db_xref="GeneID:5814"
                     /db_xref="HGNC:9702"
                     /db_xref="HPRD:12325"
                     /db_xref="MIM:608887"
     gene            44959186..44960089
                     /gene="MRPS23P1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:352290"
                     /db_xref="HGNC:29758"
     gene            complement(45002260..45018704)
                     /gene="MYO1G"
                     /gene_synonym="HA2; MGC142104; MHAG"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64005"
                     /db_xref="HGNC:13880"
                     /db_xref="HPRD:17622"
                     /db_xref="MIM:613445"
     mRNA            complement(join(45002260..45002494,45002569..45002723,
                     45003648..45003761,45004014..45004118,45004544..45004688,
                     45005236..45005459,45005672..45005879,45006271..45006437,
                     45007204..45007336,45007483..45007557,45009012..45009082,
                     45009304..45009474,45009639..45009753,45010191..45010336,
                     45010434..45010658,45011272..45011388,45011714..45011824,
                     45014773..45014826,45015083..45015248,45016163..45016256,
                     45016462..45016670,45018466..45018704))
                     /gene="MYO1G"
                     /gene_synonym="HA2; MGC142104; MHAG"
                     /product="myosin IG"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033054.2"
                     /db_xref="GI:239582754"
                     /db_xref="GeneID:64005"
                     /db_xref="HGNC:13880"
                     /db_xref="HPRD:17622"
                     /db_xref="MIM:613445"
     CDS             complement(join(45002338..45002494,45002569..45002723,
                     45003648..45003761,45004014..45004118,45004544..45004688,
                     45005236..45005459,45005672..45005879,45006271..45006437,
                     45007204..45007336,45007483..45007557,45009012..45009082,
                     45009304..45009474,45009639..45009753,45010191..45010336,
                     45010434..45010658,45011272..45011388,45011714..45011824,
                     45014773..45014826,45015083..45015248,45016163..45016256,
                     45016462..45016670,45018466..45018560))
                     /gene="MYO1G"
                     /gene_synonym="HA2; MGC142104; MHAG"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="myosin-Ig"
                     /protein_id="NP_149043.2"
                     /db_xref="GI:239582755"
                     /db_xref="CCDS:CCDS34629.1"
                     /db_xref="GeneID:64005"
                     /db_xref="HGNC:13880"
                     /db_xref="HPRD:17622"
                     /db_xref="MIM:613445"
     gene            complement(45022627..45026259)
                     /gene="C7orf40"
                     /gene_synonym="FLJ38860"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285958"
                     /db_xref="HGNC:27797"
     misc_RNA        complement(join(45022627..45022921,45023421..45023645,
                     45023956..45024025,45025620..45025696,45026124..45026259))
                     /gene="C7orf40"
                     /gene_synonym="FLJ38860"
                     /product="chromosome 7 open reading frame 40"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_003697.1"
                     /db_xref="GI:154937378"
                     /db_xref="GeneID:285958"
                     /db_xref="HGNC:27797"
     gene            complement(45024977..45025109)
                     /gene="SNORA9"
                     /gene_synonym="ACA9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:677798"
                     /db_xref="HGNC:32597"
     ncRNA           complement(45024977..45025109)
                     /gene="SNORA9"
                     /gene_synonym="ACA9"
                     /ncRNA_class="snoRNA"
                     /product="small nucleolar RNA, H/ACA box 9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_002952.1"
                     /db_xref="GI:91680819"
                     /db_xref="GeneID:677798"
                     /db_xref="HGNC:32597"
     gene            45039345..45116069
                     /gene="CCM2"
                     /gene_synonym="C7orf22; MGC4067; MGC4607; MGC74868; OSM;
                     PP10187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:83605"
                     /db_xref="HGNC:21708"
                     /db_xref="HPRD:09719"
                     /db_xref="MIM:607929"
     misc_RNA        join(45039345..45039456,45077852..45078025,
                     45103517..45103600,45104062..45104245,45108042..45108178,
                     45109425..45109560,45112325..45112382,45113059..45113170,
                     45113869..45114007,45115376..45116069)
                     /gene="CCM2"
                     /gene_synonym="C7orf22; MGC4067; MGC4607; MGC74868; OSM;
                     PP10187"
                     /product="cerebral cavernous malformation 2, transcript
                     variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_030770.1"
                     /db_xref="GI:269308191"
                     /db_xref="GeneID:83605"
                     /db_xref="HGNC:21708"
                     /db_xref="MIM:607929"
                     /db_xref="HPRD:09719"
     mRNA            join(45039787..45039962,45077852..45078025,
                     45103517..45103600,45104062..45104245,45108042..45108178,
                     45109425..45109560,45112325..45112382,45113059..45113170,
                     45113869..45114007,45115376..45116069)
                     /gene="CCM2"
                     /gene_synonym="C7orf22; MGC4067; MGC4607; MGC74868; OSM;
                     PP10187"
                     /product="cerebral cavernous malformation 2, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_031443.3"
                     /db_xref="GI:71067339"
                     /db_xref="GeneID:83605"
                     /db_xref="HGNC:21708"
                     /db_xref="HPRD:09719"
                     /db_xref="MIM:607929"
     mRNA            join(45039787..45039962,45103517..45103600,
                     45104062..45104245,45108042..45108178,45109425..45109560,
                     45112325..45112382,45113059..45113170,45113869..45114007,
                     45115376..45116069)
                     /gene="CCM2"
                     /gene_synonym="C7orf22; MGC4067; MGC4607; MGC74868; OSM;
                     PP10187"
                     /product="cerebral cavernous malformation 2, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001167934.1"
                     /db_xref="GI:269308187"
                     /db_xref="GeneID:83605"
                     /db_xref="HGNC:21708"
                     /db_xref="MIM:607929"
                     /db_xref="HPRD:09719"
     mRNA            join(45039787..45039962,45077852..45078025,
                     45103517..45103600,45104062..45104245,45112325..45112382,
                     45113059..45113170,45113869..45114007,45115376..45116069)
                     /gene="CCM2"
                     /gene_synonym="C7orf22; MGC4067; MGC4607; MGC74868; OSM;
                     PP10187"
                     /product="cerebral cavernous malformation 2, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001167935.1"
                     /db_xref="GI:269308189"
                     /db_xref="GeneID:83605"
                     /db_xref="HGNC:21708"
                     /db_xref="MIM:607929"
                     /db_xref="HPRD:09719"
     CDS             join(45039933..45039962,45077852..45078025,
                     45103517..45103600,45104062..45104245,45108042..45108178,
                     45109425..45109560,45112325..45112382,45113059..45113170,
                     45113869..45114007,45115376..45115656)
                     /gene="CCM2"
                     /gene_synonym="C7orf22; MGC4067; MGC4607; MGC74868; OSM;
                     PP10187"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="malcavernin isoform 2"
                     /protein_id="NP_113631.1"
                     /db_xref="GI:13899275"
                     /db_xref="CCDS:CCDS5500.1"
                     /db_xref="GeneID:83605"
                     /db_xref="HGNC:21708"
                     /db_xref="HPRD:09719"
                     /db_xref="MIM:607929"
     CDS             join(45039933..45039962,45103517..45103600,
                     45104062..45104245,45108042..45108178,45109425..45109560,
                     45112325..45112382,45113059..45113170,45113869..45114007,
                     45115376..45115656)
                     /gene="CCM2"
                     /gene_synonym="C7orf22; MGC4067; MGC4607; MGC74868; OSM;
                     PP10187"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="malcavernin isoform 3"
                     /protein_id="NP_001161406.1"
                     /db_xref="GI:269308188"
                     /db_xref="CCDS:CCDS55109.1"
                     /db_xref="GeneID:83605"
                     /db_xref="HGNC:21708"
                     /db_xref="HPRD:09719"
                     /db_xref="MIM:607929"
     CDS             join(45039933..45039962,45077852..45078025,
                     45103517..45103600,45104062..45104245,45112325..45112382,
                     45113059..45113170,45113869..45114007,45115376..45115656)
                     /gene="CCM2"
                     /gene_synonym="C7orf22; MGC4067; MGC4607; MGC74868; OSM;
                     PP10187"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="malcavernin isoform 4"
                     /protein_id="NP_001161407.1"
                     /db_xref="GI:269308190"
                     /db_xref="CCDS:CCDS55108.1"
                     /db_xref="GeneID:83605"
                     /db_xref="HGNC:21708"
                     /db_xref="HPRD:09719"
                     /db_xref="MIM:607929"
     mRNA            join(45067233..45067396,45077852..45078025,
                     45103517..45103600,45104062..45104245,45108042..45108178,
                     45109425..45109560,45112325..45112382,45113059..45113170,
                     45113869..45114007,45115376..45116069)
                     /gene="CCM2"
                     /gene_synonym="C7orf22; MGC4067; MGC4607; MGC74868; OSM;
                     PP10187"
                     /product="cerebral cavernous malformation 2, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001029835.2"
                     /db_xref="GI:269308186"
                     /db_xref="GeneID:83605"
                     /db_xref="HGNC:21708"
                     /db_xref="HPRD:09719"
                     /db_xref="MIM:607929"
     CDS             join(45067304..45067396,45077852..45078025,
                     45103517..45103600,45104062..45104245,45108042..45108178,
                     45109425..45109560,45112325..45112382,45113059..45113170,
                     45113869..45114007,45115376..45115656)
                     /gene="CCM2"
                     /gene_synonym="C7orf22; MGC4067; MGC4607; MGC74868; OSM;
                     PP10187"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="malcavernin isoform 1"
                     /protein_id="NP_001025006.1"
                     /db_xref="GI:71067341"
                     /db_xref="CCDS:CCDS34630.1"
                     /db_xref="GeneID:83605"
                     /db_xref="HGNC:21708"
                     /db_xref="HPRD:09719"
                     /db_xref="MIM:607929"
     gene            complement(45117402..45119610)
                     /gene="LOC100128364"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 4 ESTs, 1 Protein"
                     /db_xref="GeneID:100128364"
     misc_RNA        complement(45117402..45119610)
                     /gene="LOC100128364"
                     /product="hypothetical LOC100128364"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 4 ESTs, 1 Protein"
                     /transcript_id="XR_108776.1"
                     /db_xref="GI:310119963"
                     /db_xref="GeneID:100128364"
     gene            complement(45120036..45128493)
                     /gene="NACAD"
                     /gene_synonym="KIAA0363"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23148"
                     /db_xref="HGNC:22196"
     mRNA            complement(join(45120036..45120122,45120239..45120361,
                     45120475..45120621,45120716..45120862,45121200..45121271,
                     45121354..45121466,45121707..45125711,45128427..45128493))
                     /gene="NACAD"
                     /gene_synonym="KIAA0363"
                     /product="NAC alpha domain containing"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001146334.1"
                     /db_xref="GI:226437578"
                     /db_xref="GeneID:23148"
                     /db_xref="HGNC:22196"
     CDS             complement(join(45120108..45120122,45120239..45120361,
                     45120475..45120621,45120716..45120862,45121200..45121271,
                     45121354..45121466,45121707..45125711,45128427..45128493))
                     /gene="NACAD"
                     /gene_synonym="KIAA0363"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="NAC-alpha domain-containing protein 1"
                     /protein_id="NP_001139806.1"
                     /db_xref="GI:226437579"
                     /db_xref="CCDS:CCDS47582.1"
                     /db_xref="GeneID:23148"
                     /db_xref="HGNC:22196"
     gene            complement(45139699..45151317)
                     /gene="TBRG4"
                     /gene_synonym="CPR2; FASTKD4; KIAA0948"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9238"
                     /db_xref="HGNC:17443"
                     /db_xref="MIM:611325"
     mRNA            complement(join(45139699..45140025,45140857..45140971,
                     45141102..45141213,45141424..45141669,45141946..45142090,
                     45142932..45143042,45143698..45143855,45144137..45144308,
                     45145040..45145363,45148426..45148886,45151242..45151317))
                     /gene="TBRG4"
                     /gene_synonym="CPR2; FASTKD4; KIAA0948"
                     /product="transforming growth factor beta regulator 4,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004749.2"
                     /db_xref="GI:40217811"
                     /db_xref="GeneID:9238"
                     /db_xref="HGNC:17443"
                     /db_xref="HPRD:10263"
                     /db_xref="MIM:611325"
     mRNA            complement(join(45139699..45140025,45140857..45140971,
                     45141102..45141213,45141424..45141669,45141946..45142090,
                     45142932..45143042,45145040..45145363,45148426..45148886,
                     45151242..45151317))
                     /gene="TBRG4"
                     /gene_synonym="CPR2; FASTKD4; KIAA0948"
                     /product="transforming growth factor beta regulator 4,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_030900.2"
                     /db_xref="GI:40217813"
                     /db_xref="GeneID:9238"
                     /db_xref="HGNC:17443"
                     /db_xref="MIM:611325"
     mRNA            complement(join(45139699..45140025,45140857..45140971,
                     45141102..45141213,45141424..45141669,45141946..45142090,
                     45142932..45143042,45145040..45145363,45148426..45148886,
                     45151263..45151317))
                     /gene="TBRG4"
                     /gene_synonym="CPR2; FASTKD4; KIAA0948"
                     /product="transforming growth factor beta regulator 4,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_199122.1"
                     /db_xref="GI:40217809"
                     /db_xref="GeneID:9238"
                     /db_xref="HGNC:17443"
                     /db_xref="MIM:611325"
     CDS             complement(join(45139924..45140025,45140857..45140971,
                     45141102..45141213,45141424..45141669,45141946..45142090,
                     45142932..45143042,45143698..45143855,45144137..45144308,
                     45145040..45145363,45148426..45148836))
                     /gene="TBRG4"
                     /gene_synonym="CPR2; FASTKD4; KIAA0948"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein TBRG4 isoform 1"
                     /protein_id="NP_004740.2"
                     /db_xref="GI:40217812"
                     /db_xref="CCDS:CCDS5501.1"
                     /db_xref="GeneID:9238"
                     /db_xref="HGNC:17443"
                     /db_xref="MIM:611325"
     CDS             complement(join(45139924..45140025,45140857..45140971,
                     45141102..45141213,45141424..45141669,45141946..45142090,
                     45142932..45143042,45145040..45145363,45148426..45148836))
                     /gene="TBRG4"
                     /gene_synonym="CPR2; FASTKD4; KIAA0948"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein TBRG4 isoform 2"
                     /protein_id="NP_112162.1"
                     /db_xref="GI:13569848"
                     /db_xref="CCDS:CCDS5502.1"
                     /db_xref="GeneID:9238"
                     /db_xref="HGNC:17443"
                     /db_xref="MIM:611325"
     CDS             complement(join(45139924..45140025,45140857..45140971,
                     45141102..45141213,45141424..45141669,45141946..45142090,
                     45142932..45143042,45145040..45145363,45148426..45148836))
                     /gene="TBRG4"
                     /gene_synonym="CPR2; FASTKD4; KIAA0948"
                     /note="isoform 2 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein TBRG4 isoform 2"
                     /protein_id="NP_954573.1"
                     /db_xref="GI:40217810"
                     /db_xref="CCDS:CCDS5502.1"
                     /db_xref="GeneID:9238"
                     /db_xref="HGNC:17443"
                     /db_xref="MIM:611325"
     gene            complement(45143948..45144081)
                     /gene="SNORA5A"
                     /gene_synonym="ACA5; ACA5A/B/C"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:654319"
                     /db_xref="HGNC:32588"
     ncRNA           complement(45143948..45144081)
                     /gene="SNORA5A"
                     /gene_synonym="ACA5; ACA5A/B/C"
                     /ncRNA_class="snoRNA"
                     /product="small nucleolar RNA, H/ACA box 5A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_002919.1"
                     /db_xref="GI:86604713"
                     /db_xref="GeneID:654319"
                     /db_xref="HGNC:32588"
     gene            complement(45144505..45144641)
                     /gene="SNORA5C"
                     /gene_synonym="ACA5c"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:677796"
                     /db_xref="HGNC:32590"
                     /db_xref="MIM:611335"
     ncRNA           complement(45144505..45144641)
                     /gene="SNORA5C"
                     /gene_synonym="ACA5c"
                     /ncRNA_class="snoRNA"
                     /product="small nucleolar RNA, H/ACA box 5C"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_002991.1"
                     /db_xref="GI:91754173"
                     /db_xref="GeneID:677796"
                     /db_xref="HGNC:32590"
                     /db_xref="MIM:611335"
     gene            complement(45145567..45145698)
                     /gene="SNORA5B"
                     /gene_synonym="ACA5b"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:677795"
                     /db_xref="HGNC:32589"
     ncRNA           complement(45145567..45145698)
                     /gene="SNORA5B"
                     /gene_synonym="ACA5b"
                     /ncRNA_class="snoRNA"
                     /product="small nucleolar RNA, H/ACA box 5B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_002990.1"
                     /db_xref="GI:91754171"
                     /db_xref="GeneID:677795"
                     /db_xref="HGNC:32589"
     gene            45197367..45223849
                     /gene="RAMP3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10268"
                     /db_xref="HGNC:9845"
                     /db_xref="HPRD:05517"
                     /db_xref="MIM:605155"
     mRNA            join(45197367..45197485,45216908..45217040,
                     45222756..45223849)
                     /gene="RAMP3"
                     /product="receptor (G protein-coupled) activity modifying
                     protein 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005856.2"
                     /db_xref="GI:118572586"
                     /db_xref="GeneID:10268"
                     /db_xref="HGNC:9845"
                     /db_xref="HPRD:05517"
                     /db_xref="MIM:605155"
     CDS             join(45197428..45197485,45216908..45217040,
                     45222756..45223011)
                     /gene="RAMP3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="receptor activity-modifying protein 3 precursor"
                     /protein_id="NP_005847.1"
                     /db_xref="GI:5032023"
                     /db_xref="CCDS:CCDS5503.1"
                     /db_xref="GeneID:10268"
                     /db_xref="HGNC:9845"
                     /db_xref="HPRD:05517"
                     /db_xref="MIM:605155"
     gene            45343219..45343961
                     /gene="LOC100419775"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419775"
     gene            complement(45431072..45431737)
                     /gene="ELK1P1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:647102"
                     /db_xref="HGNC:39021"
     gene            45614125..45762715
                     /gene="ADCY1"
                     /gene_synonym="AC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:107"
                     /db_xref="HGNC:232"
                     /db_xref="HPRD:00053"
                     /db_xref="MIM:103072"
     mRNA            join(45614125..45614781,45632358..45632507,
                     45649978..45650096,45662231..45662342,45688269..45688396,
                     45697326..45697484,45699641..45699782,45701658..45701813,
                     45717468..45717662,45717765..45717862,45719308..45719392,
                     45724578..45724667,45725561..45725814,45726146..45726272,
                     45742975..45743091,45743199..45743345,45744117..45744215,
                     45747949..45748063,45750127..45750251,45753292..45762715)
                     /gene="ADCY1"
                     /gene_synonym="AC1"
                     /product="adenylate cyclase 1 (brain)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021116.2"
                     /db_xref="GI:168480138"
                     /db_xref="GeneID:107"
                     /db_xref="HGNC:232"
                     /db_xref="HPRD:00053"
                     /db_xref="MIM:103072"
     CDS             join(45614143..45614781,45632358..45632507,
                     45649978..45650096,45662231..45662342,45688269..45688396,
                     45697326..45697484,45699641..45699782,45701658..45701813,
                     45717468..45717662,45717765..45717862,45719308..45719392,
                     45724578..45724667,45725561..45725814,45726146..45726272,
                     45742975..45743091,45743199..45743345,45744117..45744215,
                     45747949..45748063,45750127..45750251,45753292..45753594)
                     /gene="ADCY1"
                     /gene_synonym="AC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="adenylate cyclase type 1"
                     /protein_id="NP_066939.1"
                     /db_xref="GI:31083193"
                     /db_xref="CCDS:CCDS34631.1"
                     /db_xref="GeneID:107"
                     /db_xref="HGNC:232"
                     /db_xref="HPRD:00053"
                     /db_xref="MIM:103072"
     gene            complement(45763386..45808617)
                     /gene="SEPT7P2"
                     /gene_synonym="DKFZp313J1114; FLJ14186; FLJ31470; SEPT13;
                     SEPT7B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:641977"
                     /db_xref="HGNC:32339"
                     /db_xref="MIM:611563"
     misc_RNA        complement(join(45763386..45764079,45765783..45765835,
                     45767777..45767912,45768431..45768625,45776386..45776509,
                     45784596..45784647,45786814..45786910,45788225..45788313,
                     45791128..45791245,45796508..45796591,45797642..45797776,
                     45798673..45798773,45808259..45808617))
                     /gene="SEPT7P2"
                     /gene_synonym="DKFZp313J1114; FLJ14186; FLJ31470; SEPT13;
                     SEPT7B"
                     /product="septin 7 pseudogene 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_024271.1"
                     /db_xref="GI:210032242"
                     /db_xref="GeneID:641977"
                     /db_xref="HGNC:32339"
                     /db_xref="MIM:611563"
     gene            45846543..45854988
                     /gene="LOC730234"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:730234"
     gene            complement(45855000..45858615)
                     /gene="LOC100129050"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129050"
     gene            45927959..45933267
                     /gene="IGFBP1"
                     /gene_synonym="AFBP; hIGFBP-1; IBP1; IGF-BP25; PP12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3484"
                     /db_xref="HGNC:5469"
                     /db_xref="HPRD:00897"
                     /db_xref="MIM:146730"
     mRNA            join(45927959..45928600,45930147..45930316,
                     45931531..45931659,45932559..45933267)
                     /gene="IGFBP1"
                     /gene_synonym="AFBP; hIGFBP-1; IBP1; IGF-BP25; PP12"
                     /product="insulin-like growth factor binding protein 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000596.2"
                     /db_xref="GI:61744447"
                     /db_xref="GeneID:3484"
                     /db_xref="HGNC:5469"
                     /db_xref="HPRD:00897"
                     /db_xref="MIM:146730"
     CDS             join(45928252..45928600,45930147..45930316,
                     45931531..45931659,45932559..45932690)
                     /gene="IGFBP1"
                     /gene_synonym="AFBP; hIGFBP-1; IBP1; IGF-BP25; PP12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="insulin-like growth factor-binding protein 1
                     precursor"
                     /protein_id="NP_000587.1"
                     /db_xref="GI:4504615"
                     /db_xref="CCDS:CCDS5504.1"
                     /db_xref="GeneID:3484"
                     /db_xref="HGNC:5469"
                     /db_xref="HPRD:00897"
                     /db_xref="MIM:146730"
     gene            complement(45951844..45960871)
                     /gene="IGFBP3"
                     /gene_synonym="BP-53; IBP3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3486"
                     /db_xref="HGNC:5472"
                     /db_xref="HPRD:00899"
                     /db_xref="MIM:146732"
     mRNA            complement(join(45951844..45953433,45954404..45954544,
                     45956147..45956266,45956812..45957038,45960319..45960871))
                     /gene="IGFBP3"
                     /gene_synonym="BP-53; IBP3"
                     /product="insulin-like growth factor binding protein 3,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001013398.1"
                     /db_xref="GI:62243247"
                     /db_xref="GeneID:3486"
                     /db_xref="HGNC:5472"
                     /db_xref="HPRD:00899"
                     /db_xref="MIM:146732"
     mRNA            complement(join(45951844..45953433,45954404..45954544,
                     45956147..45956266,45956812..45957038,45960337..45960871))
                     /gene="IGFBP3"
                     /gene_synonym="BP-53; IBP3"
                     /product="insulin-like growth factor binding protein 3,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000598.4"
                     /db_xref="GI:62243067"
                     /db_xref="GeneID:3486"
                     /db_xref="HGNC:5472"
                     /db_xref="HPRD:00899"
                     /db_xref="MIM:146732"
     CDS             complement(join(45954419..45954544,45956147..45956266,
                     45956812..45957038,45960319..45960739))
                     /gene="IGFBP3"
                     /gene_synonym="BP-53; IBP3"
                     /note="isoform a precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="insulin-like growth factor-binding protein 3
                     isoform a precursor"
                     /protein_id="NP_001013416.1"
                     /db_xref="GI:62243248"
                     /db_xref="CCDS:CCDS34632.1"
                     /db_xref="GeneID:3486"
                     /db_xref="HGNC:5472"
                     /db_xref="HPRD:00899"
                     /db_xref="MIM:146732"
     CDS             complement(join(45954419..45954544,45956147..45956266,
                     45956812..45957038,45960337..45960739))
                     /gene="IGFBP3"
                     /gene_synonym="BP-53; IBP3"
                     /note="isoform b precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="insulin-like growth factor-binding protein 3
                     isoform b precursor"
                     /protein_id="NP_000589.2"
                     /db_xref="GI:62243068"
                     /db_xref="CCDS:CCDS5505.1"
                     /db_xref="GeneID:3486"
                     /db_xref="HGNC:5472"
                     /db_xref="HPRD:00899"
                     /db_xref="MIM:146732"
     gene            complement(46037142..46037670)
                     /gene="FTLP15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442304"
                     /db_xref="HGNC:37965"
     gene            complement(46039312..46040377)
                     /gene="TTC4P1"
                     /gene_synonym="TTC4P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:222052"
                     /db_xref="HGNC:12395"
     gene            46184172..46185366
                     /gene="LOC100419776"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419776"
     gene            46821488..46823118
                     /gene="EPS15P1"
                     /gene_synonym="EPS15L2; PRO1866"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:55380"
                     /db_xref="HGNC:18166"
     gene            complement(47065720..47066070)
                     /gene="MRPL42P4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:346470"
                     /db_xref="HGNC:29713"
     gene            47092057..47094618
                     /gene="LOC647145"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:647145"
     gene            complement(47314752..47621742)
                     /gene="TNS3"
                     /gene_synonym="DKFZp686K12123; DKFZp686M1045; FLJ13732;
                     FLJ35545; MGC88434; TEM6; TENS1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64759"
                     /db_xref="HGNC:21616"
                     /db_xref="MIM:606825"
     mRNA            complement(join(47314752..47317818,47319762..47319788,
                     47319884..47319952,47323295..47323463,47331553..47331630,
                     47332426..47332503,47333331..47333426,47336680..47336811,
                     47341784..47341870,47342548..47343182,47344430..47344601,
                     47384353..47384436,47384522..47384636,47385785..47385954,
                     47407962..47409218,47436397..47436501,47439990..47440055,
                     47440382..47440511,47451325..47451400,47453535..47453595,
                     47454692..47454804,47463699..47463782,47467910..47467974,
                     47474880..47475002,47476861..47476911,47479085..47479256,
                     47481601..47481653,47520701..47520739,47546505..47546542,
                     47568634..47568745,47621649..47621742))
                     /gene="TNS3"
                     /gene_synonym="DKFZp686K12123; DKFZp686M1045; FLJ13732;
                     FLJ35545; MGC88434; TEM6; TENS1"
                     /product="tensin 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022748.11"
                     /db_xref="GI:315013560"
                     /db_xref="GeneID:64759"
                     /db_xref="HGNC:21616"
                     /db_xref="MIM:606825"
     CDS             complement(join(47317674..47317818,47319762..47319788,
                     47319884..47319952,47323295..47323463,47331553..47331630,
                     47332426..47332503,47333331..47333426,47336680..47336811,
                     47341784..47341870,47342548..47343182,47344430..47344601,
                     47384353..47384436,47384522..47384636,47385785..47385954,
                     47407962..47409218,47436397..47436501,47439990..47440055,
                     47440382..47440511,47451325..47451400,47453535..47453595,
                     47454692..47454804,47463699..47463782,47467910..47467974,
                     47474880..47475002,47476861..47476911,47479085..47479234))
                     /gene="TNS3"
                     /gene_synonym="DKFZp686K12123; DKFZp686M1045; FLJ13732;
                     FLJ35545; MGC88434; TEM6; TENS1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="tensin-3"
                     /protein_id="NP_073585.8"
                     /db_xref="GI:65288071"
                     /db_xref="CCDS:CCDS5506.2"
                     /db_xref="GeneID:64759"
                     /db_xref="HGNC:21616"
                     /db_xref="MIM:606825"
     gene            47694842..47701246
                     /gene="C7orf65"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:401335"
                     /db_xref="HGNC:34432"
     mRNA            join(47694842..47694946,47698291..47698354,
                     47698505..47701246)
                     /gene="C7orf65"
                     /product="chromosome 7 open reading frame 65"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001123065.1"
                     /db_xref="GI:178057326"
                     /db_xref="GeneID:401335"
                     /db_xref="HGNC:34432"
     CDS             join(47694877..47694946,47698291..47698354,
                     47698505..47698826)
                     /gene="C7orf65"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC401335"
                     /protein_id="NP_001116537.1"
                     /db_xref="GI:178057327"
                     /db_xref="CCDS:CCDS43580.1"
                     /db_xref="GeneID:401335"
                     /db_xref="HGNC:34432"
     gene            47801074..47806370
                     /gene="MGC16075"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84847"
     misc_RNA        join(47801074..47801111,47802971..47803176,
                     47805427..47806370)
                     /gene="MGC16075"
                     /product="hypothetical LOC84847"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038407.1"
                     /db_xref="GI:336088633"
                     /db_xref="GeneID:84847"
     gene            complement(47814250..47988071)
                     /gene="PKD1L1"
                     /gene_synonym="PRO19563"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:168507"
                     /db_xref="HGNC:18053"
                     /db_xref="HPRD:10154"
                     /db_xref="MIM:609721"
     mRNA            complement(join(47814250..47814764,47832225..47832395,
                     47835587..47835748,47840247..47840477,47842808..47842942,
                     47847845..47847985,47849071..47849175,47851415..47851649,
                     47852719..47852891,47853529..47853612,47854932..47855055,
                     47860674..47860784,47866948..47867066,47869023..47869199,
                     47869638..47869722,47870815..47870950,47872688..47872850,
                     47873937..47873983,47874565..47874637,47874731..47874841,
                     47876519..47876692,47879044..47879260,47880059..47880165,
                     47882560..47882767,47884593..47884676,47886477..47886669,
                     47892725..47892825,47894480..47894637,47894753..47894863,
                     47897203..47897430,47898271..47898483,47904814..47904870,
                     47906017..47906212,47913497..47913608,47915695..47915815,
                     47917087..47917229,47920326..47920403,47921507..47921683,
                     47924196..47924255,47925284..47925652,47927588..47927748,
                     47930140..47930361,47933475..47933656,47937585..47937791,
                     47941976..47942108,47943975..47944214,47944754..47944922,
                     47945440..47945559,47947674..47947847,47955029..47955196,
                     47968801..47969123,47970701..47970918,47971533..47971653,
                     47976443..47976555,47979790..47979914,47982993..47983108,
                     47987994..47988071))
                     /gene="PKD1L1"
                     /gene_synonym="PRO19563"
                     /product="polycystic kidney disease 1 like 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138295.3"
                     /db_xref="GI:315434237"
                     /db_xref="GeneID:168507"
                     /db_xref="HGNC:18053"
                     /db_xref="HPRD:10154"
                     /db_xref="MIM:609721"
     CDS             complement(join(47814741..47814764,47832225..47832395,
                     47835587..47835748,47840247..47840477,47842808..47842942,
                     47847845..47847985,47849071..47849175,47851415..47851649,
                     47852719..47852891,47853529..47853612,47854932..47855055,
                     47860674..47860784,47866948..47867066,47869023..47869199,
                     47869638..47869722,47870815..47870950,47872688..47872850,
                     47873937..47873983,47874565..47874637,47874731..47874841,
                     47876519..47876692,47879044..47879260,47880059..47880165,
                     47882560..47882767,47884593..47884676,47886477..47886669,
                     47892725..47892825,47894480..47894637,47894753..47894863,
                     47897203..47897430,47898271..47898483,47904814..47904870,
                     47906017..47906212,47913497..47913608,47915695..47915815,
                     47917087..47917229,47920326..47920403,47921507..47921683,
                     47924196..47924255,47925284..47925652,47927588..47927748,
                     47930140..47930361,47933475..47933656,47937585..47937791,
                     47941976..47942108,47943975..47944214,47944754..47944922,
                     47945440..47945559,47947674..47947847,47955029..47955196,
                     47968801..47969123,47970701..47970918,47971533..47971653,
                     47976443..47976555,47979790..47979914,47982993..47983108,
                     47987994..47988037))
                     /gene="PKD1L1"
                     /gene_synonym="PRO19563"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="polycystic kidney disease protein 1-like 1"
                     /protein_id="NP_612152.1"
                     /db_xref="GI:19923084"
                     /db_xref="CCDS:CCDS34633.1"
                     /db_xref="GeneID:168507"
                     /db_xref="HGNC:18053"
                     /db_xref="HPRD:10154"
                     /db_xref="MIM:609721"
     gene            47834889..47859445
                     /gene="C7orf69"
                     /gene_synonym="FLJ21075"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:80099"
                     /db_xref="HGNC:21911"
                     /db_xref="HPRD:08635"
     mRNA            join(47834889..47835041,47857624..47857793,
                     47859105..47859445)
                     /gene="C7orf69"
                     /gene_synonym="FLJ21075"
                     /product="chromosome 7 open reading frame 69"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_025031.2"
                     /db_xref="GI:153251668"
                     /db_xref="GeneID:80099"
                     /db_xref="HGNC:21911"
                     /db_xref="HPRD:08635"
     CDS             join(47834934..47835041,47857624..47857793,
                     47859105..47859195)
                     /gene="C7orf69"
                     /gene_synonym="FLJ21075"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC80099 precursor"
                     /protein_id="NP_079307.2"
                     /db_xref="GI:153251669"
                     /db_xref="CCDS:CCDS43581.1"
                     /db_xref="GeneID:80099"
                     /db_xref="HGNC:21911"
                     /db_xref="HPRD:08635"
     gene            complement(48002885..48019222)
                     /gene="HUS1"
                     /gene_synonym="hHUS1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3364"
                     /db_xref="HGNC:5309"
                     /db_xref="HPRD:04787"
                     /db_xref="MIM:603760"
     mRNA            complement(join(48002885..48005035,48007403..48007522,
                     48008816..48008915,48015210..48015284,48016327..48016434,
                     48018014..48018190,48018286..48018413,48019065..48019222))
                     /gene="HUS1"
                     /gene_synonym="hHUS1"
                     /product="HUS1 checkpoint homolog (S. pombe), transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004507.3"
                     /db_xref="GI:324711024"
                     /db_xref="GeneID:3364"
                     /db_xref="HGNC:5309"
                     /db_xref="HPRD:04787"
                     /db_xref="MIM:603760"
     misc_RNA        complement(join(48002885..48004229,48004897..48005035,
                     48007403..48007522,48008816..48008915,48015210..48015284,
                     48016327..48016434,48018014..48018190,48018286..48018413,
                     48019007..48019222))
                     /gene="HUS1"
                     /gene_synonym="hHUS1"
                     /product="HUS1 checkpoint homolog (S. pombe), transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037917.1"
                     /db_xref="GI:324711025"
                     /db_xref="GeneID:3364"
                     /db_xref="HGNC:5309"
                     /db_xref="MIM:603760"
                     /db_xref="HPRD:04787"
     CDS             complement(join(48004953..48005035,48007403..48007522,
                     48008816..48008915,48015210..48015284,48016327..48016434,
                     48018014..48018190,48018286..48018413,48019065..48019116))
                     /gene="HUS1"
                     /gene_synonym="hHUS1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="checkpoint protein HUS1"
                     /protein_id="NP_004498.1"
                     /db_xref="GI:4758576"
                     /db_xref="CCDS:CCDS34635.1"
                     /db_xref="GeneID:3364"
                     /db_xref="HGNC:5309"
                     /db_xref="HPRD:04787"
                     /db_xref="MIM:603760"
     gene            complement(48026745..48068716)
                     /gene="SUN3"
                     /gene_synonym="MGC33329; SUNC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:256979"
                     /db_xref="HGNC:22429"
                     /db_xref="HPRD:15451"
     mRNA            complement(join(48026745..48027046,48028385..48028477,
                     48033912..48034079,48035628..48035743,48045566..48045650,
                     48046762..48046924,48048632..48048672,48056859..48056962,
                     48065474..48065535,48068414..48068716))
                     /gene="SUN3"
                     /gene_synonym="MGC33329; SUNC1"
                     /product="Sad1 and UNC84 domain containing 3, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001030019.1"
                     /db_xref="GI:71834869"
                     /db_xref="GeneID:256979"
                     /db_xref="HGNC:22429"
                     /db_xref="HPRD:15451"
     mRNA            complement(join(48026745..48027046,48028385..48028477,
                     48033912..48034079,48035628..48035743,48045566..48045650,
                     48046762..48046924,48048632..48048672,48056859..48056962,
                     48065474..48065535,48068414..48068541,48068626..48068716))
                     /gene="SUN3"
                     /gene_synonym="MGC33329; SUNC1"
                     /product="Sad1 and UNC84 domain containing 3, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152782.3"
                     /db_xref="GI:71834867"
                     /db_xref="GeneID:256979"
                     /db_xref="HGNC:22429"
                     /db_xref="HPRD:15451"
     CDS             complement(join(48026927..48027046,48028385..48028477,
                     48033912..48034079,48035628..48035743,48045566..48045650,
                     48046762..48046924,48048632..48048672,48056859..48056962,
                     48065474..48065535,48068414..48068535))
                     /gene="SUN3"
                     /gene_synonym="MGC33329; SUNC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="SUN domain-containing protein 3"
                     /protein_id="NP_689995.3"
                     /db_xref="GI:71834868"
                     /db_xref="CCDS:CCDS34636.1"
                     /db_xref="GeneID:256979"
                     /db_xref="HGNC:22429"
                     /db_xref="HPRD:15451"
     CDS             complement(join(48026927..48027046,48028385..48028477,
                     48033912..48034079,48035628..48035743,48045566..48045650,
                     48046762..48046924,48048632..48048672,48056859..48056962,
                     48065474..48065535,48068414..48068535))
                     /gene="SUN3"
                     /gene_synonym="MGC33329; SUNC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="SUN domain-containing protein 3"
                     /protein_id="NP_001025190.1"
                     /db_xref="GI:71834870"
                     /db_xref="CCDS:CCDS34636.1"
                     /db_xref="GeneID:256979"
                     /db_xref="HGNC:22429"
                     /db_xref="HPRD:15451"
     gene            48075117..48100894
                     /gene="C7orf57"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:136288"
                     /db_xref="HGNC:22247"
     mRNA            join(48075117..48075227,48075805..48075960,
                     48080931..48081116,48083078..48083186,48086057..48086213,
                     48089477..48089574,48092297..48092520,48094192..48094203,
                     48099823..48100894)
                     /gene="C7orf57"
                     /product="chromosome 7 open reading frame 57"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001100159.1"
                     /db_xref="GI:154091006"
                     /db_xref="GeneID:136288"
                     /db_xref="HGNC:22247"
     CDS             join(48075906..48075960,48080931..48081116,
                     48083078..48083186,48086057..48086213,48089477..48089574,
                     48092297..48092520,48094192..48094203,48099823..48099869)
                     /gene="C7orf57"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC136288"
                     /protein_id="NP_001093629.1"
                     /db_xref="GI:154091007"
                     /db_xref="CCDS:CCDS47583.1"
                     /db_xref="GeneID:136288"
                     /db_xref="HGNC:22247"
     gene            48128355..48148330
                     /gene="UPP1"
                     /gene_synonym="UDRPASE; UP; UPASE; UPP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7378"
                     /db_xref="HGNC:12576"
                     /db_xref="HPRD:08932"
                     /db_xref="MIM:191730"
     mRNA            join(48128355..48128520,48128851..48129015,
                     48129785..48129961,48134360..48134424,48139267..48139384,
                     48141421..48141579,48142894..48143008,48146470..48146679,
                     48146958..48147104,48147815..48148330)
                     /gene="UPP1"
                     /gene_synonym="UDRPASE; UP; UPASE; UPP"
                     /product="uridine phosphorylase 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_181597.1"
                     /db_xref="GI:31742507"
                     /db_xref="GeneID:7378"
                     /db_xref="HGNC:12576"
                     /db_xref="MIM:191730"
                     /db_xref="HPRD:08932"
     mRNA            join(48128746..48129015,48129785..48129961,
                     48134360..48134424,48139267..48139384,48141421..48141579,
                     48142894..48143008,48146470..48146679,48146958..48147104,
                     48147815..48148330)
                     /gene="UPP1"
                     /gene_synonym="UDRPASE; UP; UPASE; UPP"
                     /product="uridine phosphorylase 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003364.2"
                     /db_xref="GI:31742506"
                     /db_xref="GeneID:7378"
                     /db_xref="HGNC:12576"
                     /db_xref="HPRD:08932"
                     /db_xref="MIM:191730"
     CDS             join(48134381..48134424,48139267..48139384,
                     48141421..48141579,48142894..48143008,48146470..48146679,
                     48146958..48147104,48147815..48147954)
                     /gene="UPP1"
                     /gene_synonym="UDRPASE; UP; UPASE; UPP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="uridine phosphorylase 1"
                     /protein_id="NP_003355.1"
                     /db_xref="GI:4507839"
                     /db_xref="CCDS:CCDS5507.1"
                     /db_xref="GeneID:7378"
                     /db_xref="HGNC:12576"
                     /db_xref="HPRD:08932"
                     /db_xref="MIM:191730"
     CDS             join(48134381..48134424,48139267..48139384,
                     48141421..48141579,48142894..48143008,48146470..48146679,
                     48146958..48147104,48147815..48147954)
                     /gene="UPP1"
                     /gene_synonym="UDRPASE; UP; UPASE; UPP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="uridine phosphorylase 1"
                     /protein_id="NP_853628.1"
                     /db_xref="GI:31742508"
                     /db_xref="CCDS:CCDS5507.1"
                     /db_xref="GeneID:7378"
                     /db_xref="HGNC:12576"
                     /db_xref="HPRD:08932"
                     /db_xref="MIM:191730"
     gene            48211057..48687091
                     /gene="ABCA13"
                     /gene_synonym="DKFZp313D2411; FLJ16398; FLJ33876;
                     FLJ33951"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:154664"
                     /db_xref="HGNC:14638"
                     /db_xref="HPRD:07422"
                     /db_xref="MIM:607807"
     mRNA            join(48211057..48211149,48232556..48232649,
                     48237834..48237957,48258951..48259102,48260878..48260906,
                     48266859..48267022,48269422..48269552,48273615..48273748,
                     48278838..48279002,48280464..48280663,48284173..48284300,
                     48285109..48285209,48285460..48285627,48287836..48288041,
                     48288809..48288948,48308577..48308691,48311384..48316162,
                     48317691..48319517,48320940..48321049,48327557..48327675,
                     48335297..48335460,48336829..48336908,48337963..48338084,
                     48349544..48349738,48352664..48352828,48353829..48354006,
                     48356754..48356893,48375019..48375132,48377962..48378052,
                     48390240..48390416,48391778..48392084,48407391..48407505,
                     48411765..48412094,48413944..48414013,48416038..48416169,
                     48427419..48427556,48428637..48428817,48431518..48431736,
                     48443280..48443476,48450117..48450274,48451950..48452180,
                     48467363..48467468,48494634..48494883,48506553..48506642,
                     48511127..48511196,48520633..48520751,48522673..48522760,
                     48528833..48528941,48545932..48545986,48547468..48547645,
                     48550680..48550795,48556321..48556477,48559637..48559890,
                     48563844..48564036,48567832..48567941,48619820..48619970,
                     48626750..48626884,48634306..48634409,48654881..48654973,
                     48682884..48682989,48684213..48684350,48685013..48687091)
                     /gene="ABCA13"
                     /gene_synonym="DKFZp313D2411; FLJ16398; FLJ33876;
                     FLJ33951"
                     /product="ATP-binding cassette, sub-family A (ABC1),
                     member 13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152701.3"
                     /db_xref="GI:259013576"
                     /db_xref="GeneID:154664"
                     /db_xref="HGNC:14638"
                     /db_xref="HPRD:07422"
                     /db_xref="MIM:607807"
     CDS             join(48211081..48211149,48232556..48232649,
                     48237834..48237957,48258951..48259102,48260878..48260906,
                     48266859..48267022,48269422..48269552,48273615..48273748,
                     48278838..48279002,48280464..48280663,48284173..48284300,
                     48285109..48285209,48285460..48285627,48287836..48288041,
                     48288809..48288948,48308577..48308691,48311384..48316162,
                     48317691..48319517,48320940..48321049,48327557..48327675,
                     48335297..48335460,48336829..48336908,48337963..48338084,
                     48349544..48349738,48352664..48352828,48353829..48354006,
                     48356754..48356893,48375019..48375132,48377962..48378052,
                     48390240..48390416,48391778..48392084,48407391..48407505,
                     48411765..48412094,48413944..48414013,48416038..48416169,
                     48427419..48427556,48428637..48428817,48431518..48431736,
                     48443280..48443476,48450117..48450274,48451950..48452180,
                     48467363..48467468,48494634..48494883,48506553..48506642,
                     48511127..48511196,48520633..48520751,48522673..48522760,
                     48528833..48528941,48545932..48545986,48547468..48547645,
                     48550680..48550795,48556321..48556477,48559637..48559890,
                     48563844..48564036,48567832..48567941,48619820..48619970,
                     48626750..48626884,48634306..48634409,48654881..48654973,
                     48682884..48682989,48684213..48684350,48685013..48685108)
                     /gene="ABCA13"
                     /gene_synonym="DKFZp313D2411; FLJ16398; FLJ33876;
                     FLJ33951"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ATP-binding cassette sub-family A member 13"
                     /protein_id="NP_689914.2"
                     /db_xref="GI:31657092"
                     /db_xref="CCDS:CCDS47584.1"
                     /db_xref="GeneID:154664"
                     /db_xref="HGNC:14638"
                     /db_xref="HPRD:07422"
                     /db_xref="MIM:607807"
     gene            complement(48885998..48887677)
                     /gene="CDC14BL"
                     /gene_synonym="FLJ45398"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100101112"
     gene            complement(48941422..48943599)
                     /gene="GDI2P1"
                     /gene_synonym="GDI2P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:2667"
                     /db_xref="HGNC:4228"
     gene            48964157..48967049
                     /gene="CDC14C"
                     /gene_synonym="CDC14B2; CDC14Bretro; MGC26484"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:168448"
                     /db_xref="HGNC:22427"
     misc_RNA        48964157..48967049
                     /gene="CDC14C"
                     /gene_synonym="CDC14B2; CDC14Bretro; MGC26484"
                     /product="CDC14 cell division cycle 14 homolog C (S.
                     cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003595.1"
                     /db_xref="GI:150010613"
                     /db_xref="GeneID:168448"
                     /db_xref="HGNC:22427"
     gene            complement(49298114..49299376)
                     /gene="LOC100533714"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533714"
     gene            49813257..49952138
                     /gene="VWC2"
                     /gene_synonym="MGC131845; PSST739; UNQ739"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:375567"
                     /db_xref="HGNC:30200"
                     /db_xref="HPRD:18271"
                     /db_xref="MIM:611108"
     mRNA            join(49813257..49813709,49814929..49815727,
                     49842307..49842436,49951630..49952138)
                     /gene="VWC2"
                     /gene_synonym="MGC131845; PSST739; UNQ739"
                     /product="von Willebrand factor C domain containing 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198570.3"
                     /db_xref="GI:260654088"
                     /db_xref="GeneID:375567"
                     /db_xref="HGNC:30200"
                     /db_xref="HPRD:18271"
                     /db_xref="MIM:611108"
     CDS             join(49815032..49815727,49842307..49842436,
                     49951630..49951781)
                     /gene="VWC2"
                     /gene_synonym="MGC131845; PSST739; UNQ739"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="brorin precursor"
                     /protein_id="NP_940972.2"
                     /db_xref="GI:260654089"
                     /db_xref="CCDS:CCDS5508.1"
                     /db_xref="GeneID:375567"
                     /db_xref="HGNC:30200"
                     /db_xref="HPRD:18271"
                     /db_xref="MIM:611108"
     gene            complement(49977023..50132860)
                     /gene="ZPBP"
                     /gene_synonym="FLJ93221; ZPBP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:11055"
                     /db_xref="HGNC:15662"
                     /db_xref="HPRD:18364"
                     /db_xref="MIM:608498"
     mRNA            complement(join(49977023..49977218,50022938..50023115,
                     50057836..50057912,50070688..50070906,50097585..50097737,
                     50121370..50121495,50129225..50129305,50132664..50132860))
                     /gene="ZPBP"
                     /gene_synonym="FLJ93221; ZPBP1"
                     /product="zona pellucida binding protein, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_007009.2"
                     /db_xref="GI:229577312"
                     /db_xref="GeneID:11055"
                     /db_xref="HGNC:15662"
                     /db_xref="HPRD:18364"
                     /db_xref="MIM:608498"
     mRNA            complement(join(49977023..49977218,50022938..50023115,
                     50057836..50057912,50070688..50070906,50097585..50097734,
                     50121370..50121495,50129225..50129305,50132664..50132860))
                     /gene="ZPBP"
                     /gene_synonym="FLJ93221; ZPBP1"
                     /product="zona pellucida binding protein, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001159878.1"
                     /db_xref="GI:229577314"
                     /db_xref="GeneID:11055"
                     /db_xref="HGNC:15662"
                     /db_xref="MIM:608498"
                     /db_xref="HPRD:18364"
     CDS             complement(join(49977124..49977218,50022938..50023115,
                     50057836..50057912,50070688..50070906,50097585..50097737,
                     50121370..50121495,50129225..50129305,50132664..50132790))
                     /gene="ZPBP"
                     /gene_synonym="FLJ93221; ZPBP1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zona pellucida-binding protein 1 isoform 1"
                     /protein_id="NP_008940.2"
                     /db_xref="GI:229577313"
                     /db_xref="CCDS:CCDS5509.1"
                     /db_xref="GeneID:11055"
                     /db_xref="HGNC:15662"
                     /db_xref="HPRD:18364"
                     /db_xref="MIM:608498"
     CDS             complement(join(49977124..49977218,50022938..50023115,
                     50057836..50057912,50070688..50070906,50097585..50097734,
                     50121370..50121495,50129225..50129305,50132664..50132790))
                     /gene="ZPBP"
                     /gene_synonym="FLJ93221; ZPBP1"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zona pellucida-binding protein 1 isoform 2"
                     /protein_id="NP_001153350.1"
                     /db_xref="GI:229577315"
                     /db_xref="CCDS:CCDS55110.1"
                     /db_xref="GeneID:11055"
                     /db_xref="HGNC:15662"
                     /db_xref="HPRD:18364"
                     /db_xref="MIM:608498"
     gene            complement(49981806..49984124)
                     /gene="LOC100270790"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100270790"
     gene            50135682..50198852
                     /gene="C7orf72"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100130988"
                     /db_xref="HGNC:22564"
     mRNA            join(50135682..50136234,50143910..50144007,
                     50169313..50169389,50173704..50173842,50175694..50175761,
                     50179736..50179777,50180877..50180984,50191046..50191153,
                     50198642..50198852)
                     /gene="C7orf72"
                     /product="chromosome 7 open reading frame 72"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001161834.2"
                     /db_xref="GI:332634959"
                     /db_xref="GeneID:100130988"
                     /db_xref="HGNC:22564"
     CDS             join(50135682..50136234,50143910..50144007,
                     50169313..50169389,50173704..50173842,50175694..50175761,
                     50179736..50179777,50180877..50180984,50191046..50191153,
                     50198642..50198765)
                     /gene="C7orf72"
                     /exception="mismatches in translation"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC100130988"
                     /protein_id="NP_001155306.2"
                     /db_xref="GI:332634960"
                     /db_xref="CCDS:CCDS47585.1"
                     /db_xref="GeneID:100130988"
                     /db_xref="HGNC:22564"
     gene            <50344378..>50367358
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="HPRD:04318"
                     /db_xref="MIM:603023"
     mRNA            join(<50344378..50344518,50358644..50358697,
                     50367234..>50367358)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 3"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220766.1"
                     /db_xref="GI:334085210"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50344378..50344518,50358644..50358697,
                     50367234..>50367358)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 4"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220767.1"
                     /db_xref="GI:334085212"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50344378..50344518,50358644..50358697,
                     50367234..>50367358)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 6"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220769.1"
                     /db_xref="GI:334085216"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50344378..50344518,50358644..50358697,
                     50367234..>50367358)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 7"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220770.1"
                     /db_xref="GI:334085218"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50344378..50344518,50358644..50358697,
                     50367234..>50367357)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 1"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006060.4"
                     /db_xref="GI:334085207"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="HPRD:04318"
                     /db_xref="MIM:603023"
     mRNA            join(<50344378..50344518,50358644..50358697,
                     50367234..>50367357)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 5"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220768.1"
                     /db_xref="GI:334085214"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50344378..50344518,50358644..50358697,
                     50367234..>50367353)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 2"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220765.1"
                     /db_xref="GI:334085208"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50344378..50344518,50358644..50358697,
                     50367234..>50367353)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 8"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220771.1"
                     /db_xref="GI:334085220"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(50358658..50358697,50367234..>50367358)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-binding protein Ikaros isoform 3"
                     /protein_id="NP_001207695.1"
                     /db_xref="GI:334085211"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(50358658..50358697,50367234..>50367358)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-binding protein Ikaros isoform 4"
                     /protein_id="NP_001207696.1"
                     /db_xref="GI:334085213"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(50358658..50358697,50367234..>50367358)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 6 is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-binding protein Ikaros isoform 6"
                     /protein_id="NP_001207698.1"
                     /db_xref="GI:334085217"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(50358658..50358697,50367234..>50367358)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 7 is encoded by transcript variant 7;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-binding protein Ikaros isoform 7"
                     /protein_id="NP_001207699.1"
                     /db_xref="GI:334085219"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(50358658..50358697,50367234..>50367357)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-binding protein Ikaros isoform 1"
                     /protein_id="NP_006051.1"
                     /db_xref="GI:5174501"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="HPRD:04318"
                     /db_xref="MIM:603023"
     CDS             join(50358658..50358697,50367234..>50367357)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 5 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-binding protein Ikaros isoform 5"
                     /protein_id="NP_001207697.1"
                     /db_xref="GI:334085215"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(50358658..50358697,50367234..>50367353)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-binding protein Ikaros isoform 2"
                     /protein_id="NP_001207694.1"
                     /db_xref="GI:334085209"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(50358658..50358697,50367234..>50367353)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 8 is encoded by transcript variant 8;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-binding protein Ikaros isoform 8"
                     /protein_id="NP_001207700.1"
                     /db_xref="GI:334085221"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     gene            50360502..50370140
                     /gene="LOC100507042"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 79 ESTs"
                     /db_xref="GeneID:100507042"
     misc_RNA        join(50360502..50360512,50365805..50366315,
                     50370131..50370140)
                     /gene="LOC100507042"
                     /product="hypothetical LOC100507042, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 66 ESTs"
                     /transcript_id="XR_108778.1"
                     /db_xref="GI:310119968"
                     /db_xref="GeneID:100507042"
     misc_RNA        join(50360502..50360512,50365805..50366331)
                     /gene="LOC100507042"
                     /product="hypothetical LOC100507042, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 78 ESTs"
                     /transcript_id="XR_108777.1"
                     /db_xref="GI:310119969"
                     /db_xref="GeneID:100507042"
     gap             50370632..50410631
                     /estimated_length=40000
     gene            <50444231..50472799
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="HPRD:04318"
                     /db_xref="MIM:603023"
     mRNA            join(<50444231..50444491,50450238..50450405,
                     50455043..50455168,50459427..50459561,50467616..50472799)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 1"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006060.4"
                     /db_xref="GI:334085207"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="HPRD:04318"
                     /db_xref="MIM:603023"
     mRNA            join(<50444231..50444491,50450238..50450405,
                     50459427..50459561,50467616..50472799)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 2"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220765.1"
                     /db_xref="GI:334085208"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50444231..50444491,50450238..50450405,
                     50467616..50472799)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 5"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220768.1"
                     /db_xref="GI:334085214"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50444231..50444491,50467616..50472799)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 8"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220771.1"
                     /db_xref="GI:334085220"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(<50444231..50444491,50450238..50450405,
                     50455043..50455168,50459427..50459561,50467616..50468325)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=3
                     /product="DNA-binding protein Ikaros isoform 1"
                     /protein_id="NP_006051.1"
                     /db_xref="GI:5174501"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="HPRD:04318"
                     /db_xref="MIM:603023"
     CDS             join(<50444231..50444491,50450238..50450405,
                     50459427..50459561,50467616..50468325)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=3
                     /product="DNA-binding protein Ikaros isoform 2"
                     /protein_id="NP_001207694.1"
                     /db_xref="GI:334085209"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(<50444231..50444491,50450238..50450405,
                     50467616..50468325)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 5 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=3
                     /product="DNA-binding protein Ikaros isoform 5"
                     /protein_id="NP_001207697.1"
                     /db_xref="GI:334085215"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(<50444231..50444491,50467616..50468325)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 8 is encoded by transcript variant 8;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=3
                     /product="DNA-binding protein Ikaros isoform 8"
                     /protein_id="NP_001207700.1"
                     /db_xref="GI:334085221"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50450238..50450405,50455043..50455168,
                     50459427..50459561,50467616..50472799)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 3"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220766.1"
                     /db_xref="GI:334085210"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50450238..50450405,50455043..50455168,
                     50459427..50459531,50467616..50472799)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 4"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220767.1"
                     /db_xref="GI:334085212"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50450238..50450405,50459427..50459561,
                     50467616..50472799)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 6"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220769.1"
                     /db_xref="GI:334085216"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50450238..50450405,50459427..50459531,
                     50467616..50472799)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 7"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220770.1"
                     /db_xref="GI:334085218"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(<50450238..50450405,50455043..50455168,
                     50459427..50459561,50467616..50468325)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=3
                     /product="DNA-binding protein Ikaros isoform 3"
                     /protein_id="NP_001207695.1"
                     /db_xref="GI:334085211"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(<50450238..50450405,50455043..50455168,
                     50459427..50459531,50467616..50468325)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=3
                     /product="DNA-binding protein Ikaros isoform 4"
                     /protein_id="NP_001207696.1"
                     /db_xref="GI:334085213"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(<50450238..50450405,50459427..50459561,
                     50467616..50468325)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 6 is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=3
                     /product="DNA-binding protein Ikaros isoform 6"
                     /protein_id="NP_001207698.1"
                     /db_xref="GI:334085217"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(<50450238..50450405,50459427..50459531,
                     50467616..50468325)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 7 is encoded by transcript variant 7;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=3
                     /product="DNA-binding protein Ikaros isoform 7"
                     /protein_id="NP_001207699.1"
                     /db_xref="GI:334085219"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50455032..50455168,50459427..50459561,
                     50467616..50472799)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 10"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220773.1"
                     /db_xref="GI:334085224"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50455032..50455168,50459427..50459531,
                     50467616..50472799)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 11"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220774.1"
                     /db_xref="GI:334085226"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(<50455032..50455168,50459427..50459561,
                     50467616..50468325)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 10 is encoded by transcript variant 10;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-binding protein Ikaros isoform 10"
                     /protein_id="NP_001207702.1"
                     /db_xref="GI:334085225"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(<50455032..50455168,50459427..50459531,
                     50467616..50468325)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 11 is encoded by transcript variant 11;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-binding protein Ikaros isoform 11"
                     /protein_id="NP_001207703.1"
                     /db_xref="GI:334085227"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50459422..50459561,50467616..50472799)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 12"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220775.1"
                     /db_xref="GI:334085228"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            join(<50459422..50459531,50467616..50472799)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 13"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220776.1"
                     /db_xref="GI:334085230"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(<50459422..50459561,50467616..50468325)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 12 is encoded by transcript variant 12;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=2
                     /product="DNA-binding protein Ikaros isoform 12"
                     /protein_id="NP_001207704.1"
                     /db_xref="GI:334085229"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             join(<50459422..50459531,50467616..50468325)
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 13 is encoded by transcript variant 13;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=2
                     /product="DNA-binding protein Ikaros isoform 13"
                     /protein_id="NP_001207705.1"
                     /db_xref="GI:334085231"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     mRNA            <50467613..50472799
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /product="IKAROS family zinc finger 1 (Ikaros), transcript
                     variant 9"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001220772.1"
                     /db_xref="GI:334085222"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     CDS             <50467613..50468325
                     /gene="IKZF1"
                     /gene_synonym="hIk-1; Hs.54452; IK1; IKAROS; LYF1;
                     PRO0758; ZNFN1A1"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 9 is encoded by transcript variant 9;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=3
                     /product="DNA-binding protein Ikaros isoform 9"
                     /protein_id="NP_001207701.1"
                     /db_xref="GI:334085223"
                     /db_xref="GeneID:10320"
                     /db_xref="HGNC:13176"
                     /db_xref="MIM:603023"
                     /db_xref="HPRD:04318"
     gene            complement(50511831..50518088)
                     /gene="FIGNL1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:63979"
                     /db_xref="HGNC:13286"
     mRNA            complement(join(50511831..50514995,50515879..50515987,
                     50517254..50517421,50517999..50518088))
                     /gene="FIGNL1"
                     /product="fidgetin-like 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001042762.1"
                     /db_xref="GI:112789542"
                     /db_xref="GeneID:63979"
                     /db_xref="HGNC:13286"
     mRNA            complement(join(50511831..50514995,50515879..50515987,
                     50517261..50517421,50517999..50518088))
                     /gene="FIGNL1"
                     /product="fidgetin-like 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022116.3"
                     /db_xref="GI:112789544"
                     /db_xref="GeneID:63979"
                     /db_xref="HGNC:13286"
                     /db_xref="HPRD:10958"
     CDS             complement(50512961..50514985)
                     /gene="FIGNL1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="fidgetin-like protein 1"
                     /protein_id="NP_001036227.1"
                     /db_xref="GI:112789543"
                     /db_xref="CCDS:CCDS5510.1"
                     /db_xref="GeneID:63979"
                     /db_xref="HGNC:13286"
     CDS             complement(50512961..50514985)
                     /gene="FIGNL1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="fidgetin-like protein 1"
                     /protein_id="NP_071399.2"
                     /db_xref="GI:31742536"
                     /db_xref="CCDS:CCDS5510.1"
                     /db_xref="GeneID:63979"
                     /db_xref="HGNC:13286"
     gene            complement(50526134..50633154)
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="MIM:107930"
     mRNA            complement(join(50526134..50526541,50530911..50531129,
                     50534912..50535013,50537771..50537869,50544322..50544341,
                     50547485..50547561,50563048..50563115,50566846..50566940,
                     50571691..50571757,50595835..50595978,50596906..50597040,
                     50605558..50605677,50607613..50607726,50611583..50611811,
                     50632982..50633154))
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /product="dopa decarboxylase (aromatic L-amino acid
                     decarboxylase), transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001082971.1"
                     /db_xref="GI:132814447"
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="MIM:107930"
     mRNA            complement(join(50526134..50526541,50530911..50531129,
                     50534912..50535013,50537771..50537869,50544322..50544341,
                     50547485..50547561,50563048..50563115,50566846..50566940,
                     50571691..50571757,50595835..50595978,50596906..50597040,
                     50605558..50605677,50607613..50607726,50611583..50611811,
                     50628711..50628768))
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /product="dopa decarboxylase (aromatic L-amino acid
                     decarboxylase), transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000790.3"
                     /db_xref="GI:132814459"
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="HPRD:00145"
                     /db_xref="MIM:107930"
     mRNA            complement(join(50526134..50526541,50530911..50531129,
                     50534912..50535013,50537771..50537869,50544322..50544341,
                     50547485..50547561,50563048..50563115,50566846..50566940,
                     50571691..50571757,50595835..50595978,50596906..50597040,
                     50605558..50605677,50611583..50611811,50628711..50628768))
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /product="dopa decarboxylase (aromatic L-amino acid
                     decarboxylase), transcript variant 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001242886.1"
                     /db_xref="GI:338968913"
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="MIM:107930"
     mRNA            complement(join(50526134..50526541,50530911..50531129,
                     50534912..50535013,50537771..50537869,50544322..50544341,
                     50547485..50547561,50563048..50563115,50566846..50566940,
                     50571691..50571757,50596906..50597040,50605558..50605677,
                     50607613..50607726,50611583..50611811,50628711..50628768))
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /product="dopa decarboxylase (aromatic L-amino acid
                     decarboxylase), transcript variant 4"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001242887.1"
                     /db_xref="GI:338968916"
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="MIM:107930"
     mRNA            complement(join(50526134..50526541,50530911..50531129,
                     50534912..50535013,50537771..50537869,50544322..50544341,
                     50547485..50547561,50563048..50563115,50566846..50566940,
                     50571691..50571757,50595835..50595978,50596906..50597040,
                     50611583..50611811,50628711..50628768))
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /product="dopa decarboxylase (aromatic L-amino acid
                     decarboxylase), transcript variant 5"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001242888.1"
                     /db_xref="GI:338968918"
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="MIM:107930"
     mRNA            complement(join(50526134..50526541,50530911..50531129,
                     50534912..50535013,50537771..50537869,50544322..50544341,
                     50547485..50547561,50563048..50563115,50566846..50566940,
                     50571691..50571757,50605558..50605677,50607613..50607726,
                     50611583..50611811,50628711..50628768))
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /product="dopa decarboxylase (aromatic L-amino acid
                     decarboxylase), transcript variant 6"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001242889.1"
                     /db_xref="GI:338968920"
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="MIM:107930"
     CDS             complement(join(50530929..50531129,50534912..50535013,
                     50537771..50537869,50544322..50544341,50547485..50547561,
                     50563048..50563115,50566846..50566940,50571691..50571757,
                     50595835..50595978,50596906..50597040,50605558..50605677,
                     50607613..50607726,50611583..50611783))
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /exception="mismatches in translation"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="aromatic-L-amino-acid decarboxylase isoform 1"
                     /protein_id="NP_001076440.1"
                     /db_xref="GI:132814448"
                     /db_xref="CCDS:CCDS5511.1"
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="MIM:107930"
     CDS             complement(join(50530929..50531129,50534912..50535013,
                     50537771..50537869,50544322..50544341,50547485..50547561,
                     50563048..50563115,50566846..50566940,50571691..50571757,
                     50595835..50595978,50596906..50597040,50605558..50605677,
                     50607613..50607726,50611583..50611783))
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /exception="mismatches in translation"
                     /note="isoform 1 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="aromatic-L-amino-acid decarboxylase isoform 1"
                     /protein_id="NP_000781.1"
                     /db_xref="GI:4503281"
                     /db_xref="CCDS:CCDS5511.1"
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="MIM:107930"
     CDS             complement(join(50530929..50531129,50534912..50535013,
                     50537771..50537869,50544322..50544341,50547485..50547561,
                     50563048..50563115,50566846..50566940,50571691..50571757,
                     50595835..50595978,50596906..50597040,50605558..50605677,
                     50611583..50611783))
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /exception="mismatches in translation"
                     /note="isoform 2 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="aromatic-L-amino-acid decarboxylase isoform 2"
                     /protein_id="NP_001229815.1"
                     /db_xref="GI:338968914"
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="MIM:107930"
     CDS             complement(join(50530929..50531129,50534912..50535013,
                     50537771..50537869,50544322..50544341,50547485..50547561,
                     50563048..50563115,50566846..50566940,50571691..50571757,
                     50596906..50597040,50605558..50605677,50607613..50607726,
                     50611583..50611783))
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /exception="mismatches in translation"
                     /note="isoform 3 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="aromatic-L-amino-acid decarboxylase isoform 3"
                     /protein_id="NP_001229816.1"
                     /db_xref="GI:338968917"
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="MIM:107930"
     CDS             complement(join(50530929..50531129,50534912..50535013,
                     50537771..50537869,50544322..50544341,50547485..50547561,
                     50563048..50563115,50566846..50566940,50571691..50571757,
                     50595835..50595978,50596906..50597040,50611583..50611783))
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /exception="mismatches in translation"
                     /note="isoform 4 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="aromatic-L-amino-acid decarboxylase isoform 4"
                     /protein_id="NP_001229817.1"
                     /db_xref="GI:338968919"
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="MIM:107930"
     CDS             complement(join(50530929..50531129,50534912..50535013,
                     50537771..50537869,50544322..50544341,50547485..50547561,
                     50563048..50563115,50566846..50566940,50571691..50571757,
                     50605558..50605677,50607613..50607726,50611583..50611783))
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /exception="mismatches in translation"
                     /note="isoform 5 is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="aromatic-L-amino-acid decarboxylase isoform 5"
                     /protein_id="NP_001229818.1"
                     /db_xref="GI:338968921"
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="MIM:107930"
     mRNA            complement(join(50560345..50560703,50563048..50563115,
                     50566846..50566940,50571691..50571757,50595835..50595978,
                     50596906..50597040,50605558..50605677,50607613..50607726,
                     50611583..50611811,50628711..50628768))
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /product="dopa decarboxylase (aromatic L-amino acid
                     decarboxylase), transcript variant 7"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001242890.1"
                     /db_xref="GI:338968922"
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="MIM:107930"
     CDS             complement(join(50560631..50560703,50563048..50563115,
                     50566846..50566940,50571691..50571757,50595835..50595978,
                     50596906..50597040,50605558..50605677,50607613..50607726,
                     50611583..50611783))
                     /gene="DDC"
                     /gene_synonym="AADC"
                     /exception="mismatches in translation"
                     /note="isoform 6 is encoded by transcript variant 7;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="aromatic-L-amino-acid decarboxylase isoform 6"
                     /protein_id="NP_001229819.1"
                     /db_xref="GI:338968923"
                     /db_xref="GeneID:1644"
                     /db_xref="HGNC:2719"
                     /db_xref="MIM:107930"
     gene            50599457..50611161
                     /gene="LOC100129427"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100129427"
     misc_RNA        join(50599457..50599580,50606812..50606865,
                     50607529..50607843,50609044..50609107,50609943..50611161)
                     /gene="LOC100129427"
                     /product="hypothetical LOC100129427"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033845.1"
                     /db_xref="GI:299782596"
                     /db_xref="GeneID:100129427"
     gene            complement(50657760..50861159)
                     /gene="GRB10"
                     /gene_synonym="Grb-10; GRB-IR; IRBP; KIAA0207; MEG1; RSS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2887"
                     /db_xref="HGNC:4564"
                     /db_xref="HPRD:03312"
                     /db_xref="MIM:601523"
     mRNA            complement(join(50657760..50660795,50663134..50663227,
                     50671695..50671782,50672008..50672074,50672987..50673103,
                     50674034..50674111,50680438..50680536,50682467..50682577,
                     50683907..50684044,50685768..50685836,50686867..50686982,
                     50694519..50694675,50737419..50737560,50742133..50742355,
                     50771518..50771605,50823584..50823753,50860921..50861159))
                     /gene="GRB10"
                     /gene_synonym="Grb-10; GRB-IR; IRBP; KIAA0207; MEG1; RSS"
                     /product="growth factor receptor-bound protein 10,
                     transcript variant 4"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001001555.2"
                     /db_xref="GI:219689101"
                     /db_xref="GeneID:2887"
                     /db_xref="HGNC:4564"
                     /db_xref="MIM:601523"
                     /db_xref="HPRD:03312"
     mRNA            complement(join(50657760..50660795,50663134..50663227,
                     50671695..50671782,50672008..50672074,50672987..50673103,
                     50674034..50674111,50680438..50680536,50682467..50682577,
                     50683907..50684044,50685768..50685836,50686867..50686982,
                     50694519..50694675,50737419..50737560,50742133..50742355,
                     50771518..50771605,50799969..50800050))
                     /gene="GRB10"
                     /gene_synonym="Grb-10; GRB-IR; IRBP; KIAA0207; MEG1; RSS"
                     /product="growth factor receptor-bound protein 10,
                     transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005311.4"
                     /db_xref="GI:219689098"
                     /db_xref="GeneID:2887"
                     /db_xref="HGNC:4564"
                     /db_xref="HPRD:03312"
                     /db_xref="MIM:601523"
     mRNA            complement(join(50657760..50660795,50663134..50663227,
                     50671695..50671782,50672008..50672074,50672987..50673103,
                     50674034..50674111,50680438..50680536,50682467..50682577,
                     50685768..50685836,50686867..50686982,50694519..50694675,
                     50737419..50737560,50742133..50742355,50771518..50771605,
                     50799969..50800050))
                     /gene="GRB10"
                     /gene_synonym="Grb-10; GRB-IR; IRBP; KIAA0207; MEG1; RSS"
                     /product="growth factor receptor-bound protein 10,
                     transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001001549.2"
                     /db_xref="GI:219689099"
                     /db_xref="GeneID:2887"
                     /db_xref="HGNC:4564"
                     /db_xref="MIM:601523"
                     /db_xref="HPRD:03312"
     mRNA            complement(join(50657760..50660795,50663134..50663227,
                     50671695..50671782,50672008..50672074,50672987..50673103,
                     50674034..50674111,50680438..50680536,50682467..50682577,
                     50683907..50684044,50685768..50685836,50686867..50686982,
                     50694519..50694675,50737419..50737560,50742133..50742355,
                     50771518..50771605,50772837..50772998))
                     /gene="GRB10"
                     /gene_synonym="Grb-10; GRB-IR; IRBP; KIAA0207; MEG1; RSS"
                     /product="growth factor receptor-bound protein 10,
                     transcript variant 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001001550.2"
                     /db_xref="GI:219689100"
                     /db_xref="GeneID:2887"
                     /db_xref="HGNC:4564"
                     /db_xref="MIM:601523"
                     /db_xref="HPRD:03312"
     CDS             complement(join(50660649..50660795,50663134..50663227,
                     50671695..50671782,50672008..50672074,50672987..50673103,
                     50674034..50674111,50680438..50680536,50682467..50682577,
                     50683907..50684044,50685768..50685836,50686867..50686982,
                     50694519..50694675,50737419..50737560,50742133..50742355,
                     50771518..50771605,50799969..50800019))
                     /gene="GRB10"
                     /gene_synonym="Grb-10; GRB-IR; IRBP; KIAA0207; MEG1; RSS"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="growth factor receptor-bound protein 10 isoform
                     a"
                     /protein_id="NP_005302.3"
                     /db_xref="GI:48762679"
                     /db_xref="CCDS:CCDS43582.1"
                     /db_xref="GeneID:2887"
                     /db_xref="HGNC:4564"
                     /db_xref="HPRD:03312"
                     /db_xref="MIM:601523"
     CDS             complement(join(50660649..50660795,50663134..50663227,
                     50671695..50671782,50672008..50672074,50672987..50673103,
                     50674034..50674111,50680438..50680536,50682467..50682577,
                     50685768..50685836,50686867..50686982,50694519..50694675,
                     50737419..50737560,50742133..50742355,50771518..50771605,
                     50799969..50800019))
                     /gene="GRB10"
                     /gene_synonym="Grb-10; GRB-IR; IRBP; KIAA0207; MEG1; RSS"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="growth factor receptor-bound protein 10 isoform
                     b"
                     /protein_id="NP_001001549.1"
                     /db_xref="GI:48762693"
                     /db_xref="CCDS:CCDS47586.1"
                     /db_xref="GeneID:2887"
                     /db_xref="HGNC:4564"
                     /db_xref="HPRD:03312"
                     /db_xref="MIM:601523"
     CDS             complement(join(50660649..50660795,50663134..50663227,
                     50671695..50671782,50672008..50672074,50672987..50673103,
                     50674034..50674111,50680438..50680536,50682467..50682577,
                     50683907..50684044,50685768..50685836,50686867..50686982,
                     50694519..50694675,50737419..50737560,50742133..50742320))
                     /gene="GRB10"
                     /gene_synonym="Grb-10; GRB-IR; IRBP; KIAA0207; MEG1; RSS"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="growth factor receptor-bound protein 10 isoform
                     c"
                     /protein_id="NP_001001550.1"
                     /db_xref="GI:48762695"
                     /db_xref="CCDS:CCDS43583.1"
                     /db_xref="GeneID:2887"
                     /db_xref="HGNC:4564"
                     /db_xref="HPRD:03312"
                     /db_xref="MIM:601523"
     CDS             complement(join(50660649..50660795,50663134..50663227,
                     50671695..50671782,50672008..50672074,50672987..50673103,
                     50674034..50674111,50680438..50680536,50682467..50682577,
                     50683907..50684044,50685768..50685836,50686867..50686982,
                     50694519..50694675,50737419..50737560,50742133..50742320))
                     /gene="GRB10"
                     /gene_synonym="Grb-10; GRB-IR; IRBP; KIAA0207; MEG1; RSS"
                     /note="isoform c is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="growth factor receptor-bound protein 10 isoform
                     c"
                     /protein_id="NP_001001555.1"
                     /db_xref="GI:48762697"
                     /db_xref="CCDS:CCDS43583.1"
                     /db_xref="GeneID:2887"
                     /db_xref="HGNC:4564"
                     /db_xref="HPRD:03312"
                     /db_xref="MIM:601523"
     gene            complement(50911382..50911529)
                     /gene="RPL39P23"
                     /gene_synonym="RPL39_10_809"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271203"
                     /db_xref="HGNC:36581"
     gene            complement(51083909..51384515)
                     /gene="COBL"
                     /gene_synonym="DKFZp686G13227; KIAA0633; MGC131893"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23242"
                     /db_xref="HGNC:22199"
                     /db_xref="HPRD:10843"
                     /db_xref="MIM:610317"
     mRNA            complement(join(51083909..51085265,51092806..51093069,
                     51094243..51094362,51095409..51097288,51098509..51098606,
                     51111080..51111389,51152863..51153001,51203855..51204028,
                     51251799..51251896,51258547..51258775,51261076..51261286,
                     51287438..51287641,51384290..51384515))
                     /gene="COBL"
                     /gene_synonym="DKFZp686G13227; KIAA0633; MGC131893"
                     /product="cordon-bleu homolog (mouse)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015198.3"
                     /db_xref="GI:187960112"
                     /db_xref="GeneID:23242"
                     /db_xref="HGNC:22199"
                     /db_xref="HPRD:10843"
                     /db_xref="MIM:610317"
     CDS             complement(join(51085248..51085265,51092806..51093069,
                     51094243..51094362,51095409..51097288,51098509..51098606,
                     51111080..51111389,51152863..51153001,51203855..51204028,
                     51251799..51251896,51258547..51258775,51261076..51261286,
                     51287438..51287641,51384290..51384330))
                     /gene="COBL"
                     /gene_synonym="DKFZp686G13227; KIAA0633; MGC131893"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein cordon-bleu"
                     /protein_id="NP_056013.2"
                     /db_xref="GI:31581524"
                     /db_xref="CCDS:CCDS34637.1"
                     /db_xref="GeneID:23242"
                     /db_xref="HGNC:22199"
                     /db_xref="HPRD:10843"
                     /db_xref="MIM:610317"
     gene            complement(51327129..51327864)
                     /gene="RPL7L1P2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420155"
                     /db_xref="HGNC:39484"
     gene            51449981..51452357
                     /gene="LOC642663"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:642663"
     gene            complement(51454021..51454798)
                     /gene="LOC100507138"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100507138"
     exon            complement(51454021..51454798)
                     /gene="LOC100507138"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100507138"
     gene            complement(51455251..51457317)
                     /gene="LOC100133177"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100133177"
     gene            complement(51459215..51459703)
                     /gene="LOC100652855"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100652855"
     exon            complement(51459215..51459703)
                     /gene="LOC100652855"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100652855"
     gene            complement(51459730..51460910)
                     /gene="LOC100131871"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 EST, 1 Protein"
                     /db_xref="GeneID:100131871"
     mRNA            complement(join(51459730..51460429,51460521..51460578,
                     51460806..51460910))
                     /gene="LOC100131871"
                     /product="hypothetical protein LOC100131871"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 EST, 1 Protein"
                     /transcript_id="XM_001716056.3"
                     /db_xref="GI:310119970"
                     /db_xref="GeneID:100131871"
     CDS             complement(51459730..51460353)
                     /gene="LOC100131871"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="hypothetical protein LOC100131871"
                     /protein_id="XP_001716108.3"
                     /db_xref="GI:310119971"
                     /db_xref="GeneID:100131871"
     gene            complement(52964020..52965501)
                     /gene="LOC100533661"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533661"
     gene            53070113..53071122
                     /gene="LOC392027"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392027"
     gene            53103349..53104618
                     /gene="POM121L12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285877"
                     /db_xref="HGNC:25369"
                     /db_xref="HPRD:13212"
     mRNA            53103349..53104618
                     /gene="POM121L12"
                     /product="POM121 membrane glycoprotein-like 12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182595.3"
                     /db_xref="GI:239735602"
                     /db_xref="GeneID:285877"
                     /db_xref="HGNC:25369"
                     /db_xref="HPRD:13212"
     CDS             53103365..53104255
                     /gene="POM121L12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="POM121-like protein 12"
                     /protein_id="NP_872401.3"
                     /db_xref="GI:239735603"
                     /db_xref="CCDS:CCDS43584.1"
                     /db_xref="GeneID:285877"
                     /db_xref="HGNC:25369"
                     /db_xref="HPRD:13212"
     gene            53254829..53256634
                     /gene="LOC653175"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:653175"
     gene            53383898..53384412
                     /gene="LOC100419777"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419777"
     gene            53433751..53433904
                     /gene="RNU1-14P"
                     /gene_synonym="RNU1P7; U1P17"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:26859"
                     /db_xref="HGNC:10139"
     gene            complement(53723202..53879624)
                     /gene="FLJ45974"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:401337"
     misc_RNA        complement(join(53723202..53725141,53759620..53759782,
                     53832820..53832938,53833176..53833920,53847639..53847731,
                     53879201..53879624))
                     /gene="FLJ45974"
                     /product="hypothetical LOC401337"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038371.1"
                     /db_xref="GI:335334959"
                     /db_xref="GeneID:401337"
     gene            53847442..53847956
                     /gene="LOC100422658"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100422658"
     gene            complement(54268917..54270114)
                     /gene="HPVC1"
                     /gene_synonym="HPV18E5L; PE5L"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3262"
                     /db_xref="HGNC:5169"
                     /db_xref="MIM:600762"
     misc_RNA        complement(54268917..54270114)
                     /gene="HPVC1"
                     /gene_synonym="HPV18E5L; PE5L"
                     /product="human papillomavirus (type 18) E5 central
                     sequence-like 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_004422.2"
                     /db_xref="GI:194595504"
                     /db_xref="GeneID:3262"
                     /db_xref="HGNC:5169"
                     /db_xref="MIM:600762"
     gene            54487064..54488293
                     /gene="SLC25A5P3"
                     /gene_synonym="ANTP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:222005"
                     /db_xref="HGNC:507"
     gene            54610019..54636948
                     /gene="VSTM2A"
                     /gene_synonym="MGC33530; VSTM2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222008"
                     /db_xref="HGNC:28499"
                     /db_xref="HPRD:14566"
     mRNA            join(54610019..54610502,54612315..54612481,
                     54614640..54614690,54617527..54617863,54636702..54636948)
                     /gene="VSTM2A"
                     /gene_synonym="MGC33530; VSTM2"
                     /product="V-set and transmembrane domain containing 2A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182546.2"
                     /db_xref="GI:148743775"
                     /db_xref="GeneID:222008"
                     /db_xref="HGNC:28499"
                     /db_xref="HPRD:14566"
     CDS             join(54610424..54610502,54612315..54612481,
                     54614640..54614690,54617527..54617863,54636702..54636778)
                     /gene="VSTM2A"
                     /gene_synonym="MGC33530; VSTM2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="V-set and transmembrane domain-containing
                     protein 2A"
                     /protein_id="NP_872352.2"
                     /db_xref="GI:148743776"
                     /db_xref="CCDS:CCDS5512.2"
                     /db_xref="GeneID:222008"
                     /db_xref="HGNC:28499"
                     /db_xref="HPRD:14566"
     gene            54624663..54639419
                     /gene="LOC285878"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285878"
     misc_RNA        join(54624663..54624988,54625543..54627664,
                     54638463..54638584,54638959..54639419)
                     /gene="LOC285878"
                     /product="hypothetical LOC285878"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038994.1"
                     /db_xref="GI:337756627"
                     /db_xref="GeneID:285878"
     gene            54724008..54724468
                     /gene="RPL31P35"
                     /gene_synonym="RPL31_16_810"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271199"
                     /db_xref="HGNC:36932"
     gene            complement(54819940..54826939)
                     /gene="SEC61G"
                     /gene_synonym="SSS1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23480"
                     /db_xref="HGNC:18277"
                     /db_xref="HPRD:15318"
                     /db_xref="MIM:609215"
     mRNA            complement(join(54819940..54820113,54823472..54823574,
                     54825188..54825287,54826851..54826939))
                     /gene="SEC61G"
                     /gene_synonym="SSS1"
                     /product="Sec61 gamma subunit, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014302.3"
                     /db_xref="GI:60279263"
                     /db_xref="GeneID:23480"
                     /db_xref="HGNC:18277"
                     /db_xref="HPRD:15318"
                     /db_xref="MIM:609215"
     mRNA            complement(join(54819940..54820113,54823472..54823574,
                     54825188..54825287,54826855..54826939))
                     /gene="SEC61G"
                     /gene_synonym="SSS1"
                     /product="Sec61 gamma subunit, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001012456.1"
                     /db_xref="GI:60279264"
                     /db_xref="GeneID:23480"
                     /db_xref="HGNC:18277"
                     /db_xref="HPRD:15318"
                     /db_xref="MIM:609215"
     CDS             complement(join(54820104..54820113,54823472..54823574,
                     54825188..54825281))
                     /gene="SEC61G"
                     /gene_synonym="SSS1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein transport protein Sec61 subunit gamma"
                     /protein_id="NP_055117.1"
                     /db_xref="GI:7657546"
                     /db_xref="CCDS:CCDS5513.1"
                     /db_xref="GeneID:23480"
                     /db_xref="HGNC:18277"
                     /db_xref="HPRD:15318"
                     /db_xref="MIM:609215"
     CDS             complement(join(54820104..54820113,54823472..54823574,
                     54825188..54825281))
                     /gene="SEC61G"
                     /gene_synonym="SSS1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein transport protein Sec61 subunit gamma"
                     /protein_id="NP_001012474.1"
                     /db_xref="GI:60279265"
                     /db_xref="CCDS:CCDS5513.1"
                     /db_xref="GeneID:23480"
                     /db_xref="HGNC:18277"
                     /db_xref="HPRD:15318"
                     /db_xref="MIM:609215"
     gene            55001074..55007281
                     /gene="LOC643168"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:643168"
     gene            55086725..55275031
                     /gene="EGFR"
                     /gene_synonym="ERBB; ERBB1; HER1; mENA; PIG61"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1956"
                     /db_xref="HGNC:3236"
                     /db_xref="HPRD:00579"
                     /db_xref="MIM:131550"
     mRNA            join(55086725..55087058,55209979..55210130,
                     55210998..55211181,55214299..55214433,55218987..55219055,
                     55220239..55220357,55221704..55221845,55223523..55223639,
                     55224226..55224352,55224452..55224525,55225356..55225446,
                     55227832..55228031,55229192..55229324,55231426..55231516,
                     55232973..55233130,55238868..55238906,55240676..55240817,
                     55241614..55241736,55242415..55242513,55248986..55249171,
                     55259412..55259567,55260459..55260534,55266410..55266556,
                     55268009..55268106,55268881..55269048,55269428..55269475,
                     55270210..55270318,55272949..55275031)
                     /gene="EGFR"
                     /gene_synonym="ERBB; ERBB1; HER1; mENA; PIG61"
                     /product="epidermal growth factor receptor, transcript
                     variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005228.3"
                     /db_xref="GI:41327737"
                     /db_xref="GeneID:1956"
                     /db_xref="HGNC:3236"
                     /db_xref="HPRD:00579"
                     /db_xref="MIM:131550"
     mRNA            join(55086725..55087058,55209979..55210130,
                     55210998..55211181,55214299..55214433,55218987..55219055,
                     55220239..55220357,55221704..55221845,55223523..55223639,
                     55224226..55224352,55224452..55224525,55225356..55225446,
                     55227832..55228031,55229192..55229324,55231426..55231516,
                     55232973..55233130,55238000..55238738)
                     /gene="EGFR"
                     /gene_synonym="ERBB; ERBB1; HER1; mENA; PIG61"
                     /product="epidermal growth factor receptor, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_201284.1"
                     /db_xref="GI:41327735"
                     /db_xref="GeneID:1956"
                     /db_xref="HGNC:3236"
                     /db_xref="HPRD:00579"
                     /db_xref="MIM:131550"
     mRNA            join(55086725..55087058,55209979..55210130,
                     55210998..55211181,55214299..55214433,55218987..55219055,
                     55220239..55220357,55221704..55221845,55223523..55223639,
                     55224226..55224352,55224452..55224525,55225356..55225446,
                     55227832..55228031,55229192..55229324,55231426..55231516,
                     55232973..55233130,55236216..55236328)
                     /gene="EGFR"
                     /gene_synonym="ERBB; ERBB1; HER1; mENA; PIG61"
                     /product="epidermal growth factor receptor, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_201282.1"
                     /db_xref="GI:41327731"
                     /db_xref="GeneID:1956"
                     /db_xref="HGNC:3236"
                     /db_xref="HPRD:00579"
                     /db_xref="MIM:131550"
     mRNA            join(55086725..55087058,55209979..55210130,
                     55210998..55211181,55214299..55214433,55218987..55219055,
                     55220239..55220357,55221704..55221845,55223523..55223639,
                     55224226..55224352,55224452..55224644)
                     /gene="EGFR"
                     /gene_synonym="ERBB; ERBB1; HER1; mENA; PIG61"
                     /product="epidermal growth factor receptor, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_201283.1"
                     /db_xref="GI:41327733"
                     /db_xref="GeneID:1956"
                     /db_xref="HGNC:3236"
                     /db_xref="HPRD:00579"
                     /db_xref="MIM:131550"
     CDS             join(55086971..55087058,55209979..55210130,
                     55210998..55211181,55214299..55214433,55218987..55219055,
                     55220239..55220357,55221704..55221845,55223523..55223639,
                     55224226..55224352,55224452..55224525,55225356..55225446,
                     55227832..55228031,55229192..55229324,55231426..55231516,
                     55232973..55233130,55238868..55238906,55240676..55240817,
                     55241614..55241736,55242415..55242513,55248986..55249171,
                     55259412..55259567,55260459..55260534,55266410..55266556,
                     55268009..55268106,55268881..55269048,55269428..55269475,
                     55270210..55270318,55272949..55273310)
                     /gene="EGFR"
                     /gene_synonym="ERBB; ERBB1; HER1; mENA; PIG61"
                     /note="isoform a precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="epidermal growth factor receptor isoform a
                     precursor"
                     /protein_id="NP_005219.2"
                     /db_xref="GI:29725609"
                     /db_xref="CCDS:CCDS5514.1"
                     /db_xref="GeneID:1956"
                     /db_xref="HGNC:3236"
                     /db_xref="HPRD:00579"
                     /db_xref="MIM:131550"
     CDS             join(55086971..55087058,55209979..55210130,
                     55210998..55211181,55214299..55214433,55218987..55219055,
                     55220239..55220357,55221704..55221845,55223523..55223639,
                     55224226..55224352,55224452..55224525,55225356..55225446,
                     55227832..55228031,55229192..55229324,55231426..55231516,
                     55232973..55233130,55238000..55238237)
                     /gene="EGFR"
                     /gene_synonym="ERBB; ERBB1; HER1; mENA; PIG61"
                     /note="isoform d precursor is encoded by transcript
                     variant 4; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="epidermal growth factor receptor isoform d
                     precursor"
                     /protein_id="NP_958441.1"
                     /db_xref="GI:41327736"
                     /db_xref="CCDS:CCDS5515.1"
                     /db_xref="GeneID:1956"
                     /db_xref="HGNC:3236"
                     /db_xref="HPRD:00579"
                     /db_xref="MIM:131550"
     CDS             join(55086971..55087058,55209979..55210130,
                     55210998..55211181,55214299..55214433,55218987..55219055,
                     55220239..55220357,55221704..55221845,55223523..55223639,
                     55224226..55224352,55224452..55224525,55225356..55225446,
                     55227832..55228031,55229192..55229324,55231426..55231516,
                     55232973..55233130,55236216..55236222)
                     /gene="EGFR"
                     /gene_synonym="ERBB; ERBB1; HER1; mENA; PIG61"
                     /note="isoform b precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="epidermal growth factor receptor isoform b
                     precursor"
                     /protein_id="NP_958439.1"
                     /db_xref="GI:41327732"
                     /db_xref="CCDS:CCDS5516.1"
                     /db_xref="GeneID:1956"
                     /db_xref="HGNC:3236"
                     /db_xref="HPRD:00579"
                     /db_xref="MIM:131550"
     CDS             join(55086971..55087058,55209979..55210130,
                     55210998..55211181,55214299..55214433,55218987..55219055,
                     55220239..55220357,55221704..55221845,55223523..55223639,
                     55224226..55224352,55224452..55224536)
                     /gene="EGFR"
                     /gene_synonym="ERBB; ERBB1; HER1; mENA; PIG61"
                     /note="isoform c precursor is encoded by transcript
                     variant 3; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="epidermal growth factor receptor isoform c
                     precursor"
                     /protein_id="NP_958440.1"
                     /db_xref="GI:41327734"
                     /db_xref="CCDS:CCDS47587.1"
                     /db_xref="GeneID:1956"
                     /db_xref="HGNC:3236"
                     /db_xref="HPRD:00579"
                     /db_xref="MIM:131550"
     gene            complement(55247443..55256648)
                     /gene="LOC100507500"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 mRNAs, 4 ESTs"
                     /db_xref="GeneID:100507500"
     misc_RNA        complement(join(55247443..55250170,55256550..55256648))
                     /gene="LOC100507500"
                     /product="hypothetical LOC100507500"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 mRNAs, 4 ESTs"
                     /transcript_id="XR_110544.1"
                     /db_xref="GI:310119973"
                     /db_xref="GeneID:100507500"
     gene            55311940..55313374
                     /gene="LOC100130121"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100130121"
     gene            complement(55327411..55327794)
                     /gene="CALM1P2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:804"
                     /db_xref="HGNC:1444"
     gene            55410009..55412651
                     /gene="LOC100129276"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129276"
     gene            55433141..55501435
                     /gene="LANCL2"
                     /gene_synonym="GPR69B; MGC87139; TASP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55915"
                     /db_xref="HGNC:6509"
                     /db_xref="HPRD:13956"
                     /db_xref="MIM:612919"
     mRNA            join(55433141..55433922,55459486..55459603,
                     55466116..55466323,55467650..55467797,55468867..55469013,
                     55479600..55479782,55492947..55493123,55496068..55496140,
                     55498919..55501435)
                     /gene="LANCL2"
                     /gene_synonym="GPR69B; MGC87139; TASP"
                     /product="LanC lantibiotic synthetase component C-like 2
                     (bacterial)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018697.3"
                     /db_xref="GI:50593015"
                     /db_xref="GeneID:55915"
                     /db_xref="HGNC:6509"
                     /db_xref="HPRD:13956"
                     /db_xref="MIM:612919"
     CDS             join(55433719..55433922,55459486..55459603,
                     55466116..55466323,55467650..55467797,55468867..55469013,
                     55479600..55479782,55492947..55493123,55496068..55496140,
                     55498919..55499013)
                     /gene="LANCL2"
                     /gene_synonym="GPR69B; MGC87139; TASP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="lanC-like protein 2"
                     /protein_id="NP_061167.1"
                     /db_xref="GI:8923911"
                     /db_xref="CCDS:CCDS5517.1"
                     /db_xref="GeneID:55915"
                     /db_xref="HGNC:6509"
                     /db_xref="HPRD:13956"
                     /db_xref="MIM:612919"
     gene            complement(55538306..55640200)
                     /gene="VOPP1"
                     /gene_synonym="DKFZp564K0822; ECOP; FLJ20532; GASP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:81552"
                     /db_xref="HGNC:34518"
                     /db_xref="HPRD:08526"
                     /db_xref="MIM:611915"
     mRNA            complement(join(55538306..55540738,55559975..55560111,
                     55565306..55565383,55588765..55588823,55639964..55640200))
                     /gene="VOPP1"
                     /gene_synonym="DKFZp564K0822; ECOP; FLJ20532; GASP"
                     /product="vesicular, overexpressed in cancer, prosurvival
                     protein 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_030796.3"
                     /db_xref="GI:106507238"
                     /db_xref="GeneID:81552"
                     /db_xref="HGNC:34518"
                     /db_xref="HPRD:08526"
                     /db_xref="MIM:611915"
     CDS             complement(join(55540548..55540738,55559975..55560111,
                     55565306..55565383,55588765..55588823,55639964..55640017))
                     /gene="VOPP1"
                     /gene_synonym="DKFZp564K0822; ECOP; FLJ20532; GASP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="vesicular, overexpressed in cancer, prosurvival
                     protein 1"
                     /protein_id="NP_110423.3"
                     /db_xref="GI:106507239"
                     /db_xref="CCDS:CCDS47588.1"
                     /db_xref="GeneID:81552"
                     /db_xref="HGNC:34518"
                     /db_xref="HPRD:08526"
                     /db_xref="MIM:611915"
     gene            complement(55705826..55706598)
                     /gene="CDC42P2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:643336"
                     /db_xref="HGNC:33952"
     gene            55713312..55714643
                     /gene="LOC442308"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442308"
     gene            complement(55726689..55746170)
                     /gene="LOC643348"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:643348"
     gene            complement(55748767..55772260)
                     /gene="FKBP9L"
                     /gene_synonym="MGC20531"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:360132"
                     /db_xref="HGNC:23568"
     misc_RNA        complement(join(55748767..55750518,55752865..55753028,
                     55755472..55755617,55759007..55759193,55766696..55766841,
                     55772219..55772260))
                     /gene="FKBP9L"
                     /gene_synonym="MGC20531"
                     /product="FK506 binding protein 9-like, transcript variant
                     4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003949.1"
                     /db_xref="GI:158081749"
                     /db_xref="GeneID:360132"
                     /db_xref="HGNC:23568"
     misc_RNA        complement(join(55748767..55750518,55752865..55753028,
                     55755472..55755617,55756675..55757153))
                     /gene="FKBP9L"
                     /gene_synonym="MGC20531"
                     /product="FK506 binding protein 9-like, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_027339.1"
                     /db_xref="GI:224994165"
                     /db_xref="GeneID:360132"
                     /db_xref="HGNC:23568"
     misc_RNA        complement(join(55748767..55750518,55752865..55753028,
                     55755472..55755617,55756606..55756994))
                     /gene="FKBP9L"
                     /gene_synonym="MGC20531"
                     /product="FK506 binding protein 9-like, transcript variant
                     3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_027342.1"
                     /db_xref="GI:224994167"
                     /db_xref="GeneID:360132"
                     /db_xref="HGNC:23568"
     misc_RNA        complement(join(55748767..55750518,55752865..55753028,
                     55755472..55755725))
                     /gene="FKBP9L"
                     /gene_synonym="MGC20531"
                     /product="FK506 binding protein 9-like, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_027340.1"
                     /db_xref="GI:224994166"
                     /db_xref="GeneID:360132"
                     /db_xref="HGNC:23568"
     gene            complement(55778997..55780921)
                     /gene="LOC100420539"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420539"
     gene            55799717..55800706
                     /gene="SUMO2P3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:652489"
                     /db_xref="HGNC:39013"
     gene            55804472..55808193
                     /gene="CICP11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100288904"
                     /db_xref="HGNC:37903"
     gene            complement(55808486..55809263)
                     /gene="LOC730376"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /db_xref="GeneID:730376"
     misc_RNA        complement(55808486..55809263)
                     /gene="LOC730376"
                     /product="hypothetical LOC730376"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /transcript_id="XR_110545.1"
                     /db_xref="GI:310119974"
                     /db_xref="GeneID:730376"
     gene            complement(55810070..55811221)
                     /gene="LOC100419984"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419984"
     gene            complement(55814590..55815779)
                     /gene="LOC100128326"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 4 Proteins"
                     /db_xref="GeneID:100128326"
     mRNA            complement(55814590..55815779)
                     /gene="LOC100128326"
                     /product="putative uncharacterized protein FLJ44672-like"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 4 Proteins"
                     /transcript_id="XM_002342720.2"
                     /db_xref="GI:310119977"
                     /db_xref="GeneID:100128326"
     CDS             complement(55814590..55815779)
                     /gene="LOC100128326"
                     /exception="unclassified translation discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="putative uncharacterized protein FLJ44672-like"
                     /protein_id="XP_002342761.2"
                     /db_xref="GI:310119978"
                     /db_xref="GeneID:100128326"
     gene            55832490..55841389
                     /gene="PSPHL"
                     /gene_synonym="CO9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:8781"
                     /db_xref="HGNC:9578"
                     /db_xref="MIM:604239"
     gene            complement(55861237..55930482)
                     /gene="SEPT14"
                     /gene_synonym="FLJ44060"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:346288"
                     /db_xref="HGNC:33280"
                     /db_xref="HPRD:16972"
                     /db_xref="MIM:612140"
     mRNA            complement(join(55861237..55863785,55872951..55873083,
                     55874783..55874951,55886820..55886916,55902118..55902279,
                     55910635..55910821,55912216..55912411,55914210..55914330,
                     55929636..55929704,55930381..55930482))
                     /gene="SEPT14"
                     /gene_synonym="FLJ44060"
                     /product="septin 14"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_207366.2"
                     /db_xref="GI:153252197"
                     /db_xref="GeneID:346288"
                     /db_xref="HGNC:33280"
                     /db_xref="HPRD:16972"
                     /db_xref="MIM:612140"
     CDS             complement(join(55863606..55863785,55872951..55873083,
                     55874783..55874951,55886820..55886916,55902118..55902279,
                     55910635..55910821,55912216..55912411,55914210..55914330,
                     55929636..55929689))
                     /gene="SEPT14"
                     /gene_synonym="FLJ44060"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="septin-14"
                     /protein_id="NP_997249.2"
                     /db_xref="GI:153252198"
                     /db_xref="CCDS:CCDS5519.2"
                     /db_xref="GeneID:346288"
                     /db_xref="HGNC:33280"
                     /db_xref="HPRD:16972"
                     /db_xref="MIM:612140"
     gene            55865727..55866569
                     /gene="CICP12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420224"
                     /db_xref="HGNC:37905"
     gene            complement(55878460..55879104)
                     /gene="LOC100420540"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420540"
     gene            55980331..56008433
                     /gene="ZNF713"
                     /gene_synonym="FLJ39963"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:349075"
                     /db_xref="HGNC:22043"
                     /db_xref="HPRD:13440"
     mRNA            join(55980331..55980416,55990855..55990981,
                     55991300..55991392,56006675..56008433)
                     /gene="ZNF713"
                     /gene_synonym="FLJ39963"
                     /product="zinc finger protein 713"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182633.1"
                     /db_xref="GI:33438599"
                     /db_xref="GeneID:349075"
                     /db_xref="HGNC:22043"
                     /db_xref="HPRD:13440"
     CDS             join(55980369..55980416,55990855..55990981,
                     55991300..55991392,56006675..56007699)
                     /gene="ZNF713"
                     /gene_synonym="FLJ39963"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 713"
                     /protein_id="NP_872439.1"
                     /db_xref="GI:33438600"
                     /db_xref="CCDS:CCDS34639.1"
                     /db_xref="GeneID:349075"
                     /db_xref="HGNC:22043"
                     /db_xref="HPRD:13440"
     gene            56019611..56023034
                     /gene="MRPS17"
                     /gene_synonym="HSPC011; MRP-S17; RPMS17"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51373"
                     /db_xref="HGNC:14047"
                     /db_xref="HPRD:14779"
                     /db_xref="MIM:611980"
     mRNA            join(56019611..56019623,56020872..56021011,
                     56022602..56023034)
                     /gene="MRPS17"
                     /gene_synonym="HSPC011; MRP-S17; RPMS17"
                     /product="mitochondrial ribosomal protein S17"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015969.2"
                     /db_xref="GI:16554613"
                     /db_xref="GeneID:51373"
                     /db_xref="HGNC:14047"
                     /db_xref="HPRD:14779"
                     /db_xref="MIM:611980"
     CDS             join(56020889..56021011,56022602..56022871)
                     /gene="MRPS17"
                     /gene_synonym="HSPC011; MRP-S17; RPMS17"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="28S ribosomal protein S17, mitochondrial
                     precursor"
                     /protein_id="NP_057053.1"
                     /db_xref="GI:7705425"
                     /db_xref="CCDS:CCDS5520.1"
                     /db_xref="GeneID:51373"
                     /db_xref="HGNC:14047"
                     /db_xref="HPRD:14779"
                     /db_xref="MIM:611980"
     gene            56032270..56067875
                     /gene="GBAS"
                     /gene_synonym="NIPSNAP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2631"
                     /db_xref="HGNC:4179"
                     /db_xref="HPRD:04302"
                     /db_xref="MIM:603004"
     mRNA            join(56032270..56032394,56045819..56045958,
                     56046043..56046088,56049166..56049260,56049903..56049973,
                     56051421..56051561,56052540..56052571,56062587..56062681,
                     56065059..56065142,56066701..56067875)
                     /gene="GBAS"
                     /gene_synonym="NIPSNAP2"
                     /product="glioblastoma amplified sequence, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001483.2"
                     /db_xref="GI:321267475"
                     /db_xref="GeneID:2631"
                     /db_xref="HGNC:4179"
                     /db_xref="HPRD:04302"
                     /db_xref="MIM:603004"
     mRNA            join(56032270..56032394,56045819..56045958,
                     56049166..56049260,56051421..56051561,56052540..56052571,
                     56062587..56062681,56065059..56065142,56066701..56067875)
                     /gene="GBAS"
                     /gene_synonym="NIPSNAP2"
                     /product="glioblastoma amplified sequence, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001202469.1"
                     /db_xref="GI:321267476"
                     /db_xref="GeneID:2631"
                     /db_xref="HGNC:4179"
                     /db_xref="MIM:603004"
                     /db_xref="HPRD:04302"
     CDS             join(56032303..56032394,56045819..56045958,
                     56046043..56046088,56049166..56049260,56049903..56049973,
                     56051421..56051561,56052540..56052571,56062587..56062681,
                     56065059..56065142,56066701..56066765)
                     /gene="GBAS"
                     /gene_synonym="NIPSNAP2"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein NipSnap homolog 2 isoform 1"
                     /protein_id="NP_001474.1"
                     /db_xref="GI:4503937"
                     /db_xref="CCDS:CCDS5521.1"
                     /db_xref="GeneID:2631"
                     /db_xref="HGNC:4179"
                     /db_xref="HPRD:04302"
                     /db_xref="MIM:603004"
     CDS             join(56032303..56032394,56045819..56045958,
                     56049166..56049260,56051421..56051561,56052540..56052571,
                     56062587..56062681,56065059..56065142,56066701..56066765)
                     /gene="GBAS"
                     /gene_synonym="NIPSNAP2"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein NipSnap homolog 2 isoform 2"
                     /protein_id="NP_001189398.1"
                     /db_xref="GI:321267477"
                     /db_xref="GeneID:2631"
                     /db_xref="HGNC:4179"
                     /db_xref="MIM:603004"
                     /db_xref="HPRD:04302"
     gene            complement(56078744..56119268)
                     /gene="PSPH"
                     /gene_synonym="PSP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5723"
                     /db_xref="HGNC:9577"
                     /db_xref="HPRD:01406"
                     /db_xref="MIM:172480"
     mRNA            complement(join(56078744..56079562,56082716..56082864,
                     56084927..56085072,56087293..56087427,56088766..56088924,
                     56099622..56099747,56101654..56101799,56118831..56119268))
                     /gene="PSPH"
                     /gene_synonym="PSP"
                     /product="phosphoserine phosphatase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004577.3"
                     /db_xref="GI:46249387"
                     /db_xref="GeneID:5723"
                     /db_xref="HGNC:9577"
                     /db_xref="HPRD:01406"
                     /db_xref="MIM:172480"
     CDS             complement(join(56079455..56079562,56082716..56082864,
                     56084927..56085072,56087293..56087427,56088766..56088905))
                     /gene="PSPH"
                     /gene_synonym="PSP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="phosphoserine phosphatase"
                     /protein_id="NP_004568.2"
                     /db_xref="GI:46249388"
                     /db_xref="CCDS:CCDS5522.1"
                     /db_xref="GeneID:5723"
                     /db_xref="HGNC:9577"
                     /db_xref="HPRD:01406"
                     /db_xref="MIM:172480"
     gene            56119378..56131682
                     /gene="CCT6A"
                     /gene_synonym="CCT-zeta; CCT-zeta-1; CCT6; Cctz; HTR3;
                     MGC126214; MGC126215; MoDP-2; TCP-1-zeta; TCP20; TCPZ;
                     TTCP20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:908"
                     /db_xref="HGNC:1620"
                     /db_xref="HPRD:00089"
                     /db_xref="MIM:104613"
     mRNA            join(56119378..56119678,56120115..56120178,
                     56122062..56122196,56123317..56123490,56124004..56124107,
                     56125686..56125796,56126055..56126214,56126313..56126395,
                     56127237..56127333,56127962..56128109,56128500..56128633,
                     56129440..56129542,56130376..56130448,56130706..56131682)
                     /gene="CCT6A"
                     /gene_synonym="CCT-zeta; CCT-zeta-1; CCT6; Cctz; HTR3;
                     MGC126214; MGC126215; MoDP-2; TCP-1-zeta; TCP20; TCPZ;
                     TTCP20"
                     /product="chaperonin containing TCP1, subunit 6A (zeta 1),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001762.3"
                     /db_xref="GI:58331169"
                     /db_xref="GeneID:908"
                     /db_xref="HGNC:1620"
                     /db_xref="HPRD:00089"
                     /db_xref="MIM:104613"
     mRNA            join(56119378..56119678,56120115..56120178,
                     56123317..56123490,56124004..56124107,56125686..56125796,
                     56126055..56126214,56126313..56126395,56127237..56127333,
                     56127962..56128109,56128500..56128633,56129440..56129542,
                     56130376..56130448,56130706..56131682)
                     /gene="CCT6A"
                     /gene_synonym="CCT-zeta; CCT-zeta-1; CCT6; Cctz; HTR3;
                     MGC126214; MGC126215; MoDP-2; TCP-1-zeta; TCP20; TCPZ;
                     TTCP20"
                     /product="chaperonin containing TCP1, subunit 6A (zeta 1),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001009186.1"
                     /db_xref="GI:58331170"
                     /db_xref="GeneID:908"
                     /db_xref="HGNC:1620"
                     /db_xref="HPRD:00089"
                     /db_xref="MIM:104613"
     CDS             join(56119542..56119678,56120115..56120178,
                     56122062..56122196,56123317..56123490,56124004..56124107,
                     56125686..56125796,56126055..56126214,56126313..56126395,
                     56127237..56127333,56127962..56128109,56128500..56128633,
                     56129440..56129542,56130376..56130448,56130706..56130778)
                     /gene="CCT6A"
                     /gene_synonym="CCT-zeta; CCT-zeta-1; CCT6; Cctz; HTR3;
                     MGC126214; MGC126215; MoDP-2; TCP-1-zeta; TCP20; TCPZ;
                     TTCP20"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="T-complex protein 1 subunit zeta isoform a"
                     /protein_id="NP_001753.1"
                     /db_xref="GI:4502643"
                     /db_xref="CCDS:CCDS5523.1"
                     /db_xref="GeneID:908"
                     /db_xref="HGNC:1620"
                     /db_xref="HPRD:00089"
                     /db_xref="MIM:104613"
     CDS             join(56119542..56119678,56120115..56120178,
                     56123317..56123490,56124004..56124107,56125686..56125796,
                     56126055..56126214,56126313..56126395,56127237..56127333,
                     56127962..56128109,56128500..56128633,56129440..56129542,
                     56130376..56130448,56130706..56130778)
                     /gene="CCT6A"
                     /gene_synonym="CCT-zeta; CCT-zeta-1; CCT6; Cctz; HTR3;
                     MGC126214; MGC126215; MoDP-2; TCP-1-zeta; TCP20; TCPZ;
                     TTCP20"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="T-complex protein 1 subunit zeta isoform b"
                     /protein_id="NP_001009186.1"
                     /db_xref="GI:58331171"
                     /db_xref="CCDS:CCDS34640.1"
                     /db_xref="GeneID:908"
                     /db_xref="HGNC:1620"
                     /db_xref="HPRD:00089"
                     /db_xref="MIM:104613"
     gene            56128163..56128295
                     /gene="SNORA15"
                     /gene_synonym="ACA15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:677803"
                     /db_xref="HGNC:32604"
     ncRNA           56128163..56128295
                     /gene="SNORA15"
                     /gene_synonym="ACA15"
                     /ncRNA_class="snoRNA"
                     /product="small nucleolar RNA, H/ACA box 15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_002957.1"
                     /db_xref="GI:91680824"
                     /db_xref="GeneID:677803"
                     /db_xref="HGNC:32604"
     gene            56131917..56148365
                     /gene="SUMF2"
                     /gene_synonym="DKFZp566I1024; DKFZp686I1024;
                     DKFZp686L17160; DKFZp781L1035; MGC99485; pFGE"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:25870"
                     /db_xref="HGNC:20415"
                     /db_xref="HPRD:06400"
                     /db_xref="MIM:607940"
     mRNA            join(56131917..56132071,56136175..56136331,
                     56140690..56140804,56141867..56141911,56142279..56142429,
                     56144527..56144582,56145795..56145879,56146057..56146201,
                     56147221..56148365)
                     /gene="SUMF2"
                     /gene_synonym="DKFZp566I1024; DKFZp686I1024;
                     DKFZp686L17160; DKFZp781L1035; MGC99485; pFGE"
                     /product="sulfatase modifying factor 2, transcript variant
                     2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015411.2"
                     /db_xref="GI:110227849"
                     /db_xref="GeneID:25870"
                     /db_xref="HGNC:20415"
                     /db_xref="HPRD:06400"
                     /db_xref="MIM:607940"
     mRNA            join(56131917..56132071,56136175..56136331,
                     56140690..56140804,56142279..56142429,56144527..56144582,
                     56145795..56145879,56146057..56146201,56147221..56148365)
                     /gene="SUMF2"
                     /gene_synonym="DKFZp566I1024; DKFZp686I1024;
                     DKFZp686L17160; DKFZp781L1035; MGC99485; pFGE"
                     /product="sulfatase modifying factor 2, transcript variant
                     3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001042469.1"
                     /db_xref="GI:110227850"
                     /db_xref="GeneID:25870"
                     /db_xref="HGNC:20415"
                     /db_xref="MIM:607940"
                     /db_xref="HPRD:06400"
     mRNA            join(56131917..56132071,56136175..56136331,
                     56140690..56140804,56145795..56145879,56146057..56146201,
                     56147221..56148365)
                     /gene="SUMF2"
                     /gene_synonym="DKFZp566I1024; DKFZp686I1024;
                     DKFZp686L17160; DKFZp781L1035; MGC99485; pFGE"
                     /product="sulfatase modifying factor 2, transcript variant
                     4"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001042470.1"
                     /db_xref="GI:110227852"
                     /db_xref="GeneID:25870"
                     /db_xref="HGNC:20415"
                     /db_xref="MIM:607940"
                     /db_xref="HPRD:06400"
     mRNA            join(56131917..56132071,56136175..56136331,
                     56140690..56140804,56141867..56141911,56142279..56142429,
                     56144527..56144582,56145795..56145879,56147221..56148365)
                     /gene="SUMF2"
                     /gene_synonym="DKFZp566I1024; DKFZp686I1024;
                     DKFZp686L17160; DKFZp781L1035; MGC99485; pFGE"
                     /product="sulfatase modifying factor 2, transcript variant
                     5"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130069.1"
                     /db_xref="GI:194248089"
                     /db_xref="GeneID:25870"
                     /db_xref="HGNC:20415"
                     /db_xref="MIM:607940"
                     /db_xref="HPRD:06400"
     mRNA            join(56131917..56132071,56140690..56140804,
                     56141867..56141911,56142279..56142429,56144527..56144582,
                     56145795..56145879,56146057..56146201,56147221..56148365)
                     /gene="SUMF2"
                     /gene_synonym="DKFZp566I1024; DKFZp686I1024;
                     DKFZp686L17160; DKFZp781L1035; MGC99485; pFGE"
                     /product="sulfatase modifying factor 2, transcript variant
                     7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001146333.1"
                     /db_xref="GI:226437576"
                     /db_xref="GeneID:25870"
                     /db_xref="HGNC:20415"
                     /db_xref="MIM:607940"
                     /db_xref="HPRD:06400"
     CDS             join(56131948..56132071,56136175..56136331,
                     56140690..56140804,56141867..56141911,56142279..56142429,
                     56144527..56144582,56145795..56145879,56147221..56147564)
                     /gene="SUMF2"
                     /gene_synonym="DKFZp566I1024; DKFZp686I1024;
                     DKFZp686L17160; DKFZp781L1035; MGC99485; pFGE"
                     /exception="mismatches in translation"
                     /note="isoform e precursor is encoded by transcript
                     variant 5; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="sulfatase-modifying factor 2 isoform e
                     precursor"
                     /protein_id="NP_001123541.1"
                     /db_xref="GI:194248090"
                     /db_xref="CCDS:CCDS47589.1"
                     /db_xref="GeneID:25870"
                     /db_xref="HGNC:20415"
                     /db_xref="HPRD:06400"
                     /db_xref="MIM:607940"
     CDS             join(56131948..56132071,56136175..56136331,
                     56140690..56140804,56141867..56141911,56142279..56142429,
                     56144527..56144582,56145795..56145879,56146057..56146201,
                     56147221..56147305)
                     /gene="SUMF2"
                     /gene_synonym="DKFZp566I1024; DKFZp686I1024;
                     DKFZp686L17160; DKFZp781L1035; MGC99485; pFGE"
                     /exception="mismatches in translation"
                     /note="isoform b precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="sulfatase-modifying factor 2 isoform b
                     precursor"
                     /protein_id="NP_056226.2"
                     /db_xref="GI:194248088"
                     /db_xref="CCDS:CCDS5524.2"
                     /db_xref="GeneID:25870"
                     /db_xref="HGNC:20415"
                     /db_xref="HPRD:06400"
                     /db_xref="MIM:607940"
     CDS             join(56131948..56132071,56136175..56136331,
                     56140690..56140804,56142279..56142429,56144527..56144582,
                     56145795..56145879,56146057..56146201,56147221..56147305)
                     /gene="SUMF2"
                     /gene_synonym="DKFZp566I1024; DKFZp686I1024;
                     DKFZp686L17160; DKFZp781L1035; MGC99485; pFGE"
                     /exception="mismatches in translation"
                     /note="isoform c precursor is encoded by transcript
                     variant 3; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="sulfatase-modifying factor 2 isoform c
                     precursor"
                     /protein_id="NP_001035934.2"
                     /db_xref="GI:194248087"
                     /db_xref="CCDS:CCDS43588.2"
                     /db_xref="GeneID:25870"
                     /db_xref="HGNC:20415"
                     /db_xref="HPRD:06400"
                     /db_xref="MIM:607940"
     CDS             join(56131948..56132071,56136175..56136331,
                     56140690..56140804,56145795..56145879,56146057..56146201,
                     56147221..56147305)
                     /gene="SUMF2"
                     /gene_synonym="DKFZp566I1024; DKFZp686I1024;
                     DKFZp686L17160; DKFZp781L1035; MGC99485; pFGE"
                     /exception="mismatches in translation"
                     /note="isoform d precursor is encoded by transcript
                     variant 4; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="sulfatase-modifying factor 2 isoform d
                     precursor"
                     /protein_id="NP_001035935.2"
                     /db_xref="GI:194248084"
                     /db_xref="CCDS:CCDS43589.2"
                     /db_xref="GeneID:25870"
                     /db_xref="HGNC:20415"
                     /db_xref="HPRD:06400"
                     /db_xref="MIM:607940"
     CDS             join(56140730..56140804,56141867..56141911,
                     56142279..56142429,56144527..56144582,56145795..56145879,
                     56146057..56146201,56147221..56147305)
                     /gene="SUMF2"
                     /gene_synonym="DKFZp566I1024; DKFZp686I1024;
                     DKFZp686L17160; DKFZp781L1035; MGC99485; pFGE"
                     /note="isoform g is encoded by transcript variant 7;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="sulfatase-modifying factor 2 isoform g"
                     /protein_id="NP_001139805.1"
                     /db_xref="GI:226437577"
                     /db_xref="CCDS:CCDS55111.1"
                     /db_xref="GeneID:25870"
                     /db_xref="HGNC:20415"
                     /db_xref="HPRD:06400"
                     /db_xref="MIM:607940"
     gene            complement(56148675..56160689)
                     /gene="PHKG1"
                     /gene_synonym="PHKG"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5260"
                     /db_xref="HGNC:8930"
                     /db_xref="HPRD:01404"
                     /db_xref="MIM:172470"
     mRNA            complement(join(56148675..56148992,56149323..56149448,
                     56149586..56149739,56149856..56149946,56150971..56151134,
                     56151343..56151408,56154663..56154717,56155291..56155469,
                     56156552..56156668,56160529..56160689))
                     /gene="PHKG1"
                     /gene_synonym="PHKG"
                     /product="phosphorylase kinase, gamma 1 (muscle)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006213.3"
                     /db_xref="GI:94538351"
                     /db_xref="GeneID:5260"
                     /db_xref="HGNC:8930"
                     /db_xref="HPRD:01404"
                     /db_xref="MIM:172470"
     CDS             complement(join(56148747..56148992,56149323..56149448,
                     56149586..56149739,56149856..56149946,56150971..56151134,
                     56151343..56151408,56154663..56154717,56155291..56155469,
                     56156552..56156634))
                     /gene="PHKG1"
                     /gene_synonym="PHKG"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="phosphorylase b kinase gamma catalytic chain,
                     skeletal muscle isoform"
                     /protein_id="NP_006204.1"
                     /db_xref="GI:5453882"
                     /db_xref="CCDS:CCDS5525.1"
                     /db_xref="GeneID:5260"
                     /db_xref="HGNC:8930"
                     /db_xref="HPRD:01404"
                     /db_xref="MIM:172470"
     gene            complement(56169266..56174187)
                     /gene="CHCHD2"
                     /gene_synonym="C7orf17"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51142"
                     /db_xref="HGNC:21645"
                     /db_xref="HPRD:09879"
     mRNA            complement(join(56169266..56169554,56170560..56170704,
                     56171919..56172168,56174057..56174187))
                     /gene="CHCHD2"
                     /gene_synonym="C7orf17"
                     /product="coiled-coil-helix-coiled-coil-helix domain
                     containing 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016139.2"
                     /db_xref="GI:32307179"
                     /db_xref="GeneID:51142"
                     /db_xref="HGNC:21645"
                     /db_xref="HPRD:09879"
     CDS             complement(join(56169544..56169554,56170560..56170704,
                     56171919..56172168,56174057..56174106))
                     /gene="CHCHD2"
                     /gene_synonym="C7orf17"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="coiled-coil-helix-coiled-coil-helix
                     domain-containing protein 2, mitochondrial precursor"
                     /protein_id="NP_057223.1"
                     /db_xref="GI:7705851"
                     /db_xref="CCDS:CCDS5526.1"
                     /db_xref="GeneID:51142"
                     /db_xref="HGNC:21645"
                     /db_xref="HPRD:09879"
     gene            complement(56182374..56184090)
                     /gene="LOC389493"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:389493"
     mRNA            complement(join(56182374..56182590,56183708..56184090))
                     /gene="LOC389493"
                     /product="hypothetical protein LOC389493"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145712.1"
                     /db_xref="GI:224589116"
                     /db_xref="GeneID:389493"
     CDS             complement(56183714..56184007)
                     /gene="LOC389493"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC389493"
                     /protein_id="NP_001139184.1"
                     /db_xref="GI:224589117"
                     /db_xref="GeneID:389493"
     gene            56230806..56231396
                     /gene="LOC442309"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442309"
     gene            56242160..56244177
                     /gene="LOC100130909"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100130909"
     exon            56242160..56242307
                     /gene="LOC100130909"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100130909"
     exon            56242454..56242892
                     /gene="LOC100130909"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100130909"
     exon            56242972..56243955
                     /gene="LOC100130909"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:100130909"
     exon            56243987..56244177
                     /gene="LOC100130909"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=4
                     /pseudo
                     /db_xref="GeneID:100130909"
     gene            complement(56296324..56297475)
                     /gene="CCNJP1"
                     /gene_synonym="CCNJP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100128459"
                     /db_xref="HGNC:22512"
     gene            56355480..56359674
                     /gene="LOC441228"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:441228"
     gene            complement(56371015..56373219)
                     /gene="LOC154937"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:154937"
     gene            56416079..56433841
                     /gene="CICP8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442676"
                     /db_xref="HGNC:37757"
     gene            complement(56434223..56434946)
                     /gene="LOC731631"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:731631"
     exon            complement(56434223..56434946)
                     /gene="LOC731631"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:731631"
     gene            complement(56438331..56439444)
                     /gene="LOC100419985"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419985"
     gene            complement(56439629..56440742)
                     /gene="LOC100533648"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533648"
     gene            complement(56440924..56441578)
                     /gene="LOC100419986"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419986"
     gene            complement(56442220..56443346)
                     /gene="LOC100533649"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533649"
     gene            complement(56445015..56445503)
                     /gene="LOC100132050"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /db_xref="GeneID:100132050"
     mRNA            complement(56445015..56445503)
                     /gene="LOC100132050"
                     /product="hypothetical protein LOC100132050"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /transcript_id="XM_002342721.2"
                     /db_xref="GI:310119979"
                     /db_xref="GeneID:100132050"
     CDS             complement(56445015..56445503)
                     /gene="LOC100132050"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="hypothetical protein LOC100132050"
                     /protein_id="XP_002342762.1"
                     /db_xref="GI:239743158"
                     /db_xref="GeneID:100132050"
     gene            complement(56445530..56446754)
                     /gene="LOC100507369"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 1 Protein"
                     /db_xref="GeneID:100507369"
     mRNA            complement(join(56445530..56445592,56445678..56446229,
                     56446689..56446754))
                     /gene="LOC100507369"
                     /product="putative uncharacterized protein encoded by
                     NCRNA00174-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 1 Protein"
                     /transcript_id="XM_003118987.1"
                     /db_xref="GI:310119980"
                     /db_xref="GeneID:100507369"
     CDS             complement(join(56445530..56445592,56445678..56446229,
                     56446689..56446754))
                     /gene="LOC100507369"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="putative uncharacterized protein encoded by
                     NCRNA00174-like"
                     /protein_id="XP_003119035.1"
                     /db_xref="GI:310119981"
                     /db_xref="GeneID:100507369"
     gene            complement(56491397..56516068)
                     /gene="LOC650226"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:650226"
     misc_RNA        complement(join(56491397..56492330,56493828..56493956,
                     56494528..56494703,56496078..56496134,56500181..56500394,
                     56515912..56516068))
                     /gene="LOC650226"
                     /product="ankyrin repeat domain 26 pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_029420.1"
                     /db_xref="GI:261862239"
                     /db_xref="GeneID:650226"
     gene            56515651..56535232
                     /gene="LOC728376"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:728376"
     gene            56558300..56559330
                     /gene="RBM22P3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100128867"
                     /db_xref="HGNC:39696"
     gene            56563916..56564977
                     /gene="DKFZp434L192"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222029"
     misc_RNA        56563916..56564977
                     /gene="DKFZp434L192"
                     /product="hypothetical protein DKFZp434L192"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_026929.1"
                     /db_xref="GI:223941934"
                     /db_xref="GeneID:222029"
     gene            complement(56568578..56568836)
                     /gene="VN1R24P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312781"
                     /db_xref="HGNC:37344"
     gene            complement(56569977..56570737)
                     /gene="NMD3P2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100286929"
                     /db_xref="HGNC:37820"
     gene            complement(56593121..56593806)
                     /gene="LOC100419642"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419642"
     gene            56626806..56627717
                     /gene="VN1R25P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312782"
                     /db_xref="HGNC:37345"
     gene            complement(56635602..56636640)
                     /gene="LOC100130210"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100130210"
     gene            56665244..56669238
                     /gene="LOC346296"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:346296"
     gene            56671103..56671246
                     /gene="LOC100289196"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /db_xref="GeneID:100289196"
     mRNA            56671103..56671246
                     /gene="LOC100289196"
                     /product="hypothetical protein LOC100289196"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /transcript_id="XM_002342722.1"
                     /db_xref="GI:239743159"
                     /db_xref="GeneID:100289196"
     CDS             56671103..56671246
                     /gene="LOC100289196"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="hypothetical protein LOC100289196"
                     /protein_id="XP_002342763.1"
                     /db_xref="GI:239743160"
                     /db_xref="GeneID:100289196"
     gene            complement(56699429..56700420)
                     /gene="TRIM60P16"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420412"
                     /db_xref="HGNC:38488"
     gene            complement(56707031..56718390)
                     /gene="LOC100533632"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533632"
     gene            complement(56748838..56749350)
                     /gene="VN1R26P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312783"
                     /db_xref="HGNC:37346"
     gene            complement(56752729..56753889)
                     /gene="LOC100533633"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533633"
     gene            complement(56803903..56804304)
                     /gene="LOC728416"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:728416"
     gene            56871232..56872341
                     /gene="LOC100533652"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533652"
     gene            56873032..56875346
                     /gene="LOC100287136"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100287136"
     gene            complement(56879492..56880139)
                     /gene="LOC401357"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /db_xref="GeneID:401357"
     misc_RNA        complement(56879492..56880139)
                     /gene="LOC401357"
                     /product="hypothetical LOC401357"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /transcript_id="XR_132811.1"
                     /db_xref="GI:341915385"
                     /db_xref="GeneID:401357"
     gene            complement(56881183..56881881)
                     /gene="LOC100652873"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100652873"
     exon            complement(56881183..56881365)
                     /gene="LOC100652873"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100652873"
     exon            complement(56881414..56881881)
                     /gene="LOC100652873"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100652873"
     gene            complement(56883245..56884446)
                     /gene="LOC100419987"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419987"
     gene            complement(56885131..56886281)
                     /gene="LOC100533650"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533650"
     gene            complement(56886969..56888119)
                     /gene="LOC100533651"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533651"
     gene            complement(56888951..56890152)
                     /gene="LOC100507393"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100507393"
     gene            complement(56890421..56891226)
                     /gene="LOC100652879"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100652879"
     exon            complement(56890421..56890603)
                     /gene="LOC100652879"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100652879"
     exon            complement(56890748..56891226)
                     /gene="LOC100652879"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100652879"
     gene            complement(56892268..56892966)
                     /gene="LOC100652881"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100652881"
     exon            complement(56892268..56892450)
                     /gene="LOC100652881"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100652881"
     exon            complement(56892499..56892966)
                     /gene="LOC100652881"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100652881"
     gene            complement(56892986..56894804)
                     /gene="LOC100287197"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100287197"
     exon            complement(56892986..56893460)
                     /gene="LOC100287197"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=4
                     /pseudo
                     /db_xref="GeneID:100287197"
     exon            complement(56893738..56893910)
                     /gene="LOC100287197"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:100287197"
     exon            complement(56894025..56894192)
                     /gene="LOC100287197"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100287197"
     exon            complement(56894337..56894804)
                     /gene="LOC100287197"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100287197"
     gene            complement(56898080..56898582)
                     /gene="LOC100289306"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100289306"
     misc_RNA        complement(56898080..56898582)
                     /gene="LOC100289306"
                     /product="hypothetical LOC100289306"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 1 Protein"
                     /pseudo
                     /transcript_id="XR_132812.1"
                     /db_xref="GI:341915386"
                     /db_xref="GeneID:100289306"
     gene            complement(56898609..56935716)
                     /gene="LOC100287258"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100287258"
     exon            complement(56898609..56898671)
                     /gene="LOC100287258"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=4
                     /pseudo
                     /db_xref="GeneID:100287258"
     exon            complement(56898757..56899057)
                     /gene="LOC100287258"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:100287258"
     exon            complement(56900436..56900683)
                     /gene="LOC100287258"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100287258"
     exon            complement(56935660..56935716)
                     /gene="LOC100287258"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100287258"
     gene            complement(56943078..56949839)
                     /gene="LOC100130849"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:100130849"
     misc_RNA        complement(join(56943078..56943151,56943262..56943378,
                     56945065..56945243,56947815..56947924,56949756..56949839))
                     /gene="LOC100130849"
                     /product="phosphorylase kinase, gamma 1 (muscle)
                     pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_038450.1"
                     /db_xref="GI:336285222"
                     /db_xref="GeneID:100130849"
     gene            complement(56991848..57012060)
                     /gene="LOC100287294"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /db_xref="GeneID:100287294"
     mRNA            complement(join(56991848..56991960,56993826..56993910,
                     56994669..56994791,57008048..57008139,57008630..57008743,
                     57009003..57009134,57011892..57012060))
                     /gene="LOC100287294"
                     /product="equilibrative nucleoside transporter 4-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /transcript_id="XM_002342726.2"
                     /db_xref="GI:310119983"
                     /db_xref="GeneID:100287294"
     CDS             complement(join(56991848..56991960,56993826..56993910,
                     56994669..56994791,57008048..57008139,57008630..57008743,
                     57009003..57009134,57011892..57012060))
                     /gene="LOC100287294"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="equilibrative nucleoside transporter 4-like"
                     /protein_id="XP_002342767.2"
                     /db_xref="GI:310119984"
                     /db_xref="GeneID:100287294"
     gene            complement(57023492..57023571)
                     /gene="MIR4283-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100422917"
                     /db_xref="HGNC:38238"
                     /db_xref="miRBase:MI0015892"
     ncRNA           complement(57023492..57023571)
                     /gene="MIR4283-1"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4283-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_036246.1"
                     /db_xref="GI:301172441"
                     /db_xref="GeneID:100422917"
                     /db_xref="HGNC:38238"
                     /db_xref="miRBase:MI0015892"
     gene            57063241..57076859
                     /gene="TNRC18C"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:340221"
                     /db_xref="HGNC:34015"
     gene            complement(57081992..57087978)
                     /gene="LOC402509"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402509"
     gene            complement(57128219..57129008)
                     /gene="PHKG1P4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100151641"
                     /db_xref="HGNC:33918"
     gene            complement(57135656..57142390)
                     /gene="LOC100418714"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100418714"
     gene            complement(57187321..57207571)
                     /gene="ZNF479"
                     /gene_synonym="KR19"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:90827"
                     /db_xref="HGNC:23258"
     mRNA            complement(join(57187321..57188859,57193725..57193820,
                     57194299..57194425,57199993..57200045,57207315..57207571))
                     /gene="ZNF479"
                     /gene_synonym="KR19"
                     /product="zinc finger protein 479"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033273.1"
                     /db_xref="GI:149274616"
                     /db_xref="GeneID:90827"
                     /db_xref="HGNC:23258"
     CDS             complement(join(57187547..57188859,57193725..57193820,
                     57194299..57194425,57199993..57200031))
                     /gene="ZNF479"
                     /gene_synonym="KR19"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 479"
                     /protein_id="NP_150376.1"
                     /db_xref="GI:149274617"
                     /db_xref="CCDS:CCDS43590.1"
                     /db_xref="GeneID:90827"
                     /db_xref="HGNC:23258"
     gene            complement(57214508..57218254)
                     /gene="LOC100101483"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100101483"
     gene            complement(57227866..57228239)
                     /gene="VN1R27P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312784"
                     /db_xref="HGNC:37347"
     gene            complement(57233377..57247863)
                     /gene="GUSBP10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:642006"
                     /db_xref="HGNC:42324"
     misc_RNA        complement(join(57233377..57233726,57245082..57245235,
                     57245908..57246093,57247576..57247863))
                     /gene="GUSBP10"
                     /product="glucuronidase, beta pseudogene 10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_030766.1"
                     /db_xref="GI:268834521"
                     /db_xref="GeneID:642006"
                     /db_xref="HGNC:42324"
     gene            complement(57253980..57254051)
                     /gene="TRNAQ52P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100189535"
                     /db_xref="HGNC:35112"
     gene            complement(57268531..57271376)
                     /gene="GUSBP12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:642007"
                     /db_xref="HGNC:42326"
     gene            57341960..57342561
                     /gene="LOC100419779"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419779"
     gene            57472731..57472796
                     /gene="MIR3147"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100422939"
                     /db_xref="HGNC:38300"
                     /db_xref="miRBase:MI0014173"
     ncRNA           57472731..57472796
                     /gene="MIR3147"
                     /ncRNA_class="miRNA"
                     /product="microRNA 3147"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_036102.1"
                     /db_xref="GI:301171258"
                     /db_xref="GeneID:100422939"
                     /db_xref="HGNC:38300"
                     /db_xref="miRBase:MI0014173"
     gene            complement(57482489..57483407)
                     /gene="VN1R28P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312785"
                     /db_xref="HGNC:37348"
     gene            57484219..57485383
                     /gene="LOC442317"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442317"
     gene            57509883..57533265
                     /gene="ZNF716"
                     /gene_synonym="FLJ46189"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:441234"
                     /db_xref="HGNC:32458"
     mRNA            join(57509883..57510033,57522166..57522292,
                     57522779..57522874,57528430..57533265)
                     /gene="ZNF716"
                     /gene_synonym="FLJ46189"
                     /product="zinc finger protein 716"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001159279.1"
                     /db_xref="GI:226529226"
                     /db_xref="GeneID:441234"
                     /db_xref="HGNC:32458"
     CDS             join(57509995..57510033,57522166..57522292,
                     57522779..57522874,57528430..57529655)
                     /gene="ZNF716"
                     /gene_synonym="FLJ46189"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 716"
                     /protein_id="NP_001152751.1"
                     /db_xref="GI:226529227"
                     /db_xref="CCDS:CCDS55112.1"
                     /db_xref="GeneID:441234"
                     /db_xref="HGNC:32458"
     gene            57536328..57537198
                     /gene="VN1R29P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312786"
                     /db_xref="HGNC:37349"
     gene            complement(57545123..57545458)
                     /gene="LOC100287575"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100287575"
     exon            complement(57545123..57545458)
                     /gene="LOC100287575"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100287575"
     gene            complement(57688119..57701660)
                     /gene="LOC100128575"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100128575"
     exon            complement(57688119..57688268)
                     /gene="LOC100128575"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=4
                     /pseudo
                     /db_xref="GeneID:100128575"
     gene            57688991..57689907
                     /gene="LOC100420545"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420545"
     exon            complement(57689759..57689985)
                     /gene="LOC100128575"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:100128575"
     exon            complement(57696817..57696916)
                     /gene="LOC100128575"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100128575"
     exon            complement(57701610..57701660)
                     /gene="LOC100128575"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100128575"
     gene            57710228..57712559
                     /gene="LOC100287633"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /db_xref="GeneID:100287633"
     mRNA            join(57710228..57710597,57712447..57712559)
                     /gene="LOC100287633"
                     /product="protein FAM27E2-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /transcript_id="XM_002342728.2"
                     /db_xref="GI:310119985"
                     /db_xref="GeneID:100287633"
     CDS             join(57710228..57710597,57712447..57712559)
                     /gene="LOC100287633"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="protein FAM27E2-like"
                     /protein_id="XP_002342769.2"
                     /db_xref="GI:310119986"
                     /db_xref="GeneID:100287633"
     gene            57712583..57882653
                     /gene="LOC100287663"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100287663"
     exon            57712583..57712928
                     /gene="LOC100287663"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100287663"
     exon            57821081..57821204
                     /gene="LOC100287663"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100287663"
     exon            57824175..57824328
                     /gene="LOC100287663"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:100287663"
     exon            57830683..57830796
                     /gene="LOC100287663"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=4
                     /pseudo
                     /db_xref="GeneID:100287663"
     exon            57834499..57834759
                     /gene="LOC100287663"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=5
                     /pseudo
                     /db_xref="GeneID:100287663"
     exon            57865514..57865579
                     /gene="LOC100287663"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=6
                     /pseudo
                     /db_xref="GeneID:100287663"
     exon            57877715..57877969
                     /gene="LOC100287663"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=7
                     /pseudo
                     /db_xref="GeneID:100287663"
     exon            57882528..57882653
                     /gene="LOC100287663"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=8
                     /pseudo
                     /db_xref="GeneID:100287663"
     gene            complement(57895042..57895958)
                     /gene="LOC100420541"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420541"
     gap             58054332..61054331
                     /estimated_length=3000000
     gap             61310514..61360513
                     /estimated_length=50000
     gap             61917158..61967157
                     /estimated_length=50000
     gene            62517822..62520462
                     /gene="LOC100419991"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419991"
     gene            complement(62574013..62575182)
                     /gene="LOC442318"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442318"
     gene            62669600..62672194
                     /gene="LOC100421386"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421386"
     gene            complement(62693341..62694624)
                     /gene="PHKG1P1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:643941"
                     /db_xref="HGNC:33916"
     gene            complement(62701968..62708699)
                     /gene="SEPT7P4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100418715"
                     /db_xref="HGNC:38039"
     gene            complement(62751665..62764434)
                     /gene="LOC643955"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:643955"
     misc_RNA        complement(join(62751665..62753201,62758644..62758770,
                     62764328..62764434))
                     /gene="LOC643955"
                     /product="zinc finger protein 479 pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003952.1"
                     /db_xref="GI:158262018"
                     /db_xref="GeneID:643955"
     gene            62803095..62804112
                     /gene="ARAF3P"
                     /gene_synonym="ARAFPS2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:285893"
                     /db_xref="HGNC:35474"
     gene            62806218..62807110
                     /gene="VN1R30P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100287919"
                     /db_xref="HGNC:37350"
     gene            62809448..62812152
                     /gene="LOC100287704"
                     /gene_synonym="FLJ46332"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100287704"
     misc_RNA        join(62809448..62809926,62811977..62812152)
                     /gene="LOC100287704"
                     /gene_synonym="FLJ46332"
                     /product="hypothetical LOC100287704"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_028348.1"
                     /db_xref="GI:256355158"
                     /db_xref="GeneID:100287704"
     gene            complement(62827703..62828545)
                     /gene="VN1R31P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312787"
                     /db_xref="HGNC:37351"
     gene            62837711..62838627
                     /gene="VN1R32P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312788"
                     /db_xref="HGNC:37352"
     gene            complement(62856718..62859419)
                     /gene="LOC100287834"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100287834"
     misc_RNA        complement(join(62856718..62856893,62858944..62859419))
                     /gene="LOC100287834"
                     /product="hypothetical LOC100287834"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_028349.1"
                     /db_xref="GI:284005503"
                     /db_xref="GeneID:100287834"
     gene            62857832..62859970
                     /gene="LOC100133079"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100133079"
     gene            complement(62858414..62858860)
                     /gene="LOC100506447"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /db_xref="GeneID:100506447"
     mRNA            complement(62858414..62858860)
                     /gene="LOC100506447"
                     /product="hypothetical protein LOC100506447"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /transcript_id="XM_003118594.1"
                     /db_xref="GI:310119987"
                     /db_xref="GeneID:100506447"
     CDS             complement(62858414..62858860)
                     /gene="LOC100506447"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="hypothetical protein LOC100506447"
                     /protein_id="XP_003118642.1"
                     /db_xref="GI:310119988"
                     /db_xref="GeneID:100506447"
     gene            complement(62861757..62862649)
                     /gene="VN1R33P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100288022"
                     /db_xref="HGNC:37353"
     gene            complement(62864760..62865776)
                     /gene="ARAF2P"
                     /gene_synonym="ARAF2; ARAFPS; PKS1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:644000"
                     /db_xref="HGNC:647"
     gene            62904563..62917271
                     /gene="LOC644017"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:644017"
     gene            62956177..62962914
                     /gene="SEPT7P5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100418718"
                     /db_xref="HGNC:38041"
     gene            62969681..62971337
                     /gene="PHKG1P2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:644032"
                     /db_xref="HGNC:33917"
     gene            63016976..63022966
                     /gene="LOC100132308"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100132308"
     gene            complement(63026751..63045452)
                     /gene="TNRC18B"
                     /gene_synonym="TNRC18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:27320"
                     /db_xref="HGNC:34014"
     gene            63081468..63081547
                     /gene="MIR4283-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100422848"
                     /db_xref="HGNC:38296"
                     /db_xref="miRBase:MI0015982"
     ncRNA           63081468..63081547
                     /gene="MIR4283-2"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4283-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_036270.1"
                     /db_xref="GI:301172675"
                     /db_xref="GeneID:100422848"
                     /db_xref="HGNC:38296"
                     /db_xref="miRBase:MI0015982"
     gene            63092986..63161735
                     /gene="LOC402269"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /db_xref="GeneID:402269"
     mRNA            join(63092986..63093154,63095910..63096041,
                     63096301..63096414,63096905..63096996,63110260..63110382,
                     63111141..63111225,63145721..63145828,63154649..63154769,
                     63154855..63154977,63159770..63159952,63161639..63161735)
                     /gene="LOC402269"
                     /product="hypothetical protein LOC402269"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /transcript_id="XM_377941.7"
                     /db_xref="GI:341915392"
                     /db_xref="GeneID:402269"
     CDS             join(63092986..63093154,63095910..63096041,
                     63096301..63096414,63096905..63096996,63110260..63110382,
                     63111141..63111225,63145721..63145828,63154649..63154769,
                     63154855..63154977,63159770..63159952,63161639..63161735)
                     /gene="LOC402269"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="hypothetical protein LOC402269"
                     /protein_id="XP_377941.5"
                     /db_xref="GI:341915393"
                     /db_xref="GeneID:402269"
     gene            63206505..63207007
                     /gene="LOC100287894"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100287894"
     misc_RNA        63206505..63207007
                     /gene="LOC100287894"
                     /product="hypothetical LOC100287894"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 1 Protein"
                     /pseudo
                     /transcript_id="XR_132537.1"
                     /db_xref="GI:341915399"
                     /db_xref="GeneID:100287894"
     gene            63207106..63216761
                     /gene="LOC100288187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /pseudo
                     /db_xref="GeneID:100288187"
     exon            63207106..63207150
                     /gene="LOC100288187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100288187"
     exon            63209014..63209137
                     /gene="LOC100288187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100288187"
     exon            63209782..63210161
                     /gene="LOC100288187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:100288187"
     exon            63210245..63210799
                     /gene="LOC100288187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=4
                     /pseudo
                     /db_xref="GeneID:100288187"
     exon            63210944..63211205
                     /gene="LOC100288187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=5
                     /pseudo
                     /db_xref="GeneID:100288187"
     exon            63211817..63211928
                     /gene="LOC100288187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=6
                     /pseudo
                     /db_xref="GeneID:100288187"
     exon            63212529..63212724
                     /gene="LOC100288187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=7
                     /pseudo
                     /db_xref="GeneID:100288187"
     exon            63212872..63213084
                     /gene="LOC100288187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=8
                     /pseudo
                     /db_xref="GeneID:100288187"
     exon            63213640..63213939
                     /gene="LOC100288187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=9
                     /pseudo
                     /db_xref="GeneID:100288187"
     exon            63214647..63214829
                     /gene="LOC100288187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=10
                     /pseudo
                     /db_xref="GeneID:100288187"
     exon            63215416..63215715
                     /gene="LOC100288187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=11
                     /pseudo
                     /db_xref="GeneID:100288187"
     exon            63216471..63216761
                     /gene="LOC100288187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=12
                     /pseudo
                     /db_xref="GeneID:100288187"
     gene            63217201..63218584
                     /gene="LOC100653012"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100653012"
     exon            63217201..63217281
                     /gene="LOC100653012"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100653012"
     exon            63217490..63218044
                     /gene="LOC100653012"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100653012"
     exon            63218189..63218584
                     /gene="LOC100653012"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:100653012"
     gene            63219024..63222086
                     /gene="LOC100653015"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100653015"
     exon            63219024..63219104
                     /gene="LOC100653015"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100653015"
     exon            63220117..63220273
                     /gene="LOC100653015"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100653015"
     exon            63220648..63222086
                     /gene="LOC100653015"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:100653015"
     gene            63222526..63223909
                     /gene="LOC100653019"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100653019"
     exon            63222526..63222606
                     /gene="LOC100653019"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100653019"
     exon            63222815..63223369
                     /gene="LOC100653019"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100653019"
     exon            63223514..63223909
                     /gene="LOC100653019"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:100653019"
     gene            63224349..63227328
                     /gene="LOC100288292"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100288292"
     misc_RNA        join(63224349..63224908,63226287..63226786,
                     63226950..63227094,63227232..63227328)
                     /gene="LOC100288292"
                     /product="putative uncharacterized protein FLJ44672-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /transcript_id="XR_132538.1"
                     /db_xref="GI:341915400"
                     /db_xref="GeneID:100288292"
     gene            63303824..63337748
                     /gene="LOC100653023"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100653023"
     exon            63303824..63303882
                     /gene="LOC100653023"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100653023"
     exon            63336865..63337748
                     /gene="LOC100653023"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100653023"
     gene            63353444..63358288
                     /gene="GABPAP"
                     /gene_synonym="E4TF1; E4TF1B; GABPB1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:8327"
                     /db_xref="HGNC:4072"
     gene            complement(63369338..63370830)
                     /gene="NMD3P1"
                     /gene_synonym="NMD3P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:441238"
                     /db_xref="HGNC:22672"
     gene            63391465..63392611
                     /gene="LOC644159"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:644159"
     gene            complement(63394842..63395709)
                     /gene="VN1R34P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129587"
                     /db_xref="HGNC:37354"
     gene            complement(63398281..63398896)
                     /gene="LOC100421741"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421741"
     gene            complement(63423809..63424470)
                     /gene="VN1R35P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312789"
                     /db_xref="HGNC:37355"
     gene            complement(63426156..63426526)
                     /gene="VN1R36P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312790"
                     /db_xref="HGNC:37356"
     gene            63465993..63477866
                     /gene="LOC100419780"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419780"
     gene            complement(63484794..63490480)
                     /gene="LOC100506050"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100506050"
     misc_RNA        complement(join(63484794..63487382,63488169..63488290,
                     63489664..63489739,63490375..63490480))
                     /gene="LOC100506050"
                     /product="hypothetical LOC100506050"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039987.1"
                     /db_xref="GI:337756452"
                     /db_xref="GeneID:100506050"
     gene            63505821..63538927
                     /gene="ZNF727"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:442319"
                     /db_xref="HGNC:22785"
     mRNA            join(63505821..63506002,63529269..63529395,
                     63529892..63529987,63537654..63538927)
                     /gene="ZNF727"
                     /product="zinc finger protein 727"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001159522.1"
                     /db_xref="GI:226958477"
                     /db_xref="GeneID:442319"
                     /db_xref="HGNC:22785"
     CDS             join(63506000..63506002,63529269..63529395,
                     63529892..63529987,63537654..63538927)
                     /gene="ZNF727"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative zinc finger protein 727"
                     /protein_id="NP_001152994.1"
                     /db_xref="GI:226958478"
                     /db_xref="CCDS:CCDS55113.1"
                     /db_xref="GeneID:442319"
                     /db_xref="HGNC:22785"
     gene            63545938..63546954
                     /gene="TRIM60P17"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420414"
                     /db_xref="HGNC:38489"
     gene            63560587..63580916
                     /gene="LOC653435"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:653435"
     gene            complement(63601871..63602798)
                     /gene="RPL6P20"
                     /gene_synonym="RPL6_6_811"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:285900"
                     /db_xref="HGNC:36543"
     gene            complement(63609997..63610907)
                     /gene="VN1R37P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402273"
                     /db_xref="HGNC:37357"
     gene            complement(63640366..63641294)
                     /gene="VN1R38P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100131065"
                     /db_xref="HGNC:37358"
     gene            63642088..63643271
                     /gene="LOC442320"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442320"
     gene            63667581..63680668
                     /gene="ZNF735"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:730291"
                     /db_xref="HGNC:32466"
     mRNA            join(63667581..63667619,63673470..63673596,
                     63674391..63674486,63679692..63680668)
                     /gene="ZNF735"
                     /product="zinc finger protein 735"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001159524.1"
                     /db_xref="GI:226958482"
                     /db_xref="GeneID:730291"
                     /db_xref="HGNC:32466"
     CDS             join(63667581..63667619,63673470..63673596,
                     63674391..63674486,63679692..63680668)
                     /gene="ZNF735"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative zinc finger protein 735"
                     /protein_id="NP_001152996.1"
                     /db_xref="GI:226958483"
                     /db_xref="GeneID:730291"
                     /db_xref="HGNC:32466"
     gene            63688852..63727309
                     /gene="ZNF679"
                     /gene_synonym="MGC42415"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:168417"
                     /db_xref="HGNC:28650"
                     /db_xref="HPRD:14621"
     mRNA            join(63688852..63689030,63709406..63709534,
                     63720599..63720725,63721212..63721307,63726274..63727309)
                     /gene="ZNF679"
                     /gene_synonym="MGC42415"
                     /product="zinc finger protein 679"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_153363.2"
                     /db_xref="GI:224586909"
                     /db_xref="GeneID:168417"
                     /db_xref="HGNC:28650"
                     /db_xref="HPRD:14621"
     CDS             join(63709496..63709534,63720599..63720725,
                     63721212..63721307,63726274..63727247)
                     /gene="ZNF679"
                     /gene_synonym="MGC42415"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 679"
                     /protein_id="NP_699194.2"
                     /db_xref="GI:224586910"
                     /db_xref="CCDS:CCDS47592.1"
                     /db_xref="GeneID:168417"
                     /db_xref="HGNC:28650"
                     /db_xref="HPRD:14621"
     gene            63733916..63734367
                     /gene="VN1R39P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312791"
                     /db_xref="HGNC:37359"
     gene            63773186..63810017
                     /gene="ZNF736"
                     /gene_synonym="DKFZp781H0161"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:728927"
                     /db_xref="HGNC:32467"
     mRNA            join(63773186..63773229,63774251..63774531,
                     63796637..63796763,63797265..63797360,63808468..63810017)
                     /gene="ZNF736"
                     /gene_synonym="DKFZp781H0161"
                     /product="zinc finger protein 736"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001170905.1"
                     /db_xref="GI:283135245"
                     /db_xref="GeneID:728927"
                     /db_xref="HGNC:32467"
     CDS             join(63774529..63774531,63796637..63796763,
                     63797265..63797360,63808468..63809525)
                     /gene="ZNF736"
                     /gene_synonym="DKFZp781H0161"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 736"
                     /protein_id="NP_001164376.1"
                     /db_xref="GI:283135246"
                     /db_xref="CCDS:CCDS55114.1"
                     /db_xref="GeneID:728927"
                     /db_xref="HGNC:32467"
     gene            63815396..63816577
                     /gene="TRIM60P18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420415"
                     /db_xref="HGNC:38490"
     gene            63894071..63895898
                     /gene="LOC649395"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:649395"
     misc_RNA        63894071..63895898
                     /gene="LOC649395"
                     /product="tyrosine 3-monooxygenase/tryptophan
                     5-monooxygenase activation protein, epsilon polypeptide
                     pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_029404.1"
                     /db_xref="GI:261490650"
                     /db_xref="GeneID:649395"
     gene            complement(63904138..63905054)
                     /gene="VN1R40P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312792"
                     /db_xref="HGNC:37360"
     gene            63929554..63930950
                     /gene="LOC728947"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:728947"
     gene            63935935..63936540
                     /gene="VN1R41P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312793"
                     /db_xref="HGNC:37361"
     gene            63961203..63962107
                     /gene="LOC100127907"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100127907"
     gene            complement(63980255..64023505)
                     /gene="ZNF680"
                     /gene_synonym="FLJ90430"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:340252"
                     /db_xref="HGNC:26897"
                     /db_xref="HPRD:08296"
     mRNA            complement(join(63980255..63982878,64004085..64004180,
                     64004684..64004810,64023303..64023505))
                     /gene="ZNF680"
                     /gene_synonym="FLJ90430"
                     /product="zinc finger protein 680, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178558.4"
                     /db_xref="GI:194097406"
                     /db_xref="GeneID:340252"
                     /db_xref="HGNC:26897"
                     /db_xref="HPRD:08296"
     CDS             complement(join(63981539..63982878,64004085..64004180,
                     64004684..64004810,64023303..64023332))
                     /gene="ZNF680"
                     /gene_synonym="FLJ90430"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 680 isoform 1"
                     /protein_id="NP_848653.2"
                     /db_xref="GI:194097407"
                     /db_xref="CCDS:CCDS34644.1"
                     /db_xref="GeneID:340252"
                     /db_xref="HGNC:26897"
                     /db_xref="HPRD:08296"
     mRNA            complement(join(63985034..63986895,64004085..64004180,
                     64004684..64004810,64023303..64023505))
                     /gene="ZNF680"
                     /gene_synonym="FLJ90430"
                     /product="zinc finger protein 680, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130022.1"
                     /db_xref="GI:194097408"
                     /db_xref="GeneID:340252"
                     /db_xref="HGNC:26897"
                     /db_xref="HPRD:08296"
     CDS             complement(join(63986777..63986895,64004085..64004180,
                     64004684..64004810,64023303..64023332))
                     /gene="ZNF680"
                     /gene_synonym="FLJ90430"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 680 isoform 2"
                     /protein_id="NP_001123494.1"
                     /db_xref="GI:194097409"
                     /db_xref="CCDS:CCDS47594.1"
                     /db_xref="GeneID:340252"
                     /db_xref="HGNC:26897"
                     /db_xref="HPRD:08296"
     gene            complement(64027174..64027851)
                     /gene="LOC100133092"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100133092"
     gene            complement(64028248..64030815)
                     /gene="LOC100129293"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129293"
     gene            64042988..64044129
                     /gene="LOC641746"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:641746"
     misc_RNA        64042988..64044129
                     /gene="LOC641746"
                     /product="glycine cleavage system protein H pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_033245.1"
                     /db_xref="GI:284005210"
                     /db_xref="GeneID:641746"
     gene            64126511..64171404
                     /gene="ZNF107"
                     /gene_synonym="smap-7; Y8; ZFD25; ZNF588"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51427"
                     /db_xref="HGNC:12887"
                     /db_xref="HPRD:18669"
                     /db_xref="MIM:603989"
     mRNA            join(64126511..64126663,64129415..64129556,
                     64139555..64139714,64150777..64150903,64151626..64151752,
                     64152243..64152338,64166702..64171404)
                     /gene="ZNF107"
                     /gene_synonym="smap-7; Y8; ZFD25; ZNF588"
                     /product="zinc finger protein 107, transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016220.3"
                     /db_xref="GI:62243603"
                     /db_xref="GeneID:51427"
                     /db_xref="HGNC:12887"
                     /db_xref="HPRD:18669"
                     /db_xref="MIM:603989"
     mRNA            join(64126511..64126663,64139555..64139714,
                     64151626..64151752,64152243..64152338,64166702..64171404)
                     /gene="ZNF107"
                     /gene_synonym="smap-7; Y8; ZFD25; ZNF588"
                     /product="zinc finger protein 107, transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001013746.1"
                     /db_xref="GI:62243639"
                     /db_xref="GeneID:51427"
                     /db_xref="HGNC:12887"
                     /db_xref="HPRD:18669"
                     /db_xref="MIM:603989"
     CDS             join(64152320..64152338,64166702..64169034)
                     /gene="ZNF107"
                     /gene_synonym="smap-7; Y8; ZFD25; ZNF588"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 107"
                     /protein_id="NP_057304.1"
                     /db_xref="GI:7706775"
                     /db_xref="CCDS:CCDS5527.1"
                     /db_xref="GeneID:51427"
                     /db_xref="HGNC:12887"
                     /db_xref="HPRD:18669"
                     /db_xref="MIM:603989"
     CDS             join(64152320..64152338,64166702..64169034)
                     /gene="ZNF107"
                     /gene_synonym="smap-7; Y8; ZFD25; ZNF588"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 107"
                     /protein_id="NP_001013768.1"
                     /db_xref="GI:62243640"
                     /db_xref="CCDS:CCDS5527.1"
                     /db_xref="GeneID:51427"
                     /db_xref="HGNC:12887"
                     /db_xref="HPRD:18669"
                     /db_xref="MIM:603989"
     gene            complement(64194993..64197311)
                     /gene="LOC644387"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:644387"
     gene            64254771..64294026
                     /gene="ZNF138"
                     /gene_synonym="pHZ-32"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7697"
                     /db_xref="HGNC:12922"
                     /db_xref="HPRD:07244"
                     /db_xref="MIM:604080"
     mRNA            join(64254771..64254949,64275296..64275422,
                     64291829..64294026)
                     /gene="ZNF138"
                     /gene_synonym="pHZ-32"
                     /product="zinc finger protein 138, transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006524.2"
                     /db_xref="GI:237512948"
                     /db_xref="GeneID:7697"
                     /db_xref="HGNC:12922"
                     /db_xref="HPRD:07244"
                     /db_xref="MIM:604080"
     mRNA            join(64254771..64254949,64275296..64275422,
                     64275954..64276031,64291318..64291454,64291829..64294026)
                     /gene="ZNF138"
                     /gene_synonym="pHZ-32"
                     /product="zinc finger protein 138, transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001160183.1"
                     /db_xref="GI:237512950"
                     /db_xref="GeneID:7697"
                     /db_xref="HGNC:12922"
                     /db_xref="MIM:604080"
                     /db_xref="HPRD:07244"
     misc_RNA        join(64254771..64254949,64275296..64275422,
                     64275950..64276031,64291829..64294026)
                     /gene="ZNF138"
                     /gene_synonym="pHZ-32"
                     /product="zinc finger protein 138, transcript variant 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027660.1"
                     /db_xref="GI:237512952"
                     /db_xref="GeneID:7697"
                     /db_xref="HGNC:12922"
                     /db_xref="MIM:604080"
                     /db_xref="HPRD:07244"
     misc_RNA        join(64254771..64254949,64291829..64294026)
                     /gene="ZNF138"
                     /gene_synonym="pHZ-32"
                     /product="zinc finger protein 138, transcript variant 4"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027661.1"
                     /db_xref="GI:237512953"
                     /db_xref="GeneID:7697"
                     /db_xref="HGNC:12922"
                     /db_xref="MIM:604080"
                     /db_xref="HPRD:07244"
     CDS             join(64254947..64254949,64275296..64275422,
                     64291829..64292580)
                     /gene="ZNF138"
                     /gene_synonym="pHZ-32"
                     /exception="mismatches in translation"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 138 isoform 1"
                     /protein_id="NP_006515.2"
                     /db_xref="GI:237512949"
                     /db_xref="CCDS:CCDS34645.2"
                     /db_xref="GeneID:7697"
                     /db_xref="HGNC:12922"
                     /db_xref="HPRD:07244"
                     /db_xref="MIM:604080"
     CDS             join(64254947..64254949,64275296..64275422,
                     64275954..64276031,64291318..64291454,64291829..64291864)
                     /gene="ZNF138"
                     /gene_synonym="pHZ-32"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 138 isoform 2"
                     /protein_id="NP_001153655.1"
                     /db_xref="GI:237512951"
                     /db_xref="CCDS:CCDS55115.1"
                     /db_xref="GeneID:7697"
                     /db_xref="HGNC:12922"
                     /db_xref="HPRD:07244"
                     /db_xref="MIM:604080"
     gene            complement(64310071..64324845)
                     /gene="SEPHS1P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:168474"
     misc_RNA        complement(join(64310071..64314178,64324829..64324845))
                     /gene="SEPHS1P"
                     /product="selenophosphate synthetase pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002789.2"
                     /db_xref="GI:283135106"
                     /db_xref="GeneID:168474"
     gene            64323329..64324839
                     /gene="EEF1DP4"
                     /gene_synonym="FLJ26697"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442325"
                     /db_xref="HGNC:22598"
     gene            complement(64348715..64350478)
                     /gene="LOC441239"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 1 EST, 1 Protein"
                     /db_xref="GeneID:441239"
     mRNA            complement(join(64348715..64349195,64349444..64349565,
                     64349830..64350478))
                     /gene="LOC441239"
                     /product="hypothetical protein LOC441239"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 1 EST, 1 Protein"
                     /transcript_id="XM_499305.4"
                     /db_xref="GI:310119991"
                     /db_xref="GeneID:441239"
     CDS             complement(join(64348715..64349195,64349444..64349565,
                     64349830..64350117))
                     /gene="LOC441239"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="hypothetical protein LOC441239"
                     /protein_id="XP_499305.4"
                     /db_xref="GI:310119992"
                     /db_xref="GeneID:441239"
     gene            64363620..64391955
                     /gene="ZNF273"
                     /gene_synonym="HZF9; MGC12518"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10793"
                     /db_xref="HGNC:13067"
                     /db_xref="MIM:604756"
     mRNA            join(64363620..64363797,64377959..64378085,
                     64378575..64378670,64388032..64391955)
                     /gene="ZNF273"
                     /gene_synonym="HZF9; MGC12518"
                     /product="zinc finger protein 273, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021148.2"
                     /db_xref="GI:110349777"
                     /db_xref="GeneID:10793"
                     /db_xref="HGNC:13067"
                     /db_xref="HPRD:07264"
                     /db_xref="MIM:604756"
     misc_RNA        join(64363620..64363797,64377408..64377496,
                     64377959..64378085,64378575..64378670,64388032..64391955)
                     /gene="ZNF273"
                     /gene_synonym="HZF9; MGC12518"
                     /product="zinc finger protein 273, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_003099.1"
                     /db_xref="GI:110349776"
                     /db_xref="GeneID:10793"
                     /db_xref="HGNC:13067"
                     /db_xref="MIM:604756"
     CDS             join(64363696..64363797,64377959..64378085,
                     64378575..64378670,64388032..64389416)
                     /gene="ZNF273"
                     /gene_synonym="HZF9; MGC12518"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 273"
                     /protein_id="NP_066971.2"
                     /db_xref="GI:110349778"
                     /db_xref="CCDS:CCDS5528.2"
                     /db_xref="GeneID:10793"
                     /db_xref="HGNC:13067"
                     /db_xref="MIM:604756"
     gene            64393651..64394129
                     /gene="VN1R42P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312794"
                     /db_xref="HGNC:37362"
     gene            complement(64402541..64403289)
                     /gene="LOC100418814"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100418814"
     gene            complement(64433295..64433602)
                     /gene="VN1R43P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100312795"
                     /db_xref="HGNC:37363"
     gene            complement(64434830..64451414)
                     /gene="ZNF117"
                     /gene_synonym="H-plk; HPF9; MGC22613"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:51351"
                     /db_xref="HGNC:12897"
                     /db_xref="MIM:194624"
     mRNA            complement(join(64434830..64439914,64441765..64441860,
                     64442362..64442494,64450325..64451414))
                     /gene="ZNF117"
                     /gene_synonym="H-plk; HPF9; MGC22613"
                     /product="zinc finger protein 117"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /transcript_id="NM_015852.3"
                     /db_xref="GI:134152706"
                     /db_xref="GeneID:51351"
                     /db_xref="HGNC:12897"
                     /db_xref="MIM:194624"
     CDS             complement(join(64438497..64439914,64441765..64441798))
                     /gene="ZNF117"
                     /gene_synonym="H-plk; HPF9; MGC22613"
                     /note="Krueppel-related zinc finger protein;
                     provirus-linked krueppel; zinc finger protein HPF9;
                     Derived by automated computational analysis using gene
                     prediction method: Curated Genomic."
                     /codon_start=1
                     /product="zinc finger protein 117"
                     /protein_id="NP_056936.2"
                     /db_xref="GI:115270953"
                     /db_xref="CCDS:CCDS43593.1"
                     /db_xref="GeneID:51351"
                     /db_xref="HGNC:12897"
                     /db_xref="MIM:194624"
     gene            complement(64450733..64467124)
                     /gene="ERV3-1"
                     /gene_synonym="envR; ERV-R; ERV3; ERVR; FLJ23884; HERV-R;
                     HERVR"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:2086"
                     /db_xref="HGNC:3454"
                     /db_xref="MIM:131170"
     mRNA            complement(join(64450733..64453792,64466919..64467124))
                     /gene="ERV3-1"
                     /gene_synonym="envR; ERV-R; ERV3; ERVR; FLJ23884; HERV-R;
                     HERVR"
                     /product="endogenous retrovirus group 3, member 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /transcript_id="NM_001007253.3"
                     /db_xref="GI:297515503"
                     /db_xref="GeneID:2086"
                     /db_xref="HGNC:3454"
                     /db_xref="MIM:131170"
     CDS             complement(64451590..64453404)
                     /gene="ERV3-1"
                     /gene_synonym="envR; ERV-R; ERV3; ERVR; FLJ23884; HERV-R;
                     HERVR"
                     /note="HERV-R_7q21.2 provirus ancestral Env polyprotein;
                     ERV-3 envelope protein; ERV-R envelope protein; HERV-R
                     envelope protein; endogenous retroviral sequence 3;
                     Derived by automated computational analysis using gene
                     prediction method: Curated Genomic."
                     /codon_start=1
                     /product="HERV-R_7q21.2 provirus ancestral Env polyprotein
                     precursor"
                     /protein_id="NP_001007254.2"
                     /db_xref="GI:145651814"
                     /db_xref="CCDS:CCDS47595.1"
                     /db_xref="GeneID:2086"
                     /db_xref="HGNC:3454"
                     /db_xref="MIM:131170"
     gene            64498643..64498947
                     /gene="LOC441241"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:441241"
     gene            64498732..64535091
                     /gene="CCT6P3"
                     /gene_synonym="CCT6-3P; DKFZp779B0634"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:643180"
                     /db_xref="HGNC:35137"
     misc_RNA        join(64498732..64498943,64525377..64525511,
                     64526631..64526804,64527323..64527428,64528834..64528988,
                     64529087..64529168,64530039..64530135,64530724..64530862,
                     64531287..64531420,64533819..64533892,64534156..64535091)
                     /gene="CCT6P3"
                     /gene_synonym="CCT6-3P; DKFZp779B0634"
                     /product="chaperonin containing TCP1, subunit 6 (zeta)
                     pseudogene 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_033416.1"
                     /db_xref="GI:293597532"
                     /db_xref="GeneID:643180"
                     /db_xref="HGNC:35137"
     gene            64601603..64694600
                     /gene="INTS4L1"
                     /gene_synonym="FLJ25037; MGC133166"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:285905"
                     /db_xref="HGNC:21925"
     misc_RNA        join(64601603..64601786,64613395..64613515,
                     64628127..64628198,64630565..64630739,64639670..64639875,
                     64643352..64643494,64645768..64645883,64646768..64646888,
                     64649358..64649515,64660996..64661076,64670132..64670191,
                     64691919..64692314,64693443..64693537,64693977..64694600)
                     /gene="INTS4L1"
                     /gene_synonym="FLJ25037; MGC133166"
                     /product="integrator complex subunit 4-like 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_027393.1"
                     /db_xref="GI:225637471"
                     /db_xref="GeneID:285905"
                     /db_xref="HGNC:21925"
     gene            64727289..64727877
                     /gene="LOC100418719"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100418719"
     gene            64756554..64757705
                     /gene="LOC100419781"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419781"
     gene            complement(64800087..64800918)
                     /gene="RSL24D1P3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100130721"
                     /db_xref="HGNC:37883"
     gene            64820866..64822202
                     /gene="LOC100533634"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533634"
     gene            64838768..64865998
                     /gene="ZNF92"
                     /gene_synonym="HPF12; HTF12; TF12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:168374"
                     /db_xref="HGNC:13168"
                     /db_xref="HPRD:04919"
                     /db_xref="MIM:603974"
     mRNA            join(64838768..64838913,64853719..64853814,
                     64863254..64865998)
                     /gene="ZNF92"
                     /gene_synonym="HPF12; HTF12; TF12"
                     /product="zinc finger protein 92, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_007139.2"
                     /db_xref="GI:37537683"
                     /db_xref="GeneID:168374"
                     /db_xref="HGNC:13168"
                     /db_xref="MIM:603974"
                     /db_xref="HPRD:04919"
     mRNA            join(64838768..64838913,64852815..64852941,
                     64853719..64853814,64863254..64865998)
                     /gene="ZNF92"
                     /gene_synonym="HPF12; HTF12; TF12"
                     /product="zinc finger protein 92, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152626.2"
                     /db_xref="GI:37537682"
                     /db_xref="GeneID:168374"
                     /db_xref="HGNC:13168"
                     /db_xref="HPRD:04919"
                     /db_xref="MIM:603974"
     CDS             join(64838911..64838913,64852815..64852941,
                     64853719..64853814,64863254..64864788)
                     /gene="ZNF92"
                     /gene_synonym="HPF12; HTF12; TF12"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 92 isoform 2"
                     /protein_id="NP_689839.1"
                     /db_xref="GI:23097323"
                     /db_xref="CCDS:CCDS34646.1"
                     /db_xref="GeneID:168374"
                     /db_xref="HGNC:13168"
                     /db_xref="HPRD:04919"
                     /db_xref="MIM:603974"
     CDS             join(64853796..64853814,64863254..64864788)
                     /gene="ZNF92"
                     /gene_synonym="HPF12; HTF12; TF12"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 92 isoform 1"
                     /protein_id="NP_009070.2"
                     /db_xref="GI:37537684"
                     /db_xref="CCDS:CCDS47596.1"
                     /db_xref="GeneID:168374"
                     /db_xref="HGNC:13168"
                     /db_xref="HPRD:04919"
                     /db_xref="MIM:603974"
     gene            65019171..65020372
                     /gene="LOC100288268"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 EST, 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100288268"
     misc_RNA        join(65019171..65019203,65019497..65020372)
                     /gene="LOC100288268"
                     /product="hypothetical LOC100288268"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 EST, 1 Protein"
                     /pseudo
                     /transcript_id="XR_132532.1"
                     /db_xref="GI:341915388"
                     /db_xref="GeneID:100288268"
     gene            65081995..65084067
                     /gene="LOC402279"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402279"
     gene            complement(65111924..65235797)
                     /gene="LOC441242"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:441242"
     misc_RNA        complement(join(65111924..65112954,65113248..65113333,
                     65113758..65113894,65114330..65114462,65136099..65136187,
                     65192028..65192081,65227918..65228004,65235454..65235797))
                     /gene="LOC441242"
                     /product="hypothetical LOC441242"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038378.1"
                     /db_xref="GI:335335005"
                     /db_xref="GeneID:441242"
     gene            65112777..65183632
                     /gene="INTS4L2"
                     /gene_synonym="MGC133166"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:644619"
                     /db_xref="HGNC:22351"
     misc_RNA        join(65112777..65112960,65124594..65124714,
                     65139334..65139405,65141772..65141946,65150572..65150776,
                     65154274..65154416,65156695..65156810,65157690..65157823,
                     65159981..65160138,65171319..65171399,65180623..65180682,
                     65183142..65183301,65183520..65183632)
                     /gene="INTS4L2"
                     /gene_synonym="MGC133166"
                     /product="integrator complex subunit 4-like 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_027392.1"
                     /db_xref="GI:225637470"
                     /db_xref="GeneID:644619"
                     /db_xref="HGNC:22351"
     gene            65216092..65228662
                     /gene="CCT6P1"
                     /gene_synonym="CCT6-5P; CCT6AP1; DKFZp779B0634"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:643253"
                     /db_xref="HGNC:33094"
     misc_RNA        join(65216092..65216265,65219514..65219648,
                     65220767..65220939,65221456..65221561,65222970..65223124,
                     65223223..65223304,65224162..65224258,65224847..65224985,
                     65225411..65225543,65226633..65226735,65227934..65228007,
                     65228268..65228662)
                     /gene="CCT6P1"
                     /gene_synonym="CCT6-5P; CCT6AP1; DKFZp779B0634"
                     /product="chaperonin containing TCP1, subunit 6 (zeta)
                     pseudogene 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003110.2"
                     /db_xref="GI:119709841"
                     /db_xref="GeneID:643253"
                     /db_xref="HGNC:33094"
     gene            65220513..65220646
                     /gene="SNORA22"
                     /gene_synonym="ACA22"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:677807"
                     /db_xref="HGNC:32612"
     ncRNA           65220513..65220646
                     /gene="SNORA22"
                     /gene_synonym="ACA22"
                     /ncRNA_class="snoRNA"
                     /product="small nucleolar RNA, H/ACA box 22"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_002961.1"
                     /db_xref="GI:91680829"
                     /db_xref="GeneID:677807"
                     /db_xref="HGNC:32612"
     gene            65238607..65267079
                     /gene="LOC100420546"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420546"
     gene            65305198..65305588
                     /gene="DKFZP434F142"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA"
                     /db_xref="GeneID:84214"
     misc_RNA        65305198..65305588
                     /gene="DKFZP434F142"
                     /product="hypothetical DKFZp434F142"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA"
                     /transcript_id="XR_108809.1"
                     /db_xref="GI:310119994"
                     /db_xref="GeneID:84214"
     gene            65306164..65307231
                     /gene="LOC100419992"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419992"
     gene            65338257..65419800
                     /gene="VKORC1L1"
                     /gene_synonym="DKFZp762H0113"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:154807"
                     /db_xref="HGNC:21492"
                     /db_xref="HPRD:12312"
                     /db_xref="MIM:608838"
     mRNA            join(65338257..65338552,65413658..65413767,
                     65419061..65419800)
                     /gene="VKORC1L1"
                     /gene_synonym="DKFZp762H0113"
                     /product="vitamin K epoxide reductase complex, subunit
                     1-like 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_173517.3"
                     /db_xref="GI:47717107"
                     /db_xref="GeneID:154807"
                     /db_xref="HGNC:21492"
                     /db_xref="HPRD:12312"
                     /db_xref="MIM:608838"
     CDS             join(65338359..65338552,65413658..65413767,
                     65419061..65419287)
                     /gene="VKORC1L1"
                     /gene_synonym="DKFZp762H0113"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="vitamin K epoxide reductase complex subunit
                     1-like protein 1"
                     /protein_id="NP_775788.2"
                     /db_xref="GI:46309463"
                     /db_xref="CCDS:CCDS5529.1"
                     /db_xref="GeneID:154807"
                     /db_xref="HGNC:21492"
                     /db_xref="HPRD:12312"
                     /db_xref="MIM:608838"
     gene            complement(65425671..65447301)
                     /gene="GUSB"
                     /gene_synonym="BG; FLJ39445; MPS7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2990"
                     /db_xref="HGNC:4696"
                     /db_xref="HPRD:02018"
                     /db_xref="MIM:611499"
     mRNA            complement(join(65425671..65426050,65429310..65429445,
                     65432718..65432894,65435269..65435353,65439282..65439428,
                     65439513..65439691,65439906..65440058,65441002..65441189,
                     65444386..65444528,65444714..65444898,65445211..65445396,
                     65446961..65447301))
                     /gene="GUSB"
                     /gene_synonym="BG; FLJ39445; MPS7"
                     /product="glucuronidase, beta"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000181.3"
                     /db_xref="GI:268834191"
                     /db_xref="GeneID:2990"
                     /db_xref="HGNC:4696"
                     /db_xref="HPRD:02018"
                     /db_xref="MIM:611499"
     CDS             complement(join(65425884..65426050,65429310..65429445,
                     65432718..65432894,65435269..65435353,65439282..65439428,
                     65439513..65439691,65439906..65440058,65441002..65441189,
                     65444386..65444528,65444714..65444898,65445211..65445396,
                     65446961..65447170))
                     /gene="GUSB"
                     /gene_synonym="BG; FLJ39445; MPS7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="beta-glucuronidase precursor"
                     /protein_id="NP_000172.2"
                     /db_xref="GI:268834192"
                     /db_xref="CCDS:CCDS5530.1"
                     /db_xref="GeneID:2990"
                     /db_xref="HGNC:4696"
                     /db_xref="HPRD:02018"
                     /db_xref="MIM:611499"
     gene            complement(65490168..65493644)
                     /gene="LOC100419772"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419772"
     gene            complement(65534487..65536329)
                     /gene="LOC644667"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:644667"
     gene            65540776..65558330
                     /gene="ASL"
                     /gene_synonym="ASAL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:435"
                     /db_xref="HGNC:746"
                     /db_xref="HPRD:01948"
                     /db_xref="MIM:608310"
     mRNA            join(65540776..65540843,65541026..65541080,
                     65546790..65546984,65547355..65547438,65547867..65547923,
                     65548064..65548161,65551572..65551649,65551731..65551808,
                     65552321..65552373,65552716..65552778,65553794..65553908,
                     65554078..65554162,65554263..65554322,65554599..65554682,
                     65556993..65557073,65557544..65557650,65557755..65558330)
                     /gene="ASL"
                     /gene_synonym="ASAL"
                     /product="argininosuccinate lyase, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000048.3"
                     /db_xref="GI:68303544"
                     /db_xref="GeneID:435"
                     /db_xref="HGNC:746"
                     /db_xref="HPRD:01948"
                     /db_xref="MIM:608310"
     mRNA            join(65540834..65541080,65546790..65546984,
                     65547355..65547438,65547867..65547923,65548064..65548161,
                     65551572..65551649,65551731..65551808,65552321..65552373,
                     65552716..65552778,65553794..65553908,65554078..65554162,
                     65554263..65554322,65554599..65554682,65556993..65557073,
                     65557544..65557650,65557755..65558330)
                     /gene="ASL"
                     /gene_synonym="ASAL"
                     /product="argininosuccinate lyase, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001024943.1"
                     /db_xref="GI:68303541"
                     /db_xref="GeneID:435"
                     /db_xref="HGNC:746"
                     /db_xref="HPRD:01948"
                     /db_xref="MIM:608310"
     mRNA            join(65540834..65541080,65546790..65546984,
                     65547355..65547438,65547867..65547923,65548064..65548161,
                     65551572..65551649,65551731..65551808,65552321..65552373,
                     65552716..65552778,65553794..65553908,65554078..65554162,
                     65554599..65554682,65556993..65557073,65557544..65557650,
                     65557755..65558330)
                     /gene="ASL"
                     /gene_synonym="ASAL"
                     /product="argininosuccinate lyase, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001024944.1"
                     /db_xref="GI:68303546"
                     /db_xref="GeneID:435"
                     /db_xref="HGNC:746"
                     /db_xref="HPRD:01948"
                     /db_xref="MIM:608310"
     mRNA            join(65540834..65541080,65546790..65546984,
                     65547355..65547438,65547867..65547923,65548064..65548161,
                     65551572..65551649,65552321..65552373,65552716..65552778,
                     65553794..65553908,65554078..65554162,65554263..65554322,
                     65554599..65554682,65556993..65557073,65557544..65557650,
                     65557755..65558330)
                     /gene="ASL"
                     /gene_synonym="ASAL"
                     /product="argininosuccinate lyase, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001024946.1"
                     /db_xref="GI:68303548"
                     /db_xref="GeneID:435"
                     /db_xref="HGNC:746"
                     /db_xref="HPRD:01948"
                     /db_xref="MIM:608310"
     CDS             join(65541069..65541080,65546790..65546984,
                     65547355..65547438,65547867..65547923,65548064..65548161,
                     65551572..65551649,65551731..65551808,65552321..65552373,
                     65552716..65552778,65553794..65553908,65554078..65554162,
                     65554263..65554322,65554599..65554682,65556993..65557073,
                     65557544..65557650,65557755..65557899)
                     /gene="ASL"
                     /gene_synonym="ASAL"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="argininosuccinate lyase isoform 1"
                     /protein_id="NP_001020114.1"
                     /db_xref="GI:68303542"
                     /db_xref="CCDS:CCDS5531.1"
                     /db_xref="GeneID:435"
                     /db_xref="HGNC:746"
                     /db_xref="HPRD:01948"
                     /db_xref="MIM:608310"
     CDS             join(65541069..65541080,65546790..65546984,
                     65547355..65547438,65547867..65547923,65548064..65548161,
                     65551572..65551649,65551731..65551808,65552321..65552373,
                     65552716..65552778,65553794..65553908,65554078..65554162,
                     65554263..65554322,65554599..65554682,65556993..65557073,
                     65557544..65557650,65557755..65557899)
                     /gene="ASL"
                     /gene_synonym="ASAL"
                     /note="isoform 1 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="argininosuccinate lyase isoform 1"
                     /protein_id="NP_000039.2"
                     /db_xref="GI:31541964"
                     /db_xref="CCDS:CCDS5531.1"
                     /db_xref="GeneID:435"
                     /db_xref="HGNC:746"
                     /db_xref="HPRD:01948"
                     /db_xref="MIM:608310"
     CDS             join(65541069..65541080,65546790..65546984,
                     65547355..65547438,65547867..65547923,65548064..65548161,
                     65551572..65551649,65551731..65551808,65552321..65552373,
                     65552716..65552778,65553794..65553908,65554078..65554162,
                     65554599..65554682,65556993..65557073,65557544..65557650,
                     65557755..65557899)
                     /gene="ASL"
                     /gene_synonym="ASAL"
                     /note="isoform 2 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="argininosuccinate lyase isoform 2"
                     /protein_id="NP_001020115.1"
                     /db_xref="GI:68303547"
                     /db_xref="CCDS:CCDS47597.1"
                     /db_xref="GeneID:435"
                     /db_xref="HGNC:746"
                     /db_xref="HPRD:01948"
                     /db_xref="MIM:608310"
     CDS             join(65541069..65541080,65546790..65546984,
                     65547355..65547438,65547867..65547923,65548064..65548161,
                     65551572..65551649,65552321..65552373,65552716..65552778,
                     65553794..65553908,65554078..65554162,65554263..65554322,
                     65554599..65554682,65556993..65557073,65557544..65557650,
                     65557755..65557899)
                     /gene="ASL"
                     /gene_synonym="ASAL"
                     /note="isoform 3 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="argininosuccinate lyase isoform 3"
                     /protein_id="NP_001020117.1"
                     /db_xref="GI:68303549"
                     /db_xref="CCDS:CCDS47598.1"
                     /db_xref="GeneID:435"
                     /db_xref="HGNC:746"
                     /db_xref="HPRD:01948"
                     /db_xref="MIM:608310"
     gene            65579805..65619555
                     /gene="CRCP"
                     /gene_synonym="CGRP-RCP; CGRPRCP; MGC111194; RCP; RCP9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:27297"
                     /db_xref="HGNC:17888"
                     /db_xref="HPRD:12089"
                     /db_xref="MIM:606121"
     mRNA            join(65579805..65579957,65592691..65592727,
                     65595731..65595829,65599267..65599361,65610430..65610487,
                     65617195..65619555)
                     /gene="CRCP"
                     /gene_synonym="CGRP-RCP; CGRPRCP; MGC111194; RCP; RCP9"
                     /product="CGRP receptor component, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014478.4"
                     /db_xref="GI:100913024"
                     /db_xref="GeneID:27297"
                     /db_xref="HGNC:17888"
                     /db_xref="HPRD:12089"
                     /db_xref="MIM:606121"
     mRNA            join(65579805..65579957,65592691..65592727,
                     65599267..65599361,65610430..65610487,65617195..65619555)
                     /gene="CRCP"
                     /gene_synonym="CGRP-RCP; CGRPRCP; MGC111194; RCP; RCP9"
                     /product="CGRP receptor component, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040647.1"
                     /db_xref="GI:100913025"
                     /db_xref="GeneID:27297"
                     /db_xref="HGNC:17888"
                     /db_xref="MIM:606121"
                     /db_xref="HPRD:12089"
     mRNA            join(65579805..65579957,65610430..65610487,
                     65617195..65619555)
                     /gene="CRCP"
                     /gene_synonym="CGRP-RCP; CGRPRCP; MGC111194; RCP; RCP9"
                     /product="CGRP receptor component, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040648.1"
                     /db_xref="GI:100913027"
                     /db_xref="GeneID:27297"
                     /db_xref="HGNC:17888"
                     /db_xref="MIM:606121"
                     /db_xref="HPRD:12089"
     mRNA            join(65579805..65579901,65592691..65592727,
                     65599267..65599361,65610430..65610487,65617195..65619555)
                     /gene="CRCP"
                     /gene_synonym="CGRP-RCP; CGRPRCP; MGC111194; RCP; RCP9"
                     /product="CGRP receptor component, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001142414.1"
                     /db_xref="GI:227495693"
                     /db_xref="GeneID:27297"
                     /db_xref="HGNC:17888"
                     /db_xref="MIM:606121"
                     /db_xref="HPRD:12089"
     misc_RNA        join(65579805..65579957,65592691..65592727,
                     65595114..65595235,65595731..65595829,65599267..65599361,
                     65610430..65610487,65617195..65619555)
                     /gene="CRCP"
                     /gene_synonym="CGRP-RCP; CGRPRCP; MGC111194; RCP; RCP9"
                     /product="CGRP receptor component, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024548.1"
                     /db_xref="GI:227495697"
                     /db_xref="GeneID:27297"
                     /db_xref="HGNC:17888"
                     /db_xref="MIM:606121"
                     /db_xref="HPRD:12089"
     CDS             join(65579816..65579901,65592691..65592727,
                     65599267..65599361,65610430..65610487,65617195..65617344)
                     /gene="CRCP"
                     /gene_synonym="CGRP-RCP; CGRPRCP; MGC111194; RCP; RCP9"
                     /note="isoform d is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-directed RNA polymerase III subunit RPC9
                     isoform d"
                     /protein_id="NP_001135886.1"
                     /db_xref="GI:227495694"
                     /db_xref="CCDS:CCDS55116.1"
                     /db_xref="GeneID:27297"
                     /db_xref="HGNC:17888"
                     /db_xref="HPRD:12089"
                     /db_xref="MIM:606121"
     CDS             join(65579950..65579957,65592691..65592727,
                     65595731..65595829,65599267..65599361,65610430..65610487,
                     65617195..65617344)
                     /gene="CRCP"
                     /gene_synonym="CGRP-RCP; CGRPRCP; MGC111194; RCP; RCP9"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-directed RNA polymerase III subunit RPC9
                     isoform a"
                     /protein_id="NP_055293.1"
                     /db_xref="GI:7656977"
                     /db_xref="CCDS:CCDS5532.1"
                     /db_xref="GeneID:27297"
                     /db_xref="HGNC:17888"
                     /db_xref="HPRD:12089"
                     /db_xref="MIM:606121"
     CDS             join(65579950..65579957,65592691..65592727,
                     65599267..65599361,65610430..65610487,65617195..65617344)
                     /gene="CRCP"
                     /gene_synonym="CGRP-RCP; CGRPRCP; MGC111194; RCP; RCP9"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-directed RNA polymerase III subunit RPC9
                     isoform b"
                     /protein_id="NP_001035737.1"
                     /db_xref="GI:100913026"
                     /db_xref="CCDS:CCDS47599.1"
                     /db_xref="GeneID:27297"
                     /db_xref="HGNC:17888"
                     /db_xref="HPRD:12089"
                     /db_xref="MIM:606121"
     CDS             join(65579950..65579957,65610430..65610487,
                     65617195..65617344)
                     /gene="CRCP"
                     /gene_synonym="CGRP-RCP; CGRPRCP; MGC111194; RCP; RCP9"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-directed RNA polymerase III subunit RPC9
                     isoform c"
                     /protein_id="NP_001035738.1"
                     /db_xref="GI:100913028"
                     /db_xref="CCDS:CCDS47600.1"
                     /db_xref="GeneID:27297"
                     /db_xref="HGNC:17888"
                     /db_xref="HPRD:12089"
                     /db_xref="MIM:606121"
     gene            65670259..65825438
                     /gene="TPST1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8460"
                     /db_xref="HGNC:12020"
                     /db_xref="HPRD:07216"
                     /db_xref="MIM:603125"
     mRNA            join(65670259..65670509,65705312..65706257,
                     65751498..65751696,65817492..65817542,65821812..65821858,
                     65824882..65825438)
                     /gene="TPST1"
                     /product="tyrosylprotein sulfotransferase 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003596.3"
                     /db_xref="GI:215422402"
                     /db_xref="GeneID:8460"
                     /db_xref="HGNC:12020"
                     /db_xref="HPRD:07216"
                     /db_xref="MIM:603125"
     CDS             join(65705413..65706257,65751498..65751696,
                     65817492..65817542,65821812..65821829)
                     /gene="TPST1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein-tyrosine sulfotransferase 1"
                     /protein_id="NP_003587.1"
                     /db_xref="GI:4507665"
                     /db_xref="CCDS:CCDS5533.1"
                     /db_xref="GeneID:8460"
                     /db_xref="HGNC:12020"
                     /db_xref="HPRD:07216"
                     /db_xref="MIM:603125"
     gene            complement(65841031..65865395)
                     /gene="NCRNA00174"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285908"
                     /db_xref="HGNC:27788"
     misc_RNA        complement(join(65841031..65844990,65847224..65847418,
                     65860866..65860943,65864679..65864782,65865309..65865395))
                     /gene="NCRNA00174"
                     /product="non-protein coding RNA 174"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_026873.1"
                     /db_xref="GI:223671902"
                     /db_xref="GeneID:285908"
                     /db_xref="HGNC:27788"
     gene            complement(65887829..65888973)
                     /gene="SKP1P1"
                     /gene_synonym="EMC19; OCP2; TCEB1L; TCEB1P; TCEB1P1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6922"
                     /db_xref="HGNC:33696"
     gene            complement(65899620..65900144)
                     /gene="LOC729126"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:729126"
     gene            65958693..65960461
                     /gene="LOC100289098"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 10 ESTs"
                     /db_xref="GeneID:100289098"
     misc_RNA        join(65958693..65959012,65960242..65960461)
                     /gene="LOC100289098"
                     /product="hypothetical LOC100289098, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_108825.1"
                     /db_xref="GI:310119995"
                     /db_xref="GeneID:100289098"
     misc_RNA        join(65958729..65959008,65960242..65960461)
                     /gene="LOC100289098"
                     /product="hypothetical LOC100289098, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /transcript_id="XR_108824.1"
                     /db_xref="GI:310119996"
                     /db_xref="GeneID:100289098"
     gene            complement(65969948..65971393)
                     /gene="LOC346329"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:346329"
     gene            65976393..66010659
                     /gene="LOC100420547"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420547"
     gene            complement(66018553..66043498)
                     /gene="LOC493754"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:493754"
     misc_RNA        complement(join(66018553..66019824,66025566..66025662,
                     66038372..66038537,66041742..66043498))
                     /gene="LOC493754"
                     /product="RAB guanine nucleotide exchange factor (GEF) 1
                     pseudogene"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002933.1"
                     /db_xref="GI:89886427"
                     /db_xref="GeneID:493754"
     gene            66021139..66022759
                     /gene="LOC643353"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:643353"
     gene            complement(66071690..66072144)
                     /gene="RPL35P5"
                     /gene_synonym="RPL35_4_812"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:441246"
                     /db_xref="HGNC:36955"
     gene            66093868..66108216
                     /gene="KCTD7"
                     /gene_synonym="EPM3; FLJ32069; FLJ45891"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:154881"
                     /db_xref="HGNC:21957"
                     /db_xref="MIM:611725"
     mRNA            join(66093868..66094195,66098262..66098431,
                     66103240..66103418,66103843..66108216)
                     /gene="KCTD7"
                     /gene_synonym="EPM3; FLJ32069; FLJ45891"
                     /product="potassium channel tetramerisation domain
                     containing 7, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_153033.4"
                     /db_xref="GI:319803087"
                     /db_xref="GeneID:154881"
                     /db_xref="HGNC:21957"
                     /db_xref="HPRD:13770"
                     /db_xref="MIM:611725"
     mRNA            join(66093868..66094195,66098262..66098431,
                     66103240..66103418,66103843..66104215,66105381..66108216)
                     /gene="KCTD7"
                     /gene_synonym="EPM3; FLJ32069; FLJ45891"
                     /product="potassium channel tetramerisation domain
                     containing 7, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001167961.2"
                     /db_xref="GI:319803086"
                     /db_xref="GeneID:154881"
                     /db_xref="HGNC:21957"
                     /db_xref="MIM:611725"
     CDS             join(66094052..66094195,66098262..66098431,
                     66103240..66103418,66103843..66104215,66105381)
                     /gene="KCTD7"
                     /gene_synonym="EPM3; FLJ32069; FLJ45891"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="BTB/POZ domain-containing protein KCTD7 isoform
                     2"
                     /protein_id="NP_001161433.1"
                     /db_xref="GI:269784642"
                     /db_xref="CCDS:CCDS55117.1"
                     /db_xref="GeneID:154881"
                     /db_xref="HGNC:21957"
                     /db_xref="MIM:611725"
     CDS             join(66094052..66094195,66098262..66098431,
                     66103240..66103418,66103843..66104219)
                     /gene="KCTD7"
                     /gene_synonym="EPM3; FLJ32069; FLJ45891"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="BTB/POZ domain-containing protein KCTD7 isoform
                     1"
                     /protein_id="NP_694578.1"
                     /db_xref="GI:23308551"
                     /db_xref="CCDS:CCDS5534.1"
                     /db_xref="GeneID:154881"
                     /db_xref="HGNC:21957"
                     /db_xref="MIM:611725"
     gene            66199630..66205592
                     /gene="LOC100653016"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 13 ESTs"
                     /db_xref="GeneID:100653016"
     misc_RNA        join(66199630..66199915,66205144..66205592)
                     /gene="LOC100653016"
                     /product="hypothetical LOC100653016"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 13 ESTs"
                     /transcript_id="XR_132536.1"
                     /db_xref="GI:341915394"
                     /db_xref="GeneID:100653016"
     gene            66205643..66276451
                     /gene="RABGEF1"
                     /gene_synonym="FLJ32302; rabex-5; RABEX5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:27342"
                     /db_xref="HGNC:17676"
                     /db_xref="MIM:609700"
     mRNA            join(66205643..66205779,66236870..66237065,
                     66240214..66240380,66248662..66248828,66260498..66260579,
                     66262361..66262493,66264310..66264401,66270127..66270383,
                     66273873..66276451)
                     /gene="RABGEF1"
                     /gene_synonym="FLJ32302; rabex-5; RABEX5"
                     /product="RAB guanine nucleotide exchange factor (GEF) 1"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014504.2"
                     /db_xref="GI:157412268"
                     /db_xref="GeneID:27342"
                     /db_xref="HGNC:17676"
                     /db_xref="MIM:609700"
     CDS             join(66236887..66237065,66240214..66240380,
                     66248662..66248828,66260498..66260579,66262361..66262493,
                     66264310..66264401,66270127..66270383,66273873..66274271)
                     /gene="RABGEF1"
                     /gene_synonym="FLJ32302; rabex-5; RABEX5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="rab5 GDP/GTP exchange factor"
                     /protein_id="NP_055319.1"
                     /db_xref="GI:7657496"
                     /db_xref="CCDS:CCDS5535.1"
                     /db_xref="GeneID:27342"
                     /db_xref="HGNC:17676"
                     /db_xref="MIM:609700"
     gene            66254802..66255330
                     /gene="LOC100420954"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420954"
     gene            complement(66274980..66309813)
                     /gene="LOC729156"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:729156"
     misc_RNA        complement(join(66274980..66276530,66281140..66281189,
                     66288985..66289059,66290283..66290348,66296183..66296272,
                     66297257..66297467,66297972..66298009,66301722..66301787,
                     66304527..66304616,66304884..66304921,66309663..66309813))
                     /gene="LOC729156"
                     /product="GTF2I repeat domain containing 1-like"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003934.1"
                     /db_xref="GI:157671954"
                     /db_xref="GeneID:729156"
     gene            66369107..66370643
                     /gene="LOC644794"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 3 mRNAs, 5 ESTs, 1 Protein"
                     /db_xref="GeneID:644794"
     misc_RNA        66369107..66370643
                     /gene="LOC644794"
                     /product="hypothetical LOC644794"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 3 mRNAs, 5 ESTs, 1 Protein"
                     /transcript_id="XR_108826.2"
                     /db_xref="GI:341915395"
                     /db_xref="GeneID:644794"
     gene            66379557..66379970
                     /gene="RPL31P38"
                     /gene_synonym="RPL31_17_813"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442326"
                     /db_xref="HGNC:36834"
     gene            66386203..66423538
                     /gene="C7orf42"
                     /gene_synonym="FLJ10099; FLJ13090"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55069"
                     /db_xref="HGNC:25476"
                     /db_xref="HPRD:08541"
     mRNA            join(66386203..66386448,66406835..66407011,
                     66409963..66410248,66413531..66413681,66415939..66416122,
                     66418213..66418356,66420489..66423538)
                     /gene="C7orf42"
                     /gene_synonym="FLJ10099; FLJ13090"
                     /product="chromosome 7 open reading frame 42"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017994.4"
                     /db_xref="GI:98162825"
                     /db_xref="GeneID:55069"
                     /db_xref="HGNC:25476"
                     /db_xref="HPRD:08541"
     CDS             join(66406853..66407011,66409963..66410248,
                     66413531..66413681,66415939..66416122,66418213..66418356,
                     66420489..66420509)
                     /gene="C7orf42"
                     /gene_synonym="FLJ10099; FLJ13090"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC55069"
                     /protein_id="NP_060464.1"
                     /db_xref="GI:8922229"
                     /db_xref="CCDS:CCDS5536.1"
                     /db_xref="GeneID:55069"
                     /db_xref="HGNC:25476"
                     /db_xref="HPRD:08541"
     gene            complement(66452690..66460588)
                     /gene="SBDS"
                     /gene_synonym="CGI-97; FLJ10917; SDS; SWDS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51119"
                     /db_xref="HGNC:19440"
                     /db_xref="HPRD:07393"
                     /db_xref="MIM:607444"
     mRNA            complement(join(66452690..66453486,66456124..66456288,
                     66458204..66458404,66459199..66459328,66460277..66460588))
                     /gene="SBDS"
                     /gene_synonym="CGI-97; FLJ10917; SDS; SWDS"
                     /product="Shwachman-Bodian-Diamond syndrome"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016038.2"
                     /db_xref="GI:28416939"
                     /db_xref="GeneID:51119"
                     /db_xref="HGNC:19440"
                     /db_xref="HPRD:07393"
                     /db_xref="MIM:607444"
     CDS             complement(join(66453358..66453486,66456124..66456288,
                     66458204..66458404,66459199..66459328,66460277..66460404))
                     /gene="SBDS"
                     /gene_synonym="CGI-97; FLJ10917; SDS; SWDS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ribosome maturation protein SBDS"
                     /protein_id="NP_057122.2"
                     /db_xref="GI:28416940"
                     /db_xref="CCDS:CCDS5537.1"
                     /db_xref="GeneID:51119"
                     /db_xref="HGNC:19440"
                     /db_xref="HPRD:07393"
                     /db_xref="MIM:607444"
     gene            66461817..66704499
                     /gene="TYW1"
                     /gene_synonym="FLJ10900; MGC23001; MGC60291; RSAFD1;
                     TYW1A; YPL207W"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55253"
                     /db_xref="HGNC:25598"
                     /db_xref="HPRD:07711"
                     /db_xref="MIM:611243"
     mRNA            join(66461817..66461969,66463052..66463182,
                     66463804..66463941,66474570..66474671,66479354..66479548,
                     66482840..66483130,66489887..66490009,66514936..66515053,
                     66520822..66520874,66532272..66532390,66548417..66548526,
                     66563528..66563705,66582470..66582605,66648113..66648223,
                     66660157..66660324,66703295..66704499)
                     /gene="TYW1"
                     /gene_synonym="FLJ10900; MGC23001; MGC60291; RSAFD1;
                     TYW1A; YPL207W"
                     /product="tRNA-yW synthesizing protein 1 homolog (S.
                     cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018264.2"
                     /db_xref="GI:50726980"
                     /db_xref="GeneID:55253"
                     /db_xref="HGNC:25598"
                     /db_xref="HPRD:07711"
                     /db_xref="MIM:611243"
     CDS             join(66461966..66461969,66463052..66463182,
                     66463804..66463941,66474570..66474671,66479354..66479548,
                     66482840..66483130,66489887..66490009,66514936..66515053,
                     66520822..66520874,66532272..66532390,66548417..66548526,
                     66563528..66563705,66582470..66582605,66648113..66648223,
                     66660157..66660324,66703295..66703516)
                     /gene="TYW1"
                     /gene_synonym="FLJ10900; MGC23001; MGC60291; RSAFD1;
                     TYW1A; YPL207W"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="tRNA wybutosine-synthesizing protein 1 homolog"
                     /protein_id="NP_060734.2"
                     /db_xref="GI:50726981"
                     /db_xref="CCDS:CCDS5538.1"
                     /db_xref="GeneID:55253"
                     /db_xref="HGNC:25598"
                     /db_xref="HPRD:07711"
                     /db_xref="MIM:611243"
     gene            complement(66579309..66579384)
                     /gene="MIR4650-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100616310"
                     /db_xref="HGNC:41755"
                     /db_xref="miRBase:MI0017277"
     ncRNA           complement(66579309..66579384)
                     /gene="MIR4650-1"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4650-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039793.1"
                     /db_xref="GI:337756581"
                     /db_xref="GeneID:100616310"
                     /db_xref="HGNC:41755"
                     /db_xref="miRBase:MI0017277"
     gene            66743280..66753980
                     /gene="LOC442572"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442572"
     gene            complement(66757423..66767406)
                     /gene="PMS2P4"
                     /gene_synonym="PMS2L4; PMS6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:5382"
                     /db_xref="HGNC:9129"
     misc_RNA        complement(join(66757423..66757536,66760605..66760788,
                     66762204..66762290,66764272..66764411,66767363..66767406))
                     /gene="PMS2P4"
                     /gene_synonym="PMS2L4; PMS6"
                     /product="postmeiotic segregation increased 2 pseudogene
                     4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_022007.1"
                     /db_xref="GI:182765467"
                     /db_xref="GeneID:5382"
                     /db_xref="HGNC:9129"
     gene            66767616..66786513
                     /gene="STAG3L4"
                     /gene_synonym="FLJ13195"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64940"
                     /db_xref="HGNC:33887"
                     /db_xref="HPRD:07817"
     mRNA            join(66767616..66767872,66770974..66771070,
                     66773922..66774126,66774551..66774702,66785090..66786513)
                     /gene="STAG3L4"
                     /gene_synonym="FLJ13195"
                     /product="stromal antigen 3-like 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022906.2"
                     /db_xref="GI:148806903"
                     /db_xref="GeneID:64940"
                     /db_xref="HGNC:33887"
                     /db_xref="HPRD:07817"
     CDS             join(66770984..66771070,66773922..66774126,
                     66774551..66774702,66785090..66785098)
                     /gene="STAG3L4"
                     /gene_synonym="FLJ13195"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="STAG3-like protein 4"
                     /protein_id="NP_075057.2"
                     /db_xref="GI:148806904"
                     /db_xref="CCDS:CCDS43594.1"
                     /db_xref="GeneID:64940"
                     /db_xref="HGNC:33887"
                     /db_xref="HPRD:07817"
     gene            complement(67234613..67235718)
                     /gene="LOC100289197"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100289197"
     exon            complement(67234613..67234780)
                     /gene="LOC100289197"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:100289197"
     exon            complement(67235186..67235352)
                     /gene="LOC100289197"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100289197"
     exon            complement(67235393..67235718)
                     /gene="LOC100289197"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100289197"
     gene            68105745..68106594
                     /gene="LOC100419458"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419458"
     gene            complement(69061123..69062454)
                     /gene="LOC100507468"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 7 ESTs"
                     /db_xref="GeneID:100507468"
     misc_RNA        complement(join(69061123..69061419,69062220..69062454))
                     /gene="LOC100507468"
                     /product="hypothetical LOC100507468"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 7 ESTs"
                     /transcript_id="XR_108828.1"
                     /db_xref="GI:310119999"
                     /db_xref="GeneID:100507468"
     gene            69063905..70257885
                     /gene="AUTS2"
                     /gene_synonym="FBRSL2; KIAA0442; MGC13140"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26053"
                     /db_xref="HGNC:14262"
                     /db_xref="HPRD:06276"
                     /db_xref="MIM:607270"
     mRNA            join(69063905..69064948,69364272..69364484,
                     69583118..69583219,69599522..69599557,69900738..69900767,
                     70163555..70163606,70227856..70228327,70229738..70229991,
                     70231100..70231320,70233010..70233054,70236535..70236630,
                     70239014..70239085,70240343..70240372,70242089..70242160,
                     70246601..70246742,70249928..70250005,70250941..70251024,
                     70252195..70252417,70254734..70257885)
                     /gene="AUTS2"
                     /gene_synonym="FBRSL2; KIAA0442; MGC13140"
                     /product="autism susceptibility candidate 2, transcript
                     variant 1"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015570.2"
                     /db_xref="GI:187829443"
                     /db_xref="GeneID:26053"
                     /db_xref="HGNC:14262"
                     /db_xref="HPRD:06276"
                     /db_xref="MIM:607270"
     mRNA            join(69063905..69064948,69364272..69364484,
                     69583118..69583219,69599522..69599557,69900738..69900767,
                     70163555..70163606,70227856..70228327,70229738..70229991,
                     70231100..70231320,70233010..70233054,70236535..70236630,
                     70240343..70240372,70242089..70242160,70246601..70246742,
                     70249928..70250005,70250941..70251024,70252195..70252417,
                     70254734..70257491)
                     /gene="AUTS2"
                     /gene_synonym="FBRSL2; KIAA0442; MGC13140"
                     /product="autism susceptibility candidate 2, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127231.1"
                     /db_xref="GI:187829451"
                     /db_xref="GeneID:26053"
                     /db_xref="HGNC:14262"
                     /db_xref="MIM:607270"
                     /db_xref="HPRD:06276"
     mRNA            join(69063905..69064948,69364272..69364484,
                     69583118..69583219,69599522..69599557,69755354..69755607)
                     /gene="AUTS2"
                     /gene_synonym="FBRSL2; KIAA0442; MGC13140"
                     /product="autism susceptibility candidate 2, transcript
                     variant 3"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127232.1"
                     /db_xref="GI:187829484"
                     /db_xref="GeneID:26053"
                     /db_xref="HGNC:14262"
                     /db_xref="MIM:607270"
                     /db_xref="HPRD:06276"
     CDS             join(69064640..69064948,69364272..69364484,
                     69583118..69583219,69599522..69599557,69900738..69900767,
                     70163555..70163606,70227856..70228327,70229738..70229991,
                     70231100..70231320,70233010..70233054,70236535..70236630,
                     70239014..70239085,70240343..70240372,70242089..70242160,
                     70246601..70246742,70249928..70250005,70250941..70251024,
                     70252195..70252417,70254734..70255982)
                     /gene="AUTS2"
                     /gene_synonym="FBRSL2; KIAA0442; MGC13140"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="autism susceptibility gene 2 protein isoform 1"
                     /protein_id="NP_056385.1"
                     /db_xref="GI:17864090"
                     /db_xref="CCDS:CCDS5539.1"
                     /db_xref="GeneID:26053"
                     /db_xref="HGNC:14262"
                     /db_xref="HPRD:06276"
                     /db_xref="MIM:607270"
     CDS             join(69064640..69064948,69364272..69364484,
                     69583118..69583219,69599522..69599557,69900738..69900767,
                     70163555..70163606,70227856..70228327,70229738..70229991,
                     70231100..70231320,70233010..70233054,70236535..70236630,
                     70240343..70240372,70242089..70242160,70246601..70246742,
                     70249928..70250005,70250941..70251024,70252195..70252417,
                     70254734..70255982)
                     /gene="AUTS2"
                     /gene_synonym="FBRSL2; KIAA0442; MGC13140"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="autism susceptibility gene 2 protein isoform 2"
                     /protein_id="NP_001120703.1"
                     /db_xref="GI:187829452"
                     /db_xref="CCDS:CCDS47601.1"
                     /db_xref="GeneID:26053"
                     /db_xref="HGNC:14262"
                     /db_xref="HPRD:06276"
                     /db_xref="MIM:607270"
     CDS             join(69064640..69064948,69364272..69364484,
                     69583118..69583219,69599522..69599557,69755354..69755494)
                     /gene="AUTS2"
                     /gene_synonym="FBRSL2; KIAA0442; MGC13140"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="autism susceptibility gene 2 protein isoform 3"
                     /protein_id="NP_001120704.1"
                     /db_xref="GI:187829485"
                     /db_xref="CCDS:CCDS47602.1"
                     /db_xref="GeneID:26053"
                     /db_xref="HGNC:14262"
                     /db_xref="HPRD:06276"
                     /db_xref="MIM:607270"
     gene            70597789..71178584
                     /gene="WBSCR17"
                     /gene_synonym="DKFZp434I2216; DKFZp761D2324; GALNT16;
                     GALNT20; GALNTL3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64409"
                     /db_xref="HGNC:16347"
                     /db_xref="HPRD:15655"
     mRNA            join(70597789..70598026,70800536..70800719,
                     70853221..70853387,70880875..70881049,70885894..70886091,
                     71036270..71036387,71130396..71130581,71134957..71135094,
                     71142196..71142291,71175746..71175913,71177003..71178584)
                     /gene="WBSCR17"
                     /gene_synonym="DKFZp434I2216; DKFZp761D2324; GALNT16;
                     GALNT20; GALNTL3"
                     /product="Williams-Beuren syndrome chromosome region 17"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022479.1"
                     /db_xref="GI:22538494"
                     /db_xref="GeneID:64409"
                     /db_xref="HGNC:16347"
                     /db_xref="HPRD:15655"
     CDS             join(70597789..70598026,70800536..70800719,
                     70853221..70853387,70880875..70881049,70885894..70886091,
                     71036270..71036387,71130396..71130581,71134957..71135094,
                     71142196..71142291,71175746..71175913,71177003..71177131)
                     /gene="WBSCR17"
                     /gene_synonym="DKFZp434I2216; DKFZp761D2324; GALNT16;
                     GALNT20; GALNTL3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative polypeptide
                     N-acetylgalactosaminyltransferase-like protein 3"
                     /protein_id="NP_071924.1"
                     /db_xref="GI:22538495"
                     /db_xref="CCDS:CCDS5540.1"
                     /db_xref="GeneID:64409"
                     /db_xref="HGNC:16347"
                     /db_xref="HPRD:15655"
     gene            complement(70772658..70772756)
                     /gene="MIR3914-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100500836"
                     /db_xref="HGNC:38993"
                     /db_xref="miRBase:MI0016419"
     ncRNA           complement(70772658..70772756)
                     /gene="MIR3914-1"
                     /ncRNA_class="miRNA"
                     /product="microRNA 3914-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037477.1"
                     /db_xref="GI:312147076"
                     /db_xref="GeneID:100500836"
                     /db_xref="HGNC:38993"
                     /db_xref="miRBase:MI0016419"
     gene            70772660..70772754
                     /gene="MIR3914-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100500920"
                     /db_xref="HGNC:38975"
                     /db_xref="miRBase:MI0016421"
     ncRNA           70772660..70772754
                     /gene="MIR3914-2"
                     /ncRNA_class="miRNA"
                     /product="microRNA 3914-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037479.1"
                     /db_xref="GI:312147078"
                     /db_xref="GeneID:100500920"
                     /db_xref="HGNC:38975"
                     /db_xref="miRBase:MI0016421"
     gene            complement(71244476..71877360)
                     /gene="CALN1"
                     /gene_synonym="CABP8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:83698"
                     /db_xref="HGNC:13248"
                     /db_xref="HPRD:06209"
                     /db_xref="MIM:607176"
     mRNA            complement(join(71244476..71252887,71275321..71275477,
                     71488642..71488754,71571136..71571279,71743671..71743795,
                     71868236..71868427,71877043..71877360))
                     /gene="CALN1"
                     /gene_synonym="CABP8"
                     /product="calneuron 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_031468.3"
                     /db_xref="GI:157743274"
                     /db_xref="GeneID:83698"
                     /db_xref="HGNC:13248"
                     /db_xref="HPRD:06209"
                     /db_xref="MIM:607176"
     mRNA            complement(join(71244476..71252887,71275321..71275477,
                     71488642..71488754,71571136..71571279,71743671..71743795,
                     71801689..71802208))
                     /gene="CALN1"
                     /gene_synonym="CABP8"
                     /product="calneuron 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001017440.2"
                     /db_xref="GI:157743276"
                     /db_xref="GeneID:83698"
                     /db_xref="HGNC:13248"
                     /db_xref="MIM:607176"
                     /db_xref="HPRD:06209"
     CDS             complement(join(71252760..71252887,71275321..71275477,
                     71488642..71488754,71571136..71571279,71743671..71743795,
                     71868236..71868354))
                     /gene="CALN1"
                     /gene_synonym="CABP8"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium-binding protein 8 isoform 1"
                     /protein_id="NP_113656.2"
                     /db_xref="GI:157743275"
                     /db_xref="CCDS:CCDS47603.1"
                     /db_xref="GeneID:83698"
                     /db_xref="HGNC:13248"
                     /db_xref="HPRD:06209"
                     /db_xref="MIM:607176"
     CDS             complement(join(71252760..71252887,71275321..71275477,
                     71488642..71488754,71571136..71571279,71743671..71743788))
                     /gene="CALN1"
                     /gene_synonym="CABP8"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium-binding protein 8 isoform 2"
                     /protein_id="NP_001017440.1"
                     /db_xref="GI:63054822"
                     /db_xref="CCDS:CCDS5541.1"
                     /db_xref="GeneID:83698"
                     /db_xref="HGNC:13248"
                     /db_xref="HPRD:06209"
                     /db_xref="MIM:607176"
     gene            71407218..71407601
                     /gene="RPS28P6"
                     /gene_synonym="RPS28_2_814"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:728453"
                     /db_xref="HGNC:36085"
     gene            71568157..71569194
                     /gene="LOC100422059"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100422059"
     gene            complement(72039492..72298813)
                     /gene="TYW1B"
                     /gene_synonym="MGC87315; NCRNA00069; RSAFD2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:441250"
                     /db_xref="HGNC:33908"
     mRNA            complement(join(72039492..72040704,72081657..72081824,
                     72093872..72093982,72159677..72159812,72178579..72178756,
                     72193790..72193899,72209460..72209578,72242427..72242544,
                     72267415..72267537,72277659..72277949,72281057..72281251,
                     72285959..72286060,72297434..72297564,72298651..72298813))
                     /gene="TYW1B"
                     /gene_synonym="MGC87315; NCRNA00069; RSAFD2"
                     /product="tRNA-yW synthesizing protein 1 homolog B (S.
                     cerevisiae), transcript variant 1"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145440.1"
                     /db_xref="GI:224282122"
                     /db_xref="GeneID:441250"
                     /db_xref="HGNC:33908"
     CDS             complement(join(72040483..72040704,72081657..72081824,
                     72093872..72093982,72159677..72159812,72178579..72178756,
                     72193790..72193899,72209460..72209578,72242427..72242544,
                     72267415..72267537,72277659..72277949,72281057..72281251,
                     72285959..72286060,72297434..72297564,72298651..72298654))
                     /gene="TYW1B"
                     /gene_synonym="MGC87315; NCRNA00069; RSAFD2"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="tRNA wybutosine-synthesizing protein 1 homolog B
                     isoform 1"
                     /protein_id="NP_001138912.1"
                     /db_xref="GI:224282123"
                     /db_xref="GeneID:441250"
                     /db_xref="HGNC:33908"
     mRNA            complement(join(72049671..>72049737,<72080099..>72080107,
                     72081657..72081824,72093872..72093982,72159677..72159812,
                     72178579..72178756,72193790..72193899,72209460..72209578,
                     72242427..72242544,72267415..72267537,72285959..72286060,
                     72297434..72297564,72298651..72298813))
                     /gene="TYW1B"
                     /gene_synonym="MGC87315; NCRNA00069; RSAFD2"
                     /product="tRNA-yW synthesizing protein 1 homolog B (S.
                     cerevisiae), transcript variant 2"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145441.1"
                     /db_xref="GI:224282124"
                     /db_xref="GeneID:441250"
                     /db_xref="HGNC:33908"
     CDS             complement(join(72049699..72049737,<72080099..>72080107,
                     72081657..72081824,72093872..72093982,72159677..72159812,
                     72178579..72178756,72193790..72193899,72209460..72209578,
                     72242427..72242544,72267415..72267537,72285959..72286060,
                     72297434..72297564,72298651..72298654))
                     /gene="TYW1B"
                     /gene_synonym="MGC87315; NCRNA00069; RSAFD2"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="tRNA wybutosine-synthesizing protein 1 homolog B
                     isoform 2"
                     /protein_id="NP_001138913.1"
                     /db_xref="GI:224282125"
                     /db_xref="GeneID:441250"
                     /db_xref="HGNC:33908"
     gene            72162874..72162949
                     /gene="MIR4650-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100616331"
                     /db_xref="HGNC:41810"
                     /db_xref="miRBase:MI0017278"
     ncRNA           72162874..72162949
                     /gene="MIR4650-2"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4650-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039794.1"
                     /db_xref="GI:337756586"
                     /db_xref="GeneID:100616331"
                     /db_xref="HGNC:41810"
                     /db_xref="miRBase:MI0017278"
     gene            72299952..72307978
                     /gene="SBDSP1"
                     /gene_synonym="SBDSP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:155370"
                     /db_xref="HGNC:21646"
     misc_RNA        join(72299952..72300362,72301272..72301393,
                     72302182..72302378,72304344..72304508,72307156..72307978)
                     /gene="SBDSP1"
                     /gene_synonym="SBDSP"
                     /product="Shwachman-Bodian-Diamond syndrome pseudogene 1,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_024110.1"
                     /db_xref="GI:197313648"
                     /db_xref="GeneID:155370"
                     /db_xref="HGNC:21646"
     misc_RNA        join(72299952..72300362,72302182..72302378,
                     72304344..72304508,72307156..72307978)
                     /gene="SBDSP1"
                     /gene_synonym="SBDSP"
                     /product="Shwachman-Bodian-Diamond syndrome pseudogene 1,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_024111.1"
                     /db_xref="GI:197313649"
                     /db_xref="GeneID:155370"
                     /db_xref="HGNC:21646"
     misc_RNA        join(72299952..72300362,72301272..72301393,
                     72302182..72302378,72304344..72304586)
                     /gene="SBDSP1"
                     /gene_synonym="SBDSP"
                     /product="Shwachman-Bodian-Diamond syndrome pseudogene 1,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_001588.2"
                     /db_xref="GI:197313646"
                     /db_xref="GeneID:155370"
                     /db_xref="HGNC:21646"
     misc_RNA        join(72299952..72300362,72302182..72302378,
                     72304344..72304586)
                     /gene="SBDSP1"
                     /gene_synonym="SBDSP"
                     /product="Shwachman-Bodian-Diamond syndrome pseudogene 1,
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_024109.1"
                     /db_xref="GI:197313647"
                     /db_xref="GeneID:155370"
                     /db_xref="HGNC:21646"
     gene            complement(72333318..72339655)
                     /gene="SPDYE7P"
                     /gene_synonym="MGC119297"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:441251"
                     /db_xref="HGNC:35466"
     misc_RNA        complement(72333318..72339655)
                     /gene="SPDYE7P"
                     /gene_synonym="MGC119297"
                     /product="speedy homolog E7 (Xenopus laevis), pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003666.1"
                     /db_xref="GI:153791199"
                     /db_xref="GeneID:441251"
                     /db_xref="HGNC:35466"
     gene            72349936..72418838
                     /gene="POM121"
                     /gene_synonym="DKFZp586G1822; DKFZp586P2220; FLJ41820;
                     KIAA0618; MGC3792; POM121A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9883"
                     /db_xref="HGNC:19702"
                     /db_xref="HPRD:11448"
     mRNA            join(72349936..72350456,72361166..72361292,
                     72361472..72361649,72396800..72397015,72397340..72397501,
                     72398923..72399003,72400478..72400649,72409129..72409220,
                     72409875..72409948,72410386..72410507,72410953..72411055,
                     72411356..72411532,72412376..72414061,72416125..72416247,
                     72416676..72418838)
                     /gene="POM121"
                     /gene_synonym="DKFZp586G1822; DKFZp586P2220; FLJ41820;
                     KIAA0618; MGC3792; POM121A"
                     /product="POM121 membrane glycoprotein"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_172020.2"
                     /db_xref="GI:300797408"
                     /db_xref="GeneID:9883"
                     /db_xref="HGNC:19702"
                     /db_xref="HPRD:11448"
     CDS             join(72396951..72397015,72397340..72397501,
                     72398923..72399003,72400478..72400649,72409129..72409220,
                     72409875..72409948,72410386..72410507,72410953..72411055,
                     72411356..72411532,72412376..72414061,72416125..72416247,
                     72416676..72416773)
                     /gene="POM121"
                     /gene_synonym="DKFZp586G1822; DKFZp586P2220; FLJ41820;
                     KIAA0618; MGC3792; POM121A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="nuclear envelope pore membrane protein POM 121"
                     /protein_id="NP_742017.1"
                     /db_xref="GI:26051278"
                     /db_xref="CCDS:CCDS5542.1"
                     /db_xref="GeneID:9883"
                     /db_xref="HGNC:19702"
                     /db_xref="HPRD:11448"
     gene            complement(72418832..72425302)
                     /gene="NSUN5P2"
                     /gene_synonym="DKFZp434K058; DKFZp666P104; FLJ11626;
                     MGC129801; MGC15057; NOL1R2; NSUN5C; WBSCR20B; WBSCR20C"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:260294"
                     /db_xref="HGNC:16609"
     misc_RNA        complement(join(72418832..72419136,72419207..72419347,
                     72419431..72419641,72419852..72420030,72420385..72420500,
                     72420597..72420735,72422691..72422834,72423865..72423969,
                     72424050..72424216,72424898..72425018,72425164..72425302))
                     /gene="NSUN5P2"
                     /gene_synonym="DKFZp434K058; DKFZp666P104; FLJ11626;
                     MGC129801; MGC15057; NOL1R2; NSUN5C; WBSCR20B; WBSCR20C"
                     /product="NOP2/Sun domain family, member 5 pseudogene 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_033323.2"
                     /db_xref="GI:291621681"
                     /db_xref="GeneID:260294"
                     /db_xref="HGNC:16609"
     gene            complement(72430016..72439997)
                     /gene="TRIM74"
                     /gene_synonym="MGC45440; TRIM50C"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:378108"
                     /db_xref="HGNC:17453"
                     /db_xref="HPRD:15567"
                     /db_xref="MIM:612550"
     mRNA            complement(join(72430016..72430439,72430552..72430782,
                     72431881..72431976,72436290..72436706,72439816..72439997))
                     /gene="TRIM74"
                     /gene_synonym="MGC45440; TRIM50C"
                     /product="tripartite motif containing 74"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198853.1"
                     /db_xref="GI:38524611"
                     /db_xref="GeneID:378108"
                     /db_xref="HGNC:17453"
                     /db_xref="HPRD:15567"
                     /db_xref="MIM:612550"
     CDS             complement(join(72430413..72430439,72430552..72430782,
                     72431881..72431976,72436290..72436688))
                     /gene="TRIM74"
                     /gene_synonym="MGC45440; TRIM50C"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="tripartite motif-containing protein 74"
                     /protein_id="NP_942150.1"
                     /db_xref="GI:38524612"
                     /db_xref="CCDS:CCDS5545.1"
                     /db_xref="GeneID:378108"
                     /db_xref="HGNC:17453"
                     /db_xref="HPRD:15567"
                     /db_xref="MIM:612550"
     gene            72440213..72442259
                     /gene="LOC100101148"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100101148"
     gene            72463447..72464560
                     /gene="LOC100507615"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /db_xref="GeneID:100507615"
     misc_RNA        join(72463447..72463504,72463963..72464560)
                     /gene="LOC100507615"
                     /product="hypothetical LOC100507615"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /transcript_id="XR_108829.1"
                     /db_xref="GI:310120000"
                     /db_xref="GeneID:100507615"
     gene            complement(72469013..72476455)
                     /gene="STAG3L3"
                     /gene_synonym="STAG3L1; STAG3L2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:442578"
                     /db_xref="HGNC:33845"
                     /db_xref="HPRD:18656"
     mRNA            complement(join(72469013..72469313,72469578..72469685,
                     72469994..72470073,72470284..72470382,72470881..72471004,
                     72473544..72473660,72474168..72474253,72476099..72476455))
                     /gene="STAG3L3"
                     /gene_synonym="STAG3L1; STAG3L2"
                     /product="stromal antigen 3-like 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001013739.2"
                     /db_xref="GI:148236294"
                     /db_xref="GeneID:442578"
                     /db_xref="HGNC:33845"
                     /db_xref="HPRD:18656"
     CDS             complement(join(72469628..72469685,72469994..72470073,
                     72470284..72470382,72470881..72471004,72473544..72473587))
                     /gene="STAG3L3"
                     /gene_synonym="STAG3L1; STAG3L2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="STAG3-like protein 3"
                     /protein_id="NP_001013761.2"
                     /db_xref="GI:148236295"
                     /db_xref="CCDS:CCDS34651.1"
                     /db_xref="GeneID:442578"
                     /db_xref="HGNC:33845"
                     /db_xref="HPRD:18656"
     gene            72476588..72483807
                     /gene="PMS2LP2"
                     /gene_synonym="PMSR7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100101440"
                     /db_xref="HGNC:33515"
     gene            complement(72490260..72500309)
                     /gene="SPDYE8P"
                     /gene_synonym="MGC131642; MGC48646"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:389517"
                     /db_xref="HGNC:33771"
     misc_RNA        complement(join(72490260..72491729,72492583..72492687,
                     72492810..72493053,72494760..72494845,72496073..72496131,
                     72497165..72497383,72498384..72498966,72500192..72500309))
                     /gene="SPDYE8P"
                     /gene_synonym="MGC131642; MGC48646"
                     /product="speedy homolog E8 (Xenopus laevis), pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003664.2"
                     /db_xref="GI:154816206"
                     /db_xref="GeneID:389517"
                     /db_xref="HGNC:33771"
     gene            72507939..72511870
                     /gene="PMS2P8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:729299"
                     /db_xref="HGNC:33516"
     gene            complement(72518322..72525621)
                     /gene="LOC728524"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:728524"
     gene            72569012..72621336
                     /gene="LOC100093631"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:100093631"
     misc_RNA        join(72569012..72569124,72569307..72569431,
                     72589455..72589565,72590897..72590962,72593127..72593310,
                     72594579..72594637,72596117..72596188,72597155..72597338,
                     72598701..72598759,72604106..72604177,72605411..72605594,
                     72606537..72606595,72606991..72607065,72608666..72608767,
                     72609676..72609741,72609919..72610102,72612004..72612059,
                     72612733..72612813,72613736..72613819,72614489..72614672,
                     72616152..72616180,72617463..72617504,72618603..72618644,
                     72619423..72619498,72620192..72621336)
                     /gene="LOC100093631"
                     /product="general transcription factor II, i, pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003580.1"
                     /db_xref="GI:149274644"
                     /db_xref="GeneID:100093631"
     gene            72634674..72649979
                     /gene="NCF1B"
                     /gene_synonym="NCF-1B; SH3PXD1B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:654816"
                     /db_xref="HGNC:32522"
     misc_RNA        join(72634674..72634752,72637913..72637991,
                     72641444..72641499,72643601..72644294,72645845..72645924,
                     72648648..72648752,72649223..72649368,72649703..72649979)
                     /gene="NCF1B"
                     /gene_synonym="NCF-1B; SH3PXD1B"
                     /product="neutrophil cytosolic factor 1B pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003186.1"
                     /db_xref="GI:114687641"
                     /db_xref="GeneID:654816"
                     /db_xref="HGNC:32522"
     gene            complement(72656902..72685658)
                     /gene="GTF2IRD2P1"
                     /gene_synonym="GTF2IRD2P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:401375"
                     /db_xref="HGNC:33127"
     misc_RNA        complement(join(72656902..72658904,72662610..72662638,
                     72663923..72664105,72665405..72665488,72667561..72667638,
                     72669732..72669797,72671516..72671572,72673354..72673431,
                     72680156..72680199,72680571..72680625,72683023..72683051,
                     72683220..72683403,72685539..72685658))
                     /gene="GTF2IRD2P1"
                     /gene_synonym="GTF2IRD2P"
                     /product="GTF2I repeat domain containing 2 pseudogene 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002164.1"
                     /db_xref="GI:51241786"
                     /db_xref="GeneID:401375"
                     /db_xref="HGNC:33127"
     gene            72707495..72717227
                     /gene="POM121B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100288540"
                     /db_xref="HGNC:34004"
     gene            complement(72716514..72722864)
                     /gene="NSUN5"
                     /gene_synonym="FLJ10267; MGC986; NOL1; NOL1R; NSUN5A;
                     p120; WBSCR20; WBSCR20A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55695"
                     /db_xref="HGNC:16385"
     mRNA            complement(join(72716514..72717526,72717597..72717737,
                     72717823..72718033,72718227..72718405,72718744..72718859,
                     72718956..72719094,72721391..72721499,72721580..72721754,
                     72722428..72722550,72722695..72722864))
                     /gene="NSUN5"
                     /gene_synonym="FLJ10267; MGC986; NOL1; NOL1R; NSUN5A;
                     p120; WBSCR20; WBSCR20A"
                     /product="NOP2/Sun domain family, member 5, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_148956.2"
                     /db_xref="GI:270288814"
                     /db_xref="GeneID:55695"
                     /db_xref="HGNC:16385"
                     /db_xref="HPRD:11678"
     mRNA            complement(join(72716514..72717737,72717823..72718033,
                     72718227..72718405,72718744..72718859,72718956..72719094,
                     72721391..72721499,72721580..72721754,72722428..72722550,
                     72722695..72722864))
                     /gene="NSUN5"
                     /gene_synonym="FLJ10267; MGC986; NOL1; NOL1R; NSUN5A;
                     p120; WBSCR20; WBSCR20A"
                     /product="NOP2/Sun domain family, member 5, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018044.3"
                     /db_xref="GI:270288813"
                     /db_xref="GeneID:55695"
                     /db_xref="HGNC:16385"
     mRNA            complement(join(72716514..72717521,72717597..72717737,
                     72717823..72718033,72718227..72718405,72718744..72718859,
                     72718956..72719094,72721391..72721499,72721580..72721754,
                     72722428..72722550,72722695..72722864))
                     /gene="NSUN5"
                     /gene_synonym="FLJ10267; MGC986; NOL1; NOL1R; NSUN5A;
                     p120; WBSCR20; WBSCR20A"
                     /product="NOP2/Sun domain family, member 5, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001168347.1"
                     /db_xref="GI:270288815"
                     /db_xref="GeneID:55695"
                     /db_xref="HGNC:16385"
     mRNA            complement(join(72716514..72717737,72717823..72718033,
                     72718227..72718405,72718744..72718859,72718956..72719094,
                     72721391..72721499,72721580..72721640,72722428..72722550,
                     72722695..72722864))
                     /gene="NSUN5"
                     /gene_synonym="FLJ10267; MGC986; NOL1; NOL1R; NSUN5A;
                     p120; WBSCR20; WBSCR20A"
                     /product="NOP2/Sun domain family, member 5, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001168348.1"
                     /db_xref="GI:270288817"
                     /db_xref="GeneID:55695"
                     /db_xref="HGNC:16385"
     CDS             complement(join(72717395..72717521,72717597..72717737,
                     72717823..72718033,72718227..72718405,72718744..72718859,
                     72718956..72719094,72721391..72721499,72721580..72721754,
                     72722428..72722550,72722695..72722787))
                     /gene="NSUN5"
                     /gene_synonym="FLJ10267; MGC986; NOL1; NOL1R; NSUN5A;
                     p120; WBSCR20; WBSCR20A"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative methyltransferase NSUN5 isoform 3"
                     /protein_id="NP_001161819.1"
                     /db_xref="GI:270288816"
                     /db_xref="CCDS:CCDS55119.1"
                     /db_xref="GeneID:55695"
                     /db_xref="HGNC:16385"
     CDS             complement(join(72717412..72717526,72717597..72717737,
                     72717823..72718033,72718227..72718405,72718744..72718859,
                     72718956..72719094,72721391..72721499,72721580..72721754,
                     72722428..72722550,72722695..72722787))
                     /gene="NSUN5"
                     /gene_synonym="FLJ10267; MGC986; NOL1; NOL1R; NSUN5A;
                     p120; WBSCR20; WBSCR20A"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative methyltransferase NSUN5 isoform 1"
                     /protein_id="NP_683759.1"
                     /db_xref="GI:23199998"
                     /db_xref="CCDS:CCDS5546.1"
                     /db_xref="GeneID:55695"
                     /db_xref="HGNC:16385"
     CDS             complement(join(72717593..72717737,72717823..72718033,
                     72718227..72718405,72718744..72718859,72718956..72719094,
                     72721391..72721499,72721580..72721754,72722428..72722550,
                     72722695..72722787))
                     /gene="NSUN5"
                     /gene_synonym="FLJ10267; MGC986; NOL1; NOL1R; NSUN5A;
                     p120; WBSCR20; WBSCR20A"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative methyltransferase NSUN5 isoform 2"
                     /protein_id="NP_060514.1"
                     /db_xref="GI:8922322"
                     /db_xref="CCDS:CCDS5547.1"
                     /db_xref="GeneID:55695"
                     /db_xref="HGNC:16385"
     CDS             complement(join(72717593..72717737,72717823..72718033,
                     72718227..72718405,72718744..72718859,72718956..72719094,
                     72721391..72721499,72721580..72721640,72722428..72722550,
                     72722695..72722787))
                     /gene="NSUN5"
                     /gene_synonym="FLJ10267; MGC986; NOL1; NOL1R; NSUN5A;
                     p120; WBSCR20; WBSCR20A"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative methyltransferase NSUN5 isoform 4"
                     /protein_id="NP_001161820.1"
                     /db_xref="GI:270288818"
                     /db_xref="CCDS:CCDS55118.1"
                     /db_xref="GeneID:55695"
                     /db_xref="HGNC:16385"
     gene            complement(72726535..72742085)
                     /gene="TRIM50"
                     /gene_synonym="FLJ32804; MGC138357; MGC138359; TRIM50A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:135892"
                     /db_xref="HGNC:19017"
                     /db_xref="HPRD:15566"
                     /db_xref="MIM:612548"
     mRNA            complement(join(72726535..72727506,72730564..72730688,
                     72732686..72732708,72732821..72733051,72734146..72734241,
                     72738387..72738803,72741903..72742085))
                     /gene="TRIM50"
                     /gene_synonym="FLJ32804; MGC138357; MGC138359; TRIM50A"
                     /product="tripartite motif containing 50"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178125.2"
                     /db_xref="GI:31342404"
                     /db_xref="GeneID:135892"
                     /db_xref="HGNC:19017"
                     /db_xref="HPRD:15566"
                     /db_xref="MIM:612548"
     CDS             complement(join(72726917..72727506,72730564..72730688,
                     72732686..72732708,72732821..72733051,72734146..72734241,
                     72738387..72738785))
                     /gene="TRIM50"
                     /gene_synonym="FLJ32804; MGC138357; MGC138359; TRIM50A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase TRIM50"
                     /protein_id="NP_835226.1"
                     /db_xref="GI:30023818"
                     /db_xref="CCDS:CCDS34654.1"
                     /db_xref="GeneID:135892"
                     /db_xref="HGNC:19017"
                     /db_xref="HPRD:15566"
                     /db_xref="MIM:612548"
     gene            72742155..72772641
                     /gene="FKBP6"
                     /gene_synonym="FKBP36; MGC87179; PPIase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8468"
                     /db_xref="HGNC:3722"
                     /db_xref="HPRD:05326"
                     /db_xref="MIM:604839"
     mRNA            join(72742155..72742317,72742578..72742695,
                     72743363..72743452,72744153..72744355,72745660..72745779,
                     72754640..72754834,72755272..72755381,72756807..72756899,
                     72772190..72772641)
                     /gene="FKBP6"
                     /gene_synonym="FKBP36; MGC87179; PPIase"
                     /product="FK506 binding protein 6, 36kDa, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001135211.1"
                     /db_xref="GI:206725543"
                     /db_xref="GeneID:8468"
                     /db_xref="HGNC:3722"
                     /db_xref="MIM:604839"
                     /db_xref="HPRD:05326"
     CDS             join(72742276..72742317,72742578..72742695,
                     72743363..72743452,72744153..72744355,72745660..72745779,
                     72754640..72754834,72755272..72755381,72756807..72756897)
                     /gene="FKBP6"
                     /gene_synonym="FKBP36; MGC87179; PPIase"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="peptidyl-prolyl cis-trans isomerase FKBP6
                     isoform b"
                     /protein_id="NP_001128683.1"
                     /db_xref="GI:206725544"
                     /db_xref="CCDS:CCDS47604.1"
                     /db_xref="GeneID:8468"
                     /db_xref="HGNC:3722"
                     /db_xref="HPRD:05326"
                     /db_xref="MIM:604839"
     mRNA            join(72742300..72742488,72742578..72742695,
                     72743363..72743452,72744153..72744355,72745660..72745779,
                     72754640..72754834,72755272..72755381,72756807..72756899,
                     72772190..72772641)
                     /gene="FKBP6"
                     /gene_synonym="FKBP36; MGC87179; PPIase"
                     /product="FK506 binding protein 6, 36kDa, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003602.3"
                     /db_xref="GI:146229345"
                     /db_xref="GeneID:8468"
                     /db_xref="HGNC:3722"
                     /db_xref="HPRD:05326"
                     /db_xref="MIM:604839"
     CDS             join(72742432..72742488,72742578..72742695,
                     72743363..72743452,72744153..72744355,72745660..72745779,
                     72754640..72754834,72755272..72755381,72756807..72756897)
                     /gene="FKBP6"
                     /gene_synonym="FKBP36; MGC87179; PPIase"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="peptidyl-prolyl cis-trans isomerase FKBP6
                     isoform a"
                     /protein_id="NP_003593.3"
                     /db_xref="GI:146229346"
                     /db_xref="CCDS:CCDS43595.1"
                     /db_xref="GeneID:8468"
                     /db_xref="HGNC:3722"
                     /db_xref="HPRD:05326"
                     /db_xref="MIM:604839"
     gene            72848109..72850450
                     /gene="FZD9"
                     /gene_synonym="CD349; FZD3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8326"
                     /db_xref="HGNC:4047"
                     /db_xref="HPRD:03460"
                     /db_xref="MIM:601766"
     mRNA            72848109..72850450
                     /gene="FZD9"
                     /gene_synonym="CD349; FZD3"
                     /product="frizzled family receptor 9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003508.2"
                     /db_xref="GI:62865872"
                     /db_xref="GeneID:8326"
                     /db_xref="HGNC:4047"
                     /db_xref="HPRD:03460"
                     /db_xref="MIM:601766"
     CDS             72848338..72850113
                     /gene="FZD9"
                     /gene_synonym="CD349; FZD3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="frizzled-9 precursor"
                     /protein_id="NP_003499.1"
                     /db_xref="GI:4503835"
                     /db_xref="CCDS:CCDS5548.1"
                     /db_xref="GeneID:8326"
                     /db_xref="HGNC:4047"
                     /db_xref="HPRD:03460"
                     /db_xref="MIM:601766"
     gene            complement(72854728..72936615)
                     /gene="BAZ1B"
                     /gene_synonym="WBSCR10; WBSCR9; WSTF"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9031"
                     /db_xref="HGNC:961"
                     /db_xref="HPRD:10416"
                     /db_xref="MIM:605681"
     mRNA            complement(join(72854728..72856023,72856511..72856883,
                     72857055..72857158,72858314..72858459,72861594..72861709,
                     72863872..72864019,72865177..72865324,72873866..72874048,
                     72877252..72877429,72879769..72879867,72880626..72880731,
                     72883847..72883980,72884675..72884813,72891198..72892899,
                     72903524..72903721,72907130..72907251,72912827..72913028,
                     72922657..72922801,72925066..72925182,72936157..72936615))
                     /gene="BAZ1B"
                     /gene_synonym="WBSCR10; WBSCR9; WSTF"
                     /product="bromodomain adjacent to zinc finger domain, 1B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032408.3"
                     /db_xref="GI:264681496"
                     /db_xref="GeneID:9031"
                     /db_xref="HGNC:961"
                     /db_xref="HPRD:10416"
                     /db_xref="MIM:605681"
     CDS             complement(join(72856526..72856883,72857055..72857158,
                     72858314..72858459,72861594..72861709,72863872..72864019,
                     72865177..72865324,72873866..72874048,72877252..72877429,
                     72879769..72879867,72880626..72880731,72883847..72883980,
                     72884675..72884813,72891198..72892899,72903524..72903721,
                     72907130..72907251,72912827..72913028,72922657..72922801,
                     72925066..72925182,72936157..72936263))
                     /gene="BAZ1B"
                     /gene_synonym="WBSCR10; WBSCR9; WSTF"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="tyrosine-protein kinase BAZ1B"
                     /protein_id="NP_115784.1"
                     /db_xref="GI:14670392"
                     /db_xref="CCDS:CCDS5549.1"
                     /db_xref="GeneID:9031"
                     /db_xref="HGNC:961"
                     /db_xref="HPRD:10416"
                     /db_xref="MIM:605681"
     gene            complement(72950683..72972065)
                     /gene="BCL7B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9275"
                     /db_xref="HGNC:1005"
                     /db_xref="HPRD:05786"
                     /db_xref="MIM:605846"
     mRNA            complement(join(72950683..72951720,72952264..72952343,
                     72954212..72954382,72957878..72957974,72966497..72966572,
                     72971817..72972065))
                     /gene="BCL7B"
                     /product="B-cell CLL/lymphoma 7B, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001707.3"
                     /db_xref="GI:308522769"
                     /db_xref="GeneID:9275"
                     /db_xref="HGNC:1005"
                     /db_xref="HPRD:05786"
                     /db_xref="MIM:605846"
     mRNA            complement(join(72950683..72951720,72952264..72952343,
                     72957878..72957974,72966497..72966572,72971817..72972065))
                     /gene="BCL7B"
                     /product="B-cell CLL/lymphoma 7B, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001197244.1"
                     /db_xref="GI:308522772"
                     /db_xref="GeneID:9275"
                     /db_xref="HGNC:1005"
                     /db_xref="MIM:605846"
                     /db_xref="HPRD:05786"
     misc_RNA        complement(join(72950683..72951720,72952264..72952343,
                     72954212..72954382,72957878..72957974,72966497..72966572,
                     72971371..72971602))
                     /gene="BCL7B"
                     /product="B-cell CLL/lymphoma 7B, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_036682.1"
                     /db_xref="GI:308522776"
                     /db_xref="GeneID:9275"
                     /db_xref="HGNC:1005"
                     /db_xref="MIM:605846"
                     /db_xref="HPRD:05786"
     CDS             complement(join(72951628..72951720,72952264..72952343,
                     72954212..72954382,72957878..72957974,72966497..72966572,
                     72971817..72971908))
                     /gene="BCL7B"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="B-cell CLL/lymphoma 7 protein family member B
                     isoform 1"
                     /protein_id="NP_001698.2"
                     /db_xref="GI:20336473"
                     /db_xref="CCDS:CCDS5550.1"
                     /db_xref="GeneID:9275"
                     /db_xref="HGNC:1005"
                     /db_xref="HPRD:05786"
                     /db_xref="MIM:605846"
     CDS             complement(join(72951628..72951720,72952264..72952343,
                     72957878..72957974,72966497..72966572,72971817..72971908))
                     /gene="BCL7B"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="B-cell CLL/lymphoma 7 protein family member B
                     isoform 2"
                     /protein_id="NP_001184173.1"
                     /db_xref="GI:308522773"
                     /db_xref="GeneID:9275"
                     /db_xref="HGNC:1005"
                     /db_xref="MIM:605846"
                     /db_xref="HPRD:05786"
     gene            complement(72983274..72993013)
                     /gene="TBL2"
                     /gene_synonym="DKFZp434N024; MGC134739; WBSCR13;
                     WS-betaTRP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26608"
                     /db_xref="HGNC:11586"
                     /db_xref="HPRD:09319"
                     /db_xref="MIM:605842"
     mRNA            complement(join(72983274..72985302,72985519..72985671,
                     72987174..72987300,72987650..72987801,72988268..72988452,
                     72988713..72988843,72992750..72993013))
                     /gene="TBL2"
                     /gene_synonym="DKFZp434N024; MGC134739; WBSCR13;
                     WS-betaTRP"
                     /product="transducin (beta)-like 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012453.2"
                     /db_xref="GI:84874693"
                     /db_xref="GeneID:26608"
                     /db_xref="HGNC:11586"
                     /db_xref="HPRD:09319"
                     /db_xref="MIM:605842"
     CDS             complement(join(72984837..72985302,72985519..72985671,
                     72987174..72987300,72987650..72987801,72988268..72988452,
                     72988713..72988843,72992750..72992879))
                     /gene="TBL2"
                     /gene_synonym="DKFZp434N024; MGC134739; WBSCR13;
                     WS-betaTRP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transducin beta-like protein 2"
                     /protein_id="NP_036585.1"
                     /db_xref="GI:7549793"
                     /db_xref="CCDS:CCDS5551.1"
                     /db_xref="GeneID:26608"
                     /db_xref="HGNC:11586"
                     /db_xref="HPRD:09319"
                     /db_xref="MIM:605842"
     gene            complement(73007524..73038870)
                     /gene="MLXIPL"
                     /gene_synonym="bHLHd14; CHREBP; MIO; MONDOB; WBSCR14;
                     WS-bHLH"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51085"
                     /db_xref="HGNC:12744"
                     /db_xref="MIM:605678"
     mRNA            complement(join(73007524..73008313,73008604..73008733,
                     73009967..73010090,73010172..73010299,73010483..73010602,
                     73010694..73010809,73010969..73011119,73011195..73011262,
                     73011512..73012043,73013856..73014025,73020018..73020098,
                     73020240..73020441,73021304..73021348,73021661..73021750,
                     73021920..73022002,73030401..73030507,73038530..73038870))
                     /gene="MLXIPL"
                     /gene_synonym="bHLHd14; CHREBP; MIO; MONDOB; WBSCR14;
                     WS-bHLH"
                     /product="MLX interacting protein-like, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032951.2"
                     /db_xref="GI:78711801"
                     /db_xref="GeneID:51085"
                     /db_xref="HGNC:12744"
                     /db_xref="HPRD:12033"
                     /db_xref="MIM:605678"
     mRNA            complement(join(73007524..73008313,73008604..73008733,
                     73009967..73010090,73010172..73010242,73010483..73010602,
                     73010694..73010809,73010969..73011119,73011195..73011262,
                     73011512..73012043,73013856..73014025,73020018..73020098,
                     73020240..73020441,73021304..73021348,73021661..73021750,
                     73021920..73022002,73030401..73030507,73038530..73038870))
                     /gene="MLXIPL"
                     /gene_synonym="bHLHd14; CHREBP; MIO; MONDOB; WBSCR14;
                     WS-bHLH"
                     /product="MLX interacting protein-like, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032952.2"
                     /db_xref="GI:78711800"
                     /db_xref="GeneID:51085"
                     /db_xref="HGNC:12744"
                     /db_xref="MIM:605678"
     mRNA            complement(join(73007524..73008313,73008604..73008733,
                     73009967..73010090,73010172..73010299,73010483..73010596,
                     73010694..73010809,73010969..73011119,73011195..73011262,
                     73011512..73012043,73013856..73014025,73020018..73020098,
                     73020240..73020441,73021304..73021348,73021661..73021750,
                     73021920..73022002,73030401..73030507,73038530..73038870))
                     /gene="MLXIPL"
                     /gene_synonym="bHLHd14; CHREBP; MIO; MONDOB; WBSCR14;
                     WS-bHLH"
                     /product="MLX interacting protein-like, transcript variant
                     3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032953.2"
                     /db_xref="GI:78711807"
                     /db_xref="GeneID:51085"
                     /db_xref="HGNC:12744"
                     /db_xref="MIM:605678"
     mRNA            complement(join(73007524..73008313,73008604..73008733,
                     73009967..73010090,73010172..73010242,73010483..73010596,
                     73010694..73010809,73010969..73011119,73011195..73011262,
                     73011512..73012043,73013856..73014025,73020018..73020098,
                     73020240..73020441,73021304..73021348,73021661..73021750,
                     73021920..73022002,73030401..73030507,73038530..73038870))
                     /gene="MLXIPL"
                     /gene_synonym="bHLHd14; CHREBP; MIO; MONDOB; WBSCR14;
                     WS-bHLH"
                     /product="MLX interacting protein-like, transcript variant
                     4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032954.2"
                     /db_xref="GI:78711808"
                     /db_xref="GeneID:51085"
                     /db_xref="HGNC:12744"
                     /db_xref="MIM:605678"
     CDS             complement(join(73008195..73008313,73008604..73008733,
                     73009967..73010090,73010172..73010299,73010483..73010602,
                     73010694..73010809,73010969..73011119,73011195..73011262,
                     73011512..73012043,73013856..73014025,73020018..73020098,
                     73020240..73020441,73021304..73021348,73021661..73021750,
                     73021920..73022002,73030401..73030507,73038530..73038822))
                     /gene="MLXIPL"
                     /gene_synonym="bHLHd14; CHREBP; MIO; MONDOB; WBSCR14;
                     WS-bHLH"
                     /note="isoform alpha is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="Williams-Beuren syndrome chromosomal region 14
                     protein isoform alpha"
                     /protein_id="NP_116569.1"
                     /db_xref="GI:14602433"
                     /db_xref="CCDS:CCDS5553.1"
                     /db_xref="GeneID:51085"
                     /db_xref="HGNC:12744"
                     /db_xref="MIM:605678"
     CDS             complement(join(73008195..73008313,73008604..73008733,
                     73009967..73010090,73010172..73010242,73010483..73010602,
                     73010694..73010809,73010969..73011119,73011195..73011262,
                     73011512..73012043,73013856..73014025,73020018..73020098,
                     73020240..73020441,73021304..73021348,73021661..73021750,
                     73021920..73022002,73030401..73030507,73038530..73038822))
                     /gene="MLXIPL"
                     /gene_synonym="bHLHd14; CHREBP; MIO; MONDOB; WBSCR14;
                     WS-bHLH"
                     /note="isoform beta is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="Williams-Beuren syndrome chromosomal region 14
                     protein isoform beta"
                     /protein_id="NP_116570.1"
                     /db_xref="GI:14602435"
                     /db_xref="CCDS:CCDS47605.1"
                     /db_xref="GeneID:51085"
                     /db_xref="HGNC:12744"
                     /db_xref="MIM:605678"
     CDS             complement(join(73008195..73008313,73008604..73008733,
                     73009967..73010090,73010172..73010242,73010483..73010596,
                     73010694..73010809,73010969..73011119,73011195..73011262,
                     73011512..73012043,73013856..73014025,73020018..73020098,
                     73020240..73020441,73021304..73021348,73021661..73021750,
                     73021920..73022002,73030401..73030507,73038530..73038822))
                     /gene="MLXIPL"
                     /gene_synonym="bHLHd14; CHREBP; MIO; MONDOB; WBSCR14;
                     WS-bHLH"
                     /note="isoform delta is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="Williams-Beuren syndrome chromosomal region 14
                     protein isoform delta"
                     /protein_id="NP_116572.1"
                     /db_xref="GI:14602439"
                     /db_xref="CCDS:CCDS5554.1"
                     /db_xref="GeneID:51085"
                     /db_xref="HGNC:12744"
                     /db_xref="MIM:605678"
     CDS             complement(join(73008195..73008313,73008604..73008733,
                     73009967..73010090,73010172..73010299,73010483..73010596,
                     73010694..73010809,73010969..73011119,73011195..73011262,
                     73011512..73012043,73013856..73014025,73020018..73020098,
                     73020240..73020441,73021304..73021348,73021661..73021750,
                     73021920..73022002,73030401..73030507,73038530..73038822))
                     /gene="MLXIPL"
                     /gene_synonym="bHLHd14; CHREBP; MIO; MONDOB; WBSCR14;
                     WS-bHLH"
                     /note="isoform gamma is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="Williams-Beuren syndrome chromosomal region 14
                     protein isoform gamma"
                     /protein_id="NP_116571.1"
                     /db_xref="GI:14602437"
                     /db_xref="CCDS:CCDS47606.1"
                     /db_xref="GeneID:51085"
                     /db_xref="HGNC:12744"
                     /db_xref="MIM:605678"
     gene            73082174..73086440
                     /gene="VPS37D"
                     /gene_synonym="MGC35352; WBSCR24"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:155382"
                     /db_xref="HGNC:18287"
                     /db_xref="MIM:610039"
     mRNA            join(73082174..73082426,73083749..73083920,
                     73084350..73084432,73085344..73086440)
                     /gene="VPS37D"
                     /gene_synonym="MGC35352; WBSCR24"
                     /product="vacuolar protein sorting 37 homolog D (S.
                     cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001077621.1"
                     /db_xref="GI:117938317"
                     /db_xref="GeneID:155382"
                     /db_xref="HGNC:18287"
                     /db_xref="MIM:610039"
     CDS             join(73082289..73082426,73083749..73083920,
                     73084350..73084432,73085344..73085706)
                     /gene="VPS37D"
                     /gene_synonym="MGC35352; WBSCR24"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="vacuolar protein sorting-associated protein 37D"
                     /protein_id="NP_001071089.1"
                     /db_xref="GI:117938318"
                     /db_xref="CCDS:CCDS43596.1"
                     /db_xref="GeneID:155382"
                     /db_xref="HGNC:18287"
                     /db_xref="MIM:610039"
     gene            complement(73095248..73097781)
                     /gene="DNAJC30"
                     /gene_synonym="MGC12943; WBSCR18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84277"
                     /db_xref="HGNC:16410"
                     /db_xref="HPRD:10303"
     mRNA            complement(73095248..73097781)
                     /gene="DNAJC30"
                     /gene_synonym="MGC12943; WBSCR18"
                     /product="DnaJ (Hsp40) homolog, subfamily C, member 30"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032317.2"
                     /db_xref="GI:22538496"
                     /db_xref="GeneID:84277"
                     /db_xref="HGNC:16410"
                     /db_xref="HPRD:10303"
     CDS             complement(73097073..73097753)
                     /gene="DNAJC30"
                     /gene_synonym="MGC12943; WBSCR18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="dnaJ homolog subfamily C member 30"
                     /protein_id="NP_115693.2"
                     /db_xref="GI:22538497"
                     /db_xref="CCDS:CCDS5556.1"
                     /db_xref="GeneID:84277"
                     /db_xref="HGNC:16410"
                     /db_xref="HPRD:10303"
     gene            73097898..73112542
                     /gene="WBSCR22"
                     /gene_synonym="FLJ44236; HASJ4442; HUSSY-3; MGC19709;
                     MGC2022; MGC5140; PP3381; WBMT"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:114049"
                     /db_xref="HGNC:16405"
     mRNA            join(73097898..73098003,73098097..73098134,
                     73100966..73101061,73101148..73101230,73101329..73101425,
                     73105246..73105342,73106926..73106976,73107659..73107744,
                     73107954..73107999,73108322..73108380,73111796..73111846,
                     73111935..73112024,73112162..73112542)
                     /gene="WBSCR22"
                     /gene_synonym="FLJ44236; HASJ4442; HUSSY-3; MGC19709;
                     MGC2022; MGC5140; PP3381; WBMT"
                     /product="Williams Beuren syndrome chromosome region 22,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001202560.1"
                     /db_xref="GI:321400148"
                     /db_xref="GeneID:114049"
                     /db_xref="HGNC:16405"
     mRNA            join(73097898..73098003,73098097..73098134,
                     73100966..73101061,73101148..73101230,73101329..73101425,
                     73105246..73105342,73106926..73106976,73107659..73107744,
                     73107954..73107999,73108322..73108380,73111935..73112024,
                     73112162..73112542)
                     /gene="WBSCR22"
                     /gene_synonym="FLJ44236; HASJ4442; HUSSY-3; MGC19709;
                     MGC2022; MGC5140; PP3381; WBMT"
                     /product="Williams Beuren syndrome chromosome region 22,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017528.3"
                     /db_xref="GI:321400150"
                     /db_xref="GeneID:114049"
                     /db_xref="HGNC:16405"
                     /db_xref="HPRD:15659"
     misc_RNA        join(73097898..73098003,73098097..73098330,
                     73100966..73101061,73101148..73101230,73101329..73101425,
                     73105246..73105342,73106926..73106976,73107659..73107744,
                     73107954..73107999,73108322..73108380,73111935..73112024,
                     73112162..73112542)
                     /gene="WBSCR22"
                     /gene_synonym="FLJ44236; HASJ4442; HUSSY-3; MGC19709;
                     MGC2022; MGC5140; PP3381; WBMT"
                     /product="Williams Beuren syndrome chromosome region 22,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037776.1"
                     /db_xref="GI:321400151"
                     /db_xref="GeneID:114049"
                     /db_xref="HGNC:16405"
     CDS             join(73097956..73098003,73098097..73098134,
                     73100966..73101061,73101148..73101230,73101329..73101425,
                     73105246..73105342,73106926..73106976,73107659..73107744,
                     73107954..73107999,73108322..73108380,73111796..73111846,
                     73111935..73112024,73112162..73112216)
                     /gene="WBSCR22"
                     /gene_synonym="FLJ44236; HASJ4442; HUSSY-3; MGC19709;
                     MGC2022; MGC5140; PP3381; WBMT"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="Williams Beuren syndrome chromosome region 22
                     protein isoform 1"
                     /protein_id="NP_001189489.1"
                     /db_xref="GI:321400149"
                     /db_xref="GeneID:114049"
                     /db_xref="HGNC:16405"
     CDS             join(73097956..73098003,73098097..73098134,
                     73100966..73101061,73101148..73101230,73101329..73101425,
                     73105246..73105342,73106926..73106976,73107659..73107744,
                     73107954..73107999,73108322..73108380,73111935..73112024,
                     73112162..73112216)
                     /gene="WBSCR22"
                     /gene_synonym="FLJ44236; HASJ4442; HUSSY-3; MGC19709;
                     MGC2022; MGC5140; PP3381; WBMT"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="Williams Beuren syndrome chromosome region 22
                     protein isoform 2"
                     /protein_id="NP_059998.2"
                     /db_xref="GI:23199995"
                     /db_xref="CCDS:CCDS5557.1"
                     /db_xref="GeneID:114049"
                     /db_xref="HGNC:16405"
     gene            complement(73113535..73134017)
                     /gene="STX1A"
                     /gene_synonym="HPC-1; P35-1; STX1; SYN1A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6804"
                     /db_xref="HGNC:11433"
                     /db_xref="MIM:186590"
     mRNA            complement(join(73113535..73114814,73115060..73115170,
                     73117175..73117312,73118085..73118158,73118478..73118586,
                     73118680..73118753,73119480..73119554,73122919..73123018,
                     73123375..73123452,73133932..73134017))
                     /gene="STX1A"
                     /gene_synonym="HPC-1; P35-1; STX1; SYN1A"
                     /product="syntaxin 1A (brain), transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004603.3"
                     /db_xref="GI:260166656"
                     /db_xref="GeneID:6804"
                     /db_xref="HGNC:11433"
                     /db_xref="HPRD:01721"
                     /db_xref="MIM:186590"
     mRNA            complement(join(73113535..73114814,73115060..73115124,
                     73117175..73117312,73118085..73118158,73118478..73118586,
                     73118680..73118753,73119480..73119554,73122919..73123018,
                     73123375..73123452,73133932..73134017))
                     /gene="STX1A"
                     /gene_synonym="HPC-1; P35-1; STX1; SYN1A"
                     /product="syntaxin 1A (brain), transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001165903.1"
                     /db_xref="GI:259906441"
                     /db_xref="GeneID:6804"
                     /db_xref="HGNC:11433"
                     /db_xref="MIM:186590"
     CDS             complement(join(73114737..73114814,73115060..73115170,
                     73117175..73117312,73118085..73118158,73118478..73118586,
                     73118680..73118753,73119480..73119554,73122919..73123018,
                     73123375..73123452,73133932..73133961))
                     /gene="STX1A"
                     /gene_synonym="HPC-1; P35-1; STX1; SYN1A"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="syntaxin-1A isoform 1"
                     /protein_id="NP_004594.1"
                     /db_xref="GI:4759182"
                     /db_xref="CCDS:CCDS34655.1"
                     /db_xref="GeneID:6804"
                     /db_xref="HGNC:11433"
                     /db_xref="MIM:186590"
     CDS             complement(join(73114802..73114814,73115060..73115124,
                     73117175..73117312,73118085..73118158,73118478..73118586,
                     73118680..73118753,73119480..73119554,73122919..73123018,
                     73123375..73123452,73133932..73133961))
                     /gene="STX1A"
                     /gene_synonym="HPC-1; P35-1; STX1; SYN1A"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="syntaxin-1A isoform 2"
                     /protein_id="NP_001159375.1"
                     /db_xref="GI:259906442"
                     /db_xref="CCDS:CCDS55120.1"
                     /db_xref="GeneID:6804"
                     /db_xref="HGNC:11433"
                     /db_xref="MIM:186590"
     gene            73119184..73119493
                     /gene="LOC100505484"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 10 ESTs"
                     /db_xref="GeneID:100505484"
     misc_RNA        join(73119184..73119247,73119303..73119493)
                     /gene="LOC100505484"
                     /product="hypothetical LOC100505484"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 10 ESTs"
                     /transcript_id="XR_108831.1"
                     /db_xref="GI:310120002"
                     /db_xref="GeneID:100505484"
     gene            73125647..73125727
                     /gene="MIR4284"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100422948"
                     /db_xref="HGNC:38322"
                     /db_xref="miRBase:MI0015893"
     ncRNA           73125647..73125727
                     /gene="MIR4284"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4284"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_036247.1"
                     /db_xref="GI:301172450"
                     /db_xref="GeneID:100422948"
                     /db_xref="HGNC:38322"
                     /db_xref="miRBase:MI0015893"
     gene            73149399..73150330
                     /gene="ABHD11-AS1"
                     /gene_synonym="NCRNA00035; WBSCR26"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:171022"
                     /db_xref="HGNC:18289"
                     /db_xref="MIM:612545"
     misc_RNA        join(73149399..73149420,73149571..73149829,
                     73150058..73150178,73150260..73150330)
                     /gene="ABHD11-AS1"
                     /gene_synonym="NCRNA00035; WBSCR26"
                     /product="ABHD11 antisense RNA 1 (non-protein coding)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_026690.1"
                     /db_xref="GI:222080111"
                     /db_xref="GeneID:171022"
                     /db_xref="HGNC:18289"
                     /db_xref="MIM:612545"
     gene            complement(73150424..73153190)
                     /gene="ABHD11"
                     /gene_synonym="PP1226; WBSCR21"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:83451"
                     /db_xref="HGNC:16407"
     mRNA            complement(join(73150424..73151021,73151259..73151440,
                     73151892..73152065,73152658..73152793,73152976..73153184))
                     /gene="ABHD11"
                     /gene_synonym="PP1226; WBSCR21"
                     /product="abhydrolase domain containing 11, transcript
                     variant 8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145364.1"
                     /db_xref="GI:223941838"
                     /db_xref="GeneID:83451"
                     /db_xref="HGNC:16407"
     misc_RNA        complement(join(73150427..73151021,73151259..73151440,
                     73151551..73152065,73152663..73152793,73152976..73153190))
                     /gene="ABHD11"
                     /gene_synonym="PP1226; WBSCR21"
                     /product="abhydrolase domain containing 11, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_026912.1"
                     /db_xref="GI:223941841"
                     /db_xref="GeneID:83451"
                     /db_xref="HGNC:16407"
     mRNA            complement(join(73150427..73151021,73151259..73151440,
                     73151551..73151721,73151892..73152065,73152658..73152793,
                     73152976..73153184))
                     /gene="ABHD11"
                     /gene_synonym="PP1226; WBSCR21"
                     /product="abhydrolase domain containing 11, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_148912.2"
                     /db_xref="GI:58430810"
                     /db_xref="GeneID:83451"
                     /db_xref="HGNC:16407"
                     /db_xref="HPRD:15658"
     mRNA            complement(join(73150427..73151021,73151259..73151440,
                     73151551..73151721,73151892..73152065,73152658..73152772,
                     73152976..73153184))
                     /gene="ABHD11"
                     /gene_synonym="PP1226; WBSCR21"
                     /product="abhydrolase domain containing 11, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_148913.2"
                     /db_xref="GI:58430929"
                     /db_xref="GeneID:83451"
                     /db_xref="HGNC:16407"
     misc_RNA        complement(join(73150427..73151021,73151259..73151440,
                     73151551..73151721,73151892..73152065,73152663..73152793,
                     73152976..73153184))
                     /gene="ABHD11"
                     /gene_synonym="PP1226; WBSCR21"
                     /product="abhydrolase domain containing 11, transcript
                     variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_026910.1"
                     /db_xref="GI:223941829"
                     /db_xref="GeneID:83451"
                     /db_xref="HGNC:16407"
     CDS             complement(join(73150889..73151021,73151259..73151440,
                     73151551..73151721,73151892..73152065,73152658..73152793,
                     73152976..73153127))
                     /gene="ABHD11"
                     /gene_synonym="PP1226; WBSCR21"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="abhydrolase domain-containing protein 11 isoform
                     1"
                     /protein_id="NP_683710.1"
                     /db_xref="GI:23200008"
                     /db_xref="CCDS:CCDS5558.1"
                     /db_xref="GeneID:83451"
                     /db_xref="HGNC:16407"
     CDS             complement(join(73150889..73151021,73151259..73151440,
                     73151551..73151721,73151892..73152065,73152658..73152772,
                     73152976..73153127))
                     /gene="ABHD11"
                     /gene_synonym="PP1226; WBSCR21"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="abhydrolase domain-containing protein 11 isoform
                     2"
                     /protein_id="NP_683711.1"
                     /db_xref="GI:23200012"
                     /db_xref="CCDS:CCDS47608.1"
                     /db_xref="GeneID:83451"
                     /db_xref="HGNC:16407"
     CDS             complement(join(73150889..73151021,73151259..73151440,
                     73151892..73152065,73152658..73152793,73152976..73153127))
                     /gene="ABHD11"
                     /gene_synonym="PP1226; WBSCR21"
                     /note="isoform 8 is encoded by transcript variant 8;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="abhydrolase domain-containing protein 11 isoform
                     8"
                     /protein_id="NP_001138836.1"
                     /db_xref="GI:223941839"
                     /db_xref="CCDS:CCDS47607.1"
                     /db_xref="GeneID:83451"
                     /db_xref="HGNC:16407"
     gene            complement(73183327..73184600)
                     /gene="CLDN3"
                     /gene_synonym="C7orf1; CPE-R2; CPETR2; HRVP1; RVP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1365"
                     /db_xref="HGNC:2045"
                     /db_xref="HPRD:04219"
                     /db_xref="MIM:602910"
     mRNA            complement(73183327..73184600)
                     /gene="CLDN3"
                     /gene_synonym="C7orf1; CPE-R2; CPETR2; HRVP1; RVP1"
                     /product="claudin 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001306.3"
                     /db_xref="GI:171541813"
                     /db_xref="GeneID:1365"
                     /db_xref="HGNC:2045"
                     /db_xref="HPRD:04219"
                     /db_xref="MIM:602910"
     CDS             complement(73183717..73184379)
                     /gene="CLDN3"
                     /gene_synonym="C7orf1; CPE-R2; CPETR2; HRVP1; RVP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="claudin-3"
                     /protein_id="NP_001297.1"
                     /db_xref="GI:4502875"
                     /db_xref="CCDS:CCDS5559.1"
                     /db_xref="GeneID:1365"
                     /db_xref="HGNC:2045"
                     /db_xref="HPRD:04219"
                     /db_xref="MIM:602910"
     gene            73245193..73247015
                     /gene="CLDN4"
                     /gene_synonym="CPE-R; CPER; CPETR; CPETR1; hCPE-R; WBSCR8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1364"
                     /db_xref="HGNC:2046"
                     /db_xref="HPRD:04218"
                     /db_xref="MIM:602909"
     mRNA            73245193..73247015
                     /gene="CLDN4"
                     /gene_synonym="CPE-R; CPER; CPETR; CPETR1; hCPE-R; WBSCR8"
                     /product="claudin 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001305.3"
                     /db_xref="GI:34335232"
                     /db_xref="GeneID:1364"
                     /db_xref="HGNC:2046"
                     /db_xref="HPRD:04218"
                     /db_xref="MIM:602909"
     CDS             73245532..73246161
                     /gene="CLDN4"
                     /gene_synonym="CPE-R; CPER; CPETR; CPETR1; hCPE-R; WBSCR8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="claudin-4"
                     /protein_id="NP_001296.1"
                     /db_xref="GI:4502877"
                     /db_xref="CCDS:CCDS5560.1"
                     /db_xref="GeneID:1364"
                     /db_xref="HGNC:2046"
                     /db_xref="HPRD:04218"
                     /db_xref="MIM:602909"
     gene            complement(73248920..73256855)
                     /gene="WBSCR27"
                     /gene_synonym="MGC40131"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:155368"
                     /db_xref="HGNC:19068"
                     /db_xref="HPRD:15661"
                     /db_xref="MIM:612546"
     mRNA            complement(join(73248920..73249332,73254361..73254450,
                     73254744..73254879,73255400..73255528,73256348..73256474,
                     73256820..73256855))
                     /gene="WBSCR27"
                     /gene_synonym="MGC40131"
                     /product="Williams Beuren syndrome chromosome region 27"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152559.2"
                     /db_xref="GI:30795189"
                     /db_xref="GeneID:155368"
                     /db_xref="HGNC:19068"
                     /db_xref="HPRD:15661"
                     /db_xref="MIM:612546"
     CDS             complement(join(73249073..73249332,73254361..73254450,
                     73254744..73254879,73255400..73255528,73256348..73256470))
                     /gene="WBSCR27"
                     /gene_synonym="MGC40131"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="Williams-Beuren syndrome chromosomal region 27
                     protein"
                     /protein_id="NP_689772.2"
                     /db_xref="GI:30795190"
                     /db_xref="CCDS:CCDS5561.1"
                     /db_xref="GeneID:155368"
                     /db_xref="HGNC:19068"
                     /db_xref="HPRD:15661"
                     /db_xref="MIM:612546"
     gene            73275489..73280223
                     /gene="WBSCR28"
                     /gene_synonym="MGC26719"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:135886"
                     /db_xref="HGNC:23018"
                     /db_xref="HPRD:15662"
                     /db_xref="MIM:612547"
     mRNA            join(73275489..73275596,73279323..73279751,
                     73279907..73280223)
                     /gene="WBSCR28"
                     /gene_synonym="MGC26719"
                     /product="Williams-Beuren syndrome chromosome region 28"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182504.3"
                     /db_xref="GI:153281225"
                     /db_xref="GeneID:135886"
                     /db_xref="HGNC:23018"
                     /db_xref="HPRD:15662"
                     /db_xref="MIM:612547"
     CDS             join(73275525..73275596,73279323..73279751,
                     73279907..73280203)
                     /gene="WBSCR28"
                     /gene_synonym="MGC26719"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="Williams-Beuren syndrome chromosomal region 28
                     protein"
                     /protein_id="NP_872310.2"
                     /db_xref="GI:153281226"
                     /db_xref="CCDS:CCDS43597.1"
                     /db_xref="GeneID:135886"
                     /db_xref="HGNC:23018"
                     /db_xref="HPRD:15662"
                     /db_xref="MIM:612547"
     gene            73442427..73484237
                     /gene="ELN"
                     /gene_synonym="FLJ38671; FLJ43523; SVAS; WBS; WS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2006"
                     /db_xref="HGNC:3327"
                     /db_xref="MIM:130160"
     mRNA            join(73442427..73442599,73449694..73449744,
                     73450885..73450914,73452037..73452069,73455546..73455581,
                     73456944..73457036,73457314..73457364,73457448..73457498,
                     73458209..73458250,73459552..73459623,73460518..73460547,
                     73461026..73461097,73462005..73462046,73462472..73462531,
                     73462833..73462886,73466080..73466169,73466254..73466313,
                     73467493..73467639,73469046..73469099,73470601..73470765,
                     73471002..73471043,73471970..73472026,73474216..73474377,
                     73474470..73474514,73474706..73474831,73475431..73475469,
                     73477483..73477554,73477640..73477699,73477951..73478025,
                     73480024..73480062,73480274..73480327,73481062..73481106,
                     73482987..73484237)
                     /gene="ELN"
                     /gene_synonym="FLJ38671; FLJ43523; SVAS; WBS; WS"
                     /product="elastin, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000501.2"
                     /db_xref="GI:126352439"
                     /db_xref="GeneID:2006"
                     /db_xref="HGNC:3327"
                     /db_xref="HPRD:00556"
                     /db_xref="MIM:130160"
     mRNA            join(73442427..73442599,73449694..73449744,
                     73452037..73452069,73455546..73455581,73456944..73457036,
                     73457314..73457364,73457448..73457498,73458209..73458250,
                     73459552..73459623,73460518..73460547,73461026..73461097,
                     73462005..73462046,73462472..73462531,73462833..73462886,
                     73466080..73466169,73466254..73466313,73467493..73467639,
                     73469046..73469099,73470601..73470765,73471002..73471043,
                     73474216..73474377,73474470..73474514,73474706..73474831,
                     73475431..73475469,73477483..73477554,73477640..73477699,
                     73477951..73478025,73480024..73480062,73481062..73481106,
                     73482987..73484237)
                     /gene="ELN"
                     /gene_synonym="FLJ38671; FLJ43523; SVAS; WBS; WS"
                     /product="elastin, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001081752.1"
                     /db_xref="GI:126352699"
                     /db_xref="GeneID:2006"
                     /db_xref="HGNC:3327"
                     /db_xref="MIM:130160"
     mRNA            join(73442427..73442599,73449694..73449744,
                     73450885..73450914,73452037..73452069,73455546..73455581,
                     73456944..73457036,73457314..73457364,73457433..73457498,
                     73458209..73458250,73459552..73459623,73460518..73460547,
                     73461026..73461097,73462005..73462046,73462472..73462531,
                     73462833..73462886,73466080..73466169,73466254..73466313,
                     73467493..73467639,73469046..73469099,73470601..73470765,
                     73471002..73471043,73474216..73474377,73474470..73474514,
                     73474706..73474831,73475431..73475469,73477483..73477554,
                     73477640..73477699,73477951..73478025,73480024..73480062,
                     73481062..73481106,73482987..73484237)
                     /gene="ELN"
                     /gene_synonym="FLJ38671; FLJ43523; SVAS; WBS; WS"
                     /product="elastin, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001081753.1"
                     /db_xref="GI:126352321"
                     /db_xref="GeneID:2006"
                     /db_xref="HGNC:3327"
                     /db_xref="MIM:130160"
     mRNA            join(73442427..73442599,73449694..73449744,
                     73450885..73450914,73452037..73452069,73455546..73455581,
                     73456944..73457036,73457314..73457364,73457433..73457498,
                     73458209..73458250,73459552..73459623,73460518..73460547,
                     73461026..73461097,73462005..73462046,73462472..73462531,
                     73462833..73462886,73466080..73466169,73466254..73466313,
                     73467493..73467639,73469046..73469099,73470601..73470765,
                     73471002..73471043,73471970..73472026,73474216..73474377,
                     73474470..73474514,73474706..73474831,73475431..73475469,
                     73477483..73477554,73477640..73477699,73477951..73478025,
                     73480024..73480062,73481062..73481106,73482987..73484237)
                     /gene="ELN"
                     /gene_synonym="FLJ38671; FLJ43523; SVAS; WBS; WS"
                     /product="elastin, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001081754.1"
                     /db_xref="GI:126352445"
                     /db_xref="GeneID:2006"
                     /db_xref="HGNC:3327"
                     /db_xref="MIM:130160"
     mRNA            join(73442427..73442599,73449694..73449744,
                     73450885..73450914,73452037..73452069,73455546..73455581,
                     73456944..73457036,73457314..73457364,73457448..73457498,
                     73458209..73458250,73459552..73459623,73460518..73460547,
                     73461026..73461097,73462005..73462046,73462472..73462531,
                     73462833..73462886,73466080..73466169,73466254..73466313,
                     73467493..73467639,73469046..73469099,73470601..73470765,
                     73471002..73471043,73474216..73474377,73474470..73474514,
                     73474706..73474831,73475431..73475469,73477483..73477554,
                     73477640..73477699,73477951..73478025,73480024..73480062,
                     73480274..73480327,73481062..73481106,73482987..73484237)
                     /gene="ELN"
                     /gene_synonym="FLJ38671; FLJ43523; SVAS; WBS; WS"
                     /product="elastin, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001081755.1"
                     /db_xref="GI:126352607"
                     /db_xref="GeneID:2006"
                     /db_xref="HGNC:3327"
                     /db_xref="MIM:130160"
     CDS             join(73442518..73442599,73449694..73449744,
                     73450885..73450914,73452037..73452069,73455546..73455581,
                     73456944..73457036,73457314..73457364,73457448..73457498,
                     73458209..73458250,73459552..73459623,73460518..73460547,
                     73461026..73461097,73462005..73462046,73462472..73462531,
                     73462833..73462886,73466080..73466169,73466254..73466313,
                     73467493..73467639,73469046..73469099,73470601..73470765,
                     73471002..73471043,73471970..73472026,73474216..73474377,
                     73474470..73474514,73474706..73474831,73475431..73475469,
                     73477483..73477554,73477640..73477699,73477951..73478025,
                     73480024..73480062,73480274..73480327,73481062..73481106,
                     73482987..73483030)
                     /gene="ELN"
                     /gene_synonym="FLJ38671; FLJ43523; SVAS; WBS; WS"
                     /note="isoform a precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="elastin isoform a precursor"
                     /protein_id="NP_000492.2"
                     /db_xref="GI:126352440"
                     /db_xref="CCDS:CCDS5562.2"
                     /db_xref="GeneID:2006"
                     /db_xref="HGNC:3327"
                     /db_xref="MIM:130160"
     CDS             join(73442518..73442599,73449694..73449744,
                     73452037..73452069,73455546..73455581,73456944..73457036,
                     73457314..73457364,73457448..73457498,73458209..73458250,
                     73459552..73459623,73460518..73460547,73461026..73461097,
                     73462005..73462046,73462472..73462531,73462833..73462886,
                     73466080..73466169,73466254..73466313,73467493..73467639,
                     73469046..73469099,73470601..73470765,73471002..73471043,
                     73474216..73474377,73474470..73474514,73474706..73474831,
                     73475431..73475469,73477483..73477554,73477640..73477699,
                     73477951..73478025,73480024..73480062,73481062..73481106,
                     73482987..73483030)
                     /gene="ELN"
                     /gene_synonym="FLJ38671; FLJ43523; SVAS; WBS; WS"
                     /note="isoform b precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="elastin isoform b precursor"
                     /protein_id="NP_001075221.1"
                     /db_xref="GI:126352700"
                     /db_xref="CCDS:CCDS43599.1"
                     /db_xref="GeneID:2006"
                     /db_xref="HGNC:3327"
                     /db_xref="MIM:130160"
     CDS             join(73442518..73442599,73449694..73449744,
                     73450885..73450914,73452037..73452069,73455546..73455581,
                     73456944..73457036,73457314..73457364,73457433..73457498,
                     73458209..73458250,73459552..73459623,73460518..73460547,
                     73461026..73461097,73462005..73462046,73462472..73462531,
                     73462833..73462886,73466080..73466169,73466254..73466313,
                     73467493..73467639,73469046..73469099,73470601..73470765,
                     73471002..73471043,73474216..73474377,73474470..73474514,
                     73474706..73474831,73475431..73475469,73477483..73477554,
                     73477640..73477699,73477951..73478025,73480024..73480062,
                     73481062..73481106,73482987..73483030)
                     /gene="ELN"
                     /gene_synonym="FLJ38671; FLJ43523; SVAS; WBS; WS"
                     /note="isoform c precursor is encoded by transcript
                     variant 3; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="elastin isoform c precursor"
                     /protein_id="NP_001075222.1"
                     /db_xref="GI:126352322"
                     /db_xref="CCDS:CCDS47611.1"
                     /db_xref="GeneID:2006"
                     /db_xref="HGNC:3327"
                     /db_xref="MIM:130160"
     CDS             join(73442518..73442599,73449694..73449744,
                     73450885..73450914,73452037..73452069,73455546..73455581,
                     73456944..73457036,73457314..73457364,73457433..73457498,
                     73458209..73458250,73459552..73459623,73460518..73460547,
                     73461026..73461097,73462005..73462046,73462472..73462531,
                     73462833..73462886,73466080..73466169,73466254..73466313,
                     73467493..73467639,73469046..73469099,73470601..73470765,
                     73471002..73471043,73471970..73472026,73474216..73474377,
                     73474470..73474514,73474706..73474831,73475431..73475469,
                     73477483..73477554,73477640..73477699,73477951..73478025,
                     73480024..73480062,73481062..73481106,73482987..73483030)
                     /gene="ELN"
                     /gene_synonym="FLJ38671; FLJ43523; SVAS; WBS; WS"
                     /note="isoform d precursor is encoded by transcript
                     variant 4; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="elastin isoform d precursor"
                     /protein_id="NP_001075223.1"
                     /db_xref="GI:126352446"
                     /db_xref="CCDS:CCDS43598.1"
                     /db_xref="GeneID:2006"
                     /db_xref="HGNC:3327"
                     /db_xref="MIM:130160"
     CDS             join(73442518..73442599,73449694..73449744,
                     73450885..73450914,73452037..73452069,73455546..73455581,
                     73456944..73457036,73457314..73457364,73457448..73457498,
                     73458209..73458250,73459552..73459623,73460518..73460547,
                     73461026..73461097,73462005..73462046,73462472..73462531,
                     73462833..73462886,73466080..73466169,73466254..73466313,
                     73467493..73467639,73469046..73469099,73470601..73470765,
                     73471002..73471043,73474216..73474377,73474470..73474514,
                     73474706..73474831,73475431..73475469,73477483..73477554,
                     73477640..73477699,73477951..73478025,73480024..73480062,
                     73480274..73480327,73481062..73481106,73482987..73483030)
                     /gene="ELN"
                     /gene_synonym="FLJ38671; FLJ43523; SVAS; WBS; WS"
                     /note="isoform e precursor is encoded by transcript
                     variant 5; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="elastin isoform e precursor"
                     /protein_id="NP_001075224.1"
                     /db_xref="GI:126352608"
                     /db_xref="CCDS:CCDS47612.1"
                     /db_xref="GeneID:2006"
                     /db_xref="HGNC:3327"
                     /db_xref="MIM:130160"
     gene            73498107..73536855
                     /gene="LIMK1"
                     /gene_synonym="LIMK; LIMK-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3984"
                     /db_xref="HGNC:6613"
                     /db_xref="HPRD:03210"
                     /db_xref="MIM:601329"
     mRNA            join(73498107..73498375,73500078..73500174,
                     73510952..73511090,73511410..73511519,73513362..73513568,
                     73520205..73520310,73520407..73520573,73521340..73521523,
                     73522201..73522287,73523235..73523366,73525978..73526037,
                     73526263..73526328,73530132..73530288,73534913..73534968,
                     73535222..73535379,73535469..73536855)
                     /gene="LIMK1"
                     /gene_synonym="LIMK; LIMK-1"
                     /product="LIM domain kinase 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002314.3"
                     /db_xref="GI:324715044"
                     /db_xref="GeneID:3984"
                     /db_xref="HGNC:6613"
                     /db_xref="HPRD:03210"
                     /db_xref="MIM:601329"
     CDS             join(73498321..73498375,73500078..73500174,
                     73510952..73511090,73511410..73511519,73513362..73513568,
                     73520205..73520310,73520407..73520573,73521340..73521523,
                     73522201..73522287,73523235..73523366,73525978..73526037,
                     73526263..73526328,73530132..73530288,73534913..73534968,
                     73535222..73535379,73535469..73535631)
                     /gene="LIMK1"
                     /gene_synonym="LIMK; LIMK-1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="LIM domain kinase 1 isoform 1"
                     /protein_id="NP_002305.1"
                     /db_xref="GI:4505001"
                     /db_xref="CCDS:CCDS5563.1"
                     /db_xref="GeneID:3984"
                     /db_xref="HGNC:6613"
                     /db_xref="HPRD:03210"
                     /db_xref="MIM:601329"
     mRNA            join(73507486..73507629,73510952..73511090,
                     73511410..73511519,73513362..73513568,73520205..73520310,
                     73520407..73520573,73521340..73521523,73522201..73522287,
                     73523235..73523366,73525978..73526037,73526263..73526328,
                     73530132..73530288,73534913..73534968,73535222..73535379,
                     73535469..73536855)
                     /gene="LIMK1"
                     /gene_synonym="LIMK; LIMK-1"
                     /product="LIM domain kinase 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001204426.1"
                     /db_xref="GI:324715045"
                     /db_xref="GeneID:3984"
                     /db_xref="HGNC:6613"
                     /db_xref="MIM:601329"
                     /db_xref="HPRD:03210"
     CDS             join(73507580..73507629,73510952..73511090,
                     73511410..73511519,73513362..73513568,73520205..73520310,
                     73520407..73520573,73521340..73521523,73522201..73522287,
                     73523235..73523366,73525978..73526037,73526263..73526328,
                     73530132..73530288,73534913..73534968,73535222..73535379,
                     73535469..73535631)
                     /gene="LIMK1"
                     /gene_synonym="LIMK; LIMK-1"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="LIM domain kinase 1 isoform 2"
                     /protein_id="NP_001191355.1"
                     /db_xref="GI:324715046"
                     /db_xref="GeneID:3984"
                     /db_xref="HGNC:6613"
                     /db_xref="MIM:601329"
                     /db_xref="HPRD:03210"
     gene            73588706..73611429
                     /gene="EIF4H"
                     /gene_synonym="KIAA0038; WBSCR1; WSCR1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7458"
                     /db_xref="HGNC:12741"
                     /db_xref="HPRD:11940"
                     /db_xref="MIM:603431"
     mRNA            join(73588706..73588772,73601941..73602128,
                     73604003..73604067,73604152..73604248,73604577..73604636,
                     73609071..73609208,73609499..73611429)
                     /gene="EIF4H"
                     /gene_synonym="KIAA0038; WBSCR1; WSCR1"
                     /product="eukaryotic translation initiation factor 4H,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022170.1"
                     /db_xref="GI:11559922"
                     /db_xref="GeneID:7458"
                     /db_xref="HGNC:12741"
                     /db_xref="HPRD:11940"
                     /db_xref="MIM:603431"
     mRNA            join(73588706..73588772,73601941..73602128,
                     73604003..73604067,73604152..73604248,73609071..73609208,
                     73609499..73611429)
                     /gene="EIF4H"
                     /gene_synonym="KIAA0038; WBSCR1; WSCR1"
                     /product="eukaryotic translation initiation factor 4H,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_031992.1"
                     /db_xref="GI:14702179"
                     /db_xref="GeneID:7458"
                     /db_xref="HGNC:12741"
                     /db_xref="MIM:603431"
                     /db_xref="HPRD:11940"
     CDS             join(73588714..73588772,73601941..73602128,
                     73604003..73604067,73604152..73604248,73604577..73604636,
                     73609071..73609208,73609499..73609638)
                     /gene="EIF4H"
                     /gene_synonym="KIAA0038; WBSCR1; WSCR1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="eukaryotic translation initiation factor 4H
                     isoform 1"
                     /protein_id="NP_071496.1"
                     /db_xref="GI:11559923"
                     /db_xref="CCDS:CCDS5564.1"
                     /db_xref="GeneID:7458"
                     /db_xref="HGNC:12741"
                     /db_xref="HPRD:11940"
                     /db_xref="MIM:603431"
     CDS             join(73588714..73588772,73601941..73602128,
                     73604003..73604067,73604152..73604248,73609071..73609208,
                     73609499..73609638)
                     /gene="EIF4H"
                     /gene_synonym="KIAA0038; WBSCR1; WSCR1"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="eukaryotic translation initiation factor 4H
                     isoform 2"
                     /protein_id="NP_114381.1"
                     /db_xref="GI:14702180"
                     /db_xref="CCDS:CCDS5565.1"
                     /db_xref="GeneID:7458"
                     /db_xref="HGNC:12741"
                     /db_xref="HPRD:11940"
                     /db_xref="MIM:603431"
     gene            73605528..73605624
                     /gene="MIR590"
                     /gene_synonym="hsa-mir-590; MIRN590"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:693175"
                     /db_xref="HGNC:32846"
                     /db_xref="miRBase:MI0003602"
     ncRNA           73605528..73605624
                     /gene="MIR590"
                     /gene_synonym="hsa-mir-590; MIRN590"
                     /ncRNA_class="miRNA"
                     /product="microRNA 590"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_030321.1"
                     /db_xref="GI:262205947"
                     /db_xref="GeneID:693175"
                     /db_xref="HGNC:32846"
                     /db_xref="miRBase:MI0003602"
     ncRNA           73605528..73605624
                     /gene="MIR590"
                     /gene_synonym="hsa-mir-590; MIRN590"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-590"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:693175"
                     /db_xref="miRBase:MI0003602"
                     /db_xref="HGNC:32846"
     gene            73624087..73644164
                     /gene="LAT2"
                     /gene_synonym="HSPC046; LAB; NTAL; WBSCR15; WBSCR5; WSCR5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7462"
                     /db_xref="HGNC:12749"
                     /db_xref="HPRD:09304"
                     /db_xref="MIM:605719"
     mRNA            join(73624087..73624418,73629152..73629340,
                     73630277..73630399,73631155..73631194,73634074..73634117,
                     73634290..73634338,73634547..73634584,73634914..73634949,
                     73635034..73635064,73635967..73636022,73638054..73638113,
                     73638348..73638527,73638969..73639090,73643274..73644164)
                     /gene="LAT2"
                     /gene_synonym="HSPC046; LAB; NTAL; WBSCR15; WBSCR5; WSCR5"
                     /product="linker for activation of T cells family, member
                     2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032464.2"
                     /db_xref="GI:118640874"
                     /db_xref="GeneID:7462"
                     /db_xref="HGNC:12749"
                     /db_xref="HPRD:09304"
                     /db_xref="MIM:605719"
     mRNA            join(73624087..73624418,73629152..73629270,
                     73630277..73630399,73631155..73631194,73634074..73634117,
                     73634290..73634338,73634547..73634584,73634914..73634949,
                     73635034..73635064,73635967..73636022,73638054..73638113,
                     73638348..73638527,73638969..73639090,73643274..73644164)
                     /gene="LAT2"
                     /gene_synonym="HSPC046; LAB; NTAL; WBSCR15; WBSCR5; WSCR5"
                     /product="linker for activation of T cells family, member
                     2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032463.2"
                     /db_xref="GI:88999569"
                     /db_xref="GeneID:7462"
                     /db_xref="HGNC:12749"
                     /db_xref="MIM:605719"
                     /db_xref="HPRD:09304"
     mRNA            join(73624087..73624418,73630277..73630399,
                     73631155..73631194,73634074..73634117,73634290..73634338,
                     73634547..73634584,73634914..73634949,73635034..73635064,
                     73635967..73636022,73638054..73638113,73638348..73638527,
                     73638969..73639090,73643274..73644164)
                     /gene="LAT2"
                     /gene_synonym="HSPC046; LAB; NTAL; WBSCR15; WBSCR5; WSCR5"
                     /product="linker for activation of T cells family, member
                     2, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014146.3"
                     /db_xref="GI:88999570"
                     /db_xref="GeneID:7462"
                     /db_xref="HGNC:12749"
                     /db_xref="MIM:605719"
                     /db_xref="HPRD:09304"
     CDS             join(73630306..73630399,73631155..73631194,
                     73634074..73634117,73634290..73634338,73634547..73634584,
                     73634914..73634949,73635034..73635064,73635967..73636022,
                     73638054..73638113,73638348..73638527,73638969..73639072)
                     /gene="LAT2"
                     /gene_synonym="HSPC046; LAB; NTAL; WBSCR15; WBSCR5; WSCR5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="linker for activation of T-cells family member
                     2"
                     /protein_id="NP_115853.2"
                     /db_xref="GI:118640875"
                     /db_xref="CCDS:CCDS5566.2"
                     /db_xref="GeneID:7462"
                     /db_xref="HGNC:12749"
                     /db_xref="HPRD:09304"
                     /db_xref="MIM:605719"
     CDS             join(73630306..73630399,73631155..73631194,
                     73634074..73634117,73634290..73634338,73634547..73634584,
                     73634914..73634949,73635034..73635064,73635967..73636022,
                     73638054..73638113,73638348..73638527,73638969..73639072)
                     /gene="LAT2"
                     /gene_synonym="HSPC046; LAB; NTAL; WBSCR15; WBSCR5; WSCR5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="linker for activation of T-cells family member
                     2"
                     /protein_id="NP_115852.1"
                     /db_xref="GI:14702184"
                     /db_xref="CCDS:CCDS5566.2"
                     /db_xref="GeneID:7462"
                     /db_xref="HGNC:12749"
                     /db_xref="HPRD:09304"
                     /db_xref="MIM:605719"
     CDS             join(73630306..73630399,73631155..73631194,
                     73634074..73634117,73634290..73634338,73634547..73634584,
                     73634914..73634949,73635034..73635064,73635967..73636022,
                     73638054..73638113,73638348..73638527,73638969..73639072)
                     /gene="LAT2"
                     /gene_synonym="HSPC046; LAB; NTAL; WBSCR15; WBSCR5; WSCR5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="linker for activation of T-cells family member
                     2"
                     /protein_id="NP_054865.2"
                     /db_xref="GI:14702182"
                     /db_xref="CCDS:CCDS5566.2"
                     /db_xref="GeneID:7462"
                     /db_xref="HGNC:12749"
                     /db_xref="HPRD:09304"
                     /db_xref="MIM:605719"
     gene            complement(73645832..73668738)
                     /gene="RFC2"
                     /gene_synonym="A1; MGC3665; RFC40"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5982"
                     /db_xref="HGNC:9970"
                     /db_xref="HPRD:02675"
                     /db_xref="MIM:600404"
     mRNA            complement(join(73645832..73646546,73649862..73649975,
                     73651692..73651772,73653253..73653318,73654268..73654425,
                     73657476..73657576,73660992..73661093,73663342..73663448,
                     73664069..73664110,73666759..73666828,73668601..73668738))
                     /gene="RFC2"
                     /gene_synonym="A1; MGC3665; RFC40"
                     /product="replication factor C (activator 1) 2, 40kDa,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_181471.1"
                     /db_xref="GI:31563533"
                     /db_xref="GeneID:5982"
                     /db_xref="HGNC:9970"
                     /db_xref="HPRD:02675"
                     /db_xref="MIM:600404"
     mRNA            complement(join(73645832..73646546,73649862..73649975,
                     73651692..73651772,73653253..73653318,73654268..73654425,
                     73657476..73657576,73663342..73663448,73664069..73664110,
                     73666759..73666828,73668601..73668738))
                     /gene="RFC2"
                     /gene_synonym="A1; MGC3665; RFC40"
                     /product="replication factor C (activator 1) 2, 40kDa,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002914.3"
                     /db_xref="GI:31563535"
                     /db_xref="GeneID:5982"
                     /db_xref="HGNC:9970"
                     /db_xref="MIM:600404"
                     /db_xref="HPRD:02675"
     CDS             complement(join(73646436..73646546,73649862..73649975,
                     73651692..73651772,73653253..73653318,73654268..73654425,
                     73657476..73657576,73660992..73661093,73663342..73663448,
                     73664069..73664110,73666759..73666828,73668601..73668713))
                     /gene="RFC2"
                     /gene_synonym="A1; MGC3665; RFC40"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="replication factor C subunit 2 isoform 1"
                     /protein_id="NP_852136.1"
                     /db_xref="GI:31563534"
                     /db_xref="CCDS:CCDS5568.1"
                     /db_xref="GeneID:5982"
                     /db_xref="HGNC:9970"
                     /db_xref="HPRD:02675"
                     /db_xref="MIM:600404"
     CDS             complement(join(73646436..73646546,73649862..73649975,
                     73651692..73651772,73653253..73653318,73654268..73654425,
                     73657476..73657576,73663342..73663448,73664069..73664110,
                     73666759..73666828,73668601..73668713))
                     /gene="RFC2"
                     /gene_synonym="A1; MGC3665; RFC40"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="replication factor C subunit 2 isoform 2"
                     /protein_id="NP_002905.2"
                     /db_xref="GI:28882049"
                     /db_xref="CCDS:CCDS5567.1"
                     /db_xref="GeneID:5982"
                     /db_xref="HGNC:9970"
                     /db_xref="HPRD:02675"
                     /db_xref="MIM:600404"
     gene            73703805..73820273
                     /gene="CLIP2"
                     /gene_synonym="CLIP; CLIP-115; CYLN2; KIAA0291; MGC11333;
                     WBSCR3; WBSCR4; WSCR3; WSCR4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7461"
                     /db_xref="HGNC:2586"
                     /db_xref="HPRD:09140"
                     /db_xref="MIM:603432"
     mRNA            join(73703805..73704064,73731810..73731997,
                     73752778..73753334,73768210..73768334,73770740..73770953,
                     73771610..73771807,73774505..73774608,73778585..73778645,
                     73787262..73787366,73790217..73791152,73795136..73795193,
                     73800851..73800934,73803433..73803589,73811404..73811563,
                     73814700..73814885,73815835..73815897,73818167..73820273)
                     /gene="CLIP2"
                     /gene_synonym="CLIP; CLIP-115; CYLN2; KIAA0291; MGC11333;
                     WBSCR3; WBSCR4; WSCR3; WSCR4"
                     /product="CAP-GLY domain containing linker protein 2,
                     transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003388.4"
                     /db_xref="GI:116008446"
                     /db_xref="GeneID:7461"
                     /db_xref="HGNC:2586"
                     /db_xref="HPRD:09140"
                     /db_xref="MIM:603432"
     mRNA            join(73703805..73704064,73731810..73731997,
                     73752778..73753334,73768210..73768334,73770740..73770953,
                     73771610..73771807,73774505..73774608,73778585..73778645,
                     73790217..73791152,73795136..73795193,73800851..73800934,
                     73803433..73803589,73811404..73811563,73814700..73814885,
                     73815835..73815897,73818167..73820273)
                     /gene="CLIP2"
                     /gene_synonym="CLIP; CLIP-115; CYLN2; KIAA0291; MGC11333;
                     WBSCR3; WBSCR4; WSCR3; WSCR4"
                     /product="CAP-GLY domain containing linker protein 2,
                     transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032421.2"
                     /db_xref="GI:116008448"
                     /db_xref="GeneID:7461"
                     /db_xref="HGNC:2586"
                     /db_xref="HPRD:09140"
                     /db_xref="MIM:603432"
     CDS             join(73731877..73731997,73752778..73753334,
                     73768210..73768334,73770740..73770953,73771610..73771807,
                     73774505..73774608,73778585..73778645,73787262..73787366,
                     73790217..73791152,73795136..73795193,73800851..73800934,
                     73803433..73803589,73811404..73811563,73814700..73814885,
                     73815835..73815897,73818167..73818178)
                     /gene="CLIP2"
                     /gene_synonym="CLIP; CLIP-115; CYLN2; KIAA0291; MGC11333;
                     WBSCR3; WBSCR4; WSCR3; WSCR4"
                     /exception="mismatches in translation"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="CAP-Gly domain-containing linker protein 2
                     isoform 1"
                     /protein_id="NP_003379.3"
                     /db_xref="GI:116008447"
                     /db_xref="CCDS:CCDS5569.1"
                     /db_xref="GeneID:7461"
                     /db_xref="HGNC:2586"
                     /db_xref="HPRD:09140"
                     /db_xref="MIM:603432"
     CDS             join(73731877..73731997,73752778..73753334,
                     73768210..73768334,73770740..73770953,73771610..73771807,
                     73774505..73774608,73778585..73778645,73790217..73791152,
                     73795136..73795193,73800851..73800934,73803433..73803589,
                     73811404..73811563,73814700..73814885,73815835..73815897,
                     73818167..73818178)
                     /gene="CLIP2"
                     /gene_synonym="CLIP; CLIP-115; CYLN2; KIAA0291; MGC11333;
                     WBSCR3; WBSCR4; WSCR3; WSCR4"
                     /exception="mismatches in translation"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="CAP-Gly domain-containing linker protein 2
                     isoform 2"
                     /protein_id="NP_115797.1"
                     /db_xref="GI:14702162"
                     /db_xref="CCDS:CCDS5570.1"
                     /db_xref="GeneID:7461"
                     /db_xref="HGNC:2586"
                     /db_xref="HPRD:09140"
                     /db_xref="MIM:603432"
     gene            73868120..74016931
                     /gene="GTF2IRD1"
                     /gene_synonym="BEN; CREAM1; GTF3; hMusTRD1alpha1; MUSTRD1;
                     RBAP2; WBS; WBSCR11; WBSCR12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9569"
                     /db_xref="HGNC:4661"
                     /db_xref="HPRD:08379"
                     /db_xref="MIM:604318"
     mRNA            join(73868120..73868506,73922405..73922533,
                     73927160..73927301,73929771..73929926,73932469..73932652,
                     73933739..73934049,73935538..73935627,73938401..73938484,
                     73944064..73944247,73949443..73949468,73950497..73950605,
                     73952466..73952503,73953010..73953090,73954209..73954298,
                     73959085..73959132,73960074..73960139,73961433..73961616,
                     73969504..73969553,73969723..73969824,73971969..73972052,
                     73973191..73973374,73973957..73973985,74004180..74004257,
                     74005154..74005346,74009341..74009378,74015371..74015507,
                     74016692..74016931)
                     /gene="GTF2IRD1"
                     /gene_synonym="BEN; CREAM1; GTF3; hMusTRD1alpha1; MUSTRD1;
                     RBAP2; WBS; WBSCR11; WBSCR12"
                     /product="GTF2I repeat domain containing 1, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016328.2"
                     /db_xref="GI:312836809"
                     /db_xref="GeneID:9569"
                     /db_xref="HGNC:4661"
                     /db_xref="HPRD:08379"
                     /db_xref="MIM:604318"
     mRNA            join(73868120..73868506,73922405..73922533,
                     73927160..73927301,73929771..73929926,73932469..73932652,
                     73933739..73934049,73935538..73935627,73938401..73938484,
                     73944064..73944247,73949443..73949468,73950497..73950605,
                     73952466..73952503,73953010..73953090,73954209..73954298,
                     73959085..73959132,73960074..73960139,73961433..73961616,
                     73969504..73969553,73969768..73969824,73971969..73972052,
                     73973191..73973374,73973957..73973985,74004180..74004257,
                     74005154..74005346,74009341..74009378,74015371..74015507,
                     74016692..74016931)
                     /gene="GTF2IRD1"
                     /gene_synonym="BEN; CREAM1; GTF3; hMusTRD1alpha1; MUSTRD1;
                     RBAP2; WBS; WBSCR11; WBSCR12"
                     /product="GTF2I repeat domain containing 1, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005685.3"
                     /db_xref="GI:312836810"
                     /db_xref="GeneID:9569"
                     /db_xref="HGNC:4661"
                     /db_xref="HPRD:08379"
                     /db_xref="MIM:604318"
     mRNA            join(73868120..73868506,73922405..73922533,
                     73927160..73927301,73929675..73929926,73932469..73932652,
                     73933739..73934049,73935538..73935627,73938401..73938484,
                     73944064..73944247,73949443..73949468,73950497..73950605,
                     73952466..73952503,73953010..73953090,73954209..73954298,
                     73959085..73959132,73960074..73960139,73961433..73961616,
                     73969504..73969553,73969768..73969824,73971969..73972052,
                     73973191..73973374,73973957..73973985,74004180..74004257,
                     74005154..74005346,74009341..74009378,74015371..74015507,
                     74016692..74016931)
                     /gene="GTF2IRD1"
                     /gene_synonym="BEN; CREAM1; GTF3; hMusTRD1alpha1; MUSTRD1;
                     RBAP2; WBS; WBSCR11; WBSCR12"
                     /product="GTF2I repeat domain containing 1, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199207.1"
                     /db_xref="GI:312836830"
                     /db_xref="GeneID:9569"
                     /db_xref="HGNC:4661"
                     /db_xref="MIM:604318"
                     /db_xref="HPRD:08379"
     CDS             join(73922411..73922533,73927160..73927301,
                     73929771..73929926,73932469..73932652,73933739..73934049,
                     73935538..73935627,73938401..73938484,73944064..73944247,
                     73949443..73949468,73950497..73950605,73952466..73952503,
                     73953010..73953090,73954209..73954298,73959085..73959132,
                     73960074..73960139,73961433..73961616,73969504..73969553,
                     73969723..73969824,73971969..73972052,73973191..73973374,
                     73973957..73973985,74004180..74004257,74005154..74005346,
                     74009341..74009378,74015371..74015507,74016692..74016760)
                     /gene="GTF2IRD1"
                     /gene_synonym="BEN; CREAM1; GTF3; hMusTRD1alpha1; MUSTRD1;
                     RBAP2; WBS; WBSCR11; WBSCR12"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="general transcription factor II-I repeat
                     domain-containing protein 1 isoform 1"
                     /protein_id="NP_057412.1"
                     /db_xref="GI:7705387"
                     /db_xref="CCDS:CCDS5571.1"
                     /db_xref="GeneID:9569"
                     /db_xref="HGNC:4661"
                     /db_xref="HPRD:08379"
                     /db_xref="MIM:604318"
     CDS             join(73922411..73922533,73927160..73927301,
                     73929771..73929926,73932469..73932652,73933739..73934049,
                     73935538..73935627,73938401..73938484,73944064..73944247,
                     73949443..73949468,73950497..73950605,73952466..73952503,
                     73953010..73953090,73954209..73954298,73959085..73959132,
                     73960074..73960139,73961433..73961616,73969504..73969553,
                     73969768..73969824,73971969..73972052,73973191..73973374,
                     73973957..73973985,74004180..74004257,74005154..74005346,
                     74009341..74009378,74015371..74015507,74016692..74016760)
                     /gene="GTF2IRD1"
                     /gene_synonym="BEN; CREAM1; GTF3; hMusTRD1alpha1; MUSTRD1;
                     RBAP2; WBS; WBSCR11; WBSCR12"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="general transcription factor II-I repeat
                     domain-containing protein 1 isoform 2"
                     /protein_id="NP_005676.3"
                     /db_xref="GI:312836811"
                     /db_xref="CCDS:CCDS47613.1"
                     /db_xref="GeneID:9569"
                     /db_xref="HGNC:4661"
                     /db_xref="HPRD:08379"
                     /db_xref="MIM:604318"
     CDS             join(73922411..73922533,73927160..73927301,
                     73929675..73929926,73932469..73932652,73933739..73934049,
                     73935538..73935627,73938401..73938484,73944064..73944247,
                     73949443..73949468,73950497..73950605,73952466..73952503,
                     73953010..73953090,73954209..73954298,73959085..73959132,
                     73960074..73960139,73961433..73961616,73969504..73969553,
                     73969768..73969824,73971969..73972052,73973191..73973374,
                     73973957..73973985,74004180..74004257,74005154..74005346,
                     74009341..74009378,74015371..74015507,74016692..74016760)
                     /gene="GTF2IRD1"
                     /gene_synonym="BEN; CREAM1; GTF3; hMusTRD1alpha1; MUSTRD1;
                     RBAP2; WBS; WBSCR11; WBSCR12"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="general transcription factor II-I repeat
                     domain-containing protein 1 isoform 3"
                     /protein_id="NP_001186136.1"
                     /db_xref="GI:312836831"
                     /db_xref="GeneID:9569"
                     /db_xref="HGNC:4661"
                     /db_xref="MIM:604318"
                     /db_xref="HPRD:08379"
     gene            74072030..74175022
                     /gene="GTF2I"
                     /gene_synonym="BAP135; BTKAP1; DIWS; FLJ38776; FLJ56355;
                     GTFII-I; IB291; SPIN; TFII-I; WBS; WBSCR6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2969"
                     /db_xref="HGNC:4659"
                     /db_xref="HPRD:03399"
                     /db_xref="MIM:601679"
     mRNA            join(74072030..74072394,74103458..74103561,
                     74105305..74105443,74113291..74113425,74114577..74114760,
                     74114936..74114964,74119496..74119550,74120721..74120764,
                     74125363..74125440,74129177..74129236,74131214..74131270,
                     74133198..74133260,74143124..74143234,74144567..74144632,
                     74146820..74147003,74148265..74148323,74149803..74149874,
                     74150842..74151025,74152387..74152445,74157788..74157859,
                     74159097..74159280,74160222..74160280,74160676..74160750,
                     74162352..74162453,74163362..74163427,74163605..74163788,
                     74165693..74165748,74166422..74166502,74167426..74167509,
                     74168178..74168361,74169841..74169869,74171152..74171193,
                     74172292..74172333,74173110..74173185,74173878..74175022)
                     /gene="GTF2I"
                     /gene_synonym="BAP135; BTKAP1; DIWS; FLJ38776; FLJ56355;
                     GTFII-I; IB291; SPIN; TFII-I; WBS; WBSCR6"
                     /product="general transcription factor IIi, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032999.2"
                     /db_xref="GI:169881253"
                     /db_xref="GeneID:2969"
                     /db_xref="HGNC:4659"
                     /db_xref="HPRD:03399"
                     /db_xref="MIM:601679"
     mRNA            join(74072030..74072394,74103458..74103561,
                     74105305..74105443,74113291..74113425,74114577..74114760,
                     74114936..74114964,74119496..74119550,74120721..74120764,
                     74125363..74125440,74131214..74131270,74133198..74133260,
                     74143124..74143234,74144567..74144632,74146820..74147003,
                     74148265..74148323,74149803..74149874,74150842..74151025,
                     74152387..74152445,74157788..74157859,74159097..74159280,
                     74160222..74160280,74160676..74160750,74162352..74162453,
                     74163362..74163427,74163605..74163788,74165693..74165748,
                     74166422..74166502,74167426..74167509,74168178..74168361,
                     74169841..74169869,74171152..74171193,74172292..74172333,
                     74173110..74173185,74173878..74175022)
                     /gene="GTF2I"
                     /gene_synonym="BAP135; BTKAP1; DIWS; FLJ38776; FLJ56355;
                     GTFII-I; IB291; SPIN; TFII-I; WBS; WBSCR6"
                     /product="general transcription factor IIi, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033000.2"
                     /db_xref="GI:169881254"
                     /db_xref="GeneID:2969"
                     /db_xref="HGNC:4659"
                     /db_xref="HPRD:03399"
                     /db_xref="MIM:601679"
     mRNA            join(74072030..74072394,74103458..74103561,
                     74105305..74105443,74113291..74113425,74114577..74114760,
                     74114936..74114964,74119496..74119550,74120721..74120764,
                     74125363..74125440,74129177..74129236,74131214..74131270,
                     74143124..74143234,74144567..74144632,74146820..74147003,
                     74148265..74148323,74149803..74149874,74150842..74151025,
                     74152387..74152445,74157788..74157859,74159097..74159280,
                     74160222..74160280,74160676..74160750,74162352..74162453,
                     74163362..74163427,74163605..74163788,74165693..74165748,
                     74166422..74166502,74167426..74167509,74168178..74168361,
                     74169841..74169869,74171152..74171193,74172292..74172333,
                     74173110..74173185,74173878..74175022)
                     /gene="GTF2I"
                     /gene_synonym="BAP135; BTKAP1; DIWS; FLJ38776; FLJ56355;
                     GTFII-I; IB291; SPIN; TFII-I; WBS; WBSCR6"
                     /product="general transcription factor IIi, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033001.2"
                     /db_xref="GI:169881255"
                     /db_xref="GeneID:2969"
                     /db_xref="HGNC:4659"
                     /db_xref="HPRD:03399"
                     /db_xref="MIM:601679"
     mRNA            join(74072030..74072394,74103458..74103561,
                     74105305..74105443,74113291..74113425,74114577..74114760,
                     74114936..74114964,74119496..74119550,74120721..74120764,
                     74125363..74125440,74131214..74131270,74143124..74143234,
                     74144567..74144632,74146820..74147003,74148265..74148323,
                     74149803..74149874,74150842..74151025,74152387..74152445,
                     74157788..74157859,74159097..74159280,74160222..74160280,
                     74160676..74160750,74162352..74162453,74163362..74163427,
                     74163605..74163788,74165693..74165748,74166422..74166502,
                     74167426..74167509,74168178..74168361,74169841..74169869,
                     74171152..74171193,74172292..74172333,74173110..74173185,
                     74173878..74175022)
                     /gene="GTF2I"
                     /gene_synonym="BAP135; BTKAP1; DIWS; FLJ38776; FLJ56355;
                     GTFII-I; IB291; SPIN; TFII-I; WBS; WBSCR6"
                     /product="general transcription factor IIi, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001518.3"
                     /db_xref="GI:169881251"
                     /db_xref="GeneID:2969"
                     /db_xref="HGNC:4659"
                     /db_xref="HPRD:03399"
                     /db_xref="MIM:601679"
     mRNA            join(74072030..74072394,74103458..74103561,
                     74105305..74105443,74113291..74113425,74114577..74114760,
                     74114936..74114964,74119496..74119550,74120721..74120764,
                     74125363..74125440,74129180..74129236,74131214..74131270,
                     74143124..74143234,74144567..74144632,74146820..74147003,
                     74148265..74148323,74149803..74149874,74150842..74151025,
                     74152387..74152445,74157788..74157859,74159097..74159280,
                     74160222..74160280,74160676..74160750,74162352..74162453,
                     74163362..74163427,74163605..74163788,74165693..74165748,
                     74166422..74166502,74167426..74167509,74168178..74168361,
                     74169841..74169869,74171152..74171193,74172292..74172333,
                     74173110..74173185,74173878..74175022)
                     /gene="GTF2I"
                     /gene_synonym="BAP135; BTKAP1; DIWS; FLJ38776; FLJ56355;
                     GTFII-I; IB291; SPIN; TFII-I; WBS; WBSCR6"
                     /product="general transcription factor IIi, transcript
                     variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001163636.1"
                     /db_xref="GI:254692933"
                     /db_xref="GeneID:2969"
                     /db_xref="HGNC:4659"
                     /db_xref="MIM:601679"
                     /db_xref="HPRD:03399"
     CDS             join(74103463..74103561,74105305..74105443,
                     74113291..74113425,74114577..74114760,74114936..74114964,
                     74119496..74119550,74120721..74120764,74125363..74125440,
                     74129177..74129236,74131214..74131270,74133198..74133260,
                     74143124..74143234,74144567..74144632,74146820..74147003,
                     74148265..74148323,74149803..74149874,74150842..74151025,
                     74152387..74152445,74157788..74157859,74159097..74159280,
                     74160222..74160280,74160676..74160750,74162352..74162453,
                     74163362..74163427,74163605..74163788,74165693..74165748,
                     74166422..74166502,74167426..74167509,74168178..74168361,
                     74169841..74169869,74171152..74171193,74172292..74172333,
                     74173110..74173168)
                     /gene="GTF2I"
                     /gene_synonym="BAP135; BTKAP1; DIWS; FLJ38776; FLJ56355;
                     GTFII-I; IB291; SPIN; TFII-I; WBS; WBSCR6"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="general transcription factor II-I isoform 1"
                     /protein_id="NP_127492.1"
                     /db_xref="GI:14670350"
                     /db_xref="CCDS:CCDS5573.1"
                     /db_xref="GeneID:2969"
                     /db_xref="HGNC:4659"
                     /db_xref="HPRD:03399"
                     /db_xref="MIM:601679"
     CDS             join(74103463..74103561,74105305..74105443,
                     74113291..74113425,74114577..74114760,74114936..74114964,
                     74119496..74119550,74120721..74120764,74125363..74125440,
                     74131214..74131270,74133198..74133260,74143124..74143234,
                     74144567..74144632,74146820..74147003,74148265..74148323,
                     74149803..74149874,74150842..74151025,74152387..74152445,
                     74157788..74157859,74159097..74159280,74160222..74160280,
                     74160676..74160750,74162352..74162453,74163362..74163427,
                     74163605..74163788,74165693..74165748,74166422..74166502,
                     74167426..74167509,74168178..74168361,74169841..74169869,
                     74171152..74171193,74172292..74172333,74173110..74173168)
                     /gene="GTF2I"
                     /gene_synonym="BAP135; BTKAP1; DIWS; FLJ38776; FLJ56355;
                     GTFII-I; IB291; SPIN; TFII-I; WBS; WBSCR6"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="general transcription factor II-I isoform 2"
                     /protein_id="NP_127493.1"
                     /db_xref="GI:14670352"
                     /db_xref="CCDS:CCDS5574.1"
                     /db_xref="GeneID:2969"
                     /db_xref="HGNC:4659"
                     /db_xref="HPRD:03399"
                     /db_xref="MIM:601679"
     CDS             join(74103463..74103561,74105305..74105443,
                     74113291..74113425,74114577..74114760,74114936..74114964,
                     74119496..74119550,74120721..74120764,74125363..74125440,
                     74129177..74129236,74131214..74131270,74143124..74143234,
                     74144567..74144632,74146820..74147003,74148265..74148323,
                     74149803..74149874,74150842..74151025,74152387..74152445,
                     74157788..74157859,74159097..74159280,74160222..74160280,
                     74160676..74160750,74162352..74162453,74163362..74163427,
                     74163605..74163788,74165693..74165748,74166422..74166502,
                     74167426..74167509,74168178..74168361,74169841..74169869,
                     74171152..74171193,74172292..74172333,74173110..74173168)
                     /gene="GTF2I"
                     /gene_synonym="BAP135; BTKAP1; DIWS; FLJ38776; FLJ56355;
                     GTFII-I; IB291; SPIN; TFII-I; WBS; WBSCR6"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="general transcription factor II-I isoform 3"
                     /protein_id="NP_127494.1"
                     /db_xref="GI:14670354"
                     /db_xref="CCDS:CCDS5575.1"
                     /db_xref="GeneID:2969"
                     /db_xref="HGNC:4659"
                     /db_xref="HPRD:03399"
                     /db_xref="MIM:601679"
     CDS             join(74103463..74103561,74105305..74105443,
                     74113291..74113425,74114577..74114760,74114936..74114964,
                     74119496..74119550,74120721..74120764,74125363..74125440,
                     74131214..74131270,74143124..74143234,74144567..74144632,
                     74146820..74147003,74148265..74148323,74149803..74149874,
                     74150842..74151025,74152387..74152445,74157788..74157859,
                     74159097..74159280,74160222..74160280,74160676..74160750,
                     74162352..74162453,74163362..74163427,74163605..74163788,
                     74165693..74165748,74166422..74166502,74167426..74167509,
                     74168178..74168361,74169841..74169869,74171152..74171193,
                     74172292..74172333,74173110..74173168)
                     /gene="GTF2I"
                     /gene_synonym="BAP135; BTKAP1; DIWS; FLJ38776; FLJ56355;
                     GTFII-I; IB291; SPIN; TFII-I; WBS; WBSCR6"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="general transcription factor II-I isoform 4"
                     /protein_id="NP_001509.3"
                     /db_xref="GI:169881252"
                     /db_xref="CCDS:CCDS47614.1"
                     /db_xref="GeneID:2969"
                     /db_xref="HGNC:4659"
                     /db_xref="HPRD:03399"
                     /db_xref="MIM:601679"
     CDS             join(74103463..74103561,74105305..74105443,
                     74113291..74113425,74114577..74114760,74114936..74114964,
                     74119496..74119550,74120721..74120764,74125363..74125440,
                     74129180..74129236,74131214..74131270,74143124..74143234,
                     74144567..74144632,74146820..74147003,74148265..74148323,
                     74149803..74149874,74150842..74151025,74152387..74152445,
                     74157788..74157859,74159097..74159280,74160222..74160280,
                     74160676..74160750,74162352..74162453,74163362..74163427,
                     74163605..74163788,74165693..74165748,74166422..74166502,
                     74167426..74167509,74168178..74168361,74169841..74169869,
                     74171152..74171193,74172292..74172333,74173110..74173168)
                     /gene="GTF2I"
                     /gene_synonym="BAP135; BTKAP1; DIWS; FLJ38776; FLJ56355;
                     GTFII-I; IB291; SPIN; TFII-I; WBS; WBSCR6"
                     /note="isoform 5 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="general transcription factor II-I isoform 5"
                     /protein_id="NP_001157108.1"
                     /db_xref="GI:254692934"
                     /db_xref="GeneID:2969"
                     /db_xref="HGNC:4659"
                     /db_xref="MIM:601679"
                     /db_xref="HPRD:03399"
     gene            74188309..74203659
                     /gene="NCF1"
                     /gene_synonym="FLJ79451; NCF1A; NOXO2; p47phox; SH3PXD1A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:653361"
                     /db_xref="HGNC:7660"
                     /db_xref="HPRD:01990"
                     /db_xref="MIM:608512"
     mRNA            join(74188309..74188450,74191613..74191693,
                     74193428..74193503,74193603..74193768,74195126..74195181,
                     74197282..74197404,74197868..74197975,74199528..74199645,
                     74202328..74202432,74202903..74203048,74203383..74203659)
                     /gene="NCF1"
                     /gene_synonym="FLJ79451; NCF1A; NOXO2; p47phox; SH3PXD1A"
                     /product="neutrophil cytosolic factor 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000265.4"
                     /db_xref="GI:115298671"
                     /db_xref="GeneID:653361"
                     /db_xref="HGNC:7660"
                     /db_xref="HPRD:01990"
                     /db_xref="MIM:608512"
     CDS             join(74188379..74188450,74191613..74191693,
                     74193428..74193503,74193603..74193768,74195126..74195181,
                     74197282..74197404,74197868..74197975,74199528..74199645,
                     74202328..74202432,74202903..74203048,74203383..74203504)
                     /gene="NCF1"
                     /gene_synonym="FLJ79451; NCF1A; NOXO2; p47phox; SH3PXD1A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="neutrophil cytosol factor 1"
                     /protein_id="NP_000256.3"
                     /db_xref="GI:115298672"
                     /db_xref="CCDS:CCDS34657.1"
                     /db_xref="GeneID:653361"
                     /db_xref="HGNC:7660"
                     /db_xref="HPRD:01990"
                     /db_xref="MIM:608512"
     gene            complement(74210484..74267841)
                     /gene="GTF2IRD2"
                     /gene_synonym="FLJ21423; FLJ37938; FP630; GTF2IRD2A;
                     MGC75203"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84163"
                     /db_xref="HGNC:30775"
                     /db_xref="HPRD:16402"
                     /db_xref="MIM:608899"
     mRNA            complement(join(74210484..74212604,74216326..74216354,
                     74217639..74217822,74219118..74219201,74221275..74221352,
                     74223445..74223510,74225430..74225486,74227272..74227349,
                     74234084..74234127,74234499..74234553,74236955..74236983,
                     74237152..74237335,74239462..74239581,74247928..74248066,
                     74251402..74251505,74267663..74267841))
                     /gene="GTF2IRD2"
                     /gene_synonym="FLJ21423; FLJ37938; FP630; GTF2IRD2A;
                     MGC75203"
                     /product="GTF2I repeat domain containing 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_173537.2"
                     /db_xref="GI:48762699"
                     /db_xref="GeneID:84163"
                     /db_xref="HGNC:30775"
                     /db_xref="HPRD:16402"
                     /db_xref="MIM:608899"
     CDS             complement(join(74211001..74212604,74216326..74216354,
                     74217639..74217822,74219118..74219201,74221275..74221352,
                     74223445..74223510,74225430..74225486,74227272..74227349,
                     74234084..74234127,74234499..74234553,74236955..74236983,
                     74237152..74237335,74239462..74239581,74247928..74248066,
                     74251402..74251500))
                     /gene="GTF2IRD2"
                     /gene_synonym="FLJ21423; FLJ37938; FP630; GTF2IRD2A;
                     MGC75203"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="general transcription factor II-I repeat
                     domain-containing protein 2A"
                     /protein_id="NP_775808.2"
                     /db_xref="GI:48762700"
                     /db_xref="CCDS:CCDS5576.1"
                     /db_xref="GeneID:84163"
                     /db_xref="HGNC:30775"
                     /db_xref="HPRD:16402"
                     /db_xref="MIM:608899"
     gene            complement(74299267..74306731)
                     /gene="STAG3L2"
                     /gene_synonym="MGC131759; STAG3L1; STAG3L3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:442582"
                     /db_xref="HGNC:33886"
     mRNA            complement(join(74299267..74299569,74299834..74299941,
                     74300250..74300329,74300540..74300638,74301137..74301260,
                     74303804..74303920,74304433..74304518,74306509..74306731))
                     /gene="STAG3L2"
                     /gene_synonym="MGC131759; STAG3L1; STAG3L3"
                     /product="stromal antigen 3-like 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001025202.2"
                     /db_xref="GI:148226756"
                     /db_xref="GeneID:442582"
                     /db_xref="HGNC:33886"
     CDS             complement(join(74299884..74299941,74300250..74300329,
                     74300540..74300638,74301137..74301260,74303804..74303847))
                     /gene="STAG3L2"
                     /gene_synonym="MGC131759; STAG3L1; STAG3L3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="STAG3-like protein 2"
                     /protein_id="NP_001020373.2"
                     /db_xref="GI:148226757"
                     /db_xref="CCDS:CCDS47615.1"
                     /db_xref="GeneID:442582"
                     /db_xref="HGNC:33886"
     gene            74306894..74336166
                     /gene="PMS2P5"
                     /gene_synonym="MGC34222; PMS2L5; PMS7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:5383"
                     /db_xref="HGNC:9130"
     misc_RNA        join(74306894..74306965,74310233..74310372,
                     74313768..74313951,74335467..74336166)
                     /gene="PMS2P5"
                     /gene_synonym="MGC34222; PMS2L5; PMS7"
                     /product="postmeiotic segregation increased 2 pseudogene
                     5, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_027777.1"
                     /db_xref="GI:239787878"
                     /db_xref="GeneID:5383"
                     /db_xref="HGNC:9130"
     misc_RNA        join(74306894..74306965,74310233..74310372,
                     74312263..74312349,74312526..74312628,74313768..74313951,
                     74317004..74317092,74321683..74322330)
                     /gene="PMS2P5"
                     /gene_synonym="MGC34222; PMS2L5; PMS7"
                     /product="postmeiotic segregation increased 2 pseudogene
                     5, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_027775.1"
                     /db_xref="GI:239787876"
                     /db_xref="GeneID:5383"
                     /db_xref="HGNC:9130"
     misc_RNA        join(74306894..74306965,74310233..74310372,
                     74312263..74312349,74313768..74313951,74317004..74317092,
                     74321683..74322330)
                     /gene="PMS2P5"
                     /gene_synonym="MGC34222; PMS2L5; PMS7"
                     /product="postmeiotic segregation increased 2 pseudogene
                     5, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_027776.1"
                     /db_xref="GI:239787877"
                     /db_xref="GeneID:5383"
                     /db_xref="HGNC:9130"
     gene            complement(74320406..74328423)
                     /gene="LOC100101268"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100101268"
     gene            74379083..74438803
                     /gene="GATSL1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:389523"
                     /db_xref="HGNC:37072"
     mRNA            join(74379083..74379195,74422160..74422230,
                     74431766..74431959,74432158..74432290,74433140..74433263,
                     74434207..74434317,74436042..74436124,74438544..74438638,
                     74438738..74438803)
                     /gene="GATSL1"
                     /product="GATS protein-like 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145063.1"
                     /db_xref="GI:222831642"
                     /db_xref="GeneID:389523"
                     /db_xref="HGNC:37072"
     CDS             join(74379083..74379195,74422160..74422230,
                     74431766..74431959,74432158..74432290,74433140..74433263,
                     74434207..74434317,74436042..74436124,74438544..74438638,
                     74438738..74438803)
                     /gene="GATSL1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="GATS-like protein 1"
                     /protein_id="NP_001138535.1"
                     /db_xref="GI:222831643"
                     /db_xref="GeneID:389523"
                     /db_xref="HGNC:37072"
     gene            complement(74440031..74445485)
                     /gene="LOC100505669"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 8 ESTs"
                     /db_xref="GeneID:100505669"
     misc_RNA        complement(join(74440031..74443695,74444016..74445485))
                     /gene="LOC100505669"
                     /product="hypothetical LOC100505669"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 8 ESTs"
                     /transcript_id="XR_108833.1"
                     /db_xref="GI:310120006"
                     /db_xref="GeneID:100505669"
     gene            complement(74456283..74489699)
                     /gene="WBSCR16"
                     /gene_synonym="DKFZp434D0421; MGC189739; MGC44931"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:81554"
                     /db_xref="HGNC:14948"
                     /db_xref="HPRD:15654"
     mRNA            complement(join(74456283..74457217,74466818..74466903,
                     74470008..74470181,74471636..74471723,74474400..74474581,
                     74477020..74477104,74479107..74479158,74480395..74480461,
                     74482477..74482605,74486454..74486583,74489250..74489699))
                     /gene="WBSCR16"
                     /gene_synonym="DKFZp434D0421; MGC189739; MGC44931"
                     /product="Williams-Beuren syndrome chromosome region 16"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_030798.3"
                     /db_xref="GI:94538368"
                     /db_xref="GeneID:81554"
                     /db_xref="HGNC:14948"
                     /db_xref="HPRD:15654"
     CDS             complement(join(74457140..74457217,74466818..74466903,
                     74470008..74470181,74471636..74471723,74474400..74474581,
                     74477020..74477104,74479107..74479158,74480395..74480461,
                     74482477..74482605,74486454..74486583,74489250..74489573))
                     /gene="WBSCR16"
                     /gene_synonym="DKFZp434D0421; MGC189739; MGC44931"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="Williams-Beuren syndrome chromosomal region 16
                     protein"
                     /protein_id="NP_110425.1"
                     /db_xref="GI:13540582"
                     /db_xref="CCDS:CCDS5577.1"
                     /db_xref="GeneID:81554"
                     /db_xref="HGNC:14948"
                     /db_xref="HPRD:15654"
     gene            74508347..74565623
                     /gene="GTF2IRD2B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:389524"
                     /db_xref="HGNC:33125"
                     /db_xref="HPRD:12327"
                     /db_xref="MIM:608900"
     mRNA            join(74508347..74508556,74524752..74524855,
                     74528191..74528329,74536692..74536811,74538937..74539120,
                     74539289..74539317,74541717..74541771,74542143..74542186,
                     74548943..74549020,74550811..74550867,74552592..74552657,
                     74554758..74554835,74556910..74556993,74558289..74558472,
                     74559757..74559785,74563500..74565623)
                     /gene="GTF2IRD2B"
                     /product="GTF2I repeat domain containing 2B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001003795.2"
                     /db_xref="GI:91823780"
                     /db_xref="GeneID:389524"
                     /db_xref="HGNC:33125"
                     /db_xref="HPRD:12327"
                     /db_xref="MIM:608900"
     CDS             join(74524757..74524855,74528191..74528329,
                     74536692..74536811,74538937..74539120,74539289..74539317,
                     74541717..74541771,74542143..74542186,74548943..74549020,
                     74550811..74550867,74552592..74552657,74554758..74554835,
                     74556910..74556993,74558289..74558472,74559757..74559785,
                     74563500..74565103)
                     /gene="GTF2IRD2B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="general transcription factor II-I repeat
                     domain-containing protein 2B"
                     /protein_id="NP_001003795.1"
                     /db_xref="GI:51241788"
                     /db_xref="CCDS:CCDS34659.1"
                     /db_xref="GeneID:389524"
                     /db_xref="HGNC:33125"
                     /db_xref="HPRD:12327"
                     /db_xref="MIM:608900"
     gene            complement(74572384..74587816)
                     /gene="NCF1C"
                     /gene_synonym="SH3PXD1C"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:654817"
                     /db_xref="HGNC:32523"
     misc_RNA        complement(join(74572384..74572721,74573056..74573201,
                     74573672..74573776,74576464..74576581,74578131..74578238,
                     74578702..74578824,74580929..74580984,74582342..74582507,
                     74582607..74582682,74584438..74584516,74587676..74587816))
                     /gene="NCF1C"
                     /gene_synonym="SH3PXD1C"
                     /product="neutrophil cytosolic factor 1C pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003187.2"
                     /db_xref="GI:269784660"
                     /db_xref="GeneID:654817"
                     /db_xref="HGNC:32523"
     gene            complement(74601104..74653445)
                     /gene="GTF2IP1"
                     /gene_synonym="WBSCR7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:2970"
                     /db_xref="HGNC:4660"
     misc_RNA        complement(join(74601104..74602248,74602942..74603017,
                     74603796..74603837,74604934..74604975,74606258..74606286,
                     74607766..74607949,74608618..74608701,74609624..74609704,
                     74610378..74610433,74612335..74612518,74612696..74612761,
                     74613670..74613771,74615371..74615445,74615841..74615899,
                     74616841..74617024,74618258..74618329,74623676..74623734,
                     74625097..74625280,74626247..74626318,74627798..74627856,
                     74629125..74629308,74631472..74631537,74632869..74632979,
                     74653040..74653445))
                     /gene="GTF2IP1"
                     /gene_synonym="WBSCR7"
                     /product="general transcription factor IIi, pseudogene 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002206.2"
                     /db_xref="GI:197382196"
                     /db_xref="GeneID:2970"
                     /db_xref="HGNC:4660"
     gene            74697002..74704300
                     /gene="LOC643862"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:643862"
     gene            complement(74700807..74715111)
                     /gene="LOC441259"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:441259"
     gene            74765963..74790145
                     /gene="LOC653375"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 53 ESTs, 1 Protein"
                     /db_xref="GeneID:653375"
     mRNA            join(74765963..74766022,74767260..74767311,
                     74769313..74769397,74771834..74772015,74774692..74774779,
                     74776234..74776407,74779512..74779597,74789197..74789274)
                     /gene="LOC653375"
                     /product="RCC1-like G exchanging factor-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs, 1 Protein"
                     /transcript_id="XM_001722348.3"
                     /db_xref="GI:310120007"
                     /db_xref="GeneID:653375"
     CDS             join(74765964..74766022,74767260..74767311,
                     74769313..74769397,74771834..74772015,74774692..74774779,
                     74776234..74776407,74779512..74779597,74789197..74789274)
                     /gene="LOC653375"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="hypothetical protein LOC653375"
                     /protein_id="XP_001722400.1"
                     /db_xref="GI:169171160"
                     /db_xref="GeneID:653375"
     gene            complement(74807605..74867341)
                     /gene="GATSL2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:729438"
                     /db_xref="HGNC:37073"
     mRNA            complement(join(74807605..74807670,74807770..74807864,
                     74810284..74810366,74812091..74812201,74813145..74813268,
                     74814118..74814250,74814449..74814642,74824183..74824253,
                     74867229..74867341))
                     /gene="GATSL2"
                     /product="GATS protein-like 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145064.1"
                     /db_xref="GI:222831644"
                     /db_xref="GeneID:729438"
                     /db_xref="HGNC:37073"
     CDS             complement(join(74807605..74807670,74807770..74807864,
                     74810284..74810366,74812091..74812201,74813145..74813268,
                     74814118..74814250,74814449..74814642,74824183..74824253,
                     74867229..74867341))
                     /gene="GATSL2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="GATS-like protein 2"
                     /protein_id="NP_001138536.1"
                     /db_xref="GI:222831645"
                     /db_xref="CCDS:CCDS47616.1"
                     /db_xref="GeneID:729438"
                     /db_xref="HGNC:37073"
     gene            74911266..74918564
                     /gene="LOC641776"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:641776"
     gene            complement(74925017..74928923)
                     /gene="PMS2P10"
                     /gene_synonym="PMS2L10; PMSR4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100288713"
                     /db_xref="HGNC:9124"
     gene            74939286..74946587
                     /gene="LOC643909"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:643909"
     gene            complement(74953039..74956948)
                     /gene="PMS2P6"
                     /gene_synonym="PMS2L14"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:729453"
                     /db_xref="HGNC:33514"
     gene            74967309..74974606
                     /gene="LOC441258"
                     /gene_synonym="FLJ20949"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:441258"
     gene            complement(74977964..74988215)
                     /gene="PMS2L2"
                     /gene_synonym="PMS4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:5380"
                     /db_xref="HGNC:9127"
     misc_RNA        complement(join(74977964..74978010,74981057..74981240,
                     74982537..74982649,74982816..74982902,74984790..74984939,
                     74988036..74988215))
                     /gene="PMS2L2"
                     /gene_synonym="PMS4"
                     /product="postmeiotic segregation increased 2-like 2
                     pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003614.1"
                     /db_xref="GI:153791692"
                     /db_xref="GeneID:5380"
                     /db_xref="HGNC:9127"
     gene            74988447..74996990
                     /gene="STAG3L1"
                     /gene_synonym="DKFZp434A0131; FLJ78546; MGC131759;
                     MGC40269; STAG3L2; STAG3L3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54441"
                     /db_xref="HGNC:33852"
                     /db_xref="HPRD:13150"
     mRNA            join(74988447..74988678,74990644..74990729,
                     74991242..74991358,74993902..74994025,74994524..74994622,
                     74994833..74994912,74995593..74995707,74996018..74996990)
                     /gene="STAG3L1"
                     /gene_synonym="DKFZp434A0131; FLJ78546; MGC131759;
                     MGC40269; STAG3L2; STAG3L3"
                     /product="stromal antigen 3-like 1, transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018991.2"
                     /db_xref="GI:50726993"
                     /db_xref="GeneID:54441"
                     /db_xref="HGNC:33852"
                     /db_xref="HPRD:13150"
     mRNA            join(74988447..74988678,74990644..74990729,
                     74991242..74991358,74994524..74994622,74994833..74994912,
                     74995593..74995707,74996018..74996990)
                     /gene="STAG3L1"
                     /gene_synonym="DKFZp434A0131; FLJ78546; MGC131759;
                     MGC40269; STAG3L2; STAG3L3"
                     /product="stromal antigen 3-like 1, transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001002840.1"
                     /db_xref="GI:50726988"
                     /db_xref="GeneID:54441"
                     /db_xref="HGNC:33852"
                     /db_xref="HPRD:13150"
     CDS             join(74991315..74991358,74993902..74994025,
                     74994524..74994622,74994833..74994912,74995593..74995707,
                     74996018..74996173)
                     /gene="STAG3L1"
                     /gene_synonym="DKFZp434A0131; FLJ78546; MGC131759;
                     MGC40269; STAG3L2; STAG3L3"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="STAG3-like protein 1 isoform 1"
                     /protein_id="NP_061864.2"
                     /db_xref="GI:50726994"
                     /db_xref="CCDS:CCDS34663.1"
                     /db_xref="GeneID:54441"
                     /db_xref="HGNC:33852"
                     /db_xref="HPRD:13150"
     CDS             join(74991353..74991358,74994524..74994622,
                     74994833..74994912,74995593..74995707,74996018..74996173)
                     /gene="STAG3L1"
                     /gene_synonym="DKFZp434A0131; FLJ78546; MGC131759;
                     MGC40269; STAG3L2; STAG3L3"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="STAG3-like protein 1 isoform 2"
                     /protein_id="NP_001002840.1"
                     /db_xref="GI:50726989"
                     /db_xref="CCDS:CCDS43601.1"
                     /db_xref="GeneID:54441"
                     /db_xref="HGNC:33852"
                     /db_xref="HPRD:13150"
     gene            complement(75000344..75001457)
                     /gene="LOC100505688"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /db_xref="GeneID:100505688"
     misc_RNA        complement(join(75000344..75000941,75001400..75001457))
                     /gene="LOC100505688"
                     /product="hypothetical LOC100505688"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /transcript_id="XR_108834.1"
                     /db_xref="GI:310120009"
                     /db_xref="GeneID:100505688"
     gene            complement(75021229..75024708)
                     /gene="LOC541473"
                     /gene_synonym="MGC88170"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:541473"
     misc_RNA        complement(join(75021229..75021729,75022781..75022841,
                     75023541..75023630,75024292..75024409,75024499..75024708))
                     /gene="LOC541473"
                     /gene_synonym="MGC88170"
                     /product="FK506 binding protein 6, 36kDa pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003602.1"
                     /db_xref="GI:150378496"
                     /db_xref="GeneID:541473"
     gene            75024903..75034888
                     /gene="TRIM73"
                     /gene_synonym="FLJ99347; MGC45477; TRIM50B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:375593"
                     /db_xref="HGNC:18162"
                     /db_xref="HPRD:18606"
                     /db_xref="MIM:612549"
     mRNA            join(75024903..75025084,75028200..75028616,
                     75032928..75033023,75034122..75034352,75034465..75034888)
                     /gene="TRIM73"
                     /gene_synonym="FLJ99347; MGC45477; TRIM50B"
                     /product="tripartite motif containing 73"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198924.2"
                     /db_xref="GI:65285120"
                     /db_xref="GeneID:375593"
                     /db_xref="HGNC:18162"
                     /db_xref="HPRD:18606"
                     /db_xref="MIM:612549"
     CDS             join(75028218..75028616,75032928..75033023,
                     75034122..75034352,75034465..75034491)
                     /gene="TRIM73"
                     /gene_synonym="FLJ99347; MGC45477; TRIM50B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="tripartite motif-containing protein 73"
                     /protein_id="NP_944606.2"
                     /db_xref="GI:65285121"
                     /db_xref="CCDS:CCDS34665.1"
                     /db_xref="GeneID:375593"
                     /db_xref="HGNC:18162"
                     /db_xref="HPRD:18606"
                     /db_xref="MIM:612549"
     gene            75039624..75046065
                     /gene="NSUN5P1"
                     /gene_synonym="FLJ99347; MGC129801; NSUN5B; WBSCR20B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:155400"
                     /db_xref="HGNC:19146"
     misc_RNA        join(75039624..75039743,75039889..75040009,
                     75040691..75040857,75040938..75041042,75042067..75042210,
                     75044163..75044301,75044398..75044512,75044870..75045056,
                     75045259..75045469,75045554..75045694,75045765..75046065)
                     /gene="NSUN5P1"
                     /gene_synonym="FLJ99347; MGC129801; NSUN5B; WBSCR20B"
                     /product="NOP2/Sun domain family, member 5 pseudogene 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_033322.2"
                     /db_xref="GI:325652007"
                     /db_xref="GeneID:155400"
                     /db_xref="HGNC:19146"
     gene            complement(75046065..75115568)
                     /gene="POM121C"
                     /gene_synonym="DKFZp586P2220; DKFZp779K1713; FLJ43877;
                     FLJ45082; MGC163459; MGC163461; POM121-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100101267"
                     /db_xref="HGNC:34005"
     mRNA            complement(join(75046065..75048176,75048603..75048725,
                     75050792..75052486,75053332..75053508,75053809..75053911,
                     75054357..75054478,75054918..75054991,75055644..75055735,
                     75066793..75066964,75068422..75068502,75070232..75070393,
                     75070710..75070925,75103970..75104148,75104328..75104454,
                     75115141..75115568))
                     /gene="POM121C"
                     /gene_synonym="DKFZp586P2220; DKFZp779K1713; FLJ43877;
                     FLJ45082; MGC163459; MGC163461; POM121-2"
                     /product="POM121 membrane glycoprotein C"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001099415.1"
                     /db_xref="GI:150378544"
                     /db_xref="GeneID:100101267"
                     /db_xref="HGNC:34005"
     CDS             complement(join(75048079..75048176,75048603..75048725,
                     75050792..75052486,75053332..75053508,75053809..75053911,
                     75054357..75054478,75054918..75054991,75055644..75055735,
                     75066793..75066964,75068422..75068502,75070232..75070393,
                     75070710..75070774))
                     /gene="POM121C"
                     /gene_synonym="DKFZp586P2220; DKFZp779K1713; FLJ43877;
                     FLJ45082; MGC163459; MGC163461; POM121-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="nuclear envelope pore membrane protein POM 121C"
                     /protein_id="NP_001092885.1"
                     /db_xref="GI:150378545"
                     /db_xref="CCDS:CCDS47617.1"
                     /db_xref="GeneID:100101267"
                     /db_xref="HGNC:34005"
     gene            75124299..75133628
                     /gene="SPDYE5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:442590"
                     /db_xref="HGNC:35464"
     mRNA            join(75124299..75124693,75125997..75126227,
                     75127261..75127319,75128555..75128640,75130686..75130804,
                     75130880..75131079,75131202..75131306,75132157..75133628)
                     /gene="SPDYE5"
                     /product="speedy homolog E5 (Xenopus laevis)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001099435.2"
                     /db_xref="GI:194595491"
                     /db_xref="GeneID:442590"
                     /db_xref="HGNC:35464"
     CDS             join(75124435..75124693,75125997..75126227,
                     75127261..75127319,75128555..75128640,75130686..75130804,
                     75130880..75131079,75131202..75131261)
                     /gene="SPDYE5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative speedy protein E5"
                     /protein_id="NP_001092905.2"
                     /db_xref="GI:194595492"
                     /db_xref="GeneID:442590"
                     /db_xref="HGNC:35464"
     gene            complement(75137069..75157453)
                     /gene="PMS2P3"
                     /gene_synonym="MGC126647; PMS2L3; PMS2L9; PMS5; PMSR3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:5387"
                     /db_xref="HGNC:9128"
     misc_RNA        complement(join(75137069..75137189,75140253..75140436,
                     75141633..75141745,75141913..75141999,75143970..75144109,
                     75145043..75145153,75145420..75145546,75155234..75155292,
                     75156895..75157453))
                     /gene="PMS2P3"
                     /gene_synonym="MGC126647; PMS2L3; PMS2L9; PMS5; PMSR3"
                     /product="postmeiotic segregation increased 2 pseudogene
                     3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_028059.1"
                     /db_xref="GI:254039602"
                     /db_xref="GeneID:5387"
                     /db_xref="HGNC:9128"
     gene            complement(75163409..75368279)
                     /gene="HIP1"
                     /gene_synonym="ILWEQ; MGC126506"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3092"
                     /db_xref="HGNC:4913"
                     /db_xref="HPRD:03461"
                     /db_xref="MIM:601767"
     mRNA            complement(join(75163409..75167545,75168643..75168751,
                     75171238..75171299,75172170..75172293,75173993..75174098,
                     75174386..75174486,75176237..75176330,75177053..75177111,
                     75178189..75178299,75182752..75182888,75183412..75183519,
                     75183739..75183825,75184720..75184855,75185330..75185473,
                     75186014..75186115,75186958..75187074,75187471..75187559,
                     75189036..75189219,75190633..75190705,75191377..75191474,
                     75192239..75192379,75192492..75192567,75197503..75197560,
                     75203066..75203206,75210553..75210614,75211391..75211467,
                     75216071..75216151,75221374..75221430,75221690..75221832,
                     75228502..75228565,75368119..75368279))
                     /gene="HIP1"
                     /gene_synonym="ILWEQ; MGC126506"
                     /product="huntingtin interacting protein 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005338.4"
                     /db_xref="GI:38045918"
                     /db_xref="GeneID:3092"
                     /db_xref="HGNC:4913"
                     /db_xref="HPRD:03461"
                     /db_xref="MIM:601767"
     CDS             complement(join(75167493..75167545,75168643..75168751,
                     75171238..75171299,75172170..75172293,75173993..75174098,
                     75174386..75174486,75176237..75176330,75177053..75177111,
                     75178189..75178299,75182752..75182888,75183412..75183519,
                     75183739..75183825,75184720..75184855,75185330..75185473,
                     75186014..75186115,75186958..75187074,75187471..75187559,
                     75189036..75189219,75190633..75190705,75191377..75191474,
                     75192239..75192379,75192492..75192567,75197503..75197560,
                     75203066..75203206,75210553..75210614,75211391..75211467,
                     75216071..75216151,75221374..75221430,75221690..75221832,
                     75228502..75228565,75368119..75368238))
                     /gene="HIP1"
                     /gene_synonym="ILWEQ; MGC126506"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="huntingtin-interacting protein 1"
                     /protein_id="NP_005329.3"
                     /db_xref="GI:38045919"
                     /db_xref="CCDS:CCDS34669.1"
                     /db_xref="GeneID:3092"
                     /db_xref="HGNC:4913"
                     /db_xref="HPRD:03461"
                     /db_xref="MIM:601767"
     gene            complement(75398842..75419064)
                     /gene="CCL26"
                     /gene_synonym="IMAC; MGC126714; MIP-4a; MIP-4alpha;
                     SCYA26; TSC-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10344"
                     /db_xref="HGNC:10625"
                     /db_xref="HPRD:05262"
                     /db_xref="MIM:604697"
     mRNA            complement(join(75398842..75399107,75401207..75401321,
                     75401422..75401572,75419035..75419064))
                     /gene="CCL26"
                     /gene_synonym="IMAC; MGC126714; MIP-4a; MIP-4alpha;
                     SCYA26; TSC-1"
                     /product="chemokine (C-C motif) ligand 26"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006072.4"
                     /db_xref="GI:51944958"
                     /db_xref="GeneID:10344"
                     /db_xref="HGNC:10625"
                     /db_xref="HPRD:05262"
                     /db_xref="MIM:604697"
     CDS             complement(join(75399011..75399107,75401207..75401321,
                     75401422..75401494))
                     /gene="CCL26"
                     /gene_synonym="IMAC; MGC126714; MIP-4a; MIP-4alpha;
                     SCYA26; TSC-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="C-C motif chemokine 26 precursor"
                     /protein_id="NP_006063.1"
                     /db_xref="GI:5174671"
                     /db_xref="CCDS:CCDS5578.1"
                     /db_xref="GeneID:10344"
                     /db_xref="HGNC:10625"
                     /db_xref="HPRD:05262"
                     /db_xref="MIM:604697"
     gene            complement(75441114..75443033)
                     /gene="CCL24"
                     /gene_synonym="Ckb-6; MPIF-2; MPIF2; SCYA24"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6369"
                     /db_xref="HGNC:10623"
                     /db_xref="HPRD:03931"
                     /db_xref="MIM:602495"
     mRNA            complement(join(75441114..75441282,75442624..75442741,
                     75442961..75443033))
                     /gene="CCL24"
                     /gene_synonym="Ckb-6; MPIF-2; MPIF2; SCYA24"
                     /product="chemokine (C-C motif) ligand 24"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002991.2"
                     /db_xref="GI:22165426"
                     /db_xref="GeneID:6369"
                     /db_xref="HGNC:10623"
                     /db_xref="HPRD:03931"
                     /db_xref="MIM:602495"
     CDS             complement(join(75441114..75441282,75442624..75442741,
                     75442961..75443033))
                     /gene="CCL24"
                     /gene_synonym="Ckb-6; MPIF-2; MPIF2; SCYA24"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="C-C motif chemokine 24 precursor"
                     /protein_id="NP_002982.2"
                     /db_xref="GI:22165427"
                     /db_xref="CCDS:CCDS34670.1"
                     /db_xref="GeneID:6369"
                     /db_xref="HGNC:10623"
                     /db_xref="HPRD:03931"
                     /db_xref="MIM:602495"
     gene            75464899..75465459
                     /gene="LOC100129130"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129130"
     gene            75508317..75518244
                     /gene="RHBDD2"
                     /gene_synonym="NPD007; RHBDL7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57414"
                     /db_xref="HGNC:23082"
     mRNA            join(75508317..75508578,75511147..75511554,
                     75513016..75513166,75517310..75518244)
                     /gene="RHBDD2"
                     /gene_synonym="NPD007; RHBDL7"
                     /product="rhomboid domain containing 2, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040456.1"
                     /db_xref="GI:94818789"
                     /db_xref="GeneID:57414"
                     /db_xref="HGNC:23082"
     mRNA            join(75508317..75508578,75510683..75510804,
                     75511147..75511554,75513016..75513166,75517310..75518244)
                     /gene="RHBDD2"
                     /gene_synonym="NPD007; RHBDL7"
                     /product="rhomboid domain containing 2, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040457.1"
                     /db_xref="GI:94818878"
                     /db_xref="GeneID:57414"
                     /db_xref="HGNC:23082"
     CDS             join(75508401..75508578,75511147..75511554,
                     75513016..75513166,75517310..75517667)
                     /gene="RHBDD2"
                     /gene_synonym="NPD007; RHBDL7"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="rhomboid domain-containing protein 2 isoform a"
                     /protein_id="NP_001035546.1"
                     /db_xref="GI:94818790"
                     /db_xref="CCDS:CCDS43602.1"
                     /db_xref="GeneID:57414"
                     /db_xref="HGNC:23082"
     CDS             join(75511392..75511554,75513016..75513166,
                     75517310..75517667)
                     /gene="RHBDD2"
                     /gene_synonym="NPD007; RHBDL7"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="rhomboid domain-containing protein 2 isoform b"
                     /protein_id="NP_001035547.1"
                     /db_xref="GI:94818879"
                     /db_xref="CCDS:CCDS43603.1"
                     /db_xref="GeneID:57414"
                     /db_xref="HGNC:23082"
     gene            75544420..75616173
                     /gene="POR"
                     /gene_synonym="CPR; CYPOR; DKFZp686G04235; FLJ26468;
                     P450R"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5447"
                     /db_xref="HGNC:9208"
                     /db_xref="HPRD:00485"
                     /db_xref="MIM:124015"
     mRNA            join(75544420..75544497,75583307..75583498,
                     75601731..75601779,75608769..75608897,75609657..75609806,
                     75610366..75610490,75610835..75610924,75611542..75611640,
                     75612838..75612954,75613056..75613174,75614095..75614276,
                     75614376..75614525,75614897..75615167,75615241..75615386,
                     75615477..75615559,75615655..75616173)
                     /gene="POR"
                     /gene_synonym="CPR; CYPOR; DKFZp686G04235; FLJ26468;
                     P450R"
                     /product="P450 (cytochrome) oxidoreductase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000941.2"
                     /db_xref="GI:94721355"
                     /db_xref="GeneID:5447"
                     /db_xref="HGNC:9208"
                     /db_xref="HPRD:00485"
                     /db_xref="MIM:124015"
     gene            75544515..75544587
                     /gene="MIR4651"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100616270"
                     /db_xref="HGNC:41647"
                     /db_xref="miRBase:MI0017279"
     ncRNA           75544515..75544587
                     /gene="MIR4651"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4651"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039795.1"
                     /db_xref="GI:337756588"
                     /db_xref="GeneID:100616270"
                     /db_xref="HGNC:41647"
                     /db_xref="miRBase:MI0017279"
     gene            75552068..75552773
                     /gene="RPL7L1P3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100131964"
                     /db_xref="HGNC:39485"
     gene            75573101..75573234
                     /gene="SNORA14A"
                     /gene_synonym="ACA14a"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:677801"
                     /db_xref="HGNC:32602"
     ncRNA           75573101..75573234
                     /gene="SNORA14A"
                     /gene_synonym="ACA14a"
                     /ncRNA_class="snoRNA"
                     /product="small nucleolar RNA, H/ACA box 14A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_002955.1"
                     /db_xref="GI:91680822"
                     /db_xref="GeneID:677801"
                     /db_xref="HGNC:32602"
     CDS             join(75583311..75583498,75601731..75601779,
                     75608769..75608897,75609657..75609806,75610366..75610490,
                     75610835..75610924,75611542..75611640,75612838..75612954,
                     75613056..75613174,75614095..75614276,75614376..75614525,
                     75614897..75615167,75615241..75615386,75615477..75615559,
                     75615655..75615799)
                     /gene="POR"
                     /gene_synonym="CPR; CYPOR; DKFZp686G04235; FLJ26468;
                     P450R"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="NADPH--cytochrome P450 reductase"
                     /protein_id="NP_000932.3"
                     /db_xref="GI:127139033"
                     /db_xref="CCDS:CCDS5579.1"
                     /db_xref="GeneID:5447"
                     /db_xref="HGNC:9208"
                     /db_xref="HPRD:00485"
                     /db_xref="MIM:124015"
     gene            complement(75616155..75623992)
                     /gene="TMEM120A"
                     /gene_synonym="NET29; TMPIT"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:83862"
                     /db_xref="HGNC:21697"
                     /db_xref="HPRD:15543"
     mRNA            complement(join(75616155..75616603,75616678..75616746,
                     75616856..75616920,75617036..75617128,75617241..75617302,
                     75617401..75617466,75617570..75617659,75617739..75617834,
                     75618483..75618542,75621462..75621578,75621757..75621875,
                     75623808..75623992))
                     /gene="TMEM120A"
                     /gene_synonym="NET29; TMPIT"
                     /product="transmembrane protein 120A"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_031925.2"
                     /db_xref="GI:221139702"
                     /db_xref="GeneID:83862"
                     /db_xref="HGNC:21697"
                     /db_xref="HPRD:15543"
     CDS             complement(join(75616490..75616603,75616678..75616746,
                     75616856..75616920,75617036..75617128,75617241..75617302,
                     75617401..75617466,75617570..75617659,75617739..75617834,
                     75618483..75618542,75621462..75621578,75621757..75621875,
                     75623808..75623888))
                     /gene="TMEM120A"
                     /gene_synonym="NET29; TMPIT"
                     /exception="unclassified translation discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 120A"
                     /protein_id="NP_114131.1"
                     /db_xref="GI:13994300"
                     /db_xref="GeneID:83862"
                     /db_xref="HGNC:21697"
                     /db_xref="HPRD:15543"
     gene            complement(75625655..75677321)
                     /gene="STYXL1"
                     /gene_synonym="DUSP24; MK-STYX"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51657"
                     /db_xref="HGNC:18165"
                     /db_xref="HPRD:13256"
     mRNA            complement(join(75625655..75625917,75630208..75630320,
                     75633076..75633173,75634577..75634722,75643060..75643205,
                     75651169..75651310,75657960..75658021,75659739..75659842,
                     75676980..75677321))
                     /gene="STYXL1"
                     /gene_synonym="DUSP24; MK-STYX"
                     /product="serine/threonine/tyrosine interacting-like 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016086.2"
                     /db_xref="GI:32481212"
                     /db_xref="GeneID:51657"
                     /db_xref="HGNC:18165"
                     /db_xref="HPRD:13256"
     CDS             complement(join(75625786..75625917,75630208..75630320,
                     75633076..75633173,75634577..75634722,75643060..75643205,
                     75651169..75651310,75657960..75658021,75659739..75659841))
                     /gene="STYXL1"
                     /gene_synonym="DUSP24; MK-STYX"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="serine/threonine/tyrosine-interacting-like
                     protein 1"
                     /protein_id="NP_057170.1"
                     /db_xref="GI:7706363"
                     /db_xref="CCDS:CCDS5580.1"
                     /db_xref="GeneID:51657"
                     /db_xref="HGNC:18165"
                     /db_xref="HPRD:13256"
     gene            75677393..75695931
                     /gene="MDH2"
                     /gene_synonym="M-MDH; MDH; MGC:3559; MOR1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4191"
                     /db_xref="HGNC:6971"
                     /db_xref="HPRD:01099"
                     /db_xref="MIM:154100"
     mRNA            join(75677393..75677544,75684148..75684316,
                     75686728..75686811,75687287..75687396,75689691..75689816,
                     75692833..75692910,75693657..75693756,75694120..75694271,
                     75695597..75695931)
                     /gene="MDH2"
                     /gene_synonym="M-MDH; MDH; MGC:3559; MOR1"
                     /product="malate dehydrogenase 2, NAD (mitochondrial)"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005918.2"
                     /db_xref="GI:21735620"
                     /db_xref="GeneID:4191"
                     /db_xref="HGNC:6971"
                     /db_xref="HPRD:01099"
                     /db_xref="MIM:154100"
     CDS             join(75677479..75677544,75684148..75684316,
                     75686728..75686811,75687287..75687396,75689691..75689816,
                     75692833..75692910,75693657..75693756,75694120..75694271,
                     75695597..75695728)
                     /gene="MDH2"
                     /gene_synonym="M-MDH; MDH; MGC:3559; MOR1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="malate dehydrogenase, mitochondrial precursor"
                     /protein_id="NP_005909.2"
                     /db_xref="GI:21735621"
                     /db_xref="CCDS:CCDS5581.1"
                     /db_xref="GeneID:4191"
                     /db_xref="HGNC:6971"
                     /db_xref="HPRD:01099"
                     /db_xref="MIM:154100"
     gene            complement(75742228..75742753)
                     /gene="LOC645324"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:645324"
     gene            75804786..75806500
                     /gene="LOC100420548"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420548"
     gene            75831216..75916605
                     /gene="SRRM3"
                     /gene_synonym="FLJ35271; FLJ37078"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222183"
                     /db_xref="HGNC:26729"
     mRNA            join(75831216..75831385,75864346..75864617,
                     75877506..75877607,75889224..75889352,75889435..75889515,
                     75890192..75890221,75890670..75890732,75890864..75890899,
                     75894083..75894133,75894682..75894786,75896576..75896753,
                     75910759..75911120,75911966..75912190,75912282..75912419,
                     75914933..75916605)
                     /gene="SRRM3"
                     /gene_synonym="FLJ35271; FLJ37078"
                     /product="serine/arginine repetitive matrix 3"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001110199.1"
                     /db_xref="GI:158854041"
                     /db_xref="GeneID:222183"
                     /db_xref="HGNC:26729"
     CDS             join(75864385..75864617,75877506..75877607,
                     75889224..75889352,75889435..75889515,75890192..75890221,
                     75890670..75890732,75890864..75890899,75894083..75894133,
                     75894682..75894786,75896576..75896753,75910759..75911120,
                     75911966..75912190,75912282..75912419,75914933..75915160)
                     /gene="SRRM3"
                     /gene_synonym="FLJ35271; FLJ37078"
                     /exception="unclassified translation discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="serine/arginine repetitive matrix protein 3"
                     /protein_id="NP_001103669.1"
                     /db_xref="GI:158854042"
                     /db_xref="GeneID:222183"
                     /db_xref="HGNC:26729"
     gene            75931875..75933614
                     /gene="HSPB1"
                     /gene_synonym="CMT2F; DKFZp586P1322; HMN2B; HS.76067;
                     Hsp25; HSP27; HSP28; SRP27"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3315"
                     /db_xref="HGNC:5246"
                     /db_xref="HPRD:09076"
                     /db_xref="MIM:602195"
     mRNA            join(75931875..75932393,75933119..75933182,
                     75933301..75933614)
                     /gene="HSPB1"
                     /gene_synonym="CMT2F; DKFZp586P1322; HMN2B; HS.76067;
                     Hsp25; HSP27; HSP28; SRP27"
                     /product="heat shock 27kDa protein 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001540.3"
                     /db_xref="GI:209969817"
                     /db_xref="GeneID:3315"
                     /db_xref="HGNC:5246"
                     /db_xref="HPRD:09076"
                     /db_xref="MIM:602195"
     CDS             join(75932030..75932393,75933119..75933182,
                     75933301..75933490)
                     /gene="HSPB1"
                     /gene_synonym="CMT2F; DKFZp586P1322; HMN2B; HS.76067;
                     Hsp25; HSP27; HSP28; SRP27"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="heat shock protein beta-1"
                     /protein_id="NP_001531.1"
                     /db_xref="GI:4504517"
                     /db_xref="CCDS:CCDS5583.1"
                     /db_xref="GeneID:3315"
                     /db_xref="HGNC:5246"
                     /db_xref="HPRD:09076"
                     /db_xref="MIM:602195"
     gene            complement(75956108..75988342)
                     /gene="YWHAG"
                     /gene_synonym="14-3-3GAMMA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7532"
                     /db_xref="HGNC:12852"
                     /db_xref="HPRD:05639"
                     /db_xref="MIM:605356"
     mRNA            complement(join(75956108..75959550,75988039..75988342))
                     /gene="YWHAG"
                     /gene_synonym="14-3-3GAMMA"
                     /product="tyrosine 3-monooxygenase/tryptophan
                     5-monooxygenase activation protein, gamma polypeptide"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012479.3"
                     /db_xref="GI:194733744"
                     /db_xref="GeneID:7532"
                     /db_xref="HGNC:12852"
                     /db_xref="HPRD:05639"
                     /db_xref="MIM:605356"
     CDS             complement(join(75958894..75959550,75988039..75988125))
                     /gene="YWHAG"
                     /gene_synonym="14-3-3GAMMA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="14-3-3 protein gamma"
                     /protein_id="NP_036611.2"
                     /db_xref="GI:21464101"
                     /db_xref="CCDS:CCDS5584.1"
                     /db_xref="GeneID:7532"
                     /db_xref="HGNC:12852"
                     /db_xref="HPRD:05639"
                     /db_xref="MIM:605356"
     gene            complement(76018646..76039012)
                     /gene="SRCRB4D"
                     /gene_synonym="S4D-SRCRB; SRCRB-S4D; SSC4D"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:136853"
                     /db_xref="HGNC:14461"
                     /db_xref="HPRD:06364"
                     /db_xref="MIM:607639"
     mRNA            complement(join(76018646..76019692,76021281..76021358,
                     76022722..76023033,76023147..76023221,76024570..76024647,
                     76026835..76027149,76028037..76028114,76029603..76029908,
                     76030325..76030360,76033624..76033822,76038731..76039012))
                     /gene="SRCRB4D"
                     /gene_synonym="S4D-SRCRB; SRCRB-S4D; SSC4D"
                     /product="scavenger receptor cysteine rich domain
                     containing, group B (4 domains)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_080744.1"
                     /db_xref="GI:18152778"
                     /db_xref="GeneID:136853"
                     /db_xref="HGNC:14461"
                     /db_xref="HPRD:06364"
                     /db_xref="MIM:607639"
     CDS             complement(join(76019376..76019692,76021281..76021358,
                     76022722..76023033,76023147..76023221,76024570..76024647,
                     76026835..76027149,76028037..76028114,76029603..76029908,
                     76030325..76030360,76033624..76033756))
                     /gene="SRCRB4D"
                     /gene_synonym="S4D-SRCRB; SRCRB-S4D; SSC4D"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="scavenger receptor cysteine-rich
                     domain-containing group B protein precursor"
                     /protein_id="NP_542782.1"
                     /db_xref="GI:18152779"
                     /db_xref="CCDS:CCDS5585.1"
                     /db_xref="GeneID:136853"
                     /db_xref="HGNC:14461"
                     /db_xref="HPRD:06364"
                     /db_xref="MIM:607639"
     gene            76026841..76071388
                     /gene="ZP3"
                     /gene_synonym="Zp-3; ZP3A; ZP3B; ZPC"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7784"
                     /db_xref="HGNC:13189"
                     /db_xref="HPRD:01690"
                     /db_xref="MIM:182889"
     mRNA            join(76026841..76027114,76054369..76054593,
                     76058832..76058950,76062244..76062347,76062787..76062964,
                     76063355..76063472,76069567..76069658,76069792..76069928,
                     76071159..76071388)
                     /gene="ZP3"
                     /gene_synonym="Zp-3; ZP3A; ZP3B; ZPC"
                     /product="zona pellucida glycoprotein 3 (sperm receptor),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_007155.5"
                     /db_xref="GI:160358848"
                     /db_xref="GeneID:7784"
                     /db_xref="HGNC:13189"
                     /db_xref="HPRD:01690"
                     /db_xref="MIM:182889"
     mRNA            join(76054272..76054593,76058832..76058950,
                     76062244..76062347,76062787..76062964,76063355..76063472,
                     76069567..76069658,76069792..76069928,76071159..76071388)
                     /gene="ZP3"
                     /gene_synonym="Zp-3; ZP3A; ZP3B; ZPC"
                     /product="zona pellucida glycoprotein 3 (sperm receptor),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001110354.1"
                     /db_xref="GI:160358849"
                     /db_xref="GeneID:7784"
                     /db_xref="HGNC:13189"
                     /db_xref="MIM:182889"
                     /db_xref="HPRD:01690"
     CDS             join(76054282..76054593,76058832..76058950,
                     76062244..76062347,76062787..76062964,76063355..76063472,
                     76069567..76069658,76069792..76069928,76071159..76071373)
                     /gene="ZP3"
                     /gene_synonym="Zp-3; ZP3A; ZP3B; ZPC"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zona pellucida sperm-binding protein 3 isoform 1
                     precursor"
                     /protein_id="NP_001103824.1"
                     /db_xref="GI:160358850"
                     /db_xref="CCDS:CCDS47618.1"
                     /db_xref="GeneID:7784"
                     /db_xref="HGNC:13189"
                     /db_xref="HPRD:01690"
                     /db_xref="MIM:182889"
     CDS             join(76054435..76054593,76058832..76058950,
                     76062244..76062347,76062787..76062964,76063355..76063472,
                     76069567..76069658,76069792..76069928,76071159..76071373)
                     /gene="ZP3"
                     /gene_synonym="Zp-3; ZP3A; ZP3B; ZPC"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zona pellucida sperm-binding protein 3 isoform
                     2"
                     /protein_id="NP_009086.4"
                     /db_xref="GI:38327649"
                     /db_xref="CCDS:CCDS5586.1"
                     /db_xref="GeneID:7784"
                     /db_xref="HGNC:13189"
                     /db_xref="HPRD:01690"
                     /db_xref="MIM:182889"
     gene            76090972..76135312
                     /gene="DTX2"
                     /gene_synonym="KIAA1528; MGC71098; RNF58"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:113878"
                     /db_xref="HGNC:15973"
                     /db_xref="HPRD:16841"
                     /db_xref="MIM:613141"
     mRNA            join(76090972..76091153,76092862..76093026,
                     76099617..76099736,76109738..76110094,76111825..76112464,
                     76121470..76121570,76126654..76126794,76129758..76129837,
                     76131615..76131773,76132743..76132904,76133673..76133762,
                     76134691..76135312)
                     /gene="DTX2"
                     /gene_synonym="KIAA1528; MGC71098; RNF58"
                     /product="deltex homolog 2 (Drosophila), transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020892.2"
                     /db_xref="GI:156564379"
                     /db_xref="GeneID:113878"
                     /db_xref="HGNC:15973"
                     /db_xref="HPRD:16841"
                     /db_xref="MIM:613141"
     mRNA            join(76090972..76091153,76092862..76093026,
                     76109738..76110094,76111825..76112464,76121470..76121570,
                     76126654..76126794,76129758..76129837,76131615..76131773,
                     76132743..76132904,76133673..76133762,76134691..76135312)
                     /gene="DTX2"
                     /gene_synonym="KIAA1528; MGC71098; RNF58"
                     /product="deltex homolog 2 (Drosophila), transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001102594.1"
                     /db_xref="GI:156564381"
                     /db_xref="GeneID:113878"
                     /db_xref="HGNC:15973"
                     /db_xref="MIM:613141"
                     /db_xref="HPRD:16841"
     mRNA            join(76090972..76091153,76109738..76110094,
                     76111825..76112464,76121470..76121570,76126654..76126794,
                     76129758..76129837,76131615..76131773,76132743..76132904,
                     76133673..76133762,76134691..76135312)
                     /gene="DTX2"
                     /gene_synonym="KIAA1528; MGC71098; RNF58"
                     /product="deltex homolog 2 (Drosophila), transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001102595.1"
                     /db_xref="GI:156564383"
                     /db_xref="GeneID:113878"
                     /db_xref="HGNC:15973"
                     /db_xref="MIM:613141"
                     /db_xref="HPRD:16841"
     gene            complement(76099337..76104317)
                     /gene="FDPSL2A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:619190"
     misc_RNA        complement(76099337..76104317)
                     /gene="FDPSL2A"
                     /product="MGC44478"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003262.1"
                     /db_xref="GI:117606318"
                     /db_xref="GeneID:619190"
     mRNA            join(76109827..76110094,76111825..76112464,
                     76121470..76121570,76129758..76129837,76131615..76131773,
                     76132743..76132904,76133673..76133762,76134691..76135312)
                     /gene="DTX2"
                     /gene_synonym="KIAA1528; MGC71098; RNF58"
                     /product="deltex homolog 2 (Drosophila), transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001102596.1"
                     /db_xref="GI:156564385"
                     /db_xref="GeneID:113878"
                     /db_xref="HGNC:15973"
                     /db_xref="MIM:613141"
                     /db_xref="HPRD:16841"
     CDS             join(76109827..76110094,76111825..76112464,
                     76121470..76121570,76126654..76126794,76129758..76129837,
                     76131615..76131773,76132743..76132904,76133673..76133762,
                     76134691..76134918)
                     /gene="DTX2"
                     /gene_synonym="KIAA1528; MGC71098; RNF58"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein deltex-2 isoform a"
                     /protein_id="NP_065943.2"
                     /db_xref="GI:156564380"
                     /db_xref="CCDS:CCDS5587.1"
                     /db_xref="GeneID:113878"
                     /db_xref="HGNC:15973"
                     /db_xref="HPRD:16841"
                     /db_xref="MIM:613141"
     CDS             join(76109827..76110094,76111825..76112464,
                     76121470..76121570,76126654..76126794,76129758..76129837,
                     76131615..76131773,76132743..76132904,76133673..76133762,
                     76134691..76134918)
                     /gene="DTX2"
                     /gene_synonym="KIAA1528; MGC71098; RNF58"
                     /note="isoform a is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein deltex-2 isoform a"
                     /protein_id="NP_001096064.1"
                     /db_xref="GI:156564382"
                     /db_xref="CCDS:CCDS5587.1"
                     /db_xref="GeneID:113878"
                     /db_xref="HGNC:15973"
                     /db_xref="HPRD:16841"
                     /db_xref="MIM:613141"
     CDS             join(76109827..76110094,76111825..76112464,
                     76121470..76121570,76126654..76126794,76129758..76129837,
                     76131615..76131773,76132743..76132904,76133673..76133762,
                     76134691..76134918)
                     /gene="DTX2"
                     /gene_synonym="KIAA1528; MGC71098; RNF58"
                     /note="isoform a is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein deltex-2 isoform a"
                     /protein_id="NP_001096065.1"
                     /db_xref="GI:156564384"
                     /db_xref="CCDS:CCDS5587.1"
                     /db_xref="GeneID:113878"
                     /db_xref="HGNC:15973"
                     /db_xref="HPRD:16841"
                     /db_xref="MIM:613141"
     CDS             join(76109827..76110094,76111825..76112464,
                     76121470..76121570,76129758..76129837,76131615..76131773,
                     76132743..76132904,76133673..76133762,76134691..76134918)
                     /gene="DTX2"
                     /gene_synonym="KIAA1528; MGC71098; RNF58"
                     /note="isoform b is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein deltex-2 isoform b"
                     /protein_id="NP_001096066.1"
                     /db_xref="GI:156564386"
                     /db_xref="CCDS:CCDS43605.1"
                     /db_xref="GeneID:113878"
                     /db_xref="HGNC:15973"
                     /db_xref="HPRD:16841"
                     /db_xref="MIM:613141"
     gene            76139745..76157200
                     /gene="UPK3B"
                     /gene_synonym="FLJ32198; MGC10902; P35; UPIIIb"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:80761"
                     /db_xref="HGNC:21444"
                     /db_xref="HPRD:15626"
                     /db_xref="MIM:611887"
     mRNA            join(76139745..76140369,76140974..76141199,
                     76143264..76143393,76144362..76144773,76156984..76157200)
                     /gene="UPK3B"
                     /gene_synonym="FLJ32198; MGC10902; P35; UPIIIb"
                     /product="uroplakin 3B, transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_030570.2"
                     /db_xref="GI:33149302"
                     /db_xref="GeneID:80761"
                     /db_xref="HGNC:21444"
                     /db_xref="HPRD:15626"
                     /db_xref="MIM:611887"
     mRNA            join(76139745..76140054,76140220..76140369,
                     76140974..76141199,76142401..76142480,76143264..76143393,
                     76144362..76144773,76156984..76157200)
                     /gene="UPK3B"
                     /gene_synonym="FLJ32198; MGC10902; P35; UPIIIb"
                     /product="uroplakin 3B, transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182684.1"
                     /db_xref="GI:33149305"
                     /db_xref="GeneID:80761"
                     /db_xref="HGNC:21444"
                     /db_xref="HPRD:15626"
                     /db_xref="MIM:611887"
     CDS             join(76139970..76140369,76140974..76141199,
                     76143264..76143393,76144362..76144568)
                     /gene="UPK3B"
                     /gene_synonym="FLJ32198; MGC10902; P35; UPIIIb"
                     /exception="mismatches in translation"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="uroplakin-3b isoform a"
                     /protein_id="NP_085047.1"
                     /db_xref="GI:13399330"
                     /db_xref="CCDS:CCDS5588.1"
                     /db_xref="GeneID:80761"
                     /db_xref="HGNC:21444"
                     /db_xref="HPRD:15626"
                     /db_xref="MIM:611887"
     CDS             join(76139970..76140054,76140220..76140369,
                     76140974..76141199,76142401..76142480,76143264..76143393,
                     76144362..76144521)
                     /gene="UPK3B"
                     /gene_synonym="FLJ32198; MGC10902; P35; UPIIIb"
                     /exception="mismatches in translation"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="uroplakin-3b isoform b"
                     /protein_id="NP_872625.1"
                     /db_xref="GI:33149306"
                     /db_xref="CCDS:CCDS5589.1"
                     /db_xref="GeneID:80761"
                     /db_xref="HGNC:21444"
                     /db_xref="HPRD:15626"
                     /db_xref="MIM:611887"
     gene            complement(76163011..76170776)
                     /gene="LOC100288807"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 Proteins"
                     /db_xref="GeneID:100288807"
     mRNA            complement(join(76163011..76163070,76163193..76163436,
                     76165489..76165574,76166810..76166868,76167903..76168133,
                     76169445..76169663,76170617..76170776))
                     /gene="LOC100288807"
                     /product="putative speedy protein-like protein 2-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 Proteins"
                     /transcript_id="XM_002342739.2"
                     /db_xref="GI:310120011"
                     /db_xref="GeneID:100288807"
     CDS             complement(join(76163011..76163070,76163193..76163436,
                     76165489..76165574,76166810..76166868,76167903..76168133,
                     76169445..76169663,76170617..76170776))
                     /gene="LOC100288807"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="putative speedy protein-like protein 2-like"
                     /protein_id="XP_002342780.2"
                     /db_xref="GI:310120012"
                     /db_xref="GeneID:100288807"
     gene            76178658..76257299
                     /gene="LOC100133091"
                     /gene_synonym="MGC87732"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100133091"
     misc_RNA        join(76178658..76179178,76180737..76180839,
                     76255238..76257299)
                     /gene="LOC100133091"
                     /gene_synonym="MGC87732"
                     /product="hypothetical LOC100133091"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029411.1"
                     /db_xref="GI:261598992"
                     /db_xref="GeneID:100133091"
     gene            complement(76239303..76256620)
                     /gene="POMZP3"
                     /gene_synonym="MGC8359; POM-ZP3; POM121"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:22932"
                     /db_xref="HGNC:9203"
                     /db_xref="HPRD:15974"
                     /db_xref="MIM:600587"
     mRNA            complement(join(76239303..76239532,76240771..76240908,
                     76241039..76241130,76247500..76247617,76254839..76255000,
                     76255317..76255532,76256025..76256620))
                     /gene="POMZP3"
                     /gene_synonym="MGC8359; POM-ZP3; POM121"
                     /product="POM121 and ZP3 fusion, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012230.3"
                     /db_xref="GI:111160499"
                     /db_xref="GeneID:22932"
                     /db_xref="HGNC:9203"
                     /db_xref="HPRD:15974"
                     /db_xref="MIM:600587"
     mRNA            complement(join(76239303..76239532,76247500..76247617,
                     76254839..76255000,76255317..76255532,76256025..76256620))
                     /gene="POMZP3"
                     /gene_synonym="MGC8359; POM-ZP3; POM121"
                     /product="POM121 and ZP3 fusion, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152992.2"
                     /db_xref="GI:111160589"
                     /db_xref="GeneID:22932"
                     /db_xref="HGNC:9203"
                     /db_xref="MIM:600587"
                     /db_xref="HPRD:15974"
     CDS             complement(join(76239530..76239532,76247500..76247617,
                     76254839..76255000,76255317..76255381))
                     /gene="POMZP3"
                     /gene_synonym="MGC8359; POM-ZP3; POM121"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="POM121 and ZP3 fusion protein isoform 2"
                     /protein_id="NP_694537.1"
                     /db_xref="GI:23510406"
                     /db_xref="CCDS:CCDS5590.1"
                     /db_xref="GeneID:22932"
                     /db_xref="HGNC:9203"
                     /db_xref="HPRD:15974"
                     /db_xref="MIM:600587"
     CDS             complement(join(76240782..76240908,76241039..76241130,
                     76247500..76247617,76254839..76255000,76255317..76255381))
                     /gene="POMZP3"
                     /gene_synonym="MGC8359; POM-ZP3; POM121"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="POM121 and ZP3 fusion protein isoform 1"
                     /protein_id="NP_036362.3"
                     /db_xref="GI:111160500"
                     /db_xref="CCDS:CCDS43606.1"
                     /db_xref="GeneID:22932"
                     /db_xref="HGNC:9203"
                     /db_xref="HPRD:15974"
                     /db_xref="MIM:600587"
     gene            76597453..76598627
                     /gene="FDPSP2"
                     /gene_synonym="FDPSL2; FDPSL2A; FPSL2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392063"
                     /db_xref="HGNC:3633"
     gene            complement(76597453..76598627)
                     /gene="FDPSP7"
                     /gene_synonym="FDPSL2B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:441261"
                     /db_xref="HGNC:33487"
     gene            76610139..76653078
                     /gene="DTX2P1-UPK3BP1-PMS2P11"
                     /gene_synonym="PMS2L11; PMSR6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:441263"
                     /db_xref="HGNC:42360"
     misc_RNA        join(76610139..76610577,76619586..76619686,
                     76629626..76629705,76631480..76631638,76633535..76633624,
                     76634867..76635092,76641197..76641336,76643229..76643315,
                     76644989..76645172,76648226..76648314,76652911..76653078)
                     /gene="DTX2P1-UPK3BP1-PMS2P11"
                     /gene_synonym="PMS2L11; PMSR6"
                     /product="DTX2P1-UPK3BP1-PMS2P11 readthrough (non-protein
                     coding)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_023383.1"
                     /db_xref="GI:190194394"
                     /db_xref="GeneID:441263"
                     /db_xref="HGNC:9125"
                     /db_xref="HGNC:42360"
     gene            complement(76654003..76659887)
                     /gene="LOC100132581"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /db_xref="GeneID:100132581"
     mRNA            complement(join(76654003..76654062,76654185..76654290,
                     76654366..76654428,76656146..76656231,76657459..76657517,
                     76658550..76658768,76659758..76659887))
                     /gene="LOC100132581"
                     /product="putative speedy protein E8-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /transcript_id="XM_001722903.4"
                     /db_xref="GI:341915396"
                     /db_xref="GeneID:100132581"
     CDS             complement(join(76654003..76654062,76654185..76654290,
                     76654366..76654428,76656146..76656231,76657459..76657517,
                     76658550..76658768,76659758..76659887))
                     /gene="LOC100132581"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="putative speedy protein E8-like"
                     /protein_id="XP_001722955.4"
                     /db_xref="GI:341915397"
                     /db_xref="GeneID:100132581"
     gene            76668797..76682355
                     /gene="LOC100132832"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:100132832"
     misc_RNA        join(76668797..76669406,76671294..76671380,
                     76672912..76673095,76676146..76676234,76680994..76682355)
                     /gene="LOC100132832"
                     /product="postmeiotic segregation increased 2-like 5-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_028058.1"
                     /db_xref="GI:254039601"
                     /db_xref="GeneID:100132832"
     gene            complement(76682095..76689829)
                     /gene="LOC100505767"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 Proteins"
                     /db_xref="GeneID:100505767"
     mRNA            complement(join(76682095..76682154,76682277..76682520,
                     76684553..76684638,76685867..76685925,76686954..76687184,
                     76688497..76688715,76689670..76689829))
                     /gene="LOC100505767"
                     /product="putative speedy protein-like protein 2-like,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 Proteins"
                     /transcript_id="XM_003118584.1"
                     /db_xref="GI:310120015"
                     /db_xref="GeneID:100505767"
     CDS             complement(join(76682095..76682154,76682277..76682520,
                     76684553..76684638,76685867..76685925,76686954..76687184,
                     76688497..76688715,76689670..76689829))
                     /gene="LOC100505767"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="putative speedy protein-like protein 2-like
                     isoform 1"
                     /protein_id="XP_003118632.1"
                     /db_xref="GI:310120016"
                     /db_xref="GeneID:100505767"
     gene            complement(76701045..76701808)
                     /gene="LOC100422695"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100422695"
     gene            complement(76713047..76751683)
                     /gene="FAM185BP"
                     /gene_synonym="FAM185B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:641808"
                     /db_xref="HGNC:21813"
     gene            complement(76744671..76745525)
                     /gene="RPL7AP43"
                     /gene_synonym="RPL7A_17_815"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:644236"
                     /db_xref="HGNC:35775"
     gene            76751934..76924521
                     /gene="CCDC146"
                     /gene_synonym="KIAA1505"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57639"
                     /db_xref="HGNC:29296"
                     /db_xref="HPRD:11150"
     mRNA            join(76751934..76752049,76796975..76797141,
                     76866264..76866346,76871008..76871217,76883823..76883880,
                     76885650..76885826,76888312..76888385,76889326..76889553,
                     76891438..76891624,76903011..76903106,76903799..76903969,
                     76908069..76908157,76908254..76908418,76909746..76909970,
                     76911874..76912102,76916115..76916243,76916757..76916894,
                     76922269..76922517,76923980..76924521)
                     /gene="CCDC146"
                     /gene_synonym="KIAA1505"
                     /product="coiled-coil domain containing 146"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020879.2"
                     /db_xref="GI:100814338"
                     /db_xref="GeneID:57639"
                     /db_xref="HGNC:29296"
                     /db_xref="HPRD:11150"
     CDS             join(76796986..76797141,76866264..76866346,
                     76871008..76871217,76883823..76883880,76885650..76885826,
                     76888312..76888385,76889326..76889553,76891438..76891624,
                     76903011..76903106,76903799..76903969,76908069..76908157,
                     76908254..76908418,76909746..76909970,76911874..76912102,
                     76916115..76916243,76916757..76916894,76922269..76922517,
                     76923980..76924183)
                     /gene="CCDC146"
                     /gene_synonym="KIAA1505"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="coiled-coil domain-containing protein 146"
                     /protein_id="NP_065930.2"
                     /db_xref="GI:100814339"
                     /db_xref="CCDS:CCDS34671.1"
                     /db_xref="GeneID:57639"
                     /db_xref="HGNC:29296"
                     /db_xref="HPRD:11150"
     gene            complement(76822688..76829150)
                     /gene="FGL2"
                     /gene_synonym="pT49; T49"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10875"
                     /db_xref="HGNC:3696"
                     /db_xref="HPRD:16098"
                     /db_xref="MIM:605351"
     mRNA            complement(join(76822688..76826302,76828498..76829150))
                     /gene="FGL2"
                     /gene_synonym="pT49; T49"
                     /product="fibrinogen-like 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006682.2"
                     /db_xref="GI:95147561"
                     /db_xref="GeneID:10875"
                     /db_xref="HGNC:3696"
                     /db_xref="HPRD:16098"
                     /db_xref="MIM:605351"
     CDS             complement(join(76825596..76826302,76828498..76829110))
                     /gene="FGL2"
                     /gene_synonym="pT49; T49"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="fibroleukin precursor"
                     /protein_id="NP_006673.1"
                     /db_xref="GI:5730075"
                     /db_xref="CCDS:CCDS5591.1"
                     /db_xref="GeneID:10875"
                     /db_xref="HGNC:3696"
                     /db_xref="HPRD:16098"
                     /db_xref="MIM:605351"
     gene            complement(76940068..77045717)
                     /gene="PION"
                     /gene_synonym="DKFZp667B242; GSAP; MGC126548"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54103"
                     /db_xref="HGNC:28042"
                     /db_xref="HPRD:18671"
                     /db_xref="MIM:613552"
     mRNA            complement(join(76940068..76940766,76941158..76941257,
                     76941418..76941519,76942805..76942866,76943687..76943806,
                     76950042..76950136,76950650..76950720,76952964..76953059,
                     76955529..76955590,76957923..76957954,76958650..76958708,
                     76959556..76959684,76978668..76978721,76982261..76982343,
                     76982889..76982958,76984530..76984747,76984872..76984964,
                     76990141..76990218,76991900..76991977,77003387..77003472,
                     77004375..77004418,77006165..77006224,77006603..77006707,
                     77010622..77010671,77011891..77011960,77016677..77016765,
                     77026299..77026352,77026663..77026732,77033876..77033932,
                     77035346..77035422,77045530..77045717))
                     /gene="PION"
                     /gene_synonym="DKFZp667B242; GSAP; MGC126548"
                     /product="pigeon homolog (Drosophila)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017439.3"
                     /db_xref="GI:148612804"
                     /db_xref="GeneID:54103"
                     /db_xref="HGNC:28042"
                     /db_xref="HPRD:18671"
                     /db_xref="MIM:613552"
     CDS             complement(join(76940675..76940766,76941158..76941257,
                     76941418..76941519,76942805..76942866,76943687..76943806,
                     76950042..76950136,76950650..76950720,76952964..76953059,
                     76955529..76955590,76957923..76957954,76958650..76958708,
                     76959556..76959684,76978668..76978721,76982261..76982343,
                     76982889..76982958,76984530..76984747,76984872..76984964,
                     76990141..76990218,76991900..76991977,77003387..77003472,
                     77004375..77004418,77006165..77006224,77006603..77006707,
                     77010622..77010671,77011891..77011960,77016677..77016765,
                     77026299..77026352,77026663..77026732,77033876..77033932,
                     77035346..77035422,77045530..77045638))
                     /gene="PION"
                     /gene_synonym="DKFZp667B242; GSAP; MGC126548"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="gamma-secretase-activating protein"
                     /protein_id="NP_059135.2"
                     /db_xref="GI:148612805"
                     /db_xref="CCDS:CCDS34672.2"
                     /db_xref="GeneID:54103"
                     /db_xref="HGNC:28042"
                     /db_xref="HPRD:18671"
                     /db_xref="MIM:613552"
     gene            77090473..77091456
                     /gene="GCNT1P5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421598"
                     /db_xref="HGNC:37975"
     gene            77166773..77269388
                     /gene="PTPN12"
                     /gene_synonym="PTP-PEST; PTPG1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5782"
                     /db_xref="HGNC:9645"
                     /db_xref="HPRD:02513"
                     /db_xref="MIM:600079"
     mRNA            join(77166773..77166962,77200395..77200503,
                     77210744..77210820,77212872..77212967,77214860..77214898,
                     77221502..77221573,77227159..77227218,77229981..77230123,
                     77236552..77236618,77240082..77240159,77240265..77240363,
                     77247797..77247882,77256022..77256992,77261665..77261742,
                     77265099..77265166,77266335..77266365,77267941..77268048,
                     77268536..77269388)
                     /gene="PTPN12"
                     /gene_synonym="PTP-PEST; PTPG1"
                     /product="protein tyrosine phosphatase, non-receptor type
                     12, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002835.3"
                     /db_xref="GI:196114950"
                     /db_xref="GeneID:5782"
                     /db_xref="HGNC:9645"
                     /db_xref="HPRD:02513"
                     /db_xref="MIM:600079"
     CDS             join(77166864..77166962,77200395..77200503,
                     77210744..77210820,77212872..77212967,77214860..77214898,
                     77221502..77221573,77227159..77227218,77229981..77230123,
                     77236552..77236618,77240082..77240159,77240265..77240363,
                     77247797..77247882,77256022..77256992,77261665..77261742,
                     77265099..77265166,77266335..77266365,77267941..77268048,
                     77268536..77268597)
                     /gene="PTPN12"
                     /gene_synonym="PTP-PEST; PTPG1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="tyrosine-protein phosphatase non-receptor type
                     12 isoform 1"
                     /protein_id="NP_002826.3"
                     /db_xref="GI:196114951"
                     /db_xref="CCDS:CCDS5592.1"
                     /db_xref="GeneID:5782"
                     /db_xref="HGNC:9645"
                     /db_xref="HPRD:02513"
                     /db_xref="MIM:600079"
     mRNA            join(77167352..77167423,77200395..77200503,
                     77210744..77210820,77212872..77212967,77214860..77214898,
                     77221502..77221573,77227159..77227218,77229981..77230123,
                     77236552..77236618,77240082..77240159,77240265..77240363,
                     77247797..77247882,77256022..77256992,77261665..77261742,
                     77265099..77265166,77266335..77266365,77267941..77268048,
                     77268536..77269388)
                     /gene="PTPN12"
                     /gene_synonym="PTP-PEST; PTPG1"
                     /product="protein tyrosine phosphatase, non-receptor type
                     12, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001131008.1"
                     /db_xref="GI:196114966"
                     /db_xref="GeneID:5782"
                     /db_xref="HGNC:9645"
                     /db_xref="MIM:600079"
                     /db_xref="HPRD:02513"
     mRNA            join(77167352..77167423,77200395..77200503,
                     77210744..77210820,77214860..77214898,77221502..77221573,
                     77227159..77227218,77229981..77230123,77236552..77236618,
                     77240082..77240159,77240265..77240363,77247797..77247882,
                     77256022..77256992,77261665..77261742,77265099..77265166,
                     77266335..77266365,77267941..77268048,77268536..77269388)
                     /gene="PTPN12"
                     /gene_synonym="PTP-PEST; PTPG1"
                     /product="protein tyrosine phosphatase, non-receptor type
                     12, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001131009.1"
                     /db_xref="GI:196114969"
                     /db_xref="GeneID:5782"
                     /db_xref="HGNC:9645"
                     /db_xref="MIM:600079"
                     /db_xref="HPRD:02513"
     CDS             join(77212944..77212967,77214860..77214898,
                     77221502..77221573,77227159..77227218,77229981..77230123,
                     77236552..77236618,77240082..77240159,77240265..77240363,
                     77247797..77247882,77256022..77256992,77261665..77261742,
                     77265099..77265166,77266335..77266365,77267941..77268048,
                     77268536..77268597)
                     /gene="PTPN12"
                     /gene_synonym="PTP-PEST; PTPG1"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="tyrosine-protein phosphatase non-receptor type
                     12 isoform 2"
                     /protein_id="NP_001124480.1"
                     /db_xref="GI:196114967"
                     /db_xref="CCDS:CCDS47619.1"
                     /db_xref="GeneID:5782"
                     /db_xref="HGNC:9645"
                     /db_xref="HPRD:02513"
                     /db_xref="MIM:600079"
     CDS             join(77214869..77214898,77221502..77221573,
                     77227159..77227218,77229981..77230123,77236552..77236618,
                     77240082..77240159,77240265..77240363,77247797..77247882,
                     77256022..77256992,77261665..77261742,77265099..77265166,
                     77266335..77266365,77267941..77268048,77268536..77268597)
                     /gene="PTPN12"
                     /gene_synonym="PTP-PEST; PTPG1"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="tyrosine-protein phosphatase non-receptor type
                     12 isoform 3"
                     /protein_id="NP_001124481.1"
                     /db_xref="GI:196114970"
                     /db_xref="CCDS:CCDS47620.1"
                     /db_xref="GeneID:5782"
                     /db_xref="HGNC:9645"
                     /db_xref="HPRD:02513"
                     /db_xref="MIM:600079"
     gene            complement(77286977..77290598)
                     /gene="LOC100652843"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /db_xref="GeneID:100652843"
     misc_RNA        complement(join(77286977..77287387,77290515..77290598))
                     /gene="LOC100652843"
                     /product="hypothetical LOC100652843"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_132539.1"
                     /db_xref="GI:341915401"
                     /db_xref="GeneID:100652843"
     gene            complement(77313168..77326662)
                     /gene="LOC100505854"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100505854"
     misc_RNA        complement(join(77313168..77313568,77314519..77314645,
                     77325213..77326662))
                     /gene="LOC100505854"
                     /product="hypothetical LOC100505854"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038361.1"
                     /db_xref="GI:335057549"
                     /db_xref="GeneID:100505854"
     gene            77325743..77409120
                     /gene="RSBN1L"
                     /gene_synonym="FLJ42526; FLJ45813; MGC71764"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222194"
                     /db_xref="HGNC:24765"
                     /db_xref="HPRD:15278"
     mRNA            join(77325743..77326372,77365727..77365843,
                     77378741..77379381,77394812..77394949,77397978..77398120,
                     77402464..77402631,77407655..77407763,77407847..77409120)
                     /gene="RSBN1L"
                     /gene_synonym="FLJ42526; FLJ45813; MGC71764"
                     /product="round spermatid basic protein 1-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198467.2"
                     /db_xref="GI:158534054"
                     /db_xref="GeneID:222194"
                     /db_xref="HGNC:24765"
                     /db_xref="HPRD:15278"
     CDS             join(77325787..77326372,77365727..77365843,
                     77378741..77379381,77394812..77394949,77397978..77398120,
                     77402464..77402631,77407655..77407763,77407847..77408485)
                     /gene="RSBN1L"
                     /gene_synonym="FLJ42526; FLJ45813; MGC71764"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="round spermatid basic protein 1-like protein"
                     /protein_id="NP_940869.2"
                     /db_xref="GI:158534055"
                     /db_xref="CCDS:CCDS43607.1"
                     /db_xref="GeneID:222194"
                     /db_xref="HGNC:24765"
                     /db_xref="HPRD:15278"
     gene            complement(77423045..77427747)
                     /gene="TMEM60"
                     /gene_synonym="C7orf35; DC32; MGC74482"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:85025"
                     /db_xref="HGNC:21754"
                     /db_xref="HPRD:12923"
     mRNA            complement(join(77423045..77423740,77427571..77427747))
                     /gene="TMEM60"
                     /gene_synonym="C7orf35; DC32; MGC74482"
                     /product="transmembrane protein 60"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032936.3"
                     /db_xref="GI:197304734"
                     /db_xref="GeneID:85025"
                     /db_xref="HGNC:21754"
                     /db_xref="HPRD:12923"
     CDS             complement(77423289..77423690)
                     /gene="TMEM60"
                     /gene_synonym="C7orf35; DC32; MGC74482"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 60"
                     /protein_id="NP_116325.1"
                     /db_xref="GI:14269580"
                     /db_xref="CCDS:CCDS5593.1"
                     /db_xref="GeneID:85025"
                     /db_xref="HGNC:21754"
                     /db_xref="HPRD:12923"
     gene            77428109..77586821
                     /gene="PHTF2"
                     /gene_synonym="DKFZp564F013; FLJ33324; MGC86999"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57157"
                     /db_xref="HGNC:13411"
                     /db_xref="HPRD:15130"
     mRNA            join(77428109..77428288,77469538..77469617,
                     77522925..77522981,77530028..77530097,77531079..77531237,
                     77538110..77538275,77539562..77539726,77549596..77549782,
                     77551940..77552095,77558426..77558644,77567027..77567155,
                     77569347..77569619,77569845..77569976,77572017..77572103,
                     77578995..77579150,77580934..77581029,77583086..77583211,
                     77584175..77586821)
                     /gene="PHTF2"
                     /gene_synonym="DKFZp564F013; FLJ33324; MGC86999"
                     /product="putative homeodomain transcription factor 2,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127358.1"
                     /db_xref="GI:188219570"
                     /db_xref="GeneID:57157"
                     /db_xref="HGNC:13411"
                     /db_xref="HPRD:15130"
     mRNA            join(77428109..77428288,77469538..77469617,
                     77522925..77522981,77530028..77530097,77531079..77531237,
                     77538110..77538275,77539562..77539726,77549596..77549782,
                     77551940..77553500)
                     /gene="PHTF2"
                     /gene_synonym="DKFZp564F013; FLJ33324; MGC86999"
                     /product="putative homeodomain transcription factor 2,
                     transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127360.1"
                     /db_xref="GI:188219574"
                     /db_xref="GeneID:57157"
                     /db_xref="HGNC:13411"
                     /db_xref="HPRD:15130"
     mRNA            join(77469447..77469617,77522925..77522981,
                     77523299..77523310,77530028..77530097,77531079..77531237,
                     77538110..77538275,77539562..77539726,77549596..77549782,
                     77551940..77552095,77558426..77558644,77567027..77567155,
                     77569347..77569619,77569845..77569976,77572017..77572103,
                     77578995..77579150,77580934..77581029,77583086..77583211,
                     77584175..77586821)
                     /gene="PHTF2"
                     /gene_synonym="DKFZp564F013; FLJ33324; MGC86999"
                     /product="putative homeodomain transcription factor 2,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127357.1"
                     /db_xref="GI:188219568"
                     /db_xref="GeneID:57157"
                     /db_xref="HGNC:13411"
                     /db_xref="HPRD:15130"
     mRNA            join(77469447..77469617,77522925..77522981,
                     77530028..77530097,77531079..77531237,77538110..77538275,
                     77539562..77539726,77549596..77549782,77551940..77552095,
                     77558426..77558644,77567027..77567155,77569347..77569619,
                     77569845..77569976,77572017..77572103,77578995..77579150,
                     77580934..77581029,77583086..77583211,77584175..77586821)
                     /gene="PHTF2"
                     /gene_synonym="DKFZp564F013; FLJ33324; MGC86999"
                     /product="putative homeodomain transcription factor 2,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020432.4"
                     /db_xref="GI:188219564"
                     /db_xref="GeneID:57157"
                     /db_xref="HGNC:13411"
                     /db_xref="HPRD:15130"
     mRNA            join(77469447..77469617,77522925..77522981,
                     77523299..77523310,77530028..77530097,77531079..77531237,
                     77538110..77538275,77539562..77539726,77549596..77549782,
                     77551940..77553500)
                     /gene="PHTF2"
                     /gene_synonym="DKFZp564F013; FLJ33324; MGC86999"
                     /product="putative homeodomain transcription factor 2,
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127359.1"
                     /db_xref="GI:188219572"
                     /db_xref="GeneID:57157"
                     /db_xref="HGNC:13411"
                     /db_xref="HPRD:15130"
     CDS             join(77469573..77469617,77522925..77522981,
                     77523299..77523310,77530028..77530097,77531079..77531237,
                     77538110..77538275,77539562..77539726,77549596..77549782,
                     77551940..77552095,77558426..77558644,77567027..77567155,
                     77569347..77569619,77569845..77569976,77572017..77572103,
                     77578995..77579150,77580934..77581029,77583086..77583211,
                     77584175..77584195)
                     /gene="PHTF2"
                     /gene_synonym="DKFZp564F013; FLJ33324; MGC86999"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative homeodomain transcription factor 2
                     isoform 1"
                     /protein_id="NP_001120829.1"
                     /db_xref="GI:188219569"
                     /db_xref="CCDS:CCDS47621.1"
                     /db_xref="GeneID:57157"
                     /db_xref="HGNC:13411"
                     /db_xref="HPRD:15130"
     CDS             join(77469573..77469617,77522925..77522981,
                     77530028..77530097,77531079..77531237,77538110..77538275,
                     77539562..77539726,77549596..77549782,77551940..77552095,
                     77558426..77558644,77567027..77567155,77569347..77569619,
                     77569845..77569976,77572017..77572103,77578995..77579150,
                     77580934..77581029,77583086..77583211,77584175..77584195)
                     /gene="PHTF2"
                     /gene_synonym="DKFZp564F013; FLJ33324; MGC86999"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative homeodomain transcription factor 2
                     isoform 2"
                     /protein_id="NP_065165.3"
                     /db_xref="GI:188219565"
                     /db_xref="CCDS:CCDS47622.1"
                     /db_xref="GeneID:57157"
                     /db_xref="HGNC:13411"
                     /db_xref="HPRD:15130"
     CDS             join(77469573..77469617,77522925..77522981,
                     77530028..77530097,77531079..77531237,77538110..77538275,
                     77539562..77539726,77549596..77549782,77551940..77552095,
                     77558426..77558644,77567027..77567155,77569347..77569619,
                     77569845..77569976,77572017..77572103,77578995..77579150,
                     77580934..77581029,77583086..77583211,77584175..77584195)
                     /gene="PHTF2"
                     /gene_synonym="DKFZp564F013; FLJ33324; MGC86999"
                     /note="isoform 2 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative homeodomain transcription factor 2
                     isoform 2"
                     /protein_id="NP_001120830.1"
                     /db_xref="GI:188219571"
                     /db_xref="CCDS:CCDS47622.1"
                     /db_xref="GeneID:57157"
                     /db_xref="HGNC:13411"
                     /db_xref="HPRD:15130"
     CDS             join(77469573..77469617,77522925..77522981,
                     77523299..77523310,77530028..77530097,77531079..77531237,
                     77538110..77538275,77539562..77539726,77549596..77549782,
                     77551940..77552149)
                     /gene="PHTF2"
                     /gene_synonym="DKFZp564F013; FLJ33324; MGC86999"
                     /note="isoform 3 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative homeodomain transcription factor 2
                     isoform 3"
                     /protein_id="NP_001120831.1"
                     /db_xref="GI:188219573"
                     /db_xref="CCDS:CCDS47623.1"
                     /db_xref="GeneID:57157"
                     /db_xref="HGNC:13411"
                     /db_xref="HPRD:15130"
     CDS             join(77469573..77469617,77522925..77522981,
                     77530028..77530097,77531079..77531237,77538110..77538275,
                     77539562..77539726,77549596..77549782,77551940..77552149)
                     /gene="PHTF2"
                     /gene_synonym="DKFZp564F013; FLJ33324; MGC86999"
                     /note="isoform 4 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative homeodomain transcription factor 2
                     isoform 4"
                     /protein_id="NP_001120832.1"
                     /db_xref="GI:188219575"
                     /db_xref="CCDS:CCDS47624.1"
                     /db_xref="GeneID:57157"
                     /db_xref="HGNC:13411"
                     /db_xref="HPRD:15130"
     gene            complement(77646374..79082890)
                     /gene="MAGI2"
                     /gene_synonym="ACVRIP1; AIP-1; AIP1; ARIP1; MAGI-2; SSCAM"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9863"
                     /db_xref="HGNC:18957"
                     /db_xref="HPRD:16212"
                     /db_xref="MIM:606382"
     mRNA            complement(join(77646374..77649293,77708264..77708402,
                     77755011..77755154,77756514..77756733,77762206..77762377,
                     77764338..77764523,77789342..77789590,77797233..77797425,
                     77807328..77807419,77814946..77814987,77824191..77824380,
                     77830479..77830510,77885260..77885898,77973095..77973277,
                     77975239..77975360,77998473..77998530,78119078..78119157,
                     78130894..78131104,78150747..78150962,78256436..78256555,
                     78636406..78636522,79082336..79082890))
                     /gene="MAGI2"
                     /gene_synonym="ACVRIP1; AIP-1; AIP1; ARIP1; MAGI-2; SSCAM"
                     /product="membrane associated guanylate kinase, WW and PDZ
                     domain containing 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012301.3"
                     /db_xref="GI:66346709"
                     /db_xref="GeneID:9863"
                     /db_xref="HGNC:18957"
                     /db_xref="HPRD:16212"
                     /db_xref="MIM:606382"
     CDS             complement(join(77648632..77649293,77708264..77708402,
                     77755011..77755154,77756514..77756733,77762206..77762377,
                     77764338..77764523,77789342..77789590,77797233..77797425,
                     77807328..77807419,77814946..77814987,77824191..77824380,
                     77830479..77830510,77885260..77885898,77973095..77973277,
                     77975239..77975360,77998473..77998530,78119078..78119157,
                     78130894..78131104,78150747..78150962,78256436..78256555,
                     78636406..78636522,79082336..79082636))
                     /gene="MAGI2"
                     /gene_synonym="ACVRIP1; AIP-1; AIP1; ARIP1; MAGI-2; SSCAM"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="membrane-associated guanylate kinase, WW and PDZ
                     domain-containing protein 2"
                     /protein_id="NP_036433.2"
                     /db_xref="GI:27436957"
                     /db_xref="CCDS:CCDS5594.1"
                     /db_xref="GeneID:9863"
                     /db_xref="HGNC:18957"
                     /db_xref="HPRD:16212"
                     /db_xref="MIM:606382"
     gene            77976559..77988775
                     /gene="RPL13AP17"
                     /gene_synonym="RPL13A_6_816"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:399670"
                     /db_xref="HGNC:36167"
     misc_RNA        join(77976559..77976643,77977694..77977742,
                     77979444..77979598,77981071..77981274,77982172..77982290,
                     77987593..77988775)
                     /gene="RPL13AP17"
                     /gene_synonym="RPL13A_6_816"
                     /product="ribosomal protein L13a pseudogene 17"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003680.1"
                     /db_xref="GI:154240700"
                     /db_xref="GeneID:399670"
                     /db_xref="HGNC:36167"
     gene            78115833..78116717
                     /gene="LOC100124402"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100124402"
     gene            78754055..78754947
                     /gene="LOC100421387"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421387"
     gene            79082273..79100524
                     /gene="LOC100505881"
                     /gene_synonym="DKFZp686F08110"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100505881"
     misc_RNA        join(79082273..79082507,79088163..79088315,
                     79099910..79099995,79100099..79100524)
                     /gene="LOC100505881"
                     /gene_synonym="DKFZp686F08110"
                     /product="hypothetical LOC100505881, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038345.1"
                     /db_xref="GI:334358869"
                     /db_xref="GeneID:100505881"
     misc_RNA        join(79082273..79082507,79082903..79082971,
                     79088163..79088315,79100099..79100524)
                     /gene="LOC100505881"
                     /gene_synonym="DKFZp686F08110"
                     /product="hypothetical LOC100505881, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038346.1"
                     /db_xref="GI:334358870"
                     /db_xref="GeneID:100505881"
     misc_RNA        join(79083276..79083560,79084202..79084323,
                     79088163..79088315,79099910..79099995,79100099..79100524)
                     /gene="LOC100505881"
                     /gene_synonym="DKFZp686F08110"
                     /product="hypothetical LOC100505881, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038344.1"
                     /db_xref="GI:334358868"
                     /db_xref="GeneID:100505881"
     misc_RNA        join(79083276..79083560,79084202..79084323,
                     79088163..79088315,79088852..79096786)
                     /gene="LOC100505881"
                     /gene_synonym="DKFZp686F08110"
                     /product="hypothetical LOC100505881, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038343.1"
                     /db_xref="GI:334358867"
                     /db_xref="GeneID:100505881"
     gene            complement(79725837..79726578)
                     /gene="RPL10P11"
                     /gene_synonym="RPL10_4_817"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100128030"
                     /db_xref="HGNC:36565"
     gene            79764140..79848725
                     /gene="GNAI1"
                     /gene_synonym="Gi"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2770"
                     /db_xref="HGNC:4384"
                     /db_xref="HPRD:00756"
                     /db_xref="MIM:139310"
     mRNA            join(79764140..79764594,79818267..79818309,
                     79818406..79818547,79828541..79828698,79833020..79833148,
                     79840285..79840414,79842032..79842185,79846619..79848725)
                     /gene="GNAI1"
                     /gene_synonym="Gi"
                     /product="guanine nucleotide binding protein (G protein),
                     alpha inhibiting activity polypeptide 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002069.5"
                     /db_xref="GI:156071490"
                     /db_xref="GeneID:2770"
                     /db_xref="HGNC:4384"
                     /db_xref="HPRD:00756"
                     /db_xref="MIM:139310"
     CDS             join(79764477..79764594,79818267..79818309,
                     79818406..79818547,79828541..79828698,79833020..79833148,
                     79840285..79840414,79842032..79842185,79846619..79846809)
                     /gene="GNAI1"
                     /gene_synonym="Gi"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="guanine nucleotide-binding protein G(i) subunit
                     alpha-1"
                     /protein_id="NP_002060.4"
                     /db_xref="GI:33946324"
                     /db_xref="CCDS:CCDS5595.1"
                     /db_xref="GeneID:2770"
                     /db_xref="HGNC:4384"
                     /db_xref="HPRD:00756"
                     /db_xref="MIM:139310"
     gene            complement(80006870..80007151)
                     /gene="SNRPBP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100499258"
                     /db_xref="HGNC:38665"
     gene            complement(80087987..80141242)
                     /gene="GNAT3"
                     /gene_synonym="GDCA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:346562"
                     /db_xref="HGNC:22800"
                     /db_xref="MIM:139395"
     mRNA            complement(join(80087987..80088177,80091475..80091628,
                     80091818..80091947,80103567..80103695,80108157..80108314,
                     80117851..80117992,80123921..80123963,80141125..80141242))
                     /gene="GNAT3"
                     /gene_synonym="GDCA"
                     /product="guanine nucleotide binding protein, alpha
                     transducing 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001102386.1"
                     /db_xref="GI:156139154"
                     /db_xref="GeneID:346562"
                     /db_xref="HGNC:22800"
                     /db_xref="MIM:139395"
     CDS             complement(join(80087987..80088177,80091475..80091628,
                     80091818..80091947,80103567..80103695,80108157..80108314,
                     80117851..80117992,80123921..80123963,80141125..80141242))
                     /gene="GNAT3"
                     /gene_synonym="GDCA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="guanine nucleotide-binding protein G(t) subunit
                     alpha-3"
                     /protein_id="NP_001095856.1"
                     /db_xref="GI:156139155"
                     /db_xref="CCDS:CCDS47625.1"
                     /db_xref="GeneID:346562"
                     /db_xref="HGNC:22800"
                     /db_xref="MIM:139395"
     gene            80231504..80308593
                     /gene="CD36"
                     /gene_synonym="CHDS7; FAT; GP3B; GP4; GPIV; PASIV; SCARB3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:948"
                     /db_xref="HGNC:1663"
                     /db_xref="HPRD:01430"
                     /db_xref="MIM:173510"
     mRNA            join(80231504..80231695,80275404..80275497,
                     80275968..80276176,80285856..80286016,80290379..80290526,
                     80292306..80292485,80293722..80293813,80295759..80295805,
                     80299269..80299338,80300293..80300480,80301238..80301356,
                     80302086..80302159,80302671..80302725,80303299..80303736)
                     /gene="CD36"
                     /gene_synonym="CHDS7; FAT; GP3B; GP4; GPIV; PASIV; SCARB3"
                     /product="CD36 molecule (thrombospondin receptor),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001001547.2"
                     /db_xref="GI:188536059"
                     /db_xref="GeneID:948"
                     /db_xref="HGNC:1663"
                     /db_xref="HPRD:01430"
                     /db_xref="MIM:173510"
     mRNA            join(80267832..80268062,80275404..80275497,
                     80275968..80276176,80285856..80286016,80290379..80290526,
                     80292306..80292485,80293722..80293813,80295759..80295805,
                     80299269..80299338,80300293..80300480,80301238..80301356,
                     80302086..80302159,80302671..80302725,80303299..80303463,
                     80305700..80308593)
                     /gene="CD36"
                     /gene_synonym="CHDS7; FAT; GP3B; GP4; GPIV; PASIV; SCARB3"
                     /product="CD36 molecule (thrombospondin receptor),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001001548.2"
                     /db_xref="GI:188536058"
                     /db_xref="GeneID:948"
                     /db_xref="HGNC:1663"
                     /db_xref="HPRD:01430"
                     /db_xref="MIM:173510"
     mRNA            join(80267832..80268062,80275404..80275497,
                     80275968..80276176,80285856..80286016,80290379..80290526,
                     80292306..80292485,80293722..80293813,80295759..80295805,
                     80299269..80299338,80300293..80300480,80301238..80301356,
                     80302086..80302159,80302671..80302725,80303299..80303736)
                     /gene="CD36"
                     /gene_synonym="CHDS7; FAT; GP3B; GP4; GPIV; PASIV; SCARB3"
                     /product="CD36 molecule (thrombospondin receptor),
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000072.3"
                     /db_xref="GI:188536061"
                     /db_xref="GeneID:948"
                     /db_xref="HGNC:1663"
                     /db_xref="HPRD:01430"
                     /db_xref="MIM:173510"
     mRNA            join(80275645..80275675,80275968..80276176,
                     80285856..80286016,80290379..80290526,80292306..80292485,
                     80293722..80293813,80295759..80295805,80299269..80299338,
                     80300293..80300480,80301238..80301356,80302086..80302159,
                     80302671..80302725,80303299..80303736)
                     /gene="CD36"
                     /gene_synonym="CHDS7; FAT; GP3B; GP4; GPIV; PASIV; SCARB3"
                     /product="CD36 molecule (thrombospondin receptor),
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127443.1"
                     /db_xref="GI:188536062"
                     /db_xref="GeneID:948"
                     /db_xref="HGNC:1663"
                     /db_xref="MIM:173510"
                     /db_xref="HPRD:01430"
     mRNA            join(80275762..80276176,80285856..80286016,
                     80290379..80290526,80292306..80292485,80293722..80293813,
                     80295759..80295805,80299269..80299338,80300293..80300480,
                     80301238..80301356,80302086..80302159,80302671..80302725,
                     80303299..80303736)
                     /gene="CD36"
                     /gene_synonym="CHDS7; FAT; GP3B; GP4; GPIV; PASIV; SCARB3"
                     /product="CD36 molecule (thrombospondin receptor),
                     transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127444.1"
                     /db_xref="GI:188536064"
                     /db_xref="GeneID:948"
                     /db_xref="HGNC:1663"
                     /db_xref="MIM:173510"
                     /db_xref="HPRD:01430"
     CDS             join(80276057..80276176,80285856..80286016,
                     80290379..80290526,80292306..80292485,80293722..80293813,
                     80295759..80295805,80299269..80299338,80300293..80300480,
                     80301238..80301356,80302086..80302159,80302671..80302725,
                     80303299..80303463)
                     /gene="CD36"
                     /gene_synonym="CHDS7; FAT; GP3B; GP4; GPIV; PASIV; SCARB3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="platelet glycoprotein 4"
                     /protein_id="NP_001001548.1"
                     /db_xref="GI:48375180"
                     /db_xref="CCDS:CCDS34673.1"
                     /db_xref="GeneID:948"
                     /db_xref="HGNC:1663"
                     /db_xref="HPRD:01430"
                     /db_xref="MIM:173510"
     CDS             join(80276057..80276176,80285856..80286016,
                     80290379..80290526,80292306..80292485,80293722..80293813,
                     80295759..80295805,80299269..80299338,80300293..80300480,
                     80301238..80301356,80302086..80302159,80302671..80302725,
                     80303299..80303463)
                     /gene="CD36"
                     /gene_synonym="CHDS7; FAT; GP3B; GP4; GPIV; PASIV; SCARB3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="platelet glycoprotein 4"
                     /protein_id="NP_001001547.1"
                     /db_xref="GI:48375176"
                     /db_xref="CCDS:CCDS34673.1"
                     /db_xref="GeneID:948"
                     /db_xref="HGNC:1663"
                     /db_xref="HPRD:01430"
                     /db_xref="MIM:173510"
     CDS             join(80276057..80276176,80285856..80286016,
                     80290379..80290526,80292306..80292485,80293722..80293813,
                     80295759..80295805,80299269..80299338,80300293..80300480,
                     80301238..80301356,80302086..80302159,80302671..80302725,
                     80303299..80303463)
                     /gene="CD36"
                     /gene_synonym="CHDS7; FAT; GP3B; GP4; GPIV; PASIV; SCARB3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="platelet glycoprotein 4"
                     /protein_id="NP_000063.2"
                     /db_xref="GI:48375178"
                     /db_xref="CCDS:CCDS34673.1"
                     /db_xref="GeneID:948"
                     /db_xref="HGNC:1663"
                     /db_xref="HPRD:01430"
                     /db_xref="MIM:173510"
     CDS             join(80276057..80276176,80285856..80286016,
                     80290379..80290526,80292306..80292485,80293722..80293813,
                     80295759..80295805,80299269..80299338,80300293..80300480,
                     80301238..80301356,80302086..80302159,80302671..80302725,
                     80303299..80303463)
                     /gene="CD36"
                     /gene_synonym="CHDS7; FAT; GP3B; GP4; GPIV; PASIV; SCARB3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="platelet glycoprotein 4"
                     /protein_id="NP_001120915.1"
                     /db_xref="GI:188536063"
                     /db_xref="CCDS:CCDS34673.1"
                     /db_xref="GeneID:948"
                     /db_xref="HGNC:1663"
                     /db_xref="HPRD:01430"
                     /db_xref="MIM:173510"
     CDS             join(80276057..80276176,80285856..80286016,
                     80290379..80290526,80292306..80292485,80293722..80293813,
                     80295759..80295805,80299269..80299338,80300293..80300480,
                     80301238..80301356,80302086..80302159,80302671..80302725,
                     80303299..80303463)
                     /gene="CD36"
                     /gene_synonym="CHDS7; FAT; GP3B; GP4; GPIV; PASIV; SCARB3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="platelet glycoprotein 4"
                     /protein_id="NP_001120916.1"
                     /db_xref="GI:188536065"
                     /db_xref="CCDS:CCDS34673.1"
                     /db_xref="GeneID:948"
                     /db_xref="HGNC:1663"
                     /db_xref="HPRD:01430"
                     /db_xref="MIM:173510"
     gene            complement(80371854..80548667)
                     /gene="SEMA3C"
                     /gene_synonym="SEMAE; SemE"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10512"
                     /db_xref="HGNC:10725"
                     /db_xref="HPRD:04034"
                     /db_xref="MIM:602645"
     mRNA            complement(join(80371854..80374623,80378214..80378344,
                     80380585..80380652,80387647..80387804,80390932..80390973,
                     80394471..80394559,80418622..80418844,80427408..80427552,
                     80430073..80430142,80431981..80432095,80433422..80433564,
                     80434955..80435074,80439927..80440017,80447615..80447734,
                     80456741..80456803,80457901..80458061,80545995..80546135,
                     80548144..80548667))
                     /gene="SEMA3C"
                     /gene_synonym="SEMAE; SemE"
                     /product="sema domain, immunoglobulin domain (Ig), short
                     basic domain, secreted, (semaphorin) 3C"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006379.3"
                     /db_xref="GI:335057525"
                     /db_xref="GeneID:10512"
                     /db_xref="HGNC:10725"
                     /db_xref="HPRD:04034"
                     /db_xref="MIM:602645"
     CDS             complement(join(80374210..80374623,80378214..80378344,
                     80380585..80380652,80387647..80387804,80390932..80390973,
                     80394471..80394559,80418622..80418844,80427408..80427552,
                     80430073..80430142,80431981..80432095,80433422..80433564,
                     80434955..80435074,80439927..80440017,80447615..80447734,
                     80456741..80456803,80457901..80458061,80545995..80546097))
                     /gene="SEMA3C"
                     /gene_synonym="SEMAE; SemE"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="semaphorin-3C precursor"
                     /protein_id="NP_006370.1"
                     /db_xref="GI:5454048"
                     /db_xref="CCDS:CCDS5596.1"
                     /db_xref="GeneID:10512"
                     /db_xref="HGNC:10725"
                     /db_xref="HPRD:04034"
                     /db_xref="MIM:602645"
     gene            80820677..80821325
                     /gene="LOC100420647"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420647"
     gene            complement(81092352..81092929)
                     /gene="LOC100421455"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421455"
     gene            complement(81331444..81399452)
                     /gene="HGF"
                     /gene_synonym="DFNB39; F-TCF; HGFB; HPTA; SF"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3082"
                     /db_xref="HGNC:4893"
                     /db_xref="HPRD:00799"
                     /db_xref="MIM:142409"
     mRNA            complement(join(81331444..81332073,81334706..81334851,
                     81334963..81335069,81335603..81335743,81336606..81336680,
                     81339463..81339559,81340797..81340835,81346548..81346681,
                     81350061..81350163,81355206..81355333,81358921..81359095,
                     81372669..81372787,81374316..81374436,81381436..81381578,
                     81386505..81386619,81388008..81388120,81392023..81392188,
                     81399200..81399452))
                     /gene="HGF"
                     /gene_synonym="DFNB39; F-TCF; HGFB; HPTA; SF"
                     /product="hepatocyte growth factor (hepapoietin A; scatter
                     factor), transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000601.4"
                     /db_xref="GI:58533168"
                     /db_xref="GeneID:3082"
                     /db_xref="HGNC:4893"
                     /db_xref="HPRD:00799"
                     /db_xref="MIM:142409"
     mRNA            complement(join(81331444..81332073,81334706..81334851,
                     81334963..81335069,81335603..81335743,81336606..81336680,
                     81339463..81339559,81340797..81340835,81346548..81346681,
                     81350061..81350163,81355206..81355333,81358921..81359095,
                     81372669..81372787,81374316..81374436,81381436..81381563,
                     81386505..81386619,81388008..81388120,81392023..81392188,
                     81399200..81399452))
                     /gene="HGF"
                     /gene_synonym="DFNB39; F-TCF; HGFB; HPTA; SF"
                     /product="hepatocyte growth factor (hepapoietin A; scatter
                     factor), transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001010932.1"
                     /db_xref="GI:58533169"
                     /db_xref="GeneID:3082"
                     /db_xref="HGNC:4893"
                     /db_xref="HPRD:00799"
                     /db_xref="MIM:142409"
     CDS             complement(join(81331897..81332073,81334706..81334851,
                     81334963..81335069,81335603..81335743,81336606..81336680,
                     81339463..81339559,81340797..81340835,81346548..81346681,
                     81350061..81350163,81355206..81355333,81358921..81359095,
                     81372669..81372787,81374316..81374436,81381436..81381578,
                     81386505..81386619,81388008..81388120,81392023..81392188,
                     81399200..81399287))
                     /gene="HGF"
                     /gene_synonym="DFNB39; F-TCF; HGFB; HPTA; SF"
                     /note="isoform 1 preproprotein is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hepatocyte growth factor isoform 1
                     preproprotein"
                     /protein_id="NP_000592.3"
                     /db_xref="GI:33859835"
                     /db_xref="CCDS:CCDS5597.1"
                     /db_xref="GeneID:3082"
                     /db_xref="HGNC:4893"
                     /db_xref="HPRD:00799"
                     /db_xref="MIM:142409"
     CDS             complement(join(81331897..81332073,81334706..81334851,
                     81334963..81335069,81335603..81335743,81336606..81336680,
                     81339463..81339559,81340797..81340835,81346548..81346681,
                     81350061..81350163,81355206..81355333,81358921..81359095,
                     81372669..81372787,81374316..81374436,81381436..81381563,
                     81386505..81386619,81388008..81388120,81392023..81392188,
                     81399200..81399287))
                     /gene="HGF"
                     /gene_synonym="DFNB39; F-TCF; HGFB; HPTA; SF"
                     /note="isoform 3 precursor is encoded by transcript
                     variant 3; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hepatocyte growth factor isoform 3 precursor"
                     /protein_id="NP_001010932.1"
                     /db_xref="GI:58533170"
                     /db_xref="CCDS:CCDS47626.1"
                     /db_xref="GeneID:3082"
                     /db_xref="HGNC:4893"
                     /db_xref="HPRD:00799"
                     /db_xref="MIM:142409"
     mRNA            complement(join(81372007..81372265,81372669..81372787,
                     81374316..81374436,81381436..81381578,81386505..81386619,
                     81388008..81388120,81392023..81392188,81399200..81399452))
                     /gene="HGF"
                     /gene_synonym="DFNB39; F-TCF; HGFB; HPTA; SF"
                     /product="hepatocyte growth factor (hepapoietin A; scatter
                     factor), transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001010931.1"
                     /db_xref="GI:58533162"
                     /db_xref="GeneID:3082"
                     /db_xref="HGNC:4893"
                     /db_xref="HPRD:00799"
                     /db_xref="MIM:142409"
     mRNA            complement(join(81372007..81372265,81372669..81372787,
                     81374316..81374436,81381436..81381563,81386505..81386619,
                     81388008..81388120,81392023..81392188,81399200..81399452))
                     /gene="HGF"
                     /gene_synonym="DFNB39; F-TCF; HGFB; HPTA; SF"
                     /product="hepatocyte growth factor (hepapoietin A; scatter
                     factor), transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001010933.1"
                     /db_xref="GI:58533164"
                     /db_xref="GeneID:3082"
                     /db_xref="HGNC:4893"
                     /db_xref="HPRD:00799"
                     /db_xref="MIM:142409"
     CDS             complement(join(81372258..81372265,81372669..81372787,
                     81374316..81374436,81381436..81381578,81386505..81386619,
                     81388008..81388120,81392023..81392188,81399200..81399287))
                     /gene="HGF"
                     /gene_synonym="DFNB39; F-TCF; HGFB; HPTA; SF"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hepatocyte growth factor isoform 2 precursor"
                     /protein_id="NP_001010931.1"
                     /db_xref="GI:58533163"
                     /db_xref="CCDS:CCDS47627.1"
                     /db_xref="GeneID:3082"
                     /db_xref="HGNC:4893"
                     /db_xref="HPRD:00799"
                     /db_xref="MIM:142409"
     CDS             complement(join(81372258..81372265,81372669..81372787,
                     81374316..81374436,81381436..81381563,81386505..81386619,
                     81388008..81388120,81392023..81392188,81399200..81399287))
                     /gene="HGF"
                     /gene_synonym="DFNB39; F-TCF; HGFB; HPTA; SF"
                     /note="isoform 4 precursor is encoded by transcript
                     variant 4; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hepatocyte growth factor isoform 4 precursor"
                     /protein_id="NP_001010933.1"
                     /db_xref="GI:58533165"
                     /db_xref="CCDS:CCDS47628.1"
                     /db_xref="GeneID:3082"
                     /db_xref="HGNC:4893"
                     /db_xref="HPRD:00799"
                     /db_xref="MIM:142409"
     mRNA            complement(join(81380216..81381578,81386505..81386619,
                     81388008..81388120,81392023..81392188,81399200..81399452))
                     /gene="HGF"
                     /gene_synonym="DFNB39; F-TCF; HGFB; HPTA; SF"
                     /product="hepatocyte growth factor (hepapoietin A; scatter
                     factor), transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001010934.1"
                     /db_xref="GI:58533166"
                     /db_xref="GeneID:3082"
                     /db_xref="HGNC:4893"
                     /db_xref="HPRD:00799"
                     /db_xref="MIM:142409"
     CDS             complement(join(81381428..81381578,81386505..81386619,
                     81388008..81388120,81392023..81392188,81399200..81399287))
                     /gene="HGF"
                     /gene_synonym="DFNB39; F-TCF; HGFB; HPTA; SF"
                     /note="isoform 5 precursor is encoded by transcript
                     variant 5; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hepatocyte growth factor isoform 5 precursor"
                     /protein_id="NP_001010934.1"
                     /db_xref="GI:58533167"
                     /db_xref="CCDS:CCDS47629.1"
                     /db_xref="GeneID:3082"
                     /db_xref="HGNC:4893"
                     /db_xref="HPRD:00799"
                     /db_xref="MIM:142409"
     gene            complement(81579418..82073031)
                     /gene="CACNA2D1"
                     /gene_synonym="CACNA2; CACNL2A; CCHL2A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:781"
                     /db_xref="HGNC:1399"
                     /db_xref="HPRD:00245"
                     /db_xref="MIM:114204"
     mRNA            complement(join(81579418..81579824,81588591..81588673,
                     81589036..81589145,81591210..81591339,81591756..81591811,
                     81593372..81593424,81593523..81593675,81594910..81594981,
                     81596485..81596523,81596912..81596979,81598203..81598289,
                     81599197..81599300,81599991..81600053,81601093..81601180,
                     81603771..81603868,81611883..81611943,81612630..81612650,
                     81613951..81614027,81620501..81620562,81624184..81624255,
                     81626495..81626566,81634739..81634813,81635081..81635155,
                     81636995..81637072,81641470..81641559,81642777..81642826,
                     81643717..81643795,81662113..81662217,81667393..81667551,
                     81689744..81689843,81693620..81693670,81695771..81695840,
                     81714085..81714216,81746360..81746489,81765951..81765992,
                     81799866..81799925,81964451..81964567,81978884..81978965,
                     82072681..82073031))
                     /gene="CACNA2D1"
                     /gene_synonym="CACNA2; CACNL2A; CCHL2A"
                     /product="calcium channel, voltage-dependent, alpha
                     2/delta subunit 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000722.2"
                     /db_xref="GI:54112389"
                     /db_xref="GeneID:781"
                     /db_xref="HGNC:1399"
                     /db_xref="HPRD:00245"
                     /db_xref="MIM:114204"
     CDS             complement(join(81579708..81579824,81588591..81588673,
                     81589036..81589145,81591210..81591339,81591756..81591811,
                     81593372..81593424,81593523..81593675,81594910..81594981,
                     81596485..81596523,81596912..81596979,81598203..81598289,
                     81599197..81599300,81599991..81600053,81601093..81601180,
                     81603771..81603868,81611883..81611943,81612630..81612650,
                     81613951..81614027,81620501..81620562,81624184..81624255,
                     81626495..81626566,81634739..81634813,81635081..81635155,
                     81636995..81637072,81641470..81641559,81642777..81642826,
                     81643717..81643795,81662113..81662217,81667393..81667551,
                     81689744..81689843,81693620..81693670,81695771..81695840,
                     81714085..81714216,81746360..81746489,81765951..81765992,
                     81799866..81799925,81964451..81964567,81978884..81978965,
                     82072681..82072775))
                     /gene="CACNA2D1"
                     /gene_synonym="CACNA2; CACNL2A; CCHL2A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="voltage-dependent calcium channel subunit
                     alpha-2/delta-1"
                     /protein_id="NP_000713.2"
                     /db_xref="GI:54112390"
                     /db_xref="CCDS:CCDS5598.1"
                     /db_xref="GeneID:781"
                     /db_xref="HGNC:1399"
                     /db_xref="HPRD:00245"
                     /db_xref="MIM:114204"
     gene            complement(82218082..82220079)
                     /gene="LOC442707"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442707"
     gene            complement(82383321..82792197)
                     /gene="PCLO"
                     /gene_synonym="ACZ; DKFZp779G1236"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:27445"
                     /db_xref="HGNC:13406"
                     /db_xref="MIM:604918"
     mRNA            complement(join(82383321..82388031,82389955..82390100,
                     82390675..82390809,82430834..82430907,82435004..82435145,
                     82451811..82452005,82453552..82453732,82455905..82455976,
                     82457189..82457282,82464983..82465009,82467534..82467658,
                     82470775..82470825,82474587..82474801,82475883..82475950,
                     82476455..82476563,82508653..82508778,82531967..82532057,
                     82538193..82538329,82544002..82546189,82578792..82580806,
                     82581172..82586251,82595087..82595803,82763566..82764972,
                     82784064..82785708,82791661..82792197))
                     /gene="PCLO"
                     /gene_synonym="ACZ; DKFZp779G1236"
                     /product="piccolo (presynaptic cytomatrix protein),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033026.5"
                     /db_xref="GI:160707974"
                     /db_xref="GeneID:27445"
                     /db_xref="HGNC:13406"
                     /db_xref="HPRD:16078"
                     /db_xref="MIM:604918"
     CDS             complement(join(82387891..82388031,82389955..82390100,
                     82390675..82390809,82430834..82430907,82435004..82435145,
                     82451811..82452005,82453552..82453732,82455905..82455976,
                     82457189..82457282,82464983..82465009,82467534..82467658,
                     82470775..82470825,82474587..82474801,82475883..82475950,
                     82476455..82476563,82508653..82508778,82531967..82532057,
                     82538193..82538329,82544002..82546189,82578792..82580806,
                     82581172..82586251,82595087..82595803,82763566..82764972,
                     82784064..82785708,82791661..82791908))
                     /gene="PCLO"
                     /gene_synonym="ACZ; DKFZp779G1236"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein piccolo isoform 1"
                     /protein_id="NP_149015.2"
                     /db_xref="GI:150378539"
                     /db_xref="CCDS:CCDS47630.1"
                     /db_xref="GeneID:27445"
                     /db_xref="HGNC:13406"
                     /db_xref="MIM:604918"
     mRNA            complement(join(82449796..82452005,82453552..82453732,
                     82455905..82455976,82457189..82457282,82464983..82465009,
                     82467534..82467658,82470775..82470825,82474587..82474801,
                     82475883..82475950,82476455..82476563,82508653..82508778,
                     82531967..82532057,82538193..82538329,82544002..82546189,
                     82578792..82580806,82581172..82586251,82595087..82595803,
                     82763566..82764972,82784064..82785708,82791661..82792197))
                     /gene="PCLO"
                     /gene_synonym="ACZ; DKFZp779G1236"
                     /product="piccolo (presynaptic cytomatrix protein),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014510.2"
                     /db_xref="GI:150170669"
                     /db_xref="GeneID:27445"
                     /db_xref="HGNC:13406"
                     /db_xref="MIM:604918"
     CDS             complement(join(82451794..82452005,82453552..82453732,
                     82455905..82455976,82457189..82457282,82464983..82465009,
                     82467534..82467658,82470775..82470825,82474587..82474801,
                     82475883..82475950,82476455..82476563,82508653..82508778,
                     82531967..82532057,82538193..82538329,82544002..82546189,
                     82578792..82580806,82581172..82586251,82595087..82595803,
                     82763566..82764972,82784064..82785708,82791661..82791908))
                     /gene="PCLO"
                     /gene_synonym="ACZ; DKFZp779G1236"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein piccolo isoform 2"
                     /protein_id="NP_055325.2"
                     /db_xref="GI:150170670"
                     /db_xref="CCDS:CCDS47631.1"
                     /db_xref="GeneID:27445"
                     /db_xref="HGNC:13406"
                     /db_xref="MIM:604918"
     gene            complement(82993222..83278479)
                     /gene="SEMA3E"
                     /gene_synonym="coll-5; KIAA0331; M-SEMAH; M-SemaK; SEMAH"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9723"
                     /db_xref="HGNC:10727"
                     /db_xref="HPRD:11545"
                     /db_xref="MIM:608166"
     mRNA            complement(join(82993222..82997354,83014610..83014749,
                     83016299..83016366,83021871..83022037,83023613..83023654,
                     83025954..83026045,83029344..83029566,83031948..83032092,
                     83034766..83034835,83035261..83035375,83036413..83036555,
                     83037684..83037803,83047706..83047799,83095798..83095917,
                     83098559..83098618,83119430..83119590,83277744..83278479))
                     /gene="SEMA3E"
                     /gene_synonym="coll-5; KIAA0331; M-SEMAH; M-SemaK; SEMAH"
                     /product="sema domain, immunoglobulin domain (Ig), short
                     basic domain, secreted, (semaphorin) 3E, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012431.2"
                     /db_xref="GI:296011006"
                     /db_xref="GeneID:9723"
                     /db_xref="HGNC:10727"
                     /db_xref="HPRD:11545"
                     /db_xref="MIM:608166"
     mRNA            complement(join(82993222..82997354,83014610..83014749,
                     83016299..83016366,83021871..83022037,83023613..83023654,
                     83025954..83026045,83029344..83029566,83031948..83032092,
                     83034766..83034835,83035261..83035375,83036413..83036555,
                     83037684..83037803,83047706..83047799,83095798..83095917,
                     83098559..83098618,83119430..83119590,83270648..83270747))
                     /gene="SEMA3E"
                     /gene_synonym="coll-5; KIAA0331; M-SEMAH; M-SemaK; SEMAH"
                     /product="sema domain, immunoglobulin domain (Ig), short
                     basic domain, secreted, (semaphorin) 3E, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001178129.1"
                     /db_xref="GI:296011007"
                     /db_xref="GeneID:9723"
                     /db_xref="HGNC:10727"
                     /db_xref="MIM:608166"
                     /db_xref="HPRD:11545"
     CDS             complement(join(82996902..82997354,83014610..83014749,
                     83016299..83016366,83021871..83022037,83023613..83023654,
                     83025954..83026045,83029344..83029566,83031948..83032092,
                     83034766..83034835,83035261..83035375,83036413..83036555,
                     83037684..83037803,83047706..83047799,83095798..83095917,
                     83098559..83098618,83119430..83119590,83277744..83277858))
                     /gene="SEMA3E"
                     /gene_synonym="coll-5; KIAA0331; M-SEMAH; M-SemaK; SEMAH"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="semaphorin-3E isoform 1 precursor"
                     /protein_id="NP_036563.1"
                     /db_xref="GI:6912650"
                     /db_xref="CCDS:CCDS34674.1"
                     /db_xref="GeneID:9723"
                     /db_xref="HGNC:10727"
                     /db_xref="HPRD:11545"
                     /db_xref="MIM:608166"
     CDS             complement(join(82996902..82997354,83014610..83014749,
                     83016299..83016366,83021871..83022037,83023613..83023654,
                     83025954..83026045,83029344..83029566,83031948..83032092,
                     83034766..83034835,83035261..83035375,83036413..83036555,
                     83037684..83037803,83047706..83047799,83095798..83095917,
                     83098559..83098618,83119430..83119525))
                     /gene="SEMA3E"
                     /gene_synonym="coll-5; KIAA0331; M-SEMAH; M-SemaK; SEMAH"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="semaphorin-3E isoform 2"
                     /protein_id="NP_001171600.1"
                     /db_xref="GI:296011008"
                     /db_xref="CCDS:CCDS55121.1"
                     /db_xref="GeneID:9723"
                     /db_xref="HGNC:10727"
                     /db_xref="HPRD:11545"
                     /db_xref="MIM:608166"
     gene            83292735..83293941
                     /gene="LOC100130572"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100130572"
     gene            complement(83587659..83824217)
                     /gene="SEMA3A"
                     /gene_synonym="coll-1; Hsema-I; Hsema-III; MGC133243;
                     SEMA1; SEMAD; SEMAIII; SEMAL; SemD"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10371"
                     /db_xref="HGNC:10723"
                     /db_xref="HPRD:04908"
                     /db_xref="MIM:603961"
     mRNA            complement(join(83587659..83591142,83592521..83592663,
                     83606448..83606512,83610637..83610794,83614752..83614793,
                     83631271..83631362,83634655..83634874,83636669..83636813,
                     83640338..83640407,83640499..83640613,83643525..83643667,
                     83675640..83675759,83689781..83689874,83739786..83739905,
                     83758439..83758501,83764110..83764267,83823791..83824217))
                     /gene="SEMA3A"
                     /gene_synonym="coll-1; Hsema-I; Hsema-III; MGC133243;
                     SEMA1; SEMAD; SEMAIII; SEMAL; SemD"
                     /product="sema domain, immunoglobulin domain (Ig), short
                     basic domain, secreted, (semaphorin) 3A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006080.2"
                     /db_xref="GI:100913215"
                     /db_xref="GeneID:10371"
                     /db_xref="HGNC:10723"
                     /db_xref="HPRD:04908"
                     /db_xref="MIM:603961"
     CDS             complement(join(83590687..83591142,83592521..83592663,
                     83606448..83606512,83610637..83610794,83614752..83614793,
                     83631271..83631362,83634655..83634874,83636669..83636813,
                     83640338..83640407,83640499..83640613,83643525..83643667,
                     83675640..83675759,83689781..83689874,83739786..83739905,
                     83758439..83758501,83764110..83764267,83823791..83823902))
                     /gene="SEMA3A"
                     /gene_synonym="coll-1; Hsema-I; Hsema-III; MGC133243;
                     SEMA1; SEMAD; SEMAIII; SEMAL; SemD"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="semaphorin-3A precursor"
                     /protein_id="NP_006071.1"
                     /db_xref="GI:5174673"
                     /db_xref="CCDS:CCDS5599.1"
                     /db_xref="GeneID:10371"
                     /db_xref="HGNC:10723"
                     /db_xref="HPRD:04908"
                     /db_xref="MIM:603961"
     gene            complement(84157433..84158146)
                     /gene="RPL7P30"
                     /gene_synonym="RPL7_13_818"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100270908"
                     /db_xref="HGNC:36151"
     gene            84505800..84507140
                     /gene="HMGN2P11"
                     /gene_synonym="28H; HMG17P1; HMGN2L11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:3152"
                     /db_xref="HGNC:4990"
     gene            84612811..84614155
                     /gene="HNRNPA1P8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402562"
                     /db_xref="HGNC:39126"
     gene            complement(84624869..84751247)
                     /gene="SEMA3D"
                     /gene_synonym="coll-2; MGC39708; Sema-Z2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:223117"
                     /db_xref="HGNC:10726"
                     /db_xref="HPRD:15321"
                     /db_xref="MIM:609907"
     mRNA            complement(join(84624869..84629181,84636118..84636257,
                     84642098..84642162,84644375..84644532,84647568..84647609,
                     84649549..84649637,84651707..84651929,84666205..84666349,
                     84669989..84670058,84671487..84671601,84685033..84685175,
                     84694740..84694868,84697507..84697600,84702278..84702397,
                     84710833..84710895,84727121..84727281,84751057..84751247))
                     /gene="SEMA3D"
                     /gene_synonym="coll-2; MGC39708; Sema-Z2"
                     /product="sema domain, immunoglobulin domain (Ig), short
                     basic domain, secreted, (semaphorin) 3D"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152754.2"
                     /db_xref="GI:41406085"
                     /db_xref="GeneID:223117"
                     /db_xref="HGNC:10726"
                     /db_xref="HPRD:15321"
                     /db_xref="MIM:609907"
     CDS             complement(join(84628756..84629181,84636118..84636257,
                     84642098..84642162,84644375..84644532,84647568..84647609,
                     84649549..84649637,84651707..84651929,84666205..84666349,
                     84669989..84670058,84671487..84671601,84685033..84685175,
                     84694740..84694868,84697507..84697600,84702278..84702397,
                     84710833..84710895,84727121..84727281,84751057..84751207))
                     /gene="SEMA3D"
                     /gene_synonym="coll-2; MGC39708; Sema-Z2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="semaphorin-3D precursor"
                     /protein_id="NP_689967.2"
                     /db_xref="GI:41406086"
                     /db_xref="CCDS:CCDS34676.1"
                     /db_xref="GeneID:223117"
                     /db_xref="HGNC:10726"
                     /db_xref="HPRD:15321"
                     /db_xref="MIM:609907"
     gene            84657067..84659197
                     /gene="LOC100289643"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100289643"
     gene            complement(85010421..85010787)
                     /gene="LOC729630"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:729630"
     gene            85104543..85118654
                     /gene="LOC100505913"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /db_xref="GeneID:100505913"
     misc_RNA        join(85104543..85104676,85118198..85118654)
                     /gene="LOC100505913"
                     /product="hypothetical LOC100505913"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /transcript_id="XR_108842.1"
                     /db_xref="GI:310120023"
                     /db_xref="GeneID:100505913"
     gene            complement(85846101..85847043)
                     /gene="LOC100420754"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420754"
     gene            86273230..86494192
                     /gene="GRM3"
                     /gene_synonym="GLUR3; GPRC1C; mGlu3; MGLUR3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2913"
                     /db_xref="HGNC:4595"
                     /db_xref="HPRD:03070"
                     /db_xref="MIM:601115"
     mRNA            join(86273230..86274188,86394322..86394929,
                     86415577..86416432,86468155..86469221,86479686..86479860,
                     86493598..86494192)
                     /gene="GRM3"
                     /gene_synonym="GLUR3; GPRC1C; mGlu3; MGLUR3"
                     /product="glutamate receptor, metabotropic 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000840.2"
                     /db_xref="GI:46358416"
                     /db_xref="GeneID:2913"
                     /db_xref="HGNC:4595"
                     /db_xref="HPRD:03070"
                     /db_xref="MIM:601115"
     CDS             join(86394462..86394929,86415577..86416432,
                     86468155..86469221,86479686..86479860,86493598..86493671)
                     /gene="GRM3"
                     /gene_synonym="GLUR3; GPRC1C; mGlu3; MGLUR3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="metabotropic glutamate receptor 3 precursor"
                     /protein_id="NP_000831.2"
                     /db_xref="GI:46358417"
                     /db_xref="CCDS:CCDS5600.1"
                     /db_xref="GeneID:2913"
                     /db_xref="HGNC:4595"
                     /db_xref="HPRD:03070"
                     /db_xref="MIM:601115"
     gene            complement(86506222..86689014)
                     /gene="KIAA1324L"
                     /gene_synonym="EIG121L; FLJ31340"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222223"
                     /db_xref="HGNC:21945"
                     /db_xref="MIM:614048"
     mRNA            complement(join(86506222..86509846,86521040..86521205,
                     86522238..86522416,86526822..86526948,86536986..86537087,
                     86537763..86537859,86539128..86539317,86541388..86541561,
                     86542257..86542520,86544039..86544176,86547758..86547860,
                     86548536..86548626,86554844..86554972,86556052..86556232,
                     86567442..86567530,86568124..86568276,86569326..86569431,
                     86571334..86571420,86574215..86574362,86577043..86577238,
                     86594220..86594340,86688641..86689014))
                     /gene="KIAA1324L"
                     /gene_synonym="EIG121L; FLJ31340"
                     /product="KIAA1324-like, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001142749.2"
                     /db_xref="GI:262205160"
                     /db_xref="GeneID:222223"
                     /db_xref="HGNC:21945"
                     /db_xref="MIM:614048"
     misc_RNA        complement(join(86506222..86509846,86521040..86521205,
                     86522238..86522416,86526822..86526948,86536986..86537087,
                     86537763..86537859,86539128..86539317,86541388..86541561,
                     86542257..86542520,86544039..86544176,86547758..86547860,
                     86548536..86548626,86554844..86554972,86556052..86556232,
                     86567442..86567530,86568124..86568276,86569326..86569431,
                     86571334..86571420,86574215..86574362,86577043..86577238,
                     86594220..86594340,86611332..86611463))
                     /gene="KIAA1324L"
                     /gene_synonym="EIG121L; FLJ31340"
                     /product="KIAA1324-like, transcript variant 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_030672.1"
                     /db_xref="GI:262205173"
                     /db_xref="GeneID:222223"
                     /db_xref="HGNC:21945"
                     /db_xref="MIM:614048"
     mRNA            complement(join(86506222..86509846,86521040..86521205,
                     86522238..86522416,86526822..86526948,86536986..86537087,
                     86537763..86537859,86539128..86539317,86541388..86541561,
                     86542257..86542520,86544039..86544176,86547758..86547860,
                     86548536..86548626,86554844..86554972,86556052..86556232,
                     86567442..86567530,86568124..86568276,86569326..86569431,
                     86571334..86571420,86574215..86574362,86594220..86594340,
                     86595125..86595291))
                     /gene="KIAA1324L"
                     /gene_synonym="EIG121L; FLJ31340"
                     /product="KIAA1324-like, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152748.3"
                     /db_xref="GI:262205167"
                     /db_xref="GeneID:222223"
                     /db_xref="HGNC:21945"
                     /db_xref="HPRD:13405"
                     /db_xref="MIM:614048"
     CDS             complement(join(86509787..86509846,86521040..86521205,
                     86522238..86522416,86526822..86526948,86536986..86537087,
                     86537763..86537859,86539128..86539317,86541388..86541561,
                     86542257..86542520,86544039..86544176,86547758..86547860,
                     86548536..86548626,86554844..86554972,86556052..86556232,
                     86567442..86567530,86568124..86568276,86569326..86569431,
                     86571334..86571420,86574215..86574362,86577043..86577238,
                     86594220..86594340,86688641..86688829))
                     /gene="KIAA1324L"
                     /gene_synonym="EIG121L; FLJ31340"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="estrogen-induced gene 121-like protein isoform
                     1"
                     /protein_id="NP_001136221.1"
                     /db_xref="GI:218505750"
                     /db_xref="CCDS:CCDS47632.1"
                     /db_xref="GeneID:222223"
                     /db_xref="HGNC:21945"
                     /db_xref="MIM:614048"
     CDS             complement(join(86509787..86509846,86521040..86521205,
                     86522238..86522416,86526822..86526948,86536986..86537087,
                     86537763..86537859,86539128..86539317,86541388..86541561,
                     86542257..86542520,86544039..86544176,86547758..86547860,
                     86548536..86548626,86554844..86554972,86556052..86556232,
                     86567442..86567530,86568124..86568276,86569326..86569431,
                     86571334..86571420,86574215..86574362,86594220..86594224))
                     /gene="KIAA1324L"
                     /gene_synonym="EIG121L; FLJ31340"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="estrogen-induced gene 121-like protein isoform
                     2"
                     /protein_id="NP_689961.3"
                     /db_xref="GI:262205168"
                     /db_xref="CCDS:CCDS34677.2"
                     /db_xref="GeneID:222223"
                     /db_xref="HGNC:21945"
                     /db_xref="MIM:614048"
     gene            complement(86780739..86781656)
                     /gene="LOC100505932"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 20 ESTs"
                     /db_xref="GeneID:100505932"
     misc_RNA        complement(join(86780739..86780974,86781066..86781656))
                     /gene="LOC100505932"
                     /product="hypothetical LOC100505932"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 20 ESTs"
                     /transcript_id="XR_108843.1"
                     /db_xref="GI:310120024"
                     /db_xref="GeneID:100505932"
     gene            86781677..86825648
                     /gene="DMTF1"
                     /gene_synonym="DMP1; DMTF; FLJ25188; FLJ41265; FLJ76054;
                     hDMP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9988"
                     /db_xref="HGNC:14603"
                     /db_xref="MIM:608491"
     mRNA            join(86781677..86781871,86792811..86792933,
                     86794250..86794366,86795799..86795921,86800311..86800405,
                     86802851..86802965,86803909..86803985,86808861..86809018,
                     86810625..86810657,86811544..86811653,86813713..86813941,
                     86815145..86815296,86817408..86817617,86820261..86820343,
                     86822514..86822669,86823041..86823418,86824000..86824144,
                     86824347..86825648)
                     /gene="DMTF1"
                     /gene_synonym="DMP1; DMTF; FLJ25188; FLJ41265; FLJ76054;
                     hDMP1"
                     /product="cyclin D binding myb-like transcription factor
                     1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001142327.1"
                     /db_xref="GI:215599991"
                     /db_xref="GeneID:9988"
                     /db_xref="HGNC:14603"
                     /db_xref="MIM:608491"
     mRNA            join(86781677..86781871,86792811..86792933,
                     86795799..86795921,86800311..86800405,86802851..86802965,
                     86803909..86803985,86808861..86809018,86810625..86810657,
                     86811544..86811653,86813713..86813941,86815145..86815296,
                     86817408..86817617,86820261..86820343,86822514..86822669,
                     86823041..86823418,86824000..86824144,86824347..86825648)
                     /gene="DMTF1"
                     /gene_synonym="DMP1; DMTF; FLJ25188; FLJ41265; FLJ76054;
                     hDMP1"
                     /product="cyclin D binding myb-like transcription factor
                     1, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001142326.1"
                     /db_xref="GI:215599980"
                     /db_xref="GeneID:9988"
                     /db_xref="HGNC:14603"
                     /db_xref="MIM:608491"
     misc_RNA        join(86781677..86781871,86792811..86792933,
                     86794250..86794366,86795799..86795921,86800311..86800405,
                     86802851..86802965,86803909..86803985,86808861..86809018,
                     86810625..86810657,86811333..86811653,86813713..86813941,
                     86815145..86815296,86817408..86817617,86820261..86820343,
                     86822514..86822669,86823041..86823418,86824000..86824144,
                     86824347..86825648)
                     /gene="DMTF1"
                     /gene_synonym="DMP1; DMTF; FLJ25188; FLJ41265; FLJ76054;
                     hDMP1"
                     /product="cyclin D binding myb-like transcription factor
                     1, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024549.1"
                     /db_xref="GI:215598846"
                     /db_xref="GeneID:9988"
                     /db_xref="HGNC:14603"
                     /db_xref="MIM:608491"
     misc_RNA        join(86781677..86781871,86792811..86792933,
                     86794250..86794366,86795799..86795921,86800311..86800405,
                     86802851..86802965,86803909..86803985,86808861..86809018,
                     86810625..86810657,86811372..86811653,86813713..86813941,
                     86815145..86815296,86817408..86817617,86820261..86820343,
                     86822514..86822669,86823041..86823418,86824000..86824144,
                     86824347..86825648)
                     /gene="DMTF1"
                     /gene_synonym="DMP1; DMTF; FLJ25188; FLJ41265; FLJ76054;
                     hDMP1"
                     /product="cyclin D binding myb-like transcription factor
                     1, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024550.1"
                     /db_xref="GI:215598858"
                     /db_xref="GeneID:9988"
                     /db_xref="HGNC:14603"
                     /db_xref="MIM:608491"
     mRNA            join(86781870..86782111,86783544..86783594,
                     86783706..86783844,86792811..86792933,86794250..86794366,
                     86795799..86795921,86800311..86800405,86802851..86802965,
                     86803909..86803985,86808861..86809018,86810625..86810657,
                     86811544..86811653,86813713..86813941,86815145..86815296,
                     86817408..86817617,86820261..86820343,86822514..86822669,
                     86823041..86823418,86824000..86824144,86824347..86825648)
                     /gene="DMTF1"
                     /gene_synonym="DMP1; DMTF; FLJ25188; FLJ41265; FLJ76054;
                     hDMP1"
                     /product="cyclin D binding myb-like transcription factor
                     1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021145.3"
                     /db_xref="GI:215599966"
                     /db_xref="GeneID:9988"
                     /db_xref="HGNC:14603"
                     /db_xref="HPRD:09770"
                     /db_xref="MIM:608491"
     gene            86788836..86790759
                     /gene="LOC100505951"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /db_xref="GeneID:100505951"
     misc_RNA        join(86788836..86789641,86790726..86790759)
                     /gene="LOC100505951"
                     /product="hypothetical LOC100505951"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /transcript_id="XR_108844.1"
                     /db_xref="GI:310120025"
                     /db_xref="GeneID:100505951"
     CDS             join(86794258..86794366,86795799..86795921,
                     86800311..86800405,86802851..86802965,86803909..86803985,
                     86808861..86809018,86810625..86810657,86811544..86811653,
                     86813713..86813941,86815145..86815296,86817408..86817617,
                     86820261..86820343,86822514..86822669,86823041..86823418,
                     86824000..86824144,86824347..86824456)
                     /gene="DMTF1"
                     /gene_synonym="DMP1; DMTF; FLJ25188; FLJ41265; FLJ76054;
                     hDMP1"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclin-D-binding Myb-like transcription factor 1
                     isoform a"
                     /protein_id="NP_066968.3"
                     /db_xref="GI:215599967"
                     /db_xref="CCDS:CCDS5601.1"
                     /db_xref="GeneID:9988"
                     /db_xref="HGNC:14603"
                     /db_xref="MIM:608491"
     CDS             join(86794258..86794366,86795799..86795921,
                     86800311..86800405,86802851..86802965,86803909..86803985,
                     86808861..86809018,86810625..86810657,86811544..86811653,
                     86813713..86813941,86815145..86815296,86817408..86817617,
                     86820261..86820343,86822514..86822669,86823041..86823418,
                     86824000..86824144,86824347..86824456)
                     /gene="DMTF1"
                     /gene_synonym="DMP1; DMTF; FLJ25188; FLJ41265; FLJ76054;
                     hDMP1"
                     /note="isoform a is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclin-D-binding Myb-like transcription factor 1
                     isoform a"
                     /protein_id="NP_001135799.1"
                     /db_xref="GI:215599992"
                     /db_xref="CCDS:CCDS5601.1"
                     /db_xref="GeneID:9988"
                     /db_xref="HGNC:14603"
                     /db_xref="MIM:608491"
     CDS             join(86800343..86800405,86802851..86802965,
                     86803909..86803985,86808861..86809018,86810625..86810657,
                     86811544..86811653,86813713..86813941,86815145..86815296,
                     86817408..86817617,86820261..86820343,86822514..86822669,
                     86823041..86823418,86824000..86824144,86824347..86824456)
                     /gene="DMTF1"
                     /gene_synonym="DMP1; DMTF; FLJ25188; FLJ41265; FLJ76054;
                     hDMP1"
                     /note="isoform b is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclin-D-binding Myb-like transcription factor 1
                     isoform b"
                     /protein_id="NP_001135798.1"
                     /db_xref="GI:215599981"
                     /db_xref="CCDS:CCDS47633.1"
                     /db_xref="GeneID:9988"
                     /db_xref="HGNC:14603"
                     /db_xref="MIM:608491"
     gene            complement(86825478..86849031)
                     /gene="C7orf23"
                     /gene_synonym="MGC4175; MM-TRAG"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79161"
                     /db_xref="HGNC:21707"
                     /db_xref="HPRD:12911"
     mRNA            complement(join(86825478..86826074,86827257..86827361,
                     86828323..86828373,86848742..86849031))
                     /gene="C7orf23"
                     /gene_synonym="MGC4175; MM-TRAG"
                     /product="chromosome 7 open reading frame 23"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024315.2"
                     /db_xref="GI:34147374"
                     /db_xref="GeneID:79161"
                     /db_xref="HGNC:21707"
                     /db_xref="HPRD:12911"
     CDS             complement(join(86825952..86826074,86827257..86827361,
                     86828323..86828373,86848742..86848819))
                     /gene="C7orf23"
                     /gene_synonym="MGC4175; MM-TRAG"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein C7orf23"
                     /protein_id="NP_077291.1"
                     /db_xref="GI:13236557"
                     /db_xref="CCDS:CCDS5602.1"
                     /db_xref="GeneID:79161"
                     /db_xref="HGNC:21707"
                     /db_xref="HPRD:12911"
     gene            complement(86954663..86974808)
                     /gene="TP53TG1"
                     /gene_synonym="NCRNA00096; P53TG1; P53TG1-D; TP53AP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:11257"
                     /db_xref="HGNC:17026"
     misc_RNA        complement(join(86954663..86954760,86970839..86971000,
                     86974359..86974808))
                     /gene="TP53TG1"
                     /gene_synonym="NCRNA00096; P53TG1; P53TG1-D; TP53AP1"
                     /product="TP53 target 1 (non-protein coding)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_015381.1"
                     /db_xref="GI:168823573"
                     /db_xref="GeneID:11257"
                     /db_xref="HGNC:17026"
     gene            86974951..87029112
                     /gene="CROT"
                     /gene_synonym="COT"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54677"
                     /db_xref="HGNC:2366"
                     /db_xref="HPRD:12081"
                     /db_xref="MIM:606090"
     mRNA            join(86974951..86975083,86975656..86975746,
                     86978364..86978499,86986823..86986906,86988522..86988646,
                     86990706..86990887,86991044..86991168,86998692..86998800,
                     87004948..87005041,87005144..87005269,87006665..87006766,
                     87011226..87011309,87011390..87011497,87011729..87011859,
                     87020905..87021028,87021882..87021960,87022046..87022139,
                     87022264..87022383,87027840..87029112)
                     /gene="CROT"
                     /gene_synonym="COT"
                     /product="carnitine O-octanoyltransferase, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001143935.1"
                     /db_xref="GI:221316601"
                     /db_xref="GeneID:54677"
                     /db_xref="HGNC:2366"
                     /db_xref="MIM:606090"
                     /db_xref="HPRD:12081"
     mRNA            join(86974951..86975083,86975656..86975746,
                     86978364..86978499,86988522..86988646,86990706..86990887,
                     86991044..86991168,86998692..86998800,87004948..87005041,
                     87005144..87005269,87006665..87006766,87011226..87011309,
                     87011390..87011497,87011729..87011859,87020905..87021028,
                     87021882..87021960,87022046..87022139,87022264..87022383,
                     87027840..87029112)
                     /gene="CROT"
                     /gene_synonym="COT"
                     /product="carnitine O-octanoyltransferase, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021151.3"
                     /db_xref="GI:221316600"
                     /db_xref="GeneID:54677"
                     /db_xref="HGNC:2366"
                     /db_xref="HPRD:12081"
                     /db_xref="MIM:606090"
     misc_RNA        join(86974951..86975083,86975656..86975746,
                     86978364..86978499,86988522..86989425)
                     /gene="CROT"
                     /gene_synonym="COT"
                     /product="carnitine O-octanoyltransferase, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_026585.1"
                     /db_xref="GI:221316603"
                     /db_xref="GeneID:54677"
                     /db_xref="HGNC:2366"
                     /db_xref="MIM:606090"
                     /db_xref="HPRD:12081"
     CDS             join(86978385..86978499,86986823..86986906,
                     86988522..86988646,86990706..86990887,86991044..86991168,
                     86998692..86998800,87004948..87005041,87005144..87005269,
                     87006665..87006766,87011226..87011309,87011390..87011497,
                     87011729..87011859,87020905..87021028,87021882..87021960,
                     87022046..87022139,87022264..87022383,87027840..87027960)
                     /gene="CROT"
                     /gene_synonym="COT"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="peroxisomal carnitine O-octanoyltransferase
                     isoform 1"
                     /protein_id="NP_001137407.1"
                     /db_xref="GI:221316602"
                     /db_xref="CCDS:CCDS47634.1"
                     /db_xref="GeneID:54677"
                     /db_xref="HGNC:2366"
                     /db_xref="HPRD:12081"
                     /db_xref="MIM:606090"
     CDS             join(86978385..86978499,86988522..86988646,
                     86990706..86990887,86991044..86991168,86998692..86998800,
                     87004948..87005041,87005144..87005269,87006665..87006766,
                     87011226..87011309,87011390..87011497,87011729..87011859,
                     87020905..87021028,87021882..87021960,87022046..87022139,
                     87022264..87022383,87027840..87027960)
                     /gene="CROT"
                     /gene_synonym="COT"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="peroxisomal carnitine O-octanoyltransferase
                     isoform 2"
                     /protein_id="NP_066974.2"
                     /db_xref="GI:31542325"
                     /db_xref="CCDS:CCDS5604.1"
                     /db_xref="GeneID:54677"
                     /db_xref="HGNC:2366"
                     /db_xref="HPRD:12081"
                     /db_xref="MIM:606090"
     gene            complement(87031361..87105019)
                     /gene="ABCB4"
                     /gene_synonym="ABC21; GBD1; MDR2; MDR2/3; MDR3; PFIC-3;
                     PGY3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5244"
                     /db_xref="HGNC:45"
                     /db_xref="HPRD:01371"
                     /db_xref="MIM:171060"
     mRNA            complement(join(87031361..87031618,87032451..87032597,
                     87035604..87035810,87037353..87037550,87038552..87038708,
                     87041209..87041349,87042933..87043033,87046628..87046831,
                     87047853..87047936,87049314..87049391,87051437..87051541,
                     87053222..87053368,87056066..87056236,87060720..87060881,
                     87068983..87069153,87069515..87069718,87072635..87072760,
                     87072979..87073089,87074178..87074291,87076350..87076521,
                     87079284..87079408,87080939..87081110,87082260..87082451,
                     87083851..87083908,87092074..87092224,87101937..87101991,
                     87104702..87104787,87104950..87105019))
                     /gene="ABCB4"
                     /gene_synonym="ABC21; GBD1; MDR2; MDR2/3; MDR3; PFIC-3;
                     PGY3"
                     /product="ATP-binding cassette, sub-family B (MDR/TAP),
                     member 4, transcript variant A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000443.3"
                     /db_xref="GI:112380625"
                     /db_xref="GeneID:5244"
                     /db_xref="HGNC:45"
                     /db_xref="HPRD:01371"
                     /db_xref="MIM:171060"
     mRNA            complement(join(87031361..87031618,87032451..87032597,
                     87035604..87035831,87037353..87037550,87038552..87038708,
                     87041209..87041349,87042933..87043033,87046628..87046831,
                     87047853..87047936,87049314..87049391,87051437..87051541,
                     87053222..87053368,87056066..87056236,87060720..87060881,
                     87068983..87069153,87069515..87069718,87072635..87072760,
                     87072979..87073089,87074178..87074291,87076350..87076521,
                     87079284..87079408,87080939..87081110,87082260..87082451,
                     87083851..87083908,87092074..87092224,87101937..87101991,
                     87104702..87104787,87104950..87105019))
                     /gene="ABCB4"
                     /gene_synonym="ABC21; GBD1; MDR2; MDR2/3; MDR3; PFIC-3;
                     PGY3"
                     /product="ATP-binding cassette, sub-family B (MDR/TAP),
                     member 4, transcript variant B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018849.2"
                     /db_xref="GI:112380626"
                     /db_xref="GeneID:5244"
                     /db_xref="HGNC:45"
                     /db_xref="HPRD:01371"
                     /db_xref="MIM:171060"
     mRNA            complement(join(87031361..87031618,87032451..87032597,
                     87035604..87035810,87037353..87037550,87038552..87038708,
                     87042933..87043033,87046628..87046831,87047853..87047936,
                     87049314..87049391,87051437..87051541,87053222..87053368,
                     87056066..87056236,87060720..87060881,87068983..87069153,
                     87069515..87069718,87072635..87072760,87072979..87073089,
                     87074178..87074291,87076350..87076521,87079284..87079408,
                     87080939..87081110,87082260..87082451,87083851..87083908,
                     87092074..87092224,87101937..87101991,87104702..87104787,
                     87104950..87105019))
                     /gene="ABCB4"
                     /gene_synonym="ABC21; GBD1; MDR2; MDR2/3; MDR3; PFIC-3;
                     PGY3"
                     /product="ATP-binding cassette, sub-family B (MDR/TAP),
                     member 4, transcript variant C"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018850.2"
                     /db_xref="GI:112380624"
                     /db_xref="GeneID:5244"
                     /db_xref="HGNC:45"
                     /db_xref="HPRD:01371"
                     /db_xref="MIM:171060"
     CDS             complement(join(87031412..87031618,87032451..87032597,
                     87035604..87035810,87037353..87037550,87038552..87038708,
                     87041209..87041349,87042933..87043033,87046628..87046831,
                     87047853..87047936,87049314..87049391,87051437..87051541,
                     87053222..87053368,87056066..87056236,87060720..87060881,
                     87068983..87069153,87069515..87069718,87072635..87072760,
                     87072979..87073089,87074178..87074291,87076350..87076521,
                     87079284..87079408,87080939..87081110,87082260..87082451,
                     87083851..87083908,87092074..87092224,87101937..87101991,
                     87104702..87104781))
                     /gene="ABCB4"
                     /gene_synonym="ABC21; GBD1; MDR2; MDR2/3; MDR3; PFIC-3;
                     PGY3"
                     /note="isoform A is encoded by transcript variant A;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="multidrug resistance protein 3 isoform A"
                     /protein_id="NP_000434.1"
                     /db_xref="GI:4505771"
                     /db_xref="CCDS:CCDS5605.1"
                     /db_xref="GeneID:5244"
                     /db_xref="HGNC:45"
                     /db_xref="HPRD:01371"
                     /db_xref="MIM:171060"
     CDS             complement(join(87031412..87031618,87032451..87032597,
                     87035604..87035831,87037353..87037550,87038552..87038708,
                     87041209..87041349,87042933..87043033,87046628..87046831,
                     87047853..87047936,87049314..87049391,87051437..87051541,
                     87053222..87053368,87056066..87056236,87060720..87060881,
                     87068983..87069153,87069515..87069718,87072635..87072760,
                     87072979..87073089,87074178..87074291,87076350..87076521,
                     87079284..87079408,87080939..87081110,87082260..87082451,
                     87083851..87083908,87092074..87092224,87101937..87101991,
                     87104702..87104781))
                     /gene="ABCB4"
                     /gene_synonym="ABC21; GBD1; MDR2; MDR2/3; MDR3; PFIC-3;
                     PGY3"
                     /note="isoform B is encoded by transcript variant B;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="multidrug resistance protein 3 isoform B"
                     /protein_id="NP_061337.1"
                     /db_xref="GI:9961250"
                     /db_xref="CCDS:CCDS5606.1"
                     /db_xref="GeneID:5244"
                     /db_xref="HGNC:45"
                     /db_xref="HPRD:01371"
                     /db_xref="MIM:171060"
     CDS             complement(join(87031412..87031618,87032451..87032597,
                     87035604..87035810,87037353..87037550,87038552..87038708,
                     87042933..87043033,87046628..87046831,87047853..87047936,
                     87049314..87049391,87051437..87051541,87053222..87053368,
                     87056066..87056236,87060720..87060881,87068983..87069153,
                     87069515..87069718,87072635..87072760,87072979..87073089,
                     87074178..87074291,87076350..87076521,87079284..87079408,
                     87080939..87081110,87082260..87082451,87083851..87083908,
                     87092074..87092224,87101937..87101991,87104702..87104781))
                     /gene="ABCB4"
                     /gene_synonym="ABC21; GBD1; MDR2; MDR2/3; MDR3; PFIC-3;
                     PGY3"
                     /note="isoform C is encoded by transcript variant C;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="multidrug resistance protein 3 isoform C"
                     /protein_id="NP_061338.1"
                     /db_xref="GI:9961252"
                     /db_xref="CCDS:CCDS5607.1"
                     /db_xref="GeneID:5244"
                     /db_xref="HGNC:45"
                     /db_xref="HPRD:01371"
                     /db_xref="MIM:171060"
     gene            complement(87133179..87342639)
                     /gene="ABCB1"
                     /gene_synonym="ABC20; CD243; CLCS; GP170; MDR1; MGC163296;
                     P-GP; PGY1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5243"
                     /db_xref="HGNC:40"
                     /db_xref="HPRD:01370"
                     /db_xref="MIM:171050"
     mRNA            complement(join(87133179..87133765,87135213..87135359,
                     87138591..87138797,87144547..87144744,87145825..87145981,
                     87148642..87148782,87150092..87150192,87160610..87160813,
                     87165774..87165857,87168584..87168661,87170673..87170780,
                     87173445..87173591,87174139..87174315,87175179..87175340,
                     87178664..87178834,87179167..87179370,87179487..87179612,
                     87179784..87179894,87180041..87180154,87183077..87183248,
                     87190579..87190703,87195386..87195557,87196101..87196292,
                     87199488..87199539,87214828..87214996,87225082..87225130,
                     87229433..87229506,87230071..87230394,87342477..87342639))
                     /gene="ABCB1"
                     /gene_synonym="ABC20; CD243; CLCS; GP170; MDR1; MGC163296;
                     P-GP; PGY1"
                     /product="ATP-binding cassette, sub-family B (MDR/TAP),
                     member 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000927.4"
                     /db_xref="GI:318037598"
                     /db_xref="GeneID:5243"
                     /db_xref="HGNC:40"
                     /db_xref="HPRD:01370"
                     /db_xref="MIM:171050"
     CDS             complement(join(87133559..87133765,87135213..87135359,
                     87138591..87138797,87144547..87144744,87145825..87145981,
                     87148642..87148782,87150092..87150192,87160610..87160813,
                     87165774..87165857,87168584..87168661,87170673..87170780,
                     87173445..87173591,87174139..87174315,87175179..87175340,
                     87178664..87178834,87179167..87179370,87179487..87179612,
                     87179784..87179894,87180041..87180154,87183077..87183248,
                     87190579..87190703,87195386..87195557,87196101..87196292,
                     87199488..87199539,87214828..87214996,87225082..87225130,
                     87229433..87229500))
                     /gene="ABCB1"
                     /gene_synonym="ABC20; CD243; CLCS; GP170; MDR1; MGC163296;
                     P-GP; PGY1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="multidrug resistance protein 1"
                     /protein_id="NP_000918.2"
                     /db_xref="GI:42741659"
                     /db_xref="CCDS:CCDS5608.1"
                     /db_xref="GeneID:5243"
                     /db_xref="HGNC:40"
                     /db_xref="HPRD:01370"
                     /db_xref="MIM:171050"
     gene            87150777..87151728
                     /gene="LOC100421389"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421389"
     gene            87257729..87461613
                     /gene="RUNDC3B"
                     /gene_synonym="FLJ30671; MGC26655; RPIB9; RPIP9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:154661"
                     /db_xref="HGNC:30286"
                     /db_xref="HPRD:15274"
     mRNA            join(87257729..87258261,87280138..87280253,
                     87323224..87323274,87329737..87329870,87339886..87339971,
                     87369107..87369196,87370815..87370895,87399897..87400065,
                     87407114..87407271,87436688..87436834,87445456..87445577,
                     87459200..87461613)
                     /gene="RUNDC3B"
                     /gene_synonym="FLJ30671; MGC26655; RPIB9; RPIP9"
                     /product="RUN domain containing 3B, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138290.2"
                     /db_xref="GI:197304742"
                     /db_xref="GeneID:154661"
                     /db_xref="HGNC:30286"
                     /db_xref="HPRD:15274"
     mRNA            join(87257729..87258261,87280138..87280253,
                     87329737..87329870,87339886..87339971,87369107..87369196,
                     87370815..87370895,87399897..87400065,87407114..87407271,
                     87436688..87436834,87445456..87445577,87459200..87461613)
                     /gene="RUNDC3B"
                     /gene_synonym="FLJ30671; MGC26655; RPIB9; RPIP9"
                     /product="RUN domain containing 3B, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134405.1"
                     /db_xref="GI:197304743"
                     /db_xref="GeneID:154661"
                     /db_xref="HGNC:30286"
                     /db_xref="HPRD:15274"
     mRNA            join(87257729..87258261,87280138..87280253,
                     87329737..87329870,87339886..87339971,87369107..87369196,
                     87370815..87370895,87399897..87400065,87407114..87407271,
                     87445456..87445577,87459200..87461613)
                     /gene="RUNDC3B"
                     /gene_synonym="FLJ30671; MGC26655; RPIB9; RPIP9"
                     /product="RUN domain containing 3B, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134406.1"
                     /db_xref="GI:197304745"
                     /db_xref="GeneID:154661"
                     /db_xref="HGNC:30286"
                     /db_xref="HPRD:15274"
     CDS             join(87258140..87258261,87280138..87280253,
                     87323224..87323274,87329737..87329870,87339886..87339971,
                     87369107..87369196,87370815..87370895,87399897..87400065,
                     87407114..87407271,87436688..87436834,87445456..87445577,
                     87459200..87459345)
                     /gene="RUNDC3B"
                     /gene_synonym="FLJ30671; MGC26655; RPIB9; RPIP9"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="RUN domain-containing protein 3B isoform a"
                     /protein_id="NP_612147.1"
                     /db_xref="GI:19923090"
                     /db_xref="CCDS:CCDS5609.1"
                     /db_xref="GeneID:154661"
                     /db_xref="HGNC:30286"
                     /db_xref="HPRD:15274"
     CDS             join(87258140..87258261,87280138..87280253,
                     87329737..87329870,87339886..87339971,87369107..87369196,
                     87370815..87370895,87399897..87400065,87407114..87407271,
                     87436688..87436834,87445456..87445577,87459200..87459345)
                     /gene="RUNDC3B"
                     /gene_synonym="FLJ30671; MGC26655; RPIB9; RPIP9"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="RUN domain-containing protein 3B isoform b"
                     /protein_id="NP_001127877.1"
                     /db_xref="GI:197304744"
                     /db_xref="CCDS:CCDS47635.1"
                     /db_xref="GeneID:154661"
                     /db_xref="HGNC:30286"
                     /db_xref="HPRD:15274"
     CDS             join(87258140..87258261,87280138..87280253,
                     87329737..87329870,87339886..87339971,87369107..87369196,
                     87370815..87370895,87399897..87400065,87407114..87407271,
                     87445456..87445577,87459200..87459345)
                     /gene="RUNDC3B"
                     /gene_synonym="FLJ30671; MGC26655; RPIB9; RPIP9"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="RUN domain-containing protein 3B isoform c"
                     /protein_id="NP_001127878.1"
                     /db_xref="GI:197304746"
                     /db_xref="CCDS:CCDS47636.1"
                     /db_xref="GeneID:154661"
                     /db_xref="HGNC:30286"
                     /db_xref="HPRD:15274"
     gene            complement(87463814..87505692)
                     /gene="SLC25A40"
                     /gene_synonym="MCFP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55972"
                     /db_xref="HGNC:29680"
                     /db_xref="HPRD:14372"
                     /db_xref="MIM:610821"
     mRNA            complement(join(87463814..87465676,87466045..87466125,
                     87470948..87471029,87473069..87473178,87476264..87476437,
                     87477168..87477292,87479196..87479263,87483519..87483625,
                     87485607..87485666,87487946..87488066,87489887..87489955,
                     87505411..87505692))
                     /gene="SLC25A40"
                     /gene_synonym="MCFP"
                     /product="solute carrier family 25, member 40"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018843.3"
                     /db_xref="GI:301601645"
                     /db_xref="GeneID:55972"
                     /db_xref="HGNC:29680"
                     /db_xref="HPRD:14372"
                     /db_xref="MIM:610821"
     CDS             complement(join(87465564..87465676,87466045..87466125,
                     87470948..87471029,87473069..87473178,87476264..87476437,
                     87477168..87477292,87479196..87479263,87483519..87483625,
                     87485607..87485666,87487946..87488042))
                     /gene="SLC25A40"
                     /gene_synonym="MCFP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="solute carrier family 25 member 40"
                     /protein_id="NP_061331.2"
                     /db_xref="GI:46094065"
                     /db_xref="CCDS:CCDS5610.1"
                     /db_xref="GeneID:55972"
                     /db_xref="HGNC:29680"
                     /db_xref="HPRD:14372"
                     /db_xref="MIM:610821"
     gene            87505544..87538856
                     /gene="DBF4"
                     /gene_synonym="ASK; CHIF; DBF4A; ZDBF1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10926"
                     /db_xref="HGNC:17364"
                     /db_xref="HPRD:10371"
                     /db_xref="MIM:604281"
     mRNA            join(87505544..87506093,87507368..87507540,
                     87514294..87514473,87516159..87516209,87516644..87516713,
                     87517298..87517374,87525789..87525825,87526609..87526654,
                     87529536..87529664,87530079..87530193,87533607..87533731,
                     87536503..87538856)
                     /gene="DBF4"
                     /gene_synonym="ASK; CHIF; DBF4A; ZDBF1"
                     /product="DBF4 homolog (S. cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006716.3"
                     /db_xref="GI:41393589"
                     /db_xref="GeneID:10926"
                     /db_xref="HGNC:17364"
                     /db_xref="HPRD:10371"
                     /db_xref="MIM:604281"
     CDS             join(87506048..87506093,87507368..87507540,
                     87514294..87514473,87516159..87516209,87516644..87516713,
                     87517298..87517374,87525789..87525825,87526609..87526654,
                     87529536..87529664,87530079..87530193,87533607..87533731,
                     87536503..87537478)
                     /gene="DBF4"
                     /gene_synonym="ASK; CHIF; DBF4A; ZDBF1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein DBF4 homolog A"
                     /protein_id="NP_006707.1"
                     /db_xref="GI:5729734"
                     /db_xref="CCDS:CCDS5611.1"
                     /db_xref="GeneID:10926"
                     /db_xref="HGNC:17364"
                     /db_xref="HPRD:10371"
                     /db_xref="MIM:604281"
     gene            87563566..87832204
                     /gene="ADAM22"
                     /gene_synonym="ADAM 22; MDC2; MGC149832"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:53616"
                     /db_xref="HGNC:201"
                     /db_xref="HPRD:04751"
                     /db_xref="MIM:603709"
     mRNA            join(87563566..87563865,87564341..87564501,
                     87607651..87607727,87704941..87705007,87737491..87737573,
                     87743899..87743962,87746060..87746129,87754904..87754974,
                     87757917..87757991,87759703..87759774,87760584..87760750,
                     87762182..87762266,87763644..87763734,87765295..87765346,
                     87772341..87772440,87774440..87774511,87774730..87774822,
                     87778292..87778372,87780296..87780346,87780572..87780635,
                     87782536..87782641,87785202..87785321,87792327..87792495,
                     87795147..87795261,87797452..87797542,87800859..87800876,
                     87808250..87808357,87810820..87810920,87811273..87811339,
                     87822431..87822554,87825786..87832204)
                     /gene="ADAM22"
                     /gene_synonym="ADAM 22; MDC2; MGC149832"
                     /product="ADAM metallopeptidase domain 22, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021723.3"
                     /db_xref="GI:315434189"
                     /db_xref="GeneID:53616"
                     /db_xref="HGNC:201"
                     /db_xref="HPRD:04751"
                     /db_xref="MIM:603709"
     mRNA            join(87563566..87563865,87564341..87564501,
                     87607651..87607727,87704941..87705007,87737491..87737573,
                     87743899..87743962,87746060..87746129,87754904..87754974,
                     87757917..87757991,87759703..87759774,87760584..87760750,
                     87762182..87762266,87763644..87763734,87765295..87765346,
                     87772341..87772440,87774440..87774511,87774730..87774822,
                     87778292..87778372,87780296..87780346,87780572..87780635,
                     87782536..87782641,87785202..87785321,87792327..87792495,
                     87795147..87795261,87797452..87797542,87800859..87800876,
                     87810820..87810920,87811273..87811339,87815930..87816016,
                     87822431..87822554,87825786..87832204)
                     /gene="ADAM22"
                     /gene_synonym="ADAM 22; MDC2; MGC149832"
                     /product="ADAM metallopeptidase domain 22, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021722.4"
                     /db_xref="GI:315434190"
                     /db_xref="GeneID:53616"
                     /db_xref="HGNC:201"
                     /db_xref="HPRD:04751"
                     /db_xref="MIM:603709"
     mRNA            join(87563566..87563865,87564341..87564501,
                     87607651..87607727,87704941..87705007,87737491..87737573,
                     87743899..87743962,87746060..87746129,87754904..87754974,
                     87757917..87757991,87759703..87759774,87760584..87760750,
                     87762182..87762266,87763644..87763734,87765295..87765346,
                     87772341..87772440,87774440..87774511,87774730..87774822,
                     87778292..87778372,87780296..87780346,87780572..87780635,
                     87782536..87782641,87785202..87785321,87792327..87792495,
                     87795147..87795261,87797452..87797542,87800859..87800876,
                     87810820..87810920,87811273..87811339,87822431..87822554,
                     87825786..87832204)
                     /gene="ADAM22"
                     /gene_synonym="ADAM 22; MDC2; MGC149832"
                     /product="ADAM metallopeptidase domain 22, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016351.4"
                     /db_xref="GI:315434192"
                     /db_xref="GeneID:53616"
                     /db_xref="HGNC:201"
                     /db_xref="HPRD:04751"
                     /db_xref="MIM:603709"
     mRNA            join(87563566..87563865,87564341..87564501,
                     87607651..87607727,87704941..87705007,87737491..87737573,
                     87743899..87743962,87746060..87746129,87754904..87754974,
                     87757917..87757991,87759703..87759774,87760584..87760750,
                     87762182..87762266,87763644..87763734,87765295..87765346,
                     87772341..87772440,87774440..87774511,87774730..87774822,
                     87778292..87778372,87780296..87780346,87780572..87780635,
                     87782536..87782641,87785202..87785321,87792327..87792495,
                     87795147..87795261,87797452..87797542,87800859..87800876,
                     87808250..87808357,87810820..87810920,87811273..87811428)
                     /gene="ADAM22"
                     /gene_synonym="ADAM 22; MDC2; MGC149832"
                     /product="ADAM metallopeptidase domain 22, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004194.3"
                     /db_xref="GI:315434193"
                     /db_xref="GeneID:53616"
                     /db_xref="HGNC:201"
                     /db_xref="HPRD:04751"
                     /db_xref="MIM:603709"
     mRNA            join(87563566..87563865,87564341..87564501,
                     87607651..87607727,87704941..87705007,87737491..87737573,
                     87743899..87743962,87746060..87746129,87754904..87754974,
                     87757917..87757991,87759703..87759774,87760584..87760750,
                     87762182..87762266,87763644..87763734,87765295..87765346,
                     87772341..87772440,87774440..87774511,87774730..87774822,
                     87778292..87778372,87780296..87780346,87780572..87780635,
                     87782536..87782641,87785202..87785321,87792327..87792495,
                     87795147..87795261,87797452..87797542,87800859..87800876,
                     87810820..87810920,87811273..87811428)
                     /gene="ADAM22"
                     /gene_synonym="ADAM 22; MDC2; MGC149832"
                     /product="ADAM metallopeptidase domain 22, transcript
                     variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021721.3"
                     /db_xref="GI:315434191"
                     /db_xref="GeneID:53616"
                     /db_xref="HGNC:201"
                     /db_xref="HPRD:04751"
                     /db_xref="MIM:603709"
     CDS             join(87563781..87563865,87564341..87564501,
                     87607651..87607727,87704941..87705007,87737491..87737573,
                     87743899..87743962,87746060..87746129,87754904..87754974,
                     87757917..87757991,87759703..87759774,87760584..87760750,
                     87762182..87762266,87763644..87763734,87765295..87765346,
                     87772341..87772440,87774440..87774511,87774730..87774822,
                     87778292..87778372,87780296..87780346,87780572..87780635,
                     87782536..87782641,87785202..87785321,87792327..87792495,
                     87795147..87795261,87797452..87797542,87800859..87800876,
                     87808250..87808357,87810820..87810920,87811273..87811339,
                     87822431..87822554,87825786..87825806)
                     /gene="ADAM22"
                     /gene_synonym="ADAM 22; MDC2; MGC149832"
                     /note="isoform 1 preproprotein is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="disintegrin and metalloproteinase
                     domain-containing protein 22 isoform 1 preproprotein"
                     /protein_id="NP_068369.1"
                     /db_xref="GI:11497047"
                     /db_xref="CCDS:CCDS47637.1"
                     /db_xref="GeneID:53616"
                     /db_xref="HGNC:201"
                     /db_xref="HPRD:04751"
                     /db_xref="MIM:603709"
     CDS             join(87563781..87563865,87564341..87564501,
                     87607651..87607727,87704941..87705007,87737491..87737573,
                     87743899..87743962,87746060..87746129,87754904..87754974,
                     87757917..87757991,87759703..87759774,87760584..87760750,
                     87762182..87762266,87763644..87763734,87765295..87765346,
                     87772341..87772440,87774440..87774511,87774730..87774822,
                     87778292..87778372,87780296..87780346,87780572..87780635,
                     87782536..87782641,87785202..87785321,87792327..87792495,
                     87795147..87795261,87797452..87797542,87800859..87800876,
                     87810820..87810920,87811273..87811339,87815930..87816016,
                     87822431..87822554,87825786..87825806)
                     /gene="ADAM22"
                     /gene_synonym="ADAM 22; MDC2; MGC149832"
                     /note="isoform 2 preproprotein is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="disintegrin and metalloproteinase
                     domain-containing protein 22 isoform 2 preproprotein"
                     /protein_id="NP_068368.2"
                     /db_xref="GI:21536386"
                     /db_xref="CCDS:CCDS43608.1"
                     /db_xref="GeneID:53616"
                     /db_xref="HGNC:201"
                     /db_xref="HPRD:04751"
                     /db_xref="MIM:603709"
     CDS             join(87563781..87563865,87564341..87564501,
                     87607651..87607727,87704941..87705007,87737491..87737573,
                     87743899..87743962,87746060..87746129,87754904..87754974,
                     87757917..87757991,87759703..87759774,87760584..87760750,
                     87762182..87762266,87763644..87763734,87765295..87765346,
                     87772341..87772440,87774440..87774511,87774730..87774822,
                     87778292..87778372,87780296..87780346,87780572..87780635,
                     87782536..87782641,87785202..87785321,87792327..87792495,
                     87795147..87795261,87797452..87797542,87800859..87800876,
                     87810820..87810920,87811273..87811339,87822431..87822554,
                     87825786..87825806)
                     /gene="ADAM22"
                     /gene_synonym="ADAM 22; MDC2; MGC149832"
                     /note="isoform 3 preproprotein is encoded by transcript
                     variant 3; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="disintegrin and metalloproteinase
                     domain-containing protein 22 isoform 3 preproprotein"
                     /protein_id="NP_057435.2"
                     /db_xref="GI:21536383"
                     /db_xref="CCDS:CCDS43609.1"
                     /db_xref="GeneID:53616"
                     /db_xref="HGNC:201"
                     /db_xref="HPRD:04751"
                     /db_xref="MIM:603709"
     CDS             join(87563781..87563865,87564341..87564501,
                     87607651..87607727,87704941..87705007,87737491..87737573,
                     87743899..87743962,87746060..87746129,87754904..87754974,
                     87757917..87757991,87759703..87759774,87760584..87760750,
                     87762182..87762266,87763644..87763734,87765295..87765346,
                     87772341..87772440,87774440..87774511,87774730..87774822,
                     87778292..87778372,87780296..87780346,87780572..87780635,
                     87782536..87782641,87785202..87785321,87792327..87792495,
                     87795147..87795261,87797452..87797542,87800859..87800876,
                     87808250..87808357,87810820..87810920,87811273..87811343)
                     /gene="ADAM22"
                     /gene_synonym="ADAM 22; MDC2; MGC149832"
                     /note="isoform 4 preproprotein is encoded by transcript
                     variant 4; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="disintegrin and metalloproteinase
                     domain-containing protein 22 isoform 4 preproprotein"
                     /protein_id="NP_004185.1"
                     /db_xref="GI:4757722"
                     /db_xref="CCDS:CCDS43610.1"
                     /db_xref="GeneID:53616"
                     /db_xref="HGNC:201"
                     /db_xref="HPRD:04751"
                     /db_xref="MIM:603709"
     CDS             join(87563781..87563865,87564341..87564501,
                     87607651..87607727,87704941..87705007,87737491..87737573,
                     87743899..87743962,87746060..87746129,87754904..87754974,
                     87757917..87757991,87759703..87759774,87760584..87760750,
                     87762182..87762266,87763644..87763734,87765295..87765346,
                     87772341..87772440,87774440..87774511,87774730..87774822,
                     87778292..87778372,87780296..87780346,87780572..87780635,
                     87782536..87782641,87785202..87785321,87792327..87792495,
                     87795147..87795261,87797452..87797542,87800859..87800876,
                     87810820..87810920,87811273..87811343)
                     /gene="ADAM22"
                     /gene_synonym="ADAM 22; MDC2; MGC149832"
                     /note="isoform 5 preproprotein is encoded by transcript
                     variant 5; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="disintegrin and metalloproteinase
                     domain-containing protein 22 isoform 5 preproprotein"
                     /protein_id="NP_068367.1"
                     /db_xref="GI:11497043"
                     /db_xref="GeneID:53616"
                     /db_xref="HGNC:201"
                     /db_xref="HPRD:04751"
                     /db_xref="MIM:603709"
     gene            complement(87834432..87856308)
                     /gene="SRI"
                     /gene_synonym="CP22; FLJ26259; SCN"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6717"
                     /db_xref="HGNC:11292"
                     /db_xref="HPRD:01680"
                     /db_xref="MIM:182520"
     mRNA            complement(join(87834432..87835819,87837822..87837880,
                     87838654..87838767,87839298..87839445,87840197..87840240,
                     87846437..87846506,87848174..87848257,87856224..87856308))
                     /gene="SRI"
                     /gene_synonym="CP22; FLJ26259; SCN"
                     /product="sorcin, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198901.1"
                     /db_xref="GI:38679883"
                     /db_xref="GeneID:6717"
                     /db_xref="HGNC:11292"
                     /db_xref="HPRD:01680"
                     /db_xref="MIM:182520"
     mRNA            complement(join(87834432..87835819,87837822..87837880,
                     87838654..87838767,87839298..87839445,87840197..87840240,
                     87846437..87846506,87848174..87848257,87849291..87849393))
                     /gene="SRI"
                     /gene_synonym="CP22; FLJ26259; SCN"
                     /product="sorcin, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003130.2"
                     /db_xref="GI:38679886"
                     /db_xref="GeneID:6717"
                     /db_xref="HGNC:11292"
                     /db_xref="HPRD:01680"
                     /db_xref="MIM:182520"
     CDS             complement(join(87835793..87835819,87837822..87837880,
                     87838654..87838767,87839298..87839445,87840197..87840240,
                     87846437..87846506,87848174..87848257,87856224..87856229))
                     /gene="SRI"
                     /gene_synonym="CP22; FLJ26259; SCN"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="sorcin isoform b"
                     /protein_id="NP_944490.1"
                     /db_xref="GI:38679884"
                     /db_xref="CCDS:CCDS47638.1"
                     /db_xref="GeneID:6717"
                     /db_xref="HGNC:11292"
                     /db_xref="HPRD:01680"
                     /db_xref="MIM:182520"
     CDS             complement(join(87835793..87835819,87837822..87837880,
                     87838654..87838767,87839298..87839445,87840197..87840240,
                     87846437..87846506,87848174..87848257,87849291..87849341))
                     /gene="SRI"
                     /gene_synonym="CP22; FLJ26259; SCN"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="sorcin isoform a"
                     /protein_id="NP_003121.1"
                     /db_xref="GI:4507207"
                     /db_xref="CCDS:CCDS5612.1"
                     /db_xref="GeneID:6717"
                     /db_xref="HGNC:11292"
                     /db_xref="HPRD:01680"
                     /db_xref="MIM:182520"
     gene            complement(87905744..87936228)
                     /gene="STEAP4"
                     /gene_synonym="DKFZp666D049; FLJ23153; STAMP2; TIARP;
                     TNFAIP9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79689"
                     /db_xref="HGNC:21923"
                     /db_xref="HPRD:11637"
                     /db_xref="MIM:611098"
     mRNA            complement(join(87905744..87908943,87910230..87910394,
                     87911956..87912483,87913129..87913586,87936107..87936228))
                     /gene="STEAP4"
                     /gene_synonym="DKFZp666D049; FLJ23153; STAMP2; TIARP;
                     TNFAIP9"
                     /product="STEAP family member 4, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024636.3"
                     /db_xref="GI:328887947"
                     /db_xref="GeneID:79689"
                     /db_xref="HGNC:21923"
                     /db_xref="HPRD:11637"
                     /db_xref="MIM:611098"
     mRNA            complement(join(87905744..87908943,87910230..87910394,
                     87911956..87912483,87913129..87913586,87920231..87920329,
                     87936107..87936228))
                     /gene="STEAP4"
                     /gene_synonym="DKFZp666D049; FLJ23153; STAMP2; TIARP;
                     TNFAIP9"
                     /product="STEAP family member 4, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001205315.1"
                     /db_xref="GI:328887948"
                     /db_xref="GeneID:79689"
                     /db_xref="HGNC:21923"
                     /db_xref="MIM:611098"
                     /db_xref="HPRD:11637"
     mRNA            complement(join(87905744..87908943,87910230..87910394,
                     87913129..87913586,87936107..87936228))
                     /gene="STEAP4"
                     /gene_synonym="DKFZp666D049; FLJ23153; STAMP2; TIARP;
                     TNFAIP9"
                     /product="STEAP family member 4, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001205316.1"
                     /db_xref="GI:328887950"
                     /db_xref="GeneID:79689"
                     /db_xref="HGNC:21923"
                     /db_xref="MIM:611098"
                     /db_xref="HPRD:11637"
     CDS             complement(join(87908713..87908943,87910230..87910394,
                     87911956..87912483,87913129..87913584))
                     /gene="STEAP4"
                     /gene_synonym="DKFZp666D049; FLJ23153; STAMP2; TIARP;
                     TNFAIP9"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="metalloreductase STEAP4 isoform 1"
                     /protein_id="NP_078912.2"
                     /db_xref="GI:100815815"
                     /db_xref="CCDS:CCDS43611.1"
                     /db_xref="GeneID:79689"
                     /db_xref="HGNC:21923"
                     /db_xref="HPRD:11637"
                     /db_xref="MIM:611098"
     CDS             complement(join(87908713..87908943,87910230..87910394,
                     87911956..87912483,87913129..87913584))
                     /gene="STEAP4"
                     /gene_synonym="DKFZp666D049; FLJ23153; STAMP2; TIARP;
                     TNFAIP9"
                     /note="isoform 1 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="metalloreductase STEAP4 isoform 1"
                     /protein_id="NP_001192244.1"
                     /db_xref="GI:328887949"
                     /db_xref="GeneID:79689"
                     /db_xref="HGNC:21923"
                     /db_xref="MIM:611098"
                     /db_xref="HPRD:11637"
     CDS             complement(join(87908713..87908943,87910230..87910394,
                     87913129..87913584))
                     /gene="STEAP4"
                     /gene_synonym="DKFZp666D049; FLJ23153; STAMP2; TIARP;
                     TNFAIP9"
                     /note="isoform 2 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="metalloreductase STEAP4 isoform 2"
                     /protein_id="NP_001192245.1"
                     /db_xref="GI:328887951"
                     /db_xref="GeneID:79689"
                     /db_xref="HGNC:21923"
                     /db_xref="MIM:611098"
                     /db_xref="HPRD:11637"
     gene            complement(88078103..88078341)
                     /gene="EIF4A1P13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100462826"
                     /db_xref="HGNC:37934"
     gene            complement(88141344..88142502)
                     /gene="LOC100419447"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419447"
     gene            complement(88142819..88143064)
                     /gene="LOC100128464"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100128464"
     exon            complement(88142819..88143064)
                     /gene="LOC100128464"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100128464"
     gene            complement(88193833..88195721)
                     /gene="LOC645680"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:645680"
     gene            88268266..88269936
                     /gene="EEF1A1P28"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442709"
                     /db_xref="HGNC:37902"
     gene            88388753..88966346
                     /gene="ZNF804B"
                     /gene_synonym="FLJ32110"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:219578"
                     /db_xref="HGNC:21958"
                     /db_xref="HPRD:08721"
     mRNA            join(88388753..88389398,88847469..88847609,
                     88956658..88956788,88962677..88966346)
                     /gene="ZNF804B"
                     /gene_synonym="FLJ32110"
                     /product="zinc finger protein 804B"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_181646.2"
                     /db_xref="GI:37202115"
                     /db_xref="GeneID:219578"
                     /db_xref="HGNC:21958"
                     /db_xref="HPRD:08721"
     CDS             join(88389291..88389398,88847469..88847609,
                     88956658..88956788,88962677..88966346)
                     /gene="ZNF804B"
                     /gene_synonym="FLJ32110"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 804B"
                     /protein_id="NP_857597.1"
                     /db_xref="GI:31791053"
                     /db_xref="CCDS:CCDS5613.1"
                     /db_xref="GeneID:219578"
                     /db_xref="HGNC:21958"
                     /db_xref="HPRD:08721"
     gene            complement(88423420..88425031)
                     /gene="C7orf62"
                     /gene_synonym="MGC26647"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:219557"
                     /db_xref="HGNC:22402"
                     /db_xref="HPRD:14507"
     mRNA            complement(join(88423420..88424360,88424954..88425031))
                     /gene="C7orf62"
                     /gene_synonym="MGC26647"
                     /product="chromosome 7 open reading frame 62"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152706.2"
                     /db_xref="GI:34303950"
                     /db_xref="GeneID:219557"
                     /db_xref="HGNC:22402"
                     /db_xref="HPRD:14507"
     CDS             complement(88423495..88424256)
                     /gene="C7orf62"
                     /gene_synonym="MGC26647"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC219557"
                     /protein_id="NP_689919.1"
                     /db_xref="GI:22749409"
                     /db_xref="CCDS:CCDS34678.1"
                     /db_xref="GeneID:219557"
                     /db_xref="HGNC:22402"
                     /db_xref="HPRD:14507"
     gene            89748714..89754914
                     /gene="DPY19L2P4"
                     /gene_synonym="DKFZp686L2199; FLJ25893; MGC39769;
                     MGC48509"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:442523"
                     /db_xref="HGNC:22176"
     misc_RNA        join(89748714..89749179,89751381..89751405,
                     89753388..89754914)
                     /gene="DPY19L2P4"
                     /gene_synonym="DKFZp686L2199; FLJ25893; MGC39769;
                     MGC48509"
                     /product="dpy-19-like 2 pseudogene 4 (C. elegans)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003551.1"
                     /db_xref="GI:148237621"
                     /db_xref="GeneID:442523"
                     /db_xref="HGNC:22176"
     gene            89783689..89794141
                     /gene="STEAP1"
                     /gene_synonym="MGC19484; PRSS24; STEAP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26872"
                     /db_xref="HGNC:11378"
                     /db_xref="HPRD:05106"
                     /db_xref="MIM:604415"
     mRNA            join(89783689..89783857,89789072..89789186,
                     89790119..89790631,89791228..89791392,89793791..89794141)
                     /gene="STEAP1"
                     /gene_synonym="MGC19484; PRSS24; STEAP"
                     /product="six transmembrane epithelial antigen of the
                     prostate 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012449.2"
                     /db_xref="GI:22027487"
                     /db_xref="GeneID:26872"
                     /db_xref="HGNC:11378"
                     /db_xref="HPRD:05106"
                     /db_xref="MIM:604415"
     CDS             join(89789103..89789186,89790119..89790631,
                     89791228..89791392,89793791..89794048)
                     /gene="STEAP1"
                     /gene_synonym="MGC19484; PRSS24; STEAP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="metalloreductase STEAP1"
                     /protein_id="NP_036581.1"
                     /db_xref="GI:9558759"
                     /db_xref="CCDS:CCDS5614.1"
                     /db_xref="GeneID:26872"
                     /db_xref="HGNC:11378"
                     /db_xref="HPRD:05106"
                     /db_xref="MIM:604415"
     gene            89841000..89866992
                     /gene="STEAP2"
                     /gene_synonym="IPCA1; PCANAP1; PUMPCn; STAMP1; STMP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:261729"
                     /db_xref="HGNC:17885"
                     /db_xref="MIM:605094"
     mRNA            join(89841000..89841359,89854364..89854888,
                     89856285..89856812,89859186..89859350,89861651..89866992)
                     /gene="STEAP2"
                     /gene_synonym="IPCA1; PCANAP1; PUMPCn; STAMP1; STMP"
                     /product="six transmembrane epithelial antigen of the
                     prostate 2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152999.3"
                     /db_xref="GI:100913195"
                     /db_xref="GeneID:261729"
                     /db_xref="HGNC:17885"
                     /db_xref="HPRD:05481"
                     /db_xref="MIM:605094"
     mRNA            join(89841174..89841248,89841590..89841650,
                     89854364..89854888,89856285..89856812,89859186..89859350,
                     89861651..89866992)
                     /gene="STEAP2"
                     /gene_synonym="IPCA1; PCANAP1; PUMPCn; STAMP1; STMP"
                     /product="six transmembrane epithelial antigen of the
                     prostate 2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040665.1"
                     /db_xref="GI:100913193"
                     /db_xref="GeneID:261729"
                     /db_xref="HGNC:17885"
                     /db_xref="MIM:605094"
     mRNA            join(89843134..89843174,89845805..89845917,
                     89854364..89854888,89856285..89856812,89859186..89859350,
                     89861651..89861798,89866205..89866992)
                     /gene="STEAP2"
                     /gene_synonym="IPCA1; PCANAP1; PUMPCn; STAMP1; STMP"
                     /product="six transmembrane epithelial antigen of the
                     prostate 2, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040666.1"
                     /db_xref="GI:100913197"
                     /db_xref="GeneID:261729"
                     /db_xref="HGNC:17885"
                     /db_xref="MIM:605094"
     CDS             join(89854397..89854888,89856285..89856812,
                     89859186..89859350,89861651..89861798,89866205..89866236)
                     /gene="STEAP2"
                     /gene_synonym="IPCA1; PCANAP1; PUMPCn; STAMP1; STMP"
                     /note="isoform b is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="metalloreductase STEAP2 isoform b"
                     /protein_id="NP_001035756.1"
                     /db_xref="GI:100913198"
                     /db_xref="CCDS:CCDS43612.1"
                     /db_xref="GeneID:261729"
                     /db_xref="HGNC:17885"
                     /db_xref="MIM:605094"
     CDS             join(89854397..89854888,89856285..89856812,
                     89859186..89859350,89861651..89861938)
                     /gene="STEAP2"
                     /gene_synonym="IPCA1; PCANAP1; PUMPCn; STAMP1; STMP"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="metalloreductase STEAP2 isoform a"
                     /protein_id="NP_694544.2"
                     /db_xref="GI:100913196"
                     /db_xref="CCDS:CCDS5615.1"
                     /db_xref="GeneID:261729"
                     /db_xref="HGNC:17885"
                     /db_xref="MIM:605094"
     CDS             join(89854397..89854888,89856285..89856812,
                     89859186..89859350,89861651..89861938)
                     /gene="STEAP2"
                     /gene_synonym="IPCA1; PCANAP1; PUMPCn; STAMP1; STMP"
                     /note="isoform a is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="metalloreductase STEAP2 isoform a"
                     /protein_id="NP_001035755.1"
                     /db_xref="GI:100913194"
                     /db_xref="CCDS:CCDS5615.1"
                     /db_xref="GeneID:261729"
                     /db_xref="HGNC:17885"
                     /db_xref="MIM:605094"
     gene            89874488..89940377
                     /gene="C7orf63"
                     /gene_synonym="FLJ21062"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79846"
                     /db_xref="HGNC:26107"
     mRNA            join(89874488..89874858,89884737..89884796,
                     89887412..89887477,89891261..89891370,89894615..89894691,
                     89897600..89897698,89900840..89900989,89901095..89901272,
                     89903301..89903424,89906387..89906435,89906527..89906648,
                     89908991..89909207,89912206..89912370,89915595..89915713,
                     89917548..89917666,89927063..89927144,89929181..89929373,
                     89933283..89933420,89934058..89934134,89936215..89936412,
                     89937082..89937168,89938577..89938681,89939382..89940377)
                     /gene="C7orf63"
                     /gene_synonym="FLJ21062"
                     /product="chromosome 7 open reading frame 63, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001039706.2"
                     /db_xref="GI:236463163"
                     /db_xref="GeneID:79846"
                     /db_xref="HGNC:26107"
     mRNA            join(89874488..89874858,89884737..89884796,
                     89887412..89887477,89891261..89891370,89894615..89894691,
                     89897600..89897644,89900840..89900989,89901095..89901272,
                     89903301..89903424,89906387..89906435,89906527..89906648,
                     89908991..89909207,89912206..89912370,89915595..89915713,
                     89917548..89917666,89927063..89927144,89929181..89929373,
                     89933283..89933420,89934058..89934134,89936215..89936412,
                     89937082..89937168,89938577..89938681,89939382..89940377)
                     /gene="C7orf63"
                     /gene_synonym="FLJ21062"
                     /product="chromosome 7 open reading frame 63, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001160138.1"
                     /db_xref="GI:236463299"
                     /db_xref="GeneID:79846"
                     /db_xref="HGNC:26107"
     CDS             join(89874739..89874858,89884737..89884796,
                     89887412..89887477,89891261..89891370,89894615..89894691,
                     89897600..89897698,89900840..89900989,89901095..89901272,
                     89903301..89903424,89906387..89906435,89906527..89906648,
                     89908991..89909207,89912206..89912370,89915595..89915713,
                     89917548..89917666,89927063..89927144,89929181..89929373,
                     89933283..89933420,89934058..89934134,89936215..89936412,
                     89937082..89937168,89938577..89938681,89939382..89939552)
                     /gene="C7orf63"
                     /gene_synonym="FLJ21062"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC79846 isoform 1"
                     /protein_id="NP_001034795.2"
                     /db_xref="GI:236463164"
                     /db_xref="CCDS:CCDS43613.2"
                     /db_xref="GeneID:79846"
                     /db_xref="HGNC:26107"
     CDS             join(89874739..89874858,89884737..89884796,
                     89887412..89887477,89891261..89891370,89894615..89894691,
                     89897600..89897644,89900840..89900989,89901095..89901272,
                     89903301..89903424,89906387..89906435,89906527..89906648,
                     89908991..89909207,89912206..89912370,89915595..89915713,
                     89917548..89917666,89927063..89927144,89929181..89929373,
                     89933283..89933420,89934058..89934134,89936215..89936412,
                     89937082..89937168,89938577..89938681,89939382..89939552)
                     /gene="C7orf63"
                     /gene_synonym="FLJ21062"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC79846 isoform 2"
                     /protein_id="NP_001153610.1"
                     /db_xref="GI:236463300"
                     /db_xref="CCDS:CCDS55122.1"
                     /db_xref="GeneID:79846"
                     /db_xref="HGNC:26107"
     gene            89975979..90020769
                     /gene="GTPBP10"
                     /gene_synonym="DKFZp686A10121; FLJ38242; MGC104191; ObgH2;
                     UG0751c10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:85865"
                     /db_xref="HGNC:25106"
                     /db_xref="MIM:610920"
     mRNA            join(89975979..89976088,89982130..89982323,
                     90001469..90001542,90003616..90003668,90006821..90006928,
                     90007448..90007525,90012270..90012393,90014206..90020769)
                     /gene="GTPBP10"
                     /gene_synonym="DKFZp686A10121; FLJ38242; MGC104191; ObgH2;
                     UG0751c10"
                     /product="GTP-binding protein 10 (putative), transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001042717.2"
                     /db_xref="GI:313760599"
                     /db_xref="GeneID:85865"
                     /db_xref="HGNC:25106"
                     /db_xref="MIM:610920"
     mRNA            join(89975979..89976088,89982130..89982323,
                     89983772..89983863,89984400..89984544,90001469..90001542,
                     90003616..90003668,90006821..90006928,90007448..90007525,
                     90012270..90012393,90014206..90020769)
                     /gene="GTPBP10"
                     /gene_synonym="DKFZp686A10121; FLJ38242; MGC104191; ObgH2;
                     UG0751c10"
                     /product="GTP-binding protein 10 (putative), transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033107.3"
                     /db_xref="GI:313760600"
                     /db_xref="GeneID:85865"
                     /db_xref="HGNC:25106"
                     /db_xref="HPRD:14262"
                     /db_xref="MIM:610920"
     CDS             join(89976056..89976088,89982130..89982323,
                     90001469..90001542,90003616..90003668,90006821..90006928,
                     90007448..90007525,90012270..90012393,90014206..90014468)
                     /gene="GTPBP10"
                     /gene_synonym="DKFZp686A10121; FLJ38242; MGC104191; ObgH2;
                     UG0751c10"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="GTP-binding protein 10 isoform 1"
                     /protein_id="NP_001036182.1"
                     /db_xref="GI:111955063"
                     /db_xref="CCDS:CCDS43614.1"
                     /db_xref="GeneID:85865"
                     /db_xref="HGNC:25106"
                     /db_xref="MIM:610920"
     CDS             join(89976056..89976088,89982130..89982323,
                     89983772..89983863,89984400..89984544,90001469..90001542,
                     90003616..90003668,90006821..90006928,90007448..90007525,
                     90012270..90012393,90014206..90014468)
                     /gene="GTPBP10"
                     /gene_synonym="DKFZp686A10121; FLJ38242; MGC104191; ObgH2;
                     UG0751c10"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="GTP-binding protein 10 isoform 2"
                     /protein_id="NP_149098.2"
                     /db_xref="GI:111955139"
                     /db_xref="CCDS:CCDS5617.1"
                     /db_xref="GeneID:85865"
                     /db_xref="HGNC:25106"
                     /db_xref="MIM:610920"
     gene            90032648..90045268
                     /gene="CLDN12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9069"
                     /db_xref="HGNC:2034"
                     /db_xref="MIM:611232"
     mRNA            join(90032648..90032863,90034833..90034922,
                     90041321..90041363,90041958..90045268)
                     /gene="CLDN12"
                     /product="claudin 12, transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001185072.2"
                     /db_xref="GI:313760613"
                     /db_xref="GeneID:9069"
                     /db_xref="HGNC:2034"
                     /db_xref="MIM:611232"
     mRNA            join(90032648..90032863,90034833..90034926,
                     90041958..90045268)
                     /gene="CLDN12"
                     /product="claudin 12, transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001185073.2"
                     /db_xref="GI:313760614"
                     /db_xref="GeneID:9069"
                     /db_xref="HGNC:2034"
                     /db_xref="MIM:611232"
     mRNA            join(90032648..90032863,90034833..90034922,
                     90041958..90045268)
                     /gene="CLDN12"
                     /product="claudin 12, transcript variant 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012129.4"
                     /db_xref="GI:313851094"
                     /db_xref="GeneID:9069"
                     /db_xref="HGNC:2034"
                     /db_xref="HPRD:13064"
                     /db_xref="MIM:611232"
     CDS             90041991..90042725
                     /gene="CLDN12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="claudin-12"
                     /protein_id="NP_001172001.1"
                     /db_xref="GI:297374758"
                     /db_xref="CCDS:CCDS5618.1"
                     /db_xref="GeneID:9069"
                     /db_xref="HGNC:2034"
                     /db_xref="MIM:611232"
     CDS             90041991..90042725
                     /gene="CLDN12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="claudin-12"
                     /protein_id="NP_001172002.1"
                     /db_xref="GI:297374760"
                     /db_xref="CCDS:CCDS5618.1"
                     /db_xref="GeneID:9069"
                     /db_xref="HGNC:2034"
                     /db_xref="MIM:611232"
     CDS             90041991..90042725
                     /gene="CLDN12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="claudin-12"
                     /protein_id="NP_036261.1"
                     /db_xref="GI:6912312"
                     /db_xref="CCDS:CCDS5618.1"
                     /db_xref="GeneID:9069"
                     /db_xref="HGNC:2034"
                     /db_xref="MIM:611232"
     gene            complement(90219937..90226630)
                     /gene="LOC100507508"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 7 ESTs"
                     /db_xref="GeneID:100507508"
     mRNA            complement(join(90219937..90220042,90221030..90221215,
                     90225047..90225742,90225806..90226171,90226511..90226630))
                     /gene="LOC100507508"
                     /product="hypothetical protein LOC100507508"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 7 ESTs"
                     /transcript_id="XM_003118581.1"
                     /db_xref="GI:310120026"
                     /db_xref="GeneID:100507508"
     CDS             complement(join(90221117..90221215,90225047..90225742,
                     90225806..90226171,90226511..90226630))
                     /gene="LOC100507508"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="hypothetical protein LOC100507508"
                     /protein_id="XP_003118629.1"
                     /db_xref="GI:310120027"
                     /db_xref="GeneID:100507508"
     gene            90261220..90261882
                     /gene="LOC100421599"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421599"
     gene            90338712..90839904
                     /gene="CDK14"
                     /gene_synonym="KIAA0834; PFTAIRE1; PFTK1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5218"
                     /db_xref="HGNC:8883"
                     /db_xref="HPRD:15121"
                     /db_xref="MIM:610679"
     mRNA            join(90338712..90338924,90355881..90356126,
                     90376996..90377090,90419888..90419967,90492490..90492584,
                     90528606..90528668,90546916..90547039,90585012..90585132,
                     90613463..90613556,90675212..90675275,90708747..90708795,
                     90741857..90741996,90747380..90747523,90836480..90839904)
                     /gene="CDK14"
                     /gene_synonym="KIAA0834; PFTAIRE1; PFTK1"
                     /product="cyclin-dependent kinase 14"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012395.2"
                     /db_xref="GI:32130539"
                     /db_xref="GeneID:5218"
                     /db_xref="HGNC:8883"
                     /db_xref="HPRD:15121"
                     /db_xref="MIM:610679"
     CDS             join(90338856..90338924,90355881..90356126,
                     90376996..90377090,90419888..90419967,90492490..90492584,
                     90528606..90528668,90546916..90547039,90585012..90585132,
                     90613463..90613556,90675212..90675275,90708747..90708795,
                     90741857..90741996,90747380..90747495)
                     /gene="CDK14"
                     /gene_synonym="KIAA0834; PFTAIRE1; PFTK1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclin-dependent kinase 14"
                     /protein_id="NP_036527.1"
                     /db_xref="GI:6912584"
                     /db_xref="CCDS:CCDS5619.1"
                     /db_xref="GeneID:5218"
                     /db_xref="HGNC:8883"
                     /db_xref="HPRD:15121"
                     /db_xref="MIM:610679"
     gene            90893783..90898132
                     /gene="FZD1"
                     /gene_synonym="DKFZp564G072; FLJ95923"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8321"
                     /db_xref="HGNC:4038"
                     /db_xref="HPRD:04558"
                     /db_xref="MIM:603408"
     mRNA            90893783..90898132
                     /gene="FZD1"
                     /gene_synonym="DKFZp564G072; FLJ95923"
                     /product="frizzled family receptor 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003505.1"
                     /db_xref="GI:4503824"
                     /db_xref="GeneID:8321"
                     /db_xref="HGNC:4038"
                     /db_xref="HPRD:04558"
                     /db_xref="MIM:603408"
     CDS             90894196..90896139
                     /gene="FZD1"
                     /gene_synonym="DKFZp564G072; FLJ95923"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="frizzled-1 precursor"
                     /protein_id="NP_003496.1"
                     /db_xref="GI:4503825"
                     /db_xref="CCDS:CCDS5620.1"
                     /db_xref="GeneID:8321"
                     /db_xref="HGNC:4038"
                     /db_xref="HPRD:04558"
                     /db_xref="MIM:603408"
     gene            complement(90949314..90950509)
                     /gene="NIPA2P1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100132321"
                     /db_xref="HGNC:42041"
     gene            complement(91502021..91510016)
                     /gene="MTERF"
                     /gene_synonym="MGC131634"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7978"
                     /db_xref="HGNC:21463"
                     /db_xref="HPRD:08373"
                     /db_xref="MIM:602318"
     mRNA            complement(join(91502021..91504078,91509369..91509427,
                     91509971..91510016))
                     /gene="MTERF"
                     /gene_synonym="MGC131634"
                     /product="mitochondrial transcription termination factor"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006980.3"
                     /db_xref="GI:68448540"
                     /db_xref="GeneID:7978"
                     /db_xref="HGNC:21463"
                     /db_xref="HPRD:08373"
                     /db_xref="MIM:602318"
     CDS             complement(join(91502908..91504078,91509369..91509397))
                     /gene="MTERF"
                     /gene_synonym="MGC131634"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transcription termination factor, mitochondrial
                     precursor"
                     /protein_id="NP_008911.1"
                     /db_xref="GI:5902010"
                     /db_xref="CCDS:CCDS5621.1"
                     /db_xref="GeneID:7978"
                     /db_xref="HGNC:21463"
                     /db_xref="HPRD:08373"
                     /db_xref="MIM:602318"
     gene            91570189..91739987
                     /gene="AKAP9"
                     /gene_synonym="AKAP-9; AKAP350; AKAP450; CG-NAP; HYPERION;
                     KIAA0803; MU-RMS-40.16A; PRKA9; YOTIAO"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10142"
                     /db_xref="HGNC:379"
                     /db_xref="HPRD:04921"
                     /db_xref="MIM:604001"
     mRNA            join(91570189..91570461,91603025..91603282,
                     91609603..91609647,91621472..91621525,91622199..91622369,
                     91623935..91624090,91624917..91625114,91630162..91632549,
                     91641743..91641956,91643563..91643642,91645443..91645581,
                     91646331..91646416,91651552..91651666,91652128..91652323,
                     91659209..91659305,91660826..91660918,91667733..91668086,
                     91669988..91670212,91671360..91671500,91671982..91672085,
                     91674322..91674527,91682040..91682272,91690574..91690736,
                     91691588..91691800,91694545..91694777,91695741..91695860,
                     91699344..91699520,91700219..91700323,91706169..91706321,
                     91707010..91707189,91708393..91709466,91711836..91711976,
                     91712484..91712969,91713954..91714017,91714133..91714254,
                     91714809..91715000,91715542..91715730,91718699..91718843,
                     91722411..91722630,91724337..91724487,91726003..91726671,
                     91726900..91727108,91727423..91727528,91729001..91729183,
                     91730170..91730370,91731908..91732140,91734992..91735077,
                     91736607..91736736,91737808..91737947,91739436..91739987)
                     /gene="AKAP9"
                     /gene_synonym="AKAP-9; AKAP350; AKAP450; CG-NAP; HYPERION;
                     KIAA0803; MU-RMS-40.16A; PRKA9; YOTIAO"
                     /product="A kinase (PRKA) anchor protein (yotiao) 9,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005751.4"
                     /db_xref="GI:197245395"
                     /db_xref="GeneID:10142"
                     /db_xref="HGNC:379"
                     /db_xref="HPRD:04921"
                     /db_xref="MIM:604001"
     mRNA            join(91570189..91570461,91603025..91603282,
                     91609603..91609647,91621472..91621525,91622199..91622369,
                     91623935..91624090,91624917..91625114,91630162..91632549,
                     91641743..91641956,91643563..91643642,91645443..91645581,
                     91646331..91646416,91651552..91651666,91652128..91652323,
                     91659209..91659305,91660826..91660918,91667733..91668086,
                     91669988..91670212,91671360..91671500,91671982..91672085,
                     91674322..91674527,91682040..91682272,91690574..91690736,
                     91691588..91691800,91694545..91694777,91695741..91695860,
                     91699344..91699496,91700219..91700323,91706169..91706321,
                     91707010..91707189,91708393..91709466,91711836..91711976,
                     91712484..91712969,91713954..91714017,91714133..91714254,
                     91714809..91715000,91715542..91715730,91718699..91718843,
                     91722411..91722630,91724337..91724487,91726003..91726671,
                     91726900..91727108,91727423..91727528,91729001..91729183,
                     91730170..91730370,91731908..91732140,91734992..91735077,
                     91736607..91736736,91737808..91737947,91739436..91739987)
                     /gene="AKAP9"
                     /gene_synonym="AKAP-9; AKAP350; AKAP450; CG-NAP; HYPERION;
                     KIAA0803; MU-RMS-40.16A; PRKA9; YOTIAO"
                     /product="A kinase (PRKA) anchor protein (yotiao) 9,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_147185.2"
                     /db_xref="GI:197245394"
                     /db_xref="GeneID:10142"
                     /db_xref="HGNC:379"
                     /db_xref="HPRD:04921"
                     /db_xref="MIM:604001"
     CDS             join(91570414..91570461,91603025..91603282,
                     91609603..91609647,91621472..91621525,91622199..91622369,
                     91623935..91624090,91624917..91625114,91630162..91632549,
                     91641743..91641956,91643563..91643642,91645443..91645581,
                     91646331..91646416,91651552..91651666,91652128..91652323,
                     91659209..91659305,91660826..91660918,91667733..91668086,
                     91669988..91670212,91671360..91671500,91671982..91672085,
                     91674322..91674527,91682040..91682272,91690574..91690736,
                     91691588..91691800,91694545..91694777,91695741..91695860,
                     91699344..91699520,91700219..91700323,91706169..91706321,
                     91707010..91707189,91708393..91709466,91711836..91711976,
                     91712484..91712969,91713954..91714017,91714133..91714254,
                     91714809..91715000,91715542..91715730,91718699..91718843,
                     91722411..91722630,91724337..91724487,91726003..91726671,
                     91726900..91727108,91727423..91727528,91729001..91729183,
                     91730170..91730370,91731908..91732140,91734992..91735077,
                     91736607..91736736,91737808..91737947,91739436..91739473)
                     /gene="AKAP9"
                     /gene_synonym="AKAP-9; AKAP350; AKAP450; CG-NAP; HYPERION;
                     KIAA0803; MU-RMS-40.16A; PRKA9; YOTIAO"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="A-kinase anchor protein 9 isoform 2"
                     /protein_id="NP_005742.4"
                     /db_xref="GI:22538387"
                     /db_xref="CCDS:CCDS5622.1"
                     /db_xref="GeneID:10142"
                     /db_xref="HGNC:379"
                     /db_xref="HPRD:04921"
                     /db_xref="MIM:604001"
     CDS             join(91570414..91570461,91603025..91603282,
                     91609603..91609647,91621472..91621525,91622199..91622369,
                     91623935..91624090,91624917..91625114,91630162..91632549,
                     91641743..91641956,91643563..91643642,91645443..91645581,
                     91646331..91646416,91651552..91651666,91652128..91652323,
                     91659209..91659305,91660826..91660918,91667733..91668086,
                     91669988..91670212,91671360..91671500,91671982..91672085,
                     91674322..91674527,91682040..91682272,91690574..91690736,
                     91691588..91691800,91694545..91694777,91695741..91695860,
                     91699344..91699496,91700219..91700323,91706169..91706321,
                     91707010..91707189,91708393..91709466,91711836..91711976,
                     91712484..91712969,91713954..91714017,91714133..91714254,
                     91714809..91715000,91715542..91715730,91718699..91718843,
                     91722411..91722630,91724337..91724487,91726003..91726671,
                     91726900..91727108,91727423..91727528,91729001..91729183,
                     91730170..91730370,91731908..91732140,91734992..91735077,
                     91736607..91736736,91737808..91737947,91739436..91739473)
                     /gene="AKAP9"
                     /gene_synonym="AKAP-9; AKAP350; AKAP450; CG-NAP; HYPERION;
                     KIAA0803; MU-RMS-40.16A; PRKA9; YOTIAO"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="A-kinase anchor protein 9 isoform 3"
                     /protein_id="NP_671714.1"
                     /db_xref="GI:22538393"
                     /db_xref="GeneID:10142"
                     /db_xref="HGNC:379"
                     /db_xref="HPRD:04921"
                     /db_xref="MIM:604001"
     gene            complement(91741463..91764059)
                     /gene="CYP51A1"
                     /gene_synonym="CP51; CYP51; CYPL1; LDM; P450-14DM; P450L1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1595"
                     /db_xref="HGNC:2649"
                     /db_xref="HPRD:03381"
                     /db_xref="MIM:601637"
     mRNA            complement(join(91741463..91743157,91746358..91746526,
                     91747834..91747929,91752434..91752629,91753048..91753167,
                     91755567..91755741,91756819..91756945,91758194..91758370,
                     91761088..91761186,91763980..91764059))
                     /gene="CYP51A1"
                     /gene_synonym="CP51; CYP51; CYPL1; LDM; P450-14DM; P450L1"
                     /product="cytochrome P450, family 51, subfamily A,
                     polypeptide 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001146152.1"
                     /db_xref="GI:225903398"
                     /db_xref="GeneID:1595"
                     /db_xref="HGNC:2649"
                     /db_xref="MIM:601637"
                     /db_xref="HPRD:03381"
     mRNA            complement(join(91741463..91743157,91746358..91746526,
                     91747834..91747929,91752434..91752629,91753048..91753167,
                     91755567..91755741,91756819..91756945,91758194..91758370,
                     91761088..91761186,91763487..91763840))
                     /gene="CYP51A1"
                     /gene_synonym="CP51; CYP51; CYPL1; LDM; P450-14DM; P450L1"
                     /product="cytochrome P450, family 51, subfamily A,
                     polypeptide 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000786.3"
                     /db_xref="GI:168693652"
                     /db_xref="GeneID:1595"
                     /db_xref="HGNC:2649"
                     /db_xref="HPRD:03381"
                     /db_xref="MIM:601637"
     CDS             complement(join(91742979..91743157,91746358..91746526,
                     91747834..91747929,91752434..91752629,91753048..91753167,
                     91755567..91755741,91756819..91756945,91758194..91758370,
                     91761088..91761186,91763487..91763678))
                     /gene="CYP51A1"
                     /gene_synonym="CP51; CYP51; CYPL1; LDM; P450-14DM; P450L1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="lanosterol 14-alpha demethylase isoform 1"
                     /protein_id="NP_000777.1"
                     /db_xref="GI:4503243"
                     /db_xref="CCDS:CCDS5623.1"
                     /db_xref="GeneID:1595"
                     /db_xref="HGNC:2649"
                     /db_xref="HPRD:03381"
                     /db_xref="MIM:601637"
     CDS             complement(join(91742979..91743157,91746358..91746526,
                     91747834..91747929,91752434..91752629,91753048..91753167,
                     91755567..91755741,91756819..91756945,91758194..91758346))
                     /gene="CYP51A1"
                     /gene_synonym="CP51; CYP51; CYPL1; LDM; P450-14DM; P450L1"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="lanosterol 14-alpha demethylase isoform 2"
                     /protein_id="NP_001139624.1"
                     /db_xref="GI:225903399"
                     /db_xref="CCDS:CCDS55123.1"
                     /db_xref="GeneID:1595"
                     /db_xref="HGNC:2649"
                     /db_xref="HPRD:03381"
                     /db_xref="MIM:601637"
     gene            91763176..91810039
                     /gene="LOC613126"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 3 mRNAs, 7 ESTs, 1 Protein"
                     /db_xref="GeneID:613126"
     misc_RNA        join(91763176..91764396,91768081..91768265,
                     91771716..91772048,91794294..91794378,91808165..91809227,
                     91809313..91810039)
                     /gene="LOC613126"
                     /product="hypothetical LOC613126"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 3 mRNAs, 7 ESTs, 1 Protein"
                     /transcript_id="XR_108845.1"
                     /db_xref="GI:310120028"
                     /db_xref="GeneID:613126"
     gene            complement(91774198..91794590)
                     /gene="LRRD1"
                     /gene_synonym="FLJ34004; MGC178225; MGC178229"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:401387"
                     /db_xref="HGNC:34300"
     mRNA            complement(join(91774198..91774388,91775397..91775514,
                     91779848..91780009,91788319..91788517,91792600..91794590))
                     /gene="LRRD1"
                     /gene_synonym="FLJ34004; MGC178225; MGC178229"
                     /product="leucine-rich repeats and death domain containing
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001161528.1"
                     /db_xref="GI:238908507"
                     /db_xref="GeneID:401387"
                     /db_xref="HGNC:34300"
     CDS             complement(join(91774202..91774388,91775397..91775514,
                     91779848..91780009,91788319..91788517,91792600..91794516))
                     /gene="LRRD1"
                     /gene_synonym="FLJ34004; MGC178225; MGC178229"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="leucine-rich repeat and death domain-containing
                     protein LOC401387"
                     /protein_id="NP_001155000.1"
                     /db_xref="GI:238908508"
                     /db_xref="CCDS:CCDS55124.1"
                     /db_xref="GeneID:401387"
                     /db_xref="HGNC:34300"
     gene            complement(91828283..91875414)
                     /gene="KRIT1"
                     /gene_synonym="CAM; CCM1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:889"
                     /db_xref="HGNC:1573"
                     /db_xref="HPRD:05020"
                     /db_xref="MIM:604214"
     mRNA            complement(join(91828283..91830118,91830621..91830737,
                     91842509..91842715,91843206..91843293,91843925..91844091,
                     91851216..91851367,91852136..91852292,91855034..91855141,
                     91855840..91855996,91863763..91863906,91864122..91864237,
                     91864717..91864960,91865727..91865856,91866981..91867073,
                     91870307..91870466,91871348..91871451,91873316..91873463,
                     91874216..91874485,91874741..91874909,91875220..91875414))
                     /gene="KRIT1"
                     /gene_synonym="CAM; CCM1"
                     /product="KRIT1, ankyrin repeat containing, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_194456.1"
                     /db_xref="GI:37221183"
                     /db_xref="GeneID:889"
                     /db_xref="HGNC:1573"
                     /db_xref="MIM:604214"
                     /db_xref="HPRD:05020"
     mRNA            complement(join(91828283..91830118,91830621..91830737,
                     91842509..91842715,91843206..91843293,91843925..91844091,
                     91851216..91851367,91852136..91852292,91855034..91855141,
                     91855840..91855996,91863763..91863906,91864122..91864237,
                     91864717..91864960,91865727..91865856,91866981..91867073,
                     91870307..91870466,91871348..91871451,91873316..91873463,
                     91874216..91874448,91874779..91875414))
                     /gene="KRIT1"
                     /gene_synonym="CAM; CCM1"
                     /product="KRIT1, ankyrin repeat containing, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_194455.1"
                     /db_xref="GI:37221181"
                     /db_xref="GeneID:889"
                     /db_xref="HGNC:1573"
                     /db_xref="HPRD:05020"
                     /db_xref="MIM:604214"
     mRNA            complement(join(91828283..91830118,91830621..91830737,
                     91842509..91842715,91843206..91843293,91843925..91844091,
                     91851216..91851367,91852136..91852292,91855034..91855141,
                     91855840..91855996,91863763..91863906,91864122..91864237,
                     91864717..91864960,91865727..91865856,91866981..91867073,
                     91870307..91870466,91871348..91871451,91873316..91873463,
                     91874216..91874485,91875104..91875228))
                     /gene="KRIT1"
                     /gene_synonym="CAM; CCM1"
                     /product="KRIT1, ankyrin repeat containing, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_194454.1"
                     /db_xref="GI:37221186"
                     /db_xref="GeneID:889"
                     /db_xref="HGNC:1573"
                     /db_xref="MIM:604214"
                     /db_xref="HPRD:05020"
     mRNA            complement(join(91828283..91830118,91830621..91830737,
                     91842509..91842715,91843206..91843293,91843925..91844091,
                     91851216..91851367,91852136..91852292,91855034..91855141,
                     91855840..91855996,91864122..91864237,91864717..91864960,
                     91865727..91865856,91866981..91867073,91870307..91870466,
                     91871348..91871451,91874216..91874485,91875104..91875228))
                     /gene="KRIT1"
                     /gene_synonym="CAM; CCM1"
                     /product="KRIT1, ankyrin repeat containing, transcript
                     variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001013406.1"
                     /db_xref="GI:61742816"
                     /db_xref="GeneID:889"
                     /db_xref="HGNC:1573"
                     /db_xref="HPRD:05020"
                     /db_xref="MIM:604214"
     mRNA            complement(join(91828283..91830118,91830621..91830737,
                     91842509..91842715,91843206..91843293,91843925..91844091,
                     91851216..91851367,91852136..91852292,91855034..91855141,
                     91855840..91855996,91863763..91863906,91864122..91864237,
                     91864717..91864960,91865727..91865856,91866981..91867073,
                     91870307..91870466,91871348..91871451,91873316..91873463,
                     91874216..91874485,91874741..91875212))
                     /gene="KRIT1"
                     /gene_synonym="CAM; CCM1"
                     /product="KRIT1, ankyrin repeat containing, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004912.3"
                     /db_xref="GI:37221185"
                     /db_xref="GeneID:889"
                     /db_xref="HGNC:1573"
                     /db_xref="HPRD:05020"
                     /db_xref="MIM:604214"
     CDS             complement(join(91830050..91830118,91830621..91830737,
                     91842509..91842715,91843206..91843293,91843925..91844091,
                     91851216..91851367,91852136..91852292,91855034..91855141,
                     91855840..91855996,91863763..91863906,91864122..91864237,
                     91864717..91864960,91865727..91865856,91866981..91867073,
                     91870307..91870466,91871348..91871449))
                     /gene="KRIT1"
                     /gene_synonym="CAM; CCM1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="krev interaction trapped protein 1 isoform 1"
                     /protein_id="NP_919438.1"
                     /db_xref="GI:37221184"
                     /db_xref="CCDS:CCDS5624.1"
                     /db_xref="GeneID:889"
                     /db_xref="HGNC:1573"
                     /db_xref="HPRD:05020"
                     /db_xref="MIM:604214"
     CDS             complement(join(91830050..91830118,91830621..91830737,
                     91842509..91842715,91843206..91843293,91843925..91844091,
                     91851216..91851367,91852136..91852292,91855034..91855141,
                     91855840..91855996,91863763..91863906,91864122..91864237,
                     91864717..91864960,91865727..91865856,91866981..91867073,
                     91870307..91870466,91871348..91871449))
                     /gene="KRIT1"
                     /gene_synonym="CAM; CCM1"
                     /note="isoform 1 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="krev interaction trapped protein 1 isoform 1"
                     /protein_id="NP_004903.2"
                     /db_xref="GI:31581522"
                     /db_xref="CCDS:CCDS5624.1"
                     /db_xref="GeneID:889"
                     /db_xref="HGNC:1573"
                     /db_xref="HPRD:05020"
                     /db_xref="MIM:604214"
     CDS             complement(join(91830050..91830118,91830621..91830737,
                     91842509..91842715,91843206..91843293,91843925..91844091,
                     91851216..91851367,91852136..91852292,91855034..91855141,
                     91855840..91855996,91863763..91863906,91864122..91864237,
                     91864717..91864960,91865727..91865856,91866981..91867073,
                     91870307..91870466,91871348..91871449))
                     /gene="KRIT1"
                     /gene_synonym="CAM; CCM1"
                     /note="isoform 1 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="krev interaction trapped protein 1 isoform 1"
                     /protein_id="NP_919436.1"
                     /db_xref="GI:37221187"
                     /db_xref="CCDS:CCDS5624.1"
                     /db_xref="GeneID:889"
                     /db_xref="HGNC:1573"
                     /db_xref="HPRD:05020"
                     /db_xref="MIM:604214"
     CDS             complement(join(91830050..91830118,91830621..91830737,
                     91842509..91842715,91843206..91843293,91843925..91844091,
                     91851216..91851367,91852136..91852292,91855034..91855141,
                     91855840..91855996,91863763..91863906,91864122..91864237,
                     91864717..91864960,91865727..91865856,91866981..91867073,
                     91870307..91870466,91871348..91871449))
                     /gene="KRIT1"
                     /gene_synonym="CAM; CCM1"
                     /note="isoform 1 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="krev interaction trapped protein 1 isoform 1"
                     /protein_id="NP_919437.1"
                     /db_xref="GI:37221182"
                     /db_xref="CCDS:CCDS5624.1"
                     /db_xref="GeneID:889"
                     /db_xref="HGNC:1573"
                     /db_xref="HPRD:05020"
                     /db_xref="MIM:604214"
     CDS             complement(join(91830050..91830118,91830621..91830737,
                     91842509..91842715,91843206..91843293,91843925..91844091,
                     91851216..91851367,91852136..91852292,91855034..91855141,
                     91855840..91855996,91864122..91864237,91864717..91864960,
                     91865727..91865856,91866981..91867073,91870307..91870466,
                     91871348..91871449))
                     /gene="KRIT1"
                     /gene_synonym="CAM; CCM1"
                     /note="isoform 2 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="krev interaction trapped protein 1 isoform 2"
                     /protein_id="NP_001013424.1"
                     /db_xref="GI:61742817"
                     /db_xref="CCDS:CCDS34679.1"
                     /db_xref="GeneID:889"
                     /db_xref="HGNC:1573"
                     /db_xref="HPRD:05020"
                     /db_xref="MIM:604214"
     gene            complement(91833329..91833412)
                     /gene="MIR1285-1"
                     /gene_synonym="hsa-mir-1285-1; MIRN1285-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100302218"
                     /db_xref="HGNC:35277"
                     /db_xref="miRBase:MI0006346"
     ncRNA           complement(91833329..91833412)
                     /gene="MIR1285-1"
                     /gene_synonym="hsa-mir-1285-1; MIRN1285-1"
                     /ncRNA_class="miRNA"
                     /product="microRNA 1285-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_031616.1"
                     /db_xref="GI:269847128"
                     /db_xref="GeneID:100302218"
                     /db_xref="HGNC:35277"
                     /db_xref="miRBase:MI0006346"
     gene            91875548..92030698
                     /gene="ANKIB1"
                     /gene_synonym="DKFZp434A0225; FLJ33123; KIAA1386"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54467"
                     /db_xref="HGNC:22215"
     mRNA            join(91875548..91875833,91924203..91924480,
                     91936673..91936970,91948644..91948826,91957097..91957214,
                     91972338..91972546,91974292..91974380,91980264..91980408,
                     91981790..91981956,91991499..91991587,92000791..92000921,
                     92015823..92015957,92017112..92017198,92017289..92017355,
                     92019285..92019430,92020480..92020658,92021555..92021606,
                     92025679..92025790,92027037..92027173,92027526..92030698)
                     /gene="ANKIB1"
                     /gene_synonym="DKFZp434A0225; FLJ33123; KIAA1386"
                     /product="ankyrin repeat and IBR domain containing 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_019004.1"
                     /db_xref="GI:148596952"
                     /db_xref="GeneID:54467"
                     /db_xref="HGNC:22215"
     CDS             join(91924293..91924480,91936673..91936970,
                     91948644..91948826,91957097..91957214,91972338..91972546,
                     91974292..91974380,91980264..91980408,91981790..91981956,
                     91991499..91991587,92000791..92000921,92015823..92015957,
                     92017112..92017198,92017289..92017355,92019285..92019430,
                     92020480..92020658,92021555..92021606,92025679..92025790,
                     92027037..92027173,92027526..92028263)
                     /gene="ANKIB1"
                     /gene_synonym="DKFZp434A0225; FLJ33123; KIAA1386"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ankyrin repeat and IBR domain-containing protein
                     1"
                     /protein_id="NP_061877.1"
                     /db_xref="GI:148596953"
                     /db_xref="CCDS:CCDS47639.1"
                     /db_xref="GeneID:54467"
                     /db_xref="HGNC:22215"
     gene            92071391..92071808
                     /gene="LOC645862"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:645862"
     gene            92076765..92088742
                     /gene="GATAD1"
                     /gene_synonym="FLJ22489; FLJ40695; ODAG; RG083M05.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57798"
                     /db_xref="HGNC:29941"
                     /db_xref="HPRD:17656"
     mRNA            join(92076765..92077292,92078066..92078191,
                     92080015..92080074,92083816..92083999,92085686..92088742)
                     /gene="GATAD1"
                     /gene_synonym="FLJ22489; FLJ40695; ODAG; RG083M05.2"
                     /product="GATA zinc finger domain containing 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021167.3"
                     /db_xref="GI:88759345"
                     /db_xref="GeneID:57798"
                     /db_xref="HGNC:29941"
                     /db_xref="HPRD:17656"
     CDS             join(92077044..92077292,92078066..92078191,
                     92080015..92080074,92083816..92083999,92085686..92085876)
                     /gene="GATAD1"
                     /gene_synonym="FLJ22489; FLJ40695; ODAG; RG083M05.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="GATA zinc finger domain-containing protein 1"
                     /protein_id="NP_066990.3"
                     /db_xref="GI:88759346"
                     /db_xref="CCDS:CCDS5625.1"
                     /db_xref="GeneID:57798"
                     /db_xref="HGNC:29941"
                     /db_xref="HPRD:17656"
     gene            complement(92097694..92107229)
                     /gene="ERVW-1"
                     /gene_synonym="ENV; ENVW; ERVWE1; HERV-7q; HERV-W-ENV;
                     HERV7Q; HERVW; HERVWENV"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:30816"
                     /db_xref="HGNC:13525"
                     /db_xref="MIM:604659"
     mRNA            complement(join(92097694..92099922,92106696..92107229))
                     /gene="ERVW-1"
                     /gene_synonym="ENV; ENVW; ERVWE1; HERV-7q; HERV-W-ENV;
                     HERV7Q; HERVW; HERVWENV"
                     /product="endogenous retrovirus group W, member 1,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /transcript_id="NM_001130925.1"
                     /db_xref="GI:195963432"
                     /db_xref="GeneID:30816"
                     /db_xref="HGNC:13525"
                     /db_xref="MIM:604659"
     mRNA            complement(92097695..92100738)
                     /gene="ERVW-1"
                     /gene_synonym="ENV; ENVW; ERVWE1; HERV-7q; HERV-W-ENV;
                     HERV7Q; HERVW; HERVWENV"
                     /product="endogenous retrovirus group W, member 1,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /transcript_id="NM_014590.3"
                     /db_xref="GI:48949850"
                     /db_xref="GeneID:30816"
                     /db_xref="HGNC:13525"
                     /db_xref="MIM:604659"
     CDS             complement(92098079..92099695)
                     /gene="ERVW-1"
                     /gene_synonym="ENV; ENVW; ERVWE1; HERV-7q; HERV-W-ENV;
                     HERV7Q; HERVW; HERVWENV"
                     /note="envelope glycoprotein; enverin; HERV-tryptophan
                     envelope protein; HERV-7q envelope protein; HERV-W{7q21.1}
                     provirus ancestral Env polyprotein; HERV-W Env
                     glycoprotein; HERV-W_7q21.2 provirus ancestral Env
                     polyprotein; human endogenous retrovirus W envC7-1
                     envelope protein; syncytin A; envelope polyprotein gPr73;
                     syncytin-1; env-W; HERV-W envelope protein; endogenous
                     retroviral family W, env(C7), member 1; endogenous
                     retrovirus group W member 1; Derived by automated
                     computational analysis using gene prediction method:
                     Curated Genomic."
                     /codon_start=1
                     /product="HERV-W_7q21.2 provirus ancestral Env polyprotein
                     precursor"
                     /protein_id="NP_001124397.1"
                     /db_xref="GI:195963433"
                     /db_xref="CCDS:CCDS5626.1"
                     /db_xref="GeneID:30816"
                     /db_xref="HGNC:13525"
                     /db_xref="MIM:604659"
     CDS             complement(92098079..92099695)
                     /gene="ERVW-1"
                     /gene_synonym="ENV; ENVW; ERVWE1; HERV-7q; HERV-W-ENV;
                     HERV7Q; HERVW; HERVWENV"
                     /note="envelope glycoprotein; enverin; HERV-tryptophan
                     envelope protein; HERV-7q envelope protein; HERV-W{7q21.1}
                     provirus ancestral Env polyprotein; HERV-W Env
                     glycoprotein; HERV-W_7q21.2 provirus ancestral Env
                     polyprotein; human endogenous retrovirus W envC7-1
                     envelope protein; syncytin A; envelope polyprotein gPr73;
                     syncytin-1; env-W; HERV-W envelope protein; endogenous
                     retroviral family W, env(C7), member 1; endogenous
                     retrovirus group W member 1; Derived by automated
                     computational analysis using gene prediction method:
                     Curated Genomic."
                     /codon_start=1
                     /product="HERV-W_7q21.2 provirus ancestral Env polyprotein
                     precursor"
                     /protein_id="NP_055405.3"
                     /db_xref="GI:48949851"
                     /db_xref="CCDS:CCDS5626.1"
                     /db_xref="GeneID:30816"
                     /db_xref="HGNC:13525"
                     /db_xref="MIM:604659"
     gene            complement(92116337..92157845)
                     /gene="PEX1"
                     /gene_synonym="ZWS; ZWS1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5189"
                     /db_xref="HGNC:8850"
                     /db_xref="HPRD:03682"
                     /db_xref="MIM:602136"
     mRNA            complement(join(92116337..92116855,92118607..92118737,
                     92119028..92119225,92120586..92120816,92122267..92122443,
                     92123607..92123710,92123801..92123943,92126027..92126091,
                     92129018..92129152,92130821..92130987,92131204..92131393,
                     92132355..92132509,92134046..92134216,92135562..92135658,
                     92136308..92136440,92138643..92138725,92140258..92140361,
                     92140894..92141017,92143162..92143281,92146590..92147356,
                     92147455..92147569,92148309..92148392,92151416..92151559,
                     92157621..92157845))
                     /gene="PEX1"
                     /gene_synonym="ZWS; ZWS1"
                     /product="peroxisomal biogenesis factor 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000466.2"
                     /db_xref="GI:94421467"
                     /db_xref="GeneID:5189"
                     /db_xref="HGNC:8850"
                     /db_xref="HPRD:03682"
                     /db_xref="MIM:602136"
     CDS             complement(join(92116771..92116855,92118607..92118737,
                     92119028..92119225,92120586..92120816,92122267..92122443,
                     92123607..92123710,92123801..92123943,92126027..92126091,
                     92129018..92129152,92130821..92130987,92131204..92131393,
                     92132355..92132509,92134046..92134216,92135562..92135658,
                     92136308..92136440,92138643..92138725,92140258..92140361,
                     92140894..92141017,92143162..92143281,92146590..92147356,
                     92147455..92147569,92148309..92148392,92151416..92151559,
                     92157621..92157749))
                     /gene="PEX1"
                     /gene_synonym="ZWS; ZWS1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="peroxisome biogenesis factor 1"
                     /protein_id="NP_000457.1"
                     /db_xref="GI:4505725"
                     /db_xref="CCDS:CCDS5627.1"
                     /db_xref="GeneID:5189"
                     /db_xref="HGNC:8850"
                     /db_xref="HPRD:03682"
                     /db_xref="MIM:602136"
     gene            92158087..92166823
                     /gene="C7orf64"
                     /gene_synonym="DKFZP564O0523; DKFZp686D1651; HSPC304"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84060"
                     /db_xref="HGNC:21785"
                     /db_xref="HPRD:13173"
     mRNA            join(92158087..92158238,92158790..92158980,
                     92161718..92161863,92163716..92164284,92166165..92166823)
                     /gene="C7orf64"
                     /gene_synonym="DKFZP564O0523; DKFZp686D1651; HSPC304"
                     /product="chromosome 7 open reading frame 64"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032120.2"
                     /db_xref="GI:119120843"
                     /db_xref="GeneID:84060"
                     /db_xref="HGNC:21785"
                     /db_xref="HPRD:13173"
     CDS             join(92158128..92158238,92158790..92158980,
                     92161718..92161863,92163716..92164284,92166165..92166251)
                     /gene="C7orf64"
                     /gene_synonym="DKFZP564O0523; DKFZp686D1651; HSPC304"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC84060"
                     /protein_id="NP_115496.2"
                     /db_xref="GI:119120844"
                     /db_xref="CCDS:CCDS43615.1"
                     /db_xref="GeneID:84060"
                     /db_xref="HGNC:21785"
                     /db_xref="HPRD:13173"
     gene            92167789..92169079
                     /gene="MGC16142"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84849"
     misc_RNA        92167789..92169079
                     /gene="MGC16142"
                     /product="hypothetical protein MGC16142"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_026902.1"
                     /db_xref="GI:223890253"
                     /db_xref="GeneID:84849"
     gene            complement(92169576..92187191)
                     /gene="LOC442710"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:442710"
     exon            complement(92169576..92169684)
                     /gene="LOC442710"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=7
                     /pseudo
                     /db_xref="GeneID:442710"
     exon            complement(92170128..92170222)
                     /gene="LOC442710"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=6
                     /pseudo
                     /db_xref="GeneID:442710"
     exon            complement(92178036..92178176)
                     /gene="LOC442710"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=5
                     /pseudo
                     /db_xref="GeneID:442710"
     exon            complement(92178960..92178962)
                     /gene="LOC442710"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=4
                     /pseudo
                     /db_xref="GeneID:442710"
     exon            complement(92180032..92180136)
                     /gene="LOC442710"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:442710"
     exon            complement(92181970..92182123)
                     /gene="LOC442710"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:442710"
     exon            complement(92187134..92187191)
                     /gene="LOC442710"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:442710"
     gene            complement(92190072..92219706)
                     /gene="FAM133B"
                     /gene_synonym="MGC40405"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:257415"
                     /db_xref="HGNC:28629"
     mRNA            complement(join(92190072..92191682,92195328..92195375,
                     92199137..92199229,92205085..92205135,92206417..92206509,
                     92206969..92207031,92207464..92207496,92207633..92207707,
                     92208631..92208709,92210820..92210917,92219582..92219706))
                     /gene="FAM133B"
                     /gene_synonym="MGC40405"
                     /product="family with sequence similarity 133, member B,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152789.2"
                     /db_xref="GI:91206455"
                     /db_xref="GeneID:257415"
                     /db_xref="HGNC:28629"
                     /db_xref="HPRD:17557"
     mRNA            complement(join(92190072..92191682,92195328..92195375,
                     92199137..92199229,92205085..92205135,92206417..92206509,
                     92206969..92207031,92207464..92207496,92207633..92207707,
                     92208631..92208709,92210820..92210917,92214612..92214710,
                     92219582..92219706))
                     /gene="FAM133B"
                     /gene_synonym="MGC40405"
                     /product="family with sequence similarity 133, member B,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040057.1"
                     /db_xref="GI:91206453"
                     /db_xref="GeneID:257415"
                     /db_xref="HGNC:28629"
     CDS             complement(join(92191596..92191682,92195328..92195375,
                     92199137..92199229,92205085..92205135,92206417..92206509,
                     92206969..92207031,92207464..92207496,92207633..92207707,
                     92208631..92208709,92210820..92210917,92219582..92219605))
                     /gene="FAM133B"
                     /gene_synonym="MGC40405"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC257415 isoform 1"
                     /protein_id="NP_690002.2"
                     /db_xref="GI:91206456"
                     /db_xref="CCDS:CCDS47640.1"
                     /db_xref="GeneID:257415"
                     /db_xref="HGNC:28629"
     CDS             complement(join(92191596..92191682,92195328..92195375,
                     92199137..92199229,92205085..92205135,92206417..92206509,
                     92206969..92207031,92207464..92207496,92207633..92207707,
                     92208631..92208709,92210820..92210911))
                     /gene="FAM133B"
                     /gene_synonym="MGC40405"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC257415 isoform 2"
                     /protein_id="NP_001035146.1"
                     /db_xref="GI:91206454"
                     /db_xref="CCDS:CCDS47641.1"
                     /db_xref="GeneID:257415"
                     /db_xref="HGNC:28629"
     gene            complement(92234235..92465941)
                     /gene="CDK6"
                     /gene_synonym="MGC59692; PLSTIRE"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1021"
                     /db_xref="HGNC:1777"
                     /db_xref="HPRD:04533"
                     /db_xref="MIM:603368"
     mRNA            complement(join(92234235..92244600,92247386..92247521,
                     92252350..92252400,92300740..92300849,92354940..92355107,
                     92404010..92404145,92462405..92463004,92465792..92465941))
                     /gene="CDK6"
                     /gene_synonym="MGC59692; PLSTIRE"
                     /product="cyclin-dependent kinase 6, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145306.1"
                     /db_xref="GI:223718133"
                     /db_xref="GeneID:1021"
                     /db_xref="HGNC:1777"
                     /db_xref="MIM:603368"
                     /db_xref="HPRD:04533"
     mRNA            complement(join(92234235..92244600,92247386..92247521,
                     92252350..92252400,92300740..92300849,92354940..92355107,
                     92404010..92404145,92462405..92463004,92463187..92463231))
                     /gene="CDK6"
                     /gene_synonym="MGC59692; PLSTIRE"
                     /product="cyclin-dependent kinase 6, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001259.6"
                     /db_xref="GI:223718130"
                     /db_xref="GeneID:1021"
                     /db_xref="HGNC:1777"
                     /db_xref="HPRD:04533"
                     /db_xref="MIM:603368"
     CDS             complement(join(92244454..92244600,92247386..92247521,
                     92252350..92252400,92300740..92300849,92354940..92355107,
                     92404010..92404145,92462405..92462637))
                     /gene="CDK6"
                     /gene_synonym="MGC59692; PLSTIRE"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclin-dependent kinase 6"
                     /protein_id="NP_001250.1"
                     /db_xref="GI:4502741"
                     /db_xref="CCDS:CCDS5628.1"
                     /db_xref="GeneID:1021"
                     /db_xref="HGNC:1777"
                     /db_xref="HPRD:04533"
                     /db_xref="MIM:603368"
     CDS             complement(join(92244454..92244600,92247386..92247521,
                     92252350..92252400,92300740..92300849,92354940..92355107,
                     92404010..92404145,92462405..92462637))
                     /gene="CDK6"
                     /gene_synonym="MGC59692; PLSTIRE"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclin-dependent kinase 6"
                     /protein_id="NP_001138778.1"
                     /db_xref="GI:223718134"
                     /db_xref="CCDS:CCDS5628.1"
                     /db_xref="GeneID:1021"
                     /db_xref="HGNC:1777"
                     /db_xref="HPRD:04533"
                     /db_xref="MIM:603368"
     gene            complement(92600256..92600640)
                     /gene="RN7SL7P"
                     /gene_synonym="7L23; RN7SLP4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6033"
                     /db_xref="HGNC:10042"
     gene            complement(92728826..92747336)
                     /gene="SAMD9"
                     /gene_synonym="C7orf5; DRIF1; FLJ20073; KIAA2004; NFTC;
                     OEF1; OEF2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54809"
                     /db_xref="HGNC:1348"
                     /db_xref="HPRD:11531"
                     /db_xref="MIM:610456"
     mRNA            complement(join(92728826..92735418,92744108..92744208,
                     92747176..92747336))
                     /gene="SAMD9"
                     /gene_synonym="C7orf5; DRIF1; FLJ20073; KIAA2004; NFTC;
                     OEF1; OEF2"
                     /product="sterile alpha motif domain containing 9,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017654.3"
                     /db_xref="GI:300863103"
                     /db_xref="GeneID:54809"
                     /db_xref="HGNC:1348"
                     /db_xref="HPRD:11531"
                     /db_xref="MIM:610456"
     mRNA            complement(join(92728826..92735418,92747176..92747336))
                     /gene="SAMD9"
                     /gene_synonym="C7orf5; DRIF1; FLJ20073; KIAA2004; NFTC;
                     OEF1; OEF2"
                     /product="sterile alpha motif domain containing 9,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001193307.1"
                     /db_xref="GI:300863104"
                     /db_xref="GeneID:54809"
                     /db_xref="HGNC:1348"
                     /db_xref="MIM:610456"
                     /db_xref="HPRD:11531"
     CDS             complement(92730641..92735410)
                     /gene="SAMD9"
                     /gene_synonym="C7orf5; DRIF1; FLJ20073; KIAA2004; NFTC;
                     OEF1; OEF2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="sterile alpha motif domain-containing protein 9"
                     /protein_id="NP_060124.2"
                     /db_xref="GI:38201706"
                     /db_xref="CCDS:CCDS34680.1"
                     /db_xref="GeneID:54809"
                     /db_xref="HGNC:1348"
                     /db_xref="HPRD:11531"
                     /db_xref="MIM:610456"
     CDS             complement(92730641..92735410)
                     /gene="SAMD9"
                     /gene_synonym="C7orf5; DRIF1; FLJ20073; KIAA2004; NFTC;
                     OEF1; OEF2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="sterile alpha motif domain-containing protein 9"
                     /protein_id="NP_001180236.1"
                     /db_xref="GI:300863105"
                     /db_xref="CCDS:CCDS34680.1"
                     /db_xref="GeneID:54809"
                     /db_xref="HGNC:1348"
                     /db_xref="HPRD:11531"
                     /db_xref="MIM:610456"
     gene            complement(92759368..92777680)
                     /gene="SAMD9L"
                     /gene_synonym="C7orf6; DRIF2; FLJ39885; KIAA2005; UEF1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:219285"
                     /db_xref="HGNC:1349"
                     /db_xref="HPRD:10798"
                     /db_xref="MIM:611170"
     mRNA            complement(join(92759368..92765304,92774045..92774146,
                     92774698..92775353,92776196..92776459,92777507..92777680))
                     /gene="SAMD9L"
                     /gene_synonym="C7orf6; DRIF2; FLJ39885; KIAA2005; UEF1"
                     /product="sterile alpha motif domain containing 9-like"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152703.2"
                     /db_xref="GI:51339290"
                     /db_xref="GeneID:219285"
                     /db_xref="HGNC:1349"
                     /db_xref="HPRD:10798"
                     /db_xref="MIM:611170"
     CDS             complement(92760530..92765284)
                     /gene="SAMD9L"
                     /gene_synonym="C7orf6; DRIF2; FLJ39885; KIAA2005; UEF1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="sterile alpha motif domain-containing protein
                     9-like"
                     /protein_id="NP_689916.2"
                     /db_xref="GI:51339291"
                     /db_xref="CCDS:CCDS34681.1"
                     /db_xref="GeneID:219285"
                     /db_xref="HGNC:1349"
                     /db_xref="HPRD:10798"
                     /db_xref="MIM:611170"
     gene            complement(92817899..92855782)
                     /gene="HEPACAM2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:253012"
                     /db_xref="HGNC:27364"
                     /db_xref="HPRD:14138"
     mRNA            complement(join(92817899..92818583,92821567..92821676,
                     92825141..92825214,92826554..92826591,92826686..92826710,
                     92826798..92826923,92837893..92838189,92844714..92844998,
                     92848414..92848870))
                     /gene="HEPACAM2"
                     /product="HEPACAM family member 2, transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198151.1"
                     /db_xref="GI:37700248"
                     /db_xref="GeneID:253012"
                     /db_xref="HGNC:27364"
                     /db_xref="HPRD:14138"
     mRNA            complement(join(92817900..92818583,92821567..92821676,
                     92825141..92825214,92826554..92826591,92826686..92826710,
                     92826798..92826923,92837893..92838189,92844714..92844998,
                     92848414..92848764,92855681..92855782))
                     /gene="HEPACAM2"
                     /product="HEPACAM family member 2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001039372.1"
                     /db_xref="GI:86439956"
                     /db_xref="GeneID:253012"
                     /db_xref="HGNC:27364"
                     /db_xref="HPRD:14138"
     CDS             complement(join(92818580..92818583,92821567..92821676,
                     92825141..92825214,92826554..92826591,92826686..92826710,
                     92826798..92826923,92837893..92838189,92844714..92844998,
                     92848414..92848764,92855681..92855759))
                     /gene="HEPACAM2"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="HEPACAM family member 2 isoform 1"
                     /protein_id="NP_001034461.1"
                     /db_xref="GI:86439957"
                     /db_xref="CCDS:CCDS43616.1"
                     /db_xref="GeneID:253012"
                     /db_xref="HGNC:27364"
                     /db_xref="HPRD:14138"
     CDS             complement(join(92818580..92818583,92821567..92821676,
                     92825141..92825214,92826554..92826591,92826686..92826710,
                     92826798..92826923,92837893..92838189,92844714..92844998,
                     92848414..92848807))
                     /gene="HEPACAM2"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="HEPACAM family member 2 isoform 2"
                     /protein_id="NP_937794.1"
                     /db_xref="GI:37700249"
                     /db_xref="CCDS:CCDS5629.1"
                     /db_xref="GeneID:253012"
                     /db_xref="HGNC:27364"
                     /db_xref="HPRD:14138"
     gene            92861653..92988338
                     /gene="CCDC132"
                     /gene_synonym="FLJ20097; FLJ23581; KIAA1861; MGC176659"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55610"
                     /db_xref="HGNC:25956"
     mRNA            join(92861653..92861813,92869179..92869247,
                     92881966..92882088,92883173..92883244,92885821..92885874,
                     92886706..92886776,92887471..92887588,92887669..92887704,
                     92888862..92888944,92900532..92900574,92901947..92902045,
                     92905477..92905617,92921015..92921147,92923857..92923948,
                     92926054..92926148,92926457..92926555,92932772..92932862,
                     92935140..92935316,92938136..92938254,92940478..92940584,
                     92952923..92953044,92963429..92963509,92970739..92970887,
                     92978023..92978119,92979187..92979345,92982952..92983073,
                     92985203..92985392,92987629..92988338)
                     /gene="CCDC132"
                     /gene_synonym="FLJ20097; FLJ23581; KIAA1861; MGC176659"
                     /product="coiled-coil domain containing 132, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017667.2"
                     /db_xref="GI:62865870"
                     /db_xref="GeneID:55610"
                     /db_xref="HGNC:25956"
     mRNA            join(92861653..92861813,92869179..92869247,
                     92881966..92882088,92883173..92883244,92885821..92885874,
                     92886706..92886776,92887471..92887588,92887669..92887704,
                     92888862..92888944,92900532..92900574,92901947..92902045,
                     92905477..92905740)
                     /gene="CCDC132"
                     /gene_synonym="FLJ20097; FLJ23581; KIAA1861; MGC176659"
                     /product="coiled-coil domain containing 132, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024553.2"
                     /db_xref="GI:33469927"
                     /db_xref="GeneID:55610"
                     /db_xref="HGNC:25956"
     CDS             join(92861781..92861813,92869179..92869247,
                     92881966..92882088,92883173..92883244,92885821..92885874,
                     92886706..92886776,92887471..92887588,92887669..92887704,
                     92888862..92888944,92900532..92900574,92901947..92902045,
                     92905477..92905617,92921015..92921147,92923857..92923948,
                     92926054..92926148,92926457..92926555,92932772..92932862,
                     92935140..92935316,92938136..92938254,92940478..92940584,
                     92952923..92953044,92963429..92963509,92970739..92970887,
                     92978023..92978119,92979187..92979345,92982952..92983073,
                     92985203..92985392,92987629..92987748)
                     /gene="CCDC132"
                     /gene_synonym="FLJ20097; FLJ23581; KIAA1861; MGC176659"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="coiled-coil domain-containing protein 132
                     isoform a"
                     /protein_id="NP_060137.2"
                     /db_xref="GI:62865871"
                     /db_xref="CCDS:CCDS43617.1"
                     /db_xref="GeneID:55610"
                     /db_xref="HGNC:25956"
     CDS             join(92861781..92861813,92869179..92869247,
                     92881966..92882088,92883173..92883244,92885821..92885874,
                     92886706..92886776,92887471..92887588,92887669..92887704,
                     92888862..92888944,92900532..92900574,92901947..92902045,
                     92905477..92905659)
                     /gene="CCDC132"
                     /gene_synonym="FLJ20097; FLJ23581; KIAA1861; MGC176659"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="coiled-coil domain-containing protein 132
                     isoform b"
                     /protein_id="NP_078829.1"
                     /db_xref="GI:33438577"
                     /db_xref="CCDS:CCDS5630.1"
                     /db_xref="GeneID:55610"
                     /db_xref="HGNC:25956"
     gene            complement(93053799..93204042)
                     /gene="CALCR"
                     /gene_synonym="CRT; CT-R; CTR; CTR1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:799"
                     /db_xref="HGNC:1440"
                     /db_xref="HPRD:00239"
                     /db_xref="MIM:114131"
     mRNA            complement(join(93053799..93055901,93063565..93063606,
                     93065264..93065482,93067372..93067438,93067522..93067582,
                     93072916..93073069,93090133..93090259,93091375..93091422,
                     93098027..93098118,93101687..93101799,93106870..93106980,
                     93108666..93108819,93116243..93116319,93125216..93125286,
                     93203601..93203818,93204004..93204042))
                     /gene="CALCR"
                     /gene_synonym="CRT; CT-R; CTR; CTR1"
                     /product="calcitonin receptor, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001164737.1"
                     /db_xref="GI:260064023"
                     /db_xref="GeneID:799"
                     /db_xref="HGNC:1440"
                     /db_xref="MIM:114131"
                     /db_xref="HPRD:00239"
     mRNA            complement(join(93053799..93055901,93063565..93063606,
                     93065264..93065482,93067372..93067438,93067522..93067582,
                     93072916..93073069,93090133..93090259,93098027..93098118,
                     93101687..93101799,93106870..93106980,93108666..93108819,
                     93116243..93116319,93203601..93203818,93204004..93204042))
                     /gene="CALCR"
                     /gene_synonym="CRT; CT-R; CTR; CTR1"
                     /product="calcitonin receptor, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001742.3"
                     /db_xref="GI:260064022"
                     /db_xref="GeneID:799"
                     /db_xref="HGNC:1440"
                     /db_xref="HPRD:00239"
                     /db_xref="MIM:114131"
     mRNA            complement(join(93053799..93055901,93063565..93063606,
                     93065264..93065482,93067372..93067438,93067522..93067582,
                     93072916..93073069,93090133..93090259,93098027..93098118,
                     93101687..93101799,93106870..93106980,93108666..93108819,
                     93116243..93116319,93188833..93189122))
                     /gene="CALCR"
                     /gene_synonym="CRT; CT-R; CTR; CTR1"
                     /product="calcitonin receptor, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001164738.1"
                     /db_xref="GI:260064026"
                     /db_xref="GeneID:799"
                     /db_xref="HGNC:1440"
                     /db_xref="MIM:114131"
                     /db_xref="HPRD:00239"
     CDS             complement(join(93055668..93055901,93063565..93063606,
                     93065264..93065482,93067372..93067438,93067522..93067582,
                     93072916..93073069,93090133..93090259,93091375..93091422,
                     93098027..93098118,93101687..93101799,93106870..93106980,
                     93108666..93108819,93116243..93116319,93125216..93125243))
                     /gene="CALCR"
                     /gene_synonym="CRT; CT-R; CTR; CTR1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcitonin receptor isoform 1"
                     /protein_id="NP_001158209.1"
                     /db_xref="GI:260064024"
                     /db_xref="CCDS:CCDS55125.1"
                     /db_xref="GeneID:799"
                     /db_xref="HGNC:1440"
                     /db_xref="HPRD:00239"
                     /db_xref="MIM:114131"
     CDS             complement(join(93055668..93055901,93063565..93063606,
                     93065264..93065482,93067372..93067438,93067522..93067582,
                     93072916..93073069,93090133..93090259,93098027..93098118,
                     93101687..93101799,93106870..93106980,93108666..93108819,
                     93116243..93116293))
                     /gene="CALCR"
                     /gene_synonym="CRT; CT-R; CTR; CTR1"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcitonin receptor isoform 2 precursor"
                     /protein_id="NP_001733.1"
                     /db_xref="GI:4502547"
                     /db_xref="CCDS:CCDS5631.1"
                     /db_xref="GeneID:799"
                     /db_xref="HGNC:1440"
                     /db_xref="HPRD:00239"
                     /db_xref="MIM:114131"
     CDS             complement(join(93055668..93055901,93063565..93063606,
                     93065264..93065482,93067372..93067438,93067522..93067582,
                     93072916..93073069,93090133..93090259,93098027..93098118,
                     93101687..93101799,93106870..93106980,93108666..93108819,
                     93116243..93116293))
                     /gene="CALCR"
                     /gene_synonym="CRT; CT-R; CTR; CTR1"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 3; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcitonin receptor isoform 2 precursor"
                     /protein_id="NP_001158210.1"
                     /db_xref="GI:260064027"
                     /db_xref="CCDS:CCDS5631.1"
                     /db_xref="GeneID:799"
                     /db_xref="HGNC:1440"
                     /db_xref="HPRD:00239"
                     /db_xref="MIM:114131"
     gene            complement(93112072..93112167)
                     /gene="MIR653"
                     /gene_synonym="hsa-mir-653; MIRN653"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:724023"
                     /db_xref="HGNC:32909"
                     /db_xref="miRBase:MI0003674"
     ncRNA           complement(93112072..93112167)
                     /gene="MIR653"
                     /gene_synonym="hsa-mir-653; MIRN653"
                     /ncRNA_class="miRNA"
                     /product="microRNA 653"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_030388.1"
                     /db_xref="GI:262206277"
                     /db_xref="GeneID:724023"
                     /db_xref="HGNC:32909"
                     /db_xref="miRBase:MI0003674"
     ncRNA           complement(93112072..93112167)
                     /gene="MIR653"
                     /gene_synonym="hsa-mir-653; MIRN653"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-653"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:724023"
                     /db_xref="miRBase:MI0003674"
                     /db_xref="HGNC:32909"
     gene            complement(93113248..93113331)
                     /gene="MIR489"
                     /gene_synonym="hsa-mir-489; MIRN489"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:574442"
                     /db_xref="HGNC:32074"
                     /db_xref="miRBase:MI0003124"
     ncRNA           complement(93113248..93113331)
                     /gene="MIR489"
                     /gene_synonym="hsa-mir-489; MIRN489"
                     /ncRNA_class="miRNA"
                     /product="microRNA 489"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_030164.1"
                     /db_xref="GI:262205165"
                     /db_xref="GeneID:574442"
                     /db_xref="HGNC:32074"
                     /db_xref="miRBase:MI0003124"
     ncRNA           complement(93113248..93113331)
                     /gene="MIR489"
                     /gene_synonym="hsa-mir-489; MIRN489"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-489"
                     /inference="similar to RNA sequence:INSD: AY882328"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:574442"
                     /db_xref="miRBase:MI0003124"
                     /db_xref="HGNC:32074"
     gene            complement(93299081..93299423)
                     /gene="RPS27P17"
                     /gene_synonym="RPS27_5_819"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392748"
                     /db_xref="HGNC:36291"
     gene            93346240..93346317
                     /gene="MIR4652"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100616206"
                     /db_xref="HGNC:41615"
                     /db_xref="miRBase:MI0017280"
     ncRNA           93346240..93346317
                     /gene="MIR4652"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4652"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039796.1"
                     /db_xref="GI:337756590"
                     /db_xref="GeneID:100616206"
                     /db_xref="HGNC:41615"
                     /db_xref="miRBase:MI0017280"
     gene            93474101..93474624
                     /gene="LOC402676"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402676"
     gene            complement(93515745..93520065)
                     /gene="TFPI2"
                     /gene_synonym="FLJ21164; PP5; REF1; TFPI-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7980"
                     /db_xref="HGNC:11761"
                     /db_xref="HPRD:08962"
                     /db_xref="MIM:600033"
     mRNA            complement(join(93515745..93516208,93516573..93516743,
                     93518347..93518535,93519449..93519631,93519903..93520065))
                     /gene="TFPI2"
                     /gene_synonym="FLJ21164; PP5; REF1; TFPI-2"
                     /product="tissue factor pathway inhibitor 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006528.2"
                     /db_xref="GI:31543803"
                     /db_xref="GeneID:7980"
                     /db_xref="HGNC:11761"
                     /db_xref="HPRD:08962"
                     /db_xref="MIM:600033"
     CDS             complement(join(93516132..93516208,93516573..93516743,
                     93518347..93518535,93519449..93519631,93519903..93519990))
                     /gene="TFPI2"
                     /gene_synonym="FLJ21164; PP5; REF1; TFPI-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="tissue factor pathway inhibitor 2 precursor"
                     /protein_id="NP_006519.1"
                     /db_xref="GI:5730091"
                     /db_xref="CCDS:CCDS5632.1"
                     /db_xref="GeneID:7980"
                     /db_xref="HGNC:11761"
                     /db_xref="HPRD:08962"
                     /db_xref="MIM:600033"
     gene            93535820..93540485
                     /gene="GNGT1"
                     /gene_synonym="GNG1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2792"
                     /db_xref="HGNC:4411"
                     /db_xref="HPRD:01805"
                     /db_xref="MIM:189970"
     mRNA            join(93535820..93535956,93536048..93536154,
                     93540102..93540485)
                     /gene="GNGT1"
                     /gene_synonym="GNG1"
                     /product="guanine nucleotide binding protein (G protein),
                     gamma transducing activity polypeptide 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021955.3"
                     /db_xref="GI:74316012"
                     /db_xref="GeneID:2792"
                     /db_xref="HGNC:4411"
                     /db_xref="HPRD:01805"
                     /db_xref="MIM:189970"
     CDS             join(93536059..93536154,93540102..93540230)
                     /gene="GNGT1"
                     /gene_synonym="GNG1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="guanine nucleotide-binding protein G(T) subunit
                     gamma-T1 precursor"
                     /protein_id="NP_068774.1"
                     /db_xref="GI:11386179"
                     /db_xref="CCDS:CCDS5633.1"
                     /db_xref="GeneID:2792"
                     /db_xref="HGNC:4411"
                     /db_xref="HPRD:01805"
                     /db_xref="MIM:189970"
     gene            93551016..93555826
                     /gene="GNG11"
                     /gene_synonym="GNGT11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2791"
                     /db_xref="HGNC:4403"
                     /db_xref="HPRD:11979"
                     /db_xref="MIM:604390"
     mRNA            join(93551016..93551545,93555403..93555826)
                     /gene="GNG11"
                     /gene_synonym="GNGT11"
                     /product="guanine nucleotide binding protein (G protein),
                     gamma 11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004126.3"
                     /db_xref="GI:91807126"
                     /db_xref="GeneID:2791"
                     /db_xref="HGNC:4403"
                     /db_xref="HPRD:11979"
                     /db_xref="MIM:604390"
     CDS             join(93551450..93551545,93555403..93555528)
                     /gene="GNG11"
                     /gene_synonym="GNGT11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="guanine nucleotide-binding protein
                     G(I)/G(S)/G(O) subunit gamma-11 precursor"
                     /protein_id="NP_004117.1"
                     /db_xref="GI:4758448"
                     /db_xref="CCDS:CCDS5634.1"
                     /db_xref="GeneID:2791"
                     /db_xref="HGNC:4403"
                     /db_xref="HPRD:11979"
                     /db_xref="MIM:604390"
     gene            complement(93621000..93633690)
                     /gene="BET1"
                     /gene_synonym="DKFZp781C0425; HBET1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10282"
                     /db_xref="HGNC:14562"
                     /db_xref="HPRD:16107"
                     /db_xref="MIM:605456"
     mRNA            complement(join(93621000..93623697,93625577..93625633,
                     93628482..93628606,93633510..93633690))
                     /gene="BET1"
                     /gene_synonym="DKFZp781C0425; HBET1"
                     /product="blocked early in transport 1 homolog (S.
                     cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005868.4"
                     /db_xref="GI:83779007"
                     /db_xref="GeneID:10282"
                     /db_xref="HGNC:14562"
                     /db_xref="HPRD:16107"
                     /db_xref="MIM:605456"
     CDS             complement(join(93623542..93623697,93625577..93625633,
                     93628482..93628606,93633510..93633528))
                     /gene="BET1"
                     /gene_synonym="DKFZp781C0425; HBET1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="BET1 homolog"
                     /protein_id="NP_005859.1"
                     /db_xref="GI:5031611"
                     /db_xref="CCDS:CCDS5635.1"
                     /db_xref="GeneID:10282"
                     /db_xref="HGNC:14562"
                     /db_xref="HPRD:16107"
                     /db_xref="MIM:605456"
     gene            94023873..94060544
                     /gene="COL1A2"
                     /gene_synonym="OI4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1278"
                     /db_xref="HGNC:2198"
                     /db_xref="HPRD:00363"
                     /db_xref="MIM:120160"
     mRNA            join(94023873..94024413,94027060..94027070,
                     94027694..94027708,94028361..94028396,94029508..94029600,
                     94030879..94030932,94033868..94033912,94034005..94034058,
                     94034151..94034204,94034511..94034564,94034985..94035038,
                     94035562..94035615,94037159..94037203,94037495..94037548,
                     94037648..94037692,94038082..94038135,94038634..94038732,
                     94038876..94038920,94039035..94039133,94039554..94039607,
                     94039732..94039839,94040201..94040254,94040368..94040466,
                     94041380..94041433,94041896..94041994,94042395..94042448,
                     94043002..94043055,94043206..94043259,94043534..94043587,
                     94044538..94044582,94045717..94045815,94047036..94047143,
                     94047811..94047864,94048810..94048863,94049545..94049598,
                     94049703..94049756,94049853..94049960,94050321..94050374,
                     94051211..94051264,94052269..94052430,94053648..94053755,
                     94054429..94054536,94054922..94054975,94055062..94055169,
                     94055310..94055363,94055735..94055842,94056320..94056373,
                     94056500..94056607,94056939..94057197,94057605..94057789,
                     94058500..94058742,94059559..94060544)
                     /gene="COL1A2"
                     /gene_synonym="OI4"
                     /product="collagen, type I, alpha 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000089.3"
                     /db_xref="GI:48762933"
                     /db_xref="GeneID:1278"
                     /db_xref="HGNC:2198"
                     /db_xref="HPRD:00363"
                     /db_xref="MIM:120160"
     CDS             join(94024344..94024413,94027060..94027070,
                     94027694..94027708,94028361..94028396,94029508..94029600,
                     94030879..94030932,94033868..94033912,94034005..94034058,
                     94034151..94034204,94034511..94034564,94034985..94035038,
                     94035562..94035615,94037159..94037203,94037495..94037548,
                     94037648..94037692,94038082..94038135,94038634..94038732,
                     94038876..94038920,94039035..94039133,94039554..94039607,
                     94039732..94039839,94040201..94040254,94040368..94040466,
                     94041380..94041433,94041896..94041994,94042395..94042448,
                     94043002..94043055,94043206..94043259,94043534..94043587,
                     94044538..94044582,94045717..94045815,94047036..94047143,
                     94047811..94047864,94048810..94048863,94049545..94049598,
                     94049703..94049756,94049853..94049960,94050321..94050374,
                     94051211..94051264,94052269..94052430,94053648..94053755,
                     94054429..94054536,94054922..94054975,94055062..94055169,
                     94055310..94055363,94055735..94055842,94056320..94056373,
                     94056500..94056607,94056939..94057197,94057605..94057789,
                     94058500..94058742,94059559..94059705)
                     /gene="COL1A2"
                     /gene_synonym="OI4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="collagen alpha-2(I) chain precursor"
                     /protein_id="NP_000080.2"
                     /db_xref="GI:48762934"
                     /db_xref="CCDS:CCDS34682.1"
                     /db_xref="GeneID:1278"
                     /db_xref="HGNC:2198"
                     /db_xref="HPRD:00363"
                     /db_xref="MIM:120160"
     gene            complement(94042445..94060553)
                     /gene="LOC100506027"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 28 ESTs"
                     /db_xref="GeneID:100506027"
     misc_RNA        complement(join(94042445..94042455,94059879..94060553))
                     /gene="LOC100506027"
                     /product="hypothetical LOC100506027, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 9 ESTs"
                     /transcript_id="XR_108846.2"
                     /db_xref="GI:341915403"
                     /db_xref="GeneID:100506027"
     misc_RNA        complement(join(94058513..94058740,94059557..94060553))
                     /gene="LOC100506027"
                     /product="hypothetical LOC100506027, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 27 ESTs"
                     /transcript_id="XR_132540.1"
                     /db_xref="GI:341915402"
                     /db_xref="GeneID:100506027"
     gene            94139170..94186331
                     /gene="CASD1"
                     /gene_synonym="C7orf12; FLJ21213; FLJ21879; FLJ41901;
                     NBLA04196"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64921"
                     /db_xref="HGNC:16014"
                     /db_xref="HPRD:13004"
                     /db_xref="MIM:611686"
     mRNA            join(94139170..94139529,94146872..94146968,
                     94147515..94147635,94156474..94156518,94157500..94157562,
                     94162517..94162561,94162991..94163114,94164621..94164835,
                     94166784..94167206,94168279..94168368,94173723..94173842,
                     94174857..94175013,94176408..94176487,94178845..94178946,
                     94180650..94180790,94181662..94181739,94183795..94183887,
                     94184804..94186331)
                     /gene="CASD1"
                     /gene_synonym="C7orf12; FLJ21213; FLJ21879; FLJ41901;
                     NBLA04196"
                     /product="CAS1 domain containing 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022900.4"
                     /db_xref="GI:170784864"
                     /db_xref="GeneID:64921"
                     /db_xref="HGNC:16014"
                     /db_xref="HPRD:13004"
                     /db_xref="MIM:611686"
     CDS             join(94139397..94139529,94146872..94146968,
                     94147515..94147635,94156474..94156518,94157500..94157562,
                     94162517..94162561,94162991..94163114,94164621..94164835,
                     94166784..94167206,94168279..94168368,94173723..94173842,
                     94174857..94175013,94176408..94176487,94178845..94178946,
                     94180650..94180790,94181662..94181739,94183795..94183887,
                     94184804..94185070)
                     /gene="CASD1"
                     /gene_synonym="C7orf12; FLJ21213; FLJ21879; FLJ41901;
                     NBLA04196"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="CAS1 domain-containing protein 1 precursor"
                     /protein_id="NP_075051.4"
                     /db_xref="GI:170784865"
                     /db_xref="CCDS:CCDS5636.1"
                     /db_xref="GeneID:64921"
                     /db_xref="HGNC:16014"
                     /db_xref="HPRD:13004"
                     /db_xref="MIM:611686"
     gene            complement(94214536..94285521)
                     /gene="SGCE"
                     /gene_synonym="DYT11; ESG"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8910"
                     /db_xref="HGNC:10808"
                     /db_xref="MIM:604149"
     mRNA            complement(join(94214536..94214827,94218001..94218044,
                     94227242..94227316,94228087..94228275,94229009..94229035,
                     94229958..94230169,94232602..94232764,94248070..94248268,
                     94252637..94252709,94257514..94257671,94259031..94259153,
                     94285302..94285521))
                     /gene="SGCE"
                     /gene_synonym="DYT11; ESG"
                     /product="sarcoglycan, epsilon, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001099401.1"
                     /db_xref="GI:150378453"
                     /db_xref="GeneID:8910"
                     /db_xref="HGNC:10808"
                     /db_xref="MIM:604149"
     mRNA            complement(join(94214536..94214827,94218001..94218044,
                     94228087..94228275,94229009..94229035,94229958..94230169,
                     94232602..94232764,94248070..94248268,94252637..94252709,
                     94257514..94257671,94259031..94259153,94285302..94285521))
                     /gene="SGCE"
                     /gene_synonym="DYT11; ESG"
                     /product="sarcoglycan, epsilon, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003919.2"
                     /db_xref="GI:150378491"
                     /db_xref="GeneID:8910"
                     /db_xref="HGNC:10808"
                     /db_xref="HPRD:04999"
                     /db_xref="MIM:604149"
     mRNA            complement(join(94214536..94214827,94217090..94217124,
                     94218001..94218044,94228087..94228275,94229958..94230169,
                     94232602..94232764,94248070..94248268,94252637..94252709,
                     94257514..94257671,94259031..94259153,94285302..94285521))
                     /gene="SGCE"
                     /gene_synonym="DYT11; ESG"
                     /product="sarcoglycan, epsilon, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001099400.1"
                     /db_xref="GI:150378534"
                     /db_xref="GeneID:8910"
                     /db_xref="HGNC:10808"
                     /db_xref="MIM:604149"
     CDS             complement(join(94214777..94214827,94217090..94217124,
                     94218001..94218044,94228087..94228275,94229958..94230169,
                     94232602..94232764,94248070..94248268,94252637..94252709,
                     94257514..94257671,94259031..94259153,94285302..94285410))
                     /gene="SGCE"
                     /gene_synonym="DYT11; ESG"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="epsilon-sarcoglycan isoform 3"
                     /protein_id="NP_001092870.1"
                     /db_xref="GI:150378535"
                     /db_xref="CCDS:CCDS47642.1"
                     /db_xref="GeneID:8910"
                     /db_xref="HGNC:10808"
                     /db_xref="MIM:604149"
     CDS             complement(join(94214811..94214827,94218001..94218044,
                     94227242..94227316,94228087..94228275,94229009..94229035,
                     94229958..94230169,94232602..94232764,94248070..94248268,
                     94252637..94252709,94257514..94257671,94259031..94259153,
                     94285302..94285410))
                     /gene="SGCE"
                     /gene_synonym="DYT11; ESG"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="epsilon-sarcoglycan isoform 1"
                     /protein_id="NP_001092871.1"
                     /db_xref="GI:150378454"
                     /db_xref="CCDS:CCDS47643.1"
                     /db_xref="GeneID:8910"
                     /db_xref="HGNC:10808"
                     /db_xref="MIM:604149"
     CDS             complement(join(94214811..94214827,94218001..94218044,
                     94228087..94228275,94229009..94229035,94229958..94230169,
                     94232602..94232764,94248070..94248268,94252637..94252709,
                     94257514..94257671,94259031..94259153,94285302..94285410))
                     /gene="SGCE"
                     /gene_synonym="DYT11; ESG"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="epsilon-sarcoglycan isoform 2"
                     /protein_id="NP_003910.1"
                     /db_xref="GI:10835047"
                     /db_xref="CCDS:CCDS5637.1"
                     /db_xref="GeneID:8910"
                     /db_xref="HGNC:10808"
                     /db_xref="MIM:604149"
     gene            94285637..94299007
                     /gene="PEG10"
                     /gene_synonym="EDR; HB-1; KIAA1051; Mar2; Mart2; MEF3L;
                     RGAG3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23089"
                     /db_xref="HGNC:14005"
                     /db_xref="MIM:609810"
     mRNA            join(94285637..94285892,94292646..94299007)
                     /gene="PEG10"
                     /gene_synonym="EDR; HB-1; KIAA1051; Mar2; Mart2; MEF3L;
                     RGAG3"
                     /product="paternally expressed 10, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001184961.1"
                     /db_xref="GI:296785057"
                     /db_xref="GeneID:23089"
                     /db_xref="HGNC:14005"
                     /db_xref="MIM:609810"
     mRNA            join(94285637..94285892,94292646..94299007)
                     /gene="PEG10"
                     /gene_synonym="EDR; HB-1; KIAA1051; Mar2; Mart2; MEF3L;
                     RGAG3"
                     /product="paternally expressed 10, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001184962.1"
                     /db_xref="GI:296785059"
                     /db_xref="GeneID:23089"
                     /db_xref="HGNC:14005"
                     /db_xref="MIM:609810"
     mRNA            join(94285637..94285892,94292646..94299007)
                     /gene="PEG10"
                     /gene_synonym="EDR; HB-1; KIAA1051; Mar2; Mart2; MEF3L;
                     RGAG3"
                     /product="paternally expressed 10, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040152.1"
                     /db_xref="GI:94421472"
                     /db_xref="GeneID:23089"
                     /db_xref="HGNC:14005"
                     /db_xref="MIM:609810"
     mRNA            join(94285637..94285892,94292646..94299007)
                     /gene="PEG10"
                     /gene_synonym="EDR; HB-1; KIAA1051; Mar2; Mart2; MEF3L;
                     RGAG3"
                     /product="paternally expressed 10, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015068.3"
                     /db_xref="GI:94421474"
                     /db_xref="GeneID:23089"
                     /db_xref="HGNC:14005"
                     /db_xref="MIM:609810"
     mRNA            join(94285682..94285903,94292646..94299007)
                     /gene="PEG10"
                     /gene_synonym="EDR; HB-1; KIAA1051; Mar2; Mart2; MEF3L;
                     RGAG3"
                     /product="paternally expressed 10, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001172437.1"
                     /db_xref="GI:289176995"
                     /db_xref="GeneID:23089"
                     /db_xref="HGNC:14005"
                     /db_xref="MIM:609810"
     mRNA            join(94285682..94285903,94292646..94299007)
                     /gene="PEG10"
                     /gene_synonym="EDR; HB-1; KIAA1051; Mar2; Mart2; MEF3L;
                     RGAG3"
                     /product="paternally expressed 10, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001172438.1"
                     /db_xref="GI:289176997"
                     /db_xref="GeneID:23089"
                     /db_xref="HGNC:14005"
                     /db_xref="MIM:609810"
     CDS             join(94285899..94285903,94292646..94293825,
                     94293825..94294994)
                     /gene="PEG10"
                     /gene_synonym="EDR; HB-1; KIAA1051; Mar2; Mart2; MEF3L;
                     RGAG3"
                     /ribosomal_slippage
                     /note="isoform 3 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="retrotransposon-derived protein PEG10 isoform 3"
                     /protein_id="NP_001165908.1"
                     /db_xref="GI:289176996"
                     /db_xref="GeneID:23089"
                     /db_xref="HGNC:14005"
                     /db_xref="MIM:609810"
     CDS             join(94285899..94285903,94292646..94293846)
                     /gene="PEG10"
                     /gene_synonym="EDR; HB-1; KIAA1051; Mar2; Mart2; MEF3L;
                     RGAG3"
                     /note="isoform 4 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="retrotransposon-derived protein PEG10 isoform 4"
                     /protein_id="NP_001165909.1"
                     /db_xref="GI:289176998"
                     /db_xref="GeneID:23089"
                     /db_xref="HGNC:14005"
                     /db_xref="MIM:609810"
     CDS             join(94292767..94293825,94293825..94294994)
                     /gene="PEG10"
                     /gene_synonym="EDR; HB-1; KIAA1051; Mar2; Mart2; MEF3L;
                     RGAG3"
                     /ribosomal_slippage
                     /note=";
                     isoform 5 is encoded by transcript variant 1;
                     non-AUG (CUG) translation initiation codon; Derived by
                     automated computational analysis using gene prediction
                     method: BestRefseq."
                     /codon_start=1
                     /product="retrotransposon-derived protein PEG10 isoform 5"
                     /protein_id="NP_001171890.1"
                     /db_xref="GI:296785058"
                     /db_xref="GeneID:23089"
                     /db_xref="HGNC:14005"
                     /db_xref="MIM:609810"
     CDS             94292767..94293846
                     /gene="PEG10"
                     /gene_synonym="EDR; HB-1; KIAA1051; Mar2; Mart2; MEF3L;
                     RGAG3"
                     /note=";
                     isoform 6 is encoded by transcript variant 1;
                     non-AUG (CUG) translation initiation codon; Derived by
                     automated computational analysis using gene prediction
                     method: BestRefseq."
                     /codon_start=1
                     /product="retrotransposon-derived protein PEG10 isoform 6"
                     /protein_id="NP_001171891.1"
                     /db_xref="GI:296785060"
                     /db_xref="GeneID:23089"
                     /db_xref="HGNC:14005"
                     /db_xref="MIM:609810"
     CDS             join(94292869..94293825,94293825..94294994)
                     /gene="PEG10"
                     /gene_synonym="EDR; HB-1; KIAA1051; Mar2; Mart2; MEF3L;
                     RGAG3"
                     /ribosomal_slippage
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="retrotransposon-derived protein PEG10 isoform 1"
                     /protein_id="NP_055883.2"
                     /db_xref="GI:94421475"
                     /db_xref="GeneID:23089"
                     /db_xref="HGNC:14005"
                     /db_xref="MIM:609810"
     CDS             94292869..94293846
                     /gene="PEG10"
                     /gene_synonym="EDR; HB-1; KIAA1051; Mar2; Mart2; MEF3L;
                     RGAG3"
                     /note="isoform 2 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="retrotransposon-derived protein PEG10 isoform 2"
                     /protein_id="NP_001035242.1"
                     /db_xref="GI:94421473"
                     /db_xref="CCDS:CCDS55126.1"
                     /db_xref="GeneID:23089"
                     /db_xref="HGNC:14005"
                     /db_xref="MIM:609810"
     gene            complement(94324293..94325151)
                     /gene="RPS3AP25"
                     /gene_synonym="RPS3A_9_820"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:645968"
                     /db_xref="HGNC:36801"
     gene            94367966..94368773
                     /gene="ATP5F1P2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:645973"
                     /db_xref="HGNC:39743"
     gene            94412200..94412838
                     /gene="GRPEL2P3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129871"
                     /db_xref="HGNC:41971"
     gene            94463139..94465616
                     /gene="ARF1P1"
                     /gene_synonym="ARF1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442334"
                     /db_xref="HGNC:22500"
     gene            94536949..94925727
                     /gene="PPP1R9A"
                     /gene_synonym="FLJ20068; KIAA1222; Neurabin-I; NRB1; NRBI"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55607"
                     /db_xref="HGNC:14946"
                     /db_xref="MIM:602468"
     mRNA            join(94536949..94537014,94539210..94540820,
                     94740571..94740703,94750024..94750144,94791179..94791283,
                     94827661..94827796,94832977..94833042,94855273..94855428,
                     94876785..94876838,94879338..94879567,94881074..94881170,
                     94881271..94881442,94897862..94898019,94898519..94898819,
                     94903211..94903298,94903397..94903480,94913330..94913642,
                     94915518..94915637,94917848..94918030,94919403..94925727)
                     /gene="PPP1R9A"
                     /gene_synonym="FLJ20068; KIAA1222; Neurabin-I; NRB1; NRBI"
                     /product="protein phosphatase 1, regulatory (inhibitor)
                     subunit 9A, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001166160.1"
                     /db_xref="GI:261244899"
                     /db_xref="GeneID:55607"
                     /db_xref="HGNC:14946"
                     /db_xref="MIM:602468"
     mRNA            join(94536949..94537014,94539210..94540820,
                     94740571..94740703,94750024..94750144,94791179..94791283,
                     94827661..94827796,94855273..94855428,94876785..94876838,
                     94879338..94879567,94881074..94881170,94881271..94881442,
                     94897862..94898019,94915518..94915637,94916422..94916445,
                     94917848..94918030,94919403..94925727)
                     /gene="PPP1R9A"
                     /gene_synonym="FLJ20068; KIAA1222; Neurabin-I; NRB1; NRBI"
                     /product="protein phosphatase 1, regulatory (inhibitor)
                     subunit 9A, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017650.2"
                     /db_xref="GI:93204860"
                     /db_xref="GeneID:55607"
                     /db_xref="HGNC:14946"
                     /db_xref="MIM:602468"
     mRNA            join(94539210..94540820,94740571..94740703,
                     94750024..94750144,94791179..94791283,94827661..94827796,
                     94855273..94855428,94876785..94876838,94879338..94879567,
                     94881074..94881170,94881271..94881442,94897862..94898019,
                     94898573..94898819,94903211..94903298,94903397..94903480,
                     94913330..94913528,94915518..94915637,94917848..94918030,
                     94919403..94925727)
                     /gene="PPP1R9A"
                     /gene_synonym="FLJ20068; KIAA1222; Neurabin-I; NRB1; NRBI"
                     /product="protein phosphatase 1, regulatory (inhibitor)
                     subunit 9A, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001166161.1"
                     /db_xref="GI:261244901"
                     /db_xref="GeneID:55607"
                     /db_xref="HGNC:14946"
                     /db_xref="MIM:602468"
     mRNA            join(94539210..94540820,94740571..94740703,
                     94750024..94750144,94791179..94791283,94827661..94827796,
                     94855273..94855428,94876785..94876838,94879338..94879567,
                     94881074..94881170,94881271..94881442,94897862..94898019,
                     94898519..94898819,94903211..94903298,94903397..94903480,
                     94913330..94913528,94915518..94915637,94919403..94925727)
                     /gene="PPP1R9A"
                     /gene_synonym="FLJ20068; KIAA1222; Neurabin-I; NRB1; NRBI"
                     /product="protein phosphatase 1, regulatory (inhibitor)
                     subunit 9A, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001166162.1"
                     /db_xref="GI:261244903"
                     /db_xref="GeneID:55607"
                     /db_xref="HGNC:14946"
                     /db_xref="MIM:602468"
     mRNA            join(94539210..94540820,94740571..94740703,
                     94750024..94750144,94791179..94791283,94827661..94827796,
                     94855273..94855428,94876785..94876838,94879338..94879567,
                     94881074..94881170,94881271..94881442,94897862..94898019,
                     94915518..94915637,94917848..94918030,94919403..94925727)
                     /gene="PPP1R9A"
                     /gene_synonym="FLJ20068; KIAA1222; Neurabin-I; NRB1; NRBI"
                     /product="protein phosphatase 1, regulatory (inhibitor)
                     subunit 9A, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001166163.1"
                     /db_xref="GI:261244905"
                     /db_xref="GeneID:55607"
                     /db_xref="HGNC:14946"
                     /db_xref="MIM:602468"
     CDS             join(94539426..94540820,94740571..94740703,
                     94750024..94750144,94791179..94791283,94827661..94827796,
                     94832977..94833042,94855273..94855428,94876785..94876838,
                     94879338..94879567,94881074..94881170,94881271..94881442,
                     94897862..94898019,94898519..94898819,94903211..94903298,
                     94903397..94903480,94913330..94913642,94915518..94915637,
                     94917848..94918030,94919403..94919615)
                     /gene="PPP1R9A"
                     /gene_synonym="FLJ20068; KIAA1222; Neurabin-I; NRB1; NRBI"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="neurabin-1 isoform 1"
                     /protein_id="NP_001159632.1"
                     /db_xref="GI:261244900"
                     /db_xref="CCDS:CCDS55127.1"
                     /db_xref="GeneID:55607"
                     /db_xref="HGNC:14946"
                     /db_xref="MIM:602468"
     CDS             join(94539426..94540820,94740571..94740703,
                     94750024..94750144,94791179..94791283,94827661..94827796,
                     94855273..94855428,94876785..94876838,94879338..94879567,
                     94881074..94881170,94881271..94881442,94897862..94898019,
                     94898573..94898819,94903211..94903298,94903397..94903480,
                     94913330..94913528,94915518..94915637,94917848..94918030,
                     94919403..94919615)
                     /gene="PPP1R9A"
                     /gene_synonym="FLJ20068; KIAA1222; Neurabin-I; NRB1; NRBI"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="neurabin-1 isoform 2"
                     /protein_id="NP_001159633.1"
                     /db_xref="GI:261244902"
                     /db_xref="CCDS:CCDS55129.1"
                     /db_xref="GeneID:55607"
                     /db_xref="HGNC:14946"
                     /db_xref="MIM:602468"
     CDS             join(94539426..94540820,94740571..94740703,
                     94750024..94750144,94791179..94791283,94827661..94827796,
                     94855273..94855428,94876785..94876838,94879338..94879567,
                     94881074..94881170,94881271..94881442,94897862..94898019,
                     94898519..94898819,94903211..94903298,94903397..94903480,
                     94913330..94913528,94915518..94915637,94919403..94919615)
                     /gene="PPP1R9A"
                     /gene_synonym="FLJ20068; KIAA1222; Neurabin-I; NRB1; NRBI"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="neurabin-1 isoform 3"
                     /protein_id="NP_001159634.1"
                     /db_xref="GI:261244904"
                     /db_xref="CCDS:CCDS55128.1"
                     /db_xref="GeneID:55607"
                     /db_xref="HGNC:14946"
                     /db_xref="MIM:602468"
     CDS             join(94539426..94540820,94740571..94740703,
                     94750024..94750144,94791179..94791283,94827661..94827796,
                     94855273..94855428,94876785..94876838,94879338..94879567,
                     94881074..94881170,94881271..94881442,94897862..94898019,
                     94915518..94915637,94916422..94916445,94917848..94918030,
                     94919403..94919615)
                     /gene="PPP1R9A"
                     /gene_synonym="FLJ20068; KIAA1222; Neurabin-I; NRB1; NRBI"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="neurabin-1 isoform 4"
                     /protein_id="NP_060120.2"
                     /db_xref="GI:93204861"
                     /db_xref="CCDS:CCDS34683.1"
                     /db_xref="GeneID:55607"
                     /db_xref="HGNC:14946"
                     /db_xref="MIM:602468"
     CDS             join(94539426..94540820,94740571..94740703,
                     94750024..94750144,94791179..94791283,94827661..94827796,
                     94855273..94855428,94876785..94876838,94879338..94879567,
                     94881074..94881170,94881271..94881442,94897862..94898019,
                     94915518..94915637,94917848..94918030,94919403..94919615)
                     /gene="PPP1R9A"
                     /gene_synonym="FLJ20068; KIAA1222; Neurabin-I; NRB1; NRBI"
                     /note="isoform 5 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="neurabin-1 isoform 5"
                     /protein_id="NP_001159635.1"
                     /db_xref="GI:261244906"
                     /db_xref="GeneID:55607"
                     /db_xref="HGNC:14946"
                     /db_xref="MIM:602468"
     gene            complement(94647312..94647797)
                     /gene="LOC100233146"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100233146"
     gene            complement(94927669..94953884)
                     /gene="PON1"
                     /gene_synonym="ESA; MVCD5; PON"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5444"
                     /db_xref="HGNC:9204"
                     /db_xref="HPRD:01351"
                     /db_xref="MIM:168820"
     mRNA            complement(join(94927669..94928414,94931517..94931645,
                     94935597..94935678,94937323..94937523,94940763..94940889,
                     94944634..94944802,94946046..94946101,94947635..94947705,
                     94953714..94953884))
                     /gene="PON1"
                     /gene_synonym="ESA; MVCD5; PON"
                     /product="paraoxonase 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000446.5"
                     /db_xref="GI:209413720"
                     /db_xref="GeneID:5444"
                     /db_xref="HGNC:9204"
                     /db_xref="HPRD:01351"
                     /db_xref="MIM:168820"
     CDS             complement(join(94928256..94928414,94931517..94931645,
                     94935597..94935678,94937323..94937523,94940763..94940889,
                     94944634..94944802,94946046..94946101,94947635..94947705,
                     94953714..94953787))
                     /gene="PON1"
                     /gene_synonym="ESA; MVCD5; PON"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="serum paraoxonase/arylesterase 1 precursor"
                     /protein_id="NP_000437.3"
                     /db_xref="GI:19923106"
                     /db_xref="CCDS:CCDS5638.1"
                     /db_xref="GeneID:5444"
                     /db_xref="HGNC:9204"
                     /db_xref="HPRD:01351"
                     /db_xref="MIM:168820"
     gene            94979476..94981079
                     /gene="LOC100533722"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533722"
     gene            complement(94989184..95025687)
                     /gene="PON3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5446"
                     /db_xref="HGNC:9206"
                     /db_xref="HPRD:04098"
                     /db_xref="MIM:602720"
     mRNA            complement(join(94989184..94989443,94991674..94991802,
                     94992072..94992153,94993175..94993375,94996674..94996800,
                     95001485..95001650,95019466..95019521,95023956..95024026,
                     95025589..95025687))
                     /gene="PON3"
                     /product="paraoxonase 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000940.2"
                     /db_xref="GI:94538355"
                     /db_xref="GeneID:5446"
                     /db_xref="HGNC:9206"
                     /db_xref="HPRD:04098"
                     /db_xref="MIM:602720"
     CDS             complement(join(94989285..94989443,94991674..94991802,
                     94992072..94992153,94993175..94993375,94996674..94996800,
                     95001485..95001650,95019466..95019521,95023956..95024026,
                     95025589..95025662))
                     /gene="PON3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="serum paraoxonase/lactonase 3"
                     /protein_id="NP_000931.1"
                     /db_xref="GI:29788996"
                     /db_xref="CCDS:CCDS5639.1"
                     /db_xref="GeneID:5446"
                     /db_xref="HGNC:9206"
                     /db_xref="HPRD:04098"
                     /db_xref="MIM:602720"
     gene            complement(95034174..95064384)
                     /gene="PON2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5445"
                     /db_xref="HGNC:9205"
                     /db_xref="HPRD:03903"
                     /db_xref="MIM:602447"
     mRNA            complement(join(95034174..95034800,95035431..95035559,
                     95036299..95036380,95039213..95039413,95040965..95041091,
                     95041624..95041789,95045554..95045609,95053827..95053897,
                     95064190..95064384))
                     /gene="PON2"
                     /product="paraoxonase 2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000305.2"
                     /db_xref="GI:66529293"
                     /db_xref="GeneID:5445"
                     /db_xref="HGNC:9205"
                     /db_xref="HPRD:03903"
                     /db_xref="MIM:602447"
     mRNA            complement(join(95034174..95034800,95035431..95035559,
                     95036299..95036380,95039213..95039413,95040965..95041055,
                     95041624..95041789,95045554..95045609,95053827..95053897,
                     95064190..95064384))
                     /gene="PON2"
                     /product="paraoxonase 2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001018161.1"
                     /db_xref="GI:66529395"
                     /db_xref="GeneID:5445"
                     /db_xref="HGNC:9205"
                     /db_xref="MIM:602447"
                     /db_xref="HPRD:03903"
     CDS             complement(join(95034642..95034800,95035431..95035559,
                     95036299..95036380,95039213..95039413,95040965..95041091,
                     95041624..95041789,95045554..95045609,95053827..95053897,
                     95064190..95064263))
                     /gene="PON2"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="serum paraoxonase/arylesterase 2 isoform 1"
                     /protein_id="NP_000296.2"
                     /db_xref="GI:66529294"
                     /db_xref="CCDS:CCDS5640.1"
                     /db_xref="GeneID:5445"
                     /db_xref="HGNC:9205"
                     /db_xref="HPRD:03903"
                     /db_xref="MIM:602447"
     CDS             complement(join(95034642..95034800,95035431..95035559,
                     95036299..95036380,95039213..95039413,95040965..95041055,
                     95041624..95041789,95045554..95045609,95053827..95053897,
                     95064190..95064263))
                     /gene="PON2"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="serum paraoxonase/arylesterase 2 isoform 2"
                     /protein_id="NP_001018171.1"
                     /db_xref="GI:66529396"
                     /db_xref="CCDS:CCDS47644.1"
                     /db_xref="GeneID:5445"
                     /db_xref="HGNC:9205"
                     /db_xref="HPRD:03903"
                     /db_xref="MIM:602447"
     gene            95115213..95169543
                     /gene="ASB4"
                     /gene_synonym="ASB-4; MGC142039; MGC142041"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51666"
                     /db_xref="HGNC:16009"
                     /db_xref="MIM:605761"
     mRNA            join(95115213..95115470,95125070..95125369,
                     95157125..95157615,95165749..95165862,95166883..95169543)
                     /gene="ASB4"
                     /gene_synonym="ASB-4; MGC142039; MGC142041"
                     /product="ankyrin repeat and SOCS box containing 4,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016116.2"
                     /db_xref="GI:315360676"
                     /db_xref="GeneID:51666"
                     /db_xref="HGNC:16009"
                     /db_xref="HPRD:05770"
                     /db_xref="MIM:605761"
     mRNA            join(95115213..95115470,95125070..95125369,
                     95157125..95158113)
                     /gene="ASB4"
                     /gene_synonym="ASB-4; MGC142039; MGC142041"
                     /product="ankyrin repeat and SOCS box containing 4,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145872.2"
                     /db_xref="GI:315360673"
                     /db_xref="GeneID:51666"
                     /db_xref="HGNC:16009"
                     /db_xref="MIM:605761"
     CDS             join(95115284..95115470,95125070..95125369,
                     95157125..95157615,95165749..95165862,95166883..95167071)
                     /gene="ASB4"
                     /gene_synonym="ASB-4; MGC142039; MGC142041"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ankyrin repeat and SOCS box protein 4 isoform a"
                     /protein_id="NP_057200.1"
                     /db_xref="GI:7706379"
                     /db_xref="CCDS:CCDS5641.1"
                     /db_xref="GeneID:51666"
                     /db_xref="HGNC:16009"
                     /db_xref="MIM:605761"
     CDS             join(95115284..95115470,95125070..95125369,
                     95157125..95157687)
                     /gene="ASB4"
                     /gene_synonym="ASB-4; MGC142039; MGC142041"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ankyrin repeat and SOCS box protein 4 isoform b"
                     /protein_id="NP_665879.1"
                     /db_xref="GI:22208964"
                     /db_xref="CCDS:CCDS5642.1"
                     /db_xref="GeneID:51666"
                     /db_xref="HGNC:16009"
                     /db_xref="MIM:605761"
     gene            complement(95212809..95225925)
                     /gene="PDK4"
                     /gene_synonym="FLJ40832"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5166"
                     /db_xref="HGNC:8812"
                     /db_xref="HPRD:03957"
                     /db_xref="MIM:602527"
     mRNA            complement(join(95212809..95215093,95216322..95216435,
                     95216730..95216840,95217039..95217137,95218952..95219028,
                     95221300..95221377,95221823..95221909,95222072..95222256,
                     95223011..95223082,95224335..95224476,95225476..95225925))
                     /gene="PDK4"
                     /gene_synonym="FLJ40832"
                     /product="pyruvate dehydrogenase kinase, isozyme 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002612.3"
                     /db_xref="GI:94421466"
                     /db_xref="GeneID:5166"
                     /db_xref="HGNC:8812"
                     /db_xref="HPRD:03957"
                     /db_xref="MIM:602527"
     CDS             complement(join(95214953..95215093,95216322..95216435,
                     95216730..95216840,95217039..95217137,95218952..95219028,
                     95221300..95221377,95221823..95221909,95222072..95222256,
                     95223011..95223082,95224335..95224476,95225476..95225605))
                     /gene="PDK4"
                     /gene_synonym="FLJ40832"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="pyruvate dehydrogenase kinase, isozyme 4
                     precursor"
                     /protein_id="NP_002603.1"
                     /db_xref="GI:4505693"
                     /db_xref="CCDS:CCDS5643.1"
                     /db_xref="GeneID:5166"
                     /db_xref="HGNC:8812"
                     /db_xref="HPRD:03957"
                     /db_xref="MIM:602527"
     gene            95401818..95727736
                     /gene="DYNC1I1"
                     /gene_synonym="DNCI1; DNCIC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1780"
                     /db_xref="HGNC:2963"
                     /db_xref="HPRD:04798"
                     /db_xref="MIM:603772"
     mRNA            join(95401818..95402085,95434033..95434149,
                     95439704..95439818,95442508..95442649,95457369..95457428,
                     95499195..95499310,95606824..95606913,95614127..95614289,
                     95616368..95616467,95625260..95625385,95657487..95657633,
                     95661979..95662092,95664931..95665064,95668589..95668733,
                     95705369..95705509,95709675..95709800,95726795..95727736)
                     /gene="DYNC1I1"
                     /gene_synonym="DNCI1; DNCIC1"
                     /product="dynein, cytoplasmic 1, intermediate chain 1,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004411.4"
                     /db_xref="GI:197209868"
                     /db_xref="GeneID:1780"
                     /db_xref="HGNC:2963"
                     /db_xref="HPRD:04798"
                     /db_xref="MIM:603772"
     mRNA            join(95401818..95402085,95434033..95434149,
                     95439704..95439818,95442559..95442649,95457369..95457428,
                     95499195..95499310,95606824..95606913,95614127..95614289,
                     95616368..95616467,95625260..95625385,95657487..95657633,
                     95661979..95662092,95664931..95665064,95668589..95668733,
                     95705369..95705509,95709675..95709800,95726795..95727736)
                     /gene="DYNC1I1"
                     /gene_synonym="DNCI1; DNCIC1"
                     /product="dynein, cytoplasmic 1, intermediate chain 1,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001135556.1"
                     /db_xref="GI:207113121"
                     /db_xref="GeneID:1780"
                     /db_xref="HGNC:2963"
                     /db_xref="MIM:603772"
                     /db_xref="HPRD:04798"
     mRNA            join(95401818..95402085,95434033..95434149,
                     95439704..95439818,95442559..95442649,95499195..95499310,
                     95606824..95606913,95614127..95614289,95616368..95616467,
                     95625260..95625385,95657487..95657633,95661979..95662092,
                     95664931..95665064,95668589..95668733,95705369..95705509,
                     95709675..95709800,95726795..95727736)
                     /gene="DYNC1I1"
                     /gene_synonym="DNCI1; DNCIC1"
                     /product="dynein, cytoplasmic 1, intermediate chain 1,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001135557.1"
                     /db_xref="GI:207113123"
                     /db_xref="GeneID:1780"
                     /db_xref="HGNC:2963"
                     /db_xref="MIM:603772"
                     /db_xref="HPRD:04798"
     CDS             join(95434042..95434149,95439704..95439818,
                     95442508..95442649,95457369..95457428,95499195..95499310,
                     95606824..95606913,95614127..95614289,95616368..95616467,
                     95625260..95625385,95657487..95657633,95661979..95662092,
                     95664931..95665064,95668589..95668733,95705369..95705509,
                     95709675..95709800,95726795..95726905)
                     /gene="DYNC1I1"
                     /gene_synonym="DNCI1; DNCIC1"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytoplasmic dynein 1 intermediate chain 1
                     isoform a"
                     /protein_id="NP_004402.1"
                     /db_xref="GI:4758178"
                     /db_xref="CCDS:CCDS5644.1"
                     /db_xref="GeneID:1780"
                     /db_xref="HGNC:2963"
                     /db_xref="HPRD:04798"
                     /db_xref="MIM:603772"
     CDS             join(95434042..95434149,95439704..95439818,
                     95442559..95442649,95457369..95457428,95499195..95499310,
                     95606824..95606913,95614127..95614289,95616368..95616467,
                     95625260..95625385,95657487..95657633,95661979..95662092,
                     95664931..95665064,95668589..95668733,95705369..95705509,
                     95709675..95709800,95726795..95726905)
                     /gene="DYNC1I1"
                     /gene_synonym="DNCI1; DNCIC1"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytoplasmic dynein 1 intermediate chain 1
                     isoform b"
                     /protein_id="NP_001129028.1"
                     /db_xref="GI:207113122"
                     /db_xref="CCDS:CCDS47645.1"
                     /db_xref="GeneID:1780"
                     /db_xref="HGNC:2963"
                     /db_xref="HPRD:04798"
                     /db_xref="MIM:603772"
     CDS             join(95434042..95434149,95439704..95439818,
                     95442559..95442649,95499195..95499310,95606824..95606913,
                     95614127..95614289,95616368..95616467,95625260..95625385,
                     95657487..95657633,95661979..95662092,95664931..95665064,
                     95668589..95668733,95705369..95705509,95709675..95709800,
                     95726795..95726905)
                     /gene="DYNC1I1"
                     /gene_synonym="DNCI1; DNCIC1"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytoplasmic dynein 1 intermediate chain 1
                     isoform c"
                     /protein_id="NP_001129029.1"
                     /db_xref="GI:207113124"
                     /db_xref="CCDS:CCDS47646.1"
                     /db_xref="GeneID:1780"
                     /db_xref="HGNC:2963"
                     /db_xref="HPRD:04798"
                     /db_xref="MIM:603772"
     gene            complement(95749532..95951459)
                     /gene="SLC25A13"
                     /gene_synonym="ARALAR2; CITRIN; CTLN2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10165"
                     /db_xref="HGNC:10983"
                     /db_xref="HPRD:04837"
                     /db_xref="MIM:603859"
     mRNA            complement(join(95749532..95750689,95750967..95751057,
                     95751151..95751309,95761055..95761193,95775868..95776008,
                     95799357..95799437,95800784..95800836,95813589..95813747,
                     95814239..95814326,95818606..95818690,95818893..95818986,
                     95820421..95820559,95822349..95822495,95838150..95838289,
                     95864114..95864229,95906508..95906650,95926210..95926263,
                     95951254..95951459))
                     /gene="SLC25A13"
                     /gene_synonym="ARALAR2; CITRIN; CTLN2"
                     /product="solute carrier family 25, member 13 (citrin),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001160210.1"
                     /db_xref="GI:237649018"
                     /db_xref="GeneID:10165"
                     /db_xref="HGNC:10983"
                     /db_xref="MIM:603859"
                     /db_xref="HPRD:04837"
     mRNA            complement(join(95749532..95750689,95750967..95751057,
                     95751151..95751309,95761055..95761193,95775868..95776008,
                     95799357..95799437,95800784..95800836,95813589..95813747,
                     95814239..95814323,95818606..95818690,95818893..95818986,
                     95820421..95820559,95822349..95822495,95838150..95838289,
                     95864114..95864229,95906508..95906650,95926210..95926263,
                     95951254..95951459))
                     /gene="SLC25A13"
                     /gene_synonym="ARALAR2; CITRIN; CTLN2"
                     /product="solute carrier family 25, member 13 (citrin),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014251.2"
                     /db_xref="GI:171906609"
                     /db_xref="GeneID:10165"
                     /db_xref="HGNC:10983"
                     /db_xref="HPRD:04837"
                     /db_xref="MIM:603859"
     misc_RNA        complement(join(95749532..95750689,95750967..95751057,
                     95751151..95751309,95761055..95761193,95775868..95776008,
                     95799357..95799437,95800784..95800836,95813589..95813747,
                     95814239..95814323,95818606..95818690,95818893..95818986,
                     95820421..95820559,95822349..95822495,95838150..95838289,
                     95906508..95906650,95926210..95926263,95951254..95951459))
                     /gene="SLC25A13"
                     /gene_synonym="ARALAR2; CITRIN; CTLN2"
                     /product="solute carrier family 25, member 13 (citrin),
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027662.1"
                     /db_xref="GI:237649020"
                     /db_xref="GeneID:10165"
                     /db_xref="HGNC:10983"
                     /db_xref="MIM:603859"
                     /db_xref="HPRD:04837"
     CDS             complement(join(95750503..95750689,95750967..95751057,
                     95751151..95751309,95761055..95761193,95775868..95776008,
                     95799357..95799437,95800784..95800836,95813589..95813747,
                     95814239..95814326,95818606..95818690,95818893..95818986,
                     95820421..95820559,95822349..95822495,95838150..95838289,
                     95864114..95864229,95906508..95906650,95926210..95926263,
                     95951254..95951268))
                     /gene="SLC25A13"
                     /gene_synonym="ARALAR2; CITRIN; CTLN2"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium-binding mitochondrial carrier protein
                     Aralar2 isoform 1"
                     /protein_id="NP_001153682.1"
                     /db_xref="GI:237649019"
                     /db_xref="CCDS:CCDS55130.1"
                     /db_xref="GeneID:10165"
                     /db_xref="HGNC:10983"
                     /db_xref="HPRD:04837"
                     /db_xref="MIM:603859"
     CDS             complement(join(95750503..95750689,95750967..95751057,
                     95751151..95751309,95761055..95761193,95775868..95776008,
                     95799357..95799437,95800784..95800836,95813589..95813747,
                     95814239..95814323,95818606..95818690,95818893..95818986,
                     95820421..95820559,95822349..95822495,95838150..95838289,
                     95864114..95864229,95906508..95906650,95926210..95926263,
                     95951254..95951268))
                     /gene="SLC25A13"
                     /gene_synonym="ARALAR2; CITRIN; CTLN2"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium-binding mitochondrial carrier protein
                     Aralar2 isoform 2"
                     /protein_id="NP_055066.1"
                     /db_xref="GI:7657581"
                     /db_xref="CCDS:CCDS5645.1"
                     /db_xref="GeneID:10165"
                     /db_xref="HGNC:10983"
                     /db_xref="HPRD:04837"
                     /db_xref="MIM:603859"
     gene            complement(95757139..95757374)
                     /gene="CYCSP18"
                     /gene_synonym="HCP18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:360173"
                     /db_xref="HGNC:24391"
     gene            complement(95848974..95849068)
                     /gene="MIR591"
                     /gene_synonym="hsa-mir-591; MIRN591"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:693176"
                     /db_xref="HGNC:32847"
                     /db_xref="miRBase:MI0003603"
     ncRNA           complement(95848974..95849068)
                     /gene="MIR591"
                     /gene_synonym="hsa-mir-591; MIRN591"
                     /ncRNA_class="miRNA"
                     /product="microRNA 591"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_030322.1"
                     /db_xref="GI:262205952"
                     /db_xref="GeneID:693176"
                     /db_xref="HGNC:32847"
                     /db_xref="miRBase:MI0003603"
     ncRNA           complement(95848974..95849068)
                     /gene="MIR591"
                     /gene_synonym="hsa-mir-591; MIRN591"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-591"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:693176"
                     /db_xref="miRBase:MI0003603"
                     /db_xref="HGNC:32847"
     gene            95912625..95913165
                     /gene="RPL21P74"
                     /gene_synonym="RPL21_30_821"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271184"
                     /db_xref="HGNC:35854"
     gene            complement(96110938..96132835)
                     /gene="FLJ42280"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:401388"
     mRNA            complement(join(96110938..96113300,96114137..96114166,
                     96115515..96115729,96125596..96125653,96132795..96132835))
                     /gene="FLJ42280"
                     /product="hypothetical LOC401388, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001201450.1"
                     /db_xref="GI:319803094"
                     /db_xref="GeneID:401388"
     mRNA            complement(join(96110938..96113300,96115515..96115729,
                     96125596..96125653,96132795..96132835))
                     /gene="FLJ42280"
                     /product="hypothetical LOC401388, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001201451.1"
                     /db_xref="GI:319803096"
                     /db_xref="GeneID:401388"
     CDS             complement(join(96113171..96113300,96114137..96114166,
                     96115515..96115729,96125596..96125607))
                     /gene="FLJ42280"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC401388 isoform 1"
                     /protein_id="NP_001188379.1"
                     /db_xref="GI:319803095"
                     /db_xref="GeneID:401388"
     CDS             complement(join(96113171..96113300,96115515..96115729,
                     96125596..96125607))
                     /gene="FLJ42280"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC401388 isoform 2"
                     /protein_id="NP_001188380.1"
                     /db_xref="GI:319803097"
                     /db_xref="GeneID:401388"
     gene            complement(96250969..96293650)
                     /gene="LOC100506136"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100506136"
     misc_RNA        complement(join(96250969..96251955,96275036..96275248,
                     96276741..96276852,96285769..96285897,96293515..96293650))
                     /gene="LOC100506136"
                     /product="hypothetical LOC100506136"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038948.1"
                     /db_xref="GI:336595235"
                     /db_xref="GeneID:100506136"
     gene            complement(96318079..96339203)
                     /gene="SHFM1"
                     /gene_synonym="DSS1; ECD; SEM1; SHFD1; Shfdg1; SHSF1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7979"
                     /db_xref="HGNC:10845"
                     /db_xref="HPRD:03182"
                     /db_xref="MIM:183600"
     mRNA            complement(join(96318079..96318278,96324110..96324203,
                     96339000..96339203))
                     /gene="SHFM1"
                     /gene_synonym="DSS1; ECD; SEM1; SHFD1; Shfdg1; SHSF1"
                     /product="split hand/foot malformation (ectrodactyly) type
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006304.1"
                     /db_xref="GI:5453639"
                     /db_xref="GeneID:7979"
                     /db_xref="HGNC:10845"
                     /db_xref="HPRD:03182"
                     /db_xref="MIM:183600"
     CDS             complement(join(96318236..96318278,96324110..96324203,
                     96339000..96339075))
                     /gene="SHFM1"
                     /gene_synonym="DSS1; ECD; SEM1; SHFD1; Shfdg1; SHSF1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="26S proteasome complex subunit DSS1"
                     /protein_id="NP_006295.1"
                     /db_xref="GI:5453640"
                     /db_xref="CCDS:CCDS5646.1"
                     /db_xref="GeneID:7979"
                     /db_xref="HGNC:10845"
                     /db_xref="HPRD:03182"
                     /db_xref="MIM:183600"
     gene            96487476..96488983
                     /gene="MARK2P10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402679"
                     /db_xref="HGNC:39801"
     gene            complement(96597827..96643377)
                     /gene="DLX6-AS1"
                     /gene_synonym="DLX6-AS; DLX6AS; Evf-2; FLJ34048;
                     NCRNA00212"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285987"
                     /db_xref="HGNC:37151"
     misc_RNA        complement(join(96597827..96598430,96607659..96608903,
                     96643237..96643377))
                     /gene="DLX6-AS1"
                     /gene_synonym="DLX6-AS; DLX6AS; Evf-2; FLJ34048;
                     NCRNA00212"
                     /product="DLX6 antisense RNA 1 (non-protein coding)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_015448.1"
                     /db_xref="GI:213417936"
                     /db_xref="GeneID:285987"
                     /db_xref="HGNC:37151"
     gene            96635290..96640352
                     /gene="DLX6"
                     /gene_synonym="MGC125282; MGC125283; MGC125284; MGC125285"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1750"
                     /db_xref="HGNC:2919"
                     /db_xref="HPRD:02493"
                     /db_xref="MIM:600030"
     mRNA            join(96635290..96635725,96636950..96637143,
                     96639108..96640352)
                     /gene="DLX6"
                     /gene_synonym="MGC125282; MGC125283; MGC125284; MGC125285"
                     /product="distal-less homeobox 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005222.3"
                     /db_xref="GI:294610639"
                     /db_xref="GeneID:1750"
                     /db_xref="HGNC:2919"
                     /db_xref="HPRD:02493"
                     /db_xref="MIM:600030"
     CDS             join(96635290..96635725,96636950..96637143,
                     96639108..96639359)
                     /gene="DLX6"
                     /gene_synonym="MGC125282; MGC125283; MGC125284; MGC125285"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein DLX-6"
                     /protein_id="NP_005213.3"
                     /db_xref="GI:294610640"
                     /db_xref="CCDS:CCDS47647.2"
                     /db_xref="GeneID:1750"
                     /db_xref="HGNC:2919"
                     /db_xref="HPRD:02493"
                     /db_xref="MIM:600030"
     gene            complement(96649702..96654143)
                     /gene="DLX5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1749"
                     /db_xref="HGNC:2918"
                     /db_xref="HPRD:02492"
                     /db_xref="MIM:600028"
     mRNA            complement(join(96649702..96650377,96651497..96651681,
                     96653581..96654143))
                     /gene="DLX5"
                     /product="distal-less homeobox 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005221.5"
                     /db_xref="GI:84043959"
                     /db_xref="GeneID:1749"
                     /db_xref="HGNC:2918"
                     /db_xref="HPRD:02492"
                     /db_xref="MIM:600028"
     CDS             complement(join(96650048..96650377,96651497..96651681,
                     96653581..96653935))
                     /gene="DLX5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein DLX-5"
                     /protein_id="NP_005212.1"
                     /db_xref="GI:4885187"
                     /db_xref="CCDS:CCDS5647.1"
                     /db_xref="GeneID:1749"
                     /db_xref="HGNC:2918"
                     /db_xref="HPRD:02492"
                     /db_xref="MIM:600028"
     gene            96745905..96811075
                     /gene="ACN9"
                     /gene_synonym="DC11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57001"
                     /db_xref="HGNC:21752"
                     /db_xref="HPRD:16471"
     mRNA            join(96745905..96747209,96810324..96811075)
                     /gene="ACN9"
                     /gene_synonym="DC11"
                     /product="ACN9 homolog (S. cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020186.2"
                     /db_xref="GI:187761338"
                     /db_xref="GeneID:57001"
                     /db_xref="HGNC:21752"
                     /db_xref="HPRD:16471"
     CDS             join(96747036..96747209,96810324..96810527)
                     /gene="ACN9"
                     /gene_synonym="DC11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein ACN9 homolog, mitochondrial precursor"
                     /protein_id="NP_064571.1"
                     /db_xref="GI:9910180"
                     /db_xref="CCDS:CCDS5648.1"
                     /db_xref="GeneID:57001"
                     /db_xref="HGNC:21752"
                     /db_xref="HPRD:16471"
     gene            complement(96830134..96830782)
                     /gene="RPL7AP40"
                     /gene_synonym="RPL7A_18_822"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442712"
                     /db_xref="HGNC:35883"
     gene            97361271..97369784
                     /gene="TAC1"
                     /gene_synonym="Hs.2563; NK2; NKNA; NPK; TAC2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6863"
                     /db_xref="HGNC:11517"
                     /db_xref="HPRD:08876"
                     /db_xref="MIM:162320"
     mRNA            join(97361271..97361507,97361916..97362047,
                     97363035..97363131,97363560..97363604,97364138..97364161,
                     97369186..97369784)
                     /gene="TAC1"
                     /gene_synonym="Hs.2563; NK2; NKNA; NPK; TAC2"
                     /product="tachykinin, precursor 1, transcript variant
                     alpha"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013996.2"
                     /db_xref="GI:166158920"
                     /db_xref="GeneID:6863"
                     /db_xref="HGNC:11517"
                     /db_xref="MIM:162320"
                     /db_xref="HPRD:08876"
     mRNA            join(97361271..97361507,97361916..97362047,
                     97363035..97363131,97363560..97363604,97364138..97364161,
                     97365611..97365664,97369186..97369784)
                     /gene="TAC1"
                     /gene_synonym="Hs.2563; NK2; NKNA; NPK; TAC2"
                     /product="tachykinin, precursor 1, transcript variant
                     beta"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003182.2"
                     /db_xref="GI:166158917"
                     /db_xref="GeneID:6863"
                     /db_xref="HGNC:11517"
                     /db_xref="HPRD:08876"
                     /db_xref="MIM:162320"
     mRNA            join(97361271..97361507,97361916..97362047,
                     97363035..97363131,97364138..97364161,97369186..97369784)
                     /gene="TAC1"
                     /gene_synonym="Hs.2563; NK2; NKNA; NPK; TAC2"
                     /product="tachykinin, precursor 1, transcript variant
                     delta"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013998.2"
                     /db_xref="GI:166158918"
                     /db_xref="GeneID:6863"
                     /db_xref="HGNC:11517"
                     /db_xref="MIM:162320"
                     /db_xref="HPRD:08876"
     mRNA            join(97361271..97361507,97361916..97362047,
                     97363035..97363131,97364138..97364161,97365611..97365664,
                     97369186..97369784)
                     /gene="TAC1"
                     /gene_synonym="Hs.2563; NK2; NKNA; NPK; TAC2"
                     /product="tachykinin, precursor 1, transcript variant
                     gamma"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013997.2"
                     /db_xref="GI:166158919"
                     /db_xref="GeneID:6863"
                     /db_xref="HGNC:11517"
                     /db_xref="MIM:162320"
                     /db_xref="HPRD:08876"
     CDS             join(97361925..97362047,97363035..97363131,
                     97363560..97363604,97364138..97364161,97369186..97369232)
                     /gene="TAC1"
                     /gene_synonym="Hs.2563; NK2; NKNA; NPK; TAC2"
                     /note="isoform alpha precursor is encoded by transcript
                     variant alpha; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protachykinin-1 isoform alpha precursor"
                     /protein_id="NP_054702.1"
                     /db_xref="GI:7770075"
                     /db_xref="CCDS:CCDS5650.1"
                     /db_xref="GeneID:6863"
                     /db_xref="HGNC:11517"
                     /db_xref="HPRD:08876"
                     /db_xref="MIM:162320"
     CDS             join(97361925..97362047,97363035..97363131,
                     97363560..97363604,97364138..97364161,97365611..97365664,
                     97369186..97369232)
                     /gene="TAC1"
                     /gene_synonym="Hs.2563; NK2; NKNA; NPK; TAC2"
                     /note="isoform beta precursor is encoded by transcript
                     variant beta; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protachykinin-1 isoform beta precursor"
                     /protein_id="NP_003173.1"
                     /db_xref="GI:4507341"
                     /db_xref="CCDS:CCDS5649.1"
                     /db_xref="GeneID:6863"
                     /db_xref="HGNC:11517"
                     /db_xref="HPRD:08876"
                     /db_xref="MIM:162320"
     CDS             join(97361925..97362047,97363035..97363131,
                     97364138..97364161,97369186..97369232)
                     /gene="TAC1"
                     /gene_synonym="Hs.2563; NK2; NKNA; NPK; TAC2"
                     /note="isoform delta precursor is encoded by transcript
                     variant delta; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protachykinin-1 isoform delta precursor"
                     /protein_id="NP_054704.1"
                     /db_xref="GI:7770079"
                     /db_xref="GeneID:6863"
                     /db_xref="HGNC:11517"
                     /db_xref="MIM:162320"
                     /db_xref="HPRD:08876"
     CDS             join(97361925..97362047,97363035..97363131,
                     97364138..97364161,97365611..97365664,97369186..97369232)
                     /gene="TAC1"
                     /gene_synonym="Hs.2563; NK2; NKNA; NPK; TAC2"
                     /note="isoform gamma precursor is encoded by transcript
                     variant gamma; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protachykinin-1 isoform gamma precursor"
                     /protein_id="NP_054703.1"
                     /db_xref="GI:7770077"
                     /db_xref="CCDS:CCDS5651.1"
                     /db_xref="GeneID:6863"
                     /db_xref="HGNC:11517"
                     /db_xref="HPRD:08876"
                     /db_xref="MIM:162320"
     gene            complement(97481429..97501854)
                     /gene="ASNS"
                     /gene_synonym="TS11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:440"
                     /db_xref="HGNC:753"
                     /db_xref="HPRD:00153"
                     /db_xref="MIM:108370"
     mRNA            complement(join(97481429..97481780,97482372..97482527,
                     97482617..97482698,97483892..97483992,97484665..97484771,
                     97486002..97486128,97487590..97487717,97488166..97488267,
                     97488525..97488710,97493571..97493808,97498220..97498491,
                     97499090..97499125,97501663..97501854))
                     /gene="ASNS"
                     /gene_synonym="TS11"
                     /product="asparagine synthetase (glutamine-hydrolyzing),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001673.4"
                     /db_xref="GI:296010844"
                     /db_xref="GeneID:440"
                     /db_xref="HGNC:753"
                     /db_xref="HPRD:00153"
                     /db_xref="MIM:108370"
     mRNA            complement(join(97481429..97481780,97482372..97482527,
                     97482617..97482698,97483892..97483992,97484665..97484771,
                     97486002..97486128,97487590..97487717,97488166..97488267,
                     97488525..97488710,97493571..97493808,97498220..97498491,
                     97499090..97499125,97501031..97501308,97501663..97501854))
                     /gene="ASNS"
                     /gene_synonym="TS11"
                     /product="asparagine synthetase (glutamine-hydrolyzing),
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_183356.3"
                     /db_xref="GI:296010845"
                     /db_xref="GeneID:440"
                     /db_xref="HGNC:753"
                     /db_xref="HPRD:00153"
                     /db_xref="MIM:108370"
     mRNA            complement(join(97481429..97481780,97482372..97482527,
                     97482617..97482698,97483892..97483992,97484665..97484771,
                     97486002..97486128,97487590..97487717,97488166..97488267,
                     97488525..97488710,97493571..97493808,97498220..97498417,
                     97499090..97499125,97501663..97501854))
                     /gene="ASNS"
                     /gene_synonym="TS11"
                     /product="asparagine synthetase (glutamine-hydrolyzing),
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001178075.1"
                     /db_xref="GI:296010847"
                     /db_xref="GeneID:440"
                     /db_xref="HGNC:753"
                     /db_xref="MIM:108370"
                     /db_xref="HPRD:00153"
     mRNA            complement(join(97481429..97481780,97482372..97482527,
                     97482617..97482698,97483892..97483992,97484665..97484771,
                     97486002..97486128,97487590..97487717,97488166..97488267,
                     97488525..97488710,97493571..97493808,97501663..97501854))
                     /gene="ASNS"
                     /gene_synonym="TS11"
                     /product="asparagine synthetase (glutamine-hydrolyzing),
                     transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001178076.1"
                     /db_xref="GI:296010849"
                     /db_xref="GeneID:440"
                     /db_xref="HGNC:753"
                     /db_xref="MIM:108370"
                     /db_xref="HPRD:00153"
     mRNA            complement(join(97481429..97481780,97482372..97482527,
                     97482617..97482698,97483892..97483992,97484665..97484771,
                     97486002..97486128,97487590..97487717,97488166..97488267,
                     97488525..97488710,97493571..97493808,97498220..97498491,
                     97499090..97499125,97501031..97501477))
                     /gene="ASNS"
                     /gene_synonym="TS11"
                     /product="asparagine synthetase (glutamine-hydrolyzing),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_133436.3"
                     /db_xref="GI:296010846"
                     /db_xref="GeneID:440"
                     /db_xref="HGNC:753"
                     /db_xref="HPRD:00153"
                     /db_xref="MIM:108370"
     mRNA            complement(join(97481429..97481780,97482372..97482527,
                     97482617..97482698,97483892..97483992,97484665..97484771,
                     97486002..97486128,97487590..97487717,97488166..97488267,
                     97488525..97488710,97493571..97493808,97501353..97501477))
                     /gene="ASNS"
                     /gene_synonym="TS11"
                     /product="asparagine synthetase (glutamine-hydrolyzing),
                     transcript variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001178077.1"
                     /db_xref="GI:296010851"
                     /db_xref="GeneID:440"
                     /db_xref="HGNC:753"
                     /db_xref="MIM:108370"
                     /db_xref="HPRD:00153"
     CDS             complement(join(97481571..97481780,97482372..97482527,
                     97482617..97482698,97483892..97483992,97484665..97484771,
                     97486002..97486128,97487590..97487717,97488166..97488267,
                     97488525..97488710,97493571..97493808,97498220..97498468))
                     /gene="ASNS"
                     /gene_synonym="TS11"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="asparagine synthetase [glutamine-hydrolyzing]
                     isoform a"
                     /protein_id="NP_597680.2"
                     /db_xref="GI:168229248"
                     /db_xref="CCDS:CCDS5652.1"
                     /db_xref="GeneID:440"
                     /db_xref="HGNC:753"
                     /db_xref="HPRD:00153"
                     /db_xref="MIM:108370"
     CDS             complement(join(97481571..97481780,97482372..97482527,
                     97482617..97482698,97483892..97483992,97484665..97484771,
                     97486002..97486128,97487590..97487717,97488166..97488267,
                     97488525..97488710,97493571..97493808,97498220..97498468))
                     /gene="ASNS"
                     /gene_synonym="TS11"
                     /note="isoform a is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="asparagine synthetase [glutamine-hydrolyzing]
                     isoform a"
                     /protein_id="NP_001664.3"
                     /db_xref="GI:168229250"
                     /db_xref="CCDS:CCDS5652.1"
                     /db_xref="GeneID:440"
                     /db_xref="HGNC:753"
                     /db_xref="HPRD:00153"
                     /db_xref="MIM:108370"
     CDS             complement(join(97481571..97481780,97482372..97482527,
                     97482617..97482698,97483892..97483992,97484665..97484771,
                     97486002..97486128,97487590..97487717,97488166..97488267,
                     97488525..97488710,97493571..97493808,97498220..97498468))
                     /gene="ASNS"
                     /gene_synonym="TS11"
                     /note="isoform a is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="asparagine synthetase [glutamine-hydrolyzing]
                     isoform a"
                     /protein_id="NP_899199.2"
                     /db_xref="GI:168229252"
                     /db_xref="CCDS:CCDS5652.1"
                     /db_xref="GeneID:440"
                     /db_xref="HGNC:753"
                     /db_xref="HPRD:00153"
                     /db_xref="MIM:108370"
     CDS             complement(join(97481571..97481780,97482372..97482527,
                     97482617..97482698,97483892..97483992,97484665..97484771,
                     97486002..97486128,97487590..97487717,97488166..97488267,
                     97488525..97488710,97493571..97493808,97498220..97498405))
                     /gene="ASNS"
                     /gene_synonym="TS11"
                     /note="isoform b is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="asparagine synthetase [glutamine-hydrolyzing]
                     isoform b"
                     /protein_id="NP_001171546.1"
                     /db_xref="GI:296010848"
                     /db_xref="CCDS:CCDS55132.1"
                     /db_xref="GeneID:440"
                     /db_xref="HGNC:753"
                     /db_xref="HPRD:00153"
                     /db_xref="MIM:108370"
     CDS             complement(join(97481571..97481780,97482372..97482527,
                     97482617..97482698,97483892..97483992,97484665..97484771,
                     97486002..97486128,97487590..97487717,97488166..97488267,
                     97488525..97488710,97493571..97493808))
                     /gene="ASNS"
                     /gene_synonym="TS11"
                     /note="isoform c is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="asparagine synthetase [glutamine-hydrolyzing]
                     isoform c"
                     /protein_id="NP_001171547.1"
                     /db_xref="GI:296010850"
                     /db_xref="CCDS:CCDS55131.1"
                     /db_xref="GeneID:440"
                     /db_xref="HGNC:753"
                     /db_xref="HPRD:00153"
                     /db_xref="MIM:108370"
     CDS             complement(join(97481571..97481780,97482372..97482527,
                     97482617..97482698,97483892..97483992,97484665..97484771,
                     97486002..97486128,97487590..97487717,97488166..97488267,
                     97488525..97488710,97493571..97493808))
                     /gene="ASNS"
                     /gene_synonym="TS11"
                     /note="isoform c is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="asparagine synthetase [glutamine-hydrolyzing]
                     isoform c"
                     /protein_id="NP_001171548.1"
                     /db_xref="GI:296010852"
                     /db_xref="CCDS:CCDS55131.1"
                     /db_xref="GeneID:440"
                     /db_xref="HGNC:753"
                     /db_xref="HPRD:00153"
                     /db_xref="MIM:108370"
     gene            97515180..97515971
                     /gene="LOC100310853"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100310853"
     gene            complement(97527608..97528456)
                     /gene="RPS3AP29"
                     /gene_synonym="RPS3A_10_823"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:730861"
                     /db_xref="HGNC:35531"
     gene            complement(97576295..97577301)
                     /gene="OR7E7P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392752"
                     /db_xref="HGNC:8457"
     gene            complement(97595404..97596389)
                     /gene="OR7E38P"
                     /gene_synonym="OR7E76; OST127"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:389537"
                     /db_xref="HGNC:8411"
     gene            complement(97595908..97601638)
                     /gene="MGC72080"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:389538"
     misc_RNA        complement(join(97595908..97596289,97598317..97598364,
                     97599082..97599157,97601447..97601638))
                     /gene="MGC72080"
                     /product="MGC72080 pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002822.3"
                     /db_xref="GI:218505842"
                     /db_xref="GeneID:389538"
     gene            complement(97614012..97619416)
                     /gene="OCM2"
                     /gene_synonym="OCM"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4951"
                     /db_xref="HGNC:34396"
                     /db_xref="HPRD:01274"
     mRNA            complement(join(97614012..97614295,97616359..97616468,
                     97617728..97617860,97619356..97619416))
                     /gene="OCM2"
                     /gene_synonym="OCM"
                     /product="oncomodulin 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006188.3"
                     /db_xref="GI:148277110"
                     /db_xref="GeneID:4951"
                     /db_xref="HGNC:34396"
                     /db_xref="HPRD:01274"
     CDS             complement(join(97614270..97614295,97616359..97616468,
                     97617728..97617860,97619356..97619416))
                     /gene="OCM2"
                     /gene_synonym="OCM"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative oncomodulin-2"
                     /protein_id="NP_006179.2"
                     /db_xref="GI:148277111"
                     /db_xref="CCDS:CCDS5653.1"
                     /db_xref="GeneID:4951"
                     /db_xref="HGNC:34396"
                     /db_xref="HPRD:01274"
     gene            97736197..97838945
                     /gene="LMTK2"
                     /gene_synonym="AATYK2; BREK; cprk; FLJ46659; KIAA1079;
                     KPI-2; KPI2; LMR2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:22853"
                     /db_xref="HGNC:17880"
                     /db_xref="HPRD:13994"
                     /db_xref="MIM:610989"
     mRNA            join(97736197..97736592,97766627..97766754,
                     97770709..97770853,97780694..97780767,97784070..97784188,
                     97788650..97788737,97800853..97800986,97814363..97814447,
                     97816189..97816310,97820040..97820189,97820926..97823884,
                     97832886..97833018,97833256..97833498,97834776..97838945)
                     /gene="LMTK2"
                     /gene_synonym="AATYK2; BREK; cprk; FLJ46659; KIAA1079;
                     KPI-2; KPI2; LMR2"
                     /product="lemur tyrosine kinase 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014916.3"
                     /db_xref="GI:260593715"
                     /db_xref="GeneID:22853"
                     /db_xref="HGNC:17880"
                     /db_xref="HPRD:13994"
                     /db_xref="MIM:610989"
     CDS             join(97736490..97736592,97766627..97766754,
                     97770709..97770853,97780694..97780767,97784070..97784188,
                     97788650..97788737,97800853..97800986,97814363..97814447,
                     97816189..97816310,97820040..97820189,97820926..97823884,
                     97832886..97833018,97833256..97833498,97834776..97834804)
                     /gene="LMTK2"
                     /gene_synonym="AATYK2; BREK; cprk; FLJ46659; KIAA1079;
                     KPI-2; KPI2; LMR2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="serine/threonine-protein kinase LMTK2 precursor"
                     /protein_id="NP_055731.2"
                     /db_xref="GI:38016937"
                     /db_xref="CCDS:CCDS5654.1"
                     /db_xref="GeneID:22853"
                     /db_xref="HGNC:17880"
                     /db_xref="HPRD:13994"
                     /db_xref="MIM:610989"
     gene            97841566..97842271
                     /gene="BHLHA15"
                     /gene_synonym="BHLHB8; MIST1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:168620"
                     /db_xref="HGNC:22265"
                     /db_xref="HPRD:16356"
                     /db_xref="MIM:608606"
     mRNA            97841566..97842271
                     /gene="BHLHA15"
                     /gene_synonym="BHLHB8; MIST1"
                     /product="basic helix-loop-helix family, member a15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_177455.3"
                     /db_xref="GI:116642868"
                     /db_xref="GeneID:168620"
                     /db_xref="HGNC:22265"
                     /db_xref="HPRD:16356"
                     /db_xref="MIM:608606"
     CDS             97841622..97842191
                     /gene="BHLHA15"
                     /gene_synonym="BHLHB8; MIST1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="class A basic helix-loop-helix protein 15"
                     /protein_id="NP_803238.1"
                     /db_xref="GI:29126247"
                     /db_xref="CCDS:CCDS5655.1"
                     /db_xref="GeneID:168620"
                     /db_xref="HGNC:22265"
                     /db_xref="HPRD:16356"
                     /db_xref="MIM:608606"
     gene            complement(97846036..97881468)
                     /gene="TECPR1"
                     /gene_synonym="DKFZP434B0335; FLJ23419; FLJ90593"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:25851"
                     /db_xref="HGNC:22214"
                     /db_xref="HPRD:08521"
     mRNA            complement(join(97846036..97846815,97847004..97847123,
                     97847248..97847354,97850973..97851065,97851698..97851833,
                     97852302..97852482,97852974..97853030,97854113..97854192,
                     97854318..97854414,97857326..97857428,97858351..97858478,
                     97860273..97860430,97860536..97860685,97861116..97861271,
                     97862139..97862284,97862733..97863223,97866088..97866233,
                     97867821..97867922,97870163..97870263,97870382..97870556,
                     97872779..97872904,97873883..97874005,97874197..97874379,
                     97875234..97875477,97880706..97880860,97881438..97881468))
                     /gene="TECPR1"
                     /gene_synonym="DKFZP434B0335; FLJ23419; FLJ90593"
                     /product="tectonin beta-propeller repeat containing 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015395.1"
                     /db_xref="GI:32698703"
                     /db_xref="GeneID:25851"
                     /db_xref="HGNC:22214"
                     /db_xref="HPRD:08521"
     CDS             complement(join(97846702..97846815,97847004..97847123,
                     97847248..97847354,97850973..97851065,97851698..97851833,
                     97852302..97852482,97852974..97853030,97854113..97854192,
                     97854318..97854414,97857326..97857428,97858351..97858478,
                     97860273..97860430,97860536..97860685,97861116..97861271,
                     97862139..97862284,97862733..97863223,97866088..97866233,
                     97867821..97867922,97870163..97870263,97870382..97870556,
                     97872779..97872904,97873883..97874005,97874197..97874379,
                     97875234..97875458))
                     /gene="TECPR1"
                     /gene_synonym="DKFZP434B0335; FLJ23419; FLJ90593"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="tectonin beta-propeller repeat-containing
                     protein 1"
                     /protein_id="NP_056210.1"
                     /db_xref="GI:32698704"
                     /db_xref="CCDS:CCDS47648.1"
                     /db_xref="GeneID:25851"
                     /db_xref="HGNC:22214"
                     /db_xref="HPRD:08521"
     gene            97910979..97922275
                     /gene="BRI3"
                     /gene_synonym="I3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:25798"
                     /db_xref="HGNC:1109"
                     /db_xref="HPRD:16562"
     mRNA            join(97910979..97911249,97911663..97911765,
                     97921951..97922275)
                     /gene="BRI3"
                     /gene_synonym="I3"
                     /product="brain protein I3, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001159491.1"
                     /db_xref="GI:227452378"
                     /db_xref="GeneID:25798"
                     /db_xref="HGNC:1109"
                     /db_xref="HPRD:16562"
     mRNA            join(97910979..97911249,97911663..97911765,
                     97920423..97920839)
                     /gene="BRI3"
                     /gene_synonym="I3"
                     /product="brain protein I3, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015379.4"
                     /db_xref="GI:227452355"
                     /db_xref="GeneID:25798"
                     /db_xref="HGNC:1109"
                     /db_xref="HPRD:16562"
     CDS             join(97911108..97911249,97911663..97911765,
                     97921951..97922002)
                     /gene="BRI3"
                     /gene_synonym="I3"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="brain protein I3 isoform b"
                     /protein_id="NP_001152963.1"
                     /db_xref="GI:227452379"
                     /db_xref="CCDS:CCDS55133.1"
                     /db_xref="GeneID:25798"
                     /db_xref="HGNC:1109"
                     /db_xref="HPRD:16562"
     CDS             join(97911108..97911249,97911663..97911765,
                     97920423..97920555)
                     /gene="BRI3"
                     /gene_synonym="I3"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="brain protein I3 isoform a"
                     /protein_id="NP_056194.1"
                     /db_xref="GI:7661538"
                     /db_xref="CCDS:CCDS5656.1"
                     /db_xref="GeneID:25798"
                     /db_xref="HGNC:1109"
                     /db_xref="HPRD:16562"
     gene            complement(97920962..98030427)
                     /gene="BAIAP2L1"
                     /gene_synonym="FLJ42275; IRTKS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55971"
                     /db_xref="HGNC:21649"
                     /db_xref="HPRD:11270"
                     /db_xref="MIM:611877"
     mRNA            complement(join(97920962..97922908,97923386..97923423,
                     97933508..97933688,97935751..97935828,97937001..97937208,
                     97939757..97939904,97941409..97941576,97944772..97944924,
                     97946531..97946668,97949370..97949441,97949549..97949610,
                     97984354..97984440,97991669..97991744,98030114..98030427))
                     /gene="BAIAP2L1"
                     /gene_synonym="FLJ42275; IRTKS"
                     /product="BAI1-associated protein 2-like 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018842.4"
                     /db_xref="GI:227500029"
                     /db_xref="GeneID:55971"
                     /db_xref="HGNC:21649"
                     /db_xref="HPRD:11270"
                     /db_xref="MIM:611877"
     CDS             complement(join(97922833..97922908,97923386..97923423,
                     97933508..97933688,97935751..97935828,97937001..97937208,
                     97939757..97939904,97941409..97941576,97944772..97944924,
                     97946531..97946668,97949370..97949441,97949549..97949610,
                     97984354..97984440,97991669..97991744,98030114..98030164))
                     /gene="BAIAP2L1"
                     /gene_synonym="FLJ42275; IRTKS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="brain-specific angiogenesis inhibitor
                     1-associated protein 2-like protein 1"
                     /protein_id="NP_061330.2"
                     /db_xref="GI:32171238"
                     /db_xref="CCDS:CCDS34687.1"
                     /db_xref="GeneID:55971"
                     /db_xref="HGNC:21649"
                     /db_xref="HPRD:11270"
                     /db_xref="MIM:611877"
     gene            complement(98015062..98015919)
                     /gene="RPS3AP26"
                     /gene_synonym="RPS3A_11_824"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:644972"
                     /db_xref="HGNC:36513"
     gene            complement(98083225..98083960)
                     /gene="LOC442713"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442713"
     gene            complement(98107863..98108108)
                     /gene="RPS26P33"
                     /gene_synonym="RPS26_14_825"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271239"
                     /db_xref="HGNC:36227"
     gene            98246597..98259181
                     /gene="NPTX2"
                     /gene_synonym="NARP; NP-II; NP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4885"
                     /db_xref="HGNC:7953"
                     /db_xref="HPRD:02853"
                     /db_xref="MIM:600750"
     mRNA            join(98246597..98247199,98248955..98249171,
                     98254234..98254478,98256477..98256656,98257714..98259181)
                     /gene="NPTX2"
                     /gene_synonym="NARP; NP-II; NP2"
                     /product="neuronal pentraxin II"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002523.2"
                     /db_xref="GI:223671935"
                     /db_xref="GeneID:4885"
                     /db_xref="HGNC:7953"
                     /db_xref="HPRD:02853"
                     /db_xref="MIM:600750"
     CDS             join(98246774..98247199,98248955..98249171,
                     98254234..98254478,98256477..98256656,98257714..98257941)
                     /gene="NPTX2"
                     /gene_synonym="NARP; NP-II; NP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="neuronal pentraxin-2 precursor"
                     /protein_id="NP_002514.1"
                     /db_xref="GI:28195384"
                     /db_xref="CCDS:CCDS5657.1"
                     /db_xref="GeneID:4885"
                     /db_xref="HGNC:7953"
                     /db_xref="HPRD:02853"
                     /db_xref="MIM:600750"
     gene            complement(98444111..98467673)
                     /gene="TMEM130"
                     /gene_synonym="DKFZp761L1417; FLJ42643"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222865"
                     /db_xref="HGNC:25429"
                     /db_xref="HPRD:13226"
     mRNA            complement(join(98444111..98445867,98446206..98446318,
                     98449044..98449246,98452863..98452947,98453640..98453806,
                     98457802..98457961,98460718..98461023,98467400..98467673))
                     /gene="TMEM130"
                     /gene_synonym="DKFZp761L1417; FLJ42643"
                     /product="transmembrane protein 130, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134450.1"
                     /db_xref="GI:197313778"
                     /db_xref="GeneID:222865"
                     /db_xref="HGNC:25429"
                     /db_xref="HPRD:13226"
     mRNA            complement(join(98444111..98445831,98446206..98446318,
                     98449044..98449246,98452863..98452947,98453640..98453806,
                     98457802..98457961,98460718..98461023,98467400..98467673))
                     /gene="TMEM130"
                     /gene_synonym="DKFZp761L1417; FLJ42643"
                     /product="transmembrane protein 130, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152913.2"
                     /db_xref="GI:197313777"
                     /db_xref="GeneID:222865"
                     /db_xref="HGNC:25429"
                     /db_xref="HPRD:13226"
     mRNA            complement(join(98444111..98445831,98446206..98446318,
                     98449044..98449246,98452863..98452947,98453640..98453806,
                     98457802..98457961,98467400..98467673))
                     /gene="TMEM130"
                     /gene_synonym="DKFZp761L1417; FLJ42643"
                     /product="transmembrane protein 130, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134451.1"
                     /db_xref="GI:197313780"
                     /db_xref="GeneID:222865"
                     /db_xref="HGNC:25429"
                     /db_xref="HPRD:13226"
     CDS             complement(join(98445679..98445867,98446206..98446318,
                     98449044..98449246,98452863..98452947,98453640..98453806,
                     98457802..98457961,98460718..98461023,98467400..98467484))
                     /gene="TMEM130"
                     /gene_synonym="DKFZp761L1417; FLJ42643"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 130 isoform a"
                     /protein_id="NP_001127922.1"
                     /db_xref="GI:197313779"
                     /db_xref="CCDS:CCDS47650.1"
                     /db_xref="GeneID:222865"
                     /db_xref="HGNC:25429"
                     /db_xref="HPRD:13226"
     CDS             complement(join(98445679..98445831,98446206..98446318,
                     98449044..98449246,98452863..98452947,98453640..98453806,
                     98457802..98457961,98460718..98461023,98467400..98467484))
                     /gene="TMEM130"
                     /gene_synonym="DKFZp761L1417; FLJ42643"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 130 isoform b"
                     /protein_id="NP_690877.1"
                     /db_xref="GI:23097274"
                     /db_xref="CCDS:CCDS5658.1"
                     /db_xref="GeneID:222865"
                     /db_xref="HGNC:25429"
                     /db_xref="HPRD:13226"
     CDS             complement(join(98445679..98445831,98446206..98446318,
                     98449044..98449246,98452863..98452947,98453640..98453806,
                     98457802..98457961,98467400..98467484))
                     /gene="TMEM130"
                     /gene_synonym="DKFZp761L1417; FLJ42643"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 130 isoform c"
                     /protein_id="NP_001127923.1"
                     /db_xref="GI:197313781"
                     /db_xref="CCDS:CCDS47649.1"
                     /db_xref="GeneID:222865"
                     /db_xref="HGNC:25429"
                     /db_xref="HPRD:13226"
     gene            98476113..98610864
                     /gene="TRRAP"
                     /gene_synonym="FLJ10671; PAF350/400; PAF400; STAF40;
                     TR-AP; Tra1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8295"
                     /db_xref="HGNC:12347"
                     /db_xref="HPRD:04310"
                     /db_xref="MIM:603015"
     mRNA            join(98476113..98476260,98478713..98478873,
                     98479598..98479647,98487958..98488068,98490047..98490151,
                     98491421..98491504,98493387..98493443,98495364..98495489,
                     98497045..98497122,98497302..98497390,98498247..98498343,
                     98501002..98501140,98503800..98503878,98506351..98506585,
                     98507679..98508042,98508133..98508230,98508700..98508894,
                     98509645..98509836,98513346..98513511,98515046..98515302,
                     98519376..98519576,98522735..98522886,98524790..98524989,
                     98527612..98527829,98528256..98528453,98529028..98529288,
                     98530864..98531025,98533202..98533298,98534779..98534900,
                     98535273..98535443,98540572..98540640,98545844..98545963,
                     98546189..98546308,98547040..98547204,98547283..98547464,
                     98547687..98547885,98548499..98548627,98550790..98551056,
                     98552721..98552927,98553769..98553927,98554022..98554156,
                     98555604..98555714,98556967..98557113,98558884..98559097,
                     98559925..98560050,98562252..98562398,98563319..98563518,
                     98564664..98564785,98565108..98565321,98567735..98567914,
                     98569422..98569568,98573772..98573891,98574106..98574393,
                     98574562..98574699,98575834..98575946,98576392..98576527,
                     98579392..98579583,98580887..98581082,98581716..98581981,
                     98582567..98582667,98586388..98586589,98588078..98588242,
                     98589760..98589850,98591215..98591360,98592210..98592471,
                     98601813..98602038,98602754..98602971,98606000..98606184,
                     98608675..98608878,98608964..98609158,98609694..98610864)
                     /gene="TRRAP"
                     /gene_synonym="FLJ10671; PAF350/400; PAF400; STAF40;
                     TR-AP; Tra1"
                     /product="transformation/transcription domain-associated
                     protein"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003496.2"
                     /db_xref="GI:197209876"
                     /db_xref="GeneID:8295"
                     /db_xref="HGNC:12347"
                     /db_xref="HPRD:04310"
                     /db_xref="MIM:603015"
     CDS             join(98478774..98478873,98479598..98479647,
                     98487958..98488068,98490047..98490151,98491421..98491504,
                     98493387..98493443,98495364..98495489,98497045..98497122,
                     98497302..98497390,98498247..98498343,98501002..98501140,
                     98503800..98503878,98506351..98506585,98507679..98508042,
                     98508133..98508230,98508700..98508894,98509645..98509836,
                     98513346..98513511,98515046..98515302,98519376..98519576,
                     98522735..98522886,98524790..98524989,98527612..98527829,
                     98528256..98528453,98529028..98529288,98530864..98531025,
                     98533202..98533298,98534779..98534900,98535273..98535443,
                     98540572..98540640,98545844..98545963,98546189..98546308,
                     98547040..98547204,98547283..98547464,98547687..98547885,
                     98548499..98548627,98550790..98551056,98552721..98552927,
                     98553769..98553927,98554022..98554156,98555604..98555714,
                     98556967..98557113,98558884..98559097,98559925..98560050,
                     98562252..98562398,98563319..98563518,98564664..98564785,
                     98565108..98565321,98567735..98567914,98569422..98569568,
                     98573772..98573891,98574106..98574393,98574562..98574699,
                     98575834..98575946,98576392..98576527,98579392..98579583,
                     98580887..98581082,98581716..98581981,98582567..98582667,
                     98586388..98586589,98588078..98588242,98589760..98589850,
                     98591215..98591360,98592210..98592471,98601813..98602038,
                     98602754..98602971,98606000..98606184,98608675..98608878,
                     98608964..98609158,98609694..98609978)
                     /gene="TRRAP"
                     /gene_synonym="FLJ10671; PAF350/400; PAF400; STAF40;
                     TR-AP; Tra1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transformation/transcription domain-associated
                     protein"
                     /protein_id="NP_003487.1"
                     /db_xref="GI:4507691"
                     /db_xref="CCDS:CCDS5659.1"
                     /db_xref="GeneID:8295"
                     /db_xref="HGNC:12347"
                     /db_xref="HPRD:04310"
                     /db_xref="MIM:603015"
     gene            98479273..98479352
                     /gene="MIR3609"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100500819"
                     /db_xref="HGNC:38956"
                     /db_xref="miRBase:MI0015999"
     ncRNA           98479273..98479352
                     /gene="MIR3609"
                     /ncRNA_class="miRNA"
                     /product="microRNA 3609"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037403.1"
                     /db_xref="GI:312147411"
                     /db_xref="GeneID:100500819"
                     /db_xref="HGNC:38956"
                     /db_xref="miRBase:MI0015999"
     gene            complement(98596159..98597551)
                     /gene="LOC100419643"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419643"
     gene            complement(98625058..98741743)
                     /gene="SMURF1"
                     /gene_synonym="KIAA1625"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57154"
                     /db_xref="HGNC:16807"
                     /db_xref="HPRD:06902"
                     /db_xref="MIM:605568"
     mRNA            complement(join(98625058..98628306,98630660..98630744,
                     98633138..98633339,98634690..98634810,98636011..98636148,
                     98638001..98638179,98639741..98639855,98643321..98643424,
                     98645307..98645505,98647186..98647332,98648538..98648615,
                     98648980..98649064,98649828..98650069,98652413..98652488,
                     98654828..98654893,98655041..98655174,98658222..98658330,
                     98659422..98659460,98741349..98741743))
                     /gene="SMURF1"
                     /gene_synonym="KIAA1625"
                     /product="SMAD specific E3 ubiquitin protein ligase 1,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020429.2"
                     /db_xref="GI:315434201"
                     /db_xref="GeneID:57154"
                     /db_xref="HGNC:16807"
                     /db_xref="HPRD:06902"
                     /db_xref="MIM:605568"
     mRNA            complement(join(98625058..98628306,98630660..98630744,
                     98633138..98633339,98634690..98634810,98636011..98636148,
                     98638001..98638179,98639741..98639855,98643321..98643424,
                     98645307..98645505,98647186..98647332,98648980..98649064,
                     98649828..98650069,98652413..98652488,98654828..98654893,
                     98655041..98655174,98658222..98658330,98659422..98659460,
                     98741349..98741743))
                     /gene="SMURF1"
                     /gene_synonym="KIAA1625"
                     /product="SMAD specific E3 ubiquitin protein ligase 1,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_181349.2"
                     /db_xref="GI:315434202"
                     /db_xref="GeneID:57154"
                     /db_xref="HGNC:16807"
                     /db_xref="MIM:605568"
                     /db_xref="HPRD:06902"
     mRNA            complement(join(98625058..98628306,98630660..98630735,
                     98633138..98633339,98634690..98634810,98636011..98636148,
                     98638001..98638179,98639741..98639855,98643321..98643424,
                     98645307..98645505,98647186..98647332,98648980..98649064,
                     98649828..98650069,98652413..98652488,98654828..98654893,
                     98655041..98655174,98658222..98658330,98659422..98659460,
                     98741349..98741743))
                     /gene="SMURF1"
                     /gene_synonym="KIAA1625"
                     /product="SMAD specific E3 ubiquitin protein ligase 1,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199847.1"
                     /db_xref="GI:315434203"
                     /db_xref="GeneID:57154"
                     /db_xref="HGNC:16807"
                     /db_xref="MIM:605568"
                     /db_xref="HPRD:06902"
     CDS             complement(join(98628207..98628306,98630660..98630744,
                     98633138..98633339,98634690..98634810,98636011..98636148,
                     98638001..98638179,98639741..98639855,98643321..98643424,
                     98645307..98645505,98647186..98647332,98648538..98648615,
                     98648980..98649064,98649828..98650069,98652413..98652488,
                     98654828..98654893,98655041..98655174,98658222..98658330,
                     98659422..98659460,98741349..98741403))
                     /gene="SMURF1"
                     /gene_synonym="KIAA1625"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase SMURF1 isoform 1"
                     /protein_id="NP_065162.1"
                     /db_xref="GI:31317292"
                     /db_xref="CCDS:CCDS34690.1"
                     /db_xref="GeneID:57154"
                     /db_xref="HGNC:16807"
                     /db_xref="HPRD:06902"
                     /db_xref="MIM:605568"
     CDS             complement(join(98628207..98628306,98630660..98630744,
                     98633138..98633339,98634690..98634810,98636011..98636148,
                     98638001..98638179,98639741..98639855,98643321..98643424,
                     98645307..98645505,98647186..98647332,98648980..98649064,
                     98649828..98650069,98652413..98652488,98654828..98654893,
                     98655041..98655174,98658222..98658330,98659422..98659460,
                     98741349..98741403))
                     /gene="SMURF1"
                     /gene_synonym="KIAA1625"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase SMURF1 isoform 2"
                     /protein_id="NP_851994.1"
                     /db_xref="GI:31317290"
                     /db_xref="CCDS:CCDS34689.1"
                     /db_xref="GeneID:57154"
                     /db_xref="HGNC:16807"
                     /db_xref="HPRD:06902"
                     /db_xref="MIM:605568"
     CDS             complement(join(98628207..98628306,98630660..98630735,
                     98633138..98633339,98634690..98634810,98636011..98636148,
                     98638001..98638179,98639741..98639855,98643321..98643424,
                     98645307..98645505,98647186..98647332,98648980..98649064,
                     98649828..98650069,98652413..98652488,98654828..98654893,
                     98655041..98655174,98658222..98658330,98659422..98659460,
                     98741349..98741403))
                     /gene="SMURF1"
                     /gene_synonym="KIAA1625"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase SMURF1 isoform 3"
                     /protein_id="NP_001186776.1"
                     /db_xref="GI:315434204"
                     /db_xref="GeneID:57154"
                     /db_xref="HGNC:16807"
                     /db_xref="MIM:605568"
                     /db_xref="HPRD:06902"
     gene            complement(98771197..98805089)
                     /gene="KPNA7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:402569"
                     /db_xref="HGNC:21839"
                     /db_xref="MIM:614107"
     mRNA            complement(join(98771197..98771417,98775543..98775689,
                     98779506..98779688,98782552..98782785,98785923..98786186,
                     98790642..98790724,98792693..98792961,98793707..98793789,
                     98800729..98800863,98805024..98805089))
                     /gene="KPNA7"
                     /product="karyopherin alpha 7 (importin alpha 8)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145715.1"
                     /db_xref="GI:224589128"
                     /db_xref="GeneID:402569"
                     /db_xref="HGNC:21839"
                     /db_xref="MIM:614107"
     CDS             complement(join(98771331..98771417,98775543..98775689,
                     98779506..98779688,98782552..98782785,98785923..98786186,
                     98790642..98790724,98792693..98792961,98793707..98793789,
                     98800729..98800863,98805024..98805089))
                     /gene="KPNA7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="importin subunit alpha-8"
                     /protein_id="NP_001139187.1"
                     /db_xref="GI:224589129"
                     /db_xref="CCDS:CCDS47651.1"
                     /db_xref="GeneID:402569"
                     /db_xref="HGNC:21839"
                     /db_xref="MIM:614107"
     gene            98870924..98895595
                     /gene="MYH16"
                     /gene_synonym="FLJ22037; MHC20; MYH16P; MYH5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:84176"
                     /db_xref="HGNC:31038"
                     /db_xref="MIM:608580"
     misc_RNA        join(98870924..98871046,98875162..98875335,
                     98877133..98877360,98878499..98878603,98881188..98881274,
                     98881496..98881641,98882468..98882558,98883005..98883061,
                     98885515..98885760,98886910..98887027,98888946..98889073,
                     98889935..98890131,98891641..98891773,98894324..98894540,
                     98895283..98895419,98895515..98895595)
                     /gene="MYH16"
                     /gene_synonym="FLJ22037; MHC20; MYH16P; MYH5"
                     /product="myosin, heavy chain 16 pseudogene"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002147.2"
                     /db_xref="GI:70608212"
                     /db_xref="GeneID:84176"
                     /db_xref="HGNC:31038"
                     /db_xref="MIM:608580"
     gene            98923496..98963885
                     /gene="ARPC1A"
                     /gene_synonym="Arc40; SOP2Hs; SOP2L"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10552"
                     /db_xref="HGNC:703"
                     /db_xref="HPRD:07252"
                     /db_xref="MIM:604220"
     mRNA            join(98923496..98923627,98930948..98931040,
                     98935804..98935908,98941916..98942138,98946475..98946582,
                     98951532..98951744,98955963..98956038,98957168..98957361,
                     98961166..98961256,98963514..98963885)
                     /gene="ARPC1A"
                     /gene_synonym="Arc40; SOP2Hs; SOP2L"
                     /product="actin related protein 2/3 complex, subunit 1A,
                     41kDa, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006409.3"
                     /db_xref="GI:300360513"
                     /db_xref="GeneID:10552"
                     /db_xref="HGNC:703"
                     /db_xref="HPRD:07252"
                     /db_xref="MIM:604220"
     mRNA            join(98923496..98923627,98930948..98931040,
                     98935806..98935908,98941916..98942138,98946475..98946582,
                     98951532..98951744,98955963..98956038,98957168..98957361,
                     98961166..98961256,98963514..98963885)
                     /gene="ARPC1A"
                     /gene_synonym="Arc40; SOP2Hs; SOP2L"
                     /product="actin related protein 2/3 complex, subunit 1A,
                     41kDa, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001190996.1"
                     /db_xref="GI:300360514"
                     /db_xref="GeneID:10552"
                     /db_xref="HGNC:703"
                     /db_xref="MIM:604220"
                     /db_xref="HPRD:07252"
     CDS             join(98930977..98931040,98935804..98935908,
                     98941916..98942138,98946475..98946582,98951532..98951744,
                     98955963..98956038,98957168..98957361,98961166..98961256,
                     98963514..98963552)
                     /gene="ARPC1A"
                     /gene_synonym="Arc40; SOP2Hs; SOP2L"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="actin-related protein 2/3 complex subunit 1A
                     isoform 1"
                     /protein_id="NP_006400.2"
                     /db_xref="GI:22907052"
                     /db_xref="CCDS:CCDS5660.1"
                     /db_xref="GeneID:10552"
                     /db_xref="HGNC:703"
                     /db_xref="HPRD:07252"
                     /db_xref="MIM:604220"
     CDS             join(98931017..98931040,98935806..98935908,
                     98941916..98942138,98946475..98946582,98951532..98951744,
                     98955963..98956038,98957168..98957361,98961166..98961256,
                     98963514..98963552)
                     /gene="ARPC1A"
                     /gene_synonym="Arc40; SOP2Hs; SOP2L"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="actin-related protein 2/3 complex subunit 1A
                     isoform 2"
                     /protein_id="NP_001177925.1"
                     /db_xref="GI:300360515"
                     /db_xref="GeneID:10552"
                     /db_xref="HGNC:703"
                     /db_xref="MIM:604220"
                     /db_xref="HPRD:07252"
     gene            98972298..98992424
                     /gene="ARPC1B"
                     /gene_synonym="ARC41; p40-ARC; p41-ARC"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10095"
                     /db_xref="HGNC:704"
                     /db_xref="HPRD:10366"
                     /db_xref="MIM:604223"
     mRNA            join(98972298..98972404,98983325..98983401,
                     98984308..98984412,98985662..98985884,98987528..98987635,
                     98988516..98988722,98988801..98988876,98990294..98990499,
                     98991652..98991742,98992074..98992424)
                     /gene="ARPC1B"
                     /gene_synonym="ARC41; p40-ARC; p41-ARC"
                     /product="actin related protein 2/3 complex, subunit 1B,
                     41kDa"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005720.3"
                     /db_xref="GI:325197176"
                     /db_xref="GeneID:10095"
                     /db_xref="HGNC:704"
                     /db_xref="HPRD:10366"
                     /db_xref="MIM:604223"
     CDS             join(98983338..98983401,98984308..98984412,
                     98985662..98985884,98987528..98987635,98988516..98988722,
                     98988801..98988876,98990294..98990499,98991652..98991742,
                     98992074..98992112)
                     /gene="ARPC1B"
                     /gene_synonym="ARC41; p40-ARC; p41-ARC"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="actin-related protein 2/3 complex subunit 1B"
                     /protein_id="NP_005711.1"
                     /db_xref="GI:5031601"
                     /db_xref="CCDS:CCDS5661.1"
                     /db_xref="GeneID:10095"
                     /db_xref="HGNC:704"
                     /db_xref="HPRD:10366"
                     /db_xref="MIM:604223"
     gene            complement(98992296..99006305)
                     /gene="PDAP1"
                     /gene_synonym="HASPP28; PAP; PAP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:11333"
                     /db_xref="HGNC:14634"
                     /db_xref="HPRD:06149"
                     /db_xref="MIM:607075"
     mRNA            complement(join(98992296..98994363,98995485..98995636,
                     98997926..98998047,99001021..99001128,99002485..99002576,
                     99006159..99006305))
                     /gene="PDAP1"
                     /gene_synonym="HASPP28; PAP; PAP1"
                     /product="PDGFA associated protein 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014891.6"
                     /db_xref="GI:315467839"
                     /db_xref="GeneID:11333"
                     /db_xref="HGNC:14634"
                     /db_xref="HPRD:06149"
                     /db_xref="MIM:607075"
     CDS             complement(join(98994305..98994363,98995485..98995636,
                     98997926..98998047,99001021..99001128,99002485..99002576,
                     99006159..99006171))
                     /gene="PDAP1"
                     /gene_synonym="HASPP28; PAP; PAP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="28 kDa heat- and acid-stable phosphoprotein"
                     /protein_id="NP_055706.1"
                     /db_xref="GI:7657441"
                     /db_xref="CCDS:CCDS5662.1"
                     /db_xref="GeneID:11333"
                     /db_xref="HGNC:14634"
                     /db_xref="HPRD:06149"
                     /db_xref="MIM:607075"
     gene            99006601..99017239
                     /gene="BUD31"
                     /gene_synonym="EDG-2; EDG2; fSAP17; G10; MGC111202;
                     YCR063W"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8896"
                     /db_xref="HGNC:29629"
                     /db_xref="HPRD:10351"
                     /db_xref="MIM:603477"
     mRNA            join(99006601..99006868,99007657..99007792,
                     99008687..99008809,99013761..99013883,99015052..99015218,
                     99017014..99017239)
                     /gene="BUD31"
                     /gene_synonym="EDG-2; EDG2; fSAP17; G10; MGC111202;
                     YCR063W"
                     /product="BUD31 homolog (S. cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003910.3"
                     /db_xref="GI:187960106"
                     /db_xref="GeneID:8896"
                     /db_xref="HGNC:29629"
                     /db_xref="HPRD:10351"
                     /db_xref="MIM:603477"
     CDS             join(99008716..99008809,99013761..99013883,
                     99015052..99015218,99017014..99017064)
                     /gene="BUD31"
                     /gene_synonym="EDG-2; EDG2; fSAP17; G10; MGC111202;
                     YCR063W"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein BUD31 homolog"
                     /protein_id="NP_003901.2"
                     /db_xref="GI:32171175"
                     /db_xref="CCDS:CCDS5663.1"
                     /db_xref="GeneID:8896"
                     /db_xref="HGNC:29629"
                     /db_xref="HPRD:10351"
                     /db_xref="MIM:603477"
     gene            complement(99014362..99063824)
                     /gene="ATP5J2-PTCD1"
                     /gene_synonym="FLJ56092"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100526740"
                     /db_xref="HGNC:38844"
     mRNA            complement(join(99014362..99017772,99021398..99021580,
                     99022418..99023239,99026726..99026827,99027211..99027429,
                     99030901..99031041,99032413..99032891,99057709..99057816,
                     99063752..99063824))
                     /gene="ATP5J2-PTCD1"
                     /gene_synonym="FLJ56092"
                     /product="ATP5J2-PTCD1 readthrough"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001198879.1"
                     /db_xref="GI:311893395"
                     /db_xref="GeneID:100526740"
                     /db_xref="HGNC:38844"
     gene            complement(99014362..99036462)
                     /gene="PTCD1"
                     /gene_synonym="KIAA0632"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26024"
                     /db_xref="HGNC:22198"
                     /db_xref="HPRD:11463"
     mRNA            complement(join(99014362..99017772,99021398..99021580,
                     99022418..99023239,99026726..99026827,99027211..99027429,
                     99030901..99031041,99032413..99032891,99036315..99036462))
                     /gene="PTCD1"
                     /gene_synonym="KIAA0632"
                     /product="pentatricopeptide repeat domain 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015545.3"
                     /db_xref="GI:311893394"
                     /db_xref="GeneID:26024"
                     /db_xref="HGNC:22198"
                     /db_xref="HPRD:11463"
     CDS             complement(join(99017590..99017772,99021398..99021580,
                     99022418..99023239,99026726..99026827,99027211..99027429,
                     99030901..99031041,99032413..99032891,99057709..99057816,
                     99063752..99063764))
                     /gene="ATP5J2-PTCD1"
                     /gene_synonym="FLJ56092"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ATP5J2-PTCD1 fusion protein"
                     /protein_id="NP_001185808.1"
                     /db_xref="GI:311893396"
                     /db_xref="GeneID:100526740"
                     /db_xref="HGNC:38844"
     CDS             complement(join(99017590..99017772,99021398..99021580,
                     99022418..99023239,99026726..99026827,99027211..99027429,
                     99030901..99031041,99032413..99032865))
                     /gene="PTCD1"
                     /gene_synonym="KIAA0632"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="pentatricopeptide repeat-containing protein 1"
                     /protein_id="NP_056360.2"
                     /db_xref="GI:38492358"
                     /db_xref="CCDS:CCDS34691.1"
                     /db_xref="GeneID:26024"
                     /db_xref="HGNC:22198"
                     /db_xref="HPRD:11463"
     gene            99036563..99054996
                     /gene="CPSF4"
                     /gene_synonym="CPSF30; NAR; NEB1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10898"
                     /db_xref="HGNC:2327"
                     /db_xref="HPRD:04338"
                     /db_xref="MIM:603052"
     mRNA            join(99036563..99036808,99042412..99042462,
                     99045744..99045896,99047899..99047994,99048325..99048418,
                     99049991..99050063,99051589..99051759,99054055..99054996)
                     /gene="CPSF4"
                     /gene_synonym="CPSF30; NAR; NEB1"
                     /product="cleavage and polyadenylation specific factor 4,
                     30kDa, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006693.2"
                     /db_xref="GI:125987601"
                     /db_xref="GeneID:10898"
                     /db_xref="HGNC:2327"
                     /db_xref="HPRD:04338"
                     /db_xref="MIM:603052"
     mRNA            join(99036563..99036808,99042412..99042462,
                     99045744..99045896,99047899..99047994,99048325..99048418,
                     99049991..99050063,99051664..99051759,99054055..99054996)
                     /gene="CPSF4"
                     /gene_synonym="CPSF30; NAR; NEB1"
                     /product="cleavage and polyadenylation specific factor 4,
                     30kDa, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001081559.1"
                     /db_xref="GI:125987602"
                     /db_xref="GeneID:10898"
                     /db_xref="HGNC:2327"
                     /db_xref="MIM:603052"
                     /db_xref="HPRD:04338"
     CDS             join(99036706..99036808,99042412..99042462,
                     99045744..99045896,99047899..99047994,99048325..99048418,
                     99049991..99050063,99051589..99051759,99054055..99054123)
                     /gene="CPSF4"
                     /gene_synonym="CPSF30; NAR; NEB1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cleavage and polyadenylation specificity factor
                     subunit 4 isoform 1"
                     /protein_id="NP_006684.1"
                     /db_xref="GI:5729939"
                     /db_xref="CCDS:CCDS5664.1"
                     /db_xref="GeneID:10898"
                     /db_xref="HGNC:2327"
                     /db_xref="HPRD:04338"
                     /db_xref="MIM:603052"
     CDS             join(99036706..99036808,99042412..99042462,
                     99045744..99045896,99047899..99047994,99048325..99048418,
                     99049991..99050063,99051664..99051759,99054055..99054123)
                     /gene="CPSF4"
                     /gene_synonym="CPSF30; NAR; NEB1"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cleavage and polyadenylation specificity factor
                     subunit 4 isoform 2"
                     /protein_id="NP_001075028.1"
                     /db_xref="GI:125987603"
                     /db_xref="CCDS:CCDS47652.1"
                     /db_xref="GeneID:10898"
                     /db_xref="HGNC:2327"
                     /db_xref="HPRD:04338"
                     /db_xref="MIM:603052"
     gene            complement(99039958..99041104)
                     /gene="LOC100131859"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100131859"
     gene            complement(99055784..99063824)
                     /gene="ATP5J2"
                     /gene_synonym="ATP5JL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9551"
                     /db_xref="HGNC:848"
                     /db_xref="HPRD:16520"
     mRNA            complement(join(99055784..99055978,99056770..99056886,
                     99057709..99057816,99063734..99063824))
                     /gene="ATP5J2"
                     /gene_synonym="ATP5JL"
                     /product="ATP synthase, H+ transporting, mitochondrial Fo
                     complex, subunit F2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004889.3"
                     /db_xref="GI:311893383"
                     /db_xref="GeneID:9551"
                     /db_xref="HGNC:848"
                     /db_xref="HPRD:16520"
     mRNA            complement(join(99055784..99055978,99056770..99056886,
                     99057709..99057816,99063752..99063824))
                     /gene="ATP5J2"
                     /gene_synonym="ATP5JL"
                     /product="ATP synthase, H+ transporting, mitochondrial Fo
                     complex, subunit F2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001003713.2"
                     /db_xref="GI:311893389"
                     /db_xref="GeneID:9551"
                     /db_xref="HGNC:848"
                     /db_xref="HPRD:16520"
     mRNA            complement(join(99055784..99055978,99057709..99057816,
                     99063734..99063824))
                     /gene="ATP5J2"
                     /gene_synonym="ATP5JL"
                     /product="ATP synthase, H+ transporting, mitochondrial Fo
                     complex, subunit F2, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001003714.2"
                     /db_xref="GI:311893390"
                     /db_xref="GeneID:9551"
                     /db_xref="HGNC:848"
                     /db_xref="HPRD:16520"
     mRNA            complement(join(99055784..99055978,99057709..99057816,
                     99063752..99063824))
                     /gene="ATP5J2"
                     /gene_synonym="ATP5JL"
                     /product="ATP synthase, H+ transporting, mitochondrial Fo
                     complex, subunit F2, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001039178.2"
                     /db_xref="GI:311893388"
                     /db_xref="GeneID:9551"
                     /db_xref="HGNC:848"
                     /db_xref="HPRD:16520"
     CDS             complement(join(99055950..99055978,99056770..99056886,
                     99057709..99057816,99063734..99063764))
                     /gene="ATP5J2"
                     /gene_synonym="ATP5JL"
                     /note="isoform 2a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ATP synthase subunit f, mitochondrial isoform
                     2a"
                     /protein_id="NP_004880.1"
                     /db_xref="GI:4757812"
                     /db_xref="CCDS:CCDS5665.1"
                     /db_xref="GeneID:9551"
                     /db_xref="HGNC:848"
                     /db_xref="HPRD:16520"
     CDS             complement(join(99055950..99055978,99056770..99056886,
                     99057709..99057816,99063752..99063764))
                     /gene="ATP5J2"
                     /gene_synonym="ATP5JL"
                     /note="isoform 2b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ATP synthase subunit f, mitochondrial isoform
                     2b"
                     /protein_id="NP_001003713.1"
                     /db_xref="GI:51479129"
                     /db_xref="CCDS:CCDS47654.1"
                     /db_xref="GeneID:9551"
                     /db_xref="HGNC:848"
                     /db_xref="HPRD:16520"
     CDS             complement(join(99055950..99055978,99057709..99057816,
                     99063734..99063764))
                     /gene="ATP5J2"
                     /gene_synonym="ATP5JL"
                     /note="isoform 2c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ATP synthase subunit f, mitochondrial isoform
                     2c"
                     /protein_id="NP_001003714.1"
                     /db_xref="GI:51479132"
                     /db_xref="CCDS:CCDS34692.1"
                     /db_xref="GeneID:9551"
                     /db_xref="HGNC:848"
                     /db_xref="HPRD:16520"
     CDS             complement(join(99055950..99055978,99057709..99057816,
                     99063752..99063764))
                     /gene="ATP5J2"
                     /gene_synonym="ATP5JL"
                     /note="isoform 2d is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ATP synthase subunit f, mitochondrial isoform
                     2d"
                     /protein_id="NP_001034267.1"
                     /db_xref="GI:85794908"
                     /db_xref="CCDS:CCDS47653.1"
                     /db_xref="GeneID:9551"
                     /db_xref="HGNC:848"
                     /db_xref="HPRD:16520"
     tRNA            99067307..99067378
                     /product="tRNA-Trp"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /anticodon=(pos:99067339..99067341,aa:Trp)
                     /db_xref="GeneID:100189190"
     gene            99070515..99085217
                     /gene="ZNF789"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285989"
                     /db_xref="HGNC:27801"
                     /db_xref="HPRD:14161"
     mRNA            join(99070515..99070679,99074026..99074103,
                     99077284..99077410,99081653..99081766,99084099..99085217)
                     /gene="ZNF789"
                     /product="zinc finger protein 789, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_213603.2"
                     /db_xref="GI:61676101"
                     /db_xref="GeneID:285989"
                     /db_xref="HGNC:27801"
                     /db_xref="HPRD:14161"
     mRNA            join(99070515..99070679,99074026..99074103,
                     99077284..99077410,99079786..99079949)
                     /gene="ZNF789"
                     /product="zinc finger protein 789, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001013258.1"
                     /db_xref="GI:61676103"
                     /db_xref="GeneID:285989"
                     /db_xref="HGNC:27801"
                     /db_xref="HPRD:14161"
     CDS             join(99074080..99074103,99077284..99077410,
                     99081653..99081766,99084099..99085111)
                     /gene="ZNF789"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 789 isoform 1"
                     /protein_id="NP_998768.2"
                     /db_xref="GI:61676102"
                     /db_xref="CCDS:CCDS34693.1"
                     /db_xref="GeneID:285989"
                     /db_xref="HGNC:27801"
                     /db_xref="HPRD:14161"
     CDS             join(99074080..99074103,99077284..99077410,
                     99079786..99079823)
                     /gene="ZNF789"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 789 isoform 2"
                     /protein_id="NP_001013276.1"
                     /db_xref="GI:61676104"
                     /db_xref="CCDS:CCDS34694.1"
                     /db_xref="GeneID:285989"
                     /db_xref="HGNC:27801"
                     /db_xref="HPRD:14161"
     gene            complement(99090854..99097877)
                     /gene="ZNF394"
                     /gene_synonym="FLJ12298; ZKSCAN14"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84124"
                     /db_xref="HGNC:18832"
                     /db_xref="HPRD:18333"
     mRNA            complement(join(99090854..99092254,99096339..99096465,
                     99097261..99097877))
                     /gene="ZNF394"
                     /gene_synonym="FLJ12298; ZKSCAN14"
                     /product="zinc finger protein 394"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032164.2"
                     /db_xref="GI:31982908"
                     /db_xref="GeneID:84124"
                     /db_xref="HGNC:18832"
                     /db_xref="HPRD:18333"
     CDS             complement(join(99091152..99092254,99096339..99096465,
                     99097261..99097716))
                     /gene="ZNF394"
                     /gene_synonym="FLJ12298; ZKSCAN14"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 394"
                     /protein_id="NP_115540.2"
                     /db_xref="GI:31982909"
                     /db_xref="CCDS:CCDS5666.1"
                     /db_xref="GeneID:84124"
                     /db_xref="HGNC:18832"
                     /db_xref="HPRD:18333"
     gene            99102273..99131445
                     /gene="ZKSCAN5"
                     /gene_synonym="FLJ39233; KIAA1015; MGC33710; ZFP95;
                     ZNF914"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23660"
                     /db_xref="HGNC:12867"
                     /db_xref="HPRD:10318"
                     /db_xref="MIM:611272"
     mRNA            join(99102273..99102356,99103628..99104081,
                     99110076..99110214,99117450..99117532,99117792..99117927,
                     99123436..99124041,99128731..99131445)
                     /gene="ZKSCAN5"
                     /gene_synonym="FLJ39233; KIAA1015; MGC33710; ZFP95;
                     ZNF914"
                     /product="zinc finger with KRAB and SCAN domains 5,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145102.2"
                     /db_xref="GI:126091096"
                     /db_xref="GeneID:23660"
                     /db_xref="HGNC:12867"
                     /db_xref="MIM:611272"
                     /db_xref="HPRD:10318"
     mRNA            join(99102573..99102783,99103628..99104081,
                     99110076..99110214,99117450..99117532,99117792..99117927,
                     99123436..99124041,99128731..99131445)
                     /gene="ZKSCAN5"
                     /gene_synonym="FLJ39233; KIAA1015; MGC33710; ZFP95;
                     ZNF914"
                     /product="zinc finger with KRAB and SCAN domains 5,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014569.3"
                     /db_xref="GI:126091080"
                     /db_xref="GeneID:23660"
                     /db_xref="HGNC:12867"
                     /db_xref="HPRD:10318"
                     /db_xref="MIM:611272"
     CDS             join(99103668..99104081,99110076..99110214,
                     99117450..99117532,99117792..99117927,99123436..99124041,
                     99128731..99129872)
                     /gene="ZKSCAN5"
                     /gene_synonym="FLJ39233; KIAA1015; MGC33710; ZFP95;
                     ZNF914"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein with KRAB and SCAN domains
                     5"
                     /protein_id="NP_055384.1"
                     /db_xref="GI:11036642"
                     /db_xref="CCDS:CCDS5667.1"
                     /db_xref="GeneID:23660"
                     /db_xref="HGNC:12867"
                     /db_xref="HPRD:10318"
                     /db_xref="MIM:611272"
     CDS             join(99103668..99104081,99110076..99110214,
                     99117450..99117532,99117792..99117927,99123436..99124041,
                     99128731..99129872)
                     /gene="ZKSCAN5"
                     /gene_synonym="FLJ39233; KIAA1015; MGC33710; ZFP95;
                     ZNF914"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein with KRAB and SCAN domains
                     5"
                     /protein_id="NP_659570.1"
                     /db_xref="GI:21483182"
                     /db_xref="CCDS:CCDS5667.1"
                     /db_xref="GeneID:23660"
                     /db_xref="HGNC:12867"
                     /db_xref="HPRD:10318"
                     /db_xref="MIM:611272"
     gene            complement(99138150..99138664)
                     /gene="LOC100419451"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419451"
     gene            complement(99143923..99149757)
                     /gene="FAM200A"
                     /gene_synonym="C7orf38; DKFZp727G131; FLJ36794"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221786"
                     /db_xref="HGNC:25401"
                     /db_xref="HPRD:13221"
     mRNA            complement(join(99143923..99146129,99149477..99149757))
                     /gene="FAM200A"
                     /gene_synonym="C7orf38; DKFZp727G131; FLJ36794"
                     /product="family with sequence similarity 200, member A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145111.3"
                     /db_xref="GI:301601651"
                     /db_xref="GeneID:221786"
                     /db_xref="HGNC:25401"
                     /db_xref="HPRD:13221"
     CDS             complement(99144309..99146030)
                     /gene="FAM200A"
                     /gene_synonym="C7orf38; DKFZp727G131; FLJ36794"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC221786"
                     /protein_id="NP_659802.1"
                     /db_xref="GI:21495178"
                     /db_xref="CCDS:CCDS5668.1"
                     /db_xref="GeneID:221786"
                     /db_xref="HGNC:25401"
                     /db_xref="HPRD:13221"
     gene            99156045..99174076
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
     mRNA            join(99156045..99156410,99158156..99158318,
                     99169868..99174076)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /product="zinc finger protein 655, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138494.2"
                     /db_xref="GI:58331258"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
                     /db_xref="HPRD:11673"
     mRNA            join(99156045..99156410,99158156..99158318,
                     99169311..99169415,99169868..99174076)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /product="zinc finger protein 655, transcript variant 7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001083956.1"
                     /db_xref="GI:145701014"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
     mRNA            join(99156045..99156410,99158156..99158318,
                     99159511..99159596,99159991..99160117,99161486..99162328)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /product="zinc finger protein 655, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024061.3"
                     /db_xref="GI:58331257"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
                     /db_xref="HPRD:11673"
     mRNA            join(99156045..99156410,99158156..99158318,
                     99161486..99162328)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /product="zinc finger protein 655, transcript variant 9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001085366.1"
                     /db_xref="GI:145701016"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
     mRNA            join(99156448..99156640,99158156..99158318,
                     99169868..99174076)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /product="zinc finger protein 655, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001009960.1"
                     /db_xref="GI:58331263"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
     mRNA            join(99156448..99156640,99158156..99158318,
                     99169311..99169415,99169868..99174076)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /product="zinc finger protein 655, transcript variant 8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001085368.1"
                     /db_xref="GI:145701020"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
     mRNA            join(99156448..99156640,99158156..99158318,
                     99159511..99159596,99159991..99160117,99161486..99162328)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /product="zinc finger protein 655, transcript variant 10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001085367.1"
                     /db_xref="GI:145701018"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
     mRNA            join(99156448..99156640,99158156..99158318,
                     99161486..99162328)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /product="zinc finger protein 655, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001009958.1"
                     /db_xref="GI:58331261"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
                     /db_xref="HPRD:11673"
     CDS             join(99158183..99158318,99169868..99171207)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 655 isoform a"
                     /protein_id="NP_612503.1"
                     /db_xref="GI:28416427"
                     /db_xref="CCDS:CCDS5669.1"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
     CDS             join(99158183..99158318,99169868..99171207)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /note="isoform a is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 655 isoform a"
                     /protein_id="NP_001009960.1"
                     /db_xref="GI:58331264"
                     /db_xref="CCDS:CCDS5669.1"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
     CDS             join(99158183..99158318,99169311..99169415,
                     99169868..99171207)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /note="isoform f is encoded by transcript variant 7;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 655 isoform f"
                     /protein_id="NP_001077425.1"
                     /db_xref="GI:145701015"
                     /db_xref="CCDS:CCDS47655.1"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
     CDS             join(99158183..99158318,99169311..99169415,
                     99169868..99171207)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /note="isoform f is encoded by transcript variant 8;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 655 isoform f"
                     /protein_id="NP_001078837.1"
                     /db_xref="GI:145701021"
                     /db_xref="CCDS:CCDS47655.1"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
     CDS             join(99158183..99158318,99159511..99159596,
                     99159991..99160117,99161486..99161682)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /note="isoform b is encoded by transcript variant 10;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 655 isoform b"
                     /protein_id="NP_001078836.1"
                     /db_xref="GI:145701019"
                     /db_xref="CCDS:CCDS5670.1"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
     CDS             join(99158183..99158318,99159511..99159596,
                     99159991..99160117,99161486..99161682)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 655 isoform b"
                     /protein_id="NP_076966.1"
                     /db_xref="GI:13129036"
                     /db_xref="CCDS:CCDS5670.1"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
     CDS             join(99158183..99158318,99161486..99161682)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /note="isoform c is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 655 isoform c"
                     /protein_id="NP_001009958.1"
                     /db_xref="GI:58331262"
                     /db_xref="CCDS:CCDS34695.1"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
     CDS             join(99158183..99158318,99161486..99161682)
                     /gene="ZNF655"
                     /gene_synonym="DKFZp686M1631; FLJ23461; MGC10859;
                     MGC16203; MGC5521; VIK; VIK-1"
                     /note="isoform c is encoded by transcript variant 9;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 655 isoform c"
                     /protein_id="NP_001078835.1"
                     /db_xref="GI:145701017"
                     /db_xref="CCDS:CCDS34695.1"
                     /db_xref="GeneID:79027"
                     /db_xref="HGNC:30899"
     gene            99195902..99208456
                     /gene="LOC100289187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100289187"
     mRNA            join(99195902..99196004,99197828..99197908,
                     99202009..99202219,99204371..99204517,99205296..99205433,
                     99208016..99208456)
                     /gene="LOC100289187"
                     /product="transmembrane protein 225-like, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001195541.1"
                     /db_xref="GI:306966149"
                     /db_xref="GeneID:100289187"
     mRNA            join(99195902..99196004,99197831..99197908,
                     99202009..99202219,99204371..99204517,99205296..99205433,
                     99208016..99208456)
                     /gene="LOC100289187"
                     /product="transmembrane protein 225-like, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001195542.1"
                     /db_xref="GI:306966151"
                     /db_xref="GeneID:100289187"
     mRNA            join(99195902..99195995,99197828..99197908,
                     99202009..99202219,99204371..99204517,99205296..99205433,
                     99208016..99208456)
                     /gene="LOC100289187"
                     /product="transmembrane protein 225-like, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001195543.1"
                     /db_xref="GI:306966153"
                     /db_xref="GeneID:100289187"
     CDS             join(99202012..99202219,99204371..99204517,
                     99205296..99205433,99208016..99208188)
                     /gene="LOC100289187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 225-like"
                     /protein_id="NP_001182470.1"
                     /db_xref="GI:306966150"
                     /db_xref="GeneID:100289187"
     CDS             join(99202012..99202219,99204371..99204517,
                     99205296..99205433,99208016..99208188)
                     /gene="LOC100289187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 225-like"
                     /protein_id="NP_001182471.1"
                     /db_xref="GI:306966152"
                     /db_xref="GeneID:100289187"
     CDS             join(99202012..99202219,99204371..99204517,
                     99205296..99205433,99208016..99208188)
                     /gene="LOC100289187"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 225-like"
                     /protein_id="NP_001182472.1"
                     /db_xref="GI:306966154"
                     /db_xref="GeneID:100289187"
     gene            99214571..99230030
                     /gene="ZNF498"
                     /gene_synonym="ZSCAN25"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221785"
                     /db_xref="HGNC:21961"
                     /db_xref="HPRD:15807"
     mRNA            join(99214571..99214639,99216148..99216274,
                     99216671..99216755,99217184..99217616,99218996..99219197,
                     99220172..99220263,99221680..99221803,99226814..99230030)
                     /gene="ZNF498"
                     /gene_synonym="ZSCAN25"
                     /product="zinc finger protein 498"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145115.2"
                     /db_xref="GI:64368879"
                     /db_xref="GeneID:221785"
                     /db_xref="HGNC:21961"
                     /db_xref="HPRD:15807"
     CDS             join(99217230..99217616,99218996..99219197,
                     99220172..99220263,99221680..99221803,99226814..99227643)
                     /gene="ZNF498"
                     /gene_synonym="ZSCAN25"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 498"
                     /protein_id="NP_660090.2"
                     /db_xref="GI:64368880"
                     /db_xref="CCDS:CCDS5671.2"
                     /db_xref="GeneID:221785"
                     /db_xref="HGNC:21961"
                     /db_xref="HPRD:15807"
     gene            complement(99232790..99236646)
                     /gene="LOC442603"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442603"
     gene            complement(99245813..99277621)
                     /gene="CYP3A5"
                     /gene_synonym="CP35; CYPIIIA5; DKFZp686L16231; FLJ31317;
                     P450PCN3; PCN3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1577"
                     /db_xref="HGNC:2638"
                     /db_xref="MIM:605325"
     mRNA            complement(join(99245813..99246023,99247696..99247855,
                     99250176..99250402,99258122..99258282,99260439..99260505,
                     99261591..99261718,99262789..99262937,99264224..99264312,
                     99264575..99264688,99270203..99270302,99272156..99272208,
                     99273738..99273831,99277449..99277621))
                     /gene="CYP3A5"
                     /gene_synonym="CP35; CYPIIIA5; DKFZp686L16231; FLJ31317;
                     P450PCN3; PCN3"
                     /product="cytochrome P450, family 3, subfamily A,
                     polypeptide 5, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000777.3"
                     /db_xref="GI:306518607"
                     /db_xref="GeneID:1577"
                     /db_xref="HGNC:2638"
                     /db_xref="HPRD:05617"
                     /db_xref="MIM:605325"
     misc_RNA        complement(join(99245813..99246023,99247696..99247855,
                     99250176..99250402,99258122..99258282,99260439..99261718,
                     99262789..99262937,99264224..99264312,99264575..99264688,
                     99270203..99270321,99270407..99270538,99272156..99272208,
                     99273738..99274199,99277449..99277621))
                     /gene="CYP3A5"
                     /gene_synonym="CP35; CYPIIIA5; DKFZp686L16231; FLJ31317;
                     P450PCN3; PCN3"
                     /product="cytochrome P450, family 3, subfamily A,
                     polypeptide 5, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033807.1"
                     /db_xref="GI:306518610"
                     /db_xref="GeneID:1577"
                     /db_xref="HGNC:2638"
                     /db_xref="MIM:605325"
     misc_RNA        complement(join(99245813..99246023,99247696..99247855,
                     99250176..99250402,99258122..99258282,99260439..99260505,
                     99261591..99261718,99262789..99262937,99264224..99264312,
                     99264575..99264688,99270203..99270302,99270407..99270538,
                     99272156..99272208,99273738..99274199,99277449..99277621))
                     /gene="CYP3A5"
                     /gene_synonym="CP35; CYPIIIA5; DKFZp686L16231; FLJ31317;
                     P450PCN3; PCN3"
                     /product="cytochrome P450, family 3, subfamily A,
                     polypeptide 5, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033808.1"
                     /db_xref="GI:299523033"
                     /db_xref="GeneID:1577"
                     /db_xref="HGNC:2638"
                     /db_xref="MIM:605325"
     misc_RNA        complement(join(99245813..99246023,99247696..99247855,
                     99250176..99250402,99258122..99258282,99260439..99260505,
                     99261591..99261718,99262789..99262937,99264224..99264312,
                     99264575..99264688,99270203..99270302,99272156..99272208,
                     99273738..99273831,99273940..99274199,99277449..99277621))
                     /gene="CYP3A5"
                     /gene_synonym="CP35; CYPIIIA5; DKFZp686L16231; FLJ31317;
                     P450PCN3; PCN3"
                     /product="cytochrome P450, family 3, subfamily A,
                     polypeptide 5, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033809.1"
                     /db_xref="GI:299523034"
                     /db_xref="GeneID:1577"
                     /db_xref="HGNC:2638"
                     /db_xref="MIM:605325"
     CDS             complement(join(99245928..99246023,99247696..99247855,
                     99250176..99250402,99258122..99258282,99260439..99260505,
                     99261591..99261718,99262789..99262937,99264224..99264312,
                     99264575..99264688,99270203..99270302,99272156..99272208,
                     99273738..99273831,99277449..99277519))
                     /gene="CYP3A5"
                     /gene_synonym="CP35; CYPIIIA5; DKFZp686L16231; FLJ31317;
                     P450PCN3; PCN3"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytochrome P450 3A5 isoform 1"
                     /protein_id="NP_000768.1"
                     /db_xref="GI:4503231"
                     /db_xref="CCDS:CCDS5672.1"
                     /db_xref="GeneID:1577"
                     /db_xref="HGNC:2638"
                     /db_xref="MIM:605325"
     misc_RNA        complement(join(99257842..99258282,99260439..99260505,
                     99261591..99261718,99262789..99262937,99264336..99264433,
                     99264575..99264688,99269394..99269501,99270203..99270302,
                     99270407..99270538,99272156..99272208,99273738..99273831,
                     99277449..99277621))
                     /gene="CYP3A5"
                     /gene_synonym="CP35; CYPIIIA5; DKFZp686L16231; FLJ31317;
                     P450PCN3; PCN3"
                     /product="cytochrome P450, family 3, subfamily A,
                     polypeptide 5, transcript variant 7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033811.1"
                     /db_xref="GI:299523043"
                     /db_xref="GeneID:1577"
                     /db_xref="HGNC:2638"
                     /db_xref="MIM:605325"
     misc_RNA        complement(join(99257842..99258282,99260439..99260505,
                     99261591..99261718,99262789..99262937,99264336..99264433,
                     99264575..99264688,99270203..99270302,99270407..99270538,
                     99272156..99272208,99273738..99273831,99277449..99277621))
                     /gene="CYP3A5"
                     /gene_synonym="CP35; CYPIIIA5; DKFZp686L16231; FLJ31317;
                     P450PCN3; PCN3"
                     /product="cytochrome P450, family 3, subfamily A,
                     polypeptide 5, transcript variant 8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033812.1"
                     /db_xref="GI:299523044"
                     /db_xref="GeneID:1577"
                     /db_xref="HGNC:2638"
                     /db_xref="MIM:605325"
     misc_RNA        complement(join(99257851..99257996,99258122..99258282,
                     99260439..99261718,99262789..99262937,99264224..99264312,
                     99264575..99264688,99270203..99270302,99270407..99270538,
                     99272156..99272208,99273738..99274199,99277449..99277621))
                     /gene="CYP3A5"
                     /gene_synonym="CP35; CYPIIIA5; DKFZp686L16231; FLJ31317;
                     P450PCN3; PCN3"
                     /product="cytochrome P450, family 3, subfamily A,
                     polypeptide 5, transcript variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033810.1"
                     /db_xref="GI:299523036"
                     /db_xref="GeneID:1577"
                     /db_xref="HGNC:2638"
                     /db_xref="MIM:605325"
     mRNA            complement(join(99268845..99269501,99270203..99270302,
                     99272156..99272208,99273738..99273831,99277449..99277621))
                     /gene="CYP3A5"
                     /gene_synonym="CP35; CYPIIIA5; DKFZp686L16231; FLJ31317;
                     P450PCN3; PCN3"
                     /product="cytochrome P450, family 3, subfamily A,
                     polypeptide 5, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001190484.1"
                     /db_xref="GI:306518608"
                     /db_xref="GeneID:1577"
                     /db_xref="HGNC:2638"
                     /db_xref="MIM:605325"
     CDS             complement(join(99269397..99269501,99270203..99270302,
                     99272156..99272208,99273738..99273831,99277449..99277519))
                     /gene="CYP3A5"
                     /gene_synonym="CP35; CYPIIIA5; DKFZp686L16231; FLJ31317;
                     P450PCN3; PCN3"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytochrome P450 3A5 isoform 2"
                     /protein_id="NP_001177413.1"
                     /db_xref="GI:306518609"
                     /db_xref="CCDS:CCDS55134.1"
                     /db_xref="GeneID:1577"
                     /db_xref="HGNC:2638"
                     /db_xref="MIM:605325"
     gene            complement(99282647..99297743)
                     /gene="CYP3A5P1"
                     /gene_synonym="CYP3AP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:1578"
                     /db_xref="HGNC:2639"
     gene            complement(99302660..99332819)
                     /gene="CYP3A7"
                     /gene_synonym="CP37; P450-HFLA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1551"
                     /db_xref="HGNC:2640"
                     /db_xref="HPRD:05630"
                     /db_xref="MIM:605340"
     mRNA            complement(join(99302660..99303218,99305435..99305597,
                     99306658..99306884,99308355..99308515,99311092..99311158,
                     99312178..99312305,99313381..99313529,99314800..99314888,
                     99315149..99315262,99317936..99318035,99319919..99319971,
                     99328682..99328775,99332646..99332819))
                     /gene="CYP3A7"
                     /gene_synonym="CP37; P450-HFLA"
                     /product="cytochrome P450, family 3, subfamily A,
                     polypeptide 7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000765.3"
                     /db_xref="GI:262290931"
                     /db_xref="GeneID:1551"
                     /db_xref="HGNC:2640"
                     /db_xref="HPRD:05630"
                     /db_xref="MIM:605340"
     CDS             complement(join(99303123..99303218,99305435..99305597,
                     99306658..99306884,99308355..99308515,99311092..99311158,
                     99312178..99312305,99313381..99313529,99314800..99314888,
                     99315149..99315262,99317936..99318035,99319919..99319971,
                     99328682..99328775,99332646..99332716))
                     /gene="CYP3A7"
                     /gene_synonym="CP37; P450-HFLA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytochrome P450 3A7"
                     /protein_id="NP_000756.2"
                     /db_xref="GI:262290932"
                     /db_xref="CCDS:CCDS5673.1"
                     /db_xref="GeneID:1551"
                     /db_xref="HGNC:2640"
                     /db_xref="HPRD:05630"
                     /db_xref="MIM:605340"
     gene            complement(99345872..99350114)
                     /gene="CYP3A5P2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:79424"
                     /db_xref="HGNC:18850"
     gene            complement(99354583..99381811)
                     /gene="CYP3A4"
                     /gene_synonym="CP33; CP34; CYP3A; CYP3A3; CYPIIIA3;
                     CYPIIIA4; HLP; MGC126680; NF-25; P450C3; P450PCN1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1576"
                     /db_xref="HGNC:2637"
                     /db_xref="MIM:124010"
     mRNA            complement(join(99354583..99355851,99358442..99358604,
                     99359664..99359890,99361478..99361638,99364000..99364066,
                     99364754..99364881,99365977..99366125,99367391..99367479,
                     99367745..99367858,99370213..99370312,99375651..99375703,
                     99377615..99377708,99381634..99381811))
                     /gene="CYP3A4"
                     /gene_synonym="CP33; CP34; CYP3A; CYP3A3; CYPIIIA3;
                     CYPIIIA4; HLP; MGC126680; NF-25; P450C3; P450PCN1"
                     /product="cytochrome P450, family 3, subfamily A,
                     polypeptide 4, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017460.5"
                     /db_xref="GI:322960990"
                     /db_xref="GeneID:1576"
                     /db_xref="HGNC:2637"
                     /db_xref="HPRD:00484"
                     /db_xref="MIM:124010"
     mRNA            complement(join(99354583..99355851,99358442..99358604,
                     99359664..99359890,99361478..99361638,99364000..99364066,
                     99364754..99364878,99365977..99366125,99367391..99367479,
                     99367745..99367858,99370213..99370312,99375651..99375703,
                     99377615..99377708,99381634..99381811))
                     /gene="CYP3A4"
                     /gene_synonym="CP33; CP34; CYP3A; CYP3A3; CYPIIIA3;
                     CYPIIIA4; HLP; MGC126680; NF-25; P450C3; P450PCN1"
                     /product="cytochrome P450, family 3, subfamily A,
                     polypeptide 4, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001202855.2"
                     /db_xref="GI:322960937"
                     /db_xref="GeneID:1576"
                     /db_xref="HGNC:2637"
                     /db_xref="MIM:124010"
     CDS             complement(join(99355756..99355851,99358442..99358604,
                     99359664..99359890,99361478..99361638,99364000..99364066,
                     99364754..99364881,99365977..99366125,99367391..99367479,
                     99367745..99367858,99370213..99370312,99375651..99375703,
                     99377615..99377708,99381634..99381704))
                     /gene="CYP3A4"
                     /gene_synonym="CP33; CP34; CYP3A; CYP3A3; CYPIIIA3;
                     CYPIIIA4; HLP; MGC126680; NF-25; P450C3; P450PCN1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytochrome P450 3A4 isoform 1"
                     /protein_id="NP_059488.2"
                     /db_xref="GI:13435386"
                     /db_xref="CCDS:CCDS5674.1"
                     /db_xref="GeneID:1576"
                     /db_xref="HGNC:2637"
                     /db_xref="MIM:124010"
     CDS             complement(join(99355756..99355851,99358442..99358604,
                     99359664..99359890,99361478..99361638,99364000..99364066,
                     99364754..99364878,99365977..99366125,99367391..99367479,
                     99367745..99367858,99370213..99370312,99375651..99375703,
                     99377615..99377708,99381634..99381704))
                     /gene="CYP3A4"
                     /gene_synonym="CP33; CP34; CYP3A; CYP3A3; CYPIIIA3;
                     CYPIIIA4; HLP; MGC126680; NF-25; P450C3; P450PCN1"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytochrome P450 3A4 isoform 2"
                     /protein_id="NP_001189784.1"
                     /db_xref="GI:322302351"
                     /db_xref="GeneID:1576"
                     /db_xref="HGNC:2637"
                     /db_xref="MIM:124010"
     gene            99425636..99464173
                     /gene="CYP3A43"
                     /gene_synonym="MGC119315; MGC119316"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64816"
                     /db_xref="HGNC:17450"
                     /db_xref="HPRD:05942"
                     /db_xref="MIM:606534"
     mRNA            join(99425636..99425809,99434076..99434169,
                     99436743..99436795,99441766..99441865,99445111..99445224,
                     99445789..99445877,99447169..99447317,99453214..99453341,
                     99454456..99454522,99457453..99457613,99459236..99459462,
                     99461157..99461322,99463529..99464173)
                     /gene="CYP3A43"
                     /gene_synonym="MGC119315; MGC119316"
                     /product="cytochrome P450, family 3, subfamily A,
                     polypeptide 43, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022820.3"
                     /db_xref="GI:16933531"
                     /db_xref="GeneID:64816"
                     /db_xref="HGNC:17450"
                     /db_xref="HPRD:05942"
                     /db_xref="MIM:606534"
     mRNA            join(99425636..99425809,99434076..99434169,
                     99436743..99436795,99441766..99441865,99445111..99445224,
                     99445789..99445877,99447169..99447317,99453214..99453341,
                     99454456..99454522,99457453..99457613,99459236..99459462,
                     99461160..99461322,99463529..99464173)
                     /gene="CYP3A43"
                     /gene_synonym="MGC119315; MGC119316"
                     /product="cytochrome P450, family 3, subfamily A,
                     polypeptide 43, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_057095.1"
                     /db_xref="GI:16933532"
                     /db_xref="GeneID:64816"
                     /db_xref="HGNC:17450"
                     /db_xref="HPRD:05942"
                     /db_xref="MIM:606534"
     mRNA            join(99425636..99425809,99434076..99434169,
                     99436743..99436795,99441766..99441865,99445111..99445224,
                     99445789..99445877,99447169..99447317,99453214..99453341,
                     99454456..99454522,99457453..99457613,99459236..99459462,
                     99463529..99464173)
                     /gene="CYP3A43"
                     /gene_synonym="MGC119315; MGC119316"
                     /product="cytochrome P450, family 3, subfamily A,
                     polypeptide 43, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_057096.2"
                     /db_xref="GI:17738315"
                     /db_xref="GeneID:64816"
                     /db_xref="HGNC:17450"
                     /db_xref="HPRD:05942"
                     /db_xref="MIM:606534"
     CDS             join(99425739..99425809,99434076..99434169,
                     99436743..99436795,99441766..99441865,99445111..99445224,
                     99445789..99445877,99447169..99447317,99453214..99453341,
                     99454456..99454522,99457453..99457613,99459236..99459462,
                     99461157..99461322,99463529..99463624)
                     /gene="CYP3A43"
                     /gene_synonym="MGC119315; MGC119316"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytochrome P450 3A43 isoform 1"
                     /protein_id="NP_073731.1"
                     /db_xref="GI:12383060"
                     /db_xref="CCDS:CCDS5675.1"
                     /db_xref="GeneID:64816"
                     /db_xref="HGNC:17450"
                     /db_xref="HPRD:05942"
                     /db_xref="MIM:606534"
     CDS             join(99425739..99425809,99434076..99434169,
                     99436743..99436795,99441766..99441865,99445111..99445224,
                     99445789..99445877,99447169..99447317,99453214..99453341,
                     99454456..99454522,99457453..99457613,99459236..99459462,
                     99461160..99461322,99463529..99463624)
                     /gene="CYP3A43"
                     /gene_synonym="MGC119315; MGC119316"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytochrome P450 3A43 isoform 2"
                     /protein_id="NP_476436.1"
                     /db_xref="GI:16933533"
                     /db_xref="CCDS:CCDS5676.1"
                     /db_xref="GeneID:64816"
                     /db_xref="HGNC:17450"
                     /db_xref="HPRD:05942"
                     /db_xref="MIM:606534"
     CDS             join(99425739..99425809,99434076..99434169,
                     99436743..99436795,99441766..99441865,99445111..99445224,
                     99445789..99445877,99447169..99447317,99453214..99453341,
                     99454456..99454522,99457453..99457613,99459236..99459462,
                     99463529..99463538)
                     /gene="CYP3A43"
                     /gene_synonym="MGC119315; MGC119316"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytochrome P450 3A43 isoform 3"
                     /protein_id="NP_476437.1"
                     /db_xref="GI:16933535"
                     /db_xref="CCDS:CCDS5677.1"
                     /db_xref="GeneID:64816"
                     /db_xref="HGNC:17450"
                     /db_xref="HPRD:05942"
                     /db_xref="MIM:606534"
     gene            complement(99473685..99474656)
                     /gene="OR2AE1"
                     /gene_synonym="OR2AE2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:81392"
                     /db_xref="HGNC:15087"
                     /db_xref="HPRD:14934"
     mRNA            complement(99473685..99474656)
                     /gene="OR2AE1"
                     /gene_synonym="OR2AE2"
                     /product="olfactory receptor, family 2, subfamily AE,
                     member 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001005276.1"
                     /db_xref="GI:52627150"
                     /db_xref="GeneID:81392"
                     /db_xref="HGNC:15087"
                     /db_xref="HPRD:14934"
     CDS             complement(99473685..99474656)
                     /gene="OR2AE1"
                     /gene_synonym="OR2AE2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 2AE1"
                     /protein_id="NP_001005276.1"
                     /db_xref="GI:52627151"
                     /db_xref="CCDS:CCDS34696.1"
                     /db_xref="GeneID:81392"
                     /db_xref="HGNC:15087"
                     /db_xref="HPRD:14934"
     gene            complement(99488030..99517223)
                     /gene="TRIM4"
                     /gene_synonym="RNF87"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:89122"
                     /db_xref="HGNC:16275"
                     /db_xref="HPRD:15556"
     mRNA            complement(join(99488030..99490369,99500841..99500938,
                     99501199..99501221,99506205..99506435,99507188..99507283,
                     99514325..99514402,99516632..99517223))
                     /gene="TRIM4"
                     /gene_synonym="RNF87"
                     /product="tripartite motif containing 4, transcript
                     variant alpha"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033017.3"
                     /db_xref="GI:301601614"
                     /db_xref="GeneID:89122"
                     /db_xref="HGNC:16275"
                     /db_xref="HPRD:15556"
     mRNA            complement(join(99488030..99490369,99500841..99500938,
                     99501199..99501221,99506205..99506435,99507188..99507283,
                     99516632..99517223))
                     /gene="TRIM4"
                     /gene_synonym="RNF87"
                     /product="tripartite motif containing 4, transcript
                     variant beta"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033091.2"
                     /db_xref="GI:301601616"
                     /db_xref="GeneID:89122"
                     /db_xref="HGNC:16275"
                     /db_xref="HPRD:15556"
     CDS             complement(join(99489786..99490369,99500841..99500938,
                     99501199..99501221,99506205..99506435,99507188..99507283,
                     99514325..99514402,99516632..99517024))
                     /gene="TRIM4"
                     /gene_synonym="RNF87"
                     /note="isoform alpha is encoded by transcript variant
                     alpha; Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="tripartite motif-containing protein 4 isoform
                     alpha"
                     /protein_id="NP_148977.2"
                     /db_xref="GI:301601615"
                     /db_xref="CCDS:CCDS5679.1"
                     /db_xref="GeneID:89122"
                     /db_xref="HGNC:16275"
                     /db_xref="HPRD:15556"
     CDS             complement(join(99489786..99490369,99500841..99500938,
                     99501199..99501221,99506205..99506435,99507188..99507283,
                     99516632..99517024))
                     /gene="TRIM4"
                     /gene_synonym="RNF87"
                     /note="isoform beta is encoded by transcript variant beta;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="tripartite motif-containing protein 4 isoform
                     beta"
                     /protein_id="NP_149082.1"
                     /db_xref="GI:15011941"
                     /db_xref="CCDS:CCDS5678.1"
                     /db_xref="GeneID:89122"
                     /db_xref="HGNC:16275"
                     /db_xref="HPRD:15556"
     gene            complement(99520892..99527243)
                     /gene="GJC3"
                     /gene_synonym="CX29; CX30.2; CX31.3; GJE1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:349149"
                     /db_xref="HGNC:17495"
                     /db_xref="HPRD:13580"
                     /db_xref="MIM:611925"
     mRNA            complement(join(99520892..99521226,99526463..99527243))
                     /gene="GJC3"
                     /gene_synonym="CX29; CX30.2; CX31.3; GJE1"
                     /product="gap junction protein, gamma 3, 30.2kDa"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_181538.2"
                     /db_xref="GI:289177042"
                     /db_xref="GeneID:349149"
                     /db_xref="HGNC:17495"
                     /db_xref="HPRD:13580"
                     /db_xref="MIM:611925"
     CDS             complement(join(99521168..99521226,99526463..99527243))
                     /gene="GJC3"
                     /gene_synonym="CX29; CX30.2; CX31.3; GJE1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="gap junction gamma-3 protein"
                     /protein_id="NP_853516.1"
                     /db_xref="GI:31559821"
                     /db_xref="CCDS:CCDS34697.1"
                     /db_xref="GeneID:349149"
                     /db_xref="HGNC:17495"
                     /db_xref="HPRD:13580"
                     /db_xref="MIM:611925"
     gene            complement(99564350..99573735)
                     /gene="AZGP1"
                     /gene_synonym="ZA2G; ZAG"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:563"
                     /db_xref="HGNC:910"
                     /db_xref="HPRD:01910"
                     /db_xref="MIM:194460"
     mRNA            complement(join(99564350..99564909,99565778..99566053,
                     99569369..99569629,99573568..99573735))
                     /gene="AZGP1"
                     /gene_synonym="ZA2G; ZAG"
                     /product="alpha-2-glycoprotein 1, zinc-binding"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001185.3"
                     /db_xref="GI:261862294"
                     /db_xref="GeneID:563"
                     /db_xref="HGNC:910"
                     /db_xref="HPRD:01910"
                     /db_xref="MIM:194460"
     CDS             complement(join(99564626..99564909,99565778..99566053,
                     99569369..99569629,99573568..99573643))
                     /gene="AZGP1"
                     /gene_synonym="ZA2G; ZAG"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc-alpha-2-glycoprotein precursor"
                     /protein_id="NP_001176.1"
                     /db_xref="GI:4502337"
                     /db_xref="CCDS:CCDS5680.1"
                     /db_xref="GeneID:563"
                     /db_xref="HGNC:910"
                     /db_xref="HPRD:01910"
                     /db_xref="MIM:194460"
     gene            99578385..99581860
                     /gene="AZGP1P1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:646282"
                     /db_xref="HGNC:911"
     misc_RNA        join(99578385..99578471,99580767..99581860)
                     /gene="AZGP1P1"
                     /product="alpha-2-glycoprotein 1, zinc-binding pseudogene
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_036679.1"
                     /db_xref="GI:308522765"
                     /db_xref="GeneID:646282"
                     /db_xref="HGNC:911"
     gene            99590020..99590685
                     /gene="LOC100128334"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100128334"
     gene            99613219..99635403
                     /gene="ZKSCAN1"
                     /gene_synonym="9130423L19Rik; KOX18; MGC138429; PHZ-37;
                     ZNF139; ZNF36"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7586"
                     /db_xref="HGNC:13101"
                     /db_xref="HPRD:03161"
                     /db_xref="MIM:601260"
     mRNA            join(99613219..99613349,99621042..99621555,
                     99621777..99621930,99627484..99627575,99627872..99627998,
                     99630928..99635403)
                     /gene="ZKSCAN1"
                     /gene_synonym="9130423L19Rik; KOX18; MGC138429; PHZ-37;
                     ZNF139; ZNF36"
                     /product="zinc finger with KRAB and SCAN domains 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003439.1"
                     /db_xref="GI:55769563"
                     /db_xref="GeneID:7586"
                     /db_xref="HGNC:13101"
                     /db_xref="HPRD:03161"
                     /db_xref="MIM:601260"
     CDS             join(99621130..99621555,99621777..99621930,
                     99627484..99627575,99627872..99627998,99630928..99631820)
                     /gene="ZKSCAN1"
                     /gene_synonym="9130423L19Rik; KOX18; MGC138429; PHZ-37;
                     ZNF139; ZNF36"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein with KRAB and SCAN domains
                     1"
                     /protein_id="NP_003430.1"
                     /db_xref="GI:55769564"
                     /db_xref="CCDS:CCDS34698.1"
                     /db_xref="GeneID:7586"
                     /db_xref="HGNC:13101"
                     /db_xref="HPRD:03161"
                     /db_xref="MIM:601260"
     gene            99647417..99662663
                     /gene="ZSCAN21"
                     /gene_synonym="DKFZp434L134; DKFZp686H10254; NY-REN-21;
                     Zipro1; ZNF38"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7589"
                     /db_xref="HGNC:13104"
                     /db_xref="HPRD:03162"
                     /db_xref="MIM:601261"
     mRNA            join(99647417..99647464,99654534..99655028,
                     99655321..99655513,99661411..99662663)
                     /gene="ZSCAN21"
                     /gene_synonym="DKFZp434L134; DKFZp686H10254; NY-REN-21;
                     Zipro1; ZNF38"
                     /product="zinc finger and SCAN domain containing 21"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145914.2"
                     /db_xref="GI:37537685"
                     /db_xref="GeneID:7589"
                     /db_xref="HGNC:13104"
                     /db_xref="HPRD:03162"
                     /db_xref="MIM:601261"
     CDS             join(99654630..99655028,99655321..99655513,
                     99661411..99662240)
                     /gene="ZSCAN21"
                     /gene_synonym="DKFZp434L134; DKFZp686H10254; NY-REN-21;
                     Zipro1; ZNF38"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger and SCAN domain-containing protein
                     21"
                     /protein_id="NP_666019.1"
                     /db_xref="GI:27544931"
                     /db_xref="CCDS:CCDS5681.1"
                     /db_xref="GeneID:7589"
                     /db_xref="HGNC:13104"
                     /db_xref="HPRD:03162"
                     /db_xref="MIM:601261"
     gene            complement(99661653..99679371)
                     /gene="ZNF3"
                     /gene_synonym="A8-51; FLJ20216; HF.12; KOX25; PP838;
                     Zfp113"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7551"
                     /db_xref="HGNC:13089"
                     /db_xref="HPRD:01911"
                     /db_xref="MIM:194510"
     mRNA            complement(join(99661653..99662535,99672758..99672884,
                     99673165..99673253,99674926..99675056,99677159..99677279,
                     99679258..99679371))
                     /gene="ZNF3"
                     /gene_synonym="A8-51; FLJ20216; HF.12; KOX25; PP838;
                     Zfp113"
                     /product="zinc finger protein 3, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017715.2"
                     /db_xref="GI:122114648"
                     /db_xref="GeneID:7551"
                     /db_xref="HGNC:13089"
                     /db_xref="HPRD:01911"
                     /db_xref="MIM:194510"
     CDS             complement(join(99662411..99662535,99672758..99672884,
                     99673165..99673253,99674926..99674980))
                     /gene="ZNF3"
                     /gene_synonym="A8-51; FLJ20216; HF.12; KOX25; PP838;
                     Zfp113"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 3 isoform 1"
                     /protein_id="NP_060185.2"
                     /db_xref="GI:122114649"
                     /db_xref="CCDS:CCDS43618.1"
                     /db_xref="GeneID:7551"
                     /db_xref="HGNC:13089"
                     /db_xref="HPRD:01911"
                     /db_xref="MIM:194510"
     mRNA            complement(join(99667594..99669835,99672758..99672884,
                     99673165..99673253,99674926..99675056,99677163..99677279,
                     99679258..99679371))
                     /gene="ZNF3"
                     /gene_synonym="A8-51; FLJ20216; HF.12; KOX25; PP838;
                     Zfp113"
                     /product="zinc finger protein 3, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032924.3"
                     /db_xref="GI:122114640"
                     /db_xref="GeneID:7551"
                     /db_xref="HGNC:13089"
                     /db_xref="HPRD:01911"
                     /db_xref="MIM:194510"
     CDS             complement(join(99668766..99669835,99672758..99672884,
                     99673165..99673253,99674926..99674980))
                     /gene="ZNF3"
                     /gene_synonym="A8-51; FLJ20216; HF.12; KOX25; PP838;
                     Zfp113"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 3 isoform 2"
                     /protein_id="NP_116313.3"
                     /db_xref="GI:122114641"
                     /db_xref="CCDS:CCDS43619.1"
                     /db_xref="GeneID:7551"
                     /db_xref="HGNC:13089"
                     /db_xref="HPRD:01911"
                     /db_xref="MIM:194510"
     gene            99686583..99689823
                     /gene="COPS6"
                     /gene_synonym="CSN6; MOV34-34KD"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10980"
                     /db_xref="HGNC:21749"
                     /db_xref="HPRD:16735"
     mRNA            join(99686583..99686689,99686913..99687038,
                     99687238..99687369,99688022..99688110,99688215..99688277,
                     99688525..99688572,99688661..99688775,99688861..99688953,
                     99689043..99689143,99689272..99689823)
                     /gene="COPS6"
                     /gene_synonym="CSN6; MOV34-34KD"
                     /product="COP9 constitutive photomorphogenic homolog
                     subunit 6 (Arabidopsis)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006833.4"
                     /db_xref="GI:38027945"
                     /db_xref="GeneID:10980"
                     /db_xref="HGNC:21749"
                     /db_xref="HPRD:16735"
     CDS             join(99686614..99686689,99686913..99687038,
                     99687238..99687369,99688022..99688110,99688215..99688277,
                     99688525..99688572,99688661..99688775,99688861..99688953,
                     99689043..99689143,99689272..99689412)
                     /gene="COPS6"
                     /gene_synonym="CSN6; MOV34-34KD"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="COP9 signalosome complex subunit 6"
                     /protein_id="NP_006824.2"
                     /db_xref="GI:34147637"
                     /db_xref="CCDS:CCDS5682.1"
                     /db_xref="GeneID:10980"
                     /db_xref="HGNC:21749"
                     /db_xref="HPRD:16735"
     gene            complement(99690404..99699427)
                     /gene="MCM7"
                     /gene_synonym="CDC47; MCM2; P1.1-MCM3; P1CDC47; P85MCM;
                     PNAS146"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4176"
                     /db_xref="HGNC:6950"
                     /db_xref="HPRD:01154"
                     /db_xref="MIM:600592"
     mRNA            complement(join(99690404..99690756,99690915..99691024,
                     99691796..99691964,99693010..99693093,99693397..99693790,
                     99694924..99695007,99695237..99695368,99695457..99695571,
                     99695764..99695913,99696201..99696338,99696646..99696826,
                     99696902..99697026,99697212..99697376,99697637..99697716,
                     99698887..99699427))
                     /gene="MCM7"
                     /gene_synonym="CDC47; MCM2; P1.1-MCM3; P1CDC47; P85MCM;
                     PNAS146"
                     /product="minichromosome maintenance complex component 7,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005916.3"
                     /db_xref="GI:33469967"
                     /db_xref="GeneID:4176"
                     /db_xref="HGNC:6950"
                     /db_xref="HPRD:01154"
                     /db_xref="MIM:600592"
     mRNA            complement(join(99690404..99690756,99690915..99691024,
                     99691796..99691964,99693010..99693093,99693397..99693790,
                     99694924..99695007,99695237..99695368,99695457..99695571,
                     99695764..99695913,99696201..99696338,99696646..99697026,
                     99697212..99697376,99697637..99697716,99697836..99698380))
                     /gene="MCM7"
                     /gene_synonym="CDC47; MCM2; P1.1-MCM3; P1CDC47; P85MCM;
                     PNAS146"
                     /product="minichromosome maintenance complex component 7,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182776.1"
                     /db_xref="GI:33469921"
                     /db_xref="GeneID:4176"
                     /db_xref="HGNC:6950"
                     /db_xref="HPRD:01154"
                     /db_xref="MIM:600592"
     CDS             complement(join(99690555..99690756,99690915..99691024,
                     99691796..99691964,99693010..99693093,99693397..99693790,
                     99694924..99695007,99695237..99695368,99695457..99695571,
                     99695764..99695913,99696201..99696338,99696646..99696826,
                     99696902..99697026,99697212..99697376,99697637..99697716,
                     99698887..99698917))
                     /gene="MCM7"
                     /gene_synonym="CDC47; MCM2; P1.1-MCM3; P1CDC47; P85MCM;
                     PNAS146"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA replication licensing factor MCM7 isoform 1"
                     /protein_id="NP_005907.3"
                     /db_xref="GI:33469968"
                     /db_xref="CCDS:CCDS5683.1"
                     /db_xref="GeneID:4176"
                     /db_xref="HGNC:6950"
                     /db_xref="HPRD:01154"
                     /db_xref="MIM:600592"
     CDS             complement(join(99690555..99690756,99690915..99691024,
                     99691796..99691964,99693010..99693093,99693397..99693790,
                     99694924..99695007,99695237..99695368,99695457..99695571,
                     99695764..99695913,99696201..99696338,99696646..99696699))
                     /gene="MCM7"
                     /gene_synonym="CDC47; MCM2; P1.1-MCM3; P1CDC47; P85MCM;
                     PNAS146"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA replication licensing factor MCM7 isoform 2"
                     /protein_id="NP_877577.1"
                     /db_xref="GI:33469922"
                     /db_xref="CCDS:CCDS5684.1"
                     /db_xref="GeneID:4176"
                     /db_xref="HGNC:6950"
                     /db_xref="HPRD:01154"
                     /db_xref="MIM:600592"
     gene            complement(99691183..99691266)
                     /gene="MIR25"
                     /gene_synonym="hsa-mir-25; miR-25; MIRN25"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:407014"
                     /db_xref="HGNC:31609"
                     /db_xref="MIM:612150"
                     /db_xref="miRBase:MI0000082"
     ncRNA           complement(99691183..99691266)
                     /gene="MIR25"
                     /gene_synonym="hsa-mir-25; miR-25; MIRN25"
                     /ncRNA_class="miRNA"
                     /product="microRNA 25"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029498.1"
                     /db_xref="GI:262205684"
                     /db_xref="GeneID:407014"
                     /db_xref="HGNC:31609"
                     /db_xref="MIM:612150"
                     /db_xref="miRBase:MI0000082"
     ncRNA           complement(99691183..99691266)
                     /gene="MIR25"
                     /gene_synonym="hsa-mir-25; miR-25; MIRN25"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-25"
                     /inference="similar to RNA sequence:INSD: AJ421746"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:407014"
                     /db_xref="miRBase:MI0000082"
                     /db_xref="HGNC:31609"
                     /db_xref="MIM:612150"
     gene            complement(99691391..99691470)
                     /gene="MIR93"
                     /gene_synonym="hsa-mir-93; miR-93; MIRN9; MIRN93"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:407050"
                     /db_xref="HGNC:31645"
                     /db_xref="MIM:612984"
                     /db_xref="miRBase:MI0000095"
     ncRNA           complement(99691391..99691470)
                     /gene="MIR93"
                     /gene_synonym="hsa-mir-93; miR-93; MIRN9; MIRN93"
                     /ncRNA_class="miRNA"
                     /product="microRNA 93"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029510.1"
                     /db_xref="GI:262205737"
                     /db_xref="GeneID:407050"
                     /db_xref="HGNC:31645"
                     /db_xref="MIM:612984"
                     /db_xref="miRBase:MI0000095"
     ncRNA           complement(99691391..99691470)
                     /gene="MIR93"
                     /gene_synonym="hsa-mir-93; miR-93; MIRN9; MIRN93"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-93"
                     /inference="similar to RNA sequence:INSD: AF480566"
                     /inference="similar to RNA sequence:INSD: AF480565"
                     /inference="similar to RNA sequence:INSD: AF480531"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:407050"
                     /db_xref="miRBase:MI0000095"
                     /db_xref="HGNC:31645"
                     /db_xref="MIM:612984"
     gene            complement(99691616..99691697)
                     /gene="MIR106B"
                     /gene_synonym="MIRN106B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:406900"
                     /db_xref="HGNC:31495"
                     /db_xref="MIM:612983"
                     /db_xref="miRBase:MI0000734"
     ncRNA           complement(99691616..99691697)
                     /gene="MIR106B"
                     /gene_synonym="MIRN106B"
                     /ncRNA_class="miRNA"
                     /product="microRNA 106b"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029831.1"
                     /db_xref="GI:262206053"
                     /db_xref="GeneID:406900"
                     /db_xref="HGNC:31495"
                     /db_xref="MIM:612983"
                     /db_xref="miRBase:MI0000734"
     ncRNA           complement(99691616..99691697)
                     /gene="MIR106B"
                     /gene_synonym="MIRN106B"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-106b"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:406900"
                     /db_xref="miRBase:MI0000734"
                     /db_xref="HGNC:31495"
                     /db_xref="MIM:612983"
     gene            99699130..99704803
                     /gene="AP4M1"
                     /gene_synonym="CPSQ3; MU-4; MU-ARP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9179"
                     /db_xref="HGNC:574"
                     /db_xref="HPRD:03803"
                     /db_xref="MIM:602296"
     mRNA            join(99699130..99699395,99699503..99699591,
                     99700298..99700404,99700487..99700583,99701032..99701142,
                     99701235..99701315,99701715..99701777,99702497..99702563,
                     99702668..99702721,99702863..99702969,99703068..99703162,
                     99703582..99703626,99703864..99703914,99704026..99704137,
                     99704281..99704803)
                     /gene="AP4M1"
                     /gene_synonym="CPSQ3; MU-4; MU-ARP2"
                     /product="adaptor-related protein complex 4, mu 1 subunit"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004722.3"
                     /db_xref="GI:153266831"
                     /db_xref="GeneID:9179"
                     /db_xref="HGNC:574"
                     /db_xref="HPRD:03803"
                     /db_xref="MIM:602296"
     CDS             join(99699338..99699395,99699503..99699591,
                     99700298..99700404,99700487..99700583,99701032..99701142,
                     99701235..99701315,99701715..99701777,99702497..99702563,
                     99702668..99702721,99702863..99702969,99703068..99703162,
                     99703582..99703626,99703864..99703914,99704026..99704137,
                     99704281..99704505)
                     /gene="AP4M1"
                     /gene_synonym="CPSQ3; MU-4; MU-ARP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="AP-4 complex subunit mu-1"
                     /protein_id="NP_004713.2"
                     /db_xref="GI:14917111"
                     /db_xref="CCDS:CCDS5685.1"
                     /db_xref="GeneID:9179"
                     /db_xref="HGNC:574"
                     /db_xref="HPRD:03803"
                     /db_xref="MIM:602296"
     gene            complement(99704693..99717481)
                     /gene="TAF6"
                     /gene_synonym="DKFZp781E21155; MGC:8964; TAF(II)70;
                     TAF(II)80; TAF2E; TAFII-70; TAFII-80; TAFII70; TAFII80;
                     TAFII85"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6878"
                     /db_xref="HGNC:11540"
                     /db_xref="MIM:602955"
     mRNA            complement(join(99704693..99705246,99705549..99705746,
                     99705990..99706163,99707571..99707696,99707823..99707897,
                     99708762..99708944,99709351..99709452,99709545..99709622,
                     99709731..99709876,99710421..99710540,99710972..99711028,
                     99711239..99711392,99711491..99711577,99711677..99711891,
                     99717318..99717481))
                     /gene="TAF6"
                     /gene_synonym="DKFZp781E21155; MGC:8964; TAF(II)70;
                     TAF(II)80; TAF2E; TAFII-70; TAFII-80; TAFII70; TAFII80;
                     TAFII85"
                     /product="TAF6 RNA polymerase II, TATA box binding protein
                     (TBP)-associated factor, 80kDa, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001190415.1"
                     /db_xref="GI:298676519"
                     /db_xref="GeneID:6878"
                     /db_xref="HGNC:11540"
                     /db_xref="MIM:602955"
     mRNA            complement(join(99704693..99705246,99705549..99705746,
                     99705990..99706163,99707571..99707696,99707823..99707897,
                     99708762..99708944,99709351..99709452,99709545..99709622,
                     99709731..99709876,99710421..99710540,99710972..99711028,
                     99711239..99711392,99711491..99711577,99711677..99711891,
                     99716827..99717021))
                     /gene="TAF6"
                     /gene_synonym="DKFZp781E21155; MGC:8964; TAF(II)70;
                     TAF(II)80; TAF2E; TAFII-70; TAFII-80; TAFII70; TAFII80;
                     TAFII85"
                     /product="TAF6 RNA polymerase II, TATA box binding protein
                     (TBP)-associated factor, 80kDa, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_139315.2"
                     /db_xref="GI:298676518"
                     /db_xref="GeneID:6878"
                     /db_xref="HGNC:11540"
                     /db_xref="MIM:602955"
     mRNA            complement(join(99704693..99705246,99705549..99705746,
                     99705990..99706163,99707571..99707696,99707823..99707897,
                     99708762..99708944,99709351..99709452,99709545..99709622,
                     99709731..99709876,99710421..99710540,99710972..99711028,
                     99711239..99711392,99711491..99711577,99711677..99711891,
                     99716503..99716995))
                     /gene="TAF6"
                     /gene_synonym="DKFZp781E21155; MGC:8964; TAF(II)70;
                     TAF(II)80; TAF2E; TAFII-70; TAFII-80; TAFII70; TAFII80;
                     TAFII85"
                     /product="TAF6 RNA polymerase II, TATA box binding protein
                     (TBP)-associated factor, 80kDa, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005641.3"
                     /db_xref="GI:298676521"
                     /db_xref="GeneID:6878"
                     /db_xref="HGNC:11540"
                     /db_xref="HPRD:11807"
                     /db_xref="MIM:602955"
     misc_RNA        complement(join(99704693..99705246,99705549..99705746,
                     99705990..99706163,99707571..99707696,99707823..99707897,
                     99708762..99708944,99709351..99709452,99709545..99709622,
                     99709731..99709876,99710421..99710540,99710972..99711028,
                     99711239..99711392,99711491..99711577,99711677..99711891,
                     99716952..99716995))
                     /gene="TAF6"
                     /gene_synonym="DKFZp781E21155; MGC:8964; TAF(II)70;
                     TAF(II)80; TAF2E; TAFII-70; TAFII-80; TAFII70; TAFII80;
                     TAFII85"
                     /product="TAF6 RNA polymerase II, TATA box binding protein
                     (TBP)-associated factor, 80kDa, transcript variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033792.1"
                     /db_xref="GI:298676522"
                     /db_xref="GeneID:6878"
                     /db_xref="HGNC:11540"
                     /db_xref="MIM:602955"
     CDS             complement(join(99704869..99705246,99705549..99705746,
                     99705990..99706163,99707571..99707696,99707823..99707897,
                     99708762..99708944,99709351..99709452,99709545..99709622,
                     99709731..99709876,99710421..99710540,99710972..99711028,
                     99711239..99711392,99711491..99711577,99711677..99711891,
                     99717318..99717369))
                     /gene="TAF6"
                     /gene_synonym="DKFZp781E21155; MGC:8964; TAF(II)70;
                     TAF(II)80; TAF2E; TAFII-70; TAFII-80; TAFII70; TAFII80;
                     TAFII85"
                     /note="isoform epsilon is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transcription initiation factor TFIID subunit 6
                     isoform epsilon"
                     /protein_id="NP_001177344.1"
                     /db_xref="GI:298676520"
                     /db_xref="CCDS:CCDS55135.1"
                     /db_xref="GeneID:6878"
                     /db_xref="HGNC:11540"
                     /db_xref="MIM:602955"
     CDS             complement(join(99704869..99705246,99705549..99705746,
                     99705990..99706163,99707571..99707696,99707823..99707897,
                     99708762..99708944,99709351..99709452,99709545..99709622,
                     99709731..99709876,99710421..99710540,99710972..99711028,
                     99711239..99711392,99711491..99711577,99711677..99711832))
                     /gene="TAF6"
                     /gene_synonym="DKFZp781E21155; MGC:8964; TAF(II)70;
                     TAF(II)80; TAF2E; TAFII-70; TAFII-80; TAFII70; TAFII80;
                     TAFII85"
                     /note="isoform alpha is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transcription initiation factor TFIID subunit 6
                     isoform alpha"
                     /protein_id="NP_005632.1"
                     /db_xref="GI:5032147"
                     /db_xref="CCDS:CCDS5686.1"
                     /db_xref="GeneID:6878"
                     /db_xref="HGNC:11540"
                     /db_xref="MIM:602955"
     CDS             complement(join(99704869..99705246,99705549..99705746,
                     99705990..99706163,99707571..99707696,99707823..99707897,
                     99708762..99708944,99709351..99709452,99709545..99709622,
                     99709731..99709876,99710421..99710540,99710972..99711028,
                     99711239..99711392,99711491..99711577,99711677..99711832))
                     /gene="TAF6"
                     /gene_synonym="DKFZp781E21155; MGC:8964; TAF(II)70;
                     TAF(II)80; TAF2E; TAFII-70; TAFII-80; TAFII70; TAFII80;
                     TAFII85"
                     /note="isoform alpha is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transcription initiation factor TFIID subunit 6
                     isoform alpha"
                     /protein_id="NP_647476.1"
                     /db_xref="GI:21536359"
                     /db_xref="CCDS:CCDS5686.1"
                     /db_xref="GeneID:6878"
                     /db_xref="HGNC:11540"
                     /db_xref="MIM:602955"
     gene            99717265..99723131
                     /gene="CNPY4"
                     /gene_synonym="MGC40499; PRAT4B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:245812"
                     /db_xref="HGNC:28631"
                     /db_xref="HPRD:14611"
                     /db_xref="MIM:610047"
     mRNA            join(99717265..99717485,99719882..99720008,
                     99720104..99720200,99720407..99720529,99722137..99722254,
                     99722348..99723131)
                     /gene="CNPY4"
                     /gene_synonym="MGC40499; PRAT4B"
                     /product="canopy 4 homolog (zebrafish)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152755.1"
                     /db_xref="GI:22749478"
                     /db_xref="GeneID:245812"
                     /db_xref="HGNC:28631"
                     /db_xref="HPRD:14611"
                     /db_xref="MIM:610047"
     CDS             join(99717368..99717485,99719882..99720008,
                     99720104..99720200,99720407..99720529,99722137..99722254,
                     99722348..99722511)
                     /gene="CNPY4"
                     /gene_synonym="MGC40499; PRAT4B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein canopy homolog 4 precursor"
                     /protein_id="NP_689968.1"
                     /db_xref="GI:22749479"
                     /db_xref="CCDS:CCDS34701.1"
                     /db_xref="GeneID:245812"
                     /db_xref="HGNC:28631"
                     /db_xref="HPRD:14611"
                     /db_xref="MIM:610047"
     gene            99724317..99726121
                     /gene="MBLAC1"
                     /gene_synonym="MGC39819"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:255374"
                     /db_xref="HGNC:22180"
                     /db_xref="HPRD:18584"
     mRNA            join(99724317..99724687,99724991..99726121)
                     /gene="MBLAC1"
                     /gene_synonym="MGC39819"
                     /product="metallo-beta-lactamase domain containing 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_203397.1"
                     /db_xref="GI:63025211"
                     /db_xref="GeneID:255374"
                     /db_xref="HGNC:22180"
                     /db_xref="HPRD:18584"
     CDS             99725019..99725819
                     /gene="MBLAC1"
                     /gene_synonym="MGC39819"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="metallo-beta-lactamase domain-containing protein
                     1"
                     /protein_id="NP_981942.1"
                     /db_xref="GI:63025212"
                     /db_xref="CCDS:CCDS43620.1"
                     /db_xref="GeneID:255374"
                     /db_xref="HGNC:22180"
                     /db_xref="HPRD:18584"
     gene            complement(99737257..99738305)
                     /gene="LOC100289264"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /pseudo
                     /db_xref="GeneID:100289264"
     exon            complement(99737257..99737600)
                     /gene="LOC100289264"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100289264"
     exon            complement(99737920..99738305)
                     /gene="LOC100289264"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100289264"
     gene            99746530..99751833
                     /gene="C7orf59"
                     /gene_synonym="MGC163425; MGC163431"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:389541"
                     /db_xref="HGNC:33772"
                     /db_xref="HPRD:17380"
     mRNA            join(99746530..99746598,99747122..99747202,
                     99751023..99751140,99751490..99751833)
                     /gene="C7orf59"
                     /gene_synonym="MGC163425; MGC163431"
                     /product="chromosome 7 open reading frame 59"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001008395.2"
                     /db_xref="GI:148806921"
                     /db_xref="GeneID:389541"
                     /db_xref="HGNC:33772"
                     /db_xref="HPRD:17380"
     CDS             join(99746596..99746598,99747122..99747202,
                     99751023..99751140,99751490..99751587)
                     /gene="C7orf59"
                     /gene_synonym="MGC163425; MGC163431"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC389541"
                     /protein_id="NP_001008396.1"
                     /db_xref="GI:56606127"
                     /db_xref="CCDS:CCDS34702.1"
                     /db_xref="GeneID:389541"
                     /db_xref="HGNC:33772"
                     /db_xref="HPRD:17380"
     gene            complement(99752043..99756302)
                     /gene="C7orf43"
                     /gene_synonym="DKFZp761G0712; FLJ10925"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55262"
                     /db_xref="HGNC:25604"
                     /db_xref="HPRD:07716"
     mRNA            complement(join(99752043..99752787,99752885..99753078,
                     99753294..99753448,99754009..99754172,99754257..99754339,
                     99754468..99754615,99754717..99754837,99754996..99755082,
                     99755256..99755385,99755466..99755561,99755712..99756302))
                     /gene="C7orf43"
                     /gene_synonym="DKFZp761G0712; FLJ10925"
                     /product="chromosome 7 open reading frame 43"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018275.3"
                     /db_xref="GI:34222158"
                     /db_xref="GeneID:55262"
                     /db_xref="HGNC:25604"
                     /db_xref="HPRD:07716"
     CDS             complement(join(99752634..99752787,99752885..99753078,
                     99753294..99753448,99754009..99754172,99754257..99754339,
                     99754468..99754615,99754717..99754837,99754996..99755082,
                     99755256..99755385,99755466..99755561,99755712..99756122))
                     /gene="C7orf43"
                     /gene_synonym="DKFZp761G0712; FLJ10925"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC55262"
                     /protein_id="NP_060745.3"
                     /db_xref="GI:27363480"
                     /db_xref="CCDS:CCDS5687.1"
                     /db_xref="GeneID:55262"
                     /db_xref="HGNC:25604"
                     /db_xref="HPRD:07716"
     gene            complement(99754228..99754292)
                     /gene="MIR4658"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100616439"
                     /db_xref="HGNC:41673"
                     /db_xref="miRBase:MI0017286"
     ncRNA           complement(99754228..99754292)
                     /gene="MIR4658"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4658"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039802.1"
                     /db_xref="GI:337756606"
                     /db_xref="GeneID:100616439"
                     /db_xref="HGNC:41673"
                     /db_xref="miRBase:MI0017286"
     gene            complement(99756865..99766373)
                     /gene="GAL3ST4"
                     /gene_synonym="FLJ12116; GAL3ST-4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79690"
                     /db_xref="HGNC:24145"
                     /db_xref="HPRD:12195"
                     /db_xref="MIM:608235"
     mRNA            complement(join(99756865..99758582,99764125..99764428,
                     99764594..99764906,99766169..99766373))
                     /gene="GAL3ST4"
                     /gene_synonym="FLJ12116; GAL3ST-4"
                     /product="galactose-3-O-sulfotransferase 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024637.4"
                     /db_xref="GI:124381137"
                     /db_xref="GeneID:79690"
                     /db_xref="HGNC:24145"
                     /db_xref="HPRD:12195"
                     /db_xref="MIM:608235"
     CDS             complement(join(99757551..99758582,99764125..99764428,
                     99764594..99764718))
                     /gene="GAL3ST4"
                     /gene_synonym="FLJ12116; GAL3ST-4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="galactose-3-O-sulfotransferase 4"
                     /protein_id="NP_078913.3"
                     /db_xref="GI:31542835"
                     /db_xref="CCDS:CCDS5688.1"
                     /db_xref="GeneID:79690"
                     /db_xref="HGNC:24145"
                     /db_xref="HPRD:12195"
                     /db_xref="MIM:608235"
     gene            complement(99767229..99774990)
                     /gene="GPC2"
                     /gene_synonym="DKFZp547M109; FLJ38962"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221914"
                     /db_xref="HGNC:4450"
                     /db_xref="HPRD:17051"
     mRNA            complement(join(99767229..99768106,99768884..99769059,
                     99769162..99769301,99769402..99769548,99769710..99769840,
                     99771458..99771620,99772308..99772388,99773195..99773517,
                     99773830..99773988,99774657..99774990))
                     /gene="GPC2"
                     /gene_synonym="DKFZp547M109; FLJ38962"
                     /product="glypican 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152742.1"
                     /db_xref="GI:22749458"
                     /db_xref="GeneID:221914"
                     /db_xref="HGNC:4450"
                     /db_xref="HPRD:17051"
     CDS             complement(join(99767853..99768106,99768884..99769059,
                     99769162..99769301,99769402..99769548,99769710..99769840,
                     99771458..99771620,99772308..99772388,99773195..99773517,
                     99773830..99773988,99774657..99774822))
                     /gene="GPC2"
                     /gene_synonym="DKFZp547M109; FLJ38962"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="glypican-2 precursor"
                     /protein_id="NP_689955.1"
                     /db_xref="GI:22749459"
                     /db_xref="CCDS:CCDS5689.1"
                     /db_xref="GeneID:221914"
                     /db_xref="HGNC:4450"
                     /db_xref="HPRD:17051"
     gene            99775538..99812010
                     /gene="STAG3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10734"
                     /db_xref="HGNC:11356"
                     /db_xref="HPRD:10253"
                     /db_xref="MIM:608489"
     mRNA            join(99775538..99775628,99778116..99778295,
                     99779713..99779815,99780346..99780462,99783823..99783919,
                     99786076..99786152,99786435..99786639,99787068..99787219,
                     99792932..99793005,99794779..99794902,99795401..99795499,
                     99795710..99795789,99796098..99796205,99796466..99796580,
                     99796885..99796990,99797164..99797267,99797859..99797951,
                     99798076..99798165,99798392..99798592,99798713..99798783,
                     99798887..99798974,99799409..99799489,99799572..99799664,
                     99799795..99799963,99800077..99800213,99801644..99801745,
                     99802250..99802398,99802628..99802756,99802850..99803007,
                     99808634..99808808,99809061..99809162,99809418..99809499,
                     99811358..99811429,99811630..99812010)
                     /gene="STAG3"
                     /product="stromal antigen 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012447.2"
                     /db_xref="GI:57863309"
                     /db_xref="GeneID:10734"
                     /db_xref="HGNC:11356"
                     /db_xref="HPRD:10253"
                     /db_xref="MIM:608489"
     CDS             join(99778180..99778295,99779713..99779815,
                     99780346..99780462,99783823..99783919,99786076..99786152,
                     99786435..99786639,99787068..99787219,99792932..99793005,
                     99794779..99794902,99795401..99795499,99795710..99795789,
                     99796098..99796205,99796466..99796580,99796885..99796990,
                     99797164..99797267,99797859..99797951,99798076..99798165,
                     99798392..99798592,99798713..99798783,99798887..99798974,
                     99799409..99799489,99799572..99799664,99799795..99799963,
                     99800077..99800213,99801644..99801745,99802250..99802398,
                     99802628..99802756,99802850..99803007,99808634..99808808,
                     99809061..99809162,99809418..99809499,99811358..99811429,
                     99811630..99811638)
                     /gene="STAG3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cohesin subunit SA-3"
                     /protein_id="NP_036579.2"
                     /db_xref="GI:57863310"
                     /db_xref="CCDS:CCDS34703.1"
                     /db_xref="GeneID:10734"
                     /db_xref="HGNC:11356"
                     /db_xref="HPRD:10253"
                     /db_xref="MIM:608489"
     gene            complement(99798276..99869855)
                     /gene="GATS"
                     /gene_synonym="DKFZp686B07267; STAG3OS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:352954"
                     /db_xref="HGNC:29954"
                     /db_xref="HPRD:17030"
     mRNA            complement(join(99798276..99800226,99821193..99821321,
                     99821505..99821698,99831227..99831297,99869461..99869855))
                     /gene="GATS"
                     /gene_synonym="DKFZp686B07267; STAG3OS"
                     /product="GATS, stromal antigen 3 opposite strand,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178831.6"
                     /db_xref="GI:253970398"
                     /db_xref="GeneID:352954"
                     /db_xref="HGNC:29954"
                     /db_xref="HPRD:17030"
     misc_RNA        complement(join(99798276..99800226,99809017..99809617,
                     99810670..99810756,99820220..99820343,99821193..99821321,
                     99821505..99821698,99831227..99831297,99869461..99869855))
                     /gene="GATS"
                     /gene_synonym="DKFZp686B07267; STAG3OS"
                     /product="GATS, stromal antigen 3 opposite strand,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_028039.1"
                     /db_xref="GI:253970400"
                     /db_xref="GeneID:352954"
                     /db_xref="HGNC:29954"
                     /db_xref="HPRD:17030"
     misc_RNA        complement(join(99798276..99800226,99820220..99820343,
                     99821193..99821321,99821505..99821698,99831227..99831297,
                     99869461..99869855))
                     /gene="GATS"
                     /gene_synonym="DKFZp686B07267; STAG3OS"
                     /product="GATS, stromal antigen 3 opposite strand,
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_028040.1"
                     /db_xref="GI:253970401"
                     /db_xref="GeneID:352954"
                     /db_xref="HGNC:29954"
                     /db_xref="HPRD:17030"
     misc_RNA        complement(join(99806559..99809617,99810670..99810756,
                     99820220..99820343,99821193..99821321,99821505..99821698,
                     99831227..99831297,99869461..99869855))
                     /gene="GATS"
                     /gene_synonym="DKFZp686B07267; STAG3OS"
                     /product="GATS, stromal antigen 3 opposite strand,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_028038.1"
                     /db_xref="GI:253970399"
                     /db_xref="GeneID:352954"
                     /db_xref="HGNC:29954"
                     /db_xref="HPRD:17030"
     gene            99816871..99819111
                     /gene="PVRIG"
                     /gene_synonym="C7orf15; MGC104322; MGC138295; MGC138297;
                     MGC2463"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79037"
                     /db_xref="HGNC:32190"
     mRNA            join(99816871..99817023,99817336..99817651,
                     99817737..99818087,99818170..99818296,99818383..99818443,
                     99818551..99819111)
                     /gene="PVRIG"
                     /gene_synonym="C7orf15; MGC104322; MGC138295; MGC138297;
                     MGC2463"
                     /product="poliovirus receptor related immunoglobulin
                     domain containing"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024070.3"
                     /db_xref="GI:57863284"
                     /db_xref="GeneID:79037"
                     /db_xref="HGNC:32190"
     CDS             join(99817534..99817651,99817737..99818087,
                     99818170..99818296,99818383..99818443,99818551..99818874)
                     /gene="PVRIG"
                     /gene_synonym="C7orf15; MGC104322; MGC138295; MGC138297;
                     MGC2463"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein PVRIG"
                     /protein_id="NP_076975.2"
                     /db_xref="GI:57863285"
                     /db_xref="CCDS:CCDS5690.1"
                     /db_xref="GeneID:79037"
                     /db_xref="HGNC:32190"
     CDS             complement(join(99821241..99821321,99821505..99821698,
                     99831227..99831297,99869461..99869606))
                     /gene="GATS"
                     /gene_synonym="DKFZp686B07267; STAG3OS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative protein GATS"
                     /protein_id="NP_849153.3"
                     /db_xref="GI:54020722"
                     /db_xref="CCDS:CCDS43621.1"
                     /db_xref="GeneID:352954"
                     /db_xref="HGNC:29954"
                     /db_xref="HPRD:17030"
     gene            99905325..99919819
                     /gene="SPDYE3"
                     /gene_synonym="MGC119294; MGC57359"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:441272"
                     /db_xref="HGNC:35462"
                     /db_xref="HPRD:14693"
     mRNA            join(99905325..99905614,99906597..99906815,
                     99907983..99908201,99909373..99909591,99910763..99910981,
                     99912155..99912373,99913408..99913466,99914693..99914778,
                     99917188..99917431,99917554..99917658,99918514..99919819)
                     /gene="SPDYE3"
                     /gene_synonym="MGC119294; MGC57359"
                     /product="speedy homolog E3 (Xenopus laevis)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001004351.4"
                     /db_xref="GI:282721019"
                     /db_xref="GeneID:441272"
                     /db_xref="HGNC:35462"
                     /db_xref="HPRD:14693"
     CDS             join(99905509..99905614,99906597..99906815,
                     99907983..99908201,99909373..99909591,99910763..99910981,
                     99912155..99912373,99913408..99913466,99914693..99914778,
                     99917188..99917431,99917554..99917613)
                     /gene="SPDYE3"
                     /gene_synonym="MGC119294; MGC57359"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="speedy protein E3"
                     /protein_id="NP_001004351.3"
                     /db_xref="GI:282721020"
                     /db_xref="CCDS:CCDS47658.2"
                     /db_xref="GeneID:441272"
                     /db_xref="HGNC:35462"
                     /db_xref="HPRD:14693"
     gene            complement(99918263..99933930)
                     /gene="PMS2P1"
                     /gene_synonym="PMS2L1; PMS2L13; PMS2L6; PMS2L7; PMS2L8;
                     PMS3; PMS8; PMSR1; PMSR2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:5379"
                     /db_xref="HGNC:9123"
                     /db_xref="MIM:605038"
     misc_RNA        complement(join(99918263..99918707,99923314..99923402,
                     99926459..99926642,99927805..99927907,99928086..99928172,
                     99930065..99930204,99933461..99933930))
                     /gene="PMS2P1"
                     /gene_synonym="PMS2L1; PMS2L13; PMS2L6; PMS2L7; PMS2L8;
                     PMS3; PMS8; PMSR1; PMSR2"
                     /product="postmeiotic segregation increased 2 pseudogene
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003613.1"
                     /db_xref="GI:153792443"
                     /db_xref="GeneID:5379"
                     /db_xref="HGNC:9123"
                     /db_xref="MIM:605038"
     gene            99933688..99965454
                     /gene="PILRB"
                     /gene_synonym="FDFACT1; FDFACT2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:29990"
                     /db_xref="HGNC:18297"
                     /db_xref="MIM:605342"
     misc_RNA        join(99933688..99933960,99935802..99935887,
                     99936396..99936512,99943488..99943591,99947422..99947510,
                     99948875..99949033,99949786..99950101,99950187..99950290,
                     99950384..99950537,99950620..99950746,99950833..99950893,
                     99950996..99951635,99952766..99952863,99954373..99954506,
                     99955843..99955989,99956313..99956702,99956960..99957160,
                     99964972..99965454)
                     /gene="PILRB"
                     /gene_synonym="FDFACT1; FDFACT2"
                     /product="paired immunoglobin-like type 2 receptor beta,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_036569.1"
                     /db_xref="GI:304434827"
                     /db_xref="GeneID:29990"
                     /db_xref="HGNC:18297"
                     /db_xref="MIM:605342"
     misc_RNA        join(99933688..99933960,99935802..99935887,
                     99936396..99936512,99943488..99943591,99947354..99947510,
                     99948875..99949033,99949885..99950101,99950187..99950537,
                     99950620..99950746,99950833..99950893,99950996..99951106,
                     99952766..99952863,99954373..99954506,99955843..99955989,
                     99956522..99956702,99956960..99957160,99964972..99965454)
                     /gene="PILRB"
                     /gene_synonym="FDFACT1; FDFACT2"
                     /product="paired immunoglobin-like type 2 receptor beta,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_036570.1"
                     /db_xref="GI:304434829"
                     /db_xref="GeneID:29990"
                     /db_xref="HGNC:18297"
                     /db_xref="MIM:605342"
     mRNA            join(99955626..99955989,99956313..99956702,
                     99956960..99957160,99964972..99965454)
                     /gene="PILRB"
                     /gene_synonym="FDFACT1; FDFACT2"
                     /product="paired immunoglobin-like type 2 receptor beta,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178238.2"
                     /db_xref="GI:304434522"
                     /db_xref="GeneID:29990"
                     /db_xref="HGNC:18297"
                     /db_xref="MIM:605342"
     CDS             join(99955926..99955989,99956313..99956702,
                     99956960..99957160,99964972..99965000)
                     /gene="PILRB"
                     /gene_synonym="FDFACT1; FDFACT2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="paired immunoglobulin-like type 2 receptor beta
                     precursor"
                     /protein_id="NP_839956.1"
                     /db_xref="GI:30179911"
                     /db_xref="CCDS:CCDS43622.1"
                     /db_xref="GeneID:29990"
                     /db_xref="HGNC:18297"
                     /db_xref="MIM:605342"
     gene            99971068..99997722
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:29992"
                     /db_xref="HGNC:20396"
                     /db_xref="MIM:605341"
     mRNA            join(99971068..99971343,99971667..99972056,
                     99987511..99987729,99995502..99995535,99996914..99996963,
                     99997204..99997235,99997408..99997722)
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /product="paired immunoglobin-like type 2 receptor alpha,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013439.2"
                     /db_xref="GI:30179908"
                     /db_xref="GeneID:29992"
                     /db_xref="HGNC:20396"
                     /db_xref="HPRD:05631"
                     /db_xref="MIM:605341"
     mRNA            join(99971068..99971343,99971667..99972056,
                     99995502..99995535,99996914..99996963,99997204..99997235,
                     99997408..99997722)
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /product="paired immunoglobin-like type 2 receptor alpha,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178272.1"
                     /db_xref="GI:30179904"
                     /db_xref="GeneID:29992"
                     /db_xref="HGNC:20396"
                     /db_xref="MIM:605341"
     mRNA            join(99971068..99971343,99971667..99972056,
                     99996914..99996963,99997204..99997235,99997408..99997722)
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /product="paired immunoglobin-like type 2 receptor alpha,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178273.1"
                     /db_xref="GI:30179906"
                     /db_xref="GeneID:29992"
                     /db_xref="HGNC:20396"
                     /db_xref="MIM:605341"
     CDS             join(99971280..99971343,99971667..99972056,
                     99987511..99987729,99995502..99995535,99996914..99996963,
                     99997204..99997235,99997408..99997530)
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="paired immunoglobulin-like type 2 receptor alpha
                     isoform 1 precursor"
                     /protein_id="NP_038467.2"
                     /db_xref="GI:30179909"
                     /db_xref="CCDS:CCDS5691.1"
                     /db_xref="GeneID:29992"
                     /db_xref="HGNC:20396"
                     /db_xref="MIM:605341"
     CDS             join(99971280..99971343,99971667..99972056,
                     99995502..99995535,99996914..99996963,99997204..99997235,
                     99997408..99997530)
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="paired immunoglobulin-like type 2 receptor alpha
                     isoform 2 precursor"
                     /protein_id="NP_840056.1"
                     /db_xref="GI:30179905"
                     /db_xref="CCDS:CCDS5692.1"
                     /db_xref="GeneID:29992"
                     /db_xref="HGNC:20396"
                     /db_xref="MIM:605341"
     CDS             join(99971280..99971343,99971667..99972056,
                     99996914..99996963,99997204..99997227)
                     /gene="PILRA"
                     /gene_synonym="FDF03"
                     /note="isoform 3 precursor is encoded by transcript
                     variant 3; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="paired immunoglobulin-like type 2 receptor alpha
                     isoform 3 precursor"
                     /protein_id="NP_840057.1"
                     /db_xref="GI:30179907"
                     /db_xref="CCDS:CCDS47660.1"
                     /db_xref="GeneID:29992"
                     /db_xref="HGNC:20396"
                     /db_xref="MIM:605341"
     gene            complement(99998495..100026302)
                     /gene="ZCWPW1"
                     /gene_synonym="DKFZp434N0510; FLJ10057; ZCW1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55063"
                     /db_xref="HGNC:23486"
                     /db_xref="HPRD:15706"
     mRNA            complement(join(99998495..99998959,99999512..99999664,
                     100000139..100000199,100001317..100001408,
                     100001801..100001867,100002636..100002716,
                     100004317..100004421,100004851..100004926,
                     100006162..100006282,100007051..100007167,
                     100013598..100013717,100013928..100014079,
                     100014689..100014806,100016734..100016812,
                     100017253..100017506,100018245..100018301,
                     100022653..100022759,100026191..100026302))
                     /gene="ZCWPW1"
                     /gene_synonym="DKFZp434N0510; FLJ10057; ZCW1"
                     /product="zinc finger, CW type with PWWP domain 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017984.3"
                     /db_xref="GI:94721343"
                     /db_xref="GeneID:55063"
                     /db_xref="HGNC:23486"
                     /db_xref="HPRD:15706"
     gene            99998522..100001824
                     /gene="LOC100289298"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 EST, 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100289298"
     misc_RNA        join(99998522..99998971,99999506..99999663,
                     100001316..100001407,100001800..100001824)
                     /gene="LOC100289298"
                     /product="hypothetical LOC100289298"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 EST, 1 Protein"
                     /pseudo
                     /transcript_id="XR_132541.1"
                     /db_xref="GI:341915404"
                     /db_xref="GeneID:100289298"
     CDS             complement(join(99998637..99998959,99999512..99999664,
                     100000139..100000199,100001317..100001408,
                     100001801..100001867,100002636..100002716,
                     100004317..100004421,100004851..100004926,
                     100006162..100006282,100007051..100007167,
                     100013598..100013717,100013928..100014079,
                     100014689..100014806,100016734..100016812,
                     100017253..100017506,100018245..100018272))
                     /gene="ZCWPW1"
                     /gene_synonym="DKFZp434N0510; FLJ10057; ZCW1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger CW-type PWWP domain protein 1"
                     /protein_id="NP_060454.3"
                     /db_xref="GI:94721344"
                     /db_xref="CCDS:CCDS43623.1"
                     /db_xref="GeneID:55063"
                     /db_xref="HGNC:23486"
                     /db_xref="HPRD:15706"
     gene            100026413..100031749
                     /gene="MEPCE"
                     /gene_synonym="BCDIN3; FLJ20257"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:56257"
                     /db_xref="HGNC:20247"
                     /db_xref="HPRD:07889"
                     /db_xref="MIM:611478"
     mRNA            join(100026413..100026663,100028238..100029312,
                     100030542..100030760,100030886..100031012,
                     100031125..100031749)
                     /gene="MEPCE"
                     /gene_synonym="BCDIN3; FLJ20257"
                     /product="methylphosphate capping enzyme, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001194990.1"
                     /db_xref="GI:303521309"
                     /db_xref="GeneID:56257"
                     /db_xref="HGNC:20247"
                     /db_xref="MIM:611478"
                     /db_xref="HPRD:07889"
     mRNA            join(100026413..100026663,100028653..100029312,
                     100030542..100030760,100030886..100031012,
                     100031125..100031749)
                     /gene="MEPCE"
                     /gene_synonym="BCDIN3; FLJ20257"
                     /product="methylphosphate capping enzyme, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001194991.1"
                     /db_xref="GI:303521336"
                     /db_xref="GeneID:56257"
                     /db_xref="HGNC:20247"
                     /db_xref="MIM:611478"
                     /db_xref="HPRD:07889"
     mRNA            join(100026413..100026528,100028653..100029312,
                     100030542..100030760,100030886..100031012,
                     100031125..100031749)
                     /gene="MEPCE"
                     /gene_synonym="BCDIN3; FLJ20257"
                     /product="methylphosphate capping enzyme, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001194992.1"
                     /db_xref="GI:303521459"
                     /db_xref="GeneID:56257"
                     /db_xref="HGNC:20247"
                     /db_xref="MIM:611478"
                     /db_xref="HPRD:07889"
     mRNA            join(100027254..100029312,100030542..100030760,
                     100030886..100031012,100031125..100031749)
                     /gene="MEPCE"
                     /gene_synonym="BCDIN3; FLJ20257"
                     /product="methylphosphate capping enzyme, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_019606.5"
                     /db_xref="GI:303521261"
                     /db_xref="GeneID:56257"
                     /db_xref="HGNC:20247"
                     /db_xref="HPRD:07889"
                     /db_xref="MIM:611478"
     CDS             join(100027642..100029312,100030542..100030760,
                     100030886..100031012,100031125..100031177)
                     /gene="MEPCE"
                     /gene_synonym="BCDIN3; FLJ20257"
                     /note="isoform A is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="7SK snRNA methylphosphate capping enzyme isoform
                     A"
                     /protein_id="NP_062552.2"
                     /db_xref="GI:47271406"
                     /db_xref="CCDS:CCDS5693.1"
                     /db_xref="GeneID:56257"
                     /db_xref="HGNC:20247"
                     /db_xref="HPRD:07889"
                     /db_xref="MIM:611478"
     CDS             join(100029049..100029312,100030542..100030760,
                     100030886..100031012,100031125..100031177)
                     /gene="MEPCE"
                     /gene_synonym="BCDIN3; FLJ20257"
                     /note="isoform B is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="7SK snRNA methylphosphate capping enzyme isoform
                     B"
                     /protein_id="NP_001181919.1"
                     /db_xref="GI:303521310"
                     /db_xref="CCDS:CCDS55136.1"
                     /db_xref="GeneID:56257"
                     /db_xref="HGNC:20247"
                     /db_xref="HPRD:07889"
                     /db_xref="MIM:611478"
     CDS             join(100029049..100029312,100030542..100030760,
                     100030886..100031012,100031125..100031177)
                     /gene="MEPCE"
                     /gene_synonym="BCDIN3; FLJ20257"
                     /note="isoform B is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="7SK snRNA methylphosphate capping enzyme isoform
                     B"
                     /protein_id="NP_001181920.1"
                     /db_xref="GI:303521337"
                     /db_xref="CCDS:CCDS55136.1"
                     /db_xref="GeneID:56257"
                     /db_xref="HGNC:20247"
                     /db_xref="HPRD:07889"
                     /db_xref="MIM:611478"
     CDS             join(100029049..100029312,100030542..100030760,
                     100030886..100031012,100031125..100031177)
                     /gene="MEPCE"
                     /gene_synonym="BCDIN3; FLJ20257"
                     /note="isoform B is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="7SK snRNA methylphosphate capping enzyme isoform
                     B"
                     /protein_id="NP_001181921.1"
                     /db_xref="GI:303521460"
                     /db_xref="CCDS:CCDS55136.1"
                     /db_xref="GeneID:56257"
                     /db_xref="HGNC:20247"
                     /db_xref="HPRD:07889"
                     /db_xref="MIM:611478"
     gene            complement(100032912..100034094)
                     /gene="C7orf47"
                     /gene_synonym="MGC22793"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:221908"
                     /db_xref="HGNC:28320"
                     /db_xref="HPRD:14486"
     mRNA            complement(join(100032912..100033156,100033254..100033390,
                     100033471..100033687,100033764..100034094))
                     /gene="C7orf47"
                     /gene_synonym="MGC22793"
                     /product="chromosome 7 open reading frame 47"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145030.2"
                     /db_xref="GI:142376057"
                     /db_xref="GeneID:221908"
                     /db_xref="HGNC:28320"
                     /db_xref="HPRD:14486"
     CDS             complement(join(100032983..100033156,100033254..100033390,
                     100033471..100033687,100033764..100033997))
                     /gene="C7orf47"
                     /gene_synonym="MGC22793"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC221908"
                     /protein_id="NP_659467.1"
                     /db_xref="GI:21450761"
                     /db_xref="CCDS:CCDS5694.1"
                     /db_xref="GeneID:221908"
                     /db_xref="HGNC:28320"
                     /db_xref="HPRD:14486"
     gene            complement(100054238..100061894)
                     /gene="C7orf61"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:402573"
                     /db_xref="HGNC:22135"
                     /db_xref="HPRD:17558"
     mRNA            complement(join(100054238..100054608,100060986..100061309,
                     100061586..100061894))
                     /gene="C7orf61"
                     /product="chromosome 7 open reading frame 61"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001004323.1"
                     /db_xref="GI:51972225"
                     /db_xref="GeneID:402573"
                     /db_xref="HGNC:22135"
                     /db_xref="HPRD:17558"
     CDS             complement(join(100054375..100054608,100060986..100061309,
                     100061586..100061648))
                     /gene="C7orf61"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC402573"
                     /protein_id="NP_001004323.1"
                     /db_xref="GI:51972226"
                     /db_xref="CCDS:CCDS47661.1"
                     /db_xref="GeneID:402573"
                     /db_xref="HGNC:22135"
                     /db_xref="HPRD:17558"
     gene            complement(100064142..100076902)
                     /gene="TSC22D4"
                     /gene_synonym="THG-1; THG1; TILZ2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:81628"
                     /db_xref="HGNC:21696"
                     /db_xref="HPRD:18231"
                     /db_xref="MIM:611914"
     mRNA            complement(join(100064142..100064791,100065175..100065223,
                     100071897..100072063,100074900..100075930,
                     100076417..100076902))
                     /gene="TSC22D4"
                     /gene_synonym="THG-1; THG1; TILZ2"
                     /product="TSC22 domain family, member 4"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_030935.3"
                     /db_xref="GI:37059797"
                     /db_xref="GeneID:81628"
                     /db_xref="HGNC:21696"
                     /db_xref="HPRD:18231"
                     /db_xref="MIM:611914"
     CDS             complement(join(100064582..100064791,100065175..100065223,
                     100071897..100072063,100074900..100075661))
                     /gene="TSC22D4"
                     /gene_synonym="THG-1; THG1; TILZ2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="TSC22 domain family protein 4"
                     /protein_id="NP_112197.1"
                     /db_xref="GI:13569901"
                     /db_xref="CCDS:CCDS5695.1"
                     /db_xref="GeneID:81628"
                     /db_xref="HGNC:21696"
                     /db_xref="HPRD:18231"
                     /db_xref="MIM:611914"
     gene            100081550..100092422
                     /gene="C7orf51"
                     /gene_synonym="FLJ37538"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222950"
                     /db_xref="HGNC:22009"
                     /db_xref="HPRD:13427"
     mRNA            join(100081550..100081624,100082851..100083002,
                     100084444..100084805,100085775..100087289,
                     100088140..100088352,100088609..100088718,
                     100091269..100092422)
                     /gene="C7orf51"
                     /gene_synonym="FLJ37538"
                     /product="chromosome 7 open reading frame 51"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_173564.2"
                     /db_xref="GI:37537553"
                     /db_xref="GeneID:222950"
                     /db_xref="HGNC:22009"
                     /db_xref="HPRD:13427"
     CDS             join(100082935..100083002,100084444..100084805,
                     100085775..100087289,100088140..100088352,
                     100088609..100088718,100091269..100091526)
                     /gene="C7orf51"
                     /gene_synonym="FLJ37538"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein FLJ37538"
                     /protein_id="NP_775835.2"
                     /db_xref="GI:37537554"
                     /db_xref="CCDS:CCDS5696.1"
                     /db_xref="GeneID:222950"
                     /db_xref="HGNC:22009"
                     /db_xref="HPRD:13427"
     gene            100136834..100165843
                     /gene="AGFG2"
                     /gene_synonym="HRBL; RABR"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3268"
                     /db_xref="HGNC:5177"
                     /db_xref="HPRD:04932"
                     /db_xref="MIM:604019"
     mRNA            join(100136834..100137190,100146445..100146538,
                     100148019..100148134,100150970..100151123,
                     100151716..100151881,100153233..100153358,
                     100159882..100160002,100160217..100160305,
                     100160486..100160569,100161457..100161585,
                     100161841..100161926,100162555..100165843)
                     /gene="AGFG2"
                     /gene_synonym="HRBL; RABR"
                     /product="ArfGAP with FG repeats 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006076.4"
                     /db_xref="GI:91984780"
                     /db_xref="GeneID:3268"
                     /db_xref="HGNC:5177"
                     /db_xref="HPRD:04932"
                     /db_xref="MIM:604019"
     CDS             join(100136970..100137190,100146445..100146538,
                     100148019..100148134,100150970..100151123,
                     100151716..100151881,100153233..100153358,
                     100159882..100160002,100160217..100160305,
                     100160486..100160569,100161457..100161585,
                     100161841..100161926,100162555..100162614)
                     /gene="AGFG2"
                     /gene_synonym="HRBL; RABR"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="arf-GAP domain and FG repeats-containing protein
                     2"
                     /protein_id="NP_006067.3"
                     /db_xref="GI:91984781"
                     /db_xref="CCDS:CCDS5697.1"
                     /db_xref="GeneID:3268"
                     /db_xref="HGNC:5177"
                     /db_xref="HPRD:04932"
                     /db_xref="MIM:604019"
     gene            100162878..100167751
                     /gene="IRS3P"
                     /gene_synonym="IRS3L"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442338"
                     /db_xref="HGNC:6127"
     gene            complement(100169851..100171270)
                     /gene="SAP25"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100316904"
                     /db_xref="HGNC:41908"
     mRNA            complement(join(100169851..100170194,100170277..100170374,
                     100170483..100170636,100170729..100170835,
                     100170920..100171002,100171220..100171270))
                     /gene="SAP25"
                     /product="Sin3A-associated protein, 25kDa"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001168682.1"
                     /db_xref="GI:284004890"
                     /db_xref="GeneID:100316904"
                     /db_xref="HGNC:41908"
     CDS             complement(join(100169910..100170194,100170277..100170374,
                     100170483..100170636,100170729..100170791))
                     /gene="SAP25"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone deacetylase complex subunit SAP25"
                     /protein_id="NP_001162153.1"
                     /db_xref="GI:284004891"
                     /db_xref="CCDS:CCDS55137.1"
                     /db_xref="GeneID:100316904"
                     /db_xref="HGNC:41908"
     gene            complement(100171634..100183776)
                     /gene="LRCH4"
                     /gene_synonym="FLJ40101; FLJ46315; LRN; LRRN1; LRRN4;
                     PP14183"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4034"
                     /db_xref="HGNC:6691"
                     /db_xref="HPRD:10062"
     mRNA            complement(join(100171634..100172927,100173328..100173405,
                     100173494..100173631,100173861..100173946,
                     100174317..100174400,100174525..100174628,
                     100174709..100174777,100174896..100175012,
                     100175120..100175181,100175287..100175363,
                     100175445..100175535,100175782..100175881,
                     100176022..100176134,100176273..100176409,
                     100179400..100179505,100179664..100179790,
                     100179938..100180082,100183504..100183776))
                     /gene="LRCH4"
                     /gene_synonym="FLJ40101; FLJ46315; LRN; LRRN1; LRRN4;
                     PP14183"
                     /product="leucine-rich repeats and calponin homology (CH)
                     domain containing 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002319.3"
                     /db_xref="GI:86813773"
                     /db_xref="GeneID:4034"
                     /db_xref="HGNC:6691"
                     /db_xref="HPRD:10062"
     CDS             complement(join(100172730..100172927,100173328..100173405,
                     100173494..100173631,100173861..100173946,
                     100174317..100174400,100174525..100174628,
                     100174709..100174777,100174896..100175012,
                     100175120..100175181,100175287..100175363,
                     100175445..100175535,100175782..100175881,
                     100176022..100176134,100176273..100176409,
                     100179400..100179505,100179664..100179790,
                     100179938..100180082,100183504..100183723))
                     /gene="LRCH4"
                     /gene_synonym="FLJ40101; FLJ46315; LRN; LRRN1; LRRN4;
                     PP14183"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="leucine-rich repeat and calponin homology
                     domain-containing protein 4"
                     /protein_id="NP_002310.2"
                     /db_xref="GI:30181233"
                     /db_xref="CCDS:CCDS34706.1"
                     /db_xref="GeneID:4034"
                     /db_xref="HGNC:6691"
                     /db_xref="HPRD:10062"
     gene            100183956..100198740
                     /gene="FBXO24"
                     /gene_synonym="DKFZp434I1122; FBX24"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26261"
                     /db_xref="HGNC:13595"
                     /db_xref="HPRD:16438"
                     /db_xref="MIM:609097"
     mRNA            join(100183956..100184287,100187600..100187698,
                     100187797..100187980,100189290..100189525,
                     100190406..100190640,100192006..100192164,
                     100192725..100192846,100193198..100193329,
                     100197654..100197824,100198157..100198740)
                     /gene="FBXO24"
                     /gene_synonym="DKFZp434I1122; FBX24"
                     /product="F-box protein 24, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033506.2"
                     /db_xref="GI:91807115"
                     /db_xref="GeneID:26261"
                     /db_xref="HGNC:13595"
                     /db_xref="HPRD:16438"
                     /db_xref="MIM:609097"
     CDS             join(100184249..100184287,100187600..100187698,
                     100187797..100187980,100189290..100189525,
                     100190406..100190640,100192006..100192164,
                     100192725..100192846,100193198..100193329,
                     100197654..100197824,100198157..100198522)
                     /gene="FBXO24"
                     /gene_synonym="DKFZp434I1122; FBX24"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="F-box only protein 24 isoform 1"
                     /protein_id="NP_277041.1"
                     /db_xref="GI:15812196"
                     /db_xref="CCDS:CCDS5698.1"
                     /db_xref="GeneID:26261"
                     /db_xref="HGNC:13595"
                     /db_xref="HPRD:16438"
                     /db_xref="MIM:609097"
     gene            complement(100187024..100201661)
                     /gene="LOC100129845"
                     /gene_synonym="FLJ40386"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100129845"
     misc_RNA        complement(join(100187024..100187705,100187853..100187954,
                     100190448..100190697,100197294..100197425,
                     100197663..100197812,100198346..100198475,
                     100199243..100199306,100199963..100200789,
                     100201461..100201661))
                     /gene="LOC100129845"
                     /gene_synonym="FLJ40386"
                     /product="hypothetical LOC100129845"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038910.1"
                     /db_xref="GI:336594538"
                     /db_xref="GeneID:100129845"
     mRNA            join(100187196..100187416,100187600..100187698,
                     100187797..100187980,100189290..100189525,
                     100190406..100190640,100192006..100192164,
                     100192725..100192846,100193198..100193329,
                     100197654..100197824,100198157..100198740)
                     /gene="FBXO24"
                     /gene_synonym="DKFZp434I1122; FBX24"
                     /product="F-box protein 24, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012172.4"
                     /db_xref="GI:254553387"
                     /db_xref="GeneID:26261"
                     /db_xref="HGNC:13595"
                     /db_xref="HPRD:16438"
                     /db_xref="MIM:609097"
     mRNA            join(100187196..100187266,100187600..100187698,
                     100187797..100187980,100189290..100189525,
                     100190406..100190640,100192006..100192164,
                     100192725..100192846,100193198..100193329,
                     100197654..100197824,100198157..100198740)
                     /gene="FBXO24"
                     /gene_synonym="DKFZp434I1122; FBX24"
                     /product="F-box protein 24, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001163499.1"
                     /db_xref="GI:254553389"
                     /db_xref="GeneID:26261"
                     /db_xref="HGNC:13595"
                     /db_xref="MIM:609097"
                     /db_xref="HPRD:16438"
     CDS             join(100187264..100187416,100187600..100187698,
                     100187797..100187980,100189290..100189525,
                     100190406..100190640,100192006..100192164,
                     100192725..100192846,100193198..100193329,
                     100197654..100197824,100198157..100198522)
                     /gene="FBXO24"
                     /gene_synonym="DKFZp434I1122; FBX24"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="F-box only protein 24 isoform 3"
                     /protein_id="NP_036304.2"
                     /db_xref="GI:254553388"
                     /db_xref="CCDS:CCDS5699.2"
                     /db_xref="GeneID:26261"
                     /db_xref="HGNC:13595"
                     /db_xref="HPRD:16438"
                     /db_xref="MIM:609097"
     CDS             join(100187264..100187266,100187600..100187698,
                     100187797..100187980,100189290..100189525,
                     100190406..100190640,100192006..100192164,
                     100192725..100192846,100193198..100193329,
                     100197654..100197824,100198157..100198522)
                     /gene="FBXO24"
                     /gene_synonym="DKFZp434I1122; FBX24"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="F-box only protein 24 isoform 4"
                     /protein_id="NP_001156971.1"
                     /db_xref="GI:254553390"
                     /db_xref="CCDS:CCDS55138.1"
                     /db_xref="GeneID:26261"
                     /db_xref="HGNC:13595"
                     /db_xref="HPRD:16438"
                     /db_xref="MIM:609097"
     gene            100199882..100205798
                     /gene="PCOLCE"
                     /gene_synonym="PCPE; PCPE-1; PCPE1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5118"
                     /db_xref="HGNC:8738"
                     /db_xref="HPRD:02603"
                     /db_xref="MIM:600270"
     mRNA            join(100199882..100200174,100201053..100201161,
                     100201582..100201840,100202714..100202838,
                     100203299..100203435,100204039..100204253,
                     100205075..100205146,100205260..100205430,
                     100205560..100205798)
                     /gene="PCOLCE"
                     /gene_synonym="PCPE; PCPE-1; PCPE1"
                     /product="procollagen C-endopeptidase enhancer"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002593.3"
                     /db_xref="GI:157653328"
                     /db_xref="GeneID:5118"
                     /db_xref="HGNC:8738"
                     /db_xref="HPRD:02603"
                     /db_xref="MIM:600270"
     CDS             join(100200080..100200174,100201053..100201161,
                     100201582..100201840,100202714..100202838,
                     100203299..100203435,100204039..100204253,
                     100205075..100205146,100205260..100205430,
                     100205560..100205726)
                     /gene="PCOLCE"
                     /gene_synonym="PCPE; PCPE-1; PCPE1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="procollagen C-endopeptidase enhancer 1"
                     /protein_id="NP_002584.2"
                     /db_xref="GI:157653329"
                     /db_xref="CCDS:CCDS5700.1"
                     /db_xref="GeneID:5118"
                     /db_xref="HGNC:8738"
                     /db_xref="HPRD:02603"
                     /db_xref="MIM:600270"
     gene            100209725..100213000
                     /gene="MOSPD3"
                     /gene_synonym="CDS3; NET30"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64598"
                     /db_xref="HGNC:25078"
                     /db_xref="HPRD:12370"
                     /db_xref="MIM:609125"
     mRNA            join(100209725..100209864,100210353..100210619,
                     100210817..100210892,100211100..100211329,
                     100212490..100212654,100212775..100213000)
                     /gene="MOSPD3"
                     /gene_synonym="CDS3; NET30"
                     /product="motile sperm domain containing 3, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040097.1"
                     /db_xref="GI:93141011"
                     /db_xref="GeneID:64598"
                     /db_xref="HGNC:25078"
                     /db_xref="MIM:609125"
                     /db_xref="HPRD:12370"
     mRNA            join(100210053..100210108,100210353..100210619,
                     100210817..100210892,100211100..100211329,
                     100212490..100212654,100212775..100213000)
                     /gene="MOSPD3"
                     /gene_synonym="CDS3; NET30"
                     /product="motile sperm domain containing 3, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040098.1"
                     /db_xref="GI:93141013"
                     /db_xref="GeneID:64598"
                     /db_xref="HGNC:25078"
                     /db_xref="MIM:609125"
                     /db_xref="HPRD:12370"
     mRNA            join(100210114..100210619,100210817..100210892,
                     100211100..100211329,100212490..100212654,
                     100212775..100213000)
                     /gene="MOSPD3"
                     /gene_synonym="CDS3; NET30"
                     /product="motile sperm domain containing 3, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_023948.4"
                     /db_xref="GI:93141009"
                     /db_xref="GeneID:64598"
                     /db_xref="HGNC:25078"
                     /db_xref="HPRD:12370"
                     /db_xref="MIM:609125"
     mRNA            join(100210114..100210619,100210817..100210892,
                     100211130..100211329,100212490..100212654,
                     100212775..100213000)
                     /gene="MOSPD3"
                     /gene_synonym="CDS3; NET30"
                     /product="motile sperm domain containing 3, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040099.1"
                     /db_xref="GI:93141015"
                     /db_xref="GeneID:64598"
                     /db_xref="HGNC:25078"
                     /db_xref="MIM:609125"
                     /db_xref="HPRD:12370"
     CDS             join(100210415..100210619,100210817..100210892,
                     100211100..100211329,100212490..100212654,
                     100212775..100212806)
                     /gene="MOSPD3"
                     /gene_synonym="CDS3; NET30"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="motile sperm domain-containing protein 3 isoform
                     a"
                     /protein_id="NP_076438.1"
                     /db_xref="GI:13122608"
                     /db_xref="CCDS:CCDS5701.1"
                     /db_xref="GeneID:64598"
                     /db_xref="HGNC:25078"
                     /db_xref="HPRD:12370"
                     /db_xref="MIM:609125"
     CDS             join(100210415..100210619,100210817..100210892,
                     100211100..100211329,100212490..100212654,
                     100212775..100212806)
                     /gene="MOSPD3"
                     /gene_synonym="CDS3; NET30"
                     /note="isoform a is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="motile sperm domain-containing protein 3 isoform
                     a"
                     /protein_id="NP_001035186.1"
                     /db_xref="GI:93141012"
                     /db_xref="CCDS:CCDS5701.1"
                     /db_xref="GeneID:64598"
                     /db_xref="HGNC:25078"
                     /db_xref="HPRD:12370"
                     /db_xref="MIM:609125"
     CDS             join(100210415..100210619,100210817..100210892,
                     100211100..100211329,100212490..100212654,
                     100212775..100212806)
                     /gene="MOSPD3"
                     /gene_synonym="CDS3; NET30"
                     /note="isoform a is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="motile sperm domain-containing protein 3 isoform
                     a"
                     /protein_id="NP_001035187.1"
                     /db_xref="GI:93141014"
                     /db_xref="CCDS:CCDS5701.1"
                     /db_xref="GeneID:64598"
                     /db_xref="HGNC:25078"
                     /db_xref="HPRD:12370"
                     /db_xref="MIM:609125"
     CDS             join(100210415..100210619,100210817..100210892,
                     100211130..100211329,100212490..100212654,
                     100212775..100212806)
                     /gene="MOSPD3"
                     /gene_synonym="CDS3; NET30"
                     /note="isoform b is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="motile sperm domain-containing protein 3 isoform
                     b"
                     /protein_id="NP_001035188.1"
                     /db_xref="GI:93141016"
                     /db_xref="CCDS:CCDS47662.1"
                     /db_xref="GeneID:64598"
                     /db_xref="HGNC:25078"
                     /db_xref="HPRD:12370"
                     /db_xref="MIM:609125"
     gene            complement(100218039..100239173)
                     /gene="TFR2"
                     /gene_synonym="HFE3; MGC126368; TFRC2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7036"
                     /db_xref="HGNC:11762"
                     /db_xref="HPRD:05282"
                     /db_xref="MIM:604720"
     mRNA            complement(join(100218039..100218749,100224386..100224526,
                     100224887..100225114,100225200..100225284,
                     100225367..100225443,100225530..100225597,
                     100225696..100225759,100225847..100225929,
                     100226876..100226995,100228512..100228675,
                     100229429..100229568,100229705..100229821,
                     100230624..100230746,100230852..100230963,
                     100231039..100231179,100238309..100238495,
                     100238599..100238851,100239100..100239173))
                     /gene="TFR2"
                     /gene_synonym="HFE3; MGC126368; TFRC2"
                     /product="transferrin receptor 2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003227.3"
                     /db_xref="GI:110227854"
                     /db_xref="GeneID:7036"
                     /db_xref="HGNC:11762"
                     /db_xref="HPRD:05282"
                     /db_xref="MIM:604720"
     mRNA            complement(join(100218039..100218749,100224386..100224526,
                     100224887..100225114,100225200..100225284,
                     100225367..100225443,100225530..100225597,
                     100225696..100225759,100225847..100225929,
                     100226876..100226995,100228512..100228675,
                     100229429..100229568,100229705..100229821,
                     100230624..100230746,100230852..100230963,
                     100231039..100231273))
                     /gene="TFR2"
                     /gene_synonym="HFE3; MGC126368; TFRC2"
                     /product="transferrin receptor 2, transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001206855.1"
                     /db_xref="GI:332309170"
                     /db_xref="GeneID:7036"
                     /db_xref="HGNC:11762"
                     /db_xref="MIM:604720"
                     /db_xref="HPRD:05282"
     CDS             complement(join(100218480..100218749,100224386..100224526,
                     100224887..100225114,100225200..100225284,
                     100225367..100225443,100225530..100225597,
                     100225696..100225759,100225847..100225929,
                     100226876..100226995,100228512..100228675,
                     100229429..100229568,100229705..100229821,
                     100230624..100230746,100230852..100230963,
                     100231039..100231179,100238309..100238495,
                     100238599..100238851,100239100..100239132))
                     /gene="TFR2"
                     /gene_synonym="HFE3; MGC126368; TFRC2"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transferrin receptor protein 2 isoform 1"
                     /protein_id="NP_003218.2"
                     /db_xref="GI:33589848"
                     /db_xref="CCDS:CCDS34707.1"
                     /db_xref="GeneID:7036"
                     /db_xref="HGNC:11762"
                     /db_xref="HPRD:05282"
                     /db_xref="MIM:604720"
     CDS             complement(join(100218480..100218749,100224386..100224526,
                     100224887..100225114,100225200..100225284,
                     100225367..100225443,100225530..100225597,
                     100225696..100225759,100225847..100225929,
                     100226876..100226995,100228512..100228675,
                     100229429..100229568,100229705..100229821,
                     100230624..100230746,100230852..100230963,
                     100231039..100231139))
                     /gene="TFR2"
                     /gene_synonym="HFE3; MGC126368; TFRC2"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transferrin receptor protein 2 isoform 2"
                     /protein_id="NP_001193784.1"
                     /db_xref="GI:332309171"
                     /db_xref="GeneID:7036"
                     /db_xref="HGNC:11762"
                     /db_xref="MIM:604720"
                     /db_xref="HPRD:05282"
     gene            complement(100240720..100254084)
                     /gene="ACTL6B"
                     /gene_synonym="ACTL6; BAF53B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51412"
                     /db_xref="HGNC:160"
                     /db_xref="HPRD:12419"
                     /db_xref="MIM:612458"
     mRNA            complement(join(100240720..100240949,100243872..100243958,
                     100244174..100244269,100244374..100244454,
                     100244594..100244708,100244846..100244907,
                     100245067..100245156,100246179..100246285,
                     100246352..100246446,100247661..100247758,
                     100252642..100252742,100253044..100253209,
                     100253426..100253502,100253953..100254084))
                     /gene="ACTL6B"
                     /gene_synonym="ACTL6; BAF53B"
                     /product="actin-like 6B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016188.4"
                     /db_xref="GI:198386318"
                     /db_xref="GeneID:51412"
                     /db_xref="HGNC:160"
                     /db_xref="HPRD:12419"
                     /db_xref="MIM:612458"
     CDS             complement(join(100240869..100240949,100243872..100243958,
                     100244174..100244269,100244374..100244454,
                     100244594..100244708,100244846..100244907,
                     100245067..100245156,100246179..100246285,
                     100246352..100246446,100247661..100247758,
                     100252642..100252742,100253044..100253209,
                     100253426..100253502,100253953..100253977))
                     /gene="ACTL6B"
                     /gene_synonym="ACTL6; BAF53B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="actin-like protein 6B"
                     /protein_id="NP_057272.1"
                     /db_xref="GI:7705294"
                     /db_xref="CCDS:CCDS5702.1"
                     /db_xref="GeneID:51412"
                     /db_xref="HGNC:160"
                     /db_xref="HPRD:12419"
                     /db_xref="MIM:612458"
     gene            100271363..100276792
                     /gene="GNB2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2783"
                     /db_xref="HGNC:4398"
                     /db_xref="HPRD:11820"
                     /db_xref="MIM:139390"
     mRNA            join(100271363..100271546,100273800..100273945,
                     100274158..100274196,100274316..100274422,
                     100274975..100275038,100275121..100275283,
                     100275375..100275441,100275721..100275922,
                     100276021..100276237,100276318..100276792)
                     /gene="GNB2"
                     /product="guanine nucleotide binding protein (G protein),
                     beta polypeptide 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005273.3"
                     /db_xref="GI:197245333"
                     /db_xref="GeneID:2783"
                     /db_xref="HGNC:4398"
                     /db_xref="HPRD:11820"
                     /db_xref="MIM:139390"
     CDS             join(100273889..100273945,100274158..100274196,
                     100274316..100274422,100274975..100275038,
                     100275121..100275283,100275375..100275441,
                     100275721..100275922,100276021..100276237,
                     100276318..100276424)
                     /gene="GNB2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="guanine nucleotide-binding protein
                     G(I)/G(S)/G(T) subunit beta-2"
                     /protein_id="NP_005264.2"
                     /db_xref="GI:20357529"
                     /db_xref="CCDS:CCDS5703.1"
                     /db_xref="GeneID:2783"
                     /db_xref="HGNC:4398"
                     /db_xref="HPRD:11820"
                     /db_xref="MIM:139390"
     gene            complement(100277130..100286870)
                     /gene="GIGYF1"
                     /gene_synonym="GYF1; PERQ1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64599"
                     /db_xref="HGNC:9126"
                     /db_xref="HPRD:10145"
                     /db_xref="MIM:612064"
     mRNA            complement(join(100277130..100279394,100279487..100279616,
                     100279695..100279858,100279945..100280105,
                     100280213..100280400,100280635..100280853,
                     100280927..100281067,100281173..100281255,
                     100281441..100281541,100281643..100281780,
                     100281860..100281960,100282073..100282239,
                     100282346..100282517,100282672..100282769,
                     100282967..100283104,100283597..100283702,
                     100283803..100284056,100284272..100284442,
                     100284629..100284669,100284921..100285029,
                     100285128..100285239,100285411..100285506,
                     100285604..100285733,100285827..100286870))
                     /gene="GIGYF1"
                     /gene_synonym="GYF1; PERQ1"
                     /product="GRB10 interacting GYF protein 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022574.4"
                     /db_xref="GI:197245455"
                     /db_xref="GeneID:64599"
                     /db_xref="HGNC:9126"
                     /db_xref="HPRD:10145"
                     /db_xref="MIM:612064"
     CDS             complement(join(100279342..100279394,100279487..100279616,
                     100279695..100279858,100279945..100280105,
                     100280213..100280400,100280635..100280853,
                     100280927..100281067,100281173..100281255,
                     100281441..100281541,100281643..100281780,
                     100281860..100281960,100282073..100282239,
                     100282346..100282517,100282672..100282769,
                     100282967..100283104,100283597..100283702,
                     100283803..100284056,100284272..100284442,
                     100284629..100284669,100284921..100285029,
                     100285128..100285239,100285411..100285506,
                     100285604..100285733,100285827..100285861))
                     /gene="GIGYF1"
                     /gene_synonym="GYF1; PERQ1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="PERQ amino acid-rich with GYF domain-containing
                     protein 1"
                     /protein_id="NP_072096.2"
                     /db_xref="GI:92087055"
                     /db_xref="CCDS:CCDS34708.1"
                     /db_xref="GeneID:64599"
                     /db_xref="HGNC:9126"
                     /db_xref="HPRD:10145"
                     /db_xref="MIM:612064"
     gene            100303676..100305123
                     /gene="POP7"
                     /gene_synonym="0610037N12Rik; RPP2; RPP20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10248"
                     /db_xref="HGNC:19949"
                     /db_xref="HPRD:09357"
                     /db_xref="MIM:606113"
     mRNA            join(100303676..100303927,100304444..100305123)
                     /gene="POP7"
                     /gene_synonym="0610037N12Rik; RPP2; RPP20"
                     /product="processing of precursor 7, ribonuclease P/MRP
                     subunit (S. cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005837.2"
                     /db_xref="GI:153791430"
                     /db_xref="GeneID:10248"
                     /db_xref="HGNC:19949"
                     /db_xref="HPRD:09357"
                     /db_xref="MIM:606113"
     CDS             100304454..100304876
                     /gene="POP7"
                     /gene_synonym="0610037N12Rik; RPP2; RPP20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ribonuclease P protein subunit p20"
                     /protein_id="NP_005828.2"
                     /db_xref="GI:153791431"
                     /db_xref="CCDS:CCDS5704.1"
                     /db_xref="GeneID:10248"
                     /db_xref="HGNC:19949"
                     /db_xref="HPRD:09357"
                     /db_xref="MIM:606113"
     gene            100318423..100321323
                     /gene="EPO"
                     /gene_synonym="EP; MGC138142; MVCD2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2056"
                     /db_xref="HGNC:3415"
                     /db_xref="HPRD:00586"
                     /db_xref="MIM:133170"
     mRNA            join(100318423..100318616,100319181..100319326,
                     100319585..100319671,100320287..100320466,
                     100320601..100321323)
                     /gene="EPO"
                     /gene_synonym="EP; MGC138142; MVCD2"
                     /product="erythropoietin"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000799.2"
                     /db_xref="GI:62240996"
                     /db_xref="GeneID:2056"
                     /db_xref="HGNC:3415"
                     /db_xref="HPRD:00586"
                     /db_xref="MIM:133170"
     CDS             join(100318604..100318616,100319181..100319326,
                     100319585..100319671,100320287..100320466,
                     100320601..100320756)
                     /gene="EPO"
                     /gene_synonym="EP; MGC138142; MVCD2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="erythropoietin precursor"
                     /protein_id="NP_000790.2"
                     /db_xref="GI:62240997"
                     /db_xref="CCDS:CCDS5705.1"
                     /db_xref="GeneID:2056"
                     /db_xref="HGNC:3415"
                     /db_xref="HPRD:00586"
                     /db_xref="MIM:133170"
     gene            100331249..100395419
                     /gene="ZAN"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7455"
                     /db_xref="HGNC:12857"
                     /db_xref="HPRD:03846"
                     /db_xref="MIM:602372"
     mRNA            join(100331249..100331271,100331650..100331844,
                     100333343..100333395,100334106..100334252,
                     100334432..100334703,100334885..100334972,
                     100336084..100336236,100344161..100344325,
                     100345173..100345264,100345760..100345838,
                     100345947..100346093,100348248..100348519,
                     100348805..100348889,100349335..100350852,
                     100352849..100353033,100355825..100355966,
                     100356154..100356273,100357344..100357468,
                     100358014..100358159,100359838..100359981,
                     100361429..100361539,100361650..100361819,
                     100362975..100363177,100364148..100364289,
                     100364633..100364880,100365454..100365634,
                     100366233..100366344,100367503..100367597,
                     100369467..100369643,100370908..100371116,
                     100371344..100371487,100372950..100373197,
                     100373291..100373455,100374062..100374186,
                     100377068..100377372,100382245..100382456,
                     100383619..100383763,100385511..100385758,
                     100386840..100386969,100388564..100388735,
                     100389588..100389770,100390027..100390101,
                     100391442..100391640,100391742..100391880,
                     100392818..100392958,100394988..100395087,
                     100395199..100395245,100395329..100395419)
                     /gene="ZAN"
                     /product="zonadhesin, transcript variant 3"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003386.1"
                     /db_xref="GI:16554448"
                     /db_xref="GeneID:7455"
                     /db_xref="HGNC:12857"
                     /db_xref="HPRD:03846"
                     /db_xref="MIM:602372"
     mRNA            join(100331249..100331271,100331650..100331844,
                     100333343..100333395,100334106..100334252,
                     100334432..100334703,100334885..100334972,
                     100336084..100336236,100344161..100344325,
                     100345173..100345264,100345760..100345838,
                     100345947..100346093,100348248..100348519,
                     100348805..100348889,100349335..100350852,
                     100352849..100353033,100355825..100355966,
                     100356154..100356273,100357344..100357468,
                     100358014..100358159,100359838..100359981,
                     100361429..100361539,100361650..100361819,
                     100362975..100363177,100364148..100364289,
                     100364633..100364880,100365454..100365634,
                     100366233..100366344,100367503..100367597,
                     100369467..100369643,100370908..100371116,
                     100371344..100371487,100372950..100373197,
                     100373291..100373455,100374062..100374186,
                     100377068..100377372,100382245..100382456,
                     100383619..100383763,100385511..100385758,
                     100386840..100386969,100388564..100388735,
                     100389588..100389770,100390027..100390166,
                     100392818..100392958,100394988..100395087,
                     100395199..100395245,100395329..100395419)
                     /gene="ZAN"
                     /product="zonadhesin, transcript variant 6"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_173059.1"
                     /db_xref="GI:27881493"
                     /db_xref="GeneID:7455"
                     /db_xref="HGNC:12857"
                     /db_xref="HPRD:03846"
                     /db_xref="MIM:602372"
     CDS             join(100331792..100331844,100333343..100333395,
                     100334106..100334252,100334432..100334703,
                     100334885..100334972,100336084..100336236,
                     100344161..100344325,100345173..100345264,
                     100345760..100345838,100345947..100346093,
                     100348248..100348519,100348805..100348889,
                     100349335..100350852,100352849..100353033,
                     100355825..100355966,100356154..100356273,
                     100357344..100357468,100358014..100358159,
                     100359838..100359981,100361429..100361539,
                     100361650..100361819,100362975..100363177,
                     100364148..100364289,100364633..100364880,
                     100365454..100365634,100366233..100366344,
                     100367503..100367597,100369467..100369643,
                     100370908..100371116,100371344..100371487,
                     100372950..100373197,100373291..100373455,
                     100374062..100374186,100377068..100377372,
                     100382245..100382456,100383619..100383763,
                     100385511..100385758,100386840..100386969,
                     100388564..100388735,100389588..100389770,
                     100390027..100390101,100391442..100391640,
                     100391742..100391880,100392818..100392958,
                     100394988..100395087,100395199..100395245,
                     100395329..100395354)
                     /gene="ZAN"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zonadhesin isoform 3"
                     /protein_id="NP_003377.1"
                     /db_xref="GI:16554449"
                     /db_xref="GeneID:7455"
                     /db_xref="HGNC:12857"
                     /db_xref="HPRD:03846"
                     /db_xref="MIM:602372"
     CDS             join(100331792..100331844,100333343..100333395,
                     100334106..100334252,100334432..100334703,
                     100334885..100334972,100336084..100336236,
                     100344161..100344325,100345173..100345264,
                     100345760..100345838,100345947..100346093,
                     100348248..100348519,100348805..100348889,
                     100349335..100350852,100352849..100353033,
                     100355825..100355966,100356154..100356273,
                     100357344..100357468,100358014..100358159,
                     100359838..100359981,100361429..100361539,
                     100361650..100361819,100362975..100363177,
                     100364148..100364289,100364633..100364880,
                     100365454..100365634,100366233..100366344,
                     100367503..100367597,100369467..100369643,
                     100370908..100371116,100371344..100371487,
                     100372950..100373197,100373291..100373455,
                     100374062..100374186,100377068..100377372,
                     100382245..100382456,100383619..100383763,
                     100385511..100385758,100386840..100386969,
                     100388564..100388735,100389588..100389770,
                     100390027..100390166,100392818..100392958,
                     100394988..100395087,100395199..100395245,
                     100395329..100395354)
                     /gene="ZAN"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 6 is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zonadhesin isoform 6"
                     /protein_id="NP_775082.1"
                     /db_xref="GI:27881494"
                     /db_xref="GeneID:7455"
                     /db_xref="HGNC:12857"
                     /db_xref="HPRD:03846"
                     /db_xref="MIM:602372"
     gene            complement(100400187..100425143)
                     /gene="EPHB4"
                     /gene_synonym="HTK; MYK1; TYRO11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2050"
                     /db_xref="HGNC:3395"
                     /db_xref="HPRD:02481"
                     /db_xref="MIM:600011"
     mRNA            complement(join(100400187..100401212,100402788..100402943,
                     100403123..100403316,100404042..100404191,
                     100404987..100405202,100410369..100410616,
                     100410717..100410830,100411274..100411338,
                     100411541..100411643,100414814..100414979,
                     100416142..100416266,100417179..100417511,
                     100417763..100417918,100419893..100420289,
                     100421266..100421553,100421825..100421895,
                     100424601..100425143))
                     /gene="EPHB4"
                     /gene_synonym="HTK; MYK1; TYRO11"
                     /product="EPH receptor B4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004444.4"
                     /db_xref="GI:55774978"
                     /db_xref="GeneID:2050"
                     /db_xref="HGNC:3395"
                     /db_xref="HPRD:02481"
                     /db_xref="MIM:600011"
     CDS             complement(join(100401083..100401212,100402788..100402943,
                     100403123..100403316,100404042..100404191,
                     100404987..100405202,100410369..100410616,
                     100410717..100410830,100411274..100411338,
                     100411541..100411643,100414814..100414979,
                     100416142..100416266,100417179..100417511,
                     100417763..100417918,100419893..100420289,
                     100421266..100421553,100421825..100421895,
                     100424601..100424652))
                     /gene="EPHB4"
                     /gene_synonym="HTK; MYK1; TYRO11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ephrin type-B receptor 4 precursor"
                     /protein_id="NP_004435.3"
                     /db_xref="GI:32528301"
                     /db_xref="CCDS:CCDS5706.1"
                     /db_xref="GeneID:2050"
                     /db_xref="HGNC:3395"
                     /db_xref="HPRD:02481"
                     /db_xref="MIM:600011"
     gene            100450358..100464634
                     /gene="SLC12A9"
                     /gene_synonym="CIP1; FLJ46905"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:56996"
                     /db_xref="HGNC:17435"
                     /db_xref="HPRD:11564"
     mRNA            join(100450358..100450457,100451778..100452000,
                     100452242..100452376,100453328..100453459,
                     100454490..100454798,100456457..100456564,
                     100456672..100456783,100457507..100457664,
                     100457772..100457854,100458760..100458884,
                     100459014..100459206,100459359..100459533,
                     100460303..100460449,100463341..100464634)
                     /gene="SLC12A9"
                     /gene_synonym="CIP1; FLJ46905"
                     /product="solute carrier family 12 (potassium/chloride
                     transporters), member 9"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020246.2"
                     /db_xref="GI:31881739"
                     /db_xref="GeneID:56996"
                     /db_xref="HGNC:17435"
                     /db_xref="HPRD:11564"
     CDS             join(100451820..100452000,100452242..100452376,
                     100453328..100453459,100454490..100454798,
                     100456457..100456564,100456672..100456783,
                     100457507..100457664,100457772..100457854,
                     100458760..100458884,100459014..100459206,
                     100459359..100459533,100460303..100460449,
                     100463341..100464227)
                     /gene="SLC12A9"
                     /gene_synonym="CIP1; FLJ46905"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="solute carrier family 12 member 9"
                     /protein_id="NP_064631.2"
                     /db_xref="GI:31881740"
                     /db_xref="CCDS:CCDS5707.1"
                     /db_xref="GeneID:56996"
                     /db_xref="HGNC:17435"
                     /db_xref="HPRD:11564"
     gene            100464950..100471076
                     /gene="TRIP6"
                     /gene_synonym="MGC10556; MGC10558; MGC29959; MGC3837;
                     MGC4423; OIP-1; OIP1; TRIP-6; TRIP6i2; ZRP-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7205"
                     /db_xref="HGNC:12311"
                     /db_xref="HPRD:04242"
                     /db_xref="MIM:602933"
     mRNA            join(100464950..100465228,100465483..100465610,
                     100465730..100465855,100466117..100466488,
                     100467992..100468085,100468196..100468365,
                     100469165..100469343,100470246..100470366,
                     100470794..100471076)
                     /gene="TRIP6"
                     /gene_synonym="MGC10556; MGC10558; MGC29959; MGC3837;
                     MGC4423; OIP-1; OIP1; TRIP-6; TRIP6i2; ZRP-1"
                     /product="thyroid hormone receptor interactor 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003302.2"
                     /db_xref="GI:91208422"
                     /db_xref="GeneID:7205"
                     /db_xref="HGNC:12311"
                     /db_xref="HPRD:04242"
                     /db_xref="MIM:602933"
     CDS             join(100465120..100465228,100465483..100465610,
                     100465730..100465855,100466117..100466488,
                     100467992..100468085,100468196..100468365,
                     100469165..100469343,100470246..100470366,
                     100470794..100470925)
                     /gene="TRIP6"
                     /gene_synonym="MGC10556; MGC10558; MGC29959; MGC3837;
                     MGC4423; OIP-1; OIP1; TRIP-6; TRIP6i2; ZRP-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="thyroid receptor-interacting protein 6"
                     /protein_id="NP_003293.2"
                     /db_xref="GI:91208423"
                     /db_xref="CCDS:CCDS5708.1"
                     /db_xref="GeneID:7205"
                     /db_xref="HGNC:12311"
                     /db_xref="HPRD:04242"
                     /db_xref="MIM:602933"
     gene            100472701..100486285
                     /gene="SRRT"
                     /gene_synonym="ARS2; ASR2; MGC126427; serrate"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51593"
                     /db_xref="HGNC:24101"
                     /db_xref="HPRD:10665"
     mRNA            join(100472701..100472949,100473194..100473333,
                     100478906..100479034,100479280..100479426,
                     100479674..100479862,100481691..100481860,
                     100481989..100482173,100482361..100482459,
                     100482544..100482661,100482834..100482991,
                     100483322..100483383,100483484..100483562,
                     100483868..100484056,100484416..100484589,
                     100484668..100484821,100484941..100485134,
                     100485324..100485480,100485663..100485764,
                     100485878..100486004,100486095..100486285)
                     /gene="SRRT"
                     /gene_synonym="ARS2; ASR2; MGC126427; serrate"
                     /product="serrate RNA effector molecule homolog
                     (Arabidopsis), transcript variant 1"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015908.5"
                     /db_xref="GI:192807330"
                     /db_xref="GeneID:51593"
                     /db_xref="HGNC:24101"
                     /db_xref="HPRD:10665"
     mRNA            join(100472701..100472949,100473194..100473333,
                     100478906..100479034,100479280..100479426,
                     100479674..100479862,100481691..100481860,
                     100481989..100482173,100482361..100482459,
                     100482544..100482661,100482837..100482991,
                     100483322..100483383,100483484..100483562,
                     100483868..100484056,100484416..100484589,
                     100484668..100484821,100484941..100485134,
                     100485324..100485480,100485663..100485764,
                     100485878..100486004,100486095..100486285)
                     /gene="SRRT"
                     /gene_synonym="ARS2; ASR2; MGC126427; serrate"
                     /product="serrate RNA effector molecule homolog
                     (Arabidopsis), transcript variant 3"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001128852.1"
                     /db_xref="GI:192807331"
                     /db_xref="GeneID:51593"
                     /db_xref="HGNC:24101"
                     /db_xref="HPRD:10665"
     mRNA            join(100472701..100472949,100473194..100473333,
                     100478906..100479034,100479280..100479426,
                     100479674..100479862,100481691..100481860,
                     100481989..100482173,100482361..100482459,
                     100482544..100482661,100482834..100482991,
                     100483322..100483383,100483484..100483562,
                     100483868..100484056,100484416..100484589,
                     100484668..100484821,100484941..100485134,
                     100485324..100485480,100485675..100485764,
                     100485878..100486004,100486095..100486285)
                     /gene="SRRT"
                     /gene_synonym="ARS2; ASR2; MGC126427; serrate"
                     /product="serrate RNA effector molecule homolog
                     (Arabidopsis), transcript variant 4"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001128853.1"
                     /db_xref="GI:192807333"
                     /db_xref="GeneID:51593"
                     /db_xref="HGNC:24101"
                     /db_xref="HPRD:10665"
     mRNA            join(100472701..100472949,100473194..100473333,
                     100478906..100479034,100479280..100479426,
                     100479674..100479862,100481691..100481860,
                     100481989..100482173,100482361..100482459,
                     100482544..100482661,100482837..100482991,
                     100483322..100483383,100483484..100483562,
                     100483868..100484056,100484416..100484589,
                     100484668..100484821,100484941..100485134,
                     100485324..100485480,100485675..100485764,
                     100485878..100486004,100486095..100486285)
                     /gene="SRRT"
                     /gene_synonym="ARS2; ASR2; MGC126427; serrate"
                     /product="serrate RNA effector molecule homolog
                     (Arabidopsis), transcript variant 5"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001128854.1"
                     /db_xref="GI:192807335"
                     /db_xref="GeneID:51593"
                     /db_xref="HGNC:24101"
                     /db_xref="HPRD:10665"
     CDS             join(100473212..100473333,100478906..100479034,
                     100479280..100479426,100479674..100479862,
                     100481691..100481860,100481989..100482173,
                     100482361..100482459,100482544..100482661,
                     100482834..100482991,100483322..100483383,
                     100483484..100483562,100483868..100484056,
                     100484416..100484589,100484668..100484821,
                     100484941..100485134,100485324..100485480,
                     100485663..100485764,100485878..100486004,
                     100486095..100486170)
                     /gene="SRRT"
                     /gene_synonym="ARS2; ASR2; MGC126427; serrate"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="serrate RNA effector molecule homolog isoform a"
                     /protein_id="NP_056992.4"
                     /db_xref="GI:58331218"
                     /db_xref="CCDS:CCDS34709.1"
                     /db_xref="GeneID:51593"
                     /db_xref="HGNC:24101"
                     /db_xref="HPRD:10665"
     CDS             join(100473212..100473333,100478906..100479034,
                     100479280..100479426,100479674..100479862,
                     100481691..100481860,100481989..100482173,
                     100482361..100482459,100482544..100482661,
                     100482837..100482991,100483322..100483383,
                     100483484..100483562,100483868..100484056,
                     100484416..100484589,100484668..100484821,
                     100484941..100485134,100485324..100485480,
                     100485663..100485764,100485878..100486004,
                     100486095..100486170)
                     /gene="SRRT"
                     /gene_synonym="ARS2; ASR2; MGC126427; serrate"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="serrate RNA effector molecule homolog isoform c"
                     /protein_id="NP_001122324.1"
                     /db_xref="GI:192807332"
                     /db_xref="CCDS:CCDS47666.1"
                     /db_xref="GeneID:51593"
                     /db_xref="HGNC:24101"
                     /db_xref="HPRD:10665"
     CDS             join(100473212..100473333,100478906..100479034,
                     100479280..100479426,100479674..100479862,
                     100481691..100481860,100481989..100482173,
                     100482361..100482459,100482544..100482661,
                     100482834..100482991,100483322..100483383,
                     100483484..100483562,100483868..100484056,
                     100484416..100484589,100484668..100484821,
                     100484941..100485134,100485324..100485480,
                     100485675..100485764,100485878..100486004,
                     100486095..100486170)
                     /gene="SRRT"
                     /gene_synonym="ARS2; ASR2; MGC126427; serrate"
                     /note="isoform d is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="serrate RNA effector molecule homolog isoform d"
                     /protein_id="NP_001122325.1"
                     /db_xref="GI:192807334"
                     /db_xref="CCDS:CCDS47665.1"
                     /db_xref="GeneID:51593"
                     /db_xref="HGNC:24101"
                     /db_xref="HPRD:10665"
     CDS             join(100473212..100473333,100478906..100479034,
                     100479280..100479426,100479674..100479862,
                     100481691..100481860,100481989..100482173,
                     100482361..100482459,100482544..100482661,
                     100482837..100482991,100483322..100483383,
                     100483484..100483562,100483868..100484056,
                     100484416..100484589,100484668..100484821,
                     100484941..100485134,100485324..100485480,
                     100485675..100485764,100485878..100486004,
                     100486095..100486170)
                     /gene="SRRT"
                     /gene_synonym="ARS2; ASR2; MGC126427; serrate"
                     /note="isoform e is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="serrate RNA effector molecule homolog isoform e"
                     /protein_id="NP_001122326.1"
                     /db_xref="GI:192807336"
                     /db_xref="CCDS:CCDS47667.1"
                     /db_xref="GeneID:51593"
                     /db_xref="HGNC:24101"
                     /db_xref="HPRD:10665"
     gene            complement(100486344..100487339)
                     /gene="UFSP1"
                     /gene_synonym="UFSP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:402682"
                     /db_xref="HGNC:33821"
                     /db_xref="HPRD:18630"
                     /db_xref="MIM:611481"
     mRNA            complement(100486344..100487339)
                     /gene="UFSP1"
                     /gene_synonym="UFSP"
                     /product="UFM1-specific peptidase 1 (non-functional)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001015072.3"
                     /db_xref="GI:146231965"
                     /db_xref="GeneID:402682"
                     /db_xref="HGNC:33821"
                     /db_xref="HPRD:18630"
                     /db_xref="MIM:611481"
     CDS             complement(100486464..100486892)
                     /gene="UFSP1"
                     /gene_synonym="UFSP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="inactive Ufm1-specific protease 1"
                     /protein_id="NP_001015072.2"
                     /db_xref="GI:146231966"
                     /db_xref="CCDS:CCDS34710.1"
                     /db_xref="GeneID:402682"
                     /db_xref="HGNC:33821"
                     /db_xref="HPRD:18630"
                     /db_xref="MIM:611481"
     gene            complement(100487615..100493541)
                     /gene="ACHE"
                     /gene_synonym="ARACHE; N-ACHE; YT"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:43"
                     /db_xref="HGNC:108"
                     /db_xref="HPRD:00010"
                     /db_xref="MIM:100740"
     mRNA            complement(join(100487615..100488709,100488790..100488959,
                     100489955..100490439,100490786..100491873,
                     100493423..100493541))
                     /gene="ACHE"
                     /gene_synonym="ARACHE; N-ACHE; YT"
                     /product="acetylcholinesterase, transcript variant E4-E5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015831.2"
                     /db_xref="GI:88999566"
                     /db_xref="GeneID:43"
                     /db_xref="HGNC:108"
                     /db_xref="HPRD:00010"
                     /db_xref="MIM:100740"
     mRNA            complement(join(100487615..100487956,100488790..100488959,
                     100489955..100490439,100490786..100491873,
                     100493423..100493541))
                     /gene="ACHE"
                     /gene_synonym="ARACHE; N-ACHE; YT"
                     /product="acetylcholinesterase, transcript variant E4-E6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000665.3"
                     /db_xref="GI:88999567"
                     /db_xref="GeneID:43"
                     /db_xref="HGNC:108"
                     /db_xref="HPRD:00010"
                     /db_xref="MIM:100740"
     CDS             complement(join(100487835..100487956,100488790..100488959,
                     100489955..100490439,100490786..100491853))
                     /gene="ACHE"
                     /gene_synonym="ARACHE; N-ACHE; YT"
                     /note="isoform E4-E6 precursor is encoded by transcript
                     variant E4-E6; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="acetylcholinesterase isoform E4-E6 precursor"
                     /protein_id="NP_000656.1"
                     /db_xref="GI:4557239"
                     /db_xref="CCDS:CCDS5709.1"
                     /db_xref="GeneID:43"
                     /db_xref="HGNC:108"
                     /db_xref="HPRD:00010"
                     /db_xref="MIM:100740"
     CDS             complement(join(100488579..100488709,100488790..100488959,
                     100489955..100490439,100490786..100491853))
                     /gene="ACHE"
                     /gene_synonym="ARACHE; N-ACHE; YT"
                     /note="isoform E4-E5 precursor is encoded by transcript
                     variant E4-E5; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="acetylcholinesterase isoform E4-E5 precursor"
                     /protein_id="NP_056646.1"
                     /db_xref="GI:7710112"
                     /db_xref="CCDS:CCDS5710.1"
                     /db_xref="GeneID:43"
                     /db_xref="HGNC:108"
                     /db_xref="HPRD:00010"
                     /db_xref="MIM:100740"
     gene            100525960..100526215
                     /gene="RPS29P15"
                     /gene_synonym="RPS29_10_826"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271241"
                     /db_xref="HGNC:35876"
     gene            100547257..100611619
                     /gene="MUC3A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 mRNAs, 15 ESTs, 4 Proteins"
                     /db_xref="GeneID:4584"
                     /db_xref="HGNC:7513"
                     /db_xref="MIM:158371"
     mRNA            join(100547257..100547317,100549481..100552774,
                     100552881..100553066,100554980..100555095,
                     100555515..100555579,100607746..100607894,
                     100608307..100608372,100608729..100608891,
                     100609539..100609712,100609805..100609896,
                     100610052..100610104,100610274..100611619)
                     /gene="MUC3A"
                     /product="mucin 3A, cell surface associated"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 mRNAs, 15 ESTs, 4 Proteins"
                     /transcript_id="XM_001725354.4"
                     /db_xref="GI:341915398"
                     /db_xref="GeneID:4584"
                     /db_xref="HGNC:7513"
                     /db_xref="MIM:158371"
     CDS             join(100547257..100547317,100549481..100552774,
                     100552881..100553066,100554980..100555095,
                     100555515..100555579,100607746..100607894,
                     100608307..100608372,100608729..100608891,
                     100609539..100609712,100609805..100609896,
                     100610052..100610104,100610274..100610315)
                     /gene="MUC3A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="mucin-3A"
                     /protein_id="XP_001725406.2"
                     /db_xref="GI:239743291"
                     /db_xref="GeneID:4584"
                     /db_xref="HGNC:7513"
                     /db_xref="MIM:158371"
     gene            100612904..100662230
                     /gene="MUC12"
                     /gene_synonym="MUC-11; MUC-12; MUC11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10071"
                     /db_xref="HGNC:7510"
                     /db_xref="MIM:604609"
     mRNA            join(100612904..100612970,100633912..100648800,
                     100649752..100649853,100651915..100652042,
                     100652376..100652440,100655577..100655728,
                     100656100..100656171,100656261..100656423,
                     100657194..100657355,100658896..100658972,
                     100660856..100660944,100661876..100662230)
                     /gene="MUC12"
                     /gene_synonym="MUC-11; MUC-12; MUC11"
                     /product="mucin 12, cell surface associated"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001164462.1"
                     /db_xref="GI:256600256"
                     /db_xref="GeneID:10071"
                     /db_xref="HGNC:7510"
                     /db_xref="MIM:604609"
     CDS             join(100612904..100612970,100633912..100648800,
                     100649752..100649853,100651915..100652042,
                     100652376..100652440,100655577..100655728,
                     100656100..100656171,100656261..100656423,
                     100657194..100657355,100658896..100658972,
                     100660856..100660944,100661876..100661917)
                     /gene="MUC12"
                     /gene_synonym="MUC-11; MUC-12; MUC11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="mucin-12"
                     /protein_id="NP_001157934.1"
                     /db_xref="GI:256600257"
                     /db_xref="CCDS:CCDS55139.1"
                     /db_xref="GeneID:10071"
                     /db_xref="HGNC:7510"
                     /db_xref="MIM:604609"
     gene            100663364..100702140
                     /gene="MUC17"
                     /gene_synonym="MUC3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:140453"
                     /db_xref="HGNC:16800"
                     /db_xref="MIM:608424"
     mRNA            join(100663364..100663498,100674401..100674502,
                     100674882..100687100,100691265..100691396,
                     100692126..100692253,100692605..100692663,
                     100693765..100693916,100694894..100694962,
                     100695084..100695243,100696267..100696428,
                     100696620..100696717,100699475..100699551,
                     100701284..100702140)
                     /gene="MUC17"
                     /gene_synonym="MUC3"
                     /product="mucin 17, cell surface associated"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040105.1"
                     /db_xref="GI:91982771"
                     /db_xref="GeneID:140453"
                     /db_xref="HGNC:16800"
                     /db_xref="MIM:608424"
     CDS             join(100663417..100663498,100674401..100674502,
                     100674882..100687100,100691265..100691396,
                     100692126..100692253,100692605..100692663,
                     100693765..100693916,100694894..100694962,
                     100695084..100695243,100696267..100696428,
                     100696620..100696717,100699475..100699551,
                     100701284..100701325)
                     /gene="MUC17"
                     /gene_synonym="MUC3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="mucin-17 precursor"
                     /protein_id="NP_001035194.1"
                     /db_xref="GI:91982772"
                     /db_xref="CCDS:CCDS34711.1"
                     /db_xref="GeneID:140453"
                     /db_xref="HGNC:16800"
                     /db_xref="MIM:608424"
     gene            100728786..100733909
                     /gene="TRIM56"
                     /gene_synonym="DKFZp667O116; FLJ35608; RNF109"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:81844"
                     /db_xref="HGNC:19028"
                     /db_xref="HPRD:10284"
     mRNA            join(100728786..100728852,100730287..100730449,
                     100730593..100733909)
                     /gene="TRIM56"
                     /gene_synonym="DKFZp667O116; FLJ35608; RNF109"
                     /product="tripartite motif containing 56"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_030961.1"
                     /db_xref="GI:30794215"
                     /db_xref="GeneID:81844"
                     /db_xref="HGNC:19028"
                     /db_xref="HPRD:10284"
     CDS             100730594..100732861
                     /gene="TRIM56"
                     /gene_synonym="DKFZp667O116; FLJ35608; RNF109"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase TRIM56"
                     /protein_id="NP_112223.1"
                     /db_xref="GI:30794216"
                     /db_xref="CCDS:CCDS43625.1"
                     /db_xref="GeneID:81844"
                     /db_xref="HGNC:19028"
                     /db_xref="HPRD:10284"
     gene            100770379..100782547
                     /gene="SERPINE1"
                     /gene_synonym="PAI; PAI-1; PAI1; PLANH1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5054"
                     /db_xref="HGNC:8583"
                     /db_xref="HPRD:01418"
                     /db_xref="MIM:173360"
     mRNA            join(100770379..100770525,100771674..100771945,
                     100773702..100773935,100775156..100775350,
                     100776976..100777174,100778775..100778875,
                     100778996..100779082,100780282..100780365,
                     100780686..100782547)
                     /gene="SERPINE1"
                     /gene_synonym="PAI; PAI-1; PAI1; PLANH1"
                     /product="serpin peptidase inhibitor, clade E (nexin,
                     plasminogen activator inhibitor type 1), member 1,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000602.3"
                     /db_xref="GI:259155304"
                     /db_xref="GeneID:5054"
                     /db_xref="HGNC:8583"
                     /db_xref="HPRD:01418"
                     /db_xref="MIM:173360"
     mRNA            join(100770379..100770525,100771674..100771764,
                     100771810..100771945,100773702..100773935,
                     100775156..100775350,100776976..100777174,
                     100778775..100778875,100778996..100779082,
                     100780282..100780365,100780686..100782547)
                     /gene="SERPINE1"
                     /gene_synonym="PAI; PAI-1; PAI1; PLANH1"
                     /product="serpin peptidase inhibitor, clade E (nexin,
                     plasminogen activator inhibitor type 1), member 1,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001165413.1"
                     /db_xref="GI:259155305"
                     /db_xref="GeneID:5054"
                     /db_xref="HGNC:8583"
                     /db_xref="MIM:173360"
                     /db_xref="HPRD:01418"
     CDS             join(100771675..100771945,100773702..100773935,
                     100775156..100775350,100776976..100777174,
                     100778775..100778875,100778996..100779082,
                     100780282..100780365,100780686..100780723)
                     /gene="SERPINE1"
                     /gene_synonym="PAI; PAI-1; PAI1; PLANH1"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="plasminogen activator inhibitor 1 isoform 1
                     precursor"
                     /protein_id="NP_000593.1"
                     /db_xref="GI:10835159"
                     /db_xref="CCDS:CCDS5711.1"
                     /db_xref="GeneID:5054"
                     /db_xref="HGNC:8583"
                     /db_xref="HPRD:01418"
                     /db_xref="MIM:173360"
     CDS             join(100771675..100771764,100771810..100771945,
                     100773702..100773935,100775156..100775350,
                     100776976..100777174,100778775..100778875,
                     100778996..100779082,100780282..100780365,
                     100780686..100780723)
                     /gene="SERPINE1"
                     /gene_synonym="PAI; PAI-1; PAI1; PLANH1"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="plasminogen activator inhibitor 1 isoform 2
                     precursor"
                     /protein_id="NP_001158885.1"
                     /db_xref="GI:259155306"
                     /db_xref="CCDS:CCDS55140.1"
                     /db_xref="GeneID:5054"
                     /db_xref="HGNC:8583"
                     /db_xref="HPRD:01418"
                     /db_xref="MIM:173360"
     gene            100797686..100804557
                     /gene="AP1S1"
                     /gene_synonym="AP19; CLAPS1; FLJ92436; SIGMA1A;
                     WUGSC:H_DJ0747G18.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1174"
                     /db_xref="HGNC:559"
                     /db_xref="HPRD:04635"
                     /db_xref="MIM:603531"
     mRNA            join(100797686..100797798,100799875..100800053,
                     100800658..100800766,100802340..100802477,
                     100803800..100804557)
                     /gene="AP1S1"
                     /gene_synonym="AP19; CLAPS1; FLJ92436; SIGMA1A;
                     WUGSC:H_DJ0747G18.2"
                     /product="adaptor-related protein complex 1, sigma 1
                     subunit"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001283.3"
                     /db_xref="GI:148536831"
                     /db_xref="GeneID:1174"
                     /db_xref="HGNC:559"
                     /db_xref="HPRD:04635"
                     /db_xref="MIM:603531"
     CDS             join(100797796..100797798,100799875..100800053,
                     100800658..100800766,100802340..100802477,
                     100803800..100803847)
                     /gene="AP1S1"
                     /gene_synonym="AP19; CLAPS1; FLJ92436; SIGMA1A;
                     WUGSC:H_DJ0747G18.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="AP-1 complex subunit sigma-1A"
                     /protein_id="NP_001274.1"
                     /db_xref="GI:4557471"
                     /db_xref="CCDS:CCDS47669.1"
                     /db_xref="GeneID:1174"
                     /db_xref="HGNC:559"
                     /db_xref="HPRD:04635"
                     /db_xref="MIM:603531"
     gene            100802754..100802836
                     /gene="MIR4653"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100616117"
                     /db_xref="HGNC:41562"
                     /db_xref="miRBase:MI0017281"
     ncRNA           100802754..100802836
                     /gene="MIR4653"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4653"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039797.1"
                     /db_xref="GI:337756592"
                     /db_xref="GeneID:100616117"
                     /db_xref="HGNC:41562"
                     /db_xref="miRBase:MI0017281"
     gene            complement(100805790..100808852)
                     /gene="VGF"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7425"
                     /db_xref="HGNC:12684"
                     /db_xref="HPRD:03717"
                     /db_xref="MIM:602186"
     mRNA            complement(join(100805790..100808144,
                     100808655..100808852))
                     /gene="VGF"
                     /product="VGF nerve growth factor inducible"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003378.3"
                     /db_xref="GI:194688129"
                     /db_xref="GeneID:7425"
                     /db_xref="HGNC:12684"
                     /db_xref="HPRD:03717"
                     /db_xref="MIM:602186"
     CDS             complement(100806277..100808124)
                     /gene="VGF"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="neurosecretory protein VGF precursor"
                     /protein_id="NP_003369.2"
                     /db_xref="GI:17136078"
                     /db_xref="CCDS:CCDS5712.1"
                     /db_xref="GeneID:7425"
                     /db_xref="HGNC:12684"
                     /db_xref="HPRD:03717"
                     /db_xref="MIM:602186"
     gene            complement(100813774..100823557)
                     /gene="C7orf52"
                     /gene_synonym="DKFZp547K159; FLJ39237"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:375607"
                     /db_xref="HGNC:22030"
                     /db_xref="HPRD:13434"
     mRNA            complement(join(100813774..100815932,100816577..100816801,
                     100817777..100818092,100823323..100823557))
                     /gene="C7orf52"
                     /gene_synonym="DKFZp547K159; FLJ39237"
                     /product="chromosome 7 open reading frame 52"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198571.2"
                     /db_xref="GI:284005401"
                     /db_xref="GeneID:375607"
                     /db_xref="HGNC:22030"
                     /db_xref="HPRD:13434"
     CDS             complement(join(100815360..100815932,100816577..100816801,
                     100817777..100818088))
                     /gene="C7orf52"
                     /gene_synonym="DKFZp547K159; FLJ39237"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative N-acetyltransferase C7orf52"
                     /protein_id="NP_940973.2"
                     /db_xref="GI:284005402"
                     /db_xref="CCDS:CCDS5713.1"
                     /db_xref="GeneID:375607"
                     /db_xref="HGNC:22030"
                     /db_xref="HPRD:13434"
     gene            complement(100839010..100844302)
                     /gene="MOGAT3"
                     /gene_synonym="DC7; DGAT2L7; MGAT3; MGC119203; MGC119204"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:346606"
                     /db_xref="HGNC:23249"
                     /db_xref="HPRD:11368"
                     /db_xref="MIM:610184"
     mRNA            complement(join(100839010..100839381,100839468..100839670,
                     100841472..100841646,100841907..100842111,
                     100843515..100843585,100843689..100843796,
                     100844027..100844302))
                     /gene="MOGAT3"
                     /gene_synonym="DC7; DGAT2L7; MGAT3; MGC119203; MGC119204"
                     /product="monoacylglycerol O-acyltransferase 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178176.2"
                     /db_xref="GI:31342324"
                     /db_xref="GeneID:346606"
                     /db_xref="HGNC:23249"
                     /db_xref="HPRD:11368"
                     /db_xref="MIM:610184"
     CDS             complement(join(100839227..100839381,100839468..100839670,
                     100841472..100841646,100841907..100842111,
                     100843515..100843585,100843689..100843796,
                     100844027..100844135))
                     /gene="MOGAT3"
                     /gene_synonym="DC7; DGAT2L7; MGAT3; MGC119203; MGC119204"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="2-acylglycerol O-acyltransferase 3"
                     /protein_id="NP_835470.1"
                     /db_xref="GI:30039700"
                     /db_xref="CCDS:CCDS5714.1"
                     /db_xref="GeneID:346606"
                     /db_xref="HGNC:23249"
                     /db_xref="HPRD:11368"
                     /db_xref="MIM:610184"
     gene            complement(100845043..100846804)
                     /gene="DGAT2L7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA"
                     /db_xref="GeneID:646409"
     mRNA            complement(join(100845043..100845236,100845425..100845579,
                     100845724..100845898,100846352..100846556,
                     100846784..100846804))
                     /gene="DGAT2L7"
                     /product="diacylglycerol O-acyltransferase 2 like protein
                     7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA"
                     /transcript_id="XM_003118595.1"
                     /db_xref="GI:310120052"
                     /db_xref="GeneID:646409"
     CDS             complement(join(100845043..100845236,100845425..100845579,
                     100845724..100845898,100846352..100846556,
                     100846784..100846804))
                     /gene="DGAT2L7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="diacylglycerol O-acyltransferase 2 like protein
                     7"
                     /protein_id="XP_003118643.1"
                     /db_xref="GI:310120053"
                     /db_xref="GeneID:646409"
     gene            complement(100846881..100847852)
                     /gene="RPSAP46"
                     /gene_synonym="RPSA_14_827"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:652624"
                     /db_xref="HGNC:36082"
     gene            complement(100849258..100861011)
                     /gene="PLOD3"
                     /gene_synonym="LH3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8985"
                     /db_xref="HGNC:9083"
                     /db_xref="HPRD:04347"
                     /db_xref="MIM:603066"
     mRNA            complement(join(100849258..100849717,100850060..100850185,
                     100850859..100851005,100852134..100852238,
                     100853374..100853442,100853612..100853725,
                     100853813..100853954,100854872..100854997,
                     100855127..100855231,100855534..100855655,
                     100855811..100855936,100856123..100856224,
                     100856388..100856485,100858370..100858433,
                     100859189..100859301,100859444..100859607,
                     100859691..100859827,100859976..100860067,
                     100860447..100861011))
                     /gene="PLOD3"
                     /gene_synonym="LH3"
                     /product="procollagen-lysine, 2-oxoglutarate 5-dioxygenase
                     3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001084.4"
                     /db_xref="GI:62739167"
                     /db_xref="GeneID:8985"
                     /db_xref="HGNC:9083"
                     /db_xref="HPRD:04347"
                     /db_xref="MIM:603066"
     CDS             complement(join(100849562..100849717,100850060..100850185,
                     100850859..100851005,100852134..100852238,
                     100853374..100853442,100853612..100853725,
                     100853813..100853954,100854872..100854997,
                     100855127..100855231,100855534..100855655,
                     100855811..100855936,100856123..100856224,
                     100856388..100856485,100858370..100858433,
                     100859189..100859301,100859444..100859607,
                     100859691..100859827,100859976..100860067,
                     100860447..100860555))
                     /gene="PLOD3"
                     /gene_synonym="LH3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="procollagen-lysine,2-oxoglutarate 5-dioxygenase
                     3 precursor"
                     /protein_id="NP_001075.1"
                     /db_xref="GI:4505891"
                     /db_xref="CCDS:CCDS5715.1"
                     /db_xref="GeneID:8985"
                     /db_xref="HGNC:9083"
                     /db_xref="HPRD:04347"
                     /db_xref="MIM:603066"
     gene            100860985..100867471
                     /gene="ZNHIT1"
                     /gene_synonym="CG1I; ZNFN4A1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10467"
                     /db_xref="HGNC:21688"
                     /db_xref="HPRD:15892"
     mRNA            join(100860985..100861498,100865885..100866055,
                     100866758..100866837,100866954..100867123,
                     100867218..100867471)
                     /gene="ZNHIT1"
                     /gene_synonym="CG1I; ZNFN4A1"
                     /product="zinc finger, HIT-type containing 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006349.2"
                     /db_xref="GI:37594439"
                     /db_xref="GeneID:10467"
                     /db_xref="HGNC:21688"
                     /db_xref="HPRD:15892"
     CDS             join(100861477..100861498,100865885..100866055,
                     100866758..100866837,100866954..100867123,
                     100867218..100867239)
                     /gene="ZNHIT1"
                     /gene_synonym="CG1I; ZNFN4A1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger HIT domain-containing protein 1"
                     /protein_id="NP_006340.1"
                     /db_xref="GI:5453617"
                     /db_xref="CCDS:CCDS5716.1"
                     /db_xref="GeneID:10467"
                     /db_xref="HGNC:21688"
                     /db_xref="HPRD:15892"
     gene            complement(100875373..100882101)
                     /gene="CLDN15"
                     /gene_synonym="FLJ42715; MGC19536"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:24146"
                     /db_xref="HGNC:2036"
                     /db_xref="HPRD:13065"
     mRNA            complement(join(100875373..100875796,100875885..100876001,
                     100876114..100876195,100877559..100877723,
                     100880646..100881105,100881219..100882101))
                     /gene="CLDN15"
                     /gene_synonym="FLJ42715; MGC19536"
                     /product="claudin 15, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001185080.1"
                     /db_xref="GI:297515454"
                     /db_xref="GeneID:24146"
                     /db_xref="HGNC:2036"
                     /db_xref="HPRD:13065"
     mRNA            complement(join(100875373..100875796,100875885..100876001,
                     100876114..100876195,100877559..100877723,
                     100880646..100881227))
                     /gene="CLDN15"
                     /gene_synonym="FLJ42715; MGC19536"
                     /product="claudin 15, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014343.2"
                     /db_xref="GI:297515453"
                     /db_xref="GeneID:24146"
                     /db_xref="HGNC:2036"
                     /db_xref="HPRD:13065"
     CDS             complement(join(100875691..100875796,100875885..100876001,
                     100876114..100876195,100877559..100877723,
                     100880646..100880862))
                     /gene="CLDN15"
                     /gene_synonym="FLJ42715; MGC19536"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="claudin-15"
                     /protein_id="NP_055158.1"
                     /db_xref="GI:7656981"
                     /db_xref="CCDS:CCDS5717.1"
                     /db_xref="GeneID:24146"
                     /db_xref="HGNC:2036"
                     /db_xref="HPRD:13065"
     CDS             complement(join(100875691..100875796,100875885..100876001,
                     100876114..100876195,100877559..100877723,
                     100880646..100880862))
                     /gene="CLDN15"
                     /gene_synonym="FLJ42715; MGC19536"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="claudin-15"
                     /protein_id="NP_001172009.1"
                     /db_xref="GI:297515455"
                     /db_xref="CCDS:CCDS5717.1"
                     /db_xref="GeneID:24146"
                     /db_xref="HGNC:2036"
                     /db_xref="HPRD:13065"
     gene            complement(100882893..100888371)
                     /gene="FIS1"
                     /gene_synonym="CGI-135; TTC11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51024"
                     /db_xref="HGNC:21689"
                     /db_xref="HPRD:12352"
                     /db_xref="MIM:609003"
     mRNA            complement(join(100882893..100883184,100883423..100883528,
                     100884111..100884187,100887288..100887420,
                     100888241..100888371))
                     /gene="FIS1"
                     /gene_synonym="CGI-135; TTC11"
                     /product="fission 1 (mitochondrial outer membrane) homolog
                     (S. cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016068.2"
                     /db_xref="GI:151108472"
                     /db_xref="GeneID:51024"
                     /db_xref="HGNC:21689"
                     /db_xref="HPRD:12352"
                     /db_xref="MIM:609003"
     CDS             complement(join(100883087..100883184,100883423..100883528,
                     100884111..100884187,100887288..100887420,
                     100888241..100888285))
                     /gene="FIS1"
                     /gene_synonym="CGI-135; TTC11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="mitochondrial fission 1 protein"
                     /protein_id="NP_057152.2"
                     /db_xref="GI:151108473"
                     /db_xref="CCDS:CCDS43626.1"
                     /db_xref="GeneID:51024"
                     /db_xref="HGNC:21689"
                     /db_xref="HPRD:12352"
                     /db_xref="MIM:609003"
     gene            complement(100930760..100933089)
                     /gene="AZGP1P2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:401393"
                     /db_xref="HGNC:912"
     gene            100942894..100944625
                     /gene="LOC100506507"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 5 ESTs"
                     /db_xref="GeneID:100506507"
     misc_RNA        join(100942894..100943147,100944050..100944625)
                     /gene="LOC100506507"
                     /product="hypothetical LOC100506507"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 5 ESTs"
                     /transcript_id="XR_108853.1"
                     /db_xref="GI:310120054"
                     /db_xref="GeneID:100506507"
     gene            complement(100956648..100965093)
                     /gene="RABL5"
                     /gene_synonym="DKFZp761N0823; FLJ13225; FLJ14117"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64792"
                     /db_xref="HGNC:21895"
                     /db_xref="HPRD:15204"
     mRNA            complement(join(100956648..100958563,100959621..100959823,
                     100961405..100961494,100962237..100962313,
                     100964952..100965093))
                     /gene="RABL5"
                     /gene_synonym="DKFZp761N0823; FLJ13225; FLJ14117"
                     /product="RAB, member RAS oncogene family-like 5,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022777.2"
                     /db_xref="GI:195546887"
                     /db_xref="GeneID:64792"
                     /db_xref="HGNC:21895"
                     /db_xref="HPRD:15204"
     mRNA            complement(join(100956648..100958563,100959621..100959823,
                     100962237..100962313,100964952..100965093))
                     /gene="RABL5"
                     /gene_synonym="DKFZp761N0823; FLJ13225; FLJ14117"
                     /product="RAB, member RAS oncogene family-like 5,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130820.1"
                     /db_xref="GI:195546888"
                     /db_xref="GeneID:64792"
                     /db_xref="HGNC:21895"
                     /db_xref="HPRD:15204"
     mRNA            complement(join(100956648..100958563,100959621..100959823,
                     100961405..100961494,100962237..100962344,
                     100964952..100965093))
                     /gene="RABL5"
                     /gene_synonym="DKFZp761N0823; FLJ13225; FLJ14117"
                     /product="RAB, member RAS oncogene family-like 5,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130821.1"
                     /db_xref="GI:195546890"
                     /db_xref="GeneID:64792"
                     /db_xref="HGNC:21895"
                     /db_xref="HPRD:15204"
     mRNA            complement(join(100956648..100958563,100959621..100959823,
                     100961405..100961494,100964952..100965093))
                     /gene="RABL5"
                     /gene_synonym="DKFZp761N0823; FLJ13225; FLJ14117"
                     /product="RAB, member RAS oncogene family-like 5,
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130822.1"
                     /db_xref="GI:195546893"
                     /db_xref="GeneID:64792"
                     /db_xref="HGNC:21895"
                     /db_xref="HPRD:15204"
     CDS             complement(join(100958415..100958563,100959621..100959823,
                     100961405..100961494,100962237..100962313,
                     100964952..100964990))
                     /gene="RABL5"
                     /gene_synonym="DKFZp761N0823; FLJ13225; FLJ14117"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="rab-like protein 5 isoform a"
                     /protein_id="NP_073614.1"
                     /db_xref="GI:12232463"
                     /db_xref="CCDS:CCDS5719.1"
                     /db_xref="GeneID:64792"
                     /db_xref="HGNC:21895"
                     /db_xref="HPRD:15204"
     CDS             complement(join(100958415..100958563,100959621..100959823,
                     100962237..100962313,100964952..100964990))
                     /gene="RABL5"
                     /gene_synonym="DKFZp761N0823; FLJ13225; FLJ14117"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="rab-like protein 5 isoform b"
                     /protein_id="NP_001124292.1"
                     /db_xref="GI:195546889"
                     /db_xref="CCDS:CCDS47670.1"
                     /db_xref="GeneID:64792"
                     /db_xref="HGNC:21895"
                     /db_xref="HPRD:15204"
     CDS             complement(join(100958415..100958563,
                     100959621..100959798))
                     /gene="RABL5"
                     /gene_synonym="DKFZp761N0823; FLJ13225; FLJ14117"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="rab-like protein 5 isoform c"
                     /protein_id="NP_001124293.1"
                     /db_xref="GI:195546891"
                     /db_xref="CCDS:CCDS47671.1"
                     /db_xref="GeneID:64792"
                     /db_xref="HGNC:21895"
                     /db_xref="HPRD:15204"
     CDS             complement(join(100958415..100958563,
                     100959621..100959798))
                     /gene="RABL5"
                     /gene_synonym="DKFZp761N0823; FLJ13225; FLJ14117"
                     /note="isoform c is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="rab-like protein 5 isoform c"
                     /protein_id="NP_001124294.1"
                     /db_xref="GI:195546894"
                     /db_xref="CCDS:CCDS47671.1"
                     /db_xref="GeneID:64792"
                     /db_xref="HGNC:21895"
                     /db_xref="HPRD:15204"
     gene            101006122..101202304
                     /gene="EMID2"
                     /gene_synonym="COL26A1; EMI6; EMU2; MGC129848; SH2B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:136227"
                     /db_xref="HGNC:18038"
                     /db_xref="HPRD:16405"
                     /db_xref="MIM:608927"
     mRNA            join(101006122..101006471,101063258..101063380,
                     101090971..101091068,101176363..101176424,
                     101183174..101183330,101187279..101187377,
                     101188619..101188771,101190437..101190520,
                     101192452..101192504,101194389..101194424,
                     101196607..101196657,101199068..101199152,
                     101200651..101202304)
                     /gene="EMID2"
                     /gene_synonym="COL26A1; EMI6; EMU2; MGC129848; SH2B"
                     /product="EMI domain containing 2"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_133457.2"
                     /db_xref="GI:118498338"
                     /db_xref="GeneID:136227"
                     /db_xref="HGNC:18038"
                     /db_xref="HPRD:16405"
                     /db_xref="MIM:608927"
     CDS             join(101006314..101006471,101063258..101063380,
                     101090971..101091068,101176363..101176424,
                     101183174..101183330,101187279..101187377,
                     101188619..101188771,101190437..101190520,
                     101192452..101192504,101194389..101194424,
                     101196607..101196657,101199068..101199152,
                     101200651..101200810)
                     /gene="EMID2"
                     /gene_synonym="COL26A1; EMI6; EMU2; MGC129848; SH2B"
                     /exception="unclassified translation discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="collagen alpha-1(XXVI) chain"
                     /protein_id="NP_597714.2"
                     /db_xref="GI:118498339"
                     /db_xref="GeneID:136227"
                     /db_xref="HGNC:18038"
                     /db_xref="HPRD:16405"
                     /db_xref="MIM:608927"
     gene            complement(101208597..101212230)
                     /gene="LOC100506527"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 6 ESTs"
                     /db_xref="GeneID:100506527"
     misc_RNA        complement(join(101208597..101210760,
                     101212130..101212230))
                     /gene="LOC100506527"
                     /product="hypothetical LOC100506527"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 6 ESTs"
                     /transcript_id="XR_108854.1"
                     /db_xref="GI:310120055"
                     /db_xref="GeneID:100506527"
     gene            complement(101256605..101272576)
                     /gene="MYL10"
                     /gene_synonym="MYLC2PL; PLRLC"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:93408"
                     /db_xref="HGNC:29825"
                     /db_xref="HPRD:17620"
     mRNA            complement(join(101256605..101256853,101256942..101256990,
                     101259500..101259578,101265376..101265480,
                     101266277..101266352,101267200..101267301,
                     101267452..101267544,101272321..101272576))
                     /gene="MYL10"
                     /gene_synonym="MYLC2PL; PLRLC"
                     /product="myosin, light chain 10, regulatory"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138403.4"
                     /db_xref="GI:224922752"
                     /db_xref="GeneID:93408"
                     /db_xref="HGNC:29825"
                     /db_xref="HPRD:17620"
     CDS             complement(join(101256755..101256853,101256942..101256990,
                     101259500..101259578,101265376..101265480,
                     101266277..101266352,101267200..101267301,
                     101267452..101267544,101272321..101272398))
                     /gene="MYL10"
                     /gene_synonym="MYLC2PL; PLRLC"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="myosin regulatory light chain 10"
                     /protein_id="NP_612412.2"
                     /db_xref="GI:34147532"
                     /db_xref="CCDS:CCDS34713.1"
                     /db_xref="GeneID:93408"
                     /db_xref="HGNC:29825"
                     /db_xref="HPRD:17620"
     gene            101459184..101927250
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="MIM:116896"
     mRNA            join(101459184..101459373,101559395..101559505,
                     101671378..101671425,101713619..101713697,
                     101740644..101740781,101747616..101747739,
                     101754978..101755054,101758487..101758553,
                     101801840..101801888,101813726..101813830,
                     101821749..101821937,101833093..101833151,
                     101837122..101837170,101838787..101838883,
                     101916637..101916764,101917515..101917581,
                     101918518..101918630,101921220..101921336,
                     101923329..101923412,101924096..101924152,
                     101925132..101925212,101926004..101926068,
                     101926313..101927250)
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /product="cut-like homeobox 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001913.3"
                     /db_xref="GI:321400109"
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="HPRD:00295"
                     /db_xref="MIM:116896"
     mRNA            join(101459184..101459373,101559395..101559505,
                     101671378..101671425,101713619..101713697,
                     101740644..101740781,101747616..101747739,
                     101754978..101755054,101758487..101758553,
                     101801840..101801888,101813726..101813830,
                     101821755..101821937,101833093..101833151,
                     101837122..101837170,101838787..101838883,
                     101916637..101916764,101917515..101917581,
                     101918518..101918630,101921220..101921336,
                     101923329..101923412,101924096..101924152,
                     101925132..101925212,101926004..101926068,
                     101926313..101927250)
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /product="cut-like homeobox 1, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_181500.2"
                     /db_xref="GI:321400110"
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="HPRD:00295"
                     /db_xref="MIM:116896"
     mRNA            join(101459184..101459373,101559395..101559505,
                     101713619..101713697,101740644..101740781,
                     101747616..101747739,101754978..101755054,
                     101758487..101758553,101801840..101801888,
                     101813726..101813830,101821749..101821937,
                     101833093..101833151,101837122..101837170,
                     101838787..101838883,101916637..101916764,
                     101917515..101917581,101918518..101918630,
                     101921220..101921336,101923329..101923412,
                     101924096..101924152,101925132..101925212,
                     101926004..101926068,101926313..101927250)
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /product="cut-like homeobox 1, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001202544.1"
                     /db_xref="GI:321400111"
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="MIM:116896"
     mRNA            join(101459184..101459373,101559395..101559505,
                     101671378..101671425,101713619..101713697,
                     101747616..101747739,101754978..101755054,
                     101758487..101758553,101801840..101801888,
                     101813726..101813830,101821749..101821937,
                     101833093..101833151,101837122..101837170,
                     101838787..101838883,101916637..101916764,
                     101917515..101917581,101918518..101918630,
                     101921220..101921336,101923329..101923412,
                     101924096..101924152,101925132..101925212,
                     101926004..101926068,101926313..101927250)
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /product="cut-like homeobox 1, transcript variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001202545.1"
                     /db_xref="GI:321400113"
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="MIM:116896"
     mRNA            join(101459184..101459373,101559395..101559505,
                     101671378..101671425,101713619..101713697,
                     101740644..101740781,101747616..101747739,
                     101754978..101755054,101758487..101758553,
                     101801840..101801888,101813726..101813830,
                     101821749..101821937,101833093..101833151,
                     101837122..101837170,101838787..101838883,
                     101839914..101840585,101842082..101842147,
                     101843351..101843452,101844640..101845484,
                     101847671..101847836,101848394..101848450,
                     101870647..101870949,101877332..101877520,
                     101882600..101882864,101891692..101901513)
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /product="cut-like homeobox 1, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001202543.1"
                     /db_xref="GI:321400106"
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="MIM:116896"
     mRNA            join(101459288..101459373,101671378..101671425,
                     101713619..101713697,101740644..101740781,
                     101747616..101747739,101754978..101755054,
                     101758487..101758553,101801840..101801888,
                     101813726..101813830,101821755..101821937,
                     101833093..101833151,101837122..101837170,
                     101838787..101838883,101916637..101916764,
                     101917515..101917581,101918518..101918630,
                     101921220..101921336,101923329..101923412,
                     101924096..101924152,101925132..101925212,
                     101926004..101926068,101926313..101927250)
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /product="cut-like homeobox 1, transcript variant 7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001202546.1"
                     /db_xref="GI:321400115"
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="MIM:116896"
     CDS             join(101459311..101459373,101559395..101559505,
                     101671378..101671425,101713619..101713697,
                     101740644..101740781,101747616..101747739,
                     101754978..101755054,101758487..101758553,
                     101801840..101801888,101813726..101813830,
                     101821749..101821937,101833093..101833151,
                     101837122..101837170,101838787..101838883,
                     101916637..101916764,101917515..101917581,
                     101918518..101918630,101921220..101921336,
                     101923329..101923412,101924096..101924152,
                     101925132..101925212,101926004..101926068,
                     101926313..101926382)
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein CASP isoform b"
                     /protein_id="NP_001904.2"
                     /db_xref="GI:31652236"
                     /db_xref="CCDS:CCDS5720.1"
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="MIM:116896"
     CDS             join(101459311..101459373,101559395..101559505,
                     101671378..101671425,101713619..101713697,
                     101740644..101740781,101747616..101747739,
                     101754978..101755054,101758487..101758553,
                     101801840..101801888,101813726..101813830,
                     101821755..101821937,101833093..101833151,
                     101837122..101837170,101838787..101838883,
                     101916637..101916764,101917515..101917581,
                     101918518..101918630,101921220..101921336,
                     101923329..101923412,101924096..101924152,
                     101925132..101925212,101926004..101926068,
                     101926313..101926382)
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein CASP isoform c"
                     /protein_id="NP_852477.1"
                     /db_xref="GI:31652238"
                     /db_xref="CCDS:CCDS47672.1"
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="MIM:116896"
     CDS             join(101459311..101459373,101559395..101559505,
                     101713619..101713697,101740644..101740781,
                     101747616..101747739,101754978..101755054,
                     101758487..101758553,101801840..101801888,
                     101813726..101813830,101821749..101821937,
                     101833093..101833151,101837122..101837170,
                     101838787..101838883,101916637..101916764,
                     101917515..101917581,101918518..101918630,
                     101921220..101921336,101923329..101923412,
                     101924096..101924152,101925132..101925212,
                     101926004..101926068,101926313..101926382)
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /note="isoform e is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein CASP isoform e"
                     /protein_id="NP_001189473.1"
                     /db_xref="GI:321400112"
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="MIM:116896"
     CDS             join(101459311..101459373,101559395..101559505,
                     101671378..101671425,101713619..101713697,
                     101747616..101747739,101754978..101755054,
                     101758487..101758553,101801840..101801888,
                     101813726..101813830,101821749..101821937,
                     101833093..101833151,101837122..101837170,
                     101838787..101838883,101916637..101916764,
                     101917515..101917581,101918518..101918630,
                     101921220..101921336,101923329..101923412,
                     101924096..101924152,101925132..101925212,
                     101926004..101926068,101926313..101926382)
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /note="isoform f is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein CASP isoform f"
                     /protein_id="NP_001189474.1"
                     /db_xref="GI:321400114"
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="MIM:116896"
     CDS             join(101459311..101459373,101671378..101671425,
                     101713619..101713697,101740644..101740781,
                     101747616..101747739,101754978..101755054,
                     101758487..101758553,101801840..101801888,
                     101813726..101813830,101821755..101821937,
                     101833093..101833151,101837122..101837170,
                     101838787..101838883,101916637..101916764,
                     101917515..101917581,101918518..101918630,
                     101921220..101921336,101923329..101923412,
                     101924096..101924152,101925132..101925212,
                     101926004..101926068,101926313..101926382)
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /note="isoform g is encoded by transcript variant 7;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein CASP isoform g"
                     /protein_id="NP_001189475.1"
                     /db_xref="GI:321400116"
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="MIM:116896"
     CDS             join(101459311..101459373,101559395..101559505,
                     101671378..101671425,101713619..101713697,
                     101740644..101740781,101747616..101747739,
                     101754978..101755054,101758487..101758553,
                     101801840..101801888,101813726..101813830,
                     101821749..101821937,101833093..101833151,
                     101837122..101837170,101838787..101838883,
                     101839914..101840585,101842082..101842147,
                     101843351..101843452,101844640..101845484,
                     101847671..101847836,101848394..101848450,
                     101870647..101870949,101877332..101877520,
                     101882600..101882864,101891692..101892322)
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /note="isoform d is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein CASP isoform d"
                     /protein_id="NP_001189472.1"
                     /db_xref="GI:321400107"
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="MIM:116896"
     mRNA            join(101460882..101460949,101559395..101559505,
                     101671378..101671425,101713619..101713697,
                     101740644..101740781,101747616..101747739,
                     101754978..101755054,101758487..101758553,
                     101801840..101801888,101813726..101813830,
                     101821749..101821937,101833093..101833151,
                     101837122..101837170,101838787..101838883,
                     101839914..101840585,101842082..101842147,
                     101843351..101843452,101844640..101845484,
                     101847671..101847836,101848394..101848450,
                     101870647..101870949,101877332..101877520,
                     101882600..101882864,101891692..101901513)
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /product="cut-like homeobox 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_181552.3"
                     /db_xref="GI:321400108"
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="HPRD:00295"
                     /db_xref="MIM:116896"
     CDS             join(101460920..101460949,101559395..101559505,
                     101671378..101671425,101713619..101713697,
                     101740644..101740781,101747616..101747739,
                     101754978..101755054,101758487..101758553,
                     101801840..101801888,101813726..101813830,
                     101821749..101821937,101833093..101833151,
                     101837122..101837170,101838787..101838883,
                     101839914..101840585,101842082..101842147,
                     101843351..101843452,101844640..101845484,
                     101847671..101847836,101848394..101848450,
                     101870647..101870949,101877332..101877520,
                     101882600..101882864,101891692..101892322)
                     /gene="CUX1"
                     /gene_synonym="CASP; CDP; CDP/Cut; CDP1; Clox; COY1;
                     CUTL1; CUX; Cux/CDP; FLJ31745; GOLIM6; Nbla10317; p100;
                     p110; p200; p75"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein CASP isoform a"
                     /protein_id="NP_853530.2"
                     /db_xref="GI:148277064"
                     /db_xref="CCDS:CCDS5721.1"
                     /db_xref="GeneID:1523"
                     /db_xref="HGNC:2557"
                     /db_xref="MIM:116896"
     gene            101928405..101962178
                     /gene="SH2B2"
                     /gene_synonym="APS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10603"
                     /db_xref="HGNC:17381"
                     /db_xref="HPRD:16097"
                     /db_xref="MIM:605300"
     mRNA            join(101928405..101928549,101943806..101944563,
                     101950004..101950105,101952097..>101952186,
                     <101957638..101957862,101960798..101960969,
                     101961766..101962178)
                     /gene="SH2B2"
                     /gene_synonym="APS"
                     /product="SH2B adaptor protein 2"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020979.3"
                     /db_xref="GI:242247192"
                     /db_xref="GeneID:10603"
                     /db_xref="HGNC:17381"
                     /db_xref="HPRD:16097"
                     /db_xref="MIM:605300"
     CDS             join(101928450..101928549,101943806..101944563,
                     101950004..101950105,101952097..>101952186,
                     <101957638..101957862,101960798..101960969,
                     101961766..101962097)
                     /gene="SH2B2"
                     /gene_synonym="APS"
                     /exception="unclassified translation discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="SH2B adapter protein 2"
                     /protein_id="NP_066189.3"
                     /db_xref="GI:242247193"
                     /db_xref="GeneID:10603"
                     /db_xref="HGNC:17381"
                     /db_xref="HPRD:16097"
                     /db_xref="MIM:605300"
     gene            101936369..101936453
                     /gene="MIR4285"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100422858"
                     /db_xref="HGNC:38337"
                     /db_xref="miRBase:MI0015891"
     ncRNA           101936369..101936453
                     /gene="MIR4285"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4285"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_036245.1"
                     /db_xref="GI:301172432"
                     /db_xref="GeneID:100422858"
                     /db_xref="HGNC:38337"
                     /db_xref="miRBase:MI0015891"
     gene            101977726..101979560
                     /gene="PMS2P12"
                     /gene_synonym="PMS2L12; PMSL12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392713"
                     /db_xref="HGNC:13641"
     gene            complement(101986192..101996889)
                     /gene="SPDYE6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:729597"
                     /db_xref="HGNC:35465"
     mRNA            complement(join(101986192..101987661,101988497..101988601,
                     101988724..101989117,101991168..101991253,
                     101992509..101992567,101993601..101993831,
                     101995148..101995366,101996309..101996889))
                     /gene="SPDYE6"
                     /product="speedy homolog E6 (Xenopus laevis)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001146210.1"
                     /db_xref="GI:226246594"
                     /db_xref="GeneID:729597"
                     /db_xref="HGNC:35465"
     CDS             complement(join(101988542..101988601,101988724..101989117,
                     101991168..101991253,101992509..101992567,
                     101993601..101993831,101995148..101995366,
                     101996309..101996468))
                     /gene="SPDYE6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative speedy protein E6"
                     /protein_id="NP_001139682.1"
                     /db_xref="GI:226246595"
                     /db_xref="GeneID:729597"
                     /db_xref="HGNC:35465"
     gene            102004308..102067129
                     /gene="LOC100630923"
                     /gene_synonym="FLJ40957; FLJ58924"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100630923"
     misc_RNA        join(102004308..102004858,102006402..102006523,
                     102016270..102016396,102016659..102016769,
                     102038067..102038145,102039995..102040095,
                     102045045..102045130,102047881..102047945,
                     102065461..102067129)
                     /gene="LOC100630923"
                     /gene_synonym="FLJ40957; FLJ58924"
                     /product="LOC100289561-PRKRIP1 readthrough"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038967.1"
                     /db_xref="GI:337298426"
                     /db_xref="GeneID:100630923"
     gene            102004308..102021080
                     /gene="LOC100289561"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100289561"
     mRNA            join(102004308..102004858,102006421..102006523,
                     102016270..102016396,102016659..102016769,
                     102020932..102021080)
                     /gene="LOC100289561"
                     /product="hypothetical LOC100289561"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001242713.1"
                     /db_xref="GI:337298391"
                     /db_xref="GeneID:100289561"
     CDS             join(102006509..102006523,102016270..102016396,
                     102016659..102016769,102020932..102020987)
                     /gene="LOC100289561"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC100289561"
                     /protein_id="NP_001229642.1"
                     /db_xref="GI:337298392"
                     /db_xref="GeneID:100289561"
     gene            102036804..102067129
                     /gene="PRKRIP1"
                     /gene_synonym="C114; FLJ13902; FLJ40957; KRBOX3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79706"
                     /db_xref="HGNC:21894"
                     /db_xref="HPRD:11460"
     mRNA            join(102036804..102036984,102038067..102038145,
                     102039995..102040095,102045045..102045130,
                     102047881..102047945,102065461..102067129)
                     /gene="PRKRIP1"
                     /gene_synonym="C114; FLJ13902; FLJ40957; KRBOX3"
                     /product="PRKR interacting protein 1 (IL11 inducible)"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024653.3"
                     /db_xref="GI:149192832"
                     /db_xref="GeneID:79706"
                     /db_xref="HGNC:21894"
                     /db_xref="HPRD:11460"
     CDS             join(102036859..102036984,102038067..102038145,
                     102039995..102040095,102045045..102045130,
                     102047881..102047945,102065461..102065558)
                     /gene="PRKRIP1"
                     /gene_synonym="C114; FLJ13902; FLJ40957; KRBOX3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="PRKR-interacting protein 1"
                     /protein_id="NP_078929.1"
                     /db_xref="GI:13375901"
                     /db_xref="CCDS:CCDS34714.1"
                     /db_xref="GeneID:79706"
                     /db_xref="HGNC:21894"
                     /db_xref="HPRD:11460"
     gene            complement(102046189..102046302)
                     /gene="MIR548O"
                     /gene_synonym="MIRN548O"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100313829"
                     /db_xref="HGNC:35333"
                     /db_xref="miRBase:MI0006402"
     ncRNA           complement(102046189..102046302)
                     /gene="MIR548O"
                     /gene_synonym="MIRN548O"
                     /ncRNA_class="miRNA"
                     /product="microRNA 548o"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_031669.1"
                     /db_xref="GI:269847356"
                     /db_xref="GeneID:100313829"
                     /db_xref="HGNC:35333"
                     /db_xref="miRBase:MI0006402"
     ncRNA           complement(102046189..102046302)
                     /gene="MIR548O"
                     /gene_synonym="MIRN548O"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-548o"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:100302247"
                     /db_xref="miRBase:MI0006402"
                     /db_xref="HGNC:35333"
                     /db_xref="GeneID:100313829"
     gene            102073996..102097268
                     /gene="ORAI2"
                     /gene_synonym="C7orf19; CBCIP2; FLJ12474; FLJ14733;
                     FLJ44818; MEM142B; TMEM142B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:80228"
                     /db_xref="HGNC:21667"
                     /db_xref="HPRD:09860"
                     /db_xref="MIM:610929"
     mRNA            join(102073996..102074108,102076672..102076780,
                     102079391..102079628,102086960..102097268)
                     /gene="ORAI2"
                     /gene_synonym="C7orf19; CBCIP2; FLJ12474; FLJ14733;
                     FLJ44818; MEM142B; TMEM142B"
                     /product="ORAI calcium release-activated calcium modulator
                     2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001126340.1"
                     /db_xref="GI:187607421"
                     /db_xref="GeneID:80228"
                     /db_xref="HGNC:21667"
                     /db_xref="MIM:610929"
                     /db_xref="HPRD:09860"
     mRNA            join(102073996..102074108,102079391..102079628,
                     102086960..102097268)
                     /gene="ORAI2"
                     /gene_synonym="C7orf19; CBCIP2; FLJ12474; FLJ14733;
                     FLJ44818; MEM142B; TMEM142B"
                     /product="ORAI calcium release-activated calcium modulator
                     2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032831.2"
                     /db_xref="GI:187607392"
                     /db_xref="GeneID:80228"
                     /db_xref="HGNC:21667"
                     /db_xref="HPRD:09860"
                     /db_xref="MIM:610929"
     CDS             join(102079404..102079628,102086960..102087499)
                     /gene="ORAI2"
                     /gene_synonym="C7orf19; CBCIP2; FLJ12474; FLJ14733;
                     FLJ44818; MEM142B; TMEM142B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein orai-2"
                     /protein_id="NP_116220.1"
                     /db_xref="GI:14249538"
                     /db_xref="CCDS:CCDS5722.1"
                     /db_xref="GeneID:80228"
                     /db_xref="HGNC:21667"
                     /db_xref="HPRD:09860"
                     /db_xref="MIM:610929"
     CDS             join(102079404..102079628,102086960..102087499)
                     /gene="ORAI2"
                     /gene_synonym="C7orf19; CBCIP2; FLJ12474; FLJ14733;
                     FLJ44818; MEM142B; TMEM142B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein orai-2"
                     /protein_id="NP_001119812.1"
                     /db_xref="GI:187607422"
                     /db_xref="CCDS:CCDS5722.1"
                     /db_xref="GeneID:80228"
                     /db_xref="HGNC:21667"
                     /db_xref="HPRD:09860"
                     /db_xref="MIM:610929"
     gene            complement(102096667..102105321)
                     /gene="ALKBH4"
                     /gene_synonym="ABH4; FLJ20013"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54784"
                     /db_xref="HGNC:21900"
                     /db_xref="HPRD:07875"
                     /db_xref="MIM:613302"
     mRNA            complement(join(102096667..102098428,102100051..102100248,
                     102105161..102105321))
                     /gene="ALKBH4"
                     /gene_synonym="ABH4; FLJ20013"
                     /product="alkB, alkylation repair homolog 4 (E. coli)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017621.3"
                     /db_xref="GI:304307764"
                     /db_xref="GeneID:54784"
                     /db_xref="HGNC:21900"
                     /db_xref="HPRD:07875"
                     /db_xref="MIM:613302"
     CDS             complement(join(102097841..102098428,102100051..102100248,
                     102105161..102105283))
                     /gene="ALKBH4"
                     /gene_synonym="ABH4; FLJ20013"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable alpha-ketoglutarate-dependent
                     dioxygenase ABH4"
                     /protein_id="NP_060091.1"
                     /db_xref="GI:8923019"
                     /db_xref="CCDS:CCDS5723.1"
                     /db_xref="GeneID:54784"
                     /db_xref="HGNC:21900"
                     /db_xref="HPRD:07875"
                     /db_xref="MIM:613302"
     gene            102105390..102113612
                     /gene="LRWD1"
                     /gene_synonym="DKFZp434K1815; ORCA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222229"
                     /db_xref="HGNC:21769"
                     /db_xref="HPRD:10904"
     mRNA            join(102105390..102105607,102106264..102106498,
                     102106601..102106717,102107786..102107926,
                     102108166..102108270,102108509..102108634,
                     102108710..102108824,102109001..102109101,
                     102109302..102109509,102110021..102110093,
                     102110189..102110329,102112665..102112756,
                     102112901..102113056,102113139..102113251,
                     102113356..102113612)
                     /gene="LRWD1"
                     /gene_synonym="DKFZp434K1815; ORCA"
                     /product="leucine-rich repeats and WD repeat domain
                     containing 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152892.1"
                     /db_xref="GI:23097239"
                     /db_xref="GeneID:222229"
                     /db_xref="HGNC:21769"
                     /db_xref="HPRD:10904"
     CDS             join(102105528..102105607,102106264..102106498,
                     102106601..102106717,102107786..102107926,
                     102108166..102108270,102108509..102108634,
                     102108710..102108824,102109001..102109101,
                     102109302..102109509,102110021..102110093,
                     102110189..102110329,102112665..102112756,
                     102112901..102113056,102113139..102113251,
                     102113356..102113496)
                     /gene="LRWD1"
                     /gene_synonym="DKFZp434K1815; ORCA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="leucine-rich repeat and WD repeat-containing
                     protein 1"
                     /protein_id="NP_690852.1"
                     /db_xref="GI:23097240"
                     /db_xref="CCDS:CCDS34715.1"
                     /db_xref="GeneID:222229"
                     /db_xref="HGNC:21769"
                     /db_xref="HPRD:10904"
     gene            102111916..102111978
                     /gene="MIR4467"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100616367"
                     /db_xref="HGNC:41896"
                     /db_xref="miRBase:MI0016818"
     ncRNA           102111916..102111978
                     /gene="MIR4467"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4467"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039677.1"
                     /db_xref="GI:337756923"
                     /db_xref="GeneID:100616367"
                     /db_xref="HGNC:41896"
                     /db_xref="miRBase:MI0016818"
     gene            complement(102113547..102119381)
                     /gene="POLR2J"
                     /gene_synonym="hRPB14; MGC71910; POLR2J1; RPB11; RPB11A;
                     RPB11m"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5439"
                     /db_xref="HGNC:9197"
                     /db_xref="HPRD:16038"
                     /db_xref="MIM:604150"
     mRNA            complement(join(102113547..102114131,102114808..102114982,
                     102116628..102116717,102119255..102119381))
                     /gene="POLR2J"
                     /gene_synonym="hRPB14; MGC71910; POLR2J1; RPB11; RPB11A;
                     RPB11m"
                     /product="polymerase (RNA) II (DNA directed) polypeptide
                     J, 13.3kDa"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006234.4"
                     /db_xref="GI:62422568"
                     /db_xref="GeneID:5439"
                     /db_xref="HGNC:9197"
                     /db_xref="HPRD:16038"
                     /db_xref="MIM:604150"
     CDS             complement(join(102114096..102114131,102114808..102114982,
                     102116628..102116717,102119255..102119307))
                     /gene="POLR2J"
                     /gene_synonym="hRPB14; MGC71910; POLR2J1; RPB11; RPB11A;
                     RPB11m"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-directed RNA polymerase II subunit RPB11-a"
                     /protein_id="NP_006225.1"
                     /db_xref="GI:5453932"
                     /db_xref="CCDS:CCDS5724.1"
                     /db_xref="GeneID:5439"
                     /db_xref="HGNC:9197"
                     /db_xref="HPRD:16038"
                     /db_xref="MIM:604150"
     gene            complement(102123586..102158224)
                     /gene="RASA4B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 109 ESTs, 4 Proteins"
                     /db_xref="GeneID:100271927"
                     /db_xref="HGNC:35202"
     mRNA            complement(join(102123586..102124160,102124272..102124336,
                     102125486..102125606,102128910..102129045,
                     102131433..102131570,102133563..102133732,
                     102134272..102134416,102134985..102135122,
                     102135328..102135520,102135725..102135837,
                     102136587..102136651,102136916..102137066,
                     102137294..102137411,102141146..102141240,
                     102141543..102141674,102143610..102143691,
                     102147142..102147271,102150046..102150107,
                     102150626..102150739,102152372..102152428,
                     102157991..102158224))
                     /gene="RASA4B"
                     /product="RAS p21 protein activator 4B, transcript variant
                     3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 102 ESTs, 2 Proteins"
                     /transcript_id="XM_003118598.1"
                     /db_xref="GI:310120066"
                     /db_xref="GeneID:100271927"
                     /db_xref="HGNC:35202"
     mRNA            complement(join(102123586..102124160,102124272..102124336,
                     102125486..102125606,102128910..102129045,
                     102133563..102133732,102134272..102134416,
                     102134985..102135122,102135328..102135520,
                     102135725..102135837,102136587..102136651,
                     102136916..102137066,102137294..102137411,
                     102141146..102141240,102141543..102141674,
                     102143610..102143691,102147142..102147271,
                     102150046..102150107,102150626..102150739,
                     102152372..102152428,102158093..102158224))
                     /gene="RASA4B"
                     /product="RAS p21 protein activator 4B, transcript variant
                     5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 97 ESTs, 2 Proteins"
                     /transcript_id="XM_003118600.1"
                     /db_xref="GI:310120060"
                     /db_xref="GeneID:100271927"
                     /db_xref="HGNC:35202"
     mRNA            complement(join(102123586..102124160,102124272..102124336,
                     102125486..102125606,102128910..102129045,
                     102131433..102131570,102133563..102133732,
                     102134272..102134416,102134985..102135122,
                     102135328..102135520,102135725..102135837,
                     102136587..102136651,102136916..102137066,
                     102137294..102137411,102141146..102141240,
                     102141543..102141674,102143610..102143691,
                     102147142..102147271,102150046..102150107,
                     102150626..102150739,102152372..102152428,
                     102153673..102153703))
                     /gene="RASA4B"
                     /product="RAS p21 protein activator 4B, transcript variant
                     4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 102 ESTs, 2 Proteins"
                     /transcript_id="XM_003118599.1"
                     /db_xref="GI:310120064"
                     /db_xref="GeneID:100271927"
                     /db_xref="HGNC:35202"
     CDS             complement(join(102124039..102124160,102124272..102124336,
                     102125486..102125606,102128910..102129045,
                     102133563..102133732,102134272..102134416,
                     102134985..102135122,102135328..102135520,
                     102135725..102135837,102136587..102136651,
                     102136916..102137066,102137294..102137411,
                     102141146..102141240,102141543..102141674,
                     102143610..102143691,102147142..102147271,
                     102150046..102150107,102150626..102150739,
                     102152372..102152428,102158093..102158157))
                     /gene="RASA4B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="putative Ras GTPase-activating protein 4B
                     isoform 5"
                     /protein_id="XP_003118648.1"
                     /db_xref="GI:310120061"
                     /db_xref="GeneID:100271927"
                     /db_xref="HGNC:35202"
     CDS             complement(join(102124039..102124160,102124272..102124336,
                     102125486..102125606,102128910..102129045,
                     102131433..102131570,102133563..102133732,
                     102134272..102134416,102134985..102135122,
                     102135328..102135520,102135725..102135837,
                     102136587..102136651,102136916..102137066,
                     102137294..102137411,102141146..102141240,
                     102141543..102141674,102143610..102143691,
                     102147142..102147271,102150046..102150107,
                     102150626..102150645))
                     /gene="RASA4B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="putative Ras GTPase-activating protein 4B
                     isoform 3"
                     /protein_id="XP_003118646.1"
                     /db_xref="GI:310120067"
                     /db_xref="GeneID:100271927"
                     /db_xref="HGNC:35202"
     CDS             complement(join(102124039..102124160,102124272..102124336,
                     102125486..102125606,102128910..102129045,
                     102131433..102131570,102133563..102133732,
                     102134272..102134416,102134985..102135122,
                     102135328..102135520,102135725..102135837,
                     102136587..102136651,102136916..102137066,
                     102137294..102137411,102141146..102141240,
                     102141543..102141674,102143610..102143691,
                     102147142..102147271,102150046..102150107,
                     102150626..102150645))
                     /gene="RASA4B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="putative Ras GTPase-activating protein 4B
                     isoform 4"
                     /protein_id="XP_003118647.1"
                     /db_xref="GI:310120065"
                     /db_xref="GeneID:100271927"
                     /db_xref="HGNC:35202"
     gene            complement(102178366..102213068)
                     /gene="POLR2J3"
                     /gene_synonym="MGC54043; POLR2J2; RPB11b1; RPB11b2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:548644"
                     /db_xref="HGNC:33853"
     mRNA            complement(join(102178366..102178972,102180053..102180173,
                     102180462..102180538,102181540..102181750,
                     102181948..102182109,102207444..102207530,
                     102208457..102208631,102210282..102210371,
                     102212919..102213068))
                     /gene="POLR2J3"
                     /gene_synonym="MGC54043; POLR2J2; RPB11b1; RPB11b2"
                     /product="polymerase (RNA) II (DNA directed) polypeptide
                     J3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001097615.2"
                     /db_xref="GI:332634983"
                     /db_xref="GeneID:548644"
                     /db_xref="HGNC:33853"
     gene            102191679..102202757
                     /gene="SPDYE2"
                     /gene_synonym="MGC119295"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:441273"
                     /db_xref="HGNC:33841"
     mRNA            join(102191679..102191731,102193282..102193862,
                     102194806..102195024,102196347..102196577,
                     102197611..102197669,102198914..102198999,
                     102201047..102201440,102201563..102201667,
                     102202503..102202757)
                     /gene="SPDYE2"
                     /gene_synonym="MGC119295"
                     /product="speedy homolog E2 (Xenopus laevis)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001031618.3"
                     /db_xref="GI:261490709"
                     /db_xref="GeneID:441273"
                     /db_xref="HGNC:33841"
     CDS             join(102193703..102193862,102194806..102195024,
                     102196347..102196577,102197611..102197669,
                     102198914..102198999,102201047..102201440,
                     102201563..102201622)
                     /gene="SPDYE2"
                     /gene_synonym="MGC119295"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="speedy protein E2"
                     /protein_id="NP_001026789.2"
                     /db_xref="GI:261490710"
                     /db_xref="CCDS:CCDS34716.2"
                     /db_xref="GeneID:441273"
                     /db_xref="HGNC:33841"
     CDS             complement(join(102207498..102207530,102208457..102208631,
                     102210282..102210371,102212919..102212968))
                     /gene="POLR2J3"
                     /gene_synonym="MGC54043; POLR2J2; RPB11b1; RPB11b2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-directed RNA polymerase II subunit RPB11-b2"
                     /protein_id="NP_001091084.2"
                     /db_xref="GI:332634984"
                     /db_xref="CCDS:CCDS47673.1"
                     /db_xref="GeneID:548644"
                     /db_xref="HGNC:33853"
     gene            complement(102220093..102257205)
                     /gene="RASA4"
                     /gene_synonym="CAPRI; FLJ59070; GAPL; KIAA0538; MGC131890"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10156"
                     /db_xref="HGNC:23181"
                     /db_xref="MIM:607943"
     mRNA            complement(join(102220093..102223339,102223451..102223515,
                     102224665..102224785,102228082..102228217,
                     102230606..102230743,102232732..102232901,
                     102233441..102233585,102234154..102234291,
                     102234497..102234689,102234894..102235006,
                     102235752..102235816,102236081..102236231,
                     102236459..102236576,102240307..102240401,
                     102240704..102240835,102242771..102242852,
                     102246305..102246434,102249208..102249269,
                     102249788..102249901,102251533..102251589,
                     102257072..102257205))
                     /gene="RASA4"
                     /gene_synonym="CAPRI; FLJ59070; GAPL; KIAA0538; MGC131890"
                     /product="RAS p21 protein activator 4, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006989.5"
                     /db_xref="GI:299829176"
                     /db_xref="GeneID:10156"
                     /db_xref="HGNC:23181"
                     /db_xref="HPRD:12135"
                     /db_xref="MIM:607943"
     mRNA            complement(join(102220093..102223339,102223451..102223515,
                     102224665..102224785,102228082..102228217,
                     102232732..102232901,102233441..102233585,
                     102234154..102234291,102234497..102234689,
                     102234894..102235006,102235752..102235816,
                     102236081..102236231,102236459..102236576,
                     102240307..102240401,102240704..102240835,
                     102242771..102242852,102246305..102246434,
                     102249208..102249269,102249788..102249901,
                     102251533..102251589,102257072..102257205))
                     /gene="RASA4"
                     /gene_synonym="CAPRI; FLJ59070; GAPL; KIAA0538; MGC131890"
                     /product="RAS p21 protein activator 4, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001079877.2"
                     /db_xref="GI:299829174"
                     /db_xref="GeneID:10156"
                     /db_xref="HGNC:23181"
                     /db_xref="MIM:607943"
     CDS             complement(join(102223218..102223339,102223451..102223515,
                     102224665..102224785,102228082..102228217,
                     102230606..102230743,102232732..102232901,
                     102233441..102233585,102234154..102234291,
                     102234497..102234689,102234894..102235006,
                     102235752..102235816,102236081..102236231,
                     102236459..102236576,102240307..102240401,
                     102240704..102240835,102242771..102242852,
                     102246305..102246434,102249208..102249269,
                     102249788..102249901,102251533..102251589,
                     102257072..102257136))
                     /gene="RASA4"
                     /gene_synonym="CAPRI; FLJ59070; GAPL; KIAA0538; MGC131890"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ras GTPase-activating protein 4 isoform 1"
                     /protein_id="NP_008920.5"
                     /db_xref="GI:299829177"
                     /db_xref="CCDS:CCDS5725.1"
                     /db_xref="GeneID:10156"
                     /db_xref="HGNC:23181"
                     /db_xref="MIM:607943"
     CDS             complement(join(102223218..102223339,102223451..102223515,
                     102224665..102224785,102228082..102228217,
                     102232732..102232901,102233441..102233585,
                     102234154..102234291,102234497..102234689,
                     102234894..102235006,102235752..102235816,
                     102236081..102236231,102236459..102236576,
                     102240307..102240401,102240704..102240835,
                     102242771..102242852,102246305..102246434,
                     102249208..102249269,102249788..102249901,
                     102251533..102251589,102257072..102257136))
                     /gene="RASA4"
                     /gene_synonym="CAPRI; FLJ59070; GAPL; KIAA0538; MGC131890"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ras GTPase-activating protein 4 isoform 2"
                     /protein_id="NP_001073346.2"
                     /db_xref="GI:299829175"
                     /db_xref="CCDS:CCDS47674.1"
                     /db_xref="GeneID:10156"
                     /db_xref="HGNC:23181"
                     /db_xref="MIM:607943"
     gene            102233003..102234980
                     /gene="LOC100506683"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 17 ESTs"
                     /db_xref="GeneID:100506683"
     misc_RNA        join(102233003..102233070,102233816..102234980)
                     /gene="LOC100506683"
                     /product="hypothetical LOC100506683, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 6 ESTs"
                     /transcript_id="XR_108857.1"
                     /db_xref="GI:310120068"
                     /db_xref="GeneID:100506683"
     misc_RNA        join(102233400..102233621,102233816..102234585)
                     /gene="LOC100506683"
                     /product="hypothetical LOC100506683, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 10 ESTs"
                     /transcript_id="XR_108856.1"
                     /db_xref="GI:310120069"
                     /db_xref="GeneID:100506683"
     misc_RNA        join(102233442..102233591,102233816..102234585)
                     /gene="LOC100506683"
                     /product="hypothetical LOC100506683, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_108858.1"
                     /db_xref="GI:310120070"
                     /db_xref="GeneID:100506683"
     misc_RNA        join(102233476..102233611,102233816..102234585)
                     /gene="LOC100506683"
                     /product="hypothetical LOC100506683, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_108859.1"
                     /db_xref="GI:310120071"
                     /db_xref="GeneID:100506683"
     gene            complement(102277195..102312176)
                     /gene="POLR2J2"
                     /gene_synonym="HRPB11B; MGC105050; MGC54043; RPB11b1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:246721"
                     /db_xref="HGNC:23208"
                     /db_xref="HPRD:17878"
                     /db_xref="MIM:609881"
     mRNA            complement(join(102277195..102278080,102279161..102279281,
                     102279570..102279646,102280651..102280861,
                     102281059..102281220,102306524..102306610,
                     102307537..102307711,102309362..102309451,
                     102311999..102312176))
                     /gene="POLR2J2"
                     /gene_synonym="HRPB11B; MGC105050; MGC54043; RPB11b1"
                     /product="polymerase (RNA) II (DNA directed) polypeptide
                     J2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032959.5"
                     /db_xref="GI:335892824"
                     /db_xref="GeneID:246721"
                     /db_xref="HGNC:23208"
                     /db_xref="HPRD:17878"
                     /db_xref="MIM:609881"
     gene            complement(102277472..102283238)
                     /gene="UPK3BL"
                     /gene_synonym="UPLP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100134938"
                     /db_xref="HGNC:37278"
     mRNA            complement(join(102277472..102278080,102279161..102279281,
                     102279570..102279646,102280651..102280861,
                     102281059..102281220,102283077..102283238))
                     /gene="UPK3BL"
                     /gene_synonym="UPLP"
                     /product="uroplakin 3B-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001114403.2"
                     /db_xref="GI:300116235"
                     /db_xref="GeneID:100134938"
                     /db_xref="HGNC:37278"
     CDS             complement(join(102277972..102278080,102279161..102279281,
                     102279570..102279646,102280651..102280861,
                     102281059..102281220,102283077..102283188))
                     /gene="UPK3BL"
                     /gene_synonym="UPLP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="uroplakin-3b-like protein"
                     /protein_id="NP_001107875.1"
                     /db_xref="GI:167555123"
                     /db_xref="CCDS:CCDS47675.1"
                     /db_xref="GeneID:100134938"
                     /db_xref="HGNC:37278"
     gene            102290772..102301847
                     /gene="SPDYE2L"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100310812"
     mRNA            join(102290772..102290824,102292375..102292955,
                     102293898..102294116,102295431..102295661,
                     102296695..102296753,102297998..102298083,
                     102300137..102300530,102300653..102300757,
                     102301593..102301847)
                     /gene="SPDYE2L"
                     /product="WBSCR19-like protein 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001166339.1"
                     /db_xref="GI:284005310"
                     /db_xref="GeneID:100310812"
     CDS             join(102292796..102292955,102293898..102294116,
                     102295431..102295661,102296695..102296753,
                     102297998..102298083,102300137..102300530,
                     102300653..102300712)
                     /gene="SPDYE2L"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative speedy protein E2-like protein"
                     /protein_id="NP_001159811.1"
                     /db_xref="GI:284005311"
                     /db_xref="GeneID:100310812"
     CDS             complement(join(102306578..102306610,102307537..102307711,
                     102309362..102309451,102311999..102312048))
                     /gene="POLR2J2"
                     /gene_synonym="HRPB11B; MGC105050; MGC54043; RPB11b1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA-directed RNA polymerase II subunit RPB11-b1"
                     /protein_id="NP_116581.3"
                     /db_xref="GI:62739171"
                     /db_xref="CCDS:CCDS43627.1"
                     /db_xref="GeneID:246721"
                     /db_xref="HGNC:23208"
                     /db_xref="HPRD:17878"
                     /db_xref="MIM:609881"
     gene            complement(102319153..102330918)
                     /gene="LOC100133005"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100133005"
     gene            102389399..102449672
                     /gene="FAM185A"
                     /gene_synonym="MGC35361"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222234"
                     /db_xref="HGNC:22412"
     mRNA            join(102389399..102390105,102392139..102392248,
                     102398301..102398393,102401720..102401858,
                     102412856..102412897,102417700..102417795,
                     102427782..102427916,102448737..102449672)
                     /gene="FAM185A"
                     /gene_synonym="MGC35361"
                     /product="family with sequence similarity 185, member A,
                     transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145268.1"
                     /db_xref="GI:223671924"
                     /db_xref="GeneID:222234"
                     /db_xref="HGNC:22412"
     mRNA            join(102389399..102389864,102398301..102398393,
                     102401720..102401858,102412856..102412897,
                     102417700..102417795,102427782..102427916,
                     102448737..102449672)
                     /gene="FAM185A"
                     /gene_synonym="MGC35361"
                     /product="family with sequence similarity 185, member A,
                     transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145269.1"
                     /db_xref="GI:223671926"
                     /db_xref="GeneID:222234"
                     /db_xref="HGNC:22412"
     misc_RNA        join(102389399..102389864,102392139..102392248,
                     102398301..102398393,102401720..102401858,
                     102412856..102412897,102417700..102417795,
                     102427782..102427916,102448737..102449672)
                     /gene="FAM185A"
                     /gene_synonym="MGC35361"
                     /product="family with sequence similarity 185, member A,
                     transcript variant 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_026879.1"
                     /db_xref="GI:223718698"
                     /db_xref="GeneID:222234"
                     /db_xref="HGNC:22412"
     CDS             join(102389655..102390105,102392139..102392248,
                     102398301..102398393,102401720..102401858,
                     102412856..102412897,102417700..102417795,
                     102427782..102427916,102448737..102448849)
                     /gene="FAM185A"
                     /gene_synonym="MGC35361"
                     /exception="mismatches in translation"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC222234 isoform 1"
                     /protein_id="NP_001138740.1"
                     /db_xref="GI:223671925"
                     /db_xref="CCDS:CCDS47676.1"
                     /db_xref="GeneID:222234"
                     /db_xref="HGNC:22412"
     CDS             join(102389655..102389864,102398301..102398393,
                     102401720..102401858,102412856..102412897,
                     102417700..102417795,102427782..102427916,
                     102448737..102448849)
                     /gene="FAM185A"
                     /gene_synonym="MGC35361"
                     /exception="mismatches in translation"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC222234 isoform 2"
                     /protein_id="NP_001138741.1"
                     /db_xref="GI:223671927"
                     /db_xref="CCDS:CCDS47677.1"
                     /db_xref="GeneID:222234"
                     /db_xref="HGNC:22412"
     gene            102395577..102396436
                     /gene="RPL7AP39"
                     /gene_synonym="RPL7A_12_828"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:646476"
                     /db_xref="HGNC:35881"
     gene            102439437..102440108
                     /gene="LOC100422696"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100422696"
     gene            complement(102453308..102715288)
                     /gene="FBXL13"
                     /gene_synonym="Fbl13; FLJ38068; MGC21636"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222235"
                     /db_xref="HGNC:21658"
                     /db_xref="HPRD:12364"
                     /db_xref="MIM:609080"
     mRNA            complement(join(102453308..102453978,102462487..102462650,
                     102495224..102495307,102517914..102518040,
                     102518778..102518897,102523752..102523914,
                     102524015..102524132,102524661..102524759,
                     102553533..102553662,102566721..102566821,
                     102572328..102572380,102603980..102604112,
                     102608469..102608564,102665510..102665677,
                     102667896..102668005,102669047..102669195,
                     102669798..102669865,102696091..102696194,
                     102715143..102715288))
                     /gene="FBXL13"
                     /gene_synonym="Fbl13; FLJ38068; MGC21636"
                     /product="F-box and leucine-rich repeat protein 13,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001111038.1"
                     /db_xref="GI:161333853"
                     /db_xref="GeneID:222235"
                     /db_xref="HGNC:21658"
                     /db_xref="MIM:609080"
                     /db_xref="HPRD:12364"
     mRNA            complement(join(102453308..102453978,102462487..102462650,
                     102473287..102473421,102495224..102495307,
                     102517914..102518040,102518778..102518897,
                     102523752..102523914,102524015..102524132,
                     102524661..102524759,102553533..102553662,
                     102566721..102566821,102572328..102572380,
                     102603980..102604112,102608469..102608564,
                     102665510..102665677,102667896..102668005,
                     102669047..102669195,102669798..102669865,
                     102696091..102696194,102714693..102715015))
                     /gene="FBXL13"
                     /gene_synonym="Fbl13; FLJ38068; MGC21636"
                     /product="F-box and leucine-rich repeat protein 13,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145032.3"
                     /db_xref="GI:161333851"
                     /db_xref="GeneID:222235"
                     /db_xref="HGNC:21658"
                     /db_xref="HPRD:12364"
                     /db_xref="MIM:609080"
     CDS             complement(join(102453789..102453978,102462487..102462650,
                     102473287..102473421,102495224..102495307,
                     102517914..102518040,102518778..102518897,
                     102523752..102523914,102524015..102524132,
                     102524661..102524759,102553533..102553662,
                     102566721..102566821,102572328..102572380,
                     102603980..102604112,102608469..102608564,
                     102665510..102665677,102667896..102668005,
                     102669047..102669195,102669798..102669865))
                     /gene="FBXL13"
                     /gene_synonym="Fbl13; FLJ38068; MGC21636"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="F-box/LRR-repeat protein 13 isoform 1"
                     /protein_id="NP_659469.3"
                     /db_xref="GI:161333852"
                     /db_xref="CCDS:CCDS5726.1"
                     /db_xref="GeneID:222235"
                     /db_xref="HGNC:21658"
                     /db_xref="HPRD:12364"
                     /db_xref="MIM:609080"
     CDS             complement(join(102453789..102453978,102462487..102462650,
                     102495224..102495307,102517914..102518040,
                     102518778..102518897,102523752..102523914,
                     102524015..102524132,102524661..102524759,
                     102553533..102553662,102566721..102566821,
                     102572328..102572380,102603980..102604112,
                     102608469..102608564,102665510..102665677,
                     102667896..102668005,102669047..102669195,
                     102669798..102669865))
                     /gene="FBXL13"
                     /gene_synonym="Fbl13; FLJ38068; MGC21636"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="F-box/LRR-repeat protein 13 isoform 2"
                     /protein_id="NP_001104508.1"
                     /db_xref="GI:161333854"
                     /db_xref="CCDS:CCDS47678.1"
                     /db_xref="GeneID:222235"
                     /db_xref="HGNC:21658"
                     /db_xref="HPRD:12364"
                     /db_xref="MIM:609080"
     gene            102553344..102585558
                     /gene="LRRC17"
                     /gene_synonym="P37NB"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10234"
                     /db_xref="HGNC:16895"
                     /db_xref="HPRD:10059"
     mRNA            join(102553344..102553592,102574221..102575132,
                     102579877..102580032,102584657..102585558)
                     /gene="LRRC17"
                     /gene_synonym="P37NB"
                     /product="leucine rich repeat containing 17, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001031692.2"
                     /db_xref="GI:239582716"
                     /db_xref="GeneID:10234"
                     /db_xref="HGNC:16895"
                     /db_xref="HPRD:10059"
     mRNA            join(102553344..102553592,102574221..102575132,
                     102579877..102580032,102582737..102582789,
                     102584657..102585558)
                     /gene="LRRC17"
                     /gene_synonym="P37NB"
                     /product="leucine rich repeat containing 17, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005824.2"
                     /db_xref="GI:239582713"
                     /db_xref="GeneID:10234"
                     /db_xref="HGNC:16895"
                     /db_xref="HPRD:10059"
     CDS             join(102574361..102575132,102579877..102580032,
                     102584657..102585054)
                     /gene="LRRC17"
                     /gene_synonym="P37NB"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="leucine-rich repeat-containing protein 17
                     isoform 1"
                     /protein_id="NP_001026862.1"
                     /db_xref="GI:72534676"
                     /db_xref="CCDS:CCDS34721.1"
                     /db_xref="GeneID:10234"
                     /db_xref="HGNC:16895"
                     /db_xref="HPRD:10059"
     CDS             join(102574361..102575132,102579877..102580032,
                     102582737..102582750)
                     /gene="LRRC17"
                     /gene_synonym="P37NB"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="leucine-rich repeat-containing protein 17
                     isoform 2"
                     /protein_id="NP_005815.2"
                     /db_xref="GI:239582714"
                     /db_xref="CCDS:CCDS5727.1"
                     /db_xref="GeneID:10234"
                     /db_xref="HGNC:16895"
                     /db_xref="HPRD:10059"
     gene            102613884..102619114
                     /gene="NFE4"
                     /gene_synonym="NF-E4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:58160"
                     /db_xref="MIM:612133"
     mRNA            join(102613884..102614218,102616338..102616677,
                     102618828..102619114)
                     /gene="NFE4"
                     /gene_synonym="NF-E4"
                     /product="transcription factor NF-E4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001085386.1"
                     /db_xref="GI:145976941"
                     /db_xref="GeneID:58160"
                     /db_xref="MIM:612133"
     CDS             join(102614004..102614218,102616338..102616662)
                     /gene="NFE4"
                     /gene_synonym="NF-E4"
                     /note="Region: p22 NF-E4 isoform;~non-AUG (CUG)
                     translation initiation codon; Derived by automated
                     computational analysis using gene prediction method:
                     BestRefseq."
                     /codon_start=1
                     /product="transcription factor NF-E4"
                     /protein_id="NP_001078855.1"
                     /db_xref="GI:145976942"
                     /db_xref="GeneID:58160"
                     /db_xref="MIM:612133"
     gene            102715328..102740205
                     /gene="ARMC10"
                     /gene_synonym="FLJ37850; MGC3195; PNAS112; SVH"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:83787"
                     /db_xref="HGNC:21706"
                     /db_xref="HPRD:18133"
                     /db_xref="MIM:611864"
     mRNA            join(102715328..102715858,102716224..102716328,
                     102724129..102724277,102727077..102727211,
                     102732924..102733100,102737724..102737795,
                     102738746..102740205)
                     /gene="ARMC10"
                     /gene_synonym="FLJ37850; MGC3195; PNAS112; SVH"
                     /product="armadillo repeat containing 10, transcript
                     variant A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_031905.3"
                     /db_xref="GI:238776791"
                     /db_xref="GeneID:83787"
                     /db_xref="HGNC:21706"
                     /db_xref="HPRD:18133"
                     /db_xref="MIM:611864"
     mRNA            join(102715328..102715858,102724129..102724277,
                     102727077..102727211,102732924..102733100,
                     102737724..102737795,102738746..102740205)
                     /gene="ARMC10"
                     /gene_synonym="FLJ37850; MGC3195; PNAS112; SVH"
                     /product="armadillo repeat containing 10, transcript
                     variant B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001161009.1"
                     /db_xref="GI:238776792"
                     /db_xref="GeneID:83787"
                     /db_xref="HGNC:21706"
                     /db_xref="MIM:611864"
                     /db_xref="HPRD:18133"
     mRNA            join(102715328..102715858,102716224..102716328,
                     102724129..102724277,102727077..102727211,
                     102737724..102737795,102738746..102740205)
                     /gene="ARMC10"
                     /gene_synonym="FLJ37850; MGC3195; PNAS112; SVH"
                     /product="armadillo repeat containing 10, transcript
                     variant C"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001161010.1"
                     /db_xref="GI:238776794"
                     /db_xref="GeneID:83787"
                     /db_xref="HGNC:21706"
                     /db_xref="MIM:611864"
                     /db_xref="HPRD:18133"
     mRNA            join(102715328..102715858,102724129..102724277,
                     102727077..102727211,102737724..102737795,
                     102738746..102740205)
                     /gene="ARMC10"
                     /gene_synonym="FLJ37850; MGC3195; PNAS112; SVH"
                     /product="armadillo repeat containing 10, transcript
                     variant D"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001161012.1"
                     /db_xref="GI:238776798"
                     /db_xref="GeneID:83787"
                     /db_xref="HGNC:21706"
                     /db_xref="MIM:611864"
                     /db_xref="HPRD:18133"
     mRNA            join(102715328..102715858,102724129..102724277,
                     102727077..102727211,102732924..102733100,
                     102738746..102740205)
                     /gene="ARMC10"
                     /gene_synonym="FLJ37850; MGC3195; PNAS112; SVH"
                     /product="armadillo repeat containing 10, transcript
                     variant E"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001161011.1"
                     /db_xref="GI:238776796"
                     /db_xref="GeneID:83787"
                     /db_xref="HGNC:21706"
                     /db_xref="MIM:611864"
                     /db_xref="HPRD:18133"
     mRNA            join(102715328..102715858,102724129..102724277,
                     102727077..102727211,102738746..102740205)
                     /gene="ARMC10"
                     /gene_synonym="FLJ37850; MGC3195; PNAS112; SVH"
                     /product="armadillo repeat containing 10, transcript
                     variant F"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001161013.1"
                     /db_xref="GI:238776800"
                     /db_xref="GeneID:83787"
                     /db_xref="HGNC:21706"
                     /db_xref="MIM:611864"
                     /db_xref="HPRD:18133"
     CDS             join(102715720..102715858,102716224..102716328,
                     102724129..102724277,102727077..102727211,
                     102732924..102733100,102737724..102737795,
                     102738746..102739000)
                     /gene="ARMC10"
                     /gene_synonym="FLJ37850; MGC3195; PNAS112; SVH"
                     /note="isoform a is encoded by transcript variant A;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="armadillo repeat-containing protein 10 isoform
                     a"
                     /protein_id="NP_114111.2"
                     /db_xref="GI:31377663"
                     /db_xref="CCDS:CCDS5728.1"
                     /db_xref="GeneID:83787"
                     /db_xref="HGNC:21706"
                     /db_xref="HPRD:18133"
                     /db_xref="MIM:611864"
     CDS             join(102715720..102715858,102724129..102724277,
                     102727077..102727211,102732924..102733100,
                     102737724..102737795,102738746..102739000)
                     /gene="ARMC10"
                     /gene_synonym="FLJ37850; MGC3195; PNAS112; SVH"
                     /note="isoform b is encoded by transcript variant B;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="armadillo repeat-containing protein 10 isoform
                     b"
                     /protein_id="NP_001154481.1"
                     /db_xref="GI:238776793"
                     /db_xref="CCDS:CCDS55146.1"
                     /db_xref="GeneID:83787"
                     /db_xref="HGNC:21706"
                     /db_xref="HPRD:18133"
                     /db_xref="MIM:611864"
     CDS             join(102715720..102715858,102716224..102716328,
                     102724129..102724277,102727077..102727211,
                     102737724..102737795,102738746..102739000)
                     /gene="ARMC10"
                     /gene_synonym="FLJ37850; MGC3195; PNAS112; SVH"
                     /note="isoform c is encoded by transcript variant C;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="armadillo repeat-containing protein 10 isoform
                     c"
                     /protein_id="NP_001154482.1"
                     /db_xref="GI:238776795"
                     /db_xref="CCDS:CCDS55145.1"
                     /db_xref="GeneID:83787"
                     /db_xref="HGNC:21706"
                     /db_xref="HPRD:18133"
                     /db_xref="MIM:611864"
     CDS             join(102715720..102715858,102724129..102724277,
                     102727077..102727211,102737724..102737795,
                     102738746..102739000)
                     /gene="ARMC10"
                     /gene_synonym="FLJ37850; MGC3195; PNAS112; SVH"
                     /note="isoform d is encoded by transcript variant D;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="armadillo repeat-containing protein 10 isoform
                     d"
                     /protein_id="NP_001154484.1"
                     /db_xref="GI:238776799"
                     /db_xref="CCDS:CCDS55148.1"
                     /db_xref="GeneID:83787"
                     /db_xref="HGNC:21706"
                     /db_xref="HPRD:18133"
                     /db_xref="MIM:611864"
     CDS             join(102715720..102715858,102724129..102724277,
                     102727077..102727211,102732924..102733100,
                     102738746..102739000)
                     /gene="ARMC10"
                     /gene_synonym="FLJ37850; MGC3195; PNAS112; SVH"
                     /note="isoform e is encoded by transcript variant E;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="armadillo repeat-containing protein 10 isoform
                     e"
                     /protein_id="NP_001154483.1"
                     /db_xref="GI:238776797"
                     /db_xref="CCDS:CCDS55147.1"
                     /db_xref="GeneID:83787"
                     /db_xref="HGNC:21706"
                     /db_xref="HPRD:18133"
                     /db_xref="MIM:611864"
     CDS             join(102715720..102715858,102724129..102724277,
                     102727077..102727211,102738746..102739000)
                     /gene="ARMC10"
                     /gene_synonym="FLJ37850; MGC3195; PNAS112; SVH"
                     /note="isoform f is encoded by transcript variant F;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="armadillo repeat-containing protein 10 isoform
                     f"
                     /protein_id="NP_001154485.1"
                     /db_xref="GI:238776801"
                     /db_xref="CCDS:CCDS55149.1"
                     /db_xref="GeneID:83787"
                     /db_xref="HGNC:21706"
                     /db_xref="HPRD:18133"
                     /db_xref="MIM:611864"
     gene            complement(102728148..102730222)
                     /gene="CRYZP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:1430"
                     /db_xref="HGNC:2421"
     gene            complement(102740023..102789569)
                     /gene="NAPEPLD"
                     /gene_synonym="DKFZp781D1098; FMP30; NAPE-PLD"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222236"
                     /db_xref="HGNC:21683"
                     /db_xref="HPRD:14809"
                     /db_xref="MIM:612334"
     mRNA            complement(join(102740023..102744001,102755507..102755621,
                     102760024..102760670,102768930..102769239,
                     102789258..102789569))
                     /gene="NAPEPLD"
                     /gene_synonym="DKFZp781D1098; FMP30; NAPE-PLD"
                     /product="N-acyl phosphatidylethanolamine phospholipase D,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001122838.1"
                     /db_xref="GI:170932482"
                     /db_xref="GeneID:222236"
                     /db_xref="HGNC:21683"
                     /db_xref="MIM:612334"
                     /db_xref="HPRD:14809"
     mRNA            complement(join(102740023..102743569,102743871..102744001,
                     102755507..102755621,102760024..102760670,
                     102768930..102769239,102789258..102789569))
                     /gene="NAPEPLD"
                     /gene_synonym="DKFZp781D1098; FMP30; NAPE-PLD"
                     /product="N-acyl phosphatidylethanolamine phospholipase D,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198990.4"
                     /db_xref="GI:170932480"
                     /db_xref="GeneID:222236"
                     /db_xref="HGNC:21683"
                     /db_xref="HPRD:14809"
                     /db_xref="MIM:612334"
     CDS             complement(join(102743876..102744001,102755507..102755621,
                     102760024..102760670,102768930..102769223))
                     /gene="NAPEPLD"
                     /gene_synonym="DKFZp781D1098; FMP30; NAPE-PLD"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="N-acyl-phosphatidylethanolamine-hydrolyzing
                     phospholipase D"
                     /protein_id="NP_945341.3"
                     /db_xref="GI:170932481"
                     /db_xref="CCDS:CCDS5729.1"
                     /db_xref="GeneID:222236"
                     /db_xref="HGNC:21683"
                     /db_xref="HPRD:14809"
                     /db_xref="MIM:612334"
     CDS             complement(join(102743876..102744001,102755507..102755621,
                     102760024..102760670,102768930..102769223))
                     /gene="NAPEPLD"
                     /gene_synonym="DKFZp781D1098; FMP30; NAPE-PLD"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="N-acyl-phosphatidylethanolamine-hydrolyzing
                     phospholipase D"
                     /protein_id="NP_001116310.1"
                     /db_xref="GI:170932483"
                     /db_xref="CCDS:CCDS5729.1"
                     /db_xref="GeneID:222236"
                     /db_xref="HGNC:21683"
                     /db_xref="HPRD:14809"
                     /db_xref="MIM:612334"
     gene            complement(102781717..102782850)
                     /gene="RPL19P12"
                     /gene_synonym="RPL19_4_829"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:100129424"
                     /db_xref="HGNC:36047"
     misc_RNA        complement(102781717..102782850)
                     /gene="RPL19P12"
                     /gene_synonym="RPL19_4_829"
                     /product="ribosomal protein L19 pseudogene 12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_026660.1"
                     /db_xref="GI:221139769"
                     /db_xref="GeneID:100129424"
                     /db_xref="HGNC:36047"
     gene            complement(102815460..102920913)
                     /gene="DPY19L2P2"
                     /gene_synonym="DKFZp434E092; DKFZp586E1120; DKFZp779M0267;
                     FLJ36166"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:349152"
                     /db_xref="HGNC:21764"
     misc_RNA        complement(join(102815460..102815858,102824449..102824574,
                     102825885..102825984,102835887..102836061,
                     102837634..102837753,102839042..102839066,
                     102850714..102850760,102852608..102852679,
                     102854448..102854549,102856910..102856990,
                     102865552..102865611,102874247..102874333,
                     102875096..102875173,102878203..102878302,
                     102879250..102879318,102881009..102881100,
                     102883436..102883493,102895229..102895322,
                     102898051..102898171,102912179..102912316,
                     102914517..102916074,102918061..102918085,
                     102920280..102920913))
                     /gene="DPY19L2P2"
                     /gene_synonym="DKFZp434E092; DKFZp586E1120; DKFZp779M0267;
                     FLJ36166"
                     /product="dpy-19-like 2 pseudogene 2 (C. elegans),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_027768.1"
                     /db_xref="GI:239787135"
                     /db_xref="GeneID:349152"
                     /db_xref="HGNC:21764"
     misc_RNA        complement(join(102815460..102815858,102825885..102825984,
                     102850714..102850760,102852608..102852679,
                     102854448..102854549,102856910..102856990,
                     102865552..102865611,102874247..102874333,
                     102875096..102875173,102878203..102878302,
                     102881009..102881100,102883436..102883493,
                     102895229..102895322,102898051..102898171,
                     102898891..102899039,102912179..102912316,
                     102914517..102916074,102918061..102918085,
                     102918692..102918793,102920280..102920341,
                     102920585..102920759))
                     /gene="DPY19L2P2"
                     /gene_synonym="DKFZp434E092; DKFZp586E1120; DKFZp779M0267;
                     FLJ36166"
                     /product="dpy-19-like 2 pseudogene 2 (C. elegans),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003561.2"
                     /db_xref="GI:239787136"
                     /db_xref="GeneID:349152"
                     /db_xref="HGNC:21764"
     gene            102902398..102902928
                     /gene="S100A11P1"
                     /gene_synonym="S100A11P; S100A14"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:729659"
                     /db_xref="HGNC:10491"
     gene            102937873..102955133
                     /gene="PMPCB"
                     /gene_synonym="Beta-MPP; MPP11; MPPB; MPPP52; P-52"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9512"
                     /db_xref="HGNC:9119"
                     /db_xref="HPRD:07539"
                     /db_xref="MIM:603131"
     mRNA            join(102937873..102938005,102939015..102939155,
                     102939890..102939976,102940625..102940754,
                     102944289..102944487,102944858..102944937,
                     102948043..102948155,102949399..102949542,
                     102950762..102950922,102952090..102952175,
                     102952255..102952343,102952503..102952578,
                     102952654..102955133)
                     /gene="PMPCB"
                     /gene_synonym="Beta-MPP; MPP11; MPPB; MPPP52; P-52"
                     /product="peptidase (mitochondrial processing) beta"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004279.2"
                     /db_xref="GI:94538353"
                     /db_xref="GeneID:9512"
                     /db_xref="HGNC:9119"
                     /db_xref="HPRD:07539"
                     /db_xref="MIM:603131"
     CDS             join(102937907..102938005,102939015..102939155,
                     102939890..102939976,102940625..102940754,
                     102944289..102944487,102944858..102944937,
                     102948043..102948155,102949399..102949542,
                     102950762..102950922,102952090..102952175,
                     102952255..102952343,102952503..102952578,
                     102952654..102952718)
                     /gene="PMPCB"
                     /gene_synonym="Beta-MPP; MPP11; MPPB; MPPP52; P-52"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="mitochondrial-processing peptidase subunit beta
                     precursor"
                     /protein_id="NP_004270.2"
                     /db_xref="GI:94538354"
                     /db_xref="CCDS:CCDS5730.1"
                     /db_xref="GeneID:9512"
                     /db_xref="HGNC:9119"
                     /db_xref="HPRD:07539"
                     /db_xref="MIM:603131"
     gene            complement(102952921..102985320)
                     /gene="DNAJC2"
                     /gene_synonym="MPHOSPH11; MPP11; ZRF1; ZUO1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:27000"
                     /db_xref="HGNC:13192"
                     /db_xref="MIM:605502"
     mRNA            complement(join(102952921..102953090,102953394..102953548,
                     102956211..102956318,102956435..102956535,
                     102957277..102957461,102960056..102960125,
                     102960203..102960291,102962379..102962528,
                     102962958..102963079,102963150..102963241,
                     102964045..102964110,102964929..102965009,
                     102966990..102967131,102968103..102968201,
                     102978183..102978258,102982211..102982401,
                     102985006..102985320))
                     /gene="DNAJC2"
                     /gene_synonym="MPHOSPH11; MPP11; ZRF1; ZUO1"
                     /product="DnaJ (Hsp40) homolog, subfamily C, member 2,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014377.1"
                     /db_xref="GI:94538369"
                     /db_xref="GeneID:27000"
                     /db_xref="HGNC:13192"
                     /db_xref="MIM:605502"
     mRNA            complement(join(102952921..102953090,102953394..102953548,
                     102956211..102956318,102956435..102956535,
                     102957277..102957461,102962379..102962528,
                     102962958..102963079,102963150..102963241,
                     102964045..102964110,102964929..102965009,
                     102966990..102967131,102968103..102968201,
                     102978183..102978258,102982211..102982401,
                     102985006..102985320))
                     /gene="DNAJC2"
                     /gene_synonym="MPHOSPH11; MPP11; ZRF1; ZUO1"
                     /product="DnaJ (Hsp40) homolog, subfamily C, member 2,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001129887.1"
                     /db_xref="GI:193788631"
                     /db_xref="GeneID:27000"
                     /db_xref="HGNC:13192"
                     /db_xref="MIM:605502"
     CDS             complement(join(102953016..102953090,102953394..102953548,
                     102956211..102956318,102956435..102956535,
                     102957277..102957461,102960056..102960125,
                     102960203..102960291,102962379..102962528,
                     102962958..102963079,102963150..102963241,
                     102964045..102964110,102964929..102965009,
                     102966990..102967131,102968103..102968201,
                     102978183..102978258,102982211..102982401,
                     102985006..102985069))
                     /gene="DNAJC2"
                     /gene_synonym="MPHOSPH11; MPP11; ZRF1; ZUO1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="dnaJ homolog subfamily C member 2 isoform 1"
                     /protein_id="NP_055192.1"
                     /db_xref="GI:94538370"
                     /db_xref="CCDS:CCDS43628.1"
                     /db_xref="GeneID:27000"
                     /db_xref="HGNC:13192"
                     /db_xref="MIM:605502"
     CDS             complement(join(102953016..102953090,102953394..102953548,
                     102956211..102956318,102956435..102956535,
                     102957277..102957461,102962379..102962528,
                     102962958..102963079,102963150..102963241,
                     102964045..102964110,102964929..102965009,
                     102966990..102967131,102968103..102968201,
                     102978183..102978258,102982211..102982401,
                     102985006..102985069))
                     /gene="DNAJC2"
                     /gene_synonym="MPHOSPH11; MPP11; ZRF1; ZUO1"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="dnaJ homolog subfamily C member 2 isoform 2"
                     /protein_id="NP_001123359.1"
                     /db_xref="GI:193788632"
                     /db_xref="CCDS:CCDS47679.1"
                     /db_xref="GeneID:27000"
                     /db_xref="HGNC:13192"
                     /db_xref="MIM:605502"
     gene            102987971..103009842
                     /gene="PSMC2"
                     /gene_synonym="MGC3004; MSS1; Nbla10058; S7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5701"
                     /db_xref="HGNC:9548"
                     /db_xref="HPRD:01105"
                     /db_xref="MIM:154365"
     mRNA            join(102987971..102988228,102994368..102994405,
                     102995315..102995396,102996141..102996240,
                     103002404..103002535,103003133..103003205,
                     103003791..103003886,103004590..103004754,
                     103006523..103006610,103007860..103008062,
                     103008160..103008256,103008344..103009842)
                     /gene="PSMC2"
                     /gene_synonym="MGC3004; MSS1; Nbla10058; S7"
                     /product="proteasome (prosome, macropain) 26S subunit,
                     ATPase, 2, transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002803.3"
                     /db_xref="GI:325053650"
                     /db_xref="GeneID:5701"
                     /db_xref="HGNC:9548"
                     /db_xref="HPRD:01105"
                     /db_xref="MIM:154365"
     mRNA            join(102987971..102988228,102994368..102994405,
                     102995315..102995396,102996141..102996240,
                     103002404..103002914)
                     /gene="PSMC2"
                     /gene_synonym="MGC3004; MSS1; Nbla10058; S7"
                     /product="proteasome (prosome, macropain) 26S subunit,
                     ATPase, 2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001204453.1"
                     /db_xref="GI:325053651"
                     /db_xref="GeneID:5701"
                     /db_xref="HGNC:9548"
                     /db_xref="MIM:154365"
                     /db_xref="HPRD:01105"
     CDS             join(102988159..102988228,102994368..102994405,
                     102995315..102995396,102996141..102996240,
                     103002404..103002535,103003133..103003205,
                     103003791..103003886,103004590..103004754,
                     103006523..103006610,103007860..103008062,
                     103008160..103008256,103008344..103008501)
                     /gene="PSMC2"
                     /gene_synonym="MGC3004; MSS1; Nbla10058; S7"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="26S protease regulatory subunit 7 isoform 1"
                     /protein_id="NP_002794.1"
                     /db_xref="GI:4506209"
                     /db_xref="CCDS:CCDS5731.1"
                     /db_xref="GeneID:5701"
                     /db_xref="HGNC:9548"
                     /db_xref="HPRD:01105"
                     /db_xref="MIM:154365"
     CDS             join(102988159..102988228,102994368..102994405,
                     102995315..102995396,102996141..102996240,
                     103002404..103002539)
                     /gene="PSMC2"
                     /gene_synonym="MGC3004; MSS1; Nbla10058; S7"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="26S protease regulatory subunit 7 isoform 2"
                     /protein_id="NP_001191382.1"
                     /db_xref="GI:325053652"
                     /db_xref="GeneID:5701"
                     /db_xref="HGNC:9548"
                     /db_xref="MIM:154365"
                     /db_xref="HPRD:01105"
     gene            102989019..102989306
                     /gene="RPS29P16"
                     /gene_synonym="RPS29_11_830"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100132499"
                     /db_xref="HGNC:35560"
     gene            complement(102993177..103086624)
                     /gene="SLC26A5"
                     /gene_synonym="DFNB61; MGC118886; MGC118887; MGC118888;
                     MGC118889; PRES"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:375611"
                     /db_xref="HGNC:9359"
                     /db_xref="HPRD:09224"
                     /db_xref="MIM:604943"
     mRNA            complement(join(102993177..102993373,103017255..103017309,
                     103018046..103018246,103018893..103019000,
                     103019690..103019782,103020927..103020996,
                     103029455..103029561,103029776..103029871,
                     103030876..103030953,103032069..103032182,
                     103033366..103033513,103038379..103038461,
                     103048298..103048450,103050832..103050996,
                     103051867..103052033,103053449..103053559,
                     103061185..103061324,103061810..103062014,
                     103083530..103083658,103086545..103086624))
                     /gene="SLC26A5"
                     /gene_synonym="DFNB61; MGC118886; MGC118887; MGC118888;
                     MGC118889; PRES"
                     /product="solute carrier family 26, member 5 (prestin),
                     transcript variant b"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_206883.2"
                     /db_xref="GI:269784646"
                     /db_xref="GeneID:375611"
                     /db_xref="HGNC:9359"
                     /db_xref="HPRD:09224"
                     /db_xref="MIM:604943"
     mRNA            complement(join(102993177..102993373,103029455..103029561,
                     103029776..103029871,103030876..103030953,
                     103032069..103032182,103033366..103033513,
                     103038379..103038461,103048298..103048450,
                     103050832..103050996,103051867..103052033,
                     103053449..103053559,103061185..103061324,
                     103061810..103062014,103083530..103083658,
                     103086545..103086624))
                     /gene="SLC26A5"
                     /gene_synonym="DFNB61; MGC118886; MGC118887; MGC118888;
                     MGC118889; PRES"
                     /product="solute carrier family 26, member 5 (prestin),
                     transcript variant c"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_206884.2"
                     /db_xref="GI:269784647"
                     /db_xref="GeneID:375611"
                     /db_xref="HGNC:9359"
                     /db_xref="HPRD:09224"
                     /db_xref="MIM:604943"
     mRNA            complement(join(102993177..102993373,103038379..103038461,
                     103048298..103048450,103050832..103050996,
                     103051867..103052033,103053449..103053559,
                     103061185..103061324,103061810..103062014,
                     103083530..103083658,103086545..103086624))
                     /gene="SLC26A5"
                     /gene_synonym="DFNB61; MGC118886; MGC118887; MGC118888;
                     MGC118889; PRES"
                     /product="solute carrier family 26, member 5 (prestin),
                     transcript variant d"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_206885.2"
                     /db_xref="GI:269784648"
                     /db_xref="GeneID:375611"
                     /db_xref="HGNC:9359"
                     /db_xref="HPRD:09224"
                     /db_xref="MIM:604943"
     CDS             complement(join(102993337..102993373,103029455..103029561,
                     103029776..103029871,103030876..103030953,
                     103032069..103032182,103033366..103033513,
                     103038379..103038461,103048298..103048450,
                     103050832..103050996,103051867..103052033,
                     103053449..103053559,103061185..103061324,
                     103061810..103061961))
                     /gene="SLC26A5"
                     /gene_synonym="DFNB61; MGC118886; MGC118887; MGC118888;
                     MGC118889; PRES"
                     /note="isoform c is encoded by transcript variant c;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="prestin isoform c"
                     /protein_id="NP_996767.1"
                     /db_xref="GI:45827802"
                     /db_xref="GeneID:375611"
                     /db_xref="HGNC:9359"
                     /db_xref="HPRD:09224"
                     /db_xref="MIM:604943"
     CDS             complement(join(102993337..102993373,103038379..103038461,
                     103048298..103048450,103050832..103050996,
                     103051867..103052033,103053449..103053559,
                     103061185..103061324,103061810..103061961))
                     /gene="SLC26A5"
                     /gene_synonym="DFNB61; MGC118886; MGC118887; MGC118888;
                     MGC118889; PRES"
                     /note="isoform d is encoded by transcript variant d;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="prestin isoform d"
                     /protein_id="NP_996768.1"
                     /db_xref="GI:45827804"
                     /db_xref="GeneID:375611"
                     /db_xref="HGNC:9359"
                     /db_xref="HPRD:09224"
                     /db_xref="MIM:604943"
     CDS             complement(join(102993357..102993373,103017255..103017309,
                     103018046..103018246,103018893..103019000,
                     103019690..103019782,103020927..103020996,
                     103029455..103029561,103029776..103029871,
                     103030876..103030953,103032069..103032182,
                     103033366..103033513,103038379..103038461,
                     103048298..103048450,103050832..103050996,
                     103051867..103052033,103053449..103053559,
                     103061185..103061324,103061810..103061961))
                     /gene="SLC26A5"
                     /gene_synonym="DFNB61; MGC118886; MGC118887; MGC118888;
                     MGC118889; PRES"
                     /note="isoform b is encoded by transcript variant b;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="prestin isoform b"
                     /protein_id="NP_996766.1"
                     /db_xref="GI:45827800"
                     /db_xref="CCDS:CCDS43630.1"
                     /db_xref="GeneID:375611"
                     /db_xref="HGNC:9359"
                     /db_xref="HPRD:09224"
                     /db_xref="MIM:604943"
     mRNA            complement(join(103014654..103015039,103017255..103017309,
                     103018046..103018246,103018893..103019000,
                     103019690..103019782,103020927..103020996,
                     103029455..103029561,103029776..103029871,
                     103030876..103030953,103032069..103032182,
                     103033366..103033513,103038379..103038461,
                     103048298..103048450,103050832..103050996,
                     103051867..103052033,103053449..103053559,
                     103061185..103061324,103061810..103062014,
                     103083530..103083658,103086545..103086624))
                     /gene="SLC26A5"
                     /gene_synonym="DFNB61; MGC118886; MGC118887; MGC118888;
                     MGC118889; PRES"
                     /product="solute carrier family 26, member 5 (prestin),
                     transcript variant a"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198999.2"
                     /db_xref="GI:269784649"
                     /db_xref="GeneID:375611"
                     /db_xref="HGNC:9359"
                     /db_xref="HPRD:09224"
                     /db_xref="MIM:604943"
     mRNA            complement(join(103014654..103015039,103017255..103017309,
                     103018046..103018246,103018893..103019000,
                     103019690..103019782,103020927..103020996,
                     103029455..103029561,103030876..103030953,
                     103032069..103032182,103033366..103033513,
                     103038379..103038461,103048298..103048450,
                     103050832..103050996,103051867..103052033,
                     103053449..103053559,103061185..103061324,
                     103061810..103062014,103083530..103083658,
                     103086545..103086624))
                     /gene="SLC26A5"
                     /gene_synonym="DFNB61; MGC118886; MGC118887; MGC118888;
                     MGC118889; PRES"
                     /product="solute carrier family 26, member 5 (prestin),
                     transcript variant e"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001167962.1"
                     /db_xref="GI:269784650"
                     /db_xref="GeneID:375611"
                     /db_xref="HGNC:9359"
                     /db_xref="MIM:604943"
                     /db_xref="HPRD:09224"
     CDS             complement(join(103014846..103015039,103017255..103017309,
                     103018046..103018246,103018893..103019000,
                     103019690..103019782,103020927..103020996,
                     103029455..103029561,103029776..103029871,
                     103030876..103030953,103032069..103032182,
                     103033366..103033513,103038379..103038461,
                     103048298..103048450,103050832..103050996,
                     103051867..103052033,103053449..103053559,
                     103061185..103061324,103061810..103061961))
                     /gene="SLC26A5"
                     /gene_synonym="DFNB61; MGC118886; MGC118887; MGC118888;
                     MGC118889; PRES"
                     /note="isoform a is encoded by transcript variant a;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="prestin isoform a"
                     /protein_id="NP_945350.1"
                     /db_xref="GI:39752683"
                     /db_xref="CCDS:CCDS5733.1"
                     /db_xref="GeneID:375611"
                     /db_xref="HGNC:9359"
                     /db_xref="HPRD:09224"
                     /db_xref="MIM:604943"
     CDS             complement(join(103014846..103015039,103017255..103017309,
                     103018046..103018246,103018893..103019000,
                     103019690..103019782,103020927..103020996,
                     103029455..103029561,103030876..103030953,
                     103032069..103032182,103033366..103033513,
                     103038379..103038461,103048298..103048450,
                     103050832..103050996,103051867..103052033,
                     103053449..103053559,103061185..103061324,
                     103061810..103061961))
                     /gene="SLC26A5"
                     /gene_synonym="DFNB61; MGC118886; MGC118887; MGC118888;
                     MGC118889; PRES"
                     /note="isoform e is encoded by transcript variant e;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="prestin isoform e"
                     /protein_id="NP_001161434.1"
                     /db_xref="GI:269784651"
                     /db_xref="CCDS:CCDS55150.1"
                     /db_xref="GeneID:375611"
                     /db_xref="HGNC:9359"
                     /db_xref="HPRD:09224"
                     /db_xref="MIM:604943"
     gene            complement(103112231..103629963)
                     /gene="RELN"
                     /gene_synonym="PRO1598; RL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5649"
                     /db_xref="HGNC:9957"
                     /db_xref="HPRD:02742"
                     /db_xref="MIM:600514"
     mRNA            complement(join(103112231..103113355,103118836..103118841,
                     103123320..103123418,103124100..103124297,
                     103126644..103126863,103130189..103130346,
                     103131115..103131276,103132400..103132473,
                     103136170..103136345,103136973..103137215,
                     103138267..103138373,103138524..103138699,
                     103141192..103141369,103143463..103143677,
                     103151298..103151452,103155632..103155888,
                     103159770..103159963,103162469..103162646,
                     103163838..103163978,103175763..103175931,
                     103179525..103179774,103180644..103180902,
                     103183178..103183325,103185571..103185791,
                     103191514..103191743,103193908..103194010,
                     103194107..103194278,103197424..103197606,
                     103198412..103198496,103201979..103202156,
                     103202260..103202400,103205725..103205998,
                     103206671..103206859,103207048..103207206,
                     103212631..103212707,103214539..103214746,
                     103215995..103216152,103230043..103230275,
                     103234129..103234329,103234768..103234939,
                     103236903..103237108,103243751..103243937,
                     103244793..103244930,103251142..103251254,
                     103252058..103252250,103270387..103270623,
                     103275872..103276033,103276682..103276915,
                     103280990..103281056,103290721..103290830,
                     103292108..103292236,103292998..103293206,
                     103294540..103294652,103301823..103301974,
                     103322563..103322708,103338300..103338540,
                     103341357..103341453,103363587..103363638,
                     103368558..103368654,103389873..103389951,
                     103393629..103393661,103417004..103417074,
                     103473984..103474119,103557522..103557632,
                     103629578..103629963))
                     /gene="RELN"
                     /gene_synonym="PRO1598; RL"
                     /product="reelin, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005045.3"
                     /db_xref="GI:223718138"
                     /db_xref="GeneID:5649"
                     /db_xref="HGNC:9957"
                     /db_xref="HPRD:02742"
                     /db_xref="MIM:600514"
     mRNA            complement(join(103112231..103113355,103123320..103123418,
                     103124100..103124297,103126644..103126863,
                     103130189..103130346,103131115..103131276,
                     103132400..103132473,103136170..103136345,
                     103136973..103137215,103138267..103138373,
                     103138524..103138699,103141192..103141369,
                     103143463..103143677,103151298..103151452,
                     103155632..103155888,103159770..103159963,
                     103162469..103162646,103163838..103163978,
                     103175763..103175931,103179525..103179774,
                     103180644..103180902,103183178..103183325,
                     103185571..103185791,103191514..103191743,
                     103193908..103194010,103194107..103194278,
                     103197424..103197606,103198412..103198496,
                     103201979..103202156,103202260..103202400,
                     103205725..103205998,103206671..103206859,
                     103207048..103207206,103212631..103212707,
                     103214539..103214746,103215995..103216152,
                     103230043..103230275,103234129..103234329,
                     103234768..103234939,103236903..103237108,
                     103243751..103243937,103244793..103244930,
                     103251142..103251254,103252058..103252250,
                     103270387..103270623,103275872..103276033,
                     103276682..103276915,103280990..103281056,
                     103290721..103290830,103292108..103292236,
                     103292998..103293206,103294540..103294652,
                     103301823..103301974,103322563..103322708,
                     103338300..103338540,103341357..103341453,
                     103363587..103363638,103368558..103368654,
                     103389873..103389951,103393629..103393661,
                     103417004..103417074,103473984..103474119,
                     103557522..103557632,103629578..103629963))
                     /gene="RELN"
                     /gene_synonym="PRO1598; RL"
                     /product="reelin, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_173054.2"
                     /db_xref="GI:223718142"
                     /db_xref="GeneID:5649"
                     /db_xref="HGNC:9957"
                     /db_xref="HPRD:02742"
                     /db_xref="MIM:600514"
     CDS             complement(join(103113259..103113355,103118836..103118841,
                     103123320..103123418,103124100..103124297,
                     103126644..103126863,103130189..103130346,
                     103131115..103131276,103132400..103132473,
                     103136170..103136345,103136973..103137215,
                     103138267..103138373,103138524..103138699,
                     103141192..103141369,103143463..103143677,
                     103151298..103151452,103155632..103155888,
                     103159770..103159963,103162469..103162646,
                     103163838..103163978,103175763..103175931,
                     103179525..103179774,103180644..103180902,
                     103183178..103183325,103185571..103185791,
                     103191514..103191743,103193908..103194010,
                     103194107..103194278,103197424..103197606,
                     103198412..103198496,103201979..103202156,
                     103202260..103202400,103205725..103205998,
                     103206671..103206859,103207048..103207206,
                     103212631..103212707,103214539..103214746,
                     103215995..103216152,103230043..103230275,
                     103234129..103234329,103234768..103234939,
                     103236903..103237108,103243751..103243937,
                     103244793..103244930,103251142..103251254,
                     103252058..103252250,103270387..103270623,
                     103275872..103276033,103276682..103276915,
                     103280990..103281056,103290721..103290830,
                     103292108..103292236,103292998..103293206,
                     103294540..103294652,103301823..103301974,
                     103322563..103322708,103338300..103338540,
                     103341357..103341453,103363587..103363638,
                     103368558..103368654,103389873..103389951,
                     103393629..103393661,103417004..103417074,
                     103473984..103474119,103557522..103557632,
                     103629578..103629803))
                     /gene="RELN"
                     /gene_synonym="PRO1598; RL"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="reelin isoform a"
                     /protein_id="NP_005036.2"
                     /db_xref="GI:27436938"
                     /db_xref="CCDS:CCDS47680.1"
                     /db_xref="GeneID:5649"
                     /db_xref="HGNC:9957"
                     /db_xref="HPRD:02742"
                     /db_xref="MIM:600514"
     CDS             complement(join(103113259..103113355,103123320..103123418,
                     103124100..103124297,103126644..103126863,
                     103130189..103130346,103131115..103131276,
                     103132400..103132473,103136170..103136345,
                     103136973..103137215,103138267..103138373,
                     103138524..103138699,103141192..103141369,
                     103143463..103143677,103151298..103151452,
                     103155632..103155888,103159770..103159963,
                     103162469..103162646,103163838..103163978,
                     103175763..103175931,103179525..103179774,
                     103180644..103180902,103183178..103183325,
                     103185571..103185791,103191514..103191743,
                     103193908..103194010,103194107..103194278,
                     103197424..103197606,103198412..103198496,
                     103201979..103202156,103202260..103202400,
                     103205725..103205998,103206671..103206859,
                     103207048..103207206,103212631..103212707,
                     103214539..103214746,103215995..103216152,
                     103230043..103230275,103234129..103234329,
                     103234768..103234939,103236903..103237108,
                     103243751..103243937,103244793..103244930,
                     103251142..103251254,103252058..103252250,
                     103270387..103270623,103275872..103276033,
                     103276682..103276915,103280990..103281056,
                     103290721..103290830,103292108..103292236,
                     103292998..103293206,103294540..103294652,
                     103301823..103301974,103322563..103322708,
                     103338300..103338540,103341357..103341453,
                     103363587..103363638,103368558..103368654,
                     103389873..103389951,103393629..103393661,
                     103417004..103417074,103473984..103474119,
                     103557522..103557632,103629578..103629803))
                     /gene="RELN"
                     /gene_synonym="PRO1598; RL"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="reelin isoform b"
                     /protein_id="NP_774959.1"
                     /db_xref="GI:27436940"
                     /db_xref="CCDS:CCDS34722.1"
                     /db_xref="GeneID:5649"
                     /db_xref="HGNC:9957"
                     /db_xref="HPRD:02742"
                     /db_xref="MIM:600514"
     gene            complement(103766788..103848495)
                     /gene="ORC5"
                     /gene_synonym="ORC5L; ORC5P; ORC5T"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5001"
                     /db_xref="HGNC:8491"
                     /db_xref="HPRD:09086"
                     /db_xref="MIM:602331"
     mRNA            complement(join(103766788..103767340,103777228..103777340,
                     103801520..103801630,103805683..103805730,
                     103807220..103807332,103808921..103808973,
                     103824391..103824481,103824571..103824619,
                     103828699..103828829,103835591..103835702,
                     103838173..103838247,103841206..103841406,
                     103844590..103844682,103848281..103848495))
                     /gene="ORC5"
                     /gene_synonym="ORC5L; ORC5P; ORC5T"
                     /product="origin recognition complex, subunit 5,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002553.3"
                     /db_xref="GI:309243098"
                     /db_xref="GeneID:5001"
                     /db_xref="HGNC:8491"
                     /db_xref="HPRD:09086"
                     /db_xref="MIM:602331"
     CDS             complement(join(103767295..103767340,103777228..103777340,
                     103801520..103801630,103805683..103805730,
                     103807220..103807332,103808921..103808973,
                     103824391..103824481,103824571..103824619,
                     103828699..103828829,103835591..103835702,
                     103838173..103838247,103841206..103841406,
                     103844590..103844682,103848281..103848352))
                     /gene="ORC5"
                     /gene_synonym="ORC5L; ORC5P; ORC5T"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="origin recognition complex subunit 5 isoform 1"
                     /protein_id="NP_002544.1"
                     /db_xref="GI:4505525"
                     /db_xref="CCDS:CCDS5734.1"
                     /db_xref="GeneID:5001"
                     /db_xref="HGNC:8491"
                     /db_xref="HPRD:09086"
                     /db_xref="MIM:602331"
     mRNA            complement(join(103808624..103808973,103824391..103824481,
                     103824571..103824619,103828699..103828829,
                     103835591..103835702,103838173..103838247,
                     103841206..103841406,103844590..103844682,
                     103848281..103848495))
                     /gene="ORC5"
                     /gene_synonym="ORC5L; ORC5P; ORC5T"
                     /product="origin recognition complex, subunit 5,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_181747.3"
                     /db_xref="GI:313661365"
                     /db_xref="GeneID:5001"
                     /db_xref="HGNC:8491"
                     /db_xref="MIM:602331"
                     /db_xref="HPRD:09086"
     CDS             complement(join(103808823..103808973,103824391..103824481,
                     103824571..103824619,103828699..103828829,
                     103835591..103835702,103838173..103838247,
                     103841206..103841406,103844590..103844682,
                     103848281..103848352))
                     /gene="ORC5"
                     /gene_synonym="ORC5L; ORC5P; ORC5T"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="origin recognition complex subunit 5 isoform 2"
                     /protein_id="NP_859531.1"
                     /db_xref="GI:32454754"
                     /db_xref="CCDS:CCDS47681.1"
                     /db_xref="GeneID:5001"
                     /db_xref="HGNC:8491"
                     /db_xref="HPRD:09086"
                     /db_xref="MIM:602331"
     gene            103969104..104549005
                     /gene="LHFPL3"
                     /gene_synonym="LHFPL4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:375612"
                     /db_xref="HGNC:6589"
                     /db_xref="HPRD:17273"
                     /db_xref="MIM:609719"
     mRNA            join(103969104..103969672,104377122..104377358,
                     104546634..104549005)
                     /gene="LHFPL3"
                     /gene_synonym="LHFPL4"
                     /product="lipoma HMGIC fusion partner-like 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_199000.2"
                     /db_xref="GI:108773777"
                     /db_xref="GeneID:375612"
                     /db_xref="HGNC:6589"
                     /db_xref="HPRD:17273"
                     /db_xref="MIM:609719"
     CDS             join(103969228..103969672,104377122..104377358,
                     104546634..104546662)
                     /gene="LHFPL3"
                     /gene_synonym="LHFPL4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="lipoma HMGIC fusion partner-like 3 protein"
                     /protein_id="NP_945351.1"
                     /db_xref="GI:39752685"
                     /db_xref="GeneID:375612"
                     /db_xref="HGNC:6589"
                     /db_xref="HPRD:17273"
                     /db_xref="MIM:609719"
     gene            104308180..104312032
                     /gene="EIF4BP6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:645579"
                     /db_xref="HGNC:37939"
     gene            complement(104436953..104444539)
                     /gene="LOC645591"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:645591"
     misc_RNA        complement(join(104436953..104437396,104440265..104440516,
                     104443286..104443410,104444403..104444539))
                     /gene="LOC645591"
                     /product="hypothetical LOC645591, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_034141.1"
                     /db_xref="GI:300796987"
                     /db_xref="GeneID:645591"
     misc_RNA        complement(join(104439445..104440516,104443286..104443410,
                     104444403..104444539))
                     /gene="LOC645591"
                     /product="hypothetical LOC645591, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_034142.1"
                     /db_xref="GI:300797008"
                     /db_xref="GeneID:645591"
     gene            complement(104535075..104567092)
                     /gene="LOC723809"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:723809"
     misc_RNA        complement(join(104535075..104536511,104552363..104552523,
                     104560832..104560872,104566900..104567092))
                     /gene="LOC723809"
                     /product="hypothetical LOC723809"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027374.1"
                     /db_xref="GI:225543447"
                     /db_xref="GeneID:723809"
     gene            complement(104622194..104631612)
                     /gene="LOC100216546"
                     /gene_synonym="FLJ35127; FLJ41601; FLJ44142"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100216546"
     misc_RNA        complement(104622194..104631612)
                     /gene="LOC100216546"
                     /gene_synonym="FLJ35127; FLJ41601; FLJ44142"
                     /product="hypothetical LOC100216546"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039981.1"
                     /db_xref="GI:337756418"
                     /db_xref="GeneID:100216546"
     gene            complement(104650989..104654588)
                     /gene="LOC100216545"
                     /gene_synonym="FLJ37053; FLJ41482; FLJ42052"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100216545"
     misc_RNA        complement(104650989..104654588)
                     /gene="LOC100216545"
                     /gene_synonym="FLJ37053; FLJ41482; FLJ42052"
                     /product="hypothetical LOC100216545"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024586.1"
                     /db_xref="GI:218082922"
                     /db_xref="GeneID:100216545"
     gene            104654637..104754532
                     /gene="MLL5"
                     /gene_synonym="FLJ10078; FLJ14026; HDCMC04P; KMT2E;
                     MGC70452"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55904"
                     /db_xref="HGNC:18541"
                     /db_xref="HPRD:10528"
                     /db_xref="MIM:608444"
     mRNA            join(104654637..104654982,104678573..104678646,
                     104681286..104681470,104702611..104702725,
                     104703798..104704027,104707174..104707254,
                     104714066..104714124,104715090..104715262,
                     104716490..104716528,104717410..104717640,
                     104717750..104717880,104719293..104719410,
                     104722135..104722244,104730456..104730720,
                     104731663..104731761,104741872..104742036,
                     104742333..104742641,104745886..104746140,
                     104746306..104746450,104746969..104747219,
                     104747613..104747669,104747809..104748372,
                     104749389..104749675,104750727..104750815,
                     104750924..104751049,104751218..104751315,
                     104752272..104754532)
                     /gene="MLL5"
                     /gene_synonym="FLJ10078; FLJ14026; HDCMC04P; KMT2E;
                     MGC70452"
                     /product="myeloid/lymphoid or mixed-lineage leukemia 5
                     (trithorax homolog, Drosophila), transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182931.2"
                     /db_xref="GI:91199541"
                     /db_xref="GeneID:55904"
                     /db_xref="HGNC:18541"
                     /db_xref="HPRD:10528"
                     /db_xref="MIM:608444"
     mRNA            join(104654637..104654944,104681322..104681470,
                     104702611..104702725,104703798..104704027,
                     104707174..104707254,104714066..104714124,
                     104715090..104715262,104716490..104716528,
                     104717410..104717640,104717750..104717880,
                     104719293..104719410,104722135..104722244,
                     104730456..104730720,104731663..104731761,
                     104741872..104742036,104742333..104742641,
                     104745886..104746140,104746306..104746450,
                     104746969..104747219,104747613..104747669,
                     104747809..104748372,104749389..104749675,
                     104750727..104750815,104750924..104751049,
                     104751218..104751315,104752272..104754532)
                     /gene="MLL5"
                     /gene_synonym="FLJ10078; FLJ14026; HDCMC04P; KMT2E;
                     MGC70452"
                     /product="myeloid/lymphoid or mixed-lineage leukemia 5
                     (trithorax homolog, Drosophila), transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018682.3"
                     /db_xref="GI:91199542"
                     /db_xref="GeneID:55904"
                     /db_xref="HGNC:18541"
                     /db_xref="HPRD:10528"
                     /db_xref="MIM:608444"
     CDS             join(104681400..104681470,104702611..104702725,
                     104703798..104704027,104707174..104707254,
                     104714066..104714124,104715090..104715262,
                     104716490..104716528,104717410..104717640,
                     104717750..104717880,104719293..104719410,
                     104722135..104722244,104730456..104730720,
                     104731663..104731761,104741872..104742036,
                     104742333..104742641,104745886..104746140,
                     104746306..104746450,104746969..104747219,
                     104747613..104747669,104747809..104748372,
                     104749389..104749675,104750727..104750815,
                     104750924..104751049,104751218..104751315,
                     104752272..104753780)
                     /gene="MLL5"
                     /gene_synonym="FLJ10078; FLJ14026; HDCMC04P; KMT2E;
                     MGC70452"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone-lysine N-methyltransferase MLL5"
                     /protein_id="NP_891847.1"
                     /db_xref="GI:33636768"
                     /db_xref="CCDS:CCDS34723.1"
                     /db_xref="GeneID:55904"
                     /db_xref="HGNC:18541"
                     /db_xref="HPRD:10528"
                     /db_xref="MIM:608444"
     CDS             join(104681400..104681470,104702611..104702725,
                     104703798..104704027,104707174..104707254,
                     104714066..104714124,104715090..104715262,
                     104716490..104716528,104717410..104717640,
                     104717750..104717880,104719293..104719410,
                     104722135..104722244,104730456..104730720,
                     104731663..104731761,104741872..104742036,
                     104742333..104742641,104745886..104746140,
                     104746306..104746450,104746969..104747219,
                     104747613..104747669,104747809..104748372,
                     104749389..104749675,104750727..104750815,
                     104750924..104751049,104751218..104751315,
                     104752272..104753780)
                     /gene="MLL5"
                     /gene_synonym="FLJ10078; FLJ14026; HDCMC04P; KMT2E;
                     MGC70452"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone-lysine N-methyltransferase MLL5"
                     /protein_id="NP_061152.3"
                     /db_xref="GI:91199543"
                     /db_xref="CCDS:CCDS34723.1"
                     /db_xref="GeneID:55904"
                     /db_xref="HGNC:18541"
                     /db_xref="HPRD:10528"
                     /db_xref="MIM:608444"
     gene            complement(104756823..105029341)
                     /gene="SRPK2"
                     /gene_synonym="FLJ36101; SFRSK2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6733"
                     /db_xref="HGNC:11306"
                     /db_xref="MIM:602980"
     mRNA            complement(join(104756823..104758469,104766695..104766787,
                     104767440..104767509,104773238..104773345,
                     104773451..104773551,104782455..104782937,
                     104783531..104783777,104785730..104785755,
                     104786940..104787105,104800954..104801060,
                     104807824..104807911,104808455..104808542,
                     104809604..104809712,104844075..104844232,
                     105029095..105029149,105029238..105029341))
                     /gene="SRPK2"
                     /gene_synonym="FLJ36101; SFRSK2"
                     /product="SRSF protein kinase 2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182692.1"
                     /db_xref="GI:33188448"
                     /db_xref="GeneID:6733"
                     /db_xref="HGNC:11306"
                     /db_xref="HPRD:04280"
                     /db_xref="MIM:602980"
     mRNA            complement(join(104756823..104758469,104766695..104766787,
                     104767440..104767509,104773238..104773345,
                     104773451..104773551,104782455..104782937,
                     104783531..104783777,104785730..104785755,
                     104786940..104787105,104800954..104801060,
                     104807824..104807911,104808455..104808542,
                     104809604..104809712,104844075..104844232,
                     104909253..104909477))
                     /gene="SRPK2"
                     /gene_synonym="FLJ36101; SFRSK2"
                     /product="SRSF protein kinase 2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182691.1"
                     /db_xref="GI:33188446"
                     /db_xref="GeneID:6733"
                     /db_xref="HGNC:11306"
                     /db_xref="MIM:602980"
     CDS             complement(join(104758285..104758469,104766695..104766787,
                     104767440..104767509,104773238..104773345,
                     104773451..104773551,104782455..104782937,
                     104783531..104783777,104785730..104785755,
                     104786940..104787105,104800954..104801060,
                     104807824..104807911,104808455..104808542,
                     104809604..104809712,104844075..104844232,
                     105029095..105029149,105029238..105029253))
                     /gene="SRPK2"
                     /gene_synonym="FLJ36101; SFRSK2"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="serine/threonine-protein kinase SRPK2 isoform a"
                     /protein_id="NP_872634.1"
                     /db_xref="GI:33188449"
                     /db_xref="CCDS:CCDS34724.1"
                     /db_xref="GeneID:6733"
                     /db_xref="HGNC:11306"
                     /db_xref="MIM:602980"
     CDS             complement(join(104758285..104758469,104766695..104766787,
                     104767440..104767509,104773238..104773345,
                     104773451..104773551,104782455..104782937,
                     104783531..104783777,104785730..104785755,
                     104786940..104787105,104800954..104801060,
                     104807824..104807911,104808455..104808542,
                     104809604..104809712,104844075..104844232,
                     104909253..104909290))
                     /gene="SRPK2"
                     /gene_synonym="FLJ36101; SFRSK2"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="serine/threonine-protein kinase SRPK2 isoform b"
                     /protein_id="NP_872633.1"
                     /db_xref="GI:33188447"
                     /db_xref="CCDS:CCDS5735.1"
                     /db_xref="GeneID:6733"
                     /db_xref="HGNC:11306"
                     /db_xref="MIM:602980"
     gene            104885036..104885462
                     /gene="RPL36P12"
                     /gene_synonym="RPL36_4_831"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271012"
                     /db_xref="HGNC:35590"
     gene            104941969..104942530
                     /gene="RWDD4P1"
                     /gene_synonym="FAM28BP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419903"
                     /db_xref="HGNC:23753"
     gene            complement(105096958..105162685)
                     /gene="PUS7"
                     /gene_synonym="FLJ20485; KIAA1897; MGC17720"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54517"
                     /db_xref="HGNC:26033"
                     /db_xref="HPRD:07914"
     mRNA            complement(join(105096958..105098373,105099615..105099706,
                     105103068..105103197,105105760..105105861,
                     105108784..105108910,105111135..105111295,
                     105112579..105112640,105121499..105121624,
                     105122759..105122887,105131987..105132064,
                     105135589..105135700,105142867..105143011,
                     105146402..105146503,105146636..105146720,
                     105148562..105148991,105162499..105162685))
                     /gene="PUS7"
                     /gene_synonym="FLJ20485; KIAA1897; MGC17720"
                     /product="pseudouridylate synthase 7 homolog (S.
                     cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_019042.3"
                     /db_xref="GI:50727001"
                     /db_xref="GeneID:54517"
                     /db_xref="HGNC:26033"
                     /db_xref="HPRD:07914"
     CDS             complement(join(105098237..105098373,105099615..105099706,
                     105103068..105103197,105105760..105105861,
                     105108784..105108910,105111135..105111295,
                     105112579..105112640,105121499..105121624,
                     105122759..105122887,105131987..105132064,
                     105135589..105135700,105142867..105143011,
                     105146402..105146503,105146636..105146720,
                     105148562..105148959))
                     /gene="PUS7"
                     /gene_synonym="FLJ20485; KIAA1897; MGC17720"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="pseudouridylate synthase 7 homolog"
                     /protein_id="NP_061915.2"
                     /db_xref="GI:50727002"
                     /db_xref="CCDS:CCDS34725.1"
                     /db_xref="GeneID:54517"
                     /db_xref="HGNC:26033"
                     /db_xref="HPRD:07914"
     gene            105148570..105162689
                     /gene="LOC100652896"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 10 ESTs"
                     /db_xref="GeneID:100652896"
     misc_RNA        join(105148570..105148993,105149086..105149089,
                     105162505..105162689)
                     /gene="LOC100652896"
                     /product="hypothetical LOC100652896"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 10 ESTs"
                     /transcript_id="XR_132542.1"
                     /db_xref="GI:341915405"
                     /db_xref="GeneID:100652896"
     gene            105170656..105171118
                     /gene="LOC100131785"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /pseudo
                     /db_xref="GeneID:100131785"
     exon            105170656..105171118
                     /gene="LOC100131785"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100131785"
     gene            105172532..105208124
                     /gene="RINT1"
                     /gene_synonym="DKFZp667H2324; RINT-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:60561"
                     /db_xref="HGNC:21876"
                     /db_xref="HPRD:15250"
                     /db_xref="MIM:610089"
     mRNA            join(105172532..105172804,105173271..105173316,
                     105177012..105177196,105182855..105183096,
                     105187357..105187530,105187631..105187780,
                     105189001..105189157,105190502..105190612,
                     105190708..105190933,105192017..105192154,
                     105195475..105195674,105204180..105204394,
                     105205724..105205904,105205977..105206095,
                     105207566..105208124)
                     /gene="RINT1"
                     /gene_synonym="DKFZp667H2324; RINT-1"
                     /product="RAD50 interactor 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021930.4"
                     /db_xref="GI:142370362"
                     /db_xref="GeneID:60561"
                     /db_xref="HGNC:21876"
                     /db_xref="HPRD:15250"
                     /db_xref="MIM:610089"
     CDS             join(105172763..105172804,105173271..105173316,
                     105177012..105177196,105182855..105183096,
                     105187357..105187530,105187631..105187780,
                     105189001..105189157,105190502..105190612,
                     105190708..105190933,105192017..105192154,
                     105195475..105195674,105204180..105204394,
                     105205724..105205904,105205977..105206095,
                     105207566..105207758)
                     /gene="RINT1"
                     /gene_synonym="DKFZp667H2324; RINT-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="RAD50-interacting protein 1"
                     /protein_id="NP_068749.3"
                     /db_xref="GI:62899047"
                     /db_xref="CCDS:CCDS34726.1"
                     /db_xref="GeneID:60561"
                     /db_xref="HGNC:21876"
                     /db_xref="HPRD:15250"
                     /db_xref="MIM:610089"
     gene            complement(105205580..105221976)
                     /gene="EFCAB10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100130771"
                     /db_xref="HGNC:34531"
     misc_RNA        complement(join(105205580..105205894,105207914..105207937,
                     105209650..105209737,105209854..105210018,
                     105221805..105221976))
                     /gene="EFCAB10"
                     /product="EF-hand calcium binding domain 10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027068.1"
                     /db_xref="GI:224458299"
                     /db_xref="GeneID:100130771"
                     /db_xref="HGNC:34531"
     gene            complement(105222302..105223854)
                     /gene="YBX1P2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:646531"
                     /db_xref="HGNC:22635"
     gene            complement(105245221..105517031)
                     /gene="ATXN7L1"
                     /gene_synonym="ATXN7L4; FLJ40255; FLJ58242; KIAA1218;
                     MGC10760; MGC33190"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222255"
                     /db_xref="HGNC:22210"
                     /db_xref="HPRD:12508"
     mRNA            complement(join(105245221..105248337,105250976..105251050,
                     105254309..105255263,105260647..105260768,
                     105264522..105264714,105278800..105279056,
                     105279934..105280016,105283285..105283568,
                     105305513..105305735,105429050..105429154,
                     105516258..105516326,105516824..105517031))
                     /gene="ATXN7L1"
                     /gene_synonym="ATXN7L4; FLJ40255; FLJ58242; KIAA1218;
                     MGC10760; MGC33190"
                     /product="ataxin 7-like 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020725.1"
                     /db_xref="GI:163937853"
                     /db_xref="GeneID:222255"
                     /db_xref="HGNC:22210"
                     /db_xref="HPRD:12508"
     mRNA            complement(join(105245221..105248340,105250976..105251050,
                     105254309..105255263,105260647..105260768,
                     105264522..105264714,105278800..105279056,
                     105279934..105280016,105283285..105283568,
                     105305513..105305735,105319499..105319609))
                     /gene="ATXN7L1"
                     /gene_synonym="ATXN7L4; FLJ40255; FLJ58242; KIAA1218;
                     MGC10760; MGC33190"
                     /product="ataxin 7-like 1, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138495.1"
                     /db_xref="GI:211971079"
                     /db_xref="GeneID:222255"
                     /db_xref="HGNC:22210"
                     /db_xref="HPRD:12508"
     CDS             complement(join(105248299..105248337,105250976..105251050,
                     105254309..105255263,105260647..105260768,
                     105264522..105264714,105278800..105279056,
                     105279934..105280016,105283285..105283568,
                     105305513..105305735,105429050..105429154,
                     105516258..105516326,105516824..105517004))
                     /gene="ATXN7L1"
                     /gene_synonym="ATXN7L4; FLJ40255; FLJ58242; KIAA1218;
                     MGC10760; MGC33190"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ataxin-7-like protein 1 isoform 1"
                     /protein_id="NP_065776.1"
                     /db_xref="GI:163937854"
                     /db_xref="CCDS:CCDS47682.1"
                     /db_xref="GeneID:222255"
                     /db_xref="HGNC:22210"
                     /db_xref="HPRD:12508"
     CDS             complement(join(105248299..105248340,105250976..105251050,
                     105254309..105255263,105260647..105260768,
                     105264522..105264714,105278800..105279056,
                     105279934..105280016,105283285..105283568,
                     105305513..105305718))
                     /gene="ATXN7L1"
                     /gene_synonym="ATXN7L4; FLJ40255; FLJ58242; KIAA1218;
                     MGC10760; MGC33190"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ataxin-7-like protein 1 isoform 3"
                     /protein_id="NP_612504.1"
                     /db_xref="GI:211971080"
                     /db_xref="CCDS:CCDS47683.1"
                     /db_xref="GeneID:222255"
                     /db_xref="HGNC:22210"
                     /db_xref="HPRD:12508"
     mRNA            complement(join(105400636..105401909,105429050..105429154,
                     105516258..105516326,105516824..105517031))
                     /gene="ATXN7L1"
                     /gene_synonym="ATXN7L4; FLJ40255; FLJ58242; KIAA1218;
                     MGC10760; MGC33190"
                     /product="ataxin 7-like 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152749.3"
                     /db_xref="GI:163937852"
                     /db_xref="GeneID:222255"
                     /db_xref="HGNC:22210"
                     /db_xref="HPRD:12508"
     CDS             complement(join(105401824..105401909,105429050..105429154,
                     105516258..105516326,105516824..105517004))
                     /gene="ATXN7L1"
                     /gene_synonym="ATXN7L4; FLJ40255; FLJ58242; KIAA1218;
                     MGC10760; MGC33190"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ataxin-7-like protein 1 isoform 2"
                     /protein_id="NP_689962.1"
                     /db_xref="GI:23308753"
                     /db_xref="CCDS:CCDS34727.1"
                     /db_xref="GeneID:222255"
                     /db_xref="HGNC:22210"
                     /db_xref="HPRD:12508"
     gene            105459938..105460573
                     /gene="RPL13AP16"
                     /gene_synonym="RPL13A_7_832"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129553"
                     /db_xref="HGNC:35722"
     gene            105517079..105530577
                     /gene="LOC100652903"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 5 ESTs"
                     /db_xref="GeneID:100652903"
     misc_RNA        join(105517079..105517703,105518653..105518804,
                     105520091..105520523,105529972..105530577)
                     /gene="LOC100652903"
                     /product="hypothetical LOC100652903"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 5 ESTs"
                     /transcript_id="XR_132543.1"
                     /db_xref="GI:341915406"
                     /db_xref="GeneID:100652903"
     gene            105603657..105676877
                     /gene="CDHR3"
                     /gene_synonym="CDH28; FLJ23834; FLJ43271; MGC133292;
                     MGC133293"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:222256"
                     /db_xref="HGNC:26308"
                     /db_xref="HPRD:08042"
     mRNA            join(105603657..105603810,105615290..105615492,
                     105621414..105621579,105624638..105624735,
                     105635197..105635291,105636696..105636800,
                     105641908..105642056,105644944..105645133,
                     105653306..105653477,105655557..105655659,
                     105656373..105656471,105658292..105658518,
                     105660819..105660990,105662644..105662894,
                     105664827..105665008,105667128..105667141,
                     105668997..105669028,105671238..105671286,
                     105672839..105676877)
                     /gene="CDHR3"
                     /gene_synonym="CDH28; FLJ23834; FLJ43271; MGC133292;
                     MGC133293"
                     /product="cadherin-related family member 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152750.4"
                     /db_xref="GI:194018461"
                     /db_xref="GeneID:222256"
                     /db_xref="HGNC:26308"
                     /db_xref="HPRD:08042"
     CDS             join(105603765..105603810,105615290..105615492,
                     105621414..105621579,105624638..105624735,
                     105635197..105635291,105636696..105636800,
                     105641908..105642056,105644944..105645133,
                     105653306..105653477,105655557..105655659,
                     105656373..105656471,105658292..105658518,
                     105660819..105660990,105662644..105662894,
                     105664827..105665008,105667128..105667141,
                     105668997..105669028,105671238..105671286,
                     105672839..105673143)
                     /gene="CDHR3"
                     /gene_synonym="CDH28; FLJ23834; FLJ43271; MGC133292;
                     MGC133293"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cadherin-related family member 3 precursor"
                     /protein_id="NP_689963.2"
                     /db_xref="GI:40255133"
                     /db_xref="CCDS:CCDS47684.1"
                     /db_xref="GeneID:222256"
                     /db_xref="HGNC:26308"
                     /db_xref="HPRD:08042"
     gene            complement(105730951..105753057)
                     /gene="SYPL1"
                     /gene_synonym="H-SP1; SYPL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6856"
                     /db_xref="HGNC:11507"
                     /db_xref="HPRD:15459"
     mRNA            complement(join(105730951..105732385,105733395..105733583,
                     105738136..105738343,105739604..105739728,
                     105752586..105752657,105752925..105753057))
                     /gene="SYPL1"
                     /gene_synonym="H-SP1; SYPL"
                     /product="synaptophysin-like 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006754.2"
                     /db_xref="GI:33239441"
                     /db_xref="GeneID:6856"
                     /db_xref="HGNC:11507"
                     /db_xref="HPRD:15459"
     mRNA            complement(join(105730951..105732385,105733395..105733583,
                     105738136..105738343,105739604..105739728,
                     105752586..105752758))
                     /gene="SYPL1"
                     /gene_synonym="H-SP1; SYPL"
                     /product="synaptophysin-like 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182715.1"
                     /db_xref="GI:33239442"
                     /db_xref="GeneID:6856"
                     /db_xref="HGNC:11507"
                     /db_xref="HPRD:15459"
     CDS             complement(join(105732251..105732385,105733395..105733583,
                     105738136..105738343,105739604..105739728,
                     105752586..105752657,105752925..105752975))
                     /gene="SYPL1"
                     /gene_synonym="H-SP1; SYPL"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="synaptophysin-like protein 1 isoform a"
                     /protein_id="NP_006745.1"
                     /db_xref="GI:5803185"
                     /db_xref="CCDS:CCDS5736.1"
                     /db_xref="GeneID:6856"
                     /db_xref="HGNC:11507"
                     /db_xref="HPRD:15459"
     CDS             complement(join(105732251..105732385,105733395..105733583,
                     105738136..105738343,105739604..105739728,
                     105752586..105752654))
                     /gene="SYPL1"
                     /gene_synonym="H-SP1; SYPL"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="synaptophysin-like protein 1 isoform b"
                     /protein_id="NP_874384.1"
                     /db_xref="GI:33239443"
                     /db_xref="CCDS:CCDS47685.1"
                     /db_xref="GeneID:6856"
                     /db_xref="HGNC:11507"
                     /db_xref="HPRD:15459"
     gene            105765777..105768341
                     /gene="LOC100129009"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129009"
     gene            105877311..105891391
                     /gene="LOC100509105"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /db_xref="GeneID:100509105"
     misc_RNA        join(105877311..105877320,105879939..105879942,
                     105890759..105891391)
                     /gene="LOC100509105"
                     /product="hypothetical LOC100509105"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_132544.1"
                     /db_xref="GI:341915407"
                     /db_xref="GeneID:100509105"
     gene            complement(105888731..105925638)
                     /gene="NAMPT"
                     /gene_synonym="1110035O14Rik; DKFZp666B131; MGC117256;
                     PBEF; PBEF1; VF; VISFATIN"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10135"
                     /db_xref="HGNC:30092"
                     /db_xref="HPRD:09938"
                     /db_xref="MIM:608764"
     mRNA            complement(join(105888731..105891639,105893463..105893597,
                     105894810..105894950,105902034..105902153,
                     105903838..105904063,105908910..105909046,
                     105909600..105909758,105912976..105913104,
                     105915392..105915495,105917469..105917625,
                     105925274..105925638))
                     /gene="NAMPT"
                     /gene_synonym="1110035O14Rik; DKFZp666B131; MGC117256;
                     PBEF; PBEF1; VF; VISFATIN"
                     /product="nicotinamide phosphoribosyltransferase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005746.2"
                     /db_xref="GI:111161293"
                     /db_xref="GeneID:10135"
                     /db_xref="HGNC:30092"
                     /db_xref="HPRD:09938"
                     /db_xref="MIM:608764"
     CDS             complement(join(105891529..105891639,105893463..105893597,
                     105894810..105894950,105902034..105902153,
                     105903838..105904063,105908910..105909046,
                     105909600..105909758,105912976..105913104,
                     105915392..105915495,105917469..105917625,
                     105925274..105925330))
                     /gene="NAMPT"
                     /gene_synonym="1110035O14Rik; DKFZp666B131; MGC117256;
                     PBEF; PBEF1; VF; VISFATIN"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="nicotinamide phosphoribosyltransferase
                     precursor"
                     /protein_id="NP_005737.1"
                     /db_xref="GI:5031977"
                     /db_xref="CCDS:CCDS5737.1"
                     /db_xref="GeneID:10135"
                     /db_xref="HGNC:30092"
                     /db_xref="HPRD:09938"
                     /db_xref="MIM:608764"
     gene            complement(106297211..106301634)
                     /gene="FLJ36031"
                     /gene_synonym="FLJ11436; FLJ25556; MGC16181"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:168455"
                     /db_xref="HPRD:08202"
     mRNA            complement(106297211..106301634)
                     /gene="FLJ36031"
                     /gene_synonym="FLJ11436; FLJ25556; MGC16181"
                     /product="hypothetical protein FLJ36031"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_175884.4"
                     /db_xref="GI:315583016"
                     /db_xref="GeneID:168455"
                     /db_xref="HPRD:08202"
     CDS             complement(106300635..106301342)
                     /gene="FLJ36031"
                     /gene_synonym="FLJ11436; FLJ25556; MGC16181"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC168455"
                     /protein_id="NP_787080.2"
                     /db_xref="GI:57242766"
                     /db_xref="CCDS:CCDS55151.1"
                     /db_xref="GeneID:168455"
                     /db_xref="HPRD:08202"
     gene            106505924..106547592
                     /gene="PIK3CG"
                     /gene_synonym="PI3CG; PI3K; PI3Kgamma; PIK3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5294"
                     /db_xref="HGNC:8978"
                     /db_xref="HPRD:03135"
                     /db_xref="MIM:601232"
     mRNA            join(106505924..106506221,106507995..106510001,
                     106512982..106513047,106513158..106513383,
                     106515145..106515248,106519964..106520110,
                     106522562..106522652,106523478..106523608,
                     106524600..106524711,106526580..106526737,
                     106545554..106547592)
                     /gene="PIK3CG"
                     /gene_synonym="PI3CG; PI3K; PI3Kgamma; PIK3"
                     /product="phosphoinositide-3-kinase, catalytic, gamma
                     polypeptide"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002649.2"
                     /db_xref="GI:21237724"
                     /db_xref="GeneID:5294"
                     /db_xref="HGNC:8978"
                     /db_xref="HPRD:03135"
                     /db_xref="MIM:601232"
     CDS             join(106508007..106510001,106512982..106513047,
                     106513158..106513383,106515145..106515248,
                     106519964..106520110,106522562..106522652,
                     106523478..106523608,106524600..106524711,
                     106526580..106526737,106545554..106545832)
                     /gene="PIK3CG"
                     /gene_synonym="PI3CG; PI3K; PI3Kgamma; PIK3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="phosphatidylinositol-4,5-bisphosphate 3-kinase
                     catalytic subunit gamma isoform"
                     /protein_id="NP_002640.2"
                     /db_xref="GI:21237725"
                     /db_xref="CCDS:CCDS5739.1"
                     /db_xref="GeneID:5294"
                     /db_xref="HGNC:8978"
                     /db_xref="HPRD:03135"
                     /db_xref="MIM:601232"
     gene            106685178..106802256
                     /gene="PRKAR2B"
                     /gene_synonym="PRKAR2; RII-BETA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5577"
                     /db_xref="HGNC:9392"
                     /db_xref="HPRD:01486"
                     /db_xref="MIM:176912"
     mRNA            join(106685178..106685659,106710726..106710761,
                     106762397..106762449,106768657..106768740,
                     106781292..106781398,106786753..106786906,
                     106791367..106791468,106793622..106793696,
                     106797429..106797494,106797631..106797769,
                     106799894..106802256)
                     /gene="PRKAR2B"
                     /gene_synonym="PRKAR2; RII-BETA"
                     /product="protein kinase, cAMP-dependent, regulatory, type
                     II, beta"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002736.2"
                     /db_xref="GI:47132584"
                     /db_xref="GeneID:5577"
                     /db_xref="HGNC:9392"
                     /db_xref="HPRD:01486"
                     /db_xref="MIM:176912"
     CDS             join(106685353..106685659,106710726..106710761,
                     106762397..106762449,106768657..106768740,
                     106781292..106781398,106786753..106786906,
                     106791367..106791468,106793622..106793696,
                     106797429..106797494,106797631..106797769,
                     106799894..106800027)
                     /gene="PRKAR2B"
                     /gene_synonym="PRKAR2; RII-BETA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cAMP-dependent protein kinase type II-beta
                     regulatory subunit"
                     /protein_id="NP_002727.2"
                     /db_xref="GI:47132585"
                     /db_xref="CCDS:CCDS5740.1"
                     /db_xref="GeneID:5577"
                     /db_xref="HGNC:9392"
                     /db_xref="HPRD:01486"
                     /db_xref="MIM:176912"
     gene            106809460..106842974
                     /gene="HBP1"
                     /gene_synonym="FLJ16340"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26959"
                     /db_xref="HGNC:23200"
                     /db_xref="HPRD:13634"
     mRNA            join(106809460..106809630,106820324..106820507,
                     106822818..106823046,106826246..106826387,
                     106826806..106826917,106827014..106827126,
                     106829737..106829893,106830618..106830762,
                     106836279..106836596,106840605..106840746,
                     106841859..106842974)
                     /gene="HBP1"
                     /gene_synonym="FLJ16340"
                     /product="HMG-box transcription factor 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012257.3"
                     /db_xref="GI:47834345"
                     /db_xref="GeneID:26959"
                     /db_xref="HGNC:23200"
                     /db_xref="HPRD:13634"
     gene            106810212..106815649
                     /gene="LOC100506312"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 11 ESTs"
                     /db_xref="GeneID:100506312"
     misc_RNA        join(106810212..106810575,106814893..106815649)
                     /gene="LOC100506312"
                     /product="hypothetical LOC100506312"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 11 ESTs"
                     /transcript_id="XR_108794.2"
                     /db_xref="GI:341915408"
                     /db_xref="GeneID:100506312"
     CDS             join(106820339..106820507,106822818..106823046,
                     106826246..106826387,106826806..106826917,
                     106827014..106827126,106829737..106829893,
                     106830618..106830762,106836279..106836596,
                     106840605..106840746,106841859..106841876)
                     /gene="HBP1"
                     /gene_synonym="FLJ16340"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="HMG box-containing protein 1"
                     /protein_id="NP_036389.2"
                     /db_xref="GI:21361411"
                     /db_xref="CCDS:CCDS5741.1"
                     /db_xref="GeneID:26959"
                     /db_xref="HGNC:23200"
                     /db_xref="HPRD:13634"
     gene            complement(106842189..107204959)
                     /gene="COG5"
                     /gene_synonym="CDG2I; FLJ41732; FLJ44289; GOLTC1; GTC90"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10466"
                     /db_xref="HGNC:14857"
                     /db_xref="HPRD:08436"
                     /db_xref="MIM:606821"
     mRNA            complement(join(106842189..106844075,106850971..106851050,
                     106851544..106851670,106871060..106871136,
                     106876895..106877132,106888841..106888944,
                     106897177..106897239,106898718..106898828,
                     106921745..106921844,106924016..106924177,
                     106938587..106938791,106964885..106964966,
                     107002478..107002555,107002753..107002865,
                     107013040..107013205,107052947..107053077,
                     107167682..107167802,107188556..107188625,
                     107188723..107188777,107194730..107194787,
                     107198421..107198560,107204248..107204959))
                     /gene="COG5"
                     /gene_synonym="CDG2I; FLJ41732; FLJ44289; GOLTC1; GTC90"
                     /product="component of oligomeric golgi complex 5,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006348.3"
                     /db_xref="GI:240849530"
                     /db_xref="GeneID:10466"
                     /db_xref="HGNC:14857"
                     /db_xref="HPRD:08436"
                     /db_xref="MIM:606821"
     mRNA            complement(join(106842189..106844075,106850971..106851050,
                     106851544..106851670,106871060..106871136,
                     106876895..106877132,106888841..106888944,
                     106898718..106898828,106921745..106921844,
                     106924016..106924177,106938587..106938791,
                     106964885..106964966,107002478..107002555,
                     107002753..107002865,107013040..107013205,
                     107052947..107053077,107167682..107167802,
                     107188556..107188625,107188723..107188777,
                     107194730..107194787,107198421..107198560,
                     107204248..107204959))
                     /gene="COG5"
                     /gene_synonym="CDG2I; FLJ41732; FLJ44289; GOLTC1; GTC90"
                     /product="component of oligomeric golgi complex 5,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_181733.2"
                     /db_xref="GI:240849536"
                     /db_xref="GeneID:10466"
                     /db_xref="HGNC:14857"
                     /db_xref="MIM:606821"
                     /db_xref="HPRD:08436"
     CDS             complement(join(106843961..106844075,106850971..106851050,
                     106851544..106851670,106871060..106871136,
                     106876895..106877132,106888841..106888944,
                     106897177..106897239,106898718..106898828,
                     106921745..106921844,106924016..106924177,
                     106938587..106938791,106964885..106964966,
                     107002478..107002555,107002753..107002865,
                     107013040..107013205,107052947..107053077,
                     107167682..107167802,107188556..107188625,
                     107188723..107188777,107194730..107194787,
                     107198421..107198560,107204248..107204434))
                     /gene="COG5"
                     /gene_synonym="CDG2I; FLJ41732; FLJ44289; GOLTC1; GTC90"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="conserved oligomeric Golgi complex subunit 5
                     isoform 1"
                     /protein_id="NP_006339.3"
                     /db_xref="GI:240849531"
                     /db_xref="CCDS:CCDS5742.1"
                     /db_xref="GeneID:10466"
                     /db_xref="HGNC:14857"
                     /db_xref="HPRD:08436"
                     /db_xref="MIM:606821"
     CDS             complement(join(106843961..106844075,106850971..106851050,
                     106851544..106851670,106871060..106871136,
                     106876895..106877132,106888841..106888944,
                     106898718..106898828,106921745..106921844,
                     106924016..106924177,106938587..106938791,
                     106964885..106964966,107002478..107002555,
                     107002753..107002865,107013040..107013205,
                     107052947..107053077,107167682..107167802,
                     107188556..107188625,107188723..107188777,
                     107194730..107194787,107198421..107198560,
                     107204248..107204434))
                     /gene="COG5"
                     /gene_synonym="CDG2I; FLJ41732; FLJ44289; GOLTC1; GTC90"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="conserved oligomeric Golgi complex subunit 5
                     isoform 2"
                     /protein_id="NP_859422.2"
                     /db_xref="GI:240849537"
                     /db_xref="CCDS:CCDS5743.1"
                     /db_xref="GeneID:10466"
                     /db_xref="HGNC:14857"
                     /db_xref="HPRD:08436"
                     /db_xref="MIM:606821"
     mRNA            complement(join(106848298..106851050,106851544..106851670,
                     106871060..106871136,106876895..106877132,
                     106888841..106888944,106897177..106897239,
                     106898718..106898828,106921745..106921844,
                     106924016..106924177,106938587..106938791,
                     106964885..106964966,107002478..107002555,
                     107002753..107002865,107013040..107013205,
                     107052947..107053077,107167682..107167802,
                     107188556..107188625,107188723..107188777,
                     107194730..107194787,107198421..107198560,
                     107204248..107204959))
                     /gene="COG5"
                     /gene_synonym="CDG2I; FLJ41732; FLJ44289; GOLTC1; GTC90"
                     /product="component of oligomeric golgi complex 5,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001161520.1"
                     /db_xref="GI:240849566"
                     /db_xref="GeneID:10466"
                     /db_xref="HGNC:14857"
                     /db_xref="MIM:606821"
                     /db_xref="HPRD:08436"
     CDS             complement(join(106850967..106851050,106851544..106851670,
                     106871060..106871136,106876895..106877132,
                     106888841..106888944,106897177..106897239,
                     106898718..106898828,106921745..106921844,
                     106924016..106924177,106938587..106938791,
                     106964885..106964966,107002478..107002555,
                     107002753..107002865,107013040..107013205,
                     107052947..107053077,107167682..107167802,
                     107188556..107188625,107188723..107188777,
                     107194730..107194787,107198421..107198560,
                     107204248..107204434))
                     /gene="COG5"
                     /gene_synonym="CDG2I; FLJ41732; FLJ44289; GOLTC1; GTC90"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="conserved oligomeric Golgi complex subunit 5
                     isoform 3"
                     /protein_id="NP_001154992.1"
                     /db_xref="GI:240849567"
                     /db_xref="CCDS:CCDS55152.1"
                     /db_xref="GeneID:10466"
                     /db_xref="HGNC:14857"
                     /db_xref="HPRD:08436"
                     /db_xref="MIM:606821"
     gene            107090535..107090807
                     /gene="RPL37AP6"
                     /gene_synonym="RPL37A_3_833"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271339"
                     /db_xref="HGNC:36824"
     gene            107110502..107116125
                     /gene="GPR22"
                     /gene_synonym="MGC129847"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2845"
                     /db_xref="HGNC:4477"
                     /db_xref="HPRD:03552"
                     /db_xref="MIM:601910"
     mRNA            join(107110502..107110890,107111817..107112747,
                     107114480..107116125)
                     /gene="GPR22"
                     /gene_synonym="MGC129847"
                     /product="G protein-coupled receptor 22"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005295.2"
                     /db_xref="GI:91106201"
                     /db_xref="GeneID:2845"
                     /db_xref="HGNC:4477"
                     /db_xref="HPRD:03552"
                     /db_xref="MIM:601910"
     CDS             107114506..107115807
                     /gene="GPR22"
                     /gene_synonym="MGC129847"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable G-protein coupled receptor 22"
                     /protein_id="NP_005286.2"
                     /db_xref="GI:91106202"
                     /db_xref="CCDS:CCDS5744.1"
                     /db_xref="GeneID:2845"
                     /db_xref="HGNC:4477"
                     /db_xref="HPRD:03552"
                     /db_xref="MIM:601910"
     gene            107204432..107218968
                     /gene="DUS4L"
                     /gene_synonym="DUS4; MGC133233; PP35"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:11062"
                     /db_xref="HGNC:21517"
                     /db_xref="HPRD:17886"
     mRNA            join(107204432..107204654,107205033..107205121,
                     107207495..107207631,107211590..107211711,
                     107214149..107214266,107215633..107215755,
                     107216811..107217037,107217758..107218968)
                     /gene="DUS4L"
                     /gene_synonym="DUS4; MGC133233; PP35"
                     /product="dihydrouridine synthase 4-like (S. cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_181581.1"
                     /db_xref="GI:31742495"
                     /db_xref="GeneID:11062"
                     /db_xref="HGNC:21517"
                     /db_xref="HPRD:17886"
     CDS             join(107207516..107207631,107211590..107211711,
                     107214149..107214266,107215633..107215755,
                     107216811..107217037,107217758..107218005)
                     /gene="DUS4L"
                     /gene_synonym="DUS4; MGC133233; PP35"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="tRNA-dihydrouridine synthase 4-like"
                     /protein_id="NP_853559.1"
                     /db_xref="GI:31742496"
                     /db_xref="CCDS:CCDS5745.1"
                     /db_xref="GeneID:11062"
                     /db_xref="HGNC:21517"
                     /db_xref="HPRD:17886"
     gene            107220422..107263762
                     /gene="BCAP29"
                     /gene_synonym="BAP29; DKFZp686M2086; FLJ53907"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55973"
                     /db_xref="HGNC:24131"
                     /db_xref="HPRD:16541"
     mRNA            join(107220422..107220746,107221204..107221309,
                     107224327..107224427,107234400..107234550,
                     107236312..107236447,107240842..107240950,
                     107253777..107253877,107258773..107263762)
                     /gene="BCAP29"
                     /gene_synonym="BAP29; DKFZp686M2086; FLJ53907"
                     /product="B-cell receptor-associated protein 29,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018844.3"
                     /db_xref="GI:240255593"
                     /db_xref="GeneID:55973"
                     /db_xref="HGNC:24131"
                     /db_xref="HPRD:16541"
     misc_RNA        join(107220422..107220746,107224327..107224427,
                     107234400..107234550,107236312..107236447,
                     107240842..107240950,107253777..107253877,
                     107258773..107263762)
                     /gene="BCAP29"
                     /gene_synonym="BAP29; DKFZp686M2086; FLJ53907"
                     /product="B-cell receptor-associated protein 29,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027830.1"
                     /db_xref="GI:240255595"
                     /db_xref="GeneID:55973"
                     /db_xref="HGNC:24131"
                     /db_xref="HPRD:16541"
     mRNA            join(107221204..107221309,107224327..107224427,
                     107234400..107234550,107236312..107236447,
                     107240842..107240950,107253777..107253877,
                     107254099..107254177,107258773..107263762)
                     /gene="BCAP29"
                     /gene_synonym="BAP29; DKFZp686M2086; FLJ53907"
                     /product="B-cell receptor-associated protein 29,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001008405.2"
                     /db_xref="GI:240255594"
                     /db_xref="GeneID:55973"
                     /db_xref="HGNC:24131"
                     /db_xref="HPRD:16541"
     CDS             join(107221218..107221309,107224327..107224427,
                     107234400..107234550,107236312..107236447,
                     107240842..107240950,107253777..107253877,
                     107254099..107254177,107258773..107259050)
                     /gene="BCAP29"
                     /gene_synonym="BAP29; DKFZp686M2086; FLJ53907"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="B-cell receptor-associated protein 29 isoform a"
                     /protein_id="NP_001008405.1"
                     /db_xref="GI:56549093"
                     /db_xref="CCDS:CCDS34730.1"
                     /db_xref="GeneID:55973"
                     /db_xref="HGNC:24131"
                     /db_xref="HPRD:16541"
     CDS             join(107221218..107221309,107224327..107224427,
                     107234400..107234550,107236312..107236447,
                     107240842..107240950,107253777..107253877,
                     107258773..107258808)
                     /gene="BCAP29"
                     /gene_synonym="BAP29; DKFZp686M2086; FLJ53907"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="B-cell receptor-associated protein 29 isoform b"
                     /protein_id="NP_061332.2"
                     /db_xref="GI:56549091"
                     /db_xref="CCDS:CCDS34731.1"
                     /db_xref="GeneID:55973"
                     /db_xref="HGNC:24131"
                     /db_xref="HPRD:16541"
     gene            107268911..107269992
                     /gene="LOC100506330"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100506330"
     gene            complement(107283205..107283466)
                     /gene="LOC100287065"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /pseudo
                     /db_xref="GeneID:100287065"
     exon            complement(107283205..107283466)
                     /gene="LOC100287065"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 Proteins"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100287065"
     gene            complement(107296961..107302243)
                     /gene="LOC286002"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:286002"
     misc_RNA        complement(join(107296961..107300651,
                     107302047..107302243))
                     /gene="LOC286002"
                     /product="hypothetical LOC286002"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_028137.1"
                     /db_xref="GI:254939574"
                     /db_xref="GeneID:286002"
     gene            107301080..107358254
                     /gene="SLC26A4"
                     /gene_synonym="DFNB4; EVA; PDS; TDH2B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5172"
                     /db_xref="HGNC:8818"
                     /db_xref="HPRD:05735"
                     /db_xref="MIM:605646"
     mRNA            join(107301080..107301300,107302084..107302250,
                     107303741..107303880,107312583..107312693,
                     107314609..107314793,107315390..107315554,
                     107323647..107323799,107323900..107323982,
                     107329498..107329645,107330569..107330682,
                     107334848..107334925,107335066..107335161,
                     107336378..107336484,107338487..107338556,
                     107340528..107340620,107341546..107341641,
                     107342272..107342502,107344776..107344830,
                     107350499..107350644,107352984..107353067,
                     107355868..107358254)
                     /gene="SLC26A4"
                     /gene_synonym="DFNB4; EVA; PDS; TDH2B"
                     /product="solute carrier family 26, member 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000441.1"
                     /db_xref="GI:4505696"
                     /db_xref="GeneID:5172"
                     /db_xref="HGNC:8818"
                     /db_xref="HPRD:05735"
                     /db_xref="MIM:605646"
     CDS             join(107302087..107302250,107303741..107303880,
                     107312583..107312693,107314609..107314793,
                     107315390..107315554,107323647..107323799,
                     107323900..107323982,107329498..107329645,
                     107330569..107330682,107334848..107334925,
                     107335066..107335161,107336378..107336484,
                     107338487..107338556,107340528..107340620,
                     107341546..107341641,107342272..107342502,
                     107344776..107344830,107350499..107350644,
                     107352984..107353067,107355868..107355891)
                     /gene="SLC26A4"
                     /gene_synonym="DFNB4; EVA; PDS; TDH2B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="pendrin"
                     /protein_id="NP_000432.1"
                     /db_xref="GI:4505697"
                     /db_xref="CCDS:CCDS5746.1"
                     /db_xref="GeneID:5172"
                     /db_xref="HGNC:8818"
                     /db_xref="HPRD:05735"
                     /db_xref="MIM:605646"
     gene            complement(107383198..107385026)
                     /gene="LOC100128737"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 29 ESTs"
                     /db_xref="GeneID:100128737"
     misc_RNA        complement(join(107383198..107383848,
                     107384818..107385026))
                     /gene="LOC100128737"
                     /product="hypothetical LOC100128737, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 22 ESTs"
                     /transcript_id="XR_108796.1"
                     /db_xref="GI:310120074"
                     /db_xref="GeneID:100128737"
     misc_RNA        complement(join(107383198..107383848,
                     107383930..107384496))
                     /gene="LOC100128737"
                     /product="hypothetical LOC100128737, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 22 ESTs"
                     /transcript_id="XR_108795.1"
                     /db_xref="GI:310120075"
                     /db_xref="GeneID:100128737"
     misc_RNA        complement(join(107383260..107383848,
                     107384378..107384495))
                     /gene="LOC100128737"
                     /product="hypothetical LOC100128737, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 17 ESTs"
                     /transcript_id="XR_108797.1"
                     /db_xref="GI:310120076"
                     /db_xref="GeneID:100128737"
     gene            107384279..107402083
                     /gene="CBLL1"
                     /gene_synonym="FLJ23109; HAKAI; MGC163401; MGC163403;
                     RNF188"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79872"
                     /db_xref="HGNC:21225"
                     /db_xref="HPRD:07590"
                     /db_xref="MIM:606872"
     mRNA            join(107384279..107384621,107389325..107389492,
                     107393856..107393956,107394340..107394423,
                     107395863..107395936,107398588..107402083)
                     /gene="CBLL1"
                     /gene_synonym="FLJ23109; HAKAI; MGC163401; MGC163403;
                     RNF188"
                     /product="Cas-Br-M (murine) ecotropic retroviral
                     transforming sequence-like 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024814.2"
                     /db_xref="GI:209180480"
                     /db_xref="GeneID:79872"
                     /db_xref="HGNC:21225"
                     /db_xref="HPRD:07590"
                     /db_xref="MIM:606872"
     misc_RNA        join(107384279..107384621,107389325..107389492,
                     107392990..107393062,107393856..107393956,
                     107394340..107394423,107395863..107395936,
                     107398588..107402083)
                     /gene="CBLL1"
                     /gene_synonym="FLJ23109; HAKAI; MGC163401; MGC163403;
                     RNF188"
                     /product="Cas-Br-M (murine) ecotropic retroviral
                     transforming sequence-like 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024199.1"
                     /db_xref="GI:209180482"
                     /db_xref="GeneID:79872"
                     /db_xref="HGNC:21225"
                     /db_xref="MIM:606872"
                     /db_xref="HPRD:07590"
     CDS             join(107384609..107384621,107389325..107389492,
                     107393856..107393956,107394340..107394423,
                     107395863..107395936,107398588..107399623)
                     /gene="CBLL1"
                     /gene_synonym="FLJ23109; HAKAI; MGC163401; MGC163403;
                     RNF188"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase Hakai"
                     /protein_id="NP_079090.2"
                     /db_xref="GI:209180481"
                     /db_xref="CCDS:CCDS5747.1"
                     /db_xref="GeneID:79872"
                     /db_xref="HGNC:21225"
                     /db_xref="HPRD:07590"
                     /db_xref="MIM:606872"
     gene            complement(107405912..107443678)
                     /gene="SLC26A3"
                     /gene_synonym="CLD; DRA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1811"
                     /db_xref="HGNC:3018"
                     /db_xref="HPRD:00544"
                     /db_xref="MIM:126650"
     mRNA            complement(join(107405912..107406323,107408024..107408089,
                     107408211..107408353,107412499..107412553,
                     107414365..107414598,107415222..107415317,
                     107416897..107416989,107417082..107417151,
                     107418620..107418726,107420113..107420208,
                     107423242..107423319,107423425..107423538,
                     107423650..107423797,107427272..107427354,
                     107427802..107427954,107429969..107430133,
                     107431493..107431680,107432275..107432385,
                     107434187..107434326,107434824..107435042,
                     107443556..107443678))
                     /gene="SLC26A3"
                     /gene_synonym="CLD; DRA"
                     /product="solute carrier family 26, member 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000111.2"
                     /db_xref="GI:171543859"
                     /db_xref="GeneID:1811"
                     /db_xref="HGNC:3018"
                     /db_xref="HPRD:00544"
                     /db_xref="MIM:126650"
     CDS             complement(join(107406300..107406323,107408024..107408089,
                     107408211..107408353,107412499..107412553,
                     107414365..107414598,107415222..107415317,
                     107416897..107416989,107417082..107417151,
                     107418620..107418726,107420113..107420208,
                     107423242..107423319,107423425..107423538,
                     107423650..107423797,107427272..107427354,
                     107427802..107427954,107429969..107430133,
                     107431493..107431680,107432275..107432385,
                     107434187..107434326,107434824..107434954))
                     /gene="SLC26A3"
                     /gene_synonym="CLD; DRA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="chloride anion exchanger"
                     /protein_id="NP_000102.1"
                     /db_xref="GI:4557535"
                     /db_xref="CCDS:CCDS5748.1"
                     /db_xref="GeneID:1811"
                     /db_xref="HGNC:3018"
                     /db_xref="HPRD:00544"
                     /db_xref="MIM:126650"
     gene            107449182..107450037
                     /gene="LOC100128307"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100128307"
     gene            107531586..107561643
                     /gene="DLD"
                     /gene_synonym="DLDH; E3; GCSL; LAD; PHE3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1738"
                     /db_xref="HGNC:2898"
                     /db_xref="HPRD:02006"
                     /db_xref="MIM:238331"
     mRNA            join(107531586..107531734,107533645..107533723,
                     107542183..107542262,107542770..107542838,
                     107543923..107543992,107545403..107545503,
                     107545806..107545949,107546712..107546813,
                     107555951..107556141,107557239..107557409,
                     107557718..107557907,107558369..107558506,
                     107559455..107559544,107559639..107561643)
                     /gene="DLD"
                     /gene_synonym="DLDH; E3; GCSL; LAD; PHE3"
                     /product="dihydrolipoamide dehydrogenase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000108.3"
                     /db_xref="GI:91199539"
                     /db_xref="GeneID:1738"
                     /db_xref="HGNC:2898"
                     /db_xref="HPRD:02006"
                     /db_xref="MIM:238331"
     CDS             join(107531696..107531734,107533645..107533723,
                     107542183..107542262,107542770..107542838,
                     107543923..107543992,107545403..107545503,
                     107545806..107545949,107546712..107546813,
                     107555951..107556141,107557239..107557409,
                     107557718..107557907,107558369..107558506,
                     107559455..107559544,107559639..107559704)
                     /gene="DLD"
                     /gene_synonym="DLDH; E3; GCSL; LAD; PHE3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="dihydrolipoyl dehydrogenase, mitochondrial
                     precursor"
                     /protein_id="NP_000099.2"
                     /db_xref="GI:91199540"
                     /db_xref="CCDS:CCDS5749.1"
                     /db_xref="GeneID:1738"
                     /db_xref="HGNC:2898"
                     /db_xref="HPRD:02006"
                     /db_xref="MIM:238331"
     gene            complement(107564246..107643804)
                     /gene="LAMB1"
                     /gene_synonym="CLM; MGC142015"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3912"
                     /db_xref="HGNC:6486"
                     /db_xref="HPRD:01029"
                     /db_xref="MIM:150240"
     mRNA            complement(join(107564246..107564532,107564675..107564834,
                     107566628..107566804,107569509..107569650,
                     107569857..107570064,107571801..107571945,
                     107572619..107572822,107575860..107576101,
                     107577538..107577722,107580434..107580803,
                     107591671..107591767,107592454..107592668,
                     107593975..107594199,107595912..107596075,
                     107599694..107599925,107600136..107600279,
                     107600890..107601094,107601651..107601774,
                     107601994..107602121,107603350..107603508,
                     107604997..107605132,107613437..107613516,
                     107615431..107615543,107615679..107615858,
                     107616134..107616322,107618492..107618612,
                     107621054..107621256,107626467..107626530,
                     107626620..107626808,107635332..107635405,
                     107638802..107638937,107642003..107642178,
                     107643294..107643416,107643556..107643804))
                     /gene="LAMB1"
                     /gene_synonym="CLM; MGC142015"
                     /product="laminin, beta 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002291.2"
                     /db_xref="GI:167614503"
                     /db_xref="GeneID:3912"
                     /db_xref="HGNC:6486"
                     /db_xref="HPRD:01029"
                     /db_xref="MIM:150240"
     CDS             complement(join(107564396..107564532,107564675..107564834,
                     107566628..107566804,107569509..107569650,
                     107569857..107570064,107571801..107571945,
                     107572619..107572822,107575860..107576101,
                     107577538..107577722,107580434..107580803,
                     107591671..107591767,107592454..107592668,
                     107593975..107594199,107595912..107596075,
                     107599694..107599925,107600136..107600279,
                     107600890..107601094,107601651..107601774,
                     107601994..107602121,107603350..107603508,
                     107604997..107605132,107613437..107613516,
                     107615431..107615543,107615679..107615858,
                     107616134..107616322,107618492..107618612,
                     107621054..107621256,107626467..107626530,
                     107626620..107626808,107635332..107635405,
                     107638802..107638937,107642003..107642178,
                     107643294..107643330))
                     /gene="LAMB1"
                     /gene_synonym="CLM; MGC142015"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="laminin subunit beta-1 precursor"
                     /protein_id="NP_002282.2"
                     /db_xref="GI:167614504"
                     /db_xref="CCDS:CCDS5750.1"
                     /db_xref="GeneID:3912"
                     /db_xref="HGNC:6486"
                     /db_xref="HPRD:01029"
                     /db_xref="MIM:150240"
     gene            complement(107663996..107770801)
                     /gene="LAMB4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:22798"
                     /db_xref="HGNC:6491"
                     /db_xref="HPRD:11224"
     mRNA            complement(join(107663996..107664623,107669488..107669641,
                     107671251..107671424,107674653..107674791,
                     107677833..107678040,107684197..107684341,
                     107688353..107688556,107689771..107689976,
                     107692542..107692702,107696077..107696452,
                     107698277..107698373,107703219..107703439,
                     107704206..107704430,107706207..107706364,
                     107706814..107707045,107708461..107708604,
                     107710153..107710330,107717389..107717509,
                     107718646..107718761,107720046..107720231,
                     107732071..107732221,107732782..107732861,
                     107735673..107735782,107738848..107739027,
                     107743489..107743677,107744944..107745064,
                     107746262..107746476,107746954..107747017,
                     107748076..107748264,107749616..107749689,
                     107752256..107752391,107756449..107756606,
                     107763576..107763642,107770751..107770801))
                     /gene="LAMB4"
                     /product="laminin, beta 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_007356.2"
                     /db_xref="GI:143770879"
                     /db_xref="GeneID:22798"
                     /db_xref="HGNC:6491"
                     /db_xref="HPRD:11224"
     CDS             complement(join(107664484..107664623,107669488..107669641,
                     107671251..107671424,107674653..107674791,
                     107677833..107678040,107684197..107684341,
                     107688353..107688556,107689771..107689976,
                     107692542..107692702,107696077..107696452,
                     107698277..107698373,107703219..107703439,
                     107704206..107704430,107706207..107706364,
                     107706814..107707045,107708461..107708604,
                     107710153..107710330,107717389..107717509,
                     107718646..107718761,107720046..107720231,
                     107732071..107732221,107732782..107732861,
                     107735673..107735782,107738848..107739027,
                     107743489..107743677,107744944..107745064,
                     107746262..107746476,107746954..107747017,
                     107748076..107748264,107749616..107749689,
                     107752256..107752391,107756449..107756606,
                     107763576..107763609))
                     /gene="LAMB4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="laminin subunit beta-4 precursor"
                     /protein_id="NP_031382.2"
                     /db_xref="GI:143770880"
                     /db_xref="CCDS:CCDS34732.1"
                     /db_xref="GeneID:22798"
                     /db_xref="HGNC:6491"
                     /db_xref="HPRD:11224"
     gene            complement(107788071..108096841)
                     /gene="NRCAM"
                     /gene_synonym="KIAA0343; MGC138845; MGC138846"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4897"
                     /db_xref="HGNC:7994"
                     /db_xref="HPRD:07207"
                     /db_xref="MIM:601581"
     mRNA            complement(join(107788071..107790592,107799908..107799986,
                     107800806..107800937,107816875..107817051,
                     107818435..107818557,107820667..107820871,
                     107822266..107822381,107823139..107823364,
                     107824685..107824755,107824861..107825058,
                     107830089..107830190,107832173..107832297,
                     107834468..107834615,107834706..107834872,
                     107836205..107836316,107838400..107838543,
                     107847972..107848103,107849865..107850049,
                     107864169..107864280,107866089..107866145,
                     107866652..107866822,107871475..107871597,
                     107872770..107872966,107875027..107875132,
                     107880403..107880614,107953109..107953175,
                     108039880..108040037,108096687..108096841))
                     /gene="NRCAM"
                     /gene_synonym="KIAA0343; MGC138845; MGC138846"
                     /product="neuronal cell adhesion molecule, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005010.4"
                     /db_xref="GI:302191645"
                     /db_xref="GeneID:4897"
                     /db_xref="HGNC:7994"
                     /db_xref="HPRD:07207"
                     /db_xref="MIM:601581"
     mRNA            complement(join(107788071..107790592,107799908..107799986,
                     107800806..107800937,107815767..107815802,
                     107816875..107817051,107818435..107818557,
                     107820667..107820871,107822266..107822381,
                     107823139..107823364,107824685..107824755,
                     107824861..107825058,107830089..107830190,
                     107831698..107831727,107832173..107832297,
                     107834468..107834615,107834706..107834872,
                     107836205..107836316,107838400..107838543,
                     107847972..107848103,107849865..107850049,
                     107864169..107864280,107866089..107866145,
                     107866652..107866822,107871475..107871597,
                     107872770..107872966,107875027..107875132,
                     107878196..107878213,107880403..107880614,
                     107953109..107953175,108039880..108040037,
                     108096687..108096841))
                     /gene="NRCAM"
                     /gene_synonym="KIAA0343; MGC138845; MGC138846"
                     /product="neuronal cell adhesion molecule, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001193582.1"
                     /db_xref="GI:302191646"
                     /db_xref="GeneID:4897"
                     /db_xref="HGNC:7994"
                     /db_xref="MIM:601581"
                     /db_xref="HPRD:07207"
     mRNA            complement(join(107788071..107790592,107799908..107799986,
                     107800806..107800937,107815767..107815802,
                     107816875..107817051,107818435..107818557,
                     107820667..107820871,107822266..107822381,
                     107823139..107823364,107824685..107824755,
                     107824861..107825058,107830089..107830190,
                     107831698..107831727,107832173..107832297,
                     107834468..107834615,107834706..107834872,
                     107836205..107836316,107838400..107838543,
                     107847972..107848103,107849865..107850049,
                     107864169..107864280,107866652..107866822,
                     107871475..107871597,107872770..107872966,
                     107875027..107875132,107878196..107878213,
                     107880403..107880614,107953109..107953175,
                     108039880..108040037,108096687..108096841))
                     /gene="NRCAM"
                     /gene_synonym="KIAA0343; MGC138845; MGC138846"
                     /product="neuronal cell adhesion molecule, transcript
                     variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001193583.1"
                     /db_xref="GI:302191648"
                     /db_xref="GeneID:4897"
                     /db_xref="HGNC:7994"
                     /db_xref="MIM:601581"
                     /db_xref="HPRD:07207"
     mRNA            complement(join(107788071..107790592,107799908..107799986,
                     107800806..107800937,107816875..107817051,
                     107818435..107818557,107820667..107820871,
                     107822266..107822381,107823139..107823364,
                     107824685..107824755,107824861..107825058,
                     107830089..107830190,107831698..107831727,
                     107832173..107832297,107834468..107834615,
                     107834706..107834872,107836205..107836316,
                     107838400..107838543,107847972..107848103,
                     107849865..107850049,107864169..107864280,
                     107866652..107866822,107871475..107871597,
                     107872770..107872966,107875027..107875132,
                     107878196..107878213,107880403..107880614,
                     107953109..107953175,108039880..108040037,
                     108096687..108096841))
                     /gene="NRCAM"
                     /gene_synonym="KIAA0343; MGC138845; MGC138846"
                     /product="neuronal cell adhesion molecule, transcript
                     variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001193584.1"
                     /db_xref="GI:302191650"
                     /db_xref="GeneID:4897"
                     /db_xref="HGNC:7994"
                     /db_xref="MIM:601581"
                     /db_xref="HPRD:07207"
     mRNA            complement(join(107788071..107790592,107799908..107799986,
                     107800806..107800937,107807366..107807518,
                     107808722..107808847,107815767..107815802,
                     107816875..107817051,107818435..107818557,
                     107820667..107820871,107822266..107822381,
                     107823139..107823364,107824685..107824755,
                     107824861..107825058,107830089..107830190,
                     107831698..107831727,107832173..107832297,
                     107834468..107834615,107834706..107834872,
                     107836205..107836316,107838400..107838543,
                     107847972..107848103,107849865..107850049,
                     107864169..107864280,107866089..107866145,
                     107866652..107866822,107871475..107871597,
                     107872770..107872966,107875027..107875132,
                     107878196..107878213,107880403..107880614))
                     /gene="NRCAM"
                     /gene_synonym="KIAA0343; MGC138845; MGC138846"
                     /product="neuronal cell adhesion molecule, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001037132.2"
                     /db_xref="GI:302191644"
                     /db_xref="GeneID:4897"
                     /db_xref="HGNC:7994"
                     /db_xref="HPRD:07207"
                     /db_xref="MIM:601581"
     CDS             complement(join(107790355..107790592,107799908..107799986,
                     107800806..107800937,107807366..107807518,
                     107808722..107808847,107815767..107815802,
                     107816875..107817051,107818435..107818557,
                     107820667..107820871,107822266..107822381,
                     107823139..107823364,107824685..107824755,
                     107824861..107825058,107830089..107830190,
                     107831698..107831727,107832173..107832297,
                     107834468..107834615,107834706..107834872,
                     107836205..107836316,107838400..107838543,
                     107847972..107848103,107849865..107850049,
                     107864169..107864280,107866089..107866145,
                     107866652..107866822,107871475..107871597,
                     107872770..107872966,107875027..107875132,
                     107878196..107878213,107880403..107880508))
                     /gene="NRCAM"
                     /gene_synonym="KIAA0343; MGC138845; MGC138846"
                     /note="isoform A precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="neuronal cell adhesion molecule isoform A
                     precursor"
                     /protein_id="NP_001032209.1"
                     /db_xref="GI:81158226"
                     /db_xref="CCDS:CCDS47686.1"
                     /db_xref="GeneID:4897"
                     /db_xref="HGNC:7994"
                     /db_xref="HPRD:07207"
                     /db_xref="MIM:601581"
     CDS             complement(join(107790355..107790592,107799908..107799986,
                     107800806..107800937,107816875..107817051,
                     107818435..107818557,107820667..107820871,
                     107822266..107822381,107823139..107823364,
                     107824685..107824755,107824861..107825058,
                     107830089..107830190,107832173..107832297,
                     107834468..107834615,107834706..107834872,
                     107836205..107836316,107838400..107838543,
                     107847972..107848103,107849865..107850049,
                     107864169..107864280,107866089..107866145,
                     107866652..107866822,107871475..107871597,
                     107872770..107872966,107875027..107875132,
                     107880403..107880508))
                     /gene="NRCAM"
                     /gene_synonym="KIAA0343; MGC138845; MGC138846"
                     /note="isoform B precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="neuronal cell adhesion molecule isoform B
                     precursor"
                     /protein_id="NP_005001.3"
                     /db_xref="GI:81158224"
                     /db_xref="CCDS:CCDS5751.1"
                     /db_xref="GeneID:4897"
                     /db_xref="HGNC:7994"
                     /db_xref="HPRD:07207"
                     /db_xref="MIM:601581"
     CDS             complement(join(107790355..107790592,107799908..107799986,
                     107800806..107800937,107815767..107815802,
                     107816875..107817051,107818435..107818557,
                     107820667..107820871,107822266..107822381,
                     107823139..107823364,107824685..107824755,
                     107824861..107825058,107830089..107830190,
                     107831698..107831727,107832173..107832297,
                     107834468..107834615,107834706..107834872,
                     107836205..107836316,107838400..107838543,
                     107847972..107848103,107849865..107850049,
                     107864169..107864280,107866089..107866145,
                     107866652..107866822,107871475..107871597,
                     107872770..107872966,107875027..107875132,
                     107878196..107878213,107880403..107880508))
                     /gene="NRCAM"
                     /gene_synonym="KIAA0343; MGC138845; MGC138846"
                     /note="isoform D precursor is encoded by transcript
                     variant 4; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="neuronal cell adhesion molecule isoform D
                     precursor"
                     /protein_id="NP_001180511.1"
                     /db_xref="GI:302191647"
                     /db_xref="GeneID:4897"
                     /db_xref="HGNC:7994"
                     /db_xref="MIM:601581"
                     /db_xref="HPRD:07207"
     CDS             complement(join(107790355..107790592,107799908..107799986,
                     107800806..107800937,107815767..107815802,
                     107816875..107817051,107818435..107818557,
                     107820667..107820871,107822266..107822381,
                     107823139..107823364,107824685..107824755,
                     107824861..107825058,107830089..107830190,
                     107831698..107831727,107832173..107832297,
                     107834468..107834615,107834706..107834872,
                     107836205..107836316,107838400..107838543,
                     107847972..107848103,107849865..107850049,
                     107864169..107864280,107866652..107866822,
                     107871475..107871597,107872770..107872966,
                     107875027..107875132,107878196..107878213,
                     107880403..107880508))
                     /gene="NRCAM"
                     /gene_synonym="KIAA0343; MGC138845; MGC138846"
                     /note="isoform E precursor is encoded by transcript
                     variant 5; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="neuronal cell adhesion molecule isoform E
                     precursor"
                     /protein_id="NP_001180512.1"
                     /db_xref="GI:302191649"
                     /db_xref="CCDS:CCDS55153.1"
                     /db_xref="GeneID:4897"
                     /db_xref="HGNC:7994"
                     /db_xref="HPRD:07207"
                     /db_xref="MIM:601581"
     CDS             complement(join(107790355..107790592,107799908..107799986,
                     107800806..107800937,107816875..107817051,
                     107818435..107818557,107820667..107820871,
                     107822266..107822381,107823139..107823364,
                     107824685..107824755,107824861..107825058,
                     107830089..107830190,107831698..107831727,
                     107832173..107832297,107834468..107834615,
                     107834706..107834872,107836205..107836316,
                     107838400..107838543,107847972..107848103,
                     107849865..107850049,107864169..107864280,
                     107866652..107866822,107871475..107871597,
                     107872770..107872966,107875027..107875132,
                     107878196..107878213,107880403..107880508))
                     /gene="NRCAM"
                     /gene_synonym="KIAA0343; MGC138845; MGC138846"
                     /note="isoform F precursor is encoded by transcript
                     variant 6; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="neuronal cell adhesion molecule isoform F
                     precursor"
                     /protein_id="NP_001180513.1"
                     /db_xref="GI:302191651"
                     /db_xref="GeneID:4897"
                     /db_xref="HGNC:7994"
                     /db_xref="MIM:601581"
                     /db_xref="HPRD:07207"
     gene            complement(108112071..108166638)
                     /gene="PNPLA8"
                     /gene_synonym="IPLA2(GAMMA); IPLA2-2; IPLA2G"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:50640"
                     /db_xref="HGNC:28900"
                     /db_xref="HPRD:13741"
                     /db_xref="MIM:612123"
     mRNA            complement(join(108112071..108113119,108119628..108119823,
                     108128203..108128397,108131854..108131911,
                     108137028..108137199,108137927..108138021,
                     108142935..108143086,108154588..108154737,
                     108154880..108156018,108158634..108158745,
                     108161920..108161965,108166473..108166638))
                     /gene="PNPLA8"
                     /gene_synonym="IPLA2(GAMMA); IPLA2-2; IPLA2G"
                     /product="patatin-like phospholipase domain containing 8"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015723.2"
                     /db_xref="GI:48675815"
                     /db_xref="GeneID:50640"
                     /db_xref="HGNC:28900"
                     /db_xref="HPRD:13741"
                     /db_xref="MIM:612123"
     CDS             complement(join(108112845..108113119,108119628..108119823,
                     108128203..108128397,108131854..108131911,
                     108137028..108137199,108137927..108138021,
                     108142935..108143086,108154588..108154737,
                     108154880..108155935))
                     /gene="PNPLA8"
                     /gene_synonym="IPLA2(GAMMA); IPLA2-2; IPLA2G"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium-independent phospholipase A2-gamma"
                     /protein_id="NP_056538.1"
                     /db_xref="GI:48525351"
                     /db_xref="CCDS:CCDS34733.1"
                     /db_xref="GeneID:50640"
                     /db_xref="HGNC:28900"
                     /db_xref="HPRD:13741"
                     /db_xref="MIM:612123"
     gene            108150657..108151486
                     /gene="RPL7P32"
                     /gene_synonym="RPL7_15_834; RPL7P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100130892"
                     /db_xref="HGNC:35692"
     gene            complement(108202671..108210167)
                     /gene="THAP5"
                     /gene_synonym="DKFZp313O1132"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:168451"
                     /db_xref="HGNC:23188"
                     /db_xref="MIM:612534"
     mRNA            complement(join(108202671..108205549,108206274..108206466,
                     108209934..108210167))
                     /gene="THAP5"
                     /gene_synonym="DKFZp313O1132"
                     /product="THAP domain containing 5, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130475.1"
                     /db_xref="GI:194440667"
                     /db_xref="GeneID:168451"
                     /db_xref="HGNC:23188"
                     /db_xref="MIM:612534"
     mRNA            complement(join(108202671..108205549,108206274..108206466,
                     108209543..108209897))
                     /gene="THAP5"
                     /gene_synonym="DKFZp313O1132"
                     /product="THAP domain containing 5, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182529.2"
                     /db_xref="GI:194440672"
                     /db_xref="GeneID:168451"
                     /db_xref="HGNC:23188"
                     /db_xref="HPRD:15498"
                     /db_xref="MIM:612534"
     CDS             complement(join(108204635..108205549,108206274..108206466,
                     108209934..108210013))
                     /gene="THAP5"
                     /gene_synonym="DKFZp313O1132"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="THAP domain-containing protein 5 isoform 1"
                     /protein_id="NP_001123947.1"
                     /db_xref="GI:194440668"
                     /db_xref="CCDS:CCDS47687.1"
                     /db_xref="GeneID:168451"
                     /db_xref="HGNC:23188"
                     /db_xref="MIM:612534"
     CDS             complement(join(108204635..108205549,
                     108206274..108206420))
                     /gene="THAP5"
                     /gene_synonym="DKFZp313O1132"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="THAP domain-containing protein 5 isoform 2"
                     /protein_id="NP_872335.2"
                     /db_xref="GI:194440673"
                     /db_xref="CCDS:CCDS34734.2"
                     /db_xref="GeneID:168451"
                     /db_xref="HGNC:23188"
                     /db_xref="MIM:612534"
     gene            108210189..108215294
                     /gene="DNAJB9"
                     /gene_synonym="DKFZp564F1862; ERdj4; MDG-1; MDG1; MST049;
                     MSTP049"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4189"
                     /db_xref="HGNC:6968"
                     /db_xref="HPRD:07047"
                     /db_xref="MIM:602634"
     mRNA            join(108210189..108210547,108212161..108212387,
                     108213343..108215294)
                     /gene="DNAJB9"
                     /gene_synonym="DKFZp564F1862; ERdj4; MDG-1; MDG1; MST049;
                     MSTP049"
                     /product="DnaJ (Hsp40) homolog, subfamily B, member 9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012328.2"
                     /db_xref="GI:313482783"
                     /db_xref="GeneID:4189"
                     /db_xref="HGNC:6968"
                     /db_xref="HPRD:07047"
                     /db_xref="MIM:602634"
     CDS             join(108212171..108212387,108213343..108213797)
                     /gene="DNAJB9"
                     /gene_synonym="DKFZp564F1862; ERdj4; MDG-1; MDG1; MST049;
                     MSTP049"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="dnaJ homolog subfamily B member 9"
                     /protein_id="NP_036460.1"
                     /db_xref="GI:9558755"
                     /db_xref="CCDS:CCDS5752.1"
                     /db_xref="GeneID:4189"
                     /db_xref="HGNC:6968"
                     /db_xref="HPRD:07047"
                     /db_xref="MIM:602634"
     gene            complement(108361052..108362047)
                     /gene="LOC100419644"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419644"
     gene            complement(108524038..108524637)
                     /gene="C7orf66"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:154907"
                     /db_xref="HGNC:33712"
                     /db_xref="HPRD:18563"
     mRNA            complement(join(108524038..108524306,
                     108524485..108524637))
                     /gene="C7orf66"
                     /product="chromosome 7 open reading frame 66"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001024607.1"
                     /db_xref="GI:66912163"
                     /db_xref="GeneID:154907"
                     /db_xref="HGNC:33712"
                     /db_xref="HPRD:18563"
     CDS             complement(join(108524064..108524306,
                     108524485..108524589))
                     /gene="C7orf66"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC154907"
                     /protein_id="NP_001019778.1"
                     /db_xref="GI:66912164"
                     /db_xref="CCDS:CCDS34735.1"
                     /db_xref="GeneID:154907"
                     /db_xref="HGNC:33712"
                     /db_xref="HPRD:18563"
     gene            complement(108633888..108635117)
                     /gene="LOC646614"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:646614"
     gene            109403738..109404434
                     /gene="LOC100421901"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421901"
     gene            109478927..109480671
                     /gene="LOC100128056"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100128056"
     gene            complement(109599284..109600270)
                     /gene="EIF3IP1"
                     /gene_synonym="RG208K23"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:442720"
                     /db_xref="HGNC:13277"
     misc_RNA        complement(109599284..109600270)
                     /gene="EIF3IP1"
                     /gene_synonym="RG208K23"
                     /product="eukaryotic translation initiation factor 3,
                     subunit I pseudogene 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003024.1"
                     /db_xref="GI:93204855"
                     /db_xref="GeneID:442720"
                     /db_xref="HGNC:13277"
     gene            complement(109638436..109639703)
                     /gene="RPL3P8"
                     /gene_synonym="RPL3_4_835"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:646620"
                     /db_xref="HGNC:35498"
     gene            109855956..109856607
                     /gene="LOC100419782"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419782"
     gene            complement(110303110..111202347)
                     /gene="IMMP2L"
                     /gene_synonym="IMP2; IMP2-LIKE"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:83943"
                     /db_xref="HGNC:14598"
                     /db_xref="HPRD:07297"
                     /db_xref="MIM:605977"
     mRNA            complement(join(110303110..110303777,110526649..110526751,
                     110603556..110603621,111127294..111127397,
                     111161369..111161505,111201907..111202347))
                     /gene="IMMP2L"
                     /gene_synonym="IMP2; IMP2-LIKE"
                     /product="IMP2 inner mitochondrial membrane peptidase-like
                     (S. cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032549.2"
                     /db_xref="GI:142350621"
                     /db_xref="GeneID:83943"
                     /db_xref="HGNC:14598"
                     /db_xref="HPRD:07297"
                     /db_xref="MIM:605977"
     CDS             complement(join(110303658..110303777,110526649..110526751,
                     110603556..110603621,111127294..111127397,
                     111161369..111161503))
                     /gene="IMMP2L"
                     /gene_synonym="IMP2; IMP2-LIKE"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="mitochondrial inner membrane protease subunit 2"
                     /protein_id="NP_115938.1"
                     /db_xref="GI:14211845"
                     /db_xref="CCDS:CCDS5753.1"
                     /db_xref="GeneID:83943"
                     /db_xref="HGNC:14598"
                     /db_xref="HPRD:07297"
                     /db_xref="MIM:605977"
     gene            110731062..110765510
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; FLJ11129; NLRR-3; NLRR3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54674"
                     /db_xref="HGNC:17200"
     mRNA            join(110731062..110731560,110737083..110737189,
                     110739937..110740018,110762471..110765510)
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; FLJ11129; NLRR-3; NLRR3"
                     /product="leucine rich repeat neuronal 3, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001099660.1"
                     /db_xref="GI:153791506"
                     /db_xref="GeneID:54674"
                     /db_xref="HGNC:17200"
     mRNA            join(110731062..110731560,110739937..110740018,
                     110762471..110765510)
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; FLJ11129; NLRR-3; NLRR3"
                     /product="leucine rich repeat neuronal 3, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001099658.1"
                     /db_xref="GI:153792650"
                     /db_xref="GeneID:54674"
                     /db_xref="HGNC:17200"
     mRNA            join(110731062..110731560,110762471..110765510)
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; FLJ11129; NLRR-3; NLRR3"
                     /product="leucine rich repeat neuronal 3, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018334.4"
                     /db_xref="GI:153792226"
                     /db_xref="GeneID:54674"
                     /db_xref="HGNC:17200"
                     /db_xref="HPRD:14321"
     CDS             110762829..110764955
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; FLJ11129; NLRR-3; NLRR3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="leucine-rich repeat neuronal protein 3
                     precursor"
                     /protein_id="NP_001093130.1"
                     /db_xref="GI:153791507"
                     /db_xref="CCDS:CCDS5754.1"
                     /db_xref="GeneID:54674"
                     /db_xref="HGNC:17200"
     CDS             110762829..110764955
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; FLJ11129; NLRR-3; NLRR3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="leucine-rich repeat neuronal protein 3
                     precursor"
                     /protein_id="NP_060804.3"
                     /db_xref="GI:153792227"
                     /db_xref="CCDS:CCDS5754.1"
                     /db_xref="GeneID:54674"
                     /db_xref="HGNC:17200"
     CDS             110762829..110764955
                     /gene="LRRN3"
                     /gene_synonym="FIGLER5; FLJ11129; NLRR-3; NLRR3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="leucine-rich repeat neuronal protein 3
                     precursor"
                     /protein_id="NP_001093128.1"
                     /db_xref="GI:153792651"
                     /db_xref="CCDS:CCDS5754.1"
                     /db_xref="GeneID:54674"
                     /db_xref="HGNC:17200"
     gene            111051375..111051936
                     /gene="LOC100420226"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420226"
     gene            complement(111366164..111846462)
                     /gene="DOCK4"
                     /gene_synonym="FLJ34238; KIAA0716; MGC134911; MGC134912"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9732"
                     /db_xref="HGNC:19192"
                     /db_xref="HPRD:07407"
                     /db_xref="MIM:607679"
     mRNA            complement(join(111366164..111368776,111372282..111372343,
                     111375110..111375223,111376973..111377045,
                     111379190..111379299,111379452..111379533,
                     111381150..111381270,111381596..111381717,
                     111382069..111382188,111386390..111386473,
                     111387323..111387499,111395571..111395657,
                     111398680..111398846,111400237..111400378,
                     111405174..111405278,111407088..111407174,
                     111409585..111409733,111418332..111418425,
                     111422920..111422980,111423913..111424008,
                     111428718..111428803,111430513..111430661,
                     111448877..111448935,111449357..111449457,
                     111451930..111452005,111462418..111462512,
                     111474644..111474742,111484819..111484953,
                     111487055..111487182,111503428..111503620,
                     111508040..111508210,111509630..111509711,
                     111512046..111512146,111512325..111512408,
                     111512523..111512620,111517086..111517242,
                     111535668..111535774,111540430..111540592,
                     111541733..111541857,111555834..111555959,
                     111575595..111575683,111580165..111580297,
                     111584866..111584926,111585772..111585853,
                     111617187..111617338,111624361..111624445,
                     111629070..111629218,111634190..111634286,
                     111638503..111638558,111640549..111640589,
                     111644103..111644186,111846157..111846462))
                     /gene="DOCK4"
                     /gene_synonym="FLJ34238; KIAA0716; MGC134911; MGC134912"
                     /product="dedicator of cytokinesis 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014705.3"
                     /db_xref="GI:92091571"
                     /db_xref="GeneID:9732"
                     /db_xref="HGNC:19192"
                     /db_xref="HPRD:07407"
                     /db_xref="MIM:607679"
     CDS             complement(join(111368330..111368776,111372282..111372343,
                     111375110..111375223,111376973..111377045,
                     111379190..111379299,111379452..111379533,
                     111381150..111381270,111381596..111381717,
                     111382069..111382188,111386390..111386473,
                     111387323..111387499,111395571..111395657,
                     111398680..111398846,111400237..111400378,
                     111405174..111405278,111407088..111407174,
                     111409585..111409733,111418332..111418425,
                     111422920..111422980,111423913..111424008,
                     111428718..111428803,111430513..111430661,
                     111448877..111448935,111449357..111449457,
                     111451930..111452005,111462418..111462512,
                     111474644..111474742,111484819..111484953,
                     111487055..111487182,111503428..111503620,
                     111508040..111508210,111509630..111509711,
                     111512046..111512146,111512325..111512408,
                     111512523..111512620,111517086..111517242,
                     111535668..111535774,111540430..111540592,
                     111541733..111541857,111555834..111555959,
                     111575595..111575683,111580165..111580297,
                     111584866..111584926,111585772..111585853,
                     111617187..111617338,111624361..111624445,
                     111629070..111629218,111634190..111634286,
                     111638503..111638558,111640549..111640589,
                     111644103..111644186,111846157..111846193))
                     /gene="DOCK4"
                     /gene_synonym="FLJ34238; KIAA0716; MGC134911; MGC134912"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="dedicator of cytokinesis protein 4"
                     /protein_id="NP_055520.3"
                     /db_xref="GI:92091572"
                     /db_xref="CCDS:CCDS47688.1"
                     /db_xref="GeneID:9732"
                     /db_xref="HGNC:19192"
                     /db_xref="HPRD:07407"
                     /db_xref="MIM:607679"
     gene            111448582..111461835
                     /gene="LOC100506413"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 7 ESTs"
                     /db_xref="GeneID:100506413"
     misc_RNA        join(111448582..111448669,111459434..111461835)
                     /gene="LOC100506413"
                     /product="hypothetical LOC100506413"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 7 ESTs"
                     /transcript_id="XR_108798.1"
                     /db_xref="GI:310120077"
                     /db_xref="GeneID:100506413"
     gene            complement(111611219..111612080)
                     /gene="RPL7AP42"
                     /gene_synonym="RPL7A_19_836"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271215"
                     /db_xref="HGNC:36716"
     gene            111846643..111983989
                     /gene="ZNF277"
                     /gene_synonym="NRIF4; ZNF277P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:11179"
                     /db_xref="HGNC:13070"
                     /db_xref="HPRD:05680"
                     /db_xref="MIM:605465"
     mRNA            join(111846643..111846862,111926928..111927129,
                     111935924..111936012,111936284..111936366,
                     111958237..111958328,111967772..111967882,
                     111970139..111970271,111976159..111976226,
                     111977785..111977881,111979898..111979940,
                     111980927..111981101,111982616..111983989)
                     /gene="ZNF277"
                     /gene_synonym="NRIF4; ZNF277P"
                     /product="zinc finger protein 277"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021994.2"
                     /db_xref="GI:126723500"
                     /db_xref="GeneID:11179"
                     /db_xref="HGNC:13070"
                     /db_xref="HPRD:05680"
                     /db_xref="MIM:605465"
     CDS             join(111846772..111846862,111926928..111927129,
                     111935924..111936012,111936284..111936366,
                     111958237..111958328,111967772..111967882,
                     111970139..111970271,111976159..111976226,
                     111977785..111977881,111979898..111979940,
                     111980927..111981101,111982616..111982784)
                     /gene="ZNF277"
                     /gene_synonym="NRIF4; ZNF277P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 277"
                     /protein_id="NP_068834.2"
                     /db_xref="GI:126723501"
                     /db_xref="CCDS:CCDS5755.2"
                     /db_xref="GeneID:11179"
                     /db_xref="HGNC:13070"
                     /db_xref="HPRD:05680"
                     /db_xref="MIM:605465"
     gene            112063199..112117258
                     /gene="IFRD1"
                     /gene_synonym="PC4; TIS7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3475"
                     /db_xref="HGNC:5456"
                     /db_xref="HPRD:04612"
                     /db_xref="MIM:603502"
     mRNA            join(112063199..112063487,112090563..112090837,
                     112095818..112095922,112096057..112096141,
                     112096969..112097093,112098916..112099073,
                     112101921..112101971,112102056..112102234,
                     112102325..112102433,112108036..112108170,
                     112112274..112112402,112112821..112112916,
                     112115485..112117258)
                     /gene="IFRD1"
                     /gene_synonym="PC4; TIS7"
                     /product="interferon-related developmental regulator 1,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001007245.2"
                     /db_xref="GI:308193306"
                     /db_xref="GeneID:3475"
                     /db_xref="HGNC:5456"
                     /db_xref="MIM:603502"
                     /db_xref="HPRD:04612"
     mRNA            join(112063199..112063487,112095818..112095922,
                     112096057..112096141,112096969..112097093,
                     112098916..112099073,112101921..112101971,
                     112102056..112102234,112102325..112102433,
                     112108036..112108170,112112274..112112402,
                     112112821..112112916,112115485..112117258)
                     /gene="IFRD1"
                     /gene_synonym="PC4; TIS7"
                     /product="interferon-related developmental regulator 1,
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001197080.1"
                     /db_xref="GI:308193309"
                     /db_xref="GeneID:3475"
                     /db_xref="HGNC:5456"
                     /db_xref="MIM:603502"
                     /db_xref="HPRD:04612"
     mRNA            join(112090483..112090837,112095818..112095922,
                     112096057..112096141,112096969..112097093,
                     112098916..112099073,112101921..112101971,
                     112102056..112102234,112102325..112102433,
                     112108036..112108170,112112274..112112402,
                     112112821..112112916,112115485..112117258)
                     /gene="IFRD1"
                     /gene_synonym="PC4; TIS7"
                     /product="interferon-related developmental regulator 1,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001550.3"
                     /db_xref="GI:308193305"
                     /db_xref="GeneID:3475"
                     /db_xref="HGNC:5456"
                     /db_xref="HPRD:04612"
                     /db_xref="MIM:603502"
     CDS             join(112090744..112090837,112095818..112095922,
                     112096057..112096141,112096969..112097093,
                     112098916..112099073,112101921..112101971,
                     112102056..112102234,112102325..112102433,
                     112108036..112108170,112112274..112112402,
                     112112821..112112916,112115485..112115574)
                     /gene="IFRD1"
                     /gene_synonym="PC4; TIS7"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="interferon-related developmental regulator 1
                     isoform 1"
                     /protein_id="NP_001541.2"
                     /db_xref="GI:55953129"
                     /db_xref="CCDS:CCDS34736.1"
                     /db_xref="GeneID:3475"
                     /db_xref="HGNC:5456"
                     /db_xref="HPRD:04612"
                     /db_xref="MIM:603502"
     CDS             join(112090744..112090837,112095818..112095922,
                     112096057..112096141,112096969..112097093,
                     112098916..112099073,112101921..112101971,
                     112102056..112102234,112102325..112102433,
                     112108036..112108170,112112274..112112402,
                     112112821..112112916,112115485..112115574)
                     /gene="IFRD1"
                     /gene_synonym="PC4; TIS7"
                     /note="isoform 1 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="interferon-related developmental regulator 1
                     isoform 1"
                     /protein_id="NP_001007246.1"
                     /db_xref="GI:55953131"
                     /db_xref="CCDS:CCDS34736.1"
                     /db_xref="GeneID:3475"
                     /db_xref="HGNC:5456"
                     /db_xref="HPRD:04612"
                     /db_xref="MIM:603502"
     mRNA            join(112092113..112092566,112095818..112095922,
                     112096057..112096141,112096969..112097093,
                     112098916..112099073,112101921..112101971,
                     112102056..112102234,112102325..112102433,
                     112108036..112108170,112112274..112112402,
                     112112821..112112916,112115485..112117258)
                     /gene="IFRD1"
                     /gene_synonym="PC4; TIS7"
                     /product="interferon-related developmental regulator 1,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001197079.1"
                     /db_xref="GI:308193307"
                     /db_xref="GeneID:3475"
                     /db_xref="HGNC:5456"
                     /db_xref="MIM:603502"
                     /db_xref="HPRD:04612"
     CDS             join(112095874..112095922,112096057..112096141,
                     112096969..112097093,112098916..112099073,
                     112101921..112101971,112102056..112102234,
                     112102325..112102433,112108036..112108170,
                     112112274..112112402,112112821..112112916,
                     112115485..112115574)
                     /gene="IFRD1"
                     /gene_synonym="PC4; TIS7"
                     /note="isoform 2 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="interferon-related developmental regulator 1
                     isoform 2"
                     /protein_id="NP_001184008.1"
                     /db_xref="GI:308193308"
                     /db_xref="GeneID:3475"
                     /db_xref="HGNC:5456"
                     /db_xref="MIM:603502"
                     /db_xref="HPRD:04612"
     CDS             join(112095874..112095922,112096057..112096141,
                     112096969..112097093,112098916..112099073,
                     112101921..112101971,112102056..112102234,
                     112102325..112102433,112108036..112108170,
                     112112274..112112402,112112821..112112916,
                     112115485..112115574)
                     /gene="IFRD1"
                     /gene_synonym="PC4; TIS7"
                     /note="isoform 2 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="interferon-related developmental regulator 1
                     isoform 2"
                     /protein_id="NP_001184009.1"
                     /db_xref="GI:308193310"
                     /db_xref="GeneID:3475"
                     /db_xref="HGNC:5456"
                     /db_xref="MIM:603502"
                     /db_xref="HPRD:04612"
     gene            112120908..112130943
                     /gene="C7orf53"
                     /gene_synonym="FLJ39575; MGC161427; MGC163440; MGC42850"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:286006"
                     /db_xref="HGNC:22036"
                     /db_xref="HPRD:08258"
     mRNA            join(112120908..112121037,112124867..112124998,
                     112126978..112127106,112129865..112130943)
                     /gene="C7orf53"
                     /gene_synonym="FLJ39575; MGC161427; MGC163440; MGC42850"
                     /product="chromosome 7 open reading frame 53, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134468.1"
                     /db_xref="GI:197333855"
                     /db_xref="GeneID:286006"
                     /db_xref="HGNC:22036"
                     /db_xref="HPRD:08258"
     mRNA            join(112121066..112121401,112124867..112124998,
                     112126978..112127106,112129865..112130943)
                     /gene="C7orf53"
                     /gene_synonym="FLJ39575; MGC161427; MGC163440; MGC42850"
                     /product="chromosome 7 open reading frame 53, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182597.2"
                     /db_xref="GI:197333854"
                     /db_xref="GeneID:286006"
                     /db_xref="HGNC:22036"
                     /db_xref="HPRD:08258"
     CDS             join(112124872..112124998,112126978..112127106,
                     112129865..112130004)
                     /gene="C7orf53"
                     /gene_synonym="FLJ39575; MGC161427; MGC163440; MGC42850"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC286006"
                     /protein_id="NP_872403.1"
                     /db_xref="GI:32699019"
                     /db_xref="CCDS:CCDS5756.1"
                     /db_xref="GeneID:286006"
                     /db_xref="HGNC:22036"
                     /db_xref="HPRD:08258"
     CDS             join(112124872..112124998,112126978..112127106,
                     112129865..112130004)
                     /gene="C7orf53"
                     /gene_synonym="FLJ39575; MGC161427; MGC163440; MGC42850"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC286006"
                     /protein_id="NP_001127940.1"
                     /db_xref="GI:197333856"
                     /db_xref="CCDS:CCDS5756.1"
                     /db_xref="GeneID:286006"
                     /db_xref="HGNC:22036"
                     /db_xref="HPRD:08258"
     gene            112160451..112162038
                     /gene="NPM1P14"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:10833"
                     /db_xref="HGNC:7916"
     gene            complement(112375221..112378750)
                     /gene="MIPEPP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533682"
                     /db_xref="HGNC:39456"
     gene            complement(112405787..112430478)
                     /gene="TMEM168"
                     /gene_synonym="DKFZp564C012; FLJ13576"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64418"
                     /db_xref="HGNC:25826"
                     /db_xref="HPRD:07831"
     mRNA            complement(join(112405787..112407799,112412836..112413110,
                     112415231..112415373,112423753..112425008,
                     112430215..112430478))
                     /gene="TMEM168"
                     /gene_synonym="DKFZp564C012; FLJ13576"
                     /product="transmembrane protein 168"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022484.4"
                     /db_xref="GI:98961140"
                     /db_xref="GeneID:64418"
                     /db_xref="HGNC:25826"
                     /db_xref="HPRD:07831"
     CDS             complement(join(112407252..112407799,112412836..112413110,
                     112415231..112415373,112423753..112424880))
                     /gene="TMEM168"
                     /gene_synonym="DKFZp564C012; FLJ13576"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 168"
                     /protein_id="NP_071929.3"
                     /db_xref="GI:98961141"
                     /db_xref="CCDS:CCDS5757.1"
                     /db_xref="GeneID:64418"
                     /db_xref="HGNC:25826"
                     /db_xref="HPRD:07831"
     gene            complement(112459202..112579932)
                     /gene="C7orf60"
                     /gene_synonym="FLJ31818"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:154743"
                     /db_xref="HGNC:26475"
                     /db_xref="HPRD:08108"
     mRNA            complement(join(112459202..112462428,112472616..112472730,
                     112535624..112535794,112555361..112555502,
                     112579646..112579932))
                     /gene="C7orf60"
                     /gene_synonym="FLJ31818"
                     /product="chromosome 7 open reading frame 60"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152556.2"
                     /db_xref="GI:116812631"
                     /db_xref="GeneID:154743"
                     /db_xref="HGNC:26475"
                     /db_xref="HPRD:08108"
     CDS             complement(join(112461799..112462428,112472616..112472730,
                     112535624..112535794,112555361..112555502,
                     112579646..112579805))
                     /gene="C7orf60"
                     /gene_synonym="FLJ31818"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC154743"
                     /protein_id="NP_689769.2"
                     /db_xref="GI:116812632"
                     /db_xref="CCDS:CCDS43634.1"
                     /db_xref="GeneID:154743"
                     /db_xref="HGNC:26475"
                     /db_xref="HPRD:08108"
     gene            complement(112720468..112727833)
                     /gene="GPR85"
                     /gene_synonym="FLJ50993; FLJ51159; FLJ99433; SREB; SREB2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54329"
                     /db_xref="HGNC:4536"
                     /db_xref="HPRD:05543"
                     /db_xref="MIM:605188"
     mRNA            complement(join(112720468..112724946,112726047..112726164,
                     112727495..112727833))
                     /gene="GPR85"
                     /gene_synonym="FLJ50993; FLJ51159; FLJ99433; SREB; SREB2"
                     /product="G protein-coupled receptor 85, transcript
                     variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001146265.1"
                     /db_xref="GI:226342975"
                     /db_xref="GeneID:54329"
                     /db_xref="HGNC:4536"
                     /db_xref="MIM:605188"
                     /db_xref="HPRD:05543"
     mRNA            complement(join(112720468..112724946,112726047..112726161,
                     112727495..112727833))
                     /gene="GPR85"
                     /gene_synonym="FLJ50993; FLJ51159; FLJ99433; SREB; SREB2"
                     /product="G protein-coupled receptor 85, transcript
                     variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018970.6"
                     /db_xref="GI:226342974"
                     /db_xref="GeneID:54329"
                     /db_xref="HGNC:4536"
                     /db_xref="HPRD:05543"
                     /db_xref="MIM:605188"
     mRNA            complement(join(112720468..112724946,112726047..112726164,
                     112726377..112726542))
                     /gene="GPR85"
                     /gene_synonym="FLJ50993; FLJ51159; FLJ99433; SREB; SREB2"
                     /product="G protein-coupled receptor 85, transcript
                     variant 4"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001146267.1"
                     /db_xref="GI:226342979"
                     /db_xref="GeneID:54329"
                     /db_xref="HGNC:4536"
                     /db_xref="MIM:605188"
                     /db_xref="HPRD:05543"
     mRNA            complement(join(112720468..112724946,
                     112726047..112726393))
                     /gene="GPR85"
                     /gene_synonym="FLJ50993; FLJ51159; FLJ99433; SREB; SREB2"
                     /product="G protein-coupled receptor 85, transcript
                     variant 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001146266.1"
                     /db_xref="GI:226342977"
                     /db_xref="GeneID:54329"
                     /db_xref="HGNC:4536"
                     /db_xref="MIM:605188"
                     /db_xref="HPRD:05543"
     CDS             complement(112723664..112724776)
                     /gene="GPR85"
                     /gene_synonym="FLJ50993; FLJ51159; FLJ99433; SREB; SREB2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable G-protein coupled receptor 85"
                     /protein_id="NP_061843.3"
                     /db_xref="GI:153266936"
                     /db_xref="CCDS:CCDS5758.1"
                     /db_xref="GeneID:54329"
                     /db_xref="HGNC:4536"
                     /db_xref="HPRD:05543"
                     /db_xref="MIM:605188"
     CDS             complement(112723664..112724776)
                     /gene="GPR85"
                     /gene_synonym="FLJ50993; FLJ51159; FLJ99433; SREB; SREB2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable G-protein coupled receptor 85"
                     /protein_id="NP_001139737.1"
                     /db_xref="GI:226342976"
                     /db_xref="CCDS:CCDS5758.1"
                     /db_xref="GeneID:54329"
                     /db_xref="HGNC:4536"
                     /db_xref="HPRD:05543"
                     /db_xref="MIM:605188"
     CDS             complement(112723664..112724776)
                     /gene="GPR85"
                     /gene_synonym="FLJ50993; FLJ51159; FLJ99433; SREB; SREB2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable G-protein coupled receptor 85"
                     /protein_id="NP_001139738.1"
                     /db_xref="GI:226342978"
                     /db_xref="CCDS:CCDS5758.1"
                     /db_xref="GeneID:54329"
                     /db_xref="HGNC:4536"
                     /db_xref="HPRD:05543"
                     /db_xref="MIM:605188"
     CDS             complement(112723664..112724776)
                     /gene="GPR85"
                     /gene_synonym="FLJ50993; FLJ51159; FLJ99433; SREB; SREB2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable G-protein coupled receptor 85"
                     /protein_id="NP_001139739.1"
                     /db_xref="GI:226342980"
                     /db_xref="CCDS:CCDS5758.1"
                     /db_xref="GeneID:54329"
                     /db_xref="HGNC:4536"
                     /db_xref="HPRD:05543"
                     /db_xref="MIM:605188"
     gene            complement(112756773..112758637)
                     /gene="LOC401397"
                     /gene_synonym="MGC104490"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:401397"
     misc_RNA        complement(join(112756773..112757662,112758123..112758216,
                     112758495..112758637))
                     /gene="LOC401397"
                     /gene_synonym="MGC104490"
                     /product="hypothetical LOC401397, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024412.1"
                     /db_xref="GI:212276287"
                     /db_xref="GeneID:401397"
     misc_RNA        complement(join(112756773..112757662,112758123..112758216,
                     112758583..112758637))
                     /gene="LOC401397"
                     /gene_synonym="MGC104490"
                     /product="hypothetical LOC401397, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_015442.1"
                     /db_xref="GI:212276296"
                     /db_xref="GeneID:401397"
     gene            113091130..113091456
                     /gene="TSRM"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 1 Protein"
                     /db_xref="GeneID:100287664"
     misc_RNA        113091130..113091456
                     /gene="TSRM"
                     /product="zinc finger domain-related protein TSRM"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 1 Protein"
                     /transcript_id="XR_132531.1"
                     /db_xref="GI:341915387"
                     /db_xref="GeneID:100287664"
     gene            complement(113516882..113559082)
                     /gene="PPP1R3A"
                     /gene_synonym="GM; PP1G; PPP1R3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5506"
                     /db_xref="HGNC:9291"
                     /db_xref="HPRD:02950"
                     /db_xref="MIM:600917"
     mRNA            complement(join(113516882..113520180,113522094..113522218,
                     113522317..113522375,113558270..113559082))
                     /gene="PPP1R3A"
                     /gene_synonym="GM; PP1G; PPP1R3"
                     /product="protein phosphatase 1, regulatory (inhibitor)
                     subunit 3A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002711.3"
                     /db_xref="GI:167614501"
                     /db_xref="GeneID:5506"
                     /db_xref="HGNC:9291"
                     /db_xref="HPRD:02950"
                     /db_xref="MIM:600917"
     CDS             complement(join(113517778..113520180,113522094..113522218,
                     113522317..113522375,113558270..113559051))
                     /gene="PPP1R3A"
                     /gene_synonym="GM; PP1G; PPP1R3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein phosphatase 1 regulatory subunit 3A"
                     /protein_id="NP_002702.2"
                     /db_xref="GI:167614502"
                     /db_xref="CCDS:CCDS5759.1"
                     /db_xref="GeneID:5506"
                     /db_xref="HGNC:9291"
                     /db_xref="HPRD:02950"
                     /db_xref="MIM:600917"
     gene            113726365..114333827
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="HPRD:05611"
                     /db_xref="MIM:605317"
     misc_RNA        join(113726365..113726666,113928074..113928164,
                     114066557..114066734,114174672..114174761,
                     114178381..114178438,114210862..114210936,
                     114268595..114268732,114269647..114269697,
                     114269860..114270060,114271583..114271760,
                     114282465..114282678,114284740..114284844,
                     114292258..114292345,114293981..114294064,
                     114299411..114299487,114299627..114299728,
                     114302120..114302241,114303505..114303574,
                     114304328..114304491,114329837..114333827)
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /product="forkhead box P2, transcript variant 7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033766.1"
                     /db_xref="GI:298566296"
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="MIM:605317"
                     /db_xref="HPRD:05611"
     gene            complement(113937122..113937517)
                     /gene="RPL36P13"
                     /gene_synonym="RPL36_5_837"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271013"
                     /db_xref="HGNC:36941"
     mRNA            join(114055052..114055415,114066557..114066734,
                     114174672..114174761,114268595..114268732,
                     114269860..114270060,114271583..114271760,
                     114282465..114282678,114284740..114284844,
                     114292258..114292345,114293981..114294064,
                     114298121..114298322,114299411..114299487,
                     114299627..114299728,114302120..114302241,
                     114303505..114303574,114304328..114304491,
                     114329837..114333827)
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /product="forkhead box P2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014491.3"
                     /db_xref="GI:298566288"
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="HPRD:05611"
                     /db_xref="MIM:605317"
     mRNA            join(114055052..114055415,114066557..114066734,
                     114174672..114174761,114210862..114210936,
                     114268595..114268732,114269860..114270060,
                     114271583..114271760,114282465..114282678,
                     114284740..114284844,114292258..114292345,
                     114293981..114294064,114298121..114298322,
                     114299411..114299487,114299627..114299728,
                     114302120..114302241,114303505..114303574,
                     114304328..114304491,114329837..114333827)
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /product="forkhead box P2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_148898.3"
                     /db_xref="GI:298566289"
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="MIM:605317"
                     /db_xref="HPRD:05611"
     mRNA            join(114055052..114055415,114066557..114066734,
                     114174672..114174761,114268595..114268732,
                     114269647..114269697,114269860..114270060,
                     114271583..114271760,114282465..114282678,
                     114284740..114284844,114292258..114292345,
                     114293981..114294064,114298121..114298322,
                     114299411..114299487,114299627..114299728,
                     114302120..114302241,114303505..114303574,
                     114304328..114304491,114329837..114333827)
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /product="forkhead box P2, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_148900.3"
                     /db_xref="GI:298566292"
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="MIM:605317"
                     /db_xref="HPRD:05611"
     mRNA            join(114055052..114055415,114066557..114066734,
                     114174672..114174761,114268595..114268732,
                     114269860..114270060,114271586..114271760,
                     114282465..114282678,114284740..114284844,
                     114292258..114292345,114293981..114294064,
                     114298121..114298322,114299411..114299487,
                     114299627..114299728,114302120..114302241,
                     114303505..114303574,114304328..114304491,
                     114329837..114333827)
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /product="forkhead box P2, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001172766.2"
                     /db_xref="GI:298566293"
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="MIM:605317"
                     /db_xref="HPRD:05611"
     misc_RNA        join(114055052..114055415,114066557..114066734,
                     114174672..114174761,114178381..114178438,
                     114268595..114268732,114269860..114270060,
                     114271583..114271760,114282465..114282678,
                     114284740..114284844,114292258..114292345,
                     114293981..114294064,114298121..114298322,
                     114299411..114299487,114299627..114299728,
                     114302120..114302241,114303505..114303574,
                     114304328..114304491,114329837..114333827)
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /product="forkhead box P2, transcript variant 8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033767.1"
                     /db_xref="GI:298566295"
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="MIM:605317"
                     /db_xref="HPRD:05611"
     mRNA            join(114066557..114066734,114174672..114174761,
                     114268595..114268732,114269860..114270060,
                     114271583..114271760,114282465..114282678,
                     114284740..114284844,114292258..114292345,
                     114293981..114294198)
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /product="forkhead box P2, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_148899.3"
                     /db_xref="GI:298566290"
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="MIM:605317"
                     /db_xref="HPRD:05611"
     mRNA            join(114066557..114066734,114174672..114174761,
                     114210862..114210936,114268595..114268732,
                     114269860..114270060,114271583..114271760,
                     114282465..114282678,114284740..114284844,
                     114292258..114292345,114293981..114294198)
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /product="forkhead box P2, transcript variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001172767.2"
                     /db_xref="GI:298566294"
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="MIM:605317"
                     /db_xref="HPRD:05611"
     CDS             join(114066567..114066734,114174672..114174761,
                     114268595..114268732,114269860..114270060,
                     114271583..114271760,114282465..114282678,
                     114284740..114284844,114292258..114292345,
                     114293981..114294064,114298121..114298322,
                     114299411..114299487,114299627..114299728,
                     114302120..114302241,114303505..114303574,
                     114304328..114304491,114329837..114329981)
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /note="isoform I is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="forkhead box protein P2 isoform I"
                     /protein_id="NP_055306.1"
                     /db_xref="GI:17017963"
                     /db_xref="CCDS:CCDS5760.1"
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="HPRD:05611"
                     /db_xref="MIM:605317"
     CDS             join(114066567..114066734,114174672..114174761,
                     114210862..114210936,114268595..114268732,
                     114269860..114270060,114271583..114271760,
                     114282465..114282678,114284740..114284844,
                     114292258..114292345,114293981..114294064,
                     114298121..114298322,114299411..114299487,
                     114299627..114299728,114302120..114302241,
                     114303505..114303574,114304328..114304491,
                     114329837..114329981)
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /note="isoform II is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="forkhead box protein P2 isoform II"
                     /protein_id="NP_683696.2"
                     /db_xref="GI:149999352"
                     /db_xref="CCDS:CCDS43635.1"
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="HPRD:05611"
                     /db_xref="MIM:605317"
     CDS             join(114066567..114066734,114174672..114174761,
                     114268595..114268732,114269647..114269697,
                     114269860..114270060,114271583..114271760,
                     114282465..114282678,114284740..114284844,
                     114292258..114292345,114293981..114294064,
                     114298121..114298322,114299411..114299487,
                     114299627..114299728,114302120..114302241,
                     114303505..114303574,114304328..114304491,
                     114329837..114329981)
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /note="isoform IV is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="forkhead box protein P2 isoform IV"
                     /protein_id="NP_683698.2"
                     /db_xref="GI:289666774"
                     /db_xref="CCDS:CCDS55154.1"
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="HPRD:05611"
                     /db_xref="MIM:605317"
     CDS             join(114066567..114066734,114174672..114174761,
                     114268595..114268732,114269860..114270060,
                     114271586..114271760,114282465..114282678,
                     114284740..114284844,114292258..114292345,
                     114293981..114294064,114298121..114298322,
                     114299411..114299487,114299627..114299728,
                     114302120..114302241,114303505..114303574,
                     114304328..114304491,114329837..114329981)
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /note="isoform V is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="forkhead box protein P2 isoform V"
                     /protein_id="NP_001166237.1"
                     /db_xref="GI:289666732"
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="MIM:605317"
                     /db_xref="HPRD:05611"
     CDS             join(114066567..114066734,114174672..114174761,
                     114268595..114268732,114269860..114270060,
                     114271583..114271760,114282465..114282678,
                     114284740..114284844,114292258..114292345,
                     114293981..114294097)
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /note="isoform III is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="forkhead box protein P2 isoform III"
                     /protein_id="NP_683697.2"
                     /db_xref="GI:298566291"
                     /db_xref="CCDS:CCDS5761.2"
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="HPRD:05611"
                     /db_xref="MIM:605317"
     CDS             join(114066567..114066734,114174672..114174761,
                     114210862..114210936,114268595..114268732,
                     114269860..114270060,114271583..114271760,
                     114282465..114282678,114284740..114284844,
                     114292258..114292345,114293981..114294097)
                     /gene="FOXP2"
                     /gene_synonym="CAGH44; DKFZp686H1726; SPCH1; TNRC10"
                     /note="isoform VI is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="forkhead box protein P2 isoform VI"
                     /protein_id="NP_001166238.1"
                     /db_xref="GI:289666734"
                     /db_xref="GeneID:93986"
                     /db_xref="HGNC:13875"
                     /db_xref="MIM:605317"
                     /db_xref="HPRD:05611"
     gene            114293400..114293510
                     /gene="MIR3666"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100500896"
                     /db_xref="HGNC:38940"
                     /db_xref="miRBase:MI0016067"
     ncRNA           114293400..114293510
                     /gene="MIR3666"
                     /ncRNA_class="miRNA"
                     /product="microRNA 3666"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037439.1"
                     /db_xref="GI:312147459"
                     /db_xref="GeneID:100500896"
                     /db_xref="HGNC:38940"
                     /db_xref="miRBase:MI0016067"
     gene            114562209..114659970
                     /gene="MDFIC"
                     /gene_synonym="HIC"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:29969"
                     /db_xref="HGNC:28870"
                     /db_xref="HPRD:17103"
     mRNA            join(114562209..114562691,114562982..114563182,
                     114582330..114582452,114619561..114619836,
                     114655742..114659970)
                     /gene="MDFIC"
                     /gene_synonym="HIC"
                     /product="MyoD family inhibitor domain containing,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_199072.4"
                     /db_xref="GI:261599040"
                     /db_xref="GeneID:29969"
                     /db_xref="HGNC:28870"
                     /db_xref="HPRD:17103"
     mRNA            join(114562209..114562691,114562982..114563182,
                     114582330..114582452,114619561..114619836,
                     114655742..114659970)
                     /gene="MDFIC"
                     /gene_synonym="HIC"
                     /product="MyoD family inhibitor domain containing,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001166345.1"
                     /db_xref="GI:261599041"
                     /db_xref="GeneID:29969"
                     /db_xref="HGNC:28870"
                     /db_xref="HPRD:17103"
     mRNA            join(114562209..114562691,114562982..114563182,
                     114563514..114563720)
                     /gene="MDFIC"
                     /gene_synonym="HIC"
                     /product="MyoD family inhibitor domain containing,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001166346.1"
                     /db_xref="GI:261599043"
                     /db_xref="GeneID:29969"
                     /db_xref="HGNC:28870"
                     /db_xref="HPRD:17103"
     CDS             join(114562472..114562691,114562982..114563182,
                     114582330..114582452,114619561..114619836,
                     114655742..114655989)
                     /gene="MDFIC"
                     /gene_synonym="HIC"
                     /note=";
                     isoform p40 is encoded by transcript variant 1;
                     non-AUG (GUG) translation initiation codon; Derived by
                     automated computational analysis using gene prediction
                     method: BestRefseq."
                     /codon_start=1
                     /transl_except=(pos:114562472..114562474,aa:Met)
                     /product="myoD family inhibitor domain-containing protein
                     isoform p40"
                     /protein_id="NP_951038.1"
                     /db_xref="GI:40018612"
                     /db_xref="CCDS:CCDS34737.1"
                     /db_xref="GeneID:29969"
                     /db_xref="HGNC:28870"
                     /db_xref="HPRD:17103"
     CDS             join(114562472..114562691,114562982..114563182,
                     114563514..114563551)
                     /gene="MDFIC"
                     /gene_synonym="HIC"
                     /note=";
                     isoform c is encoded by transcript variant 2;
                     non-AUG (GUG) translation initiation codon; Derived by
                     automated computational analysis using gene prediction
                     method: BestRefseq."
                     /codon_start=1
                     /transl_except=(pos:114562472..114562474,aa:Met)
                     /product="myoD family inhibitor domain-containing protein
                     isoform c"
                     /protein_id="NP_001159818.3"
                     /db_xref="GI:289547634"
                     /db_xref="GeneID:29969"
                     /db_xref="HGNC:28870"
                     /db_xref="HPRD:17103"
     CDS             join(114563089..114563182,114582330..114582452,
                     114619561..114619836,114655742..114655989)
                     /gene="MDFIC"
                     /gene_synonym="HIC"
                     /note="isoform p32 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="myoD family inhibitor domain-containing protein
                     isoform p32"
                     /protein_id="NP_001159817.1"
                     /db_xref="GI:261599042"
                     /db_xref="CCDS:CCDS55155.1"
                     /db_xref="GeneID:29969"
                     /db_xref="HGNC:28870"
                     /db_xref="HPRD:17103"
     gene            complement(114776630..114777216)
                     /gene="RAC1P6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100422657"
                     /db_xref="HGNC:42006"
     gene            complement(115319399..115322672)
                     /gene="LOC100506489"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 4 ESTs"
                     /db_xref="GeneID:100506489"
     misc_RNA        complement(join(115319399..115320425,
                     115322443..115322672))
                     /gene="LOC100506489"
                     /product="hypothetical LOC100506489"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 4 ESTs"
                     /transcript_id="XR_108799.1"
                     /db_xref="GI:310120078"
                     /db_xref="GeneID:100506489"
     gene            complement(115575202..115670798)
                     /gene="TFEC"
                     /gene_synonym="bHLHe34; TCFEC; TFECL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:22797"
                     /db_xref="HGNC:11754"
                     /db_xref="HPRD:05294"
                     /db_xref="MIM:604732"
     mRNA            complement(join(115575202..115580985,115581947..115582094,
                     115590928..115591003,115594640..115594696,
                     115596733..115596847,115614224..115614310,
                     115624316..115624567,115670687..115670798))
                     /gene="TFEC"
                     /gene_synonym="bHLHe34; TCFEC; TFECL"
                     /product="transcription factor EC, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012252.2"
                     /db_xref="GI:64762384"
                     /db_xref="GeneID:22797"
                     /db_xref="HGNC:11754"
                     /db_xref="HPRD:05294"
                     /db_xref="MIM:604732"
     mRNA            complement(join(115575202..115580985,115581947..115582094,
                     115590928..115591003,115594640..115594696,
                     115596733..115596847,115624316..115624567,
                     115670687..115670798))
                     /gene="TFEC"
                     /gene_synonym="bHLHe34; TCFEC; TFECL"
                     /product="transcription factor EC, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001018058.1"
                     /db_xref="GI:64762401"
                     /db_xref="GeneID:22797"
                     /db_xref="HGNC:11754"
                     /db_xref="MIM:604732"
                     /db_xref="HPRD:05294"
     CDS             complement(join(115580605..115580985,115581947..115582094,
                     115590928..115591003,115594640..115594696,
                     115596733..115596847,115614224..115614310,
                     115624316..115624495))
                     /gene="TFEC"
                     /gene_synonym="bHLHe34; TCFEC; TFECL"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transcription factor EC isoform a"
                     /protein_id="NP_036384.1"
                     /db_xref="GI:6912702"
                     /db_xref="CCDS:CCDS5762.1"
                     /db_xref="GeneID:22797"
                     /db_xref="HGNC:11754"
                     /db_xref="HPRD:05294"
                     /db_xref="MIM:604732"
     CDS             complement(join(115580605..115580985,115581947..115582094,
                     115590928..115591003,115594640..115594696,
                     115596733..115596847,115624316..115624495))
                     /gene="TFEC"
                     /gene_synonym="bHLHe34; TCFEC; TFECL"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transcription factor EC isoform b"
                     /protein_id="NP_001018068.1"
                     /db_xref="GI:64762402"
                     /db_xref="CCDS:CCDS34738.1"
                     /db_xref="GeneID:22797"
                     /db_xref="HGNC:11754"
                     /db_xref="HPRD:05294"
                     /db_xref="MIM:604732"
     gene            115850547..115898837
                     /gene="TES"
                     /gene_synonym="DKFZp586B2022; MGC1146; TESS; TESS-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26136"
                     /db_xref="HGNC:14620"
                     /db_xref="HPRD:05833"
                     /db_xref="MIM:606085"
     mRNA            join(115850547..115850788,115874588..115874673,
                     115889074..115889326,115890215..115890550,
                     115891814..115892029,115892372..115892530,
                     115897348..115898837)
                     /gene="TES"
                     /gene_synonym="DKFZp586B2022; MGC1146; TESS; TESS-2"
                     /product="testis derived transcript (3 LIM domains),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015641.3"
                     /db_xref="GI:325197160"
                     /db_xref="GeneID:26136"
                     /db_xref="HGNC:14620"
                     /db_xref="HPRD:05833"
                     /db_xref="MIM:606085"
     CDS             join(115850762..115850788,115874588..115874673,
                     115889074..115889326,115890215..115890550,
                     115891814..115892029,115892372..115892530,
                     115897348..115897536)
                     /gene="TES"
                     /gene_synonym="DKFZp586B2022; MGC1146; TESS; TESS-2"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="testin isoform 1"
                     /protein_id="NP_056456.1"
                     /db_xref="GI:7661666"
                     /db_xref="CCDS:CCDS5763.1"
                     /db_xref="GeneID:26136"
                     /db_xref="HGNC:14620"
                     /db_xref="HPRD:05833"
                     /db_xref="MIM:606085"
     mRNA            join(115863005..115863080,115874588..115874673,
                     115889074..115889326,115890215..115890550,
                     115891814..115892029,115892372..115892530,
                     115897348..115898837)
                     /gene="TES"
                     /gene_synonym="DKFZp586B2022; MGC1146; TESS; TESS-2"
                     /product="testis derived transcript (3 LIM domains),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152829.2"
                     /db_xref="GI:325197169"
                     /db_xref="GeneID:26136"
                     /db_xref="HGNC:14620"
                     /db_xref="MIM:606085"
                     /db_xref="HPRD:05833"
     CDS             join(115874588..115874673,115889074..115889326,
                     115890215..115890550,115891814..115892029,
                     115892372..115892530,115897348..115897536)
                     /gene="TES"
                     /gene_synonym="DKFZp586B2022; MGC1146; TESS; TESS-2"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="testin isoform 2"
                     /protein_id="NP_690042.1"
                     /db_xref="GI:23238188"
                     /db_xref="CCDS:CCDS5764.1"
                     /db_xref="GeneID:26136"
                     /db_xref="HGNC:14620"
                     /db_xref="HPRD:05833"
                     /db_xref="MIM:606085"
     gene            116139655..116148595
                     /gene="CAV2"
                     /gene_synonym="CAV; MGC12294"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:858"
                     /db_xref="HGNC:1528"
                     /db_xref="HPRD:03029"
                     /db_xref="MIM:601048"
     mRNA            join(116139655..116139985,116140314..116140501,
                     116146025..116148595)
                     /gene="CAV2"
                     /gene_synonym="CAV; MGC12294"
                     /product="caveolin 2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001233.4"
                     /db_xref="GI:332164661"
                     /db_xref="GeneID:858"
                     /db_xref="HGNC:1528"
                     /db_xref="HPRD:03029"
                     /db_xref="MIM:601048"
     mRNA            join(116139655..116139985,116140314..116140501,
                     116146025..116148595)
                     /gene="CAV2"
                     /gene_synonym="CAV; MGC12294"
                     /product="caveolin 2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001206747.1"
                     /db_xref="GI:332164663"
                     /db_xref="GeneID:858"
                     /db_xref="HGNC:1528"
                     /db_xref="MIM:601048"
                     /db_xref="HPRD:03029"
     mRNA            join(116139655..116139985,116146025..116148595)
                     /gene="CAV2"
                     /gene_synonym="CAV; MGC12294"
                     /product="caveolin 2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198212.2"
                     /db_xref="GI:332164662"
                     /db_xref="GeneID:858"
                     /db_xref="HGNC:1528"
                     /db_xref="HPRD:03029"
                     /db_xref="MIM:601048"
     CDS             join(116139836..116139985,116146025..116146213)
                     /gene="CAV2"
                     /gene_synonym="CAV; MGC12294"
                     /note="isoform c is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caveolin-2 isoform c"
                     /protein_id="NP_937855.1"
                     /db_xref="GI:38176292"
                     /db_xref="CCDS:CCDS5765.1"
                     /db_xref="GeneID:858"
                     /db_xref="HGNC:1528"
                     /db_xref="HPRD:03029"
                     /db_xref="MIM:601048"
     CDS             join(116139836..116139985,116140314..116140501,
                     116146025..116146175)
                     /gene="CAV2"
                     /gene_synonym="CAV; MGC12294"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caveolin-2 isoform a"
                     /protein_id="NP_001224.1"
                     /db_xref="GI:4557413"
                     /db_xref="CCDS:CCDS5766.1"
                     /db_xref="GeneID:858"
                     /db_xref="HGNC:1528"
                     /db_xref="HPRD:03029"
                     /db_xref="MIM:601048"
     CDS             join(116139875..116139985,116140314..116140501,
                     116146025..116146175)
                     /gene="CAV2"
                     /gene_synonym="CAV; MGC12294"
                     /note="isoform b is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caveolin-2 isoform b"
                     /protein_id="NP_001193676.1"
                     /db_xref="GI:332164664"
                     /db_xref="GeneID:858"
                     /db_xref="HGNC:1528"
                     /db_xref="MIM:601048"
                     /db_xref="HPRD:03029"
     mRNA            join(116140098..116140501,116146025..116148595)
                     /gene="CAV2"
                     /gene_synonym="CAV; MGC12294"
                     /product="caveolin 2, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001206748.1"
                     /db_xref="GI:332164665"
                     /db_xref="GeneID:858"
                     /db_xref="HGNC:1528"
                     /db_xref="MIM:601048"
                     /db_xref="HPRD:03029"
     CDS             join(116140413..116140501,116146025..116146175)
                     /gene="CAV2"
                     /gene_synonym="CAV; MGC12294"
                     /note="isoform d is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caveolin-2 isoform d"
                     /protein_id="NP_001193677.1"
                     /db_xref="GI:332164666"
                     /db_xref="GeneID:858"
                     /db_xref="HGNC:1528"
                     /db_xref="MIM:601048"
                     /db_xref="HPRD:03029"
     gene            116164839..116201239
                     /gene="CAV1"
                     /gene_synonym="BSCL3; CGL3; MSTP085; VIP21"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:857"
                     /db_xref="HGNC:1527"
                     /db_xref="HPRD:03028"
                     /db_xref="MIM:601047"
     mRNA            join(116164839..116165146,116166579..116166743,
                     116199000..116201239)
                     /gene="CAV1"
                     /gene_synonym="BSCL3; CGL3; MSTP085; VIP21"
                     /product="caveolin 1, caveolae protein, 22kDa, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001753.4"
                     /db_xref="GI:290542357"
                     /db_xref="GeneID:857"
                     /db_xref="HGNC:1527"
                     /db_xref="HPRD:03028"
                     /db_xref="MIM:601047"
     mRNA            join(116165063..116165859,116166579..116166743,
                     116199000..116201239)
                     /gene="CAV1"
                     /gene_synonym="BSCL3; CGL3; MSTP085; VIP21"
                     /product="caveolin 1, caveolae protein, 22kDa, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001172895.1"
                     /db_xref="GI:290542358"
                     /db_xref="GeneID:857"
                     /db_xref="HGNC:1527"
                     /db_xref="MIM:601047"
                     /db_xref="HPRD:03028"
     CDS             join(116165117..116165146,116166579..116166743,
                     116199000..116199341)
                     /gene="CAV1"
                     /gene_synonym="BSCL3; CGL3; MSTP085; VIP21"
                     /note="isoform alpha is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caveolin-1 isoform alpha"
                     /protein_id="NP_001744.2"
                     /db_xref="GI:15451856"
                     /db_xref="CCDS:CCDS5767.1"
                     /db_xref="GeneID:857"
                     /db_xref="HGNC:1527"
                     /db_xref="HPRD:03028"
                     /db_xref="MIM:601047"
     mRNA            join(116166347..116166743,116199000..116201239)
                     /gene="CAV1"
                     /gene_synonym="BSCL3; CGL3; MSTP085; VIP21"
                     /product="caveolin 1, caveolae protein, 22kDa, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001172896.1"
                     /db_xref="GI:290542360"
                     /db_xref="GeneID:857"
                     /db_xref="HGNC:1527"
                     /db_xref="MIM:601047"
                     /db_xref="HPRD:03028"
     mRNA            join(116166412..116166442,116166579..116166743,
                     116199000..116201239)
                     /gene="CAV1"
                     /gene_synonym="BSCL3; CGL3; MSTP085; VIP21"
                     /product="caveolin 1, caveolae protein, 22kDa, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001172897.1"
                     /db_xref="GI:290542362"
                     /db_xref="GeneID:857"
                     /db_xref="HGNC:1527"
                     /db_xref="MIM:601047"
                     /db_xref="HPRD:03028"
     CDS             join(116166642..116166743,116199000..116199341)
                     /gene="CAV1"
                     /gene_synonym="BSCL3; CGL3; MSTP085; VIP21"
                     /note="isoform beta is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caveolin-1 isoform beta"
                     /protein_id="NP_001166366.1"
                     /db_xref="GI:290542359"
                     /db_xref="CCDS:CCDS55156.1"
                     /db_xref="GeneID:857"
                     /db_xref="HGNC:1527"
                     /db_xref="HPRD:03028"
                     /db_xref="MIM:601047"
     CDS             join(116166642..116166743,116199000..116199341)
                     /gene="CAV1"
                     /gene_synonym="BSCL3; CGL3; MSTP085; VIP21"
                     /note="isoform beta is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caveolin-1 isoform beta"
                     /protein_id="NP_001166367.1"
                     /db_xref="GI:290542361"
                     /db_xref="CCDS:CCDS55156.1"
                     /db_xref="GeneID:857"
                     /db_xref="HGNC:1527"
                     /db_xref="HPRD:03028"
                     /db_xref="MIM:601047"
     CDS             join(116166642..116166743,116199000..116199341)
                     /gene="CAV1"
                     /gene_synonym="BSCL3; CGL3; MSTP085; VIP21"
                     /note="isoform beta is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caveolin-1 isoform beta"
                     /protein_id="NP_001166368.1"
                     /db_xref="GI:290542363"
                     /db_xref="CCDS:CCDS55156.1"
                     /db_xref="GeneID:857"
                     /db_xref="HGNC:1527"
                     /db_xref="HPRD:03028"
                     /db_xref="MIM:601047"
     gene            116312459..116438440
                     /gene="MET"
                     /gene_synonym="AUTS9; c-Met; HGFR; RCCP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4233"
                     /db_xref="HGNC:7029"
                     /db_xref="MIM:164860"
     mRNA            join(116312459..116312631,116339125..116340338,
                     116371722..116371913,116380004..116380138,
                     116380906..116381079,116395409..116395569,
                     116397491..116397593,116397692..116397828,
                     116398513..116398674,116399391..116399544,
                     116403104..116403322,116409699..116409845,
                     116411552..116411708,116411903..116412043,
                     116414935..116415165,116417443..116417523,
                     116418830..116419011,116422042..116422151,
                     116423358..116423523,116435709..116435845,
                     116435941..116438440)
                     /gene="MET"
                     /gene_synonym="AUTS9; c-Met; HGFR; RCCP2"
                     /product="met proto-oncogene (hepatocyte growth factor
                     receptor), transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127500.1"
                     /db_xref="GI:188595715"
                     /db_xref="GeneID:4233"
                     /db_xref="HGNC:7029"
                     /db_xref="MIM:164860"
     mRNA            join(116312459..116312631,116339125..116340338,
                     116371722..116371913,116380004..116380138,
                     116380906..116381079,116395409..116395569,
                     116397491..116397593,116397692..116397828,
                     116398513..116398674,116399445..116399544,
                     116403104..116403322,116409699..116409845,
                     116411552..116411708,116411903..116412043,
                     116414935..116415165,116417443..116417523,
                     116418830..116419011,116422042..116422151,
                     116423358..116423523,116435709..116435845,
                     116435941..116438440)
                     /gene="MET"
                     /gene_synonym="AUTS9; c-Met; HGFR; RCCP2"
                     /product="met proto-oncogene (hepatocyte growth factor
                     receptor), transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000245.2"
                     /db_xref="GI:42741654"
                     /db_xref="GeneID:4233"
                     /db_xref="HGNC:7029"
                     /db_xref="HPRD:01280"
                     /db_xref="MIM:164860"
     CDS             join(116339139..116340338,116371722..116371913,
                     116380004..116380138,116380906..116381079,
                     116395409..116395569,116397491..116397593,
                     116397692..116397828,116398513..116398674,
                     116399391..116399544,116403104..116403322,
                     116409699..116409845,116411552..116411708,
                     116411903..116412043,116414935..116415165,
                     116417443..116417523,116418830..116419011,
                     116422042..116422151,116423358..116423523,
                     116435709..116435845,116435941..116436178)
                     /gene="MET"
                     /gene_synonym="AUTS9; c-Met; HGFR; RCCP2"
                     /note="isoform a precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hepatocyte growth factor receptor isoform a
                     precursor"
                     /protein_id="NP_001120972.1"
                     /db_xref="GI:188595716"
                     /db_xref="CCDS:CCDS47689.1"
                     /db_xref="GeneID:4233"
                     /db_xref="HGNC:7029"
                     /db_xref="MIM:164860"
     CDS             join(116339139..116340338,116371722..116371913,
                     116380004..116380138,116380906..116381079,
                     116395409..116395569,116397491..116397593,
                     116397692..116397828,116398513..116398674,
                     116399445..116399544,116403104..116403322,
                     116409699..116409845,116411552..116411708,
                     116411903..116412043,116414935..116415165,
                     116417443..116417523,116418830..116419011,
                     116422042..116422151,116423358..116423523,
                     116435709..116435845,116435941..116436178)
                     /gene="MET"
                     /gene_synonym="AUTS9; c-Met; HGFR; RCCP2"
                     /note="isoform b precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hepatocyte growth factor receptor isoform b
                     precursor"
                     /protein_id="NP_000236.2"
                     /db_xref="GI:42741655"
                     /db_xref="CCDS:CCDS43636.1"
                     /db_xref="GeneID:4233"
                     /db_xref="HGNC:7029"
                     /db_xref="MIM:164860"
     gene            116502563..116559313
                     /gene="CAPZA2"
                     /gene_synonym="CAPPA2; CAPZ"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:830"
                     /db_xref="HGNC:1490"
                     /db_xref="HPRD:11871"
                     /db_xref="MIM:601571"
     mRNA            join(116502563..116502704,116528181..116528244,
                     116533048..116533099,116538826..116538889,
                     116544231..116544437,116546317..116546396,
                     116550287..116550365,116552123..116552194,
                     116556114..116556176,116557781..116559313)
                     /gene="CAPZA2"
                     /gene_synonym="CAPPA2; CAPZ"
                     /product="capping protein (actin filament) muscle Z-line,
                     alpha 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006136.2"
                     /db_xref="GI:41327721"
                     /db_xref="GeneID:830"
                     /db_xref="HGNC:1490"
                     /db_xref="HPRD:11871"
                     /db_xref="MIM:601571"
     CDS             join(116502666..116502704,116528181..116528244,
                     116533048..116533099,116538826..116538889,
                     116544231..116544437,116546317..116546396,
                     116550287..116550365,116552123..116552194,
                     116556114..116556176,116557781..116557921)
                     /gene="CAPZA2"
                     /gene_synonym="CAPPA2; CAPZ"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="F-actin-capping protein subunit alpha-2"
                     /protein_id="NP_006127.1"
                     /db_xref="GI:5453599"
                     /db_xref="CCDS:CCDS5768.1"
                     /db_xref="GeneID:830"
                     /db_xref="HGNC:1490"
                     /db_xref="HPRD:11871"
                     /db_xref="MIM:601571"
     gene            complement(116513505..116515596)
                     /gene="LOC100418716"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100418716"
     gene            complement(116592500..116594388)
                     /gene="ST7-AS1"
                     /gene_synonym="ST7AS1; ST7OT1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:93653"
                     /db_xref="HGNC:16000"
     ncRNA           complement(116592500..116594388)
                     /gene="ST7-AS1"
                     /gene_synonym="ST7AS1; ST7OT1"
                     /ncRNA_class="antisense_RNA"
                     /product="ST7 antisense RNA 1 (non-protein coding)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_002330.1"
                     /db_xref="GI:70778877"
                     /db_xref="GeneID:93653"
                     /db_xref="HGNC:16000"
     gene            116593381..116870077
                     /gene="ST7"
                     /gene_synonym="DKFZp762O2113; ETS7q; FAM4A; FAM4A1; HELG;
                     RAY1; SEN4; TSG7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7982"
                     /db_xref="HGNC:11351"
                     /db_xref="HPRD:09015"
                     /db_xref="MIM:600833"
     mRNA            join(116593381..116593745,116739816..116739898,
                     116759615..116759774,116769847..116769901,
                     116770545..116770660,116771939..116772014,
                     116776135..116776289,116778489..116778586,
                     116810916..116811030,116829375..116829447,
                     116830888..116830990,116849841..116849991,
                     116859138..116859230,116861977..116862116,
                     116869816..116870077)
                     /gene="ST7"
                     /gene_synonym="DKFZp762O2113; ETS7q; FAM4A; FAM4A1; HELG;
                     RAY1; SEN4; TSG7"
                     /product="suppression of tumorigenicity 7, transcript
                     variant a"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018412.3"
                     /db_xref="GI:54112123"
                     /db_xref="GeneID:7982"
                     /db_xref="HGNC:11351"
                     /db_xref="MIM:600833"
                     /db_xref="HPRD:09015"
     mRNA            join(116593381..116593745,116739816..116739898,
                     116759615..116759774,116769847..116769901,
                     116770545..116770660,116771939..116772014,
                     116774178..116774246,116776135..116776289,
                     116778489..116778586,116810916..116811030,
                     116829375..116829447,116830888..116830990,
                     116849841..116849991,116859138..116859230,
                     116861977..116862116,116862915..116863961)
                     /gene="ST7"
                     /gene_synonym="DKFZp762O2113; ETS7q; FAM4A; FAM4A1; HELG;
                     RAY1; SEN4; TSG7"
                     /product="suppression of tumorigenicity 7, transcript
                     variant b"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021908.2"
                     /db_xref="GI:54112122"
                     /db_xref="GeneID:7982"
                     /db_xref="HGNC:11351"
                     /db_xref="HPRD:09015"
                     /db_xref="MIM:600833"
     CDS             join(116593595..116593745,116739816..116739898,
                     116759615..116759774,116769847..116769901,
                     116770545..116770660,116771939..116772014,
                     116776135..116776289,116778489..116778586,
                     116810916..116811030,116829375..116829447,
                     116830888..116830990,116849841..116849991,
                     116859138..116859230,116861977..116862116,
                     116869816..116869911)
                     /gene="ST7"
                     /gene_synonym="DKFZp762O2113; ETS7q; FAM4A; FAM4A1; HELG;
                     RAY1; SEN4; TSG7"
                     /note="isoform a is encoded by transcript variant a;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="suppressor of tumorigenicity 7 protein isoform
                     a"
                     /protein_id="NP_060882.2"
                     /db_xref="GI:11761624"
                     /db_xref="CCDS:CCDS5769.1"
                     /db_xref="GeneID:7982"
                     /db_xref="HGNC:11351"
                     /db_xref="HPRD:09015"
                     /db_xref="MIM:600833"
     CDS             join(116593595..116593745,116739816..116739898,
                     116759615..116759774,116769847..116769901,
                     116770545..116770660,116771939..116772014,
                     116774178..116774246,116776135..116776289,
                     116778489..116778586,116810916..116811030,
                     116829375..116829447,116830888..116830990,
                     116849841..116849991,116859138..116859230,
                     116861977..116862116,116862915..116863034)
                     /gene="ST7"
                     /gene_synonym="DKFZp762O2113; ETS7q; FAM4A; FAM4A1; HELG;
                     RAY1; SEN4; TSG7"
                     /note="isoform b is encoded by transcript variant b;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="suppressor of tumorigenicity 7 protein isoform
                     b"
                     /protein_id="NP_068708.1"
                     /db_xref="GI:11761626"
                     /db_xref="CCDS:CCDS5770.1"
                     /db_xref="GeneID:7982"
                     /db_xref="HGNC:11351"
                     /db_xref="HPRD:09015"
                     /db_xref="MIM:600833"
     gene            116593953..116599867
                     /gene="ST7OT4"
                     /gene_synonym="NCRNA00042"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:338069"
                     /db_xref="HGNC:18835"
     misc_RNA        join(116593953..116594163,116594515..116594733,
                     116595028..116595207,116596477..116596777,
                     116599207..116599867)
                     /gene="ST7OT4"
                     /gene_synonym="NCRNA00042"
                     /product="ST7 overlapping transcript 4 (non-protein
                     coding)"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_002329.1"
                     /db_xref="GI:70778880"
                     /db_xref="GeneID:338069"
                     /db_xref="HGNC:18835"
     gene            complement(116610951..116613034)
                     /gene="TPM3P1"
                     /gene_synonym="TPM3L2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:252956"
                     /db_xref="HGNC:16350"
     gene            complement(116752346..116785614)
                     /gene="ST7-AS2"
                     /gene_synonym="ST7AS2; ST7OT2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:93654"
                     /db_xref="HGNC:16044"
     ncRNA           complement(join(116752346..116752721,116757955..116758037,
                     116768351..116768397,116770582..116770741,
                     116784221..116784307,116785450..116785614))
                     /gene="ST7-AS2"
                     /gene_synonym="ST7AS2; ST7OT2"
                     /ncRNA_class="antisense_RNA"
                     /product="ST7 antisense RNA 2 (non-protein coding)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_002331.2"
                     /db_xref="GI:197304737"
                     /db_xref="GeneID:93654"
                     /db_xref="HGNC:16044"
     gene            116822735..116861227
                     /gene="ST7OT3"
                     /gene_synonym="NCRNA00026"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:93655"
                     /db_xref="HGNC:16045"
     misc_RNA        join(116822735..116822799,116824179..116824253,
                     116829375..116829447,116830187..116830322,
                     116830888..116830990,116831689..116831815,
                     116838374..116838594,116839126..116839198,
                     116849841..116849991,116861221..116861227)
                     /gene="ST7OT3"
                     /gene_synonym="NCRNA00026"
                     /product="ST7 overlapping transcript 3 (non-protein
                     coding)"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_002332.1"
                     /db_xref="GI:194440730"
                     /db_xref="GeneID:93655"
                     /db_xref="HGNC:16045"
     gene            complement(116902872..116904946)
                     /gene="LOC100421782"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421782"
     gene            complement(116916685..116963343)
                     /gene="WNT2"
                     /gene_synonym="INT1L1; IRP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7472"
                     /db_xref="HGNC:12780"
                     /db_xref="HPRD:00999"
                     /db_xref="MIM:147870"
     mRNA            complement(join(116916685..116918438,116937666..116937930,
                     116955125..116955402,116960621..116960847,
                     116962961..116963343))
                     /gene="WNT2"
                     /gene_synonym="INT1L1; IRP"
                     /product="wingless-type MMTV integration site family
                     member 2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003391.2"
                     /db_xref="GI:195230749"
                     /db_xref="GeneID:7472"
                     /db_xref="HGNC:12780"
                     /db_xref="HPRD:00999"
                     /db_xref="MIM:147870"
     misc_RNA        complement(join(116916685..116918438,116937666..116937930,
                     116955125..116955338,116960621..116960847,
                     116962961..116963343))
                     /gene="WNT2"
                     /gene_synonym="INT1L1; IRP"
                     /product="wingless-type MMTV integration site family
                     member 2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024047.1"
                     /db_xref="GI:195230751"
                     /db_xref="GeneID:7472"
                     /db_xref="HGNC:12780"
                     /db_xref="MIM:147870"
                     /db_xref="HPRD:00999"
     CDS             complement(join(116918209..116918438,116937666..116937930,
                     116955125..116955402,116960621..116960847,
                     116962961..116963043))
                     /gene="WNT2"
                     /gene_synonym="INT1L1; IRP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein Wnt-2 precursor"
                     /protein_id="NP_003382.1"
                     /db_xref="GI:4507927"
                     /db_xref="CCDS:CCDS5771.1"
                     /db_xref="GeneID:7472"
                     /db_xref="HGNC:12780"
                     /db_xref="HPRD:00999"
                     /db_xref="MIM:147870"
     gene            complement(117003276..117067577)
                     /gene="ASZ1"
                     /gene_synonym="ALP1; ANKL1; C7orf7; CT1.19; GASZ;
                     MGC26634; Orf3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:136991"
                     /db_xref="HGNC:1350"
                     /db_xref="HPRD:10677"
                     /db_xref="MIM:605797"
     mRNA            complement(join(117003276..117003802,117007406..117007519,
                     117008666..117008771,117019992..117020101,
                     117021065..117021121,117022123..117022198,
                     117023040..117023164,117024780..117024914,
                     117025752..117025863,117060217..117060328,
                     117062291..117062413,117066890..117066989,
                     117067410..117067577))
                     /gene="ASZ1"
                     /gene_synonym="ALP1; ANKL1; C7orf7; CT1.19; GASZ;
                     MGC26634; Orf3"
                     /product="ankyrin repeat, SAM and basic leucine zipper
                     domain containing 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_130768.2"
                     /db_xref="GI:187608269"
                     /db_xref="GeneID:136991"
                     /db_xref="HGNC:1350"
                     /db_xref="HPRD:10677"
                     /db_xref="MIM:605797"
     misc_RNA        complement(join(117003369..117003802,117007406..117008771,
                     117019992..117020101,117021065..117021121,
                     117022123..117022198,117023040..117023164,
                     117024780..117024914,117025752..117025863,
                     117060217..117060328,117062291..117062413,
                     117066890..117066989,117067410..117067577))
                     /gene="ASZ1"
                     /gene_synonym="ALP1; ANKL1; C7orf7; CT1.19; GASZ;
                     MGC26634; Orf3"
                     /product="ankyrin repeat, SAM and basic leucine zipper
                     domain containing 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_023315.1"
                     /db_xref="GI:187608276"
                     /db_xref="GeneID:136991"
                     /db_xref="HGNC:1350"
                     /db_xref="MIM:605797"
                     /db_xref="HPRD:10677"
     CDS             complement(join(117003650..117003802,117007406..117007519,
                     117008666..117008771,117019992..117020101,
                     117021065..117021121,117022123..117022198,
                     117023040..117023164,117024780..117024914,
                     117025752..117025863,117060217..117060328,
                     117062291..117062413,117066890..117066989,
                     117067410..117067514))
                     /gene="ASZ1"
                     /gene_synonym="ALP1; ANKL1; C7orf7; CT1.19; GASZ;
                     MGC26634; Orf3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ankyrin repeat, SAM and basic leucine zipper
                     domain-containing protein 1"
                     /protein_id="NP_570124.1"
                     /db_xref="GI:18640738"
                     /db_xref="CCDS:CCDS5772.1"
                     /db_xref="GeneID:136991"
                     /db_xref="HGNC:1350"
                     /db_xref="HPRD:10677"
                     /db_xref="MIM:605797"
     gene            complement(117080039..117080827)
                     /gene="LOC100130680"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100130680"
     gene            117120017..117308719
                     /gene="CFTR"
                     /gene_synonym="ABC35; ABCC7; CF; CFTR/MRP; dJ760C5.1;
                     MRP7; TNR-CFTR"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1080"
                     /db_xref="HGNC:1884"
                     /db_xref="HPRD:03883"
                     /db_xref="MIM:602421"
     mRNA            join(117120017..117120201,117144307..117144417,
                     117149088..117149196,117170953..117171168,
                     117174330..117174419,117175302..117175465,
                     117176602..117176727,117180154..117180400,
                     117182070..117182162,117188695..117188877,
                     117199518..117199709,117227793..117227887,
                     117230407..117230493,117231988..117232711,
                     117234984..117235112,117242880..117242917,
                     117243586..117243836,117246728..117246807,
                     117250573..117250723,117251635..117251862,
                     117254667..117254767,117267576..117267824,
                     117282492..117282647,117292896..117292985,
                     117304742..117304914,117305513..117305618,
                     117306962..117308719)
                     /gene="CFTR"
                     /gene_synonym="ABC35; ABCC7; CF; CFTR/MRP; dJ760C5.1;
                     MRP7; TNR-CFTR"
                     /product="cystic fibrosis transmembrane conductance
                     regulator (ATP-binding cassette sub-family C, member 7)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000492.3"
                     /db_xref="GI:90421312"
                     /db_xref="GeneID:1080"
                     /db_xref="HGNC:1884"
                     /db_xref="HPRD:03883"
                     /db_xref="MIM:602421"
     CDS             join(117120149..117120201,117144307..117144417,
                     117149088..117149196,117170953..117171168,
                     117174330..117174419,117175302..117175465,
                     117176602..117176727,117180154..117180400,
                     117182070..117182162,117188695..117188877,
                     117199518..117199709,117227793..117227887,
                     117230407..117230493,117231988..117232711,
                     117234984..117235112,117242880..117242917,
                     117243586..117243836,117246728..117246807,
                     117250573..117250723,117251635..117251862,
                     117254667..117254767,117267576..117267824,
                     117282492..117282647,117292896..117292985,
                     117304742..117304914,117305513..117305618,
                     117306962..117307162)
                     /gene="CFTR"
                     /gene_synonym="ABC35; ABCC7; CF; CFTR/MRP; dJ760C5.1;
                     MRP7; TNR-CFTR"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cystic fibrosis transmembrane conductance
                     regulator"
                     /protein_id="NP_000483.3"
                     /db_xref="GI:90421313"
                     /db_xref="CCDS:CCDS5773.1"
                     /db_xref="GeneID:1080"
                     /db_xref="HGNC:1884"
                     /db_xref="HPRD:03883"
                     /db_xref="MIM:602421"
     gene            complement(117350705..117513561)
                     /gene="CTTNBP2"
                     /gene_synonym="C7orf8; CORTBP2; FLJ34229; KIAA1758;
                     MGC104579; Orf4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:83992"
                     /db_xref="HGNC:15679"
                     /db_xref="HPRD:09890"
                     /db_xref="MIM:609772"
     mRNA            complement(join(117350705..117351836,117358072..117358173,
                     117359558..117359690,117361121..117361184,
                     117364601..117364786,117365106..117365311,
                     117368143..117368321,117374967..117375154,
                     117375323..117375475,117385885..117385984,
                     117386067..117386153,117396609..117396688,
                     117397929..117398024,117400489..117400764,
                     117407113..117407230,117417565..117417819,
                     117420495..117420645,117422916..117423015,
                     117424305..117424508,117431182..117432835,
                     117450819..117451043,117501263..117501370,
                     117513389..117513561))
                     /gene="CTTNBP2"
                     /gene_synonym="C7orf8; CORTBP2; FLJ34229; KIAA1758;
                     MGC104579; Orf4"
                     /product="cortactin binding protein 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033427.2"
                     /db_xref="GI:92091570"
                     /db_xref="GeneID:83992"
                     /db_xref="HGNC:15679"
                     /db_xref="HPRD:09890"
                     /db_xref="MIM:609772"
     CDS             complement(join(117351591..117351836,117358072..117358173,
                     117359558..117359690,117361121..117361184,
                     117364601..117364786,117365106..117365311,
                     117368143..117368321,117374967..117375154,
                     117375323..117375475,117385885..117385984,
                     117386067..117386153,117396609..117396688,
                     117397929..117398024,117400489..117400764,
                     117407113..117407230,117417565..117417819,
                     117420495..117420645,117422916..117423015,
                     117424305..117424508,117431182..117432835,
                     117450819..117451043,117501263..117501370,
                     117513389..117513469))
                     /gene="CTTNBP2"
                     /gene_synonym="C7orf8; CORTBP2; FLJ34229; KIAA1758;
                     MGC104579; Orf4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cortactin-binding protein 2"
                     /protein_id="NP_219499.1"
                     /db_xref="GI:16975496"
                     /db_xref="CCDS:CCDS5774.1"
                     /db_xref="GeneID:83992"
                     /db_xref="HGNC:15679"
                     /db_xref="HPRD:09890"
                     /db_xref="MIM:609772"
     gene            117824086..117844093
                     /gene="NAA38"
                     /gene_synonym="FLJ33242; LSM8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51691"
                     /db_xref="HGNC:20471"
                     /db_xref="HPRD:06288"
                     /db_xref="MIM:607288"
     mRNA            join(117824086..117824308,117825708..117825748,
                     117828332..117828459,117831966..117844093)
                     /gene="NAA38"
                     /gene_synonym="FLJ33242; LSM8"
                     /product="N(alpha)-acetyltransferase 38, NatC auxiliary
                     subunit"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016200.4"
                     /db_xref="GI:284172355"
                     /db_xref="GeneID:51691"
                     /db_xref="HGNC:20471"
                     /db_xref="HPRD:06288"
                     /db_xref="MIM:607288"
     CDS             join(117824278..117824308,117825708..117825748,
                     117828332..117828459,117831966..117832056)
                     /gene="NAA38"
                     /gene_synonym="FLJ33242; LSM8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="N-alpha-acetyltransferase 38, NatC auxiliary
                     subunit"
                     /protein_id="NP_057284.1"
                     /db_xref="GI:7706425"
                     /db_xref="CCDS:CCDS5775.1"
                     /db_xref="GeneID:51691"
                     /db_xref="HGNC:20471"
                     /db_xref="HPRD:06288"
                     /db_xref="MIM:607288"
     gene            117864712..117882785
                     /gene="ANKRD7"
                     /gene_synonym="TSA806"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:56311"
                     /db_xref="HGNC:18588"
                     /db_xref="MIM:610731"
     mRNA            join(117864712..117865063,117874485..117874599,
                     117874755..117874928,117876095..117876201,
                     117876844..117876980,117879963..117880052,
                     117882403..117882785)
                     /gene="ANKRD7"
                     /gene_synonym="TSA806"
                     /product="ankyrin repeat domain 7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_019644.3"
                     /db_xref="GI:237681201"
                     /db_xref="GeneID:56311"
                     /db_xref="HGNC:18588"
                     /db_xref="MIM:610731"
     CDS             join(117864885..117865063,117874485..117874599,
                     117874755..117874928,117876095..117876201,
                     117876844..117876980,117879963..117880015)
                     /gene="ANKRD7"
                     /gene_synonym="TSA806"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ankyrin repeat domain-containing protein 7"
                     /protein_id="NP_062618.2"
                     /db_xref="GI:118150656"
                     /db_xref="CCDS:CCDS43638.1"
                     /db_xref="GeneID:56311"
                     /db_xref="HGNC:18588"
                     /db_xref="MIM:610731"
     gene            complement(118520241..118521304)
                     /gene="LOC100135063"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100135063"
     gene            complement(118590442..118591321)
                     /gene="LOC648442"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:648442"
     gene            119913722..120390387
                     /gene="KCND2"
                     /gene_synonym="KIAA1044; KV4.2; MGC119702; MGC119703; RK5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3751"
                     /db_xref="HGNC:6238"
                     /db_xref="HPRD:09254"
                     /db_xref="MIM:605410"
     mRNA            join(119913722..119915801,120372957..120373119,
                     120381588..120381683,120382564..120382656,
                     120385834..120386081,120387735..120390387)
                     /gene="KCND2"
                     /gene_synonym="KIAA1044; KV4.2; MGC119702; MGC119703; RK5"
                     /product="potassium voltage-gated channel, Shal-related
                     subfamily, member 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012281.2"
                     /db_xref="GI:27436982"
                     /db_xref="GeneID:3751"
                     /db_xref="HGNC:6238"
                     /db_xref="HPRD:09254"
                     /db_xref="MIM:605410"
     CDS             join(119914687..119915801,120372957..120373119,
                     120381588..120381683,120382564..120382656,
                     120385834..120386081,120387735..120387912)
                     /gene="KCND2"
                     /gene_synonym="KIAA1044; KV4.2; MGC119702; MGC119703; RK5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="potassium voltage-gated channel subfamily D
                     member 2"
                     /protein_id="NP_036413.1"
                     /db_xref="GI:9789987"
                     /db_xref="CCDS:CCDS5776.1"
                     /db_xref="GeneID:3751"
                     /db_xref="HGNC:6238"
                     /db_xref="HPRD:09254"
                     /db_xref="MIM:605410"
     gene            complement(120386792..120392921)
                     /gene="LOC100506586"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /db_xref="GeneID:100506586"
     misc_RNA        complement(join(120386792..120386960,120391886..120392072,
                     120392378..120392921))
                     /gene="LOC100506586"
                     /product="hypothetical LOC100506586"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_108803.1"
                     /db_xref="GI:310120082"
                     /db_xref="GeneID:100506586"
     gene            complement(120427374..120498177)
                     /gene="TSPAN12"
                     /gene_synonym="EVR5; NET-2; NET2; TM4SF12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23554"
                     /db_xref="HGNC:21641"
                     /db_xref="HPRD:15509"
                     /db_xref="MIM:613138"
     mRNA            complement(join(120427374..120428951,120446603..120446746,
                     120450517..120450624,120455783..120455857,
                     120478831..120478966,120480081..120480163,
                     120496752..120496887,120497874..120498177))
                     /gene="TSPAN12"
                     /gene_synonym="EVR5; NET-2; NET2; TM4SF12"
                     /product="tetraspanin 12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012338.3"
                     /db_xref="GI:48255911"
                     /db_xref="GeneID:23554"
                     /db_xref="HGNC:21641"
                     /db_xref="HPRD:15509"
                     /db_xref="MIM:613138"
     CDS             complement(join(120428646..120428951,120446603..120446746,
                     120450517..120450624,120455783..120455857,
                     120478831..120478966,120480081..120480163,
                     120496752..120496817))
                     /gene="TSPAN12"
                     /gene_synonym="EVR5; NET-2; NET2; TM4SF12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="tetraspanin-12"
                     /protein_id="NP_036470.1"
                     /db_xref="GI:6912528"
                     /db_xref="CCDS:CCDS5777.1"
                     /db_xref="GeneID:23554"
                     /db_xref="HGNC:21641"
                     /db_xref="HPRD:15509"
                     /db_xref="MIM:613138"
     gene            120590817..120615711
                     /gene="ING3"
                     /gene_synonym="Eaf4; FLJ20089; ING2; MEAF4; p47ING3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54556"
                     /db_xref="HGNC:14587"
                     /db_xref="HPRD:06321"
                     /db_xref="MIM:607493"
     mRNA            join(120590817..120590978,120591218..120591289,
                     120593358..120593458,120595613..120595678,
                     120604796..120604892,120606680..120606751,
                     120607583..120607702,120607988..120608145,
                     120609065..120609258,120610742..120610934,
                     120613259..120613297,120614782..120615711)
                     /gene="ING3"
                     /gene_synonym="Eaf4; FLJ20089; ING2; MEAF4; p47ING3"
                     /product="inhibitor of growth family, member 3, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_019071.2"
                     /db_xref="GI:38201654"
                     /db_xref="GeneID:54556"
                     /db_xref="HGNC:14587"
                     /db_xref="HPRD:06321"
                     /db_xref="MIM:607493"
     mRNA            join(120590817..120590978,120591218..120591289,
                     120593358..120593458,120595613..120595678,
                     120596214..120597034)
                     /gene="ING3"
                     /gene_synonym="Eaf4; FLJ20089; ING2; MEAF4; p47ING3"
                     /product="inhibitor of growth family, member 3, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198267.1"
                     /db_xref="GI:38201658"
                     /db_xref="GeneID:54556"
                     /db_xref="HGNC:14587"
                     /db_xref="MIM:607493"
                     /db_xref="HPRD:06321"
     CDS             join(120590951..120590978,120591218..120591289,
                     120593358..120593458,120595613..120595678,
                     120604796..120604892,120606680..120606751,
                     120607583..120607702,120607988..120608145,
                     120609065..120609258,120610742..120610934,
                     120613259..120613297,120614782..120614898)
                     /gene="ING3"
                     /gene_synonym="Eaf4; FLJ20089; ING2; MEAF4; p47ING3"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="inhibitor of growth protein 3 isoform 1"
                     /protein_id="NP_061944.2"
                     /db_xref="GI:38201655"
                     /db_xref="CCDS:CCDS5778.1"
                     /db_xref="GeneID:54556"
                     /db_xref="HGNC:14587"
                     /db_xref="HPRD:06321"
                     /db_xref="MIM:607493"
     CDS             join(120590951..120590978,120591218..120591289,
                     120593358..120593458,120595613..120595678,
                     120596214..120596225)
                     /gene="ING3"
                     /gene_synonym="Eaf4; FLJ20089; ING2; MEAF4; p47ING3"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="inhibitor of growth protein 3 isoform 3"
                     /protein_id="NP_938008.1"
                     /db_xref="GI:38201659"
                     /db_xref="CCDS:CCDS35497.1"
                     /db_xref="GeneID:54556"
                     /db_xref="HGNC:14587"
                     /db_xref="HPRD:06321"
                     /db_xref="MIM:607493"
     gene            120628751..120937498
                     /gene="C7orf58"
                     /gene_synonym="FLJ21986; FLJ26813"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79974"
                     /db_xref="HGNC:26159"
                     /db_xref="HPRD:08647"
     mRNA            join(120628751..120628966,120629445..120629924,
                     120655719..120655902,120686941..120687047,
                     120704292..120704367,120737753..120737885,
                     120739980..120740148,120764385..120764527,
                     120765874..120765946,120767144..120767311,
                     120768436..120768540,120770179..120770348,
                     120773877..120773947,120776094..120776144,
                     120780881..120781067,120782027..120782195,
                     120876768..120876885,120884256..120884392,
                     120906281..120906501,120906761..120906862,
                     120907269..120907356,120911338..120911484,
                     120935494..120937498)
                     /gene="C7orf58"
                     /gene_synonym="FLJ21986; FLJ26813"
                     /product="chromosome 7 open reading frame 58, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024913.4"
                     /db_xref="GI:157671944"
                     /db_xref="GeneID:79974"
                     /db_xref="HGNC:26159"
                     /db_xref="HPRD:08647"
     mRNA            join(120629445..120629924,120655719..120655902,
                     120686941..120687047,120704292..120704367,
                     120737753..120737885,120739980..120740148,
                     120764385..120764527,120765874..120765946,
                     120767144..120767311,120768436..120768540,
                     120770179..120770348,120773877..120773947,
                     120776094..120776144,120780881..120781067,
                     120782027..120782195,120876768..120876885,
                     120884256..120884392,120901686..120901972)
                     /gene="C7orf58"
                     /gene_synonym="FLJ21986; FLJ26813"
                     /product="chromosome 7 open reading frame 58, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001105533.1"
                     /db_xref="GI:157671946"
                     /db_xref="GeneID:79974"
                     /db_xref="HGNC:26159"
                     /db_xref="HPRD:08647"
     CDS             join(120629676..120629924,120655719..120655902,
                     120686941..120687047,120704292..120704367,
                     120737753..120737885,120739980..120740148,
                     120764385..120764527,120765874..120765946,
                     120767144..120767311,120768436..120768540,
                     120770179..120770348,120773877..120773947,
                     120776094..120776144,120780881..120781067,
                     120782027..120782195,120876768..120876885,
                     120884256..120884392,120906281..120906501,
                     120906761..120906862,120907269..120907356,
                     120911338..120911484,120935494..120935706)
                     /gene="C7orf58"
                     /gene_synonym="FLJ21986; FLJ26813"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC79974 isoform 1"
                     /protein_id="NP_079189.4"
                     /db_xref="GI:157671945"
                     /db_xref="CCDS:CCDS34739.1"
                     /db_xref="GeneID:79974"
                     /db_xref="HGNC:26159"
                     /db_xref="HPRD:08647"
     CDS             join(120629676..120629924,120655719..120655902,
                     120686941..120687047,120704292..120704367,
                     120737753..120737885,120739980..120740148,
                     120764385..120764527,120765874..120765946,
                     120767144..120767311,120768436..120768540,
                     120770179..120770348,120773877..120773947,
                     120776094..120776144,120780881..120781067,
                     120782027..120782195,120876768..120876885,
                     120884256..120884392,120901686..120901727)
                     /gene="C7orf58"
                     /gene_synonym="FLJ21986; FLJ26813"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC79974 isoform 2"
                     /protein_id="NP_001099003.1"
                     /db_xref="GI:157671947"
                     /db_xref="CCDS:CCDS47690.1"
                     /db_xref="GeneID:79974"
                     /db_xref="HGNC:26159"
                     /db_xref="HPRD:08647"
     gene            120965421..120981158
                     /gene="WNT16"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51384"
                     /db_xref="HGNC:16267"
                     /db_xref="MIM:606267"
     mRNA            join(120965421..120965534,120969621..120969871,
                     120971732..120972018,120978935..120981158)
                     /gene="WNT16"
                     /product="wingless-type MMTV integration site family,
                     member 16, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016087.2"
                     /db_xref="GI:17402913"
                     /db_xref="GeneID:51384"
                     /db_xref="HGNC:16267"
                     /db_xref="MIM:606267"
     CDS             join(120965470..120965534,120969621..120969871,
                     120971732..120972018,120978935..120979399)
                     /gene="WNT16"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein Wnt-16 isoform 2"
                     /protein_id="NP_057171.2"
                     /db_xref="GI:17402914"
                     /db_xref="CCDS:CCDS5780.1"
                     /db_xref="GeneID:51384"
                     /db_xref="HGNC:16267"
                     /db_xref="MIM:606267"
     mRNA            join(120969090..120969441,120969621..120969871,
                     120971732..120972018,120978935..120981158)
                     /gene="WNT16"
                     /product="wingless-type MMTV integration site family,
                     member 16, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_057168.1"
                     /db_xref="GI:17402915"
                     /db_xref="GeneID:51384"
                     /db_xref="HGNC:16267"
                     /db_xref="HPRD:05882"
                     /db_xref="MIM:606267"
     CDS             join(120969347..120969441,120969621..120969871,
                     120971732..120972018,120978935..120979399)
                     /gene="WNT16"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein Wnt-16 isoform 1 precursor"
                     /protein_id="NP_476509.1"
                     /db_xref="GI:17402916"
                     /db_xref="CCDS:CCDS5781.1"
                     /db_xref="GeneID:51384"
                     /db_xref="HGNC:16267"
                     /db_xref="MIM:606267"
     gene            complement(120988905..121036422)
                     /gene="FAM3C"
                     /gene_synonym="GS3786; ILEI"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10447"
                     /db_xref="HGNC:18664"
                     /db_xref="HPRD:12270"
                     /db_xref="MIM:608618"
     mRNA            complement(join(120988905..120990604,120991197..120991323,
                     121000097..121000181,121002951..121003001,
                     121004184..121004242,121011354..121011477,
                     121012164..121012193,121018964..121019068,
                     121023011..121023064,121036216..121036422))
                     /gene="FAM3C"
                     /gene_synonym="GS3786; ILEI"
                     /product="family with sequence similarity 3, member C,
                     transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014888.2"
                     /db_xref="GI:91807123"
                     /db_xref="GeneID:10447"
                     /db_xref="HGNC:18664"
                     /db_xref="HPRD:12270"
                     /db_xref="MIM:608618"
     mRNA            complement(join(120988905..120990604,120991197..120991323,
                     121000097..121000181,121002951..121003001,
                     121004184..121004242,121011354..121011477,
                     121012164..121012193,121018964..121019068,
                     121023011..121023064,121036256..121036422))
                     /gene="FAM3C"
                     /gene_synonym="GS3786; ILEI"
                     /product="family with sequence similarity 3, member C,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040020.1"
                     /db_xref="GI:91807124"
                     /db_xref="GeneID:10447"
                     /db_xref="HGNC:18664"
                     /db_xref="MIM:608618"
                     /db_xref="HPRD:12270"
     CDS             complement(join(120990515..120990604,120991197..120991323,
                     121000097..121000181,121002951..121003001,
                     121004184..121004242,121011354..121011477,
                     121012164..121012193,121018964..121019068,
                     121023011..121023023))
                     /gene="FAM3C"
                     /gene_synonym="GS3786; ILEI"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="family with sequence similarity 3, member C
                     precursor"
                     /protein_id="NP_055703.1"
                     /db_xref="GI:7661714"
                     /db_xref="CCDS:CCDS5782.1"
                     /db_xref="GeneID:10447"
                     /db_xref="HGNC:18664"
                     /db_xref="HPRD:12270"
                     /db_xref="MIM:608618"
     CDS             complement(join(120990515..120990604,120991197..120991323,
                     121000097..121000181,121002951..121003001,
                     121004184..121004242,121011354..121011477,
                     121012164..121012193,121018964..121019068,
                     121023011..121023023))
                     /gene="FAM3C"
                     /gene_synonym="GS3786; ILEI"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="family with sequence similarity 3, member C
                     precursor"
                     /protein_id="NP_001035109.1"
                     /db_xref="GI:91807125"
                     /db_xref="CCDS:CCDS5782.1"
                     /db_xref="GeneID:10447"
                     /db_xref="HGNC:18664"
                     /db_xref="HPRD:12270"
                     /db_xref="MIM:608618"
     gene            121038508..121038824
                     /gene="CYCSP19"
                     /gene_synonym="HCP19"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:360174"
                     /db_xref="HGNC:24392"
     gene            complement(121080866..121081315)
                     /gene="RPL18P4"
                     /gene_synonym="RPL18_1_838"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392979"
                     /db_xref="HGNC:36144"
     gene            complement(121483502..121485266)
                     /gene="LOC100533721"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533721"
     gene            121513159..121702090
                     /gene="PTPRZ1"
                     /gene_synonym="HPTPZ; HPTPzeta; phosphacan; PTP-ZETA;
                     PTP18; PTPRZ; PTPZ; RPTPB; RPTPbeta"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5803"
                     /db_xref="HGNC:9685"
                     /db_xref="MIM:176891"
     mRNA            join(121513159..121513611,121568210..121568275,
                     121608005..121608184,121612595..121612746,
                     121616227..121616322,121616839..121616905,
                     121623719..121623876,121624021..121624171,
                     121636436..121636620,121637934..121638060,
                     121644668..121644714,121650388..121653943,
                     121659178..121659322,121668606..121668697,
                     121671528..121671613,121674149..121674169,
                     121674336..121674432,121676654..121676736,
                     121678809..121678943,121679508..121679642,
                     121680870..121681033,121682662..121682797,
                     121684476..121684622,121691482..121691575,
                     121691920..121691993,121693964..121694092,
                     121694995..121695141,121698854..121698996,
                     121699807..121699942,121701134..121702090)
                     /gene="PTPRZ1"
                     /gene_synonym="HPTPZ; HPTPzeta; phosphacan; PTP-ZETA;
                     PTP18; PTPRZ; PTPZ; RPTPB; RPTPbeta"
                     /product="protein tyrosine phosphatase, receptor-type, Z
                     polypeptide 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002851.2"
                     /db_xref="GI:91208427"
                     /db_xref="GeneID:5803"
                     /db_xref="HGNC:9685"
                     /db_xref="HPRD:01481"
                     /db_xref="MIM:176891"
     mRNA            join(121513159..121513611,121568210..121568275,
                     121608005..121608184,121612595..121612746,
                     121616227..121616322,121616839..121616905,
                     121623719..121623876,121624021..121624171,
                     121636436..121636620,121637934..121638060,
                     121644668..121644714,121650388..121651363,
                     121659178..121659322,121668606..121668697,
                     121671528..121671613,121674149..121674169,
                     121674336..121674432,121676654..121676736,
                     121678809..121678943,121679508..121679642,
                     121680870..121681033,121682662..121682797,
                     121684476..121684622,121691482..121691575,
                     121691920..121691993,121693964..121694092,
                     121694995..121695141,121698854..121698996,
                     121699807..121699942,121701134..121702090)
                     /gene="PTPRZ1"
                     /gene_synonym="HPTPZ; HPTPzeta; phosphacan; PTP-ZETA;
                     PTP18; PTPRZ; PTPZ; RPTPB; RPTPbeta"
                     /product="protein tyrosine phosphatase, receptor-type, Z
                     polypeptide 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001206838.1"
                     /db_xref="GI:332205942"
                     /db_xref="GeneID:5803"
                     /db_xref="HGNC:9685"
                     /db_xref="MIM:176891"
     mRNA            join(121513159..121513611,121568210..121568275,
                     121608005..121608184,121612595..121612746,
                     121616227..121616322,121616839..121616905,
                     121623719..121623876,121624021..121624171,
                     121636436..121636620,121637934..121638060,
                     121644668..121644714,121650388..121651363,
                     121659178..121659322,121668606..121668697,
                     121671528..121671613,121674336..121674432,
                     121676654..121676736,121678809..121678943,
                     121679508..121679642,121680870..121681033,
                     121682662..121682797,121684476..121684622,
                     121691482..121691575,121691920..121691993,
                     121693964..121694092,121694995..121695141,
                     121698854..121698996,121699807..121699942,
                     121701134..121702090)
                     /gene="PTPRZ1"
                     /gene_synonym="HPTPZ; HPTPzeta; phosphacan; PTP-ZETA;
                     PTP18; PTPRZ; PTPZ; RPTPB; RPTPbeta"
                     /product="protein tyrosine phosphatase, receptor-type, Z
                     polypeptide 1, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001206839.1"
                     /db_xref="GI:332205944"
                     /db_xref="GeneID:5803"
                     /db_xref="HGNC:9685"
                     /db_xref="MIM:176891"
     CDS             join(121513554..121513611,121568210..121568275,
                     121608005..121608184,121612595..121612746,
                     121616227..121616322,121616839..121616905,
                     121623719..121623876,121624021..121624171,
                     121636436..121636620,121637934..121638060,
                     121644668..121644714,121650388..121653943,
                     121659178..121659322,121668606..121668697,
                     121671528..121671613,121674149..121674169,
                     121674336..121674432,121676654..121676736,
                     121678809..121678943,121679508..121679642,
                     121680870..121681033,121682662..121682797,
                     121684476..121684622,121691482..121691575,
                     121691920..121691993,121693964..121694092,
                     121694995..121695141,121698854..121698996,
                     121699807..121699942,121701134..121701274)
                     /gene="PTPRZ1"
                     /gene_synonym="HPTPZ; HPTPzeta; phosphacan; PTP-ZETA;
                     PTP18; PTPRZ; PTPZ; RPTPB; RPTPbeta"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="receptor-type tyrosine-protein phosphatase zeta
                     isoform 1 precursor"
                     /protein_id="NP_002842.2"
                     /db_xref="GI:91208428"
                     /db_xref="CCDS:CCDS34740.1"
                     /db_xref="GeneID:5803"
                     /db_xref="HGNC:9685"
                     /db_xref="MIM:176891"
     CDS             join(121513554..121513611,121568210..121568275,
                     121608005..121608184,121612595..121612746,
                     121616227..121616322,121616839..121616905,
                     121623719..121623876,121624021..121624171,
                     121636436..121636620,121637934..121638060,
                     121644668..121644714,121650388..121651363,
                     121659178..121659322,121668606..121668697,
                     121671528..121671613,121674149..121674169,
                     121674336..121674432,121676654..121676736,
                     121678809..121678943,121679508..121679642,
                     121680870..121681033,121682662..121682797,
                     121684476..121684622,121691482..121691575,
                     121691920..121691993,121693964..121694092,
                     121694995..121695141,121698854..121698996,
                     121699807..121699942,121701134..121701274)
                     /gene="PTPRZ1"
                     /gene_synonym="HPTPZ; HPTPzeta; phosphacan; PTP-ZETA;
                     PTP18; PTPRZ; PTPZ; RPTPB; RPTPbeta"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="receptor-type tyrosine-protein phosphatase zeta
                     isoform 2 precursor"
                     /protein_id="NP_001193767.1"
                     /db_xref="GI:332205943"
                     /db_xref="GeneID:5803"
                     /db_xref="HGNC:9685"
                     /db_xref="MIM:176891"
     CDS             join(121513554..121513611,121568210..121568275,
                     121608005..121608184,121612595..121612746,
                     121616227..121616322,121616839..121616905,
                     121623719..121623876,121624021..121624171,
                     121636436..121636620,121637934..121638060,
                     121644668..121644714,121650388..121651363,
                     121659178..121659322,121668606..121668697,
                     121671528..121671613,121674336..121674432,
                     121676654..121676736,121678809..121678943,
                     121679508..121679642,121680870..121681033,
                     121682662..121682797,121684476..121684622,
                     121691482..121691575,121691920..121691993,
                     121693964..121694092,121694995..121695141,
                     121698854..121698996,121699807..121699942,
                     121701134..121701274)
                     /gene="PTPRZ1"
                     /gene_synonym="HPTPZ; HPTPzeta; phosphacan; PTP-ZETA;
                     PTP18; PTPRZ; PTPZ; RPTPB; RPTPbeta"
                     /note="isoform 3 precursor is encoded by transcript
                     variant 3; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="receptor-type tyrosine-protein phosphatase zeta
                     isoform 3 precursor"
                     /protein_id="NP_001193768.1"
                     /db_xref="GI:332205945"
                     /db_xref="GeneID:5803"
                     /db_xref="HGNC:9685"
                     /db_xref="MIM:176891"
     gene            complement(121713598..121784344)
                     /gene="AASS"
                     /gene_synonym="LKR/SDH; LKRSDH; LORSDH"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10157"
                     /db_xref="HGNC:17366"
                     /db_xref="HPRD:05489"
                     /db_xref="MIM:605113"
     mRNA            complement(join(121713598..121716661,121717892..121718068,
                     121718916..121719004,121719651..121719766,
                     121721554..121721649,121726066..121726233,
                     121731757..121731897,121732897..121733005,
                     121733102..121733212,121738504..121738630,
                     121738799..121738920,121741425..121741492,
                     121741675..121741734,121753172..121753283,
                     121753652..121753774,121755128..121755276,
                     121756687..121756814,121756933..121757011,
                     121758361..121758507,121758617..121758684,
                     121766429..121766513,121769415..121769591,
                     121773571..121773795,121784215..121784344))
                     /gene="AASS"
                     /gene_synonym="LKR/SDH; LKRSDH; LORSDH"
                     /product="aminoadipate-semialdehyde synthase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005763.3"
                     /db_xref="GI:197927212"
                     /db_xref="GeneID:10157"
                     /db_xref="HGNC:17366"
                     /db_xref="HPRD:05489"
                     /db_xref="MIM:605113"
     CDS             complement(join(121716543..121716661,121717892..121718068,
                     121718916..121719004,121719651..121719766,
                     121721554..121721649,121726066..121726233,
                     121731757..121731897,121732897..121733005,
                     121733102..121733212,121738504..121738630,
                     121738799..121738920,121741425..121741492,
                     121741675..121741734,121753172..121753283,
                     121753652..121753774,121755128..121755276,
                     121756687..121756814,121756933..121757011,
                     121758361..121758507,121758617..121758684,
                     121766429..121766513,121769415..121769591,
                     121773571..121773780))
                     /gene="AASS"
                     /gene_synonym="LKR/SDH; LKRSDH; LORSDH"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="alpha-aminoadipic semialdehyde synthase,
                     mitochondrial precursor"
                     /protein_id="NP_005754.2"
                     /db_xref="GI:13027640"
                     /db_xref="CCDS:CCDS5783.1"
                     /db_xref="GeneID:10157"
                     /db_xref="HGNC:17366"
                     /db_xref="HPRD:05489"
                     /db_xref="MIM:605113"
     gene            121799333..121802835
                     /gene="LOC100130618"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100130618"
     gene            121874562..121875002
                     /gene="RPL31P37"
                     /gene_synonym="RPL31_18_839"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:646787"
                     /db_xref="HGNC:36197"
     gene            complement(121941448..121944565)
                     /gene="FEZF1"
                     /gene_synonym="FEZ; ZNF312B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:389549"
                     /db_xref="HGNC:22788"
                     /db_xref="HPRD:18614"
                     /db_xref="MIM:613301"
     mRNA            complement(join(121941448..121942409,121942853..121942985,
                     121943231..121943365,121943691..121944565))
                     /gene="FEZF1"
                     /gene_synonym="FEZ; ZNF312B"
                     /product="FEZ family zinc finger 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001024613.2"
                     /db_xref="GI:237681193"
                     /db_xref="GeneID:389549"
                     /db_xref="HGNC:22788"
                     /db_xref="HPRD:18614"
                     /db_xref="MIM:613301"
     mRNA            complement(join(121941448..121942409,121942853..121942985,
                     121943231..121943365,121943691..121943912,
                     121944063..121944565))
                     /gene="FEZF1"
                     /gene_synonym="FEZ; ZNF312B"
                     /product="FEZ family zinc finger 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001160264.1"
                     /db_xref="GI:237681195"
                     /db_xref="GeneID:389549"
                     /db_xref="HGNC:22788"
                     /db_xref="MIM:613301"
                     /db_xref="HPRD:18614"
     CDS             complement(join(121942051..121942409,121942853..121942985,
                     121943231..121943365,121943691..121944491))
                     /gene="FEZF1"
                     /gene_synonym="FEZ; ZNF312B"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="fez family zinc finger protein 1 isoform 1"
                     /protein_id="NP_001019784.2"
                     /db_xref="GI:237681194"
                     /db_xref="CCDS:CCDS34741.2"
                     /db_xref="GeneID:389549"
                     /db_xref="HGNC:22788"
                     /db_xref="HPRD:18614"
                     /db_xref="MIM:613301"
     CDS             complement(join(121942051..121942409,121942853..121942985,
                     121943231..121943365,121943691..121943912,
                     121944063..121944491))
                     /gene="FEZF1"
                     /gene_synonym="FEZ; ZNF312B"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="fez family zinc finger protein 1 isoform 2"
                     /protein_id="NP_001153736.1"
                     /db_xref="GI:237681196"
                     /db_xref="CCDS:CCDS55157.1"
                     /db_xref="GeneID:389549"
                     /db_xref="HGNC:22788"
                     /db_xref="HPRD:18614"
                     /db_xref="MIM:613301"
     gene            121943712..121950131
                     /gene="LOC154860"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:154860"
     misc_RNA        join(121943712..121944322,121944627..121944797,
                     121945342..121946316,121946570..121946714,
                     121947357..121947542,121948541..121948611,
                     121949638..121950131)
                     /gene="LOC154860"
                     /product="hypothetical LOC154860"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_036484.1"
                     /db_xref="GI:302318963"
                     /db_xref="GeneID:154860"
     gene            complement(121958478..122526813)
                     /gene="CADPS2"
                     /gene_synonym="FLJ40851; KIAA1591"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:93664"
                     /db_xref="HGNC:16018"
                     /db_xref="HPRD:12996"
                     /db_xref="MIM:609978"
     mRNA            complement(join(121958478..121960392,121965531..121965635,
                     121985628..121985735,122000842..122000874,
                     122000984..122001067,122019422..122019496,
                     122027080..122027227,122028637..122028792,
                     122033250..122033369,122033495..122033636,
                     122047594..122047750,122054122..122054130,
                     122056115..122056218,122078395..122078518,
                     122081566..122081629,122091428..122091529,
                     122111429..122111616,122114435..122114571,
                     122120906..122120914,122130135..122130335,
                     122131366..122131474,122153303..122153369,
                     122194604..122194743,122221233..122221344,
                     122255235..122255353,122261535..122261771,
                     122269302..122269382,122303291..122303623,
                     122377009..122377122,122526053..122526813))
                     /gene="CADPS2"
                     /gene_synonym="FLJ40851; KIAA1591"
                     /product="Ca++-dependent secretion activator 2, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017954.10"
                     /db_xref="GI:269308216"
                     /db_xref="GeneID:93664"
                     /db_xref="HGNC:16018"
                     /db_xref="HPRD:12996"
                     /db_xref="MIM:609978"
     mRNA            complement(join(121958478..121960392,121965531..121965635,
                     121985628..121985735,122000842..122000874,
                     122000984..122001067,122019422..122019496,
                     122026349..122026363,122027080..122027227,
                     122028637..122028792,122033495..122033636,
                     122047594..122047750,122056115..122056218,
                     122078395..122078518,122081566..122081629,
                     122091428..122091529,122111429..122111616,
                     122114435..122114571,122130135..122130335,
                     122131366..122131474,122153303..122153369,
                     122194604..122194743,122221233..122221344,
                     122255235..122255353,122261535..122261771,
                     122269302..122269382,122303291..122303623,
                     122377009..122377122,122526053..122526813))
                     /gene="CADPS2"
                     /gene_synonym="FLJ40851; KIAA1591"
                     /product="Ca++-dependent secretion activator 2, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001009571.3"
                     /db_xref="GI:269308217"
                     /db_xref="GeneID:93664"
                     /db_xref="HGNC:16018"
                     /db_xref="MIM:609978"
                     /db_xref="HPRD:12996"
     mRNA            complement(join(121958478..121960392,121965531..121965635,
                     121985628..121985735,122000842..122000874,
                     122000984..122001067,122019422..122019496,
                     122027080..122027227,122028637..122028792,
                     122033250..122033369,122033495..122033636,
                     122047594..122047750,122056115..122056218,
                     122076414..122076434,122078395..122078518,
                     122081566..122081629,122091428..122091529,
                     122111429..122111616,122114435..122114571,
                     122120906..122120914,122130135..122130335,
                     122131366..122131474,122153303..122153369,
                     122194604..122194743,122221233..122221344,
                     122255235..122255353,122261535..122261771,
                     122269302..122269382,122303291..122303623,
                     122377009..122377122,122526053..122526813))
                     /gene="CADPS2"
                     /gene_synonym="FLJ40851; KIAA1591"
                     /product="Ca++-dependent secretion activator 2, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001167940.1"
                     /db_xref="GI:269308218"
                     /db_xref="GeneID:93664"
                     /db_xref="HGNC:16018"
                     /db_xref="MIM:609978"
                     /db_xref="HPRD:12996"
     CDS             complement(join(121960219..121960392,121965531..121965635,
                     121985628..121985735,122000842..122000874,
                     122000984..122001067,122019422..122019496,
                     122027080..122027227,122028637..122028792,
                     122033250..122033369,122033495..122033636,
                     122047594..122047750,122054122..122054130,
                     122056115..122056218,122078395..122078518,
                     122081566..122081629,122091428..122091529,
                     122111429..122111616,122114435..122114571,
                     122120906..122120914,122130135..122130335,
                     122131366..122131474,122153303..122153369,
                     122194604..122194743,122221233..122221344,
                     122255235..122255353,122261535..122261771,
                     122269302..122269382,122303291..122303623,
                     122377009..122377122,122526053..122526391))
                     /gene="CADPS2"
                     /gene_synonym="FLJ40851; KIAA1591"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium-dependent secretion activator 2 isoform
                     a"
                     /protein_id="NP_060424.9"
                     /db_xref="GI:148839294"
                     /db_xref="CCDS:CCDS55158.1"
                     /db_xref="GeneID:93664"
                     /db_xref="HGNC:16018"
                     /db_xref="HPRD:12996"
                     /db_xref="MIM:609978"
     CDS             complement(join(121960219..121960392,121965531..121965635,
                     121985628..121985735,122000842..122000874,
                     122000984..122001067,122019422..122019496,
                     122026349..122026363,122027080..122027227,
                     122028637..122028792,122033495..122033636,
                     122047594..122047750,122056115..122056218,
                     122078395..122078518,122081566..122081629,
                     122091428..122091529,122111429..122111616,
                     122114435..122114571,122130135..122130335,
                     122131366..122131474,122153303..122153369,
                     122194604..122194743,122221233..122221344,
                     122255235..122255353,122261535..122261771,
                     122269302..122269382,122303291..122303623,
                     122377009..122377122,122526053..122526391))
                     /gene="CADPS2"
                     /gene_synonym="FLJ40851; KIAA1591"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium-dependent secretion activator 2 isoform
                     b"
                     /protein_id="NP_001009571.2"
                     /db_xref="GI:148839284"
                     /db_xref="CCDS:CCDS47691.1"
                     /db_xref="GeneID:93664"
                     /db_xref="HGNC:16018"
                     /db_xref="HPRD:12996"
                     /db_xref="MIM:609978"
     CDS             complement(join(121960219..121960392,121965531..121965635,
                     121985628..121985735,122000842..122000874,
                     122000984..122001067,122019422..122019496,
                     122027080..122027227,122028637..122028792,
                     122033250..122033369,122033495..122033636,
                     122047594..122047750,122056115..122056218,
                     122076414..122076434,122078395..122078518,
                     122081566..122081629,122091428..122091529,
                     122111429..122111616,122114435..122114571,
                     122120906..122120914,122130135..122130335,
                     122131366..122131474,122153303..122153369,
                     122194604..122194743,122221233..122221344,
                     122255235..122255353,122261535..122261771,
                     122269302..122269382,122303291..122303623,
                     122377009..122377122,122526053..122526391))
                     /gene="CADPS2"
                     /gene_synonym="FLJ40851; KIAA1591"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calcium-dependent secretion activator 2 isoform
                     c"
                     /protein_id="NP_001161412.1"
                     /db_xref="GI:269308219"
                     /db_xref="GeneID:93664"
                     /db_xref="HGNC:16018"
                     /db_xref="MIM:609978"
                     /db_xref="HPRD:12996"
     gene            122321347..122321780
                     /gene="RPS26P31"
                     /gene_synonym="RPS26_8_840"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:645979"
                     /db_xref="HGNC:36614"
     gene            complement(122337766..122339208)
                     /gene="RNF133"
                     /gene_synonym="MGC27072"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:168433"
                     /db_xref="HGNC:21154"
                     /db_xref="HPRD:11505"
     mRNA            complement(122337766..122339208)
                     /gene="RNF133"
                     /gene_synonym="MGC27072"
                     /product="ring finger protein 133"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_139175.1"
                     /db_xref="GI:21040268"
                     /db_xref="GeneID:168433"
                     /db_xref="HGNC:21154"
                     /db_xref="HPRD:11505"
     CDS             complement(122337842..122338972)
                     /gene="RNF133"
                     /gene_synonym="MGC27072"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase RNF133"
                     /protein_id="NP_631914.1"
                     /db_xref="GI:21040269"
                     /db_xref="CCDS:CCDS5784.1"
                     /db_xref="GeneID:168433"
                     /db_xref="HGNC:21154"
                     /db_xref="HPRD:11505"
     gene            complement(122341720..122343021)
                     /gene="RNF148"
                     /gene_synonym="MGC35222"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:378925"
                     /db_xref="HGNC:22411"
                     /db_xref="HPRD:11512"
     mRNA            complement(122341720..122343021)
                     /gene="RNF148"
                     /gene_synonym="MGC35222"
                     /product="ring finger protein 148"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198085.1"
                     /db_xref="GI:37675276"
                     /db_xref="GeneID:378925"
                     /db_xref="HGNC:22411"
                     /db_xref="HPRD:11512"
     CDS             complement(122341887..122342804)
                     /gene="RNF148"
                     /gene_synonym="MGC35222"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="RING finger protein 148 precursor"
                     /protein_id="NP_932351.1"
                     /db_xref="GI:37675277"
                     /db_xref="CCDS:CCDS47692.1"
                     /db_xref="GeneID:378925"
                     /db_xref="HGNC:22411"
                     /db_xref="HPRD:11512"
     gene            122489824..122490414
                     /gene="LOC100422456"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100422456"
     gene            complement(122634759..122635754)
                     /gene="TAS2R16"
                     /gene_synonym="T2R16"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:50833"
                     /db_xref="HGNC:14921"
                     /db_xref="HPRD:05334"
                     /db_xref="MIM:604867"
     mRNA            complement(122634759..122635754)
                     /gene="TAS2R16"
                     /gene_synonym="T2R16"
                     /product="taste receptor, type 2, member 16"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016945.2"
                     /db_xref="GI:68160949"
                     /db_xref="GeneID:50833"
                     /db_xref="HGNC:14921"
                     /db_xref="HPRD:05334"
                     /db_xref="MIM:604867"
     CDS             complement(122634813..122635688)
                     /gene="TAS2R16"
                     /gene_synonym="T2R16"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="taste receptor type 2 member 16"
                     /protein_id="NP_058641.1"
                     /db_xref="GI:8394395"
                     /db_xref="CCDS:CCDS5785.1"
                     /db_xref="GeneID:50833"
                     /db_xref="HGNC:14921"
                     /db_xref="HPRD:05334"
                     /db_xref="MIM:604867"
     gene            complement(122753588..122840025)
                     /gene="SLC13A1"
                     /gene_synonym="NAS1; NaSi-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6561"
                     /db_xref="HGNC:10916"
                     /db_xref="HPRD:08394"
                     /db_xref="MIM:606193"
     mRNA            complement(join(122753588..122755709,122757525..122757662,
                     122759135..122759296,122763180..122763289,
                     122765623..122765729,122768899..122769000,
                     122769437..122769535,122774464..122774583,
                     122787213..122787364,122808428..122808476,
                     122808558..122808615,122809202..122809389,
                     122811822..122811958,122821027..122821155,
                     122839902..122840025))
                     /gene="SLC13A1"
                     /gene_synonym="NAS1; NaSi-1"
                     /product="solute carrier family 13 (sodium/sulfate
                     symporters), member 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022444.3"
                     /db_xref="GI:32967608"
                     /db_xref="GeneID:6561"
                     /db_xref="HGNC:10916"
                     /db_xref="HPRD:08394"
                     /db_xref="MIM:606193"
     CDS             complement(join(122755572..122755709,122757525..122757662,
                     122759135..122759296,122763180..122763289,
                     122765623..122765729,122768899..122769000,
                     122769437..122769535,122774464..122774583,
                     122787213..122787364,122808428..122808476,
                     122808558..122808615,122809202..122809389,
                     122811822..122811958,122821027..122821155,
                     122839902..122840000))
                     /gene="SLC13A1"
                     /gene_synonym="NAS1; NaSi-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="solute carrier family 13 member 1"
                     /protein_id="NP_071889.2"
                     /db_xref="GI:19923838"
                     /db_xref="CCDS:CCDS5786.1"
                     /db_xref="GeneID:6561"
                     /db_xref="HGNC:10916"
                     /db_xref="HPRD:08394"
                     /db_xref="MIM:606193"
     gene            complement(122870118..122870808)
                     /gene="LOC100129401"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129401"
     gene            complement(123092235..123174718)
                     /gene="IQUB"
                     /gene_synonym="FLJ35834; MGC149284; MGC149285"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:154865"
                     /db_xref="HGNC:21995"
                     /db_xref="HPRD:08194"
     mRNA            complement(join(123092235..123092979,123097435..123097620,
                     123101411..123101659,123104887..123105063,
                     123109268..123109438,123119849..123120024,
                     123136750..123136960,123142651..123142806,
                     123142998..123143170,123143256..123143417,
                     123149955..123150089,123151998..123152398,
                     123174546..123174718))
                     /gene="IQUB"
                     /gene_synonym="FLJ35834; MGC149284; MGC149285"
                     /product="IQ motif and ubiquitin domain containing"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178827.4"
                     /db_xref="GI:223972684"
                     /db_xref="GeneID:154865"
                     /db_xref="HGNC:21995"
                     /db_xref="HPRD:08194"
     CDS             complement(join(123092797..123092979,123097435..123097620,
                     123101411..123101659,123104887..123105063,
                     123109268..123109438,123119849..123120024,
                     123136750..123136960,123142651..123142806,
                     123142998..123143170,123143256..123143417,
                     123149955..123150089,123151998..123152394))
                     /gene="IQUB"
                     /gene_synonym="FLJ35834; MGC149284; MGC149285"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="IQ and ubiquitin-like domain-containing protein"
                     /protein_id="NP_849149.3"
                     /db_xref="GI:223972685"
                     /db_xref="CCDS:CCDS5787.1"
                     /db_xref="GeneID:154865"
                     /db_xref="HGNC:21995"
                     /db_xref="HPRD:08194"
     gene            complement(123181083..123197958)
                     /gene="NDUFA5"
                     /gene_synonym="B13; CI-13kB; CI-13KD-B; DKFZp781K1356;
                     FLJ12147; NUFM; UQOR13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4698"
                     /db_xref="HGNC:7688"
                     /db_xref="HPRD:03398"
                     /db_xref="MIM:601677"
     mRNA            complement(join(123181083..123182274,123185665..123185730,
                     123190524..123190640,123197458..123197502,
                     123197829..123197958))
                     /gene="NDUFA5"
                     /gene_synonym="B13; CI-13kB; CI-13KD-B; DKFZp781K1356;
                     FLJ12147; NUFM; UQOR13"
                     /product="NADH dehydrogenase (ubiquinone) 1 alpha
                     subcomplex, 5, 13kDa"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005000.2"
                     /db_xref="GI:13699821"
                     /db_xref="GeneID:4698"
                     /db_xref="HGNC:7688"
                     /db_xref="HPRD:03398"
                     /db_xref="MIM:601677"
     gene            123181822..123188916
                     /gene="LOC100652957"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /db_xref="GeneID:100652957"
     misc_RNA        join(123181822..123182276,123188907..123188916)
                     /gene="LOC100652957"
                     /product="hypothetical LOC100652957"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_132533.1"
                     /db_xref="GI:341915389"
                     /db_xref="GeneID:100652957"
     CDS             complement(join(123182173..123182274,123185665..123185730,
                     123190524..123190640,123197458..123197502,
                     123197829..123197849))
                     /gene="NDUFA5"
                     /gene_synonym="B13; CI-13kB; CI-13KD-B; DKFZp781K1356;
                     FLJ12147; NUFM; UQOR13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="NADH dehydrogenase [ubiquinone] 1 alpha
                     subcomplex subunit 5"
                     /protein_id="NP_004991.1"
                     /db_xref="GI:4826848"
                     /db_xref="CCDS:CCDS5788.1"
                     /db_xref="GeneID:4698"
                     /db_xref="HGNC:7688"
                     /db_xref="HPRD:03398"
                     /db_xref="MIM:601677"
     gene            123249112..123277932
                     /gene="ASB15"
                     /gene_synonym="DKFZp779M1258; FLJ43370"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:142685"
                     /db_xref="HGNC:19767"
                     /db_xref="HPRD:10669"
     mRNA            join(123249112..123249151,123254555..123254663,
                     123256275..123256327,123256418..123256549,
                     123257633..123257791,123264623..123264868,
                     123267164..123267335,123268918..123269488,
                     123270020..123270173,123276863..123277932)
                     /gene="ASB15"
                     /gene_synonym="DKFZp779M1258; FLJ43370"
                     /product="ankyrin repeat and SOCS box containing 15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_080928.3"
                     /db_xref="GI:92087059"
                     /db_xref="GeneID:142685"
                     /db_xref="HGNC:19767"
                     /db_xref="HPRD:10669"
     CDS             join(123254557..123254663,123256275..123256327,
                     123256418..123256549,123257633..123257791,
                     123264623..123264868,123267164..123267335,
                     123268918..123269488,123270020..123270173,
                     123276863..123277035)
                     /gene="ASB15"
                     /gene_synonym="DKFZp779M1258; FLJ43370"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ankyrin repeat and SOCS box protein 15"
                     /protein_id="NP_563616.3"
                     /db_xref="GI:92087060"
                     /db_xref="CCDS:CCDS34742.1"
                     /db_xref="GeneID:142685"
                     /db_xref="HGNC:19767"
                     /db_xref="HPRD:10669"
     gene            123295861..123304147
                     /gene="LMOD2"
                     /gene_synonym="C-LMOD"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:442721"
                     /db_xref="HGNC:6648"
                     /db_xref="MIM:608006"
     mRNA            join(123295861..123296290,123301914..123303257,
                     123303773..123304147)
                     /gene="LMOD2"
                     /gene_synonym="C-LMOD"
                     /product="leiomodin 2 (cardiac)"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_207163.1"
                     /db_xref="GI:150378502"
                     /db_xref="GeneID:442721"
                     /db_xref="HGNC:6648"
                     /db_xref="MIM:608006"
     CDS             join(123296018..123296290,123301914..123303257,
                     123303773..123303799)
                     /gene="LMOD2"
                     /gene_synonym="C-LMOD"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="leiomodin-2"
                     /protein_id="NP_997046.1"
                     /db_xref="GI:150378503"
                     /db_xref="CCDS:CCDS47693.1"
                     /db_xref="GeneID:442721"
                     /db_xref="HGNC:6648"
                     /db_xref="MIM:608006"
     gene            complement(123321997..123389116)
                     /gene="WASL"
                     /gene_synonym="DKFZp779G0847; MGC48327; N-WASP; NWASP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8976"
                     /db_xref="HGNC:12735"
                     /db_xref="HPRD:05448"
                     /db_xref="MIM:605056"
     mRNA            complement(join(123321997..123324634,123329096..123329204,
                     123332401..123332921,123334769..123334922,
                     123335877..123335919,123336633..123336801,
                     123344688..123344711,123346331..123346427,
                     123346794..123346880,123349143..123349277,
                     123388672..123389116))
                     /gene="WASL"
                     /gene_synonym="DKFZp779G0847; MGC48327; N-WASP; NWASP"
                     /product="Wiskott-Aldrich syndrome-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003941.2"
                     /db_xref="GI:33946268"
                     /db_xref="GeneID:8976"
                     /db_xref="HGNC:12735"
                     /db_xref="HPRD:05448"
                     /db_xref="MIM:605056"
     CDS             complement(join(123324573..123324634,123329096..123329204,
                     123332401..123332921,123334769..123334922,
                     123335877..123335919,123336633..123336801,
                     123344688..123344711,123346331..123346427,
                     123346794..123346880,123349143..123349277,
                     123388672..123388788))
                     /gene="WASL"
                     /gene_synonym="DKFZp779G0847; MGC48327; N-WASP; NWASP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="neural Wiskott-Aldrich syndrome protein"
                     /protein_id="NP_003932.3"
                     /db_xref="GI:51702526"
                     /db_xref="CCDS:CCDS34743.1"
                     /db_xref="GeneID:8976"
                     /db_xref="HGNC:12735"
                     /db_xref="HPRD:05448"
                     /db_xref="MIM:605056"
     gene            123454193..123459484
                     /gene="HYALP1"
                     /gene_synonym="HYAL6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:26062"
                     /db_xref="HGNC:5324"
     misc_RNA        join(123454193..123455085,123459395..123459484)
                     /gene="HYALP1"
                     /gene_synonym="HYAL6"
                     /product="hyaluronoglucosaminidase pseudogene 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002731.1"
                     /db_xref="GI:84872015"
                     /db_xref="GeneID:26062"
                     /db_xref="HGNC:5324"
     gene            123485223..123517532
                     /gene="HYAL4"
                     /gene_synonym="CSHY"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23553"
                     /db_xref="HGNC:5323"
                     /db_xref="HPRD:05148"
                     /db_xref="MIM:604510"
     mRNA            join(123485223..123485739,123488143..123488212,
                     123508277..123509281,123514815..123514904,
                     123516808..123517532)
                     /gene="HYAL4"
                     /gene_synonym="CSHY"
                     /product="hyaluronoglucosaminidase 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012269.2"
                     /db_xref="GI:166235887"
                     /db_xref="GeneID:23553"
                     /db_xref="HGNC:5323"
                     /db_xref="HPRD:05148"
                     /db_xref="MIM:604510"
     CDS             join(123508328..123509281,123514815..123514904,
                     123516808..123517209)
                     /gene="HYAL4"
                     /gene_synonym="CSHY"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hyaluronidase-4"
                     /protein_id="NP_036401.2"
                     /db_xref="GI:166235888"
                     /db_xref="CCDS:CCDS5789.1"
                     /db_xref="GeneID:23553"
                     /db_xref="HGNC:5323"
                     /db_xref="HPRD:05148"
                     /db_xref="MIM:604510"
     gene            123565286..123611464
                     /gene="SPAM1"
                     /gene_synonym="HYA1; HYAL1; HYAL3; HYAL5; MGC26532; PH-20;
                     PH20; SPAG15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6677"
                     /db_xref="HGNC:11217"
                     /db_xref="HPRD:02958"
                     /db_xref="MIM:600930"
     mRNA            join(123565286..123565406,123589926..123590037,
                     123593419..123594578,123595051..123595140,
                     123599538..123599978,123610252..123610350,
                     123611061..123611464)
                     /gene="SPAM1"
                     /gene_synonym="HYA1; HYAL1; HYAL3; HYAL5; MGC26532; PH-20;
                     PH20; SPAG15"
                     /product="sperm adhesion molecule 1 (PH-20 hyaluronidase,
                     zona pellucida binding), transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003117.4"
                     /db_xref="GI:291290977"
                     /db_xref="GeneID:6677"
                     /db_xref="HGNC:11217"
                     /db_xref="HPRD:02958"
                     /db_xref="MIM:600930"
     mRNA            join(123565286..123565406,123589926..123590037,
                     123593419..123594578,123595051..123595140,
                     123599538..123600100)
                     /gene="SPAM1"
                     /gene_synonym="HYA1; HYAL1; HYAL3; HYAL5; MGC26532; PH-20;
                     PH20; SPAG15"
                     /product="sperm adhesion molecule 1 (PH-20 hyaluronidase,
                     zona pellucida binding), transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_153189.2"
                     /db_xref="GI:291290976"
                     /db_xref="GeneID:6677"
                     /db_xref="HGNC:11217"
                     /db_xref="HPRD:02958"
                     /db_xref="MIM:600930"
     mRNA            join(123565286..123565585,123589926..123590037,
                     123593419..123594578,123595051..123595140,
                     123599538..123600100)
                     /gene="SPAM1"
                     /gene_synonym="HYA1; HYAL1; HYAL3; HYAL5; MGC26532; PH-20;
                     PH20; SPAG15"
                     /product="sperm adhesion molecule 1 (PH-20 hyaluronidase,
                     zona pellucida binding), transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001174044.1"
                     /db_xref="GI:291290978"
                     /db_xref="GeneID:6677"
                     /db_xref="HGNC:11217"
                     /db_xref="MIM:600930"
                     /db_xref="HPRD:02958"
     mRNA            join(123565909..123566118,123587758..123587842,
                     123589926..123590037,123593419..123594578,
                     123595051..123595140,123599538..123600100)
                     /gene="SPAM1"
                     /gene_synonym="HYA1; HYAL1; HYAL3; HYAL5; MGC26532; PH-20;
                     PH20; SPAG15"
                     /product="sperm adhesion molecule 1 (PH-20 hyaluronidase,
                     zona pellucida binding), transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001174045.1"
                     /db_xref="GI:291290980"
                     /db_xref="GeneID:6677"
                     /db_xref="HGNC:11217"
                     /db_xref="MIM:600930"
                     /db_xref="HPRD:02958"
     mRNA            join(123565909..123566118,123589926..123590037,
                     123593419..123594578,123595051..123595140,
                     123599538..123600100)
                     /gene="SPAM1"
                     /gene_synonym="HYA1; HYAL1; HYAL3; HYAL5; MGC26532; PH-20;
                     PH20; SPAG15"
                     /product="sperm adhesion molecule 1 (PH-20 hyaluronidase,
                     zona pellucida binding), transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001174046.1"
                     /db_xref="GI:291290982"
                     /db_xref="GeneID:6677"
                     /db_xref="HGNC:11217"
                     /db_xref="MIM:600930"
                     /db_xref="HPRD:02958"
     CDS             join(123593625..123594578,123595051..123595140,
                     123599538..123599978,123610252..123610302)
                     /gene="SPAM1"
                     /gene_synonym="HYA1; HYAL1; HYAL3; HYAL5; MGC26532; PH-20;
                     PH20; SPAG15"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hyaluronidase PH-20 isoform 1"
                     /protein_id="NP_003108.2"
                     /db_xref="GI:21314606"
                     /db_xref="CCDS:CCDS5790.1"
                     /db_xref="GeneID:6677"
                     /db_xref="HGNC:11217"
                     /db_xref="HPRD:02958"
                     /db_xref="MIM:600930"
     CDS             join(123593625..123594578,123595051..123595140,
                     123599538..123600023)
                     /gene="SPAM1"
                     /gene_synonym="HYA1; HYAL1; HYAL3; HYAL5; MGC26532; PH-20;
                     PH20; SPAG15"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hyaluronidase PH-20 isoform 2"
                     /protein_id="NP_694859.1"
                     /db_xref="GI:23510418"
                     /db_xref="CCDS:CCDS5791.1"
                     /db_xref="GeneID:6677"
                     /db_xref="HGNC:11217"
                     /db_xref="HPRD:02958"
                     /db_xref="MIM:600930"
     CDS             join(123593625..123594578,123595051..123595140,
                     123599538..123600023)
                     /gene="SPAM1"
                     /gene_synonym="HYA1; HYAL1; HYAL3; HYAL5; MGC26532; PH-20;
                     PH20; SPAG15"
                     /note="isoform 2 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hyaluronidase PH-20 isoform 2"
                     /protein_id="NP_001167515.1"
                     /db_xref="GI:291290979"
                     /db_xref="CCDS:CCDS5791.1"
                     /db_xref="GeneID:6677"
                     /db_xref="HGNC:11217"
                     /db_xref="HPRD:02958"
                     /db_xref="MIM:600930"
     CDS             join(123593625..123594578,123595051..123595140,
                     123599538..123600023)
                     /gene="SPAM1"
                     /gene_synonym="HYA1; HYAL1; HYAL3; HYAL5; MGC26532; PH-20;
                     PH20; SPAG15"
                     /note="isoform 2 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hyaluronidase PH-20 isoform 2"
                     /protein_id="NP_001167516.1"
                     /db_xref="GI:291290981"
                     /db_xref="CCDS:CCDS5791.1"
                     /db_xref="GeneID:6677"
                     /db_xref="HGNC:11217"
                     /db_xref="HPRD:02958"
                     /db_xref="MIM:600930"
     CDS             join(123593625..123594578,123595051..123595140,
                     123599538..123600023)
                     /gene="SPAM1"
                     /gene_synonym="HYA1; HYAL1; HYAL3; HYAL5; MGC26532; PH-20;
                     PH20; SPAG15"
                     /note="isoform 2 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hyaluronidase PH-20 isoform 2"
                     /protein_id="NP_001167517.1"
                     /db_xref="GI:291290983"
                     /db_xref="CCDS:CCDS5791.1"
                     /db_xref="GeneID:6677"
                     /db_xref="HGNC:11217"
                     /db_xref="HPRD:02958"
                     /db_xref="MIM:600930"
     gene            complement(123670970..123673523)
                     /gene="TMEM229A"
                     /gene_synonym="MGC189723"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:730130"
                     /db_xref="HGNC:37279"
     mRNA            complement(123670970..123673523)
                     /gene="TMEM229A"
                     /gene_synonym="MGC189723"
                     /product="transmembrane protein 229A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001136002.1"
                     /db_xref="GI:209862781"
                     /db_xref="GeneID:730130"
                     /db_xref="HGNC:37279"
     CDS             complement(123671915..123673057)
                     /gene="TMEM229A"
                     /gene_synonym="MGC189723"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 229A"
                     /protein_id="NP_001129474.1"
                     /db_xref="GI:209862782"
                     /db_xref="CCDS:CCDS47694.1"
                     /db_xref="GeneID:730130"
                     /db_xref="HGNC:37279"
     gene            124116425..124117009
                     /gene="LOC136157"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:136157"
     gene            124120556..124121490
                     /gene="RPS2P31"
                     /gene_synonym="RPS2_15_841"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392781"
                     /db_xref="HGNC:36965"
     gene            complement(124386114..124405681)
                     /gene="GPR37"
                     /gene_synonym="EDNRBL; hET(B)R-LP; PAELR"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2861"
                     /db_xref="HGNC:4494"
                     /db_xref="HPRD:03992"
                     /db_xref="MIM:602583"
     mRNA            complement(join(124386114..124387397,
                     124404008..124405681))
                     /gene="GPR37"
                     /gene_synonym="EDNRBL; hET(B)R-LP; PAELR"
                     /product="G protein-coupled receptor 37 (endothelin
                     receptor type B-like)"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005302.2"
                     /db_xref="GI:31377788"
                     /db_xref="GeneID:2861"
                     /db_xref="HGNC:4494"
                     /db_xref="HPRD:03992"
                     /db_xref="MIM:602583"
     CDS             complement(join(124386579..124387397,
                     124404008..124405030))
                     /gene="GPR37"
                     /gene_synonym="EDNRBL; hET(B)R-LP; PAELR"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable G-protein coupled receptor 37
                     precursor"
                     /protein_id="NP_005293.1"
                     /db_xref="GI:4885323"
                     /db_xref="CCDS:CCDS5792.1"
                     /db_xref="GeneID:2861"
                     /db_xref="HGNC:4494"
                     /db_xref="HPRD:03992"
                     /db_xref="MIM:602583"
     gene            complement(124417346..124430864)
                     /gene="LOC154872"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:154872"
                     /db_xref="HPRD:18562"
     mRNA            complement(join(124417346..124417616,124422057..124422130,
                     124427870..124427926,124430598..124430864))
                     /gene="LOC154872"
                     /product="hypothetical protein LOC154872"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001024603.1"
                     /db_xref="GI:66912169"
                     /db_xref="GeneID:154872"
                     /db_xref="HPRD:18562"
     CDS             complement(join(124417556..124417616,124422057..124422130,
                     124427870..124427926,124430598..124430678))
                     /gene="LOC154872"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC154872"
                     /protein_id="NP_001019774.1"
                     /db_xref="GI:66912170"
                     /db_xref="GeneID:154872"
                     /db_xref="HPRD:18562"
     gene            complement(124462440..124570037)
                     /gene="POT1"
                     /gene_synonym="DKFZp586D211; HPOT1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:25913"
                     /db_xref="HGNC:17284"
                     /db_xref="MIM:606478"
     mRNA            complement(join(124462440..124464128,124465306..124465411,
                     124467268..124467359,124469308..124469396,
                     124475333..124475468,124481027..124481232,
                     124482861..124483017,124486996..124487052,
                     124491926..124492005,124493026..124493192,
                     124499011..124499166,124503404..124503694,
                     124510965..124511095,124532320..124532434,
                     124537219..124537266,124538315..124538428,
                     124555628..124555700,124568869..124569053,
                     124569848..124570037))
                     /gene="POT1"
                     /gene_synonym="DKFZp586D211; HPOT1"
                     /product="protection of telomeres 1 homolog (S. pombe),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015450.2"
                     /db_xref="GI:98991775"
                     /db_xref="GeneID:25913"
                     /db_xref="HGNC:17284"
                     /db_xref="HPRD:07572"
                     /db_xref="MIM:606478"
     mRNA            complement(join(124462440..124464128,124465306..124465411,
                     124467268..124467359,124469308..124469396,
                     124475333..124475468,124481027..124481232,
                     124482861..124483017,124486996..124487052,
                     124491926..124492005,124493026..124493192,
                     124499011..124499166,124503404..124503694,
                     124532320..124532434,124537219..124537266,
                     124538315..124538428,124555628..124555700,
                     124568869..124569053,124569848..124570037))
                     /gene="POT1"
                     /gene_synonym="DKFZp586D211; HPOT1"
                     /product="protection of telomeres 1 homolog (S. pombe),
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001042594.1"
                     /db_xref="GI:110671313"
                     /db_xref="GeneID:25913"
                     /db_xref="HGNC:17284"
                     /db_xref="MIM:606478"
     misc_RNA        complement(join(124462440..124464128,124465306..124465411,
                     124467268..124467359,124469308..124469396,
                     124475333..124475468,124481027..124481232,
                     124482861..124483017,124486996..124487052,
                     124488594..124488713,124491926..124492005,
                     124493026..124493192,124499011..124499166,
                     124503404..124503694,124510965..124511095,
                     124532320..124532434,124537219..124537266,
                     124538315..124538428,124555628..124555700,
                     124568869..124569053,124569848..124570037))
                     /gene="POT1"
                     /gene_synonym="DKFZp586D211; HPOT1"
                     /product="protection of telomeres 1 homolog (S. pombe),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_003102.1"
                     /db_xref="GI:110671311"
                     /db_xref="GeneID:25913"
                     /db_xref="HGNC:17284"
                     /db_xref="MIM:606478"
     misc_RNA        complement(join(124462440..124464128,124465306..124465411,
                     124467268..124467359,124475333..124475468,
                     124481027..124481232,124482861..124483017,
                     124486996..124487052,124491926..124492005,
                     124493026..124493192,124499011..124499166,
                     124503404..124503694,124510965..124511095,
                     124532320..124532434,124537219..124537266,
                     124538315..124538428,124555628..124555700,
                     124568869..124569053,124569848..124570037))
                     /gene="POT1"
                     /gene_synonym="DKFZp586D211; HPOT1"
                     /product="protection of telomeres 1 homolog (S. pombe),
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_003103.1"
                     /db_xref="GI:110671312"
                     /db_xref="GeneID:25913"
                     /db_xref="HGNC:17284"
                     /db_xref="MIM:606478"
     misc_RNA        complement(join(124462440..124464128,124465306..124465411,
                     124467268..124467359,124469308..124469396,
                     124475333..124475468,124477174..124477270,
                     124481027..124481232,124482861..124483017,
                     124486996..124487052,124491926..124492005,
                     124493026..124493192,124499011..124499166,
                     124503404..124503694,124510965..124511095,
                     124532320..124532434,124537219..124537266,
                     124538315..124538428,124555628..124555700,
                     124568869..124569053,124569848..124570037))
                     /gene="POT1"
                     /gene_synonym="DKFZp586D211; HPOT1"
                     /product="protection of telomeres 1 homolog (S. pombe),
                     transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_003104.1"
                     /db_xref="GI:110671315"
                     /db_xref="GeneID:25913"
                     /db_xref="HGNC:17284"
                     /db_xref="MIM:606478"
     CDS             complement(join(124464016..124464128,124465306..124465411,
                     124467268..124467359,124469308..124469396,
                     124475333..124475468,124481027..124481232,
                     124482861..124483017,124486996..124487052,
                     124491926..124492005,124493026..124493192,
                     124499011..124499166,124503404..124503694,
                     124510965..124511095,124532320..124532434,
                     124537219..124537227))
                     /gene="POT1"
                     /gene_synonym="DKFZp586D211; HPOT1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protection of telomeres protein 1 isoform 1"
                     /protein_id="NP_056265.2"
                     /db_xref="GI:98991776"
                     /db_xref="CCDS:CCDS5793.1"
                     /db_xref="GeneID:25913"
                     /db_xref="HGNC:17284"
                     /db_xref="MIM:606478"
     CDS             complement(join(124464016..124464128,124465306..124465411,
                     124467268..124467359,124469308..124469396,
                     124475333..124475468,124481027..124481232,
                     124482861..124483017,124486996..124487052,
                     124491926..124492005,124493026..124493192,
                     124499011..124499166,124503404..124503556))
                     /gene="POT1"
                     /gene_synonym="DKFZp586D211; HPOT1"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="protection of telomeres protein 1 isoform 4"
                     /protein_id="NP_001036059.1"
                     /db_xref="GI:110671314"
                     /db_xref="GeneID:25913"
                     /db_xref="HGNC:17284"
                     /db_xref="MIM:606478"
     gene            124673487..124675443
                     /gene="LOC646837"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:646837"
     gene            complement(124800027..124800599)
                     /gene="LOC100420864"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420864"
     gene            complement(124940517..124940958)
                     /gene="RPL31P39"
                     /gene_synonym="RPL31_11_842"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:641790"
                     /db_xref="HGNC:35995"
     gene            124985026..124985808
                     /gene="LOC100134507"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100134507"
     gene            125078276..125102007
                     /gene="LOC100506664"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /db_xref="GeneID:100506664"
     misc_RNA        join(125078276..125078351,125101535..125102007)
                     /gene="LOC100506664"
                     /product="hypothetical LOC100506664"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_108804.1"
                     /db_xref="GI:310120083"
                     /db_xref="GeneID:100506664"
     gene            complement(126078652..126892428)
                     /gene="GRM8"
                     /gene_synonym="FLJ41058; GLUR8; GPRC1H; MGC126724; mGlu8;
                     MGLUR8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2918"
                     /db_xref="HGNC:4600"
                     /db_xref="HPRD:03071"
                     /db_xref="MIM:601116"
     mRNA            complement(join(126078652..126079222,126086125..126086426,
                     126173006..126173941,126249416..126249552,
                     126409919..126410119,126542596..126542733,
                     126544026..126544180,126544602..126544737,
                     126746550..126746766,126882749..126883569,
                     126892183..126892428))
                     /gene="GRM8"
                     /gene_synonym="FLJ41058; GLUR8; GPRC1H; MGC126724; mGlu8;
                     MGLUR8"
                     /product="glutamate receptor, metabotropic 8, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127323.1"
                     /db_xref="GI:187960068"
                     /db_xref="GeneID:2918"
                     /db_xref="HGNC:4600"
                     /db_xref="MIM:601116"
                     /db_xref="HPRD:03071"
     mRNA            complement(join(126078652..126079222,126086180..126086426,
                     126173006..126173941,126249416..126249552,
                     126409919..126410119,126542596..126542733,
                     126544026..126544180,126544602..126544737,
                     126746550..126746766,126882749..126883569))
                     /gene="GRM8"
                     /gene_synonym="FLJ41058; GLUR8; GPRC1H; MGC126724; mGlu8;
                     MGLUR8"
                     /product="glutamate receptor, metabotropic 8, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000845.2"
                     /db_xref="GI:187960066"
                     /db_xref="GeneID:2918"
                     /db_xref="HGNC:4600"
                     /db_xref="HPRD:03071"
                     /db_xref="MIM:601116"
     misc_RNA        complement(join(126078652..126079222,126086180..126086426,
                     126173006..126173941,126249416..126249552,
                     126341811..126341881,126409919..126410119,
                     126542596..126542733,126544026..126544180,
                     126544602..126544737,126746550..126746766,
                     126882749..126883569))
                     /gene="GRM8"
                     /gene_synonym="FLJ41058; GLUR8; GPRC1H; MGC126724; mGlu8;
                     MGLUR8"
                     /product="glutamate receptor, metabotropic 8, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_028041.1"
                     /db_xref="GI:253970408"
                     /db_xref="GeneID:2918"
                     /db_xref="HGNC:4600"
                     /db_xref="MIM:601116"
                     /db_xref="HPRD:03071"
     CDS             complement(join(126079173..126079222,126086180..126086426,
                     126173006..126173941,126249416..126249552,
                     126409919..126410119,126542596..126542733,
                     126544026..126544180,126544602..126544737,
                     126746550..126746766,126882749..126883258))
                     /gene="GRM8"
                     /gene_synonym="FLJ41058; GLUR8; GPRC1H; MGC126724; mGlu8;
                     MGLUR8"
                     /note="isoform a precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="metabotropic glutamate receptor 8 isoform a
                     precursor"
                     /protein_id="NP_000836.2"
                     /db_xref="GI:187960067"
                     /db_xref="CCDS:CCDS5794.1"
                     /db_xref="GeneID:2918"
                     /db_xref="HGNC:4600"
                     /db_xref="HPRD:03071"
                     /db_xref="MIM:601116"
     CDS             complement(join(126086130..126086426,126173006..126173941,
                     126249416..126249552,126409919..126410119,
                     126542596..126542733,126544026..126544180,
                     126544602..126544737,126746550..126746766,
                     126882749..126883258))
                     /gene="GRM8"
                     /gene_synonym="FLJ41058; GLUR8; GPRC1H; MGC126724; mGlu8;
                     MGLUR8"
                     /note="isoform b precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="metabotropic glutamate receptor 8 isoform b
                     precursor"
                     /protein_id="NP_001120795.1"
                     /db_xref="GI:187960069"
                     /db_xref="CCDS:CCDS47696.1"
                     /db_xref="GeneID:2918"
                     /db_xref="HGNC:4600"
                     /db_xref="HPRD:03071"
                     /db_xref="MIM:601116"
     gene            126151192..126152850
                     /gene="LOC100422325"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100422325"
     gene            complement(126698142..126698238)
                     /gene="MIR592"
                     /gene_synonym="hsa-mir-592; MIRN592"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:693177"
                     /db_xref="HGNC:32848"
                     /db_xref="miRBase:MI0003604"
     ncRNA           complement(126698142..126698238)
                     /gene="MIR592"
                     /gene_synonym="hsa-mir-592; MIRN592"
                     /ncRNA_class="miRNA"
                     /product="microRNA 592"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_030323.1"
                     /db_xref="GI:262205957"
                     /db_xref="GeneID:693177"
                     /db_xref="HGNC:32848"
                     /db_xref="miRBase:MI0003604"
     ncRNA           complement(126698142..126698238)
                     /gene="MIR592"
                     /gene_synonym="hsa-mir-592; MIRN592"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-592"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:693177"
                     /db_xref="miRBase:MI0003604"
                     /db_xref="HGNC:32848"
     gene            126935674..126936254
                     /gene="LOC646873"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:646873"
     gene            complement(127010353..127032767)
                     /gene="ZNF800"
                     /gene_synonym="FLJ43301; MGC130032; MGC130033"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:168850"
                     /db_xref="HGNC:27267"
                     /db_xref="HPRD:14112"
     mRNA            complement(join(127010353..127011868,127013396..127015088,
                     127017240..127017383,127026114..127026209,
                     127031551..127031669,127032114..127032767))
                     /gene="ZNF800"
                     /gene_synonym="FLJ43301; MGC130032; MGC130033"
                     /product="zinc finger protein 800"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_176814.3"
                     /db_xref="GI:39753952"
                     /db_xref="GeneID:168850"
                     /db_xref="HGNC:27267"
                     /db_xref="HPRD:14112"
     CDS             complement(join(127011868,127013396..127015088,
                     127017240..127017383,127026114..127026209,
                     127031551..127031611))
                     /gene="ZNF800"
                     /gene_synonym="FLJ43301; MGC130032; MGC130033"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 800"
                     /protein_id="NP_789784.2"
                     /db_xref="GI:39753953"
                     /db_xref="CCDS:CCDS5795.1"
                     /db_xref="GeneID:168850"
                     /db_xref="HGNC:27267"
                     /db_xref="HPRD:14112"
     gene            127116932..127125858
                     /gene="LOC100506682"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /db_xref="GeneID:100506682"
     misc_RNA        join(127116932..127117023,127117651..127117722,
                     127119187..127119291,127125166..127125858)
                     /gene="LOC100506682"
                     /product="hypothetical LOC100506682"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /transcript_id="XR_108805.1"
                     /db_xref="GI:310120084"
                     /db_xref="GeneID:100506682"
     gene            complement(127220682..127225654)
                     /gene="GCC1"
                     /gene_synonym="FLJ22035; GCC1P; GCC88; MGC20706"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79571"
                     /db_xref="HGNC:19095"
                     /db_xref="HPRD:07599"
                     /db_xref="MIM:607418"
     mRNA            complement(join(127220682..127223363,
                     127224205..127225654))
                     /gene="GCC1"
                     /gene_synonym="FLJ22035; GCC1P; GCC88; MGC20706"
                     /product="GRIP and coiled-coil domain containing 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024523.5"
                     /db_xref="GI:34305454"
                     /db_xref="GeneID:79571"
                     /db_xref="HGNC:19095"
                     /db_xref="HPRD:07599"
                     /db_xref="MIM:607418"
     CDS             complement(join(127222068..127223363,
                     127224205..127225236))
                     /gene="GCC1"
                     /gene_synonym="FLJ22035; GCC1P; GCC88; MGC20706"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="GRIP and coiled-coil domain-containing protein
                     1"
                     /protein_id="NP_078799.2"
                     /db_xref="GI:22208850"
                     /db_xref="CCDS:CCDS5796.1"
                     /db_xref="GeneID:79571"
                     /db_xref="HGNC:19095"
                     /db_xref="HPRD:07599"
                     /db_xref="MIM:607418"
     gene            127228406..127231759
                     /gene="ARF5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:381"
                     /db_xref="HGNC:658"
                     /db_xref="HPRD:00055"
                     /db_xref="MIM:103188"
     mRNA            join(127228406..127228619,127229137..127229217,
                     127229539..127229648,127230120..127230191,
                     127231017..127231142,127231267..127231759)
                     /gene="ARF5"
                     /product="ADP-ribosylation factor 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001662.3"
                     /db_xref="GI:313760590"
                     /db_xref="GeneID:381"
                     /db_xref="HGNC:658"
                     /db_xref="HPRD:00055"
                     /db_xref="MIM:103188"
     CDS             join(127228553..127228619,127229137..127229217,
                     127229539..127229648,127230120..127230191,
                     127231017..127231142,127231267..127231353)
                     /gene="ARF5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ADP-ribosylation factor 5"
                     /protein_id="NP_001653.1"
                     /db_xref="GI:4502209"
                     /db_xref="CCDS:CCDS34745.1"
                     /db_xref="GeneID:381"
                     /db_xref="HGNC:658"
                     /db_xref="HPRD:00055"
                     /db_xref="MIM:103188"
     gene            127233689..127241851
                     /gene="FSCN3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:29999"
                     /db_xref="HGNC:3961"
                     /db_xref="HPRD:17020"
     mRNA            join(127233689..127234051,127235361..127236057,
                     127236382..127236500,127238489..127238648,
                     127239435..127239605,127240248..127240453,
                     127241677..127241851)
                     /gene="FSCN3"
                     /product="fascin homolog 3, actin-bundling protein,
                     testicular (Strongylocentrotus purpuratus)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020369.2"
                     /db_xref="GI:313760589"
                     /db_xref="GeneID:29999"
                     /db_xref="HGNC:3961"
                     /db_xref="HPRD:17020"
     CDS             join(127233908..127234051,127235361..127236057,
                     127236382..127236500,127238489..127238648,
                     127239435..127239605,127240248..127240453)
                     /gene="FSCN3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="fascin-3"
                     /protein_id="NP_065102.1"
                     /db_xref="GI:9966791"
                     /db_xref="CCDS:CCDS34746.1"
                     /db_xref="GeneID:29999"
                     /db_xref="HGNC:3961"
                     /db_xref="HPRD:17020"
     gene            complement(127250346..127255780)
                     /gene="PAX4"
                     /gene_synonym="KPD; MGC129960; MODY9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5078"
                     /db_xref="HGNC:8618"
                     /db_xref="HPRD:01333"
                     /db_xref="MIM:167413"
     mRNA            complement(join(127250346..127251260,127251589..127251730,
                     127251999..127252054,127253076..127253145,
                     127253504..127253586,127253810..127253935,
                     127254536..127254611,127254934..127255149,
                     127255455..127255780))
                     /gene="PAX4"
                     /gene_synonym="KPD; MGC129960; MODY9"
                     /product="paired box 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006193.2"
                     /db_xref="GI:170784823"
                     /db_xref="GeneID:5078"
                     /db_xref="HGNC:8618"
                     /db_xref="HPRD:01333"
                     /db_xref="MIM:167413"
     CDS             complement(join(127251118..127251260,127251589..127251730,
                     127251999..127252054,127253076..127253145,
                     127253504..127253586,127253810..127253935,
                     127254536..127254611,127254934..127255149,
                     127255455..127255574))
                     /gene="PAX4"
                     /gene_synonym="KPD; MGC129960; MODY9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="paired box protein Pax-4"
                     /protein_id="NP_006184.2"
                     /db_xref="GI:170784824"
                     /db_xref="CCDS:CCDS5797.1"
                     /db_xref="GeneID:5078"
                     /db_xref="HGNC:8618"
                     /db_xref="HPRD:01333"
                     /db_xref="MIM:167413"
     gene            127292202..127732659
                     /gene="SND1"
                     /gene_synonym="p100; TDRD11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:27044"
                     /db_xref="HGNC:30646"
                     /db_xref="HPRD:03714"
                     /db_xref="MIM:602181"
     mRNA            join(127292202..127292505,127326667..127326816,
                     127334882..127335002,127338929..127339007,
                     127341217..127341377,127342489..127342580,
                     127343219..127343377,127344893..127344999,
                     127347611..127347701,127361341..127361454,
                     127447538..127447627,127484377..127484477,
                     127527955..127528065,127544800..127544872,
                     127569241..127569382,127631000..127631109,
                     127714554..127714742,127721412..127721553,
                     127724776..127724899,127725763..127725832,
                     127726990..127727103,127729541..127729744,
                     127731889..127731933,127732045..127732659)
                     /gene="SND1"
                     /gene_synonym="p100; TDRD11"
                     /product="staphylococcal nuclease and tudor domain
                     containing 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014390.2"
                     /db_xref="GI:77404396"
                     /db_xref="GeneID:27044"
                     /db_xref="HGNC:30646"
                     /db_xref="HPRD:03714"
                     /db_xref="MIM:602181"
     CDS             join(127292428..127292505,127326667..127326816,
                     127334882..127335002,127338929..127339007,
                     127341217..127341377,127342489..127342580,
                     127343219..127343377,127344893..127344999,
                     127347611..127347701,127361341..127361454,
                     127447538..127447627,127484377..127484477,
                     127527955..127528065,127544800..127544872,
                     127569241..127569382,127631000..127631109,
                     127714554..127714742,127721412..127721553,
                     127724776..127724899,127725763..127725832,
                     127726990..127727103,127729541..127729744,
                     127731889..127731933,127732045..127732110)
                     /gene="SND1"
                     /gene_synonym="p100; TDRD11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="staphylococcal nuclease domain-containing
                     protein 1"
                     /protein_id="NP_055205.2"
                     /db_xref="GI:77404397"
                     /db_xref="CCDS:CCDS34747.1"
                     /db_xref="GeneID:27044"
                     /db_xref="HGNC:30646"
                     /db_xref="HPRD:03714"
                     /db_xref="MIM:602181"
     gene            complement(127497590..127498524)
                     /gene="LOC100196944"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100196944"
     gene            127637562..127640130
                     /gene="C7orf54"
                     /gene_synonym="MGC138346; NAG8; NSG-X"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:27099"
                     /db_xref="HGNC:24158"
     misc_RNA        127637562..127640130
                     /gene="C7orf54"
                     /gene_synonym="MGC138346; NAG8; NSG-X"
                     /product="chromosome 7 open reading frame 54"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027330.1"
                     /db_xref="GI:224922761"
                     /db_xref="GeneID:27099"
                     /db_xref="HGNC:24158"
     gene            complement(127667124..127671002)
                     /gene="LRRC4"
                     /gene_synonym="MGC133342; MGC133343; NAG14; NGL-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64101"
                     /db_xref="HGNC:15586"
                     /db_xref="HPRD:10060"
                     /db_xref="MIM:610486"
     mRNA            complement(join(127667124..127670793,
                     127670966..127671002))
                     /gene="LRRC4"
                     /gene_synonym="MGC133342; MGC133343; NAG14; NGL-2"
                     /product="leucine rich repeat containing 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022143.4"
                     /db_xref="GI:116174787"
                     /db_xref="GeneID:64101"
                     /db_xref="HGNC:15586"
                     /db_xref="HPRD:10060"
                     /db_xref="MIM:610486"
     CDS             complement(127668732..127670693)
                     /gene="LRRC4"
                     /gene_synonym="MGC133342; MGC133343; NAG14; NGL-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="leucine-rich repeat-containing protein 4
                     precursor"
                     /protein_id="NP_071426.1"
                     /db_xref="GI:15029530"
                     /db_xref="CCDS:CCDS5799.1"
                     /db_xref="GeneID:64101"
                     /db_xref="HGNC:15586"
                     /db_xref="HPRD:10060"
                     /db_xref="MIM:610486"
     gene            127721913..127722012
                     /gene="MIR593"
                     /gene_synonym="hsa-mir-593; MIRN593"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:693178"
                     /db_xref="HGNC:32849"
                     /db_xref="miRBase:MI0003605"
     ncRNA           127721913..127722012
                     /gene="MIR593"
                     /gene_synonym="hsa-mir-593; MIRN593"
                     /ncRNA_class="miRNA"
                     /product="microRNA 593"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_030324.1"
                     /db_xref="GI:262205962"
                     /db_xref="GeneID:693178"
                     /db_xref="HGNC:32849"
                     /db_xref="miRBase:MI0003605"
     ncRNA           127721913..127722012
                     /gene="MIR593"
                     /gene_synonym="hsa-mir-593; MIRN593"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-593"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:693178"
                     /db_xref="miRBase:MI0003605"
                     /db_xref="HGNC:32849"
     gene            127847925..127847996
                     /gene="MIR129-1"
                     /gene_synonym="MIR-129b; MIRN129-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:406917"
                     /db_xref="HGNC:31512"
                     /db_xref="miRBase:MI0000252"
     ncRNA           127847925..127847996
                     /gene="MIR129-1"
                     /gene_synonym="MIR-129b; MIRN129-1"
                     /ncRNA_class="miRNA"
                     /product="microRNA 129-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029596.1"
                     /db_xref="GI:262206156"
                     /db_xref="GeneID:406917"
                     /db_xref="HGNC:31512"
                     /db_xref="miRBase:MI0000252"
     ncRNA           127847925..127847996
                     /gene="MIR129-1"
                     /gene_synonym="MIR-129b; MIRN129-1"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-129-1"
                     /inference="similar to RNA sequence:INSD: AJ560751"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:406917"
                     /db_xref="miRBase:MI0000252"
                     /db_xref="HGNC:31512"
     gene            127881331..127897682
                     /gene="LEP"
                     /gene_synonym="FLJ94114; OB; OBS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3952"
                     /db_xref="HGNC:6553"
                     /db_xref="HPRD:01249"
                     /db_xref="MIM:164160"
     mRNA            join(127881331..127881359,127892044..127892215,
                     127894457..127897682)
                     /gene="LEP"
                     /gene_synonym="FLJ94114; OB; OBS"
                     /product="leptin"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000230.2"
                     /db_xref="GI:169790920"
                     /db_xref="GeneID:3952"
                     /db_xref="HGNC:6553"
                     /db_xref="HPRD:01249"
                     /db_xref="MIM:164160"
     CDS             join(127892072..127892215,127894457..127894816)
                     /gene="LEP"
                     /gene_synonym="FLJ94114; OB; OBS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="leptin precursor"
                     /protein_id="NP_000221.1"
                     /db_xref="GI:4557715"
                     /db_xref="CCDS:CCDS5800.1"
                     /db_xref="GeneID:3952"
                     /db_xref="HGNC:6553"
                     /db_xref="HPRD:01249"
                     /db_xref="MIM:164160"
     gene            complement(127944170..127948588)
                     /gene="MGC27345"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 3 mRNAs, 49 ESTs, 1 Protein"
                     /db_xref="GeneID:157247"
     misc_RNA        complement(127944170..127948588)
                     /gene="MGC27345"
                     /product="hypothetical protein MGC27345"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 3 mRNAs, 49 ESTs, 1 Protein"
                     /transcript_id="XR_108807.1"
                     /db_xref="GI:310120085"
                     /db_xref="GeneID:157247"
     gene            127946761..127947638
                     /gene="LOC100418961"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100418961"
     gene            complement(127950436..127983962)
                     /gene="RBM28"
                     /gene_synonym="FLJ10377"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55131"
                     /db_xref="HGNC:21863"
                     /db_xref="HPRD:07668"
                     /db_xref="MIM:612074"
     mRNA            complement(join(127950436..127950984,127953228..127953327,
                     127954817..127955073,127957712..127957786,
                     127958010..127958159,127961319..127961477,
                     127963580..127963644,127964612..127964747,
                     127965871..127965944,127970872..127970981,
                     127973344..127973416,127975597..127975733,
                     127975901..127976096,127977185..127977256,
                     127978304..127978396,127978780..127978855,
                     127979281..127979375,127979687..127979845,
                     127983730..127983962))
                     /gene="RBM28"
                     /gene_synonym="FLJ10377"
                     /product="RNA binding motif protein 28, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018077.2"
                     /db_xref="GI:187960108"
                     /db_xref="GeneID:55131"
                     /db_xref="HGNC:21863"
                     /db_xref="HPRD:07668"
                     /db_xref="MIM:612074"
     mRNA            complement(join(127950436..127950984,127953228..127953327,
                     127954817..127955073,127957712..127957786,
                     127958010..127958159,127961319..127961477,
                     127963580..127963644,127964612..127964747,
                     127965871..127965944,127970872..127970981,
                     127973344..127973416,127975597..127975733,
                     127975901..127976096,127977185..127977256,
                     127983730..127983962))
                     /gene="RBM28"
                     /gene_synonym="FLJ10377"
                     /product="RNA binding motif protein 28, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001166135.1"
                     /db_xref="GI:260898762"
                     /db_xref="GeneID:55131"
                     /db_xref="HGNC:21863"
                     /db_xref="MIM:612074"
                     /db_xref="HPRD:07668"
     CDS             complement(join(127950850..127950984,127953228..127953327,
                     127954817..127955073,127957712..127957786,
                     127958010..127958159,127961319..127961477,
                     127963580..127963644,127964612..127964747,
                     127965871..127965944,127970872..127970981,
                     127973344..127973416,127975597..127975733,
                     127975901..127976096,127977185..127977256,
                     127978304..127978396,127978780..127978855,
                     127979281..127979375,127979687..127979845,
                     127983730..127983847))
                     /gene="RBM28"
                     /gene_synonym="FLJ10377"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="RNA-binding protein 28 isoform 1"
                     /protein_id="NP_060547.2"
                     /db_xref="GI:187960109"
                     /db_xref="CCDS:CCDS5801.1"
                     /db_xref="GeneID:55131"
                     /db_xref="HGNC:21863"
                     /db_xref="HPRD:07668"
                     /db_xref="MIM:612074"
     CDS             complement(join(127950850..127950984,127953228..127953327,
                     127954817..127955073,127957712..127957786,
                     127958010..127958159,127961319..127961477,
                     127963580..127963644,127964612..127964747,
                     127965871..127965944,127970872..127970981,
                     127973344..127973416,127975597..127975733,
                     127975901..127976096,127977185..127977256,
                     127983730..127983847))
                     /gene="RBM28"
                     /gene_synonym="FLJ10377"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="RNA-binding protein 28 isoform 2"
                     /protein_id="NP_001159607.1"
                     /db_xref="GI:260898763"
                     /db_xref="CCDS:CCDS55159.1"
                     /db_xref="GeneID:55131"
                     /db_xref="HGNC:21863"
                     /db_xref="HPRD:07668"
                     /db_xref="MIM:612074"
     gene            127984136..127984193
                     /gene="RNU7-27P"
                     /gene_synonym="U7.27"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100147814"
                     /db_xref="HGNC:34123"
     gene            complement(127990379..128001739)
                     /gene="PRRT4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:401399"
                     /db_xref="HGNC:37280"
     mRNA            complement(join(127990379..127992732,127998735..127998854,
                     127999203..127999307,127999394..128000117,
                     128001360..128001476,128001615..128001739))
                     /gene="PRRT4"
                     /product="proline-rich transmembrane protein 4, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001174164.1"
                     /db_xref="GI:292658792"
                     /db_xref="GeneID:401399"
                     /db_xref="HGNC:37280"
     mRNA            complement(join(127990379..127991468,127992503..127992732,
                     127998735..127998854,127999203..127999307,
                     127999394..128000117,128001615..128001739))
                     /gene="PRRT4"
                     /product="proline-rich transmembrane protein 4, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001114726.2"
                     /db_xref="GI:292658790"
                     /db_xref="GeneID:401399"
                     /db_xref="HGNC:37280"
     CDS             complement(join(127990910..127992732,127998735..127998854,
                     127999203..127999307,127999394..128000045))
                     /gene="PRRT4"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="proline-rich transmembrane protein 4 isoform 1"
                     /protein_id="NP_001167635.1"
                     /db_xref="GI:292658793"
                     /db_xref="CCDS:CCDS55160.1"
                     /db_xref="GeneID:401399"
                     /db_xref="HGNC:37280"
     CDS             complement(join(127991286..127991468,127992503..127992732,
                     127998735..127998854,127999203..127999307,
                     127999394..128000045))
                     /gene="PRRT4"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="proline-rich transmembrane protein 4 isoform 2"
                     /protein_id="NP_001108198.2"
                     /db_xref="GI:292658791"
                     /db_xref="CCDS:CCDS47698.2"
                     /db_xref="GeneID:401399"
                     /db_xref="HGNC:37280"
     gene            complement(128032331..128050036)
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="HPRD:08853"
                     /db_xref="MIM:146690"
     mRNA            complement(join(128032331..128033082,128034332..128034415,
                     128034510..128034653,128034943..128035087,
                     128035185..128035328,128036654..128036749,
                     128036986..128037076,128038468..128038667,
                     128040149..128040236,128040387..128040593,
                     128040871..128040945,128041069..128041170,
                     128043760..128043808,128045821..128045919,
                     128049343..128049406,128049495..128049538,
                     128049810..128050036))
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /product="IMP (inosine 5'-monophosphate) dehydrogenase 1,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000883.3"
                     /db_xref="GI:156616276"
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="HPRD:08853"
                     /db_xref="MIM:146690"
     mRNA            complement(join(128032331..128033082,128034332..128034415,
                     128034510..128034653,128034943..128035087,
                     128035185..128035328,128036654..128036749,
                     128036986..128037076,128038468..128038667,
                     128040149..128040236,128040387..128040593,
                     128040871..128040945,128041069..128041170,
                     128043760..128043808,128045821..128045919,
                     128049810..128050036))
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /product="IMP (inosine 5'-monophosphate) dehydrogenase 1,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_183243.2"
                     /db_xref="GI:156616277"
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="MIM:146690"
                     /db_xref="HPRD:08853"
     mRNA            complement(join(128032331..128033082,128034332..128034415,
                     128034510..128034653,128034943..128035087,
                     128035185..128035328,128036654..128036749,
                     128036986..128037076,128038468..128038667,
                     128040149..128040236,128040387..128040593,
                     128040871..128040945,128041069..128041170,
                     128043760..128043808,128045821..128045919,
                     128049343..128049420,128049810..128050036))
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /product="IMP (inosine 5'-monophosphate) dehydrogenase 1,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001102605.1"
                     /db_xref="GI:156616278"
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="MIM:146690"
                     /db_xref="HPRD:08853"
     mRNA            complement(join(128032331..128033082,128034332..128034415,
                     128034510..128034653,128034943..128035087,
                     128035185..128035328,128036654..128036749,
                     128036986..128037076,128038468..128038667,
                     128040149..128040236,128040387..128040593,
                     128040871..128040945,128041069..128041170,
                     128043760..128043808,128049343..128049406,
                     128049495..128049538,128049810..128050036))
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /product="IMP (inosine 5'-monophosphate) dehydrogenase 1,
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001142576.1"
                     /db_xref="GI:217035151"
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="MIM:146690"
                     /db_xref="HPRD:08853"
     mRNA            complement(join(128032331..128033082,128034332..128034415,
                     128034510..128034653,128034943..128035087,
                     128035185..128035328,128036654..128036749,
                     128036986..128037076,128038468..128038667,
                     128040149..128040236,128040387..128040593,
                     128040871..128040945,128041069..128041170,
                     128043760..128043808,128045821..128046024))
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /product="IMP (inosine 5'-monophosphate) dehydrogenase 1,
                     transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001142573.1"
                     /db_xref="GI:217035145"
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="MIM:146690"
                     /db_xref="HPRD:08853"
     mRNA            complement(join(128032331..128033082,128034332..128034415,
                     128034510..128034653,128034943..128035087,
                     128035185..128035328,128036654..128036749,
                     128036986..128037076,128038468..128038667,
                     128040149..128040236,128040387..128040593,
                     128040886..128040945,128041069..128041170,
                     128043760..128043808,128045821..128046024))
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /product="IMP (inosine 5'-monophosphate) dehydrogenase 1,
                     transcript variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001142574.1"
                     /db_xref="GI:217035147"
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="MIM:146690"
                     /db_xref="HPRD:08853"
     mRNA            complement(join(128032331..128033082,128034332..128034415,
                     128034510..128034653,128034943..128035087,
                     128035185..128035328,128036654..128036749,
                     128036986..128037076,128038468..128038667,
                     128040149..128040236,128040387..128040593,
                     128041069..128041170,128043760..128043808,
                     128045821..128046024))
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /product="IMP (inosine 5'-monophosphate) dehydrogenase 1,
                     transcript variant 7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001142575.1"
                     /db_xref="GI:217035149"
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="MIM:146690"
                     /db_xref="HPRD:08853"
     CDS             complement(join(128033061..128033082,128034332..128034415,
                     128034510..128034653,128034943..128035087,
                     128035185..128035328,128036654..128036749,
                     128036986..128037076,128038468..128038667,
                     128040149..128040236,128040387..128040593,
                     128040871..128040945,128041069..128041170,
                     128043760..128043808,128045821..128045919,
                     128049343..128049406,128049495..128049538,
                     128049810..128049955))
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="inosine-5'-monophosphate dehydrogenase 1 isoform
                     a"
                     /protein_id="NP_000874.2"
                     /db_xref="GI:34328930"
                     /db_xref="CCDS:CCDS34749.1"
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="HPRD:08853"
                     /db_xref="MIM:146690"
     CDS             complement(join(128033061..128033082,128034332..128034415,
                     128034510..128034653,128034943..128035087,
                     128035185..128035328,128036654..128036749,
                     128036986..128037076,128038468..128038667,
                     128040149..128040236,128040387..128040593,
                     128040871..128040945,128041069..128041170,
                     128043760..128043808,128045821..128045919,
                     128049810..128049955))
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="inosine-5'-monophosphate dehydrogenase 1 isoform
                     b"
                     /protein_id="NP_899066.1"
                     /db_xref="GI:34328928"
                     /db_xref="CCDS:CCDS34748.1"
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="HPRD:08853"
                     /db_xref="MIM:146690"
     CDS             complement(join(128033061..128033082,128034332..128034415,
                     128034510..128034653,128034943..128035087,
                     128035185..128035328,128036654..128036749,
                     128036986..128037076,128038468..128038667,
                     128040149..128040236,128040387..128040593,
                     128040871..128040945,128041069..128041170,
                     128043760..128043808,128045821..128045919,
                     128049343..128049420,128049810..128049955))
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="inosine-5'-monophosphate dehydrogenase 1 isoform
                     c"
                     /protein_id="NP_001096075.1"
                     /db_xref="GI:156616279"
                     /db_xref="CCDS:CCDS43643.1"
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="HPRD:08853"
                     /db_xref="MIM:146690"
     CDS             complement(join(128033061..128033082,128034332..128034415,
                     128034510..128034653,128034943..128035087,
                     128035185..128035328,128036654..128036749,
                     128036986..128037076,128038468..128038667,
                     128040149..128040236,128040387..128040593,
                     128040871..128040945,128041069..128041170,
                     128043760..128043808,128049343..128049406,
                     128049495..128049538,128049810..128049955))
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /note="isoform d is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="inosine-5'-monophosphate dehydrogenase 1 isoform
                     d"
                     /protein_id="NP_001136048.1"
                     /db_xref="GI:217035152"
                     /db_xref="CCDS:CCDS47699.1"
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="HPRD:08853"
                     /db_xref="MIM:146690"
     CDS             complement(join(128033061..128033082,128034332..128034415,
                     128034510..128034653,128034943..128035087,
                     128035185..128035328,128036654..128036749,
                     128036986..128037076,128038468..128038667,
                     128040149..128040236,128040387..128040593,
                     128040871..128040945,128041069..128041170,
                     128043760..128043808,128045821..128045918))
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /note="isoform e is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="inosine-5'-monophosphate dehydrogenase 1 isoform
                     e"
                     /protein_id="NP_001136045.1"
                     /db_xref="GI:217035146"
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="MIM:146690"
                     /db_xref="HPRD:08853"
     CDS             complement(join(128033061..128033082,128034332..128034415,
                     128034510..128034653,128034943..128035087,
                     128035185..128035328,128036654..128036749,
                     128036986..128037076,128038468..128038667,
                     128040149..128040236,128040387..128040593,
                     128040886..128040945,128041069..128041170,
                     128043760..128043808,128045821..128045918))
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /note="isoform f is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="inosine-5'-monophosphate dehydrogenase 1 isoform
                     f"
                     /protein_id="NP_001136046.1"
                     /db_xref="GI:217035148"
                     /db_xref="CCDS:CCDS55161.1"
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="HPRD:08853"
                     /db_xref="MIM:146690"
     CDS             complement(join(128033061..128033082,128034332..128034415,
                     128034510..128034653,128034943..128035087,
                     128035185..128035328,128036654..128036749,
                     128036986..128037076,128038468..128038667,
                     128040149..128040236,128040387..128040593,
                     128041069..128041170,128043760..128043808,
                     128045821..128045918))
                     /gene="IMPDH1"
                     /gene_synonym="DKFZp781N0678; IMPD; IMPD1; LCA11; RP10;
                     sWSS2608"
                     /note="isoform g is encoded by transcript variant 7;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="inosine-5'-monophosphate dehydrogenase 1 isoform
                     g"
                     /protein_id="NP_001136047.1"
                     /db_xref="GI:217035150"
                     /db_xref="CCDS:CCDS47700.1"
                     /db_xref="GeneID:3614"
                     /db_xref="HGNC:6052"
                     /db_xref="HPRD:08853"
                     /db_xref="MIM:146690"
     gene            complement(128073476..128073767)
                     /gene="RPL37P16"
                     /gene_synonym="RPL37_6_843"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271021"
                     /db_xref="HGNC:35949"
     gene            complement(128083504..128083564)
                     /gene="RNU7-54P"
                     /gene_synonym="U7.54"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100151650"
                     /db_xref="HGNC:34150"
     gene            128095884..128098472
                     /gene="C7orf68"
                     /gene_synonym="FLJ21076; HIG-2; HIG2; MGC138388"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:29923"
                     /db_xref="HGNC:28859"
     mRNA            join(128095884..128096077,128097255..128098472)
                     /gene="C7orf68"
                     /gene_synonym="FLJ21076; HIG-2; HIG2; MGC138388"
                     /product="chromosome 7 open reading frame 68, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013332.3"
                     /db_xref="GI:149192860"
                     /db_xref="GeneID:29923"
                     /db_xref="HGNC:28859"
                     /db_xref="HPRD:17105"
     mRNA            join(128095884..128095963,128097255..128098472)
                     /gene="C7orf68"
                     /gene_synonym="FLJ21076; HIG-2; HIG2; MGC138388"
                     /product="chromosome 7 open reading frame 68, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001098786.1"
                     /db_xref="GI:149192827"
                     /db_xref="GeneID:29923"
                     /db_xref="HGNC:28859"
     CDS             128097323..128097514
                     /gene="C7orf68"
                     /gene_synonym="FLJ21076; HIG-2; HIG2; MGC138388"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypoxia-inducible gene 2 protein"
                     /protein_id="NP_001092256.1"
                     /db_xref="GI:149192828"
                     /db_xref="CCDS:CCDS5802.1"
                     /db_xref="GeneID:29923"
                     /db_xref="HGNC:28859"
     CDS             128097323..128097514
                     /gene="C7orf68"
                     /gene_synonym="FLJ21076; HIG-2; HIG2; MGC138388"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypoxia-inducible gene 2 protein"
                     /protein_id="NP_037464.1"
                     /db_xref="GI:7019409"
                     /db_xref="CCDS:CCDS5802.1"
                     /db_xref="GeneID:29923"
                     /db_xref="HGNC:28859"
     gene            128116783..128142978
                     /gene="METTL2B"
                     /gene_synonym="FLJ11350; FLJ12760; METL; METTL2; METTL2A;
                     PSENIP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55798"
                     /db_xref="HGNC:18272"
                     /db_xref="HPRD:09705"
                     /db_xref="MIM:607846"
     mRNA            join(128116783..128116929,128117136..128117227,
                     128119212..128119567,128120701..128120750,
                     128128155..128128215,128133858..128133997,
                     128138090..128138196,128140957..128141022,
                     128141816..128142978)
                     /gene="METTL2B"
                     /gene_synonym="FLJ11350; FLJ12760; METL; METTL2; METTL2A;
                     PSENIP1"
                     /product="methyltransferase like 2B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018396.2"
                     /db_xref="GI:93141203"
                     /db_xref="GeneID:55798"
                     /db_xref="HGNC:18272"
                     /db_xref="HPRD:09705"
                     /db_xref="MIM:607846"
     CDS             join(128116820..128116929,128117136..128117227,
                     128119212..128119567,128120701..128120750,
                     128128155..128128215,128133858..128133997,
                     128138090..128138196,128140957..128141022,
                     128141816..128141970)
                     /gene="METTL2B"
                     /gene_synonym="FLJ11350; FLJ12760; METL; METTL2; METTL2A;
                     PSENIP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="methyltransferase-like protein 2B"
                     /protein_id="NP_060866.2"
                     /db_xref="GI:93141204"
                     /db_xref="CCDS:CCDS5803.2"
                     /db_xref="GeneID:55798"
                     /db_xref="HGNC:18272"
                     /db_xref="HPRD:09705"
                     /db_xref="MIM:607846"
     gene            complement(128210249..128210779)
                     /gene="RPS10P15"
                     /gene_synonym="RPS10_3_844"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:654029"
                     /db_xref="HGNC:35860"
     gene            128281295..128301052
                     /gene="FLJ45340"
                     /gene_synonym="FLJ53525"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:402483"
     misc_RNA        join(128281295..128281433,128282271..128282335,
                     128288846..128289036,128291092..128291149,
                     128291243..128301052)
                     /gene="FLJ45340"
                     /gene_synonym="FLJ53525"
                     /product="hypothetical LOC402483"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024368.1"
                     /db_xref="GI:211938434"
                     /db_xref="GeneID:402483"
     gene            complement(128295178..128298845)
                     /gene="CICP14"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100130600"
                     /db_xref="HGNC:38542"
     gene            128312346..128323375
                     /gene="FAM71F2"
                     /gene_synonym="FAM137B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:346653"
                     /db_xref="HGNC:27998"
                     /db_xref="HPRD:17840"
     mRNA            join(128312346..128312604,128315702..128315913,
                     128317618..128317867,128320085..128320203,
                     128323018..128323375)
                     /gene="FAM71F2"
                     /gene_synonym="FAM137B"
                     /product="family with sequence similarity 71, member F2,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001012454.3"
                     /db_xref="GI:149192823"
                     /db_xref="GeneID:346653"
                     /db_xref="HGNC:27998"
                     /db_xref="HPRD:17840"
     mRNA            join(128312346..128312604,128315729..128315913,
                     128317618..128317867,128320085..128320203,
                     128323018..128323309)
                     /gene="FAM71F2"
                     /gene_synonym="FAM137B"
                     /product="family with sequence similarity 71, member F2,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001128926.1"
                     /db_xref="GI:193083149"
                     /db_xref="GeneID:346653"
                     /db_xref="HGNC:27998"
                     /db_xref="HPRD:17840"
     CDS             join(128312452..128312604,128315702..128315913,
                     128317618..128317867,128320085..128320203,
                     128323018..128323213)
                     /gene="FAM71F2"
                     /gene_synonym="FAM137B"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC346653 isoform a"
                     /protein_id="NP_001012457.3"
                     /db_xref="GI:149192824"
                     /db_xref="CCDS:CCDS47701.1"
                     /db_xref="GeneID:346653"
                     /db_xref="HGNC:27998"
                     /db_xref="HPRD:17840"
     CDS             join(128312452..128312604,128315729..128315913,
                     128317618..128317867,128320085..128320203,
                     128323018..128323213)
                     /gene="FAM71F2"
                     /gene_synonym="FAM137B"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC346653 isoform b"
                     /protein_id="NP_001122398.1"
                     /db_xref="GI:193083150"
                     /db_xref="CCDS:CCDS47702.1"
                     /db_xref="GeneID:346653"
                     /db_xref="HGNC:27998"
                     /db_xref="HPRD:17840"
     gene            128355443..128371797
                     /gene="FAM71F1"
                     /gene_synonym="FAM137A; NYD-SP18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84691"
                     /db_xref="HGNC:30704"
                     /db_xref="HPRD:14861"
     mRNA            join(128355443..128355744,128356867..128357051,
                     128358885..128359137,128363251..128363372,
                     128366882..128366925,128369956..128370123,
                     128371154..128371797)
                     /gene="FAM71F1"
                     /gene_synonym="FAM137A; NYD-SP18"
                     /product="family with sequence similarity 71, member F1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032599.2"
                     /db_xref="GI:85797668"
                     /db_xref="GeneID:84691"
                     /db_xref="HGNC:30704"
                     /db_xref="HPRD:14861"
     CDS             join(128355496..128355744,128356867..128357051,
                     128358885..128359137,128363251..128363372,
                     128366882..128366925,128369956..128370123,
                     128371154..128371167)
                     /gene="FAM71F1"
                     /gene_synonym="FAM137A; NYD-SP18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="testes development-related NYD-SP18"
                     /protein_id="NP_115988.1"
                     /db_xref="GI:14211935"
                     /db_xref="CCDS:CCDS5804.1"
                     /db_xref="GeneID:84691"
                     /db_xref="HGNC:30704"
                     /db_xref="HPRD:14861"
     gene            128379346..128413477
                     /gene="CALU"
                     /gene_synonym="FLJ90608"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:813"
                     /db_xref="HGNC:1458"
                     /db_xref="HPRD:04569"
                     /db_xref="MIM:603420"
     mRNA            join(128379346..128379486,128388627..128388858,
                     128394316..128394509,128398925..128399091,
                     128399846..128399906,128407510..128407709,
                     128409117..128413477)
                     /gene="CALU"
                     /gene_synonym="FLJ90608"
                     /product="calumenin, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001219.4"
                     /db_xref="GI:314122174"
                     /db_xref="GeneID:813"
                     /db_xref="HGNC:1458"
                     /db_xref="HPRD:04569"
                     /db_xref="MIM:603420"
     mRNA            join(128379346..128379486,128388627..128388858,
                     128394583..128394776,128398925..128399091,
                     128399846..128399906,128407510..128407709,
                     128409117..128413477)
                     /gene="CALU"
                     /gene_synonym="FLJ90608"
                     /product="calumenin, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130674.2"
                     /db_xref="GI:314122175"
                     /db_xref="GeneID:813"
                     /db_xref="HGNC:1458"
                     /db_xref="MIM:603420"
                     /db_xref="HPRD:04569"
     mRNA            join(128379346..128379486,128387607..128388421,
                     128388627..128388858,128394316..128394509,
                     128398925..128399091,128399846..128399906,
                     128407510..128407709,128409117..128413477)
                     /gene="CALU"
                     /gene_synonym="FLJ90608"
                     /product="calumenin, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199671.1"
                     /db_xref="GI:314122176"
                     /db_xref="GeneID:813"
                     /db_xref="HGNC:1458"
                     /db_xref="MIM:603420"
                     /db_xref="HPRD:04569"
     mRNA            join(128379346..128379486,128387607..128388421,
                     128388627..128388858,128394583..128394776,
                     128398925..128399091,128399846..128399906,
                     128407510..128407709,128409117..128413477)
                     /gene="CALU"
                     /gene_synonym="FLJ90608"
                     /product="calumenin, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199672.1"
                     /db_xref="GI:314122178"
                     /db_xref="GeneID:813"
                     /db_xref="HGNC:1458"
                     /db_xref="MIM:603420"
                     /db_xref="HPRD:04569"
     mRNA            join(128379346..128379486,128388627..128388858,
                     128394316..128394509,128398925..128399091,
                     128399846..128399906,128409117..128413477)
                     /gene="CALU"
                     /gene_synonym="FLJ90608"
                     /product="calumenin, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199673.1"
                     /db_xref="GI:314122180"
                     /db_xref="GeneID:813"
                     /db_xref="HGNC:1458"
                     /db_xref="MIM:603420"
                     /db_xref="HPRD:04569"
     mRNA            join(128379346..128379486,128398925..128399091,
                     128399846..128399906,128407510..128407709,
                     128409117..128413477)
                     /gene="CALU"
                     /gene_synonym="FLJ90608"
                     /product="calumenin, transcript variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199674.1"
                     /db_xref="GI:314122182"
                     /db_xref="GeneID:813"
                     /db_xref="HGNC:1458"
                     /db_xref="MIM:603420"
                     /db_xref="HPRD:04569"
     CDS             join(128388409..128388421,128388627..128388858,
                     128394316..128394509,128398925..128399091,
                     128399846..128399906,128407510..128407709,
                     128409117..128409221)
                     /gene="CALU"
                     /gene_synonym="FLJ90608"
                     /note="isoform c precursor is encoded by transcript
                     variant 3; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="calumenin isoform c precursor"
                     /protein_id="NP_001186600.1"
                     /db_xref="GI:314122177"
                     /db_xref="GeneID:813"
                     /db_xref="HGNC:1458"
                     /db_xref="MIM:603420"
                     /db_xref="HPRD:04569"
     CDS             join(128388409..128388421,128388627..128388858,
                     128394583..128394776,128398925..128399091,
                     128399846..128399906,128407510..128407709,
                     128409117..128409221)
                     /gene="CALU"
                     /gene_synonym="FLJ90608"
                     /note="isoform d precursor is encoded by transcript
                     variant 4; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="calumenin isoform d precursor"
                     /protein_id="NP_001186601.1"
                     /db_xref="GI:314122179"
                     /db_xref="GeneID:813"
                     /db_xref="HGNC:1458"
                     /db_xref="MIM:603420"
                     /db_xref="HPRD:04569"
     CDS             join(128388638..128388858,128394316..128394509,
                     128398925..128399091,128399846..128399906,
                     128407510..128407709,128409117..128409221)
                     /gene="CALU"
                     /gene_synonym="FLJ90608"
                     /note="isoform a precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="calumenin isoform a precursor"
                     /protein_id="NP_001210.1"
                     /db_xref="GI:4502551"
                     /db_xref="CCDS:CCDS5805.1"
                     /db_xref="GeneID:813"
                     /db_xref="HGNC:1458"
                     /db_xref="HPRD:04569"
                     /db_xref="MIM:603420"
     CDS             join(128388638..128388858,128394583..128394776,
                     128398925..128399091,128399846..128399906,
                     128407510..128407709,128409117..128409221)
                     /gene="CALU"
                     /gene_synonym="FLJ90608"
                     /note="isoform b precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="calumenin isoform b precursor"
                     /protein_id="NP_001124146.1"
                     /db_xref="GI:194578885"
                     /db_xref="CCDS:CCDS47703.1"
                     /db_xref="GeneID:813"
                     /db_xref="HGNC:1458"
                     /db_xref="HPRD:04569"
                     /db_xref="MIM:603420"
     CDS             join(128388638..128388858,128394316..128394509,
                     128398925..128399091,128399846..128399906,
                     128409117..128409148)
                     /gene="CALU"
                     /gene_synonym="FLJ90608"
                     /note="isoform e precursor is encoded by transcript
                     variant 5; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="calumenin isoform e precursor"
                     /protein_id="NP_001186602.1"
                     /db_xref="GI:314122181"
                     /db_xref="GeneID:813"
                     /db_xref="HGNC:1458"
                     /db_xref="MIM:603420"
                     /db_xref="HPRD:04569"
     CDS             join(128398963..128399091,128399846..128399906,
                     128407510..128407709,128409117..128409221)
                     /gene="CALU"
                     /gene_synonym="FLJ90608"
                     /note="isoform f is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="calumenin isoform f"
                     /protein_id="NP_001186603.1"
                     /db_xref="GI:314122183"
                     /db_xref="GeneID:813"
                     /db_xref="HGNC:1458"
                     /db_xref="MIM:603420"
                     /db_xref="HPRD:04569"
     gene            complement(128412543..128415844)
                     /gene="OPN1SW"
                     /gene_synonym="BCP; BOP; CBT"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:611"
                     /db_xref="HGNC:1012"
                     /db_xref="HPRD:01836"
                     /db_xref="MIM:613522"
     mRNA            complement(join(128412543..128412713,128413703..128413942,
                     128414552..128414717,128415040..128415208,
                     128415493..128415844))
                     /gene="OPN1SW"
                     /gene_synonym="BCP; BOP; CBT"
                     /product="opsin 1 (cone pigments), short-wave-sensitive"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001708.2"
                     /db_xref="GI:183979967"
                     /db_xref="GeneID:611"
                     /db_xref="HGNC:1012"
                     /db_xref="HPRD:01836"
                     /db_xref="MIM:613522"
     CDS             complement(join(128412594..128412713,128413703..128413942,
                     128414552..128414717,128415040..128415208,
                     128415493..128415844))
                     /gene="OPN1SW"
                     /gene_synonym="BCP; BOP; CBT"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="short-wave-sensitive opsin 1"
                     /protein_id="NP_001699.1"
                     /db_xref="GI:4502387"
                     /db_xref="CCDS:CCDS5806.1"
                     /db_xref="GeneID:611"
                     /db_xref="HGNC:1012"
                     /db_xref="HPRD:01836"
                     /db_xref="MIM:613522"
     tRNA            128423504..128423575
                     /product="tRNA-Pro"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /anticodon=(pos:128423536..128423538,aa:Pro)
                     /db_xref="GeneID:100189276"
     gene            128431464..128462187
                     /gene="CCDC136"
                     /gene_synonym="DKFZp434G156; MGC129657; MGC176632; NAG6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64753"
                     /db_xref="HGNC:22225"
                     /db_xref="HPRD:10887"
                     /db_xref="MIM:611902"
     mRNA            join(128431464..128431605,128432374..128432481,
                     128434402..128434656,128434748..128434822,
                     128441240..128441527,128444704..128444815,
                     128445413..128445578,128445815..128445955,
                     128457812..128457918,128461853..128462187)
                     /gene="CCDC136"
                     /gene_synonym="DKFZp434G156; MGC129657; MGC176632; NAG6"
                     /product="coiled-coil domain containing 136, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001201372.1"
                     /db_xref="GI:319655557"
                     /db_xref="GeneID:64753"
                     /db_xref="HGNC:22225"
                     /db_xref="MIM:611902"
                     /db_xref="HPRD:10887"
     CDS             join(128431548..128431605,128432374..128432481,
                     128434402..128434656,128434748..128434822,
                     128441240..128441527,128444704..128444815,
                     128445413..128445578,128445815..128445955,
                     128457812..128457913)
                     /gene="CCDC136"
                     /gene_synonym="DKFZp434G156; MGC129657; MGC176632; NAG6"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="coiled-coil domain-containing protein 136
                     isoform 2"
                     /protein_id="NP_001188301.1"
                     /db_xref="GI:319655558"
                     /db_xref="GeneID:64753"
                     /db_xref="HGNC:22225"
                     /db_xref="MIM:611902"
                     /db_xref="HPRD:10887"
     mRNA            join(128432050..128432481,128434402..128434656,
                     128434748..128434822,128441240..128441563,
                     128444704..128444815,128445413..128445578,
                     128445815..128445955,128446291..128446449,
                     128446742..128446912,128447414..128447599,
                     128449504..128449698,128450193..128450420,
                     128451854..128452366,128452762..128452983,
                     128454692..128454973,128455668..128455985,
                     128457812..128457918,128461853..128462187)
                     /gene="CCDC136"
                     /gene_synonym="DKFZp434G156; MGC129657; MGC176632; NAG6"
                     /product="coiled-coil domain containing 136, transcript
                     variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022742.4"
                     /db_xref="GI:319655555"
                     /db_xref="GeneID:64753"
                     /db_xref="HGNC:22225"
                     /db_xref="HPRD:10887"
                     /db_xref="MIM:611902"
     CDS             join(128432466..128432481,128434402..128434656,
                     128434748..128434822,128441240..128441563,
                     128444704..128444815,128445413..128445578,
                     128445815..128445955,128446291..128446449,
                     128446742..128446912,128447414..128447599,
                     128449504..128449698,128450193..128450420,
                     128451854..128452366,128452762..128452983,
                     128454692..128454973,128455668..128455985,
                     128457812..128457913)
                     /gene="CCDC136"
                     /gene_synonym="DKFZp434G156; MGC129657; MGC176632; NAG6"
                     /exception="mismatches in translation"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="coiled-coil domain-containing protein 136
                     isoform 1"
                     /protein_id="NP_073579.4"
                     /db_xref="GI:319655556"
                     /db_xref="CCDS:CCDS47704.1"
                     /db_xref="GeneID:64753"
                     /db_xref="HGNC:22225"
                     /db_xref="HPRD:10887"
                     /db_xref="MIM:611902"
     gene            128470483..128499328
                     /gene="FLNC"
                     /gene_synonym="ABP-280; ABP280A; ABPA; ABPL; FLJ10186;
                     FLN2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2318"
                     /db_xref="HGNC:3756"
                     /db_xref="HPRD:00018"
                     /db_xref="MIM:102565"
     mRNA            join(128470483..128471043,128475380..128475628,
                     128477214..128477311,128477452..128477602,
                     128477691..128477809,128478041..128478118,
                     128478321..128478483,128478657..128478857,
                     128480077..128480214,128480602..128480728,
                     128480888..128481024,128481224..128481417,
                     128481508..128481621,128482285..128482428,
                     128482629..128482752,128482848..128483008,
                     128483283..128483373,128483462..128483631,
                     128483850..128483967,128484058..128484320,
                     128484712..128485309,128486044..128486217,
                     128486355..128486517,128486799..128486959,
                     128487751..128487918,128487999..128488122,
                     128488615..128488771,128488847..128489036,
                     128489235..128489258,128489385..128489632,
                     128490030..128490128,128490438..128490537,
                     128490857..128490997,128491286..128491414,
                     128491509..128491682,128492645..128492806,
                     128492882..128493085,128493523..128493675,
                     128493769..128493891,128494028..128494270,
                     128494467..128494736,128494829..128494966,
                     128495253..128495368,128496572..128496704,
                     128496799..128496975,128497172..128497390,
                     128498062..128498271,128498390..128499328)
                     /gene="FLNC"
                     /gene_synonym="ABP-280; ABP280A; ABPA; ABPL; FLJ10186;
                     FLN2"
                     /product="filamin C, gamma, transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001458.4"
                     /db_xref="GI:188595685"
                     /db_xref="GeneID:2318"
                     /db_xref="HGNC:3756"
                     /db_xref="HPRD:00018"
                     /db_xref="MIM:102565"
     mRNA            join(128470483..128471043,128475380..128475628,
                     128477214..128477311,128477452..128477602,
                     128477691..128477809,128478041..128478118,
                     128478321..128478483,128478657..128478857,
                     128480077..128480214,128480602..128480728,
                     128480888..128481024,128481224..128481417,
                     128481508..128481621,128482285..128482428,
                     128482629..128482752,128482848..128483008,
                     128483283..128483373,128483462..128483631,
                     128483850..128483967,128484058..128484320,
                     128484712..128485309,128486044..128486217,
                     128486355..128486517,128486799..128486959,
                     128487751..128487918,128487999..128488122,
                     128488615..128488771,128488847..128489036,
                     128489235..128489258,128489385..128489632,
                     128490438..128490537,128490857..128490997,
                     128491286..128491414,128491509..128491682,
                     128492645..128492806,128492882..128493085,
                     128493523..128493675,128493769..128493891,
                     128494028..128494270,128494467..128494736,
                     128494829..128494966,128495253..128495368,
                     128496572..128496704,128496799..128496975,
                     128497172..128497390,128498062..128498271,
                     128498390..128499328)
                     /gene="FLNC"
                     /gene_synonym="ABP-280; ABP280A; ABPA; ABPL; FLJ10186;
                     FLN2"
                     /product="filamin C, gamma, transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127487.1"
                     /db_xref="GI:188595686"
                     /db_xref="GeneID:2318"
                     /db_xref="HGNC:3756"
                     /db_xref="MIM:102565"
                     /db_xref="HPRD:00018"
     CDS             join(128470692..128471043,128475380..128475628,
                     128477214..128477311,128477452..128477602,
                     128477691..128477809,128478041..128478118,
                     128478321..128478483,128478657..128478857,
                     128480077..128480214,128480602..128480728,
                     128480888..128481024,128481224..128481417,
                     128481508..128481621,128482285..128482428,
                     128482629..128482752,128482848..128483008,
                     128483283..128483373,128483462..128483631,
                     128483850..128483967,128484058..128484320,
                     128484712..128485309,128486044..128486217,
                     128486355..128486517,128486799..128486959,
                     128487751..128487918,128487999..128488122,
                     128488615..128488771,128488847..128489036,
                     128489235..128489258,128489385..128489632,
                     128490030..128490128,128490438..128490537,
                     128490857..128490997,128491286..128491414,
                     128491509..128491682,128492645..128492806,
                     128492882..128493085,128493523..128493675,
                     128493769..128493891,128494028..128494270,
                     128494467..128494736,128494829..128494966,
                     128495253..128495368,128496572..128496704,
                     128496799..128496975,128497172..128497390,
                     128498062..128498271,128498390..128498577)
                     /gene="FLNC"
                     /gene_synonym="ABP-280; ABP280A; ABPA; ABPL; FLJ10186;
                     FLN2"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="filamin-C isoform a"
                     /protein_id="NP_001449.3"
                     /db_xref="GI:116805322"
                     /db_xref="CCDS:CCDS43644.1"
                     /db_xref="GeneID:2318"
                     /db_xref="HGNC:3756"
                     /db_xref="HPRD:00018"
                     /db_xref="MIM:102565"
     CDS             join(128470692..128471043,128475380..128475628,
                     128477214..128477311,128477452..128477602,
                     128477691..128477809,128478041..128478118,
                     128478321..128478483,128478657..128478857,
                     128480077..128480214,128480602..128480728,
                     128480888..128481024,128481224..128481417,
                     128481508..128481621,128482285..128482428,
                     128482629..128482752,128482848..128483008,
                     128483283..128483373,128483462..128483631,
                     128483850..128483967,128484058..128484320,
                     128484712..128485309,128486044..128486217,
                     128486355..128486517,128486799..128486959,
                     128487751..128487918,128487999..128488122,
                     128488615..128488771,128488847..128489036,
                     128489235..128489258,128489385..128489632,
                     128490438..128490537,128490857..128490997,
                     128491286..128491414,128491509..128491682,
                     128492645..128492806,128492882..128493085,
                     128493523..128493675,128493769..128493891,
                     128494028..128494270,128494467..128494736,
                     128494829..128494966,128495253..128495368,
                     128496572..128496704,128496799..128496975,
                     128497172..128497390,128498062..128498271,
                     128498390..128498577)
                     /gene="FLNC"
                     /gene_synonym="ABP-280; ABP280A; ABPA; ABPL; FLJ10186;
                     FLN2"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="filamin-C isoform b"
                     /protein_id="NP_001120959.1"
                     /db_xref="GI:188595687"
                     /db_xref="CCDS:CCDS47705.1"
                     /db_xref="GeneID:2318"
                     /db_xref="HGNC:3756"
                     /db_xref="HPRD:00018"
                     /db_xref="MIM:102565"
     gene            128502857..128505903
                     /gene="ATP6V1F"
                     /gene_synonym="ATP6S14; MGC117321; MGC126037; MGC126038;
                     VATF; Vma7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9296"
                     /db_xref="HGNC:16832"
                     /db_xref="HPRD:06198"
                     /db_xref="MIM:607160"
     mRNA            join(128502857..128503116,128505431..128505903)
                     /gene="ATP6V1F"
                     /gene_synonym="ATP6S14; MGC117321; MGC126037; MGC126038;
                     VATF; Vma7"
                     /product="ATPase, H+ transporting, lysosomal 14kDa, V1
                     subunit F, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004231.3"
                     /db_xref="GI:312032444"
                     /db_xref="GeneID:9296"
                     /db_xref="HGNC:16832"
                     /db_xref="HPRD:06198"
                     /db_xref="MIM:607160"
     mRNA            join(128502857..128503116,128505174..128505257,
                     128505431..128505903)
                     /gene="ATP6V1F"
                     /gene_synonym="ATP6S14; MGC117321; MGC126037; MGC126038;
                     VATF; Vma7"
                     /product="ATPase, H+ transporting, lysosomal 14kDa, V1
                     subunit F, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001198909.1"
                     /db_xref="GI:312032452"
                     /db_xref="GeneID:9296"
                     /db_xref="HGNC:16832"
                     /db_xref="MIM:607160"
                     /db_xref="HPRD:06198"
     CDS             join(128502959..128503116,128505431..128505632)
                     /gene="ATP6V1F"
                     /gene_synonym="ATP6S14; MGC117321; MGC126037; MGC126038;
                     VATF; Vma7"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="V-type proton ATPase subunit F isoform 1"
                     /protein_id="NP_004222.2"
                     /db_xref="GI:20357547"
                     /db_xref="CCDS:CCDS5807.1"
                     /db_xref="GeneID:9296"
                     /db_xref="HGNC:16832"
                     /db_xref="HPRD:06198"
                     /db_xref="MIM:607160"
     CDS             join(128502959..128503116,128505174..128505257,
                     128505431..128505632)
                     /gene="ATP6V1F"
                     /gene_synonym="ATP6S14; MGC117321; MGC126037; MGC126038;
                     VATF; Vma7"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="V-type proton ATPase subunit F isoform 2"
                     /protein_id="NP_001185838.1"
                     /db_xref="GI:312032453"
                     /db_xref="GeneID:9296"
                     /db_xref="HGNC:16832"
                     /db_xref="MIM:607160"
                     /db_xref="HPRD:06198"
     gene            128506464..128512101
                     /gene="LOC100130705"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100130705"
     mRNA            join(128506464..128506884,128508720..128512101)
                     /gene="LOC100130705"
                     /product="hypothetical protein LOC100130705"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001195150.1"
                     /db_xref="GI:304376315"
                     /db_xref="GeneID:100130705"
     CDS             join(128506464..128506884,128508720..128508829)
                     /gene="LOC100130705"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC100130705"
                     /protein_id="NP_001182079.1"
                     /db_xref="GI:304376316"
                     /db_xref="GeneID:100130705"
     gene            complement(128516919..128550773)
                     /gene="KCP"
                     /gene_synonym="CRIM2; KCP1; NET67"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:375616"
                     /db_xref="HGNC:17585"
                     /db_xref="MIM:609344"
     mRNA            complement(join(128516919..128517365,128517538..128517844,
                     128518612..128518776,128519576..128519677,
                     128519772..128519883,128519967..128520139,
                     128520440..128520582,128521680..128521779,
                     128521991..128522070,128524056..128524176,
                     128524835..128524917,128525151..128525324,
                     128526518..128526611,128526709..128526791,
                     128526930..128527020,128527269..128527354,
                     128528917..128529093,128530397..128530567,
                     128530959..128531141,128531239..128531332,
                     128531505..128531587,128531700..128531873,
                     128532568..128532661,128532742..128532848,
                     128532923..128533075,128533292..128533373,
                     128533445..128533529,128533859..128533952,
                     128534029..128534108,128534253..128534346,
                     128542830..128542912,128544346..128544433,
                     128547154..128547230,128547317..128547506,
                     128548479..128548621,128550654..128550773))
                     /gene="KCP"
                     /gene_synonym="CRIM2; KCP1; NET67"
                     /product="kielin/chordin-like protein, transcript variant
                     1"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001135914.1"
                     /db_xref="GI:209571518"
                     /db_xref="GeneID:375616"
                     /db_xref="HGNC:17585"
                     /db_xref="MIM:609344"
     CDS             complement(join(128517097..128517365,128517538..128517844,
                     128518612..128518776,128519576..128519677,
                     128519772..128519883,128519967..128520139,
                     128520440..128520582,128521680..128521779,
                     128521991..128522070,128524056..128524176,
                     128524835..128524917,128525151..128525324,
                     128526518..128526611,128526709..128526791,
                     128526930..128527020,128527269..128527354,
                     128528917..128529093,128530397..128530567,
                     128530959..128531141,128531239..128531332,
                     128531505..128531587,128531700..128531873,
                     128532568..128532661,128532742..128532848,
                     128532923..128533075,128533292..128533373,
                     128533445..128533529,128533859..128533952,
                     128534029..128534108,128534253..128534346,
                     128542830..128542912,128544346..128544433,
                     128547154..128547230,128547317..128547506,
                     128548479..128548621,128550654..128550730))
                     /gene="KCP"
                     /gene_synonym="CRIM2; KCP1; NET67"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="kielin/chordin-like protein isoform 1"
                     /protein_id="NP_001129386.1"
                     /db_xref="GI:209571519"
                     /db_xref="GeneID:375616"
                     /db_xref="HGNC:17585"
                     /db_xref="MIM:609344"
     mRNA            complement(join(128530001..128530567,128530959..128531150,
                     128531239..128531332,128531505..128531587,
                     128531700..128531873,128532568..128532661,
                     128532742..128532848,128532923..128533075,
                     128533292..128533373,128533445..128533529,
                     128533859..128533952,128534029..128534108,
                     128534253..128534346,128542830..128542912,
                     128543780..128543873,128544109..128544191,
                     128546332..128546416,128547154..128547230,
                     128547317..128547506,128548479..128548621,
                     128550654..128550773))
                     /gene="KCP"
                     /gene_synonym="CRIM2; KCP1; NET67"
                     /product="kielin/chordin-like protein, transcript variant
                     2"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_199349.2"
                     /db_xref="GI:209571520"
                     /db_xref="GeneID:375616"
                     /db_xref="HGNC:17585"
                     /db_xref="HPRD:14196"
                     /db_xref="MIM:609344"
     CDS             complement(join(128530287..128530567,128530959..128531150,
                     128531239..128531332,128531505..128531587,
                     128531700..128531873,128532568..128532661,
                     128532742..128532848,128532923..128533075,
                     128533292..128533373,128533445..128533529,
                     128533859..128533952,128534029..128534108,
                     128534253..128534346,128542830..128542912,
                     128543780..128543873,128544109..128544191,
                     128546332..128546416,128547154..128547230,
                     128547317..128547506,128548479..128548621,
                     128550654..128550730))
                     /gene="KCP"
                     /gene_synonym="CRIM2; KCP1; NET67"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="kielin/chordin-like protein isoform 2"
                     /protein_id="NP_955381.2"
                     /db_xref="GI:209571521"
                     /db_xref="GeneID:375616"
                     /db_xref="HGNC:17585"
                     /db_xref="HPRD:14196"
                     /db_xref="MIM:609344"
     gene            complement(128552714..128563124)
                     /gene="LOC392787"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392787"
     gene            128577994..128590089
                     /gene="IRF5"
                     /gene_synonym="SLEB10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3663"
                     /db_xref="HGNC:6120"
                     /db_xref="MIM:607218"
     mRNA            join(128577994..128578103,128582125..128582330,
                     128585899..128586088,128586555..128586616,
                     128587077..128587110,128587284..128587589,
                     128587783..128588175,128588264..128588382,
                     128588627..128590089)
                     /gene="IRF5"
                     /gene_synonym="SLEB10"
                     /product="interferon regulatory factor 5, transcript
                     variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001098629.1"
                     /db_xref="GI:148833493"
                     /db_xref="GeneID:3663"
                     /db_xref="HGNC:6120"
                     /db_xref="MIM:607218"
     mRNA            join(128577994..128578103,128582125..128582330,
                     128585899..128586088,128586555..128586616,
                     128587077..128587110,128587332..128587589,
                     128587783..128588175,128588264..128588382,
                     128588627..128590089)
                     /gene="IRF5"
                     /gene_synonym="SLEB10"
                     /product="interferon regulatory factor 5, transcript
                     variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001098630.1"
                     /db_xref="GI:148833495"
                     /db_xref="GeneID:3663"
                     /db_xref="HGNC:6120"
                     /db_xref="MIM:607218"
     mRNA            join(128577994..128578103,128582125..128582330,
                     128585899..128586088,128586555..128586616,
                     128587077..128587110,128587783..128588175,
                     128588264..128588382,128588627..128590089)
                     /gene="IRF5"
                     /gene_synonym="SLEB10"
                     /product="interferon regulatory factor 5, transcript
                     variant 8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001242452.1"
                     /db_xref="GI:334883189"
                     /db_xref="GeneID:3663"
                     /db_xref="HGNC:6120"
                     /db_xref="MIM:607218"
     mRNA            join(128578271..128578299,128582125..128582330,
                     128585899..128586088,128586555..128586616,
                     128587077..128587110,128587332..128587589,
                     128587783..128588175,128588264..128588382,
                     128588627..128590089)
                     /gene="IRF5"
                     /gene_synonym="SLEB10"
                     /product="interferon regulatory factor 5, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032643.3"
                     /db_xref="GI:38683858"
                     /db_xref="GeneID:3663"
                     /db_xref="HGNC:6120"
                     /db_xref="MIM:607218"
     mRNA            join(128580772..128580929,128582125..128582330,
                     128585899..128586088,128586555..128586616,
                     128587077..128587110,128587332..128587589,
                     128587783..128588175,128588264..128588382,
                     128588627..128590089)
                     /gene="IRF5"
                     /gene_synonym="SLEB10"
                     /product="interferon regulatory factor 5, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001098627.2"
                     /db_xref="GI:291190718"
                     /db_xref="GeneID:3663"
                     /db_xref="HGNC:6120"
                     /db_xref="MIM:607218"
     CDS             join(128582136..128582330,128585899..128586088,
                     128586555..128586616,128587077..128587110,
                     128587332..128587589,128587783..128588175,
                     128588264..128588382,128588627..128588872)
                     /gene="IRF5"
                     /gene_synonym="SLEB10"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="interferon regulatory factor 5 isoform b"
                     /protein_id="NP_116032.1"
                     /db_xref="GI:14249182"
                     /db_xref="CCDS:CCDS5808.1"
                     /db_xref="GeneID:3663"
                     /db_xref="HGNC:6120"
                     /db_xref="MIM:607218"
     CDS             join(128582136..128582330,128585899..128586088,
                     128586555..128586616,128587077..128587110,
                     128587332..128587589,128587783..128588175,
                     128588264..128588382,128588627..128588872)
                     /gene="IRF5"
                     /gene_synonym="SLEB10"
                     /note="isoform b is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="interferon regulatory factor 5 isoform b"
                     /protein_id="NP_001092097.2"
                     /db_xref="GI:291190719"
                     /db_xref="CCDS:CCDS5808.1"
                     /db_xref="GeneID:3663"
                     /db_xref="HGNC:6120"
                     /db_xref="MIM:607218"
     CDS             join(128582136..128582330,128585899..128586088,
                     128586555..128586616,128587077..128587110,
                     128587332..128587589,128587783..128588175,
                     128588264..128588382,128588627..128588872)
                     /gene="IRF5"
                     /gene_synonym="SLEB10"
                     /note="isoform b is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="interferon regulatory factor 5 isoform b"
                     /protein_id="NP_001092100.1"
                     /db_xref="GI:148833496"
                     /db_xref="CCDS:CCDS5808.1"
                     /db_xref="GeneID:3663"
                     /db_xref="HGNC:6120"
                     /db_xref="MIM:607218"
     CDS             join(128582136..128582330,128585899..128586088,
                     128586555..128586616,128587077..128587110,
                     128587284..128587589,128587783..128588175,
                     128588264..128588382,128588627..128588872)
                     /gene="IRF5"
                     /gene_synonym="SLEB10"
                     /note="isoform d is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="interferon regulatory factor 5 isoform d"
                     /protein_id="NP_001092099.1"
                     /db_xref="GI:148833494"
                     /db_xref="CCDS:CCDS43645.1"
                     /db_xref="GeneID:3663"
                     /db_xref="HGNC:6120"
                     /db_xref="MIM:607218"
     CDS             join(128582136..128582330,128585899..128586088,
                     128586555..128586616,128587077..128587110,
                     128587783..128588175,128588264..128588382,
                     128588627..128588872)
                     /gene="IRF5"
                     /gene_synonym="SLEB10"
                     /note="isoform e is encoded by transcript variant 8;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="interferon regulatory factor 5 isoform e"
                     /protein_id="NP_001229381.1"
                     /db_xref="GI:334883190"
                     /db_xref="GeneID:3663"
                     /db_xref="HGNC:6120"
                     /db_xref="MIM:607218"
     gene            complement(128594234..128695227)
                     /gene="TNPO3"
                     /gene_synonym="IPO12; MTR10A; TRN-SR; TRN-SR2; TRNSR"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23534"
                     /db_xref="HGNC:17103"
                     /db_xref="HPRD:18209"
                     /db_xref="MIM:610032"
     mRNA            complement(join(128594234..128595439,128597278..128597369,
                     128607334..128607446,128610202..128610369,
                     128612480..128612636,128614922..128615016,
                     128615873..128615989,128619037..128619177,
                     128620025..128620085,128622302..128622378,
                     128624222..128624313,128626783..128626974,
                     128630015..128630154,128632053..128632144,
                     128633861..128633968,128637443..128637589,
                     128640483..128640621,128641113..128641288,
                     128645070..128645213,128655033..128655189,
                     128657037..128657110,128658011..128658211,
                     128694705..128695227))
                     /gene="TNPO3"
                     /gene_synonym="IPO12; MTR10A; TRN-SR; TRN-SR2; TRNSR"
                     /product="transportin 3, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012470.3"
                     /db_xref="GI:300794233"
                     /db_xref="GeneID:23534"
                     /db_xref="HGNC:17103"
                     /db_xref="HPRD:18209"
                     /db_xref="MIM:610032"
     mRNA            complement(join(128594234..128595439,128597278..128597369,
                     128607334..128607446,128610202..128610369,
                     128612480..128612636,128614922..128615016,
                     128615873..128615989,128619037..128619177,
                     128620025..128620085,128622302..128622378,
                     128624222..128624313,128630015..128630154,
                     128632053..128632144,128633861..128633968,
                     128637443..128637589,128640483..128640621,
                     128641113..128641288,128645070..128645213,
                     128655033..128655189,128657037..128657110,
                     128658011..128658211,128694705..128695227))
                     /gene="TNPO3"
                     /gene_synonym="IPO12; MTR10A; TRN-SR; TRN-SR2; TRNSR"
                     /product="transportin 3, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001191028.2"
                     /db_xref="GI:300934781"
                     /db_xref="GeneID:23534"
                     /db_xref="HGNC:17103"
                     /db_xref="MIM:610032"
                     /db_xref="HPRD:18209"
     misc_RNA        complement(join(128594234..128595439,128597278..128597369,
                     128607334..128607446,128610202..128610369,
                     128612480..128612636,128614922..128615016,
                     128615873..128615989,128619037..128619177,
                     128620025..128620085,128622302..128622378,
                     128624222..128624313,128626783..128626974,
                     128630015..128630154,128632053..128632144,
                     128633861..128633968,128637443..128637589,
                     128640483..128640621,128641113..128641288,
                     128645070..128645213,128655033..128655189,
                     128657037..128657110,128658011..128658211,
                     128681611..128681771,128694705..128695227))
                     /gene="TNPO3"
                     /gene_synonym="IPO12; MTR10A; TRN-SR; TRN-SR2; TRNSR"
                     /product="transportin 3, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_034053.2"
                     /db_xref="GI:300934784"
                     /db_xref="GeneID:23534"
                     /db_xref="HGNC:17103"
                     /db_xref="MIM:610032"
                     /db_xref="HPRD:18209"
     CDS             complement(join(128597309..128597369,128607334..128607446,
                     128610202..128610369,128612480..128612636,
                     128614922..128615016,128615873..128615989,
                     128619037..128619177,128620025..128620085,
                     128622302..128622378,128624222..128624313,
                     128626783..128626974,128630015..128630154,
                     128632053..128632144,128633861..128633968,
                     128637443..128637589,128640483..128640621,
                     128641113..128641288,128645070..128645213,
                     128655033..128655189,128657037..128657110,
                     128658011..128658211,128694705..128694824))
                     /gene="TNPO3"
                     /gene_synonym="IPO12; MTR10A; TRN-SR; TRN-SR2; TRNSR"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transportin-3 isoform 1"
                     /protein_id="NP_036602.1"
                     /db_xref="GI:6912734"
                     /db_xref="CCDS:CCDS5809.1"
                     /db_xref="GeneID:23534"
                     /db_xref="HGNC:17103"
                     /db_xref="HPRD:18209"
                     /db_xref="MIM:610032"
     CDS             complement(join(128597309..128597369,128607334..128607446,
                     128610202..128610369,128612480..128612636,
                     128614922..128615016,128615873..128615989,
                     128619037..128619177,128620025..128620085,
                     128622302..128622378,128624222..128624313,
                     128630015..128630154,128632053..128632144,
                     128633861..128633968,128637443..128637589,
                     128640483..128640621,128641113..128641288,
                     128645070..128645213,128655033..128655189,
                     128657037..128657110,128658011..128658211,
                     128694705..128694824))
                     /gene="TNPO3"
                     /gene_synonym="IPO12; MTR10A; TRN-SR; TRN-SR2; TRNSR"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transportin-3 isoform 2"
                     /protein_id="NP_001177957.2"
                     /db_xref="GI:300934782"
                     /db_xref="CCDS:CCDS55162.1"
                     /db_xref="GeneID:23534"
                     /db_xref="HGNC:17103"
                     /db_xref="HPRD:18209"
                     /db_xref="MIM:610032"
     gene            128668552..128671091
                     /gene="ODCP"
                     /gene_synonym="ODC2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:4954"
                     /db_xref="HGNC:8110"
     gene            128695277..128697293
                     /gene="TPI1P2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:286016"
                     /db_xref="HGNC:38069"
     misc_RNA        128695277..128697293
                     /gene="TPI1P2"
                     /product="triosephosphate isomerase 1 pseudogene 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002187.3"
                     /db_xref="GI:301171420"
                     /db_xref="GeneID:286016"
                     /db_xref="HGNC:38069"
     gene            complement(128757567..128757881)
                     /gene="CYCSP20"
                     /gene_synonym="HCP20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:349158"
                     /db_xref="HGNC:24394"
     gene            128766325..128768061
                     /gene="LOC407835"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:407835"
     misc_RNA        128766325..128768061
                     /gene="LOC407835"
                     /product="mitogen-activated protein kinase kinase 2
                     pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002144.1"
                     /db_xref="GI:47174756"
                     /db_xref="GeneID:407835"
     gene            <128784712..128809534
                     /gene="TSPAN33"
                     /gene_synonym="MGC50844; PEN"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:340348"
                     /db_xref="HGNC:28743"
                     /db_xref="HPRD:14669"
                     /db_xref="MIM:610120"
     mRNA            join(<128784712..128784922,128801520..128801577,
                     128802235..128802362,128802674..128802748,
                     128804315..128804410,128806619..128806747,
                     128807240..128807401,128807614..128809534)
                     /gene="TSPAN33"
                     /gene_synonym="MGC50844; PEN"
                     /product="tetraspanin 33"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178562.3"
                     /db_xref="GI:288557356"
                     /db_xref="GeneID:340348"
                     /db_xref="HGNC:28743"
                     /db_xref="HPRD:14669"
                     /db_xref="MIM:610120"
     CDS             join(128784821..128784922,128801520..128801577,
                     128802235..128802362,128802674..128802748,
                     128804315..128804410,128806619..128806747,
                     128807240..128807401,128807614..128807715)
                     /gene="TSPAN33"
                     /gene_synonym="MGC50844; PEN"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="tetraspanin-33"
                     /protein_id="NP_848657.1"
                     /db_xref="GI:30425534"
                     /db_xref="CCDS:CCDS5810.1"
                     /db_xref="GeneID:340348"
                     /db_xref="HGNC:28743"
                     /db_xref="HPRD:14669"
                     /db_xref="MIM:610120"
     gene            128828713..128853386
                     /gene="SMO"
                     /gene_synonym="FZD11; Gx; SMOH"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6608"
                     /db_xref="HGNC:11119"
                     /db_xref="HPRD:03294"
                     /db_xref="MIM:601500"
     mRNA            join(128828713..128829323,128843225..128843430,
                     128845044..128845253,128845451..128845623,
                     128845991..128846210,128846305..128846428,
                     128848600..128848692,128849130..128849238,
                     128850204..128850389,128850806..128850954,
                     128851477..128851611,128851865..128853386)
                     /gene="SMO"
                     /gene_synonym="FZD11; Gx; SMOH"
                     /product="smoothened, frizzled family receptor"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005631.4"
                     /db_xref="GI:300116182"
                     /db_xref="GeneID:6608"
                     /db_xref="HGNC:11119"
                     /db_xref="HPRD:03294"
                     /db_xref="MIM:601500"
     CDS             join(128828993..128829323,128843225..128843430,
                     128845044..128845253,128845451..128845623,
                     128845991..128846210,128846305..128846428,
                     128848600..128848692,128849130..128849238,
                     128850204..128850389,128850806..128850954,
                     128851477..128851611,128851865..128852292)
                     /gene="SMO"
                     /gene_synonym="FZD11; Gx; SMOH"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="smoothened homolog precursor"
                     /protein_id="NP_005622.1"
                     /db_xref="GI:5032099"
                     /db_xref="CCDS:CCDS5811.1"
                     /db_xref="GeneID:6608"
                     /db_xref="HGNC:11119"
                     /db_xref="HPRD:03294"
                     /db_xref="MIM:601500"
     gene            128864855..129070052
                     /gene="AHCYL2"
                     /gene_synonym="ADOHCYASE3; FLJ21719; KIAA0828"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23382"
                     /db_xref="HGNC:22204"
     mRNA            join(128864855..128865280,129019479..129019590,
                     129028897..129029040,129029475..129029575,
                     129037063..129037165,129040131..129040225,
                     129043220..129043326,129044938..129045054,
                     129045677..129045740,129046219..129046307,
                     129049317..129049387,129053435..129053529,
                     129062681..129062779,129064715..129064783,
                     129064904..129064982,129066284..129066404,
                     129066880..129070052)
                     /gene="AHCYL2"
                     /gene_synonym="ADOHCYASE3; FLJ21719; KIAA0828"
                     /product="adenosylhomocysteinase-like 2, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015328.3"
                     /db_xref="GI:298286487"
                     /db_xref="GeneID:23382"
                     /db_xref="HGNC:22204"
                     /db_xref="HPRD:11113"
     mRNA            join(128864855..128865280,129019482..129019590,
                     129028897..129029040,129029475..129029575,
                     129037063..129037165,129040131..129040225,
                     129043220..129043326,129044938..129045054,
                     129045677..129045740,129046219..129046307,
                     129049317..129049387,129053435..129053529,
                     129062681..129062779,129064715..129064783,
                     129064904..129064982,129066284..129066404,
                     129066880..129070052)
                     /gene="AHCYL2"
                     /gene_synonym="ADOHCYASE3; FLJ21719; KIAA0828"
                     /product="adenosylhomocysteinase-like 2, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130720.2"
                     /db_xref="GI:298286486"
                     /db_xref="GeneID:23382"
                     /db_xref="HGNC:22204"
     CDS             join(128864918..128865280,129019479..129019590,
                     129028897..129029040,129029475..129029575,
                     129037063..129037165,129040131..129040225,
                     129043220..129043326,129044938..129045054,
                     129045677..129045740,129046219..129046307,
                     129049317..129049387,129053435..129053529,
                     129062681..129062779,129064715..129064783,
                     129064904..129064982,129066284..129066404,
                     129066880..129066886)
                     /gene="AHCYL2"
                     /gene_synonym="ADOHCYASE3; FLJ21719; KIAA0828"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative adenosylhomocysteinase 3 isoform a"
                     /protein_id="NP_056143.1"
                     /db_xref="GI:24308043"
                     /db_xref="CCDS:CCDS5812.1"
                     /db_xref="GeneID:23382"
                     /db_xref="HGNC:22204"
     CDS             join(128864918..128865280,129019482..129019590,
                     129028897..129029040,129029475..129029575,
                     129037063..129037165,129040131..129040225,
                     129043220..129043326,129044938..129045054,
                     129045677..129045740,129046219..129046307,
                     129049317..129049387,129053435..129053529,
                     129062681..129062779,129064715..129064783,
                     129064904..129064982,129066284..129066404,
                     129066880..129066886)
                     /gene="AHCYL2"
                     /gene_synonym="ADOHCYASE3; FLJ21719; KIAA0828"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative adenosylhomocysteinase 3 isoform b"
                     /protein_id="NP_001124192.1"
                     /db_xref="GI:195539337"
                     /db_xref="CCDS:CCDS47706.1"
                     /db_xref="GeneID:23382"
                     /db_xref="HGNC:22204"
     mRNA            join(129007964..129008392,129019482..129019590,
                     129028897..129029040,129029475..129029575,
                     129037063..129037165,129040131..129040225,
                     129043220..129043326,129044938..129045054,
                     129045677..129045740,129046219..129046307,
                     129049317..129049387,129053435..129053529,
                     129062681..129062779,129064715..129064783,
                     129064904..129064982,129066284..129066404,
                     129066880..129070052)
                     /gene="AHCYL2"
                     /gene_synonym="ADOHCYASE3; FLJ21719; KIAA0828"
                     /product="adenosylhomocysteinase-like 2, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130723.2"
                     /db_xref="GI:298286490"
                     /db_xref="GeneID:23382"
                     /db_xref="HGNC:22204"
     CDS             join(129008336..129008392,129019482..129019590,
                     129028897..129029040,129029475..129029575,
                     129037063..129037165,129040131..129040225,
                     129043220..129043326,129044938..129045054,
                     129045677..129045740,129046219..129046307,
                     129049317..129049387,129053435..129053529,
                     129062681..129062779,129064715..129064783,
                     129064904..129064982,129066284..129066404,
                     129066880..129066886)
                     /gene="AHCYL2"
                     /gene_synonym="ADOHCYASE3; FLJ21719; KIAA0828"
                     /note="isoform d is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative adenosylhomocysteinase 3 isoform d"
                     /protein_id="NP_001124195.1"
                     /db_xref="GI:195539349"
                     /db_xref="CCDS:CCDS47708.1"
                     /db_xref="GeneID:23382"
                     /db_xref="HGNC:22204"
     mRNA            join(129015484..129015767,129019482..129019590,
                     129028897..129029040,129029475..129029575,
                     129037063..129037165,129040131..129040225,
                     129043220..129043326,129044938..129045054,
                     129045677..129045740,129046219..129046307,
                     129049317..129049387,129053435..129053529,
                     129062681..129062779,129064715..129064783,
                     129064904..129064982,129066284..129066404,
                     129066880..129070052)
                     /gene="AHCYL2"
                     /gene_synonym="ADOHCYASE3; FLJ21719; KIAA0828"
                     /product="adenosylhomocysteinase-like 2, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130722.2"
                     /db_xref="GI:298286488"
                     /db_xref="GeneID:23382"
                     /db_xref="HGNC:22204"
     CDS             join(129015711..129015767,129019482..129019590,
                     129028897..129029040,129029475..129029575,
                     129037063..129037165,129040131..129040225,
                     129043220..129043326,129044938..129045054,
                     129045677..129045740,129046219..129046307,
                     129049317..129049387,129053435..129053529,
                     129062681..129062779,129064715..129064783,
                     129064904..129064982,129066284..129066404,
                     129066880..129066886)
                     /gene="AHCYL2"
                     /gene_synonym="ADOHCYASE3; FLJ21719; KIAA0828"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative adenosylhomocysteinase 3 isoform c"
                     /protein_id="NP_001124194.2"
                     /db_xref="GI:298286489"
                     /db_xref="CCDS:CCDS47707.2"
                     /db_xref="GeneID:23382"
                     /db_xref="HGNC:22204"
     gene            129045476..129045537
                     /gene="RNU7-16P"
                     /gene_synonym="U7.16"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100147764"
                     /db_xref="HGNC:34112"
     gene            complement(129049694..129050397)
                     /gene="CDC26P1"
                     /gene_synonym="CDC26P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:729948"
                     /db_xref="HGNC:22770"
     gene            129074274..129128240
                     /gene="FAM40B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57464"
                     /db_xref="HGNC:22209"
                     /db_xref="HPRD:16880"
     mRNA            join(129074274..129074442,129079863..129079932,
                     129083865..129083939,129091454..129091588,
                     129093068..129093188,129093983..129094051,
                     129094262..129094368,129095085..129095212,
                     129096280..129096483,129098056..129098291,
                     129098553..129098618,129099358..129099421,
                     129100142..129100213,129102807..129102881,
                     129103885..129103982,129104453..129104579,
                     129107191..129107291,129110490..129110556,
                     129120626..129120730,129122683..129122887,
                     129125420..129128240)
                     /gene="FAM40B"
                     /product="family with sequence similarity 40, member B,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020704.2"
                     /db_xref="GI:197245442"
                     /db_xref="GeneID:57464"
                     /db_xref="HGNC:22209"
                     /db_xref="HPRD:16880"
     mRNA            join(129074274..129074442,129079863..129079932,
                     129083865..129083939,129091454..129091588,
                     129093068..129093188,129093983..129094051,
                     129094262..129094368,129095085..129095212,
                     129096280..129096483,129098056..129098291,
                     129098553..129098618,129099358..129099421,
                     129100142..129100213,129102807..129102881,
                     129103885..129103982,129104453..129104579,
                     129107191..129107291,129110490..129110556,
                     129120626..129120730,129122683..129123472)
                     /gene="FAM40B"
                     /product="family with sequence similarity 40, member B,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134336.1"
                     /db_xref="GI:197245443"
                     /db_xref="GeneID:57464"
                     /db_xref="HGNC:22209"
                     /db_xref="HPRD:16880"
     CDS             join(129074314..129074442,129079863..129079932,
                     129083865..129083939,129091454..129091588,
                     129093068..129093188,129093983..129094051,
                     129094262..129094368,129095085..129095212,
                     129096280..129096483,129098056..129098291,
                     129098553..129098618,129099358..129099421,
                     129100142..129100213,129102807..129102881,
                     129103885..129103982,129104453..129104579,
                     129107191..129107291,129110490..129110556,
                     129120626..129120730,129122683..129122887,
                     129125420..129125670)
                     /gene="FAM40B"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC57464 isoform a"
                     /protein_id="NP_065755.1"
                     /db_xref="GI:55742705"
                     /db_xref="CCDS:CCDS34752.1"
                     /db_xref="GeneID:57464"
                     /db_xref="HGNC:22209"
                     /db_xref="HPRD:16880"
     CDS             join(129074314..129074442,129079863..129079932,
                     129083865..129083939,129091454..129091588,
                     129093068..129093188,129093983..129094051,
                     129094262..129094368,129095085..129095212,
                     129096280..129096483,129098056..129098291,
                     129098553..129098618,129099358..129099421,
                     129100142..129100213,129102807..129102881,
                     129103885..129103982,129104453..129104579,
                     129107191..129107291,129110490..129110556,
                     129120626..129120730,129122683..129122910)
                     /gene="FAM40B"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC57464 isoform b"
                     /protein_id="NP_001127808.1"
                     /db_xref="GI:197245444"
                     /db_xref="CCDS:CCDS47709.1"
                     /db_xref="GeneID:57464"
                     /db_xref="HGNC:22209"
                     /db_xref="HPRD:16880"
     gene            129142320..129152773
                     /gene="LOC100287482"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100287482"
     mRNA            join(129142320..129142668,129152088..129152773)
                     /gene="LOC100287482"
                     /product="hypothetical protein LOC100287482"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001195243.1"
                     /db_xref="GI:305410808"
                     /db_xref="GeneID:100287482"
     CDS             join(129142666..129142668,129152088..129152282)
                     /gene="LOC100287482"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC100287482"
                     /protein_id="NP_001182172.1"
                     /db_xref="GI:305410809"
                     /db_xref="GeneID:100287482"
     gene            complement(129232744..129251495)
                     /gene="LOC100127891"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 8 ESTs"
                     /db_xref="GeneID:100127891"
     misc_RNA        complement(join(129232744..129232753,
                     129250959..129251495))
                     /gene="LOC100127891"
                     /product="hypothetical LOC100127891"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 8 ESTs"
                     /transcript_id="XR_108812.1"
                     /db_xref="GI:310120091"
                     /db_xref="GeneID:100127891"
     gene            129251555..129396922
                     /gene="NRF1"
                     /gene_synonym="ALPHA-PAL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4899"
                     /db_xref="HGNC:7996"
                     /db_xref="HPRD:02930"
                     /db_xref="MIM:600879"
     mRNA            join(129251555..129251665,129297186..129297414,
                     129311269..129311383,129317472..129317598,
                     129330246..129330386,129348915..129349073,
                     129350214..129350411,129351315..129351416,
                     129357059..129357216,129367081..129367205,
                     129394858..129396922)
                     /gene="NRF1"
                     /gene_synonym="ALPHA-PAL"
                     /product="nuclear respiratory factor 1, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005011.3"
                     /db_xref="GI:93141036"
                     /db_xref="GeneID:4899"
                     /db_xref="HGNC:7996"
                     /db_xref="HPRD:02930"
                     /db_xref="MIM:600879"
     mRNA            join(129269919..129270009,129297183..129297414,
                     129311269..129311383,129317472..129317598,
                     129330246..129330386,129348915..129349073,
                     129350214..129350411,129351315..129351416,
                     129357059..129357216,129367081..129367205,
                     129394858..129396922)
                     /gene="NRF1"
                     /gene_synonym="ALPHA-PAL"
                     /product="nuclear respiratory factor 1, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040110.1"
                     /db_xref="GI:93141038"
                     /db_xref="GeneID:4899"
                     /db_xref="HGNC:7996"
                     /db_xref="MIM:600879"
                     /db_xref="HPRD:02930"
     CDS             join(129297192..129297414,129311269..129311383,
                     129317472..129317598,129330246..129330386,
                     129348915..129349073,129350214..129350411,
                     129351315..129351416,129357059..129357216,
                     129367081..129367205,129394858..129395021)
                     /gene="NRF1"
                     /gene_synonym="ALPHA-PAL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="nuclear respiratory factor 1"
                     /protein_id="NP_005002.3"
                     /db_xref="GI:93141037"
                     /db_xref="CCDS:CCDS5813.2"
                     /db_xref="GeneID:4899"
                     /db_xref="HGNC:7996"
                     /db_xref="HPRD:02930"
                     /db_xref="MIM:600879"
     CDS             join(129297192..129297414,129311269..129311383,
                     129317472..129317598,129330246..129330386,
                     129348915..129349073,129350214..129350411,
                     129351315..129351416,129357059..129357216,
                     129367081..129367205,129394858..129395021)
                     /gene="NRF1"
                     /gene_synonym="ALPHA-PAL"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="nuclear respiratory factor 1"
                     /protein_id="NP_001035199.1"
                     /db_xref="GI:93141039"
                     /db_xref="CCDS:CCDS5813.2"
                     /db_xref="GeneID:4899"
                     /db_xref="HGNC:7996"
                     /db_xref="HPRD:02930"
                     /db_xref="MIM:600879"
     gene            complement(129410223..129410332)
                     /gene="MIR182"
                     /gene_synonym="MIRN182; miRNA182"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:406958"
                     /db_xref="HGNC:31553"
                     /db_xref="MIM:611607"
                     /db_xref="miRBase:MI0000272"
     ncRNA           complement(129410223..129410332)
                     /gene="MIR182"
                     /gene_synonym="MIRN182; miRNA182"
                     /ncRNA_class="miRNA"
                     /product="microRNA 182"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029614.1"
                     /db_xref="GI:262206242"
                     /db_xref="GeneID:406958"
                     /db_xref="HGNC:31553"
                     /db_xref="MIM:611607"
                     /db_xref="miRBase:MI0000272"
     ncRNA           complement(129410223..129410332)
                     /gene="MIR182"
                     /gene_synonym="MIRN182; miRNA182"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-182"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:406958"
                     /db_xref="miRBase:MI0000272"
                     /db_xref="HGNC:31553"
                     /db_xref="MIM:611607"
     gene            complement(129414532..129414609)
                     /gene="MIR96"
                     /gene_synonym="DFNA50; hsa-mir-96; miR-96; MIRN96;
                     miRNA96"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:407053"
                     /db_xref="HGNC:31648"
                     /db_xref="MIM:611606"
                     /db_xref="miRBase:MI0000098"
     ncRNA           complement(129414532..129414609)
                     /gene="MIR96"
                     /gene_synonym="DFNA50; hsa-mir-96; miR-96; MIRN96;
                     miRNA96"
                     /ncRNA_class="miRNA"
                     /product="microRNA 96"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029512.1"
                     /db_xref="GI:262205747"
                     /db_xref="GeneID:407053"
                     /db_xref="HGNC:31648"
                     /db_xref="MIM:611606"
                     /db_xref="miRBase:MI0000098"
     ncRNA           complement(129414532..129414609)
                     /gene="MIR96"
                     /gene_synonym="DFNA50; hsa-mir-96; miR-96; MIRN96;
                     miRNA96"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-96"
                     /inference="similar to RNA sequence:INSD: AF480568"
                     /inference="similar to RNA sequence:INSD: AF480534"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:407053"
                     /db_xref="miRBase:MI0000098"
                     /db_xref="HGNC:31648"
                     /db_xref="MIM:611606"
     gene            complement(129414745..129414854)
                     /gene="MIR183"
                     /gene_synonym="miR-183; MIRN183; miRNA183"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:406959"
                     /db_xref="HGNC:31554"
                     /db_xref="MIM:611608"
                     /db_xref="miRBase:MI0000273"
     ncRNA           complement(129414745..129414854)
                     /gene="MIR183"
                     /gene_synonym="miR-183; MIRN183; miRNA183"
                     /ncRNA_class="miRNA"
                     /product="microRNA 183"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029615.1"
                     /db_xref="GI:262206247"
                     /db_xref="GeneID:406959"
                     /db_xref="HGNC:31554"
                     /db_xref="MIM:611608"
                     /db_xref="miRBase:MI0000273"
     ncRNA           complement(129414745..129414854)
                     /gene="MIR183"
                     /gene_synonym="miR-183; MIRN183; miRNA183"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-183"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:406959"
                     /db_xref="miRBase:MI0000273"
                     /db_xref="HGNC:31554"
                     /db_xref="MIM:611608"
     gene            complement(129470572..129592800)
                     /gene="UBE2H"
                     /gene_synonym="E2-20K; UBC8; UBCH; UBCH2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7328"
                     /db_xref="HGNC:12484"
                     /db_xref="HPRD:03052"
                     /db_xref="MIM:601082"
     mRNA            complement(join(129470572..129474901,129479047..129479175,
                     129497351..129497403,129498742..129498781,
                     129519408..129519482,129520735..129520811,
                     129592343..129592800))
                     /gene="UBE2H"
                     /gene_synonym="E2-20K; UBC8; UBCH; UBCH2"
                     /product="ubiquitin-conjugating enzyme E2H, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003344.3"
                     /db_xref="GI:321267497"
                     /db_xref="GeneID:7328"
                     /db_xref="HGNC:12484"
                     /db_xref="HPRD:03052"
                     /db_xref="MIM:601082"
     mRNA            complement(join(129470572..129474901,129479047..129479175,
                     129519408..129519482,129520735..129520811,
                     129592343..129592800))
                     /gene="UBE2H"
                     /gene_synonym="E2-20K; UBC8; UBCH; UBCH2"
                     /product="ubiquitin-conjugating enzyme E2H, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182697.2"
                     /db_xref="GI:321267498"
                     /db_xref="GeneID:7328"
                     /db_xref="HGNC:12484"
                     /db_xref="HPRD:03052"
                     /db_xref="MIM:601082"
     mRNA            complement(join(129470572..129474901,129479047..129479175,
                     129497351..129497403,129498742..129498781,
                     129519408..129519482,129520735..129520811,
                     129592722..129592783))
                     /gene="UBE2H"
                     /gene_synonym="E2-20K; UBC8; UBCH; UBCH2"
                     /product="ubiquitin-conjugating enzyme E2H, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001202498.1"
                     /db_xref="GI:321267499"
                     /db_xref="GeneID:7328"
                     /db_xref="HGNC:12484"
                     /db_xref="MIM:601082"
                     /db_xref="HPRD:03052"
     CDS             complement(join(129474777..129474901,129479047..129479175,
                     129497351..129497403,129498742..129498781,
                     129519408..129519482,129520735..129520811,
                     129592343..129592395))
                     /gene="UBE2H"
                     /gene_synonym="E2-20K; UBC8; UBCH; UBCH2"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ubiquitin-conjugating enzyme E2 H isoform 1"
                     /protein_id="NP_003335.1"
                     /db_xref="GI:4507783"
                     /db_xref="CCDS:CCDS5814.1"
                     /db_xref="GeneID:7328"
                     /db_xref="HGNC:12484"
                     /db_xref="HPRD:03052"
                     /db_xref="MIM:601082"
     CDS             complement(join(129474777..129474901,129479047..129479175,
                     129519408..129519482,129520735..129520811,
                     129592343..129592395))
                     /gene="UBE2H"
                     /gene_synonym="E2-20K; UBC8; UBCH; UBCH2"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ubiquitin-conjugating enzyme E2 H isoform 2"
                     /protein_id="NP_874356.1"
                     /db_xref="GI:33356154"
                     /db_xref="CCDS:CCDS47710.1"
                     /db_xref="GeneID:7328"
                     /db_xref="HGNC:12484"
                     /db_xref="HPRD:03052"
                     /db_xref="MIM:601082"
     CDS             complement(join(129474777..129474901,129479047..129479175,
                     129497351..129497403,129498742..129498776))
                     /gene="UBE2H"
                     /gene_synonym="E2-20K; UBC8; UBCH; UBCH2"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ubiquitin-conjugating enzyme E2 H isoform 3"
                     /protein_id="NP_001189427.1"
                     /db_xref="GI:321267500"
                     /db_xref="GeneID:7328"
                     /db_xref="HGNC:12484"
                     /db_xref="MIM:601082"
                     /db_xref="HPRD:03052"
     gene            complement(129658126..129691233)
                     /gene="ZC3HC1"
                     /gene_synonym="1110054L24Rik; HSPC216; NIPA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51530"
                     /db_xref="HGNC:29913"
     mRNA            complement(join(129658126..129658572,129662159..129662365,
                     129663351..129663563,129664103..129664346,
                     129665998..129666152,129668742..129668869,
                     129679304..129679387,129680791..129680941,
                     129688873..129688984,129691061..129691233))
                     /gene="ZC3HC1"
                     /gene_synonym="1110054L24Rik; HSPC216; NIPA"
                     /product="zinc finger, C3HC-type containing 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016478.3"
                     /db_xref="GI:66348044"
                     /db_xref="GeneID:51530"
                     /db_xref="HGNC:29913"
     CDS             complement(join(129658504..129658572,129662159..129662365,
                     129663351..129663563,129664103..129664346,
                     129665998..129666152,129668742..129668869,
                     129679304..129679387,129680791..129680941,
                     129688873..129688984,129691061..129691206))
                     /gene="ZC3HC1"
                     /gene_synonym="1110054L24Rik; HSPC216; NIPA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="nuclear-interacting partner of ALK"
                     /protein_id="NP_057562.3"
                     /db_xref="GI:66348045"
                     /db_xref="CCDS:CCDS34753.1"
                     /db_xref="GeneID:51530"
                     /db_xref="HGNC:29913"
     gene            129710349..129775560
                     /gene="KLHDC10"
                     /gene_synonym="KIAA0265; slim"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23008"
                     /db_xref="HGNC:22194"
                     /db_xref="HPRD:17182"
     mRNA            join(129710349..129710649,129736761..129736847,
                     129756285..129756506,129760589..129760743,
                     129761894..129762042,129764291..129764375,
                     129765705..129765771,129767244..129767291,
                     129769277..129769416,129770377..129775560)
                     /gene="KLHDC10"
                     /gene_synonym="KIAA0265; slim"
                     /product="kelch domain containing 10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014997.3"
                     /db_xref="GI:301171678"
                     /db_xref="GeneID:23008"
                     /db_xref="HGNC:22194"
                     /db_xref="HPRD:17182"
     CDS             join(129710484..129710649,129736761..129736847,
                     129756285..129756506,129760589..129760743,
                     129761894..129762042,129764291..129764375,
                     129765705..129765771,129767244..129767291,
                     129769277..129769416,129770377..129770586)
                     /gene="KLHDC10"
                     /gene_synonym="KIAA0265; slim"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="kelch domain-containing protein 10"
                     /protein_id="NP_055812.1"
                     /db_xref="GI:44917619"
                     /db_xref="CCDS:CCDS5815.1"
                     /db_xref="GeneID:23008"
                     /db_xref="HGNC:22194"
                     /db_xref="HPRD:17182"
     gene            complement(129804555..129845338)
                     /gene="TMEM209"
                     /gene_synonym="FLJ14803; NET31"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84928"
                     /db_xref="HGNC:21898"
                     /db_xref="HPRD:07871"
     mRNA            complement(join(129804555..129806345,129810240..129810313,
                     129813472..129813569,129813665..129813779,
                     129815352..129815449,129818242..129818367,
                     129821463..129821559,129824024..129824095,
                     129825032..129825207,129832462..129832663,
                     129841690..129841931,129842372..129842503,
                     129843628..129843686,129843814..129843950,
                     129845213..129845338))
                     /gene="TMEM209"
                     /gene_synonym="FLJ14803; NET31"
                     /product="transmembrane protein 209"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032842.3"
                     /db_xref="GI:134133309"
                     /db_xref="GeneID:84928"
                     /db_xref="HGNC:21898"
                     /db_xref="HPRD:07871"
     CDS             complement(join(129806291..129806345,129810240..129810313,
                     129813472..129813569,129813665..129813779,
                     129815352..129815449,129818242..129818367,
                     129821463..129821559,129824024..129824095,
                     129825032..129825207,129832462..129832663,
                     129841690..129841931,129842372..129842503,
                     129843628..129843686,129843814..129843950,
                     129845213..129845215))
                     /gene="TMEM209"
                     /gene_synonym="FLJ14803; NET31"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 209"
                     /protein_id="NP_116231.2"
                     /db_xref="GI:66348165"
                     /db_xref="CCDS:CCDS47712.1"
                     /db_xref="GeneID:84928"
                     /db_xref="HGNC:21898"
                     /db_xref="HPRD:07871"
     gene            129847704..129856684
                     /gene="C7orf45"
                     /gene_synonym="FLJ40316"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:136263"
                     /db_xref="HGNC:29580"
                     /db_xref="HPRD:14060"
     mRNA            join(129847704..129847933,129853320..129853374,
                     129855814..129856684)
                     /gene="C7orf45"
                     /gene_synonym="FLJ40316"
                     /product="chromosome 7 open reading frame 45"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145268.3"
                     /db_xref="GI:197304739"
                     /db_xref="GeneID:136263"
                     /db_xref="HGNC:29580"
                     /db_xref="HPRD:14060"
     CDS             join(129847751..129847933,129853320..129853374,
                     129855814..129856310)
                     /gene="C7orf45"
                     /gene_synonym="FLJ40316"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC136263"
                     /protein_id="NP_660311.1"
                     /db_xref="GI:21687171"
                     /db_xref="CCDS:CCDS5816.1"
                     /db_xref="GeneID:136263"
                     /db_xref="HGNC:29580"
                     /db_xref="HPRD:14060"
     gene            129906703..129929638
                     /gene="CPA2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1358"
                     /db_xref="HGNC:2297"
                     /db_xref="HPRD:02821"
                     /db_xref="MIM:600688"
     mRNA            join(129906703..129906792,129908769..129908850,
                     129909509..129909643,129910533..129910628,
                     129912916..129913017,129914989..129915087,
                     129916468..129916578,129917666..129917756,
                     129919303..129919502,129921944..129922028,
                     129929400..129929638)
                     /gene="CPA2"
                     /product="carboxypeptidase A2 (pancreatic)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001869.2"
                     /db_xref="GI:217416389"
                     /db_xref="GeneID:1358"
                     /db_xref="HGNC:2297"
                     /db_xref="HPRD:02821"
                     /db_xref="MIM:600688"
     CDS             join(129906722..129906792,129908769..129908850,
                     129909509..129909643,129910533..129910628,
                     129912916..129913017,129914989..129915087,
                     129916468..129916578,129917666..129917756,
                     129919303..129919502,129921944..129922028,
                     129929400..129929587)
                     /gene="CPA2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="carboxypeptidase A2 precursor"
                     /protein_id="NP_001860.2"
                     /db_xref="GI:217416390"
                     /db_xref="CCDS:CCDS5817.2"
                     /db_xref="GeneID:1358"
                     /db_xref="HGNC:2297"
                     /db_xref="HPRD:02821"
                     /db_xref="MIM:600688"
     gene            129932974..129964020
                     /gene="CPA4"
                     /gene_synonym="CPA3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51200"
                     /db_xref="HGNC:15740"
                     /db_xref="HPRD:07405"
                     /db_xref="MIM:607635"
     mRNA            join(129932974..129933088,129938586..129938667,
                     129939110..129939244,129940656..129940754,
                     129944318..129944419,129945656..129945760,
                     129946627..129946737,129948147..129948237,
                     129950627..129950826,129951878..129951962,
                     129962329..129964020)
                     /gene="CPA4"
                     /gene_synonym="CPA3"
                     /product="carboxypeptidase A4, transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016352.3"
                     /db_xref="GI:223941942"
                     /db_xref="GeneID:51200"
                     /db_xref="HGNC:15740"
                     /db_xref="HPRD:07405"
                     /db_xref="MIM:607635"
     mRNA            join(129932974..129933088,129938586..129938667,
                     129939110..129939244,129944318..129944419,
                     129945656..129945760,129946627..129946737,
                     129948147..129948237,129950627..129950826,
                     129951878..129951962,129962329..129964020)
                     /gene="CPA4"
                     /gene_synonym="CPA3"
                     /product="carboxypeptidase A4, transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001163446.1"
                     /db_xref="GI:254540195"
                     /db_xref="GeneID:51200"
                     /db_xref="HGNC:15740"
                     /db_xref="MIM:607635"
                     /db_xref="HPRD:07405"
     CDS             join(129933021..129933088,129938586..129938667,
                     129939110..129939244,129944318..129944419,
                     129945656..129945760,129946627..129946737,
                     129948147..129948237,129950627..129950826,
                     129951878..129951962,129962329..129962516)
                     /gene="CPA4"
                     /gene_synonym="CPA3"
                     /note="isoform 2 preproprotein is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="carboxypeptidase A4 isoform 2 preproprotein"
                     /protein_id="NP_001156918.1"
                     /db_xref="GI:254540196"
                     /db_xref="CCDS:CCDS55163.1"
                     /db_xref="GeneID:51200"
                     /db_xref="HGNC:15740"
                     /db_xref="HPRD:07405"
                     /db_xref="MIM:607635"
     CDS             join(129933021..129933088,129938586..129938667,
                     129939110..129939244,129940656..129940754,
                     129944318..129944419,129945656..129945760,
                     129946627..129946737,129948147..129948237,
                     129950627..129950826,129951878..129951962,
                     129962329..129962516)
                     /gene="CPA4"
                     /gene_synonym="CPA3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="carboxypeptidase A4 preproprotein preproprotein"
                     /protein_id="NP_057436.2"
                     /db_xref="GI:61743916"
                     /db_xref="CCDS:CCDS5818.1"
                     /db_xref="GeneID:51200"
                     /db_xref="HGNC:15740"
                     /db_xref="HPRD:07405"
                     /db_xref="MIM:607635"
     gene            129984630..130008571
                     /gene="CPA5"
                     /gene_synonym="FLJ35969"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:93979"
                     /db_xref="HGNC:15722"
                     /db_xref="HPRD:07097"
                     /db_xref="MIM:609561"
     mRNA            join(129984630..129985045,129985679..129985736,
                     129986234..129986442,129987607..129987688,
                     129989816..129989950,129999430..129999528,
                     130000984..130001085,130002279..130002380,
                     130002725..130002835,130003260..130003350,
                     130007213..130007412,130007747..130007831,
                     130008251..130008571)
                     /gene="CPA5"
                     /gene_synonym="FLJ35969"
                     /product="carboxypeptidase A5, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_080385.4"
                     /db_xref="GI:188536050"
                     /db_xref="GeneID:93979"
                     /db_xref="HGNC:15722"
                     /db_xref="HPRD:07097"
                     /db_xref="MIM:609561"
     mRNA            join(129984630..129985045,129986234..129986442,
                     129987607..129987688,129989816..129989950,
                     129999430..129999528,130000984..130001085,
                     130002279..130002380,130002725..130002835,
                     130003260..130003350,130007213..130007412,
                     130008251..130008571)
                     /gene="CPA5"
                     /gene_synonym="FLJ35969"
                     /product="carboxypeptidase A5, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127442.1"
                     /db_xref="GI:188536054"
                     /db_xref="GeneID:93979"
                     /db_xref="HGNC:15722"
                     /db_xref="MIM:609561"
                     /db_xref="HPRD:07097"
     mRNA            join(129984630..129985045,129985679..129985736,
                     129986022..129986088,129986248..129986442,
                     129987607..129987688,129989816..129989950,
                     129999430..129999528,130000984..130001085,
                     130002279..130002380,130002725..130002835,
                     130003260..130003350,130007213..130007412,
                     130007747..130007831,130008251..130008569)
                     /gene="CPA5"
                     /gene_synonym="FLJ35969"
                     /product="carboxypeptidase A5, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001127441.1"
                     /db_xref="GI:188536052"
                     /db_xref="GeneID:93979"
                     /db_xref="HGNC:15722"
                     /db_xref="MIM:609561"
                     /db_xref="HPRD:07097"
     CDS             join(129986327..129986442,129987607..129987688,
                     129989816..129989950,129999430..129999528,
                     130000984..130001085,130002279..130002380,
                     130002725..130002835,130003260..130003350,
                     130007213..130007412,130007747..130007831,
                     130008251..130008438)
                     /gene="CPA5"
                     /gene_synonym="FLJ35969"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="carboxypeptidase A5 isoform 1"
                     /protein_id="NP_525124.3"
                     /db_xref="GI:188536051"
                     /db_xref="CCDS:CCDS5819.1"
                     /db_xref="GeneID:93979"
                     /db_xref="HGNC:15722"
                     /db_xref="HPRD:07097"
                     /db_xref="MIM:609561"
     CDS             join(129986327..129986442,129987607..129987688,
                     129989816..129989950,129999430..129999528,
                     130000984..130001085,130002279..130002380,
                     130002725..130002835,130003260..130003350,
                     130007213..130007412,130007747..130007831,
                     130008251..130008438)
                     /gene="CPA5"
                     /gene_synonym="FLJ35969"
                     /note="isoform 1 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="carboxypeptidase A5 isoform 1"
                     /protein_id="NP_001120913.1"
                     /db_xref="GI:188536053"
                     /db_xref="CCDS:CCDS5819.1"
                     /db_xref="GeneID:93979"
                     /db_xref="HGNC:15722"
                     /db_xref="HPRD:07097"
                     /db_xref="MIM:609561"
     CDS             join(129986327..129986442,129987607..129987688,
                     129989816..129989950,129999430..129999528,
                     130000984..130001085,130002279..130002380,
                     130002725..130002835,130003260..130003350,
                     130007213..130007412,130008251..130008424)
                     /gene="CPA5"
                     /gene_synonym="FLJ35969"
                     /note="isoform 2 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="carboxypeptidase A5 isoform 2"
                     /protein_id="NP_001120914.1"
                     /db_xref="GI:188536055"
                     /db_xref="CCDS:CCDS47713.1"
                     /db_xref="GeneID:93979"
                     /db_xref="HGNC:15722"
                     /db_xref="HPRD:07097"
                     /db_xref="MIM:609561"
     gene            130020290..130027949
                     /gene="CPA1"
                     /gene_synonym="CPA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1357"
                     /db_xref="HGNC:2296"
                     /db_xref="HPRD:00269"
                     /db_xref="MIM:114850"
     mRNA            join(130020290..130020426,130020939..130021020,
                     130021471..130021704,130021949..130022050,
                     130023232..130023333,130023525..130023635,
                     130024377..130024467,130024987..130025186,
                     130025680..130025764,130027665..130027949)
                     /gene="CPA1"
                     /gene_synonym="CPA"
                     /product="carboxypeptidase A1 (pancreatic)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001868.2"
                     /db_xref="GI:221316610"
                     /db_xref="GeneID:1357"
                     /db_xref="HGNC:2296"
                     /db_xref="HPRD:00269"
                     /db_xref="MIM:114850"
     CDS             join(130020362..130020426,130020939..130021020,
                     130021471..130021704,130021949..130022050,
                     130023232..130023333,130023525..130023635,
                     130024377..130024467,130024987..130025186,
                     130025680..130025764,130027665..130027852)
                     /gene="CPA1"
                     /gene_synonym="CPA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="carboxypeptidase A1 precursor"
                     /protein_id="NP_001859.1"
                     /db_xref="GI:4502997"
                     /db_xref="CCDS:CCDS5820.1"
                     /db_xref="GeneID:1357"
                     /db_xref="HGNC:2296"
                     /db_xref="HPRD:00269"
                     /db_xref="MIM:114850"
     gene            complement(130036375..130080854)
                     /gene="TSGA14"
                     /gene_synonym="Cep41; DKFZp762H1311"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:95681"
                     /db_xref="HGNC:12370"
                     /db_xref="HPRD:15574"
                     /db_xref="MIM:610523"
     mRNA            complement(join(130036375..130038880,130039880..130040095,
                     130040548..130040662,130041722..130041789,
                     130042489..130042640,130044405..130044549,
                     130050963..130051032,130052020..130052081,
                     130056760..130056807,130067796..130067859,
                     130080775..130080854))
                     /gene="TSGA14"
                     /gene_synonym="Cep41; DKFZp762H1311"
                     /product="testis specific, 14"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018718.1"
                     /db_xref="GI:16306478"
                     /db_xref="GeneID:95681"
                     /db_xref="HGNC:12370"
                     /db_xref="HPRD:15574"
                     /db_xref="MIM:610523"
     CDS             complement(join(130038732..130038880,130039880..130040095,
                     130040548..130040662,130041722..130041789,
                     130042489..130042640,130044405..130044549,
                     130050963..130051032,130052020..130052081,
                     130056760..130056807,130067796..130067859,
                     130080775..130080807))
                     /gene="TSGA14"
                     /gene_synonym="Cep41; DKFZp762H1311"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="centrosomal protein of 41 kDa"
                     /protein_id="NP_061188.1"
                     /db_xref="GI:16306479"
                     /db_xref="CCDS:CCDS5821.1"
                     /db_xref="GeneID:95681"
                     /db_xref="HGNC:12370"
                     /db_xref="HPRD:15574"
                     /db_xref="MIM:610523"
     gene            130126046..130146133
                     /gene="MEST"
                     /gene_synonym="DKFZp686L18234; MGC111102; MGC8703; PEG1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4232"
                     /db_xref="HGNC:7028"
                     /db_xref="MIM:601029"
     mRNA            join(130126046..130126236,130135209..130135363,
                     130136997..130137076,130137777..130137854,
                     130137980..130138116,130138260..130138318,
                     130139716..130139756,130140303..130140373,
                     130140630..130140731,130142485..130142561,
                     130143774..130143837,130144780..130146133)
                     /gene="MEST"
                     /gene_synonym="DKFZp686L18234; MGC111102; MGC8703; PEG1"
                     /product="mesoderm specific transcript homolog (mouse),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_177524.1"
                     /db_xref="GI:29294634"
                     /db_xref="GeneID:4232"
                     /db_xref="HGNC:7028"
                     /db_xref="MIM:601029"
     gene            complement(130126898..130131013)
                     /gene="MESTIT1"
                     /gene_synonym="MEST-IT; MESTIT1; NCRNA00040; PEG1-AS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:317751"
                     /db_xref="HGNC:17991"
                     /db_xref="MIM:607794"
     misc_RNA        complement(join(130126898..130129808,
                     130130683..130131013))
                     /gene="MESTIT1"
                     /gene_synonym="MEST-IT; MESTIT1; NCRNA00040; PEG1-AS"
                     /product="MEST intronic transcript 1, antisense RNA
                     (non-protein coding)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_004382.1"
                     /db_xref="GI:161087002"
                     /db_xref="GeneID:317751"
                     /db_xref="HGNC:17991"
                     /db_xref="MIM:607794"
     mRNA            join(130131173..130131327,130135209..130135363,
                     130136997..130137076,130137777..130137854,
                     130137980..130138116,130138260..130138318,
                     130139716..130139756,130140303..130140373,
                     130140630..130140731,130142485..130142561,
                     130143774..130143837,130144780..130146133)
                     /gene="MEST"
                     /gene_synonym="DKFZp686L18234; MGC111102; MGC8703; PEG1"
                     /product="mesoderm specific transcript homolog (mouse),
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_177525.1"
                     /db_xref="GI:29294636"
                     /db_xref="GeneID:4232"
                     /db_xref="HGNC:7028"
                     /db_xref="MIM:601029"
     mRNA            join(130131938..130132180,130135209..130135363,
                     130136997..130137076,130137777..130137854,
                     130137980..130138116,130138260..130138318,
                     130139716..130139756,130140303..130140373,
                     130140630..130140731,130142485..130142561,
                     130143774..130143837,130144780..130146133)
                     /gene="MEST"
                     /gene_synonym="DKFZp686L18234; MGC111102; MGC8703; PEG1"
                     /product="mesoderm specific transcript homolog (mouse),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002402.2"
                     /db_xref="GI:29294638"
                     /db_xref="GeneID:4232"
                     /db_xref="HGNC:7028"
                     /db_xref="HPRD:06776"
                     /db_xref="MIM:601029"
     CDS             join(130132155..130132180,130135209..130135363,
                     130136997..130137076,130137777..130137854,
                     130137980..130138116,130138260..130138318,
                     130139716..130139756,130140303..130140373,
                     130140630..130140731,130142485..130142561,
                     130143774..130143837,130144780..130144897)
                     /gene="MEST"
                     /gene_synonym="DKFZp686L18234; MGC111102; MGC8703; PEG1"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="mesoderm-specific transcript homolog protein
                     isoform a"
                     /protein_id="NP_002393.2"
                     /db_xref="GI:29294639"
                     /db_xref="CCDS:CCDS5822.1"
                     /db_xref="GeneID:4232"
                     /db_xref="HGNC:7028"
                     /db_xref="MIM:601029"
     CDS             join(130135210..130135363,130136997..130137076,
                     130137777..130137854,130137980..130138116,
                     130138260..130138318,130139716..130139756,
                     130140303..130140373,130140630..130140731,
                     130142485..130142561,130143774..130143837,
                     130144780..130144897)
                     /gene="MEST"
                     /gene_synonym="DKFZp686L18234; MGC111102; MGC8703; PEG1"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="mesoderm-specific transcript homolog protein
                     isoform b"
                     /protein_id="NP_803490.1"
                     /db_xref="GI:29294635"
                     /db_xref="CCDS:CCDS5823.1"
                     /db_xref="GeneID:4232"
                     /db_xref="HGNC:7028"
                     /db_xref="MIM:601029"
     CDS             join(130135210..130135363,130136997..130137076,
                     130137777..130137854,130137980..130138116,
                     130138260..130138318,130139716..130139756,
                     130140303..130140373,130140630..130140731,
                     130142485..130142561,130143774..130143837,
                     130144780..130144897)
                     /gene="MEST"
                     /gene_synonym="DKFZp686L18234; MGC111102; MGC8703; PEG1"
                     /note="isoform b is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="mesoderm-specific transcript homolog protein
                     isoform b"
                     /protein_id="NP_803491.1"
                     /db_xref="GI:29294637"
                     /db_xref="CCDS:CCDS5823.1"
                     /db_xref="GeneID:4232"
                     /db_xref="HGNC:7028"
                     /db_xref="MIM:601029"
     gene            130135952..130136045
                     /gene="MIR335"
                     /gene_synonym="hsa-mir-335; MIRN335; miRNA335"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:442904"
                     /db_xref="HGNC:31773"
                     /db_xref="MIM:611768"
                     /db_xref="miRBase:MI0000816"
     ncRNA           130135952..130136045
                     /gene="MIR335"
                     /gene_synonym="hsa-mir-335; MIRN335; miRNA335"
                     /ncRNA_class="miRNA"
                     /product="microRNA 335"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029899.1"
                     /db_xref="GI:262205112"
                     /db_xref="GeneID:442904"
                     /db_xref="HGNC:31773"
                     /db_xref="MIM:611768"
                     /db_xref="miRBase:MI0000816"
     ncRNA           130135952..130136045
                     /gene="MIR335"
                     /gene_synonym="hsa-mir-335; MIRN335; miRNA335"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-335"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:442904"
                     /db_xref="miRBase:MI0000816"
                     /db_xref="HGNC:31773"
                     /db_xref="MIM:611768"
     gene            complement(130146079..130353598)
                     /gene="COPG2"
                     /gene_synonym="2-COP; DKFZp761N09121; FLJ11781"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26958"
                     /db_xref="HGNC:2237"
                     /db_xref="HPRD:05074"
                     /db_xref="MIM:604355"
     mRNA            complement(join(130146079..130146647,130147115..130147213,
                     130147526..130147664,130148403..>130148520,
                     <130152304..130152328,130153698..130153718,
                     130255188..>130255196,<130269205..>130269213,
                     <130273723..>130273731,130277154..>130277166,
                     <130287349..>130287357,<130295826..130295981,
                     130297023..130297109,130298415..130298507,
                     130301861..130301936,130337709..130337788,
                     130347807..130347878,130351689..130351769,
                     130352322..130352374,130353472..130353598))
                     /gene="COPG2"
                     /gene_synonym="2-COP; DKFZp761N09121; FLJ11781"
                     /product="coatomer protein complex, subunit gamma 2"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012133.4"
                     /db_xref="GI:256985143"
                     /db_xref="GeneID:26958"
                     /db_xref="HGNC:2237"
                     /db_xref="HPRD:05074"
                     /db_xref="MIM:604355"
     CDS             complement(join(130146517..130146647,130147115..130147213,
                     130147526..130147664,130148403..>130148520,
                     <130152304..130152328,130153698..130153718,
                     130255188..>130255196,<130269205..>130269213,
                     <130273723..>130273731,130277154..>130277166,
                     <130287349..>130287357,<130295826..130295981,
                     130297023..130297109,130298415..130298507,
                     130301861..130301936,130337709..130337788,
                     130347807..130347878,130351689..130351769,
                     130352322..130352374,130353472..130353508))
                     /gene="COPG2"
                     /gene_synonym="2-COP; DKFZp761N09121; FLJ11781"
                     /exception="unclassified translation discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="coatomer subunit gamma-2"
                     /protein_id="NP_036265.3"
                     /db_xref="GI:109134349"
                     /db_xref="GeneID:26958"
                     /db_xref="HGNC:2237"
                     /db_xref="HPRD:05074"
                     /db_xref="MIM:604355"
     gene            complement(130353486..130371406)
                     /gene="TSGA13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:114960"
                     /db_xref="HGNC:12369"
                     /db_xref="HPRD:11650"
     mRNA            complement(join(130353486..130354023,130356501..130356628,
                     130357574..130357716,130363993..130364205,
                     130365784..130365855,130368432..130368510,
                     130370026..130370198,130371100..130371406))
                     /gene="TSGA13"
                     /product="testis specific, 13"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_052933.2"
                     /db_xref="GI:31377632"
                     /db_xref="GeneID:114960"
                     /db_xref="HGNC:12369"
                     /db_xref="HPRD:11650"
     CDS             complement(join(130353854..130354023,130356501..130356628,
                     130357574..130357716,130363993..130364205,
                     130365784..130365855,130368432..130368510,
                     130370026..130370048))
                     /gene="TSGA13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="testis-specific gene 13 protein"
                     /protein_id="NP_443165.1"
                     /db_xref="GI:16418411"
                     /db_xref="CCDS:CCDS5824.1"
                     /db_xref="GeneID:114960"
                     /db_xref="HGNC:12369"
                     /db_xref="HPRD:11650"
     gene            complement(130417396..130418888)
                     /gene="KLF14"
                     /gene_synonym="BTEB5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:136259"
                     /db_xref="HGNC:23025"
                     /db_xref="HPRD:13919"
                     /db_xref="MIM:609393"
     mRNA            complement(130417396..130418888)
                     /gene="KLF14"
                     /gene_synonym="BTEB5"
                     /product="Kruppel-like factor 14"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138693.2"
                     /db_xref="GI:269784639"
                     /db_xref="GeneID:136259"
                     /db_xref="HGNC:23025"
                     /db_xref="HPRD:13919"
                     /db_xref="MIM:609393"
     CDS             complement(130417889..130418860)
                     /gene="KLF14"
                     /gene_synonym="BTEB5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="Krueppel-like factor 14"
                     /protein_id="NP_619638.1"
                     /db_xref="GI:20162554"
                     /db_xref="CCDS:CCDS5825.1"
                     /db_xref="GeneID:136259"
                     /db_xref="HGNC:23025"
                     /db_xref="HPRD:13919"
                     /db_xref="MIM:609393"
     gene            complement(130507218..130507984)
                     /gene="LOC347674"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:347674"
     gene            complement(130524966..130528484)
                     /gene="LOC100133252"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100133252"
     gene            130538479..130613408
                     /gene="LOC100506860"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 12 ESTs"
                     /db_xref="GeneID:100506860"
     misc_RNA        join(130538479..130538555,130546883..130546961,
                     130599721..130599861,130600659..130600891,
                     130612321..130613408)
                     /gene="LOC100506860"
                     /product="hypothetical LOC100506860, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 4 ESTs"
                     /transcript_id="XR_108814.1"
                     /db_xref="GI:310120092"
                     /db_xref="GeneID:100506860"
     gene            complement(130561506..130561569)
                     /gene="MIR29A"
                     /gene_synonym="hsa-mir-29; hsa-mir-29a; MIRN29; MIRN29A;
                     miRNA29A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:407021"
                     /db_xref="HGNC:31616"
                     /db_xref="MIM:610782"
                     /db_xref="miRBase:MI0000087"
     ncRNA           complement(130561506..130561569)
                     /gene="MIR29A"
                     /gene_synonym="hsa-mir-29; hsa-mir-29a; MIRN29; MIRN29A;
                     miRNA29A"
                     /ncRNA_class="miRNA"
                     /product="microRNA 29a"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029503.1"
                     /db_xref="GI:262205706"
                     /db_xref="GeneID:407021"
                     /db_xref="HGNC:31616"
                     /db_xref="MIM:610782"
                     /db_xref="miRBase:MI0000087"
     ncRNA           complement(130561506..130561569)
                     /gene="MIR29A"
                     /gene_synonym="hsa-mir-29; hsa-mir-29a; MIRN29; MIRN29A;
                     miRNA29A"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-29a"
                     /inference="similar to RNA sequence:INSD: AJ421751"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:407021"
                     /db_xref="miRBase:MI0000087"
                     /db_xref="RFAM:RF00074"
                     /db_xref="HGNC:31616"
                     /db_xref="MIM:610782"
     gene            complement(130562218..130562298)
                     /gene="MIR29B1"
                     /gene_synonym="MIRN29B1; miRNA29B1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:407024"
                     /db_xref="HGNC:31619"
                     /db_xref="MIM:610783"
                     /db_xref="miRBase:MI0000105"
     ncRNA           complement(130562218..130562298)
                     /gene="MIR29B1"
                     /gene_synonym="MIRN29B1; miRNA29B1"
                     /ncRNA_class="miRNA"
                     /product="microRNA 29b-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029517.1"
                     /db_xref="GI:262205770"
                     /db_xref="GeneID:407024"
                     /db_xref="HGNC:31619"
                     /db_xref="MIM:610783"
                     /db_xref="miRBase:MI0000105"
     ncRNA           complement(130562218..130562298)
                     /gene="MIR29B1"
                     /gene_synonym="MIRN29B1; miRNA29B1"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-29b-1"
                     /inference="similar to RNA sequence:INSD: AF480542"
                     /inference="similar to RNA sequence:INSD: AF480541"
                     /inference="similar to RNA sequence:INSD: AF480500"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:407024"
                     /db_xref="miRBase:MI0000105"
                     /db_xref="RFAM:RF00074"
                     /db_xref="HGNC:31619"
                     /db_xref="MIM:610783"
     gene            complement(130565751..130598069)
                     /gene="LOC646329"
                     /gene_synonym="FLJ38230; hCG_2038586"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:646329"
     misc_RNA        complement(join(130565751..130567495,130569076..130569155,
                     130596869..130596911,130597710..130598069))
                     /gene="LOC646329"
                     /gene_synonym="FLJ38230; hCG_2038586"
                     /product="hypothetical LOC646329"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_034120.1"
                     /db_xref="GI:300796423"
                     /db_xref="GeneID:646329"
     misc_RNA        join(130597978..130598384,130599721..130599861,
                     130600659..130600891,130606295..130606704)
                     /gene="LOC100506860"
                     /product="hypothetical LOC100506860, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 8 ESTs"
                     /transcript_id="XR_108813.1"
                     /db_xref="GI:310120093"
                     /db_xref="GeneID:100506860"
     gene            complement(130628919..130793562)
                     /gene="FLJ43663"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:378805"
     misc_RNA        complement(join(130628919..130630594,130668812..130668868,
                     130737184..130737314,130792479..130793562))
                     /gene="FLJ43663"
                     /product="hypothetical LOC378805, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_015431.1"
                     /db_xref="GI:205277371"
                     /db_xref="GeneID:378805"
     misc_RNA        complement(join(130628919..130630594,130668812..130668868,
                     130791502..130791789))
                     /gene="FLJ43663"
                     /product="hypothetical LOC378805, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024153.1"
                     /db_xref="GI:205277373"
                     /db_xref="GeneID:378805"
     gene            130794855..131181398
                     /gene="MKLN1"
                     /gene_synonym="FLJ11162; TWA2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4289"
                     /db_xref="HGNC:7109"
                     /db_xref="MIM:605623"
     mRNA            join(130794855..130794966,130827579..130827700,
                     131060183..131060252,131071879..131072021,
                     131073643..131073731,131082026..131082135,
                     131084000..131084192,131096065..131096142,
                     131099404..131099469,131113792..131113904,
                     131122544..131122756,131128240..131128461,
                     131130533..131130662,131147976..131148123,
                     131149053..131149167,131151035..131151174,
                     131155601..131155703,131163382..131163436,
                     131172366..131181398)
                     /gene="MKLN1"
                     /gene_synonym="FLJ11162; TWA2"
                     /product="muskelin 1, intracellular mediator containing
                     kelch motifs, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145354.1"
                     /db_xref="GI:223890245"
                     /db_xref="GeneID:4289"
                     /db_xref="HGNC:7109"
                     /db_xref="MIM:605623"
     CDS             join(130827672..130827700,131060183..131060252,
                     131071879..131072021,131073643..131073731,
                     131082026..131082135,131084000..131084192,
                     131096065..131096142,131099404..131099469,
                     131113792..131113904,131122544..131122756,
                     131128240..131128461,131130533..131130662,
                     131147976..131148123,131149053..131149167,
                     131151035..131151174,131155601..131155703,
                     131163382..131163436,131172366..131172487)
                     /gene="MKLN1"
                     /gene_synonym="FLJ11162; TWA2"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="muskelin isoform 1"
                     /protein_id="NP_001138826.1"
                     /db_xref="GI:223890246"
                     /db_xref="GeneID:4289"
                     /db_xref="HGNC:7109"
                     /db_xref="MIM:605623"
     gene            130927314..130927803
                     /gene="RPL27P11"
                     /gene_synonym="RPL27_6_845"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442723"
                     /db_xref="HGNC:36533"
     gene            complement(130994503..131012538)
                     /gene="LOC100506881"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 12 ESTs"
                     /db_xref="GeneID:100506881"
     misc_RNA        complement(join(130994503..130995532,130995889..130995982,
                     131008124..131008627,131009062..131009184,
                     131011565..131011694,131012374..131012538))
                     /gene="LOC100506881"
                     /product="hypothetical LOC100506881, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 5 ESTs"
                     /transcript_id="XR_108815.1"
                     /db_xref="GI:310120094"
                     /db_xref="GeneID:100506881"
     misc_RNA        complement(join(131007691..131008627,131009062..131009184,
                     131011565..131011694,131012374..131012538))
                     /gene="LOC100506881"
                     /product="hypothetical LOC100506881, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 6 ESTs"
                     /transcript_id="XR_108816.1"
                     /db_xref="GI:310120095"
                     /db_xref="GeneID:100506881"
     misc_RNA        complement(join(131007691..131008627,131009011..131009184,
                     131011565..131011654,131012374..131012489))
                     /gene="LOC100506881"
                     /product="hypothetical LOC100506881, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_108817.1"
                     /db_xref="GI:310120096"
                     /db_xref="GeneID:100506881"
     misc_RNA        complement(join(131007691..131008627,131009011..131009184,
                     131011565..131011694,131012374..131012476))
                     /gene="LOC100506881"
                     /product="hypothetical LOC100506881, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_108818.1"
                     /db_xref="GI:310120097"
                     /db_xref="GeneID:100506881"
     mRNA            join(131012595..131012756,131060183..131060252,
                     131071879..131072021,131073643..131073731,
                     131082026..131082135,131084000..131084192,
                     131096065..131096142,131099404..131099469,
                     131113792..131113904,131122544..131122756,
                     131128240..131128461,131130533..131130662,
                     131147976..131148123,131149053..131149167,
                     131151035..131151174,131155601..131155703,
                     131163382..131163436,131172366..131181398)
                     /gene="MKLN1"
                     /gene_synonym="FLJ11162; TWA2"
                     /product="muskelin 1, intracellular mediator containing
                     kelch motifs, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013255.4"
                     /db_xref="GI:223890247"
                     /db_xref="GeneID:4289"
                     /db_xref="HGNC:7109"
                     /db_xref="HPRD:16129"
                     /db_xref="MIM:605623"
     CDS             join(131012659..131012756,131060183..131060252,
                     131071879..131072021,131073643..131073731,
                     131082026..131082135,131084000..131084192,
                     131096065..131096142,131099404..131099469,
                     131113792..131113904,131122544..131122756,
                     131128240..131128461,131130533..131130662,
                     131147976..131148123,131149053..131149167,
                     131151035..131151174,131155601..131155703,
                     131163382..131163436,131172366..131172487)
                     /gene="MKLN1"
                     /gene_synonym="FLJ11162; TWA2"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="muskelin isoform 2"
                     /protein_id="NP_037387.2"
                     /db_xref="GI:31881798"
                     /db_xref="CCDS:CCDS34754.1"
                     /db_xref="GeneID:4289"
                     /db_xref="HGNC:7109"
                     /db_xref="MIM:605623"
     gene            complement(131185021..131241376)
                     /gene="PODXL"
                     /gene_synonym="Gp200; MGC138240; PC; PCLP; PCLP-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5420"
                     /db_xref="HGNC:9171"
                     /db_xref="MIM:602632"
     mRNA            complement(join(131185021..131189267,131190627..131190794,
                     131191019..131191080,131191338..131191485,
                     131193710..131193787,131194124..131194344,
                     131194995..131195090,131195587..131196192,
                     131241019..131241376))
                     /gene="PODXL"
                     /gene_synonym="Gp200; MGC138240; PC; PCLP; PCLP-1"
                     /product="podocalyxin-like, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001018111.2"
                     /db_xref="GI:144094253"
                     /db_xref="GeneID:5420"
                     /db_xref="HGNC:9171"
                     /db_xref="MIM:602632"
     mRNA            complement(join(131185021..131189267,131190627..131190794,
                     131191019..131191080,131191338..131191485,
                     131193710..131193787,131194124..131194344,
                     131195587..131196192,131241019..131241376))
                     /gene="PODXL"
                     /gene_synonym="Gp200; MGC138240; PC; PCLP; PCLP-1"
                     /product="podocalyxin-like, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005397.3"
                     /db_xref="GI:144094254"
                     /db_xref="GeneID:5420"
                     /db_xref="HGNC:9171"
                     /db_xref="HPRD:04025"
                     /db_xref="MIM:602632"
     CDS             complement(join(131189070..131189267,131190627..131190794,
                     131191019..131191080,131191338..131191485,
                     131193710..131193787,131194124..131194344,
                     131194995..131195090,131195587..131196192,
                     131241019..131241118))
                     /gene="PODXL"
                     /gene_synonym="Gp200; MGC138240; PC; PCLP; PCLP-1"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="podocalyxin isoform 1 precursor"
                     /protein_id="NP_001018121.1"
                     /db_xref="GI:66277202"
                     /db_xref="CCDS:CCDS34755.1"
                     /db_xref="GeneID:5420"
                     /db_xref="HGNC:9171"
                     /db_xref="MIM:602632"
     CDS             complement(join(131189070..131189267,131190627..131190794,
                     131191019..131191080,131191338..131191485,
                     131193710..131193787,131194124..131194344,
                     131195587..131196192,131241019..131241118))
                     /gene="PODXL"
                     /gene_synonym="Gp200; MGC138240; PC; PCLP; PCLP-1"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="podocalyxin isoform 2 precursor"
                     /protein_id="NP_005388.2"
                     /db_xref="GI:33598950"
                     /db_xref="CCDS:CCDS47714.1"
                     /db_xref="GeneID:5420"
                     /db_xref="HGNC:9171"
                     /db_xref="MIM:602632"
     gene            131204873..131205305
                     /gene="RPL31P36"
                     /gene_synonym="RPL31_19_846"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271200"
                     /db_xref="HGNC:36676"
     gene            complement(131346659..131347424)
                     /gene="LOC647030"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:647030"
     gene            131350338..131350544
                     /gene="RPS14P10"
                     /gene_synonym="RPS14_7_847"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:647034"
                     /db_xref="HGNC:35517"
     gene            complement(131386983..131387440)
                     /gene="RPS15AP22"
                     /gene_synonym="RPS15A_11_848"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271557"
                     /db_xref="HGNC:36305"
     gene            complement(131438412..131460814)
                     /gene="LOC100128596"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /pseudo
                     /db_xref="GeneID:100128596"
     exon            complement(131438412..131439056)
                     /gene="LOC100128596"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=3
                     /pseudo
                     /db_xref="GeneID:100128596"
     exon            complement(131460337..131460434)
                     /gene="LOC100128596"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=2
                     /pseudo
                     /db_xref="GeneID:100128596"
     exon            complement(131460511..131460814)
                     /gene="LOC100128596"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /number=1
                     /pseudo
                     /db_xref="GeneID:100128596"
     gene            complement(131577371..131578262)
                     /gene="LOC100130704"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100130704"
     gene            131770965..131774078
                     /gene="LOC100533635"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533635"
     gene            complement(131808091..132333447)
                     /gene="PLXNA4"
                     /gene_synonym="DKFZp434G0625; DKFZp566O0546; FAYV2820;
                     FLJ35026; FLJ38287; KIAA1550; PLEXA4; PLXNA4A; PLXNA4B;
                     PRO34003"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:91584"
                     /db_xref="HGNC:9102"
                     /db_xref="HPRD:10901"
                     /db_xref="MIM:604280"
     mRNA            complement(join(131808091..131815333,131817808..131817958,
                     131825358..131825570,131829878..131830047,
                     131831269..131831459,131832659..131832758,
                     131833302..131833405,131844232..131844391,
                     131848901..131849047,131849893..131849959,
                     131853063..131853331,131859537..131859679,
                     131864446..131864680,131865345..131865491,
                     131866140..131866379,131866856..131866949,
                     131870058..131870222,131872230..131872366,
                     131878821..131878938,131883244..131883395,
                     131887405..131887595,131888082..131888178,
                     131895702..131895902,131908286..131908400,
                     131910920..131911019,131912210..131912363,
                     131913105..131913228,131925825..131925925,
                     131982850..131982981,132174051..132174233,
                     132192265..132193538,132261181..132261323))
                     /gene="PLXNA4"
                     /gene_synonym="DKFZp434G0625; DKFZp566O0546; FAYV2820;
                     FLJ35026; FLJ38287; KIAA1550; PLEXA4; PLXNA4A; PLXNA4B;
                     PRO34003"
                     /product="plexin A4, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020911.1"
                     /db_xref="GI:157738644"
                     /db_xref="GeneID:91584"
                     /db_xref="HGNC:9102"
                     /db_xref="MIM:604280"
                     /db_xref="HPRD:10901"
     CDS             complement(join(131815238..131815333,131817808..131817958,
                     131825358..131825570,131829878..131830047,
                     131831269..131831459,131832659..131832758,
                     131833302..131833405,131844232..131844391,
                     131848901..131849047,131849893..131849959,
                     131853063..131853331,131859537..131859679,
                     131864446..131864680,131865345..131865491,
                     131866140..131866379,131866856..131866949,
                     131870058..131870222,131872230..131872366,
                     131878821..131878938,131883244..131883395,
                     131887405..131887595,131888082..131888178,
                     131895702..131895902,131908286..131908400,
                     131910920..131911019,131912210..131912363,
                     131913105..131913228,131925825..131925925,
                     131982850..131982981,132174051..132174233,
                     132192265..132193452))
                     /gene="PLXNA4"
                     /gene_synonym="DKFZp434G0625; DKFZp566O0546; FAYV2820;
                     FLJ35026; FLJ38287; KIAA1550; PLEXA4; PLXNA4A; PLXNA4B;
                     PRO34003"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="plexin-A4 isoform 1"
                     /protein_id="NP_065962.1"
                     /db_xref="GI:157738645"
                     /db_xref="CCDS:CCDS43646.1"
                     /db_xref="GeneID:91584"
                     /db_xref="HGNC:9102"
                     /db_xref="HPRD:10901"
                     /db_xref="MIM:604280"
     mRNA            complement(join(132068247..132070054,132174051..132174233,
                     132192265..132193538,132261181..132261323))
                     /gene="PLXNA4"
                     /gene_synonym="DKFZp434G0625; DKFZp566O0546; FAYV2820;
                     FLJ35026; FLJ38287; KIAA1550; PLEXA4; PLXNA4A; PLXNA4B;
                     PRO34003"
                     /product="plexin A4, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001105543.1"
                     /db_xref="GI:157738646"
                     /db_xref="GeneID:91584"
                     /db_xref="HGNC:9102"
                     /db_xref="MIM:604280"
                     /db_xref="HPRD:10901"
     CDS             complement(join(132069947..132070054,132174051..132174233,
                     132192265..132193452))
                     /gene="PLXNA4"
                     /gene_synonym="DKFZp434G0625; DKFZp566O0546; FAYV2820;
                     FLJ35026; FLJ38287; KIAA1550; PLEXA4; PLXNA4A; PLXNA4B;
                     PRO34003"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="plexin-A4 isoform 3"
                     /protein_id="NP_001099013.1"
                     /db_xref="GI:157738647"
                     /db_xref="CCDS:CCDS43647.1"
                     /db_xref="GeneID:91584"
                     /db_xref="HGNC:9102"
                     /db_xref="HPRD:10901"
                     /db_xref="MIM:604280"
     mRNA            complement(join(132169521..132169772,132174051..132174233,
                     132192265..132193538,132330687..132330802,
                     132333273..132333447))
                     /gene="PLXNA4"
                     /gene_synonym="DKFZp434G0625; DKFZp566O0546; FAYV2820;
                     FLJ35026; FLJ38287; KIAA1550; PLEXA4; PLXNA4A; PLXNA4B;
                     PRO34003"
                     /product="plexin A4, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_181775.3"
                     /db_xref="GI:157738642"
                     /db_xref="GeneID:91584"
                     /db_xref="HGNC:9102"
                     /db_xref="HPRD:10901"
                     /db_xref="MIM:604280"
     CDS             complement(join(132169575..132169772,132174051..132174233,
                     132192265..132193452))
                     /gene="PLXNA4"
                     /gene_synonym="DKFZp434G0625; DKFZp566O0546; FAYV2820;
                     FLJ35026; FLJ38287; KIAA1550; PLEXA4; PLXNA4A; PLXNA4B;
                     PRO34003"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="plexin-A4 isoform 2"
                     /protein_id="NP_861440.2"
                     /db_xref="GI:157738643"
                     /db_xref="CCDS:CCDS5826.1"
                     /db_xref="GeneID:91584"
                     /db_xref="HGNC:9102"
                     /db_xref="HPRD:10901"
                     /db_xref="MIM:604280"
     gene            132344290..132357053
                     /gene="FLJ40288"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /db_xref="GeneID:286023"
     misc_RNA        join(132344290..132344374,132346240..132346304,
                     132346750..132346841,132356695..132357053)
                     /gene="FLJ40288"
                     /product="hypothetical FLJ40288"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_132534.1"
                     /db_xref="GI:341915390"
                     /db_xref="GeneID:286023"
     gene            132443730..132445392
                     /gene="LOC100506937"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /db_xref="GeneID:100506937"
     misc_RNA        join(132443730..132444165,132445078..132445392)
                     /gene="LOC100506937"
                     /product="hypothetical LOC100506937"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_108820.1"
                     /db_xref="GI:310120101"
                     /db_xref="GeneID:100506937"
     gene            complement(132469623..132766833)
                     /gene="CHCHD3"
                     /gene_synonym="FLJ20420"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54927"
                     /db_xref="HGNC:21906"
                     /db_xref="HPRD:13044"
                     /db_xref="MIM:613748"
     mRNA            complement(join(132469623..132470421,132481203..132481338,
                     132523159..132523229,132570422..132570505,
                     132659929..132660046,132709306..132709387,
                     132754902..132754989,132766617..132766833))
                     /gene="CHCHD3"
                     /gene_synonym="FLJ20420"
                     /product="coiled-coil-helix-coiled-coil-helix domain
                     containing 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017812.2"
                     /db_xref="GI:142365297"
                     /db_xref="GeneID:54927"
                     /db_xref="HGNC:21906"
                     /db_xref="HPRD:13044"
                     /db_xref="MIM:613748"
     CDS             complement(join(132470398..132470421,132481203..132481338,
                     132523159..132523229,132570422..132570505,
                     132659929..132660046,132709306..132709387,
                     132754902..132754989,132766617..132766697))
                     /gene="CHCHD3"
                     /gene_synonym="FLJ20420"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="coiled-coil-helix-coiled-coil-helix
                     domain-containing protein 3, mitochondrial precursor"
                     /protein_id="NP_060282.1"
                     /db_xref="GI:8923390"
                     /db_xref="CCDS:CCDS5828.1"
                     /db_xref="GeneID:54927"
                     /db_xref="HGNC:21906"
                     /db_xref="HPRD:13044"
                     /db_xref="MIM:613748"
     gene            complement(132719275..132720700)
                     /gene="LOC729998"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:729998"
     gene            complement(132719620..132719675)
                     /gene="MIR3654"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100500804"
                     /db_xref="HGNC:38896"
                     /db_xref="miRBase:MI0016054"
     ncRNA           complement(132719620..132719675)
                     /gene="MIR3654"
                     /ncRNA_class="miRNA"
                     /product="microRNA 3654"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037427.1"
                     /db_xref="GI:338797799"
                     /db_xref="GeneID:100500804"
                     /db_xref="HGNC:38896"
                     /db_xref="miRBase:MI0016054"
     gene            complement(132852760..132855356)
                     /gene="ST13P7"
                     /gene_synonym="FAM10A7; FAM10A7P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:155019"
                     /db_xref="HGNC:18558"
     gene            132937823..133750514
                     /gene="EXOC4"
                     /gene_synonym="MGC27170; REC8; SEC8; SEC8L1; Sec8p"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:60412"
                     /db_xref="HGNC:30389"
                     /db_xref="HPRD:12185"
                     /db_xref="MIM:608185"
     mRNA            join(132937823..132937943,132959737..132959926,
                     132973676..132973870,132990631..132990815,
                     133002038..133002144,133041084..133041327,
                     133059582..133059756,133160082..133160227,
                     133164804..133164892,133314798..133314894,
                     133502078..133502297,133580352..133580488,
                     133602336..133602491,133622644..133622822,
                     133682245..133682386,133689665..133689843,
                     133692429..133692588,133749044..133750514)
                     /gene="EXOC4"
                     /gene_synonym="MGC27170; REC8; SEC8; SEC8L1; Sec8p"
                     /product="exocyst complex component 4, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_021807.3"
                     /db_xref="GI:82546829"
                     /db_xref="GeneID:60412"
                     /db_xref="HGNC:30389"
                     /db_xref="HPRD:12185"
                     /db_xref="MIM:608185"
     mRNA            join(132937823..132937943,132959737..132959926,
                     132973676..132973870,132990631..132990815,
                     133002038..133002144,133041084..133041327,
                     133059582..133059756,133160082..133160227,
                     133164804..133164892,133168794..133168951)
                     /gene="EXOC4"
                     /gene_synonym="MGC27170; REC8; SEC8; SEC8L1; Sec8p"
                     /product="exocyst complex component 4, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001037126.1"
                     /db_xref="GI:82546831"
                     /db_xref="GeneID:60412"
                     /db_xref="HGNC:30389"
                     /db_xref="HPRD:12185"
                     /db_xref="MIM:608185"
     CDS             join(132937858..132937943,132959737..132959926,
                     132973676..132973870,132990631..132990815,
                     133002038..133002144,133041084..133041327,
                     133059582..133059756,133160082..133160227,
                     133164804..133164892,133314798..133314894,
                     133502078..133502297,133580352..133580488,
                     133602336..133602491,133622644..133622822,
                     133682245..133682386,133689665..133689843,
                     133692429..133692588,133749044..133749281)
                     /gene="EXOC4"
                     /gene_synonym="MGC27170; REC8; SEC8; SEC8L1; Sec8p"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="exocyst complex component 4 isoform a"
                     /protein_id="NP_068579.3"
                     /db_xref="GI:82546830"
                     /db_xref="CCDS:CCDS5829.1"
                     /db_xref="GeneID:60412"
                     /db_xref="HGNC:30389"
                     /db_xref="HPRD:12185"
                     /db_xref="MIM:608185"
     CDS             join(132937858..132937943,132959737..132959926,
                     132973676..132973870,132990631..132990815,
                     133002038..133002144,133041084..133041327,
                     133059582..133059756,133160082..133160227,
                     133164804..133164892,133168794..133168798)
                     /gene="EXOC4"
                     /gene_synonym="MGC27170; REC8; SEC8; SEC8L1; Sec8p"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="exocyst complex component 4 isoform b"
                     /protein_id="NP_001032203.1"
                     /db_xref="GI:82546832"
                     /db_xref="CCDS:CCDS43648.1"
                     /db_xref="GeneID:60412"
                     /db_xref="HGNC:30389"
                     /db_xref="HPRD:12185"
                     /db_xref="MIM:608185"
     gene            complement(132999763..133000165)
                     /gene="RPS15AP23"
                     /gene_synonym="RPS15A_12_849"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271558"
                     /db_xref="HGNC:36718"
     gene            complement(133412033..133412521)
                     /gene="COX5BP3"
                     /gene_synonym="COX5BL3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:1332"
                     /db_xref="HGNC:2272"
     gene            complement(133417246..133417973)
                     /gene="RPS3AP27"
                     /gene_synonym="RPS3A_12_850"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271255"
                     /db_xref="HGNC:35978"
     gene            133812105..133948933
                     /gene="LRGUK"
                     /gene_synonym="FLJ32786"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:136332"
                     /db_xref="HGNC:21964"
                     /db_xref="HPRD:08734"
     mRNA            join(133812105..133812417,133821776..133821883,
                     133824189..133824270,133827815..133827915,
                     133832991..133833072,133842788..133842912,
                     133848149..133848292,133859308..133859388,
                     133861729..133861815,133863255..133863361,
                     133868486..133868605,133876407..133876503,
                     133881744..133881857,133883972..133884173,
                     133886233..133886328,133906531..133906670,
                     133932308..133932396,133933703..133933828,
                     133943009..133943157,133948597..133948933)
                     /gene="LRGUK"
                     /gene_synonym="FLJ32786"
                     /product="leucine-rich repeats and guanylate kinase domain
                     containing"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_144648.1"
                     /db_xref="GI:21389482"
                     /db_xref="GeneID:136332"
                     /db_xref="HGNC:21964"
                     /db_xref="HPRD:08734"
     CDS             join(133812121..133812417,133821776..133821883,
                     133824189..133824270,133827815..133827915,
                     133832991..133833072,133842788..133842912,
                     133848149..133848292,133859308..133859388,
                     133861729..133861815,133863255..133863361,
                     133868486..133868605,133876407..133876503,
                     133881744..133881857,133883972..133884173,
                     133886233..133886328,133906531..133906670,
                     133932308..133932396,133933703..133933828,
                     133943009..133943157,133948597..133948727)
                     /gene="LRGUK"
                     /gene_synonym="FLJ32786"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="leucine-rich repeat and guanylate kinase
                     domain-containing protein"
                     /protein_id="NP_653249.1"
                     /db_xref="GI:21389483"
                     /db_xref="CCDS:CCDS5830.1"
                     /db_xref="GeneID:136332"
                     /db_xref="HGNC:21964"
                     /db_xref="HPRD:08734"
     gene            complement(133974089..134001827)
                     /gene="SLC35B4"
                     /gene_synonym="FLJ14697; YEA; YEA4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84912"
                     /db_xref="HGNC:20584"
                     /db_xref="HPRD:11578"
                     /db_xref="MIM:610923"
     mRNA            complement(join(133974089..133979831,133981143..133981218,
                     133984275..133984350,133984904..133985013,
                     133986513..133986573,133986781..133986862,
                     133989557..133989606,133991424..133991526,
                     133994118..133994231,134001427..134001827))
                     /gene="SLC35B4"
                     /gene_synonym="FLJ14697; YEA; YEA4"
                     /product="solute carrier family 35, member B4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032826.4"
                     /db_xref="GI:197304722"
                     /db_xref="GeneID:84912"
                     /db_xref="HGNC:20584"
                     /db_xref="HPRD:11578"
                     /db_xref="MIM:610923"
     CDS             complement(join(133979585..133979831,133981143..133981218,
                     133984275..133984350,133984904..133985013,
                     133986513..133986573,133986781..133986862,
                     133989557..133989606,133991424..133991526,
                     133994118..133994231,134001427..134001503))
                     /gene="SLC35B4"
                     /gene_synonym="FLJ14697; YEA; YEA4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="UDP-xylose and UDP-N-acetylglucosamine
                     transporter"
                     /protein_id="NP_116215.1"
                     /db_xref="GI:14249528"
                     /db_xref="CCDS:CCDS34756.1"
                     /db_xref="GeneID:84912"
                     /db_xref="HGNC:20584"
                     /db_xref="HPRD:11578"
                     /db_xref="MIM:610923"
     gene            complement(134127107..134143888)
                     /gene="AKR1B1"
                     /gene_synonym="ADR; ALDR1; ALR2; AR; MGC1804"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:231"
                     /db_xref="HGNC:381"
                     /db_xref="HPRD:00071"
                     /db_xref="MIM:103880"
     mRNA            complement(join(134127107..134127522,134129990..134130072,
                     134132050..134132133,134132732..134132813,
                     134133139..134133245,134133749..134133871,
                     134134472..134134549,134135538..134135654,
                     134136338..134136505,134143749..134143888))
                     /gene="AKR1B1"
                     /gene_synonym="ADR; ALDR1; ALR2; AR; MGC1804"
                     /product="aldo-keto reductase family 1, member B1 (aldose
                     reductase)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001628.2"
                     /db_xref="GI:24497579"
                     /db_xref="GeneID:231"
                     /db_xref="HGNC:381"
                     /db_xref="HPRD:00071"
                     /db_xref="MIM:103880"
     CDS             complement(join(134127480..134127522,134129990..134130072,
                     134132050..134132133,134132732..134132813,
                     134133139..134133245,134133749..134133871,
                     134134472..134134549,134135538..134135654,
                     134136338..134136505,134143749..134143814))
                     /gene="AKR1B1"
                     /gene_synonym="ADR; ALDR1; ALR2; AR; MGC1804"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="aldose reductase"
                     /protein_id="NP_001619.1"
                     /db_xref="GI:4502049"
                     /db_xref="CCDS:CCDS5831.1"
                     /db_xref="GeneID:231"
                     /db_xref="HGNC:381"
                     /db_xref="HPRD:00071"
                     /db_xref="MIM:103880"
     gene            134212344..134226166
                     /gene="AKR1B10"
                     /gene_synonym="AKR1B11; AKR1B12; ALDRLn; ARL-1; ARL1; HIS;
                     HSI; MGC14103"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57016"
                     /db_xref="HGNC:382"
                     /db_xref="HPRD:05271"
                     /db_xref="MIM:604707"
     mRNA            join(134212344..134212729,134215395..134215562,
                     134216660..134216776,134217756..134217833,
                     134221402..134221524,134221803..134221909,
                     134222332..134222413,134222946..134223029,
                     134223687..134223769,134225799..134226166)
                     /gene="AKR1B10"
                     /gene_synonym="AKR1B11; AKR1B12; ALDRLn; ARL-1; ARL1; HIS;
                     HSI; MGC14103"
                     /product="aldo-keto reductase family 1, member B10 (aldose
                     reductase)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020299.4"
                     /db_xref="GI:223468662"
                     /db_xref="GeneID:57016"
                     /db_xref="HGNC:382"
                     /db_xref="HPRD:05271"
                     /db_xref="MIM:604707"
     CDS             join(134212664..134212729,134215395..134215562,
                     134216660..134216776,134217756..134217833,
                     134221402..134221524,134221803..134221909,
                     134222332..134222413,134222946..134223029,
                     134223687..134223769,134225799..134225841)
                     /gene="AKR1B10"
                     /gene_synonym="AKR1B11; AKR1B12; ALDRLn; ARL-1; ARL1; HIS;
                     HSI; MGC14103"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="aldo-keto reductase family 1 member B10"
                     /protein_id="NP_064695.3"
                     /db_xref="GI:223468663"
                     /db_xref="CCDS:CCDS5832.1"
                     /db_xref="GeneID:57016"
                     /db_xref="HGNC:382"
                     /db_xref="HPRD:05271"
                     /db_xref="MIM:604707"
     gene            134233849..134264592
                     /gene="AKR1B15"
                     /gene_synonym="AKR1B10L"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:441282"
                     /db_xref="HGNC:37281"
     mRNA            join(134233849..134234001,134241488..134241611,
                     134249350..134249521,134252910..134253077,
                     134254165..134254281,134256356..134256433,
                     134260172..134260294,134260573..134260679,
                     134261101..134261182,134261715..134261798,
                     134262456..134262538,134264259..134264592)
                     /gene="AKR1B15"
                     /gene_synonym="AKR1B10L"
                     /product="aldo-keto reductase family 1, member B15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001080538.2"
                     /db_xref="GI:291291011"
                     /db_xref="GeneID:441282"
                     /db_xref="HGNC:37281"
     CDS             join(134249372..134249521,134252910..134253077,
                     134254165..134254281,134256356..134256433,
                     134260172..134260294,134260573..134260679,
                     134261101..134261182,134261715..134261798,
                     134262456..134262538,134264259..134264301)
                     /gene="AKR1B15"
                     /gene_synonym="AKR1B10L"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative aldo-keto reductase family 1 member
                     B15"
                     /protein_id="NP_001074007.2"
                     /db_xref="GI:291291012"
                     /db_xref="CCDS:CCDS47715.2"
                     /db_xref="GeneID:441282"
                     /db_xref="HGNC:37281"
     gene            134331531..134364568
                     /gene="BPGM"
                     /gene_synonym="DPGM"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:669"
                     /db_xref="HGNC:1093"
                     /db_xref="MIM:613896"
     mRNA            join(134331531..134331689,134346199..134346860,
                     134363605..134364568)
                     /gene="BPGM"
                     /gene_synonym="DPGM"
                     /product="2,3-bisphosphoglycerate mutase, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001724.4"
                     /db_xref="GI:223718105"
                     /db_xref="GeneID:669"
                     /db_xref="HGNC:1093"
                     /db_xref="HPRD:01961"
                     /db_xref="MIM:613896"
     mRNA            join(134331531..134331689,134343100..134343420,
                     134346199..134346860,134363605..134364568)
                     /gene="BPGM"
                     /gene_synonym="DPGM"
                     /product="2,3-bisphosphoglycerate mutase, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_199186.2"
                     /db_xref="GI:223718101"
                     /db_xref="GeneID:669"
                     /db_xref="HGNC:1093"
                     /db_xref="MIM:613896"
     CDS             join(134346260..134346860,134363605..134363783)
                     /gene="BPGM"
                     /gene_synonym="DPGM"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="bisphosphoglycerate mutase"
                     /protein_id="NP_954655.1"
                     /db_xref="GI:40353764"
                     /db_xref="CCDS:CCDS5833.1"
                     /db_xref="GeneID:669"
                     /db_xref="HGNC:1093"
                     /db_xref="MIM:613896"
     CDS             join(134346260..134346860,134363605..134363783)
                     /gene="BPGM"
                     /gene_synonym="DPGM"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="bisphosphoglycerate mutase"
                     /protein_id="NP_001715.1"
                     /db_xref="GI:4502445"
                     /db_xref="CCDS:CCDS5833.1"
                     /db_xref="GeneID:669"
                     /db_xref="HGNC:1093"
                     /db_xref="MIM:613896"
     gene            134464164..134655480
                     /gene="CALD1"
                     /gene_synonym="CDM; H-CAD; HCAD; L-CAD; LCAD; MGC21352;
                     NAG22"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:800"
                     /db_xref="HGNC:1441"
                     /db_xref="HPRD:00251"
                     /db_xref="MIM:114213"
     mRNA            join(134464164..134464500,134528635..134528722,
                     134552444..134552555,134613505..134613651,
                     134617739..134618828,134620439..134620516,
                     134625843..134625988,134632259..134632520,
                     134635125..134635265,134642820..134642863,
                     134642960..134643041,134644725..134644862,
                     134645284..134645379,134650057..134650137,
                     134653091..134655480)
                     /gene="CALD1"
                     /gene_synonym="CDM; H-CAD; HCAD; L-CAD; LCAD; MGC21352;
                     NAG22"
                     /product="caldesmon 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033138.3"
                     /db_xref="GI:261490655"
                     /db_xref="GeneID:800"
                     /db_xref="HGNC:1441"
                     /db_xref="HPRD:00251"
                     /db_xref="MIM:114213"
     mRNA            join(134464164..134464500,134528635..134528722,
                     134552444..134552555,134613505..134613651,
                     134617739..134618141,134625843..134625988,
                     134632259..134632520,134635125..134635265,
                     134642820..134642863,134642960..134643041,
                     134644725..134644862,134645284..134645379,
                     134650057..134650137,134653091..134655480)
                     /gene="CALD1"
                     /gene_synonym="CDM; H-CAD; HCAD; L-CAD; LCAD; MGC21352;
                     NAG22"
                     /product="caldesmon 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004342.6"
                     /db_xref="GI:261490654"
                     /db_xref="GeneID:800"
                     /db_xref="HGNC:1441"
                     /db_xref="HPRD:00251"
                     /db_xref="MIM:114213"
     mRNA            join(134464164..134464500,134528635..134528722,
                     134552444..134552555,134613505..134613651,
                     134617739..134618141,134620439..134620516,
                     134625843..134625988,134632259..134632520,
                     134635125..134635265,134642820..134642863,
                     134642963..134643041,134644725..134644862,
                     134645284..134645379,134650057..134650137,
                     134653091..134655480)
                     /gene="CALD1"
                     /gene_synonym="CDM; H-CAD; HCAD; L-CAD; LCAD; MGC21352;
                     NAG22"
                     /product="caldesmon 1, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033157.3"
                     /db_xref="GI:261490658"
                     /db_xref="GeneID:800"
                     /db_xref="HGNC:1441"
                     /db_xref="HPRD:00251"
                     /db_xref="MIM:114213"
     CDS             join(134552485..134552555,134613505..134613651,
                     134617739..134618828,134620439..134620516,
                     134625843..134625988,134632259..134632520,
                     134635125..134635265,134642820..134642863,
                     134642960..134643041,134644725..134644862,
                     134645284..134645379,134650057..134650137,
                     134653091..134653096)
                     /gene="CALD1"
                     /gene_synonym="CDM; H-CAD; HCAD; L-CAD; LCAD; MGC21352;
                     NAG22"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caldesmon isoform 1"
                     /protein_id="NP_149129.2"
                     /db_xref="GI:44680105"
                     /db_xref="CCDS:CCDS5835.1"
                     /db_xref="GeneID:800"
                     /db_xref="HGNC:1441"
                     /db_xref="HPRD:00251"
                     /db_xref="MIM:114213"
     CDS             join(134552485..134552555,134613505..134613651,
                     134617739..134618141,134625843..134625988,
                     134632259..134632520,134635125..134635265,
                     134642820..134642863,134642960..134643041,
                     134644725..134644862,134645284..134645379,
                     134650057..134650137,134653091..134653096)
                     /gene="CALD1"
                     /gene_synonym="CDM; H-CAD; HCAD; L-CAD; LCAD; MGC21352;
                     NAG22"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caldesmon isoform 2"
                     /protein_id="NP_004333.1"
                     /db_xref="GI:4826657"
                     /db_xref="CCDS:CCDS5834.1"
                     /db_xref="GeneID:800"
                     /db_xref="HGNC:1441"
                     /db_xref="HPRD:00251"
                     /db_xref="MIM:114213"
     CDS             join(134552485..134552555,134613505..134613651,
                     134617739..134618141,134620439..134620516,
                     134625843..134625988,134632259..134632520,
                     134635125..134635265,134642820..134642863,
                     134642963..134643041,134644725..134644862,
                     134645284..134645379,134650057..134650137,
                     134653091..134653096)
                     /gene="CALD1"
                     /gene_synonym="CDM; H-CAD; HCAD; L-CAD; LCAD; MGC21352;
                     NAG22"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caldesmon isoform 3"
                     /protein_id="NP_149347.2"
                     /db_xref="GI:261490659"
                     /db_xref="CCDS:CCDS5836.2"
                     /db_xref="GeneID:800"
                     /db_xref="HGNC:1441"
                     /db_xref="HPRD:00251"
                     /db_xref="MIM:114213"
     mRNA            join(134576151..134576424,134613505..134613651,
                     134617739..134618141,134620439..134620516,
                     134625843..134625988,134632259..134632520,
                     134635125..134635265,134642820..134642863,
                     134642960..134643041,134644725..134644862,
                     134645284..134645379,134650057..134650137,
                     134653091..134655480)
                     /gene="CALD1"
                     /gene_synonym="CDM; H-CAD; HCAD; L-CAD; LCAD; MGC21352;
                     NAG22"
                     /product="caldesmon 1, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033139.3"
                     /db_xref="GI:261490656"
                     /db_xref="GeneID:800"
                     /db_xref="HGNC:1441"
                     /db_xref="HPRD:00251"
                     /db_xref="MIM:114213"
     mRNA            join(134576151..134576424,134613505..134613651,
                     134617739..134618141,134625843..134625988,
                     134632259..134632520,134635125..134635265,
                     134642820..134642863,134642960..134643041,
                     134644725..134644862,134645284..134645379,
                     134650057..134650137,134653091..134655480)
                     /gene="CALD1"
                     /gene_synonym="CDM; H-CAD; HCAD; L-CAD; LCAD; MGC21352;
                     NAG22"
                     /product="caldesmon 1, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033140.3"
                     /db_xref="GI:261490657"
                     /db_xref="GeneID:800"
                     /db_xref="HGNC:1441"
                     /db_xref="HPRD:00251"
                     /db_xref="MIM:114213"
     CDS             join(134576372..134576424,134613505..134613651,
                     134617739..134618141,134620439..134620516,
                     134625843..134625988,134632259..134632520,
                     134635125..134635265,134642820..134642863,
                     134642960..134643041,134644725..134644862,
                     134645284..134645379,134650057..134650137,
                     134653091..134653096)
                     /gene="CALD1"
                     /gene_synonym="CDM; H-CAD; HCAD; L-CAD; LCAD; MGC21352;
                     NAG22"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caldesmon isoform 4"
                     /protein_id="NP_149130.1"
                     /db_xref="GI:15149463"
                     /db_xref="CCDS:CCDS47716.1"
                     /db_xref="GeneID:800"
                     /db_xref="HGNC:1441"
                     /db_xref="HPRD:00251"
                     /db_xref="MIM:114213"
     CDS             join(134576372..134576424,134613505..134613651,
                     134617739..134618141,134625843..134625988,
                     134632259..134632520,134635125..134635265,
                     134642820..134642863,134642960..134643041,
                     134644725..134644862,134645284..134645379,
                     134650057..134650137,134653091..134653096)
                     /gene="CALD1"
                     /gene_synonym="CDM; H-CAD; HCAD; L-CAD; LCAD; MGC21352;
                     NAG22"
                     /note="isoform 5 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caldesmon isoform 5"
                     /protein_id="NP_149131.1"
                     /db_xref="GI:15149465"
                     /db_xref="CCDS:CCDS47717.1"
                     /db_xref="GeneID:800"
                     /db_xref="HGNC:1441"
                     /db_xref="HPRD:00251"
                     /db_xref="MIM:114213"
     gene            134671259..134820530
                     /gene="AGBL3"
                     /gene_synonym="FLJ12983; MGC32955"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:340351"
                     /db_xref="HGNC:27981"
                     /db_xref="HPRD:14175"
     mRNA            join(134671259..134671452,134672626..134672747,
                     134674001..134674061,134678244..134678429,
                     134701803..134701910,134717595..134717733,
                     134718900..134719679,134722169..134722331,
                     134728776..134728902,134730225..134730325,
                     134730550..134730662,134743920..134743986,
                     134761149..134761220,134764955..134765012,
                     134766471..134766542,134800132..134800363,
                     134819593..134820530)
                     /gene="AGBL3"
                     /gene_synonym="FLJ12983; MGC32955"
                     /product="ATP/GTP binding protein-like 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178563.3"
                     /db_xref="GI:222352157"
                     /db_xref="GeneID:340351"
                     /db_xref="HGNC:27981"
                     /db_xref="HPRD:14175"
     CDS             join(134672685..134672747,134674001..134674061,
                     134678244..134678429,134701803..134701910,
                     134717595..134717733,134718900..134719679,
                     134722169..134722331,134728776..134728902,
                     134730225..134730325,134730550..134730662,
                     134743920..134743986,134761149..134761220,
                     134764955..134765012,134766471..134766542,
                     134800132..134800363,134819593..134820013)
                     /gene="AGBL3"
                     /gene_synonym="FLJ12983; MGC32955"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cytosolic carboxypeptidase 3"
                     /protein_id="NP_848658.3"
                     /db_xref="GI:222352158"
                     /db_xref="CCDS:CCDS47718.1"
                     /db_xref="GeneID:340351"
                     /db_xref="HGNC:27981"
                     /db_xref="HPRD:14175"
     gene            complement(134778131..134833045)
                     /gene="LOC653739"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 mRNAs, 3 ESTs, 1 Protein"
                     /db_xref="GeneID:653739"
     misc_RNA        complement(join(134778131..134779334,
                     134832729..134833045))
                     /gene="LOC653739"
                     /product="hypothetical LOC653739"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 mRNAs, 3 ESTs, 1 Protein"
                     /transcript_id="XR_108832.1"
                     /db_xref="GI:310120102"
                     /db_xref="GeneID:653739"
     gene            134813198..134814441
                     /gene="LOC100419645"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100419645"
     gene            134832766..134850967
                     /gene="TMEM140"
                     /gene_synonym="FLJ11000"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55281"
                     /db_xref="HGNC:21870"
                     /db_xref="HPRD:07723"
     mRNA            join(134832766..134833022,134849170..134850967)
                     /gene="TMEM140"
                     /gene_synonym="FLJ11000"
                     /product="transmembrane protein 140"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018295.3"
                     /db_xref="GI:256355110"
                     /db_xref="GeneID:55281"
                     /db_xref="HGNC:21870"
                     /db_xref="HPRD:07723"
     CDS             134849194..134849751
                     /gene="TMEM140"
                     /gene_synonym="FLJ11000"
                     /exception="mismatches in translation"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 140"
                     /protein_id="NP_060765.3"
                     /db_xref="GI:256355111"
                     /db_xref="CCDS:CCDS5837.1"
                     /db_xref="GeneID:55281"
                     /db_xref="HGNC:21870"
                     /db_xref="HPRD:07723"
     gene            complement(134850532..134855532)
                     /gene="C7orf49"
                     /gene_synonym="FLJ22450; FLJ27285; MGC5242; MRI"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:78996"
                     /db_xref="HGNC:22432"
                     /db_xref="HPRD:08333"
     mRNA            complement(join(134850532..134851623,134852484..134852559,
                     134853538..134853812,134855404..134855532))
                     /gene="C7orf49"
                     /gene_synonym="FLJ22450; FLJ27285; MGC5242; MRI"
                     /product="chromosome 7 open reading frame 49, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024033.2"
                     /db_xref="GI:208022702"
                     /db_xref="GeneID:78996"
                     /db_xref="HGNC:22432"
                     /db_xref="HPRD:08333"
     misc_RNA        complement(join(134850532..134851623,134852484..134852559,
                     134853501..134853812,134855151..134855532))
                     /gene="C7orf49"
                     /gene_synonym="FLJ22450; FLJ27285; MGC5242; MRI"
                     /product="chromosome 7 open reading frame 49, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024185.1"
                     /db_xref="GI:208022704"
                     /db_xref="GeneID:78996"
                     /db_xref="HGNC:22432"
                     /db_xref="HPRD:08333"
     misc_RNA        complement(join(134850532..134851623,134852484..134852559,
                     134853501..134853812,134855404..134855532))
                     /gene="C7orf49"
                     /gene_synonym="FLJ22450; FLJ27285; MGC5242; MRI"
                     /product="chromosome 7 open reading frame 49, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024186.1"
                     /db_xref="GI:208022705"
                     /db_xref="GeneID:78996"
                     /db_xref="HGNC:22432"
                     /db_xref="HPRD:08333"
     CDS             complement(join(134851363..134851623,134852484..134852559,
                     134853538..134853674))
                     /gene="C7orf49"
                     /gene_synonym="FLJ22450; FLJ27285; MGC5242; MRI"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="modulator of retrovirus infection homolog"
                     /protein_id="NP_076938.2"
                     /db_xref="GI:208022703"
                     /db_xref="CCDS:CCDS5838.2"
                     /db_xref="GeneID:78996"
                     /db_xref="HGNC:22432"
                     /db_xref="HPRD:08333"
     gene            complement(134868590..134896316)
                     /gene="WDR91"
                     /gene_synonym="HSPC049"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:29062"
                     /db_xref="HGNC:24997"
                     /db_xref="HPRD:11035"
     mRNA            complement(join(134868590..134871067,134871724..134871921,
                     134873185..134873297,134874096..134874204,
                     134877983..134878151,134878330..134878424,
                     134879686..134879836,134880896..134881089,
                     134882745..134882903,134889020..134889185,
                     134890680..134890810,134891872..134891954,
                     134893543..134893750,134894328..134894507,
                     134896132..134896316))
                     /gene="WDR91"
                     /gene_synonym="HSPC049"
                     /product="WD repeat domain 91"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014149.3"
                     /db_xref="GI:222080091"
                     /db_xref="GeneID:29062"
                     /db_xref="HGNC:24997"
                     /db_xref="HPRD:11035"
     CDS             complement(join(134870903..134871067,134871724..134871921,
                     134873185..134873297,134874096..134874204,
                     134877983..134878151,134878330..134878424,
                     134879686..134879836,134880896..134881089,
                     134882745..134882903,134889020..134889185,
                     134890680..134890810,134891872..134891954,
                     134893543..134893750,134894328..134894507,
                     134896132..134896254))
                     /gene="WDR91"
                     /gene_synonym="HSPC049"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="WD repeat-containing protein 91"
                     /protein_id="NP_054868.3"
                     /db_xref="GI:222080092"
                     /db_xref="CCDS:CCDS34758.1"
                     /db_xref="GeneID:29062"
                     /db_xref="HGNC:24997"
                     /db_xref="HPRD:11035"
     gene            134916731..134943244
                     /gene="STRA8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:346673"
                     /db_xref="HGNC:30653"
                     /db_xref="HPRD:18123"
                     /db_xref="MIM:609987"
     mRNA            join(134916731..134916790,134925271..134925468,
                     134927533..134927608,134928078..134928162,
                     134930055..134930081,134931169..134931454,
                     134936548..134936621,134939866..134939977,
                     134943170..134943244)
                     /gene="STRA8"
                     /product="stimulated by retinoic acid gene 8 homolog
                     (mouse)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_182489.1"
                     /db_xref="GI:32698789"
                     /db_xref="GeneID:346673"
                     /db_xref="HGNC:30653"
                     /db_xref="HPRD:18123"
                     /db_xref="MIM:609987"
     CDS             join(134916731..134916790,134925271..134925468,
                     134927533..134927608,134928078..134928162,
                     134930055..134930081,134931169..134931454,
                     134936548..134936621,134939866..134939977,
                     134943170..134943244)
                     /gene="STRA8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="stimulated by retinoic acid gene 8 protein
                     homolog"
                     /protein_id="NP_872295.1"
                     /db_xref="GI:32698790"
                     /db_xref="CCDS:CCDS5839.1"
                     /db_xref="GeneID:346673"
                     /db_xref="HGNC:30653"
                     /db_xref="HPRD:18123"
                     /db_xref="MIM:609987"
     gene            complement(134961969..134998313)
                     /gene="SLC23A4P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:641842"
                     /db_xref="HGNC:20602"
     gene            complement(135046547..135194875)
                     /gene="CNOT4"
                     /gene_synonym="CLONE243; NOT4; NOT4H"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4850"
                     /db_xref="HGNC:7880"
                     /db_xref="HPRD:05369"
                     /db_xref="MIM:604911"
     mRNA            complement(join(135046547..135047938,135078670..135079167,
                     135080386..135080635,135082921..135082978,
                     135095274..135095398,135098237..135098362,
                     135099080..135099181,135099925..135100011,
                     135106905..135107102,135122906..135123171,
                     135194637..135194875))
                     /gene="CNOT4"
                     /gene_synonym="CLONE243; NOT4; NOT4H"
                     /product="CCR4-NOT transcription complex, subunit 4,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013316.3"
                     /db_xref="GI:300069008"
                     /db_xref="GeneID:4850"
                     /db_xref="HGNC:7880"
                     /db_xref="HPRD:05369"
                     /db_xref="MIM:604911"
     mRNA            complement(join(135046547..135047938,135078670..135079167,
                     135080386..135080635,135082921..135082978,
                     135095265..135095398,135098237..135098362,
                     135099080..135099181,135099925..135100011,
                     135106905..135107102,135122906..135123171,
                     135194637..135194875))
                     /gene="CNOT4"
                     /gene_synonym="CLONE243; NOT4; NOT4H"
                     /product="CCR4-NOT transcription complex, subunit 4,
                     transcript variant 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001190847.1"
                     /db_xref="GI:300069010"
                     /db_xref="GeneID:4850"
                     /db_xref="HGNC:7880"
                     /db_xref="MIM:604911"
                     /db_xref="HPRD:05369"
     mRNA            complement(join(135046547..135047938,135048606..135048818,
                     135078670..135079167,135080386..135080635,
                     135082921..135082978,135095274..135095398,
                     135098237..135098362,135099080..135099181,
                     135099925..135100011,135106905..135107102,
                     135122906..135123171,135194637..135194875))
                     /gene="CNOT4"
                     /gene_synonym="CLONE243; NOT4; NOT4H"
                     /product="CCR4-NOT transcription complex, subunit 4,
                     transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001190849.1"
                     /db_xref="GI:300069014"
                     /db_xref="GeneID:4850"
                     /db_xref="HGNC:7880"
                     /db_xref="MIM:604911"
                     /db_xref="HPRD:05369"
     mRNA            complement(join(135046547..135047938,135048606..135048818,
                     135078670..135079167,135080386..135080635,
                     135082921..135082978,135095265..135095398,
                     135098237..135098362,135099080..135099181,
                     135099925..135100011,135106905..135107102,
                     135122906..135123171,135194637..135194875))
                     /gene="CNOT4"
                     /gene_synonym="CLONE243; NOT4; NOT4H"
                     /product="CCR4-NOT transcription complex, subunit 4,
                     transcript variant 6"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001190850.1"
                     /db_xref="GI:300069016"
                     /db_xref="GeneID:4850"
                     /db_xref="HGNC:7880"
                     /db_xref="MIM:604911"
                     /db_xref="HPRD:05369"
     CDS             complement(join(135047637..135047938,135078670..135079167,
                     135080386..135080635,135082921..135082978,
                     135095274..135095398,135098237..135098362,
                     135099080..135099181,135099925..135100011,
                     135106905..135107102,135122906..135123079))
                     /gene="CNOT4"
                     /gene_synonym="CLONE243; NOT4; NOT4H"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="CCR4-NOT transcription complex subunit 4 isoform
                     a"
                     /protein_id="NP_037448.2"
                     /db_xref="GI:56550057"
                     /db_xref="CCDS:CCDS43650.1"
                     /db_xref="GeneID:4850"
                     /db_xref="HGNC:7880"
                     /db_xref="HPRD:05369"
                     /db_xref="MIM:604911"
     CDS             complement(join(135047637..135047938,135078670..135079167,
                     135080386..135080635,135082921..135082978,
                     135095265..135095398,135098237..135098362,
                     135099080..135099181,135099925..135100011,
                     135106905..135107102,135122906..135123079))
                     /gene="CNOT4"
                     /gene_synonym="CLONE243; NOT4; NOT4H"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="CCR4-NOT transcription complex subunit 4 isoform
                     c"
                     /protein_id="NP_001177776.1"
                     /db_xref="GI:300069011"
                     /db_xref="CCDS:CCDS55164.1"
                     /db_xref="GeneID:4850"
                     /db_xref="HGNC:7880"
                     /db_xref="HPRD:05369"
                     /db_xref="MIM:604911"
     CDS             complement(join(135047637..135047938,135048606..135048818,
                     135078670..135079167,135080386..135080635,
                     135082921..135082978,135095274..135095398,
                     135098237..135098362,135099080..135099181,
                     135099925..135100011,135106905..135107102,
                     135122906..135123079))
                     /gene="CNOT4"
                     /gene_synonym="CLONE243; NOT4; NOT4H"
                     /note="isoform e is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="CCR4-NOT transcription complex subunit 4 isoform
                     e"
                     /protein_id="NP_001177778.1"
                     /db_xref="GI:300069015"
                     /db_xref="CCDS:CCDS55167.1"
                     /db_xref="GeneID:4850"
                     /db_xref="HGNC:7880"
                     /db_xref="HPRD:05369"
                     /db_xref="MIM:604911"
     CDS             complement(join(135047637..135047938,135048606..135048818,
                     135078670..135079167,135080386..135080635,
                     135082921..135082978,135095265..135095398,
                     135098237..135098362,135099080..135099181,
                     135099925..135100011,135106905..135107102,
                     135122906..135123079))
                     /gene="CNOT4"
                     /gene_synonym="CLONE243; NOT4; NOT4H"
                     /note="isoform f is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="CCR4-NOT transcription complex subunit 4 isoform
                     f"
                     /protein_id="NP_001177779.1"
                     /db_xref="GI:300069017"
                     /db_xref="CCDS:CCDS55165.1"
                     /db_xref="GeneID:4850"
                     /db_xref="HGNC:7880"
                     /db_xref="HPRD:05369"
                     /db_xref="MIM:604911"
     mRNA            complement(join(135071822..135073646,135078670..135079167,
                     135080386..135080635,135082921..135082978,
                     135095274..135095398,135098237..135098362,
                     135099080..135099181,135099925..135100011,
                     135106905..135107102,135122906..135123171,
                     135194637..135194875))
                     /gene="CNOT4"
                     /gene_synonym="CLONE243; NOT4; NOT4H"
                     /product="CCR4-NOT transcription complex, subunit 4,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001008225.2"
                     /db_xref="GI:300069009"
                     /db_xref="GeneID:4850"
                     /db_xref="HGNC:7880"
                     /db_xref="MIM:604911"
                     /db_xref="HPRD:05369"
     mRNA            complement(join(135071822..135073646,135078670..135079167,
                     135080386..135080635,135082921..135082978,
                     135095265..135095398,135098237..135098362,
                     135099080..135099181,135099925..135100011,
                     135106905..135107102,135122906..135123171,
                     135194637..135194875))
                     /gene="CNOT4"
                     /gene_synonym="CLONE243; NOT4; NOT4H"
                     /product="CCR4-NOT transcription complex, subunit 4,
                     transcript variant 4"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001190848.1"
                     /db_xref="GI:300069012"
                     /db_xref="GeneID:4850"
                     /db_xref="HGNC:7880"
                     /db_xref="MIM:604911"
                     /db_xref="HPRD:05369"
     CDS             complement(join(135073546..135073646,135078670..135079167,
                     135080386..135080635,135082921..135082978,
                     135095274..135095398,135098237..135098362,
                     135099080..135099181,135099925..135100011,
                     135106905..135107102,135122906..135123079))
                     /gene="CNOT4"
                     /gene_synonym="CLONE243; NOT4; NOT4H"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="CCR4-NOT transcription complex subunit 4 isoform
                     b"
                     /protein_id="NP_001008226.1"
                     /db_xref="GI:56550059"
                     /db_xref="CCDS:CCDS47719.1"
                     /db_xref="GeneID:4850"
                     /db_xref="HGNC:7880"
                     /db_xref="HPRD:05369"
                     /db_xref="MIM:604911"
     CDS             complement(join(135073546..135073646,135078670..135079167,
                     135080386..135080635,135082921..135082978,
                     135095265..135095398,135098237..135098362,
                     135099080..135099181,135099925..135100011,
                     135106905..135107102,135122906..135123079))
                     /gene="CNOT4"
                     /gene_synonym="CLONE243; NOT4; NOT4H"
                     /note="isoform d is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="CCR4-NOT transcription complex subunit 4 isoform
                     d"
                     /protein_id="NP_001177777.1"
                     /db_xref="GI:300069013"
                     /db_xref="CCDS:CCDS55166.1"
                     /db_xref="GeneID:4850"
                     /db_xref="HGNC:7880"
                     /db_xref="HPRD:05369"
                     /db_xref="MIM:604911"
     gene            135129188..135130488
                     /gene="SDHDP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:647081"
                     /db_xref="HGNC:10685"
     gene            135242662..135333501
                     /gene="NUP205"
                     /gene_synonym="C7orf14"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23165"
                     /db_xref="HGNC:18658"
                     /db_xref="HPRD:17653"
     mRNA            join(135242662..135242720,135255853..135255995,
                     135258402..135258573,135261018..135261162,
                     135261717..135261876,135262544..135262772,
                     135263499..135263663,135269580..135269755,
                     135272323..135272439,135272603..135272740,
                     135276198..135276348,135277735..135277940,
                     135279295..135279477,135282116..135282166,
                     135282746..135282955,135285618..135285717,
                     135286118..135286255,135287553..135287742,
                     135289088..135289208,135290893..135290974,
                     135291499..135291663,135291995..135292119,
                     135298907..135299021,135300664..135300813,
                     135301403..135301474,135301838..135301995,
                     135302350..135302430,135303160..135303351,
                     135304171..135304438,135304538..135304636,
                     135307525..135307673,135309912..135310103,
                     135310988..135311109,135312721..135312859,
                     135315092..135315218,135320329..135320405,
                     135322679..135322807,135323305..135323431,
                     135327940..135328106,135329643..135329766,
                     135330216..135330344,135330906..135330979,
                     135333152..135333501)
                     /gene="NUP205"
                     /gene_synonym="C7orf14"
                     /product="nucleoporin 205kDa"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015135.2"
                     /db_xref="GI:223468614"
                     /db_xref="GeneID:23165"
                     /db_xref="HGNC:18658"
                     /db_xref="HPRD:17653"
     CDS             join(135242693..135242720,135255853..135255995,
                     135258402..135258573,135261018..135261162,
                     135261717..135261876,135262544..135262772,
                     135263499..135263663,135269580..135269755,
                     135272323..135272439,135272603..135272740,
                     135276198..135276348,135277735..135277940,
                     135279295..135279477,135282116..135282166,
                     135282746..135282955,135285618..135285717,
                     135286118..135286255,135287553..135287742,
                     135289088..135289208,135290893..135290974,
                     135291499..135291663,135291995..135292119,
                     135298907..135299021,135300664..135300813,
                     135301403..135301474,135301838..135301995,
                     135302350..135302430,135303160..135303351,
                     135304171..135304438,135304538..135304636,
                     135307525..135307673,135309912..135310103,
                     135310988..135311109,135312721..135312859,
                     135315092..135315218,135320329..135320405,
                     135322679..135322807,135323305..135323431,
                     135327940..135328106,135329643..135329766,
                     135330216..135330344,135330906..135330979,
                     135333152..135333304)
                     /gene="NUP205"
                     /gene_synonym="C7orf14"
                     /exception="mismatches in translation"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="nuclear pore complex protein Nup205"
                     /protein_id="NP_055950.1"
                     /db_xref="GI:57634534"
                     /db_xref="CCDS:CCDS34759.1"
                     /db_xref="GeneID:23165"
                     /db_xref="HGNC:18658"
                     /db_xref="HPRD:17653"
     gene            135344786..135345400
                     /gene="RPL15P11"
                     /gene_synonym="RPL15_5_851"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402694"
                     /db_xref="HGNC:36093"
     gene            135347221..135361160
                     /gene="PL-5283"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:647087"
     mRNA            join(135347221..135347342,135357501..135357554,
                     135358839..135361160)
                     /gene="PL-5283"
                     /product="PL-5283 protein"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130929.1"
                     /db_xref="GI:195963434"
                     /db_xref="GeneID:647087"
     CDS             join(135347328..135347342,135357501..135357554,
                     135358839..135358913)
                     /gene="PL-5283"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="PL-5283 protein"
                     /protein_id="NP_001124401.1"
                     /db_xref="GI:195963435"
                     /db_xref="CCDS:CCDS55168.1"
                     /db_xref="GeneID:647087"
     gene            complement(135365985..135412933)
                     /gene="SLC13A4"
                     /gene_synonym="SUT-1; SUT1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26266"
                     /db_xref="HGNC:15827"
                     /db_xref="HPRD:10372"
                     /db_xref="MIM:604309"
     mRNA            complement(join(135365985..135366448,135368872..135369009,
                     135370270..135370431,135375949..135376073,
                     135376296..135376393,135377071..135377172,
                     135378885..135378986,135380116..135380235,
                     135384112..135384296,135386428..135386508,
                     135387593..135387629,135390344..135390398,
                     135390876..135391048,135392862..135392998,
                     135406143..135406271,135412146..135412933))
                     /gene="SLC13A4"
                     /gene_synonym="SUT-1; SUT1"
                     /product="solute carrier family 13 (sodium/sulfate
                     symporters), member 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012450.2"
                     /db_xref="GI:31795545"
                     /db_xref="GeneID:26266"
                     /db_xref="HGNC:15827"
                     /db_xref="HPRD:10372"
                     /db_xref="MIM:604309"
     CDS             complement(join(135366311..135366448,135368872..135369009,
                     135370270..135370431,135375949..135376073,
                     135376296..135376393,135377071..135377172,
                     135378885..135378986,135380116..135380235,
                     135384112..135384296,135386428..135386508,
                     135387593..135387629,135390344..135390398,
                     135390876..135391048,135392862..135392998,
                     135406143..135406271,135412146..135412244))
                     /gene="SLC13A4"
                     /gene_synonym="SUT-1; SUT1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="solute carrier family 13 member 4"
                     /protein_id="NP_036582.2"
                     /db_xref="GI:31795546"
                     /db_xref="CCDS:CCDS5840.1"
                     /db_xref="GeneID:26266"
                     /db_xref="HGNC:15827"
                     /db_xref="HPRD:10372"
                     /db_xref="MIM:604309"
     gene            complement(135414346..135433594)
                     /gene="FAM180A"
                     /gene_synonym="UNQ1940"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:389558"
                     /db_xref="HGNC:33773"
                     /db_xref="HPRD:15613"
     mRNA            complement(join(135414346..135415029,135418394..135419067,
                     135421847..135421947,135433253..135433594))
                     /gene="FAM180A"
                     /gene_synonym="UNQ1940"
                     /product="family with sequence similarity 180, member A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_205855.3"
                     /db_xref="GI:253795478"
                     /db_xref="GeneID:389558"
                     /db_xref="HGNC:33773"
                     /db_xref="HPRD:15613"
     CDS             complement(join(135418723..135419067,135421847..135421947,
                     135433253..135433328))
                     /gene="FAM180A"
                     /gene_synonym="UNQ1940"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC389558 precursor"
                     /protein_id="NP_995327.1"
                     /db_xref="GI:45504351"
                     /db_xref="CCDS:CCDS5841.1"
                     /db_xref="GeneID:389558"
                     /db_xref="HGNC:33773"
                     /db_xref="HPRD:15613"
     gene            135611203..135617629
                     /gene="LOC100506957"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 9 ESTs"
                     /db_xref="GeneID:100506957"
     misc_RNA        join(135611203..135611333,135616957..135617629)
                     /gene="LOC100506957"
                     /product="hypothetical LOC100506957"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 9 ESTs"
                     /transcript_id="XR_108821.1"
                     /db_xref="GI:310120103"
                     /db_xref="GeneID:100506957"
     gene            complement(135611503..135662204)
                     /gene="LUZP6"
                     /gene_synonym="MPD6; MTPNUT"
                     /note="dicistronic gene; Derived by automated
                     computational analysis using gene prediction method:
                     BestRefseq."
                     /db_xref="GeneID:767558"
                     /db_xref="HGNC:33955"
                     /db_xref="MIM:611050"
     gene            complement(135611503..135662204)
                     /gene="MTPN"
                     /gene_synonym="FLJ31098; FLJ99857; GCDP; V-1"
                     /note="dicistronic gene; Derived by automated
                     computational analysis using gene prediction method:
                     BestRefseq."
                     /db_xref="GeneID:136319"
                     /db_xref="HGNC:15667"
                     /db_xref="HPRD:07574"
                     /db_xref="MIM:606484"
     mRNA            complement(join(135611503..135614760,135635347..135635430,
                     135636265..135636378,135661777..135662204))
                     /gene="LUZP6"
                     /gene_synonym="MPD6; MTPNUT"
                     /product="leucine zipper protein 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001128619.1"
                     /db_xref="GI:190886450"
                     /db_xref="GeneID:767558"
                     /db_xref="HGNC:33955"
                     /db_xref="MIM:611050"
     mRNA            complement(join(135611503..135614760,135635347..135635430,
                     135636265..135636378,135661777..135662204))
                     /gene="MTPN"
                     /gene_synonym="FLJ31098; FLJ99857; GCDP; V-1"
                     /product="myotrophin"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145808.3"
                     /db_xref="GI:190886458"
                     /db_xref="GeneID:136319"
                     /db_xref="HGNC:15667"
                     /db_xref="HPRD:07574"
                     /db_xref="MIM:606484"
     CDS             complement(135612022..135612198)
                     /gene="LUZP6"
                     /gene_synonym="MPD6; MTPNUT"
                     /note="non-AUG (ATT) translation initiation codon; non-AUG
                     (AUU) translation initiation codon; Derived by automated
                     computational analysis using gene prediction method:
                     BestRefseq."
                     /codon_start=1
                     /transl_except=(pos:complement(135612196..135612198),
                     aa:Met)
                     /product="leucine zipper protein 6"
                     /protein_id="NP_001122091.2"
                     /db_xref="GI:301898339"
                     /db_xref="GeneID:767558"
                     /db_xref="HGNC:33955"
                     /db_xref="MIM:611050"
     CDS             complement(join(135614674..135614760,135635347..135635430,
                     135636265..135636378,135661777..135661848))
                     /gene="MTPN"
                     /gene_synonym="FLJ31098; FLJ99857; GCDP; V-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="myotrophin"
                     /protein_id="NP_665807.1"
                     /db_xref="GI:21956645"
                     /db_xref="CCDS:CCDS5842.1"
                     /db_xref="GeneID:136319"
                     /db_xref="HGNC:15667"
                     /db_xref="HPRD:07574"
                     /db_xref="MIM:606484"
     gene            136170787..136171313
                     /gene="LOC100421642"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421642"
     gene            136398573..136400158
                     /gene="PSMC1P3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392100"
                     /db_xref="HGNC:39778"
     gene            136553399..136701771
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     mRNA            join(136553399..136553739,136554008..136554165,
                     136676934..136677011,136699567..136701771)
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /product="cholinergic receptor, muscarinic 2, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001006630.1"
                     /db_xref="GI:54792112"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     mRNA            join(136553399..136553739,136554008..136554165,
                     136699567..136701771)
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /product="cholinergic receptor, muscarinic 2, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001006627.1"
                     /db_xref="GI:54792106"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     mRNA            join(136553832..136553920,136554008..136554165,
                     136676934..136677011,136699567..136701771)
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /product="cholinergic receptor, muscarinic 2, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000739.2"
                     /db_xref="GI:54792103"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     mRNA            join(136553832..136553864,136554008..136554165,
                     136676934..136677011,136699567..136701771)
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /product="cholinergic receptor, muscarinic 2, transcript
                     variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001006631.1"
                     /db_xref="GI:54792114"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     mRNA            join(136553832..136553920,136554008..136554165,
                     136699567..136701771)
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /product="cholinergic receptor, muscarinic 2, transcript
                     variant 7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001006632.1"
                     /db_xref="GI:54792116"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     mRNA            join(136553869..136553920,136554008..136554165,
                     136635750..136635827,136676934..136677011,
                     136699567..136701771)
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /product="cholinergic receptor, muscarinic 2, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001006626.1"
                     /db_xref="GI:54792104"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     mRNA            join(136553984..136554165,136699567..136701771)
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /product="cholinergic receptor, muscarinic 2, transcript
                     variant 8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001006629.1"
                     /db_xref="GI:54792110"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     mRNA            join(136553993..136554165,136676934..136677011,
                     136699567..136701771)
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /product="cholinergic receptor, muscarinic 2, transcript
                     variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001006628.1"
                     /db_xref="GI:54792108"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     gene            136587914..136588041
                     /gene="MIR490"
                     /gene_synonym="hsa-mir-490; MIRN490"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:574443"
                     /db_xref="HGNC:32075"
                     /db_xref="miRBase:MI0003125"
     ncRNA           136587914..136588041
                     /gene="MIR490"
                     /gene_synonym="hsa-mir-490; MIRN490"
                     /ncRNA_class="miRNA"
                     /product="microRNA 490"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_030165.1"
                     /db_xref="GI:262205171"
                     /db_xref="GeneID:574443"
                     /db_xref="HGNC:32075"
                     /db_xref="miRBase:MI0003125"
     ncRNA           136587914..136588041
                     /gene="MIR490"
                     /gene_synonym="hsa-mir-490; MIRN490"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-490"
                     /inference="similar to RNA sequence:INSD: AY882316"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:574443"
                     /db_xref="miRBase:MI0003125"
                     /db_xref="HGNC:32075"
     CDS             136699613..136701013
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="muscarinic acetylcholine receptor M2"
                     /protein_id="NP_000730.1"
                     /db_xref="GI:4502817"
                     /db_xref="CCDS:CCDS5843.1"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     CDS             136699613..136701013
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="muscarinic acetylcholine receptor M2"
                     /protein_id="NP_001006627.1"
                     /db_xref="GI:54792105"
                     /db_xref="CCDS:CCDS5843.1"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     CDS             136699613..136701013
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="muscarinic acetylcholine receptor M2"
                     /protein_id="NP_001006628.1"
                     /db_xref="GI:54792107"
                     /db_xref="CCDS:CCDS5843.1"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     CDS             136699613..136701013
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="muscarinic acetylcholine receptor M2"
                     /protein_id="NP_001006629.1"
                     /db_xref="GI:54792109"
                     /db_xref="CCDS:CCDS5843.1"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     CDS             136699613..136701013
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="muscarinic acetylcholine receptor M2"
                     /protein_id="NP_001006630.1"
                     /db_xref="GI:54792111"
                     /db_xref="CCDS:CCDS5843.1"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     CDS             136699613..136701013
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="muscarinic acetylcholine receptor M2"
                     /protein_id="NP_001006631.1"
                     /db_xref="GI:54792113"
                     /db_xref="CCDS:CCDS5843.1"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     CDS             136699613..136701013
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="muscarinic acetylcholine receptor M2"
                     /protein_id="NP_001006632.1"
                     /db_xref="GI:54792115"
                     /db_xref="CCDS:CCDS5843.1"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     CDS             136699613..136701013
                     /gene="CHRM2"
                     /gene_synonym="FLJ43243; HM2; MGC120006; MGC120007"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="muscarinic acetylcholine receptor M2"
                     /protein_id="NP_001006633.1"
                     /db_xref="GI:54792117"
                     /db_xref="CCDS:CCDS5843.1"
                     /db_xref="GeneID:1129"
                     /db_xref="HGNC:1951"
                     /db_xref="HPRD:00328"
                     /db_xref="MIM:118493"
     gene            136848778..136849395
                     /gene="RPL18P5"
                     /gene_synonym="RPL18_3_852"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100270944"
                     /db_xref="HGNC:36425"
     gene            complement(136912088..137028546)
                     /gene="PTN"
                     /gene_synonym="HARP; HBGF8; HBNF; NEGF1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5764"
                     /db_xref="HGNC:9630"
                     /db_xref="HPRD:01199"
                     /db_xref="MIM:162095"
     mRNA            complement(join(136912088..136912822,136935977..136936138,
                     136938211..136938384,136939606..136939721,
                     137028185..137028546))
                     /gene="PTN"
                     /gene_synonym="HARP; HBGF8; HBNF; NEGF1"
                     /product="pleiotrophin"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002825.5"
                     /db_xref="GI:42476152"
                     /db_xref="GeneID:5764"
                     /db_xref="HGNC:9630"
                     /db_xref="HPRD:01199"
                     /db_xref="MIM:162095"
     CDS             complement(join(136912767..136912822,136935977..136936138,
                     136938211..136938384,136939606..136939720))
                     /gene="PTN"
                     /gene_synonym="HARP; HBGF8; HBNF; NEGF1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="pleiotrophin"
                     /protein_id="NP_002816.1"
                     /db_xref="GI:4506281"
                     /db_xref="CCDS:CCDS5844.1"
                     /db_xref="GeneID:5764"
                     /db_xref="HGNC:9630"
                     /db_xref="HPRD:01199"
                     /db_xref="MIM:162095"
     gene            136936018..136939712
                     /gene="LOC100287705"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /db_xref="GeneID:100287705"
     mRNA            join(136936018..136936144,136938205..136938384,
                     136939606..136939712)
                     /gene="LOC100287705"
                     /product="hypothetical protein LOC100287705"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /transcript_id="XM_002342757.1"
                     /db_xref="GI:239743353"
                     /db_xref="GeneID:100287705"
     CDS             join(136936018..136936144,136938205..136938384,
                     136939606..136939712)
                     /gene="LOC100287705"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="hypothetical protein LOC100287705"
                     /protein_id="XP_002342798.1"
                     /db_xref="GI:239743354"
                     /db_xref="GeneID:100287705"
     gene            137003339..137011700
                     /gene="LOC100507000"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 5 ESTs"
                     /db_xref="GeneID:100507000"
     misc_RNA        join(137003339..137003604,137010132..137011700)
                     /gene="LOC100507000"
                     /product="hypothetical LOC100507000"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 5 ESTs"
                     /transcript_id="XR_108822.1"
                     /db_xref="GI:310120104"
                     /db_xref="GeneID:100507000"
     gene            complement(137074385..137531609)
                     /gene="DGKI"
                     /gene_synonym="DGK-IOTA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9162"
                     /db_xref="HGNC:2855"
                     /db_xref="HPRD:07238"
                     /db_xref="MIM:604072"
     mRNA            complement(join(137074385..137076082,137080344..137080443,
                     137082123..137082159,137092621..137092741,
                     137096916..137096953,137128823..137128848,
                     137148235..137148357,137150654..137150781,
                     137151648..137151658,137154296..137154365,
                     137170120..137170164,137172356..137172435,
                     137178529..137178582,137206612..137206712,
                     137237115..137237314,137255921..137256032,
                     137257511..137257584,137261968..137262030,
                     137263016..137263071,137266596..137266674,
                     137269955..137270092,137271843..137271956,
                     137282593..137282653,137284569..137284651,
                     137293712..137293810,137294281..137294355,
                     137304570..137304686,137308229..137308300,
                     137330218..137330283,137339478..137339534,
                     137341212..137341286,137363303..137363398,
                     137374640..137374748,137531208..137531609))
                     /gene="DGKI"
                     /gene_synonym="DGK-IOTA"
                     /product="diacylglycerol kinase, iota"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004717.2"
                     /db_xref="GI:32483395"
                     /db_xref="GeneID:9162"
                     /db_xref="HGNC:2855"
                     /db_xref="HPRD:07238"
                     /db_xref="MIM:604072"
     CDS             complement(join(137075966..137076082,137080344..137080443,
                     137082123..137082159,137092621..137092741,
                     137096916..137096953,137128823..137128848,
                     137148235..137148357,137150654..137150781,
                     137151648..137151658,137154296..137154365,
                     137170120..137170164,137172356..137172435,
                     137178529..137178582,137206612..137206712,
                     137237115..137237314,137255921..137256032,
                     137257511..137257584,137261968..137262030,
                     137263016..137263071,137266596..137266674,
                     137269955..137270092,137271843..137271956,
                     137282593..137282653,137284569..137284651,
                     137293712..137293810,137294281..137294355,
                     137304570..137304686,137308229..137308300,
                     137330218..137330283,137339478..137339534,
                     137341212..137341286,137363303..137363398,
                     137374640..137374748,137531208..137531608))
                     /gene="DGKI"
                     /gene_synonym="DGK-IOTA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="diacylglycerol kinase iota"
                     /protein_id="NP_004708.1"
                     /db_xref="GI:4758156"
                     /db_xref="CCDS:CCDS5845.1"
                     /db_xref="GeneID:9162"
                     /db_xref="HGNC:2855"
                     /db_xref="HPRD:07238"
                     /db_xref="MIM:604072"
     gene            137184049..137199006
                     /gene="LOC100652998"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 66 ESTs"
                     /db_xref="GeneID:100652998"
     misc_RNA        join(137184049..137184060,137198578..137199006)
                     /gene="LOC100652998"
                     /product="hypothetical LOC100652998"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 66 ESTs"
                     /transcript_id="XR_132535.1"
                     /db_xref="GI:341915391"
                     /db_xref="GeneID:100652998"
     gene            complement(137352554..137354168)
                     /gene="NAG20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 6 ESTs, 1 Protein"
                     /db_xref="GeneID:100129703"
     misc_RNA        complement(137352554..137354168)
                     /gene="NAG20"
                     /product="NAG20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 6 ESTs, 1 Protein"
                     /transcript_id="XR_108823.1"
                     /db_xref="GI:310120105"
                     /db_xref="GeneID:100129703"
     gene            137404799..137407632
                     /gene="RPL6P19"
                     /gene_synonym="RPL6_14_853"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:646483"
                     /db_xref="HGNC:36754"
     gene            complement(137559725..137686846)
                     /gene="CREB3L2"
                     /gene_synonym="BBF2H7; MGC131709; MGC71006"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64764"
                     /db_xref="HGNC:23720"
                     /db_xref="HPRD:16391"
                     /db_xref="MIM:608834"
     mRNA            complement(join(137559725..137565297,137567158..137567374,
                     137569741..137569867,137570149..137570248,
                     137586100..137586168,137588705..137588763,
                     137590448..137590594,137592998..137593182,
                     137597737..137597824,137600583..137600758,
                     137612896..137613112,137686350..137686846))
                     /gene="CREB3L2"
                     /gene_synonym="BBF2H7; MGC131709; MGC71006"
                     /product="cAMP responsive element binding protein 3-like
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_194071.2"
                     /db_xref="GI:56550066"
                     /db_xref="GeneID:64764"
                     /db_xref="HGNC:23720"
                     /db_xref="HPRD:16391"
                     /db_xref="MIM:608834"
     CDS             complement(join(137565222..137565297,137567158..137567374,
                     137569741..137569867,137570149..137570248,
                     137586100..137586168,137588705..137588763,
                     137590448..137590594,137592998..137593182,
                     137597737..137597824,137600583..137600758,
                     137612896..137613112,137686350..137686451))
                     /gene="CREB3L2"
                     /gene_synonym="BBF2H7; MGC131709; MGC71006"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclic AMP-responsive element-binding protein
                     3-like protein 2"
                     /protein_id="NP_919047.2"
                     /db_xref="GI:56550067"
                     /db_xref="CCDS:CCDS34760.1"
                     /db_xref="GeneID:64764"
                     /db_xref="HGNC:23720"
                     /db_xref="HPRD:16391"
                     /db_xref="MIM:608834"
     gene            137638094..137642712
                     /gene="LOC100130880"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 EST"
                     /db_xref="GeneID:100130880"
     mRNA            join(137638094..137638270,137639994..137640082,
                     137641330..137641391,137642464..137642712)
                     /gene="LOC100130880"
                     /product="hypothetical protein LOC100130880"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 EST"
                     /transcript_id="XM_001726692.1"
                     /db_xref="GI:169171152"
                     /db_xref="GeneID:100130880"
     CDS             join(137638215..137638270,137639994..137640082,
                     137641330..137641391,137642464..137642571)
                     /gene="LOC100130880"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="hypothetical protein LOC100130880"
                     /protein_id="XP_001726744.1"
                     /db_xref="GI:169171153"
                     /db_xref="GeneID:100130880"
     gene            137707044..137709096
                     /gene="LOC100128052"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100128052"
     gene            137732000..137732643
                     /gene="LOC100420648"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420648"
     gene            137761178..137803050
                     /gene="AKR1D1"
                     /gene_synonym="3o5bred; CBAS2; SRD5B1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6718"
                     /db_xref="HGNC:388"
                     /db_xref="HPRD:07263"
                     /db_xref="MIM:604741"
     mRNA            join(137761178..137761357,137773347..137773514,
                     137776514..137776630,137782612..137782689,
                     137790053..137790175,137791354..137791463,
                     137792161..137792326,137798436..137798518,
                     137801366..137803050)
                     /gene="AKR1D1"
                     /gene_synonym="3o5bred; CBAS2; SRD5B1"
                     /product="aldo-keto reductase family 1, member D1 (delta
                     4-3-ketosteroid-5-beta-reductase), transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005989.3"
                     /db_xref="GI:300116269"
                     /db_xref="GeneID:6718"
                     /db_xref="HGNC:388"
                     /db_xref="HPRD:07263"
                     /db_xref="MIM:604741"
     mRNA            join(137761178..137761357,137773347..137773514,
                     137776514..137776630,137782612..137782689,
                     137791354..137791463,137792161..137792326,
                     137798436..137798518,137801366..137803050)
                     /gene="AKR1D1"
                     /gene_synonym="3o5bred; CBAS2; SRD5B1"
                     /product="aldo-keto reductase family 1, member D1 (delta
                     4-3-ketosteroid-5-beta-reductase), transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001190906.1"
                     /db_xref="GI:300116270"
                     /db_xref="GeneID:6718"
                     /db_xref="HGNC:388"
                     /db_xref="MIM:604741"
                     /db_xref="HPRD:07263"
     mRNA            join(137761178..137761357,137773347..137773514,
                     137776514..137776630,137782612..137782689,
                     137790053..137790175,137791354..137791463,
                     137792161..137792326,137801366..137803050)
                     /gene="AKR1D1"
                     /gene_synonym="3o5bred; CBAS2; SRD5B1"
                     /product="aldo-keto reductase family 1, member D1 (delta
                     4-3-ketosteroid-5-beta-reductase), transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001190907.1"
                     /db_xref="GI:300116272"
                     /db_xref="GeneID:6718"
                     /db_xref="HGNC:388"
                     /db_xref="MIM:604741"
                     /db_xref="HPRD:07263"
     CDS             join(137761265..137761357,137773347..137773514,
                     137776514..137776630,137782612..137782689,
                     137790053..137790175,137791354..137791463,
                     137792161..137792326,137798436..137798518,
                     137801366..137801408)
                     /gene="AKR1D1"
                     /gene_synonym="3o5bred; CBAS2; SRD5B1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="3-oxo-5-beta-steroid 4-dehydrogenase isoform 1"
                     /protein_id="NP_005980.1"
                     /db_xref="GI:5174695"
                     /db_xref="CCDS:CCDS5846.1"
                     /db_xref="GeneID:6718"
                     /db_xref="HGNC:388"
                     /db_xref="HPRD:07263"
                     /db_xref="MIM:604741"
     CDS             join(137761265..137761357,137773347..137773514,
                     137776514..137776630,137782612..137782689,
                     137791354..137791463,137792161..137792326,
                     137798436..137798518,137801366..137801408)
                     /gene="AKR1D1"
                     /gene_synonym="3o5bred; CBAS2; SRD5B1"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="3-oxo-5-beta-steroid 4-dehydrogenase isoform 2"
                     /protein_id="NP_001177835.1"
                     /db_xref="GI:300116271"
                     /db_xref="CCDS:CCDS55170.1"
                     /db_xref="GeneID:6718"
                     /db_xref="HGNC:388"
                     /db_xref="HPRD:07263"
                     /db_xref="MIM:604741"
     CDS             join(137761265..137761357,137773347..137773514,
                     137776514..137776630,137782612..137782689,
                     137790053..137790175,137791354..137791463,
                     137792161..137792326,137801366..137801383)
                     /gene="AKR1D1"
                     /gene_synonym="3o5bred; CBAS2; SRD5B1"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="3-oxo-5-beta-steroid 4-dehydrogenase isoform 3"
                     /protein_id="NP_001177836.1"
                     /db_xref="GI:300116273"
                     /db_xref="CCDS:CCDS55169.1"
                     /db_xref="GeneID:6718"
                     /db_xref="HGNC:388"
                     /db_xref="HPRD:07263"
                     /db_xref="MIM:604741"
     gene            137806949..137809003
                     /gene="RCC2P3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100131932"
                     /db_xref="HGNC:42379"
     gene            137808504..137808567
                     /gene="MIR4468"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100616226"
                     /db_xref="HGNC:41533"
                     /db_xref="miRBase:MI0016819"
     ncRNA           137808504..137808567
                     /gene="MIR4468"
                     /ncRNA_class="miRNA"
                     /product="microRNA 4468"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_039678.1"
                     /db_xref="GI:338797764"
                     /db_xref="GeneID:100616226"
                     /db_xref="HGNC:41533"
                     /db_xref="miRBase:MI0016819"
     gene            complement(137982806..137983252)
                     /gene="RPS17P12"
                     /gene_synonym="RPS17_5_854"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442726"
                     /db_xref="HGNC:35930"
     gene            complement(138088705..138089396)
                     /gene="LOC442727"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442727"
     gene            138125338..138127685
                     /gene="IMPDH1P3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:136307"
                     /db_xref="HGNC:33958"
     gene            138145079..138270333
                     /gene="TRIM24"
                     /gene_synonym="hTIF1; PTC6; RNF82; TF1A; TIF1; TIF1A;
                     TIF1ALPHA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8805"
                     /db_xref="HGNC:11812"
                     /db_xref="HPRD:04556"
                     /db_xref="MIM:603406"
     mRNA            join(138145079..138145657,138189035..138189153,
                     138199957..138200104,138203934..138204066,
                     138209986..138210102,138213861..138213975,
                     138223402..138223548,138235808..138235925,
                     138239443..138239711,138252226..138252399,
                     138255575..138255748,138258252..138258387,
                     138261118..138261190,138262165..138262333,
                     138263949..138264277,138265307..138265439,
                     138266442..138266516,138268595..138268744,
                     138269487..138270333)
                     /gene="TRIM24"
                     /gene_synonym="hTIF1; PTC6; RNF82; TF1A; TIF1; TIF1A;
                     TIF1ALPHA"
                     /product="tripartite motif containing 24, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015905.2"
                     /db_xref="GI:47419910"
                     /db_xref="GeneID:8805"
                     /db_xref="HGNC:11812"
                     /db_xref="HPRD:04556"
                     /db_xref="MIM:603406"
     mRNA            join(138145079..138145657,138189035..138189153,
                     138199957..138200104,138203934..138204066,
                     138209986..138210102,138213861..138213975,
                     138223402..138223548,138235808..138235925,
                     138239443..138239609,138252226..138252399,
                     138255575..138255748,138258252..138258387,
                     138261118..138261190,138262165..138262333,
                     138263949..138264277,138265307..138265439,
                     138266442..138266516,138268595..138268744,
                     138269487..138270333)
                     /gene="TRIM24"
                     /gene_synonym="hTIF1; PTC6; RNF82; TF1A; TIF1; TIF1A;
                     TIF1ALPHA"
                     /product="tripartite motif containing 24, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003852.3"
                     /db_xref="GI:47419908"
                     /db_xref="GeneID:8805"
                     /db_xref="HGNC:11812"
                     /db_xref="HPRD:04556"
                     /db_xref="MIM:603406"
     CDS             join(138145294..138145657,138189035..138189153,
                     138199957..138200104,138203934..138204066,
                     138209986..138210102,138213861..138213975,
                     138223402..138223548,138235808..138235925,
                     138239443..138239711,138252226..138252399,
                     138255575..138255748,138258252..138258387,
                     138261118..138261190,138262165..138262333,
                     138263949..138264277,138265307..138265439,
                     138266442..138266516,138268595..138268744,
                     138269487..138269696)
                     /gene="TRIM24"
                     /gene_synonym="hTIF1; PTC6; RNF82; TF1A; TIF1; TIF1A;
                     TIF1ALPHA"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transcription intermediary factor 1-alpha
                     isoform a"
                     /protein_id="NP_056989.2"
                     /db_xref="GI:47419911"
                     /db_xref="CCDS:CCDS5847.1"
                     /db_xref="GeneID:8805"
                     /db_xref="HGNC:11812"
                     /db_xref="HPRD:04556"
                     /db_xref="MIM:603406"
     CDS             join(138145294..138145657,138189035..138189153,
                     138199957..138200104,138203934..138204066,
                     138209986..138210102,138213861..138213975,
                     138223402..138223548,138235808..138235925,
                     138239443..138239609,138252226..138252399,
                     138255575..138255748,138258252..138258387,
                     138261118..138261190,138262165..138262333,
                     138263949..138264277,138265307..138265439,
                     138266442..138266516,138268595..138268744,
                     138269487..138269696)
                     /gene="TRIM24"
                     /gene_synonym="hTIF1; PTC6; RNF82; TF1A; TIF1; TIF1A;
                     TIF1ALPHA"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transcription intermediary factor 1-alpha
                     isoform b"
                     /protein_id="NP_003843.3"
                     /db_xref="GI:47419909"
                     /db_xref="CCDS:CCDS47720.1"
                     /db_xref="GeneID:8805"
                     /db_xref="HGNC:11812"
                     /db_xref="HPRD:04556"
                     /db_xref="MIM:603406"
     gene            complement(138175288..138176118)
                     /gene="RPS3AP28"
                     /gene_synonym="RPS3A_13_855"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271257"
                     /db_xref="HGNC:35738"
     gene            complement(138279030..138363790)
                     /gene="SVOPL"
                     /gene_synonym="MGC46715"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:136306"
                     /db_xref="HGNC:27034"
                     /db_xref="MIM:611700"
     mRNA            complement(join(138279030..138279366,138281162..138281275,
                     138305791..138305880,138310714..138310795,
                     138312095..138312206,138312903..138313108,
                     138314794..138314867,138329462..138329590,
                     138333757..138333882,138341193..138341256,
                     138344609..138344733,138347819..138347890,
                     138356764..138356862,138363179..138363270,
                     138363709..138363790))
                     /gene="SVOPL"
                     /gene_synonym="MGC46715"
                     /product="SVOP-like, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001139456.1"
                     /db_xref="GI:213021147"
                     /db_xref="GeneID:136306"
                     /db_xref="HGNC:27034"
                     /db_xref="MIM:611700"
     mRNA            complement(join(138279030..138279366,138281162..138281275,
                     138305791..138305880,138310714..138310795,
                     138312095..138312206,138312903..138313108,
                     138314794..138314867,138329462..138329590,
                     138333757..138333882,138341193..138341256,
                     138347819..138347890,138348955..138348969))
                     /gene="SVOPL"
                     /gene_synonym="MGC46715"
                     /product="SVOP-like, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_174959.2"
                     /db_xref="GI:213021151"
                     /db_xref="GeneID:136306"
                     /db_xref="HGNC:27034"
                     /db_xref="HPRD:11235"
                     /db_xref="MIM:611700"
     CDS             complement(join(138279355..138279366,138281162..138281275,
                     138305791..138305880,138310714..138310795,
                     138312095..138312206,138312903..138313108,
                     138314794..138314867,138329462..138329590,
                     138333757..138333882,138341193..138341256,
                     138344609..138344733,138347819..138347890,
                     138356764..138356862,138363179..138363270,
                     138363709..138363790))
                     /gene="SVOPL"
                     /gene_synonym="MGC46715"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative transporter SVOPL isoform 1"
                     /protein_id="NP_001132928.1"
                     /db_xref="GI:213021148"
                     /db_xref="CCDS:CCDS47721.1"
                     /db_xref="GeneID:136306"
                     /db_xref="HGNC:27034"
                     /db_xref="MIM:611700"
     CDS             complement(join(138279355..138279366,138281162..138281275,
                     138305791..138305880,138310714..138310795,
                     138312095..138312206,138312903..138313108,
                     138314794..138314867,138329462..138329590,
                     138333757..138333882,138341193..138341256,
                     138347819..138347832))
                     /gene="SVOPL"
                     /gene_synonym="MGC46715"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative transporter SVOPL isoform 2"
                     /protein_id="NP_777619.1"
                     /db_xref="GI:33457322"
                     /db_xref="CCDS:CCDS5848.1"
                     /db_xref="GeneID:136306"
                     /db_xref="HGNC:27034"
                     /db_xref="MIM:611700"
     gene            complement(138330855..138331193)
                     /gene="RPL21P73"
                     /gene_synonym="RPL21_28_856"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271182"
                     /db_xref="HGNC:36794"
     gene            138373684..138374300
                     /gene="RPL17P27"
                     /gene_synonym="RPL17_17_857"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:202789"
                     /db_xref="HGNC:36038"
     gene            138386404..138387812
                     /gene="UQCRFS1P2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:647123"
                     /db_xref="HGNC:39172"
     gene            complement(138391039..138482941)
                     /gene="ATP6V0A4"
                     /gene_synonym="A4; ATP6N1B; ATP6N2; MGC130016; MGC130017;
                     RDRTA2; RTA1C; RTADR; STV1; VPH1; VPP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:50617"
                     /db_xref="HGNC:866"
                     /db_xref="HPRD:05576"
                     /db_xref="MIM:605239"
     mRNA            complement(join(138391039..138391462,138394369..138394540,
                     138400509..138400626,138406642..138406770,
                     138413506..138413607,138417622..138417838,
                     138418881..138418999,138424285..138424378,
                     138429868..138430025,138432170..138432309,
                     138433912..138434062,138437370..138437582,
                     138440434..138440527,138441203..138441285,
                     138444497..138444623,138447085..138447179,
                     138447645..138447770,138453525..138453619,
                     138453918..138453996,138455876..138456009,
                     138470903..138471005,138482779..138482941))
                     /gene="ATP6V0A4"
                     /gene_synonym="A4; ATP6N1B; ATP6N2; MGC130016; MGC130017;
                     RDRTA2; RTA1C; RTADR; STV1; VPH1; VPP2"
                     /product="ATPase, H+ transporting, lysosomal V0 subunit
                     a4, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020632.2"
                     /db_xref="GI:85386052"
                     /db_xref="GeneID:50617"
                     /db_xref="HGNC:866"
                     /db_xref="HPRD:05576"
                     /db_xref="MIM:605239"
     mRNA            complement(join(138391039..138391462,138394369..138394540,
                     138400509..138400626,138406642..138406770,
                     138413506..138413607,138417622..138417838,
                     138418881..138418999,138424285..138424378,
                     138429868..138430025,138432170..138432309,
                     138433912..138434062,138437370..138437582,
                     138440434..138440527,138441203..138441285,
                     138444497..138444623,138447085..138447179,
                     138447645..138447770,138453525..138453619,
                     138453918..138453996,138455876..138456009,
                     138482779..138482941))
                     /gene="ATP6V0A4"
                     /gene_synonym="A4; ATP6N1B; ATP6N2; MGC130016; MGC130017;
                     RDRTA2; RTA1C; RTADR; STV1; VPH1; VPP2"
                     /product="ATPase, H+ transporting, lysosomal V0 subunit
                     a4, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_130840.2"
                     /db_xref="GI:85386055"
                     /db_xref="GeneID:50617"
                     /db_xref="HGNC:866"
                     /db_xref="MIM:605239"
                     /db_xref="HPRD:05576"
     mRNA            complement(join(138391039..138391462,138394369..138394540,
                     138400509..138400626,138406642..138406770,
                     138413506..138413607,138417622..138417838,
                     138418881..138418999,138424285..138424378,
                     138429868..138430025,138432170..138432309,
                     138433912..138434062,138437370..138437582,
                     138440434..138440527,138441203..138441285,
                     138444497..138444623,138447085..138447179,
                     138447645..138447770,138453525..138453619,
                     138453918..138453996,138455876..138456009,
                     138458562..138458782))
                     /gene="ATP6V0A4"
                     /gene_synonym="A4; ATP6N1B; ATP6N2; MGC130016; MGC130017;
                     RDRTA2; RTA1C; RTADR; STV1; VPH1; VPP2"
                     /product="ATPase, H+ transporting, lysosomal V0 subunit
                     a4, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_130841.2"
                     /db_xref="GI:85386546"
                     /db_xref="GeneID:50617"
                     /db_xref="HGNC:866"
                     /db_xref="MIM:605239"
                     /db_xref="HPRD:05576"
     CDS             complement(join(138391369..138391462,138394369..138394540,
                     138400509..138400626,138406642..138406770,
                     138413506..138413607,138417622..138417838,
                     138418881..138418999,138424285..138424378,
                     138429868..138430025,138432170..138432309,
                     138433912..138434062,138437370..138437582,
                     138440434..138440527,138441203..138441285,
                     138444497..138444623,138447085..138447179,
                     138447645..138447770,138453525..138453619,
                     138453918..138453996,138455876..138455992))
                     /gene="ATP6V0A4"
                     /gene_synonym="A4; ATP6N1B; ATP6N2; MGC130016; MGC130017;
                     RDRTA2; RTA1C; RTADR; STV1; VPH1; VPP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="V-type proton ATPase 116 kDa subunit a isoform
                     4"
                     /protein_id="NP_065683.2"
                     /db_xref="GI:85386053"
                     /db_xref="CCDS:CCDS5849.1"
                     /db_xref="GeneID:50617"
                     /db_xref="HGNC:866"
                     /db_xref="HPRD:05576"
                     /db_xref="MIM:605239"
     CDS             complement(join(138391369..138391462,138394369..138394540,
                     138400509..138400626,138406642..138406770,
                     138413506..138413607,138417622..138417838,
                     138418881..138418999,138424285..138424378,
                     138429868..138430025,138432170..138432309,
                     138433912..138434062,138437370..138437582,
                     138440434..138440527,138441203..138441285,
                     138444497..138444623,138447085..138447179,
                     138447645..138447770,138453525..138453619,
                     138453918..138453996,138455876..138455992))
                     /gene="ATP6V0A4"
                     /gene_synonym="A4; ATP6N1B; ATP6N2; MGC130016; MGC130017;
                     RDRTA2; RTA1C; RTADR; STV1; VPH1; VPP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="V-type proton ATPase 116 kDa subunit a isoform
                     4"
                     /protein_id="NP_570855.2"
                     /db_xref="GI:85386056"
                     /db_xref="CCDS:CCDS5849.1"
                     /db_xref="GeneID:50617"
                     /db_xref="HGNC:866"
                     /db_xref="HPRD:05576"
                     /db_xref="MIM:605239"
     CDS             complement(join(138391369..138391462,138394369..138394540,
                     138400509..138400626,138406642..138406770,
                     138413506..138413607,138417622..138417838,
                     138418881..138418999,138424285..138424378,
                     138429868..138430025,138432170..138432309,
                     138433912..138434062,138437370..138437582,
                     138440434..138440527,138441203..138441285,
                     138444497..138444623,138447085..138447179,
                     138447645..138447770,138453525..138453619,
                     138453918..138453996,138455876..138455992))
                     /gene="ATP6V0A4"
                     /gene_synonym="A4; ATP6N1B; ATP6N2; MGC130016; MGC130017;
                     RDRTA2; RTA1C; RTADR; STV1; VPH1; VPP2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="V-type proton ATPase 116 kDa subunit a isoform
                     4"
                     /protein_id="NP_570856.2"
                     /db_xref="GI:85386547"
                     /db_xref="CCDS:CCDS5849.1"
                     /db_xref="GeneID:50617"
                     /db_xref="HGNC:866"
                     /db_xref="HPRD:05576"
                     /db_xref="MIM:605239"
     gene            138482739..138490769
                     /gene="TMEM213"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:155006"
                     /db_xref="HGNC:27220"
     mRNA            join(138482739..138482931,138486072..138486143,
                     138487645..138490769)
                     /gene="TMEM213"
                     /product="transmembrane protein 213"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001085429.1"
                     /db_xref="GI:146229351"
                     /db_xref="GeneID:155006"
                     /db_xref="HGNC:27220"
     CDS             join(138482850..138482931,138486072..138486143,
                     138487645..138487814)
                     /gene="TMEM213"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 213"
                     /protein_id="NP_001078898.1"
                     /db_xref="GI:146229352"
                     /db_xref="CCDS:CCDS47722.1"
                     /db_xref="GeneID:155006"
                     /db_xref="HGNC:27220"
     gene            complement(138516126..138666064)
                     /gene="KIAA1549"
                     /gene_synonym="FLJ11731; FLJ38703; FLJ40644"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57670"
                     /db_xref="HGNC:22219"
                     /db_xref="MIM:613344"
     mRNA            complement(join(138516126..138522857,138524878..138525023,
                     138529062..138529219,138536969..138537015,
                     138545885..138546202,138552721..138552874,
                     138554284..138554507,138555903..138556108,
                     138564284..138564399,138566134..138566330,
                     138579088..138579272,138583701..138583878,
                     138588334..138588482,138589768..138589827,
                     138591665..138591848,138593737..138593867,
                     138595892..138596069,138597118..138597206,
                     138601494..138604184,138665829..138666064))
                     /gene="KIAA1549"
                     /gene_synonym="FLJ11731; FLJ38703; FLJ40644"
                     /product="KIAA1549, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020910.2"
                     /db_xref="GI:257467651"
                     /db_xref="GeneID:57670"
                     /db_xref="HGNC:22219"
                     /db_xref="MIM:613344"
     mRNA            complement(join(138516126..138522905,138524878..138525023,
                     138529062..138529219,138536969..138537015,
                     138545885..138546202,138552721..138552874,
                     138554284..138554507,138555903..138556108,
                     138564284..138564399,138566134..138566330,
                     138579088..138579272,138583701..138583878,
                     138588334..138588482,138589768..138589827,
                     138591665..138591848,138593737..138593867,
                     138595892..138596069,138597118..138597206,
                     138601494..138604184,138665829..138666064))
                     /gene="KIAA1549"
                     /gene_synonym="FLJ11731; FLJ38703; FLJ40644"
                     /product="KIAA1549, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001164665.1"
                     /db_xref="GI:257467653"
                     /db_xref="GeneID:57670"
                     /db_xref="HGNC:22219"
                     /db_xref="MIM:613344"
     CDS             complement(join(138522651..138522857,138524878..138525023,
                     138529062..138529219,138536969..138537015,
                     138545885..138546202,138552721..138552874,
                     138554284..138554507,138555903..138556108,
                     138564284..138564399,138566134..138566330,
                     138579088..138579272,138583701..138583878,
                     138588334..138588482,138589768..138589827,
                     138591665..138591848,138593737..138593867,
                     138595892..138596069,138597118..138597206,
                     138601494..138604184,138665829..138666015))
                     /gene="KIAA1549"
                     /gene_synonym="FLJ11731; FLJ38703; FLJ40644"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC57670 isoform 1"
                     /protein_id="NP_065961.2"
                     /db_xref="GI:257467652"
                     /db_xref="CCDS:CCDS47723.1"
                     /db_xref="GeneID:57670"
                     /db_xref="HGNC:22219"
                     /db_xref="MIM:613344"
     CDS             complement(join(138522651..138522905,138524878..138525023,
                     138529062..138529219,138536969..138537015,
                     138545885..138546202,138552721..138552874,
                     138554284..138554507,138555903..138556108,
                     138564284..138564399,138566134..138566330,
                     138579088..138579272,138583701..138583878,
                     138588334..138588482,138589768..138589827,
                     138591665..138591848,138593737..138593867,
                     138595892..138596069,138597118..138597206,
                     138601494..138604184,138665829..138666015))
                     /gene="KIAA1549"
                     /gene_synonym="FLJ11731; FLJ38703; FLJ40644"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC57670 isoform 2"
                     /protein_id="NP_001158137.1"
                     /db_xref="GI:257467654"
                     /db_xref="GeneID:57670"
                     /db_xref="HGNC:22219"
                     /db_xref="MIM:613344"
     gene            complement(138710452..138720775)
                     /gene="ZC3HAV1L"
                     /gene_synonym="C7orf39; MGC14289"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:92092"
                     /db_xref="HGNC:22423"
                     /db_xref="HPRD:14440"
     mRNA            complement(join(138710452..138711306,138711454..138711579,
                     138713448..138713706,138719289..138719424,
                     138720399..138720775))
                     /gene="ZC3HAV1L"
                     /gene_synonym="C7orf39; MGC14289"
                     /product="zinc finger CCCH-type, antiviral 1-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_080660.3"
                     /db_xref="GI:259906439"
                     /db_xref="GeneID:92092"
                     /db_xref="HGNC:22423"
                     /db_xref="HPRD:14440"
     CDS             complement(join(138711290..138711306,138711454..138711579,
                     138713448..138713706,138719289..138719424,
                     138720399..138720763))
                     /gene="ZC3HAV1L"
                     /gene_synonym="C7orf39; MGC14289"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger CCCH-type antiviral protein 1-like"
                     /protein_id="NP_542391.2"
                     /db_xref="GI:259906440"
                     /db_xref="CCDS:CCDS5850.1"
                     /db_xref="GeneID:92092"
                     /db_xref="HGNC:22423"
                     /db_xref="HPRD:14440"
     gene            complement(138728266..138794465)
                     /gene="ZC3HAV1"
                     /gene_synonym="DKFZp686F2052; DKFZp686H1869;
                     DKFZp686O19171; FLB6421; FLJ13288; MGC48898; PARP13; ZAP;
                     ZC3H2; ZC3HDC2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:56829"
                     /db_xref="HGNC:23721"
                     /db_xref="MIM:607312"
     mRNA            complement(join(138728266..138732599,138738197..138738327,
                     138738711..138738841,138739951..138740041,
                     138745782..138745884,138749625..138749745,
                     138758602..138758776,138761032..138761155,
                     138763298..138763399,138764216..138764989,
                     138768526..138768778,138774370..138774505,
                     138793770..138794465))
                     /gene="ZC3HAV1"
                     /gene_synonym="DKFZp686F2052; DKFZp686H1869;
                     DKFZp686O19171; FLB6421; FLJ13288; MGC48898; PARP13; ZAP;
                     ZC3H2; ZC3HDC2"
                     /product="zinc finger CCCH-type, antiviral 1, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020119.3"
                     /db_xref="GI:33946332"
                     /db_xref="GeneID:56829"
                     /db_xref="HGNC:23721"
                     /db_xref="HPRD:09534"
                     /db_xref="MIM:607312"
     CDS             complement(join(138732340..138732599,138738197..138738327,
                     138738711..138738841,138739951..138740041,
                     138745782..138745884,138749625..138749745,
                     138758602..138758776,138761032..138761155,
                     138763298..138763399,138764216..138764989,
                     138768526..138768778,138774370..138774505,
                     138793770..138794077))
                     /gene="ZC3HAV1"
                     /gene_synonym="DKFZp686F2052; DKFZp686H1869;
                     DKFZp686O19171; FLB6421; FLJ13288; MGC48898; PARP13; ZAP;
                     ZC3H2; ZC3HDC2"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger CCCH-type antiviral protein 1
                     isoform 1"
                     /protein_id="NP_064504.2"
                     /db_xref="GI:27477136"
                     /db_xref="CCDS:CCDS5851.1"
                     /db_xref="GeneID:56829"
                     /db_xref="HGNC:23721"
                     /db_xref="MIM:607312"
     gene            complement(138734202..138734752)
                     /gene="RPL17P28"
                     /gene_synonym="RPL17_7_858"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100270940"
                     /db_xref="HGNC:36055"
     mRNA            complement(join(138745084..138745884,138749625..138749745,
                     138758602..138758776,138761032..138761155,
                     138763298..138763399,138764216..138764989,
                     138768526..138768778,138774370..138774505,
                     138793770..138794465))
                     /gene="ZC3HAV1"
                     /gene_synonym="DKFZp686F2052; DKFZp686H1869;
                     DKFZp686O19171; FLB6421; FLJ13288; MGC48898; PARP13; ZAP;
                     ZC3H2; ZC3HDC2"
                     /product="zinc finger CCCH-type, antiviral 1, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024625.3"
                     /db_xref="GI:27477137"
                     /db_xref="GeneID:56829"
                     /db_xref="HGNC:23721"
                     /db_xref="MIM:607312"
     CDS             complement(join(138745778..138745884,138749625..138749745,
                     138758602..138758776,138761032..138761155,
                     138763298..138763399,138764216..138764989,
                     138768526..138768778,138774370..138774505,
                     138793770..138794077))
                     /gene="ZC3HAV1"
                     /gene_synonym="DKFZp686F2052; DKFZp686H1869;
                     DKFZp686O19171; FLB6421; FLJ13288; MGC48898; PARP13; ZAP;
                     ZC3H2; ZC3HDC2"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger CCCH-type antiviral protein 1
                     isoform 2"
                     /protein_id="NP_078901.3"
                     /db_xref="GI:27477138"
                     /db_xref="CCDS:CCDS55171.1"
                     /db_xref="GeneID:56829"
                     /db_xref="HGNC:23721"
                     /db_xref="MIM:607312"
     gene            138818490..138874550
                     /gene="TTC26"
                     /gene_synonym="dyf-13; DYF13; FLJ12571; MGC163211"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:79989"
                     /db_xref="HGNC:21882"
     mRNA            join(138818490..138818606,138819401..138819538,
                     138822593..138822685,138824636..138824750,
                     138827002..138827051,138831891..138832036,
                     138832952..138833123,138845694..138845768,
                     138849878..138849980,138851586..138851641,
                     138853090..138853143,138854035..138854098,
                     138862960..138863048,138863261..138863344,
                     138864320..138864389,138865838..138865944,
                     138872152..138872285,138874067..138874550)
                     /gene="TTC26"
                     /gene_synonym="dyf-13; DYF13; FLJ12571; MGC163211"
                     /product="tetratricopeptide repeat domain 26, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024926.2"
                     /db_xref="GI:222136633"
                     /db_xref="GeneID:79989"
                     /db_xref="HGNC:21882"
                     /db_xref="HPRD:07776"
     mRNA            join(138818490..138818606,138819401..138819538,
                     138822593..138822685,138824636..138824750,
                     138827002..138827051,138831891..138832036,
                     138832952..138833123,138845694..138845768,
                     138849878..138849980,138851586..138851641,
                     138853090..138853143,138854035..138854098,
                     138862960..138863048,138863261..138863344,
                     138864320..138864389,138865838..138865944,
                     138874067..138874550)
                     /gene="TTC26"
                     /gene_synonym="dyf-13; DYF13; FLJ12571; MGC163211"
                     /product="tetratricopeptide repeat domain 26, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001144920.1"
                     /db_xref="GI:222136604"
                     /db_xref="GeneID:79989"
                     /db_xref="HGNC:21882"
     mRNA            join(138818490..138818606,138819401..138819538,
                     138824636..138824750,138827002..138827051,
                     138831891..138832036,138832952..138833123,
                     138845694..138845768,138849878..138849980,
                     138851586..138851641,138853090..138853143,
                     138854035..138854098,138862960..138863048,
                     138863261..138863344,138864320..138864389,
                     138865838..138865944,138872152..138872285,
                     138874067..138874550)
                     /gene="TTC26"
                     /gene_synonym="dyf-13; DYF13; FLJ12571; MGC163211"
                     /product="tetratricopeptide repeat domain 26, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001144923.1"
                     /db_xref="GI:222136606"
                     /db_xref="GeneID:79989"
                     /db_xref="HGNC:21882"
     CDS             join(138818604..138818606,138819401..138819538,
                     138822593..138822685,138824636..138824750,
                     138827002..138827051,138831891..138832036,
                     138832952..138833123,138845694..138845768,
                     138849878..138849980,138851586..138851641,
                     138853090..138853143,138854035..138854098,
                     138862960..138863048,138863261..138863344,
                     138864320..138864389,138865838..138865944,
                     138872152..138872285,138874067..138874178)
                     /gene="TTC26"
                     /gene_synonym="dyf-13; DYF13; FLJ12571; MGC163211"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="tetratricopeptide repeat protein 26 isoform 1"
                     /protein_id="NP_079202.2"
                     /db_xref="GI:222136634"
                     /db_xref="CCDS:CCDS5852.1"
                     /db_xref="GeneID:79989"
                     /db_xref="HGNC:21882"
     CDS             join(138818604..138818606,138819401..138819538,
                     138824636..138824750,138827002..138827051,
                     138831891..138832036,138832952..138833123,
                     138845694..138845768,138849878..138849980,
                     138851586..138851641,138853090..138853143,
                     138854035..138854098,138862960..138863048,
                     138863261..138863344,138864320..138864389,
                     138865838..138865944,138872152..138872285,
                     138874067..138874178)
                     /gene="TTC26"
                     /gene_synonym="dyf-13; DYF13; FLJ12571; MGC163211"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="tetratricopeptide repeat protein 26 isoform 3"
                     /protein_id="NP_001138395.1"
                     /db_xref="GI:222136607"
                     /db_xref="CCDS:CCDS55173.1"
                     /db_xref="GeneID:79989"
                     /db_xref="HGNC:21882"
     CDS             join(138818604..138818606,138819401..138819538,
                     138822593..138822685,138824636..138824750,
                     138827002..138827051,138831891..138832036,
                     138832952..138833123,138845694..138845768,
                     138849878..138849980,138851586..138851641,
                     138853090..138853143,138854035..138854098,
                     138862960..138863048,138863261..138863344,
                     138864320..138864389,138865838..138865944,
                     138874067..138874111)
                     /gene="TTC26"
                     /gene_synonym="dyf-13; DYF13; FLJ12571; MGC163211"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="tetratricopeptide repeat protein 26 isoform 2"
                     /protein_id="NP_001138392.1"
                     /db_xref="GI:222136605"
                     /db_xref="CCDS:CCDS55172.1"
                     /db_xref="GeneID:79989"
                     /db_xref="HGNC:21882"
     gene            complement(138856562..138859185)
                     /gene="LOC100499191"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100499191"
     gene            complement(138883302..138883888)
                     /gene="LOC100132310"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100132310"
     gene            complement(138912224..138912605)
                     /gene="RPL37AP5"
                     /gene_synonym="RPL37A_2_859"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129856"
                     /db_xref="HGNC:36977"
     gene            138916231..138992982
                     /gene="UBN2"
                     /gene_synonym="FLJ25778"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:254048"
                     /db_xref="HGNC:21931"
                     /db_xref="MIM:613841"
     mRNA            join(138916231..138916698,138921751..138921843,
                     138936702..138936803,138943234..138943371,
                     138944013..138944116,138945998..138946487,
                     138951079..138951149,138954140..138954269,
                     138957068..138957186,138958043..138958156,
                     138958677..138958820,138960843..138960893,
                     138964064..138964106,138966751..138966801,
                     138967770..138969320,138977978..138978209,
                     138978635..138978727,138982533..138992982)
                     /gene="UBN2"
                     /gene_synonym="FLJ25778"
                     /product="ubinuclein 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_173569.3"
                     /db_xref="GI:236459850"
                     /db_xref="GeneID:254048"
                     /db_xref="HGNC:21931"
                     /db_xref="MIM:613841"
     CDS             join(138916231..138916698,138921751..138921843,
                     138936702..138936803,138943234..138943371,
                     138944013..138944116,138945998..138946487,
                     138951079..138951149,138954140..138954269,
                     138957068..138957186,138958043..138958156,
                     138958677..138958820,138960843..138960893,
                     138964064..138964106,138966751..138966801,
                     138967770..138969320,138977978..138978209,
                     138978635..138978727,138982533..138982582)
                     /gene="UBN2"
                     /gene_synonym="FLJ25778"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ubinuclein-2"
                     /protein_id="NP_775840.3"
                     /db_xref="GI:236459851"
                     /db_xref="CCDS:CCDS43655.2"
                     /db_xref="GeneID:254048"
                     /db_xref="HGNC:21931"
                     /db_xref="MIM:613841"
     tRNA            139025446..139025518
                     /product="tRNA-Arg"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /anticodon=(pos:139025479..139025481,aa:Arg)
                     /db_xref="GeneID:100189406"
     gene            139025897..139030541
                     /gene="C7orf55"
                     /gene_synonym="FLJ35699; FMC1; HSPC268"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:154791"
                     /db_xref="HGNC:26946"
                     /db_xref="HPRD:13714"
     mRNA            join(139025897..139026268,139030247..139030541)
                     /gene="C7orf55"
                     /gene_synonym="FLJ35699; FMC1; HSPC268"
                     /product="chromosome 7 open reading frame 55"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_197964.3"
                     /db_xref="GI:188219594"
                     /db_xref="GeneID:154791"
                     /db_xref="HGNC:26946"
                     /db_xref="HPRD:13714"
     CDS             join(139026131..139026268,139030247..139030450)
                     /gene="C7orf55"
                     /gene_synonym="FLJ35699; FMC1; HSPC268"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="formation of mitochondrial complexes 1 homolog"
                     /protein_id="NP_932068.2"
                     /db_xref="GI:188219595"
                     /db_xref="CCDS:CCDS5853.1"
                     /db_xref="GeneID:154791"
                     /db_xref="HGNC:26946"
                     /db_xref="HPRD:13714"
     gene            139044634..139108200
                     /gene="LUC7L2"
                     /gene_synonym="CGI-59; CGI-74; FLJ10657; hLuc7B2; LUC7B2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51631"
                     /db_xref="HGNC:21608"
                     /db_xref="HPRD:17456"
                     /db_xref="MIM:613056"
     mRNA            join(139044634..139045068,139060808..139060902,
                     139083345..139083443,139086883..139086993,
                     139090390..139090533,139091920..139092096,
                     139094309..139094400,139097297..139097326,
                     139102284..139102475,139106909..139108200)
                     /gene="LUC7L2"
                     /gene_synonym="CGI-59; CGI-74; FLJ10657; hLuc7B2; LUC7B2"
                     /product="LUC7-like 2 (S. cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016019.2"
                     /db_xref="GI:116812576"
                     /db_xref="GeneID:51631"
                     /db_xref="HGNC:21608"
                     /db_xref="HPRD:17456"
                     /db_xref="MIM:613056"
     CDS             join(139045008..139045068,139060808..139060902,
                     139083345..139083443,139086883..139086993,
                     139090390..139090533,139091920..139092096,
                     139094309..139094400,139097297..139097326,
                     139102284..139102475,139106909..139107086)
                     /gene="LUC7L2"
                     /gene_synonym="CGI-59; CGI-74; FLJ10657; hLuc7B2; LUC7B2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative RNA-binding protein Luc7-like 2"
                     /protein_id="NP_057103.2"
                     /db_xref="GI:116812577"
                     /db_xref="CCDS:CCDS43656.1"
                     /db_xref="GeneID:51631"
                     /db_xref="HGNC:21608"
                     /db_xref="HPRD:17456"
                     /db_xref="MIM:613056"
     gene            complement(139102208..139112272)
                     /gene="LOC100129148"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100129148"
     misc_RNA        complement(join(139102208..139102441,139108031..139108131,
                     139112147..139112272))
                     /gene="LOC100129148"
                     /product="hypothetical LOC100129148"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033999.1"
                     /db_xref="GI:300244511"
                     /db_xref="GeneID:100129148"
     gene            complement(139138088..139168457)
                     /gene="KLRG2"
                     /gene_synonym="CLEC15B; FLJ44186; MGC131846"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:346689"
                     /db_xref="HGNC:24778"
                     /db_xref="HPRD:13485"
     mRNA            complement(join(139138088..139138453,139138857..139138960,
                     139164373..139164518,139164892..139164993,
                     139167632..139168457))
                     /gene="KLRG2"
                     /gene_synonym="CLEC15B; FLJ44186; MGC131846"
                     /product="killer cell lectin-like receptor subfamily G,
                     member 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198508.2"
                     /db_xref="GI:87080809"
                     /db_xref="GeneID:346689"
                     /db_xref="HGNC:24778"
                     /db_xref="HPRD:13485"
     CDS             complement(join(139138333..139138453,139138857..139138960,
                     139164373..139164518,139164892..139164993,
                     139167632..139168388))
                     /gene="KLRG2"
                     /gene_synonym="CLEC15B; FLJ44186; MGC131846"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="killer cell lectin-like receptor subfamily G
                     member 2"
                     /protein_id="NP_940910.1"
                     /db_xref="GI:38348332"
                     /db_xref="CCDS:CCDS5854.1"
                     /db_xref="GeneID:346689"
                     /db_xref="HGNC:24778"
                     /db_xref="HPRD:13485"
     gene            139187200..139188560
                     /gene="ST13P17"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:442730"
                     /db_xref="HGNC:38859"
     gene            139208674..139229731
                     /gene="CLEC2L"
                     /gene_synonym="FLJ32986"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:154790"
                     /db_xref="HGNC:21969"
     mRNA            join(139208674..139208863,139221020..139221094,
                     139225067..139225233,139226767..139226867,
                     139228977..139229731)
                     /gene="CLEC2L"
                     /gene_synonym="FLJ32986"
                     /product="C-type lectin domain family 2, member L"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001080511.2"
                     /db_xref="GI:168229213"
                     /db_xref="GeneID:154790"
                     /db_xref="HGNC:21969"
     CDS             join(139208674..139208863,139221020..139221094,
                     139225067..139225233,139226767..139226867,
                     139228977..139229088)
                     /gene="CLEC2L"
                     /gene_synonym="FLJ32986"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="C-type lectin domain family 2 member L"
                     /protein_id="NP_001073980.2"
                     /db_xref="GI:168229214"
                     /db_xref="CCDS:CCDS47724.1"
                     /db_xref="GeneID:154790"
                     /db_xref="HGNC:21969"
     gene            139218940..139219707
                     /gene="ERHP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100507125"
                     /db_xref="HGNC:41916"
     gene            complement(139246316..>139342363)
                     /gene="HIPK2"
                     /gene_synonym="DKFZp686K02111; FLJ23711; PRO0593"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:28996"
                     /db_xref="HGNC:14402"
                     /db_xref="MIM:606868"
     mRNA            complement(join(139246316..139258143,139259874..139260034,
                     139268563..139268810,139281463..139281744,
                     139285163..139285342,139288827..139288969,
                     139297948..139298069,139299032..139299239,
                     139305147..139305309,139311347..139311531,
                     139313699..139313785,139315911..139316030,
                     139316348..>139316493,<139342333..>139342363))
                     /gene="HIPK2"
                     /gene_synonym="DKFZp686K02111; FLJ23711; PRO0593"
                     /product="homeodomain interacting protein kinase 2,
                     transcript variant 1"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022740.4"
                     /db_xref="GI:257470982"
                     /db_xref="GeneID:28996"
                     /db_xref="HGNC:14402"
                     /db_xref="HPRD:06039"
                     /db_xref="MIM:606868"
     mRNA            complement(join(139246316..139258143,139259874..139260034,
                     139268563..139268810,139281463..139281744,
                     139285163..139285342,139288827..139288969,
                     139297948..139298069,139299032..139299158,
                     139305147..139305309,139311347..139311531,
                     139313699..139313785,139315911..139316030,
                     139316348..>139316493,<139342333..>139342363))
                     /gene="HIPK2"
                     /gene_synonym="DKFZp686K02111; FLJ23711; PRO0593"
                     /product="homeodomain interacting protein kinase 2,
                     transcript variant 2"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001113239.2"
                     /db_xref="GI:256985144"
                     /db_xref="GeneID:28996"
                     /db_xref="HGNC:14402"
                     /db_xref="MIM:606868"
     CDS             complement(join(139257673..139258143,139259874..139260034,
                     139268563..139268810,139281463..139281744,
                     139285163..139285342,139288827..139288969,
                     139297948..139298069,139299032..139299239,
                     139305147..139305309,139311347..139311531,
                     139313699..139313785,139315911..139316030,
                     139316348..>139316493,<139342333..>139342363))
                     /gene="HIPK2"
                     /gene_synonym="DKFZp686K02111; FLJ23711; PRO0593"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=2
                     /product="homeodomain-interacting protein kinase 2 isoform
                     1"
                     /protein_id="NP_073577.3"
                     /db_xref="GI:164420685"
                     /db_xref="GeneID:28996"
                     /db_xref="HGNC:14402"
                     /db_xref="HPRD:06039"
                     /db_xref="MIM:606868"
     CDS             complement(join(139257673..139258143,139259874..139260034,
                     139268563..139268810,139281463..139281744,
                     139285163..139285342,139288827..139288969,
                     139297948..139298069,139299032..139299158,
                     139305147..139305309,139311347..139311531,
                     139313699..139313785,139315911..139316030,
                     139316348..>139316493,<139342333..>139342363))
                     /gene="HIPK2"
                     /gene_synonym="DKFZp686K02111; FLJ23711; PRO0593"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=2
                     /product="homeodomain-interacting protein kinase 2 isoform
                     2"
                     /protein_id="NP_001106710.1"
                     /db_xref="GI:164420691"
                     /db_xref="GeneID:28996"
                     /db_xref="HGNC:14402"
                     /db_xref="MIM:606868"
     gap             139379378..139404377
                     /estimated_length=25000
     gene            complement(<139415730..139477693)
                     /gene="HIPK2"
                     /gene_synonym="DKFZp686K02111; FLJ23711; PRO0593"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:28996"
                     /db_xref="HGNC:14402"
                     /db_xref="MIM:606868"
     mRNA            complement(join(<139415730..139416814,
                     139477404..139477693))
                     /gene="HIPK2"
                     /gene_synonym="DKFZp686K02111; FLJ23711; PRO0593"
                     /product="homeodomain interacting protein kinase 2,
                     transcript variant 1"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022740.4"
                     /db_xref="GI:257470982"
                     /db_xref="GeneID:28996"
                     /db_xref="HGNC:14402"
                     /db_xref="HPRD:06039"
                     /db_xref="MIM:606868"
     mRNA            complement(join(<139415730..139416814,
                     139477404..139477693))
                     /gene="HIPK2"
                     /gene_synonym="DKFZp686K02111; FLJ23711; PRO0593"
                     /product="homeodomain interacting protein kinase 2,
                     transcript variant 2"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001113239.2"
                     /db_xref="GI:256985144"
                     /db_xref="GeneID:28996"
                     /db_xref="HGNC:14402"
                     /db_xref="MIM:606868"
     CDS             complement(join(<139415730..139416814,
                     139477404..139477422))
                     /gene="HIPK2"
                     /gene_synonym="DKFZp686K02111; FLJ23711; PRO0593"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeodomain-interacting protein kinase 2 isoform
                     1"
                     /protein_id="NP_073577.3"
                     /db_xref="GI:164420685"
                     /db_xref="GeneID:28996"
                     /db_xref="HGNC:14402"
                     /db_xref="HPRD:06039"
                     /db_xref="MIM:606868"
     CDS             complement(join(<139415730..139416814,
                     139477404..139477422))
                     /gene="HIPK2"
                     /gene_synonym="DKFZp686K02111; FLJ23711; PRO0593"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeodomain-interacting protein kinase 2 isoform
                     2"
                     /protein_id="NP_001106710.1"
                     /db_xref="GI:164420691"
                     /db_xref="GeneID:28996"
                     /db_xref="HGNC:14402"
                     /db_xref="MIM:606868"
     gene            139478047..139720125
                     /gene="TBXAS1"
                     /gene_synonym="CYP5; CYP5A1; FLJ52771; GHOSAL; THAS; TS;
                     TXAS; TXS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6916"
                     /db_xref="HGNC:11609"
                     /db_xref="HPRD:02035"
                     /db_xref="MIM:274180"
     mRNA            join(139478047..139478270,139480539..139480623,
                     139482465..139482528,139487137..139487225,
                     139529111..139529278,139572034..139572127,
                     139575384..139575436,139611024..139611120,
                     139635990..139636106,139653167..139653255,
                     139655258..139655406,139657433..139657563,
                     139661718..139662032,139706891..139706982,
                     139715523..139715660,139717471..139717633,
                     139719825..139720125)
                     /gene="TBXAS1"
                     /gene_synonym="CYP5; CYP5A1; FLJ52771; GHOSAL; THAS; TS;
                     TXAS; TXS"
                     /product="thromboxane A synthase 1 (platelet), transcript
                     variant 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130966.2"
                     /db_xref="GI:261278366"
                     /db_xref="GeneID:6916"
                     /db_xref="HGNC:11609"
                     /db_xref="MIM:274180"
                     /db_xref="HPRD:02035"
     mRNA            join(139478047..139478270,139482465..139482528,
                     139487137..139487225,139572034..139572127,
                     139575384..139575436,139611024..139611120,
                     139635990..139636106,139653167..139653255,
                     139655258..139655406,139657433..139657563,
                     139661718..139662032,139706891..139706982,
                     139715523..139715660,139717471..139717633,
                     139719825..139720125)
                     /gene="TBXAS1"
                     /gene_synonym="CYP5; CYP5A1; FLJ52771; GHOSAL; THAS; TS;
                     TXAS; TXS"
                     /product="thromboxane A synthase 1 (platelet), transcript
                     variant 5"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001166254.1"
                     /db_xref="GI:261278371"
                     /db_xref="GeneID:6916"
                     /db_xref="HGNC:11609"
                     /db_xref="MIM:274180"
                     /db_xref="HPRD:02035"
     mRNA            join(139528952..139529278,139572034..139572127,
                     139575384..139575436,139611024..139611120,
                     139635990..139636106,139653167..139653255,
                     139655258..139655406,139657433..139657563,
                     139661718..139662032,139706891..139706982,
                     139715523..139715660,139717471..139717633,
                     139719825..139720125)
                     /gene="TBXAS1"
                     /gene_synonym="CYP5; CYP5A1; FLJ52771; GHOSAL; THAS; TS;
                     TXAS; TXS"
                     /product="thromboxane A synthase 1 (platelet), transcript
                     variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001061.4"
                     /db_xref="GI:261278363"
                     /db_xref="GeneID:6916"
                     /db_xref="HGNC:11609"
                     /db_xref="HPRD:02035"
                     /db_xref="MIM:274180"
     mRNA            join(139528952..139529278,139572034..139572127,
                     139575384..139575436,139611024..139611120,
                     139635990..139636106,139653167..139653255,
                     139655258..139655406,139657433..139657563,
                     139661718..139662032,139706891..139706982,
                     139715523..139715660,139719825..139720125)
                     /gene="TBXAS1"
                     /gene_synonym="CYP5; CYP5A1; FLJ52771; GHOSAL; THAS; TS;
                     TXAS; TXS"
                     /product="thromboxane A synthase 1 (platelet), transcript
                     variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_030984.3"
                     /db_xref="GI:261278364"
                     /db_xref="GeneID:6916"
                     /db_xref="HGNC:11609"
                     /db_xref="HPRD:02035"
                     /db_xref="MIM:274180"
     mRNA            join(139528952..139529278,139572034..139572127,
                     139575384..139575436,139611024..139611120,
                     139635990..139636106,139652350..139652487,
                     139653167..139653255,139655258..139655406,
                     139657433..139657563,139661718..139662032,
                     139706891..139706982,139715523..139715660,
                     139717471..139717633,139719825..139720125)
                     /gene="TBXAS1"
                     /gene_synonym="CYP5; CYP5A1; FLJ52771; GHOSAL; THAS; TS;
                     TXAS; TXS"
                     /product="thromboxane A synthase 1 (platelet), transcript
                     variant 4"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001166253.1"
                     /db_xref="GI:261278369"
                     /db_xref="GeneID:6916"
                     /db_xref="HGNC:11609"
                     /db_xref="MIM:274180"
                     /db_xref="HPRD:02035"
     misc_RNA        join(139528952..139529278,139572034..139572127,
                     139575384..139575465,139611024..139611120,
                     139635990..139636106,139653167..139653255,
                     139655258..139655406,139657433..139657563,
                     139661718..139662032,139706891..139706982,
                     139715523..139715660,139717471..139717633,
                     139719825..139720125)
                     /gene="TBXAS1"
                     /gene_synonym="CYP5; CYP5A1; FLJ52771; GHOSAL; THAS; TS;
                     TXAS; TXS"
                     /product="thromboxane A synthase 1 (platelet), transcript
                     variant 6"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029394.1"
                     /db_xref="GI:261278373"
                     /db_xref="GeneID:6916"
                     /db_xref="HGNC:11609"
                     /db_xref="MIM:274180"
                     /db_xref="HPRD:02035"
     CDS             join(139529187..139529278,139572034..139572127,
                     139575384..139575436,139611024..139611120,
                     139635990..139636106,139653167..139653255,
                     139655258..139655406,139657433..139657563,
                     139661718..139662032,139706891..139706982,
                     139715523..139715660,139717471..139717633,
                     139719825..139719899)
                     /gene="TBXAS1"
                     /gene_synonym="CYP5; CYP5A1; FLJ52771; GHOSAL; THAS; TS;
                     TXAS; TXS"
                     /exception="mismatches in translation"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="thromboxane-A synthase isoform 1"
                     /protein_id="NP_001052.2"
                     /db_xref="GI:195972898"
                     /db_xref="CCDS:CCDS5855.1"
                     /db_xref="GeneID:6916"
                     /db_xref="HGNC:11609"
                     /db_xref="HPRD:02035"
                     /db_xref="MIM:274180"
     CDS             join(139529187..139529278,139572034..139572127,
                     139575384..139575436,139611024..139611120,
                     139635990..139636106,139653167..139653255,
                     139655258..139655406,139657433..139657563,
                     139661718..139662032,139706891..139706982,
                     139715523..139715660,139717471..139717633,
                     139719825..139719899)
                     /gene="TBXAS1"
                     /gene_synonym="CYP5; CYP5A1; FLJ52771; GHOSAL; THAS; TS;
                     TXAS; TXS"
                     /exception="mismatches in translation"
                     /note="isoform 1 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="thromboxane-A synthase isoform 1"
                     /protein_id="NP_001124438.1"
                     /db_xref="GI:195972896"
                     /db_xref="CCDS:CCDS5855.1"
                     /db_xref="GeneID:6916"
                     /db_xref="HGNC:11609"
                     /db_xref="HPRD:02035"
                     /db_xref="MIM:274180"
     CDS             join(139529187..139529278,139572034..139572127,
                     139575384..139575436,139611024..139611120,
                     139635990..139636106,139652350..139652487,
                     139653167..139653255,139655258..139655406,
                     139657433..139657563,139661718..139662032,
                     139706891..139706982,139715523..139715660,
                     139717471..139717633,139719825..139719899)
                     /gene="TBXAS1"
                     /gene_synonym="CYP5; CYP5A1; FLJ52771; GHOSAL; THAS; TS;
                     TXAS; TXS"
                     /exception="mismatches in translation"
                     /note="isoform 3 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="thromboxane-A synthase isoform 3"
                     /protein_id="NP_001159725.1"
                     /db_xref="GI:261278370"
                     /db_xref="CCDS:CCDS55174.1"
                     /db_xref="GeneID:6916"
                     /db_xref="HGNC:11609"
                     /db_xref="HPRD:02035"
                     /db_xref="MIM:274180"
     CDS             join(139529187..139529278,139572034..139572127,
                     139575384..139575436,139611024..139611120,
                     139635990..139636106,139653167..139653255,
                     139655258..139655406,139657433..139657563,
                     139661718..139662032,139706891..139706982,
                     139715523..139715660,139719825..139719840)
                     /gene="TBXAS1"
                     /gene_synonym="CYP5; CYP5A1; FLJ52771; GHOSAL; THAS; TS;
                     TXAS; TXS"
                     /exception="mismatches in translation"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="thromboxane-A synthase isoform 2"
                     /protein_id="NP_112246.2"
                     /db_xref="GI:195972900"
                     /db_xref="CCDS:CCDS5856.1"
                     /db_xref="GeneID:6916"
                     /db_xref="HGNC:11609"
                     /db_xref="HPRD:02035"
                     /db_xref="MIM:274180"
     CDS             join(139575402..139575436,139611024..139611120,
                     139635990..139636106,139653167..139653255,
                     139655258..139655406,139657433..139657563,
                     139661718..139662032,139706891..139706982,
                     139715523..139715660,139717471..139717633,
                     139719825..139719899)
                     /gene="TBXAS1"
                     /gene_synonym="CYP5; CYP5A1; FLJ52771; GHOSAL; THAS; TS;
                     TXAS; TXS"
                     /exception="mismatches in translation"
                     /note="isoform 4 is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="thromboxane-A synthase isoform 4"
                     /protein_id="NP_001159726.1"
                     /db_xref="GI:261278372"
                     /db_xref="CCDS:CCDS55175.1"
                     /db_xref="GeneID:6916"
                     /db_xref="HGNC:11609"
                     /db_xref="HPRD:02035"
                     /db_xref="MIM:274180"
     gene            complement(139723549..139763521)
                     /gene="PARP12"
                     /gene_synonym="FLJ22693; MST109; MSTP109; ZC3H1; ZC3HDC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64761"
                     /db_xref="HGNC:21919"
                     /db_xref="HPRD:15696"
                     /db_xref="MIM:612481"
     mRNA            complement(join(139723549..139724685,139725997..139726148,
                     139727076..139727206,139728413..139728488,
                     139734035..139734131,139737515..139737656,
                     139741444..139741639,139746684..139746807,
                     139754462..139754563,139756656..139756953,
                     139757699..139757834,139762322..139763521))
                     /gene="PARP12"
                     /gene_synonym="FLJ22693; MST109; MSTP109; ZC3H1; ZC3HDC1"
                     /product="poly (ADP-ribose) polymerase family, member 12"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022750.2"
                     /db_xref="GI:52345407"
                     /db_xref="GeneID:64761"
                     /db_xref="HGNC:21919"
                     /db_xref="HPRD:15696"
                     /db_xref="MIM:612481"
     CDS             complement(join(139724360..139724685,139725997..139726148,
                     139727076..139727206,139728413..139728488,
                     139734035..139734131,139737515..139737656,
                     139741444..139741639,139746684..139746807,
                     139754462..139754563,139756656..139756953,
                     139757699..139757834,139762322..139762647))
                     /gene="PARP12"
                     /gene_synonym="FLJ22693; MST109; MSTP109; ZC3H1; ZC3HDC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="poly [ADP-ribose] polymerase 12"
                     /protein_id="NP_073587.1"
                     /db_xref="GI:12232413"
                     /db_xref="CCDS:CCDS5857.1"
                     /db_xref="GeneID:64761"
                     /db_xref="HGNC:21919"
                     /db_xref="HPRD:15696"
                     /db_xref="MIM:612481"
     gene            complement(139784546..139876741)
                     /gene="JHDM1D"
                     /gene_synonym="KDM7A; KIAA1718"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:80853"
                     /db_xref="HGNC:22224"
     mRNA            complement(join(139784546..139790988,139791604..139791877,
                     139793856..139793938,139796355..139796563,
                     139796699..139796847,139797345..139797442,
                     139798679..139798833,139799699..139799823,
                     139801751..139801960,139810895..139810984,
                     139813291..139813382,139818913..139819019,
                     139820242..139820329,139824421..139824583,
                     139826437..139826623,139827242..139827383,
                     139829293..139829453,139833339..139833456,
                     139838905..139838990,139876544..139876741))
                     /gene="JHDM1D"
                     /gene_synonym="KDM7A; KIAA1718"
                     /product="jumonji C domain containing histone demethylase
                     1 homolog D (S. cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_030647.1"
                     /db_xref="GI:90093354"
                     /db_xref="GeneID:80853"
                     /db_xref="HGNC:22224"
     CDS             complement(join(139790894..139790988,139791604..139791877,
                     139793856..139793938,139796355..139796563,
                     139796699..139796847,139797345..139797442,
                     139798679..139798833,139799699..139799823,
                     139801751..139801960,139810895..139810984,
                     139813291..139813382,139818913..139819019,
                     139820242..139820329,139824421..139824583,
                     139826437..139826623,139827242..139827383,
                     139829293..139829453,139833339..139833456,
                     139838905..139838990,139876544..139876737))
                     /gene="JHDM1D"
                     /gene_synonym="KDM7A; KIAA1718"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="lysine-specific demethylase 7"
                     /protein_id="NP_085150.1"
                     /db_xref="GI:90093355"
                     /db_xref="CCDS:CCDS43658.1"
                     /db_xref="GeneID:80853"
                     /db_xref="HGNC:22224"
     gene            139877061..139879440
                     /gene="LOC100134229"
                     /gene_synonym="FLJ22719"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100134229"
     misc_RNA        139877061..139879440
                     /gene="LOC100134229"
                     /gene_synonym="FLJ22719"
                     /product="hypothetical LOC100134229"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024451.1"
                     /db_xref="GI:213021164"
                     /db_xref="GeneID:100134229"
     gene            139992552..139993139
                     /gene="LOC100130972"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100130972"
     gene            complement(140033552..140098311)
                     /gene="SLC37A3"
                     /gene_synonym="FLJ16367; MGC32939"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84255"
                     /db_xref="HGNC:20651"
                     /db_xref="HPRD:15381"
     mRNA            complement(join(140033552..140035304,140037084..140037149,
                     140043212..140043363,140045016..140045063,
                     140045669..140045770,140048426..140048567,
                     140051073..140051251,140051862..140051946,
                     140055468..140055564,140058440..140058585,
                     140064208..140064291,140069390..140069482,
                     140080082..140080190,140082238..140082396,
                     140098216..140098311))
                     /gene="SLC37A3"
                     /gene_synonym="FLJ16367; MGC32939"
                     /product="solute carrier family 37 (glycerol-3-phosphate
                     transporter), member 3, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_207113.1"
                     /db_xref="GI:46361975"
                     /db_xref="GeneID:84255"
                     /db_xref="HGNC:20651"
                     /db_xref="HPRD:15381"
     mRNA            complement(join(140033552..140035304,140037084..140037149,
                     140048426..140048567,140051073..140051251,
                     140051862..140051946,140055468..140055564,
                     140058440..140058585,140064208..140064291,
                     140069390..140069482,140080082..140080190,
                     140082238..140082396,140098216..140098311))
                     /gene="SLC37A3"
                     /gene_synonym="FLJ16367; MGC32939"
                     /product="solute carrier family 37 (glycerol-3-phosphate
                     transporter), member 3, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032295.2"
                     /db_xref="GI:46361974"
                     /db_xref="GeneID:84255"
                     /db_xref="HGNC:20651"
                     /db_xref="HPRD:15381"
     CDS             complement(join(140035063..140035304,140037084..140037149,
                     140048426..140048567,140051073..140051251,
                     140051862..140051946,140055468..140055564,
                     140058440..140058585,140064208..140064291,
                     140069390..140069482,140080082..140080190,
                     140082238..140082326))
                     /gene="SLC37A3"
                     /gene_synonym="FLJ16367; MGC32939"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="sugar phosphate exchanger 3 isoform 2"
                     /protein_id="NP_115671.1"
                     /db_xref="GI:14150047"
                     /db_xref="CCDS:CCDS5858.1"
                     /db_xref="GeneID:84255"
                     /db_xref="HGNC:20651"
                     /db_xref="HPRD:15381"
     CDS             complement(join(140035212..140035304,140037084..140037149,
                     140043212..140043363,140045016..140045063,
                     140045669..140045770,140048426..140048567,
                     140051073..140051251,140051862..140051946,
                     140055468..140055564,140058440..140058585,
                     140064208..140064291,140069390..140069482,
                     140080082..140080190,140082238..140082326))
                     /gene="SLC37A3"
                     /gene_synonym="FLJ16367; MGC32939"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="sugar phosphate exchanger 3 isoform 1"
                     /protein_id="NP_996996.1"
                     /db_xref="GI:46361976"
                     /db_xref="CCDS:CCDS5859.1"
                     /db_xref="GeneID:84255"
                     /db_xref="HGNC:20651"
                     /db_xref="HPRD:15381"
     gene            140103843..140126050
                     /gene="RAB19"
                     /gene_synonym="RAB19B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:401409"
                     /db_xref="HGNC:19982"
                     /db_xref="HPRD:17946"
     mRNA            join(140103843..140104017,140107424..140107647,
                     140111674..140111857,140125682..140126050)
                     /gene="RAB19"
                     /gene_synonym="RAB19B"
                     /product="RAB19, member RAS oncogene family"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001008749.2"
                     /db_xref="GI:239915975"
                     /db_xref="GeneID:401409"
                     /db_xref="HGNC:19982"
                     /db_xref="HPRD:17946"
     CDS             join(140107447..140107647,140111674..140111857,
                     140125682..140125950)
                     /gene="RAB19"
                     /gene_synonym="RAB19B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ras-related protein Rab-19"
                     /protein_id="NP_001008749.2"
                     /db_xref="GI:239915976"
                     /db_xref="CCDS:CCDS34762.2"
                     /db_xref="GeneID:401409"
                     /db_xref="HGNC:19982"
                     /db_xref="HPRD:17946"
     gene            complement(140135113..140146606)
                     /gene="LOC642355"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:642355"
     gene            complement(140152840..140179369)
                     /gene="MKRN1"
                     /gene_synonym="FLJ21334; RNF61"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23608"
                     /db_xref="HGNC:7112"
                     /db_xref="HPRD:09673"
                     /db_xref="MIM:607754"
     mRNA            complement(join(140152840..140154529,140154895..140155033,
                     140155590..140155700,140156452..140156666,
                     140158807..140159033,140159507..140159736,
                     140171683..140171811,140178960..140179369))
                     /gene="MKRN1"
                     /gene_synonym="FLJ21334; RNF61"
                     /product="makorin ring finger protein 1, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013446.3"
                     /db_xref="GI:223468619"
                     /db_xref="GeneID:23608"
                     /db_xref="HGNC:7112"
                     /db_xref="HPRD:09673"
                     /db_xref="MIM:607754"
     CDS             complement(join(140154317..140154529,140154895..140155033,
                     140155590..140155700,140156452..140156666,
                     140158807..140159033,140159507..140159736,
                     140171683..140171811,140178960..140179144))
                     /gene="MKRN1"
                     /gene_synonym="FLJ21334; RNF61"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase makorin-1 isoform 1"
                     /protein_id="NP_038474.2"
                     /db_xref="GI:223468620"
                     /db_xref="CCDS:CCDS5860.1"
                     /db_xref="GeneID:23608"
                     /db_xref="HGNC:7112"
                     /db_xref="HPRD:09673"
                     /db_xref="MIM:607754"
     mRNA            complement(join(140155983..140156666,140158807..140159033,
                     140159507..140159736,140171683..140171811,
                     140178960..140179369))
                     /gene="MKRN1"
                     /gene_synonym="FLJ21334; RNF61"
                     /product="makorin ring finger protein 1, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001145125.1"
                     /db_xref="GI:223468621"
                     /db_xref="GeneID:23608"
                     /db_xref="HGNC:7112"
                     /db_xref="MIM:607754"
                     /db_xref="HPRD:09673"
     CDS             complement(join(140156448..140156666,140158807..140159033,
                     140159507..140159736,140171683..140171811,
                     140178960..140179144))
                     /gene="MKRN1"
                     /gene_synonym="FLJ21334; RNF61"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase makorin-1 isoform 2"
                     /protein_id="NP_001138597.1"
                     /db_xref="GI:223468622"
                     /db_xref="CCDS:CCDS47725.1"
                     /db_xref="GeneID:23608"
                     /db_xref="HGNC:7112"
                     /db_xref="HPRD:09673"
                     /db_xref="MIM:607754"
     gene            complement(140218220..140302342)
                     /gene="DENND2A"
                     /gene_synonym="FAM31D; KIAA1277"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:27147"
                     /db_xref="HGNC:22212"
                     /db_xref="HPRD:17210"
     mRNA            complement(join(140218220..140218538,140219432..140219518,
                     140221655..140221900,140223107..140223224,
                     140225551..140225592,140227118..140227295,
                     140244418..140244566,140246599..140246739,
                     140255436..140255513,140257943..140258012,
                     140259508..140259617,140266886..140267073,
                     140268563..140268613,140269445..140269538,
                     140273608..140273808,140285389..140285510,
                     140287453..140287580,140301203..140302342))
                     /gene="DENND2A"
                     /gene_synonym="FAM31D; KIAA1277"
                     /product="DENN/MADD domain containing 2A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015689.3"
                     /db_xref="GI:154813194"
                     /db_xref="GeneID:27147"
                     /db_xref="HGNC:22212"
                     /db_xref="HPRD:17210"
     CDS             complement(join(140218507..140218538,140219432..140219518,
                     140221655..140221900,140223107..140223224,
                     140225551..140225592,140227118..140227295,
                     140244418..140244566,140246599..140246739,
                     140255436..140255513,140257943..140258012,
                     140259508..140259617,140266886..140267073,
                     140268563..140268613,140269445..140269538,
                     140273608..140273808,140285389..140285510,
                     140287453..140287580,140301203..140302197))
                     /gene="DENND2A"
                     /gene_synonym="FAM31D; KIAA1277"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="DENN domain-containing protein 2A"
                     /protein_id="NP_056504.3"
                     /db_xref="GI:154813195"
                     /db_xref="CCDS:CCDS43659.1"
                     /db_xref="GeneID:27147"
                     /db_xref="HGNC:22212"
                     /db_xref="HPRD:17210"
     gene            140372953..140394908
                     /gene="ADCK2"
                     /gene_synonym="AARF; MGC20727"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:90956"
                     /db_xref="HGNC:19039"
                     /db_xref="HPRD:10631"
     mRNA            join(140372953..140374063,140374411..140374557,
                     140378955..140379083,140380842..140380937,
                     140386790..140387041,140389397..140389525,
                     140390560..140390613,140394463..140394908)
                     /gene="ADCK2"
                     /gene_synonym="AARF; MGC20727"
                     /product="aarF domain containing kinase 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_052853.3"
                     /db_xref="GI:41393591"
                     /db_xref="GeneID:90956"
                     /db_xref="HGNC:19039"
                     /db_xref="HPRD:10631"
     CDS             join(140373131..140374063,140374411..140374557,
                     140378955..140379083,140380842..140380937,
                     140386790..140387041,140389397..140389525,
                     140390560..140390613,140394463..140394603)
                     /gene="ADCK2"
                     /gene_synonym="AARF; MGC20727"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="aarF domain containing kinase 2"
                     /protein_id="NP_443085.2"
                     /db_xref="GI:32261307"
                     /db_xref="CCDS:CCDS5861.1"
                     /db_xref="GeneID:90956"
                     /db_xref="HGNC:19039"
                     /db_xref="HPRD:10631"
     gene            complement(140395136..140396877)
                     /gene="LOC100134713"
                     /gene_synonym="FLJ26073"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100134713"
     misc_RNA        complement(join(140395136..140396620,
                     140396715..140396877))
                     /gene="LOC100134713"
                     /gene_synonym="FLJ26073"
                     /product="hypothetical LOC100134713"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024454.1"
                     /db_xref="GI:213021181"
                     /db_xref="GeneID:100134713"
     gene            140396481..140406446
                     /gene="NDUFB2"
                     /gene_synonym="AGGG; CI-AGGG; MGC70788"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4708"
                     /db_xref="HGNC:7697"
                     /db_xref="HPRD:11953"
                     /db_xref="MIM:603838"
     mRNA            join(140396481..140396642,140402666..140402810,
                     140404660..140404763,140406363..140406446)
                     /gene="NDUFB2"
                     /gene_synonym="AGGG; CI-AGGG; MGC70788"
                     /product="NADH dehydrogenase (ubiquinone) 1 beta
                     subcomplex, 2, 8kDa"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004546.2"
                     /db_xref="GI:33519465"
                     /db_xref="GeneID:4708"
                     /db_xref="HGNC:7697"
                     /db_xref="HPRD:11953"
                     /db_xref="MIM:603838"
     CDS             join(140396545..140396642,140402666..140402810,
                     140404660..140404734)
                     /gene="NDUFB2"
                     /gene_synonym="AGGG; CI-AGGG; MGC70788"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="NADH dehydrogenase [ubiquinone] 1 beta
                     subcomplex subunit 2, mitochondrial precursor"
                     /protein_id="NP_004537.1"
                     /db_xref="GI:4758778"
                     /db_xref="CCDS:CCDS5862.1"
                     /db_xref="GeneID:4708"
                     /db_xref="HGNC:7697"
                     /db_xref="HPRD:11953"
                     /db_xref="MIM:603838"
     gene            complement(140433812..140624564)
                     /gene="BRAF"
                     /gene_synonym="B-RAF1; BRAF1; FLJ95109; MGC126806;
                     MGC138284; NS7; RAFB1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:673"
                     /db_xref="HGNC:1097"
                     /db_xref="HPRD:01264"
                     /db_xref="MIM:164757"
     mRNA            complement(join(140433812..140434570,140439612..140439746,
                     140449087..140449218,140453075..140453193,
                     140453987..140454033,140476712..140476888,
                     140477791..140477875,140481376..140481493,
                     140482821..140482957,140487348..140487384,
                     140494108..140494267,140500162..140500281,
                     140501212..140501360,140507760..140507862,
                     140508692..140508795,140534409..140534672,
                     140549911..140550012,140624366..140624564))
                     /gene="BRAF"
                     /gene_synonym="B-RAF1; BRAF1; FLJ95109; MGC126806;
                     MGC138284; NS7; RAFB1"
                     /product="v-raf murine sarcoma viral oncogene homolog B1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004333.4"
                     /db_xref="GI:187608632"
                     /db_xref="GeneID:673"
                     /db_xref="HGNC:1097"
                     /db_xref="HPRD:01264"
                     /db_xref="MIM:164757"
     CDS             complement(join(140434397..140434570,140439612..140439746,
                     140449087..140449218,140453075..140453193,
                     140453987..140454033,140476712..140476888,
                     140477791..140477875,140481376..140481493,
                     140482821..140482957,140487348..140487384,
                     140494108..140494267,140500162..140500281,
                     140501212..140501360,140507760..140507862,
                     140508692..140508795,140534409..140534672,
                     140549911..140550012,140624366..140624503))
                     /gene="BRAF"
                     /gene_synonym="B-RAF1; BRAF1; FLJ95109; MGC126806;
                     MGC138284; NS7; RAFB1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="serine/threonine-protein kinase B-raf"
                     /protein_id="NP_004324.2"
                     /db_xref="GI:33188459"
                     /db_xref="CCDS:CCDS5863.1"
                     /db_xref="GeneID:673"
                     /db_xref="HGNC:1097"
                     /db_xref="HPRD:01264"
                     /db_xref="MIM:164757"
     gene            complement(140697740..140699594)
                     /gene="CCT4P1"
                     /gene_synonym="CCT4-2P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:650172"
                     /db_xref="HGNC:35151"
     gene            complement(140705961..140714781)
                     /gene="MRPS33"
                     /gene_synonym="CGI-139; FLJ21123; MRP-S33; PTD003"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51650"
                     /db_xref="HGNC:16634"
                     /db_xref="HPRD:17598"
                     /db_xref="MIM:611993"
     mRNA            complement(join(140705961..140706335,140710219..140710460,
                     140714711..140714781))
                     /gene="MRPS33"
                     /gene_synonym="CGI-139; FLJ21123; MRP-S33; PTD003"
                     /product="mitochondrial ribosomal protein S33, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_053035.2"
                     /db_xref="GI:187167259"
                     /db_xref="GeneID:51650"
                     /db_xref="HGNC:16634"
                     /db_xref="HPRD:17598"
                     /db_xref="MIM:611993"
     mRNA            complement(join(140705961..140706335,140710219..140710460,
                     140714351..140714479))
                     /gene="MRPS33"
                     /gene_synonym="CGI-139; FLJ21123; MRP-S33; PTD003"
                     /product="mitochondrial ribosomal protein S33, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016071.3"
                     /db_xref="GI:187167257"
                     /db_xref="GeneID:51650"
                     /db_xref="HGNC:16634"
                     /db_xref="HPRD:17598"
                     /db_xref="MIM:611993"
     CDS             complement(join(140706230..140706335,
                     140710219..140710433))
                     /gene="MRPS33"
                     /gene_synonym="CGI-139; FLJ21123; MRP-S33; PTD003"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="28S ribosomal protein S33, mitochondrial"
                     /protein_id="NP_057155.1"
                     /db_xref="GI:7706349"
                     /db_xref="CCDS:CCDS5864.1"
                     /db_xref="GeneID:51650"
                     /db_xref="HGNC:16634"
                     /db_xref="HPRD:17598"
                     /db_xref="MIM:611993"
     CDS             complement(join(140706230..140706335,
                     140710219..140710433))
                     /gene="MRPS33"
                     /gene_synonym="CGI-139; FLJ21123; MRP-S33; PTD003"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="28S ribosomal protein S33, mitochondrial"
                     /protein_id="NP_444263.1"
                     /db_xref="GI:16950597"
                     /db_xref="CCDS:CCDS5864.1"
                     /db_xref="GeneID:51650"
                     /db_xref="HGNC:16634"
                     /db_xref="HPRD:17598"
                     /db_xref="MIM:611993"
     gene            140774032..141180180
                     /gene="LOC100507421"
                     /gene_synonym="DKFZp547G036; FLJ39162; FLJ42883"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100507421"
     mRNA            join(140774032..140774492,140912391..140912504,
                     141137408..141137545,141170336..141180180)
                     /gene="LOC100507421"
                     /gene_synonym="DKFZp547G036; FLJ39162; FLJ42883"
                     /product="transmembrane protein 178-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001195278.1"
                     /db_xref="GI:305632806"
                     /db_xref="GeneID:100507421"
     CDS             join(140774111..140774492,140912391..140912504,
                     141137408..141137545,141170336..141170586)
                     /gene="LOC100507421"
                     /gene_synonym="DKFZp547G036; FLJ39162; FLJ42883"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 178-like"
                     /protein_id="NP_001182207.1"
                     /db_xref="GI:305632807"
                     /db_xref="GeneID:100507421"
     gene            141115747..141116169
                     /gene="LOC100130169"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /db_xref="GeneID:100130169"
     misc_RNA        141115747..141116169
                     /gene="LOC100130169"
                     /product="hypothetical LOC100130169"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 Protein"
                     /transcript_id="XR_108782.1"
                     /db_xref="GI:310120111"
                     /db_xref="GeneID:100130169"
     gene            141251078..141354209
                     /gene="AGK"
                     /gene_synonym="FLJ10842; MULK"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55750"
                     /db_xref="HGNC:21869"
                     /db_xref="HPRD:08554"
                     /db_xref="MIM:610345"
     mRNA            join(141251078..141251234,141255253..141255367,
                     141292946..141292985,141296362..141296441,
                     141301005..141301080,141310995..141311087,
                     141313946..141313978,141315271..141315365,
                     141321532..141321601,141333701..141333780,
                     141336760..141336817,141341048..141341198,
                     141341611..141341708,141349063..141349133,
                     141351325..141351409,141352587..141354209)
                     /gene="AGK"
                     /gene_synonym="FLJ10842; MULK"
                     /product="acylglycerol kinase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018238.3"
                     /db_xref="GI:187607258"
                     /db_xref="GeneID:55750"
                     /db_xref="HGNC:21869"
                     /db_xref="HPRD:08554"
                     /db_xref="MIM:610345"
     CDS             join(141255267..141255367,141292946..141292985,
                     141296362..141296441,141301005..141301080,
                     141310995..141311087,141313946..141313978,
                     141315271..141315365,141321532..141321601,
                     141333701..141333780,141336760..141336817,
                     141341048..141341198,141341611..141341708,
                     141349063..141349133,141351325..141351409,
                     141352587..141352724)
                     /gene="AGK"
                     /gene_synonym="FLJ10842; MULK"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="acylglycerol kinase, mitochondrial precursor"
                     /protein_id="NP_060708.1"
                     /db_xref="GI:8922701"
                     /db_xref="CCDS:CCDS5865.1"
                     /db_xref="GeneID:55750"
                     /db_xref="HGNC:21869"
                     /db_xref="HPRD:08554"
                     /db_xref="MIM:610345"
     gene            complement(141356528..141401953)
                     /gene="KIAA1147"
                     /gene_synonym="LCHN; PRO2561"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57189"
                     /db_xref="HGNC:29472"
     mRNA            complement(join(141356528..141362651,141363972..141364040,
                     141364704..141364854,141364987..141365118,
                     141366087..141366225,141373867..141374020,
                     141385278..141385436,141386359..141386458,
                     141401686..141401953))
                     /gene="KIAA1147"
                     /gene_synonym="LCHN; PRO2561"
                     /product="KIAA1147"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001080392.1"
                     /db_xref="GI:122937184"
                     /db_xref="GeneID:57189"
                     /db_xref="HGNC:29472"
     CDS             complement(join(141362456..141362651,141363972..141364040,
                     141364704..141364854,141364987..141365118,
                     141366087..141366225,141373867..141374020,
                     141385278..141385436,141386359..141386458,
                     141401686..141401953))
                     /gene="KIAA1147"
                     /gene_synonym="LCHN; PRO2561"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein LCHN"
                     /protein_id="NP_001073861.1"
                     /db_xref="GI:122937185"
                     /db_xref="CCDS:CCDS47726.1"
                     /db_xref="GeneID:57189"
                     /db_xref="HGNC:29472"
     gene            complement(141404138..141438030)
                     /gene="FLJ40852"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285962"
     misc_RNA        complement(join(141404138..141405557,141413989..141414174,
                     141423716..141423824,141427004..141427178,
                     141427792..141427945,141437183..141437367,
                     141437998..141438030))
                     /gene="FLJ40852"
                     /product="hypothetical LOC285962"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_015392.1"
                     /db_xref="GI:213417881"
                     /db_xref="GeneID:285962"
     gene            141408153..141431071
                     /gene="WEE2"
                     /gene_synonym="FLJ16107; WEE1B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:494551"
                     /db_xref="HGNC:19684"
                     /db_xref="MIM:614084"
     mRNA            join(141408153..141408900,141414009..141414205,
                     141416022..141416067,141418872..141419044,
                     141420735..141420856,141422934..141423080,
                     141423741..141423848,141423990..141424075,
                     141424826..141424996,141427104..141427246,
                     141429331..141429473,141430095..141431071)
                     /gene="WEE2"
                     /gene_synonym="FLJ16107; WEE1B"
                     /product="WEE1 homolog 2 (S. pombe)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001105558.1"
                     /db_xref="GI:157738686"
                     /db_xref="GeneID:494551"
                     /db_xref="HGNC:19684"
                     /db_xref="MIM:614084"
     CDS             join(141408559..141408900,141414009..141414205,
                     141416022..141416067,141418872..141419044,
                     141420735..141420856,141422934..141423080,
                     141423741..141423848,141423990..141424075,
                     141424826..141424996,141427104..141427246,
                     141429331..141429473,141430095..141430120)
                     /gene="WEE2"
                     /gene_synonym="FLJ16107; WEE1B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="wee1-like protein kinase 2"
                     /protein_id="NP_001099028.1"
                     /db_xref="GI:157738687"
                     /db_xref="CCDS:CCDS43660.1"
                     /db_xref="GeneID:494551"
                     /db_xref="HGNC:19684"
                     /db_xref="MIM:614084"
     gene            141438176..141450257
                     /gene="SSBP1"
                     /gene_synonym="Mt-SSB; mtSSB; SOSS-B1; SSBP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6742"
                     /db_xref="HGNC:11317"
                     /db_xref="HPRD:02703"
                     /db_xref="MIM:600439"
     mRNA            join(141438176..141438210,141438924..141438990,
                     141441969..141442029,141443361..141443501,
                     141443702..141443789,141445296..141445384,
                     141450111..141450257)
                     /gene="SSBP1"
                     /gene_synonym="Mt-SSB; mtSSB; SOSS-B1; SSBP"
                     /product="single-stranded DNA binding protein 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003143.1"
                     /db_xref="GI:4507230"
                     /db_xref="GeneID:6742"
                     /db_xref="HGNC:11317"
                     /db_xref="HPRD:02703"
                     /db_xref="MIM:600439"
     CDS             join(141438967..141438990,141441969..141442029,
                     141443361..141443501,141443702..141443789,
                     141445296..141445384,141450111..141450154)
                     /gene="SSBP1"
                     /gene_synonym="Mt-SSB; mtSSB; SOSS-B1; SSBP"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="single-stranded DNA-binding protein,
                     mitochondrial precursor"
                     /protein_id="NP_003134.1"
                     /db_xref="GI:4507231"
                     /db_xref="CCDS:CCDS5866.1"
                     /db_xref="GeneID:6742"
                     /db_xref="HGNC:11317"
                     /db_xref="HPRD:02703"
                     /db_xref="MIM:600439"
     gene            141463897..141464997
                     /gene="TAS2R3"
                     /gene_synonym="T2R3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:50831"
                     /db_xref="HGNC:14910"
                     /db_xref="HPRD:05335"
                     /db_xref="MIM:604868"
     mRNA            141463897..141464997
                     /gene="TAS2R3"
                     /gene_synonym="T2R3"
                     /product="taste receptor, type 2, member 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016943.2"
                     /db_xref="GI:67944636"
                     /db_xref="GeneID:50831"
                     /db_xref="HGNC:14910"
                     /db_xref="HPRD:05335"
                     /db_xref="MIM:604868"
     CDS             141463959..141464909
                     /gene="TAS2R3"
                     /gene_synonym="T2R3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="taste receptor type 2 member 3"
                     /protein_id="NP_058639.1"
                     /db_xref="GI:8394398"
                     /db_xref="CCDS:CCDS5867.1"
                     /db_xref="GeneID:50831"
                     /db_xref="HGNC:14910"
                     /db_xref="HPRD:05335"
                     /db_xref="MIM:604868"
     gene            141478289..141479188
                     /gene="TAS2R4"
                     /gene_synonym="MGC163311; T2R4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:50832"
                     /db_xref="HGNC:14911"
                     /db_xref="HPRD:05336"
                     /db_xref="MIM:604869"
     mRNA            141478289..141479188
                     /gene="TAS2R4"
                     /gene_synonym="MGC163311; T2R4"
                     /product="taste receptor, type 2, member 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016944.1"
                     /db_xref="GI:8394401"
                     /db_xref="GeneID:50832"
                     /db_xref="HGNC:14911"
                     /db_xref="HPRD:05336"
                     /db_xref="MIM:604869"
     CDS             141478289..141479188
                     /gene="TAS2R4"
                     /gene_synonym="MGC163311; T2R4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="taste receptor type 2 member 4"
                     /protein_id="NP_058640.1"
                     /db_xref="GI:8394402"
                     /db_xref="CCDS:CCDS5868.1"
                     /db_xref="GeneID:50832"
                     /db_xref="HGNC:14911"
                     /db_xref="HPRD:05336"
                     /db_xref="MIM:604869"
     gene            141487614..141488436
                     /gene="PS3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:448990"
     gene            141490017..141491166
                     /gene="TAS2R5"
                     /gene_synonym="MGC126635; MGC126637; T2R5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54429"
                     /db_xref="HGNC:14912"
                     /db_xref="HPRD:05453"
                     /db_xref="MIM:605062"
     mRNA            141490017..141491166
                     /gene="TAS2R5"
                     /gene_synonym="MGC126635; MGC126637; T2R5"
                     /product="taste receptor, type 2, member 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018980.2"
                     /db_xref="GI:67944637"
                     /db_xref="GeneID:54429"
                     /db_xref="HGNC:14912"
                     /db_xref="HPRD:05453"
                     /db_xref="MIM:605062"
     CDS             141490162..141491061
                     /gene="TAS2R5"
                     /gene_synonym="MGC126635; MGC126637; T2R5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="taste receptor type 2 member 5"
                     /protein_id="NP_061853.1"
                     /db_xref="GI:9507173"
                     /db_xref="CCDS:CCDS5869.1"
                     /db_xref="GeneID:54429"
                     /db_xref="HGNC:14912"
                     /db_xref="HPRD:05453"
                     /db_xref="MIM:605062"
     gene            141503357..141503428
                     /gene="TRNAQ48P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100189516"
                     /db_xref="HGNC:35091"
     gene            complement(141503495..141504432)
                     /gene="MTND1P3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100288984"
                     /db_xref="HGNC:42052"
     gene            141511710..141512057
                     /gene="MYL6P4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:642627"
                     /db_xref="HGNC:37813"
     gene            complement(141536078..141541221)
                     /gene="PRSS37"
                     /gene_synonym="TRYX2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:136242"
                     /db_xref="HGNC:29211"
                     /db_xref="HPRD:17297"
     mRNA            complement(join(141536078..141536335,141536912..141537048,
                     141537660..141537913,141539138..141539279,
                     141540816..141541221))
                     /gene="PRSS37"
                     /gene_synonym="TRYX2"
                     /product="protease, serine, 37, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001008270.2"
                     /db_xref="GI:285394163"
                     /db_xref="GeneID:136242"
                     /db_xref="HGNC:29211"
                     /db_xref="HPRD:17297"
     mRNA            complement(join(141536078..141536335,141536912..141537048,
                     141537663..141537913,141539138..141539279,
                     141540816..141541221))
                     /gene="PRSS37"
                     /gene_synonym="TRYX2"
                     /product="protease, serine, 37, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001171951.1"
                     /db_xref="GI:285394226"
                     /db_xref="GeneID:136242"
                     /db_xref="HGNC:29211"
                     /db_xref="HPRD:17297"
     CDS             complement(join(141536195..141536335,141536912..141537048,
                     141537660..141537913,141539138..141539279,
                     141540816..141540849))
                     /gene="PRSS37"
                     /gene_synonym="TRYX2"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable inactive serine protease 37 isoform 1
                     precursor"
                     /protein_id="NP_001008271.2"
                     /db_xref="GI:285394164"
                     /db_xref="CCDS:CCDS34764.1"
                     /db_xref="GeneID:136242"
                     /db_xref="HGNC:29211"
                     /db_xref="HPRD:17297"
     CDS             complement(join(141536195..141536335,141536912..141537048,
                     141537663..141537913,141539138..141539279,
                     141540816..141540849))
                     /gene="PRSS37"
                     /gene_synonym="TRYX2"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="probable inactive serine protease 37 isoform 2
                     precursor"
                     /protein_id="NP_001165422.1"
                     /db_xref="GI:285394227"
                     /db_xref="GeneID:136242"
                     /db_xref="HGNC:29211"
                     /db_xref="HPRD:17297"
     gene            141562659..141563618
                     /gene="OR9A3P"
                     /gene_synonym="OR9A6P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392106"
                     /db_xref="HGNC:15094"
     gene            141586948..141587736
                     /gene="OR9A1P"
                     /gene_synonym="HSHTPCRX06; HTPCRX06; OR9A1; OR9A5P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:26495"
                     /db_xref="HGNC:8486"
     gene            141611202..141611822
                     /gene="OR9N1P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:81383"
                     /db_xref="HGNC:15096"
     gene            141618676..141619620
                     /gene="OR9A4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:130075"
                     /db_xref="HGNC:15095"
                     /db_xref="HPRD:17797"
     mRNA            141618676..141619620
                     /gene="OR9A4"
                     /product="olfactory receptor, family 9, subfamily A,
                     member 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001001656.1"
                     /db_xref="GI:48717230"
                     /db_xref="GeneID:130075"
                     /db_xref="HGNC:15095"
                     /db_xref="HPRD:17797"
     CDS             141618676..141619620
                     /gene="OR9A4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 9A4"
                     /protein_id="NP_001001656.1"
                     /db_xref="GI:48717231"
                     /db_xref="CCDS:CCDS43661.1"
                     /db_xref="GeneID:130075"
                     /db_xref="HGNC:15095"
                     /db_xref="HPRD:17797"
     gene            complement(141627157..141646783)
                     /gene="CLEC5A"
                     /gene_synonym="CLECSF5; MDL-1; MDL1; MGC138304"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23601"
                     /db_xref="HGNC:2054"
                     /db_xref="HPRD:09229"
                     /db_xref="MIM:604987"
     mRNA            complement(join(141627157..141630018,141631520..141631626,
                     141635614..141635750,141643696..141643764,
                     141645141..141645200,141646014..141646112,
                     141646607..141646783))
                     /gene="CLEC5A"
                     /gene_synonym="CLECSF5; MDL-1; MDL1; MGC138304"
                     /product="C-type lectin domain family 5, member A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013252.2"
                     /db_xref="GI:31747574"
                     /db_xref="GeneID:23601"
                     /db_xref="HGNC:2054"
                     /db_xref="HPRD:09229"
                     /db_xref="MIM:604987"
     CDS             complement(join(141629904..141630018,141631520..141631626,
                     141635614..141635750,141643696..141643764,
                     141645141..141645200,141646014..141646092))
                     /gene="CLEC5A"
                     /gene_synonym="CLECSF5; MDL-1; MDL1; MGC138304"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="C-type lectin domain family 5 member A"
                     /protein_id="NP_037384.1"
                     /db_xref="GI:10281669"
                     /db_xref="CCDS:CCDS5870.1"
                     /db_xref="GeneID:23601"
                     /db_xref="HGNC:2054"
                     /db_xref="HPRD:09229"
                     /db_xref="MIM:604987"
     gene            complement(141672431..141673573)
                     /gene="TAS2R38"
                     /gene_synonym="PTC; T2R38; T2R61"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5726"
                     /db_xref="HGNC:9584"
                     /db_xref="HPRD:09672"
                     /db_xref="MIM:607751"
     mRNA            complement(141672431..141673573)
                     /gene="TAS2R38"
                     /gene_synonym="PTC; T2R38; T2R61"
                     /product="taste receptor, type 2, member 38"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_176817.4"
                     /db_xref="GI:261490644"
                     /db_xref="GeneID:5726"
                     /db_xref="HGNC:9584"
                     /db_xref="HPRD:09672"
                     /db_xref="MIM:607751"
     CDS             complement(141672488..141673489)
                     /gene="TAS2R38"
                     /gene_synonym="PTC; T2R38; T2R61"
                     /exception="mismatches in translation"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="taste receptor type 2 member 38"
                     /protein_id="NP_789787.4"
                     /db_xref="GI:261490645"
                     /db_xref="CCDS:CCDS34765.1"
                     /db_xref="GeneID:5726"
                     /db_xref="HGNC:9584"
                     /db_xref="HPRD:09672"
                     /db_xref="MIM:607751"
     gene            141695679..141806547
                     /gene="MGAM"
                     /gene_synonym="MG; MGA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8972"
                     /db_xref="HGNC:7043"
                     /db_xref="HPRD:01104"
                     /db_xref="MIM:154360"
     mRNA            join(141695679..141695730,141705329..141705457,
                     141708306..141708505,141718999..141719119,
                     141720774..141720883,141721386..141721537,
                     141722068..141722239,141724850..141724949,
                     141726915..141727027,141727410..141727535,
                     141730162..141730293,141730441..141730557,
                     141731480..141731593,141732625..141732709,
                     141734062..141734179,141734470..141734641,
                     141735969..141736085,141736623..141736777,
                     141738331..141738415,141739915..141739971,
                     141740522..141740646,141747585..141747673,
                     141750035..141750084,141750497..141750664,
                     141752094..141752246,141752584..141752784,
                     141754554..141754708,141755358..141755526,
                     141755800..141755896,141756630..141756742,
                     141758003..141758128,141759272..141759400,
                     141759656..141759766,141760111..141760173,
                     141762368..141762502,141763299..141763386,
                     141764184..141764322,141765135..141765268,
                     141794420..141794454,141794547..141794663,
                     141795365..141795513,141796131..141796215,
                     141797393..141797449,141799413..141799537,
                     141800602..141800690,141802430..141802479,
                     141803069..141803239,141805614..141806547)
                     /gene="MGAM"
                     /gene_synonym="MG; MGA"
                     /product="maltase-glucoamylase (alpha-glucosidase)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004668.2"
                     /db_xref="GI:221316698"
                     /db_xref="GeneID:8972"
                     /db_xref="HGNC:7043"
                     /db_xref="HPRD:01104"
                     /db_xref="MIM:154360"
     CDS             join(141705331..141705457,141708306..141708505,
                     141718999..141719119,141720774..141720883,
                     141721386..141721537,141722068..141722239,
                     141724850..141724949,141726915..141727027,
                     141727410..141727535,141730162..141730293,
                     141730441..141730557,141731480..141731593,
                     141732625..141732709,141734062..141734179,
                     141734470..141734641,141735969..141736085,
                     141736623..141736777,141738331..141738415,
                     141739915..141739971,141740522..141740646,
                     141747585..141747673,141750035..141750084,
                     141750497..141750664,141752094..141752246,
                     141752584..141752784,141754554..141754708,
                     141755358..141755526,141755800..141755896,
                     141756630..141756742,141758003..141758128,
                     141759272..141759400,141759656..141759766,
                     141760111..141760173,141762368..141762502,
                     141763299..141763386,141764184..141764322,
                     141765135..141765268,141794420..141794454,
                     141794547..141794663,141795365..141795513,
                     141796131..141796215,141797393..141797449,
                     141799413..141799537,141800602..141800690,
                     141802430..141802479,141803069..141803239,
                     141805614..141805691)
                     /gene="MGAM"
                     /gene_synonym="MG; MGA"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="maltase-glucoamylase, intestinal"
                     /protein_id="NP_004659.2"
                     /db_xref="GI:221316699"
                     /db_xref="CCDS:CCDS47727.1"
                     /db_xref="GeneID:8972"
                     /db_xref="HGNC:7043"
                     /db_xref="HPRD:01104"
                     /db_xref="MIM:154360"
     gene            141776438..141794663
                     /gene="LOC100421262"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421262"
     gene            141811549..141843783
                     /gene="LOC93432"
                     /gene_synonym="MGC138178; MGC138180"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:93432"
     misc_RNA        join(141811549..141811607,141816674..141816779,
                     141820102..141820181,141830748..141830871,
                     141831318..141831427,141831731..141831885,
                     141833781..141833952,141836341..141836440,
                     141837233..141837345,141838342..141838467,
                     141840602..141840733,141840821..141840919,
                     141843569..141843783)
                     /gene="LOC93432"
                     /gene_synonym="MGC138178; MGC138180"
                     /product="maltase-glucoamylase-like pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003715.1"
                     /db_xref="GI:156713455"
                     /db_xref="GeneID:93432"
     gene            141870970..141921088
                     /gene="LOC100124692"
                     /gene_synonym="FLJ16351"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:100124692"
     misc_RNA        join(141870970..141871240,141871898..141871994,
                     141872452..141872564,141873029..141873154,
                     141875452..141875580,141883066..141883173,
                     141884877..141884939,141885789..141885923,
                     141887550..141887634,141889167..141889305,
                     141895954..141896087,141896365..141896399,
                     141896500..141896616,141897200..141897348,
                     141897444..141897528,141897939..141897995,
                     141898415..141898539,141899680..141899768,
                     141908020..141908106,141908373..141908422,
                     141918161..141918331,141919670..141919974,
                     141920098..141920240,141920364..141921088)
                     /gene="LOC100124692"
                     /gene_synonym="FLJ16351"
                     /product="maltase-glucoamylase-like pseudogene"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_003717.1"
                     /db_xref="GI:156713482"
                     /db_xref="GeneID:100124692"
     gene            complement(141940556..141946886)
                     /gene="MOXD2P"
                     /gene_synonym="MOXD2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100289017"
                     /db_xref="HGNC:33605"
     misc_RNA        complement(join(141940556..141940690,141942123..141942182,
                     141942317..141942413,141942701..141942792,
                     141943143..141943309,141943502..141943604,
                     141943796..141943963,141944780..141944863,
                     141945109..141945270,141945806..141945888,
                     141945890..141945952,141946599..141946886))
                     /gene="MOXD2P"
                     /gene_synonym="MOXD2"
                     /product="monooxygenase, DBH-like 2, pseudogene"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /transcript_id="NR_024346.2"
                     /db_xref="GI:269985699"
                     /db_xref="GeneID:100289017"
                     /db_xref="HGNC:33605"
     gene            complement(141951958..141957878)
                     /gene="PRSS58"
                     /gene_synonym="FLJ16649; MGC35022; PRSS1; TRY1; TRYX3;
                     UNQ2540"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:136541"
                     /db_xref="HGNC:39125"
     mRNA            complement(join(141951958..141952190,141952292..141952431,
                     141954875..141955131,141955355..141955493,
                     141957488..141957568,141957811..141957878))
                     /gene="PRSS58"
                     /gene_synonym="FLJ16649; MGC35022; PRSS1; TRY1; TRYX3;
                     UNQ2540"
                     /product="protease, serine, 58"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /transcript_id="NM_001001317.3"
                     /db_xref="GI:325995179"
                     /db_xref="GeneID:136541"
                     /db_xref="HGNC:39125"
     CDS             complement(join(141952041..141952190,141952292..141952431,
                     141954875..141955131,141955355..141955493,
                     141957488..141957527))
                     /gene="PRSS58"
                     /gene_synonym="FLJ16649; MGC35022; PRSS1; TRY1; TRYX3;
                     UNQ2540"
                     /EC_number="3.4.21.4"
                     /note="trypsin-X3; trypsin X3; serine protease 58; Derived
                     by automated computational analysis using gene prediction
                     method: Curated Genomic."
                     /codon_start=1
                     /product="serine protease 58 precursor"
                     /protein_id="NP_001001317.1"
                     /db_xref="GI:48255915"
                     /db_xref="CCDS:CCDS5871.1"
                     /db_xref="GeneID:136541"
                     /db_xref="HGNC:39125"
     gene            complement(141965647..141971117)
                     /gene="TRY2P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:207147"
     gene            complement(141968101..141972068)
                     /gene="LOC730441"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:730441"
     misc_RNA        complement(join(141968101..141969704,141970967..141971120,
                     141971772..141972068))
                     /gene="LOC730441"
                     /product="trypsin X3 pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_036483.1"
                     /db_xref="GI:302318959"
                     /db_xref="GeneID:730441"
     gene            complement(141987077..141991436)
                     /gene="TRY3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:136540"
     gene            141998851..142510972
                     /gene="TRB@"
                     /gene_synonym="TCRB; TRB"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:6957"
                     /db_xref="HGNC:12155"
                     /db_xref="MIM:186930"
     gene            141998851..141999300
                     /gene="TRBV1"
                     /gene_synonym="TCRBV1S1P; TCRBV27S1P"
                     /note="this gene has a stop codon in exon 1 and lacks a
                     conserved cysteine in exon 2; Derived by automated
                     computational analysis using gene prediction method:
                     Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28621"
                     /db_xref="HGNC:12176"
                     /db_xref="IMGT/GENE-DB:TRBV1"
     CDS             join(141998851..141998891,141999009..>141999300)
                     /gene="TRBV1"
                     /gene_synonym="TCRBV1S1P; TCRBV27S1P"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28621"
                     /db_xref="HGNC:12176"
                     /db_xref="IMGT/GENE-DB:TRBV1"
     V_segment       join(141998851..141998891,141999009..141999300)
                     /gene="TRBV1"
                     /gene_synonym="TCRBV1S1P; TCRBV27S1P"
                     /standard_name="TRBV1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28621"
     gene            142000821..142001255
                     /gene="TRBV2"
                     /gene_synonym="TCRBV22S1A2N1T; TCRBV2S1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28620"
                     /db_xref="HGNC:12195"
                     /db_xref="IMGT/GENE-DB:TRBV2"
     CDS             join(142000821..142000869,142000958..>142001255)
                     /gene="TRBV2"
                     /gene_synonym="TCRBV22S1A2N1T; TCRBV2S1"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28620"
                     /db_xref="HGNC:12195"
                     /db_xref="IMGT/GENE-DB:TRBV2"
     V_segment       join(142000821..142000869,142000958..142001255)
                     /gene="TRBV2"
                     /gene_synonym="TCRBV22S1A2N1T; TCRBV2S1"
                     /standard_name="TRBV2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28620"
     gene            142008412..142008871
                     /gene="TRBV3-1"
                     /gene_synonym="TCRBV3S1; TCRBV9S1A1T; TRBV31"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28619"
                     /db_xref="HGNC:12212"
                     /db_xref="IMGT/GENE-DB:TRBV3-1"
     CDS             join(142008412..142008460,142008577..>142008871)
                     /gene="TRBV3-1"
                     /gene_synonym="TCRBV3S1; TCRBV9S1A1T; TRBV31"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28619"
                     /db_xref="HGNC:12212"
                     /db_xref="IMGT/GENE-DB:TRBV3-1"
     V_segment       join(142008412..142008460,142008577..142008871)
                     /gene="TRBV3-1"
                     /gene_synonym="TCRBV3S1; TCRBV9S1A1T; TRBV31"
                     /standard_name="TRBV3-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28619"
     gene            142013036..142013489
                     /gene="TRBV4-1"
                     /gene_synonym="BV07S1J2.7; TCRBV4S1; TCRBV7S1A1N2T;
                     TRBV41"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28617"
                     /db_xref="HGNC:12215"
                     /db_xref="IMGT/GENE-DB:TRBV4-1"
     CDS             join(142013036..142013084,142013195..>142013489)
                     /gene="TRBV4-1"
                     /gene_synonym="BV07S1J2.7; TCRBV4S1; TCRBV7S1A1N2T;
                     TRBV41"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28617"
                     /db_xref="HGNC:12215"
                     /db_xref="IMGT/GENE-DB:TRBV4-1"
     V_segment       join(142013036..142013084,142013195..142013489)
                     /gene="TRBV4-1"
                     /gene_synonym="BV07S1J2.7; TCRBV4S1; TCRBV7S1A1N2T;
                     TRBV41"
                     /standard_name="TRBV4-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28617"
     gene            142020894..142021363
                     /gene="TRBV5-1"
                     /gene_synonym="TCRBV5S1; TCRBV5S1A1T; TRBV51"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28614"
                     /db_xref="HGNC:12218"
                     /db_xref="IMGT/GENE-DB:TRBV5-1"
     CDS             join(142020894..142020942,142021070..>142021363)
                     /gene="TRBV5-1"
                     /gene_synonym="TCRBV5S1; TCRBV5S1A1T; TRBV51"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28614"
                     /db_xref="HGNC:12218"
                     /db_xref="IMGT/GENE-DB:TRBV5-1"
     V_segment       join(142020894..142020942,142021070..142021363)
                     /gene="TRBV5-1"
                     /gene_synonym="TCRBV5S1; TCRBV5S1A1T; TRBV51"
                     /standard_name="TRBV5-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28614"
     gene            142028178..142028610
                     /gene="TRBV6-1"
                     /gene_synonym="TCRBV13S3; TCRBV6S1; TRBV61"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28606"
                     /db_xref="HGNC:12226"
                     /db_xref="IMGT/GENE-DB:TRBV6-1"
     CDS             join(142028178..142028226,142028316..>142028610)
                     /gene="TRBV6-1"
                     /gene_synonym="TCRBV13S3; TCRBV6S1; TRBV61"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28606"
                     /db_xref="HGNC:12226"
                     /db_xref="IMGT/GENE-DB:TRBV6-1"
     V_segment       join(142028178..142028226,142028316..142028610)
                     /gene="TRBV6-1"
                     /gene_synonym="TCRBV13S3; TCRBV6S1; TRBV61"
                     /standard_name="TRBV6-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28606"
     gene            142032039..142032527
                     /gene="TRBV7-1"
                     /gene_synonym="TCRBV6S7P; TCRBV7S1; TRBV71"
                     /note="this gene lacks the nonamer recombination signal;
                     Derived by automated computational analysis using gene
                     prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28597"
                     /db_xref="HGNC:12235"
                     /db_xref="IMGT/GENE-DB:TRBV7-1"
     CDS             join(142032039..142032087,142032230..>142032527)
                     /gene="TRBV7-1"
                     /gene_synonym="TCRBV6S7P; TCRBV7S1; TRBV71"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28597"
                     /db_xref="HGNC:12235"
                     /db_xref="IMGT/GENE-DB:TRBV7-1"
     V_segment       join(142032039..142032087,142032230..142032527)
                     /gene="TRBV7-1"
                     /gene_synonym="TCRBV6S7P; TCRBV7S1; TRBV71"
                     /standard_name="TRBV7-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28597"
     gene            142045363..142045816
                     /gene="TRBV4-2"
                     /gene_synonym="TCRBV4S2; TCRBV7S3A2; TCRBV7S3A2T; TRBV42"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28616"
                     /db_xref="HGNC:12216"
                     /db_xref="IMGT/GENE-DB:TRBV4-2"
     CDS             join(142045363..142045411,142045522..>142045816)
                     /gene="TRBV4-2"
                     /gene_synonym="TCRBV4S2; TCRBV7S3A2; TCRBV7S3A2T; TRBV42"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28616"
                     /db_xref="HGNC:12216"
                     /db_xref="IMGT/GENE-DB:TRBV4-2"
     V_segment       join(142045363..142045411,142045522..142045816)
                     /gene="TRBV4-2"
                     /gene_synonym="TCRBV4S2; TCRBV7S3A2; TCRBV7S3A2T; TRBV42"
                     /standard_name="TRBV4-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28616"
     gene            complement(142099455..142099938)
                     /gene="TRBV7-8"
                     /gene_synonym="TCRBV6S2A1N1T; TCRBV7S8; TRBV78"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28590"
                     /db_xref="HGNC:12242"
                     /db_xref="IMGT/GENE-DB:TRBV7-8"
     CDS             complement(join(<142099455..142099752,
                     142099890..142099938))
                     /gene="TRBV7-8"
                     /gene_synonym="TCRBV6S2A1N1T; TCRBV7S8; TRBV78"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28590"
                     /db_xref="HGNC:12242"
                     /db_xref="IMGT/GENE-DB:TRBV7-8"
     V_segment       complement(join(142099455..142099752,
                     142099890..142099938))
                     /gene="TRBV7-8"
                     /gene_synonym="TCRBV6S2A1N1T; TCRBV7S8; TRBV78"
                     /standard_name="TRBV7-8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28590"
     gene            complement(142104121..142104553)
                     /gene="TRBV6-9"
                     /gene_synonym="TCRBV13S4; TCRBV6S9; TRBV69"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28598"
                     /db_xref="HGNC:12234"
                     /db_xref="IMGT/GENE-DB:TRBV6-9"
     CDS             complement(join(<142104121..142104415,
                     142104505..142104553))
                     /gene="TRBV6-9"
                     /gene_synonym="TCRBV13S4; TCRBV6S9; TRBV69"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28598"
                     /db_xref="HGNC:12234"
                     /db_xref="IMGT/GENE-DB:TRBV6-9"
     V_segment       complement(join(142104121..142104415,
                     142104505..142104553))
                     /gene="TRBV6-9"
                     /gene_synonym="TCRBV13S4; TCRBV6S9; TRBV69"
                     /standard_name="TRBV6-9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28598"
     gene            complement(142111393..142111859)
                     /gene="TRBV5-7"
                     /gene_synonym="TCRBV5S7; TCRBV5S7P; TRBV57"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28608"
                     /db_xref="HGNC:12224"
                     /db_xref="IMGT/GENE-DB:TRBV5-7"
     CDS             complement(join(<142111393..142111686,
                     142111811..142111859))
                     /gene="TRBV5-7"
                     /gene_synonym="TCRBV5S7; TCRBV5S7P; TRBV57"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28608"
                     /db_xref="HGNC:12224"
                     /db_xref="IMGT/GENE-DB:TRBV5-7"
     V_segment       complement(join(142111393..142111686,
                     142111811..142111859))
                     /gene="TRBV5-7"
                     /gene_synonym="TCRBV5S7; TCRBV5S7P; TRBV57"
                     /standard_name="TRBV5-7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28608"
     gene            complement(142119820..142120321)
                     /gene="TRBV7-7"
                     /gene_synonym="TCRBV6S6A2T; TCRBV7S7; TRBV77"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28591"
                     /db_xref="HGNC:12241"
                     /db_xref="IMGT/GENE-DB:TRBV7-7"
     CDS             complement(join(<142119820..142120117,
                     142120273..142120321))
                     /gene="TRBV7-7"
                     /gene_synonym="TCRBV6S6A2T; TCRBV7S7; TRBV77"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28591"
                     /db_xref="HGNC:12241"
                     /db_xref="IMGT/GENE-DB:TRBV7-7"
     V_segment       complement(join(142119820..142120117,
                     142120273..142120321))
                     /gene="TRBV7-7"
                     /gene_synonym="TCRBV6S6A2T; TCRBV7S7; TRBV77"
                     /standard_name="TRBV7-7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28591"
     gene            complement(142124137..142124565)
                     /gene="TRBV6-8"
                     /gene_synonym="TCRBV13S7P; TCRBV6S8; TRBV68"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28599"
                     /db_xref="HGNC:12233"
                     /db_xref="IMGT/GENE-DB:TRBV6-8"
     CDS             complement(join(<142124137..142124428,
                     142124517..142124565))
                     /gene="TRBV6-8"
                     /gene_synonym="TCRBV13S7P; TCRBV6S8; TRBV68"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28599"
                     /db_xref="HGNC:12233"
                     /db_xref="IMGT/GENE-DB:TRBV6-8"
     V_segment       complement(join(142124137..142124428,
                     142124517..142124565))
                     /gene="TRBV6-8"
                     /gene_synonym="TCRBV13S7P; TCRBV6S8; TRBV68"
                     /standard_name="TRBV6-8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28599"
     gene            complement(142131412..142131877)
                     /gene="TRBV5-6"
                     /gene_synonym="TCRBV5S2; TCRBV5S6; TRBV56"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28609"
                     /db_xref="HGNC:12223"
                     /db_xref="IMGT/GENE-DB:TRBV5-6"
     CDS             complement(join(<142131412..142131705,
                     142131829..142131877))
                     /gene="TRBV5-6"
                     /gene_synonym="TCRBV5S2; TCRBV5S6; TRBV56"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28609"
                     /db_xref="HGNC:12223"
                     /db_xref="IMGT/GENE-DB:TRBV5-6"
     V_segment       complement(join(142131412..142131705,
                     142131829..142131877))
                     /gene="TRBV5-6"
                     /gene_synonym="TCRBV5S2; TCRBV5S6; TRBV56"
                     /standard_name="TRBV5-6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28609"
     gene            complement(142139278..142139770)
                     /gene="TRBV7-6"
                     /gene_synonym="TCRBV6S3A1N1T; TCRBV7S6; TRBV76"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28592"
                     /db_xref="HGNC:12240"
                     /db_xref="IMGT/GENE-DB:TRBV7-6"
     CDS             complement(join(<142139278..142139575,
                     142139722..142139770))
                     /gene="TRBV7-6"
                     /gene_synonym="TCRBV6S3A1N1T; TCRBV7S6; TRBV76"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28592"
                     /db_xref="HGNC:12240"
                     /db_xref="IMGT/GENE-DB:TRBV7-6"
     V_segment       complement(join(142139278..142139575,
                     142139722..142139770))
                     /gene="TRBV7-6"
                     /gene_synonym="TCRBV6S3A1N1T; TCRBV7S6; TRBV76"
                     /standard_name="TRBV7-6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28592"
     gene            complement(142143652..142144084)
                     /gene="TRBV6-7"
                     /gene_synonym="TCRBV13S8P; TCRBV6S7; TRBV67"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28600"
                     /db_xref="HGNC:12232"
                     /db_xref="IMGT/GENE-DB:TRBV6-7"
     CDS             complement(join(<142143652..142143946,
                     142144036..142144084))
                     /gene="TRBV6-7"
                     /gene_synonym="TCRBV13S8P; TCRBV6S7; TRBV67"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28600"
                     /db_xref="HGNC:12232"
                     /db_xref="IMGT/GENE-DB:TRBV6-7"
     V_segment       complement(join(142143652..142143946,
                     142144036..142144084))
                     /gene="TRBV6-7"
                     /gene_synonym="TCRBV13S8P; TCRBV6S7; TRBV67"
                     /standard_name="TCRBV6-7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28600"
     gene            complement(142148928..142149392)
                     /gene="TRBV5-5"
                     /gene_synonym="TCRBV5S3A2T; TCRBV5S5; TRBV55"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28610"
                     /db_xref="HGNC:12222"
                     /db_xref="IMGT/GENE-DB:TRBV5-5"
     CDS             complement(join(<142148928..142149221,
                     142149344..142149392))
                     /gene="TRBV5-5"
                     /gene_synonym="TCRBV5S3A2T; TCRBV5S5; TRBV55"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28610"
                     /db_xref="HGNC:12222"
                     /db_xref="IMGT/GENE-DB:TRBV5-5"
     V_segment       complement(join(142148928..142149221,
                     142149344..142149392))
                     /gene="TRBV5-5"
                     /gene_synonym="TCRBV5S3A2T; TCRBV5S5; TRBV55"
                     /standard_name="TRBV5-5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28610"
     gene            complement(142157378..142157849)
                     /gene="TRBV7-5"
                     /gene_synonym="TCRBV6S9P; TCRBV7S5; TRBV75"
                     /note="this gene has a frameshift in exon 2; Derived by
                     automated computational analysis using gene prediction
                     method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28593"
                     /db_xref="HGNC:12239"
                     /db_xref="IMGT/GENE-DB:TRBV7-5"
     CDS             complement(join(<142157378..142157673,
                     142157801..142157849))
                     /gene="TRBV7-5"
                     /gene_synonym="TCRBV6S9P; TCRBV7S5; TRBV75"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28593"
                     /db_xref="HGNC:12239"
                     /db_xref="IMGT/GENE-DB:TRBV7-5"
     V_segment       complement(join(142157378..142157673,
                     142157801..142157849))
                     /gene="TRBV7-5"
                     /gene_synonym="TCRBV6S9P; TCRBV7S5; TRBV75"
                     /standard_name="TRBV7-5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28593"
     gene            complement(142161931..142162363)
                     /gene="TRBV6-6"
                     /gene_synonym="TCRBV13S6A2T; TCRBV6S6; TRBV66"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28601"
                     /db_xref="HGNC:12231"
                     /db_xref="IMGT/GENE-DB:TRBV6-6"
     CDS             complement(join(<142161931..142162225,
                     142162315..142162363))
                     /gene="TRBV6-6"
                     /gene_synonym="TCRBV13S6A2T; TCRBV6S6; TRBV66"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28601"
                     /db_xref="HGNC:12231"
                     /db_xref="IMGT/GENE-DB:TRBV6-6"
     V_segment       complement(join(142161931..142162225,
                     142162315..142162363))
                     /gene="TRBV6-6"
                     /gene_synonym="TCRBV13S6A2T; TCRBV6S6; TRBV66"
                     /standard_name="TRBV6-6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28601"
     gene            complement(142168380..142168844)
                     /gene="TRBV5-4"
                     /gene_synonym="TCRBV5S4; TCRBV5S6A3N2T; TRBV54"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28611"
                     /db_xref="HGNC:12221"
                     /db_xref="IMGT/GENE-DB:TRBV5-4"
     CDS             complement(join(<142168380..>142168661,
                     <142168664..142168673,142168796..142168844))
                     /gene="TRBV5-4"
                     /gene_synonym="TCRBV5S4; TCRBV5S6A3N2T; TRBV54"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28611"
                     /db_xref="HGNC:12221"
                     /db_xref="IMGT/GENE-DB:TRBV5-4"
     V_segment       complement(join(142168380..>142168661,
                     <142168664..142168673,142168796..142168844))
                     /gene="TRBV5-4"
                     /gene_synonym="TCRBV5S4; TCRBV5S6A3N2T; TRBV54"
                     /standard_name="TRBV5-4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28611"
     gene            complement(142176329..142176790)
                     /gene="TRBV7-4"
                     /gene_synonym="TCRBV6S8A2T; TCRBV7S4; TRBV74"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28594"
                     /db_xref="HGNC:12238"
                     /db_xref="IMGT/GENE-DB:TRBV7-4"
     CDS             complement(join(<142176329..142176626,
                     142176742..142176790))
                     /gene="TRBV7-4"
                     /gene_synonym="TCRBV6S8A2T; TCRBV7S4; TRBV74"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28594"
                     /db_xref="HGNC:12238"
                     /db_xref="IMGT/GENE-DB:TRBV7-4"
     V_segment       complement(join(142176329..142176626,
                     142176742..142176790))
                     /gene="TRBV7-4"
                     /gene_synonym="TCRBV6S8A2T; TCRBV7S4; TRBV74"
                     /standard_name="TRBV7-4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28594"
     gene            complement(142180515..142180950)
                     /gene="TRBV6-5"
                     /gene_synonym="TCRBV13S1; TCRBV6S5; TRBV65"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28602"
                     /db_xref="HGNC:12230"
                     /db_xref="IMGT/GENE-DB:TRBV6-5"
     CDS             complement(join(<142180515..142180809,
                     142180902..142180950))
                     /gene="TRBV6-5"
                     /gene_synonym="TCRBV13S1; TCRBV6S5; TRBV65"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28602"
                     /db_xref="HGNC:12230"
                     /db_xref="IMGT/GENE-DB:TRBV6-5"
     V_segment       complement(join(142180515..142180809,
                     142180902..142180950))
                     /gene="TRBV6-5"
                     /gene_synonym="TCRBV13S1; TCRBV6S5; TRBV65"
                     /standard_name="TRBV6-5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28602"
     gene            complement(142190638..142191080)
                     /gene="TRBV12-2"
                     /gene_synonym="TCRBV12S2; TCRBV8S5P; TRBV122"
                     /note="this gene has a stop codon in exon 2; Derived by
                     automated computational analysis using gene prediction
                     method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28578"
                     /db_xref="HGNC:12184"
                     /db_xref="IMGT/GENE-DB:TRBV12-2"
     CDS             complement(join(<142190638..142190935,
                     142191035..142191080))
                     /gene="TRBV12-2"
                     /gene_synonym="TCRBV12S2; TCRBV8S5P; TRBV122"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28578"
                     /db_xref="HGNC:12184"
                     /db_xref="IMGT/GENE-DB:TRBV12-2"
     V_segment       complement(join(142190638..142190935,
                     142191035..142191080))
                     /gene="TRBV12-2"
                     /gene_synonym="TCRBV12S2; TCRBV8S5P; TRBV122"
                     /standard_name="TRBV12-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28578"
     gene            complement(142197570..142198008)
                     /gene="TRBV11-2"
                     /gene_synonym="TCRBV11S2; TCRBV21S3A2N2T; TRBV112"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28581"
                     /db_xref="HGNC:12181"
                     /db_xref="IMGT/GENE-DB:TRBV11-2"
     CDS             complement(join(<142197570..142197867,
                     142197960..142198008))
                     /gene="TRBV11-2"
                     /gene_synonym="TCRBV11S2; TCRBV21S3A2N2T; TRBV112"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28581"
                     /db_xref="HGNC:12181"
                     /db_xref="IMGT/GENE-DB:TRBV11-2"
     V_segment       complement(join(142197570..142197867,
                     142197960..142198008))
                     /gene="TRBV11-2"
                     /gene_synonym="TCRBV11S2; TCRBV21S3A2N2T; TRBV112"
                     /standard_name="TRBV11-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28581"
     gene            complement(142206511..142206960)
                     /gene="TRBV10-2"
                     /gene_synonym="TCRBV10S2; TCRBV12S3; TRBV102"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28584"
                     /db_xref="HGNC:12178"
                     /db_xref="IMGT/GENE-DB:TRBV10-2"
     CDS             complement(join(<142206511..142206805,
                     142206912..142206960))
                     /gene="TRBV10-2"
                     /gene_synonym="TCRBV10S2; TCRBV12S3; TRBV102"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28584"
                     /db_xref="HGNC:12178"
                     /db_xref="IMGT/GENE-DB:TRBV10-2"
     V_segment       complement(join(142206511..142206805,
                     142206912..142206960))
                     /gene="TRBV10-2"
                     /gene_synonym="TCRBV10S2; TCRBV12S3; TRBV102"
                     /standard_name="TRBV10-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28584"
     gene            complement(142216290..142216732)
                     /gene="TRBV12-1"
                     /gene_synonym="TCRBV12S1; TCRBV8S4P; TRBV121"
                     /note="this gene has a stop codon in exon 2; Derived by
                     automated computational analysis using gene prediction
                     method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28579"
                     /db_xref="HGNC:12183"
                     /db_xref="IMGT/GENE-DB:TRBV12-1"
     CDS             complement(join(<142216290..142216587,
                     142216687..142216732))
                     /gene="TRBV12-1"
                     /gene_synonym="TCRBV12S1; TCRBV8S4P; TRBV121"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28579"
                     /db_xref="HGNC:12183"
                     /db_xref="IMGT/GENE-DB:TRBV12-1"
     V_segment       complement(join(142216290..142216587,
                     142216687..142216732))
                     /gene="TRBV12-1"
                     /gene_synonym="TCRBV12S1; TCRBV8S4P; TRBV121"
                     /standard_name="TRBV12-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28579"
     gene            complement(142223790..142224267)
                     /gene="TRBV11-1"
                     /gene_synonym="TCRBV11S1; TCRBV21S1; TRBV111"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28582"
                     /db_xref="HGNC:12180"
                     /db_xref="IMGT/GENE-DB:TRBV11-1"
     CDS             complement(join(<142223820..142224117,
                     142224219..142224267))
                     /gene="TRBV11-1"
                     /gene_synonym="TCRBV11S1; TCRBV21S1; TRBV111"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28582"
                     /db_xref="HGNC:12180"
                     /db_xref="IMGT/GENE-DB:TRBV11-1"
     V_segment       complement(join(142223820..142224117,
                     142224219..142224267))
                     /gene="TRBV11-1"
                     /gene_synonym="TCRBV11S1; TCRBV21S1; TRBV111"
                     /standard_name="TRBV11-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28582"
     gene            complement(142231573..142232022)
                     /gene="TRBV10-1"
                     /gene_synonym="TCRBV10S1; TCRBV12S2; TCRBV12S2A1T;
                     TRBV101"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28585"
                     /db_xref="HGNC:12177"
                     /db_xref="IMGT/GENE-DB:TRBV10-1"
     CDS             complement(join(<142231573..142231867,
                     142231974..142232022))
                     /gene="TRBV10-1"
                     /gene_synonym="TCRBV10S1; TCRBV12S2; TCRBV12S2A1T;
                     TRBV101"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28585"
                     /db_xref="HGNC:12177"
                     /db_xref="IMGT/GENE-DB:TRBV10-1"
     V_segment       complement(join(142231573..142231867,
                     142231974..142232022))
                     /gene="TRBV10-1"
                     /gene_synonym="TCRBV10S1; TCRBV12S2; TCRBV12S2A1T;
                     TRBV101"
                     /standard_name="TRBV10-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28585"
     gene            complement(142239537..142240011)
                     /gene="TRBV9"
                     /gene_synonym="TCRBV1S1A1N1; TCRBV9S1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28586"
                     /db_xref="HGNC:12246"
                     /db_xref="IMGT/GENE-DB:TRBV9"
     CDS             complement(join(<142239537..142239830,
                     142239963..142240011))
                     /gene="TRBV9"
                     /gene_synonym="TCRBV1S1A1N1; TCRBV9S1"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28586"
                     /db_xref="HGNC:12246"
                     /db_xref="IMGT/GENE-DB:TRBV9"
     V_segment       complement(join(142239537..142239830,
                     142239963..142240011))
                     /gene="TRBV9"
                     /gene_synonym="TCRBV1S1A1N1; TCRBV9S1"
                     /standard_name="TRBV9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28586"
     gene            complement(142242281..142242747)
                     /gene="TRBV5-3"
                     /gene_synonym="TCRBV5S3; TCRBV5S5P; TRBV53"
                     /note="this gene has a defective splice donor; Derived by
                     automated computational analysis using gene prediction
                     method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28612"
                     /db_xref="HGNC:12220"
                     /db_xref="IMGT/GENE-DB:TRBV5-3"
     CDS             complement(join(<142242281..142242574,
                     142242699..142242747))
                     /gene="TRBV5-3"
                     /gene_synonym="TCRBV5S3; TCRBV5S5P; TRBV53"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28612"
                     /db_xref="HGNC:12220"
                     /db_xref="IMGT/GENE-DB:TRBV5-3"
     V_segment       complement(join(142242281..142242574,
                     142242699..142242747))
                     /gene="TRBV5-3"
                     /gene_synonym="TCRBV5S3; TCRBV5S5P; TRBV53"
                     /standard_name="TRBV5-3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28612"
     gene            complement(142245303..142245763)
                     /gene="TRBV8-2"
                     /gene_synonym="TCRBV32S1P; TRBV82"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28587"
                     /db_xref="HGNC:12245"
                     /db_xref="IMGT/GENE-DB:TRBV8-2"
     CDS             complement(join(<142245303..142245581,
                     142245718..142245763))
                     /gene="TRBV8-2"
                     /gene_synonym="TCRBV32S1P; TRBV82"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28587"
                     /db_xref="HGNC:12245"
                     /db_xref="IMGT/GENE-DB:TRBV8-2"
     V_segment       complement(join(142245303..142245581,
                     142245718..142245763))
                     /gene="TRBV8-2"
                     /gene_synonym="TCRBV32S1P; TRBV82"
                     /standard_name="TRBV8-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28587"
     gene            complement(142247109..142247565)
                     /gene="TRBV7-3"
                     /gene_synonym="TCRBV6S1A1N1; TCRBV7S3; TRBV73"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28595"
                     /db_xref="HGNC:12237"
                     /db_xref="IMGT/GENE-DB:TRBV7-3"
     CDS             complement(join(<142247109..142247406,
                     142247517..142247565))
                     /gene="TRBV7-3"
                     /gene_synonym="TCRBV6S1A1N1; TCRBV7S3; TRBV73"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28595"
                     /db_xref="HGNC:12237"
                     /db_xref="IMGT/GENE-DB:TRBV7-3"
     V_segment       complement(join(142247109..142247406,
                     142247517..142247565))
                     /gene="TRBV7-3"
                     /gene_synonym="TCRBV6S1A1N1; TCRBV7S3; TRBV73"
                     /standard_name="TRBV7-3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28595"
     gene            complement(142250703..142251137)
                     /gene="TRBV6-4"
                     /gene_synonym="TCRBV13S5; TCRBV6S4; TRBV64"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28603"
                     /db_xref="HGNC:12229"
                     /db_xref="IMGT/GENE-DB:TRBV6-4"
     CDS             complement(join(<142250703..142250997,
                     142251089..142251137))
                     /gene="TRBV6-4"
                     /gene_synonym="TCRBV13S5; TCRBV6S4; TRBV64"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28603"
                     /db_xref="HGNC:12229"
                     /db_xref="IMGT/GENE-DB:TRBV6-4"
     V_segment       complement(join(142250703..142250997,
                     142251089..142251137))
                     /gene="TRBV6-4"
                     /gene_synonym="TCRBV13S5; TCRBV6S4; TRBV64"
                     /standard_name="TRBV6-4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28603"
     gene            complement(142259058..142259498)
                     /gene="TRBV5-2"
                     /gene_synonym="TCRBV31S1; TCRBV5S2P; TRBV52"
                     /note="this gene has  frameshifts in exon 2; Derived by
                     automated computational analysis using gene prediction
                     method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28613"
                     /db_xref="HGNC:12219"
                     /db_xref="IMGT/GENE-DB:TRBV5-2"
     CDS             complement(join(<142259058..142259340,
                     142259450..142259498))
                     /gene="TRBV5-2"
                     /gene_synonym="TCRBV31S1; TCRBV5S2P; TRBV52"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28613"
                     /db_xref="HGNC:12219"
                     /db_xref="IMGT/GENE-DB:TRBV5-2"
     V_segment       complement(join(142259058..142259340,
                     142259450..142259498))
                     /gene="TRBV5-2"
                     /gene_synonym="TCRBV31S1; TCRBV5S2P; TRBV52"
                     /standard_name="TRBV5-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28613"
     gene            complement(142273056..142273342)
                     /gene="TRBV8-1"
                     /gene_synonym="TCRBV30S1P; TCRBV8S1P; TRBV81"
                     /note="this gene has frameshifts in exon 2; Derived by
                     automated computational analysis using gene prediction
                     method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28588"
                     /db_xref="HGNC:12244"
                     /db_xref="IMGT/GENE-DB:TRBV8-1"
     CDS             complement(<142273056..142273342)
                     /gene="TRBV8-1"
                     /gene_synonym="TCRBV30S1P; TCRBV8S1P; TRBV81"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28588"
                     /db_xref="HGNC:12244"
                     /db_xref="IMGT/GENE-DB:TRBV8-1"
     V_segment       complement(142273056..142273342)
                     /gene="TRBV8-1"
                     /gene_synonym="TCRBV30S1P; TCRBV8S1P; TRBV81"
                     /standard_name="TRBV8-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28588"
     gene            142326571..142327046
                     /gene="TRBV19"
                     /gene_synonym="TCRBV17S1A1T; TCRBV19S1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28568"
                     /db_xref="HGNC:12194"
                     /db_xref="IMGT/GENE-DB:TRBV19"
     CDS             join(142326571..142326619,142326752..>142327046)
                     /gene="TRBV19"
                     /gene_synonym="TCRBV17S1A1T; TCRBV19S1"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28568"
                     /db_xref="HGNC:12194"
                     /db_xref="IMGT/GENE-DB:TRBV19"
     V_segment       join(142326571..142326619,142326752..142327046)
                     /gene="TRBV19"
                     /gene_synonym="TCRBV17S1A1T; TCRBV19S1"
                     /standard_name="TRBV19"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28568"
     gene            142334241..142334913
                     /gene="TRBV20-1"
                     /gene_synonym="TCRBV20S1; TCRBV2S1; TRBV201"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28567"
                     /db_xref="HGNC:12196"
                     /db_xref="IMGT/GENE-DB:TRBV20-1"
     CDS             join(142334241..142334271,142334610..>142334913)
                     /gene="TRBV20-1"
                     /gene_synonym="TCRBV20S1; TCRBV2S1; TRBV201"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28567"
                     /db_xref="HGNC:12196"
                     /db_xref="IMGT/GENE-DB:TRBV20-1"
     V_segment       join(142334241..142334271,142334610..142334913)
                     /gene="TRBV20-1"
                     /gene_synonym="TCRBV20S1; TCRBV2S1; TRBV201"
                     /standard_name="TRBV20-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28567"
     gene            142344427..142344894
                     /gene="TRBV21-1"
                     /gene_synonym="TCRBV10S1P; TCRBV21S1; TRBV211"
                     /note="this gene has a frameshift in exon 1; Derived by
                     automated computational analysis using gene prediction
                     method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28566"
                     /db_xref="HGNC:12198"
                     /db_xref="IMGT/GENE-DB:TRBV21-1"
     CDS             join(142344427..142344476,142344590..>142344887)
                     /gene="TRBV21-1"
                     /gene_synonym="TCRBV10S1P; TCRBV21S1; TRBV211"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28566"
                     /db_xref="HGNC:12198"
                     /db_xref="IMGT/GENE-DB:TRBV21-1"
     V_segment       join(142344427..142344476,142344590..142344887)
                     /gene="TRBV21-1"
                     /gene_synonym="TCRBV10S1P; TCRBV21S1; TRBV211"
                     /standard_name="TCRBV21-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28566"
     gene            142349249..>142349699
                     /gene="TRBV22-1"
                     /gene_synonym="TCRBV22S1; TCRBV29S1P; TRBV22"
                     /note="this gene has a frameshift in exon 2; Derived by
                     automated computational analysis using gene prediction
                     method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28565"
                     /db_xref="HGNC:12200"
                     /db_xref="IMGT/GENE-DB:TRBV22-1"
     CDS             join(142349249..142349297,142349404..>142349699)
                     /gene="TRBV22-1"
                     /gene_synonym="TCRBV22S1; TCRBV29S1P; TRBV22"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28565"
                     /db_xref="HGNC:12200"
                     /db_xref="IMGT/GENE-DB:TRBV22-1"
     V_segment       join(142349249..142349297,142349404..142349699)
                     /gene="TRBV22-1"
                     /gene_synonym="TCRBV22S1; TCRBV29S1P; TRBV22"
                     /standard_name="TRBV22"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28565"
     gene            142353468..142353971
                     /gene="TRBV23-1"
                     /gene_synonym="TCRBV19S1P; TCRBV23S1; TRBV231"
                     /note="this gene has a defective splice donor; Derived by
                     automated computational analysis using gene prediction
                     method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28564"
                     /db_xref="HGNC:12201"
                     /db_xref="IMGT/GENE-DB:TRBV23-1"
     CDS             join(142353468..142353516,142353667..>142353964)
                     /gene="TRBV23-1"
                     /gene_synonym="TCRBV19S1P; TCRBV23S1; TRBV231"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28564"
                     /db_xref="HGNC:12201"
                     /db_xref="IMGT/GENE-DB:TRBV23-1"
     V_segment       join(142353468..142353516,142353667..142353964)
                     /gene="TRBV23-1"
                     /gene_synonym="TCRBV19S1P; TCRBV23S1; TRBV231"
                     /standard_name="TRBV23-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28564"
     gene            142364234..142364710
                     /gene="TRBV24-1"
                     /gene_synonym="TCRBV15S1; TCRBV24S1; TRBV241"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28563"
                     /db_xref="HGNC:12203"
                     /db_xref="IMGT/GENE-DB:TRBV24-1"
     CDS             join(142364234..142364282,142364415..>142364710)
                     /gene="TRBV24-1"
                     /gene_synonym="TCRBV15S1; TCRBV24S1; TRBV241"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28563"
                     /db_xref="HGNC:12203"
                     /db_xref="IMGT/GENE-DB:TRBV24-1"
     V_segment       join(142364234..142364282,142364415..142364710)
                     /gene="TRBV24-1"
                     /gene_synonym="TCRBV15S1; TCRBV24S1; TRBV241"
                     /standard_name="TRBV24-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28563"
     gene            142374131..142375525
                     /gene="MTRNR2L6"
                     /gene_synonym="HN6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100463482"
                     /db_xref="HGNC:37163"
     mRNA            142374131..142375525
                     /gene="MTRNR2L6"
                     /gene_synonym="HN6"
                     /product="MT-RNR2-like 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001190487.1"
                     /db_xref="GI:299523051"
                     /db_xref="GeneID:100463482"
                     /db_xref="HGNC:37163"
     CDS             142375063..142375137
                     /gene="MTRNR2L6"
                     /gene_synonym="HN6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="humanin-like protein 6"
                     /protein_id="NP_001177416.1"
                     /db_xref="GI:299523052"
                     /db_xref="GeneID:100463482"
                     /db_xref="HGNC:37163"
     gene            142378609..142379076
                     /gene="TRBV25-1"
                     /gene_synonym="TCRBV11S1A1T; TCRBV25S1; TRBV251"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28562"
                     /db_xref="HGNC:12205"
                     /db_xref="IMGT/GENE-DB:TRBV25-1"
     CDS             join(142378609..142378657,142378782..>142379076)
                     /gene="TRBV25-1"
                     /gene_synonym="TCRBV11S1A1T; TCRBV25S1; TRBV251"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28562"
                     /db_xref="HGNC:12205"
                     /db_xref="IMGT/GENE-DB:TRBV25-1"
     V_segment       join(142378609..142378657,142378782..142379076)
                     /gene="TRBV25-1"
                     /gene_synonym="TCRBV11S1A1T; TCRBV25S1; TRBV251"
                     /standard_name="TRBV25-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28562"
     gene            142389237..142389691
                     /gene="TRBVA"
                     /gene_synonym="TCRBV33S1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28556"
                     /db_xref="HGNC:12247"
                     /db_xref="IMGT/GENE-DB:TRBVA"
     CDS             join(142389237..142389284,142389424..142389691)
                     /gene="TRBVA"
                     /gene_synonym="TCRBV33S1"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28556"
                     /db_xref="HGNC:12247"
                     /db_xref="IMGT/GENE-DB:TRBVA"
     V_segment       join(142389237..142389284,142389424..142389691)
                     /gene="TRBVA"
                     /gene_synonym="TCRBV33S1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28556"
     gene            142403511..142403995
                     /gene="TRBV26"
                     /gene_synonym="TCRBV26S1; TCRBV28S1P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28561"
                     /db_xref="HGNC:12207"
                     /db_xref="IMGT/GENE-DB:TRBV26"
     CDS             join(142403511..142403559,142403701..>142403995)
                     /gene="TRBV26"
                     /gene_synonym="TCRBV26S1; TCRBV28S1P"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28561"
                     /db_xref="HGNC:12207"
                     /db_xref="IMGT/GENE-DB:TRBV26"
     V_segment       join(142403511..142403559,142403701..142403995)
                     /gene="TRBV26"
                     /gene_synonym="TCRBV26S1; TCRBV28S1P"
                     /standard_name="TRBV26"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28561"
     gene            142419212..142419752
                     /gene="TRBVB"
                     /gene_synonym="TCRBV34S1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28555"
                     /db_xref="HGNC:12248"
                     /db_xref="IMGT/GENE-DB:TRBVB"
     CDS             join(142419212..142419260,142419394..142419752)
                     /gene="TRBVB"
                     /gene_synonym="TCRBV34S1"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28555"
                     /db_xref="HGNC:12248"
                     /db_xref="IMGT/GENE-DB:TRBVB"
     V_segment       join(142419212..142419260,142419394..142419752)
                     /gene="TRBVB"
                     /gene_synonym="TCRBV34S1"
                     /standard_name="TRBVB"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28555"
     gene            142423216..142423688
                     /gene="TRBV27"
                     /gene_synonym="FLJ35984; TCRBV14S1; TCRBV27S1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28560"
                     /db_xref="HGNC:12208"
                     /db_xref="IMGT/GENE-DB:TRBV27"
     CDS             join(142423216..142423264,142423394..>142423688)
                     /gene="TRBV27"
                     /gene_synonym="FLJ35984; TCRBV14S1; TCRBV27S1"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28560"
                     /db_xref="HGNC:12208"
                     /db_xref="IMGT/GENE-DB:TRBV27"
     V_segment       join(142423216..142423264,142423394..142423688)
                     /gene="TRBV27"
                     /gene_synonym="FLJ35984; TCRBV14S1; TCRBV27S1"
                     /standard_name="TRBV27"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28560"
     gene            142428504..142428984
                     /gene="TRBV28"
                     /gene_synonym="TCRBV28S1; TCRBV3S1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28559"
                     /db_xref="HGNC:12209"
                     /db_xref="IMGT/GENE-DB:TRBV28"
     CDS             join(142428504..142428552,142428690..>142428984)
                     /gene="TRBV28"
                     /gene_synonym="TCRBV28S1; TCRBV3S1"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28559"
                     /db_xref="HGNC:12209"
                     /db_xref="IMGT/GENE-DB:TRBV28"
     V_segment       join(142428504..142428552,142428690..142428984)
                     /gene="TRBV28"
                     /gene_synonym="TCRBV28S1; TCRBV3S1"
                     /standard_name="TRBV28"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28559"
     gene            142448120..142448741
                     /gene="TRBV29-1"
                     /gene_synonym="TCRBV29S1; TCRBV4S1A1T; TRBV291"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28558"
                     /db_xref="HGNC:12210"
                     /db_xref="IMGT/GENE-DB:TRBV29-1"
     CDS             join(142448120..142448153,142448441..>142448741)
                     /gene="TRBV29-1"
                     /gene_synonym="TCRBV29S1; TCRBV4S1A1T; TRBV291"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28558"
                     /db_xref="HGNC:12210"
                     /db_xref="IMGT/GENE-DB:TRBV29-1"
     V_segment       join(142448120..142448153,142448441..142448741)
                     /gene="TRBV29-1"
                     /gene_synonym="TCRBV29S1; TCRBV4S1A1T; TRBV291"
                     /standard_name="TRBV29-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28558"
     gene            142457319..142460927
                     /gene="PRSS1"
                     /gene_synonym="DKFZp779A0837; FLJ57296; MGC120175;
                     MGC149362; TRP1; TRY1; TRY4; TRYP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:5644"
                     /db_xref="HGNC:9475"
                     /db_xref="MIM:276000"
     mRNA            join(142457319..142457375,142458406..142458565,
                     142459625..142459878,142460282..142460418,
                     142460719..142460927)
                     /gene="PRSS1"
                     /gene_synonym="DKFZp779A0837; FLJ57296; MGC120175;
                     MGC149362; TRP1; TRY1; TRY4; TRYP1"
                     /product="protease, serine, 1 (trypsin 1)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /transcript_id="NM_002769.4"
                     /db_xref="GI:310923201"
                     /db_xref="GeneID:5644"
                     /db_xref="HGNC:9475"
                     /db_xref="MIM:276000"
     CDS             join(142457336..142457375,142458406..142458565,
                     142459625..142459878,142460282..142460418,
                     142460719..142460871)
                     /gene="PRSS1"
                     /gene_synonym="DKFZp779A0837; FLJ57296; MGC120175;
                     MGC149362; TRP1; TRY1; TRY4; TRYP1"
                     /EC_number="3.4.21.4"
                     /note="trypsinogen 1; trypsinogen A; cationic trypsinogen;
                     nonfunctional trypsin 1; digestive zymogen; beta-trypsin;
                     Derived by automated computational analysis using gene
                     prediction method: Curated Genomic."
                     /codon_start=1
                     /product="trypsin-1 preproprotein"
                     /protein_id="NP_002760.1"
                     /db_xref="GI:4506145"
                     /db_xref="CCDS:CCDS5872.1"
                     /db_xref="GeneID:5644"
                     /db_xref="HGNC:9475"
                     /db_xref="MIM:276000"
     gene            142468264..142471830
                     /gene="TRY5"
                     /note="this gene contains two internal stop codons and
                     exon 1 splice donor violates consensus; Derived by
                     automated computational analysis using gene prediction
                     method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:168330"
     gene            142478757..142482400
                     /gene="TRY6"
                     /gene_synonym="T6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:154754"
     misc_RNA        join(142478757..142478879,142479909..142480068,
                     142481127..142481380,142481776..142481912,
                     142482212..142482400)
                     /gene="TRY6"
                     /gene_synonym="T6"
                     /product="trypsinogen C"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /transcript_id="NR_001296.3"
                     /db_xref="GI:251823861"
                     /db_xref="GeneID:154754"
     gene            <142494022..>142494030
                     /gene="TRBD1"
                     /gene_synonym="TCRBD1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28637"
                     /db_xref="HGNC:12158"
                     /db_xref="IMGT/GENE-DB:TRBD1"
     CDS             <142494022..>142494030
                     /gene="TRBD1"
                     /gene_synonym="TCRBD1"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28637"
                     /db_xref="HGNC:12158"
                     /db_xref="IMGT/GENE-DB:TRBD1"
     D_segment       142494022..>142494030
                     /gene="TRBD1"
                     /gene_synonym="TCRBD1"
                     /standard_name="TRBD1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28637"
     gene            <142494049..>142494098
                     /gene="TRBJ2-1"
                     /gene_synonym="TCRBJ2S1; TRBJ21"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28629"
                     /db_xref="HGNC:12168"
                     /db_xref="IMGT/GENE-DB:TRBJ2-1"
     CDS             <142494049..>142494098
                     /gene="TRBJ2-1"
                     /gene_synonym="TCRBJ2S1; TRBJ21"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=2
                     /db_xref="GeneID:28629"
                     /db_xref="HGNC:12168"
                     /db_xref="IMGT/GENE-DB:TRBJ2-1"
     J_segment       142494049..142494098
                     /gene="TRBJ2-1"
                     /gene_synonym="TCRBJ2S1; TRBJ21"
                     /standard_name="TRBJ2-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28629"
     gene            <142494244..>142494294
                     /gene="TRBJ2-2"
                     /gene_synonym="TCRBJ2S2; TRBJ22"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28628"
                     /db_xref="HGNC:12169"
                     /db_xref="IMGT/GENE-DB:TRBJ2-2"
     CDS             <142494244..>142494294
                     /gene="TRBJ2-2"
                     /gene_synonym="TCRBJ2S2; TRBJ22"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=3
                     /db_xref="GeneID:28628"
                     /db_xref="HGNC:12169"
                     /db_xref="IMGT/GENE-DB:TRBJ2-2"
     J_segment       142494244..142494294
                     /gene="TRBJ2-2"
                     /gene_synonym="TCRBJ2S2; TRBJ22"
                     /standard_name="TRBJ2-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28628"
     gene            142494381..142494426
                     /gene="TRBJ2-2P"
                     /gene_synonym="TRBJ22P"
                     /note="this gene lacks the nonamer recombination signal;
                     Derived by automated computational analysis using gene
                     prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28627"
                     /db_xref="HGNC:12170"
                     /db_xref="IMGT/GENE-DB:TRBJ2-2P"
     CDS             142494381..142494426
                     /gene="TRBJ2-2P"
                     /gene_synonym="TRBJ22P"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /codon_start=1
                     /db_xref="GeneID:28627"
                     /db_xref="HGNC:12170"
                     /db_xref="IMGT/GENE-DB:TRBJ2-2P"
     J_segment       142494381..142494426
                     /gene="TRBJ2-2P"
                     /gene_synonym="TRBJ22P"
                     /standard_name="TRBJ2-2P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:28627"
     gene            <142494531..>142494579
                     /gene="TRBJ2-3"
                     /gene_synonym="TCRBJ2S3; TRBJ23"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28626"
                     /db_xref="HGNC:12171"
                     /db_xref="IMGT/GENE-DB:TRBJ2-3"
     CDS             <142494531..>142494579
                     /gene="TRBJ2-3"
                     /gene_synonym="TCRBJ2S3; TRBJ23"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28626"
                     /db_xref="HGNC:12171"
                     /db_xref="IMGT/GENE-DB:TRBJ2-3"
     J_segment       142494531..142494579
                     /gene="TRBJ2-3"
                     /gene_synonym="TCRBJ2S3; TRBJ23"
                     /standard_name="TRBJ2-3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28626"
     gene            <142494682..>142494731
                     /gene="TRBJ2-4"
                     /gene_synonym="TCRBJ2S4; TRBJ24"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28625"
                     /db_xref="HGNC:12172"
                     /db_xref="IMGT/GENE-DB:TRBJ2-4"
     CDS             <142494682..>142494731
                     /gene="TRBJ2-4"
                     /gene_synonym="TCRBJ2S4; TRBJ24"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28625"
                     /db_xref="HGNC:12172"
                     /db_xref="IMGT/GENE-DB:TRBJ2-4"
     J_segment       142494682..142494731
                     /gene="TRBJ2-4"
                     /gene_synonym="TCRBJ2S4; TRBJ24"
                     /standard_name="TRBJ2-4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28625"
     gene            <142494803..>142494922
                     /gene="TRBJ2-5"
                     /gene_synonym="TCRBJ2S5; TRBJ25"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28624"
                     /db_xref="HGNC:12173"
                     /db_xref="IMGT/GENE-DB:TRBJ2-5"
     CDS             <142494803..>142494850
                     /gene="TRBJ2-5"
                     /gene_synonym="TCRBJ2S5; TRBJ25"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28624"
                     /db_xref="HGNC:12173"
                     /db_xref="IMGT/GENE-DB:TRBJ2-5"
     J_segment       142494803..142494850
                     /gene="TRBJ2-5"
                     /gene_synonym="TCRBJ2S5; TRBJ25"
                     /standard_name="TRBJ2-5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28624"
     gene            <142494895..>142494975
                     /gene="TRBJ2-6"
                     /gene_synonym="TCRBJ2S6; TRBJ26"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28623"
                     /db_xref="HGNC:12174"
                     /db_xref="IMGT/GENE-DB:TRBJ2-6"
     CDS             <142494923..>142494975
                     /gene="TRBJ2-6"
                     /gene_synonym="TCRBJ2S6; TRBJ26"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28623"
                     /db_xref="HGNC:12174"
                     /db_xref="IMGT/GENE-DB:TRBJ2-6"
     J_segment       142494923..142494975
                     /gene="TRBJ2-6"
                     /gene_synonym="TCRBJ2S6; TRBJ26"
                     /standard_name="TRBJ2-6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28623"
     gene            <142495140..>142495186
                     /gene="TRBJ2-7"
                     /gene_synonym="TCRBJ2S7; TRBJ27"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28622"
                     /db_xref="HGNC:12175"
                     /db_xref="IMGT/GENE-DB:TRBJ2-7"
     CDS             <142495140..>142495186
                     /gene="TRBJ2-7"
                     /gene_synonym="TCRBJ2S7; TRBJ27"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28622"
                     /db_xref="HGNC:12175"
                     /db_xref="IMGT/GENE-DB:TRBJ2-7"
     J_segment       142495140..142495186
                     /gene="TRBJ2-7"
                     /gene_synonym="TCRBJ2S7; TRBJ27"
                     /standard_name="TRBJ2-7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28622"
     gene            142498725..142500213
                     /gene="TRBC2"
                     /gene_synonym="TCRBC2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28638"
                     /db_xref="HGNC:12157"
                     /db_xref="IMGT/GENE-DB:TRBC2"
     CDS             join(<142498725..142499111,142499628..142499645,
                     142499789..142499897,142500187..142500213)
                     /gene="TRBC2"
                     /gene_synonym="TCRBC2"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=3
                     /db_xref="GeneID:28638"
                     /db_xref="HGNC:12157"
                     /db_xref="IMGT/GENE-DB:TRBC2"
     C_region        join(142498725..142499111,142499628..142499645,
                     142499789..142499897,142500187..142500213)
                     /gene="TRBC2"
                     /gene_synonym="TCRBC2"
                     /standard_name="TRBC2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28638"
     gene            complement(142510271..142510972)
                     /gene="TRBV30"
                     /gene_synonym="TCRBV20S1A1N2; TCRBV30S1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28557"
                     /db_xref="HGNC:12214"
                     /db_xref="IMGT/GENE-DB:TRBV30"
     CDS             complement(join(<142510271..142510562,
                     142510930..142510972))
                     /gene="TRBV30"
                     /gene_synonym="TCRBV20S1A1N2; TCRBV30S1"
                     /exception="rearrangement required for product"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /codon_start=1
                     /db_xref="GeneID:28557"
                     /db_xref="HGNC:12214"
                     /db_xref="IMGT/GENE-DB:TRBV30"
     V_segment       complement(join(142510271..142510562,
                     142510930..142510972))
                     /gene="TRBV30"
                     /gene_synonym="TCRBV20S1A1N2; TCRBV30S1"
                     /standard_name="TRBV30"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /db_xref="GeneID:28557"
     gene            142552792..142568847
                     /gene="EPHB6"
                     /gene_synonym="HEP; MGC129910; MGC129911"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2051"
                     /db_xref="HGNC:3396"
                     /db_xref="HPRD:04133"
                     /db_xref="MIM:602757"
     mRNA            join(142552792..142553147,142558810..142558944,
                     142559775..142559891,142560514..142560591,
                     142560885..142561085,142561389..142561453,
                     142561724..142562504,142563230..142563385,
                     142563715..142564071,142564236..142564360,
                     142564661..142564823,142565363..142565477,
                     142565752..142565804,142565996..142566115,
                     142566247..142566494,142566727..142566900,
                     142567570..142567719,142567967..142568160,
                     142568283..142568438,142568549..142568847)
                     /gene="EPHB6"
                     /gene_synonym="HEP; MGC129910; MGC129911"
                     /product="EPH receptor B6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004445.3"
                     /db_xref="GI:194097331"
                     /db_xref="GeneID:2051"
                     /db_xref="HGNC:3396"
                     /db_xref="HPRD:04133"
                     /db_xref="MIM:602757"
     CDS             join(142560986..142561085,142561389..142561453,
                     142561724..142562504,142563230..142563385,
                     142563715..142564071,142564236..142564360,
                     142564661..142564823,142565363..142565477,
                     142565752..142565804,142565996..142566115,
                     142566247..142566494,142566727..142566900,
                     142567570..142567719,142567967..142568160,
                     142568283..142568438,142568549..142568657)
                     /gene="EPHB6"
                     /gene_synonym="HEP; MGC129910; MGC129911"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ephrin type-B receptor 6 precursor"
                     /protein_id="NP_004436.2"
                     /db_xref="GI:194097332"
                     /db_xref="CCDS:CCDS5873.2"
                     /db_xref="GeneID:2051"
                     /db_xref="HGNC:3396"
                     /db_xref="HPRD:04133"
                     /db_xref="MIM:602757"
     gene            complement(142568960..142583477)
                     /gene="TRPV6"
                     /gene_synonym="ABP/ZF; CAT1; CATL; ECAC2; HSA277909;
                     LP6728; ZFAB"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55503"
                     /db_xref="HGNC:14006"
                     /db_xref="HPRD:05982"
                     /db_xref="MIM:606680"
     mRNA            complement(join(142568960..142569742,142570125..142570231,
                     142571201..142571469,142571829..142571895,
                     142572244..142572409,142572657..142572733,
                     142572831..142572917,142573221..142573433,
                     142573511..142573657,142574161..142574336,
                     142574492..142574590,142574895..142575032,
                     142575404..142575526,142575682..142575779,
                     142583134..142583477))
                     /gene="TRPV6"
                     /gene_synonym="ABP/ZF; CAT1; CATL; ECAC2; HSA277909;
                     LP6728; ZFAB"
                     /product="transient receptor potential cation channel,
                     subfamily V, member 6"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018646.2"
                     /db_xref="GI:21314681"
                     /db_xref="GeneID:55503"
                     /db_xref="HGNC:14006"
                     /db_xref="HPRD:05982"
                     /db_xref="MIM:606680"
     CDS             complement(join(142569460..142569742,142570125..142570231,
                     142571201..142571469,142571829..142571895,
                     142572244..142572409,142572657..142572733,
                     142572831..142572917,142573221..142573433,
                     142573511..142573657,142574161..142574336,
                     142574492..142574590,142574895..142575032,
                     142575404..142575526,142575682..142575779,
                     142583134..142583261))
                     /gene="TRPV6"
                     /gene_synonym="ABP/ZF; CAT1; CATL; ECAC2; HSA277909;
                     LP6728; ZFAB"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transient receptor potential cation channel
                     subfamily V member 6"
                     /protein_id="NP_061116.2"
                     /db_xref="GI:21314682"
                     /db_xref="CCDS:CCDS5874.1"
                     /db_xref="GeneID:55503"
                     /db_xref="HGNC:14006"
                     /db_xref="HPRD:05982"
                     /db_xref="MIM:606680"
     gene            complement(142605648..142630820)
                     /gene="TRPV5"
                     /gene_synonym="CAT2; ECAC1; OTRPC3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:56302"
                     /db_xref="HGNC:3145"
                     /db_xref="HPRD:05981"
                     /db_xref="MIM:606679"
     mRNA            complement(join(142605648..142605974,142606656..142606762,
                     142609648..142609916,142611810..142611876,
                     142612051..142612216,142612477..142612553,
                     142612652..142612738,142622624..142622836,
                     142625183..142625329,142625786..142625961,
                     142626117..142626215,142626523..142626660,
                     142627153..142627275,142627444..142627541,
                     142630429..142630820))
                     /gene="TRPV5"
                     /gene_synonym="CAT2; ECAC1; OTRPC3"
                     /product="transient receptor potential cation channel,
                     subfamily V, member 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_019841.4"
                     /db_xref="GI:83722285"
                     /db_xref="GeneID:56302"
                     /db_xref="HGNC:3145"
                     /db_xref="HPRD:05981"
                     /db_xref="MIM:606679"
     CDS             complement(join(142605680..142605974,142606656..142606762,
                     142609648..142609916,142611810..142611876,
                     142612051..142612216,142612477..142612553,
                     142612652..142612738,142622624..142622836,
                     142625183..142625329,142625786..142625961,
                     142626117..142626215,142626523..142626660,
                     142627153..142627275,142627444..142627541,
                     142630429..142630556))
                     /gene="TRPV5"
                     /gene_synonym="CAT2; ECAC1; OTRPC3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transient receptor potential cation channel
                     subfamily V member 5"
                     /protein_id="NP_062815.2"
                     /db_xref="GI:17505200"
                     /db_xref="CCDS:CCDS5875.1"
                     /db_xref="GeneID:56302"
                     /db_xref="HGNC:3145"
                     /db_xref="HPRD:05981"
                     /db_xref="MIM:606679"
     gene            142636603..142637957
                     /gene="C7orf34"
                     /gene_synonym="ctm-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:135927"
                     /db_xref="HGNC:21750"
                     /db_xref="HPRD:12922"
     mRNA            join(142636603..142636851,142637439..142637957)
                     /gene="C7orf34"
                     /gene_synonym="ctm-1"
                     /product="chromosome 7 open reading frame 34"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178829.4"
                     /db_xref="GI:170671737"
                     /db_xref="GeneID:135927"
                     /db_xref="HGNC:21750"
                     /db_xref="HPRD:12922"
     CDS             join(142636644..142636851,142637439..142637674)
                     /gene="C7orf34"
                     /gene_synonym="ctm-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC135927"
                     /protein_id="NP_849151.2"
                     /db_xref="GI:170671738"
                     /db_xref="CCDS:CCDS5876.2"
                     /db_xref="GeneID:135927"
                     /db_xref="HGNC:21750"
                     /db_xref="HPRD:12922"
     gene            complement(142638201..142659503)
                     /gene="KEL"
                     /gene_synonym="CD238; ECE3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3792"
                     /db_xref="HGNC:6308"
                     /db_xref="HPRD:00194"
                     /db_xref="MIM:110900"
     mRNA            complement(join(142638201..142638500,142639521..142639616,
                     142639962..142640131,142640363..142640430,
                     142640573..142640683,142640870..142640970,
                     142641410..142641487,142641730..142641828,
                     142643294..142643404,142649596..142649725,
                     142650895..142651043,142651271..142651459,
                     142651552..142651614,142654914..142655060,
                     142655391..142655515,142658015..142658191,
                     142658447..142658588,142658882..142658959,
                     142659291..142659503))
                     /gene="KEL"
                     /gene_synonym="CD238; ECE3"
                     /product="Kell blood group, metallo-endopeptidase"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000420.2"
                     /db_xref="GI:17025233"
                     /db_xref="GeneID:3792"
                     /db_xref="HGNC:6308"
                     /db_xref="HPRD:00194"
                     /db_xref="MIM:110900"
     CDS             complement(join(142638339..142638500,142639521..142639616,
                     142639962..142640131,142640363..142640430,
                     142640573..142640683,142640870..142640970,
                     142641410..142641487,142641730..142641828,
                     142643294..142643404,142649596..142649725,
                     142650895..142651043,142651271..142651459,
                     142651552..142651614,142654914..142655060,
                     142655391..142655515,142658015..142658191,
                     142658447..142658588,142658882..142658959,
                     142659291..142659293))
                     /gene="KEL"
                     /gene_synonym="CD238; ECE3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="kell blood group glycoprotein"
                     /protein_id="NP_000411.1"
                     /db_xref="GI:4557691"
                     /db_xref="CCDS:CCDS34766.1"
                     /db_xref="GeneID:3792"
                     /db_xref="HGNC:6308"
                     /db_xref="HPRD:00194"
                     /db_xref="MIM:110900"
     gene            complement(142723287..142724219)
                     /gene="OR9A2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:135924"
                     /db_xref="HGNC:15093"
                     /db_xref="HPRD:15088"
     mRNA            complement(142723287..142724219)
                     /gene="OR9A2"
                     /product="olfactory receptor, family 9, subfamily A,
                     member 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001001658.1"
                     /db_xref="GI:48717233"
                     /db_xref="GeneID:135924"
                     /db_xref="HGNC:15093"
                     /db_xref="HPRD:15088"
     CDS             complement(142723287..142724219)
                     /gene="OR9A2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 9A2"
                     /protein_id="NP_001001658.1"
                     /db_xref="GI:48717234"
                     /db_xref="CCDS:CCDS34767.1"
                     /db_xref="GeneID:135924"
                     /db_xref="HGNC:15093"
                     /db_xref="HPRD:15088"
     gene            complement(142744168..142744873)
                     /gene="OR9P1P"
                     /gene_synonym="OR9P2P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:81382"
                     /db_xref="HGNC:15097"
     gene            142749438..142750379
                     /gene="OR6V1"
                     /gene_synonym="GPR138"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:346517"
                     /db_xref="HGNC:15090"
                     /db_xref="HPRD:11417"
     mRNA            142749438..142750379
                     /gene="OR6V1"
                     /gene_synonym="GPR138"
                     /product="olfactory receptor, family 6, subfamily V,
                     member 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001001667.1"
                     /db_xref="GI:48717322"
                     /db_xref="GeneID:346517"
                     /db_xref="HGNC:15090"
                     /db_xref="HPRD:11417"
     CDS             142749438..142750379
                     /gene="OR6V1"
                     /gene_synonym="GPR138"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 6V1"
                     /protein_id="NP_001001667.1"
                     /db_xref="GI:48717323"
                     /db_xref="CCDS:CCDS47728.1"
                     /db_xref="GeneID:346517"
                     /db_xref="HGNC:15090"
                     /db_xref="HPRD:11417"
     gene            complement(142759381..142760882)
                     /gene="OR6W1P"
                     /gene_synonym="OR6W1; sdolf"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:89883"
                     /db_xref="HGNC:15091"
     misc_RNA        complement(142759381..142760882)
                     /gene="OR6W1P"
                     /gene_synonym="OR6W1; sdolf"
                     /product="olfactory receptor, family 6, subfamily W,
                     member 1 pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002140.1"
                     /db_xref="GI:46395477"
                     /db_xref="GeneID:89883"
                     /db_xref="HGNC:15091"
     gene            142829174..142836834
                     /gene="PIP"
                     /gene_synonym="GCDFP-15; GCDFP15; GPIP4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5304"
                     /db_xref="HGNC:8993"
                     /db_xref="HPRD:07179"
                     /db_xref="MIM:176720"
     mRNA            join(142829174..142829304,142832287..142832392,
                     142836168..142836282,142836611..142836834)
                     /gene="PIP"
                     /gene_synonym="GCDFP-15; GCDFP15; GPIP4"
                     /product="prolactin-induced protein"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002652.2"
                     /db_xref="GI:46309847"
                     /db_xref="GeneID:5304"
                     /db_xref="HGNC:8993"
                     /db_xref="HPRD:07179"
                     /db_xref="MIM:176720"
     CDS             join(142829210..142829304,142832287..142832392,
                     142836168..142836282,142836611..142836735)
                     /gene="PIP"
                     /gene_synonym="GCDFP-15; GCDFP15; GPIP4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="prolactin-inducible protein precursor"
                     /protein_id="NP_002643.1"
                     /db_xref="GI:4505821"
                     /db_xref="CCDS:CCDS34768.1"
                     /db_xref="GeneID:5304"
                     /db_xref="HGNC:8993"
                     /db_xref="HPRD:07179"
                     /db_xref="MIM:176720"
     gene            142880512..142881528
                     /gene="TAS2R39"
                     /gene_synonym="T2R39; T2R57"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:259285"
                     /db_xref="HGNC:18886"
                     /db_xref="HPRD:18149"
     mRNA            142880512..142881528
                     /gene="TAS2R39"
                     /gene_synonym="T2R39; T2R57"
                     /product="taste receptor, type 2, member 39"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_176881.2"
                     /db_xref="GI:116875818"
                     /db_xref="GeneID:259285"
                     /db_xref="HGNC:18886"
                     /db_xref="HPRD:18149"
     CDS             142880512..142881528
                     /gene="TAS2R39"
                     /gene_synonym="T2R39; T2R57"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="taste receptor type 2 member 39"
                     /protein_id="NP_795362.2"
                     /db_xref="GI:116875819"
                     /db_xref="CCDS:CCDS47729.1"
                     /db_xref="GeneID:259285"
                     /db_xref="HGNC:18886"
                     /db_xref="HPRD:18149"
     gene            142919172..142920143
                     /gene="TAS2R40"
                     /gene_synonym="GPR60; MGC126844; MGC126846; T2R40; T2R58"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:259286"
                     /db_xref="HGNC:18885"
                     /db_xref="HPRD:18150"
                     /db_xref="MIM:613964"
     mRNA            142919172..142920143
                     /gene="TAS2R40"
                     /gene_synonym="GPR60; MGC126844; MGC126846; T2R40; T2R58"
                     /product="taste receptor, type 2, member 40"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_176882.1"
                     /db_xref="GI:28882032"
                     /db_xref="GeneID:259286"
                     /db_xref="HGNC:18885"
                     /db_xref="HPRD:18150"
                     /db_xref="MIM:613964"
     CDS             142919172..142920143
                     /gene="TAS2R40"
                     /gene_synonym="GPR60; MGC126844; MGC126846; T2R40; T2R58"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="taste receptor type 2 member 40"
                     /protein_id="NP_795363.1"
                     /db_xref="GI:28882033"
                     /db_xref="CCDS:CCDS43662.1"
                     /db_xref="GeneID:259286"
                     /db_xref="HGNC:18885"
                     /db_xref="HPRD:18150"
                     /db_xref="MIM:613964"
     gene            142960522..142966222
                     /gene="GSTK1"
                     /gene_synonym="GST; GST 13-13; GST13; GST13-13; GSTK1-1;
                     hGSTK1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:373156"
                     /db_xref="HGNC:16906"
                     /db_xref="MIM:602321"
     mRNA            join(142960522..142960678,142961179..142961260,
                     142961641..142961769,142962085..142962185,
                     142962354..142962389,142964710..142964826,
                     142965184..142965277,142965881..142966222)
                     /gene="GSTK1"
                     /gene_synonym="GST; GST 13-13; GST13; GST13-13; GSTK1-1;
                     hGSTK1"
                     /product="glutathione S-transferase kappa 1, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015917.2"
                     /db_xref="GI:219842315"
                     /db_xref="GeneID:373156"
                     /db_xref="HGNC:16906"
                     /db_xref="MIM:602321"
     mRNA            join(142960522..142960678,142961179..142961260,
                     142961641..142961769,142962085..142962389,
                     142964710..142964826,142965184..142965277,
                     142965881..142966222)
                     /gene="GSTK1"
                     /gene_synonym="GST; GST 13-13; GST13; GST13-13; GSTK1-1;
                     hGSTK1"
                     /product="glutathione S-transferase kappa 1, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001143679.1"
                     /db_xref="GI:219842316"
                     /db_xref="GeneID:373156"
                     /db_xref="HGNC:16906"
                     /db_xref="MIM:602321"
     mRNA            join(142960522..142960678,142961179..142961260,
                     142961641..142961769,142962085..142962185,
                     142964710..142964826,142965184..142965277,
                     142965881..142966222)
                     /gene="GSTK1"
                     /gene_synonym="GST; GST 13-13; GST13; GST13-13; GSTK1-1;
                     hGSTK1"
                     /product="glutathione S-transferase kappa 1, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001143680.1"
                     /db_xref="GI:219842332"
                     /db_xref="GeneID:373156"
                     /db_xref="HGNC:16906"
                     /db_xref="MIM:602321"
     mRNA            join(142960522..142960678,142961179..142961260,
                     142962085..142962185,142962354..142962389,
                     142964710..142964826,142965184..142965277,
                     142965881..142966222)
                     /gene="GSTK1"
                     /gene_synonym="GST; GST 13-13; GST13; GST13-13; GSTK1-1;
                     hGSTK1"
                     /product="glutathione S-transferase kappa 1, transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001143681.1"
                     /db_xref="GI:219842334"
                     /db_xref="GeneID:373156"
                     /db_xref="HGNC:16906"
                     /db_xref="MIM:602321"
     CDS             join(142960607..142960678,142961179..142961260,
                     142961641..142961769,142962085..142962185,
                     142962354..142962389,142964710..142964826,
                     142965184..142965277,142965881..142965930)
                     /gene="GSTK1"
                     /gene_synonym="GST; GST 13-13; GST13; GST13-13; GSTK1-1;
                     hGSTK1"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="glutathione S-transferase kappa 1 isoform a"
                     /protein_id="NP_057001.1"
                     /db_xref="GI:7705704"
                     /db_xref="CCDS:CCDS5877.1"
                     /db_xref="GeneID:373156"
                     /db_xref="HGNC:16906"
                     /db_xref="MIM:602321"
     CDS             join(142960607..142960678,142961179..142961260,
                     142961641..142961769,142962085..142962389,
                     142964710..142964826,142965184..142965277,
                     142965881..142965930)
                     /gene="GSTK1"
                     /gene_synonym="GST; GST 13-13; GST13; GST13-13; GSTK1-1;
                     hGSTK1"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="glutathione S-transferase kappa 1 isoform b"
                     /protein_id="NP_001137151.1"
                     /db_xref="GI:219842317"
                     /db_xref="CCDS:CCDS47730.1"
                     /db_xref="GeneID:373156"
                     /db_xref="HGNC:16906"
                     /db_xref="MIM:602321"
     CDS             join(142960607..142960678,142961179..142961260,
                     142961641..142961769,142962085..142962185,
                     142964710..142964826,142965184..142965277,
                     142965881..142965930)
                     /gene="GSTK1"
                     /gene_synonym="GST; GST 13-13; GST13; GST13-13; GSTK1-1;
                     hGSTK1"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="glutathione S-transferase kappa 1 isoform c"
                     /protein_id="NP_001137152.1"
                     /db_xref="GI:219842333"
                     /db_xref="CCDS:CCDS47731.1"
                     /db_xref="GeneID:373156"
                     /db_xref="HGNC:16906"
                     /db_xref="MIM:602321"
     CDS             join(142960607..142960678,142961179..142961260,
                     142962085..142962185,142962354..142962389,
                     142964710..142964826,142965184..142965277,
                     142965881..142965930)
                     /gene="GSTK1"
                     /gene_synonym="GST; GST 13-13; GST13; GST13-13; GSTK1-1;
                     hGSTK1"
                     /note="isoform d is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="glutathione S-transferase kappa 1 isoform d"
                     /protein_id="NP_001137153.1"
                     /db_xref="GI:219842335"
                     /db_xref="CCDS:CCDS47732.1"
                     /db_xref="GeneID:373156"
                     /db_xref="HGNC:16906"
                     /db_xref="MIM:602321"
     gene            142982040..142985141
                     /gene="TMEM139"
                     /gene_synonym="FLJ90586"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:135932"
                     /db_xref="HGNC:22058"
     mRNA            join(142982040..142982067,142983034..142983295,
                     142983517..142985141)
                     /gene="TMEM139"
                     /gene_synonym="FLJ90586"
                     /product="transmembrane protein 139, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_153345.2"
                     /db_xref="GI:338222095"
                     /db_xref="GeneID:135932"
                     /db_xref="HGNC:22058"
                     /db_xref="HPRD:08298"
     mRNA            join(142982040..142982067,142982441..142982538,
                     142983034..142983295,142983517..142985141)
                     /gene="TMEM139"
                     /gene_synonym="FLJ90586"
                     /product="transmembrane protein 139, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001242773.1"
                     /db_xref="GI:338221711"
                     /db_xref="GeneID:135932"
                     /db_xref="HGNC:22058"
     mRNA            join(142982040..142982091,142982441..142982538,
                     142982647..142982733,142983034..142983295,
                     142983517..142985141)
                     /gene="TMEM139"
                     /gene_synonym="FLJ90586"
                     /product="transmembrane protein 139, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001242774.1"
                     /db_xref="GI:338221713"
                     /db_xref="GeneID:135932"
                     /db_xref="HGNC:22058"
     mRNA            join(142982040..142982091,142982441..142982538,
                     142983034..142983295,142983517..142985141)
                     /gene="TMEM139"
                     /gene_synonym="FLJ90586"
                     /product="transmembrane protein 139, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001242775.1"
                     /db_xref="GI:338221715"
                     /db_xref="GeneID:135932"
                     /db_xref="HGNC:22058"
     mRNA            join(142982040..142982067,142982438..142982538,
                     142983517..142985141)
                     /gene="TMEM139"
                     /gene_synonym="FLJ90586"
                     /product="transmembrane protein 139, transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001242776.1"
                     /db_xref="GI:338222096"
                     /db_xref="GeneID:135932"
                     /db_xref="HGNC:22058"
     mRNA            join(142982040..142982067,142983517..142985141)
                     /gene="TMEM139"
                     /gene_synonym="FLJ90586"
                     /product="transmembrane protein 139, transcript variant 6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001242777.1"
                     /db_xref="GI:338221717"
                     /db_xref="GeneID:135932"
                     /db_xref="HGNC:22058"
     misc_RNA        join(142982040..142982538,142983517..142985141)
                     /gene="TMEM139"
                     /gene_synonym="FLJ90586"
                     /product="transmembrane protein 139, transcript variant 7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_040003.1"
                     /db_xref="GI:338221719"
                     /db_xref="GeneID:135932"
                     /db_xref="HGNC:22058"
     CDS             join(142983051..142983295,142983517..142983922)
                     /gene="TMEM139"
                     /gene_synonym="FLJ90586"
                     /note="isoform a precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 139 isoform a precursor"
                     /protein_id="NP_699176.1"
                     /db_xref="GI:23503271"
                     /db_xref="CCDS:CCDS5878.1"
                     /db_xref="GeneID:135932"
                     /db_xref="HGNC:22058"
     CDS             join(142983051..142983295,142983517..142983922)
                     /gene="TMEM139"
                     /gene_synonym="FLJ90586"
                     /note="isoform a precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 139 isoform a precursor"
                     /protein_id="NP_001229702.1"
                     /db_xref="GI:338221712"
                     /db_xref="GeneID:135932"
                     /db_xref="HGNC:22058"
     CDS             join(142983051..142983295,142983517..142983922)
                     /gene="TMEM139"
                     /gene_synonym="FLJ90586"
                     /note="isoform a precursor is encoded by transcript
                     variant 3; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 139 isoform a precursor"
                     /protein_id="NP_001229703.1"
                     /db_xref="GI:338221714"
                     /db_xref="GeneID:135932"
                     /db_xref="HGNC:22058"
     CDS             join(142983051..142983295,142983517..142983922)
                     /gene="TMEM139"
                     /gene_synonym="FLJ90586"
                     /note="isoform a precursor is encoded by transcript
                     variant 4; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 139 isoform a precursor"
                     /protein_id="NP_001229704.1"
                     /db_xref="GI:338221716"
                     /db_xref="GeneID:135932"
                     /db_xref="HGNC:22058"
     CDS             142983701..142983922
                     /gene="TMEM139"
                     /gene_synonym="FLJ90586"
                     /note="isoform b is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 139 isoform b"
                     /protein_id="NP_001229705.1"
                     /db_xref="GI:338222097"
                     /db_xref="GeneID:135932"
                     /db_xref="HGNC:22058"
     CDS             142983701..142983922
                     /gene="TMEM139"
                     /gene_synonym="FLJ90586"
                     /note="isoform b is encoded by transcript variant 6;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 139 isoform b"
                     /protein_id="NP_001229706.1"
                     /db_xref="GI:338221718"
                     /db_xref="GeneID:135932"
                     /db_xref="HGNC:22058"
     gene            142985308..143004789
                     /gene="CASP2"
                     /gene_synonym="CASP-2; ICH1; NEDD-2; NEDD2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:835"
                     /db_xref="HGNC:1503"
                     /db_xref="HPRD:02800"
                     /db_xref="MIM:600639"
     mRNA            join(142985308..142985622,142988633..142988783,
                     142989393..142989560,142989710..142989791,
                     142991323..142991417,142991690..142991866,
                     142997016..142997144,142997297..142997387,
                     143000877..143001026,143001767..143001876,
                     143002033..143004789)
                     /gene="CASP2"
                     /gene_synonym="CASP-2; ICH1; NEDD-2; NEDD2"
                     /product="caspase 2, apoptosis-related cysteine peptidase,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032982.3"
                     /db_xref="GI:320461578"
                     /db_xref="GeneID:835"
                     /db_xref="HGNC:1503"
                     /db_xref="HPRD:02800"
                     /db_xref="MIM:600639"
     mRNA            join(142985308..142985622,142988633..142988783,
                     142989393..142989474,142991373..142991417,
                     142991690..142991866,142997016..142997144,
                     142997297..142997387,143000877..143001026,
                     143001767..143001876,143002033..143004789)
                     /gene="CASP2"
                     /gene_synonym="CASP-2; ICH1; NEDD-2; NEDD2"
                     /product="caspase 2, apoptosis-related cysteine peptidase,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032983.3"
                     /db_xref="GI:320461587"
                     /db_xref="GeneID:835"
                     /db_xref="HGNC:1503"
                     /db_xref="HPRD:02800"
                     /db_xref="MIM:600639"
     CDS             join(142985549..142985622,142988633..142988783,
                     142989393..142989560,142989710..142989791,
                     142991323..142991417,142991690..142991866,
                     142997016..142997144,142997297..142997387,
                     143000877..143001026,143001767..143001876,
                     143002033..143002164)
                     /gene="CASP2"
                     /gene_synonym="CASP-2; ICH1; NEDD-2; NEDD2"
                     /note="isoform 1 preproprotein is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="caspase-2 isoform 1 preproprotein"
                     /protein_id="NP_116764.2"
                     /db_xref="GI:39995059"
                     /db_xref="CCDS:CCDS5879.1"
                     /db_xref="GeneID:835"
                     /db_xref="HGNC:1503"
                     /db_xref="HPRD:02800"
                     /db_xref="MIM:600639"
     CDS             join(142985549..142985622,142988633..142988783,
                     142989393..142989474,142991373..142991392)
                     /gene="CASP2"
                     /gene_synonym="CASP-2; ICH1; NEDD-2; NEDD2"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caspase-2 isoform 3"
                     /protein_id="NP_116765.2"
                     /db_xref="GI:39995061"
                     /db_xref="CCDS:CCDS47733.1"
                     /db_xref="GeneID:835"
                     /db_xref="HGNC:1503"
                     /db_xref="HPRD:02800"
                     /db_xref="MIM:600639"
     mRNA            join(142986681..142986749,142988633..142988783,
                     142989393..142989560,142989710..142989791,
                     142991323..142991417,142991690..142991866,
                     142997016..142997144,142997297..142997387,
                     142997473..142997533,143000877..143001026,
                     143001767..143001876,143002033..143004789)
                     /gene="CASP2"
                     /gene_synonym="CASP-2; ICH1; NEDD-2; NEDD2"
                     /product="caspase 2, apoptosis-related cysteine peptidase,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001224.4"
                     /db_xref="GI:331999981"
                     /db_xref="GeneID:835"
                     /db_xref="HGNC:1503"
                     /db_xref="HPRD:02800"
                     /db_xref="MIM:600639"
     CDS             join(142988652..142988783,142989393..142989560,
                     142989710..142989791,142991323..142991417,
                     142991690..142991866,142997016..142997144,
                     142997297..142997387,142997473..142997533,
                     143000877..143000880)
                     /gene="CASP2"
                     /gene_synonym="CASP-2; ICH1; NEDD-2; NEDD2"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="caspase-2 isoform 2"
                     /protein_id="NP_001215.1"
                     /db_xref="GI:4502575"
                     /db_xref="GeneID:835"
                     /db_xref="HGNC:1503"
                     /db_xref="HPRD:02800"
                     /db_xref="MIM:600639"
     gene            complement(143009623..143010216)
                     /gene="HINT1P1"
                     /gene_synonym="HINTP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:730647"
                     /db_xref="HGNC:18467"
     gene            143013219..143049097
                     /gene="CLCN1"
                     /gene_synonym="CLC1; MGC138361; MGC142055"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1180"
                     /db_xref="HGNC:2019"
                     /db_xref="HPRD:00320"
                     /db_xref="MIM:118425"
     mRNA            join(143013219..143013485,143016848..143016968,
                     143017757..143017888,143018458..143018586,
                     143018808..143018941,143020402..143020479,
                     143021507..143021585,143027865..143027990,
                     143028325..143028409,143028644..143028745,
                     143029512..143029596,143029817..143029966,
                     143036346..143036415,143036604..143036714,
                     143039022..143039235,143039465..143039598,
                     143042614..143042855,143043233..143043344,
                     143043672..143043751,143044004..143044042,
                     143047465..143047569,143047661..143047747,
                     143048687..143049097)
                     /gene="CLCN1"
                     /gene_synonym="CLC1; MGC138361; MGC142055"
                     /product="chloride channel 1, skeletal muscle"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000083.2"
                     /db_xref="GI:119433676"
                     /db_xref="GeneID:1180"
                     /db_xref="HGNC:2019"
                     /db_xref="HPRD:00320"
                     /db_xref="MIM:118425"
     CDS             join(143013306..143013485,143016848..143016968,
                     143017757..143017888,143018458..143018586,
                     143018808..143018941,143020402..143020479,
                     143021507..143021585,143027865..143027990,
                     143028325..143028409,143028644..143028745,
                     143029512..143029596,143029817..143029966,
                     143036346..143036415,143036604..143036714,
                     143039022..143039235,143039465..143039598,
                     143042614..143042855,143043233..143043344,
                     143043672..143043751,143044004..143044042,
                     143047465..143047569,143047661..143047747,
                     143048687..143049058)
                     /gene="CLCN1"
                     /gene_synonym="CLC1; MGC138361; MGC142055"
                     /exception="mismatches in translation"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="chloride channel protein 1"
                     /protein_id="NP_000074.2"
                     /db_xref="GI:119433677"
                     /db_xref="CCDS:CCDS5881.1"
                     /db_xref="GeneID:1180"
                     /db_xref="HGNC:2019"
                     /db_xref="HPRD:00320"
                     /db_xref="MIM:118425"
     gene            complement(143050493..143059840)
                     /gene="FAM131B"
                     /gene_synonym="KIAA0773"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9715"
                     /db_xref="HGNC:22202"
                     /db_xref="HPRD:13816"
     mRNA            complement(join(143050493..143054115,143054373..143054516,
                     143055920..143056117,143056419..143056512,
                     143056825..143056860,143057133..143057242,
                     143059669..143059840))
                     /gene="FAM131B"
                     /gene_synonym="KIAA0773"
                     /product="family with sequence similarity 131, member B,
                     transcript variant a"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001031690.2"
                     /db_xref="GI:164565451"
                     /db_xref="GeneID:9715"
                     /db_xref="HGNC:22202"
                     /db_xref="HPRD:13816"
     mRNA            complement(join(143050493..143054115,143054373..143054516,
                     143055920..143056117,143056419..143056512,
                     143056825..143056860,143057133..143057242,
                     143059109..143059173))
                     /gene="FAM131B"
                     /gene_synonym="KIAA0773"
                     /product="family with sequence similarity 131, member B,
                     transcript variant b"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014690.4"
                     /db_xref="GI:164519060"
                     /db_xref="GeneID:9715"
                     /db_xref="HGNC:22202"
                     /db_xref="HPRD:13816"
     CDS             complement(join(143053643..143054115,143054373..143054516,
                     143055920..143056117,143056419..143056512,
                     143056825..143056860,143057133..143057242,
                     143059669..143059696))
                     /gene="FAM131B"
                     /gene_synonym="KIAA0773"
                     /note="isoform a is encoded by transcript variant a;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC9715 isoform a"
                     /protein_id="NP_001026860.2"
                     /db_xref="GI:164565452"
                     /db_xref="CCDS:CCDS47734.1"
                     /db_xref="GeneID:9715"
                     /db_xref="HGNC:22202"
                     /db_xref="HPRD:13816"
     CDS             complement(join(143053643..143054115,143054373..143054516,
                     143055920..143056117,143056419..143056512,
                     143056825..143056860,143057133..143057186))
                     /gene="FAM131B"
                     /gene_synonym="KIAA0773"
                     /note="isoform b is encoded by transcript variant b;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC9715 isoform b"
                     /protein_id="NP_055505.3"
                     /db_xref="GI:164519061"
                     /db_xref="CCDS:CCDS5882.1"
                     /db_xref="GeneID:9715"
                     /db_xref="HGNC:22202"
                     /db_xref="HPRD:13816"
     gene            complement(143076248..143077588)
                     /gene="LOC100507507"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 10 ESTs"
                     /db_xref="GeneID:100507507"
     misc_RNA        complement(join(143076248..143077202,
                     143077359..143077588))
                     /gene="LOC100507507"
                     /product="hypothetical LOC100507507"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 10 ESTs"
                     /transcript_id="XR_108783.1"
                     /db_xref="GI:310120114"
                     /db_xref="GeneID:100507507"
     gene            143078360..143088204
                     /gene="ZYX"
                     /gene_synonym="ESP-2; HED-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7791"
                     /db_xref="HGNC:13200"
                     /db_xref="HPRD:03592"
                     /db_xref="MIM:602002"
     mRNA            join(143078360..143078502,143078650..143078872,
                     143079341..143079540,143079686..143079778,
                     143079894..143080415,143085312..143085432,
                     143085582..143085751,143085860..143086038,
                     143086950..143087070,143087671..143088204)
                     /gene="ZYX"
                     /gene_synonym="ESP-2; HED-2"
                     /product="zyxin, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003461.4"
                     /db_xref="GI:58530843"
                     /db_xref="GeneID:7791"
                     /db_xref="HGNC:13200"
                     /db_xref="HPRD:03592"
                     /db_xref="MIM:602002"
     mRNA            join(143078360..143078502,143078653..143078872,
                     143079341..143079540,143079686..143079778,
                     143079894..143080415,143085312..143085432,
                     143085582..143085751,143085860..143086038,
                     143086950..143087070,143087671..143088204)
                     /gene="ZYX"
                     /gene_synonym="ESP-2; HED-2"
                     /product="zyxin, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001010972.1"
                     /db_xref="GI:58530844"
                     /db_xref="GeneID:7791"
                     /db_xref="HGNC:13200"
                     /db_xref="MIM:602002"
                     /db_xref="HPRD:03592"
     CDS             join(143078665..143078872,143079341..143079540,
                     143079686..143079778,143079894..143080415,
                     143085312..143085432,143085582..143085751,
                     143085860..143086038,143086950..143087070,
                     143087671..143087775)
                     /gene="ZYX"
                     /gene_synonym="ESP-2; HED-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zyxin"
                     /protein_id="NP_003452.1"
                     /db_xref="GI:4508047"
                     /db_xref="CCDS:CCDS5883.1"
                     /db_xref="GeneID:7791"
                     /db_xref="HGNC:13200"
                     /db_xref="HPRD:03592"
                     /db_xref="MIM:602002"
     CDS             join(143078665..143078872,143079341..143079540,
                     143079686..143079778,143079894..143080415,
                     143085312..143085432,143085582..143085751,
                     143085860..143086038,143086950..143087070,
                     143087671..143087775)
                     /gene="ZYX"
                     /gene_synonym="ESP-2; HED-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zyxin"
                     /protein_id="NP_001010972.1"
                     /db_xref="GI:58530845"
                     /db_xref="CCDS:CCDS5883.1"
                     /db_xref="GeneID:7791"
                     /db_xref="HGNC:13200"
                     /db_xref="HPRD:03592"
                     /db_xref="MIM:602002"
     gene            complement(143088205..143105985)
                     /gene="EPHA1"
                     /gene_synonym="EPH; EPHT; EPHT1; MGC163163"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2041"
                     /db_xref="HGNC:3385"
                     /db_xref="HPRD:01554"
                     /db_xref="MIM:179610"
     mRNA            complement(join(143088205..143088628,143088713..143088868,
                     143090764..143090957,143091287..143091436,
                     143091901..143092107,143092214..143092275,
                     143092412..143092597,143093478..143093603,
                     143094397..143094455,143094654..143094750,
                     143095013..143095163,143095414..143095541,
                     143095694..143096038,143096351..143096506,
                     143096744..143097146,143098417..143098698,
                     143104704..143104771,143105817..143105985))
                     /gene="EPHA1"
                     /gene_synonym="EPH; EPHT; EPHT1; MGC163163"
                     /product="EPH receptor A1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005232.4"
                     /db_xref="GI:221316649"
                     /db_xref="GeneID:2041"
                     /db_xref="HGNC:3385"
                     /db_xref="HPRD:01554"
                     /db_xref="MIM:179610"
     CDS             complement(join(143088550..143088628,143088713..143088868,
                     143090764..143090957,143091287..143091436,
                     143091901..143092107,143092214..143092275,
                     143092412..143092597,143093478..143093603,
                     143094397..143094455,143094654..143094750,
                     143095013..143095163,143095414..143095541,
                     143095694..143096038,143096351..143096506,
                     143096744..143097146,143098417..143098698,
                     143104704..143104771,143105817..143105898))
                     /gene="EPHA1"
                     /gene_synonym="EPH; EPHT; EPHT1; MGC163163"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ephrin type-A receptor 1 precursor"
                     /protein_id="NP_005223.4"
                     /db_xref="GI:221316650"
                     /db_xref="CCDS:CCDS5884.1"
                     /db_xref="GeneID:2041"
                     /db_xref="HGNC:3385"
                     /db_xref="HPRD:01554"
                     /db_xref="MIM:179610"
     gene            143104906..143220542
                     /gene="LOC285965"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285965"
     misc_RNA        join(143104906..143104979,143112161..143112292,
                     143201867..143201923,143215375..143215610,
                     143216024..143220542)
                     /gene="LOC285965"
                     /product="hypothetical LOC285965"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033897.1"
                     /db_xref="GI:299829233"
                     /db_xref="GeneID:285965"
     gene            143134128..143135066
                     /gene="TAS2R62P"
                     /gene_synonym="PS1; T2R62; TAS2R62"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:338399"
                     /db_xref="HGNC:20640"
     gene            143140546..143141502
                     /gene="TAS2R60"
                     /gene_synonym="MGC119154; MGC119155; T2R56; T2R60"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:338398"
                     /db_xref="HGNC:20639"
                     /db_xref="HPRD:18159"
                     /db_xref="MIM:613968"
     mRNA            143140546..143141502
                     /gene="TAS2R60"
                     /gene_synonym="MGC119154; MGC119155; T2R56; T2R60"
                     /product="taste receptor, type 2, member 60"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_177437.1"
                     /db_xref="GI:28973794"
                     /db_xref="GeneID:338398"
                     /db_xref="HGNC:20639"
                     /db_xref="HPRD:18159"
                     /db_xref="MIM:613968"
     CDS             143140546..143141502
                     /gene="TAS2R60"
                     /gene_synonym="MGC119154; MGC119155; T2R56; T2R60"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="taste receptor type 2 member 60"
                     /protein_id="NP_803186.1"
                     /db_xref="GI:28973795"
                     /db_xref="CCDS:CCDS5885.1"
                     /db_xref="GeneID:338398"
                     /db_xref="HGNC:20639"
                     /db_xref="HPRD:18159"
                     /db_xref="MIM:613968"
     gene            143174966..143175889
                     /gene="TAS2R41"
                     /gene_synonym="MGC119928; MGC119929; T2R41; T2R59"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:259287"
                     /db_xref="HGNC:18883"
                     /db_xref="HPRD:18151"
                     /db_xref="MIM:613965"
     mRNA            143174966..143175889
                     /gene="TAS2R41"
                     /gene_synonym="MGC119928; MGC119929; T2R41; T2R59"
                     /product="taste receptor, type 2, member 41"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_176883.2"
                     /db_xref="GI:116268092"
                     /db_xref="GeneID:259287"
                     /db_xref="HGNC:18883"
                     /db_xref="HPRD:18151"
                     /db_xref="MIM:613965"
     CDS             143174966..143175889
                     /gene="TAS2R41"
                     /gene_synonym="MGC119928; MGC119929; T2R41; T2R59"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="taste receptor type 2 member 41"
                     /protein_id="NP_795364.2"
                     /db_xref="GI:116268093"
                     /db_xref="CCDS:CCDS43663.1"
                     /db_xref="GeneID:259287"
                     /db_xref="HGNC:18883"
                     /db_xref="HPRD:18151"
                     /db_xref="MIM:613965"
     gene            143181443..143193865
                     /gene="LOC100507525"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 7 ESTs"
                     /db_xref="GeneID:100507525"
     misc_RNA        join(143181443..143181544,143193059..143193865)
                     /gene="LOC100507525"
                     /product="hypothetical LOC100507525"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 7 ESTs"
                     /transcript_id="XR_108784.1"
                     /db_xref="GI:310120115"
                     /db_xref="GeneID:100507525"
     gene            complement(143185555..143186502)
                     /gene="OR2R1P"
                     /gene_synonym="OR2R1; OST058"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392132"
                     /db_xref="HGNC:8274"
     gene            complement(143208060..143209004)
                     /gene="OR10AC1P"
                     /gene_synonym="OR10AC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392133"
                     /db_xref="HGNC:14758"
     gene            complement(143229787..143230303)
                     /gene="RPL26P22"
                     /gene_synonym="RPL26_5_860"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:643101"
                     /db_xref="HGNC:36244"
     gene            complement(143242134..143243404)
                     /gene="PAICSP5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:780811"
                     /db_xref="HGNC:38098"
     gene            143268890..143271244
                     /gene="CTAGE15P"
                     /gene_synonym="MGC167090"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:441294"
                     /db_xref="HGNC:37295"
                     /db_xref="HPRD:17404"
     mRNA            143268890..143271244
                     /gene="CTAGE15P"
                     /gene_synonym="MGC167090"
                     /product="CTAGE family, member 15, pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001008747.1"
                     /db_xref="GI:56847633"
                     /db_xref="GeneID:441294"
                     /db_xref="HGNC:37295"
                     /db_xref="HPRD:17404"
     CDS             143268911..143271244
                     /gene="CTAGE15P"
                     /gene_synonym="MGC167090"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="CTAGE6-like"
                     /protein_id="NP_001008747.1"
                     /db_xref="GI:56847634"
                     /db_xref="GeneID:441294"
                     /db_xref="HGNC:37295"
                     /db_xref="HPRD:17404"
     gene            143295130..143306072
                     /gene="FAM115B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:653199"
                     /db_xref="HGNC:33604"
     gene            143318045..143427173
                     /gene="FAM115C"
                     /gene_synonym="FAM139A; FLJ40722; MGC142090"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285966"
                     /db_xref="HGNC:26878"
                     /db_xref="HPRD:07117"
     mRNA            join(143318045..143318113,143400074..143400710,
                     143416776..143417767,143418374..143418471,
                     143419751..143419964,143420304..143420543,
                     143421453..143422176)
                     /gene="FAM115C"
                     /gene_synonym="FAM139A; FLJ40722; MGC142090"
                     /product="family with sequence similarity 115, member C,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130025.1"
                     /db_xref="GI:194097427"
                     /db_xref="GeneID:285966"
                     /db_xref="HGNC:26878"
                     /db_xref="HPRD:07117"
     mRNA            join(143318542..143318596,143400074..143400710,
                     143416776..143417767,143418374..143418471,
                     143419751..143419964,143420304..143420543,
                     143421453..143422176)
                     /gene="FAM115C"
                     /gene_synonym="FAM139A; FLJ40722; MGC142090"
                     /product="family with sequence similarity 115, member C,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_173678.2"
                     /db_xref="GI:194097424"
                     /db_xref="GeneID:285966"
                     /db_xref="HGNC:26878"
                     /db_xref="HPRD:07117"
     gene            complement(143339347..143344742)
                     /gene="LOC100533814"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100533814"
     CDS             join(143400088..143400710,143416776..143417767,
                     143418374..143418471,143419751..143419964,
                     143420304..143420543,143421453..143421823)
                     /gene="FAM115C"
                     /gene_synonym="FAM139A; FLJ40722; MGC142090"
                     /note="isoform A is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC285966 isoform A"
                     /protein_id="NP_001123497.1"
                     /db_xref="GI:194097428"
                     /db_xref="CCDS:CCDS34769.1"
                     /db_xref="GeneID:285966"
                     /db_xref="HGNC:26878"
                     /db_xref="HPRD:07117"
     CDS             join(143400088..143400710,143416776..143417767,
                     143418374..143418471,143419751..143419964,
                     143420304..143420543,143421453..143421823)
                     /gene="FAM115C"
                     /gene_synonym="FAM139A; FLJ40722; MGC142090"
                     /note="isoform A is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC285966 isoform A"
                     /protein_id="NP_775949.2"
                     /db_xref="GI:194097425"
                     /db_xref="CCDS:CCDS34769.1"
                     /db_xref="GeneID:285966"
                     /db_xref="HGNC:26878"
                     /db_xref="HPRD:07117"
     mRNA            join(143412939..143413093,143416776..143417767,
                     143417899..143418078,143418374..143418471,
                     143419751..143419964,143420304..143420543,
                     143421453..143421790,143424506..143427173)
                     /gene="FAM115C"
                     /gene_synonym="FAM139A; FLJ40722; MGC142090"
                     /product="family with sequence similarity 115, member C,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001130026.2"
                     /db_xref="GI:293651620"
                     /db_xref="GeneID:285966"
                     /db_xref="HGNC:26878"
                     /db_xref="HPRD:07117"
     CDS             join(143412963..143413093,143416776..143417767,
                     143417899..143418078,143418374..143418471,
                     143419751..143419964,143420304..143420543,
                     143421453..143421790,143424506..143424760)
                     /gene="FAM115C"
                     /gene_synonym="FAM139A; FLJ40722; MGC142090"
                     /note="isoform B is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC285966 isoform B"
                     /protein_id="NP_001123498.2"
                     /db_xref="GI:293651621"
                     /db_xref="CCDS:CCDS47735.2"
                     /db_xref="GeneID:285966"
                     /db_xref="HGNC:26878"
                     /db_xref="HPRD:07117"
     gene            complement(143452182..143454843)
                     /gene="CTAGE6P"
                     /gene_synonym="CTAGE6; MGC41943"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:340307"
                     /db_xref="HGNC:28644"
     mRNA            complement(143452182..143454843)
                     /gene="CTAGE6P"
                     /gene_synonym="CTAGE6; MGC41943"
                     /product="CTAGE family, member 6, pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_178561.4"
                     /db_xref="GI:146262004"
                     /db_xref="GeneID:340307"
                     /db_xref="HGNC:28644"
     CDS             complement(143452418..143454751)
                     /gene="CTAGE6P"
                     /gene_synonym="CTAGE6; MGC41943"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative protein cTAGE-6"
                     /protein_id="NP_848656.2"
                     /db_xref="GI:146262005"
                     /db_xref="GeneID:340307"
                     /db_xref="HGNC:28644"
     gene            143480220..143481372
                     /gene="PAICSP6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:780812"
                     /db_xref="HGNC:38099"
     gene            143493346..143493862
                     /gene="RPL26P24"
                     /gene_synonym="RPL26_12_861"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:728311"
                     /db_xref="HGNC:35774"
     gene            143497824..143515065
                     /gene="FAM115D"
                     /gene_synonym="FAM139B"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:653691"
                     /db_xref="HGNC:33603"
     gene            complement(143509061..143533810)
                     /gene="LOC154761"
                     /gene_synonym="FLJ58905"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:154761"
     misc_RNA        complement(join(143509061..143510872,143530340..143530976,
                     143533733..143533810))
                     /gene="LOC154761"
                     /gene_synonym="FLJ58905"
                     /product="hypothetical LOC154761"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_015421.1"
                     /db_xref="GI:211971086"
                     /db_xref="GeneID:154761"
     gene            complement(143548461..143599278)
                     /gene="FAM115A"
                     /gene_synonym="FLJ56782; KIAA0738"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9747"
                     /db_xref="HGNC:22201"
                     /db_xref="HPRD:13813"
     mRNA            complement(join(143548461..143551235,143554167..143554443,
                     143555917..143556254,143557301..143557540,
                     143558188..143558401,143559509..143559606,
                     143559895..143560889,143573082..143573715,
                     143599120..143599278))
                     /gene="FAM115A"
                     /gene_synonym="FLJ56782; KIAA0738"
                     /product="family with sequence similarity 115, member A,
                     transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001206938.1"
                     /db_xref="GI:332635044"
                     /db_xref="GeneID:9747"
                     /db_xref="HGNC:22201"
                     /db_xref="HPRD:13813"
     mRNA            complement(join(143548461..143551235,143554193..143554443,
                     143555917..143556254,143557301..143557540,
                     143558188..143558401,143559509..143559606,
                     143559895..143560889,143573082..143573715,
                     143599054..143599172))
                     /gene="FAM115A"
                     /gene_synonym="FLJ56782; KIAA0738"
                     /product="family with sequence similarity 115, member A,
                     transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014719.2"
                     /db_xref="GI:332635038"
                     /db_xref="GeneID:9747"
                     /db_xref="HGNC:22201"
                     /db_xref="HPRD:13813"
     mRNA            complement(join(143548461..143551235,143554193..143554443,
                     143555917..143556254,143557301..143557540,
                     143558188..143558401,143559509..143559606,
                     143559895..143560889,143582303..143582466))
                     /gene="FAM115A"
                     /gene_synonym="FLJ56782; KIAA0738"
                     /product="family with sequence similarity 115, member A,
                     transcript variant 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001206941.1"
                     /db_xref="GI:332635056"
                     /db_xref="GeneID:9747"
                     /db_xref="HGNC:22201"
                     /db_xref="HPRD:13813"
     CDS             complement(join(143551226..143551235,143554193..143554443,
                     143555917..143556254,143557301..143557540,
                     143558188..143558401,143559509..143559606,
                     143559895..143560889,143573082..143573701))
                     /gene="FAM115A"
                     /gene_synonym="FLJ56782; KIAA0738"
                     /exception="mismatches in translation"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC9747 isoform 1"
                     /protein_id="NP_055534.1"
                     /db_xref="GI:7662276"
                     /db_xref="CCDS:CCDS5886.1"
                     /db_xref="GeneID:9747"
                     /db_xref="HGNC:22201"
                     /db_xref="HPRD:13813"
     CDS             complement(join(143551226..143551235,143554193..143554443,
                     143555917..143556254,143557301..143557540,
                     143558188..143558401,143559509..143559606,
                     143559895..143560237))
                     /gene="FAM115A"
                     /gene_synonym="FLJ56782; KIAA0738"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC9747 isoform 3"
                     /protein_id="NP_001193870.1"
                     /db_xref="GI:332635057"
                     /db_xref="GeneID:9747"
                     /db_xref="HGNC:22201"
                     /db_xref="HPRD:13813"
     CDS             complement(join(143554189..143554443,143555917..143556254,
                     143557301..143557540,143558188..143558401,
                     143559509..143559606,143559895..143560889,
                     143573082..143573701))
                     /gene="FAM115A"
                     /gene_synonym="FLJ56782; KIAA0738"
                     /exception="mismatches in translation"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC9747 isoform 2"
                     /protein_id="NP_001193867.1"
                     /db_xref="GI:332635045"
                     /db_xref="GeneID:9747"
                     /db_xref="HGNC:22201"
                     /db_xref="HPRD:13813"
     gene            143632326..143633279
                     /gene="OR2F2"
                     /gene_synonym="OR7-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:135948"
                     /db_xref="HGNC:8247"
                     /db_xref="HPRD:14939"
     mRNA            143632326..143633279
                     /gene="OR2F2"
                     /gene_synonym="OR7-1"
                     /product="olfactory receptor, family 2, subfamily F,
                     member 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001004685.1"
                     /db_xref="GI:52317195"
                     /db_xref="GeneID:135948"
                     /db_xref="HGNC:8247"
                     /db_xref="HPRD:14939"
     CDS             143632326..143633279
                     /gene="OR2F2"
                     /gene_synonym="OR7-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 2F2"
                     /protein_id="NP_001004685.1"
                     /db_xref="GI:52317196"
                     /db_xref="CCDS:CCDS43666.1"
                     /db_xref="GeneID:135948"
                     /db_xref="HGNC:8247"
                     /db_xref="HPRD:14939"
     gene            143657020..143658108
                     /gene="OR2F1"
                     /gene_synonym="OLF3; OR14-60; OR2F3; OR2F3P; OR2F4; OR2F5;
                     OR7-139; OR7-140"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26211"
                     /db_xref="HGNC:8246"
                     /db_xref="HPRD:16340"
                     /db_xref="MIM:608497"
     mRNA            143657020..143658108
                     /gene="OR2F1"
                     /gene_synonym="OLF3; OR14-60; OR2F3; OR2F3P; OR2F4; OR2F5;
                     OR7-139; OR7-140"
                     /product="olfactory receptor, family 2, subfamily F,
                     member 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012369.2"
                     /db_xref="GI:92110012"
                     /db_xref="GeneID:26211"
                     /db_xref="HGNC:8246"
                     /db_xref="HPRD:16340"
                     /db_xref="MIM:608497"
     CDS             143657064..143658017
                     /gene="OR2F1"
                     /gene_synonym="OLF3; OR14-60; OR2F3; OR2F3P; OR2F4; OR2F5;
                     OR7-139; OR7-140"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 2F1"
                     /protein_id="NP_036501.2"
                     /db_xref="GI:92110013"
                     /db_xref="CCDS:CCDS5887.1"
                     /db_xref="GeneID:26211"
                     /db_xref="HGNC:8246"
                     /db_xref="HPRD:16340"
                     /db_xref="MIM:608497"
     gene            complement(143676187..143676722)
                     /gene="LOC100422324"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100422324"
     gene            143677898..143679025
                     /gene="OR2Q1P"
                     /gene_synonym="OR7-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:346524"
                     /db_xref="HGNC:8273"
     gene            143682235..143683610
                     /gene="LOC100422547"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100422547"
     gene            143701090..143702025
                     /gene="OR6B1"
                     /gene_synonym="OR7-3; OR7-9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:135946"
                     /db_xref="HGNC:8354"
                     /db_xref="HPRD:15055"
     mRNA            143701090..143702025
                     /gene="OR6B1"
                     /gene_synonym="OR7-3; OR7-9"
                     /product="olfactory receptor, family 6, subfamily B,
                     member 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001005281.1"
                     /db_xref="GI:52627214"
                     /db_xref="GeneID:135946"
                     /db_xref="HGNC:8354"
                     /db_xref="HPRD:15055"
     CDS             143701090..143702025
                     /gene="OR6B1"
                     /gene_synonym="OR7-3; OR7-9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 6B1"
                     /protein_id="NP_001005281.1"
                     /db_xref="GI:52627215"
                     /db_xref="CCDS:CCDS43667.1"
                     /db_xref="GeneID:135946"
                     /db_xref="HGNC:8354"
                     /db_xref="HPRD:15055"
     gene            143747495..143748430
                     /gene="OR2A5"
                     /gene_synonym="OR2A11P; OR2A26; OR2A8; OR7-138; OR7-141"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:393046"
                     /db_xref="HGNC:8232"
                     /db_xref="HPRD:14932"
     mRNA            143747495..143748430
                     /gene="OR2A5"
                     /gene_synonym="OR2A11P; OR2A26; OR2A8; OR7-138; OR7-141"
                     /product="olfactory receptor, family 2, subfamily A,
                     member 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012365.1"
                     /db_xref="GI:53850571"
                     /db_xref="GeneID:393046"
                     /db_xref="HGNC:8232"
                     /db_xref="HPRD:14932"
     CDS             143747495..143748430
                     /gene="OR2A5"
                     /gene_synonym="OR2A11P; OR2A26; OR2A8; OR7-138; OR7-141"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 2A5"
                     /protein_id="NP_036497.1"
                     /db_xref="GI:53850572"
                     /db_xref="CCDS:CCDS43668.1"
                     /db_xref="GeneID:393046"
                     /db_xref="HGNC:8232"
                     /db_xref="HPRD:14932"
     gene            143771313..143772245
                     /gene="OR2A25"
                     /gene_synonym="OR2A24P; OR2A25P; OR2A27"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:392138"
                     /db_xref="HGNC:19562"
                     /db_xref="HPRD:17691"
     mRNA            143771313..143772245
                     /gene="OR2A25"
                     /gene_synonym="OR2A24P; OR2A25P; OR2A27"
                     /product="olfactory receptor, family 2, subfamily A,
                     member 25"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001004488.1"
                     /db_xref="GI:52317187"
                     /db_xref="GeneID:392138"
                     /db_xref="HGNC:19562"
                     /db_xref="HPRD:17691"
     CDS             143771313..143772245
                     /gene="OR2A25"
                     /gene_synonym="OR2A24P; OR2A25P; OR2A27"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 2A25"
                     /protein_id="NP_001004488.1"
                     /db_xref="GI:52317188"
                     /db_xref="CCDS:CCDS43669.1"
                     /db_xref="GeneID:392138"
                     /db_xref="HGNC:19562"
                     /db_xref="HPRD:17691"
     gene            143774486..143774947
                     /gene="OR2A41P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:403234"
                     /db_xref="HGNC:31246"
     gene            143792201..143793133
                     /gene="OR2A12"
                     /gene_synonym="OR2A12P; OR2A16P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:346525"
                     /db_xref="HGNC:15082"
                     /db_xref="HPRD:14929"
     mRNA            143792201..143793133
                     /gene="OR2A12"
                     /gene_synonym="OR2A12P; OR2A16P"
                     /product="olfactory receptor, family 2, subfamily A,
                     member 12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001004135.1"
                     /db_xref="GI:51921272"
                     /db_xref="GeneID:346525"
                     /db_xref="HGNC:15082"
                     /db_xref="HPRD:14929"
     CDS             143792201..143793133
                     /gene="OR2A12"
                     /gene_synonym="OR2A12P; OR2A16P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 2A12"
                     /protein_id="NP_001004135.1"
                     /db_xref="GI:51921273"
                     /db_xref="CCDS:CCDS43670.1"
                     /db_xref="GeneID:346525"
                     /db_xref="HGNC:15082"
                     /db_xref="HPRD:14929"
     gene            143806676..143807632
                     /gene="OR2A2"
                     /gene_synonym="OR2A17P; OR2A2P; OR7-11; OST008"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:442361"
                     /db_xref="HGNC:8230"
                     /db_xref="HPRD:14931"
     mRNA            143806676..143807632
                     /gene="OR2A2"
                     /gene_synonym="OR2A17P; OR2A2P; OR7-11; OST008"
                     /product="olfactory receptor, family 2, subfamily A,
                     member 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001005480.2"
                     /db_xref="GI:154759241"
                     /db_xref="GeneID:442361"
                     /db_xref="HGNC:8230"
                     /db_xref="HPRD:14931"
     CDS             143806676..143807632
                     /gene="OR2A2"
                     /gene_synonym="OR2A17P; OR2A2P; OR7-11; OST008"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 2A2"
                     /protein_id="NP_001005480.2"
                     /db_xref="GI:154759242"
                     /db_xref="CCDS:CCDS43671.1"
                     /db_xref="GeneID:442361"
                     /db_xref="HGNC:8230"
                     /db_xref="HPRD:14931"
     gene            complement(143815557..143816453)
                     /gene="OR2A15P"
                     /gene_synonym="OR2A23P; OR2A28P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:135942"
                     /db_xref="HGNC:15085"
     gene            143826206..143827138
                     /gene="OR2A14"
                     /gene_synonym="OR2A14P; OR2A6; OST182"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:135941"
                     /db_xref="HGNC:15084"
                     /db_xref="HPRD:14930"
     mRNA            143826206..143827138
                     /gene="OR2A14"
                     /gene_synonym="OR2A14P; OR2A6; OST182"
                     /product="olfactory receptor, family 2, subfamily A,
                     member 14"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001001659.1"
                     /db_xref="GI:48717235"
                     /db_xref="GeneID:135941"
                     /db_xref="HGNC:15084"
                     /db_xref="HPRD:14930"
     CDS             143826206..143827138
                     /gene="OR2A14"
                     /gene_synonym="OR2A14P; OR2A6; OST182"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 2A14"
                     /protein_id="NP_001001659.1"
                     /db_xref="GI:48717236"
                     /db_xref="CCDS:CCDS43672.1"
                     /db_xref="GeneID:135941"
                     /db_xref="HGNC:15084"
                     /db_xref="HPRD:14930"
     gene            143839028..143840234
                     /gene="OR2A13P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392140"
                     /db_xref="HGNC:15083"
     gene            143854119..143855452
                     /gene="OR2A3P"
                     /gene_synonym="OR2A18P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:202861"
                     /db_xref="HGNC:8231"
     gene            143873834..143874610
                     /gene="OR2AO1P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:403235"
                     /db_xref="HGNC:31247"
     gene            143880548..143883173
                     /gene="CTAGE4"
                     /gene_synonym="cTAGE-4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100128553"
                     /db_xref="HGNC:24772"
                     /db_xref="MIM:608910"
     mRNA            143880548..143883173
                     /gene="CTAGE4"
                     /gene_synonym="cTAGE-4"
                     /product="CTAGE family, member 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198495.2"
                     /db_xref="GI:193290159"
                     /db_xref="GeneID:100128553"
                     /db_xref="HGNC:24772"
                     /db_xref="MIM:608910"
     CDS             143880597..143882930
                     /gene="CTAGE4"
                     /gene_synonym="cTAGE-4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cutaneous T-cell lymphoma-associated antigen 4"
                     /protein_id="NP_940897.2"
                     /db_xref="GI:193290160"
                     /db_xref="CCDS:CCDS55176.1"
                     /db_xref="GeneID:100128553"
                     /db_xref="HGNC:24772"
                     /db_xref="MIM:608910"
     gene            complement(143883176..143892791)
                     /gene="ARHGEF35"
                     /gene_synonym="ARHGEF5L; CTAGE4; FLJ43692"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:445328"
                     /db_xref="HGNC:33846"
                     /db_xref="HPRD:13476"
     mRNA            complement(join(143883176..143885488,
                     143892631..143892791))
                     /gene="ARHGEF35"
                     /gene_synonym="ARHGEF5L; CTAGE4; FLJ43692"
                     /product="Rho guanine nucleotide exchange factor (GEF) 35"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001003702.2"
                     /db_xref="GI:270265794"
                     /db_xref="GeneID:445328"
                     /db_xref="HGNC:33846"
                     /db_xref="HPRD:13476"
     CDS             complement(143884022..143885476)
                     /gene="ARHGEF35"
                     /gene_synonym="ARHGEF5L; CTAGE4; FLJ43692"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="rho guanine nucleotide exchange factor 35"
                     /protein_id="NP_001003702.2"
                     /db_xref="GI:270265795"
                     /db_xref="CCDS:CCDS34770.1"
                     /db_xref="GeneID:445328"
                     /db_xref="HGNC:33846"
                     /db_xref="HPRD:13476"
     gene            complement(143929004..143929936)
                     /gene="OR2A42"
                     /gene_synonym="OR2A1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:402317"
                     /db_xref="HGNC:31230"
                     /db_xref="HPRD:18486"
     mRNA            complement(143929004..143929936)
                     /gene="OR2A42"
                     /gene_synonym="OR2A1"
                     /product="olfactory receptor, family 2, subfamily A,
                     member 42"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001001802.2"
                     /db_xref="GI:333360868"
                     /db_xref="GeneID:402317"
                     /db_xref="HGNC:31230"
                     /db_xref="HPRD:18486"
     CDS             complement(143929004..143929936)
                     /gene="OR2A42"
                     /gene_synonym="OR2A1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 2A1/2A42"
                     /protein_id="NP_001001802.2"
                     /db_xref="GI:333360869"
                     /db_xref="GeneID:402317"
                     /db_xref="HGNC:31230"
                     /db_xref="HPRD:18486"
     gene            complement(143947767..143948696)
                     /gene="OR2A20P"
                     /gene_synonym="OR2A20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:401428"
                     /db_xref="HGNC:15413"
     misc_RNA        complement(143947767..143948696)
                     /gene="OR2A20P"
                     /gene_synonym="OR2A20"
                     /product="olfactory receptor, family 2, subfamily A,
                     member 20 pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002158.1"
                     /db_xref="GI:49227780"
                     /db_xref="GeneID:401428"
                     /db_xref="HGNC:15413"
     gene            complement(143955789..143956721)
                     /gene="OR2A7"
                     /gene_synonym="HSDJ0798C17; OR2A21"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:401427"
                     /db_xref="HGNC:8234"
                     /db_xref="HPRD:14933"
     mRNA            complement(143955789..143956721)
                     /gene="OR2A7"
                     /gene_synonym="HSDJ0798C17; OR2A21"
                     /product="olfactory receptor, family 2, subfamily A,
                     member 7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001005328.1"
                     /db_xref="GI:52693944"
                     /db_xref="GeneID:401427"
                     /db_xref="HGNC:8234"
                     /db_xref="HPRD:14933"
     CDS             complement(143955789..143956721)
                     /gene="OR2A7"
                     /gene_synonym="HSDJ0798C17; OR2A21"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 2A7"
                     /protein_id="NP_001005328.1"
                     /db_xref="GI:52693945"
                     /db_xref="CCDS:CCDS55177.1"
                     /db_xref="GeneID:401427"
                     /db_xref="HGNC:8234"
                     /db_xref="HPRD:14933"
     gene            complement(143956089..143983096)
                     /gene="LOC728377"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:728377"
     misc_RNA        complement(join(143956089..143956725,143969538..143969608,
                     143971053..143971214,143971839..143971996,
                     143973445..143973534,143973972..143974046,
                     143974301..143974430,143974700..143974852,
                     143975408..143975567,143979374..143979627,
                     143979819..143979883,143980317..143980374,
                     143980906..143983096))
                     /gene="LOC728377"
                     /product="Rho guanine nucleotide exchange factor (GEF) 5
                     pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_033942.1"
                     /db_xref="GI:300068984"
                     /db_xref="GeneID:728377"
     gene            complement(143963767..143966392)
                     /gene="LOC100289604"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100289604"
     gene            143996614..143997598
                     /gene="OR2A9P"
                     /gene_synonym="FKSG35; HSDJ0798C17; OR2A19; OR2A22P;
                     OR2A9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:441295"
                     /db_xref="HGNC:8236"
     misc_RNA        143996614..143997598
                     /gene="OR2A9P"
                     /gene_synonym="FKSG35; HSDJ0798C17; OR2A19; OR2A22P;
                     OR2A9"
                     /product="olfactory receptor, family 2, subfamily A,
                     member 9 pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002157.1"
                     /db_xref="GI:49227711"
                     /db_xref="GeneID:441295"
                     /db_xref="HGNC:8236"
     gene            144015218..144016150
                     /gene="OR2A1"
                     /gene_synonym="OR2A42"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:346528"
                     /db_xref="HGNC:8229"
                     /db_xref="HPRD:14928"
     mRNA            144015218..144016150
                     /gene="OR2A1"
                     /gene_synonym="OR2A42"
                     /product="olfactory receptor, family 2, subfamily A,
                     member 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001005287.1"
                     /db_xref="GI:52627212"
                     /db_xref="GeneID:346528"
                     /db_xref="HGNC:8229"
                     /db_xref="HPRD:14928"
     CDS             144015218..144016150
                     /gene="OR2A1"
                     /gene_synonym="OR2A42"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="olfactory receptor 2A1/2A42"
                     /protein_id="NP_001005287.1"
                     /db_xref="GI:52627213"
                     /db_xref="CCDS:CCDS43673.1"
                     /db_xref="GeneID:346528"
                     /db_xref="HGNC:8229"
                     /db_xref="HPRD:14928"
     gene            144052489..144077725
                     /gene="ARHGEF5"
                     /gene_synonym="DKFZp686N1969; GEF5; P60; TIM; TIM1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7984"
                     /db_xref="HGNC:13209"
                     /db_xref="HPRD:02932"
                     /db_xref="MIM:600888"
     mRNA            join(144052489..144052594,144059751..144062916,
                     144063448..144063505,144063939..144064003,
                     144064195..144064448,144068254..144068414,
                     144068970..144069122,144069392..144069521,
                     144069776..144069850,144070288..144070377,
                     144071825..144071982,144072607..144072768,
                     144074213..144074283,144075855..144075959,
                     144076992..144077725)
                     /gene="ARHGEF5"
                     /gene_synonym="DKFZp686N1969; GEF5; P60; TIM; TIM1"
                     /product="Rho guanine nucleotide exchange factor (GEF) 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005435.3"
                     /db_xref="GI:50959190"
                     /db_xref="GeneID:7984"
                     /db_xref="HGNC:13209"
                     /db_xref="HPRD:02932"
                     /db_xref="MIM:600888"
     CDS             join(144059763..144062916,144063448..144063505,
                     144063939..144064003,144064195..144064448,
                     144068254..144068414,144068970..144069122,
                     144069392..144069521,144069776..144069850,
                     144070288..144070377,144071825..144071982,
                     144072607..144072768,144074213..144074283,
                     144075855..144075959,144076992..144077149)
                     /gene="ARHGEF5"
                     /gene_synonym="DKFZp686N1969; GEF5; P60; TIM; TIM1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="rho guanine nucleotide exchange factor 5"
                     /protein_id="NP_005426.2"
                     /db_xref="GI:50959191"
                     /db_xref="CCDS:CCDS34771.1"
                     /db_xref="GeneID:7984"
                     /db_xref="HGNC:13209"
                     /db_xref="HPRD:02932"
                     /db_xref="MIM:600888"
     gene            complement(144094333..144107320)
                     /gene="NOBOX"
                     /gene_synonym="OG-2; OG2; OG2X; POF5; TCAG_12042"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:135935"
                     /db_xref="HGNC:22448"
                     /db_xref="MIM:610934"
     mRNA            complement(join(144094333..144094634,144095375..144095679,
                     144096043..144096271,144096490..144096575,
                     144096850..144096956,144097203..144097405,
                     144098139..144098690,144098962..144099043,
                     144101649..144101773,144107236..144107320))
                     /gene="NOBOX"
                     /gene_synonym="OG-2; OG2; OG2X; POF5; TCAG_12042"
                     /product="NOBOX oogenesis homeobox"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001080413.3"
                     /db_xref="GI:333470750"
                     /db_xref="GeneID:135935"
                     /db_xref="HGNC:22448"
                     /db_xref="MIM:610934"
     CDS             complement(join(144094333..144094634,144095375..144095679,
                     144096043..144096271,144096490..144096575,
                     144096850..144096956,144097203..144097405,
                     144098139..144098690,144098962..144099043,
                     144101649..144101773,144107236..144107320))
                     /gene="NOBOX"
                     /gene_synonym="OG-2; OG2; OG2X; POF5; TCAG_12042"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein NOBOX"
                     /protein_id="NP_001073882.3"
                     /db_xref="GI:333470751"
                     /db_xref="GeneID:135935"
                     /db_xref="HGNC:22448"
                     /db_xref="MIM:610934"
     gene            complement(144149034..144533146)
                     /gene="TPK1"
                     /gene_synonym="HTPK1; PP20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:27010"
                     /db_xref="HGNC:17358"
                     /db_xref="HPRD:06967"
                     /db_xref="MIM:606370"
     mRNA            complement(join(144149034..144150756,144245584..144245695,
                     144288516..144288662,144320259..144320354,
                     144345900..144345972,144380002..144380071,
                     144462973..144463044,144532653..144532711,
                     144533060..144533146))
                     /gene="TPK1"
                     /gene_synonym="HTPK1; PP20"
                     /product="thiamin pyrophosphokinase 1, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022445.3"
                     /db_xref="GI:110227855"
                     /db_xref="GeneID:27010"
                     /db_xref="HGNC:17358"
                     /db_xref="HPRD:06967"
                     /db_xref="MIM:606370"
     mRNA            complement(join(144149034..144150756,144245584..144245695,
                     144320259..144320354,144345900..144345972,
                     144380002..144380071,144462973..144463044,
                     144532653..144532711,144533060..144533146))
                     /gene="TPK1"
                     /gene_synonym="HTPK1; PP20"
                     /product="thiamin pyrophosphokinase 1, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001042482.1"
                     /db_xref="GI:110227856"
                     /db_xref="GeneID:27010"
                     /db_xref="HGNC:17358"
                     /db_xref="MIM:606370"
                     /db_xref="HPRD:06967"
     CDS             complement(join(144150638..144150756,144245584..144245695,
                     144288516..144288662,144320259..144320354,
                     144345900..144345972,144380002..144380071,
                     144462973..144463044,144532653..144532695))
                     /gene="TPK1"
                     /gene_synonym="HTPK1; PP20"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="thiamin pyrophosphokinase 1 isoform a"
                     /protein_id="NP_071890.2"
                     /db_xref="GI:21362110"
                     /db_xref="CCDS:CCDS5888.1"
                     /db_xref="GeneID:27010"
                     /db_xref="HGNC:17358"
                     /db_xref="HPRD:06967"
                     /db_xref="MIM:606370"
     CDS             complement(join(144150638..144150756,144245584..144245695,
                     144320259..144320354,144345900..144345972,
                     144380002..144380071,144462973..144463044,
                     144532653..144532695))
                     /gene="TPK1"
                     /gene_synonym="HTPK1; PP20"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="thiamin pyrophosphokinase 1 isoform b"
                     /protein_id="NP_001035947.1"
                     /db_xref="GI:110227857"
                     /db_xref="CCDS:CCDS55178.1"
                     /db_xref="GeneID:27010"
                     /db_xref="HGNC:17358"
                     /db_xref="HPRD:06967"
                     /db_xref="MIM:606370"
     gene            complement(144344282..144345668)
                     /gene="LOC100421829"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100421829"
     gene            144702155..144703238
                     /gene="LOC100420072"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420072"
     gene            144707146..144708295
                     /gene="LOC402715"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402715"
     gene            complement(144737444..144738056)
                     /gene="LOC643308"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:643308"
     gene            145280294..145281915
                     /gene="LOC100420073"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420073"
     gene            145813453..148118090
                     /gene="CNTNAP2"
                     /gene_synonym="AUTS15; CASPR2; CDFE; DKFZp781D1846; NRXN4;
                     PTHSL1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26047"
                     /db_xref="HGNC:13830"
                     /db_xref="HPRD:05197"
                     /db_xref="MIM:604569"
     mRNA            join(145813453..145814065,146471363..146471473,
                     146536803..146536996,146740999..146741146,
                     146805239..146805442,146818071..146818255,
                     146825785..146825928,146829337..146829601,
                     146997233..146997382,147092701..147092872,
                     147183027..147183133,147259230..147259349,
                     147336198..147336398,147600657..147600813,
                     147674954..147675081,147815210..147815380,
                     147844583..147844801,147869334..147869570,
                     147914380..147914616,147926738..147926871,
                     147964125..147964218,148080741..148080980,
                     148106483..148106563,148112509..148118090)
                     /gene="CNTNAP2"
                     /gene_synonym="AUTS15; CASPR2; CDFE; DKFZp781D1846; NRXN4;
                     PTHSL1"
                     /product="contactin associated protein-like 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014141.5"
                     /db_xref="GI:289802978"
                     /db_xref="GeneID:26047"
                     /db_xref="HGNC:13830"
                     /db_xref="HPRD:05197"
                     /db_xref="MIM:604569"
     CDS             join(145813969..145814065,146471363..146471473,
                     146536803..146536996,146740999..146741146,
                     146805239..146805442,146818071..146818255,
                     146825785..146825928,146829337..146829601,
                     146997233..146997382,147092701..147092872,
                     147183027..147183133,147259230..147259349,
                     147336198..147336398,147600657..147600813,
                     147674954..147675081,147815210..147815380,
                     147844583..147844801,147869334..147869570,
                     147914380..147914616,147926738..147926871,
                     147964125..147964218,148080741..148080980,
                     148106483..148106563,148112509..148112708)
                     /gene="CNTNAP2"
                     /gene_synonym="AUTS15; CASPR2; CDFE; DKFZp781D1846; NRXN4;
                     PTHSL1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="contactin-associated protein-like 2 precursor"
                     /protein_id="NP_054860.1"
                     /db_xref="GI:7662350"
                     /db_xref="CCDS:CCDS5889.1"
                     /db_xref="GeneID:26047"
                     /db_xref="HGNC:13830"
                     /db_xref="HPRD:05197"
                     /db_xref="MIM:604569"
     gene            146289110..146289752
                     /gene="LOC100420074"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420074"
     gene            complement(147075109..147075213)
                     /gene="MIR548F4"
                     /gene_synonym="hsa-mir-548f-4; MIR548F-4; MIRN548F4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100313895"
                     /db_xref="HGNC:35308"
                     /db_xref="miRBase:MI0006377"
     ncRNA           complement(147075109..147075213)
                     /gene="MIR548F4"
                     /gene_synonym="hsa-mir-548f-4; MIR548F-4; MIRN548F4"
                     /ncRNA_class="miRNA"
                     /product="microRNA 548f-4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_031645.1"
                     /db_xref="GI:269847249"
                     /db_xref="GeneID:100313895"
                     /db_xref="HGNC:35308"
                     /db_xref="miRBase:MI0006377"
     gene            147368791..147370236
                     /gene="LOC100507538"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /db_xref="GeneID:100507538"
     misc_RNA        join(147368791..147369225,147369543..147370236)
                     /gene="LOC100507538"
                     /product="hypothetical LOC100507538"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_108785.1"
                     /db_xref="GI:310120116"
                     /db_xref="GeneID:100507538"
     gene            148142902..148143487
                     /gene="LOC392145"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:392145"
     gene            148277493..148286036
                     /gene="RPL32P17"
                     /gene_synonym="RPL32_9_862"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:402716"
                     /db_xref="HGNC:36251"
     gene            148287657..148312952
                     /gene="C7orf33"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:202865"
                     /db_xref="HGNC:21724"
                     /db_xref="HPRD:12921"
     mRNA            join(148287657..148288221,148311134..148311388,
                     148312419..148312952)
                     /gene="C7orf33"
                     /product="chromosome 7 open reading frame 33"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145304.2"
                     /db_xref="GI:34147719"
                     /db_xref="GeneID:202865"
                     /db_xref="HGNC:21724"
                     /db_xref="HPRD:12921"
     CDS             join(148288018..148288221,148311134..148311388,
                     148312419..148312493)
                     /gene="C7orf33"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC202865"
                     /protein_id="NP_660347.1"
                     /db_xref="GI:21687070"
                     /db_xref="CCDS:CCDS5890.1"
                     /db_xref="GeneID:202865"
                     /db_xref="HGNC:21724"
                     /db_xref="HPRD:12921"
     gene            148334272..148337615
                     /gene="LOC643438"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:643438"
     gene            148346568..148347435
                     /gene="LOC100301516"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100301516"
     gene            148395933..148498202
                     /gene="CUL1"
                     /gene_synonym="MGC149834; MGC149835"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8454"
                     /db_xref="HGNC:2551"
                     /db_xref="HPRD:04389"
                     /db_xref="MIM:603134"
     mRNA            join(148395933..148396121,148427054..148427354,
                     148451068..148451242,148454075..148454242,
                     148456396..148456446,148456640..148456730,
                     148457425..148457588,148463653..148463815,
                     148464711..148464841,148480875..148480982,
                     148481063..148481169,148483643..148483691,
                     148484081..148484212,148485649..148485766,
                     148486842..148486918,148487402..148487533,
                     148489818..148489910,148494904..148494951,
                     148495029..148495111,148495664..148495769,
                     148496367..148496480,148497594..148498202)
                     /gene="CUL1"
                     /gene_synonym="MGC149834; MGC149835"
                     /product="cullin 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003592.2"
                     /db_xref="GI:32307160"
                     /db_xref="GeneID:8454"
                     /db_xref="HGNC:2551"
                     /db_xref="HPRD:04389"
                     /db_xref="MIM:603134"
     CDS             join(148427215..148427354,148451068..148451242,
                     148454075..148454242,148456396..148456446,
                     148456640..148456730,148457425..148457588,
                     148463653..148463815,148464711..148464841,
                     148480875..148480982,148481063..148481169,
                     148483643..148483691,148484081..148484212,
                     148485649..148485766,148486842..148486918,
                     148487402..148487533,148489818..148489910,
                     148494904..148494951,148495029..148495111,
                     148495664..148495769,148496367..148496480,
                     148497594..148497674)
                     /gene="CUL1"
                     /gene_synonym="MGC149834; MGC149835"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="cullin-1"
                     /protein_id="NP_003583.2"
                     /db_xref="GI:32307161"
                     /db_xref="CCDS:CCDS34772.1"
                     /db_xref="GeneID:8454"
                     /db_xref="HGNC:2551"
                     /db_xref="HPRD:04389"
                     /db_xref="MIM:603134"
     gene            complement(148497133..148498102)
                     /gene="LOC100507558"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 7 ESTs"
                     /db_xref="GeneID:100507558"
     misc_RNA        complement(join(148497133..148497740,
                     148498063..148498102))
                     /gene="LOC100507558"
                     /product="hypothetical LOC100507558"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 7 ESTs"
                     /transcript_id="XR_108786.1"
                     /db_xref="GI:310120117"
                     /db_xref="GeneID:100507558"
     gene            complement(148504464..148581441)
                     /gene="EZH2"
                     /gene_synonym="ENX-1; ENX1; EZH1; KMT6; KMT6A; MGC9169"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2146"
                     /db_xref="HGNC:3527"
                     /db_xref="HPRD:03342"
                     /db_xref="MIM:601573"
     mRNA            complement(join(148504464..148504798,148506163..148506247,
                     148506402..148506482,148507425..148507506,
                     148508717..148508812,148511051..148511229,
                     148512006..148512131,148512598..148512638,
                     148513776..148513870,148514314..148514483,
                     148514969..148515209,148516688..148516779,
                     148523546..148523724,148524256..148524358,
                     148525832..148525972,148526820..148526940,
                     148529726..148529842,148543562..148543690,
                     148544274..148544397,148581256..148581441))
                     /gene="EZH2"
                     /gene_synonym="ENX-1; ENX1; EZH1; KMT6; KMT6A; MGC9169"
                     /product="enhancer of zeste homolog 2 (Drosophila),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004456.4"
                     /db_xref="GI:322506095"
                     /db_xref="GeneID:2146"
                     /db_xref="HGNC:3527"
                     /db_xref="HPRD:03342"
                     /db_xref="MIM:601573"
     mRNA            complement(join(148504464..148504798,148506163..148506247,
                     148506402..148506482,148507425..148507506,
                     148508717..148508812,148511051..148511229,
                     148512006..148512131,148512598..148512638,
                     148513776..148513870,148514314..148514483,
                     148514969..148515209,148516688..148516779,
                     148523561..148523724,148524256..148524358,
                     148525832..148525972,148526820..148526940,
                     148543562..148543690,148544274..148544397,
                     148581256..148581441))
                     /gene="EZH2"
                     /gene_synonym="ENX-1; ENX1; EZH1; KMT6; KMT6A; MGC9169"
                     /product="enhancer of zeste homolog 2 (Drosophila),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152998.2"
                     /db_xref="GI:322506094"
                     /db_xref="GeneID:2146"
                     /db_xref="HGNC:3527"
                     /db_xref="HPRD:03342"
                     /db_xref="MIM:601573"
     mRNA            complement(join(148504464..148504798,148506163..148506247,
                     148506402..148506482,148507425..148507506,
                     148508717..148508812,148511051..148511229,
                     148512006..148512131,148512598..148512638,
                     148513776..148513870,148514314..148514483,
                     148514969..148515209,148516688..148516779,
                     148523561..148523724,148524256..148524358,
                     148525832..148525972,148526820..148526940,
                     148529726..148529842,148543562..148543690,
                     148544274..148544397,148581256..148581441))
                     /gene="EZH2"
                     /gene_synonym="ENX-1; ENX1; EZH1; KMT6; KMT6A; MGC9169"
                     /product="enhancer of zeste homolog 2 (Drosophila),
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001203247.1"
                     /db_xref="GI:322506096"
                     /db_xref="GeneID:2146"
                     /db_xref="HGNC:3527"
                     /db_xref="MIM:601573"
                     /db_xref="HPRD:03342"
     mRNA            complement(join(148504464..148504798,148506163..148506247,
                     148506402..148506482,148507425..148507506,
                     148508717..148508812,148511051..148511229,
                     148512006..148512131,148512598..148512638,
                     148513776..148513870,148514314..148514483,
                     148514969..148515209,148516688..148516779,
                     148523561..148523724,148524256..148524358,
                     148525832..148525972,148526820..148526940,
                     148529726..148529842,148543589..148543690,
                     148544274..148544397,148581256..148581441))
                     /gene="EZH2"
                     /gene_synonym="ENX-1; ENX1; EZH1; KMT6; KMT6A; MGC9169"
                     /product="enhancer of zeste homolog 2 (Drosophila),
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001203248.1"
                     /db_xref="GI:322506098"
                     /db_xref="GeneID:2146"
                     /db_xref="HGNC:3527"
                     /db_xref="MIM:601573"
                     /db_xref="HPRD:03342"
     mRNA            complement(join(148504464..148504798,148506163..148506247,
                     148506402..148506482,148507425..148507506,
                     148508717..148508812,148511051..148511229,
                     148512598..148512638,148513776..148513870,
                     148514314..148514483,148514969..148515209,
                     148516688..148516779,148523561..148523724,
                     148524256..148524358,148525832..148525972,
                     148526820..148526940,148529726..148529842,
                     148543589..148543690,148544274..148544397,
                     148580289..148580601))
                     /gene="EZH2"
                     /gene_synonym="ENX-1; ENX1; EZH1; KMT6; KMT6A; MGC9169"
                     /product="enhancer of zeste homolog 2 (Drosophila),
                     transcript variant 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001203249.1"
                     /db_xref="GI:322506100"
                     /db_xref="GeneID:2146"
                     /db_xref="HGNC:3527"
                     /db_xref="MIM:601573"
                     /db_xref="HPRD:03342"
     CDS             complement(join(148504738..148504798,148506163..148506247,
                     148506402..148506482,148507425..148507506,
                     148508717..148508812,148511051..148511229,
                     148512006..148512131,148512598..148512638,
                     148513776..148513870,148514314..148514483,
                     148514969..148515209,148516688..148516779,
                     148523546..148523724,148524256..148524358,
                     148525832..148525972,148526820..148526940,
                     148529726..148529842,148543562..148543690,
                     148544274..148544390))
                     /gene="EZH2"
                     /gene_synonym="ENX-1; ENX1; EZH1; KMT6; KMT6A; MGC9169"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone-lysine N-methyltransferase EZH2 isoform
                     a"
                     /protein_id="NP_004447.2"
                     /db_xref="GI:21361095"
                     /db_xref="CCDS:CCDS5891.1"
                     /db_xref="GeneID:2146"
                     /db_xref="HGNC:3527"
                     /db_xref="HPRD:03342"
                     /db_xref="MIM:601573"
     CDS             complement(join(148504738..148504798,148506163..148506247,
                     148506402..148506482,148507425..148507506,
                     148508717..148508812,148511051..148511229,
                     148512006..148512131,148512598..148512638,
                     148513776..148513870,148514314..148514483,
                     148514969..148515209,148516688..148516779,
                     148523561..148523724,148524256..148524358,
                     148525832..148525972,148526820..148526940,
                     148543562..148543690,148544274..148544390))
                     /gene="EZH2"
                     /gene_synonym="ENX-1; ENX1; EZH1; KMT6; KMT6A; MGC9169"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone-lysine N-methyltransferase EZH2 isoform
                     b"
                     /protein_id="NP_694543.1"
                     /db_xref="GI:23510384"
                     /db_xref="CCDS:CCDS5892.1"
                     /db_xref="GeneID:2146"
                     /db_xref="HGNC:3527"
                     /db_xref="HPRD:03342"
                     /db_xref="MIM:601573"
     CDS             complement(join(148504738..148504798,148506163..148506247,
                     148506402..148506482,148507425..148507506,
                     148508717..148508812,148511051..148511229,
                     148512006..148512131,148512598..148512638,
                     148513776..148513870,148514314..148514483,
                     148514969..148515209,148516688..148516779,
                     148523561..148523724,148524256..148524358,
                     148525832..148525972,148526820..148526940,
                     148529726..148529842,148543562..148543690,
                     148544274..148544390))
                     /gene="EZH2"
                     /gene_synonym="ENX-1; ENX1; EZH1; KMT6; KMT6A; MGC9169"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone-lysine N-methyltransferase EZH2 isoform
                     c"
                     /protein_id="NP_001190176.1"
                     /db_xref="GI:322506097"
                     /db_xref="GeneID:2146"
                     /db_xref="HGNC:3527"
                     /db_xref="MIM:601573"
                     /db_xref="HPRD:03342"
     CDS             complement(join(148504738..148504798,148506163..148506247,
                     148506402..148506482,148507425..148507506,
                     148508717..148508812,148511051..148511229,
                     148512006..148512131,148512598..148512638,
                     148513776..148513870,148514314..148514483,
                     148514969..148515209,148516688..148516779,
                     148523561..148523724,148524256..148524358,
                     148525832..148525972,148526820..148526940,
                     148529726..148529842,148543589..148543690,
                     148544274..148544390))
                     /gene="EZH2"
                     /gene_synonym="ENX-1; ENX1; EZH1; KMT6; KMT6A; MGC9169"
                     /note="isoform d is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone-lysine N-methyltransferase EZH2 isoform
                     d"
                     /protein_id="NP_001190177.1"
                     /db_xref="GI:322506099"
                     /db_xref="GeneID:2146"
                     /db_xref="HGNC:3527"
                     /db_xref="MIM:601573"
                     /db_xref="HPRD:03342"
     CDS             complement(join(148504738..148504798,148506163..148506247,
                     148506402..148506482,148507425..148507506,
                     148508717..148508812,148511051..148511229,
                     148512598..148512638,148513776..148513870,
                     148514314..148514483,148514969..148515209,
                     148516688..148516779,148523561..148523724,
                     148524256..148524358,148525832..148525972,
                     148526820..148526940,148529726..148529842,
                     148543589..148543690,148544274..148544390))
                     /gene="EZH2"
                     /gene_synonym="ENX-1; ENX1; EZH1; KMT6; KMT6A; MGC9169"
                     /note="isoform e is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone-lysine N-methyltransferase EZH2 isoform
                     e"
                     /protein_id="NP_001190178.1"
                     /db_xref="GI:322506101"
                     /db_xref="GeneID:2146"
                     /db_xref="HGNC:3527"
                     /db_xref="MIM:601573"
                     /db_xref="HPRD:03342"
     gene            148518107..148518161
                     /gene="RNU7-20P"
                     /gene_synonym="U7.20"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100147768"
                     /db_xref="HGNC:34116"
     ncRNA           148638580..148638654
                     /gene="MIR1975"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-1975"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:100302248"
                     /db_xref="miRBase:MI0009985"
     gene            148660407..148660502
                     /gene="RNY4"
                     /gene_synonym="HY4; Y4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6086"
                     /db_xref="HGNC:10244"
                     /db_xref="MIM:601823"
     ncRNA           148660407..148660502
                     /gene="RNY4"
                     /gene_synonym="HY4; Y4"
                     /ncRNA_class="scRNA"
                     /product="RNA, Ro-associated Y4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_004393.1"
                     /db_xref="GI:161087013"
                     /db_xref="GeneID:6086"
                     /db_xref="HGNC:10244"
                     /db_xref="MIM:601823"
     gene            148680847..148680948
                     /gene="RNY3"
                     /gene_synonym="HY3; Y3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6085"
                     /db_xref="HGNC:10243"
                     /db_xref="MIM:601822"
     ncRNA           148680847..148680948
                     /gene="RNY3"
                     /gene_synonym="HY3; Y3"
                     /ncRNA_class="scRNA"
                     /product="RNA, Ro-associated Y3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_004392.1"
                     /db_xref="GI:161087012"
                     /db_xref="GeneID:6085"
                     /db_xref="HGNC:10243"
                     /db_xref="MIM:601822"
     gene            complement(148684228..148684340)
                     /gene="RNY1"
                     /gene_synonym="HY1; Y1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6084"
                     /db_xref="HGNC:10242"
                     /db_xref="MIM:601821"
     misc_RNA        complement(148684228..148684340)
                     /gene="RNY1"
                     /gene_synonym="HY1; Y1"
                     /product="RNA, Ro-associated Y1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_004391.1"
                     /db_xref="GI:161087011"
                     /db_xref="GeneID:6084"
                     /db_xref="HGNC:10242"
                     /db_xref="MIM:601821"
     gene            complement(148700154..148725782)
                     /gene="PDIA4"
                     /gene_synonym="ERp-72; ERP70; ERP72"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9601"
                     /db_xref="HGNC:30167"
                     /db_xref="HPRD:06501"
     mRNA            complement(join(148700154..148701301,148702233..148702466,
                     148702989..148703145,148705251..148705402,
                     148708938..148709096,148709247..148709452,
                     148711996..148712134,148716084..148716289,
                     148718059..148718239,148725413..148725782))
                     /gene="PDIA4"
                     /gene_synonym="ERp-72; ERP70; ERP72"
                     /product="protein disulfide isomerase family A, member 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004911.4"
                     /db_xref="GI:157427676"
                     /db_xref="GeneID:9601"
                     /db_xref="HGNC:30167"
                     /db_xref="HPRD:06501"
     CDS             complement(join(148700886..148701301,148702233..148702466,
                     148702989..148703145,148705251..148705402,
                     148708938..148709096,148709247..148709452,
                     148711996..148712134,148716084..148716289,
                     148718059..148718239,148725413..148725500))
                     /gene="PDIA4"
                     /gene_synonym="ERp-72; ERP70; ERP72"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein disulfide-isomerase A4 precursor"
                     /protein_id="NP_004902.1"
                     /db_xref="GI:4758304"
                     /db_xref="CCDS:CCDS5893.1"
                     /db_xref="GeneID:9601"
                     /db_xref="HGNC:30167"
                     /db_xref="HPRD:06501"
     gene            148750959..148751399
                     /gene="COX6B1P1"
                     /gene_synonym="COX6BP-1; COX6BP1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:140603"
                     /db_xref="HGNC:2281"
     gene            complement(148766733..148787869)
                     /gene="ZNF786"
                     /gene_synonym="DKFZp762I137; MGC156120"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:136051"
                     /db_xref="HGNC:21806"
                     /db_xref="HPRD:13232"
     mRNA            complement(join(148766733..148769565,148771478..148771630,
                     148777683..148777809,148787715..148787869))
                     /gene="ZNF786"
                     /gene_synonym="DKFZp762I137; MGC156120"
                     /product="zinc finger protein 786"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152411.3"
                     /db_xref="GI:170932472"
                     /db_xref="GeneID:136051"
                     /db_xref="HGNC:21806"
                     /db_xref="HPRD:13232"
     CDS             complement(join(148767515..148769565,148771478..148771630,
                     148777683..148777809,148787715..148787732))
                     /gene="ZNF786"
                     /gene_synonym="DKFZp762I137; MGC156120"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 786"
                     /protein_id="NP_689624.2"
                     /db_xref="GI:170932473"
                     /db_xref="CCDS:CCDS47738.1"
                     /db_xref="GeneID:136051"
                     /db_xref="HGNC:21806"
                     /db_xref="HPRD:13232"
     gene            complement(148799876..148823438)
                     /gene="ZNF425"
                     /gene_synonym="MGC150568"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:155054"
                     /db_xref="HGNC:20690"
                     /db_xref="HPRD:11715"
     mRNA            complement(join(148799876..148802658,148809229..148809387,
                     148815314..148815440,148823288..148823438))
                     /gene="ZNF425"
                     /gene_synonym="MGC150568"
                     /product="zinc finger protein 425"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001001661.2"
                     /db_xref="GI:296531446"
                     /db_xref="GeneID:155054"
                     /db_xref="HGNC:20690"
                     /db_xref="HPRD:11715"
     CDS             complement(join(148800704..148802658,148809229..148809387,
                     148815314..148815440,148823288..148823305))
                     /gene="ZNF425"
                     /gene_synonym="MGC150568"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 425"
                     /protein_id="NP_001001661.1"
                     /db_xref="GI:48717241"
                     /db_xref="CCDS:CCDS34773.1"
                     /db_xref="GeneID:155054"
                     /db_xref="HGNC:20690"
                     /db_xref="HPRD:11715"
     gene            148823508..148880134
                     /gene="ZNF398"
                     /gene_synonym="KIAA1339; P51; P71; ZER6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57541"
                     /db_xref="HGNC:18373"
                     /db_xref="HPRD:18336"
     mRNA            join(148823508..148823747,148825915..148826036,
                     148851037..148851432,148863250..148863376,
                     148863909..148864022,148873560..148873673,
                     148875740..148880134)
                     /gene="ZNF398"
                     /gene_synonym="KIAA1339; P51; P71; ZER6"
                     /product="zinc finger protein 398, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020781.3"
                     /db_xref="GI:194328796"
                     /db_xref="GeneID:57541"
                     /db_xref="HGNC:18373"
                     /db_xref="HPRD:18336"
     mRNA            join(148844560..148844858,148851037..148851432,
                     148863250..148863376,148863909..148864022,
                     148873560..148873673,148875740..148880134)
                     /gene="ZNF398"
                     /gene_synonym="KIAA1339; P51; P71; ZER6"
                     /product="zinc finger protein 398, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_170686.2"
                     /db_xref="GI:194328795"
                     /db_xref="GeneID:57541"
                     /db_xref="HGNC:18373"
                     /db_xref="HPRD:18336"
     CDS             join(148844835..148844858,148851037..148851432,
                     148863250..148863376,148863909..148864022,
                     148873560..148873673,148875740..148876893)
                     /gene="ZNF398"
                     /gene_synonym="KIAA1339; P51; P71; ZER6"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 398 isoform a"
                     /protein_id="NP_733787.1"
                     /db_xref="GI:25777704"
                     /db_xref="CCDS:CCDS5894.1"
                     /db_xref="GeneID:57541"
                     /db_xref="HGNC:18373"
                     /db_xref="HPRD:18336"
     gene            148861520..148862513
                     /gene="LOC100420549"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100420549"
     CDS             join(148863343..148863376,148863909..148864022,
                     148873560..148873673,148875740..148876893)
                     /gene="ZNF398"
                     /gene_synonym="KIAA1339; P51; P71; ZER6"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 398 isoform b"
                     /protein_id="NP_065832.1"
                     /db_xref="GI:24308225"
                     /db_xref="CCDS:CCDS47739.1"
                     /db_xref="GeneID:57541"
                     /db_xref="HGNC:18373"
                     /db_xref="HPRD:18336"
     gene            148892577..148923339
                     /gene="ZNF282"
                     /gene_synonym="HUB1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:8427"
                     /db_xref="HGNC:13076"
                     /db_xref="HPRD:04549"
                     /db_xref="MIM:603397"
     mRNA            join(148892577..148892846,148895425..148895844,
                     148903788..148903914,148904443..148904562,
                     148907677..148907796,148909450..148909563,
                     148910793..148910906,148920904..148923339)
                     /gene="ZNF282"
                     /gene_synonym="HUB1"
                     /product="zinc finger protein 282"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003575.2"
                     /db_xref="GI:120586995"
                     /db_xref="GeneID:8427"
                     /db_xref="HGNC:13076"
                     /db_xref="HPRD:04549"
                     /db_xref="MIM:603397"
     CDS             join(148892682..148892846,148895425..148895844,
                     148903788..148903914,148904443..148904562,
                     148907677..148907796,148909450..148909563,
                     148910793..148910906,148920904..148921739)
                     /gene="ZNF282"
                     /gene_synonym="HUB1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 282"
                     /protein_id="NP_003566.1"
                     /db_xref="GI:31657109"
                     /db_xref="CCDS:CCDS5895.1"
                     /db_xref="GeneID:8427"
                     /db_xref="HGNC:13076"
                     /db_xref="HPRD:04549"
                     /db_xref="MIM:603397"
     gene            148936742..148952700
                     /gene="ZNF212"
                     /gene_synonym="C2H2-150; MGC9707; ZNF182; ZNFC150"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7988"
                     /db_xref="HGNC:13004"
                     /db_xref="HPRD:03859"
                     /db_xref="MIM:602386"
     mRNA            join(148936742..148936893,148947250..148947639,
                     148947772..148947898,148949797..148949886,
                     148950650..148952700)
                     /gene="ZNF212"
                     /gene_synonym="C2H2-150; MGC9707; ZNF182; ZNFC150"
                     /product="zinc finger protein 212"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_012256.3"
                     /db_xref="GI:300116290"
                     /db_xref="GeneID:7988"
                     /db_xref="HGNC:13004"
                     /db_xref="HPRD:03859"
                     /db_xref="MIM:602386"
     CDS             join(148936870..148936893,148947250..148947639,
                     148947772..148947898,148949797..148949886,
                     148950650..148951506)
                     /gene="ZNF212"
                     /gene_synonym="C2H2-150; MGC9707; ZNF182; ZNFC150"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 212"
                     /protein_id="NP_036388.2"
                     /db_xref="GI:24797065"
                     /db_xref="CCDS:CCDS5896.1"
                     /db_xref="GeneID:7988"
                     /db_xref="HGNC:13004"
                     /db_xref="HPRD:03859"
                     /db_xref="MIM:602386"
     gene            148959262..148982085
                     /gene="ZNF783"
                     /gene_synonym="DKFZp762P2111; FLJ12914; FLJ16713"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100289678"
                     /db_xref="HGNC:27222"
     mRNA            join(148959262..148959448,148963426..148963821,
                     148963910..148964036,148964188..148964313,
                     148975490..148975618,148978596..148982085)
                     /gene="ZNF783"
                     /gene_synonym="DKFZp762P2111; FLJ12914; FLJ16713"
                     /product="zinc finger family member 783"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001195220.1"
                     /db_xref="GI:304647594"
                     /db_xref="GeneID:100289678"
                     /db_xref="HGNC:27222"
     CDS             join(148959425..148959448,148963426..148963821,
                     148963910..148964036,148964188..148964313,
                     148975490..148975618,148978596..148979434)
                     /gene="ZNF783"
                     /gene_synonym="DKFZp762P2111; FLJ12914; FLJ16713"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein ZNF783"
                     /protein_id="NP_001182149.1"
                     /db_xref="GI:304647595"
                     /db_xref="GeneID:100289678"
                     /db_xref="HGNC:27222"
     gene            148982372..148994403
                     /gene="LOC155060"
                     /gene_synonym="DKFZp667J212; DKFZp762P2111; FLJ16713;
                     FLJ17438; FLJ17495; FLJ17722; FLJ25485; FLJ36716;
                     FLJ38357; FLJ61016; MGC149135"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:155060"
     misc_RNA        join(148982372..148982587,148984656..148984867,
                     148985522..148986548,148986639..148986817,
                     148987029..148987129,148989302..148989399,
                     148990468..148990583,148990842..148991107,
                     148991471..148991503,148991631..148992274,
                     148994142..148994403)
                     /gene="LOC155060"
                     /gene_synonym="DKFZp667J212; DKFZp762P2111; FLJ16713;
                     FLJ17438; FLJ17495; FLJ17722; FLJ25485; FLJ36716;
                     FLJ38357; FLJ61016; MGC149135"
                     /product="AI894139 pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_036573.1"
                     /db_xref="GI:304766526"
                     /db_xref="GeneID:155060"
     tRNA            149007281..149007352
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /anticodon=(pos:149007313..149007315,aa:Cys)
                     /db_xref="GeneID:100189144"
     tRNA            149028220..149028291
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /anticodon=(pos:149028252..149028254,aa:Cys)
                     /db_xref="GeneID:100189413"
     gene            149031005..149032261
                     /gene="NPM1P12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:10835"
                     /db_xref="HGNC:7914"
     tRNA            complement(149052766..149052837)
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /db_xref="GeneID:100189357"
     gene            complement(149053745..149053820)
                     /gene="TRNAY17P"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100189507"
                     /db_xref="HGNC:35082"
     tRNA            complement(149072850..149072921)
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /db_xref="GeneID:100189049"
     tRNA            complement(149074601..149074672)
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /db_xref="GeneID:100189305"
     tRNA            complement(149112229..149112300)
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /db_xref="GeneID:100189008"
     gene            complement(149128454..149158053)
                     /gene="ZNF777"
                     /gene_synonym="KIAA1285"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:27153"
                     /db_xref="HGNC:22213"
                     /db_xref="HPRD:13849"
     mRNA            complement(join(149128454..149130023,149133666..149133917,
                     149148090..149148203,149151202..149151328,
                     149152268..149153128,149157906..149158053))
                     /gene="ZNF777"
                     /gene_synonym="KIAA1285"
                     /product="zinc finger protein 777"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015694.2"
                     /db_xref="GI:118918410"
                     /db_xref="GeneID:27153"
                     /db_xref="HGNC:22213"
                     /db_xref="HPRD:13849"
     CDS             complement(join(149128867..149130023,149133666..149133917,
                     149148090..149148203,149151202..149151328,
                     149152268..149153113))
                     /gene="ZNF777"
                     /gene_synonym="KIAA1285"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 777"
                     /protein_id="NP_056509.2"
                     /db_xref="GI:118918411"
                     /db_xref="CCDS:CCDS43675.1"
                     /db_xref="GeneID:27153"
                     /db_xref="HGNC:22213"
                     /db_xref="HPRD:13849"
     gene            complement(149169884..149194898)
                     /gene="ZNF746"
                     /gene_synonym="FLJ31413; PARIS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:155061"
                     /db_xref="HGNC:21948"
                     /db_xref="HPRD:08099"
                     /db_xref="MIM:613914"
     mRNA            complement(join(149169884..149172574,149174013..149174138,
                     149174655..149174846,149189950..149190063,
                     149191080..149191161,149191295..149191594,
                     149194604..149194898))
                     /gene="ZNF746"
                     /gene_synonym="FLJ31413; PARIS"
                     /product="zinc finger protein 746, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001163474.1"
                     /db_xref="GI:254553271"
                     /db_xref="GeneID:155061"
                     /db_xref="HGNC:21948"
                     /db_xref="MIM:613914"
                     /db_xref="HPRD:08099"
     mRNA            complement(join(149169884..149172571,149174013..149174138,
                     149174655..149174846,149189950..149190063,
                     149191080..149191161,149191295..149191594,
                     149194604..149194898))
                     /gene="ZNF746"
                     /gene_synonym="FLJ31413; PARIS"
                     /product="zinc finger protein 746, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_152557.4"
                     /db_xref="GI:254553270"
                     /db_xref="GeneID:155061"
                     /db_xref="HGNC:21948"
                     /db_xref="HPRD:08099"
                     /db_xref="MIM:613914"
     CDS             complement(join(149171475..149172574,149174013..149174138,
                     149174655..149174846,149189950..149190063,
                     149191080..149191161,149191295..149191594,
                     149194604..149194627))
                     /gene="ZNF746"
                     /gene_synonym="FLJ31413; PARIS"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 746 isoform 1"
                     /protein_id="NP_001156946.1"
                     /db_xref="GI:254553272"
                     /db_xref="CCDS:CCDS55180.1"
                     /db_xref="GeneID:155061"
                     /db_xref="HGNC:21948"
                     /db_xref="HPRD:08099"
                     /db_xref="MIM:613914"
     CDS             complement(join(149171475..149172571,149174013..149174138,
                     149174655..149174846,149189950..149190063,
                     149191080..149191161,149191295..149191594,
                     149194604..149194627))
                     /gene="ZNF746"
                     /gene_synonym="FLJ31413; PARIS"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 746 isoform 2"
                     /protein_id="NP_689770.3"
                     /db_xref="GI:46358366"
                     /db_xref="CCDS:CCDS5897.1"
                     /db_xref="GeneID:155061"
                     /db_xref="HGNC:21948"
                     /db_xref="HPRD:08099"
                     /db_xref="MIM:613914"
     tRNA            149243631..149243702
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /anticodon=(pos:149243663..149243665,aa:Cys)
                     /db_xref="GeneID:100189146"
     gene            complement(149244245..149321881)
                     /gene="ZNF767"
                     /gene_synonym="FLJ12700; FLJ42870; MGC51818"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:79970"
                     /db_xref="HGNC:21884"
     misc_RNA        complement(join(149244245..149246465,149247959..149248037,
                     149248746..149248917,149249892..149250107,
                     149255699..149255930,149317015..149317128,
                     149318351..149318650,149321633..149321881))
                     /gene="ZNF767"
                     /gene_synonym="FLJ12700; FLJ42870; MGC51818"
                     /product="zinc finger family member 767, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_027788.1"
                     /db_xref="GI:239916008"
                     /db_xref="GeneID:79970"
                     /db_xref="HGNC:21884"
     misc_RNA        complement(join(149244245..149244867,149246284..149246465,
                     149247959..149248037,149248665..149248917,
                     149249892..149250107,149317015..149317128,
                     149318137..149318263,149318351..149318650,
                     149321633..149321881))
                     /gene="ZNF767"
                     /gene_synonym="FLJ12700; FLJ42870; MGC51818"
                     /product="zinc finger family member 767, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_027789.1"
                     /db_xref="GI:239916009"
                     /db_xref="GeneID:79970"
                     /db_xref="HGNC:21884"
     tRNA            149253802..149253873
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /anticodon=(pos:149253834..149253836,aa:Cys)
                     /db_xref="GeneID:100189029"
     tRNA            149281816..149281887
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /anticodon=(pos:149281848..149281850,aa:Cys)
                     /db_xref="GeneID:100189267"
     tRNA            complement(149286164..149286235)
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /db_xref="GeneID:100189097"
     tRNA            complement(149292305..149292376)
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /db_xref="GeneID:100189194"
     tRNA            149295046..149295117
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /anticodon=(pos:149295078..149295080,aa:Cys)
                     /db_xref="GeneID:100189355"
     tRNA            149305467..149305538
                     /product="tRNA-Ser"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /anticodon=(pos:149305499..149305501,aa:Ser)
                     /db_xref="GeneID:100189432"
     tRNA            complement(149310156..149310227)
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /db_xref="GeneID:100189177"
     tRNA            149332778..149332849
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /anticodon=(pos:149332810..149332812,aa:Cys)
                     /db_xref="GeneID:100189376"
     tRNA            complement(149344046..149344117)
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /db_xref="GeneID:100189075"
     tRNA            149361915..149361986
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /anticodon=(pos:149361947..149361949,aa:Cys)
                     /db_xref="GeneID:100189375"
     tRNA            complement(149388272..149388343)
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /db_xref="GeneID:100189289"
     tRNA            149404760..149404831
                     /product="tRNA-Cys"
                     /note="tRNA features were annotated by tRNAscan-SE."
                     /anticodon=(pos:149404792..149404794,aa:Cys)
                     /db_xref="GeneID:100189379"
     gene            149412148..149431664
                     /gene="KRBA1"
                     /gene_synonym="KIAA1862; MGC176633"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:84626"
                     /db_xref="HGNC:22228"
                     /db_xref="HPRD:11167"
     mRNA            join(149412148..149412440,149416624..149416763,
                     149417099..149417218,149417926..149418081,
                     149418471..149418626,149419513..149419644,
                     149419874..149420047,149420825..149420980,
                     149421743..149421940,149422406..149422579,
                     149422978..149423151,149425614..149425766,
                     149426279..149426460,149427237..149427431,
                     149427518..149427658,149428762..149428866,
                     149430295..149431664)
                     /gene="KRBA1"
                     /gene_synonym="KIAA1862; MGC176633"
                     /product="KRAB-A domain containing 1"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_032534.2"
                     /db_xref="GI:116292167"
                     /db_xref="GeneID:84626"
                     /db_xref="HGNC:22228"
                     /db_xref="HPRD:11167"
     CDS             join(149416730..149416763,149417099..149417218,
                     149417926..149418081,149418471..149418626,
                     149419513..149419644,149419874..149420047,
                     149420825..149420980,149421743..149421940,
                     149422406..149422579,149422978..149423151,
                     149425614..149425766,149426279..149426460,
                     149427237..149427431,149427518..149427658,
                     149428762..149428866,149430295..149431136)
                     /gene="KRBA1"
                     /gene_synonym="KIAA1862; MGC176633"
                     /exception="unclassified translation discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein KRBA1"
                     /protein_id="NP_115923.2"
                     /db_xref="GI:116292168"
                     /db_xref="GeneID:84626"
                     /db_xref="HGNC:22228"
                     /db_xref="HPRD:11167"
     gene            complement(149461452..149470295)
                     /gene="ZNF467"
                     /gene_synonym="EZI; Zfp467"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:168544"
                     /db_xref="HGNC:23154"
                     /db_xref="HPRD:18343"
                     /db_xref="MIM:614040"
     mRNA            complement(join(149461452..149463328,149466179..149466289,
                     149467529..149467645,149468088..149468163,
                     149470197..149470295))
                     /gene="ZNF467"
                     /gene_synonym="EZI; Zfp467"
                     /product="zinc finger protein 467"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_207336.1"
                     /db_xref="GI:46409309"
                     /db_xref="GeneID:168544"
                     /db_xref="HGNC:23154"
                     /db_xref="HPRD:18343"
                     /db_xref="MIM:614040"
     CDS             complement(join(149461803..149463328,149466179..149466289,
                     149467529..149467645,149468088..149468121))
                     /gene="ZNF467"
                     /gene_synonym="EZI; Zfp467"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 467"
                     /protein_id="NP_997219.1"
                     /db_xref="GI:46409310"
                     /db_xref="CCDS:CCDS5899.1"
                     /db_xref="GeneID:168544"
                     /db_xref="HGNC:23154"
                     /db_xref="HPRD:18343"
                     /db_xref="MIM:614040"
     gene            149473131..149531054
                     /gene="SSPO"
                     /gene_synonym="FLJ36112; FLJ45737; KIAA2036; SCO-spondin"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:23145"
                     /db_xref="HGNC:21998"
     mRNA            join(149473131..149473180,149473435..149473617,
                     149474024..149474106,149474273..149474452,
                     149474698..149474942,149475041..149475134,
                     149475870..149476028,149476117..149476196,
                     149476623..149476774,149477048..149477219,
                     149477326..149477566,149477867..149478011,
                     149479270..149479387,149479935..149480110,
                     149480195..149480422,149480599..149480764,
                     149480989..149481223,149481916..149482104,
                     149482219..149482313,149482572..149482828,
                     149483177..149483311,149484457..149484653,
                     149484755..149484882,149484950..149485059,
                     149485409..149485558,149485655..149485748,
                     149485840..149486009,149486253..149486486,
                     149486689..149486910,149487371..149487607,
                     149488390..149488481,149488563..149488794,
                     149488905..149489057,149489154..149489294,
                     149489387..149489569,149489667..149489817,
                     149490398..149490551,149490654..149490708,
                     149491882..149491986,149492299..149492517,
                     149492627..149492754,149493459..149493603,
                     149493684..149493834,149494360..149494432,
                     149495156..149495213,149496922..149497092,
                     149497375..149497518,149498825..149499043,
                     149499128..149499292,149500035..149500214,
                     149500315..149500437,149500563..149500692,
                     149500776..149500901,149501084..149501175,
                     149502499..149502672,149502982..149503146,
                     149503823..149504079,149505346..149505392,
                     149505572..149505742,149506130..149506260,
                     149506477..149506622,149508003..149508097,
                     149508753..149508805,149508999..149509205,
                     149509354..149509524,149509649..149509728,
                     149510718..149510887,149511422..149511468,
                     149511560..149511751,149511862..149512032,
                     149512263..149512463,149512777..149512873,
                     149512978..149513177,149513460..149513626,
                     149514706..149514836,149514989..149515213,
                     149515545..149515586,149515741..149515896,
                     149516395..149516604,149516806..149516973,
                     149517739..149517870,149517965..149518211,
                     149518486..149518638,149518714..149518760,
                     149518951..149519286,149519601..149519768,
                     149520441..149520571,149520813..149520937,
                     149521175..149521221,149521483..149521761,
                     149522054..149522213,149522369..149522480,
                     149522889..149523027,149523164..149523366,
                     149523539..149523666,149523768..149523910,
                     149524002..149524048,149524860..149525074,
                     149525727..149525822,149526025..149526085,
                     149528224..149528354,149529857..149530012,
                     149530901..149531054)
                     /gene="SSPO"
                     /gene_synonym="FLJ36112; FLJ45737; KIAA2036; SCO-spondin"
                     /product="SCO-spondin homolog (Bos taurus)"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198455.2"
                     /db_xref="GI:134031944"
                     /db_xref="GeneID:23145"
                     /db_xref="HGNC:21998"
     CDS             join(149473131..149473180,149473435..149473617,
                     149474024..149474106,149474273..149474452,
                     149474698..149474942,149475041..149475134,
                     149475870..149476028,149476117..149476196,
                     149476623..149476774,149477048..149477219,
                     149477326..149477566,149477867..149478011,
                     149479270..149479387,149479935..149480110,
                     149480195..149480422,149480599..149480764,
                     149480989..149481223,149481916..149482104,
                     149482219..149482313,149482572..149482828,
                     149483177..149483311,149484457..149484653,
                     149484755..149484882,149484950..149485059,
                     149485409..149485558,149485655..149485748,
                     149485840..149486009,149486253..149486486,
                     149486689..149486910,149487371..149487607,
                     149488390..149488481,149488563..149488794,
                     149488905..149489057,149489154..149489294,
                     149489387..149489569,149489667..149489817,
                     149490398..149490551,149490654..149490708,
                     149491882..149491986,149492299..149492517,
                     149492627..149492754,149493459..149493603,
                     149493684..149493834,149494360..149494432,
                     149495156..149495213,149496922..149497092,
                     149497375..149497518,149498825..149499043,
                     149499128..149499292,149500035..149500214,
                     149500315..149500437,149500563..149500692,
                     149500776..149500901,149501084..149501175,
                     149502499..149502672,149502982..149503146,
                     149503823..149504079,149505346..149505392,
                     149505572..149505742,149506130..149506260,
                     149506477..149506622,149508003..149508097,
                     149508753..149508805,149508999..149509205,
                     149509354..149509524,149509649..149509728,
                     149510718..149510887,149511422..149511468,
                     149511560..149511751,149511862..149512032,
                     149512263..149512463,149512777..149512873,
                     149512978..149513177,149513460..149513626,
                     149514706..149514836,149514989..149515213,
                     149515545..149515586,149515741..149515896,
                     149516395..149516604,149516806..149516973,
                     149517739..149517870,149517965..149518211,
                     149518486..149518638,149518714..149518760,
                     149518951..149519286,149519601..149519768,
                     149520441..149520571,149520813..149520937,
                     149521175..149521221,149521483..149521761,
                     149522054..149522213,149522369..149522480,
                     149522889..149523027,149523164..149523366,
                     149523539..149523666,149523768..149523910,
                     149524002..149524048,149524860..149525074,
                     149525727..149525822,149526025..149526085,
                     149528224..149528354,149529857..149530012,
                     149530901..149530918)
                     /gene="SSPO"
                     /gene_synonym="FLJ36112; FLJ45737; KIAA2036; SCO-spondin"
                     /exception="unclassified translation discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="SCO-spondin precursor"
                     /protein_id="NP_940857.2"
                     /db_xref="GI:134031945"
                     /db_xref="GeneID:23145"
                     /db_xref="HGNC:21998"
     gene            149535509..149564568
                     /gene="ZNF862"
                     /gene_synonym="FLJ30362; KIAA0543"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:643641"
                     /db_xref="HGNC:34519"
     mRNA            join(149535509..149535724,149541714..149541825,
                     149543240..149543344,149544824..149545521,
                     149547250..149547427,149556511..149556615,
                     149557472..149559583,149561198..149564568)
                     /gene="ZNF862"
                     /gene_synonym="FLJ30362; KIAA0543"
                     /product="zinc finger protein 862"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001099220.1"
                     /db_xref="GI:149773448"
                     /db_xref="GeneID:643641"
                     /db_xref="HGNC:34519"
     CDS             join(149535701..149535724,149541714..149541825,
                     149543240..149543344,149544824..149545521,
                     149547250..149547427,149556511..149556615,
                     149557472..149559583,149561198..149561373)
                     /gene="ZNF862"
                     /gene_synonym="FLJ30362; KIAA0543"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 862"
                     /protein_id="NP_001092690.1"
                     /db_xref="GI:149773449"
                     /db_xref="CCDS:CCDS47741.1"
                     /db_xref="GeneID:643641"
                     /db_xref="HGNC:34519"
     gene            complement(149564783..149570951)
                     /gene="LOC401431"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:401431"
     misc_RNA        complement(join(149564783..149566947,149567331..149567440,
                     149568731..149568885,149570313..149570951))
                     /gene="LOC401431"
                     /product="hypothetical LOC401431"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027040.1"
                     /db_xref="GI:224451010"
                     /db_xref="GeneID:401431"
     gene            149570057..149577787
                     /gene="ATP6V0E2"
                     /gene_synonym="ATP6V0E2L; C7orf32"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:155066"
                     /db_xref="HGNC:21723"
                     /db_xref="HPRD:12920"
                     /db_xref="MIM:611019"
     mRNA            join(149570057..149571258,149572687..149572734,
                     149575767..149575879,149576424..149577787)
                     /gene="ATP6V0E2"
                     /gene_synonym="ATP6V0E2L; C7orf32"
                     /product="ATPase, H+ transporting V0 subunit e2,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145230.2"
                     /db_xref="GI:154689665"
                     /db_xref="GeneID:155066"
                     /db_xref="HGNC:21723"
                     /db_xref="HPRD:12920"
                     /db_xref="MIM:611019"
     mRNA            join(149570057..149571258,149572687..149572734,
                     149576424..149577738)
                     /gene="ATP6V0E2"
                     /gene_synonym="ATP6V0E2L; C7orf32"
                     /product="ATPase, H+ transporting V0 subunit e2,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001100592.1"
                     /db_xref="GI:154689795"
                     /db_xref="GeneID:155066"
                     /db_xref="HGNC:21723"
                     /db_xref="MIM:611019"
                     /db_xref="HPRD:12920"
     CDS             join(149571008..149571258,149572687..149572734,
                     149576424..149576766)
                     /gene="ATP6V0E2"
                     /gene_synonym="ATP6V0E2L; C7orf32"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="V-type proton ATPase subunit e 2 isoform 2"
                     /protein_id="NP_001094062.1"
                     /db_xref="GI:154689796"
                     /db_xref="CCDS:CCDS47742.1"
                     /db_xref="GeneID:155066"
                     /db_xref="HGNC:21723"
                     /db_xref="HPRD:12920"
                     /db_xref="MIM:611019"
     CDS             join(149571008..149571258,149572687..149572734,
                     149575767..149575860)
                     /gene="ATP6V0E2"
                     /gene_synonym="ATP6V0E2L; C7orf32"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="V-type proton ATPase subunit e 2 isoform 1"
                     /protein_id="NP_660265.2"
                     /db_xref="GI:154689666"
                     /db_xref="CCDS:CCDS55181.1"
                     /db_xref="GeneID:155066"
                     /db_xref="HGNC:21723"
                     /db_xref="HPRD:12920"
                     /db_xref="MIM:611019"
     gene            complement(149944301..150020758)
                     /gene="ACTR3C"
                     /gene_synonym="ARP11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:653857"
                     /db_xref="HGNC:37282"
     mRNA            complement(join(149944301..149944658,149946037..149946143,
                     149981842..149981934,149983456..149983629,
                     149986539..149986682,149990401..149990508,
                     149992341..149992436,150020558..150020758))
                     /gene="ACTR3C"
                     /gene_synonym="ARP11"
                     /product="ARP3 actin-related protein 3 homolog C (yeast),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001164458.1"
                     /db_xref="GI:256574834"
                     /db_xref="GeneID:653857"
                     /db_xref="HGNC:37282"
     mRNA            complement(join(149944301..149944658,149946037..149946143,
                     149981842..149981934,149983456..149983629,
                     149986539..149986682,149990401..149990508,
                     149992341..149992436,149999931..150000069))
                     /gene="ACTR3C"
                     /gene_synonym="ARP11"
                     /product="ARP3 actin-related protein 3 homolog C (yeast),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001164459.1"
                     /db_xref="GI:256574836"
                     /db_xref="GeneID:653857"
                     /db_xref="HGNC:37282"
     CDS             complement(join(149946075..149946143,149981842..149981934,
                     149983456..149983629,149986539..149986682,
                     149990401..149990508,149992341..149992385))
                     /gene="ACTR3C"
                     /gene_synonym="ARP11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="actin-related protein 3C precursor"
                     /protein_id="NP_001157930.1"
                     /db_xref="GI:256574835"
                     /db_xref="CCDS:CCDS47744.1"
                     /db_xref="GeneID:653857"
                     /db_xref="HGNC:37282"
     CDS             complement(join(149946075..149946143,149981842..149981934,
                     149983456..149983629,149986539..149986682,
                     149990401..149990508,149992341..149992385))
                     /gene="ACTR3C"
                     /gene_synonym="ARP11"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="actin-related protein 3C precursor"
                     /protein_id="NP_001157931.1"
                     /db_xref="GI:256574837"
                     /db_xref="CCDS:CCDS47744.1"
                     /db_xref="GeneID:653857"
                     /db_xref="HGNC:37282"
     gene            150020296..150035245
                     /gene="LRRC61"
                     /gene_synonym="FLJ22216; FLJ31392; HSPC295; MGC3036"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:65999"
                     /db_xref="HGNC:21704"
                     /db_xref="HPRD:08326"
     mRNA            join(150020296..150020649,150022930..150023099,
                     150033807..150035245)
                     /gene="LRRC61"
                     /gene_synonym="FLJ22216; FLJ31392; HSPC295; MGC3036"
                     /product="leucine rich repeat containing 61, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001142928.1"
                     /db_xref="GI:218931216"
                     /db_xref="GeneID:65999"
                     /db_xref="HGNC:21704"
                     /db_xref="HPRD:08326"
     mRNA            join(150020296..150020649,150033807..150035245)
                     /gene="LRRC61"
                     /gene_synonym="FLJ22216; FLJ31392; HSPC295; MGC3036"
                     /product="leucine rich repeat containing 61, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_023942.2"
                     /db_xref="GI:218931215"
                     /db_xref="GeneID:65999"
                     /db_xref="HGNC:21704"
                     /db_xref="HPRD:08326"
     gene            150026938..150029810
                     /gene="C7orf29"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:113763"
                     /db_xref="HGNC:21720"
                     /db_xref="HPRD:12917"
     mRNA            150026938..150029810
                     /gene="C7orf29"
                     /product="chromosome 7 open reading frame 29"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138434.2"
                     /db_xref="GI:49574496"
                     /db_xref="GeneID:113763"
                     /db_xref="HGNC:21720"
                     /db_xref="HPRD:12917"
     CDS             150027494..150028204
                     /gene="C7orf29"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC113763"
                     /protein_id="NP_612443.1"
                     /db_xref="GI:19923961"
                     /db_xref="CCDS:CCDS5900.1"
                     /db_xref="GeneID:113763"
                     /db_xref="HGNC:21720"
                     /db_xref="HPRD:12917"
     CDS             150033951..150034730
                     /gene="LRRC61"
                     /gene_synonym="FLJ22216; FLJ31392; HSPC295; MGC3036"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="leucine-rich repeat-containing protein 61"
                     /protein_id="NP_076431.1"
                     /db_xref="GI:13027616"
                     /db_xref="CCDS:CCDS5901.1"
                     /db_xref="GeneID:65999"
                     /db_xref="HGNC:21704"
                     /db_xref="HPRD:08326"
     CDS             150033951..150034730
                     /gene="LRRC61"
                     /gene_synonym="FLJ22216; FLJ31392; HSPC295; MGC3036"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="leucine-rich repeat-containing protein 61"
                     /protein_id="NP_001136400.1"
                     /db_xref="GI:218931217"
                     /db_xref="CCDS:CCDS5901.1"
                     /db_xref="GeneID:65999"
                     /db_xref="HGNC:21704"
                     /db_xref="HPRD:08326"
     gene            complement(150035407..150038763)
                     /gene="RARRES2"
                     /gene_synonym="HP10433; TIG2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5919"
                     /db_xref="HGNC:9868"
                     /db_xref="HPRD:03577"
                     /db_xref="MIM:601973"
     mRNA            complement(join(150035407..150035528,150035704..150035830,
                     150036075..150036170,150037189..150037293,
                     150037525..150037718,150038667..150038763))
                     /gene="RARRES2"
                     /gene_synonym="HP10433; TIG2"
                     /product="retinoic acid receptor responder (tazarotene
                     induced) 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002889.3"
                     /db_xref="GI:218931208"
                     /db_xref="GeneID:5919"
                     /db_xref="HGNC:9868"
                     /db_xref="HPRD:03577"
                     /db_xref="MIM:601973"
     CDS             complement(join(150035714..150035830,150036075..150036170,
                     150037189..150037293,150037525..150037698))
                     /gene="RARRES2"
                     /gene_synonym="HP10433; TIG2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="retinoic acid receptor responder protein 2
                     precursor"
                     /protein_id="NP_002880.1"
                     /db_xref="GI:4506427"
                     /db_xref="CCDS:CCDS5902.1"
                     /db_xref="GeneID:5919"
                     /db_xref="HGNC:9868"
                     /db_xref="HPRD:03577"
                     /db_xref="MIM:601973"
     gene            150065879..150071133
                     /gene="REPIN1"
                     /gene_synonym="AP4; RIP60; Zfp464; ZNF464"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:29803"
                     /db_xref="HGNC:17922"
                     /db_xref="HPRD:17966"
     mRNA            join(150065879..150066030,150066760..150066957,
                     150067849..150067973,150068317..150071133)
                     /gene="REPIN1"
                     /gene_synonym="AP4; RIP60; Zfp464; ZNF464"
                     /product="replication initiator 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_013400.3"
                     /db_xref="GI:153791993"
                     /db_xref="GeneID:29803"
                     /db_xref="HGNC:17922"
                     /db_xref="HPRD:17966"
     mRNA            join(150065879..150066030,150068317..150071133)
                     /gene="REPIN1"
                     /gene_synonym="AP4; RIP60; Zfp464; ZNF464"
                     /product="replication initiator 1, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001099696.2"
                     /db_xref="GI:197304796"
                     /db_xref="GeneID:29803"
                     /db_xref="HGNC:17922"
                     /db_xref="HPRD:17966"
     mRNA            join(150065879..150066030,150066760..150066957,
                     150068317..150071133)
                     /gene="REPIN1"
                     /gene_synonym="AP4; RIP60; Zfp464; ZNF464"
                     /product="replication initiator 1, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001099695.1"
                     /db_xref="GI:153792646"
                     /db_xref="GeneID:29803"
                     /db_xref="HGNC:17922"
                     /db_xref="HPRD:17966"
     CDS             join(150066801..150066957,150068317..150070034)
                     /gene="REPIN1"
                     /gene_synonym="AP4; RIP60; Zfp464; ZNF464"
                     /note="isoform 3 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="replication initiator 1 isoform 3"
                     /protein_id="NP_001093165.1"
                     /db_xref="GI:153792647"
                     /db_xref="CCDS:CCDS47745.1"
                     /db_xref="GeneID:29803"
                     /db_xref="HGNC:17922"
                     /db_xref="HPRD:17966"
     mRNA            150068258..150071133
                     /gene="REPIN1"
                     /gene_synonym="AP4; RIP60; Zfp464; ZNF464"
                     /product="replication initiator 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014374.3"
                     /db_xref="GI:153792538"
                     /db_xref="GeneID:29803"
                     /db_xref="HGNC:17922"
                     /db_xref="HPRD:17966"
     CDS             150068331..150070034
                     /gene="REPIN1"
                     /gene_synonym="AP4; RIP60; Zfp464; ZNF464"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="replication initiator 1 isoform 1"
                     /protein_id="NP_037532.2"
                     /db_xref="GI:153791994"
                     /db_xref="CCDS:CCDS43677.1"
                     /db_xref="GeneID:29803"
                     /db_xref="HGNC:17922"
                     /db_xref="HPRD:17966"
     CDS             150068331..150070034
                     /gene="REPIN1"
                     /gene_synonym="AP4; RIP60; Zfp464; ZNF464"
                     /note="isoform 1 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="replication initiator 1 isoform 1"
                     /protein_id="NP_055189.2"
                     /db_xref="GI:153792539"
                     /db_xref="CCDS:CCDS43677.1"
                     /db_xref="GeneID:29803"
                     /db_xref="HGNC:17922"
                     /db_xref="HPRD:17966"
     CDS             150068331..150070034
                     /gene="REPIN1"
                     /gene_synonym="AP4; RIP60; Zfp464; ZNF464"
                     /note="isoform 1 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="replication initiator 1 isoform 1"
                     /protein_id="NP_001093166.1"
                     /db_xref="GI:153791350"
                     /db_xref="CCDS:CCDS43677.1"
                     /db_xref="GeneID:29803"
                     /db_xref="HGNC:17922"
                     /db_xref="HPRD:17966"
     gene            150076406..150095719
                     /gene="ZNF775"
                     /gene_synonym="MGC33584"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285971"
                     /db_xref="HGNC:28501"
                     /db_xref="HPRD:14567"
     mRNA            join(150076406..150076481,150085510..150085589,
                     150093601..150095719)
                     /gene="ZNF775"
                     /gene_synonym="MGC33584"
                     /product="zinc finger protein 775"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_173680.3"
                     /db_xref="GI:116256459"
                     /db_xref="GeneID:285971"
                     /db_xref="HGNC:28501"
                     /db_xref="HPRD:14567"
     CDS             join(150085559..150085589,150093601..150095183)
                     /gene="ZNF775"
                     /gene_synonym="MGC33584"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="zinc finger protein 775"
                     /protein_id="NP_775951.2"
                     /db_xref="GI:116256460"
                     /db_xref="CCDS:CCDS43678.1"
                     /db_xref="GeneID:285971"
                     /db_xref="HGNC:28501"
                     /db_xref="HPRD:14567"
     gene            150102840..150109558
                     /gene="LOC728743"
                     /gene_synonym="FLJ12702; FLJ12789"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:728743"
     misc_RNA        join(150102840..150102992,150104672..150105576,
                     150107248..150109558)
                     /gene="LOC728743"
                     /gene_synonym="FLJ12702; FLJ12789"
                     /product="zinc finger protein pseudogene"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_027237.1"
                     /db_xref="GI:224549007"
                     /db_xref="GeneID:728743"
     gene            150130742..150145228
                     /gene="LOC285972"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285972"
     misc_RNA        join(150130742..150130917,150139637..150140248,
                     150143788..150143977,150144164..150145228)
                     /gene="LOC285972"
                     /product="hypothetical LOC285972"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_034033.1"
                     /db_xref="GI:300360530"
                     /db_xref="GeneID:285972"
     gene            150147962..150176483
                     /gene="GIMAP8"
                     /gene_synonym="DKFZp667I133; hIAN6; IAN-9; IAN6; IANT;
                     MGC129545"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:155038"
                     /db_xref="HGNC:21792"
                     /db_xref="HPRD:13577"
     mRNA            join(150147962..150148263,150163759..150164422,
                     150167917..150167962,150171100..150171726,
                     150174180..150176483)
                     /gene="GIMAP8"
                     /gene_synonym="DKFZp667I133; hIAN6; IAN-9; IAN6; IANT;
                     MGC129545"
                     /product="GTPase, IMAP family member 8"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_175571.2"
                     /db_xref="GI:55953077"
                     /db_xref="GeneID:155038"
                     /db_xref="HGNC:21792"
                     /db_xref="HPRD:13577"
     CDS             join(150163787..150164422,150167917..150167962,
                     150171100..150171726,150174180..150174868)
                     /gene="GIMAP8"
                     /gene_synonym="DKFZp667I133; hIAN6; IAN-9; IAN6; IANT;
                     MGC129545"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="GTPase IMAP family member 8"
                     /protein_id="NP_783161.1"
                     /db_xref="GI:28416956"
                     /db_xref="CCDS:CCDS34777.1"
                     /db_xref="GeneID:155038"
                     /db_xref="HGNC:21792"
                     /db_xref="HPRD:13577"
     gene            complement(150209062..150211135)
                     /gene="STRADBP1"
                     /gene_synonym="ALS2CR2P1; STLK6ps1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:389599"
                     /db_xref="HGNC:22478"
     gene            150211945..150218161
                     /gene="GIMAP7"
                     /gene_synonym="hIAN7; IAN7; MGC27027"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:168537"
                     /db_xref="HGNC:22404"
                     /db_xref="HPRD:17039"
     mRNA            join(150211945..150212033,150217022..150218161)
                     /gene="GIMAP7"
                     /gene_synonym="hIAN7; IAN7; MGC27027"
                     /product="GTPase, IMAP family member 7"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_153236.3"
                     /db_xref="GI:55774985"
                     /db_xref="GeneID:168537"
                     /db_xref="HGNC:22404"
                     /db_xref="HPRD:17039"
     CDS             150217063..150217965
                     /gene="GIMAP7"
                     /gene_synonym="hIAN7; IAN7; MGC27027"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="GTPase IMAP family member 7"
                     /protein_id="NP_694968.1"
                     /db_xref="GI:23397516"
                     /db_xref="CCDS:CCDS5903.1"
                     /db_xref="GeneID:168537"
                     /db_xref="HGNC:22404"
                     /db_xref="HPRD:17039"
     gene            complement(150238720..150239243)
                     /gene="ALDH7A1P3"
                     /gene_synonym="ATQL3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:543"
                     /db_xref="HGNC:880"
     gene            150264458..150271041
                     /gene="GIMAP4"
                     /gene_synonym="FLJ11110; hIAN1; HIMAP4; IAN1; IMAP4;
                     MSTP062"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55303"
                     /db_xref="HGNC:21872"
                     /db_xref="HPRD:16281"
                     /db_xref="MIM:608087"
     mRNA            join(150264458..150264525,150266976..150267047,
                     150269217..150271041)
                     /gene="GIMAP4"
                     /gene_synonym="FLJ11110; hIAN1; HIMAP4; IAN1; IMAP4;
                     MSTP062"
                     /product="GTPase, IMAP family member 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018326.2"
                     /db_xref="GI:28416432"
                     /db_xref="GeneID:55303"
                     /db_xref="HGNC:21872"
                     /db_xref="HPRD:16281"
                     /db_xref="MIM:608087"
     CDS             join(150266990..150267047,150269217..150270148)
                     /gene="GIMAP4"
                     /gene_synonym="FLJ11110; hIAN1; HIMAP4; IAN1; IMAP4;
                     MSTP062"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="GTPase IMAP family member 4"
                     /protein_id="NP_060796.1"
                     /db_xref="GI:8922873"
                     /db_xref="CCDS:CCDS5904.1"
                     /db_xref="GeneID:55303"
                     /db_xref="HGNC:21872"
                     /db_xref="HPRD:16281"
                     /db_xref="MIM:608087"
     gene            complement(150311158..150311873)
                     /gene="LOC100288724"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100288724"
     gene            complement(150322463..150329680)
                     /gene="GIMAP6"
                     /gene_synonym="DKFZp686A01175; FLJ22690; hIAN2; hIAN6;
                     IAN-2; IAN-6; IAN2; IAN6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:474344"
                     /db_xref="HGNC:21918"
                     /db_xref="HPRD:13576"
     mRNA            complement(join(150322463..150325600,150327146..150327230,
                     150329257..150329680))
                     /gene="GIMAP6"
                     /gene_synonym="DKFZp686A01175; FLJ22690; hIAN2; hIAN6;
                     IAN-2; IAN-6; IAN2; IAN6"
                     /product="GTPase, IMAP family member 6, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024711.4"
                     /db_xref="GI:197333697"
                     /db_xref="GeneID:474344"
                     /db_xref="HGNC:21918"
                     /db_xref="HPRD:13576"
     misc_RNA        complement(join(150322463..150325376,150327146..150327230,
                     150329257..150329680))
                     /gene="GIMAP6"
                     /gene_synonym="DKFZp686A01175; FLJ22690; hIAN2; hIAN6;
                     IAN-2; IAN-6; IAN2; IAN6"
                     /product="GTPase, IMAP family member 6, transcript variant
                     3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024115.1"
                     /db_xref="GI:197333708"
                     /db_xref="GeneID:474344"
                     /db_xref="HGNC:21918"
                     /db_xref="HPRD:13576"
     CDS             complement(join(150324807..150325600,
                     150327146..150327230))
                     /gene="GIMAP6"
                     /gene_synonym="DKFZp686A01175; FLJ22690; hIAN2; hIAN6;
                     IAN-2; IAN-6; IAN2; IAN6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="GTPase IMAP family member 6"
                     /protein_id="NP_078987.3"
                     /db_xref="GI:56119214"
                     /db_xref="CCDS:CCDS34778.1"
                     /db_xref="GeneID:474344"
                     /db_xref="HGNC:21918"
                     /db_xref="HPRD:13576"
     gene            150382794..150390729
                     /gene="GIMAP2"
                     /gene_synonym="DKFZp586D0824; HIMAP2; IMAP2; MGC24275"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26157"
                     /db_xref="HGNC:21789"
                     /db_xref="HPRD:16279"
                     /db_xref="MIM:608085"
     mRNA            join(150382794..150382873,150384140..150384175,
                     150389403..150390729)
                     /gene="GIMAP2"
                     /gene_synonym="DKFZp586D0824; HIMAP2; IMAP2; MGC24275"
                     /product="GTPase, IMAP family member 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_015660.2"
                     /db_xref="GI:55774983"
                     /db_xref="GeneID:26157"
                     /db_xref="HGNC:21789"
                     /db_xref="HPRD:16279"
                     /db_xref="MIM:608085"
     CDS             join(150384148..150384175,150389403..150390388)
                     /gene="GIMAP2"
                     /gene_synonym="DKFZp586D0824; HIMAP2; IMAP2; MGC24275"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="GTPase IMAP family member 2"
                     /protein_id="NP_056475.1"
                     /db_xref="GI:28416431"
                     /db_xref="CCDS:CCDS5905.1"
                     /db_xref="GeneID:26157"
                     /db_xref="HGNC:21789"
                     /db_xref="HPRD:16279"
                     /db_xref="MIM:608085"
     gene            150413645..150440737
                     /gene="GIMAP1-GIMAP5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100527949"
     mRNA            join(150413645..150413778,150416130..150416178,
                     150417136..150417494,150434593..150434796,
                     150437967..150438015,150439271..150440737)
                     /gene="GIMAP1-GIMAP5"
                     /product="GIMAP1-GIMAP5 readthrough"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199577.1"
                     /db_xref="GI:313760637"
                     /db_xref="GeneID:100527949"
     gene            150413645..150421368
                     /gene="GIMAP1"
                     /gene_synonym="HIMAP1; IMAP1; IMAP38"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:170575"
                     /db_xref="HGNC:23237"
                     /db_xref="HPRD:16278"
                     /db_xref="MIM:608084"
     mRNA            join(150413645..150413778,150416130..150416178,
                     150417136..150421368)
                     /gene="GIMAP1"
                     /gene_synonym="HIMAP1; IMAP1; IMAP38"
                     /product="GTPase, IMAP family member 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_130759.3"
                     /db_xref="GI:313760609"
                     /db_xref="GeneID:170575"
                     /db_xref="HGNC:23237"
                     /db_xref="HPRD:16278"
                     /db_xref="MIM:608084"
     CDS             join(150416136..150416178,150417136..150417494,
                     150434593..150434796,150437967..150438015,
                     150439271..150440151)
                     /gene="GIMAP1-GIMAP5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="GIMAP1-GIMAP5 protein"
                     /protein_id="NP_001186506.1"
                     /db_xref="GI:313760638"
                     /db_xref="GeneID:100527949"
     CDS             join(150416136..150416178,150417136..150418013)
                     /gene="GIMAP1"
                     /gene_synonym="HIMAP1; IMAP1; IMAP38"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="GTPase IMAP family member 1"
                     /protein_id="NP_570115.1"
                     /db_xref="GI:18594498"
                     /db_xref="CCDS:CCDS5906.1"
                     /db_xref="GeneID:170575"
                     /db_xref="HGNC:23237"
                     /db_xref="HPRD:16278"
                     /db_xref="MIM:608084"
     gene            150434436..150440737
                     /gene="GIMAP5"
                     /gene_synonym="FLJ11296; HIMAP3; IAN-5; IAN4; IAN4L1;
                     IAN5; IMAP3; IROD"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55340"
                     /db_xref="HGNC:18005"
                     /db_xref="HPRD:16280"
                     /db_xref="MIM:608086"
     mRNA            join(150434436..150434796,150437967..150438015,
                     150439271..150440737)
                     /gene="GIMAP5"
                     /gene_synonym="FLJ11296; HIMAP3; IAN-5; IAN4; IAN4L1;
                     IAN5; IMAP3; IROD"
                     /product="GTPase, IMAP family member 5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018384.4"
                     /db_xref="GI:313760632"
                     /db_xref="GeneID:55340"
                     /db_xref="HGNC:18005"
                     /db_xref="HPRD:16280"
                     /db_xref="MIM:608086"
     CDS             join(150437973..150438015,150439271..150440151)
                     /gene="GIMAP5"
                     /gene_synonym="FLJ11296; HIMAP3; IAN-5; IAN4; IAN4L1;
                     IAN5; IMAP3; IROD"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="GTPase IMAP family member 5"
                     /protein_id="NP_060854.2"
                     /db_xref="GI:28416949"
                     /db_xref="CCDS:CCDS5907.1"
                     /db_xref="GeneID:55340"
                     /db_xref="HGNC:18005"
                     /db_xref="HPRD:16280"
                     /db_xref="MIM:608086"
     gene            complement(150444013..150444819)
                     /gene="GIMAP3P"
                     /gene_synonym="GIMAP3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:474345"
                     /db_xref="HGNC:30975"
     gene            150446824..150487837
                     /gene="LOC100128542"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100128542"
     mRNA            join(150446824..150447058,150487587..150487837)
                     /gene="LOC100128542"
                     /product="hypothetical protein LOC100128542"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001162367.1"
                     /db_xref="GI:240849210"
                     /db_xref="GeneID:100128542"
     CDS             join(150446824..150447058,150487587..150487837)
                     /gene="LOC100128542"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="hypothetical protein LOC100128542"
                     /protein_id="NP_001155839.1"
                     /db_xref="GI:240849211"
                     /db_xref="GeneID:100128542"
     gene            complement(150488375..150498448)
                     /gene="TMEM176B"
                     /gene_synonym="FLJ26014; LR8; MGC110857"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:28959"
                     /db_xref="HGNC:29596"
                     /db_xref="HPRD:17443"
                     /db_xref="MIM:610385"
     mRNA            complement(join(150488375..150488711,150489144..150489263,
                     150490176..150490403,150490632..150490688,
                     150491049..150491159,150493454..150493662,
                     150498081..150498448))
                     /gene="TMEM176B"
                     /gene_synonym="FLJ26014; LR8; MGC110857"
                     /product="transmembrane protein 176B, transcript variant
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014020.3"
                     /db_xref="GI:156416013"
                     /db_xref="GeneID:28959"
                     /db_xref="HGNC:29596"
                     /db_xref="HPRD:17443"
                     /db_xref="MIM:610385"
     mRNA            complement(join(150488375..150488711,150489144..150489263,
                     150490176..150490403,150490632..150490688,
                     150491049..150491159,150493454..150493662,
                     150496699..150496706,150497386..150497621))
                     /gene="TMEM176B"
                     /gene_synonym="FLJ26014; LR8; MGC110857"
                     /product="transmembrane protein 176B, transcript variant
                     2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001101311.1"
                     /db_xref="GI:156416015"
                     /db_xref="GeneID:28959"
                     /db_xref="HGNC:29596"
                     /db_xref="MIM:610385"
                     /db_xref="HPRD:17443"
     mRNA            complement(join(150488375..150488711,150489144..150489263,
                     150490176..150490403,150490632..150490688,
                     150491049..150491159,150493454..150493662,
                     150497386..150497621))
                     /gene="TMEM176B"
                     /gene_synonym="FLJ26014; LR8; MGC110857"
                     /product="transmembrane protein 176B, transcript variant
                     3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001101312.1"
                     /db_xref="GI:156416017"
                     /db_xref="GeneID:28959"
                     /db_xref="HGNC:29596"
                     /db_xref="MIM:610385"
                     /db_xref="HPRD:17443"
     mRNA            complement(join(150488375..150488711,150489144..150489263,
                     150490176..150490403,150490632..150490688,
                     150493454..150493662,150497386..150497621))
                     /gene="TMEM176B"
                     /gene_synonym="FLJ26014; LR8; MGC110857"
                     /product="transmembrane protein 176B, transcript variant
                     5"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001101314.1"
                     /db_xref="GI:156416021"
                     /db_xref="GeneID:28959"
                     /db_xref="HGNC:29596"
                     /db_xref="MIM:610385"
                     /db_xref="HPRD:17443"
     CDS             complement(join(150488619..150488711,150489144..150489263,
                     150490176..150490403,150490632..150490688,
                     150491049..150491159,150493454..150493657))
                     /gene="TMEM176B"
                     /gene_synonym="FLJ26014; LR8; MGC110857"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 176B isoform a"
                     /protein_id="NP_054739.3"
                     /db_xref="GI:156416014"
                     /db_xref="CCDS:CCDS5908.1"
                     /db_xref="GeneID:28959"
                     /db_xref="HGNC:29596"
                     /db_xref="HPRD:17443"
                     /db_xref="MIM:610385"
     CDS             complement(join(150488619..150488711,150489144..150489263,
                     150490176..150490403,150490632..150490688,
                     150491049..150491159,150493454..150493657))
                     /gene="TMEM176B"
                     /gene_synonym="FLJ26014; LR8; MGC110857"
                     /note="isoform a is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 176B isoform a"
                     /protein_id="NP_001094781.1"
                     /db_xref="GI:156416016"
                     /db_xref="CCDS:CCDS5908.1"
                     /db_xref="GeneID:28959"
                     /db_xref="HGNC:29596"
                     /db_xref="HPRD:17443"
                     /db_xref="MIM:610385"
     CDS             complement(join(150488619..150488711,150489144..150489263,
                     150490176..150490403,150490632..150490688,
                     150491049..150491159,150493454..150493657))
                     /gene="TMEM176B"
                     /gene_synonym="FLJ26014; LR8; MGC110857"
                     /note="isoform a is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 176B isoform a"
                     /protein_id="NP_001094782.1"
                     /db_xref="GI:156416018"
                     /db_xref="CCDS:CCDS5908.1"
                     /db_xref="GeneID:28959"
                     /db_xref="HGNC:29596"
                     /db_xref="HPRD:17443"
                     /db_xref="MIM:610385"
     CDS             complement(join(150488619..150488711,150489144..150489263,
                     150490176..150490403,150490632..150490688,
                     150493454..150493657))
                     /gene="TMEM176B"
                     /gene_synonym="FLJ26014; LR8; MGC110857"
                     /note="isoform b is encoded by transcript variant 5;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 176B isoform b"
                     /protein_id="NP_001094784.1"
                     /db_xref="GI:156416022"
                     /db_xref="CCDS:CCDS47746.1"
                     /db_xref="GeneID:28959"
                     /db_xref="HGNC:29596"
                     /db_xref="HPRD:17443"
                     /db_xref="MIM:610385"
     gene            150497854..150502208
                     /gene="TMEM176A"
                     /gene_synonym="GS188; HCA112"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55365"
                     /db_xref="HGNC:24930"
                     /db_xref="HPRD:13635"
                     /db_xref="MIM:610334"
     mRNA            join(150497854..150497916,150498624..150498812,
                     150499303..150499413,150500488..150500544,
                     150500708..150500920,150501450..150501560,
                     150501915..150502208)
                     /gene="TMEM176A"
                     /gene_synonym="GS188; HCA112"
                     /product="transmembrane protein 176A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018487.2"
                     /db_xref="GI:32484986"
                     /db_xref="GeneID:55365"
                     /db_xref="HGNC:24930"
                     /db_xref="HPRD:13635"
                     /db_xref="MIM:610334"
     CDS             join(150498639..150498812,150499303..150499413,
                     150500488..150500544,150500708..150500920,
                     150501450..150501560,150501915..150501956)
                     /gene="TMEM176A"
                     /gene_synonym="GS188; HCA112"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane protein 176A"
                     /protein_id="NP_060957.2"
                     /db_xref="GI:32484987"
                     /db_xref="CCDS:CCDS5909.1"
                     /db_xref="GeneID:55365"
                     /db_xref="HGNC:24930"
                     /db_xref="HPRD:13635"
                     /db_xref="MIM:610334"
     gene            150549573..150558379
                     /gene="ABP1"
                     /gene_synonym="ABP; AOC1; DAO; DAO1; KAO"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:26"
                     /db_xref="HGNC:80"
                     /db_xref="HPRD:00088"
                     /db_xref="MIM:104610"
     mRNA            join(150549573..150549646,150553543..150555128,
                     150555851..150556136,150557589..150557721,
                     150558031..150558379)
                     /gene="ABP1"
                     /gene_synonym="ABP; AOC1; DAO; DAO1; KAO"
                     /product="amiloride binding protein 1 (amine oxidase
                     (copper-containing))"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001091.2"
                     /db_xref="GI:73486660"
                     /db_xref="GeneID:26"
                     /db_xref="HGNC:80"
                     /db_xref="HPRD:00088"
                     /db_xref="MIM:104610"
     CDS             join(150553559..150555128,150555851..150556136,
                     150557589..150557721,150558031..150558297)
                     /gene="ABP1"
                     /gene_synonym="ABP; AOC1; DAO; DAO1; KAO"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="amiloride-sensitive amine oxidase
                     [copper-containing] precursor"
                     /protein_id="NP_001082.2"
                     /db_xref="GI:73486661"
                     /db_xref="CCDS:CCDS43679.1"
                     /db_xref="GeneID:26"
                     /db_xref="HGNC:80"
                     /db_xref="HPRD:00088"
                     /db_xref="MIM:104610"
     gene            complement(150642044..150675402)
                     /gene="KCNH2"
                     /gene_synonym="ERG1; HERG; HERG1; Kv11.1; LQT2; SQT1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3757"
                     /db_xref="HGNC:6251"
                     /db_xref="HPRD:01069"
                     /db_xref="MIM:152427"
     mRNA            complement(join(150642044..150642602,150643965..150644142,
                     150644416..150644602,150644694..150644966,
                     150645532..150645631,150645944..150646137,
                     150647256..150647508,150648009..150648208,
                     150648536..150648923,150649513..150649941,
                     150654379..150654590,150655147..150655590,
                     150656660..150656824,150671799..150672029,
                     150674926..150675402))
                     /gene="KCNH2"
                     /gene_synonym="ERG1; HERG; HERG1; Kv11.1; LQT2; SQT1"
                     /product="potassium voltage-gated channel, subfamily H
                     (eag-related), member 2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000238.3"
                     /db_xref="GI:325651830"
                     /db_xref="GeneID:3757"
                     /db_xref="HGNC:6251"
                     /db_xref="HPRD:01069"
                     /db_xref="MIM:152427"
     mRNA            complement(join(150642044..150642602,150643965..150644142,
                     150644416..150644602,150644694..150644966,
                     150645532..150645631,150645944..150646137,
                     150647256..150647508,150648009..150648208,
                     150648536..150648923,150649513..150649941,
                     150652484..150652917))
                     /gene="KCNH2"
                     /gene_synonym="ERG1; HERG; HERG1; Kv11.1; LQT2; SQT1"
                     /product="potassium voltage-gated channel, subfamily H
                     (eag-related), member 2, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_172057.2"
                     /db_xref="GI:325651832"
                     /db_xref="GeneID:3757"
                     /db_xref="HGNC:6251"
                     /db_xref="HPRD:01069"
                     /db_xref="MIM:152427"
     CDS             complement(join(150642453..150642602,150643965..150644142,
                     150644416..150644602,150644694..150644966,
                     150645532..150645631,150645944..150646137,
                     150647256..150647508,150648009..150648208,
                     150648536..150648923,150649513..150649941,
                     150654379..150654590,150655147..150655590,
                     150656660..150656824,150671799..150672029,
                     150674926..150675001))
                     /gene="KCNH2"
                     /gene_synonym="ERG1; HERG; HERG1; Kv11.1; LQT2; SQT1"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="potassium voltage-gated channel subfamily H
                     member 2 isoform a"
                     /protein_id="NP_000229.1"
                     /db_xref="GI:4557729"
                     /db_xref="CCDS:CCDS5910.1"
                     /db_xref="GeneID:3757"
                     /db_xref="HGNC:6251"
                     /db_xref="HPRD:01069"
                     /db_xref="MIM:152427"
     CDS             complement(join(150642453..150642602,150643965..150644142,
                     150644416..150644602,150644694..150644966,
                     150645532..150645631,150645944..150646137,
                     150647256..150647508,150648009..150648208,
                     150648536..150648923,150649513..150649941,
                     150652484..150652591))
                     /gene="KCNH2"
                     /gene_synonym="ERG1; HERG; HERG1; Kv11.1; LQT2; SQT1"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="potassium voltage-gated channel subfamily H
                     member 2 isoform c"
                     /protein_id="NP_742054.1"
                     /db_xref="GI:26051273"
                     /db_xref="CCDS:CCDS5911.1"
                     /db_xref="GeneID:3757"
                     /db_xref="HGNC:6251"
                     /db_xref="HPRD:01069"
                     /db_xref="MIM:152427"
     mRNA            complement(join(150646497..150647508,150648009..150648208,
                     150648536..150648923,150649513..150649941,
                     150654379..150654590,150655147..150655590,
                     150656660..150656824,150671799..150672029,
                     150674926..150675402))
                     /gene="KCNH2"
                     /gene_synonym="ERG1; HERG; HERG1; Kv11.1; LQT2; SQT1"
                     /product="potassium voltage-gated channel, subfamily H
                     (eag-related), member 2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_172056.2"
                     /db_xref="GI:325651831"
                     /db_xref="GeneID:3757"
                     /db_xref="HGNC:6251"
                     /db_xref="HPRD:01069"
                     /db_xref="MIM:152427"
     mRNA            complement(join(150646497..150647508,150648009..150648208,
                     150648536..150648923,150649513..150649941,
                     150652484..150652917))
                     /gene="KCNH2"
                     /gene_synonym="ERG1; HERG; HERG1; Kv11.1; LQT2; SQT1"
                     /product="potassium voltage-gated channel, subfamily H
                     (eag-related), member 2, transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001204798.1"
                     /db_xref="GI:325651833"
                     /db_xref="GeneID:3757"
                     /db_xref="HGNC:6251"
                     /db_xref="MIM:152427"
                     /db_xref="HPRD:01069"
     CDS             complement(join(150646987..150647508,150648009..150648208,
                     150648536..150648923,150649513..150649941,
                     150654379..150654590,150655147..150655590,
                     150656660..150656824,150671799..150672029,
                     150674926..150675001))
                     /gene="KCNH2"
                     /gene_synonym="ERG1; HERG; HERG1; Kv11.1; LQT2; SQT1"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="potassium voltage-gated channel subfamily H
                     member 2 isoform b"
                     /protein_id="NP_742053.1"
                     /db_xref="GI:26051271"
                     /db_xref="CCDS:CCDS47747.1"
                     /db_xref="GeneID:3757"
                     /db_xref="HGNC:6251"
                     /db_xref="HPRD:01069"
                     /db_xref="MIM:152427"
     CDS             complement(join(150646987..150647508,150648009..150648208,
                     150648536..150648923,150649513..150649941,
                     150652484..150652591))
                     /gene="KCNH2"
                     /gene_synonym="ERG1; HERG; HERG1; Kv11.1; LQT2; SQT1"
                     /note="isoform d is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="potassium voltage-gated channel subfamily H
                     member 2 isoform d"
                     /protein_id="NP_001191727.1"
                     /db_xref="GI:325651834"
                     /db_xref="GeneID:3757"
                     /db_xref="HGNC:6251"
                     /db_xref="MIM:152427"
                     /db_xref="HPRD:01069"
     gene            150688144..150711687
                     /gene="NOS3"
                     /gene_synonym="ECNOS; eNOS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:4846"
                     /db_xref="HGNC:7876"
                     /db_xref="HPRD:01224"
                     /db_xref="MIM:163729"
     mRNA            join(150688144..150688388,150690841..150691049,
                     150692291..150692402,150693492..150693640,
                     150693851..150694013,150695445..150695536,
                     150695627..150695768,150696034..150696173,
                     150696278..150696452,150697586..150697687,
                     150698319..150698513,150698632..150698705,
                     150698909..150699053,150699288..150699392,
                     150703515..150703582,150703977..150704093,
                     150704190..150704364,150706018..150706150,
                     150706277..150706355,150706486..150706673,
                     150707203..150707375,150707685..150707895,
                     150707987..150708074,150709439..150709560,
                     150710319..150710467,150710812..150711006,
                     150711096..150711687)
                     /gene="NOS3"
                     /gene_synonym="ECNOS; eNOS"
                     /product="nitric oxide synthase 3 (endothelial cell),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000603.4"
                     /db_xref="GI:231571207"
                     /db_xref="GeneID:4846"
                     /db_xref="HGNC:7876"
                     /db_xref="HPRD:01224"
                     /db_xref="MIM:163729"
     CDS             join(150690892..150691049,150692291..150692402,
                     150693492..150693640,150693851..150694013,
                     150695445..150695536,150695627..150695768,
                     150696034..150696173,150696278..150696452,
                     150697586..150697687,150698319..150698513,
                     150698632..150698705,150698909..150699053,
                     150699288..150699392,150703515..150703582,
                     150703977..150704093,150704190..150704364,
                     150706018..150706150,150706277..150706355,
                     150706486..150706673,150707203..150707375,
                     150707685..150707895,150707987..150708074,
                     150709439..150709560,150710319..150710467,
                     150710812..150711006,150711096..150711257)
                     /gene="NOS3"
                     /gene_synonym="ECNOS; eNOS"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="nitric oxide synthase, endothelial isoform 1"
                     /protein_id="NP_000594.2"
                     /db_xref="GI:40254422"
                     /db_xref="CCDS:CCDS5912.1"
                     /db_xref="GeneID:4846"
                     /db_xref="HGNC:7876"
                     /db_xref="HPRD:01224"
                     /db_xref="MIM:163729"
     mRNA            join(150690892..150691049,150692291..150692402,
                     150693492..150693640,150693851..150694013,
                     150695445..150695536,150695627..150695768,
                     150696034..150696173,150696278..150696452,
                     150697586..150697687,150698319..150698513,
                     150698632..150698705,150698909..150699053,
                     150699288..150699392,150700745..150701023)
                     /gene="NOS3"
                     /gene_synonym="ECNOS; eNOS"
                     /product="nitric oxide synthase 3 (endothelial cell),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001160109.1"
                     /db_xref="GI:231571313"
                     /db_xref="GeneID:4846"
                     /db_xref="HGNC:7876"
                     /db_xref="MIM:163729"
                     /db_xref="HPRD:01224"
     mRNA            join(150690892..150691049,150692291..150692402,
                     150693492..150693640,150693851..150694013,
                     150695445..150695536,150695627..150695768,
                     150696034..150696173,150696278..150696452,
                     150697586..150697687,150698319..150698513,
                     150698632..150698705,150698909..150699053,
                     150699288..150699392,150700399..150701023)
                     /gene="NOS3"
                     /gene_synonym="ECNOS; eNOS"
                     /product="nitric oxide synthase 3 (endothelial cell),
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001160110.1"
                     /db_xref="GI:231571328"
                     /db_xref="GeneID:4846"
                     /db_xref="HGNC:7876"
                     /db_xref="MIM:163729"
                     /db_xref="HPRD:01224"
     mRNA            join(150690892..150691049,150692291..150692402,
                     150693492..150693640,150693851..150694013,
                     150695445..150695536,150695627..150695768,
                     150696034..150696173,150696278..150696452,
                     150697586..150697687,150698319..150698513,
                     150698632..150698705,150698909..150699053,
                     150699288..150699392,150700239..150701023)
                     /gene="NOS3"
                     /gene_synonym="ECNOS; eNOS"
                     /product="nitric oxide synthase 3 (endothelial cell),
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001160111.1"
                     /db_xref="GI:231571355"
                     /db_xref="GeneID:4846"
                     /db_xref="HGNC:7876"
                     /db_xref="MIM:163729"
                     /db_xref="HPRD:01224"
     CDS             join(150690892..150691049,150692291..150692402,
                     150693492..150693640,150693851..150694013,
                     150695445..150695536,150695627..150695768,
                     150696034..150696173,150696278..150696452,
                     150697586..150697687,150698319..150698513,
                     150698632..150698705,150698909..150699053,
                     150699288..150699392,150700745..150700783)
                     /gene="NOS3"
                     /gene_synonym="ECNOS; eNOS"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="nitric oxide synthase, endothelial isoform 2"
                     /protein_id="NP_001153581.1"
                     /db_xref="GI:231571314"
                     /db_xref="GeneID:4846"
                     /db_xref="HGNC:7876"
                     /db_xref="MIM:163729"
                     /db_xref="HPRD:01224"
     CDS             join(150690892..150691049,150692291..150692402,
                     150693492..150693640,150693851..150694013,
                     150695445..150695536,150695627..150695768,
                     150696034..150696173,150696278..150696452,
                     150697586..150697687,150698319..150698513,
                     150698632..150698705,150698909..150699053,
                     150699288..150699392,150700399..150700491)
                     /gene="NOS3"
                     /gene_synonym="ECNOS; eNOS"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="nitric oxide synthase, endothelial isoform 3"
                     /protein_id="NP_001153582.1"
                     /db_xref="GI:231571329"
                     /db_xref="CCDS:CCDS55183.1"
                     /db_xref="GeneID:4846"
                     /db_xref="HGNC:7876"
                     /db_xref="HPRD:01224"
                     /db_xref="MIM:163729"
     CDS             join(150690892..150691049,150692291..150692402,
                     150693492..150693640,150693851..150694013,
                     150695445..150695536,150695627..150695768,
                     150696034..150696173,150696278..150696452,
                     150697586..150697687,150698319..150698513,
                     150698632..150698705,150698909..150699053,
                     150699288..150699392,150700239..150700376)
                     /gene="NOS3"
                     /gene_synonym="ECNOS; eNOS"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="nitric oxide synthase, endothelial isoform 4"
                     /protein_id="NP_001153583.1"
                     /db_xref="GI:231571356"
                     /db_xref="CCDS:CCDS55182.1"
                     /db_xref="GeneID:4846"
                     /db_xref="HGNC:7876"
                     /db_xref="HPRD:01224"
                     /db_xref="MIM:163729"
     gene            complement(150709297..150721586)
                     /gene="ATG9B"
                     /gene_synonym="APG9L2; NOS3AS; SONE"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285973"
                     /db_xref="HGNC:21899"
                     /db_xref="HPRD:08253"
                     /db_xref="MIM:612205"
     mRNA            complement(join(150709297..150710496,150710818..150711000,
                     150711170..150711377,150712091..150712211,
                     150712970..150713111,150713197..150713323,
                     150713519..150713615,150713776..150713908,
                     150714123..150714359,150714958..150715137,
                     150715381..150715534,150715707..150716461,
                     150718275..150718416,150720132..150720293,
                     150720532..150720596,150720774..150720817,
                     150720961..150721586))
                     /gene="ATG9B"
                     /gene_synonym="APG9L2; NOS3AS; SONE"
                     /product="ATG9 autophagy related 9 homolog B (S.
                     cerevisiae)"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_173681.5"
                     /db_xref="GI:239582719"
                     /db_xref="GeneID:285973"
                     /db_xref="HGNC:21899"
                     /db_xref="HPRD:08253"
                     /db_xref="MIM:612205"
     CDS             complement(join(150712984..150713111,150713197..150713323,
                     150713519..150713615,150713776..150713908,
                     150714123..150714359,150714958..150715137,
                     150715381..150715534,150715707..150716461,
                     150718275..150718416,150720132..150720293,
                     150720532..150720596,150720774..150720817,
                     150720961..150721510))
                     /gene="ATG9B"
                     /gene_synonym="APG9L2; NOS3AS; SONE"
                     /exception="unclassified translation discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="autophagy-related protein 9B"
                     /protein_id="NP_775952.4"
                     /db_xref="GI:239582720"
                     /db_xref="CCDS:CCDS43680.1"
                     /db_xref="GeneID:285973"
                     /db_xref="HGNC:21899"
                     /db_xref="HPRD:08253"
                     /db_xref="MIM:612205"
     gene            150725510..150744869
                     /gene="ABCB8"
                     /gene_synonym="EST328128; M-ABC1; MABC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:11194"
                     /db_xref="HGNC:49"
                     /db_xref="HPRD:10400"
                     /db_xref="MIM:605464"
     mRNA            join(150725510..150725697,150730692..150731004,
                     150731360..150731515,150731592..150731686,
                     150731811..150731916,150732668..150732829,
                     150732969..150733054,150733160..150733257,
                     150733631..150733736,150737355..150737388,
                     150737585..150737721,150737915..150738009,
                     150738186..150738319,150739048..150739195,
                     150741058..150741308,150742296..150744869)
                     /gene="ABCB8"
                     /gene_synonym="EST328128; M-ABC1; MABC1"
                     /product="ATP-binding cassette, sub-family B (MDR/TAP),
                     member 8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_007188.3"
                     /db_xref="GI:156105684"
                     /db_xref="GeneID:11194"
                     /db_xref="HGNC:49"
                     /db_xref="HPRD:10400"
                     /db_xref="MIM:605464"
     gene            complement(150725510..150731235)
                     /gene="LOC100507614"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 20 ESTs"
                     /db_xref="GeneID:100507614"
     misc_RNA        complement(join(150725510..150725690,150729264..150729269,
                     150730690..150731235))
                     /gene="LOC100507614"
                     /product="hypothetical LOC100507614, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 20 ESTs"
                     /transcript_id="XR_108787.1"
                     /db_xref="GI:310120121"
                     /db_xref="GeneID:100507614"
     CDS             join(150725603..150725697,150730692..150731004,
                     150731360..150731515,150731592..150731686,
                     150731811..150731916,150732668..150732829,
                     150732969..150733054,150733160..150733257,
                     150733631..150733736,150737355..150737388,
                     150737585..150737721,150737915..150738009,
                     150738186..150738319,150739048..150739195,
                     150741058..150741308,150742296..150742436)
                     /gene="ABCB8"
                     /gene_synonym="EST328128; M-ABC1; MABC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ATP-binding cassette sub-family B member 8,
                     mitochondrial"
                     /protein_id="NP_009119.2"
                     /db_xref="GI:156105685"
                     /db_xref="CCDS:CCDS5913.1"
                     /db_xref="GeneID:11194"
                     /db_xref="HGNC:49"
                     /db_xref="HPRD:10400"
                     /db_xref="MIM:605464"
     gene            150745605..150749843
                     /gene="ACCN3"
                     /gene_synonym="ASIC3; DRASIC; SLNAC1; TNaC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9311"
                     /db_xref="HGNC:101"
                     /db_xref="HPRD:10626"
                     /db_xref="MIM:611741"
     mRNA            join(150745605..150746506,150747193..150747343,
                     150747568..150747695,150747845..150748040,
                     150748126..150748182,150748259..150748406,
                     150748897..150748988,150749070..150749149,
                     150749253..150749324,150749503..150749561,
                     150749661..150749843)
                     /gene="ACCN3"
                     /gene_synonym="ASIC3; DRASIC; SLNAC1; TNaC1"
                     /product="amiloride-sensitive cation channel 3, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004769.2"
                     /db_xref="GI:166063997"
                     /db_xref="GeneID:9311"
                     /db_xref="HGNC:101"
                     /db_xref="HPRD:10626"
                     /db_xref="MIM:611741"
     mRNA            join(150745605..150746506,150747193..150747343,
                     150747568..150747695,150747845..150748040,
                     150748126..150748182,150748259..150748406,
                     150748897..150748988,150749070..150749149,
                     150749253..150749324,150749503..150749561,
                     150749641..150749843)
                     /gene="ACCN3"
                     /gene_synonym="ASIC3; DRASIC; SLNAC1; TNaC1"
                     /product="amiloride-sensitive cation channel 3, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020321.2"
                     /db_xref="GI:166063996"
                     /db_xref="GeneID:9311"
                     /db_xref="HGNC:101"
                     /db_xref="HPRD:10626"
                     /db_xref="MIM:611741"
     mRNA            join(150745605..150746506,150747193..150747343,
                     150747568..150747695,150747845..150748040,
                     150748126..150748182,150748259..150748406,
                     150748897..150748988,150749070..150749149,
                     150749253..150749324,150749661..150749843)
                     /gene="ACCN3"
                     /gene_synonym="ASIC3; DRASIC; SLNAC1; TNaC1"
                     /product="amiloride-sensitive cation channel 3, transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020322.2"
                     /db_xref="GI:166063993"
                     /db_xref="GeneID:9311"
                     /db_xref="HGNC:101"
                     /db_xref="HPRD:10626"
                     /db_xref="MIM:611741"
     CDS             join(150745973..150746506,150747193..150747343,
                     150747568..150747695,150747845..150748040,
                     150748126..150748182,150748259..150748406,
                     150748897..150748988,150749070..150749149,
                     150749253..150749324,150749661..150749834)
                     /gene="ACCN3"
                     /gene_synonym="ASIC3; DRASIC; SLNAC1; TNaC1"
                     /note="isoform c is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="amiloride-sensitive cation channel 3 isoform c"
                     /protein_id="NP_064718.1"
                     /db_xref="GI:9998948"
                     /db_xref="CCDS:CCDS5914.1"
                     /db_xref="GeneID:9311"
                     /db_xref="HGNC:101"
                     /db_xref="HPRD:10626"
                     /db_xref="MIM:611741"
     CDS             join(150745973..150746506,150747193..150747343,
                     150747568..150747695,150747845..150748040,
                     150748126..150748182,150748259..150748406,
                     150748897..150748988,150749070..150749149,
                     150749253..150749324,150749503..150749561,
                     150749641..150749773)
                     /gene="ACCN3"
                     /gene_synonym="ASIC3; DRASIC; SLNAC1; TNaC1"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="amiloride-sensitive cation channel 3 isoform b"
                     /protein_id="NP_064717.1"
                     /db_xref="GI:9998946"
                     /db_xref="CCDS:CCDS5915.1"
                     /db_xref="GeneID:9311"
                     /db_xref="HGNC:101"
                     /db_xref="HPRD:10626"
                     /db_xref="MIM:611741"
     CDS             join(150745973..150746506,150747193..150747343,
                     150747568..150747695,150747845..150748040,
                     150748126..150748182,150748259..150748406,
                     150748897..150748988,150749070..150749149,
                     150749253..150749324,150749503..150749561,
                     150749661..150749739)
                     /gene="ACCN3"
                     /gene_synonym="ASIC3; DRASIC; SLNAC1; TNaC1"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="amiloride-sensitive cation channel 3 isoform a"
                     /protein_id="NP_004760.1"
                     /db_xref="GI:4757710"
                     /db_xref="CCDS:CCDS5916.1"
                     /db_xref="GeneID:9311"
                     /db_xref="HGNC:101"
                     /db_xref="HPRD:10626"
                     /db_xref="MIM:611741"
     gene            complement(150750899..150755052)
                     /gene="CDK5"
                     /gene_synonym="PSSALRE"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1020"
                     /db_xref="HGNC:1774"
                     /db_xref="MIM:123831"
     mRNA            complement(join(150750899..150751182,150751299..150751379,
                     150751492..150751552,150752114..150752183,
                     150752364..150752460,150752619..150752693,
                     150752840..150752935,150753667..150753723,
                     150753823..150753883,150753995..150754062,
                     150754159..150754247,150754899..150755052))
                     /gene="CDK5"
                     /gene_synonym="PSSALRE"
                     /product="cyclin-dependent kinase 5, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_004935.3"
                     /db_xref="GI:256574768"
                     /db_xref="GeneID:1020"
                     /db_xref="HGNC:1774"
                     /db_xref="HPRD:00449"
                     /db_xref="MIM:123831"
     mRNA            complement(join(150750902..150751182,150751299..150751379,
                     150751492..150751552,150752114..150752183,
                     150752364..150752460,150752619..150752693,
                     150753667..150753723,150753823..150753883,
                     150753995..150754062,150754159..150754247,
                     150754899..150755052))
                     /gene="CDK5"
                     /gene_synonym="PSSALRE"
                     /product="cyclin-dependent kinase 5, transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001164410.1"
                     /db_xref="GI:256542305"
                     /db_xref="GeneID:1020"
                     /db_xref="HGNC:1774"
                     /db_xref="MIM:123831"
     CDS             complement(join(150751096..150751182,150751299..150751379,
                     150751492..150751552,150752114..150752183,
                     150752364..150752460,150752619..150752693,
                     150752840..150752935,150753667..150753723,
                     150753823..150753883,150753995..150754062,
                     150754159..150754247,150754899..150754935))
                     /gene="CDK5"
                     /gene_synonym="PSSALRE"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclin-dependent kinase 5 isoform 1"
                     /protein_id="NP_004926.1"
                     /db_xref="GI:4826675"
                     /db_xref="CCDS:CCDS47748.1"
                     /db_xref="GeneID:1020"
                     /db_xref="HGNC:1774"
                     /db_xref="MIM:123831"
     CDS             complement(join(150751096..150751182,150751299..150751379,
                     150751492..150751552,150752114..150752183,
                     150752364..150752460,150752619..150752693,
                     150753667..150753723,150753823..150753883,
                     150753995..150754062,150754159..150754247,
                     150754899..150754935))
                     /gene="CDK5"
                     /gene_synonym="PSSALRE"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="cyclin-dependent kinase 5 isoform 2"
                     /protein_id="NP_001157882.1"
                     /db_xref="GI:256542306"
                     /db_xref="CCDS:CCDS55184.1"
                     /db_xref="GeneID:1020"
                     /db_xref="HGNC:1774"
                     /db_xref="MIM:123831"
     gene            150755299..150773614
                     /gene="SLC4A2"
                     /gene_synonym="AE2; BND3L; EPB3L1; FLJ59028; HKB3; NBND3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6522"
                     /db_xref="HGNC:11028"
                     /db_xref="HPRD:02728"
                     /db_xref="MIM:109280"
     mRNA            join(150755299..150756275,150759012..150759125,
                     150761289..150761454,150761613..150761854,
                     150761935..150762053,150763604..150763848,
                     150763938..150764080,150764961..150765141,
                     150767034..150767169,150767268..150767433,
                     150767544..150767658,150767814..150767998,
                     150768159..150768384,150768477..150768692,
                     150768776..150768924,150769029..150769223,
                     150771126..150771380,150771486..150771575,
                     150771762..150771928,150772342..150772595,
                     150772693..150772862,150773100..150773273,
                     150773374..150773614)
                     /gene="SLC4A2"
                     /gene_synonym="AE2; BND3L; EPB3L1; FLJ59028; HKB3; NBND3"
                     /product="solute carrier family 4, anion exchanger, member
                     2 (erythrocyte membrane protein band 3-like 1), transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199692.1"
                     /db_xref="GI:314122219"
                     /db_xref="GeneID:6522"
                     /db_xref="HGNC:11028"
                     /db_xref="MIM:109280"
                     /db_xref="HPRD:02728"
     mRNA            join(150756657..150756849,150759012..150759125,
                     150761289..150761454,150761613..150761854,
                     150761935..150762053,150763604..150763848,
                     150763938..150764080,150764961..150765141,
                     150767034..150767169,150767268..150767433,
                     150767544..150767658,150767814..150767998,
                     150768159..150768384,150768477..150768692,
                     150768776..150768924,150769029..150769223,
                     150771126..150771380,150771486..150771575,
                     150771762..150771928,150772342..150772595,
                     150772693..150772862,150773100..150773273,
                     150773374..150773614)
                     /gene="SLC4A2"
                     /gene_synonym="AE2; BND3L; EPB3L1; FLJ59028; HKB3; NBND3"
                     /product="solute carrier family 4, anion exchanger, member
                     2 (erythrocyte membrane protein band 3-like 1), transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003040.3"
                     /db_xref="GI:156071473"
                     /db_xref="GeneID:6522"
                     /db_xref="HGNC:11028"
                     /db_xref="HPRD:02728"
                     /db_xref="MIM:109280"
     CDS             join(150759075..150759125,150761289..150761454,
                     150761613..150761854,150761935..150762053,
                     150763604..150763848,150763938..150764080,
                     150764961..150765141,150767034..150767169,
                     150767268..150767433,150767544..150767658,
                     150767814..150767998,150768159..150768384,
                     150768477..150768692,150768776..150768924,
                     150769029..150769223,150771126..150771380,
                     150771486..150771575,150771762..150771928,
                     150772342..150772595,150772693..150772862,
                     150773100..150773273,150773374..150773454)
                     /gene="SLC4A2"
                     /gene_synonym="AE2; BND3L; EPB3L1; FLJ59028; HKB3; NBND3"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="anion exchange protein 2 isoform 1"
                     /protein_id="NP_003031.3"
                     /db_xref="GI:156071474"
                     /db_xref="CCDS:CCDS5917.1"
                     /db_xref="GeneID:6522"
                     /db_xref="HGNC:11028"
                     /db_xref="HPRD:02728"
                     /db_xref="MIM:109280"
     CDS             join(150759075..150759125,150761289..150761454,
                     150761613..150761854,150761935..150762053,
                     150763604..150763848,150763938..150764080,
                     150764961..150765141,150767034..150767169,
                     150767268..150767433,150767544..150767658,
                     150767814..150767998,150768159..150768384,
                     150768477..150768692,150768776..150768924,
                     150769029..150769223,150771126..150771380,
                     150771486..150771575,150771762..150771928,
                     150772342..150772595,150772693..150772862,
                     150773100..150773273,150773374..150773454)
                     /gene="SLC4A2"
                     /gene_synonym="AE2; BND3L; EPB3L1; FLJ59028; HKB3; NBND3"
                     /note="isoform 1 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="anion exchange protein 2 isoform 1"
                     /protein_id="NP_001186621.1"
                     /db_xref="GI:314122220"
                     /db_xref="GeneID:6522"
                     /db_xref="HGNC:11028"
                     /db_xref="MIM:109280"
                     /db_xref="HPRD:02728"
     mRNA            join(150759634..150759750,150761289..150761454,
                     150761613..150761854,150761935..150762053,
                     150763604..150763848,150763938..150764080,
                     150764961..150765141,150767034..150767169,
                     150767268..150767433,150767544..150767658,
                     150767814..150767998,150768159..150768384,
                     150768477..150768692,150768776..150768924,
                     150769029..150769223,150771126..150771380,
                     150771486..150771575,150771762..150771928,
                     150772342..150772595,150772693..150772862,
                     150773100..150773273,150773374..150773614)
                     /gene="SLC4A2"
                     /gene_synonym="AE2; BND3L; EPB3L1; FLJ59028; HKB3; NBND3"
                     /product="solute carrier family 4, anion exchanger, member
                     2 (erythrocyte membrane protein band 3-like 1), transcript
                     variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199693.1"
                     /db_xref="GI:314122221"
                     /db_xref="GeneID:6522"
                     /db_xref="HGNC:11028"
                     /db_xref="MIM:109280"
                     /db_xref="HPRD:02728"
     CDS             join(150759727..150759750,150761289..150761454,
                     150761613..150761854,150761935..150762053,
                     150763604..150763848,150763938..150764080,
                     150764961..150765141,150767034..150767169,
                     150767268..150767433,150767544..150767658,
                     150767814..150767998,150768159..150768384,
                     150768477..150768692,150768776..150768924,
                     150769029..150769223,150771126..150771380,
                     150771486..150771575,150771762..150771928,
                     150772342..150772595,150772693..150772862,
                     150773100..150773273,150773374..150773454)
                     /gene="SLC4A2"
                     /gene_synonym="AE2; BND3L; EPB3L1; FLJ59028; HKB3; NBND3"
                     /note="isoform 2 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="anion exchange protein 2 isoform 2"
                     /protein_id="NP_001186622.1"
                     /db_xref="GI:314122222"
                     /db_xref="GeneID:6522"
                     /db_xref="HGNC:11028"
                     /db_xref="MIM:109280"
                     /db_xref="HPRD:02728"
     mRNA            join(150759739..150760276,150761289..150761454,
                     150761613..150761854,150761935..150762053,
                     150763604..150763848,150763938..150764080,
                     150764961..150765141,150767034..150767169,
                     150767268..150767433,150767544..150767658,
                     150767814..150767998,150768159..150768384,
                     150768477..150768692,150768776..150768924,
                     150769029..150769223,150771126..150771380,
                     150771486..150771575,150771762..150771928,
                     150772342..150772595,150772693..150772862,
                     150773100..150773273,150773374..150773614)
                     /gene="SLC4A2"
                     /gene_synonym="AE2; BND3L; EPB3L1; FLJ59028; HKB3; NBND3"
                     /product="solute carrier family 4, anion exchanger, member
                     2 (erythrocyte membrane protein band 3-like 1), transcript
                     variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001199694.1"
                     /db_xref="GI:314122223"
                     /db_xref="GeneID:6522"
                     /db_xref="HGNC:11028"
                     /db_xref="MIM:109280"
                     /db_xref="HPRD:02728"
     CDS             join(150760268..150760276,150761289..150761454,
                     150761613..150761854,150761935..150762053,
                     150763604..150763848,150763938..150764080,
                     150764961..150765141,150767034..150767169,
                     150767268..150767433,150767544..150767658,
                     150767814..150767998,150768159..150768384,
                     150768477..150768692,150768776..150768924,
                     150769029..150769223,150771126..150771380,
                     150771486..150771575,150771762..150771928,
                     150772342..150772595,150772693..150772862,
                     150773100..150773273,150773374..150773454)
                     /gene="SLC4A2"
                     /gene_synonym="AE2; BND3L; EPB3L1; FLJ59028; HKB3; NBND3"
                     /note="isoform 3 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="anion exchange protein 2 isoform 3"
                     /protein_id="NP_001186623.1"
                     /db_xref="GI:314122224"
                     /db_xref="GeneID:6522"
                     /db_xref="HGNC:11028"
                     /db_xref="MIM:109280"
                     /db_xref="HPRD:02728"
     gene            complement(150773708..150777951)
                     /gene="FASTK"
                     /gene_synonym="FAST"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10922"
                     /db_xref="HGNC:24676"
                     /db_xref="HPRD:07368"
                     /db_xref="MIM:606965"
     mRNA            complement(join(150773708..150773919,150774000..150774114,
                     150774188..150774323,150774397..150774488,
                     150774708..150774867,150774966..150775179,
                     150775649..150775788,150775929..150776108,
                     150776587..150777009,150777772..150777951))
                     /gene="FASTK"
                     /gene_synonym="FAST"
                     /product="Fas-activated serine/threonine kinase,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_006712.3"
                     /db_xref="GI:39995105"
                     /db_xref="GeneID:10922"
                     /db_xref="HGNC:24676"
                     /db_xref="HPRD:07368"
                     /db_xref="MIM:606965"
     mRNA            complement(join(150773708..150773919,150774000..150774114,
                     150774188..150774323,150774397..150774488,
                     150774708..150774867,150774966..150775179,
                     150775649..150775788,150775929..150776108,
                     150777772..150777951))
                     /gene="FASTK"
                     /gene_synonym="FAST"
                     /product="Fas-activated serine/threonine kinase,
                     transcript variant 4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_033015.2"
                     /db_xref="GI:39995106"
                     /db_xref="GeneID:10922"
                     /db_xref="HGNC:24676"
                     /db_xref="MIM:606965"
                     /db_xref="HPRD:07368"
     CDS             complement(join(150773812..150773919,150774000..150774114,
                     150774188..150774323,150774397..150774488,
                     150774708..150774867,150774966..150775179,
                     150775649..150775788,150775929..150776108,
                     150776587..150777009,150777772..150777853))
                     /gene="FASTK"
                     /gene_synonym="FAST"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="fas-activated serine/threonine kinase isoform 1"
                     /protein_id="NP_006703.1"
                     /db_xref="GI:5729822"
                     /db_xref="CCDS:CCDS5918.1"
                     /db_xref="GeneID:10922"
                     /db_xref="HGNC:24676"
                     /db_xref="HPRD:07368"
                     /db_xref="MIM:606965"
     CDS             complement(join(150773812..150773919,150774000..150774114,
                     150774188..150774323,150774397..150774488,
                     150774708..150774867,150774966..150775179,
                     150775649..150775788,150775929..150776108,
                     150777772..150777853))
                     /gene="FASTK"
                     /gene_synonym="FAST"
                     /note="isoform 4 is encoded by transcript variant 4;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="fas-activated serine/threonine kinase isoform 4"
                     /protein_id="NP_148936.2"
                     /db_xref="GI:39995107"
                     /db_xref="CCDS:CCDS5919.1"
                     /db_xref="GeneID:10922"
                     /db_xref="HGNC:24676"
                     /db_xref="HPRD:07368"
                     /db_xref="MIM:606965"
     gene            complement(150778172..150780620)
                     /gene="TMUB1"
                     /gene_synonym="C7orf21; MGC5442; SB144"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:83590"
                     /db_xref="HGNC:21709"
     mRNA            complement(join(150778172..150778987,150779262..150779680,
                     150780521..150780620))
                     /gene="TMUB1"
                     /gene_synonym="C7orf21; MGC5442; SB144"
                     /product="transmembrane and ubiquitin-like domain
                     containing 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001136044.1"
                     /db_xref="GI:209862888"
                     /db_xref="GeneID:83590"
                     /db_xref="HGNC:21709"
     mRNA            complement(join(150778172..150778987,150779262..150779680,
                     150779851..150780413))
                     /gene="TMUB1"
                     /gene_synonym="C7orf21; MGC5442; SB144"
                     /product="transmembrane and ubiquitin-like domain
                     containing 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_031434.3"
                     /db_xref="GI:217035134"
                     /db_xref="GeneID:83590"
                     /db_xref="HGNC:21709"
                     /db_xref="HPRD:12910"
     CDS             complement(join(150778636..150778987,
                     150779262..150779650))
                     /gene="TMUB1"
                     /gene_synonym="C7orf21; MGC5442; SB144"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane and ubiquitin-like
                     domain-containing protein 1 isoform 1"
                     /protein_id="NP_113622.1"
                     /db_xref="GI:13899257"
                     /db_xref="CCDS:CCDS5920.1"
                     /db_xref="GeneID:83590"
                     /db_xref="HGNC:21709"
     CDS             complement(join(150778636..150778987,
                     150779262..150779650))
                     /gene="TMUB1"
                     /gene_synonym="C7orf21; MGC5442; SB144"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="transmembrane and ubiquitin-like
                     domain-containing protein 1 isoform 2"
                     /protein_id="NP_001129516.1"
                     /db_xref="GI:209862889"
                     /db_xref="CCDS:CCDS5920.1"
                     /db_xref="GeneID:83590"
                     /db_xref="HGNC:21709"
     gene            150783826..150841523
                     /gene="AGAP3"
                     /gene_synonym="CENTG3; CRAG; FLJ16146; FLJ34452; MRIP-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:116988"
                     /db_xref="HGNC:16923"
                     /db_xref="HPRD:16707"
     mRNA            join(150783826..150784159,150813880..150813938,
                     150814182..150814269,150814458..150814543,
                     150814723..150814864,150815297..150815431,
                     150815592..150815719,150817074..150817232,
                     150820881..150820973,150825667..150825771,
                     150831487..150831655,150835230..150835400,
                     150837066..150837203,150838985..150839139,
                     150839250..150839340,150839499..150839721,
                     150840428..150840683,150840824..150841523)
                     /gene="AGAP3"
                     /gene_synonym="CENTG3; CRAG; FLJ16146; FLJ34452; MRIP-1"
                     /product="ArfGAP with GTPase domain, ankyrin repeat and PH
                     domain 3, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_031946.4"
                     /db_xref="GI:110227612"
                     /db_xref="GeneID:116988"
                     /db_xref="HGNC:16923"
                     /db_xref="HPRD:16707"
     mRNA            join(150783826..150784159,150813880..150813938,
                     150814182..150814269,150814458..150814543,
                     150814723..150814864,150815297..150815431,
                     150815592..150815719,150817074..150817232,
                     150819812..150820725)
                     /gene="AGAP3"
                     /gene_synonym="CENTG3; CRAG; FLJ16146; FLJ34452; MRIP-1"
                     /product="ArfGAP with GTPase domain, ankyrin repeat and PH
                     domain 3, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001042535.1"
                     /db_xref="GI:110227616"
                     /db_xref="GeneID:116988"
                     /db_xref="HGNC:16923"
                     /db_xref="HPRD:16707"
     CDS             join(150783829..150784159,150813880..150813938,
                     150814182..150814269,150814458..150814543,
                     150814723..150814864,150815297..150815431,
                     150815592..150815719,150817074..150817232,
                     150820881..150820973,150825667..150825771,
                     150831487..150831655,150835230..150835400,
                     150837066..150837203,150838985..150839139,
                     150839250..150839340,150839499..150839721,
                     150840428..150840683,150840824..150841030)
                     /gene="AGAP3"
                     /gene_synonym="CENTG3; CRAG; FLJ16146; FLJ34452; MRIP-1"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="arf-GAP with GTPase, ANK repeat and PH
                     domain-containing protein 3 isoform a"
                     /protein_id="NP_114152.3"
                     /db_xref="GI:110227613"
                     /db_xref="CCDS:CCDS43681.1"
                     /db_xref="GeneID:116988"
                     /db_xref="HGNC:16923"
                     /db_xref="HPRD:16707"
     CDS             join(150783829..150784159,150813880..150813938,
                     150814182..150814269,150814458..150814543,
                     150814723..150814864,150815297..150815431,
                     150815592..150815719,150817074..150817232,
                     150819812..150819874)
                     /gene="AGAP3"
                     /gene_synonym="CENTG3; CRAG; FLJ16146; FLJ34452; MRIP-1"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="arf-GAP with GTPase, ANK repeat and PH
                     domain-containing protein 3 isoform b"
                     /protein_id="NP_001036000.1"
                     /db_xref="GI:110227617"
                     /db_xref="CCDS:CCDS55185.1"
                     /db_xref="GeneID:116988"
                     /db_xref="HGNC:16923"
                     /db_xref="HPRD:16707"
     gene            complement(150845676..150864867)
                     /gene="GBX1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2636"
                     /db_xref="HGNC:4185"
                     /db_xref="MIM:603354"
     mRNA            complement(join(150845676..150846229,
                     150864098..150864867))
                     /gene="GBX1"
                     /product="gastrulation brain homeobox 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001098834.1"
                     /db_xref="GI:149588929"
                     /db_xref="GeneID:2636"
                     /db_xref="HGNC:4185"
                     /db_xref="MIM:603354"
     CDS             complement(join(150845676..150846229,
                     150864098..150864635))
                     /gene="GBX1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein GBX-1"
                     /protein_id="NP_001092304.1"
                     /db_xref="GI:149588930"
                     /db_xref="CCDS:CCDS43682.1"
                     /db_xref="GeneID:2636"
                     /db_xref="HGNC:4185"
                     /db_xref="MIM:603354"
     gene            complement(150872785..150884919)
                     /gene="ASB10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:136371"
                     /db_xref="HGNC:17185"
     mRNA            complement(join(150872785..150873053,150873199..150873384,
                     150873650..150873763,150878026..150878545,
                     150883479..150883746,150884539..150884919))
                     /gene="ASB10"
                     /product="ankyrin repeat and SOCS box containing 10,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_080871.3"
                     /db_xref="GI:215598805"
                     /db_xref="GeneID:136371"
                     /db_xref="HGNC:17185"
     mRNA            complement(join(150872785..150873053,150873199..150873384,
                     150873650..150873763,150878026..150878545,
                     150883479..150883746,150883902..150884478))
                     /gene="ASB10"
                     /product="ankyrin repeat and SOCS box containing 10,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001142459.1"
                     /db_xref="GI:215598818"
                     /db_xref="GeneID:136371"
                     /db_xref="HGNC:17185"
     mRNA            complement(join(150872785..150873053,150873199..150873384,
                     150878026..150878545,150883479..150883746,
                     150883902..150884478))
                     /gene="ASB10"
                     /product="ankyrin repeat and SOCS box containing 10,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001142460.1"
                     /db_xref="GI:215598823"
                     /db_xref="GeneID:136371"
                     /db_xref="HGNC:17185"
     CDS             complement(join(150873199..150873384,150873650..150873763,
                     150878026..150878545,150883479..150883746,
                     150884539..150884809))
                     /gene="ASB10"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ankyrin repeat and SOCS box protein 10 isoform
                     3"
                     /protein_id="NP_543147.2"
                     /db_xref="GI:215598806"
                     /db_xref="CCDS:CCDS5921.2"
                     /db_xref="GeneID:136371"
                     /db_xref="HGNC:17185"
     CDS             complement(join(150873199..150873384,150873650..150873763,
                     150878026..150878545,150883479..150883746,
                     150883902..150884217))
                     /gene="ASB10"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ankyrin repeat and SOCS box protein 10 isoform
                     1"
                     /protein_id="NP_001135931.2"
                     /db_xref="GI:294337037"
                     /db_xref="CCDS:CCDS47750.2"
                     /db_xref="GeneID:136371"
                     /db_xref="HGNC:17185"
     CDS             complement(join(150873199..150873384,150878026..150878545,
                     150883479..150883746,150883902..150884217))
                     /gene="ASB10"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ankyrin repeat and SOCS box protein 10 isoform
                     2"
                     /protein_id="NP_001135932.2"
                     /db_xref="GI:294337038"
                     /db_xref="CCDS:CCDS47749.2"
                     /db_xref="GeneID:136371"
                     /db_xref="HGNC:17185"
     gene            complement(150887960..150889474)
                     /gene="IQCA1P1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 ESTs"
                     /pseudo
                     /db_xref="GeneID:392843"
                     /db_xref="HGNC:22831"
     misc_RNA        complement(join(150887960..150888174,150888725..150888963,
                     150889363..150889474))
                     /gene="IQCA1P1"
                     /product="IQ motif containing with AAA domain 1 pseudogene
                     1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 2 ESTs"
                     /pseudo
                     /transcript_id="XR_132530.1"
                     /db_xref="GI:341915409"
                     /db_xref="GeneID:392843"
                     /db_xref="HGNC:22831"
     gene            complement(150892673..150902582)
                     /gene="LOC100652970"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 EST"
                     /db_xref="GeneID:100652970"
     mRNA            complement(join(150892673..150892744,150893534..150893640,
                     150894908..150894960,150895884..150896089,
                     150897221..150897268,150897469..150897540,
                     150899997..150900182,150900481..150900600,
                     150901595..150901922,150902530..150902582))
                     /gene="LOC100652970"
                     /product="putative IQ and AAA domain-containing protein
                     1-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 EST"
                     /transcript_id="XM_003403442.1"
                     /db_xref="GI:341915410"
                     /db_xref="GeneID:100652970"
     CDS             complement(join(150892673..150892744,150893534..150893640,
                     150894908..150894960,150895884..150896089,
                     150897221..150897268,150897469..150897540,
                     150899997..150900182,150900481..150900600,
                     150901595..150901922,150902530..150902540))
                     /gene="LOC100652970"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /codon_start=1
                     /product="putative IQ and AAA domain-containing protein
                     1-like"
                     /protein_id="XP_003403490.1"
                     /db_xref="GI:341915411"
                     /db_xref="GeneID:100652970"
     gene            complement(150904923..150924317)
                     /gene="ABCF2"
                     /gene_synonym="ABC28; DKFZp586K1823; EST133090; HUSSY-18;
                     HUSSY18; M-ABC1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10061"
                     /db_xref="HGNC:71"
                     /db_xref="HPRD:12403"
                     /db_xref="MIM:612510"
     mRNA            complement(join(150904923..150905193,150911144..150911277,
                     150911965..150912168,150912690..150912818,
                     150913053..150913115,150915167..150915277,
                     150915647..150915736,150915840..150915959,
                     150916150..150916245,150918664..150918766,
                     150919607..150919702,150920764..150920935,
                     150921018..150921200,150921862..150922074,
                     150923391..150923586,150924249..150924317))
                     /gene="ABCF2"
                     /gene_synonym="ABC28; DKFZp586K1823; EST133090; HUSSY-18;
                     HUSSY18; M-ABC1"
                     /product="ATP-binding cassette, sub-family F (GCN20),
                     member 2, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005692.3"
                     /db_xref="GI:27881504"
                     /db_xref="GeneID:10061"
                     /db_xref="HGNC:71"
                     /db_xref="HPRD:12403"
                     /db_xref="MIM:612510"
     CDS             complement(join(150905157..150905193,150911144..150911277,
                     150911965..150912168,150912690..150912818,
                     150913053..150913115,150915167..150915277,
                     150915647..150915736,150915840..150915959,
                     150916150..150916245,150918664..150918766,
                     150919607..150919702,150920764..150920935,
                     150921018..150921200,150921862..150922074,
                     150923391..150923544))
                     /gene="ABCF2"
                     /gene_synonym="ABC28; DKFZp586K1823; EST133090; HUSSY-18;
                     HUSSY18; M-ABC1"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ATP-binding cassette sub-family F member 2
                     isoform b"
                     /protein_id="NP_005683.2"
                     /db_xref="GI:10947137"
                     /db_xref="CCDS:CCDS5922.1"
                     /db_xref="GeneID:10061"
                     /db_xref="HGNC:71"
                     /db_xref="HPRD:12403"
                     /db_xref="MIM:612510"
     mRNA            complement(join(150909576..150911277,150911965..150912168,
                     150912690..150912818,150913053..150913115,
                     150915167..150915277,150915647..150915736,
                     150915840..150915959,150916150..150916245,
                     150918664..150918766,150919607..150919702,
                     150920764..150920935,150921018..150921200,
                     150921862..150922074,150923391..150923586,
                     150924249..150924317))
                     /gene="ABCF2"
                     /gene_synonym="ABC28; DKFZp586K1823; EST133090; HUSSY-18;
                     HUSSY18; M-ABC1"
                     /product="ATP-binding cassette, sub-family F (GCN20),
                     member 2, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_007189.1"
                     /db_xref="GI:27881505"
                     /db_xref="GeneID:10061"
                     /db_xref="HGNC:71"
                     /db_xref="MIM:612510"
                     /db_xref="HPRD:12403"
     CDS             complement(join(150911140..150911277,150911965..150912168,
                     150912690..150912818,150913053..150913115,
                     150915167..150915277,150915647..150915736,
                     150915840..150915959,150916150..150916245,
                     150918664..150918766,150919607..150919702,
                     150920764..150920935,150921018..150921200,
                     150921862..150922074,150923391..150923544))
                     /gene="ABCF2"
                     /gene_synonym="ABC28; DKFZp586K1823; EST133090; HUSSY-18;
                     HUSSY18; M-ABC1"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ATP-binding cassette sub-family F member 2
                     isoform a"
                     /protein_id="NP_009120.1"
                     /db_xref="GI:27881506"
                     /db_xref="CCDS:CCDS5923.1"
                     /db_xref="GeneID:10061"
                     /db_xref="HGNC:71"
                     /db_xref="HPRD:12403"
                     /db_xref="MIM:612510"
     gene            150929585..150935905
                     /gene="CHPF2"
                     /gene_synonym="ChSy-3; CSGLCA-T; CSGlcAT; KIAA1402"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54480"
                     /db_xref="HGNC:29270"
                     /db_xref="HPRD:10474"
                     /db_xref="MIM:608037"
     mRNA            join(150929585..150931360,150932134..150932698,
                     150933494..150933676,150934460..150935905)
                     /gene="CHPF2"
                     /gene_synonym="ChSy-3; CSGLCA-T; CSGlcAT; KIAA1402"
                     /product="chondroitin polymerizing factor 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_019015.1"
                     /db_xref="GI:48717494"
                     /db_xref="GeneID:54480"
                     /db_xref="HGNC:29270"
                     /db_xref="HPRD:10474"
                     /db_xref="MIM:608037"
     CDS             join(150931098..150931360,150932134..150932698,
                     150933494..150933676,150934460..150935767)
                     /gene="CHPF2"
                     /gene_synonym="ChSy-3; CSGLCA-T; CSGlcAT; KIAA1402"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="chondroitin sulfate glucuronyltransferase"
                     /protein_id="NP_061888.1"
                     /db_xref="GI:48717495"
                     /db_xref="CCDS:CCDS34779.1"
                     /db_xref="GeneID:54480"
                     /db_xref="HGNC:29270"
                     /db_xref="HPRD:10474"
                     /db_xref="MIM:608037"
     gene            150935507..150935624
                     /gene="MIR671"
                     /gene_synonym="hsa-mir-671; MIRN671"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:768213"
                     /db_xref="HGNC:33134"
                     /db_xref="miRBase:MI0003760"
     ncRNA           150935507..150935624
                     /gene="MIR671"
                     /gene_synonym="hsa-mir-671; MIRN671"
                     /ncRNA_class="miRNA"
                     /product="microRNA 671"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_030407.1"
                     /db_xref="GI:262206365"
                     /db_xref="GeneID:768213"
                     /db_xref="HGNC:33134"
                     /db_xref="miRBase:MI0003760"
     ncRNA           150935507..150935624
                     /gene="MIR671"
                     /gene_synonym="hsa-mir-671; MIRN671"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-671"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:768213"
                     /db_xref="miRBase:MI0003760"
                     /db_xref="HGNC:33134"
     gene            complement(150936059..150974231)
                     /gene="SMARCD3"
                     /gene_synonym="BAF60C; CRACD3; MGC111010; Rsc6p"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6604"
                     /db_xref="HGNC:11108"
                     /db_xref="HPRD:03440"
                     /db_xref="MIM:601737"
     mRNA            complement(join(150936059..150936242,150936482..150936583,
                     150936710..150936832,150937198..150937333,
                     150937511..150937608,150938578..150938739,
                     150938963..150939064,150939223..150939318,
                     150939567..150939689,150939807..150939929,
                     150940745..150940787,150942546..150942757,
                     150972200..150972337,150974163..150974231))
                     /gene="SMARCD3"
                     /gene_synonym="BAF60C; CRACD3; MGC111010; Rsc6p"
                     /product="SWI/SNF related, matrix associated, actin
                     dependent regulator of chromatin, subfamily d, member 3,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003078.3"
                     /db_xref="GI:51477705"
                     /db_xref="GeneID:6604"
                     /db_xref="HGNC:11108"
                     /db_xref="HPRD:03440"
                     /db_xref="MIM:601737"
     mRNA            complement(join(150936059..150936242,150936482..150936583,
                     150936710..150936832,150937198..150937333,
                     150937511..150937608,150938578..150938739,
                     150938963..150939064,150939223..150939318,
                     150939567..150939689,150939807..150939929,
                     150940745..150940787,150942546..150942757,
                     150972200..150972337,150973791..150973820))
                     /gene="SMARCD3"
                     /gene_synonym="BAF60C; CRACD3; MGC111010; Rsc6p"
                     /product="SWI/SNF related, matrix associated, actin
                     dependent regulator of chromatin, subfamily d, member 3,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001003802.1"
                     /db_xref="GI:51477703"
                     /db_xref="GeneID:6604"
                     /db_xref="HGNC:11108"
                     /db_xref="MIM:601737"
                     /db_xref="HPRD:03440"
     mRNA            complement(join(150936059..150936242,150936482..150936583,
                     150936710..150936832,150937198..150937333,
                     150937511..150937608,150938578..150938739,
                     150938963..150939064,150939223..150939318,
                     150939567..150939689,150939807..150939929,
                     150940745..150940787,150942546..150942757,
                     150945571..150945749))
                     /gene="SMARCD3"
                     /gene_synonym="BAF60C; CRACD3; MGC111010; Rsc6p"
                     /product="SWI/SNF related, matrix associated, actin
                     dependent regulator of chromatin, subfamily d, member 3,
                     transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001003801.1"
                     /db_xref="GI:51477701"
                     /db_xref="GeneID:6604"
                     /db_xref="HGNC:11108"
                     /db_xref="HPRD:03440"
                     /db_xref="MIM:601737"
     CDS             complement(join(150936189..150936242,150936482..150936583,
                     150936710..150936832,150937198..150937333,
                     150937511..150937608,150938578..150938739,
                     150938963..150939064,150939223..150939318,
                     150939567..150939689,150939807..150939929,
                     150940745..150940787,150942546..150942757,
                     150972200..150972238))
                     /gene="SMARCD3"
                     /gene_synonym="BAF60C; CRACD3; MGC111010; Rsc6p"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="SWI/SNF-related matrix-associated
                     actin-dependent regulator of chromatin subfamily D member
                     3 isoform 1"
                     /protein_id="NP_001003802.1"
                     /db_xref="GI:51477704"
                     /db_xref="CCDS:CCDS5924.1"
                     /db_xref="GeneID:6604"
                     /db_xref="HGNC:11108"
                     /db_xref="HPRD:03440"
                     /db_xref="MIM:601737"
     CDS             complement(join(150936189..150936242,150936482..150936583,
                     150936710..150936832,150937198..150937333,
                     150937511..150937608,150938578..150938739,
                     150938963..150939064,150939223..150939318,
                     150939567..150939689,150939807..150939929,
                     150940745..150940787,150942546..150942757,
                     150972200..150972238))
                     /gene="SMARCD3"
                     /gene_synonym="BAF60C; CRACD3; MGC111010; Rsc6p"
                     /note="isoform 1 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="SWI/SNF-related matrix-associated
                     actin-dependent regulator of chromatin subfamily D member
                     3 isoform 1"
                     /protein_id="NP_003069.2"
                     /db_xref="GI:21264353"
                     /db_xref="CCDS:CCDS5924.1"
                     /db_xref="GeneID:6604"
                     /db_xref="HGNC:11108"
                     /db_xref="HPRD:03440"
                     /db_xref="MIM:601737"
     CDS             complement(join(150936189..150936242,150936482..150936583,
                     150936710..150936832,150937198..150937333,
                     150937511..150937608,150938578..150938739,
                     150938963..150939064,150939223..150939318,
                     150939567..150939689,150939807..150939929,
                     150940745..150940787,150942546..150942757,
                     150945571..150945648))
                     /gene="SMARCD3"
                     /gene_synonym="BAF60C; CRACD3; MGC111010; Rsc6p"
                     /note="isoform 2 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="SWI/SNF-related matrix-associated
                     actin-dependent regulator of chromatin subfamily D member
                     3 isoform 2"
                     /protein_id="NP_001003801.1"
                     /db_xref="GI:51477702"
                     /db_xref="CCDS:CCDS34780.1"
                     /db_xref="GeneID:6604"
                     /db_xref="HGNC:11108"
                     /db_xref="HPRD:03440"
                     /db_xref="MIM:601737"
     gene            151038858..151075535
                     /gene="NUB1"
                     /gene_synonym="BS4; NUB1L; NYREN18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51667"
                     /db_xref="HGNC:17623"
                     /db_xref="HPRD:07450"
                     /db_xref="MIM:607981"
     mRNA            join(151038858..151038932,151042434..151042552,
                     151046159..151046326,151048510..151048568,
                     151049898..151049968,151052854..151053036,
                     151053214..151053308,151057227..151057333,
                     151064025..151064211,151064947..151065054,
                     151065821..151065973,151071183..151071287,
                     151072934..151073029,151073720..151073897,
                     151074133..151075535)
                     /gene="NUB1"
                     /gene_synonym="BS4; NUB1L; NYREN18"
                     /product="negative regulator of ubiquitin-like proteins 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016118.3"
                     /db_xref="GI:32483375"
                     /db_xref="GeneID:51667"
                     /db_xref="HGNC:17623"
                     /db_xref="HPRD:07450"
                     /db_xref="MIM:607981"
     CDS             join(151042436..151042552,151046159..151046326,
                     151048510..151048568,151049898..151049968,
                     151052854..151053036,151053214..151053308,
                     151057227..151057333,151064025..151064211,
                     151064947..151065054,151065821..151065973,
                     151071183..151071287,151072934..151073029,
                     151073720..151073897,151074133..151074311)
                     /gene="NUB1"
                     /gene_synonym="BS4; NUB1L; NYREN18"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="NEDD8 ultimate buster 1"
                     /protein_id="NP_057202.2"
                     /db_xref="GI:19923477"
                     /db_xref="CCDS:CCDS47751.1"
                     /db_xref="GeneID:51667"
                     /db_xref="HGNC:17623"
                     /db_xref="HPRD:07450"
                     /db_xref="MIM:607981"
     gene            complement(151078207..151107124)
                     /gene="WDR86"
                     /gene_synonym="FLJ51355; MGC129839"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:349136"
                     /db_xref="HGNC:28020"
                     /db_xref="HPRD:14183"
     mRNA            complement(join(151078207..151078832,151078964..151079067,
                     151082174..151082309,151092862..151093282,
                     151097186..151097327,151106513..151107124))
                     /gene="WDR86"
                     /gene_synonym="FLJ51355; MGC129839"
                     /product="WD repeat domain 86"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198285.2"
                     /db_xref="GI:157266265"
                     /db_xref="GeneID:349136"
                     /db_xref="HGNC:28020"
                     /db_xref="HPRD:14183"
     CDS             complement(join(151078668..151078832,151078964..151079067,
                     151082174..151082309,151092862..151093282,
                     151097186..151097327,151106513..151106675))
                     /gene="WDR86"
                     /gene_synonym="FLJ51355; MGC129839"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="WD repeat-containing protein 86"
                     /protein_id="NP_938026.2"
                     /db_xref="GI:157266266"
                     /db_xref="CCDS:CCDS5925.2"
                     /db_xref="GeneID:349136"
                     /db_xref="HGNC:28020"
                     /db_xref="HPRD:14183"
     gene            complement(151103955..151106058)
                     /gene="LOC100507673"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 8 ESTs"
                     /db_xref="GeneID:100507673"
     misc_RNA        complement(join(151103955..151104706,
                     151105573..151106058))
                     /gene="LOC100507673"
                     /product="hypothetical LOC100507673"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 8 ESTs"
                     /transcript_id="XR_108790.1"
                     /db_xref="GI:310120123"
                     /db_xref="GeneID:100507673"
     gene            151106322..151110134
                     /gene="LOC100131176"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100131176"
     misc_RNA        join(151106322..151106468,151108314..151108398,
                     151108756..151108878,151109053..151109156,
                     151109805..151110134)
                     /gene="LOC100131176"
                     /product="hypothetical LOC100131176"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_034012.1"
                     /db_xref="GI:300244556"
                     /db_xref="GeneID:100131176"
     misc_RNA        join(151106322..151106468,151108756..151108878,
                     151109053..151109156,151109805..151110134)
                     /gene="LOC100131176"
                     /product="hypothetical LOC100131176"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_034013.1"
                     /db_xref="GI:300244557"
                     /db_xref="GeneID:100131176"
     gene            complement(151127056..151137099)
                     /gene="CRYGN"
                     /gene_synonym="MGC119042; MGC119043; MGC119044; MGC119045"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:155051"
                     /db_xref="HGNC:20458"
                     /db_xref="HPRD:16761"
                     /db_xref="MIM:609603"
     mRNA            complement(join(151127056..151127266,151133266..151133411,
                     151135082..151135330,151136983..151137099))
                     /gene="CRYGN"
                     /gene_synonym="MGC119042; MGC119043; MGC119044; MGC119045"
                     /product="crystallin, gamma N"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_144727.1"
                     /db_xref="GI:21389516"
                     /db_xref="GeneID:155051"
                     /db_xref="HGNC:20458"
                     /db_xref="HPRD:16761"
                     /db_xref="MIM:609603"
     CDS             complement(join(151127134..151127266,151133266..151133411,
                     151135082..151135330,151136983..151137003))
                     /gene="CRYGN"
                     /gene_synonym="MGC119042; MGC119043; MGC119044; MGC119045"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="gamma-crystallin N"
                     /protein_id="NP_653328.1"
                     /db_xref="GI:21389517"
                     /db_xref="CCDS:CCDS5926.1"
                     /db_xref="GeneID:155051"
                     /db_xref="HGNC:20458"
                     /db_xref="HPRD:16761"
                     /db_xref="MIM:609603"
     gene            complement(151130575..151130725)
                     /gene="MIR3907"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100500835"
                     /db_xref="HGNC:38988"
                     /db_xref="miRBase:MI0016410"
     ncRNA           complement(151130575..151130725)
                     /gene="MIR3907"
                     /ncRNA_class="miRNA"
                     /product="microRNA 3907"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_037468.1"
                     /db_xref="GI:312147066"
                     /db_xref="GeneID:100500835"
                     /db_xref="HGNC:38988"
                     /db_xref="miRBase:MI0016410"
     gene            complement(151163098..151217010)
                     /gene="RHEB"
                     /gene_synonym="MGC111559; RHEB2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6009"
                     /db_xref="HGNC:10011"
                     /db_xref="HPRD:03188"
                     /db_xref="MIM:601293"
     mRNA            complement(join(151163098..151164297,151167657..151167738,
                     151168480..151168527,151168635..151168691,
                     151174419..151174501,151181823..151181890,
                     151188029..151188100,151216546..151217010))
                     /gene="RHEB"
                     /gene_synonym="MGC111559; RHEB2"
                     /product="Ras homolog enriched in brain"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005614.3"
                     /db_xref="GI:100913214"
                     /db_xref="GeneID:6009"
                     /db_xref="HGNC:10011"
                     /db_xref="HPRD:03188"
                     /db_xref="MIM:601293"
     CDS             complement(join(151164205..151164297,151167657..151167738,
                     151168480..151168527,151168635..151168691,
                     151174419..151174501,151181823..151181890,
                     151188029..151188100,151216546..151216597))
                     /gene="RHEB"
                     /gene_synonym="MGC111559; RHEB2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="GTP-binding protein Rheb precursor"
                     /protein_id="NP_005605.1"
                     /db_xref="GI:5032041"
                     /db_xref="CCDS:CCDS5927.1"
                     /db_xref="GeneID:6009"
                     /db_xref="HGNC:10011"
                     /db_xref="HPRD:03188"
                     /db_xref="MIM:601293"
     gene            151198918..151201398
                     /gene="ETF1P2"
                     /gene_synonym="SUP45L3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:6825"
                     /db_xref="HGNC:3479"
     gene            complement(151253200..151574316)
                     /gene="PRKAG2"
                     /gene_synonym="AAKG; AAKG2; CMH6; H91620p; WPWS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51422"
                     /db_xref="HGNC:9386"
                     /db_xref="MIM:602743"
     mRNA            complement(join(151253200..151254318,151257610..151257703,
                     151261164..151261310,151262432..151262469,
                     151262806..151262971,151265802..151265928,
                     151267257..151267311,151269750..151269795,
                     151271977..151272035,151273457..151273538,
                     151292431..151292540,151329155..151329224,
                     151372506..151372723,151478238..151478517,
                     151483556..151483627,151573592..151574316))
                     /gene="PRKAG2"
                     /gene_synonym="AAKG; AAKG2; CMH6; H91620p; WPWS"
                     /product="protein kinase, AMP-activated, gamma 2
                     non-catalytic subunit, transcript variant a"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016203.3"
                     /db_xref="GI:100913190"
                     /db_xref="GeneID:51422"
                     /db_xref="HGNC:9386"
                     /db_xref="HPRD:04119"
                     /db_xref="MIM:602743"
     mRNA            complement(join(151253200..151254318,151257610..151257703,
                     151261164..151261310,151262432..151262469,
                     151262806..151262971,151265802..151265928,
                     151267257..151267311,151269750..151269795,
                     151271977..151272035,151273457..151273538,
                     151292431..151292540,151329155..151329224,
                     151372506..151372723,151478238..151478517,
                     151483556..151483627,151511502..151511957))
                     /gene="PRKAG2"
                     /gene_synonym="AAKG; AAKG2; CMH6; H91620p; WPWS"
                     /product="protein kinase, AMP-activated, gamma 2
                     non-catalytic subunit, transcript variant c"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040633.1"
                     /db_xref="GI:100913191"
                     /db_xref="GeneID:51422"
                     /db_xref="HGNC:9386"
                     /db_xref="MIM:602743"
     mRNA            complement(join(151253200..151254318,151257610..151257703,
                     151261164..151261310,151262432..151262469,
                     151262806..151262971,151265802..151265928,
                     151267257..151267311,151269750..151269795,
                     151271977..151272035,151273457..151273538,
                     151292431..151292540,151329155..151329344))
                     /gene="PRKAG2"
                     /gene_synonym="AAKG; AAKG2; CMH6; H91620p; WPWS"
                     /product="protein kinase, AMP-activated, gamma 2
                     non-catalytic subunit, transcript variant b"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024429.1"
                     /db_xref="GI:100913188"
                     /db_xref="GeneID:51422"
                     /db_xref="HGNC:9386"
                     /db_xref="MIM:602743"
     CDS             complement(join(151254287..151254318,151257610..151257703,
                     151261164..151261310,151262432..151262469,
                     151262806..151262971,151265802..151265928,
                     151267257..151267311,151269750..151269795,
                     151271977..151272035,151273457..151273538,
                     151292431..151292540,151329155..151329224,
                     151372506..151372723,151478238..151478517,
                     151483556..151483627,151573592..151573705))
                     /gene="PRKAG2"
                     /gene_synonym="AAKG; AAKG2; CMH6; H91620p; WPWS"
                     /note="isoform a is encoded by transcript variant a;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="5'-AMP-activated protein kinase subunit gamma-2
                     isoform a"
                     /protein_id="NP_057287.2"
                     /db_xref="GI:33186925"
                     /db_xref="CCDS:CCDS5928.1"
                     /db_xref="GeneID:51422"
                     /db_xref="HGNC:9386"
                     /db_xref="MIM:602743"
     CDS             complement(join(151254287..151254318,151257610..151257703,
                     151261164..151261310,151262432..151262469,
                     151262806..151262971,151265802..151265928,
                     151267257..151267311,151269750..151269795,
                     151271977..151272035,151273457..151273538,
                     151292431..151292540,151329155..151329224,
                     151372506..151372723,151478238..151478517,
                     151483556..151483609))
                     /gene="PRKAG2"
                     /gene_synonym="AAKG; AAKG2; CMH6; H91620p; WPWS"
                     /note="isoform c is encoded by transcript variant c;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="5'-AMP-activated protein kinase subunit gamma-2
                     isoform c"
                     /protein_id="NP_001035723.1"
                     /db_xref="GI:100913192"
                     /db_xref="CCDS:CCDS43683.1"
                     /db_xref="GeneID:51422"
                     /db_xref="HGNC:9386"
                     /db_xref="MIM:602743"
     CDS             complement(join(151254287..151254318,151257610..151257703,
                     151261164..151261310,151262432..151262469,
                     151262806..151262971,151265802..151265928,
                     151267257..151267311,151269750..151269795,
                     151271977..151272035,151273457..151273538,
                     151292431..151292540,151329155..151329185))
                     /gene="PRKAG2"
                     /gene_synonym="AAKG; AAKG2; CMH6; H91620p; WPWS"
                     /note="isoform b is encoded by transcript variant b;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="5'-AMP-activated protein kinase subunit gamma-2
                     isoform b"
                     /protein_id="NP_077747.1"
                     /db_xref="GI:100913189"
                     /db_xref="CCDS:CCDS47752.1"
                     /db_xref="GeneID:51422"
                     /db_xref="HGNC:9386"
                     /db_xref="MIM:602743"
     gene            151574127..151576308
                     /gene="LOC100505483"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100505483"
     misc_RNA        join(151574127..151574225,151574922..151574951,
                     151575647..151576308)
                     /gene="LOC100505483"
                     /product="hypothetical LOC100505483"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038926.1"
                     /db_xref="GI:336594917"
                     /db_xref="GeneID:100505483"
     gene            151653464..151717019
                     /gene="GALNTL5"
                     /gene_synonym="GALNT15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:168391"
                     /db_xref="HGNC:21725"
                     /db_xref="HPRD:13565"
     mRNA            join(151653464..151653694,151664293..151664578,
                     151668030..151668150,151680071..151680237,
                     151684244..151684366,151699799..151700048,
                     151704912..151705029,151711729..151711878,
                     151716731..151717019)
                     /gene="GALNTL5"
                     /gene_synonym="GALNT15"
                     /product="UDP-N-acetyl-alpha-D-galactosamine:polypeptide
                     N-acetylgalactosaminyltransferase-like 5, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_145292.3"
                     /db_xref="GI:281485546"
                     /db_xref="GeneID:168391"
                     /db_xref="HGNC:21725"
                     /db_xref="HPRD:13565"
     misc_RNA        join(151653464..151653694,151654868..151654971,
                     151664293..151664578,151668030..151668150,
                     151679926..151680237,151684244..151684366,
                     151699799..151700048,151704912..151705029,
                     151711729..151711878,151716731..151717019)
                     /gene="GALNTL5"
                     /gene_synonym="GALNT15"
                     /product="UDP-N-acetyl-alpha-D-galactosamine:polypeptide
                     N-acetylgalactosaminyltransferase-like 5, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_033169.1"
                     /db_xref="GI:281485548"
                     /db_xref="GeneID:168391"
                     /db_xref="HGNC:21725"
                     /db_xref="HPRD:13565"
     CDS             join(151664332..151664578,151668030..151668150,
                     151680071..151680237,151684244..151684366,
                     151699799..151700048,151704912..151705029,
                     151711729..151711878,151716731..151716886)
                     /gene="GALNTL5"
                     /gene_synonym="GALNT15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="putative polypeptide
                     N-acetylgalactosaminyltransferase-like protein 5"
                     /protein_id="NP_660335.2"
                     /db_xref="GI:281485547"
                     /db_xref="CCDS:CCDS5929.1"
                     /db_xref="GeneID:168391"
                     /db_xref="HGNC:21725"
                     /db_xref="HPRD:13565"
     gene            151722778..151819427
                     /gene="GALNT11"
                     /gene_synonym="FLJ21634; MGC71630"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:63917"
                     /db_xref="HGNC:19875"
                     /db_xref="HPRD:13560"
     mRNA            join(151722778..151722969,151791275..151791607,
                     151797883..151798006,151800197..151800363,
                     151802330..151802455,151805123..151805372,
                     151807613..151807730,151810331..151810483,
                     151814242..151814460,151815763..151815867,
                     151817916..151818053,151818631..151819427)
                     /gene="GALNT11"
                     /gene_synonym="FLJ21634; MGC71630"
                     /product="UDP-N-acetyl-alpha-D-galactosamine:polypeptide
                     N-acetylgalactosaminyltransferase 11 (GalNAc-T11)"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022087.2"
                     /db_xref="GI:153792094"
                     /db_xref="GeneID:63917"
                     /db_xref="HGNC:19875"
                     /db_xref="HPRD:13560"
     CDS             join(151791313..151791607,151797883..151798006,
                     151800197..151800363,151802330..151802455,
                     151805123..151805372,151807613..151807730,
                     151810331..151810483,151814242..151814460,
                     151815763..151815867,151817916..151818053,
                     151818631..151818762)
                     /gene="GALNT11"
                     /gene_synonym="FLJ21634; MGC71630"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="polypeptide N-acetylgalactosaminyltransferase
                     11"
                     /protein_id="NP_071370.2"
                     /db_xref="GI:153792095"
                     /db_xref="CCDS:CCDS5930.1"
                     /db_xref="GeneID:63917"
                     /db_xref="HGNC:19875"
                     /db_xref="HPRD:13560"
     gene            151825922..151826741
                     /gene="LOC100131012"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100131012"
     gene            complement(151832010..152133090)
                     /gene="MLL3"
                     /gene_synonym="DKFZp686C08112; FLJ12625; FLJ38309; HALR;
                     KIAA1506; KMT2C; MGC119851; MGC119852; MGC119853"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:58508"
                     /db_xref="HGNC:13726"
                     /db_xref="HPRD:06016"
                     /db_xref="MIM:606833"
     mRNA            complement(join(151832010..151834009,151835881..151835989,
                     151836271..151836344,151836760..151836876,
                     151841798..151841966,151842238..151842380,
                     151843684..151843820,151845118..151846237,
                     151847985..151848092,151848527..151848666,
                     151849790..151850039,151851095..151851231,
                     151851352..151851530,151852995..151853142,
                     151853290..151853431,151855948..151856157,
                     151859202..151860911,151864231..151864463,
                     151866271..151866334,151868349..151868427,
                     151871216..151871327,151873276..151875095,
                     151876919..151877211,151877796..151879679,
                     151880059..151880241,151882643..151882716,
                     151884347..151884561,151884800..151884932,
                     151891094..151891213,151891314..151891346,
                     151891525..151891653,151892992..151893096,
                     151896364..151896544,151900019..151900149,
                     151902191..151902310,151904385..151904513,
                     151917608..151917820,151919086..151919151,
                     151919658..151919767,151921100..151921264,
                     151921520..151921701,151927008..151927112,
                     151927305..151927406,151932902..151933018,
                     151935792..151935911,151944987..151945705,
                     151946961..151947038,151947938..151948051,
                     151949024..151949175,151949631..151949800,
                     151960101..151960215,151962123..151962294,
                     151970790..151970952,152007051..152007160,
                     152008883..152009031,152012223..152012423,
                     152027686..152027824,152055672..152055760,
                     152132711..152133090))
                     /gene="MLL3"
                     /gene_synonym="DKFZp686C08112; FLJ12625; FLJ38309; HALR;
                     KIAA1506; KMT2C; MGC119851; MGC119852; MGC119853"
                     /product="myeloid/lymphoid or mixed-lineage leukemia 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_170606.2"
                     /db_xref="GI:91718901"
                     /db_xref="GeneID:58508"
                     /db_xref="HGNC:13726"
                     /db_xref="HPRD:06016"
                     /db_xref="MIM:606833"
     CDS             complement(join(151833917..151834009,151835881..151835989,
                     151836271..151836344,151836760..151836876,
                     151841798..151841966,151842238..151842380,
                     151843684..151843820,151845118..151846237,
                     151847985..151848092,151848527..151848666,
                     151849790..151850039,151851095..151851231,
                     151851352..151851530,151852995..151853142,
                     151853290..151853431,151855948..151856157,
                     151859202..151860911,151864231..151864463,
                     151866271..151866334,151868349..151868427,
                     151871216..151871327,151873276..151875095,
                     151876919..151877211,151877796..151879679,
                     151880059..151880241,151882643..151882716,
                     151884347..151884561,151884800..151884932,
                     151891094..151891213,151891314..151891346,
                     151891525..151891653,151892992..151893096,
                     151896364..151896544,151900019..151900149,
                     151902191..151902310,151904385..151904513,
                     151917608..151917820,151919086..151919151,
                     151919658..151919767,151921100..151921264,
                     151921520..151921701,151927008..151927112,
                     151927305..151927406,151932902..151933018,
                     151935792..151935911,151944987..151945705,
                     151946961..151947038,151947938..151948051,
                     151949024..151949175,151949631..151949800,
                     151960101..151960215,151962123..151962294,
                     151970790..151970952,152007051..152007160,
                     152008883..152009031,152012223..152012423,
                     152027686..152027824,152055672..152055760,
                     152132711..152132871))
                     /gene="MLL3"
                     /gene_synonym="DKFZp686C08112; FLJ12625; FLJ38309; HALR;
                     KIAA1506; KMT2C; MGC119851; MGC119852; MGC119853"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="histone-lysine N-methyltransferase MLL3"
                     /protein_id="NP_733751.2"
                     /db_xref="GI:91718902"
                     /db_xref="CCDS:CCDS5931.1"
                     /db_xref="GeneID:58508"
                     /db_xref="HGNC:13726"
                     /db_xref="HPRD:06016"
                     /db_xref="MIM:606833"
     gene            152064592..152065572
                     /gene="SEPT7P6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100418720"
                     /db_xref="HGNC:38042"
     gene            152133980..152140101
                     /gene="FABP5P3"
                     /gene_synonym="FABP5L3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /db_xref="GeneID:220832"
                     /db_xref="HGNC:22573"
     misc_RNA        join(152133980..152134113,152139380..152140101)
                     /gene="FABP5P3"
                     /gene_synonym="FABP5L3"
                     /product="fatty acid binding protein 5 pseudogene 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /pseudo
                     /transcript_id="NR_002935.1"
                     /db_xref="GI:89941461"
                     /db_xref="GeneID:220832"
                     /db_xref="HGNC:22573"
     gene            152142302..152144354
                     /gene="CCT8L1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:155100"
                     /db_xref="HGNC:32153"
     gene            152161209..152162630
                     /gene="LOC100128822"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100128822"
     misc_RNA        152161209..152162630
                     /gene="LOC100128822"
                     /product="hypothetical LOC100128822"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_027387.1"
                     /db_xref="GI:225579107"
                     /db_xref="GeneID:100128822"
     gene            complement(152287631..152288149)
                     /gene="RPS20P19"
                     /gene_synonym="RPS20_7_863"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:644309"
                     /db_xref="HGNC:36503"
     gene            complement(152299239..152299600)
                     /gene="RPL36AP28"
                     /gene_synonym="RPL36A_10_864"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271509"
                     /db_xref="HGNC:36702"
     gene            complement(152343583..152373250)
                     /gene="XRCC2"
                     /gene_synonym="DKFZp781P0919"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7516"
                     /db_xref="HGNC:12829"
                     /db_xref="HPRD:02656"
                     /db_xref="MIM:600375"
     mRNA            complement(join(152343583..152346448,152357786..152357867,
                     152373126..152373250))
                     /gene="XRCC2"
                     /gene_synonym="DKFZp781P0919"
                     /product="X-ray repair complementing defective repair in
                     Chinese hamster cells 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005431.1"
                     /db_xref="GI:4885656"
                     /db_xref="GeneID:7516"
                     /db_xref="HGNC:12829"
                     /db_xref="HPRD:02656"
                     /db_xref="MIM:600375"
     CDS             complement(join(152345727..152346448,152357786..152357867,
                     152373126..152373164))
                     /gene="XRCC2"
                     /gene_synonym="DKFZp781P0919"
                     /note="Xrcc2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="DNA repair protein XRCC2"
                     /protein_id="NP_005422.1"
                     /db_xref="GI:4885657"
                     /db_xref="CCDS:CCDS5933.1"
                     /db_xref="GeneID:7516"
                     /db_xref="HGNC:12829"
                     /db_xref="HPRD:02656"
                     /db_xref="MIM:600375"
     gene            152446057..152446820
                     /gene="ATP5F1P3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:644333"
                     /db_xref="HGNC:39744"
     gene            152456851..152552463
                     /gene="ACTR3B"
                     /gene_synonym="ARP11; ARP3BETA; DKFZp686O24114"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57180"
                     /db_xref="HGNC:17256"
     mRNA            join(152456851..152457011,152480272..152480327,
                     152497616..152497740,152498706..152498816,
                     152511635..152511730,152513566..152513673,
                     152517384..152517527,152520427..152520600,
                     152522115..152522207,152549211..152549336,
                     152550579..152550662,152551543..152552463)
                     /gene="ACTR3B"
                     /gene_synonym="ARP11; ARP3BETA; DKFZp686O24114"
                     /product="ARP3 actin-related protein 3 homolog B (yeast),
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020445.4"
                     /db_xref="GI:92373412"
                     /db_xref="GeneID:57180"
                     /db_xref="HGNC:17256"
                     /db_xref="HPRD:12489"
     mRNA            join(152456851..152457011,152480272..152480327,
                     152497616..152497740,152498706..152498816,
                     152511635..152511730,152513566..152513673,
                     152517384..152517527,152520427..152520600,
                     152522115..152522207,152551543..152552463)
                     /gene="ACTR3B"
                     /gene_synonym="ARP11; ARP3BETA; DKFZp686O24114"
                     /product="ARP3 actin-related protein 3 homolog B (yeast),
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001040135.1"
                     /db_xref="GI:92373392"
                     /db_xref="GeneID:57180"
                     /db_xref="HGNC:17256"
     CDS             join(152456968..152457011,152480272..152480327,
                     152497616..152497740,152498706..152498816,
                     152511635..152511730,152513566..152513673,
                     152517384..152517527,152520427..152520600,
                     152522115..152522207,152549211..152549336,
                     152550579..152550662,152551543..152551638)
                     /gene="ACTR3B"
                     /gene_synonym="ARP11; ARP3BETA; DKFZp686O24114"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="actin-related protein 3B isoform 1"
                     /protein_id="NP_065178.1"
                     /db_xref="GI:9966913"
                     /db_xref="CCDS:CCDS5934.1"
                     /db_xref="GeneID:57180"
                     /db_xref="HGNC:17256"
     CDS             join(152456968..152457011,152480272..152480327,
                     152497616..152497740,152498706..152498816,
                     152511635..152511730,152513566..152513673,
                     152517384..152517527,152520427..152520600,
                     152522115..152522207,152551543..152551638)
                     /gene="ACTR3B"
                     /gene_synonym="ARP11; ARP3BETA; DKFZp686O24114"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="actin-related protein 3B isoform 2"
                     /protein_id="NP_001035225.1"
                     /db_xref="GI:92373393"
                     /db_xref="CCDS:CCDS34782.1"
                     /db_xref="GeneID:57180"
                     /db_xref="HGNC:17256"
     gene            153584419..>154264025
                     /gene="DPP6"
                     /gene_synonym="DPPX; FLJ55680; MGC46605; VF2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1804"
                     /db_xref="HGNC:3010"
                     /db_xref="HPRD:00525"
                     /db_xref="MIM:126141"
     mRNA            join(153584419..153584819,154143299..154143413,
                     154172024..154172122,154237617..154237711,
                     154263927..>154264025)
                     /gene="DPP6"
                     /gene_synonym="DPPX; FLJ55680; MGC46605; VF2"
                     /product="dipeptidyl-peptidase 6, transcript variant 3"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001039350.1"
                     /db_xref="GI:86792862"
                     /db_xref="GeneID:1804"
                     /db_xref="HGNC:3010"
                     /db_xref="MIM:126141"
                     /db_xref="HPRD:00525"
     CDS             join(153584769..153584819,154143299..154143413,
                     154172024..154172122,154237617..154237711,
                     154263927..>154264025)
                     /gene="DPP6"
                     /gene_synonym="DPPX; FLJ55680; MGC46605; VF2"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="dipeptidyl aminopeptidase-like protein 6 isoform
                     3"
                     /protein_id="NP_001034439.1"
                     /db_xref="GI:86792863"
                     /db_xref="GeneID:1804"
                     /db_xref="HGNC:3010"
                     /db_xref="MIM:126141"
                     /db_xref="HPRD:00525"
     mRNA            join(153749777..153750148,154143299..154143413,
                     154172024..154172122,154237617..154237711,
                     154263927..>154264025)
                     /gene="DPP6"
                     /gene_synonym="DPPX; FLJ55680; MGC46605; VF2"
                     /product="dipeptidyl-peptidase 6, transcript variant 1"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_130797.2"
                     /db_xref="GI:86792773"
                     /db_xref="GeneID:1804"
                     /db_xref="HGNC:3010"
                     /db_xref="HPRD:00525"
                     /db_xref="MIM:126141"
     CDS             join(153749906..153750148,154143299..154143413,
                     154172024..154172122,154237617..154237711,
                     154263927..>154264025)
                     /gene="DPP6"
                     /gene_synonym="DPPX; FLJ55680; MGC46605; VF2"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="dipeptidyl aminopeptidase-like protein 6 isoform
                     1"
                     /protein_id="NP_570629.2"
                     /db_xref="GI:86792774"
                     /db_xref="GeneID:1804"
                     /db_xref="HGNC:3010"
                     /db_xref="HPRD:00525"
                     /db_xref="MIM:126141"
     mRNA            join(154002347..154002636,154143299..154143413,
                     154172024..154172122,154237617..154237711,
                     154263927..>154264025)
                     /gene="DPP6"
                     /gene_synonym="DPPX; FLJ55680; MGC46605; VF2"
                     /product="dipeptidyl-peptidase 6, transcript variant 2"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001936.3"
                     /db_xref="GI:86792777"
                     /db_xref="GeneID:1804"
                     /db_xref="HGNC:3010"
                     /db_xref="HPRD:00525"
                     /db_xref="MIM:126141"
     CDS             join(154002580..154002636,154143299..154143413,
                     154172024..154172122,154237617..154237711,
                     154263927..>154264025)
                     /gene="DPP6"
                     /gene_synonym="DPPX; FLJ55680; MGC46605; VF2"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="dipeptidyl aminopeptidase-like protein 6 isoform
                     2"
                     /protein_id="NP_001927.3"
                     /db_xref="GI:86792778"
                     /db_xref="GeneID:1804"
                     /db_xref="HGNC:3010"
                     /db_xref="HPRD:00525"
                     /db_xref="MIM:126141"
     gap             154270635..154370634
                     /estimated_length=100000
     gene            <154400205..154685995
                     /gene="DPP6"
                     /gene_synonym="DPPX; FLJ55680; MGC46605; VF2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:1804"
                     /db_xref="HGNC:3010"
                     /db_xref="HPRD:00525"
                     /db_xref="MIM:126141"
     mRNA            join(<154400205..>154400234,<154406933..>154406941,
                     <154408704..>154408712,<154410635..>154410655,
                     <154416177..>154416188,<154420926..>154420940,
                     <154423535..>154423549,<154427453..154427461,
                     154429531..154429583,154461070..154461151,
                     154519477..154519597,154561127..154561281,
                     154564555..154564652,154585789..154585912,
                     154587555..154587593,154593065..154593172,
                     154595574..154595665,154596627..154596674,
                     154598704..154598822,154645490..154645537,
                     154659705..154659803,154664334..154664403,
                     154667616..154667810,154672598..154672652,
                     154677343..154677454,154679386..154679444,
                     154680982..154681054,154681167..154681240,
                     154684044..154685995)
                     /gene="DPP6"
                     /gene_synonym="DPPX; FLJ55680; MGC46605; VF2"
                     /product="dipeptidyl-peptidase 6, transcript variant 3"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001039350.1"
                     /db_xref="GI:86792862"
                     /db_xref="GeneID:1804"
                     /db_xref="HGNC:3010"
                     /db_xref="MIM:126141"
                     /db_xref="HPRD:00525"
     CDS             join(<154408704..>154408712,<154410635..>154410655,
                     <154416177..>154416188,<154420926..>154420940,
                     <154423535..>154423549,<154427453..154427461,
                     154429531..154429583,154461070..154461151,
                     154519477..154519597,154561127..154561281,
                     154564555..154564652,154585789..154585912,
                     154587555..154587593,154593065..154593172,
                     154595574..154595665,154596627..154596674,
                     154598704..154598822,154645490..154645537,
                     154659705..154659803,154664334..154664403,
                     154667616..154667810,154672598..154672652,
                     154677343..154677454,154679386..154679444,
                     154680982..154681054,154681167..154681240,
                     154684044..154684190)
                     /gene="DPP6"
                     /gene_synonym="DPPX; FLJ55680; MGC46605; VF2"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="dipeptidyl aminopeptidase-like protein 6 isoform
                     3"
                     /protein_id="NP_001034439.1"
                     /db_xref="GI:86792863"
                     /db_xref="GeneID:1804"
                     /db_xref="HGNC:3010"
                     /db_xref="MIM:126141"
                     /db_xref="HPRD:00525"
     mRNA            join(<154429531..154429583,154461070..154461151,
                     154519477..154519597,154561127..154561281,
                     154564555..154564652,154585789..154585912,
                     154587555..154587593,154593065..154593172,
                     154595574..154595665,154596627..154596674,
                     154598704..154598822,154645490..154645537,
                     154659705..154659803,154664334..154664403,
                     154667616..154667810,154672598..154672652,
                     154677343..154677454,154679386..154679444,
                     154680982..154681054,154681167..154681240,
                     154684044..154685995)
                     /gene="DPP6"
                     /gene_synonym="DPPX; FLJ55680; MGC46605; VF2"
                     /product="dipeptidyl-peptidase 6, transcript variant 1"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_130797.2"
                     /db_xref="GI:86792773"
                     /db_xref="GeneID:1804"
                     /db_xref="HGNC:3010"
                     /db_xref="HPRD:00525"
                     /db_xref="MIM:126141"
     mRNA            join(<154429531..154429583,154461070..154461151,
                     154519477..154519597,154561127..154561281,
                     154564555..154564652,154585789..154585912,
                     154587555..154587593,154593065..154593172,
                     154595574..154595665,154596627..154596674,
                     154598704..154598822,154645490..154645537,
                     154659705..154659803,154664334..154664403,
                     154667616..154667810,154672598..154672652,
                     154677343..154677454,154679386..154679444,
                     154680982..154681054,154681167..154681240,
                     154684044..154685995)
                     /gene="DPP6"
                     /gene_synonym="DPPX; FLJ55680; MGC46605; VF2"
                     /product="dipeptidyl-peptidase 6, transcript variant 2"
                     /exception="unclassified transcription discrepancy"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001936.3"
                     /db_xref="GI:86792777"
                     /db_xref="GeneID:1804"
                     /db_xref="HGNC:3010"
                     /db_xref="HPRD:00525"
                     /db_xref="MIM:126141"
     CDS             join(<154429531..154429583,154461070..154461151,
                     154519477..154519597,154561127..154561281,
                     154564555..154564652,154585789..154585912,
                     154587555..154587593,154593065..154593172,
                     154595574..154595665,154596627..154596674,
                     154598704..154598822,154645490..154645537,
                     154659705..154659803,154664334..154664403,
                     154667616..154667810,154672598..154672652,
                     154677343..154677454,154679386..154679444,
                     154680982..154681054,154681167..154681240,
                     154684044..154684190)
                     /gene="DPP6"
                     /gene_synonym="DPPX; FLJ55680; MGC46605; VF2"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="dipeptidyl aminopeptidase-like protein 6 isoform
                     1"
                     /protein_id="NP_570629.2"
                     /db_xref="GI:86792774"
                     /db_xref="GeneID:1804"
                     /db_xref="HGNC:3010"
                     /db_xref="HPRD:00525"
                     /db_xref="MIM:126141"
     CDS             join(<154429531..154429583,154461070..154461151,
                     154519477..154519597,154561127..154561281,
                     154564555..154564652,154585789..154585912,
                     154587555..154587593,154593065..154593172,
                     154595574..154595665,154596627..154596674,
                     154598704..154598822,154645490..154645537,
                     154659705..154659803,154664334..154664403,
                     154667616..154667810,154672598..154672652,
                     154677343..154677454,154679386..154679444,
                     154680982..154681054,154681167..154681240,
                     154684044..154684190)
                     /gene="DPP6"
                     /gene_synonym="DPPX; FLJ55680; MGC46605; VF2"
                     /exception="unclassified translation discrepancy"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="dipeptidyl aminopeptidase-like protein 6 isoform
                     2"
                     /protein_id="NP_001927.3"
                     /db_xref="GI:86792778"
                     /db_xref="GeneID:1804"
                     /db_xref="HGNC:3010"
                     /db_xref="HPRD:00525"
                     /db_xref="MIM:126141"
     gene            154720227..154741200
                     /gene="LOC100132707"
                     /gene_synonym="FLJ18763; FLJ32047"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100132707"
     misc_RNA        join(154720227..154720477,154720666..154720734,
                     154735737..154736330,154738070..154738203,
                     154738303..154738501,154739403..154739483,
                     154739608..154739800,154741008..154741200)
                     /gene="LOC100132707"
                     /gene_synonym="FLJ18763; FLJ32047"
                     /product="hypothetical LOC100132707, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024476.1"
                     /db_xref="GI:213511921"
                     /db_xref="GeneID:100132707"
     misc_RNA        join(154720227..154720477,154720666..154720734,
                     154735737..154736330,154738070..154738203,
                     154738350..154738562)
                     /gene="LOC100132707"
                     /gene_synonym="FLJ18763; FLJ32047"
                     /product="hypothetical LOC100132707, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024477.1"
                     /db_xref="GI:213511959"
                     /db_xref="GeneID:100132707"
     gene            complement(154735400..154794682)
                     /gene="PAXIP1"
                     /gene_synonym="CAGF28; CAGF29; FLJ41049; PACIP1; PAXIP1L;
                     PTIP; TNRC2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:22976"
                     /db_xref="HGNC:8624"
                     /db_xref="HPRD:08491"
                     /db_xref="MIM:608254"
     mRNA            complement(join(154735400..154735874,154738075..154738135,
                     154738222..154738297,154738389..154738523,
                     154739613..154739713,154745965..154746133,
                     154747239..154747341,154748934..154749004,
                     154751600..154751643,154752603..154752787,
                     154753237..154753358,154754031..154754168,
                     154755381..154755476,154759526..154759620,
                     154760113..154760836,154767406..154768041,
                     154774929..154775042,154782716..154782779,
                     154785436..154785479,154790360..154790494,
                     154794559..154794682))
                     /gene="PAXIP1"
                     /gene_synonym="CAGF28; CAGF29; FLJ41049; PACIP1; PAXIP1L;
                     PTIP; TNRC2"
                     /product="PAX interacting (with transcription-activation
                     domain) protein 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_007349.3"
                     /db_xref="GI:93141032"
                     /db_xref="GeneID:22976"
                     /db_xref="HGNC:8624"
                     /db_xref="HPRD:08491"
                     /db_xref="MIM:608254"
     CDS             complement(join(154735859..154735874,154738075..154738135,
                     154738222..154738297,154738389..154738523,
                     154739613..154739713,154745965..154746133,
                     154747239..154747341,154748934..154749004,
                     154751600..154751643,154752603..154752787,
                     154753237..154753358,154754031..154754168,
                     154755381..154755476,154759526..154759620,
                     154760113..154760836,154767406..154768041,
                     154774929..154775042,154782716..154782779,
                     154785436..154785479,154790360..154790494,
                     154794559..154794639))
                     /gene="PAXIP1"
                     /gene_synonym="CAGF28; CAGF29; FLJ41049; PACIP1; PAXIP1L;
                     PTIP; TNRC2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="PAX-interacting protein 1"
                     /protein_id="NP_031375.3"
                     /db_xref="GI:93141033"
                     /db_xref="CCDS:CCDS47753.1"
                     /db_xref="GeneID:22976"
                     /db_xref="HGNC:8624"
                     /db_xref="HPRD:08491"
                     /db_xref="MIM:608254"
     gene            154795143..154797413
                     /gene="LOC202781"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:202781"
     misc_RNA        154795143..154797413
                     /gene="LOC202781"
                     /product="hypothetical LOC202781"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_028090.1"
                     /db_xref="GI:254553257"
                     /db_xref="GeneID:202781"
     gene            complement(154858777..154863267)
                     /gene="LOC100128264"
                     /gene_synonym="FLJ50038"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100128264"
     misc_RNA        complement(join(154858777..154860955,
                     154862744..154863267))
                     /gene="LOC100128264"
                     /gene_synonym="FLJ50038"
                     /product="hypothetical LOC100128264"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038945.1"
                     /db_xref="GI:336595170"
                     /db_xref="GeneID:100128264"
     gene            154862546..154877459
                     /gene="HTR5A"
                     /gene_synonym="5-HT5A; MGC138226"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3361"
                     /db_xref="HGNC:5300"
                     /db_xref="HPRD:03198"
                     /db_xref="MIM:601305"
     mRNA            join(154862546..154863350,154875865..154877459)
                     /gene="HTR5A"
                     /gene_synonym="5-HT5A; MGC138226"
                     /product="5-hydroxytryptamine (serotonin) receptor 5A"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_024012.2"
                     /db_xref="GI:91807129"
                     /db_xref="GeneID:3361"
                     /db_xref="HGNC:5300"
                     /db_xref="HPRD:03198"
                     /db_xref="MIM:601305"
     CDS             join(154862610..154863350,154875865..154876197)
                     /gene="HTR5A"
                     /gene_synonym="5-HT5A; MGC138226"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="5-hydroxytryptamine receptor 5A"
                     /protein_id="NP_076917.1"
                     /db_xref="GI:13236497"
                     /db_xref="CCDS:CCDS5936.1"
                     /db_xref="GeneID:3361"
                     /db_xref="HGNC:5300"
                     /db_xref="HPRD:03198"
                     /db_xref="MIM:601305"
     gene            155089486..155101945
                     /gene="INSIG1"
                     /gene_synonym="CL-6; CL6; MGC1405"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3638"
                     /db_xref="HGNC:6083"
                     /db_xref="MIM:602055"
     mRNA            join(155089486..155089669,155089969..155090407,
                     155093276..155093400,155093961..155094127,
                     155094457..155094556,155099951..155101945)
                     /gene="INSIG1"
                     /gene_synonym="CL-6; CL6; MGC1405"
                     /product="insulin induced gene 1, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005542.4"
                     /db_xref="GI:241982792"
                     /db_xref="GeneID:3638"
                     /db_xref="HGNC:6083"
                     /db_xref="MIM:602055"
     mRNA            join(155089486..155089669,155089969..155090076,
                     155093961..155094127,155094457..155094556,
                     155095535..155095605,155099951..155101945)
                     /gene="INSIG1"
                     /gene_synonym="CL-6; CL6; MGC1405"
                     /product="insulin induced gene 1, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198336.2"
                     /db_xref="GI:241982793"
                     /db_xref="GeneID:3638"
                     /db_xref="HGNC:6083"
                     /db_xref="HPRD:03633"
                     /db_xref="MIM:602055"
     mRNA            join(155089486..155089669,155089969..155090407,
                     155094457..155094556,155099951..155101945)
                     /gene="INSIG1"
                     /gene_synonym="CL-6; CL6; MGC1405"
                     /product="insulin induced gene 1, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_198337.2"
                     /db_xref="GI:241982795"
                     /db_xref="GeneID:3638"
                     /db_xref="HGNC:6083"
                     /db_xref="MIM:602055"
     CDS             join(155089996..155090076,155093961..155094127,
                     155094457..155094556,155095535..155095605,
                     155099951..155100068)
                     /gene="INSIG1"
                     /gene_synonym="CL-6; CL6; MGC1405"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="insulin-induced gene 1 protein isoform 2"
                     /protein_id="NP_938150.2"
                     /db_xref="GI:241982794"
                     /db_xref="GeneID:3638"
                     /db_xref="HGNC:6083"
                     /db_xref="HPRD:03633"
                     /db_xref="MIM:602055"
     CDS             join(155089996..155090407,155093276..155093400,
                     155093961..155094127,155094457..155094556,
                     155099951..155099980)
                     /gene="INSIG1"
                     /gene_synonym="CL-6; CL6; MGC1405"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="insulin-induced gene 1 protein isoform 1"
                     /protein_id="NP_005533.2"
                     /db_xref="GI:28882053"
                     /db_xref="CCDS:CCDS5938.1"
                     /db_xref="GeneID:3638"
                     /db_xref="HGNC:6083"
                     /db_xref="MIM:602055"
     CDS             join(155089996..155090407,155094457..155094539)
                     /gene="INSIG1"
                     /gene_synonym="CL-6; CL6; MGC1405"
                     /note="isoform 3 is encoded by transcript variant 3;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="insulin-induced gene 1 protein isoform 3"
                     /protein_id="NP_938151.1"
                     /db_xref="GI:38327531"
                     /db_xref="CCDS:CCDS5939.1"
                     /db_xref="GeneID:3638"
                     /db_xref="HGNC:6083"
                     /db_xref="MIM:602055"
     gene            155250824..155257526
                     /gene="EN2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:2020"
                     /db_xref="HGNC:3343"
                     /db_xref="HPRD:08836"
                     /db_xref="MIM:131310"
     mRNA            join(155250824..155251757,155255066..155257526)
                     /gene="EN2"
                     /product="engrailed homeobox 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001427.3"
                     /db_xref="GI:126090912"
                     /db_xref="GeneID:2020"
                     /db_xref="HGNC:3343"
                     /db_xref="HPRD:08836"
                     /db_xref="MIM:131310"
     CDS             join(155251073..155251757,155255066..155255382)
                     /gene="EN2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="homeobox protein engrailed-2"
                     /protein_id="NP_001418.2"
                     /db_xref="GI:7710121"
                     /db_xref="CCDS:CCDS5940.1"
                     /db_xref="GeneID:2020"
                     /db_xref="HGNC:3343"
                     /db_xref="HPRD:08836"
                     /db_xref="MIM:131310"
     gene            complement(155293953..155326539)
                     /gene="CNPY1"
                     /gene_synonym="MGC125606"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285888"
                     /db_xref="HGNC:27786"
                     /db_xref="MIM:612493"
     mRNA            complement(join(155293953..155295800,155299715..155299811,
                     155301589..155301792,155326455..155326539))
                     /gene="CNPY1"
                     /gene_synonym="MGC125606"
                     /product="canopy 1 homolog (zebrafish)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001103176.1"
                     /db_xref="GI:157042799"
                     /db_xref="GeneID:285888"
                     /db_xref="HGNC:27786"
                     /db_xref="MIM:612493"
     CDS             complement(join(155295763..155295800,155299715..155299811,
                     155301589..155301732))
                     /gene="CNPY1"
                     /gene_synonym="MGC125606"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="protein canopy homolog 1"
                     /protein_id="NP_001096646.1"
                     /db_xref="GI:157042800"
                     /db_xref="CCDS:CCDS43684.1"
                     /db_xref="GeneID:285888"
                     /db_xref="HGNC:27786"
                     /db_xref="MIM:612493"
     gene            complement(155434610..155437074)
                     /gene="LOC100506302"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 20 ESTs"
                     /db_xref="GeneID:100506302"
     misc_RNA        complement(join(155434610..155435664,155436162..155436298,
                     155436908..155437074))
                     /gene="LOC100506302"
                     /product="hypothetical LOC100506302"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 20 ESTs"
                     /transcript_id="XR_108708.1"
                     /db_xref="GI:310120130"
                     /db_xref="GeneID:100506302"
     gene            155437203..155574179
                     /gene="RBM33"
                     /gene_synonym="DKFZp434D1319; MGC20460; PRR8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:155435"
                     /db_xref="HGNC:27223"
                     /db_xref="HPRD:11317"
     mRNA            join(155437203..155437613,155457869..155457947,
                     155465561..155465609,155471302..155471378,
                     155473284..155473602,155493467..155493638,
                     155499554..155499762,155503897..155504149,
                     155511079..155511137,155530224..155530356,
                     155530754..155531097,155532409..155532720,
                     155534513..155534800,155537655..155538296,
                     155556506..155556712,155559161..155559349,
                     155567253..155567341,155567687..155574179)
                     /gene="RBM33"
                     /gene_synonym="DKFZp434D1319; MGC20460; PRR8"
                     /product="RNA binding motif protein 33"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_053043.2"
                     /db_xref="GI:151301052"
                     /db_xref="GeneID:155435"
                     /db_xref="HGNC:27223"
                     /db_xref="HPRD:11317"
     CDS             join(155437571..155437613,155457869..155457947,
                     155465561..155465609,155471302..155471378,
                     155473284..155473602,155493467..155493638,
                     155499554..155499762,155503897..155504149,
                     155511079..155511137,155530224..155530356,
                     155530754..155531097,155532409..155532720,
                     155534513..155534800,155537655..155538296,
                     155556506..155556712,155559161..155559349,
                     155567253..155567341,155567687..155567735)
                     /gene="RBM33"
                     /gene_synonym="DKFZp434D1319; MGC20460; PRR8"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="RNA-binding protein 33"
                     /protein_id="NP_444271.2"
                     /db_xref="GI:151301053"
                     /db_xref="CCDS:CCDS5941.2"
                     /db_xref="GeneID:155435"
                     /db_xref="HGNC:27223"
                     /db_xref="HPRD:11317"
     gene            complement(155595558..155604967)
                     /gene="SHH"
                     /gene_synonym="HHG1; HLP3; HPE3; MCOPCB5; SMMCI; TPT;
                     TPTPS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:6469"
                     /db_xref="HGNC:10848"
                     /db_xref="HPRD:02838"
                     /db_xref="MIM:600725"
     mRNA            complement(join(155595558..155596420,155598990..155599251,
                     155604517..155604967))
                     /gene="SHH"
                     /gene_synonym="HHG1; HLP3; HPE3; MCOPCB5; SMMCI; TPT;
                     TPTPS"
                     /product="sonic hedgehog"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_000193.2"
                     /db_xref="GI:21071042"
                     /db_xref="GeneID:6469"
                     /db_xref="HGNC:10848"
                     /db_xref="HPRD:02838"
                     /db_xref="MIM:600725"
     CDS             complement(join(155595594..155596420,155598990..155599251,
                     155604517..155604816))
                     /gene="SHH"
                     /gene_synonym="HHG1; HLP3; HPE3; MCOPCB5; SMMCI; TPT;
                     TPTPS"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="sonic hedgehog protein preproprotein
                     preproprotein"
                     /protein_id="NP_000184.1"
                     /db_xref="GI:4506939"
                     /db_xref="CCDS:CCDS5942.1"
                     /db_xref="GeneID:6469"
                     /db_xref="HGNC:10848"
                     /db_xref="HPRD:02838"
                     /db_xref="MIM:600725"
     gene            155755251..155759037
                     /gene="LOC389602"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 7 ESTs, 1 Protein"
                     /db_xref="GeneID:389602"
     misc_RNA        join(155755251..155755969,155757146..155759037)
                     /gene="LOC389602"
                     /product="hypothetical LOC389602"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 7 ESTs, 1 Protein"
                     /transcript_id="XR_108709.1"
                     /db_xref="GI:310120131"
                     /db_xref="GeneID:389602"
     gene            complement(156230483..156238282)
                     /gene="LOC285889"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:285889"
     misc_RNA        complement(join(156230483..156231689,156233924..156234074,
                     156236943..156238282))
                     /gene="LOC285889"
                     /product="hypothetical LOC285889"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038232.1"
                     /db_xref="GI:333440444"
                     /db_xref="GeneID:285889"
     gene            complement(156264795..156398461)
                     /gene="LOC100506380"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 11 ESTs"
                     /db_xref="GeneID:100506380"
     misc_RNA        complement(join(156264795..156265405,156397882..156398074,
                     156398352..156398461))
                     /gene="LOC100506380"
                     /product="hypothetical LOC100506380, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 8 ESTs"
                     /transcript_id="XR_108713.1"
                     /db_xref="GI:310120134"
                     /db_xref="GeneID:100506380"
     misc_RNA        complement(join(156264795..156265405,
                     156395745..156395889))
                     /gene="LOC100506380"
                     /product="hypothetical LOC100506380, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 11 ESTs"
                     /transcript_id="XR_108712.1"
                     /db_xref="GI:310120135"
                     /db_xref="GeneID:100506380"
     gene            156333185..156333795
                     /gene="NCRNA00244"
                     /gene_synonym="C7orf4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64433"
                     /db_xref="HGNC:13245"
     misc_RNA        156333185..156333795
                     /gene="NCRNA00244"
                     /gene_synonym="C7orf4"
                     /product="non-protein coding RNA 244"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024119.1"
                     /db_xref="GI:198041698"
                     /db_xref="GeneID:64433"
                     /db_xref="HGNC:13245"
     gene            156426008..156426514
                     /gene="RPL26P23"
                     /gene_synonym="RPL26_13_865"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129517"
                     /db_xref="HGNC:36634"
     gene            complement(156431060..156433348)
                     /gene="C7orf13"
                     /gene_synonym="MY040"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:129790"
                     /db_xref="HGNC:17126"
                     /db_xref="MIM:610242"
     misc_RNA        complement(156431060..156433348)
                     /gene="C7orf13"
                     /gene_synonym="MY040"
                     /product="chromosome 7 open reading frame 13"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_026865.1"
                     /db_xref="GI:223634015"
                     /db_xref="GeneID:129790"
                     /db_xref="HGNC:17126"
                     /db_xref="MIM:610242"
     gene            156433353..156469824
                     /gene="RNF32"
                     /gene_synonym="FKSG33; HSD15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:140545"
                     /db_xref="HGNC:17118"
                     /db_xref="MIM:610241"
     mRNA            join(156433353..156433505,156436495..156436586,
                     156437193..156437451,156447270..156447412,
                     156450235..156450267,156450822..156450946,
                     156451156..156451264,156468390..156468557,
                     156469113..156469824)
                     /gene="RNF32"
                     /gene_synonym="FKSG33; HSD15"
                     /product="ring finger protein 32, transcript variant 3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_030936.3"
                     /db_xref="GI:319996749"
                     /db_xref="GeneID:140545"
                     /db_xref="HGNC:17118"
                     /db_xref="HPRD:11517"
                     /db_xref="MIM:610241"
     mRNA            join(156433441..156433698,156436495..156436586,
                     156437193..156437451,156447270..156447412,
                     156450235..156450267,156450822..156450946,
                     156451156..156451264,156468390..156468557,
                     156469113..156469824)
                     /gene="RNF32"
                     /gene_synonym="FKSG33; HSD15"
                     /product="ring finger protein 32, transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001184996.1"
                     /db_xref="GI:297139738"
                     /db_xref="GeneID:140545"
                     /db_xref="HGNC:17118"
                     /db_xref="MIM:610241"
     mRNA            join(156435671..156435781,156436495..156436586,
                     156437193..156437451,156447270..156447412,
                     156450235..156450267,156450822..156450946,
                     156451156..156451264,156468390..156468557,
                     156469113..156469824)
                     /gene="RNF32"
                     /gene_synonym="FKSG33; HSD15"
                     /product="ring finger protein 32, transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001184997.1"
                     /db_xref="GI:297139740"
                     /db_xref="GeneID:140545"
                     /db_xref="HGNC:17118"
                     /db_xref="MIM:610241"
     CDS             join(156436572..156436586,156437193..156437451,
                     156447270..156447412,156450235..156450267,
                     156450822..156450946,156451156..156451264,
                     156468390..156468557,156469113..156469349)
                     /gene="RNF32"
                     /gene_synonym="FKSG33; HSD15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="RING finger protein 32"
                     /protein_id="NP_001171925.1"
                     /db_xref="GI:297139739"
                     /db_xref="CCDS:CCDS5944.1"
                     /db_xref="GeneID:140545"
                     /db_xref="HGNC:17118"
                     /db_xref="MIM:610241"
     CDS             join(156436572..156436586,156437193..156437451,
                     156447270..156447412,156450235..156450267,
                     156450822..156450946,156451156..156451264,
                     156468390..156468557,156469113..156469349)
                     /gene="RNF32"
                     /gene_synonym="FKSG33; HSD15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="RING finger protein 32"
                     /protein_id="NP_001171926.1"
                     /db_xref="GI:297139741"
                     /db_xref="CCDS:CCDS5944.1"
                     /db_xref="GeneID:140545"
                     /db_xref="HGNC:17118"
                     /db_xref="MIM:610241"
     CDS             join(156436572..156436586,156437193..156437451,
                     156447270..156447412,156450235..156450267,
                     156450822..156450946,156451156..156451264,
                     156468390..156468557,156469113..156469349)
                     /gene="RNF32"
                     /gene_synonym="FKSG33; HSD15"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="RING finger protein 32"
                     /protein_id="NP_112198.1"
                     /db_xref="GI:13569903"
                     /db_xref="CCDS:CCDS5944.1"
                     /db_xref="GeneID:140545"
                     /db_xref="HGNC:17118"
                     /db_xref="MIM:610241"
     gene            complement(156473570..156685902)
                     /gene="LMBR1"
                     /gene_synonym="ACHP; C7orf2; DIF14; FLJ11665; PPD2; TPT"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64327"
                     /db_xref="HGNC:13243"
                     /db_xref="HPRD:05700"
                     /db_xref="MIM:605522"
     mRNA            complement(join(156473570..156476857,156480724..156480885,
                     156516806..156516872,156518129..156518219,
                     156518458..156518531,156520624..156520701,
                     156521338..156521414,156526871..156526951,
                     156549087..156549159,156554828..156554892,
                     156555802..156555870,156556363..156556489,
                     156589083..156589186,156619299..156619438,
                     156626447..156626486,156629507..156629579,
                     156685622..156685902))
                     /gene="LMBR1"
                     /gene_synonym="ACHP; C7orf2; DIF14; FLJ11665; PPD2; TPT"
                     /product="limb region 1 homolog (mouse)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_022458.3"
                     /db_xref="GI:126513134"
                     /db_xref="GeneID:64327"
                     /db_xref="HGNC:13243"
                     /db_xref="HPRD:05700"
                     /db_xref="MIM:605522"
     CDS             complement(join(156476772..156476857,156480724..156480885,
                     156516806..156516872,156518129..156518219,
                     156518458..156518531,156520624..156520701,
                     156521338..156521414,156526871..156526951,
                     156549087..156549159,156554828..156554892,
                     156555802..156555870,156556363..156556489,
                     156589083..156589186,156619299..156619438,
                     156626447..156626486,156629507..156629579,
                     156685622..156685687))
                     /gene="LMBR1"
                     /gene_synonym="ACHP; C7orf2; DIF14; FLJ11665; PPD2; TPT"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="limb region 1 protein homolog"
                     /protein_id="NP_071903.2"
                     /db_xref="GI:21362112"
                     /db_xref="CCDS:CCDS5945.1"
                     /db_xref="GeneID:64327"
                     /db_xref="HGNC:13243"
                     /db_xref="HPRD:05700"
                     /db_xref="MIM:605522"
     gene            156742417..156765876
                     /gene="NOM1"
                     /gene_synonym="C7orf3; FLJ16401; SGD1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:64434"
                     /db_xref="HGNC:13244"
                     /db_xref="HPRD:18485"
                     /db_xref="MIM:611269"
     mRNA            join(156742417..156743418,156745168..156745292,
                     156746797..156746992,156752545..156752868,
                     156754845..156754955,156755702..156755869,
                     156756599..156756720,156758964..156759096,
                     156759655..156759786,156761781..156761890,
                     156762223..156765876)
                     /gene="NOM1"
                     /gene_synonym="C7orf3; FLJ16401; SGD1"
                     /product="nucleolar protein with MIF4G domain 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_138400.1"
                     /db_xref="GI:61097911"
                     /db_xref="GeneID:64434"
                     /db_xref="HGNC:13244"
                     /db_xref="HPRD:18485"
                     /db_xref="MIM:611269"
     CDS             join(156742432..156743418,156745168..156745292,
                     156746797..156746992,156752545..156752868,
                     156754845..156754955,156755702..156755869,
                     156756599..156756720,156758964..156759096,
                     156759655..156759786,156761781..156761890,
                     156762223..156762397)
                     /gene="NOM1"
                     /gene_synonym="C7orf3; FLJ16401; SGD1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="nucleolar MIF4G domain-containing protein 1"
                     /protein_id="NP_612409.1"
                     /db_xref="GI:61097912"
                     /db_xref="CCDS:CCDS34787.1"
                     /db_xref="GeneID:64434"
                     /db_xref="HGNC:13244"
                     /db_xref="HPRD:18485"
                     /db_xref="MIM:611269"
     gene            complement(156797547..156803347)
                     /gene="MNX1"
                     /gene_synonym="HB9; HLXB9; HOXHB9; SCRA1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:3110"
                     /db_xref="HGNC:4979"
                     /db_xref="MIM:142994"
     mRNA            complement(join(156797547..156798567,156799173..156799333,
                     156802354..156803347))
                     /gene="MNX1"
                     /gene_synonym="HB9; HLXB9; HOXHB9; SCRA1"
                     /product="motor neuron and pancreas homeobox 1, transcript
                     variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005515.3"
                     /db_xref="GI:89257347"
                     /db_xref="GeneID:3110"
                     /db_xref="HGNC:4979"
                     /db_xref="HPRD:00874"
                     /db_xref="MIM:142994"
     mRNA            complement(join(156797547..156798567,156799173..156799333,
                     156801692..156802129))
                     /gene="MNX1"
                     /gene_synonym="HB9; HLXB9; HOXHB9; SCRA1"
                     /product="motor neuron and pancreas homeobox 1, transcript
                     variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001165255.1"
                     /db_xref="GI:259155339"
                     /db_xref="GeneID:3110"
                     /db_xref="HGNC:4979"
                     /db_xref="MIM:142994"
     CDS             complement(join(156798214..156798567,156799173..156799333,
                     156802354..156803044))
                     /gene="MNX1"
                     /gene_synonym="HB9; HLXB9; HOXHB9; SCRA1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="motor neuron and pancreas homeobox protein 1
                     isoform 1"
                     /protein_id="NP_005506.3"
                     /db_xref="GI:89257348"
                     /db_xref="CCDS:CCDS34788.1"
                     /db_xref="GeneID:3110"
                     /db_xref="HGNC:4979"
                     /db_xref="MIM:142994"
     CDS             complement(join(156798214..156798567,156799173..156799333,
                     156801692..156801746))
                     /gene="MNX1"
                     /gene_synonym="HB9; HLXB9; HOXHB9; SCRA1"
                     /note="isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="motor neuron and pancreas homeobox protein 1
                     isoform 2"
                     /protein_id="NP_001158727.1"
                     /db_xref="GI:259155340"
                     /db_xref="CCDS:CCDS55187.1"
                     /db_xref="GeneID:3110"
                     /db_xref="HGNC:4979"
                     /db_xref="MIM:142994"
     gene            156803551..156809118
                     /gene="LOC645249"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:645249"
     misc_RNA        join(156803551..156804001,156808583..156809118)
                     /gene="LOC645249"
                     /product="hypothetical LOC645249"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038835.1"
                     /db_xref="GI:336285466"
                     /db_xref="GeneID:645249"
     gene            complement(156880802..156881071)
                     /gene="LOC645272"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:645272"
     gene            156931655..157062066
                     /gene="UBE3C"
                     /gene_synonym="KIAA0010; KIAA10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:9690"
                     /db_xref="HGNC:16803"
                     /db_xref="HPRD:15604"
     mRNA            join(156931655..156932032,156956504..156956557,
                     156961742..156961816,156962998..156963144,
                     156967613..156967728,156971384..156971541,
                     156974212..156974365,156974802..156975022,
                     156976572..156976723,156979528..156979715,
                     156994415..156994501,157000092..157000249,
                     157000397..157000629,157009561..157009665,
                     157013383..157013470,157015948..157016045,
                     157018101..157018233,157023774..157024021,
                     157041062..157041274,157046648..157046836,
                     157046938..157047004,157049608..157049738,
                     157060279..157062066)
                     /gene="UBE3C"
                     /gene_synonym="KIAA0010; KIAA10"
                     /product="ubiquitin protein ligase E3C"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_014671.2"
                     /db_xref="GI:187960099"
                     /db_xref="GeneID:9690"
                     /db_xref="HGNC:16803"
                     /db_xref="HPRD:15604"
     CDS             join(156931967..156932032,156956504..156956557,
                     156961742..156961816,156962998..156963144,
                     156967613..156967728,156971384..156971541,
                     156974212..156974365,156974802..156975022,
                     156976572..156976723,156979528..156979715,
                     156994415..156994501,157000092..157000249,
                     157000397..157000629,157009561..157009665,
                     157013383..157013470,157015948..157016045,
                     157018101..157018233,157023774..157024021,
                     157041062..157041274,157046648..157046836,
                     157046938..157047004,157049608..157049738,
                     157060279..157060449)
                     /gene="UBE3C"
                     /gene_synonym="KIAA0010; KIAA10"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="ubiquitin-protein ligase E3C"
                     /protein_id="NP_055486.2"
                     /db_xref="GI:187960100"
                     /db_xref="CCDS:CCDS34789.1"
                     /db_xref="GeneID:9690"
                     /db_xref="HGNC:16803"
                     /db_xref="HPRD:15604"
     gene            156985030..156985574
                     /gene="RPS27AP12"
                     /gene_synonym="RPS27A_5_866"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100130446"
                     /db_xref="HGNC:35732"
     gene            complement(156986368..156990953)
                     /gene="LOC777650"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:777650"
     gene            complement(157055716..157056095)
                     /gene="RPL36AP30"
                     /gene_synonym="RPL36A_11_867"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100271511"
                     /db_xref="HGNC:36216"
     gene            157056843..157059007
                     /gene="LOC100506458"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 3 ESTs, 1 Protein"
                     /db_xref="GeneID:100506458"
     misc_RNA        157056843..157059007
                     /gene="LOC100506458"
                     /product="putative uncharacterized protein LOC65996-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 3 ESTs, 1 Protein"
                     /transcript_id="XR_132523.1"
                     /db_xref="GI:341915412"
                     /db_xref="GeneID:100506458"
     gene            157129710..157210133
                     /gene="DNAJB6"
                     /gene_synonym="DJ4; DKFZp566D0824; DnaJ; FLJ42837; HHDJ1;
                     HSJ-2; HSJ2; MGC1152; MGC117297; MRJ; MSJ-1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10049"
                     /db_xref="HGNC:14888"
                     /db_xref="MIM:611332"
     mRNA            join(157129710..157129838,157151241..157151331,
                     157155855..157155964,157159196..157159255,
                     157160067..157160177,157174940..157175071,
                     157177561..157177702,157178235..157179018)
                     /gene="DNAJB6"
                     /gene_synonym="DJ4; DKFZp566D0824; DnaJ; FLJ42837; HHDJ1;
                     HSJ-2; HSJ2; MGC1152; MGC117297; MRJ; MSJ-1"
                     /product="DnaJ (Hsp40) homolog, subfamily B, member 6,
                     transcript variant 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005494.2"
                     /db_xref="GI:24234719"
                     /db_xref="GeneID:10049"
                     /db_xref="HGNC:14888"
                     /db_xref="MIM:611332"
     mRNA            join(157129711..157129838,157151241..157151331,
                     157155855..157155964,157159196..157159255,
                     157160067..157160177,157174940..157175071,
                     157177561..157177702,157178235..157178305,
                     157202489..157202695,157208710..157210133)
                     /gene="DNAJB6"
                     /gene_synonym="DJ4; DKFZp566D0824; DnaJ; FLJ42837; HHDJ1;
                     HSJ-2; HSJ2; MGC1152; MGC117297; MRJ; MSJ-1"
                     /product="DnaJ (Hsp40) homolog, subfamily B, member 6,
                     transcript variant 1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_058246.3"
                     /db_xref="GI:34328906"
                     /db_xref="GeneID:10049"
                     /db_xref="HGNC:14888"
                     /db_xref="HPRD:07107"
                     /db_xref="MIM:611332"
     CDS             join(157151267..157151331,157155855..157155964,
                     157159196..157159255,157160067..157160177,
                     157174940..157175071,157177561..157177702,
                     157178235..157178305,157202489..157202695,
                     157208710..157208792)
                     /gene="DNAJB6"
                     /gene_synonym="DJ4; DKFZp566D0824; DnaJ; FLJ42837; HHDJ1;
                     HSJ-2; HSJ2; MGC1152; MGC117297; MRJ; MSJ-1"
                     /note="isoform a is encoded by transcript variant 1;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="dnaJ homolog subfamily B member 6 isoform a"
                     /protein_id="NP_490647.1"
                     /db_xref="GI:17388799"
                     /db_xref="CCDS:CCDS5946.1"
                     /db_xref="GeneID:10049"
                     /db_xref="HGNC:14888"
                     /db_xref="MIM:611332"
     CDS             join(157151267..157151331,157155855..157155964,
                     157159196..157159255,157160067..157160177,
                     157174940..157175071,157177561..157177702,
                     157178235..157178340)
                     /gene="DNAJB6"
                     /gene_synonym="DJ4; DKFZp566D0824; DnaJ; FLJ42837; HHDJ1;
                     HSJ-2; HSJ2; MGC1152; MGC117297; MRJ; MSJ-1"
                     /note="isoform b is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="dnaJ homolog subfamily B member 6 isoform b"
                     /protein_id="NP_005485.1"
                     /db_xref="GI:4885495"
                     /db_xref="CCDS:CCDS47755.1"
                     /db_xref="GeneID:10049"
                     /db_xref="HGNC:14888"
                     /db_xref="MIM:611332"
     gene            157294016..157296283
                     /gene="LOC100506534"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /db_xref="GeneID:100506534"
     misc_RNA        join(157294016..157294209,157295678..157295803,
                     157296046..157296283)
                     /gene="LOC100506534"
                     /product="hypothetical LOC100506534"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 5 ESTs"
                     /transcript_id="XR_108717.1"
                     /db_xref="GI:310120144"
                     /db_xref="GeneID:100506534"
     gene            157318393..157320019
                     /gene="LOC100506557"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 1 EST"
                     /db_xref="GeneID:100506557"
     misc_RNA        157318393..157320019
                     /gene="LOC100506557"
                     /product="hypothetical LOC100506557"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON. Supporting evidence
                     includes similarity to: 1 mRNA, 1 EST"
                     /transcript_id="XR_132524.1"
                     /db_xref="GI:341915413"
                     /db_xref="GeneID:100506557"
     gene            complement(157331750..158380482)
                     /gene="PTPRN2"
                     /gene_synonym="IA-2beta; IAR; ICAAR; PTPRP; R-PTP-N2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:5799"
                     /db_xref="HGNC:9677"
                     /db_xref="MIM:601698"
     mRNA            complement(join(157331750..157333479,157341640..157341713,
                     157361594..157361658,157364132..157364185,
                     157369305..157369471,157370713..157370832,
                     157387930..157388007,157396694..157396767,
                     157414054..157414201,157449049..157449243,
                     157475417..157475629,157691365..157691429,
                     157873990..157874069,157903521..157903607,
                     157926369..157926751,157929347..157929387,
                     157930986..157931207,157959623..157959983,
                     157985019..157985187,157997863..157997965,
                     158109511..158109624,158282427..158282477,
                     158380250..158380482))
                     /gene="PTPRN2"
                     /gene_synonym="IA-2beta; IAR; ICAAR; PTPRP; R-PTP-N2"
                     /product="protein tyrosine phosphatase, receptor type, N
                     polypeptide 2, transcript variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_002847.3"
                     /db_xref="GI:194097439"
                     /db_xref="GeneID:5799"
                     /db_xref="HGNC:9677"
                     /db_xref="HPRD:03413"
                     /db_xref="MIM:601698"
     mRNA            complement(join(157331750..157333479,157341640..157341713,
                     157361594..157361658,157364132..157364185,
                     157369305..157369471,157370713..157370832,
                     157387930..157388007,157396694..157396767,
                     157414054..157414201,157449049..157449243,
                     157475417..157475629,157691365..157691429,
                     157873990..157874069,157903521..157903607,
                     157926369..157926751,157929347..157929387,
                     157930986..157931207,157959623..157959983,
                     157985019..157985187,157997863..157997965,
                     158109511..158109624,158380250..158380482))
                     /gene="PTPRN2"
                     /gene_synonym="IA-2beta; IAR; ICAAR; PTPRP; R-PTP-N2"
                     /product="protein tyrosine phosphatase, receptor type, N
                     polypeptide 2, transcript variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_130842.2"
                     /db_xref="GI:194097437"
                     /db_xref="GeneID:5799"
                     /db_xref="HGNC:9677"
                     /db_xref="MIM:601698"
     mRNA            complement(join(157331750..157333479,157341640..157341713,
                     157361594..157361658,157364132..157364185,
                     157369305..157369471,157370713..157370832,
                     157387930..157388007,157396694..157396767,
                     157414054..157414201,157449049..157449243,
                     157475417..157475629,157691365..157691429,
                     157873990..157874069,157926369..157926751,
                     157929347..157929387,157930986..157931207,
                     157959623..157959983,157985019..157985187,
                     157997863..157997965,158109511..158109624,
                     158282427..158282477,158380250..158380482))
                     /gene="PTPRN2"
                     /gene_synonym="IA-2beta; IAR; ICAAR; PTPRP; R-PTP-N2"
                     /product="protein tyrosine phosphatase, receptor type, N
                     polypeptide 2, transcript variant 3"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_130843.2"
                     /db_xref="GI:194097441"
                     /db_xref="GeneID:5799"
                     /db_xref="HGNC:9677"
                     /db_xref="MIM:601698"
     CDS             complement(join(157333408..157333479,157341640..157341713,
                     157361594..157361658,157364132..157364185,
                     157369305..157369471,157370713..157370832,
                     157387930..157388007,157396694..157396767,
                     157414054..157414201,157449049..157449243,
                     157475417..157475629,157691365..157691429,
                     157873990..157874069,157903521..157903607,
                     157926369..157926751,157929347..157929387,
                     157930986..157931207,157959623..157959983,
                     157985019..157985187,157997863..157997965,
                     158109511..158109624,158282427..158282477,
                     158380250..158380361))
                     /gene="PTPRN2"
                     /gene_synonym="IA-2beta; IAR; ICAAR; PTPRP; R-PTP-N2"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="receptor-type tyrosine-protein phosphatase N2
                     isoform 1 precursor"
                     /protein_id="NP_002838.2"
                     /db_xref="GI:194097440"
                     /db_xref="CCDS:CCDS5947.1"
                     /db_xref="GeneID:5799"
                     /db_xref="HGNC:9677"
                     /db_xref="MIM:601698"
     CDS             complement(join(157333408..157333479,157341640..157341713,
                     157361594..157361658,157364132..157364185,
                     157369305..157369471,157370713..157370832,
                     157387930..157388007,157396694..157396767,
                     157414054..157414201,157449049..157449243,
                     157475417..157475629,157691365..157691429,
                     157873990..157874069,157903521..157903607,
                     157926369..157926751,157929347..157929387,
                     157930986..157931207,157959623..157959983,
                     157985019..157985187,157997863..157997965,
                     158109511..158109624,158380250..158380361))
                     /gene="PTPRN2"
                     /gene_synonym="IA-2beta; IAR; ICAAR; PTPRP; R-PTP-N2"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="receptor-type tyrosine-protein phosphatase N2
                     isoform 2 precursor"
                     /protein_id="NP_570857.2"
                     /db_xref="GI:194097438"
                     /db_xref="CCDS:CCDS5948.1"
                     /db_xref="GeneID:5799"
                     /db_xref="HGNC:9677"
                     /db_xref="MIM:601698"
     CDS             complement(join(157333408..157333479,157341640..157341713,
                     157361594..157361658,157364132..157364185,
                     157369305..157369471,157370713..157370832,
                     157387930..157388007,157396694..157396767,
                     157414054..157414201,157449049..157449243,
                     157475417..157475629,157691365..157691429,
                     157873990..157874069,157926369..157926751,
                     157929347..157929387,157930986..157931207,
                     157959623..157959983,157985019..157985187,
                     157997863..157997965,158109511..158109624,
                     158282427..158282477,158380250..158380361))
                     /gene="PTPRN2"
                     /gene_synonym="IA-2beta; IAR; ICAAR; PTPRP; R-PTP-N2"
                     /note="isoform 3 precursor is encoded by transcript
                     variant 3; Derived by automated computational analysis
                     using gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="receptor-type tyrosine-protein phosphatase N2
                     isoform 3 precursor"
                     /protein_id="NP_570858.2"
                     /db_xref="GI:194097442"
                     /db_xref="CCDS:CCDS5949.1"
                     /db_xref="GeneID:5799"
                     /db_xref="HGNC:9677"
                     /db_xref="MIM:601698"
     gene            complement(157367028..157367114)
                     /gene="MIR153-2"
                     /gene_synonym="MIRN153-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:406945"
                     /db_xref="HGNC:31540"
                     /db_xref="miRBase:MI0000464"
     ncRNA           complement(157367028..157367114)
                     /gene="MIR153-2"
                     /gene_synonym="MIRN153-2"
                     /ncRNA_class="miRNA"
                     /product="microRNA 153-2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_029689.1"
                     /db_xref="GI:262205343"
                     /db_xref="GeneID:406945"
                     /db_xref="HGNC:31540"
                     /db_xref="miRBase:MI0000464"
     ncRNA           complement(157367028..157367114)
                     /gene="MIR153-2"
                     /gene_synonym="MIRN153-2"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-153-2"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:406945"
                     /db_xref="miRBase:MI0000464"
                     /db_xref="HGNC:31540"
     gene            157647277..157658784
                     /gene="LOC100506585"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:100506585"
     misc_RNA        join(157647277..157647567,157648619..157648822,
                     157649982..157650240,157655237..157658784)
                     /gene="LOC100506585"
                     /product="hypothetical LOC100506585"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_038966.1"
                     /db_xref="GI:337298412"
                     /db_xref="GeneID:100506585"
     gene            complement(158325410..158325505)
                     /gene="MIR595"
                     /gene_synonym="hsa-mir-595; MIRN595"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:693180"
                     /db_xref="HGNC:32851"
                     /db_xref="miRBase:MI0003607"
     ncRNA           complement(158325410..158325505)
                     /gene="MIR595"
                     /gene_synonym="hsa-mir-595; MIRN595"
                     /ncRNA_class="miRNA"
                     /product="microRNA 595"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_030325.1"
                     /db_xref="GI:262205966"
                     /db_xref="GeneID:693180"
                     /db_xref="HGNC:32851"
                     /db_xref="miRBase:MI0003607"
     ncRNA           complement(158325410..158325505)
                     /gene="MIR595"
                     /gene_synonym="hsa-mir-595; MIRN595"
                     /ncRNA_class="miRNA"
                     /product="microRNA:hsa-mir-595"
                     /note="Data source: miRBase"
                     /db_xref="GeneID:693180"
                     /db_xref="miRBase:MI0003607"
                     /db_xref="HGNC:32851"
     gene            complement(158414865..158416073)
                     /gene="LOC285872"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:285872"
     gene            complement(158424003..158497520)
                     /gene="NCAPG2"
                     /gene_synonym="CAP-G2; FLJ20311; hCAP-G2; LUZP5; MTB"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:54892"
                     /db_xref="HGNC:21904"
                     /db_xref="HPRD:10539"
                     /db_xref="MIM:608532"
     mRNA            complement(join(158424003..158424409,158436981..158437080,
                     158438211..158438311,158439152..158439255,
                     158443524..158443664,158444985..158445172,
                     158447287..158447386,158447810..158447950,
                     158448031..158448147,158448952..158449125,
                     158449244..158449397,158451030..158451100,
                     158454886..158455059,158456876..158456988,
                     158457220..158457442,158464206..158464358,
                     158468169..158468348,158472652..158472777,
                     158473413..158473508,158475992..158476078,
                     158478864..158478933,158480040..158480134,
                     158482511..158482645,158483260..158483414,
                     158485534..158485648,158486001..158486189,
                     158494513..158494629,158497415..158497520))
                     /gene="NCAPG2"
                     /gene_synonym="CAP-G2; FLJ20311; hCAP-G2; LUZP5; MTB"
                     /product="non-SMC condensin II complex, subunit G2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_017760.5"
                     /db_xref="GI:116812585"
                     /db_xref="GeneID:54892"
                     /db_xref="HGNC:21904"
                     /db_xref="HPRD:10539"
                     /db_xref="MIM:608532"
     CDS             complement(join(158424358..158424409,158436981..158437080,
                     158438211..158438311,158439152..158439255,
                     158443524..158443664,158444985..158445172,
                     158447287..158447386,158447810..158447950,
                     158448031..158448147,158448952..158449125,
                     158449244..158449397,158451030..158451100,
                     158454886..158455059,158456876..158456988,
                     158457220..158457442,158464206..158464358,
                     158468169..158468348,158472652..158472777,
                     158473413..158473508,158475992..158476078,
                     158478864..158478933,158480040..158480134,
                     158482511..158482645,158483260..158483414,
                     158485534..158485648,158486001..158486189,
                     158494513..158494590))
                     /gene="NCAPG2"
                     /gene_synonym="CAP-G2; FLJ20311; hCAP-G2; LUZP5; MTB"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="condensin-2 complex subunit G2"
                     /protein_id="NP_060230.5"
                     /db_xref="GI:116812586"
                     /db_xref="CCDS:CCDS43686.1"
                     /db_xref="GeneID:54892"
                     /db_xref="HGNC:21904"
                     /db_xref="HPRD:10539"
                     /db_xref="MIM:608532"
     gene            158512363..158512894
                     /gene="RPL21P76"
                     /gene_synonym="RPL21_31_868"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:645373"
                     /db_xref="HGNC:37042"
     gene            complement(158523689..158622319)
                     /gene="ESYT2"
                     /gene_synonym="CHR2SYT; E-Syt2; FAM62B; KIAA1228"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:57488"
                     /db_xref="HGNC:22211"
                     /db_xref="HPRD:13053"
     mRNA            complement(join(158523689..158526943,158527113..158527162,
                     158528194..158528299,158529739..158529870,
                     158531714..158531812,158534214..158534587,
                     158536220..158536369,158540885..158540971,
                     158542340..158542414,158552177..158552272,
                     158552749..158552838,158554187..158554235,
                     158555774..158555856,158557368..158557544,
                     158560345..158560465,158566032..158566087,
                     158580695..158580784,158581036..158581108,
                     158586341..158586417,158590633..158590767,
                     158591722..158591763,158621780..158622319))
                     /gene="ESYT2"
                     /gene_synonym="CHR2SYT; E-Syt2; FAM62B; KIAA1228"
                     /product="extended synaptotagmin-like protein 2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_020728.2"
                     /db_xref="GI:197245447"
                     /db_xref="GeneID:57488"
                     /db_xref="HGNC:22211"
                     /db_xref="HPRD:13053"
     CDS             complement(join(158526898..158526943,158527113..158527162,
                     158528194..158528299,158529739..158529870,
                     158531714..158531812,158534214..158534587,
                     158536220..158536369,158540885..158540971,
                     158542340..158542414,158552177..158552272,
                     158552749..158552838,158554187..158554235,
                     158555774..158555856,158557368..158557544,
                     158560345..158560465,158566032..158566087,
                     158580695..158580784,158581036..158581108,
                     158586341..158586417,158590633..158590767,
                     158591722..158591763,158621780..158622253))
                     /gene="ESYT2"
                     /gene_synonym="CHR2SYT; E-Syt2; FAM62B; KIAA1228"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="extended synaptotagmin-2"
                     /protein_id="NP_065779.1"
                     /db_xref="GI:45387945"
                     /db_xref="CCDS:CCDS34791.1"
                     /db_xref="GeneID:57488"
                     /db_xref="HGNC:22211"
                     /db_xref="HPRD:13053"
     gene            158649269..158738883
                     /gene="WDR60"
                     /gene_synonym="FLJ10300; FLJ23575"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:55112"
                     /db_xref="HGNC:21862"
                     /db_xref="HPRD:08545"
     mRNA            join(158649269..158649441,158662546..158662599,
                     158663833..158664253,158669300..158669382,
                     158672375..158672680,158677255..158677310,
                     158679712..158679766,158683956..158684024,
                     158694430..158694507,158695067..158695286,
                     158698680..158698782,158704241..158704370,
                     158705676..158705787,158706924..158707012,
                     158711431..158711560,158715068..158715240,
                     158716262..158716424,158718878..158718991,
                     158719093..158719154,158719683..158719734,
                     158723146..158723206,158726820..158726919,
                     158727109..158727240,158734616..158734839,
                     158738272..158738883)
                     /gene="WDR60"
                     /gene_synonym="FLJ10300; FLJ23575"
                     /product="WD repeat domain 60"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_018051.4"
                     /db_xref="GI:155030241"
                     /db_xref="GeneID:55112"
                     /db_xref="HGNC:21862"
                     /db_xref="HPRD:08545"
     CDS             join(158649427..158649441,158662546..158662599,
                     158663833..158664253,158669300..158669382,
                     158672375..158672680,158677255..158677310,
                     158679712..158679766,158683956..158684024,
                     158694430..158694507,158695067..158695286,
                     158698680..158698782,158704241..158704370,
                     158705676..158705787,158706924..158707012,
                     158711431..158711560,158715068..158715240,
                     158716262..158716424,158718878..158718991,
                     158719093..158719154,158719683..158719734,
                     158723146..158723206,158726820..158726919,
                     158727109..158727240,158734616..158734839,
                     158738272..158738470)
                     /gene="WDR60"
                     /gene_synonym="FLJ10300; FLJ23575"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="WD repeat-containing protein 60"
                     /protein_id="NP_060521.4"
                     /db_xref="GI:155030242"
                     /db_xref="CCDS:CCDS47757.1"
                     /db_xref="GeneID:55112"
                     /db_xref="HGNC:21862"
                     /db_xref="HPRD:08545"
     gene            158801045..158818929
                     /gene="LOC154822"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:154822"
     misc_RNA        join(158801045..158802129,158809149..158810337,
                     158812998..158813539,158814364..158814488,
                     158817858..158818929)
                     /gene="LOC154822"
                     /product="hypothetical LOC154822"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NR_024394.1"
                     /db_xref="GI:211971087"
                     /db_xref="GeneID:154822"
     gene            complement(158820866..158937649)
                     /gene="VIPR2"
                     /gene_synonym="FLJ16511; VPAC2; VPCAP2R"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:7434"
                     /db_xref="HGNC:12695"
                     /db_xref="HPRD:03576"
                     /db_xref="MIM:601970"
     mRNA            complement(join(158820866..158823480,158824519..158824560,
                     158824629..158824758,158826904..158826995,
                     158827272..158827341,158828643..158828703,
                     158829443..158829593,158835726..158835867,
                     158851172..158851269,158896448..158896545,
                     158902503..158902610,158935138..158935237,
                     158937413..158937649))
                     /gene="VIPR2"
                     /gene_synonym="FLJ16511; VPAC2; VPCAP2R"
                     /product="vasoactive intestinal peptide receptor 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_003382.4"
                     /db_xref="GI:194733740"
                     /db_xref="GeneID:7434"
                     /db_xref="HGNC:12695"
                     /db_xref="HPRD:03576"
                     /db_xref="MIM:601970"
     CDS             complement(join(158823307..158823480,158824519..158824560,
                     158824629..158824758,158826904..158826995,
                     158827272..158827341,158828643..158828703,
                     158829443..158829593,158835726..158835867,
                     158851172..158851269,158896448..158896545,
                     158902503..158902610,158935138..158935237,
                     158937413..158937463))
                     /gene="VIPR2"
                     /gene_synonym="FLJ16511; VPAC2; VPCAP2R"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="vasoactive intestinal polypeptide receptor 2"
                     /protein_id="NP_003373.2"
                     /db_xref="GI:21361557"
                     /db_xref="CCDS:CCDS5950.1"
                     /db_xref="GeneID:7434"
                     /db_xref="HGNC:12695"
                     /db_xref="HPRD:03576"
                     /db_xref="MIM:601970"
     gene            159023686..159028019
                     /gene="PIP5K1P2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Curated Genomic."
                     /pseudo
                     /db_xref="GeneID:100129824"
                     /db_xref="HGNC:38068"
     gap             159128664..159138663
                     /estimated_length=10000
CONTIG      join(gap(10000),NT_007819.17:1..50360631,gap(40000),
            NT_033968.6:1..7643700,gap(3000000),NT_023603.5:1..256182,
            gap(50000),NT_077528.2:1..556644,gap(50000),
            NT_007933.15:1..77412220,gap(25000),NT_007914.15:1..14866257,
            gap(100000),NT_007741.14:1..4758029,gap(10000))
//
BioPerl-1.007002/t/data/NC_001284.gbk000444000766000024    223424613155576321 16570 0ustar00cjfieldsstaff000000000000LOCUS       NC_001284             366924 bp    DNA     circular PLN 16-OCT-2003
DEFINITION  Arabidopsis thaliana mitochondrion, complete genome.
ACCESSION   NC_001284
VERSION     NC_001284.2  GI:26556996
KEYWORDS    .
SOURCE      mitochondrion Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1
  AUTHORS   Giege,P. and Brennicke,A.
  TITLE     RNA editing in Arabidopsis mitochondria effects 441 C to U changes
            in ORFs
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 96 (26), 15324-15329 (1999)
  MEDLINE   20079652
   PUBMED   10611383
REFERENCE   2  (bases 1 to 366924)
  AUTHORS   Unseld,M., Marienfeld,J.R., Brandt,P. and Brennicke,A.
  TITLE     The mitochondrial genome of Arabidopsis thaliana contains 57 genes
            in 366,924 nucleotides
  JOURNAL   Nat. Genet. 15 (1), 57-61 (1997)
  MEDLINE   97141919
   PUBMED   8988169
REFERENCE   3  (bases 1 to 366924)
  AUTHORS   Marienfeld,J., Unseld,M., Brandt,P. and Brennicke,A.
  TITLE     Genomic recombination of the mitochondrial atp6 gene in Arabidopsis
            thaliana at the protein processing site creates two different
            presequences
  JOURNAL   DNA Res. 3 (5), 287-290 (1996)
  MEDLINE   97191539
   PUBMED   9039497
REFERENCE   4  (bases 1 to 366924)
  AUTHORS   Marienfeld,J.R.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-SEP-1996) J.R. Marienfeld, Institut fuer
            Genbiologische Forschung GmbH, Ihnestrasse 63, 14195 Berlin, FRG
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from Y08501 and
            Y08502.
            On Dec 12, 2002 this sequence version replaced gi:13449290.
FEATURES             Location/Qualifiers
     source          1..366924
                     /organism="Arabidopsis thaliana"
                     /organelle="mitochondrion"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:3702"
                     /sub_clone="pUC19"
                     /sub_clone="pUC18"
                     /sub_clone="pBluescript SK"
                     /sub_clone="pBluescript KS"
                     /clone_lib="Lorist X"
     CDS             complement(join(327890..328078,329735..330306,
                     332945..333105,79740..80132,81113..81297))
                     /EC_number="1.6.99.3"
                     /codon_start=1
                     /exception="trans-splicing"
                     /label=nad2_cds
                     /product="NADH dehydrogenase subunit 2"
                     /protein_id="NP_085584.1"
                     /db_xref="GI:13449314"
                     /db_xref="UniProt/TrEMBL:O05000"
                     /translation="MKAEFVRILPHMFNLFLAVSPEIFIINATSILLIHGVVFSTSKK
                     YDYPPLASNVGWLGLLSVLITLLLLAAGAPLLTIAHLFWNNLFRRDNFTYFCQIFLLL
                     STAGTISMCFDSSDQERFDAFEFIVLIPLPTRGMLFMISAHDLIAMYLAIEPQSLCFY
                     VIAASKRKSEFSTEAGSKYLILGAFSSGILLFGCSMIYGSTGATHFDQLAKILTGYEI
                     TGARSSGIFMGILSIAVGFLFKITAVPFHMWAPDIYEGSPTPVTAFLSIAPKISISAN
                     ILRVSIYGSYGATLQQIFFFCSIASMILGALAAMAQTKVKRPLAHSSIGHVGYIRTGF
                     SCGTIEGIQSLLIGIFIYALMTMDAFAIVSALRQTRVKYIADLGALAKTNPISAITFS
                     ITMFSYAGIPPLAGFCSKFYLFFAALGCGAYFLAPVGVVTSVIGRFYYIRLVKRMFFD
                     TPRTWILYEPMDRNKSLLLAMTSFFITSSLLYPSPLFSVTHQMALSSYL"
     CDS             complement(273..734)
                     /note="orf153a"
                     /codon_start=1
                     /protein_id="NP_085474.1"
                     /db_xref="GI:13449291"
                     /db_xref="UniProt/TrEMBL:P93275"
                     /translation="MSLLFQQTVPLSHLHRSLDPPLCFRTHILLILLLLSRHLPGFTG
                     SDCESADPSIVSAIAPGTATTSERDCPVRTAGSDPVPIGDSGTFFDVGTAAPELLSPN
                     RHHMITRAKDGIRKPNPRYNLFTQKYTPSEPKTITSASQDGDKLCKKRCRH"
     promoter        complement(2485..2493)
                     /note="orf153a"
                     /evidence=not_experimental
     gene            complement(8848..11415)
                     /gene="rrn26"
                     /db_xref="GeneID:814566"
     rRNA            complement(8848..11415)
                     /gene="rrn26"
                     /product="26S ribosomal RNA protein"
                     /db_xref="GeneID:814566"
     CDS             11918..12241
                     /note="orf107a"
                     /codon_start=1
                     /protein_id="NP_085475.1"
                     /db_xref="GI:13449292"
                     /db_xref="UniProt/TrEMBL:P93276"
                     /translation="MFQFAKFSKSKERRLATELGYGFPIGDPWITDGISPWPFASESV
                     LPSQCPGIHPMHSFRSCTQGTLNTTKISMKLTISDCGFEPLTEGFTVLHSTRATTCYH
                     FLFNS"
     CDS             complement(16844..17791)
                     /note="orf315"
                     /codon_start=1
                     /protein_id="NP_085476.1"
                     /db_xref="GI:13449293"
                     /db_xref="UniProt/TrEMBL:P93278"
                     /translation="MTKREYNSQPEMLEGAKSIGAGAATIASAGAAIGIGNVFSSLIH
                     SVARNPSLATTTVLVVTLTLLGGVAAFYLHSFRLKGPLKKIIYLFLVFFIAVGISLIR
                     IKAIHLLGLALPLLVPPLVWNAIGGGGEALPSTGPNGASSYSEWFTYTSDLEDSASSG
                     RTSSSVNQPIQREQAGPSNALPEPAASPVAQQQDHLDQPFGEGGEREARAQEHDRISA
                     EVETITSACENLEAAMVRKAHILLHQRGVTLGDPEDVKRALQLALHDDWEHDIDDRKR
                     HFTVLRRDFGTARCERWNPFIDELRGLGNRQVNARHYVD"
     CDS             16856..17251
                     /note="orf131"
                     /codon_start=1
                     /protein_id="NP_085477.1"
                     /db_xref="GI:13449294"
                     /db_xref="UniProt/TrEMBL:P93277"
                     /translation="MSGVYLTVPQAPELINERIPSFTASCSEVAPEHSEMPLTVIYIV
                     LPVVMESQLESTLDILWIPESYSTLMQENMGFPYHGRLQILAGARDSLYLGRDAVVLL
                     CPSLPFPTFTKWLIQVILLLSYWGSGGFG"
     gene            complement(20571..333105)
                     /gene="nad5"
                     /db_xref="GeneID:814567"
     mRNA            complement(join(20571..20717,21692..22086,190740..190761,
                     140724..141939,142769..142998))
                     /gene="nad5"
                     /note="trans-splicing, RNA editing"
                     /db_xref="GeneID:814567"
     CDS             complement(join(20571..20717,21692..22086,190740..190761,
                     140724..141939,142769..142998))
                     /gene="nad5"
                     /EC_number="1.6.99.3"
                     /codon_start=1
                     /exception="trans-splicing, RNA editing"
                     /product="NADH dehydrogenase subunit 5"
                     /protein_id="NP_085478.1"
                     /db_xref="GI:13449295"
                     /db_xref="UniProt/Swiss-Prot:P29388"
                     /db_xref="GeneID:814567"
                     /translation="MYLLIVFLPLLGSSVAGFFGRFLGSEGSAIMTTTCVSFSSILSL
                     IAFYEVAPGASACYLRIAPWISSEMFDASWGFLFDSPTVVMLIVVTSISSLVHLYSIS
                     YMSEDPHSPRFMCYLSILTFFMPMLVTGDNSLQLFLGWEGVGLASYLLIHFWFTRLQA
                     DKAATKAMLVNRVGDFGLALGISGRFTLFQTVDFSTIFARASAPRNSWISCNMRLNAI
                     SLICILLLIGAVGKSAQIGSHTWSPDAMEGPTPVSASIHAATMVTAGVFMIARCSPLF
                     EYPPTALIVITSAGATTSFLAATTGILQNDLKRVIAYSTCSQLGYMIFACGISNYSVS
                     VFHLMNHAFFKALLFLSAGSVIHAMSDEQDMRKMGGLASSFPLTYAMMLIGSLSLIGF
                     PFLTGFYSKDVILELAYTKYTISGNFAFWLGSVSVLFTSYYSFRLLFLTFLVPTNSFG
                     RDISRCHDAPIPMAIPLILLALGSLFVGYLAKDMMIGLGTNFWANSPLVLPKNEILAE
                     SEFAAPTITKLIPILFSTSGAFVAYNVNPVADQFQRAFQTSTFCNRLYSFFNKRWFFD
                     QVLNDFLVRSFLRFGYEVSFEALDKGAIEILGPYGISYTFRRLAERISQLQSGFVYHY
                     AFAMLLGSTLFVTFSRMWDSLSSWVDNRSSFILIVSSFYTKSSQE"
     exon            complement(20571..20717)
                     /gene="nad5"
                     /number=5
     misc_feature    20623
                     /note="C to U RNA editing"
     misc_feature    20652
                     /note="C to U RNA editing"
     misc_feature    20663
                     /note="C to U RNA editing"
     misc_feature    20665
                     /note="C to U RNA editing"
     misc_feature    20686
                     /note="C to U RNA editing"
     intron          complement(20718..21691)
                     /gene="nad5"
                     /number=4
     exon            complement(21692..22086)
                     /gene="nad5"
                     /number=4
     misc_feature    21975
                     /note="C to U RNA editing"
     misc_feature    22005
                     /note="C to U RNA editing"
     misc_feature    22065
                     /note="C to U RNA editing"
     intron          complement(22087..190739)
                     /gene="nad5"
                     /note="transpliced intron"
                     /number=3
     gene            complement(23663..24235)
                     /gene="nad9"
                     /db_xref="GeneID:814568"
     CDS             complement(23663..24235)
                     /gene="nad9"
                     /EC_number="1.6.99.3"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="NADH dehydrogenase subunit 9"
                     /protein_id="NP_085479.1"
                     /db_xref="GI:13449296"
                     /db_xref="UniProt/Swiss-Prot:Q95748"
                     /db_xref="GeneID:814568"
                     /translation="MDNQFIFKYSWETLPKKWVKKMERSEHGNRSDTNTDYLFQLLCF
                     LKLHTYTRVQVSIDICGVDHPSRKRRFEVVYNLLSTRYNSRIRVQTSADEVTRISPVV
                     SLFPSAGRWEREVWDMFGVSFINHPDLRRISTDYGFEGHPLRKDLPLSGYVQVRYDDP
                     EKRVVSEPIEMTQEFRYFDFASPWEQRSDG"
     misc_feature    23797
                     /note="C to U RNA editing"
     misc_feature    23838
                     /note="C to U RNA editing"
     misc_feature    23908
                     /note="C to U RNA editing"
     misc_feature    23938
                     /note="C to U RNA editing"
     misc_feature    24046
                     /note="C to U RNA editing"
     misc_feature    24069
                     /note="C to U RNA editing"
     misc_feature    24144
                     /note="C to U RNA editing"
     misc_feature    24685
                     /note="C to U RNA editing"
     misc_feature    24693
                     /note="C to U RNA editing"
     misc_feature    24749
                     /note="C to U RNA editing"
     misc_feature    24801
                     /note="C to U RNA editing"
     misc_feature    25004
                     /note="C to U RNA editing"
     misc_feature    25075
                     /note="C to U RNA editing"
     gene            complement(25076..25615)
                     /gene="rpl16"
                     /db_xref="GeneID:814569"
     CDS             complement(25076..25615)
                     /gene="rpl16"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="ribosomal protein L16"
                     /protein_id="NP_085480.1"
                     /db_xref="GI:13449297"
                     /db_xref="UniProt/Swiss-Prot:Q95747"
                     /db_xref="GeneID:814569"
                     /translation="MYLTIKSIMLLRKYLLVTESQVSKCGFHIVKKKGDVLYPKRTKY
                     SKYRKGRCSRGCKPDGTKLGFGRYGTKSCKAGRLSYRAIEAARRAIIGHFHRAMSGQF
                     RRNGKIWVRVFADLPITGKPTEVRMGRGKGNPTGWIARVSTGQIPFEMDGVSLANARQ
                     AATLAAHKPCSSTKFVQWS"
     misc_feature    25104
                     /note="C to U RNA editing"
     misc_feature    25110
                     /note="C to U RNA editing"
     misc_feature    25176
                     /note="C to U RNA editing"
     misc_feature    25387
                     /note="C to U RNA editing"
     misc_feature    25407
                     /note="C to U RNA editing"
     gene            complement(25482..28733)
                     /gene="rps3"
                     /db_xref="GeneID:814570"
     mRNA            complement(join(25482..27077,28659..28733))
                     /gene="rps3"
                     /db_xref="GeneID:814570"
     CDS             complement(join(25482..27077,28659..28733))
                     /gene="rps3"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="ribosomal protein S3"
                     /protein_id="NP_085481.1"
                     /db_xref="GI:13449298"
                     /db_xref="UniProt/TrEMBL:Q95749"
                     /db_xref="GeneID:814570"
                     /translation="MARKGNPISVRLGKNRSSDSSRFSEYYYGKFVYQDVNLRSYFGS
                     IRPPTRLTFGFRLGRCIILHFPKRTFIHFFLPRRPRRLKRREKTRPGKEKGRWWTTFG
                     KAGPIECLHSSDDTEEERNEVRGRGARKRVESIRLDDRKKQNEIRGWPKKKQRYGYHD
                     RLPSIKKNLSKSLRISGAFKHPKYAGVVNDIAFLIENDDSFKKTKLFKLFFQNKSRSD
                     GPTSYLRTLPAVRPSLNFLVMQYFFNTKNQINFDPVVVLNHFVAPGAAEPSTMGRANA
                     QGRSLQKRIRSRIAFFVESSTSEKKCLAEAKNRLTHFIRLANDLRFAGTTKTTISLFP
                     FFGATFFFLRDGVGVYNNLDAREQLLNQLRVKCWNLVGKDKIMELIEKLKNLGGIEEL
                     IKVIDMMIEIILRKRGIPYRYNSYFYEVKKMRSFLSNRTNTKTLIESVKIKSVYQSAS
                     PIAQDISFQLKNKRRSFHSIFAKIVKEIPKGVEGIRICFSGRLKDAAEKAQTKCYKHR
                     KTSRNVFNHKIDYAPAEVSTRYGISGVKVWISYSQKKGRRAISETYEI"
     exon            complement(25482..27077)
                     /gene="rps3"
                     /number=2
     misc_feature    25555
                     /note="C to U RNA editing"
     misc_feature    25573
                     /note="C to U RNA editing"
     misc_feature    25582
                     /note="C to U RNA editing"
     misc_feature    25619
                     /note="C to U RNA editing"
     misc_feature    25683
                     /note="C to U RNA editing"
     misc_feature    25801
                     /note="C to U RNA editing"
     misc_feature    25809
                     /note="C to U RNA editing"
     misc_feature    26266
                     /note="C to U RNA editing"
     misc_feature    26550
                     /note="C to U RNA editing"
     misc_feature    26638
                     /note="C to U RNA editing"
     misc_feature    26966
                     /note="C to U RNA editing"
     misc_feature    27027
                     /note="C to U RNA editing"
     intron          complement(27078..28658)
                     /gene="rps3"
                     /number=1
     exon            complement(28659..28733)
                     /gene="rps3"
                     /number=1
     misc_feature    28670
                     /note="C to U RNA editing"
     gene            complement(28898..28970)
                     /gene="tRNA-Lys"
                     /db_xref="GeneID:814571"
     tRNA            complement(28898..28970)
                     /gene="tRNA-Lys"
                     /product="tRNA-Lys"
                     /db_xref="GeneID:814571"
     gene            30463..31083
                     /gene="ccb206"
                     /db_xref="GeneID:814572"
     CDS             30463..31083
                     /gene="ccb206"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="cytochrome c biogenesis orf206"
                     /protein_id="NP_085482.1"
                     /db_xref="GI:13449299"
                     /db_xref="UniProt/TrEMBL:P93280"
                     /db_xref="GeneID:814572"
                     /translation="MRRLFLELYHKLIFSSTPITSFSSFLSYIVVTPLMLGFEKDFSC
                     HSHLGPIRIPPLFPFPPAPFPRNEKEDGTLELYYLSTYCLPKILLLQLVGHRVIQISR
                     VFCGFPMLQLSYQFGRSGMDRLNIPLGSLVLTLLCGIHSRSALGITSSSGWNSSQNPT
                     TSPTLLPLTVSRTSIETEWFHVLSSIGYSSLFVSLFPISVSISLQD"
     misc_feature    30478
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30490
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30533
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30537
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30540
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30542
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30590
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30599
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30610
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30611
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30616
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30621
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30622
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30626
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30634
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30641
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30643
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30650
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30655
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30656
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30748
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30766
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30800
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30829
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30841
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30842
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30868
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30886
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30890
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30929
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30937
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30938
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30947
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30974
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    30976
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    31013
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    31016
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    31028
                     /gene="ccb206"
                     /note="C to U RNA editing"
     misc_feature    31031
                     /gene="ccb206"
                     /note="C to U RNA editing"
     CDS             complement(32041..32472)
                     /gene="nad5"
                     /note="orf143"
                     /codon_start=1
                     /protein_id="NP_085483.1"
                     /db_xref="GI:13449300"
                     /db_xref="UniProt/TrEMBL:P93281"
                     /db_xref="GeneID:814567"
                     /translation="MAGQCLMQEIALYELFFFSLLKTGSFGLSARMEIFFSKTAWNLI
                     RQTYPKVDYAGIVRNKFNIPNPSHSIIAWMALNSGLQQIELADFIPTNTVTLCGLCML
                     EDESAEHLFSAAMQGGFFLSSVRNVDMISLQPTFMMFANGL"
     CDS             34190..34555
                     /note="orf121a"
                     /codon_start=1
                     /protein_id="NP_085484.1"
                     /db_xref="GI:13449301"
                     /db_xref="UniProt/TrEMBL:P93282"
                     /translation="MASKIRKVTNQNMRINSSLSKSSTFSTRLRITDSYLSSPSVTEL
                     APLTLTTGDDFTVTLSVTPTMNSLESQVICPRAYDCKERIPPNQHIVSLELTYHPASI
                     EPTATGSPETRDPDPSAYA"
     CDS             34599..35102
                     /note="orf167"
                     /codon_start=1
                     /protein_id="NP_085485.1"
                     /db_xref="GI:13449302"
                     /db_xref="UniProt/TrEMBL:P93283"
                     /translation="MNQLDQYSQPMQHLILLWFWLLDLSPPPSFHLSVKSVDLSLFSL
                     SPLFLLLSISSLIFSRVNKFGIRRVGYAMAPKPDPTVLPDLQEKKAILGTQIEMITQA
                     MTTLESRVTDLQQESNDHRTWVREALDKLLKRDLGDENRPKPTTNKMIATGEQHKGEV
                     STSLFHD"
     promoter        35638..35646
                     /note="orf116"
                     /evidence=not_experimental
     CDS             35782..36132
                     /note="orf116"
                     /codon_start=1
                     /protein_id="NP_085486.1"
                     /db_xref="GI:13449303"
                     /db_xref="UniProt/TrEMBL:P93284"
                     /translation="MSRSSIGPELEVNSKPLKGPIICPIRTYYSKVPLELLFPTTDRR
                     FYFLKSYVFCSANSVPLYLLLLTSALHFNSYILLFDFQLKSKLLAYKRRARCVAGLLK
                     SMERYPESTVTAMI"
     gene            complement(40502..42628)
                     /gene="cox2"
                     /db_xref="GeneID:814573"
     mRNA            complement(join(40502..40585,41930..42628))
                     /gene="cox2"
                     /db_xref="GeneID:814573"
     CDS             complement(join(40502..40585,41930..42628))
                     /gene="cox2"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="cytochrome c oxidase subunit 2"
                     /protein_id="NP_085487.1"
                     /db_xref="GI:13449304"
                     /db_xref="UniProt/TrEMBL:P93285"
                     /db_xref="GeneID:814573"
                     /translation="MIVLKWLFLTISPCDAAEPWQLGSQDAATPIMQGIIDLHHDIFF
                     FLILILVFVLWILVRALWHFHYKKNAIPQRIVHGTTIEILRTIFPSIISMFIAIPSFA
                     LLYSMDEVVVDPAITIKAIGHQWYRTYEYSDYNSSDEQSLTFDSYMIPEEDLELGQSR
                     LLEVDNRVVVPAKTHLRIIVTSADVPHSWAVPSSGVKCDAVPGRLNQISILVQREGVY
                     YGQCSEICGTNHAFTSIVVEAVPRKDYGSRVSNQLIPQTGEA"
     exon            complement(40502..40585)
                     /gene="cox2"
                     /number=2
     misc_feature    40543
                     /note="C to U RNA editing"
     misc_feature    40564
                     /note="C to U RNA editing"
     intron          complement(40586..41929)
                     /gene="cox2"
                     /number=1
     exon            complement(41930..42628)
                     /gene="cox2"
                     /number=1
     misc_feature    41931
                     /note="C to U RNA editing"
     misc_feature    42048
                     /note="C to U RNA editing"
     misc_feature    42072
                     /note="C to U RNA editing"
     misc_feature    42153
                     /note="C to U RNA editing"
     misc_feature    42250
                     /note="C to U RNA editing"
     misc_feature    42351
                     /note="C to U RNA editing"
     misc_feature    42368
                     /note="C to U RNA editing"
     misc_feature    42376
                     /note="C to U RNA editing"
     misc_feature    42491
                     /note="C to U RNA editing"
     misc_feature    42558
                     /note="C to U RNA editing"
     misc_feature    42602
                     /note="C to U RNA editing"
     misc_feature    42604
                     /note="C to U RNA editing"
     misc_feature    42605
                     /note="C to U RNA editing"
     repeat_unit     44698..48894
                     /note="repeat I"
     promoter        46909..48917
                     /note="orf139a"
                     /evidence=not_experimental
     CDS             48113..48532
                     /note="orf139a
                     identical to orf139b"
                     /codon_start=1
                     /protein_id="NP_085488.1"
                     /db_xref="GI:13449305"
                     /db_xref="UniProt/TrEMBL:P94024"
                     /translation="MIQRTRNQSIMLSLPSNQSANHAILTFQPIGQSRYLLTFQPTPS
                     IPLLQQYIISVPYLDAYSSICFPVMARIRSAKYCFFFFLVLFLNGIIATRGKAMLPTL
                     PQKGAAFFPPKMPVPPSGPSKQHNSAPRSDFVQFFYM"
     gene            complement(51293..53611)
                     /gene="ccb452"
                     /db_xref="GeneID:814574"
     mRNA            complement(join(51293..51871,52832..53611))
                     /gene="ccb452"
                     /db_xref="GeneID:814574"
     CDS             complement(join(51293..51871,52832..53611))
                     /gene="ccb452"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="cytochrome c biogenesis orf452"
                     /protein_id="NP_085489.1"
                     /db_xref="GI:13449306"
                     /db_xref="UniProt/TrEMBL:P93286"
                     /db_xref="GeneID:814574"
                     /translation="MVQLHNFFFFIIFMVVPCGTAAPVLLKWFVSRDVPTGAPFSNGT
                     IIPIPISSFPLLVYLHSRKIIRSMDGAKSGVLVRASRPILLPDIIGRSSSETRARKAL
                     FFFVPVLHFRLLESKGDFSYLESFCGVLCLLFFRTFLFLARDRSAKRERARRRKGQTL
                     RPNGNEQRRNDKMRCSGHPHLDLERRVEGFGPLAFPVPPELGGACVGGVPPEIGLEAL
                     ALPRSRQLMAMAVGHDYYQKVPMKMNISHGGVCICMLGVLLSNTKKIQFTQRLPLGYE
                     LHMGKERCCLRGLDHLHGPTFHSICGNLMIYKPSLTNDRLMFEHDESLHADLLLINFP
                     ASYKNGKLEHFLHWWMKNRKHNNFWLTMFPEKRYFRERTSTAEVAIHTNLFTDLYASI
                     GTGSSRTGGWYTTIMKLPFIFFIRIGFMLASLGGSPSLLRQLQKDKLRWNRESSVEFI
                     IA"
     exon            complement(51293..51871)
                     /gene="ccb452"
                     /number=2
     misc_feature    51325
                     /note="C to U RNA editing"
     misc_feature    51372
                     /note="C to U RNA editing"
     misc_feature    51406
                     /note="C to U RNA editing"
     misc_feature    51437
                     /note="C to U RNA editing"
     misc_feature    51480
                     /note="C to U RNA editing"
     misc_feature    51727
                     /note="C to U RNA editing"
     intron          complement(51872..52831)
                     /gene="ccb452"
                     /number=1
     exon            complement(52832..53611)
                     /gene="ccb452"
                     /number=1
     misc_feature    53197
                     /note="C to U RNA editing"
     misc_feature    53206
                     /note="C to U RNA editing"
     misc_feature    53278
                     /note="C to U RNA editing"
     misc_feature    53437
                     /note="C to U RNA editing"
     misc_feature    53452
                     /note="C to U RNA editing"
     misc_feature    53457
                     /note="C to U RNA editing"
     misc_feature    53466
                     /note="C to U RNA editing"
     misc_feature    53490
                     /note="C to U RNA editing"
     misc_feature    53509
                     /note="C to U RNA editing"
     misc_feature    53562
                     /note="C to U RNA editing"
     gene            complement(53736..53809)
                     /gene="tRNA-Gly"
                     /db_xref="GeneID:814575"
     tRNA            complement(53736..53809)
                     /gene="tRNA-Gly"
                     /product="tRNA-Gly"
                     /db_xref="GeneID:814575"
     CDS             complement(55767..56090)
                     /gene="nad5"
                     /note="orf107b"
                     /codon_start=1
                     /protein_id="NP_085490.1"
                     /db_xref="GI:13449307"
                     /db_xref="UniProt/TrEMBL:P93287"
                     /db_xref="GeneID:814567"
                     /translation="MLNAFAFPQTNECFPAKRGFCANERTKCLNPKMPSKSMFGGSVS
                     ENLFLSKIRIGLSFPLPLSEIKLQNQDFRLEGQMSSFDPFVDESKALVRRLGQKVKAK
                     SFLCR"
     gene            57774..58331
                     /gene="rpl5"
                     /db_xref="GeneID:814576"
     CDS             57774..58331
                     /gene="rpl5"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="ribosomal protein L5"
                     /protein_id="NP_085491.1"
                     /db_xref="GI:13449308"
                     /db_xref="UniProt/Swiss-Prot:P42793"
                     /db_xref="GeneID:814576"
                     /translation="MFPLNFHYEDVSRQDPLLKPNHANVMEVPGSCEIRVVPKAPYNF
                     IIKNGKLAMEIPRGQKFIQTQRGSTGKSFRSNPFLGSNKDKGYVSDLARQSTLRGHGM
                     SNFSVRISTVMSLLDFPVEIRKNSIQFSMETEFCEFSPELEDHFEIFEHIRGFNVTII
                     TSANTQDETLPLWSGFLQKDEGETQ"
     misc_feature    57808
                     /gene="rpl5"
                     /note="C to U RNA editing"
     misc_feature    57820
                     /gene="rpl5"
                     /note="C to U RNA editing"
     misc_feature    57831
                     /gene="rpl5"
                     /note="C to U RNA editing"
     misc_feature    57832
                     /gene="rpl5"
                     /note="C to U RNA editing"
     misc_feature    57837
                     /gene="rpl5"
                     /note="C to U RNA editing"
     misc_feature    57865
                     /gene="rpl5"
                     /note="C to U RNA editing"
     misc_feature    57942
                     /gene="rpl5"
                     /note="C to U RNA editing"
     misc_feature    58090
                     /gene="rpl5"
                     /note="C to U RNA editing"
     misc_feature    58102
                     /gene="rpl5"
                     /note="C to U RNA editing"
     misc_feature    58285
                     /gene="rpl5"
                     /note="C to U RNA editing"
     misc_feature    58526
                     /note="C to U RNA editing"
     gene            60235..61416
                     /gene="cob"
                     /db_xref="GeneID:814577"
     CDS             60235..61416
                     /gene="cob"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="apocytochrome B"
                     /protein_id="NP_085492.1"
                     /db_xref="GI:13449309"
                     /db_xref="UniProt/TrEMBL:P93289"
                     /db_xref="GeneID:814577"
                     /translation="MTIRNQRFSLLKQPISSTLNQHLVDYPTPSNLSYWWGFGPLAGI
                     CLVIQIVTGVFLAMHYTPHVDLAFNSVEHIMRDVEGGWLLRYMHANGASMFLIVVYLH
                     IFRGLYHASYSSPREFVWCLGVVIFLLMIVTAFIGYVLPWGQMSFWGATVITSLASAI
                     PVVGDTIVTWLWGGFSVDNATLNRFFSLHHLLPFILVGASLLHLAALHQYGSNNPLGV
                     HSEMDKIAFYPYFYVKDLVGWVAFAIFFSIWIFYAPNVLGHPDNYIPANPMSTPPHIV
                     PEWYFLPIHAILRSIPDKAGGVAAIAPVFICLLALPFFKSMYVRSSSFRPIHQGMFWL
                     LLADCLLLGWIGCQPVEAPFVTIGQISPLVFFLFFAITPILGRVGRGIPNSYTDETDH
                     T"
     misc_feature    60520
                     /gene="cob"
                     /note="C to U RNA editing"
     misc_feature    60559
                     /gene="cob"
                     /note="C to U RNA editing"
     misc_feature    60802
                     /gene="cob"
                     /note="C to U RNA editing"
     misc_feature    61087
                     /gene="cob"
                     /note="C to U RNA editing"
     misc_feature    61142
                     /gene="cob"
                     /note="C to U RNA editing"
     misc_feature    61216
                     /gene="cob"
                     /note="C to U RNA editing"
     misc_feature    61318
                     /gene="cob"
                     /note="C to U RNA editing"
     gene            62349..62433
                     /gene="tRNA-Ser"
                     /db_xref="GeneID:814578"
     tRNA            62349..62433
                     /gene="tRNA-Ser"
                     /product="tRNA-Ser"
                     /db_xref="GeneID:814578"
     CDS             complement(68918..69253)
                     /gene="nad5"
                     /note="orf111a"
                     /codon_start=1
                     /protein_id="NP_085493.1"
                     /db_xref="GI:13449310"
                     /db_xref="UniProt/TrEMBL:P93290"
                     /db_xref="GeneID:814567"
                     /translation="MYLTITRPDLTFAVNRLSQFSSASRTAQMQAVYKVLHYVKGTVG
                     QGLFYSATSDLQLKAFADSDWASCPDTRRSVTGFCSLVPLWFLGALRKSILSPGLLQR
                     QNIEALHLL"
     gene            71349..71526
                     /gene="tRNA-fMet"
                     /db_xref="GeneID:814579"
     promoter        71349..71357
                     /gene="tRNA-fMet"
                     /evidence=not_experimental
     tRNA            71453..71526
                     /gene="tRNA-fMet"
                     /product="tRNA-Met"
                     /note="fMet"
                     /db_xref="GeneID:814579"
     CDS             76132..76437
                     /note="orf101a"
                     /codon_start=1
                     /protein_id="NP_085494.1"
                     /db_xref="GI:13449311"
                     /db_xref="UniProt/TrEMBL:P93291"
                     /translation="MSRLELGKEAVALLTLYEEGVKSLAIVDTLRSARQEQYRKHRMP
                     WFLLQTRLQVRVIESAQLGMLPMPIPELLKEAVAVQPLNLNGIAHSSSSINSFLLFE"
     gene            complement(76642..77259)
                     /gene="nad6"
                     /db_xref="GeneID:814580"
     CDS             complement(76642..77259)
                     /gene="nad6"
                     /EC_number="1.6.99.3"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="NADH dehydrogenase subunit 6"
                     /protein_id="NP_085495.1"
                     /db_xref="GI:13449312"
                     /db_xref="UniProt/Swiss-Prot:Q01825"
                     /db_xref="GeneID:814580"
                     /translation="MILSVLSSPALVSGLMVARAKNPVHSVLFPIPVFRDTSGLLLLL
                     GLDFFAMIFPVVHIGAIAVSFLFVVMMFHIQIAEIHEEVLRYLPVSGIIGLIFWWEMF
                     FILDNESIPLLPTQRNTTSLRYTVYAGKVRSWTNLETLGNLLYTYYSVWFLVPSLILL
                     VAMIGAIVLTMHRTTKVKRQDVFRRNAIDFRRTIMRRTTDPLTIY"
     misc_feature    76814
                     /note="C to U RNA editing"
     misc_feature    77069
                     /note="C to U RNA editing"
     misc_feature    77091
                     /note="C to U RNA editing"
     misc_feature    77099
                     /note="C to U RNA editing"
     misc_feature    77157
                     /note="C to U RNA editing"
     misc_feature    77165
                     /note="C to U RNA editing"
     misc_feature    77171
                     /note="C to U RNA editing"
     misc_feature    77172
                     /note="C to U RNA editing"
     misc_feature    77207
                     /note="C to U RNA editing"
     misc_feature    77234
                     /note="C to U RNA editing"
     misc_feature    77332
                     /note="C to U RNA editing"
     CDS             complement(77819..78151)
                     /gene="nad5"
                     /note="orf110a"
                     /codon_start=1
                     /protein_id="NP_085496.1"
                     /db_xref="GI:13449313"
                     /db_xref="UniProt/TrEMBL:P93292"
                     /db_xref="GeneID:814567"
                     /translation="MNNAAKRADCWFGAKNYGRAVYECLRGGLYFTKDDENVNSQPFM
                     RWRDRFLFCAEAVYKAQAETGGIKGHYLNATAGTCEEMIKRAVFARELGVPIVMHDYL
                     NRGIHRKY"
     mRNA            complement(join(79740..<80132,81113..81297))
                     /gene="nad5"
                     /label=nad2_mrna
                     /db_xref="GeneID:814567"
     exon            complement(79740..80132)
                     /gene="nad2"
                     /label=nad2_ex2
     misc_feature    79760
                     /note="C to U RNA editing"
     misc_feature    79788
                     /note="C to U RNA editing"
     misc_feature    79790
                     /note="C to U RNA editing"
     misc_feature    79857
                     /note="C to U RNA editing"
     misc_feature    79877
                     /note="C to U RNA editing"
     misc_feature    79891
                     /note="C to U RNA editing"
     misc_feature    79918
                     /note="C to U RNA editing"
     misc_feature    79924
                     /note="C to U RNA editing"
     misc_feature    79929
                     /note="C to U RNA editing"
     misc_feature    79974
                     /note="C to U RNA editing"
     misc_feature    79977
                     /note="C to U RNA editing"
     intron          complement(80133..81112)
                     /gene="nad2"
                     /number=1
     exon            complement(81113..>81297)
                     /gene="nad2"
                     /label=ex1
     misc_feature    81208
                     /note="C to U RNA editing"
     misc_feature    81209
                     /note="C to U RNA editing"
     misc_feature    81239
                     /note="C to U RNA editing"
     gene            complement(82028..83116)
                     /gene="rps4"
                     /db_xref="GeneID:814581"
     CDS             complement(82028..83116)
                     /gene="rps4"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="ribosomal protein S4"
                     /protein_id="NP_085497.1"
                     /db_xref="GI:13449315"
                     /db_xref="UniProt/Swiss-Prot:Q31708"
                     /db_xref="GeneID:814581"
                     /translation="MWLLKKLIQRDIDLSPLRFQTCRLLSGNVRNRELTIIQRRILRR
                     LRNRKRSIKKRKIYPKKYLTSYIQLQTTRKLPLFHGDLPITEMHRGTKRTSYIPFPLN
                     PETRFDVIPLRLHFLETIPQARQPISHRRVCVNKGMVSITHFKLSHGDIISFQENNAI
                     IRGEEIRRSFYKEISVEKIIGKLLHQPLRMWRRSKTEWFHLLKTKRGCRLLLKSRFLQ
                     QLRSSMQEEDLERTKKFGSEKVCLGSSFAEHKRMKRNLLKSLFLSKRRKDKNLNLPTR
                     TISPIVYNSSLSLYSNSTYCFASPHKLTMKRRIKRIELPTHYSEVNHRTPKAVVSYGP
                     NIGHIPHDIRLKDPNLPLRSRNGRGQNI"
     misc_feature    82060
                     /note="C to U RNA editing"
     misc_feature    82065
                     /note="C to U RNA editing"
     misc_feature    82074
                     /note="C to U RNA editing"
     misc_feature    82075
                     /note="C to U RNA editing"
     misc_feature    82125
                     /note="C to U RNA editing"
     misc_feature    82150
                     /note="C to U RNA editing"
     misc_feature    82161
                     /note="C to U RNA editing"
     misc_feature    82593
                     /note="C to U RNA editing"
     misc_feature    82740
                     /note="C to U RNA editing"
     misc_feature    82774
                     /note="C to U RNA editing"
     misc_feature    82809
                     /note="C to U RNA editing"
     misc_feature    82818
                     /note="C to U RNA editing"
     misc_feature    82882
                     /note="C to U RNA editing"
     misc_feature    82888
                     /note="C to U RNA editing"
     misc_feature    83029
                     /note="C to U RNA editing"
     CDS             complement(89617..90054)
                     /gene="nad5"
                     /note="orf145a"
                     /codon_start=1
                     /protein_id="NP_085498.1"
                     /db_xref="GI:13449316"
                     /db_xref="UniProt/TrEMBL:P93293"
                     /db_xref="GeneID:814567"
                     /translation="MRKGERMLATSKEWERPRPVEASCSEGVLKVLKGCRTILKGNRH
                     DSLYILQGSVETGESNLAETAKDETRLWHSRLAHMSQRGMELLVKKGFLDSSKVSSLK
                     FCEDCIYGKTHRVNFSTGQHTTKNPLDYVHSDLWGAPSVPLSF"
     CDS             complement(90883..91347)
                     /gene="nad5"
                     /note="orf154"
                     /codon_start=1
                     /protein_id="NP_085499.1"
                     /db_xref="GI:13449317"
                     /db_xref="UniProt/TrEMBL:P93295"
                     /db_xref="GeneID:814567"
                     /translation="MALPVYAMSCFRLSKLLCKKLTSAMTEFWWSSCENKRKISWVAW
                     QKLCKSKEDDGGLGFRDLGWFNQALLAKQSFRIIHQPHTLLSRLLRSRYFPHSSMMEC
                     SVGTRPSYAWRSIIHGRELLSRGLLRTIGDGIHTKVWLDRWIMDETPLPPLN"
     CDS             91001..91384
                     /note="orf127"
                     /codon_start=1
                     /protein_id="NP_085500.1"
                     /db_xref="GI:13449318"
                     /db_xref="UniProt/TrEMBL:P93294"
                     /translation="MILLQAYEGLVPTLHSIIELCGKYRLRRSRDSSVCGWCIIRKDC
                     FARRAWLNQPKSRKPKPPSSSLDLHNFCQATHEIFLLFSQELHQNSVIALVNFLHSSF
                     ESRKHDIAYTGKAIAIDFSSTSFPP"
     promoter        complement(92271..92279)
                     /gene="nad5"
                     /note="orf145a"
                     /evidence=not_experimental
     gene            98939..103914
                     /gene="tRNA-Ser"
                     /db_xref="GeneID:814582"
     promoter        98939..98947
                     /gene="tRNA-Ser"
                     /evidence=not_experimental
     gene            103752..104295
                     /gene="tRNA-Tyr"
                     /db_xref="GeneID:814583"
     promoter        103752..103760
                     /gene="tRNA-Tyr"
                     /evidence=not_experimental
     repeat_unit     103805..104337
                     /note="repeat II"
     tRNA            103827..103914
                     /gene="tRNA-Ser"
                     /product="tRNA-Ser"
     tRNA            104221..104295
                     /gene="tRNA-Tyr"
                     /product="tRNA-Tyr"
                     /db_xref="GeneID:814583"
     gene            104457..104531
                     /gene="tRNA-Pro"
                     /db_xref="GeneID:814584"
     tRNA            104457..104531
                     /gene="tRNA-Pro"
                     /product="tRNA-Pro"
                     /db_xref="GeneID:814584"
     gene            104885..104995
                     /gene="tRNA-Cys"
                     /db_xref="GeneID:814585"
     tRNA            104885..104995
                     /gene="tRNA-Cys"
                     /product="tRNA-Cys"
                     /db_xref="GeneID:814585"
     CDS             complement(104954..105553)
                     /gene="nad5"
                     /note="orf199"
                     /codon_start=1
                     /protein_id="NP_085501.1"
                     /db_xref="GI:13449319"
                     /db_xref="UniProt/TrEMBL:P93296"
                     /db_xref="GeneID:814567"
                     /translation="MVFQSFILGNLVYLCMKIINSVVVVGLYYGFLTTFSIGPSYLFL
                     LRARVMDEGEEGTEKKVSATTGFIAGQLMMFISIYYAPLHLALGRPHTITVLALPYLL
                     FHFFFWNNHKHFFDYGSTTRNEMRNLRIQCVFPNNLIFKLFNHLILPSSMLARLVNIY
                     MFRCNNKMLFVTSSFVVCVRMLLVEWAFPLFQLFLVMKV"
     promoter        complement(105653..105661)
                     /gene="nad5"
                     /note="orf199"
                     /evidence=not_experimental
     gene            105887..105948
                     /gene="tRNA-Asn"
                     /db_xref="GeneID:814586"
     tRNA            105887..105948
                     /gene="tRNA-Asn"
                     /product="tRNA-Asn"
                     /db_xref="GeneID:814586"
     gene            106797..106879
                     /gene="tRNA-Tyr"
                     /db_xref="GeneID:814587"
     tRNA            106797..106879
                     /gene="tRNA-Tyr"
                     /product="tRNA-Tyr"
                     /db_xref="GeneID:814587"
     CDS             complement(110930..111403)
                     /gene="nad5"
                     /note="orf157"
                     /codon_start=1
                     /protein_id="NP_085502.1"
                     /db_xref="GI:13449320"
                     /db_xref="UniProt/TrEMBL:P93297"
                     /db_xref="GeneID:814567"
                     /translation="MGDLEGQDRPDPISTMVGPSGTGNLRLTSFQQVRRSILSQERRN
                     PAPLATCTKKKLGRKEEPLLIPATINNYRRAIHLKNGARISLDVGLYFFRRARFGTLK
                     QDMIYIIRHHRRLEIKVRFIALLIQACCRIVGYDYLFFYEVRNHLLLAALLIIIR"
     gene            111587..112907
                     /gene="atp6-1"
                     /db_xref="GeneID:814588"
     promoter        111587..111595
                     /gene="atp6-1"
                     /evidence=not_experimental
     CDS             111750..112907
                     /gene="atp6-1"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="ATPase subunit 6"
                     /protein_id="NP_085503.1"
                     /db_xref="GI:13449321"
                     /db_xref="UniProt/TrEMBL:P93298"
                     /db_xref="GeneID:814588"
                     /translation="MRRIFLFDENSLNSSSTIDTSSASTIDTSFASQCTNFSSGQASG
                     TQDTHAGIFEDCPGLNPNDERVVELQCEIREKCEALTQDPEMGLILGEALHAESDNVP
                     FLQSIADDLTQNGVSGEAFQEALNIVGQAAASPLDQFEIVPLIPMHIGNFYFSFTNPS
                     LFMLLTLSFFLLLIHFVTKKGGGNLVPNAWQSLVELLYDFVLNLVKEQIGGLSGNVKQ
                     MFFPCILVTFLFLLFCNLQGMIPYSFTVTSHFLITLALSFSIFIGITIVGFQRHGLHF
                     FSFLLPAGVPLPLAPFLVLLELISYCFRALSLGIRLFANMMAGHSLVKILSGFAWTML
                     CMNDIFYFIGALGPLFIVLALTGLELGVAILQAYVFTILICIYLNDAINLH"
     repeat_unit     112147..118736
                     /note="repeat III"
     misc_feature    112224
                     /gene="atp6-1"
                     /note="C to U RNA editing"
     gene            112953..113039
                     /gene="tRNA-Ser"
                     /db_xref="GeneID:814589"
     tRNA            112953..113039
                     /gene="tRNA-Ser"
                     /product="tRNA-Ser"
                     /db_xref="GeneID:814589"
     CDS             115431..115751
                     /note="orf106a
                     identical to orf106g"
                     /codon_start=1
                     /protein_id="NP_085504.1"
                     /db_xref="GI:13449322"
                     /db_xref="UniProt/TrEMBL:P93299"
                     /translation="MLHRGRSCLTGLFPCYLLSNWLNSNLCWIPLKLVIPCFQLIVES
                     YLLEFLLLLAISTCLLGEDSLIWLTLVVAHSKSRQSSSQEPLDTRMATRALLDQLRSD
                     RRHN"
     CDS             116296..116754
                     /note="orf152a
                     identical to orf152b"
                     /codon_start=1
                     /protein_id="NP_085505.1"
                     /db_xref="GI:13449323"
                     /db_xref="UniProt/TrEMBL:P93300"
                     /translation="MPTILSSKPAFNSLFSYHLIGLISNKLVTLAPDYTGTKKTTWGA
                     RLHLQELRVQTKHRQIEPDIKNLPLQPIRYGSFRPVFHWIEKPCMLIGLCGLHSEVSF
                     IANWPWGKPSEIGGCSIPCMLTGRGSELSYHIRASRRPLPGNRFHFQSFF"
     CDS             complement(119381..119701)
                     /gene="nad5"
                     /note="orf106b"
                     /codon_start=1
                     /protein_id="NP_085506.1"
                     /db_xref="GI:13449324"
                     /db_xref="UniProt/TrEMBL:P93301"
                     /db_xref="GeneID:814567"
                     /translation="MVVTAYPKSSAGMGVTVLPEYLKQSSYEAYSRPYSAFFLSGCTK
                     QERSPLLARRLVDAWLSFHSILMINEEVSDWEQLSDHYTRRSLFKTIAFRNLQREEEY
                     RPGG"
     gene            complement(127021..127094)
                     /gene="tRNA-Ile"
                     /db_xref="GeneID:814590"
     tRNA            complement(127021..127094)
                     /gene="tRNA-Ile"
                     /product="tRNA-Ile"
                     /db_xref="GeneID:814590"
     CDS             complement(127475..127843)
                     /gene="nad5"
                     /note="orf122a"
                     /codon_start=1
                     /protein_id="NP_085507.1"
                     /db_xref="GI:13449325"
                     /db_xref="UniProt/TrEMBL:P93302"
                     /db_xref="GeneID:814567"
                     /translation="MILNLDTNIFNHGLSRHNILAFSQGFPIGLPCRNWIEVGLRLRL
                     RLLLELAVGNFPQGFKIHLSGSFQAVRLALFSSFTSLRTDELLLIETRPSYLSSVQGL
                     KYYVIFIDNYSQGSVGCSRN"
     misc_feature    129794
                     /note="C to U RNA editing"
     misc_feature    129825
                     /note="C to U RNA editing"
     gene            129909..130385
                     /gene="orfB"
                     /db_xref="GeneID:814591"
     CDS             129909..130385
                     /gene="orfB"
                     /codon_start=1
                     /protein_id="NP_085508.1"
                     /db_xref="GI:13449326"
                     /db_xref="UniProt/TrEMBL:P93303"
                     /db_xref="GeneID:814591"
                     /translation="MPQLDKFTYFSQFFWLCLFFFTFYIFICNDGDGVLGISRILKLR
                     NQLLSHRGKTIRSKDPNSLEDLLRKGFSTGVSYMYASLFEVSQWCKAVDLLGKRRKIT
                     LISCFGEISGSRGMERNILYNISKSSPSNTGRWITCRNCRNDIMLIHVVHGQGSIK"
     CDS             130817..131140
                     /note="orf107c"
                     /codon_start=1
                     /protein_id="NP_085509.1"
                     /db_xref="GI:13449327"
                     /db_xref="UniProt/TrEMBL:P93304"
                     /translation="MAVRCSKIQRTDGRPGHSLQPAKVSFVAGQPLGYYSSWPLFALS
                     HHMVVWYAAEHVYPSSFFFQSKLPPSEVFAYPGMEVFNEYTLYHAWVDEALSGVSKME
                     LYAKA"
     CDS             130968..131393
                     /note="orf141"
                     /codon_start=1
                     /protein_id="NP_085510.1"
                     /db_xref="GI:13449328"
                     /db_xref="UniProt/TrEMBL:P93305"
                     /translation="MRQNMSILPPSSFSRNFLLVRCSPIQVWKYSMNTLCTMHGWMKL
                     YLEYQRWNCMLRLSASIELEVFMDVPIFIRTYYRPANMDDSFRYGIIFRMYDLAVQLQ
                     WGNVMKLLLVTKTQVEKKKALNLNVSKTRDGRGGLNQQG"
     misc_feature    132032
                     /note="C to U RNA editing"
     gene            132071..138153
                     /gene="nad7"
                     /db_xref="GeneID:814592"
     mRNA            join(132071..132213,133177..133245,134309..134775,
                     135829..136072,137892..138153)
                     /gene="nad7"
                     /db_xref="GeneID:814592"
     CDS             join(132071..132213,133177..133245,134309..134775,
                     135829..136072,137892..138153)
                     /gene="nad7"
                     /EC_number="1.6.99.3"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="NADH dehydrogenase subunit 7"
                     /protein_id="NP_085511.1"
                     /db_xref="GI:13449329"
                     /db_xref="UniProt/Swiss-Prot:P93306"
                     /db_xref="GeneID:814592"
                     /translation="MTTRKRQIKNFTSNFGPQHPAAHGVSRLVLEMNGEVVERAEPHI
                     GSLHRGTEKLIEYKTYLQALPYSDRSDYVSMMAQEHAHSSAVEKLLNCEVPLRAQYIR
                     VLFREITRISNHSLALTTHAMDVGALTPFLWAFEEREKLLEFYERVSGARMHASFIRP
                     GGVAQDLPLGLCRDIDSFTQQFASRIDELEEMSTGNRIWKQRLVDIGTVTAQQAKDWG
                     FSGVMLRGPGVCWDSRRAAPYDVHDQSDLDVPVGTRGDRYDRYCIRIEEMRQSLRIIV
                     QCLNQMPSGMIKADDRKLCPPSRCRMKLSMESSIHHFELYTEGFSVPASSTYTAVEAP
                     KGEFGVFLVSNGSNRPYRRKIRAPGSAHSQGLDSMSKHHMPADVVTIIGTQDIVFGEV
                     DR"
     exon            132071..132213
                     /gene="nad7"
                     /number=1
     misc_feature    132094
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    132108
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    132147
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    132207
                     /gene="nad7"
                     /note="C to U RNA editing"
     intron          132214..133176
                     /gene="nad7"
                     /number=1
     exon            133177..133245
                     /gene="nad7"
                     /number=2
     misc_feature    133233
                     /gene="nad7"
                     /note="C to U RNA editing"
     intron          133246..134308
                     /gene="nad7"
                     /number=2
     misc_feature    134300
                     /gene="nad7"
                     /note="C to U RNA editing"
     exon            134309..134775
                     /gene="nad7"
                     /number=3
     misc_feature    134309
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    134340
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    134347
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    134412
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    134431
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    134440
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    134674
                     /gene="nad7"
                     /note="C to U RNA editing"
     intron          134776..135828
                     /gene="nad7"
                     /number=3
     exon            135829..136072
                     /gene="nad7"
                     /number=4
     misc_feature    135847
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    135873
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    135883
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    135888
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    135918
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    135938
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    135944
                     /gene="nad7"
                     /note="C to U RNA editing"
     intron          136073..137891
                     /gene="nad7"
                     /number=4
     exon            137892..138153
                     /gene="nad7"
                     /number=5
     misc_feature    137931
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    138018
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    138025
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    138047
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    138056
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    138071
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    138092
                     /gene="nad7"
                     /note="C to U RNA editing"
     misc_feature    138105
                     /gene="nad7"
                     /note="C to U RNA editing"
     intron          complement(140723..190762)
                     /gene="nad5"
                     /note="transpliced intron"
                     /number=2
     exon            complement(140724..141939)
                     /gene="nad5"
                     /number=2
     misc_feature    140895
                     /note="C to U RNA editing"
     misc_feature    141295
                     /note="C to U RNA editing"
     misc_feature    141335
                     /note="C to U RNA editing"
     misc_feature    141406
                     /note="C to U RNA editing"
     misc_feature    141445
                     /note="C to U RNA editing"
     misc_feature    141457
                     /note="C to U RNA editing"
     misc_feature    141494
                     /note="C to U RNA editing"
     misc_feature    141541
                     /note="C to U RNA editing"
     misc_feature    141561
                     /note="C to U RNA editing"
     misc_feature    141562
                     /note="C to U RNA editing"
     misc_feature    141572
                     /note="C to U RNA editing"
     misc_feature    141617
                     /note="C to U RNA editing"
     misc_feature    141622
                     /note="C to U RNA editing"
     misc_feature    141676
                     /note="C to U RNA editing"
     misc_feature    141772
                     /note="C to U RNA editing"
     misc_feature    141796
                     /note="C to U RNA editing"
     misc_feature    141812
                     /note="C to U RNA editing"
     misc_feature    141928
                     /note="C to U RNA editing"
     intron          complement(141940..142768)
                     /gene="nad5"
                     /number=1
     misc_feature    141949
                     /note="C to U RNA editing"
     misc_feature    141961
                     /note="C to U RNA editing"
     misc_feature    142139
                     /note="C to U RNA editing"
     exon            complement(142769..142998)
                     /gene="nad5"
                     /number=1
     misc_feature    142844
                     /note="C to U RNA editing"
     gene            complement(143219..>318390)
                     /gene="nad1"
                     /db_xref="GeneID:814625"
     mRNA            complement(join(143219..143477,146990..147048,
                     287917..288108,289003..289083,318004..>318390))
                     /gene="nad1"
                     /label=nad1_mrna
                     /db_xref="GeneID:814625"
     CDS             complement(join(143219..143477,146990..147048,
                     287917..288108,289003..289083,318004..>318390))
                     /gene="nad1"
                     /codon_start=1
                     /label=nad1_cds
                     /product="NADH dehydrogenase subunit 1"
                     /protein_id="NP_085565.2"
                     /db_xref="GI:26557004"
                     /db_xref="UniProt/TrEMBL:P92558"
                     /db_xref="GeneID:814625"
                     /translation="TYIAVPAEILGIILPLLLGVAFLVLAERKVMAFVQRRKGPDVVG
                     SFGLLQPLADGSKLILKEPISPSSANFFLFRMAPVATFMLSLVARAVVPFDYGMVLSD
                     PNIGLLYLFAISSLGVYGIIIAGRSSNSKYAFLGALRSAAQMVSYEVSIGLILITVLI
                     CVGPRNSSEIVMAQKQIWSGIPLFPVLVMFLISRLAETNRAPFDLPEAEAESVAGYNV
                     EYSSMGSALFFLGEYANMILMSGPCTLFFPGGWPPILDLPIFKKIPGSIWFSIKVLLF
                     LFLYIWVRAAFPRYRYDQLMGLGRKVFLPLSLARVVPVSGLLVTFQWLP"
     exon            complement(143219..143477)
                     /gene="nad1"
                     /usedin=Y08502:nad1_cds
                     /usedin=Y08502:nad1_mrna
                     /label=nad1_ex5
     misc_feature    143260
                     /note="C to U RNA editing"
     misc_feature    143269
                     /note="C to U RNA editing"
     misc_feature    143299
                     /note="C to U RNA editing"
     misc_feature    143374
                     /note="C to U RNA editing"
     misc_feature    143400
                     /note="C to U RNA editing"
     misc_feature    143434
                     /note="C to U RNA editing"
     misc_feature    143442
                     /note="C to U RNA editing"
     misc_feature    143454
                     /note="C to U RNA editing"
     misc_feature    143472
                     /note="C to U RNA editing"
     intron          complement(143478..146989)
                     /gene="nad1"
                     /number=4
     misc_feature    143590
                     /note="C to U RNA editing"
     misc_feature    144105
                     /note="C to U RNA editing"
     gene            complement(144294..146312)
                     /gene="matR"
                     /db_xref="GeneID:814593"
     CDS             complement(144294..>146312)
                     /gene="matR"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="maturase"
                     /protein_id="NP_085512.1"
                     /db_xref="GI:13449330"
                     /db_xref="UniProt/TrEMBL:P93307"
                     /db_xref="GeneID:814593"
                     /translation="GLKFRPLTVVLPIEKIMKEAIRMVLESIYDPEFPDTSHFRSGQG
                     CHSVLRRIKEEWGISRWFLEFDIRKCFHTIDRHRLIQILKEEIDDPKFFYSIQKVFSA
                     GRLVGVERGPYSVPHSVLLSALPGNIYLHKLDQEIGRIRQKYEIPIVQRVRSVLLRTG
                     RRIDDQENPGEEASFNAPQDNRAIIVGSVKSMQRKAAFHSLVSSWHTPPTSTLRLRGD
                     QKRPFVFPPSSALAVFLNKPSSLLCAAFLIEAAGLTPKAEFYGGERCNNNWAMRDLLK
                     YCKRKGLLIELGGEAILVIRSERGLARKQAPLKTHYLIRICYARYADDLLLGIVGAVE
                     LLIEIQKRIAHFLQSGLNLWVGSAGSTTIAARSTVEFLGTVIREVPPRTTPIQFLREL
                     EKRLRVKHRIHITACHLRSAIHSKFRNLGDSIPIKQLTKGMSKTGSLQDGVQLAETLG
                     TAGVRSPQVSVLWGTVKHIRQGSRGISFLHSSGRSNASSDVQQVVSRSGTHARKLSLY
                     TPPGRKAAGEGGGHWAGSISSEFPIKIEAPIKKILRRLRDRGIISRRRPWPIHVACLT
                     NVSDEDIVNWSAGIAISPLSYYRCRDNLYQVRTIVDHQIRWSAIFTLAHKHKSSAPNI
                     ILKYSKDSNIVNQEGGKILAEFPNSIELGKLGPGQDLNKKEHSTTSLV"
     misc_feature    144418
                     /note="C to U RNA editing"
     misc_feature    144506
                     /note="C to U RNA editing"
     misc_feature    144542
                     /note="C to U RNA editing"
     misc_feature    144562
                     /note="C to U RNA editing"
     misc_feature    144583
                     /note="C to U RNA editing"
     misc_feature    145939
                     /note="C to U RNA editing"
     misc_feature    146029
                     /note="C to U RNA editing"
     misc_feature    146072
                     /note="C to U RNA editing"
     misc_feature    146233
                     /note="C to U RNA editing"
     exon            complement(146990..147048)
                     /gene="nad1"
                     /usedin=Y08502:nad1_cds
                     /usedin=Y08502:nad1_mrna
                     /label=nad1_ex4
     CDS             complement(147282..147611)
                     /gene="nad1"
                     /note="orf109"
                     /codon_start=1
                     /protein_id="NP_085513.1"
                     /db_xref="GI:13449331"
                     /db_xref="UniProt/TrEMBL:P93308"
                     /db_xref="GeneID:814625"
                     /translation="MALFFFLLLLISHREQLLLVQGHQMRDLLPTPRNRSNGRLPSPF
                     SRVINPSTHLSIHKKALPRGERKLQDEYALDSRIHSRPDPLWNFRNLQKHSRKGLVMI
                     FSKITRC"
     CDS             150783..151151
                     /note="orf102b"
                     /codon_start=1
                     /protein_id="NP_085514.1"
                     /db_xref="GI:13449332"
                     /db_xref="UniProt/TrEMBL:P93309"
                     /translation="MYRYEISCPFNLRSPAVPVSSKASSTSFIKTKALRISEVNRELS
                     VPRVYREKSFTRRLNAPIFGSLFVDKESRFANPYSFTLNQGLTRGRGKQAKLAPDRRG
                     KSVVTEVDYRTGVGENIVKD"
     CDS             complement(151265..151747)
                     /gene="nad1"
                     /note="orf160"
                     /codon_start=1
                     /protein_id="NP_085515.1"
                     /db_xref="GI:13449333"
                     /db_xref="UniProt/TrEMBL:P93310"
                     /db_xref="GeneID:814625"
                     /translation="MDLRLLHGVAYGHSWFGKWGYRFCSGSFGVEEHHYHRAIAFLTS
                     ISLVDDITANFRENKANLNIGDIVRCYRDMSEIQLTTLQDLLRFMLTIKSRAPPIRIP
                     IGKIEAPSVVLPSMKAYGTRACPQVKQCPKDKEKSVKCRKFALPLPYRLAFTSLSVVV
                     "
     promoter        complement(153106..153114)
                     /gene="nad1"
                     /note="orf160"
                     /evidence=not_experimental
     gene            154744..157345
                     /gene="rpl2"
                     /db_xref="GeneID:814594"
     mRNA            join(154744..155660,157213..157345)
                     /gene="rpl2"
                     /db_xref="GeneID:814594"
     CDS             join(154744..155660,157213..157345)
                     /gene="rpl2"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="ribosomal protein L2"
                     /protein_id="NP_085516.1"
                     /db_xref="GI:13449334"
                     /db_xref="UniProt/TrEMBL:P93311"
                     /db_xref="GeneID:814594"
                     /translation="MRPGRARALRQFTLSTGKSAGRNSSGRITVFHRGGGSKRLLRRI
                     DLKRSTSSMGIVESIEYDPNRSSQIAPVRWIKGGCQKKMNTIEKFAPPRKILEPTTNT
                     ISGLFSFSFLPGKVDKRKVACFSPGLMAAYVVVGLPTGMPPLSSSKSAFASKGAGSTK
                     TLVKDVFFSAFSSPKAKRETASLAFASSFGFPRIAVAGAKPAFFAPRMRQKVRGKSTF
                     SLCEVQKGRTHSILWAHRIKGKAGLSWQSFRRQDTLGLVGAAGHKKSKPKTDQGNLPA
                     KPIGERAKQLKALRGLRAKDGACKVDRAPVTYIIASHQLEAGKMVMNCDWSKPSTSSF
                     LQSAQNDHPKPLFTV"
     exon            154744..155660
                     /gene="rpl2"
                     /number=1
     misc_feature    155454
                     /gene="rpl2"
                     /note="C to U RNA editing"
     intron          155661..157212
                     /gene="rpl2"
                     /number=1
     exon            157213..157345
                     /gene="rpl2"
                     /number=2
     gene            157491..158351
                     /gene="orfX"
                     /db_xref="GeneID:814595"
     CDS             <157491..158351
                     /gene="orfX"
                     /codon_start=1
                     /exception="RNA editing"
                     /protein_id="NP_085517.1"
                     /db_xref="GI:13449335"
                     /db_xref="UniProt/TrEMBL:P93312"
                     /db_xref="GeneID:814595"
                     /translation="NPSLLALNYLYISYEFNFASETILGEVRIRSVRILIGLGLTWFT
                     CYWFPEELISPLASPFLTLPFDSYFVCTQLTEAFSTFVATSSIACSYFVFPLISYQIW
                     CFLIPSCYGEQRTKYNRFLHLSGSRFFLFLFLTPPRVVPNVWHFPYFVGATSTNSLMI
                     KLQPKIYDHIMLTVRISFIPSVCSQVPVIVICLPEPRGLSLETFTNNRRFLMVFPLLT
                     AALSTPPDIWCQIVARFLISLIIELAIFVASIVQVREEGWTSGMRESGSIEKKNKSSP
                     PPRTWQSNYQ"
     misc_feature    157549
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157634
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157635
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157651
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157654
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157663
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157690
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157851
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157854
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157867
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157869
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157897
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157899
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157902
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157930
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157964
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    157995
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    158028
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    158071
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    158133
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    158155
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    158183
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    158190
                     /gene="orfX"
                     /note="C to U RNA editing"
     misc_feature    158236
                     /gene="orfX"
                     /note="C to U RNA editing"
     gene            161693..169674
                     /gene="nad4"
                     /db_xref="GeneID:814596"
     mRNA            join(161693..162153,163625..164139,167221..167642,
                     169585..169674)
                     /gene="nad4"
                     /db_xref="GeneID:814596"
     CDS             join(161693..162153,163625..164139,167221..167642,
                     169585..169674)
                     /gene="nad4"
                     /EC_number="1.6.99.3"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="NADH dehydrogenase subunit 4"
                     /protein_id="NP_085518.1"
                     /db_xref="GI:13449336"
                     /db_xref="UniProt/TrEMBL:P93313"
                     /db_xref="GeneID:814596"
                     /translation="MLEHFCECYSNLSGLILCPVLGSITLLFIPNSRIRPIRLIGLCA
                     SLITFLYSPVPRIQFDSSTAKSQFVESLRWLPYENINFYLGIDGISLFFVILTTFLIP
                     ICISVGWSGMRSYGKEYITAFLIREFLMIAVFRMLDLLLFYVFPESVPIPMFIIIGVW
                     GSRQRKIKAAYQFFLYTLLGSLFMLLAILLILFQTGTTDLQISLTTEFSERRQIFLWI
                     ASFASFAVKVPMVPVHIWLPEAHVEAPTAGSVILAGIPLKFGTHGFLRFSIPMFPEAT
                     LCSTPFIYTLSAIAIIYTSLTTSRQIDLKKIIAYSSVAHMNLVTIGMFSPNIQGIGGS
                     ILPMLSHGLVPSALFLCVGVLYDRHKTRLVRYYGGLVSTMPNLSTIFFSFTLANMSSP
                     GTSSFIGEFLILVGAFQRNSLVATLAALGMILGAAYSLWLYNRVVSGNLKPDFLHKFS
                     DSNGREVSIFIPFLVGLVRMGVHPKVFPDCMHTSVSNLVQHGKFH"
     exon            161693..162153
                     /gene="nad4"
                     /number=1
     misc_feature    161721
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    161766
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    161776
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    161799
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    161816
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    161850
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    161856
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    161858
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    161889
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    162009
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    162054
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    162068
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    162094
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    162095
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    162110
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    162141
                     /gene="nad4"
                     /note="C to U RNA editing"
     intron          162154..163624
                     /gene="nad4"
                     /number=1
     exon            163625..164139
                     /gene="nad4"
                     /number=2
     misc_feature    163771
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    163822
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    163930
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    163947
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    163999
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    164059
                     /gene="nad4"
                     /note="C to U RNA editing"
     intron          164140..167220
                     /gene="nad4"
                     /number=2
     exon            167221..167642
                     /gene="nad4"
                     /number=3
     misc_feature    167254
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    167277
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    167345
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    167373
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    167416
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    167599
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    167617
                     /gene="nad4"
                     /note="C to U RNA editing"
     intron          167643..169584
                     /gene="nad4"
                     /number=3
     exon            169585..169674
                     /gene="nad4"
                     /number=4
     misc_feature    169591
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    169603
                     /gene="nad4"
                     /note="C to U RNA editing"
     misc_feature    169619
                     /gene="nad4"
                     /note="C to U RNA editing"
     CDS             169796..170737
                     /note="orf313"
                     /codon_start=1
                     /protein_id="NP_085519.1"
                     /db_xref="GI:13449337"
                     /db_xref="UniProt/TrEMBL:P93314"
                     /translation="MTIRNQRFSLLKQPISSTLNQHLVDYPTPSNLSYWWGFGPLAGT
                     MILSVLSSPALVSGLMVARAKNLVHSVLFPIPIFFSINQLFHYFCRLPIIKHLATKCQ
                     LLLFLISHFLLLLVLTKLVLDLGGYLFMDDLSRALSQFVPGFSGGLGGGSNTPPNPSG
                     DFFLSSYQTSDPDYHDQRRGDSYFSSAPGVQETHRHASGSSTNLHLNLNDQSQDPIFL
                     EVERLSLKCDKVKEKTILKTQSLLLERGYHIPDERDIERAINVVMTEHETIDIDRRRK
                     RFYYLYSCLGKTGNKFWMELLETLADYNINIKSDSDN"
     CDS             174205..174525
                     /note="orf106c"
                     /codon_start=1
                     /protein_id="NP_085520.1"
                     /db_xref="GI:13449338"
                     /db_xref="UniProt/TrEMBL:P93315"
                     /translation="MTPCFINGKCAEQLTSTTAYKLLFLPPLTEHTTSLYPKQYPDKQ
                     LVLLLDPRSGTRLTYYSQPFFIALSSPYSGSSLSAKFHFAPHLYAFLVVASITRSDIA
                     YSVN"
     promoter        176194..176202
                     /evidence=not_experimental
     CDS             complement(176542..177027)
                     /gene="nad1"
                     /note="orf161"
                     /codon_start=1
                     /protein_id="NP_085521.1"
                     /db_xref="GI:13449339"
                     /db_xref="UniProt/TrEMBL:P93316"
                     /db_xref="GeneID:814625"
                     /translation="MLYGLRLYAFQEISFLDPWQLAAIFSGSCVLFISLEKRTLTGYM
                     LTFILYSVLALFVSVWLSSAAGKAGIPIEGMVFLLFLIGGICFICLIQKIFQLTPNTV
                     QALIPILFSALFFFLEELPALEGLPLLKWLKGLDLLLLLVGLLLLIFNENRQGGDGEG
                     S"
     repeat_unit     178863..183059
                     /note="repeat I"
     promoter        181074..181082
                     /note="orf139b"
                     /evidence=not_experimental
     CDS             182278..182697
                     /note="orf139b
                     identical to orf139a"
                     /codon_start=1
                     /protein_id="NP_085522.1"
                     /db_xref="GI:13449340"
                     /db_xref="UniProt/TrEMBL:P94024"
                     /translation="MIQRTRNQSIMLSLPSNQSANHAILTFQPIGQSRYLLTFQPTPS
                     IPLLQQYIISVPYLDAYSSICFPVMARIRSAKYCFFFFLVLFLNGIIATRGKAMLPTL
                     PQKGAAFFPPKMPVPPSGPSKQHNSAPRSDFVQFFYM"
     CDS             183111..183443
                     /note="orf110b"
                     /codon_start=1
                     /protein_id="NP_085523.1"
                     /db_xref="GI:13449341"
                     /db_xref="UniProt/TrEMBL:P93317"
                     /translation="MPSPILPMLPISHLIGTEVRNLISVRTPNITMDQLKNGCCSILT
                     QLETLLRSQSPSEMTIFQTLCDRCCGAEVANEATVECGKTMETTNLTSGGRYWPFHNG
                     TNLSRISL"
     gene            complement(188084..188662)
                     /gene="orf25"
                     /db_xref="GeneID:814597"
     CDS             complement(188084..188662)
                     /gene="orf25"
                     /codon_start=1
                     /exception="RNA editing"
                     /protein_id="NP_085524.1"
                     /db_xref="GI:13449342"
                     /db_xref="UniProt/Swiss-Prot:Q04613"
                     /db_xref="GeneID:814597"
                     /translation="MRLSITNMDGRKMLFAAILSICALSSKKISIYNEEMIVALCFIG
                     FIIFSRKSLGTTFKVTLDGSLQAIQEESQQFPNPNEVVPPESNEQQRLLRISLRICGT
                     VVESLPMARCAPKCEKTVQALLCRNLNVKSATLTNATSSRRIRFQDDLVTKFYTLVGK
                     QFAYSCISKAERVEFIRESLVVLRMVRGGVFS"
     misc_feature    188247
                     /note="C to U RNA editing"
     misc_feature    188268
                     /note="C to U RNA editing"
     misc_feature    188412
                     /note="C to U RNA editing"
     misc_feature    188413
                     /note="C to U RNA editing"
     misc_feature    188415
                     /note="C to U RNA editing"
     misc_feature    188448
                     /note="C to U RNA editing"
     misc_feature    188525
                     /note="C to U RNA editing"
     misc_feature    188574
                     /note="C to U RNA editing"
     gene            complement(188929..189231)
                     /gene="nad4L"
                     /db_xref="GeneID:814598"
     CDS             complement(188929..189231)
                     /gene="nad4L"
                     /EC_number="1.6.99.3"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="NADH dehydrogenase subunit 4L"
                     /protein_id="NP_085525.1"
                     /db_xref="GI:13449343"
                     /db_xref="UniProt/Swiss-Prot:Q04614"
                     /db_xref="GeneID:814598"
                     /translation="MDLIKYFTFSMIISILGIRGILLNRRNIPIMSMPIESMLLAVNS
                     NFLVFSVSSDDMMGQVFASLVPTVAAAESAIGLAIFVITFRVRGTIAVEFINSIQG"
     misc_feature    189035
                     /note="C to U RNA editing"
     misc_feature    189044
                     /note="C to U RNA editing"
     misc_feature    189074
                     /note="C to U RNA editing"
     misc_feature    189122
                     /note="C to U RNA editing"
     misc_feature    189132
                     /note="C to U RNA editing"
     misc_feature    189137
                     /note="C to U RNA editing"
     misc_feature    189146
                     /note="C to U RNA editing"
     misc_feature    189177
                     /note="C to U RNA editing"
     misc_feature    189191
                     /note="C to U RNA editing"
     CDS             complement(190104..190553)
                     /gene="nad1"
                     /note="orf149"
                     /codon_start=1
                     /protein_id="NP_085526.1"
                     /db_xref="GI:13449344"
                     /db_xref="UniProt/TrEMBL:P93318"
                     /db_xref="GeneID:814625"
                     /translation="MRPFGEAKFLSGHQTLQLMRKKALWSKGKRVRCHTPCLPKVPRG
                     RARRSGATTREQSPHRQGDRRRPSQGTSRPTGKTGETREGNPIGSQRIHSTCSPTDFI
                     FLILESGGKGSLFCNEKKKRSRFDSAQPNDTSNTNDLCLECVARSLF"
     exon            complement(190740..190761)
                     /gene="nad1"
                     /number=3
     CDS             complement(191055..191882)
                     /gene="nad1"
                     /note="orf275"
                     /codon_start=1
                     /protein_id="NP_085527.1"
                     /db_xref="GI:13449345"
                     /db_xref="UniProt/TrEMBL:P93319"
                     /db_xref="GeneID:814625"
                     /translation="MKKYKMVINIDMLRLFLPLLGGSVSGSLFGRFLGSEGSAIMITT
                     CVSFCALVVFIFGLFYFRKKGPLKRILYLFLVGFVLSLIRIKVVYLLGGQALPLLDPI
                     LMYAVGAGALLGPNGAESSATWEEDSFELDVLGESFSSSKTDMDSQVAEAPQTEEGEP
                     SVNQVPQEAGASHRVGPYQDQGLATDRNGNPIDLNDSLPPSSLLYGEIESSASVRARD
                     LELEKDIKRVQRLTRNFDNAEDPARRLEVAARLDPEVRELDQKWALFQEKDASGLGR"
     intron          complement(200001..<287916)
                     /gene="nad1"
                     /note="transpliced intron"
                     /number=3
     CDS             201729..202097
                     /note="orf122c"
                     /codon_start=1
                     /protein_id="NP_085528.1"
                     /db_xref="GI:13449346"
                     /db_xref="UniProt/TrEMBL:P92510"
                     /translation="MKHASFCLSSRILLLAPCRYLGTLLLLLPYPCSTLRQFLFLLRS
                     LFIRDVEWIPAGLSHHIPYFPLASPPLTVETLLIARLLLSIKQLSLPPAKTASLSASL
                     DAKTKGRSLLSSCSYCYMPT"
     CDS             complement(203588..204310)
                     /gene="nad1"
                     /note="orf240a"
                     /codon_start=1
                     /protein_id="NP_085529.1"
                     /db_xref="GI:13449347"
                     /db_xref="UniProt/TrEMBL:P92511"
                     /db_xref="GeneID:814625"
                     /translation="MRSSVLRSLRGRLVINLESTRKLRLSRTNIVPGRKKGQKSIKSK
                     NMARKGNPILVRLGKNRSSDSSRFSAEALLGCLYFFIYFVAPTLGPVLFLLRLIHFVW
                     GLRLGLGNENFHFGVGPDGGATGLDLNQPPQEQQPTLGVNRAALDLNELPPVHLLYAE
                     VEGPQSTKAQNDVMLAHLNQVQNLTRDLQTEPNIWRRQALIDILDWEVRSLQRHFRIF
                     RQRDRLREVQRSWLREQLNRYR"
     misc_feature    204112
                     /note="C to U RNA editing"
     gene            complement(204340..204412)
                     /gene="tRNA-Lys"
                     /db_xref="GeneID:814600"
     tRNA            complement(204340..204412)
                     /gene="tRNA-Lys"
                     /product="tRNA-Lys"
                     /db_xref="GeneID:814600"
     CDS             complement(207553..207915)
                     /gene="nad1"
                     /note="orf120"
                     /codon_start=1
                     /protein_id="NP_085530.1"
                     /db_xref="GI:13449348"
                     /db_xref="UniProt/TrEMBL:P92512"
                     /db_xref="GeneID:814625"
                     /translation="MNRTIIEKVRSMLCECGLPKTFRADAANTAVHIINKYPSTAINF
                     HVPDEVWFQSVPTYSYLRRFGCVAYIHCDEGKLKPRAKKGEEKGSYLINRIVSILYTI
                     GIGKTSSPRKASHLGIKG"
     CDS             209499..209822
                     /note="orf107d"
                     /codon_start=1
                     /protein_id="NP_085531.1"
                     /db_xref="GI:13449349"
                     /db_xref="UniProt/TrEMBL:P92513"
                     /translation="MEDFGFTTALRSESVYIVFRFISSSSLSYNTLSSAFIRLDWIKT
                     PRHRAASRALGIQSNGQICTACPHLSALFGFLSVASCFPSNKDDGLHTRIYFDLEFQP
                     DSAVF"
     gene            217631..219077
                     /gene="cox3"
                     /db_xref="GeneID:814601"
     promoter        217631..217639
                     /gene="cox3"
                     /evidence=not_experimental
     CDS             218280..219077
                     /gene="cox3"
                     /codon_start=1
                     /evidence=not_experimental
                     /exception="RNA editing"
                     /product="cytochrome c oxidase subunit 3"
                     /protein_id="NP_085532.2"
                     /db_xref="GI:26556997"
                     /db_xref="UniProt/Swiss-Prot:P92514"
                     /db_xref="GeneID:814601"
                     /translation="MIESQRHSYHLVDPSPWPISGSLGALATTVGGVMYMHPFQGGAR
                     LLSLGLIFILYTMFVWWRDVLRESTLEGHHTKVVQLGPRYGSILFIVSEVMFFFAFFW
                     ASSHSSLAPAVEIGGIWPPKGIEVLDPWEIPFLNTPILPSSGAAVTWAHHAILAGKEK
                     RAVYALVATVLLALVFTGFQGMEYYQAPFTISDSIYGSTFFLATGFHGFHVIIGTLFL
                     IICGIRQYLGHLTKEHHVGFEAAAWYWHFVDVVWLFLFVSIYWWGGI"
     misc_feature    218391
                     /gene="cox3"
                     /note="C to U RNA editing"
     misc_feature    218524
                     /gene="cox3"
                     /note="C to U RNA editing"
     misc_feature    218536
                     /gene="cox3"
                     /note="C to U RNA editing"
     misc_feature    218590
                     /gene="cox3"
                     /note="C to U RNA editing"
     misc_feature    218593
                     /gene="cox3"
                     /note="C to U RNA editing"
     misc_feature    218692
                     /gene="cox3"
                     /note="C to U RNA editing"
     misc_feature    218701
                     /gene="cox3"
                     /note="C to U RNA editing"
     misc_feature    218882
                     /gene="cox3"
                     /note="C to U RNA editing"
     misc_feature    219126
                     /note="C to U RNA editing"
     misc_feature    219159
                     /note="C to U RNA editing"
     misc_feature    219207
                     /note="C to U RNA editing"
     misc_feature    219244
                     /note="C to U RNA editing"
     misc_feature    219263
                     /note="C to U RNA editing"
     CDS             complement(220471..220773)
                     /gene="nad1"
                     /note="orf100a"
                     /codon_start=1
                     /protein_id="NP_085533.1"
                     /db_xref="GI:13449351"
                     /db_xref="UniProt/TrEMBL:P92515"
                     /db_xref="GeneID:814625"
                     /translation="MLHISQEFLLPISMEHWRLLITSQVIKKIGIPWKVIFHAFQNHN
                     RGILFLQIFEHIIDFLFGEAIIYRYVLLDPKSRQVIRDSILNSFLVLYNQIKLLEK"
     CDS             220830..221189
                     /note="orf119"
                     /codon_start=1
                     /protein_id="NP_085534.1"
                     /db_xref="GI:13449352"
                     /db_xref="UniProt/TrEMBL:P92516"
                     /translation="MHFKRGSEGHSLPLPCMHRSMQDISQHLKQWPRFVLQAGFYWPT
                     TFKDAHGFVSSCDACQRKGNFTKRNEMPQHFILEVEVFDVWGIYFMKKTIFSWKPIHP
                     NGGRLCLKMGGSSCEPH"
     CDS             complement(221700..222029)
                     /gene="nad1"
                     /note="orf109b"
                     /codon_start=1
                     /protein_id="NP_085535.1"
                     /db_xref="GI:13449353"
                     /db_xref="UniProt/TrEMBL:P92517"
                     /db_xref="GeneID:814625"
                     /translation="MLRSGKELEEVVRDDKEEEQVVVRKAKQIVNFPLLGMLSSARYG
                     LRRWPFTVKCSPLTSQSTTAPYGFTSFMRKGKKHLDLNFPGNNLSLELRSSTWSFTLN
                     SLGKIFL"
     CDS             complement(222687..222989)
                     /gene="nad1"
                     /note="orf100b"
                     /codon_start=1
                     /protein_id="NP_085536.1"
                     /db_xref="GI:13449354"
                     /db_xref="UniProt/TrEMBL:P92518"
                     /db_xref="GeneID:814625"
                     /translation="MGLSTHCQLVFSWKPMNTHMVSRAMEGSLKSYPFPSNINITSCV
                     SIKLNDRNYLLYDEGRVRLSLLNLGERCDFVPFLSVELFKPLQSSGVYEKLHESNN"
     repeat_unit     227087..227619
                     /note="repeat II"
     gene            227109..227196
                     /gene="tRNA-Ser"
                     /db_xref="GeneID:814602"
     tRNA            227109..227196
                     /gene="tRNA-Ser"
                     /product="tRNA-Ser"
                     /db_xref="GeneID:814602"
     gene            227502..227577
                     /gene="tRNA-Tyr"
                     /db_xref="GeneID:814603"
     tRNA            227502..227577
                     /gene="tRNA-Tyr"
                     /product="tRNA-Tyr"
                     /db_xref="GeneID:814603"
     gene            227615..227686
                     /gene="tRNA-Glu"
                     /db_xref="GeneID:814604"
     tRNA            227615..227686
                     /gene="tRNA-Glu"
                     /product="tRNA-Glu"
                     /db_xref="GeneID:814604"
     CDS             complement(227709..228431)
                     /gene="nad1"
                     /note="orf240b"
                     /codon_start=1
                     /protein_id="NP_085537.1"
                     /db_xref="GI:13449355"
                     /db_xref="UniProt/TrEMBL:P92519"
                     /db_xref="GeneID:814625"
                     /translation="MYLLLYVDDILLTGSSNTLLNMLIFQLSSTFSMKDLGPVHYFLG
                     IQIKTHPSGLFLSQTKYAEQILNNAGMLDCKPMSTPLPLKLNSSVSTAKYPDPSDFRS
                     IVGALQYLTLTRPDISYAVNIVCQRMHEPTLADFDLLKRVLRYVKGTIFHGLYIHKNS
                     KLNVQAFCDSDWAGCTSTRRSTTGFCTFLGCNIISWSAKRQPTVSRSSTETEYRALAL
                     TAAELTWSSASRSRDPSAMNTN"
     CDS             complement(228573..229085)
                     /gene="nad1"
                     /note="orf170"
                     /codon_start=1
                     /protein_id="NP_085538.1"
                     /db_xref="GI:13449356"
                     /db_xref="UniProt/TrEMBL:P92520"
                     /db_xref="GeneID:814625"
                     /translation="MLTRSKAGINKLNPKYSLTITTTIKKEPKSVIFALKDPGWCQAM
                     QEELDALSRNKTWILVPPPVNQNILGCKWVFKTKLHSDGTLDRLKARLVAKGFHQEEG
                     IYFVETYSPVVRTATIRTILNVAQQLEVGQSINWMFKMHFSMGIFKKKFICINLLVLR
                     ILFIHPMCVC"
     gene            complement(231894..233042)
                     /gene="ccb382"
                     /db_xref="GeneID:814605"
     CDS             complement(231894..233042)
                     /gene="ccb382"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="cytochrome c biogenesis orf382"
                     /protein_id="NP_085539.2"
                     /db_xref="GI:26556998"
                     /db_xref="UniProt/TrEMBL:Q9T6H8"
                     /db_xref="GeneID:814605"
                     /translation="MSISIYEFFHYSLFPGLFVAFTYNKKQPPAFGAAPAFWCILLSF
                     LGLSFCHIPNNLSNYNVLTANAPFFYQISGTWSNHEGSILLWCRIPNFYGFFLCYRGR
                     PQSHNVLKQGGHRESLFFFFVSNFVKNSILSLPRYEQESGLKNQLYTPFVLRTLVDSE
                     LRSRRNRTFDGPALFYAPLYPERKIKNPLDAWRSRGSREGKRTHPLLHLARDDKERAS
                     SIDEQRIDGALGIALFFSPFLSASSDPFVRNFFVCTEPLAESNPVPQDPISAIHPPCI
                     YAGDVASAEGFGLCRSKMMNGIVALHSPPMRKDAAEKNGTLLRSAGCVGSRITSELFT
                     LKFKHVGAKCYPALLLRSNRSPLMLLRRRFFAFSSFWAGARSHSTKRY"
     misc_feature    232088
                     /note="C to U RNA editing"
     misc_feature    232237
                     /note="C to U RNA editing"
     misc_feature    232252
                     /note="C to U RNA editing"
     misc_feature    232264
                     /note="C to U RNA editing"
     misc_feature    232324
                     /note="C to U RNA editing"
     misc_feature    232333
                     /note="C to U RNA editing"
     misc_feature    232334
                     /note="C to U RNA editing"
     misc_feature    232462
                     /note="C to U RNA editing"
     misc_feature    232464
                     /note="C to U RNA editing"
     misc_feature    232559
                     /note="C to U RNA editing"
     misc_feature    232639
                     /note="C to U RNA editing"
     misc_feature    232665
                     /note="C to U RNA editing"
     misc_feature    232672
                     /note="C to U RNA editing"
     misc_feature    232703
                     /note="C to U RNA editing"
     misc_feature    232754
                     /note="C to U RNA editing"
     misc_feature    232774
                     /note="C to U RNA editing"
     misc_feature    232781
                     /note="C to U RNA editing"
     misc_feature    232843
                     /note="C to U RNA editing"
     misc_feature    232886
                     /note="C to U RNA editing"
     misc_feature    232900
                     /note="C to U RNA editing"
     misc_feature    232939
                     /note="C to U RNA editing"
     misc_feature    232999
                     /note="C to U RNA editing"
     CDS             complement(234538..234903)
                     /gene="nad1"
                     /note="orf121b"
                     /codon_start=1
                     /protein_id="NP_085540.1"
                     /db_xref="GI:13449358"
                     /db_xref="UniProt/TrEMBL:P92521"
                     /db_xref="GeneID:814625"
                     /translation="MKLLVAPESIKTMTSCPAICPLILMDLSQLLNLPSTAKTTRVIP
                     LLHPHLILLSFSLFQLHQPHPTHLLHPQPYTLILCPYICDQDSTCHHNENKAPCSFYP
                     DQTVSGMVPFYVLGIGRAR"
     CDS             235338..235661
                     /note="orf107e"
                     /codon_start=1
                     /protein_id="NP_085541.1"
                     /db_xref="GI:13449359"
                     /db_xref="UniProt/TrEMBL:P92522"
                     /translation="MKTCLRCRKDYPQNVAGNMLSTLRKEQNQLTSVLTGIHILRRTR
                     LKNWLGEMLEARIIQPSISPYSSPVLLVQKKDGGWPTARGLPSLLQAHGTRQVPNSRD
                     RGTVG"
     CDS             235916..236392
                     /note="orf158"
                     /codon_start=1
                     /protein_id="NP_085542.1"
                     /db_xref="GI:13449360"
                     /db_xref="UniProt/TrEMBL:P92523"
                     /translation="MNHLGMVLQIWEQHQFYANRKKCAFGQPQIAYLGHRHIISGEGV
                     SADPAKLEAMVGWPEPKNTTELRGFLGLTGYYRRFVKNYGKIVRPLTELLKKNSLKWT
                     EMAALAFKALKGAVTTLPVLALPDLKLPFVTRVGKWNWSCFITREQACCVSQPRVF"
     CDS             complement(236927..237481)
                     /gene="nad1"
                     /note="orf184"
                     /codon_start=1
                     /protein_id="NP_085543.1"
                     /db_xref="GI:13449361"
                     /db_xref="UniProt/TrEMBL:P92525"
                     /db_xref="GeneID:814625"
                     /translation="MVSSSRIARSFTRYTSALQRHTIVTKIKQKFPCPRSRTQGQSRR
                     SETHTISRRRSCRAIARSNLGRVSSVTLPWFSCPSPAVVALAKKPFRTARSSCPRSRK
                     SSRCRKSLLSWTAHHLLDEFPKRRIWVFLSFRIGGSLHRRHAMEKNICSTRARIRLIS
                     AISLLSKPIVEIVVGYPQSEDRRL"
     CDS             237053..237616
                     /note="orf187"
                     /codon_start=1
                     /protein_id="NP_085544.1"
                     /db_xref="GI:13449362"
                     /db_xref="UniProt/TrEMBL:P92524"
                     /translation="MTTMKRSADPEAEEDPDPSLGKFIEQVVSGPTQKGFPASGAFAT
                     PRARRSRGPKRFLGKRNYRRARARKPGKRDRAHSSKVRSSDGSTRPSARYGMRFRSPT
                     LPLCSRPRTWEFLLDLGYDSMSLKSARVASERPCDPGRANHVWEPGGLSPEQAQWDWV
                     GKVYSRDRVLKLMGELHELVYRESGRR"
     CDS             complement(239636..239956)
                     /gene="nad1"
                     /note="orf106d"
                     /codon_start=1
                     /protein_id="NP_085545.1"
                     /db_xref="GI:13449363"
                     /db_xref="UniProt/TrEMBL:P92526"
                     /db_xref="GeneID:814625"
                     /translation="MHLERSVQSQLTESKEIARPYSLWGISLAQHSFKTSTRSTGKKR
                     SKGSTSQDGKKQESLESRNDLGPTIVGLIRKILSYSSKKEFSNLTGLESGGSSPPFSL
                     AVSK"
     gene            complement(239988..240758)
                     /gene="ccb256"
                     /db_xref="GeneID:814606"
     CDS             complement(239988..240758)
                     /gene="ccb256"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="cytochrome c biogenesis orf256"
                     /protein_id="NP_085546.2"
                     /db_xref="GI:26556999"
                     /db_xref="UniProt/TrEMBL:P92527"
                     /db_xref="GeneID:814606"
                     /translation="MSVSLLQPSFLMSKTRSYAQILIGSWLFLTAMAIHLSLGVAPLD
                     LQQGGNSRILYVHVPAARMSIIVYIATAINTFLFLLTKHPLYLRSSGTGIEMGAFFTL
                     FTLVTGGFRGRPMWGTFWVWDARLTSVFISFLIYLGALRFQKLPVEPASISIRAGPID
                     IPIIKSSVNWWNTSHQPGSISRSGTSIHVPMPIPILSNFANFPFSTRILFVLETRLPI
                     PSFLESPITEEIEAREGIPKPSSLALFASMAEWLKRPT"
     misc_feature    240086
                     /note="C to U RNA editing"
     misc_feature    240103
                     /note="C to U RNA editing"
     misc_feature    240109
                     /note="C to U RNA editing"
     misc_feature    240135
                     /note="C to U RNA editing"
     misc_feature    240140
                     /note="C to U RNA editing"
     misc_feature    240141
                     /note="C to U RNA editing"
     misc_feature    240145
                     /note="C to U RNA editing"
     misc_feature    240151
                     /note="C to U RNA editing"
     misc_feature    240184
                     /note="C to U RNA editing"
     misc_feature    240191
                     /note="C to U RNA editing"
     misc_feature    240211
                     /note="C to U RNA editing"
     misc_feature    240238
                     /note="C to U RNA editing"
     misc_feature    240262
                     /note="C to U RNA editing"
     misc_feature    240282
                     /note="C to U RNA editing"
     misc_feature    240286
                     /note="C to U RNA editing"
     misc_feature    240292
                     /note="C to U RNA editing"
     misc_feature    240296
                     /note="C to U RNA editing"
     misc_feature    240301
                     /note="C to U RNA editing"
     misc_feature    240313
                     /note="C to U RNA editing"
     misc_feature    240338
                     /note="C to U RNA editing"
     misc_feature    240359
                     /note="C to U RNA editing"
     misc_feature    240364
                     /note="C to U RNA editing"
     misc_feature    240428
                     /note="C to U RNA editing"
     misc_feature    240497
                     /note="C to U RNA editing"
     misc_feature    240575
                     /note="C to U RNA editing"
     misc_feature    240580
                     /note="C to U RNA editing"
     misc_feature    240626
                     /note="C to U RNA editing"
     misc_feature    240656
                     /note="C to U RNA editing"
     CDS             complement(241306..241953)
                     /gene="nad1"
                     /note="orf215a"
                     /codon_start=1
                     /protein_id="NP_085547.1"
                     /db_xref="GI:13449365"
                     /db_xref="UniProt/TrEMBL:P92528"
                     /db_xref="GeneID:814625"
                     /translation="MPTANQLIRHGREEKRRTDRTEVLVFGLLVTRIIRFVHSVLFPI
                     PVFCSIKVLLDYFCSLPIIDKLSKKWQLIWFYVLSVILCKSLFAVGYLWMDDLSRAIS
                     QFYPVVSGGLGGGNTPMPPTNPSEGGLLEGYYAHENEHSHDQQRGSPFWSKEYKESGS
                     KRLFLNLEVEDQNTDTIGEQVKAESGKCEKIKAKIIAKTHELLVSEDTKFQIKTI"
     CDS             complement(249272..249919)
                     /gene="nad1"
                     /note="orf215b"
                     /codon_start=1
                     /protein_id="NP_085548.1"
                     /db_xref="GI:13449366"
                     /db_xref="UniProt/TrEMBL:P92529"
                     /db_xref="GeneID:814625"
                     /translation="MKMKSPLFRGPLVNSSTENPIHILTREKLRHQTSGTNSTEKVIL
                     PNILHSYIKNLNLDFTSPYGSTGNNEVLSILRSRFKQSIFPSSGLKCLDTTGDFLIKN
                     VLHKRYESVQKNISNALSSSINSRTAVFFCILFSITVLMEIAPGPLLKKPSLLFSDNL
                     PNVLQYTRDVYVNHVCIIHKSLSPCECEEPLNRIIRDMFPQTTFDPLELQKPSPQ"
     gene            complement(250080..250153)
                     /gene="tRNA-Trp"
                     /db_xref="GeneID:814607"
     tRNA            complement(250080..250153)
                     /gene="tRNA-Trp"
                     /product="tRNA-Trp"
                     /db_xref="GeneID:814607"
     CDS             complement(251403..251897)
                     /gene="nad1"
                     /note="orf164"
                     /codon_start=1
                     /protein_id="NP_085549.1"
                     /db_xref="GI:13449367"
                     /db_xref="UniProt/TrEMBL:P92530"
                     /db_xref="GeneID:814625"
                     /translation="MRKSADEMFIGVRRAPISSNVGGTSFYGGDEYCSYYQSNGGVAK
                     EDDGSAKKGFRRTGKGKLTAEAVSEAINRAAQGLPFEVVYYPTAGWSDFVVKAEDVEA
                     SMAIFWTPGTRVKMAMETEDSSRITWFQGIVFYTYQETGPWRGSPWNSFRYKIPFTIP
                     LIFL"
     gene            complement(254505..254571)
                     /gene="tRNA-Gln"
                     /db_xref="GeneID:814608"
     tRNA            complement(254505..254571)
                     /gene="tRNA-Gln"
                     /product="tRNA-Gln"
                     /db_xref="GeneID:814608"
     gene            complement(256865..257476)
                     /gene="ccb203"
                     /db_xref="GeneID:814609"
     CDS             complement(256865..>257476)
                     /gene="ccb203"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="cytochrome c biogenesis orf203"
                     /protein_id="NP_085550.2"
                     /db_xref="GI:26557000"
                     /db_xref="UniProt/TrEMBL:Q9T6H7"
                     /db_xref="GeneID:814609"
                     /translation="VDTGREQAKRVVRNGKKETTTSPLCWTAGANTVVSDQDQEPIRI
                     WILTCWWFLTVGILPGSWWAYHELGRGGWWFRDPVENASFMPRVLATARIHSVILPLL
                     HSWTSFLNIVTFPCCVSGTFSIRSGLLAPVHSFATDDTRGIFLWWFFLLMTGISMILF
                     YQMKQQASVRRTYKKEMVVARSTLVHLRHSARAQPRPVMLWKN"
     misc_feature    257010
                     /note="C to U RNA editing"
     misc_feature    257086
                     /note="C to U RNA editing"
     misc_feature    257121
                     /note="C to U RNA editing"
     misc_feature    257133
                     /note="C to U RNA editing"
     misc_feature    257157
                     /note="C to U RNA editing"
     misc_feature    257176
                     /note="C to U RNA editing"
     misc_feature    257200
                     /note="C to U RNA editing"
     misc_feature    257218
                     /note="C to U RNA editing"
     misc_feature    257251
                     /note="C to U RNA editing"
     misc_feature    257269
                     /note="C to U RNA editing"
     misc_feature    257301
                     /note="C to U RNA editing"
     misc_feature    257412
                     /note="C to U RNA editing"
     CDS             complement(258045..258398)
                     /gene="nad1"
                     /note="orf117"
                     /codon_start=1
                     /protein_id="NP_085551.1"
                     /db_xref="GI:13449369"
                     /db_xref="UniProt/TrEMBL:P92531"
                     /db_xref="GeneID:814625"
                     /translation="MVASDSRPMRLRLRAELFLASFAVREESIRSKKEWTYISKYIKG
                     ILKSRLSRREQSRWNIIDDTTSMAFFEEFASLNPVFHTFLFYGRRDGEDLSFHIVGFF
                     RLSIRGYIFFLWESF"
     gene            complement(260224..260601)
                     /gene="rpsl2"
                     /db_xref="GeneID:814610"
     CDS             complement(260224..260601)
                     /gene="rpsl2"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="ribosomal protein L2"
                     /protein_id="NP_085552.2"
                     /db_xref="GI:26557001"
                     /db_xref="UniProt/Swiss-Prot:P92532"
                     /db_xref="GeneID:814610"
                     /translation="MPTFNQLIRHGREEKRRTDRTRALDKCPQKTGVCPRVSTRTPKK
                     PNSAPRKIAKVRLSNRHDIFAHIPGEGHNSQEHSTVLIRGGRVKDSPGVKSHCIRGVK
                     DLMGIPGRRRGRSKYGAEKPKSI"
     misc_feature    260317
                     /note="C to U RNA editing"
     misc_feature    260318
                     /note="C to U RNA editing"
     misc_feature    260333
                     /note="C to U RNA editing"
     misc_feature    260381
                     /note="C to U RNA editing"
     misc_feature    260406
                     /note="C to U RNA editing"
     misc_feature    260456
                     /note="C to U RNA editing"
     misc_feature    260498
                     /note="C to U RNA editing"
     misc_feature    260518
                     /note="C to U RNA editing"
     gene            complement(260647..261006)
                     /gene="nad3"
                     /db_xref="GeneID:814611"
     CDS             complement(260647..261006)
                     /gene="nad3"
                     /EC_number="1.6.99.3"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="NADH dehydrogenase subunit 3"
                     /protein_id="NP_085553.2"
                     /db_xref="GI:26557002"
                     /db_xref="UniProt/Swiss-Prot:P92533"
                     /db_xref="GeneID:814611"
                     /translation="MMSEFAPISIYLVISLLVSLILLGVPFPFASNSSTYPEKLSAYE
                     CGFDPSGDARSRFDIRFYLVSILFLIPDLEVTFFFPWAVPPNKIDLFGFWSMMAFLFI
                     LTIGFLYEWKRGASDRE"
     misc_feature    260655
                     /note="C to U RNA editing"
     misc_feature    260660
                     /note="C to U RNA editing"
     misc_feature    260753
                     /note="C to U RNA editing"
     misc_feature    260757
                     /note="C to U RNA editing"
     misc_feature    260795
                     /note="C to U RNA editing"
     misc_feature    260796
                     /note="C to U RNA editing"
     misc_feature    260858
                     /note="C to U RNA editing"
     misc_feature    260924
                     /note="C to U RNA editing"
     misc_feature    260938
                     /note="C to U RNA editing"
     misc_feature    260943
                     /note="C to U RNA editing"
     gene            complement(260963..261307)
                     /gene="orf114"
                     /db_xref="GeneID:814623"
     CDS             complement(260963..261307)
                     /gene="orf114"
                     /codon_start=1
                     /exception="RNA editing"
                     /protein_id="NP_085554.1"
                     /db_xref="GI:13449372"
                     /db_xref="UniProt/TrEMBL:P92534"
                     /db_xref="GeneID:814623"
                     /translation="MTQPAIGWRVGLGPSIIRGPLVGKSPWSVFMIYGRTSKKPGPSR
                     TSFLVYKRKYSSRKAALGGTLSHKVCKPFGMGFCFFLYFSICRFFASKERENKVGCND
                     VRICTNFYLFSD"
     misc_feature    260981
                     /note="C to U RNA editing"
     misc_feature    260999
                     /note="C to U RNA editing"
     gene            complement(261105..261461)
                     /gene="orf118"
                     /db_xref="GeneID:814624"
     CDS             complement(261105..261461)
                     /gene="orf118"
                     /codon_start=1
                     /protein_id="NP_085555.1"
                     /db_xref="GI:13449373"
                     /db_xref="UniProt/TrEMBL:P92535"
                     /db_xref="GeneID:814624"
                     /translation="MIGGDSVEAIERRLLAKYPEGSPSAEIIEMARIEAEDLFEIKAQ
                     IIQRMALYDPTGDWMARGARALDNPRTTSGEESLERLYDIWKDLQETGPLSDEFSRLQ
                     EKVFLKKGGPGGDPIA"
     CDS             complement(261617..262078)
                     /gene="nad1"
                     /note="orf153b"
                     /codon_start=1
                     /protein_id="NP_085556.1"
                     /db_xref="GI:13449374"
                     /db_xref="UniProt/TrEMBL:P92536"
                     /db_xref="GeneID:814625"
                     /translation="MKNMVRLLLPLLGALAGSFCARFLGSEGSAIMTTTRVSFSSILV
                     VSFLFCFHFHSFRLKGPQKKIIYLFLVFSMGFVGSLIRIEVIHLVGGLALPVLGPLVL
                     NAIGGQALPSTGPSGSGSSSMWEEDSFELGVLEESDSPPAGGPERKRGNPR"
     CDS             complement(264113..264433)
                     /gene="nad1"
                     /note="orf106e"
                     /codon_start=1
                     /protein_id="NP_085557.1"
                     /db_xref="GI:13449375"
                     /db_xref="UniProt/TrEMBL:P92537"
                     /db_xref="GeneID:814625"
                     /translation="MQQVFRREGINLYYYSNKTKKFSLDSWYLPQLHLLESKGNKKSK
                     AATDQYFIHPSRTRQERDLTDRKHRPEQQQLQRRVTRWKKEVTTRSRPKETSSTHLPY
                     HGSY"
     CDS             complement(270238..270561)
                     /gene="nad1"
                     /note="orf107f"
                     /codon_start=1
                     /protein_id="NP_085558.1"
                     /db_xref="GI:13449376"
                     /db_xref="UniProt/TrEMBL:P92538"
                     /db_xref="GeneID:814625"
                     /translation="MTERNASGRMNTKGRSIKETKKAMNEEVGPFTLFLVTLGADLIN
                     ALQREGRLGLSHLGMAEHKRFENQVKIRKGREKTERKAVAPVRAREIKNKDSCFPHTH
                     IGCEK"
     CDS             complement(272944..273423)
                     /gene="nad1"
                     /note="orf159"
                     /codon_start=1
                     /protein_id="NP_085559.1"
                     /db_xref="GI:13449377"
                     /db_xref="UniProt/TrEMBL:P92539"
                     /db_xref="GeneID:814625"
                     /translation="MAFNLFTTFTERLRLVSWRSVFEDTRSLRRFLIRIALVATGLVS
                     KESAIVCHVLAGKVLRMYKTSRDPCLRIIVSLPLLSIYFRPDSIAKSNRKQRPWKEKI
                     FHPDSRKMSCHCEPLPYQTRFDRQAPLQEYSIYPKSRKRLELDPQQNSTVVVQHDKF"
     gene            274899..275222
                     /gene="orf107g"
                     /db_xref="GeneID:814599"
     CDS             274899..275222
                     /gene="orf107g"
                     /codon_start=1
                     /product="ORF107g"
                     /protein_id="NP_085560.1"
                     /db_xref="GI:13449378"
                     /db_xref="UniProt/TrEMBL:P92540"
                     /db_xref="GeneID:814599"
                     /translation="MEFFQLSRKIGCNITQSPIYLFLARKTNRCLCPAHTDFILAVVG
                     PTTLLLSFEISYEKKVDKKNNFKTGIVVQSVRAPPCQGGSCGFEPRQSRPSHNCVLRP
                     GLATK"
     gene            275103..275176
                     /gene="tRNA-Asp"
                     /db_xref="GeneID:814612"
     tRNA            275103..275176
                     /gene="tRNA-Asp"
                     /product="tRNA-Asp"
                     /db_xref="GeneID:814612"
     gene            278649..279152
                     /gene="atp9"
                     /db_xref="GeneID:814613"
     promoter        278649..278656
                     /gene="atp9"
                     /evidence=not_experimental
     CDS             278895..279152
                     /gene="atp9"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="ATPase subunit 9"
                     /protein_id="NP_085561.2"
                     /db_xref="GI:26557003"
                     /db_xref="GeneID:814613"
                     /translation="MTKREYNSQPEMLEGAKSIGAGAATIASAGAAIGIGNVFSSLIH
                     SVARNPSLAKQSFGYAILGFALTEAIALFAPMMAFLILFVF"
     misc_feature    278947
                     /gene="atp9"
                     /note="C to U RNA editing"
     misc_feature    278977
                     /gene="atp9"
                     /note="C to U RNA editing"
     misc_feature    279061
                     /gene="atp9"
                     /note="C to U RNA editing"
     misc_feature    279118
                     /gene="atp9"
                     /note="C to U RNA editing"
     CDS             279463..280251
                     /note="orf262"
                     /codon_start=1
                     /protein_id="NP_085562.1"
                     /db_xref="GI:13449380"
                     /db_xref="UniProt/TrEMBL:P92541"
                     /translation="MYLLIVFLSMLSSSVAGFFGRFLGSESVSRFNLIIFLILLVFSI
                     CLFRSLKQYLGKRMTQWCYLALVCQISLFLVLLRSHILAGFGTFSADVFTVFMGTFSV
                     TGSSGGIVNHQDGASSEWFTYTSDMVEDSASSGRTSSSVNQPIPEEQAWEREARAQEH
                     DRISAEVETITSACENLEAAMVRKAQILLHQRGVTLGDPEDVKRALQLALHDDWEHAI
                     DDRKRHFTVLRRNFGTARCERWNPFIDELRGLGNHQVNARHYVD"
     CDS             281614..281931
                     /note="orf105a"
                     /codon_start=1
                     /protein_id="NP_085563.1"
                     /db_xref="GI:13449381"
                     /db_xref="UniProt/TrEMBL:P92542"
                     /translation="MQSPAMKRIKSSSHSRWDGSGSVNEMPFPSTIRLQGSFWECSTR
                     RHMCYILRYLFRANGHRHFSYERLDCRNQTLRLPDHLYQPSRPHLLPHLSQLLLVRDS
                     GYL"
     CDS             complement(283034..283789)
                     /gene="nad1"
                     /note="orf251"
                     /codon_start=1
                     /protein_id="NP_085564.1"
                     /db_xref="GI:13449382"
                     /db_xref="UniProt/TrEMBL:P92543"
                     /db_xref="GeneID:814625"
                     /translation="MSVLRRIPQDGTFHQEGPIHRLAKRRPRFIASFDLSAATDRWPV
                     PVIYELMACLFGQTMASCIVNGALALNSCSLKSVTGRHDEVVFVAGQPLGYYGSWALF
                     ALSHHAIVWLAALRAYPHQTRPFLDYALLGDDIVIADRSVAKEYRSLLDALQVDISDA
                     KSIVSETGCLEFAKRFWVKIMSKDLSPVSAKAVLESYFLVGTQQLAYKYKLSPKTCLR
                     LNKAGYRVLGQMDTTLRPYPGVLVGFRRYLVSF"
     exon            complement(287917..288108)
                     /gene="nad1"
                     /label=nad1_ex3
     misc_feature    287942
                     /note="C to U RNA editing"
     misc_feature    287997
                     /note="C to U RNA editing"
     misc_feature    288006
                     /note="C to U RNA editing"
     misc_feature    288031
                     /note="C to U RNA editing"
     misc_feature    288041
                     /note="C to U RNA editing"
     misc_feature    288077
                     /note="C to U RNA editing"
     misc_feature    288084
                     /note="C to U RNA editing"
     misc_feature    288085
                     /note="C to U RNA editing"
     misc_feature    288087
                     /note="C to U RNA editing"
     intron          complement(288109..289004)
                     /gene="nad1"
                     /number=2
     exon            complement(289003..289083)
                     /gene="nad1"
                     /label=nad1_ex2
     intron          complement(289084..318003)
                     /gene="nad1"
                     /number=1
     CDS             complement(289197..289517)
                     /gene="nad1"
                     /note="orf106f"
                     /codon_start=1
                     /protein_id="NP_085566.1"
                     /db_xref="GI:13449384"
                     /db_xref="UniProt/TrEMBL:P92544"
                     /db_xref="GeneID:814625"
                     /translation="MMVTALQILFSLIRYVTETIRSVSVLFSDSEDEPDDEASSSDKD
                     VSDATLPARTTYSIVIFLAGSVRRDKREMLSISQKGTLSPAMLPRPAYRGIEREDRGG
                     VQSK"
     repeat_unit     290991..297580
                     /note="repeat III"
     CDS             complement(292973..293431)
                     /gene="nad1"
                     /note="orf152b
                     identical to orf152a"
                     /codon_start=1
                     /protein_id="NP_085567.1"
                     /db_xref="GI:13449385"
                     /db_xref="UniProt/TrEMBL:P92545"
                     /db_xref="GeneID:814625"
                     /translation="MPTILSSKPAFNSLFSYHLIGLISNKLVTLAPDYTGTKKTTWGA
                     RLHLQELRVQTKHRQIEPDIKNLPLQPIRYGSFRPVFHWIEKPCMLIGLCGLHSEVSF
                     IANWPWGKPSEIGGCSIPCMLTGRGSELSYHIRASRRPLPGNRFHFQSFF"
     CDS             complement(293976..294296)
                     /gene="nad1"
                     /note="orf106g"
                     /codon_start=1
                     /protein_id="NP_085568.1"
                     /db_xref="GI:13449386"
                     /db_xref="UniProt/TrEMBL:P92546"
                     /db_xref="GeneID:814625"
                     /translation="MLHRGRSCLTGLFPCYLLSNWLNSNLCWIPLKLVIPCFQLIVES
                     YLLEFLLLLAISTCLLGEDSLIWLTLVVAHSKSRQSSSQEPLDTRMATRALLDQLRSD
                     RRHN"
     gene            complement(296688..296784)
                     /gene="tRNA-Ser"
                     /db_xref="GeneID:814614"
     tRNA            complement(296688..296784)
                     /gene="tRNA-Ser"
                     /product="tRNA-Ser"
                     /db_xref="GeneID:814614"
     gene            complement(296820..298204)
                     /gene="atp6-2"
                     /db_xref="GeneID:814615"
     CDS             complement(296820..297869)
                     /gene="atp6-2"
                     /codon_start=1
                     /product="ATPase subunit 6"
                     /protein_id="NP_085569.1"
                     /db_xref="GI:13449387"
                     /db_xref="UniProt/TrEMBL:P92547"
                     /db_xref="GeneID:814615"
                     /translation="MERLTRLNHFLVNMRWDFYEGVIQAGYIRNLQRELDHTPAELLG
                     SKLDLIFFRESLNLSTYVNNWYMQNLGVPGPVNFIEKYHDACFSNYMKLMEIPSPLDQ
                     FEIVPLIPMHIGNFYFSFTNPSLFMLLTLSFFLLLIHFVTKKGGGNLVPNAWQSLVEL
                     LYDFVLNLVKEQIGGLSGNVKQMFFPCILVTFLFLLFCNLQGMIPYSFTVTSHFLITL
                     ALSFSIFIGITIVGFQRHGLHFFSFLLPAGVPLPLAPFLVLLELISYCFRALSLGIRL
                     FANMMAGHSLVKILSGFAWTMLCMNDIFYFIGALGPLFIVLALTGLELGVAILQAYVF
                     TILICIYLNDAINLH"
     promoter        complement(298196..298204)
                     /gene="atp6-2"
                     /evidence=not_experimental
     CDS             complement(300966..301301)
                     /gene="nad1"
                     /note="orf111b"
                     /codon_start=1
                     /protein_id="NP_085570.1"
                     /db_xref="GI:13449388"
                     /db_xref="UniProt/TrEMBL:P92548"
                     /db_xref="GeneID:814625"
                     /translation="MMTLFTQEPSFSIKCLPTTPSKPHRSLLAARLLFLSISDFSCRC
                     PKIKLSLKGYRFIYCVRVVPSPSSLAKAQSDRLNIGLIRRSLKLCCARDIRLELGQVL
                     ISIPLLLFL"
     gene            complement(302166..303689)
                     /gene="atp1"
                     /db_xref="GeneID:814616"
     CDS             complement(302166..303689)
                     /gene="atp1"
                     /codon_start=1
                     /exception="RNA editing"
                     /product="ATPase subunit 1"
                     /protein_id="NP_085571.2"
                     /db_xref="GI:26557005"
                     /db_xref="UniProt/Swiss-Prot:P92549"
                     /db_xref="GeneID:814616"
                     /translation="MELSPRAAELTNLFESRIRNFYANFQVDEIGRVVSVGDGIAQVY
                     GLNEIQAGEMVLFANGVKGMALNLENENVGIVVFGGDTAIKEGDLVKRTGSIVDVPAG
                     KAMLGRVVDAMGVPIDGKGALSDHEQRRVEVKAPGILERKSVHEPMQTGLKAVDSLVP
                     IGRGQRELLIGGRQTGKTTIAIDTILNQKQINSRATSESETMYCVYVAIGQKRSTVGQ
                     LIQTLEEANALEYSILVAATASDPAPLQFLAPYSGCAMGEYFRDNGMHALIIYDDLSK
                     QAVAYRQMSLLLRRPPGREAFPGDVFYLHSRLLERAAKRSDQTGAGSLTALPVIETQA
                     GDVSAYIPTNVISITDGQICLETELFYRGIRPAINVGLSVSRVGSAAQLKAMKQVCGS
                     SKLELAQYREVAAFAQFGSDLDAATQALLNRGARLTEVPKQPQYAPLPIEKQILVIYA
                     AVNGFCDRMPLDRISQYEKAIPNSVKPELLQALKGGLTNERKMEPDAFLKERALALI"
     misc_feature    302206
                     /note="C to U RNA editing"
     misc_feature    302275
                     /note="C to U RNA editing"
     misc_feature    302398
                     /note="C to U RNA editing"
     misc_feature    302512
                     /note="C to U RNA editing"
     misc_feature    302580
                     /note="C to U RNA editing"
     CDS             complement(303836..304720)
                     /gene="nad1"
                     /note="orf294"
                     /codon_start=1
                     /protein_id="NP_085572.1"
                     /db_xref="GI:13449390"
                     /db_xref="UniProt/TrEMBL:P92550"
                     /db_xref="GeneID:814625"
                     /translation="MITRLFAQLVSLSIVTYWNDAIVATNFSWLFITFFVMTFTFRTF
                     SRYFKKPIIWTLYFFLCLIAFLLLWAARIHINILFSFAFGDVYSFFMAGVFLFYGFGE
                     LLPIGSDSDVGEASWVVNPATGASGSGGNGWTESAANDPAREVSLAPFPPQLTHPVPF
                     PAEPGSPDPVSPPPPIASFYSRIERAESLHAGNIELAEDLQRIQEMERNLENERSPYR
                     GRELAARIDWEVRELEGKVARNRAWDMVRDAQLDIWRQGLDQELVRQQENESRLEERR
                     FQSHSTNSLFEADSSRDN"
     CDS             complement(304779..305084)
                     /gene="nad1"
                     /note="orf101b"
                     /codon_start=1
                     /protein_id="NP_085573.1"
                     /db_xref="GI:13449391"
                     /db_xref="UniProt/TrEMBL:P92551"
                     /db_xref="GeneID:814625"
                     /translation="MIHQINSINMEIILTDVARDALQEKIVSQLSILLRVYRDTNTSE
                     SVTLPLSGVNLQEVAARSFFNNESIPWFFHLFRPCQSGHEKKPLCPQALELVLSFSS"
     CDS             complement(305221..305562)
                     /gene="nad1"
                     /note="orf113"
                     /codon_start=1
                     /protein_id="NP_085574.1"
                     /db_xref="GI:13449392"
                     /db_xref="UniProt/TrEMBL:P92552"
                     /db_xref="GeneID:814625"
                     /translation="MKRYATMLSEFTGVVPSTFLSKLFLKCEINLSIGRVQDRKEPYR
                     QAKSAVRLHGLNNTQYCTGRIRFAARSIPQSPLVPFRLFPQFPTPSVRQNLTTLHFDT
                     REEDRALVSSG"
     promoter        complement(305586..305594)
                     /gene="nad1"
                     /note="orf113"
                     /evidence=not_experimental
     CDS             308932..309369
                     /note="orf145b"
                     /codon_start=1
                     /protein_id="NP_085575.1"
                     /db_xref="GI:13449393"
                     /db_xref="UniProt/TrEMBL:P92553"
                     /translation="MWSYEGKCGFLLLSVYKEQVLDSYSPLTKENGISSNPRYIKRKF
                     PFDSGFPFTRKLPAKVESFLCLPLFLSFLVANLILWLSFHSARVGHQKLSYHLLEWKA
                     FPSSFRNKESKATCDLSSWSNPYFKRKAQIPFSFSRYLLKYLF"
     CDS             complement(309338..309640)
                     /gene="nad1"
                     /note="orf100c"
                     /codon_start=1
                     /protein_id="NP_085576.1"
                     /db_xref="GI:13449394"
                     /db_xref="UniProt/TrEMBL:P92554"
                     /db_xref="GeneID:814625"
                     /translation="MSPTLSTGNRDQRGSSRSYAFVSLASHHFTPQGKITITSSLTRK
                     IDPGNFQGQDVVDFSPWVVLPDEDKVAFLISCRVTAKIRKSGLPQLFKTNTSRDIG"
     CDS             310514..310882
                     /note="orf102"
                     /codon_start=1
                     /protein_id="NP_085577.1"
                     /db_xref="GI:13449395"
                     /db_xref="UniProt/TrEMBL:P92555"
                     /translation="MGYGVCHFYLLFIINGAPQGLVTPSRGLRQGDPLSPYLFILCTE
                     VLSGLCRRAQEQGRLPGIRVSNNSPRINHLLFADDTSSARWIPLAAQIWPIFFLSMRL
                     FQGNPVNHPMSNLYFLGSLP"
     CDS             complement(312545..313162)
                     /gene="nad1"
                     /note="orf205"
                     /codon_start=1
                     /protein_id="NP_085578.1"
                     /db_xref="GI:13449396"
                     /db_xref="UniProt/TrEMBL:P92556"
                     /db_xref="GeneID:814625"
                     /translation="MQPDLTLLGKLRSTWASATVNVIHPISLCLSWFLGTIGCSSPLP
                     LRCADLRILLLKKKEFCLLPLFYHLGIFQHLFYPIIPLLAFCFYAPRLVCPAASLEFQ
                     RRYVVWILAVSRHIVFLENSYYIMLLHPHHLHHPHPPFLIFLFLILRKLRRNRSVKAQ
                     RIMQRSCHRLLFAPVGNDSELSAPSAPSESVVPLRRFNRQSVSTV"
     misc_feature    314410
                     /note="C to U RNA editing"
     misc_feature    314421
                     /note="C to U RNA editing"
     gene            314627..315073
                     /gene="rps7"
                     /db_xref="GeneID:814617"
     CDS             314627..315073
                     /gene="rps7"
                     /codon_start=1
                     /product="ribosomal protein S7"
                     /protein_id="NP_085579.1"
                     /db_xref="GI:13449397"
                     /db_xref="UniProt/Swiss-Prot:P92557"
                     /db_xref="GeneID:814617"
                     /translation="MGGLDGEQKLLIKKLVNFRMKEGKRTRVRAIVYQTFHRPARTER
                     DVIKLMVDAVENIKPICEVAKVGVAGTIYDVPGIVARDRQQTLAIRWILEAAFKRRIS
                     YRISLEKCSFAEILDAYQKRGSARRKRENLHGLASTNRSFAHFRWW"
     exon            complement(318004..>318390)
                     /gene="nad1"
                     /label=nad1_ex1
     misc_feature    318015
                     /note="C to U RNA editing"
     misc_feature    318083
                     /note="C to U RNA editing"
     misc_feature    318084
                     /note="C to U RNA editing"
     misc_feature    318126
                     /note="C to U RNA editing"
     misc_feature    318224
                     /note="C to U RNA editing"
     misc_feature    318389
                     /note="C to U RNA editing"
     CDS             complement(318588..319463)
                     /gene="nad5"
                     /note="orf291"
                     /codon_start=1
                     /exception="RNA editing"
                     /protein_id="NP_085580.1"
                     /db_xref="GI:13449398"
                     /db_xref="UniProt/TrEMBL:P92559"
                     /db_xref="GeneID:814567"
                     /translation="MIVLKWLFLTISPCDAAEPWQLGSQDAATPIMQGIIDLHHDIFF
                     FLILILVFVLWILVRALWHFHYKKNAIPQRIVHGTTIEILRTIFPCFISIFIVEPSFA
                     LALDDAAEALFPNTAPTPSNTSSSEDSFGLRVLSEPWPITRNLGLESSICNRIRLLEA
                     ANSPFLLGKEKGQYWGEIQECLYNVSEQREYYRLLDFENRDLQIRERKHSCLEVFRGV
                     LLRNPYLEERAAYSPQEAFFDFLNERRDALDISNPGSSPAEMDRLEILFLGEIERDLL
                     RRGDESLYIKQLLGD"
     CDS             324259..324594
                     /note="orf111c"
                     /codon_start=1
                     /protein_id="NP_085581.1"
                     /db_xref="GI:13449399"
                     /db_xref="UniProt/TrEMBL:P92560"
                     /translation="MTFVPTDFLIRTPDDPAYFKDRLASPFSFRGCSKTTSTSSSIYS
                     KKKASTATYFRVDPVPRGSQSSRVCEPKTKLIVYQPGNYQKKVKRQVTDPLSLMDKVK
                     KRIDKTEIL"
     CDS             325300..325710
                     /note="orf136a"
                     /codon_start=1
                     /protein_id="NP_085582.1"
                     /db_xref="GI:13449400"
                     /db_xref="UniProt/TrEMBL:P92561"
                     /translation="MPRTELILNAAVILYTMIPPDAHSLGSEGRVVNGNWRDTSDVKE
                     GSLPREVTKQVNGSLSSRTKQVNEFSKHTRFLVDISFSCCSLINRSLWESAQKDELSD
                     SFGKALTTKPECLAVRETPRNFRRNLCLVIPSLN"
     CDS             326099..326509
                     /note="orf136b"
                     /codon_start=1
                     /protein_id="NP_085583.1"
                     /db_xref="GI:13449401"
                     /db_xref="UniProt/TrEMBL:P92562"
                     /translation="MLKRKLKPKRLQLPPQDVVFEGEAAMNEYTFYRNWVESWLQHIR
                     SYYLLFIDGDPSLSKFFEIEICAHSWKRSTFDQQVFKFGLLWECVDIARSRTVYWQCA
                     LGTGHIQEDKVSEATSPFTDDSCTNSCLSRMTGQ"
     gene            complement(327890..333105)
                     /gene="nad2"
                     /db_xref="GeneID:814618"
     exon            complement(327890..328078)
                     /gene="nad2"
                     /usedin=Y08501:nad2_cds
                     /usedin=Y08501:nad2_mrna
                     /label=nad2_ex5
     misc_feature    327900
                     /note="C to U RNA editing"
     misc_feature    327954
                     /note="C to U RNA editing"
     misc_feature    327957
                     /note="C to U RNA editing"
     intron          complement(328079..329734)
                     /gene="nad2"
                     /number=4
     CDS             complement(329082..329465)
                     /gene="nad2"
                     /note="orf107h"
                     /codon_start=1
                     /protein_id="NP_085585.1"
                     /db_xref="GI:13449402"
                     /db_xref="UniProt/TrEMBL:P92563"
                     /db_xref="GeneID:814618"
                     /translation="MLPAGCWNDTSRDGPGFRKMKGPKVEIGGYKFPISLGAENESTS
                     RCDTAFSFLVGKERRSPSEPNRPMKNKRRAKPNGEAHAEQARRKISVEEKQPSSFPSH
                     PGPKAVQSFLAKSRIWGFLLRYLTI"
     exon            complement(329735..330306)
                     /gene="nad2"
                     /usedin=Y08501:nad2_cds
                     /usedin=Y08501:nad2_mrna
                     /label=nad2_ex4
     misc_feature    329737
                     /note="C to U RNA editing"
     misc_feature    329766
                     /note="C to U RNA editing"
     misc_feature    329767
                     /note="C to U RNA editing"
     misc_feature    329813
                     /note="C to U RNA editing"
     misc_feature    329886
                     /note="C to U RNA editing"
     misc_feature    329955
                     /note="C to U RNA editing"
     misc_feature    330051
                     /note="C to U RNA editing"
     misc_feature    330055
                     /note="C to U RNA editing"
     misc_feature    330085
                     /note="C to U RNA editing"
     misc_feature    330093
                     /note="C to U RNA editing"
     misc_feature    330204
                     /note="C to U RNA editing"
     misc_feature    330225
                     /note="C to U RNA editing"
     intron          complement(330307..332944)
                     /gene="nad2"
                     /number=3
     exon            complement(332945..333105)
                     /gene="nad2"
                     /usedin=Y08501:nad2_cds
                     /usedin=Y08501:nad2_mrna
                     /label=nad2_ex3
     misc_feature    332989
                     /note="C to U RNA editing"
     misc_feature    333042
                     /note="C to U RNA editing"
     misc_feature    333099
                     /note="C to U RNA editing"
     gene            337669..337741
                     /gene="tRNA-met"
                     /db_xref="GeneID:814619"
     tRNA            337669..337741
                     /gene="tRNA-met"
                     /product="tRNA-Met"
                     /db_xref="GeneID:814619"
     CDS             346757..347194
                     /note="orf145c"
                     /codon_start=1
                     /protein_id="NP_085586.1"
                     /db_xref="GI:13449403"
                     /db_xref="UniProt/TrEMBL:P92564"
                     /translation="MTKREYNSQPEMKEEVLAYLLQLSASLVLPVAIWLIAAGQIFTC
                     LRGYTISNYQEKVEEKLCSTLVDKISEKLADLFPVYGITPSRNAPFPTILEQLLATVS
                     QEERLAYLSNMYNSLIEMGIDSPCFYPIVQTFLFLMGGGGGPA"
     gene            complement(349830..351413)
                     /gene="cox1"
                     /db_xref="GeneID:814620"
     CDS             complement(349830..351413)
                     /gene="cox1"
                     /codon_start=1
                     /product="cytochrome c oxidase subunit 1"
                     /protein_id="NP_085587.1"
                     /db_xref="GI:13449404"
                     /db_xref="UniProt/Swiss-Prot:Q07063"
                     /db_xref="GeneID:814620"
                     /translation="MKNLVRWLFSTNHKDIGTLYFIFGAIAGVMGTCFSVLIRMELAR
                     PGDQILGGNHQLYNVLITAHAFLMIFFMVMPAMIGGFGNWFVPILIGAPDMAFPRLNN
                     ISFWLLPPSLLLLLSSALVEVGSGTGWTVYPPLSGITSHSGGAVDLAIFSLHLSGVSS
                     ILGSINFITTIFNMRGPGMTMHRLPLFVWSVLVTAFLLLLSLPVLAGAITMLLTDRNF
                     NTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIVSTFSGKPVFGYLGMV
                     YAMISIGVLGFLVWAHHMFTVGLDVDTRAYFTAATMIIAVPTGIKIFSWIATMWGGSI
                     QYKTPMLFAVGFIFLFTIGGLTGIVLANSGLDIALHDTYYVVAHFHYVLSMGAVFALF
                     AGFYYWVGKIFGRTYPETLGQIHFWITFFGVNLTFFPMHFLGLSGMPRRIPDYPDAYA
                     GWNALSSFGSYISVVGICCFFVVVTITLSSGNNKRCAPSPWALELNSTTLEWMVQSPP
                     AFHTFGELPAIKETKSYVK"
     promoter        355212..355220
                     /evidence=not_experimental
     CDS             complement(360717..361052)
                     /note="orf111d"
                     /codon_start=1
                     /protein_id="NP_085588.1"
                     /db_xref="GI:13449405"
                     /db_xref="UniProt/TrEMBL:P92565"
                     /translation="MKISYFIRRGKKTSRRSHFIKMKKNIITTQLFKPDNAFIFFSGI
                     HGSVNRATYKYKISKTFGRFLAHISCLICILSKRIFVLSFSVIGSFCHPSIVHFDCLL
                     FFLDTTPCL"
     gene            complement(361062..361179)
                     /gene="rrn5"
                     /db_xref="GeneID:814621"
     rRNA            complement(361062..361179)
                     /gene="rrn5"
                     /product="5S ribosomal RNA"
                     /db_xref="GeneID:814621"
     gene            complement(361350..363284)
                     /gene="rrn18"
                     /db_xref="GeneID:814622"
     rRNA            complement(361350..363284)
                     /gene="rrn18"
                     /product="18S ribosomal RNA"
                     /db_xref="GeneID:814622"
     CDS             363725..364042
                     /note="orf105b"
                     /codon_start=1
                     /protein_id="NP_085589.1"
                     /db_xref="GI:13449406"
                     /db_xref="UniProt/TrEMBL:P92566"
                     /translation="MKYHFSSMEPWWKREFSFCIPAIYIKMASISLFQNSWLKMKHLP
                     SCLFTQTTNTLGIYRKKKPNHSRDNPRINSNLSTNYAQAKSVERSRSNSLNSGPNPLE
                     NAT"
     CDS             complement(366086..366700)
                     /note="orf204"
                     /codon_start=1
                     /protein_id="NP_085590.1"
                     /db_xref="GI:13449407"
                     /db_xref="UniProt/TrEMBL:P92567"
                     /translation="MFGGRRRRLPQDGTFNQTQPFDRLVGSRHSFSFDLKSATDRWPL
                     VFLFEVVQYLFDRSFASSVVNSAFACNIFEVPFVKLKRRFSQVCFVAGQPLGYHGSWP
                     TFALSHHILVWWCAKQVHPGVRFTSYAVLGDDVVIADQEVAKVYESALGGLGVKISYQ
                     KSLIPIQVLLSLLNASGLGNLVLKREIFPRESGVLSLMSVPSLA"
ORIGIN      
        1 ggatccgttc gaaacaggtt agcctactat aatataagga ttggattcta ataagttcga
       61 aacaggttag ccttagccta ctataggatt agatctttct tatcaaccta ctaacttctt
      121 ccttgttggg atgagaaacc cttttgcaac caagcgtgct ttgagtttgt caagggaccc
      181 atctgcattc agtttcactc tgaaaaccca tttacaaccg agaagattca tgtcaggtga
      241 tgcgggaact aagtcccaag tgtgattctg tgttaatgcc gacatctctt cttgcatagc
      301 ttgtctccat cctgggaggc agacgtaatg gtttttggtt cagagggagt gtatttttgt
      361 gtaaacaggt tgtaacgagg attaggcttg cgaataccat cctttgcccg agtgatcata
      421 tgatgtctat taggtgaaag tagctcagga gcagctgtcc caacatcaaa aaaggtaccg
      481 ctgtcgccaa taggaacagg atctgagcct gccgtacgca caggacagtc tctttctgat
      541 gtggtagcag ttccaggagc aatcgcagag acaattgaag gatctgcaga ttcgcaatca
      601 gagcctgtga aaccgggaag atgtcgagat agcaggagaa gaattagcag tatgtgagtg
      661 cggaagcaga gtggaggatc gagggacctg tgaaggtgtg ataaaggaac tgtctgttga
      721 aacagaaggg acatatgaag gtttagaacc aagctgccaa gcacgaagca gagaacttgg
      781 atacggtggg atgagatggt gataacagtc ctgaaaacga aagactagag ctcttgccca
      841 actgacaggc ttcacaaaca gaaagatccc ttttattaat aactatagct ttactagtct
      901 tgagttgttg gagaacttga ggatttggat gcccaagcct ataatgccaa gtgagctcac
      961 tagctgcttg ttgtcttgta gagtagaaga cttatagatt aaaattctcc aacatataga
     1021 tgtccttaca ccgttttcct ttgctcagca ggctccgtgt ttgcttgtcc tttatgcata
     1081 cttcgttagc atcaaactca aagaagcatg gataaatcat cacaaagttt ggacacagag
     1141 agaagagact tagttatgaa aggacaaaca agaacttcat ttaatggtaa actacctgat
     1201 gagcttggta gattggtaga tccaacatga gtgatgggca agaaggctcc atccccaacc
     1261 atcacactgt cggatcccac ataaggttgt gactgttgga ggtgatgagc agaattggta
     1321 atgtgagagg aggcaccaga atctggaaac cattctgtac cagaggtatc cgtgatctga
     1381 agagcagcaa gagcttgcgg aatatcactg ttctggaagg agttgtcata ttggttccag
     1441 cattttaggg ctgagtgacc agtttagcca cagatttggc aaacgggtcg agaagagaac
     1501 tgatcagagg agtgggattg atgcaaacta gttgagggct tgatagcgtt gatgaaaccc
     1561 tcttcctctt gtagagaatg agccgcgacc acggtagtta ccaaaccgag aataggactg
     1621 tcatacgagt ataccagagg ctgaaggtat tgagtgatga tccttcctca accctaagct
     1681 aggcgaatca ataacaaagc aagactactt tccatcagta cggggtacgc cataaacgaa
     1741 gtcagaaggt tgtcaatcaa atatggtacg cgatgcttgt ccaaataaaa aacgatccct
     1801 taaaagtgag ttagaaaggt aagagtcttg tacctagtag aacttctaat aactaataaa
     1861 agctattttc tcagaagcga gagcgcacct ctcgcaacaa gtgctcgagt cactccgcac
     1921 ctcgaaaaac aagtctcagg aagtgagtga gttatagtat tacaggagct aatagcttca
     1981 gcagagaaat aagcacagga aatactggtg ggaatctcac ctccaagcct ttcatgggcc
     2041 cgcgttgaaa tacccaacaa aaatccaaag atcattgata gcagaatgaa gaaactgaag
     2101 atcctgctat aaagatctcc tcataatgta atgaaattat tataagaaat aaaatgaaag
     2161 cgcagctaac attatccagg aacaaggaac aggtgatgga ttgagcagta ataaaggtaa
     2221 tggttggaag ctgatggatg gccgagtaaa gaacccagat attagaaggg agaccgttac
     2281 agtggttcaa ggtagctaaa ttcatgtttc gcgaatcata gaaaagaaag aagaagggat
     2341 attggaaaaa agaagtcatg gatttagcaa tacaaagagg ttcagctgtt tccaaatacg
     2401 gcggatctgg tgataaaggc caagggcgtg ctcttctatt aaaggaagaa cagaaacgaa
     2461 aaagctctct ttgcgtacta tggatctctt acgtgcgata ttccttgctt tgactttgac
     2521 gagcagcatc cagtacattc accccggctg ggcagtagcg ccaagaagaa cttcaagcta
     2581 agagcgaaga gaaggtaatg atttcgctca gtagaaggtc acctacatgg atattaaggc
     2641 tataagccgc aggtaagata tagttcatcg aaggggaatc ttgaatcaaa tgtcgattca
     2701 tcttaattgt acgtcaattc taattcaatt tgttctaaac ttcctcgggg ctaaagcctc
     2761 gtgattcaat tatggctctt tgctgctatt aaggtgatag tatctgctta gcccatagta
     2821 ataagatggt agtgaccgct tatcctaagt cttccgctgg catgggtgta actgtccttc
     2881 cagagtacct caaacagtcc tcttacgaag cctattcccg gccttactct gcattctttc
     2941 tttctggttg tactaagcag gagcgttccc ccttactggc taggcggcta gtagatgctt
     3001 ggctttcatt ccattccatt ctgatgataa atgaagaaag aggtgtcgga ctgggcatat
     3061 aagcagctat cagaaatttc actcatgata ccaggcgcga ggagcctgtt taagaccata
     3121 gcttttcgaa acctgcaaag agaagaagag tatcgaccgg gaggttgaga catgactctt
     3181 ttcggttaag tgaccctgta gaaaagcgtt gttgacatcc aattgacgaa gagtccagcc
     3241 atggtataga gtaagactct cagacgaata gtgataggct taaccacagg gcttaatcta
     3301 tcaaaagact ctctcccagg ccgctgattc ctgtctaaaa cacgagagaa ccttgccttg
     3361 tgggtgtccg atgccgaccc cgttgtgctg tgcgtcttgt ctttcccaac gaaagtgatg
     3421 ccgattcagc gtgtgtggcc tgatgcggtt cagcctacca attagtgggg caaggagata
     3481 tggtttcctt aggcataagc atgtcatgta tatgtacaca aggggaatag caactaaagc
     3541 tcaatagcac cttagtgaac tacaagggct ctaccgctcg ggtccctcaa ccgagagccc
     3601 ctcctcgcta cgatccaccc tttctctagc cctctactca accgctttag ctggcccgct
     3661 tctgacagaa gtagcagatt caatctgtga atcccgtcta gagctcctca cactgtccgc
     3721 atcatcatca acggcaagcg gatcagattt taagagcttc aaaatacata caatacccta
     3781 aggagtgagg gatgtacctt ttggaaaggg actgactgaa cggaatcaat gacttacatt
     3841 aacattgctc ttaaaagaag tcgaattccc ttcattcaga gcataattaa tctagtcact
     3901 gatttgagtt atatagttat tattcatgtt tgttgttcgt tggacctttt ttgaaaggct
     3961 ttgttaatgc ttatcgagtt atgatataag aaagggggac gactgaggaa atgccatgct
     4021 aaggcctatt tccctgctgt ttcaacttct ttctatagcg attggacaca agtttttctc
     4081 aagttaatgc aactccgttt caattccata atttgactca aactacatgt caatccccca
     4141 gtccactata ggggagagtt cactccagtt agggggtatt accagcggct tcgaccacat
     4201 cctatcctct ctagctactg gcttctgtgg ggagggcaaa cttctatatt tccctgctag
     4261 tgcactactt ccttttcttt cagaacagag acggagccct gctttaaatt gacagaggag
     4321 ttattggacg ccgggtatat ccagccatcc aaagcacctt atgaagcccc agtgttgttc
     4381 cagaagaagc gggagcctac gtctatgcat cgactaacct atatctaaac aaggttaccc
     4441 tcaagaaaat aagtacctga ttctgcgcgt agaagaccta ttcgatccgt tgggagatgc
     4501 aagcttcttc accaagttgg atctaaagcc ggggtactac caggtgcgca tcgccgaggg
     4561 taatgaacca aagaggagta tactttatga atgggaaagc agtcatcaag ccagatgcgg
     4621 atgaaattct aactgctgcg cttacgcctt ttgattagac aactcctagt gccaagctaa
     4681 ctaactagga ttcgttcaaa ggattcgtga aaacagaaag aagagctagc gactctgacg
     4741 aatctaatgt tgcccgcgtt gaggcgaaaa gaaaggcgga ttccctatat aagtgaattt
     4801 gttcttcaat cgattcatct cggccttaga ctgctacggt tagctcttgc cccgagcacc
     4861 tggactggct atctcgaaag aaatgctttc atatcatagc tgctgacttg gctttgaaac
     4921 tataggagct gaaggaacgg ctactgattt ggacctaaat catttcatcc ggaagtgact
     4981 gcactcgcct aagccaaaac caagctactt tcataaccac caggaaagcc tagctacttc
     5041 ttcgttcctc accctgtccc ttacctctta ccgtaggaaa agccgttgat attcgtagat
     5101 cgttcgttga ttcccttgct tttgggcgat gattcgattc ttctgggctt gttgccacta
     5161 aagaaagagt tctgccttct agccaagcct ttgagaccaa gtcaagcttc ccagcagtca
     5221 accaagaaag agtgtttctc ccctactgaa gaaatggaag tcagtctgct ttccttctta
     5281 gctttgttca catctgctct ttccaggact ggctatctct caatgtattc acgcatctcg
     5341 aaatagtgaa aagaagtagt ccctcctccc agagctgaaa tagctggaaa aaaacttcaa
     5401 cagaagtaat gccgactctt ctacttcctg gtacttttga ataaggcaag gcctttacct
     5461 attccctatc acaaccactt tcagtagagg aacttcctct ccttttagtc gagttatagc
     5521 tttcgcttct tcagatcctg atccttcatc agaggagatc gctttacttt tttataagag
     5581 ccattggcag gaccaagaaa ctcccattca aggcgccaat cattcataaa taattcttat
     5641 atatgatatg caattcgatg attcaatttc ttgtggaaaa gactagcgca atggcttaat
     5701 gcatttcatt ggcagtttgg tcctaacaaa ttatgcttct tgggagagga gaacttccac
     5761 caagcaatat atttgagttg gctaacccaa tgattgagct agcttctaat ccatttcaat
     5821 ctcatcttac acagcagaag ttgtggattc atacctggaa gcaggcaatg ccgccacatc
     5881 tcccctgtga aagaaggtta cgcagctgat tcggttaatc acatgtcaga ggcatctatc
     5941 taaatcgcac atgtcagaac aagacctagg gatccggtgg caccaggagc gggtagccga
     6001 gttgagatca ttccgttaag acacaaccac ttttacagta aacatgcatc cgcccagcgc
     6061 cccctcctta cgaatggtta cgggactaga gcgagtctct ttttctttgc aagaataggt
     6121 ctgagcctga tgacattcct gctttccttg ccatgtccaa ctaaagtgaa agttaatcaa
     6181 ctgcaaggag gaatcgacct ttttctacta ttcatttgcg ccggaaaacc ccttcatcat
     6241 ttgccctgaa ctggtgaaag gaataggagg acttttccct cggtggaagt agggatttaa
     6301 gcacagttgt gattccgctt tcatgtcttg gattgagctt tctcactctt tctatgcctc
     6361 ttccttgtcg gcgtcctttg ttcgctactg ctttaaagaa tgggatgagg ctacctgatc
     6421 gtcgagtcga cttccatcaa tcaattggat tggatcttat tatcccatag tcataaatct
     6481 gattcttcac ccagtgggaa cagtcttcat ggtggtacca gtgcgtatat atgtagatga
     6541 gttttggttc ccaccctcga ttttccatcc aatcttccta tcttcttttc cctgctttgg
     6601 aagcattcga tctctcgtaa agcaaaccct cgtcagagaa agggggcggg aagcctgcgt
     6661 gcgattcctg ggttggatat ccctggctct cttctctctg agtccccgct agctttcaag
     6721 cgttcattca atctccctcc caacgcaagg aaaccgatcg atgcacttgg ctttaggttt
     6781 cgatcgataa taatttatat tatatataaa aacgcttctc gctggagact cgggtggggc
     6841 gcttgctctc cactggcggt tgaatgaaag acgtacccat aaagttgacc taagttggta
     6901 tgcctcccat cgaactaaag caagaaatct tccttcgatg cgagtctatc aaatgtttag
     6961 ccacatctgc tgcgccccgg tcagtggagt caatagcctt atcagctgtc cctcccttct
     7021 tttaaaatat tacccaggat cttatcccag gccgctgatg aattggcaac gaggcgagcc
     7081 ttgtaccgct caacactgcc atcaggtttc cgcttaaccc gataagaaga cccacaacaa
     7141 tcttttgatg aggagatgat ggtactagtt cccgggtgcc atggagaatt aatgcatcaa
     7201 attcagcaga catggatggt ggcactagga tctgcatacg aggcttttgg tgtgcggacg
     7261 tatgtgacca atgcacttat gctgccttca ctcaaaggaa agcactttca aagaagcaag
     7321 ggatgaaggg gaggtaagcc tgtcttaaaa tcgattaact aagctagctt aattcttgaa
     7381 ctacttgaac tagaggagcg gtacgagcgg cttactacaa aagaaaggct atttgagatg
     7441 ctttttccgg gccaaagtac tctgacccat gataccgatt caagctcact gagaacggat
     7501 ttccctagtt ttaaattcaa ctacggacca acaaagattg attgttgtcc cgttgacagg
     7561 aagatggagg gttgttctcg tactcgcttg gcggggtggg cattcttatt tgtttaagac
     7621 ttctcacagc ttttaggcgc taggagggct tgatagcttt gatgtaaccg ttttggtcgt
     7681 tgttggaatt gatgagccaa acaagccagt tctcagcctt ctatagtatc cgtttgaata
     7741 cgagacaaag gaatctatag gcctatctct cactttctaa tactactatt gctagtgcta
     7801 aggagctaga gtatactagt ctagaaaaga atcccacata gttggctgtc ttactctaat
     7861 accaatgcga agaaactcat taattcattg atgaggaggg cgaagaaact ttcagcttta
     7921 gagaatccag ttccagcgga agactaagta cggtagcaag tcaaatcaat ctcctccaac
     7981 agaaggctct gacctgacca cagtcaatca gtctattgtt ctggttctag agagtctaac
     8041 cgagaagaaa tcgtctcatc gctttgagcc tggtccaggt gtgggggaat gagtcctcca
     8101 tctagtagcc cagcccttcc gacaagagca gttacgcctt ttcctaaagc tcttactaaa
     8161 ccaccgccta gcgaccacgg aaagcatagt cagaagagct gaaacaatag ccatgtcata
     8221 ttcctcggga attgcctttc gaactgaact accacgactc tcgttaactg catcggattc
     8281 gtgaatcaat tgctgcagat tatctcattc aattgcagcg gctttagcag acatctcttc
     8341 aatttgcgta gatagaagat ccggctagaa actccttttc attgccttct actttaagtt
     8401 ttaaattaat ttctctatat ctaattccaa gtgagatgtc caaaatcaaa ggatggaggg
     8461 taagaatcga cgaggaatct ataagataaa atcgttcatt caaaaggaag aagaagaaga
     8521 atcggacgat tgaagactag aatcgctaat agtcagtcgg agtggattga gaaagaattg
     8581 taggactaga tagctctttc cttttttgat gtgctttctt gcgggaaaga aaaggtattt
     8641 agttagctag gctttgacgc ttgttctcgg attcctttgc ttgtatattg tccgaaatct
     8701 ctatggcaag tagtaggacc ctcacactct gttcgttctc ctgtccctat ctctctctgt
     8761 cacatcctat cccgttcaga atctttggga tcaagaactc tcttccattt ctctgctcgg
     8821 aaagaaggtt ggcaagagat atttttaaat tagggtgcgg caactaaaga ggtatcgaga
     8881 ctgaccgcaa ttgcaggttg acttttcttt tcattttgtt tatggcaagt gaaagtcgtt
     8941 tcgtttagta cgagatggct tcacaacctc gcggtgcttc cacctctcgc ctatcgaagt
     9001 tctgttctaa aacctgttcc gagaacttgt atagagaagg atttcccgct aagcagcagt
     9061 tcttccatac caacttagct gcccggcgct gctattggca taacaaccgg tacaccatag
     9121 gttggcccaa cccagtcctc tcgtactagg gttggctcct cgcagttctc cctttaacac
     9181 caacggtaga taggaaccga actgtctcac gacgttctaa acccaactca cgtaccactt
     9241 gaatcggcga acaaccgaac ccttgggacc ttcttcaacc ccaggatgtg atgagtcgac
     9301 atcgaggtgc caaacgactc cgtcgataag agctcttggg agtcatcagc ctgttatccc
     9361 cggcgtacct ttgatccgtt gagcgagagc ccttccacac gggactcccg gatcactatg
     9421 gccgactttc gtctctgttc gaccagtcgg tctcacagtc aggcaggctt ataccattac
     9481 gctcacgagc agaatcttag cttgagccta ccttcgcaca cctccgttac tctttaggag
     9541 gcatccgccc cagataaact acccacctcg cagtgtcccg cctccccccg aattctcggt
     9601 gcggcggtta ggcaccctta gacgaaagag tggtctttca ggattggtcc ttctatgtca
     9661 cgacctccca cctatcctac acattcgatc aaggttgtca ctgcgaagct atagtgaagg
     9721 tgcacggggt cttaccgtct agccgttggt actccgcatc ttcacggaga attcaatttc
     9781 accgggtcca tgtcggagac agcggggcag tcgttacacc attcgtgcag gtcgctactt
     9841 atgcgacaag gaatttcgct accttaggac agttagagtt actgccgccg tttaccgggg
     9901 cttccattca aagcttataa cacttctcct tttgactttc cagcaccggg caggtgtcag
     9961 actctataca tcgtgttacc acttagcaga gtcctgtgtt tttaataaac agtcgctacc
    10021 ccctggtatg tgccgctttc ctaatcaaaa gataggagag caccccttct cccgaagtta
    10081 cggggtcatt ttgccgagtt ccttcgacat ggttctctca agcgccctag tatactctac
    10141 ttgttcacct gtgtcggttt ggggtacggt cagttcaccg ggaggatcgc cctcccaatt
    10201 cgaagttttt tcctggaagt ttcaaccttc ttgactatga caagagtcgc gactataaac
    10261 agactcgcga ctatggcagg gcggtacgct ctgctctctc gcgaccccta ctctaatcaa
    10321 aagactaaag gcccctactg aaggtcgcca aactacgacg agactttcgc cttttgaagc
    10381 gccagtagcg tagggcgacc gggccaggcc gagtcagaaa ggctttgatg actcaaggtt
    10441 catattaggg aaaggagagt gaggggaaga gggctacgct gccctcggcc cgatcatcca
    10501 attcgctcca agagagaggc atggttttgt agtcaaagca acttcgtcac tttcgtgtac
    10561 ccatcggacg gcagcccttt cgggggttcc ttagggaccg attcactctg cgtagattga
    10621 ctgaacgcag aaagccttcc actggcaggc gatcgtgttt ttcacaggat ttatcgttac
    10681 tcatgtcagc attctcactt ctgatatctc caggtcttgt caccaaaaac cttccccgat
    10741 tgacagaacg ttccgctact gacacttgaa aaagcagctt tcaaggtctc gtcgcttcgg
    10801 tgaatcactt gagccctgat acattttcgg tgccatggag ctagaccagt gagctattac
    10861 gctttcttca aaggatggct gcttccaagc ccacctcctg gttgtcatcg ctcgatcact
    10921 tccttttcca ctaagtgatt gcttagggac cttagcgtac gatctgggct gtttccctct
    10981 cgactttgga tcttagcacc ccaaaagtct gtctgtacaa acgagaacgg cctgtattcg
    11041 gagtttccct ggggttggta aggcgaaatg gggccaccct agcccattga gtgctctacc
    11101 tcgggccatc gacatcatac gctctactga aatagatttc gcggaaaacc agctatatcc
    11161 gatcttggtt ggcctttcac ccctagccac aagtcatccc cgtattttgc cacatacgtg
    11221 ggttcggtcc tccaaggcct gttagagctc tcttcaacct gctcatggct agatcgatcg
    11281 gtttcgggtc aaataggaag aactagaaga ttccaccttt ggaaagcgcc tacacctaat
    11341 ggcttaagcc gctcttccca tttcctcgct gacccatcat gcaaaaggta cgccgttaga
    11401 gtgagtgcgc ttgactactc cttcgactga ttgttcgcat cggatctcag gttctctatt
    11461 gcactcccgt catagggttc ttttcacctt tccctcacgg tacttgtacg ctatcggtca
    11521 ttgaggaata cttaggctta gagggtggtc cccctttctc gcgtaaaagc gatcagaatt
    11581 cgaacacgcc gcgttttact gggaaggatc gaaccatagg aacgaatcta cagggctatc
    11641 accttctttg gccagatctt ccaacctttt cacaattaca gttcacagcg ccctttagga
    11701 atcttcagtc aaggtacgaa gtaaactcga ctgaaagaag aggggctttc tggtttttcc
    11761 atcatccaat ccacaataaa tcgaatgaaa cctggcgaaa aagaagtgaa cactttggaa
    11821 cgaagcttcg tctttctttt tcttaaaatc ccaaatccgc tctcgctcgc cgctactaac
    11881 ggggtctcgg ttgatttccc ttcctttagc tacttagatg tttcagttcg ctaagttttc
    11941 aaagtccaaa gagcgcagac tagccacgga gcttggatac ggtttcccga tcggagatcc
    12001 atggatcaca gacggtatct ccccatggcc tttcgcctct gaaagcgtcc ttccttctca
    12061 atgcccgggc atccatccaa tgcattcttt tcgatcttgt actcagggta cactgaacac
    12121 cacaaaaata tcgatgaaac taactataag tgattgcgga ttcgaaccgc tcacagaagg
    12181 atttacagtc ctgcactcta ccagagctac tacctgttac cactttcttt tcaactcgta
    12241 aaggcaaaga aaaaagggat ccgcctcgaa tcaaaacgtt ctttcttttc taaaaacgat
    12301 ctttcttctc ttatgaaatt gatagtttgt gagagggatg caataactcg actgtgtaag
    12361 gtccaccagg tccgtaggag agtcagtctt tctctaagca agctgttttc tggcctatac
    12421 ggaaagagtt ttcaaggtct ttccctttcc ccgaagggaa gttaaagctt gcctgtaaag
    12481 ggaagggaag cacagcaata acgccttttt ccttttttct cccgattaga cgaaagacgt
    12541 gttggggctg tatccgaaac atttttgaac tgccggcccg acaaccaagc ctataaccgg
    12601 caataagagg tcaagttgag acatacaaag gcgccagtga agagcttaaa atcagtacaa
    12661 gggctgctat tgaagggatt aaatctccca atcaaggact gcttaggtcc cttctagtcc
    12721 gtcctgtatt ttagtatgat cgacgtattg tattttacct atacgggcat atgttcgact
    12781 tcctgatcaa gggcatccgt ccacaaatta ttttatgtaa atatagatat tccctacttt
    12841 tcataccatg ggaaatccac tcggacgaag acatagatga taggattatt tgagagaaga
    12901 gccgtgccct acctattcta caaaacctta tcctagtttt tactttattt tttttatata
    12961 taagcattca tcaacggatt ctgcttccac tgccttagtg ctaattacaa actaattatc
    13021 ctcatcccaa aaccccttac aaagaaaggt aggcgtgcaa taagagaaag cttaccttgc
    13081 cccgagagag accataggat aaagtaagcg tgcaagagct agagaatccc ggggtatagt
    13141 gagagacctg gtgcaagctt ttagagtatg gctatcagtc ccaagtttaa gctaatcact
    13201 cgtaaggtta tgtagtccgc ctatagccca gcctttaagc atcaacagaa gatccagcgg
    13261 tatagtcgtt ctctgtatcc aaatgctaga gtaggagagg agtaagctaa ccttatccaa
    13321 cctttgtatc cgtaaatccc tatatagcct accagcgttg tacccttttg cgagcaagtc
    13381 agcctctatt tattaaaccc tttctagagt caccagctaa tcctaaaatc cctggtgcgt
    13441 aagcacaagc taccctttag tagtcagcaa ccctcctaag ccttgttttt aggagtaacc
    13501 tgggatcttt ttaagctcgt tataggaaga cgcgctatat gagtaatcta tcctagtaga
    13561 cattatacta ggaagctcct gagtcaacct ctaatctata agccagtcag cgggatatat
    13621 gaatatgaac ttctctaaga gaacagttca acgggtttaa ttgaattccg ttatctgatc
    13681 agattagata ttatctaaga ctgtataata gagacctaac taactggatt gctagcagtg
    13741 atcatacccg atgatgtgaa cccgattgaa tcagctcttg tgatcatatc ccatgctatc
    13801 aatgggagtg aagtccgcct atccatcaac ataaaagtga aaggagcccg ctaactactg
    13861 cacttcctaa tgtgatattg agttttgcct aaacttgccc gcccatactc ttaacttttc
    13921 gcttaagctc tcagactaga gctattctca ctaaaccgaa aattataata tacccctctc
    13981 tcctctctcc tcaatggcta aataccaaag ctaaccttaa atgggttaaa gaccgagcca
    14041 gaacaggagc ttagcctcaa tcttagatag gagattaccc ataacaactc aactacgtcg
    14101 agccttgtct tgaacaagcc aatcaacctc aatcctagga aatgatttca ggtgaagctc
    14161 acccctcttg ttctcatctt aagggaaggc ccaggcgcag aaggaagact ctttgatcgg
    14221 gtagttcctg ttctcagtca tcttaggtgc ggttggccaa ttaattactt aaatttatag
    14281 cgcgagcccc actcatacaa gtaggggaaa actctagttc aactgttttt ttattcagat
    14341 tcagaattgg ctgggcctta accgtagctt tagggccaaa agcctatcta tggccttttg
    14401 gctgggggta gctatggcaa gggtagtttc ctcggaaaaa ggaggggaag ccccgacttt
    14461 ccaataaggc ccgggggaat gaaaacactc aaccgatggg gggaggaatg aacagcagct
    14521 ctaggggata aatgtggata tccagtggca actgagcagg agcagctcta cccgcacata
    14581 gctaaatatc ccccttccac gccacccagt tggtgagctc cgcccttaag ggagcccatc
    14641 cgtcggtcgg ccaatattgg atagtaaact agcgcacagg gtaactcgaa tatcaaatat
    14701 aagaatagca gccccggtct caaaaacaag catggaaaca gcagtcaatc agaaagataa
    14761 gttgaagtta gctttcagct gttcaaccac taaagactaa agtgggtgaa gcatagtttc
    14821 gtccgtccct ctcgctttca gcgcgggata gagttatcag tacgtgcgac accaactctt
    14881 gcgttttcac ttttttttta tacatatata gataaattcc taccatattt cgttacttta
    14941 tcccgaaaaa ggggagctgc tgggctcctt cctgttttat tagcatcaaa cccactcaac
    15001 aggatattcc ataagcactc cggaaggtat agtgtgaagg aaagtaggtc ccttacatga
    15061 gagtttgcga acacgggggg cttatgctcc tgctgctcat atggaacagg ttggccccca
    15121 aaagccccaa gggaacgagc gaaagggctg cttgccggaa cagcagatcg agcagcctat
    15181 tatttattac atttctgccc caactattcc aaaaagggta aaaaatgggt ctaattctga
    15241 gacaaaagta atttaacatc cctgattcgg aaactgctgc agtgggaact ctacttgcca
    15301 ttcctccttc cgaagtgaaa gttttcattc tccccttggc ccagttgaaa agcctaaccc
    15361 caggtgaagt accagattct taagtgaaag taaggaattg cccctgtctg attcgtaaag
    15421 ctttcggaga aggaggggag atccgcggag gtagaattct gaatacgggt acgaagggtc
    15481 atccagaagc gctggaaggg ctggaggaag gggacgaacc gcatcgattg agttatatcc
    15541 ggcaggctaa cacccacgta cctagaaagg aaggggaaag tcttaccttt tggaaacata
    15601 aggcgcatca gaaaggaatc cggatatatt tagatagcca gattcacgag ctgaggacta
    15661 agtcgaagcg aaagtctgtg ccattgttag tgccaagacc ctagaatagt gaacaccaag
    15721 tgaagagcca cctccgggaa cgtcgagaag ggggacgaac agctttgatt ggatccgatc
    15781 tggtagacag agacgaagac aaggatgaat aatctgaaga aggctatgcc gaatccgagg
    15841 gaagaagaag actacgaaga aggaagccga tgcctaggcc gaggctggtg cctaattcta
    15901 tgcttgaagc ctaagctaga gctggagctg aagcctaatt ataagtttca tctaaagctg
    15961 aagttagggc tggagcctga gttggtgttg atgtcctaga gtagcgaaac tacaagtgaa
    16021 ggggcgctat ccggaaccct taaggtcggg gacaatctgc ttcgattggg ccttgcaggc
    16081 agacaggcta acttgtggag acgaaatgga atcctataag aatgtcgagt cccgagggtc
    16141 tgcatgcaag aggctgagct aacaagctgg ctgaatatat catggggatg cccgatttgc
    16201 gattgagcta gccgataagt ataatctctc cggtctggca tgagccactc cattcctact
    16261 tccactcaac aaaaaagata ggattcttgg gctctacctc cagagtgcgt acggctattt
    16321 cagaccaaag ggggccaagg gggatcccat aaataataaa gtaagagaag taacccgggc
    16381 tatgagctat ttcgtcgttt tcttgccgga gttcgctagc cgttcaatcc gatcttccct
    16441 tcgcatggca gaagagcgcg gctcgagact actctttcaa ttaaaaatga aaggcaagca
    16501 ggaatttaac ccactaatgg gccagctgca taatcacgta tgtaagcaag tgatcctctt
    16561 ctttcgcagg aagcattact catttcttca gagttgaaga aaaggctacc gatttcccac
    16621 tgactattat gtaagggctt gaccttggat gataaattca tggctaagtt agtccgtagt
    16681 acgaagcttt caattcaagc accttttttc tatactaaag gccaaaggga agttgaagcc
    16741 caacatcccg tggtcgggat ggacaccggt ctggcccaca cctacatgga cttcaaattg
    16801 acttctgatc gtaactactt taaaaacctg tggttcctca cgcctagtcg acataatgtc
    16861 tggcgtttac ctgacggttc cccaagcccc tgagctcatc aatgaacgga ttccatcttt
    16921 cacagcgagc tgttccgaag tcgcgcctga gcacagtgaa atgcctctta cggtcatcta
    16981 tatcgtgctc ccagtcgtca tggagagcca actggagagc acgcttgaca tcctctggat
    17041 ccccgagagt tactccacgt tgatgcaaga gaatatgggc tttccgtacc atggccgcct
    17101 ccaaattctc gcaggcgctc gtgatagtct ctacctcggc agagatgcgg tcgtgctctt
    17161 gtgcccgagc ctccctttcc ccaccttcac caaatggttg atccaggtga tcctgctgtt
    17221 gagctactgg ggaagcggcg ggttcgggta aggcattgga tggcccagcc tgttccctct
    17281 gaatcggttg attcaccgac gaggaggtac gcccggaact ggccgaatcc tccaaatcag
    17341 acgtgtaggt aaaccactct gaataggaag atgccccgtt agggcccgta gaaggaagtg
    17401 cttcccctcc ccctcctatg gcattccaga ccaaaggagg taccaacagg ggcaaagcca
    17461 gacccagtag gtggatggct ttgatccgta tcaaagatat tcccaccgcg atgaaaaaga
    17521 ccaaaaagag atagataatc ttcttcagtg gccctttcaa ccggaaggaa tgcaaataaa
    17581 aggcggcgac cccgccgagg agtgtaagtg taaccactaa aacagtggtg gtcgccaatg
    17641 atggatttcg agccacagaa tggatcaaag aactgaatac gtttccaata ccgatagcag
    17701 ctcccgctga agcaattgta gcagctccgg cacctattga ttttgcacct tctaacatct
    17761 cgggttgaga attatactca cgctttgtca ttcacttatc ttatatctta ttgattcctc
    17821 gtcgattctt accctcgttc ctttgatctt ggacatctca cttggaatgc attctttgcg
    17881 atcttatacc cacggagtgg tagactgaag accaactgaa tctcgacaaa gagaagtaca
    17941 agcaagtaga tcattcgacg tcagaggggc tgatgtgggt cgggctatct atcttgctat
    18001 cttttttttt atacataccg tattattcta tcaatcggga agttggcctc actcaatagc
    18061 gggaagttgg cctcactcaa tcaatagtcg gatacaatcg tggacaccgt agacctgctt
    18121 cgcctagagt ggatcaggtc cttatacgta aggcgatccc gcgaagccgg tcaccggagg
    18181 tgaagtcaac catcatttct tttcttacta aattcaacta tgtattctga ttaaagagct
    18241 tattctcttg attcatgtcc accttgcccc tggtaactta aggatgagtt tcgaaattag
    18301 gaaggattgg actgcagatt tagaaagaga atggggagcc ctcatcaatg aattaatgag
    18361 tttcttcgcc ctctcttggt gatagtagct cttcatcagc ttatagtagg agctgagctc
    18421 ttccgctagc ttactagctc tggtagtcag gctcttcggt caatagttct actggaaaca
    18481 gcttcctgta tcactgcttt ttaatttttt tttaatgctt atattttctg taaagatctc
    18541 gatgaccgct taattcatct ttcctttccc gctcctgaat gaaaagtggt tttttttatt
    18601 cctacggtct tggcgtgatc tctgaaactg aaattcgact gaaaagttac caatagaata
    18661 ggctttagag tagctctttc caaataggtc gagtagccat ttctagaaat agaatgaatt
    18721 aaaaggagcc aaatagttgg gattcacacg cacagcctta tcctatgagt ctgcctatgc
    18781 tacgcgcctg cctttgagag cctttaccgc tggttccctt catcggcgtc attgaacctc
    18841 gttagcattt cgaaaagaat tggaggctca aaacgaatgg tcaaaggaat tgatgattcg
    18901 tgtttagtct ccgatcttcg cctagtctta gaacctgcac tgtagagagg cgctgcgctg
    18961 cctctttctg ccgctctcct cccagatgta ggtcttcccg gaagtgagaa cactgctgcc
    19021 caacttataa ttcggtcact ccccgtcttc atcctagacg ccactggtac tattcatcta
    19081 tactatatat ggatgactcc tgctttctcc ccaatggaat gatcaggacc ctaaagaagg
    19141 atcgtctcac tccaactaga ataaagatga gctagttagc gctggagttt tcttgcttct
    19201 tcgcctctgg atagtagttt gaatgaatct ttgatactgg gattaactct tgaaggaaag
    19261 atcttccact cctatgcttt caagcgattt ggattccaag acgatagata ggccggttat
    19321 gaaaaagagg gatcgagcag gacgaagtca acccggaaag aaagtcggat aatatgaaag
    19381 gtcatccgtc tcattctaag cgtaaaatta atttttttca gagaaagaag agcccatcag
    19441 ttctcactct tccttaccag tcagttcccg ggtctataac aaagcagtca cagtgtgtca
    19501 tcttcttgcg tggaagtgag tcctccatta atggtatcaa tgcctgtccc cctctcatcc
    19561 ctgtctattg ggcttcacgc tagcccccat ttcgatcaag aagaaacttc ccagtcccaa
    19621 gtgagaaagt gagaatagtc agatgatccc atctcataga taattggctg tctcggaaag
    19681 agaggaagtg atgaatatag aagatctagc tctcattcct acagaataga cgacatcaga
    19741 aggaaagatc agtcgataga atagaatccg aggatttgct tggatttgtc cgcttcatct
    19801 cccccggttt acgcttccag gttctcacat ttggttcttg gaaaagaaca attgaattcg
    19861 gatgtgattt gacttcttcc ctgatgatct tgtcggccct atctatcctg aaaaagaagc
    19921 attccagaat caaaaagaag aaaggtctcg acgagcatta actagttgat gaggtctcaa
    19981 cgagcgactg aaaggagagg agaaaaaagc tgctagaaag aaagtgagct acgatcggat
    20041 aaggtatgcg ccttctatta ttgatgttgt cactgcctca acttaacctc agaataagat
    20101 tgaacgtcaa cgagaagcgt cagtccaagc taaagaggaa tgatggagag caagaaaagt
    20161 cctgtgctga ctctgtgttc taagctgcca tttcgatcaa aagtatactt atttttcctc
    20221 ctactcgaga atgatggatc cggggaggca aggaagtagt agaaatgttg aagaaggaga
    20281 cttaaaggca actcgagtaa aacgagaggt ccattaggga ctcgacttaa aggagaggta
    20341 cggagtgact cgagcaaagc aagaggttta aataactcga gtgtaaacga gaggagacaa
    20401 cccgctcttg aacttgaaac tatgcgcgtc cgtcttcgat ctagcaatct tggacaattg
    20461 ttttgatgag ctgtcactaa actaaaaaaa gagagaagag aaagaactgg gaatgggcgc
    20521 ctggttgctt gcttaccaag ccatcctggc aagctcctcc agttcgatta ttattcttga
    20581 cttgactttg tataaaaact actcactatc aaaatgaaag acgatcgatt atctacccaa
    20641 gaagatagag agtcccacat acgagaaaag gtcacaaata gagttgaacc aagtaacatt
    20701 gcaaaggcat aatgatagta gggtcgggat atccccgccc tccgaaccgg acgtgaaggt
    20761 ctcccctcat ccggctctcc gcaggggaat ctccactcac tgcttcccct aatatcctcc
    20821 tttaccacat catgggggtt tacaggagat cccagaggca cgcacggaaa ggctgctata
    20881 ccataccttt gactcaactc tactctagta gtcatagact cactagaata gtccgtccgg
    20941 ctgctcttgc tgaaatacat tactcttcat tctcccgtgc tctagcaatt gcgctcccta
    21001 gaccactacc atgtagttag gtagggacat ccgtaatgac gggaatctag gaatgaatgg
    21061 ggatccctat caataagaat atgaagaata tctaattagt tacactacct ttctctcact
    21121 caatagatct atctggtctg gatacggtac agtacaatac gagacgatgg aatgctatgg
    21181 gatggatggt agagggatgc cagcgcccaa aagcgatgat tcacttgtcc ccttgtccat
    21241 agggacctcg tggcatacaa ccgaaacgac tcccgctaga tagccgcccc tatctctctt
    21301 tttacagcct cgtggacgga cgaaagaagg caagttacag aacggtgcag tgaaggctcg
    21361 cgaagtagac agcaagcaac tgcttttcag ccccttctct attatattag taaagggaag
    21421 gggactctat caggatctta cgaatctaaa gatctccaaa ttgaagaacg gactcttttg
    21481 ctgcccccgg agcgtaagca cttcactcgc taggggatgg gattcattca cttgcattcc
    21541 tgctagcact acaaaaagct cggtcttaac gcccttacta ctgctgtgca gcctttcctc
    21601 gggttcgtag agtcgggttt cccgtttacc cacaacggag gagggccccc caccaggcag
    21661 gcggccacgg gtcataacgc actcttcgca caacaaatcc actttgaagt tgacttattc
    21721 gctcggccaa tcgtcggaat gtgtacgaga taccataagg gcccaatatc tcaatagcac
    21781 ctttgtctaa agcttcgaat gagacttcat atccgaaacg caggaacgat ctgactagaa
    21841 agtcattcaa aacttgatcg aagaaccagc gtttattgaa gaagctatag agtcgattac
    21901 aaaaagtact agtttgaaag gctcgttgga attgatccgc tacgggattt acattatacg
    21961 caacaaaagc acctgaagta ctaaacagaa taggtattag tttggtaatg gttggagcag
    22021 caaactcgga ttcggcaaga atctcatttt ttggtagtac gaggggggaa ttggcccaaa
    22081 aattggatag gggtcaagac gcagtcgggc gccggcggct tactcaagtg ccccccgaac
    22141 cgcgcgaaat ggtcgcctat tacacggctc actaactctg cctggggtgg gggtacgtac
    22201 ctatttatta ttcgtcgccg gtccggctta atggagaagg aaattcattc ttaatctaga
    22261 gagttccctt ttgttaagcg catcgagcca aaagactttt cagtcagaaa attaggaagc
    22321 atggactcac tctactcctc gcggcggtat tgccgcataa tggaatagat agcatctttt
    22381 tccttttgag tttgaaaggg aaaaggaata tggttcccgc cattataata atggcgagca
    22441 aggtatcgac tcgcgaaagg agctcacgat aaaaacccac cggattttct ttttccaata
    22501 ttaaattgat cgtatggaaa gacgcctaca cggaacctat acgaaggagc aaacaagcaa
    22561 cggtaactac tctactttac tttgatttga ctaggcaatt gattccccat ctcggtcaat
    22621 caatcggcct ctaggactgt tgtttaaaga atctgacctt gacaaccgaa acgtgagcgg
    22681 ggaagctgac tacaccttac cccttgactt cgatttccgc agtgctctat gagacgactg
    22741 cgagcacata cctatggatc tatgtcaacc aaaagcaacc actccagcaa gtttaccaac
    22801 cagcacagat cctcccaagc aacttccact gcgccaacta gaaaacttat gcgcttgtca
    22861 attctttctt atcttactat atttctaatt acctaaataa aataataaat actgtagtta
    22921 tagctaaagc tcgacttctt tcttcttttg gatctgcttt gccttgcttt gctaccgggc
    22981 ttctagctgc ccttcctcca ccgttagctc agtagagcat tttctcctcc actcatgtca
    23041 cggattcagt tcaaaaatga caacagtctc tagtttacaa tggctcagaa gtatggttgg
    23101 agatggtgct tatcttccta tttctcatgt cggttcaaca actcttgcta ccacagaagg
    23161 tagaatacct gttagtgatg tttcttcttg ttcctactaa aaaaagaatc cttgctctca
    23221 gtctctcaat ttaccccttg gtcctaaacc atgctcagtc cttgattgtc agctgctaga
    23281 acaagcacca gacacctttc aagaaagagc aagagcggcc gggaaagata aatcggatta
    23341 gcctttcatc gatccccgaa gagaaacatt ttgttgttga atctgtgaga aaagcataag
    23401 gataggtgag gatagattct ctagattaac tttatcgaac gaatgagaag cttagcaatt
    23461 catctcggtt aaaggattct acggcgaggg tttaagcgca taaactgctt ggagaaggac
    23521 ttctgacaag gcggctatct tgatagaagc aattctcttt tgaaacactt tcatagaagt
    23581 cttcttacaa agcaaatagc atttcctata gcatttccta ttgatttgtc ccctggactg
    23641 gtggacctat tctgattctg aattatccgt cgctacgctg ttcccaagga ctagcaaaat
    23701 cgaaatagcg aaattcttgg gtcatctcaa tgggttcaga aaccacacgt ttctctggat
    23761 catcatagcg tacttggaca tatccactca gaggaaggtc ttttcgtaat ggatgaccct
    23821 cgaaaccata atcagttgat atacggcgta gatccggatg attgatgaaa gaaacaccaa
    23881 acatatccca aacttctcgc tcccaccggc cggctgatgg aaatagactt actaccggag
    23941 atattcgtgt tacttcgtct gcactggttt gtacacgaat gcgtgagtta taccgagtac
    24001 tcagtaaatt atagaccact tcaaatcttc gttttcgaga gggatgatca actccgcaaa
    24061 tatcgatcga aacttgaacc cttgtatagg tatgcaattt gagaaagcac aacaattgaa
    24121 ataggtagtc cgtattggta tcagatctat tcccatgttc cgatctttcc atttttttga
    24181 cccatttctt gggtaaagtc tcccaactat atttgaaaat gaattggtta tccataaaga
    24241 taaagaaagc tttcttgtag ttccgcttct tgctcttcaa attctgaaag actcgtcgga
    24301 aattgccggt gccggttggt ccaaccaaga aaggcatggg agtctttggg cattacttgg
    24361 gtcgagttaa gtaaagactg gttacctata aagatccctt actttttttc gcaccggaca
    24421 atctaatttg attgaaagcg aatgatcaaa ttcgtggatc gcctgccata ttggactttt
    24481 tgtttttcca atacaggcga gcacgctttt gagatgccct agacgactcg catttgaaag
    24541 gaagctgtgc agatcgctta agtaggctta aatacctatg cgaatatcgc tctcctcgat
    24601 atttagatct cggagatccc tttcttttcc ttcaattaaa cttttgagag ttccttctcc
    24661 atacatatcg agggctttat caatgattct ttggatcttt tgttcgcaaa agtggaaatg
    24721 gcgctctgtg aatcgccact ccttagatga aatcagatct ttccacactt tatcttcatt
    24781 tagttccaca gttctaaata gatcatctgg ctttctaaca acataacgga tgaagtcccc
    24841 cccacgggta aagtctgtgg aacttgcagc atagggacaa ttccttgtcc cacctcctgg
    24901 attactccaa gaaaaggttc gaccattggc aacagttcgg attcgaacat tgtctatctc
    24961 gtaatcattt gattccgtct gactcctcct actcctcctt tccgaaaaga ttatccttgg
    25021 tccttacttt tgacataaga ttctcggccc gctttatccc cattaaccaa ttacgttacg
    25081 accactgaac aaacttggtt gacgaacatg gtttatgagc cgctaatgta gcggcttgtc
    25141 gagcatttgc caaactcaca ccatccattt caaatgggat ttgtcccgtg gacacacgag
    25201 caatccaacc cgtaggattt ccttttcctc ttcccattct tacttctgtg ggtttcccgg
    25261 taatagggag atccgcgaaa actcttaccc atatcttacc atttcttcgg aattgtccgc
    25321 tcatagcacg atgaaagtgt ccgattatag cccgacgcgc tgcttcaatg gctcgatatg
    25381 aaagacgacc agctttacaa cttttagtgc catatcttcc aaaacccagt tttgtaccat
    25441 ccggtttgca acccctacta catctgcctt tacgatattt actatatttc gtacgtttcg
    25501 gatatagcac gtctcccttt tttttgacta tatgaaatcc acactttgac acctgagatt
    25561 ccgtaacgag tagatacttc cgcaggagca taatcgattt tatggttaaa tacattacga
    25621 gaagtttttc tatgcttata gcatttagtt tgagcttttt ctgctgcgtc ttttaatcga
    25681 ccggaaaaac atatacggat tccctccacc ccttttggaa tctccttcac tattttagca
    25741 aaaatggaat gaaatgatct tcttttgttc ttcagttgaa aagagatgtc ttgagcaatc
    25801 ggagaagcgc tttgataaac agattttatt ttgactgact caattaaggt cttagtgttt
    25861 gttctattag acaagaaaga tcgcattttt ttgacttcgt aaaaataaga gttgtacctg
    25921 tacggaattc ctctctttct cagtatgatc tctatcatca tatctattac ctttatcaat
    25981 tcttctatcc cacctaggtt ttttaatttc tctatcaatt ccattatctt atccttaccc
    26041 acgaggttcc aacatttgac ccttaattga ttgaggagtt gttcccgagc atcaaggtta
    26101 ttatacaccc caaccccatc tcttagaaag aaaaaggtag caccgaagaa tggaaagagc
    26161 gagatggtgg ttttagttgt tcccgcgaag cgaagatcat tcgccaagcg aatgaagtgg
    26221 gtcaacctat ttttggcttc ggccaaacac tttttctcgc tggtcgagct ttctacaaaa
    26281 aaagcgatac gagaacgtat tctcttctgt aagcttcttc cctgtgcatt cgctctcccc
    26341 atcgtagatg gttcagcggc gcccggtgcc acgaaatgat tgagaactac gacggggtcg
    26401 aaattaattt ggttctttgt attaaaaaag tattgcatga ccaaaaaatt caaggagggg
    26461 cgcactgcag ggagggtccg tagataactc gtcgggccgt cggagcggga cttattttgg
    26521 aaaaataact tgaataactt cgtttttttg aaggagtcgt cattttctat caggaacgct
    26581 atgtcattta caaccccggc gtatttcgga tgcttgaagg ccccgctgat ccgaagtgat
    26641 ttagaaagat tcttctttat cgagggtaat cggtcatggt atccatagcg ttgttttttt
    26701 ttcggccaac cccggatttc gttttgcttt tttcggtcgt cgagcctgat cgactcgact
    26761 cttttccttg ccccccggcc tctcacttcg tttcgttctt cttctgtatc gtcgcttgaa
    26821 tgaagacact cgatcggccc ggctttcccg aatgtcgtcc accaccggcc cttctccttt
    26881 ccgggtctag ttttttcacg tcgtttcagt cgtcgtggtc gacggggaag aaagaaatga
    26941 atgaatgttc ttttaggaaa atgtagaata atacacctac cgagacgaaa gccgaaggtg
    27001 agtctcgtag gtggacgtat cgaaccgaaa taagatctca gattgacatc ttgatacaca
    27061 aatttaccat aataataaat agagtcaata gtgaccccgc cgtagaaaga gccgcttatt
    27121 ttttgcttga taggggggct tccattcacc aacaaagact aaaagtgctc tccgaaccgt
    27181 gctggatagt cacccatcac acggctctca aacccaacct gtggtggatc ccgggagaca
    27241 aagtaaaagc gcttgatcct ttgccccata ctttgagatg ctcctccccg cgcagcacgc
    27301 tgctcgtgag aggcttagct ttaagtttaa gctgctatcg ttcggttcgg ataagtcaag
    27361 tccctttgat cggttcgctc aggtggtctt atcttcccta acgttcagag tcgttttggt
    27421 ttgagaaagg agcaccggcc gagcgccctg aatgaataag aaatggacag gagagagaat
    27481 caatgattct tattcaaccg agttgaagct agcaacatgt tgattacaca ccggaggtta
    27541 gtaagaactg agggcaatgc cctcctaacc taagtaggct acccgcgctg cgaagcaact
    27601 ggtacttgat tggggcgggg ggcggtttgg tttcgtgcaa ggccctcgca acaggaagag
    27661 gcagttgtca ttaacctttc gcctttattg atataaaaca agcttactta ccggcaacaa
    27721 gcaccttttt ttctcaaagt aaagtttctc gcttgtttct ttagaaagat tgcagcctta
    27781 gcgaaacaac ttatcctttt ctacgaatct tccctttatt gagcaaaatt ctatctatat
    27841 ttattcccgg aatattttct atttcaattc tatcatttgt ttgacagctt aaactaggct
    27901 tcattttaga taggttttcg gtctcttaat caaaatcggt caggggtgcc gtcggaacgg
    27961 tcggtggctg cttagtctca tccgagagtc taatctcttt gtactgcttt ttttcaaaga
    28021 aaaaaaaaga agaaaggggt cgatttaggc tccttccctt ccactgcata gctacgctaa
    28081 caggtactac gagccctctg tcccacacat ctaaccagct cgcgtggttc accggttcca
    28141 ccgaaaactc tcatttgtta aaacggagca tagtgcgctt taggcgccga gcgagaaacc
    28201 tctcttcttt cgtttcggtt tattcactat ctgaaactta gcacttgttt gatttttctt
    28261 attgggcggc ggcgttcttt tttgaagtct atccgaaccg aattagcact tctcagatca
    28321 gactaggcct cccccgcaga gctgggcgcc ggggacctgg atgcgctagc gatcggcgca
    28381 tagggggggt tagttgcccg ggtttctcgg cctggtatcc tacacctcgc gttaatgata
    28441 tctacattca actgtgcccc ggagacacgg tcgaagcacg cccatccaat gtgcttcttt
    28501 cacgacatgc tctggttccg ggtgttttcc agtggtcttc tagcgttaga agaagtcgtg
    28561 tccgtcccgg acatctgcaa cgtcctccca cgcttttttg aaaatatagg ataaactgaa
    28621 ggaaaagact tacccattcg gtgactttcg cggtcgccct cactgaaccg acttgaatct
    28681 gaactacgat tttttccaag tcttaccgaa atcggatttc cttttcgtgc catatttttt
    28741 gactttatgg atttctgtcc cttttttctt cccggtacaa tatttgttct cgaaagtctg
    28801 agtttccgtg tactctccaa atttatgacc aaccttcccc tcagtgatct tagaacgcta
    28861 ctacgcatct ttactatata gtgtggtaag gtaggtttgg gtatagcagg acttgaacct
    28921 gcgaccatta ggttaaaagc ccaatgctct accaactgag ctatacaccc aaataaagat
    28981 gtagtagtca attaagattg gtgcggaaaa gagaagaggt ctcaacaagt attaactagt
    29041 tgatgctgat cgaaccctca gttcgaagct cttcgccaac atgttacgag gctccagtct
    29101 taggcgggtc accattactt gacttagctt agaaaggcga acatctgggc aagggaaagc
    29161 gcagtgcgcc tggtcctttc gaaccagtct ttataaacct ggtgcaaatg gctttctttt
    29221 tttatgatat accaatcaga atggaaggcc ctacgtacat gattgataga agcactacgt
    29281 atggggggtc cacttgatgc gggagaggca tgagtgcagt tcgatcttgt ggtgtattcg
    29341 tttgtagtga gtagggcctc tttctcgttg atcagttcgc ctccgctcta ttgaatggtc
    29401 cccattccta cggcggtttt gtcaacgaat gcgtctcggg ccggattgac taacctaacc
    29461 cttaaggtaa gggggccttg ccatagttgg gtgctctgct ttagtgtgat tgacgaaggc
    29521 gctaggctag gtttggtaat accaaaaaca aattaaaaga gattggagtc gatagttggc
    29581 aaggaacttt tttcccctcc cccccccaaa aaaaaaaagg agctgcggtc gaactctaat
    29641 tctgaaaata agtcggggcc cttttaccaa gtctactaga tagaaatgat agagggccaa
    29701 ccatggttgc gttgcacaag acggtgccgc ctcacctcga gttcctttct tcgtagtcaa
    29761 atcagatgat aggcttcggc gatgttacct accaaataaa aaaaaggcct gctaggtgat
    29821 cgaaatcgct caggtcagtg aggactcact cactcatcta cgtattacta ataatttttt
    29881 ctatctactg aattaaagac ccgccacgcc gggctataag atacagctgt tgtactactt
    29941 gactggtaag aaaaagctaa cgtaagaact ggaagagtct tgtatgtaca gtacccctct
    30001 cttccgctat tggtggactg ttgaacagaa aggccgacag aagcaacctt tcttagcgcg
    30061 cttttcaagc gcttagcttt tgctagcgac ggggcggcaa ggctataaag taagtaaagt
    30121 tggaagccta agccaagaag gtacgaacga agtgacgggc ccctttagag ataggatagg
    30181 gggctcttgt ggtagtaatt gcgaacatct ctctttttct cgtagtgtgc acagtttgct
    30241 tgcatgccgc cttaggcaca tctctctttc ttagtttcat gcttcctaat gaacgaaagt
    30301 cagtctttta gtaagcgtat ataagcagca gtttagtgta taagcaattc tttagtggct
    30361 gtgcaccgaa aggtacgtac ggtggaggtt ggttgaagat gatgttacgc ggcgttcaga
    30421 accagccttg aagtgaatga attagaaaga agaagtaagg aaatgagacg actttttctt
    30481 gaactatatc ataaactgat cttctcctcc acaccaatca cgagtttttc ttcattcctc
    30541 tcgtatatcg tcgtaacgcc cttaatgcta ggttttgaaa aagacttttc atgtcattcc
    30601 catttaggtc cgattcggat ccctccgttg tttccttttc ctcctgcacc ttttcctcga
    30661 aatgagaaag aagatggtac actcgaattg tattatttaa gtacttattg cttgccaaag
    30721 atcctacttc tacaattggt gggtcaccgg gttattcaaa taagtcgtgt tttctgtggt
    30781 tttcccatgt tacaactttc gtaccaattc ggtcgatccg gaatggatcg gttaaacatt
    30841 ccattaggga gcctggtctt gactcttctg tgtggtattc attctcgttc ggctcttgga
    30901 atcacatcca gcagtggttg gaacagctcg caaaatccaa ccacttcacc tactttattg
    30961 cccctaaccg tttctcgtac ctctattgaa acagaatggt ttcatgttct ttcatcgatt
    31021 ggttattcct ctctgttcgt atctcttttt ccaatttcgg tctcgattag tttacaagat
    31081 taaatggcca attctcttct ggaccctcga ttctttagtt ttccgagaat gttgggccgg
    31141 gtatgtaagc catgtatcta ggaggaatta gaaagaaggg cttttgtttt tttgcatcct
    31201 gtgttgtatt ggtcttgcag ctatatatta gaataagaaa tattattctt gtcttatatt
    31261 attatataat acataataat attagaaaga tggtacataa tatctcatac acgtacataa
    31321 agaagttcct gcatatcctc tctaataatg taattaaggg ctaagggagg tttcttgggt
    31381 acattaagac ataactcgac atcccgaaat caagtcggcg gctctattgc tctccctcca
    31441 acaatgtgtg actctaaaaa acaaactgct ctggcatttt cagtgaagct cagcagcata
    31501 tttcgcgctt atggggcttg gagttaatca tcttgactgc atataatgag tcagactcta
    31561 cccaaaggtt acgaatgcct attcgcgaag catctccccc gtatggcgga ttgcataaag
    31621 ttccaccttc aaaatatctc tccactcaac cgtcttccgg aaagcccaaa gaggccgata
    31681 aagtctcttg ctatcacaag ccgcaccgca gcagcctcta ttgctactga accgtctgtg
    31741 ttcacttttg tttacggagg gttcgaagaa gagtaagatt cagctgagca gggtaaccat
    31801 gcattcccaa aaacggagtt gagtgcaaaa agagtccata actctcagtt taatctgaga
    31861 ggaaaccaaa tgcagtctca gttttacttt tcccttacaa ttctccaaaa ctacgttctg
    31921 cttacagctt ggattccctt catggcgcct ggaatttctc tcacgcccat agtatatgac
    31981 tgcagtaaag cagagcttta ggatcaggcc agtaaaggtc taattcttag tttttctatt
    32041 ttataatcca ttggcaaaca tcatgaaggt tggttgcagg ctgatcatat ctacatttcg
    32101 aactgagctg agaaaaaacc caccctgcat agctgcactg aagagatgtt cggcactttc
    32161 atcttcaagc atgcacaggc cacaaagagt cacggtgttg gttgggataa aatctgctaa
    32221 ctcgatctgc tgaagcccag agttgagggc catccaggcg ataatactgt ggcttgggtt
    32281 ggggatatta aatttattcc gaacgatgcc tgcatagtcg accttaggat aggtctgcct
    32341 aatgaggttc caggctgttt tggagaaaaa aatttccatc cgggctgaga gaccaaacga
    32401 tcctgtcttc aacagggaga aaaaaaagag ttcatacagg gcaatctctt gcattagaca
    32461 ctgtccagcc attctgcggc taggaggaag ggtccaatgc aatgcccatt ttttattaaa
    32521 tcgcttacta gagcatgggt ccgggagacc tctttccctt ataacagtga cctcgtacct
    32581 gtagctgatc gggccatttc taagccacgg acaatgccac agcttcgtgc tttcgccatt
    32641 aaatctgaca ctttatagta ttatattagc cacatcttcc cttaccgaca ctcctccaag
    32701 actaagatca gtcggatgga agcttagcca ccaaaataga atgtctccag agatatctca
    32761 aattaaccca ttgagtccaa atggacccat tatcattaac tactctccag aaaagcttta
    32821 acatggcagt cctattccag ccctcaattg ttcttaaacc caatccacct tcatccttcg
    32881 gtctacattg gaccagctga tcatatggat cttataggtg ggttcggggc ctgaccaaaa
    32941 gaaatcccga atgctcaatg aaatggattt ctatatcttc tccggaagcc tgaaagcgga
    33001 cgaccaatag atgtgaaggc ttgcaagcac tgaggtctgc aagcctttca tgacagcagc
    33061 cttcttttct tttccaattt aaaatttggc gattgaactt gtccaagagg gggagacagt
    33121 cagagtgtct caatctggta gatactagga aaaaaaccag tatttgagag ggagctgcac
    33181 ctcacgtaag ccaagagtac gaatgatttt tagttttact tttttttaac tggtggccga
    33241 gaatgatagg gaacatttgg ctttattaat ccaaagaccc gcctagctgt gaaactaatt
    33301 cagcacttgg ttgatgacca acgcattacg cacggagctc tccgcgaaaa tgagcacatc
    33361 agcatatatt atatgagaaa gatagagttt atgaaatctt cttgaatggg ttatccgctt
    33421 gttgtttact tccctgttaa aaagctggct gaatattcag ggtaaaaaga taggctctaa
    33481 gaaacttgtc tcaatcaaac cgcggccccc cctgaagaag ctagatggag atccgttaat
    33541 cataactgca aatgacacta tggagataca ttatctaatc tatcttacct aaattgaagg
    33601 aaacttcaag gattcaaggg tattgaggac agcatcccaa ggtactgaca tgactcgact
    33661 gaaaggagag gtgctttagc aactcgactt aaaaggagag gtgctttagc aactcgactt
    33721 aaaaggagag gataagaaaa agccaacttg aagttcagtt acttgccttc cccattcttt
    33781 cgaagttgct agcattctct ctcctttgct ccaagggaat ctgtaatagt aaaccacgca
    33841 cagatgctag gaatgaagcc agccaatgcc ccttacatta caagaagatc gctagtagaa
    33901 gaagataccc acacccacgg ccagagaata ggcgaatagg ggaaaaacat gaatagggct
    33961 ttttgaaata aatagggttt gcgcaattcc atttctaata gaatgccgtc tttagcaaaa
    34021 gcaaaggagg aatgatctac gaatgccggg catgatgtat tagtattacc cgagctaagt
    34081 gcgctgtttt cagaacaaat gcacagtgaa tctacgaagt cttcccctta atgttaatgt
    34141 cctaaagcag gagagagtta atcaacgggt agccctctgt caatctctga tggcatcaaa
    34201 aatccgcaaa gtgacaaatc aaaatatgag aatcaacagc agtctcagta agagtagcac
    34261 gttttcgacc aggcttagga taaccgattc ttatttatca agcccttctg taacagaact
    34321 agcaccgctt actttgacaa caggggatga tttcacagtg actttatctg taacaccgac
    34381 aatgaactca ctagaaagtc aagtcatctg tcccagagcc tatgattgca aagaacgcat
    34441 tcctcctaac caacatatcg tttctctcga actaacatat catccagctt ctatcgaacc
    34501 aacggctacg ggttctcccg aaacaagaga tcccgatcct tctgcatacg cataagccgt
    34561 ttcattcgcc gaagcatcag tctcaagatc cgaatcctat gaatcaactg gatcaatatt
    34621 cgcaaccgat gcaacatctg attcttttat ggttttggtt gctggacctt tctccgccac
    34681 cgtcttttca tctatcagtt aaatcagttg acctttctct cttctctctc tctcctcttt
    34741 ttctcctcct ttctatttct tctcttatct tttctagggt taacaaattt ggtatcagac
    34801 gcgtaggtta cgcaatggca ccgaaaccag atcccactgt tcttcctgat cttcaggaga
    34861 aaaaggcgat cctgggaacc cagatcgaaa tgataaccca agccatgaca acactggagt
    34921 ctcgtgtgac agatctgcag caagaaagca acgaccatag gacttgggtc agggaagctc
    34981 tagacaagtt gttgaagagg gatttgggag atgaaaacag gccgaaaccc actaccaaca
    35041 agatgatagc aacaggcgag cagcacaagg gagaggtctc gacgagcctc ttccacgatt
    35101 aacggttcct ccgagacaag ctcccaacgg aaagagctca cttaggcttg atagctttga
    35161 tgtgagcgtt tgtccaattc aaagattcta agctctcaca gcactgattt ccgatggaaa
    35221 ctacagacct tcatcacaga gaaacttcca ggaagatgga gggttctcgt actcgcttgg
    35281 cgggggatga agtaaaccct ctttctgagc agctatcgag cctattagct tcttgcccgc
    35341 atcccaaagt acgattcccc cggacaacca caatggttac tcaactaaga agcaagtcct
    35401 tcaaagagac agctttactt accttttctc cctagatgga acaactcaac tccttactta
    35461 gatttcaggg ggttaaggta gttgactttc tggctgataa atcaggtaac gaagcctaag
    35521 atttagatga ctgattagat tactagtttg tttaactgag attccccgcc taaatcccat
    35581 atcttaaagt aaagactata actcaacagc aagctgcctt tacttggctt caagtcccat
    35641 aagagaagga agaatagcta gaagctagag agtagctgcc tagctacaaa ctcaaaagcc
    35701 tggtgaaagg aaggcctttt ccttacttag cttagagtcc caaaaggtgt tataagctgg
    35761 aagctaagaa gctagtcgtt tatgagtagg agttccatcg gtccagaact agaagtcaac
    35821 tcaaaaccgc taaaaggacc tattatttgc cctattagga cctattattc taaagtacca
    35881 ttggagctcc ttttcccgac aacagatcgg agattttact ttctcaagtc atacgtcttt
    35941 tgttcagcca acagtgttcc gctctactta ttattactta ctagcgccct tcacttcaac
    36001 tcatacatac tactttttga ctttcagctc aaatcaaagc tacttgctta taagagaaga
    36061 gcaaggtgcg tagctggctt gttaaaaagc atggaaaggt atccagaaag cacagtaaca
    36121 gctatgatat aggcaccctc tcgcctaata cccactacta aggattgaag tagcacaatc
    36181 ggctatagaa ctccagatct atgaatagcc agagcctagc ttgattactg gaactaaaca
    36241 gcaagctgct cctaccttac ttatcgataa ggagtacagg gactgagtcg acttctttta
    36301 gttctctttc ccctagcagc ctttccttct tgcttagagc ttctattcct tttgcattgc
    36361 ccatcattct actcaaaaga ggacgaaggc tactttcggg acattggttg cagcgatttg
    36421 tagaccaata gcaaaagcag caacgattcg atgctctctt cctccaagag cgcattcaag
    36481 gtctaatgaa attcccggat cgagcattct tgggctaagt attcactgat tcaagatttc
    36541 cggtccacgg taaccgatac ccctattaag cagcatacac attgagtcaa ctctgttcac
    36601 tccgaggcca ttcaatcaag gagataagcg ctgatattcc gatctgccta attcgtcgag
    36661 tcttccgtcg gcgaagtttt tcatttcaaa ataaagtgga aactgaggac tgggctaagt
    36721 ctttaatttc ctctatgtga ggaattacat tcgccctata gatcaaggag agtttcagca
    36781 tagatgaagt agtgccctgg tagctcttcc gagggctggt gctttccttc cctcccgggc
    36841 gagaagggta ggtttttaat cctggctctc ttcttttatc tttttggggg ttctccagtt
    36901 tcataattag aaatcttgag cagagcttgt gcagcacatt agttcactct ttggcaatcc
    36961 tttgaatctt ctactagtga agcagcccta gcgtagcaat tttagttttc cttcctccac
    37021 acactttcgg ttgataagtc aagcacataa aaggatactt cttttcggag ggatttatga
    37081 tggatcacgg atgttccaac agatggatct atcgggaatg aagaaatatc gaacaggcct
    37141 acgtctatcc aaatgctaag ccttgtcact agccatctat ggtatcctcg gtatgacgat
    37201 gaatgtctct aacctagcta gagccctgtt gagatcctat tctctcgtat agtcagctac
    37261 tatagaccct attccgccct ttcttttcta cattccttta ttgagccgaa tcaccatcat
    37321 tatattatat attcattgtt ggtttggctg ctggtctagc gaagcaacct ccttctatag
    37381 tttatttctg gctggcctgt cggagtccta ttattgtaga tgacaaggag ctatataatc
    37441 cctcttcttt tccaagaaca acgacatgct cttagatctg gaaggctaga agagagtagc
    37501 tcatgcccta gaagtccgat cgtataatat ccaaatgttt cccccggagt ggttcaagct
    37561 tatgtgacca aagctggaaa gaaagattct tctaaacttt acccaaaccc aatgcctgac
    37621 catcgatggt agagcggtca gtatgatgac ggagaggtcc tgtcttcaaa tcctaggcgg
    37681 ggttccttag aatgatcata ctcacgaaga tggcatcgaa aagctaaggt aaaggcaaag
    37741 ctactccacc ttcaattgta actagccggg catcagaaag agcacgaggg taatgcctgt
    37801 aagacagaag cacttccatt ttatgggctc tccaactggc tcaaaataag gactgggagg
    37861 caaggaaagg agaaaaaatt tctcactccc ggaagttttg gtaaggacgt caaaaatata
    37921 cgtccgaggg ttcaattcag tgatcggatg cccccggact aaagtcaaga tttcatacat
    37981 atcgaaaaca atagctagat actctgcggg acctctttga gaagctctca ctgttcatac
    38041 attctttcta attaatcgtt ttaccgggaa tactatagtg taagattcat tcctttgttc
    38101 acaacaattg cccgcaagat gtttctctct acgttggatg atcggagatc catggatcac
    38161 tgacggtatc ttcccatggc taagcgtcta aaatacttta ctatatcgaa gatttctctc
    38221 ctaaagtgtt ttccctttgt cagaaacaac ctcaagcttg gaatggatct tacactattg
    38281 gtttaccggc ctacgcggat cgtacgcaat gtacctgacc tagattgcga ggcactactt
    38341 gggccctagc ttctcgatgc caattccgta atgaggctct tcttcgatta gattgagatc
    38401 tgattttctt ctcttacgat attatcgatt tctagattga ataggaatgg gtcagcacgg
    38461 tgcagcggca acttaaatat atctaaacgg attgcgtggt acccccggac cgaaggaagg
    38521 gcttcaaaaa tgaattgaat caatgaaatg ttgcttggtc ttcactgaga acttgagtaa
    38581 ggagtagatt cttttggggt aactcgaaaa aggctttttt ctaggcaatc gaccactgca
    38641 tctgcatttc acaaaaagat ggttccgctc gccacaagca agcccttccc tttacaggga
    38701 agctttcacc cttccccatc gagtcgagta gcctcgaata actctcttct ccctctttac
    38761 tttcgcgtac tcctctgtct ctttcttctg tcctttgtcc ttctcttccg agcagtagca
    38821 gcagcggtag agtcggtaag tcaattgaaa gagatgctca tctgctctgg ttagctcggt
    38881 agagtggcag gcgaaatccg tctctcttta tagatataga ataggcggct agtcacttct
    38941 tactcgtgta gtgagaaaat ccttcttttt ttcatgataa tagtttttga ctctttattt
    39001 tgaagcaagg tggatctata cgggaaccgg taagtagata gttagaatcg tattcttctt
    39061 tcttcttgat tgtttgcacg tttgtatgag aataaagctc atctccttcg gtaagcacat
    39121 atagggtatc gagccctcgg cgcttgagag gaccccgggg agctcttctg tgataggctc
    39181 cgagttcctg actctactag gcaactaaga cattagatga gggagttgct tgtctgttta
    39241 gcgctctgta gttcatagat tggatattga attctccgaa gatgagtctc cctcgagcct
    39301 tacttccaag cactgcttct atagtcaaca aagaagtagg gtttcagact tcgtcatgag
    39361 tttgaccttc tgttctaaga aagaatgcct gagcttctgt agcgcgaaga caagaactag
    39421 tcaatttatt atctccaatc tggaataacc ttcttcctcc atccatacac tgacatcagt
    39481 tactgaaaac cgagatatgg gcataaagaa aataaaactc tttgctttga atagctatcc
    39541 cgtcgtactc aagggatgaa ggaagtgaag ttgagtttcc tgcctctatc ttctagttat
    39601 gtaccttata gcccgcctag tccccctttt gggaggagta gtgccagtaa gggtaagact
    39661 ctcatatgat cattcctagt ttccagccat cgattgagtt gcagtccttt gctcaaccag
    39721 ttacacgcct gttgaattgg acttttttca aattgaccct tcaagcagtc ttacagccga
    39781 gtctttcttt gtttagttca aagaggagta gagggtttgc tgggaattcc tggtggaaaa
    39841 agatcgtgaa atggcaatgg cttttattag tcagatccgc ccttctcggt ggtcgttagc
    39901 agctgctatt tgaaatccat tcccgctgct gtcgtcaacg gtagaactct tcgggcatcc
    39961 gtccgttctt cttctgtctg aggcaaaggc gaatccctta tactgtatac ggtcgagctg
    40021 gcttggctgg tacatcaagc atatcggcat attgcttgtt cggtgtggta cacatatctg
    40081 tcaatgtcaa tcaagtaata gaattcattc ccactgtctg aagaaaacgt gaataattgc
    40141 ctgtttatga gcttggaaga cccgttgaag tccccgaata aaggggaaaa ggctataagt
    40201 aggccgtttg ctattgctag aagggctgct cgcctttata cggcttggct tcgctatcgc
    40261 tcctatgtag tgatcggcct caaaagtggt attcctgcca tacaagccta ttttttctag
    40321 tgctagaagc ttcgccagaa gcaagcaaga cgagggagcg gagcttcgta gacaaggctc
    40381 gttacgtact tgactgacga gctgtctact aaacgagcgt tagagcgagc gagttaagcc
    40441 tctaaagttt gatagctctt ccccctcccc cccctccctc accttactct taaatttccg
    40501 cttaagcttc cccggtttgg gggattaatt gattggatac ccgagaacca taatctttcc
    40561 taggaacagc ttctacgacg atagataggg gtcagctttc tttggcatct atgccccctg
    40621 ccctccaaac agtatgggag cctttcagct cgtactgctc acactcctag atcttcacgg
    40681 cacctcctcc accatagtgt gagctgctcc cagcggagaa aagcaaggcc tacttcctaa
    40741 ttagctttca acaacgtcaa caacaccacg aaaaaagtaa acaatggttg cccactaatc
    40801 tgatcatagg tgaaatccaa tcccttcgct tcgcgccagg ctttgaaacc gtaagtcagg
    40861 ctcctttcgc ctctcctttc agtcgagtca cgtcagtacc tctcagaagc gagaaagcga
    40921 gcagcaagct gaaaaaagga gaaagtggtt ttataaagca aaataagcta agggggctgg
    40981 ctaggaatcg caagaattga gaagggtggg aaagacaggt tcggtaatgg ccggattagc
    41041 aggaggaagg tcttgaagag cctgaaacaa agaaaggtgt acataaaaaa agaggctggt
    41101 tatggccttt acttgatagg actcctttcc catcccggga agaggggata aaaaaaacct
    41161 tgcggaagcc ctgcccaccc ttccggatcc ctcatattta tgattccagg cttcccggac
    41221 tcgtaataga cggctaagaa caagaagagg gtcagtagtc tctgccgttg caggtccttc
    41281 tccttccgct gagacggccc tctttttttg tttgttcacc gcggcacgaa atcgaaatca
    41341 tgaagaagct ggaataactc agaaagagag tggcgcctag ccgttgagag cgtctattat
    41401 ctttgtagag gaacagtacg atcttggact ggcccccttc gcatgaccta gaaagatcaa
    41461 gaagtccatg ctactataag gcctctaaac tcctccctca ggacactatt gcccatgggg
    41521 acggggtagc cccgacttcc ataggtcctt ggttcgacct cctaatgaga attgaggtcc
    41581 ttgcgcgggc gtctcatccc taagacttgc ttgctctgta tggagtgccc tgtggttcct
    41641 cgagtgccag ccgcagagag gaatgccatc aactagggcg ctattggcca ctaaccactc
    41701 gctcgccagc cgctcgggct ccgcgtttca agttcgttat cctaaccgtc ccctctgctc
    41761 caccgggtgc ctggcccttt tcttctatct tatctactac cttgctcctc ggctccctac
    41821 agctccagcc gctcactgta atagcttgct tctcgggtgg ctcgcacccc gggtggtgcg
    41881 gctgagccag agtggggctc aacagtcggc ctatgtttcc gggcgcacgc gtaaaggcat
    41941 gattagttcc acaaatctca ctgcactgac catagtaaac tccttctcgt tgtaccaaaa
    42001 tagagatttg atttaaacga ccaggtacag catcacattt gacacctgag gaaggtacag
    42061 cccaactatg aggtacatca gcagatgtta caataatacg tagatgagtt ttggctggta
    42121 caaccactct attgtccact tctaataaac gtgattgacc caattctaga tcttcttctg
    42181 gaatcatata actgtcaaaa gtgagtgact gctcatcgga actgttatag tcagaatact
    42241 cataagtccg ataccattga tgtccaatag ctttgatagt aatggctgga tctactacta
    42301 cctcgtccat tgagtataag agagcaaatg atggtatagc aatgaacatc gagatgatac
    42361 taggaaagat ggtccgaaga atctcgatag tagttccatg aacaatcctt tgcgggattg
    42421 catttttttt atagtggaaa tgccataaag cgcgaaccaa gatccataat acgaaaacca
    42481 aaatcagaat gaggaagaaa aagatatcgt gatgtaagtc tattattcct tgcattatag
    42541 gtgtagctgc gtcttgagat cctaattgcc atggttccgc tgcatcacaa ggagaaattg
    42601 tgaggaataa ccattttaga acaatcattt tcaaagcaaa ggttccttca ttttctgctc
    42661 cccccaaaca aagagagact gattctgact ctcccaatta aggaagacgg aaatggctgg
    42721 tgccggttgg tccaaccaag aaaaaagaga tgggaatttg gggcgtaaga ttcttcttct
    42781 tcttacaata ttttgagtta gatgaacaga tcactctcct aaaagcagca gtcttcttat
    42841 atacgaaacc aacatcctta taatactact aggccccacc acactgaatt atgaactttg
    42901 cgcctccagg agggtcaagg cagaattcca ttcctatctc cttcgtctgg tcgagaaggg
    42961 actctgactc ttctattact acagtacaga ggattagtcc cattttttcg tcacgatcga
    43021 tccacgtccg ggcttagaaa gctagcttac taaggcgaag gaccgctttt tattgattgc
    43081 acgagctaag aacagatcca caatctatta tctaatgaat attcattaga tagctaatta
    43141 tcctttgcct agctgcccat tgctagaact tccagcgcta aggtggttgg tgtggtaagg
    43201 caaggcaact cctctttcct acgctaagcg caaaaggcac tcgaaggagt actgggacca
    43261 accatcacta ccatagggtt atagtggtaa atcctgccac ctcagattct tattttacct
    43321 tacgtgtcaa caagcaagtt gggatgctct cccttaacgt ggtagggctc tgtttcaggt
    43381 cttgacgttg gccttattaa aaaaggcatc ctcgtcgcag caaagcccgt gtacaatgct
    43441 caaaaaaaac tgagtcaaaa acgagacttt cacaggaata acacatcttt ctaaacaaca
    43501 acgggttcta ataaattaag ccttgtcatg gctggttgag gttagaattt cataaagata
    43561 aaggtgggta gagaaggccg cagtagattc ttccgaccga gtcccagtgg cagagtcttg
    43621 aggcacgaat ccaacggcag gggaatcagc ggctgatcgc gattcatcag tcgcaattct
    43681 cccagcagct atccatttta gttcaccagt ccattactga gctgtgattg cataggtaat
    43741 agagcaagct ggagcggagg cagcagagat gaaggtgaga acaggggggg gtaggagtag
    43801 ggcacctagt tagttacagt ttgcccgaag catcgttaga ggcataggca gtcagaaata
    43861 aaaatcgtgg tcgatctttt tcaggctatc aaatcagcaa gggtacttga atagtcaagg
    43921 ctactcgata aaggatggct ggcattcatc agtacgtgtg gatccgccgt aggggttggt
    43981 tcagccactc gacgaccggc acttgccatt gaaaaaccgc ttaatcgtgc tttctattcc
    44041 tatgaataaa agaagaagat aaggaagggt agtgatacca atattcactc aacgccaaag
    44101 aaagcttcta aaacaaggtc aaaacttcac ggatttcata aggattaata gtcataggaa
    44161 aggtacactc aaacgaagaa aagatctttt ttgcaaggtc accatagttc tatttgaaat
    44221 tcgactgttt actacattac ttcctgaaag tgtgcccgtg ccctcagagg ggaaggggtt
    44281 ttggaatagg ggtaggaagg acctttatgg gtataatcat gttcggtcct ccactcaaca
    44341 agccactgga ttagcttccg gcggaatccg cttttgaagg ccttggcctt ccattgagac
    44401 aagagatgat tcacgctgaa ctaggatgct tggaaattgc gtactttttt tctgacacct
    44461 ggcacaaaga actcgagtgc cgcctgctac tacggtgtat tagagttcga gcaacagatc
    44521 aaggttcgag ctaaagctaa ttccgagttt tcgcgggaag aagtacggtt tcggacagct
    44581 catgatgaac tattgaatcc ttctccatcc gaatccgtct cagttccagg tattgaactg
    44641 aaagatgact cgaccggagg aaaaagccac tcggggatca attttccaca tcagtctaag
    44701 tggctttttg gttggtagca ggacggtaat tggcaacgaa gcagagattt attttaccca
    44761 ttaaaaagta tatttcacca ttcctctcgt cgtccagaat gggtgactca aagaaaacgt
    44821 ttcattcacg atgaggcaga attgacataa tataaccaag attggatggt gacatataat
    44881 atagtaaagt aaggggttcc tccgcccgtc ttcgatacaa tcattgcgat gtgtcactca
    44941 aggatagcta gccattcttc tctacccatg ccatgattta cagatgagct cgagaccatt
    45001 attgaatata ttatgaacac aatttgccaa gagttggttg tgacaaaagt gattgggatg
    45061 cccatctttg gtccagaagg ggttctctat gaaaagagtt tccacctttc tctactcgaa
    45121 aagccctatc taaaagggct tgtctggatg aatgcagtgt cggaagccgt gatcacatag
    45181 taacttccgc ccacagtgct attacgacgg cgggtcaccg ggagtgaagt aaactcggct
    45241 cctgatgtag cattcattcg gaccattcga cgtttgattc tttttatcag ggataccgat
    45301 gactctgtga gaggtgttct tcggccaagt ttcccatgac gggttacccg gttcaaggct
    45361 tttctatata atgagaaata ctactttctt tctagcttaa gtgttcacgt aggtaaaata
    45421 gcttctatag ctccatccaa tagtaatcaa cggagataga gtccagcggt tcaaccaacg
    45481 cttctaagga gagcggggca agcaagaaag caggcaaagt cattgagcct attctattcc
    45541 gaaagttcaa ctactggata aacaacgaaa gccgtcggca ttcttctcct actgtagctg
    45601 ctacaattgc tttagcgcga gcagcaagga ggaggcagct cttactaaaa aagcaaaaag
    45661 ggaagggcat gacagaaggg agatagacct cctataagca ttactctctt ttgaggtaac
    45721 ttacttactt actctgatat gatgagttcc gtgggctagt aagataacta ttgaggtgag
    45781 ggtccgaagg agatctttca ctatttatgc ttgtacagtt ttatgatagt tttgtaaggg
    45841 aaagcaaatc ctgagaatgg aatgtaagtt agggaacagt agtcagacgc ggaccagcgc
    45901 aggtgggcgc cacagctgtc ttcctccatg tgatatctga tatcacgcaa caggagattc
    45961 ttcaccctta tttattgaca cgatttacaa aagaagaacc aacccggtcg tgctatatgt
    46021 atttgggatc aaaaaggctc actgctgtat gatataaatc tttctgaatg agagttcatg
    46081 agctacagga agagatcgag tctagaataa accttagaag tggcaaaaac gacttacttt
    46141 gttgcaacgg gaactactcg ccccgggcac tggtgaaata gaatcttatg tgttgcagct
    46201 acttatgctt tcccaactag aaatcaaacg gaacaaaacc gagtcttgct atttagagcc
    46261 agggttcctc cgggggtcac aaccagagac ctaccagccc catgtaaacc actttcggaa
    46321 gggacaaagc agttgaactc tttagaggaa gagtctaacc acaagtcaaa ctgtgaacat
    46381 cagaaggatc gatatattgg taatagctct acacgagaga attgaaactc cacctgcaat
    46441 tccgagtata ggagagtcca gtcaataata aagtcctggt tgcagcatcg ggtaaatggg
    46501 atccaggtaa atggcttact gttcggtcaa catttcatga ttcgtaatta gtcaagctcc
    46561 ggccggttcc tatgtggtga atagggatat atttagtatt aaagacatgc gagtgctccg
    46621 ttcgtcagta agcgaaagag actgaaacct gggagaattc cgctctgtta agagagagaa
    46681 ctaacgaaaa ttggagactg acggaaggaa aggggttcct cccttctcct ttaggggaga
    46741 agcttggttc ctccttctcc gctgagaggg gagaagagct gggttcctct ttgaaaactc
    46801 tttccgtata ggccagaaaa cagcttgctt agagaaagac tgactctcct acggacctgg
    46861 tggaccttac agtcgagtta ttgcatcgat ctcacaaact atcaatttca taagagaaga
    46921 aagatcgttt ttagatcatc aagtgaggac aggtagtagc tctggtagag cgagggactg
    46981 aaaatccttc tgtctgcggt tcgaatccgg actcacttct agctctggca caagttcctc
    47041 atccttagtt gtttgatgag cctgcgtagt attaggtagt tggttaggta aaggctgacc
    47101 aagccgatga tgcttagccg gttagagcaa aggacttgaa atccttagag caaagccagg
    47161 gacttgaaat cctttttgtg tcagctcttt ggaagtgcct tttcctttac ttcagtaagg
    47221 agtctcaaaa taggaaatac ctagctagca aagtaagcaa taacggaagg taacgaattc
    47281 tccgtttcga tattaacaat ccggatctag ggaaagtagg ttcccgcatc acgtaaattt
    47341 catttctttt gggaaaataa tacataaacc ttttgagtca cagccacctc agcacaagtt
    47401 actcgagtag cacagaagcc atcatcaata gcttgcttgc ctgggagctc aaccacgaat
    47461 tctctgtctt ctaacctttc tatcacttga ggattatcta cgcaattcgt aaatgatcaa
    47521 actagatagt cccttatctt actggccagt agtagaaggg gatcttgaat caaagagttc
    47581 ctgtccaaca agcaaggaat gtcagtcata aataatgaaa tccatataac tctactccgg
    47641 gttgtgagaa catcgtgcct gttgcgattg tgtggctttc cgcatggttg gagaccccct
    47701 atgaacaaac aaaacagtag ggtggtgtag gagaaccccg actccctaat gcaagataga
    47761 gctcttaggg tgcgtttcgt ctttgtcagg aagaaaaaag tggcaagagg agtgtatcca
    47821 tacccgtacc gaagagatct tgggaaggca tctctataga tttagtagtt ggactaccaa
    47881 agacccagac agcttcaagg ttaggtcttc agtgttaggt cagttcgagg tcagttgttc
    47941 cctccgtact gttgctagag agctgctttc catctatctt cctacatgaa aggatctaag
    48001 tctatccaaa taaaatagcc cagaaaatga cagccatcaa aaggcgcgca cccatatagc
    48061 ctcggcctgt ccaaatgatg ttcagcggtc tctacccaag tagctgtggc ccatgatcca
    48121 aaggacccgc aaccagtcaa tcatgctatc cttaccttcc aaccaatcgg ccaatcacgc
    48181 tatccttacc ttccaaccaa tcggccaatc acgctatctc cttacctttc aaccaacccc
    48241 ttcgattccg cttctgcagc agtatataat ctcggtccct taccttgatg cctacagctc
    48301 aatttgtttt ccagtgatgg caagaatccg atccgcgaaa tactgctttt tcttttttct
    48361 tgtgttgttt ctgaatggca tcatagctac acgagggaaa gcgatgctgc ccactctgcc
    48421 gcaaaagggg gccgctttct tcccccccaa aatgccagtt ccaccatcag ggcccagcaa
    48481 gcagcataat tctgctcctc gatcggactt cgtgcaattc ttttatatgt aaataaggga
    48541 ggggtctcga ccacattttt gagtaatagt aataggctaa ggcggattcg tctgcttcgc
    48601 ttacgtagtc aaaacattct cgctggacac ctggtaagga atatttgtat atgcgggaaa
    48661 gatactctca cctacagctc ccgttactag tagttccggt tagcccactt gcccgagcac
    48721 actctcaact tgtagatgat ccaacagaaa aagcaagaga ccacgaaagc acgcatgaaa
    48781 acagcccttt tgaaagcata cccaaggcac ccatccaatc tgaacttata gacatcaaga
    48841 agaagatcta ttaacacgca tggctaccta tataacaagt tacctctgac ctcttctgaa
    48901 agcatttgag acttctcgtg ctgaaaaaga taatttcatt gacctacggc acggaaggaa
    48961 agcaccgctg ctagctcgcc ttgtccacgg aacttatcct gttgagaatc ctatcttgct
    49021 tgactgcgct gggaagtctt tccttaaagc attgatttta cttggagtat ccgcttaagt
    49081 gagaaaagga acttgattta gcttgaacct tgagccgtag aagaggacct ttcagaagga
    49141 cggctggctt tagcccttga gcatggacga gagtgaacct atttaaaggt ttactgtatc
    49201 gtttactggt gatgggaata tgtaatattg ttgtagaagt ttccagcctc acaggcttta
    49261 gattgaacta tggaaccgag cgaagacctt tgagattgag attccccagt ccacttatga
    49321 aatggatccg gattaaccgc tttcgactga gatgtaaagt caccttcgct tttgcttttc
    49381 gtattctatg cggctttctc caactctaat ctcaggtttt tccttctcta tgaactctat
    49441 agattgatcc acaaagagat tgtacctata cctacttcag tataagttta tcctgaaccc
    49501 tatggcactt cgttgcttgc tccagtgagc tacctattta atgaaaggga tatttttatc
    49561 ctttttcagt gtgtgtacac gcttgaaagc ggaaaagatg aactcagact aataaaagga
    49621 aacggaactt agaaaacaaa acaactaagg atgggctctc cggtggatga aacgacccct
    49681 aggagtccct tcgattgggt gagggcgaag caaatctaca atccttatgg gaggatggga
    49741 ggcctaccac aaatatgggg attgaaaaca ggcaaacggt ctcatacgtc gtaaataagc
    49801 attcttaatg tcaagttggt agataggcca tagctgtcgc caaccaagtc tattagaacc
    49861 atcacagttt aaaatttagt aagcgaaggt ctctttatca tccttcccaa tcacttgcgt
    49921 ctacccttta gctactaatg acgctttcta tctctcaata gaaccatcag gatgagactg
    49981 gatcttatac attagagcct ataagccttt gtattaggtg gtaatgtccg aagtcttctt
    50041 ggatttgagt gcaccaattt atttttgcat ggcctctttg gtctcattct ttttctgaga
    50101 agaaggttca gagacagcaa gaagattgtt caaagaagct agatagtctg ctgggaatgt
    50161 gtgtctatta tgcagaggaa ttgaaagaga atgtgaacag agaatcaaca gaaagtttcc
    50221 cttcttcttt ggtaccgtag aagcttggcg atgtgaaaag atagaattct tgaacgagcg
    50281 aagaagcaat cggggcagcg tatagcctta gtcacgcgca tccctttcct gcataaagat
    50341 gagctagata gcacggcttt gaaagaaaga tatctgaggc aattttccat tcaccttttc
    50401 ttgctggtca agatagtaag ccgagacttc tgtagtagct ttctgttcct tggataagga
    50461 gtcagttgaa agtggtgaat aagacccgca aatccccctc taaatggttt tttcattttc
    50521 aatctgtaaa ttcatgaagt caagaagtgt agccgaatca aatagttggc tctagtctaa
    50581 ttgactactt ggaaagaaaa aagtgattta gtgaagtctc tttgatgcgc tacgaaggtc
    50641 aagcaggaaa cagggaagcc ctttcgacct aagccaggct aataggttga gtgaccagga
    50701 gagtagacca gagaaaggtt atgtaataga ggcaatagtg agccccgaag agtgcttttc
    50761 tattcttccc cttattcgct acgtattcct ttcactggga tttttcatcg ctcctaatac
    50821 tatgacaagg ctcgcttatg gctcgctccc gtggctctag tagtagtcca ttttattcag
    50881 aattattctt tctttttgtt gatggtgcgt tggaagggac gaaaggagct agtgagcaat
    50941 gacatccgcg cggggaatag gcttgcttct tcctagcgat cgggcggtcc tccctcttcc
    51001 tgttcaccgc cggttcgccc actgctgctt tcatagatgt cgtgcgaagg gacagagcta
    51061 atggatgcct attccgttct cctgctcctg ctccagctca agagttcaaa cggacagaag
    51121 agagtcctgc taccgaaaaa aaagtgcata atattggatt caaacaaagg ggatttattc
    51181 acgaatacga tttctattga ttgaaagctt tcctattact gatggcagac gggcgagacg
    51241 gagaccgtcg aagaagtgcc ttgacgcgcc gcagccacta ctttgactcc ttttatgcaa
    51301 ttatgaactc cacggaactt tctcgattcc aacgcaactt atccttttgg agctgacgta
    51361 acaaactagg cgagcctccc aacgaagcca acataaatcc tatccgaata aaaaaaataa
    51421 aaggcagttt cattatggtg gtataccaac ctcctgttct ggaacttcca gttccaatcg
    51481 aagcatatag atccgtaaat agatttgtat gtatagccac ttcagccgtg ctcgtccttt
    51541 ctcgaaagta tcttttttct gggaacatgg ttaaccaaaa attattatgt ttgcgattct
    51601 tcatccacca atgcagaaaa tgctcaagtt ttccattctt atatgaggcc ggaaagttta
    51661 ttagcaagag gtcggcatga agtgattcat catgctcaaa catgagccga tcgttcgtta
    51721 gggacggttt atagatcatc aaattcccac aaatggaatg aaaagtgggt ccatgtaaat
    51781 gatcgagacc tcgcaaacaa caacgttcct tccccatatg gagttcgtaa cccaaaggca
    51841 atcgttgagt gaactgtatc ttctttgtgt tagttgacct aagccgcacc attactgctg
    51901 gggtggggct cggcctccga accgtacgtg ggacgagttt ctgcctcata cagctcgggc
    51961 cgaagaccgg gggaagttta ggagagatgg ggagacccag cagctgccgg tcggggcggg
    52021 ggtaagcttg tgaagaagcg agcttatccc ccccaaaaaa tcctatagcg ctagcgcttc
    52081 gcgttctttc tattttatct atctcatttc attccgggat aggcggctaa tactaatcta
    52141 ataaagtgaa gtagtcgtcg tctgaccaat tgactcggac accagaccgc tcgtgcccgc
    52201 ccattctgtc tcgccctaaa tggaatggct ctcttagtta cgctgcaccc cgacccgagt
    52261 ccccacgtcc gctcttctcc gtccgcaacc taagaagttg gctttgccaa cacaacatta
    52321 gggccgtccc cttcattcta tgctgacccc gcccggcccg gggctggctt tttgggaagc
    52381 ccgttcccac cgcgctcatg gcccggctgg cctgccagcg gtagtgggaa ttatcccgtt
    52441 ccctggtcaa agacttggtt ggatgcggga tctactccac gaggagcggt acggacgtag
    52501 atgatatcat cacgacctct cttttcgtac cgctagggat gcttaacgcc acttcgccaa
    52561 ctagcgttac ccgcgctttc gtgtctctca gtgtggtcag cactgggtgt ttccgagcag
    52621 cgaagcttac acccattcgc attagttcat ccaaagttcc ttacccttat gcacgaattt
    52681 tggaataagc catcttccta tcaaggttaa ggagtcaact gagcatctca gcggcgggat
    52741 tgaatacccg gatcgaatca gagttcacgc cgcccgccct gaacaaatag gaggcgtggg
    52801 ccacaggtcg cacataagcc gccgggtcgc acgacagaag aacacccaac atacagatgc
    52861 acactcctcc atgtgaaata ttcatcttca ttggaacctt ttggtagtag tcgtgaccaa
    52921 cagccatagc catcagctgt cggctccttg gtaaggcgag agcttcaagc ccgatttctg
    52981 gtggcacgcc ccccacacaa gcaccaccca actcaggggg gacggggaaa gctagaggcc
    53041 caaaaccttc gacccttctt tctaaatcta aatgggggtg cccggagcac ctcatcttgt
    53101 catttcgtcg ttgctcattc ccgttcggcc gaagtgtttg gcctttcctt ctccgcgccc
    53161 gctcacgctt cgctgaccta tcgcgtgcta aaaagaggaa agtacgaaag aatagtaaac
    53221 agagcacacc gcagaaagat tctaaatatg agaagtcccc cttggattcg agaagacgga
    53281 aatgaagaac gggaacgaaa aaaaataagg cctttctagc tctagtttca gatgagcttc
    53341 tcccaattat gtctggtaat agaatagggc gacttgctct gaccaagact ccactttttg
    53401 ctccgtccat ggagcgtatg attttccttg aatgtagata gaccaaaaga gggaatgaag
    53461 agataggaat aggaattata gtaccattgg aaaaaggggc acccgtggga acatctctac
    53521 tgacgaacca tttcaatagt acgggtgctg ccgtgccaca aggcacgacc ataaaaataa
    53581 taaaaaagaa aaagttatgt agttggacca tctgctctat ccgttcgagt ttggcttctc
    53641 taaagaagag aaggcgctaa aaatgaaaat gttcgcaagg cataccgaaa ggataccaat
    53701 gaagccgacc attaatgact agttcgaaca ccaggagcgg aaggagggac ttgaaccctc
    53761 aaccttagcc ttggcaaggc tatgctctac cattaagcta tttccgccag ctacggtagt
    53821 ggcgaagcac tactgagcaa ttcacgtatt acttgatacg gacgacttcc gtttttccgc
    53881 cggaccacgg ctcttgacct ccgatcgagc tacgagcacg agtaggtagg cggcatctgt
    53941 cttttttttt ttgaagttga gtcatttcct ttcctaagac ggctcctctt attctacgat
    54001 aatccaagca gcagctgccc gagtccgctc ggaaccagtc gattcctgag cctggactca
    54061 aggtctctcc tgcctgcgag tttgctgcga atgctgcgag taaatacatg aacgagacga
    54121 gtgagttagt ctccgagcga atccggcggg tctttcaaac atccaagttg ccacttttca
    54181 gctacttgga atgcatgaga cccctgcatt taggaatctt aggttacctc cagccttctg
    54241 aagcgagttg accttctgtt gaccttatat ctgtctacct tatataataa tgaatatgaa
    54301 aggaaagcac taactcctga gcttgggcaa agttggctaa tcgatttaga ctattataat
    54361 agaataataa atccgcgact tgggaaaccc tttcttcatt cgtttggcgg gaaaggagaa
    54421 accatttctt cattcattgg cgagaaagca tttcgtgcct tcgtcctagg ctcggctact
    54481 tctttctcaa ataagacaaa gattgcacta gaccttgagc ccgggaagac cgctactagc
    54541 cctttactct attggattga tttggtcgag acccggtttc tccttcctag aaacctgaaa
    54601 ctgcaatccg cgaacgaccg ctttcttcct tattagccta atatcttact ctcggactac
    54661 atttgtctaa gagcagttga ggaatctgca actgaaagaa aggaatcatg gaatctgaac
    54721 ccaaggttaa aaaaagggga aagaactacg gaaaaggttc tatcacgtta atcgtcaccc
    54781 acttacgctc ccaagccatc tctggaattg aacttcctcg gaacagctac aatgctttga
    54841 attcctctgt gctttcacga acaagccgaa taaccttcta tttcggaaga ggcattctga
    54901 taccattcac ccatagatga tattgagaat tctcaggttg aaagcccatc aacttaacgc
    54961 tatctggggc cattcagaaa ttataatcca cgaaaggagc catcaccgga ctcgagccgg
    55021 gagaaccttt gaacaatact ggctgccttt gctcgttgac gactagcctt tgttctttga
    55081 ccgagatgtc gacctgatca cttttctcaa atttcagcaa caacaataag aaatagtaga
    55141 gccttcaacg ggacattcga acgcaacaaa gggtttcttg accgcctttg aacgacaact
    55201 cgataataga atagaagact ttcttcgtcg acttactcgc tcgcatgaca gcatttagtg
    55261 gtctcttcac tggcttaggc tatattgggg aacgctcggc tacaagattg aaaagaccga
    55321 tatgatagct ccacggccgg agccgatact tctctctcaa accattacct ttccccgcca
    55381 cattcttttt tgacggagag acgattcaag aggatccagc taggctgaaa gcggaggatt
    55441 ctttctttac ctgtgccccg gacccaagct cggctgaagg caaggaattc tttctagact
    55501 gacacgcaag ctaggctgaa agcaacccgg gttacagcaa tggggattct ctcttctatt
    55561 agaaatgata ttatattggt gactactccc ttcagattga agatttgaaa gataacacgc
    55621 ccaccgccgg atactcttca cgtgctgata cctatattgg attggtgaac aaccctggag
    55681 tttaggacat ttgaaactat agaaagacct tagccgcttt tatgatatag tcctgaagac
    55741 ctaactctta gaaatgacct actaactcat cgacaaagaa aggacttcgc cttgaccttc
    55801 tgacctagac gtcgaaccag tgccttggat tcatcaacaa agggatcaaa ggaactcatc
    55861 tgtccctcca aacggaaatc ttggttttgt aatttgatct ctgacaaagg gagagggaaa
    55921 gaaagaccaa tccgtatctt tgaaagaaaa agattctcag aaacgctacc accgaacatc
    55981 gacttactcg gcatcttcgg attcaagcat ttcgttcgtt cgttggcgca aaagcctcgt
    56041 ttggcgggaa agcattcatt cgtttgcggg aaagcaaaag cgttcagcat tgacttccta
    56101 aagcgacttc ttagcgtgct tcaacagcgc ccagataatg ccttgaccgg agccggaggg
    56161 agacctaaac agaagaacga cctcgcagtg gcaacatagc ccatcctcaa ctcatacctc
    56221 agattttgaa ccatactttg agtcctcaaa ctttgagatg gactggacca acactcttct
    56281 ttgagatgga attcccacca ctcttatttg acatgaactg taacgctact ctttcaaaga
    56341 tacctaacaa ccttagctgg cattgatcac tcttccttcc caatccctcc atttagaatt
    56401 gcaaacatcc caacttccag agctacctat gagccaaggg cggagggaga tatattagac
    56461 tgatcaactt caaacaaaac gaccttcctg gactcgcttt catctccttc tttgaaacga
    56521 ctcaaataat tgagtgggca ttgggagcct tatttaatgg tggattcctg agctatgaat
    56581 gtctctgaaa tcgtgatgtc aaaaaggaat gatatgcgat tattaacttg cttccttccc
    56641 tctaattttc atgcagtagt tgaatttttg cactcttacc tggatgcgat tttccgcctt
    56701 gaatagatgg aggtgttttc caccttgaat tgagaatttt tgcatgctcg atgggatttc
    56761 tgccttgaat tatgatacat ttattatgaa tttttgcatg ctcgatctga tttccttcgc
    56821 tgtatggagt gcataggcct attctagcat ggggtttctc ggggtaaggc ttgtgctttt
    56881 ccttccatat aagactagct atgtgctccc tcggtacgcc tgtattcctt tcgtggattg
    56941 gaacctacgt actgttgtat tgtagcgtga tgttttccca ctgctttctg gcttgactca
    57001 cataaagtac gtgcgtaact ggcactatca tgtaggtgcg aaatctgtct tctcctatgt
    57061 cttgttctcc cagtttgatt cctatgtttc gaagtccagc taattagtga aggaaagtgg
    57121 tatggatgtt tggagctcaa tccatcgaat tcactcgctt ctttgcgctg cgttgtagct
    57181 cttagattat tgggaggagg tcatttcgaa tgttttgtaa tttggaatcg ttttttcttc
    57241 aaggcacggc ttcttgaatc gtctttgtct tgtagaatgg ttgtcatctg gaatctaact
    57301 aaatagttag ttaagaagac gcgtgctttg tttggttttg atctggaatt tcactataag
    57361 ataagataag agtgaagtgc tttgtttggg caatctgcct ccctaaatct agtggaggtc
    57421 ccggtcccgc cgctcctgtt tgtaatgggg ccgctttgtg ccaaatgtgt aagttgtttt
    57481 ttcaatccgt tctaactgta ataagagaag agggaagtcc gtctaaagaa attagtgaag
    57541 gaaagttata tggatgttca ttagttcagt aaagtgttag taatgttgct gggagtaacc
    57601 ctttgatctg atctgtcttt gtacgtgtta tcttgcgagg ctgtcaggtt ggcttgtgag
    57661 gatggggaga aagcgggccg agaatcttat gtcaaaagga ccaaggatga tcttttcgga
    57721 aaggaggagt aggaggagtc agcttattct atagatactg taaaagccaa ctcatgtttc
    57781 cactcaattt tcattacgaa gatgtatcac gtcaagatcc gttgctcaaa ccgaatcacg
    57841 ccaacgttat ggaagttcct ggatcgtgtg aaataagagt agtaccaaag gcaccctata
    57901 atttcataat aaaaaatgga aaattggcta tggagattcc gcgcggtcag aaattcatac
    57961 agacacaaag gggttcgaca ggaaagtcct ttcgatctaa tccattcttg gggtcaaata
    58021 aagacaaagg atatgtaagt gacctagcac gacaaagcac tctccgaggg catggaatgt
    58081 ctaatttttc ggtcagaatc tcgacagtaa tgtctctatt agattttccg gtcgaaatac
    58141 ggaaaaactc cattcaattc tcgatggaaa cggagttttg cgaattctcc ccggaactgg
    58201 aagatcattt cgagatcttc gaacatattc gggggttcaa tgtgactatt atcacttcgg
    58261 ccaacacaca agatgagact ttaccactgt ggagcggttt tttgcaaaaa gatgaggggg
    58321 aaactcagta agatgtcgta gaagcaaaat agtagagatc acaaacgtag attgctcgcg
    58381 gctaaatttg aattgagacg aaagctttat aaagcctttt gtaaagatcc cgatcttcct
    58441 agtgatatgc gggacaaaca ttgttataag ttgtccaagt tgccaagaaa tagttccttt
    58501 gcacgagtca gaaaccgatg tatttccacg gtcgccctcg ttctgtatct gagttctttc
    58561 gaatttctcg tatcgttttt cgtggattag catctcgagg ttctttgatg ggcataaata
    58621 aatcgtcttg gtagcaacca ccaaaccaat agaacaaaga aaggttagct ccgcagctgg
    58681 tccacaagca aggtaagtaa gcccattacc agccggctcc ggaccgaaaa gtaacgtatt
    58741 taaaaccctt atcttggatc ggagatgcga acggggcggg aatcgaagtg ggggacctct
    58801 ctaccgcttg tgtctatttc ctgtcaagta tgctccccat acatagacta cgtacaggta
    58861 gtactcttgg aaagaaagat ataatgcatg aacataacat taagttacga atgtaactcc
    58921 cgaccactct tctaaatata ctaaggcgga gaactcttgt tcattggagc gccgtagtgc
    58981 ggaggttctt cccatcatgg aagtccgagt tgggactgag ccttccgaat gataatgctt
    59041 tgtttcgttg gaaaaaccaa cgcaaatctc atattgactt tctatcgccc tacttctaag
    59101 gatagataga gagagttact ttatgaaatt atctcccttc taaagcagcg caagtcggcc
    59161 cccccagaac aaagccccta ctcccgagag gtataaatga ctcgactaaa aggagaggta
    59221 tttattactc gagcacttgt tgcgagaggt ccaacgtaat ttattactct tataaaagag
    59281 ggaactcgac tgaaaggaga ggttgtttac atactcgact aaaaggagag gtccaaatgg
    59341 acttctgtga attacagtga tccagtctca cggatatgga gcttcgccgg agatggcagg
    59401 gcaaaacctg atggaccttt tttttttttt tctcaagagg tgatttcgag aatcaaccaa
    59461 ccgacgagac taattcgagg atgtgttaaa agagagtcta accgccaagg caagtcccat
    59521 ggataagccc cagcctccct ctcgtttcac tctcgttcct ctccttacag tcgagctcct
    59581 ttgttccttc ggacctctcg cccaaatgaa atgggatgaa tccaatcaat aagcttattg
    59641 attgattcag agcgcagcga agccaaattc aatcaaggca aaggggggct tacttttcct
    59701 gacgctgagt catcctattc aaatttagct atgctaatgt aacaggaaaa gttttcacag
    59761 atgatatgga tcccaagaga tgagcgagaa cctccaattg cttaaggatc gcactccgct
    59821 atcccgcttg gtggacgaga tcttctctcg ggtcatccat cctgggttac tgaagggttg
    59881 tccgactgct cggtgaccga atcagagaag ttttgaccgc tttctcttct ctccagcact
    59941 ctcggactga tcatccaatc catcttgctg cgacaaagca agcttaggaa tgaatctaag
    60001 aaatttaggt ctctgcccgc ttgaaagatt cttctttcct tttcggtgaa agagggcaaa
    60061 agtgtgtagg agaaagaatt ctaaaaacgt cgacgcttaa ttcgccccct ccatccttca
    60121 aaagtaaaag aaaggctcaa atatcaatat tatatatata tttgaggata ttttagggcc
    60181 ctagaacgca aaaaaaaggt gggtgaacaa gagttgtcac gataggaaag agaaatgact
    60241 ataaggaacc aacgattctc tcttcttaaa caacctatat cctccacact taatcagcat
    60301 ttagtagatt atccaacccc gagcaatctt agttattggt gggggttcgg tccgttagct
    60361 ggtatttgtt tagtcattca gatagtgact ggcgtttttt tagctatgca ttacacacct
    60421 catgtggatt tagctttcaa cagcgtagaa cacattatga gagatgttga agggggctgg
    60481 ttgctccgtt atatgcatgc taatggggca agtatgtttc ttattgtggt ttaccttcat
    60541 atttttcgtg gtctatatca tgcgagttat agcagtccta gggaatttgt ttggtgtctt
    60601 ggagttgtaa tcttcctatt aatgattgtg acagctttta taggatatgt actaccttgg
    60661 ggtcagatga gcttttgggg agctacagta attacaagct tagctagcgc catacctgta
    60721 gtaggagata ccatagtgac ttggctttgg ggtggtttct ccgtggacaa tgccacctta
    60781 aatcgttttt ttagtcttca tcatttactc ccctttattt tagtaggcgc cagtcttctt
    60841 catctggccg cattgcatca atatggatca aataatccat tgggtgtaca ttctgagatg
    60901 gataaaatag ctttttaccc ttatttttat gtcaaggatc tagttggttg ggtagctttt
    60961 gctatctttt tttctatttg gattttttat gctcctaatg ttttgggaca tcccgacaat
    61021 tatatacctg ctaatccgat gtccaccccg cctcatattg tgccggaatg gtatttccta
    61081 ccgatccatg ccattcttcg tagtatacct gacaaagcgg gaggtgtagc cgcaatagca
    61141 ccagttttta tatgtctctt ggctttacct ttttttaaaa gtatgtatgt gcgtagttca
    61201 agttttcgac cgattcacca aggaatgttt tggttgcttt tggcggattg cttactacta
    61261 ggttggatcg gatgtcaacc tgtggaggct ccatttgtta ctattggaca aatttctcct
    61321 ttggttttct tcttgttctt tgccataacg cccattctgg gacgagttgg aagaggaatt
    61381 cctaattctt acacggatga gactgatcac acctgatcag tgaaaaattc tgacaccaat
    61441 catttacata ttacaccaag aattgacaag cagataagtt ttctagtttg ctatgttgat
    61501 atagcttaga tagggaaaag ataactccac tatagagtag ggctgtactt caaaaatcaa
    61561 aaagggtccc tctccccctt tttttattaa aaaatcaaaa aagaggcccc gccccccaag
    61621 gcctaaggaa aaaacctctg ataaagaaag aaaaaatata gaactaacct ttacactata
    61681 accattaagt caagttatta acaatcctat actaagagga gaattcggat cagctcgggc
    61741 ggaagaggag aggcgaagaa gaagacaata agcactcaga ttggaccaac ctttcattta
    61801 aggttcgtca ttatcttttc aatcctgact agaatcaggc ttctcttgaa aaaaggtaag
    61861 gagttattcg atataatatg gtattaaccc tagcgcctaa gtcacccccg caaggtagga
    61921 agaagataaa ggagaaagtg aacggaggaa aaaaaggcga taagcgaacc ggcgggcggt
    61981 aaaaaccaca aagaatttat atagaaaaat aggtactacc aatatgaaat taagaaagac
    62041 atatatacct gaaacaaaat tctgtaatga ctatgtgacc atgaagggag tagttgattc
    62101 gcgttccaat tcattggcaa aatccggtat aaatataata atataacggg atcgtcgtct
    62161 tgacaaagat gaatagaaag agtgcttttt ttttaatggt aacaattctt attgtttttt
    62221 tttcttcgaa ggaagatctt tctttgacta aaaaggtttc catttttaat agattgtttg
    62281 tggttgtacc tttactgcaa gaatataaat gactcgctat tcactcgagg tttctgggtc
    62341 ataatgtagg agagatggcc gagtggttta aggcgtagca ttggaactgc tatgtaggct
    62401 tttgtttacc gagggttcga atccctctct ttccgtacct ttacctaatt caccaacgtt
    62461 accgaccgcg caataccaat cgagacctct aagacgaact aaagggatgt ctctaagcag
    62521 ccaaggccaa gagcaagcag gagtggtcct atccgcccat tcatttttaa gtgacttata
    62581 agacgtgaga gatactctaa agtcataacg gggaaggcca gagacttcgt tcaaatgggg
    62641 ggaggttttc tcttcaataa aatgaaaggc aggtattttt atacgaaaat tgagaattca
    62701 ataataaatg ttcacttgag attaggttcg cgaagaagaa gatcacaaat gagatcttga
    62761 gcttgaagct tactctccag aatcgaaaga tctcttatcc ccgaggcgag gatggcttca
    62821 taaacttttt ttgccgaagg aaagatagat aaggggtttc atccatattt ttctcccatt
    62881 tacgtatcac gttcagagat tttaattagt tgtccgctct ttccgtacct ttacttaccg
    62941 accaaatacc aagactactt acaacaggtg gtgaggatca gcacactgcg ggaatctaag
    63001 gaattgattg ctgtgcatcg accaatctca gaaagggaac tataaaagaa ggtgaagatg
    63061 caccgaggga tttatgaaga cgcatggtat gctgtggaga aaggggtgaa aggagtagaa
    63121 gcggcagggc aagaaaagga tagtgataaa tggacagacg ctgagaagaa gaagtcgaaa
    63181 gtataacagc aaagcactgt cagcaatcgc aagtgacaca ttcaagggtg aatcatccaa
    63241 agatgcttgg gatatcctac agaagggttg acaagtgtaa agagatctcg tattgatatg
    63301 ctgctggctt cacggaggaa agagagacca ttgaacaatt catctgtgct ttgccaatgc
    63361 tgctcaaaat gaaagacaaa gacaaaagtc aaaaagcttc tgttctgtag cacactcccg
    63421 gcgaagagcc cttcgcaagc catgaatgac acagataccc ttgcgtttga tgttgttgta
    63481 ggtcacctac aagcgtatga aatggagact gagaagtccg agaaaaagca ttgctgcagc
    63541 acacactaag acaacaagag agatattgaa gattcaatcg gcagcacact gcttgctaga
    63601 aactttggca aagtagtaaa gaagaatgga caaagtagga aaaacccttt tacacagaac
    63661 acaacaacaa atcgtgatcg tgtgtcaaag aagggagaac aacagtgtag ggatatggca
    63721 aagctgagca ctgccttttt ttagagaaga gacttcaaat gtttttaatg caaaggttgc
    63781 ttcgctaggg gcacacaaaa gctgaatgtg tgaatactcc cttattggtt tgcttggagc
    63841 gagagcgaaa cagacgagga tgatgatgca gaggaagtct ctggattcgt agcatttgtg
    63901 ataaagatga gacgcttcat tcggacaatt gctttgctag tgaaacaaat ttgctgcttt
    63961 actcaagccc acaccctcaa ggggttactt cgtcacctcc gtcaaacccg cgtcaaagcc
    64021 cctcgtcaaa gacctacgtc aaagtaggtt gcttcgccac ctccgtcaaa cctccgtcaa
    64081 aggaggctgc gggaggctac ggggctgcgg gaggctgcgg gaggctacgg ggctgcggga
    64141 ggctgcgggg gctacttcgc tgggagtgtg cgcttatgct gaagaaagaa agcaggtcca
    64201 ggttcaaagc gtaaaacggt gaaaccaaag gcttcttcaa ctcgaagaaa aagcaggaac
    64261 ggaaagaact ttacttcctg gtgaagcaat tttcaggata gaattctgcc agcttaggaa
    64321 tctgaacata agcagtagag cgagggcata gattactctg gtcatgccac cccagcaatt
    64381 ccaagaatta atgcaagcaa agcataggag tgtgatttgt cgtttacctt cttttgctct
    64441 taggaataaa ggtaaaaaga aaagcagtgt gctggacagc acctttccta cgtttgaaaa
    64501 cgaattgccg gtactccact tagacttctg cacctgacct agtggctgaa gaaggatctc
    64561 cctcaagtga tttgctgctt cctccccgac gtaggtttga cggaggtatc agtctcgttg
    64621 ctaaagcacc ttcggacctc ttttttcgtc tattctttgg ttaaagctaa aaatatttct
    64681 tttcattttg gatcattcag tagctcagac tggaacttga gagctataac cttttttcct
    64741 taatttcttc cgttgccgta tcttgcatat ataagatcga gatatctcta gtattcataa
    64801 tccaggattt cgccatactc ttacacctta cccagatctt ataacttata ataagatcat
    64861 ctaggctagg acgaggcaga ctaccatcaa taaaagagcg cttcagtcaa catatacaaa
    64921 gtccagcata gttagatcca ttaagagttg agccagaccc ggatgatcac cgaagataat
    64981 aagggctaga aacattatct ggtgaatctg agacaacgaa gctgcgatcg gcaacacaaa
    65041 ccattggagt gtgctgggga ggatctgagc tgtagaaacc cttgatccac taggtaaggt
    65101 tacttccaga gcggagtatg ctcaggtgaa actggtggtg atgccgatct cttctttctc
    65161 gatttctagt tccgtttcgc cattgttgag gaaaaaaagt gatccgagac tcaacaaatc
    65221 gaagagaaaa ggaaaacttt gttgattcag gaactgtgaa acggaaagtc tcaccagaaa
    65281 gtcattgcac tctctttgaa gagggtcttc cctttgtaag caaaggtaat aaatgctcaa
    65341 tgaggaaaga ttatgaattt attctttcat ttcggcttaa catctcttaa taattgtttc
    65401 cctgttttta atacaaaatt tgaggtgaag ccttctctaa tgctacgtgt cttcatctta
    65461 gcagatctct aaagcttgga gcgtatggta acggttagaa gtgggatttg agccgctgta
    65521 ctgtggcaga gaatgacgtc gctgtacgtt catggcttca gctctggttt tgttttaagt
    65581 gataaataag acagaggata ctttgggctt cggtttgtag acaaaactcg tcttgggctt
    65641 atgtcttgta gtcataggag agctgagcct tgtgttggcc cagttttggt tcatttagtg
    65701 aaacagtgtc gttttgagtt gtaaccggaa atatctcctt cttcctttga ctgtcgatct
    65761 cggtgtgggt ggcttaacga gatgttaggg ctaatgttag tatgtagtga tgtgctgttg
    65821 aaggtagata cactttatac cttcttcctg aagcagacga agcgagctgg aacgtacaag
    65881 gaaagagaag atgcctccta atctacttat ggatgtcaga gttgatggtc gagcataggt
    65941 ccattagcag atggaaagaa gattctgctt agcgacactg cagagtcaga tcggccccta
    66001 ctaatgagaa ggccttgaag gaagtgaaga ttgaggcttt cagggtttag ttaagacttt
    66061 gccggtgact cttttcctct cgcttcgtaa aaagaaaact cttccatact aagattaatg
    66121 agattttccg gtatacttcc cagtcgacta tgtgaacagc acaaagcaaa gttttaccct
    66181 ttagtgtcca atgatatcaa tggtatcttt ctgtttgtta ccaaacagga gggaagcttt
    66241 atggtttcgt aggttttctt ctactttttc ttctacttta gggtttgata gaatcgtccg
    66301 ctattacaga ctttgattat ctgtggggca gtgcgttaga cgaaggaagt agcaaggaag
    66361 atgaagaccg gatattaaaa ggaatatttc acaaagccga agcattacaa gcatacataa
    66421 aagaggaagc ctaccgtaga cccccacaca agacaaagtt cactaataac atagtacgtg
    66481 aacacaaaaa gacatagaaa tagaacaaaa ggagaacaaa gaaaagccat gcagtacttt
    66541 gggtcgaccg gactccttat ttaaatatta gaagagagtg gttctagtct ccctggcgct
    66601 ggagagcgtg ttcgatagta cacacaatta ggtagttccg ctcctgcagg agaccagaaa
    66661 tcctttgttg caggccgcga atgcggtccc gtaagacttg catccttgca cccacaaatt
    66721 ccgggtccag agcaggcggg tgctcccaga acaagcccag catttcctcc cagtggagct
    66781 ttgcgttttc cgcggcttcg atttcttgtg gaatggtcgc cagcctgtta tagatctcca
    66841 tatcatccat ctctcttaac tttcgacttc taagtgttct caaatataga cggaaagctg
    66901 cttctattta taggcaggct agtcttctta tcttaactta atgagtcttc ttacgtaaca
    66961 cgtttaatat ggaacaccct ttagtccgct gaagaattaa ttaagtacgc tgaagacttt
    67021 aaaggcccca tccatcaaag agttcttttt ggcgggtatt gccacgcggc ttaataccga
    67081 tcactccctc agaaagaaga ggcaataata gaacgcacag tagagagtac tcccccgcgt
    67141 ttctcgcaaa gcccagagca ctccttactc gacagctcct gaccagagtc ctcgttggcc
    67201 ctacttgcat tagctctgcc tgctcagagc tcgcttttct ttgtctattt ttgattggct
    67261 gattcccagg tacataacag ccctcggcca atccttactc gacagctccg tcctttctta
    67321 ggtgagctaa gaccgaagct agctctcttg aatttccccg gaaagacgga acctttccag
    67381 ctcactctgt cagtccacta agacgcgtat agagtaaatg agcactagca ataacttttt
    67441 cagtacaata agtccccttc tccacgacca cttttgtttt tgggctttct tggattcgtt
    67501 tccccagtaa ttccattttg gactcggagg cttttccatt gggctcagta tcataattat
    67561 cccaaaagcc ccctctcctc tagcttgctt ctttaaaaaa caaagcacac tgcttgttaa
    67621 tgggcttata tggatcaaag cattagatag aatgctaagt ccaattcctc aatattcttc
    67681 ttcttcagtg gcccaagcaa gatcatctat cagagaggat agggtccaag gtctgactct
    67741 tagatatatc ccctactacg agttactccg tacctctgcc tattactgaa caattaccta
    67801 atgagtgcgg gtagcataag acaaggtgag caaagagagg tctcaaaaag taaaaagacg
    67861 ggttttactt tttgacacag ttttgccctc gtatctagaa aaggataatt tacggaaata
    67921 gtaaaagata ggacctccta actttcctgc tacgagtgat taaagacggg gtttactcta
    67981 aaaaaacgtc aaaatattgt acgggattcc attccccggt tggtttgttt aatcaaacaa
    68041 gagaaagcac ctcttttcca aaggcagact cggctgtaaa cagaacagaa ttattactaa
    68101 aaggatgtta atgacttatg gctcctgtct tacttttctg atagggaaac ggaaatccat
    68161 aactagggat cctcctacgt ggacataaag ggattggaga cagagaaagt gattgtgcta
    68221 atactataat ggttcgctag ttgctctccc ttgttctcta ggttcggtaa cctgggtaaa
    68281 ggctgccttg cttcccgttg tggaatcttt tctaatcctt ttggccgctt ctttccactc
    68341 ggaccatagg gaagtcagaa cggaaaccaa caaaggacaa cacaaacagt ctatctcggc
    68401 aggagcagag cggctacgca aacccgtctg gctattcata ttccgacctg aggagtaaga
    68461 ctctcgcagc tactcagggt attgagctac tactagggag gctccggagc tttaaccaaa
    68521 ggagagaaaa gtacctacac cggtttatac aacaccggtt cacagactca actatacaat
    68581 tcatcacaat cacagatgca actatacaat tcatcacatt acatcacaaa attccccggg
    68641 atcaaataga gatcaaaccc atcttactta ccaagttgtg gaaaggagtt ggatgtaatg
    68701 cctttgtgag aacatctgca atttgtagat cagttcggag agaagcttga atagacctgc
    68761 aaccaacttc taacacacag tcgatctcta tatgtttagt acgctgaaaa caggatagca
    68821 agatgtctgg cagcagtgtt atcacaaaag ggaggagcag aagaactcat ttgaatgcca
    68881 agttcctgca agaaatttgt gagccaaacc atttcactta cagcagatgc aaggcttcga
    68941 tattctgcct ctgcagaaga cctggagaca gtatgctctt tcttagagcg ccaagaaacc
    69001 agagaggaac caatgaacag aagccagtta cagagcgccg tgtgtcggga caagaagccc
    69061 agtcagaatc agcaaaagcc ttgagctgaa gatcagatgt agcagaataa aaaagaccct
    69121 gcccaactgt ccctttcaca tagtgtaaaa ccttgtaaac tgcctgcatc tgggctgtac
    69181 gagatgctga tgagaactgg cttaacctgt tgacagcaaa agtgagatct ggacgagtaa
    69241 tagtcagata catcaacctg ccaataagcc tacgatacaa ctctgcatca accagatcac
    69301 caccagaatc cttagacaga gattaggttc catagggata gaagaggtct cagcgagcca
    69361 acaaacctgt ctagatccag agcatatttg cgttgacaaa ctgaaatacc ctctgtagac
    69421 cgagcaattt caagcccaag gaagtaagag gaccgaggta tgaagttgca actgatcttc
    69481 gagagtgtat cagctggaaa aatagcttct ctgcgccaag gaaatccgga tctctctaca
    69541 tactatacga aaagcctctt tcttcacaaa gctggacctt cgttcgggct attggaaagt
    69601 cagaattaca gaaggaaacg agcctaaaac cacttacttc tgttaccaga tatggcttta
    69661 cgagttcctt gtcatgctga taagaggcca gtcgatgagg ctcttgaaca agttcccggc
    69721 ggaagttagc cctataagct aaccgcctgc catgtctacc ccgaaggtat ctttggtgct
    69781 gttgttccta aaagtctctt ctttaacttt gtttccaaca acttcccctg ctttgttgtt
    69841 tcagaattga gaggcacgaa atagccccca aaaaaaggcg aaatccacta tttcatcaat
    69901 caaattttcg ttcgagggtt gaaagcgcca gaacttttga agagttttcg ccccaggcct
    69961 gtcatccggg ggatctcttt atgctcgtcc actcggggat gacccctact gatctctctc
    70021 atcggatcga atcgaatcca ctcctgaact ccagaagcaa gaacggacgg atgcccgaag
    70081 agttctaccg ttgacgacag cagcgggaat ggatttcaaa tagcagctgc taacgaccac
    70141 cgagaagggc gagtcaagac ttccagtttt atgaaataga agatccagat cttggagcac
    70201 ctaatcaacc agttgaggaa gaggaacgaa ggtactcagc ctcctggggc aagtgggagc
    70261 gacacactga atgaaccaac tccaatggag caggatcaag aagaagtgaa gctacgtaaa
    70321 agtgagcgtg gtagaatctc tcgtcgtcga tttgagattg agggagatcc ggggaatctt
    70381 attctgtcac ccaaaacgac cactccttct gtcggaaaaa ggacttgccc tatattgaaa
    70441 tgaaatcgaa acgaatggaa ccgcgacaga gcactcccta tcatcaggta gtgcgcgcca
    70501 ttcagaacta tgatatcgtc ttctagtcta ttcggcaggt ccaagttgtt ttggtcttat
    70561 aagctcaggt tcttgagttt tgggaatttc cttccattgg ctggttaaaa ttcaatacgg
    70621 atggtgcttc caagaggaac cttttcttgc atggtgctgc aacgggacat tctggtaagt
    70681 cgggtgctgg tggccttctc cgagactgtt caggaacatg gatctatggg tatacctgca
    70741 aaatagcttt ctctacgagc ctacaagctt cactttggtt tagcttccaa ctaaggctaa
    70801 gggagttgtt tccacgggat tgagtgaacg agctcatagc cctccacccg taccacaaaa
    70861 gcgctaattt atataaaaaa gaccgggaaa acgtgaatct atcccgaaca tttcctaaaa
    70921 tactggataa actgactcag atcggtctcc ctcaatcgag aggctcgctt gcttcacttc
    70981 aacttcatag aagagggaag gagctatgca taggggtgat tccggtggag atggaatgaa
    71041 tgcattgaca gttcggtctg atccgtctta ttcgtatatc ttattatggg atatttgcct
    71101 taacggaatc attagaaggc tttgggcggg gaaacccaac tgcaagacca gaggctactg
    71161 aaaggaagat actatctctt cttgagcttc cgattgacat accgagattg attcaatgaa
    71221 agtccctagc gcaggtgaga cctaattcta tgtttacttt tcattcaaat cagcttcctg
    71281 atgactaaag aagactttta tcctggcggt tgttggtcca acgactctac ttctttcttt
    71341 tgaaatatcg taagagaaga aggttgacaa gaagaataat ttgtctcctg tgattgtagt
    71401 tcaatcggtc gtttgtctct agaagaaaga agcctacttg tagaagagaa gaagcggggt
    71461 agaggaattg gtcaactcat caggctcatg acctgaagat tacaggttcg aatcctgtcc
    71521 ccgcataaag aacaaacaaa caatagaaaa aataaaaaat gggatttgaa gagtcaaagt
    71581 caaataaatg atcattcggt ggggactgct ccgccgacat tggaacgagg ccaaccgctg
    71641 cttatcacaa cctctggtgc cggtggaggt ttgacctcgg cgccgatgag gattaactat
    71701 gtgaggatta aggtgccgga cgtcatccgc aacgtaaaga tcgtggtgca cagtgtgtac
    71761 ttgccatttc cacatattaa tcctgtggct gcggcttacg aagtatccta ggaggctcag
    71821 aagtctcagg aggagatcag acgatggaag gaaggatttc gatcttcgat cttcgttacc
    71881 attccaaagt taattattta gctttcgatt aagtgagtgt ttgtttgctc agactcagac
    71941 taaaatgcga ctctatgcct tcccggtaga aaacgacctc tgtggcggga tttaccaggt
    72001 caaattcaac gggaccctag cctgcagtcg tcaaccggtc cgcttccttg aatgagagta
    72061 ggtcttcccg atccacgaat actgtctgtt gtcctttact tgtttagtgg catctggaat
    72121 tgtctgtttc ggtattcact cttgtaaagg gccgcgaact aagctaagcg cttggcttgt
    72181 cttcttatag ggtcccaacc gaccagtaca ttcaatatcg aaatccgtta ctgttacaga
    72241 agagaattaa gataacgagg cttggagtat ctaaaactaa gtccagcgaa ctggaagtct
    72301 cttcagactc cctcattgct tggctatcga agtggacttg tacctttttc gcgtgcgtcg
    72361 acacgacaat gcttaccttt ctagctttta cccttcttct ccggaaggaa tagaaagaag
    72421 acaactagaa taaggggaac tactctatat attacagcag gagaaattcc aacatgaaag
    72481 aaagcaggcg gtgcacttaa atctaaatag ggtgagaaag cttggcttgg gattgggatt
    72541 gttgactcat catgataggg catgaattgc gtatagataa ggtccagttc attaagttga
    72601 gacagctgta ggctcaaacc aaactgacgt gtaaagagcc ctagttgaaa taaaccctgg
    72661 tgaatctttt ggtgtcttag ggtaggagta agtggaggtt aggtaaccca gccagaggat
    72721 tccgttagcg ggttgattcc gagctggtaa tcgaacaggt caccaatcgt cctcgaaagg
    72781 gcggttcaag cgcatgagtt cagaggtcta tagatcgtga tctgaatata aagtggattc
    72841 caggggcagc tgcttctata aacacaagaa aaggtcttgt ggacttacgg attgataact
    72901 tgccagtaca cgctgagcct cgtcgatgag atgaggtacc tcatttagga tgactattgg
    72961 aaacgcgcgg tgccgcgtta ggttagggag cggggctcat ttcatcgatc atttctgcac
    73021 gagcaaagct caatagtaca tatagattca gatagcataa taaactaagt gaacatggct
    73081 aaaattaaaa ttgataaaca agagcataag attgcctacg tcaccataaa actcgacaca
    73141 gaaattcata agtaaaagcg gcgtaagtta ctaacatgcc acatgcgagg gacagaactg
    73201 ccattgacag cctccagggc aggtagctcc cagctcggct tgcttctact accttatagg
    73261 gtccccccca gttaggatct aacttgcgct ttcacttaag taaggaaagt cctattctaa
    73321 aagaaaagta gatttctccc tagatgcttg gaaattttaa ttactccacc acttcgcccg
    73381 gtgaacttct aaccatcctt ttctagagaa gaatagctat ctttcgtcag aattgatttc
    73441 ttttataccc gagtgaattg aagcattcct ttatgtggga acgtccatct ctagcgtgga
    73501 taagcctgaa ggtcctacta agcggtctaa ctcgactccc ctttctaggg agatgtggac
    73561 gaaggctact tgagctcatt ctcacatttc ggggtaagag gctaggctag gaatagggta
    73621 cagaggcgta gggggaatga aagaatttgc ttagtcataa tagtgctttc aaagtgaaag
    73681 gatataaagt aattaattcc tctgcttgca agctacctat gattttcttc gtcaccaacc
    73741 atttccgctg actcaagcat ggcatctttc ctcaagcccc tggcatttcc aggatcgata
    73801 ggtgcatccc ctcctcaacc ctattttctt atacagccta tcagttattg aataagaaat
    73861 aggcacctcg ctaaagcctg actatgccac cggtcgttct agcatagtca ctgagaccca
    73921 acttgcgtac tcggattact tcaggcggcc cattggaaaa tatacttcta ccaggcctac
    73981 tcaatcctat cttaggaagc ccgcatctct gtgtcaaacc tttttgaaaa ggctctactt
    74041 gaattgaata atatttcttt attccgactt cgccaatgaa agagggtagt tgaatagacc
    74101 gatatatcta gaaagtgtgg agtgagtgaa tggtggaaaa aaagtaactg gcaccgcccc
    74161 ttgctggata gaatatcgag atgcacatgg gattggggtg ctctctaagt gaggggccgt
    74221 ggaactatag cttagataga aaggtttttt aggccggaca aaggtctagg ttaagtccgg
    74281 agagaaggct tgatgaacac cacctcctgg ttagtgattg ggcacatgct tcctttacgg
    74341 cgtagaatcg gcttcttttt ttgacgtatc agaaagggcc tctcttctac cgcccgaagt
    74401 ttctatttat gcaagtatct tcacttcaat accccagcct atacatttaa tgataaccga
    74461 acccaagcaa ggagcttaaa tcttgtctat ttccttgaat ggtcgggttg gaaattcttt
    74521 tatgtgccaa cgcaggccta tcacctaatc tccactgcga aatcctttgt tggaaggctt
    74581 gctgatttac acctctctcc gccgcttctt aacagttgac tctgcgctgc gagattagca
    74641 ctttcttagt tactaacaga tatatctttt ccgcgcgagc tagttcaaca gttcattctt
    74701 gtaagccccc ttgtcagcca cactaagact tcgggtcatc attacctctg ttgaaggaat
    74761 aagcccggct atttcagctc tgggaggaag gactactttt ttcaccgcga attgcctttg
    74821 atgcaaaacc atataccgat cctgttaagt cttgaattga cttctgatgt cctggctgcc
    74881 ccttaagcct ggaagaagag tgactcggga agaaatctcc tgctggagag gtatatccgg
    74941 cccttctacg aagcctcaac tgcaactgag actgataata ggagcagtat ttttaaattg
    75001 aattgctggt gccggttggt taaaggcatg gggactgctt tcaattggac agctaactaa
    75061 caatcgattc cccataaaca aatagttatg aaacattgga ttggatgcct tttaaacaag
    75121 gaaagtaaag acagctaagg taagtattcc ccacattgaa agatatctat ttctttcttc
    75181 tgttcccttt gtctaataag atgggactgc aggaaagtaa gtggaaagta agaacacagt
    75241 tgttagctta tagcggggaa gaaagaacta gctcgactga aaggagaggt ccaaggtaat
    75301 ttattactct tataaaagag ggaactcgag catttattgc gagagggaaa gcttagagtt
    75361 ccactccagg agaagtagct tatggtaggg attataggta ggctggctaa ggagttgctc
    75421 ctggaaaggt agcagcttgg tcccttgatt gcggggtttc aaacctcata ccaagagaaa
    75481 gattccaaac cagcatacgc aaagcaaaga gcggaaaggt gctttgtacc tcatttcgct
    75541 aagcagcgag aattgtactg aagctctctt tcaaacgccc gccgatcgta ctacttcatt
    75601 cttagtgtgc tgaccagata cccccaccct gagctaagag ccatagcaag agatatagcg
    75661 ttggctgtag gcttagtgag ctcataaact ggcgaatcaa ttcatttgaa agagaaagtc
    75721 gggtctagct gattcccgag ttgaccaatg atagataggt aggaatggca ggacctaaac
    75781 gagctaggct tcgttagcca gttctccttt tagaagctat tcttaatgcc gctcgggctc
    75841 ccttttttat gggattccat cgctcttgga acagatgata taagatctta ctaaaataaa
    75901 aaaagtatga aaattaaata tacagatata ctctataccg gtatacagca ataacaatgt
    75961 cagccaatta gcaaagatca agcgaactca ctcaagcgta ctacagcttt tccgtctttc
    76021 ttccctaagc gcaatagccc cttgaataga taggatagaa ttagtgcgct tgaaagagat
    76081 ttggcttagt gaaaattcct agtcttactc atctcagatg cgggattacc aatgtcacga
    76141 ttggaattag gaaaggaagc tgtggcactt cttactttat atgaggaagg ggttaaatca
    76201 ctagcaatag tagacacgct acgatctgct agacaggagc agtacaggaa gcatcgaatg
    76261 ccatggttct tgttacagac taggctgcaa gtgagagtga tagaatcagc tcaactggga
    76321 atgttgccga tgccgatacc ggagctgcta aaggaagcag tagcagtaca accattaaat
    76381 ttgaatggaa ttgcacattc atcttcctct atcaattcat ttcttttgtt tgaataagct
    76441 attaaggtgc ctaggacact agtagacacc cagaaggagt tgtaagggag aacggaaatt
    76501 taagatcgga cgattttcaa cagacaagat cagatcgtag aatagagaag gatttgctgc
    76561 cgctactgaa tcagagtcca cggtgcaaca atttctcatc tgctcacgaa ttggattcga
    76621 accaatcaag ctacttgccc tttagtagat cgtgagtggg tcagtcgtcc tcctcattat
    76681 agtcctccta aaatcaatag catttcgtcg gaatacatcc tgtcttttca ccttagtagt
    76741 cctatgcata gtcagtacta tagccccaat catggctact aataaaataa gactaggaac
    76801 caaaaaccag acagaatagt aggtataaag taaattgccc aatgtttcca aattagtcca
    76861 acttcgtacc tttccggcat aaaccgtata tctaagagag gtcgtatttc tttgggttgg
    76921 tagtaatgga atgctttcat tatctaaaat gaaaaacatt tcccaccaaa agatcagtcc
    76981 aataatccca ctcactggta aatagcgcaa tacttcttcg tgaatctccg ctatttgaat
    77041 atggaacatc ataacaacga aaaggaatga aacggctata gctcctatat gaactactgg
    77101 gaagatcata gcgaagaagt cgagacctaa caaaagaagt aaacctgaag tgtcgcgaaa
    77161 gactgggatg ggaaacaaaa cggaatgtac cggattttta gcacgtgcaa ccatcaaacc
    77221 agagaccaaa gcagggctcg acaaaacaga aagtatcatg gtaccgtcgt ccttccctga
    77281 aatggaactt tcatgctagt tcttgcttca gcatgaaagt cgatctatta cgaccagcgc
    77341 ggttgttcct atttcatttt cttcttccaa gcccttcttt cttagaaagc actcactgag
    77401 ttacttacgg aatctcaatg catccattta atgcattctt ttcgatcttg tacccacgga
    77461 gcggtagact gaacaccaca aaaatatcga ttcaaaaaaa ggtacaggca actaaacctg
    77521 tgaactcaga tagccttgtg gtatggtagc gagatccaat cttgagtgaa aaagataccg
    77581 cggcttcgat ctttttcaac ataatcatcg cgcagtaaat caacaaagcc caaagttgac
    77641 tctctgtctc cttcaagttt acctactact gtacccgcgt gaatatgatc tccaccagat
    77701 agacgtaaag ctttagctag tacacggaag tgcaaaccat gattcttctg tctatcaata
    77761 acagcatgca ttgcacggtg gatgtgaaga agtaggccat tatctcgaat gagccaaact
    77821 agtatttgcg gtgaatcccc ctgtttaagt agtcatgcat tacgatagga actcccaatt
    77881 ctctggcaaa tacagctctt ttgatcattt cttcgcatgt acccgcagta gcattcaaat
    77941 aatgcccttt gattccacct gtttcagcct gtgctttata aacagcttcg gcacaaaata
    78001 agaaacggtc tctccaacgc ataaatggtt gggagttcac attctcatca tctttggtaa
    78061 aataaagtcc accacgtaga cattcataaa ctgctctacc atagttcttc gcgccaaacc
    78121 aacaatctgc acgcttagcc gcattgttca tcttgcctta accctacccg aaggaaggct
    78181 atgaattgag ctaacgccct ctgtaacagc ttaaatgata taggaggggg ttgatcctcg
    78241 atttgattct cgtgttgcga gtgtcgtgtc tcgcgtttcg aattcatttc gattgggaaa
    78301 gtgagccgat ccagacctaa ttgatctggt ttctgagagc actgacaagg ctaaactcgc
    78361 cggttgaaga gagcactgaa tcattcgaaa ggggaagcct cgactggaat ccctgctata
    78421 aagggcagcg gaggaatacc tacagattgc tcgccttaac cttaagattg ctagaaaata
    78481 tctaatgcag gagaataact aacaatttat gtggaatact atttcatttc gggggtaacg
    78541 actttaaaac ttgcctatag gatcgcttga cctagaacct gtttacactg gtcctgctgt
    78601 gaggaacgga ctttatcgag caaaaaaagc gattctatgc gcagacgtga aagctctatt
    78661 gataggaaac attctagcca attttagagg aacgattccc ttgtctgaga accgccattc
    78721 ccgcactatt cctccccaca ttgagaatct cgataactcc aaattaagaa gtgagcgaat
    78781 cccaaagctc tctctttccc ccttttcacc tttaattggt gaaagtctaa aatctgatgt
    78841 gaatagaaga aaaagaaaga agaaagatag gcggacgact ttactatagt ataggtcgaa
    78901 aaaaccgtga gcagtaagca gcggatctcc ccttcttttg ggaaagcagg tggccgcgtg
    78961 tgaattcttt caaggcaagg ggcggcctga tttcgacatt gttgtttcac tctgatccgg
    79021 tcgaggtggt tttcgtttac cagcgcgtag gtggtctaag ttcctatgac cgagtctttc
    79081 tggcccctgt gaacatcttt tcttaatgta ttaaagaggg cctctctaac cggtgaaaag
    79141 tagtgggtgt ccactaacgg ccgttcccgg ctcggctccg ataacgaaat tccgggagga
    79201 gtcggtagtt gggcactgga tcccttcgga cctggagaac gtgtgacgct gggtaggggt
    79261 ttggtgaacc aactggtcgc tcctctagtt gaagtatcgg gccccttttc gttgcctagg
    79321 ttacaccttc ggaatacccc agaagggaat ttatctctac ttccctaaat cttcacttga
    79381 tgccacgccg actctccttt cgtcataagg cgtggaatta gaccaagggg aatctccata
    79441 gaaacaggtc cctctgattt cgcgcgtagg agatcgagac acagcccaag ggctatggag
    79501 aaagatgtag atcgatcgcc ctagatagac aactacatag agggtcttta caagtctata
    79561 tattctttga tttcgttccc cccccccgta agatcaatat cacaactaat gaggtcttaa
    79621 agtttcacat ctaagtaata cccgatccga tagtttacaa tataaataga tatttatcta
    79681 tttaacaaca acattctaaa aaaagatatt aattgatatc ggtagttgtc cggtcgtacc
    79741 caaacaataa tattccagag gaaaatgcac ctaagatcaa atatttcgag ccggcttccg
    79801 tggaaaattc agactttctt tttgatgctg cgattacata aaaacataaa ctttgaggct
    79861 caatagctaa atacatggca attaaatcat gagccgagat cataaagagc ataccgcgag
    79921 taggaagtgg aattaataca atgaattcaa aagcatcaaa cctctcttgg tcggaagaat
    79981 cgaaacacat cgaaatggta ccagccgtac ttaataatag aaagatttgg cagaaatatg
    80041 taaaattgtc cctcctaaaa agattattcc agaataaatg ggcaatagtt aggagaggtg
    80101 cgccagcggc gagcagaagc aaggttatta gatacctcag gaaagcccgg ccagaaccac
    80161 acgtgcaagt ttccctgcat gtggctcgtc cgtgataact tcttcggatt tgcgtgaact
    80221 agcagaccga tcactaagtg gaaaaaaccc tccagcataa gcgaaccttt tctccactgg
    80281 ttaggaatgg gctaagagag gaagccaaac aaaccgacct attaagcaca gctaagctaa
    80341 tatgcgccgg ggaaagccag gtgccggagg taagctttat tcggcccgga gcattgattc
    80401 cccataacga ataggctagc tctatctttc aattgcctat cctgtgctcg agaaggtctc
    80461 ccagttcctc ggcagcacct cggggtgcat ttagttgtct tacatgagac tcgggatatt
    80521 cctcacccca tggcaccttt tgctcatcca ttccgcccgc ccgtacagac gcggcgccct
    80581 ttttcattat catctaccgc cctttctttc ctcccggcta ttcacgcatg aagatcgtcc
    80641 tatgtatgct ttacttcggt tgccggtgct ataggtagga gtacattatg gcaggatcag
    80701 tcacccgggc aaaccaaccc ccctccaaga ggaattgtgc tatgcccccc cgatccctat
    80761 agagcgaaag agctgcctgg tgatccctag gttgcagcac gtccggtcgt taactcctcg
    80821 cgccgttgcc gccgtttcta ggaccgaccg acgcctcacc tgcactggta cctacgtagt
    80881 gtcggtcgca cattcaacat agcgttcgga ctcatgtgcc ttccagaacc agggggtctt
    80941 cgagcctgct gcgtacgatt agccagcctt gcggcggcaa aaggattaga cgtccccccc
    81001 cccatgctac ggttcctgcg gtccgaatcc ggcgccgcat taggttaggg tagggggctg
    81061 ggcgataata gttcctctgc atccccaagc gcgctgccct cctaggcgcg caacactaag
    81121 taatccaagc caacccacat tactggctaa cggcggataa tcatatttct tagaggtact
    81181 aaatacaact ccatgaatga gcaaaatgga ggttgcatta atgataaaga tctctgggga
    81241 aaccgctaaa aaaagattga acatgtgtgg gaggatccga acgaattctg ctttcatttc
    81301 ccccgtatgg agcactgagt cacttacgtt acggtcttca gcgggcaggc tgcactctag
    81361 gcgacggcta ggaaggatcg ctagaccagc agccaaacca acaatgaata tataatataa
    81421 tgatagtgat tcggctcaat aaaaaaatgt agaaaagaaa gggcggaata gcataattgt
    81481 ccgatttatt cctcgatctt ctttgaagac ttactcctcc tttccgaaaa gatcgtcctt
    81541 ggtccttttg acataagatt ctcggccgct caagagactc tctctcgtat atatatttat
    81601 acgcaatatc ttgactccta ctacccctcc tttccgaaaa attgattgag tctttgtcta
    81661 agcgagtttt ctaggccggg tgacctggcc acttctattg cttatctttt cattacatct
    81721 tttgttctct agcggacttt ccgacttcaa ctggaccacc cacccggact aggaacccga
    81781 atttatccgc ccatccccgt cgaagaaggg gcgacggcct tgattatgcc gggcatgctc
    81841 cccgaacccc acccaattaa taagactaag taaaaaaaaa tggaaatagt gaatcaagat
    81901 ctagatggat ccctatcttt ctctctatcc acgggatacc tatctagatg aaaaaatcca
    81961 tctatgaatc gatctagact atcctctatc cggatagaga tgtccctatg agtgactacg
    82021 ccgatcttta tatgttttgg ccacgtccgt ttctgctccg aagaggaagg tttggatctt
    82081 ttaatcttat gtcgtgaggg atatgaccta tgttaggtcc ataagatacc acagcttttg
    82141 gtgttctatg attaacctcc gaataatgag taggtagttc gatccttttg attcttctct
    82201 tcatagtcaa cttatggggg gatgcgaagc aataggtcga attactatat aaagataaag
    82261 aagagttgta aactatagga ctgattgttc gagtaggaag atttaggttt ttatccttcc
    82321 ttctcttcga taagaatagg gattttaaca aattcctctt cattctcttg tgctcagcga
    82381 aggaacttcc taagcatact ttttcggatc caaacttctt tgttctttct aagtcttctt
    82441 cttgcataga agaacgcaac tgttgcaaaa accgggattt tagtagtagg cggcatcccc
    82501 tcttagtttt gagtaggtgg aaccattcag ttttgcttct tctccacatt cttagcggtt
    82561 gatgcagtaa tttgcctatg attttttcaa ctgaaatttc tttatagaaa gatctcctta
    82621 tttcttcacc gcgtattatc gcgttatttt cttgaaaaga tattatatca ccgtgggaaa
    82681 gtttaaaatg agtaatgctt accattcctt tattcacaca aacccttcga tgacttatcg
    82741 gctgccttgc ttgaggaata gtttcaagaa aatggagacg aagcggaata acgtcaaatc
    82801 ttgtttctgg attgagtgga aaagggatat atgaagttcg ttttgttcct ctgtgcatct
    82861 ctgtgatggg taaatcccca tgaaaaaggg gcaactttcg tgtagtttgt aattgtatat
    82921 aactggtaag atattttttc ggataaatct ttctcttctt aatagatctc ttcctgttcc
    82981 tcaatcttcg gagaatgcgg cgttgtatta ttgtcagttc tctgttccga acatttcctg
    83041 aaagtagacg acaagtttga aatcttaatg gggacaaatc tatatctcgt tgaatcagtt
    83101 ttttaagcag ccacattgcg tccctgggac tcgaacccaa ttctgcaaca acccctgttc
    83161 ctgtcctttc tttgttttgt tgatctattc ctcttcacgt tgtcttttta aaaaaagact
    83221 gaaagtatgg gctattgaca ccatggtcag aaagatattt taggactttt ctaagtcccg
    83281 cttctacgat aaagtctttc cggttttaat aaagcgagcg ccactctgaa tccacgatcc
    83341 gtaaggatct agctccgcca cattttgagt agcacttctt tattttttga aaaggccaca
    83401 aaactctttt caaaaaataa atctacagtt tttggtagtt catttttttg tgaaagaaag
    83461 aggcggaaag ctatgtcctg tacagtttct cctcccacct gagggcgaag tcatgactcg
    83521 acctttagtt ttgtgactcg agtacttgtt gcgagaggta ctttagtaac tcgactaaaa
    83581 ggagaggttg tttacatact tgagctttct gcgagaggga tttattactc gactaaaagg
    83641 agagagagca aggtgaactc ttcccattgc taacattcca gggattccag aaccaactaa
    83701 tctaatttcc taacctggga ttccttaacc aactaccaat ttaaagagta aaacacttcc
    83761 ttgggataaa ctgattcaaa cagataggca gattgaaatg gaactttcta caaacaaaaa
    83821 ctccttacct tacttggctt acctctccca ttcctctaat ccctaaccaa aacaaaccta
    83881 atctcatcac ctcattgcta atattgctgg gattccctcc taaccaacta atctccttac
    83941 ctcctattcc tgggattact gggattactg gttctcccat tcctaacatt cctaggaatt
    84001 cgcaagacac cataggcaac atgggaatcc ttgatctact tgtttctcag attccctttg
    84061 aggttaggag agtgagtcga ttcgacgagg ctagcttgta ggttagcctt tagtttccgt
    84121 caaagaattg gattttcata cttccttccc ctttggtcga ttcaagtgga ctttatccta
    84181 gatttgtcga tttatccctg gttgaggacc tttggatgcc agttttctag atgccagttt
    84241 tctataagaa gggtcagcct taaaggaaaa aaaccaatcc caaggtaagg tctaaactga
    84301 tctaatcggt aaagcccgta aaaagagctg agtttaacgg cgagaagctc ctttcaaagg
    84361 aaggagtgac agaaaaggtc gggacagtgg ctgctaccgc attgacttcg taagatttgg
    84421 atgtgttaag gctaacctcc caaaactcac taaatttacg ttgcttcaca aggtaattcc
    84481 tatttgctta cttgttagag taaggaaagg agaagagctt caaggtagaa cctatgaacg
    84541 tagatcgcat ataatgtgtc gatctcatca ccttaccaac cagggcctat gtatacgaaa
    84601 ctggtgcacc atctgcaatc gctatatata cctgacctat cttctcgtgt atcacccttt
    84661 ctttcttcct ttcctaacta tcactgaccg cgggggaaat gctgacagaa tgccaatact
    84721 tgttcgatcg aaattctaac agttgttccg ggcgtttaat gtttgttctg gttcaagcta
    84781 gaaaacggtc aagtgtgttt ctaatcaggg ttatctaaat tggaataagt actttttgat
    84841 aactttgtct catgcggagc aaagcccttc ttagtcaagc ttagtccctt tggagtatat
    84901 ttaaagggaa gtgcggatct ggagtgtttt gtttagacga gctatgcagc aagctgagtt
    84961 ctatcgaaac aacgttttcc gggcatacga gaaaagagtc cagcccagca tatttatttg
    85021 cgactttctt gatcccggaa atcttgtact cagagtcacg gataaagata aagtggacta
    85081 ccctgtatga cctacagttc tttttagtgg ctttttcttg tcctggacca ttcagccctt
    85141 tctcaaccaa gtataggtag aagccctctt ttccatacag ataaaggttc gacttccaag
    85201 agaaaagata aggaagtcgg tattgatcgt ggaaatatct tagaaagtct tcaaaatcgc
    85261 ttctcttcct tcattctcag taggctaccg tcctcggaac caatgcctaa gatttgcctt
    85321 gcggtctgcc cttagtctaa agacttctat ccactacgat ggaatctgtt tagtggagag
    85381 aaggcctagt taatctagca ctatggtgga atctaagtgt aagatattgt tccgcggttg
    85441 gaaaactagc tcctatgcgc ctgtaggtag gacgttagaa aaagaatccg aattaggctt
    85501 gcagacctac tattaggctt tcagtgtagt aacctagatg ctgaatatag actcccatct
    85561 atagtaaaag agaagaaagt caggcggaca ctggcagctg caagtcagtc ggttggcttc
    85621 cgtcacttct ataaaacgct gcccaacaga ctgaaatgac tatcttcggg atatgatgcc
    85681 agagttggtg cttttgcggc atctagttca gtatcagagg gctgcgctgc ccttggctaa
    85741 gaaggtttac ttctctgtca cttccgtact tctgtaactt ctctttagct tattaatgga
    85801 attggttaga aagtctttcc ggctagaaga gagggattag tacacctcca acactgactt
    85861 cttagtcgag tagttctctt tctcctgggc tgagacgtga cctcttctcc tcgttttcat
    85921 tgggagggaa gatatagata caaaggtaag cacgaacgga agtattcgaa agagctattt
    85981 agctgaaaac tctatagcta aattactcta tcatagaagc cattactgac tgaatctggg
    86041 agggcaaaag gcttagtaat agtaagcttc tcaaccctgg taagggttta cttcgtccca
    86101 ggccaggtcg ttgctcgttg cacggtaggc ggctttgagg aaaggtatga agtcactcgc
    86161 cctttagctt tagaaagcag gagaggtgct ttagcaactc gactgaaagg agaggttgtg
    86221 aacacaaact cgactgaaag gagaggttgt gaacacaaac tcgactgaaa ggagaggttg
    86281 tgaacacaaa ctcgactgaa aggagaggtc caaggtaatt tattactctt ataaaagagg
    86341 gaactcgact gaaaggagag ggagagggat ttgacttttt ctgtcaggcc aatttctttc
    86401 tagtggtaag tgctttcagc cagttctagt ccttttctta tacgcttatt ggcgttagca
    86461 cattcctctt tcttattgga tggagttgtt ttgccacctg gagttttaat ggaagtttga
    86521 gtgcgtccta aaagccaatg cttctgcctt ttggaagtgt ctgcctatat ctgtcctccc
    86581 catttaatca gtctctgtcc ttaccttcga cggtaacccc tttatagtac agcagtcccg
    86641 tttccggcag tgccttcccc ccccctagtc tagaccgagt atcaatagtt gtagttcctg
    86701 tccgttatgg acccttcgta tctttcaaat ccaatcaatg tgtggtgtgt atccaagggc
    86761 aaatgcaatc tctgaatctg ttacagccat tgtagcacta ggtgcctacc cataagcagt
    86821 agttgccctt gaatgtgcat caaatcctaa gacaagccta tctaatctca cttcttagtc
    86881 taaagcactc aaatcccttc taaggagcca gccctttttg aatccctctc ttttcttcat
    86941 gctgtgaaga aattttccct atccccctga ctggcgaggc ttcttctaaa cgagtggagt
    87001 tcagttagac tgccccttct ttctcgtgct ctccgtccaa gcgagctaac tcctgatctc
    87061 ctgttgtaaa gatctccaga ccaaggctat tcttaccagt tgacatccat cccgttgcat
    87121 tcccagcggt tttagttcta ttggatgggg ttctatacga gcgttccata ccgtctcttg
    87181 ggatcaaact gaattaagtt ggactccctt caagagatag atttctttcc acgataatat
    87241 ctatattttc ttaagaaaga agactagaat atcattggga gtgcacttaa gccaattgga
    87301 gtactaggcc ttctgttcca gtgacagtta tagaaaaaag cgaagccctc cactcataag
    87361 taataagtaa tttcatccct taccagtccg tcctaccagc tcttctgtct tcctttttaa
    87421 aaggagctaa cgatacgatg ttcaagcttt gccagaagcc ttttgcagag agaaagttcg
    87481 aagatcagga tcaggattgg attgaaaata aatctcctca gcattcaatt caagtgggtc
    87541 tatcgataca agtggtaaga ccgataattc agcatccaag acctggccga tgtctacttc
    87601 aaattcaagt gccacttatc ttaacacaac tcggggctaa tcgactccca gcctatcccg
    87661 acctggtcct ttcgaaccag tctttataaa cctggtgaaa gcaatcaagc aggacttacc
    87721 tgctgggagc cccttccttc tattccgaaa cctagaagtt ttttttccag ctcttgagct
    87781 gattgaatga ttttgttcac tgctaagcta atccttctgt cctactttac tctattatga
    87841 gacctcaccc taggctaggg agctggttta agccatgccc ttatttgact cccaagaccg
    87901 gatacatagc tcttctgagc gggtcaaatt caaatacaat gagtgcttag ggaaagtaag
    87961 aaagaaagac ataaagcgga atccggtaat cctactgcta ctaagactac tccgtcttag
    88021 ggctaggagt tcaagcgcgg cgtaacgggg gttgtcagcg taacagctgg tgctctaatc
    88081 tgagctgaga aataggaact gcacttcgac ttgatttatt tatttactat attcccccct
    88141 ctctaaccca agtcctagaa gtgaatgagg aatgaaagaa cttctgcttc cgcaatgaga
    88201 cgctaaagtc cttaaatcaa ggaaatcaca atgcttctct tattcagtag ttcaatctta
    88261 ctttcttacc ccgccgggga agcgttgaat gaatgtgtaa tgatgtccat caggggagat
    88321 cttgaccgat ggccgcgcga tgtccgagtt ccttcgaatg ctttttccaa gccccttctt
    88381 gcgctttacg aaattcgttg ttaaggccag tccttctctc accttcacag aagaaaagag
    88441 attcttctga atggttgata tattcattcc agaggagatg ccggtgaaga ctaccagcca
    88501 atgatggacc tgggcttact accgccaagt agcctattaa gtctcaaatt gagtactaaa
    88561 gtcaaactac ttgtcctccc caaaagagca gctgaaagaa acccatggca aagcaacata
    88621 cccgtttaag catagtcgct cgtctaacgt ttcgggacaa gaggagagga acgcctttga
    88681 gatcaggatg ttctaccgct tttcctaggg aaggtatata ctactgatag tattccgctt
    88741 tgtgaaagtg ccataaaagc tctcttcgcg tcaacgacat ccatctaacc atctaacgag
    88801 atatgcttcg ggtaagattc cctgatctga aatttcgtta gtgagctggt tcggtctatc
    88861 ccttcactta acctaaagcg tacattcgat agggaacttt gattatcaaa tgggttggtt
    88921 tattagcgca ctcacgccaa gtgctaccgg ctcatcctgg tgaggcatcc caagcccctg
    88981 taatatttcg cttttttcgt cctctcgctt tgtccattcc ttgatctacg aaaggtattc
    89041 agtattagga tcagaggcct atgggatttc agtagccttt aatcaattac aaactcatca
    89101 ctcttcttga aggttaactt cacatcttgt gtgtgttccc ttgatgtatc ttaagaccca
    89161 tttcacagcc tgccaatgac tcctcaatgg cttactcata tatctgctaa tcactcctac
    89221 tggataaggg taatctggtc ttgtaccaat cattgcgtac atcacacttc caacagcact
    89281 tgaatatggg agtgatttca tatagtccat ttgttcctgc agttcttctt ctgtagctgt
    89341 ttggaatctg aagtgaactc ccaaaggagg taggaaaggt ttggcacaac gctcatagga
    89401 ctatcggtgt gcggagttca tctcttggtt agcaaggaaa gattcttcaa ccagacatct
    89461 cccatttaat cggaacagaa gtaagaaatc taatatcagt acggaccagg ggaaaggtgt
    89521 tacaattgta gcatcaagtg cactcaatcc ggttgttagt atttgttagg tcttccgtgt
    89581 taggtcatct ataagactta gaaaatactg acactttcaa aaagataatg ggactgaagg
    89641 tgctccccat aaatctgaat gcacataatc cagaggattc ttagtagtgt gctggcccgt
    89701 agagaaattc actctatgtg tctttccata gatgcaatct tcacaaaatt tgagacttga
    89761 aaccttgctg ctatctagga aacctttctt gaccagtaac tccattcctc tttggctcat
    89821 atgtgcaagc ctactgtgcc aaagccttgt ctcatcctta gctgtttctg caaggttaga
    89881 ctctcctgtt tcaacagagc cttgaagaat gtaaagtgaa tcatgtctgt tccctttcag
    89941 tattgttctg catcctttaa gaaccttcag aactccttca ctacaacttg cttcaacggg
    90001 ccggggcctt tcccattctt tcgaagttgc tagcattctc tctcctttgc gcatgtgtgg
    90061 gaataaattg actccatctg tctctgagaa tgggggaagg ccacactttg ttctcttctc
    90121 tctctctagt ccaatgtcca attaaaccta accgatcaac cctttcagtg gtccaatacg
    90181 cgcgctgtag ggcgctgaca cttgggtcaa cgatgattgt acctaaaatg agaagagagg
    90241 agataaagaa agagagcgta ttgaaactct taggtgagga atttggaagt actttaaggc
    90301 ttgacggaga agagagagat gagagggaag gatagcagtt accgagtagg agtagttgat
    90361 cctcacatca aaatatgttt ataagaaagt ttcctcattc aagtgagaaa taggataaac
    90421 caccgcccaa agttgcttag ccaagagtag tcctatatgg gctcgcgaag ccggtctccg
    90481 gtgggaaaga tcctatctaa ctatttggga gaacttctct tcttttcttt gattgtgctt
    90541 tgcttaacac aatcgaagtg ggatcatcgt ggagaaaaat atcttgcggt cagtctttcc
    90601 atatcttctt ctttagctca ttcgcaacag tttcctccat tcctgcgatt tcctcaggat
    90661 tcctcgcttg ttgtgatagc aatctataac cgctctgtac cgtgtacatg ccactcttag
    90721 tgtaagccca cacattatca tccataagat ttgcccctgg tatcatcgag atgataaatg
    90781 ccacattctg tggaggaaaa atattatgca acatatccag tttccacgac tgcctattca
    90841 tgtcgtacaa gtcagacgaa gattaaggtc aatagatagg tttcaattca gtggaggtag
    90901 aggtgtctca tccattatcc atctgtctaa ccaaaccttc gtgtgtatac cgtctccaat
    90961 cgtccttagg agcccgcgag agaggagttc tctgccatga atgatacttc tccaagcata
    91021 tgaaggtctt gtcccaacac tacactccat cattgagcta tgtgggaaat atcggctacg
    91081 gagaagtcga gatagtagcg tatgtggttg gtgtataatc cggaaagatt gttttgcaag
    91141 aagagcttgg ttaaaccaac ctaaatcccg aaaacccaaa ccaccatcat cttctttaga
    91201 tttgcataat ttctgccaag ctacccatga gatcttcctt ttgttttcgc aagaactcca
    91261 ccaaaattcc gtcatcgcac ttgttaactt cttgcatagc agctttgaaa gccggaagca
    91321 cgacatcgca tacaccggta aggccattgc tatagatttc agcagcacct cctttccccc
    91381 ctgagatcaa aattttgcaa accaaccatt aaggcgggat tgaagcttgt cccgaatgaa
    91441 ggctaacaac ttcttatttt atctacaaca gcagaatcgc agcaataatc aacagataga
    91501 aagaaataga ttagaggaga gggtaagggt ggatagggta tggacagccg tagaactcgc
    91561 gaagcatgca ttagaagcag atcctactag ggtttgttaa cctactcggc ggggtaggag
    91621 atagatatgt tcctcgtagg gatgacctag tcgaaggaaa gaagatgttc ccaaagagat
    91681 gttgaggaag gatagcagta tacataatct taatgcaatc aaacggttat cctccttttt
    91741 ataggtatcc aaactcggaa gatgttatga gactgagccg gctaccgtac ttcgtgctgg
    91801 aacaggggtg actcctaaca atggatccac cacagtaggg gttatatcac aacttattac
    91861 catccggaca aaggaaaagg gaatagtagt gaaatgacag gaacgacagc tttcactgct
    91921 acggctattg gctttagcta tactatggca ttccctgtag ttcttggagt cactcaaact
    91981 cgaactcctg ttacagctcg gctatagact acgcctctat taatcctttg ttcgtgatca
    92041 ctcccagcaa tcacttcact ggctaacagt tagttagaaa gtgttccggc taaggcctat
    92101 agaactcatt tcactccggt tatagctgaa agtggctttg ttcttatcgt tcagtggtca
    92161 ctctttatag gtaagtaaag aagggattct attgtattcc gatactgcta cgagctgtct
    92221 taactccact tacttctagg ccattagctc agtaagctca gtaactccat tctcttatgc
    92281 cagccttacc tcaattccct tcttagcctc aacagctaaa gcatcccttt ctacagctcc
    92341 tgaaacagcc gaagaaccac aggcctaagt aagtgttgtg ttcaaccttt ctataagtaa
    92401 tatgggttgg ctggttggaa ggacagcttt atgtcgtaag taagtaaata gtcgtcaact
    92461 atcgagaacc tgtctgaagt gttattccag cgcttcctag tctttacata gtctttttcc
    92521 ctataatcaa gaaacgtctc tcaagtcgtg ttccaaccag atgactccat ctctctcttg
    92581 gactgtttcc ttcatcctca gaataggtgt ctgagggtct tcatctccgc tggaatcttt
    92641 acttgcaatt tgatcaagtc agctatccaa aatgagtttt cattcaagaa ccactttact
    92701 ttgagctcgt agcggaaaga gcagattaac tttcagtttc tcatatggag tcccatatgc
    92761 ttagccatca gctgagaaag attgatacca agtcggagca tatcccgttc gagggtccac
    92821 ctattcggga gccagtacga gggtcaattc cagtttcgga tacctgcgcc tattgcatat
    92881 ttagtatttg cagttcaccc cgctgttaga taggcagagt aagcataggc tgtggtataa
    92941 atcttttgag tttgaagata ttttatcgac cggagcaaga tccattcata agggtttgga
    93001 gatttctcaa tctaaaaaat caaatacgat tcaacagcgg gagagatcag cattgatagg
    93061 acatggagat gtgggctcag aagggagtgg aatagagtca tttgatagct tagatgccgc
    93121 cactagagag aggttcactt gcttaccttg ccgggtcacc aggagaggtt gtgcagaaca
    93181 agaccaataa cccgatctct gctaaggagc aatacggatc ggataagaga ggatccatct
    93241 tctcggggga gtctaaaaga agaccaccac ttccatacgg aaaagtgtag acgatgatcc
    93301 gggacttttc gatctttttt ctgttaccta actcttcaat cactctttct tagggggcga
    93361 caggattcga acctgcagtc ttcaggtcat gagcctgatg agttttcttc ctctacccag
    93421 cggtcttccc cttctctttc tttcacaatt cccacctagg tcccccgctt tgttagcttg
    93481 gccgggatag aagctgcgct tagtaagcgc cccttgtctt gtataggttg gagctatgaa
    93541 gcttagcctt cttattagaa aaaggtatga aatgactcga ctaaaagagg aactttcctt
    93601 tgtgaacatt tacttgcctt tgcctttcct tcccgcctta agaaaaagaa agcccggatc
    93661 cggataagca gctatcggct tcatgccatc ttcattcatt tgtccaattc cgggcactgt
    93721 aagaacctat tctctgattc aatcaaatat cccaaaccaa aggcctatga aagcccgctc
    93781 aatagcaaga aggctttttc aacgattttc atgcttcctt cctcgattga tgaggccgtc
    93841 ggggtgcctt ttgtgctttg cttgcctgtt agttttgcgt atcagttact agctttcctt
    93901 ccctagcttg aagttcagtt cttcctttcc ttgggtcatt agtggcatta gtttgaaaat
    93961 gaatatcaga tcatctgtcc aaattgatgg aggaagattc tttcacagcg cattcaattc
    94021 ctaactattg tgacgtagcc cgatgtagtg tgactcgacc tttcttcttc ttttttctgg
    94081 agagcttcaa tttagctgtc atccacggag aagcttcttg ggctctagcc tcatgtctca
    94141 tattctttca tattctttct cgttggatat ggtatcaact tcaagactgc agacatgaac
    94201 tcaagatccc accaatccct tcttcttgtt atatgcgacg acctaccgaa gacaagagat
    94261 gattagctcc tttcttattg gattggagaa gatggctcgc tcacttcctt tgtgcacctc
    94321 ccgctatcga tctcatttct tcccttctaa aagaaactga agaaagaagt agagtcgcct
    94381 aggaagtaaa gaaagttgtg ttggttcttt ccctggttcc ttgttcccct gttgccctaa
    94441 gagaaaggct gttgtgattc tacggtttag agcatttcca agataggcat tgttagcctt
    94501 gcgcttgaac ctacaaggag gaagagatag caaagtctta tcttataggg ggcctcgaaa
    94561 tcagaataag ttgaggggga gggaattcaa tgaatctgaa gcatcagata gcaacaccac
    94621 aggataatcc attcctactt tagaaaaagg gaaggcgtga gggtaaggta aagtagaata
    94681 ctactcaaaa agctggtaaa agaccttggt tgatcgggta tcgaaggaat ccctttagtt
    94741 tgaaactaat acccccttgg aaattgattt gatctggcta cgtatctcac ttcctcagca
    94801 accggtaaaa agtagattca tcaagatagg aaggaaagac gcagtgctcc tgtggtgaaa
    94861 ctgcaggata aagataggaa aagtggtgct tgtcttgaag gtgaggaagg gaagaggaag
    94921 tgaatttgct ttgggtgtgg gttaagctct tccttatctt aggacgaatc agcagagaag
    94981 ggccttcgct tcgaactcgg atgtttagga agaaagctgt ccacttgaag ctgaaacctt
    95041 agacttcctc tcgggctatc tatgaattag aaagctaacc cttagatccg ggaagaggga
    95101 actggcagta agggtattac acttcaagaa aagtggaact cactcgaata gagagagtct
    95161 aggctcactc acagacccag ctgtctttgc tttgttcaca acgtcagccc gcaagaactc
    95221 accctcgtgt gaaagatagc aagatgtggt tgatggaagt aggtatgtgt cataagttca
    95281 ggcacagtgt cttctaggaa gaaactttgt gtaaggatct tttacagtaa agcaaggtat
    95341 tgatcaaagt gacagtggtg agggtaacct tgtgaaaaaa aaaatggtta ggtgtgccct
    95401 ttcctatggt gtctcttctg tgttagctag tataagtctt agtgcttttg ttttagtaag
    95461 gtcaatagga gttagctggt agggcaatct ctcgtgcaat caggaataat ccttgaacct
    95521 tccaccccgg agtttcttct ttcttcaaag ctttggattg aaaacctttg cttagcctta
    95581 taaagtagcc aattttccaa ctataattag aatgaatgtg aaaagaagat gaaagaatcg
    95641 tgtgatacta tagctagcta cgatccccta caagaggaat cactctactt accctttggc
    95701 gggcttcgag gaccctactg actaattctt tatgcatgga tgcaggaaga gcctacgagt
    95761 tcatttgtaa caatatgaaa gaagaacctt gcgtgcccga tcatgatata ggtacagctt
    95821 ccagccagaa aggtgattgt gctagaaaga tggcagtgaa gatcatggat aaagagctag
    95881 tcaagcagca tcctgatgat atccacgtac caactactgg cactgctagt gcttttgtgg
    95941 attaacctac ttcccagggc cggcggtcag agagaaaaga tctctatgaa aagcaggaga
    96001 cgggaaaata ggctcgctcg aattcgaatg ggttttaaga gttcccggta atcaataatg
    96061 gcaatgcttt ccttagaaat ccaataagac aaaagggcgt aacggtaccc tacgaaatcg
    96121 gcagatgatt gctttgattg gcctgctgta tcagtttatt cgactacttc ctccataccg
    96181 tagtggactt ccttcctaga tagatgtagg agcagcggaa agggctgctt tagaagcttc
    96241 aatagttccc tcatcaacgg atggtttagc cgccaggtga tagggatgtc aaatagaaaa
    96301 ggcaagcagg cgtagaaggc cacgttcgat agctgaaaag tcaagctgcg gtagagggtg
    96361 taaactaaat agttacagct gggcttggca attatctagc cgaagtggaa ggttaaacgg
    96421 gataaaatcc tggtcattct atagttgcag gatcggtaaa tgaagccgga aagagtatct
    96481 agagataaaa gtccaggcgt cgaagccaat taaacacttg gacaagatag tgaagggtct
    96541 ggggagaagt aaattctaga gttcattact cggatgggga ctacagtaaa gaaatctatt
    96601 ctagaggact aaatgtcaac aaactttagc gagagtacca agatcggact caacttccta
    96661 ttccaaaggc aactttacta gcgtggttat gaatcaactt acaattcttg tacaggagga
    96721 actgttaatg aaagacaact atagtagtaa tagctgtgaa ttccacttct gagttagagt
    96781 tcaatccttt ccatctgaaa gtacgtactt cttatagctt gagaagagga aggatgcatt
    96841 cgtcagcata ggaaggccca atcaaatacc ccatcatagt ataagttttc cctcttgatt
    96901 gacttgaaca aaaggaaaga aagaaagatg cacaaacgaa acaggaaact acgaaggtct
    96961 caggagcaat atcaactacc tagaccgacc tgctataaga attccataaa gaccttgcga
    97021 agatacctgt actgaatgac tggatcgtac tagatagata gtcttagata gacttgaata
    97081 cgcaattcct gccaatctcg cacttgacac gcaataaaca gcagtctatc ttcacagaga
    97141 aggatggcaa ggggtgaaag gcttagacct tatctgctct aggctagttt cattctattc
    97201 ttgttcagca tatttagttt caaaagatag aggtccggag gcattaatta gttgatgagg
    97261 agaaaggcca gccacgaaac actcacccaa tcaaccttca aaggcaagta aggactctct
    97321 caaactgaaa attgctgttc acattgcaag atctgtctca agatgttttg aaaatgagaa
    97381 acagcagcag aataaatagt atactttatc gagaaaaggg aggaagtatc ttctttctct
    97441 gacgtagacg ggcattccta tcgagattac ttccttagga ccgggaggtc gaagaatcta
    97501 tatgctacct tactttcagg atggctttac gaaagattcc atttagctga agtaggacga
    97561 agcggtatga gataagaggt ctcaacgagc cttcagcatc tgaaacggga gctttaacct
    97621 gcatatcata cgggagtctt agtggagagc gttctctggt tatcatccct agttaaattt
    97681 gaagtgacgg aggaacccct attcgataaa gaagggaacg gtgcaaataa agctatttcg
    97741 agtcctctat caacaaccaa ccaaaccacc cgcttgtcgg gcttaaagcg aaactgagct
    97801 tctcactaac aaaatcaatc gtaagcttca tgtccgagac tcggaaagag tggcgttaaa
    97861 gagggcgtca gagcctctcg aagtctccga tctcacagat ggttaggctg caattccttc
    97921 gcttgtgaag aagcttggat agttctcctt actcggacat tctattcatt cgaccaccgc
    97981 ccatgcttaa agattgaagt tttgttttga cccggtaaaa aaaaagaacg ttgtaacgtc
    98041 ggttaacgca gcctcacagg cagcctgaga agtttttgac ccctttacct atcttgggtg
    98101 agctacatcc atacatagtc taagcctctg attgacagta ctagatacgg aatcttagtc
    98161 ccaagagttc tgcggaagcg ggctaaaagg caatagttcg ctagggtggt tatcccaatt
    98221 ctttgataag atcgctaccg aacagcccca aaagcctagt ctttagaagg aacgaacgga
    98281 tttctttgtt tgttcgtgca atgaagaatc ttatctgaag aaggtaatac ggaaagaaaa
    98341 aaactcaacc tgatgctact ggaatagaga agcaagcaaa gtgggtcggg ctggccaatt
    98401 gaaaaaagcg gtatttcttc cgcgaagact aactaacggg gcgcactcaa tttctacctt
    98461 ccccgagctt accaccaccc gtggtacaat agaatgaaaa cagagtaatg accaagggaa
    98521 ttttctatta accaacggga gatcctcctt ttctcgctaa tctaggtctc caggttcccc
    98581 agcacagact tcttgttagt ttaaactagt aaaatgggag tgaagctatg ctgttaaaca
    98641 agacaaacca atcgcagatg tactatcatg cgaggaaggc cccccattat tgttgaaaaa
    98701 ggactattcc caacacgtct ttcgtctaat cgggagaaaa aaggaaaaag gcgttattgc
    98761 tgtgcttccc ttccctttac aggcaagctt taacttcctt cggggaaagg gaaagacctt
    98821 gaaaactctt tccgtatagg ccagaaaaca gcttgcttag agaaagactg actctcctac
    98881 ggacctggtg gaccttacac agtcgagtta ttgcatccct ctcacaaact atcaatttca
    98941 taagagaaga aagatcgttt ttagaaaaga aagaacgttt tgattcgagg cggatccctt
    99001 ttttctttgc ctttacgagt tgaaaagaaa gtggtaacag gtagtagctc tggtagagtg
    99061 caggactgta aatccttctg tgagcggttc gaatccgcaa tcacttatag ttagtttcat
    99121 cgatattttt gtggtgttca gtgtaccctg agtacaagat cgaagaggat cctcattccc
    99181 tctttagtca atcccaatcg aaaaatcagc ggagccaatg gcttgatcat aatgctgcgg
    99241 cggggtcaga gagccggcaa accgtttctg gttctagtag aaagggattt actgattcgg
    99301 gttgaggatg acgagcaaaa gagtggagga aaagctgtta tatagttagt ctatttctat
    99361 cttcctatct ttgtcatgtc agtcttattc ctatcttggt atctttgtca tgaggtatgc
    99421 agcacactca accaaaatat atagaattgg atcatcaacg ggtgtgctaa agaaacgcct
    99481 ctacgtaaac ggatgaacgg gatcatcata tagtgagctt cgtttgggat acttaaaccc
    99541 acaaaaatta gctctttagc tgatatacga ccaccaacta tctggctatc gagaagatct
    99601 aatatgcagg gaagtaattc aatagaataa cgcaaggttc gataaatcaa ttgatgcaaa
    99661 agcagggaat tagaccactc catcctttat ttcacctagg agccatctta gcagcagggc
    99721 tttcgactct cgaatgtcaa agaaggtcct ttttatcatc tgagctttct cacttgtgcc
    99781 ctcagccctc aagacttcgc cagaccttga ttttcgattg aagataatcg tttcttcgct
    99841 atcccgatac caaaatggga agatctccct tctgggttgg tagatgaatt gttctgggta
    99901 acaggcggtg gacatcttcg ttgacagatc tgagttatcg acttggtcat atgccctaaa
    99961 gttaccctaa gccctcgggg ctccatccga acctgtgact caaccttctc tttagcggag
   100021 gagaatagtt tcgagtgagt gtgctcccga accaacgatt tgtatactct ttgccccagg
   100081 taccaatacc catgtcttcc tgcttctttt gattctctta ctcttcaaaa ataaaagcaa
   100141 agcacaccgc taaacaaaaa gctggtatta ccaaccttct cagaggttag gcgattcatt
   100201 gagtcgatca gtcatctttt tcccaagaca actttattgt gtgtaggcgc acaaaggaag
   100261 atcgtaaaat caggattact cgtccacttt catcgccttt tgttgatccg tgtcatcctt
   100321 gctgcttcat ccaattattc tttattcctc ctctcacttg ggcgaaacac tagaaacggc
   100381 cattaattta cggatcggtt atacaaggag catacctact aatacttcgg cgtgtgctgc
   100441 attcgagtgg ttaacagcat acatctattc ccaaatcccc aacggagata gatagtatcc
   100501 ttctgtgcta tcccctatat cctcgtagta gggttgaggg cagcgaagtc tcccgtttat
   100561 cctgtctcct tcctcttggt tagtgcgtac tacttccaac gtatcttata tagagacatt
   100621 ggaggagcct gatcttccat ctacgcagaa gagatgcttg agttcttcca tccgcgaagg
   100681 cggtgtgctc aaataagtta gtttgttacg agactatcag gtccaccagg ataattcgag
   100741 gtggatagcc ctgactgaca ggggactaag attaggaagc atccacaaga gcgaaagagc
   100801 ccttttatgt ttgtttcgct aatcttatag attggaagtt tgcccagcac agagtagtag
   100861 ggttatgctt tcgaaagtct tttcggagta taagggaggt ccatctttag agatctgaat
   100921 gaaagttctg agcttaatgg attcccggaa ccccaggact ttagagagtc ccaaccctaa
   100981 gaaggcttgc tcgggttgaa agatgtgatg cagcacagac agaggtgcga tagtaagtca
   101041 attgatcagg agaggtggta gcttctggtc tctcaagctg acaatggtag tctagataga
   101101 tataaagttc tatgctgttt gcttgctcaa ggctagaagc aggagtctgt tattgatagc
   101161 tcccgttgcc attggctgtt ccgcccgtgg tctttcagat agacgttcaa aataaaattc
   101221 ttttcatcct ctcctcctgg ctaccagtat atggagatgg tttgattctg agagttgagg
   101281 aacaccaagc aagatttgat tgacatcatc tacggctttg cgccaatatg aattatgaat
   101341 ataggttaag tgaaatctga caaccagcac actgcttgat ctcattagca gctccggcga
   101401 agcagcacag accaaggtaa gcacaggata ggcagtatct ttatgaagtc tcgtaaggct
   101461 cagatcttta atagaagtaa acttcaggtc tttgttctaa taaatagcca tcttcgtcct
   101521 caatggcaag aaagaaaggc tgctaggagt aagtgggaag tgccagggta aagcccctga
   101581 tggatcgatc aacggattct gcaatttcat ctctttcata agcgattaat tcttgtttag
   101641 ccttagttgg gatttggact cagaagccga acacagttct tagatcgatt aaaagcctgc
   101701 cgcttatcga cactcttttt ctaaggatct taggcagcgg ttgaagttac cagggatgga
   101761 accataggtg ctttagcaac agcaactcga ctattagaac atgcgtacgt gaggagcaac
   101821 tcgagtgaag aagcaagtta tggtgtattg tccaatgtgc cccgcttttc tccatgctga
   101881 ggactattcg acttgtgagt cagattccga tttagtggag gaacttcctt tgaaggcacc
   101941 cgagagccta tataagatta ccaatttcct cagctagatg atcaaagtct tggatgcagg
   102001 atggctccaa tctgacagat gtggcaccaa aacctaaaga ttcctttact agggtttggt
   102061 ggaatgatag cccaaagaag atttttggtg tagaaagtct caaattcagg atcttccgct
   102121 gtacggattt cctgggaaac gaagtcatag gcacgtaggt tcagagccag accgatcact
   102181 cacaatatcc ctgggcaagc caaagatttt gaccacatgc ttaaggaaca actccgcagc
   102241 atcatggacg gtgcatgcat gttgcgctgc tatgaacaca gcatacttag aaaagcgatc
   102301 caccactacc atcacggacc taatcttttt aggaatggaa cccacaaaca aggtcttgaa
   102361 gagccttgtg ttacctaact aaagagctcc caaggccacc tgattcggag tagagcactc
   102421 ctatttacac ttcgattccg cccactgatt cagatccagc taagccccgc aaccaaagag
   102481 gagacacttg caccggggta atgctaccac acaggttttg aggcgaggcg ctgccctctt
   102541 tcgggcaatc aactctttct tgtacctggc actagtcaaa ttgtatctcg gttcatggca
   102601 tgccacaacg actctatcgg cttatagtca ttcctggcac tcggcgcatg tctttgatca
   102661 accccggttc cgtcactcgt atctggttga accagtactt cctttccgcc gttcctaggg
   102721 accacccact cccgttccat gagtgatccg agacagtacg cggagattaa tcggtctctt
   102781 ttggttctca ttccaaaagt tgagcagcct gttagcataa aaatgcaatt acctccttct
   102841 tatcgttctg ggtacgggcc tagtcctgag tgcgctgtct gtcttctcgg ctggcccaaa
   102901 caacgggatt ggtcctgtgg gattagcacc aaaattcctc ggcatctcat cctcctgttg
   102961 ctggtcattt cctaaaggat cgaaggttca gccgacgcct caaagtggat ttgttgtgcg
   103021 aagggtgcga ccgggattta gagttagaat agcggggaag acttgacctc aggcagcgtg
   103081 aaaccagttt atttcattcg atgtagtggt ccgattgcct agtggaagcc ctgaggcact
   103141 tgattcttgc gtacgctcgg ctcctctacc aatcaccaca gcgcgagatg cgcaagagtg
   103201 acccatctct ccacaccaac tggaccatac aatacactct ttataagaaa aaaagatttg
   103261 gaaccgaaag ataggaaata aatttacttc cagagcggaa gggaatactt aaccacgcct
   103321 cgagtcccag tctcctagtg gtgagatggt aaagggcaat gtccggttct ggccaagaga
   103381 tgtctttgct ccgtccccct tcttgttggt tggcacaagc ccttgtagta gtaagtcttt
   103441 cctccggccg gatcggatgt tagagtcaat tccattgtag gtttgaccat taagtgaatg
   103501 caaatatagg tagaatttga atcaacgacc taagagtctt cttttgccta tcgtagttac
   103561 cttgatgtga taaatggtcc aactttcttg aaagatatca gatctttaaa gtcctgctca
   103621 tatacatact aatatgatcg ctaccaggtc atcccactac acaccatcaa gcaaccacta
   103681 ctgaagctat caactcaatt ctctcgttcg aatggggaga tagataaaag aaacgaaact
   103741 ctataaaata tcataagaga agaagatttt aattccagct taaataagta agacttgact
   103801 ctttaaaaaa ttccgatcaa caacttggag ggatggctga gtggcttaag gcattggttt
   103861 gctaaatcga catacaagaa gattgtatca tgggttcgaa tcccatttcc tccggcgcgg
   103921 aagtgaaacg ggcgggcgaa atgagaagag cactacttag tgactaggag cggggagccc
   103981 gttgcgcgtt tttttgtttg accggcctat cttcataagt aagctcccta tggccgtcca
   104041 gtccctgggc ggctctcggt tcttgagcat gttgggagat tagtcgtcaa ttgaaagagc
   104101 tgctctaaag cttgacgaag aagttttccc tattaattag attagtaaag ggcttttccc
   104161 ttactagtca agtggtaagg tagggcgctc ttcgatgaag aaaagaagag acttttggaa
   104221 aagtggttca gctcagctgg ttagagcaaa ggactgtaaa tccttgtgtc agtggttcga
   104281 atccacaacc acttctattc tcggagctga ggtatatgaa gaatggcctt ttggtccttt
   104341 ggacacgtag ccgagagcga gccggatttt taaaattcaa gtgaaagaag gaagaaggca
   104401 aaaagccgta tagtgcagga ggcagatgaa aaaaaaaaag caattacagt gagacgcgag
   104461 gtgtagcgca gtctggtcag cgcatctgtt ttgggtacag agggccatag gttcgaatcc
   104521 tgtcaccttg attaatgtct ttttttttgg aacctttgtt ttggagtttt cccaaaccta
   104581 taccttactc atcttactaa gaaaatgggg cttatgtttt tcagccgcat cgcactgctg
   104641 cataaacaat agatccgctg ggctggatga gcaaccttct atctggcctc tgtactagta
   104701 gtagagttgc ttgctacttt caatcataaa acgaaaattg agcaaggcaa gggagaaaga
   104761 agttgtcccc tcctctctgg taacccgccg ccggtcatat agagcgtccg cccgccccag
   104821 catatgtata aaaaagagga agaaagaaca accgttttac tttggcacat gaggtggcgg
   104881 gtttggctag gtaacataat ggaaatgtat cggactgcaa atcctgtaat gacggttcga
   104941 ctccgtcctt ggcctacacc ttcatgacca gaaataactg gaacaaaggg aaagcccact
   105001 caactagtaa catacggaca caaacaacaa aactacttgt tacaaataac atcttgttgt
   105061 tgcatcgaaa catataaatg tttactaatc tggctaacat tgaacttggt aaaattaaat
   105121 ggttgaataa tttaaaaatt agattattcg ggaatacaca ttgaatgcga agattacgca
   105181 tttcatttct ggtagtagat ccataatcaa aaaagtgttt gtgattgttc cagaagaaga
   105241 aatgaaacaa aagatacggt agagctagga cagttattgt atgaggtcta cccaatgcta
   105301 aatgcagagg cgcataatag atcgatatga acatcatgag ctgtcccgca ataaaacctg
   105361 ttgttgctga tactttcttc tcggttcctt cttctccttc gtccataacc cgagctcgga
   105421 gaaggaagag ataagagggc cctatggaga atgtggtcag aaatccataa tagagtccga
   105481 ccacaacgac cgaattgatt atcttcatgc ataagtatac tagattacct agtataaaag
   105541 attgaaaaac catcacaaac ctcccctttt tcttttctat ttctggatta ttatatgatg
   105601 attttgcaac tttccatata tagaaataga aagagataga ctagaaacga catctcttat
   105661 gtcaatgaca ccaaagggat attaaatgaa tggaattggg atatggatag aatataatga
   105721 aataaataga gccgctttga ggttccctat gaaatgaggc atggaacgga gccactacga
   105781 agaagttccg ggggttacga aggaaacttc gagttcatat tggtcatgtg ggttgagaac
   105841 gggaattgaa ctctataaga tctaatctcc cgttgttcct cagtagctca gtggtagagc
   105901 ggtcggctgt taactgattg gtcgtaggtt caaatcctac ttggggagat ttgttagtta
   105961 tcgcttttct gacctaacgg cccctgtcct tctcctttgt ttctaaacta gctgaatcgt
   106021 gtcaaaagtg gaaagttgat tgttggtttt gattcctcac tctcgtatag gtgaacttgg
   106081 ttcgttaaat tcttaggaag aaaagaagga tcaactggga atgaatggga agactggagt
   106141 agtatctctt cattagtcgg aaggaatttg tctccactag cctcattcga aaaagaacag
   106201 aatccgaaca aacaagaaaa gggtttaggt aggatagtgc gatgtagtcc aatggctaaa
   106261 gctctgccag cttcttgtag actgaactct ctttaggctc ctagtggttt tcgggtggga
   106321 tggttgaaat tttattcgcc actagtggca acgaagttct tggtaatttt aaagggggaa
   106381 ggcttgcaga ccactcattt cattcattca gtgcctgcgg tgaggcgcga cccacaacaa
   106441 aaacaaaggg ggaaagcttg cttactgtag ccctctttta gtagactagg cttggtaagc
   106501 gtaactattt taagtaggct cgagaagggt agggctcgca gcttcgccgg aagcgacgaa
   106561 ggggggctgg ggaaggccga cgactacatg agggggaagc tgtcgtagaa gctttgtccc
   106621 ttgctttaca gagattgtta tgaattgact aaatgactag gattctcccg gaacgctagc
   106681 taagctaaga aatagtatta gttcccttca atcaaatcaa taagtttatt ttttttattg
   106741 attcagggaa aaaacctcct tcttagaacc cattgagggg gcctcggccc gggaagggga
   106801 gagtggccga gtggtcaaaa gcggcagact gtaaatctgt tgaagttttt ctacgtaggt
   106861 tcgaatcctg cctctcccac ttgttgtagt tttagcttgt atatgtgaaa aaacgagatt
   106921 tctttcatag aataactctt tcacataaga aagtggaggc aggcttgggg gtacgactaa
   106981 aatgattcca catgaaaagg gaccggcaat ccccctcttt tttaatgaag aagcgggcta
   107041 gtccccggga atgcccgtta atcaagcaag ttggggaaaa aatcttacct attagacgga
   107101 acacgaagag gtgaactgcc ggaacaggag gacttaaagc tgaggaaaca ggaagggcag
   107161 ctaagggaac ttgcttcggt aggagtgtgc tgaagttggc ttcaaacaaa gagaaagaaa
   107221 gtagtgtgct gaaggaaaga agaaagagag aaggttaaga agaggatact ggcttcgtaa
   107281 gtaaagtatc tgaagatgag atagatcgga gaggtgagtt accagcgaaa ctattcactc
   107341 tgatgtccat ttcctgcctt ttctttgtgc cgatagagga tttaatatgt agattccttt
   107401 ccttattccc tttctggtaa ccataacacg tccctgcttt tttctgtcgt tgactgctag
   107461 agcaagaggg gacgaccttt cctaccttat gatagactga actgctacgg cggctttagc
   107521 tctactatgg cagaaggaat cgccaacttt catttcatat agctgtaaaa gttagcaacc
   107581 ccatttctaa gggaaagagc aatctttttt tgaaaagttt catctacagt caaaagaaag
   107641 caaacctcgg cagcacagaa gagagctact actattattg catgcgtgct cacgtgtaag
   107701 agtgtgctaa ataaggaaac ttcggtctaa tcctcgggtg tgctatcaca aggaactcgt
   107761 ccggtgtagg attgtagatt acctgtccta ttcagcacac tcctccatta cagcacagag
   107821 gattagctcg ggttaggaaa acaagtagct ggtcaaagct atcggaaaag cagaggagtg
   107881 tgctgacttc aagcagtagc tagtcaacca acttctgctc aaccctagga acaaggaaag
   107941 tatcagccga taactctgtt cacttggtgt gggattccta aaagtgtact attatcgcac
   108001 gccaaagagt gtgctgaaaa gggaatagtt ggttaactac cgaagctaga aacaaatacc
   108061 tgctaaaacc aagggaagca agagtaggaa ctacccaccc aggaatcagc attctaaact
   108121 gcagcacaag cacaccagcg tgtatcaggg gtgtgctata aaagatcaca gctaaggttg
   108181 agtccttacc ttcttattcc ttccgtagtt agcagaacat actagcctgg cttatccatt
   108241 cctcgtattt gaggaaagta gggtttgaca tcccattctc ggatgcacga attatgcgtt
   108301 taatcccacg caacaaactc ctctgtgctg ggttgtgatc ttaaaaagga gctttactgt
   108361 atagtgttac agtaggaata cctactagat cgaggattcg gaacagtact atcctgttta
   108421 tattgacatt cttctgttaa gatttcccgt ttgagaaacc ctttaagatc tgagtatctc
   108481 ggaattgaaa ataggacttt atttgcatcc cttccatttc ataggaatac agctaaggat
   108541 accatcagct cgcatactat ttacgggaaa cagaagtagg gcaaagagga aaagagcaac
   108601 tccctctatt agaacaatat tctcgaatcg ttgccctttt attcatgaag aaagaaaaca
   108661 catcggtcta tctaaagcaa caaaattcgt tctatctttc tttctctcct attaataaaa
   108721 ctggacttct cctctgctcc tatcttagcg cgacggagaa gccagcactg agagaagacc
   108781 tccctttcaa agtccatcgc ctgcacttga accggatacc tactatttat tttattgaac
   108841 tagacgatca gcggactttt atatcatatc accaacaacg ggtttcgccc acagtacaga
   108901 gatgatctca atcgcatcgg cataaaggtc cggattccaa ctttcaaaaa ggatttacgc
   108961 gcgaattcaa ctatagacaa aggtccggat tccacttcaa aaggatttac gcgcgaattc
   109021 aactatagac atatctcttt ggcgacccag ggacggggat tcatcaatcc cggggttcga
   109081 gggagacttt agaaccccta tatatgagtc tcgaaaccat tatttataca tttctcgatg
   109141 acagagatca tctttaagga gaataaacat tggtccttta tttaataacc ccgatattat
   109201 caaaaccatg atttccttat ttctcgatgg cataggttcc agggaaggaa aacagtccgg
   109261 tcctttttca ccccgaaatt cgagagtagc cgtataaacc aataccggca gaaccaccca
   109321 aactcggctc aaagcaggaa caaagacatc tagaaagccc acatcacgtg gggacttggc
   109381 cttggtggga cattcaaccg acatacacaa ccaaataata ataggtttta gccatgtatt
   109441 ccgctacacc gccctattga tctacgcttt cgaagcaacc accggtacca ttttcacaca
   109501 acagagccga cttacttatt acatttatag gacagggaac ccgtctcggt aggacttcca
   109561 aatcctacct caagcaaccg acatctcttt acttacttga ccgctagcca ggggcttgaa
   109621 accccttaca accttccttg cttgccgggc ttacatcgct atcatcgcta gccagggact
   109681 ggaaatccct tacaatcaca tgcctgcgct cgtcgtgcct ttaatactta tttattaacc
   109741 aaaccctcct tggccccaat tggtctaaga ctcaccaaca tcttacgatg agacatcggg
   109801 ctacctggca agagtcaata aattggtgaa cctatgagag acgcttctaa ttcttttctt
   109861 tctcctgaca ctcactatcc tacccgatcc tgctaacagg aaatttgatg aaataaggaa
   109921 acttaggctg ttgttgaatc aacttagaat acaaccggta cccacgtcgc aactaaagca
   109981 ctcgtagcat acgttccatc cacatccggc cagttgaagt gaagatcgag aaaatgttct
   110041 tcaaagcttg ctaataacca aaaaagaatt ggactagtgt aagggacttc cttttcaagc
   110101 tagcatttta gaccaatgca atcgagtgaa agtgcttcct atcatttgtc tgcttgaaac
   110161 cttgcattga gtgtgcacct tgggaatact tgagtttgga ggtcttcaag cctttctatg
   110221 ggaaaggttt ccaatacgta ttcttgccgt tgttcgagct taaaagcgga tgatgatcct
   110281 aatcaagagt ttggtctagc ttttcgattc atttgagtct gtcctcgcaa agatatgaag
   110341 ggcgctttca ggacggatac ggatacaggt gacccctttt tcccctttgc tttctttatt
   110401 acttctcgta cgtgcccagt ctcaacgtca cttccaaaac cgcctttccc agatctatga
   110461 aaggtgaaag gttgaaggtc cacaaaaggt aacataaatg aacaagttta ttttgtattc
   110521 gagctgctga gggccggagc tcgtatggat acattacttc attgttctat gaggccttgc
   110581 acaaagccca tactcggata aggatcgcga agtgcaaaga tccggtcttt gacaacccaa
   110641 ccgtcgtaag gacaacaaaa cctatactta tgtgtgttcg acactatagg cgagaccagt
   110701 tgtcagatga tcgccgagtg gcgttctgct tgattaggcg aatgcgagtg aggtatctaa
   110761 tcccgttcgc taggagggaa actcaggaag agttcgggca gaaatagatg gtgaaaagcc
   110821 ctttatatta tataataaag cgcgctcctt gcatgactcc atatcattca ttattaaagc
   110881 gaaagcacaa cgtgtcaccc taaccttcaa atcgataaac gggaatgcgt tacctaataa
   110941 taatgagcaa tgctgctaag agcaaatggt tcctaacctc ataaaaaaag agatagtcat
   111001 atccgactat ccggcaacac gcttggataa gtaaggcgat gaaccgtacc tttatctcta
   111061 ggcgcctatg atgtcttatt atgtagatca tgtcttgctt gagagttcca aacctcgccc
   111121 ttctaaaaaa gtacaaaccc acgtctaggg atatacgagc gccattcttc agatggatcg
   111181 ctcttcgata gttatttatt gtagccggga taagcagggg ttcctccttc cgtcctagtt
   111241 tttttttagt acaagtagct aagggggctg ggttgcgtct ttcttgtgaa agaatacttc
   111301 tgcgcacctg ctgaaaggaa gtcaaacgga gattaccggt tccggaggga ccaaccattg
   111361 tacttatagg gtcaggtcta tcttgccctt ccaaatcacc catgtgtagc tccaccgcac
   111421 gagtcagacc ttgtacgggc ttttccacag gcttgaggca gactctttcc ttattgggct
   111481 tcaatccgtt tgtctttgcc tcctctactg agtcagtgac agaagtgcag cagccaataa
   111541 tacgtatata agaagaggac tgcttacggg atcaaactat caatctcata agagaagaaa
   111601 tctctatgcc ccctttttct tggttttctc ccatgctttt gttggtcaac aaccaaccac
   111661 aactttctat agttcttcac tactcctaga ggcttgacgg agtgaagctg tctggaggga
   111721 atcattttgt tgaaatcaat taatccaata tgcgacgaat ctttttgttt gatgaaaata
   111781 gtcttaattc aagttccacc attgatacat cttctgcttc caccattgat acatcttttg
   111841 cgagtcaatg cactaacttt tctagtggtc aagcgtccgg tactcaggat actcatgctg
   111901 gtatttttga ggattgtccg ggccttaatc ctaacgatga gcgtgtagta gagctgcaat
   111961 gtgagatacg cgagaagtgt gaggcattaa cgcaagatcc cgaaatgggc ttgattttgg
   112021 gcgaagcttt acatgcggaa agcgacaatg tccctttttt gcagtccatt gctgatgatt
   112081 taacccaaaa cggagtatcc ggggaagcct ttcaagaagc tctgaatata gtgggacagg
   112141 cggcggcctc cccactggac caatttgaga ttgtcccatt gattcctatg catatcggaa
   112201 acttctattt ctcattcaca aatccatctt tgttcatgct gctaactctg agttttttcc
   112261 tacttctgat tcattttgtt actaaaaagg gaggaggaaa cttagtccca aatgcttggc
   112321 aatccttggt agagcttctt tatgatttcg tgctgaacct ggtaaaggaa caaataggtg
   112381 gtctttccgg gaatgtgaaa caaatgtttt tcccttgcat cttggtcact tttctttttt
   112441 tgttattttg taatcttcag ggtatgatac cttatagctt cacagtgaca agtcattttc
   112501 tcattacttt ggctctctca ttttcgattt ttattggcat tactatagtg ggatttcaaa
   112561 gacatgggct tcattttttc agctttttat tacccgcagg agtcccactg ccgttagcac
   112621 cttttttagt actccttgag ctaatttctt attgttttcg cgcattaagc ttaggaatac
   112681 gtttatttgc taatatgatg gccggtcata gtttagtaaa gattttaagt gggttcgctt
   112741 ggactatgct atgtatgaat gatattttct attttatagg ggctcttggt cctttattta
   112801 tagttcttgc attaaccggt ctggaattag gtgtagctat attacaagct tatgttttta
   112861 cgatcttaat ctgtatttac ttgaatgatg ctataaatct ccattaaagt tcttctttct
   112921 tttatttata tttataattg aacaaaagcg agggatggat gtctgagcgg ttgaaagagt
   112981 cggtcttgaa aaccgaagta tttctaggaa taccgggggt tcgaatccct ctccatccgc
   113041 gaagtcataa gttctctctt gccgcctgat aagaacgaat cggatcgact cgactgatat
   113101 gatagatgga atgggtacct tgtgttatga ttttgttagg aactttgtct ccctttcgtt
   113161 atcttctctt tttttcttgg tcggcaaggg ttagggcctt tctcgctggg cgagcgcatc
   113221 cgattagtcc tttcctaagc cacttcccgt tcagttgctg aaaaaaaaat ggggataagc
   113281 tatgcgacga cagagaaatc tgaatctact ttttgccagt tccacgaatt ctgcagataa
   113341 cgacgttctg ccaggagtgc cagttctgga catgtttcct aatatatcag tagacaccat
   113401 aattaaccac cccttctact gttcgggtac agtagctctc gcagaagaat tggtggatcc
   113461 tattattatg gagaggtgga tagataggac gactagttgc tcgatcagga ccttagcttt
   113521 attgcgagcc tagaagtctc tcttttttcg gaacagcctt taagtaaaat ccaacctaat
   113581 atcattcaga gtaaaaggac tacggaacca aagagaacca cacttgcttc gctaggaatg
   113641 aagcagcaca ccaatgggca aagggtatgg gcgacctatc tgctgcgcta gagaaagaaa
   113701 gaaagtgctt cgggctgctt tgctgcgcta gaggaaggag actgataagg agaggagtga
   113761 tccaagctca actcgatact ccactcatct ttctcgattc tattgacata atttggtttc
   113821 ttctatatta gtgaaatcat tacatgacag tggatcttgc ttggtacttg tccgagggga
   113881 gatccatact caactcatct ttctcaattc tactgacatg attacttgga attgattgtc
   113941 gtgaactcaa tctctcatat aggcatagtt gaatatcgcg aagcaaaaac ccaaacttga
   114001 atatcgcgaa gcaaaaggct acatcagacg atgtacaagt ttttcaaaaa tgatttgatc
   114061 gattggtgtg tttcgatctt gttgattcac taggtaaatc acagcctcat ccttctatat
   114121 tacctgttga tcgatcaaaa aaagcacctt acctcggatc aagaaaaaag aagaaaccga
   114181 atctcggaaa acgacaaatc acacagttga acaaggtggg agtagctcgt gtgatctagt
   114241 cgaaggtcca taggaaactg ataaggagag gggtcttcca tctcactatt ctagattcta
   114301 ccgaattagt tggaattgaa ttcgtccaag attaaatgcc agttgaatgt cgactagtgt
   114361 tgaaggtcca agctgtactc gactcataat tttgcttttc tataccttac tcgtgaaatc
   114421 gatgatgatt acatgacagt ttaatgtcgc cttattgctt gatccttatc ttgtatccaa
   114481 accatactca actcagaatc tactgacgat cgaccaccaa ctcatgatta caaaaaccct
   114541 ctcttcgaaa acccaataat cataaaccaa ctcgtcgact ttggttgatc cttcacttgg
   114601 ccaaaggtcc tagccgtact tccctccact cataatcacc aactctatca aatttttaga
   114661 attgaaatgt ttgactatta caaaagtaca ttttccatag agtgcaggaa ccccatcccc
   114721 tcacccctca tcatctagca cacccttggg gttcacatac ggttttaaaa agcgaagcaa
   114781 ctcttcatac tcatggcgaa gcacgcaaca agccgaaccc tcaatcccag tgaggactac
   114841 tccgttgggg gttacttcgc aaggacgccg catgtgcagt tcctcagtct tccttctcct
   114901 ccatatgaag atttatccca tacggtgcta gcgaagcaag tcttccgagt tcatactgca
   114961 tctcgaacga aggtcactca cagttccgaa ggtcactacg gtttccgagt cttattgttc
   115021 ttcttcttcc acgtatgaca gataccctca accctcaggc ccacgggggg ttgctacgcc
   115081 cagggctact ccgttggccc tgaagggtta cttcgttagg gctacttgga ggagttgacc
   115141 aacccgaaca tggtgccttg atcttcagct ttccaataag aagatcattg atgcagcaca
   115201 ctgagctaaa ttcttaaact atctttaccg gtgtgctgcc tcgcagagat tctcaaccta
   115261 gtccgcgcat actctttccg tttctgtctt acagtctttc ttgttcttct tttccctata
   115321 gttagaagat gagcccctgg ggtgccctgc ccttctttta cggctgatgg acattcaata
   115381 gatttatctg ctgttgcctg atctacgacc ccctcaatct gtcgaagcaa atgctgcaca
   115441 gagggagaag ttgcctgacc gggctattcc cttgttatct gttatccaac tggttgaata
   115501 gtaatctgtg ctggatccct ctgaagctgg tcattccttg tttccagtta atagtggagt
   115561 cttacttact tgaattccta ttactgttag ctattagcac ttgcttgtta ggtgaggact
   115621 ctcttatctg gttaacctta gtggtagcac actccaagtc tagacaatct tcctcccaag
   115681 aacctctcga taccagaatg gctaccaggg cgctactaga ccaactcaga tcagatcgtc
   115741 ggcataatta attcttttta cttgcccagt agtggtctct gaagtttact actagtggta
   115801 gtgcagaaga cctctttacc tacccggcta ctgacaggaa aggatgattt tagattcttt
   115861 gcttgcccat acgccgatcc tgttagctga ctggtactac gaagatctat gccattcaaa
   115921 ggagagatat gaatacacca actacagaca agaaagagac tctaagtcca acccatgtcg
   115981 tgggcaggga gagacaggca ggcagctaac acagatatca gatattagac ttggcaacag
   116041 acgctttgat atgtgttaca cagacgccct gtagacattg aatcggctca ctccgacttc
   116101 gattgctaaa atgttgacgt gaatagtgaa tacgcttgct ggttgtgata tgttccctac
   116161 tatactacta ttgaagacct tgacttttga tcttccttct aggagaattc atcaaacctt
   116221 gcttatcctt ctgatgagca ttcctctaac taagttagac tgcctcttac gagcaggtaa
   116281 cctaccttct aaaccatgcc cactatactt tcttctaagc cagcttttaa ctctttgttt
   116341 tcgtatcatc tcattggact tatttcaaac aaactcgtta cactcgcacc tgattacacg
   116401 ggaacgaaga aaactacatg gggagcacgc ttacacctgc aagaactaag ggtccagacc
   116461 aagcacagac agatagaacc agacatcaaa aatcttcctt tgcagcctat cagatatgga
   116521 agttttcgac ctgtctttca ctggattgaa aagccttgta tgttgatagg actatgtggg
   116581 ctgcattctg aagtttcttt catcgcaaac tggccatggg gtaaaccctc tgagataggg
   116641 ggctgctcaa tcccatgtat gttgacaggg agagggagcg aactttctta tcatatcaga
   116701 gcaagccgaa gacctcttcc gggaaatcgg ttccacttcc aatctttttt ttgaagaaag
   116761 aaaagtagca agagaatggt tcaagttcgg atcgagtaac ggtgattgaa gggatgagat
   116821 cggaagctcc tgattcaaat agttaactgg gctgtggttg tcgagtctgc tttccctctc
   116881 tatcaaagcc cttgcacctg ccttctcagt tcctcgtgct tagcgggact ccttttctaa
   116941 ttagaaggag acagattagg tcaagttgct ccaggtatga aatcaatccc atgttggtcg
   117001 taagagtggc aagccatgag gtaggtctta tggaaataaa taagcatctt cctcaagcaa
   117061 ctccttcatc tgtggcggct gctcctccaa gacaactgcc cagcataact aaactcttat
   117121 ctttgacttg actctctttt gttctatgcc ccttaggtag gagtcagatc tgttttgtag
   117181 cttgtttcac ccttctttgt agcttgccgt ttggtgtgtt catccccgcc ctccctgaac
   117241 ggagctgttg ctaaagcata actaatatct tagctgtttg gaacgtatag ctacccggtt
   117301 cttcctttct ttagcggagg cgtaggtaac atatctatct atgagttgct gagaacgtct
   117361 ccaaagcata aggagttgtt cttcaatttc aaccaagaag cacaggttcc cgcaaccctg
   117421 acgccagaag agttgcaaga cgtggtctgg tcgaacagat tacgaccgct gacctttaca
   117481 gatcaattat tttccatctt gaaagaacag ccggaaggta tgaagctcta gtccttcttt
   117541 ctagccgtaa atcaagaact cgaaaggttt attactttgt ttaatcgctt gactagcttc
   117601 gaaagagcaa tctcctcttc tagtcttacc acaaatcaat gctttcaaga aagtgctcag
   117661 ttcctgacaa catggttccc ggtcgcgcat ccccatggag gtggatattt cacacattgg
   117721 ggtcatcagc cgtcgaacac agtcaagtta gcaaagattc gtacgaagga aaagaagaaa
   117781 gatagatggt ttctaatggg aaggtagcag ctgtcatcat tatgatgatt caatccatat
   117841 taatccctat ttcagaacta tgtattagtt agacgacgtc aacggaacaa gaactccttc
   117901 ctttacaggc aagcggggta gctgctgtct cgtttaggaa cttgagttag tcgactaaga
   117961 ggtagaaagt ggaaagaagc ggcctaaagg attagcgacg acccctctcg gcttaaagta
   118021 aaggaagcgg cttgtcccat ccaatgccct acttttaagt actcggtatg ttcactcaat
   118081 cagaagaagc tttcggaagt tcattggcct ctgcggagca tgaaaaggcc tgttttgaag
   118141 ctccggggac ttattagccc gtcagcctta cttcttagga agaagagaaa tgtgcttgac
   118201 ttcttcatct tataagatga cggcaacatc ctagataaga tctacgattc ctgcttatga
   118261 atcatggcaa accggtggtg aaaacagtat tacagagtag gttggttaaa ttaaagcggg
   118321 ttactttgat cttatcgtct agccgggcat gagagcccaa taaaaaagga ccgacgacga
   118381 tccgagaagg acgaatcaat aaatcgactt cctttagagc agacagacta cgcgctaaca
   118441 gctttagaaa ctttgctata ctaacaaagc aagcatagca aagtcaaagt ttgagttaga
   118501 ccgggtatga ggcaaagcca aaggcagaag tggtttatcc aggtcggttg aatccccgaa
   118561 ataagcacca attgctaccg tccaatcgct atcattatca tggttggagc atagatagca
   118621 aaggtatggt tagaggtcaa atacacatat ctaccaggta ggtgaaacga attccatacc
   118681 catatcgggt aatgggcctc caattacttc agcctaaaac gaagtctgag gtcgggcctt
   118741 cctggacctg ccttaaaccc tccatcttcc tgtcaacggg actcctctct ctctgaggag
   118801 gtccgtagag tctcactagg gatctccgtt ctcagtgagc gagaatcggt atggtcagag
   118861 tactgaggcc tggtcaaagc atctcagcct ttcttttgta gtaagccgct cgtatcgctc
   118921 ctctagttta gttaattaag ctagcttagt ttctcgattg aaagacaggc ttacctcccc
   118981 ttcatccctt gcttctttga aagtgctttc ctgagagtgt cggcagagtg cattggtcac
   119041 agacgtccgc acaccaaaag cctcgtatgc agatcctagt gccaccatct ctgctgaaga
   119101 tgatgccttc tccatggcac ctgggaacta gtaccatcat ctcctcatca tcagagagtt
   119161 gtgggtctta tcgggttaag gggatccctg atggcagtgt tgagcggtac aaggctcgcc
   119221 tcgttgccca tcagcggcct gggagagagt cttttgatag attaagccct gtggttaagc
   119281 ctatcactat tcgtctgaga gtcttactct ataccatggc tggactcttc gtcaattgga
   119341 tgtctttcta cagggtcact taaccgaaaa gagtcatgtc tcaacctccc ggtcgatact
   119401 cttcttctct ttgcaggttt cgaaaagcta tggtcttaaa caggctcctc ctggtatagt
   119461 gatctgatag ctgctcccag tccgacacct cttcatttat catcagaatg gaatggaatg
   119521 aaagccaagc atctactagc cgcctagcca gtaaggggga acgctcctgc ttagtacaac
   119581 cagaaagaaa gaatgcagag taaggccggg aataggcttc gtaagaggac tgtttgaggt
   119641 actctggaag gacagttaca cccatgccag cggaagactt aggataagcg gtcactacca
   119701 tcttattact atgggctaag cagatactat caccttaata gcagcaaaga gcaatagtcc
   119761 ttggactcga ggaaggatag aacagaagtc gtacgtacaa ttaagatgaa tcgatgatta
   119821 ttccccttcg atgaactata tcttacctgc ggcttatagc ctatctaggt gaccgactac
   119881 tgagctatct accttctctt tgctcttaga agttcttctt gttataacat taatggagaa
   119941 gacaagttat tgtacgttag ttgaaatata gatagaaata caaacctttt cctgttctgt
   120001 cctaggactt tctaacattt gaagcttacc gggatttgct cttccctacc tatgataaag
   120061 gctgagaggg gacttcagca gtataatttc attccgcttt ggacacgcaa caaaaagtga
   120121 gggaggggca aatatttcac cgaaaggtgg gagggggggc caatatcctg cagcccagct
   120181 ggatcttccc atcattgatc gactaaagag aaagtcggcg gatatattgg ttcgaatcca
   120241 attaatgatt acaatttaga aggacttcat tcaatcgatg tttaggatgg aacagactag
   120301 tcgttcagta gtcttacaga gcggttactc aatggtacag tacagacgtc tttgatcctt
   120361 cttggtacgg gagttgaggt tgaataagtc gttcagatag ccatacagac agacagaatc
   120421 taatcttttg tgaaagaaaa aaggggatag ggagctggca atgtcggaga tcctacctca
   120481 gaatctttct atttagaagt tagggataga aggtgagtac caactcgaaa agtatactca
   120541 catccccatg tctttagcca accgtcttga ttgaatagat ttcctgatgt ctagttttcc
   120601 tactgtggaa atcctattta gagtagactc acttcaatga aagctattac ttagtgggtc
   120661 aaaaagattt actttcaaac gtcagcatct tatcctatta gggaaatagg ctaaactatt
   120721 ggtgtgtaac ggaagaaggg gaagaaaata aatgatccta gctgtcgaat gcagcttgat
   120781 cttaatcaga ggaatgaagg tctttgaatc gcttatctct cagattgaac tgaccgggga
   120841 gtacctgagc tctttctctg tttaaatctg tattccttag ttctgttatt agctgttagg
   120901 tgggggaagt ataattccct aaggtaagtt cttctgatct catatgtatg tatactcagg
   120961 ttctactggg attctcgaaa gagctccttt tgttcttctc tttggtttgg agtgagagga
   121021 agtatcggaa ggtgccttgt tcagcacact cctctgcttt gctttgcttt tccgagacca
   121081 gctatttgcg atcgaagttg aatagttcct atgaagatgc gtaatcccat tccgttgtcg
   121141 tccttcttct tcttgcattt attttaattg taaactgagc ttgtcgatca aactgtggct
   121201 taggtcggac cgttccctaa attattcact tcctcacaac cgagcccttc gagtctttgt
   121261 cctgaaacag ttccttcttc gcatctctca agtgagaagg atttggtctc atcttcttcc
   121321 ttcttccttt tagtcgagac tcttcctctc cttttagtcg agactcttcc tctcctttta
   121381 gtcgagactc ttcctggaaa gcctaaaccc tcactcttcc aagcggacat caatcccgga
   121441 atagtgtaag taagaagaag accggttagg atcacactag tcctggctgg cctataactt
   121501 ctcagaaaca aaaagaggct tgcaggtcta gtcgcatacc cctatcgtct tattgttcta
   121561 ttcgttgcag tggtaaactc attgaatact caaatatggt ttagtcacac ccttagtgta
   121621 cattctgatt caatagcaaa cagagcattc ctttgcttcc tgattccatc cctgaaacaa
   121681 ttctatcggc gaatcgagga ctctcccaca gctttgctta ttcgtgcaag atccagcatt
   121741 ccttcactta tcatatagat aacgatcgac agtcagagtg tgcacaacga gagatgaagt
   121801 acgctgcaga ttcccgatag cagcatctct ctatatgtga tgagaagtca gttaagtcag
   121861 tctacgttcc ggaccagaaa gcattgaata cggctgtcag gctagcaact gattctccgg
   121921 taagatagat cagtcagtcc gcccgcattc aataataaaa taaatggcat tgagctaagt
   121981 caagcttttt ccaagtgttg taaagaacgg gctacaacga aagtaaaaaa gatgaaaact
   122041 tccgtcactg cgcaccactt tgggctctgg tccactttcg ctccgtttac gcgaattggt
   122101 tgtatctgcc cgctaggaac gctggcatct gttgacaaca gtcccgctaa aggccgctgt
   122161 ctcttctcgg caaggtaagt tagttaggaa tcatagcagt cggtgaagct ttttctttgt
   122221 tatgcacaga tggttgggcg cagctgctaa ggaaaaagtg ctaaagcttt agctgctttg
   122281 attgaccgaa gagcctgact accagagcta gtaagctagc ggaagagctc agctcctact
   122341 ataagctgat aaagagctac tatcaccaag agagggcgaa gaaactcatt aattcattga
   122401 tgagggctcc ccattctctt tctaaatctg cagtccaatc cttcctaatt tcgaaactca
   122461 tccttaagtt accaggggca aggtggacat gaatcaagag aataagctct ttaatcagaa
   122521 tacatagttg aatttagtaa gaaaagaaat gatggttgac tcattcaagt gataaatcgg
   122581 atcaagaaaa caccgcccaa ataagcttcg ccatgagtgg atcaggtcct ttaaggcgat
   122641 cccgcgaagc cggtccccgg tgtctaagat cctatctgac tattgaggag agctgatctt
   122701 cacgacgaac ttttgttgat agtgctttgc ttaacactaa gaagttcgat catccaacgt
   122761 agagagaaac atcttgcggg cagttgttgt gaacaaagga atgaatcttt gggtttcctc
   122821 tcaacaacag aattttgttc aggagtttca gggcaagaat gataagaaag aatgcctttt
   122881 tatttaaaaa gagtgtgaaa tttgagttca tgagcattat cggctctaac agctttggct
   122941 acccttttgt attgagtttc tatgagcttt agaaaccctg ggaagacagt gagaacctca
   123001 ctttgacttt tgagaagata gacccaagta gcccttgaat gatcatccac tatggttcaa
   123061 aaatatcgaa aaccttctgt tctgaggttt caactgaaaa agggcccaaa atgtcaatgt
   123121 gaatcagatc aaaaggttca tcacaaatgt tattatgaga tttaaaaggt aagtgttttt
   123181 gtttagccaa aggacagatt ttacaaatgg tctgattgac ctttttattc ttatgagtag
   123241 ggagtcaatc tgaaaggata gcagttttag aagaagaagg atggcctagc ctgttatgcc
   123301 aagtgtgaga atctgcaata acagaggcac taaaaaaagt agtacctgaa agagatggat
   123361 cagaatccaa aacatagagg tttgatactt cacataaatt ttcattttta cgaattcgtc
   123421 tttctaaatt caactattag catagcatta agtagtaaac attttacact aggagctgcg
   123481 cccataccac acacatacat gcaaacataa caaatcaaac aaagacaaag aaaagctatt
   123541 tctagtatac ttcttcactt cagataatcc aaccgagatg tgattgcgat gatgctacca
   123601 gaaggaggtg atgtcttcgc gctacgatcg aaagatcaag aatcaaataa tgacttttcg
   123661 aggaatcatg ttaacgaaac gaatccaaca ggcttgaccg catacctact cctgaaagga
   123721 gtcaagctta ttacttttag ttactagtta tagttatccc gggtaagcat acttttgagt
   123781 agtttcagtg tattcaactc ttatctatag aaagcgagcg gagtccagta gtgaaattac
   123841 tttatttagt aaatgaatac agtgtctact aagaaaagtt agaggtaagg cgggaacagc
   123901 ttccatcttt atctttatta agctggaaaa tagaaagccg gggctccagt ccagagattg
   123961 gatcatctct acgttcattt ttaggaagta gggtacgtct aaggtaaggt ctgaagccga
   124021 tgttcattgg ccttccgcgc ctatgatttc ttgaattcct cgcaggtcaa gcggctgaac
   124081 tctttttatc tttttttttg tgtctatccg gtcttccact gttcttgcct tcttatctta
   124141 agcagtcgct aggctaatgg gtatggtcca atcaatggaa cattcttctg aactgaagac
   124201 ggaagcaagc gcatttagta ataaatttct tatacaggat ttctttcact attagattca
   124261 gtattagaaa ggtctgggtg atcgcagtat attcggacct gtagttagct cagcttgggc
   124321 agcaccccat ttttaggtac catcaacagc aagaccatac aaatgtcatc gcttattctt
   124381 tcaacatttg cggagcgtct cactgaactg ggtcaaagaa ctaccttcct ggagctacct
   124441 ccttacttag atcgttcgtt ccccaattca aactcgggca aagttgtcca ggtgggaaaa
   124501 tatctaccac ctgaggtaaa acataaagct gtagacctgc ttcgtgagta caaagacgtc
   124561 taatccttcg cctgtgagac atctacttag ttatcggtac tcggacaccc aatcccatcc
   124621 ccgaaagaca gaaggaaaga caaagattac cattaggcga aagcaggtcc acaaggtgaa
   124681 gactctctat cgtcagatcg ttggcagtct agttctgctt tctttggaat cgaagtttaa
   124741 ggcattcaga catgggattt tttaagtgca ttcagcatca gtatctgctt tctttcctga
   124801 tgtaattgca gagaagatgt agacaaaact tacttaattt aattcaaacc ctgtgcgaag
   124861 gaactcagga atcacttccc cttcattgaa aacaacataa gaaggagtgt tctaaggcca
   124921 atagacagaa agtgagtgct tgatgtagca tatctgctgt tcactatcaa ccataggcag
   124981 actaagcaag gctcgatgga attgaggttc gatgtaattg acctgcctta tgttggactt
   125041 cccaacttac ctagcggaag aaaagggcta ggacctataa atataaatat gtataggtca
   125101 cttccaccaa caactcaagc tatttcttac tgggattctc cacaagtact agaaagtatg
   125161 ggatctctac aacttgttcc acaaactcaa actatcggtc aaggaagcat acgcctctaa
   125221 ctcggttcat tccctaggta cccattcttg ggttcttaca aggtaggctc gtgcccgggt
   125281 tcactcgtga aagaaaggtt atagcggtaa agtaaagaaa atcctccctt cttgcttcct
   125341 tagggtacgt cccctatcgc ctttcattcg gaaaagctcg agtcattatc cttcctgtac
   125401 ttcaagtgag agctagagcg cttctttctc aattacatcg acccttcgca ccttggaata
   125461 ttgaatagac acttttgaat cccccctttc gattagtagg ggattcctta gctgagcatc
   125521 aatcccattc tttgcggata aagtacacta cccgcttgcc tgtaaccttc tgcttgcttg
   125581 actacagtca ctcctattag gtcacgaaca tccttaactt aagagagcag gaagagttta
   125641 ctatcatagc agcacataca gagtgccgga actacaaatg gactaatgct ttctctgctt
   125701 tccctcttgg tttcgttcat ggaagatgcg gcatagatag aaagagagca ttccagacta
   125761 ttctctagca tccgagtctg ggcatgaatg gaagactcct agctccctcc taccacactt
   125821 aagtatctct tctttagcgg gcgcttcata atcaaaagat tgttccatac catatgaccc
   125881 aggctttgtc acgagctgga ttcgaaccag cacttccgga tgagttacat ccgacgaatt
   125941 cccacaacta tagtgatttc ccggttcctc attccattca tttcagccgg attgtacggc
   126001 gaaactcgct aatagataga gaaattttct cagggaagaa gaacatctat ctccggtctt
   126061 gtggaacttc tgtcgtcccg ttcattgtgc ttcctcggcc ctgctagcca tttgcttgct
   126121 cgaacaactg gaagtccccc caccccattc tttgcctcat cctggggagc ggtttgttgc
   126181 cattgaaatc ccttgttgaa ggggctggct taccaaacca acttaccaaa tcgactctcc
   126241 ctctactctc tacctttctt ccctacaaac tcttaacctc aatccagggc taaggggact
   126301 aacaactggc ttcccatcac taaccagcta acctccttag aaaaactcta tctcctgttt
   126361 caagtaacct taatctaggg ctaggggaac tagggacaga tctaactccc attcctccaa
   126421 tccttaacca actaccaatt aaaagattca aagctcactg agaacagatt tctatagtta
   126481 taatttcaat tactgacctt tctcaccctc gctcaattca ttgataattt tggctcaatt
   126541 cttccattag ttaaatggga aagaaaggct aagtaaggaa gtccgtagag tagcggagct
   126601 aatttcaggg agaaataaat cactgaaaca cagtattcgc accttacttg attcattcct
   126661 tccacccgaa gcccctgctg cctgcctggg atgagcgtcc tctgatctaa ataagagctc
   126721 ctgtttgctt tctggcaatg agctagctta accctgattg cgacaggctt aatacagtca
   126781 tgttggatct cctattcgtt ctgctaccag gaagagaaag aaagactgat tgcgacagct
   126841 caaccggatg agacatctct tatttacaga actgtgccaa ccgtgccttc ctaccaactc
   126901 cgccaacccc agacggggat attgatttag ccgcacctga acccgcaact gctgcctcta
   126961 ctccgcctac ttcttgtgcc gacttcgact gccttatttc gggtgaagag taaggggtgg
   127021 taggcttagt agggctcgaa cctacaatat aaccgttatg agcggtacgt ttcaaccaat
   127081 taaactataa gcccctacgg atctctacat gcaatttgct cacttcggga agagcggacg
   127141 caagcaaagg ggaggccttt gctctatctg cttcttcctc ttcccaggaa tgcccaatta
   127201 gataaaataa tgattttaat attgtttata gatagataat cttatatatc tattatttat
   127261 aataataaga aaataaagca agcggtcctt tcgcgactaa aactgccggt acgctttccg
   127321 gctcgcaacg actcaaaacg ggcggggggc tctctatttg cttgcaatgc cggctgttcg
   127381 cgtttagtta aaagtagaag tagagggcgc ccttttcccc acacttaaaa aaagtataaa
   127441 agtctaaagt acataaaaag taagaaagaa aaacttagtt acgggaacat ccaacagaac
   127501 cttgtgaata attgtcgatg aaaataacat agtacttcaa accttgaaca gaggagaggt
   127561 aactggggcg ggtctcaata agtaagagtt catccgttct caaggaagta aagcttgaga
   127621 acagagcgag ccttacagct tgaaaggaac ctgaaagatg gatcttgaaa ccttggggaa
   127681 agtttcctac ggcgagctcg agcagaaggc gcagccgaag gcgcagccct acttctatcc
   127741 aattccggca aggtaatcca attggaaaac cctgactgaa cgcgaggatg ttatgtcgac
   127801 ttaatccgtg gttgaatatg ttagtatcta gattgagtat cataccattt tccaaagaaa
   127861 gatagtatgc taaaatatta tgctaatatg gtcatttggt atgctcttat agggatagag
   127921 cactatgtaa gaggtctcga cgagcctcca ccatactaag ctaaggtcta ctagctatag
   127981 tagctagatg ggaatgtagc ctagcagcta gtagctctct tcttatagct cggtagttgg
   128041 atctttcata attcctttat ggttagagca cactgggata gaagaataga tgagtttgta
   128101 tctttcttcc tacttttttt ttatcggaaa acagagctag aacaaggaac aagcaacact
   128161 agcacttaaa ataaggtagg cggctaaaac aattgggcat ttccttgatg tccggaaatg
   128221 gtatatctga aaacagaaga aagactttct tttgaaccaa aactaaagat gatccgatcc
   128281 gtgcaccgct tttcttctct accctttaga atccaaggaa aaggcaaaga gaaagaggtt
   128341 gcagagggca cctaaccttc caaagacaca gcagctctag cctaacttcg gattcgaaac
   128401 catacttccc tgacttcctc tcaacaagaa gttaaggctg aaagtcctaa tcttcttatc
   128461 ccgatgcctg gagtagcggg tcttagttcg gattagtacc ttttgagcaa ggtaagttaa
   128521 gtttcggcag tgaaagaaag taaccaggat ccgcttaacc agttatggat gaaggtaggt
   128581 ctactccaat ccctcagcca ataaacaata aagtaggcac atttccctcg gcaaagaaag
   128641 tagtccctcg ctaaagagta gacttgagta tcttcgaagt caaagccgag gaataagact
   128701 cagttcgggt agagcaacca tttatatttt cattattctt acccgtttac ataaatgaaa
   128761 aataaaagtg aattaccacg gaaaatatcc acctaaaaaa atttctgggg ttacttggca
   128821 tagtcctcta aagaccctat ttagatactc tttcttccga gttcgagata aggaggaaga
   128881 atggggcgac agataaaatt aaataaagag caaaaatgct tgactttcat tttattaaat
   128941 ataatggtag gtagggcttc ttttaggtca taaagggaat agtactttta gctcgttcat
   129001 ctaattctgc tggtctatag gagtggctcc cagggctatg tgatagcacc caaaatacga
   129061 cggcctgatc aagagagcca gaagctgggt ccgcccgccg gagcttcttt caatttccgg
   129121 ggggcttagc ttgaaccact cccaagtgcc aagaaccggc gaatgaaggc tccgtggcgg
   129181 catcggagct gccaataagc taatccgttc ccagtgagct attacgcgct ctttcaaggg
   129241 tggctgcttc taggcaaacc tccttggctg tctctgcacc cctacctcct ttataactga
   129301 gcggccattt gggggcctta gctggtgatc cgggctgttt ccctctccta gagaaagaag
   129361 ttctctagtc actaaagtgc gtttcactct cgttcctctc gtttcactcg ggttgctaaa
   129421 gcacctctcc tctgccaagc tctctgtctt ggttaatggt tatccaaaag gatatttctc
   129481 atgttaggcg gtgtgagaca gggggataaa ggatcccccg ttgttatttt gtattgcgga
   129541 agatgtctta tcacggggtc ttaccgggct taatcacctg ggcattcttt cttcaattac
   129601 cgagacctgt acatacaaag atctaggcag ctcatcttct tctaacgaag tcagatcttt
   129661 ttccatacca taacatatat agaatcgatt ttcttttctg atcgctagcc tgccgggccg
   129721 cccccgcgat caaactatca atctcataag agaagaaatc tctatgcccc ctttttcttg
   129781 gttttctccc atgcttttgt tggtcaacaa ccaaccacaa ctttctatag ttcttcacta
   129841 ctcctagaga cttgacggag tgaagctgtc tggagggaat cattttgttg aaatcaatta
   129901 atctaatcat gcctcaactg gataaattca cttatttttc acaattcttc tggttatgcc
   129961 ttttcttctt tactttctat attttcatat gcaatgatgg agatggagta cttgggatca
   130021 gcagaattct aaaactacgg aaccaactgc tttcacaccg ggggaagacc atccggagca
   130081 aggaccccaa cagtttggaa gatctcttga gaaagggttt tagcactggt gtatcctata
   130141 tgtacgctag tttattcgaa gtatcccaat ggtgtaaggc cgtcgactta ttgggaaaaa
   130201 ggaggaaaat cactttgatc tcttgtttcg gagaaataag tggctcacga ggaatggaaa
   130261 gaaacatatt atataatata tcgaagtcct ctccttcaaa tactggaagg tggatcactt
   130321 gtaggaattg taggaatgac ataatgctaa tccatgttgt acatggccaa ggaagcataa
   130381 aatgattctt tcattctata gatacctctg gtaggtaaag cactcgactg tgctttattg
   130441 aaagttccca tcgcgggggc gaggatactt gccttcgcgg ttcgactttc ttttcaggct
   130501 tgactcattc gctagcttct cctccccttt agagctcttt atgatgccca ctgagtaaga
   130561 ttcggggact tccggcgcag aagctcattc tgaaccgcgg gaaccttcgt ctcaatcttc
   130621 ataatcaatt tatgccatct taaaaaaatt ggaatcttgt taggtacccg tacgacagct
   130681 ctaataatga gctaacgtac tcatctttag agtggtttgt gcgcaggctc gagaagttgc
   130741 tgcccgcttc agaagacctt agggtgcctt cgattcctgg acgactttgt tcgtcgtgta
   130801 caggggacgg gaagagatgg ctgttcgctg tagcaaaatt caacgaaccg acgggcgtcc
   130861 cggacatagc cttcaacccg caaaggttag ctttgttgct ggacaaccac tagggtacta
   130921 ttcttcctgg cccctcttcg ccctatcaca tcacatggtg gtgtggtatg cggcagaaca
   130981 tgtctatcct tcctccttct tctttcagtc gaaacttcct cctagtgagg tgttcgccta
   131041 tccaggtatg gaagtattca atgaatacac tctgtaccat gcatgggtgg atgaagcttt
   131101 atctggagta tcaaagatgg aattgtatgc taaggcttag tgccagtata gagcttgaag
   131161 tctttatgga tgtgccgatc tttatccgta catattaccg acctgcgaac atggatgatt
   131221 cgttcaggta cgggataata tttaggatgt acgatttggc tgtccagtta cagtggggca
   131281 atgtcatgaa attgctacta gtaactaaga ctcaagtgga gaaaaaaaaa gcactcaatt
   131341 tgaatgtaag taaaacacgg gatggaagag gaggcctgaa ccaacaggga tgaaacagta
   131401 tagattcccc tgggcgaagc aagtcaccga ttagtaacct aagaaagagt tgtcaacggg
   131461 cgagtgtcct gctataaggt aaactcctac tatttcagct tcttttcccg tggtcgaaag
   131521 ctaaatatct caagatgata ttttccaaac tctcgacaag cagcaaatag aaaattaaaa
   131581 gaagattttg aaggatctga tttcatctaa ggagtggcgg ttaacagaag gccatttcaa
   131641 cttatgctct aaaaagatag aaagcattgt tgataaagcc ctctctttat ataaagaggg
   131701 ctttgcgcct tcggataaag gaagattccg atattcgcat aggtattgaa gcggggatat
   131761 gaacagctag cttcccctca aatgggagcc gtttaagtaa tcttaaaaga gtcctcgact
   131821 gtattggaaa aacaaaaagt tcaatatggc gggagatcca taattttatt gagagctttc
   131881 aatcaaatta gattgtaaag tagtagtcct gtgtaaaaaa aaaagctggt ggggcggggt
   131941 ccaagcaagc gtaataaggg gagggggact aggggtggaa gggtcgtcga aggagatgca
   132001 tttctggtac aagtggtatt ggacaagatc tcagggaatc atctctttca gatttctgcc
   132061 tttctttccc atgacgacta ggaaaaggca aatcaaaaat tttacttcga attttggacc
   132121 tcaacatcct gctgctcatg gtgtttcacg attagtattg gaaatgaacg gagaagtggt
   132181 ggaacgtgcg gaaccacata ttggatcact ccagtgcggc acgaagccgc tgacgccgag
   132241 tcggctccta tgccgctagc tatgccctgc ttggtccccc ggcacggtgg aggttccgta
   132301 gcgggtcatg agcaccgggc taaggggcga agtcactcga ctgaaaagag aggggcggtt
   132361 gagcaactca agcgaaccgc cctaccttac tacaacatag ggacagaggg ggagaaggtt
   132421 gtgaaggtgg cctcgttatc cacacctccg gtcggatgaa tggaggaccg cccgacccgg
   132481 gtttcatgag cgttggcggg tcctggagtg cctgtcaagg gcgctagcgc ataccccggg
   132541 gtgatcatca tcacctgcac ctcacatctc ggcgtagtgg aacgtgtaac ccgcctgctg
   132601 tctcattcaa ctacatttgt tactgtaatc tatagcctaa cagaaggcag cgtcgagggg
   132661 ctttaggaac tcgactgaaa ggagaggaga taaattccca tacagccagc ggggaggatg
   132721 gcactacagg caaagaccgt ctggcgaaaa cgccgcaggc gcgaagcgtg gtaggcctgc
   132781 gccgggtgag catagggggg gaaagggatc ccggacggtg taagagccag gggaggccgg
   132841 gtcatttgac ggaaatggaa ggcttttccc ctcttataga aagccctatg aagttaaggg
   132901 aagtgaatga attcttggaa aaagaaggag cgagcctata tataaaatgt aagaaagtca
   132961 attattcaat gaatagatga taaagtcaac cgtacgacag acagcgctgc ctacacgcga
   133021 attagcttcc aaggtcgagc agtctcaatt tcactacagg atttgcgaat gaatgctggg
   133081 ctgggccacc tcgaatggcg tgagcgcatg cggggagacc cgcacgtacg gtttttaggg
   133141 ggatctggcc gaaagaccgg ccggcgccca cccgactaga gggactgaga aattaataga
   133201 gtacaaaact tatcttcaag ctttacctta ttctgatcgt tcagagggcg atcgcggagt
   133261 cactgaatga agtcctccgt ttctttcgga ggtgctgacc cgcagcgagg cagagatgac
   133321 taagtgacat atggaatatg acgacaacaa cagcatgtcg tagaaggaga gaacaggtgg
   133381 agctaacgac ccacgttgac taacgtatct acaactacat ccccgagcgg cagtcaaacg
   133441 gaggcgtgaa tgcaagatgc cagcggaatg atcggccgga cagaggctag ggctgcttcc
   133501 ttcccaccgc gtccttcctt gtgtatcgga gatataaagc gagtgcaccg gaaaagaacg
   133561 ggaactgggt cgatctattg cgaagcatcc gaagcataac tgcacactca cacgatcttt
   133621 gccgagagat aggagcattc ggtggaaccg gtgaactaca cttgcttctg gatagatgtg
   133681 tgggacagag ggctcgtggt accttctgcc cacccttcct cctctgcttt gagaactgtg
   133741 tgaacggaga gtgggcagaa gggaaggagg tcctcataca gagaaaatca tggaatgggt
   133801 cgagatagat gacagcgcct ttttcctctc ttccttgccg ggagggcaat cttctcttat
   133861 ggtcttcacc tcccgcccgg cctggaaatt gaatccagcc cccttctttc tgatccattc
   133921 atttctgcaa gcccagagcg ttgcctccct tctattgcat aacctaaaaa gctataagca
   133981 aagtaacaaa agcgcgctcc gcccggtgac taagaaagag gtttgcgcaa caattaaagt
   134041 gataaggtcg agggaagtag ggctcctatt gaaaggcttt ccctccctca aaagaagact
   134101 agctttcaat actagttctt acgttacgct gccatttttc caatattatt gaatagcatg
   134161 gcctggggct aaagtaactc aagtgggaga gccgtgttat gggtgacctt attgcacggt
   134221 tcagagagca cttgtgtatg tgatgcaagt gaacgtgtac gaaaaagctg tcgtaaagtt
   134281 tcgtttttcg ttccgttttc gaccctatct atgtttctat gatggcccaa gaacacgctc
   134341 attcttcagc tgtagagaaa cttttgaatt gcgaggtacc attacgagct caatatatac
   134401 gagtgttatt ccgtgaaata actcgaattt caaatcattc acttgcttta actactcatg
   134461 ctatggatgt gggagcatta actccgttcc tgtgggcttt tgaggagcgg gagaaattgt
   134521 tggaattcta tgaaagagtc tcgggagcca ggatgcatgc cagtttcata cgaccaggtg
   134581 gagtggcaca agatctgcct cttggcttat gtcgagatat tgattccttc acacaacaat
   134641 ttgcttctcg tatcgatgaa ttagaagaga tgtcaaccgg caaccgtatc tggaaacaac
   134701 gattagtgga tattggtact gtcactgcac agcaagcaaa ggattgggga ttcagtggtg
   134761 taatgttaag aggtcgtgcg acatgaagac attgatagca atatggggga agttcccatc
   134821 aggcaacaat ggttccgcct gactctactt aagcatgcat attatgtaag tgaagacttg
   134881 gtgtgaagcc ttggagctta cgttagaaga gcaaaaggcc cggggctagg gtgagctggg
   134941 gggggacagc gtaagtgagc gaatgtgtgt aagcccagtc aaagatgact gttctaagcg
   135001 gggggagcca cccacctttg aatggtgttg gtcctacgga ccgtgaacgg atttcgcctc
   135061 tggcctctgg gcacgtcgga accgcgtgag ttcaccgggg tggagcacgg tccgccaaaa
   135121 ccggcataga ttaggtgcta ttgatggaac atggtaagcc tatctttctc catatggaag
   135181 tgctgcgagc acttagagat gcgggtagag gaagcctcaa aaagcgaagg ccgagctgta
   135241 ggtcacgtga cctgcaccga gttggtggct gactgggctt tttccttgat caaagcagat
   135301 caactcgcct tctttcttgt tacccaaaac taaagttggt cgaatggttt ttttcctgcc
   135361 ccggaacgtc gaatgaaata gggggccggg ttctctttct acaacccttt tgatatgata
   135421 ggcctggcta cctttcccct atcccttatg attagggggc tgttaagccc aagaacaacc
   135481 agtcttgtgg tggtacggaa ggaacggact ccgcgaacgt cccgcgcccc ggaaagaaag
   135541 tctcaaccag aaccacattc cttttgcgtg cggatgtagc taagtgtctg actctattgg
   135601 tcatagtttc ctgctgttgc ggctggtgct cgtttgcgcg cgcgtgaacc aactcaacaa
   135661 agaaggaaag gatgcccggg gaggcatctg agaatgattc gagccgtatg aagggaaact
   135721 ctcacgtaca gtttgttttt tttggggggg gcaggagccc gacagggtcc cccactgact
   135781 tggcccgggc ctaagttaaa gtgaagtggt gggcctaccc atcccaacca ggggtatgct
   135841 gggattcgcg aagagcagca ccttacgatg ttcatgacca atcggatctt gacgtaccag
   135901 taggtaccag aggagatcgc tatgatcgtt actgtatccg tatcgaagag atgcgacaaa
   135961 gtcttcggat cattgtgcaa tgtcttaatc aaatgcctag cggcatgatc aaagccgatg
   136021 atcgtaagct atgtcctcca tcacgatgtc gaatgaaact atccatggaa tcgtgcgtcg
   136081 tgtgaaacgt agatcatcgc cgttcttaac caagactcag gttaagctcc gtctcggaac
   136141 cttgtgggtt aggagtaaag catcccgggg ttggcgcatc tcattgggcg tagagaagca
   136201 ttgggaaccc caatttattt cttcggagcc gtttcttttc ccgtcccccc caccccggca
   136261 tagcgcttcg cttccggttc ttcggaagaa tcaacttact tctaccttct tcattgatct
   136321 gggggaaaag gaaccgtcta ccagttggga agctagacat caagtaagtg gcttgatgag
   136381 gataactaag ctgacacgcc ggagttggct gctggcacaa cagggtggtg ccttaccgca
   136441 ccgcaggcga acgcgcggta gcgttcgtgg tggtgcttca ggattccaat gtactgcgtc
   136501 caagatcaga acgagcttgc cggcggacca ctgccgtccc attcttgagt gagctggagc
   136561 gcagccatct tatccactga actagctaga agctatcgct tcgggtcgaa gcactaaaag
   136621 aaaagcaccg ggaaacgcgg cggcatagga accacgggac ccccacccta ctagtaaagg
   136681 gaaaacggaa gtgcgctcct gcgcaccagc tgaaaaaagc cctttcccct ttctctgata
   136741 ataaggaaag cttcttagct ccaacctata caaggggttt ttatgtcctt tttataggtt
   136801 gggttgttgg atacgggatc ctcgtagtag gctggaccaa catccagccg agagagggca
   136861 gcctctagaa gcaacaggtt gggaaaccaa gagaacgctt cgccttttct tatcttcttt
   136921 ctgccctagg agtagaagta gcacaaaaag agggattcgc attattgacc caatgataaa
   136981 ccactaacac cttcctcgtt ggggctccgc gcactgggaa aacgcttgac gcgattggga
   137041 aaccggccac tagttacaaa gctccaataa ggtatcgaga gggctatcac agtcaggtgc
   137101 gaagaattac ccctatttgg aaagtaccct tcttcctatt tagggggtta aggcgagaaa
   137161 tggcttgatg aatcgttccg ttcgccatgc accggcccca ttcacttgct tatcgtagag
   137221 gctgtaagta cacagtgccc cacaactatc aatagtatag tggggttgaa agacgagagt
   137281 gcccgccctt tcttttcttt caagtgggcc acttttttcc cgaacgcagt ccgggatcac
   137341 cgtggccgtg tatatatata tatatatctt cgatgctgtc atttcgaaat gtccgcttca
   137401 atcgctcttt cacctccccc caaaaaaagc aaagttggct taacgagcgc agatgtgagg
   137461 aagcgggagc aataaaacaa aaaaatatct ttcttgtcct tctacttaag gggcaaagag
   137521 aagcgctttt gctactgaga aagcgaacgg tcagcgcgaa ggttcaagac ttttctgagc
   137581 gttagcgaag ctagattctc atagcgaggc gcttcgagtt agcgaagcct gtagtagcgc
   137641 cgaagcccta tgtgctataa tgctgagcca aggacactcc gccttattct tataagaagc
   137701 agtcaactga gttctgaacg aattagatcc ttggtaaatg gctcaatcta tagatagaaa
   137761 gccttatgat gggaaactac cacgttaggt ttggagagag atgggaccgg ttatataata
   137821 gagggagcag atgcaagctt ttttctttca atagccggcc aaatgactac aggatcatcg
   137881 gtctactcta cctcaattca ccatttcgaa ctttatacag aaggtttttc cgtaccagct
   137941 tcttctacct ataccgcagt tgaagcacct aaaggagaat ttggtgtctt tctggtcagt
   138001 aatggaagca atcgtcccta ccgtcgtaaa ataagagcac ccggctctgc ccattcacaa
   138061 ggactcgatt ctatgtccaa acatcacatg ccagcagatg tggtcaccat cataggtact
   138121 caagatattg tgtttggaga ggtggataga taggacgact agttgctcga tcaggacctt
   138181 agctttattg cgagcccaga agtctctctt tttttcggcc ttcaggaaca gcctttaagt
   138241 aaaatccaac ctaatataat gaatatcctt ctacatagaa gaaagacact ctaagatcct
   138301 ttttcaaacc tgctcccatt tcgagtcaag agatagataa atagacacgt cccattgcac
   138361 tgatcggggg cgttcgttgt atgttgaagc agagatgaat agggtggctg tgaagagagt
   138421 gatggttgat cctgactcca cagtcaatct catacctatg tccactaggc attccaaaag
   138481 aaaagattgg aggagcactt ctcgaggtat ataatttgag ttcgaattgt caaatcaatt
   138541 ttctaggaat ggtatggtca gagtcaattg caacgttgga ccttttcaaa gtccgataga
   138601 gttccaggtt gtttttgcac cgacgacaca ttatgctctt ctgggcagac tctagattca
   138661 taaagaccaa gcggtcccat cgacatacca tcaatgtata aaaggtataa tcaaaggaaa
   138721 ataagtactc gtaccagcgg tgagcactcc cttcgaaaga tctgaaatcc atttttgctg
   138781 acgctataca ttattcggag tttgccgagg atggagagct ttcagggtcc agggagctgt
   138841 tggcttactc gttgggagga cttattaatt aaggaagatt cagttcgtat ctatttatag
   138901 aaaagagacc accggtatgc aaaagttgag aaaagccgtc tttagcctgt cactaagttg
   138961 ccaatcgaca tgatctattt gctcacattc caggcgaagg tcataattcg ctgtttccta
   139021 caggtactgg gacggaaaca tcatattccc gaaaaaaatg cgggacttcg gtagcgagga
   139081 gggccctcac agcaaagccc attgccaagg ccagaccccc agccgatctt gatgatcaag
   139141 aaagaaagat ggctcgactc cctactaggt ataccccaac cttagatagt agggccataa
   139201 aaggtttccc taggaaaaaa gaaagagaat caaatatagc gagaacacat aaaagaatcg
   139261 agattctgat gagaatgcaa ccactgcgat tagaaagggt tccgcgattg taattcacag
   139321 tcatttcttc aagatgtttc tgccattccc aacaaatcat ctttagaaag ctgcagattt
   139381 tccattcttt ttaatgcctt aaatacggat tttttataat catctgtctc agtactcatc
   139441 tttttactta tttacttatc cttcctgaga cttttttcag tttatcgtag aaattagtcc
   139501 acaaaactga taagaacgac acgagtttaa aaatttcgat tacgctgggc catgcctggc
   139561 actttcattt tattgagtca taagattaat ttaatcaatt gcctcttatt ttaggcaaaa
   139621 aaaacaatcc catttgttct ccgcagtcct tctgtgtgta gaacattggc cagctccatc
   139681 taccaatggg tgcacctgac tgtctccagt tcagttagaa cagaaggccg ccagcttaca
   139741 tagtatataa ttgtagcggg gggagctgac tgttgcctcc ctagttgaca aatgagccaa
   139801 atataattta atcctatgtg ctctacatat tttctattta tttcttatct atcccattta
   139861 gcgataagat actcgggtta tgtttggtga actggggccg tgttttatat cctccttccc
   139921 cacgggaaaa cgtttgcaga tgcgatcatg aatcgaacca gatcgaaaca ttcagctgtc
   139981 gacggacaaa ccttgccgaa acgtcgaccg caaacgaagg atggccaggc cccggttccc
   140041 agagttatag tattccctat tcctcgccta ctcaaataag aactagttga ttctctttcg
   140101 cctatcggcc ggccggcttg ttgcaacctt cgcatttcct gctgagatcc taagtctcca
   140161 agtgggccct cttggccacc cgcgaccttg gctttttaaa gaatcccgct cctgagtcgt
   140221 ggaacttgta gctcggcagt ccaccgggtg ggtttgttta tccttccagt ttcgagtgtc
   140281 ttcttggata gttatagcgg cccataggcg cgagatgtac cttgtggggg ggggggcggc
   140341 ggtcccctgg acatagtcgt ttcaggcagt ggccgtttag tccatggtcc attagatggg
   140401 aggtgcaagg ccagaaaatt gaacacattg attccgctcg ttcccgtcct tcgcttcagg
   140461 gcctgcccct cggtgtggtc agtactccat actgtcgggc agcgaagctt acacttgttc
   140521 actaattatg acggttcgcc agggcctctt tcctcctccc ttttctgctc actcgtaggg
   140581 gtccggaccc ccacaaaggg ggagggagtc gactgaacat ctcagccatt ggcggaaatt
   140641 tcgcccgcat ccgatgtacg atcgtgtcgg gtgagcaaca gccgcttcgt cacagtactt
   140701 acttatgggc taacgggtca cactttggcc aagtatccta caaagagact cccgagagcc
   140761 agaagtatta aaggaatggc cataggaatg ggcgcatcat gacatcgtga gatgtctcgc
   140821 ccgaacgaat tagttggtac tagaaatgtt agaaaaagta aacgaaaaga gtaataagaa
   140881 gtgaaaagga cagagacact tcccaaccag aaagcaaagt tcccactgat ggtatactta
   140941 gtgtaagcga gctctaagat cacatctttg gaataaaatc cagttagaaa aggaaatcca
   141001 attagagata agctgcctat gagcatcatg gcataggtca aagggaagga ggaggcaagc
   141061 ccccccatct tccgcatatc ttgctcatcc gacatggcat gaatcaccga accagcactc
   141121 aggaatagta atgctttgaa aaaggcgtga ttcattaagt gaaagacgct aaccgaatag
   141181 ttagagatgc cgcaagcaaa gatcatatag cctaattgac tacaagttga ataagcgatg
   141241 accctcttta gatcgttctg taatattcca gtggttgccg caaggaatga cgtcgtagct
   141301 cctgcagaag taataacaat caaagccgta ggtgggtatt caaataaagg ggagcacctt
   141361 gctatcatga aaacgccagc tgttaccata gtagctgcat gaatcgaagc ggatactgga
   141421 gtgggaccct ccatagcatc gggtgaccaa gtatgcgatc ctatctgcgc ggatttccca
   141481 acagcaccaa taagaagtaa aatacaaata agacttatgg cattcaatct catattgcaa
   141541 gaaatccaag aatttctggg ggcactagca cgagcaaaaa tggttgaaaa gtctactgtt
   141601 tgaaagagag taaaacgacc cgaaatccca agagctaatc caaaatcacc tactcgattg
   141661 acaagcatag cttttgtagc tgctttatct gcctgaagtc gtgtaaacca aaaatgaatt
   141721 aacaaatatg aagcaagacc tactccctcc catcccagga ataattgaag agagttatct
   141781 ccagtcacca acattggcat aaaaaaagta agaatggata aataacacat aaatcgaggg
   141841 ctatgcggat cctcggacat atatgaaatg gaataaagat ggaccaagct acttatggat
   141901 gtaaccacaa ttaacatcac tacggtcggg ctatcgaaca cagagtcaga agtgaattac
   141961 gagtcggacc tatttgcgaa tcgagcgagc tccccttgca tgcaatgatg tggtggtgaa
   142021 cctctcattc taattcagtg ctctccgaac cgtgcgggaa ggtttcccat cacacggctc
   142081 accaacttga tcttccggcg ggaaccgtat gtccaaacag gcctagaaaa acaggtacga
   142141 ttgccactaa agtgtacgaa aaaatccgtg cttaggcccc ttcttccctt ccaagagtca
   142201 ccaccgcctt agtagtctca caaatagggc gtgcaggcct ccctattttt tgagtaggta
   142261 attcactacc gaagcgcgaa gaaaaggctg gatcaagaaa agggggtact acgagccctc
   142321 tgccccacgc atctaaccag ctcgcgtggt tcaccggttc caccgactag accaaaaaga
   142381 gttattcagt cgatacagag gtgcgcttga agcggggggt gtgctgtccc tattggctgg
   142441 gcccttcccc ataaggcccc accgtcgggg cataagcgcc ctcttgctac ccatatgcag
   142501 ggcgccgtct tagccttccc tgaccaggat cgctcccaca cctgtagcgt tcgtgatcgg
   142561 cctactcaac tgtgtatcga ttgaaaggca ggaatttccc acaaccaaag ggagtggtta
   142621 cgtccagtat gtcccccctt attcccgaca tgctatggtg ccccggggtg ggtaggagcg
   142681 ggtcgagtcc gtatcgccgc ggagcaacag ccgcgtccgg atcagatcta tctactcggc
   142741 aattcatccg gtgacttcac ggtcgccaaa gaagccccaa gaagcatcaa acatttccga
   142801 tgagatccat ggagcaattc ttagatagca agcactagct cccggtgcga cttcataaaa
   142861 agcaatcaaa gataagatcg aagagaatga aacgcacgta gtggtcatta tagcgcttcc
   142921 ttctgatcct agaaaacgtc cgaaaaaacc tgctacggaa ctaccgagca ggggcaaaaa
   142981 tacgataagt agatacataa tttaatttcg agtgtgatca aaaacctaaa atcaagacaa
   143041 tgacagagcg gccagtgatt gagtgataga tttctcgacg tccggagaac gctcgaccga
   143101 agaaatgagt aactaacaag gaagattttg ttccccaact tgcttgatta acgggcattt
   143161 tcggggacta gcccgcttcc cattactcca agagggcaat tcctcgcaca taataaaatt
   143221 aaggaagcca ttgaaaggtg actaaaagac cagaaacagg gactacccga gctaatgata
   143281 gaggcaagaa cactttccgg ccaagtccca ttaattgatc ataacgatat cgtggaaatg
   143341 ctgcacggac ccatatatat aggaacagaa agagaagaac cttgatacta aaccagatcg
   143401 agcccgggat cttcttgaaa atgggaagat ctaggatagg cggccaacct cctggaaaga
   143461 acaatgtgca tggaccaggt gagtagggat gcagctccgt ggaccgctcg tcgggcctga
   143521 taggtggtgg tatcacaccc ttctcaaaga aaccgtacgt gacactctcg cgtcatacgg
   143581 ctccgccccg gaatcatttt tatacctctc cttttagtcg agtttgtttc acaacctctc
   143641 ccaacaagtg gtcgagttcc tttgtacctt tcctttgacc aaggggtcct cgaaccaacc
   143701 tgtccttcct ttctattcct agtcaggcgt tttcattcat tcattgattg attcaaggta
   143761 cgaagtgaca agtccaagcg atagcgtaaa agctagtcgc cggaagcgaa cttccgggcc
   143821 gggaaggggc caaaaaacgt gagcgccccc cgcaatcttt ctaaagaaac aagctagaaa
   143881 ctttactttg agaaatacct tattatatat atataattag taaaggcgtg ttagcctatc
   143941 tagtagtaag gggccttttc ttgatcgtta gcgctttact aataacaagg acttttctcg
   144001 cttgtttagt attgctttgg cttcgctgtc cgtatcttgc tggcgcggaa gctaccgcaa
   144061 ctaaaagaaa atgaatgaag gaagaaggca ttagaaagac taccgaggca ttccgggccg
   144121 actacaatac aagtcatgag cgatagcgaa gccaagccta tccggctttt ttatgtcaaa
   144181 agccctaccc caaaactagc tctatcttat agcagacaac tcaggcaagt ctactcaact
   144241 aatctcataa gtaaacgcct gttcgcatcg caactaatag aaaaaaacga ctactagact
   144301 agactagtag ttgagtgttc cttcttgttc aggtcttgac cgggtccgag cttcccaagc
   144361 tctatgctgt tggggaactc tgcaaggatc ttgccacctt cttgatttac aatatttgag
   144421 tctttggagt acttgaggat tatattcggc gccgaggatt tgtgcttgtg ggctagggtg
   144481 aatattgcag accagcgaat ctggtggtcg acaatcgttc ggacttgata aaggttgtcg
   144541 cggcacctgt agtaggacag aggacttatc gcgatgcccg cggaccaatt tacgatgtct
   144601 tcgtcgctga cgttcgtcaa acaggccacg tggattggcc agggtcttct tcggctaatg
   144661 atacctcgat cccgaagcct tcggagtatc ttttttatag gtgcctctat ctttatgggg
   144721 aattcgctgc tgatagatcc cgcccagtgt cctcctccct cccccgccgc cttccgaccc
   144781 gggggagtat acaatgacaa cttacgggca tgagtgcccg atcgtgagac tacctgttga
   144841 acgtccgatg acgcgttgct ccgacctgag ctatgcaaga acgagatccc ccttgatcct
   144901 tgccggatgt gcttgacggt cccccataat acgctaactt ggggacttct gactccagct
   144961 gttccaagag tctccgctag ttgaaccccg tcctgtagac tccctgtttt gctcatcccc
   145021 ttcgtcagct gtttgatcgg gatactatca cctaggttcc taaactttga atggatggcg
   145081 gagcgtaggt ggcaagcagt tatatggata cggtgcttta cccgtagacg cttttccagc
   145141 tctcgcaaaa attgtatggg agtcgtcctc ggagggactt cccgaatgac cgtaccaagg
   145201 aattctaccg tactccgtgc agctattgtt gttgatcctg cggagcctac ccaaaggttc
   145261 aggccagatt gtaggaaatg ggcgatacgt ttttgtattt ctatgagaag ctctacggca
   145321 cccacgattc ccagtagtaa gtcgtcggca tatcgcgcgt aacaaatcct tattaagtaa
   145381 tgggttttta agggggcctg cttacgggcc aggcctctct ctgacctgat aactagtatc
   145441 gcctccccgc ccagctctat cagcaggccc tttcttttgc aatacttaag aaggtctctc
   145501 atggcccaat tattattaca gcgttctcca ccatagaatt cagccttcgg ggtcaacccg
   145561 gcggcttcta tgaggaaggc ggcgcaaaga aggctcgagg gcttgttaag gaagacggca
   145621 agggccgacg aaggggggaa aacgaaaggc cttttctggt cccccctgag ccggagggtg
   145681 cttgtggggg gggtgtgcca cgacgaaaca agggaatgaa aggccgcttt gcgttgcatg
   145741 ctcttaacgc tccccacaat gatggctctg ttgtcttggg gagcgttgaa gcttgcttct
   145801 tctccagggt tttcttggtc atcaatacga cgacctgtcc ttaatagaac cgatctgact
   145861 ctctgaacaa tcggaatttc gtacttctgt cggatcctcc ctatctcctg atcgagcttg
   145921 tgtaggtaga tgttgcctgg tagggccgat agtagtacac tgtgtgggac ggagtaaggg
   145981 cccctctcaa ctcctacgag tcgtccggcg gaaaatactt tctgaatgga gtaaaagaac
   146041 ttgggatcgt cgatctcttc cttcaaaatt tggatgagtc gatgtcggtc gatggtgtga
   146101 aaacacttcc tgatgtcgaa ttctaaaaac cagcgagaga ttccccactc ttctttgatc
   146161 cgtcttagga ccgagtggca gccttgaccc gagcggaaat gcgatgtgtc tggaaactcg
   146221 ggatcgtaaa tggattcgag taccattctg atcgcctctt tcatgatctt ttctataggt
   146281 agaactactg tgagcggtct aaacttcaac ccttctttct ttcttcatat tgtaaagggg
   146341 ggaaaagctc gttttttgct cccctttttt ataatcaaag gccccctcct gccgtcgttt
   146401 cagtgactca tagggcttcc ctcagttcag tctttttggt tcttgaaaat ggtcgccacc
   146461 tctcctcttc tttcagtcga tggggttcct ctccttttag tcgagtaatc aatacctctc
   146521 ccaggaccgg aatgattatc cctgcccgat gggtctacat ccatccctga atgtcgtcgg
   146581 gtactgttca cttccccgca ttcttgtaac cgtcacctgt aatccgcgcg ggtgtgtccg
   146641 cacccccctg agtggacgag aaagaaagga tttctcggag caacccccca ggttccagac
   146701 ccaggagtca actttcccgt atgagcattc ggtacatgta tcagtccgtg ggaagaggtg
   146761 aaagggtcac cactactgag gatctccccc ccccctaatc ttagataggt cgtctgaggg
   146821 ttcgccgcgg ttcattgctg tgcttacaca caaggctacc cttctccgaa agctacgcgg
   146881 gaccacctac cactagtctt cggccggagg ggtttattgc acaaaaacgg ccgggacgca
   146941 ggctcccgaa gagggaagcc caacgaatgt cagatgcaaa gttccgcacc tcattaagat
   147001 catattggca tactctccca aaaaaaaaag agcagacccc attgaagacg agagtaaggt
   147061 acaacaaggc catttctgtc caccgccctt ctcacggaac cgtacgtgga cgttaccgct
   147121 catacagctc ccagccagca agcacagtta gccttcctct acaagaaatg gaaatgtgga
   147181 tgaatcgaat gaaatcgagg aattcggttt ttcttttcag acatgataag taagagcatc
   147241 cctttcacaa aaactacgga tccccctcct atcctgccac ttcagcacct tgtgatcttt
   147301 gagaagatca ttacgagccc tttcctagaa tgtttttgta gattccgaaa attccagagt
   147361 ggatcaggac gagaatgaat ccgggaatcc agggcatact catcctggag cttccgctct
   147421 cctctgggaa gggctttttt atggatagag agatgagtcg agggattgat tactcgacta
   147481 aaaggagagg gtagcctccc gtttgaccga tttctcggag tcggaagaag atctctcatc
   147541 tgatgaccct gaacaagaag gagctgctct cgatgtgaga tcagcagcaa aagaaagaag
   147601 aaaagggcca tgatgatgat cctatgttcg ttttcgccct gcccctatga tgcgctccta
   147661 gctcgcagag cataagtcag cgcaaaggag agatacatcc ttttaagact gtgaagagaa
   147721 tccttggttt gacctacgga ctacgtggga aatacgagat ctaggcaagc cgctacatgt
   147781 tctccccttg cccttgaacg atagaagaac tacttatctt ctcttagata gcagtcgatc
   147841 ggttctatga tctatggtca atcaataggc ccacggatct attcttctat acgataaatt
   147901 gccatctcgt agcaccacag cctgggggta agactagaag aggagatttg cttggtcttc
   147961 tgtgcggaat ctgcttccta atcagtgtag ctcttgggtc agctcacagc taggacgtca
   148021 tcagttctaa aggattcctc actagggaga ctctctcctt atgggcaagg gaggcagatt
   148081 ttgacgggga gaaggattcg gaatatagtt acataagtcc ccttccctct cctcaatata
   148141 gtttcactcg agtcacgtca gtacctctcc ttttagtcgc tcgtcgagac ctcatcaact
   148201 agttaatacc tccggacctc tcctttatca gtcgagtttg tgttcacaac ctctcgagaa
   148261 acaagttcga gagttacgta ctttcaatgc tctctctatt ccttgctaat caaggcctgc
   148321 aagggaactg gttacgacta taggcgggac gacatgcttt tagcttccct gaaataggcg
   148381 acttgctcgc tttggcagga agtatttttt ttgaagaatt gaacaaaaaa aactgaaatt
   148441 tctgtaaatc attaaaacgg gactttcttt aaagaaaaat ggtctctcag gctggttcaa
   148501 agccctattt ttagataata ggaaaaatcc catttcattc gggttttcta ttctgtcctt
   148561 atccccactg agggaagtag ctaacctaac ttcatattat ggattagtaa ggatccactg
   148621 ggtgggagga atcaaactca acgttgcgag ctcaaaaagt gatcctggaa ggcccacggg
   148681 taagcaaaga ttctaattcg agattggcag agaaacggcc cgtgcgagca cgaaccaaaa
   148741 gaaggtgcca agccgaagtg tacaaatctc ataggtctat atctgctcag tctctgttag
   148801 cagcttcagt aggattctgg tcttttcttt ctttcctgcg agtgttgaag tggggaagtc
   148861 cggatcaatc cgtcgaaaga gacgccatct ctcagtctaa atggaagtag accaagtagt
   148921 ttcataggaa gaaatgtgaa agtaggggct gctaagcgcc cagacccatg ggaggtgagg
   148981 tgagatagtc aatgaatggg gtggtagatt ctggcgcagt gtcaattgag aaagcgattg
   149041 tgactctgac cttcttatcg gctgctggtc ttgaagtctc gctaactact tggatacctt
   149101 ctctcattcc tcgggaacga aaaagcgaga gtacattctc ctttttagtg catttcagct
   149161 gcgtcagcag tttattcttt cttattccct ttcccgtgtt cattttaaag tggtggatag
   149221 gatgaactta ctggccgttg gtccttctct tctctttctt attagtaatc ttgttcaagt
   149281 gagagggact gacatcttct tttcatttct ttcatatctc ccttgattct gtttcagttt
   149341 gaagtaatag ggaggcttgc agaccttaca attgtctttg ttaaatactt ttatgaccga
   149401 ctgacttgaa tatgcttgcc attggtcctt atcttatctt taagataatg gtaagagtgg
   149461 taatgtaggg ctaggggtat agaatggaga gcctttgtag gccgataggt tgattgagtc
   149521 agtacacttg acgtatgctt ctagaaagaa aaagaatgag attcagctct gatcaccacc
   149581 accggatgca tttttcttga tcttctcgga ctccagtaaa gtttatgcgt tgggcctaga
   149641 aagcggtaaa cgtcagcaat gagtgcttcg attgtattaa attcttcttc tcgattgggg
   149701 aaagtccgtt acatgctaag acgcaccaga tctatgatct ctattttcta cagaatcgtc
   149761 tagcgagaaa actctttcac taatttttct tcttggcact ttcggtcttc tgcagaatag
   149821 tagcattgca tcgtcaattc acaattgatg tggggagagc ttgttcaaag aactcgagtc
   149881 aacacgccac tctgcacctt gtgtgagcta gacgaagaaa gcacaaagta cttaccctac
   149941 atatgcagga aagaaagtta actatggata ccatagctac tcgggcactt ggcgtcattc
   150001 tcacccctaa tgcttctttc tattcggatt ctatttgaag gtttttctcc ggattatatt
   150061 ttttttataa aatgaaaaaa gggggctttg ttccctcgta ctaatagctg aacagttgta
   150121 gaattaatgt ggtcagcata acacaagtac tcttcgcccg ttgtggaatc atgcaaaaaa
   150181 tagacgaaaa aagacgggtt ttgtcaactt tttgacactg tttagacatc tatctaacag
   150241 ccagaaagat aaagcagctt tgataactaa gaaagcagtc tatgggatcc tttttagcaa
   150301 gaatagcaat tggattagga tatagatggc atgtctcatt agccggcact ggctttcgat
   150361 tcggggaaaa actagactaa tccgtatagg agaagtttaa gtggaagcag tggaggcaga
   150421 agggcgaaaa tccccaccac tctccctgaa agtagctaat tcaaagcaga acgagaacag
   150481 atggcttgca cgctctacct tttcatctct tgcaacatct catctgcaac tatcacttat
   150541 cgatttcttg cacctatatc ttatgttggg tacagaaagg gatcaagaat agggtggatt
   150601 caccaaaggg tattgacacc ccagggcaaa tcacacctcg acctgccttg ggcaaaaaag
   150661 tctccgtgcg gatcacctag gggcaactcg taccggcttc taacaagtcg aagaagcact
   150721 ctttccttca gtcaacccat ctccttcggt ttagtggaaa gaaaactctc ctagctgagt
   150781 tgatgtaccg atatgaaatc tcctgcccct tcaacctaag gagtccggca gtacccgtct
   150841 catcaaaagc cagcagtacc tctttcatca aaacaaaggc cctcagaata agcgaagtaa
   150901 accgtgagtt aagcgtccct cgcgtttacc gtgagaagag tttcacgcgg cggctaaacg
   150961 cacctatttt tggcagccta ttcgtagaca aagaaagccg attcgctaat ccttattcct
   151021 ttactttgaa tcaaggtctt acccgaggaa gagggaagca agcaaagctt gccccggatc
   151081 gtaggggaaa gagtgttgta accgaagtag actaccgaac gggtgtgggg gagaatatcg
   151141 tcaaagattg agctaatccg aatccctctc acaacaagag ctaaccgtag cagtctaagg
   151201 ccgagatgaa tcaattcgaa agctgttctt cacgtttatg atctgaaaga cccggacaga
   151261 agagtcatac tactacggaa agggaagtga aagcaagcct gtaagggagg gggagggcaa
   151321 acttccgaca tttcactgat ttctccttat ctttaggaca ttgctttact tgagggcatg
   151381 ctcgtgtacc atacgctttc atcgatggaa gcacaacaga aggtgcttca atctttccta
   151441 tgggtattct gatgggcggg gctcgggatt tgatagtaag catgaatcta aggagatctt
   151501 gcagagtagt cagctggatc tcgctcatgt ctctatagca cctgactatg tcgcctatat
   151561 ttagattggc tttattctct ctgaaattag cagttatatc atccaccaaa gatatggagg
   151621 ttagaaacgc aattgccctg tgataatggt gttcttccac accaaagctc ccactgcaaa
   151681 agcggtaacc ccatttacca aaccatgaat gaccataagc aactccatgc aatagcctaa
   151741 gatccattga cctcttttgt gattcatcct ccagagtgat tttcctacaa aagcaacatt
   151801 aaaatcgctc atcataagag ataaaccgaa cattaatcaa gttaacccaa acaaaccgac
   151861 aagttatcaa atatcgtcag atttcaagcc aacccaaatt ggtttctcgc aagaaggata
   151921 aacaggtcta tccgatttgt ttattttcca tcgaattact aacctagcat cgtttttttg
   151981 gggtaaaacc taacttcgag ttttagcaat tttttagggc aaaacttacc gagtatgcag
   152041 gttaacacaa aaacgatccc aaagatccat aatctctctc ccatgaaggt gcttggaccc
   152101 accttcaatc cccttcgagc aagtgaccga acccgttcaa atggaccatt ccatgcaggt
   152161 ccgggtcagt ggatctgtgc cttacccgcg ggggctttct cattgagtca tttccgtagt
   152221 cagggaggga tcgatatctt ggtccatggg cccattctca attagtcttc ctggactatg
   152281 tttcttaccc acccgaacca tccctgctag cataaaaaca agttcgggca gtgagtcaca
   152341 tgttggaatg tcaggatgtg gaattttttt attgagatta gattagtgat taattagtca
   152401 cacctaccgt aacctatatt ggtaaggtta agcagctgac ttagcccccc gtcttcttaa
   152461 ggaggtcttt ctcacaggac ggagataggt tatgcaatta tgacttattc aagaggtcct
   152521 cccttcccta ctggagcgct aactcctatt tttttgtaga gaatccttgt gtagtgtatt
   152581 ctactggtat agaatctttg tgcgctgact cctacgaata taccgaacta gtccatccat
   152641 tttgattgat tcactgttcc tcgtccaatc cctctcgtat caatccttcg gatctgcctt
   152701 tccctgggtt actttttgta gctgttgttt catcccccta tctaacgagg gaattgagct
   152761 ggtgaatcac agcttatttc tcgagtgatc cctttgtaag tgtagctaaa gcaggggcga
   152821 tagccccttt ttaaatatct ttcctatctt tcttacttcg tttaccagct tggaatatca
   152881 ctgataaccc ttcatatgtc attcgttgtt atctgttgat ttccctgtgt ttgccgatca
   152941 ctgatgtaat ggctgttccg tcctttcttt cctctgagtt ggcttgcaga ccaaggagga
   153001 tcaacgtctc attgtattcc agttagtttc acagctaccc cttcccctac atcttctttc
   153061 ttcttctctg tatctttcgc tgttggccag cttgaatcgt agttttctct tatgggaagg
   153121 gcggacgaag ccactttcac tttggcaaac aggaaccagc caagtaaaaa agaaaggtga
   153181 tgggaaattt ccaattagat cgagattctt ctttcttctt atggatagag gttaggttat
   153241 ctttgccagc tcgatgccac aaaggtttaa aatggggatt ccttggtgcc gttcgcttga
   153301 cttgaggtca gtcctttcaa ctagcctaga cccatcatat ggggagcttt aaatggtgcc
   153361 tagcctttcg aaaggaagcc tgtctgtctg ttagtatgga ctatagaata gaattctttt
   153421 atcactgcta agcaataagt ctcagctagg gcacaggaga actgaggtcg gggggggggt
   153481 gaaataatat agattagcaa actcgttcga ttccagattg gcgagtcagg gggatcttat
   153541 taccaaggat cgatcaggga taaagaaaaa aaaagggttc cggccgggct aaaggtttca
   153601 aatcaaggtg taggtgggca tatccatgtt tgggcatttc acatgatgag tagagcgatg
   153661 ggtcttcctc ttgcaatcga gagaggcaaa taggcggaaa tcggtacact tttagtacgg
   153721 tggtatgcga gcagcaaaac agtatatgca atacagaaat acgagcaagc tcactaatca
   153781 tagtacggta aataagcaca agcagcagca aggaaagaaa gccagctagc ccttatagtg
   153841 cccgaagcga gatcggagta ggaagaccat gagcggaaag gaagaaagct tcaatgccaa
   153901 gagcagatag gataagagct gctacggtgg gggaacctca cccagtcaat cctaggagta
   153961 agccctttta ctaagaagta gaagttcaca tgcccatctt ttctcttgca tgcgccttcg
   154021 ttcctcatta attcaaatca aagtaagcga catcgcatcg ggaagggata gggatagcgc
   154081 atttgcttgg ttggcggctg gctagcttag ctctcgtcct gtagctgctg cttatcgacc
   154141 ggcagaccgg ctaccagcag caagaattga atcttttgag ccttaagttc ttcttgcccc
   154201 agtttcacta tctctttcac ttcttcgatt ccccttgaag tagggggttt cagtgggaac
   154261 gagatcaatc aatgaagggt caagagaaag aagaaaagaa gactaatctg gatattcccg
   154321 aagatgcttg acttcgagtt cttggagtga cagctttgta aacaagggtc ccttactttt
   154381 gagtttcgaa aatgcatctt tctttctccc atgcttttca ttggtcaaca accaaaccaa
   154441 ccactaattc ttccttcact actaatccag gaagaagtct tgtcttcttc tgttcggaat
   154501 acattttttt caaaagaaag actcaaaaat aatataaata ataatatata gaatatagaa
   154561 agaattgctt aaataactca gcgatctaaa atcatagtta cgatctacta aaagtaaagt
   154621 tgagcacccg gaccagacag aggtggccga gaatcttatg tcaaaagtaa ggaccaagga
   154681 tgatcttttc ggaaaggagg agtaggagga gtcagacgga atcaaatgat tacgagatag
   154741 acaatgagac cagggagagc aagagcactt agacaattca ctttgagtac aggaaagtct
   154801 gctggtagga attcctcagg gcgtattacg gtttttcacc gagggggtgg ctcgaagcga
   154861 ttgctgcgaa gaattgatct gaaacgaagc acttcctcta tgggcattgt agagagtata
   154921 gaatatgacc ctaatcgttc ttctcagatc gctccagtac gatggatcaa agggggctgc
   154981 cagaaaaaaa tgaacacgat cgagaagttc gctccgccgc gcaagatcct cgaacctacc
   155041 acgaacacca tcagcggcct cttttcgttc tctttcctgc ccgggaaggt ggataaaaga
   155101 aaggtagctt gcttctctcc tggactgatg gccgcttatg tagtggtcgg ccttcctacc
   155161 ggaatgcctc ctttgtcttc gtctaagagc gcctttgcta gtaagggcgc aggaagcaca
   155221 aaaactttag tgaaggacgt cttcttctct gccttctcct ctccaaaggc caagagagag
   155281 actgcatccc ttgccttcgc tagctctttt ggtttcccaa ggatagcggt agctggggca
   155341 aagcccgctt tcttcgctcc gcgaatgaga cagaaagtga gaggaaaaag cacgttctct
   155401 ctttgcgagg tccaaaaggg gagaacgcat agcattctct gggcacatag gatcaaaggt
   155461 aaagcagggc tttcttggca gagttttagg cggcaagata ctttagggct tgttggagct
   155521 gctgggcata aaaaatcgaa gccgaagacg gatcaaggta acttgcctgc caagccaata
   155581 ggcgaaaggg cgaagcaact caaagctctc cggggtttga gggcgaagga tggagcgtgc
   155641 aaagtcgatc gtgcacctgt cgtgtgaccc gttggtccta agcaatgtct tgcgcgaagc
   155701 gacccaccta gaaagagctc tcctttatct gggggcacta aaatgaaact tcgatcagat
   155761 gcgggtataa aatcccgccg ctgagatgtc cagcggattc ctgagccttg acgaaaggtc
   155821 ggccaccttt tttttacgga gagcaaaagg cccggggcat agcaggatga accaatgtga
   155881 atgagtgtaa gcttcgttgc ccgaacacga ttggtgctga ccacactagg tgctaccgcg
   155941 gtagcaagag aggccaggca atgacaattg agaggttgtc actgaacatt tctagtcaca
   156001 cgggaagaga ggtccaatgg caaggccata cgcccgtttg gctcctcgcg gagtatagct
   156061 cacatccaaa tatcatatct gattggggaa cggggcaaca cccatgaagc tccgacggaa
   156121 agggaaggcc tgccaggccg tatgcccatg ggtgcaggat tcttcgaaaa agcgcgggct
   156181 gactcggaga cctgggacct tggcttagca acgaatgaat atttctcctc gagctttctc
   156241 cgccagcggc ttatgtagtg atcggccagc tcgctaagct ttccttcttg tagtcggccc
   156301 gtaatgcctc ccttcatttg cttgcctcct tccttacttt tcagagaagc attttacgac
   156361 tataaggggc gctgttcacc tttggaaact tagctacacc ggtcacgata tcttgttgat
   156421 attgattgag gactttcgct gactaaatcc ataaacctag aaagtcaccg tcactggtac
   156481 ttttttgact cgataggtag gtattggtgg agcttgcgta atgtagttgt agttaaggtt
   156541 gcattgaagt ctttcttttt tttgaagatc tactgaacaa aggcgaacgg ggttcccaag
   156601 gcgggacgtc tggcagaatg cttggcctcc cgcgctggaa gcgagacccg aagggtgagc
   156661 ttctggcggt tagcttctag aacttataat aggcattagg cattctgagc tggaaggagg
   156721 caagcaaaag gccgaccact ctatcatttc ccatttctga tgggaaggcc gaccactaca
   156781 cggactctat aacaagtcat gagcgatatc gaaaccaagc caaagcctat aggctttggg
   156841 atgaaagcca gcccgacgaa ggcctatgat agagtaagaa aaaaagtacg ttaaagtgac
   156901 gaagtaactt agccgtctac aaagggaaag gcgtcggtac ggagtcaccg tcagctgtgg
   156961 atatagacta tactataagg aacggagtct taaactatgg accgagacta cactaaggaa
   157021 caaggaagct tgactgagca aagaagtcaa ggaacgaagc tgcttctcta atagccccgt
   157081 tgaataggag ggcgaaggct ttaaaaaaaa gtttgattta gggagagggg gcttcaagtt
   157141 cttaggaaga gccgtacgag gcagctcacg tacggttcgg gagccgagcc cctgcacagg
   157201 ggcttaggtc aacacttata taatagccag tcatcaatta gaagcaggca aaatggtgat
   157261 gaattgcgat tggtccaaac cttcgaccag ctccttcttg caatccgccc agaatgacca
   157321 tcctaagccc ttattcactg tgtgaagaac ggggcagtcc gctggagtgt aggcttcttg
   157381 gccacgcccc ctgcttatag atacgaaata cttgagataa attatcaaat aggaaattgc
   157441 ataccattag ccgatatacg tttaggaaca tgggtacatg aaccctataa aatccttcac
   157501 ttttagcttt gaattactta tatatatcct atgaatttaa tttcgcatcg gaaacgattc
   157561 taggagaagt tcgaatccgt tccgttcgga tattgatcgg tcttggtttg acatggttta
   157621 cgtgttactg gttcccggaa gagttaatat ctccattagc gtcacccttt cttaccctgc
   157681 cttttgactc gtattttgtt tgtacacaat taacggaggc cttttcgaca tttgttgcaa
   157741 cgtcttcaat agcatgctct tatttcgtct ttcctttaat aagttatcaa atttggtgct
   157801 ttttgatccc cagttgctat ggagaacaaa ggacgaaata caatcgattc ctccatttaa
   157861 gtggttctcg cttcttcttg ttcctgttcc taactcctcc ccgggtcgtt cccaatgttt
   157921 ggcactttcc atacttcgtg ggtgcaacat caacaaattc gctcatgatc aagttacaac
   157981 ctaagatcta tgaccatatt atgttaactg ttcgtatttc gttcattcca tcggtatgct
   158041 cccaggtacc tgtaattgtg atctgtttgc cagaaccaag gggtctttct ttggaaacct
   158101 tcacgaacaa tcgtcgtttt ttgatggttt ttccgcttct cacagctgct ctttccacac
   158161 ctccggatat ctggtgccaa atcgtcgccc gtttccttat ttctttgata atagagttgg
   158221 ctatttttgt ggcatcgatt gtacaagttc gtgaagaggg ctggacgagt ggaatgaggg
   158281 agagcggctc gatcgagaaa aaaaataaga gtagcccccc ccctagaacc tggcaaagta
   158341 actatcaatg aattccaata aagattataa cacacagagg actccttacc agcgggatga
   158401 gtgatacatt cggtgagcgc cgtagttaag ttttccttat tcgttagcta tgctaaagga
   158461 atggattgtt ctctttaggg agtgcagaat caactagggt taacctctct ttagcctatc
   158521 tgtcctcatg ctagtcaatc tcaggtaatt ggtctatggc aaaggggttc ctctttcctt
   158581 cacctgatgg caaatacaag aagagttcgg caacgcaaaa gcgggcttaa taatcaaata
   158641 ataagatcga gttaagagaa ctcgtcccct aaactatcta gttaacggcg gcgtgatctt
   158701 gctgtagggt cagagctgca ccgaagaaca gttattatcg actcgatggc tctgatccgc
   158761 gtgaatcaga cggtgagtta ctggttcttg aatgggaatc ccgagcacca aagagcagag
   158821 tgatcctctg ctcgagatag gaccgggtaa agggaaaaag acagaaaaga ccatagaata
   158881 gcaataggaa tcgctgctat ccgacaactt tctccgtgga gcccgcagct aaaggttaac
   158941 aaaagattgt agaacccatg gacttactat ctaaacgata cgagacgggt cagtcaaggg
   159001 ccaccagagg cacaaagctg gcgaatatcc gtgagagcgg aagatataaa aggtataggt
   159061 aagtaagctc ttttaagatc aagggcaata agacgtcgaa ggaagaatcc gcaatgcttt
   159121 gacattcctt ttcaaatgag ttgtgcccag cccagttagt ccactactac agatagtaac
   159181 tagcacagaa aaacaagatg gaatcaaata cggtgttaat taatttactg aagtgaagca
   159241 aggaacgtag taactcgact ggttggagag aaactttgtt attagggttg aatttccagt
   159301 cttcgggcct caacaccgga gcttatcctg aggcctaggt aggtaggtag tgacgtctct
   159361 tgctgggtct ttcataagga atggtcctgt tagtcttaat ccagcgactg gccttgctcc
   159421 gagccgatat ccgaagtatg gttcgctcgc tagttatatg cttaacacat gcatctgagg
   159481 tcagaggtgc cgctaaggtg aacgctcagc ttcaactctg actatatatt atatataagt
   159541 gcactgaagg ttaactatgt caatctacaa ctcaatgtga ttggcttcgc ccgggctcag
   159601 tctctttcgg ccggtatgta gaatcgtcgg agcgagcaaa gcagcggagc gaagtgggct
   159661 gtgtaatcat tttatttttt gacttttttt taatatataa gggtaagtaa ggagctgaaa
   159721 acgagtcctt cggagggcga agaaactcat taattcattt tgatgagggc ccctcattca
   159781 aatgttatgc ttagtgcttc cctcacattt tgagttgatt atttccaatt tcgagagtga
   159841 gattgatccg accaagtagt agtgcggaag ccagtacata catggctagt ttccaggcaa
   159901 gccatccata ttggcataac cttcttctat gccatctagc ttcatagccg atagtttccg
   159961 ttgatcatta tcttcatcca tcggatcagc tccttctttt ctgatttttt tcaatgactg
   160021 cttcttatgc ttgccctcgt tcttctctct tctcctagac ccacccccct tactgtctgt
   160081 ttaggccccc tgccaggtac tccagtctca ttgcgtaccg tcgtctgcat cttcttgccc
   160141 tgttttcata gttgtttgct tttcttatat ggattaggct tggttaaaag cgtaccgtca
   160201 agcaagaaaa ggaaccgtaa actagcttta ccgagttggc ttcttcgtat gagccctagc
   160261 agcatctatt ccttactctg ttttctgctt tcaagcccct aagtaggatc gtctaacgaa
   160321 gtcaggtacg agggaatatg ttaatgcaaa agaggcgagg aggctggtga ccagagaagg
   160381 tctgtgatgg aagcaattcc tggctttctg gtctgtgata aaagcaatct ctctccggtc
   160441 ggttcgactg ttaatggaaa aatgaataga tccttaggaa gaaaaaggct cttttgctct
   160501 tgtgtagaat cagttgttac agagaaggag cggttttcgt ttcgcaatgg aatcagaatt
   160561 agctacgatc aattaaaata tcgtagtata gtaagagcca acgaagtagc tgtaacgtga
   160621 acagctaaag ctccttacct tatatgggct gcaccgcgct gaatgatcaa atcccattta
   160681 ttcttatttt tttacattac aactcccatg cctttccgtt ggtcaacaac caaccgtcga
   160741 tttacctttt ccttcatttt gagaacaagt ctctcttggg gggagcagag catgcaaaat
   160801 cgagcaatag atggatctta gaagaattcc actttgaacg gcacgactct ttcgattttt
   160861 gcgctggcat ttgagttgtc tcccctcctc tttcaatcga cacactcgac gcagatagct
   160921 ccggtggccc cggcttctgc ctctatcagg cttaggctgc ccccaccccc acagagccac
   160981 agcatggagt agctgctccc gcgctacaac caatcaaaat tttatacgga tcgatatatg
   161041 atgatgctaa accgagatag agaaagaggg cgaagaaact cattaattca tcgatgaggg
   161101 ttgccgcgcc tccctttgtt ggctcttcga gacaaaaaca ctcataggaa tggtgctaat
   161161 tcccatgttc cttctagtct cgtttggttt cgaaagcctc cccctccctg tctcttactc
   161221 tttgaaagct gtcatcctgg atttattttt gaatggtttc tttgttctct tatttggatt
   161281 gaaagaaaga caaaacttca ttttcttcga cgaatttcgg ctatgaccaa tgcaccaata
   161341 gctgaatagg cgtaacaaag ctacctgaaa aggcaaggtg caccttggga ttgaaatcga
   161401 cgaattgcgt tttgcccgag agatttattt agaaagatta tccatcggat aaagaatgca
   161461 aaaatagaaa gaatataaat aaaggcgtat acacgggaag ggggcaccac tacttccagg
   161521 gggagactag cctcattact tcttagtggg cgagaggtgc gcctaaccca cctacccact
   161581 cataaatcac ggtgttcagc tgacttgaac tgatagaccc ttattgtatt ggaatttagc
   161641 gcccatcttt tgactgttgt caacaaatct cttcaatgtt cgattctact ctatgttaga
   161701 acatttctgt gaatgctatt ctaatctaag tggtcttatt ctgtgtcctg tgctaggaag
   161761 cattactctt cttttcattc caaattcaag aatacgaccg atacgattaa ttggtctgtg
   161821 tgcctctctt attacttttt tgtattctcc tgttcctcgg atacaattcg actcttctac
   161881 ggccaaatct caatttgtgg aaagccttcg atggcttcct tatgaaaaca tcaattttta
   161941 tttgggtata gacggtatct ctttattctt cgtgatattg accacatttc tgatccctat
   162001 ttgcatttca gtgggttggt ctggtatgag aagttatggg aaagagtata ttacagcatt
   162061 tttaattcgt gaatttctaa tgatcgccgt gttccgcatg ctagatcttc tactattcta
   162121 tgtttttccc gaaagcgtgc caatccctat gttgtgcgga gcggagtatc ttatattcgc
   162181 tgggagaaag cttttcctct gcaggggcct tgtgcagtaa acccctacgg gcggtcgtcc
   162241 gtcgtcgtaa agtagtcccc gcgaagcttt cgggaagagg ggtagtcttg tgtgtaagca
   162301 tagcatttct ggtcgaaccc gcccaatcca actaagaaga accgaacctg acaaacacat
   162361 ctttttcctt ttgggagggt actccgagta tagtgggtac ctcgtaggac ctcgacccgc
   162421 ctactcgggt cttgtatgga tatgcaggaa ggggtgctcc taggtgtgtg taggggttgt
   162481 gtttgttcgc gagaatggat tcctcgtcaa gtctgtttgg ggggtgtgga cacacttgcg
   162541 cgaattcagg taacggctac aagggagaaa taaaaaggaa actgtacccg accagggatg
   162601 gacgtaaact cgtaagctac cgaggttagg gataatcgtc caggtcttat tgtgaaacaa
   162661 aaaagccgcc ccgccacagc aagcgggttg gttcctctgt cgtcgccgga tagctcttgg
   162721 cgaggtactt ttgtcactcg actgaaagga gaggagacct taggataagt tgctaaaaca
   162781 aaggggagta gaggatcgac ccgttcagta gaattccgaa gaaagactgt tgacagctgg
   162841 tggagacatt tctttggccc ccggcaaatc aaaaggaaat gcgggcaggt ttaagctcgg
   162901 cagagggttc aagaataggg tcctgccctt cagattctca gaataaaaaa atagttccaa
   162961 acctttatgc atgcacctcc gtataagtgc tgcgtacaag ttccggccag gataattggg
   163021 aaagatcaaa cccgaaagaa ccgctcacat cacagtagta gtagcgtaaa ggccgtaagt
   163081 cgggtagcgg ccataccata aggtaagggg ctattacttt cacatctctc cttctgtcgt
   163141 actataagaa agagagatcc gctgcgtgag caacccgact gtgcgttaca tgtgctctac
   163201 aggccgaact ccatctttct tcttaacaag cccatttatc tttagatttt gaagacgggc
   163261 gttgcgttcg gttcgaaagg tatggttttc agtatgtctc cagatagggc gccccactag
   163321 tccggctagc tagtgagcgg ttctttcggg cgagaagcag gccgggccct acgggcgggg
   163381 gcatctcccg caacgaaagc tgcatagttc gccaccaccc gaaaagtaaa agattagaga
   163441 gtccagacta aaaatacatg catagatagt gatctaatga caagggccga cgacggaagc
   163501 tcgggacgga gccgtatgat gcggaagtct cacgtacggt tccctgagaa gggagtggct
   163561 acctactgga gcttcgacca agcacccccg gtcaattccg ctttggggcc accccttact
   163621 ctaccattat tataggagta tggggttcga gacaaagaaa gatcaaggca gcatatcagt
   163681 ttttccttta tactttactt ggatctcttt ttatgctatt agctattctg ttgattcttt
   163741 tccaaacagg aaccaccgat ttacaaatat cattaaccac agaatttagt gagcggcgcc
   163801 aaatctttct atggattgct tctttcgcct ctttcgccgt caaagtgcct atggtaccag
   163861 ttcatatttg gttacctgaa gctcatgtag aggcacctac ggcaggatcc gtcatcttgg
   163921 caggaattcc tttaaaattt ggaacccacg ggtttttaag attttcaata cccatgtttc
   163981 ccgaagcgac actttgttct actcctttca tttatacttt aagcgcgatt gctataatat
   164041 atacttcctt gaccacttca agacagatcg atctaaagaa gatcattgct tactcctcag
   164101 tagcccatat gaatctggtg actattggta tgtttagtcg ggcggcggcc gttaggtcac
   164161 ctattttgag ttatggacac acaaggccaa aacatgtgtg tcgggcgtgc gacccatcaa
   164221 cctactagca atgggggaga aaacatagca tgtcgcaaca aaagcttgat tcgaggcgtc
   164281 agcaaaacac tgccgtctgt tcccttcagt cccttagcgc cccgggacgg gagtggggga
   164341 cggctctacg cgcaggcaac agcagcaccg gctccacgaa gtctgaatcg aatctttctg
   164401 ttggctttcc caaattcatt cgtaaatcaa aatcaaaggg ctagaagcga gcgcttctag
   164461 ctgcttcgcc tgcttcttct tattatggcg gccatgttgg cgtggcgaaa atgaacgaaa
   164521 agcgagatga acgtgctatt ttcaaatcgg attgatagat tgatctgttc tgatagatct
   164581 aaagagtaga aatagataga gaatagagag ggaatcaata ataaggtctt tgagcctatt
   164641 tctatctatt gatgagacaa ctatctattc ttgatccatc agaaagaaat tatttatcca
   164701 tcagaaagaa atcgatatgt atctgatgga gtcttctaca tcgtacgtag agcgcccaag
   164761 cgctttttgg gccagctcag ttctcttatc catcggtcca atgcactggg ctcatctcat
   164821 ggagggaaaa gccaaaatgt agttgtcttg ttgttgttcg ccgcctcgac gcattccctt
   164881 ctctccccgg catcgtccca cacagaaaga aagagcgcgg agccccggcc cgagccgtag
   164941 gtccgctaac gtaaagcgag gagttgagcc tgaactggcg aaccgaagtc actttcggaa
   165001 ccatacttcc tacagctgct aacatgtgcc cagtcctgcg gaaaggcgca aacgaacgtg
   165061 agctgctata ccggaatccc ccgctggcca tcggggaccg agtggtaagg ccatgatctg
   165121 caggggaacg gatcactcat tcttccattg gggacaggtg cacgaacgac aactccaaac
   165181 gtcacacatc cgccgcctac ttaccgttta ggtggcacca gcgagatcca gctaaggaaa
   165241 aagagtgtcg cggctgctcc actccgccgc ggtctcatga acttcacttc gttgccttcc
   165301 cgcgcgcaaa gcgaatgggc gctgtgctgt gggtcagttt cggggcgggg ggcgcagaga
   165361 taccagaata aatgattcat ttgtttggat cgacgagctt tttcagcccc aaaactcaga
   165421 atcaatggaa tgtctgtcca taaacatcta ttctatctgt atatataggg gatctctcta
   165481 tacatatcaa agtcttttat ggcattgata tgatcgccta gctgtagccg catatcacag
   165541 ctgcactcaa tatgcggatt tctgttggat cagatctttt ctttcgcttt gacggaagct
   165601 ttttgaccta gcgaaaagca ctttcgcgca agcaaagtag aagctttgcc agaagcaaga
   165661 cgaggaagtg gagctgtcgt ataagcggta gcttcccccg accgactaaa atacaagagt
   165721 cgcggcctac tttgattgcg aaggggtttg gcaacaagca aacggctttc tatcatagtt
   165781 gcaagggttc aaaaccttag ttcgctgctt ttcccagtac cagagaaggg cttatactgc
   165841 tcgcctttgt ttggtttgat atattcattc agtcaaaata caaactacaa caaagtggaa
   165901 gtggaagggc cgctatagaa gctagaactt gctttataag tcggcctaac caaagcgtca
   165961 cgacaacaaa aaattatcct tatgaatgga atcttaagta gggggggctt tgaccgcccg
   166021 cctaccaatc aaagaggcag agagtaaacg taagctcacc cgtaagctcg aagagagctt
   166081 cccttcattc gcttcgcggg agccgcacaa gcacatagct ggaagtcaga gggcccatac
   166141 tacctgccta accctttgtt ccgagggacc gtagatcgga aagcacccca tttatccaaa
   166201 agagaaggga aggggcctat gtatttgcat gacccctgcg gatttgaccc tatcccggag
   166261 ccaatcccct attggtcctg ccaccacgcc gcagaacgag agctcgtgtg gaaccttttc
   166321 tttctggcgt aacagccggt ggaacgtaac aaaagattac ggtcgcctaa cattaacata
   166381 agggcggggg gtacggtaaa ctcggccaaa atatgacacc cgaagggccc gaacgcacaa
   166441 tcctatccca tccgagtccg agtttacccc ttgcacttcg gacagccgac cgtagcatca
   166501 taaggaggac cccctttcga ggtaaaaaaa aaaaaaggta cggtacatat aggaggttgg
   166561 actttctcaa cgtggtgtat agcacgaaaa acttttcgat acaagaaagg gccgttctca
   166621 catgaaagaa gagaagaaat cctttcttct cttctttctc tttctcgaga aggaaagaaa
   166681 gaggatgggg ggaggggggg aatggggccg gtgcccttct tttacggccg tcactcttat
   166741 ttgtcagccg tgaggaacta ccggctcggt ctcggtggga aaggaaaggc ttgggcctac
   166801 ctatcccgat aagacctcat aaaggaacgg cgggagtgat aggttccata ttgccgagct
   166861 gaagggcaag acttttgtac gtgatcgtag tatgtgacgt cgtctcgtcc acgctgcatt
   166921 gaagagtacc tacgcactaa gttccggttc actgataagg aagatagagt tgggcggggg
   166981 tctacgatgt gatactcaag tatatgaccc ggggagatac atgctaacta tgggtaggaa
   167041 gcaggaaccc ttatgtaaat aatttcgggg gggggttaca gatctcttat actaccctcg
   167101 atcgacagag cggaacgacc agaaaaataa gtgatgttag aaagccgtat gataggtggt
   167161 aactatcttg tacggttcgg ggggtaatcg gcgtactccg ggagaaatct ttcgctctat
   167221 cgaacataca gggaattgga ggtagcattc taccgatgtt aagtcatgga ctggttcctt
   167281 cagccctttt tctatgtgtt ggtgttttat atgaccgaca taagactcga cttgttagat
   167341 attacggagg tttagtgagc accatgccga atctctctac cattttcttt tcttttactt
   167401 tggccaatat gagttcacct ggtactagca gctttatcgg ggaatttctc atcttagtag
   167461 gagctttcca aagaaatagc ttagtagcca cattagcagc gcttgggatg attttaggtg
   167521 cggcctattc cctttggcta tataatcgtg tggtttctgg aaatttaaaa cctgatttcc
   167581 tccataaatt ctccgattca aatggcagag aagtttccat atttatacct tttcttgttg
   167641 gaggggcgac cgtccgttga actaccaaag aaaaagggta aacctatgtg atcatgacat
   167701 tgtaggtgct tgcgatggga cggatgcgac ttccctcagt tggtttgggt ggcatagccc
   167761 gttgcataag tccccctttt tttgattcat tttttgagtc tttagggagc caaagcttta
   167821 ctttactaat aaaggctcgc gcaggggcgc tcactttttt ttgctaagcc gtctctttct
   167881 gggtgggacc gagagaaata aaggacagag ggcaaccatg catggtactt ctcgaccctg
   167941 tctccgaggg acagttgaac gagcgactca tgaatgctgc cgggtcggac gagccaataa
   168001 ctcgaacgcg ttcggtctgt tttttgagca agaatcacag cgttacctta ccttcaccat
   168061 gatacggact ccaagttctt atggcagagc acgaggagat ttatcatcaa tattctaatg
   168121 ggaatggaaa ccagaagcac gaccgaggtc ttcgtagtct aaaataataa aaccatcaat
   168181 aacagtaatg taagcatgag actttttggt agtaccggtg aaccagatgg ccgcggcgat
   168241 ggaatctggg acggaggact cgtagtatct ctctagatcc ggcaaaagcg aaagaccccc
   168301 tagttccatt cgaatgaagg ctgactgctg agcccactct ggccccggcg ggcccccgtg
   168361 gttgcgagcc ggagctgcca tagcttatgg ctagagcaat gggaggggcc tcagcagaga
   168421 gaacagaaca gaaccaccgt aaggataacg agtgctccgc ccgtcaagcg ggcggcagga
   168481 gcagcaggca agtacttggt aggccaacag tccagtgggc actcgacgaa agggggcaca
   168541 cggagcaagt acgagaaatt ggccccgctc cgctttataa aaagcaagga cccactacgg
   168601 gaggtcaaaa acccaggacc tatggaagtc ggggctcgtc cccggtcaat attggatcaa
   168661 acaaaacaag caataggggc ccgtagcact gacctctttt tttattgatt caatataata
   168721 ggggaaaaga tcgtacagtt ccctaccgag acaagagaca ctcttaacag atcctccgcg
   168781 cgctgggcat acctcttccg tgcgtctttc tcgtggcagg aacagaacaa cagggaaaga
   168841 aagacccggg gccgacctgc ccagggctcg agggcgagct ttatttaaga gagaatgggg
   168901 agcgaatcga aaggcttccg ttttagttct tggtttggtt cgggctcctc tcgatctttt
   168961 tcgtagtagg gaagggggaa ggagtctaaa tctatggaca ttaatgaacc atcattgatg
   169021 gacgttgcac atgacacgat caattcgact cagggtccgg cgctaataga ggttgcttac
   169081 tttcctagta gcgaaggaaa agggcagggc ttttttcgtg gtaatagtgg gcgggtctcc
   169141 tttcgaagta aaggccttcg cattcctaat ccgccccacc aaccccggac ggcttagttt
   169201 gtcccagctt ggtgaatcgc atccccgcgc aacgacatag tttgtgcgcc ctttaccgtt
   169261 ctcgctcagt gtttgcaacg gctggggagg cagtcgtaga agcgaagtct atcgccacgc
   169321 caaccatcaa atacgagatt gggccccttc tcaaagattt gatggaatgg cccacccaat
   169381 agcgcttatg tcatatggga actcatggct ggaaacaatc cttatggttt tgatatccgg
   169441 taggaataat aagaatcaaa gtccaggtag gttggtgagc ctagtgatag gagactatct
   169501 agcttggttc ggagagcact tgttgggtta aaaacttttt ttgttgctaa atgttacagc
   169561 ctaaatgctg aactattgac tctactcgtt cggatgggtg ttcaccccaa agtgttcccg
   169621 gactgcatgc atacatccgt aagtaactta gtgcaacatg gcaaatttca ttgagaggaa
   169681 tcagcaaaga aaagaaaaac gggtcaacat cttaatgtgt atttgaggat attttagggc
   169741 cctagaacgc aaaaaaaagg tgggtgaaca agagttgtca cgataggaaa gagaaatgac
   169801 tataaggaac caacggttct ctcttcttaa acaacctata tcctccacac ttaatcagca
   169861 tttagtagat tatccaaccc cgagcaatct tagttattgg tgggggttcg gtccgttagc
   169921 tggtaccatg atactttctg ttttgtcgag ccctgctttg gtctctggtt tgatggttgc
   169981 acgtgctaaa aatctggtac attccgtttt gtttcccatc cctatctttt tttctatcaa
   170041 tcaacttttc cattactttt gtaggcttcc tattataaag cacctggcaa caaaatgcca
   170101 actccttctt tttttgattt ctcactttct gcttttgctg gttcttacca aattggtact
   170161 tgatctgggc ggctatctct ttatggacga cctgagtcgt gccctttctc aattcgtccc
   170221 cggtttttcc gggggattgg gagggggttc taatacgccg cccaacccct caggggattt
   170281 ttttctctct tcttatcaaa cttcagaccc ggactatcac gatcagcgga ggggtgattc
   170341 ctacttttcc tccgcgcccg gagtacagga aacccaccgg cacgcgtcgg gaagttccac
   170401 aaaccttcac ttgaacctaa acgaccaaag ccaagatccc atttttttag aggttgagcg
   170461 cctaagcttg aaatgcgata aagtgaaaga aaaaacgata ttaaagaccc agtctttatt
   170521 gctagaaaga ggttaccata ttccggatga acgggatata gaacgagcaa taaatgttgt
   170581 gatgactgaa catgaaacga tcgatataga tcggcgtagg aaacggttct actaccttta
   170641 ctcgtgttta ggaaaaaccg gaaacaagtt ttggatggag ctactggaaa cgctggctga
   170701 ctacaatata aatataaaaa gcgattccga caactaacct gccatttcag gttttttgtt
   170761 aggtctcgac tttcttttca ggcttgactc attattttgc taggtatagg tcctctcctt
   170821 caaatactgg aaggtggatc acttgtagga attgtaggaa tgacataatg ctaatccatg
   170881 ttgtacatgg ccaaggaagc ataaaatgat tctttcattc tatagatacc tctggtaggt
   170941 aaagcactcg actgtgcttt attgaaagtt cccatcgcgg gggcgaggat acttgccttc
   171001 gcggttcgac tttcttttca ggcttgactc attcgctagc ttctcctccc ctttagagct
   171061 ctttatgatg cccactgagt aagattcggg gacttccggc gcagaagctc attctgaacc
   171121 gcgggaacct tcgtctcaat cttcataatc aatttatgca cttttttctt atgtgatttc
   171181 atagttcgag gcgcttaatg aagaagcagc tatagttcct ctcgggctag aatgactgac
   171241 ttggctttcg actgatatag tgcatgggtc tgtacttcag gctgaggttc ttggattgaa
   171301 atcttatgat gttctgactg accttttccc tcctcgactt gagtagatag tcagggtttc
   171361 agaatatgtt tgttggatgg gaatatggtg cttgatggtg ttgttgttca gacctcggct
   171421 ttctcccttc ctttcgtata tgccatgcca gctgacaggg agatcttcgt tgttcagctt
   171481 atattagagt cgttctacct tctatgggtc caagggaaat ggggcagttg ttccatcttc
   171541 ccatgcctgg actaccgata gttccctctt cttcctctta ttgtttccct ctttcgtacg
   171601 tacacacgtc gtcaagggat tgatgctaaa caaccaaagc tgccttggct gctgtgactg
   171661 cctctccttg cctcctatcc tttaagtcga gtacttcgtt ccttttcagt cgagttatcg
   171721 ctttcgcttc ttttgatcct gcagaggcag gacaaactcc cggcgagcaa ggtcaagatg
   171781 ccgatgctgt cggtctgcag cctcctttag tcaacgaagc gaactggctg aactctatgt
   171841 cttttggctt cgtcttgctg aaagaaaaag agtgaggaaa acaaagcaac aaaagagagt
   171901 ggcaacaaga agaatggaag gcttcccgtt actgaagtga acttctcggt aagtccggca
   171961 ctctgcccca tataccttat tcgtagtatc gctcctatct cgatgaagct tctagcctac
   172021 accggggttc ctctcgatac atcttgcaag ggatttctag ttgactgttg cctctccttc
   172081 tccaccaccg aatccttacc ctcctcttct ctccggctag acatctgctt tggcttcacc
   172141 ggctgactcg gatgtaagcg atgaactagt ctctcctaca gttaatcatt tctatggtgt
   172201 gggtagcgag gttcttcttc tccattgaag aaatgagcag ccttgagacc caggagaata
   172261 gcttcaacat agccttcacc atctgacccg gagcccttgc cgttcacttc actactacgt
   172321 acgccaggat ctagccctta gctgcagaga ttcggataaa gctctgtgct ctctccaaca
   172381 gcgtattatc ccgtagctac cgctctttcc tgccacttca aagtggaatt ctttctctgt
   172441 gttgctttgc gaattgggat tgagtctcag ccaagaaaga taaggtgatc gaaaggtcaa
   172501 atcagagatc tcctcgctta cccctgaagg agctgatcga ggaccaatgt cagaacactc
   172561 gagttggcct tccttcccta cggatgagga gatgaaacag attatggttt agaagccgaa
   172621 caaagagcat tggtgtgacc gttagcagcc cagtcgtgcc ctcccctgaa cactcggacg
   172681 agagggtgag ggtgggtgcc tctctatgat tcgtctatct atgttcctat ctatcggaat
   172741 gactcccacc gctgcttcaa tctatatctc ccggtaaagt gaaatcatca atctgaatca
   172801 attgaatcct tcgatatcag tgaaatcctc catctatgat tgctccttca tttcctcaat
   172861 cggaagagtc ttcttctctt ctgtcagttg atcagcatcc cttttccaag aacacctcga
   172921 attcggccta ctctacttcc cggaatgaga cgggggtcga gtcataggag ctgcttctct
   172981 ctgctattgg acttgcaaca gcggtctctc tataggaaag agatagctcg ttcactccgt
   173041 ctctctctgc tttgccgacc agaaactttc cgtatcgtac ttaagagccc gaaagcacac
   173101 tcctctgctt tgattccagg ttagggataa gaactcttca ctgttgaata gagagattca
   173161 attgctagta agttattcaa tcgatacttc tgggcctgcc tacgctgatg aatccctcct
   173221 ttcttcaggt agcatgagaa gatggaatct cagacttgca aagcagacct acgactcagg
   173281 tctcgaagag ccttgccata gcgtacagag aaagcaagag gactggtagc tctagagtcc
   173341 agggggtctt cacctttact tatagtcgag tgggcagcgt tgacggaagg agagtcaggt
   173401 attcacttag ttgacgctat cgtccttcta atccatcttt ccgtttagct cggcattgct
   173461 attgatctct atctctgctg aagcatgtta ttgatcggga atcgttcctt gaccatattg
   173521 gtcttatcca tcctcctcta acccctacca acttcgatag cgatcactaa ggcaacctac
   173581 atcctctatc ccttagcctc tctcaatgta tgcaagagtc tccctgcgag gagaaggaag
   173641 gcaaacaaca gaaaggagag ggcaccagca agtgaaacac acatggaagt cagtctagca
   173701 atctatccca gccaagaagc cgttaaaaag aagtcaggat acccgaggta agccaaccaa
   173761 gccaatgatc caaccaagcc aatgatgtgg tttgatgcat cgatcttctt ccgaacaagg
   173821 tagccaacca agaaagtatc tgatcaccca tccgatacga agacctttga tagtcaacct
   173881 ctccagcttg atagtccctc tccagtcaat aaagaacctt cccttgcgaa ataaccttcc
   173941 cttgccaggc agttggcttt gttccttggt aaagaagaga aagctaacgg gtaagcggat
   174001 ggcaaagaag agaaagctag cctttgcttg ggtgaagatg tgaaagagga gaaatccaaa
   174061 gaaagaagag aaagctgcta tagtttaagc taactcctcc gacagcgaaa agaaagagga
   174121 gaaagctgcc agtactcact cagccgagga tccttacttc ctttcataga cgaaacgggg
   174181 cttgaatcgg tatattggtt gagaatgact ccctgcttca ttaatgggaa atgcgcggag
   174241 caactaacta gtaccactgc atacaagctt ctcttccttc ctccgttaac agaacatacg
   174301 acttctctgt atccaaagca gtaccccgat aaacaactag tacttttact agaccccagg
   174361 agcggaactc gattaacata ctacagccag cccttcttca ttgccctctc ttccccatat
   174421 tctgggtcct ctttgtctgc taagttccac tttgctcctc atctctatgc attcttggtg
   174481 gttgctagca taaccagatc tgacatagct tactcagtga actgactttc tgatcgaaga
   174541 gagatcagaa ggtttaccag tttatattcc ttcctagaaa acgctttctc tgttgagata
   174601 tcttctctcg acctctctcc ttgcgtagta gctgagtcat cagtttatct tgtagtgagg
   174661 gattcacctc tggcttattc ttcgtgtcag gcttgttaga ccacttcttg tcttcctagt
   174721 attcttgctg cttttactta ttctgagtga gagctcagtc ttatcttctt agccttctat
   174781 ccgcatactt ccaacacaaa gagaaagaag gtaaatggcc tctggagagg taagatttgt
   174841 agggaaaggt aagccaatac atcaaatttc tcactcacaa ctggcatgct accagcaaga
   174901 atagaatctt ccattttcgg tgaatgctct ctcttcaaca acaggagttc taaataaagt
   174961 aacgaaggag agctgcggaa ccgctagcag cacttgccaa cacttgtcag cagccaaggg
   175021 gtcctcttct tgccagccaa tgactaacag atagatgttt gggattcaga cttgtatgca
   175081 tcgggggaaa catggctccg cctaaggttc gaggaattcc tttgacctag tttgctgcgt
   175141 ttccgttctt gcttgctcga cttatgactc acaactggtg gagctttgcc cttggcttgc
   175201 tgtaaagagc ttggccaaat aggatggttc ctcactcttt aggggaagga acggtgcttc
   175261 tcaaagtagg attggagaag tctcccccta acaggaaatg tacacaacgc tgtttgtggg
   175321 acgggaactt cctggtgatt tgactttgtc gaagtctctc tagtgcttcc gatgtgataa
   175381 tgttaagcat atagctagta acgcctttga agcaaggttg ccaccgaagt tcatcaaaaa
   175441 aagacggggt attgcaactt ttgaaggctt ttcggctctc taaaataaga tcagatacta
   175501 tacgaaatta gccttttcga ggacccaaaa atgggtcttt ctttactgat tcattaaaaa
   175561 accacggctc tttaaaaaaa gaaagagttg aaaaagctga ttgcatagcc gttttattca
   175621 cgtcgggcat tcactttagc agctttagcg agtaaaggca tatagctagt atagcagttg
   175681 agtcggtgaa ctcggataag taagcttaca gtatccgtta tcttattcct tagggcaggc
   175741 ctctatcttg ttccaatccc agtagcaaaa cgcgggctag gagtggcttg ttcctcactc
   175801 gggggactgc ttgatccgct cctcccgtct atatttctta ccttgtcgct tcccgttctc
   175861 catcgtactg atatgactgc tatggtagga gaatctcaag tgcttgcgat aaaggtcggc
   175921 cccttccaag tcggaccttg gcttgtagcc tggacttctc atttgatgag gaggaaaagg
   175981 ggcatgtaag tgtaaggatg aaacctcggg taggtgagat tggagcctat tattgtatgc
   176041 gtgatggaat tccgatcttc cctctcttcc tctggagccc ttacctcgca ggggcctgac
   176101 tttggggtgt ggttcttggc ctgtattatt tgtccgatcg cattatcttt tattccggtt
   176161 catcatagtc tcgtatctct caaccatcta tatcataaga gaagccggtt ccaagactag
   176221 tcgagatgcc ctattcagaa aggtagatga gagcttgcgg agaaggaaag ttttcatggt
   176281 tggctgatcc atcgaatact gtcctttccc ctttttacca ttttttcgtc gagttgctga
   176341 tacgttcttc tccagcaaca gcctacgtag caatcttcct cttttcaagg acaaggaaga
   176401 aagcatcaga cacgtccgta gttctaggtc tttttgccca gttcctggag cactcttgtg
   176461 gtttagtgtg ctaagtaatc tgggagccca ctgtcatttt attcgggctc agctcaatcg
   176521 gcatcgaaac tcttaattct attatgaccc ttcgccatct cctccctgtc gattctcatt
   176581 aaaaattaag agcaggagac ccacaagtag taaaagcaag tctagacctt ttagccattt
   176641 caagagaggt agaccctcca gcgcaggaag ttcttctaaa aagaagaaga gtgcactgaa
   176701 gaggatagga atcagggcct gtactgtatt gggagtgagt tgaaatatct tttgtataag
   176761 acatataaaa caaatcccac cgatcagaaa taaaaggaag accatccctt cgatcggtat
   176821 tcccgctttg cccgccgcgg acgagagcca aacggataca aaaagggcga gaaccgaata
   176881 aagtataaag gtcagcatat atcctgttag cgtgcgtttc tccagggaaa taaaaagaac
   176941 gcacgatccc gagaatatag cggctagttg ccaggggtct aagaaagaga tctcctgaaa
   177001 agcgtataac cttagtccat ataacatgag acaaagcaaa atgagaggta gaattccccc
   177061 tcgtagagct acaggggatt ctcttcttcc tagacagaat gaaagcgcgg agtatcctaa
   177121 aagctgcgaa gctaatagga acccccactc cgcgagttct ctatctagtc caaagaacag
   177181 taaaaaaata aaaggcgaca agggagggga accccaagac cagaacaccg gagaaaatgc
   177241 caagcaaccc tacttgggcg aaagccaacc ctcttaaaaa aagggtggaa agttggcata
   177301 gggcgaatag tcctaggaga tatggcctta gtctcggatc tatagaaagt gtgcagtgag
   177361 agatctttat aggtagagtt aagtaaagcc agtctttact taactcggcc caaacaattt
   177421 tgattattca atataaaact gtcccatgct ttccgttggt caacaaccaa ccaaaccaca
   177481 tattttcgtc tttccaaatt aggagagcaa ataagcaagt cctttccaac tagagctctg
   177541 gcggtctttt aagctgttca actagttagg gcattagcct cagaggcagg ggtttgaagt
   177601 caggaatttc ccactcccac tggacgacat gcggatagag aaatgcgact aagctagatt
   177661 caggaacagc ttctattagt acacaatctt tttgaatata gatcagcagc ggatgttgcg
   177721 acagtaactt caacatcgac aacagccttc agtcgtcgaa gtaaggaatt actaggaact
   177781 gctttcattc ccacgatatg cgccaacagg gcttttagga agagtagtaa cagcaccagt
   177841 aaccgctttc tttattccgg actttcagta aggaatgata gaaccgctga tacaaagtat
   177901 agtgagaaga gctgatatgc ttaagcgtcg aaaggactgt ttgcttacgt gccggattgc
   177961 ttttctaact agccagtata gttacagctg atatttctat atgaaagaaa gctttaataa
   178021 tagatgcgat tgtgagcagg cttacttatc agtgctagct tgtatgcgct ttctattaca
   178081 gcaacagctt ttatgcgaaa aacaagaaaa aggaaaactg cagctctgcg acataaccag
   178141 tcttgcagaa ctggaagaac gaatttactc gacaaggaaa ccaagtcaaa aggttgcgcc
   178201 tgacagccaa gcgccagttt ttgtaatctc tttccttcca aggagtcctt gtcttcttgc
   178261 atcacggcct cgatctacgc aatgaaaacg tatttcctct aactgcccgt aaagtcagaa
   178321 ttcaacgaag agcactcatt tatgatgtaa ctattatgta cctagaccgg ccttacccga
   178381 tacattactt gcttcccata ggaagaaggt ctgcaagcct ccatatgatt gattctcgca
   178441 atgaagtctt cccgttgatt ccacttcttt ctcctctgac tcagtctagc aaccccacct
   178501 tggtctcgta gcccacttgt agccatcact accgcgggtc tttgctcata gtcacgaata
   178561 agcttctcct aagtcctctc agcaattcaa agatgagact gactgacttc tattaagtaa
   178621 tcggataaga ctgatgcact cacttttaag acttccccga tctcctaccc ggctaaaaac
   178681 tagaagtcag cattctattc taatctccgg ccttcatgcc aggggttcct cctccgtacc
   178741 ttttccttct gtttggcttt tccccagccc gtgagaaatt gataagccaa tagagtcaat
   178801 cgtcaagtcg ggatatccaa taggtttttt tccaggtaag gaactagaat agattcatac
   178861 gaaagtggct ttttggttgg tagcaggacg gtaattggca acgaagcaga gatttatttt
   178921 acccattaaa aagtatattt caccattcct ctcgtcgtcc agaatgggtg actcaaagaa
   178981 aacgtttcat tcacgatgag gcagaattga cataatataa ccaagattgg atggtgacat
   179041 ataatatagt aaagtaaggg gttcctccgc ccgtcttcga tacaatcatt gcgatgtgtc
   179101 actcaaggat agctagccat tcttctctac ccatgccatg atttacagat gagctcgaga
   179161 ccattattga atatattatg aacacaattt gccaagagtt ggttgtgaca aaagtgattg
   179221 ggatgcccat ctttggtcca gaaggggttc tctatgaaaa gagtttccac ctttctctac
   179281 tcgaaaagcc ctatctaaaa gggcttgtct ggatgaatgc agtgtcggaa gccgtgatca
   179341 catagtaact tccgcccaca gtgctattac gacggcgggt caccgggagt gaagtaaact
   179401 cggctcctga tgtagcattc attcggacca ttcgacgttt gattcttttt atcagggata
   179461 ccgatgactc tgtgagaggt gttcttcggc caagtttccc atgacgggtt acccggttca
   179521 aggcttttct atataatgag aaatactact ttctttctag cttaagtgtt cacgtaggta
   179581 aaatagcttc tatagctcca tccaatagta atcaacggag atagagtcca gcggttcaac
   179641 caacgcttct aaggagagcg gggcaagcaa gaaagcaggc aaagtcattg agcctattct
   179701 attccgaaag ttcaactact ggataaacaa cgaaagccgt cggcattctt ctcctactgt
   179761 agctgctaca attgctttag cgcgagcagc aaggaggagg cagctcttac taaaaaagca
   179821 aaaagggaag ggcatgacag aagggagata gacctcctat aagcattact ctcttttgag
   179881 gtaacttact tacttactct gatatgatga gttccgtggg ctagtaagat aactattgag
   179941 gtgagggtcc gaaggagatc tttcactatt tatgcttgta cagttttatg atagttttgt
   180001 aagggaaagc aaatcctgag aatggaatgt aagttaggga acagtagtca gacgcggacc
   180061 agcgcaggtg ggcgccacag ctgtcttcct ccatgtgata tctgatatca cgcaacagga
   180121 gattcttcac ccttatttat tgacacgatt tacaaaagaa gaaccaaccc ggtcgtgcta
   180181 tatgtatttg ggatcaaaaa ggctcactgc tgtatgatat aaatctttct gaatgagagt
   180241 tcatgagcta caggaagaga tcgagtctag aataaacctt agaagtggca aaaacgactt
   180301 actttgttgc aacgggaact actcgccccg ggcactggtg aaatagaatc ttatgtgttg
   180361 cagctactta tgctttccca actagaaatc aaacggaaca aaaccgagtc ttgctattta
   180421 gagccagggt tcctccgggg gtcacaacca gagacctacc agccccatgt aaaccacttt
   180481 cggaagggac aaagcagttg aactctttag aggaagagtc taaccacaag tcaaactgtg
   180541 aacatcagaa ggatcgatat attggtaata gctctacacg agagaattga aactccacct
   180601 gcaattccga gtataggaga gtccagtcaa taataaagtc ctggttgcag catcgggtaa
   180661 atgggatcca ggtaaatggc ttactgttcg gtcaacattt catgattcgt aattagtcaa
   180721 gctccggccg gttcctatgt ggtgaatagg gatatattta gtattaaaga catgcgagtg
   180781 ctccgttcgt cagtaagcga aagagactga aacctgggag aattccgctc tgttaagaga
   180841 gagaactaac gaaaattgga gactgacgga aggaaagggg ttcctccctt ctcctttagg
   180901 ggagaagctt ggttcctcct tctccgctga gaggggagaa gagctgggtt cctctttgaa
   180961 aactctttcc gtataggcca gaaaacagct tgcttagaga aagactgact ctcctacgga
   181021 cctggtggac cttacagtcg agttattgca tcgatctcac aaactatcaa tttcataaga
   181081 gaagaaagat cgtttttaga tcatcaagtg aggacaggta gtagctctgg tagagcgagg
   181141 gactgaaaat ccttctgtct gcggttcgaa tccggactca cttctagctc tggcacaagt
   181201 tcctcatcct tagttgtttg atgagcctgc gtagtattag gtagttggtt aggtaaaggc
   181261 tgaccaagcc gatgatgctt agccggttag agcaaaggac ttgaaatcct tagagcaaag
   181321 ccagggactt gaaatccttt ttgtgtcagc tctttggaag tgccttttcc tttacttcag
   181381 taaggagtct caaaatagga aatacctagc tagcaaagta agcaataacg gaaggtaacg
   181441 aattctccgt ttcgatatta acaatccgga tctagggaaa gtaggttccc gcatcacgta
   181501 aatttcattt cttttgggaa aataatacat aaaccttttg agtcacagcc acctcagcac
   181561 aagttactcg agtagcacag aagccatcat caatagcttg cttgcctggg agctcaacca
   181621 cgaattctct gtcttctaac ctttctatca cttgaggatt atctacgcaa ttcgtaaatg
   181681 atcaaactag atagtccctt atcttactgg ccagtagtag aaggggatct tgaatcaaag
   181741 agttcctgtc caacaagcaa ggaatgtcag tcataaataa tgaaatccat ataactctac
   181801 tccgggttgt gagaacatcg tgcctgttgc gattgtgtgg ctttccgcat ggttggagac
   181861 cccctatgaa caaacaaaac agtagggtgg tgtaggagaa ccccgactcc ctaatgcaag
   181921 atagagctct tagggtgcgt ttcgtctttg tcaggaagaa aaaagtggca agaggagtgt
   181981 atccataccc gtaccgaaga gatcttggga aggcatctct atagatttag tagttggact
   182041 accaaagacc cagacagctt caaggttagg tcttcagtgt taggtcagtt cgaggtcagt
   182101 tgttccctcc gtactgttgc tagagagctg ctttccatct atcttcctac atgaaaggat
   182161 ctaagtctat ccaaataaaa tagcccagaa aatgacagcc atcaaaaggc gcgcacccat
   182221 atagcctcgg cctgtccaaa tgatgttcag cggtctctac ccaagtagct gtggcccatg
   182281 atccaaagga cccgcaacca gtcaatcatg ctatccttac cttccaacca atcggccaat
   182341 cacgctatcc ttaccttcca accaatcggc caatcacgct atctccttac ctttcaacca
   182401 accccttcga ttccgcttct gcagcagtat ataatctcgg tcccttacct tgatgcctac
   182461 agctcaattt gttttccagt gatggcaaga atccgatccg cgaaatactg ctttttcttt
   182521 tttcttgtgt tgtttctgaa tggcatcata gctacacgag ggaaagcgat gctgcccact
   182581 ctgccgcaaa agggggccgc tttcttcccc cccaaaatgc cagttccacc atcagggccc
   182641 agcaagcagc ataattctgc tcctcgatcg gacttcgtgc aattctttta tatgtaaata
   182701 agggaggggt ctcgaccaca tttttgagta atagtaatag gctaaggcgg attcgtctgc
   182761 ttcgcttacg tagtcaaaac attctcgctg gacacctggt aaggaatatt tgtatatgcg
   182821 ggaaagatac tctcacctac agctcccgtt actagtagtt ccggttagcc cacttgcccg
   182881 agcacactct caacttgtag atgatccaac agaaaaagca agagaccacg aaagcacgca
   182941 tgaaaacagc ccttttgaaa gcatacccaa ggcacccatc caatctgaac ttatagacat
   183001 caagaagaag atctattaac acgcatggct acctatataa caagttacct ctgacctctg
   183061 tctcacgacc gcaaatataa tctgtagctt catgccctga cctgaacctg atgccaagtc
   183121 ccatcttgcc tatgttgccc atctcccatt taatcggaac ggaagtaaga aatctaatat
   183181 ctgtacggac cccaaacatc acaatggatc aactgaaaaa tggctgttgt tctattctca
   183241 ctcaactgga aactctcctc cgcagccaga gtccaagtga aatgactatc tttcaaacac
   183301 tctgtgatag gtgctgtggt gctgaagttg cgaatgaagc gacggtagaa tgtggcaaga
   183361 ctatggaaac tacgaacctt actagtggag gtaggtactg gccattccac aatggcacta
   183421 acctttcccg gatcagcctt tgactccttc agctgaaatg caaaatctca agaacaaaaa
   183481 aaggatcccc cggaggcttc ttcaaattga tatagagttt ctcttgttgc aacactatca
   183541 ttaattggcg aagatgttcc atatgttcaa cggcattttt acgaaagacc aatatctcat
   183601 caaaagatac caaaacaaac cgaccatggg cgcaagacct gcgtcattaa ttgcataaac
   183661 gtacttggag cgttgcttcg accaaacggc atcatcatcc actgacccct tgctcccaag
   183721 ccaagtccag gttttttttc catctctata tgagccacgt aatgatttgc ataggatcaa
   183781 aatccagaga cacactttct atagcattaa caaaccggaa cccggactca agtcattcgg
   183841 tcatagtaat gatttttaac aaagaccaat tgttaggatt ctttgcctcc ctatcacatg
   183901 aacatcttaa tgagatagaa atgaatagcc atcaagaaag ggactctcga agattcccac
   183961 tggaaacgga ataagaagga aaagcagaag gtccgaaggg cttgatagat ctcattattg
   184021 gatagattat cctagtggtt ctcacttatt ttatggtact attatcctag tggttctcac
   184081 ttattttatg gtacttttga accatttttt ttgaatacat agtagaaaaa aagtcatgca
   184141 aaagagcgta gtgtaagaga aagagcctgt caagtaggtc tactcaatct tctatcaggc
   184201 agtttcaaag tcatagatct ttcaaagtca tagatttcca agtcatagat tctgctggca
   184261 gtttcaaagt catagattct tctcgaagaa aataagtcat agttcgcttg ataatcagag
   184321 ttcacttcat agttatagat cacactttct tctaaacaga cttctatcaa tcctttggag
   184381 aatcctaatc cacccgtctt ccccagtccc tgagcccagc ttgtagcaag ccaactgttt
   184441 gactttgcta agagaagaga gagaagggaa agacagacgg cagaaagcct tagttgctat
   184501 ggagtttgat tgcttcccct gggcctctgg cgtaaaagga ttcgcacctt tgctagcccg
   184561 gtcccaatga accgagcggg gcgcacactg cagcttcctg cattcgtact tctgactagc
   184621 tcccatccta ttcttttagt cagtctagct agtatcggat tcggaaaatg aaagtgagat
   184681 ccttgtactg tggtactttg cctattcact catctccttt agtcgcaagg aggcaaccca
   184741 aaacagcaga gccaaaccaa accctaagtc aagcacagtc acatcagcac agcactcgag
   184801 accagtctag tacaggcgca gacattagag ttatagatcc acagcaaaag cctactttga
   184861 aaccttggag tacttattcc aggttattta aaaggccaaa gtcgggtctt tctttcacct
   184921 tgaataacta tcgataaata aagggctttg agaattaacc tcaccctttt tctaaggcga
   184981 agtgggaaat gtaagataag gattccggaa gcattggaaa agcagcgaga cgggcctaca
   185041 gtaaaaaaag gtaaactgaa gctacatcaa ctatcgaagc tgttgagtcg gcagaagaag
   185101 tgaaatcatc tgcagtagcc aattaaatta ggaaccatca gactgatcaa tccctagtta
   185161 aagctatggt tctttgtagg ctcttccccg gctagtcctc aagccatgcc agtcataata
   185221 gaatctcttc cagccaaggc agttaaaaaa ggactagagt aaagggaggg gcacacaagg
   185281 ctcgttccgt acttgactta cgagctcgcc tctatctcta acaaaggaaa aggattcaat
   185341 ccagtcccaa gcgtacccgg ggctaacctg ttttaccgta tccttagagg tctgcccgtc
   185401 ggtacctcat ttaattaagg cggcccttca accgcttttg gggtcttttt cgacttgtaa
   185461 ttgcaaaagc tcatcgggag tacgtatcct ataaaagctg ttacaatcat taaaaagaag
   185521 gtaaaccaca atgagaaacc tacttgtact agtaagttga ttaccatttg aagcaaaaag
   185581 tgcattaaga gtcacgatta tgctcagggc gactgctcca gtcagtactg gtatggtctt
   185641 agtggctctt gactatttgc atctttctat gagttggcta ctagagtaat caaagagtga
   185701 cggattcagg aattacttgc tagagattgg acaagtgagg attatcggga gggtcgcaga
   185761 tttgctcgcg aacaactatt cggatgggga acttcggagt gaaaattctt ctttacccac
   185821 cccaactgcg atgcaggatc ttcttgtcgc ggacaaatgt ggaatagcat ggcctagatt
   185881 gtgtgtgtat taggtagttc tctctctttt ataagaaaga actattatac aacatcccca
   185941 ggcttgagtt ttcttctcaa ctctttctat ccaatagttt gctgctgctt tctttgattt
   186001 accccacaag gaagaatcag gcttatccta ttatctttat gccaactgta tttaaatcta
   186061 tcatcacatt atggttacac cacaccattc gaaagacgaa catcaagatc acatttcagg
   186121 gactacaaga ttttgagatt ggcagcatta agtagaaagc attattgtag aagggccccc
   186181 catccaatag atcaggggtc ttgccctata acctagtgaa tagggaagaa cagatcaaat
   186241 atgtctagtt aaaatgtctt tcctttgcgg cggagtgaac taagcaccaa tcggaatgcc
   186301 tagcgtgctt gcccctcttc cctctgcttc gacttaaaat gtgatctata cgctcttcga
   186361 tatttttaag gagatctttt ggtcgtatcg tagaaaaaga aagatcaagg cggagtgaga
   186421 tgtccctgtc ctgtaactat caatcacttg aataatcgaa gagagatggg atcctagggc
   186481 agatgaaaga gatgcccgtt tcatgatcta ggtgccgttg attgattcta cttcttttcc
   186541 ttctttctcg agatgttgtt ggtcttcaat ctactgatca taggtagaag agagagaaaa
   186601 ttcatcttat ataaggataa gttcgttctg ttgcacttct tcatgtcttg gttcactgtc
   186661 catctgaaga taggaagtga ggggcgcacg gaaggaggta gcttcttttt cggtcttgtt
   186721 tttcaacaag cggaataacc caatttgtat ctcggaaatg aatcccctat tgaattgaga
   186781 tctttagtac agaaatcatt ttccattctt tttgtccttg gccgcattag caaaacattc
   186841 ttatctgact ttggatccag accttcgaac cctggaacga tggaagctat cgaaaaacta
   186901 acttcactcc atcttcccac ccattctgtc gatcaaatgg ttataatgac ccaaccctgg
   186961 aatgaattag atgcataaag tggtagagat gtttgactga gatggatgtg tcacttgaag
   187021 cttagagttc catgtgtcag tcaagcgaga gggctagatc aaggtggcaa gcggaaggaa
   187081 gagggcatag agtcaccgac taaagcaagc caggaaaggt aattgcttac agacagacca
   187141 gatttttgaa tagcagctta ctctcaaaca ccgtattccg ccaaaaccat ttactacgca
   187201 aacaagaccg gcaactggtt gagctgatag gaccacagct gagattgact caagagcgtc
   187261 tgtggctaaa agactagcag catattcttt cttcaattgc gacaggagct cattctttcg
   187321 cagcttattc gtcgtttggg caaatggatg tgggatggag cttgaactaa gggacccggg
   187381 gcgtagcctt gattcaaagt gtctaggtac caagagtaaa ggaaggaggg ctaactaata
   187441 taataggggt aggggggcgc taacgagcca gaaagggccc ctttattagt aaggttgctt
   187501 gcttgtcaca caggtcgtct ttggctcgtc tccttccgcg atacgcacct ggtagtatcc
   187561 cgcccggcca tagatccaac ttcgagaagt atctcgcgcg ggcgaagaag tctgcaataa
   187621 aagtggatac ttgtttttga tagttaggtt accttgttga gcgcccgata atcaatgcac
   187681 aaggctcccg ctttttctgg aaaggggctc cccaaccttt tcccagcagg caatcaatat
   187741 agggaaaaac tgccttggag gctggaatca aaataaggcc tccatgagtt cctgaaattt
   187801 attcctgagt tcaaccaatc cccttaacta atagatgcta gttggggggc catccgctta
   187861 acccatagcc ccagtctaaa tagttggggg tttggctcca gctccaactc gatcttgtgg
   187921 tagactgccc tactagggcg acttggcaac taattcgtgg ggcatgatat cccaaaattc
   187981 ctcaagtact tgctgcactt cctgagaaag aagtagtctt ggtattggat ccgctcttct
   188041 gagagcatga acatcaatta gattcaattc ctcttcttta ttcttaagag aaaacccccc
   188101 cccgaaccat tcttaagacc accaagctct ctcgaatgaa ttctactctt tctgctttcg
   188161 agatacaaga gtaggcaaat tgcttcccca ctaaggtgta aaactttgtg actagatcgt
   188221 cctgaaaacg gatgcgacgg gaagaagtgg catttgtaag tgttgctgac ttaacattta
   188281 ggtttcggca taacaaagct tgcactgtct tttcgcactt aggcgcacag cgtgccattg
   188341 gtaatgattc tactacggtg ccacaaattc gcaagctgat cctaagtaat cgttgttgtt
   188401 cattggattc cggaggaact acttcgttag gattggggaa ttgctgcgat tcttcctgaa
   188461 tagcctggag gctcccgtcg agagtcactt tgaaagtcgt acctaaactc ttacgactga
   188521 atatgataaa gcctataaaa caaagagcta ctatcatttc ttcattatag attgagatct
   188581 tcttcgaact taatgcacaa atagatagaa tagcagcaaa taacatcttt ctaccatcca
   188641 tattcgtaat actcaatctc atttagaaag cttatcccca tttttttttc agcaactgaa
   188701 cgggaagtgg cttaggaaag gactaatcgg atgcgctcgc ccagcgagaa aggccctgac
   188761 cctgccgacc aagaaaaaaa gagaacgaaa ggagaagaga acttcgtatt ttccttattt
   188821 gagaagaggt acaaagtgac tcgactgaaa gaagaggtcc gaaggaacaa aggagctcga
   188881 ctgtaaggtc caccaggtct cgacgagcga ctgaaaggag aggaatggtt aaccttgaat
   188941 gctattaata aattctacag caatagtacc tcggactcgg aaagttataa cgaaaatggc
   189001 taacccaata gcggattccg cagctgccac cgttggaacc aatgaagcaa atacttgacc
   189061 catcatatca tccgaagaaa cggaaaatac caaaaagttc gaattcacag ctaataacat
   189121 tgattcaatt ggcattgaca taataggaat atttcgtcta ttaaggagga ttccccgaat
   189181 acctaaaata gaaataatca tagaaaatgt gaaatatttg ataagatcca tttcgggaac
   189241 gtggaatcta agataaattc aaatgttatt agatgacaag ctcgaccgaa cacctgaagt
   189301 ccttgatatt taggttaggg agacacgcgc gcattcctga caacaggcac gggcgataat
   189361 ccaggcaagc ttccccgcaa gcctcacaac agacacgtcc cagctgtccg accgtaggcc
   189421 ccgctgctgc ggcaaggcgc ggcagccctc tgaccctgcg aaaaagagct tcccgtcggt
   189481 tcaggcacca tttttttgaa taggtgggac ttcggtgata ggttgttttt gatcccatga
   189541 gggatctagt gatttccccc gttcccccca agaggagatt ggttaggaac gggatgggca
   189601 acttcagccg gtgctggcgc ctgcgtaagc ggctcaagag ccgctaaaga gaaccaatag
   189661 acacgacagc tgggccagca ccagaagtgg atttactaaa tcccccttat ctatttctgg
   189721 gtaaataagt tggtgactaa caacaaagac aaaaaaactt gctaccaaga agacgatgga
   189781 taagagaaaa attagggtat tttctccttc cggtttgact ttagaaaaaa aaaaggaata
   189841 atttacaccg actaagatca aagaaactag cagactaatc actaaaaagg cctttggttc
   189901 aaattgttac atctatctta acttactcaa ttatctcgtg aactatctgc ttcaaaaaga
   189961 gagttggttg aatgagactg aaaccttctt tcttcgagga gggcaccact tcgactgatg
   190021 cgggcgcggt tccctcgtcg tgaaataagt aatgaaaggg aagacccgcc cctggtcaac
   190081 tttattgttg cctgtatagc tttttagaac agagatctag caacgcattc taggcacaga
   190141 tcattggtat tggatgtatc gttaggttgt gccgagtcaa atctgctccg tttttttttt
   190201 tcgttgcaga aaagagatcc cttccctccg ctttctaaaa tgaggaatat gaagtccgtg
   190261 gggctgcagg tactatggat cctctgactc ccaatcgggt tgccttccct ggtctcgccg
   190321 gtcttacctg taggtcgtga tgtgccttga gatggccgtc tcctgtcccc ctgccggtgg
   190381 ggactctgct cccgggttgt cgctccgctg cgtctggccc gtcctctagg cacctttgga
   190441 aggcagggag tgtgacaacg tacacgcttc cctttactcc atagggcctt ctttctcatc
   190501 agttgcaggg tttggtggcc cgaaagaaac ttggcttcgc caaaaggcct catctctgga
   190561 agcccggctc gcgaggcgtc cctcccgctg tagggttcca aaactcgcct cgctcttggg
   190621 acatgctatc tttcccctct ttattctcaa gtaaagggtg agtcccatgc gtcagtttgt
   190681 ggatcgcggt ctcacgcact aatccctaca ggcgggtgcc cgtagtaggc cggccgccct
   190741 acctaaacca atcatcatat cggtccctaa gccccattgc tggaaaggct cggcttcaaa
   190801 accgtacgtg gggcttccgc ctcatacggc tcctctaagg atggaggtag gcccagccca
   190861 ggcttgcgcg gttaaggttg ttgtacacct gccaatcaag taaaaaaaaa gaagagaacg
   190921 aaagctttag ttttgggggg gttggttatt ccgtgtatgg atgatcacct tgagccacga
   190981 atttagtaat gcaaggcggg cttctttctc ccttcccgcc gctaaatcct ccgaaaacgt
   191041 ctccctccat tcggctatct gcctagcccg gaggcatcct tttcttgaaa gagtgcccac
   191101 ttctgatcta gctcgcgcac ctccggatcc aggcgcgcgg ctacttccag acgacgggcg
   191161 ggatcctccg cgttatcgaa gttccgcgtc aacctctgga cccgcttaat atctttctcc
   191221 aattcgagat cccgcgctcg cacagaggcg gaactctcta tttctccgta taacaacgaa
   191281 gaggggggga gcgaatcatt aagatctatc gggttaccat tcctatcagt agctaggccc
   191341 tggtcctgat aggggcccac tctatgagat gccccagctt cctggggcac ttgatttacc
   191401 gagggttccc cctcttccgt ttggggcgcc tccgccacct gggagtccat gtccgttttg
   191461 gaggaggaga atgattctcc gagaacgtcc agttcaaagg aatcctcctc ccacgtggcg
   191521 gagctctcag ccccgttagg gcccagaagt gctcccgctc cgactgcata cataagaatg
   191581 ggatctaaca ggggcaaagc ctgaccaccc agtagataga cgactttgat ccggatcaaa
   191641 gatagcacga accccactaa gaagagatag agaatcctct tcagcggtcc tttcttacga
   191701 aagtaaaaaa gtccaaatat aaataccact agcgcacaga atgaaacgca cgtagtgatc
   191761 attatagcgc ttccttctga tcctagaaaa cgtccgaata aagaacctga tacggaacca
   191821 ccgaggaggg gcaaaaatag tcgaagcata tcaatattaa taaccatttt atattttttc
   191881 atttttgata ttatttgaga gtatttttga ataaataatt tacggcgagc tcttccgagg
   191941 aatgcttaca atagaagtgg ttgtggattc gaaccactgc aagggtttac agtcctttgc
   192001 tctaaccaac tgagctgaac cactttgttc tcaactgaat ctctttctct tatttcattc
   192061 cactttgttt cgtttagtga tagttagaga gaaagatcac tccacaaagc agccttctga
   192121 ttatatacgt attattctat caatcggaaa gtagagtctg gaatgagatg aatcttctta
   192181 tatacgtatt tggataagca atcgataagc ctggtttgtc tgtctcttct tttggaacga
   192241 gatttaactc tttcttcttt gggaactaaa agttgtttag ctttcattct tccttacggt
   192301 accctttcag tccaactgag caaattagtc aaactttgta ctcgaaatgc tacttccctg
   192361 agttttgttt caaatacttt cttacttcac tgggaatatg ctgttattga actgtgttct
   192421 ttccttattc ccctggtttc accggttggc ctgtgcccgt actactcgta agctaaccac
   192481 taacctaatc cgcatctatc atccggaaca tcttctgttg ttttctgaaa cttttttgta
   192541 ttagcttgtt tcgttatcaa agggttcgtt tgtgtaaggc gtagttcacc ccctatagaa
   192601 gtgagctggt taatcacagc ttacttcttg agtgatcccg gaggcagggc taaggcagag
   192661 ggaaggtgta gttcgcttac ttctacctgg gagagaaagt cccctccttg agaagcggaa
   192721 gaaggggaag gaagactaat gggatggtta aggcatagcc gaggccatta gtctgagtga
   192781 gcggctcctg ttgctttgca gctgcggtat aactcctatc cctgtttgtt cgatgggaat
   192841 aggtattact aagccagcta gtttcctacg gcgagctcga gcagaaggtc tgcaagccta
   192901 acaatttacg tacctcggga gggaaatcag actcagtgga atctatttat ctaatcttac
   192961 ttgaattgga gtagcaagcc cttcaactgg cacaacacaa gcaaaaggaa agaggcaagt
   193021 ctgctatctt cgcctcgttg tctgccttga cttagtcttt ctttccgaac agaaatccgg
   193081 gtttcatcgg aaagatcaca aaaattaatc cactgaggga cttttacgag aaggcttttt
   193141 ttcttagcgt ttaatggcat atttatgagc cggttgtccc aactactata cgaacagtcc
   193201 tctccattgc tctaggccaa ggctggcaaa tcaaacaact ttatgttaat aacaccttta
   193261 acttatgaca ttttaatgaa tgaggtgcgg gcaacaggcg ggaataacaa gactctatgg
   193321 cttaattcct tccccaccaa aacccttact cgggcctcga cagggtgaga gtagttggaa
   193381 atgagcgtct cctttgtttg cgaggaggtt gcgttgcttt cgcgtgaaga ggacctgcag
   193441 acggcataat ttgcttatgt taataaggat atgaggtggt gggatgccga atggtagtct
   193501 tattctgtgg agtcgatcta agtcgagcta gccctagtat ggacggtttt gagtgccggg
   193561 acctttacca attctgatct acgatagggg tattccagtg gtatgttaat ttgattttcc
   193621 tccttcacac aggccttcca atgtagattc ttccaaagat atactgacta aaaggtattt
   193681 atggattcgg attggaggtc ttgggaatga aagtcttata gaggagactg gcttcgtaag
   193741 taaagtaaat taattttaga tagatagctc ggagaagctg gagaggcacg gagtcgagaa
   193801 caacatctgt tctgtatact agtcgaccag agagaagccg acttatccga caaggctaaa
   193861 aaagaatggt ttattgacca gtttccacgg actttcgata accggcttgt ggaggtgccc
   193921 attatgtcgt tcgttatgat gcttcttgtg attgaggtgt ccggtgggtg gacgttccct
   193981 tatgttcacc tctcgccctt cgcttaaaaa caaggatcga atggacgtgc tatttttgaa
   194041 ctcttccagt gaaaaaaagc gatctatgca tttatcatag gcaaaaaaaa taaggtattg
   194101 aataagctca gttctactca tatctatgtc aatttgatga aagcaattcc tacctttggt
   194161 agctctcctt aagctcggaa gtcacggaac tctcttccta aactgaaact caaataggaa
   194221 agtacactga ctgagttcag tcgtgccggt ctttcttatt ctgattttca gagagtgaag
   194281 tagttctggg aaagagaaat agacttactt tccagtaaga taagagccaa ggaagagaag
   194341 gtaacgagag ctagagcttg aatcaaacag gtcctaggag tcaagtcatg agcgtacgag
   194401 tctagagtga atgtcttatt tgtttgaatg gtcctgttat tgctaggaag gtatggaaca
   194461 cgggtaagct agccaacaca gggcaataca atagtacaag agagggagta agggatgggt
   194521 caagtaagta aagcacgcat aggaataaag agagcttccc ctgccttcct cggcacacgc
   194581 atataagata taaaggtacc ccgtgggcac acacacgcga gagttggaaa tgcatgattg
   194641 gccgattcga taatatccgc ataatagagg gaactcaaga ttggatactc tatgtctttc
   194701 tttccttctg agtatttgga gatatctgaa ctggatactc tatgtggaat ggacactcta
   194761 tgcctttctt gactaatagg aatttctacg tgttaaacac tcaactggtt tcttccctgg
   194821 attgttagct ggaatggctc aattcgaata tttacgtgtt aaacactcaa ctgtaatggc
   194881 tactctatgt cttcctccta cttaactcag tggttagagt attgctttca tagggcacta
   194941 gtgattggtt cgactccaat ccaatagtag gtaactgctt tccttctgtt gcttgtctga
   195001 gactttccgc gtatatgata gaacgataga ttgatactct atgtcccttt ttgatcccta
   195061 actaggaata gatgggtgac tgttaaccac gagactgagc tctttcacct tgttattcat
   195121 agataggttt gttctgcttg cctggcttgc cttgattcct ttccttgctt gtattttatt
   195181 gattggcttg gaataattgt ttgataactc ctccttctat cactggctta tatctaggga
   195241 acaccggtag gcaaatacag gtgagtgacc acactccctg gcttaatgga cctgcttgta
   195301 gtaaagagag aagtcttggg tcaaggaagt aaagaaagaa caggccaagc aagtaaggaa
   195361 ccgggaaagc gagccaagca agccctcgag tattggagtt gggatgggcg cgtaagtgca
   195421 catcaaatga gaggttgaat tccttccacg cgagagagct tttgaatcaa gctaagcaaa
   195481 tcaagctaag caaatcaaag aaggggttcc ggtcaagcta attaagggag gcccaggttt
   195541 tggttctcaa aagtcatgca cttaatagct tgcaaaagga aagcgagcct atatataagc
   195601 aggtgatcct ttcttagaga gctcaagttc ctaaagctaa agagaaagcc aagcaagcca
   195661 agccagatga tacgcgcatt tgaaccattg accgaaagga aatgcactcc caagcaatga
   195721 gagaaggatt cgaactagac ttctcatata aagagaaaga tctacagcta caactccaaa
   195781 tagactctta taggaaagga atcccagtag ctacttatct gataggctgg ctcatccaca
   195841 gcccattcct actacttatc tattgatcgg aaactccttc acatgaggct tcttaggagc
   195901 ccttctcttt cttccgttac tgtgctgcac gtattcgcag cagcggatgg gagatgaacc
   195961 gagcaactaa ctagtaccgg ggaactccca ctccaagcct tgactatacc ccactcaaag
   196021 ccttaactac aatcttatct tggaattcct tcctccgtta gcagaacata cgacttctct
   196081 gtatccaaag caggggatta ccccgatcaa ctagtaccga ccccaggaac tcgattagca
   196141 gaacatacgg cttctctatt agcagaacat acggcttctc tatatccaaa gcagcggatt
   196201 gggaaaggag taaaccctag aaaccgaagc caatagccaa gacatgaata cacttttgtc
   196261 gatccatctc acagacaaag aaagtaggct tatgtacggg acaccaagat cggtatgatg
   196321 ccctggccct tacccattca cctggaccct accattcata cctaagcgga ataactagaa
   196381 agactgccga ggctaactcc cggaatcgcc aacccgaatt cagctaacag ctgctaaccc
   196441 gccaacctac catcaaccta ccaataagaa tgaagctaac tgctaaagcc atgcccttct
   196501 ctaacagcta aagctaagtc ctcaagaaag gggaatccta tggttaccta ggcatccggc
   196561 tacctatcag gacgagaagt tacgtagaaa gggaagagtt ctagagattc ctccgatacc
   196621 ttttagctgc ttcacgcaga gactccaagg cgttctaacg gaagaggaaa gagttgttta
   196681 tgccttccct tcgcccggaa agagtttatg ccctctgtct tagggttcat tcaacagccc
   196741 catctgatcg ttcatatgat tcagcacact cttccgtcta acatagtttc cttgttgctc
   196801 ctcctcgaga tgcccggatg gatagaagac ttatagattg aataactaga ttccgcggat
   196861 gtaatgtagc tgatagtagg agtcaacgta ggaaggggaa gatcctcacc caagcacacg
   196921 ctagccttta tacgttagca acatccgcta gcctttctac tggagattcg catctcaaca
   196981 tccgaataca ctgaactcct ctatcaggca tctcattcac atcattcctc tatcctggca
   197041 gctggatatt ccatcactcc tctggcatct caacatccga atccccgagt tgacttccct
   197101 tctatcagcg gaatagcatc ccttcggaac agcagacctt ctgccatttt ctttagtcct
   197161 ccattccttc tttagtttgg taggattagc agagccttct atcagtttgg taggaacagg
   197221 atcccatcta tcaggagcat ctcttctctc agttgaacag catcccattg atcttccttg
   197281 ccatagcgag agatgtatcg acggacacta tagagtgaac tcggcgagag gggtccctaa
   197341 ctccaggaga agagttgtca atgggcttag attaggaaag tgttgtcaat ggcttagatg
   197401 aatcaaagca ttagcttcct cttaccaagc aagatcatat agggagggaa tacccactat
   197461 ctatgggcgt aggcaataag tagctccctg tttgtgttca ggtaaagccg accctgcttc
   197521 ctctccgttc tcaaagcagc aatacactca agcactttac tcgattgaac aaggaaattg
   197581 tattaggtga agaggactca gattccggaa caaggaaacg gcttatgtct tccctatctg
   197641 cagaagcagc aggaatgggg ctctgactca ccgaatacct tcatcatcca caagcaccca
   197701 actgagggaa ctgttcttca acatacgaca atcttccttc ccaacaatca agctagtcct
   197761 ttcttccgta cttttgttgc aagattcgat tggccgcttc tccttaccct ctcatattct
   197821 gtgtttcata tgcctctctc ctccgctttg cttccttagg gcctcgctgc tttgaagtgg
   197881 aagatgaata gaccgaggct ccggctactt taccaggacc aggagtctct gttaaccttg
   197941 cagacctttc ccacctatag ttcgttgact gaggaacttt cctacctata gacttcacag
   198001 ctacgacttg cttgctgata ctgatgagga gcaagaggac caatccaaac ctatagactt
   198061 cactgctacg gctgctttag ctctactatg ggtcgggagt cctgctgatc tgtccttcct
   198121 cgtcttctcc atgtcaagac atactggact tctcaatcag taagagagaa agggctaacc
   198181 actaagtagg agaattgttc gggagatccc gctgtctctg aacttgctta cctagttgac
   198241 aaaggagggc agttgctatt gctaaaccaa aggagaacac taagccttac cactaagagg
   198301 agcaggtata aggggggaag gctaagatag cagggttgaa ggatcgttga gacatctgtt
   198361 tattcttttt ttacattgaa cagggatttg accgactcgc aggcagcgct cccgaagcga
   198421 gaaaggggat tggctcaccg gccggcgctg cgtcaacaag gcccttgggc gacattccag
   198481 gtctctcgaa tgcctattca gagggatacg ggacagagca actcgaagtg aagtaaagtg
   198541 ttctagttac accagttgga ttattaaagt caaaaacact gattccagta aggagttcaa
   198601 atttctattc tcaggcccgg ctatgtgatc agattttctt tggctattgg ggcagaggac
   198661 cggatgtcgc cttctcttac ttgctcaata gagcgaacag gggcatgcta cttttttttt
   198721 ggtcttgtct catttcagtc ctcaaaaggg gagaagaggc gcgtctcacg ccgctttcct
   198781 cacttctgtt tgttagtaaa ggttcgatct aattgaaata ttctatgacg ggatccccgt
   198841 ctcctctttc cttccgatga atggattgac agcttacagt gccttgtaga aaagcattgc
   198901 ctcattgttc attcactgat ctacgactga tatagggcct acctggctca tagagactcc
   198961 gcctggaaaa tagagaatag ggccacatac acctttcttt tccacaaaaa tctctcctta
   199021 agcgttgagg ggacaattga ttcgtaggac cattaactga tattttcact tcttgtttag
   199081 caaatggctg gtagatcttc attgttctta ccggaggaat cataaatagt cgcccagtca
   199141 acttcctgtc aaatcaagac cgaaaagagt tctctatatg gaacgtaaac tcatcttacc
   199201 gggcgaaagg gcacataact gactcttcct tctttagctg aagcgaaagc attggacagc
   199261 aggtcttgcc tgccccaatc aatacagaga tctcgtccca cactacttca tctttccttt
   199321 actcctttta ggggtcaggt ccgcttaaca tcactggtgt agaccgaagc ctatactcac
   199381 tcctccccat cagaacgact ctcagcttca gccattcgag tcagaaggga gagagggggt
   199441 cgaagcgcga tgcttctgat ctgccgattc cgaggtcagg gatgatgatg gctgtggtga
   199501 ctaggcctag tggcagctaa tccaactgta attgatacaa accttgactc tcgctatgac
   199561 aaggaagctt tcaatcaaca gaagcaacaa ctatgcctta aacggagaat ataactattg
   199621 ctcacttaag accgatttca agcaatcatc caagcagaaa tctcttcctt tcgataagcc
   199681 ttgcctggcc ctgctttacc tgccccctca aaccaaaaag gcagctaagc cataccccaa
   199741 aaccgactat cagatatatg ggtagagtca gagtacgagc tcaatatgga cactaccctt
   199801 aaagaaatag gcttctccgt cggagacaga atggctcaga cctggagaca aacaggcgaa
   199861 acttttctga taatgggtgg gaatgaagga gcaggcgtgg taaactgaga tcaggctcgt
   199921 tctcacaacc agaatgagaa ctcctctcga agttattact tctcaacaca gaagctctga
   199981 tccgagcgag actcttcttt catttcgata caactgtaaa caagagtagt gccggtactc
   200041 attgatgttt ttgtaattct ttcagcgggg gttgataatg ctaataccag aggagagtag
   200101 ttcccatagg tgatatcagt gaccaaaccg gaccgggagg agtacgggcg ggcttccttt
   200161 cgagcggggt ggcgagagtg gtcaataaat ctcactttct agactacggt tacggtctgg
   200221 atagtaagaa aggaaaagaa aggtagtaga tcgaagttta ccagagagat cttccggaga
   200281 cttggtagta gtagcgagcc ttcccagatc gagaagcgag aaatcttccc ccattacaga
   200341 ggcgcagctt gcctctgtct ttcccccata taccttattt taagtatcag actctcgaat
   200401 gcgactgcac ctatcccttc ttcggtgcct cttactccga acgagtcacc cttgaatatt
   200461 tcaattggtg tgctagtcaa ccagtcgtca tcccggaatc ccactgagtt ggtaagcaag
   200521 cctgggcgtg gtaatatgcc cattgagggc caagcagctg catctgattc cgactcttct
   200581 ttctgagact caaccatcag gagctcgtgt ttcatgggaa gcagtcaaac tctaacgttt
   200641 cgcctagcgg agccgatagt acatctttct tcctatcccg ataatcgtac atctttccgg
   200701 taggagcaaa gcagaggaag gtgctttatc gagtagttct attgggagga aacgaaagga
   200761 aaaggtaaga gacccgggaa aggcggggac atccattggt gcatactctg aacgagagac
   200821 ggtaggttca tcagaggaag aaagatcggc acttaggttc tctgaccaag catctatata
   200881 tctctcggtt tcggcatctc cctcctactc atcagtctcc agagtggtag aggaatcagc
   200941 ctcatcagtg ttagagtcat ccccctcccg agttgtagtt gaacagatgg aatcaggaac
   201001 atctgtgtgt ggagggccca agtgatacgg agctcctttc tagcgctagt ctttgaatcc
   201061 cgtccttcgg ctaaggttga tacagaacag agaagaggaa ccaatacgaa atcaaagtag
   201121 tgagccggag agtccctttt ccgcccccaa ctctcgattg cccgacctgt tcacataagt
   201181 cattctcaag ggtaatggga aagagagata gaatacccaa taggcatagg gtagctcctc
   201241 tcgtacaagt gttcaggatg tagcgataga agactaaaag gataggatat cgaggagatc
   201301 atagaagagt gatcctcgca tcaaaataca gggcagaagg aaaagaagag acatccagaa
   201361 actagggaca gaaacctgac atccatttcc attgaatagg agacagaagt gacacacatt
   201421 caatccattg agaagccaaa gaaagtcctt caccctttac ccacccatct ctctcagcac
   201481 agtgctgctt cttcccttgt tgcggaatac cacctctctc tccgaatctt tcatctccta
   201541 cacttccgat acatcagaga cattcgcgcc tcgctcttac cgccactcaa ctcaggctta
   201601 ttctcctact caaggtaaac ggcatctcca cccaactgcc aagccgatct ataagattcg
   201661 cgtatagcct ctaccttccc cgagtgtacg cccgccaagc agcgcaaacg atccaattcg
   201721 aataggccat gaaacatgcc tctttctgcc tctctagccg gattctgctc ttagccccat
   201781 gtagatacct ggggacacta ctcttgcttc ttccctatcc gtgctccacc ctacgccagt
   201841 tcctattcct actccggagc ctattcatac gcgatgtaga atggatccct gcaggtctga
   201901 gtcatcatat cccttatttt ccgctagctt ctcctcccct gacagttgag actcttctga
   201961 tagcaagact tcttctctcg ataaagcaac tttcattgcc tccggccaag actgcatccc
   202021 tctcggcttc gctagatgct aaaaccaagg gaaggagttt gttatcttcc tgcagctact
   202081 gttatatgcc tacgtaaaga tatgtgtccg gccccgcagg gggcttccca taggtgtgag
   202141 cgcagggcgt taatgcagct actccgtcaa ccataggaaa cagtactctt atcccctatg
   202201 tcttgtacct ttcagagctt cggctggtta ggtaaaagat gaataaaggt tagcttgctt
   202261 gcttccgccc ctcactccgc ctcgtggcca cgttcatgac ttcatccctc cagctcaaac
   202321 tacgacgata tggtgacctc tcccaccacg ggtctcttta tagcacctat tccgcacttc
   202381 cggcgcagaa agaaagctcg aacccttcct tgcagaggag tattatcaag ctactgttac
   202441 gtttgtgacg caaagacctg attcaactag accgttgaac aaagaatccc agctcgtgta
   202501 aatatggcac aaagaaaaga cgacacctgc cccttcctcg ttctagcctt cctcgttctc
   202561 agtcaacgaa tcggaatcgg gatgttgcca gtgcccaagc gaactttatt taagaaggaa
   202621 atgagcgtag attgatctct gatgctagaa atgatttatt ctttcaagct agtctctgat
   202681 cgtaaagaga tgaaattcca cctgctaatg ggatgttagg ataggtctat ctctttccct
   202741 tctatcagtt tggtgagaat agcatccctt cttattaagc acacaaagca gggatgcaca
   202801 tatatagtaa gttgatcacc ctgagtagtt tccttgccat agcgagagcg ttggactagc
   202861 tgaacaggta tccgaactta aataaaaccc tgactctcca ccttcttcgt atgggaccga
   202921 gtggtagatc aaattggaag tagaaatgtg aacgaaggtg aagattaagg cttggttgct
   202981 attgggatgg gaactaggtg gaaccggccg atcgatggca atcactggtt cagtagcctg
   203041 cagtcagtcg agcttacagg tgtcacatat agcagacttc tttctccgga ttggggcaag
   203101 tgtagagggt cacggcctag ttactaattc ctttcctctt ccaacgctct ctttcttctg
   203161 gacgaggtta ccctatctcg acttacttat gctatcggga atggtgttgc acccatagta
   203221 gttgttctct tctcatcggt acctctcatc catctatttc ataagagaat aaaagttgag
   203281 ccagttgaaa gactagtcga gaagccctat tcagaaaggt agatgagagc ttgcggagaa
   203341 ggcaaagttc tcatttgtcc aatccaccga atactatcct ttccttcttt taccaatttt
   203401 atcgtcgagt tgctgatacg tttgttgaac agcaacagcc tacatagccc gtctccctct
   203461 tttcaaggaa gaaagcatca gacaaatctg tagttctagg tccttttgtc cagttcctga
   203521 aagcaccatc gtggtttctt cactcaggtt tgctaagtag tctgggagcc cgactgtcat
   203581 tttaaattta tcgataacga tttagctgct cgcgcaacca ggacctttgg acctccctga
   203641 gtcgatctcg ctggcgaaag atacgaaaat ggcgctggag gcttctgacc tcccagtcca
   203701 gtatatctat caacgcctga cgacgccaga tattaggctc agtctggagg tccctagtta
   203761 agttttgtac ttgatttaga tgagctaaca ttacgtcatt ttgcgccttc gtagactggg
   203821 ggccctcgac ctctgcgtac aataaatgta ctggaggaag ctcgttgaga tcgagagcag
   203881 cacgattgac tcctagggtg ggctgctgct cttggggcgg ctggttgaga tcgagaccag
   203941 tcgcgccgcc atcaggccca acgccaaaat gaaagttctc atttcccaat cccaacctca
   204001 gcccccaaac aaaatgtatt aatcgcagta gaaacagaac aggccccaat gttggggcta
   204061 cgaaatatat aaaaaagtat aaacacccta acagtgcctc ggcactgaac cgacttgaat
   204121 ctgaactacg attttttcca agtcttacca aaatcggatt tccttttcgt gccatatttt
   204181 ttgactttat ggatttctgt cccttttttc ttcccggtac aatatttgtt ctcgaaagtc
   204241 tgagtttccg tgtactctcc aaatttatga ccaaccttcc cctcagtgat cttagaacgc
   204301 tactacgcat ctttactata tagtgtggta aggtaggttt gggtatagca ggacttgaac
   204361 ctgcgaccat taggttaaaa gcccaatgct ctaccaactg agctatacac ccaaataaag
   204421 atgtagtagt caattaagat tggtgcggaa aagagaagag gtctcaacaa gtattaacta
   204481 gttgatgctg atcgaaccct cagttcgaag ctcttcgcca acatgttacg aggctccagt
   204541 cttaggcggg tcaccattac ttgacttagc ttagaaaggc gaacatctgg gcaagggaaa
   204601 gcgcagtgcg cctggtcctt tcgaaccagt ctttataaac ctggtgcaaa tggctttcga
   204661 tagttgcatc gtaaacgggc atccaataga ttctactcat aaagagatag atcagtagtt
   204721 taggaatgta tgcttgcttt atttttttct ttctttcctt tcatcggaaa atcaacaacc
   204781 taattcaact cacttctttt accgggcgat ggaagactag ggatatatca tttaatcagg
   204841 aagggcatca ccagctacag tagttgcatt ctcaccagcc ttcatagcaa gatttcataa
   204901 agagtattta cttaggaggg ctatagataa gattctaagg tagggttcta tataatctat
   204961 ttatttcctg ttgaggatag tttaataatc tcatagcgca tcgacgtaga tcgcccagtt
   205021 ggttctaggt ggggtctcga gtaagggtag ccgcactctc cttcttttat aacaaaaagc
   205081 ggaggacctt ccctcttagc tcttaaggaa ttctgaaacc tatacacgtt gttaacgagc
   205141 taacctaact aatatagata gaaaaacctg agcgaagtag ctaagggact aggtcggtta
   205201 tttcagttcc gaggaaagag aggactagag ctaattctta taagctaatg tgcgatacgc
   205261 gttacacgtg ttaagcatat acgcgtgtaa catgttcata tgtatgttca ttcacatgtt
   205321 cacatcagtg gtagcttgaa caaacaacaa tttatccctt ctcacatagc atgtctcatt
   205381 catattcaaa gcagactgtc ttcatgctca atcagtagca agtttacttc atccccgggg
   205441 accgtccagt agaggagcgg aaacgactct gttatcttac attcctcatt cgcattagag
   205501 cattagagta tgaatataag caagctttcc ttattccgaa atctaaaaaa aaaagagctc
   205561 tagaagttca gtcggtgttc tctcatctct taattaagat atttcttaat cgagaatcgt
   205621 gagactcccc aacctagtaa aggggcttga atcggtattt tgtttaggga gaaaccctac
   205681 taaggaaagg atgagatata gcattaactc cacttgttgg tattcgttgg gacgcatgct
   205741 tggaacggcc tctaaggggt tgttgtataa caagtgcata attgtccact agaacgtccg
   205801 tgtattttat catcaacctg atgaatgaat ttcaagatat agggctttcc tattatcaca
   205861 ggctgttcaa aaggatctcc tgttcttcca tcaaaaaatc tgctttttcc tggatactcg
   205921 ggttcaaata cccatggatt cgctgtttgc ttactggctt catataatta agaaaacact
   205981 agttttctcg aagcctcttg ttcatatctc tcatcaaaag gggctattcg ataatgtcta
   206041 tctagcagac ttcccgctaa cccaagcgag cattcaaata tctgtcctac attcattcgt
   206101 gagggtactc ctaatgggta tgggttgaag accatatcca cgggtcttcc cgcttaggaa
   206161 gaattgcgag ccggagtttt gttttagtcc atacaatgcc tttctgagtc tactaactag
   206221 atgtgaagaa actgatcacc ctggcgaagg tgtaaactaa acccgactct aaatctagaa
   206281 tcgttttcca ttcataaaag cattccccac atctcactgg aactgagtat caagggctac
   206341 agtaagaaag acaagagaaa ggtaagatgc cgtggtgatc taagccgtca acgagcaatt
   206401 tgtctcagtt gaatccaaag aaagagggcg aagaaactca ttaattcatt gatgagggct
   206461 aggccgagag aaaataaata tgaaagggaa ggagatattc aggtgggtcg aatccataag
   206521 gtcatgatcg agttaagctt gcgcttacgt tttacagcat tgagaacttc gaatcatcct
   206581 ccacaaccct aacctcacaa taaaatcttt taaaattatc tttttagctg tgatttgaat
   206641 gtctaaagtt tgtcttcaac ctccctggtt tcgatatggg ttcaaaactc ccggttaaga
   206701 tcaaaagtag gagctaattc gtctatcaca ggtagtagct cacccgcctc tctttctcaa
   206761 gtgagacaaa ggcattcaag atggactgct aaaagacata tcttaccttt actttacatc
   206821 gcatttattc tttcagaacc ttactatcta ttgagcttga actactaaat ctctattatt
   206881 acataccagg gtttactaca gtttcactgc cctgaaggga gctagccctg cttcttcttc
   206941 agtgtttgct aactgcttct gtgcttaatc ccgcatgata agaggaggtt tctgaaacgg
   207001 acacggactc aaaactccct gagtctatac ctggtgaact ccctggggct gagaagaaag
   207061 cttataattc gattggaaca tttacttcga gggcactcat aactaaagta ctggggagcg
   207121 gtttgttgcc cttgtaggta gtccttgttg gagagtcata gcttatctca attgagagtc
   207181 ctgcgctgcg tcttatctag accgctgcca gccggattga aattccagtt gttggaagag
   207241 ctactgcaac taaagcaaca gatactagaa ctattgaatt cacagctact tctgcaacta
   207301 actactgaga ctcttacttg aatcatttat ggaactctcg tcggagcctg ttctttcttc
   207361 tacgaagcct cctgtaaagg catcatttcc atccgtctca gtaaaggctt cagttgttga
   207421 attacctgga gtttcctcaa cacccactac tagagaaagt gaagatggtt catttacaga
   207481 ccctgtcact ctttcttatc ctgtagtttc atatggaatg gtttcagctt cctctactcc
   207541 tactaggtct acttagcctt ttattcctag gtggcttgct ttcctggggc tgctagtctt
   207601 tcctatccct atggtgtaaa gaatgcttac tatcctattt attaggtaac tccccttctc
   207661 ctctcctttc ttagctctag gcttcagctt tccttcatca cagtgaatgt aagcaacaca
   207721 cccaaatctc ctgagatatg aataagtagg gactgattga aaccatacct catctggaac
   207781 atggaaattg attgctgtgg aagggtattt gttgatgatg tgcacagctg tgtttgcagc
   207841 atctgccctg aaagtcttgg gaagtccaca ctcacaaagc atacttctga ccttttcaat
   207901 gattgtgcgg ttcatccttt cagctacccc gttttgttga ggggtgtatg cacatgtctt
   207961 acaatcccat ttctccgatt tacagatctt ccattaaggg atctaacatt aagggatcta
   208021 acattgattt accattcctc ctatgaagtg aacaactaac caaaccgctc cgccccttgg
   208081 cttacttggc ttcccttcgt ttcctaccat tcccaactaa cctactttcc tagttctttg
   208141 attctgatat tcctattcct gggattacta gttctcacat tcctcttttc tttctggttt
   208201 cccggatttc tcttcttcct actttctttg ctctcctggc tttctggatg tgagggttag
   208261 cttaaaaaga actatctcta gctctcccag ctaagatgta cgatgtctga taccgattca
   208321 agctcactca gagatatatg atttatgtgt tctatgggtt tgaaaacagg gatggtaggg
   208381 gtttcttcca ttgaaaagaa agaaagctta tttaggacct ctgagaccgt ttagctctta
   208441 ttcctctttg gaagttactt tgtgatggga ttgggtcttc tgtgagggat cattctatta
   208501 aacgaataaa gtgaacgttt ccggacgttt tctggttggg agagcgtaca aagcaaggac
   208561 tcggaggtcg gtgtagttag gatagtaata taacctatta cctattggta acctattgct
   208621 gtacgtatcc cctataagat cttgtccagc atctttgtct agctaatctt agggactgta
   208681 agcaaaggat gtcactatag ctaaccttcc caagtaacag tacctaattt gaccaatttt
   208741 tattttataa gaaaacaagg aaagtcaact accctattcc caaaccatcg gtacaggaaa
   208801 acaaggaaag tcaactaccc tattcccaat tcccaagcca accaaaccag ggaagctagg
   208861 tccaaccatt acccttttcg agcagactca gaaaaagaac cattagttgg tcgctggtct
   208921 tatggtaatg gtgactatct gcttcgtttc caatgcgtag tagttctcaa gtgtaggagg
   208981 tgcttttagg ttttaccgtg ttttgagctt gccggtgttt tcactctttg aaatcataac
   209041 aaaaagtgaa gagttgcgtt ttaccgggaa ttttggttgt aaactcaatt catacttaga
   209101 aagccgatca aaaagagaca agcgacgcaa accccggtat tttggctatc gatgaatttg
   209161 actcttagga atcatggaaa aatgatcaaa tttgctaggt tttggccatg gtggaacgca
   209221 acatttctct ttccgatggg tccccaaaga gtgaaacagg gtttctaggt tttcccctag
   209281 ggggagatgg aagattctac tttttcatgt catccaaaga gtcaaagtgc cttgctaggt
   209341 tttgtccatg gtggagtgta aactttttgt tttctcatgt ggtcttacga agtcaaaagg
   209401 gtttgcatgt ttttgccact atatgagatg gaagttcttc attccaacag aggtcttacg
   209461 aagtaaaaca aggtttcatc aattcgtcgc tatatgagat ggaagatttt ggtttcacca
   209521 cggccctacg aagtgaatct gtctatattg tcttccgctt catctcttca tcttccttat
   209581 cttataatac actgtctagc gcctttattc gattagactg gattaagact cctcgtcacc
   209641 gggcagcttc ccgagccctc ggaatccagt ccaatggtca gatctgcaca gcctgtccac
   209701 atctctctgc tctcttcgga ttcctttctg ttgcgtcttg ctttccctct aacaaagatg
   209761 acggactaca caccaggatc tattttgact tagaatttca gccggatagc gccgtgtttt
   209821 agggttacga caagctgacc tctgccctaa tcaactgctt tatagccggt catagttata
   209881 ccgggaaaga aactccaact ggaaatcaaa atggggggac ttacacttca actagatagg
   209941 catctctttt aggaaagaaa atatctgata ataacctgcc tcaaaggata tgtcgtactc
   210001 tccaatcccc tcactcagga aactatagcc acagataggc ttcattgcca tatcccgagg
   210061 tagccttcca acaagaattg agctagatgc gcttggaaaa cagtgaacta ccactccaac
   210121 tggcttgtcg ggccaggata aggtattata ttcaggcagg gcgtcttaca aaagagatat
   210181 ataaaaaagg gctggccgta cttctgtttc gacgaatgga atcttagtta agagaacaag
   210241 accgtagaca aagccttcca acataagtta ttcaaacctt tttcgagttg accatcaaga
   210301 gcaaagcgtg gctttttgcc ccggggcact agggcctgat catctttatg gctataaatc
   210361 tgccttcaca gtgatcagct ttttgatccg agtggaaaga ggagtcttcc cagatgtgat
   210421 tagagaataa cccaaaagag gcatgtcggc atcagctgag gaaagggttg gctaggggtt
   210481 agcaatcaag aaagcaatca aagacgatga aagaatcaat tagtactgcg ccctgatgca
   210541 agaacggaga gtttctggtc tctaaaagag tcagacgacg actaataaga agccgataga
   210601 agagctacgc cccttcttct ctgttctaga tagaatagga atcccagagc ctggcgaaga
   210661 tgaataagag gaattttact agtagtgtta tggaagtttc agagcgagag aaggttccat
   210721 atctgttttt tttctctaag ggatgagaga gtgagggagg tcagatctat ctatcaaagc
   210781 ggaaagtcca gagccggctg tacagcactc ttccgccgag taccggataa aggtaaaggg
   210841 ttagctttct agcaagagag tcaaagccct atccacagcc aagaagcaag ggctgtctaa
   210901 agaccggatt ccctctctga atcacagggt attcactgga ctttttatca aactcgtctg
   210961 agtaataagc caaggcaatc gggaaaagaa ctcaatgaaa aagggcctat tctcttaagg
   211021 ctaacggatt cttagtcgag tctcgtccct ctcctttaaa gtagagtcag cacacttccc
   211081 cccccccttc aaagaagctt acctgagttt agtctcgggg gactgatgac cttctattga
   211141 aagagtagaa ggtagcaaat ggagattgag attgaaggtg gcccgacgag gaagtcttgc
   211201 ccattaaagt cgcttccggc aaccgcttat ccgtgggaaa gagaggatgg aacttgagaa
   211261 ggcttcatgc cgattcggca actgattgac tattattcag gtacggatga ggctgggaag
   211321 ggctgataag catcggctag tggaaccact cctgtccttc tttcgtatcc gaggtgggcg
   211381 ctttacacaa tatggaaatc tagtacggtg aataaggtag gggctgatcg attaggcgaa
   211441 ccagtccaac tagtcaaaaa aagttaaccc cttttgcttt agcaaagctt aggtccccgg
   211501 gtccaatcgg cagaggctcg tcgagacctc gatttgctgc acagaggtga gagcccctct
   211561 gatgcgagcc cttcccccct actatccacg taacaccaag ctcagaaagt gtacctgacg
   211621 agggcttcct cccctccaag cctgtctact ctggaaaaaa aaataactcc catctctcag
   211681 tgagtcccat caaatcaaca gccccgagtt gttggcctga cctgttgatg gaaggtccga
   211741 gctgctttgt catccagagc ctgggggtcc cctcggttta ttaataggcc ccaatagtct
   211801 tagaggaagt caaaggtcct cccaaaatac acagttgaat aaggtgagtg aagtgaaaga
   211861 agagaaaaaa gcccgaggtt cgaaggctcg gactctcatc cggtcaccca agagggctct
   211921 tctagaagca ctactatcta ctgttccttc tttagtgagt agacggtttt gaacggagaa
   211981 tgcagaatag aatcatcaga ataatggata ttccatctag ctggggttgg ctgactctca
   212041 ccaggtcagg gggagaccac agcagatgaa tgagggattc agtagcacgg acaccattcc
   212101 caaggaatgg aaagaaggaa ccatcaacta gaagaacagg caaggaagag ccctctcagg
   212161 tcgactcagg agaaggagct tacgatccac cccgtccacc ggaagaccga acccagagat
   212221 ttattacctg tgctttgctc ggtacggaga taggagctcc gaacctgcag agacgagatc
   212281 tctactccta gaagtttggg gcaccgtagc tcacctttca ctaaaaagaa gtgtagccag
   212341 gttgctaaca tcggctaccc ctgaccttct ccttccgcat ctagatttat tcagagcgca
   212401 caatcggacg ctaacctgga actgaccctt caactgacta ggcgcttggg aattctgaaa
   212461 cccccccctg aaatgagact tcctccttgc ttgaaccttt gcgacgacta tggcaccttt
   212521 tggtactcct ctgagacctt tggaaggggc acggactcca ctttagagtc tgattggaat
   212581 tcgcattctc gataagagcc gctacgagat ctcaaaacag aaagtacctt atcgtagaag
   212641 acgacttctt tctattctat tttgatcttg cagaatggaa ccctactctg agaggcaggg
   212701 aagaccctct ccagagaatc cagagaggaa agaggaaggt tatttcaagc tgctttcagg
   212761 cgtgcgccca cgtcgtcctg ccatcagaaa gagcctacca gtggtcccta ctggcacagt
   212821 actggcccct cggtcaactt ttcatctgaa agaaggtagc ccttctcccc ttctgaacag
   212881 aacatttcta agcttgaagc tctttcggat tagatctttt ttcactggat tcacctgagt
   212941 agctcagtct gatttccaaa aacggatcga attcttggct cggcaaccct tattcattcg
   213001 atttgtcccc tcagatattc taattgaatg aaattaggcc caacggcaaa gagtaggcga
   213061 ggaaggaggg aggggttctt tttttctttt tcccctaaat agctttttag aagtgccagt
   213121 ccgttcccgg gtaatagtca gaacgaagag ctagaatagg agttctagta gagtaagcgc
   213181 ggacgtcttc ctactttcat ttgtcacaat aggttgaatc tctaaataaa aagcgagccg
   213241 gcacatgggt tctttgccaa ccctagctct atccatagtg taggatgaga agagatcagc
   213301 gacctgaatt caccatcctt ttctccttca ccacaaaata caaactgctt gtagaaggag
   213361 gtgccttctc cctttctgag acttctttcc acttattagt gctggcagat cctctttatt
   213421 gattgcccac cgaaagttcc ctctacctct aaatatcggg ttgtcatcgt ccttttccca
   213481 gtttgcgcca ggagcctccg acagcctggc agactgcaaa atcattgcac ttccttctca
   213541 cgatggatgg aaccaggaga gctaggcacg ggaagggaag ctaggctcac tcccgacaat
   213601 tatatacctg cattccagac aatggtccaa ccctttgata ttcctaaggt aacagagtac
   213661 ataggtgaga aaggagcgct tttctaagct cagcaagacc gaatggaatt caagtatatg
   213721 gcactctaac tacgaaagga atgccaacaa gaaagctaat agggatagga ctactagctg
   213781 ctagtataga aaccgaaaag aactcctaat agcattggtt gccgctctat ctattctgtt
   213841 agttccatag ccgcgcttcc tactagtcgg ataggaacaa ctaactgcct agctacaaga
   213901 agagagctac gaggaaagaa gagctagcag ctaggatagg aactctaaac tagctactag
   213961 aggaagtcaa gctactaaca gagctcaaag cggataagaa atcggaagag acagacgcaa
   214021 ggaagatcag aggcgttcct cggtgctatt gccctcttgt cctagcagcc gatcactcac
   214081 taatagctac taccaggagg agaggaattt ttttcgaaca ggatcctttc cggtggattg
   214141 gaatttgact cagatttgct taatccccaa gaagctcaat cctcggttaa tgacatagat
   214201 gcgacccatt agtctttgct cagtcatgta taagatcata tcaaagatca tggtggccag
   214261 actcaaaccg attctgcctt cccttgtgtc tcctacacag tctgcatttg tttcggaaag
   214321 gcttatatct gacaatattt taatagccca tgagttggtt tacaatctac gtactcaccc
   214381 ctcatttcat cagctactct cccctcattt cattggtcac tggcttagtt gcggaggaac
   214441 ctagcttctt cagcgaagct ggaggaaccc ctatggctag cattgttctt gcttcactca
   214501 cttacattcc cttcattcaa acttcttcta attcacattc acttacccaa cttctctggc
   214561 ttagggtcag ggttactcac attcctagtt ataagattcc tagttctggg tctgggtaag
   214621 ggaagggtct aggctcctaa cattccttcc caactcacca cttatctccc tagttcttga
   214681 attcaaagtt ctgggattct ttgattctta gttctgagat tgttagttct gggactgaga
   214741 gtgccaggct gcgacccatc tttgcaaagc aagagcgagg ccaagaagca gcagcactcg
   214801 tacactagaa gtgagtatag ccttgccgga aagagattta gctttgactt tgcttagcag
   214861 gctggctggt ttgtttggct tggctgtctt cgtagttgag cacactgatg taccagtttc
   214921 aagggttaaa gttggaagct gcttcccttt tgtgcagcac acaggttcat ctcatatgta
   214981 gctctttcta ccaatgtgct gcattaatcc ctagctatca agctgaaact tgaacagaaa
   215041 ttgctctaaa cctgttcgct acaactatag gagtccaatc tactgaggtt cggcttctgt
   215101 tgaatctcca gttcacttgc gatggaaagg cttcactcct agcgcagcaa atgaagcgca
   215161 gcaattttaa gtagcttctc ctctagcaca gtgctgcatt tagtcgtcag cacacaccta
   215221 gaacatctcc tttagacgca agcaaagacc tgtcttcgtc taaacgtcgt ccagcccttg
   215281 aaaggatcct tgaagaaaac ccaattcagc acactcctcg tgaagcagcg ggtaatcatt
   215341 caaatgctaa agataaaggg ccagctttag agcgacttga gctccctgtc gatgaggctg
   215401 gtacctctaa atctaaagaa aagcggcctg ctttggaaag aatcgagacc caaccagtct
   215461 tccagcacac tcctcctacg gtcttcgata ggcttggaga tcctgatctg ttaactttct
   215521 ttcgtctatg agccgtctta tcttccatag cagtgtgctg gctttccact cctgcttcct
   215581 tttagatcaa agttcgacaa gtgcacctct attgattaaa ggcgtgattc gtacatcttt
   215641 gaatagtatg ccaccgatta tccaatcaat catttccatc ttttgctttt attgatcaca
   215701 tatgtttatc tagtttaaat cagctggtaa tgcaggacaa taagcagaac tgtaaacatc
   215761 cccttgtcat ctgagtaatc taagtcttcc tctttttaaa gcagcaattt aagttgagtt
   215821 cctttggacc tcttctgaaa ccggttcttc ttcttttggt aatcagagga tttctctttt
   215881 cccttttctt gatcttatgc ttttcctctc ttttcgcagg gatggacccc gggtaatatg
   215941 agaaatcaga attctttttt tctgatgctt gcccttacgc atccctagcg catcaaagga
   216001 aattcttgac tttatcttac acgtgcgtgc tgtcacgcat ctgccaatag taggagctag
   216061 cacaaagctg ctaatcccgg gacctatccc ttgaaaggta cccttcgttt ttattggctc
   216121 ttcagtttta ggggtatcag cacctgaaaa gttatgaaac gtgcgattgc cagtaagcaa
   216181 cttgaaaggt ttttacaagg acctacccta aatctgatac tttattgggt cggatgccca
   216241 gctttcttgg atgggataga tacaacaggt gattgatctc ccatttctgt catccttaat
   216301 ttcccaattc ctagcgcagc aactttgact tttcttgatc ttttgctttt ccttttcttt
   216361 tcgcagggat ttatactttg acttgataga ggtaagggct cctgcccaat atgtcaacat
   216421 gccaacacat gccacaccaa tatgagttga gttggccctg ataagtggtg ttcaatcttc
   216481 ctacccttat atttcagagg tcctatcacc ttcatacccc tcgaaacgtg ggttttcgac
   216541 tatagacatt tcgatgagca acctaaaagt agaagtttat tgtgggagat agatgaatct
   216601 ccaattgata tcatctcgaa ttacgaagat tggttctttc ttttcattcc gaattagcag
   216661 ggatatctcc caccttctac caacaagtcg attatcaact gacgagaaat ttgattgaag
   216721 ctttcctctt tcctttcctc tgctgcttct tgccagggat ctaccaccaa gtcgatatga
   216781 aacatgaaaa gtgtgatgtt ggttttcgtc gatcgatagt aatgtatata aaagcgatgg
   216841 atttgagttg acgatcgaag gtgtaaggta gataatagcg attgttgagt tgagtacggc
   216901 ttggatcaat cctcccctcg acaaggatca accaagaaat aatcgtcgat gattacaatt
   216961 tcaacatatc atgtattgat aggattggtt gatttgattg atttgaagtg tgattcccct
   217021 cgtatgaagc ggagaatcaa tgagtcccaa acccgacaat tgatcaaccc ttctcgtctt
   217081 ttttcattga ttgattaatc gttttgaatc gattgtgttt ctggttttaa aatatagtca
   217141 agtgttacaa catttgaatg ttgatgttga ggagaaagca ggagtgtgct gaggagctca
   217201 gggttgcttc gctcacttaa ctggctcata ctacttgttc acagacggac aaagagatag
   217261 ttgtacgttt gctgctcaga cgattaacaa agtgtttagt gcaaggaaaa aaagcatagt
   217321 ttgatgagtg ccaagatgat tcggagagtg ttcagtgcag cacaaaggaa gaagatctct
   217381 cttggcaggg ccggaaacag gtgcgcgcag ttgggaggat gccggggtgt gctagtaagc
   217441 aaatgggaag ttgatccgat cttaagtagc ccaggatcca tcccagggga agatctatcg
   217501 agtaaccagg aaagagatgg gtaggtagaa cagccagaaa gatagaaaga gctgttgctg
   217561 gaaatcagag aaatagtcga gttcttccct ctcgtttttc ggacctctaa ctatcactaa
   217621 aaaagaatct cataagagaa gaaatcaagt tgatagatca gttagttgag gcggatcctt
   217681 tctttacctt tacgagcacg gaatcgccta ttgtcggagt cttgggaacg ggtcgagggg
   217741 acggaacggg ccctccagaa cgagggggat ccaggccggc gtcgggaatt aaccgcgcgc
   217801 ctggatcagg aaatacgaac cctccaacga caaatccatc tcggtcgaag agctgattcc
   217861 attcgggatc ggcaaatcgc cgagtggagg ggaaggttta atacggaatt agcagggata
   217921 gaggaggaaa gcgcacgccg tgcgttcctt aattggtgtc tccgtgtgct catccatgca
   217981 cacgaggacc aacctcccca gaactaaatc cgttcgttcg ttctcttctt tcttttcata
   218041 gatttaagtc tgtttgtgca tctttctttc tcccatgctt tccgtcggtc aaaccaacga
   218101 ttctcttctc aaagtaatag agagatcctt ttctagttag aacttctatc aatgcaatta
   218161 aagaaccatc ccttcctatt agtttgtcct gtcagataga aagaaaatta ggccccaaag
   218221 ataaagagcc cggtgggggt gaagggtggg gtttacatat aaccgagaca aagtggttta
   218281 tgattgaatc tcagaggcat tcttatcatt tggtagatcc aagtccatgg cctatttcgg
   218341 gttcactcgg agctttggca accaccgtag gaggtgtgat gtacatgcac ccatttcaag
   218401 ggggtgcaag acttctaagt ttgggcctca tatttatcct atataccatg ttcgtatggt
   218461 ggcgcgatgt tctacgtgaa tccacgttgg aaggacatca taccaaagtc gtacaattag
   218521 gacctcgata tggttctatt ctgttcatcg tatcggaggt tatgttcttt tttgcttttt
   218581 tttgggcttc ttctcattct tctttggcac ctgcggtaga gatcggaggt atttggcccc
   218641 caaaagggat tgaggtttta gatccttggg aaatcccttt tcttaatacc cctattctcc
   218701 cttcatccgg agctgccgta acttgggctc atcatgctat actcgcgggg aaagaaaaac
   218761 gagcagttta tgctttagta gctaccgttt tattggctct agtatttact ggctttcaag
   218821 gaatggaata ttatcaagca cccttcacta tttcggatag tatttatggt tctacctttt
   218881 tcttagcaac aggctttcat ggttttcatg tgattatagg tactcttttc ttgattatat
   218941 gtggtattcg gcaatatctt ggtcatctga cgaaggagca tcacgttggc tttgaagcag
   219001 ctgcatggta ctggcatttt gtagacgtag tttggttatt cctatttgtc tctatctatt
   219061 ggtggggagg tatatgaagg aacgaaagag tggattacaa aatgaaagct cgaagacaaa
   219121 gagaaccggg cttttccaaa gaattactgc agctttccca ctccctttga ttatcatata
   219181 caataaagtc tcttccactt tcctaccaaa tctatcttta ttctggcaca taaatgaagg
   219241 aatcgaagag attatggcag atcatgttca ccaagaaatg acccgaaatt agatcttggt
   219301 ctatttgaga ttgttccttt taatcgtaat caaagatgtt ttcttgtttc ttgtttcttt
   219361 tctgaacaaa ttgaagaacc taatggatcg aactcatcct acgaaagata tcggaacacc
   219421 aaaaccagaa agaaagaaag tagagctaat tgcgagagtt cctcgttaaa agtgcaagct
   219481 gtaattatac gtttcagaat cccacttaat aatttcctca aaaaattaaa tctgcttttc
   219541 gtaagacgtg tctttagaat actgttcaaa acaagtaaaa aattcgttga ccaagcgaag
   219601 attgaggtga tgacaagttt gcaaccacca aacttggtaa agggtattcg aagcttctta
   219661 ggacattagg gttttataga agatttctca aggatttatc gaagattgct aggccactca
   219721 cacaactctt atgcaaagat gtggcttttg tgtttgatga gaaatgcctt gaggcattct
   219781 tgatgcttaa agaggctcta gtgaccgcgc ccatagtcca actggaattt accatttgag
   219841 gtcatgtgcg atgcaagtga ctacgcggtt ggagccgttt tggggcaaag gaaggacagg
   219901 aagttgagcg ccatctactt agtgccatag ggcgaagcgg gacatgttcg acctcacgtc
   219961 taaccagcgt caggtcgaac gagcccccta gctctttctt gtttgaagac cggaacatta
   220021 gcaaagatgg attaggaaca ttagcaagat ggattaggat ggctctgggg gtaagccccg
   220081 taggaatact agcaaatcca atgttacatg tattttaggg caaggaaggg ctatctttac
   220141 tctttagttt gagagggaga aggcttcctt ttccgcgtag gcagattagc aatccatagt
   220201 cttactaaaa gagtcttgga cttagatttc ctcctcctcg aggatgatgg atccggggag
   220261 ggggaaaaga tgaggctagt agaaccttgg acgacgcgca agtcaactat gccaccaccg
   220321 cgcttacgct cctcgccata gttttcgcct ttgagaagtt taggtcggtc ttacttggtg
   220381 ggctccaaag taatagtgca cacggaccac gcggctttga gatacttatt ggcaaagaag
   220441 gacgcgaaac cgaggctact tagatggatt ctacttctcc aagagtttga tttggttata
   220501 aaggacaaga aaggaattga gaatggagtc gcgaatcact tgtctagact tcgggtcgag
   220561 gaggacatac cgatagatga tagcctcccc gaagagaaag tctattatgt gctcgaatat
   220621 ttgaaggaag agtatcccgc ggttatgatt ttggaaagca tggaagatga ccttccatgg
   220681 tatgccgatt tttttaatta cttggcttgt gatcaagagc ctccaatgtt ccatggatat
   220741 aggaagaaga aattcttgcg agatgtgcaa cattattttt tggatgagcc atttttgtat
   220801 aagagatgct ccgatggtct ttttaggaga tgcatttcaa aagaggaagt gaagggcatt
   220861 ctctaccatt gccatgcatg catcggagta tgcaggacat ttcgcaacat ttaaaacagt
   220921 ggccaaggtt tgttttacaa gcaggattct attggccaac cacgttcaag gatgctcatg
   220981 ggtttgtttc ttcttgcgac gcttgccaaa ggaagggcaa ctttacaaag aggaatgaga
   221041 tgccacaaca ctttatcttg gaagtagaag tatttgatgt gtggggcatc tatttcatga
   221101 aaaaaaccat cttctcatgg aaaccaatac atcctaatgg cggtagatta tgtttaaaaa
   221161 tgggtggaag ctcttgcgag ccccactaat gacgccaagg ttgtgctaaa aatgtttaag
   221221 aaagtgattt tcccaagatt cggtatacca cgagtggtta ttagtgatgg gggatctcac
   221281 ttcatcaaca aagtttttga gaaccttttg aagaaaacat ggtgtgaagc ataaggttgc
   221341 cactccttac catcctcaaa caagtggcca agtggaaatc tccaaccgat aaatcaaagc
   221401 gagaagacgg ttgggaaaac aagaaaggat tggtccacca agcttgacga tgcgctatgg
   221461 gcatatagga cggcatacaa gacacccata agaaccacac ctttcaatct tgtctatggg
   221521 aagtcttgcc atttgccggt tgagattgag cacaaagctt tttgggctac aaaattgttg
   221581 aactatgaca taaaaaccgc ttcggaaagg cggttggtcc aattgaacca cctcgacgaa
   221641 ataaggcaag aggcctacga gaacacaaag atctacaagg agaggactaa ggcttggcat
   221701 tataagaaga tcttaccaag ggagttcaag gtaaatgacc aagtgctgct cctcaactct
   221761 agactcaagt tatttccagg aaagttgaga tctagatgtt ttttaccctt tcgcataaag
   221821 gaagtgaaac cgtatggagc ggtagtgctt tgggatgtca atggtgaaca cttcacggtg
   221881 aatggccagc gccttaagcc ataccttgct gatgagagca tgccaagcaa gggaaagttg
   221941 acgatctgtt tagcctttct cacaacaact tgctcctctt ccttatcatc tctcacaact
   222001 tcctcaagct cttttccact tctaagcatt atgtaaaatg ttcccttggg tttgcttccg
   222061 gtttaccggg tagtgttccc atgggtctct ttgatgaaga ggcggtttaa gcaacttggt
   222121 tgtcaagaga tttgacatga gaggccaaag tttaaaactt cccattaaga tcattgtaca
   222181 tgttgtccat ctttgtgttc atctcaatgg tacttttctt ttgtccttca aggaattgtt
   222241 gcaacattag cttcacctca ctatctggtg cagttggagc agaaaaagaa ctcccttgag
   222301 cttggtaagg ggcttggtaa ggtgcttggt agggcgcttg gtaaggtggt ctttgttgga
   222361 gcagtagccc ctctagcttg gaacccttgg ttgaaaggcc ttggttggaa tccttgacct
   222421 ccaacatagt tcaactcttc ttgtggctcc tcataccctt caacaccaaa gtcttggtac
   222481 ccttgatatc caccatactc ttcacaagag tttaccgtca tcttttcttt tggtcacgct
   222541 tcaatatctt atccattttt gcattcagct cttggatggc atgatgagat tcatcattgt
   222601 ttttccttgt agtccgatca taatccgagc catgactccc attgctttat gcgagattct
   222661 ctaccaaagt ataagtatcg gcttcctcaa ttgtttgact catgaagctt ctcgtagaca
   222721 ccagagctct ggagaggttt aaataactcg actgaaagga aaggaacgaa gtcacatctc
   222781 tcgcccaagt tcagcagact caatcgcacc cttccttcgt cgtataaaag atagttccga
   222841 tcgttgagtt taatggagac acaactagta atattgatat tggaaggaaa aggataagac
   222901 ttaagagaac cctccatggc tcttgatacc atgtgagtgt tcatgggctt ccaactaaaa
   222961 accaattggc aatgagtgga gaggcccatg tcctttatat actagtgtag gtcccttctc
   223021 actttcaatt agggattcct aacaaaggga agtctggata cttgacacag gttgttcttt
   223081 cggaagaaga gaatggtttg taagtttatc agatgctggt agtgaaacaa gtaaagatgg
   223141 caaatgacac catgtcaaca gtaaagggaa taggaagtgt gagactgaga aatgaagatg
   223201 gttctactgt tttgctgaca aaggtgagat atgtccccag ggtgagagca ttactaatcg
   223261 gggaagtttt aactagctgg agagtaagga tctcttctcg aaagctatta tcaacgttca
   223321 gcgattgaat taccttcagt aaatctaacc agctaagcta ccctttataa ttaagttaag
   223381 aaagggcagt tctgtcgatt cccaatctcg aaactgagag tgtgcgaagt cacaagctga
   223441 tgggctatat gtgaagttaa aaaacccagt taagaaagga aagatatagc tatcaagctg
   223501 aaacttgaac agaaatttcc ctagctttta acctttctcg ttagtacact atctttcacc
   223561 cttccacatc ttctctttat tattggatgg tttatggtca aaaagcttag gctgtgtatc
   223621 ctcagctgtt gtctgttcag tattctcact ggcatctccg tctgtgataa catctactta
   223681 tctcctttca ctctctcctt ctcctctcct tcttccaatc ccgtagagag gcctggaaaa
   223741 atttattgaa aataacaaga cgattgacat cttaaataaa gacatcatgc cctagatgcg
   223801 aaggttagta agagacccaa gtgaattctg cgaagataga agagcggact tctgaggaga
   223861 ctggaagcct ataaataata ggaatggcga actggaacct catccttcaa agggttggtg
   223921 tatatttgtc ctattcgtaa agaccccgac cttgcgtcag gaaaagtgga aaaaccccta
   223981 agactctacg ggctagccgg gcctaaagaa gcttataaaa ttccacctat gtaatgactc
   224041 gcattcaaca actaagagtc ttccttgctt tcgtcacaaa tcccatcgct cgaaagaaag
   224101 agggtttgga gttagttaca agctggacta agactgaaat gaaggaacca gatggaggct
   224161 gatgcaacgg ataggagtta tgctttttgg aaatgaggat tagcaatcat tcgacagttg
   224221 ggatgccgct ttcactagta aaagatatcc acgcaaggaa agaaaatgcc ccgccggaaa
   224281 gaaaagtaat taagttaaag agtgtcggtt tggggtgagg cttactcctc gaccaaaaga
   224341 attgaaaaaa agcaagacta acaagtagag gtggtttttt tcctaagcca aagaagggtt
   224401 tgattccacc tcaactgaaa gagagtcagt agcagaactt aactaagcag ctgcagagtt
   224461 tcgctcagtc taatctaagt agctaggcta agagtcagac agtaggcttc cggtagggac
   224521 agggatcggg tggcctgaat ggctcaacta attagtagag gaggaacttg agttactcga
   224581 ccactcggaa gaggaacgaa ggtactcgac caaaagaaaa ggttagaacc tgctcggccg
   224641 actaaagcta aagggatagg ggaaagaaaa ctgcttgaat aactagtggg ttactactcg
   224701 atcgactaaa acagaagtca gggaaaaaaa ccaccatcat actgtctttt cccttaaaga
   224761 aagtaaggca tcccaaggca gggaaggaat ctgaaccaag gaaggattct gctggagctg
   224821 cagtctcgga gtttaaaact gacctttagg cactgacgtg actcttccac ttgttgatga
   224881 ggagagggat tgattactcg actaaaagga gagggtagca gaataccatt aataaaaata
   224941 tcccattagt gctgctcttt cctaagtaaa atacctaaca acgagaatca ggagggagct
   225001 tctgggtagc atcaggagac ttacttacta gaaactaata aaatagtgaa ggttgtagag
   225061 aagggttctt ataagataaa ggtacagtag ctcgtatcga agaatattcc cgagatgtga
   225121 atctcactaa agcatttcaa ataaagagag gggccaagct taagaattcg ctttccagga
   225181 cgtactcagg gcagggagac agggcgcaac aattgtgact ggccattttg atcgatgagg
   225241 gaaggcaagg ccttaaccaa gagtcatcgc attcgtcgca ccaatcatag atagaacccg
   225301 atccttggat agaatccata atcagaagtt atcggtaccc ttagcatctt ccctttgatt
   225361 agaatgtgaa ggtccttggt tcgggcaagc agcgtattta gaagcctgct accgaaatgg
   225421 aattcctcgg tcgataactt tcatgataaa gcagaattcc gttggaccaa ttaagtacct
   225481 tctcgtttca gtcgagtcac tgagcgccca ccgggttgat tgaaagtgcc cctacggact
   225541 gggacacctt cttccagagc attctcacca tctgtactag ccttgcatga aaaaaggatg
   225601 aaccatgaag aattctccac tctatgaact catagcgctc ttgggatggg catgtgtctt
   225661 gcagtaggta aaagttaaag aataaataag cacgagggag atgctaggct gatcaaaaga
   225721 agaaggatta gcgagaagta tatctaactt tattctccaa ttgcaattga ctgattatag
   225781 attttctata ttctttttct attttcctag cgaactagca gctcccccgc cctacacagg
   225841 attggatact gaacctgatc agatagaccg atcggtgcgt aagatgatag tgacgcacta
   225901 ggtttgattt gatctcgcta cctactatgt atactgttat agctcttctt ctacctctat
   225961 ctactgagga tattggagca ctaacccgca actttcatct acgctaacag ctctcttctc
   226021 ttaatccgcc ttcgattatt cattagcgct ccgcgggtcc tcctgctact caaacagctt
   226081 tctttaggaa atgccgacat ctactactaa tggcttgaca ttccagaaca ggaagtcatt
   226141 tgaatgcccg aagtctgcat cttctattac atctccgaaa gagtgaaaag tccccttctt
   226201 gcctgatgag ttcttctttc ttttcttgct cctcacagtc aagatcccgc aaattctgac
   226261 tgacttgaaa ttaatagtcg ttttatctga tgatatgaga tgacgagcgt cagacagaga
   226321 aagatcaaaa agtctagtca agaagcttaa cggtgaagat ggagaatgaa ttgaatcttt
   226381 cacccacctc agtccaacta gcactcttgt gcctcatcga tctgccttct cactccagga
   226441 gagccatttc gccattcaaa aagaactgta cacgcgcgta tggatcatcc atcagaatca
   226501 atcagtcttt cagagtagtc atcaagcaag ctatagaagt acgtgtgagg aaagagaaag
   226561 aagtgagttg agtgacttgt gaccatcctt ataatttcga attgcataaa aggagtcagt
   226621 cactgacgcc gctcccagaa tcttaggttg atttcttttc gttttaggta aaataaccaa
   226681 ggttctaaaa agctatgggg ggccctcata aatccaccac ttatcagact gcgaatgcta
   226741 acagtatcga agcgcaccaa gagattcccg gtcgaacaaa tttcgtatag aaaaaaaaga
   226801 tgtgttttgt cgagtttgct tcgtcctctt tttttttctt attttccttc ctttaggcgc
   226861 ttgctctcaa aaaaaaggga aaggggtcaa ataaaaagct accttttatc aaggctaatt
   226921 ccaacggact tcgcccagat cttcattcaa tgggacgacg tcagtgcatc tttctggatg
   226981 atgaacgcct gtctcgctca tagatagagg aagagtacgc gcgctagcgc gctacggctt
   227041 acgaagttga tcgggtcaga tagccccttc gggcaaccaa ccgcacaaaa aattccgatc
   227101 aacaacttgg agggatggct gagtggctta aggcattggt ttgctaaatc gacatacaag
   227161 aagattgtat catgggttcg aatcccattt cctccggcgc ggaagtgaaa cgggcgggcg
   227221 aaatgagaag agcactactt agtgactagg agcggggagc ccgttgcgcg tttttttgtt
   227281 tgaccggcct atcttcataa gtaagctccc tatggccgtc cagtccctgg gcggctctcg
   227341 gttcttgagc atgttgggag attagtcgtc aattgaaaga gctgctctaa agcttgacga
   227401 agaagttttc cctattaatt agattagtaa agggcttttc ccttactagt caagtggtaa
   227461 ggtagggcgc tcttcgatga agaaaagaag agacttttgg aaaagtggtt cagctcagct
   227521 ggttagagca aaggactgta aatccttgtg tcagtggttc gaatccacaa ccacttctat
   227581 tctcggagct gaggtatatg aagaatggcc ttttggtccc tttcgtccag tggttaggac
   227641 atcgtctttt catgtcgaag acacgggttc gattcccgta agggataggt actcattctc
   227701 ggccgctttc agttagtgtt cattgctgag ggatcccgag atctcgaagc agatgaccaa
   227761 gtgagctccg cagccgttag tgcaagggct cgatattccg tttccgtaga agaacgagac
   227821 actgtaggct ggcgttttgc ggaccaggag ataatattgc atccgagaaa cgtacagaat
   227881 ccagttgtag acctcctcgt ggatgtacat cctgcccagt cactatcaca gaaggcctga
   227941 acattgagct tgctgttttt gtgaatatac agcccatgaa agatggtgcc tttaacatag
   228001 cgaaggacac gcttcaggag atcaaaatca gcgagtgtag gctcatgcat tcgctgacag
   228061 acaatgttca cggcataact tatgtctggt cgagtgagag ttaagtattg gagagcacct
   228121 acaatgctgc gaaagtctga aggatccgga tacttagcag tggaaacaga ggagttgagc
   228181 ttaaggggca gaggagtaga cataggtttg caatctaaca tccctgcatt gttcagaatc
   228241 tgttcagcat acttggtttg ggatagaaac agacccgaag gatgagtttt gatctgaatt
   228301 cccagaaaat agtggactgg tccaaggtct ttcattgaga aggtggagct gagctgaaag
   228361 atcaacatat tgagcagagt gttggaactg cccgtgagaa gaatatcatc cacgtagaga
   228421 agcagataca tgacatcaga attgttgtga tacgtgaaca gagaaggatc agctgagctg
   228481 cagacaaacc caaactccag aagaaaatcg aaaatcgcta aacttgtcga accaagcacg
   228541 aggcgcctgt ttcaatccgt agagagcctt tttcaacaga cacacatggg atggatgaat
   228601 aggattcgta aaaccaggag attgatgcat ataaactttt tcttgaagat acccatggag
   228661 aaatgcattt tgaacatcca attgattgat tggccaacct ctaactgttg tgcaacattc
   228721 aagatagtac gaatagtggc tgtcctcaca accggactgt aggtctcaac aaagtaaata
   228781 ccttcttctt gatgaaaccc tttagcaacc aagcgagcct ttaggcgatc aagagtacca
   228841 tcagaatgta atttggtttt gaagacccat ttacaaccaa gaatattctg attaactgga
   228901 ggtggaacaa gtatccaagt cttgttccga gagagagcat caagttcttc ctgcattgct
   228961 tgacaccatc ctggatcctt aagggcaaaa ataacagatt ttggttcttt tttaatagtg
   229021 gtagtaatag tgagactata cttgggattt agtttgttta tgccagcctt tgatctggta
   229081 agcatggggt gagaggagtg gttttgaggt agtggaagaa ctgtagatga agaaagcggt
   229141 atttgagagg gaagtagaag aacatggaga ggaaggtggg tctggttctc tgtttagtaa
   229201 agaagaaggt gggttagggg aaggtggatt aggtcagttg gttagggatg tgaggaaagg
   229261 aagggaaggt tgggccaggc aagctaggga agttgagaag gttgggctag ggaagttggg
   229321 agttggtgtt tcccttgttc ccagttgcta gtgcctgtgt agcttgttcc cttgttccct
   229381 tgttccctgt agctagtccc ctgttgttag gaatgggact aaagagctct aacagaagag
   229441 cggcaagagc ttctctgaaa agacctgttc tcttatcgct ttgaacattc tcctgggttc
   229501 ctagcccaaa gaaaaagaca aggctgagtt gccccttcta ccatctgagg tggaatacgg
   229561 atcaagattt gctgagtttg ttctatggaa taggccaggc cctctcactc tatctcatgt
   229621 cggagaagat tatgtatgaa tttgaatacc cacgaacgtc taagaggtca gctacttagt
   229681 tgattttatt taaggtatct cttgatcgaa gggttcaagc cgctaaagcg gaaagatata
   229741 tctcttcgcc tgaagcgttg tggatttagg cgtgtcacgc caaccttctg taagttcctg
   229801 gataatcgtt cccggataat gcctgccgca gggactaacc ctatcttcgc gcatacttcc
   229861 ttgtttgtct gggagttgaa tcagaagcat cgaatgaaag cttctttaca ggacctcttc
   229921 tatttccctc cattcttctt cctagtgacc taggagttgg gttcgtgaca ttttttcttt
   229981 ctgcttattc aagtagcccg gtctggtaag taaggacttt gctctcagta gaagtcaaaa
   230041 agccttcaac aagaccacat ccgctattga atcagctgct atagacttag ctaaagaatg
   230101 tcttgcacga gattcaatgt tatgtgcttg attgcgatca catttttctc gtagttgatg
   230161 agctgccaac ctccggaatt gagggttgta ggtagagttt cctgcgttca acttggagtt
   230221 ggaagagttg gatttggagt ttataaaagc tgttattagt tccgactccc cggtctaggc
   230281 ctggtacttg ttagttctaa ggtatcagtg tcgctacttt ctgtaaaaaa tttcctgcga
   230341 agggaagcgg gaaagacaag gtttcgaatc ttggtctaag aacttacact acactacgga
   230401 ggcacgggcc aagagatcat aacagtcaaa tcctcaacct cacaagcaga caagctggtg
   230461 gatcatctga tcttgaaata ggtcatccca gctatcccga tcttttctct ctttatttcg
   230521 tcaggtatct gaatcatacg attcctcgga tgtagctttt cacattggac caaaacaagg
   230581 cccggaaacc ccgctagctt tgttgataga aagttagctt cccgtgcttg actagtaggg
   230641 ctaatgaacg acccttaact atggaatgtt acgcctttcc tcggttactc acaacgtaat
   230701 caactccatt ggttattttc cccgggggaa cacctatagc cccaatagac tgatttagta
   230761 ggtatgatgt attactagga gtctctaagt tcctgctttg gttgtccctg tccgggctaa
   230821 gcggagttta gctttggccg ttaataagag cttccctcca ttccttcagt ccagtcacgc
   230881 ttttcttttc ggcttttgct tcagtctctt cttttcgtcc tttcaggtgg catttcgctt
   230941 agtcttgtca ttccttccgt catgctactg tcatgtgcta taaattgatc ctcccgtcta
   231001 gtgtttcctc tctcatgtta tacagaccgc tcctttaatc caatgaatag gcggcgaggg
   231061 tgacaaaggc ttagaagcag gggcgggcag aagcagcatt aattctttcg cccgcgcgta
   231121 catattctat tgagcgtata cgatcattga gctgatcacc ggtggcttcc tcacttgtga
   231181 tgtgaagctg ctttccattt ctcatttttg aggatatcga tattctctta agagaaaggg
   231241 tagccttttg tcacgagctg gactcgaacc agcgcgtctg gcaaaaagac catccagatt
   231301 tcaaccttag actgatcgtg actttggtta ctcggttccc cacgcgaacc ccacacgcca
   231361 tgggtacgtc cgaggtagat taactacgaa cttttttcaa aaaaagtgtg atatattttc
   231421 ctcacttact agcaaagaac tggaccagga ttcgtccttg gctgcctacg tacccctttg
   231481 ggaatcaagt aaatcgtagt tctcttaact tattgtcttc tttctaagtc ttgctttctt
   231541 ctctctttac tattgcttct ttttcttttc tttctataaa atgttcctca atagcactga
   231601 ttcttcatat atttttgtca aagcaattgg gttcacaaag cattattttc tcggtccatt
   231661 ttccacctct ttcttttgtc gaaccatgct aagcaaagat gcacggttcc agtcttcttt
   231721 ccctccccgt gtccactagc gctcctatcc tctccttttc agtcgagtca ctagggttcc
   231781 tctcctttta gtcgagtcat tagggttcct ctccttttag tcgagtcatt agggttcctc
   231841 tccttttagt cgagtcatta gggttcctct ccttttttta gttgagagtt acgtcagtac
   231901 cttttagtcg agtggcttct cgctcctgcc cagaacgaag agaaggcgaa aaagcgccgc
   231961 cgaagcagca tgagcgggct tctattgcta cgtaacaata gagcaggata gcattttgcg
   232021 cccacatgtt tgaattttag ggtaaaaagc tcgcttgtta tacgggatcc gacgcatcca
   232081 gcagagcgaa gcagcgttcc attcttttcg gcggcatcct tccgcattgg cggcgagtgg
   232141 agtgccacaa tcccattcat catttttgat ctacataagc caaagccctc cgcactggcg
   232201 acgtccccgg cataaatgca aggaggatgt atagctgata taggatcttg tggaacagga
   232261 tttgattctg caagcggttc ggtacaaaca aagaaatttc gaacaaaagg atcggaactc
   232321 gctgatagga aaggagagaa aaacaaagca atgccaagag ctccgtcaat tcgctgttca
   232381 tcgatagacg aagctctctc tttatcatct cgtgccagat gcaacaaagg atgagtcctt
   232441 tttccttctc gcgaaccacg ggagcgccaa gcgtccagag gatttttaat tttcctttca
   232501 ggataaagcg gcgcataaaa aagggctggt ccgtcaaaag tccggttcct tcgcgaacga
   232561 agttcagaat caacaagggt tcgtagaacg aagggagtgt acaactggtt tttcaaacca
   232621 ctttcttgtt cgtaacgagg gagagataaa attgagttct tcacgaagtt cgagacaaaa
   232681 aaaaaaaaaa gactttccct atggcctcct tgttttaaga cattatggct ctggggtcga
   232741 ccccggtaac aaagaaaaaa tccataaaaa tttgggatcc gacaccataa taaaatacta
   232801 ccctcatgat tagaccatgt tcctgagatt tgataaaaga aaggtgcatt agcggttaat
   232861 acgttgtaat tggataagtt attaggaata tgacagaacg aaagaccaag gaaagaaaga
   232921 agaatgcacc aaaatgcagg tgctgcacca aacgctggtg gttgtttctt gttgtaagtg
   232981 aatgcaacga aaagacccgg aaataacgaa taatgaaaga attcatatat tgatattgac
   233041 atttcgtgct catttcaaga tttctgcttc gttattccca tcatccggta accacaggat
   233101 gatccacaag aaaggtggca ggattcgaac ctatggccgg cccaaccctg acctgttggg
   233161 ttgggtggcc tgcttcgccc tcgtcgcctc tgtacccgaa acagatgcgc tgcgctaccc
   233221 agcgcgtaac cttgtccccc tatccctctt ctgcttatgc cattaccaat cgcgggtaac
   233281 ccccggaccg gccgccccta acctaataag aacgattatc cttatgacca aacaaggacc
   233341 agcttacttt tcgagcgaga gtttcacgat cccgaccagc aacttgttgt gggagtaagg
   233401 gcatccaagc ttgcccaacc tagtaaaggg gcttggagat agagggtttt ctggggggat
   233461 ttggcttctt tggaaagctg agttggaggt gaagattgtt catcgccagt atgttcattt
   233521 tagtgtttat cggaataatg cttttctgtc ctgggtaacg gcagtctatg ctagtcctaa
   233581 tgctactttg cggcgtgctc tctgggagca gttgagtagc ttggcatcta tgatatctga
   233641 tccttggcta ataggtgggg ggactttcat tccattctgt gtagttcaga tagccggggt
   233701 ggctcagcta gtggtaatcg gccgtgtcgt ttgagttggt tccattcctc tagtctctat
   233761 gacatgaagt tcgttggtcc gaagttgact tgggctcgca agggtttgct gaagcgttta
   233821 gatagagcta cacttgagag tctttctatt acttccttgc ttacctgggc tcacttcgca
   233881 acaaagagaa gttgtttatt tgcttgctta gctagaagat gccaacttcg ttcacttacg
   233941 tctctcgttt acttgttagc tagccctatt cctcaccttt gctttgaggg tatctaaata
   234001 aaaaaaatat acagtggtgt gctcgttaga ggatgctttt ttagttagct aagcgactac
   234061 cttagttgaa ggtgggagga gagcagcaaa gtctcttatc tttccaaaga aggcggaaat
   234121 cgagatgtga gaaaaagaat agctattcac tctccaaaga agccctcaaa attctttcta
   234181 gcaaatgtga agagaggatt gttgacaatt caataaccac tgcaataccc tcttacggaa
   234241 tgatctcggt gttctcgcta tgtcgtcaat ctcagtatac ggaaatggtc tgaccaagag
   234301 gcatcgatct ggagtgggtc ttgcattgcc ggatgacagg agccctttac ctccactctt
   234361 caattatatc cataccaggt gaacacagat gatcgacctt cagtgcctgg tcaaccatta
   234421 aagaagagaa gaggagcgga acaatgagaa ggagttcgta gccctccaac cagaactaat
   234481 caacccgcct cttcaacatc tccatttccc attccatctc tgggatccaa tgcttcttca
   234541 ccgggcccgc ccgatcccca gaacgtaaaa tggaaccata ccggaaaccg tttgatcagg
   234601 atagaaagag caaggggctt tgttttcgtt gtggtgacaa gtggaatcct ggtcacagat
   234661 gtaagggcag agaattaaag tatatggctg tggatgaagg agatgagttg gatgaggctg
   234721 atgaagctga aacagggaaa aagatagaag aatcagatga ggatgaagta aaggaattac
   234781 tctggttgtc tttgcggtcg atggcaggtt taacaactga gagagatcca tgaggatgag
   234841 aggacaaatt gcaggacaag aagtcattgt tttaattgat tcaggggcta caagcaattt
   234901 catagcagag agtgtagcac atcggtgtgg tctgcaaatc acagaaactc gtggatttgg
   234961 ggtttctatt ggaaatggtc aagtcgttcc aagtgccggg aaatgcagcg gagtagagct
   235021 aacggtccaa gatgtgcaga tacgtgcgga cttcttcctg taaccatgga tatagtgctg
   235081 ggttatgcgt ggttggctac tctgggtgac accagaatga attggggaag acacaccttg
   235141 agtttccgta gggaagatca gtgggtcacc ttagcaggcg atccgtcact ggtgcgagct
   235201 caaatctctc tcaattcggt agtcaaagag ggaaggaagg cttattatct cctagagctc
   235261 accgcactgt tttgcaggag gaattaagac tcaaaatttt cctgaggatg ctcaagtgaa
   235321 acagttgttg gaatggcatg aaaacgtgtt tgagatgccg caaggattac ccccaaaatg
   235381 tggcagggaa catgctatca accttaagga aggagcagaa ccagttaaca tccgtcctta
   235441 ccggtataca tatactcaga aggacgagat tgaaaaattg gttaggggag atgttagaag
   235501 cacggatcat ccagccgagc atcagtccat attcaagtcc agttttgctc gtccaaaaga
   235561 aggacggagg atggcctacg gcgcgtggat taccgagcct tttacaagct cacggtacca
   235621 gacaggtacc caattcccgt gatcgaggaa ctgttggatg agttacaagg agcttctgta
   235681 ttctccaaac tcgatctcaa atccgggtac caccaaatac gtgtacgagc cacagacgtg
   235741 aagaaaactg cctttcgaac tcacgaaggg cactatgagt tcctggtcat gccatttggg
   235801 cttaccaacg caccagcaac attccaatcc gtgatgaacg atattttccg cagggaagtt
   235861 tgtgttggta ttttttgatg acatactagt ctatagcaag ggcacggagg aacacatgaa
   235921 tcacttggga atggtgctcc agatttggga acaacaccag ttttatgcaa acagaaagaa
   235981 gtgtgctttt ggacaaccac agattgcata tttgggacat agacatatta tatcgggcga
   236041 aggggtgtca gctgatccag ctaagttaga agcaatggtg ggttggccag aaccaaagaa
   236101 cacaacagaa ttgcgaggct tcttgggctt gacggggtac tacaggagat tcgttaagaa
   236161 ttatgggaaa attgtgagac cgttgaccga gttactcaaa aagaacagtt taaaatggac
   236221 agaaatggca gcactagctt tcaaggctct caaaggagca gtgacgacgc ttcctgttct
   236281 agccttgcca gatttgaagc taccttttgt gacccgcgtc gggaaatgga attggagctg
   236341 ttttattaca agggaacagg cctgttgcgt atctcagcca agggttttct gaaaaagggg
   236401 agcttgaaat cagtgtacga acgagagctc ttagcaatag tcttggcagt ccaacgttgg
   236461 agacatcagg gcaacgtttc acgatacgca cagaccagaa gagtctaaag cacttgctgg
   236521 aacaaaggtt tgtcaccaag gaacaacaga ggatgggcta ccaaactgtt aggcttggat
   236581 tttctcattg agtataagcc gggaactgaa aataaggctg ctgatgcgtt gtcaagacga
   236641 gtgcaacctg agcgtctgtt ggaacttgta ttcgcacctc ctccctcttt cgatgcagca
   236701 gaattactat ctcaagttga agctgatccg gagttaagaa ctgtgttaca acaagcccga
   236761 tagggaaaga acctggaatc tggttatacg gaaaaaagag gggctgctat gtaaagatgg
   236821 aagagtggcg tctcgaatca gccaagcttt ctcccaattt cttctatatt ttcatctctt
   236881 tctctattct accgagaaga tccatctcgg gtcttatcag atggtatcag agccttcggt
   236941 cttctgactg tgggtatcca acgacgattt cgacaatggg tttggatagt aacgatatag
   237001 cgctgatcag gcggattctc gctcgggtgg agcagatgtt tttttccatc gcatgacgac
   237061 gatgaagaga tccgccgatc ctgaagctga ggaagaccca gatccgtcgc ttgggaaatt
   237121 catcgagcag gtggtgagcg gtccaactca gaagggattt cctgcatctg gagcttttgc
   237181 gactcctcgg gcaagacgat ctcgcggtcc gaaaaggttt cttggcaagc gcaactaccg
   237241 cagggctcgg gcaagaaaac cagggaagcg tgacagagct cactcgtcca aggttagatc
   237301 tagcgatggc tctacacgac cttctgcgag atatggtatg cgtttccgat ctcctacttt
   237361 gcccttgtgt tctagacctc ggacatggga atttctgctt gatcttggtt acgatagtat
   237421 gtcgctgaag agcgctcgtg tagcgagtga acgaccttgc gatcctggac gagctaacca
   237481 tgtgtgggag ccgggtggat tatcgcctga acaagctcag tgggactggg tagggaaggt
   237541 ttacagtcgt gatagagttc tgaagctaat gggagagctt catgaattgg tttacaggga
   237601 atcaggaaga cggtaaggat cttagattgt caaggatctt cctcataaac acgtttccgc
   237661 ttgcagctga aacaagcgga gaagatggga ccaacgagat cagccaccag gaagttaata
   237721 agatctgatt tttggcatcc tttgatcctg gaagaacttg tgctgaaaag tgagttcgtc
   237781 aaagagctct ggcgaggcat tagagctgtg aagggaaaga aggttaagaa gaggaagaaa
   237841 cgggaaccta gcctgccagc tttggaaccc cagaattttc cctgtgttgg ggggttggag
   237901 gtatgattag taggcttaat tataaagttc tcgttcaacc agaactagat aaagctacaa
   237961 gggcagtctc tagaattact tacggattgg ttgctgttgg taaagctgat gggtatagtt
   238021 ttgaggttgt ggattgatca agttaactcc actgacgaag ataagcttgt gagtttcatt
   238081 ggatctggtg ggtgtcaaac acactttaag aagcagctag tagcaaggaa gttagcattg
   238141 tttaatcccg aaaaattcat gaacctaaga ctacctcatg acaagggaat tctagtcttt
   238201 gctggtcata gaattgctca aaccacattg tgagattgat gccattttga tagaaatcgt
   238261 cggtatataa agagaaagtt tgcgatgtaa gatgtgctct tacgaaggaa aataggattg
   238321 ctaacttttc catctatata aaatgaaaag caagtttttg tatcaggaaa gaggcaagga
   238381 cagatccgcc gaagaaggat cggggttaga actagtctga agcttaaggc ttttgctatt
   238441 caagaaggct ctccctgctg gctccatgta tgctatagct cctgaaagtg tgagtttggc
   238501 ccctggatag agagaaaggt aaaataaaga ggagagtgat gtttcgtttc aagttcgaga
   238561 tctcgtgtag gtatacatga gaacagagaa gtgtcctacg gattcagaac cggaaggtca
   238621 gaaaaaagtg ggaatgacag tccggctacc ggaggagcta ttcaactatt atcaactatt
   238681 gagtctctga gtggattttc caatagatgg gagcaaggat attctgtctg aagaaggacg
   238741 cagaagttag tgcgtacgct tgatacatca aagtatgcct cccgcttaca catcagcagt
   238801 cgttctaatt tttcaatcaa agtagtagct gtcgtattcc agaaggaagg gggattgata
   238861 taagaagagt cagacttctt tttaagcagc aatcttttac agaaaagaga gtagttgtcg
   238921 tcgatgtggg atagtccctg aagaatagta cccatgtcaa cggattgcag gcatagttca
   238981 actcatagcc ccaatccacg ggtgacgata ttgtcattgg ggatctgtat gctttcaaaa
   239041 gagtcgttag ctgatctagg agtcagtggt caataagtag gcaaaagact ctggggaagt
   239101 aagcgaagct attgattggt tgagcccctc aacaaagcat gtccagcact tatcttaagt
   239161 tcctttaagc agatctgtga gcaatcctag gcctctcttt cagtaatttc caaagagtat
   239221 aggctcaatt aaaattattt atggtaggca gagcaatcgt agacccttac ctagctagtg
   239281 acctggctct cttcttcata cttactgcac gcaggataag atctacttgt cctcctccct
   239341 tccctttacc tttaaatgaa agctttcacc ctctccctca tctgcatcca aaccggagcg
   239401 actttgttca atcgcttttg cacttttttc tctgcctggc aggcttttca tagttcacgg
   239461 cccctgttga gtagggtcgg tataggtaag gcaatcgatt caaaagtaga ctgagagtgg
   239521 aggtttagaa taacctaagg cgtactgtag aaggaaagaa aggtaagcaa tcccagaccc
   239581 aatagggcta cctttcttcg actgagacct atctgcttca ttcccgagtt tcacttcact
   239641 tggacacagc caaagaaaaa ggggggcttg atccaccgct ttcaagtcca gttaaattag
   239701 agaactcctt tttagaagaa taggatagaa tcttccgaat cagtcctact atggttggac
   239761 caaggtcatt tcgactctct agactttctt gcttctttcc atcctgagaa gtagatcctt
   239821 tggacctttt ctttcctgtt gaacgagtgg atgttttgaa cgagtgttga gcgagtgaaa
   239881 tgccccataa gctataaggg cgagctatct ctttagattc tgtgagctgc gattgaactg
   239941 aacgttccaa gtgcatccag caggaatcga acctacttgc ctctttatta ggttgggcgc
   240001 tttaaccatt cagccatgga tgcaaagaga gcgagtgaac taggttttgg tattccttct
   240061 cgagcttcaa tttcttccgt tataggagat tcgagaaaag atggaatagg aagacgtgtt
   240121 tccagaacaa acaagatacg ggttgagaag gggaagttag caaagttaga caagattgga
   240181 atgggcatag gaacatgtat tgatgtacca gatcggctaa tgctcccagg ttgatgcgat
   240241 gtattccacc agttgactga agactttatt attggtatat cgatcggtcc agcacgaatt
   240301 gaaatagaag ccggttcgac aggaagcttt tgaaaacgca gtgcacccag gtaaataaga
   240361 aacgagatga atacagaggt caaacgagca tcccacaccc aaaaggtccc ccacattggt
   240421 cttccccgaa accccccagt aactaaggta aacaacgtaa aaaaagcacc catttctata
   240481 ccggttccgg aagagcgaag ataaagggga tgttttgtta ataggaacaa gaaagtgttt
   240541 atagccgtgg cgatataaac aataatactc atccgagccg caggaacatg tacatagaga
   240601 atacgagaat ttccaccttg ttgaagatct agtggtgcta ccccaagact taaatgaata
   240661 gccatcgctg ttaagaacaa ccaagaccca atgagaattt gcgcgtagct tctggtcttt
   240721 gacatcaaaa aagaaggttg taataacgaa acggacatgt gcaaattttg tcctagctag
   240781 tggaacaaga aagacatgga tctataatac gcaatcaaag gatttccccc aacgaataat
   240841 tccccctccc ctgctttgtt tgttttcgct ctgcttgtgc gtggcactcc ttgctggcgg
   240901 agcggcgcat agcgaaaaaa agaaaaaagg aaactcacca ccaaaagatc agtccaataa
   240961 tcccactcac tggtaaatag cgcaatactt cttcgtgaat ctccgctatt tgaatatgga
   241021 acatcataac aacgaaaagg aatgaaacgg ctatagctcc tatatgaact accgggaaga
   241081 tcatagcgaa gaagtcgaga cctaacaaaa gacgtaaacc tgaaatggcg gtttagtcgt
   241141 cggaatcgct tttatttatg tcgtagtcag acagcaattc cagtagctcc atccaaaact
   241201 tgtctccgtt ttttcctaac cgggaataaa gatagtagaa tcgtttctta cgccgatcga
   241261 tatcgatcaa ctcatcgtca aacatcgcta catcgataat tctttttata tcgtttttat
   241321 ctggaatttt gtatcttcgg atactaagag ttcatgtgtt tttgctatta tttttgcctt
   241381 gattttttcg catttaccac tctctgcttt tacttgctcc ccgatggtat ctgtgttttg
   241441 atcctctacc tcgaggttca agaaaaggcg ttttgagcca ctttccttgt actctttcga
   241501 ccagaaaggt gaacccctct gctgatcgtg agagtgctca ttctcatgag cataatatcc
   241561 ttctaaaaga ccaccctcag atggatttgt cgggggcatt ggcgtatttc ctcctcctag
   241621 tcctccggat accaccgggt agaactgaga aatggcacga cttaagtcgt ccatccacaa
   241681 gtatcctaca gcaaataaag atttacagag aataactgaa agaacataaa accaaatgag
   241741 ttgccatttt ttggaaagtt tgtctataat aggaagcgaa caaaagtaat ctaaaaggac
   241801 ttttatgctg caaaagactg ggatgggaaa caaaacagaa tgtacaaaac ggataatacg
   241861 tgtaaccagc aaaccaaaga ccaaaacttc agtacggtcc gtgcgccgtt tttcttctct
   241921 accatgacga atcaattgat tagctgtagg cattattctc tttcctttct tttccccccc
   241981 attttgtgcc ctatcacttt actcccgatc cgaagcaccc cttttccatt catatagaaa
   242041 tccaatcgtc aaaataaata aaaagagtcc atcatggacc aaaatctgcc cgagacaaag
   242101 ctgagctgtc aaataagacc aacaagggat aagataggga ggctcctcta aagctggaac
   242161 ctcttccaac cccagcacgg ctcttccccg tcgactcctc gtacgcgtat cacaggggca
   242221 aacacgcctt caaaacatct ggatcataca aacttctcat tcagtggaaa aaaccttacc
   242281 aagactagtt gcctcaacga attgatatgc ttttgctttt tgtgacaccg gcgcgaatgc
   242341 tgaatacgga ggaatacaat gaaatcagaa caaagcaggt agaccaagct agcttacaga
   242401 attcgaggaa ttaaaactca gaataagctc ttttattagc acgtttggta gccagaaagg
   242461 aaagaggttc tcattcacag tgccttctcc ttctgtgatc actgatcaaa aggacattca
   242521 ttcagtaagg gattgatcct caaagtggtt cttttagcac aatgaattac ttatcttata
   242581 atgaattact tatcttatat agtagtgtaa ccttctcttc gtacaaaaaa gcctattctg
   242641 aaagccgtct ttcaatgcct gtaccctagg gcgggctagg ttcaagggta cgcacctagt
   242701 agctgcgagc ctaagattaa aggcaagttc ccttggttcg gcacgctttc actcagtatg
   242761 ataggctacg gtcagattcg ctcggtctag gtatcacctt gatgcgcgta gttattgcct
   242821 tgatcccttt cctttgctcg ggtcattcca ttgcctgaaa aagtgagcct ggatcttcgg
   242881 agaaaggatt ttagagctct gtggagaaag tcttgaaata ttggatgctt tctttcgtgg
   242941 ttaggcgggc atggcatcaa ctctgtatag gtgggttggc ccggccggcc aaagctagat
   243001 atagatcggt tggcactgga tctgctggat agaggtagcg gcacagacag ctacggatgg
   243061 atagaattac gtcagcttgt cgggtcagta gatatgccca gcatccattt tgactagaaa
   243121 tgaaatggta cagagaagcg cagtgagcgg tagcaaccat tgactactcg ggccgggcct
   243181 tgcagccaga aaatgggact cgatcagctc agcccattga ctcttttatg gggaactatt
   243241 agagacctag gaaagtcaag atgccaccgg ggcgtagaaa gaaaaaggct tcttcggcat
   243301 gatagctctg ctctgtcgga taatatgagc cccttatgga acagctcact ccggggtgat
   243361 tctggtttag tcatagaata aagtaaatcc atgcgtttgt cttcgccttt tcggaagacc
   243421 aagacagcta gacgatagat taaccaaagc cataaagaga agatcgatat cgcacagaaa
   243481 tcctggatct atcaaaaaag cccgccaaag gtgtcctcac atgaaatcat gaaaaggatc
   243541 cgagcccatc aaagactcta ctacatgaaa ggatctgaat ctatccaaat agctgtggcc
   243601 catgatccaa gggacccgca accagtcaat catgctatcc ttaccttcca accaatcgga
   243661 aaaaattacg ttcaattcag gatcgaatac atctttggct tatgagttat gcgttttctc
   243721 ttcttggcac tttatgtctg ctagtgcata atcatgctta tggaaatagt ggaggttgag
   243781 cagtttccct gatgaagaga actctccttc tctaaacaag cttgcctgtg ggcgtcgagt
   243841 aagagcatct gggaattgat cttttacgag acagcccgga gttggtctcg tggctaggtc
   243901 tttaaccgaa ccggttcgga atagaaagtc tcggtcaatg aagtggagtg ggctgaaaca
   243961 gaaagttggg tattgtattt ttatgctcgc ttggccggaa tcccctatag tgcttttcgg
   244021 gcgaagtgac ggattacttt ttgagtgact accctcagtc tttcagagcc tcgggataag
   244081 ctgttcttgt ttcataagca aatgtggcaa cctggtggta tagtgagctc tctctctgga
   244141 ttaagcttcg gtcattgata gagaggaatc acctagccta gcattagact cgactagcta
   244201 gccttccttg ggcggattgc tttgaatagc gtagttttct tagctccggg gactgcctta
   244261 tctacactat gagaaatgtt agatgcaacc attatagtat agatatattc ttagatgatt
   244321 actatatgtg atttctttca tacagtctta acaaatatag agatcttcac cataggagac
   244381 tagcttgaac taaatcctcc aaccttaaag cagtatgaga gaggacggat accagaaaga
   244441 atcacctcgg agccgctatg ccactatgag aaacgttata ctatagatag acatgagatg
   244501 atattctata aggaatacaa tgtttgaaaa gcaagaatag atagagttga aagaaaggcg
   244561 ctcgtataga gccctcgact atgtatcgga catatggcag gttgggaaag cgcgcttgga
   244621 aaagaaagac tatcctcgag gtaaatgtaa atcaatctat ctcgcattgc ccaatctgaa
   244681 tgctaaaggc tcgtaacccc ctaaaaggaa actcaccacc aaaagaaaaa ggtaggttaa
   244741 ctaacgaaac tcaaaactac attttaattc ttgctcaccg ataatccttt agaaaaaata
   244801 ttatacagct gtatacagga ttattggtat agctgtccac tagccgaaaa tcggacacca
   244861 aattattgta gactgaatta agtaattgca tagctgccgg ggatgccgga ttgcttgagt
   244921 tccttcctat agaaaaagaa ttaattcagg agttccaggc aggaaaagta tacaaccata
   244981 cttaaaaata ctgggcgcca ttcggaatag aaagaataga gatgttgggg gtggaaagat
   245041 tccatggatg tcttatagag ccatatggga aagataagtc tgtgttcggt ctctgggcat
   245101 cggtatcgtc ttatgggctt gtcgactcta gaacccgaaa agggaatacc aaaaatgaag
   245161 ttaggggatt ccggcgcgga tgatctgtct tagagtctct tgctaagcca ctcggattcg
   245221 ggtgttctca aacggtgaag actttaaggt accaggtctg cgagcctatt cagttcttgt
   245281 tcttccgaca tcggatattg cccgactaaa acgacgtgtc ttgcaatcct aaccaacatc
   245341 gcttcggtag ctcagtcagc atcaaaggac acatgggggt ctcgaaacga acgttttcga
   245401 ttagtaacat ggggtcggtc gccccattcc ttcttaggta ccagcataat aggcagagac
   245461 agagctacga ttccccaggg cgagggaaaa agactgacta gacccggctc gaggagattc
   245521 aaagggcaga ccctcttcac aatcagcttt ttaagaagca agaaatgcca cttttggccc
   245581 tcctgggtca tacctatggg gttggctctc acgtttattc gtattcaagg aaaggtgtca
   245641 atctagcgta agccgcaata ctagatcgat acgagatagc agtcaaaagc agcacccatt
   245701 gaggaatgaa aaaaatccac cccctaacta gactatggaa gatcttctcg ttttggctaa
   245761 acggatcttc cctgtactgt aacagggtca acaccgcctt ttgaggttgg tgtccgagct
   245821 ttccgcccag ctttcttcga tcgtatgcca cgaactatgt cttagatacg taagggcccc
   245881 tgtccaagtt tggctttctt agtacattgc ctttgtactg gaagctggat catacgaacc
   245941 agcaatgacc tgaagctttc ttgcagcaag atgatcagtc cgagagtgct gggcattcat
   246001 ctctagcttt tacaatggtt atttcattcg ccggatattc accaaaagaa agtgctcgct
   246061 agccgtaagc ggaatgactt tcttgatatg gaccgatcga agcccttaag gatagcttac
   246121 tatggtaaat agctagaccc cgaacctatt cccagtttcc gagtaactat cattggtcaa
   246181 tttcctgttt cccatggtct atcattggtc cggtccttca gaggcaggag aagtacaaga
   246241 tgcaagctca taaacgagac ggtaggatgg cgctaatgcc aggcgatcat tagacttcgg
   246301 ttaatggaaa gtggaactta gaaatagctt cttaagaaag agatatatag tagtgcttcc
   246361 ccctccttag aatggtaatg gttcgttctt cgccaggatc atctccaggt agtgctgctc
   246421 cgtcttcgcc ttgaccttgt gctggccgct tttgtacagc atgaaggggg gaaggttccg
   246481 tctctgtttt atcttttgct gcgaactttt ttttcctctg ttctctgtac agcacactgc
   246541 tgctttttct cggtactcct ctgctttctc tagcacagtg ctgggttact ccttcctaac
   246601 tctcctaact gttatcctcc tctgtgctct acctgaagca cactcctctc tctgtgctgg
   246661 tatactccta actcttaata gtacgcacac acgtaactct taatagtacg cacacacgaa
   246721 agtgaaagta aagggattgt ctggccctgc tacctagcca acatgagcac acccagctgt
   246781 atttcctaga tttaggtttg attacttttc tcggtatagc agcgctacta cgcttcgctc
   246841 acactctctc gaccaatgct gccttctcta acaactctca gggagactaa agaactgaag
   246901 gcttcggagc ctagcctcta actcaggtga caggccagag aagaacttcc tagctagagt
   246961 caactcgctt caggtgcctg ccaaatatac ctgcgggctt agttgaacct cctgatgtag
   247021 accttaacag agtagctaaa ctgatccaat catcatccca gtgattaggc taactacatt
   247081 cctttttttc gaaagagaaa gaagtcaaag gcgttcctct cctattagtc gagtagtagg
   247141 cgttcctctc ctattagtcg agtagtaggc gttcctctcc gagtaagaga ctgagccggc
   247201 taccttactt cgtctggaac aggaacagct aacaacagta cgaagagtat gaccgctgac
   247261 cttctgtgga aagaaagaaa agatattgat tctacgggtt cctcctatga gataggagaa
   247321 gctgggttcc tcctacctac ttgaacagat aactaactac acctactgga ctggctactc
   247381 tgcttctaag ggcgcgtagc cagatacaag ggttaacaac agatacaata gttcccatcc
   247441 gaacaaagag aggaggagat tattaactga cagcagaacg cagatcgtac ttagctacac
   247501 atgataactc agccagggac tacggacaac agatgaactc ttcatgctac ttattcccag
   247561 agaacaaaga aaggaagtgg aagctgcaca gcgggaagca gacacaaccc agaaacaata
   247621 cctgcaagac ggagaggggg aacttagtga tataaagtgg tagacccctt ctcctatccc
   247681 acgtatcaac gggaggactg cttcgcctac ttcacgccta ctcatacaca ttccgcccag
   247741 aagaaggaag actcttttac cgcagcagca agggatcccg ggccccgcca tgcatgaaca
   247801 ggggttcctc cactggaagc aaccaactgg ttattcatgg ctagtccgaa cgaagagaag
   247861 ggagattctt tcacaaatat gccatgtcgc ttacgctcct cgcccagaat atacagctgc
   247921 aagtgctggt tcagctacaa cggtaactag aggaagaagc cctagtatgc acgcacctta
   247981 ggaacactct agctacattc acattattcc ctggaccgga acattcataa gatattgact
   248041 aaagacagct gagcaacaag caacccttaa ccgctcacac ggcttacccg tcgtcgtcga
   248101 caagctcgct tcccgggtaa tcctaacatg agctacactt catgacagaa ctcactggaa
   248161 caaagaagag cagactagta agggaccaac agggaacttc tagacaatac ttacatattc
   248221 cagcctatac taacacatat tctaggaaat gacaggactg gcaacaaccg aagtgccaac
   248281 acccgataca ccgctagaga gaagtatcca ctagcagaga accacaggga agacatctag
   248341 ctacttcttc cacattacag acgatactaa gatattgact cattccagta tgacaaccgg
   248401 aggcaacaac tgaactaaga tattgactcc agtatgccag ctacaccttc tacactggaa
   248461 gcaaggaagt aggaactagt caagacccta gggaaacatc tagcatcttc taccccttcc
   248521 cggaaacttt cttaataagg tcaaatctgt gcagtgtaag cttgatctct ttgaattggg
   248581 tattccccca acctgtcaaa caaagaaagc tagtataggc atgaaaacag cttgcttaga
   248641 gagcttgcct tccccttaca ggcaagcttt aacttccctt cctaacgagc caacaagtta
   248701 gagatgtaaa gacggttcct taccaggagt caatcccaca agaatcctag cttgattggt
   248761 ttgatgtaag cgaatgcgag tacagggaaa cgagacagct cacaacaaag cttaggctca
   248821 cttctgaccg aaagtccaat tcaatcattt aaagctcact gagcacttct ttccttagtt
   248881 tgaggacgtt aatgagtttc aaaggataat agctgatcta gaaaacctga aagtctctat
   248941 atcagacgag gatcaatact gatgtcctta ccaaaacata attcaattca attcaacagc
   249001 aaaagaagga tagcttgatc ctcaatgcct ttgatcatct ttttctaggt agggaattgc
   249061 ttatctcggt aagctaagaa tgttagaaac aaagaactag gacagaacgg gaaatggaga
   249121 aggaggttag aatcaaagaa cagtaaatgg agaaggaggt taatgtgtat ttcattctat
   249181 ctacatttta actaattgag tgtatccagt cttatccatt aatgtaatta caagaagaat
   249241 agtaccaagc atgtaggtta tagttttcac tttactgggg tgaaggtttc tgtagttcaa
   249301 gtgggtcaaa agtggtttgc ggaaacatat ctctaataat tcgattgaga ggctcctcgc
   249361 actcacatgg acttaaactt ttgtgtatta tacaaacatg attcacatac acatctcgtg
   249421 tatattgcaa tacatttggt aaattatctg aaaataataa tgaaggtttc ttcaaaagag
   249481 gtccaggagc tatttccatt aacactgtta tactgaacag tatacaaaag aagactgcag
   249541 tgcgagaatt tatggaggat gataatgcat ttgagatatt cttctgaaca ctttcatatc
   249601 ttttatgtaa aacatttttg atgagaaaat caccagtagt atccaaacac tttaatccag
   249661 atgatgggaa aatgctttgt ttaaacctac tacgaagtat gcttaatact tcattattac
   249721 cagttgatcc atatggtgat gtgaaatcta agtttaggtt tttgatataa ctatgaagta
   249781 tattaggtag tattactttc tctgttgagt ttgtaccact ggtctgatgt ctcaatttct
   249841 ctcgcgttag gatatgaatt ggattttctg tggaactgtt gaccagtggt cctctaaata
   249901 aaggagattt cattttcata tctaaattca ccaatatgta tagagcacca ctggtcagaa
   249961 gtaagaaaga taatatatat gtctattggt taaatcaatt ctggcgagag atcaaattca
   250021 gattactgtt caattatttg agttcagtct aattttcgac ctaacaagag caacggaatc
   250081 acgctctgta ggatttgaac ctacgacatt gggttttgga gacccacgtt ctaccgaact
   250141 gaactaagag cgctttctta tcacaattga taagactgta aagacgagga ttcttttttt
   250201 ttttataacc ccaataaatt ttccacgcct atattatcat atataatatg agaaattgaa
   250261 agattatcta tgtccaattt gaatcgatta ccaagccatg tcccctcatg ctatatgaga
   250321 ctgaactctc agtttgtata tgtggaaaga gacctaagag aactgaaact gacttctaac
   250381 ctaggctctt actctcttat tttgacttct ttccttcttt tcccgtagat ctcccaagaa
   250441 aaagccaata tcctgagagt gatctataaa ttcccacgaa ggccaatcag catcactaaa
   250501 acaagagcaa gttgagagga aggtgtcaag tgcagacaat tcagagaaga tatctcaaca
   250561 atcttttgaa agcgtttaat aggaaggaat agaaacttta atctaaacct tcttttctat
   250621 ctaaggtctc atcagaaatt gtgaaagttc actgagtaag ctatgtcagg tctggttatg
   250681 ctagcaacca ccaagaatgc tctagctacg atagagatga ggattagcag caaagtggaa
   250741 cttacaacag cagagcagac aaagaggacc cagaagtgac tatgggagaa gggagaggtt
   250801 ctttccatgc cagccttgac caatagatca gtaatgtttt gagaaagata gaagcagaag
   250861 ttctactcac tttttgacca agattgagcc agatacttta tagaaaagat ggcatttttg
   250921 atgcatacta tgtcatcaat atgaagagga ttggaccatg tgattctaag atcatcaaca
   250981 tatactagaa tgtacagagc atgatcaccg ctcagaaaga gagagagaga aagagaccgt
   251041 aatgtctgag agaaaggaga gattgaaaac ggaagcaagc ggagggatag gagaagagag
   251101 aagagagatt gtagcgattt actgtatctg agtgcaacac aaacaatact aagaccaaga
   251161 tcttccgact tctttttcca atgtatcttt gttgaagatg aatctcaaac aacaaaacta
   251221 agggatatgg cattcatttg aaaatgaact aactaatact gcttccaatc aacatatttc
   251281 gatttcaaac cacgaatccc cccaacacag caatccaaac ttgacacaac tggaacctca
   251341 cattccaaac ccaaattagc attcgaataa ccagatttat atattttccc atcagctcaa
   251401 catcagagga atattaaggg aatagtgaag gggatcttat acctgaagct gttccaagga
   251461 gatccacgcc atggaccagt ttcctgatat gtatagaaga caatcccctg aaaccaagta
   251521 atccgcgaag agtcctcagt ctccatggcc atcttcactc tagtaccagg agtccagaat
   251581 atagccatgg aagcctcaac atcttctgcc ttcaccacaa agtccgacca tccagccgta
   251641 ggataataaa ccacctcaaa cggcaaaccc tgagctgctc tattaatcgc ctcagagaca
   251701 gcttcagccg tcaatttccc tttcccagtc ctcctaaacc ccttcttcgc acttccgtcg
   251761 tcttccttag caacgcctcc attgctctga taataactac agtactcatc tccgccgtag
   251821 aagcttgttc ctccgacgtt actagagatt ggtgctcgcc ttacaccaat aaacatctca
   251881 tcagccgatt tcctcataaa tacaacagaa tcaccagcga ttagcttctt attgttcacg
   251941 aacttgctcc atccggtggt taacaagtgc ctcctcggtg tggttcgact tgacgaagag
   252001 cctttatgcc aacaacaact gctttcgaag cggagctttt tgagtgtttt ttgggctgct
   252061 gaaagtttaa gcaccaacag gtgagagtgg aattttaaac tgactgtaga gaggtggcgg
   252121 aggcaatcaa ccacaggtgt ggcctttgca tcggaacctc ctaagtcaaa ttgataatta
   252181 tcctgccatt gaaggttggt ctgttaccgt cattgaaaaa gaagcgaaca gagcggcaac
   252241 attgctcgga gtgtcgcaag agaccgaagt accagtccta tatatctagt gaggaacctc
   252301 ggtggttggc tgctgttcta tttcataaag agaggaaacc cttcgaggtt ggccctagag
   252361 tgaagttgtg aagttctcga acagaccctt ccaaaggtcc gcccggttca acttgagtac
   252421 tccattcggg gtgatatata aaggctaaaa tcgtcagcag aatagcgagt tttgaagccg
   252481 gttgaagggg cctctgagac aaggaagccc ttgcttgaaa gagtcaacgg agcaatggat
   252541 tattttccgt tacttatttt ataataaagt ctgatgacca caacagggct tgttgaatgg
   252601 caggcttgac tggcaatgga aaggagatgg ctcatccatc tcagatgatc ctcaatcaaa
   252661 gactccttct agtggttcgc ttaaaagatc tgtactaaaa acatccctcc ctaccgggaa
   252721 atcacaaaaa aagagtacgc gaaaaaagca cctttaggtg ccaggagtgc ggcgtccagc
   252781 catgcttcga atcgagtacc ggcaccgatg tcctatttcg tctgattcaa caagcctcct
   252841 atcccggacc aaaagaagtg gctggataac ctttcttccc ttctactttt agtagtcgat
   252901 gttataccgg tactaaagag aagtaattga tagtgttcaa catccctatc aatgacttct
   252961 aacggtcagt ctatagcgct tctagccagt ctgacttaat aaaagatctt ccagccaagc
   253021 ctgtttcagt tgaaatagaa gtcagccttt ctctggtttt atatatccct gtgactggtc
   253081 ttactaagag cagctactgg gtttgcttac tacagaccct tcattaccac tttatcgata
   253141 aagggattga ctgctctagc tacaacggtc tcgctcctac tacttttacc tcttattaca
   253201 taggataaac cgagaagact accgacaaac agcaggaatg aatgtgaccc acggctacaa
   253261 acgaatgaat agaggggttt ggaactagaa ccgtatccca actcaaggcc ctagaaaggt
   253321 agggcgatgc agtaggaaca gattacttgc tgcttgatac tgaaggaatt tagtgtactc
   253381 atcctcacat acagatagag ttttatgctc agtagtggta gaaggattag gagggggaac
   253441 atagtcagaa gtagctacat tcgcaaggtc taccaaatct caacaagaat tcactaggct
   253501 taacgccctc ttcaccgaat caccatagtg agaacacttc atcctcatcc acttctccac
   253561 tgccataaaa agagccttaa tctccttctc gggcaggcca taacaccttc tttccctcag
   253621 ctaaacacca tataaagagt cactcctcga ggtaggtcag cgactggaag agtcgtttga
   253681 aggcgatcag cagtcggtct gataaagaag tctgtatgac catctctgtc tgttctcctc
   253741 atccccctat cataactcgg caaagcgtta gtgcctttcc agctagtcgt tccaacagga
   253801 atgcttaaga taacgaacct tgaccaactt gttcaaaaac agaggtcggc ctcttcatcc
   253861 ttcaagcttt gagtggaccg ggtagcgtca atcagagtgt gaatgaaagg tcaagggaac
   253921 aagcaacgga ttgaacaacg ttagcgaaag ccgttgcgct aacgcgcatc cgttttcttg
   253981 ctcgtcttcc ttgatctttt aatatggaag gaaggctaga atcttctttc cgctttcaaa
   254041 tcttccgatt tcgatgagaa taaaaaagat caaagcctgc agggtcagaa taatggaatt
   254101 agactagtta agttcagtta gcaattcaat cagccttagc taataaagcg aatatccttc
   254161 cgcttcaacc caatcttact cgaagaacta gttatgtttg ccggaagtac gatcagtgtg
   254221 aggggtagta taagtgatca aggggtggta actcatatta ctggaggaaa ctttgcacag
   254281 agttccatta ctattaatgg gtggaattgc cacaacatgg gcgttcttct tagcaagaat
   254341 tattgcagta ggataatggc taggaggatt ttaaaggcat tatggcatta agatttccaa
   254401 ggcttagctc agggactgct gtcagtcgct tcccctcatc aactaattaa tgagagcttc
   254461 cgtcgtcagc tcgttcttga cagatccgat cgggtgttca taatctggag taaaaggatt
   254521 cgaacctttg catgccggta ccaaaaaccg gtgccttacc acttggctat actccatacg
   254581 gcctctgagt tttggacggt aagggggggg agggggaagg gagaagcagg gcggggttgc
   254641 gcgcgagccg tgcaagaacg cgggaatata gcaagtaagc agcaaggttc tttaggaccg
   254701 actacaacaa gctcgcgact ctcatagaaa gaaagggtaa gctctctgct ctctatttgc
   254761 tcgcaatgct atacctatca aagttggcga acgcttctgt aaccttagac tcgttacgct
   254821 cttcgactga actcgtttgg ctccgcgtcc accgaaagtc ggtaaccttc gtcaccgtca
   254881 gcatttggta ctctctcgat agcttcaata gttcactgaa agcctttggt gtaatgaacc
   254941 gcaagccctt ctgaaagaaa gaataagaga aaggcttggt tgcgggaacc gacggtgacg
   255001 aagcgggccg atgcggccgt ttccctttgt aaggtaggcc ttttgataac taattagagt
   255061 tgacatgaaa tggatcacgg gaaaagacgt atccgatgaa tgaatgattc aatcctccca
   255121 ctcacacggg ttcttctatt gaagggcttc ccccttcttc tatgtgaggt ggggaaaggt
   255181 cagagcggaa cctagataga aacgcggagc gccgacccct tagccgatac agttaccatg
   255241 cttaccagct cttaccattg ccgcttatag atgggaggta ggcgaagggt agcttgcttc
   255301 tcttctccta ggctacctcc actccacatg gttattcgcg aagaaaaggc agcgagcggt
   255361 tcttcgctta gtagagctac cggccggcgt acgacgaccg cttcttgttc tcgcccagcc
   255421 gcttcttttg atttgattat tatttgaaat cctagactaa agaagaagct ccagaatccg
   255481 cgcagggcaa aatctgcagc aggagaagaa agagggtcca ggtcaatttg ataatgaagc
   255541 gaaggtcccc cttactccct attccctctt aaagctttat aaagctgggc ggttggttaa
   255601 gaactactga ctgtaaacta tagatagcag ttacagtcac tcaattgaaa tgttcgcctt
   255661 tggaatgaag atagatgagc aggggagttt tcactcctac gtggtattct cttccaacaa
   255721 gggttacggc taaaacaccg cttacttttc aaagacaaac tgctcctaaa ccaagcctga
   255781 acacgtttcc agttgttgat cgacgcgtgt cgtgatcacc agcatagtcg gcgtcacaat
   255841 agccaactat cttacactgt tctcctttct tatacagaag accatagtca agtcttcctt
   255901 tcatgtacct caatattcgt cgaaagtgag gtttctttgg attttgcatg aatcgactaa
   255961 ccactccaac tgcatatgcg atgtagggcc ttgtcagggt tagcgcttgt gctaagcgat
   256021 aagaattcgt tctggaatgc cggcgcggac tgaaggatga tgtttattag ctagacaaat
   256081 ccttcattcg aaagacgaca atcaaagcat aacgactcgt ggaacattca ttcctaaaag
   256141 gtgtaaacct gtgagatcgg acaacccgta aaaggaagcc gctaggcatc aagccctatt
   256201 atcttacacc tagggagggt ggccgttgtt gggtttttct caattagagt cgcaaggagt
   256261 ttgctgctcg ttggtagtgg aatgctgact aaccgtctcc gtccccctat gatgagaaaa
   256321 agctttccga gtggacgagg accgatcttc tctttcttta gtcttgctcg tcttatggca
   256381 ttagcctttg cggattcctt aatccgcggg acagctgtct cggcacatgt caatccttat
   256441 gtccccagcg agcaggtcaa ggtactctat gttgctgctt gcctttatct tccagtctgc
   256501 caagcaagct tgtttattct atgttattga taaatcgcta tttcccccaa accgctagtt
   256561 ttcatacgac tcagaactta taacgttgtt ctgtctccaa acagagagct tgtaggcctt
   256621 attctttgga taaaagtagc gacgagccga ctactacgac cacatgcgca tctagcgcag
   256681 tggcttgtca cttcgtacct tgaccatctt ccgaagttct aaataatcta ctgatcaaac
   256741 gctgtagggg cggactgctc tacattcagc cacgccacag tgaccccccg aagcgatctg
   256801 cctcattgca ggacgaaatc cggcagccaa ttgctggctc tgaataacca gcccagcaag
   256861 aagttcaatt cttccataac ataacggggc ggggttgcgc gcgagccgag tgacgtagat
   256921 gcacaagagt acttcgcgcc acaaccatct cttttttata cgttctacgg accgatgcct
   256981 gctgcttcat ctggtagaaa agaatcatag atatgccggt cattagaagg aagaaccacc
   257041 ataaaaagat tcctcgtgta tcatctgtag caaaactatg aacgggagct agcaatccgg
   257101 accgtattga aaaggttcct gagacacagc atggaaaagt cacaatatta agaaacgagg
   257161 tccaagaatg aagaaggggt aaaattacag aatgaatacg agctgtggct aatacccgag
   257221 gcataaaaga agcattttct acgggatccc gaaaccacca gccaccccga cctaattcat
   257281 gataagccca ccaacttcct ggcaagatgc ctacggttaa aaaccaccaa catgtcaaga
   257341 tccaaattcg aattggttcc tggtcctgat cagagaccac tgtgttcgcg ccggcggtcc
   257401 aacaaagagg cgaagtagtg gtctctttct ttccattacg aacgacacgc ttcgcctgct
   257461 ccctccccgt gtccacgtcg tcgaagaaag ggtcttttgc cccgatttac cgtcgtaggg
   257521 agcactcttc tgagccccac atgattcgcc gaaggatgag atcttgccta tgcagtagga
   257581 ttaaaaggaa agttatccga acagtgagac ccgggaagac tactacttct gtatttttga
   257641 taaatcaaag ggctatttcc tgattcattc cacatttcac attccccttg ggattagcaa
   257701 aatcaaatac ctttttctcg ttatagctat cctttgcttg tgtaatgact cgaactttct
   257761 catttatgaa gacttgaaat cgcatgcata agtgttggtc catcagagct tacagttgga
   257821 gatgccgcaa agcaaagatc tggacgaaat gagagtcctt ccgcgttgga gctagggaac
   257881 ctagggccag attgatcggt aactgaatca gttaaccaaa agatgctgac acgatcatta
   257941 cttgcacaaa gataaaaaaa ttgagtactc tgcccttcca gtgctacctt tcttcgatgt
   258001 gatttgattc tagaagatga gcttgctcgg atccttttcg gtagctaaaa gctttcccat
   258061 aaaaagaata tgtaaccccg tatcgataga cgaaaaaacc caacaatgtg aaaagaaaga
   258121 tcttctccgt ctctcctccc gtaaaataag aaagtatgaa aaactggatt aagagacgca
   258181 aattcttcaa agaaagccat agaagttgta tcatctatta tattccagcg tgactgctca
   258241 cgtcgggata atcttgattt tagaatacct ttaatatact ttgaaatata agtccactcc
   258301 ttcttactgc gtatgctctc ttctctcact gcgaatgatg ccaaaaagag ttcagctcgc
   258361 aagcggagtc tcattggccg tgaatcagaa gctaccatgt tctaacttgc acttagtcaa
   258421 ttgggaagat taaccacaac aaatcgtaaa catcagatcg gacctttatt ttattagcgt
   258481 tctttctttt agtttgaaca acaaagtccg ggccaacaat atcccaagtt aatctgtaaa
   258541 agtcagctgg aaaaccatcc gagccagggg atttgtcgag cggcatgctg aaaagacaat
   258601 ttggaatctc ctccgtagtt aacctgttgc agaagattcg cttgcatcta gttggagcat
   258661 ctgatgaagt cgataagaga gcgaagggat gagatagagg ctcgagtgtg gttcaccggt
   258721 gaaaactgaa acaggttgga gaagtaacga atggcttctt cttggatatc acttgttcga
   258781 aatagatcca caccttgatc tgatgtaatt ctgcggattg cattagcaga ttttctggct
   258841 cgcactctat gaagatcgcc gatgaaaaaa aggcatatcc actcgtagat cgggttggtt
   258901 atatttatat aagggctatt ttgcatattt ttaatgttga taggcagtag ggtaaggaaa
   258961 ggatcatcaa tctatgataa tttccgagtt gcaaaatcca aatacaacct gacttgaatc
   259021 cttactggac tacttcatat gccttccgca cacaggacag aggaattcac tccacacacg
   259081 agccaactcc cctaaaaggc ctttctttca tgcaattggc gacgccatcg ccttatatct
   259141 ttcttgttaa gatcttaagc ttcctggacg tctacaaatc tgttaggcag gaaatgttta
   259201 catcggggga agagttcatg ctatcatgtc gctaaaaagt gggctttttg cctctacctt
   259261 tgaaagtagt gttaaaaagc cttacttcat tggttcgatc agtcttttcg tataaatagc
   259321 attgggcgtt tagcaccggc cttctattca ttcccaccct gaagcagtta ttcggactaa
   259381 gatcgtcatc gtaccctcaa ggcaagctcc tgaagtagaa gtgtgaggca agacgggctg
   259441 ataaactacg aaaatcgttt tttgagggtg gaataaggca cgcggaagac ttaggagtcg
   259501 gagatcatca aaaaataaat ccaatgcttg tcgtgggcaa tcctatagcc cctttcctcg
   259561 ggatcggctt aggctggcta gccttttcta tctgcaaatc tgctaaccga ccgacggata
   259621 ccactaactg actaagctag agaacaggag accaaaggtc ttcctgctta atcgagcttc
   259681 ttttagaacg ggtaaaataa ggagctttcc ctccttccac tgtcactttt ctcattcttt
   259741 tccctaaaaa aaattcataa gctaaagaag gaaataactt acaatgctac aaagaaggga
   259801 acttcaaact attctcaacg aaaaagcctt tcaattagtc ggtctaacct tcctaacttg
   259861 gcacacatat gacataaagc catcaaccaa gtcagccaac taccagcagt cgatgagagg
   259921 gtaaggagga agcgatagcc tgctctcatt gatgatttcg aaccttctta ccctctcttg
   259981 gatgaagcaa ccatataact gacgatatgg attgagtagc gagatcagtt acactagccc
   260041 gggcatgcct taggcttcct ctgccacctc cacgggcgaa gtgagtcaaa tgcactcttt
   260101 cttggctagt gtagtagact ccattatggt cattcgtaac ggctccatat agttttattt
   260161 tggggcgtaa cgttgtgatt gttccaccga ctgaccgata ctagttccag aggcatcttc
   260221 cattcatatc gatttgggtt tttctgcacc atattttgat ctgcctcttc ttcgacccgg
   260281 aattcccatc aaatccttta ctcctcgaat acaatgggat tttacacctg gcgaatcttt
   260341 cactctacct cctcttatta acaccgtaga atgttcctgc gaattatgac cttcgcccgg
   260401 gatgtgagca aatatatcat gtcgattgct caaccgtact ttggctatct tacgtggagc
   260461 ggaattaggt tttttcggtg ttctcgttga aacacgcggg catactcctg ttttctgggg
   260521 acatttatcc aaagctcgag tacggtccgt gcgccgtttt tcttctctac catgacgaat
   260581 caattgatta aacgtgggca ttattctctt tcctttcttt ttccccccat tttgtgccct
   260641 atcactttac tcccgatccg aagcacccct tttccattca tatagaaatc caatcgtcaa
   260701 aataaataaa aaggccatca tggaccaaaa tccaaacaga tcaatcttgt tgggaggtac
   260761 tgcccaagga aagaaaaagg ttacttccag atcagggatt aaaaataaaa ttgaaacaag
   260821 ataaaatcgt atatcgaaac gacttctggc atcaccggaa ggatcgaaac cacattcgta
   260881 ggccgacaat ttttctgggt aggtagaact attggaagca aatggaaaag gaacaccgag
   260941 taggatcaaa gaaactagca gactaatcac taaatagata gaaattggtg caaattctga
   261001 catcattaca gcccactttg ttttctcgct ccttgctggc gaagaagcgg catatcgaaa
   261061 aataaagaaa gaagcaaaag cccatcccga aaggcttgca gaccttatgc gatagggtcc
   261121 cccccagggc cgcctttctt gaggaatact ttctcttgta aacgagaaaa ctcgtccgag
   261181 aggggcccgg tttcttggag gtccttccat atatcataaa gacgctccaa ggactcttcc
   261241 ccactagtgg tcctcggatt atcgagggcc cgagccccac gcgccatcca atcgccggtt
   261301 gggtcatata gagccatccg ttggatgatt tgggctttga tctcgaatag atcttcggcc
   261361 tctattcggg ccatctctat gatctccgca gagggagagc cttcggggta tttcgccaga
   261421 aggcggcgtt ctatcgcctc tacgctatcc cccccaatca tttcatccct cctgtatgga
   261481 taggggacta ctggcccagc ttcctccccc ccgggaggga ctggattagc tggaagcgca
   261541 ggcccagctt cctggggcac ttgatttacc gagggttccc cctcttccgt ttgggacggg
   261601 aggggactgc cctgatttac cgagggttcc ccctcttccg ttcgggaccc cctgccgggg
   261661 gggagtcgga ttcctcgaga actcccagtt caaaggaatc ttcctcccac atggaagaac
   261721 tgcccgaccc ggaagggccg gtagaaggaa gtgcttgccc ccctattgca ttcaagacca
   261781 aaggtcccaa cacgggcaaa gccagacccc ccactaggtg gatgacttcg atccggatca
   261841 aagatcccac gaaccccatg gaaaagacca aaaagagata gataatcttt ttctgcggcc
   261901 ctttcaaacg aaaggaatga aaatgaaagc aaaataggaa gcttacgact aagatcgaag
   261961 agaatgaaac gcgcgtagtg gtcattatag cgcttccttc tgatcctaga aaacgggcgc
   262021 aaaaactacc tgccaaagct ccgagcaggg gcaacaacag tcgaaccata tttttcataa
   262081 atttgagatt ctgtagtttg cttcgttatt agcgtccgag gaacgcatag aagtggttgt
   262141 ggaatcgaac cactaacaca aggatttaca gtcctttgct ctaaccatct gagctacctg
   262201 tgaaccactt tgttctcaac ttatccaacg aatctctttc tcttattcaa ttccactttg
   262261 tttagtttag tgatagttag aggttagaga gctagatcac tcctctaagc agccttctga
   262321 ttatatacgt attattctat ctatctgtcc ctaccttata ctatccttcc tatctgccat
   262381 tacttgtatt ctatcgatag gaatggttag ttagtgtgca tagctgcctt gtttctgtgt
   262441 atgcacagca gttgtttctg tgtgaagcat gtatggaggt agtgaagaac ggcctgcgaa
   262501 ctaccgtagc taagcggcac tagttcctgt tgcttgcagc ttcagtagaa ttcatatccc
   262561 ttgttggtat gtgagtaagt tgttgcatga atggtcaggt aggtaagcgt agcagtattc
   262621 ctgttcatgc atgtatccct gcaggttgtc ttccctatcg aatgagggaa gtgagctggt
   262681 taatcgcagc ttacttctgg agtggtccct aggcgggtgt agctattgtt gcttgtagct
   262741 gctgttaagt atctatcttt gtttgccgat cactgatgta atggctgttc cgtgctgtgc
   262801 agcgcgttcc gaggtctgct ttcctttctt tgtcatttga ctatctctct acgttcgatg
   262861 ggaacagttg tttcacgact aagtaagaaa ggttagcgaa gccgggttcc tatgtatgca
   262921 tgatatttgt tccgaggtgg ttgttttctc ttcttttgga aattgcccgg ggtttaaata
   262981 gggcaagaac atcaggaagg tcttttcgtt cggatacaga catggcaatc tacgtatatg
   263041 aagtctcgat ttaagctgcc taagcataga tccaacgcgc tactcaagta ggcgggaaag
   263101 aaatgccctt ctagcattgc cacttgcttc aagctgctct ttctataagc tatattccag
   263161 tagtgattcg agaaggaatt catgagtgac tgaccatcca gcctttcctt cgtatgagac
   263221 cggacatgcc agcgaatcga atagcgtagg aagtcaacaa gtcttaatgg tggaaagcta
   263281 gaaagggaaa aagcattagt ttcaggttgt ttacatactc gactaaaagg aggaacccct
   263341 cgggcgaata aagtatgtaa ctggcttaag aacaagaaag caagaaaaag gtatgaagtt
   263401 ctaattgtac aatgctatta cttcatccgc tgtgaatagg ctgaaggaat tggatcttgt
   263461 ctctttgaat ctgcttttaa ggcaggaagt cagaactata aactttctct ttagatatcc
   263521 ccatacgttc ccttgtgtga aagagctgta gaataagtcc tagctatctg ataatagcag
   263581 tcttgttgct atgggcttag cactagtctg caatactcaa ttcataccag tagtacggtt
   263641 gctaacttgt ctttcaaagt tgccctggtg tatatcccgg agtacttcga ggaacgccag
   263701 taggcctatt agtgtataga tccttcccgg gttgtttgct gtgtttcact gtttcttcct
   263761 tgggaactgt ttgttttttc tcttctgtta tagtaagagt tctcactcct tcacctcatc
   263821 ggtcaagtgg aagagtcacg tcagtcccga ggaacgcctt tccgctcatg gtcttcctac
   263881 tccgatctcg cttcgggcac tataagggct agctggcttg ttgctagagc acagttaaga
   263941 gtcactcctc tcctggttct acgtagcttg atgagataga ttgctggcgt agctgtgatt
   264001 cctaagtaaa caagttgtag ggaaggagtg ccttccgggt tgtgcgtatg catctactga
   264061 ggtaaggcac gattgagcgg ctagctgctc tgtcattact agagagtctt tcttagtatg
   264121 agccgtgata gggaagatgt gtgctcgaag tctccttagg tcttgatcta gttgtgactt
   264181 cttttttcca gcgagttacc cgtcgttgta gttgttgctg ttccgggcgg tgcttcctgt
   264241 ctgtaagatc cctttcttgt ctcgtccggg aaggatgtat gaagtattgg tccgtagctg
   264301 ccttgctttt cttgtttcct ttgctttcga gtaggtgcag ctgaggcagg taccaagagt
   264361 caagagagaa cttctttgtt ttgtttgaat aatagtatag atttatacct tctctacgga
   264421 atacctgttg catcctgtct ctcctgccaa gcgaatggat ttgtcatgca tttgttgcta
   264481 actgccgaca caagctggct tgttaggaaa aaaacccttt tcttcttctt atgaatgttg
   264541 cttactctgt ccactgcgat acaactgttg taagctctgt tttacagctt gtaatgggat
   264601 ttctgctctc ttttcaatat atcccctctc tttttcctag gaaagcctct gttgaatcta
   264661 tctctctccg ttcggaatgg gaactccaag ctgtttagct ttcattcttc cttccggtac
   264721 cttttcacag tgcaactgag caaattagtc aaactttgta ctcggaatgt tactttcctt
   264781 agttttgttt caaatatctg ccgtttcatc tgcttcagga aaggcagttg acttggtcga
   264841 atcccgatta cgatcaaaag gaaaatcttg acttgcagtg gaataacggc tttgcggagg
   264901 aagatcatca aaggctgttg ctgggagagg tccattagtc cggggtcgat tgcttccatc
   264961 ctcaattgct tcttttgaag gttacatgcc tgctgttgaa agcctgggac gagacagagt
   265021 tagtaggcgc ctccggccct gcggttgaag gtgatatacc aacaacatga gctagcatgg
   265081 tttcgagtgc gataacatgg gatatggata tgttttcttc gatgcctagg caggctggga
   265141 ttggaactgc tcgtgattag accttctata tgactgaact tccccgcaac aagatagaaa
   265201 gaagagtata attcggagaa agatgaagat cgtccaatag tgatctacgg atagctaccg
   265261 acgtgagagg cctagagtga agctctggca gagtggctcc cttgttaagt gtagggcccc
   265321 ttggctttgg acaactcacc aagccataga gactaaagaa agagctaaat aagtccttgc
   265381 tgcaactgaa ggaacgaaag aaatctactt ccgaactgag cgctaaaggt acatacggag
   265441 agacctatga tttccattct gtttaggcta tgaaaacctc cccggatgaa ggaatgtaat
   265501 acattgaaga cttcgaactg cttacgtaat ggaaaaaggg gctagatggc ttacggggta
   265561 tagggttttg aggaggaaaa tgactcactt tttgacagaa tcaaggtcct atcatttctt
   265621 ctttctgagt gaaatcaaag ctagaccata aagggaagaa ggttggttac ctgctatact
   265681 aagagtaagc gagctaacga ggcctaatcc tgggttcacg gcattccatt cctaccaatt
   265741 ccatttcgag gggtagcagt agattagatc ctgttgattc aaaaccttgt tcgaactctc
   265801 tttggcatct cacaaatgtt tcaaaatata tagtacagat tggatcctga tcaagctcaa
   265861 gctaaaactt acctacaaga gaatccatac tgaatctatt atcatagatc ttgctttcgt
   265921 cggatacgtc tctttctccc caatttggat ggatcctctc attctaattc atcgctacta
   265981 actagaagaa gttcctaaaa atcgaaagct cccctctttt tctccatcca taaccaccag
   266041 ttgtagcgga ggaagtagca gtcagtggct tctcccgggg cccttaccct tgctcttttc
   266101 tttctcgggc gcagtaaaaa gatatacgag gttatagaga aatagacaaa gaagttcagc
   266161 tgcaagagtg gatcctatcc cgccgtattt accagcggga ttcatccgtc taggcattcc
   266221 tcggaggaac tcgtccaagc acatgatgtc tcctttatct gttttcagcc agcctaagcg
   266281 ccctacttta cctacttgaa atgtcaattt tcctttcatc aaagccttcg tgttcatcga
   266341 atactcgctt cactatgtgt agctcgctcc cctctcttga aagccgaacc ggcgccttct
   266401 tttgataact gggttagggt taccgaaggc aatctggcag gcaaagtttc cccttttatt
   266461 cggcagccac ctttgatgta actaaactag atagagtttg ggtcacgaat tcggatttac
   266521 cgatccgagg gaaccaaatg aagcatcttt ttctccttcc gaaagaaaag aggaagactt
   266581 attcccaccg aagtgcacta atagaaaacc cctaccagtc gaagtggaat gatgagctaa
   266641 aagtcccttg tacgatgaag ctgagtcaca gaagcgggag aggtgtcttc tttgaagatc
   266701 gtttcctatc gagtggataa aatcccaagc cttaagagcc cattaaccca tcttctgttc
   266761 cgctagccag ctaagctaaa gcttgccatc gaccggttcg ttcggaagta acgcatgcgc
   266821 tcacctatcc atcaaccaag acagaaggga atgaccaacc aagcgagcag agcccaacta
   266881 ccaatcctat gttctcccaa ttctggaact ggtggcaatc taacgaattc gggaaagcaa
   266941 gatgatcgac actggaaaag acgtcttggc gagaggtgct ttagcaactc gactgaaaag
   267001 gagagggcga agtcatgact caagcacttg tctagagagg agagggagct tacagcattc
   267061 tcaggcgcgg atgccctaga cgagagagtt attgagagag aaaagttagg taggtcgtca
   267121 gtaagttagc gagatagagc gagactgttt gttaggtagc ttagcgagat agggagcagc
   267181 tatggaacaa ggggtctgtt aaaacagaac taattaccct tttttttgtt tgttcaaggg
   267241 gttcctcgga agagctcgca gtgaatgccc agtgcaatcc aataaaacaa cctaacagaa
   267301 ccgctccgcc cctccatgta cagaaaagta aacccaaaga agttgttctg gacgagagag
   267361 tgagattaga ctgcttaaac cgtagatagg cgttcctctc cctttagtcg actaactggc
   267421 gttcctcggg aagtacacct taggtttaca aacctaacac agaataacga gacgaagtcg
   267481 actttagaac ctattgatta gagcttggct gctcaagagc tacaaatgcg aggggatagc
   267541 tgcaataaac ccatgtaagc acagggagaa gccggctaaa gcctacatac ctgttccctt
   267601 aatgcaacct attcccaacg gaggagaaga ggaatactaa tgaaatgaca gaagctacag
   267661 cgcggacttc gtgcttgcag gaacagcagc actactatgc aattaattag ctgccccatt
   267721 catgcgccct ctaaacaacg aaagctacaa catcaacgaa gggaatgggt tcctccggca
   267781 tctaggtaga accttccaga aaaacgggga gtagacccaa ggagcgaagc tacagccaag
   267841 gaagaaatcc cgggcaggga catgaacaag atagatattc tacgcagcca agccccacag
   267901 cacaggagag gtgtaggagt aggaagattc gctttttata gatggtcaaa gcgctcaaac
   267961 ctgcttacag gatgaattag aaaaggagat agtaccaagt caagatacga aaagatgtgc
   268021 tgcacgactc agttgaccac aaggggcata gtcaggaggg tgtaaaggac tggagattga
   268081 tcacattatc cttcttccat tagctcctat tacatccttt gagataaagt catgacgggc
   268141 cactgcctga attagggatt ttttctataa tgcccttatc acgatctagc cccttgtcta
   268201 tatcatggtc tgttttcata taaccttact actgtatagc atgctaaata aagcgctgtg
   268261 ggatcaatca ttgcattttt ccattcataa ccatcatata cgctctttca agaaaaggga
   268321 tagaatgaca gtctatcagt cttaccagca tgcatacaaa agggagtgta gttgcctatc
   268381 agctggttaa acagataaga ttctgatata ttatataagg aataaggatc ccatatcgat
   268441 cgaatgaaga tggatgggtt gagataggtt cgttccaact taaggtaagg ccggctgtta
   268501 gcagggatcg ttagctgtag aagtccattc agtagaggta gggcccggga ctcctttctt
   268561 tattagacga gaaaagggtt ggcacaaggg gcgtagcgct gaatgaaaat agaaaagcat
   268621 tccaaggggt tcttccaagt actcgactag acacaaaata aatgaatcct tacttcatca
   268681 agaaaggaga cggagagcca cgaacctact ttcctgtgcc ggaggagaac cagaaagaag
   268741 tcttgatcca tggccgggtg caggggaggt agggacggag aaaacgtgct tcatatacgc
   268801 cagcggtcga agattggcga aagttggtct agtcctatac tatatataaa gcgagtggtg
   268861 acatcgcaag ataaaagcat ttttttgaag tattattctc aaagcaagag attcaagtaa
   268921 gaaccagcag aaccatcatc ggtcaactga ggttaggact actctgacac tcgcttattc
   268981 ctctctaata ctttcttctg tctattcctt tctttcccgc tttcaagctg aaggaagaaa
   269041 gtcaatcttt cgtagtcccg tccggatcaa tagattgggt cagatcaatt ccttttcatc
   269101 cccgaggaac gccaattcct cgactaatag gtctgcaagc cttatctttt ctttttctgt
   269161 tgtaaaccgg cctgttagga tcttctcgcc gtaactagta ataggcttat ctgccctttc
   269221 attcgcatta tcgtgagcgg gtctggtgaa ctaccctttc actggttcta gctactattg
   269281 gatttgaacc ctagcttagc actccctctt gttattgtta gggcgctagc gtcccgtcga
   269341 atcttgattc tccttgacag accagcagac cttacatacg caatttatcg attaattaac
   269401 gtgcaagaga aagcgatcca caagagggtt cgttcatcta acacttaccc actatcggct
   269461 tcaagcaact atcgatgtag tctgataacc tattgtataa ggtgtttgac tatgtgtgag
   269521 aatttattga caattttttt tcacatactc gatttaccta ggaagtcctg agagagcaac
   269581 agcagctgga attggaccta agggctgaaa gcttcagact gtctcaatcc aggtaactct
   269641 tactccatta cttacaaacg gattaaggta gctcagatct agctaggtta gacggtaaag
   269701 aagtccctca agcattgaag aaaggaagaa agcctgtaaa ctaccttact aaactgcttt
   269761 ctgactctct ctagccagta aactacctct ccttccagtg ttttttcctt tgtacctcca
   269821 cctctctgaa gagtcgatcc cgacttggga agcaagggtc tcggagttca ggaagcagtt
   269881 cagcaacaca caaagaaggg ttggagtgcc cgaactacta aaaaccaagc aaaggtataa
   269941 tgaacctgtc atggaattca ctgcaaggtg gcgagctttt acttttgcct gtccccataa
   270001 gtttacttag caagagctcc tcaagatgtg catgaacaac ttcaggcacg acttgtcgtc
   270061 gatactcctg ccccaaacct ttcctttaag ggattcgacg acttgtgcac taaagactca
   270121 cgatgtggaa gcacatctta gcaaacggcg gcgtcctacg aaggacttga agttcgttcc
   270181 gttaccttat taagaaagta gacgaatcac tcactttctc tattaaaaaa agtagactta
   270241 tttttcacag cctatatgcg tatgcggaaa acaagagtcc ttatttttta tttctcttgc
   270301 cctgacgggg gctaccgctt tacgttcagt tttctctcta ccttttctta ttttgacttg
   270361 attttcaaat cttttatgct cggccatacc aagatgggaa agacctagcc ttccctccct
   270421 ttgaagtgca tttatcagat cagctcccag agtaactaga aagagggtga aaggcccaac
   270481 ttcttcattc atggcctttt ttgtttcttt gattgatctc cctttcgtat tcattcgacc
   270541 tgaggcgttc ctctcagtca tacaaaaaag aaaggttatt tcatgctctg gttccgggtg
   270601 ttttccagat gaaatgaaaa caaaaaggaa aagggtcaaa ccatatctta cttaataatc
   270661 tggcttaaag gacggaacca ccgaggaata ccggttagca gctctagtag gatgtatact
   270721 gtgctttgtt ccctgtctct ttctttcatc ctccgagtag ttctccaagc ctaataggaa
   270781 catcgctagc tcggtcagtt tgtgtttctc ctgctttctt tccttctgct tccgaagaac
   270841 tgttggtctc tttgtatcca ctgaacactc tcctaatctg tcttccttct cccgtactct
   270901 tcattccgac taggtttact agcctaggag gataaccgtt tgaatttggt atataagagc
   270961 tctactgcta tcctttcccc tatcatactc tctatcttcc ttctctcaat cgttcagatc
   271021 tttgtttaca tcggtatatg taagggacat cttatgggtt cttctgtagt aatctttcga
   271081 cagttccggt taaacttcta ctttcactcg gaacatcccg ggtgttggct tccctgtaat
   271141 tccgtgtaag gaaggttagt aagtaagcta agccctgtca ggaagtaatc ccaggaatgt
   271201 ttgttagttg ttagtaaggt aagccaggta agccatgtca gttggtaaga aagtaatccc
   271261 ttccagagtt gtaaggttag taagcttttc ccgtttatag gaatgggttt ctaagcctag
   271321 gaagtcaagg aagttgtgtt ggtctttccc ctggttcctt gttcccctgt tgcctttctc
   271381 ttcatttcat tgacgggttg gagaaatgtt cacgacgtaa gtcagtggaa gcaaacgggc
   271441 aatcggctgc ctaaaggacc ccatttgtgg ttgaaggcta agttcattct tcgatatata
   271501 tcactccgct atgctagaag actgagcagc ttcagtttat taccaacctc gagttcaaca
   271561 actattgggt aaagcctaaa ccttactcct ttccttctat cggaactggc aacagatctc
   271621 tagatccgat gcaactagaa gtcagtcgat tccgtctgaa aatggtttca gtccaaacct
   271681 tttttgtcga gtgaaactcc gcttcttaag agcttctttg gacagactca ctcccttact
   271741 cgctgggttg gcgtatccaa ggtagcgcca gcagcaagcg taggggttac tacgtaagtg
   271801 cgttcgttag cgcgttacgt tttctcgctt gctagacacg acaactaagg atagacgcgc
   271861 tgggatagca agcaagtttg ttgaaagagg ggcagtagat tctagatctg ctgaaaacca
   271921 ggttataggg ctatatcttt attccatggt agggctaggg gcagggtggt ttaaaataac
   271981 tccttttact ttccctccta caattacaat gggaagggac gagacaaagc cttcttttaa
   272041 actaaataaa gtaggattcc gctttcactg ttctcaaggt atctcctgac tcgaagatta
   272101 gggcttcttc ccagccggag gcatccgaaa ctggagaatc atcaaccctc gcataaagaa
   272161 acaactaaac tatacgcggc aggttggtca aaaagggaaa gaaaaaggtg acatacattc
   272221 tattcgggga cataatagtg attcctatcg agcacactct gttatatcga tcccaatcaa
   272281 tagtttttgg gggaagtcga tggtcccccc catgctttat gacatctttt ctcttctccg
   272341 tagtgatcag tgtatgcacg tagcatcaca gtcaatcttt tatgcttggt tccggtcgcg
   272401 ctcttcttct aactgcagga gcccgacagg gctgtcttac tctttttgtt gctaatgaat
   272461 aacctttttc ttggtgattc atttccaagg gaataaaaga aagacctgtg actcattgtc
   272521 tcaatcataa cttcaaacag aacctcactg tagagaggga gacccccgaa agcgtaagaa
   272581 cgacgatttt tgagcctgag ggtgaggttc tccatcgacg agtgagaaaa gggcctggtc
   272641 tcggaagaga tgcagctaac gtgagtaata gctgaacagt tgcctaatgc atgtggtcag
   272701 catcagacaa ggttataaaa tacatcttta catcccggtc aaagtaacga aaaaagacga
   272761 gttttagcaa ctttttcata cagttttgcc ctcttttata taaaaaacta acttacgcaa
   272821 atagtaaatg agaggacctt agcacttttc gttatggagt gattcatcta aaattcccgg
   272881 ggttttgtga atgaattcaa ctagaaaatc tcaattgcac gggattcgcg attcggtgta
   272941 agttcaaaat ttatcgtgct ggacgaccac ggttgagttt tgttgtggat ccaactccaa
   273001 gcgtttgcgg gattttggat agatggaata ctcttgcaac ggagcttgtc tgtcaaatct
   273061 ggtctggtat ggtagcggtt cacaatggca gctcattttc ctggaatccg ggtgaaagat
   273121 cttttctttc caaggtcttt gctttctatt cgacttagcg atggagtcgg gtcggaaata
   273181 aatactaagt aaaggcagac ttacaataat acgcaaacaa gggtcccgcg atgtcttgta
   273241 cattctaagt actttgcctg ctaagacgtg acaaacaatc gctgattctt tactaacgag
   273301 cccagtagcc actaaggcga tccgaatgag gaaacgccgg agtgaccgag tgtcttcaaa
   273361 aacactgcgc caagagacca agcggagcct ctcggtgaat gtggtaaaca aattgaaagc
   273421 catatcaatc ggtataaaat gacaaacctt ttggtatgta ccacaaaaca ctaagaaaga
   273481 ccccgccggt tctactctcc ttgacccgtg gacaaacgcc acgtgatgga cggcgcccgg
   273541 ctctgacgaa gaaccagtaa gattaggtat tgcctaatcc gtaaggttgt cataccctta
   273601 tcagctttct gaccaaacct ctgtgttgcc actttggtaa ggaaagtcca ccaaccgggc
   273661 atagtacctc gttagcagga ccactattgc tccttttaaa gctttgtgct caagtgatct
   273721 gggagggtgt caaacctccc ccagcccctt attcagggga tggtgccagg gagtttgaac
   273781 tgttaacaaa agattttctc gatacaaaga agagccccac tcctagaata gttagccact
   273841 cagtccacag attcggctta gtgaaaatag ccctagaaag atcaaggtgc ggaaggataa
   273901 tttcctccgt taatgatagc tataccatag agttttccat caaggaaaga caatgccttc
   273961 tcttctccat cctccaggta ccagggaaga actctatatt ccgggtccaa ggatgatggt
   274021 tgcaacgccc cgcgcttcca ccaataagag gtgcggggga tggtgatatc ccttgaaaga
   274081 cataactaac ttacaagact taaaatgaaa agtaaactaa cggaacaagg cgccggagga
   274141 acccccttct aaaagtctaa gagctagaag gcggggtaca gcggttgctt cctgtaagat
   274201 ttgaatagtc atggcctcat ggtcaagcca gaaaggaaag aaaaagtcta tatcttctgt
   274261 cctctctatt actcgctcca ggtattacac tcgttgggct caaggtagca ttactaaacc
   274321 tataaagagc gggatgctat tctaagagga atttactgta aaatagatat ctctttgctc
   274381 ttcagccagt aagtctgaaa gcaagtcagt tgtaggccag acctgtcatc agtagttcta
   274441 cttttgtaga ttgaagcttt tataaggcag gaatgggagc tgcaaaggca gagataaagc
   274501 tgcgattgct cttgctcgac tcttcatggc acggttggcc gggaatgaga acaaaaggag
   274561 taagaagaaa ctggctaaga ttcaattgac ctatatagca accagttcaa ctaaaggggc
   274621 gtagcgggct taaggctgct agggactctg gggcgagaag aagcttttcc cgcattcctg
   274681 ttgatgcaga gatcagacga gaaggcccat ctctttacta gaatccgatg tgatagaagg
   274741 agcagttcta gcttaagcct aaggcctaag ttgatcctta cttaatagaa tagccataga
   274801 gctcatcccc ggtgaaatag ttgatgattt cttgatggtt gactgctata tcttaattag
   274861 agaatccgac tgggaacgaa tactttgagc tcttcttcat ggaatttttc cagctctcaa
   274921 ggaagattgg atgtaatatt acacaatctc caatttatct ctttctcgct cggaaaacaa
   274981 acaggtgtct ttgccccgct cacacagatt ttatcctggc ggttgttggt ccaacgactc
   275041 tacttctttc ttttgaaatt tcgtatgaga agaaggttga caagaagaat aattttaaaa
   275101 ctgggattgt agttcaatcg gtcagagcac cgccctgtca aggcggaagc tgcgggttcg
   275161 agccccgtca gtcccgacct agtcataatt gcgttttaag acctggtcta gcaacaaagt
   275221 agaatcataa gcacactccc ttgtcacaac taaagagggg agcggcaggc ccttgataag
   275281 acgcctttgc tttagcgcac ccaaccgtcc tggttgaaag gtcgacccac tctatcttta
   275341 atggaatgtc gtctttggct ttacggaatg agactgaact gatctcatat cttcatctga
   275401 ttcaattagc tcatccgaaa ggaagaacaa ttaacccacc tatatccatg tgattaggag
   275461 acttaaaggc aactcgagtc aaacgagagg agacgtcccc agtgatcacg attcaatttg
   275521 ttaatgaacc agattttttt gggaagaaaa gaaactggtc aaagcagtcc gggctgatct
   275581 atgcacagtg gattcatcta ggggtctata tgcacgtgtg tgtgtggagg tagatttcaa
   275641 attcaaaaag agttcccagt tttgtcttaa tgatgacatc cagagggtcg aatacgaagg
   275701 cttgcatctt atatgttttt gagtgtgggg aatatggcca ccggatagag ctttgtccga
   275761 agcaaaacca gactgatgta gaaaactcac cggcggcgaa ggaggttctc ccaaacccgg
   275821 atccgcaagt cgggtcggaa caaaggcctt tcggaccttg gatgctacct cccaacagac
   275881 gtcgcaagag gaccacgtgg tcagcctaag aatcagggac cacaagatag caaataccca
   275941 aaaggagaag gaaggatgtt aacaaaccca gaaaggtcgt atcggtcagg gagccagaag
   276001 cgagatgcgt gcgcacgggt gagaaatcaa ccgtatttca gcctagtgga aagaagacac
   276061 tcagtgctag caggagtact ttctcggata cgatcccttt ttataggttt gctgccctgc
   276121 gacacgtggc agaagaggac tcaaggacac atgccagatc tttgggtcgg tatttcttcc
   276181 ttaagatctc aaccaaccac cctttggtgg ttttccacga ccgaaccata ggtcatgagg
   276241 cattcaaaat ttgacatgca tcgaggtcaa tctttgcacc ttagatgtga tgagactatt
   276301 tattttcaaa gcgacccgtt gaacccaaag cccagagcga acgaccttga caaaggtccc
   276361 ataaagaccc ttttttgggg gtcttgtttc aaggtcttat tccttccata ggaggacacc
   276421 ttggttccaa gatctctatg tctttaatgc cccttgggac gttgaaagga gtgagtactt
   276481 ggaggacttt ggggtcggcc ggcctctgta ctaaatcata tttcggatta cggggaactc
   276541 cctatctcct acgcctctca gtcaaaagag tgcgggttcc catcccgaat ctccttagct
   276601 tagttgaaag tgaaaaacct ctctctatcg cccttccttc ttttagcagt tcatctcgag
   276661 aatcttgaat gtttagcgaa tcgatcgtaa ttggtctgac cgctcaaggc ttatctcttc
   276721 tattcccctt tctggtctcc ggtcattggt agaaagcctg taaatggaat ttatctcctc
   276781 tcctttcagt cgagttccct cttttataag agtaataaat tacgttggac ctctccgatg
   276841 gccattgctg gggcattcta tcaagttaga gctagggctt tctatcaagt tttcctgatc
   276901 tctgagtccc taaagatgct acccataaag tactagcttt tgactgtaga catatcacag
   276961 taagtcgata gtgtccttaa cagtaaactg ctgggtgccc cccaaaaaag gggcagaagc
   277021 tgtgaacgat ggatactatt ggcgaactgg aacatatgtc ggctacagag aatatttcat
   277081 tgtaatcgat gcgagaatat ccctttccca ccaatcttgc cttaaaccgt ggagaatatg
   277141 ggagcaagcc tacatcgagc aagttgacat tgcgaaattg tgtgaaataa atcaaagatg
   277201 gatctttttc acgcccgatt cgagatgctt ccttaagcgc cttagattct cacgaggagt
   277261 attggtcatt gtaagtgatc catctagtgc atgaagggaa aggcttgatc tgctcattcc
   277321 ccctctttct ttgaagcaga aaggcaaaga gctgcttctt caggacagga agagaccccc
   277381 aatcctatga tacgatgaac gggaaagaaa ccgatcctcc tttatttgag tccctcgtgg
   277441 aagaagaatt agctgatgta gaaggtttct ttcttatcct atccaccaca tcttttacat
   277501 actcagacag actccagcgc ctatttcaag ctaaagagat cacaatagtc aattcgctac
   277561 gcccctactc tttagactta gactcaccaa cttaaccaat ggcttagagg gcgaaggaca
   277621 agaaagtcaa ttggcagaaa agattcgcta cagatcgatg atcaaccctc atttctcatt
   277681 agactgcaac ccccactgaa acgaaaggag ctgtggttag cctgaacttc attctcaccc
   277741 gttcccttca gattattagg ggaaagcaaa agtcgatccg ctcaacgcct tgctctcgag
   277801 actctttcgc taacttctcc aatcaagttg agtgcttgga tctttcttca aaggaattct
   277861 tccggagagt cgctccaact tagaatgggc ccaacgctcc tcaaccatag gagccgtgag
   277921 agccctctaa taagagaagg agttgtacgc aacgcaggaa agcaagaaaa gaagaaaaag
   277981 caattcatgg gggaagtcac agcatcaaaa ccaggagttc aagtagaaag gggtcggacg
   278041 ggatcgcatg agtacgagag aaagcaattc atgggggaaa gaaaggacga tgccattcaa
   278101 ttatgggact gattctttga cttgctttag ctttccattc tttggataat ggtctagccg
   278161 agtaacttga tcttccttta ccatctatat ctgaatggac tttaccatcc atatctgaat
   278221 tgaaaagaag attgaagtaa ggagcaggtt caagtcatag ttctcaccaa ctatagaaga
   278281 atagggatcg actcgtgcta aagaagattg atagccaact aacatcttat ctgttcggaa
   278341 cgaactccta tgtcttattg gtatgtgatt gaaatctatc ggatcctcct atgtcttatt
   278401 ggtatgtgat acaagcatat taaaggaaag aatgcggaag gagattggaa aagctttcca
   278461 taggcttggc cctagaggtt gtcattgagt tgaactagct cgccttcttt cctcgatcag
   278521 aatacgaata agatctttac ttttgggata agtgaaatcg tatgtatcca tccatggtgt
   278581 atctggtgct ctcgtatata agagaagggc agcatttatg agtaatcgat ctcacaaact
   278641 atcaatttca taagagaaga cgaagacgga tcaaattgaa taatcgaaga gagatgggac
   278701 cctagctacg agtcattccc tctgacgtcg aatgatctac ttgcttgtac ttctctttgt
   278761 cgagattcag ttggtcttca gtctaccact ccgtgggtat aagatcgcaa agaatgcatt
   278821 ccaagtgaga tgtccaagat caaaggaacg agggtaagaa tcgacgagga atcaataaga
   278881 tataagataa gtgaatgaca aagcgtgagt ataattctca acccgagatg ttagaaggtg
   278941 caaaatcaat aggtgccgga gctgctacaa ttgcttcagc gggagctgct atcggtattg
   279001 gaaacgtatt cagttctttg attcattctg tggcgcgaaa tccatcattg gctaaacaat
   279061 catttggtta tgccattttg ggctttgctc taaccgaagc tattgcattg tttgccccaa
   279121 tgatggcctt tttgatctta ttcgtattct gatcgaagaa agaaggtttc cattcagtct
   279181 cataaagcaa gcacctcttt cacataagaa agtggaggca ggcttgggga tacgatctaa
   279241 aatgattcca aggaccgggc aatcgccctc ttttttaatg aagaagcggg ctagtccccg
   279301 aaaatgcccg ttaatcaagc aagttgggga acaaaatctt ccttgttagt tactcatttc
   279361 ttcggtcgag cgttctccgg acgtcgagaa atctatcact caatcactgg ccgctctgta
   279421 attgtctgat tttaggtttt tgatcacact cgaaattaaa ttatgtatct acttatcgta
   279481 tttttgtcca tgctcagtag ttccgtagca ggttttttcg gacgttttct aggatcagaa
   279541 agcgtttccc gtttcaatct tataatcttc ttgattctat tggttttttc aatttgccta
   279601 tttagatcct taaagcagta tttaggaaag aggatgacac aatggtgcta tctagccctt
   279661 gtttgtcaaa tctccctctt tctcgttctt ctacgtagcc atatcttggc gggttttggt
   279721 acattctccg cggatgtatt tactgtcttt atgggcacat tttcagttac cggttcatcg
   279781 ggggggatag tgaatcacca agacggggcc tcgtctgagt ggttcacgta tacatccgat
   279841 atggtcgaag attcggccag ttccgggcgt acctcctcgt cggtcaatca accgattcct
   279901 gaggagcagg cttgggaaag ggaggctcgg gcacaagagc acgaccgcat ctctgccgag
   279961 gtagagacta tcacgagcgc ctgcgagaat ttggaggcgg ccatggtacg gaaagcccaa
   280021 attctcttgc atcaacgtgg agtaactctc ggggatccag aggatgtcaa gcgtgctctc
   280081 cagttggctc tacatgacga ctgggagcac gctatagatg accgtaagag gcatttcact
   280141 gtgctcaggc gcaacttcgg aacagctcgc tgtgaaaggt ggaatccgtt cattgatgag
   280201 ctcaggggct tggggaacca tcaggtgaat gcccggcatt acgtcgactg aggcataccg
   280261 tgctgggatc ttcgactggg gtgaagtcgt aacaaggtag ccgtagggga acctgcggct
   280321 ggattgaatc cttctataga aaagttgtta agcaaagact ggagaggccc ccggtcgaga
   280381 tgtagtaagt aggtctccaa tactgggaga ctgaggagaa tgggagtttg tgggttgagg
   280441 gtggcatgct ccccagggcc ctcttttttt tagataggta gggtaatgca tttcagtatg
   280501 aatttgatct agcagtgtaa acctgagatt ttcaagagtt ggcttccgct tattttgatt
   280561 attaagcgta acgagactaa aagagtcgtg aagcgagtcg gaaagaaaga ggcgaatcta
   280621 caagagtctg attttttata tgttaacggg cggagattaa gaggtgggca agttggtagg
   280681 ctccggagaa tagaatgcaa tggaggacct aacgcctagt aagacgggga aggagtgtta
   280741 tgaaagggag gaagaggaaa agctactctt gagcctcctt gctcaaacct gccttcttcg
   280801 ggaactaatg gatgtctatt ccgttctcca gctccatcag tccactagcc agtaccactt
   280861 tcaagtaagt cttcagtact agtgtcagcg ggcaggtttg aagatgtctt tcctggtcta
   280921 tctccagact tggccagaga gtaaaatatg cgttttcgca cagtaaggca ctttagactt
   280981 tgatttccgc taaatcttca agataaaatg tctttgcctc agcttcacat atggcttacc
   281041 atcctcttct agtaaggaag tccttcccgc ccttcctaac cttacccgta accacgactc
   281101 cctttgatta tcataagtta atattcaaaa tgtgggtctt tctcgtcagg tctatgttct
   281161 tgctttcaat tcaatctttc caatcgggtc tagaatgaca atttatccca gacaaacaag
   281221 tctcctctag cttaaggagt agtccatagc taataatcta tggtactagc ttattccagt
   281281 cattgagcac aacttccttt tctgtttaca gagaatagga taaacctcta ttccatccgg
   281341 gcaaataaga tgctcgctca ctccactacg ccacttgctg tgcagtctcc aatacgccac
   281401 ttgcagttcc acagagtgtt tttctaatct tcttgagtat aaagaggaat ctaagggaag
   281461 acacttcatt gcgggaagca ccacacgcct gcttcctcct ctaagcaagc aatagccaga
   281521 gctctgaagc tgaagtgagc caagctcaac aatcttgaat ggcttactca ctcaagcagt
   281581 aaggcgactc cgcgggctca atcagaggtt cctatgcaaa gcccagctat gaagcgaata
   281641 aagagcagtt cgcactctcg gtgggatggg tcgggttcgg tcaatgaaat gccttttcca
   281701 agcacgatca ggcttcaggg tagcttctgg gagtgctcta cgagaaggca tatgtgttac
   281761 atcttgagat atttgtttag ggcaaacggt caccgccatt tctcgtatga aaggctggac
   281821 tgtcgcaatc aaactctccg cctgccggat catctctatc aaccgtctcg gccgcacctt
   281881 cttccgcatc tgtctcaact gctccttgtg cgggactctg gatacctata aagctcctct
   281941 gggcaatcgt attggttcca atcagcattc ctaacctccg tcttctcctg agcgtctgga
   282001 ctgcactgag tgcctggact gaaaggattc tctttcgcca tttagaactt ccccgtggta
   282061 gcatagcata gtagtgcaag tgaaagtaaa taatcaaaga cgttgaaaaa aaaaccttgt
   282121 gatcgatgtg ggaccttaga taacaaagta gcgatagggc gcctaattct ggtcatttag
   282181 agcatcttct cttgattcac tcagaaatta ccctttctct gaaaagcttc aactcaatca
   282241 cttggacaga gggatttggc ctaccaactg caggctctgg tgggggaacg gtatccattg
   282301 cctgctgccc catcccaata aaacgtgttt ctcaaccacc cctgtcgact tcgcacaagc
   282361 caaccttgca ctaaccctaa aagaaaaatc cagtataaaa tcccgagcgg ggaaccacca
   282421 agtgcagcta aagcagggcc gctaggtccg aagagtaact gcccttctga cttccctgtc
   282481 cgggatctct tcactgaatg tggaggcgcg tagcgctgcg aaaaagaaag ggttgccttc
   282541 catgccaagc cagcacatgg accggattgt tactcgctac gcgcctctgc atggtgagat
   282601 gggaacaagt tgtcatgatg tatgcaggta agtgagcgat gaacgcctgt ctctgttgct
   282661 gcatgtgctg tttgtttgtt tccgaggtgg tgtggtctgc ccccgaggaa tgtctaggag
   282721 aagggttttc tgctgtgatt gcaccaagtg cagctgcggg ttagtatctc ttcctaggtg
   282781 ggaaggggca cgacgaggaa cgaagtcaaa ccataccacg tactcacacc attgttcata
   282841 caatgtctat aagcggtgtt ttctgcgata tgtgcttctg gctctccaca aaggaacatc
   282901 tccaagggag ggggcgtgag ctgcttaagc ttcatcccat cccgaatcct tgcaattaac
   282961 acaccacgaa gatagggact gagaggtaat cctcttccaa tccaccactc gagtggtaac
   283021 cgatcaggac cgactaaaag cttactagat aacgcctgaa tccgactaaa acgccgggat
   283081 agggccttag tgtagtgtcc atttgtccta gcacgcggta tccagcttta tttaacctta
   283141 aacaagtctt aggacttaac ttgtacttat aggccaactg ctgagtacca acgaggaagt
   283201 agctctcaag cacagctttc gcagatactg gggataagtc cttcgacatt atcttaaccc
   283261 agaaccgctt ggcgaactca agacaacccg tctcagatac aatagacttg gcatcagata
   283321 tatctacttg caaagcatca agtagagaac ggtactcctt agccacacta cgatcggcaa
   283381 tgacgatgtc atcacctaac aaagcgtagt cgagaaatgg tctcgtctga tgaggatatg
   283441 ctcgtaatgc tgccaaccac acaatagcat ggtgggacaa cgcgaataga gcccaggagc
   283501 cgtaataacc caaaggttga cctgcaacaa acacaacttc gtcatgccgt ccagtaacgg
   283561 acttcaaaga gcatgagttg agtgctaagg caccattgac aatgcacgat gccatcgttt
   283621 gaccgaaaag gcacgccata agctcatata tgactggaac gggccaccga tcggtggcag
   283681 cgctcaagtc aaaacttgct ataaatcttg ggcgtctctt tgccagacga tggataggac
   283741 cttcttgatg gaaggtaccg tcttgtggaa tacgcctcag aacagacata ccccacacat
   283801 gcacggggta taacagacgt tgtttaaacc agttaccgat tacaaacaaa cgccgctttc
   283861 cggccaccct ctaaggactg agccaaacgt ccggaataaa taggttgaga agaacggtcg
   283921 aagcccatgg cgagggaatc aaacaccaag ccaggccaag cctcataaaa cctcaaccct
   283981 tcattagctg cccaggtact aaattgcgta tcaaacgggt acaaagtata cccaggttga
   284041 aagagaatac ctggactgaa aataccatcc ggttctgaat gaatgattcg cagctggcgg
   284101 gcaaaagccg cgatttccaa gaacatcgca gagaagaaac aagtctcctt ccgttcttta
   284161 ggagcaggct gctcatctac ctgtaacctt tttagaacac atgtgcaact gaaggattcg
   284221 gtttcggcgg acgcagtttt ttgagcttac gctcttcacg aagttgcctc cgtgcttcac
   284281 ggcgcgcttc ctcctcttca gggctccgtt ggatcttatg ttgaacaagg ttacttaaat
   284341 cattaggggt ggacttccag gacgggacaa actgaaatcc cttttctaag gggattgagt
   284401 tcacccaggg gagatagcgt ctgaacaaat tttctacatt ttgtttaagt tcagaacaca
   284461 cctctttaac ccgacccata tctttaatgg gagtcacaat ggtacggaat gtgctagcct
   284521 ttataggctt cgccaattta ataatccgac acactgagaa ccaagaaaga tacaatcgga
   284581 ccaactgatc tgcccgatca tcccgcactt tgatcaattg gcggtgatgg gtagggattc
   284641 tagttggtat cccaagcaag ccaggaaggc agctgcgcgc tacggtcctt tgctgtgtta
   284701 agcatgtgtt gctgagctaa ccatgtcaac agtatggaac cccgctcgta gagaccttaa
   284761 aaagaataca agcaagtgta gctcactctc ccgaagggag cttagcaaca gtagttagtt
   284821 agaaacagca gccgcggatc agtcggagaa gtcgtttcta ccatttcaat cggacaataa
   284881 attccgagac ctttcaaaca gcgtattctc ggcacgaacc aggcccgctg ggagagtcaa
   284941 ctttctgatt tccgaattga ttggaaaaaa ctcctttttg ggccagagac aggtacggaa
   285001 aattctcagg ggccgaagcg ccaagtagga gaggtcagag tcaatatctc gtccgatact
   285061 cgtcctatcc tttctttaaa gtggaaacgg cgttaccgtc attgaaaaat aagcgaacag
   285121 ggaacggcgg gagaaagact cggcattcag gccatgctag tacagtttgt tttcttagct
   285181 acacttgctt ccatcaagct tccatcaaga gctcccaagg ccacctgatt cggagtagcc
   285241 cgttcgtggc agagatttta attccagttg gacttggcca aatgccaatc ctcctagttg
   285301 tggaagtggt tggaacggtt tcctattcct atcgagcagc tgagccagtg aaaagcagga
   285361 cagggtcaca atcttccaaa ttttaaaagc aaataaaaaa aagtcggagc tggtaacgcc
   285421 ttggtgagca aatcggcagg ttgttcttta gtagagatgt gttcggttgt aatgagtttg
   285481 tcttgaaccg catcacgcac ctgatgacaa tcagattcaa tgtgcttcgt gcgctccatg
   285541 aaacacagga ttggcagcaa tattcatagc agacttgcta tcacaaaatc acttcattgg
   285601 ttcgtcatgt ttgataccaa acgagagaag taactccttg aaccatttaa gctcgcacaa
   285661 agcaaacgcc atagatctat actcggcttc ggcggaagac cttgacactg ttggttgttt
   285721 cctagttttc caagagatcg gagaactacc aagatagaac cgttcaagca ggacttgctt
   285781 gcttcgcctg ttgattacct ctctcctttc agtcgagtta tttcaacctc tcctgaagcg
   285841 tcttattcag atatagatat tacagattcg catacgaaag attggaatga ccggataact
   285901 gcccaaagca ctactaaatg ggtgtcaaag aggaatgaaa tgggatgact gattgatgga
   285961 tacgtggtaa ttttccactc ctgaacgact tggtactccc tctttctcta tggatcgagc
   286021 atatgaggtg ccactctacc gcaccaatgc aggttatgaa attatagatg ctccccccgg
   286081 tgtcttgcca gaagctcgtt ttctaaccaa aaaatggaag attttaaaac cccatccccg
   286141 ggaaaaggac ctaaactcgt gatagaagcc gtctttctct agtaggaaat caaagacatc
   286201 gggaaggctc gcgtattcct attcttgtta tgggagactg tccataccct atctcgactc
   286261 cgttcacaag accataaagt aggggaaggc gggtttgatc ctatcatttg ttattttagt
   286321 ttgaaatggc aacactaaag aagtgtggaa acagagattt agaaagcaga gttagagacc
   286381 ccttacccag ggatgtgatt gggaaaagag ccattggaag gtgactaaaa gaccagaaac
   286441 aggggctacc cgagctaatg atagaggcaa gaacactttc cggccaggcc tgactataac
   286501 caaccttaca gatcccactc aaccttttac accgatgtat cgtactctct cgaccaggtc
   286561 atcataagaa aatactgcta aatctttcca aagttataga aggagggaag gcgcgctaca
   286621 actaaataac agccagctga aaaatgctag ctagttaggc tagcgcgcaa tggctttctc
   286681 tgctctgata ggggcttgct tcttcaagct ctgcccaacc tatacaaggt gctgctcgct
   286741 ttctctcagc cactagtggc ttatgtggtg gtcgacattc ctacgcgctc ctccttgccc
   286801 cctacttcag aatccaaagg taaactttgg atgttgtcgt gacgctttgg ttacgaaggt
   286861 taccggggtc taggtttatg gatggagtca gtcagcgaaa gtcctcaatc aatatcaaca
   286921 agatgtcgtg accgcttaga cttggtggat tttgtcagaa aataaagttg gtttcggggg
   286981 ttcattgatt agtacacctc tggtgctggt aaggtcggaa ccgtggtcgt ccgtctccgg
   287041 tttgccggcc gataagatct ctgagattga tcagccagct gggttggttt ggctattcct
   287101 ttctattgaa aaggagtcag ctgtctgcgc gagtcacctt cttttaggct ccgctgaacg
   287161 acacggcatt ctcgttcaaa tataggccgg ccgtacttgt gatggttccc aaggatccaa
   287221 tatgaccact taggtctacg ttgccgcgat atttttctat ggaagcgggc gggctgttag
   287281 aagttcggcc cggttttttt ggtgtcgtag gggagggatt gacctttcta acgcatattc
   287341 agtcgtaccg gcatggcccc actgatttgt tttcgatcgg agcatcaagc agcgcaaccc
   287401 ggttctactt gactaagccc cgtgctcgtc caaggaggga gtttgcttta cccaacaact
   287461 tcctttttga taacaaggca gaaacctctg acccgacatt caaaagtttc gaatgaagaa
   287521 tgaagagtgc cctgccccag caagcaccta ctcaattcta aataaaaaag cgtgacttta
   287581 ctaaacaagc aagaaaagcc ctttcgcact tcttagtaaa gcctaagcgc ccttgttgct
   287641 aaaggtaagg ccggctttct tcgcatgctt gagcgcatta cgcattaata taatacatat
   287701 atatcaagct ttccttgagt tttcaataag gggcatctat agtaaggggc cttttcaata
   287761 agactcgcgc taggcgatca cgttttttgt cttcccaaaa atcgaatatt tttgagttgg
   287821 taaagaccca cccctagttt cagtcagaat gagtccccgg gaccccggga cattggcttc
   287881 cgccaacagt ggactattaa ggatcgcatc ccgcgcatat tctacattat agcctgcaac
   287941 tgattcagct tccgcttctg ggagatcaaa cggagctcga ttagtttctg ctagacgaga
   288001 aataaggaac ataaccaata cagggaacag gggaatacca gaccatatct gcttttgcgc
   288061 catgacaatc tcactcgaat tacggggacc tacacatatt agtacagtat accgggggtg
   288121 tccccggcca gaaccacacg tgcaagtttc cctgcaatgt ggctcgtccg tgctttccga
   288181 ggcgctgcct gtgactcagc atgagagaag ggggcggaac tgcacactct cgtgttcaga
   288241 gcattgtccg agtgagtagg cagcgcctac caagcaaagc tttcttgaag aggctgggct
   288301 gcttcctttt cggcgcccgc ctttattcat ctatactaaa gccacacacg acccaatagg
   288361 aacgatttca gcgcccctct ctagataaga agcaaaacgc gccatcacct acagcccttt
   288421 cctctgccgg ggacttccat gaaatgaaaa cgggcggcat cgttgtatgc tcgacatttg
   288481 ttgccctggt ttatatcccg gagtactcct atggccgatc tgtcacccaa cctacttaaa
   288541 caacctaaag gcttggccct gtcccgcttt tagaattacc cttatggcac agcttagtca
   288601 gttattctcg cagttcagat aagattcgga ccgccacttc tctgaaagca tggtgcttgc
   288661 ctcctccctc cttggagctc gtccattcgt tgggtgatcc cttgctctca cgttcgagtg
   288721 ttttctcgtc gtttaggccg gtgagtgaga tttctgctca ttgcagtcac ctccggggtt
   288781 cttcgcacct ggatagtacc aggacccgtg tgccccggcc cttgatcaga taaagctgcc
   288841 cgcccgaagc ccgacctatg acccacaact caaaatgagc cttgcgacga gacgcggaca
   288901 ttacccatgc tgcggttccc tccggtccgt tcccgggttg ggttagggga acatccgagc
   288961 gatgattgcc ttcgcggata caaacgcgct cacaaggcgc acaataagaa taagaccaat
   289021 agatacttca taagagacca tttgagctgc agatcgtaat gctcctagaa aggcatattt
   289081 cgaatataga ggagttcaag ttaccaacaa tcaacgagtt gatcataccc ttctatgaac
   289141 cgtacgagca cgtcctctct cacaccccac cgcgcttacg gctctatacc ccaaccctac
   289201 ttgctctgga cccccccccg gtcctccctt tctattcctc ggtaagcggg ccgtgggagc
   289261 atggcgggag acaaagtccc cttttgactg atagaaagca tctctctttt gtctctcctg
   289321 accgaacccg ccaaaaaaat cacaatagaa taagttgttc ttgccgggag agtagcgtct
   289381 gagacatctt tatctgagga ggaggcttcg tcgtccggct catcctcgga atccgaaaat
   289441 aaaactgaga cagaacggat tgtttcagtg acatatctaa tcagactgaa taggatttga
   289501 agagctgtca ccatcattca attcacatca atttaagcag gcaggaaggg cgcggaagtt
   289561 accgtttata gaatgcaagc aaggtagctt gcctgccaag ccgataggcg aaagggcgaa
   289621 ctgatcgact tgcatgtgtt aagcatatag ctagcgttcc ttagtctcaa tcacagacct
   289681 ttttccattt taggtgaacg agggttaccg gctctacgac cttgcaaggc actacagtag
   289741 agctcttttg gcctgccact ttctcaatcg aaaatgtcaa ctgtgaagat tctcgcgttt
   289801 ctttatgtaa tttcaggatt tcttttcgtt gatcggatcg agcacatagg aatatttccc
   289861 taagtcaatt cattctcttt ggctgaagtc aatcttcatc aagacagctg accgagtcga
   289921 aacctactgc tcaagtctga tgaatgcccc gttcatgagc tggtaaagtc gagatcaatc
   289981 aactgggatc ggagactgga cgtctatttc actatcccgc ttttgtctaa gaaagtaaga
   290041 tacctatgcg ggatcattat gaacaggtta cgaggcctga agcggaagcg ctattgaact
   290101 gtcgggggga cttggatcaa tcaaagacac tagtcggtaa acccgatctc ttacaggcac
   290161 tggaattgga cgatatagtg gcggctatgc atcccgagga aaaatttggt actggcatcc
   290221 ttgcttctgt ccccgttgcc tctgatagct atgcccccgc ctctcttttt gtctctgtga
   290281 ctcgagaagc gagtctcgat ctcaaaaggg tacttgtatt aaaaaaatcg agatctttca
   290341 ggtgctccca gatctggagc aggcgatggc tcttgaaatg ggctagggat gcctagaaaa
   290401 ggtgaataat taggctattc tgctgctggt catggaaaaa aaatggatga aactgaaggg
   290461 tctgcttcga cgctcccgac cttcaactcc gaattatgct atgcctttcc tttcggggag
   290521 cttccgccgg ctcagatgct ttctttgcca cggatgcctt cggtttgagg tcagggactt
   290581 tttttttccg gctggtggct gtgatgctag gctaaatgct gttagtgaga ctcggtaaac
   290641 ccggtccatt gtaggtgcta cttcttgctc ttttgccccc atttctctgt gattggcttt
   290701 agaaccggga aaaaagagtc aacaacaatc aatcagttat gcctctcctc ttcctgcctc
   290761 tctagctggc ttgatcttag actccgctac cagagaagag cccttgtgtc cctagctaat
   290821 ggatgcctct tccattagtg ctccttcctc tgatgtctcc gctcggtcaa ccgtctctgg
   290881 aatttcttac tttttcggtt ctaaagccac tccgcccgcc atccagtgga tcttcacctg
   290941 gctaggattc tgactctcga acgggggaag gcaacctatt agattgttga cccgacctca
   291001 gacttcgttt taggctgaag taattggagg cccattaccc gatatgggta tggaattcgt
   291061 ttcacctacc tggtagatat gtgtatttga cctctaacca tacctttgct atctatgctc
   291121 caaccatgat aatgatagcg attggacggt agcaattggt gcttatttcg gggattcaac
   291181 cgacctggat aaaccacttc tgcctttggc tttgcctcat acccggtcta actcaaactt
   291241 tgactttgct atgcttgctt tgttagtata gcaaagtttc taaagctgtt agcgcgtagt
   291301 ctgtctgctc taaaggaagt cgatttattg attcgtcctt ctcggatcgt cgtcggtcct
   291361 tttttattgg gctctcatgc ccggctagac gataagatca aagtaacccg ctttaattta
   291421 accaacctac tctgtaatac tgttttcacc accggtttgc catgattcat aagcaggaat
   291481 cgtagatctt atctaggatg ttgccgtcat cttataagat gaagaagtca agcacatttc
   291541 tcttcttcct aagaagtaag gctgacgggc taataagtcc ccggagcttc aaaacaggcc
   291601 ttttcatgct ccgcagaggc caatgaactt ccgaaagctt cttctgattg agtgaacata
   291661 ccgagtactt aaaagtaggg cattggatgg gacaagccgc ttcctttact ttaagccgag
   291721 aggggtcgtc gctaatcctt taggccgctt ctttccactt tctacctctt agtcgactaa
   291781 ctcaagttcc taaacgagac agcagctacc ccgcttgcct gtaaaggaag gagttcttgt
   291841 tccgttgacg tcgtctaact aatacatagt tctgaaatag ggattaatat ggattgaatc
   291901 atcataatga tgacagctgc taccttccca ttagaaacca tctatctttc ttcttttcct
   291961 tcgtacgaat ctttgctaac ttgactgtgt tcgacggctg atgaccccaa tgtgtgaaat
   292021 atccacctcc atggggatgc gcgaccggga accatgttgt caggaactga gcactttctt
   292081 gaaagcattg atttgtggta agactagaag aggagattgc tctttcgaag ctagtcaagc
   292141 gattaaacaa agtaataaac ctttcgagtt cttgatttac ggctagaaag aaggactaga
   292201 gcttcatacc ttccggctgt tctttcaaga tggaaaataa ttgatctgta aaggtcagcg
   292261 gtcgtaatct gttcgaccag accacgtctt gcaactcttc tggcgtcagg gttgcgggaa
   292321 cctgtgcttc ttggttgaaa ttgaagaaca actccttatg ctttggagac gttctcagca
   292381 actcatagat agatatgtta cctacgcctc cgctaaagaa aggaagaacc gggtagctat
   292441 acgttccaaa cagctaagat attagttatg ctttagcaac agctccgttc agggagggcg
   292501 gggatgaaca caccaaacgg caagctacaa agaagggtga aacaagctac aaaacagatc
   292561 tgactcctac ctaaggggca tagaacaaaa gagagtcaag tcaaagataa gagtttagtt
   292621 atgctgggca gttgtcttgg aggagcagcc gccacagatg aaggagttgc ttgaggaaga
   292681 tgcttattta tttccataag acctacctca tggcttgcca ctcttacgac caacatggga
   292741 ttgatttcat acctggagca acttgaccta atctgtctcc ttctaattag aaaaggagtc
   292801 ccgctaagca cgaggaactg agaaggcagg tgcaagggct ttgatagaga gggaaagcag
   292861 actcgacaac cacagcccag ttaactattt gaatcaggag cttccgatct catcccttca
   292921 atcaccgtta ctcgatccga acttgaacca ttctcttgct acttttcttt cttcaaaaaa
   292981 aagattggaa gtggaaccga tttcccggaa gaggtcttcg gcttgctctg atatgataag
   293041 aaagttcgct ccctctccct gtcaacatac atgggattga gcagccccct atctcagagg
   293101 gtttacccca tggccagttt gcgatgaaag aaacttcaga atgcagccca catagtccta
   293161 tcaacataca aggcttttca atccagtgaa agacaggtcg aaaacttcca tatctgatag
   293221 gctgcaaagg aagatttttg atgtctggtt ctatctgtct gtgcttggtc tggaccctta
   293281 gttcttgcag gtgtaagcgt gctccccatg tagttttctt cgttcccgtg taatcaggtg
   293341 cgagtgtaac gagtttgttt gaaataagtc caatgagatg atacgaaaac aaagagttaa
   293401 aagctggctt agaagaaagt atagtgggca tggtttagaa ggtaggttac ctgctcgtaa
   293461 gaggcagtct aacttagtta gaggaatgct catcagaagg ataagcaagg tttgatgaat
   293521 tctcctagaa ggaagatcaa aagtcaaggt cttcaatagt agtatagtag ggaacatatc
   293581 acaaccagca agcgtattca ctattcacgt caacatttta gcaatcgaag tcggagtgag
   293641 ccgattcaat gtctacaggg cgtctgtgta acacatatca aagcgtctgt tgccaagtct
   293701 aatatctgat atctgtgtta gctgcctgcc tgtctctccc tgcccacgac atgggttgga
   293761 cttagagtct ctttcttgtc tgtagttggt gtattcatat ctctcctttg aatggcatag
   293821 atcttcgtag taccagtcag ctaacaggat cggcgtatgg gcaagcaaag aatctaaaat
   293881 catcctttcc tgtcagtagc cgggtaggta aagaggtctt ctgcactacc actagtagta
   293941 aacttcagag accactactg ggcaagtaaa aagaattaat tatgccgacg atctgatctg
   294001 agttggtcta gtagcgccct ggtagccatt ctggtatcga gaggttcttg ggaggaagat
   294061 tgtctagact tggagtgtgc taccactaag gttaaccaga taagagagtc ctcacctaac
   294121 aagcaagtgc taatagctaa cagtaatagg aattcaagta agtaagactc cactattaac
   294181 tggaaacaag gaatgaccag cttcagaggg atccagcaca gattactatt caaccagttg
   294241 gataacagat aacaagggaa tagcccggtc aggcaacttc tccctctgtg cagcatttgc
   294301 ttcgacagat tgagggggtc gtagatcagg caacagcaga taaatctatt gaatgtccat
   294361 cagccgtaaa agaagggcag ggcaccccag gggctcatct tctaactata gggaaaagaa
   294421 gaacaagaaa gactgtaaga cagaaacgga aagagtatgc gcggactagg ttgagaatct
   294481 ctgcgaggca gcacaccggt aaagatagtt taagaattta gctcagtgtg ctgcatcaat
   294541 gatcttctta ttggaaagct gaagatcaag gcaccatgtt cgggttggtc aactcctcca
   294601 agtagcccta acgaagtaac ccttcagggc caacggagta gccctgggcg tagcaacccc
   294661 ccgtgggcct gagggttgag ggtatctgtc atacgtggaa gaagaagaac aataagactc
   294721 ggaaaccgta gtgaccttcg gaactgtgag tgaccttcgt tcgagatgca gtatgaactc
   294781 ggaagacttg cttcgctagc accgtatggg ataaatcttc atatggagga gaaggaagac
   294841 tgaggaactg cacatgcggc gtccttgcga agtaaccccc aacggagtag tcctcactgg
   294901 gattgagggt tcggcttgtt gcgtgcttcg ccatgagtat gaagagttgc ttcgcttttt
   294961 aaaaccgtat gtgaacccca agggtgtgct agatgatgag gggtgagggg atggggttcc
   295021 tgcactctat ggaaaatgta cttttgtaat agtcaaacat ttcaattcta aaaatttgat
   295081 agagttggtg attatgagtg gagggaagta cggctaggac ctttggccaa gtgaaggatc
   295141 aaccaaagtc gacgagttgg tttatgatta ttgggttttc gaagagaggg tttttgtaat
   295201 catgagttgg tggtcgatcg tcagtagatt ctgagttgag tatggtttgg atacaagata
   295261 aggatcaagc aataaggcga cattaaactg tcatgtaatc atcatcgatt tcacgagtaa
   295321 ggtatagaaa agcaaaatta tgagtcgagt acagcttgga ccttcaacac tagtcgacat
   295381 tcaactggca tttaatcttg gacgaattca attccaacta attcggtaga atctagaata
   295441 gtgagatgga agacccctct ccttatcagt ttcctatgga ccttcgacta gatcacacga
   295501 gctactccca ccttgttcaa ctgtgtgatt tgtcgttttc cgagattcgg tttcttcttt
   295561 tttcttgatc cgaggtaagg tgcttttttt gatcgatcaa caggtaatat agaaggatga
   295621 ggctgtgatt tacctagtga atcaacaaga tcgaaacaca ccaatcgatc aaatcatttt
   295681 tgaaaaactt gtacatcgtc tgatgtagcc ttttgcttcg cgatattcaa gtttgggttt
   295741 ttgcttcgcg atattcaact atgcctatat gagagattga gttcacgaca atcaattcca
   295801 agtaatcatg tcagtagaat tgagaaagat gagttgagta tggatctccc ctcggacaag
   295861 taccaagcaa gatccactgt catgtaatga tttcactaat atagaagaaa ccaaattatg
   295921 tcaatagaat cgagaaagat gagtggagta tcgagttgag cttggatcac tcctctcctt
   295981 atcagtctcc ttcctctagc gcagcaaagc agcccgaagc actttctttc tttctctagc
   296041 gcagcagata ggtcgcccat accctttgcc cattggtgtg ctgcttcatt cctagcgaag
   296101 caagtgtggt tctctttggt tccgtagtcc ttttactctg aatgatatta ggttggattt
   296161 tacttaaagg ctgttccgaa aaaagagaga cttctaggct cgcaataaag ctaaggtcct
   296221 gatcgagcaa ctagtcgtcc tatctatcca cctctccata ataataggat ccaccaattc
   296281 ttctgcgaga gctactgtac ccgaacagta gaaggggtgg ttaattatgg tgtctactga
   296341 tatattagga aacatgtcca gaactggcac tcctggcaga acgtcgttat ctgcagaatt
   296401 cgtggaactg gcaaaaagta gattcagatt tctctgtcgt cgcatagctt atccccattt
   296461 ttttttcagc aactgaacgg gaagtggctt aggaaaggac taatcggatg cgctcgccca
   296521 gcgagaaagg ccctaaccct tgccgaccaa gaaaaaaaga gaagataacg aaagggagac
   296581 aaagttccta acaaaatcat aacacaaggt acccattcca tctatcatat cagtcgagtc
   296641 gatccgattc gttcttatca ggcggcaaga gagaacttat gacttcgcgg atggagaggg
   296701 attcgaaccc ccggtattcc tagaaatact tcggttttca agaccgactc tttcaaccgc
   296761 tcagacatcc atccctcgct tttgttcaat tataaatata aataaaagaa agaagaactt
   296821 taatggagat ttatagcatc attcaagtaa atacagatta agatcgtaaa aacataagct
   296881 tgtaatatag ctacacctaa ttccagaccg gttaatgcaa gaactataaa taaaggacca
   296941 agagccccta taaaatagaa aatatcattc atacatagca tagtccaagc gaacccactt
   297001 aaaatcttta ctaaactatg accggccatc atattagcaa ataaacgtat tcctaagctt
   297061 aatgcgcgaa aacaataaga aattagctca aggagtacta aaaaaggtgc taacggcagt
   297121 gggactcctg cgggtaataa aaagctgaaa aaatgaagcc catgtctttg aaatcccact
   297181 atagtaatgc caataaaaat cgaaaatgag agagccaaag taatgagaaa atgacttgtc
   297241 actgtgaagc tataaggtat cataccctga agattacaaa ataacaaaaa aagaaaagtg
   297301 accaagatgc aagggaaaaa catttgtttc acattcccgg aaagaccacc tatttgttcc
   297361 tttaccaggt tcagcacgaa atcataaaga agctctacca aggattgcca agcatttggg
   297421 actaagtttc ctcctccctt tttagtaaca aaatgaatca gaagtaggaa aaaactcaga
   297481 gttagcagca tgaacaaaga tggatttgtg aatgagaaat agaagtttcc gatatgcata
   297541 ggaatcaatg ggacaatctc aaattggtcc agtggggagg ggatttccat aagtttcata
   297601 tagttagaaa aacaggcgtc gtgatatttt tcaataaaat tgacagggcc aggaacgccc
   297661 aaattctgca tataccagtt attaacgtac gtagataaat taagcgattc cctaaaaaaa
   297721 ataaggtcca gtttgctccc gaggagttcc gcgggagtat gatccaattc tcgctggagg
   297781 ttcctaatat atccggcctg aatcactccc tcgtaaaaat cccagcgcat attaactaag
   297841 aagtgattca accgggttaa cctctccata ataataggat ccaccaattc ttctgcgaga
   297901 gctactgtac ccgaacacta gaaggggtgg ttaattatgg tgtctactta tatattagga
   297961 aacatgtcca gaataggcac tcctggcaga acgtcgttag ttccggaatt cgtggaactg
   298021 caaaaaagta gatttggctt ttgaggcatg attagattaa ttgatttcaa caaaatgatt
   298081 ccctccagac agcttacgtc aagcctctag gagtaacaac tataaaaagt tgtggttggt
   298141 tgttgaccaa caaaaacatg gtagaaaacc aagaacaggg ggcatagaga tttcttctct
   298201 tatgagattg atagtttgat ggggggcccg gcaggctagc gatcagaaac ctaaaatcag
   298261 acaatgatag agcgcccgta ccctacctga agtagcatcc cgccgatctt tcgaataaac
   298321 aaaaggatca actaatacaa ggattgagaa atcttggcaa ctcaacagaa acgggattga
   298381 ggaaacttga ctttattgaa attcgagcag cgaacccgat aaacacctca ataggatcgc
   298441 taatactacc acttctagac ttggcacaga caacacttct tttctatata cttaattcaa
   298501 gatgaaagca atgaatgatt gatccaacac gccaagccat acttttcatt cttattacta
   298561 tacttaattt atctaggtga tcgacggaac acggagaggt gctttagtca ggacgagggg
   298621 atttagacgg aactgagagg agaaccgaat gaatgcaagt gcaagagtgg aagattgatc
   298681 ggactctcta cgaaagctgt ccttcttctc gcacaaacat atccgactcg tacgaaacaa
   298741 aagattgaac cttcacccaa aaccgtacga agctgagtag caaagatgac agcacgccaa
   298801 gcagccgtcg aaagaaagtt gacagatcag gagctgaaag actctactga tgattcccaa
   298861 gccagctgta caaaacatag attacagatt aatcaggatg gaacacgaaa gaaagaatat
   298921 actgaaatga tgattagcac aaaggcagtg ctcgtaccga aacaaatcta cagcactttg
   298981 accaagcatt actcctccac tttctactga tgattagcac aaaggagcag tttggcatac
   299041 aaaactgatt agcagcacaa aggatcagga gcagaagcag gatggagtct caatattgaa
   299101 atgattagca cattgatcac gggatggagt caagtacgaa actccacact tcgcacacgc
   299161 tctatggaaa caaaagccct cacacaactg atcagtagca catcactcaa gtacaaaact
   299221 catactttca cattcttctt tattttagtt atcacattat cgcaaaagca cgaacgactg
   299281 atcagcacaa tcgtacacag aagcactaat acacttatgc cccgaagcag gtcacaggtc
   299341 cgaagcagga ctctccctcc cttccccgac tgataaaatg gacttaatta cgaaagaaag
   299401 aaaaagaaat aagattccct acacaggtgc agtaaccatt ggagcattat cactatctgt
   299461 actgaaccat aatccactga ccaaggaaag aaagattaca gcaccaagcc gtacgagaag
   299521 ccaagacgct ttacgtcgat tagtcaaggt caaggtgccg atgaataaac aacacgctca
   299581 tactccgccc taaaacccct gtaagcatac cgaaacccca acctcgagga aaaggtgcaa
   299641 aggtgcttta tcaacaggac gaggaacatc tgaatgacat ggatcagcag caggcgcaga
   299701 gtggaagatt gatcaggagc caggagctga agagtctact gatgaacaca aagattgata
   299761 aatagcatta ctcgtatgaa agaaacccaa gccaaaacaa aggaaataat aagattgatg
   299821 gaaccaatca ttactcctcc actttcccgt ttactgaaat ggattagcac aaagatagca
   299881 gtatgcaaag aatatactat actgattagc agcacaaaga tagcacggtg gagtaaacaa
   299941 cgccaagcct acgcacaaca agaaggaaca gtgaagctgc caagcatcag cattaccata
   300001 aatgtgagtt aattactgca aggaaagaga aggaataaaa gacaggtctt caaaggaaca
   300061 atgatcggac gaaggtctcg aaatggcaca gtaacaaagg aacaactgtg ctggactcag
   300121 cacctaccat aggtcaacgt ctttcgagaa taagtcctgg ggaagatgtc taggcataag
   300181 cagcacccgg tcataagtaa acaaatgttg cttaaggagc caatacaaca caatcagagg
   300241 actactttac gcttgagagg gccgatcagc tcataccaac aaaacaaaga agatggcaat
   300301 gctgtggagt aaaccggcag taagtaaata cctgggaaag gctcggtagc acaccggagg
   300361 caacaaagaa agataggtgc tttagcaact cgaccaagag gagaggaaga gacggacgat
   300421 cggacaaagg aaaagtgctg gactcagaag aagactcgac taatcaaaac acttggaaac
   300481 agctcgtaca aaacaaagag gcacttggga aggggaccac cggtctatgc ctctccttat
   300541 agagtttcta cgaaccttgg ttatacggtc atagctattg ttcattggta attggatagc
   300601 tggtaaagag ctgataaagg gaacggggaa cagcaacaaa agaccaaggg tcactgggcc
   300661 acggagtagt cccttgaggg taatggttca aagaaaagaa taaaggaagc ggctgtactt
   300721 accgagtcga gcaaacaaag atgtgctggg tagtcaactc ttccatatca gaaggaaccg
   300781 atcaaagcat cggaagaata ggattctaga tgacctgtcc ttctactgct ctgctcgttt
   300841 ggctgcttat cttgcggatt ctgattcaat tagatcaagg attgccaagc aaagcagcac
   300901 caacctagct ctactctagc taatcaatca tggcctactt ctaactgtaa atgtgatcac
   300961 cagcatcaca aaaacaacag aagcggtatc gaaataagca cctgtcccaa ctcaagcctg
   301021 atatccctgg cacaacagag tttgagactt cgccggataa gcccgatatt gagcctatct
   301081 gactgagcct tagccagaga tgaagggctt ggcaccaccc taacgcagta aatgaagcga
   301141 tatcccttga gcgaaagctt tatttttggg catctacagg agaagtcgct tatggaaaga
   301201 aacagaagcc tagctgctaa caaagaccta tgcggcttgc ttggggtagt gggcaggcat
   301261 ttaatcgaga aagaaggctc ttgagtaaac agagtcatca tatgagactt ctgtcggagt
   301321 gctgtggaaa gactttcgtc cgcataagca aagatgattg ctgctcaaga ctgggaggca
   301381 agtaagggag aaagagagaa ggttgtgcgc taggagagtg ttgaagctat agatttattt
   301441 agtagagact aggagtctct aacttactgt gctttggccg agggtgaaag tcgaaaagat
   301501 atatcagagg gctgcccttt cttcttagag accgagtcaa ataaagctcc tccaaactga
   301561 cctgatctat tgtttgagtc taaccgagaa gtctcatcgc tttgagcctg gtttaggcgc
   301621 atacgcccat agagtagccc agcccgacca atcatcagtg tacgtggtcc aaggaaatca
   301681 aggctttatg gccaatgaag aggtgggcta tgaaggaatg gaaaagcagg gttgtgcttg
   301741 tgctgcataa cttacttcta cattcctcag attacccagg agtgtgctgg aatgagaaag
   301801 tgaagtattc cttgggcgaa aaatagtcaa ctcttacttt gcttgggtag ggctttgcaa
   301861 cacaccgata tccctttctt tctagggtgt atggttccta gacctgtaca catgtaatta
   301921 taaggccaac tcttgaaaat ctcaggttta cactgctaga tcaaattcat actgaaatgc
   301981 attaccctac ctatctaaaa aaaagagggc cctggggagc atgccaccct caacccacaa
   302041 actcccattc tcctcagtct cccagtattg gagacctact tactacatct cgaccggggg
   302101 cctctccagt ctttgcttaa caacttttct ttcttactga ttgaggattc ctaatgtgat
   302161 gaaagctaaa ttaaagctaa agctctttct tttaagaaag catctggttc catttttctt
   302221 tcgttagtta atccaccttt aagggcttgt agtaattcag gtttgacact atttggaatg
   302281 gctttctcat attgagagat tctgtctagt ggcattcgat cacagaatcc attgacagct
   302341 gcataaatga ctagtatttg tttttcaatt ggaagtggtg catattgtgg ttgtttcggt
   302401 acttctgtca gccttgcacc tctattgagt aatgcctgag tcgcagcatc aaggtctgag
   302461 ccaaattgag caaaggcggc cacttcgcga tattgtgcca attccagttt tgaactaccg
   302521 catacttgtt tcatagcttt caactgagcg gcagacccga cgcgactgac agataagccg
   302581 acgttaatag caggtctaat tccgcgataa aagagctctg tttccaaaca gatttgtcca
   302641 tcagtaatgg agatcacatt ggtgggaata taggccgata cgtctccagc ttgtgtttca
   302701 atgacgggta aggcggtcaa gctacctgca cctgtctggt ccgatcgttt agccgctctt
   302761 tctaagagac gggaatgtaa atagaaaaca tcacctggga aagcctcacg gcctggtggt
   302821 cggcgtaaca ataatgacat ttgtcgatat gccaccgcct gtttactaag atcatcatag
   302881 attattaatg cgtgcattcc attatcgcgg aaatattccc ccatggcaca cccggaatat
   302941 ggggccaaaa attgcagagg agcaggatcc gaagcggtgg ctgctacaag aatggaatat
   303001 tccaaagcat tcgcttcttc aagagtttga attaattgtc ccacagtcga gcgtttctgt
   303061 ccaatcgcta catagacaca atacattgtc tcactctcag aggtggccct tgagtttatt
   303121 tgcttttggt ttaatatggt atcgatagca atagtcgttt ttccagtttg tcggccaccg
   303181 attagaagtt ctcgttgacc acggcctata ggaaccaggc tatctaccgc ttttaaccct
   303241 gtttgcatag gctcgtgcac tgatttacgt tcaagaatcc caggggcttt cacttcgaca
   303301 cgtctttgct cgtgatcgct tagagcccct tttccatcaa taggtactcc catcgcgtcg
   303361 accacacgcc ctagcatagc ctttcccgcg ggaacatcca caatagatcc agtgcgcttg
   303421 acaagatctc cttcttttat agcggtatca ccaccaaaga caacaatccc gacattctca
   303481 ttctcaagat tcaaggccat tcctttcaca ccgttggcaa aaagaaccat ttccccagct
   303541 tgaatctcgt tcaatccata aacttgtgca atcccatctc caactgagac cactcgaccg
   303601 atctcatcca cttgaaaatt cgcgtaaaag ttcctaattc gactttcgaa tagattcgtt
   303661 agttccgcag ctctaggaga taattccata attccatttt ttaattaaga ggcaaggagg
   303721 aataccgctt tagaaaaaaa aaaggaataa tttacaccga ctaagatcaa agaaactagc
   303781 agactaatca ctaaaaaggc ctttggttca aattgttaca tctatcttaa cttactcaat
   303841 tatctcgtga actatctgct tcaaaaagag agttggttga atgagactga aaccttcttt
   303901 cttcgaggcg ggactcattc tcctgttgcc ttactaattc ctgatcaagc ccctgcctcc
   303961 atatgtcgag ttgagcatct cgtaccatat cccaggcgcg attgcgcgcc acttttccct
   304021 ccagctcgcg cacctcccaa tcgatgcggg cggctagttc ccgcccacgg tagggagacc
   304081 tctcgttctc caggttacgt tccatttcct ggatccgttg tagatcctcc gccaattcta
   304141 tatttccggc gtgtaaggac tcagcccttt ctattcggga gtagaacgag gctatggggg
   304201 gagggggaga aaccgggtcc ggagagccag gttcggcagg aaagggcacg ggatgtgtaa
   304261 gttgcggagg aaagggggcg agggaaactt cccttgccgg atcatttgca gcagactcag
   304321 tccagccgtt ccccccacta ccgctcgccc ctgtagcagg gtttacgacc caacttgcct
   304381 caccaacatc ggaatctgat ccgatgggca gcaattcccc gaaaccataa aacaagaaca
   304441 cccctgccat gaagaagcta taaacatctc caaaagcaaa tgagaaaagg atatttatat
   304501 ggattcgggc tgcccaaaga aggagaaagg ctattaaaca taaaaaaaaa tataaagtcc
   304561 aaatgatcgg ttttttgaag tagcgcgaga aggtacgaaa ggtgaaagtc ataacaaaga
   304621 aagttatgaa gagccaggaa aagtttgtcg caacaatagc gtcattccaa taagttacaa
   304681 ttgataacga taccagttgg gcgaacagcc gagtaatcat attagatttg aggattagag
   304741 gcaaggagga ataccgcttt agaaaaaaaa agtctacctt atgaactgaa cgaaagcact
   304801 aactccagag cttgtgggca aagtggtttt ttttcgtgcc ctgattgaca aggtctaaat
   304861 agatgaaaaa accatggaat gctctcgttg ttaaaaaaac tacgagcggc gacttcttgg
   304921 agatttactc cggataaagg taaggtcaca ctctcactag tattagtatc cctatatact
   304981 ctcaacagaa ttgagagttg ggacacgatt ttttcttgaa gcgcatctcg cgctacatca
   305041 gtcaggatta tttccatatt aatactattt atttgatgga tcatttggcc agacctaacg
   305101 gctacaagaa taaaagtaca ggcagagcca aacccatcct agaaacgaaa tcagcaataa
   305161 gttgatccat gagataagga gtatttgatt tgagttttct taaaagaaga ccgataactc
   305221 ctatcccgaa gatacaagcg cccggtcctc ttctcttgtg tcgaagtgta gtgtggtgag
   305281 gttttgcctc acagaaggag tgggaaattg gggaaaaagc cgaaacggaa ctaacggaga
   305341 ttgaggtata ctccgtgctg cgaaacggat tcggccagta caatactgag tattattgag
   305401 gccatgaaga cggacagcgc ttttagcctg cctatagggt tcttttcgat cttgtactct
   305461 accaattgat aggtttattt cgcactttag aaaaagtttg gaaagaaaag tagacggaac
   305521 gacacctgtg aactcggata gcattgtggc ataccttttc atctgaacta ggctactttc
   305581 tttcttctct tatgaaattg atagtttcag atcattctta aaagaagctc tctcttatat
   305641 acgataccac cagatgtgcc ccttccaccc tcgtccaatc ttcctaagtg ccagcctagc
   305701 ttcataggaa gctgaacaat acgtccagct ccttaaggaa tgaatacttg ggcttggacc
   305761 atcaacgggc gaagcaggtt tcctgtttgc atcacctttt ctccggtatt ttctttttga
   305821 aactcaatct ttaaatcatt caattataaa tagcttatat aacgaaaaat tggaattcga
   305881 ttgaaaactc tctcaactca attggaagat aacatagtaa gtagctttcg cccaaaaaag
   305941 cttcgcctag agtggatcag gtccttatac gtaaggcgat cccgcgaagc cggtcaccgg
   306001 agtgaagtca acttcctttt ctttttgagc agatgttgct tgcaaataaa aagataataa
   306061 gtgttttctt attacccgtt tttttaagag aaaagattta attagctctt agatatccca
   306121 agtaagcttt taggtcaaaa tagatatgat gatatcagac agcagtgaac ccccttatcc
   306181 ccatctgcat ggacttggct agtagtgaag cacaaccact cttctttcca tagagagtgc
   306241 taccctagag taagatgagc gaccccagtg gcaacgtggg ccccaaggaa aaacccttca
   306301 ctagtcaacg aagtgcatca acggatgtag gcacgttctt gcttgatcat ttgctctcac
   306361 tagaccgacc tatcataaac gacggcattt gaccaggtaa acataatggc taacggtgaa
   306421 gagtcgttct caggcttgtt tccgagtaac attctgtgct tccggcttat gcaacgtggt
   306481 tctttaagcc atcaccactc ctttctcttc ctctcttcca aggggttgga agaaaatctc
   306541 ccttatcgat gtcggccgac tgagtttcag tgcccagcag ttgcaagcta gcaaacaagt
   306601 gagatagaag catttgaagg aaaaagctat acgattgggc gaactctttc tttcttttca
   306661 ttgctcgaat taccattccc aatttcttca ttcttttatt gagctacttc ggtcacctcc
   306721 tgcattggct ctatcctatc tcaatggttg ttgatcagcg tgggggggaa caaaaaggtc
   306781 cttacggaag aagagatagc tagaaagaaa aagggataga gtcgatagct agaaaggacg
   306841 caaaagggat cgatagcgag aggtagagga ctgaccgctc tcccgcccac atcctccctt
   306901 gcagcaccag cttcgcactt aggtgcacta aagggcctga acgagcacaa ttctaagagt
   306961 tctcgactcg tggcaccact ttcgcagcag tctgcttcat ccgataggtc agccgatttc
   307021 cttcagaatc catctttccc tcaaacttct tcaacacgac tggggaagag cgcgtcgaca
   307081 ctctcctgac atcagtacct ctgctaaaaa agaagctctc atcttctgag accagacaat
   307141 ttccttgtga tagcactctc tggtatggct gggttgcgca gaggagtttg aggaaggtag
   307201 cttcttctac gcgggtacgc ctatgagaat aagttagcac actcctagcg aagcaagcta
   307261 tctactcttc tgtgctgtcc tgtcctagcg aagaagcttt gagtgctcct taatagtaat
   307321 agtaggagct ttcctctcca aaggtaatcc caggatctct ggcacaccta actctttcct
   307381 ttagaatcct tattcttggc agttacatga ttagctggta ttctcgctcg tacagttaaa
   307441 caaaggtgta ctgtgagcag cttttgttct aattcttggg tagacagttc cactagctcc
   307501 tcctcagctt tagtcccatg ctttagtctt ccttttcctt ttcaggtttg gaagtataaa
   307561 gtatcatagt ttcatagatg gctagggagt ttggtaaacc ttagttctta tagggaaggt
   307621 gaaaccaact ctcccttttc ctttcctagc gaagcaagtt ctctctactt ctcggtattc
   307681 ctctgctttc tctagcgcag tgctgggtta ttccttccta actgttatct gtatactcct
   307741 agcgaagaag cccgataaac tagtattgca cacattccag cacacacccg tggatgaaga
   307801 ttggtcccta tctcgtgcta aaatcaattg ggtgccacta tagtataaac gcgggcgaaa
   307861 gaccctaaga gtcggtttac cccttcccag gagtgtgctc aaccaaccaa cttagtagat
   307921 tagctgccca tcttcaccta acctagttga cttacttatc tgtgttctat cctctgtgct
   307981 gggatcagat caaaggaact ctcctgaaaa ggatagccaa tttagcaact tcacaagggt
   308041 gtgttgtaaa caagcgtagc cctgtgttgg caaaagggat gaactacgga aggtaagaga
   308101 tcagattcgg aactagcgct gcaatcttct gataaaagaa agtataaatc cctgcttact
   308161 tagcagactt agcttagttc ctatccatcc atggaactag aaacccatca gcattagcaa
   308221 ctgcccaaaa gagtcaccct tcgcgctacc tatgaaatat aaggaacgtc agttagtcga
   308281 ctaaagggat ccttagaccc ggactcccac gactattaag aaagcactgc tctttctttc
   308341 ttcttttgca tttcctactg aggaatccat tgcaagagct cttcttcccc caaacttctt
   308401 ttcttagaga ggcggccctt caccttaagg cccggttcca gtaaacatag atagcggggc
   308461 atgtcatgga aagatatcga cgcaatacaa agctgctcga gctcgccgta ggaaactaac
   308521 tggcttagtc atgcctattc ccacaaaaca aacagaggag agtctttctt catgcaagca
   308581 aaggaacaag gcagataagc taactacctt ttctcatcat gcacattccc aacgaaccaa
   308641 gaaagagact ctttaatcaa agctagctac aggggaatga tccggcaggc ggagagtttg
   308701 attgcgacag tccagccttt catacgagaa atggcggtga ccgtttgccc taaacaaata
   308761 tctcaagatg taacacatat gccttctcgt agagcacacc cagctcgtat ttcctagatt
   308821 tgcttacttt tcaccatgct gagaaggcat ttttccaaaa aagatttgtc ttacgaaggg
   308881 aaatgtggtt tcttactttt caccatgtgg agaaggcttt tttgattcca aatgtggtct
   308941 tacgaaggga aatgtggttt cttacttttg tcggtatata aagagcaagt tttggattcc
   309001 tacagtcctc ttacgaagga aaatgggatt tcatcaaatc ctcgctatat aaagaggaag
   309061 tttccctttg actctggttt cccttttacg aggaagctac cagctaaagt ggaatccttt
   309121 ctctgtctcc ctctctttct ttcctttcta gtagcaaact tgattctgtg gctttccttc
   309181 cattccgcga gagtagggca ccaaaagctg tcctatcatt tattggagtg gaaggccttc
   309241 ccatcctcat tccgaaacaa agagagtaag gccacttgtg acctatcttc ttggtccaac
   309301 ccctacttta agaggaaagc acaaatcccc ttttcgttta gccgatatct cttgaagtat
   309361 ttgttttgaa aagctgcggt aatccactct tccttatttt tgctgtaact cgacaagata
   309421 tgagaaaggc gaccttgtct tcgtctggca acactaccca aggcgagaaa tcaactacgt
   309481 cttggccttg gaagttcccg gggtctatct ttctagtaag gctggacgta atcgtaatct
   309541 tcccttgtgg agtgaagtga tgggatgcta aagatacaaa agcgtaggat ctggaggaac
   309601 ccctttggtc tcgattccct gtagagagcg taggactcat gggatggtgt agtcgttaga
   309661 cggccatgag tccgagtgat cggctagctg ggctgctgct tctgtcatta tataatatct
   309721 cttcctctac tttaagtcga gttccgttgg tggggacagg agcaccggat acttttacgc
   309781 agtaacaaga ggaagaagaa cgataaacag attcactgtg ttggaggatg aaaacggagt
   309841 tgaagtcaag aagctcaaat agcgaacgtc atctcctcat actttaatga catcttcacg
   309901 gcgagagctt cgggtaattt ccaactcgtc cgtgaagctc tttctccttg catttctgat
   309961 gaaatgaact cagccctcac ggcttctcct agtgatgaag agattaaggc agcagtcctc
   310021 tcaattcaaa taaggctcca ggccccgatg ggttttccgc caagttctac cataaatact
   310081 gggatatcat tggaccagaa atttcaaaga agatcaaaga attcttcacc tcggcctcct
   310141 ttcctcctcg ggttaacgaa actcatattt gtttaatccc aaaagtgaga gctccgaaga
   310201 aagtctcaga ttatcgacct attgctctat gcaatgttta ctacaagatt gtagcaaaga
   310261 tgttaacgaa gcgcctccaa ccgtatctgc ctttgattat ttcagagaat cagtctgctt
   310321 ttgttccggg tagagtgatc tctgataatg tactgatcac ccatgagaca ctccattact
   310381 taagaatatc gaaagctact gttagaggtt ccatggctgt gaaaacagat atgagcaaag
   310441 catacgatcg catcgaatgg ggctttctaa gataagtttt gacttgcttt ggcttccata
   310501 atcaatggat tgaatgggtt atggagtgtg tcacttctat ctcctattca ttatcaatgg
   310561 agcccctcaa ggtttagtca ccccatctcg aggtcttcgt caaggagatc cactttcccc
   310621 atacctcttt atcctatgta cggaggtgct ctcaggatta tgtcgaagag ctcaggaaca
   310681 aggacgtttg cctggtatta gagtatcaaa caacagcccc cgtatcaacc atctcctctt
   310741 tgcagatgac acttcttctg caagatggat cccactagct gctcaaatct ggccgatatt
   310801 ctttctaagt atgaggctgt ttcagggcaa cccagtcaac cacccgatgt cgaaccttta
   310861 ctttctcggc tcacttccat gatagtgcag aatcctaaaa gaagatcaat ctattgctac
   310921 tgaaggtgag aaagaaagag tgatttgctt cttgcaaacc ctagtgagtt atctaccgcg
   310981 tctgatatgc ttgctaagct cttgatgaac gaaactggat agaaagattc ctcttgatgt
   311041 acgaaaacct tggattcctt actagttggt acttgatcca atgctacatc ggaaccggga
   311101 tatcgatttc ccaagcctta ctcagagcga tgctcgatac gaggaggaaa gcaggtcttc
   311161 tcactctctc tcatcttgaa atgcccctat ctcaataagg cagtgaaatt acattacatc
   311221 aaagtctggg tctcgttatc cacccttttc cttttatcct ggcactgtgc ccctcagcac
   311281 ttggacgatt gagtgatcat agggaaagta catatctaga tgcttctcat agggttgaag
   311341 aaggtataac gaagctatgg tacatcagtt ccctacagcg gccgtcttag ccgaacccgg
   311401 aaagaattaa aaaagacgag tgctcattat tctatttcat agccttccgg gagagaattc
   311461 tttctcgatt cgtaccaaat tcctagggtg tgaggcgata gttttccacc catggcattg
   311521 gcctacttac ttctccaatc tagatgtgcg tcttagtctg ctgtcaacgc gttatgggaa
   311581 atcttctttg atcttcccag tagttctgtt accgctctgt gaggggaagg gcaggctgac
   311641 gagtgactat tcatcatccg aaacaaggat ctttgaaata gtctcgtttc aagccaactc
   311701 cagagctcta ttccataacc aggtgctgtg gcgagtgtgg tttccgatac ttgattgagt
   311761 tcgattgctt gcccggaaag aagaattgtg ccatcgacgg ttgggagtca aataagagga
   311821 agacaagttc tactgaaaga cttctggtca gacacaagaa aaggaatata ataataatag
   311881 ttggtacggc caagagcact tgtaattgtt actagttgtc ttctctatat cttctccggc
   311941 aaagaaacat ggaatagtcg tgcgaactct ggcggaatct agcactaaaa agagtggttt
   312001 cattattggt agcaaatggt tatacttaat caagctgaaa tccgatggta gtatagatag
   312061 gtataaagct cgtctgcttg ctcaaggcta taagcaggag tatggcatcg attatgaaga
   312121 aagatttgct cccgttgcca aaatgactac tgttcgtacc ccgttggctg ttcgtacccc
   312181 gttggctgtt ccgcccattc actataggtc tttacatcag atggacgttc aaaatgaatt
   312241 tcttcatggt catcttaagg agacagttta tatgctatgc aacctcctcc tggctaccag
   312301 gaagcggaaa aaactctcgt ttgtcgtctt cgtaaatctc tatatggatt gtgaaacaag
   312361 tgcatggttt gataaatttc aaactatctg agagttgagg aacaccaagt atgatttgat
   312421 tctagggcct ggagctcatc atctatggct ttgcgccaac atgcgagttc tgctgcctgc
   312481 ttataggtag aagggacatg aacagaatga aaagtagtca aaaaagaaga tgataatacc
   312541 catatcagac agtagataca gattgacgat tgaaacgtcg aagaggaact acagattcag
   312601 atggtgcaga aggagcagag agttctgagt cattacctac tggggcaaaa agaaggcggt
   312661 ggcacgaacg ttgcattatt cgctgggctt tgacagaccg attccgtcga agttttctca
   312721 agatcaaaaa aaggaagata agaaatggag gatgtgggtg gtgcaagtgg tgtgggtgaa
   312781 gaagcataat ataataagaa ttttccaaga agacaatgtg tcgggaaaca gctaggatcc
   312841 agacgacata cctcctctgg aattccaatg aagcggccgg acaaacaaga cgaggggcat
   312901 agaaacagaa agccaaaagt ggaatgattg gataaaagag atgctggaag atgccgagat
   312961 ggtaaaacag tgggaggagg cagaattcct ttttctttag aagaagtatc ctcagatcag
   313021 cacaccttag aggtagaggc gatgagcagc ctatggtgcc cagaaaccag ctcaaacata
   313081 atgagatggg gtgaatcaca ttcactgtcg cggacgccca tgtgcttcgt aatttgccta
   313141 aaagagtcaa gtctggctgc atacgataaa gtagccaaga aaacgatgtt gaattaatgg
   313201 atcacatact tccgaacaaa agtaacagga gatccactta tccccccgat aggtttatat
   313261 gccgcctggc ttagcaagtt catcttccct ttgagccccc tactacctaa tagggagaga
   313321 cttcgctcca gtttcagttt ggttagtgct cagtcagtag taactagatc tcacggcagg
   313381 tgccgcttaa tcagtctacc ggattccttc tgtctttatc acagattttt ttcttctcca
   313441 gaagtacaga tcagtgctcc tacactacag ctcaaaacat actttgcatc gatcgattgg
   313501 cttagcttat aagtaggaac ggaaccttct tttctcaact caaatgcttc gagtttaagt
   313561 tagtgttcat tgcttactag taaattgata ttataagttt atcctaagtg gggagaagaa
   313621 gataattgcg gatttcacac aaaataaatt ctaccaaagc attctccttt gaattagatc
   313681 gctcgcgacc tatgtcaatc aaaggaatga atggttgaca ggcgatggat aaaaataagt
   313741 ggaagaaaat gtgcgattac cacttcgatt ggactttatt ctttctttag ccataataga
   313801 agctctgttc aagcggagga ataaaaatgc gttagtgact tcgatttgaa ggaaggtata
   313861 cctaacggcc caagaagggg cagttcacca agaaggagcc aggggctagc gaagaagaag
   313921 aatcaggggc ccctgattct ccgacttttg cagaagcaga attgaaagac tttttatttg
   313981 ttgaaactcc tacaattgag gaggacctcg agttcgatag attgttcgag gagatctacg
   314041 acagaatcct ttccattttt gaaagggaaa atcttattct cccccccccc ccaaatccac
   314101 tttcttctat gatggatata gtcaatttcg tcctcgtgga cgattcagat atgtctgaac
   314161 tcatatatat atatatatga tgacttatat ctaaatggaa tccagtctat atatttagaa
   314221 gagtttgact ctacctacgt ccaggaaatg ctactttttt ttagcgtggg agggtaattc
   314281 ttggagattg agggaggaca ggttggttcg aggacccctt ggtcaaagga aaggtacaaa
   314341 ggaacttgac cacttgttgg gagaggttgt gaaacaaact cgactaaaag aagaggtata
   314401 aaatgattcc ggggcggagc catatgacgc gagagtgtag actctggaac tcagggagca
   314461 agaccctaaa gaaagttcaa gaagctatga agagtggtaa actctaaaag gaaagataga
   314521 aactggggag ttggctgata aagatggaca gtaacgattg cgtaatataa atttatcggc
   314581 ctcgtcatcg aaagcggctt ccaattgctc ggaaattttc agctatatgg ggggcttgga
   314641 tggtgagcaa aaactattga tcaagaagtt ggtcaatttt cgcatgaaag aaggtaaaag
   314701 aacgagagtt cgtgctattg tttatcaaac ttttcatcgc ccagctcgaa ctgaacgcga
   314761 tgtaatcaaa cttatggttg acgccgtaga gaatataaag cccatatgcg aagtagcaaa
   314821 agtaggagta gcgggtacta tttatgatgt ccctgggatt gtagccaggg atcgtcaaca
   314881 aaccttagct attcgttgga tccttgaagc agctttcaaa cgacgtataa gctataggat
   314941 aagcttagag aaatgttcat ttgctgagat actggatgct taccaaaaga ggggaagtgc
   315001 acgtaggaaa agggagaatc ttcatggact ggcttccacc aatcgaagtt tcgcgcattt
   315061 cagatggtgg taaagtgaga ccacataaag agctcttcgt cattcagtca gattattaag
   315121 taagatatgg tttgaccctt ttcctttttg ttttcatttt catccagaaa gccggccttc
   315181 ctcatactcc tcccttcatt cattgagtta gaggaatcca taggaggccc acccgttatg
   315241 cattgcatga aagaaccttt cttttttgta tgactgagag gaacgcctca ggtcgaatga
   315301 atacgaaagg gagatcaatc caaagaaaca aaaaaggcca tgaatgaaga agttgggcct
   315361 ttcaccctct ttctagttac tctgggagct gatctgataa atgcacttca aagggaggga
   315421 aggctaggaa tctcgttttt gctcctcgta cacatcttcc tcagtccggg cattccgacc
   315481 ggcggaatag gcattcatat aatccattta gccatctgag gcacctctat tggatgagtt
   315541 gacctcacct ctttcattca gatctgcaga gacaactgga acagaagctt cactggaaga
   315601 ggtagctaag cctgccgaat cttgggaatt caaatctgtt accgacctac gttgaaaata
   315661 aaccagcagc taactgctga gtaagaaggg cagggtcggt actgtgtagg tggaacaaag
   315721 taaggtcgag agtcgcgagt caagaaagaa atcttcttag caccaaagga ttataagtta
   315781 gagttagacg atggttcaga tgttatgaag cacaagggtg caggtaaaga ctacgtcact
   315841 gaagagtggt ttgaagaaca atacaacgat ccctgctcgg acagtaactg gtcgaaaagc
   315901 ctctgctaaa gatcgtcttc ctagcaaaat gacattctcc taactgagag agtcaagggc
   315961 agctcttacc ctgccaagcc aatctagatg tcttacgcat aacacaagct aagccgcttc
   316021 cagtgaaagc agtagtgagg tagctcaata aacctagcaa acaccggcta gataagtggg
   316081 gcaggctgct aactcagggg ggattctttg tcgatagaag gcattcgcga aagtcgccga
   316141 tgaagagaag ctttactaaa agagggcttc tcattatgtg gatacaaagg cttcaagtgg
   316201 tgcggttccc acaggaattg caaacacctg aagagagcgg gtccaacccg atacgatatc
   316261 cttctttccc tagaaagaag tattcacata gtccaatcca ttacagcccg gcagtctaac
   316321 aggcgtagat cacactggaa ctggagtagt ggaactagca cgacgaacaa tgctcggcac
   316381 tctggtcaag tgagcccctc tcattctcta taatccctat agttgccctg tataagcatt
   316441 cttaatatgc cctctcaggc taatgaaagc aaaaaaaagc agaaggccct tactacacta
   316501 agcgctacga gagcccccta tacggaagga gactctattt ggtcaaagtc actttccaga
   316561 agagatcaag tcgtttactt cttatttgtg actcttgcca acaattagtt ctgtaactgg
   316621 cacttgactc aaaccgcttg tctaaatact ggaaaagagg gaattgattc aagattccct
   316681 tgtgccctac aaccctcgag gcttttaagt ccatagcgcc cgattcgatc actctatcga
   316741 atagaagtcc agggatgctt caatcgattc ttaacacctt gaaaactccc ttctttattt
   316801 ttgatgagaa ggcaaatttt tagctttctc ggcttaacga ctctttcttc gaaccttttg
   316861 gtatgtattg ccccataact atagatcaga tccaccagac gagaaactca attccgcact
   316921 gctgctgagt cgtcggactt atccaccaag ggattcgtgg aatttctgtg aattgcgttg
   316981 ggggaaatct accaaagcta ggcagataga tagactcctt tcccgctgct aagggagagc
   317041 aagaaataaa ataaaattct tgttttttaa ttagcgcctc cttttgagta tgccgatact
   317101 aagagtcctc tcactaccaa ccagcagaca tcatctggct gggtcttgcc ggtatcaaca
   317161 acgagaaaaa aacaaccaaa tggaaacagc aactaactat gactcttggc ccagacaacg
   317221 tcctaggcgt agggtagatc ggagcaagag ggaacgccta gacgacgttt ttattcctgg
   317281 gctgctgtaa gtagatcgag aggtcgttcc gccccttgtc cccgaagatg gggtaatatg
   317341 ttctcaaaaa atgttgcttc aatctgacct agctggcgag cgatcccagt tcgcggcaga
   317401 gaacaagaca gcaagcgagc gtacctttgt tcgcttcttc tccaccaagc acggaagttt
   317461 aaggataact gtaggtcggt ggctacctaa ggaaactgcg attcgatccg ccccccgaaa
   317521 aggaggcatt tacctcatcc cgatcacaag gagaggttca ccatgatggg ggtacttata
   317581 attttccttt ctagaaagaa tgaaatgcat aggggaccat ccttttgttg cggcatgctc
   317641 ctcaatttac ggattcgcag ggggcggaac gacctactta gttgactgac aatgacaaag
   317701 gcttgcgaaa ctaagtatgg cctttcaaat tgaatcttta gtagtctatc agtggtgcga
   317761 agagaaacat atctttttat gacttctact tattgatccc ggcccggaaa agtgagcgac
   317821 caggtttata aagactggtt cgaaaggcgc gtctagccct cttgatgaat gaaagaaagg
   317881 gtttctgagc cctagccctg taagcccaca cctgtgtaga gtagatcgtt caacacctgc
   317941 ggcacaaacc aatttttgac ctattggtcc tagtctcata ggcgaccgaa cggccgcccc
   318001 ctaattacta gaccgacccg ctataataat tccataaaca cctagcgaag atatggcaaa
   318061 caaataaagt agccctatgt tcggatctga caataccata ccataatcaa aaggtacaac
   318121 ggcccgagcg accagactta acataaatgt agccactgga gccattctaa aaaggaaaaa
   318181 attagcacta cttggtgaaa taggttcttt tagaatcaat ttcgaaccat ctgctagagg
   318241 ttgtaacaat ccgaacgatc ccactacatc aggacccttt ctacgttgca caaaagccat
   318301 tactttacgt tcagctagca ctaaaaaggc tactcctagt agaagtggta gaattattcc
   318361 aagtatttca gctggaacag ctatgtacgt tttcgatttt ttatttactc atgatctggc
   318421 ctggtcgacc caatcatgat attgaaggat gggacctttt ctcgaaaaac tcccgatacc
   318481 gagaagagtt gaagatggtg caatattcca tctattctca atggaacgaa ccccctatca
   318541 ctttactccc gaaataaagc accccttccc cttctccgcg aactatctca atccccaagt
   318601 aattgtttaa tataaagaga ttcgtcgccc cgtctgagaa ggtcacgctc tatttcgcct
   318661 agaaataaga tctctaggcg gtccatttcg gccgggctag atccggggtt cgaaatgtcc
   318721 agcgcgtccc gcctctcgtt caagaagtcg aaaaaagcct cttgaggaga gtaggcggcc
   318781 ctttcttcca aataaggatt cctcaaaagc actccccgaa agacttctaa acaggagtgc
   318841 ttccgttccc ttatttggag atcccggttc tcgaaatcca agagtctata atactccctt
   318901 tgttcggaaa cattataaag acattcttga atttcccccc aatactgccc tttctctttt
   318961 ccaagcagaa aaggggaatt cgccgcctcg agcaggcgaa ttcgattaca aatcgaagac
   319021 tccaacccga gatttcgggt aatgggccag ggttccgaaa gaaccctcag cccaaaagaa
   319081 tcctccgacg aggaggtgtt ggaaggggtc ggggctgtgt tggggaagag agcctccgcc
   319141 gcgtcgtcaa gggccaaagc aaaggatggt tcaacaatga atatcgaaat gaaacaagga
   319201 aaaatggtcc gaagaatctc gatagtagtt ccatgaacaa ttctttgcgg gattgcattt
   319261 tttttatagt ggaaatgcca taaagcgcga accaagatcc ataatacgaa aaccaaaatc
   319321 agaatgagga agaaaaagat atcgtgatgt aagtctatta ttccttgcat tataggtgta
   319381 gctgcgtctt gagatcctaa ttgccatggt tccgctgcat cacaaggaga aattgtgagg
   319441 aataaccatt ttagaacaat cattttcaaa gcaaaggttc cttcattttc tgctcccccc
   319501 aaacaaagag agactgattc tgactctccc aattaaggaa gacggaaatg gctggtgccg
   319561 gttggtccaa ccaagaaaaa agagatggga atttggggcg taagattcta tcaatcggga
   319621 agttggcctc actcaatagt cggatacaat cgtggacacc gtagacctgc ttcgcgggat
   319681 cgccttaaaa ggacttgatc cgcacatggc gaacggtatt ttggcagtgt tttcttaatt
   319741 gatatctcta actggaatga taatctgatt atatacgtat tattccaagg aggatcaaca
   319801 tcccattcca ttacaaatgg ttaaacagct atcctttacc atacatctct tcccgctacg
   319861 cgcctcacag ccggtattgg cccttgctgt gctccccctg gaactgtagt tcacttcctt
   319921 cctccgggag ctgcagctat cttctcaaca atcaactatc caatcttgtt gctaatgtgc
   319981 aaaaagttga agcaggtgtt gcgaagctgc cctgctgctt tgattgcgta gctacctccc
   320041 gcagggaaat gcagctaact ccttaaaaag agtaaacagt ttgttagtag gtatgagttg
   320101 caaggaagtg ttgcgtagct gccttgctcc ttagtaaagt aagcacggga accctcccgc
   320161 agggagctgt agctagagct ccttattaag aactcccttg cttgttttgc ctaggcatga
   320221 gtagttcagt tcgaaaatgg atcctcaata aaaaaaatgg aatatctgtg cggatatgtt
   320281 cagctttggg tggaaaggta aggaatttta ctccgactaa gattattgtc catggtgtaa
   320341 cggacacagc caaaataact ctcgggtaca acatgctaca gatgcctgtg gatcgctggg
   320401 aggcgtacat acaatgaatg ttattgatgc tactccttct taccattttt gactggggcg
   320461 accccccatt gatcttggct tgcttctttg ttcttggcta ctgcttggtt aactattgcg
   320521 aattatttaa tggtataaaa aatacttatt ccttctcgca tcgcgcccta gaggggccgc
   320581 tcggacgaag aaagtcaggg atagagttcg agtgagacat caaccataga tttcggaact
   320641 ttcgagatgc tttcttgcga aagccaacgg aatctgtaac tcaaccttct cacccatggg
   320701 ggattcaatc atattcgatg aaaaatttca atcgagggca ccctcatttc cagagataaa
   320761 atcaggctgc acagaagggg aaaagccctc ctactgagca agatcattaa tgaataagga
   320821 agcacttaac ttaggacagc cggtctcact tcacgcagca tagcgccttg ctatttgcat
   320881 tcatccttgt aacttaccga agtgaggaaa gaaagccaca ttggggatcg cgagtcggga
   320941 gggtggcgaa gatattgtgt gtgtcagcgg agtctttccg gggttggttg aaagcatgag
   321001 cgatgaactt ctcgacttcg atctttttct tttaagttat gggttgattg tgacctagta
   321061 taggactgat ccaggtcaat tcaaaggcta agcccaagaa ttccaatagt tcgcttttta
   321121 gttttagcgc tacttggata cttcaagaaa accatgaatg accattgtgc cttcataaag
   321181 aggtacgtta gcggcgactt tctcatactt ttgctatatg tcgatgattg attgtgggcc
   321241 atgaccgcac caagataacc gctctaaaga aagatttgaa caagtgcttt gccatgaaag
   321301 tggggccagc aaaacattgg gatgaagatc actcgtgata gatcgagaaa cctgttatcc
   321361 taagaacgat ctgttgggtg gagagattca atatacacaa ggcaaagcct acttgctgga
   321421 catttaaaat taagctcgga acaaagtcca acaaatgaga aggaggaaat gaagactacc
   321481 ccatatgcat ctgcagtagg cagtcttctg tatgccgtgg tgtgtacaag gccagatatc
   321541 gcctatgcag ttgtgagtcg ctttctagcc aatccagact gcaaatggat cctccactat
   321601 ttacgtaaaa gttgtctatg ctttggtaat gagaagcttg agctgatggg ctataccgat
   321661 gtggtgtgct gccgacgaca aagattctag gaaataaact tcagggtata taactacctt
   321721 tgcaggagga gctgtttcct ggcaatcaaa actacagctt tgttccacga ctgaagcaga
   321781 attgctgcca cagaagcttg caaggagatg ttgtggatga agaacttctt gcttgagttg
   321841 ggagtaaagc aagataaata tatctatgtg ataaccagag cgctattcac ttagcaaaga
   321901 attcgacctt gcactcccgc tcaatcgata tacgacatcg ttggatccga gaagttctga
   321961 aagatctcaa caaagtggag gagaactggt cagacgacct aggtgttgtc gattcccttt
   322021 cctaatataa aaagagtttt cttgcattcc tattgtctaa ttcccatctt catcacacga
   322081 aagaatattg ggtaaatttc ccaacaatgt ctggaacagc cactatcaaa cagggaatac
   322141 tctcatctta gcacactcct gtcacatgca tttgagttct ccttcatctc gaaaaatcac
   322201 tcgcgcactc agacttcact acagcttgag ttctgtaatc aggttttctg catctctgtt
   322261 gtatctccgt ctgtaggtgt ttagcacact gctgtgagcc ccatatagat ctgtcctttt
   322321 gatccatgct tgattacgtc aaccgtagag cgcatccaat ctgtcaaaat agtcgtagca
   322381 gtaagaatca gtaattacag cgtggccttc ttttctttct gatacgtatg cttgctcctt
   322441 ctgctttcct ttgacgaata cattccgtat ttgagacgcc ttgatatcct agaccttact
   322501 ttctcactct tcttatttga ctgttcagaa tcttgtctag ttcttttgtt cctgagttca
   322561 gcatccttat cagcttgagc tgcgtgtcta ggtctgtctg aagcttagct gatttcgatg
   322621 tctgtcttta gcttctctat aagacttcgt agctctgtgc tgtgttctca ttttccagaa
   322681 taaaattctc tttagggttt cacacatagc cctgtcctcc ttttcaacat ctttgccttc
   322741 gacatcgacc tgatgaatca gactctgtgt cactttcttc tgttatccct gaccatgcaa
   322801 cgaatcatgc ctaacgaatc ctcagattca tcttcatctg cattcactgt catcagcaca
   322861 cagaagagag cgagtattcc caatccctca gcacaatgca cacacctaga acaacacctt
   322921 gtccctttct cggttatccg gcacaacatc gtcactccat aacgattcgg agccaagctg
   322981 gcatccgcaa acccaagttg atactctctc ttctagcctt ccagatctaa gagcatgtcg
   323041 ttgttcttgg aaaagaagag ggattatata gctccttgtc atctacaata ataggactcc
   323101 gacaggccag ccagaaataa actatagaag gaggttgctt cgctagagct gaagaagttt
   323161 cgggctgaaa agctgcctca ccaggaagac ctgcttctta ctttctggtc gtatgcccga
   323221 taggatttcc gtagtataaa ttgaaactcg ggtaccctta tcatttcact aatcaaaaga
   323281 ctcaaggtct gtgctcttca cctgttcacc tgttctcttc acttgcttag cagcctcact
   323341 tcgaaggtgt gctgcatact ccttcctgct tgctcttgag cacactcctt ttggagattc
   323401 catacactac taagtaaaac gtcgtcaccc aagtggaaaa gaatcacttg aatccagaag
   323461 atctagagtt ttgtttggag ctggcttgtg cagcacactc ccacccaact catcttcttt
   323521 gggaactaaa agttgtttag ctgtcattct tccttccggt accctttcag tccaactgag
   323581 caaattagtc aaactttgta ctcacaatga gagaggaacc tgtaggagct ccccataggt
   323641 ctgaatgaac ataatccagc ttttcttcct ttgtatcatg ttgagctaaa tcaaaactaa
   323701 ctctcttagc tctgccgtat atgcaatctt caaagatgct gaaggttgac actttctttc
   323761 tgtcaaggaa tcctcttttt actaagagat ccatgttctt ctggctcatg tgcccaagcc
   323821 tttgatgcca caagactgtg ttatcaactc tcttctccac tgatagagag tgtccagttt
   323881 aaggtgtccc acgcaatatg tataaagtat ctagcctctt cctcaaagcc gatgcttctg
   323941 actcaattgc gaaaaccatt ctaagactaa ctgccgtaat cccactaatg attgaatcga
   324001 gagtcatcct tcttgctaaa ctcctccctt ctgtgaaact cactttaagt aagcagatga
   324061 gcctcttacc cgtgcaacat cagaacatgc attctcgcga tctacagagt ccttatgggc
   324121 ttgctcttga aaaagaagaa tgaaccttct tgttacagaa catacattcg aattcgttcc
   324181 ttccccagca ctgactcttt cgatgctaca gtcggctcta ctgattagtc aactagtcaa
   324241 atcgctttca catctcagat gacatttgta ccaacagact tcttgataag aactccagat
   324301 gatccagctt attttaaaga taggttagcc agccccttct ccttcagggg atgcagcaag
   324361 actacgtcca cttcttcctc aatctactct aagaaaaagg caagtacagc tacttacttt
   324421 agagtcgatc cagttcctcg ggggtctcaa tcaagtaggg tatgtgagcc taaaactaaa
   324481 ctaatagtct atcaacctgg gaactatcaa aaaaaagtaa agagacaagt aaccgatcct
   324541 ctttctttaa tggataaagt aaaaaaacga attgataaaa cagaaatact ctgaggggtc
   324601 ttggattgta gagctgatca cagcagccag acagaagaca ataataatcc ccgaaactat
   324661 aatccgccgg gcgaaaaaag tgcaagtgtg tgcaggtcaa gctcagggga agttgaatct
   324721 agcggagggg tctttgcttt tgcttttcat gactcagcta ctattgaatc cgatcctagg
   324781 gcattaaaag aagagtacga gttagcaggg ctgtctcacc ttgggcttgt tggccggcgg
   324841 aataaccgca gtaacctcct tcacttcatg cctttgatag aacggagatg gtaattaggc
   324901 tgctggtagt acaactaggc tctttctttg caagattctc agcatctacg gggagaatgt
   324961 cccaaagccc cttttctcca attgcaattc cagagggata tccttttaga cgctctcccg
   325021 gcattagcgg aataagagca gtgggacttg agctagtgag atagattcac tttcactatt
   325081 tgaatgcccc tcttcgattt cgatgagcag aggattttcg gacattagct ttagcagacc
   325141 atttgcggca tatactacta tttccatgaa gactataact gaagacttac tttcttatta
   325201 ataaacttac actaggaata gccccgagaa cccatagttg cccgctacgc cccttctgct
   325261 actttctttc taggtccaat aggctctttg tcggtcttga tgccgagaac tgagttaatc
   325321 ctaaatgcag ccgtgatctt atatacgatg ataccaccag acgcgcattc cttgggatca
   325381 gaaggaagag ttgtcaacgg gaactggcga gacacttctg acgttaaaga aggaagtctt
   325441 ccccgggagg taactaaaca agttaatgga agtctgtctt cccgaactaa gcaagttaat
   325501 gagttcagca agcacacaag gtttcttgta gacataagtt tcagttgttg ttccctaata
   325561 aatagatctc tttgggaatc agcacagaaa gatgagctta gtgattcctt cgggaaagca
   325621 cttacaacaa agccagaatg tttagctgtg agagaaaccc ctaggaactt tagaagaaat
   325681 ctgtgcttag tgattccttc tttgaattga aatgcttact atagctaaga aatcatacgg
   325741 gattacttgg accttaccac gttccctccc ctctcttagt atgggtcctg ccccgtacga
   325801 gcaaatcgct tcaaaaggat ttgtctccaa tctctttaaa ggcactatta acttttcggt
   325861 cttcacttgg aatctgtgca ctatgagtgc gttacaattg ttctttgaat actgtggcgc
   325921 gcctttcagg tgctggtttc cgggtgaggg caaaccttca atcaaatgtg tccaagaaat
   325981 ggactagatt gaggacaata tattctaaac ccccgtcatc gtctcaacta cctttagagt
   326041 ggtggattgc tggagacaaa gtcccctctc tccatacata aagggaattc tagttgagat
   326101 gctgaagaga aaattgaagc ctaaacgact tcaattgcct cctcaggatg tcgtctttga
   326161 aggggaggca gctatgaatg agtatacttt ctatcgtaac tgggtggaat cctggttaca
   326221 gcacatccgt tcatactacc ttcttttcat tgatggagat ccttctcttt caaagttctt
   326281 tgagattgag atatgtgccc actcttggaa gcgttcgact ttcgaccaac aggtctttaa
   326341 gtttggcctt ctatgggagt gtgtggatat tgctcgctct agaacagttt attggcaatg
   326401 tgctttaggc acaggtcata tacaggaaga taaggtatcg gaggcaacaa gcccctttac
   326461 cgatgacagt tgtaccaaca gctgtttatc aaggatgact ggacaataaa gaatgggaac
   326521 tgggaaagtc actgctattg gcggatcttt gcctagaacc gaaactgatc tttagctagc
   326581 cgaccacgtg ccagaagttt atactggcat tgcaataggt caagcaagtc tgctggcaac
   326641 cctgtagcct attggcttct tcctatatcc ctattcgggc aaacttttga ttccattacc
   326701 gagccaaaga agattcttcc cctagttcta cttatcacct tttcatactg ggcagcatct
   326761 attgagagtg gattgacggt gttgagagat ttccagcata agcagtagtt gaaccagcat
   326821 aatgaaaaag ctagaaaaag gggcaagtag gtcggcttca gccagaagag cttaaccgaa
   326881 tttttccaat acaacttaag ctccaggaag aaagcaaagc cttgagggag tgagcttagt
   326941 tacttttttt cggtcggttt gctaaagcac ctctcgggca ctaaacaaaa agtaatcaaa
   327001 aagtaatact taataggtcc ctatccacct ttctaagaca acagatcgaa ctcctatact
   327061 cccttcgttc gaagaccact cttgaagagc ttttccttac ctatgcccct tagccaatca
   327121 agccggactt tccctttttt tcttgcctcg gtctttcttt ggtctatttc tgcgggtcac
   327181 taaactaacc ttctctggtc cgctttggct attgaactaa tattcttccc ccccaggccc
   327241 caagccagtc agtttgacca ggaatgcctg cgaacggtat aatcatgaat aagaagagca
   327301 agcggtaaac gagtgcgaag ggagcgaagc gagtttttct ttttaaggaa gtctagtctc
   327361 cttcaggcga gttgaacgaa cggtctactc aagctcctga gagcgagcgg aatagcctgg
   327421 tctttctaat caaataagta gttaacccgc gattgacctt tatcttgtct acctctgtct
   327481 cgcatgagaa atcgaattcg gggtgatcaa aactagccaa cgaactcagc tggcgagtgt
   327541 gaggctatag atatagtcta taaaaaaaaa gaattgagct gacaaaaggg aagaaagagt
   327601 tgttacgccg ccttcgacaa tcgtgaaacc aaccaacagg tgctttcttt tgttgtgtcg
   327661 ctaaataagc aggcttccgt caagcgaggt cagccacaaa gggaaagaag aaagagtgag
   327721 cgagaaagcg gtgagcttac tctttaagaa ttgattaccg ttgatggcgg ggggcggaaa
   327781 cctttccctt tctagttgtg aattccgtat ttttgaaaaa aaaaaagtgc ataatattgg
   327841 attcaaaccg acggcctacc ctttctttga accttgtcaa tgatcgaact taaagatatg
   327901 aactgagtgc catttgatga gtaactgaga acaaaggaga ggggtatagc aaggatgaag
   327961 taatgaaaaa ggaagtcatt gctagtagta acgacttatt acgatccatt ggttcatata
   328021 gaatccatgt cctaggtgta tcaaaaaaca ttcttttcac taagcgtata taataaaata
   328081 gagtgaaaaa gggtccaccc cgaaaccaag gggatactaa ctaacagctg agtcctctcc
   328141 aaaccgcagg agatagttgc ccatcatacg gctcaccaac ttggcctcta tgggaggctc
   328201 actccgggca ggttcggatc acttataata caaagctcgg agaaggaagg ggttaggtta
   328261 ggaacgcagt aactcgaccc ctcatcaact aattaatgag accttatcct tgggagagcc
   328321 ggaaaggcac tcgactaaaa ggttaaaaga tctcgactga aaaggagagg gcgaagtcat
   328381 gactcgagca cttgttgcga gaggtccata ggaacaaagg agctcgactg taaggaaagg
   328441 aacgagagtg aaacgagagg agaggtgagg ttttcaatat gattcttttt tcgtatttgt
   328501 tcgatgagaa atgcgagtcc aggttttgtc cattttttct atccccctct atcaaacaaa
   328561 atgatcaaaa aggaagttta ctggcttctt attctcgtct ttgatctctt ccatctctgc
   328621 ctcgctcgtt gtcacctata ttgaagaaag aaaccctgta gagaatgaag aggggcctag
   328681 gatcttcttc tcaacagtgc ttctcgaggc tccccccctg aataagtaag gccccgttag
   328741 cctgggcgaa gatggggata aggaataagg attgaagccc ccttagctct gccaggcact
   328801 gacaggggtt agctcggtaa atgtgtagag ccaagtgtag tatggtgtag tagtagtagg
   328861 cacttctagg ccccttcccg gctactggat cactccagtg ctttgggtac tacggaccct
   328921 ctgccatcca ttgcagcaga gccgtttcat gagcgggggg gctaggcgca gttctttgaa
   328981 tcaaacgttg aatgaaatcg attctttttt agatatgaaa atggaaatcg gataggatag
   329041 atggatggat ctatctttcc atttatatat tactaaagga tttatatagt taagtatcgt
   329101 agcaagaagc cccaaatcct tgatttggcc aggaaagact gcactgcttt gggcccagga
   329161 tgcgaaggga atgagctcgg ctgcttctcc tccacactga tttttctccg tgcctgctcc
   329221 gcatgcgctt ccccattggg ctttgctctc ctcttattct tcattggacg gttcggttcg
   329281 gatggacttc gccgttcttt cccaactaaa aaagaaaagg ctgtatcaca tcgagatgtc
   329341 gattcgtttt ccgcccccaa tgagatgggg aatttgtaac cccctatttc tactttgggg
   329401 cccttcatct ttctgaatcc aggcccgtcc cggctcgtgt cgttccaaca accggcgggg
   329461 agcatctcag tatacgatcg cgcgcagtaa ctgggagtcc tattacacct aaggcgaact
   329521 tcaattcacc aaaccaaggt tcatctcgtg tagtgattgt ggactctact aaggatattg
   329581 agtagacggt tgatgtatca gactcgaccc tatctttcgt agcatgcatt cccatcggtg
   329641 tcgcaactga ttcggtaagc tacgtgtccg gtgcacggag aactgccttc ggtcctccaa
   329701 acttacttat tcgtggcaac cttccggccg cccaacgacc tataacgcta gtcactactc
   329761 ccactggggc tagaaagtaa gccccacaac ccaaagcggc gaagaacaaa tagaatttgc
   329821 tacaaaagcc ggctaacggg ggtattcctg cgtatgagaa catagtaatg gagaaggtaa
   329881 tagccgaaat aggattcgtt ttggctagag cgcccaaatc cgctatatat ttgacacggg
   329941 tttgccgtaa tgctgaaact atggcgaatg catccatcgt cattaatgca taaataaaga
   330001 taccaattag tagtgattga attccttcta tggttccaca tgagaaacca gtacgaatat
   330061 aacctacatg tccaattgaa ctatgagcta gaggtctttt gactttcgtt tgggccatgg
   330121 cggccagtgc tcctaagatc atagaagcaa tgctgcagaa aaagaagatt tgttgcaatg
   330181 tagctccata ggaaccataa atagaaacac gtaaaatatt agcagaaata gagattttag
   330241 gcgcaataga aaggaatgct gtaaccgggg tgggtgaacc ctcatagata tctggtgccc
   330301 acatatatag agtcaaaggg aatatggagt ccgaggggga gggggttttc ttcggggctc
   330361 gagagattga atagacccac aagtttgaaa ttcgccactg gggaattcac acgaaaggga
   330421 acgaggaatt ctcaacgaaa aaagtgctct ctgaaccgaa cgtgaaagtt tttttccatc
   330481 agacggctgt tcctgtaact ccactctcga cttggattat atatccaaaa aggtccgctc
   330541 tcggccattc cacacgctgc ctagccgagg tgtggtttct gaagtggatt ctctcttttc
   330601 tagtagatgc cgaacctgct gccccattga ctaagaagag gggcgggcgc agcagctaca
   330661 tggacccctt cctttctgtt gttgccagcg ctttcccggg ccgagccgga atttttgatt
   330721 attattctaa tgggcaggca aagccgcagg ctgctatccc aataggccag cgggcggttc
   330781 gaggagaggc tccggcaatc atagcaccgc ggtcgaaaaa gcgtgctccc ttcagataac
   330841 acgcaccgta gctatcctcg gccttcttcg ttttcgatgc aaaagaaagg aaatctctcg
   330901 atctccgaaa gccttttcct taccccgccg catctccctc ccttcgtcga gcctttccgg
   330961 ggttgttcct tccttatcag aacttggcgg gcattctttc cagccggggg atgggttttg
   331021 tttgaacata ggctcaaaca taattttaag gtcctagcta cgccatgcgt tcaataccaa
   331081 atctggaaag ctgcagaaat gacaaaaaga gggccgcttt cctatgttgc actgaaaaaa
   331141 gaaggaccta agagcgtctt ctcttaggtt ttttcctccc gcgcccgccg ccgcctggcc
   331201 cccgttagag ggaaggggaa gattagcaaa gcgaaaaaag acagaggaag ggggagcagc
   331261 atcttattct cttcgcgaga acttccggat tgaagaagca ttcggaacgg gctccagcgt
   331321 tcatttcatt ggcgggaaac gatccaatcc attcggggct tcggccaaaa acgaattcga
   331381 cttgattcat agatagaatc aatgataaat aaacaaaaga tagatgttcg agatatcttt
   331441 tctttctata aaaaaagagg aatagaatag acatcccttt ctttagatgt ctatctatcc
   331501 ttccgatttt atatcgttat atctgctctc tcaatttttt tttagagaga gcagatagat
   331561 cctatcccct atatcgaaca ctaattccta tctattgata ggaagatctt cgtctaatag
   331621 cggactttgc ctttttttag gaatttctca tatccaaggc agcttaccac aagaacccca
   331681 ccccatacaa ctagttgggg gggctgttcg ccttttgaat caaacaaaga ttgaagtagg
   331741 taggggcttc atagctactt tcattctaaa ggaaagcgaa gaaccaatct ttagtcaata
   331801 ggagccctac ttccctcgac ctcatcactt caattgttgc gcaaacctct ttcttagtca
   331861 ccgggggagc gcacctttgt cacagtattt cgagctgttt gatagtgact tcttgcgttt
   331921 ggtagggcga cgaaagggct acttccttca atctaggaaa cagccggaaa ctcgagaagg
   331981 tcgcctttgg aacggttcgc cagtaaccaa agcctcactc cttccttttg attatgtcgt
   332041 gacgctgact gaatccaatc tataaaaaaa cccggaaact caacaaagtg cgttcccttc
   332101 gtcaagtagg taaagtaggc atacgaacca cttttgcttt gcggaataaa acaatgaatg
   332161 aggcggaatg gagaaaggaa aggtctgcag gtatttatta ctcttataaa agaggaactc
   332221 gagcttattg cgagaggtgc tttacgaact cgactaaaag gagaggggcg aagtcactcg
   332281 agcacttgtc tagagaggtt gtgaacacaa actcgactga aaggagaggg acaagggcgg
   332341 tcttgcttgg cgcgaaggct gctggtttgg gggtacggta ctaaaggtcc tcggacttcc
   332401 aggcggtttt tattttgggc agctgttcac cgttggatct cgccaataca gccccctatg
   332461 gtttttgtta ccgagatatc tttttttttc attgttccca gggatttttt gggtaatctg
   332521 ctcccatgct gcaaacagtc aaatctgaac tcaaccttgt cgctcttctt tctttcctcg
   332581 cgggctggaa gcacaccagc agcgtgcgtt gcgtgattct actgtgtttt ttgcacttga
   332641 ctgggtggac agttgaccgg aagagaactt cgattcgccc ggccagcagg cgggcgacgt
   332701 gcttatcttg tgtgacaaca ctacagagcg agtgactctt ctaggcgggc agctgtgtga
   332761 caacactaca agggtttttt tcctcgtgta acatgctatg gtctcaatgc ccttacgagg
   332821 tagtgatgag tttcactcgc tctaagcccg gcccgcgcgc ggttaggaag attggccgca
   332881 atctgagcgg taccacccac cctaccctac cacctatagg cggccgtccg tcctacagcc
   332941 gcccgaaaag gaactgcagt gatcttgaat aggaatccta cagcgataga cagaatcccc
   333001 ataaaaatac cactagatcg agcaccagtg atttcgtatc cggtcaaaat cttggctaat
   333061 tgatcgaagt gggtagctcc agtagaccca tagatcatgg aacaaatagg gtgggtaggc
   333121 ccaaccacca cactacacgt atagacgcga accccccctc gttaccgtac gtgcgactct
   333181 caccgcatac ggctcgcaca aagactccta aatccatccc gagccttttc ttcccacttc
   333241 tcccttcagt cgagttacta aagtacctct ccaatcctcg atcaaacttg cccaggcgct
   333301 attaaataaa tgggggtctt tccttcgcct atcgtatatt gtatgtatcg gcttggcttc
   333361 gtccaaaact aaaacaagga ggcattccgg cgggctctag cgtgtaggaa ggccgaccat
   333421 tacataagct aaaagactag gactataagc cagccggaag cgactcgctt ctattccccg
   333481 ttgggattgg atatagatgg ggaatctatt gatcgtagta gttcgccaac ctctctaact
   333541 aacatacgat caaattttcg gcacggccca aaaaaaagaa agagcttcgc tcggtgggcc
   333601 ttcctacgct gacgaatgcc tcctttctct tctcttcagt ctacaacaag tgggagaggc
   333661 aggattcgaa cctacgtaga aaaacttcaa cagatttaca gtctgccgct tttgaccact
   333721 ctcccctttc ccttttctct taccttctgc cttctcccct tcccctagtt ccaatcgttt
   333781 taggaaagtc ggcattcttt gtggaaagga cttataccat gaacggactc tttgccttgg
   333841 gtcaatcagt tccttggctt actaatgacc acttcgagaa gaacctattt gaaaacagtc
   333901 taatgccaca tctgactcaa cagctccttc ttccttttct tcttcataca agcccccttc
   333961 aactatatgc aaccacttct tgaacaacct attcctattc atgcgatctt cagctcattc
   334021 tatgccatct tacttatact attattaaac caagcttcaa ttgcacaagc cattctaagg
   334081 aagattagac tggcatctgc ttagccctgt ctccctctct agctaattga ataccagctt
   334141 tctcttatat tagtattata tgtcacttcc ttgtcctatt cttttagttt tagtatgcat
   334201 gggggtaagg agatattgat tacacagtag ttaggagctc atagtttcgt gcgcttacgg
   334261 cgtgctcttt cttttatttt tatgacaaat ggccgccagt agacgacaat aggtgaggtg
   334321 tccggtacgt gcttctaatg attattccag gctgagcact tcattcttat gcacccattt
   334381 cacatgttag gtgtagctgg tgtattcggc ggctccctat ttagtgctat acatgggttc
   334441 cttggtaact tctagtttga tcagggaaac catagaaaat gaatctgcta atcaaggtta
   334501 cagattcggt caagaagaat aaacttacaa cattgtagct gctcatggtt attttggccg
   334561 attgatcttc cgtttcaaca attctcgttc tttacatttc ttcttagcgg cttggccggt
   334621 agtaggtatt tggtttactg ctttaggtat tagcactatg gctttcaacc taaatggttt
   334681 aaatttcaac caatcagtag ttgatagtca agggcgtgtt attaatactt gggctgatat
   334741 tattaaccgt gctaactttg gtatagaagt tatgcatgaa cgtaatgctc acaacttccc
   334801 tctagaccta gctgctgttg aggctccatc taagagggaa cactgtaaca acaactagat
   334861 cgggtctatt cccattcctt caccgaagtg gttgacgagc tcaaaagttc cttttttctt
   334921 acttttcgtg gctgattaga tcactgaact tggttcactg acgctaagag aaggaaccat
   334981 tggattattt atatatccct ccctttccac taggcttaaa tcggccagta aattcctggt
   335041 ggaccaaata cagcaacctc acctttagcc atgcagaaga ggagattccc agactatgat
   335101 gcctggcacc gatcaactct gaaagtcctg gattttttgt actctctctg aagaaactat
   335161 tggatatgta tttagacttg caacagctca ggaggtctct ctttggctga tcatttcaat
   335221 cattgttcta tcttctatct cccgtgactt ttctttgcta ataagctagc tctctgcaaa
   335281 tgataagaaa ggtagaacta gggagataag agataagaga tttctttcca attccctttt
   335341 ttggaggcca agcgagctaa atggtataaa aataactcgc cagtcaatgg gagtttgctt
   335401 aggaaaataa gtgcaggtca ggttcggttc gttcctttca gcagtatcga ataagccaaa
   335461 tgaaagtgag aaagcaggcc atctatccgt tgacttgccc cggagtgagc tgcatcgaca
   335521 gaagagagaa gagagagtgg aagcggtaag tgaacttgac ttgaaagaga attcccactt
   335581 gacgcccgaa cagcattttc agagggaaga tatcgaccat acatagggag agagctcaag
   335641 ttagacggcg ccttagcgaa actttctcac tctacattca ttccctaatc acacatgact
   335701 ttgaacgttg atttgacttc acatagcttt tcgtctcctt gatagctgga agagaacgtt
   335761 gagaagctga tctgtctttc cgcgcagaat cctctttatc taaagtaaag agcagagttg
   335821 cgatagagaa cctatttgct ttcttcgact cccttgcccc tgtccttgca gcaaattcaa
   335881 agagttgtgt ggcattgact aactcactat tcctgcctga aggaaatgca tgagcgaatc
   335941 tttcagttgc aattcccctt tccaaatctg aatcaaagaa cgggattaag gggaaataaa
   336001 agtcggcgat gggactgatg ctctttcatt gcttcgagga tcacatttct tttcaggtca
   336061 gaatctgatt gatgcgttgt aacatccact gactcaaaga actacccttt agtaaataaa
   336121 tcccagggaa agtccattta tgttaaaatc tctagtgtag tggctggttc ctatacaact
   336181 acatcataag aagaagccag gtctgaggcc agcgagctca agatcaggag ccaaagcgga
   336241 ccgaagaagg cttcatctgc tccaagcccc taaagaagtg aagggacttg ctttcctaaa
   336301 aaaaaatgaa atggaaagag ttcgtttctt cctcaaattg taaacatggg ttgtccaact
   336361 ggaaatgata acagaatgca taggtcaaac gaaggagtcc caataagcgg atgaatatag
   336421 tatacctatt tcctctatga gggagaaagc aaattgaaga acccgcggat atgtgcaaaa
   336481 cttcaattct tcttagccaa ggctttccaa ctcttatagt agataatatc taaagcgata
   336541 gagctggtgg atggaaatta aaatgtcctc cagaatgaaa gtgataaaat agataaagaa
   336601 agggcgcaaa acgcagtcct ccaacggaat caatggcatt cctttcttac tagtccttac
   336661 gaactctaca ttgcttacaa ggttgaatag cagaaagcct tagctttagc tacttcaatc
   336721 tctcctttcc tcatattcga gcaaggaaag ctgtacaaag gaaaaggtat tctaaagact
   336781 tgtttgcaaa aaaatgcaaa atctcttact tagaaaaagt acctgcagat tcctgcccaa
   336841 aatcaactgc tattgaatct aagccaattg aatggaatca gatcatccgt ttctggtatg
   336901 ttgggtgtca tcctatccag tactggatgc agtagaaggt gctctcgggc gaattcccgg
   336961 ctaaaaagta cactgagtta ggcgagaatt gtctcgagat tgacagattg acttagggga
   337021 attaggagtt gtttggaggt gggtaccacg gaagaggtag gttatccctg aaaaagggac
   337081 tcggatagga atagagacta gaagctgaca gcaagctctt agtcttggct tcttcttcct
   337141 ttattttatg gagacagggt tactaccata cttggagcac gaattcatat gtaagatgcc
   337201 cagttggatc actaattcgt aaattgacaa cctctagaaa gggccttttt cccaaaagat
   337261 tcctaattta atttcgtcga tattgaatac cttattgact ttgagactac taataaatag
   337321 caacgaagct gactcgacca gtttacaact tcgaaagaag gagagcggag atctttcttt
   337381 caatcgaagg gtcatgggtt ttttcatagg caccggactg aggtatgaaa tgaaggacga
   337441 gtttcactcg cttcgggctc aagtttagat aaaagagtcc aatgagccca aatggaaatt
   337501 cgatagaaaa ctaaagctga gaaagtcaca atccattgaa taagatcggc taaaggtgag
   337561 agctcaaaaa agaaagaaaa gaagtcgctc acccgcctac gattgattgg agacttattc
   337621 aataggtcct cctttagggg tctattttct ctgacttgac tcagcttgac ctacttgact
   337681 cagcggttag agtatcgctt tcatacggcg agagtcattg gttcaaatcc aatagtaggt
   337741 aaacccggcc gaaaccccag caagaaaacc tcctcaaaat atttccctgg caacctttta
   337801 agggaacccg cccagaagct tcgatttgtc aaagctgcgc taaaagcctt gaattcaaaa
   337861 gttgaaggtc gataaaagaa taagaaaggc catagaagaa ctagacgcca ttcaatccca
   337921 gctatccttt ttccagttca atgaaaggct cgcagagcag aagagtatat tatcaaattg
   337981 gatgagttga acggatacag aaaaggattg ggaccacaat atcaaagact tccacgctac
   338041 actcacagaa agaagggcaa ggaagactat caatatcagt atcaagagaa taaaggatga
   338101 gagtggaacc tgtggaagcc tacatcaaaa gaaaagacag gcggaactct actttattaa
   338161 tctagtgggc acagctagca gagtggaggg cctctataat ataataggtt aggcttcttt
   338221 cttctgggaa ttggcagttg ctttagcagc tgtgcatatc ttaactagtg ggcttagtcc
   338281 gaaaagaata ttgcctgctc ttcgtagagc aactatgtca cttctgtcta ttagtgaaag
   338341 gctaaggctc catccatccg aactttcgaa tgattcctct atcaaagtta tgaaataagt
   338401 ttgttagaga aagctaggtt tccctaaaaa agggttttct cgctcagtgt catcgttccg
   338461 gtgatcacct tcaggtcagg atactaaagt ggaatggatt gcatttcaat cttgcctata
   338521 atgttgatta ttttccccag cgtatgtggt cttgaagagc ctttcagcgg cttaataaag
   338581 gctggaattt acggaccgga ctactacgtg tcggttcctt ttcaatctaa aagagcaaaa
   338641 gcctattctc ccacctacca gcagcctaat tccccctctt tccaatccta gctctacggt
   338701 tgattcgaga aagaggaaga ggaccgaagg aacaacctaa gagaccaatc caaatccaaa
   338761 cctcacctct tcgcttcttc aacaagaaag aagaagactc ccacctgtac gccgacgcag
   338821 cactcgcggt tacttagcgg aattcacgga gcagtcacgg ataccaccat ctgggcagac
   338881 tagaaattcg ctatcgcttt tctgtttttt aagattaggc taaaaaagtg gttagtagca
   338941 ccttgacgtg ccatgatatt tactttgctt ctgtgaggcg gtaggctcga ttgttttcca
   339001 tgtgatgata gaccctttcg cccataccgt gaccacgtga agcaggcgaa gagctttgtg
   339061 tcaccatgtc aacttgtatg tgttcagcat atcatatatt cttttggata gttggacgga
   339121 agtcctatca acctacagga tctgacgctc aaaagtaccc acgcgtttcc tacgagtact
   339181 tatcatggcg gtgtagcgcc cttggcaagc cctgcaaacg acaccactgg taccctaact
   339241 tagtctaatc atagatctgt atgaagcact catttctgat tctaccaatt cccaagacgg
   339301 aaagtacttt tgatcataca ttcgcacgtg ttctatggat gcagtggtcg atccatatgt
   339361 cgtgcagagg caagggtatt caaatgtcat agttgagcca gctcatcagc atcaataaaa
   339421 gaaccttttg tatatcaatt gcgtcatcac gactagcacg gttatcatag cttcaagatc
   339481 tcatgcttcc atagctcagc tgctttctcc tttctctgca ctgtgccctt gcccagctta
   339541 ctctggtgcc tctagggaag aaaagaggct ttaaaggttt tgctactata actataggag
   339601 atgaactttt gcaattccaa tataggtctt acgaaaggaa atcgcgttgg taactttctc
   339661 gctatgggag atggaatgga tttctcgata agcccactac tgcatgggat cggtatagat
   339721 cgtgacgctc atctcaagat ctaaggagat gtaaatgtgt caaggaaatg gcatctgact
   339781 ttaattccca ctattctata atagcactca atatggtgac gaaacaatgg tgaccaactc
   339841 ccacaattga ggagcaagcc gggatccaag cccaagcagc caatgaaaaa gccacttgtc
   339901 tctgtcaact tcatttcatt ttcgctctag gattgacatg caaagtaagg acttagatta
   339961 gccgaggagc tgtggctgct ggactcgatt tgacttttgt taacgatcga ctaattaacc
   340021 ctttatcaga tggaagcatg ggatagactt gtctgaaatg agctggtcat aataggaatt
   340081 agtgtctgca ctgtctgctt tagcgtcgtg gtcccaccat ttggtggcgg aaagagagca
   340141 tattcacgct tctatataag gacgagagcc ctggaccggg ttttgcatga cagcccatct
   340201 cgcgacccta actaactttt gttctaaacg gggactccag tgcattctga agcaagtacg
   340261 tatgctttta agccaaagga acgaaaactc ccgagcaaca ctatcggtag tcaaaggaag
   340321 agagaaggtc ctacgatcat tcctaaacag aggagaggga gtagaaattg ctaaggattt
   340381 tacagaaaaa tcacagatca aacttaacac agagaaaaat gatgtgactg tttatcggtt
   340441 gagtatagag tcatctcgcg tagagtcatt tctaaaagta atgtagtcat atggtatcag
   340501 ccagtagcac taaggagcat tctatagcat ggtgcatcgg ttgactatca agagtggtca
   340561 agtccattga gaactatttc cgggtatagg agcatttcag ggtcaagatc caatcgaaga
   340621 aagggcacag ggcatgccag tattccagtt cttagcttct tggcttgggc taatcacgag
   340681 cctgggtcta gctaattggc tgcaggcacc ggtgatgaga ttgggcacct ttcgcgtttc
   340741 aaattgaaag gattccagga ccagaatgaa ggtcgtcagt ccctcccgat cactgctctc
   340801 gacgactcga cgaggtaagg tctcgagatg cgtgtccctc ttttcgtatt gattagcgcc
   340861 cggacgatag tagtttgccc ttgctgtttc ttcgactgtt gctttgtcgc attgatgctt
   340921 tccatcgctg ctttactccg cttgtcatct tgctcttgct gctccccatg tttgttcttt
   340981 tgcattggta gctctttgta gtattccatg agttgggcta aaacgctacc ctccgttact
   341041 ttgatgctag ataggtggga ttcgattgat tatgtgatgt tgccgctgct gctcctcgtc
   341101 gcgatgaaca gaccaagtta ggctaacgca atcctagtca gaagacaaaa acttctcttt
   341161 ttattcctat acttggacaa ataaggcgag tagaagaata gactgagatg cttcttcaaa
   341221 acaaagaagt cacatcaata atgggactaa ccataaggga gttggtagta tcccattggg
   341281 gggaagcagt agaatggcaa tcgcaaggtt tgacctcttt gtagctagcc tcccttctat
   341341 gtgttagtga gcgcccattt agtggaaaag cgagggatca ggtggagtta tcccttgtag
   341401 tcaaaacaca gtccgaaatc cgcctcattg ttttcgtcat cagcattgtc ttcggcatag
   341461 ctttagccgt tagccctcca tctcgattcc ggaatttggt gcagacttgg agtgacttcg
   341521 cagagggaag ggttgtggct ttgacagata aataggttgt cattagacaa atcggggagt
   341581 taggcctggc acagctgaat ctagctaggg aactaagtag cagcgggttg cggcacaaaa
   341641 gaagttgaca cttcagccat cggcacaatc caataatctc aagtcaactc agggtggcat
   341701 agagtattag ccccttagct tttagtcgaa aagtttaggc ctgatgggaa tacagactac
   341761 aaagtttgct cagcagcgga agcacttttt tttagttatc aaattagaga gtagtgccag
   341821 gcaatgaagg cccggtttat gcgagcaaga tattcatacc tttcatacca tccgaaggct
   341881 gaactaagag tgcatatgta ctatcttcta ttctttctat tctattggat tattggattt
   341941 ctatcttcta tttcatttca acattccttc taattattgt tattggattt cagcaatcta
   342001 agcagaaaag catgaagtta aggaaagcac ggaagaagaa aaggccaatg cgaagtagtt
   342061 tgccaacctt tgactagtcc cattctatcg gttaaggagg ccaggaaaga tcctcaggta
   342121 gaactcagtt tgggaacaaa aacttttccg agcccagcaa aataatcgca aggagcccag
   342181 cttcaaacta atagcccagc tccataacag gcgagcagcc aacaaactat gacccgaggc
   342241 aaggaacatt ccccatccag ctcagcccgg caagtgaaac ataaaacaca atttgcactc
   342301 ttccagccga cttctcagca tagcaggacc aaccaatcag cacatttggc acttacgcca
   342361 gcaaagcata tatgcaagtc aggctcaaga ttcacaccca aactaggctc agcagcataa
   342421 agatgcccgt ggtatagact actcgactta gactaagaag gaaccgagaa agtaagccaa
   342481 gcggcgtaga ccaataatca atgtagactt tgacacctaa caattgcact agattcaagg
   342541 aaacctacca aggaacaatc acatcgggat tagcaagtca ggctccgcat tcgtactacc
   342601 aagctaagca gaaagattac cggtaaatgg attcctttac ttagaagtcc actcacccga
   342661 gcaaggaaga aaagcaatgc aaggaccaat ccaactaagg acaatcaaac aataccagca
   342721 tgggagaaaa aggagactca tcacattcca tcagtcactc gagtcaaagc ataaagcaga
   342781 gcaatcgtac tccactcaag aataatccca tcaaacaaaa atgggcgatt cacatttccc
   342841 ttccctcgac ctggctctct tcaacttgtt tcgaccggct tctatattct gaatgtttca
   342901 accaatttaa ctttcaccct tatcgttcta aatgatcttt ctctttgact tcgagtttca
   342961 gtattcgtgt gacttatgct ccacttgatt agcgtagctg ccttagcttg ccccgacttg
   343021 actgattggc tgggttcgct tcacctcgct cggcttagtt ggaggactac agaaagagaa
   343081 gcatgacaag catgacgttc cttaattata tctatatata gttaactatc cgtatatcat
   343141 agtaaggaac cgaaaagtag ttacccattc acgtacatcg gttgtgtcga atatttgtaa
   343201 tcaatcggtc aaccagacat cacgtaacta ttcagatcca acttctagaa ataggtttca
   343261 gtcagctcga tgaaatagac taatattgac catttatgtc agatccaata gcttgcctcg
   343321 aatgccagca tgaaacctaa ttacgatagc ggtggcgaag acttgaagta atcacttttt
   343381 cctggacaat cggccagcta aaggtcagac ccaataatag cataatttca cccatcagtg
   343441 gttggtacca gtccgtaaaa gtccagcact taggtagcag ccccatcaac tgtacaatac
   343501 cgacctaaca ggaccagtat ccaccataaa aaccgtagca taacaagcta ggttcccata
   343561 gcatataaag gtagggccta gtctaataga ctgaagcact aatcacaagg aatcacaaat
   343621 agcatcccat ggacaagtat ttcaccaaca tacagaggag cggaccaatt tcaacgagta
   343681 gacaaatcca tttgaaaaga caactaaaga tttattaaat ttccggttaa cttatgatcc
   343741 cggcctagct cgtcttttct tctataatag cttttggtca ccgctaatca tcaggtgacg
   343801 ctggtcaaga tcagtactct tattaacttt ctgattggca ttagtataga atgggcgact
   343861 aatataatag aagcatcaat ctaaaatcaa caatcacaag tatctacatg tttactcaat
   343921 gcctggacca ccttaactac tatgtctagt cttcaaaatg cctggctacg ctataataaa
   343981 ggcttgcaat gattgtgatc tcttattgta tttgatccta ttaaagtatc atgagaaagc
   344041 tacgaatgtt actatgcacg cataaaaaga agtgagtcga atatcttgag tgagaaatat
   344101 ggtagcttta cgtgctagaa tggaccaata cattataaaa aaggatctct ctttgaaacc
   344161 tttatagacc ccaggcttca aaccggacct tagaaccctc caagctcaag agtacttatc
   344221 tagacatcgc aagtcaggct caacagtcgt actacaagct cagcagcaat atgaccatgg
   344281 aatggagtca ttgagaagaa agggagatcc tacctccaat acgagaggga atcgtacgaa
   344341 aggaacaaac tcaacttcaa gctcttagcc cagcagcaac aaactatggg attggtccga
   344401 gacaaagaag acagaaacag cccggcccag taccaatatc atctaacgaa ttgtacgaga
   344461 aagctaccaa tccagcccgg ctcagcaagg cgtggaaaat gaagcacatc gggtccacat
   344521 gggacagcgc aagttagact caagattcgt accatccacg actgagtgaa gtaggacgaa
   344581 agcaaccaat ctaactaaac tagatagaat aatgtttcaa ctaattaaac tataaacctt
   344641 gttcgttctg aactatctcc tttcttcgac gttcactggg ttggcgtgac tggcttaaac
   344701 tctctgaaac ctgctattat atcaaccgat gaactaacta tctcttacat atctctatat
   344761 agaatagatt atctataatg tttgattctt agtctactgc ccgtttaatt cccttgactt
   344821 ggccttactt cttttccttt cttcgcttgg gcgttcctat caaaagaatc tgtcatgcca
   344881 aagacccaat ccatgaggta gtccaccgat ccagtaaacg atggaaatgc acaagtcctg
   344941 aaagcataag accgaagtat gagaccgagt gacgagcaaa ttcagtattt ttgtttccca
   345001 ggaaaaaagg aaaagggggg cgagagaagg aaaggggaca cagtggtgac aaggatgact
   345061 caggtcagtc ttccacccat aagcaccatc aggaaaaaat aaaggaaggt agggacaagc
   345121 ataagccacg tgagcttcat tctttcctat gcaatggacc tcactgggaa ggtaataaaa
   345181 aataaaaaaa aaaagccatc cactctctca cagacaagct aagtgaggag gagccagatg
   345241 aggagttggg atctatacag ctgatcaatg ccatggccaa atcaaaaggg ctcatccacg
   345301 ttgaagtcgg aatcaatggg aagaacactc gggccatcat aaagaggtct caacgagcca
   345361 ctactttctc tcagtagagg aggcaaagac aaacggattg aagcccaata aggaaagagt
   345421 ctgcctcaag cctgtggaaa agcccgtaca aggtctgact cgtgcggtgg agctacacat
   345481 gggtgattgg aagggcaaga tagacctgac cctataagta caatggttgg tccctccgga
   345541 accggtaatc tccgtttgac ttcctttcag caggtgcgca gaagtattct ttcacaagtt
   345601 tgacgcaagt cgtacctccc agccccctta gctacttgta ctaaaaaaaa ctaggacgga
   345661 agttgctaat cagaggtggg cagggttcct ctccacactc tcaaccttaa ttatctttct
   345721 cctctgtggc tatagcctcg ggttcgtatg gatgaatcaa ccgactgtgg aattttcttt
   345781 gcctttgcat ctccgtcttt cgcgtgccat ggaaatttct ttgctttctt caacccttac
   345841 ggacctttac tttattccta tctgtgtggt tactcctagt acgcactgtt taagtatccg
   345901 gtttccttaa ggcctagatt caatcgtatt tttgatactt gggagatatc cgacgagtac
   345961 ctgtttggca aaccaaggaa gctgtatact caacctctgt cccgaaagta gctttaaggt
   346021 ctaatgaccc ggatcgagta cactgattca atctttccgg tcttaacacc tctactaagt
   346081 aagcagctcc attcaatgac gatctgtcta aggagtcttc cgtcgtcgaa gtgattcatt
   346141 tattctgtca gtgggctcat agatcaagga gtgtgcagca gcacattgtg ctaaaagccg
   346201 gttatcgtgt ctgcctcttt cctctctagc cgcccttcag gctggtctat ccaaacaaaa
   346261 agcagaaaaa gaaactctag ctagctaaca aacctttgct ttctctaaga ctccgggtga
   346321 ttgtactggc taaccttttc agaggagaaa cgccgagggc atcaagagca gaataaaaaa
   346381 caaggcatgt tcaatgagaa ggtatgggat aaagacccaa gggatattct aacgacagat
   346441 acgttctttc gatacggaga aggggctcca aggttcgttg agaccaaacc aatgaaacga
   346501 ttcggtagtt aacaatcttt cgattgagct gctatcttat tgaacgcaga gagtggctac
   346561 tgcttcaaag ctttgaaaag gagctgccct tctctatccc gtactcctat tcttcttttc
   346621 ctctaataat acaaagcatc tgtttgtagg taaacaggtc aagcactatc ttcagaacag
   346681 tgagaagatg cctaaagcta agaataagaa cgagggtaag aatcgacgag gaatcaataa
   346741 gatataagat aagtgaatga caaagcgtga gtataattct caacccgaga tgaaggagga
   346801 ggtgttagcc tacttgctgc agctgtctgc gtcgctagtt ctgccggtag ccatttggct
   346861 gattgctgcc ggacagattt ttacctgttt acgcggatat actatctcca attaccaaga
   346921 aaaagtagag gagaagctct gctcgacttt agtagataag atttcagaga aactggccga
   346981 tttatttccc gtatatggta tcacgccgtc aaggaacgca ccctttccta ctattctcga
   347041 gcaattgctc gccacagttt cgcaagagga gcgcttggcc tacctctcca atatgtataa
   347101 cagtttgata gaaatgggta tcgacagccc ctgtttttat cccatagttc aaacatttct
   347161 ttttctaatg ggcggcggcg gcgggcccgc ttgacctcaa ttttccatac ccctagcccc
   347221 cggatgtagt ccttgcttag tcttctagcg gcgaaccggg taaacaacgc gatccgaata
   347281 aaaggaagtt cgctgggatt gtatttattc attttccaga ggtactggtt cgactccagt
   347341 tcgcgactac cgtgatttca ttttatacga gcatcaaatc aaacctgtcg gctatttctg
   347401 tttcatctct ttctaatctt cgttgcgtgc aaattcatat ttctcgcgga attctccatt
   347461 ttatagatct cagcaaacaa atgtacaaag tggatcgcct agcaaacgtt gctgcctatg
   347521 atatgccaac aggttcgaaa gaagctttct gggaagccat cgggaccagg ggatattctt
   347581 ctcgaagacc gtgcttttga tctcgtcctc atctggcata gcagttagga aagcattgtc
   347641 atcctcggat accactggag gaatcgattc caggagttcc ggatgggctt tcctggggct
   347701 ggaggtgtac acaacttatc aaagaattgg aatatgtact aataaatcat gttggtcatc
   347761 ttggatttcg tataaagagt ttttcgatct atgtatttga cccgagattt ttgcttccac
   347821 atcctatatt gaagtcacaa cgcattatgg aggtcccttt tcagctgtaa tttatccctc
   347881 tcccgatctc tttcttctcc tgctgttcgc ttcgcttctt tctttcgtta gcttcctttc
   347941 ttttctcctg agaaaaagat tgtttgttgt ggcatgcatg actaagccac ctttcgatag
   348001 cctcggactc tacattaatc tggttgggag taagacaggg ttagaagcag acaagaagga
   348061 gcagaagagg atctttgtta tctgcttact ttatgtttga gtttgatctc tgacttgtct
   348121 aactccatct gtactttagc attcactaat ccatcacttc cctatcttat ctatcttaaa
   348181 tccaacttgg cagtttccct gaccacccat aagaaaaaaa aagatgatta aataggcata
   348241 atctaaagga aataagttta ttagaataag aaagaaaaac aaaactaaag aaaggatttc
   348301 ccaatctatc ccttgcacaa aagactactt agaacgctca taaaaaacac agaagaataa
   348361 gtcatcgaag aagtaataat ggggtaggaa gaggtaaact aactttattg ctagtctttg
   348421 tctttctagt gtcctcaatt gtccgcctct gaatggcttt gtcagagctt tctgtcgttc
   348481 cgttccctca ggtcttgggg gagtagagct gcttctttca actcggagga acacacctca
   348541 ttggagaact tgttgtagtt tcaggtatga ctaggaaatg caatatacgc taggtcaatc
   348601 cattcctata aggccggtga gccgccgtta ggccgttaag gctaattaca tgaagggatc
   348661 caagagaagg taggtatgga attggcttta gtgctctatt aggtaaaggg gtgctttagt
   348721 agcctcccct cactctcctt gacccgtgga caaacgccac gtgatggacg gcgcccggct
   348781 ctgacgaaga accagtaaga ttaggtattg cctaatccgt aaggttgtca tacccttatc
   348841 agctttctga ccaatcctcc tatcctatgg gaatgctttc ctaaactctg attgctcttg
   348901 ccgactcgga acgaaaagat agcgagggat tgatagattc ctcgttggat tgggagacca
   348961 actcggaaag aaagaaagag gcttggatgc tagggatagc ttgaagaacg agtaccggga
   349021 gaaaggacct tcttttgagg aatgaggatt aggaagctta ctcgtagaaa attaagttgg
   349081 cacctactaa accaagtgcc tgaaaagggg tagtgaaaaa ggagaaggca atctcggatt
   349141 gttcagacac tgcctttggt tcattacccg ttgagaaggc agtagaagag gtagcattcg
   349201 cagaccaaag caaagacggc tggggattct tcatagcata gcaagaagga agggcgtgct
   349261 taatatataa ggactagtag aggcagtaga ggtccttcac catgaagatt gtatgctttc
   349321 cttttttcac tcaacaatga aagctaaacg aaaccgattc caatctcttt tccattcaga
   349381 aagagaatcg attatgtagc tcacagaagg ggtgatcaaa gaagttgact aagtgaatgg
   349441 gaatccgata gctctaccag ccttggaaga gtagtcagag gcaattcgct aatatttaac
   349501 cttttctatc atctttcttt cctcaagcat gaaacggagt tgagcggtag gcattccttt
   349561 ccattacagt gggaaagcgt atgcgagtca tagagttctt ccagtaaggt ttgaggtcac
   349621 aggtaccgat gcagtggaaa aggaaaacta ggatataaac aagacccatt tgtttcaagt
   349681 ttagggcccc ctagtgttac aagctactgc ttgcgaagga aagaaagagt tgctaaagct
   349741 ccatgaaaat agtctcctta agataaccat gcataaattt ctaaaagttc tgttaggttc
   349801 ttagtagcag tcggcgacct tttcttcttt tacttcacat agcttttcgt ctccttgata
   349861 gctggaagtt ctccaaaagt atgaaaagca ggaggacttt gtaccatcca ttccagtgta
   349921 gttgaattca gttcaagagc ccaaggactc ggagcacatc ttttgttatt tccactgctt
   349981 aaagtgattg ttacgaccac gaagaaacaa caaatcccaa ctacggatat ataagagcca
   350041 aaactggaaa gggcattcca tccagcgtaa gcatccggat aatctggaat acgacgtggc
   350101 atacctgaaa gccctaagaa atgcatagga aagaaggtca aattaacccc gaaaaaagtg
   350161 atccaaaaat ggatttgacc taaagtttca gggtatgtcc gaccaaagat tttacccacc
   350221 caatagtaaa atcctgcaaa taaagcaaaa acggctccca tagaaagtac ataatggaaa
   350281 tgtgcaacca cataataagt atcatgtaga gcaatgtcta gccctgaatt tgccaggact
   350341 attccagtga gtcctcctat ggtgaacaaa aagatgaatc ctacagcaaa taacatgggt
   350401 gttttgtatt gtatcgaacc cccccacatg gtagcgatcc aactaaagat tttgattcca
   350461 gtggggacag ctatgatcat ggtagctgcg gtgaagtagg cacgggtatc tacgtctaag
   350521 cccacagtaa acatatgatg agcccaaaca agaaatccta agacaccaat actgatcatg
   350581 gcataaacca tgcctagata cccgaagacc ggttttcccg aaaaagtcga aacgatatga
   350641 cttatgatac cgaatccagg cagaatgaga atatacacct ctggatgacc gaagaaccaa
   350701 aagagatgct ggtataaaat tgggtctccc cctccagcgg gatcaaaaaa ggttgtatta
   350761 aagtttcgat cggttaataa catggtaatt gcccctgcca gtaccgggag tgataataaa
   350821 agtaggaatg ctgtcactag aacggaccac acaaataggg gtaatctatg catagtcatt
   350881 ccaggtccac gcatgttgaa gatagttgtt ataaaattga tagaacctaa aatggatgaa
   350941 acaccagata gatgaagact aaaaattgct aaatcaactg ctcctccaga atgactggta
   351001 ataccactta agggcggata gaccgtccac ccagtgccgc tacctacttc tactaaggct
   351061 gagcttaata ggagcaagag acttggtggc aacaaccaga atgaaatatt atttaatcgt
   351121 ggaaatgcca tgtcaggtgc acctatcaga atcggaacaa accaattacc aaatccacct
   351181 atcatcgccg gcataaccat aaaaaagatc attaaaaaag catgagctgt tattaaaaca
   351241 ttataaagtt gatgattccc accaagaatt tgatcgccgg gtcgtgctaa ttccatacga
   351301 atcagtactg agaagcatgt gcccatcact ccagcaatgg caccgaaaat gaaatagaga
   351361 gtccctatat ccttgtggtt tgtggagaac agccatcgaa ccagattttt cataaatttg
   351421 agattctttc gtttattacc ttatcagaga ggggttaggt atttagtaac tctcgcgctt
   351481 tcctggaacg ggttccatag tctacgagtt cttgagagtc ccgtggaacg gtcaaatttt
   351541 tgctagtaaa ctagctcaag caggaaattc caacctagct gatggttttg ctaggaacgc
   351601 tagctcatgg caggaaatca taccttgcct gattctcctg cgtaggagag cccaggccta
   351661 ccattggatt cgaaccaatc agcatcgtcc tacaaaagat aatgctctca ccaattagag
   351721 aagtaggaaa atacaacaaa cacatttcga cagaacataa ttattattat ataattgaat
   351781 aaattctcag gaaaagagaa acagtggtgc aaactctact acaatagggt ttcacagatc
   351841 aaaactttct tcctcgaatt gaagttttgg gagctacatt ctatattaag acaacccaga
   351901 agccctagga ctatactcca acaagatcac ggaacggacg ttacgaccac tcaacaaagt
   351961 ctcgacaata cacccaaata atcacaactt ttttcttcgc tacctttagt attcggataa
   352021 acactcggac agtattgaca aatcgcgtgt gttaagcaaa tcacaagact tctcttttct
   352081 ttgcctcatt tgaaacttct ttattaaacc tgacttcagt ctatcatttt aagaaaagga
   352141 agactcttat taaacctgag ggaaagtata gagttatgac agaggccaca tttcatacac
   352201 tttaggcagg tgaaacactt caaacaggaa acacttacag aggaacagga aacagctcac
   352261 cttacagagt tacgcacaac agagaggcag cgcggggcag tcaaggaaca cattcggctt
   352321 tcacatacaa ttactttact taccttaccc tacagtctta gcgaacctta cagatccttt
   352381 tacaaacctg gaagcggggg aatacctatc aacgggggga cccatccgac tcttctatat
   352441 atatgcccgg gggacacaaa gaacttcttt cgggatccca gtgcgagtca catcaatcag
   352501 ctttctaaca accactcgta ctattttcac acaaaagatc cgccattgat cacttttcgg
   352561 tcacaataca gacatttagc aacaggggag attagagact atcgaagtaa gcccgaccta
   352621 ggctgaaacc agcagctaca accaagtcag ctgaaagcag tagctatatc taagctcagc
   352681 tgaaaacagt gacacttcaa aagctagcgt tcccagttcc gatacaagac aaccaaggag
   352741 gttcagaatt tagactatcg aaaggacctt tagccgctca tacgtaacgc ctcctcggtt
   352801 acgccttccc tcgcacgggg cgccactact gagctacaaa caagctcggc agaagcagga
   352861 ctaagtacgg ctgaaagcag gtataagact ttagacggag gagcccaagc taggctgaag
   352921 gcagaccaag cggaggctga aggcatacat tcactcagag ctatacgcgt tacggcagct
   352981 gctaccttcc ttcaaaggag ataccaaata gaggctgaaa acaaccaagt aggctgaaca
   353041 gaacaatcta ggcagaagca gcagaccggg agtagatcct tagctctttg cccgggggcc
   353101 ccatagaact tcttgagcgg aaactcgaaa cggggcggat ctacagaccc tctttcacgg
   353161 tgacagtcca agtaccatca gacgggggtg caagtactca cattatcacg cggggcagag
   353221 ggaccatctc atccagtcaa tacgggtcca ccacttcatc ctccccagcc atcgggtcag
   353281 ccatgccaaa cagctaggac atctcaggac cggtcaacca gaggagatcc atcgccaaca
   353341 ggggctccag tacaaacagt agggaggcgg atagaccatt tgtcagttcc aatagccaat
   353401 cagtcaggct atttagcagt cgggacatcc ggaacattct actaaaaacc atacgataca
   353461 gatttttatc tatttaaaac attggcatca tccgggagtg ggagtggtat acctcagact
   353521 ttgaggacct gaaagcagca gaactagatt tggtggacct tcgtagcgga agaataagac
   353581 tttcttgacc ttcgaagcaa cagttttacc tgacatccca gtggcagcat tctttgactt
   353641 ggaggcccta agcgatcgtc ctacctcgaa aggagtggca gcagcggcag gaatacccaa
   353701 gtcatagtct ttttcgggag agggctcggc atagtcttta tgcgacagta ccagcatgcc
   353761 atagtcttta tgcgacagta ccagcatgcc atagtctttt atgcgacagt aacagcgtca
   353821 tagtctttat tatgcggctt cagcagcacc cggttaggac ttcaaccaca gaagacccgt
   353881 ctttgccttc acgtcagaaa caacaacgca ttgaacttcg accgcttgac ttccaacaga
   353941 agtggatgat tctttcgcct ttcttcgttg acctgacacg acattcaaaa tggagagtcc
   354001 caatagtcca gaggtagcag cacgatcagg gaaccaaaat ggctgtctcg cgcttcgaag
   354061 ccacagcatt tagagggccc ttggcacatc ttgcaatgac aacacgtctc accacccaaa
   354121 cttggttttc gacggcgaat cagcaatgtg tgtcaagcaa ccaattctgc tcctaggcca
   354181 gttctgatct taggaattcc ctgatccaga atatctgagc cggaaggtgg cgttcaaaga
   354241 cttaaacgag tagtgggcca aagggctcta taatgatagt tcgccctcag cttttgtcca
   354301 ggattggcat tctcaaagga gaaagatctg atcagggaag gattgatcga tcaagatcag
   354361 gaagaggaga acgaggaaca attaacgaaa gaaggggaaa gggctaaagc atctgcttcc
   354421 acttccgctg cagaagaagt tgggggaggt tacaaagccc ttatttcaac agactgttaa
   354481 ccactttaat gcctttatcc ggctttgcaa caaagtgatc ttcgatcgca ctaaggcgca
   354541 taagacagta cacttcaccg agattcacca agtaacccta cggaattgat gttgtgacac
   354601 ttgaaacgca tgaaaggaat ctaggaacaa aacaaagagt tgcacccctt gcatttgaat
   354661 gccggtatac tgctccgcca ctcagggcac actaccaaag gactccaatc ctcatcattg
   354721 ggcaattcaa gacgcaagtg gtgtgtatca tctctagcct cctcggtgat gtttcatatg
   354781 ggtcactaga atctccatct ggggccgaag aacgtacgat caaagacttc tgaagcgtcg
   354841 tctaaaggct ccgatctaat aagttacgtg cgtgatgtcg atgagatgtc ggcaggagat
   354901 gtcggcaaag aaagaggaag gcgcgcagaa ggtaggtaat agatctcata ccgaacgtga
   354961 ccgagtccac ccaaccgtac acgatccttg agtcaagtat gcgaatgaaa aagaaggagt
   355021 aattcgagca ggaagaagaa aggctgacgc tgcagcttca acttccgctg caaaagacag
   355081 gggatggggg agtttcaaag ccattcttat aacggattac tgtaccttat atacctttat
   355141 tggctttttc aactaaaagt gctccgctcc actaccactc ataaggttcc gccactacaa
   355201 tagggcacag tcataagaga atcgagagct ttatcctggc tcaggcaaac ggaactacct
   355261 taggtctcgc tgggaaccca gctcaggaac ctaaaccaca gtgctttctt aaggagttgc
   355321 cgagtcctac ctcgctatca aagatactaa ctgaggaact cacctatgac ccaagggaag
   355381 agcctagaag aaggtttctc acgttgatcg tcacccctgg gtctaagaga cccccaagct
   355441 gtctcaccgg gatcgaatcg ggctcacctc ggatcaggaa cagctacaat atacgccgct
   355501 taaacaagca gattaaagga aagagaccca tctatctaag gctaaaagaa gggaaagaag
   355561 ccgtagctag tcgtagaagt cagtgaaggg gaacaagcaa gccgaaccgt aggcgagcaa
   355621 agctttcatt caacagcaga ggaagacgta gaaagaccag caaaaagaat gaacacgtgc
   355681 caagaaccca ttccattcac ggacgcgggg aaggaggaaa gtcaaggcac aagtttctct
   355741 attaagaacc aaggccctac tgagctacat ttactcttta caccaagaac agctcagata
   355801 tgcgaccccg gggactgggc tttggtcttc gaccgacggc tcctttttcg gcatatgaag
   355861 caacaataaa taaaagagaa ctacagatga acgaagggaa gaggtagatc atacagttca
   355921 aactcaaaca acaaagacat tctaacagtt gcctcgcttt catccttata agtggacaga
   355981 ctcatccgca ttctccgctt tgaacagagt ttgcttcttc gttcgccttc cctcacacta
   356041 ctgagctaca accaagctcg gcagaagcag gacagagatt taagaaccgt gaagtgagcc
   356101 caaacaaggc agaaacagca gctgcaacca aataggctga aaacagtgcg gcagcactag
   356161 ccgtccccag taacagcagc agtacgagca ttccttagga gggtcaaacg acggactacg
   356221 tcctatcctc aggtgaatac ttttacttca gttggatact ttgatagttc actactacga
   356281 taggggaata ctaggctagg gaatgggaac tacttgggaa gtcatctctt tacttaacga
   356341 actaaccact cagggattca aatccacgat actcctacca tctgcttgat ccagttgaaa
   356401 actttactcc gacttcacat cagcccttag ggtcaacaca gctcctctta tcctttactc
   356461 tttctatgcc tggattccta tgcctgtttt acctcgagtt ggaattcagt gggagaaatt
   356521 ccaacaaaat tcagtgggag aaattccaac aaaattcagt gggagaaatt ctccagaaaa
   356581 cgaaaacggc gattccaact ctacaatcaa ggcagaacgc agggaggaga agagaataga
   356641 ttatagacgg cggaccggac ccaagctagg ctgaaggcag gactctatta agtacggcta
   356701 aaggcagact ctattaagta cgactgaagg caaaccaagt aagtgcggtt tcaaacaaag
   356761 gtgaaggaaa ggtacgatcg gtggacaagg aatcggttga gatcgaaacc atattcgtag
   356821 gacgcgtacc caatagcgtt tccaggggcc tcatcccggg ggcaagccgg ggcatcagta
   356881 cgcgctaggc ctatcactcg gagcccgggc gatctactcc tactctttat ttagaggcgg
   356941 gaaatcttac tcttcttgag cgggggatag accaatcttc ttcagcggga aatccaatcc
   357001 ataccttggg ggaaatacat agcttggtag acaatccata gcttggtata caatcactct
   357061 acttcaagtg ggctaactta ctcatctttt gggattggtc tttcttcaat gtataagtgg
   357121 agtaaggtct ttttccccac cgaaagaaaa gaaggtttcc attcccattc cagtagtaag
   357181 aaaagatcag aggcaccgtt gcctacttcg cgggatcgcc ttacgtagaa ggacttgtga
   357241 tccactctcg gctaagtttc tatggtcggt cctctctcga ttaatagcta actggaaaga
   357301 gaatcctctt ttatacttaa ttatcgatca agagggaagt tcctaacgtg ttcttaggaa
   357361 cgaaggtctg tcgaaggcgg gcgaacgtgt ctttctatgg tacgctcggt acgccttgtt
   357421 tctattgttc tccgatagct ctatcagtga ttatttaaag tagtgctttt tgtctgttac
   357481 cggatatgta tagaagtttc cttatggtat tcctctccgg tgttgctgaa tacacgtcac
   357541 cggttcgact cctatttata tttagtggtc catttattga ttgatgggcg aatggagctc
   357601 gggatgctga aaatgtaaag gccaaggcct ctctcggttg ttgctttacc tgtcctatta
   357661 gactagctag gccctccttc ggtatgtctt gttccttggc ttctccttgt tggaattcat
   357721 ggttgattgt aacctaaggg ttgttatatc actgtccttc tgtgggggag aaagaggggg
   357781 tgttgctagc tcggtaggca cacaggcgcg ggttccggtt gaagagtcaa attctccttc
   357841 ttgtttttat tgtgagaatc tttctctata ctctatataa gatgccatct gttttcttta
   357901 ctcgtttcct ccttagcttt gaatctatct gtgactgttc tccttcttct ctaaggtctg
   357961 ttcctttgtt ccttctttgt gccttcattt gctttctttt gtttgactgt taacttaaag
   358021 tatctacctt cttcctttgg tttcttgtag ttctatcagt tagttcttca atggttagct
   358081 ctgcctgagc tggagttgtc cctccagcga gagttgcttt cttccttgct tgatcggtag
   358141 gagttgccga gatagcaggt attagctgtt agccgtcgga ctcatttaaa ggagtcctat
   358201 cgggctacac tagtctaagg gcagttgagt aaccgattcc tacgcttcct ccgcttacct
   358261 ccgtcgctta actattaata cgtcgcttac ccgcctccgc ttacccgcct ccgtcgcttg
   358321 ttatctgctt cccttagcta aaacgttagg cgatagtgaa agccttcact ctcttatatt
   358381 tacgtacacg tgggaagaag acctagtaat tgagtgacag cattcctgga ccaattctat
   358441 aaacagccaa tcaggcatat catggtacag gtgaaagaaa cttatccaat acagatctta
   358501 tcacctgccc atcaacgctc aaccgtctgc tcctctcgtg cgtgtaggaa taatcaaaag
   358561 aggagacagc atgcctatta ttaagaaccc aattctacta aaaacgataa caacgattcg
   358621 aggttctcaa tcaaggcaga aagcaagaaa cccatccagc taggaggaaa gcaaatcaag
   358681 gagaccaatc agacatctag attctatagt acgcgtatgt gtacgtaccc aggctaaaac
   358741 agcaaatcaa acttggctat cgtttgagag caacctatcg ctaaacacaa accaatcctt
   358801 ttacacagtc cattgaaagg aagaaaacaa gggtggaaat tcatgttcct ttttacacag
   358861 acctccaaaa ctcgaatagg ccaatcttac ttttcctcat tctagaggtt gcaagggaag
   358921 aaaacaagat tggttcttta tgaaacctgg ttcaaagcaa cgaactccgc tctctcccgt
   358981 gggcacattc ctattatagt aaacggggac ttctctcttt attcctatgc gtgctttact
   359041 tgactcctct gaattcagaa caatgacttt taggctattt ttccccaccg gcaagaatga
   359101 acttctatgt gttaagcaaa gaagaacaga agatctattc cagtagttag gtacaatctt
   359161 ggacggccgg ggacctactt cgcgggaccg cctaaaagga cttggtccac acgcggcgaa
   359221 gtttctttgg gcggcgtttt atcgattgat atctaaagtg actggaattc gaatcttctt
   359281 atataaggaa ttatcgatta taaacttctt atataaggaa ttatcgatta taaacgagga
   359341 tgaaagaagt taggaataaa aacccgatgt tgtgttctca tgcccggtcg aagtccaagg
   359401 ccaacccggt ctgttgccaa tgagttgtga ggaagtccac cgtcaagtgc gggatgtgag
   359461 gccacgtcaa ctgtgtatgt tgctgcgaag gtcaaccaag tcgaggaatg cgctgcggaa
   359521 aaaataaaag tcactgagga tttgccttcg cggataccaa ttgcttggat ggatgcgttt
   359581 gaaagcctcg agatgacttg cagaaaaaat gctttctagg tttgtcttgt gtctccgtaa
   359641 caaatggtcc atttattgat taatgggcga acgacgggaa ttgaacccgc gcatggtgga
   359701 ttcacaatcc actgccttga tccacttggc tacatccgcc cctaccctcc ccgcccttaa
   359761 ttttgtttca ctgtcataaa acctattaaa caactcattt acatttgtat cttagcacca
   359821 aactaaaatg aaattattct ctgcctaatc attaataatc attaatgaag gggcccgcct
   359881 caccactcca cttccccttt ttatggaagc aaccaaactc accatgacaa gggccagcgc
   359941 tcttacagcg aaaggctcct tttctctagc caaaaacatt atgccatcaa gccaagccag
   360001 ctcccgaatg tctttaatcg agagaggtac agaatagtcg aagaaagtaa gcaactgcga
   360061 caagaaagga cttataagat aacatggaaa atgagatttc acttctagtt atccgccaag
   360121 gaaatgccgg aggaattcta tatatagctg agcgatgacc gtttcgttgt gcatcttgga
   360181 tacagtaccg aaggtctgct ctactaaaac tttgtcataa tgagagcggg gatcatgaag
   360241 attgaaacta ttcatgttgt tttctataaa ctccaaggct tctggtctta tggcccaggg
   360301 tgattgagat caaattttga ttaggcgcgc atccggttcg tttaccaata aagtaaaaag
   360361 tttattttgt aaatgtgctt tccgctccat tattataatg tcgaatagct cgttgtttag
   360421 ggcactttga tagtgatgaa tgttgactgc gtggtccaaa taatctctga aaaaggtttc
   360481 gtatttaccg aagtggaggc aatccatgaa ctaatttttg aggtttcgta tgcgcgaaaa
   360541 gagtttcgct ctcaacttcg acgttctctg ccctatattg tccagccagg gatgtaaatc
   360601 aagttggctg gttaaaaaca ttggtccagc ttaagcttga cgttgaatgg gaatttagag
   360661 ttccaatcca gctagaagaa gcgttgttag aagcggcaaa agctatgaga ttcgaatcat
   360721 aggcaaggag ttgtgtcaag aaaaaacaaa agacaatcga aatggacaat cgacggatgg
   360781 caaaaagatc caataactga gaaagacaaa acaaagattc ttttcgataa aatacaaata
   360841 agacaagata tatgagcaag aaatctgcca aaggtcttcg agattttgta tttatatgtc
   360901 gctctattaa cagagccgtg tataccggaa aaaaaaataa aagcgttatc gggtttgaac
   360961 aactgagttg ttataatgtt ctttttcatt ttaataaagt gactccgtcg cgatgttttt
   361021 tttcctcttc ttatgaaata tgaaattttc attttatttc ttcaccgggc ttggaccatg
   361081 tctcccgaac aatctcagta catatggcgc aagacgattc cacatatcga ggtcggaatg
   361141 ggatcgggtg ttttcacgtc tcaccgtagt gcccggtttg tcttgatttc cgattgatga
   361201 acaagaagga aaatggaact attggattta gttgtgactc gcccccggct acctgtccaa
   361261 aggaccaaaa gcccgcccgc cgccagtggg tgggaaggaa gctagccccc tatcttggtt
   361321 gggggaagag gaacgaagtc catcgcgaag gattcaatcc agccacaggt tcccctacgg
   361381 ctaccttgtt acgacttcac cccagtcgaa gaccccaccg tggtatgcgc caataagacc
   361441 accaaaagcc tttgtggcac tagtggtaca cagaagtcat gggtgatcat tggtccgatg
   361501 cttcgggcga aaccaattcc cagggtgtga cgggcggtgt gtacagggcc cgggtacata
   361561 ttcaccgcgg catgctgatc cgcgattact agcgattcca acttcatgtt cccgagttgc
   361621 agagaacaat ccgaactgag gcaatctttc cggattcgct ccgccttaca gccttgcttc
   361681 ccattgtaat tgccattgta gcacgtgtgt ggcccagccc ataagggcca tgcggacttg
   361741 acgtcatccc caccttcctc cagtatatca ctggcagtcc ctcgtgagtg cggcacgcac
   361801 ctttttgttt gtttcggagc cgttttggca gggcgtacta aacccactta cttcgtccca
   361861 caccaccggg cggctcgcct gaatgccgag tctttctccg ccgccaactc gacgtcgtcg
   361921 tcacctgggt caaaaacttg actttactaa acaagcgaga aaagcccttt cgcacttctt
   361981 agtaaagcgc ggcgctagct gcaatcaaac tcaagcgcag actagaaagg gcttggaaag
   362041 gcgccgtctc ccttcttact gagagcagag ctagttgctg tcactcaatt actaggtctg
   362101 gcacgtcact cggctccttg gctcacttcg gttttcaagc ctttctcctt aggcgcatgt
   362161 ctgagcaaca caagacgagg gtttcgctcg ttataggact tgaccaaaca tctcacgaca
   362221 cgagctgacg acagccatgc agcacctgta tgaaagtgag taccatcccg ttaaggatag
   362281 gttttgttgt tcatatgtca agggctggta aggttttgcg cgttgtatcg aattaaacca
   362341 catgctccac cgcttgtgca ggcccccgtc aattcctttg agttttggtc ttgcgaccgt
   362401 actccccagg cggagtgttc acgcgttagc tgagcccctg atctgcgtag accaagggcg
   362461 aacactcatc gtttacggca tggactacca gggtatctaa tcccgttcgc tcccccatgc
   362521 tttcgcaccc ccagcgtcgg tagggaccca gagagctgcc ttcgcttttg gcgttccttc
   362581 gtagatctgt agatttcacc cctccacacg aaattccact ctcctctgtc tcactcaagt
   362641 gaattggttt cgaaagcatt ccgccacttt ttggcgactt tcactttcaa cccgattcac
   362701 cgcctacgtg ccctttacgc ccagtcattc cgaagaacac ttgccccccc cgttttaccg
   362761 cggctgctgg cacggagtta gccggggctt cttcctcgag tcctgtcatg atcgcgcact
   362821 cgacgaaaga gctttacaag cggcattgcc tttcttcact cacgcgatat tgctggatcg
   362881 gctttcgccc attgtccaag attccccact gctgcccccc gtgggagtcc gggccgtgtc
   362941 tcagtcccag tgtggctgat catccgaaaa gaccagctaa gcatcattgg cttggtcagc
   363001 ctttacctaa ccaactacct aatactacgc aggctcatca aacagcgctt tttagctttc
   363061 ttcaggattt ggcccgaact gttcggcaga ttcccacgcc ttacgcaccc gttcgccact
   363121 ttgttctcaa ctcttcccgc ctcctgggcg agacaagcta ccttgagcta ggagcctctt
   363181 ttccttctgc ctagctcccc gagaacaacg ttcgacttgc atgtgttaag catatagcta
   363241 gcgttccttc tgagccagga tcaaactctt cttttgacta tgattgggcc ctgcagtggt
   363301 agaacctcgt gaaccgggcg tactacttcc caaccttctg tggacctttc ttctcttatt
   363361 caattccact ttgtttagtt tagtgatagt tagaggttag agaagagagc tagatcactc
   363421 ctctaagcag ccttctgatt atatacgtat tattctatca atcgataagc aagggtaggg
   363481 ttcctggatc ggtctcgacc agaagaccga gaggtacttt tgtcacgagc tggcttaacc
   363541 cattccctta acaccaagcc tggataagca actgaaaagt caagtagaat ccctggcttg
   363601 tgtaggcgag ctaaacacaa atctttcttt tcattttata tagatggaaa agtaagaaat
   363661 cctattttcc ttcgtaagag cacatcttac atcgcaaact ttctctttat ataccgagga
   363721 tttgatgaaa taccatttta gctctatgga gccgtggtgg aaaagagaat tttcattttg
   363781 tataccggcg atttatatca aaatggcatc aatctcactt tttcaaaata gttggctgaa
   363841 gatgaaacat ctccctagtt gcctattcac ccagacaacc aacactttag gcatttacag
   363901 gaaaaaaaaa cctaaccata gtcgtgacaa ccctagaatc aactcaaacc tttcgaccaa
   363961 ctatgcccaa gctaagtcag ttgagagatc aagatccaat agcctcaact caggcccaaa
   364021 cccattagag aatgccacgt agagaaccat cgggcacata aacttctata ttccacccga
   364081 tgagactaat gctgtcactc gaaaccaagc tgctcaaact aatgctagct aggctgtgaa
   364141 ctttgaaggg gtagatagca atccaagtct tatacccgaa atgctgcaaa taacttgaga
   364201 agtgcctaga gagttcctac gaaaagatac tacatcatca tcgataagct gagctccacc
   364261 cgcataagca tttccatgtt agagctgctt aaaactttgc ttgtgcgtag ggatgctttc
   364321 gtgagagaag tgctactctc ggtttggatc aaaagaatat actgctgaac ctattgactg
   364381 actactttat gcaactactc gctataaagc cttaaagcta gctctcacta acaaagccag
   364441 tgaaatctct attagcccat agggtatact ctcaaccatt acttgccctt tactagattg
   364501 tctgaaactt gtcttattgc tgctttgtct taggataacc accctgcaaa ggcatgggga
   364561 aagctatagg catcagcaga aaggcaagca aaggcgtagg tagccaaatg gtctagtccc
   364621 tgccagagaa caactgcagc tgagacgaga gctgacaagt atgtaacacc tacttccacc
   364681 ccatcgggga gtgaaataga acatgaaacc gtaagctccc aagcagtggg aggagccctg
   364741 ggctctgacc gcgtgcctgt tgaagaatga gccggcgact cataggcagt ggcttggtta
   364801 agggaaccca ccggagccgt agcgaaaggc gagtcttcat agggcaattg tcactgctta
   364861 tggacccgaa cctgggtgat ctatctatga ccaggatgaa gcttgggtga aactaagtgg
   364921 aggtccgaac cgactgatgt tgaaaaatca gcggatgagt tgtggttagg ggtgaaatgc
   364981 cactcgaacc cagagctagc tggttctccc cgaaatgcgt tgaggcgcag cagttgactg
   365041 gacatctagg ggtaaagcac tgtttcggtg cgggccgcga gagcggtacc aaatcgaggc
   365101 aaactctgaa tactagatat gacctcaaaa taacaggggt caaggtcggc cagtgagacg
   365161 gtgggggata agcttcatcg tcgagaggtt gtttacatac tcgactaaaa ggagaggtcc
   365221 aaaatcgact gataaaggag aggtccggag gtattaacta gttgatgagg tctcgacgag
   365281 cgactgaaag gttcacctag tgctcgagag agaattgggt cgcgcacctt ctgaacccga
   365341 ccaccaccta taagacgacg tcaagaaagc caactctcag gccaagagaa catacctcgc
   365401 ctaatagact ggaggaggtg tcccgtaccc ttagaatcgt ctaataaaaa aaatgtgctt
   365461 accttcatga gagctgacat tacttctttt gatatcgatg ccttagtcag gctaactata
   365521 tgcgatgcgt caaacataaa atgaaattca tcctaccgaa accagaccag agaaaagagg
   365581 atctccggag ctcaaccatc gaatcgggaa agcactcttt ccagcttaaa acagagcaca
   365641 gaaaggacac tcaaagcagg tccgtctgta tttcattata gtagtgatcc ccttctcttg
   365701 atcaattaga caagaacttt actttgttaa agacataaaa ggaggtccca ctatgactat
   365761 tagcggttcc tagcaggcat gggagaagag caggaagaga aagaaaaaag agacaaagat
   365821 agactagcca cttccttatt atacgaaaag tttttgattg atgagttctc accttctctc
   365881 atggagtagg tagatgagac agaagggaaa aggagtgacc cctactatga ctcatctcag
   365941 ttactcttca tcacaggaca agatacgagc agaatcagag gaaaatcgaa caactacaag
   366001 ctaagatgaa aaatctaagt gaaagactaa ctgataggcc ctggctggac cgatggaatg
   366061 tttcaagtaa agggctaact cttaactagg ctagcgaagg aactgacatt agggaaagaa
   366121 ctcctgactc tcggggaaag atctctctct ttaatacgag attccctaac cctgaagcat
   366181 ttagcaaact cagcaaaacc tgaatgggga tcaaggactt ttgataactt attttgaccc
   366241 ccaatccacc caaagcagat tcatagactt tggcgacttc ctgatcggca atgacaacat
   366301 catcaccgag taccgcgtac gatgtaaagc gtacaccagg atgcacctgt ttcgcacacc
   366361 accacactaa tatatggtgt gatagcgcga aagtaggcca agaaccgtga tatcccaatg
   366421 gctgccctgc cacaaagcat acttgagaga accttcgttt aagtttaaca aaaggcacct
   366481 caaagatatt gcatgcaaat gcagaattaa ccacacttga ggcaaaggag cggtcaaata
   366541 ggtactgcac cacctcaaac agaaagacta aaggccaacg atcagtggcc gactttaagt
   366601 caaaggagaa agagtgccta ctgccaacca gtcgatcaaa aggctgtgtt tggttaaaag
   366661 tcccatcttg ggggagacgt cttctccgcc ccccaaacat ggaaggggtg taacaaccta
   366721 ttattaacgt agttcccaat ggcgaataga aggcttttgc cacctccctc aacaacctga
   366781 cctagtcggc ccatcctccg aggtttttgt tctgctgata tgatagctct tttaaagaag
   366841 aggtctcaac gagcctcctg aatttaattt catccataca ggagaatgca tcattcttat
   366901 cgcagaatgg aaacaaaccg gatt
//

BioPerl-1.007002/t/data/NC_002058_multDBLINK_bug3375.gb000444000766000024      6155413155576321 21457 0ustar00cjfieldsstaff000000000000LOCUS       NC_002058               7440 bp ss-RNA     linear   VRL 08-DEC-2008
DEFINITION  Poliovirus, complete genome.
ACCESSION   NC_002058
VERSION     NC_002058.3  GI:12408699
DBLINK      BioProject: PRJNA15288
DBLINK      Project:100,200,300
DBLINK      NC_002058.3
KEYWORDS    coat protein; complementary DNA; genome; polyprotein.
SOURCE      Human enterovirus C
  ORGANISM  Human enterovirus C
            Viruses; ssRNA positive-strand viruses, no DNA stage;
            Picornavirales; Picornaviridae; Enterovirus.
REFERENCE   1  (sites)
  AUTHORS   Dorner,A.J., Dorner,L.F., Larsen,G.R., Wimmer,E. and Anderson,C.W.
  TITLE     Identification of the initiation site of poliovirus polyprotein
            synthesis
  JOURNAL   J. Virol. 42 (3), 1017-1028 (1982)
   PUBMED   6284987
REFERENCE   2  (sites)
  AUTHORS   Emini,E.A., Elzinga,M. and Wimmer,E.
  TITLE     Carboxy-terminal analysis of poliovirus proteins: termination of
            poliovirus RNA translation and location of unique poliovirus
            polyprotein cleavage sites
  JOURNAL   J. Virol. 42 (1), 194-199 (1982)
   PUBMED   6283138
REFERENCE   3  (bases 1 to 7440)
  AUTHORS   Racaniello,V.R. and Baltimore,D.
  TITLE     Molecular cloning of poliovirus cDNA and determination of the
            complete nucleotide sequence of the viral genome
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 78 (8), 4887-4891 (1981)
   PUBMED   6272282
REFERENCE   4  (bases 1 to 7440)
  AUTHORS   Kitamura,N., Semler,B.L., Rothberg,P.G., Larsen,G.R., Adler,C.J.,
            Dorner,A.J., Emini,E.A., Hanecak,R., Lee,J.J., van der Werf,S.,
            Anderson,C.W. and Wimmer,E.
  TITLE     Primary structure, gene organization and polypeptide expression of
            poliovirus RNA
  JOURNAL   Nature 291 (5816), 547-553 (1981)
   PUBMED   6264310
REFERENCE   5  (bases 5360 to 5527)
  AUTHORS   Kitamura,N., Adler,C.J., Rothberg,P.G., Martinko,J., Nathenson,S.G.
            and Wimmer,E.
  TITLE     The genome-linked protein of picornaviruses. VII. Genetic mapping
            of poliovirus VPg by protein and RNA sequence studies
  JOURNAL   Cell 21 (1), 295-302 (1980)
   PUBMED   6250717
REFERENCE   6  (bases 6383 to 7440)
  AUTHORS   Kitamura,N. and Wimmer,E.
  TITLE     Sequence of 1060 3'-terminal nucleotides of poliovirus RNA as
            determined by a modification of the dideoxynucleotide method
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 77 (6), 3196-3200 (1980)
   PUBMED   6158042
REFERENCE   7  (bases 1 to 7440)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (01-AUG-2000) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from V01149.
            On Jan 24, 2001 this sequence version replaced gi:12331600.
            See also entries V01148 (POLIO1A, for another version of this
            genome) and V01150 (POLIOS1, for the genome of the Sabin 1 strain).
            See the entry V01148 (POLIO1A) for the sequence reported in [3].
            Mature peptides were added to the annotation by NCBI RefSeq Genomes
            staff.
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..7440
                     /organism="Human enterovirus C"
                     /mol_type="genomic RNA"
                     /strain="Human poliovirus 1 Mahoney"
                     /db_xref="taxon:138950"
     conflict        284..288
                     /note="CGCUC is GUU in [3]"
                     /citation=[4]
     conflict        352
                     /note="G is U in [3]"
                     /citation=[4]
     conflict        387
                     /note="GC is C in [3]"
                     /citation=[4]
     conflict        488
                     /note="G is GU in [3]"
                     /citation=[4]
     gene            743..7372
                     /locus_tag="PVgp1"
                     /db_xref="GeneID:919920"
     CDS             743..7372
                     /locus_tag="PVgp1"
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="NP_041277.1"
                     /db_xref="GI:9627037"
                     /db_xref="GOA:P03300"
                     /db_xref="UniProtKB/Swiss-Prot:P03300"
                     /db_xref="GeneID:919920"
                     /translation="MGAQVSSQKVGAHENSNRAYGGSTINYTTINYYRDSASNAASKQ
                     DFSQDPSKFTEPIKDVLIKTAPMLNSPNIEACGYSDRVLQLTLGNSTITTQEAANSVV
                     AYGRWPEYLRDSEANPVDQPTEPDVAACRFYTLDTVSWTKESRGWWWKLPDALRDMGL
                     FGQNMYYHYLGRSGYTVHVQCNASKFHQGALGVFAVPEMCLAGDSNTTTMHTSYQNAN
                     PGEKGGTFTGTFTPDNNQTSPARRFCPVDYLLGNGTLLGNAFVFPHQIINLRTNNCAT
                     LVLPYVNSLSIDSMVKHNNWGIAILPLAPLNFASESSPEIPITLTIAPMCCEFNGLRN
                     ITLPRLQGLPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEIDT
                     MIPFDLSATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTH
                     WAGSLKFTFLFCGFMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMV
                     VPWISNTTYRQTIDDSFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLL
                     RDTTHIEQKALAQGLGQMLESMIDNTVRETVGAATSRDALPNTEASGPTHSKEIPALT
                     AVETGATNPLVPSDTVQTRHVVQHRSRSESSIESFFARGACVTIMTVDNPASTTNKDK
                     LFAVWKITYKDTVQLRRKLEFFTYSRFDMELTFVVTANFTETNNGHALNQVYQIMYVP
                     PGAPVPEKWDDYTWQTSSNPSIFYTYGTAPARISVPYVGISNAYSHFYDGFSKVPLKD
                     QSAALGDSLYGAASLNDFGILAVRVVNDHNPTKVTSKIRVYLKPKHIRVWCPRPPRAV
                     AYYGPGVDYKDGTLTPLSTKDLTTYGFGHQNKAVYTAGYKICNYHLATQDDLQNAVNV
                     MWSRDLLVTESRAQGTDSIARCNCNAGVYYCESRRKYYPVSFVGPTFQYMEANNYYPA
                     RYQSHMLIGHGFASPGDCGGILRCHHGVIGIITAGGEGLVAFSDIRDLYAYEEEAMEQ
                     GITNYIESLGAAFGSGFTQQISDKITELTNMVTSTITEKLLKNLIKIISSLVIITRNY
                     EDTTTVLATLALLGCDASPWQWLRKKACDVLEIPYVIKQGDSWLKKFTEACNAAKGLE
                     WVSNKISKFIDWLKEKIIPQARDKLEFVTKLRQLEMLENQISTIHQSCPSQEHQEILF
                     NNVRWLSIQSKRFAPLYAVEAKRIQKLEHTINNYIQFKSKHRIEPVCLLVHGSPGTGK
                     SVATNLIARAIAERENTSTYSLPPDPSHFDGYKQQGVVIMDDLNQNPDGADMKLFCQM
                     VSTVEFIPPMASLEEKGILFTSNYVLASTNSSRISPPTVAHSDALARRFAFDMDIQVM
                     NEYSRDGKLNMAMATEMCKNCHQPANFKRCCPLVCGKAIQLMDKSSRVRYSIDQITTM
                     IINERNRRSNIGNCMEALFQGPLQYKDLKIDIKTSPPPECINDLLQAVDSQEVRDYCE
                     KKGWIVNITSQVQTERNINRAMTILQAVTTFAAVAGVVYVMYKLFAGHQGAYTGLPNK
                     KPNVPTIRTAKVQGPGFDYAVAMAKRNIVTATTSKGEFTMLGVHDNVAILPTHASPGE
                     SIVIDGKEVEILDAKALEDQAGTNLEITIITLKRNEKFRDIRPHIPTQITETNDGVLI
                     VNTSKYPNMYVPVGAVTEQGYLNLGGRQTARTLMYNFPTRAGQCGGVITCTGKVIGMH
                     VGGNGSHGFAAALKRSYFTQSQGEIQWMRPSKEVGYPIINAPSKTKLEPSAFHYVFEG
                     VKEPAVLTKNDPRLKTDFEEAIFSKYVGNKITEVDEYMKEAVDHYAGQLMSLDINTEQ
                     MCLEDAMYGTDGLEALDLSTSAGYPYVAMGKKKRDILNKQTRDTKEMQKLLDTYGINL
                     PLVTYVKDELRSKTKVEQGKSRLIEASSLNDSVAMRMAFGNLYAAFHKNPGVITGSAV
                     GCDPDLFWSKIPVLMEEKLFAFDYTGYDASLSPAWFEALKMVLEKIGFGDRVDYIDYL
                     NHSHHLYKNKTYCVKGGMPSGCSGTSIFNSMINNLIIRTLLLKTYKGIDLDHLKMIAY
                     GDDVIASYPHEVDASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEKY
                     PFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCLLAWHNGEEEYNKFLAKIRSVPIG
                     RALLLPEYSTLYRRWLDSF"
     mat_peptide     746..949
                     /locus_tag="PVgp1"
                     /product="coat protein VP4"
                     /protein_id="NP_740468.1"
                     /db_xref="GI:25121840"
     mat_peptide     950..1765
                     /locus_tag="PVgp1"
                     /product="coat protein VP2"
                     /protein_id="NP_740469.1"
                     /db_xref="GI:25121841"
     mat_peptide     1766..2479
                     /locus_tag="PVgp1"
                     /product="coat protein VP3"
                     /protein_id="NP_740470.1"
                     /db_xref="GI:25121842"
     mat_peptide     2480..3385
                     /locus_tag="PVgp1"
                     /product="coat protein VP1"
                     /protein_id="NP_740471.1"
                     /db_xref="GI:25121843"
     mat_peptide     3386..3832
                     /locus_tag="PVgp1"
                     /product="Picornain 2A"
                     /note="Small chymotrypsin-like cysteine proteinase"
                     /protein_id="NP_740477.1"
                     /db_xref="GI:25121849"
     mat_peptide     3833..4123
                     /locus_tag="PVgp1"
                     /product="protein 2B"
                     /protein_id="NP_740472.1"
                     /db_xref="GI:25121844"
     mat_peptide     4124..5110
                     /locus_tag="PVgp1"
                     /product="protein 2C (NTPase)"
                     /note="Involved in initiation and elongation of RNA
                     synthesis, RNA encapsidation, virus uncoating and
                     guanidine resistance (Asn179-Gly mutation). Putative
                     helicase III."
                     /protein_id="NP_740473.1"
                     /db_xref="GI:25121845"
     mat_peptide     5111..5371
                     /locus_tag="PVgp1"
                     /product="protein 3A"
                     /protein_id="NP_740474.1"
                     /db_xref="GI:25121846"
     mat_peptide     5372..5437
                     /locus_tag="PVgp1"
                     /product="genome linked protein VPg"
                     /protein_id="NP_740475.1"
                     /db_xref="GI:25121847"
     mat_peptide     5438..5986
                     /locus_tag="PVgp1"
                     /product="Picornain 3C"
                     /note="Chymotrypsin-like cystein proteinase 3C"
                     /protein_id="NP_740476.2"
                     /db_xref="GI:62871476"
     mat_peptide     5987..7369
                     /locus_tag="PVgp1"
                     /product="RNA-directed RNA-polymerase 3D"
                     /protein_id="NP_740478.2"
                     /db_xref="GI:62871477"
     conflict        1467..1468
                     /locus_tag="PVgp1"
                     /note="GG is G in [3]"
                     /citation=[4]
     conflict        1529..1530
                     /locus_tag="PVgp1"
                     /note="CC is C in [3]"
                     /citation=[4]
     conflict        1534..1535
                     /locus_tag="PVgp1"
                     /note="CC is C in [3]"
                     /citation=[4]
     conflict        1547
                     /locus_tag="PVgp1"
                     /note="C is U in [3]"
                     /citation=[4]
     conflict        1579
                     /locus_tag="PVgp1"
                     /note="C is A in [3]"
                     /citation=[4]
     conflict        1601
                     /locus_tag="PVgp1"
                     /note="A is C in [3]"
                     /citation=[4]
     conflict        1668
                     /locus_tag="PVgp1"
                     /note="C is U in [3]"
                     /citation=[4]
     conflict        2001
                     /locus_tag="PVgp1"
                     /note="A is C in [3]"
                     /citation=[4]
     conflict        2004..2006
                     /locus_tag="PVgp1"
                     /note="AUC is CCU in [3]"
                     /citation=[4]
     conflict        2035
                     /locus_tag="PVgp1"
                     /note="U is C in [3]"
                     /citation=[4]
     conflict        2133
                     /locus_tag="PVgp1"
                     /note="U is C in [3]"
                     /citation=[4]
     conflict        2286
                     /locus_tag="PVgp1"
                     /note="C is G in [3]"
                     /citation=[4]
     conflict        2983
                     /locus_tag="PVgp1"
                     /note="G is A in [3]"
                     /citation=[4]
     conflict        3043
                     /locus_tag="PVgp1"
                     /note="A is G in [3]"
                     /citation=[4]
     conflict        3303..3304
                     /locus_tag="PVgp1"
                     /note="GG is G in [3]"
                     /citation=[4]
     conflict        3308
                     /locus_tag="PVgp1"
                     /note="G is GC in [3]"
                     /citation=[4]
     conflict        3657
                     /locus_tag="PVgp1"
                     /note="C is U in [3]"
                     /citation=[4]
     conflict        3696
                     /locus_tag="PVgp1"
                     /note="C is A in [3]"
                     /citation=[4]
     conflict        3766
                     /locus_tag="PVgp1"
                     /note="C is A in [3]"
                     /citation=[4]
     conflict        4158
                     /locus_tag="PVgp1"
                     /note="C is CC in [3]"
                     /citation=[4]
     conflict        4163..4164
                     /locus_tag="PVgp1"
                     /note="GC is G in [3]"
                     /citation=[4]
     conflict        4174
                     /locus_tag="PVgp1"
                     /note="A is C in [3]"
                     /citation=[4]
     conflict        5113
                     /locus_tag="PVgp1"
                     /note="A is C in [3]"
                     /citation=[4]
     conflict        5598
                     /locus_tag="PVgp1"
                     /note="U is C in [3]"
                     /citation=[4]
     conflict        5619..5623
                     /locus_tag="PVgp1"
                     /note="CGCUC is UGUUU in [3]"
                     /citation=[4]
     conflict        5645
                     /locus_tag="PVgp1"
                     /note="C is U in [3]"
                     /citation=[4]
     conflict        5786
                     /locus_tag="PVgp1"
                     /note="G is C in [3]"
                     /citation=[4]
     conflict        5903..5905
                     /locus_tag="PVgp1"
                     /note="AAA is AA in [3]"
                     /citation=[4]
     conflict        5927..5931
                     /locus_tag="PVgp1"
                     /note="GGGAA is GGA in [3]"
                     /citation=[4]
     conflict        5970..5971
                     /locus_tag="PVgp1"
                     /note="AC is UA in [3]"
                     /citation=[4]
     conflict        5997
                     /locus_tag="PVgp1"
                     /note="A is C in [3]"
                     /citation=[4]
     conflict        6019
                     /locus_tag="PVgp1"
                     /note="A is C in [3]"
                     /citation=[4]
     conflict        6021
                     /locus_tag="PVgp1"
                     /note="U is C in [3]"
                     /citation=[4]
     conflict        6261
                     /locus_tag="PVgp1"
                     /note="C is U in [3]"
                     /citation=[4]
     conflict        6845..6847
                     /locus_tag="PVgp1"
                     /note="CCA is CA in [2]"
                     /citation=[5]
     conflict        6978..6979
                     /locus_tag="PVgp1"
                     /note="UU is UUU in [2]"
                     /citation=[5]
     conflict        7258
                     /locus_tag="PVgp1"
                     /note="U is UU in [2]"
                     /citation=[5]
     conflict        7410
                     /note="U is C in [3] and [2]"
                     /citation=[4]
                     /citation=[5]
     conflict        7440
                     /note="G is GG in [3] and [2]"
                     /citation=[4]
                     /citation=[5]
ORIGIN      
        1 ttaaaacagc tctggggttg tacccacccc agaggcccac gtggcggcta gtactccggt
       61 attgcggtac ccttgtacgc ctgttttata ctcccttccc gtaacttaga cgcacaaaac
      121 caagttcaat agaagggggt acaaaccagt accaccacga acaagcactt ctgtttcccc
      181 ggtgatgtcg tatagactgc ttgcgtggtt gaaagcgacg gatccgttat ccgcttatgt
      241 acttcgagaa gcccagtacc acctcggaat cttcgatgcg ttgcgctcag cactcaaccc
      301 cagagtgtag cttaggctga tgagtctgga catccctcac cggtgacggt ggtccaggct
      361 gcgttggcgg cctacctatg gctaacgcca tgggacgcta gttgtgaaca aggtgtgaag
      421 agcctattga gctacataag aatcctccgg cccctgaatg cggctaatcc caacctcgga
      481 gcaggtggtc acaaaccagt gattggcctg tcgtaacgcg caagtccgtg gcggaaccga
      541 ctactttggg tgtccgtgtt tccttttatt ttattgtggc tgcttatggt gacaatcaca
      601 gattgttatc ataaagcgaa ttggattggc catccggtga aagtgagact cattatctat
      661 ctgtttgctg gatccgctcc attgagtgtg tttactctaa gtacaatttc aacagttatt
      721 tcaatcagac aattgtatca taatgggtgc tcaggtttca tcacagaaag tgggcgcaca
      781 tgaaaactca aatagagcgt atggtggttc taccattaat tacaccacca ttaattatta
      841 tagagattca gctagtaacg cggcttcgaa acaggacttc tctcaagacc cttccaagtt
      901 caccgagccc atcaaggatg tcctgataaa aacagcccca atgctaaact cgccaaacat
      961 agaggcttgc gggtatagcg atagagtact gcaattaaca ctgggaaact ccactataac
     1021 cacacaggag gcggctaatt cagtagtcgc ttatgggcgt tggcctgaat atctgaggga
     1081 cagcgaagcc aatccagtgg accagccgac agaaccagac gtcgctgcat gcaggtttta
     1141 tacgctagac accgtgtctt ggacgaaaga gtcgcgaggg tggtggtgga agttgcctga
     1201 tgcactgagg gacatgggac tctttgggca aaatatgtac taccactacc taggtaggtc
     1261 cgggtacacc gtgcatgtac agtgtaacgc ctccaaattc caccaggggg cactaggggt
     1321 attcgccgta ccagagatgt gtctggccgg ggatagcaac accactacca tgcacaccag
     1381 ctatcaaaat gccaatcctg gcgagaaagg aggcactttc acgggtacgt tcactcctga
     1441 caacaaccag acatcacctg cccgcaggtt ctgcccggtg gattacctcc ttggaaatgg
     1501 cacgttgttg gggaatgcct ttgtgttccc gcaccagata ataaacctac ggaccaacaa
     1561 ctgtgctaca ctggtactcc cttacgtgaa ctccctctcg atagatagta tggtaaagca
     1621 caataattgg ggaattgcaa tattaccatt ggccccatta aattttgcta gtgagtcctc
     1681 cccagagatt ccaatcacct tgaccatagc ccctatgtgc tgtgagttca atggattaag
     1741 aaacatcacc ctgccacgct tacagggcct gccggtcatg aacacccctg gtagcaatca
     1801 atatcttact gcagacaact tccagtcacc gtgtgcgctg cctgaatttg atgtgacccc
     1861 acctattgac atacccggtg aagtaaagaa catgatggaa ttggcagaaa tcgacaccat
     1921 gattcccttt gacttaagtg ccacaaaaaa gaacaccatg gaaatgtata gggttcggtt
     1981 aagtgacaaa ccacatacag acgatcccat actctgcctg tcactctctc cagcttcaga
     2041 tcctaggttg tcacatacta tgcttggaga aatcctaaat tactacacac actgggcagg
     2101 atccctgaag ttcacgtttc tgttctgtgg attcatgatg gcaactggca aactgttggt
     2161 gtcatacgcg cctcctggag ccgacccacc aaagaagcgt aaggaggcga tgttgggaac
     2221 acatgtgatc tgggacatag gactgcagtc ctcatgtact atggtagtgc catggattag
     2281 caacaccacg tatcggcaaa ccatagatga tagtttcacc gaaggcggat acatcagcgt
     2341 cttctaccaa actagaatag tcgtccctct ttcgacaccc agagagatgg acatccttgg
     2401 ttttgtgtca gcgtgtaatg acttcagcgt gcgcttgttg cgagatacca cacatataga
     2461 gcaaaaagcg ctagcacagg ggttaggtca gatgcttgaa agcatgattg acaacacagt
     2521 ccgtgaaacg gtgggggcgg caacatctag agacgctctc ccaaacactg aagccagtgg
     2581 accaacacac tccaaggaaa ttccggcact caccgcagtg gaaactgggg ccacaaatcc
     2641 actagtccct tctgatacag tgcaaaccag acatgttgta caacataggt caaggtcaga
     2701 gtctagcata gagtctttct tcgcgcgggg tgcatgcgtg accattatga ccgtggataa
     2761 cccagcttcc accacgaata aggataagct atttgcagtg tggaagatca cttataaaga
     2821 tactgtccag ttacggagga aattggagtt cttcacctat tctagatttg atatggaact
     2881 tacctttgtg gttactgcaa atttcactga gactaacaat gggcatgcct taaatcaagt
     2941 gtaccaaatt atgtacgtac caccaggcgc tccagtgccc gagaaatggg acgactacac
     3001 atggcaaacc tcatcaaatc catcaatctt ttacacctac ggaacagctc cagcccggat
     3061 ctcggtaccg tatgttggta tttcgaacgc ctattcacac ttttacgacg gtttttccaa
     3121 agtaccactg aaggaccagt cggcagcact aggtgactcc ctttatggtg cagcatctct
     3181 aaatgacttc ggtattttgg ctgttagagt agtcaatgat cacaacccga ccaaggtcac
     3241 ctccaaaatc agagtgtatc taaaacccaa acacatcaga gtctggtgcc cgcgtccacc
     3301 gagggcagtg gcgtactacg gccctggagt ggattacaag gatggtacgc ttacacccct
     3361 ctccaccaag gatctgacca catatggatt cggacaccaa aacaaagcgg tgtacactgc
     3421 aggttacaaa atttgcaact accacttggc cactcaggat gatttgcaaa acgcagtgaa
     3481 cgtcatgtgg agtagagacc tcttagtcac agaatcaaga gcccagggca ccgattcaat
     3541 cgcaaggtgc aattgcaacg caggggtgta ctactgcgag tctagaagga aatactaccc
     3601 agtatccttc gttggcccaa cgttccagta catggaggct aataactatt acccagctag
     3661 gtaccagtcc catatgctca ttggccatgg attcgcatct ccaggggatt gtggtggcat
     3721 actcagatgt caccacgggg tgatagggat cattactgct ggtggcgaag ggttggttgc
     3781 attttcagac attagagact tgtatgccta cgaagaagaa gccatggaac aaggcatcac
     3841 caattacata gagtcacttg gggccgcatt tggaagtgga tttactcagc agattagcga
     3901 caaaataaca gagttgacca atatggtgac cagtaccatc actgaaaagc tacttaagaa
     3961 cttgatcaag atcatatcct cactagttat tataactagg aactatgaag acaccacaac
     4021 agtgctcgct accctggccc ttcttgggtg tgatgcttca ccatggcagt ggcttagaaa
     4081 gaaagcatgc gatgttctgg agatacctta tgtcatcaag caaggtgaca gttggttgaa
     4141 gaagtttact gaagcatgca acgcagctaa gggactggag tgggtgtcaa acaaaatctc
     4201 aaaattcatt gattggctca aggagaaaat tatcccacaa gctagagata agttggaatt
     4261 tgtaacaaaa cttagacaac tagaaatgct ggaaaaccaa atctcaacta tacaccaatc
     4321 atgccctagt caggaacacc aggaaattct attcaataat gtcagatggt tatccatcca
     4381 gtctaagagg tttgcccctc tttacgcagt ggaagccaaa agaatacaga aactagagca
     4441 tactattaac aactacatac agttcaagag caaacaccgt attgaaccag tatgtttgct
     4501 agtacatggc agccccggaa caggtaaatc tgtagcaacc aacctgattg ctagagccat
     4561 agctgaaaga gaaaacacgt ccacgtactc gctacccccg gatccatcac acttcgacgg
     4621 atacaaacaa cagggagtgg tgattatgga cgacctgaat caaaacccag atggtgcgga
     4681 catgaagctg ttctgtcaga tggtatcaac agtggagttt ataccaccca tggcatccct
     4741 ggaggagaaa ggaatcctgt ttacttcaaa ttacgttcta gcatccacaa actcaagcag
     4801 aatttccccc cccactgtgg cacacagtga tgcattagcc aggcgctttg cgttcgacat
     4861 ggacattcag gtcatgaatg agtattctag agatgggaaa ttgaacatgg ccatggctac
     4921 tgaaatgtgt aagaactgtc accaaccagc aaactttaag agatgctgtc ctttagtgtg
     4981 tggtaaggca attcaattaa tggacaaatc ttccagagtt agatacagta ttgaccagat
     5041 cactacaatg attatcaatg agagaaacag aagatccaac attggcaatt gtatggaggc
     5101 tttgtttcaa ggaccactcc agtataaaga cttgaaaatt gacatcaaga cgagtccccc
     5161 tcctgaatgt atcaatgact tgctccaagc agttgactcc caggaggtga gagattactg
     5221 tgagaagaag ggttggatag tcaacatcac cagccaggtt caaacagaaa ggaacatcaa
     5281 cagggcaatg acaattctac aagcggtgac aaccttcgcc gcagtggctg gagttgtcta
     5341 tgtcatgtat aaactgtttg ctggacacca gggagcatac actggtttac caaacaaaaa
     5401 acccaacgtg cccaccattc ggacagcaaa ggtacaagga ccagggttcg attacgcagt
     5461 ggctatggct aaaagaaaca ttgttacagc aactactagc aagggagagt tcactatgtt
     5521 aggagtccac gacaacgtgg ctattttacc aacccacgct tcacctggtg aaagcattgt
     5581 gatcgatggc aaagaagtgg agatcttgga tgccaaagcg ctcgaagatc aagcaggaac
     5641 caatcttgaa atcactataa tcactctaaa gagaaatgaa aagttcagag acattagacc
     5701 acatatacct actcaaatca ctgagacaaa tgatggagtc ttgatcgtga acactagcaa
     5761 gtaccccaat atgtatgttc ctgtcggtgc tgtgactgaa cagggatatc taaatctcgg
     5821 tgggcgccaa actgctcgta ctctaatgta caactttcca accagagcag gacagtgtgg
     5881 tggagtcatc acatgtactg ggaaagtcat cgggatgcat gttggtggga acggttcaca
     5941 cgggtttgca gcggccctga agcgatcata cttcactcag agtcaaggtg aaatccagtg
     6001 gatgagacct tcgaaggaag tgggatatcc aatcataaat gccccgtcca aaaccaagct
     6061 tgaacccagt gctttccact atgtgtttga aggggtgaag gaaccagcag tcctcactaa
     6121 aaacgatccc aggcttaaga cagactttga ggaggcaatt ttctccaagt acgtgggtaa
     6181 caaaattact gaagtggatg agtacatgaa agaggcagta gaccactatg ctggccagct
     6241 catgtcacta gacatcaaca cagaacaaat gtgcttggag gatgccatgt atggcactga
     6301 tggtctagaa gcacttgatt tgtccaccag tgctggctac ccttatgtag caatgggaaa
     6361 gaagaagaga gacatcttga acaaacaaac cagagacact aaggaaatgc aaaaactgct
     6421 cgacacatat ggaatcaacc tcccactggt gacttatgta aaggatgaac ttagatccaa
     6481 aacaaaggtt gagcagggga aatccagatt aattgaagct tctagtttga atgactcagt
     6541 ggcaatgaga atggcttttg ggaacctata tgctgctttt cacaaaaacc caggagtgat
     6601 aacaggttca gcagtggggt gcgatccaga tttgttttgg agcaaaattc cggtattgat
     6661 ggaagagaag ctgtttgctt ttgactacac agggtatgat gcatctctca gccctgcttg
     6721 gttcgaggca ctaaagatgg tgcttgagaa aatcggattc ggagacagag ttgactacat
     6781 cgactaccta aaccactcac accacctgta caagaataaa acatactgtg tcaagggcgg
     6841 tatgccatct ggctgctcag gcacttcaat ttttaactca atgattaaca acttgattat
     6901 caggacactc ttactgaaaa cctacaaggg catagattta gaccacctaa aaatgattgc
     6961 ctatggtgat gatgtaattg cttcctaccc ccatgaagtt gacgctagtc tcctagccca
     7021 atcaggaaaa gactatggac taactatgac tccagctgac aaatcagcta catttgaaac
     7081 agtcacatgg gagaatgtaa cattcttgaa gagattcttc agggcagacg agaaataccc
     7141 atttcttatt catccagtaa tgccaatgaa ggaaattcat gaatcaatta gatggactaa
     7201 agatcctagg aacactcagg atcacgttcg ctctctgtgc cttttagctt ggcacaatgg
     7261 cgaagaagaa tataacaaat tcctagctaa aatcaggagt gtgccaattg gaagagcttt
     7321 attgctccca gagtactcaa cattgtaccg ccgttggctt gactcatttt agtaacccta
     7381 cctcagtcga attggattgg gtcatactgt tgtaggggta aatttttctt taattcggag
//

BioPerl-1.007002/t/data/NC_006346.gb000444000766000024       551713155576321 16334 0ustar00cjfieldsstaff000000000000LOCUS       NC_006346              21657 bp    DNA     circular VRT 12-JAN-2005
DEFINITION  Bolitoglossa n. sp. RLM-2004 mitochondrion, complete genome.
ACCESSION   NC_006346
VERSION     NC_006346.1  GI:53686544
KEYWORDS    .
SOURCE      mitochondrion Bolitoglossa n. sp. RLM-2004 (mushroomtongue
            salamander)
  ORGANISM  Bolitoglossa n. sp. RLM-2004
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Amphibia; Batrachia; Caudata; Salamandroidea; Plethodontidae;
            Plethodontinae; Bolitoglossini; Bolitoglossa.
REFERENCE   1  (bases 1 to 21657)
  AUTHORS   Mueller,R.L., Macey,J.R., Jaekel,M., Wake,D.B. and Boore,J.L.
  TITLE     Morphological homoplasy, life history evolution, and historical
            biogeography of plethodontid salamanders inferred from complete
            mitochondrial genomes
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 101 (38), 13820-13825 (2004)
   PUBMED   15365171
REFERENCE   2  (bases 1 to 21657)
  AUTHORS   .
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (01-OCT-2004) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
REFERENCE   3  (bases 1 to 21657)
  AUTHORS   Mueller,R.L., Macey,J.R., Jaekel,M., Wake,D.B. and Boore,J.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-AUG-2004) Museum of Vertebrate Zoology and
            Evolutionary Genomics, University of California at Berkeley and DOE
            Joint Genome Institute, 3101 Valley Life Sciences Bldg., Berkeley,
            CA 94720-3160, USA
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AY728235.
FEATURES             Location/Qualifiers
     source          1..21657
                     /organism="Bolitoglossa n. sp. RLM-2004"
                     /organelle="mitochondrion"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:291262"
                     /common="mushroomtongue salamander"
     tRNA            1..64
                     /product="tRNA-Phe"
     rRNA            65..96
                     /product="s-rRNA"
     D-loop          152..216
                     /note="putative control region"
ORIGIN      
        1 gcaagtgtag tttataaaaa catagcactg aaaatgctaa aataaatatt atatttcact
       61 agcaatagat ttggtcctaa tctttttatt aattataact ataattatac atgcaagttt
      121 caccacccca gtgagtaagc cccacatccc cgcttagtga tgaaggagct ggtatcaggc
      181 atacacaccc aaaacaccac gcttagccac acctacacag gaactcagca gtaattaaca
      241 ttaaaccata agtgaaaact tgatttagta atagtattta aagttggtaa atctcgtgcc
      301 agccaccgcg gttacacgaa agacttaaat taatatatgc ggcccaaagg acagtttaag
      361 gttttatagg aacttaagag cctttaaggc cgttatacgt ttaaaaggtc aaaaacacaa
      421 atcaccccac caacttgaat ctgttaaagc cgggggacac actgggatta gataccccac
//

BioPerl-1.007002/t/data/NC_006511-short.gbk000444000766000024      1430313155576321 17647 0ustar00cjfieldsstaff000000000000LOCUS       NC_006511            4585229 bp    DNA     circular BCT 03-DEC-2005
DEFINITION  Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC
            9150, complete genome.
ACCESSION   NC_006511
VERSION     NC_006511.1  GI:56412276
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC
            9150
  ORGANISM  Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC
            9150
            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 4585229)
  AUTHORS   McClelland,M., Sanderson,K.E., Clifton,S.W., Latreille,P.,
            Porwollik,S., Sabo,A., Meyer,R., Bieri,T., Ozersky,P., McLellan,M.,
            Harkins,C.R., Wang,C., Nguyen,C., Berghoff,A., Elliott,G.,
            Kohlberg,S., Strong,C., Du,F., Carter,J., Kremizki,C., Layman,D.,
            Leonard,S., Sun,H., Fulton,L., Nash,W., Miner,T., Minx,P.,
            Delehaunty,K., Fronick,C., Magrini,V., Nhan,M., Warren,W.,
            Florea,L., Spieth,J. and Wilson,R.K.
  TITLE     Comparison of genome degradation in Paratyphi A and Typhi,
            human-restricted serovars of Salmonella enterica that cause typhoid
  JOURNAL   Nat. Genet. 36 (12), 1268-1274 (2004)
   PUBMED   15531882
REFERENCE   2  (bases 1 to 4585229)
  AUTHORS   .
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (08-DEC-2004) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
REFERENCE   3  (bases 1 to 4585229)
  AUTHORS   McClelland,M., Sanderson,K.E., Clifton,S.W., Latreille,P.,
            Porwollik,S., Sabo,A., Meyer,R., Bieri,T., Ozersky,P., McLellan,M.,
            Harkins,R., Wang,C., Nguyen,C., Burghoff,A., Elliott,G.,
            Kohlberg,S., Strong,C., Ali,J., Dante,M., Du,F., Layman,D.,
            Leonard,S., Sun,H., Fulton,L., Nash,W., Miner,T., Delehaunty,K.,
            Fronick,C., Florea,L., Spieth,J., Nhan,M. and Wilson,R.K.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-OCT-2004) Genome Sequencing Center, Washington
            University, 4444 Forest Park Ave., St. Louis, MO 63108, USA
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from CP000026.
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..4585229
                     /organism="Salmonella enterica subsp. enterica serovar
                     Paratyphi A str. ATCC 9150"
                     /mol_type="genomic DNA"
                     /strain="ATCC 9150"
                     /db_xref="ATCC:9150"
                     /db_xref="taxon:295319"
     gene            190..255
                     /gene="thrL"
                     /locus_tag="SPA0001"
                     /db_xref="GeneID:3175747"
     CDS             190..255
                     /gene="thrL"
                     /locus_tag="SPA0001"
                     /note="similar to Salmonella typhi CT18 thr operon leader
                     peptide"
                     /codon_start=1
                     /transl_table=11
                     /product="thr operon leader peptide"
                     /protein_id="YP_149352.1"
                     /db_xref="GI:56412277"
                     /db_xref="GeneID:3175747"
                     /translation="MNRISTTTITTITITTGNGAG"
                     /transl_table=11
                     /product="putative major fimbrial subunit"
                     /protein_id="YP_153436.1"
                     /db_xref="GI:56416361"
                     /db_xref="GeneID:3177061"
                     /translation="MRRLYLALILLFAYSSHGYASCRRSGNEGAITITPPSQLVVDSH
                     AYTAGEVLWQSGWVSTSEVTMDGCSRDYKVGFLYEPGSAQSNTSATINANDGNNTPVF
                     STGISGVDIAIKTQTNAGPYDNVMPIDNTYHNGDGNKTHHAMAPAYNVELVALGGPIT
                     SDTATFQSPLARVSFRDSATEDSGGDILTHLYLGNTQLIMKAMGCRVETPAITVDLGS
                     VNLGSFANSQTAGTGEQDILLTCEQGTAISASLSAQPASGNNPDNSVIQLSNASAPTS
                     ATGVGVQLGIQAPDAGFFTDSLPINQKIDLFTHTITTNADGSQTVNGGTMNMSTTLKI
                     SARYYKTAATVTAGQANATATLNLTYN"
     gene            4584519..4585205
                     /gene="lasT"
                     /locus_tag="SPA4410"
                     /db_xref="GeneID:3177689"
     CDS             4584519..4585205
                     /gene="lasT"
                     /locus_tag="SPA4410"
                     /note="similar to Salmonella typhi CT18 putative RNA
                     methyltransferase"
                     /codon_start=1
                     /transl_table=11
                     /product="putative RNA methyltransferase"
                     /protein_id="YP_153444.1"
                     /db_xref="GI:56416369"
                     /db_xref="GeneID:3177689"
                     /translation="MRVTIVLVAPARAENIGAAARAMKTMGFTDLRIVDSQAHLEPAT
                     RWVAHGSGDIIDNIEVFHTLADALHDVDFTVATTARSRAKFHYYASPAELVPLLQEKS
                     RWMRHAALVFGREDSGLTNDELALADVLTGVPMAADYPSLNLGQAVMVYCYQLAGLMQ
                     QATESVDIADESQLQALRARLLRLLTTLEAADDHKLTDWLQQRIGLLGQRDTVMLHRL
                     VHDIEKKLTK"
ORIGIN      
        1 agagattacg tctggtttca agagatcata acagagggaa ttggttgaaa ataaatatat
       61 cgccagcagc acatgaacaa atttcggaat gtgatcaatt taaaaattta ttgacttagg
      121 cgggcagata ctttaaccaa tataggaata caagacagac aaataaaaat gacagagtac
      181 acaacatcca tgaaccgcat cagcaccacc accattacca ccatcaccat taccacaggt
      241 aacggtgcgg gctgacgcgt acaggaaaca cagaaaaaag cccgcacctg aacagtgcgg
      301 gctttttttt cgaccagaga tcacgaggta acaaccatgc gagtgttgaa gttcggcggt
      361 acatcagtgg caaatgcaga acgttttctg cgtgttgccg atattctgga aagcaatgcc
      421 aggcaagggc aggtagcgac cgtactttcc gcccccgcga aaattaccaa ccatctggtg
      481 gcgatgattg aaaaaactat cggcggtcag gatgctttgc cgaatatcag cgatgccgaa
      541 cgtatttttt ctgacctgct cgcaggactt gccagcgcgc agccgggatt cccgcttgca
      601 cggttgaaaa tggttgtcga acaagaattc gctcagatca aacatgtttt gcatggtatc
      661 agcctgctgg gtcagtgccc ggacagcatc aacgccgcgc tgatttgccg tggcgaaaaa
      721 atgtcgatcg cgattatggc gggacttctg gaggcgcgtg ggcatcgcgt cacggtgatc
      781 gatccggtag aaaaactgct ggcggtgggc cattaccttg agtctaccgt cgatatcgcg
//
BioPerl-1.007002/t/data/NC_008536.gb000444000766000024      2651713155576321 16362 0ustar00cjfieldsstaff000000000000LOCUS       NC_008536               2001 bp    DNA     linear   BCT 21-JUL-2008
DEFINITION  Solibacter usitatus Ellin6076, complete genome.
ACCESSION   NC_008536 REGION: 1000..3000
VERSION     NC_008536.1  GI:116619145
PROJECT     GenomeProject:12638
KEYWORDS    .
SOURCE      Solibacter usitatus Ellin6076
  ORGANISM  Solibacter usitatus Ellin6076
            Bacteria; Acidobacteria; Solibacteres; Solibacterales;
            Solibacteraceae; Solibacter.
REFERENCE   1  (bases 1 to 2001)
  AUTHORS   Copeland,A., Lucas,S., Lapidus,A., Barry,K., Detter,J.C., Glavina
            del Rio,T., Hammon,N., Israni,S., Dalin,E., Tice,H., Pitluck,S.,
            Thompson,L.S., Brettin,T., Bruce,D., Han,C., Tapia,R., Gilna,P.,
            Schmutz,J., Larimer,F., Land,M., Hauser,L., Kyrpides,N.,
            Mikhailova,N., Janssen,P.H., Kuske,C.R. and Richardson,P.
  CONSRTM   US DOE Joint Genome Institute
  TITLE     Complete sequence of Solibacter usitatus Ellin6076
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2001)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (24-OCT-2006) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
REFERENCE   3  (bases 1 to 2001)
  AUTHORS   Copeland,A., Lucas,S., Lapidus,A., Barry,K., Detter,J.C., Glavina
            del Rio,T., Hammon,N., Israni,S., Dalin,E., Tice,H., Pitluck,S.,
            Thompson,L.S., Brettin,T., Bruce,D., Han,C., Tapia,R., Gilna,P.,
            Schmutz,J., Larimer,F., Land,M., Hauser,L., Kyrpides,N.,
            Mikhailova,N., Janssen,P.H., Kuske,C.R. and Richardson,P.
  CONSRTM   US DOE Joint Genome Institute
  TITLE     Direct Submission
  JOURNAL   Submitted (06-OCT-2006) US DOE Joint Genome Institute, 2800
            Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from CP000473.
            URL -- http://www.jgi.doe.gov
            JGI Project ID: 3634513
            Source DNA and bacteria available from Cheryl R. Kuske
            (kuske@lanl.gov)
            Contacts: Cheryl R. Kuske (kuske@lanl.gov)
                 Paul Richardson (microbes@cuba.jgi-psf.org)
            Quality assurance done by JGI-Stanford
            Annotation done by JGI-ORNL and JGI-PGF
            Finishing done by JGI-LANL
            Finished microbial genomes have been curated to close all gaps with
            greater than 98% coverage of at least two independent clones. Each
            base pair has a minimum q (quality) value of 30 and the total error
            rate is less than one per 50000.
            The JGI and collaborators endorse the principles for the
            distribution and use of large scale sequencing data adopted by the
            larger genome sequencing community and urge users of this data to
            follow them. It is our intention to publish the work of this
            project in a timely fashion and we welcome collaborative
            interaction on the project and analysis.
            (http://www.genome.gov/page.cfm?pageID=10506376).
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..2001
                     /organism="Solibacter usitatus Ellin6076"
                     /mol_type="genomic DNA"
                     /strain="Ellin6076"
                     /db_xref="taxon:234267"
     gene            <1..403
                     /locus_tag="Acid_0001"
                     /db_xref="GeneID:4431688"
     CDS             <1..403
                     /locus_tag="Acid_0001"
                     /note="KEGG: aba:Acid345_0001 chromosomal replication
                     initiator protein DnaA
                     TIGRFAM: chromosomal replication initiator protein DnaA
                     PFAM: Chromosomal replication initiator, DnaA C-terminal
                     domain; Chromosomal replication initiator, DnaA
                     SMART: AAA ATPase"
                     /codon_start=1
                     /transl_table=11
                     /product="chromosomal replication initiator protein DnaA"
                     /protein_id="YP_821302.1"
                     /db_xref="GI:116619146"
                     /db_xref="InterPro:IPR001957"
                     /db_xref="InterPro:IPR003593"
                     /db_xref="InterPro:IPR013159"
                     /db_xref="InterPro:IPR013317"
                     /db_xref="GeneID:4431688"
                     /translation="MNYWDQIRHYLQSKVSADGYDNWLKSTAFVGQNGDTLYVSVPDR
                     ETRAWLETEYTQLIQGGIQALGLPVRHVSFEAEQSRPAAPAATIAVNANTEPDAAATV
                     LNPKFTFNSFVVGACNQFAHAAAKSVATNPSRSYNPLFLYGGVGMGKTHLMHAIGRQL
                     IDQFGSMRIIYTSSERFMNEMISCIRTERMQQFHQRYREADVLLIDDIQLLGNKERTQ
                     EEFFHTFNELHDHQKQIVISSDSPPKDIPGLLERLRSRFEWGLMADIQPPDLETKMAI
                     LDKKAEIEGVELPDDVRTFMASKTKSNVRELEGALVKLIAYSSLTGTPIHLQMAQQVL
                     KHLVHVQDRRVTMDSIQKAVAEKFSIKQSQLKEKSNTKKVVYPRQVAMYLVKELTNAS
                     LPEIGRAFGGKHHTTVIHSINKIEKDRQSDPELNRLLHSLMDSLQ"
     gene            638..1756
                     /locus_tag="Acid_0002"
                     /db_xref="GeneID:4431689"
     CDS             638..1756
                     /locus_tag="Acid_0002"
                     /EC_number="2.7.7.7"
                     /note="KEGG: aba:Acid345_0002 DNA polymerase III, beta
                     subunit
                     TIGRFAM: DNA polymerase III, beta subunit
                     PFAM: DNA polymerase III, beta chain"
                     /codon_start=1
                     /transl_table=11
                     /product="DNA polymerase III, beta subunit"
                     /protein_id="YP_821303.1"
                     /db_xref="GI:116619147"
                     /db_xref="InterPro:IPR001001"
                     /db_xref="GeneID:4431689"
                     /translation="MEFTVSKSDLVRELSLSQGVVEKKTTIPILSNVLLEAADDRITL
                     TATDLELGIRCSCPARVKKEGSGTVPARKLLDYMRLLPEGDVNMKFLDNHWASITSGR
                     SRTRIAGMSRESFPELPQMPEPIAQVPVKTLASMIARTSFAISMEESRFTLNGALLLM
                     RPEGLTMVATDGHRLAYVQAEPAESGSADKPFRALVPKKAMSELTKLSDDAGEGAMAI
                     VAGDDNHLFFQIGHRLLITRKLTGNFPDYERVLPKDHQFMAKLEKGEIRSAIERVAQF
                     ADERSRAIRVQFNSGEVRVFSSSVETGESEESVPAEYTGPDIEIGFNAQYLLDFLRAI
                     SQDHVAFELKDQKSAGELRPAGDAIADQYRYVVMPMRI"
     gene            1782..>2001
                     /locus_tag="Acid_0003"
                     /db_xref="GeneID:4431690"
     CDS             1782..>2001
                     /locus_tag="Acid_0003"
                     /EC_number="5.99.1.3"
                     /note="KEGG: aba:Acid345_0008 DNA gyrase, B subunit
                     TIGRFAM: DNA gyrase, B subunit
                     PFAM: DNA gyrase, subunit B domain protein; ATP-binding
                     region, ATPase domain protein domain protein; TOPRIM
                     domain protein; DNA topoisomerase, type IIA, subunit B,
                     region 2 domain protein
                     SMART: DNA topoisomerase II"
                     /codon_start=1
                     /transl_table=11
                     /product="DNA gyrase subunit B"
                     /protein_id="YP_821304.1"
                     /db_xref="GI:116619148"
                     /db_xref="InterPro:IPR000565"
                     /db_xref="InterPro:IPR001241"
                     /db_xref="InterPro:IPR002288"
                     /db_xref="InterPro:IPR003594"
                     /db_xref="InterPro:IPR006171"
                     /db_xref="InterPro:IPR011557"
                     /db_xref="InterPro:IPR011558"
                     /db_xref="InterPro:IPR013506"
                     /db_xref="GeneID:4431690"
                     /translation="MPNEVNPVGGNGNVYDSSSIKVLEGLEAVRLRPAMYIGSTGEMG
                     LHHLVYEVVDNSVDEALAGYATHIEVTIHDDNSVTVEDDGRGIPVGIHEEEGVSAAQV
                     VMTKLHAGGKFDSNSYKVSGGLHGVGVSCVNALSEKLELEIWREGYTWTQEYSCGKPK
                     ADLVRAGKAGKRTGTRVTFKPDSTIMEVAVFNYDTLAQRLRELAFLNKGLKITLTDER
                     VDPEKVTPFEYQGGISEFIKHLNRGKSVLHEKPIHFEAEREMPEKGTITMEVALQYND
                     AYSENVFSFANNINTVDGGTHLSGFRSALTRTINAFGQKNGLFKDVKENLSGDDVREG
                     LTAVVSVKVPQPQFEGQTKGKLNSDIAGYMTQFVNDKLSEYFDKNSAVGRKIVGKAIE
                     ASRAREAARKARDLTRRKGALDSGGLPGKLADCQEKDPKLCELFLVEGESAGGTAKQG
                     RERRFQAILPLKGKILNVEKARYDKMLGHEEIRCMITALGTGIGKDDFDVAKLRYDKI
                     IIMTDADVDGSHIRTLLLTFFFRHMNELITRGKVYIAQPPLYRIKKGKSEKYIKDEKE
                     FTKEIMRRATENLTVEIHSNGDGKPKSSLEGQELRTFLLNLDEFQQIFHKVERRLRDS
                     RAVDVLTNVDLHVDNKAEFQVEANLKPVFEAMKAKGLNPQMKKDEEHSAWAVVFHDST
                     GAERSVGLQLAAQPEYRRFRALARTIAKFNEPPFVVVKNEHRDAQPDWVELLEYVKNE
                     GKKDASVQRYKGLGEMNAEQLADTTMNPEKRTLLEVRLEDAVQCEEIFSTLMGEDVES
                     RRKFIEENALDVKNLDV"
ORIGIN      
        1 ccgcgaactc gaaggcgccc tggttaaatt gatcgcgtac tcctccctca ccggaacgcc
       61 gatccacctg cagatggcgc aacaggtcct gaagcacctg gtccacgtgc aggaccgccg
      121 cgtcaccatg gattccatcc aaaaggccgt cgcggagaaa ttcagcatta agcagtccca
      181 gctcaaggaa aagagcaata ccaagaaggt ggtctatccg cggcaggtgg caatgtacct
      241 ggtcaaggag ctcaccaacg cgtcgctacc tgagatcggg cgcgctttcg gcggaaagca
      301 tcacaccacc gtgatccact cgatcaacaa aatcgagaag gatcgccaga gcgaccctga
      361 attgaacagg ttactacaca gcctaatgga ctcattacaa tgaccttcca ccgttttcca
      421 caattgccct tgcaccgggc atggggaaat ctgtgtatat cgcatgacag cgttggtttt
      481 gcgcaatttt ccgcgccgca atccgcagct tgacgtagca gaaagtggct gagtttagta
      541 taatttagat agtcttcaac actttgcaca gggcctatga atacggttat ttatcaggcc
      601 tatctataga gacagcaaag aactaggagc cgtgggcatg gaattcaccg tcagcaagag
      661 cgatctggta cgtgagctga gtctctcgca gggtgtggtg gaaaaaaaga ccaccattcc
      721 aatcctgtcg aacgtgctcc tggaggccgc ggacgatcgc attacgttga ctgcgaccga
      781 cctggaactg ggcatccgct gttcttgccc ggcgcgcgtc aagaaagaag ggtccggcac
      841 ggtgccggcg cgcaaactgc tcgattacat gcgtctgttg cccgaaggcg acgtgaacat
      901 gaagttcctg gacaatcact gggccagtat caccagcgga cgttctcgca ccaggattgc
      961 gggcatgtcg cgcgagagct tccccgaact gccgcagatg ccggagccga tcgcgcaggt
     1021 gcccgtcaaa acgctggcct ccatgatcgc ccgtacgtcc ttcgccatct ccatggagga
     1081 gtcgcgcttt acgctcaacg gcgcgctcct gctgatgcgc cccgaaggcc tcaccatggt
     1141 cgccaccgat ggccaccgcc tcgcctacgt gcaggccgag cccgcggaga gcggcagcgc
     1201 cgacaaaccc ttccgcgccc tcgtccccaa gaaggcgatg agcgaattga ccaagctcag
     1261 cgatgatgcc ggcgaaggcg ccatggccat cgtcgccggt gatgacaatc acctgttctt
     1321 ccaaattggc caccgcctgc tgatcacgcg aaagctcacc ggcaacttcc cggattacga
     1381 gcgcgtcttg cccaaagatc accagttcat ggccaagctc gagaagggcg aaatccgctc
     1441 ggcaatcgaa cgcgtggcgc agttcgccga tgaacggtcg cgcgccattc gggtgcaatt
     1501 caacagcggc gaagtccgcg tcttcagttc cagcgtcgaa accggcgaga gcgaagagag
     1561 cgttcccgcc gagtacacgg gtcccgatat cgagatcggt ttcaatgccc aatacctgct
     1621 cgatttcctg cgtgcgattt ctcaggatca cgttgccttc gaattgaagg atcaaaaaag
     1681 cgcgggcgaa ctccgtcccg ccggcgatgc catcgcggac cagtaccgct atgtagtcat
     1741 gccgatgcgt atttgaagtt tagtcaaacc agtaaggaac tatgccaaac gaagtcaatc
     1801 ccgtcggggg aaatggaaac gtctacgatt ccagcagtat caaagtcctg gaaggcctcg
     1861 aagcagtgcg cctgcgccct gccatgtaca tcgggtctac aggcgagatg gggctgcacc
     1921 atctggtcta tgaggtcgtc gataattccg tcgatgaagc tctagccggc tacgccaccc
     1981 atatcgaggt gacgatccac g
//

BioPerl-1.007002/t/data/NM_002254.gb000444000766000024      2422113155576321 16351 0ustar00cjfieldsstaff000000000000LOCUS       KIF3C                   4913 bp    mRNA    linear   PRI 06-APR-2003
DEFINITION  Homo sapiens kinesin family member 3C (KIF3C), mRNA.
ACCESSION   NM_002254
VERSION     NM_002254.2  GI:19923139
KEYWORDS    .
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 4913)
  AUTHORS   Sardella,M., Navone,F., Rocchi,M., Rubartelli,A., Viggiano,L.,
            Vignali,G., Consalez,G.G., Sitia,R. and Cabibbo,A.
  TITLE     KIF3C, a novel member of the kinesin superfamily: sequence,
            expression, and mapping to human chromosome 2 at 2p23
  JOURNAL   Genomics 47 (3), 405-408 (1998)
  MEDLINE   98149989
   PUBMED   9480755
REFERENCE   2  (bases 1 to 4913)
  AUTHORS   Telford,E.A., Wightman,P., Leek,J., Markham,A.F., Lench,N.J. and
            Bonthron,D.T.
  TITLE     cDNA cloning, genomic organization, and chromosomal localization of
            a novel human gene that encodes a kinesin-related protein highly
            similar to mouse Kif3C
  JOURNAL   Biochem. Biophys. Res. Commun. 242 (2), 407-412 (1998)
  MEDLINE   98113366
   PUBMED   9446808
REFERENCE   3  (bases 1 to 4913)
  AUTHORS   Telford,E.A.R., Wightman,P., Leek,J., Lench,N.J., Markham,A.F. and
            Bonthron,D.T.
  TITLE     Homo sapiens kinesin family member 3C (KIF3C), mRNA
  JOURNAL   Unpublished (1997)
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AF035621.1.
            On Apr 4, 2002 this sequence version replaced gi:4504868.
FEATURES             Location/Qualifiers
     source          1..4913
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2p23"
     gene            1..4913
                     /gene="KIF3C"
                     /db_xref="LocusID:3797"
                     /db_xref="MIM:602845"
     CDS             154..2535
                     /gene="KIF3C"
                     /codon_start=1
                     /product="kinesin family member 3C"
                     /protein_id="NP_002245.2"
                     /db_xref="GI:19923140"
                     /db_xref="LocusID:3797"
                     /db_xref="MIM:602845"
                     /translation="MASKTKASEALKVVARCRPLSRKEEAAGHEQILTMDVKLGQVTL
                     RNPRAAPGELPKTFTFDAVYDASSKQADLYDETVRPLIDSVLQGFNGTVFAYGQTGTG
                     KTYTMQGTWVEPELRGVIPNAFEHIFTHISRSQNQQYLVRASYLEIYQEEIRDLLSKE
                     PGKRLELKENPETGVYIKDLSSFVTKNVKEIEHVMNLGNQTRAVGSTHMNEVSSRSHA
                     IFIITVECSERGSDGQDHIRVGKLNLVDLAGSERQNKAGPNTAGGAATPSSGGGGGGG
                     GSGGGAGGERPKEASKINLSLSALGNVIAALAGNRSTHIPYRDSKLTRLLQDSLGGNA
                     KTIMVATLGPASHSYDESLSTLRFANRAKNIKNKPRVNEDPKDTLLREFQEEIARLKA
                     QLEKRGMLGKRPRRKSSRRKKAVSAPPGYPEGPVIEAWVAEEEDDNNNNHRPPQPILE
                     SALEKNMENYLQEQKERLEEEKAAIQDDRSLVSEEKQKLLEEKEKMLEDLRREQQATE
                     LLAAKYKAMESKLLIGGRNIMDHTNEQQKMLELKRQEIAEQKRREREMQQEMMLRDEE
                     TMELRGTYTSLQQEVEVKTKKLKKLYAKLQAVKAEIQDQHDEYIRVRQDLEEAQNEQT
                     RELKLKYLIIENFIPPEEKNKIMNRLFLDCEEEQWKFQPLVPAGVSSSQMKKRPTSAV
                     GYKRPISQYARVAMAMGSHPRYRAENIMFLELDVSPPAVFEMEFSHDQEQDPRALHME
                     RLMRLDSFLERPSTSKVRKSRSWCQSPQRPPPSTTHASLASASLRPATVADHE"
     misc_feature    199..1251
                     /gene="KIF3C"
                     /note="kinesin; Region: Kinesin motor domain"
                     /db_xref="CDD:pfam00225"
     misc_feature    442..465
                     /gene="KIF3C"
                     /note="encodes ATP/GTP-binding site motif"
     misc_feature    871..906
                     /gene="KIF3C"
                     /note="encodes kinesin motor domain signature"
     polyA_signal    4889..4894
                     /gene="KIF3C"
BASE COUNT     1150 a   1342 c   1355 g   1066 t
ORIGIN      
        1 cctcccagcg tccccaccct aggaggctgc atgcggattg aagacgtgcg cctgggggct
       61 gggccggccc cgctgatccc gacctagcga gcaggatagc aggaccgccc aggctgcgga
      121 ggggctcggg ggcaggaagg tcagagcagc aagatggcca gtaagaccaa ggccagcgag
      181 gccctcaagg tggtggcccg gtgccgcccc ctcagcagga aggaggaggc tgctggtcac
      241 gagcagatcc tgaccatgga cgtgaaactg ggccaggtga ccctgcggaa cccccgcgcc
      301 gccccggggg agctgcccaa gaccttcacc tttgacgccg tgtatgatgc cagctccaag
      361 caggccgacc tgtatgacga aaccgtgagg cccctgatag actccgtgct ccagggtttc
      421 aatggcacgg tgtttgccta tggccagacg ggcactggca agacctatac catgcagggg
      481 acctgggtgg agcccgagct gcgcggggtc atcccgaatg cctttgagca catcttcacc
      541 cacatctccc gctcccagaa ccaacagtac ctggtccggg cctcctattt ggagatctac
      601 caggaagaga ttcgagacct gctctccaag gagccgggca agaggctaga gctgaaagag
      661 aaccccgaga ctggcgtcta catcaaggac ctctcctcct tcgtcaccaa gaatgtcaag
      721 gagattgagc atgtgatgaa cctggggaac cagacccggg ctgtgggcag cacccacatg
      781 aatgaggtca gctcccgctc ccatgccatc ttcatcatca ctgtggagtg cagcgaacgt
      841 ggctctgatg gccaggacca catccgagtg ggcaagctca acctcgtgga cctggctggc
      901 agcgagaggc agaacaaggc aggccccaac acagcgggag gggcagccac accatcctcg
      961 ggtggcggtg gtggcggtgg aggcagtggt ggtggtgctg gtggagagag gcctaaggaa
     1021 gcctccaaaa tcaacctctc attatctgcc ctgggcaacg tgattgctgc cctggcgggc
     1081 aacaggagca cccacattcc ctaccgggac tccaagctga cccggctgct ccaggactcc
     1141 ctggggggga atgcgaagac catcatggta gccacactgg ggccagcttc tcacagctac
     1201 gatgagagcc tctccacctt gcgctttgcc aaccgagcca agaacatcaa gaacaagccc
     1261 cgggtgaacg aggaccccaa ggacacactg ctgcgggaat tccaagagga gattgcccgc
     1321 ctgaaggccc agctggagaa gagggggatg ctggggaagc ggccccggag gaagagcagc
     1381 cgcaggaaga aggccgtgtc cgccccgcct gggtaccctg agggcccagt gattgaggct
     1441 tgggtggcag aagaggagga tgacaacaac aacaaccacc gcccgcccca gcccatcctg
     1501 gagtcagcct tggagaagaa catggagaat tacctgcagg aacagaagga gcggctggag
     1561 gaggagaagg cagccatcca ggatgaccgc agcctggtga gcgaggagaa gcagaagctg
     1621 ctggaggaga aggagaagat gctggaggac ctgcggcggg aacagcaggc cacagagctg
     1681 cttgcggcca agtacaaggc catggagagc aagctcctca tcgggggcag gaacatcatg
     1741 gatcacacca acgaacagca gaagatgttg gaactgaaga ggcaggagat tgccgagcag
     1801 aaacgtcgtg agcgggagat gcagcaggag atgatgctcc gggacgagga gactatggag
     1861 ctccggggca cctacacatc cctgcagcag gaggtggagg tcaaaaccaa gaaactcaag
     1921 aagctctacg ccaagctgca ggcggtgaag gcggagatcc aggaccagca tgatgagtat
     1981 atccgcgtgc ggcaggacct ggaggaggcg cagaacgagc agacccgcga actcaagctc
     2041 aagtacctaa tcatcgagaa cttcatcccg ccggaggaga agaacaagat catgaaccgg
     2101 cttttcctgg actgtgagga ggagcagtgg aagttccagc cactggtgcc agccggcgtc
     2161 agtagcagcc agatgaagaa gcggccaaca tctgcagtgg gctacaagag gcctatcagc
     2221 cagtatgctc gggttgccat ggcaatgggg tcccacccca ggtacagggc tgaaaacata
     2281 atgtttctgg agttggatgt gtcccctcca gctgtctttg agatggaatt ctctcacgac
     2341 caagaacaag accctcgtgc gctacacatg gagaggctca tgcgattgga cagctttctg
     2401 gaaagacctt ccacgtctaa agtccgaaag tccagatcct ggtgccagag tcctcagcgg
     2461 cctccacctt ccaccacaca tgcctccctg gcctctgctt ctctgcgccc tgcaacagtg
     2521 gcggaccatg agtgacaacc atcacgtcag gctgcccatc caatagactc ctgggatggg
     2581 gcagccaacc ctggctcatc tcatctgccg cttggtgcgt gtgcgtgtgc gtgcatgtgc
     2641 gtgtgcgtgt gtgcaggggt gagaatctgg cagatggtgc ctctgcctgc tcttcttcgc
     2701 ctcctttatt taattcatgt tatttattcg cggacgtctg ttcgtgttgg ggagatgccc
     2761 tcgcctgagc cgtctgggcc taccgtggtc actgcgtacg ctctttttct tctgacttga
     2821 gagctccccc agtcagatct caggcttgtc cccctgtcag ctgcctccag aagggaaggt
     2881 agccagtgcc tgagaagaca gtcccttttc tacccaccgc actccataac ctccatcttc
     2941 tcccacactg atggcgagca gcccctgagc actttctggg actgggagac tgcttggtgt
     3001 tccctgagga caagagacat cctgacagtg ttgggcatct gctccccgtg gacacagccc
     3061 cactctccac tttctgagcc tcagacaacc tcattcagcc tcttgggctc cttttcaagg
     3121 acattaataa cctcaccaac atagctcatg cccttcagct ttgacaagaa ctcacggctt
     3181 cccaaactct gctttctgcc caccttggat gggaactgtg gaccaagcaa ttaccatcgc
     3241 cttggaacct gcaggaaatg gaacagcaat tgagacaact tgaacagtca tcaacggaag
     3301 tccctccact ggattccttt gtttctgtcc cctccgagga gtcattttgg tcgacaggct
     3361 ctcaaggcaa ctccccattt tcaagaggct gctcctgcct gcttcgatca tttctccctg
     3421 cagctgccta gaccccgttc acagtgggag gagtcaatgt cattctaccc ctcgctaaac
     3481 gaagatatta acatctattg ctttttccct tcatctgtca caggaaacag aagcccaggc
     3541 acaatctttt ccagctttgc ctgttacccc tgtttctgaa ttgcatcttt aaggtattat
     3601 tttgttgaca atagatcctt tattcactag ttacgcaaat tggttcctag ggggatactc
     3661 cttaccttcc tttgtgatgg cccaaaatgt ctctaggtat ctcaagtgat aagtaaattt
     3721 ctacaaaaaa aaaatggtta atgttcattg actggctttt taagtgtata ttttggagga
     3781 cgggtgaaga ggtcataacg aaagcaagcg agtgaattag gatttcaaag tgccctaata
     3841 gtgtgagtct ccagttccta gaatatgaag agtgctgtcg ttggggtgaa accatgagac
     3901 tgacagatct gcctgaaatg gggggtgtgg gaggtggtgg cgggggttat tctctttcct
     3961 tcaggaaatg aacccttctt acatcattca agttctgctc tgaggatcaa gcttgggtct
     4021 gatttaactc agcgacactg tcatttctgc ttcattactg gactagaggg ttgagccacc
     4081 cacttgccat ttgctcctgt ccttccagga aatcacaatt ttcatcagag cccaagagat
     4141 tatttgagac tcaggattca gatcagaggt tcgactgtgg ctgggacagg agttgtgtgt
     4201 agaaattcac caggtggcct gagcgcaggg ggacctccag gctgcgttga gcagcctctc
     4261 ccactgacct ctttctcgtt tgtggacaaa gcagcacgta tcacctcatt catcacttgg
     4321 acacatcgcc tttgcattgt cttgtcacac ctccctcaca gtcttatagc acaatatacc
     4381 caaatcagcc cccccagtcc gaggctgggc ccaaggtatg gtcggaggag gagctcctgc
     4441 ctgcggtttt gtgtatgtgt gtatgtgtgt gcgtgtttgt gtgcgtgttt acctccacag
     4501 gggacactct acactcagtg taagatctgc tgggaacagg gccaccagga gtgcgtggat
     4561 ctcagtctct ctgtctctct ttctctcctt ttaattttgg tgtatcaaat atttgattga
     4621 caaagtaagg gccttgatta ggaccaaatt ctcgtgtgtt gctatggtct ttatttagga
     4681 caacaattaa caatgcagtg gcccattctt gtcactctac acatatgact atacgggaca
     4741 tatgtaatat ataaatatat atataaaaca ttcccctctg tccccttggc ttcggatgga
     4801 ggaatttctg ttgagctgaa atgcacctgc agctgggtgc tgccagcagc ttgcaggccc
     4861 cagccctgtt ccaatcaatg cagttgacaa taaaggaatg agtatcgtca cgg
//

BioPerl-1.007002/t/data/NT_021877.gbk000444000766000024      4017613155576321 16556 0ustar00cjfieldsstaff000000000000LOCUS       NT_021877              10001 bp    DNA     linear   CON 17-OCT-2003
DEFINITION  Homo sapiens chromosome 1 genomic contig.
ACCESSION   NT_021877 REGION: 13920000..13930000
VERSION     NT_021877.16  GI:37539616
KEYWORDS    .
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 10001)
  AUTHORS   International Human Genome Sequencing Consortium.
  TITLE     The DNA sequence of Homo sapiens
  JOURNAL   Unpublished (2003)
COMMENT     GENOME ANNOTATION REFSEQ:  Features on this sequence have been
            produced for build 34 of the NCBI's genome annotation [see
            documentation].
            On Oct 7, 2003 this sequence version replaced gi:29789880.
            The DNA sequence is part of the second release of the finished
            human reference genome. It was assembled from individual clone
            sequences by the Human Genome Sequencing Consortium in consultation
            with NCBI staff.
            COMPLETENESS: not full length.
FEATURES             Location/Qualifiers
     source          1..10001
                     /organism="Homo sapiens"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
     source          <1..>10001
                     /organism="Homo sapiens"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:9606"
                     /clone="RP11-302I18"
                     /note="Accession AL451081 sequenced by The Sanger Centre"
     gene            complement(3024..6641)
                     /gene="LOC127086"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /db_xref="GeneID:127086"
                     /db_xref="InterimID:127086"
     mRNA            complement(join(3024..4108,4110..4258,4357..4533,
                     5985..6225,6324..6641))
                     /gene="LOC127086"
                     /product="similar to ATP-dependent DNA helicase II, 70 kDa
                     subunit (Lupus Ku autoantigen protein p70) (Ku70) (70 kDa
                     subunit of Ku antigen) (Thyroid-lupus autoantigen) (TLAA)
                     (CTC box binding factor 75 kDa subunit) (CTCBF) (CTC75)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GNOMON."
                     /transcript_id="XM_060320.3"
                     /db_xref="GI:37539614"
                     /db_xref="GeneID:127086"
                     /db_xref="InterimID:127086"
     CDS             complement(join(3024..4108,4110..4258,4357..4533,
                     5985..6225,6324..6641))
                     /gene="LOC127086"
                     /note="overriding stop codons"
                     /codon_start=1
                     /transl_except=(pos:complement(6444..6446),aa:OTHER)
                     /transl_except=(pos:complement(4224..4226),
		     aa:OTHER)
                     /transl_except=(pos:complement(4067..4069),aa:OTHER)
                     /transl_except=(pos:complement(4049..4051),aa:OTHER)
                     /transl_except=(pos:complement(4046..4048),aa:OTHER)
                     /transl_except=(pos:complement(3791..3793),aa:OTHER)
                     /transl_except=(pos:complement(3678..3680),aa:OTHER)
                     /transl_except=(pos:complement(3036..3038),aa:OTHER)
                     /protein_id="XP_060320.3"
                     /db_xref="GI:37539615"
                     /db_xref="GeneID:127086"
                     /db_xref="InterimID:127086"
ORIGIN      
        1 atctctatgt gtcttttgta tccaatgtta actctagtcg ctgggaagtt ggatgtccct
       61 ccttaatcag atttgatata acagcaagag atttccaaga aaataccaaa aaatctaatt
      121 tcagcaaaaa gaaaaaattt ggcctccagt tttccagatg taggtagatt ctgtccaaaa
      181 cagatatcat ttaaaattta attttaaatc ctttgagttc ttcaaaagaa gatatttaac
      241 aaaatgtggg agctgatgac aattttaatt atttacaaag taattttctc agtaaaatga
      301 gccatgcttc aaaagggaaa ataccaacaa tttgccaggc attgtacctt ctttaatttt
      361 cttctttctt tctttctttc tttctttctt tctttctttc tttctttctt tctttctttc
      421 tttctttctt tcttttcttt ctttctttct ttctttcttt cttgagacgt tgtctcgctc
      481 tgtcacccag actagagtgc agtggcacca tctttgctca ctgcaagctc cgcctcctgg
      541 gttcacgcca ttctcctgcc acagcctcct gtgaagctgg gactacaggt gcctgccacc
      601 acgcccagct aattttttgt atttttggta gacacggggt ttcaccgtgt tagccaggat
      661 ggtctcgatc tcctgacctc gtgatctgcc tgccttggcc tcccaaagtg ctgggattat
      721 aggtgtgagc cactgtgccc ggccgccgcc tttaattttt ataaccactg tgaggagtgg
      781 tattattatt tgtgctcaaa cgggctcaca gaagtaggta acttggttaa aatcacttag
      841 ccattaagtg gtgaagttgg aattggaact cagatgtgtg tgaccctaat tttattgcta
      901 ttcctttaca cttggaattt tggtattttc attgctgtag aagaatgaag ttagccacca
      961 ctcattttgt tgacagattg accatatggc cttcctagaa gtgatcattg aactgatggt
     1021 attagctatt tctcctcaga cttactgatt gattgccttt gtgtgcaaaa agctctgtgt
     1081 tatgacagaa acaccaaaga atagcaaaga tctttacttt ccaggatatt caaatctaac
     1141 tggaggaaga gaacatgtaa ataaaaacta tatatcacca ggtagtaatt aattagtcag
     1201 agacaaccta atgtctcttc ttttttttat tctaaagata ataactacat attgcaggaa
     1261 aatctcctct aatctcacca ttatttcctc aactcttttt ttcaatgcac acatatattt
     1321 agatatttaa ttggatgata tttataaaca cttttatatc ctatttttta ttgaatattg
     1381 tattatgagc actctttcat gacatattat tccaatgtat aatttttaat ggcagaataa
     1441 tattcatagt attttaattt ataatatctt ctggacattt agattgtttc taatattttt
     1501 aattttttat aaattatatt gcattgaaca tcctagacca caaatctttt ctcatgtctc
     1561 tacttattga cttaggataa atttattcag gagaaatcga gaataaattt ctggagattc
     1621 ctgatatatg ttgagaagac ataagagaga atggagatcc ctaaacagat ttcgggtgca
     1681 ccacttcagt caccaccatt gtgggcacca ggccctagag gctaaagtac cacattatat
     1741 ctccaattcg tttgccaggt ggtctgtatt ctttgcttct ttgatttctc tgaatagagc
     1801 tttccattca tttgaagggg cactttctgg tggtgcctga tggcattttg cattacattt
     1861 tatttactgc aaaataaatt ttatttaatg caaaatgcca ccagggtgcc atcagaaagt
     1921 gccccttcaa atgagtagaa agtctccttt tatgattgca gtatagtttg acagagttag
     1981 aattctttgc tgttttcata ttagctactt aggatctata taaatctcat tgcaacggaa
     2041 ataccagagt gtcttgaggc tggctgactg gggccttatt tctagcattc taagaaggtg
     2101 caagagaaag aaactagcac tagatgagac tcatgagcat aaaccccttc aaattgggag
     2161 agatgtctgc atttgcagcc aaacttctat catcagcctt gattcctgac ataatgagtt
     2221 gtgagttgtt ataatcatgg aagaaaaatg acttgagagg ataacatgga tgatgtgatt
     2281 tgaagatgag ttcagtataa actttggtga aaaatcattc tgataaactg atcttaagac
     2341 atcatgccat gtttgatggc tcatgcctgt aatcccagaa ctttgcagca gtttgggagg
     2401 ctgaggcagg caggttgctt gagcccagga gtttgacacc agcctgggca acatggcgaa
     2461 accctatctc ttaaaaaaaa aatacaaaaa gtagccagtc atggtggctc atgcctggag
     2521 acccagctac ctgggaggct gacaggggag gttcacctga accgggggaa gatctgagcc
     2581 atgattgtgc cactacactc cagcctagga ctctctctgt ctcttaaaaa acaaaaaaaa
     2641 caaaaaaaaa aaaacaaaaa aaaacaaagg catcacattg tttactccct tgtgatgccg
     2701 gctggagtga cacttggcat caggagggca gtatagtctc tcttttttct tacagtacaa
     2761 agttagggct cctcattcag gcagtagagt aaagaacagc aaagtgggag ggctacacca
     2821 ttgccatggc aacagaaagc ctcctgaaga taaagtccct ctgcttctgt caggcagact
     2881 cttcctagat caggagacac ctgttttcac tggctgagaa caaggccagg tagcctggtt
     2941 acagtgtgga agggcagctg gacacatggc ctctggtcag ttctggaagt gattggtgaa
     3001 ggcttccagt ggctcctgct tcttcagcct gctcttcagc ccatacccca gcaggtctct
     3061 ttcagcatgg gcacggcaaa cttgcccagc atgctgttgc ttatgtgggt cttcagctcc
     3121 tcttctgaat actccacctt gggccttttg cttctgaaac cttcattatt gtgttttatg
     3181 ttgctaactt tcccttcagg attgtaatct ggtgggtaga gaagttcctt aaacttatcc
     3241 accagtgggg agcccagtct tttattcatt gcttcaacct caggcaatgt caggtccact
     3301 gcttgttcag gctccatcaa atccaaggcc aaggcctcca ggttcctgga acactgctgc
     3361 agcacagagt tctcaaagct gtcacttctg tatttgaatc ggagcttctg aacaatagcc
     3421 ttcaccttgt ccccctgctc tggggttgcc atgacttttt tagcaaaggg caccttccct
     3481 ttattatcag cataacataa aaagaccagc tggaagcctg caggaggcac ctgaattttc
     3541 tgatcatcca actcctcttc ctgtggcacc aaagccacaa aataaggggg gatgttcctg
     3601 cagggtgtgt atctgcacaa tgctgtgacc tccttctcca gacacttgat gagtagagca
     3661 ctgaacaggg ttgagctcta attcatcagt gactcttcag agtacacaaa caaggagggc
     3721 ctcaggtaac ggtgcttctt cagctttacc aagggcttaa acccatgaga atcaaacctg
     3781 gttcatcaaa ctattttagc tcttctgttt cctctttctc cagtataatc tgacgccttc
     3841 catagatctg agacctcttg gtatctctag acagaagcca actgcctgta tttacattaa
     3901 atatccaggt cttggttttc actgattcat ctatttctcg atagggcttt attggaggag
     3961 gcttgagagc cttctggatc ggattataaa tgcccacaga gagcactata tctttattga
     4021 gcttcagctt taacctgctg agtgttcact aactgatctc cttggctcaa acctgcctca
     4081 acaggtcttc tagctttctg gattcctcag tgagccctgg ggtcctcatc ctctgctatg
     4141 ctggtgatat ctctgtagaa gaaaggtata tcaaagccct cagttttctt caggtgcatc
     4201 aagtcaagga agatgcctgt atctcagtga ttattggctt tggtcctggc ccagctggct
     4261 ttggcatgtc attgccatgg gggttatcct cattggtgaa caacatgact cctcttgtac
     4321 agtacattgc taaagaggtt gttggcacag actcacagca cttcactgag tgagtagtca
     4381 gatccatgcc catcaggtct tggaaacgtt tttgtccctg ctgctcctta aaccggtcaa
     4441 gctctagaat tcgttttgcc cctggattat ccaactcctg gatgctcatg tcaaaaggag
     4501 tcaactcatc ttcactctga gattcaaaca tagctctgga ggcatcaacc aaaaaaatca
     4561 aactatttct tcctgaatat ttatagactc cacttgcttc acatgattct catgggtttc
     4621 aagcccttgg taatgctgaa gtgctgtgga tctgtgccaa cctctttagc gatgtccagt
     4681 tcaaaatgtt cttcttctgc ttcttcatca cccctggttt tgtaataaga ctttcaccct
     4741 gacatgttgc ttactgctca ctttggtgca ggccagagca gtatgatttc ttaaaattct
     4801 ctctgccagt ctggcctctg tcccactaca ttatttcaga gacccaagag tgttccaaag
     4861 gaatgttctg atattgataa caatacatat catcaaattg ctctctagaa atgtataaat
     4921 gtacaactcc atcgtaagag tatgtgatag tgctccttac agtgtatcct caccaacatg
     4981 gaatattatc ttttaaatat ctttgatgta ttattaattg tttttgtgga gtgctgtgac
     5041 tcaggctttt agaagaagcc taggataaca caaacataat tctggttaaa atcgatcagc
     5101 acagatgagt ggtgctggca atgactcgtc ttggctgaca ctggagaaaa taaaaggttt
     5161 agccaatggg aagagaaaat gataagtttg gtttgagata agataaattt ggattatctg
     5221 tgggacatcc aagaggtgat atgcagtagg tcattgagta tctctgtgtg ggggtgtgag
     5281 atgtaaatag aaaatgaaag tattaatata tggtaagtag gtaaaatcat aaatgtaggt
     5341 actatggttc aaggagaatt cagaatggga aaggagttga atatgaaatc ttggggaata
     5401 tcaacattta aagggtcgca aaagacacat aagctaaagg tactgaattt tttttttttt
     5461 tttttttttt agagatgagg tcttgcccta ttgcacaggc tggagtgcag cggtgcaatc
     5521 atagctcact gaagccttga attcctgggc tgaagcaatt ctcccacatc agcctctgga
     5581 gtagctaaga ctacaggcac aagccagcat gcccagagga aggcactttt ttttttcttt
     5641 ttaaagaagt ctttatttcc ttgttctgca aataaagctg gctgagttgg ttgctttttg
     5701 gtgattagtc agggaccaaa tcccatatcc ttgtccaatt cctccgactc ttccttggct
     5761 tcaaccttag ttggggtagc agcagcagca ggagcagtca tggcagcagt gtccacaggg
     5821 gcagcagcca caaaggcaga tggattaacc aagaaggcct tgaccttttc agcaagtggg
     5881 aaggtgtaat caatctccac agacaaagcc aggactcgtt tgtacccatt gatgatagaa
     5941 tggggtactg atgcaacagt tgggtagcca atctgcaaac agaccctgga aacatcgcag
     6001 acactctcca gaaagtgaga atgcagtttc ctctgtgatg tcaagccctt cagggttgta
     6061 gatgctgcca ttgtcgaaca cctgctgaat gaccagccca aagaagggag agatgttcag
     6121 cagtgtggct tcgctggctc ccactttgtc tccagtcttg atcagctgca catcactcag
     6181 gatttcagtg gcgcccctgg agattttagt ggtgatgcct aaaacctgga gaaacgaggt
     6241 cttcttgggc cctagaccag tgttctggac tggcacagtg acttcacagg ggcaatggaa
     6301 ccagcatgag ccacagctgg caccttgttg gccagcagca ggtccctgat ctcagtgagg
     6361 tcctccttga tgaacacaaa gcccacattc ccctgaatat gaggcaacag tttctctaga
     6421 gctgggttgt tttccaggtg ccttcagatg gccttgacca tcgtggtgtt cttgcctagc
     6481 agcaccatgg ccttcctgca gagggatatg cggatctgct gcatctgctt agagcccata
     6541 ttgtctgctc ccatgatgaa acatttcgga taatcatcca aaagttggat gatcttaagg
     6601 aagtagttgg gcttccaggt caccctgtct tccctgggca tcacagcggt gtgtcaggga
     6661 tttaaagaca caagggttta aagatgatgt cacttaaacg acgacacctg gtgagaggag
     6721 gcacttttta tgaagagcca cagaggtaga aagaaaactc agagagtatt gtcattgaaa
     6781 ataaagactt tcagaaagga gagaatagca tgtcacagag aaagaaaatt gagtaaatat
     6841 tagtgattgt aaaatggtga tttagtctgt tttgtgctgc tattacaaaa tacctgagac
     6901 tggataattt ataaagaaaa gaaatttatt ttctcacagt tctgagtgct agaaagtcta
     6961 agattaaggt gacagcaggt tgcattttct ggtgagttct gcatcatcca gagggaagga
     7021 acgctgtgtc ctcacatggt ggaaggctaa agagcaagcc agctgagtga ggcaagaaga
     7081 ttctttaata aaggccttaa ttccattcat gaggggacca gctctcatga ccttatcatc
     7141 tctagaaaac tccacctctt catactatca cattgcacta agtttcaaca tctgaatttt
     7201 ggagcggaca cattcagact atagcagatg aagttttaat agaaataatt aatgtttagc
     7261 aaccaagaag taccctcata cttccctgct tgttaatttc tacctttcag gttccccaag
     7321 gggtggtaca cagaggaata tcaaataata accaaattgc aattttatta aggcccaagt
     7381 caatgtcatt aacactcaat gcagctttgg cagggatagg tggacctctg gtttaggctc
     7441 aaggcataaa tgagattttc taccctgtgt ttccatcccc gttccccact atgggtcaaa
     7501 tctaaagctt aggatgttac ctacctgtgg tttgctgcat gatgaaagga tgtcaacgta
     7561 agatctgaca gagcctcctg gggaaggcct gaatccactt atttatcacg ccacatggag
     7621 taggaaacag agctcagaga aagactgtgt gcctgtgtga ccccaagaat cctatctttt
     7681 ggccatggaa gcaactctgt ctcctgagca ggtggggagg ttcttgaaaa actaggaaca
     7741 aaggctgtct gcttcatctt gtccctttag taggagaaag cagatccctt ctgcactcta
     7801 ggaacttcac atacatacag ctcggacaat agcacttgaa aaattaccat cttctaagaa
     7861 tagacccctt cactcatgag gatgtcttct agagcagtgc cattcaatag aattttctgt
     7921 gatgatgaag atgctattta aatctgtcct gtccagtact gtagttacta tgtgaggtca
     7981 ctgaagttat tattagcatt taaatttaaa tagccccctg tggatagtgg tgatcctatt
     8041 atacagtgaa gctctaggga tttcagggaa ttgtgaaatc tgctgatact ttcatgatag
     8101 tcttgttttc tcttttcagc ctctccatct ttatttgatt gattattcct ggttattcta
     8161 ggtctgctct taaggtatgg attaatattc atgtatagct gatacaactt atggagcctc
     8221 aggttctcga tctatgaaat gggaatgcta ataacaagtg ttccgttgtg gagattaaat
     8281 gacataatta aaccataagt tccaaatatg caaatggctt tcttacttaa ttgcaaattg
     8341 tcagggttta cccaatgcct gtaccaccat tgtatcttag aggtaaataa cttgtttttc
     8401 atcttacagg ctcatagctg aaaggaactt accttgagtc tctaatgaga ctttggactt
     8461 tagacttttg agatgatgct ggaatgagtt aagacttttg ggactattgg gaaaggatga
     8521 ttgtattttg caatgtgaga agaacatgag tttgctaggg ggggcaggag tggaatgcta
     8581 tggtttggat ataatttgtt tgtccccacc aaatcacatg ttgaaattta atccccagtg
     8641 tagcgatgtt gggtggtggg gcctagtggg aagtatttgg gtcacaggag tggatcgttc
     8701 atgaatatat caacgccctt ccactctgga gtggtgagtt ctcactatgt tagttcccat
     8761 gtgagctggt tgttaaaaca atcctcgctt ctccctgccc tgccctcctc tcttagcgtg
     8821 cagcctctgc acacaccagc tcctcttcgc catccaccac gagtggaagc agcctgaagg
     8881 ttttatcaga tgcagatgcc caatcttgaa ctttccagcc atccagaatc ataaaacaaa
     8941 taaaccttct ttttctttat aaattaccca acctccagta ttcctttata gcaaaacaaa
     9001 acagactaag acagtcagtt ttctgcattg atttttgtga ttcagggttc cagccctctg
     9061 gtgccatcaa taaatcacta ttcccaagtt aaagcaaatc cccatgagca ctggggatgt
     9121 gcagatagtg agtggtggtg atggtgaggt gcaaccacga tctttttttt tttttttgag
     9181 atgagtttta ctccatcacc aaggctgggg ctcagtggca tgatctcaac tcactgcaac
     9241 ctcggcctcc tgggttcaag caattcttgt gcctcagcct cttaaatagc tgggactagg
     9301 ggtgtgccac catgcctggc taatttttgc acttttatta gagatgaggc tttgccatgt
     9361 tggtcagact ggtctctaac tcctgacctc aagtgatcca cctgcctggg cctcccaaag
     9421 tgctgggatt acaggcatga gccaccgcac ccggcaccat gttcgattga agggagagat
     9481 ggggagggaa cctcattact gtattcacat gataaagctc ccatagaaac tcagcatcaa
     9541 ctaagtcaat tctagttttc attctaccaa caggcctccg ggctctggct tcctgaaggg
     9601 taggagtgat atatacaaag acgtcaagtg ggtgaaaaaa aactccacct gtcccctcag
     9661 aacgtggaga acctctttaa agttatgggg ctgaagactg atggcatcca cttatcagag
     9721 ctcccccagg tatgaaagga gtagaagatt tttcagggtg gggcattaat gaattttcag
     9781 aaataaagaa ataattgatt agtaatggtt ctactcaaca ggcactgttt actaacacca
     9841 caatcctaca tattcctaaa gctgaggatg aacaaaagtt cattactttg agactctaat
     9901 ttagacaaaa cttgaagcaa atcagtgatg aaagaaatcc tgctagctca gcaatcttcc
     9961 tgtggtactt gtgtgtgtgt gtgtttgtgt gtgtatgcgt g
//

BioPerl-1.007002/t/data/ORTHOMCL2345.cluster.aa.fa.aln.aa.phy.txt000444000766000024       606213155576321 23557 0ustar00cjfieldsstaff00000000000018  162
A5703     MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A57307    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A61002    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A65082    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A1895     MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARLLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A53685    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A9694     MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A13531    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A21170    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A17451    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A30004    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A34040    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A38189    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A72804    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A42101    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLXXXQVQP
A45935    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A76877    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A49905    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
BioPerl-1.007002/t/data/O_sat.wgs000444000766000024      1405713155576321 16506 0ustar00cjfieldsstaff000000000000LOCUS       AAAA02000000           50231 rc    DNA     linear   PLN 11-MAR-2005
DEFINITION  Oryza sativa (indica cultivar-group) whole genome shotgun
            sequencing project.
ACCESSION   AAAA00000000
VERSION     AAAA00000000.2  GI:54362548
KEYWORDS    WGS.
SOURCE      Oryza sativa (indica cultivar-group)
  ORGANISM  Oryza sativa (indica cultivar-group)
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
            clade; Ehrhartoideae; Oryzeae; Oryza.
REFERENCE   1  (bases 1 to 50231)
  AUTHORS   Yu,J., Wang,J., Lin,W., Li,S., Li,H., Zhou,J., Ni,P., Dong,W.,
            Hu,S., Zeng,C., Zhang,J., Zhang,Y., Li,R., Xu,Z., Li,S., Li,X.,
            Zheng,H., Cong,L., Lin,L., Yin,J., Geng,J., Li,G., Shi,J., Liu,J.,
            Lv,H., Li,J., Wang,J., Deng,Y., Ran,L., Shi,X., Wang,X., Wu,Q.,
            Li,C., Ren,X., Wang,J., Wang,X., Li,D., Liu,D., Zhang,X., Ji,Z.,
            Zhao,W., Sun,Y., Zhang,Z., Bao,J., Han,Y., Dong,L., Ji,J., Chen,P.,
            Wu,S., Liu,J., Xiao,Y., Bu,D., Tan,J., Yang,L., Ye,C., Zhang,J.,
            Xu,J., Zhou,Y., Yu,Y., Zhang,B., Zhuang,S., Wei,H., Liu,B., Lei,M.,
            Yu,H., Li,Y., Xu,H., Wei,S., He,X., Fang,L., Zhang,Z., Zhang,Y.,
            Huang,X., Su,Z., Tong,W., Li,J., Tong,Z., Li,S., Ye,J., Wang,L.,
            Fang,L., Lei,T., Chen,C., Chen,H., Xu,Z., Li,H., Huang,H.,
            Zhang,F., Xu,H., Li,N., Zhao,C., Li,S., Dong,L., Huang,Y., Li,L.,
            Xi,Y., Qi,Q., Li,W., Zhang,B., Hu,W., Zhang,Y., Tian,X., Jiao,Y.,
            Liang,X., Jin,J., Gao,L., Zheng,W., Hao,B., Liu,S., Wang,W.,
            Yuan,L., Cao,M., McDermott,J., Samudrala,R., Wang,J., Wong,G.K. and
            Yang,H.
  TITLE     The Genomes of Oryza sativa: A History of Duplications
  JOURNAL   PLoS Biol. 3 (2), E38 (2005)
   PUBMED   15685292
REFERENCE   2  (bases 1 to 50231)
  AUTHORS   Yu,J., Hu,S., Wang,J., Li,S., Wong,K.-S.G., Liu,B., Deng,Y.,
            Dai,L., Zhou,Y., Zhang,X., Cao,M., Liu,J., Sun,J., Tang,J.,
            Chen,Y., Huang,X., Lin,W., Ye,C., Tong,W., Cong,L., Geng,J.,
            Han,Y., Li,L., Li,W., Hu,G., Huang,X., Li,W., Li,J., Liu,Z., Li,L.,
            Liu,J., Qi,Q., Liu,J., Li,L., Wang,X., Lu,H., Wu,T., Zhu,M., Ni,P.,
            Han,H., Dong,W., Ren,X., Feng,X., Cui,P., Li,X., Wang,H., Xu,X.,
            Zhai,W., Xu,Z., Zhang,J., He,S., Zhang,J., Xu,J., Zhang,K.,
            Zheng,X., Dong,J., Zeng,W., Tao,L., Chen,X., He,J., Liu,D.,
            Tian,W., Tian,C., Xia,H., Li,G., Gao,H., Li,P., Chen,W., Wang,X.,
            Zhang,Y., Hu,J., Wang,J., Liu,S., Yang,J., Zhang,G., Bao,Q.,
            Xiong,Y., Li,Z., Mao,L., Zhou,C., Chen,R., Zhu,Z., Hao,B.,
            Zheng,W., Chen,S., Guo,W., Li,G., Liu,S., Huang,G., Tao,M.,
            Wang,J., Zhu,L., Yuan,L. and Yang,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-JAN-2002) Beijing Genomics Institute/Center of
            Genomics & Bioinformatics, Institute of Genomics, Chinese Academy
            of Sciences, Beijing Airport Industrial Zone B6, Beijing, Beijing
            101300, P.R.China
REFERENCE   3  (bases 1 to 50231)
  AUTHORS   Yu,J., Wang,J., Lin,W., Li,S., Li,H., Zhou,J., Ni,P., Dong,W.,
            Hu,S., Zeng,C., Zhang,J., Zhang,Y., Li,R., Xu,Z., Li,S., Li,X.,
            Zheng,H., Cong,L., Lin,L., Yin,J., Geng,J., Li,G., Shi,J., Liu,J.,
            Lv,H., Li,J., Wang,J., Deng,Y., Ran,L., Shi,X., Wang,X., Wu,Q.,
            Li,C., Ren,X., Wang,J., Wang,X., Li,D., Liu,D., Zhang,X., Ji,Z.,
            Zhao,W., Sun,Y., Zhang,Z., Bao,J., Han,Y., Dong,L., Ji,J., Chen,P.,
            Wu,S., Liu,J., Xiao,Y., Bu,D., Tan,J., Yang,L., Ye,C., Zhang,J.,
            Xu,J., Zhou,Y., Yu,Y., Zhang,B., Zhuang,S., Wei,H., Liu,B., Lei,M.,
            Yu,H., Li,Y., Xu,H., Wei,S., He,X., Fang,L., Zhang,Z., Zhang,Y.,
            Huang,X., Su,Z., Tong,W., Li,J., Tong,Z., Li,S., Ye,J., Wang,L.,
            Fang,L., Lei,T., Chen,C., Chen,H., Xu,Z., Li,H., Huang,H.,
            Zhang,F., Xu,H., Li,N., Zhao,C., Li,S., Dong,L., Huang,Y., Li,L.,
            Xi,Y., Qi,Q., Li,W., Zhang,B., Hu,W., Zhang,Y., Zheng,W., Hao,B.,
            Liu,S., Wang,W., Yuan,L., Cao,M.L., McDermott,J., Samudrala,R.,
            Wang,J., Wong,G.K.-S. and Yang,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-SEP-2003) Beijing Institute of Genomics, Chinese
            Academy of Sciences, Beijing Airport Industrial Zone B6, Beijing,
            Beijing 101300, P.R.China
COMMENT     On Oct 21, 2004 this sequence version replaced gi:19924305.
            The Oryza sativa (indica cultivar-group) whole genome shotgun (WGS)
            project has the project accession AAAA00000000.  This version of
            the project (02) has the accession number AAAA02000000, and
            consists of sequences AAAA02000001-AAAA02050231.
            The improved whole-genome shotgun (WGS) sequences for the genomes
            of indica and japonica rice, AAAA02000000 and AACV01000000,
            respectively, have multi-megabase contiguity and are nearly
            1000-fold improved over the drafts of 2002. Tested against a
            non-redundant collection of 19,079 full-length cDNAs, 98.1% of the
            genes are aligned without fragmentation to the mapped
            super-scaffolds of one or the other genome. Despite having only a
            small variation in gene content, there is an enormous variation in
            intergenic regions. At least a quarter of the two sequences could
            not be aligned, and in the aligned region
            single-nucleotide-polymorphism (SNP) rates varied from as little as
            3.0 SNP/kb in the coding regions, to 27.6 SNP/kb in the
            transposable elements.
FEATURES             Location/Qualifiers
     source          1..50231
                     /organism="Oryza sativa (indica cultivar-group)"
                     /mol_type="genomic DNA"
                     /cultivar="93-11"
                     /db_xref="taxon:39946"
WGS         AAAA02000001-AAAA02050231
WGS_SCAFLD  CM000126-CM000137
WGS_SCAFLD  CH398081-CH401163
//

BioPerl-1.007002/t/data/P33897000444000766000024      7033213155576321 15455 0ustar00cjfieldsstaff000000000000ID   ALD_HUMAN      STANDARD;      PRT;   745 AA.
AC   P33897;
DT   01-FEB-1994 (Rel. 28, Created)
DT   01-FEB-1994 (Rel. 28, Last sequence update)
DT   15-JUN-2004 (Rel. 44, Last annotation update)
DE   Adrenoleukodystrophy protein (ALDP).
GN   ABCD1 OR ALD.
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   SEQUENCE FROM N.A.
RX   MEDLINE=93180910; PubMed=8441467;
RA   Mosser J., Douar A.-M., Sarde C.-O., Kioschis P., Feil R., Moser H.,
RA   Poustka A.-M., Mandel J.-L., Aubourg P.;
RT   "Putative X-linked adrenoleukodystrophy gene shares unexpected
RT   homology with ABC transporters.";
RL   Nature 361:726-730(1993).
RN   [2]
RP   SEQUENCE FROM N.A.
RA   Platzer M., Bauer D., Brenner V., Drescher B., Nyakatura G.,
RA   Reichwald K., Sandoval N., Coy J., Kioschis P., Korn B.,
RA   Poustka A.-M., Rosenthal A.;
RL   Submitted (MAY-1996) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   SUBUNITS, AND CHARACTERIZATION OF VARIANTS X-ALD HIS-389; GLN-401;
RP   ARG-484 AND GLN-591.
RX   MEDLINE=20020240; PubMed=10551832;
RA   Liu L.X., Janvier K., Berteaux-Lecellier V., Cartier N., Benarous R.,
RA   Aubourg P.;
RT   "Homo- and heterodimerization of peroxisomal ATP-binding cassette
RT   half-transporters.";
RL   J. Biol. Chem. 274:32738-32743(1999).
RN   [4]
RP   FUNCTION, AND CHARACTERIZATION OF VARIANTS X-ALD SER-512 AND LEU-606.
RX   MEDLINE=21145507; PubMed=11248239;
RA   Roerig P., Mayerhofer P., Holzinger A., Gaertner J.;
RT   "Characterization and functional analysis of the nucleotide binding
RT   fold in human peroxisomal ATP binding cassette transporters.";
RL   FEBS Lett. 492:66-72(2001).
RN   [5]
RP   REVIEW.
RX   MEDLINE=93283453; PubMed=8507690;
RA   Aubourg P., Mosser J., Douar A.-M., Sarde C.-O., Lopez J.,
RA   Mandel J.-L.;
RT   "Adrenoleukodystrophy gene: unexpected homology to a protein involved
RT   in peroxisome biogenesis.";
RL   Biochimie 75:293-302(1993).
RN   [6]
RP   REVIEW ON VARIANTS.
RX   MEDLINE=97338663; PubMed=9195223;
RA   Dodd A., Rowland S.A., Hawkes S.L.J., Kennedy M.A., Love D.R.;
RT   "Mutations in the adrenoleukodystrophy gene.";
RL   Hum. Mutat. 9:500-511(1997).
RN   [7]
RP   REVIEW ON VARIANTS.
RX   MEDLINE=21614879; PubMed=11748843;
RA   Kemp S., Pujol A., Waterham H.R., van Geel B.M., Boehm C.D.,
RA   Raymond G.V., Cutting G.R., Wanders R.J.A., Moser H.W.;
RT   "ABCD1 mutations and the X-linked adrenoleukodystrophy mutation
RT   database: role in diagnosis and clinical correlations.";
RL   Hum. Mutat. 18:499-515(2001).
RN   [8]
RP   VARIANT X-ALD LYS-291.
RX   MEDLINE=94108454; PubMed=7904210;
RA   Cartier N., Sarde C.-O., Douar A.-M., Mosser J., Mandel J.-L.,
RA   Aubourg P.;
RT   "Abnormal messenger RNA expression and a missense mutation in
RT   patients with X-linked adrenoleukodystrophy.";
RL   Hum. Mol. Genet. 2:1949-1951(1993).
RN   [9]
RP   VARIANTS X-ALD SER-148; ASP-174; ARG-266; GLN-401; TRP-418 AND
RP   PHE-515.
RX   MEDLINE=95152524; PubMed=7849723;
RA   Fuchs S., Sarde C.-O., Wedemann H., Schwinger E., Mandel J.-L.,
RA   Gal A.;
RT   "Missense mutations are frequent in the gene for X-chromosomal
RT   adrenoleukodystrophy (ALD).";
RL   Hum. Mol. Genet. 3:1903-1905(1994).
RN   [10]
RP   VARIANTS X-ALD TRP-518; LEU-606; CYS-617 AND HIS-617.
RX   MEDLINE=94314951; PubMed=8040304;
RA   Fanen P., Guidoux S., Sarde C.-O., Mandel J.-L., Goossens M.,
RA   Aubourg P.;
RT   "Identification of mutations in the putative ATP-binding domain of
RT   the adrenoleukodystrophy gene.";
RL   J. Clin. Invest. 94:516-520(1994).
RN   [11]
RP   VARIANTS X-ALD.
RX   MEDLINE=95126139; PubMed=7825602;
RA   Ligtenberg M.J.L., Kemp S., Sarde C.-O., van Geel B.M., Kleijer W.J.,
RA   Barth P.G., Mandel J.-L., van Oost B.A., Bolhuis P.A.;
RT   "Spectrum of mutations in the gene encoding the adrenoleukodystrophy
RT   protein.";
RL   Am. J. Hum. Genet. 56:44-50(1995).
RN   [12]
RP   VARIANTS X-ALD HIS-104; GLU-178; LEU-560 AND GLY-528 DEL.
RX   MEDLINE=95233433; PubMed=7717396;
RA   Braun A., Ambach H., Kammerer S., Rolinski B., Stoeckler S., Rabl W.,
RA   Gaertner J., Zierz S., Roscher A.A.;
RT   "Mutations in the gene for X-linked adrenoleukodystrophy in patients
RT   with different clinical phenotypes.";
RL   Am. J. Hum. Genet. 56:854-861(1995).
RN   [13]
RP   VARIANTS X-ALD.
RX   MEDLINE=96047143; PubMed=7581394;
RA   Kok F., Neumann S., Sarde C.-O., Zheng S., Wu K.-H., Wei H.-M.,
RA   Bergin J., Watkins P.A., Gould S., Sack G., Moser H., Mandel J.-L.,
RA   Smith K.D.;
RT   "Mutational analysis of patients with X-linked adrenoleukodystrophy.";
RL   Hum. Mutat. 6:104-115(1995).
RN   [14]
RP   VARIANTS X-ALD.
RX   MEDLINE=96213748; PubMed=8651290;
RA   Feigenbaum V., Lombard-Platet G., Guidoux S., Sarde C.-O.,
RA   Mandel J.-L., Aubourg P.;
RT   "Mutational and protein analysis of patients and heterozygous women
RT   with X-linked adrenoleukodystrophy.";
RL   Am. J. Hum. Genet. 58:1135-1144(1996).
RN   [15]
RP   VARIANTS X-ALD.
RX   MEDLINE=96163493; PubMed=8566952;
RA   Krasemann E.W., Meier V., Korenke G.C., Hunneman D.H., Hanefeld F.;
RT   "Identification of mutations in the ALD-gene of 20 families with
RT   adrenoleukodystrophy/adrenomyeloneuropathy.";
RL   Hum. Genet. 97:194-197(1996).
RN   [16]
RP   VARIANT X-ALD ARG-679.
RX   MEDLINE=98112466; PubMed=9452087;
RA   Korenke G.C., Krasemann E., Meier V., Beuche W., Hunneman D.H.,
RA   Hanefeld F.;
RT   "First missense mutation (W679R) in exon 10 of the
RT   adrenoleukodystrophy gene in siblings with adrenomyeloneuropathy.";
RL   Hum. Mutat. Suppl. 1:S204-S206(1998).
RN   [17]
RP   VARIANTS X-ALD.
RX   MEDLINE=99408241; PubMed=10480364;
RA   Wichers M., Kohler W., Brennemann W., Boese V., Sokolowski P.,
RA   Bidlingmaier F., Ludwig M.;
RT   "X-linked adrenomyeloneuropathy associated with 14 novel ALD-gene
RT   mutations: no correlation between type of mutation and age of onset.";
RL   Hum. Genet. 105:116-119(1999).
RN   [18]
RP   VARIANTS X-ALD LEU-108 AND SER-143.
RX   MEDLINE=99299442; PubMed=10369742;
RA   Perusi C., Gomez-Lira M., Mottes M., Pignatti P.F., Bertini E.,
RA   Cappa M., Vigliani M.C., Schiffer D., Rizzuto N., Salviati A.;
RT   "Two novel missense mutations causing adrenoleukodystrophy in Italian
RT   patients.";
RL   Mol. Cell. Probes 13:179-182(1999).
RN   [19]
RP   VARIANTS X-ALD.
RX   MEDLINE=20202141; PubMed=10737980;
RA   Lachtermacher M.B., Seuanez H.N., Moser A.B., Moser H.W., Smith K.D.;
RT   "Determination of 30 X-linked adrenoleukodystrophy mutations,
RT   including 15 not previously described.";
RL   Hum. Mutat. 15:348-353(2000).
RN   [20]
RP   VARIANTS X-ALD GLN-401; TRP-418; LEU-543 AND ARG-556.
RX   MEDLINE=20438355; PubMed=10980539;
RA   Lira M.G., Mottes M., Pignatti P.F., Medica I., Uziel G., Cappa M.,
RA   Bertini E., Rizzuto N., Salviati A.;
RT   "Detection of mutations in the ALD gene (ABCD1) in seven Italian
RT   families: description of four novel mutations.";
RL   Hum. Mutat. 16:271-271(2000).
RN   [21]
RP   VARIANTS X-ALD LEU-98; ASP-99; GLU-217; GLN-518; ASP-608; ILE-633 AND
RP   PRO-660, AND VARIANT THR-13.
RX   MEDLINE=21331689; PubMed=11438993;
RA   Dvorakova L., Storkanova G., Unterrainer G., Hujova J., Kmoch S.,
RA   Zeman J., Hrebicek M., Berger J.;
RT   "Eight novel ABCD1 gene mutations and three polymorphisms in patients
RT   with X-linked adrenoleukodystrophy: the first polymorphism causing an
RT   amino acid exchange.";
RL   Hum. Mutat. 18:52-60(2001).
RN   [22]
RP   VARIANT X-ALD VAL-GLY-GLN-300 INS.
RX   MEDLINE=21668186; PubMed=11810273; DOI=10.1007/s00439-001-0632-z;
RA   Guimaraes C.P., Lemos M., Menezes I., Coelho T., Sa-Miranda C.,
RA   Azevedo J.E.;
RT   "Characterisation of two mutations in the ABCD1 gene leading to low
RT   levels of normal ALDP.";
RL   Hum. Genet. 109:616-622(2001).
RN   [23]
RP   INVOLVEMENT IN CONTIGUOUS ABCD1/DXS1375E DELETION SYNDROME.
RX   PubMed=11992258;
RA   Corzo D., Gibson W., Johnson K., Mitchell G., LePage G., Cox G.F.,
RA   Casey R., Zeiss C., Tyson H., Cutting G.R., Raymond G.V., Smith K.D.,
RA   Watkins P.A., Moser A.B., Moser H.W., Steinberg S.J.;
RT   "Contiguous deletion of the X-linked adrenoleukodystrophy gene (ABCD1)
RT   and DXS1357E: a novel neonatal phenotype similar to peroxisomal
RT   biogenesis disorders.";
RL   Am. J. Hum. Genet. 70:1520-1531(2002).
CC   -!- FUNCTION: Probable transporter. The nucleotide-binding fold acts
CC       as an ATP-binding subunit with ATPase activity.
CC   -!- SUBUNIT: Can form homo- and heterodimers with ABCD2/ALDR and
CC       ABCD3/PMP70. Dimerization is necessary to form an active
CC       transporter.
CC   -!- SUBCELLULAR LOCATION: Integral membrane protein. Peroxisomal.
CC   -!- DISEASE: Defects in ABCD1 are the cause of recessive X-linked
CC       adrenoleukodystrophy (X-ALD) [MIM:300100]. X-ALD is a rare
CC       peroxisomal metabolic disorder that occurs in boys and is
CC       characterized by progressive multifocal demyelination of the
CC       central nervous system and by adrenocortical insufficiency. It
CC       produces mental deterioration, corticospinal tract dysfunction,
CC       and cortical blindness. There is laboratory evidence of adrenal
CC       cortical dysfunction. Different clinical manifestations exist
CC       like: cerebral childhood ALD (CALD), adult cerebral ALD (ACALD),
CC       adrenomyeloneuropathy (AMN) and "Addison disease only" (ADO)
CC       phenotype.
CC   -!- DISEASE: Microdeletions in ABCD1 are involved in the contiguous
CC       ABCD1/DXS1375E deletion syndrome (CADDS) [MIM:300475]. Patients
CC       manifest profound neonatal hypotonia, subsequent failure to
CC       thrive, and cholestatic liver disease.
CC   -!- SIMILARITY: Belongs to the ABC transporter family. ALD subfamily.
CC   -!- DATABASE: NAME=X-ALD gene mutation database;
CC       WWW="http://www.x-ald.nl/".
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; Z21876; CAA79922.1; -.
DR   EMBL; Z31348; CAA83230.1; -.
DR   EMBL; Z31006; CAA83230.1; JOINED.
DR   EMBL; Z31007; CAA83230.1; JOINED.
DR   EMBL; Z31008; CAA83230.1; JOINED.
DR   EMBL; Z31009; CAA83230.1; JOINED.
DR   EMBL; Z31010; CAA83230.1; JOINED.
DR   EMBL; U52111; -; NOT_ANNOTATED_CDS.
DR   PIR; G02500; G02500.
DR   Genew; HGNC:61; ABCD1.
DR   MIM; 300371; -.
DR   MIM; 300100; -.
DR   MIM; 300475; -.
DR   GO; GO:0005779; C:integral to peroxisomal membrane; NAS.
DR   GO; GO:0004009; F:ATP-binding cassette (ABC) transporter acti...; NAS.
DR   GO; GO:0005215; F:transporter activity; NAS.
DR   GO; GO:0015919; P:peroxisomal membrane transport; NAS.
DR   GO; GO:0007031; P:peroxisome organization and biogenesis; NAS.
DR   InterPro; IPR003593; AAA_ATPase.
DR   InterPro; IPR003439; ABC_transporter.
DR   InterPro; IPR005283; FA_transporter.
DR   Pfam; PF00005; ABC_tran; 1.
DR   Pfam; PF06472; Ald_N; 1.
DR   ProDom; PD000006; ABC_transporter; 1.
DR   TIGRFAMs; TIGR00954; 3a01203; 1.
DR   PROSITE; PS50929; ABC_TM1F; 1.
DR   PROSITE; PS00211; ABC_TRANSPORTER_1; 1.
DR   PROSITE; PS50893; ABC_TRANSPORTER_2; 1.
KW   ATP-binding; Glycoprotein; Transmembrane; Transport; Peroxisome;
KW   Disease mutation; Polymorphism.
FT   TRANSMEM     92    112       Potential.
FT   TRANSMEM    131    151       Potential.
FT   TRANSMEM    238    258       Potential.
FT   TRANSMEM    333    353       Potential.
FT   TRANSMEM    473    493       Potential.
FT   NP_BIND     507    514       ATP (By similarity).
FT   VARIANT      13     13       N -> T (very rare polymorphism; does not
FT                                affect ALDP function).
FT                                /FTId=VAR_013340.
FT   VARIANT      90     90       E -> K (in X-ALD).
FT                                /FTId=VAR_009349.
FT   VARIANT      98     98       S -> L (in X-ALD; CALD type).
FT                                /FTId=VAR_000024.
FT   VARIANT      99     99       A -> D (in X-ALD; AMN-type).
FT                                /FTId=VAR_013341.
FT   VARIANT     103    103       S -> R (in X-ALD).
FT                                /FTId=VAR_009350.
FT   VARIANT     104    104       R -> C (in X-ALD).
FT                                /FTId=VAR_000025.
FT   VARIANT     104    104       R -> H (in X-ALD; ADO-type).
FT                                /FTId=VAR_000026.
FT   VARIANT     105    105       T -> I (in X-ALD; ADO-type).
FT                                /FTId=VAR_000027.
FT   VARIANT     105    105       T -> P (in X-ALD).
FT                                /FTId=VAR_009351.
FT   VARIANT     107    107       L -> P (in X-ALD; ALD/AMN/ADO-types and
FT                                asymptomatic).
FT                                /FTId=VAR_000028.
FT   VARIANT     108    108       S -> L (in X-ALD).
FT                                /FTId=VAR_009352.
FT   VARIANT     108    108       S -> W (in X-ALD; CALD and AMN-types).
FT                                /FTId=VAR_000029.
FT   VARIANT     113    113       R -> C (in X-ALD).
FT                                /FTId=VAR_009353.
FT   VARIANT     113    113       R -> P (in X-ALD).
FT                                /FTId=VAR_013342.
FT   VARIANT     116    116       G -> R (in X-ALD; CALD-type).
FT                                /FTId=VAR_000030.
FT   VARIANT     123    123       A -> V.
FT                                /FTId=VAR_000031.
FT   VARIANT     138    141       Missing (in X-ALD; ALD-type).
FT                                /FTId=VAR_000032.
FT   VARIANT     141    141       A -> T (in X-ALD).
FT                                /FTId=VAR_000033.
FT   VARIANT     143    143       P -> S (in X-ALD).
FT                                /FTId=VAR_009354.
FT   VARIANT     148    148       N -> S (in X-ALD; ADO-type).
FT                                /FTId=VAR_000034.
FT   VARIANT     149    149       S -> N (in X-ALD).
FT                                /FTId=VAR_000035.
FT   VARIANT     152    152       R -> C (in X-ALD; ADO-type).
FT                                /FTId=VAR_000036.
FT   VARIANT     152    152       R -> L (in X-ALD).
FT                                /FTId=VAR_009355.
FT   VARIANT     152    152       R -> P (in X-ALD).
FT                                /FTId=VAR_000037.
FT   VARIANT     152    152       R -> S (in X-ALD).
FT                                /FTId=VAR_009356.
FT   VARIANT     161    161       S -> P (in X-ALD).
FT                                /FTId=VAR_009357.
FT   VARIANT     163    163       R -> H (in X-ALD).
FT                                /FTId=VAR_000038.
FT   VARIANT     163    163       R -> P (in X-ALD).
FT                                /FTId=VAR_009358.
FT   VARIANT     174    174       Y -> C (in X-ALD).
FT                                /FTId=VAR_009359.
FT   VARIANT     174    174       Y -> D (in X-ALD; ALD-type).
FT                                /FTId=VAR_000039.
FT   VARIANT     174    174       Y -> S (in X-ALD; CALD-type).
FT                                /FTId=VAR_000040.
FT   VARIANT     178    178       Q -> E (in X-ALD; AMN-type).
FT                                /FTId=VAR_000041.
FT   VARIANT     181    181       Y -> C (in X-ALD; ALMD-type).
FT                                /FTId=VAR_000042.
FT   VARIANT     182    182       R -> P (in X-ALD).
FT                                /FTId=VAR_000043.
FT   VARIANT     189    189       R -> W (in X-ALD).
FT                                /FTId=VAR_009360.
FT   VARIANT     190    190       L -> P (in X-ALD).
FT                                /FTId=VAR_009361.
FT   VARIANT     194    194       D -> H (in X-ALD).
FT                                /FTId=VAR_000044.
FT   VARIANT     198    198       T -> K (in X-ALD).
FT                                /FTId=VAR_009362.
FT   VARIANT     200    200       D -> N (in X-ALD).
FT                                /FTId=VAR_009363.
FT   VARIANT     200    200       D -> V (in X-ALD; CALD-type).
FT                                /FTId=VAR_000045.
FT   VARIANT     207    207       S -> SAAS (in X-ALD).
FT                                /FTId=VAR_013343.
FT   VARIANT     211    211       L -> P (in X-ALD).
FT                                /FTId=VAR_000046.
FT   VARIANT     213    213       S -> C (in X-ALD).
FT                                /FTId=VAR_009364.
FT   VARIANT     214    214       N -> D (in X-ALD).
FT                                /FTId=VAR_009365.
FT   VARIANT     217    217       K -> E (in X-ALD).
FT                                /FTId=VAR_013344.
FT   VARIANT     218    218       P -> T (in X-ALD).
FT                                /FTId=VAR_009366.
FT   VARIANT     220    220       L -> P (in X-ALD).
FT                                /FTId=VAR_000047.
FT   VARIANT     221    221       D -> G (in X-ALD; CALD and AMN-types).
FT                                /FTId=VAR_000048.
FT   VARIANT     224    224       V -> E (in X-ALD).
FT                                /FTId=VAR_013345.
FT   VARIANT     229    229       L -> P (in X-ALD).
FT                                /FTId=VAR_009367.
FT   VARIANT     254    254       T -> M (in X-ALD; AMN-type).
FT                                /FTId=VAR_000049.
FT   VARIANT     254    254       T -> P (in X-ALD; AMN-type).
FT                                /FTId=VAR_000050.
FT   VARIANT     263    263       P -> L (in X-ALD; CALD, AMN and AD-
FT                                typeS).
FT                                /FTId=VAR_000051.
FT   VARIANT     266    266       G -> R (in X-ALD).
FT                                /FTId=VAR_000052.
FT   VARIANT     271    271       E -> K (in X-ALD).
FT                                /FTId=VAR_009368.
FT   VARIANT     274    274       R -> W (in X-ALD).
FT                                /FTId=VAR_013346.
FT   VARIANT     276    276       K -> E (in X-ALD; CALD-type).
FT                                /FTId=VAR_000053.
FT   VARIANT     277    277       G -> R (in X-ALD; AMN-type).
FT                                /FTId=VAR_000054.
FT   VARIANT     277    277       G -> GN (in X-ALD; ADO-type).
FT                                /FTId=VAR_000055.
FT   VARIANT     277    277       G -> W (in X-ALD).
FT                                /FTId=VAR_000056.
FT   VARIANT     280    280       R -> C (in X-ALD).
FT                                /FTId=VAR_013347.
FT   VARIANT     285    285       R -> P (in X-ALD).
FT                                /FTId=VAR_009369.
FT   VARIANT     291    291       E -> D (in X-ALD; ACALD and CALD-types).
FT                                /FTId=VAR_000057.
FT   VARIANT     291    291       E -> K (in X-ALD).
FT                                /FTId=VAR_000058.
FT   VARIANT     291    291       Missing (in X-ALD; ALD-type).
FT                                /FTId=VAR_000059.
FT   VARIANT     294    294       A -> T (in X-ALD; AMN-type).
FT                                /FTId=VAR_000060.
FT   VARIANT     296    296       Y -> C (in X-ALD).
FT                                /FTId=VAR_009370.
FT   VARIANT     298    298       G -> D (in X-ALD).
FT                                /FTId=VAR_009371.
FT   VARIANT     300    300       E -> EVGQ (in X-ALD).
FT                                /FTId=VAR_013348.
FT   VARIANT     302    302       E -> K (in X-ALD).
FT                                /FTId=VAR_009372.
FT   VARIANT     322    322       L -> P (in X-ALD).
FT                                /FTId=VAR_009373.
FT   VARIANT     336    336       K -> M (in X-ALD).
FT                                /FTId=VAR_009374.
FT   VARIANT     339    339       W -> R (in X-ALD).
FT                                /FTId=VAR_013349.
FT   VARIANT     342    342       S -> P (in X-ALD; AMN-type).
FT                                /FTId=VAR_000061.
FT   VARIANT     343    343       G -> D (in X-ALD).
FT                                /FTId=VAR_013350.
FT   VARIANT     389    389       R -> G (in X-ALD; AMN-type).
FT                                /FTId=VAR_000062.
FT   VARIANT     389    389       R -> H (in X-ALD; does not affect protein
FT                                stability, homo- and heterodimerization
FT                                with ALDR and PMP70).
FT                                /FTId=VAR_000063.
FT   VARIANT     401    401       R -> Q (in X-ALD; ALD and AMN-types; does
FT                                not affect protein stability, homo- and
FT                                heterodimerization with ALDR and PMP70).
FT                                /FTId=VAR_000064.
FT   VARIANT     401    401       R -> W (in X-ALD).
FT                                /FTId=VAR_009375.
FT   VARIANT     418    418       R -> W (in X-ALD; AMN-type).
FT                                /FTId=VAR_000065.
FT   VARIANT     427    427       Missing (in X-ALD).
FT                                /FTId=VAR_013351.
FT   VARIANT     484    484       P -> R (in X-ALD; CALD, AMN and ADO-
FT                                types; significantly decreases
FT                                homodimerization and abolishes
FT                                heterodimerization with ALDR and PMP70).
FT                                /FTId=VAR_000066.
FT   VARIANT     507    507       G -> V (in X-ALD; CALD-types).
FT                                /FTId=VAR_000067.
FT   VARIANT     512    512       G -> S (in X-ALD; CALD and AS-types;
FT                                reduced ATPase activity).
FT                                /FTId=VAR_000068.
FT   VARIANT     515    515       S -> F (in X-ALD).
FT                                /FTId=VAR_000069.
FT   VARIANT     518    518       R -> Q (in X-ALD; CALD-type).
FT                                /FTId=VAR_000070.
FT   VARIANT     518    518       R -> W (in X-ALD; CALD-type).
FT                                /FTId=VAR_000071.
FT   VARIANT     522    522       G -> W (in X-ALD; AD-type).
FT                                /FTId=VAR_000072.
FT   VARIANT     528    528       Missing (in X-ALD; CALD-type).
FT                                /FTId=VAR_000073.
FT   VARIANT     529    529       G -> S (in X-ALD).
FT                                /FTId=VAR_009376.
FT   VARIANT     534    534       P -> L (in X-ALD; CALD-type).
FT                                /FTId=VAR_000074.
FT   VARIANT     540    540       F -> S (in X-ALD).
FT                                /FTId=VAR_009377.
FT   VARIANT     543    543       P -> L (in X-ALD).
FT                                /FTId=VAR_009378.
FT   VARIANT     544    544       Q -> R (in X-ALD).
FT                                /FTId=VAR_009379.
FT   VARIANT     552    552       S -> P (in X-ALD).
FT                                /FTId=VAR_009380.
FT   VARIANT     554    554       R -> H (in X-ALD).
FT                                /FTId=VAR_009381.
FT   VARIANT     556    556       Q -> R (in X-ALD; ACALD type).
FT                                /FTId=VAR_013352.
FT   VARIANT     560    560       P -> L (in X-ALD; CALD-type).
FT                                /FTId=VAR_000075.
FT   VARIANT     560    560       P -> R (in X-ALD; AMN and ALMD-types).
FT                                /FTId=VAR_000076.
FT   VARIANT     560    560       P -> S (in X-ALD).
FT                                /FTId=VAR_013353.
FT   VARIANT     566    566       M -> K (in X-ALD).
FT                                /FTId=VAR_000077.
FT   VARIANT     591    591       R -> P (in X-ALD).
FT                                /FTId=VAR_013354.
FT   VARIANT     591    591       R -> Q (in X-ALD; AMN-type; significantly
FT                                decreases homodimerization and abolishes
FT                                heterodimerization with ALDR and PMP70).
FT                                /FTId=VAR_000078.
FT   VARIANT     591    591       R -> W (in X-ALD).
FT                                /FTId=VAR_009382.
FT   VARIANT     606    606       S -> L (in X-ALD; decreased ATP-binding
FT                                affinity).
FT                                /FTId=VAR_000079.
FT   VARIANT     606    606       S -> P (in X-ALD; CALD, AMN and ALMD-
FT                                types).
FT                                /FTId=VAR_000080.
FT   VARIANT     608    608       G -> D (in X-ALD; CALD-type).
FT                                /FTId=VAR_013355.
FT   VARIANT     609    609       E -> G (in X-ALD).
FT                                /FTId=VAR_000081.
FT   VARIANT     609    609       E -> K (in X-ALD; AMN-type).
FT                                /FTId=VAR_000082.
FT   VARIANT     616    616       A -> V (in X-ALD).
FT                                /FTId=VAR_009383.
FT   VARIANT     617    617       R -> C (in X-ALD; ALD-type and
FT                                asymptomatic).
FT                                /FTId=VAR_000083.
FT   VARIANT     617    617       R -> G (in X-ALD; ADO and AMN-types with
FT                                cerebral involvement).
FT                                /FTId=VAR_000084.
FT   VARIANT     617    617       R -> H (in X-ALD).
FT                                /FTId=VAR_000085.
FT   VARIANT     626    626       A -> D (in X-ALD).
FT                                /FTId=VAR_013356.
FT   VARIANT     626    626       A -> T (in X-ALD; CALD and AMN-types).
FT                                /FTId=VAR_000086.
FT   VARIANT     629    629       D -> H (in X-ALD).
FT                                /FTId=VAR_000087.
FT   VARIANT     630    630       E -> G (in X-ALD).
FT                                /FTId=VAR_009384.
FT   VARIANT     631    631       C -> Y (in X-ALD).
FT                                /FTId=VAR_009385.
FT   VARIANT     632    632       T -> I (in X-ALD).
FT                                /FTId=VAR_013357.
FT   VARIANT     633    633       S -> I (in X-ALD; asymptomatic).
FT                                /FTId=VAR_013358.
FT   VARIANT     633    633       S -> R (in X-ALD).
FT                                /FTId=VAR_009386.
FT   VARIANT     635    635       V -> M (in X-ALD).
FT                                /FTId=VAR_013359.
FT   VARIANT     636    636       S -> I (in X-ALD).
FT                                /FTId=VAR_009387.
FT   VARIANT     638    638       D -> Y (in X-ALD).
FT                                /FTId=VAR_009388.
FT   VARIANT     646    646       A -> P (in X-ALD).
FT                                /FTId=VAR_009389.
FT   VARIANT     654    654       L -> P (in X-ALD).
FT                                /FTId=VAR_009390.
FT   VARIANT     657    657       Missing (in X-ALD; CALD-type).
FT                                /FTId=VAR_000088.
FT   VARIANT     660    660       R -> P (in X-ALD; CALD-type).
FT                                /FTId=VAR_013360.
FT   VARIANT     660    660       R -> W (in X-ALD; CALD, ALMD and AS-
FT                                types).
FT                                /FTId=VAR_000089.
FT   VARIANT     667    667       H -> D (in X-ALD).
FT                                /FTId=VAR_009391.
FT   VARIANT     668    668       T -> I (in X-ALD).
FT                                /FTId=VAR_009392.
FT   VARIANT     679    679       W -> R (in X-ALD; AMN-type).
FT                                /FTId=VAR_000090.
FT   VARIANT     693    693       T -> M (in X-ALD).
FT                                /FTId=VAR_009393.
SQ   SEQUENCE   745 AA;  82908 MW;  13A8EFDE9EB1E7FA CRC64;
     MPVLSRPRPW RGNTLKRTAV LLALAAYGAH KVYPLVRQCL APARGLQAPA GEPTQEASGV
     AAAKAGMNRV FLQRLLWLLR LLFPRVLCRE TGLLALHSAA LVSRTFLSVY VARLDGRLAR
     CIARKDPRAF GWQLLQWLLI ALPATFVNSA IRYLEGQLAL SFRSRLVAHA YRLYFSQQTY
     YRVSNMDGRL RNPDQSLTED VVAFAASVAH LYSNLTKPLL DVAVTSYTLL RAARSRGAGT
     AWPSAIAGLV VFLTANVLRA FSPKFGELVA EEARRKGELR YMHSRVVANS EEIAFYGGHE
     VELALLQRSY QDLASQINLI LLERLWYVML EQFLMKYVWS ASGLLMVAVP IITATGYSES
     DAEAVKKAAL EKKEEELVSE RTEAFTIARN LLTAAADAIE RIMSSYKEVT ELAGYTARVH
     EMFQVFEDVQ RCHFKRPREL EDAQAGSGTI GRSGVRVEGP LKIRGQVVDV EQGIICENIP
     IVTPSGEVVV ASLNIRVEEG MHLLITGPNG CGKSSLFRIL GGLWPTYGGV LYKPPPQRMF
     YIPQRPYMSV GSLRDQVIYP DSVEDMQRKG YSEQDLEAIL DVVHLHHILQ REGGWEAMCD
     WKDVLSGGEK QRIGMARMFY HRPKYALLDE CTSAVSIDVE GKIFQAAKDA GIALLSITHR
     PSLWKYHTHL LQFDGEGGWK FEKLDSAARL SLTEEKQRLE QQLAGIPKMQ RRLQELCQIL
     GEAVAPAHVP APSPQGPGGL QGAST
//
BioPerl-1.007002/t/data/P35527.gb000444000766000024      3401413155576321 16031 0ustar00cjfieldsstaff000000000000LOCUS       P35527                   623 aa            linear   PRI 19-SEP-2006
DEFINITION  Keratin, type I cytoskeletal 9 (Cytokeratin-9) (CK-9) (Keratin-9)
            (K9).
ACCESSION   P35527
VERSION     P35527  GI:81175178
DBSOURCE    swissprot: locus K1C9_HUMAN, accession P35527;
            class: standard.
            extra accessions:O00109,Q14665
            created: Jun 1, 1994.
            sequence updated: Nov 8, 2005.
            annotation updated: Sep 19, 2006.
            xrefs: Z29074.1, CAA82315.1, S69510.1, AAC60619.1, X75015.1,
            CAA52924.1, AB001594.1, BAA19418.1, I37984
            xrefs (non-sequence databases): HSSP:P08670, IntAct:P35527,
            Ensembl:ENSG00000171403, KEGG:hsa:3857, HGNC:6447, MIM:144200,
            MIM:607606, ArrayExpress:P35527, GO:0005200, GO:0008544,
            InterPro:IPR011000, InterPro:IPR001664, InterPro:IPR002957,
            Pfam:PF00038, PRINTS:PR01248, PROSITE:PS00226
KEYWORDS    Coiled coil; Direct protein sequencing; Disease mutation;
            Intermediate filament; Keratin.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (residues 1 to 623)
  AUTHORS   Langbein,L., Heid,H.W., Moll,I. and Franke,W.W.
  TITLE     Molecular characterization of the body site-specific human
            epidermal cytokeratin 9: cDNA cloning, amino acid sequence, and
            tissue specificity of gene expression
  JOURNAL   Differentiation 55 (1), 57-71 (1993)
   PUBMED   7507869
  REMARK    NUCLEOTIDE SEQUENCE [MRNA], AND PARTIAL PROTEIN SEQUENCE.
            TISSUE=Foot sole tissue
            Erratum:[Differentiation. 1994 Jan;55(2):164. PMID: 7511549]
REFERENCE   2  (residues 1 to 623)
  AUTHORS   Reis,A., Hennies,H.-C., Langbein,L., Digweed,M., Mischke,D.,
            Dreschler,M., Schroek,E., Royer-Pokora,B., Franke,W.W., Sperling,K.
            and Kuester,W.
  TITLE     Keratin 9 gene mutations in epidermolytic palmoplantar keratoderma
            (EPPK)
  JOURNAL   Nat. Genet. 6 (2), 174-179 (1994)
   PUBMED   7512862
  REMARK    NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANTS EPPK LYS-161;
            GLN-163 AND TRP-163.
REFERENCE   3  (residues 1 to 623)
  AUTHORS   Bienvenut,W.V.
  JOURNAL   Unpublished
  REMARK    PROTEIN SEQUENCE OF 14-29, AND MASS SPECTROMETRY.
            TISSUE=Cervix carcinoma
REFERENCE   4  (residues 1 to 623)
  AUTHORS   Kobayashi,S., Tanaka,T., Matsuyoshi,N. and Imamura,S.
  TITLE     Keratin 9 point mutation in the pedigree of epidermolytic
            hereditary palmoplantar keratoderma perturbs keratin intermediate
            filament network formation
  JOURNAL   FEBS Lett. 386 (2-3), 149-155 (1996)
   PUBMED   8647270
  REMARK    NUCLEOTIDE SEQUENCE [MRNA] OF 147-372, AND VARIANT EPPK GLN-163.
REFERENCE   5  (residues 1 to 623)
  AUTHORS   Rosen,E.M., Meromsky,L., Romero,R., Setter,E. and Goldberg,I.
  TITLE     Human placenta contains an epithelial scatter protein
  JOURNAL   Biochem. Biophys. Res. Commun. 168 (3), 1082-1088 (1990)
   PUBMED   2140676
  REMARK    PROTEIN SEQUENCE OF 450-466.
REFERENCE   6  (residues 1 to 623)
  AUTHORS   Hennies,H.C., Zehender,D., Kunze,J., Kuster,W. and Reis,A.
  TITLE     Keratin 9 gene mutational heterogeneity in patients with
            epidermolytic palmoplantar keratoderma
  JOURNAL   Hum. Genet. 93 (6), 649-654 (1994)
   PUBMED   7516304
  REMARK    VARIANTS EPPK VAL-157 AND PRO-172.
REFERENCE   7  (residues 1 to 623)
  AUTHORS   Bonifas,J.M., Matsumura,K., Chen,M.A., Berth-Jones,J.,
            Hutchison,P.E., Zloczower,M., Fritsch,P.O. and Epstein,E.H. Jr.
  TITLE     Mutations of keratin 9 in two families with palmoplantar
            epidermolytic hyperkeratosis
  JOURNAL   J. Invest. Dermatol. 103 (4), 474-477 (1994)
   PUBMED   7523529
  REMARK    VARIANT EPPK SER-161.
REFERENCE   8  (residues 1 to 623)
  AUTHORS   Torchard,D., Blanchet-Bardon,C., Serova,O., Langbein,L., Narod,S.,
            Janin,N., Goguel,A.F., Bernheim,A., Franke,W.W., Lenoir,G.M. and
            Feunteun,J.
  TITLE     Epidermolytic palmoplantar keratoderma cosegregates with a keratin
            9 mutation in a pedigree with breast and ovarian cancer
  JOURNAL   Nat. Genet. 6 (1), 106-110 (1994)
   PUBMED   7511021
  REMARK    VARIANT EPPK TYR-161.
REFERENCE   9  (residues 1 to 623)
  AUTHORS   Rothnagel,J.A., Wojcik,S., Liefer,K.M., Dominey,A.M., Huber,M.,
            Hohl,D. and Roop,D.R.
  TITLE     Mutations in the 1A domain of keratin 9 in patients with
            epidermolytic palmoplantar keratoderma
  JOURNAL   J. Invest. Dermatol. 104 (3), 430-433 (1995)
   PUBMED   7532199
  REMARK    VARIANTS EPPK TRP-163 AND SER-168.
REFERENCE   10 (residues 1 to 623)
  AUTHORS   Endo,H., Hatamochi,A. and Shinkai,H.
  TITLE     A novel mutation of a leucine residue in coil 1A of keratin 9 in
            epidermolytic palmoplantar keratoderma
  JOURNAL   J. Invest. Dermatol. 109 (1), 113-115 (1997)
   PUBMED   9204965
  REMARK    VARIANT EPPK VAL-160.
REFERENCE   11 (residues 1 to 623)
  AUTHORS   Covello,S.P., Irvine,A.D., McKenna,K.E., Munro,C.S., Nevin,N.C.,
            Smith,F.J., Uitto,J. and McLean,W.H.
  TITLE     Mutations in keratin K9 in kindreds with epidermolytic palmoplantar
            keratoderma and epidemiology in Northern Ireland
  JOURNAL   J. Invest. Dermatol. 111 (6), 1207-1209 (1998)
   PUBMED   9856842
  REMARK    VARIANTS EPPK THR-157; VAL-157 AND GLN-163.
COMMENT     On Nov 8, 2005 this sequence version replaced gi:547748.
            [FUNCTION] May serve an important special function either in the
            mature palmar and plantar skin tissue or in the morphogenic program
            of the formation of these tissues.
            [SUBUNIT] Heterotetramer of two type I and two type II keratins.
            [TISSUE SPECIFICITY] Expressed in the terminally differentiated
            epidermis of palms and soles.
            [DISEASE] Defects in KRT9 are a cause of epidermolytic palmoplantar
            keratoderma (EPPK) [MIM:144200]; also abbreviated EHPPK. EPPK is an
            autosomal dominant disease characterized by diffuse thickening of
            the epidermis on the entire surface of palms and soles sharply
            bordered with erythematous margins.
            [MISCELLANEOUS] There are two types of cytoskeletal and
            microfibrillar keratin, I (acidic) and II (neutral to basic) (40-55
            and 56-70 kDa, respectively).
            [SIMILARITY] Belongs to the intermediate filament family.
            [CAUTION] Was originally (Ref.4) thought to be a 60 kDa chain of
            placental scatter protein.
            [WEB RESOURCE] NAME=Human Intermediate Filament Mutation Database;
            URL='http://www.interfil.org'.
            [WEB RESOURCE] NAME=GeneReviews;
            URL='http://www.genetests.org/query?gene=KRT9'.
FEATURES             Location/Qualifiers
     source          1..623
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
     gene            1..623
                     /gene="KRT9"
     Protein         1..623
                     /gene="KRT9"
                     /product="Keratin, type I cytoskeletal 9"
     Region          1..623
                     /gene="KRT9"
                     /region_name="Mature chain"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="Keratin, type I cytoskeletal 9.
                     /FTId=PRO_0000063640."
     Region          1..152
                     /gene="KRT9"
                     /region_name="Region of interest in the sequence"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="Head."
     Region          12..13
                     /gene="KRT9"
                     /region_name="Conflict"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="SR -> T (in Ref. 1; AAC60619 and 2)."
     Region          15..26
                     /gene="KRT9"
                     /region_name="Compositionally biased region"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="Poly-Gly."
     Region          152..463
                     /gene="KRT9"
                     /region_name="Filament"
                     /note="Intermediate filament protein; pfam00038"
                     /db_xref="CDD:40140"
     Region          153..461
                     /gene="KRT9"
                     /region_name="Region of interest in the sequence"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="Rod."
     Region          153..188
                     /gene="KRT9"
                     /region_name="Region of interest in the sequence"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="Coil 1A."
     Region          157
                     /gene="KRT9"
                     /region_name="Variant"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="M -> T (in EPPK). /FTId=VAR_010499."
     Region          157
                     /gene="KRT9"
                     /region_name="Variant"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="M -> V (in EPPK). /FTId=VAR_010500."
     Region          160
                     /gene="KRT9"
                     /region_name="Variant"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="L -> V (in EPPK). /FTId=VAR_010501."
     Region          161
                     /gene="KRT9"
                     /region_name="Variant"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="N -> K (in EPPK). /FTId=VAR_003822."
     Region          161
                     /gene="KRT9"
                     /region_name="Variant"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="N -> S (in EPPK). /FTId=VAR_010502."
     Region          161
                     /gene="KRT9"
                     /region_name="Variant"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="N -> Y (in EPPK). /FTId=VAR_010503."
     Region          163
                     /gene="KRT9"
                     /region_name="Variant"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="R -> Q (in EPPK). /FTId=VAR_003823."
     Region          163
                     /gene="KRT9"
                     /region_name="Variant"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="R -> W (in EPPK). /FTId=VAR_003824."
     Region          168
                     /gene="KRT9"
                     /region_name="Variant"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="L -> S (in EPPK). /FTId=VAR_003825."
     Region          172
                     /gene="KRT9"
                     /region_name="Variant"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="Q -> P (in EPPK). /FTId=VAR_010504."
     Region          189..207
                     /gene="KRT9"
                     /region_name="Region of interest in the sequence"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="Linker 1."
     Region          208..299
                     /gene="KRT9"
                     /region_name="Region of interest in the sequence"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="Coil 1B."
     Region          300..322
                     /gene="KRT9"
                     /region_name="Region of interest in the sequence"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="Linker 12."
     Region          323..461
                     /gene="KRT9"
                     /region_name="Region of interest in the sequence"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="Coil 2."
     Region          462..623
                     /gene="KRT9"
                     /region_name="Region of interest in the sequence"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="Tail."
ORIGIN      
        1 mscrqfsssy lsrsgggggg glgsggsirs sysrfsssgg rggggrfsss sgygggssrv
       61 cgrggggsfg ysygggsggg fsasslgggf gggsrgfgga sgggysssgg fgggfgggsg
      121 ggfgggygsg fgglggfggg agggdggilt anekstmqel nsrlasyldk vqaleeannd
      181 lenkiqdwyd kkgpaaiqkn yspyyntidd lkdqivdltv gnnktlldid ntrmtlddfr
      241 ikfemeqnlr qgvdadingl rqvldnltme ksdlemqyet lqeelmalkk nhkeemsqlt
      301 gqnsgdvnve invapgkdlt ktlndmrqey eqliaknrkd ienqyetqit qiehevsssg
      361 qevqssakev tqlrhgvqel eielqsqlsk kaaleksled tknrycgqlq miqeqisnle
      421 aqitdvrqei ecqnqeysll lsikmrleke ietyhnlleg gqedfessga gkiglggrgg
      481 sggsygrgsr ggsggsyggg gsgggygggs gsrggsggsy gggsgsgggs gggygggsgg
      541 ghsggsgggh sggsggnygg gsgsgggsgg gygggsgsrg gsggshgggs gfggesggsy
      601 gggeeasgsg ggygggsgks shs
//

BioPerl-1.007002/t/data/P39765.gb000444000766000024      4635213155576321 16051 0ustar00cjfieldsstaff000000000000LOCUS       P39765                   181 aa            linear   BCT 03-MAR-2009
DEFINITION  RecName: Full=Bifunctional protein pyrR; Includes: RecName:
            Full=Pyrimidine operon regulatory protein; Includes: RecName:
            Full=Uracil phosphoribosyltransferase; Short=UPRTase.
ACCESSION   P39765
VERSION     P39765.2  GI:20141743
DBSOURCE    UniProtKB: locus PYRR_BACSU, accession P39765;
            class: standard.
            extra accessions:P25982,Q45483
            created: Feb 1, 1995.
            sequence updated: Jan 31, 2002.
            annotation updated: Mar 3, 2009.
            xrefs: M59757.2, AAA21265.2, Z99112.2, CAB13421.1, U48870.1,
            AAB57770.1, B57986, NP_389430.1, 1A3C_A, 1A4X_A, 1A4X_B
            xrefs (non-sequence databases): PDBsum:1A3C, PDBsum:1A4X,
            GeneID:938030, GenomeReviews:AL009126_GR, KEGG:bsu:BSU15470,
            NMPDR:fig|224308.1.peg.1549, SubtiList:BG10712, HOGENOM:P39765,
            BioCyc:BSUB224308:BSU1549-MON, BRENDA:2.4.2.9, GO:0003723,
            GO:0004845, GO:0009116, GO:0006355, GO:0006353, HAMAP:MF_01219,
            InterPro:IPR000836, Pfam:PF00156, PROSITE:PS00103
KEYWORDS    3D-structure; Complete proteome; Glycosyltransferase; RNA-binding;
            Transcription; Transcription regulation; Transcription termination;
            Transferase.
SOURCE      Bacillus subtilis
  ORGANISM  Bacillus subtilis
            Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus.
REFERENCE   1  (residues 1 to 181)
  AUTHORS   Quinn,C.L., Stephenson,B.T. and Switzer,R.L.
  TITLE     Functional organization and nucleotide sequence of the Bacillus
            subtilis pyrimidine biosynthetic operon
  JOURNAL   J. Biol. Chem. 266 (14), 9113-9127 (1991)
   PUBMED   1709162
  REMARK    NUCLEOTIDE SEQUENCE [GENOMIC DNA].
            STRAIN=1A610, and JH861
REFERENCE   2  (residues 1 to 181)
  AUTHORS   Turner,R.J., Lu,Y. and Switzer,R.L.
  TITLE     Regulation of the Bacillus subtilis pyrimidine biosynthetic (pyr)
            gene cluster by an autogenous transcriptional attenuation mechanism
  JOURNAL   J. Bacteriol. 176 (12), 3708-3722 (1994)
   PUBMED   8206849
  REMARK    SEQUENCE REVISION, AND CHARACTERIZATION.
REFERENCE   3  (residues 1 to 181)
  AUTHORS   Switzer,R.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (??-MAY-1999)
  REMARK    SEQUENCE REVISION TO 34 AND 53.
REFERENCE   4  (residues 1 to 181)
  AUTHORS   Kunst,F., Ogasawara,N., Moszer,I., Albertini,A.M., Alloni,G.,
            Azevedo,V., Bertero,M.G., Bessieres,P., Bolotin,A., Borchert,S.,
            Borriss,R., Boursier,L., Brans,A., Braun,M., Brignell,S.C.,
            Bron,S., Brouillet,S., Bruschi,C.V., Caldwell,B., Capuano,V.,
            Carter,N.M., Choi,S.-K., Codani,J.-J., Connerton,I.F.,
            Cummings,N.J., Daniel,R.A., Denizot,F., Devine,K.M.,
            Duesterhoeft,A., Ehrlich,S.D., Emmerson,P.T., Entian,K.-D.,
            Errington,J., Fabret,C., Ferrari,E., Foulger,D., Fritz,C.,
            Fujita,M., Fujita,Y., Fuma,S., Galizzi,A., Galleron,N., Ghim,S.-Y.,
            Glaser,P., Goffeau,A., Golightly,E.J., Grandi,G., Guiseppi,G.,
            Guy,B.J., Haga,K., Haiech,J., Harwood,C.R., Henaut,A., Hilbert,H.,
            Holsappel,S., Hosono,S., Hullo,M.-F., Itaya,M., Jones,L.-M.,
            Joris,B., Karamata,D., Kasahara,Y., Klaerr-Blanchard,M., Klein,C.,
            Kobayashi,Y., Koetter,P., Koningstein,G., Krogh,S., Kumano,M.,
            Kurita,K., Lapidus,A., Lardinois,S., Lauber,J., Lazarevic,V.,
            Lee,S.-M., Levine,A., Liu,H., Masuda,S., Mauel,C., Medigue,C.,
            Medina,N., Mellado,R.P., Mizuno,M., Moestl,D., Nakai,S., Noback,M.,
            Noone,D., O'Reilly,M., Ogawa,K., Ogiwara,A., Oudega,B., Park,S.-H.,
            Parro,V., Pohl,T.M., Portetelle,D., Porwollik,S., Prescott,A.M.,
            Presecan,E., Pujic,P., Purnelle,B., Rapoport,G., Rey,M.,
            Reynolds,S., Rieger,M., Rivolta,C., Rocha,E., Roche,B., Rose,M.,
            Sadaie,Y., Sato,T., Scanlan,E., Schleich,S., Schroeter,R.,
            Scoffone,F., Sekiguchi,J., Sekowska,A., Seror,S.J., Serror,P.,
            Shin,B.-S., Soldo,B., Sorokin,A., Tacconi,E., Takagi,T.,
            Takahashi,H., Takemaru,K., Takeuchi,M., Tamakoshi,A., Tanaka,T.,
            Terpstra,P., Tognoni,A., Tosato,V., Uchiyama,S., Vandenbol,M.,
            Vannier,F., Vassarotti,A., Viari,A., Wambutt,R., Wedler,E.,
            Wedler,H., Weitzenegger,T., Winters,P., Wipat,A., Yamamoto,H.,
            Yamane,K., Yasumoto,K., Yata,K., Yoshida,K., Yoshikawa,H.-F.,
            Zumstein,E., Yoshikawa,H. and Danchin,A.
  TITLE     The complete genome sequence of the gram-positive bacterium
            Bacillus subtilis
  JOURNAL   Nature 390 (6657), 249-256 (1997)
   PUBMED   9384377
  REMARK    NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
            STRAIN=168
REFERENCE   5  (residues 1 to 181)
  AUTHORS   Pragai,Z., Tjalsma,H., Bolhuis,A., van Dijl,J.M., Venema,G. and
            Bron,S.
  TITLE     The signal peptidase II (Isp) gene of Bacillus subtilis
  JOURNAL   Microbiology (Reading, Engl.) 143 (PT 4), 1327-1333 (1997)
   PUBMED   9141696
  REMARK    NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-173.
            STRAIN=168
REFERENCE   6  (residues 1 to 181)
  AUTHORS   Martinussen,J., Glaser,P., Andersen,P.S. and Saxild,H.H.
  TITLE     Two genes encoding uracil phosphoribosyltransferase are present in
            Bacillus subtilis
  JOURNAL   J. Bacteriol. 177 (1), 271-274 (1995)
   PUBMED   7798145
  REMARK    ENZYME ACTIVITY.
REFERENCE   7  (residues 1 to 181)
  AUTHORS   Turner,R.J., Bonner,E.R., Grabner,G.K. and Switzer,R.L.
  TITLE     Purification and characterization of Bacillus subtilis PyrR, a
            bifunctional pyr mRNA-binding attenuation protein/uracil
            phosphoribosyltransferase
  JOURNAL   J. Biol. Chem. 273 (10), 5932-5938 (1998)
   PUBMED   9488732
  REMARK    CHARACTERIZATION, AND MASS SPECTROMETRY.
REFERENCE   8  (residues 1 to 181)
  AUTHORS   Savacool,H.K. and Switzer,R.L.
  TITLE     Characterization of the interaction of Bacillus subtilis PyrR with
            pyr mRNA by site-directed mutagenesis of the protein
  JOURNAL   J. Bacteriol. 184 (9), 2521-2528 (2002)
   PUBMED   11948166
  REMARK    MUTAGENESIS OF ARG-15; THR-18; ARG-19; HIS-22; ARG-27; THR-41;
            HIS-140; ARG-141; ARG-146 AND LYS-152.
REFERENCE   9  (residues 1 to 181)
  AUTHORS   Tomchick,D.R., Turner,R.J., Switzer,R.L. and Smith,J.L.
  TITLE     Adaptation of an enzyme to regulatory function: structure of
            Bacillus subtilis PyrR, a pyr RNA-binding attenuation protein and
            uracil phosphoribosyltransferase
  JOURNAL   Structure 6 (3), 337-350 (1998)
   PUBMED   9551555
  REMARK    X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
COMMENT     On or before Sep 27, 2005 this sequence version replaced
            gi:11376215, gi:730440.
            [FUNCTION] Regulates transcriptional attenuation of the pyrimidine
            nucleotide (pyr) operon by binding in a uridine-dependent manner to
            specific sites on pyr mRNA. This disrupts an antiterminator hairpin
            in the RNA and favors formation of a downstream transcription
            terminator, leading to a reduced expression of downstream genes.
            [FUNCTION] Also displays a weak uracil phosphoribosyltransferase
            activity which is not physiologically significant.
            [CATALYTIC ACTIVITY] UMP + diphosphate = uracil +
            5-phospho-alpha-D-ribose 1-diphosphate.
            [BIOPHYSICOCHEMICAL PROPERTIES] pH dependence: Optimum pH is 8.2
            for UPRTase activity.
            [SUBUNIT] Homodimer and homohexamer; in equilibrium.
            [MASS SPECTROMETRY] Mass=20263; Mass_error=2; Method=Electrospray;
            Range=1-181; Source=PubMed:9488732.
            [MISCELLANEOUS] Mutagenesis studies identified four amino acid
            residues that seem to be involved directly in binding of the
            protein to pyr mRNA: Thr-18, His-22, Arg-141 and Arg-146. Arg-27
            and Lys-152 were also likely to be involved in RNA-binding, but
            mutations may have altered their subunit-subunit interactions.
            Arg-19 was implicated in pyr regulation, but a specific role in
            RNA-binding could not be demonstrated.
            [MISCELLANEOUS] UMP and UTP incresase the affinity of pyrR for RNA.
            [SIMILARITY] Belongs to the purine/pyrimidine
            phosphoribosyltransferase family. PyrR subfamily.
FEATURES             Location/Qualifiers
     source          1..181
                     /organism="Bacillus subtilis"
                     /db_xref="taxon:1423"
     gene            1..181
                     /gene="pyrR"
                     /locus_tag="BSU15470"
     Protein         1..181
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /product="Bifunctional protein pyrR"
                     /EC_number="2.4.2.9"
     Region          1..181
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Mature chain"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="Bifunctional protein pyrR. /FTId=PRO_0000183030."
     Region          3..179
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Pribosyltran"
                     /note="Phosphoribosyl transferase domain; cl00309"
                     /db_xref="CDD:119714"
     Region          4..8
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Beta-strand region"
                     /experiment="experimental evidence, no additional details
                     recorded"
     Region          10..28
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Helical region"
                     /experiment="experimental evidence, no additional details
                     recorded"
     Site            15
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /site_type="mutagenized"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="R->Q: No effect on ability to regulate the pyr
                     operon; no effect on uprtase activity."
     Site            18
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /site_type="mutagenized"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="T->A: No effect on ability to regulate the pyr
                     operon only in presence of excess pyrimidines; reduced
                     affinity for RNA; no effect on UPRTase activity."
     Site            19
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /site_type="mutagenized"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="R->Q: Loss of ability to regulate the pyr operon;
                     no effect on UPRTase activity."
     Site            22
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /site_type="mutagenized"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="H->A: Loss of ability to regulate the pyr operon
                     and to bind to RNA; no effect on UPRTase activity."
     Site            27
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /site_type="mutagenized"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="R->Q: No effect on ability to regulate the pyr
                     operon only in presence of excess pyrimidines; reduced
                     affinity for RNA; no effect on UPRTase activity."
     Region          35..40
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Beta-strand region"
                     /experiment="experimental evidence, no additional details
                     recorded"
     Region          41..58
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Helical region"
                     /experiment="experimental evidence, no additional details
                     recorded"
     Region          41..42
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Region of interest in the sequence"
                     /inference="non-experimental evidence, no additional
                     details recorded"
                     /note="Substrate-binding (By similarity)."
     Site            41
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /site_type="mutagenized"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="T->I: Reduced ability to regulate the pyr operon;
                     reduced affinity for RNA; loss of UPRTase activity."
     Region          63..70
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Beta-strand region"
                     /experiment="experimental evidence, no additional details
                     recorded"
     Region          86..91
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Beta-strand region"
                     /experiment="experimental evidence, no additional details
                     recorded"
     Region          99..111
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Beta-strand region"
                     /experiment="experimental evidence, no additional details
                     recorded"
     Region          101..113
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Short sequence motif of biological interest"
                     /inference="non-experimental evidence, no additional
                     details recorded"
                     /note="PRPP-binding (By similarity)."
     Region          105..113
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Region of interest in the sequence"
                     /inference="non-experimental evidence, no additional
                     details recorded"
                     /note="Substrate binding (By similarity)."
     Region          112..124
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Helical region"
                     /experiment="experimental evidence, no additional details
                     recorded"
     Region          128..137
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Beta-strand region"
                     /experiment="experimental evidence, no additional details
                     recorded"
     Site            138
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /site_type="binding"
                     /inference="non-experimental evidence, no additional
                     details recorded"
                     /note="Substrate (By similarity)."
     Site            140
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /site_type="mutagenized"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="H->A: Reduced ability to regulate the pyr operon;
                     decreased UPRTase activity."
     Site            141
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /site_type="mutagenized"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="R->Q: Loss of ability to regulate the pyr operon;
                     highly reduced affinity for RNA; no effect on UPRTase
                     activity."
     Region          142..144
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Beta-strand region"
                     /experiment="experimental evidence, no additional details
                     recorded"
     Site            146
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /site_type="mutagenized"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="R->Q: Reduced ability to regulate the pyr operon,
                     and loss of ability to bind to RNA; no effect on UPRTase
                     activity."
     Region          148..153
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Beta-strand region"
                     /experiment="experimental evidence, no additional details
                     recorded"
     Site            152
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /site_type="mutagenized"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="K->Q: No effect on ability to regulate the pyr
                     operon only in presence of excess pyrimidines; reduced
                     affinity for RNA; no effect on UPRTase activity."
     Region          161..165
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Beta-strand region"
                     /experiment="experimental evidence, no additional details
                     recorded"
     Site            162
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /site_type="binding"
                     /inference="non-experimental evidence, no additional
                     details recorded"
                     /note="Substrate (By similarity)."
     Region          167..170
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Helical region"
                     /experiment="experimental evidence, no additional details
                     recorded"
     Region          174..178
                     /gene="pyrR"
                     /locus_tag="BSU15470"
                     /region_name="Beta-strand region"
                     /experiment="experimental evidence, no additional details
                     recorded"
ORIGIN      
        1 mnqkavilde qairraltri ahemiernkg mnncilvgik trgiylakrl aerieqiegn
       61 pvtvgeidit lyrddlskkt sndeplvkga dipvditdqk vilvddvlyt grtvragmda
      121 lvdvgrpssi qlavlvdrgh relpiradyi gkniptskse kvmvqldevd qndlvaiyen
      181 e
//

BioPerl-1.007002/t/data/PAM250000444000766000024       402413155576321 15457 0ustar00cjfieldsstaff000000000000#
# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
#
# PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049
#
# Expected score = -0.844, Entropy = 0.354 bits
#
# Lowest score = -8, Highest score = 17
#
   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
A  2 -2  0  0 -2  0  0  1 -1 -1 -2 -1 -1 -3  1  1  1 -6 -3  0  0  0  0 -8
R -2  6  0 -1 -4  1 -1 -3  2 -2 -3  3  0 -4  0  0 -1  2 -4 -2 -1  0 -1 -8
N  0  0  2  2 -4  1  1  0  2 -2 -3  1 -2 -3  0  1  0 -4 -2 -2  2  1  0 -8
D  0 -1  2  4 -5  2  3  1  1 -2 -4  0 -3 -6 -1  0  0 -7 -4 -2  3  3 -1 -8
C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3  0 -2 -8  0 -2 -4 -5 -3 -8
Q  0  1  1  2 -5  4  2 -1  3 -2 -2  1 -1 -5  0 -1 -1 -5 -4 -2  1  3 -1 -8
E  0 -1  1  3 -5  2  4  0  1 -2 -3  0 -2 -5 -1  0  0 -7 -4 -2  3  3 -1 -8
G  1 -3  0  1 -3 -1  0  5 -2 -3 -4 -2 -3 -5  0  1  0 -7 -5 -1  0  0 -1 -8
H -1  2  2  1 -3  3  1 -2  6 -2 -2  0 -2 -2  0 -1 -1 -3  0 -2  1  2 -1 -8
I -1 -2 -2 -2 -2 -2 -2 -3 -2  5  2 -2  2  1 -2 -1  0 -5 -1  4 -2 -2 -1 -8
L -2 -3 -3 -4 -6 -2 -3 -4 -2  2  6 -3  4  2 -3 -3 -2 -2 -1  2 -3 -3 -1 -8
K -1  3  1  0 -5  1  0 -2  0 -2 -3  5  0 -5 -1  0  0 -3 -4 -2  1  0 -1 -8
M -1  0 -2 -3 -5 -1 -2 -3 -2  2  4  0  6  0 -2 -2 -1 -4 -2  2 -2 -2 -1 -8
F -3 -4 -3 -6 -4 -5 -5 -5 -2  1  2 -5  0  9 -5 -3 -3  0  7 -1 -4 -5 -2 -8
P  1  0  0 -1 -3  0 -1  0  0 -2 -3 -1 -2 -5  6  1  0 -6 -5 -1 -1  0 -1 -8
S  1  0  1  0  0 -1  0  1 -1 -1 -3  0 -2 -3  1  2  1 -2 -3 -1  0  0  0 -8
T  1 -1  0  0 -2 -1  0  0 -1  0 -2  0 -1 -3  0  1  3 -5 -3  0  0 -1  0 -8
W -6  2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4  0 -6 -2 -5 17  0 -6 -5 -6 -4 -8
Y -3 -4 -2 -4  0 -4 -4 -5  0 -1 -1 -4 -2  7 -5 -3 -3  0 10 -2 -3 -4 -2 -8
V  0 -2 -2 -2 -2 -2 -2 -1 -2  4  2 -2  2 -1 -1 -1  0 -6 -2  4 -2 -2 -1 -8
B  0 -1  2  3 -4  1  3  0  1 -2 -3  1 -2 -4 -1  0  0 -5 -3 -2  3  2 -1 -8
Z  0  0  1  3 -5  3  3  0  2 -2 -3  0 -2 -5  0  0 -1 -6 -4 -2  2  3 -1 -8
X  0 -1  0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1  0  0 -4 -2 -1 -1 -1 -1 -8
* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8  1
BioPerl-1.007002/t/data/PX1CG.gb000444000766000024      5534013155576321 16053 0ustar00cjfieldsstaff000000000000LOCUS       PX1CG                   5386 bp ss-DNA     circular PHG 16-JUN-2004
DEFINITION  Coliphage phi-X174, complete genome.
ACCESSION   J02482 M10348 M10379 M10714 M10749 M10750 M10866 M10867 M24859
            V01128
VERSION     J02482.1  GI:216019
KEYWORDS    .
SOURCE      Enterobacteria phage phiX174
  ORGANISM  Enterobacteria phage phiX174
            Viruses; ssDNA viruses; Microviridae; Microvirus.
REFERENCE   1  (bases 1047 to 1094)
  AUTHORS   Ziff,E.B., Sedat,J.W. and Galibert,F.
  TITLE     Determination of the nucleotide sequence of a fragment of
            bacteriophage phiX 174 DNA
  JOURNAL   Nature New Biol. 241 (106), 34-37 (1973)
   PUBMED   4349156
REFERENCE   2  (bases 2370 to 2421)
  AUTHORS   Robertson,H.D., Barrell,B.G., Weith,H.L. and Donelson,J.E.
  TITLE     Isolation and sequence analysis of a ribosome-protected fragment
            from bacteriophage phiX 174 DNA
  JOURNAL   Nature New Biol. 241 (106), 38-40 (1973)
   PUBMED   4572838
REFERENCE   3  (bases 2370 to 2420)
  AUTHORS   Barrell,B.G., Weith,H.L., Donelson,J.E. and Robertson,H.D.
  TITLE     Sequence analysis of the ribosome-protected bacteriophase phiX174
            DNA fragment containing the gene G initiation site
  JOURNAL   J. Mol. Biol. 92 (3), 377-393 (1975)
   PUBMED   1095758
REFERENCE   4  (bases 2365 to 2591)
  AUTHORS   Air,G.M., Blackburn,E.H., Sanger,F. and Coulson,A.R.
  TITLE     The nucleotide and amino acid sequences of the N (5') terminal
            region of gene G of bacteriophage phiphiX 174
  JOURNAL   J. Mol. Biol. 96 (4), 703-719 (1975)
   PUBMED   1081600
REFERENCE   5  (bases 2263 to 2421)
  AUTHORS   Fiddes,J.C.
  TITLE     Nucleotide sequence of the intercistronic region between genes G
            and F in bacteriophage phiX174 DNA
  JOURNAL   J. Mol. Biol. 107 (1), 1-24 (1976)
   PUBMED   826639
REFERENCE   6  (bases 1017 to 1081)
  AUTHORS   Sedat,J., Ziff,E. and Galibert,F.
  TITLE     Direct determination of DNA nucleotide sequences. Structure of
            large specific fragments of bacteriophage phiX174 DNA
  JOURNAL   J. Mol. Biol. 107 (4), 391-416 (1976)
   PUBMED   1003475
REFERENCE   7  (bases 730 to 903)
  AUTHORS   Blackburn,E.H.
  TITLE     Transcription and sequence analysis of a fragment of bacteriophage
            phiX174 DNA
  JOURNAL   J. Mol. Biol. 107 (4), 417-431 (1976)
   PUBMED   826641
REFERENCE   8  (bases 1017 to 1762)
  AUTHORS   Air,G.M., Blackburn,E.H., Coulson,A.R., Galibert,F., Sanger,F.,
            Sedat,J.W. and Ziff,E.B.
  TITLE     Gene F of bacteriophage phiX174. Correlation of nucleotide
            sequences from the DNA and amino acid sequences from the gene
            product
  JOURNAL   J. Mol. Biol. 107 (4), 445-458 (1976)
   PUBMED   1088826
REFERENCE   9  (bases 2395 to 2922)
  AUTHORS   Air,G.M., Sanger,F. and Coulson,A.R.
  TITLE     Nucleotide and amino acid sequences of gene G of omegaX174
  JOURNAL   J. Mol. Biol. 108 (3), 519-533 (1976)
   PUBMED   1088827
REFERENCE   10 (bases 4137 to 4207)
  AUTHORS   Mansfeld,A.D., Vereijken,J.M. and Jansz,H.S.
  TITLE     The nucleotide sequence of a DNA fragment, 71 base pairs in length,
            near the origin of DNA replication of bacteriophage 0X174
  JOURNAL   Nucleic Acids Res. 3 (10), 2827-2844 (1976)
   PUBMED   995652
REFERENCE   11 (bases 4505 to 5374)
  AUTHORS   Brown,N.L. and Smith,M.
  TITLE     The sequence of a region of bacteriophage phiX174 DNA coding for
            parts of genes A and B
  JOURNAL   J. Mol. Biol. 116 (1), 1-28 (1977)
   PUBMED   592379
REFERENCE   12 (bases 1 to 5375)
  AUTHORS   Sanger,F., Air,G.M., Barrell,B.G., Brown,N.L., Coulson,A.R.,
            Fiddes,C.A., Hutchison,C.A., Slocombe,P.M. and Smith,M.
  TITLE     Nucleotide sequence of bacteriophage phi X174 DNA
  JOURNAL   Nature 265 (5596), 687-695 (1977)
   PUBMED   870828
REFERENCE   13 (bases 5022 to 5132)
  AUTHORS   Brown,N.L. and Smith,M.
  TITLE     DNA sequence of a region of the phi X174 genome coding for a
            ribosome binding site
  JOURNAL   Nature 265 (5596), 695-698 (1977)
   PUBMED   859573
REFERENCE   14 (bases 5346 to 5386; 1 to 159)
  AUTHORS   Smith,M., Brown,N.L., Air,G.M., Barrell,B.G., Coulson,A.R.,
            Hutchison,C.A. III and Sanger,F.
  TITLE     DNA sequence at the C termini of the overlapping genes A and B in
            bacteriophage phi X174
  JOURNAL   Nature 265 (5596), 702-705 (1977)
   PUBMED   859575
REFERENCE   15 (sites)
  AUTHORS   Fiddes,J.C.
  TITLE     The nucleotide sequence of a viral DNA
  JOURNAL   Sci. Am. 237 (6), 54-67 (1977)
   PUBMED   929160
REFERENCE   16 (bases 1 to 5386)
  AUTHORS   Sanger,F., Coulson,A.R., Friedmann,T., Air,G.M., Barrell,B.G.,
            Brown,N.L., Fiddes,J.C., Hutchison,C.A. III, Slocombe,P.M. and
            Smith,M.
  TITLE     The nucleotide sequence of bacteriophage phiX174
  JOURNAL   J. Mol. Biol. 125 (2), 225-246 (1978)
   PUBMED   731693
REFERENCE   17 (bases 1290 to 1302; 1340 to 1430; 1510 to 1570; 1600 to 1750)
  AUTHORS   Air,G.M., Coulson,A.R., Fiddes,J.C., Friedmann,T., Hutchison,C.A.
            III, Sanger,F., Slocombe,P.M. and Smith,A.J.
  TITLE     Nucleotide sequence of the F protein coding region of bacteriophage
            phiX174 and the amino acid sequence of its product
  JOURNAL   J. Mol. Biol. 125 (2), 247-254 (1978)
   PUBMED   731694
REFERENCE   18 (bases 4256 to 4317)
  AUTHORS   Langeveld,S.A., van Mansfeld,A.D., de Winter,J.M. and Weisbeek,P.J.
  TITLE     Cleavage of single-stranded DNA by the A and A* proteins of
            bacteriophage phi X174
  JOURNAL   Nucleic Acids Res. 7 (8), 2177-2188 (1979)
   PUBMED   160544
REFERENCE   19 (bases 4248 to 4332)
  AUTHORS   Heidekamp,F., Langeveld,S.A., Baas,P.D. and Jansz,H.S.
  TITLE     Studies of the recognition sequence of phi X174 gene A protein.
            Cleavage site of phi X gene A protein in St-1 RFI DNA
  JOURNAL   Nucleic Acids Res. 8 (9), 2009-2021 (1980)
   PUBMED   6253953
REFERENCE   20 (bases 436 to 490; 630 to 669; 930 to 979)
  AUTHORS   Takeshita,M., Kappen,L.S., Grollman,A.P., Eisenberg,M. and
            Goldberg,I.H.
  TITLE     Strand scission of deoxyribonucleic acid by neocarzinostatin,
            auromomycin, and bleomycin: studies on base release and nucleotide
            sequence specificity
  JOURNAL   Biochemistry 20 (26), 7599-7606 (1981)
   PUBMED   6173064
REFERENCE   22 (bases 1064 to 1757)
  AUTHORS   Merville,M.P., Piette,J., Lopez,M., Decuyper,J. and van de Vorst,A.
  TITLE     Termination sites of the in vitro DNA synthesis on single-stranded
            DNA photosensitized by promazines
  JOURNAL   J. Biol. Chem. 259 (24), 15069-15077 (1984)
   PUBMED   6239864
REFERENCE   23 (bases 2380 to 2512; 2593 to 2786; 2788 to 2947)
  AUTHORS   Air,G.M., Els,M.C., Brown,L.E., Laver,W.G. and Webster,R.G.
  TITLE     Location of antigenic sites on the three-dimensional structure of
            the influenza N2 virus neuraminidase
  JOURNAL   Virology 145 (2), 237-248 (1985)
   PUBMED   2411049
REFERENCE   24 (bases 449 to 482; 504 to 598; 1047 to 1111)
  AUTHORS   Ueda,K., Morita,J. and Komano,T.
  TITLE     Sequence specificity of heat-labile sites in DNA induced by
            mitomycin C
  JOURNAL   Biochemistry 23 (8), 1634-1640 (1984)
   PUBMED   6232949
COMMENT     On Apr 28, 2004 this sequence version replaced gi:15535.
            [8]  intermittent sequences.
            [15]  review; discussion of complete genome.
            Double checked with sumex tape.
            Single-stranded circular DNA which codes for eleven proteins.
            Replicative form is duplex, icosahedron, related to s13 & g4. [21]
            indicates that mitomycin C reduced with sodium borohydride induced
            heat-labile sites in DNA most preferentially at dinucleotide
            sequence 'gt' (especially 'Pu-g-t').
            Bacteriophage phi-X174 single stranded DNA molecules were
            irradiated with near UV light in the presence of promazine
            derivatives, after priming with restriction fragments or synthetic
            primers [22].  The resulting DNA fragments were used as templates
            for in vitro complementary chain synthesis by E.coli DNA polymerase
            I [22].  More than 90% of the observed chain terminations were
            mapped one nucleotide before a guanine residue [22].  Photoreaction
            occurred more predominantly with guanine residues localized in
            single-stranded parts of the genome [22].  These same guanine
            residues could also be damaged when the reaction was performed in
            the dark, in the presence of promazine cation radicals [22].
FEATURES             Location/Qualifiers
     source          1..5386
                     /organism="Enterobacteria phage phiX174"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:10847"
     CDS             join(3981..5386,1..136)
                     /function="viral strand synthesis"
                     /note="rf replication"
                     /codon_start=1
                     /transl_table=11
                     /product="A"
                     /protein_id="AAA32570.1"
                     /db_xref="GI:216020"
                     /translation="MVRSYYPSECHADYFDFERIEALKPAIEACGISTLSQSPMLGFH
                     KQMDNRIKLLEEILSFRMQGVEFDNGDMYVDGHKAASDVRDEFVSVTEKLMDELAQCY
                     NVLPQLDINNTIDHRPEGDEKWFLENEKTVTQFCRKLAAERPLKDIRDEYNYPKKKGI
                     KDECSRLLEASTMKSRRGFAIQRLMNAMRQAHADGWFIVFDTLTLADDRLEAFYDNPN
                     ALRDYFRDIGRMVLAAEGRKANDSHADCYQYFCVPEYGTANGRLHFHAVHFMRTLPTG
                     SVDPNFGRRVRNRRQLNSLQNTWPYGYSMPIAVRYTQDAFSRSGWLWPVDAKGEPLKA
                     TSYMAVGFYVAKYVNKKSDMDLAAKGLGAKEWNNSLKTKLSLLPKKLFRIRMSRNFGM
                     KMLTMTNLSTECLIQLTKLGYDATPFNQILKQNAKREMRLRLGKVTVADVLAAQPVTT
                     NLLKFMRASIKMIGVSNLQSFIASMTQKLTLSDISDESKNYLDKAGITTACLRIKSKW
                     TAGGK"
     CDS             join(4497..5386,1..136)
                     /function="shut off host DNA synthesis"
                     /codon_start=1
                     /transl_table=11
                     /product="A*"
                     /protein_id="AAA32571.1"
                     /db_xref="GI:216021"
                     /translation="MKSRRGFAIQRLMNAMRQAHADGWFIVFDTLTLADDRLEAFYDN
                     PNALRDYFRDIGRMVLAAEGRKANDSHADCYQYFCVPEYGTANGRLHFHAVHFMRTLP
                     TGSVDPNFGRRVRNRRQLNSLQNTWPYGYSMPIAVRYTQDAFSRSGWLWPVDAKGEPL
                     KATSYMAVGFYVAKYVNKKSDMDLAAKGLGAKEWNNSLKTKLSLLPKKLFRIRMSRNF
                     GMKMLTMTNLSTECLIQLTKLGYDATPFNQILKQNAKREMRLRLGKVTVADVLAAQPV
                     TTNLLKFMRASIKMIGVSNLQSFIASMTQKLTLSDISDESKNYLDKAGITTACLRIKS
                     KWTAGGK"
     CDS             join(5075..5386,1..51)
                     /function="capsid morphogenesis"
                     /codon_start=1
                     /transl_table=11
                     /product="B"
                     /protein_id="AAA32572.1"
                     /db_xref="GI:216022"
                     /translation="MEQLTKNQAVATSQEAVQNQNEPQLRDENAHNDKSVHGVLNPTY
                     QAGLRRDAVQPDIEAERKKRDEIEAGKSYCSRRFGGATCDDKSAQIYARFDKNDWRIQ
                     PAEFYRFHDAEVNTFGYF"
     variation       23
                     /note="in am18 and am35 [14]"
                     /replace="t"
     variation       25
                     /note="ts116 [14]"
                     /replace="c"
     CDS             51..221
                     /codon_start=1
                     /transl_table=11
                     /product="K"
                     /protein_id="AAA32573.1"
                     /db_xref="GI:216023"
                     /translation="MSRKIILIKQELLLLVYELNRSGLLAENEKIRPILAQLEKLLLC
                     DLSPSTNDSVKN"
     variation       57
                     /note="am6 [14]"
                     /replace="c"
     variation       117
                     /note="am6 [14]"
                     /replace="a"
     CDS             133..393
                     /note="DNA maturation"
                     /codon_start=1
                     /transl_table=11
                     /product="C"
                     /protein_id="AAA32574.1"
                     /db_xref="GI:216024"
                     /translation="MRKFDLSLRSSRSSYFATFRHQLTILSKTDALDEEKWLNMLGTF
                     VKDWFRYESHFVHGRDSLVDILKERGLLSESDAVQPLIGKKS"
     mRNA            358..3975
                     /product="major transcript"
     mRNA            358..991
                     /product="minor transcript"
     CDS             390..848
                     /function="capsid morphogenesis"
                     /codon_start=1
                     /transl_table=11
                     /product="D"
                     /protein_id="AAA32575.1"
                     /db_xref="GI:216025"
                     /translation="MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWI
                     ATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAE
                     FTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM"
     CDS             568..843
                     /function="cell lysis"
                     /codon_start=1
                     /transl_table=11
                     /product="E"
                     /protein_id="AAA32576.1"
                     /db_xref="GI:216026"
                     /translation="MVRWTLWDTLAFLLLLSLLLPSLLIMFIPSTFKRPVSSWKALNL
                     RKTLLMASSVRLKPLNCSRLPCVYAQETLTFLLTQKKTCVKNYVRKE"
     CDS             848..964
                     /note="core protein; DNA condensation"
                     /codon_start=1
                     /transl_table=11
                     /product="J"
                     /protein_id="AAA32577.1"
                     /db_xref="GI:216027"
                     /translation="MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF"
     CDS             1001..2284
                     /note="major coat protein"
                     /codon_start=1
                     /transl_table=11
                     /product="F"
                     /protein_id="AAA32578.1"
                     /db_xref="GI:216028"
                     /translation="MSNIQTGAERMPHDLSHLGFLAGQIGRLITISTTPVIAGDSFEM
                     DAVGALRLSPLRRGLAIDSTVDIFTFYVPHRHVYGEQWIKFMKDGVNATPLPTVNTTG
                     YIDHAAFLGTINPDTNKIPKHLFQGYLNIYNNYFKAPWMPDRTEANPNELNQDDARYG
                     FRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMGLQAAYANLHTDQERDYFMQRYHD
                     VISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRF
                     FVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVLYGNLPPREISMKDV
                     FRSGDSSKKFKIAEGQWYRYAPSYVSPAYHLLEGFPFIQEPPSGDLQERVLIRHHDYD
                     QCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS"
     CDS             2395..2922
                     /note="major spike protein"
                     /codon_start=1
                     /transl_table=11
                     /product="G"
                     /protein_id="AAA32579.1"
                     /db_xref="GI:216029"
                     /translation="MFQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYF
                     DSLTVNAGNGGFLHCIQMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESSSVPTT
                     LPTAYDVYPLNGRHDGGYYTVKDCVTIDVLPRTPGNNVYVGFMVWSNFTATKCRGLVS
                     LNQVIKEIICLQPLK"
     CDS             2931..3917
                     /function="adsorption"
                     /note="minor spike protein"
                     /codon_start=1
                     /transl_table=11
                     /product="H"
                     /protein_id="AAA32580.1"
                     /db_xref="GI:216030"
                     /translation="MFGAIAGGIASALAGGAMSKLFGGGQKAASGGIQGDVLATDNNT
                     VGMGDAGIKSAIQGSNVPNPDEAAPSFVSGAMAKAGKGLLEGTLQAGTSAVSDKLLDL
                     VGLGGKSAADKGKDTRDYLAAAFPELNAWERAGADASSAGMVDAGFENQKELTKMQLD
                     NQKEIAEMQNETQKEIAGIQSATSRQNTKDQVYAQNEMLAYQQKESTARVASIMENTN
                     LSKQQQVSEIMRQMLTQAQTAGQYFTNDQIKEMTRKVSAEVDLVHQQTQNQRYGSSHI
                     GATAKDISNVVTDAASGVVDIFHGIDKAVADTWNNFWKDGKADGIGSNLSRK"
     misc_feature    3962
                     /note="transcription start site"
     rep_origin      4306
                     /note="origin of viral strand synthesis"
     misc_feature    4899
                     /note="transcription start site"
ORIGIN      
        1 gagttttatc gcttccatga cgcagaagtt aacactttcg gatatttctg atgagtcgaa
       61 aaattatctt gataaagcag gaattactac tgcttgttta cgaattaaat cgaagtggac
      121 tgctggcgga aaatgagaaa attcgaccta tccttgcgca gctcgagaag ctcttacttt
      181 gcgacctttc gccatcaact aacgattctg tcaaaaactg acgcgttgga tgaggagaag
      241 tggcttaata tgcttggcac gttcgtcaag gactggttta gatatgagtc acattttgtt
      301 catggtagag attctcttgt tgacatttta aaagagcgtg gattactatc tgagtccgat
      361 gctgttcaac cactaatagg taagaaatca tgagtcaagt tactgaacaa tccgtacgtt
      421 tccagaccgc tttggcctct attaagctca ttcaggcttc tgccgttttg gatttaaccg
      481 aagatgattt cgattttctg acgagtaaca aagtttggat tgctactgac cgctctcgtg
      541 ctcgtcgctg cgttgaggct tgcgtttatg gtacgctgga ctttgtggga taccctcgct
      601 ttcctgctcc tgttgagttt attgctgccg tcattgctta ttatgttcat cccgtcaaca
      661 ttcaaacggc ctgtctcatc atggaaggcg ctgaatttac ggaaaacatt attaatggcg
      721 tcgagcgtcc ggttaaagcc gctgaattgt tcgcgtttac cttgcgtgta cgcgcaggaa
      781 acactgacgt tcttactgac gcagaagaaa acgtgcgtca aaaattacgt gcggaaggag
      841 tgatgtaatg tctaaaggta aaaaacgttc tggcgctcgc cctggtcgtc cgcagccgtt
      901 gcgaggtact aaaggcaagc gtaaaggcgc tcgtctttgg tatgtaggtg gtcaacaatt
      961 ttaattgcag gggcttcggc cccttacttg aggataaatt atgtctaata ttcaaactgg
     1021 cgccgagcgt atgccgcatg acctttccca tcttggcttc cttgctggtc agattggtcg
     1081 tcttattacc atttcaacta ctccggttat cgctggcgac tccttcgaga tggacgccgt
     1141 tggcgctctc cgtctttctc cattgcgtcg tggccttgct attgactcta ctgtagacat
     1201 ttttactttt tatgtccctc atcgtcacgt ttatggtgaa cagtggatta agttcatgaa
     1261 ggatggtgtt aatgccactc ctctcccgac tgttaacact actggttata ttgaccatgc
     1321 cgcttttctt ggcacgatta accctgatac caataaaatc cctaagcatt tgtttcaggg
     1381 ttatttgaat atctataaca actattttaa agcgccgtgg atgcctgacc gtaccgaggc
     1441 taaccctaat gagcttaatc aagatgatgc tcgttatggt ttccgttgct gccatctcaa
     1501 aaacatttgg actgctccgc ttcctcctga gactgagctt tctcgccaaa tgacgacttc
     1561 taccacatct attgacatta tgggtctgca agctgcttat gctaatttgc atactgacca
     1621 agaacgtgat tacttcatgc agcgttacca tgatgttatt tcttcatttg gaggtaaaac
     1681 ctcttatgac gctgacaacc gtcctttact tgtcatgcgc tctaatctct gggcatctgg
     1741 ctatgatgtt gatggaactg accaaacgtc gttaggccag ttttctggtc gtgttcaaca
     1801 gacctataaa cattctgtgc cgcgtttctt tgttcctgag catggcacta tgtttactct
     1861 tgcgcttgtt cgttttccgc ctactgcgac taaagagatt cagtacctta acgctaaagg
     1921 tgctttgact tataccgata ttgctggcga ccctgttttg tatggcaact tgccgccgcg
     1981 tgaaatttct atgaaggatg ttttccgttc tggtgattcg tctaagaagt ttaagattgc
     2041 tgagggtcag tggtatcgtt atgcgccttc gtatgtttct cctgcttatc accttcttga
     2101 aggcttccca ttcattcagg aaccgccttc tggtgatttg caagaacgcg tacttattcg
     2161 ccaccatgat tatgaccagt gtttccagtc cgttcagttg ttgcagtgga atagtcaggt
     2221 taaatttaat gtgaccgttt atcgcaatct gccgaccact cgcgattcaa tcatgacttc
     2281 gtgataaaag attgagtgtg aggttataac gccgaagcgg taaaaatttt aatttttgcc
     2341 gctgaggggt tgaccaagcg aagcgcggta ggttttctgc ttaggagttt aatcatgttt
     2401 cagactttta tttctcgcca taattcaaac tttttttctg ataagctggt tctcacttct
     2461 gttactccag cttcttcggc acctgtttta cagacaccta aagctacatc gtcaacgtta
     2521 tattttgata gtttgacggt taatgctggt aatggtggtt ttcttcattg cattcagatg
     2581 gatacatctg tcaacgccgc taatcaggtt gtttctgttg gtgctgatat tgcttttgat
     2641 gccgacccta aattttttgc ctgtttggtt cgctttgagt cttcttcggt tccgactacc
     2701 ctcccgactg cctatgatgt ttatcctttg aatggtcgcc atgatggtgg ttattatacc
     2761 gtcaaggact gtgtgactat tgacgtcctt ccccgtacgc cgggcaataa cgtttatgtt
     2821 ggtttcatgg tttggtctaa ctttaccgct actaaatgcc gcggattggt ttcgctgaat
     2881 caggttatta aagagattat ttgtctccag ccacttaagt gaggtgattt atgtttggtg
     2941 ctattgctgg cggtattgct tctgctcttg ctggtggcgc catgtctaaa ttgtttggag
     3001 gcggtcaaaa agccgcctcc ggtggcattc aaggtgatgt gcttgctacc gataacaata
     3061 ctgtaggcat gggtgatgct ggtattaaat ctgccattca aggctctaat gttcctaacc
     3121 ctgatgaggc cgcccctagt tttgtttctg gtgctatggc taaagctggt aaaggacttc
     3181 ttgaaggtac gttgcaggct ggcacttctg ccgtttctga taagttgctt gatttggttg
     3241 gacttggtgg caagtctgcc gctgataaag gaaaggatac tcgtgattat cttgctgctg
     3301 catttcctga gcttaatgct tgggagcgtg ctggtgctga tgcttcctct gctggtatgg
     3361 ttgacgccgg atttgagaat caaaaagagc ttactaaaat gcaactggac aatcagaaag
     3421 agattgccga gatgcaaaat gagactcaaa aagagattgc tggcattcag tcggcgactt
     3481 cacgccagaa tacgaaagac caggtatatg cacaaaatga gatgcttgct tatcaacaga
     3541 aggagtctac tgctcgcgtt gcgtctatta tggaaaacac caatctttcc aagcaacagc
     3601 aggtttccga gattatgcgc caaatgctta ctcaagctca aacggctggt cagtatttta
     3661 ccaatgacca aatcaaagaa atgactcgca aggttagtgc tgaggttgac ttagttcatc
     3721 agcaaacgca gaatcagcgg tatggctctt ctcatattgg cgctactgca aaggatattt
     3781 ctaatgtcgt cactgatgct gcttctggtg tggttgatat ttttcatggt attgataaag
     3841 ctgttgccga tacttggaac aatttctgga aagacggtaa agctgatggt attggctcta
     3901 atttgtctag gaaataaccg tcaggattga caccctccca attgtatgtt ttcatgcctc
     3961 caaatcttgg aggctttttt atggttcgtt cttattaccc ttctgaatgt cacgctgatt
     4021 attttgactt tgagcgtatc gaggctctta aacctgctat tgaggcttgt ggcatttcta
     4081 ctctttctca atccccaatg cttggcttcc ataagcagat ggataaccgc atcaagctct
     4141 tggaagagat tctgtctttt cgtatgcagg gcgttgagtt cgataatggt gatatgtatg
     4201 ttgacggcca taaggctgct tctgacgttc gtgatgagtt tgtatctgtt actgagaagt
     4261 taatggatga attggcacaa tgctacaatg tgctccccca acttgatatt aataacacta
     4321 tagaccaccg ccccgaaggg gacgaaaaat ggtttttaga gaacgagaag acggttacgc
     4381 agttttgccg caagctggct gctgaacgcc ctcttaagga tattcgcgat gagtataatt
     4441 accccaaaaa gaaaggtatt aaggatgagt gttcaagatt gctggaggcc tccactatga
     4501 aatcgcgtag aggctttgct attcagcgtt tgatgaatgc aatgcgacag gctcatgctg
     4561 atggttggtt tatcgttttt gacactctca cgttggctga cgaccgatta gaggcgtttt
     4621 atgataatcc caatgctttg cgtgactatt ttcgtgatat tggtcgtatg gttcttgctg
     4681 ccgagggtcg caaggctaat gattcacacg ccgactgcta tcagtatttt tgtgtgcctg
     4741 agtatggtac agctaatggc cgtcttcatt tccatgcggt gcactttatg cggacacttc
     4801 ctacaggtag cgttgaccct aattttggtc gtcgggtacg caatcgccgc cagttaaata
     4861 gcttgcaaaa tacgtggcct tatggttaca gtatgcccat cgcagttcgc tacacgcagg
     4921 acgctttttc acgttctggt tggttgtggc ctgttgatgc taaaggtgag ccgcttaaag
     4981 ctaccagtta tatggctgtt ggtttctatg tggctaaata cgttaacaaa aagtcagata
     5041 tggaccttgc tgctaaaggt ctaggagcta aagaatggaa caactcacta aaaaccaagc
     5101 tgtcgctact tcccaagaag ctgttcagaa tcagaatgag ccgcaacttc gggatgaaaa
     5161 tgctcacaat gacaaatctg tccacggagt gcttaatcca acttaccaag ctgggttacg
     5221 acgcgacgcc gttcaaccag atattgaagc agaacgcaaa aagagagatg agattgaggc
     5281 tgggaaaagt tactgtagcc gacgttttgg cggcgcaacc tgtgacgaca aatctgctca
     5341 aatttatgcg cgcttcgata aaaatgattg gcgtatccaa cctgca
//
BioPerl-1.007002/t/data/Primate_mtDNA.nex000444000766000024      7513613155576321 20064 0ustar00cjfieldsstaff000000000000#NEXUS 


BEGIN DATA;
DIMENSIONS  NTAX=12 NCHAR=898;

[!A portion of primate mitochondrial DNA.   Site names correspond to Anderson (1981) numbering scheme.

This portion includes parts of two protein-coding genes, as well as 3 tRNA's:

tRNA His:  459-528
tRNA Ser (AGY):  529-588
tRNA Leu (CUN):  589-659

Data from:

Hayasaka, K., T. Gojobori, and S. Horai. 1988. Molecular phylogeny and evolution of primate mitochondrial DNA. Mol. Biol. Evol., 5:626-644.

See pp. 335-339 of the MacClade book.]
FORMAT DATATYPE=DNA  MISSING=? GAP=-  MATCHCHAR=.  INTERLEAVE ;OPTIONS  IGNORE=UNINFORM ;

CHARLABELS
	[1]	A_11680	[2]	A_11681	[3]	A_11682	[4]	A_11683	[5]	A_11684
	[6]	A_11685	[7]	A_11686	[8]	A_11687	[9]	A_11688	[10]	A_11689
	[11]	A_11690	[12]	A_11691	[13]	A_11692	[14]	A_11693	[15]	A_11694
	[16]	A_11695	[17]	A_11696	[18]	A_11697	[19]	A_11698	[20]	A_11699
	[21]	A_11700	[22]	A_11701	[23]	A_11702	[24]	A_11703	[25]	A_11704
	[26]	A_11705	[27]	A_11706	[28]	A_11707	[29]	A_11708	[30]	A_11709
	[31]	A_11710	[32]	A_11711	[33]	A_11712	[34]	A_11713	[35]	A_11714
	[36]	A_11715	[37]	A_11716	[38]	A_11717	[39]	A_11718	[40]	A_11719
	[41]	A_11720	[42]	A_11721	[43]	A_11722	[44]	A_11723	[45]	A_11724
	[46]	A_11725	[47]	A_11726	[48]	A_11727	[49]	A_11728	[50]	A_11729
	[51]	A_11730	[52]	A_11731	[53]	A_11732	[54]	A_11733	[55]	A_11734
	[56]	A_11735	[57]	A_11736	[58]	A_11737	[59]	A_11738	[60]	A_11739
	[61]	A_11740	[62]	A_11741	[63]	A_11742	[64]	A_11743	[65]	A_11744
	[66]	A_11745	[67]	A_11746	[68]	A_11747	[69]	A_11748	[70]	A_11749
	[71]	A_11750	[72]	A_11751	[73]	A_11752	[74]	A_11753	[75]	A_11754
	[76]	A_11755	[77]	A_11756	[78]	A_11757	[79]	A_11758	[80]	A_11759
	[81]	A_11760	[82]	A_11761	[83]	A_11762	[84]	A_11763	[85]	A_11764
	[86]	A_11765	[87]	A_11766	[88]	A_11767	[89]	A_11768	[90]	A_11769
	[91]	A_11770	[92]	A_11771	[93]	A_11772	[94]	A_11773	[95]	A_11774
	[96]	A_11775	[97]	A_11776	[98]	A_11777	[99]	A_11778	[100]	A_11779
	[101]	A_11780	[102]	A_11781	[103]	A_11782	[104]	A_11783	[105]	A_11784
	[106]	A_11785	[107]	A_11786	[108]	A_11787	[109]	A_11788	[110]	A_11789
	[111]	A_11790	[112]	A_11791	[113]	A_11792	[114]	A_11793	[115]	A_11794
	[116]	A_11795	[117]	A_11796	[118]	A_11797	[119]	A_11798	[120]	A_11799
	[121]	A_11800	[122]	A_11801	[123]	A_11802	[124]	A_11803	[125]	A_11804
	[126]	A_11805	[127]	A_11806	[128]	A_11807	[129]	A_11808	[130]	A_11809
	[131]	A_11810	[132]	A_11811	[133]	A_11812	[134]	A_11813	[135]	A_11814
	[136]	A_11815	[137]	A_11816	[138]	A_11817	[139]	A_11818	[140]	A_11819
	[141]	A_11820	[142]	A_11821	[143]	A_11822	[144]	A_11823	[145]	A_11824
	[146]	A_11825	[147]	A_11826	[148]	A_11827	[149]	A_11828	[150]	A_11829
	[151]	A_11830	[152]	A_11831	[153]	A_11832	[154]	A_11833	[155]	A_11834
	[156]	A_11835	[157]	A_11836	[158]	A_11837	[159]	A_11838	[160]	A_11839
	[161]	A_11840	[162]	A_11841	[163]	A_11842	[164]	A_11843	[165]	A_11844
	[166]	A_11845	[167]	A_11846	[168]	A_11847	[169]	A_11848	[170]	A_11849
	[171]	A_11850	[172]	A_11851	[173]	A_11852	[174]	A_11853	[175]	A_11854
	[176]	A_11855	[177]	A_11856	[178]	A_11857	[179]	A_11858	[180]	A_11859
	[181]	A_11860	[182]	A_11861	[183]	A_11862	[184]	A_11863	[185]	A_11864
	[186]	A_11865	[187]	A_11866	[188]	A_11867	[189]	A_11868	[190]	A_11869
	[191]	A_11870	[192]	A_11871	[193]	A_11872	[194]	A_11873	[195]	A_11874
	[196]	A_11875	[197]	A_11876	[198]	A_11877	[199]	A_11878	[200]	A_11879
	[201]	A_11880	[202]	A_11881	[203]	A_11882	[204]	A_11883	[205]	A_11884
	[206]	A_11885	[207]	A_11886	[208]	A_11887	[209]	A_11888	[210]	A_11889
	[211]	A_11890	[212]	A_11891	[213]	A_11892	[214]	A_11893	[215]	A_11894
	[216]	A_11895	[217]	A_11896	[218]	A_11897	[219]	A_11898	[220]	A_11899
	[221]	A_11900	[222]	A_11901	[223]	A_11902	[224]	A_11903	[225]	A_11904
	[226]	A_11905	[227]	A_11906	[228]	A_11907	[229]	A_11908	[230]	A_11909
	[231]	A_11910	[232]	A_11911	[233]	A_11912	[234]	A_11913	[235]	A_11914
	[236]	A_11915	[237]	A_11916	[238]	A_11917	[239]	A_11918	[240]	A_11919
	[241]	A_11920	[242]	A_11921	[243]	A_11922	[244]	A_11923	[245]	A_11924
	[246]	A_11925	[247]	A_11926	[248]	A_11927	[249]	A_11928	[250]	A_11929
	[251]	A_11930	[252]	A_11931	[253]	A_11932	[254]	A_11933	[255]	A_11934
	[256]	A_11935	[257]	A_11936	[258]	A_11937	[259]	A_11938	[260]	A_11939
	[261]	A_11940	[262]	A_11941	[263]	A_11942	[264]	A_11943	[265]	A_11944
	[266]	A_11945	[267]	A_11946	[268]	A_11947	[269]	A_11948	[270]	A_11949
	[271]	A_11950	[272]	A_11951	[273]	A_11952	[274]	A_11953	[275]	A_11954
	[276]	A_11955	[277]	A_11956	[278]	A_11957	[279]	A_11958	[280]	A_11959
	[281]	A_11960	[282]	A_11961	[283]	A_11962	[284]	A_11963	[285]	A_11964
	[286]	A_11965	[287]	A_11966	[288]	A_11967	[289]	A_11968	[290]	A_11969
	[291]	A_11970	[292]	A_11971	[293]	A_11972	[294]	A_11973	[295]	A_11974
	[296]	A_11975	[297]	A_11976	[298]	A_11977	[299]	A_11978	[300]	A_11979
	[301]	A_11980	[302]	A_11981	[303]	A_11982	[304]	A_11983	[305]	A_11984
	[306]	A_11985	[307]	A_11986	[308]	A_11987	[309]	A_11988	[310]	A_11989
	[311]	A_11990	[312]	A_11991	[313]	A_11992	[314]	A_11993	[315]	A_11994
	[316]	A_11995	[317]	A_11996	[318]	A_11997	[319]	A_11998	[320]	A_11999
	[321]	A_12000	[322]	A_12001	[323]	A_12002	[324]	A_12003	[325]	A_12004
	[326]	A_12005	[327]	A_12006	[328]	A_12007	[329]	A_12008	[330]	A_12009
	[331]	A_12010	[332]	A_12011	[333]	A_12012	[334]	A_12013	[335]	A_12014
	[336]	A_12015	[337]	A_12016	[338]	A_12017	[339]	A_12018	[340]	A_12019
	[341]	A_12020	[342]	A_12021	[343]	A_12022	[344]	A_12023	[345]	A_12024
	[346]	A_12025	[347]	A_12026	[348]	A_12027	[349]	A_12028	[350]	A_12029
	[351]	A_12030	[352]	A_12031	[353]	A_12032	[354]	A_12033	[355]	A_12034
	[356]	A_12035	[357]	A_12036	[358]	A_12037	[359]	A_12038	[360]	A_12039
	[361]	A_12040	[362]	A_12041	[363]	A_12042	[364]	A_12043	[365]	A_12044
	[366]	A_12045	[367]	A_12046	[368]	A_12047	[369]	A_12048	[370]	A_12049
	[371]	A_12050	[372]	A_12051	[373]	A_12052	[374]	A_12053	[375]	A_12054
	[376]	A_12055	[377]	A_12056	[378]	A_12057	[379]	A_12058	[380]	A_12059
	[381]	A_12060	[382]	A_12061	[383]	A_12062	[384]	A_12063	[385]	A_12064
	[386]	A_12065	[387]	A_12066	[388]	A_12067	[389]	A_12068	[390]	A_12069
	[391]	A_12070	[392]	A_12071	[393]	A_12072	[394]	A_12073	[395]	A_12074
	[396]	A_12075	[397]	A_12076	[398]	A_12077	[399]	A_12078	[400]	A_12079
	[401]	A_12080	[402]	A_12081	[403]	A_12082	[404]	A_12083	[405]	A_12084
	[406]	A_12085	[407]	A_12086	[408]	A_12087	[409]	A_12088	[410]	A_12089
	[411]	A_12090	[412]	A_12091	[413]	A_12092	[414]	A_12093	[415]	A_12094
	[416]	A_12095	[417]	A_12096	[418]	A_12097	[419]	A_12098	[420]	A_12099
	[421]	A_12100	[422]	A_12101	[423]	A_12102	[424]	A_12103	[425]	A_12104
	[426]	A_12105	[427]	A_12106	[428]	A_12107	[429]	A_12108	[430]	A_12109
	[431]	A_12110	[432]	A_12111	[433]	A_12112	[434]	A_12113	[435]	A_12114
	[436]	A_12115	[437]	A_12116	[438]	A_12117	[439]	A_12118	[440]	A_12119
	[441]	A_12120	[442]	A_12121	[443]	A_12122	[444]	A_12123	[445]	A_12124
	[446]	A_12125	[447]	A_12126	[448]	A_12127	[449]	A_12128	[450]	A_12129
	[451]	A_12130	[452]	A_12131	[453]	A_12132	[454]	A_12133	[455]	A_12134
	[456]	A_12135	[457]	A_12136	[458]	A_12137	[459]	A_12138	[460]	A_12139
	[461]	A_12140	[462]	A_12141	[463]	A_12142	[464]	A_12143	[465]	A_12144
	[466]	A_12145	[467]	A_12146	[468]	A_12147	[469]	A_12148	[470]	A_12149
	[471]	A_12150	[472]	A_12151	[473]	A_12152	[474]	A_12153	[475]	A_12154
	[476]	A_12155	[477]	A_12156	[478]	A_12157	[479]	A_12158	[480]	A_12159
	[481]	A_12160	[482]	A_12161	[483]	A_12162	[484]	A_12163	[485]	A_12164
	[486]	A_12165	[487]	A_12166	[488]	A_12167	[489]	A_12168	[490]	A_12169
	[491]	A_12170	[492]	A_12171	[493]	A_12172	[494]	A_12173	[495]	A_12174
	[496]	A_12175	[497]	A_12176	[498]	A_12177	[499]	A_12178	[500]	A_12179
	[501]	A_12180	[502]	A_12181	[503]	A_12182	[504]	A_12183	[505]	A_12184
	[506]	A_12185	[507]	A_12186	[508]	A_12187	[509]	A_12188	[510]	A_12189
	[511]	A_12190	[512]	A_12190a	[513]	A_12191	[514]	A_12192	[515]	A_12193
	[516]	A_12194	[517]	A_12195	[518]	A_12196	[519]	A_12197	[520]	A_12198
	[521]	A_12199	[522]	A_12200	[523]	A_12201	[524]	A_12202	[525]	A_12203
	[526]	A_12204	[527]	A_12205	[528]	A_12206	[529]	A_12207	[530]	A_12208
	[531]	A_12209	[532]	A_12210	[533]	A_12211	[534]	A_12212	[535]	A_12213
	[536]	A_12214	[537]	A_12215	[538]	A_12215a	[539]	A_12216	[540]	A_12217
	[541]	A_12218	[542]	A_12219	[543]	A_12220	[544]	A_12221	[545]	A_12222
	[546]	A_12223	[547]	A_12224	[548]	A_12225	[549]	A_12226	[550]	A_12227
	[551]	A_12228	[552]	A_12229	[553]	A_12230	[554]	A_12231	[555]	A_12232
	[556]	A_12233	[557]	A_12234	[558]	A_12235	[559]	A_12236	[560]	A_12237
	[561]	A_12238	[562]	A_12239	[563]	A_12240	[564]	A_12241	[565]	A_12242
	[566]	A_12243	[567]	A_12244	[568]	A_12245	[569]	A_12246	[570]	A_12247
	[571]	A_12248	[572]	A_12249	[573]	A_12250	[574]	A_12251	[575]	A_12252
	[576]	A_12253	[577]	A_12254	[578]	A_12255	[579]	A_12256	[580]	A_12257
	[581]	A_12258	[582]	A_12259	[583]	A_12260	[584]	A_12261	[585]	A_12262
	[586]	A_12263	[587]	A_12264	[588]	A_12265	[589]	A_12266	[590]	A_12267
	[591]	A_12268	[592]	A_12269	[593]	A_12270	[594]	A_12271	[595]	A_12272
	[596]	A_12273	[597]	A_12274	[598]	A_12275	[599]	A_12276	[600]	A_12277
	[601]	A_12278	[602]	A_12279	[603]	A_12280	[604]	A_12281	[605]	A_12282
	[606]	A_12283	[607]	A_12284	[608]	A_12285	[609]	A_12286	[610]	A_12287
	[611]	A_12288	[612]	A_12289	[613]	A_12290	[614]	A_12291	[615]	A_12292
	[616]	A_12293	[617]	A_12294	[618]	A_12295	[619]	A_12296	[620]	A_12297
	[621]	A_12298	[622]	A_12299	[623]	A_12300	[624]	A_12301	[625]	A_12302
	[626]	A_12303	[627]	A_12304	[628]	A_12305	[629]	A_12306	[630]	A_12307
	[631]	A_12308	[632]	A_12309	[633]	A_12310	[634]	A_12311	[635]	A_12312
	[636]	A_12313	[637]	A_12314	[638]	A_12315	[639]	A_12316	[640]	A_12317
	[641]	A_12318	[642]	A_12319	[643]	A_12320	[644]	A_12321	[645]	A_12322
	[646]	A_12323	[647]	A_12324	[648]	A_12325	[649]	A_12326	[650]	A_12327
	[651]	A_12328	[652]	A_12329	[653]	A_12330	[654]	A_12331	[655]	A_12332
	[656]	A_12333	[657]	A_12334	[658]	A_12335	[659]	A_12336	[660]	A_12337
	[661]	A_12338	[662]	A_12339	[663]	A_12340	[664]	A_12341	[665]	A_12342
	[666]	A_12343	[667]	A_12344	[668]	A_12345	[669]	A_12346	[670]	A_12347
	[671]	A_12348	[672]	A_12349	[673]	A_12350	[674]	A_12351	[675]	A_12352
	[676]	A_12353	[677]	A_12354	[678]	A_12355	[679]	A_12356	[680]	A_12357
	[681]	A_12358	[682]	A_12359	[683]	A_12360	[684]	A_12361	[685]	A_12362
	[686]	A_12363	[687]	A_12364	[688]	A_12365	[689]	A_12366	[690]	A_12367
	[691]	A_12368	[692]	A_12369	[693]	A_12370	[694]	A_12371	[695]	A_12372
	[696]	A_12373	[697]	A_12374	[698]	A_12375	[699]	A_12376	[700]	A_12377
	[701]	A_12378	[702]	A_12379	[703]	A_12380	[704]	A_12381	[705]	A_12382
	[706]	A_12383	[707]	A_12384	[708]	A_12385	[709]	A_12386	[710]	A_12387
	[711]	A_12388	[712]	A_12389	[713]	A_12390	[714]	A_12391	[715]	A_12392
	[716]	A_12393	[717]	A_12394	[718]	A_12395	[719]	A_12396	[720]	A_12397
	[721]	A_12398	[722]	A_12399	[723]	A_12400	[724]	A_12401	[725]	A_12402
	[726]	A_12403	[727]	A_12404	[728]	A_12405	[729]	A_12406	[730]	A_12407
	[731]	A_12408	[732]	A_12409	[733]	A_12410	[734]	A_12411	[735]	A_12412
	[736]	A_12413	[737]	A_12414	[738]	A_12415	[739]	A_12416	[740]	A_12417
	[741]	A_12418	[742]	A_12419	[743]	A_12420	[744]	A_12421	[745]	A_12422
	[746]	A_12423	[747]	A_12424	[748]	A_12425	[749]	A_12426	[750]	A_12427
	[751]	A_12428	[752]	A_12429	[753]	A_12430	[754]	A_12431	[755]	A_12432
	[756]	A_12433	[757]	A_12434	[758]	A_12435	[759]	A_12436	[760]	A_12437
	[761]	A_12438	[762]	A_12439	[763]	A_12440	[764]	A_12441	[765]	A_12442
	[766]	A_12443	[767]	A_12444	[768]	A_12445	[769]	A_12446	[770]	A_12447
	[771]	A_12448	[772]	A_12449	[773]	A_12450	[774]	A_12451	[775]	A_12452
	[776]	A_12453	[777]	A_12454	[778]	A_12455	[779]	A_12456	[780]	A_12457
	[781]	A_12458	[782]	A_12459	[783]	A_12460	[784]	A_12461	[785]	A_12462
	[786]	A_12463	[787]	A_12464	[788]	A_12465	[789]	A_12466	[790]	A_12467
	[791]	A_12468	[792]	A_12469	[793]	A_12470	[794]	A_12471	[795]	A_12472
	[796]	A_12473	[797]	A_12474	[798]	A_12475	[799]	A_12476	[800]	A_12477
	[801]	A_12478	[802]	A_12479	[803]	A_12480	[804]	A_12481	[805]	A_12482
	[806]	A_12483	[807]	A_12484	[808]	A_12485	[809]	A_12486	[810]	A_12487
	[811]	A_12488	[812]	A_12489	[813]	A_12490	[814]	A_12491	[815]	A_12492
	[816]	A_12493	[817]	A_12494	[818]	A_12495	[819]	A_12496	[820]	A_12497
	[821]	A_12498	[822]	A_12499	[823]	A_12500	[824]	A_12501	[825]	A_12502
	[826]	A_12503	[827]	A_12504	[828]	A_12505	[829]	A_12506	[830]	A_12507
	[831]	A_12508	[832]	A_12509	[833]	A_12510	[834]	A_12511	[835]	A_12512
	[836]	A_12513	[837]	A_12514	[838]	A_12515	[839]	A_12516	[840]	A_12517
	[841]	A_12518	[842]	A_12519	[843]	A_12520	[844]	A_12521	[845]	A_12522
	[846]	A_12523	[847]	A_12524	[848]	A_12525	[849]	A_12526	[850]	A_12527
	[851]	A_12528	[852]	A_12529	[853]	A_12530	[854]	A_12531	[855]	A_12532
	[856]	A_12533	[857]	A_12534	[858]	A_12535	[859]	A_12536	[860]	A_12537
	[861]	A_12538	[862]	A_12539	[863]	A_12540	[864]	A_12541	[865]	A_12542
	[866]	A_12543	[867]	A_12544	[868]	A_12545	[869]	A_12546	[870]	A_12547
	[871]	A_12548	[872]	A_12549	[873]	A_12550	[874]	A_12551	[875]	A_12552
	[876]	A_12553	[877]	A_12554	[878]	A_12555	[879]	A_12556	[880]	A_12557
	[881]	A_12558	[882]	A_12559	[883]	A_12560	[884]	A_12561	[885]	A_12562
	[886]	A_12563	[887]	A_12564	[888]	A_12565	[889]	A_12566	[890]	A_12567
	[891]	A_12568	[892]	A_12569	[893]	A_12570	[894]	A_12571	[895]	A_12572
	[896]	A_12573	[897]	A_12574	[898]	A_12575
	;

MATRIX

[                            10        20        30        40        50        60        70        80        90        100]
[                            .         .         .         .         .         .         .         .         .         .]

Homo_sapiens        AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGC   [100]
Pan                 ................A.T..C.................A...............T......................T..T........C.........   [100]
Gorilla             ..................TG....T.....T........A........A......T...............................A..C.....C...   [100]
Pongo               ................AC..CC.....G..T.....T..A..C........CC....G.............................A..C.....C...   [100]
Hylobates           ......T..A..T...AC.G.C.................A..A..C..T..CC.G...........T....................A........C...   [100]
Macaca_fuscata      ......TT........AC...C..T..G.....T.....A..C..C..T..CA..TAT...........C..T........T.............AC..T   [100]
M._mulatta          ......TT.T......AC...C.....G..T..T.....A..C..C..T..CA..TAT...........C..T........T.............AC..T   [100]
M._fascicularis     .......T........AC..CC..T.................C..C..T..CA.GTAT......T.G..C..T........T..G........T.AC..T   [100]
M._sylvanus         .......T....T...ACT..C..T...G.T.....T..A..C..C..T..CA..TAC......T.G..C....................C.....C...   [100]
Saimiri_sciureus    ................A.G..C..A........T......T....T..G..TA.G.......................T........A.T......C..A   [100]
Tarsius_syrichta    ...T....TT..A..CAC..C...T.....T.....T..C..C..C.....CC..T....T...........TA.............AGTC........A   [100]
Lemur_catta         ........TA..A...AC......A........A..T..C........A..CA..T.......T.....C.....T...........A.TC..T..C..T   [100]

[                            110       120       130       140       150       160       170       180       190       200]
[                            .         .         .         .         .         .         .         .         .         .]

Homo_sapiens        ATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTA   [200]
Pan                 ........T.....C................................C...........C........................C.......T..C....   [200]
Gorilla             ........T..............C.....C.................CC.............G...........C....................C....   [200]
Pongo               ....................C.................C........CC.C.....................A.......T...C....A.....C..C.   [200]
Hylobates           ...........A....G...G..C...G.CT..........G.....C..C........CGC......................C...............   [200]
Macaca_fuscata      .C....C.A..G..C.G...........TC.....T.......C...C.........T.AAC.........TA.......T...C.............C.   [200]
M._mulatta          .C....C.A..G..C.GG..........TC.....T.......C......C......T.AAC.........TA.......T...C.............C.   [200]
M._fascicularis     .C....C.A..A..C.G...........T......T...T.G.C...C..C........CAC.........TA.......T...C...............   [200]
M._sylvanus         ......C.A..A..C.G......C....TC.............C...C..C......T.CAC.........TA....T..T..TC.....T.........   [200]
Saimiri_sciureus    .CA....CAT.TA...G...G..C.....A...T....G..T....GCC.C........C.......AT...............C.....A.AG......   [200]
Tarsius_syrichta    .CA...GCA..AG.C.GT..C........C...T.A..T..TGC...AACA........C..C..C...T.AA.C.....G...C.T.....A..A....   [200]
Lemur_catta         .CA...C.A..AG.A.G...GA.C.....CA.T.....T..T.....CACC........A..C..C.....AA.......A...C.....A..T....C.   [200]

[                            210       220       230       240       250       260       270       280       290       300]
[                            .         .         .         .         .         .         .         .         .         .]

Homo_sapiens        ACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTC   [300]
Pan                 .T..C..A..G........C............T.A................C............C......T...........A..........G.....   [300]
Gorilla             .......A.....G.....C..A...........A..............C.C...C..TT...........TCT.........A.T........G.....   [300]
Pongo               ....T..A...........C..A...A..G...TA.....T.....T..C.....CA.......A..................A.....A..........   [300]
Hylobates           ....C..A..T.......TC..A...A.GG..T.C........GG....C.CT...A.TAC...C..C..G......G.....A....G...........   [300]
Macaca_fuscata      .T.....A..T.......T...AA.C.C....T.A...........CC.......CA.TA.G..A........T......T..A.T..G.....C.....   [300]
M._mulatta          .......A..T.......T...AA.C.CG...T.A........G..CC.......CA.TA..T.A......T.T.........A.T..G.....C.....   [300]
M._fascicularis     .T.....A..C.......T...AA.CAC...TT.A..T........CC.......CA.TG.GT.A..G..C..T..T......A..........C.....   [300]
M._sylvanus         .T........C.......TC..AA.C.C....T.A..T........CC.C.....CA..A....A........G.........A.T........C.....   [300]
Saimiri_sciureus    .T...G.A......T.ACTCACAA.C...T.TT.C.....T.....C..CT.T...A.TA..T.C........T..T......A.T.....A..C.....   [300]
Tarsius_syrichta    .TT..A.C..T.....G..C..AA..A..G.AG.A..T..A..G...C.CC.A...A.TA.CT.AGT...C..T....CC..TA....C........T..   [300]
Lemur_catta         .TT..A.T..C.....A.TC..CACTA..G.AT.C.....A........C..T..AA.TA.CT.A.T...CT.A..T..G..CA....C..T..C..T..   [300]

[                            310       320       330       340       350       360       370       380       390       400]
[                            .         .         .         .         .         .         .         .         .         .]

Homo_sapiens        CCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACAC   [400]
Pan                 .........G.................A.......................T........G....................T..T.....A..TT.....   [400]
Gorilla             ...T..T....................A...C.......A........C.C..................T.............T......A.....G...   [400]
Pongo               T.....T.....C............C.A..TA...C...A........C..............T..T........C.....T.........C........   [400]
Hylobates           ...T..........T..T.......C.A...A....T..A...........A...............C...............TAT.A..AC.T..G...   [400]
Macaca_fuscata      T...C.......C..T.........C.A..AA.......A..T.....A.T.........G...C.C.................AT.A..A.........   [400]
M._mulatta          ....C.......C............C.A..AG.......A..T.....A.T.............C.C................TAT.A..A.........   [400]
M._fascicularis     T...C....G..C.TT...GT....C.A..AA.......A........A.T...T.........C.C................TAT.A..A.........   [400]
M._sylvanus         T..TC.......C............C.A..AG.G.....A........A.TT...........AC.T................TAT.A..AC........   [400]
Saimiri_sciureus    A..TC.T..G.A.G..T.T.....GC.A..TC....T..AT..AG..CC.G...T........AAT...T...........T..G..A..A..T.....T   [400]
Tarsius_syrichta    ...A..T...C.A.T..T...T...C.A..AAA.TA...AT.T..T..C.....T..C.TG...C.T.....C........T..AT.A..AA........   [400]
Lemur_catta         ......T.....A..T..T......C.A..AAA......AT.T..TTCGC.....C....C..A..C..T.................T..A.C.......   [400]

[                            410       420       430       440       450       460       470       480       490       500]
[                            .         .         .         .         .         .         .         .         .         .]

Homo_sapiens        CTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACA   [500]
Pan                 ...........C.....T...........T..T..T.....C..T..A..CA....C...........................................   [500]
Gorilla             ...........C.......................T..T..C........CA....C.........................................T.   [500]
Pongo               ...........C......T..............AG......CG.T.....CG...AC.........................T.............A.T.   [500]
Hylobates           ..C.T....C.C.........A..........TA..........T..C...A.TC.C......C.........T........T.............A...   [500]
Macaca_fuscata      ..CG.T..A...A....T...............A.......CCTG......A....C....G............T......CT.............A..C   [500]
M._mulatta          ..CG.T..A..CA..........T.........A.......CCTG......A.T..C....G............T.......T.............A..C   [500]
M._fascicularis     ..CG.T..A...A....T.....T.........A.......CCTG......A....C.................T.......T.............A..T   [500]
M._sylvanus         ..CG.T..A...A.T..T.....T..T......A........CTA..A...A.T..C................TT.......T...C.........A..T   [500]
Saimiri_sciureus    A..A.A..A..C........TA..T.G.G....A.GG.A....TA..ACCC..AC.......T.........G.T.......T.............A.T.   [500]
Tarsius_syrichta    ....TT...T.AA....A.....TAC.......A.AG.A....TA..AACCATG.AC................A........T.........G...A.T.   [500]
Lemur_catta         A..CT....C.......AT.TA..T.A......A.A..T...CTA..ACCCA.G.AC................A-......CT............CAGA.   [499]

[                            510       520       530       540       550       560       570       580       590       600]
[                            .         .         .         .         .         .         .         .         .         .]

Homo_sapiens        ACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGA   [598]
Pan                 .........C.-.........................-T.T............T....AT.......C..G.............................   [598]
Gorilla             .........C.-.A.......................-.GT....G............A.....G..CT.G.............................   [598]
Pongo               .T..G.C.CC.-.A.......................-..................TCA.T-......G.G.................G...........   [597]
Hylobates           .T.......CG-AA...T...GC.............C-...................CTAT.......A.G.............................   [598]
Macaca_fuscata      .T....A..C.-.C...T................A..-.G....G.........C....TA...G.AC....A.TT.C..T...................   [598]
M._mulatta          .T....A....-.C...T................A..-.G.G..G.........C....TAT..G.AC....A.TT.C..T...................   [598]
M._fascicularis     .T......C..-.C..TT................A..-.G....G........TC......T..G.ACT...A.CT.C..T..C................   [598]
M._sylvanus         .T...A.....-.C..TT................A..-TG....G..C.....TC..CA..T..G.ACT...A.CT.C..T...................   [598]
Saimiri_sciureus    .T...A.AA..-TA..TT....A............TG-.G.............T......T....A.A........T......C................   [598]
Tarsius_syrichta    .T...A..CC.AA..TTT..........A......TA-TG.....................T....A.A......TG.........T-............   [598]
Lemur_catta         .T...A...C.AAC-.TT.................TAATGT.T.............TGCA.T..G.A.A...A..T.C....A.................   [598]

[                            610       620       630       640       650       660       670       680       690       700]
[                            .         .         .         .         .         .         .         .         .         .]

Homo_sapiens        TAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTC   [698]
Pan                 .......C....G.......................................................T.T.....C.........T.......A...C.   [698]
Gorilla             ........................A.......................................T...T..G....C.........T..G....A.....   [698]
Pongo               ............C...........AT..................................C.G.....TTT..C..C.....TG....C...T.A.....   [697]
Hylobates           ........................A.....................................G.A...T....C..C...G...TT.....G..A..C..   [698]
Macaca_fuscata      ................AC......AGT......CA............................T.........CC.C..C.TT.TAAC......T.TC..   [698]
M._mulatta          ................AC......AGT.......A............................T.........CC....C.TA.TAAC......T.TC..   [698]
M._fascicularis     ................AC......AGT......CA............................T.........CC.C..C.TA.TAAC......C.TC..   [698]
M._sylvanus         .................C......AGT.......A............................T....T.T..CC.C..C.TA.TAAC...T..C.TC..   [698]
Saimiri_sciureus    ..GT..T.................AG.......CA...........................---..A...TTCT.C..C..TCTAA....A..A.T.AG   [695]
Tarsius_syrichta    ..GA..TA......C.........AA..G....-A............................ATT.ATTTT.AT.CTCC.TTTTA...T.A..T..ACT   [697]
Lemur_catta         ..GA..TA.........C......AG.......-A............................ATC.ATTAT.CT..T.C...CTTG.C..A....T.AT   [697]

[                            710       720       730       740       750       760       770       780       790       800]
[                            .         .         .         .         .         .         .         .         .         .]

Homo_sapiens        CCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGT   [798]
Pan                 .T......T.........C.........A.........................T...........G.........A....G...........C..T..C   [798]
Gorilla             .T..........T............T..A.C..T.............G...............C........T..C.................C.....C   [798]
Pongo               ......C........TACCG.T......A.......C............C..........C.........A.GGCCA........G......C......C   [797]
Hylobates           ...............TACAG.......TA.......C..T.....G....T......G..C..C......ATG.CCA.T..C..T........A.....C   [798]
Macaca_fuscata      .....C..T...A..TT..G........A.C......T........CGTC.......AG....C......A.A.CC..AAT..ATG.T..C..C.....C   [798]
M._mulatta          .....C..T...A..TT..G........A.C......T........CGTC.......AG....C......A.A.CC..AAT..ATG.T..C..C.....C   [798]
M._fascicularis     ...G.CC.TT..A..TT..G........ACC.....CT.T......CGT........AG.C..C......A.A.CC..AAT..ATG.T.......C....   [798]
M._sylvanus         .....C..TT..A..TT.CG.T.....TA.C.....C.........C..CT...T..AA.C..C......A.AGCC..AAT..ATG.T..C....C...C   [798]
Saimiri_sciureus    ....C.AG.G..A.....AG.T......A...............GC.CACT......GT.C..C......CTAGCCA..ATC.A.G..C.C....C....   [795]
Tarsius_syrichta    .T.....A....AT.TA...TT..AACAAC...AAAAT.TG...C.C.TG.......TT.C..C......AA.TC.A....C.G.G.A.....A.CA..C   [797]
Lemur_catta         .....C.TTA..T...A...TA.A.G.TACA...ATAT.......CT..C.C..TG.A.CA..C........TTC.A.T....GTG....C..C.CT..C   [797]

[                            810       820       830       840       850       860       870       880       890      ]
[                            .         .         .         .         .         .         .         .         .        ]

Homo_sapiens        CTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT   [896]
Pan                 ..T....................A................C.........A.....G........A................................   [896]
Gorilla             ....................TC.A................C.........A.G............A.............TT..A..............   [896]
Pongo               ..TA....A...........T..C.......GA......ACC..CG..A.A......TG....A.A..C.....G...CTA..A.....A........   [895]
Hylobates           ..A..T.......T.............AC..........ACC.....T..A............A.TG..........GCTAG.A..............   [896]
Macaca_fuscata      ...CC.T.A.....TT.......C.T.TC.A........ACA.CC..T.G..G......T...ATA.TG.........CTAG.C..AA.G........   [896]
M._mulatta          ...CC.T.A.....TT.......C.T.TC.A........ACA.CC..T.GA.G......T...ATA.T..........CTAG.C..AA.A........   [896]
M._fascicularis     ...CC.T.A.....CC.......CCT.TC.A........ACA.CC..T.G..GT.....T...ATA............TTAG.C..AA.A........   [896]
M._sylvanus         ....CTT.A.....TT...AT..A.T.T..A........ACA..C....GA.G...G......ATA.T..........CTAAGC..AA.AT.......   [896]
Saimiri_sciureus    AC...AT.T.T..T.T.C..T..CCTTAC..G.......TCA..A..T..A............ATA..T.T......C.T.A.A..A...........   [893]
Tarsius_syrichta    ..AG....A.TGCTC.....TC.A.A.AC.A.T......A.A..C..T..C........T...ATA..G.TT..T..T.T.A.AT.A.G.........   [895]
Lemur_catta         ...A....A..T.T.T....T..C.C.TC..GA......ACA..C..T..C........T...ATA....T......CCTAA.A..A..TA.T.....   [895]
;
END;
BEGIN GENETICCode;
StandardNUCLEAR;
END;

BEGIN CODONS;
CODONPOSSET * UNTITLED = 
		N: 1 458-659 897 898, 
		1: 2-455\3 660-894\3, 
		2: 3-456\3 661-895\3, 
		3: 4-457\3 662-896\3;
CODESET * UNTITLED = mtDNA.mam: all ;
END;

BEGIN ASSUMPTIONS;
	USERTYPE ttbias STEPMATRIX= 4
	     A C G T
	 [A] . 6 1 6
	 [C] 6 . 6 1
	 [G] 1 6 . 6
	 [T] 6 1 6 .
	;

	OPTIONS  DEFTYPE=unord PolyTcount=MINSTEPS ;
	CHARSET  tRNA_His  =  459-528;
	CHARSET  'tRNA_Ser_(AGY)'  =  529-588;
	CHARSET  'tRNA_Leu_(CUN)'  =  589-659;
	CHARSET  noncoding = 1 458-659 897 898; 
	CHARSET  position1 =  2-455\3 660-894\3; 
	CHARSET  position2 =  3-456\3 661-895\3; 
	CHARSET  position3 =  4-457\3 662-896\3;
	EXSET  protein_only  =  noncoding;
	EXSET  non_protein  =  position1 position2 position3;
	EXSET  only_3rds = position1 position2 noncoding;
	EXSET  only_2nds = position1 position3 noncoding;
	EXSET  only_1sts = position2 position3 noncoding;
END; 

BEGIN TREES; 

[!
Heuristic search settings:

   Addition sequence: random
      Number of replications = 10
      Starting seed = 1
   Global branch-swapping performed
   MULPARS option in effect
   Steepest descent option not in effect
   Initial MAXTREES setting = 100
   Branches having maximum length zero collapsed to yield polytomies
   Trees are unrooted
   Length of shortest tree found = 998
   Number of trees retained = 2
   Time used = 50.0 sec
]
	TRANSLATE
		1	Homo_sapiens,
		2	Pan,
		3	Gorilla,
		4	Pongo,
		5	Hylobates,
		6	Macaca_fuscata,
		7	M._mulatta,
		8	M._fascicularis,
		9	M._sylvanus,
		10	Saimiri_sciureus,
		11	Tarsius_syrichta,
		12	Lemur_catta
	;
	TREE  * 'Homo-Pan' =  [&R] (12,(((((((1,2),3),4),5),(((6,7),8),9)),10),11));
	TREE 'Pan-Gorilla' =  [&R] (12,((((((1,(2,3)),4),5),(((6,7),8),9)),10),11));
	TREE 'Homo-Gorilla' =  [&R] (12,(((((((1,3),2),4),5),(((6,7),8),9)),10),11));

END;



BEGIN MACCLADE;
Version 3.05;
LastModified -1425155069;
Singles 0000&/0;
END;
BioPerl-1.007002/t/data/Q8GBD3.swiss000444000766000024       417713155576321 16663 0ustar00cjfieldsstaff000000000000ID   CH10_ACEAC              Reviewed;          97 AA.
AC   Q8GBD3;
DT   11-APR-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-MAR-2003, sequence version 1.
DT   12-JUN-2007, entry version 26.
DE   10 kDa chaperonin (Protein Cpn10) (groES protein).
GN   Name=groS; Synonyms=groES;
OS   Acetobacter aceti.
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales;
OC   Acetobacteraceae; Acetobacter; Acetobacter subgen. Acetobacter.
OX   NCBI_TaxID=435;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=IFO 3283 / LMG 1513;
RX   PubMed=16233284; DOI=10.1263/jbb.94.140;
RA   Okamoto-Kainuma A., Yan W., Kadono S., Tayama K., Koizumi Y.,
RA   Yanagida F.;
RT   "Cloning and characterization of groESL operon in Acetobacter aceti.";
RL   J. Biosci. Bioeng. 94:140-147(2002).
CC   -!- FUNCTION: Binds to Cpn60 in the presence of Mg-ATP and suppresses
CC       the ATPase activity of the latter.
CC   -!- SUBUNIT: Heptamer of 7 subunits arranged in a ring (By
CC       similarity).
CC   -!- SUBCELLULAR LOCATION: Cytoplasm (By similarity).
CC   -!- SIMILARITY: Belongs to the groES chaperonin family.
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------
DR   EMBL; AB081586; BAC16231.1; -; Genomic_DNA.
DR   HSSP; P09621; 1HX5.
DR   GO; GO:0006457; P:protein folding; IEA:HAMAP.
DR   HAMAP; MF_00580; -; 1.
DR   InterPro; IPR001476; Chaprnin_Cpn10.
DR   Gene3D; G3DSA:2.30.33.40; Chaprnin_Cpn10; 1.
DR   PANTHER; PTHR10772; Chaprnin_Cpn10; 1.
DR   Pfam; PF00166; Cpn10; 1.
DR   PRINTS; PR00297; CHAPERONIN10.
DR   ProDom; PD000566; Chaprnin_Cpn10; 1.
DR   PROSITE; PS00681; CHAPERONINS_CPN10; 1.
KW   Chaperone.
FT   CHAIN         1     97       10 kDa chaperonin.
FT                                /FTId=PRO_0000174677.
SQ   SEQUENCE   97 AA;  10514 MW;  4DF9365DE3CDA23E CRC64;
     MTKFRPLHDR VVVRRLEGEQ KTAGGIIIPD TAQEKPMEGE VVAVGPGARN EQGQIVALDV
     KAGDRVLFGK WSGTEVKIDG EELLIMKESD IMGVVTA
//
BioPerl-1.007002/t/data/Rab1.chaos-xml000444000766000024      4736313155576321 17327 0ustar00cjfieldsstaff000000000000


  
    1
    chaos
    gene:EMBL/GenBank/SwissProt:AE003734:52204:55287
    feature_id
    chado_1_01
    1114399206
    Sun Apr 24 20:20:06 2005
    
    cjm
    :/Users/cjm/cvs/DBIx-DBStag:/Users/cjm/stag:/Users/cjm/cvs/sqlfairy/lib:/Users/cjm/chaos-xml/lib::/Users/cjm/cabal::/Users/cjm/biostag/lib::/Users/cjm/amigo/perl::/Users/cjm/go-db-perl::/Users/cjm/go-perl::/Users/cjm/cvs/bioperl-live::/users/cjm/cvs/gmod/XML-XORT/lib:/sw/lib/perl5:/sw/lib/perl5/darwin
    /Users/cjm/chaos-xml/bin/cx-genbank2chaos.pl
  
  
    AE003734.2
    SEQDB:AE003734.2
    AE003734
    Drosophila_melanogaster:AE003734.2
    databank_entry
    
      comment
      On Sep 18, 2002 this sequence version replaced gi:7300718.
    
    Drosophila melanogaster (fruit fly)
  
  
    contig:AE003734.2:55787:51703
    contig-Rab1-500-500
    contig-Drosophila_melanogaster:Rab1-500-500
    contig
    
      55787
      51703
      -1
      AE003734.2
    
    AACCTGTGCTATCTGGAGGCCATTCACAACTTCGTGGAGGTGCTCAACGAATACTTCCATAATGTGTGCGAGCTGGATCTGGTCTTCAACTTCTACAAGGTGTACAGTGTGGTGGACGAGATGTTCCTGGCGGGCGAGATCCGGGAGACCTCGCAGACGAAGGTGCTCAAGCAGCTGCTCACGCTAAATTCGCTGGAGTAGCGGCCCAATTCATACATATGTATATCGGATCTGCCAGATGCATTCCCCCAGGCGCTACACCCGCCTATCGAATCTTCTTTCATATACTATTACGCGTATTATTATTATTATCTTTAATGTGTTCTCTATGCAAACACTCAAATGTTAAAGGCCGTGTTTAGAAACAAATGATGTACCATAAGAGATTGTATGCAAAAGTTAAGTATTTTTGTTTTTATATGGGGTGTGTTAGGGGTCATTTGGCGATAATCCATATATTTTCTTCTCTGGTTCCGCCCACTCACCTCCGTAGACAAGATAATGTGTAGCCCTGGTTGGAAGAGGGCCCCGCGCATTTTCCAACACTGCCGCTAATGCCACTTCGTCATTTTTTCAGTCGCCATTGTTCTCGTTCTCGGCCGTCGAATTTGTGGAAATAAACGTATTTCCCATTTAAATTCGCTGCAATAATTACAATAGCGAACTGCAAAACACAACACAAGCCGAGTGCGTGTCGATTTCCAGTATTTCGGAACGCGCAAATCAAATAAAAACACTCTGAACAGCAGCCAGTCCAGGGCCAGAAATCGAATATTTGTTCGTGGCAAATATATAATCTTGTGAAAAAGCCAGAAAATGTCATCTGTGAATCCGGAATAGTAAGTCGTCACACGTAATTATGCGCAGTTATCTGGAGTTAAAACAGTGACTGGGCTTCCACTTCCTTTTCTGGCCTTCGAAAATAGTTTCTTTTATTTTTTCTGCGACGTCATTTCTGCTACGTTTCATTCCCATTCATTATCGAGCAGCCCCACTCCACTCCCTTTTGCCCTCGTTGGCAACTCCAAAAAAACAGACCATTTGCTAAAAACAAAATACACACTCGGACCTAACAACCGACCCAATCGAGAAACCATAACCAAAACTGTGTGTTTCAGCTGGATTTCAATGTAGTGCCCACGGGCGAGGCGATGAAAAGCGCGTTCGAAACTCTCATCGGAATCTGCATATGTATAAAGTCCACACATATATACAGCGAGATCCCAGTTGACGGGCCAAATCGCTAGTCGGGCGGATGAGTCACCTGCGTGGAGAGCCTTTCCCACCCCCAGCGCAGTGCTACGTAATCAAAGGCCATTCCAGTGCTACTTAATTGCCGCTCTCACTCAAGGCAATTAAATCTGAACCGATCTTGGTTCGCACTCTCCAGAAAGCCTCCTTCAATAGCCAGCATACATGTGTGCAGAGGATTGGAACACTATCGCATATCATTCAGCAATTGGGGGTTGATGTTGGACATAGCATGATAAGATAAAGCCTAAACCAAACCGGTTTTATGTATATATTAGTATCTGCCCGACTAAACTATGCCCGCAAAACACCTCTCTAAATGTTTTGCTTGAATCAATGATTTCTAACTGATTGTCATCCAACTTATTTCCCTTTAAATGTATACTAAACCTTTTACACTCTGATTTTAAACATTTCGTCTTGTAATATCACTATCGCAAATATGCATCATCAGTTTTATTTAGATTTCTCTGAAGTTTTATATGTTTCAGCATAGGGTCTGAACTATTCCCACATCGCAGCACAAATTTATATCATTAACTATTAAATTAACTATAATTTATTAACTATATAACTATTTTATAACATTAACTATATTAACTATCTCCAAATCCACAGCGATTATCTCTTTAAGTTGCTGCTTATTGGAGACTCGGGCGTTGGAAAGTCCTGTCTTCTGTTGCGATTTGCCGATGACACATATACAGAAAGTTATATCAGCACAATCGGAGTGGATTTCGTAAGCCAACCGGAAATTTGTGAAAATTCTTTATGTCTGACTCATAAACCTTTATCTTGCAGAAAATCAGGACTATAGAACTCGACGGAAAGACCATTAAACTGCAAATCGTAAGCATAAAAACGCCAGAGGCAATCTAGTCCAGAGCTAATTAGTCTGTTTACAGTGGGATACTGCTGGCCAGGAGCGCTTCCGCACCATCACGTCTTCATATTATAGGGGCGCCCATGGCATCATTGTCGTATACGATTGCACGGACCAGGAGTCTTTCAACAATGTGAAGCAGTGGCTGGAGGAGATCGAGCGGTATGCCTGTGAGAATGTCAACAAGTTGCTGGTTGGCAACAAGAGCGACTTGACCACCAAGAAAGTAGTCGACCACACCACAGCTGCGGTGCGTATATTGCTGGTTTAGTCCTGGGAATCATAGATGCACGTATATACTAATCTGGGTCTTTGTTTCCAAAATTCCAGGAGTACGCCGCCCAGTTAGGCATTCCATTCCTTGAAACTTCGGCCAAGAGCGCCACCAACGTTGAGCAGGCCTTCATGACGATGGCGGCGGAGATCAAGAATCGCGTCGGGCCGCCGTCCAGCGCCACTGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAACACCAAATCCGGTTGCTGCTGAATAACTCTGATTGTGAATCATTATTTTATTATACAATTAAACAAAATTTAAATATAATAAATTAAAACGGAAACCACACAATAATAATAAAACAAGCGAAACCGATGGCGGATCCACGAAATCGTAATTATAATAACTAATTCTGTAATAACAATAATGGTGAGGAATGACGAGTAGTGCGTTTGTATGATCCTAACCGTGATCCAATTCGATAAACAATTTAAGCAAATATGTATTAGGTACGTAGCCAACCAGCTCCAGATCCAGATCCCGATCCAGACTTCAGACATCCCCAACTAAACTCGAGCAACAAGGACATCGATCCTAATACTAACCGTCACTCTGATTTCCGCAGTTCTGTTCATAAGTAGTGCAAAGCAAGCAAATTCGGTGTAGCAATTAACCTAATATTACTTTAACCTACAATAAGAAGTTACCTATCACAGCAGCGCGAAACCATACCGAAACTAATATGTACTATTAACTACACATTAATTGAGCGCAGGCGACGGCAGGAGCAATTGTACTTGTCCTGTGTCAGCTACTACTTACCACTATGTATACATATGTATGTGTTTAAATTACAAATACAATTTTCTAAACATATTATCTCTAGCGAACGTGATCGTCACTTGAAATTTTATGTAAATCGAACCCAAAACCGAACGAACATTTTTAGATTTAACGTCGAGCGATTGTGTGTTTGAATTATCGTGTGACACAAGGGATTTGTTTAGGCACATAATTAGTGTAATAATGACGACATAGCGATGAAGTTTAATAAAAATTATTGCGTGTGCGTATTTAAATTGCAAGGTTTGGGATCAAGGACACACTTTAGTTTCGGTTTTTACTGTCGCCCGAATTTGAATCTTAATTTGACCTGAGTCTAATAAAATCGATCTGTACCGATGCCTACAAACGACTTGTTTTATTTCTTGACTTTGGAAAGATTGCAAAACTTAAGTGAAGGCCGGAACTGATCCGCACGCACCCAAATACTTGGCAGAAACTTTAAGGGCGAGGCGATTTGTGTAGAATCTTCCTGTTTTTGGAGCAAGTTTTTGGCTGATTTAAAACTTGGATCATGCCAATGTATTTAGAATATATTCAAAGCACTCTATACGAGTGCTTAGATGTTGAAGAATCAGATGTATAAATATATTTCTATTTAAAAATGTTTTATATCTGCATTATTTCACAAATCAGATTAGTTAGTGCACTGCCGTTAAGTTAACTGCACATAGGTAATCAATTTTTGTAAACCTGATACGTTGGCAAATCTTCTAGGATACTTACGAAAAATGTATGTATCCACTTATTTTATAAATTATATACATATATTCGGAAAGATATTTTTCTTTTTAGGACATACTCTACCTTTATGTATTGCATTGTATACATACAGGACTTATTATTTTT
  
  
    gene:EMBL/GenBank/SwissProt:AE003734:52204:55287
    Rab1
    Drosophila_melanogaster:Rab1
    gene
    Drosophila melanogaster (fruit fly)
    
      contig:AE003734.2:55787:51703
      500
      3584
      -1
      0
    
    
      FLYBASE:FBgn0016700
    
    
      map
      93D2-93D2
      0
    
    
      note
      last curated on Mon Apr 01 10:37:17 PST 2002
      0
    
    
      db_xref
      FLYBASE:FBgn0016700
      0
    
    
      gene
      Rab1
      0
    
    
      locus_tag
      CG3320
      0
    
  
  
    mRNA:EMBL/GenBank/SwissProt:AE003734:52204:55287
    Rab1-mRNA-2
    Drosophila_melanogaster:Rab1-mRNA-2
    mRNA
    Drosophila melanogaster (fruit fly)
    
      contig:AE003734.2:55787:51703
      500
      3584
      -1
      0
    
    
      FLYBASE:FBgn0016700
    
    
      product
      CG3320-RB
      0
    
    
      db_xref
      FLYBASE:FBgn0016700
      0
    
    
      gene
      Rab1
      0
    
    
      locus_tag
      CG3320
      0
    
  
  
    mRNA:EMBL/GenBank/SwissProt:AE003734:52204:55287
    gene:EMBL/GenBank/SwissProt:AE003734:52204:55287
    part_of
  
  
    mRNA:EMBL/GenBank/SwissProt:AE003734:52204:55287
    gene:EMBL/GenBank/SwissProt:AE003734:52204:55287
    part_of
  
  
    AAF55873.1
    Rab1-CDS-1
    Drosophila_melanogaster:Rab1-CDS-1
    polypeptide
    MSSVNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQESFNNVKQWLEEIERYACENVNKLLVGNKSDLTTKKVVDHTTAAEYAAQLGIPFLETSAKSATNVEQAFMTMAAEIKNRVGPPSSATDNASKVKIDQGRPVENTKSGCC
    205
    Drosophila melanogaster (fruit fly)
    
      contig:AE003734.2:55787:51703
      816
      2662
      -1
      0
    
    
      GI:7300727
    
    
      FLYBASE:FBgn0016700
    
    
      protein:AAF55873.1
    
    
      product
      CG3320-PA
      0
    
    
      note
      Rab1 gene product from transcript CG3320-RA
      0
    
    
      db_xref
      GI:7300727
      0
    
    
      db_xref
      FLYBASE:FBgn0016700
      1
    
    
      protein_id
      AAF55873.1
      0
    
    
      gene
      Rab1
      0
    
    
      translation
      MSSVNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQESFNNVKQWLEEIERYACENVNKLLVGNKSDLTTKKVVDHTTAAEYAAQLGIPFLETSAKSATNVEQAFMTMAAEIKNRVGPPSSATDNASKVKIDQGRPVENTKSGCC
      0
    
    
      locus_tag
      CG3320
      0
    
    
      codon_start
      1
      0
    
  
  
    AAF55873.1
    mRNA:EMBL/GenBank/SwissProt:AE003734:52204:55287
    derives_from
  
  
    AAN13857.1
    Rab1-CDS-2
    Drosophila_melanogaster:Rab1-CDS-2
    polypeptide
    MSSVNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQESFNNVKQWLEEIERYACENVNKLLVGNKSDLTTKKVVDHTTAAVRILLV
    146
    Drosophila melanogaster (fruit fly)
    
      contig:AE003734.2:55787:51703
      816
      2405
      -1
      0
    
    
      GI:23171868
    
    
      FLYBASE:FBgn0016700
    
    
      protein:AAN13857.1
    
    
      product
      CG3320-PB
      0
    
    
      note
      Rab1 gene product from transcript CG3320-RB
      0
    
    
      db_xref
      GI:23171868
      0
    
    
      db_xref
      FLYBASE:FBgn0016700
      1
    
    
      protein_id
      AAN13857.1
      0
    
    
      gene
      Rab1
      0
    
    
      translation
      MSSVNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQESFNNVKQWLEEIERYACENVNKLLVGNKSDLTTKKVVDHTTAAVRILLV
      0
    
    
      locus_tag
      CG3320
      0
    
    
      codon_start
      1
      0
    
  
  
    AAN13857.1
    mRNA:EMBL/GenBank/SwissProt:AE003734:52204:55287
    derives_from
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:52204:53323
    Rab1-exon-1
    Drosophila_melanogaster:Rab1-exon-1
    exon
    Drosophila melanogaster (fruit fly)
    
      contig:AE003734.2:55787:51703
      2464
      3584
      -1
      0
    
    
      gene
      Rab1
      0
    
    
      locus_tag
      CG3320
      0
    
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:52204:53323
    mRNA:EMBL/GenBank/SwissProt:AE003734:52204:55287
    part_of
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:52204:53631
    Rab1-exon-6
    Drosophila_melanogaster:Rab1-exon-6
    exon
    Drosophila melanogaster (fruit fly)
    
      contig:AE003734.2:55787:51703
      2156
      3584
      -1
      0
    
    
      gene
      Rab1
      0
    
    
      locus_tag
      CG3320
      0
    
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:52204:53631
    mRNA:EMBL/GenBank/SwissProt:AE003734:52204:55287
    part_of
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:53404:53631
    Rab1-exon-2
    Drosophila_melanogaster:Rab1-exon-2
    exon
    Drosophila melanogaster (fruit fly)
    
      contig:AE003734.2:55787:51703
      2156
      2384
      -1
      0
    
    
      gene
      Rab1
      0
    
    
      locus_tag
      CG3320
      0
    
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:53404:53631
    mRNA:EMBL/GenBank/SwissProt:AE003734:52204:55287
    part_of
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:53688:53735
    Rab1-exon-3
    Drosophila_melanogaster:Rab1-exon-3
    exon
    Drosophila melanogaster (fruit fly)
    
      contig:AE003734.2:55787:51703
      2052
      2100
      -1
      0
    
    
      id
      exon:EMBL/GenBank/SwissProt:AE003734:53688:53735
      0
    
    
      gene
      Rab1
      0
    
    
      locus_tag
      CG3320
      0
    
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:53688:53735
    mRNA:EMBL/GenBank/SwissProt:AE003734:52204:55287
    part_of
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:53688:53735
    mRNA:EMBL/GenBank/SwissProt:AE003734:52204:55287
    part_of
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:53798:53918
    Rab1-exon-4
    Drosophila_melanogaster:Rab1-exon-4
    exon
    Drosophila melanogaster (fruit fly)
    
      contig:AE003734.2:55787:51703
      1869
      1990
      -1
      0
    
    
      id
      exon:EMBL/GenBank/SwissProt:AE003734:53798:53918
      0
    
    
      gene
      Rab1
      0
    
    
      locus_tag
      CG3320
      0
    
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:53798:53918
    mRNA:EMBL/GenBank/SwissProt:AE003734:52204:55287
    part_of
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:53798:53918
    mRNA:EMBL/GenBank/SwissProt:AE003734:52204:55287
    part_of
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:54949:55287
    Rab1-exon-5
    Drosophila_melanogaster:Rab1-exon-5
    exon
    Drosophila melanogaster (fruit fly)
    
      contig:AE003734.2:55787:51703
      500
      839
      -1
      0
    
    
      id
      exon:EMBL/GenBank/SwissProt:AE003734:54949:55287
      0
    
    
      gene
      Rab1
      0
    
    
      locus_tag
      CG3320
      0
    
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:54949:55287
    mRNA:EMBL/GenBank/SwissProt:AE003734:52204:55287
    part_of
  
  
    exon:EMBL/GenBank/SwissProt:AE003734:54949:55287
    mRNA:EMBL/GenBank/SwissProt:AE003734:52204:55287
    part_of
  

BioPerl-1.007002/t/data/SPAN_Family4nl.nex000444000766000024      7512013155576321 20111 0ustar00cjfieldsstaff000000000000#NEXUS
begin taxa;
	dimensions ntax=27;
	taxlabels
	Chlamydomonas_reinhardtii_AAB04944.1	Trypanosoma_cruzi_AAB39949.1	Caenorhabditis_elegans_AAB53822.1	Mus_musculus_AAB60902.1	Saccharomyces_cerevisiae_AAB68939.1	Babesia_bovis_AAB69755.1	Candida_albicans_AAB86583.1	Pneumocystis_carinii_AAC24764.1	Penicillium_chrysogenum_AAC36585.1	Tritrichomonas_foetus_AAC47734.1	Tritrichomonas_foetus_AAC47735.1	Trichomonas_vaginalis_AAC48291.1	Toxoplasma_gondii_AAC63943.1	Neurospora_crassa_AAD28503.1	Arabidopsis_thaliana_AAF01529.1	Schizosaccharomyces_pombe_AAF19051.1	Drosophila_melanogaster_AAF57955.1	Oryza_sativa_BAA92737.1	Arabidopsis_thaliana_BAA97372.1	Arabidopsis_thaliana_BAB11186.1	Escherichia_coli_CAA27580.1	Rattus_norvegicus_CAA39937.1	Entamoeba_histolytica_CAA50204.1	Onchocerca_volvulus_CAA57658.1	Candida_sp_CAA72335.1	Caenorhabditis_elegans_CAB02913.1	Arabidopsis_thaliana_CAB87434.1;
end;

begin characters;
	dimensions nchar=1035;
	format datatype=dna missing=? gap=-;
	matrix
Chlamydomonas_reinhardtii_AAB04944.1	???atggccctcgcgatgaaggctcaggcttccagcctggtggctggc---------------------------cagcgccgcgctgtgcgccccgcttcgggccgtcgcgctgtgatcactcgc------------------------gctgctctggagctgaagtctcccccctacgctctggatgctctggagccccac---atgagcaagcagaccctggagttccactggggcaagcaccaccgcgcctacgtggataacatgaacaagcaggtcgctggcactccc---ctggac---------------------------ggcaagtcgctggaggagatcgtcctggccagctggaacaatggccag------cccaccccggtgttcaacaacgccgctcaggtctggaaccacactttcttctgggagagcatgaagccc---------aacggtggcggtgcccccaccggc---------gcgctggctgaggccatcacccgcgacttcggcagcctggacaagttcaaggaggagttcaagcaggctggcatgacccagttcggctctggctgggcctggctgaacgccgacaag------------------------------------------------acc------ggcaagctgtcgatcagcaagtcgcccaacgccgtgaaccccgtggtggag------------------ggcaagacccccatcctgactgtcgatgtgtgggagcacgcctactacattgacgtgcagaaccgccgccccgactacatcaccaccttcatggagaagctgatcaactgggacgccgttgctcagcgctacgcccgtgccaccaag??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Trypanosoma_cruzi_AAB39949.1	??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggtcttcagcattcctccgctcccatggggctacgatgggcttgcggcaaaaggcctctcaaagcagcaggtgacgctccactacgacaaacaccatcaggggtatgtgacgaaactcaacgccgcggcgcagacaaactccgcgcttgca---------------------------acgaaaagcatcgaggaaatcatcaggacggag---aaaggc------------------cccatattcaaccttgcggcgcagatttttaaccacacgttctactgggagagcatgtgtcct---------aatggcggtggcgagccgacggga---------aaagttgccgacgagatcaacgcttcatttggcagttttgcgaagttcaaggaggagtttacaaacgtggctgtgggccactttggctcgggtttggcgtggcttgtgaaggacacc---------------------------------------------aattcc------ggcaaactgaaagtctaccagacgcatgacgcgggatgtccactgacagagccc---------------aacttgaagcctctccttacatgcgatgtatgggagcatgcgtactacgtggactacaagaacgaccgtgcggcatatgtgcagaccttttggaac---gttgtcaactgg------------aagaacgtggaacggcaactt?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Caenorhabditis_elegans_AAB53822.1	???????????????????????????????????????????????????????????????????????????atgctgcaatctactgctcgcactgcttcaaagcttgttcaaccggttgcgggagttctcgccgtccgc------tccaagcacactctcccagatctcccattcgactatgcagatttggaacctgta---atcagccatgaaatcatgcagcttcatcatcaaaagcatcatgccacctacgtgaacaatctcaatcagatcgaggagaaacttcacgaggctgtttcg---------------------aaagggaatctaaaagaagcaattgctctccaacca---------------------------gcgctgaaattcaatggtggtggacacatcaatcattctatcttctggaccaacttggct------------aaggatggtggagaaccttcaaag---------gagctgatggacactattaagcgcgacttcggttccctggataacttgcaaaaacgtctttctgacatcactattgcggttcaaggctctggctggggatggttgggatattgcaag---------------------------------------------aaagac------aaaatcttgaagatcgccacctgtgcaaaccaggat---cctttggaagga---------------------atggtcccactttttggaattgacgtttgggagcacgcctactacttgcagtacaaaaatgtccgcccagactatgtccatgctatttggaag---attgccaactggaagaatatcagcgagagatttgccaatgctcgacaa??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Mus_musculus_AAB60902.1	???????????????????????????????????????????????????????????????????????????atgttgtgtcgggcggcgtgcagcacgggcaggaggctgggccctgtggccggtgccgcgggctcccgg------cacaagcacagcctcccagacctgccttacgactatggcgcgctggagccacac---attaacgcgcagatcatgcagctgcaccacagcaagcaccatgcggcctacgtgaacaacctcaacgccaccgaggagaagtaccacgaggctctggcc---------------------aagggagatgttacaactcaggtcgctcttcagcct---------------------------gcactgaagttcaatggtgggggacatattaatcacaccattttctggacaaacctgagccct---------aagggtggtggagaacctaaagga---------gagttgctggaggctatcaagcgtgactttgggtcttttgagaagtttaaggagaagctgacagccatgtctgtgggagtccaaggttcaggctggggctggcttggcttcaataag---------------------------------------------gagcaa------ggtcgcttacagattgctgcctgctctaatcaggac---ccattgcaaggaacaacaggc------------cttattccgctgctggggattgacgtgtgggagcacgcttactaccttcagtataaaaacgtcagacctgactatctgaaagctatttggaat---gtaatcaactgggagaatgttactgaaagatacacagcttgcaagaag??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Saccharomyces_cerevisiae_AAB68939.1	?????????????????????????????????????????????atgttc---------------------gcgaaaacagcagctgctaatttaaccaagaagggtggtttgtcattgctctccacc---acagcaaggaga------accaaagtcaccttgccagacttgaagtgggacttcggtgcattggaaccttat---atctccggtcaaatcaacgaattgcattacaccaagcaccatcaaacttatgtgaacggattcaacactgctgttgaccaattccaagaactctcagatcttctggccaaggagccctctcccgcaaacgcaagaaaaatgattgctatccaacaa---------------------------aacatcaagttccatggcggtggtttcacaaaccactgtctattctgggaaaacctggctccagagtcg---cagggcggtggtgaaccacccaccggc------gctttggcaaaggcaatcgacgagcagtttggcagtctggacgagctgattaagttgaccaacacaaagctagcaggcgtgcagggctccggatgggccttcattgtgaaaaacctc---------------------------------------------tctaat---ggaggcaagctggacgttgttcaaacctacaaccaggat---accgtcacaggccca------------------ctagttcctctagttgccattgacgcctgggaacacgcctactacttgcagtaccaaaacaagaaagccgactacttcaaagccatttggaat---gtggtcaactggaaagaagcatccagaagattcgatgctggcaagatc??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Babesia_bovis_AAB69755.1	??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggccttcaaactaccagcgctcccttacggcatgagggaactcatccctcac---atcagcgaggaaaccttgagcttccactacggcaaacaccatgcaggctacgtcaacaaactaaacagtctcatcaagggc---acacctatggaa---------------------------tcatgcactatcgaagagttgatactcggacaa---accggt------------------gccgtattcaacaacgcagcacaaatatggaaccacaccttctactggaactccatgggacct---------aactgtggaggcgagcccaccggt---------cccatccgcaagaagatcgaggaaaagttcggttctttcagcgcattcaagaccgatttctctaaccttctcgcagggcatttcggatccggttggggatggttggtgctaaaggat---------------------------------------------gatggc---------acagctgatattgtccaaacacatgatgcaggatcaccattaaaagagaat---------------ctagggcgcccactactttgctgtgatgtctgggagcatgcttactacattgactacaagaatgaccgtttgagctacattaacagctggtggaat---cttgtcaactgggacttcgccaataagaacctcgaagctcccttcaagtggtct????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Candida_albicans_AAB86583.1	?????????????????????????????????????????????atgttttctatcagatcatcatctcgtgttttattaaaggcttcttccgcaaccacccgtgctactttgaacgccgctgcttccaagactttcactaga------tctaaatatagtttaccagaattggactatgaattctccgctactgaaccatac---atttctggtcaaataaacgaaattcactacactaaacatcaccaaacttatgttaacaaccttaatgcttcaattgaacaagccgttgaagccaaatct---------------------aaaggtgaagttaaaaaattggttgccttagaaaaa---------------------------gccatcaatttcaacggtggtggttacctcaatcattgtttgtggtggaaaaacttggctcctgtctct---caaggtggtggtcaaccaccaagtgaagattccaaattaggtaaacaaatcgtcaaacaatttggttctttggataaattgattgaaatcaccaatggcaaattggctggtattcaaggttctggatgggcttttattgttaaaaacaaa---------------------------------------------gccaat---ggtgatactattgatgtcatcaccactgctaaccaagat---actgttactgatccaaac---------------ttggttccattgattgctattgatgcttgggaacatgcttattatttgcaataccaaaatgttaaagctgattacttcaagaacctttggcat---gttatcaactggaaggaagctgaaagaagatttgaattt???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Pneumocystis_carinii_AAC24764.1	????????????????????????????????????????????????????????????????????????atgttaaagtcatttagagatttggttttcaaaaaaactattaaaaactctcgtttt------ttttctcat------tcaaaacatgttttaccaagtcttccttatgattatcaggcattagaaccatat---ctttcagcagatttaattgagcttcattataatcaacatcatcgggcatatgttacaaatttaaataagacgatagagaaatattatgagggaaatgaa---------------tcatcattagattcgtttattaaccggttaaatcttttaaca---------------------------tctataaaattttttgcaggtggtcatattaatcattcattatattgggaaaatcttcttcctaataaa---caaggaggcggggaaataattaatgga------cctttagtagaagctattaagaaagaatggaaaagtgtcgatgaatttattcgtatatttaatatgcaattggcaggaattcaaggaagtggatgggcatggcttgtaaaatcg------------------------------------------------cctttt---agtcaacgtctaagtattcaaataacaatgaatcaagat---gttgtgacacagggt---------------------aaagttattcttggaatcgatgcatgggaacattcatattatgttcaatatttaaataataaaacaaaatattttgaaaatatatggaat---gtgatcaattggaaagttatgaatcaacgatttgagcaa???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Penicillium_chrysogenum_AAC36585.1	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgacttct------------------------caaacacacacactgcctcctctcccctatgcctacgatgcgttggagcccgtc---atctccaagcagataatggagctgcatcatcagaagcaccaccaaacttacatcaacaatctgaacgcagcgctctccgcccaagcttctgcaacagca---------------------tcaaatgatgtccccaccttgatttcattgcaacaa---------------------------aagcttcgctttaacggtggaggccatatcaatcactccctgttctggaagaacctgactccccccggt---acacctgcgaatgacatcgctggt---gctcccgctctgcgcgaagccatcgtctcccgctggggctcgcatgaagcgtttgtcaaggcttttggcgccgagctgctcggtcttcaggggagtggctggggatggctggtgagcaagggt---------------------------------------------ggtgcc---aagggacgacttgagatcgttacgactaaggaccaggac---cctgttaatgcacctgat------------------gtgcctgtcttcggtgtggatatgtgggagcatgcctactacctccagtacctgaacaacaaggctggctatgttgaggggatttggaag---atcattcactgggctgaagctgagaagcgttacactgctggcgttgagaacccg---------ctgaagctg??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tritrichomonas_foetus_AAC47734.1	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgttcagcatcgctccaatcccatacatggaaacaggaatcagtggattc---cttaccaagcacgccgtcgagatccacgtcacaaagcaccaccaagcctacgtcgacttcgctaacaagaatgttccaggaacagaa---ttcgaa---------------------------ggcaagccaatcgaagaaatcatccaaaaggctacagga---------------------ccactcttcaacaacgttgcccaacatttcaaccacgccttcttctggaactgcctcacagcc---------aagaagcaagaagttcca---gct---------ggcgtcgcatctttcctcgccaagcactttgaaagcgttgacaacttcaaggcccaattcgtccaaaaggcttcaacagtcttcggctccggatggtgctacctcgcccaaaacaag------------------------------------------------gac------aagacaatctcaatcaatcaatactcaaacgccctcaacccagtcaaggac------------------ggaggtgttccactcctttgcgttgacacctgggagcacgcctggtacatcgactacgaaaaccgcaaggccgaatacttcaacaaattctgggat---gcctgcaactgggaattccttgagaagaaccttaaggccgccggtctcatt???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tritrichomonas_foetus_AAC47735.1	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgttcagcatcgaaccagtttcattcttagagtcaggacttccaaacttc---ctcacaccacacgctgtccagatccacgttacaaagcaccaccaaggctacgtcgacatggccaacaaaattgtcccagaaagcgaa---ttcaag---------------------------ggcaaatccgttgaagaaatcattcaaaatgcttcaggt---------------------ccagtcttcaataacgtcgcccagcacttcaatcacagctttttctggaaatgtttgacagca---------acaacacaagaagttcca---gcc---------gccgttgcctcgttcctttcaaagcatttcgaaagcgtcgataacttcaaggcccagttcgtccaaaaggcatcaacagttttcggaagcggatggtgctatcttgccgtcaacaag------------------------------------------------gat------ggctcagtttcaatcaaccaatactcaaacgctctcaatccagtaaaggat------------------ggcggtgttccactcctttgcgttgacacatgggagcacgcctggtatatcgattatgaaaaccgcaaggccgaatacttcaacaaattctggggt---gttgtcaactggaactttgttgaagaaaaccttaagaaagccaaattaatc???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Trichomonas_vaginalis_AAC48291.1	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgttcacaatggagcatcctgcctacttgaagactggtcttccaggcttc---ctcacacagcacgctgtcgaggtccatgttacaaagcaccatcagtcctacattgatacagctaacaagcttatcgttggctctggc---ttcgaa---------------------------ggcaagccaattgaagaaatcatccaaaaggctcagggc---------------------ccactcttcaacaacgttgcccagcacttcaaccactccttcttctggaagtccctctccgct---------gagaaggttgctgttcca---gct---------catgttgctgagctcctcaagaagaacttcggctctgtcgagaagttccaggaaacattcacagctaaggcttcaacagtcttcggctctggctgggcttacctttacaagacaaag------------------------------------------------gac------ggcaagcttgagatcggccagtactccaacgctgctaacccagtcaaggat------------------ggccttacaccaattctcacagtcgatacatgggaacatgcttggtacatcgactacgagaacagaaaggctgagtacttcaagaactactggaac---cacgtcaactggaactttgttgagcagaacttaaaggctgctggtttg??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Toxoplasma_gondii_AAC63943.1	??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggtattcactttgcccccgctcccctacgcgcatgacgcgcttgctccccat---atcagctcggagacacttcagttccatcatggcaaacaccatgcaggctacgtggctaagctgaatggcttcattgaagga---accgctttcgcg---------------------------ggaaagactctagaagaggtgatccgtacgtct---actgga------------------gccattttcaataatgcggctcaagtgtggaatcatacattctacttcagcagcatgaagccaccaatgtctggtggtggtggagaacctactggg---------agacttctcgacgaaatcaagaaggaattcacatctgttgagaactttaaggacgagttttcgaaggttgccgctggccactttggctcaggttgggcatggcttgtttgggacaaa---------------------------------------------caaggc------aagaaggtcggcattgagcaaactcatgatgcgggcaccccgataacggagccg---------------atgaaggttccgctcctttgctgtgatgtatgggagcatgcctactaccttgacagaaagaacgacaggccagcgtacatcaaagcatggtggaat---gttgtaaactgggacttcgccagcaagaacttggagaatgccttgaaa??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Neurospora_crassa_AAD28503.1	?????????????????????????????????????????????????????????atggtcaatctaggaagcatttggcaaaaccttctcgcctcgcaagctcctctccagtccatgacaggcaacgcaaccaccatggccggcctcgcgacttattcccttccgcagctaccatatgcctacaatgctctggagccctac---atctcagcccagatcatggagcttcaccacagcaagcaccatcagacttacgtgaccaatctcaacaacgccttgaaagttcacgtcgccgccatcgcc---------------------tctagcgatatccccgcccagatcgcccagcagccc---------------------------gccatcaagttcaacggcggcggccacatcaatcactcgctcttctggaagaacctggcccccgctgag---accccagagaccaactactcgaaggcggctccttcgctggcggccgaaattgagaagacatggggtagttttgacgagttcaagaaggccttctctgctgcgctcttgggcatccagggcagtggctggggttggctcgttaaggagtct---------------------------------------------actgccgagaagggaaggctgcgtatcattactaccaaggatcaggat---cccgtcgtgggcggtgag------------------gtccctgtgttcggggtggacatgtgggagcatgcgtactacctccagtacctaaacggaaaggctgcgtatgttgagaatatctggaag---gtgatcaactggaagacagccgaggagcgcttccagggtagtcgtgaggacgcttttgcggacctcaaggctttgcta????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Arabidopsis_thaliana_AAF01529.1	??????????????????????????????????????????????????????????????????atggcgattcgttgtgtagcgagtagaaaaaccctagccggcttgaaggagacatcatcgaggctattgaggatcagagggattcagacttttacgcttcctgatcttccttacgattatggcgcattggaaccggcc---attagtggagagatcatgcagattcatcaccagaagcatcaccaggcttatgttactaattacaataatgctcttgagcagcttgatcaagctgtgaac---------------------aagggagatgcttccactgttgttaagttgcagagc---------------------------gccatcaaattcaacggcggaggtcatgtcaaccattcgattttctggaagaaccttgctccttccagt---gaaggtggtggagagccaccaaaa------ggatctcttggtagtgccattgacgctcactttggctcccttgaaggtctggtgaaaaagatgagtgctgagggtgctgcagtgcaaggctcaggatgggtgtggctcggactagacaaa---------------------------------------------gaactg------aagaagctagttgttgacacaactgccaatcaggat---ccattagtgacaaaaggaggaagc---------ttggtacctctggtgggtatagatgtttgggagcacgcctactacttgcagtacaaaaatgtgaggcctgagtatctgaagaatgtatggaaa---gtgatcaactggaaatatgcaagcgaggtttatgagaaggaaaacaac??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Schizosaccharomyces_pombe_AAF19051.1	?????????????????????????????????????????????????????????????????????atgcttcgctttttgtct------aagaactctgtagccgctattaggaacgtctcaattgccaggggagttcat------actaaggctactcttccccctttaccttatgcttacaatgcacttgaacctgct---ttgtcggaaacgattatgaagttacatcatgacaagcatcaccaaacatatgttaacaacttgaatgccgctcaggagaagctggccgatcccaac---------------------------ctcgatttggagggagaggttgcccttcaagct---------------------------gctattaaattcaatggcggtggtcacatcaatcattctctcttttggaagattttagcacctcaaaag---gaaggtggtggcaaacccgtcacc---tctggatctttacataaggctataacctctaaatggggttctttggaggatttccagaaggaaatgaatgccgccttagctagcatccaaggtagtggttgggcatggctaatcgtggataaa---------------------------------------------gacggt------agt---ctccgtattactactactgctaaccaagac---acgattgtcaagtccaag---------------------cccattattggaattgatgcttgggaacatgcctactatcctcaatacgagaatcgtaaggccgaatactttaaagctatttggaat---gtgattaattggaaagaggccgagtctcgttattccaaccgt????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Drosophila_melanogaster_AAF57955.1	??????????????????????????????????????????????????????????????????????????????????????????atgttcgtggcccgtaaaatttcgcaaactgcaagc------ctggcggtgcgt------ggcaagcacaccctaccgaagctgccctacgactatgccgccctggagcctatc---atctgccgggagatcatggagctgcatcaccagaagcaccaccagacctacgtcaacaatctaaatgccgccgaggagcagctggaggaggccaagtcg---------------------aagagcgacaccaccaagctgattcagctggctcct---------------------------gccctgcgtttcaatggcggtggccacatcaaccacaccatcttctggcagaacctctcg------------cccaacaagacccagcccagcgat---------gatctgaagaaggccatcgagtcgcagtggaagagcctcgaggagttcaaaaaggagctgaccacgctgaccgtggcggtccagggctccggctggggctggctgggcttcaacaag---------------------------------------------aagtcg------ggcaaactgcaactggccgccctgcccaaccaggat---cccctggaggcctccaccggc------------ctgatcccgctcttcggcatcgatgtctgggagcacgcctactatctgcagtacaagaacgtgcgtccctcctacgtggaggccatctgggac---atcgccaactgggatgacatctcgtgccgcttccaggaggccaagaagctcggttgc?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Oryza_sativa_BAA92737.1	???atggatgaggatgctgaagcaaatggt------------------------------------------------------gatgagtcgtcaggcactgatgaagatgcttctgtctcc------------------------------tggatagagcagcagcctcttccttatccttcagatgccctagagccatac---atcagcaaggagacggtggaacagcactggggagttcatcagaacattcacgtcgagaggctcaatggcatgattggtggcagtgag---tgggag---------------------------gggatgtcgctggggcagatgatgctatcctccttcaatgagggcagggaggcaccccatccccccttcttccatgctgcacagatatggaaccatgatttctattggcgatctatgcaacct---------ggtggcgggggaaaacccccagaa---------cgccttttgaaatttatcaacagggactttggatcctatgatggcatgattcgacaatttatggatgctgcatcaactcaatttggttctggatgggtttggctttgttacaaaacaagcaagttgcctcatgtgaaatcaagaagcccaatcccatctgataattat------ggtagactggtcatctcaaagtctccgaatgccatcaatcctcttgtctgg------------------ggtcactct---------------------------catgcatactacctggattatgaggatcggagatctgactatgtctccacatttctagagaagcttgtgtcatgggaaactgttgagtccaggcttaagaaggccgtacaacgggcagtagaaagagatgaatatgttagcacaaagcatataaggaagcaacttttagctcgggcaaagagccaaatcagagctatgcctcagcaggtcaatggggatgcaagagagcagaccagcggtcaagagaagtccctaggggtg
Arabidopsis_thaliana_BAA97372.1	atgatgaatgttgcagtgacagccactccctcgtctctcttgtactctcctctgcttcttccttctcaagggccaaaccggcgaatgcaatggaaaagaaacggaaagagacggttagggacaaaggtggctgtttccggtgttatcacagctggatttgagctgaagccacctccatatcctcttgatgctctggaaccgcat---atgagccgggaaaccttggattatcactggggcaaacatcacaaaacttatgtagagaacctgaacaagcaaatcttaggcacggat---ctagat---------------------------gcattatccttggaagaagttgtgcttctttcatacaacaaaggcaat------atgcttcctgctttcaacaacgctgcacaggcttggaaccacgagttcttctgggagtctatccaacct---------ggaggtggaggaaagccaactgga---------gagctcctcagattaatagaaagagattttgggtctttcgaagagtttttggaaaggttcaagtcggctgcagcttcgaattttggttcgggttggacatggcttgcatataaggcgaatagacttgacgttgcaaatgccgttaatcctctcccaaaggaggaagac------aagaaacttgttatagtgaagacgcccaatgcagtaaatccgctcgtatgg------------------gattattctccacttctcaccattgatacctgggagcacgcttactatctggattttgagaaccgaagagctgaatacataaatacattcatggaaaagcttgtgtcatgggaaactgtaagcacaaggttggaatccgcaattgctcgagcagtgcaaagagaacaagaaggaacagagacagaagat------------------------gaagagaatccagatgatgaagtaccagaggtctatttagatagtgacatcgatgtatctgaggttgac???????????????
Arabidopsis_thaliana_BAB11186.1	???atgagttcttgtgttgtgacgacaagctgtttctatacaatttcagattctagtatacgtttgaaatcccccaagctcctcaatctgagtaaccagcagagaagacgctctcttaggtctcgaggtggtttaaag------gttgaagcttactacggtctaaagacacctccttatccacttgatgctttggagccgtat---atgagtagaagaacactagaagtgcattggggaaaacaccatcgaggttatgtagataatctgaataaacagttagggaaagatgatagactctat---------------------------ggatacaccatggaagagcttatcaaggctacatacaacaacgggaat------cctttacccgagttcaacaacgctgcacaggtctataaccatgatttcttctgggagtcgatgcaacct---------ggtggtggagacacgcctcaaaag---------ggtgttcttgagcagattgataaggattttggttctttcacaaattttagagaaaagttcactaatgcagctcttactcagtttggttctggatgggtctggcttgtcttaaagagg---------------------------------------------gaagag------agaaggcttgaggtggtcaaaacctcaaacgccattaacccactcgtgtgg------------------gacgatattccaatcatctgcgtggatgtgtgggagcactcttattatctggactacaagaacgacagggctaagtatataaacacatttctgaaccacttggtgtcgtggaacgctgccatgagtcggatggcccgtgcagaagcgtttgtgaatcttggtgaa------------------------------------------------------------------------------------------cccaacatcccaatcgct????????????????????????
Escherichia_coli_CAA27580.1	??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgagctataccctgccatccctgccgtatgcttacgatgccctggaaccgcac---ttcgataagcagaccatggaaatccaccacaccaaacaccatcagacctacgtaaacaacgccaacgcggcgctggaaagcctgccagaatttgccaacctgccggttgaagagctgattaccaaactggaccagctgccagcagacaagaaaacc---------------------------gtactgcgcaacaacgctggcggtcacgctaaccacagcctgttctggaaaggtctgaaa---------------aaaggcaccaccctgcagggt---------gacctgaaagcggctatcgaacgtgacttcggctccgttgataacttcaaagcagaatttgaaaaagcggcagcttcccgctttggttccggctgggcatggctggtgctgaaaggc---------------------------------------------gataaa------------ctggcggtggtttctactgctaaccaggattctccgctgatgggtgaagctatttctggcgcttccggcttcccgattatgggcctggatgtgtgggaacatgcttactacctgaaattccagaaccgccgtccggactacattaaagagttctggaac---gtggtgaactgggacgaagcagcggcacgttttgcggcgaaaaaa?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Rattus_norvegicus_CAA39937.1	???????????????????????????????????????????????????????????????????????????atgttgtgtcgggcggcgtgcagcgcgggcagaagactgggccccgcggccagtaccgcgggctcccgg------cacaagcacagcctccctgacctgccttacgactatggcgcgctggagccgcac---attaacgcgcagatcatgcagctgcaccacagcaagcaccacgcgacctacgtgaacaatctgaacgtcaccgaggagaagtaccacgaggcgctggcc---------------------aagggagatgttacaactcaggttgctcttcagcct---------------------------gcactgaagttcaatggcgggggccatatcaatcacagcattttctggacaaacctgagccct---------aagggtggtggagaacccaaagga---------gagttgctggaggctatcaagcgtgactttgggtcttttgagaagtttaaggagaaactgacagctgtgtctgtgggagtccaaggttcaggctggggctggcttggcttcaataag---------------------------------------------gagcaa------ggtcgcttacagattgccgcctgctctaatcaggac---ccactgcaaggaaccacaggc------------cttattccactgctggggattgatgtgtgggagcacgcttactatcttcagtataaaaacgtcagacctgactatctgaaagccatttggaat---gtaatcaactgggagaatgttagccaaagatacatagtttgcaagaag??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Entamoeba_histolytica_CAA50204.1	??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgtctttccaattaccacaattaccttatgcttataatgctcttgagcctcat---attagtaaagagactcttgaattccatcatgataagcatcacgctacttatgttaataagttaaatggtcttgtaaaagga---actgaacaagaa---------------------------cataaaactcttgaagaattaattaaacaaaagccaactcaa------------------gcaatttataataatgcagcccaagcatggaatcatgcattctattggaaatgtatgtgtgga------------tgtggagttaaaccatctgaa---------caattaattgctaaattaactgctgcttttggaggattagaagaatttaagaagaagtttactgagaaagctgttggacattttggaagtggatggtgttggttggttgaacatgat---------------------------------------------ggt------------aagttagagattattgatactcatgatgctgttaatccaatgaccaat------------------ggaatgaaaccattattaacttgtgatgtttgggaacatgcttattacattgacactagaaacaacagagctgcttacttagaacattggtggaat---gtagtcaactgg------------aagttcgttgaagaacaactc?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Onchocerca_volvulus_CAA57658.1	???????????????????????????????????????????????????????????????????????????atgaatctgattattggcgtcgcaggtcgcttattggttggcaagaactattgtctgaatacacaacga------ctaaaacatgttcttcctgatttaccatacgattatggagccttggagccgata---ttgtcggccgaaattatgcaagttcatcacggtaaacatcatgctgcatatgtaaatgctcttaatcaagccgaagagaaagtaaaagaagcgctagca---------------------aaaggagatacacaggctgctgttgctggcacaaaa---------------------------ttaatgaatttcaacactggcggacacattaatcatacactgttctgggaaggattaactgccgta------aagaatagcggagaaccgaattct---------gaattaatgacggctataaagaaggatttcgggtctttggaaacgatgatagataagttaaatgctaaaacaattgcgatccaaggttccggatggggatggcttgcttatgacaag---------------------------------------------gaaatg------aaacgtttgcaacttgcttgttgtcccaaccaagat---cttcttgagccaacaacaggt------------ctaattccactattttgcatcgatgtctgggaacatgcttattatctgcagtataaaaatttacggccagatttcgtgaaagctatttggaaa---attgcgaattggaaaataatcagtgatcgctacattaaagctagagga??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Candida_sp_CAA72335.1	?????????????????????????????????????????????atgctt------------tcttctgctatcaagagatccgccgtcggtattgctagacgttccgtcgtgtcttcttccgttgga------gccgtcaga------accaaagtatcgttaccagacttggattgggacttcggagccttggagcctcac---atttcgggacagatcaacgaaatccactacaccaagcaccaccaaacttacgttaacggttacaaccaagccattgagcaagcagccaggccaagg------------------------caaggggaggtcaagaagaccattgaattgcaaaag---------------------------gccatcaacttccacggtggtggatacaccaaccactgtttgttctggaagaacttggctccagagaag---caaggaggtggtgagccacctgctgaagactctgagtttgccaagagaatcgttgagcaatacggctccctcgacaacttgaaggctatcaccaacggtaagttggccggtatccaaggttctggttgggctttcattgtcaagaacaag---------------------------------------------gaaaac---ggtggtgctttagatgttatcactactgcaaaccaagat---actgttcttggacca------------------tttgttccattggttgctattgatgcttgggaacatgcctactacttgcaataccagaacgtcaaggctgactacttcaaggccatctggaac---gttatcaactggaaggaagccgagaagagatacttgatcaac????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Caenorhabditis_elegans_CAB02913.1	???????????????????????????????????????????????????????????????????????????atgcttcaaaacaccgttcgctgtgtctcaaagcttgttcaaccgatcacaggagtcgctgctgttcgc------tcgaagcactcgctgccagatttaccatacgactatgctgatttggagcctgta---atcagtcacgagattatgcaacttcatcatcaaaagcatcatgccacttatgtgaacaatctcaaccaaattgaggaaaagcttcacgaggcggtctcc---------------------aaaggaaacgtcaaagaagctatcgctcttcagcca---------------------------gctctcaagttcaatggaggaggacatatcaaccactccatcttctggactaatttggca------------aaggacggaggagaaccatcggcg---------gagttgctcaccgcaattaagagcgacttcggatctctggataatcttcaaaaacagctttcggcatcaactgtcgctgttcaaggatcaggatggggatggttgggatactgtcca---------------------------------------------aaggga------aagatcttgaaggttgccacatgtgccaatcaggat---ccacttgaggcaacaactgga------------cttgttccactgttcggaattgacgtctgggagcacgcttactacttgcagtacaagaatgttcgaccagattatgtcaatgctatttggaag---atcgccaactggaagaacgtcagcgagcgttttgcaaaggcacagcaa??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Arabidopsis_thaliana_CAB87434.1	???????????????????????????????????????????????????atgacgaccaccgttattatcattatcttcgttgccatcttcgctacgactcttcacgacgccagaggagcaaccatggaaccgtgtctcgaatcaatgaagactgcttcgcttcctgatcttccgtatgcttatgatgcgctagagccagca---atcagtgaggagatcatgcggctacaccatcagaaacaccaccagacttatgtcactcagtacaacaaagccctcaacagccttcgttctgccatggct---------------------gacggtgatcactcctccgtcgtcaaactccaaagc---------------------------ctcatcaagttcaacggcggagggcacgttaaccatgcaatcttctggaaaaacctagccccggttcat---gaaggaggtggcaaaccaccgcat------gatcctttggcttcggcgatcgatgctcatttcggatcactagaaggattgatccaaaaaatgaacgcggaaggcgctgctgtacagggatctggatgggtgtggtttggattagacaga---------------------------------------------gagctt------aagagacttgtcgttgaaaccacagccaaccaggat---ccattggtgactaagggatcacac---------ctagttcctctaattgggattgacgtgtgggagcatgcctactatccacagtacaagaatgcaagagcggagtacttgaagaacatatggact---gtaatcaactggaaatatgcagcggacgtcttcgagaagcacactcgtgatctt------gatattaac?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
;
end;

begin trees;
	tree Mn_Fe_superoxide_dismutase = (((((Penicillium_chrysogenum_AAC36585.1:0.34051,Neurospora_crassa_AAD28503.1:0.27339)7:0.26409[1],(Schizosaccharomyces_pombe_AAF19051.1:0.36196,Pneumocystis_carinii_AAC24764.1:0.71151)8:0.12214[0.943])6:0.06412[0.513],(Candida_albicans_AAB86583.1:0.24934,(Candida_sp_CAA72335.1:0.18954,Saccharomyces_cerevisiae_AAB68939.1:0.32136)5:0.07268[0.61])4:0.25434[1])3:0.08564[0.791],((Arabidopsis_thaliana_CAB87434.1:0.31765,Arabidopsis_thaliana_AAF01529.1:0.21348)10:0.27524[1],(Drosophila_melanogaster_AAF57955.1:0.35616,((Onchocerca_volvulus_CAA57658.1:0.50902,(Caenorhabditis_elegans_CAB02913.1:0.15628,Caenorhabditis_elegans_AAB53822.1:0.11313)15:0.15295[1])14:0.11584[0.994],(Rattus_norvegicus_CAA39937.1:0.03387,Mus_musculus_AAB60902.1:0.02684)13:0.23219[1])12:0.08725[0.873])11:0.14599[1])9:0.10103[0.724])2:0.21049[1],(((Toxoplasma_gondii_AAC63943.1:0.21401,(Babesia_bovis_AAB69755.1:0.3377,Entamoeba_histolytica_CAA50204.1:0.47354)19:0.08578[0.743])18:0.09059[0.924],Trypanosoma_cruzi_AAB39949.1:0.35308)17:0.14755[1],((Trichomonas_vaginalis_AAC48291.1:0.12536,(Tritrichomonas_foetus_AAC47735.1:0.1604,Tritrichomonas_foetus_AAC47734.1:0.09764)22:0.20185[1])21:0.38885[1],(Chlamydomonas_reinhardtii_AAB04944.1:0.28584,((Arabidopsis_thaliana_BAA97372.1:0.29163,Oryza_sativa_BAA92737.1:0.56464)25:0.13153[0.967],Arabidopsis_thaliana_BAB11186.1:0.43387)24:0.21097[1])23:0.12537[0.998])20:0.09524[0.633])16:0.25459[1],Escherichia_coli_CAA27580.1:0.39688)1;
end;

BioPerl-1.007002/t/data/SPAN_Family7n.nex000444000766000024     33645413155576321 17772 0ustar00cjfieldsstaff000000000000#NEXUS
begin taxa;
	dimensions ntax=71;
	taxlabels
	otu_1	otu_2	otu_3	otu_4	otu_5	otu_6	otu_7	otu_8	otu_9	otu_10	otu_11	otu_12	otu_13	otu_14	otu_15	otu_16	otu_17	otu_18	otu_19	otu_20	otu_21	otu_22	otu_23	otu_24	otu_25	otu_26	otu_27	otu_28	otu_29	otu_30	otu_31	otu_32	otu_33	otu_34	otu_35	otu_36	otu_37	otu_38	otu_39	otu_40	otu_41	otu_42	otu_43	otu_44	otu_45	otu_46	otu_47	otu_48	otu_49	otu_50	otu_51	otu_52	otu_53	otu_54	otu_55	otu_56	otu_57	otu_58	otu_59	otu_60	otu_61	otu_62	otu_63	otu_64	otu_65	otu_66	otu_67	otu_68	otu_69	otu_70	otu_71;
end;

begin characters;
	dimensions nchar=1557;
	format datatype=dna missing=? gap=-;
	matrix
otu_1	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgtcgaag------atcggaatcaac---------------------------------------ggatttggccgcatcggccgcttggtgctccgcgccgccatcgataag---------ggc------gcctccgtggtggccgtcaacgatcccttcatcgatgtcaactacatggtttacctgtttaaattcgactcgactcacggtcgtttcaag------------------------ggc------accgttgcggctgagggcggattcctggtggtgaac---------------ggccagaagatcaccgtgttcagcgag---cgcgacccggccaacatcaactgggccagtgctggagccgagtatgtggtggagtccaccggagtgttc---------------------------------accaccatcgacaaggcgtccacccacttgaagggcggtgccaagaaggtcatcatctcggccccatcc---gcc---gatgcgcccatgttcgtgtgcggcgttaacctggacgcctacagcccc---gacatgaaggtggtctcc---------------------------aacgcctcgtgcaccaccaactgcctggctcccctggccaaggtcatcaat---gacaacttcgagatcgtcgagggtctgatgaccaccgtgcacgccaccactgccacccagaagaccgtcgacggtccctctggcaaactgtggcgcgatggacgtggcgccgcccagaacatcatcccggccgccaccggagccgccaaggctgtgggcaaggtcatccccgccctgaac---ggcaagctgaccggcatggctttccgcgtgcccacgcccaatgtctccgttgtggatcttaccgtccgcctgggcaaggga---gccacctatgacgaaatcaaggctaaggtcgaggaggcctccaaggga------------cccctgaagggaatcctgggctacaccgacgaggaggtggtctccaccgacttcctcagcgacacccattcgtctgtgttcgacgccaaggctggcatttcgctgaac------------gataagttcgtcaagctaatctcgtggtacgacaacgagttcggttactccaaccgcgtcatcgacctgatcaagtatatgcagagcaaggac??????????????????????????????????????????????????????????????????????????????????????????
otu_2	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggttaatgttggaatcaat---------------------------------------gggtttgggaggatcggacgtctcgtcctcagaaatgcattacaaatg---------caa---attctcactgttgtagctgttaatgatcctttccttgacgttgaatacatggcgtatctgttcaagtatgattccgttcatggacgatatcaa------------------------gga------aaagtcgaaaccaaggacgggaaattgatcattgat---------------ggacataaaatcgcggctttcgcagaa---cgtgaaccggcaaatattaaatgggccgattgcggcgctgagtacatcgttgaatctaccggcgtgttc---------------------------------aaaacagaagaattagcgaaggagcatttgaagggtggggccaaaaaagttgtcatcaccgctcctggg---agt---ggcgtacccacatacgtcgttggtgtcaatctggataaatacgatcct---aaagaagttgtgatttca---------------------------aatgcttcgtgcactaccaattgcctagcagtcctggcgaaggtcatcaat---gacaaatttggaattgtggaaggcttgatgacgacagtgcatgccaccacagccacgcagaagactgtcgatgctcctgcaaagaaggattggcgttctggaaggagtgttacaaataacatcattccagcatctacgggtgccgctaaagctgttacaaaggcgattcctgatttggag---ggaaaactcactggactggcattccgagtcccgacactcgacgtatcggttgttgacctcgtcgttcgcctcgaaaaggaa---accagttacgatgacgtcaaaaaagccatgagggacgcagccgacggtaaacacccgggcatcgagaaaggcattgtcgactatacggaagaagacgttgtttccaccgatttcgttgggagcaactattcgatgatctttgacgcaaaagccgggatcgcgttgaac------------tcgcgttttatgaagttggttgcatggtatgataatgagtggggatatgcgcgtagagtctgcgatgaggttgtgtatgtagcgaagaagaat??????????????????????????????????????????????????????????????????????????????????????????
otu_3	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggttaaagttggaatcaac---------------------------------------ggtttcggtcgtatcggccgcattgtcctccgtaatgctctccaattc---------cag---gacatcgaagttgtcgccgtgaacgacccgttcattgacctcgaatacatggcatacatgttcaagtacgactccgtccacggtcgcttcaag------------------------ggt------accgttgaggtcaagaacggcagctttgtcgttgac---------------ggcaggcctatgaaagtctttgctgaa---cgcgatcccgctgccatcccttggggttcagtcggcgcggactacgtcgtggaatccacaggtgtattc---------------------------------actactatcgacaaggcttcggctcacttgaaggggggcgccaaaaaagtcgttatctccgctccttcg---gcc---gatgcgccgatgtatgtctgcggtgttaaccttgacaagtacaatccc---aaggacacaattatctcg---------------------------aacgcttcttgcacaaccaattgcttggctactcttgctaaagtcattcac---gataactttggtatcgttgagggtctgatgaccactgttcacgccaccaccgctactcaaaagactgtggatggtccttctcacaaggactggcgtggtggccgtggtgtcggcaataacatcattccttcctctactggcgccgccaaggccgtcggaaaggttatcccttcactcaac---ggcaagctcactggtctctcgatgcgtgttcccactcaggacgtttccgttgtcgatcttgttgttcgtcttgagaagccc---gcttcctatgaacagatcaaggaggtcatgcgcaaggccgctgaaggc------------gaatacaagggaattatcgcatacaccgacgaggacgtggtttccactgacttcattagtgataacaattcttgtgtcttcgatgcgaaggccggaattcagcttagc------------ccgaactttgtcaagctgattgcttggtacgataacgaatggggatactcgcgccgtgtttgcaacctcctccaatacgttgcaaaggaggacgccaaggctggcatt???????????????????????????????????????????????????????????????????????????
otu_4	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctgacaagaagattaggatcggaatcaac---------------------------------------ggattcggaagaattggtcgtttggttgctagagttgttctccagagg---------gac---gatgttgagctcgtcgctgtcaacgaccccttcatcactactgagtacatgacctacatgttcaagtacgacagtgttcacggtcaatggaaa------------------------cacaatgaactcaagatcaaggatgagaagacccttctcttcggt---------------gagaagccagtcactgttttcggcatc---aggaaccctgaggatatcccatgggccgaggctggagctgactacgttgttgagtctactggtgtcttc---------------------------------actgacaaagacaaggctgcagctcacttgaagggtggtgccaagaaggttgttatctctgaacccagc---aaa---gacgctccaatgtttgttgttggtgtcaacgagcacgaatacaagtcc---gaccttgacattgtctcc---------------------------aacgctagctgcaccactaactgccttgctccccttgccaaggttatcaat---gacagatttggaattgttgagggtcttatgactacagtccactcaatcactgctactcagaagactgttgatgggccttcaatgaaggactggagaggtggaagagctgcttcattcaacattattcccagcagcactggagctgccaaggctgtcggaaaggtgcttccagctcttaac---ggaaagttgactggaatgtctttccgtgtcccaaccgttgatgtctcagttgttgaccttactgtcagactcgagaaagct---gctacctacgaagaaatcaaaaaggctatcaaggaggaatccgaaggc------------aaactcaagggaatccttggatacaccgaggatgatgttgtctcaactgacttcgttggcgacaacaggtcgagcatttttgacgccaaggctggaattgcattgagc------------gacaagtttgtgaaattggtgtcatggtacgacaacgaatggggttacagttcccgtgtggtcgacttgatcgtccacatgtcaaaggcc?????????????????????????????????????????????????????????????????????????????????????????????
otu_5	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctcccaaggtcggaatcaac---------------------------------------ggcttcggtcgtattggacgcatcgttttccgtaacgccatcgaggcg---------ggt---accgtcgatgttgttgccgtcaacgaccctttcatcgagacccactacgctgcctacatgctcaagtatgactcacagcacggtcagttcaag------------------------ggc------accattgagacctacgacgagggtcttattgtcaac---------------ggcaagaagatccgcttccacaccgag---cgtgaccccgccaacatcccctggggccaggacggtgctgaatacattgtcgagtccaccggtgtcttc---------------------------------actacccaggagaaggctagcgctcacctgaagggtggtgccaagaaggttgtcatctctgccccatct---gct---gatgcccctatgttcgtcatgggtgtcaacaacgagacctacaagaag---gacattcaggtcctctcc---------------------------aacgcttcttgcaccaccaactgccttgcccctctcgccaaggtcatcaac---gacaacttcggtatcatcgagggtctgatgaccaccgtccactcctacactgctacccagaaggtcgtcgacggcccctcggccaaggactggcgtggtggccgtaccgctgctaccaacatcatcccctcctccactggtgctgccaaggctgtcggcaaggtcattccttcgctcaat---ggcaagctcaccggcatggcgatgcgtgttcccacctccaacgtctccgttgttgacctgaccgtccgcaccgagaaggct---gttacctacgaccagatcaaggatgccgtcaagaaggcttctgagaac------------gagctcaagggcatccttggctacaccgaggacgacatcgtctctaccgacctcaacggtgacacccgctcttccatcttcgatgctaaggcgggtattgccctcaac------------tccaacttcatcaagctcgtttcctggtacgacaacgagtggggttactcccgccgtgttgttgacctcatcacctacatctccaaggttgatgcccaa????????????????????????????????????????????????????????????????????????????????????
otu_6	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgccggtcaaagcaggaatcaac---------------------------------------ggtttcggtcgtattggccgtatcgtcctccgtaatgctctccttcac---------gga---gacattgacgtcgtcgcggtcaacgaccccttcattgacctcgagtacatggtctacatgttcaagtacgactccgttcacggtcgcttcaag------------------------ggt------tccgtcgaggccaaggacggcaagctctatgtcgag---------------ggcaagcctatccacgtcttcgctgag---aaggacccggccaacatcccttggggctctgtcggcgctgagtacatcgtcgagtcgaccggtgtgttc---------------------------------accaccaccgagaaggcctctgcccacttgaagggcgtgtgcaagaaggtcatcatctcggccccctct---gct---gatgcccccatgtttgtctgcggtgtcaacctcgacgcgtacgactcc---aagtacaaggtcatctcg---------------------------aacgcgtcctgcaccaccaactgcttggcgccccttgccaaggtcatccac---gacaagttcggcattgtgcagggtctcatgacctccgtccacgctaccaccgctacccagaagaccgtcgatggcccctcgaacaaggactggctgggtggccgttccgtcggcaacaacatcatcccctcgtcgactggtgccgccaaggccgtcggcaaggtcatcccttcgctcaac---ggcaagctgaacggtctcgccttccgtgtccccaccgtcgatgtctccgtcgtcgacctcgtcgtccgtctcgagaagccc---gcttcttacgacgagatcaagcaggccatcaaggaggcgtcggagacc------------acccacaagggcatcctcggctacaccgaggagaaggtcgtctccaccgacttcaccggcaacgacaactcgtcgatcttcgatcgtgacgcgggtatcgcgctcaac------------aagacattcgtcaagctcatctcctggtacgacaacgagtggggctactcccgccgttgctgcgacctcctcggttacgccgcgaaggtcgacggtgccctc?????????????????????????????????????????????????????????????????????????????????
otu_7	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggccgtgaaggttggaattaac---------------------------------------gggttcggtcgcattggccgtatcgttctccgtaatgcccttcagctg---------ggc---aacatcgaggtcgtcgccatcaacgacccgttcatcgcccttgactacatggtctacatgttcaagtacgacaccgtccacggccgctacaag------------------------ggc------accgtcgaggtgaaggacggcaagctcgtcgtcgac---------------ggccatgccatcaccgtcttcgctgag---aagaaccccgccgacatcaagtggggctctgctggcgccgactacatcgtcgagtccaccggtgtcttc---------------------------------accaccgtcgagaaggcgtcgctgcacttgcagggcggcgcgaagaaggtcgtcatctcggcgccctcc---gcc---gacgccccgatgttcgtcgtcggcgtcaacctcgacaagtacgactcg---aagtaccaggtcatctcg---------------------------aacgcgtcctgcacgaccaactgcctggcgccgctcgcgaaggtcatccac---gacaagtacggcatcgcggagggtctcatgaccaccgtgcacgccacgaccgcgacccagaagaccgtcgacggcccgtcgcacaaggactggcgcggtggccgctcggtcaacaacaacatcatcccctcgtcgactggtgcggctaaggccgtcggcaaggtcatcccctcgctcaac---gggcgcctcaccggcctcgccttccgtgtcccgaccctcgacgtctccgtcgtcgacctcgtcgtccgcctcgagaaggag---gcctcgtacgacgagatcgtcgcgaccgtcaaggaggcgtccgagggc------------ccgctcaagggcatcctcggcttcaccgacgagtccgtcgtctcgaccgacttcaccggcgcgaacgagtcgtccatcttcgactccaaggccggcatcgcgatcagc------------aagagcttcgtgaagctcattgcctggtacgacaacgagtggggctactcccgccgtgtctgcgacctgctcgtctacgcggcgaagcaggacggcgcgctc?????????????????????????????????????????????????????????????????????????????????
otu_8	atggcaactcatgctgctttagcttctacaagaatcccaacaaacacaaggtttccatctaagacctct---cactctttcccatctcaatgtgcctcaaagagacttgaggtaggtgaattctctggactcaaatcaacttcatgtatttcctatgttcatagtgctagagattcttctttttatgatgttgtagctgctcaactcacttccaaggcaaatgga---tcaactgctgtgaaggga---------gtgactgtggctaagttgaaggtagcaatcaat---------------------------------------ggttttggacgcatcggtagaaatttccttcgatgctggcacggtcgaaaggactcg------ccacttgaagtcattgttgtcaatgac---agtggaggtgtcaagaatgcttcacatttgttgaaatatgattctatgcttggaacttttaaa------------------------gca------gaagtgaagatactaaacaatgagactattacagtt------------gatggtaaacccatcaaggttgtctctagcagagat---cctcttaagcttccttgggccgaacttggaattgacattgttattgagggaacaggagtgttt---------------------------------gtggacggccctggcgcgggcaaacacatccaagcaggtgccaagaaagttatcatcactgctcctgcaaagggtgctgatattccgacttacgttattggagtgaacgaacaagactacggccatgaagtagccgacatcataagc---------------------------aatgcttcttgcaccacaaactgtcttgctccctttgctaaggtcctggat---gaagagttcggaatcgttaagggaaccatgacaaccacacattcctacaccggagaccagaggcttttggat---gcttcacatagggacttgagaagagctagagctgcagcactgaacattgttccgaccagcacaggagcagccaaggctgtatctctagtgttgccacagctcaag---ggaaagctcaacggaatcgccctccgtgtgcctacgcctaatgtttcagttgttgaccttgtggtcaatgttgcgaagaagggtatatcagctgaagatgtcaatgcagcattcagaaaggcagctgaggga------------ccactgaaaggtatattggatgtctgtgatgttccgctcgtgtctgttgacttccgctgctccgatgtttctacaactattgactcttccttgactatggtcatgggagatgat------------atggttaaggtggttgcttggtatgacaatgaatggggttacagccaaagagtggtggatttggcacatctagtagcaaacaaatggccaggaacccctaaagtagggagtggagatccattggaggacttctgcgagacgaatccggccgacgaggaatgcaaagtttatgaa???
otu_9	??????????????????atggccgccatgatgcag---------------------------------------------------------------------------aagagcgccttcaccggcagcgccgtgtcctccaag---------------------------------------------------tctggcgtccgcgccaaggctgcccgcgccgtcgtcgacgtgcgc---------------gcggagaagaagatccgcgtggccatcaac---------------------------------------ggcttcggtcgcattggccgcaacttcctgcgctgctggcacggtcgccagaacacc------ctgctggacgtggttgccatcaacgac---agcggcggtgtcaagcaggccagccacctgctgaagtacgactccaccctgggcacgttcgcc------------------------gcc------gatgttaagatcgtcgacgacagccacatctcggtg------------gacggcaagcagatcaagattgtgtccagccgcgac---cccctgcagctgccctggaaggagatgaacatcgacctggtcattgagggcactggtgtcttc---------------------------------attgacaaggttggcgctggcaagcacatccaggccggtgcctccaaggtgctgatcaccgcccccgccaaggacaaggacatccccaccttcgtggtcggtgtgaacgagggcgactacaagcacgagtacccc---atcatctcc---------------------------aacgcctcgtgcaccaccaactgcctggcccccttcgtcaaggtgctggag---cagaagttcggcattgtcaagggcacgatgaccaccacccactcctacaccggtgaccagcgcctgctggac---gcgtcccaccgcgacctgcgccgcgcccgcgccgccgccctgaacattgtgcccaccaccaccggtgccgccaaggccgtgtcgctggtgctgcccagcctgaag---ggcaagctgaacggcattgccctgcgcgtgcccacccccaccgtgtcggtcgtcgacctggtcgtccaggttgagaagaag---accttcgccgaggaggtgaacgccgccttccgcgaggccgccaacggc------------cccatgaagggcgtgctgcacgtcgaggacgcccccctggtgtccattgacttcaagtgcaccgaccagtcgacctccatcgacgcctccctgaccatggtcatgggcgacgac------------atggtcaaggtcgtggcctggtacgacaacgagtggggctactcccagcgcgtggtcgacctggctgaggtcaccgccaagaagtgggtggcg????????????????????????????????????????????????????????????????????????????????????
otu_10	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgggcaagatcaagatcggaatcaac---------------------------------------ggtttcggaaggatcggcaggctcgtggccagggtcgccctgcagagc---------gag---gatgtcgagctcgtcgccgtcaacgaccccttcatcaccacggattacatgacgtacatgttcaagtacgacaccgtgcacggccaatggaag------------------------cacagcgacatcgccctcaaggactccaagacgcttctcttcggc---------------gagaagccggtcaccgtctttggcatc---aggaaccccgaggagatcccgtggggtgaggctggtgctgagtatgtcgtggagtccaccggtgtcttc---------------------------------actgacaaggacaaggctgctgcacatctgaagggtggtgccaagaaggttgttatctctgccccaagc---aaa---gatgcgcccatgtttgttgttggtgtcaatgaggacaagtacacctcc---gatgttaacattgtttcc---------------------------aatgctagctgcaccacaaactgccttgctccccttgctaaggtcattcat---gacaactttggcattattgagggcttgatgacaactgttcatgccatcactgccacccagaagactgttgatggaccctcagccaaggactggagaggtggcagggctgccagctttaacatcattcccagcagcaccggtgctgccaaggctgtcggtaaggttcttcctgaattgaat---ggcaagctcactggcatgtccttccgggttcccaccgtggatgtgtcagttgttgacctcactgtcagaatcgagaagggg---gcctcttacgaggaaatcaagaaagctattaaggctgcttctgagggc------------ccactcaagggtattatgggctacgtggaggaggatctggtttccaccgacttcaccggtgacagcaggtcgagcatcttcgacgccaaggccgggattgccctgaac------------gaccacttcatcaagctcgtctcttggtacgacaacgagtggggctacagcaaccgcgtcgtcgacctgatccgccacatgttcaagacccag??????????????????????????????????????????????????????????????????????????????????????????
otu_11	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggttgtcaggattgcaatcaac---------------------------------------ggtttcggcagaattggacgtcttgtcttccgcgcagttcgcgatctctatccaaaa------gaatgccaaattgtcgctgttcacgat---ctttgcgatatcgccactaacgttcatttattgaactacgattccgctcatcaaaggttccca------------------------gaa------caacttacagttacagctgaagataccttcgaagttggcacaggctccgacaagtgggttgtcaaaaatcttacaggcagattaggtccatcccaactcccatggaaggaattagatgtcgatgtcgttttagaatccactggactcttccgcacccactgtgttaagggagaagacggaagcgtcacaaaagatggatatgacggacatttattagccggtgccaagaaagtcgttttatcagtaccttcagccgacgaaatcgaatgcacacttgttttaggggtcaacgacgaagacctcaagccagatacaaac---tgcatttca---------------------------aacgcctcatgcacaacaaattgcctcgcaccagtcatcaaagtgttgaac---gacacattcggcatcagaaacggatacatgacaactgttcacgcctacacaaacgatcaagttgtttcagat---atcatgcataaggatctccgccgtgcccgtgcagctgcaatgaacatcattccaacatcaacaggagctgccatcgccctcacacgtgttgttaagaacctcacacgcggatgcatggatggcctcgctttacgcgttccagccatcacaggcagcctcgtcgacatcaccgtcaacacacgtgaaaag---gtaaccaaggatcaagttaatcaagccctcaaggctgcttcagaatccgaa---------gccctccgtggaatccttggctacactgacgagccaatcgtcagctcagatataattggtgacagacattcatccatcgttgactcactctctacaatggttctcgacaacgaaaagggtggaagcctcgtaaaggtcctctcatggtacgataacgaatggatgtactcatgccgctgcgctgatattttccaccatcttgaacagtacacaaag???????????????????????????????????????????????????????????????????????????????????????
otu_12	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctcccatcaaggttggcatcaac---------------------------------------ggtttcggccgtatcggtcgtatcgtcttccgcaacgctgtcgagcac---------ccc---gacgtcgagatcgttgccgtcaacgaccccttcattgagaccaagtacgctgcctacatgctcaagtacgactccacccacggcattttcaac------------------------ggc------gagattgcgcaggatggcaacgaccttgtcatcaac---------------ggcaagaaggtcaagttctacactgag---cgcgaccccgctgtcatcccctggaaggagaccggcgccgactacgtcgtcgagtccactggtgtcttc---------------------------------accaccatcgacaaggccaaggcacatcttcagggcggtgccaagaaggtcatcatctctgctccctcc---gcc---gacgcccccatgtacgtgatgggtgtcaacgagaagtcctacgacggc---agc---gcagtcatctcc---------------------------caagcttcttgcaccaccaactgcctggctcccctcgccaaggtcatcaac---gacaagtacaccatcattgagggtctcatgaccaccgtccactcctacaccgctacccagaagaccgttgacggtccctccgccaaggactggcgtggtggccgcactgctgctcagaacatcattcccagcagcactggcgcgcccaaggctgtcggcaaggtcattcctgagctcaac---ggcaagctcaccggcatgtccatgcgtgtccctaccgccaacgtctccgtcgttgacctgactgtccgcatcgagaagggc---gccacgtacgacgagatcaagcaggccatcaaggaggcggctgagggt------------cccctcaagggcgtcttggcctacaccgaggacgacttcgtctccaccgacatgatcggcaaccccaactcctccatcttcgacgccaaggccggtatctccctgaac------------aacaacttcgttaagctggtctcctggtacgacaacgagtggggttactcccgccgtgtcctcgacctcttggcccacgtcgccaaggtcgatgcctccaag?????????????????????????????????????????????????????????????????????????????????
otu_13	?????????????????????????????????????????????atgtcgaagcgcgacatcgtcctcaccaatgtcaccgttgtccagttgctgcgacagccgtgcccggtgaccagagcaccgcccccacctgagcctaaggctgaagtagagccccagccacaaccagagcccacaccagtcagggaggaaataaagccaccaccgccaccactgcctcctcaccccgctactcctcctcctaagatggtgtctgtggcccgggagctgactgtgggcatcaat---------------------------------------ggatttggacgcatcggtcgcctggtcctgcgcgcctgcatggagaag---------ggt------gttaaggtggtggctgtgaatgatccattcattgacccggaatacatggtgtacatgtttaagtatgactccacccacggccgatacaag------------------------gga------agtgtggaattcaggaatggacaactggtcgtggac---------------aaccatgagatctctgtctaccagtgc---aaagagcccaaacagatcccctggagggctgtcgggagcccctacgtggtggagtccacaggcgtgtac---------------------------------ctctccatacaggcagcttcggaccacatctctgcaggtgctcaacgtgtggtcatctccgcgccctca---ccg---gatgcaccaatgttcgtcatgggtgtcaatgaaaatgactataaccctggctccatgaacattgtgagtgtccgtgcacaccttggctgtttcagcaacgcgtcctgcaccaccaactgtttggctcccctcgccaaagtcatccac---gagcgatttgggatcgtggaagggttgatgaccacagtccattcctacacggccacccagaagacagtggacgggccatcaaggaaggcctggcgagatgggcggggtgcccaccagaacatcatcccagcctccactggggctgcgaaagctgtgaccaaagtcatcccagagctcaaa---gggaagctgacagggatggcgttccgggtaccaaccccggatgtgtctgtcgtggacctgacctgccgcctcgcccagcct---gccccctactcagccatcaaggaggctgtaaaagcagcagccaagggg------------cccatggctggcatccttgcctacaccgaggatgaggtcgtctctacggacttcctcggtgatacccactcgtccatcttcgatgctaaggccggcattgcgctcaat------------gacaatttcgtgaagctcatttcatggtacgacaacgaatatggctacagtcaccgggtggtcgacctcctccgctacatgttcagccgagacaag???????????????????????????????????????????????????????????????????????????????????????
otu_14	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggtcgtcaaggtcggcatcaac---------------------------------------ggtttcggccgtatcggtcgcattgtcttccgcaatgccattgagcac---------gat---gacatccacatcgtcgctgtcaacgaccccttcattgagcccaagtacgctgcttacatgctccgctacgacaccacccacggcaacttcaag------------------------ggc------accatcgaggttgacggtgctgacctcgtcgtcaac---------------ggcaagaaggtcaagttctacactgag---cgcgaccccgctgccatcccctggtccgagaccggtgccgactacattgtcgagtccactggtgtcttc---------------------------------accaccaccgagaaggcctccgcccacttgaagggtggtgccaagaaggtcatcatctctgccccctct---gct---gatgcccccatgtacgttatgggtgtcaacaacgagacctacgatggc---tccgccgacgtcatctcc---------------------------aacgcctcttgcaccaccaactgcttggctcccctcgccaaggtcatccac---gacaacttcaccatcgtcgagggtctcatgaccaccgtccactcctacaccgccacccagaagaccgtcgatggtccttccgccaaggactggcgcggtggccgcactgctgctcagaacatcattcccagcagcactggttccgccaaggccgtcggcaaggtcatccccgacctcaac---ggcaagctcactggtatggccatgcgtgtccccaccgccaacgtctccgttgtcgatcttactgcccgcatcgagaagggt---gctacctacgatgagatcaaggaggtcatcaagaaggcctctgagggt------------cccctcgctggcatccttgcctacaccgaggatgaggttgtctcttccgacatgaacggcaaccccgcctcctccatcttcgatgccaaggctggtatctccctcaac------------aagaacttcgtcaagcttgtctcctggtacgacaacgagtggggctactctcgccgtgtcctcgacctcatctcctacatctccaaggtcgatgccaagaaggct??????????????????????????????????????????????????????????????????????????????
otu_15	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgaccgcaaacgttggaattaat---------------------------------------ggatttggaagaattggtagactggtgttgagaattgccttgagcaga---------gac---gacatcaacgtcattgctatcaatgatccattcattgctcctgattacgccgcttacatgttcaagtacgactctacccacggaaagttcaag------------------------gga------actgtcacccacgagggcaagtacttggtcattaac---------------ggcaagaagattgaggtcttccaagag---agagacccagcaaacatcccatggggtaaggagggcgtcgactacgttcttgactccactggagttttc---------------------------------accaccatcgagggtgctcaaaagcacattgatgctggtgccaagaaggtcatcatcactgctccatct---aag---gacgctccaatgttcgtcgtcggtgtgaaccacgaggagtacactcca---gacatcaagatcctgtct---------------------------aacgcttcttgtaccaccaactgtctggctccactggccaaggttatcaac---gacatcttcggaatcgaggaaggtttgatgaccaccgtccactccatcaccgctactcaaaagactgtcgacggtccatcccacaaggactggagaggtggtagaactgcttctggtaacatcatcccatcctccaccggtgctgccaaggctgtcggaaaggtccttccagcattggcc---ggtaagctcactggtatgtccatgagagtcccaaccactgatgtttctgttgttgacttgaccgtcaaccttaagaagcca---accacctacgaggacatttgtgccaccatgaagaaggctgctgagggc------------ccattggctggaattcttggatacaccgacgaggctgttgtttcgtctgacttcttgaccgacagcagatcctctgtctttgacgccaaggccggtatcttgttgacc------------ccaaccttcgtcaagctcgtttcctggtacgacaatgagtacggttactctaccagagttgttgacttgcttcagcacgttgctaaggtttccgcc???????????????????????????????????????????????????????????????????????????????????????
otu_16	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctatcactgtcggtattaac---------------------------------------ggtttcggacgtattggacgtctcgttctgagagtcgctctttccaga---------gct---gacatcaaggttgttgctatcaacgacccattcattgctccagaatacgctgcttacatgttcaagtacgactctacccacaaggcttacaag------------------------ggt------gaggtttctgccagcggcaacaagatcaacattgac---------------ggtaaagaaatcaccgttttccaagag---agagaccctgtcaacatcccatggggtaaggctggtgtcgactacgtcattgagtccaccggtgttttc---------------------------------accactttggagggtgcccaaaagcacatcgacgccggtgccaagaaggtggtcatcactgctccatcc---aag---gatgctccaatgttcgttgtcggtgtcaacgaggagaaatacacttct---gacttgaacattgtctcc---------------------------aatgcttcttgtactaccaactgtttggctccattggccaaggttgtcaac---gacactttcggaattgagtccggtttgatgaccaccgtccactccatgaccgccactcaaaagaccgttgacggtccatcccacaaggactggagaggtggtagaacggcttctggtaacatcattccatcttccactggtgctgctaaggccgtcggtaaggttattccagaattgaac---ggtaagctgaccggtttggctttccgtgtcccaaccgtcgatgtctccgttgttgacttgaccgtcaacttgaagaaggag---actacctacgaggagatcaagtctgttatcaaggctgcttccgagggt------------aagctcaagggtgttttgggttacactgaagatgccgttgtctcttctgacttcttgggtgacgagagatcctccatcttcgacgcttctgccggtattcaattgact------------ccatctttcgtcaagctgatctcttggtacgacaacgagtacggttactccaccagagtcgtcgacttgttgcaacacgttgctaaggct?????????????????????????????????????????????????????????????????????????????????????????????
otu_17	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctattaaaattggtattaac---------------------------------------ggtttcggtagaatcggtagattagtcttaagagttgctttgggcaga---------aaa---gacattgaagttgtcgccgtcaacgatccattcattgctccagactatgctgcttacatgttcaaatacgattctactcacggtagatacaag------------------------ggt------gaagtcactgcttctggtgacgacttggtcattgat---------------ggtcacaagattaaagttttccaagaa---agagacccagctaacattccatggggtaaatctggtgttgactacgttattgaatccaccggtgttttc---------------------------------accaaagtcgaaggtgctcaaaagcacattgatgctggtgccaaaaaagttatcatcactgctccatct---gct---gatgccccaatgtttgttgtcggtgttaacgaagacaaatacactcca---gacttgaagattatctcc---------------------------aatgcttcttgtaccaccaactgtttggctccattagctaaagtcgtcaac---gatactttcggtattgaagaaggtttgatgaccactgtccactccatcactgctacccaaaagaccgttgacggtccatcccacaaggactggagaggtggtagaactgcttctggtaacattatcccatcttccactggtgctgctaaagccgttggtaaggttattccagaattgaac---ggtaaattgactggtatgtctttgagactcccaaccaccgatgtttccgttgttgacttgactgtcagattgaagaaagct---gcttcttacgaagaaattgctccagctatcaagaaagcttctgaaggt------------ccattgaaaggtgttttgggctacactgaagatgctgttgtctccaccgatttcttgggttcaagctactcatctatctttgatgaaaaagccggtatcttgttgtcc------------ccaactttcgtcaaattgatttcctggtacgataacgaatacggttactccaccaaagttgttgacttgttggaacacgttgcc???????????????????????????????????????????????????????????????????????????????????????????????????
otu_18	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctccgatcaaggttggcatcaac---------------------------------------ggctttggccgcatcggccgcatggtgttccagtccatgtgcgaggacaacgtgctcggcaccgagctggacgttgtcgccgtggtggacatgagcacggacgccgagtacttcgcgtaccagatgaagttcgacacggtgcacggccgcccgaag---tacacggtggaggtggcgaagagctcgccgtcggcgaag---aagccggacgtgctggtggtgaac---------------ggccaccgcatcctgtgcgtgaaggcggaccgcaacccggcggacctgccgtggggcaagctcggcgtggactacgtgatcgagtccaccggcctgttc---------------------------------acggacaaggcgaaggcggagggccacgtgaagggcggcgcgaagaaggtggtgatcagcgcgccggcgtctggc---ggcgccaagacgatcgtgatgggcgtgaaccagcacgagtacaacccggccacgcaccacgtcgtgtcg---------------------------aacgcgtcctgcacgaccaactgcctggcgccgatcgtgcacgtgctgaccaaggagaacttcggcatcgagaccggcctgatgaccaccatccactcctacacggcgacgcagaagacggtggacggcgtgtcgatcaaggactggcgcggcggccgcgcggctgcggtgaacatcatccccagcacgaccggcgctgccaaggccgtgggcatggtgatcccgtccaccaag---ggcaagctgaccggcatgtcgttccgcgtgccgacgccggatgtgtcggtggtcgacctgaccttccgcgccacccgcgac---acgtccatccaggagatcgacgcggccctcaagaaggcgtcgcagacc------------tacatgaagggcatcctcggcttcacggacgaggagctggtgagcagcgacttcatcaacgacgcgcgcagctccatctacgactccaaggcgacgctgcagaacaacctgcccggcgagaagcgcttcttcaaggtggtgtcgtggtacgacaacgagtggggctactcgcaccgcgtggtggaccttgtgcgcttcatgggcgccaaggac---cgctccagctccaagctg?????????????????????????????????????????????????????????????????????
otu_19	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctcccgtcaaggttggcatcaac---------------------------------------ggtttcggccgcattggccgcatggtcttccaggccatgtgcgagcagggcgtgctcggcaaggacttcgacgttgtcgcggtcgtggatatgtcgacggacgctgagtactttgcgtaccagatgaagtacgactctgtgcacggcaagcccaag---tacacggtggaggtcgcgaagagctctccgtctgtgaag---aagccggatgtgcttgtggtgaac---------------ggccaccgcatccagtgcgtgaaggcgcagcgcaaccccgctgacctgccctggagcaagctcggcgtggagtacgtgatcgagtcgactggtctgttc---------------------------------acgaacaaggccaaggctgagggccacctcaagggcggcgcgaagaaggtgatcatcagcgcgcctgcctctggc---ggcgccaagacgatcgtgatgggcgtgaacaaccaggagtacaaccccagcagccacagcgttgtgtcg---------------------------aacgcgtcctgcacgaccaactgccttgccccgctggtgcacgtgctgctgaaggagggcttcggcgtggagactggcctgatgaccaccatccactcgtacaccgccacgcagaagaccgtcgatggcgtctccctgaaggactggcgcggcggccgtgctgctgccatgaacatcatcccgtcgacgacgggtgctgccaaggccgttggtgaggtgctgcccgtgaccaag---ggcaagctgaccggcatgtccttccgtgtgccgacgccggatgtgtccgtggtggacctgaccttcaccgctgccaaggac---acgtcgatcaaggagattgacgaggccttcaagcgcgcgtccaagacg------------tacatgaagggcatcctcagctacaccgacgaggagcttgtgtcgtcggacttctacaacaacaacaacagctccatctacgactccaaggcgacgctgcagaacaacctgcccggcgagaagcgcttcttcaaggttgtgtcctggtacgacaacgagtggggctactctcaccgtgtcgtgaacctgctgtccttcatgatcaagaaggac---cgcgccggctccaagatc?????????????????????????????????????????????????????????????????????
otu_20	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctccgctcaaggttggcatcaac---------------------------------------ggcttcggtcgcattggccgcatggtgttccagtcgatgtgcgaggacaacgtcctcggcaacgagatcgatgtcgtggcggtggtggacatgagcacggacgccgagtacttcgcgtaccagatgaagtacgacacggtgcacggccgcccgaag---tacacggtggaggtggcgaagagctctgccgcggtgaag---aagccggatgtgcttgtggtgaac---------------ggccaccgcatcctgtgcgtgaaggcgcagcgcaacccggcggacctgccgtggggcaagcttggcgtggactacgtgatcgagtcgaccggcctgttc---------------------------------acggacaaggtgaaggctgagggccacgtgaagggcggcgcgaagaaggtggtgatcagcgcgccggcgtccggc---ggtgcgaagacgatcgtgatgggcgtgaaccagaacgagtacgactccgccaagcaccacgtcgtgtcg---------------------------aacgcgtcctgcacgaccaactgcctcgccccgatcgtgcacgtgctgacgaaggagggcttcggcgtcgagaccggcctgatgacgaccatccactcctacactgccacgcagaagacggtggacggcgtgtcgatcaaggactggcgcggtggccgcgctgctgcggtgaacatcatcccgagcacgaccggtgcggccaaggccgtgggcatggtgatcccgtcgacgaag---ggcaagctgaccggcatgtccttccgcgtgccgacgccggatgtgtccgtggtggacctgacgttccgcgcgacccgcgac---acgtcgatccaggagatcgacgcggcgctgaagaaggcgtccaagacg------------tacatgaagggcatcctcggcttcacggacgaggagctggtgagcgccgacttcatcaacgacgcccgcagctcgatctacgactccaaggcgacgctgcagaacaacctgcccggcgagaagcgcttcttcaaggtcgtgtcgtggtacgacaacgagtggggctactcccaccgcgtggtggacctggtgcgcttcatgggcgccaaggac---cgcgcgagctcgaagatg?????????????????????????????????????????????????????????????????????
otu_21	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctcccatcaaggttggaattaac---------------------------------------ggcttcggtcgtattggccgcaatgtcttccaggcgatctgcgagggaaaccatctcggcactgacatcgacgtggttgcggttgcggatatgagcacagacgccgagtacttctcctaccagatcgtggacgactccgtgcacggcaagccgcgctcctatggcgtcgaggtggcgaagagcaacccgtctgtggag---aagccggatgtgctcgtggtgaac---------------ggccaccgcatccagtgtgtgaaggcagcccgcaaccccgctgatctgccgtggggtaagcttgatatcgagtatgtgatcgagtccaccgggctcttc---------------------------------acgaagaagacccaggctgagggtcacatcaagggaggggccaagaaggtggtcatcagcgctcccgcatctggc---ggtgtcaagacgatcgtgatgggcgtgaacgagaaggagtatgacccgtcgtctcaccacatcgtgtcg---------------------------aacgcgtcgtgcacgaccaactgcctcgcgccccttgtgcacgttctgacgaaggagggcttcgggctggagactggtctgatgaccacgatccactcgtacacggcgacccagaagactgtggacggcgtgtcgatcaaggactggcgtggtggccgcgctgccgcgatcaacataatccccagcacgactggtgcggccaaggctgtgggcgaggtgatccccacgaccaag---ggcaagttgacgggcatggccttccgcgtcccgacacccgacgtgtcggtggtggacttgactttcacggccacccgcgac---acatcgatcaaggagatcgacgccgcgctgaagaaggcg---gtgacg------------tacataaagggcatcctcagctttaccgacgaggagttggtgagcacagactttatcaacgacaaccacagctccatctacgactccaaggcgacgctccaaaacaacctgcccaacgagaagcgcttcttcaagctcgtgtcctggtacgataacgaatggggctactcccaccgtgttgtggatctaattatctacatggctaagagggac---gctgcctccgccaagcta?????????????????????????????????????????????????????????????????????
otu_22	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctaccaaggtcggcatcaac---------------------------------------ggtttcggtcgcattggccgcatcgtgctccgcaacgccctcgagcac---------ggc---gacattgacgtcgttgccatcaacgaccccttcattgacctcgactacatggtctacatgttcaagtacgactcgacccacggccgcttcaag------------------------ggc------aaggttgagaccaaggacggcaagctcgtcattgag---------------ggcaagcccatctcggtcttcggcgag---cgtgaccccgctgccatcccttggggcaaggccggcgccgactacgtcgtcgagtcgaccggtgtcttc---------------------------------accaccattgagaaggcctcgctccacctcaagggtggtgccaagaaggtcatcatctcggccccttcg---gct---gacgcccccatgttcgtttgcggtgtcaacctcgaggcttacaagccc---gagtacgaggtcatctcg---------------------------aacgcctcgtgcaccaccaactgccttgcgccccttgccaaggtcatccac---gacaacttcggcatcgtcgagggtctcatgaccaccgtccacgccaccaccgccacccagaagaccgttgacggcccttcgcacaaggactggcgtggcggccgtggcgctgccgccaacatcattccctcgtcgaccggtgccgccaaggccgtcggcaaggtcatcccctcgctcaac---ggcaagctcaccggcatgtcgttccgtatccccacctcggacgtttcggtcgttgaccttgtcgtccgtcttgagaagggc---gcctcgtacgaccagatcaaggaggtcatcaagaaggcctcggagggc------------gagctcaagggcatcctcggctacactgaggacgaggttgtctcgaccgacttcctcggctcgaccgagtcgtcggtctttgacgccaaggcgggtatccccctcaac------------gacaagttcgtcaagctcatctcgtggtacgacaacgagtacggctactcgcgccgcgtctgcgacctcatcgcctacgttgccaagaaggacaagtcggcg?????????????????????????????????????????????????????????????????????????????????
otu_23	???????????????????????????????????????????????????atggccttctcttctctcctcagatctgccgcctcctacacggttgccgctcctcgccctgactttttctcgtcgccggcgtctgatcattctaaggtgttgtcaagtcttggatttagtcgcaacctgaagccatcaagattttcttctgggatatcttcatctctacaaaatggcaatgcaagaagtgtgcaacccatcaaggccacggctacagaagtgccatctgcagttcgaaggtcaagtagcagtggaaagacaaaggttgggatcaacggttttggtcggattggaaggttggtcctccgcattgcaacatcaagg---------gat---gatattgaggttgtagcagtgaatgacccattcattgatgccaagtacatggcttacatgttgaagtatgattctactcatggaaatttcaag------------------------gga---agcatcaatgtcattgatgattctactttggagatcaat---------------gggaagaaggtcaatgttgtcagcaag---agagatccatctgagatcccatgggctgatcttggagctgattatgttgttgagtcttccggtgtattc---------------------------------accaccctgtcaaaggctgcatcccatttgaagggcggtgccaagaaagttataatttctgccccttct---gct---gacgcacctatgtttgttgttggagtaaacgagcacacataccaacca---aacatggatatagtctcc---------------------------aatgcaagttgtaccaccaattgtcttgcccctcttgccaaggtggtgcat---gaggaatttggtattcttgaaggcttgatgacaactgtccacgcaactacagctactcagaaaactgttgatgggccatcaatgaaggactggagaggaggtcggggcgctagtcaaaacatcattcctagctcaaccggcgccgcgaaggctgtaggtaaagttcttccagaactgaat---gggaaacttacgggaatggccttccgtgtaccaacatcgaatgtttctgtggtggatttaacttgtcgacttgagaagggt---gcctcttacgaagatgttaaggcagccattaagcatgcctcagaagga------------cctcttaaaggcattctcgggtacacagatgaagatgtcgtctccaatgatttcgtcggtgattcaaggtccagtatctttgacgccaatgctggtattggattgagc------------aagtcctttgtgaaacttgtctcttggtacgacaacgaatggggttacagcaaccgagttcttgaccttatagagcacatggctttggtagctgccagccac?????????????????????????????????????????????????????????????????????????????????
otu_24	???????????????????????????????????????????????????atggccttatcttctctcctcagatctgccgccact---tccgccgcagctcctcgtgtcgagctttatccatcgtcatcgtacaatcattctcaggtcacgtcaagtcttggattcagtcatagcctgacctcgtctagattttct---ggtgctgcagtttcaaccggaaaatacaatgcgaagagggttcaacccatcaaggccacagctacggaagcacctcctgctgttcat------------agt---------------------------tttggtcgaattggaagattggtcctccgcatcgcaacctttagg---------gat---gatatcgaggttgtagcagtcaacgatccattcatagatgccaagtacatggcttacatgttcaagtatgattctactcatggaaattacaaa------------------------gga---actatcaatgtaattgatgattcaactttggagatcaat---------------ggaaaacaagtcaaagttgtcagcaag---agagacccagctgaaatcccgtgggctgatcttggagctgagtatgttgttgagtcttcaggggtattc---------------------------------accaccgttggacaagcttcatcacatttgaagggtggtgctaagaaggtcatcatttctgcaccttca---gcg---gacgcgcccatgtttgttgttggagtaaatgaaaagacatacctgcct---aacatggatatagtctcc---------------------------aatgcaagttgtaccaccaattgtcttgcacctcttgccaaggtggtgcat---gaggaatttggtattcttgaaggcttgatgacaacagtccacgcgaccacagctactcagaaaactgtggacggcccatcaatgaaggactggagaggaggccgaggcgcaagtcaaaacatcattcctagctcaacaggcgctgcaaaggctgttggtaaggtccttccggaactcaat---ggaaaactaacaggaatggccttccgtgtcccaacaccaaatgtctctgttgtggatttaacttgtcgacttgagaaggat---gcatcgtatgaagacgtcaaggcagccataaagtttgcatcagaagga------------ccacttaggggcattcttggatatacagaagaagatgtcgtctctaatgattttcttggagattcaaggtcaagtatctttgatgctaatgctgggattggattaagc------------aagtccttcatgaaacttgtctcctggtatgacaacgaatggggttacagcaaccgagtccttgacctgatagaacacatggcgttagttgcagccagccgc?????????????????????????????????????????????????????????????????????????????????
otu_25	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctgtcaaggttggaatcaac---------------------------------------ggtttcggacgaatcggacgaatcgtccttcgaaacgctatcatccac---------ggt---gatatcgatgtcgtcgccatcaacgaccctttcatcgatcttgagtacatggtctacatgttcaagtacgactccacccacggtgtcttcaag------------------------gga------tccgtcgagatcaaggacggcaagctcgtgatcgag---------------ggcaagcccatcgtcgtctacggtgag---cgagaccccgccaacatccagtggggagctgccggtgccgactacgtcgtcgagtccaccggtgtcttc---------------------------------accacccaggagaaggccgagctccacctcaagggaggagccaagaaggtcgtcatctctgccccttcg---gcc---gatgcccccatgttcgtctgcggtgttaacctcgacaagtacgacccc---aagtacaccgtcgtctcc---------------------------aacgcttcgtgcaccaccaactgcttggctcccctcgccaaggtcatccac---gacaactacaccattgtcgagggtctcatgaccaccgtccacgccaccaccgccacccagaagaccgtcgacggtccttccaacaaggactggcgaggaggtcgaggagctggtgccaacatcatcccctcctccaccggagccgccaaggccgtcggtaaggttatcccctccctcaac---ggaaagctcaccggaatggccttccgagtgcccacccccgatgtctccgtcgtcgatcttgtcgtccgaatcgagaaggcc---gcctcttacgaggagatcaaggagaccatcaagaaggcctcccagacccct---------gagctcaagggtatcctgaactacaccgacgaccaggtcgtctccaccgatttcaccggtgactctgcctcctccaccttcgacgcccaggccggtatctcccttaac------------ggaaacttcgtcaagcttgtctcctggtacgacaacgagtggggatactctgcccgagtctgcgaccttgtttcttacatcgccgcccaggacgccaaggcc?????????????????????????????????????????????????????????????????????????????????
otu_26	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctatcacagttggtattaac---------------------------------------ggtttcggtcgtattggtcgtttagtcctaagaattgctctttcaaga---------aaa---gatattcaaattgttgcaattaatgatccattcattgcaccagaatatgcttcatatatgtttaaatatgattctactcatggtcgttattca------------------------ggt------gaagtttctcatgaaggtgaaaacattgttattgat---------------ggtaaaaaaatcagagtttatcaagaa---cgtgatccagttaatatcccatggggtaaagatggtgttgattatgttattgattcaactggtgttttt---------------------------------aaagaattagattctgctcaaaaacatattgatgccggtgctaaaaaagttgttattactgctccatca---tca---actgctccaatgtttgttgttggtgttaatgaagataaatatactcca---gatttaaacattatttca---------------------------aatgcttcatgtacaacaaattgtttagctccattagctaaaattattaac---aataaatttggtattgaagaaggtttaatgactactgttcattcaattactgctactcaaaaaactgttgatggtccatctcataaagattggagaagtggtcctactgcttcaggtaatattattccatcatcaactggtgctgctaaagctgttggtaaagttattccagaattggct---ggtaaattaactggtatgtctttaagagttccaactgttgatgtttcagttgttgatttaactgttaaattattaaaagat---gccacttatgatgaaattaaagctgctgttaaagaagctgctgaaggt------------ccattaaaaggtgttgttggttatactgaagatcaagttgtttcttcagatttcttaactgataacagatcatcaatttttgatgctgaagctggtatttggttatca------------ccaagatttgttaaattaattgcttggtatgataatgaatatggttactctaccagagttgttgatttattagaatacgttgcttcaaagaac??????????????????????????????????????????????????????????????????????????????????????????
otu_27	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctgacaagaagattaggatcggaatcaac---------------------------------------ggattcggaagaattggtcgtttggttgctagagttgttctccagagg---------gac---gatgttgagctcgtcgctgtcaacgaccccttcatcactactgagtacatgacctacatgttcaagtacgacagtgttcacggtcaatggaaa------------------------cacaatgaactcaagatcaaggatgagaagacccttctcttcggt---------------gagaagccagtcactgttttcggcatc---aggaaccctgaggatatcccatgggccgaggctggagctgactacgttgttgagtctactggtgtcttc---------------------------------actgacaaagacaaggctgcagctcacttgaagggtggtgccaagaaggttgttatctctgcccccagc---aaa---gacgctccaatgtttgttgttggtgtcaacgagcacgaatacaagtcc---gaccttgacattgtctcc---------------------------aacgctagctgcaccactaactgccttgctccccttgccaaggttatcaat---gacagatttggaattgttgagggtcttatgactacagtccactcaatcactgctactcagaagactgttgatgggccttcaatgaaggactggagaggtggaagagctgcttcattcaacattattcccagcagcactggagctgccaaggctgtcggaaaggtgcttccagctcttaac---ggaaagttgactggaatgtctttccgtgtcccaaccgttgatgtctcagttgttgaccttactgtcagactcgagaaagct---gctacctacgatgaaatcaaaaaggctatcaaggaggaatccgaaggc------------aaactcaagggaatccttggatacaccgaggatgatgttgtctcaactgacttcgttggcgacaacaggtcgagcatttttgacgccaaggctggaattgcattgagc------------gacaagtttgtgaaattggtgtcatggtacgacaacgaatggggttacagttcccgtgtggtcgacttgatcgtccacatgtcaaaggcc?????????????????????????????????????????????????????????????????????????????????????????????
otu_28	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgaagttctctgccgccacttttgctgcccttgtaggatctgccgctgcctactccagttcttcctttaccggatcggccctcaagagctcggcgtccaatgatgcctccatgtcgatggctaccggtatgggagtcaac---------------------------------------ggattcggacgtatcggacgtctcgtcacccgcatcatgatggaagac---------gac---gaatgcgatttggtcggaatcaacgccggttccgccactccggactacatggcctaccagtacaagtacgataccatccacggcaaggccaag------------------------cag------acggtcgaaatcgatggcgacttcctcgtcttggac---------------ggcaagaagatcatcacttcgcgctgc---cgtgaccccaaggaagtgggctggggcgcactcggagccgactacgtctgcgaatccaccggagtcttc---------------------------------ctcaccaaggaatccgcacagtccatcattgacggaggcgccaagaaggtcatctactcggcacccgccaaggac---gactcactcaccattgtcatgggagtcaaccaggaagcctacgatggt---tcggaagatttcatctcc---------------------------tgcgcttcttgcaccaccaacggacttgcccctatggttaaggccattcac---gacgaattcgtcattgaggaagccctcatgaccaccgtccacgccatgaccgccacccaggccgttgtcgactcctcatcccgcaaggactggcgcggaggacgtgcggcctcgggaaatatcatcccatcctccaccggagccgccaaagccgtcaccaaggtcattccttccctcgtt---ggaaagatcaccggcatggccttccgtgtccccaccattgacgtctccgtcgtcgacttgaccgcaaaactcgaaaagtcc---accacttacgaagaaatctgtgccgtcatcaaggccaagtccgagggt------------gaaatgaagggattcctcggatactccgacgaaccgttggtctccaccgactttgaaggtgacttgcgctcctccatctttgatgccgatgccggtatcatgctcaac------------cccaactttgtcaagctcatcgcctggtacgacaacgaatacggttactccggccgtgtcgtcgacctcatgaagcacgtcgcggccgtcgacgccaagatcaaggcc???????????????????????????????????????????????????????????????????????????
otu_29	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgtcgaag------attggtatcaat---------------------------------------ggatttggtcgcatcggccgcttggttctccgcgccgccattgataag---------ggc------gccaacgttgtggccgtcaacgatcccttcatcgatgtgaactacatggtctacctgttcaagttcgattcgacccacggacgttttaag------------------------ggc------accgttgccgccgagggcggtttcctggtggtcaac---------------ggccagaagatcaccgtcttcagcgaa---cgcgacccggccaacatcaactgggccagcgctggtgccgaatacatcgtggagtccactggcgtgttc---------------------------------accaccatcgacaaggcatccactcacttgaagggcggtgccaagaaggttatcatctcggccccatcc---gcc---gatgctcccatgttcgtttgcggcgtcaacttggatgcctacaagccc---gacatgaaggtggtctcc---------------------------aacgcatcgtgcaccaccaactgcttggctcctctggccaaggtgatcaac---gacaacttcgagatcgtcgagggtctgatgaccaccgttcatgccaccaccgctacccagaagaccgtcgatggaccttccggcaagttgtggcgtgatggacgtggcgctgcccagaacatcattccagcttccactggagctgccaaggccgtgggcaaggttatccccgccctcaac---ggtaagctcaccggaatggcattccgtgtgcccactcccaacgtttccgtggtcgatttgaccgtgcgcttgggcaagggt---gcgtcctatgatgaaattaaggccaaggttcaggaggccgccaacgga------------cccctgaagggtatcctgggatacaccgatgaggaggtcgtttctaccgatttcctcagcgacacccactcgtcggtgttcgatgccaaggctggcatttcgctaaac------------gacaagttcgtgaagctgatctcttggtacgacaacgagtttggctactccaaccgcgtcatcgacctgatcaagtacatgcagagcaaggat??????????????????????????????????????????????????????????????????????????????????????????
otu_30	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgtccggtattggcatcaat---------------------------------------ggctttggccgaatcggtcgcatgtttgcccgccaggctctagttcgc---------aaa---gatgtcaagatcgtggcaatcaacgatccctcactggatcccaagtatctggcctacatgctgcgatacgactccactcatggacagttcaat------------------------cag------aagatctctgtcgacgggaacaatcttgttgttaat---------------ggcaagaagatccagctgcttaaggag---tcggacgtcaagaagattaaatggtgcgacctgggcgtgcatacggtggtggagtgctccggtaggttt---------------------------------accaccctgaaagcctgtcaaggtcacttggatagtggggccaaaaaggtggtcatatcggcaccatct---gcc---gatgctccgatgtttgtgtgcggagtgaatcttgaggcatacaagccg---ggcacagcaatcatctcg---------------------------aatgcctcatgcacaaccaattgcctggcgccgctggccaaggtggtgcac---gataactttgaaatatgtgagggccttatgaccaccgttcatgcggctacagctacccaaaagatcatcgacggacccagcagcaaactctggcgggatggacgcagtggcatgaccaacatcatacccgcatccacgggagccgctaaagccgtcggcaaggtgattccggatctaaac---gggaagctaacgggtatggctttccgtgtaccagttcccaatgtctcggtggtggacctcacctgtaggctttctaagccc---gccaaaatggacgatatcaagaagtgcataaaggctgcatccaaatgc------------gaaatgaagggaatcctggggtatgtggaggaggaggtggtgtccaccgattttaacggctcacgatttgcatccgtctttgatgccaaggcctgtattgccctaaac------------gataacttcgtcaagttgatcagttggtacgataacgagaccggatattcctgccgtctccttgacctagttctctatgcccagttggtcgaccaatgcgatgcgaaggaaaagggtgcttgc????????????????????????????????????????????????????????????
otu_31	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgtcaatcactgtcggcatcaac---------------------------------------ggcttcggccctgtcgggaagtccgccttattcgcggccctagccgatccg------------ctgttcaccgtcacggcagtcgttgacgtctccgtgtgtgcggcctacattgcgtatgtgattgagcaagagtatccgcatcgcaacccaacaggg------------------cctccgattcgggtgacggacaagcagaaggatcagattgtactgaac---------------aacacccacgtcattcacgtgtcggccgcgcaagatccgcagtcatccatgtggaagaagtacggtgcgcagtacgtgctagagtgcacaggcctctac---------------------------------accacacgtagccgcagctggggtcatgtgacaggtggtgcggtgggcgtcttcatcgccgccgccagcgctgatacgaacacagtcatggcatcaagcggcttggaaagactcgcggcatcgttgcctgtgtgcgccgcaggagcgccc------------------------atcggggccgtcgtagctccagtgctggacgcgctggcgaaggtgttggagatcgagcaggtgagttacacggcc---ctctatgggcctcagccacagcacccgatcggcgctaagtcggacgactcgcgcgactggcggcaagtacgactacagccatttgccagctgtgcgatggcgtccagtcgcgacaacggcgctgaaacagttggcgcgctcctgccgcatcttgtt---ggtcgcgtgagtgctagtgctttccaggttcctgtggcgcaagggtgtgcgatcgacctcgttgtctacacgaaggaggcc---gcgtcggcggatgtggtggcgagcgccttcgcgcccgccgcggcggactcg---------gagccgcttgtaaaggtctgcatcgccaacggacccatgatcagcgttgactgcattggcagctca---agtgtcatactcgacgccacttcgttgagcagcagcaccgaaggc---------aaggtgcatcgcatggtgctgtgggtggacgtagcgtgctactacgctgccctgttgttgtcattagcgaagcaggtgcacagcattcacgcaccgccgtcgtcg???????????????????????????????????????????????????????????????????????????
otu_32	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggcagcccgc---gtcggcatcaac---------------------------------------ggcttcggccgcatcggtcgcctcgtcctccgcgtcctcctctcccgc---------ggcatgcccgccaacgtcgtcctgatcaacgacccgttcatcacgactgacgccatggcgtacatcttcaagtacgacaccgtccacggccgcttcccc------------------------ggc------accgtcgtcggcaaggagggcaagctcgagatcaccctcaacggc---cacgtctacgacatcgccgtctcggcctgc---aagaaccccgccgagatcccgtggggcgcgagcaacgtcgaggtcgtcatcgagtcctcgggcgccttc---------------------------------accaccatggagaaggcccacctccaccagcagggtggtgcgaagaaggtcctgatcaccgccccgtcg---gcc---gacgcccccatgttcgtctacggtgtcaaccaccagtcgctcaaggcc---gaccagacggtcttctcg---------------------------aacgcctcgtgcacgaccaactgcctggcgcccctcaccaaggtcatcaac---gacaagttcggcatcgtccgcggcctgatgaccaccgtccactcgacgacggccacccagaagaccgtcgacggcccctcgggcaaggcgtggcgcgacggccgtgccgccgccggcaacatcatcccctcgagcactggcgccgccaaggccgtcactgccgtcatccccgagctcaag---ggccgcctgactggcatgtcgttccgcgtccccacgctcaacgtctcggtcgtcgacctgactgccgagctcaagaccccc---gccacgtacgaggagatctgcaacgccgtccgtgaggccgccaacggc------------gagctcaagggcgtcctcggctacaccgacgagcaggtcgtctcgtcggacttcgtcggcgagcccatgtcgtcgatcttcgacgccaaggcgggaatcgccctggac------------aagaccttcgtcaagctggtctcgtggtacgacaacgagtggggctactcgaaccgcgtcgtcgacctgctcctccactcgctctccctccac??????????????????????????????????????????????????????????????????????????????????????????
otu_33	??????????????????atggcttcggctactttctctgtggccaaaccatctcttcagggt------------------------------------------------ttttctgagttctcaggacttcgaaactcctctgct------cttccctttgccaagagatcttcttccgatgagtttgtttccttcgtcagtttccaaacttctgcaatgagaagcaatggtggatacaggaaaggg------gtgaccgaggccaagataaaggtagccatcaat---------------------------------------gggttcggtaggattggtaggaacttcttgaggtgttggcatggtcgtaaggactct------cctcttgatgtcgttgtcattaacgac---actggtggtgttaaacaagcatcacatctcctcaaatacgactcaactcttggaatctttgac------------------------gct------gatgtcaaaccttcaggagactcagctctctctgtt------------gatggaaagatcatcaagattgtatctgatcgtaac---ccatctaatctcccctggggggaactaggcattgacttagttatcgaaggaaccggagtgttt---------------------------------gttgacagagacggtgctgggaagcaccttcaggctggagccaagaaggttcttatcactgcacctggaaaaggt---gacatcccaacttatgtcgttggtgtcaatgctgaactttacagccatgaagatacg---atcatcagc---------------------------aatgcgtcttgtactactaactgtctcgctccattcgtcaaggttcttgac---cagaaatttgggatcataaagggtacaatgacaactactcactcatacactggtgaccaaaggttgttagat---gcgagccaccgtgatctaaggagagcaagagcagcagctttgaacattgttccaacatctacaggagcagccaaagctgtggctcttgtgcttcctaacctcaaa---ggaaaacttaacggaattgcattgcgtgtgccaactccaaacgtttcagtggttgacttagtcgtgcaagtctccaagaaa---acttttgctgaagaagtcaatgctgctttcagagatgcagctgagaaa------------gagcttaaaggtatccttgacgtctgtgatgagcctcttgtctctgttgacttcaggtgctctgatgtatcctccactattgattcttccctcacaatggttatgggagatgat------------atggttaaagtgattgcttggtatgacaatgaatggggttactcacagagagtcgttgatttggctgacattgttgccaataactggaag???????????????????????????????????????????????????????????????????????????????????????
otu_34	?????????????????????????????????????????????atgtcgaagcgcgacatcgtcctcaccaatgtcaccgttgtccagttgctgcgacagccgtgcccggtgaccagagcaccgcccccacctgagcctaaggctgaagtagagccccagccacaaccagagcccacaccagtcagggaggaaataaagccaccaccgccaccactgcctcctcaccccgctactcctcctcctaagatggtgtctgtggcccgggagctgactgtgggcatcaat---------------------------------------ggatttggacgcatcggtcgcctggtcctgcgcgcctgcatggagaag---------ggt------gttaaggtggtggctgtgaatgatccattcattgacccggaatacatggtgtacatgtttaagtatgactccacccacggccgatacaag------------------------gga------agtgtggaattcaggaatggacaactggtcgtggac---------------aaccatgagatctctgtctaccagtgc---aaagagcccaaacagatcccctggagggctgtcgggagcccctacgtggtggagtccacaggcgtgtac---------------------------------ctctccatacaggcagcttcggaccacatctctgcaggtgctcaacgtgtggtcatctccgcgccctca---ccg---gatgcaccaatgttcgtcatgggtgtcaatgaaaatgactataaccctggctccatgaacattgtgagc---------------------------aacgcgtcctgcaccaccaactgtttggctcccctcgccaaagtcatccac---gagcgatttgggatcgtggaagggttgatgaccacagtccattcctacacggccacccagaagacagtggacgggccatcaaggaaggcctggcgagatgggcggggtgcccaccagaacatcatcccagcctccactggggctgcgaaagctgtgaccaaagtcatcccagagctcaaa---gggaagctgacagggatggcgttccgggtaccaaccccggatgtgtctgtcgtggacctgacctgccgcctcgcccagcct---gccccctactcagccatcaaggaggctgtaaaagcagcagccaagggg------------cccatgcgtggcatccttgcctacaccgaggatgaggtcgtctctacggacttcctcggtgatacccactcgtccatcttcgatgctaaggccggcattgcgctcaat------------gacaatttcgtgaagctcatttcatggtacgacaacgaatatggctacagtcaccgggtggtcgacctcctccgctacatgttcagccgagacaag???????????????????????????????????????????????????????????????????????????????????????
otu_35	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctgacaagaagatcagaatcggaatcaac---------------------------------------ggtttcggaagaatcggtcgtttggttgctagagttgttcttcagagg---------gat---gatgttgagctcgtcgctgttaacgatcctttcatcaccaccgagtacatgacatacatgtttaagtatgacagtgttcacggtcagtggaag------------------------caccatgagcttaaggtgaaggatgacaaaactcttctcttcggt---------------gagaagccagtcactgttttcggcatc---aggaaccctgaggacatcccatggggtgaggctggagctgactttgttgttgagtctactggtgtcttc---------------------------------actgacaaagacaaggctgctgctcacttgaagggtggtgctaaaaaggttgtcatctctgccccaagc---aaa---gatgcgcccatgttcgttgttggtgtcaacgagcacgagtacaagtct---gaccttgacattgtttcc---------------------------aacgctagttgcaccactaactgccttgctcctcttgccaaggttattaat---gacaggtttggcattgttgagggactcatgaccactgtccactctatcactgctactcagaagacagttgatggtccatcaatgaaggactggagaggtggaagagctgcttccttcaacattattcctagcagcactggtgccgccaaggctgttgggaaagtgttgccatccctcaat---ggaaaattgaccggaatgtctttccgtgttccaaccgttgatgtctcagttgttgatctcaccgttagacttgagaaagct---gcaacatacgacgaaatcaagaaggccatcaaggaggaatctgaaggc------------aaaatgaagggaattttgggatacactgaggatgatgttgtgtctaccgactttgttggtgacaacaggtcaagcattttcgatgccaaggctgggattgcattgagc------------gacaagtttgtgaagttggtgtcatggtacgacaacgaatggggttacagttctcgtgtcgttgaccttatcgttcacatgtcaaaggcc?????????????????????????????????????????????????????????????????????????????????????????????
otu_36	atggccacacatgcagctctcgccgtctcaagaatcccggtcacacagcgactgcagtctaagagtgccattcactctttccctgctcaatgctcctccaagaggctagaagtcgctgaattctccggtctgcgtatgagtagtatcggt------------------ggggaagcatctttcttcgatgctgtagctgcacaaatcatccctaaggctgtgacaacatcaactcctgttagagga---------gagacagtggcgaaactgaaagttgcgattaac---------------------------------------ggttttggaaggattggtaggaactttcttaggtgttggcatggtcgtaaagactct------cctctcgaagttgttgtacttaacgac---agtggtggtgtcaagaatgcatcccacttgcttaagtatgactccatgcttggaaccttcaag------------------------gct------gaagtgaaaattgtggacaatgaaactattagtgtt------------gatggtaagctcatcaaagttgtctccaacagagac---cctcttaagcttccatgggctgagctcggcattgacattgttatcgagggaacaggagtgttt---------------------------------gttgatgggccaggagcagggaagcatatccaagccggagcctcgaaagttatcatcactgcaccagccaaaggtgctgatatccctacctatgttatgggagtcaatgagcaagactatggtcacgatgtcgctaacattattagc---------------------------aatgcatcttgcaccaccaactgtttggcaccttttgctaaagtcttggat---gaagaatttggaattgtcaaggggacaatgacaaccacacactcctacaccggagaccaaaggcttctagat---gcatcacacagggacctaaggcgtgcaagagccgcagcactgaacatagtgcctaccagcacaggagcagccaaggcggtgtcattagtgttgccgcagctgaag---ggtaaacttaacggcattgcactccgtgtgccaacaccaaacgtctcagtggttgaccttgttataaacgttgagaagaaaggtttgacagcagaggatgtgaacgaggcctttagaaaagccgctaatgga------------ccgatgaaaggcattttagacgtttgcgatgcgcctcttgtctctgttgacttcaggtgctctgatgtctctaccaccattgactcgtccctcactatggttatgggtgatgat------------atggtcaaggtggttgcttggtatgataacgagtggggttacagccaaagagtggtggatttggctcacctagtggctagcaagtggccgggagcggaagctgttggaagtggagatcctttggaggatttctgcaagacaaacccggctgatgaggaatgcaaagtctatgac???
otu_37	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggttaacgtctcagtcaac---------------------------------------ggtttcggtagaattggtagattagtcaccagaattgctatcagcaga---------aag---gacatcaacttggtcgctatcaacgacccattcatctccactgactacgctgcttacatgttcaagtacgactccacccacggtcgtttcgac------------------------ggt------gaagtctcccacgacaaagaccacattatcttgaac---------------ggtaagaaggtcgctgtcttcaacgaa---aaggacccagccgctttgccatggggtaagttgggtgttgatgtcgccatcgactccactggtatcttc---------------------------------aaggaaatggactctgctaacaagcacattgaagctggtgccaagaaggttgtcatcaccgctccatct---ggt---tccgccccaatgtacgtcatgggtgtcaacgaagaaacctacactcca---gaccaaaagatcgtctcc---------------------------aacgcttcctgtaccaccaactgtttggccccattggctaaggtcatccac---aacgaattcggtatcaaggaaggtttgatgaccactgtccactctatgaccgccacccaaaagactgttgacggtccatcccacaaggactggagaggtggtagaaccgcttctggtaacatcatcccatcttccactggtgctgccaaggctgtcggtaaggtcttgccatccttgcaa---ggtaagttgaccggtatggctttcagagttccaaccgtcgatgtctccgttgttgacttgactgttaacttggccaaggaa---acctcttacgacgaaatcaaggctgctttgaagaaggcttccgaaggt------------tccatgaagggtatcttgggttacactgaagacgacgttgtctcttctgacttcttgggtgatgctcactcttccatcgtcgatgctgctgccggtatccaattgacc------------ccaactttcgtcaagttggtctcctggtacgacaacgaattcggttactccaccagagttgtcgacttggttgaacacgtcgctaagtccgct??????????????????????????????????????????????????????????????????????????????????????????
otu_38	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggttaacgttggtatcaac---------------------------------------ggattcggtcgtatcggccgtatcgtcttccgcaatgccctcctcaac---------ccc---aaaatccaggtcgtagccatcaacgacccattcatcaaccttgaatacatggtctacatgttcaagtacgactccgttcacggtcgcttcaag------------------------gga------accgtcgaggcaaaagatggcaagctttggattcag---------------ggcaagcccgtcatcgtctacggcgag---aagaatccctctgacatcaaatggggcgccgccggccgtgactacgttgtcgaatccacgggtgttttc---------------------------------acaacagtcgaaaaggctgaaggacacttgaagggcggtgccaagaaagtcatcatctctgctccttcg---gcc---gacgcgccaatgttcgttatgggttgcaatctcgaccagtacgatccc---aagtacaccgtcatttcg---------------------------aacgcttcatgcacgaccaactgccttgcgcccctcaccaaggtcatccac---gacaagtatggcatcattgagggcttgatgagcaccattcatgccaccaccgccacccaaaagaccgtggacggtccctccaacaaggactggcgcggtggacgcgccgtcgttaacaacatcatcccttcgtccaccggtgccgctaaggctgttggaaaggtcatcccttcgctcaac---ggcaagctcactggcctctccttccgtgtgcccaccatcgacgtctccgtgatcgaccttgtcgtccgcctcgagaagccc---gcaagctacgaggatatcaagaaaactgtcaaggaggcttcagagggt------------gcctacaaaggcatcatcgagtacaccgaggaacaggtcgtctccgccgacttcatcggccaccacgcctcctcgatcttcgacgcacaagctggcatccagctcaac------------cccaacttcgtcaagctcatcgtttggtacgacaacgagtggggctactccgcccgcgtgtgcgacctcctcgtcttcgccgccgagcaggacgccaagcaacag??????????????????????????????????????????????????????????????????????????????
otu_39	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggccgtcaaagtcggtatcaac---------------------------------------ggtttcggtcgtatcggccgtatcgtactcagaaatgctttgttgaac---------cct---gaagtcaacgttgttgcagtcaacgaccctttcattgctcttgagtacatggtctacatgttcaagtatgactccgtccacggacgtttcaaa------------------------ggc------actgtcgagactaagggcggcaagctcatcgtcgac---------------ggaaaggaaatctccgtcttcggtgag---aaggatgctggtgctattccttggagctctgtcggtgcagagtacatagtcgagtctaccggtgtcttc---------------------------------accacgattgaaaaggcctctgctcacttgaagggtggtgccaagaaagtcatcatctctgctccttcc---gct---gatgcacctatgtacgtttgcggtgtcaatctcgactcttatgactcg---caacatgctgttatctcc---------------------------aatgcttcttgcacgacgaactgcctcgcacctctcgccaaggttatccac---gacaaattcggtatcgttgaggctctgatgactaccgtccatgccaccaccgctacccagaagactgttgatggtccttcgaacaaagattggcgtggaggtcgttctgtcaacggaaacatcatcccttcttcaactggtgctgccaaggctgtcggaaaggttattccttcgctcaac---ggaaagttgaccggtcttgccttccgtgttcctaccctcgacgtttcggtagtcgaccttgtttgccgtaccgaaaagagt---gcaacctacgacgagatcaaagctgctgtcaaagaagcctccaagggt------------cctctcaagggtatcttaggctacactgaggaccatgttgtttccaccgacttcattggggacaaccactcttcgatcttcgatgctaccgccggaatccagctcaac------------aagaactttgtcaagttgattgcttggtacgacaacgagtggggttactctggaagagttgttgatctcttggtgtttgctgccaagaaggatggtgctctc?????????????????????????????????????????????????????????????????????????????????
otu_40	atggccacacacgcagcgctcgcggcgtcccgcattccggccaccgcccggctgcacagcaaggcggcg------------------tccaag------cagagggtggacttcgccgacttctccggactgaggccgggatcgtgctcc---atcagccacgccgcgagggaggcgtccttctccgatgtccttggctcgcagctcgtcgccagggctaccgga---gagaacgccgtgagggcg---------ccggctgaggcgaagctcaaggttgccatcaac---------------------------------------ggcttcggccgcattggccgcaacttcctccggtgctggcacgaacgcgagaactcc------ccgctcgaggtcgtcgtcgtcaacgac---agcggaggcgtcaggaacgcatcacaccttctcaagtacgactcgatgctcggcaccttcaag------------------------gcc------gacgtcaagatcgtcgacgaccagaccatcagcgtc------------gacggcaagctgatcaaggtcgtctccaacagggac---cccctcaagctgccatgggctgagctcggcatcgacattgtcatcgagggtaccggagtgttc---------------------------------gtcgacggccccggcgccgggaagcacatccaggccggcgcgaagaaggtcatcatcactgctccggcgaagggtgctgacatccctacctacgtcctcggtgtcaacgagggagactactcccacgaagtggccaacattatcagc---------------------------aatgcttcctgcacaaccaactgcctcgctccgttcgtcaagatcttggac---gaagagttcggaatcgtaaagggaaccatgaccacaactcactcctacaccggcgaccagaggttgctggac---gcgtcgcaccgtgacctgaggagggcccgggcggcggcgctgaacatcgtgccgacgagcaccggcgccgcgaaggccgtggcgctggtgctcccgcagctgaag---gggaagctcaacggcatcgcgctgcgcgtgccgaccccgaacgtgtccgtggtggacctggtgatcaacaccgtgaagaccggcatcaccgccgacgacgtgaacgccgcgttccgcaaggccgcggcgggg------------ccactcagcggcatcctcgacgtctgcgacgtgccgctggtgtccgtcgacttccgctgctccgacgtctcctccaccatcgacgcctcgctcaccatggtcatgggcgacgac------------atggtcaaggtggtcgcctggtacgacaacgagtggggctacagccaacgcgtggtcgatctggcgcatctggtggcgagcaagtggcccggcgcggcggtgcagggcagcggcgacccactggaggacttctgcaaggacaacccggagaccgacgagtgcaaagtgtacgaaaac
otu_41	??????????????????atggcttcggttactttctctgtccccaag---------ggt---------------------------------------------------ttcactgaattctcaggattgcgaagctcctctgcttct---cttcccttcggcaagaaactttcttccgatgagttcgtttccatcgtctccttccagacttctgcaatgggaagcagtggtggatacaggaaaggt------gtgactgaggccaagcttaaggtggccattaat---------------------------------------ggattcggtaggatcgggaggaacttcctgagatgttggcatggtcgcaaggactct------cctcttgatatcattgccattaatgac---actggtggcgtcaagcaggcttcgcatttacttaaatacgactctactctcggaatctttgat------------------------gct------gatgtcaaaccttctggagagactgcaatctctgtt------------gatggaaagatcatccaagttgtctctaaccgaaac---ccgtctcttctcccttggaaggagctaggaattgacattgtcatcgaaggaaccggagtgttt---------------------------------gtggatagagaaggtgcagggaaacacattgaagctggtgccaagaaggttatcattactgctccaggcaaagga---gatattccaacttatgtcgttggtgtcaatgcagatgcttacagtcatgatgaacct---atcatcagc---------------------------aatgcatcttgcactaccaactgtcttgctccctttgtcaaagttcttgac---cagaaattcggtatcataaagggtacaatgacgactactcactcttacaccggtgaccagaggttgctagac---gcgagtcaccgtgatctaaggagagcaagagcagctgctttgaacattgttcctacttctacaggagcagctaaagctgtggctcttgtgctccctaacctcaaa---ggaaaactcaacgggatcgctctccgtgtaccaacaccaaacgtatcagtggttgatctcgttgtgcaggtctcaaagaag---acatttgctgaggaagtcaacgctgctttcagagattctgcagagaaa------------gagcttaaaggtatactcgatgtctgcgatgagccactagtgtccgttgatttcagatgctcagatttttcaacgaccattgattcatcactcactatggttatgggagatgat------------atggttaaggtgattgcttggtatgataatgaatggggttactcacagagagttgttgacttggctgacattgttgccaacaactggaag???????????????????????????????????????????????????????????????????????????????????????
otu_42	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggcaattcctaaagttggtatcaac---------------------------------------ggtttcggtcgtattggccgtatcgtcctccgtaacgccatcctcact---------ggc---aagatccaagttgtcgctgtcaacgatcctttcatcgatcttgactacatggcatatatgttcaagtacgactctacccacggtcgctttgag------------------------ggc------tccgttgagaccaagggtggcaagcttgtcatcgac---------------ggtcactccatcgatgtccacaacgag---cgtgaccccgccaacatcaagtggtctgcctctggtgctgagtacgttattgagtccactggtgtcttc---------------------------------actaccaaggagactgcctctgctcacttgaagggtggtgccaagcgtgtcatcatctctgctccttcc---aag---gatgctcccatgttcgtcgtcggtgttaacttggagaagttcaacccc---tccgagaaggttatctcc---------------------------aacgcctcttgcaccaccaactgtttggctccccttgccaaggtcatcaac---gacaccttcggtattgaagagggtctcatgaccactgttcacgctaccactgccacccaaaagaccgttgacggtccctctaagaaggactggcgtggtggtcgtggcgccagcgccaacatcatcccctcctccactggtgccgccaaggccgtcggtaaggttattcccgctcttaac---ggtaagcttaccggtatggctttccgtgtccctacccccgatgtttccgttgttgacttgaccgtcaagttggccaagcct---accaactacgaggacatcaaggctgctatcaaggctgcctctgag------------ggtcccatgaagggtgtgttgggttacaccgaggactctgttgtctccaccgacttctgtggtgacaaccactcctccatcttcgatgcctctgccggtatccaactttct------------cctcaattcgtcaagctcgtctcttggtacgataacgaatggggttactcccaccgtgttgttgacttggttgcctacactgcttccaaggat??????????????????????????????????????????????????????????????????????????????????????????
otu_43	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggcaattcctaaggttggtattaac---------------------------------------ggtttcggtcgtattggacgtattgtcctccgtaacgctttggtcgct---------aag---accatccaagtcgttgctatcaacgatccttttatcgatcttgaatacatggcctacatgttcaagtacgactctacccacggtcgcttcgat------------------------ggc------tccgtcgagatcaaggatggtaagctcgtcattgat---------------ggcaatgccatcgatgtccacaacgag---cgtgaccccgccgacatcaagtggtctacctctggtgctgactacgttatcgagtccaccggtgtcttc---------------------------------accactcaagagactgcctctgctcacttgaagggtggtgccaagcgtgtcatcatctctgctccttcc---aag---gacgcccccatgtacgttgtcggtgtcaacgaggagaagttcaacccc---tctgagaaggttatctcc---------------------------aacgcttcttgcaccaccaactgtttggctccccttgccaaggtcatcaac---gacaccttcggtatcgaggagggtctcatgaccactgtccacgctaccactgccacccaaaagaccgttgacggtccctccaagaaggactggcgtggtggtcgtggcgccagcgccaacatcatcccctcctccactggtgccgccaaggccgtcggtaaggttattcccgctcttaac---ggtaagcttaccggtatggctttccgtgtccctacccccgatgtttccgttgttgacttgaccgtcaagttggccaagcct---accaactacgaggacatcaaggccgccatcaaggctgcctctgag------------ggccccatgaagggtgtgttgggttacaccgaggacgctgttgtctccactgacttctgcggtgacaaccactcctccatcttcgatgcctctgccggtatccaactttct------------cctcaattcgtcaagctcgtctcttggtacgataacgaatggggttactcccgccgtgtcgttgacttggttgcctacactgccgccaaggacaac???????????????????????????????????????????????????????????????????????????????????????
otu_44	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgactatcaaagtaggtatcaac---------------------------------------ggttttggccgtatcggtcgcattgttttccgtgctgctcagaaacgt---------tct---gacatcgagatcgttgcaatcaacgac---ctgttagacgctgattacatggcatacatgctgaaatatgactccactcacggccgtttcgac------------------------ggt------accgttgaagtgaaagacggtcatctgatcgttaac---------------ggtaaaaaaatccgtgttaccgctgaa---cgtgatccggctaacctgaaatgggacgaagttggtgttgacgttgtcgctgaagcaactggtctgttc---------------------------------ctgactgacgaaactgctcgtaaacacatcaccgctggtgcgaagaaagtggttatgactggtccgtctaaagac---aacactccgatgttcgttaaaggcgctaacttcgacaaatatgct------ggccaggacatcgtttcc---------------------------aacgcttcctgcaccaccaactgcctggctccgctggctaaagttatcaac---gataacttcggcatcatcgaaggtctgatgaccaccgttcacgctactaccgctactcagaaaaccgttgatggcccgtctcacaaagactggcgcggcggccgcggcgcttcccagaacatcatcccgtcctctaccggtgctgctaaagctgtaggtaaagtactgccagaactgaat---ggcaaactgactggtatggcgttccgcgttccgaccccgaacgtatctgtagttgacctgaccgttcgtctggaaaaagct---gcaacttacgagcagatcaaagctgccgttaaagctgctgctgaaggc------------gaaatgaaaggcgttctgggctacaccgaagatgacgtagtatctaccgatttcaacggcgaagtttgcacttccgtgttcgatgctaaagctggtatcgctctgaac------------gacaacttcgtgaaactggtatcctggtacgacaacgaaaccggttactccaacaaagttctggacctgatcgctcacatctccaaa????????????????????????????????????????????????????????????????????????????????????????????????
otu_45	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgtctcaggtcaacatcggtatcaac---------------------------------------ggcttcggtcgtatcggacgtatcgtcttccgtaactcggtcgtccac---------aac---acggccaacgtcgttgccatcaacgaccccttcattgacctagaatacatggtgtacatgctcaagtacgactccacccacggtgtcttcaac------------------------ggt------gacatctccaccaaggatggcaagctcattgttaac---------------ggcaagtcgatcgctgtcttcgccgag---aaggacccctccaacatcccctggggtcaggctggtgcccactacgttgtcgagtccaccggtgtcttc---------------------------------accaccattgacaaggcctcggcccacatcaagggtggtgccaagaaggtcgtcatctcggctccctcg---gct---gacgcccctatgtacgtctgtggtgtcaaccttgacgcctacgacccc---aaggcccaggtcgtctcg---------------------------aacgcctcatgcaccaccaactgccttgctcccctcgccaaggtcatccac---gacaagttcggtatcgttgagggtctcatgaccactgtccatgccaccaccgccacccagaagaccgtcgacggcccctcggccaaggactggcgtggaggccgtgccgccgctgccaacatcatcccctcgtccactggtgccgccaagcgcgtcggcaaggtcatcccttcgctcaac---ggcaagctcaccggtatggctttccgtgtgcccaccaccaacgtctcggttgttgacctgaccgcccgcctcgagaagggc---gccagctacgacgagatcaaggccgaggtcaagcgcgcttccgagaac------------gagctgaagggtatcctcggctacactgaggacgccgttgtgtctcaggacttcattggcaactcgcactcgtcgatcttcgatgctgctgccggtatctctctcaac------------aacaactttgtcaagcttgtctcgtggtacgacaacgagtggggttactcgaaccgatgcctcgacctcctcgtcttcatggctcagaaggacagcgcg????????????????????????????????????????????????????????????????????????????????????
otu_46	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgccaaagccaaatgtcggaatcaac---------------------------------------ggattcggaagaatcggacgtcttgtcctccgcgccgctgtcgagaag---------gacagt---gtcaacgttgatgccgtcaacgatccattcatctccatcgactacatggtctacttgttccagtacgactccacccacggacgcttcaag------------------------gga------accgttgctcacgagggagactaccttcttgtcgccaaggaagggaagtcgcagcacaagatcaaggtctacaactca---agagacccagctgaaatccaatggggagcctctggagccgactatgtcgttgagtccaccggagtcttc---------------------------------accaccatcgagaaggccaacgctcacttgaagggaggagccaagaaggtcatcatctctgctccatct---gct---gatgctccaatgttcgtcgtcggagtcaaccacgagaagtacgatcatgccaacgaccacatcatctcc---------------------------aatgcttcctgcaccactaactgccttgctccacttgccaaggtcatcaat---gacaacttcggaattattgagggacttatgaccactgtccacgccgtcaccgccacccaaaagactgttgacggaccatcaggaaagctctggagagacggacgtggagctggacagaacatcatcccagcctctactggagccgctaaggctgttggaaaggttatcccagagctcaat---ggaaagctcaccggaatggctttccgtgtcccaaccccagatgtgtctgttgttgatctcactgctcgtcttgagaagcca---gcttccctcgatgacatcaagaaagttatcaaggctgccgctgacgga------------ccaatgaagggaattctcgcttacactgaggatcaagttgtctccaccgactttgtctccgataccaactcttccatcttcgatgccggagcatccatctcactcaac------------ccacacttcgtcaagctcgtctcgtggtacgataacgagttcggatactccaacagagttgttgatctcatctcgtacatcgccaccaaggcc??????????????????????????????????????????????????????????????????????????????????????????
otu_47	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgaccaagccaagtgtcggaatcaac---------------------------------------ggattcggaagaatcggacgtcttgtcctccgcgccgctgtcgagaag---------gacagt---gtcaatgttgttgccgtcaacgatccattcatctccatcgactacatggtctacttgttccagtacgattccactcacggacgcttcaag------------------------gga------accgttgcccacgagggagactaccttcttgtcgccaaggaaggaaagtcccagcacaagatcaaggtctacaactca---agagacccagctgagatccaatggggagcctctggagccgactatgtcgttgagtccaccggagtcttc---------------------------------accaccatcgagaaggccaatgctcacttgaagggaggagccaagaaggtcatcatctctgctccatct---gct---gatgctccaatgttcgtcgtcggagtcaaccacgagaagtacgatcatgccaacgaccacatcatctcc---------------------------aatgcttcctgcaccactaactgccttgctccacttgccaaggtcatcaat---gacaacttcggaattattgagggacttatgaccactgtccacgccgtcaccgccacccaaaagactgttgacggaccatcaggaaagctctggagagacggacgtggagctggacaaaacatcatcccagcctctactggagccgctaaggctgtcggcaaggttatcccagagctcaat---ggaaagctcaccggaatggctttccgtgtcccaaccccagatgtctctgttgttgatctcactgctcgtcttgagaagcca---gcttccctcgatgacattaagaaggttatcaaggctgccgctgacgga------------ccaatgaagggaattctcgcttacaccgaggatcaagttgtctccactgactttgtctccgataccaactcttccatcttcgatgccggagcatccatctcactcaac------------ccacactttgtcaagctcgtctcatggtacgataacgagttcggatactccaacagagtcgtcgaccttatctcctacattgctaccaaggcc??????????????????????????????????????????????????????????????????????????????????????????
otu_48	??????????????????atggcgtcgtccatgctctccgctaccaccgtgccactccagcaggggggc---------------------------------------ggcctgtccgagttctccgggctcaggagctccgcgtcg------ctgcccatgcgccggaatgccacctccgacgacttcatgtccgccgtctccttcaggacccacgcggtcggcacgagcggcgggccgcggcgggcgccg------acggaggcgaagctgaaggtggccatcaat---------------------------------------gggttcggccgcatcgggcgcaacttcctgcggtgctggcacgggcgcggcgacgcctcg---cccctcgacgtcatcgccatcaacgac---accggaggcgtcaagcaggcgtcccacctgctcaagtacgactccacgctcggcatcttcgat------------------------gcc------gacgtcaagcccgtcggcgacaacgccatctccgtc------------gacggcaaggtcatcaaggtcgtgtccgaccgcaac---cccagcaacctgccgtggggcgagctcggcatcgacctcgtcatcgagggcaccggcgtcttc---------------------------------gtcgaccgcgagggcgcggggaagcacatccaggcgggggccaagaaggtgctcatcacggcgcccggcaagggc---gacatccccacctacgtcgtcggcgttaatgccgaccagtacaaccccgacgagccc---atcatcagc---------------------------aacgcctcctgcaccaccaactgcctcgcgccattcgtcaaggtcctcgac---caaaagttcggcatcatcaagggcaccatgaccaccacccactcctacaccggcgaccagaggctgctggac---gcgagccaccgcgacctgcgccgcgcccgcgccgccgcgctcaacatcgtgcccacgtccaccggtgccgccaaggccgtctcgctggtgctccccaaccttaag---ggcaagctcaacgggatcgcgctccgggtgcccaccccgaacgtctccgtcgtcgacctcgtcgtgcaggtctccaagaag---accctcgccgaggaggtgaaccaggcgttccgcgacgccgcggccaac------------gagctcacgggcatcctcgaggtctgcgacgtgccgctcgtgtccgtcgacttcaggtgctccgacgtctcctccaccatcgacgcctccctcaccatggtcatgggcgacgac------------atggtcaaggtcatctcctggtacgacaacgagtggggctactcgcagagggtcgtcgacctcgctgacatctgcgccaaccagtggaag???????????????????????????????????????????????????????????????????????????????????????
otu_49	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgggcaagattaagatcggaatcaac---------------------------------------ggcttcggaaggatcggcaggctcgtggccagggtcgccctccagagc---------gag---gatgtcgagctcgtcgccgtcaacgaccccttcatcaccacggactacatgacctacatgttcaagtacgacaccgtccacggccactggaag------------------------cacagcgacatcacactcaaggactccaagacccttctcttcggt---------------gacaagccggtcaccgtctttggcatc---aggaaccctgaggaaatcccgtggggtgaggctggcgctgagtacgtcgtggagtccaccggcgtcttc---------------------------------actgacaaggacaaggctgctgcacatctcaagggtggtgccaagaaggttgttatctctgccccaagc---aaa---gacgcacccatgtttgttgttggtgtcaatgaggacaagtacacctcg---gatgttaacattgtttcc---------------------------aatgctagctgcaccacaaactgccttgctccccttgctaaggtcattcat---gacaacttcggcattgttgagggtctgatgacaactgttcatgccatcactgccacccagaaaactgttgacggaccctcagccaaggactggagaggtggcagggctgccagctttaacatcattccgagcagcaccggtgctgccaaggctgttggtaaagttctccctgatctgaat---ggcaagctcactggtatgtccttccgcgttcctactgtggatgtctcggttgttgacctcaccgtcagaatcgagaagggg---gcctcctatgaggatatcaagaaagctattaaggctgcttccgagggt------------ccactcaagggtatcatgggttatgtggaggaggatctggtttctaccgacttccttggtgacagcaggtcgagcatcttcgacgccaaggccgggatcgctctgaac------------gaccacttcgtcaagcttgtctcgtggtacgacaacgagtggggctacagcaaccgcgtcgtcgacctgatccgccacatgttcaagacccag??????????????????????????????????????????????????????????????????????????????????????????
otu_50	??????????????????atggcttcggctactttctctgtagccaaaccagctattaaggcaaatggg------------------------------------aaaggcttctctgaattctctggtctccgcaactcttcaagacat---cttcccttttctagaaaa---tcttcagatgattttcattctcttgttaccttccaaaccaatgcagttggaagtagtggaggacacaagaaaagtcttgtagtggaagcaaaacaactgaaggtagccataaat---------------------------------------ggatttggaagaattggaaggaacttcttgagatgttggcatggtcgcaaggactcg------cctcttgatgtcattgcaatcaatgac---accggaggtgtaaagcaagcttctcaccttctcaagtatgattccacacttggaatctttgat------------------------gct------gatgttaagcctgttggtactgatggcatctcagtt------------gatggaaaggttatcaaagttgtctccgaccgcaac---cctgccaaccttccttggaaggagttggggatagacttggtgattgaaggaactggagtgttt---------------------------------gtggacagagaaggtgcagggaggcacattacagcaggggctaagaaggttctcatcactgcccctggaaaagga---gacatccctacttatgtggttggtgtcaatgctgatgcttacacccacgccgacgac---attatcagc---------------------------aatgcttcttgcaccactaactgccttgctccctttgtcaaggtccttgat---cagaaattcggtatcatcaagggtaccatgactactactcactcctacaccggtgaccaacggcttcttgac---gcgagccaccgtgacctaaggcgtgcgagagcagcagccctcaacatagtcccaacatcaacaggagcagctaaagcagtggcccttgtcctcccaacactcaaa---ggcaagctcaacggtattgcgcttcgtgtgccaacaccaaacgtttcggtggtggacctcgtcgttcaagtctcaaagaag---acatttgctgaagaagtgaatgaggcttttagagagagtgcagccaag------------gagctgactggtattctctcggtctgtgacgagccactcgtgtctgtagattttaggtgcaccgatgtgtcgtctaccgttgattcgtcattgacaatggtcatgggcgatgac------------ctggttaaggtgattgcttggtatgataatgagtggggttactcacaaagggttgttgatttggctgacattgttgccaataactggaag???????????????????????????????????????????????????????????????????????????????????????
otu_51	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggttaaggttgctattaac---------------------------------------gggtttggtagaatcggtagattggttttgagaattgctttgcaaaga---------aag---gctctagaagttgttgccgttaacgatccattcatttctgttgattatgccgcttacatgttcaagtacgattccacccatggtagatacaag------------------------ggt------gaagttactaccagcggtaacgacttggtcattgac---------------ggtcacaagattgctgttttccaagaa---aaggatccagctaacttgccatggggtaagctaggtgtcgatatcgttatcgactctactggtgtcttc---------------------------------aaggaattggactccgctcaaaagcatctagacgctggtgccaagaaggtcgtcatcactgctccttcc---aag---actgctccaatgtttgtcgttggtgttaacgaagacaagtacaac------ggtgaaaccattgtttct---------------------------aacgcttcttgtactaccaactgtttggctccaattgctaagattatcaac---gatgaattcggtattgacgaagctttgatgactaccgttcattccatcactgctactcaaaagactgttgatggtccatcccacaaggactggagaggtggtagaactgcttccggtaacattatcccatcctctactggtgctgctaaggctgtcggtaaagtcttgccagaattgcaa---ggtaaattgaccggtatggctttcagagtcccaaccgtcgatgtttctgtcgttgatttgaccgtcaagttggctaaggaa---gccacttacgatgaaatcaaggccgctgttaagaaggcttctcaaggt------------aagctaaagaatgttgttggttacactgaagactctgttgtttccagcgatttccttggtgacactcactccaccatctttgacgcctctgctggtattcaattgtct------------ccaaagttcgtcaaggttgttgcttggtacgataacgaatacggttactctgaaagagttgtcgatttggttgagcacgttgct???????????????????????????????????????????????????????????????????????????????????????????????????
otu_52	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggtaataagagtcggcatcaat---------------------------------------gggtttggccgtattggccgcgttgtgttccgagctgcgcagcgccga---------aac---gacattgaaattgttgggatcaacgat---ttgctcgatgcggattacatggcttacatgttgaagtatgattccactcacggccgcttcgaa------------------------ggt------gcggtagaggttcaaggtggtgcacttgtggtaaat---------------ggcaagaagattcgcgtcacgtccgag---cgggatcccgcgaacttgaagtggaatgaaattaatgtggacgttgttgtggagtctactggacttttt---------------------------------ctctccgacgatacggcacgaaagcacatccaggctggtgccaagaaggtcgtcatcacaggtccttcgaaggac---gacacaccaatgttcgttatgggtgtaaaccacacgacttacaag------ggggaagccatcgtctca---------------------------aacgcatcatgcacgacgaactgccttgccccccttgcaaaggtgctcaac---gacaagtttggcatcgtggaaggactcatgacaaccgttcacgcaacaacggcgacacagaaaactgtcgatggcccctcgcagaaggactggcgtggcggcaggggtgcggcgcagaatattattccttcatccaccggtgcggcgaaagcggtgggcaaaatcatcccgtcgctcaat---ggcaaactcactggtatggccttccgtgtaccaactcccaacgtttccgtggtggatctcacagtgcggctagagcgtccc---gcgacctacaagcaaatttgcgacgccattaaggctgcatcagagggt------------gaactgaaggggattttgggttatgtggacgaagagattgtttccagtgacatcaacggcattccgctcacatccgtcttcgatgccagggcgggtatttcgctgaac------------gacaacttcgttaagctggtctcgtggtatgacaacgaaaccgggtactcaaacaaggtccatgacctcattgcgcacatcacaaag????????????????????????????????????????????????????????????????????????????????????????????????
otu_53	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggtcgtcaaggtcggcatcaac---------------------------------------ggatttggccgtattggccgtatcgtcttccgcaacgctcacgagcac---------tcc---gacgtcgagatcgttgccgtcaacgaccccttcattgagccccactacgctgcctacatgctcaagtatgactctcaacacggcaacttcaag------------------------ggc------gacgtcaccgtcgagggcagcgacctggtcgttggt---------------ggcaagaaggtccgcttctacaccgag---cgtgaccccgctgccatcccctggagcgagactggcgccgactacattgtcgagtccactggtgtcttc---------------------------------accaccaccgagaaggccaaggctcatctgaagggtggtgccaagaaagtcatcatctctgccccctcg---gcc---gatgcccccatgtacgtgatgggcgtcaacgagaagacctacgacggc---tccggcatggtcatctcc---------------------------aacgcctcctgcaccaccaactgcctggctcccctcgccaaggtcatcaac---gacgagttcaagatcattgagggtctcatgaccaccgtccactcctacaccgccacccagaagaccgtcgacggtccctccgccaaggactggcgtggtggacgtaccgccgcccagaacatcatcccctcctccaccggtgccgccaaggctgtcggcaaggtcatccccgagctcaac---ggcaagctcaccggcatgtccatgcgtgtgcccacatccaacgtctccgttgttgacttgactgtccgcatcgagaagggc---gccacctacgagcagatcaagaccgccgtcaagaaggccgccgatggt------------cccctcaagggtgttctggcctacactgaggacgacgtcgtctccactgacatgaacggcaaccccaactcctccatctttgacgccaaggctggtatctccctgaac------------gaccactttgtcaagctggtctcctggtacgacaacgagtggggctactcccgccgtgtccttgacctgatctcccacgtcgccaaggtcgatggcaacgcc?????????????????????????????????????????????????????????????????????????????????
otu_54	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgactgtcaaggttggcatcaac---------------------------------------ggtttcggccgcattggccgtatcgtcttccgcaatgcggttgagcac---------ccc---gacgtcgagatcgttgccgttaacgaccccttcattgagcccaagtacgctgagtacatgctcaagtacgactctacccacggcgtcttcaag------------------------ggc------accattcaggtctccggcagcgatctgatcgtcaac---------------ggcaagaccgtcaagttctacactgag---cgcgacccctctgccatcccctggaaggacaccggcgccgagtacatcgtcgagtccaccggtgtcttc---------------------------------accaccactgagaaggctagcgcccacttgaagggtggtgccaagcgcgtcatcatctctgccccctcg---gcc---gatgcccccatgtacgtgatgggtgtcaacgagaagacctacgacggc---aaggccgctgtcatctcc---------------------------aacgcctcttgcaccaccaactgcctggctcccctcgccaaggttgtcaac---gacaagttcggcatcgttgagggtctcatgaccaccgtccactcctacactgccacccagaagaccgtcgatggtccctcggccaaggactggcgcggtggccgtggcgctgctcagaacatcatccccagcagcaccggtgccgccaaggccgtcggcaaggttatccccgagctcaac---ggcaagcttaccggcatggccttccgtgtccccacctccaacgtctccgttgtcgacctcacctgccgtctcgagaagccc---gccagctacgagaccatcaaggccgccctcaaggaggcttccgagggt------------gagctcaagggcattctcggctacaccgaggacgagattgtctcctctgacctcaacggcaatgccaactcttccatcttcgacgccaaggctggtatctccctgaac------------gacaactttgtcaagcttgtctcctggtacgacaacgagtggggctacagcagacgtgtgctcgacctcctctcctatgtcgccaagtatgatgcttctcat?????????????????????????????????????????????????????????????????????????????????
otu_55	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggtcgtcaaggttggtatcaac---------------------------------------ggcttcggtcgcattggccgcatcgtcttccgcaatgccatcgagcac---------aac---gacgtcgacattgtcgccgtaaacgaccctttcatcgagccccactacgctgcatacatgctcaagtatgacagcacacacggccagttcaag------------------------ggt------gacatcaaggttgacggcaacaacctgactgtcaac---------------ggcaagaccatccgtttccacatggag---aaggaccccgccaacattccatggagcgagactggcgcttactacgtcgtcgagtctaccggtgtcttc---------------------------------accaccaccgagaaggccaaggcccacttgaagggcggagccaagaaggttgtcatctctgctccctcg---cct---gacgcccccatgttcgtcatgggtgtcaaccacgagacctacaagccc---gacatcgaggcactctcc---------------------------aacgcctcttgcacaaccaactgcttggctcctctcgccaaggtcatccac---gacaagtacaccatcattgagggtctcatgaccaccatccactcatacactgccacccagaaggtcgttgacggcccctccgcaaaggactggcgtggtggacgtactgctgctcaaaacatcattcccagcagcactggtgccgccaaggctgtcggcaaggttatccccgagctcaac---ggtaagctcactggtatggccatgcgtgtccctaccgccaatgtctcggttgtcgacttgactgttcgcatcgagaagggt---gcttcctacgacgagatcaagcaggccgtcaaggaggcctctgagggc------------tccctcaacggtatccttggttacactgaggatgacattgtttccactgacttgaacggcgacaaccgctcctccatcttcgacgccaaggccggtatctcccttaac------------aagaactttgtcaagctcgtctcctggtacgacaacgagtggggttactcccgccgtgtcctcgacctcctggtctacattgccaagattgatggcaacgct?????????????????????????????????????????????????????????????????????????????????
otu_56	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggtcaaggtaggcatcaac---------------------------------------ggtttcggacgcatcggccgtgtcgtctttcgagcggcacagatgcgc---------ccc---gacatcgagattgtcggcattaacgat---ctgctcgatgccgagtacatggcctacagcctcaagtatgactccacgcatggccgctttgat------------------------ggg------acggtggaggtgataaaaggggcacttgttgtgaac---------------ggcaagagcatccgcgtcacgagcgag---cgtgacccggcaaacctcaagtgggacgaaatcggtgtggaggtggtggtggagtctacgggcttattc---------------------------------ctcacgcaggagacagctcacaagcacatcgaggcaggggcaaggcgcgtcgtcatgacggggccgccgaaagat---gacacaccgatgtttgtgatgggcgtgaaccacacaacgtacaag------gggcaaccgattatatct---------------------------aacgcgtcgtgtacgacgaactgcctcgccccactggcaaaggtggtgaac---gagaagtacggtattgttgaaggcctcatgactactgtgcacgcgactacggcaacgcagaagacggtggatggtccctctctgaaagactggcgaggtggtcgcggcgcgtcgcagaacatcatcccctcctccaccggcgctcctaaggccgtcggcaaggtgtacccggctctggat---ggaaagctcactggtatggcttttcgcgttccgaccccgaacgtgtcagtggtcgacctcaccgtgcgtctagagaagcca---gcaacctataaggacatctgcgccgcaatcaaggctgcagcggagggc------------gagatgaaaggcatccttggatacaccgacgatgaggtcgtgtcttcggacttcaacggtgtggcgctgacatctgtttttgacgtgaaggccggtatctcactgaac------------gatcactttgtcaagctcgtgtcttggtatgacaacgaaacaggctactcgcacaaggtactcgatctcatcctacatacgtccgcgagg?????????????????????????????????????????????????????????????????????????????????????????????
otu_57	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgacagcaccgaaggtcggcatcaac---------------------------------------ggcttcggccgcatcggccgcctcgtcctgcgcgccgccatcgagaag---------gga---acgtgccaggtcgtcgccatcaacgacccgttcatcgacctcgactacatggcctacatgctcaagtacgactcgacgcacggccgctacgcc------------------------ggt------gacgtctccatcaaggacggcaagctgcaggtcgac---------------ggcaactccatcaccgtctttgcccac---cgcgaccccgccgagatcccgtgggccacggccgccgccgactacatcgtcgaggccaccggcgtcttc---------------------------------acgctcaaggacaaggccgccgcccacttcaagggcggcgccaagaaggtcgtcatctcggccccctcc---aag---gacgcccccatgtttgtgtgtggcgtcaacgaggccaagtacaccccg---gacttggacatcatctcc---------------------------aacgcctcgtgcaccactaattgcctcgcccccctcgtcaaggtcatccat---gagaagtacggcatcgaggagggcctcatgaccaccgttcacgccaccaccgccacgcagaagaccgtcgacggtcccagcaacaaggactggcgcggcggccgcggccgtggccgtaacatcatcccgtccagcaccggcgccgcaaaggccgtcggcaaggtcatgcccgagctcaac---ggtaagctcaccggcatggccttccgcgtccccacccccgatgtctccgtcgtcgatctcaccgtccgcctcacgtccgag---actacctacgaggacatcaaggccaccatgaaggccgccgccgac------------gactccatgaagggcatcatgaagtacaccgaagacgccgttgtcagtaccgactttatccatgacgacgcgtcgtgcatatttgacgccagcgcgggcatcatgcttaac------------agcaagttttgcaagctcgtcgcatggtacgacaatgagtggggatattctaaccgcgtcgttgacctcatcgcacacatctccaaggtccag??????????????????????????????????????????????????????????????????????????????????????????
otu_58	??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgggtgccaagatcaagatcggaatcaac---------------------------------------ggattcggaagaatcggacgtttagttgctagagtagctttgaagaga---------gat---gatgttgaactcgttgcagttaacgatcctttcatcaccactgattacatgacgtatatgtttaagtacgacagtgttcacggacagtggaag------------------------aacgacgaactcaccgtcaaggactctaacactcttctcttcggt---------------cagaagccagttactgtctttgcacac---aggaacccagaagagatcccatgggccagcactggtgctgatatcattgttgagtctactggtgttttt---------------------------------actgataaggacaaggctgctgctcatttgaagggtggtgccaagaaggtcatcatttctgctcccagt---aaa---gatgctcccatgtttgttgttggtgttaatgagaatgaatacaagcca---gagtttgacattatttcc---------------------------aatgctagctgcaccaccaactgccttgcaccacttgcaaaggttattaat---gacaggtttggcattgttgagggtctcatgaccactgtccattccatcaccgccacccagaagactgttgatggaccatcaagcaaggactggagaggtggaagagctgcttcatttaacatcattcccagcagtaccggagctgctaaggctgtcggcaaagtgcttcctgctttgaat---ggaaagttgaccggtatgtcattccgtgtcccaactgtggatgtctccgttgttgaccttacagtgaggcttgagaaggcc---gccacctatgatgaaatcaaagctgctatcaaggaagagtctgagggc------------aagttgaaaggaatccttggttacactgaagacgatgtggtctccactgactttattggtgacaccaggtcaagtatctttgatgccaaggcaggaattgccttaaat------------gacaagtttgttaagcttgtctcatggtatgacaacgagttgggttacagtacccgtgtggttgacctcattgttcacattgctaaacaactt??????????????????????????????????????????????????????????????????????????????????????????
otu_59	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctgtcaaggttggcatcaac---------------------------------------ggcttcggtcgcattggccgtatcgtcttccgcaacgccgtcgagcac---------ccc---gagattgaggtcgttgccgtcaacgaccctttcatcgaccccgaatatgctgcctacatgctcaagtatgactcttcccacggcgtcttcaag------------------------ggc------gagatcaagaaggacgcggacggcttgattgtcaat---------------ggcaagaaggtcaagttccacactgag---cgcgacccttctgctattccctggaaggcgtctggagccgagtacattgtcgagtccaccggtgtcttc---------------------------------accaccaccgagaaggccaaggcccatttgactggtggcgccaagaaggtcatcatctcggctccttct---gcc---gatgctcccatgtacgttatgggagtcaacgagaagacctatgacggc---aaggccgatgtcatttcc---------------------------aacgcttcttgcaccaccaactgcctggctcccctggccaaggttatccac---gacaagtacaccattgttgagggtctgatgaccactgtccactcgtacactgccacccagaagaccgtcgacggtccctcaggcaaggactggcgaggtggccgtggtgctgcccagaacatcattcccagcagcaccggtgccgccaaggccgtcggcaaggtcattcccgacctcaac---ggcaagctcactggcatgtccatgcgagtgcctactcccaacgtctccgtcgttgacttgactgtccgcatcgagaagggt---gctacttacgacgagatcaaggcgactgtcaaggaggccgccaacggt------------tcccttgccggcattctcggctacaccgaggacgacattgtgtccagcgacatgaacggcaacaccaactcctccatcttcgatgccaaggccggtatctccctcaac------------aagaactttgtcaagctcattgcttggtacgacaacgagtggggctactcccgccgtgttctcgacctccttgcctacgttgccaaggctgacgctagcaag?????????????????????????????????????????????????????????????????????????????????
otu_60	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctccaatcaaagtaggaattaac---------------------------------------ggatttggccgcatcggtcgtatggtcttgcaagccatatgcgaccagggccttctcggtactgagattgatgttgtcgctgtagttgtcagatcccctgacgctgattacttatcttatcggttgcgctatgactctgttcatggccgcttcaag---cataaggtagatgttgccgcaagtcccgaatgtgagcccggaaagcatgatacccttgtggtaaat---------------ggccataaagtaaagtgcgtgaagggaggccctgatccttctacactcccatggggaaaactgggtgttgactatgtcattgaatccacaggatttttc---------------------------------acagataagtccaaggccgagggtcacatcaaagctggtgctaagaaggttatcatttcagccccagctaaggga---ggcgccaagaccattgtgatgggtgtaaaccagcatgagtacaaccctaatgagcattctgttgtatcc---------------------------aatgcatcttgtactactaatggtctcgcacctattgtacacgtgttgaataaagaaggctttggcataaaggtgggcctgatcactacattgcacgcttataccgctactcagaagacagttgacggcgtctcccagaaggactggcgcggcggacgtgccgcatctgtgaacatcatccccagcagcactggtgccgccaaagctgtaggtgaggtactgcccgagaccaaa---ggtaaactgaccggtatggccttccgtgtgcccacacctgacgtgtccgtagtcgaccttacatttaccactactaaagat---acaagcattaaagagatcgatgccgctctgaagcgtgctgctgcatcg------------tacctccgtggtatcctggacatctccaaagaagagctcgtcagcactgactttatccataatccgaacagctccatctatgactcactggccacactacagaacaacctgcctacagagaagcgcttcttcaaggttgtttcgtggtatgataacgagtggggatactccaatcgcgtggtagacctcgtacgctttatgaattccaaagactccaaatgccatgcaaagttg?????????????????????????????????????????????????????????????????????
otu_61	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctccaatcaaagtaggaattaac---------------------------------------ggatttgggcgcatcggtcgtatggtcttacaagccatatgcgatcagggccttctcggtactgagattgatgttgtggctgtagttgacatgtccactgacgctgattacttttcttatcaaatccgctatgactctgttcatggccgcttcaag---cataaggtagatgttgccgcaagtcccgaatgtgagcccggaaagcatgatacccttgtgataaat---------------ggccataaagtaaagtgcgtgaaggcaacccgtaacccttctgatcttccatggggaaaactgggtgttgactatgtcattgaatccacagggctattc---------------------------------acagataagtccaaggccgagggtcacatcaaagctggtgctaagaaggttatcatttcagccccagctaaggga---ggcgccaagaccattgtgatgggtgtaaaccagcatgagtacaaccctaatgagcattctgttgtatcc---------------------------aacgcatcttgtactaccaattgcctcgcacctattgtacacgtgttgaataaagaaggctttggcataaaggttggcctgatgactaccatccacgcttataccgctactcagaagacagttgacggcgtctcccagaaggactggcgcggcggacgtgccgcatctgtgaacatcatccccagcagcactggtgccgccaaagctgtaggtgaggtactgcccgagaccaaa---ggtaaactgaccggtatggccttccgtgtgcccacacctgacgtgtccgtagtcgaccttacatttaccactactaaagat---acaagcattaaagagatcgatgccgctctgaagcgtgctgctgcatcg------------tacctccgtggtatcctggacatctccaaagaagagctcgtcagcactgactttatccataatccgaacagctccatctatgactcactggccacactacagaataacctgcctacagagaagcgcttcttcaaggttgtttcgtggtatgataacgagtggggatactccaatcgcgtggtagacctcgtacgctttatgaattccaaagactccaaaagccatgcaaagttg?????????????????????????????????????????????????????????????????????
otu_62	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggttagagttgctattaac---------------------------------------ggtttcggtagaatcggtagattggtcatgagaattgctttgtctaga---------cca---aacgtcgaagttgttgctttgaacgacccattcatcaccaacgactacgctgcttacatgttcaagtacgactccactcacggtagatacgct------------------------ggt------gaagtttcccacgatgacaagcacatcattgtcgat---------------ggtaagaagattgctacttaccaagaa---agagacccagctaacttgccatggggttcttccaacgttgacatcgccattgactccactggtgttttc---------------------------------aaggaattagacactgctcaaaagcacattgacgctggtgccaagaaggttgttatcactgctccatct---tcc---accgccccaatgttcgtcatgggtgttaacgaagaaaaatacacttct---gacttgaagattgtttcc---------------------------aacgcttcttgtaccaccaactgtttggctccattggccaaggttatcaac---gatgctttcggtattgaagaaggtttgatgaccactgtccactctttgactgctactcaaaagactgttgacggtccatcccacaaggactggagaggtggtagaaccgcttccggtaacatcatcccatcctccaccggtgctgctaaggctgtcggtaaggtcttgccagaattgcaa---ggtaagttgaccggtatggctttcagagtcccaaccgtcgatgtctccgttgttgacttgactgtcaagttgaacaaggaa---accacctacgatgaaatcaagaaggttgttaaggctgccgctgaaggt------------aagttgaagggtgttttgggttacaccgaagacgctgttgtctcctctgacttcttgggtgactctcactcttccatcttcgatgcttccgctggtatccaattgtct------------ccaaagttcgtcaagttggtctcctggtacgacaacgaatacggttactctaccagagttgtcgacttggttgaacacgttgccaaggct?????????????????????????????????????????????????????????????????????????????????????????????
otu_63	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????attggcccagttgcaaaagtattaaat---gatgaatttggtatcgtgaacggtctgatgactacagtacacgcaattactaatgaccaaaagaatattgat---aatggccataaagatttgcgtagagcacgttcatgtaatgaaagtattattccgacatctacaggcgcacgtaaagcattaaaagaagtgctacctgaagtagaa---ggtaaattacatggaatggcattaagagtaccaactaaaaacgtttctcttgtagacttagtagtagatttagaacaaaat---gtaacagctgatcaaattaatgacgctttcaaaaatgcaaat---------------------ttagatggtgtattggatgtagaaagtgaaccacttgtttcagtagattttaatacaaatcctaattctgcagtaattgatgcacaatcaacaatggttatgggcgataat------------aaagttaaagtaatcgct???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
otu_64	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggctcccaaggtcggtatcaac---------------------------------------ggcttcggtcgtatcggacgtatcgtcttccgtaacgccatcaaccac---------ggc---gaggttgacgtcgttgctgtcaacgaccccttcatcgagacccactatgctgcctacatgctcaagtacgacagcacccacggccagttcaag------------------------ggc------accatcgagacctacgaggagggtctgattgtcaac---------------ggcaagaagatccgcttcttcgctgag---cgtgaccccgctgccatcccctggggcaccaccggcgctgactacatcgtcgagtccactggtgtcttc---------------------------------accacccaggagaaggccgccgctcacttgaagggtggtgccaagaaggtcgtcatctctgctccttcc---gct---gatgcccccatgttcgtcatgggtgtcaacaacacctcctacaccaag---gacatcaacgtcctctcc---------------------------aacgcttcttgcaccaccaactgccttgctcccctcgccaaggtcatcaac---gacaagttcggcatcgttgagggtctcatgaccaccgtccactcctacaccgctacccagaaggtcgtcgatgccccctccagcaaggactggcgtggtggccgtactgcggcccagaacatcatcccctcttccaccggtgctgccaaggctgtcggcaaggtcatccctacccttaac---ggcaagctcaccggtatggccatgcgtgtccccacctccaacgtctccgttgtcgacttgacctgccgcctcgagaaggcc---accagctacgacgagatcaagaaggccctcaaggacgcttccgagaac------------gagctcaagggcatcctcggctacactgaggacgacatcgtctcctccgacctgaacggtgacgaccactcctccatcttcgatgccaaggccggtatcgcccttaac------------tccaacttcgtcaagctcgtctcctggtacgacaacgagtggggttactcccgccgtgtcgtcgacctcattgcctacatctccaaggttgatgcccag????????????????????????????????????????????????????????????????????????????????????
otu_65	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgtcgaag------attggtattaat---------------------------------------ggatttggccgcattggtcgtctggtgctccgtgccgccgtcgacaaa---------ggt------gccagcgtcgtggccgttaacgatcccttcatcgatgtgaactacatggtctacttgttcaagttcgattctacccacggccgtttcaag------------------------ggc------accgtttccgctgagggcggcttcctggtcgtcaat---------------ggccagaagatcaccgtgttcagcgaa---cgcgaccccgctaacatcaactgggccagcgctggcgctgagtacgtggttgagtctaccggtgtcttc---------------------------------accaccaccgagaaggcctccactcacttgaagggcggtgccaagaaggttgtcatttcggcaccatcc---gct---gatgcgcccatgttcgtgtgcggcgtgaacttggatgcgtacagcccc---gacatgaaggtcgtgtcg---------------------------aacgcttcttgcaccaccaactgcttggccccattggctaaggttatcaac---gataacttcgagattgtggaggtcttgatgaccactgtgcatgccaccacagccacccagaagaccgtcgatggcccctccggcaagttgtggcgtgatggccgtggtgcttgccaaaacatcattccagcatccactggtgccgccaaggccgtcggcaaagtcattccagctctgaat---ggaaaactgactggcatggctttccgtgtgcccacaccaaatgtgtccgttgtcgatttgactgtccgcttgggcaagggc---gccagctacgatgagattaaggccaaggtacaagaggctgccaacggt------------ccattgaagggcattctgggctacaccgatgaggaggttgtctccactgacttccttagcgatactcactcgtctgtgttcgagcccaaggccggcatctcgctcaac------------gacaagttcgtgaagctgatttcctggtacgacaacgagttcggctactccaaccgtgtcattgacttgatcaagtacatgcagagcaaggat??????????????????????????????????????????????????????????????????????????????????????????
otu_66	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgtcgaaagccaacgtcggaatcaac---------------------------------------ggtttcggaagaatcggacgtctcgtgctccgcgcggctgtcgaaaag---------gacacg---gttcaagtggtcgccgtcaacgatccgtttatcacaatcgactacatggtctaccttttcaagtatgactcgacccacggtcaattcaaa------------------------gga------actgttacctacgatggagactttctgattgtccagaaagatggcaaatcatcgcacaagatcaaggtcttcaacagc---aaggatccagctgccatcgcatggggatcagtcaaagccgatttcgttgtcgagtctactggagttttc---------------------------------acgacaaaggaaaaggcctctgcccatcttcaaggaggagccaagaaggtcatcatctctgctccatct---gct---gatgctccaatgtacgtggttggagtaaaccatgagaagtacgacgcttcgaatgatcacgttatttct---------------------------aacgcatcgtgcaccaccaactgtctggcaccactggcgaaggttatcaat---gataacttcggtatcatcgaaggactcatgacgacagtgcacgctgtaaccgcaacccagaagacagtcgatggaccatccggaaagctgtggagagatggacgcggtgctggacaaaacatcattccagcttccactggagccgccaaggctgtgggaaaagtcattccggagctgaac---ggaaagctcactggaatggctttccgtgtccctacaccagatgtttccgtcgttgatctgaccgttcgcctcgagaaacca---gcttcgatggatgacatcaagaaggtagtcaaggccgctgccgatgga------------ccaatgaagggaatcctcgcctacaccgaagatcaagttgtgtcgactgacttcgtgtccgaccctcactcgtccattttcgatactggagcatgcatttcgctcaac------------ccgaacttcgtcaagctcgtctcttggtacgacaatgaatatggatactcgaaccgtgttgtcgacctcatcggatacatcgccacccgtgga??????????????????????????????????????????????????????????????????????????????????????????
otu_67	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgtcgaaggccaacgtcggaatcaac---------------------------------------ggtttcggaagaatcggacgtctcgtgctccgcgcggctgtcgaaaag---------gacacg---gttcaagtggtcgccgtcaacgatccgtttatcacaatcgactacatggtctaccttttcaagtatgactcgacccacggtcaattcaaa------------------------gga------actgttacctacgatggagactttctgattgtccagaaagatggcaaatcatcgcacaagatcaaggtcttcaacagc---aaggatccagctgccatcgcatggggatcagtcaaagccgatttcgttgtcgagtctactggagttttc---------------------------------acgacaaaggaaaaggcttctgctcatcttcaaggaggagccaagaaggtcatcatctctgctccatct---gct---gatgctccaatgtacgtggttggagtaaaccatgagaagtacgacgcttcgaatgatcacgttgtttct---------------------------aacgcatcgtgcaccaccaactgtctggcaccactggcgaaggttatcaat---gataacttcggtatcatcgaaggactcatgacgacagtgcacgctgtaaccgcaacccagaagacagtcgatggaccatccggaaagctgtggagagatggacgcggtgctggacaaaacatcattccagcttccactggagccgccaaggctgtgggaaaagtcattccggagctgaac---ggaaaactcactggaatggctttccgtgtccctacaccagatgtttccgtcgttgatctgaccgttcgcctcgagaagcca---gcttcgatggacgacatcaagaaggtagtcaaggccgctgccgatgga------------ccaatgaagggaatcctcgcctacactgaagatcaagttgtgtcgactgatttcgtgtccgaccctcactcgtccattttcgatgctggagcatgcatttcgctcaac------------ccgaacttcgtcaagctcgtctcttggtacgacaatgaatatggatactcgaaccgtgttgtcgacctcatcggatacatcgccacccgtgga??????????????????????????????????????????????????????????????????????????????????????????
otu_68	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atgatcagaattgctattaac---------------------------------------ggtttcggtagaatcggtagattggtcttgagattggctttgcaaaga---------aaa---gacattgaggttgttgctgtcaacgatccatttatctctaacgattatgctgcttacatggtcaagtacgattctactcatggtagatacaag------------------------ggt------actgtttcccatgacgacaagcacatcatcattgat---------------ggtgtcaagatcgctacctaccaagaa---agagacccagctaacttgccatggggttctctaaagatcgatgtcgctgttgactccactggtgttttc---------------------------------aaggaattggacaccgctcaaaagcacattgacgctggtgccaagaaggttgtcatcactgctccatct---tct---tctgctccaatgtttgttgttggtgttaaccacactaaatacactcca---gacaagaagattgtctcc---------------------------aacgcttcttgtaccaccaactgtttggctccattggccaaggttatcaac---gatgctttcggtattgaagaaggtttgatgaccactgttcactccatgaccgccactcaaaagactgttgatggtccatcccacaaggactggagaggtggtagaaccgcttccggtaacattatcccatcctctaccggtgctgctaaggctgtcggtaaggtcttgccagaattgcaa---ggtaagttgaccggtatggctttcagagtcccaaccgtcgatgtttccgttgttgacttgactgtcaagttggaaaaggaa---gctacttacgaccaaatcaagaaggctgttaaggctgccgctgaaggt------------ccaatgaagggtgttttgggttacaccgaagatgccgttgtctcctctgatttcttgggtgacactcacgcttccatcttcgatgcctccgctggtatccaattgtct------------ccaaagttcgtcaagttgatttcctggtacgataacgaatacggttactccgccagagttgttgacttgatcgaatatgttgccaaggct?????????????????????????????????????????????????????????????????????????????????????????????
otu_69	???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggttagagttgctattaac---------------------------------------ggtttcggtagaatcggtagattggttatgagaattgctttgcaaaga---------aag---aacgtcgaagttgttgctttgaacgatcctttcatctctaacgactactccgcttacatgttcaagtacgactctactcacggtagatacgct------------------------ggt------gaagtttcccacgatgacaagcacatcatcgttgat---------------ggtcacaagatcgccactttccaagaa---agagacccagctaacttgccatgggcttctctaaacattgacatcgccattgactccactggtgttttc---------------------------------aaggaattggacactgctcaaaagcacattgacgctggtgccaagaaggttgtcatcactgctccatct---tcc---accgccccaatgttcgtcatgggtgttaacgaagaaaaatacacttct---gacttgaagattgtttcc---------------------------aacgcttcttgtaccaccaactgtttggctccattggccaaggttatcaac---gatgctttcggtattgaagaaggtttgatgaccactgttcactccatgaccgccacccaaaagactgttgacggtccatcccacaaggactggagaggtggtagaaccgcttccggtaacatcatcccatcctctaccggtgctgctaaggctgtcggtaaggtcttgccagaattgcaa---ggtaagttgaccggtatggctttcagagtcccaaccgtcgatgtttccgttgttgacttgactgtcaagttgaacaaggaa---accacctacgatgaaatcaagaaggttgtcaaggctgccgctgaaggt------------aagttgaagggtgtcttgggttacactgaagacgctgttgtctcctctgacttcttgggtgactctaactcttccatcttcgatgctgccgctggtatccaattgtct------------ccaaagttcgtcaagttggtttcctggtacgacaacgaatacggttactctaccagagttgtcgacttggttgaacacgttgccaaggct?????????????????????????????????????????????????????????????????????????????????????????????
otu_70	?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggttgtccccaaggttggaatcaac---------------------------------------ggcttcggtcgtatcggccgtattgtcttccgtaacgctatcgagcac---------gag---ggtgttgacatcgttgccgtcaacgaccccttcattgag------------gcctacatgctcaagtatgacagcacccacggccgcttcaac------------------------gga------gccgtcgagttcgacggcaacacgctcatcgtcaac---------------ggcaagaagatcaagttctacgcagag---agggaccccgctcagatcccctggagcgagactggc---cagtacgtcgttgagtccactggtgtcttc---------------------------------accaagcaggagaaggcctcccttcacctgagagggtgtgccaagaaggtcatcatctccgctccctct---tcc---gactcccccatgtttgtcatgggtgtcaacaacgaccaatacaccaag---gacatcaccgtcctttcc---------------------------aacgcctcttgcaccaccaactgcttggctccccttgccaaggtcatcaat---gacaagttcggcatcgtcgagggtctgatgaccacagtccactcctacactgctacccagaaggtcgtcgatggcccctccaacaaggactggagaggtggccgtaccgctgcccagaacatcatccccagctccaccggtgtgcctaaggcagtcggcaaggtcattccttccttgaac---ggcaagctcactggcatgtctatgcgtgtgcctacttccaacgcctccgttgtcgaccttactgcccgtctcgagaaggcc---gccacctacgacgagatcaagcaggccgtcaagaaggcctctgagcgc------------cctctgaagggcatcctcggctacactgaggatgacgttgtctcctccgatctcaacggagacccccactcctccatcttcgatgccaaggctggtatcgccctcaac------------tcgaacttcgtcaagctgttttcctggtacgacaacgagtggggttactcccgccgtgttatcgacctcattgcctatgcc---caggtcgatgcccag????????????????????????????????????????????????????????????????????????????????????
otu_71	????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????atggtcgtcaaggttggtatcaac---------------------------------------ggcttcggtcgcattggccgtatcgtcttccgcaatgccatcgagcac---------aac---gacgtcgagatcgtcgccgtcaacgaccctttcatcgagccacactacgctgcctacatgctcaagtatgacagccagcacggccagttcaag------------------------ggc------gacatcaaggtcgagggcaacgacctgaccatcaac---------------ggcaagaccatccgcttctacactgag---aaggaccccgccaacatcccatggagcgagaccggcgcatactacgtcgttgagtccaccggtgtcttc---------------------------------accaccaccgacaaggccaaggcccacttgaagggtggtgctaagaaggtcgtcatctccgctccctcg---gct---gatgctcccatgttcgtcatgggtgtcaacaacgagacctacaccaag---gacattgaggtgctctcc---------------------------aacgcctcctgcacaaccaactgcttggctcccctcgccaaggtcatccac---gacaagttcaccatcattgagggtttgatgaccaccgtccactcctacaccgctacccagaaagtcgttgacggcccttccgccaaggactggcgtggtggccgcactgcggcccagaacatcattcccagcagcactggtgccgccaaggctgtcggcaaggtcattcctgacctcaac---ggcaagctcaccggaatgtccatgcgtgttcccacctccaacgtttctgtggttgacttgactgtccgcctcgagaagggt---gctacctacgatgagatcaaggaggccgtcaaggccgccgctgatggt------------cctcttaacggcattctcggatacactgaggacgagatcgtctccaccgacttgaacggtgacacccgctcttccatcttcgacgccaaggccggtatctccctgaac------------aagaacttcgtcaagctcgtctcctggtacgacaacgagtggggttactcccgccgtgtcctcgacctcttggtctacattgccaaggtcgatggtaacgcc?????????????????????????????????????????????????????????????????????????????????
;
end;

begin trees;
	tree glyceraldehyde-3-phosphate_dehydrogenase = ((otu_30:0.49051,((otu_28:0.49077,(((otu_31:2.01423,((otu_19:0.06892,((otu_20:0.03391,otu_18:0.04913)67:0.06131[1],otu_21:0.17073)66:0.05144[1])65:0.15044[1],(otu_60:0.03246,otu_61:0.0051)68:0.24938[1])64:0.25626[1])63:0.09208[0.586],(((((otu_40:0.12574,(otu_36:0.13995,otu_8:0.17533)59:0.19561[1])58:0.17743[1],(otu_48:0.09594,((otu_41:0.08423,otu_33:0.09024)62:0.06736[1],otu_50:0.14704)61:0.26418[1])60:0.11592[1])57:0.0924[1],otu_9:0.15489)56:0.38086[1],otu_63:0.6026)55:0.0988[0.746],otu_11:0.70361)54:0.18437[0.988])53:0.12048[0.994],(((otu_32:0.3374,(otu_45:0.17225,((((otu_38:0.17276,(otu_2:0.45585,otu_3:0.1545)50:0.06724[0.971])49:0.03913[1],otu_39:0.21582)48:0.03959[0.907],(otu_7:0.12835,otu_6:0.09868)51:0.0189[0.894])47:0.04402[1],(otu_22:0.10484,otu_25:0.16061)52:0.02817[0.999])46:0.02715[1])45:0.02351[0.999])44:0.02505[0.935],(((otu_1:0.06459,(otu_65:0.12251,otu_29:0.05151)38:0.03182[0.848])37:0.14809[1],(((otu_47:0.01586,otu_46:0.01469)43:0.08936[1],(otu_67:0.0074,otu_66:0.00478)42:0.16879[1])41:0.12119[1],(otu_34:0.00116,otu_13:0.00225)40:0.45393[1])39:0.05934[0.962])36:0.08529[1],((otu_43:0.03399,otu_42:0.04004)35:0.17074[1],otu_57:0.24799)34:0.04464[1])33:0.03287[0.998])32:0.03751[0.995],((otu_64:0.05167,otu_5:0.09417)24:0.0371[1],(otu_70:0.13406,((otu_14:0.08084,((otu_59:0.1093,otu_54:0.10356)29:0.02172[0.999],(otu_12:0.0721,otu_53:0.08486)30:0.01661[0.856])28:0.02685[1])27:0.04636[1],(otu_71:0.05705,otu_55:0.07532)31:0.05053[1])26:0.03818[1])25:0.02449[0.973])23:0.06116[1])22:0.04736[0.998])21:0.038[0.307])20:0.03735[0.319],((((otu_10:0.02615,otu_49:0.03557)8:0.12455[1],(otu_58:0.13279,((otu_27:0.00127,otu_4:0.00359)11:0.04842[1],otu_35:0.06224)10:0.06368[1])9:0.06089[1])7:0.1334[1],(otu_23:0.0696,otu_24:0.11442)6:0.32447[1])5:0.1036[1],(((((otu_37:0.15673,((otu_69:0.01483,otu_62:0.02881)18:0.03515[1],otu_68:0.06013)17:0.03773[1])16:0.0128[0.45],otu_51:0.13459)15:0.07285[1],(otu_26:0.21596,otu_17:0.07616)19:0.04614[0.858])14:0.04159[0.8],otu_16:0.13043)13:0.05611[1],otu_15:0.13292)12:0.16149[1])4:0.09891[0.998])3:0.10067[1])2:0.0983[1],(otu_56:0.21641,otu_52:0.19337)69:0.09771[1],otu_44:0.17553)1;
end;

BioPerl-1.007002/t/data/SPAN_Family8a.nex000444000766000024      2453113155576321 17724 0ustar00cjfieldsstaff000000000000#NEXUS
begin taxa;
	dimensions ntax=32;
	taxlabels
	otu_1	otu_2	otu_3	otu_4	otu_5	otu_6	otu_7	otu_8	otu_9	otu_10	otu_11	otu_12	otu_13	otu_14	otu_15	otu_16	otu_17	otu_18	otu_19	otu_20	otu_21	otu_22	otu_23	otu_24	otu_25	otu_26	otu_27	otu_28	otu_29	otu_30	otu_31	otu_32;
end;

begin characters;
	dimensions nchar=280;
	format datatype=protein missing=? gap=-;
	matrix
otu_1	?????????????????????????????????MTVYSYLVILFILLDNYCSAYGYG-----YSYYHRRHFDPAIASFTK-------EPYIGAVWFTQHGDY----MYVNGSVAGLPPGKLLGTHVHRYG--------GLGNMCLEAGPHFNPFNQ-RHGPRHG--YPRHAGDLGNIRVGRGGVAKFDFYVTIKGLGPFDGFIGRALVIHANRDDLGRN---RDEGSRTTGNSGPRLACATIGFRAP?????????????????????????????????
otu_2	?????????????????????????????????????????????????????????????????????MAMKAVCVLKG------DGPVQGTIHFEQKASGE--PVVLSGQITGLTE-GQHGFHVHQYG--------DNTQGCTSAGPHFNPHSK-KHGGPAD--EERHVGDLGNVTAGKDGVANVSIEHRVISLSGEHSIIGRTMVVHEKQDDLGKG-G--NEESTKTGNAGSRLACGVIGIAQ??????????????????????????????????
otu_3	?????????????????????????????????????????????????????????????????????MVVKAVCVING------DV--KGTVHFEQQDAKS--PVLVTGEVNGLAK-GLHGFHVHEFG--------DNTNGCTSAGPHFNPYGN-SHGAPSD--LNRHLGDLGNIEASGDGATKVEISDKLITLFGENSIVGRTIVVHADPDDLGKG---GHELSKTTGNAGARLGCGVIGICKI?????????????????????????????????
otu_4	??????????????????????????????????????????????????????????????????????MVKAVAVVRG------DSNVKGTVIFEQESESA--PTTITYDISGNDPNAKRGFHIHTFG--------DNTNGCTSAGPHFNPHGT-THGDRTA--EVRHVGDLGNIETDAQGNAKGTVTDNLVKLIGPESVIGRTVVVHAGTDDLGKG---GNEESLKTGNAGPRPACGVIGISQ??????????????????????????????????
otu_5	????????????????????????????????????MDILSDIANAVLPQDVVSKVE-------------SKRAVAVLRG------TA-VFGTVWLTQKAEGE--ETEFEGEIKGLSP-GLHGFHIHQYG--------DSTDGCTSAGPHFNPCKM-NHGGRDS--VVRHVGDLGNVEAGADGVAKIKFSDKVVSLFGANTVIGRSMVVHVDRDDLGQGIDDKAEESLKTGNAGARAACGVIALAAPA????????????????????????????????
otu_6	????????????????????????????????????MKRFSLAILALVVATGAQAAS-----------EKVEMNLVTSQG------VGQSIGSVTITETDKG----LEFSPDLKALPP-GEHGFHIHAKGSCQPATKDGKASAAESAGGHLDPQNTGKHEGPEG---AGHLGDLPALVVNNDGKATDAVIAP--RLKSLDEIKDKALMVHVGGDNMSDQ-------PKPLGGGGERYACGVIK?????????????????????????????????????
otu_7	??????????????????????????????????????????????????????????????????????MVKAVAVLGS------SDGVKGTIFFTQEGDG---PTAVTGSVSGLKP-GLHGFHVHALG--------DTTNGCMSTGHDYNPASK-EHGAPED--ENRHAGDLGNVTAGADGVANINVTDSQIPLTGPNSIIGRAVVVHADPDDLGKG---GHELSKSTGNAGGRVACGIIGLQG??????????????????????????????????
otu_8	????????????????????????????????????????????????????????M-------------STNAIAVLRG------DT-VSGIIRFKQDKEGL--PTTVTGEVKGLTP-GLHGFHIHQYG--------DTTNGCISAGPHFNPYNK-THGDRTD--EIRHVGDLGNIEAGADGTAHISISDQHIQLLGPNSIIGRSIVVHADQDDLGKGVGAKKDESLKTGNAGARVACGIVAIGAAS????????????????????????????????
otu_9	???????????????????????????MINSFIVIFLSFLIFINYANLVYVEATHVYGRRSHSNGMHGNGARRAVAVLRG------DAGVSGIIYFQQDSGGS--ITTISGSVSGLTP-GLHGFHVHQYG--------DQTNGCTSAGGHYNPYGK-THGDPND--RIKHIGDLGNIVAGANGVAEVYINSYHIKLRGPLSVIGRSLVVHENPDDLGQGTGNMREESLKTGNAGSRLACAVIGIAAVS????????????????????????????????
otu_10	??????????????????????????????????????????????????????????????????????MVKAVAVVRG------DSKVQGTVHFEQESESA--PTTISWEIEGNDPNALRGFHIHQFG--------DNTNGCTSAGPHFNPFGK-QHGAPED--DERHVGDLGNISTDGNGVAKGTKQDLLIKLIGKDSILGRTIVVHAGTDDYGKG---GFEDSKTTGHAGARPACGVIGLTQ??????????????????????????????????
otu_11	??????????????????????????????????????????????????????????????????????MVKAVVVLGS------SEIVKGTIHFVQEGDG---PTTVTGSVSGLKP-GLHGFHIHALG--------DTTNGCMSTGPHYNPAGK-EHGAPED--ETRHAGDLGNVTAGEDGVANIHVVDSQIPLTGPNSIIGRAVVVHADPDDLGKG---GHELSKTTGNAGGRVACGIIGLQG??????????????????????????????????
otu_12	??????????????????????????????????????????????????????????????????????MVKAVAVLAS------SEGVKGTIFFSQEGDG---PTSVTGSVSGLKP-GLHGFHVHALG--------DTTNGCMSTGPHFNPTGK-EHGAPQD--ENRHAGDLGNITAGADGVANVNVSDSQIPLTGAHSIIGRAVVVHADPDDLGKG---GHELSKTTGNAGGRVACGIIGLQG??????????????????????????????????
otu_13	???????????????????????????????????????????????????????????????????????MKAVCVMTG------TAGVKGVVKFTQETDNG--PVHVHAEFSGLKA-GKHGFHVHEFG--------DTTNGCTSAGAHFNPTKQ-EHGAPED--SIRHVGDLGNVVAGADGNAVYNATDKLISLNGSHSIIGRTMVIHENEDDLGRG---GHELSKVTGNAGGRLACGVVGLAAE?????????????????????????????????
otu_14	??????????????????????????????????????????????????????????????????????MVKAVAVLNS------SEGVSGTIFFTQEGDG---PTTVTGNLSGLKP-GLHGFHVHALG--------DTTNGCMSTGPHFNPVGK-EHGAPED--ENRHAGDLGNVTVGDDGTAAFTIIDFQIPLTGPHSIIGRAVVVHGDPDDLGKG---GHELSKTTGNAGGRVACGIIGLQG??????????????????????????????????
otu_15	???????MAATNTILAFSSPSRLLIPPSSNPSTLRSSFRGVSLNNNNLHRLQSVSFAVKAPSKALTVVSAAKKAVAVLKG------TSDVEGVVTLTQDDSG---PTTVNVRITGLTP-GPHGFHLHEFG--------DTTNGCISTGPHFNPNNM-THGAPED--ECRHAGDLGNINANADGVAETTIVDNQIPLTGPNSVVGRAFVVHELKDDLGKG---GHELSLTTGNAGGRLACGMFKLSITMT???????????????????????????????
otu_16	?????????????????????????????????????????????????????????????????????MVVKAVCVING------DA--KGTVFFEQESSET--PVKVSGEVCGLAK-GLHGFHVHEFG--------DNTNGCMSSGPHFNPYGK-EHGAPVD--ENRHLGDLGNIEATGDCPTKVSITDSRITLFGADSIIGRTVVVHADADDLGKG---GHELSKSTGNAGARIGCGVIGIAKV?????????????????????????????????
otu_17	?????????????????????????????????????????????????????????????????????MVVKAVCVING------DA--KGTVFFEQESSET--PVKVSGEVCGLAK-CLHGFHVHEFG--------DNTNGCMSSGPHFNPHGK-EHGAPVD--ENRHLGDLGNIEATGDCPTKVSITDSKITLFGADSIIGRTVVVHADADDLGKG---GHELSKSTGNAGARIGCGVIGIAKV?????????????????????????????????
otu_18	?????????????????????????????????????????????????????????????????????MVVKAVCVING------DA--KGTVFFEQESSGT--PVKVSGEVCGLAK-GLHGFHVHEFG--------DNTNGCMSSGPHFNPYGK-EHGAPVD--ENRHLGDLGNIEATGDCPTKVNITDSKITLFGADSIIGRTVVVHADADDLGQG---GHELSKSTGNAGARIGCGVIGIAKV?????????????????????????????????
otu_19	?????????????????????????????????????????????????????????????????????MVVKAVCVING------DA--KGTVFFEQESSGT--PVKVSGEVCGLAK-GLHGFHVHEFG--------DNTNGCMSSGPHFNPYGK-EHGAPVD--ENRHLGDLGNIEATGDCPTKVNITDSKITLFGADSIIGRTVVVHADADDLGQG---GHELSKSTGNAGARIGCGVIGIAKV?????????????????????????????????
otu_20	?????????????????????????????????????????????????????????????????????MVVKAVCVING------DA--KGTVFFEQESSET--PVKVSGEVCGLAK-GLHGFHVHEFG--------DNTNGCMSSGPHFNPYGK-EHGAPVD--ENRHLGDLGNIEATGDCPTKVSITDSKITLFGADSIIGRTVVVHADADDLGKG---GHELSKSTGNAGARIGCGVIGIAKV?????????????????????????????????
otu_21	?????????????????????????????????????????????????????????????????????MVVKAVCVING------DA--KGTVFFEQESSET--PVKVSGEVCGLAK-GLHGFHVHEFG--------DNTNGCMSSGPHFNPYGK-EHGAPVD--ENRHLGDLGNIEATGDCPTKVSITDSKITLFGADSIIGRTVVVHADADDLGQG---GHELSKSTGNAGARIGCGVIGIAKV?????????????????????????????????
otu_22	??????????????????????????????????MFMNLLTQVSNAIFPQVEAAQKM-------------SNRAVAVLRG------ET-VTGTIWITQKSEND--QAVIEGEIKGLTP-GLHGFHVHQYG--------DSTNGCISAGPHFNPFGK-THGGPKS--EIRHVGDLGNVEAGADGVAKIKLTDTLVTLYGPNTVVGRSMVVHAGQDDLGEGVGDKAEESKKTGNAGARAACGVIALAAPQ????????????????????????????????
otu_23	?????????????????????????????????????????????????????????????????????MVVKAVCVING------DA--KGTVFFEQESSGT--PVKVSGEVCGLAK-GLHGFHVHEFG--------DNTNGCMSSGPHFNPYGK-EHGAPVD--ENRHLGDLGNIEATGDCPTKVNITDSKITLFGADSIIGRTVVVHADADDLGQG---GHELSKSTGNAGARIGCGVIGIAKV?????????????????????????????????
otu_24	MSSIKIEFAVQMRRGDESYAGALRSALDGVGQVEIDTQEGRVIIQTQRPWSEIQDKIEATGVRAVLSGFGGQSAVALINTTGSVVDKTPIQGVVRFTTITADKKPGVVVDGVVDGLSP-GLHGLHIHESG--------DTSAGCSSVGEHYNPRQS-PHGSPAAGAEERHAGDLGNIRADENGRATFRFVDPVLEVWD---IIGRAVVLTANADDLGRG---GNDQSLIDGNSGERIACGIIARSAGILENFKRICACDGVTLWDERNKPLAGKERSQKL
otu_25	??????????????????????????????????????????????????????????????????????MAKGVAVLNS------SEGVTGTIFFTQEGDG---VTTVSGTVSGLKP-GLHGFHVHALG--------DTTNGCMSTGPHFNPDGK-THGAPED--ANRHAGDLGNITVGDDGTATFTITDCQIPLTGPNSIVGRAVVVHADPDDLGKG---GHELSLATGNAGGRVACGK???????????????????????????????????????
otu_26	???????????????????????????????????MMQYLVVSLALCATICSAAQTRN-----------MPIQAIAYLIGPVQ-SDNTQVKGNVTFTQNDCGQ--NVHVRVQLEGLKE-GKHGFHIHEKG--------DLTNGCISMGAHYNPDKV-DHGGPDH--EVRHVGDLGNLEANSTGIIDVTYTDQVITLTGKLGIIGRGVVVHELEDDLGLG---NHTDSKKTGNAGGRIACGVIGIK???????????????????????????????????
otu_27	????????????????????????????????????????????????????????????????MEAPRGNLRAVALIAG------DNNVRGCLQFVQDISG---TTHVTGKISGLSP-GFHGFHIHSFG--------DTTNGCISTGPHFNPLNR-VHGPPNE--EERHAGDLGNILAGSNGVAEILIKDKHIPLSGQYSILGRAVVVHADPDDLGKG---GHKLSKSTGNAGSRVGCGIIGLQSSADAKL????????????????????????????
otu_28	?????????????????????????????????????????????????????????????????????MVVKAVCVING------DA--KGTVFFEQEGEGC--PVKVTGEVTGLAK-GQHGFHVHEFG--------DNTNGCMSSGPHFNPYQK-EHGAPTD--ENRHLGDLGNIIANGDGPTPVNICDCKITLLGANSIIGRTVVVHADPDDLGKG---GHELSKTTGNAGARIGCGVIGIAKI?????????????????????????????????
otu_29	?????????????????????????????????????????????????????????????????????MVVKAVCVING------DA--KGTVFFEQESSGT--PVKVSGEVCGLAK-GLHGFHVHEFG--------DNTNGCMSSGPHFNPYGK-EHGAPVD--ENRHLGDLGNIEATGDCPTKVNITDSKITLFGADSIIGRTVVVHADADDLGQG---GHELSKSTGNAGARIGCGVIGIAKV?????????????????????????????????
otu_30	??????????????????????????????????????????????????????????????????????MVQAVAVLKG------DAGVSGVVKFEQASESE--PTTVSYEIAGNSPNAERGFHIHEFG--------DATNGCVSAGPHFNPFKK-THGAPTD--EVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVIHAGQDDLGKG---DTEESLKTGNAGPRPACGVIGLTN??????????????????????????????????
otu_31	??????????????????????????????????????????????????????????????????????MVRAVAVLRG------DSKVSGVVTFEQVDQNS--QVSVIVDLVGNDANAKRGFHIHQFG--------DNTNGCTSAGPHFNPEGK-THGDRTA--AVRHVGDLGNLESDAQGNIKTTFSDSVISLFGANSIIGRTIVIHAGEDDLGKG---TSEESLKTGNAGARNACGVIGIAV??????????????????????????????????
otu_32	????????????????????????????????????MKTRVVLILALSVCIEAAS--------------EVIRARAYIFKAEAGKIPTELIGTIDFDQ--SGS--FLKLNGSVSGLAA-GKHGFHIHEKG--------DTGNGCLSAGGHYNPHKL-SHGAPDD--SNRHIGDLGNIESPASGDTLISVSDSLASLSGQYSIIGRSVVIHEKTDDLGRG---TSDQSKTTGNAGSRLACGTIGTV???????????????????????????????????
;
end;

begin trees;
	tree Cu_Zn_superoxide_dismutase = ((otu_24:0.9929,(((otu_26:0.68297,otu_32:0.55754)30:0.14493[0.82],otu_13:0.29491)29:0.06243[0.44],(((((otu_9:0.31741,otu_8:0.13498)27:0.20268[1],(otu_22:0.14579,otu_5:0.27311)28:0.2533[1])26:0.12655[0.98],((otu_30:0.28255,otu_10:0.25631)25:0.08358[0.91],(otu_31:0.3159,otu_4:0.1635)24:0.11954[0.97])23:0.17514[1])22:0.08988[0.77],(otu_2:0.49149,(otu_3:0.18945,(otu_28:0.11453,(((otu_17:0.00661,otu_16:0.00769)17:0.00497[0.92],(otu_21:0.004,otu_20:0.01012)18:0.0073[0.87])16:0.01271[0.88],(((otu_23:0.00836,otu_19:0.00552)21:0.00203[0.28],otu_18:0.01103)20:0.00398[0.7],otu_29:0.00595)19:0.00739[0.75])15:0.11795[1])14:0.11754[1])13:0.12932[1])12:0.10326[1])11:0.0712[0.9],(((((otu_7:0.05142,otu_11:0.09031)10:0.02799[0.98],otu_12:0.06915)9:0.05245[0.99],(otu_25:0.17064,otu_14:0.1075)8:0.08023[1])7:0.08596[1],otu_27:0.46052)6:0.06401[0.75],otu_15:0.42442)5:0.14252[0.94])4:0.15394[0.91])3:0.16508[0.85])2:0.16387[0.45],otu_1:1.03491,otu_6:1.06056)1;
end;

BioPerl-1.007002/t/data/SwissProt.dat000444000766000024       401713155576321 17341 0ustar00cjfieldsstaff000000000000ID   1433_CANAL     STANDARD;      PRT;   264 AA.
AC   O42766;
DT   15-JUL-1998 (Rel. 36, Created)
DT   01-MAR-2002 (Rel. 41, Last sequence update)
DT   01-MAR-2002 (Rel. 41, Last annotation update)
DE   14-3-3 protein homolog.
GN   BMH1 OR BMH.
OS   Candida albicans (Yeast).
OC   Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; mitosporic Saccharomycetales; Candida.
OX   NCBI_TaxID=5476;
RN   [1]
RP   SEQUENCE FROM N.A.
RC   STRAIN=SC5314;
RA   Cognetti D., Devine D., Sturtevant J.;
RT   "The Candida 14-3-3 gene (BMH1) is essential for growth.";
RL   Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases.
CC   -!- SIMILARITY: BELONGS TO THE 14-3-3 FAMILY.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; AF038154; AAB96910.2; -.
DR   HSSP; P29312; 1A38.
DR   InterPro; IPR000308; 14-3-3.
DR   Pfam; PF00244; 14-3-3; 1.
DR   PRINTS; PR00305; 1433ZETA.
DR   ProDom; PD000600; 14-3-3; 1.
DR   SMART; SM00101; 14_3_3; 1.
DR   PROSITE; PS00796; 1433_1; 1.
DR   PROSITE; PS00797; 1433_2; 1.
SQ   SEQUENCE   264 AA;  29480 MW;  192EC2FFEFD52BB6 CRC64;
     MPASREDSVY LAKLAEQAER YEEMVENMKA VASSGQELSV EERNLLSVAY KNVIGARRAS
     WRIVSSIEQK EEAKGNESQV ALIRDYRAKI EAELSKICED ILSVLSDHLI TSAQTGESKV
     FYYKMKGDYH RYLAEFAIAE KRKEAADLSL EAYKAASDVA VTELPPTHPI RLGLALNFSV
     FYYEILNSPD RACHLAKQAF DDAVADLETL SEDSYKDSTL IMQLLRDNLT LWTDLSEAPA
     ATEEQQQSSQ APAAQPTEGK ADQE
//
BioPerl-1.007002/t/data/T7.aln000444000766000024      5171613155576321 15710 0ustar00cjfieldsstaff000000000000CLUSTAL W (1.82) multiple sequence alignment


AF419503        ATGGCTAACGTAATTAAAACCGTTTTGACTTACCAGTTAGATGGCTCCAATCGTGATTTT
AF419511        ATGGCTAACGTAATTAAAACCGTTTTGACTTACCAGTTAGATGGCTCCAATCGTGATTTT
AF419509        ATGGCTAACGTAATTAAAACCGTTTTGACTTATCAGTTAGATGGCTCCAATCGTGATTTT
AF419507        ATGGCTAACGTAATTAAAACCGTTTTGACTTACCAGTTAGATGGCTCCAATCGTGATTTT
AF419508        ATGGCTAACGTAATTAAAACCGTTTTGACTTACCAGTTAGATGGCTCCAATCGTGATTTT
AF419504        ATGGCTAACGTAATTAAAACCGTTTTGACTTACCAGTTAGATGGCTCCAATCGTGATTTT
AF419506        ATGGCTAACGTAATTAAAACCGTTTTGACTTACCAGTTAGATGGCTCCAATCGTGATTTT
AF419510        ATGGCTAACGTAATTAAAACCGTTTTGACTTACCAGTTAGATGGCTCCAATCGTGATTTT
AF419505        ATGGCTAACGTAATTAAAACCGTTTTGACTTATCAGTTAGATGGCTCCAATCGTGATTTT
                ******************************** ***************************

AF419503        AATATCCCGTTTGAATATCTAGCCCGTAAGTTCGTAGTGGTAACTCTTATTGGTGTAGAC
AF419511        AATATTCCGTTTGAATATCTAGCCCGTAAGTTCGTAGTGATAACTCTTATTGGTGTAGAC
AF419509        AATATTCCGTTTGAATATCTAGCCCGTAAGTTCGTAGTGGTAACTCTTATTGGTGTAGAC
AF419507        AATATCCCGTTTGAATATCTAGCCCGTAAGTTCGTAGTGGTAACTCTTATTGGTGTAGAC
AF419508        AATATTCCATTTGAGTATCTAGCCCGTAAGTTCATAGTGGTAACTCTTATTGGTGTAGAC
AF419504        AATATTCCGTTTGAATATCTAGCCCGTAAGTTCGTAGTGGTAACTCTTATTGGTGTAGAC
AF419506        AATATTCCGTTTGAATATCTAGCCCGTAAGTTCGTAGTGGTAACTCTTATTGGTGTAGAC
AF419510        AATATTCCGTTTGAATATCTAGCCCGTAAGTTCGTAGTGGTAACTCTTATTGGTGTAGAT
AF419505        AATATCCCGTTTGAATATCTAGCCCGTAAGTTCATAGTGGTAACTCTTATTGGTGTAGAC
                ***** ** ***** ****************** ***** ******************* 

AF419503        CGAAAGATCCTTACGATTAATACAGACTATCGTTTTGCTACACGTACTACTATTTCTCTG
AF419511        CGAAAGATCCTTACGATTAATACAGACTATCGTTTTGCTACACGTACTACTATTTCTCTG
AF419509        CGAAAGATTCTTACGATTAATACAGACTATCGTTTTGCTACACGTACTACTATTTCTCTG
AF419507        CGAAAGATCCTTACGATTAATACAGACTATCGTTTTGCTACACGTACTACTATCTCTCTG
AF419508        CGAAAGATTCTTACGATTAATACAGACTATCGTTTTGCTACACGTACTACTATTTCTCTG
AF419504        CGAAAGATCCTTACGATTAATACAGACTATCGTTTTGCTACACGTACTACTATTTCTCTG
AF419506        CGAAAGATTCTTACGATTAATACAGACTATCGTTTTGCTACACGTACTACTATTTCTCTG
AF419510        CGAAAGATTCTTACGATTAATACAGACTATCGTTTTGCTACACGTACTATTATCTCTCTG
AF419505        CGAAAGATTCTTACGATTAATACAGACTATCGTTTTGCTACACGTACTACTATTTCTCTG
                ******** **************************************** *** ******

AF419503        ACAAAGGCTTGGGGTCCAGCCGATGGCTACATGACTATCGAGTTACGTCGAGTAACCTCC
AF419511        ACAAAGGCTTGGGGTCCAGCCGATGGCTACACAACCATCGAGTTACGTCGAGTAACCTCC
AF419509        ACAAAGGCTTGGGGTCCAGCCGATGGCTACATGACCATCGAGTTACGTCGAGTAACTTCC
AF419507        ACAAAAGCTTGGGGTCCAGCCGATGGCTACACGACCATCGAGTTACGTCGAGTAACTTCC
AF419508        ACAAAGGCTTGGGGTCCAACCGATGGCTACATGACTATCGAGTTACGTCGAGTAACCTCC
AF419504        ACAAAGGCTTGGGGTCCAACCGATGGCTACATGACTATCGAGTTACGTCGAGTAACCTCC
AF419506        ACAAAGGCTTGGGGTCCAGCCGATGGCTACATGACTATCGAGTTACGTCGAGTAACCTCC
AF419510        ACAAAGGCTTGGGGTCCAACCGATGGTTATACGACCATCGAGTTACGTCGAGTAACCTCC
AF419505        ACAAAGGCTTGGGGTCCAGCCGATGGCTACACGACCATCGAGTTACGTCGAATAACTTCC
                ***** ************ ******* ** *  ** *************** **** ***

AF419503        ACTACCGACCGATTGGTTGACTTTACGGATGGTTCAATCCTCCGCGCATATGACCTTAAC
AF419511        ACTACCGACCGATTGGTTGACTTTACGGATGGTTCAATTCTCCGCGCATATGACCTTAAC
AF419509        ACTACCGACCGATTGGTTGACTTTACGGATGGTTCAATCCTCCGCGCATATGATCTTAAC
AF419507        ACTACCGACCGATTGGTTGACTTTACGGATGGTTCAATTCTCCGCGCGTATGATCTTAAC
AF419508        ACTACCGACCGATTGGTTGACTTTACGGATGGTTCAATCCTCCGTGCATATGATCTTAAC
AF419504        ACTACCGACCGATTGGTTGACTTTACGGATGGTTCAATCCTCCGTGCGTATGATCTTAAC
AF419506        ACTACCGACCGATTGGTTGACTTTACGGATGGTTCAATCCTCCGCGCGTATGATCTTAAC
AF419510        ACTACCGACCGATTGGTTGACTTTACGGATGGTTCAATCCTCCGCGCGTATGATCTTAAC
AF419505        ACTACCGATCGATTGGTTGACTTTACGGATGGTTCAATCCTCCGCGCGTATGATCTTAAC
                ******** ***************************** ***** ** ***** ******

AF419503        GTCGCTCAAATTCAAACGATGCACGTAGCGGAAGAGGCCCGTAATCTCACTACGGACACT
AF419511        GTCGCTCAGATTCAAACGATGCATGTAGCAGAAGAGGCCCGTAATCTCACTACGGATACT
AF419509        GTTGCTCAAATTCAAACGATGCACGTAGCGGAAGAGGCCCGTAATCTCACTACGGATACT
AF419507        GTTGCTCAGATTCAAACGATGCACGTAGCAGAAGAGGCTCGTAATCTCACTACGGACACT
AF419508        GTCGCTCAGATTCAAACGATGCACGTAGCGGAAGAGGCCCGTGATCTCACTACAGATACT
AF419504        GTCGCTCAGATTCAAACGATGCACGTAGCGGAAGAGGCCCGTGACCTCACTACGGATACT
AF419506        GTCGCTCAGATTCAAACGATGCACGTAGCGGAAGAGGCCCGTGACCTCACTACGGATACT
AF419510        GTCGCTCAGATTCAAACGATGCACGTAGCGAAAGAGGCCCGTGACCTCACTACGGATACT
AF419505        GTCGCTCAGATTCAAACGATGCACGTAGCAGAAGAGGCTCGTAATCTCACTACGGATACT
                ** ***** ************** *****  ******* *** * ******** ** ***

AF419503        ATCGGTGTCAATAACGATGGTCACTTGGATGCTCGTGGTCGTCGAATTGTGAATCTAGCG
AF419511        ATCGGTGTCAATAACGATGGTCACTTGGATGCTCGTGGTCGTCGAATTGTGAACCTAGCG
AF419509        ATCGGTGTCAATAACGATGGTCATTTGGATGCTCGTGGTCGTCGAATTGTGAACCTAGCG
AF419507        ATCGGTGTCAATAACGATGGTCACTTGGATGCTCGTGGTCGTCGAATTGTGAACTTAGCG
AF419508        ATCGGTGTCAATAACGATGGTCACTTGGATGCTCGTGGTCGTCGAATTGTGAACTTAGCG
AF419504        ATCGGTGTCAATAACGATGGTCACTTGGATGCTCGTGGTCGTCGAATTATGAACCTAGCG
AF419506        ATCGGTGTCAATAACGATGGTCACTTAGATGCTCGTGGTCGTCGAATTGTGAACTTAGCG
AF419510        ATCGGTGTCAATAACGATGGTCATTTGGATGCTCGTGGTCGTCGAATTGTGAACCTAGCG
AF419505        ATCGGTGTCAATAACGATGGTCACTTGGATGCTCGTGGTCGTCGAATTGTGAACCTAGCG
                *********************** ** ********************* ****  *****

AF419503        AACGCCGTGGATGATCGCGATGTTGTTCCGTTTGGTCAACTAAAGACCATGAACCAGAAC
AF419511        AACGCCGTGGACGACCGCGATGCTGTTTCGTTTGGTCAACTAAAGATCATGAACCAGAAT
AF419509        AACGCCGTGGATGATCGTGATGCTGTTTCGTTTGGTCAACTAAAGACCATGAACCAGAAC
AF419507        AACGCCGTGGATGATCGCGATGTTGTTCCGTTTGGTCAACTAAAGACCATGAACCAGAAC
AF419508        AACGCCGTGGATGATCGCGATGTTGTTCCGTTTGGTCAACTAAAGACCATGAACCAGAAC
AF419504        AACGCCGTGGACGATCGTGATGCTGTTTCGTTTGGTCAACTAAAGATCATGAACCAAAAC
AF419506        AACGCCGTGGATGATCGCGATGCTGTTTCATTTGGTCAATTAAAGACCATGAACCAGAAC
AF419510        AATGCCGTGGATGATCGCGATGTTGTTCCGTTTGGTCAACTAAAGACCATGAACCAGAAC
AF419505        AACGCCGTGGATGATCGCGATGTTGTTCCATTTGGTCAACTAAAGACCATGAACCAGAAC
                ** ******** ** ** **** **** * ********* ****** ********* ** 

AF419503        TCATGGCAAGCACGTAATGAAACCTTACAGTTCCGTAATGAGGCTGAGACTTTCAGAAAC
AF419511        TCATGGCAAGCACGTAATGAAACCTTACAGTTCCGTAATGAGGCTGAGACTTTCAAAAAC
AF419509        TCATGGCAAGCACGTAATGAAACCTTACAGTTTCGTAATGAGGCTGAGACTTTCAGAAAC
AF419507        TCATGGCAAGCACGTAATGAAACCTTACAGTTTCGTAATGAGGCTGAGACTTTCAGAAAC
AF419508        TCATGGCAAGCACGTAATGAAACCTTACAGTTTCGTAATGAGGCTGAGACTTTCAGAAAC
AF419504        TCATGGCAAGCACGTAATGAAACCTTACAGTTCCGTAATGAGACTGAGACTTTCAAAAAC
AF419506        TCATGGCAAGCACGTAATGAAACCTTACAGTTTCGTAATGAGGCTGAGACTTTCAGAAAC
AF419510        TCATGGCAAGCACGTAATGAAACCTTACAGTTCCGTAATGAGGCTGAGACTTTCAGAAAC
AF419505        TCATGGCAAGCACGTAATGAAACCTTACAGTTCCGTAATGAGGCTGAGACTTTCAGAAAC
                ******************************** ********* ************ ****

AF419503        CAAGCGGAGGACTTTAAGGACGAGTCCAGTATCAACGCTACGAACACAAAACAGTGGCGC
AF419511        CAAGCGGAGGACTTTAAGAACGAGTCCAGTATCAACGCTACGAATACAAAGCAATGGTAT
AF419509        CAAGCGGAGGGCTTTAAGGACGAGTCCAGTATCAACGCTACGAACACAAAGCAGTGGCGC
AF419507        CAAGCGGAGAGCTTTAAGGACGAGTCCAGTACCAACGTTACGAACACAAAGCAGTGGCGC
AF419508        CAAGCGGAGGGCTTTAAGGACGAGTCCAGTACCAACGCTACGAACACAAAGCAGTGGCGC
AF419504        CAAGTGGAGGACTTTAAGAACGAGTCCAGTATCAACGCTACGAACACAAAACAGTGGCGC
AF419506        CAAGCGGAGAGCTTTAAGGACGAGTCCAGTACCAACGCTACGAACACAAAGCAGTGGCGC
AF419510        CAAGCGGAGGGCTTTAAGGACGAGTCCAGTACCAACGCTACGAACACAAAGCAGTGGCGC
AF419505        CAAGCGGAGGGCTTTAAGGACGAGTCCAGTACCAACGCTACGAACACAAAGCAATGGCGC
                **** ****  ******* ************ ***** ****** ***** ** ***   

AF419503        GATGAAATCAAGGATTTTCGAGACGAAGCCAAGCGGTTCAAGAATACGGCTGATCAATAC
AF419511        GATGAGATCAAGGATTTTCGAGACGAAGCCAAACGGTTCAAGAATACGGCTGATCAATAC
AF419509        GATGAGATCAAGGATTTTCGAGACGAAGCCAAGCGGTTCAAGAATACGGCTGATCAATAC
AF419507        GATGAAATCAAGAATTTCCGAGACGAAGCCAAGCGATTCAAGAATATGGCTGATCAATAC
AF419508        GATGAAATCAAGGATTTCCGAGACGAAGCCAAGCGATTCAAGAATACGGCTGATCAATAC
AF419504        GATGAAATCAAGGATTTCCGAGACGAAGCCAAGCGGTTCAAGAATACGGCTGATCAATAC
AF419506        GATGAAATCAAGGATTTCCGAGACGAAGCCAAGCGATTCAAGAATACGGCTGATCAATAC
AF419510        GATGAGATCAAAGGTTTTCGAGACGAAGCCAAGCGGTTCAAGAATACGGCTGATCAATAC
AF419505        GATGAGATCAAGGATTTTCGAGACGAAGCCAAGCGGTTTAAAAATACGGCTGATCAATAC
                ***** *****   *** ************** ** ** ** **** *************

AF419503        GCTACATCTGCTGGGAACTCTGCTTCCGCTGCGTATCAATCTGAGGTAAACGCTGAGAAC
AF419511        GCTACATCTGCTGGGAACTCTGCTTCCGCTGCGCATCAATCTGAGGTAAACGCTGAGAAC
AF419509        GCTACATCTGCTGGGAACTTTGCTTCCGCTGCGCATCAATCTGAGGTAAACGCTGAGAAT
AF419507        GCTACATCTGCTGAGAACTCTGCTTCCACTGCGCATCAATCTGAGGTAAACGCTGAGAAT
AF419508        GCTACATCTGCTGGAAACTCTGCTTCCGCTGCGCATCAATCTGAGGTAAACGCTGAGAAT
AF419504        GCTACATCTGCTGGGAACTCTGCTTCCGCTGCGCATCAATCTGAGATAAACGCTGAGAAT
AF419506        GCTACATCTGCTGGGAACTCTGCTTCCGCTGCGCATCAATCTGAGGTAAACGCTGAGAAT
AF419510        GCTACATCTGCTGGGAATTCTGCTTCCGCTGCGCATCAATCTGAGGTAAACGCTGAGAAC
AF419505        GCTACATCTGCTGAGAACTCTGCTTCCGCTGCGCATCAATCTGAGGTAAACGCTGAGAAC
                *************  ** * ******* ***** *********** ************* 

AF419503        TCTGCCATAGTATCCGCTAACTCTGCTCATTTGGCAGAACAGCAAGCAGACCGTGCGGAA
AF419511        TCTGCCACAGCATCCGCTAACTCTGCTCATTTGGCAGAACAGCAAGCAGACCGTGCGAAA
AF419509        TCTGCCACAGCATCCGCTAATTCTGCTCATTTGGCAGAACAGCAAGCAGACCGTGCGAAA
AF419507        TCTGCCACAGCATCCGCTAACTCTGCTCATTTGGCAGAACAGCAAGCAGACCGTGCGGAA
AF419508        TCTGCCACAGCATCCGCTAACTCTGCTCATTTGGCAGAACAGCAAGCAGACCGTGCGGAA
AF419504        TTTGCCACAACATCCGCTAACTCTGCTCATTTGGCAGAACAGCAAGCAGATCGTGCGGAA
AF419506        TCTGCCACAGCATCCGCTAACTCTGCTCATTTGGCAGAACAGCAAGCAGATCGTGCGGAA
AF419510        TCTGCCACAACATCCACTAATTCTGCTCATTTGGCAAAACAGCAAGCAGACCGTGCGGAA
AF419505        TCTGCCACAACATCCGCTAACTCTGCTCATTTGGCAGAACAGCAAGCAGATCGTGCGGAA
                * ***** *  **** **** *************** ************* ****** **

AF419503        CGTGAGGCAGACAAGTTGAAAAATTACAATGGATTGGCTAGTGCAATTGATAAGATAGAT
AF419511        CGTGAGACAGACAAATTGGAAAATTACAATGGATTGGCTAGTGCAATTGATAAGATAGAT
AF419509        CGTGAGACAGACAAGCTGGAAAATTACAATGGATTGGCTAGTGCAATTGATAAGATAGAT
AF419507        CGTGAGGCAGATAAGCTGGAAAATTACAATGGATTGGCTAGTGCAATTGATAAGATAGAT
AF419508        CGTGAGGCAGACAAGCTGGAAAATTACAATGGATTGGCTAGTGCAATTGATAAGATAGAT
AF419504        CGTGAGGCAGACAAATTGGAAAATTACAATGGATTGGCTAGTGCAATTGATAAGATAGAT
AF419506        CGTGAGGCAGACAAATTGGAAAATTACAATGGATTGGCTAGTGCAATTGATAAGATAGAT
AF419510        CGTGAGGCAGACAAGCTGAAAAATTACAATGGATTGGCTGGTGCAATTGATAAAATAGAT
AF419505        CGTGAGGCAGACAAATTGGAAAATTACAATGGATTGGCTAGTGCAATTGATAAAATAGAT
                ****** **** **  ** ******************** ************* ******

AF419503        GGAACCAATGTGTACTGGAAAGGAAATATTCACGCTAACGGGCGTCTTTACATGACCACA
AF419511        GGAACCAATGTGTACTGGAAAGGAAATATTCACGCTAACGGGCGTCTTTATATGACCACA
AF419509        GGAACTAATGTGTACTGGAAAGGAAATATTCACGCTAACGGACGTCTTTACATGACCACA
AF419507        GGAACCAATGTGTACTGGAAAGGAAATATTCACGCTAACGGACGTTTTTACATGACCACA
AF419508        GGAACCAATGTGTACTGGAAAGGAAATATTCACGCTAACGGGCGTCTTTACATGACCACA
AF419504        GGAACCAATGTGTACTGGAAAGGAAATATTCACGCTAATGGGCGTCTTTACATGACCACA
AF419506        GGAACCAATGTGTACTGGAAAGGAAATATTCACGCTAACGGGCGTCTTTACATGACCACA
AF419510        GGAACCAATGTGTATTGGAAAGGAAATATTCACGCTAACGGGCGTCTTTACATGACCACA
AF419505        GGAACCAATGTGTACTGGAAAGGAAATATTCACGCTAACGGGCGTCTTTACATGACCACA
                ***** ******** *********************** ** *** **** *********

AF419503        AACGATTTTGACTGTGGCCAGTATCAACAGTTCTTTGGTGGTGTCACTAATCGTTACTCT
AF419511        AACGGTTTTGATTGTGGCCAGTATCAACAGTTCTTTGGTGGTGTCACTAATCGTTACTCT
AF419509        AATGATTTTGACTGTGGCCAGTATCAACAGTTCTTTGGTGGTGTCACTAATCGTTATTCT
AF419507        AACGGTTTTGACTGTGGCCAGTATCAACAGTTCTTTGGTGGTGTCACTAATCGTTACTCT
AF419508        AACGGTTTTGACTGTGGCCAGTATCAACAGTTCTTTGGTGGTGTTACTAATCGTTACTCT
AF419504        AACGATTTTGACTGTGGCCAGTATCAACAGTTCTTTGGTGGTGTCACTAATCGTTACTCT
AF419506        AACGATTTTGACTGTGGTCAGTATCAACAATTCTTTGGTGATGTTACTAATCGTTACTCT
AF419510        AACGATTTTGACTGTGGCCAGTATCAACAGTTCTTTGGTGGTGTCACTAATCGTTACTCT
AF419505        AACGATTTTGACTGTGGCCAGTATCAACAGTTCTTTGGTGGTGTCACTAATCGTTACTCT
                ** * ****** ***** *********** ********** *** *********** ***

AF419503        GTCATGGAGTGGGGAGATGAGAACGGATGGTTGATGTATGTTCAACGTAGAGAGTGGACA
AF419511        GTCATGGAATGGGGAGATGAGAATGGATGGCTGATGTATGTTCAACGTAGAGAATGGACA
AF419509        GTCATGGAGTGGGGAGATGAGAACGGATGGTTGATGTATGTTCAACGTAGAGAGTGGACA
AF419507        GTCATGGAGTGGGGAGATGAGAATGGATGGCTGATGTATGTTCAACGTAGAGAATGGACA
AF419508        GTCATGGAGTGGGGAGATGAGAACGGATGGCTGATGTATGTTCAACGTAGAGAGTGGACA
AF419504        GTCATGGAGTGGGGAGATGAGAACGGATGGTTGATGTATGTTCAACGTAGAGAGTGGACA
AF419506        GTCATGGAATGGGGAGATAAGAACGGATGGTTGATGTATGTTCAACGTAGAGAATGGACA
AF419510        GTCATGGAGTGGGGAGATGAGAACGGATGGTTGATGTATGTTCAACGTAGAGAATGGACA
AF419505        GTCATGGAGTGGGGAGATGAGAACGGATGGTTGATGTATGTTCAACGTAGAGAGTGGACA
                ******** ********* **** ****** ********************** ******

AF419503        ACAGCGATAGGCGATAACATTCAGTTAGTAGTAAACGGACAGATCATCACCCAAGGTGGA
AF419511        ACAGCGATAGGTGATAACATTCAGTTAGTAGTAAACGGACAGATCATCACCCAAGGTGGA
AF419509        ACAGCGATAGGTGATAACATTCAGTTAGTAGTAAACGGACAGATCATCACTCAAGGTGGA
AF419507        ACAGCGATAGGTGATAACATTCAGTTAGTAGTAAACGGACAGATCATCACTCAAGGTGGA
AF419508        ACAGCAATAGGCGATAACATTCAGTTAGTAGTAAACGGACAGATCATCACCCAAGGTGGA
AF419504        ACAGCGATAGGCGATAACATTCAGTTAGTAGTAAATGGACAGATCATCACCCAAGGTGGA
AF419506        ACAGCAATAGGCGATAACATTCAGTTAGTAGTAAACGGACAGATCATCACCCAAGGTGGA
AF419510        ACAGCGATAGGCAATAACATTCAGTTAGTAGTAAACGGACAGATTATCACCCAAGGTGGA
AF419505        ACAGCGATAGGCGATAACATTCAGTTAGTAGTAAACGGACAGATCATCACCCAAGGTGGA
                ***** *****  ********************** ******** ***** *********

AF419503        GCCATGACTGGTCAGCTAAAATTGCAGAATGGGCATGTTCTTCAATTAGAATCCGCATTC
AF419511        GCCATGACCGGTCAGCTAAAATTGCAGAATGGGCATGTTCTTCAATTAGAATCCGCATTC
AF419509        GCCATGACCGGTCAGCTAAAATTGCAGAATGGGCATGTTCTTCAATTAGAATCCGCATCC
AF419507        GCCATGACCGGTCAGCTAAAATTGCAGAATGGGCATGTTCTTCAATTAGAATCCGCATCC
AF419508        GCCATGACCGGTCAGCTAAAATTGCAGAATGGACATGTTCTTCAATTAGAATCCGCATCC
AF419504        GCCATGACCGGTCAGCTAAAATTGCAGAATGGGCATGTTCTTCAATTAGAATCCGCATCC
AF419506        GCCATGACCGGTCAGCTAAAATTGCAGAATGGGCATGTTCTTCAATTAGAATCCGCATCC
AF419510        GCCATGACCGGTCAGCTAAAATTGCAGAATGGGCATGTTCTTCAATTAGAATCCGCATCC
AF419505        GCCATGACCGGTCAGCTAAAATTGCAGAATGGGCATGTTCTTCAATTAGAGTCCGCATCC
                ******** *********************** ***************** ******* *

AF419503        GACAAGGCGCACTATATTCTATCTAAAGATGGTAACAGGAATAACTGGTACATTGGTAGA
AF419511        GACAAGGCGCACTATATTCTATCTAAAGATGGTAACAGGAATAACTGGTACATTGGTAGA
AF419509        GACAAAGCGCACTATATTCTATCTAAAGATGGTAACAGGAATAACTGGTACATTGGTAGA
AF419507        GACAAGGCACACTATATTCTATCTAAAGATGGTAACAGGAATAACTGGTACATTGGTAGA
AF419508        GACAAGGCGCACTATATTCTATCTAAAGATGGTAACAGGAATAACTGGTACATTGGTAGA
AF419504        GACAAGGCGCACTATATTCTATCTAAAGATGGTAACAGGAATAACTGGTACATTGGTAGA
AF419506        GACAAGGCGCACTATATTCTATCTAAAGATGGTAACAGGAATAACTGGTACATTGGTAGA
AF419510        GACAAGGCGCACTATATTTTATCTAAAGATGGTAACAGGAATAACTGGTACATTGGTAGA
AF419505        GACAAGGCACACTATATTCTATCTAAAGATGGTAACAGGAATAATTGGTACATTGGTAGA
                ***** ** ********* ************************* ***************

AF419503        GGGTCAGATAACAACAATGACTGTACTTTCCATTCTTATGTACATGGTACGACTTTAACA
AF419511        GGGTCAGATAACAACAATGACTGTACTTTCCATTCTTATGTACATGGTACGACTTTAACA
AF419509        AGGTCAGATAACAACAATGACTGTATCTTCCATTCTTATGTACATGGTACGACTTTAACA
AF419507        GGGTCAGATAACAACAATGACTGTACCTTCCATTCTTATGTACATGGTACGACCTTAACA
AF419508        GGGTCAGATAACAACAATGACTGTACTTTCCATTCTTATGTACATGGTACGACTTTAACA
AF419504        GGGTCAGATAACAACAATGACTGTACTTTCCATTCTTATGTACATGGTACGACTTTAACA
AF419506        GGATCAGATAACAACAATGACTGTACTTTCCATTCTTATGTACATGGTACGACTTTAACA
AF419510        GGGTCAAATAACAACAATGACTGTACCTTTCATTCTTATGTACATGGTACGACTTTAACA
AF419505        GGGTCAGATAACAACAATGATTGTACCTTTCATTCTTATGTACATGATACAACTTTAACA
                 * *** ************* ****  ** **************** *** ** ******

AF419503        CTCAAGCAGGACTATGCAGTAGTTAACAAACACTTCCACGTAGGTCAGGCCGTTGTGGCC
AF419511        CTCAAGCAGGACTATGCAATAGTTAACAAACACTTCCACGTAGGTCAGGCCGTTGTGGCC
AF419509        CTCAAGCAGGACTATGCAGTAGTTAACAAACACTTCCACGTAGGTCAGGCCGTTGTGGCC
AF419507        CTCAAGCAGGATTATGCAGTAGTTAACAAACATTTCCACGTAGGTCAGGCCGTTGTGGCC
AF419508        CTCAAGCAGGACTATGCAATAGTTAACAAACACTTCCACGTAGGTCAGGCCGTTGTGGCC
AF419504        CTCAAGCAGGACTATGCAGTAGTTAACAAACACTTCCACGTAGGTCAGGCCGTTGTGGCC
AF419506        CTCAAGCAGGACTATGCAGTAGTTAACAAACACTTCCACGTAGGTCAGGCCGTTGTGGCC
AF419510        CTCAAACAGGACTATGCAGTAGTTAACAAACACTTCCACGTAGGTCAGGCCGTTGTGGCC
AF419505        CTCAAGCAGGACTATGCAGTAGTTAACAAACACTTTCACGTAGGTCAGGCTGTTGTGGCC
                ***** ***** ****** ************* ** ************** *********

AF419503        ACTGATGGTAATATTCAAGGTACTAAGTGGGGAGGTAAATGGCTGGATGCTTACCTACGT
AF419511        ACTGATGGTAATATTCAAGGTACTAAATGGGGAGGTAAATGGCTGGATGCTTACTTACGT
AF419509        ACTGATGGTAATATTCAAGGTACTAAGTGGGGAGGTAAATGGCTGGATGCTTACCTACGT
AF419507        ACTGATGGTAATATTCAAGGTACTAAGTGGGAAGGTAAATGGTTGGATGTTTACCTACGT
AF419508        ACTGATGGTAATATTCAAGGTACTAAGTGGGAAGGTAAATGGCTGGATGTTTACCTACGT
AF419504        ACTGATGGTAATATTCAAGGTACTAAGTGGGGAGGTAAATGGCTGGATGCTTATCTACGT
AF419506        ACTGATGGTAATATTCAAGGTACTAAGTGGGGAGGTAAATGGCTGGATGCTTACCTACGT
AF419510        ACTGATGGTAATATTCAAGGTACTAAGTGGGGAGATAAATGGCTGGATGCTTACCTACGT
AF419505        ACTGATGGTAATATTCAAGGTACTAAGTGGGAAGGTAAATGGTTGGATGCTTATCTACGT
                ************************** **** ** ******* ****** ***  *****

AF419503        GACAGCTTCGTTGCAAAGTCCAAAACGTGGACTCAGGTGTGGTCTGGTAGAGCTGGCGGT
AF419511        GACAGCTTCGTTGCAAAGTCCAAAACGTGGACTCAGGTGTGGTCTGGTAGAGCTGGCGGT
AF419509        GACAGCTTCGTTGCAAAGTCCAAAACGTGGACTCAGGTGTGGTCTGGTAGAGCTGGCGGT
AF419507        GATAGCTTCATTGCAAAGTCCAAGACATGGACTCAGGTGTGGTCTGGTAGGGCTGGCGGT
AF419508        GACAACTTCGTTGCAAAGTCCAAAACGTGGACTCAGGTGTGGTCTGGTAGGGCTGGCGGT
AF419504        GACAGCTTCGTTGCAAAGTCCAAAACGTGGACTCAGGTGTGGTCTGGTAGGGCTGGCGGT
AF419506        GACAGCTTCGTTGCAAAGTCCAAGACGTGGACTCAGGTGTGGTCTGGTAGGGCTGGCGGT
AF419510        GACAGCTTCGTTGCAAAGTCCAAAACGTGGACTCAGGTGTGGTCTGGTAGAGCTGGCGGT
AF419505        GACAATTTCGTTGCGAAGTCCAAGGCGTGGACTCAAGTGTGGTCTGGTAGGGCTGGCGGT
                ** *  *** **** ********  * ******** ************** *********

AF419503        GGGGTAAGTGTGACTGTTTCACAGGATCTCCGCTTCCGCAATATCTGGATTAAGTGTGCC
AF419511        GGGGTAAGTGTGACTGTTTCACAGGATCTCCGCTTCCGCAATATCTGGATTAAGTGTGCC
AF419509        GGGGTAAGTGTGACTGTTTCACAGGATCTCCGCTTCCGCAATATCTGGATTAAGTGTGCC
AF419507        GGGGTAAGTGTGACTGTTTCACAGGATCTCCGTTTCCGCAATATCTGGATTAAGTGTGCC
AF419508        GGGATAAGTGTGACTGTTTCACAGGATCTCCGCTTCCGCAATATCTGGATTAAGTGTGCC
AF419504        GGGGTAAGTGTGACTGTTTCACAGGATCTCCGTTTCCGCAATATCTGGATTAAGTGTGCC
AF419506        GGGGTAAGTGTGACTGTTTCACAGGATCTCCGCTTTCGCAATATCTGGATTAAGTGTGCC
AF419510        GGGGTAAGTGTGACTGTTTCACAGGATCTCCGCTTCCGCAATATCTGGATTAAGTGTGCC
AF419505        GGGGTAAGTGTGACTGTTTCACAGGATCTCCGCTTCCGCAATATCTGGATTAAGTGTGCC
                *** **************************** ** ************************

AF419503        AACAATTCTTGGAACTTCTTTCGTACTGGCCCCGATGGAATTTATTTCATAGCCTCTGAT
AF419511        AACAACTCTTGGAACTTCTTTCGTACTGGCCCCGATGGAATTTACTTCATAGCCTCTGAT
AF419509        AACAATTCTTGGAACTTCTTTCGTACTGGCCCCGATGGAATTTACTTCATAGCCTCTGAT
AF419507        AACAACTCTTGGAACTTCTTTCGTACTGGCCCCGATGGAATTTACTTCATAGCCTCTGAT
AF419508        AACAACTCTTGGAACTTCTTTCGTACTGGCCCCGATGGAATTTACTTCATAGCCTCTGAT
AF419504        AACAACTCTTGGAACTTCTTCCGTACTGGTCCCGATGGAATCTACTTCATAGCCTCTGAT
AF419506        AACAACTCTTGGAACTTCTTTCGTACTGGCCCCGATGGAATCTACTTCATAGCTTCTGAT
AF419510        AACAATTCTTGGAACTTCTTTCGTACTGGCCCCGATGGAATTTACTTCATAGCCTCTGAT
AF419505        AACAATTCTTGGAACTTCTTCCGTACTGGCCCCGATGGAATCTACTTCATAGCCTCTGAT
                ***** ************** ******** *********** ** ******** ******

AF419503        GGTGGATGGTTACGATTCCAAATACACTCCAACGGTCTCGGATTCAAGAATATTGCAGAC
AF419511        GGTGGATGGTTACGATTCCAAATACATTCCAACGGTCTCGGATTTAAGAATATTGCAGAC
AF419509        GGTGGATGGTTACGATTTCAAATACACTCCAACGGTCTCGGATTCAAGAATATTGCAGAC
AF419507        GGTGGATGGTTACGATTTCAAATACACTCCAACGGTCTCGGATTCAAGAATATTGCAGAC
AF419508        GGTGGATGGTTACGATTTCAAATACACTCCAACGGTCTCGGATTCAAGAATATTGCAGAC
AF419504        GGTGGATGGTTACGATTCCAAATACATTCCAACGGTCTCGGATTCAAGAATATTGCAGAC
AF419506        GGTGGATGGTTACGATTCCAAATACACTCCAACGGTCTCGGATTCAAGAATATTGCAGAC
AF419510        GGTGGATGGTTACGATTTCAAATACACTCCAACGGTCTCGGATTCAAGAATATTGCAGAC
AF419505        GGTGGATGGTTACGATTCCAAATACACTCCAACGGTTTTGGATTTAAGAATATTGCAGAC
                ***************** ******** ********* * ***** ***************

AF419503        AGTCATTCAGTACCTAATGCAATCATGGTGGAGAACGAGTAA
AF419511        AGGCATTCAGTACCTAATGCAATCATGGTGGAAAACGAGTAA
AF419509        AGTCATTCAGTACCTAATGCAATCATGGTGGAAAACGAGTAA
AF419507        AGTCATTCAGTACCTAATGCAATCATGGTGGAGAACGAGTAA
AF419508        AGTCATTCAGTACCTAATGCAATCATGGTGGAAAACGAGTAA
AF419504        AGTCATTCAGTACCTAATGCAATCATGGTGGAGAACGAGTAA
AF419506        AGTCATTCAGTACCTAATGCAATCATGGTGGAGAACGAGTAA
AF419510        AGTCATTCAGTACCTAATGCAATCATGGTGGAGAACGAGTAA
AF419505        AGTCATTCAGTACCTAATGCAATCATGGTGGAGAACGAGTAA
                ** ***************************** *********
BioPerl-1.007002/t/data/Treebase-chlamy-dna.nex000444000766000024      3461713155576321 21204 0ustar00cjfieldsstaff000000000000#NEXUS
[File created by TreeBASE:  12/13/00  11:58:39]
[Matrix accession#: M809]
BEGIN DATA;
DIMENSIONS  NTAX=14 NCHAR=629;

[!This data set was downloaded from TreeBASE, a prototype relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, and UC Davis. Please do not remove this acknowledgment from the Nexus file. 
TreeBASE © 1994-2000.

Study reference: 
Coleman, A. W., L. Jaenicke, and R. C. Starr. 2001. Genetics and sexual behavior of the pheromone producer, Chlamydomonas allensworthii (Chlorophyceae). J. Phycology 37, in press.

Study accession number = S549
Matrix accession number = M809
]
FORMAT DATATYPE = DNA MISSING = - GAP = # INTERLEAVE  ;
MATRIX

'Chlamydomonas_reinhardtii_Crein'         AATCTATCACAATCCACACCGCGAACTAACACTGTTGGCCTCCGTCTGTG-TAAAAGCA-----AACGGGCCAGGTCTGGGCGCAATGTAAAAGTTACGC
'Chlamydomonas_allensworthii_Cat'         AATCTATCAATACCAACACCGAGAACCGATTCGTCTGACC-CCGTC-GTGGCGCAAGCG---ACGACGG-CGCTTGCCGATCCG----TAAATT-CGGAT
'Chlamydomonas_allensworthii_21A'         AATCTATCAATACCAACACCGAGAACCAATTCGTCTGACC-CCGTC-GTGGCGCAAGCG---ACGACGG-CGCTTGCCGATCCG----TTTATT-CTGAT
'Chlamydomonas_allensworthii_Neb'         AATCTATCAATACCAACACCGAGAACCGATTCGTCTGACC-CCGTC-GTGGCGCAAGCG---ACGACGG-CGCTTGCCGTTCCG----TTTATT-CGGAT
'Chlamydomonas_allensworthii_Hon2'        AATCTATCAATACCAACACCGAGAACCGATTCGTCTGACC-CCGTC-GTGGCGCAAGCG---ACGACGG-CGCTTGCCGATCCG----TTTATT-CGGAT
'Chlamydomonas_allensworthii_Hon9'        AATCTATCAATACCAACACCGAGAACCAATTCGTCTGACC-CTGTT-GATGCGCAAGCA---GCAACGG-CGCTTGCCGATGCG----TTAACT-CGGGT
'Chlamydomonas_allensworthii_Chile'       AATCTATCAATAACAACACCGAGAACCATTTCGTCTGACC-CT-TTATAAGCCTTTGGGTTTATAACGG-CGCCTGTTGTTTGG----TTAATT-CCAAG
'Chlamydomonas_allensworthii_Flam'        AATCTATCAATAACAACACCGAGAACCATTTCGTCTGACC-CT-TTATAAGCCTTTGGGTTTATAACGG-CGCCTGTTGTTTGG----TTAATT-CCAAG
'Chlamydomonas_allensworthii_88.10'       AATCTATCAATAACAACACCGAGAACCATTTCGTCTGACC-CTTTTATAAGCCTTTGGGTTTATAACGG-CGCCTGTTGTTTGG----TTAATT-CCAAG
'Chlamydomonas_allensworthii_266'         AATCTATCAATAACAACACCGAGAACCATTTCGTCTGACC-CTTTTATAAGCCTTTGGGTTTATAACGG-CGCCTGTTGTTTGG----TTAATT-CCAAG
'Chlamydomonas_allensworthii_Krueger'     AATCTATCAATAACAACACCGAGAACCATTTCGTCTGACC-CTTTTATAAAC-TTCGGGTTTATAACGG-CGCCTGTTGTTTGG----TTAATT-CTAAG
'Chlamydomonas_allensworthii_LCA'         AATCTATCAATACCAACACCGAGAACCATTTCGTCTGACC-CTCCTAT--GCTTTCGGG--TATAGAAG-CGCTCGGAGCCTAG----TTAATT-CTAAG
'Chlamydomonas_allensworthii_LCH'         AATCTATCAATACCAACACCGAGAACCATTTCGTCTGACC-CTTCTAT--GCTTTCGGG--TATAGAGG-CGCTCGTTGCCTAG----TTAATT-CTAAG
'Chlamydomonas_allensworthii_LCN'         AATCTATCAATACCAACACCGAGAACCATTTCGTCTGACC-CTTCTAT--GCTTTCGGG--TATAGAGG-CGCTTGGAGCCTAG----TTAATT-CTAAG


'Chlamydomonas_reinhardtii_Crein'         CTGGCCTGGGT------TGCCGCAA------GGCATCGGTCTCTTATACTAACCAACCAACACCAAACCAAAACTAAATTAAAACCGAGTATCTAGCTTA
'Chlamydomonas_allensworthii_Cat'         CGGCGATCGGGCTCCGGGGCCTCAAAACCCTAGGGTCGGTCTCT----GTCCAACAACAACACCAAACCAATACCTCTAACTAAAC-TGCATTCGGCTC-
'Chlamydomonas_allensworthii_21A'         CGGCGATCGGGCTCCGGGGCCTCAAAACCCTAGGGTCGGTCTCT----GTCCAACAACAACACCAAACCAATACCTCTAACTAAAC-TGCATTCGGCTC-
'Chlamydomonas_allensworthii_Neb'         CGGCGATCGGGCTCCGGGGCCTCAAAACCCTAGGGTCGGTCTAT----GTCCAACAACAACACCAAACCAATACCTCTAACTAAAC-TGCATTCGGCTC-
'Chlamydomonas_allensworthii_Hon2'        CGGCGATCGGGCTCCGGGGCCTCAAAACCCTAGGGTCGGTCTAT----GTCCAACAACAACACCAAACCAATACCTCTAACTAAAC-TGCATTCGGCTC-
'Chlamydomonas_allensworthii_Hon9'        CGGTGATCGGGCTCTAGGGCTTAACAACCCTAGGGTCGGTCCCT----GTCCAACAACAACACCAAACCAATACCTCTAACTAAAC-TGCATTCGGCTC-
'Chlamydomonas_allensworthii_Chile'       CACCAGGTGGGCTC---GGCTT-------GCCGAGTTGGTCTCT----GTCCAACAACAACACCAAACCAATAATTCTAATTATCC-TGCATTCGGCAT-
'Chlamydomonas_allensworthii_Flam'        CACCAGGTGGGCTC---GGCTT-------GCCGAGTTGGTCTCT----GTCCAACAACAACACCAAACCAATAATTCTAATTATCC-TGCATTCGGCAT-
'Chlamydomonas_allensworthii_88.10'       CACCAGGTGGGCTC---GGCTT-------GCCGAGTTGGTCTCT----GTCCAACAACAACACCAAACCAATAATTCTAATTATCC-TGCATTCGGCAT-
'Chlamydomonas_allensworthii_266'         CACCAGGTGGGCTC---GGCTT-------GCCGAGTTGGTCTCT----GTCCAACAACAACACCAAACCAATAATTCTAATTATCC-TGCATTCGGCAT-
'Chlamydomonas_allensworthii_Krueger'     CACCAGGTGGGCTC---GGCTT-------GCCGAGTTGGTCTCT----GTCCAACAACAACACCAAACCAATAATTCTAATTATCC-TGCATTCGGCAT-
'Chlamydomonas_allensworthii_LCA'         CTCCGGGTGGGCTC---GGCTTC-----GGCTGGGTTGGTTCCT----GTCCAACAACAACACCAAACAAATAATTCTAAATAATC-TGCATTCGGCA--
'Chlamydomonas_allensworthii_LCH'         CTCCGGGTGGGCTC---AGCTTC-----GGCTGGGTTGGTTCTT----GTCCAACAACAACACCAAACAAATAATTCTAAATAATC-TGCATTCGGCA--
'Chlamydomonas_allensworthii_LCN'         CTCCGGGTGGGCTC---GGCTTC-----GGCTGGGTTGGTCCTT----GTCCAACAACAACACCAAACAAATAATTCTAAATAATC-TGCATTCGGCA--


'Chlamydomonas_reinhardtii_Crein'         GAGCTAGTGCTCACTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGGATCGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGC
'Chlamydomonas_allensworthii_Cat'         -AGCCGGTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGC
'Chlamydomonas_allensworthii_21A'         -AGCCGGTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGC
'Chlamydomonas_allensworthii_Neb'         -AGCCGGTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGC
'Chlamydomonas_allensworthii_Hon2'        -AGCCGGTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGC
'Chlamydomonas_allensworthii_Hon9'        -AGCCGGTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGC
'Chlamydomonas_allensworthii_Chile'       -AGCCGATGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGC
'Chlamydomonas_allensworthii_Flam'        -AGCCGATGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGC
'Chlamydomonas_allensworthii_88.10'       -AGCCGATGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGC
'Chlamydomonas_allensworthii_266'         -AGCCGATGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGC
'Chlamydomonas_allensworthii_Krueger'     -AGCCGATGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGC
'Chlamydomonas_allensworthii_LCA'         -ATCGGCTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGC
'Chlamydomonas_allensworthii_LCH'         -ATCGGCTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGC
'Chlamydomonas_allensworthii_LCN'         -ATCGGCTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGC


'Chlamydomonas_reinhardtii_Crein'         AGAAATACGTGAATCATCGAATCTTTGAACGCATATTGCGCTCGAGGCTTCGGCCAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCCCTA-CT
'Chlamydomonas_allensworthii_Cat'         AGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATT
'Chlamydomonas_allensworthii_21A'         AGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATT
'Chlamydomonas_allensworthii_Neb'         AGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATT
'Chlamydomonas_allensworthii_Hon2'        AGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATT
'Chlamydomonas_allensworthii_Hon9'        AGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATT
'Chlamydomonas_allensworthii_Chile'       AGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATT
'Chlamydomonas_allensworthii_Flam'        AGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATT
'Chlamydomonas_allensworthii_88.10'       AGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATT
'Chlamydomonas_allensworthii_266'         AGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATT
'Chlamydomonas_allensworthii_Krueger'     AGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATT
'Chlamydomonas_allensworthii_LCA'         AGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATA
'Chlamydomonas_allensworthii_LCH'         AGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATT
'Chlamydomonas_allensworthii_LCN'         AGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATA


'Chlamydomonas_reinhardtii_Crein'         CCAACATACACTTGTGTGTTTGGAGCAAGAGCGGACCTGGCTGTCTCGGTGTTTGATTTTCGGATCAGACGCCGGGTCAGCTGAAGTACAGAGGTTGATG
'Chlamydomonas_allensworthii_Cat'         CCACA--------------------TTGGAACGGATCTGGCAGTCTCAGTCTGC------------AAAGACTGGGTCTGCTGAAGTGCAGAGGTTGATG
'Chlamydomonas_allensworthii_21A'         CCACA--------------------TTGGAACGGATCTGGCAGTCTCAGTTTGC------------AAAGACTGGGTCTGCTGAAGTGCAGAGGTTGATG
'Chlamydomonas_allensworthii_Neb'         CCACA--------------------TTGGAACGGATCTGGCAGTCTCAGTTTGC------------AAAGACTGGGTCTGCTGAAGTGCAGAGGTTGATG
'Chlamydomonas_allensworthii_Hon2'        CCACA--------------------TTGGAACGGATCTGGCAGTCTCAGTTTGC------------AAAAACTGGGTCTGCTGAAGTGCAGAGGTTGATG
'Chlamydomonas_allensworthii_Hon9'        CCACA--------------------TTGGAACGGATCTGGCAGTCTCGGTTTGC------------AAAAACCGGGTCTGCTGAAGTGCAGAGGTTGATG
'Chlamydomonas_allensworthii_Chile'       CCCCAA-------------------TTGGAACGGATCTGGCAGTCTCAGCTTTTTC--------AATAGAGCTGGGCCTGCTGAAGTGCAGAGGTTGATG
'Chlamydomonas_allensworthii_Flam'        CCCCAA-------------------TTGGAACGGATCTGGCAGTCTCAGCTTTTTC--------AATAGAGCTGGGTCTGCTGAAGTGCAGAGGTTGATG
'Chlamydomonas_allensworthii_88.10'       CCCCAA-------------------TTGGATCGGATCTGGCAGTCTCAGCTTTTTC--------AATAGAGCTGGGTCTGCTGAAGTGCAGAGGTTGATG
'Chlamydomonas_allensworthii_266'         CCCCAA-------------------TTGGAACGGATCTGGCAGTCTCAGCTTTTTC--------AATAGAGCTGGGTCTGCTGAAGTGCAGAGGTTGATG
'Chlamydomonas_allensworthii_Krueger'     CCCCAA-------------------TTGGAACGGATCTGGCAGTCTCAGCTTTTTC--------AATAGAGCTGGGTCTGCTGAAGTGCAGAGGTTGATG
'Chlamydomonas_allensworthii_LCA'         CCACA--------------------TTGGAACGGACCTGGCAGTCTCAGTTCTTTG--------ATTAGAGCTGGGTCTGCTGAAGTGCAGAGATTGATG
'Chlamydomonas_allensworthii_LCH'         CCACA--------------------TTGGAACGGACCTGGCAGTCTCAGTTCTTTT--------AATAGAGCTGGGTCTGCTGAAGTGCAGAGATTGATG
'Chlamydomonas_allensworthii_LCN'         CCACA--------------------TTGGAACGGACCTGGCAGTCTCAGTTCTTTG--------ATTAGAGCTGGGTCTGCTGAAGTGCAGAGATTGATG


'Chlamydomonas_reinhardtii_Crein'         CATGGACCCGCTTATGGGCCTCTACTGGGTAGGCAACTCGTTGCTAATGCTTTAGTAGATGGCTTGGAGCTGTGCTTGTCGACCCAAACCAGGAACTTTG
'Chlamydomonas_allensworthii_Cat'         TA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACT-
'Chlamydomonas_allensworthii_21A'         TA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACC-
'Chlamydomonas_allensworthii_Neb'         TA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACT-
'Chlamydomonas_allensworthii_Hon2'        TA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACT-
'Chlamydomonas_allensworthii_Hon9'        TA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACA-
'Chlamydomonas_allensworthii_Chile'       TA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACC-
'Chlamydomonas_allensworthii_Flam'        TA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACC-
'Chlamydomonas_allensworthii_88.10'       TA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACC-
'Chlamydomonas_allensworthii_266'         TA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACC-
'Chlamydomonas_allensworthii_Krueger'     TA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACC-
'Chlamydomonas_allensworthii_LCA'         TA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGATCCTCAACAGGAAAAC--
'Chlamydomonas_allensworthii_LCH'         TA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGATCCTCAACAGGAAAAC--
'Chlamydomonas_allensworthii_LCN'         TA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGATCCTCAACAGGAAAAC--


'Chlamydomonas_reinhardtii_Crein'         GCCCTGTGCCGAAGCAAACCCCTATTTTC
'Chlamydomonas_allensworthii_Cat'         ---------------ATTAACCTATTTTC
'Chlamydomonas_allensworthii_21A'         ---------------ATTAACCTATTTTC
'Chlamydomonas_allensworthii_Neb'         ---------------ATTAACCTATTTTC
'Chlamydomonas_allensworthii_Hon2'        ---------------ATTAACCTATTTTC
'Chlamydomonas_allensworthii_Hon9'        ---------------ATTAACCTATTTTC
'Chlamydomonas_allensworthii_Chile'       ---------------ATTAACCTATTTTC
'Chlamydomonas_allensworthii_Flam'        ---------------ATTAACCTATTTTC
'Chlamydomonas_allensworthii_88.10'       ---------------ATTAACCTATTTTC
'Chlamydomonas_allensworthii_266'         ---------------ATTAACCTATTTTC
'Chlamydomonas_allensworthii_Krueger'     ---------------ATTAACCTATTTTC
'Chlamydomonas_allensworthii_LCA'         ---------------ATTAACCTATTTTC
'Chlamydomonas_allensworthii_LCH'         ---------------ATTAACCTATTTTC
'Chlamydomonas_allensworthii_LCN'         ---------------ATTAACCTATTTTC
;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions = 
 N: 1 - 629 ; 
 CODESET * UNTITLED = Universal: all ; 
 END;
BEGIN ASSUMPTIONS;
OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; 
 END;
BEGIN TREEBASE;
END;

BEGIN TREES;

[! 1 trees. TreeBASE accession#: Tree1641 ]
	TRANSLATE
		1	'Chlamydomonas_allensworthii_Krueger',
		2	'Chlamydomonas_allensworthii_88.10',
		3	'Chlamydomonas_allensworthii_Chile',
		4	'Chlamydomonas_allensworthii_Flam',
		5	'Chlamydomonas_allensworthii_Hon9',
		6	'Chlamydomonas_allensworthii_Hon2',
		7	'Chlamydomonas_allensworthii_LCN',
		8	'Chlamydomonas_allensworthii_LCH',
		9	'Chlamydomonas_allensworthii_LCA',
		10	'Chlamydomonas_allensworthii_266',
		11	'Chlamydomonas_allensworthii_Neb',
		12	'Chlamydomonas_allensworthii_21A',
		13	'Chlamydomonas_allensworthii_Cat',
		14	'Chlamydomonas_reinhardtii_Crein',
		15	'Chlamydomonas_allensworthii',
		16	'Chlamydomonas',
	;
	TREE 'Fig._2' =  [&R] (((((7,9),8),(1,(10,2,4,3))),(5,((6,11),12,13))),14);


END;
BioPerl-1.007002/t/data/U58726.gb000444000766000024     20014013155576321 16057 0ustar00cjfieldsstaff000000000000LOCUS       U58726                 31931 bp    DNA     linear   INV 29-APR-2011
DEFINITION  Caenorhabditis elegans cosmid T01C8, complete sequence.
ACCESSION   U58726
VERSION     U58726.1  GI:1326250
KEYWORDS    HTG.
SOURCE      Caenorhabditis elegans
  ORGANISM  Caenorhabditis elegans
            Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida;
            Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis.
REFERENCE   1  (bases 1 to 31931)
  CONSRTM   C. elegans Sequencing Consortium
  TITLE     Genome sequence of the nematode C. elegans: a platform for
            investigating biology
  JOURNAL   Science 282 (5396), 2012-2018 (1998)
   PUBMED   9851916
  REMARK    Erratum:[Science 1999 Jan 1;283(5398):35]
REFERENCE   2  (bases 1 to 31931)
  AUTHORS   Wohldmann,P. and Hawkins,J.
  TITLE     The sequence of C. elegans cosmid T01C8
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 31931)
  AUTHORS   Waterston,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-MAY-1996) Robert Waterston
REFERENCE   4  (bases 1 to 31931)
  AUTHORS   Waterston,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-JUL-2001) Department of Genetics, Washington
            University, Genome Sequencing Center, 4444 Forest Park Avenue, St.
            Louis, MO 63110, USA
REFERENCE   5  (bases 1 to 31931)
  AUTHORS   Waterston,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-MAY-2002) Department of Genetics, Washington
            University, Genome Sequencing Center, 4444 Forest Park Avenue, St.
            Louis, MO 63110, USA
REFERENCE   6  (bases 1 to 31931)
  AUTHORS   Waterston,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-JUN-2002) Department of Genetics, Washington
            University, Genome Sequencing Center, 4444 Forest Park Avenue, St.
            Louis, MO 63110, USA
REFERENCE   7  (bases 1 to 31931)
  AUTHORS   Waterston,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-NOV-2002) Department of Genetics, Washington
            University, Genome Sequencing Center, 4444 Forest Park Avenue, St.
            Louis, MO 63110, USA
REFERENCE   8  (bases 1 to 31931)
  AUTHORS   Waterston,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-NOV-2002) Department of Genetics, Washington
            University, Genome Sequencing Center, 4444 Forest Park Avenue, St.
            Louis, MO 63110, USA
REFERENCE   9  (bases 1 to 31931)
  AUTHORS   Waterston,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-APR-2003) Department of Genetics, Washington
            University, Genome Sequencing Center, 4444 Forest Park Avenue, St.
            Louis, MO 63110, USA
REFERENCE   10 (bases 1 to 31931)
  CONSRTM   WormBase Consortium
  TITLE     Direct Submission
  JOURNAL   Submitted (21-SEP-2004) Department of Genetics, Washington
            University, Genome Sequencing Center, 4444 Forest Park Avenue, St.
            Louis, MO 63110, USA
REFERENCE   11 (bases 1 to 31931)
  CONSRTM   WormBase Consortium
  TITLE     Direct Submission
  JOURNAL   Submitted (10-SEP-2005) Department of Genetics, Washington
            University, Genome Sequencing Center, 4444 Forest Park Avenue, St.
            Louis, MO 63110, USA
REFERENCE   12 (bases 1 to 31931)
  CONSRTM   WormBase Consortium
  TITLE     Direct Submission
  JOURNAL   Submitted (06-MAY-2006) Department of Genetics, Washington
            University, Genome Sequencing Center, 4444 Forest Park Avenue, St.
            Louis, MO 63110, USA
REFERENCE   13 (bases 1 to 31931)
  CONSRTM   WormBase Consortium
  TITLE     Direct Submission
  JOURNAL   Submitted (29-APR-2011) Department of Genetics, Washington
            University, Genome Sequencing Center, 4444 Forest Park Avenue, St.
            Louis, MO 63110, USA
COMMENT     [WARNING] On Oct 13, 2011 this sequence was replaced by
            gi:351061076.
            Submitted by:
                   Genome Sequencing Center
                   Department of Genetics, Washington University
                   St. Louis , MO  63110, USA, and
                   Sanger Centre, Hinxton Hall
                   Cambridge CB10 IRQ, England
                   email: stlouis@wormbase.org and sanger@wormbase.org
            
            NOTICE:  This sequence may not be the entire insert of this clone.
            It may be shorter because we only sequence overlapping sections
            once, or longer because we provide a small overlap between
            neighboring submissions.
            
            This sequence was finished as follows unless otherwise noted: all
            regions were double stranded, sequenced with an alternate chemistry
            or covered by high quality data (i.e., phred quality >= 30); an
            attempt was made to resolve all sequencing problems, such as
            compressions and repeats; all regions were covered by sequence from
            more than one m13 subclone.
            
            For a graphical representation of this clone sequence and its
            analysis see:
            http://www.wormbase.org/db/seq/sequence?name=T01C8
            
                        NEIGHBORING CLONE INFORMATION
            
            The 5' clone is EGAP8, 200 bp overlap; the 3' clone is F41G4, 2000
            bp overlap. Actual start of this clone is at base position 1 of
            T01C8; actual end is at 10488 of F41G4.
            
            NOTES:
            
            Coding seqences below are the result of integration and manual
            review of the following data : computer analysis using the program
            Genefinder (P. Green and L. Hillier, personal communication), the
            large scale EST projects of Yuji Kohara
            (http://www.ddbj.nig.ac.jp/c-elegans/html/CE_INDEX.html) and The C.
            elegans ORFeome cloning project (http://worfdb.dfci.harvard.edu/),
            similarity to other proteins from BlastX analyses
            (http://blast.wustl.edu/), sequence conservation with C. briggsae
            using Jim Kent's WABA alignment program (Genome Research
            10:1115-1125, 2000), individual C. elegans GenBank submissions,
            and personal communications with C. elegans researchers. tRNAs
            are predicted using the program tRNAscan-SE (Lowe, T.M. and
            Eddy, S.R., 1997, Nucl. Acids. Res., 25, 955-964).
FEATURES             Location/Qualifiers
     source          1..31931
                     /organism="Caenorhabditis elegans"
                     /mol_type="genomic DNA"
                     /strain="Bristol N2"
                     /db_xref="taxon:6239"
                     /chromosome="X"
                     /clone="T01C8"
     gene            1698..1819
                     /locus_tag="T01C8.8"
                     /db_xref="WormBase:WBGene00196318"
     ncRNA           1698..1819
                     /locus_tag="T01C8.8"
                     /ncRNA_class="other"
                     /product="T01C8.8"
                     /db_xref="WormBase:T01C8.8"
                     /db_xref="WormBase:WBGene00196318"
     gene            complement(5778..7678)
                     /locus_tag="T01C8.3"
                     /db_xref="WormBase:WBGene00020144"
     CDS             complement(join(5778..5951,5996..6076,6123..6219,
                     6268..6317,6359..6509,6555..6631,7562..7678))
                     /locus_tag="T01C8.3"
                     /standard_name="T01C8.3"
                     /note="contains similarity to Paramecium tetraurelia
                     Chromosome undetermined scaffold_129, whole genome shotgun
                     sequence.; TR:A0BUB6; coded for by the following C.
                     elegans cDNAs: FM864997"
                     /codon_start=1
                     /product="Hypothetical protein T01C8.3"
                     /protein_id="AAB00575.3"
                     /db_xref="GI:331028906"
                     /db_xref="WormBase:T01C8.3"
                     /db_xref="WormBase:WBGene00020144"
                     /translation="MQLLENCNFRCTNCTGDYCYAVNYKHLNPSLKNEQSYYQGCFTS
                     PTDLPLGCSTNSRGSIFCICNSTDYCNEMTNVKEEKNITYLICEYAKDSMFRGADCVQ
                     PWCVKTASSYMDEMVECGEGTYEMEMYDIGFVYSGMLLPINSCYAVADDSRYDKSQIC
                     TYKVNKTTPYKLKVPGSTKCFAPGEVMTRMKNSTCIGQFCYSASAVFGCISQFNREGA
                     ILKVTIFHFEILNKNNNICLTIRNFCKKKL"
     misc_feature    11227..11228
                     /note="SL1 trans-splice acceptor; see yk1591b07.5"
     misc_feature    11227..11228
                     /note="SL2 defined by RNASeq short reads (Hillier et al.);
                     see RNASeq_Hillier.dauer_daf-2"
     gene            11238..12262
                     /locus_tag="T01C8.2"
                     /db_xref="WormBase:WBGene00020143"
     CDS             join(11238..11384,12167..12262)
                     /locus_tag="T01C8.2"
                     /standard_name="T01C8.2"
                     /note="contains similarity to Escherichia coli Type 4
                     prepilin-like proteins leader peptide-processing
                     enzymes[Includes: Leader peptidase (EC 3.4.23.43)
                     (Prepilin peptidase); N-smethyltransferase (EC 2.1.1.-)].;
                     SW:P25960; coded for by the following C. elegans cDNAs:
                     OSTF201H6_1, OSTR201H6_1, yk725a4.3, yk1428d07.3,
                     yk1428d07.5, yk1591b07.3, yk1591b07.5,
                     MM454_FPK17YK01E1TJO"
                     /codon_start=1
                     /product="Hypothetical protein T01C8.2"
                     /protein_id="AAB00576.1"
                     /db_xref="GI:1326252"
                     /db_xref="WormBase:T01C8.2"
                     /db_xref="WormBase:WBGene00020143"
                     /translation="MPKQEFNPLDYTGPLIVGAIFCVFLFVISFFVINFFCITKYDDI
                     TKFELMGGKYGWRLGPHPLIVVKKGGFVAEEEVDDA"
     gene            complement(12416..13336)
                     /locus_tag="T01C8.4"
                     /db_xref="WormBase:WBGene00020145"
     CDS             complement(join(12416..12555,12785..13093,13138..13336))
                     /locus_tag="T01C8.4"
                     /standard_name="T01C8.4"
                     /note="contains similarity to Pfam domain PF00155
                     (Aminotransferase class I and II); coded for by the
                     following C. elegans cDNAs: FN888767, FN888768, FN888770,
                     FM864682"
                     /codon_start=1
                     /product="Hypothetical protein T01C8.4"
                     /protein_id="AAB00577.2"
                     /db_xref="GI:331028907"
                     /db_xref="WormBase:T01C8.4"
                     /db_xref="WormBase:WBGene00020145"
                     /translation="MDPTREQWIQMAQVIKQKNLFTFFHIADQGLASGDADADAWAVR
                     FFVEQGLEMIVSQSFSKNFGLYNDRVGSLTVIVNKPSHIANLKSQLTLVNVSNFSNPP
                     AYGARIVHEILKSPKYREQWQNSIKMMAFRIKKTRQELIRELNMLQTSGKWDRITQQS
                     GLFSYTGLTPCQVDHLIAHHKIYLLSDGRINICGLNMSNLDYVARAIDDTVRTIH"
     gene            complement(16309..17896)
                     /locus_tag="T01C8.5"
                     /db_xref="WormBase:WBGene00020146"
     CDS             complement(join(16309..16457,16507..16815,16863..17233,
                     17499..17896))
                     /locus_tag="T01C8.5"
                     /standard_name="T01C8.5"
                     /note="contains similarity to Pfam domain PF00155
                     (Aminotransferase class I and II); coded for by the
                     following C. elegans cDNAs: OSTR040A9_1, OSTR040A9_2,
                     yk204c10.5, yk327b7.3, yk327b7.5, yk468h3.5, yk503d6.3,
                     yk503d6.5, yk512b9.3, yk512b9.5, yk597a11.3, yk597a11.5,
                     yk829h10.3, yk829h10.5, yk899e07.3, yk1020c11.5,
                     yk1023a07.3, yk1023a07.5, yk1070e06.3, yk1070e06.5,
                     yk1318d04.3, yk1318d04.5, cm20g8.5, yk1400g10.3,
                     yk1400g10.5, yk1444g09.3, yk1444g09.5, yk1452e06.3,
                     yk1452e06.5, yk1471h11.3, yk1471h11.5, yk1500a04.3,
                     yk1546b06.3, yk1546b06.5, yk1560g10.5, yk1611e03.3,
                     yk1611e03.5, yk1613g08.3, yk1630a11.5, yk1672d12.3,
                     yk1672d12.5, yk1675b02.3, yk1675b02.5, yk1755e02.3,
                     yk1755e02.5, yk899b12.3, yk899b12.5, EC036254, EC029162,
                     MM454_contig05811, FN906088, FN906090, FN906089, FN906091"
                     /codon_start=1
                     /product="Hypothetical protein T01C8.5"
                     /protein_id="AAB00578.1"
                     /db_xref="GI:1326254"
                     /db_xref="WormBase:T01C8.5"
                     /db_xref="WormBase:WBGene00020146"
                     /translation="MSFFDGIPVAPPIEVFHKNKMYLDETAPVKVNLTIGAYRTEEGQ
                     PWVLPVVHETEVEIANDTSLNHEYLPVLGHEGFRKAATELVLGAESPAIKEERSFGVQ
                     CLSGTGALRAGAEFLASVCNMKTVYVSNPTWGNHKLVFKKAGFTTVADYTFWDYDNKR
                     VHIEKFLSDLESAPEKSVIILHGCAHNPTGMDPTQEQWKLVAEVIKRKNLFTFFDIAY
                     QGFASGDPAADAWAIRYFVDQGMEMVVSQSFAKNFGLYNERVGNLTVVVNNPAVIAGF
                     QSQMSLVIRANWSNPPAHGARIVHKVLTTPARREQWNQSIQAMSSRIKQMRAALLRHL
                     MDLGTPGTWDHIIQQIGMFSYTGLTSAQVDHLIANHKVFLLRDGRINICGLNTKNVEY
                     VAKAIDETVRAVKSNI"
     gene            16755..16901
                     /locus_tag="T01C8.10"
                     /db_xref="WormBase:WBGene00201366"
     ncRNA           16755..16901
                     /locus_tag="T01C8.10"
                     /ncRNA_class="other"
                     /product="T01C8.10"
                     /db_xref="WormBase:T01C8.10"
                     /db_xref="WormBase:WBGene00201366"
     gene            17202..17310
                     /locus_tag="T01C8.11"
                     /db_xref="WormBase:WBGene00202374"
     ncRNA           17202..17310
                     /locus_tag="T01C8.11"
                     /ncRNA_class="other"
                     /product="T01C8.11"
                     /db_xref="WormBase:T01C8.11"
                     /db_xref="WormBase:WBGene00202374"
     misc_feature    complement(17910..17911)
                     /note="SL1 trans-splice acceptor; see cm20g8.5"
     misc_feature    complement(17910..17911)
                     /note="SL2 defined by RNASeq short reads (Hillier et al.);
                     see RNASeq_Hillier.L1_larva"
     misc_feature    20870..20871
                     /note="SL1 trans-splice acceptor; see yk1146c08.5"
     misc_feature    20870..20871
                     /note="SL2 defined by RNASeq short reads (Hillier et al.);
                     see RNASeq_Hillier.dauer_entry_daf-2"
     gene            20873..27634
                     /gene="aak-2"
                     /locus_tag="T01C8.1"
                     /db_xref="WormBase:WBGene00020142"
     CDS             join(20873..21015,24491..24654,24830..25298,25473..25591,
                     25817..25922,26012..26117,26167..26374,26476..26787,
                     27198..27349,27533..27634)
                     /gene="aak-2"
                     /locus_tag="T01C8.1"
                     /standard_name="T01C8.1b"
                     /note="contains similarity to Pfam domains PF07714
                     (Protein tyrosine kinase), PF00069 (Protein kinase
                     domain); coded for by the following C. elegans cDNAs:
                     OSTF004G3_1, OSTR004G3_1, yk114d1.5, yk133b5.5, yk222d7.5,
                     yk273e10.5, yk298g7.5, yk390b1.5, yk443g12.5, yk507b7.5,
                     yk607a4.5, yk652d12.5, yk677a2.5, yk848d05.3, yk1005g04.3,
                     yk1005g04.5, yk1146c08.3, yk1146c08.5, yk1235g04.3,
                     yk1235g04.5, yk1251g04.3, yk1251g04.5, yk848d05.5,
                     yk1552h06.3, yk1625b07.3, yk237e11.5, MM454_contig01620"
                     /codon_start=1
                     /product="Amp-activated kinase protein 2, isoform b,
                     confirmed by transcript evidence"
                     /protein_id="AAM69096.1"
                     /db_xref="GI:21629470"
                     /db_xref="WormBase:T01C8.1b"
                     /db_xref="WormBase:WBGene00020142"
                     /translation="MFSHQDRDRDRKEDGGGDGTEMKSKSRSQPSGLNRVKNLSRKLS
                     AKSRKERKDRDSTDNSSKMSSPGGETSTKQQQELKAQIKIGHYILKETLGVGTFGKVK
                     VGIHETTQYKVAVKILNRQKIKSLDVVGKIRREIQNLSLFRHPHIIRLYQVISTPSDI
                     FMIMEHVSGGELFDYIVKHGRLKTAEARRFFQQIISGVDYCHRHMVVHRDLKPENLLL
                     DEQNNVKIADFGLSNIMTDGDFLRTSCGSPNYAAPEVISGKLYAGPEVDVWSCGVILY
                     ALLCGTLPFDDEHVPSLFRKIKSGVFPTPDFLERPIVNLLHHMLCVDPMKRATIKDVI
                     AHEWFQKDLPNYLFPPINESEASIVDIEAVREVTEFQRYHVAEEEVTSALLGDDPHHH
                     LSIAYNLIVDNKRIADETAKLSIEEFYQVTPNKGPGPVHRHPERIAASVSSKITPTLD
                     NTEASGANRNKRAKWHLGIRSQSRPEDIMFEVFRAMKQLDMEWKVLNPYHVIVRRKPD
                     APAADPPKMSLQLYQVDQRSYLLDFKSLADEESGSASASSSRHASMSMPQKPAGIRGT
                     RTSSMPQAMSMEASIEKMEVHDFSDMSCDVTPPPSPGGAKLSQTMQFFEICAALIGTL
                     AR"
     CDS             join(20873..21015,24491..24654,24830..25298,25473..25591,
                     25817..25922,26012..26117,26173..26374,26476..26787,
                     27198..27349,27533..27634)
                     /gene="aak-2"
                     /locus_tag="T01C8.1"
                     /standard_name="T01C8.1a"
                     /note="contains similarity to Pfam domains PF07714
                     (Protein tyrosine kinase), PF00069 (Protein kinase
                     domain); coded for by the following C. elegans cDNAs:
                     OSTF004G3_1, OSTR004G3_1, yk114d1.5, yk133b5.5, yk222d7.5,
                     yk273e10.5, yk298g7.5, yk390b1.5, yk402f12.5, yk443g12.5,
                     yk507b7.5, yk607a4.5, yk617g6.5, yk652d12.5, yk677a2.5,
                     yk848d05.3, yk1005g04.3, yk1005g04.5, yk1146c08.3,
                     yk1146c08.5, yk1235g04.3, yk1235g04.5, yk1251g04.3,
                     yk1251g04.5, yk848d05.5, yk1552h06.3, yk1625b07.3,
                     yk114d1.3, yk133b5.3, yk222d7.3, yk273e10.3, yk390b1.3,
                     yk402f12.3, yk607a4.3, yk617g6.3, yk652d12.3, yk677a2.3,
                     yk1552h06.5, yk1625b07.5, AY347273, MM454_contig01620"
                     /codon_start=1
                     /product="Amp-activated kinase protein 2, isoform a,
                     confirmed by transcript evidence"
                     /protein_id="AAM69095.1"
                     /db_xref="GI:21629469"
                     /db_xref="WormBase:T01C8.1a"
                     /db_xref="WormBase:WBGene00020142"
                     /translation="MFSHQDRDRDRKEDGGGDGTEMKSKSRSQPSGLNRVKNLSRKLS
                     AKSRKERKDRDSTDNSSKMSSPGGETSTKQQQELKAQIKIGHYILKETLGVGTFGKVK
                     VGIHETTQYKVAVKILNRQKIKSLDVVGKIRREIQNLSLFRHPHIIRLYQVISTPSDI
                     FMIMEHVSGGELFDYIVKHGRLKTAEARRFFQQIISGVDYCHRHMVVHRDLKPENLLL
                     DEQNNVKIADFGLSNIMTDGDFLRTSCGSPNYAAPEVISGKLYAGPEVDVWSCGVILY
                     ALLCGTLPFDDEHVPSLFRKIKSGVFPTPDFLERPIVNLLHHMLCVDPMKRATIKDVI
                     AHEWFQKDLPNYLFPPINESEASIVDIEAVREVTERYHVAEEEVTSALLGDDPHHHLS
                     IAYNLIVDNKRIADETAKLSIEEFYQVTPNKGPGPVHRHPERIAASVSSKITPTLDNT
                     EASGANRNKRAKWHLGIRSQSRPEDIMFEVFRAMKQLDMEWKVLNPYHVIVRRKPDAP
                     AADPPKMSLQLYQVDQRSYLLDFKSLADEESGSASASSSRHASMSMPQKPAGIRGTRT
                     SSMPQAMSMEASIEKMEVHDFSDMSCDVTPPPSPGGAKLSQTMQFFEICAALIGTLAR
                     "
     gene            complement(21899..21958)
                     /locus_tag="T01C8.9"
                     /db_xref="WormBase:WBGene00199326"
     ncRNA           complement(21899..21958)
                     /locus_tag="T01C8.9"
                     /ncRNA_class="other"
                     /product="T01C8.9"
                     /db_xref="WormBase:T01C8.9"
                     /db_xref="WormBase:WBGene00199326"
     misc_feature    24490..24491
                     /gene="aak-2"
                     /locus_tag="T01C8.1"
                     /note="SL1 trans-splice acceptor; see yk848d05.5"
     misc_feature    24490..24491
                     /gene="aak-2"
                     /locus_tag="T01C8.1"
                     /note="SL2 defined by RNASeq short reads (Hillier et al.);
                     see RNASeq_Hillier.L1_larva"
     CDS             join(24534..24654,24830..25298,25473..25591,25817..25922,
                     26012..26117,26173..26374,26476..26787,27198..27349,
                     27533..27634)
                     /gene="aak-2"
                     /locus_tag="T01C8.1"
                     /standard_name="T01C8.1c"
                     /note="contains similarity to Pfam domains PF07714
                     (Protein tyrosine kinase), PF00069 (Protein kinase
                     domain); coded for by the following C. elegans cDNAs:
                     OSTF004G3_1, OSTR004G3_1, yk114d1.5, yk133b5.5, yk222d7.5,
                     yk273e10.5, yk298g7.5, yk390b1.5, yk402f12.5, yk443g12.5,
                     yk507b7.5, yk607a4.5, yk617g6.5, yk652d12.5, yk677a2.5,
                     yk848d05.3, yk848d05.5, yk1005g04.3, yk1005g04.5,
                     yk1146c08.3, yk1146c08.5, yk1235g04.3, yk1235g04.5,
                     yk1251g04.3, yk1251g04.5, yk1552h06.3, yk1552h06.5,
                     yk1625b07.3, yk1625b07.5, FN880253, MM454_contig01620"
                     /codon_start=1
                     /product="Amp-activated kinase protein 2, isoform c,
                     confirmed by transcript evidence"
                     /protein_id="AAP13770.1"
                     /db_xref="GI:30025106"
                     /db_xref="WormBase:T01C8.1c"
                     /db_xref="WormBase:WBGene00020142"
                     /translation="MSSPGGETSTKQQQELKAQIKIGHYILKETLGVGTFGKVKVGIH
                     ETTQYKVAVKILNRQKIKSLDVVGKIRREIQNLSLFRHPHIIRLYQVISTPSDIFMIM
                     EHVSGGELFDYIVKHGRLKTAEARRFFQQIISGVDYCHRHMVVHRDLKPENLLLDEQN
                     NVKIADFGLSNIMTDGDFLRTSCGSPNYAAPEVISGKLYAGPEVDVWSCGVILYALLC
                     GTLPFDDEHVPSLFRKIKSGVFPTPDFLERPIVNLLHHMLCVDPMKRATIKDVIAHEW
                     FQKDLPNYLFPPINESEASIVDIEAVREVTERYHVAEEEVTSALLGDDPHHHLSIAYN
                     LIVDNKRIADETAKLSIEEFYQVTPNKGPGPVHRHPERIAASVSSKITPTLDNTEASG
                     ANRNKRAKWHLGIRSQSRPEDIMFEVFRAMKQLDMEWKVLNPYHVIVRRKPDAPAADP
                     PKMSLQLYQVDQRSYLLDFKSLADEESGSASASSSRHASMSMPQKPAGIRGTRTSSMP
                     QAMSMEASIEKMEVHDFSDMSCDVTPPPSPGGAKLSQTMQFFEICAALIGTLAR"
     gene            complement(28176..31898)
                     /gene="mec-4"
                     /locus_tag="T01C8.7"
                     /db_xref="WormBase:WBGene00003168"
     CDS             complement(join(28176..28361,28501..28576,28625..28753,
                     28811..28871,28916..29030,29154..29249,29301..29473,
                     29567..29655,29698..29855,29903..30051,30149..30309,
                     30526..30637,30690..31052,31100..31355,31716..31898))
                     /gene="mec-4"
                     /locus_tag="T01C8.7"
                     /standard_name="T01C8.7"
                     /note="contains similarity to Pfam domain PF00858
                     (Amiloride-sensitive sodium channel); coded for by the
                     following C. elegans cDNAs: yk411c2.3, yk411c2.5,
                     yk1105a08.3, yk1105a08.5, EC002941, RST5_376858, FM864873"
                     /codon_start=1
                     /product="Mechanosensory abnormality protein 4, partially
                     confirmed by transcript evidence"
                     /protein_id="AAB00580.3"
                     /db_xref="GI:74356167"
                     /db_xref="WormBase:T01C8.7"
                     /db_xref="WormBase:WBGene00003168"
                     /translation="MSWMQNLKNYQHLRDPSEYMSQVYGDPLAYLQETTKFVTEREYY
                     EDFGYGECFNSTESEVQCELITGEFDPKLLPYDKRLAWHFKEFCYKTSAHGIPMIGEA
                     PNVYYRAVWVVLFLGCMIMLYLNAQSVLDKYNRNEKIVDIQLKFDTAPFPAITLCNLN
                     PYKASLATSVDLVKRTLSAFDGAMGKAGGNKDHEEEREVVTEPPTTPAPTTKPARRRG
                     KRDLSGAFFEPGFARCLCGSQGSSEQEDKDEEKEEELLETTTKKVFNINDADEEWDGM
                     EEYDNEHYENYDVEATTGMNMMEECQSERTKFDEPTGFDDRCICAFDRSTHDAWPCFL
                     NGTWETTECDTCNEHAFCTKDNKTAKGHRSPCICAPSRFCVAYNGKTPPIEIWTYLQG
                     GTPTEDPNFLEAMGFQGMTDEVAIVTKAKENIMFAMATLSMQDRERLSTTKRELVHKC
                     SFNGKACDIEADFLTHIDPAFGSCFTFNHNRTVNLTSIRAGPMYGLRMLVYVNASDYM
                     PTTEATGVRLTIHDKEDFPFPDTFGYSAPTGYVSSFGLRLRKMSRLPAPYGDCVPDGK
                     TSDYIYSNYEYSVEGCYRSCFQQLVLKECRCGDPRFPVPENARHCDAADPIARKCLDA
                     RMNDLGGLHGSFRCRCQQPCRQSIYSVTYSPAKWPSLSLQIQLGSCNGTAVECNKHYK
                     ENGAMVEVFYEQLNFEMLTESEAYGFVNLLADFGGQLGLWCGISFLTCCEFVFLFLET
                     AYMSAEHNYSLYKKKKAEKAKKIASGSF"
ORIGIN      
        1 gatcaaaacc caaaaaaaaa tttcattcaa aaatttggtt ctttcttaca agcaaaatgc
       61 gaggaatagg tgagaaggaa ctgagactga aactaaaaat ttgtgaatag aaactaaaaa
      121 aaaactttat caaggtgttg caattttggt ttctgcaaaa ctgacttgac agtgataagc
      181 tgatagcagc cagaaaccga tagcggtttc aatgacaatt cggggcaagt tggagatcaa
      241 ggactcgttc cacgtggagc gatgtaaagg tctgtttgtt ttgtattgaa tcaaaatcag
      301 aaaaaaaaag aatcagaaac agcaatagat gaaacagaag aaagaaaaat atgataaaat
      361 tgataatgaa attgaaaacc acgccgacgc tgttcgttga ttgattgagg tgggaaacgt
      421 gagcgagaaa aaagtcaaaa gatgataagt ctatgtgaac aagtcacgtt gcttgaatgg
      481 acccctcgag gcgtgagtgt gtcctccgtt atcaagtgat catagtgggt aggtgggtgt
      541 atgatttgaa attgtgaaca ccgacgaata tacataactt acgccgaaca gttgttcgct
      601 cgcaagacaa ggtacttacc aaactctcaa cgttttccat ttctcactct gccgaccccc
      661 catcacttta ccgaagtgtt taggtgtgtt ggtgtgttgg tactcaaaac catagttgag
      721 ttgacatttc atgagtcagc gtagaacgat atacaaagat cataagtgaa atgtatgtag
      781 gttagtggaa aaaagatttg ttagtatgta agtacattaa attttgaaaa atcagacttt
      841 taatatatat ggctgtgaat tcaaaattta aaaaaatata ggttaaaaat gacctaattt
      901 tagttgaaat cttcaatacg acaggatgga agaagcttaa aggtggtgta gtcgaatttg
      961 agactatgct taaaaacatt ctctatgctc gtacaagtcg atatgataaa gcgaaacatc
     1021 tcaaaaattt ctctaacgga agttatgagc cttcaaagtg ccgaaaaaaa tctctttctt
     1081 cactgtcaaa attttttttg ttgaaaattt agcaatttac caaaacttcc actacaactt
     1141 ttgaaaggaa ggatcaatgc aacaaagttc aggcgtagta ggcaataaat gcatttttcg
     1201 aataatttta gctattttcg aattagcatt taagttgcac ttttgaaaat gatatttttc
     1261 agtttcaaga tgttttatct tttcagtaat attccaaact aggaaagtca tatggaaaaa
     1321 atgacaagga acatgatttc gattcaaagt tacactatat gttatattaa aaagggagca
     1381 atactttttc agagtagcgc ggcaagcgca atattactac ggaggctatg ataatagaag
     1441 gagtacggta aaactagagt tcaaatagtt caaggagaac aagtcttaga catatgacaa
     1501 tgatcacaat tctacgagaa tcttgctcat tttaatgcta tttaaggaaa ggaatcactt
     1561 gtcataaatt gtaaagcaaa taaacaaagt tcaagtaagc gggggatgac cgttcttcct
     1621 aattgtttat cttttcttat cctcttttca caatcgagca gaaggatgca tcacggaatg
     1681 agaatacgaa tacacagaaa aacatctgca caccattatt gtttacaagc cttgcatatt
     1741 tcaaggtctt caaggaactg atcaaaaagt gacggacaac acattgtaca ggtcagttga
     1801 tgaacgagag aaagagtttc aaaaaagtgt tatatattga gtatcgggtt acaaggaagg
     1861 aaacggcaga gttaaaacgt gtcgggttac aaaacaacac aattgttgat tggattaatc
     1921 cagaggaatt gaacaaagaa tggaaagaga aaaacaaaag cgaagtcaac attcagaaac
     1981 taatgcgctt gggaactttc gatcaaatgg agaaaaaatt attgcattgg agggctagag
     2041 caaagagttg ctatactttt tcagtttggc acaatattgt actctgttaa tttctccaat
     2101 tagttactta agttgattaa ttaattggtt tatttttcag ttgaggtaaa aaaaaacaaa
     2161 aaataccgcg tcttgttatt ttattatcgc atgcaaaatt atcgcatgtt attttattat
     2221 cgcatgttca tatttagtgc aatactgaaa ttggagacaa ttttcacgtt tttttggtca
     2281 cataatttga gttttacaaa aaaggcattt tttacgtcaa tttgaagcag cttatcaatt
     2341 gtttttggtg actataatag agcaatagaa aaaaattcgc tactctagca ggaaatcaat
     2401 aaacttaggt atgcagtgct ttaaggaacg ctcggggata ctaatagata aatttcaatt
     2461 ttatagtact tcataaatat caatcaccaa tgttcagagc gttttgaaac tgagaaattg
     2521 tttacaaatg atgcgatcgt ttgtaatgtg caattaaacg tttgaaaaca tttcaaaaat
     2581 cttccaggaa caatgtgagt ttctgaccga tgattgtatc atttcacatt tggatatctt
     2641 tatcattttg aaaactttac atacatttaa tttttacaac actaatacaa gtacaataga
     2701 cgacaatttc taaatttagc tttacatgac ataactcatt gaaccatgtt ttaattgttc
     2761 cctaacctca ttaactcaga ttttacactt gatagaaaaa ccgaaattca tagaccaaat
     2821 acgtgaaaat aaaataaaat aggaaaaagc tggttgggtt gtttttgttt tccttattgt
     2881 atactactca catttctcaa caaaaacact tgaagaatta gtttttttat cgcatttcca
     2941 gatcttttgc agcagaaatg tagcaaaaaa aattgaaaaa aaaaagaaaa aagcttgaag
     3001 aaaaaagaaa gatgaactac aaaggaagtt gagggaaaca ctaaacagaa gctagaacat
     3061 tttagatctg caaaaaacat ttaaaaaagt attggctatg ttggggttga agaaacatta
     3121 ttggaaactt tgaaacaact tgtaaatact caacctttaa aaatttgtta tattttcttg
     3181 tgacaacaat ttattttctt aatctcatat tttttttgta tgccgtttca tttttcatgc
     3241 tcaacaactt aaaaacaata atcattctaa aacagcaaag tcaatacaga caagaacaca
     3301 aaaattcaat tcttaacatt ccaaaatgtt tcttaaaagc tttaagcttg acgctttcta
     3361 aattgaaatt taatgtatgc aaactagtgg ggagaaaagc agaccaacga ggtggtcatt
     3421 cgtagaaaga gcggcagacc cccccccccc ctttgtgttg ttgctcatac tcctccaaat
     3481 gtgatgcaat ctctctgtct gcctcacacc gcttcaaaag cctcccgcgc tccgtgtccg
     3541 tcagaatatt cgaatgcatt tcattttcat ctgccgttta tgagatgtga gggctgctga
     3601 aatagaaatt gaaaaatgtc tggaaagcat tgtcgtcgaa tccaccctaa aaaggctaca
     3661 atcgacgacc ttgcagcgct ataacatagt tctcattgga atatcccact attcttaaac
     3721 tatgttaaca ctgccagatt ctcctaatta ctctcttgtt aattcctttt atttcattca
     3781 aaaccgttaa gtataagccg agatacactc aacttacata atcaccaaac gagctagttg
     3841 cattcaaact acgcgcccga tcgccaccgt acctctcttc ccctcgagac ccacgcggca
     3901 ccactacttg gcaccgcgcc aagaaagggg gagaggtggc ggcgcgcgct atgtttgttc
     3961 gtacacgaag atatgcgtgc cacccaacgg ttaattctac tcgaaaatac cttttaatcg
     4021 agcaagaata ttattatttg ttagaattaa ttaaatatta aagtttgaac caaattgata
     4081 gtctaaagat caaaatcgta ttccatttcg ccatgaggat ttcggaccac aagaacagtt
     4141 ttttataaca cctacttttc tgttctttaa tgtattaccc actttttact tgttattttc
     4201 ttatttattg atggcctgcg cgaccctagg gcgtggttgt acaataaata agtttttgag
     4261 ttatcttcgt ttgtgttatt cgtttctttc tctctattgc aggttttagg tgtattccgt
     4321 cgtgaagggg gtgtttggga gtgggaaggg ttgtccacga tgccgactac gtacacttta
     4381 ttggatttcg ccacaagcat gttggattca tatatttcaa tttttaaccg gttcaattca
     4441 ttaacttggt ggtttcattt atataaggtt taatgcaatt atgattctct cagaagcacc
     4501 gagaaaattg cggtttccac tgaacacaat ataaagaaat ttgatttaaa taggcgcaat
     4561 aaatttaaaa aaacaactta ttgtaatttc cttcccgatg actaagtatg taaatttgga
     4621 atatcactga atttttaatt tttcaagctt gaaacggctt caaaaaaatg tatttccttc
     4681 gctcagttct ttttaaaaac aaaattttta cctataatta tttttctaca tacatggata
     4741 gagccaacta gacacatttt tattttgtag atattcagga acagaaaaaa aaacaaattt
     4801 ttccaaaaaa taaaaacaaa gtgtttagaa aatttaaaaa ttctagcttt tcttatcatt
     4861 aataaatttt tcttatcact tgtctgtgca aaaaacgaaa tcaaataacg gatgacatct
     4921 ttattggaaa atccaaatat tttagagaaa caagcaaaag aaatatggga aagaatgaga
     4981 aaatgatctt tgcaacgacg gcggccaaga aaagggcatg ttctgaaagt gcttttcctt
     5041 gaaggcaaac tctctgagca actgagcaac tgggaattag acatacacca accacaccaa
     5101 ttgtatcaaa atgagcacta cgaagcattg cttctttgca gaactccaca cataagttgt
     5161 cgggtaagaa tatcttcctt cgacatcatc ttccaactga aatagttgtt cttcgaaccg
     5221 gggtgaaagg tgtgaatgtc aatgataaga aacagacact agtacatacc gtttgattgt
     5281 tgcaaaagtc gctatcacag atttggaagg gtgttaaaaa cggtgtaaga tggtataagc
     5341 cggcctgaac acgtcttgat tgcacttttt cgtttgctcg gtttgggggt acttttgttc
     5401 ttgctcgaaa tatttggact tgagaatatg aaagaggggt caagtgaata cgaaactgtc
     5461 aacaacaaaa aaattccaga ccttgtcttc gtgacccaaa ttaaggtttt cttcgtgacc
     5521 caaattaagg cttgtaaaat aatattaaaa aaacaaaaat cttaaaatat ttttcttcgg
     5581 caagtttagg tatggtatag tttcatcaaa cttgaatttg atagaaactt tcagaaagtc
     5641 ttttcagatt tcaacatgac tttcgcggta actcaaagta tgaaatgaag aaatacctga
     5701 atttagtcgt atgtatttct acaatttgtt aattttccca gaaaaaatgt gacgtcactc
     5761 gtgtttttaa taacgtttta cagttttttt ttgcagaaat ttctgatggt caaacaaatg
     5821 ttgttgtttt tgtttaaaat ttcaaaatga aaaatggtta ctttcaatat ggctccttcc
     5881 ctattgaatt gagaaatgca tccaaaaaca gcgctggctg agtaacagaa ctgcccaata
     5941 cacgttgaat tctaaatttt cattttctcg ttgttttgtt ttttttcatt ctcactttca
     6001 tccttgtcat gacttctcct ggagcaaagc atttggtact tccgggcact ttcagtttgt
     6061 atggagttgt tttgttctga actttaacta tgtaatattt gcggtcttca atcataactt
     6121 accactttat atgtacaaat ttgacttttg tcataacgtg agtcatctgc aacggcatag
     6181 catgagttga taggtagtaa cataccactg tagacgaatc tataaaaata ttctttatta
     6241 gtttcaagtc atacagtttt cctttaccca atatcataca tctccatttc atatgtccct
     6301 tctccgcatt caaccatcta aattattaac atagttatat atataatcac agccttacct
     6361 catccatata actagatgct gtcttcacac accacggttg cacacaatcg gctcctctga
     6421 acatcgaatc tttagcgtat tcacaaatta aatacgtgat atttttctcc tcttttacgt
     6481 tggtcatctc attacagtaa tccgtactgc tggaaaaaaa aatgtagagt tttaactttc
     6541 tataggaatt ttacttgcaa atacagaaaa tgcttcctcg gctgtttgtg gaacatccca
     6601 atggcaagtc ggtaggagat gtgaagcacc cctaaaattt ttttaaaaat tgtctttttg
     6661 aaattttgcg gtagtttaga attttaccct cttttcgttt aatttgaaat taaggaatac
     6721 tatttattgc cggaacggta taaaatttta aagaataatg ctactaaata tttattttcc
     6781 acgtgtgttg ggcagaaaac tataattttc tgaaactgca gtccattttt ttctgaaact
     6841 gctgtctttt tccaaacttc tggcaaactg tggttgagca ttttttttta tggaagtttt
     6901 tgaatgtcta ttttcaaact acaaaaattg aaggaacttg ttcgaggatt aagaaaaaaa
     6961 aatttcaaat gttttcaaaa aaggttttct ttaaaaatat taaaaaagaa ccgaaaactt
     7021 cgaaaacatt tacatagttt tttagttttg gttataaaaa aggtaaacga aaaatttccg
     7081 agtacaaaaa atttggcaaa tcggcaaact gccctttctc agattttttc ctgatatcat
     7141 acccgatacc tgaatcaaga ttcaaagaga ctgaaattta ataatggtgt tatacgcgtg
     7201 gtgtcagagt gtctcatttc ggcttgatct acgtagatct acaaaaaaat gcgagaaaag
     7261 agacgcagag ttctgaactg atttcgtatg agagaacgtg ctgacgtcac atatttttcg
     7321 gcacaacatt tccgcaattt ttgtagatca aaacgtaatg ggacagcctg gcaccacgtg
     7381 ttttaatata ttcaaattag ctattgcaaa aagtcaaaac attttatgag agaatcaaaa
     7441 ttcataactt ttcatttcgt tattcaaaaa aatcagcttt cagttctcta ttaattcgtt
     7501 ttgggaagtt ttttacattt tcagaatcaa cattagcatt tatacattga gtaaaacaaa
     7561 cctgataata agactgctcg tttttcagag acgggttcag gtgtttataa tttacggcgt
     7621 aacagtaatc tccggtgcag tttgtacatc tgaagttaca gttttcaagc agttgcattt
     7681 acaggaaaaa ttacgtttta tctaccgaaa taacccttcc atcacatttg acacattcaa
     7741 gttcgcaatc acaaaaagtc gataaaaata gtaaaaacca taaaatccga agcaacattt
     7801 gactgaaagc tacttgacag cgccggctta cttgctccgt ttcaaattac gttgttctta
     7861 tcaatttctt ggttttcatt ttcagctgtc gcgcccccaa atcaccattt taggggactc
     7921 gtttctatag caatttgtat catgtgtaat tggaaaaaaa accaattttc gtgtgataaa
     7981 tgacagaaag aaaaacgaaa aagaaggaag agattttccc tttgattaaa atgatagaca
     8041 gttggtcagt gcgggaagaa gaagagattt tggaaaaaaa gtgcagaggg ataccggaag
     8101 aattgggaaa agtgtgattt tgaaacaatc agagctcatt catttgtact tggttttttg
     8161 ctcgggttca ttgcatcccg agaatctgtc tgtgttgggc aactgtattg gcaaaatttt
     8221 aaacatcctg aatgaaattt cagattcact tttttttgtt cgaagttcta ttcagaagct
     8281 atttttgtga caatattttt ataatgtgtt ctatcataca acacagattt tgtttggaat
     8341 ttcgagattt ccgggttttc cgaagttttt ctttattaac attaattacg actaaatatt
     8401 aaataacttg aaaaaataaa aattattgaa tttctcaatc aaaacgtttt tatcttgttc
     8461 cttgatggct taaattgtat tctcagaggt tcccttccat attctcacat ttcaagtgtc
     8521 atttagaatt cttgtcagat gagtaatatt aggaaggcgt ctagactaaa taataaaagt
     8581 aatacatagt acggaatttt gacagcgctt ttactaattt actaaatttt tgtacttcac
     8641 atttaataag aaaacaattc atttccgttt ttccgatttg cgatcgaatc aattgaaaat
     8701 aaaacaggtt ttggtttgtg tccgttttta tttataatat ttttgatatt caaaattaaa
     8761 caaaaatttt gcataatatt caaaatcata aaaaatattg gttcttttat tggctcaatg
     8821 aatcttcttc acaattcctc ccaactaacc ttttttcaaa gttcccctat gaatcaatct
     8881 cccgccccag cccatgtttc cttccactaa tttttctgtt tttcatttta attcttctct
     8941 attgccacgc atcgattcca ccccagcaaa aattgaaaaa gtaacgaagg tcaccgagag
     9001 atcgaccatt ttcatctacg tcgattcttt ttaaaagatg cgcgcacctc cccccgaaaa
     9061 tagatcaatc tgtctcagtt ttgctggttt ttattagtga gtttttatct gacaattgtg
     9121 agaaggtgat actagagata atcaaagaat tcatttgatt caatgatcca gaagtctttt
     9181 tttttatatt ttcaaaaaag tgaaactagc aatattaaaa gaatcccaat cctacaaaat
     9241 tttcgaagta aattcaatta aaattaaaat taaaattaga aaaaaaactt taatttatca
     9301 agattgatgc gatatcatcg tcaacaattg ctactcaatt attagattta ttttatttat
     9361 ttcatttaga cataaatatg tacgtgagaa acaattgttt tctgttacac tgaataaact
     9421 aaactcattt tatttttttt gagcttacga taattgctat gaattattca taacattttc
     9481 taatgtcgag tgcacttttg cagatatgac tcactttttt ttgttttgtg agttgagcag
     9541 cctaggactt tgtatgaatt aatttgcaaa aaactaggta aatttaatca tttacgtttt
     9601 ttttcaaatc aattgcaaat ataaattctt gtctgaaatg tatattaccg tatttctttt
     9661 attagtatat atgtaactac attttttaac aagtttttca aaagtctccc aataacgcaa
     9721 aatcataaaa aattctacac ataggtacat attatttaga gttttctcaa gacctatatc
     9781 acctcatttt caatttttcc ttatcaatca atctcgtttt cttcaaaaat tgaatcatct
     9841 tttgatacaa cagacgtatt ctattcatag cctcatattg gcattggcta tcaatcaaga
     9901 tgccaatatt ttacaatgca tttttcattt ccggtgaaaa tctagaatct agaattgaga
     9961 atcgagaatc tagaatccgg cccgcttcaa ctattttata tatatacaaa tatataaatt
    10021 tctgcccact ctttcttgat ttatttgcga tttggttgca tgacgcaggc gtgttgctct
    10081 tactacccaa acaaggaata aagatcttta aatgcggatt tcatatatta atttttttct
    10141 tctttcaatt ttattttgtt tgccaagaaa aaaaaaacgt gtcctttact acccttcaat
    10201 atttttgttt caactgaaaa tataggtttt ttaaattaaa ggattaaaaa tgaattaaaa
    10261 ctttttttta aagtaagaaa gtctgtttta gatttgtttt tattttaaac ttgaaaccat
    10321 acctacaaaa ataccattaa aaattttaac aaaatctttg taacatttga agtcaacttt
    10381 aaatacttca aataagcatt tgattatgag aagtgtgcat atgtatattt attactatta
    10441 ttttttgtag aattttttaa aacgtatgta aaatttacat cttatgaaac atgtatgggg
    10501 aaattttcag atgaatggta agagggttag taagtttatt aggtttatct attcaatcac
    10561 aatgtaattt tttgactgaa atgcgcctgg ttttaaaatt tgagagcatg tacctttaat
    10621 ttttgtccta catttttact ttatgggctg tttgttataa attttgtata tttacagaaa
    10681 gatttcaact cttcattttt tatgaatctt ttttattgta aagagcatta gtcaatgctc
    10741 accaaatgat ttctcaatta aaaatcaccg atctgagagc tcaaaatgct ccgttctcgt
    10801 aacgccaaca tttttatctg tttgtgtctt cacattagtc taccaccacc aacactcaaa
    10861 atatcaaatt tttctcaatt ttcattcacc gatcattgtc tccactcttc gcctcaatct
    10921 ccgtcgacct gtaactaacc agttgtcgaa tcgcattgga tcgtcgcgta tcgctctctc
    10981 atttcctcat ggtcttcccc ctcagggcac tactcctctt cttttcccaa aatgcccatg
    11041 attttcactt ttcattctgt gttgttgttg acacgacgac tgtctcgttt cgtcctttcc
    11101 tcttgtttca tccctcccac ggttacctct tcaagtcttt tctcattgat ttttgaaagt
    11161 ttttcaattc ttttgtaccg taatgatagt gatattgata agttgaacta ttttagtaca
    11221 gtttcaggtg actagagatg ccaaagcaag agttcaaccc acttgattac actggaccac
    11281 tgatagttgg agcaattttc tgcgtctttt tgtttgtgat ttcgttcttt gttatcaact
    11341 tcttctgtat taccaaatac gatgatatta caaagtttga attggtgagt ttagtacttt
    11401 gtagttttat ctttaaatta tttacaaata gaaggaaacc aatagcattg tacgttctaa
    11461 aggttgggtt tgctagagag cctgctttat gttaattaaa aagttgagta tctatacaac
    11521 atacacattt gatttttggc tttgctgcgt accattatta ctcaagaatt ggtatgtatt
    11581 caaataatgc aataacgttg tgaaattttt tctctagaaa tcgttcataa tttctaagta
    11641 gaaaagtcaa ttatttctga caatttctaa tttttttata aataaaaatg cacattaaga
    11701 acttttgata atgttgcaag aaagttggga aagttatttg tctggtcact tactttcgaa
    11761 atgtattaat cgatccttga acttttttgt tccgcagagg ctggcggagt ttacaagcgt
    11821 acgacgtggt tcaattttca tttaaagctt taaaaatgga acatagatga acatttcgaa
    11881 tgctaaatgc aaaatcaaat aatttaattt tcacgactct ataaagtttg ccagcttcct
    11941 ataactgaca caaataaaaa ggaatccttt aatgagaacg agtataattt ctggaaaccc
    12001 ccgcccctgc ataatactca aattctcaaa aaatttccaa ttgtctttac tgcagacgtt
    12061 caatgaactt ttcccccacc atatcaatga taagtgtttt actacctaaa catgatttat
    12121 agtttgaacc aatcagtctc tttcctttat atgcattttt tttcagatgg gaggtaaata
    12181 tggatggcgc ctaggaccac atccattgat cgttgtcaag aagggtggat ttgtcgccga
    12241 ggaggaggtt gatgatgctt aaatacttag ttccattcca acaacaaatc tatattttgc
    12301 ttttaatggt tttgtttttg aaatatgcag tacgtttatt gcatttttaa taattccgca
    12361 actttttgct gcaaactttt attcgaataa aattttaatt tgaagtgaat actttttaat
    12421 gaattgttcg tacagtgtca tcaattgctc tagccacata atccaagtta ctcatgttaa
    12481 gcccgcagat attaatacga ccgtcactga gaaggtagat cttgtgatgg gctatgagat
    12541 ggtcgacttg acaagctgaa aaccatttca tttatttttt aggtttttca gaaaatgtct
    12601 aatctaaaat tgctttttat taattttatt ccccacgacc atacggactt aaagctggat
    12661 gtaacttttg tgcaaaatgg cacaattccg tccggagctt tggggtgttt tacgagaata
    12721 ggtaaaataa cctaatgctt tttcactatg ctaaatagtt ttttgaaaaa tattgcttac
    12781 ttacgcgtca atccggtata actgaacaac cccgattgtt gagtaatacg atcccatttt
    12841 ccagaagttt gaagcatatt caactctcga atcagttctt gtcttgtttt cttaatacga
    12901 aaagccatca ttttaatgga attttgccat tgttctctgt acttcggcga cttgagaatc
    12961 tcatgcacaa tacgtgctcc gtaagctgga gggttagaaa aattagaaac attaacaagt
    13021 gtcagttggg attttaggtt cgcaatatga cttggtttgt tcacgatcac agtaaggctt
    13081 ccaacacgat catctgaaaa ttttaatcct aactaataat attcaattca aacttactgt
    13141 aaagcccaaa attctttgag aaagattgag agacaatcat ttccaaaccc tgttcgacaa
    13201 agaaccgaac agcccaagca tctgcatcag cgtcgccaga agctaatccc tgatcagcaa
    13261 tatgaaaaaa agtgaaaaga ttcttctgtt tgatgacttg cgccatttgt atccattgct
    13321 ctcgagttgg gtccattcct gttggattat agcacaggct tgaagaagaa cagctgatct
    13381 ttccggagct tggcggaggt cgtcaagtaa ctgtgtgatg ttaatttctc tgttatgcaa
    13441 gtcccagtac gtatattccc taattgaatt gaaaccactc ttttgaaatg tacgctcgta
    13501 gtttcccctg gaaaaagaaa catcacacaa ttggtcgttt taataatcgg ttgaaaaaat
    13561 tttgattttc tcattaaaaa atacccccaa aaagcattta cttaccagca tggattgctg
    13621 acataaatcg tcttcatact aagaacttga gcaagaaact ctgctccaac acatatggca
    13681 cctgtaccag agatgcactg aacactaaat gatcttccct ctttgatagc caaagaatca
    13741 tttccgagta gcaaagcggt ggctgatttg cagaatccat catgtccaag aatcggtagg
    13801 tactcatgat tgtgatgagg ctcgtgaggg aatttaagtt cgatttctcg aaccactggc
    13861 aaaacccacg gctctccatc ttccgtgcga taagcttcta ttgcaagatt tattttcaca
    13921 gggcaaattt ctttctggaa gagttccgat gtatggagct ctttgattgg cgaagcaaca
    13981 tgaattccat caaagaaaga tagccgcata ttttaactga aatttatttg ctgtttaagc
    14041 ttagataaca ttaaccctta gcctaagatg gacaaaaaag tcacgtaaaa ctatgtataa
    14101 gaatggccac catttctggg tcagttgaac tacacaagta ccaaaagttg aatagttcca
    14161 tgcataacac gaaatagaaa aatgggagtt ttttggagca ggtggcgata agaaaacgaa
    14221 attttaattt atagctgacg ttgaaaaaaa ctcttgaact cagaaagtgc aagaaacaaa
    14281 atttctggga ctgcaaattc agtacatttt atactttgac tataaaacat ttttgtagct
    14341 cactgtcttc tgaaaaaaag aactgggagt actttttttc cttagcgcaa tcctgtttat
    14401 atacggttgc aaaaatcgtt atagcgttcg caacatggta attttgttca agaatcaaaa
    14461 aactgcggta ctaagttttt ttttttttta gtttattttt ttttagtttt tttatttttt
    14521 taaatttatt tagtttaact atgtaaagtt tttctgttcg tttgaaaatg aatttgtgtt
    14581 cctgattact tcctggcacg tattcacatt ttcatggtga atcgagtctg gtgaagatgg
    14641 gcgtacccac ggttcgacat gttgctggaa ttctcgtgct ttttgaaaaa tgaatatgcc
    14701 gttctattaa ttttgtaacc ccgtaacaaa tgaaaaccgt tttgtaacgg ggtttcttag
    14761 taataatatt gggtataagt acaacaataa caaccataat aacaatataa taataataat
    14821 aataacaata acaataataa gtacaaccgc ttgataattg agtttgccat ttttagagca
    14881 atggaaaata ttacattgtc attttctatt tattaattgt tatgatcaaa taaaaccttt
    14941 ttcatccttc ccatattcat tggtaatgat tactctattt ttttccataa aacaactact
    15001 tgatgaacga tgttacggcg aaacacgaag gttcgaaaaa aactaagaca gcttaaagtg
    15061 cattgcaata aaaaatgatt tatcacttga ttgacgttga taagaaaata gaagcctacc
    15121 tcaactttga atactccggg aaatgaagtt cgtgtagatg agaatgcgaa agtttgacgt
    15181 ggtcagttat agaattaaat cagtttttca aactgtagta acaaatatta acagctgctc
    15241 gaaaaaaagt ttttaaacat ggtgccaggt ggtcagtaat acactgtatt ttgaagcata
    15301 tgacagaagt tgaaacactt ttttttcaat taactacaag aaaattacaa aaataaaata
    15361 aagcctagtg atgattagta tttgcaccat atatcataat tgcttgaaca gaaaacattg
    15421 ttcataaatc cccgcaattt tttaactgtc tttcacactc cgggtcatcg aagtttgcaa
    15481 gacgtaagct tttcaggtaa tggaacactg atgtatcctt acctgtacac gtgatttcag
    15541 aaagttggag agccgttttt gaattggtgc tccgttcaaa ttgactctaa aagttattca
    15601 cgaaatccac atatagttga atgttttttt agtattgtgg aataatttta aaacaattat
    15661 tctaaatact agagaaccat ttttagtaca aaactgatta ttttatccca tcccgttgta
    15721 caacgtaaca gaaaagcata atttgaaagt ttctcggagc acactttcaa tccaatgaac
    15781 tgtaaagaaa attgttgtaa caagattttt ctcaaatttt gccacatgac ttcgaggaga
    15841 ctgaaaaatt ttaaccaaat cgacaggtgt ctaaacaata gatagatggc aaatattctt
    15901 aatctaaact tggggtgacc agaattacaa actttgtaac aaaatgtcgt agacttttcg
    15961 cacaacagtt ttagttttat ttttgttccg gcaattctga tgttcctctt gcttccatat
    16021 gccaaaaatc cgctgcttca tgcattatgg cagtgtatcc ataattgtcg cggttaggag
    16081 cgaatatttt atgaaatagt tccccaagta aacgtccaca tcacacggat aataatagca
    16141 atgattcatt ttccattcaa gaaaaaaaag taatcgggtt aaaataaata aaagtacaca
    16201 cgggaaatta aaactaagtg catagaaata ctcaatctac acttaatgct caaacttgaa
    16261 gagcacaaaa actcaatttt tcacataaaa ttcataaatt tcaaagcttt agatgttgct
    16321 cttcacggca cgcacagtct catcaatcgc cttggcgaca tattccacgt ttttcgtgtt
    16381 aagaccacaa atgttgatgc ggccgtctct gagcaggaat actttgtgat tggcaatcag
    16441 gtgatccact tgggcagctg aaaattaaga ttgtcctcat cagagtgtta aaaaaagcaa
    16501 actcacaagt aagtccggtg tagctgaaca ttccaatttg ttgaatgatg tgatcccaag
    16561 ttccaggagt gccaagatcc atcaaatggc gcaataaggc ggctctcatc tgcttgatac
    16621 gagaagacat cgcttgaata gactggttcc attgttcacg gcgagctggg gtggtgagca
    16681 ccttgtgcac aattcttgct ccatgtgctg gtggattgga ccagttggca cggataacca
    16741 acgacatttg agactggaat ccggcaatga cagctggatt gttgacgacg acagtaaggt
    16801 ttccgacacg ctcgtctgaa attttgaagt attttacttt tcatcttcta ttcaaaactt
    16861 actgtaaagt ccaaagttct tggcaaatga ttgggacaca accatctcca ttccctggtc
    16921 tacaaagtag cggatcgccc aggcgtccgc agctggatca ccagatgcga atccttggta
    16981 agcaatgtca aagaaggtga agaggttctt tctcttgatc acctcggcaa ccaacttcca
    17041 ttgctcctga gttgggtcca ttccagttgg gttgtgagca catccgtgaa gaatgatgac
    17101 agacttctct ggggctgact caagatcgga gaggaacttc tcaatgtgca cacgtttgtt
    17161 atcatagtcc cagaaggtgt agtcggcgac ggtggtgaaa ccagccttct tgaagacaag
    17221 cttgtgattt cccctgaaaa tgataaaaat tcatgatttg atgaatttcg cccagcatta
    17281 tcagaggttc aggaaaagta ccttacacct ctttgaaaga gccttgctga aactcatttt
    17341 ttacctagat tacctaggtt tatggtaata ctgccaagaa ttgggcggct attttaagaa
    17401 gttgaagttc tggttgactg ctactcactc tggccaatac aagacttgtt atattttatc
    17461 agataagtat gtttggctcc gatttttcga ccacttacca tgttgggttg ctcacgtaga
    17521 cggtcttcat gttacacact gaagcaagaa actcggctcc agcacgaaga gctccggttc
    17581 cagagagaca ctgtactcca aacgatcttt cctccttgat agctggcgat tcggctccga
    17641 ggacaagctc ggtggcagcc ttgcggaaac cctcgtgacc gagaactgga agatactcgt
    17701 gattgagcga ggtgtcgttg gcgatttcga cttcagtctc atgaacgact ggaagcaccc
    17761 atggctgtcc ctcctctgtg cggtaggctc caattgtcag gttaactttg acgggagccg
    17821 tctcatcgag gtacatcttg ttcttgtgga acacctcgat tggtggagca actgggattc
    17881 cgtcaaagaa ggacatgttg agtgttgttt ctggaattaa aaaaaatcaa taagtttagt
    17941 tatagaaatt gaagagatga aaagagtggc ggtatgccgc aaaacgcgat aatgaggtgt
    18001 atttatatag cgaaagagat caaaatcgaa aaatgaccac gttaaaagga ggtcacctca
    18061 tcgacattcg agaggattta cttggaaaca aaaaacgttt taggtgtttc caataaaaat
    18121 cgatttgatg ataaaaatta ttatacgata agaaacgtaa aactttctac tttcttattt
    18181 tagcactcaa gaaatcaaca gaaacgtgtg ttgataagac tacgggccca gtttcaagac
    18241 tgaactagat ggttactttc tattgcacca aagtcgacag ttcacaacaa aagttacagg
    18301 aaattttgcc tagttttcgg acaaattgag gaaagggggt ctcaaaaacg gactgcctct
    18361 tctcgacaac tctttctcgt cggcccgccc tccaataagc acacactatt tccgagaaaa
    18421 caacacatgc gggtagaaaa cgagaggcag cgttgttgtt tgccagagac gtttttcgag
    18481 acgtgaccat tttgaaaatt tttatttcga ggaaaacgtg atggcaaggt ggagagaacg
    18541 ggcaaaacgc agcgcaatga gatcgaaatg tgtcatttgt gagggtttca aagtgttctt
    18601 tgataaggca aattactttt ttgaaaattg aaaaaaaaga ttggatattt atctaggtta
    18661 atgtaataag atcctaggaa taaatgaaat tatatcaaaa ttccctcacc aaaaatgaaa
    18721 aactattttt ttttttgaaa ttttctagtg gaagttttct tctgtttttg cctatagaaa
    18781 aaccttgaaa gagctgattt tttcaaaatc cctttacaaa aggaatcaag gttaacctat
    18841 acaactacct cgtgaacttc aaagattcaa aaaccaaacg accacttcaa aaattattgg
    18901 caaaatgacc ttttgaaatg agtgatggtg cgaaaccgcc tagataaata aatataacaa
    18961 tctcacgtgg ccaggcggaa aaacatgttt atgtaaattt tcgaaacgaa aaataatcgg
    19021 ttttcttttt ggggtgatga tggcgggaca tgatgaaaag aaatggaaca gtatacacga
    19081 gaaaatccaa gttgctgggt atttagaaat atggatgaga actaaacaac attccgcccg
    19141 gtaaacgcct ttgaatgaat gagaagtaaa aatgaaaaaa aatcacagaa aaatattcac
    19201 cgtaatgaga atttgcatac aagatttccg gtagaaagaa gggtgagaga agaggtaaag
    19261 aaaaaggcga taagaggcgc ctccgggccg ccttaaagcc tcaattctac gtggcgaagt
    19321 tctcaacaaa gttttgtaaa atttacgaca actaaaaatt ttttcagcac attctgattt
    19381 attattttag tcaccgactt taatgggtgg cctttaatga ttttgaagtt aatttgaaaa
    19441 tttttaaaat caataaagat gaacatggac atggattttt cacaaaacta acaattaaga
    19501 ggcaacaaaa acaaacataa tgatagttgt tagaaaaatg gaaattgaac aaaaatttca
    19561 aaaacaaaga aagcaagtca acaagtgtct aacgaagaag taaacttttc tcatcacttg
    19621 gacgccgagt gtgctcaaaa ccattgtgct ccgaaatatg acacttttca actcgtccca
    19681 tcgttcaaag ttattattcc ctctcatttt ttttcccgcg ctctcgttgg ctctcgtatc
    19741 atgagctctc gttgacaagt aacttttaag tttcaaaatt tatctatagt tgttaaagta
    19801 taatgttttc ctagaagctg taagcttggc aggtgacttt ccctgcggga attgcgaaaa
    19861 aaatagagac tgaataaaac gcatatactg tttcatattg tctggcacgt gccttgtggc
    19921 aggaggtata ccaatacact gccccgttct gatccgatta ctttgacaaa agtcgccgag
    19981 tctgatactc acaaacagta gcgtcaagtg aggagggctc actttaccag aatttattat
    20041 gaatgtttct ggtatcatca cattgtttca actttccacg cgctgttaca ttgcgttttg
    20101 aatcgatttt ttggtattct gccaaatata gcttcagtgc gttgcactcg agcatctgaa
    20161 catatttgct ttttgtttgg cgagaggaag gaaaaagcac tgaaaagtgc ttaaaaatcg
    20221 ttttgaaata aggattagta actggattag agctagagca ttaagtgata ttaggcaatt
    20281 tttgttattt ctaaaaatat ggaactatgc gggtggaatt ttttgttcac atgaacgtgt
    20341 caaaaaaatt gttaatgttc ataccctcat ttacatttcc acttttatgg cattttggaa
    20401 aaagatggct atattcgccc tgttagtttt agaaaacctt ttccactaga tattgaaatt
    20461 tcgaagtgaa gttttcgctt tcatcaaaca ttcttcgaga gctagcttca attgttctcc
    20521 ttcatttttt ctattgcttt atgttgcatt gaatagctaa aaaaaaattc aaaaagctat
    20581 cccttcaaaa aaagaaaatt cgctgcttct cgacgtgaaa aacaatgaaa aaagtgttcg
    20641 gtgagtactt gttctattta cacagcaaac ctttttagca gccgagctgt tagaaaaacc
    20701 aaaaaacgcc accaaaatat gcttattcac attttccgtc atcaccatcg ccgccgattt
    20761 ctgcgcatga caaagtggct tttctctctt tttttggatt tcaaggtcta acattgccgt
    20821 tctaatgccc gttttttagg ttacatttca aaataaccga ctattttcag aaatgttttc
    20881 tcatcaagat cgagaccgcg ataggaagga ggacggtggt ggagacggta ctgagatgaa
    20941 atccaagagt cggagtcagc caagtggact taatcgcgtg aaaaatcttt caagaaagct
    21001 atcggcaaag tcaaggttag tttttgaggg gttttcgggg ggtcaaggga agtcaaaaac
    21061 cgcaattcta aaattttgcg atgggtagcc acagaaggga tgttcttttc atttgaaaat
    21121 gtgaaaaaga ttaatttttt ttaaaaccac actgatgagt ttagtgaaaa aattaaacat
    21181 gcttctagcg cctcagctaa tcaactcaga ttttccgtac aaattacttt agtattacga
    21241 aatattgaaa aattcatcgg ccctcagcaa attagattcc aattcgggaa aatactgaat
    21301 tttccctgaa ttccgtgttt tgtctgtgtg aattaaagat tgttcacatt taaaataacg
    21361 taccaaggtt tttttttgaa aactttctag atcactagtt tttgaaagac taaatattaa
    21421 ttttcagcaa ctttttgtaa acgcccatta cgattagcaa aacagaaaaa gataacagca
    21481 aaaatgttca atgcaaaaac aaaagaaaag agactggagc cttaatgcaa aacgaacaat
    21541 gtgggggccc ttcccgaata agtgagccgc gcggaacgct gccgccctcc actaaacaac
    21601 gcgcggtacg atactccgtt catcggacca acttcccccc tctttaccta gttggcaaca
    21661 ttttcttcgt attctcacgg attctcctca ttcattccgc tttcaaaccc aatttccgtg
    21721 catttagcat tggaaaaaca cgtgccgcaa cgtatccgaa aatagtgtga gacgcagacg
    21781 gctggcgccc cgcgtgaggc gaccaaaagg cttttcttct ttttgtcctc cgttgaaaat
    21841 catggtaaat tgagtgatct cgtttgcgta tttgtgtgta tgagagagtg tgagtgtgtg
    21901 tgtgtgtgtg tgtggacacg ccaaagcttg atggagtcac atgtatatca tgaaaaacac
    21961 aaacagatac cacaccaacg aatcttgaac cttgagttct tccgccagtg ttcattttta
    22021 acatctcttc atcgttctgc aaggagacct gtcaaaattt ccaacaaaaa aaagagtttc
    22081 ccataaatta ggaaaattct gataggttcg gaagttttcc gtgaagtaac tgaatatatt
    22141 ttcaatgatc acgagaaggc aattgaataa atgttagttg gaaaattttt attgagcttc
    22201 tagattttgt tgtctaatat ttgagcctca aacttttaat ataggttatt attttttatt
    22261 gcagccgaca attttttgtg gcaatttata tacaaaagca taaatatctg agatgcttag
    22321 tttcatagaa attcagttca agaggcttca ccgtataata taatatattc ttgctgaaac
    22381 tacaggaaaa tttagtggga acttgtgaaa tttgaaagct cccagattcg attttgtcat
    22441 tcttttatgc aatgcaaaaa ttatttttaa aaaactgttt tcgacatttt ctcatgattt
    22501 gtgaaaaagt ttttttctca aatagaagtt aagctcattt ttctaaatag tttttctaaa
    22561 ccctggattg tctcaaatcc gctgtagaaa agttgaagcg actgacatct tatgagctaa
    22621 atttttcctg agtttttgaa atagactaca tcttgataat tgaacattac agtttgacaa
    22681 aatttataaa aatattgatc agttggattt tattattttt ctgttgtttt gttctagctc
    22741 cagtagggtg gatatttttc aaaaatctca aatttttgtg caacttctat tagtacaaat
    22801 ataaaaatat ttcaaacgtg cactttttga acatggacat acgttaaatt tccaatataa
    22861 agggcaaact ttcagctgag ttaggagaat atgagcagct gttaatcaca taaatctaac
    22921 aaaaaaacca catgttccaa cttaaaattg atttcaaaat tttgtggcca aaatgaaacc
    22981 ctacgatgtc agccgagttt actttttcaa agtgcagtta gaaaaattgt ctcaattttt
    23041 tatcagtgga aacgtttttg gtagtctcac taattttaaa gtttaactcg ttttagtaga
    23101 agtcatttaa aaaattcaaa aattgcggtg taacagttct tttaatactt tttcaaatgc
    23161 cataaatcgt ctgtaattaa ttttctacca acttgacaat ttcaattagt aaaatcacag
    23221 ttttaatgca taactttttg atgctagtcg tatcaaattg tgattattgt tgttatcttc
    23281 accacttata ttacgagtgt atcaaatttc gatgacacaa tacggctatt attcattgag
    23341 cgcttgtgtt ttctctatcg tctccactgt ctgaccttcg atgatgtttt tctacatgtt
    23401 tttttgttct ctcaaaatag atgtttcagt tcctccaacc ttttgaaaat ctgtaattgg
    23461 tgttgatttt ggaacctttc ctattgtctc ttctaccatt catatccggc acatttatgt
    23521 caaaacactg actgcacctg ctgtttttga aatttagtgt ctggtgtctg ggcggcagtc
    23581 ataagacctg atgggcatac ggttttccta gagactccta ctgcaatggt cattctgtga
    23641 taagaagttg cttttttgtt tatccattca aaattaccat ccaaaaacca caccagttat
    23701 caatttttaa gtctttgaga cccgtaaaat caatcaatca tgtccacatt gcacttttgc
    23761 ctgtagaaaa acgcgatttt cggttttcaa tcttatctca tttctggttt tcgttcccat
    23821 ttgactactt gttgtcaatt ttttaggtta ggtctaaata aatattaaag attttttaaa
    23881 aatttaaatg aaagttcaat ttcttctttc tatttttttg ttcctaccta ccaacgctgt
    23941 ttgcgccgga ggacgataga cataaggaaa cgaacacacg ggatgccttt cccttctatt
    24001 tttctcctct ttttctctat ctctcgccat tgctttgtgc tgtatggtca actctcgttg
    24061 tcttcgctgt gcgtgtgtgt ttgtctgttg ttagaaaacg aggaaaattg tgagaaagag
    24121 tgagcgagga agatcgagag agaagagtgt gcgtgtgaga ggtgtagggg tcgcgagagt
    24181 gtgcgggagg ttggcggacc ttttaccaca ttttcggcca aaggaaaaaa ggcatcgatc
    24241 tttgttggtt gtagttctag acattttttg tttctgctat gttctcaaaa caccaaaact
    24301 tgttcttaga tttctgatct ttgaaaaata catgctcttt atacacttgt ttttctcgtt
    24361 gttttgctat ttgcaggagg ttcctcgtga ctgtatttat tgatttttta actgaacaat
    24421 tattctgagg aacttgtgaa ttcgagattt tacttacgat catttaccta ccaacaacgt
    24481 acgttttcag aaaggaacgc aaggaccgcg atagcacaga caacagttcg aaaatgtcgt
    24541 ctccaggagg agaaacgtcg acgaagcagc aacaagagct caaagctcaa atcaaaatcg
    24601 gacattacat tctcaaggag acactcggag ttggtacttt tggtaaagta aaaggtaagc
    24661 tacaacacct taaaattcaa ccaaaccgga aagttagaaa ctttttcatt tgctgcaact
    24721 tcctggcaac accataagct gccaaattgt tgcaaaaatt ttgtcccaat ctgccaaata
    24781 ctgacatatt tatctttctt ttctgttcat ctagttttca cattttcagt tggaatccat
    24841 gagacaactc aatacaaagt ggctgtcaag attctgaacc gtcagaagat caagtcactg
    24901 gatgtcgttg gaaagattcg ccgcgaaatc caaaacctct cgctcttccg ccatccgcat
    24961 atcatccgcc tctaccaagt catcagtaca ccttctgaca ttttcatgat tatggagcac
    25021 gtttccggcg gggagctctt tgactacatt gttaagcacg gacggctgaa gaccgcagaa
    25081 gctcgtcgct tctttcaaca aatcatttcc ggcgttgact actgtcatcg tcatatggtt
    25141 gtccatagag atttgaagcc agagaatttg ttgctcgatg agcagaacaa tgtgaagatt
    25201 gcggactttg gactttcaaa tattatgacg gatggtgact tcttacgcac cagctgcgga
    25261 tcgccaaatt atgctgcccc tgaggttatt agcggaaagt gagtgattat ggtggtctcc
    25321 tgatcatggt tcaatgtaaa ataaaaacca aattagaact gaataacaaa acatgaaaca
    25381 tgtgttcgca aacaccaaga cgacattttg cactagtaga aatccaatta aagtaattga
    25441 acaagattag acacaacaac tttgttttgc aggttgtacg caggtcccga agttgatgta
    25501 tggtcgtgtg gagtcatttt gtatgcactt ctttgtggaa ccctgccatt tgatgatgag
    25561 cacgtgccaa gtcttttcag aaaaattaaa tgtacgttag tgtgacatga gaatcaaaac
    25621 acaaaaatgg caaaggatta cgacaacata ccaatttcat ttagacatat gaaagcgaaa
    25681 tgggatttga aaattgaaat atccctatta caaaaggcac tattactatg ttttggcgca
    25741 ctgcccgggt gataaatgtt tgaaatttaa attggaatca ttaaaaatta taacgttcac
    25801 gaaatatgtt ttttagctgg cgtattccca actccagact ttctggagcg cccaattgta
    25861 aatctgcttc accatatgct ctgcgtagac ccgatgaaga gggccaccat caaggacgtc
    25921 atgtaagtgg tcttctaaaa agaaaaaaaa aacaaacatc gttgctatga gacgccaagg
    25981 aaacaagaca ataactgctt tatattttca gtgctcacga gtggttccag aaggatttgc
    26041 cgaactactt gttcccacca atcaacgaga gtgaggcttc cattgttgat attgaggctg
    26101 tccgagaggt cactgaggta ttaatcgtgt tcgataggag cagaagtttc taatcacaat
    26161 gaaaagtttc agcgctatca tgtcgccgaa gaggaagtca cctcagcatt gctgggagat
    26221 gatccacatc accatttgtc gattgcatat aacttgattg ttgataacaa gagaattgcc
    26281 gatgagactg ccaagttgtc aattgaggag ttttatcaag tgacgccgaa taagggacct
    26341 ggaccagttc atcgccatcc agagcgcatt gcaggtagga gagggtgcat agaaaaactc
    26401 ttggtggcaa agaataataa aacttttgca tcgaacatga aattcgtaaa acaatatcta
    26461 aatcttcaat ttcagcgtca gtcagcagca agatcacacc aactctcgac aacacggaag
    26521 ccagtggcgc gaaccgcaac aaacgtgcca agtggcatct gggtatccga tcccaaagtc
    26581 gtccggaaga catcatgttc gaggtgttcc gtgcgatgaa gcagctggac atggagtgga
    26641 aggtgctcaa cccatatcat gtgattgttc gtcgcaagcc tgatgcaccc gctgccgacc
    26701 cgccaaagat gtcgttgcag ttgtaccaag tggatcagag aagttacttg ttggatttca
    26761 agagtttggc cgacgaggag tctggatgta agggttttct ttgtttagat tgaacttttt
    26821 gaaagtggaa cctgtttaaa atatttagtt aatcgttcta gaaaatacta gaaaatacaa
    26881 gttagtgcat ttttttaaac taaaatcaca atttgaattt gaaaagccgt agaataatat
    26941 tttgcaatgg tctctgaaca tgcccctcta taacctaagt ttctgcatgt agtctagctt
    27001 aacgtgtcac aataattttg ttcagaaatg tttaaaacga agtttgcttt gcagttggaa
    27061 aaataaaaag gtcaatggaa attctttttc aatagcgtca agtcttctca agacgatttt
    27121 ttttgtatgc attttttcct aatgggtcaa atgaatatat aatttccacc tcaaccaata
    27181 ttcattaaaa atttcagccg ccagtgcatc ttcatcccga cacgcatcaa tgtctatgcc
    27241 gcagaagccg gccggaattc gtggaactag aacgtcaagc atgccacagg cgatgagtat
    27301 ggaggcgagt attgagaaaa tggaagtgca tgatttttcg gacatgtcgg tgagaattaa
    27361 tatttttctt ttatttcaat atttttattg tgaagtatta caaataactg gaattgtatt
    27421 tggagtggtt gatatagtta taggtttttt aaaaatcttc gagtgacaag aagttgatgc
    27481 cactaccttt aaataattaa cgcactaatt ttcaatgacc gagtattttc agtgcgatgt
    27541 gacaccacca ccatctcctg gaggagctaa gctttcccag actatgcaat tctttgagat
    27601 ttgcgccgca ttgattggaa cactggctcg ttaagcactc cttgatgcca acaatgctct
    27661 gtgtaaaatt caacttttct gtctcaaaat ttatttcttc cattccttgt attaagcttg
    27721 aaacccccgt ttcttatatt ggttcacttt gttgcagctt acagtatctt tgtatttttt
    27781 ttcttgactc tgtttggttt tgcccctccc cccttcacct ccgtaaatgc cacgtatttt
    27841 aattgatgct attctagtgc cgctttcatt ttcagccaat tttgacaagt aaccatacaa
    27901 ataattattt aaagttatga cttgacttgt cacccccttt gtttctgtga atagattttc
    27961 cttcagcgag tgattgtttc tgttttttat atgtttctct tcagtagttt ttttttctgt
    28021 cttttaaact ccccttctcc tacttctttg tgtctattgt aagtaaaata ttaattgaat
    28081 aatttcctac ccaaaattat tcaattattc tcatgtaaat ttttatttta agacacaaca
    28141 ttgcaatggt aactttaaaa caagaaaaaa caaattcaga aagatccaga cgcaattttc
    28201 tttgccttct cagccttctt ctttttgtac agagagtagt tatgttcggc actcatgtag
    28261 gcagtttcca agaaaaggaa cacaaattcg caacaggtaa ggaaggatat tccgcaccaa
    28321 agaccgagtt gtccaccaaa atcggctagc aagttgacaa actagaaata gttgagataa
    28381 attttttgga ataaaaataa attttttttt gcctgctcgc tagtagtaat tcggcatttt
    28441 ttcgaatttt tttgatacat ttctttgata cacgttcttt gcctaaattt ttcaactcac
    28501 cccataagcc tctgattcag tgagcatttc aaaattcaac tgctcgtaga acacttccac
    28561 cattgctccg ttctctctca aataggccca attttaaagt gtgttttttc ttgaattaac
    28621 ttacttataa tgcttattac actctaccgc tgtaccatta cacgatccta gttgaatttg
    28681 caaagataac gacggccact ttgccggcga gtatgtaacg gagtagattg actggcggca
    28741 tggttgttgg catcttaaaa ttgaaattgc agttttttat ttaaaaagta tataacaatt
    28801 caaaagttac ctgcaacgga aagatccgtg taggcctccc aagtcattca ttctggcgtc
    28861 aagacatttt cctgcagaaa aaaatattta tggagatgtc aaatttgaaa ctaacttgca
    28921 atagggtctg ctgcatcgca atgccgtgca ttttcaggga ctgggaaacg tggatctcca
    28981 catctgcact ctttcagcac gagttgttgg aagcaagaac ggtagcagcc ctggaatagt
    29041 tccctctgtt atcatattaa gttctatatt taattgctat tttaacaaga atcacaaagt
    29101 ttctatgacc catttttcct actaaacttg cttaaattct gtttactatt cacctctacc
    29161 gaatattcat aattgctgta aatatagtcc gatgttttgc catctggcac acaatctcca
    29221 taaggtgctg gcaaacgtga catctttcgc tgaaaacaac aacaccatta ctctataaaa
    29281 agagtttgaa tttctaatac caatcgtaat ccaaatgagg atacatatcc agttggagca
    29341 gaataaccga acgtatcagg aaatgggaaa tcttctttgt catgaatagt caaacgaacg
    29401 cctgtggctt ccgtggttgg catatagtca gacgcgttta cataaaccag catacgtaat
    29461 ccgtacatgg gacctggaat cggaacacgt tttttggttt atacataacg gacttcaaaa
    29521 attattttag aaaaaaatat gtggaaaaaa ttttgaggaa actaacctgc tcgaatacta
    29581 gtcaagttta ctgttcgatt atgattgaag gtaaagcacg aaccaaacgc agggtcaata
    29641 tgagtcagaa aatctctgaa taattgaatt tatatcatat ctgaaagcct aactaacgct
    29701 tcgatatcac acgcttttcc gttaaacgag cacttgtgga caagttccct ttttgtagta
    29761 cttagccgtt ccctatcttg cattgacaag gtagccattg caaacatgat gttttccttg
    29821 gctttagtga caattgcaac ttcatctgtc attccctgaa acttttcagt ttccacttga
    29881 tttatatatt tgtgattgtt acctgaaatc ccatagcttc aaggaagttt ggatcttcag
    29941 ttggagttcc tccttgaaga tatgtccaaa tttcaattgg tggcgtcttt ccgttgtatg
    30001 ctacacagaa tctagatgga gcacaaatac atggggatct atggcccttc gctgaaaaat
    30061 tccgatttag aaaaaaacaa caataaaaat taagaagagt aaaatcaaac aagtgaagct
    30121 agtttggcaa agtgattgaa aaacctacca gttttgttat ctttggtgca gaaagcatgt
    30181 tcattgcaag tatcacattc ggtggtttcc caggttccgt tcagaaaaca gggccacgca
    30241 tcatgagttg atctatcgaa agcgcaaata caccgatcgt caaatcccgt cggctcgtcg
    30301 aattttgttc tgaacgagaa aaaagatttg tggagaacat ttcgaaacgt ctcattatga
    30361 acttctgtat tttggaacca tatgaatttc aaatttatgg aaggcaaaat tgagccttct
    30421 caaaaattgg acttatcaaa atggacaaac tttaccgtac ctcaaaattg taagactaga
    30481 ctttttcaaa cacttttttg tcaaagttgt tagactagac tttacctctc tgattgacat
    30541 tcttccatca tattcattcc agtagttgct tccacatcgt aattctcata atgctcattg
    30601 tcatattctt ccattccatc ccattcctca tcggcatctg tgttcaaaag aatgttttac
    30661 gcgatgctca tttgacatgc aacactcacc attaatatta aatacctttt tggtagttgt
    30721 ttcaagtaac tcttcctcct tctcctcatc cttatcctct tgctcactag acccttggct
    30781 tccacaaagg catcttgcaa atcctggctc aaaaaatgct ccagataaat cacgttttcc
    30841 tcgacgacgt gccggttttg tggtgggtgc aggggtggtg ggtggttcgg tgacaacttc
    30901 gcgttcctct tcgtgatctt tgtttcctcc ggcttttccc attgctccat caaatgctga
    30961 caacgttcgc tttactaaat ccacgcttgt tgctaaactt gctttgtaag gattcaaatt
    31021 acaaagcgta attgctggaa aaggtgcagt gtctggaaat aaaaaagctc agtaaggagc
    31081 acatgatttt tcaaactacc aaatttcaat tgaatatcga caattttctc attcctgttg
    31141 tatttgtcaa gcacagattg agcattaaga tagagcatta tcatacatcc aagaaaaagt
    31201 acgacccaaa ctgctcgata atatacgttt ggagcttcac caatcatggg aattccgtga
    31261 gcagatgttt tgtagcaaaa ctctttgaaa tgccaggcta gacgtttgtc atagggtagc
    31321 aattttggat cgaattctcc cgtaataagt tcacactgaa attcggaaat gttagattac
    31381 tcagctgcga ctttttgcaa gttttatttt ttttaccgtt tattgaacat tttaagcgtt
    31441 ttgattatat tgttccaaaa caaaaaatct tggtttttaa ttttggtaca gttttgcaga
    31501 taagctatca aagtaaaata aacaagttga ttcagcaaaa acttagtagt tataaagaca
    31561 aaatacttat cgaagaatta agaaaatacg ggccttcaaa tttacagttg aaaaacttca
    31621 atgtatataa cgaatatttc aaaaactggg aacaaaatac aattgcatac aaaaataaaa
    31681 tttaccgttg caatttgaaa attacgtaaa ctcacttgta cttctgattc tgtagagttg
    31741 aaacattcgc cataaccaaa atcttcataa tattctcttt ctgtcacaaa tttagtcgtc
    31801 tcttgtaagt acgctaacgg gtctccataa acctgggaca tgtactcgga tgggtcccga
    31861 aggtgttggt agtttttcag gttttgcatc catgacattc tataacttga tagcgataaa
    31921 aaaaatagca t
//
BioPerl-1.007002/t/data/U71225.gb000444000766000024       616513155576321 16017 0ustar00cjfieldsstaff000000000000LOCUS       U71225                  1164 bp    DNA     linear   VRT 27-NOV-2001
DEFINITION  Desmognathus quadramaculatus 12S ribosomal RNA gene, partial
            sequence; tRNA-Val gene, complete sequence; and 16S ribosomal RNA
            gene, partial sequence, mitochondrial genes for mitochondrial RNAs.
ACCESSION   U71225
VERSION     U71225.1  GI:2804359
KEYWORDS    .
SOURCE      mitochondrion Desmognathus quadramaculatus (black-bellied
            salamander)
  ORGANISM  Desmognathus quadramaculatus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Amphibia; Batrachia; Caudata; Salamandroidea; Plethodontidae;
            Desmognathinae; Desmognathus.
REFERENCE   1  (bases 1 to 1164)
  AUTHORS   Titus,T.A. and Larson,A.
  TITLE     Molecular phylogenetics of Desmognathine salamanders (Caudata:
            Plethodontidae): A reevaluation of evolution in ecology, life
            history, and morphology
  JOURNAL   Syst. Biol. 45, 451-472 (1996)
REFERENCE   2  (bases 1 to 1164)
  AUTHORS   Titus,T.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-SEP-1996) Biology, University of Oregon, Eugene, OR
            97403, USA
FEATURES             Location/Qualifiers
     source          1..1164
                     /organism="Desmognathus quadramaculatus"
                     /organelle="mitochondrion"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:52105"
     rRNA            <1..638
                     /product="12S ribosomal RNA"
     tRNA            639..706
                     /product="tRNA-Val"
     rRNA            707..>1164
                     /product="16S ribosomal RNA"
ORIGIN      
        1 ggcccaaagg gtagttttag gtgaaataaa atagaattta aaatttatct agtagttata
       61 tataaacata aaatgtaaaa tcaaaaacga aagtcatact atataacctt gaatctacta
      121 cagctgagaa acaaactagg attagatacc ctactatgct caactttaaa atggaccttc
      181 ccgccagagc actacgagcc acagcttaaa actcaaagga cttggcggtg ctctacaccc
      241 acctagagga gcctgttcta taatcgacac tccccgataa acctcaccac ctcttgctaa
      301 tacagcctat ataccaccgc cctcagttca cccttcaaaa gaataatagt gaacaaaata
      361 atttaaaata aaaaagtcag gtcaaggtgc agcaaatgaa gtggaaagaa atgggctaca
      421 ttttttatag taaaaaatac ggaatattct atgaaataaa atataaagga ggatttagaa
      481 gtaaaaagaa aaaagagtgt tctttttaaa ttggcaatag agcacgcaca caccgcccgt
      541 caccctcttc aaaattaaat aaactaaata aatatataaa tttataagaa aaggtaagtc
      601 gtaacatggt aagtctaccg gaaggtggcc ttggatatcg aagtatagct taaataaagc
      661 attttgctta caccaaaaaa atatttgtta acccaaatta ccttaaattt taaatctatg
      721 ctaaatataa aatactactt cctaatacac aaaacattat tatatgatag tacgggcgac
      781 agaaaactta ttagcgcaat agaaaaagta ctgtaaagga aagatgaaat aaaattgaaa
      841 taaaataaaa atataaaaga gcaaagatta taacttttac ctttagcata atggtctagc
      901 cagtctatat taacataaag aattttagtt atataccccg aaaccaggcg agctacccta
      961 aaacagcaat atatgagcga actcttctct gtggcaaaag agtgagaaga atttttggta
     1021 gaggcgaaaa accaaacgag cccggatata gctggttact tgagaatgaa ttttagttca
     1081 attaaaagca taaatattat aaaaacataa cgcttttatt ataattaatt gaggtacagc
     1141 ccaattaata aaggaaacaa ccta
//
BioPerl-1.007002/t/data/U71225.gb.mac000444000766000024       616513155576321 16556 0ustar00cjfieldsstaff000000000000LOCUS       U71225                  1164 bp    DNA     linear   VRT 27-NOV-2001
DEFINITION  Desmognathus quadramaculatus 12S ribosomal RNA gene, partial
            sequence; tRNA-Val gene, complete sequence; and 16S ribosomal RNA
            gene, partial sequence, mitochondrial genes for mitochondrial RNAs.
ACCESSION   U71225
VERSION     U71225.1  GI:2804359
KEYWORDS    .
SOURCE      mitochondrion Desmognathus quadramaculatus (black-bellied
            salamander)
  ORGANISM  Desmognathus quadramaculatus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Amphibia; Batrachia; Caudata; Salamandroidea; Plethodontidae;
            Desmognathinae; Desmognathus.
REFERENCE   1  (bases 1 to 1164)
  AUTHORS   Titus,T.A. and Larson,A.
  TITLE     Molecular phylogenetics of Desmognathine salamanders (Caudata:
            Plethodontidae): A reevaluation of evolution in ecology, life
            history, and morphology
  JOURNAL   Syst. Biol. 45, 451-472 (1996)
REFERENCE   2  (bases 1 to 1164)
  AUTHORS   Titus,T.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-SEP-1996) Biology, University of Oregon, Eugene, OR
            97403, USA
FEATURES             Location/Qualifiers
     source          1..1164
                     /organism="Desmognathus quadramaculatus"
                     /organelle="mitochondrion"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:52105"
     rRNA            <1..638
                     /product="12S ribosomal RNA"
     tRNA            639..706
                     /product="tRNA-Val"
     rRNA            707..>1164
                     /product="16S ribosomal RNA"
ORIGIN      
        1 ggcccaaagg gtagttttag gtgaaataaa atagaattta aaatttatct agtagttata
       61 tataaacata aaatgtaaaa tcaaaaacga aagtcatact atataacctt gaatctacta
      121 cagctgagaa acaaactagg attagatacc ctactatgct caactttaaa atggaccttc
      181 ccgccagagc actacgagcc acagcttaaa actcaaagga cttggcggtg ctctacaccc
      241 acctagagga gcctgttcta taatcgacac tccccgataa acctcaccac ctcttgctaa
      301 tacagcctat ataccaccgc cctcagttca cccttcaaaa gaataatagt gaacaaaata
      361 atttaaaata aaaaagtcag gtcaaggtgc agcaaatgaa gtggaaagaa atgggctaca
      421 ttttttatag taaaaaatac ggaatattct atgaaataaa atataaagga ggatttagaa
      481 gtaaaaagaa aaaagagtgt tctttttaaa ttggcaatag agcacgcaca caccgcccgt
      541 caccctcttc aaaattaaat aaactaaata aatatataaa tttataagaa aaggtaagtc
      601 gtaacatggt aagtctaccg gaaggtggcc ttggatatcg aagtatagct taaataaagc
      661 attttgctta caccaaaaaa atatttgtta acccaaatta ccttaaattt taaatctatg
      721 ctaaatataa aatactactt cctaatacac aaaacattat tatatgatag tacgggcgac
      781 agaaaactta ttagcgcaat agaaaaagta ctgtaaagga aagatgaaat aaaattgaaa
      841 taaaataaaa atataaaaga gcaaagatta taacttttac ctttagcata atggtctagc
      901 cagtctatat taacataaag aattttagtt atataccccg aaaccaggcg agctacccta
      961 aaacagcaat atatgagcga actcttctct gtggcaaaag agtgagaaga atttttggta
     1021 gaggcgaaaa accaaacgag cccggatata gctggttact tgagaatgaa ttttagttca
     1081 attaaaagca taaatattat aaaaacataa cgcttttatt ataattaatt gaggtacagc
     1141 ccaattaata aaggaaacaa ccta
//
BioPerl-1.007002/t/data/U71225.gb.unix000444000766000024       616513155576321 17001 0ustar00cjfieldsstaff000000000000LOCUS       U71225                  1164 bp    DNA     linear   VRT 27-NOV-2001
DEFINITION  Desmognathus quadramaculatus 12S ribosomal RNA gene, partial
            sequence; tRNA-Val gene, complete sequence; and 16S ribosomal RNA
            gene, partial sequence, mitochondrial genes for mitochondrial RNAs.
ACCESSION   U71225
VERSION     U71225.1  GI:2804359
KEYWORDS    .
SOURCE      mitochondrion Desmognathus quadramaculatus (black-bellied
            salamander)
  ORGANISM  Desmognathus quadramaculatus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Amphibia; Batrachia; Caudata; Salamandroidea; Plethodontidae;
            Desmognathinae; Desmognathus.
REFERENCE   1  (bases 1 to 1164)
  AUTHORS   Titus,T.A. and Larson,A.
  TITLE     Molecular phylogenetics of Desmognathine salamanders (Caudata:
            Plethodontidae): A reevaluation of evolution in ecology, life
            history, and morphology
  JOURNAL   Syst. Biol. 45, 451-472 (1996)
REFERENCE   2  (bases 1 to 1164)
  AUTHORS   Titus,T.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-SEP-1996) Biology, University of Oregon, Eugene, OR
            97403, USA
FEATURES             Location/Qualifiers
     source          1..1164
                     /organism="Desmognathus quadramaculatus"
                     /organelle="mitochondrion"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:52105"
     rRNA            <1..638
                     /product="12S ribosomal RNA"
     tRNA            639..706
                     /product="tRNA-Val"
     rRNA            707..>1164
                     /product="16S ribosomal RNA"
ORIGIN      
        1 ggcccaaagg gtagttttag gtgaaataaa atagaattta aaatttatct agtagttata
       61 tataaacata aaatgtaaaa tcaaaaacga aagtcatact atataacctt gaatctacta
      121 cagctgagaa acaaactagg attagatacc ctactatgct caactttaaa atggaccttc
      181 ccgccagagc actacgagcc acagcttaaa actcaaagga cttggcggtg ctctacaccc
      241 acctagagga gcctgttcta taatcgacac tccccgataa acctcaccac ctcttgctaa
      301 tacagcctat ataccaccgc cctcagttca cccttcaaaa gaataatagt gaacaaaata
      361 atttaaaata aaaaagtcag gtcaaggtgc agcaaatgaa gtggaaagaa atgggctaca
      421 ttttttatag taaaaaatac ggaatattct atgaaataaa atataaagga ggatttagaa
      481 gtaaaaagaa aaaagagtgt tctttttaaa ttggcaatag agcacgcaca caccgcccgt
      541 caccctcttc aaaattaaat aaactaaata aatatataaa tttataagaa aaggtaagtc
      601 gtaacatggt aagtctaccg gaaggtggcc ttggatatcg aagtatagct taaataaagc
      661 attttgctta caccaaaaaa atatttgtta acccaaatta ccttaaattt taaatctatg
      721 ctaaatataa aatactactt cctaatacac aaaacattat tatatgatag tacgggcgac
      781 agaaaactta ttagcgcaat agaaaaagta ctgtaaagga aagatgaaat aaaattgaaa
      841 taaaataaaa atataaaaga gcaaagatta taacttttac ctttagcata atggtctagc
      901 cagtctatat taacataaag aattttagtt atataccccg aaaccaggcg agctacccta
      961 aaacagcaat atatgagcga actcttctct gtggcaaaag agtgagaaga atttttggta
     1021 gaggcgaaaa accaaacgag cccggatata gctggttact tgagaatgaa ttttagttca
     1081 attaaaagca taaatattat aaaaacataa cgcttttatt ataattaatt gaggtacagc
     1141 ccaattaata aaggaaacaa ccta
//
BioPerl-1.007002/t/data/U71225.gb.win000444000766000024       625713155576321 16615 0ustar00cjfieldsstaff000000000000LOCUS       U71225                  1164 bp    DNA     linear   VRT 27-NOV-2001
DEFINITION  Desmognathus quadramaculatus 12S ribosomal RNA gene, partial
            sequence; tRNA-Val gene, complete sequence; and 16S ribosomal RNA
            gene, partial sequence, mitochondrial genes for mitochondrial RNAs.
ACCESSION   U71225
VERSION     U71225.1  GI:2804359
KEYWORDS    .
SOURCE      mitochondrion Desmognathus quadramaculatus (black-bellied
            salamander)
  ORGANISM  Desmognathus quadramaculatus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Amphibia; Batrachia; Caudata; Salamandroidea; Plethodontidae;
            Desmognathinae; Desmognathus.
REFERENCE   1  (bases 1 to 1164)
  AUTHORS   Titus,T.A. and Larson,A.
  TITLE     Molecular phylogenetics of Desmognathine salamanders (Caudata:
            Plethodontidae): A reevaluation of evolution in ecology, life
            history, and morphology
  JOURNAL   Syst. Biol. 45, 451-472 (1996)
REFERENCE   2  (bases 1 to 1164)
  AUTHORS   Titus,T.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-SEP-1996) Biology, University of Oregon, Eugene, OR
            97403, USA
FEATURES             Location/Qualifiers
     source          1..1164
                     /organism="Desmognathus quadramaculatus"
                     /organelle="mitochondrion"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:52105"
     rRNA            <1..638
                     /product="12S ribosomal RNA"
     tRNA            639..706
                     /product="tRNA-Val"
     rRNA            707..>1164
                     /product="16S ribosomal RNA"
ORIGIN      
        1 ggcccaaagg gtagttttag gtgaaataaa atagaattta aaatttatct agtagttata
       61 tataaacata aaatgtaaaa tcaaaaacga aagtcatact atataacctt gaatctacta
      121 cagctgagaa acaaactagg attagatacc ctactatgct caactttaaa atggaccttc
      181 ccgccagagc actacgagcc acagcttaaa actcaaagga cttggcggtg ctctacaccc
      241 acctagagga gcctgttcta taatcgacac tccccgataa acctcaccac ctcttgctaa
      301 tacagcctat ataccaccgc cctcagttca cccttcaaaa gaataatagt gaacaaaata
      361 atttaaaata aaaaagtcag gtcaaggtgc agcaaatgaa gtggaaagaa atgggctaca
      421 ttttttatag taaaaaatac ggaatattct atgaaataaa atataaagga ggatttagaa
      481 gtaaaaagaa aaaagagtgt tctttttaaa ttggcaatag agcacgcaca caccgcccgt
      541 caccctcttc aaaattaaat aaactaaata aatatataaa tttataagaa aaggtaagtc
      601 gtaacatggt aagtctaccg gaaggtggcc ttggatatcg aagtatagct taaataaagc
      661 attttgctta caccaaaaaa atatttgtta acccaaatta ccttaaattt taaatctatg
      721 ctaaatataa aatactactt cctaatacac aaaacattat tatatgatag tacgggcgac
      781 agaaaactta ttagcgcaat agaaaaagta ctgtaaagga aagatgaaat aaaattgaaa
      841 taaaataaaa atataaaaga gcaaagatta taacttttac ctttagcata atggtctagc
      901 cagtctatat taacataaag aattttagtt atataccccg aaaccaggcg agctacccta
      961 aaacagcaat atatgagcga actcttctct gtggcaaaag agtgagaaga atttttggta
     1021 gaggcgaaaa accaaacgag cccggatata gctggttact tgagaatgaa ttttagttca
     1081 attaaaagca taaatattat aaaaacataa cgcttttatt ataattaatt gaggtacagc
     1141 ccaattaata aaggaaacaa ccta
//
BioPerl-1.007002/t/data/U83300.bsml000444000766000024      1033413155576321 16372 0ustar00cjfieldsstaff000000000000





 
  
   
    
    
    
    
    
    
    
    
    
     
      
       Moore W.S., DeFilippis V.R.
       The window of taxonomic resolution for phylogenies based on mitochondrial cytochrome b
       (in) Mindell D.R. (eds.). AVIAN MOLECULAR EVOLUTION AND SYSTEMATICS:81-116. Academic Press, Inc., San Diego, CA, USA (1997)
      
      
       Moore W.S., DeFilippis V.R.
       Submitted (27-DEC-1996) to the EMBL/GenBank/DDBJ databases. Biological Sciences, Wayne State University, Biological Sciences Building, Detroit, MI 48202, USA
      
      
       
       
       
       
       
      
      
       
       
       
       
       
       
       
      
     
    
    aantttggatctctcctaggcatttgcctaataacacaaattgtcacagg
cctcctgcttgccacccactacactgccgacacaaccctagccttttctt
ccgtcgcccatacatgccgcaacgttcaatacggctgactaatccgtaac
ctccatgccaacggggcctcattctttttcatctgcatctacttacacat
cggacgtggattctactacggatcctacttatttaaagaaacttgaaaca
cgggagtcatccttctcctcaccctcatagccaccgccttcgtcggctac
gtcctcccctgaggacaaatatcatcctgaggagcaaccgttattacaaa
tttattctcagccctcccctacgtaggacaaactatcgtcgaatgagcct
gaggaggattctctgtagacaaccccactctcacccgattcttcgnccta
cactttctcctcccattcttaattgnaggactcaccctaattcacttcac
tttcctccacgaatccggntcgaacaatcccctcggaatcgtatccgaca
gngataaaatcccctttcanccctacttctccntaaaagatatcctagga
ttcatattcatactcctccccctcgtnnccctagcnctattctcacctaa
cctcctaggagaccnggaaaatttnacgcccgcaaaccccctagtnacac
ccccccacatcaaaccagaatggtacttcctatttgcatatgctatccta
cgctcaatccccaataaactaggaggagtcctagccctagctgcctcagt
cctaattctattcctagcccccctccttcatacatccaaacaacgcacga
tagccttccgacccttttcccaactcctattctgaatactagtcgccaac
ctcctcatcctcacctgaatcggnagncaaccagnagaacatccct

   
  
 

BioPerl-1.007002/t/data/UnaSmithHIV-both.nex000444000766000024     27152613155576321 20512 0ustar00cjfieldsstaff000000000000#NEXUS
[Complete genomes of HIV-1, all "non-recombinant".]

begin data;
  dimensions ntax=10 nchar=9281;
  format datatype=dna gap=-;
  matrix
'A1.BY.97.97BL006'
AYRGGTGCGAGAGCGTCAGTATTAAGCGGGGG---AAAATTAGATGCATA
GGAAAAAATTCGGTTAAGGCCAGRRGGAAAGAAAAAATATAGAATAAAAC
ACCTAGTATGGGCAAGCAGGGAGCTGGAAAGATTCGCGCTTAACCCTGGC
CTTTTAGAAACATCAGAAGGATGTCAACAAATACTGGAACAGTTACAACC
AACTCTCAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAG
CAACTCTCTATTGTGTACATCAACGGATAGAGATAAAAGACACCAAGGAA
GCTTTAG---AT--AAA-ATAGAGGAAATACA------------AAATNA
NAGCAAG------------CAAAAGACC---------CA---ACAG----
--------------GCA---GCA---------------------ACT---
------------------------GGCACAGGA-----------------
-------AGCAGCAGC------------AAG------GTCAGTCAAAATT
ACCCCATAGTRCAAAATGCACAAGGGCAAATGACACACCAGTCCATGTCA
CCTAGGACTTTGAATGCATRGGTGAAAGTAATAGAAGAAAAGGCTTTCAG
CCCAGAAGTAATACCCATGTTTTCAGCATTGTCAGAGGGAGCCACCCCAC
AAGATTTAAACATGATGCTGAATATAGTGGGGGGACACCA---GGCAGCT
ATGCAAATGTTGAAAGATACCATCAATGAGGAAGCTGCTRAATRGGATAG
GTTACATCCAGCACAGGCAGGGCCTTTTCCACCAGGGCAGATGAGAGAAC
CAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAAGAACAAATA
GGATRGATGACAAGCAACCCACCTATCCCAGTRGGAGACATCTATAAAAG
ATRGATAATCCTAGGATTAAATAAGATAGTAAGAATGTATAGCCCTGTTA
GCATTTTAGACATAAGACAAGGGCCAAAAGAACCCTTCAGAGATTATGTA
GATAGGTTCTTTAAAACTCTTARAGCTGAGCAAGCTACACAGGATGTAAA
GAACTGGATGACAGAAACCCTGCTGGTCCAAAATGCAAATCCAGATTGTA
AAACCATTTTAAGAGCATTAGGATCAGAGGCTACATTAGAAGAAATGATG
ACAGCATGCCAGGGAGTGGGAGGACCCGGCCATAAAGCAARGGTTTTRGC
CGAGGCAATGAGTCAAGT---AC---AAA---A---TG--C---A-----
-----------------AACATA---ATGATGCAGAAAAGTAATTTTAGG
GGCCCAAAA---AGAATTAAGTGTYTCAACTGTGGCAAAGAAGGACACCT
AGCCAGAAATTGCAGGGCCCCTAGGAAAAARGGCTGTTGGAAATGTGGAA
AGGAAGGCCATCAAATGAAAGACTGCACT------GAGAGACAGGCTAAT
TTTTTAGGAAGAATTTGGCCTTC---CAGCAAAGGG---AGGCCAGGAAA
TTTTCCTCAGAGCAGA---------------CCAGAGCCATCAGCCCCA-
-----------------------------------CCA---GCAGAAAAC
TTTAGGATGGGGGAAGAGATA---------------ACCCCCTCCCTG--
----AAACAGGAACAG------------AAAGA---CAGGGAACAGTAT-
-----CCT------CCTTCAATTTCCCTCAAATCACTCTTTGGCAACGAC
CCCTTGTCACAGTAAGAATAGGAGGACAGCTAAAAGAAGCTCTATTAGAT
ACAGGAGCAGATRATACAGTATTAGAAGACATAAATTTGCCAGGAAAATG
GAAACCAAAAATGATAGGRGGAATTRGAGGTTTTATCAAGGTAAGACAGT
ATGATCAGATACTTGTAGAAATTTGTGRAAAAAAGGCTATARGTACGGTA
TTAGTAGGACCTACCCCTGYCAACA---TAATTRGAAGAAATATGTTGAC
TCAGCTTGGTTGTACTTTAAATTTTCCAATAAGTCCTATTGAAACTGTAC
CAGTAACATTAAAGCCAGGAATGG---ATGGCCCAAAGGTTAAACAATGG
CCATTAACAGAAGAGAAAATAAAAGCATTAMCAGACATTTGTAAG-----
-GAGATRGAAAAGGAAGGAAAAATTTCAAAAATTRGGCCTGAAAATCCAT
ACAATACTCCAGTATTTGCTATAAAGAAAAAGGACAGCACTAAGTGGAGG
AAATTAGTASATTTCASRGAGCTCAATAAAAGAACTCAGGACTTTTSRGA
AGTTCAATTAGGAATACCCCATCC---AGCGGGTTTAAAAAAGAAAAAAT
CAGTAA---CAGTACTAGATGTGGGGGATGCATATTTTTCAGTACCTTTA
GATGAAAGCTTCAGAAAGTNTACNGCATTCACTATACCAAGTGTAAACAA
TGAGACACCARGGATCAGATATCAGTACAATGTACTTCCACAGGGATGGA
AAGGATCACCATCAATATTCCAGAGTAG---CATGACAAAAATCTTAGAG
CCCTTTAGATTAAAAAATCCAGAAATAGTTATCTATCAATACATRGATGA
CTTGTATGTAGGCTCTGATTTAGAAACAGGGCAACATAGAACAAAAATAG
AGGAGTTAAGAGCTCATCTATTGAGCTGGGGATTTACTACACCAGAC---
AAAAAGCATCAGAAAGAACCTCCATTTCTTTGGATWRGATATGAANTCCA
TCCTGACAAATGGACAGTCCAGCCTATAATGCTGCCAGATAAAGACAGCT
GGACTGTCAATGATAT---ACAGAAATTAGTRGGAAAACTAAATTGGGCA
AGTCAGATTTATCCAGAGATTAAAGTAAGGCAATTGTGTAAACTCCTTAR
RGGAGCCAAAGCACTGACAGATATAGTGACACTGACTGAGGAAGCAGAAT
TAGAATTGGCAGAGAACA---GAGAGATTCTAAAARAACCTGTGCATGRA
GTATATTATGACCCATCAAAAGATTTAGTAGCAGAAATACAGAAACAAGG
ACAAGACCAATGGACATATCAAATTTATCAGGAGCCATTTAAGAATCTAA
AAACAGGAAAATATGCAAAAAARRGGTCTGCTCACACTAATRATGTAAAA
CAATTAACAGCAGTGGTGCAAAAAGTGGCCACAGAAAGCWTAATACTATR
GGGAAAGA---CTCCTAAATTTAGACTAC--CCCATACAAAARGAAACAT
RGGAAGCMT--TGGTRGATGGARTWCTGGCAGGCTACCTRGATTCCTGAA
TAGGAGTTTGTCAATACCCCTCCTCTAGTAAAACTATGGTACCAGTTGGA
GAAAGAACCCATAGTAAGAGCAGAGACTTTCTATGTAGATAGGGCAGCTA
ACAGGGAGACTAAGATAGGAAAGGCAGGGTATGTTACTGACTGAAGAAGA
CAAAAGGTTGTTCCTCTAACTGAGAC--CAACGAATCAAAAGACTGAATT
ACATGCAATCCATCTAGTTTTGCAGGATTCAGGATCAGAAGTAGATATAG
TA--AACAGACTCACAATATGCATTAGGAATTAT--TTCAGGCACAACCA
GACAGGAGTGAATCAGAGATAGTCAATAAAATAATAGAGAAACTAATAAA
AAAAGAAAGWGTCTACCTGT--TCWTAGGTACCAGCGCACAAGAGGATTR
GAGRAAATGAACAAGTAGATAAATTAGTCAGTAATRGAATCAGGARGGTG
TTATTTTTAGAARRGATAGATAAGGCTCAAG---AARAACATGAAAAATA
T--TCACAGCAATTGAAAAGCAATGGCTAGTGATTTTAATCTGCCACCTA
TAGTAGCAAARGAAATAGTAGCCAGCTNTGATAAAT---GTCA---ACTA
AAARGGGAAGNTATGCATRGACAGGTAGACTGTAGTCCARRGATATGGCA
ATTAGATTGCACACATCTARAARGAAAAGTAATCATAGTRGCAGTCCAYG
TAGCCAGTGGCTATATAGAAGCAGAAGTTATCCCAGCAGAAACAGGACAG
GAGACAGCATACTTTCTGCTAAAATTAGCAGGAAGATGGCCAGTAAAAGT
AGTACACACAGATAATGGCCCCAATTTCACCAGCAGTGCAGTTAAGGCTG
CCTGTTGGTAGGCAAATATCCAACAGGAATTTARGATTCCCTACAATYCC
CAAAGTCAAGGAGTAGTGGAGTCTATGAATAARGAATTAAAGAAAATCAT
AAGGCAGGTAAGAGAGCAAGCTGAATACCTTAAGACAGCAGTACAAATGG
CAGTATTCATTCACAATTTTAAAAGAAAA---GGGGGGATTGGGGGGTAC
AGTGCAGGNGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAA
AGAATTACAAAAACARATTACAAAAATTCAAAATTTTYSGGTTTATTACA
GAGACAGCAGAGATCCAATTTGGAAAGGACCAGCAAAACTACTCTRGAAA
GGTGAAGGGGC---AGTGGTAATACAGGACAATNACGATATAAAAGTAGT
ACCAAGAAGAAAAGCAAAGATCATTNGGGATTNTRGAAAACAGATGGCAG
GTGNTGATTGTGTGGCAAGTAGACAGGATGAGGATTAGA---ACATGGAA
CAGTTTAGTAAAACATCATATGTATGTCTCAAAGAAAGCTAGAGAGTAGG
TTTATAGACATCACTATGAAAGCAGGCAGCCAAGAGTAAGTTCAGAAGTA
CACATCCCACTAGGGG---ATG---CTAGGCTAGTAGTAAAAACATATTR
RGGTCTGCATGCAGRAGAAAAAGACTGGCAATTAGGTCATRGGGTCTCCA
TAGAATRGAGACAGGAAARGTATAGCACACAA------ATAGACCCTGAC
CTGGCGGACCAACTAATTCATCTGTATTATTTTGACTGTTTTTCAGAATC
---TGCCATAAGGAAAGCCATAGTAGGACACATAGTTAGCCCTAGGTGTA
ACTATCCAGCAGGACACA---ACAAGGTAGGATCTCTACAATACTTGGCA
CTGAAAGCATTAGTAACACC---AACAAGGGAAAGGCCACCTTTGCCTAG
TGTTAGGAANCTAACAGAGGATAGATRGAACAAGCCCCAGAAGACCAGGG
GCCGCAGARGGAACCACACAATGAATRGATGTTAGAACTGTTAGAAGATA
TTAAGCATGAAGCTGTCAGACATTTTCCAAGGCCRTGGCTCCATGGATTA
GGACAACATATCTATAACACCTATRGGGATACTTRGGAAGARGTTGAAG-
--CTATAATAAGAACTTTGCAA---CAACTACTGTTTGTTCAT---TTCA
GAATTARGTGCC---AACATAGCAGA--AATAGGCATT---GTGCAAARG
AGAAGAGTCA----------GGAATRGATCCAGTAGATCCTAACCTAGAG
CCCTRGAATCATCCRRGAAGTCAGCCTAAAACTGRTTGTAG--GCAATTG
TTACTGTAAAAAGTGTTGCTGGCATTGCCAA---------------ATTT
GCTTTCTAAAA--AAAAGGCTTAGGCATCTCCTATGGCAGGAAGAAGCGG
AGGC------A---CAGACGCGGA------A---CTTCTCACAGCAGTAA
GGATCATCANATTCCTATATCAAAGCAGTAAGTAC--TA-----------
-AATAAATGTA---ATG---------------------------------
---------ACACCTTTAR---------------AAATTTATGCAATAGT
A---GCATTAGTAGTAGT---GT--TTGTTA-TAGCNNTAGTTGTGTGGA
CTATAGTAGGTATARAATAT---ANNN------------NATTGCTAAAA
CAA---AGAAAAATAGACAGGTTARTTGAGAGAANNNNAGANAGAGCAGA
AGACAGTGGCAATGAAAGCGAGGGGGATGCARAGGAATTATCAACACTT-
--ATGGAGGTG------------------------RGGAACTATG---CT
CTTTTGG---ATGATAATAAT------------GTGT------AAGGCTG
C---------AGA---A------------G---A------CTTG------
TAGGTCACRGTATACTATARGGTACCTGTGTRGARAGATGCAG---CG--
ACCACCC-TATTTTGTGCATCAGATGCTAAAGCAYATGATAAAGAAGTAC
ACAATGTCTGGGCTACACATGCCTGTGTACCCACAGACCCTGACCCACAA
GAAATAATTTTAGGAAATGTGACAGAAAAATTTGACATGTRGAAAAATAA
CATRGTAGAACAAATGCAAACAGATATAATCAGTCTCTAGGACCAAAGCC
TAAAGCCATGTGTAAAGTTAACCCCTCTCTGCGTTACTTTAAATTGTGCT
G---AAC---CC--AAC---------------------------------
-----------AG--CACT---AG---ATC-TA-ACA---AC--------
-------A-GTAGCGTT---AA--C-------------------------
--------------------------AGC---AA--C---AG--C-----
AGC---GATAGCTTGTTT-RAA-RA-AATGA-AGAACTGCTCTTTCAACA
TGACCACAGAACTAAGAGATAAAAGGAAAACTGTACATTCAC---TTTTT
TATAAACTTGATATAGTATCAACTAGTAAT--------------------
------------------AA--TGATAGT---RGG---------------
---------------------C---AG--TATAGA-C-TAATAAATTGTA
-ATACATCAGCCATGACACAGGCCTGTCCTAARGTAACCTTTGAGCCAAT
TCCTATATATTATTGTGCCCCAGCTGGTTTTGCGATTCTAAAGTGCAARG
ATACAAATTTTACTAGAACARGGCCATGCAAGAATGTCAGCACAGTACAA
TGCACACATRGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTAAATGG
CAGTCTAGCAGAG---AAAGA---RGTAATGATTAGATCTGAAAATATCA
CAGACAATGTCAAAATCATAATAGTACAGCTTACTGAGCCTGTAAACATC
ACTTGTATCAGACC------T------GGCAACA---AT---ACAAGAAC
AAGTATACGTATA---------GGACCAGGACAAACCTTCTATGCA---A
CAGGTGAT------GTAATARRGGACATAAGAAAAGCATATTGTAATGTC
AGCAGAGCAGCATRGAATAGCACTTTACAAAAGATAAGT---AC--ACAA
TTAAGAAAA------TACTTT---A----AT--AAC------AAAACA--
----ATAATCTTTAAG----AGCTC---CACAGGARAGGATTTAGAAGTT
ACAACAC------ATAGTTTCAATTGTGGAG---GAGAATTTTTCTATTG
CAATACAACAGACCTGTTCAAT---AGCACT---TR---G----------
------GAT-----------------------------------GGCACT
G---TCACA-----------------AAT---AG-CAC---A---A----
--AG--GC--CAA---T---------------GGAACTATAACT------
---CTACCATG-CA-GAATAAAGCAAATTATAAATATGTGGCA---GAGA
GTAGGACAAGCAATGTATGCCCNTCCTATCAAARGAAGTATAAGGTGTGA
ATCAAACATTACAGGACTACTACTAACAAGAGATGG---TRGAGG---TR
GA------ACT---------------AAT--NGCA---GC--AATGAGAC
CTTCAGACCTATAR-GAGGAG-ATWTGAGGAACAATTGGAGAAGTGAACT
ATATAAGNATAAAGTAGTAAAAATTGAACCAATARRAGTAGCACCTACCA
GGGCAAAGAGAAGAGTRGTRGA------GAGAGAAAAAAGAGCAA---TT
GGA-------CTARGAGC---TG--C---CTTCCTTARGT---TCTTAGG
----AG-CAGCAGRAAG-TACTATRGGCGCGGCGTCAATGACGCTGACGG
TACAGGCCAGACAATTATTGTCTGGCATAGTGCAACAGCAAAGCAATTTG
CTGARGGCTATAWARGCTCAGCAGCAYCTGCTGAAACTCACGGTCTRGGG
CATTAAACAGCTCCAGGCAAGARTCCTGGCTGTGGAAAGRTACCTAAAGG
ATCAGCAGYTCCTAAGAATTTGRGGTTGCTCTARAAAACTCATCTGCACC
ACTAATGTGCCCTRGAAYTCTAGTTRGAG---T---AAT-----------
-AAATYTCAGAG---TGAGATAT---ARG---ATAACATGACCTAGATGC
AATAGGACAARGAAGTTATCAATWACACAGACATAATATATGATCTAATT
RAAAAATCGCAAAACCAGCAGGAAAAGAATGARCAAGATTTATTGGCATT
AGATAAGTAGGCAGGTCTGTRRAGTTRGTTWGACATATCAAATTGGTTAT
RGTATATARAAATATTTATAATAATAGTAGGAGGCTTAATARGATTAAGA
ATAATTTTTGCTGTGCTTTCTATAATAAATAGAGCCAGGCARRGATACTC
ACCCTTGTC---ATTGCAGACC---CTTACCC---CACACCCAGAAAGA-
-----CCAGACAGGCCCRGAAGAATCAAAGAAGAAGGTRGAGAGCAAGGC
AGAGACAGATCAATTCGATTAGTAAGCGGATTTTTAGCACTTGCCTRGGA
CGATCTACRGAGCCTGTGTCTCTTCAGCTACCACCGATTGAGAGACTTCA
TCTCGATTGCAGCGAGGACTGTRGAACTTCTGAAA---CGCAGCAGTCTC
AARGGACTGAGACTGRGGTARGARGGCCTCAAATATCT---RRGGAATCT
T---CTRGGATATTRRGGTCAGGAACTAAAGAGTAGTGCTATTAATCTGA
TAGATA---CCATAGCAATAGCAGTAGCTRGGTRGACAGATARGGTTATA
GAAATAGGACAAAGATTTTGTAGAGCTATTCGTAACATACCTAGGAGAAT
CAGACARGGCGCAGAAAAAGCTTTGCAATAA
'A1.KE.00.KER2008'
------GCGAGAGCGTCAGTATTAAGTGGGGG---AAAATTAGATGCATG
GGAGAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGACTGAAAC
ACTTAGTATGGGCAAGCAGGGAGCTGGAAAAATTCGCACTTAACCCTGGC
CTTTTAGAAACTTCAGAAGGATGTCAGCAAATAATGAACCAAATACAACC
AGCTCTTCAGACAGGAACAGAAGAACTTAGATCATTATTTAATGCAGTAG
CAACCCTCTATTGTGTACATCAGCGGATAGAGGTAAAAGACACCAAGGAA
GCTTTAG---AT--AAA-GTAGAGGAAATACA------------AAACAA
GAGCAAA------------CAAAAGACA---------CA---ACAG----
--------------GCA---GCA---------------------GCT---
------------------------GATACAGGA-----------------
-------AACAACAGC------------AAG------GTCAGCCATAATT
ACCCTATAGTGCAAAATGCACAAGGGCAAATGATACATCAGTCCTTATCA
CCAAGGACTTTGAATGCATGGGTAAAGGTAATAGAAGAAAGGGGTTTTAG
CCCAGAAGTAATACCCATGTTCTCAGCATTATCAGAAGGAGCCACCCCAC
AAGATTTAAATATGATGCTGAACATAGTGGGGGGACACCA---GGCAGCT
ATGCAAATGTTAAAAGAAACCATCAATGAGGAAGCTGCAGAATGGGACAG
ATTACATCCAGCACAGGCAGGGCCTATTCCACCAGGCCAGATAAGAGACC
CAAGGGGAAGTGACATAGCAGGAACTACTAGCACCCCTCAAGAACAAATA
ACATGGATGACAAACAACCCACCTATCCCAGTGGGAGACATCTATAAAAG
ATGGATAATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTA
GCATTCTGGATATAAAACAAGGGCCAAAAGAACCCTTCAGAGACTATGTA
GATAGGTTCTTTAAAGTTCTCAGAGCCGAACAAGCTACACAGGAAGTAAA
AGGTTGGATGACAGAGACCCTGCTGGTTCAAAATGCAAATCCAGATTGTA
AATCCATCCTAAGAGCATTAGGAACAGGGGCTACATTAGAAGAAATGATG
ACAGCATGCCAGGGAGTGGGAGGACCCAGCCATAAAGCAAGGGTTTTAGC
TGAGGCAATGAGTCAAGC---AC---AAC---A---GG--C---A-----
-----------------AATGTA---ATGATGCAGAGGGGCAATTTTAAG
GGCCAGAAA---AGAATTAAGTGTTTCAACTGTGGCAAAGAGGGACACCT
AGCCAGAAATTGCAGAGCCCCTAGGAAAAAAGGCTGTTGGAAGTGTGGGA
AAGAAGGACACCAAATGAAAGATTGCATT------GAGAGACAGGCTAAT
TTTTTAGGGAAAATTTGGCCTTC---CAGCAAAGGG---AGGCCAGGGAA
TTTTCCTCAGAGCAGA---------------CCGGAGCCAACAGCCCCA-
-----------------------------------CCA---GCAGAGATC
TTTGGGATGGGGGAAGAGATA---------------ACCTCCCCTCCG--
----AAGCAGGAGCAG------------AAAGA---GAGGGAACAAACC-
-----CCA------CCCTTTGTTTCCCTCAAATCACTCTTTGGCAACGAC
CCGTTGTCACAGTAAAAGTAGGAGGAGAGATGAGAGAAGCTCTATTAGAT
ACAGGAGCAGATGATACAGTATTAGAAGATATAAATTTGCCAGGAAAATG
GAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAGGTAAAACAAT
ATGATCAGGTATCTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTA
TTAGTAGGACCTACACCTGTCAACA---TAATTGGAAGAAATATGTTGAC
TCAAATTGGTTGTACTTTAAATTTTCCAATTAGTCCTATTGAAACTGTAC
CAGTAACATTAAAGCCAGGAATGG---ATGGCCCAAGGGTTAAACAATGG
CCATTGACAGAAGAAAAAATAAAAGCATTGACAGAAATTTGTCAA-----
-GAGATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCAT
ACAATACTCCAATATTTGCAATAAAGAAAAAAGATAGCACTAAATGGAGG
AAATTAGTAGATTTCAGAGAGCTCAATAAAAGAACACAAGACTTTTGGGA
AGTTCAATTAGGGATACCGCACCC---AGCGGGACTAAAAAGGAAAAAAT
CAGTAA---CAGTACTAGATGTGGGGGACGCATATTTCTCAGTTCCCCTA
GATAAAAACTTTAGAAAGTATACTGCATTTACCATACCTAGTTTAAATAA
TGAAACACCAGGAATTAGGTATCAATACAATGTGCTTCCACAAGGATGGA
AAGGATCACCAGCAATATTCCAGTGCAG---TATGACAAAAATCTTAGAG
CCCTTTAGATCAAAAAATCCAGAAATAATTATCTATCAATATATGGATGA
CCTGTATGTAGGATCAGATTTAGAAATAGGGCAGCATAGAGCAAAAATAG
AAGAATTAAGAGCTCATCTACTGAGCTGGGGATTTACTACACCAGAC---
AAAAAGCATCAGAAAGAACCTCCATTCCTTTGGATGGGATATGAGCTCCA
TCCTGACAAGTGGACAGTCCAGCCTATAGAGCTGCCAGAAAAAGAAAGCT
GGACTGTCAATGATAT---ACAGAAATTAGTGGGAAAACTAAATTGGGCC
AGTCAAATTTATCCAGGAATTAAAGTAAAGCAATTATGTAAACTTCTTAG
GGGAGCCAAAGCACTAACAGATATAGTAACACTGACTGAGGAAGCAGAAT
TAGAATTAGCAGAGAACA---GGGAGATTCTAAAAGACCCTGTACATGGA
GTATATTATGACCCATCAAAAGACTTAACAGCAGAAATACAGAAGCAAGG
GCAAGACCAATGGACATACCAAATTTATCAGGAGCCATTTAAAAATTTAA
AGACAGGAAAATATGCAAGAAAAAGGTCTGCCCACACTAATGATGTAAGA
CAATTAGCAGAAGTGGTGCAGAAAGTGGTCATGGAAAGCATAGTAATATG
GGGAAAGA---CTCCTAAATTTAAACTA---CCCATACAAAAAGAGACAT
GGGAGACA---TGGTGGATGGACTATTGGCAGGCTACCTGGATTCCTGAA
TGGGAGTTTGTCAATACCCCTCCCCTAGTAAAATTATGGTACCAGTTGGA
GAAAGACCCCATAGCAGGAGCAGAGACTTTCTATGTAGATGGGGCAGCCC
ATAGGGAGACTAAGCTAGGAAAGGCAGGATATGTCACTGACAGGGGAAGA
CAAAAGGTTGTTTCCCTGACTGAGA---CAACAAATCAAAAAACTGAACT
ACATGCAATTTATCTAGCCTTGCAGGATTCAGGATCAGAAGTAAATATAG
T---AACAGACTCACAGTATGCATTAGGAATCA---TTCAGGCACAACCA
GACAGAAGTGAATCAGAGATAGTTAATCAAATAATAGAGAAGCTAATAGG
AAAGGACAAAGTCTACCTG---TCATGGGTACCAGCACACAAAGGGATTG
GAGGAAATGAACAAGTAGATAAATTAGTCAGCTCTGGAATCAGGAGGGTA
CTATTTCTAGATGGGATAGATAAGGCTCAAG---AAGAACATGAAAGATA
---TCACAACAATTGGAGAGCAATGGCTAGTGATTTTAATATCCCACCTA
TAATAGCAAAGGAAATAGTAGCCAGCTGTGATAAAT---GTCA---ACTA
AAAGGGGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGGATGTGGCA
ATTAGATTGCACACATCTAGAAGGAAAAGTAATTCTGGTAGCAGTCCATG
TAGCCAGTGGCTATATAGAAGCAGAAGTTATCCCAGCAGAAACAGGACAG
GAGACAGCATACTTTCTGCTAAAATTAGCAGGAAGATGGCCAGTAAAAGT
AGTACACACAGACAATGGCAGCAACTTCACCAGCGCTGCATTTAAAGCAG
CCTGTTGGTGGGCAAATGTCCAACAAGAATATGGAATTCCCTACAATCCC
CAAAGTCAAGGAGTAGTGGAATCTATGAATAAGGAATTAAAGAAAATCAT
AGGGCAGGTAAGGGACCAAGCTGAACACCTCAAGACAGCAGTACAAATGG
CAGTATTCATTCACAATTTTAAAAGAAAA---GGGGGGATTGGGGGGTAC
AGTGCAGGGGAAAGAATAATAGACATAATAGCATCAGACATACAAACCAA
AGAACTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACA
GGGACAGCAGAGATCCACTTTGGAAAGGACCAGCAAAACTACTCTGGAAA
GGTGAAGGGGC---AGTAGTAATACAGGACAATAGTGATATAAAGGTAGT
ACCAAGGAGAAAAGCAAAGATTATCAGGGACTATGGAAAACAGATGGCAG
GTGATGATTGTGTGGCAGGTAGACAGGATGAGGATTAGA---ACATGGAA
CAGTTTAGTAAAACATCATATGTATATTTCAAAGAAAGCTAAAGGTTGGT
TTTATAGACATCACTATGAAAGCAGGCATCCAAAAGTAAGTTCAGAAGTA
CACATCCCACTAGGGG---ATG---CTAAATTAGTAGTAAGGACATATTG
GGGTCTGCATCCAGGAGAAAAAGATTGGCACTTGGGTCATGGGGTCTCCA
TAGAATGGAGGCTAAAAAGATATAGCACACAA------GTAGATCCTGAA
CTGGCAGACCAACTAATTCATCTGCATTATTTTAACTGTTTTTCAGAATC
---TGCCATAAGGAAAGCCATATTAGGACAAGTAGTTAGCCCTAGTTGTG
AATATCAAGCAGGACATA---ACAAGGTAGGATCTCTACAATATTTGGCA
CTGAAAGCATTAGTAACACC---AAAGAAGACAAAGCCACCTTTGCCTAG
TGTTAAGAAACTAGCAGAGGATAGATGGAACAAGCCCCAGAAGATCAGGG
GCCACAGAGAGAGCCATACAATGAATGGACATTAGAATTGTTAGAAGAGC
TTAAAAATGAAGCTGTTAGACATTTTCCTGGGCCATGGCTTCATGGATTA
GGACAATATATCTATCACACCTATGGGGATACTTGGGAAGGAGTTGAAG-
--CTATGCTAAGAATTTTGCAA---CAACTACTGTTTGTTCAT---TTCA
GAATTGGGTGCA---CACATAGCAG---AATAGGCATT---ATTCCCAGG
AGAAGAGCCA----------GGGATGGATCCGGTAGATCCTAACCTAGCG
CCCTGGCAACACCCGGGAAGTCAGCCTACAACTCCTTGTA---ACAAGTG
TTTCTGTAAAAAGTGTTGCTATCATTGTCCA---------------GTTT
GCTTGCTGAA---CAAAGGCTTAGGCATCTCCTATGGCAGGAAGAAGCGG
AGAC------A---GCGACGAGGA------A---CTCCTCAAAGCAATAA
GGATCATCAAAATCCTATACCAAAGCAGTAAGTAC--TTAGTAACT----
-AATATATGTA---ATGTTG------------------------------
---------TCTGCTTTAG---------------AAATCTGTGCAATTGC
A---GGACTGGTAATAGC---TT--TAATCA-TAGCAATAGTTGTGTGGA
CTATAGTAGGTATAGAATAT---AGGA------------GATTGTTAAAA
CAA---AGAAAAATAGACAGGTTAATTGAGAGAATAAGAGAAAGAGCAGA
AGACAGTGGCAATGAGAGTGATGGGGACACAGAGGAATTGGCAGCCCTT-
--ATTGAGATG------------------------GGGAACTATG---AT
CTTGGGG---ATGCTAATGAT------------CTGT------AGTGCTG
C---------AGA---C------------A---A------CTTG------
TGGGTTACTGTCTATTATGGGGTACCTGTGTGGAAAGATGCAG---AG--
ACCACCT-TATTTTGTGCATCAGATGCTAAAGCATATGAGACAGAAAAAC
ATAATGTCTGGGCTACACATGCCTGTGTACCCACAGACCCCAGCCCACAA
GAAATACCTTTGAAAAATGTGACAGAAAAGTTTAACATGTGGAAAAATAA
CATGGTAGAACAGATGCATACAGATATAATCAGTCTATGGGACCAAAGCC
TAAAGCCATGTGTACAGTTAACCCCTCTCTGCGTCACTCTAAATTGTAGT
G---ACG---TC--ACCACCAATAACACCAAG------------------
-----------GT--CAAT---AC---CAC-CA-GTG---CC--------
-------C-CTACCACC---GC--T-------------------------
--------------------------GCC---AC--T---GT--C-----
AAC---AATGA------C-AGT-GA-CATGA-AAAACTGTTCTTACAATA
TGACCACAGAACTAAGGGATAAGAAACAGAAAATGTATTCAC---TCTTT
TATAGACTTGATGTAGAACTAATAAATAAG--------------------
-------AATA---AT--AG--TAATAGC---ACT---------------
---------------------G---AG--TATGTA-T-TAATAAATTGTA
-AAACCTCAACCCTTACACAGGCTTGTCCAAAGGTATCCTTTGAGCCAAT
TCCCATACATTATTGTGCTCCAGCTGGTTTTGCGATTCTAATGTGTAAGG
ATAAGGAGTTCAATGGAACAGGGCTATGCAAGAATGTCAGCACAGTACAA
TGCACACATGGAATCAAGCCAGTAGTGTCTACTCAACTACTATTAAATGG
CAGTTTAGCGGAA---AAAAG---GGTAATGATTAGATCTGCAAATATCA
CAGACAATACCAAAAACATAATAGTACAACTTAAGGATCCTGTAGAAATT
AATTGTACCAGACC------T------AACAACA---AT---ACAAGAAG
AGGTGTACATATA---------GGGCTAGGGAGAAGATTCTATACA---A
CA---CAG------GTAGTAGGGGATATAAGACAAGCATATTGTAATGTC
AGTAAATCAAAATGGGATGATACTTTGAAAAAAGTAGTT---TA--CCAA
TTAAGAAAA------TACTTT---A----AC-----------AAAACA--
----ATAATCTTTAAC----TCCTC---CTCAGGAGGGGATGTAGAAATT
ACAACAC------ATATGTTTACTTGTGGAG---GAGAGTTTTTCTATTG
TAATACATCAGGCCTGTTCAAT---AGCACT---TG---G----------
------CCT-----------------------------------GTCAAT
C---AGGAG---T-C-------A---AAT---AG-CAC---A---A----
--AG--TC--AAA---T---------------GGCATTATAACT------
---CTCCGATG-CA-GAATAAAGCAAATCATAAATATGTGGCA---GAGA
ACAGGACAAGCAATGTATGCCCCTCCCATTCAAGGAATAATAAAGTGTGT
ATCAAACATTACAGGACTACTGTTAACAAGAGATGG---TGGGAA---TA
GT-----------------------------ACTG---TC--AATGAAAC
TTTCAGACCTGGAG-GAGGAG-ATATGAGGGACAATTGGAGAAGTGAATT
ATATAAGTATAAAGTAGTAAAAATTGAACCACTAGGAGTAGCACCCACCA
AGGCAAGGAGAAGAGTGGTGGG------AAGAGAAAAAAGAGCAG---TT
GGA-------ATAGGAGC---TG--T---TTTCCTTGGGT---TCTTAGG
----AG-CAGCTGGCAG-CACTATGGGCGCGGCGTCAATAACGCTGACGG
TACAGGCCAGACAATTACTGTCTGGCATAGTGCAACAGCAAAACAATTTG
CTGAGGGCTATAGAGGCTCAACAACAACTGTTGAAACTCACGGTCTGGGG
CATTAAACAGCTCCAGGCAAGAGTCCTGGCTGTGGAAAGATACCTAAGGG
ATCAACAGCTCCTAGGAATTTGGGGCTGCTCTGGAAAACTCATCTGCACC
ACTAATGTGCCTTGGAACTCCAGTTGGAG---T---AAT-----------
-AAGTCTCAGAG---TGAGATAT---GGG---ACAACATGACCTGGCTGC
AATGGGATAGAGAAATTAACAATTATACAGACATAATATATAGACTACTT
GAAGATTCGCAAAACCAGCAGGAAAAGAATGAACAAGACTTATTGGCATT
GGACAAGTGGGCAAGCCTGTGGACTTGGTTTGACCTATCAAACTGGCTGT
GGTACATAAAAATATTTATAATGATAGTAGGAGGTTTAATAGGATTAAGA
ATAGTTTTTGCTGTGCTTGCTGTAATAAATAGAGTTAGGCAGGGATACTC
ACCTTTGTC---GTTCCAGACC---CTTACCC---CAAACCCAAGGGAA-
-----CTCGACAGGCCCGGAAGAATCGAAGAAGAAGGTGGAGAGCAAGAC
AGAGGCAGATCGATTCGCTTAGTGAGCGGATTCTTAGCACTTGCCTGGGA
CGACCTGCGGAGCCTGTGCCTCTTCAGCTACCACCACTTGAGAGACTTCA
TCTTGATTGCAGCGAGGATTGTGGGACTTCTGGGA---CGCAGG------
---------------GGGTGGGAAGGCCTCAAGTATCT---GTGGAATCT
C---CTGATATATTGGGGTCAGGAACTAAAAACTAGTGCTGTTAGCTTGC
TTGATA---CCACAGCAATAGTAGTAGCTGGCTGGACAGATAGGGTTCTA
GAAATAGGACAAAGAATTGGTAGGGCTTTTATCAACATACCTAGAAGAAT
TAGACAGGGTTTTGAAAGGGCTTTGCTGTAA
'A1.KE.00.KER2009'
------GCGAGAGCGTCAGTATTAAGCGGGGG---AAAATTAGATGCATG
GGAGAGGATTCGGCTAAGGCCAGGGGGAAAGAAAAAATATAGACTGAAAC
ATTTAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCTGGC
CTTTTAGAAACAGCAGAAGGATGTCAGCAAATAATAGAACAGTTACAACC
AGCTCTCAAGACAGGAACAGAAGAACTTAAATCATTATTCAATGCAGTAG
CAGTCCTCTATTGTGTACATCAAAGAATAGATGTAAAAGACACCAAGGAA
GCTCTAG---AT--AAA-ATAGAGGAAATACA------------AAATAA
GAGCAAG------------CAAAAGACA---------CA---ACAG----
--------------ACA---GCA---------------------GCT---
------------------------GACACAGGA-----------------
-------AACAGCAGC------------AAG------GTCAGCCAAAATT
ACCCTATAGTGCAAAATGCACAGGGGCAAATGATACACCAGACCGTGTCA
CCTAGGACTTTGAATGCATGGGTAAAAGTAATAGAAGAGAAGGCTTTCAG
CCCAGAAGTAATACCCATGTTCTCAGCATTAGCAGAAGGAGCCACCCCTG
GAGATTTAAATACGATGCTGAATATAGTGGGGGGACACCA---GGCAGCC
ATGCAAATGTTAAAAGATACCATCAATGAGGAGGCTGCAGAATGGGACAG
ACAACATCCAGTACATGCTGGACCTATTCCACCAGGCCAGATGAGAGAAC
CAAGGGGAAGTGACATAGCAGGAACTACTAGTACCACTCAAGAGCAAATA
GGATGGATGACAAGTAACCCACCTATCCCAGTGGGAGAAATCTATAAAAG
ATGGATAATCCTGGGATTAAATAAGATAGTAAGAATGTATAGCCCTGTTA
GCATTCTGGATATAAGACAAGGGCCAAAAGAACCCTTCAAAGATTATGTA
GATAGGTTCTTTAAAACTCTCAGAGCTGAGCAAGCTACGCAGGAGGTAAA
AAATTGGATGACAGAAACATTACTGGTCCAAAATGCAAATCCAGATTGTA
AAACCATTCTAAGAGCATTAGGACCAGGGGCTACATTAGAAGAAATGATG
ACAGCATGCCAGGGAGTGGGAGGACCCAGCCATAAAGCAAAGATTTTGGC
TGAGGCAATGAGTCAGGC---AC---AAC---A---TA--C---A-----
-----------------AACATA---ATGATGCAGAGAGGTAATTTTAGG
GGTCAAAAA---AGGATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCT
AGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGGA
AGGAGGGACACCAAATGAAAGACTGCACG------GAAAGACAGGCTAAT
TTTTTAGGGAAAATCTGGCCTTC---CAGCAAGGGG---AGGCCAGGAAA
TTTTCCACAGAAAAGA---------------CTGGAGCCAACAGCCCCA-
-----------------------------------CCA---GCAGAGATC
TATGGGATGGGGGAAGAGATA---------------GCCTCTCCTCCG--
----AAGCAGGAGCAG------------AAAGA---CAGGGAACAGGGT-
-----CCA------CCTGCAATTTCCCTCAAATCACTCTTTGGCAACGAC
CTATTGTCACAGTAAAAATAGGGGGACAGCTAAGAGAAGCTTTATTAGAT
ACAGGAGCAGATGATACAGTATTAGAAGACATAGATTTGCCAGGAAAATG
GAAACCAAGAATGATAGGGGGAATTGGAGGTTTCATCAAAGTAAAACAGT
ATGATCAGATACTTATAGAAATTTGTGGAAAAAGGGCTATAGGTACAGTA
TTAGTAGGACCTACACCTGTCAACA---TAATTGGAAGAAACATGTTGAC
CCAGATTGGTTGTACTTTAAATTTCCCAATTAGTCCTATTGAGACTGTAC
CAGTAAAATTAAAGCCAGGAATGG---ATGGCCCAAAGGTTAAACAATGG
CCATTAACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACA-----
-GAGATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCAT
ACAATACTCCAATATTTGCAATAAAGAAAAAAGATAGTACTAAATGGAGA
AAATTAGTAGATTTCAGAGAGCTTAATAAAAGAACACAAGACTTTTGGGA
AGTTCAATTAGGAATACCGCATCC---AGCGGGCTTAAAAAAGAAAAAAT
CAGTAA---CAGTACTGGATGTGGGGGACGCATATTTCTCAGTTCCTTTA
GATGAAAGCTTTAGAAAATATACTGCGTTCACCATACCTAGCACAAACAA
TGCGACACCAGGAATCAGATATCAGTACAATGTGCTTCCACAGGGATGGA
AAGGATCACCAGCAATATTCCAGTGTAG---CATGACAAAAATCTTAGAG
CCCTTTAGATCAAAAAATCCAGACATAATTATCTATCAATACATGGATGA
CTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAACAAAAATAG
AAGAATTAAGAGCTCATCTATTGAGCTGGGGATTAACTACACCAGAC---
AAAAAGCATCAGAAAGAACCCCCATTCCTTTGGATGGGATATGAGCTCCA
TCCTGACAAGTGGACTGTCCAGCCTATAGTGCTGCCAGAAAAAGAAAGCT
GGACTGTCAATGATAT---ACAGAAATTAGTAGGGAAACTAAATTGGGCA
AGTCAAATTTATCCAGGGATTAAAGTAAAGCAATTGTGTAAACTTCTCAG
GGGAGCCAAAGCACTAACAGATATAGTAACATTGACTGAGGAAGCAGAAT
TAGAATTGGCAGAGAACA---GGGAGATCCTAAAAGACCCTGTGCATGGA
GTATACTATGACCCATCAAAAGAATTAATAGCAGAAATACAAAAACAAGG
GCAAGACCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTAA
AAACAGGAAAATATGCAAGAAAAAGGTCTGCTCACACTAATGATGTAAGA
CAATTAACAGAGGTGGTGCAAAAGGTGGTCCTGGAAAGCATAGTAATATG
GGGAAAGA---CCCCTAAATTTAAACTG---CCCATACAGAAAGAGACAT
GGGAAACA---TGGTGGATGGACTATTGGCAGGCTACCTGGATTCCTGAA
TGGGAGTTTGTTAATACCCCTCCTCTAGTAAAATTGTGGTACCAGTTAGA
GAAAGACCCCATAGTAGGAGCAGAGACTTTCTATGTAGATGGGGCGGCCA
ATAAAGAGACTAAGCTAGGAAAAGCAGGGTATGTCACTGACAGGGGAAGA
CAAAAGGTTGTTTCCCTAACTGAGA---CAACAAATCAAAAGACTGAACT
ACATGCAATCTATCTAGCCTTGCAGGATTCAGGATCAGAAGTAAACATAG
T---AACAGACTCACAGTATGCATTAGGAATCA---TTCAGGCACAACCA
GACAGGAGTGAATCAGAAATAGTCAATCAAATAATAGAGAAGCTAATAGA
AAAGGACAAAATCTACCTG---TCATGGGTACCGGCACACAAAGGGATTG
GAGGAAATGAACAAGTAGATAAATTAGTCAGTTCCGGAATCAGAAAGGTA
CTGTTCTTAGATGGGATAGATAAAGCTCAAG---AGGAACATGAAAGATA
---TCACAGCAATTGGAGAACAATGGCTAGTGATTTTAATCTGCCACCTG
TAGTAGCAAAGGAAATAGTAGCCAGCTGTGATAAAT---GTCA---GCTA
AAAGGGGAAGCCATGCATGGACAAGTAGACTGCAGTCCAGGGATATGGCA
ATTAGATTGCACACATCTAGAAGGAAAAATAATTCTGGTAGCAGTTCATG
TAGCCAGTGGCTATATAGAAGCAGAAGTTATCCCAGCAGAAACAGGACAA
GAGACAGCATACTTTTTACTGAAATTAGCAGGAAGATGGCCAGTAAAAGT
AGTACACACAGACAATGGCAGCAATTTCACCAGCGCTGCAGTTAAAGCAG
CCTGTTGGTGGGCAGGTATCCAACAGGAATTTGGAATTCCCTACAATCCC
CAAAGTCAAGGAGTAGTGGAATCTATGAATAAGGAATTAAAGAAAATCAT
AGGACAGGTAAGAGAACAAGCTGAACACCTTAAAACAGCGGTACAAATGG
CAGTATTCATTCACAATTTTAAAAGAAAA---GGGGGGATTGGGGGGTAC
AGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAA
AGAACTACAAAAACAAATTACAAAAGTTCAAAATTTTCGGGTTTATTTCA
GGGACAGCAGAGATCCACTTTGGAAAGGACCAGCAAAACTACTCTGGAAA
GGTGAAGGGGC---AGTAGTAATACAGGATAATAGTGAGATAAAAGTAGT
ACCAAGGAGAAAAGCAAAGATCATCAGGGACTATGGAAAACAGATGGCAG
GTGATGATTGTGTGGCAGGTAGACAGGATGAGGATTAGA---ACATGGAA
CAGTCTAGTGAAACATCATATGTATGTCTCAAAGAAAGCTAAAAGGTGGT
TTTATAGACATCACTATGAAAGCAGGCATCCAAAAGTAAGTTCAGAAGTA
CACATCCCAGTAGGGG---AGG---CTATGTTAGTAATAACAACATATTG
GGGTCTGCATACAGGAGAAAAAGACTGGCAGTTGGGTCATGGGGTTTCCA
TAGTATGGAGGCTAAGAAGATATAGCACACAA------ATAGATCCTGAC
CAGGCAGACCAACTAATTCATCTGCATTATTTTGACTGTTTTTCAGGCTC
---TGCCATAAGGAAGGCCATATTAGGACAAATAGTTAGGCCTAGTTGTG
AATATCCTACAGGACATA---ACAAGGTAGGATCTCTACAATATTTAGCA
CTGAAAGCATTAGTAACACC---AACAAGGAGAAAGCCACCTTTGCCTAG
TGTTAGGAAATTAACAGAGGATAGATGGAACAAGCCCCAGAAGACCAGGG
GCCGCAGAGAGAGCCATACAATGAATGGATGTTAGAGTTGTTAGAAGATC
TTAAGCATGAAGCTGTTAGACATTTTCCTAGGCCATGGCTTCATGGATTA
GGACAACATATCTATAACACCTATGGGGATACTTGGGAGGGAGTTGAAG-
--CTATAATAAGAACTCTGCAA---CAACTACTGTTTGTTCAT---TTCA
GAATTGGGTGCC---AACATAGCAG---AATAGGCATT---ACTCAGACG
AGAAGAGGCA----------GGAATGGACCCGGTAGATCCTAACTTAGAG
CCCTGGAACCATCCGGGAAGTCAGCCTACAACACCTTGTA---GCAAATG
TTACTGTAAAAAGTGTTGCTATCATTGCCCG---------------CTTT
GCTTCATAAA---CAAAGGCTTAGGCATCTCCTATGGCAGGAAGAAGCGG
AGAC------A---GCGACGAGGA------A---CTCCTCAGAGCTATAA
GGATCATCAAAATCTTGTACCAAAGCAGTAAGTAT--TAGTAACT-----
-AGTATATGTA---ATGACTCCTG--------------------------
---------AAACCTGTG----------------------CAGCAATAGT
A---GGACTGATAGTAGC---GC--TAATCC-TAGCAATAGTTGTGTGGA
CTATAGTAGGTATAGAATAT---AAGA------------AAATATTAAAA
CAA---AGGAAAATAGACAGGGTAATTGAAAGAATAAGAGAAAGAGCAGA
AGATAGTGGCAATGAGAGTGATGGGGATACAGAGGAATTGTCAGCACTT-
--GTTGGGATG------------------------GGGAACTATG---AT
CTTGGGA---ATATTAATAAT------------GTGT------AGTGCTG
C---------AGA---A------------C---A------CTTG------
TGGGTTACTGTCTACTATGGGGTACCTGTGTGGAAAGAAGCAG---AA--
ACCACCT-TATTTTGTGCATCAGAAGCTAAAGCATATGATCCAGAACAGC
ATAACGTCTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAA
GAAATAAATTTGATAAATGTGACAGAAAAGTTTAACATGTGGAAAAATAC
CATGGTAGAGCAAATGCATACAGATATAATCAGTCTATGGGACGAAAGTC
TAAAGCCATGTGTAAAGTTAACCCCTCTCTGTGTTACTTTACGTTGTAAC
A---ATA---CC--AAT---------------------------------
-----------GT--CAAT---GT---CAA-TA-ACA---CG--------
-------A-TTGACAAC---AG--C-------------------------
--------------------------ACG---GA--C---AG--G-----
-------------------GGG-GA-AATGA-AAAACTGCTCTTTCAAAG
TGACCACAGAGCTAAGGGATAAGGAACAGAAGGTACATTCAC---TTTTT
TATAGACTTGACTTAGTACAATTGGATAATACAACGCCA-----------
-------GAAA---AT--AG--TAGTAAC---AAG---------------
---------------------G---AG--TATAGA-T-TAATAAATTGTA
-ATACCTCAGCCATCACACAGGCTTGCCCAAAGGTATCTTTTGAGCCAAT
TCCCATACATTATTGTGCCCCAGCTGGTTATGCGATCCTAAAGTGTAATG
ATAAGAAGTTCAATGGAACAGGGCCATGCACGAATGTCAGCACAGTACAA
TGCACACATGGAATCAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGG
AAGTCTAGCAGAA---GAAGA---GGTAATAATTAGATCTGAAAACATCA
CAGACAATGCCAAAACTATAATAGTACAACTTACTGAGCCTGTAAAAATT
AATTGTACCAGACC------T------AACAACA---AT---ACAAGAAG
GAGTATAACTATG---------GGACCAGGAAAAGCATTCTATACA---A
AT---GAC------ATCATAGGAAATATAAGACAAGCATATTGTACTGTC
AATAGATCAGAATGGAATAACACTTTACAAAAGGTAGCT---AC--ACAA
TTAAGAGAA------CACTTT---G----AA--AAC------AAAACA--
----ATAATATTTACT----CACTC---CTCAGGAGGGGATCTAGAAGTC
ACAACAC------ATATGTTTAATTGTGGAG---GAGAATTCTTCTATTG
TAATACATCAGGCCTGTTTAAC---AGCACC---TG---GC--ACTATAA
CAGC--AATGG--TACTTGG------------------------CACAAT
A---ACAGC---A-C-------A---AAT---AG-CAT---G---G----
--AC--TC--AAA---T---------------GAAACTATAACT------
---CTCACATG-CA-GAATAAAGCAAATTATAAATATGTGGCA---GAGA
GTAGGAAAAGCAATGTATGCTAATCCCATCCAAGGAATAATAAAGTGTGA
ATCAAACATTACAGGACTACTCTTAACAAGAGATGG---TGGGAA---TA
CT------AGC--------------------AGTA---CA--AATGAAAC
CTTCAGACCTGGAG-GAGGAG-ATATGAGGGACAATTGGAGAAGTGAATT
ATACAAATATAAAGTAGTAAAGATTGAGCCACTAGGAGTAGCACCCACCA
GGGCACAGAGAAGAGTGGTGGG------GAGAGAAAAAAGAGCAA---TT
GGA-------ATAGGAGC---TG--T---CTTCCTTGGGT---TCTTAGG
----AG-CAGCAGGAAG-CACTATGGGCGCGGCGTCAATGACGCTGACGG
TACAGGCCAGACAATTATTGTCTGGCATAGTGCAACAGCAAAGCAATTTG
CTGAGGGCTATAGAGGCTCAACAACAACTGTTGAAACTCACGGTCTGGGG
CATTAAACAGCTCCAGGCACGAGTCCTGGCTGTGGAAAGATACCTACAGG
ATCAACAGCTCCTAGGAATTTGGGGATGCTCTGGAAAACTCATCTGCCCC
ACTAATGTGCCCTGGAACTCTACTTGGAG---T---AAT-----------
-AAATCTTATAG---TGAGATAT---GGG---ATAACATGACCTGGCTGC
AATGGGATGAAGAAGTTAGCAATTACACACAAATAATATATGACCTAATT
GAAAAATCGCAGAACCAGCAGGAAAAGAATGAACAAGACTTATTGGCATT
GGACAAGTGGGCAAGTCTGTGGAGTTGGTTTAGCATATCAAACTGGCTGT
GGTATATAAGAATATTTATAATGGTAGTAGGAGGTTTAATAGGATTAAGA
ATAGTTTTTGCTGTGTTTTCTGTAATAAATAGAGTTAGGCAGGGATACTC
ACCTCTGTC---ATTTCAGACC---CATTCCC---CAGCCCCAGGGGGT-
-----CTCGACAGGCCCGGAAGAATCGAAGAAGAAGGTGGAGAGCAAGGC
AGAGACAGATCGATTCGATTAGTGAGCGGATTCTTAACACTTGCCTGGGA
CGACCTACGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAAACTTCA
TCTTGATTGTAGCGAGGACTGTGGAACTTCTGGGA---CACAGCAGTCTC
AAGGGGTTGAGACTGGGATGGGAAGGCCTCAAGTATCT---GTGGAATCT
C---CTGATATATTGGGGTCGGGAACTAAAAATTAGTGCTACTAATTTGA
TAGATA---CTATAGCAATAGTAGTAGCTGGCTGGACAGATAGGGTGATA
GAAATAGGACAGAGCATTGGTAGAGCTATCCTCCACATACCTAGAAGAAT
CAGACAGGGCTTTGAAAGAGCTTTGCTATAA
'A1.KE.00.KER2012'
------GCGAGAGCGTCAGTATTAAGTGGGGG---AAAATTAGATGCATG
GGAGAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAGACTGAAAC
ATCTAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTTAACCCTAGC
CTTTTAGAAACAACAGAAGGATGTCAACAAATAATAACACAGTTACAACC
AGCTATCGGAACAGGAACAGAAGAACTTAAATCATTATATAATACAGTAG
CAACCCTCTATTGTGTACATCAGGGGATAAAGGTAAAAGACACCAAGGAA
GCTCTAG---AT--AAA-ATAGAGGAAATACA------------AAAGAA
AAGCAAA------------CAACAGACA----------------------
--------------------GCA---------------------GCT---
------------------------GACACAGGA-----------------
----------AGCAGC------------------------AGCCAAAATT
ACCCTATAGTGCAAAATGCACAAGGGCAAATGATACACCAGTCCTTGTCA
CCTAGGACTTTGAATGCATGGGTGAAAGTAATAGAAGAAAAGGCTTTCAG
CCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCAC
AAGATTTAAATATGATGCTGAACATAGTGGGGGGACACCA---GGCAGCT
ATGCAAATGTTAAAAGACACCATCAATGAGGAAGCTGCAGAATGGGACAG
GCTACATCCAGTACATGCAGGGCCTCCTGCACCAGGCCAGCTGAGAGAAC
CAAGGGGAAGTGATATAGCAGGAACTACTAGCACCCCTCAAGAACAGATA
GGATGGATGACAGGCAACCCACCTATCCCAGTGGGAGACATCTATAAAAG
ATGGATAATTCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTA
GCATTCTGGATATAAAACAAGGGCCAAAAGAACCCTTCAGAGATTATGTA
GATAGGTTCTTTAAAGTTCTCAGAGCTGAGCAAGCTACACAGGAGGTAAA
AGGTTGGATGACAGAAACATTATTGATCCAAAATGCAAATCCAGATTGTA
AGTCCATTTTAAGAGCATTAGGAGCAGGGGCTACATTAGAAGAAATGATG
ACAGCATGCCAGGGAGTGGGAGGACCCGGCCATAAAGCAAGGGTCTTGGC
AGAGGCAATGAGCCAAGT---AC---AAC---A---AA--C---A-----
-----------------AACATA---ATGATGCAGAGAGGCAATTTTAGG
GGCCAAAAA---AGGATTAAGTGTTTCAACTGTGGCAAAGAAGGACACCT
AGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGCTGGAAATGTGGGA
AGGAGGGACACCAGATGAAAGACTGCACT------GAGAGACAGGCCAAT
TTTTTAGGGAAAATTTGGCCTTC---CAGCAAGGGG---AGGCCAGGGAA
TTTTCCTCAGAGCAGG---------------CCAGAGCCAACAGCCCCA-
-----------------------------------CCA---GCAGAGTTC
TTTGGAACGAGGGAAGAGATG---------------ACCCCCCCTCCG--
----AAGCAGGAGCAG------------AAGGA---CAGGGAACAGAAC-
-----TCA------CCTTCAGTTTCCCTCAAATCACTCTTTGGCAACGAC
CTATTGTCACAGTAAAAATAGGGGGACAGCTAAAAGAAGCTCTACTAGAT
ACAGGAGCAGATGATACAGTATTAGAAGACATAAATTTACCAGGAAAATG
GAAACCAAAAATGATAGGGGGAATTGGAGGTTTCATTAAGGTAAAACAGT
ATGATCAGATAGTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTA
TTGGTAGGACCTACACCTGTCAACA---TAATTGGAAGAAATATGTTGAC
CCAGATTGGCTGTACTTTAAATTTCCCAATTAGTCCTATTAGTACTGTAC
CGGTAAAACTAAAGCCAGGAATGG---ATGGCCCAAGGGTTAAACAATGG
CCATTGACAGAAGAAAAAATAAAAGCATTAACAGAGATTTGTAAA-----
-GAGATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCAT
ACAATACCCCAATATTTGCTATAAAGAAAAAAGACAGCACTAAATGGAGA
AAATTAGTAGATTTCAGAGAGCTCAATAAAAGAACTCAAGACTTTTGGGA
AGTTCAATTAGGAATACCGCATCC---AGCGGGCTTAAAAAAGAAAAAAT
CAGTAA---CAGTACTAGATGTGGGGGACGCATATTTTTCAGTTCCCTTA
GATGAAAGCTTTAGAAAGTATACTGCATTCACCATACCTAGTACAAACAA
TGAGACACCAGGAATCAGGTATCAGTACAATGTGCTTCCACAGGGATGGA
AAGGATCACCGGCAATATTTCAGAGTAG---CATGACAACAATTTTAGAG
CCCTTTAGATCAAAAAATCCAGAAATAATTATCTATCAATACATGGATGA
CTTATATGTAGGATCTGATTTAGAAATAGGGCAACATAGAGCAAAAATAG
AGGAGTTGAGAGCTCATCTATTGAGCTGGGGACTTACTACACCAGAC---
AAAAAGCATCAGAAAGAACCCCCATTTCTTTGGATGGGATATGAACTCCA
TCCTGACAAGTGGACAGTCCAACCTATACAGCTGCCAGAGAAAGAAAGCT
GGACTGTCAATGATAT---ACAGAAATTAGTGGGAAAACTAAATTGGGCA
AGCCAAATTTACCCAGGGATTAAAGTAAAACAATTGTGTAGACTCCTCAG
GGGAGCCAAAGCACTGACAGATGTAGTAACATTGACTGAGGAAGCAGAAT
TAGAACTGGCAGAAAACA---GGGAGATTCTAAAAGACCCTGTGCATGGA
GTATATTATGACCCATCAAAAGACTTGATAGCAGAAATACAGAAACAAGG
GCAAGACCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATTTAA
AAACAGGAAAATATGCAAGAAAGAAATCTGCTCATACTAATGATGTAAAA
CAATTAGCAGAAGTGGTGCAAAAGGTGGTCATGGAAAGCATAGTAATATG
GGGAAAGA---CTCCTAAATTTAAACTA---CCCATACAAAAGGAAACAT
GGGAAACA---TGGTGGATGGATTATTGGCAGGCTACCTGGATTCCTGAA
TGGGAATTTGTCAATACCCCTCCTCTGGTAAAATTATGGTACCAGTTAGA
GAAAGACCCCATAGCAGGAGCAGAAACTTTCTATGTAGATGGGGCAGCCA
ATAGGGAGACTAAACTAGGGAAGGCAGGGTATGTCACTGACAGAGGAAGA
CAAAAGGTTGTTCCCCTAACTGAGA---CAACAAATCAAAAGACTGAATT
ATATGCAATAGATTTAGCCTTGCAGGATTCAGGATCAGAAGTAAACATAG
T---AACAGATTCACAGTATGCATTAGGAATCA---TCCAGGCACAACCA
GACAGGAGTGAATCAGAGATAGTCAATCAAATAATAGAGAAGCTAATAGG
AAAGGACAAGGTCTACCTG---TCATGGGTACCAGCACACAAAGGAATTG
GAGGAAATGAACAAGTAGATAAATTAGTCAGTTCTGGAATCAGGAAGGTG
CTATTTTTAGATGGAATAGATAAAGCTCAAG---AAGAACATGAAAGATA
---TCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAATCTGCCACCTA
TAGTAGCAAAGGAAATAGTAGCCAGCTGTGATAAAT---GCCA---GCTA
AAAGGGGAAGCCATACATGGACAAGTAGACTGCAGTCCAGGGATGTGGCA
ATTAGATTGCACACATCTAGAAGGAAAAGTAATTCTGGTAGCAGTCCATG
TAGCCAGTGGCTATATAGAAGCAGAAGTAATCCCAGCAGAAACAGGACAG
GAGACAGCCTACTTTCTACTAAAATTAGCAGGAAGATGGCCAGTAAAAGT
AGTACACACAGATAATGGCAGCAATTTTACCAGTGCTGCATTTAAAGCAG
CCTGTTGGTGGGCAGGTGTCCAACAGGAATTTGGGATTCCCTACAATCCC
CAAAGTCAAGGAGTAGTGGAATCTATGAATAGAGAATTAAAGAAAATCAT
AGGACAAGTAAGGGAGCAGGCTGAACACCTTAAGACAGCAGTACAAATGG
CAGTATTCATTCACAATTTTAAAAGAAAA---GGGGGGATTGGGGGGTAC
AGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAA
AGAATTACAAAAACAAATTACAAAAATTCAAAAATTTCGGGTTTATTACA
GGGACAGCAGAGATCCAATTTGGAAAGGACCAGCAAAACTACTCTGGAAA
GGTGAAGGGGC---AGTGGTGATACAGGACAATAGTGATATAAAGGTAGT
ACCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGGTGGCAG
GTGATGATTGTGTGGCAGGTAGACAGGATGAGGATTAGA---ACATGGAA
CAGTTTAGTAAAATACCATATGTATGTCTCAAAGGAAGCTAAAGGTTGGT
TTTATAGACATCACTATGAAAGTAGTCATCCAAAAGTAAGTTCAGAAGTA
CACATCCCACTAGGGG---ATG---CTAAAATAGTAGTAAGAACATATTG
GGGTCTGCATACAGGAGAAAAAGATTGGCACTTGGGTCATGGGGTCTCCA
TAGAATGGAGGCTAAAAAGATATAGCACACAA------ATAGATCCTGAC
GTGGCAGACCAACTAATTCATCAACATTATTTTGCCTGTTTTTCAGACTC
---TGCCATAAGGAGAGCCATATTAGGGCATGTAGTTAGCCCTAGGTGTG
AATATCAAACAGGACATA---ACAAGGTAGGATCTCTACAATATTTAGCA
CTGAAAGCATTAGTAAAACC---AACAAGGAGAAAGCCACCTTTGCCTAG
TGTTAGGAAATTAACAGAGGATAGATGGAACAAGCCCCGGAAGACCAGGG
GCCACAGAGGGAGCCATACAATGAATGGATGTTAGAGCTGTTAGAAGATC
TTAAGCATGAAGCTGTAAGGCATTTTCCTAGGCCATGGCTTCATGGATTA
GGACAACATATCTATAACACCTATGGGGACACTTGGGAAGGAGTTGAGG-
--CTATAATAAGAATCTTGCAA---CAACTACTGTTTGTTCAT---TTCA
GAATTGGGTGCC---AACACAGCAG---AATAGGCATT---ATTCGAGGG
AGAAGAGCCA----------GGGATGGATCCGGTAGATCATAAACTAGAG
CCCTGGAACCATCCGGGAAGTCAGCCTACAACTCCTTGTA---GCAAATG
CTACTGTAAAAAATGTTGCTATCATTGCATA---------------GTTT
GCTTTCAGAC---CAAAGGCTTAGGCATCTCCTATGGCAGGAAGAAGCGG
AGAC------A---GCGACGAGGA------G---CTTCTCAAAGCAGTAA
GGATCATCAAAATCCTGTACCAAAGCAGTAAGTAG--TAGTAATT-----
-AACATATGTA---ATG---------------------------------
---------TCTCCTTTGG---------------AAGTTTGGGCAATAGT
A---GGACTCGTAGTAGC---GC--TAATAC-TAGCAATAGTTGTGTGGA
CTATAGTAGGTATAGAATAT---AGAA------------AAGTGTTAAAG
CAA---AGAAAAATAGACAGGTTAATTGAGAGAATAACAGAAAGAGCAGA
AGACAGTGGCAATGAGAGTGATGGGGATACAGAGGAATTGTCAGCACTT-
--GTTGAGATG------------------------GGGAATTATA---AT
CTTGGGT---ATGATAATGAT------------CTGT------AGTATGG
C---------ACA---A------------A---A------CTTG------
TGGGTTACTGTCTATTATGGGGTACCTGTGTGGAGAGATGCAG---AC--
ACCACCC-TATTTTGTGCATCAGATGCTAAAGCATATAAGACAGAAGTGC
ATAATGTCTGGGCTACACATGCCTGTGTGCCCACAGACCCCAACCCACAA
GAAATATATTTGACAAATGTGACAGAAAATTTTAACATGTGGAAAAATAA
AATGGTAGAGCAGATGCATGAAGACATAATTAGTCTATGGGACCAAAGCC
TAAAGCCATGTGTACAGTTAACCCCTCTCTGCGTTACGTTAAACTGTAGC
G---ATG---TC--ACGAATAACACCCTC---------------------
-----------AG--GAAT---GC---CAC-TG-TGAATGCC--------
-------A-ATGCCAAT---GC--C-------------------------
--------------------------ACT---GT--C---AC--TGG--G
GAC---ATGGA------A-GGA-GA-AATGA-AAAACTGCTCTTACAATA
TGACCACAGCAGTAAGGGATAAGCAAAAGAAAGTATACTCAC---TTTTT
TATAGGCTAGATGTAGTGCAAATTAGCAAT--------------------
-------AATA---GT--AG--CAGTAGT---AGT---------------
---------------------G---AG--TATAGA-T-TAATAAATTGTA
-ATACCTCAGCCATTACACAAGCTTGTCCAAAAGTAACCTTTGAGCCAAT
TCCCATACATTATTGTGCCCCAGCTGGTTTTGCGATCCTAAAGTGTAATG
AAGAAGGGTTCAATGGAACAGGACCATGCAAAAATGTCAGCACAGTACAA
TGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTAAATGG
CAGTCTAGCAGAA---AAAGG---GGTAATAATCAGATCTGAAAACATCT
CAAACAATGCTAAAACCATAATAGTACAACTTGCCGAGCCTGTAACAATT
AATTGTACCAGACC------T------AACAACA---AT---ACAAGAAA
AGGTATACATATA---------GGACCAGGACGAGCATTCTATGCA---A
CAGGTGAC------ATAATAGGGGATATAAGAAAAGCATATTGTAATGTC
AGTAGAACACAATGGAATAAAACTTTGGCACAGGTAGCT---GC--ACAA
TTAACAAAA------TATTGG---A----AC-----------AAAACA--
----ATAAACTTTACT----AGCTC---CTCAGGAGGGGATGTAGAAATT
ACAACAC------ATAGTTTTAATTGTGGGG---GAGAATTTTTCTATTG
TAATACAACAAACCTGTTTAAT---AGCACC---TG---G----------
------AGAGG--AAAT---------------------------AAAACT
G---TCAGC-----------------AAT---AG-CAC---A---G----
--AG--TT--AGA---TGAAAAT---------GGCACTATAACT------
---CTCCCATG-CA-GAATAAAGCAAATTATAAATATGTGGCA---GAGA
ACAGGACAAGCAATGTATGCCCCTCCCATCCAAGGAGTAATAAAGTGTGT
ATCAAACATTACAGGACTACTATTAACAAGAGATGG---TGGAAG---TG
AT------AAC---------------AAT--ATAA---GT--AGTGAAAC
CTTCAGACCAGGAG-GAGGAG-ATATGAGGGACAATTGGAGAAGTGAATT
ATATAAGTATAAAGTAGTGAAACTTGAACCACTAGGAGTAGCACCCAACA
AGGCAAGGAGAAGAGTGGTGGA------GAGAGAAAAAAGAGCAG---TT
GGA-------CTGGGAGC---TG--T---ATTCATTGGGT---TCTTAGG
----AG-CAGCAGGAAG-CACTATGGGCGCGGCGTCAATAACGCTGACGG
CACAGGCCAGACAATTATTGTCTGGCATAGTGCAACAGCAAAGCAATTTG
CTGAAGGCTATAGAGGCTCAACAGCATCTGTTGAAACTCACGGTCTGGGG
CATTAAACAGCTCCAGGCAAGAGTCCTGGCTCTGGAAAGATACCTAAAGG
ATCAACAGCTCCTAGGAATTTGGGGCTGCTCTGGAAAACTCATCTGCACC
ACTAGTGTGCCCTGGAACTCTAGTTGGAG---T---AAT-----------
-AAATCTTTTGA---GCAAATAT---GGA---ATAACATGACCTGGTTGG
AATGGGATAAAGAAGTTAGCAATTACACACAAATAATATATGAGCTACTT
GAAGTATCGCAGAACCAGCAAGAAAAGAATGAACAAGACTTATTGTCATT
GGACAAATGGGCAAGTCTGTGGAATTGGTTTGACATATCAAAATGGCTGT
GGTATATAAAAATATTTATAATGATAGTAGGAGGCTTAATAGGCTTAAGA
ATAGTTTTTGCTGTGCTTTCTATAATAAATAGAGTTAGGCAGGGATACTC
ACCTTTGTC---ATTTCAGACC---CTTACCC---CAAACCCAGGGGGA-
-----CTCGACAGGCCCGGAAGAATCGAAGAAGAAGGTGGAGAGCAAGGC
AGAGACAGATCGATTCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGA
CGATCTGAGGAACCTGTGCCTTTTCAGCTACCACCGCTTGAGAGACTTCA
TCTTGATTGCCGCGAGGACTGTGGAACTTCTGGGA---CACAGCAGTCTC
AAGGGGTTGAGACTGGGGTGGGAAGGGATCAAGTATCT---GGGGAATCT
C---CTGTTGTATTGGGGTCGGGAACTGAAAAATAGTGCTATTAATTTGT
TAGATA---CTATAGCAATAGCAGTAGCTGGCTGGACAGATAGGGTTATA
GAAATAGGACAAAGAATTGGTAGAGCTATTCTCAACATACCTAGAAGAAT
CAGACAGGGCGCTGAAAGAATCTTAGTATAA
'A1.KE.00.KER2018'
------GCGAGAGCGTCAGTATTAAGTAGGGG---AAAATTAGATGCATA
AGAAAAAATTCGGTTAAGGCCAGGAAGAAAGAAAAAATATAAATTAAAAC
ATCTAGTATAGGCAAGCAAAGAGCTGGACAGATTTGCACTTAACCCTAGC
CTTTTAGAAACAACAGAAGGATGTCAACAAATAATAGAACAGTTACAACC
AAGTCTCAAGACAGAAACAGATGAACTTAGATCATTATTTAATACAGTAG
CAACTCTCTATTGTGTACATCAACAGATAGATGTAAAAGACACCAAAGAA
GCTCTAG---AT--AAA-ATAGAAGAAATACA------------AAATAA
AAGCAAG------------CAAAAGGCA---------CA---ACAG----
--------------GCA---GCA---------------------GCT---
------------------------GACACAAGA-----------------
-------AGCAGCAGC------------AAG------GTCAGCCAAAATT
ACCCTATAGTGCAAAATGCACAAAGGCAAATGATACACCAGTCCTTGTCA
CCTAAGACTTTGAATGCATAAGTAAAAGTAATAGAAGAAAAGGCTTTCAG
CCCAGAAGTAATACCCATGTTCTCAGCATTATCAGAAGGAGCCACCCCAC
AAGATTTAAACATGATGCTGAACATAGTAAAGAGGCACCA---GGCAGCT
ATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAAAGTAAGACAG
GCTACATCCAGCACATGCAAGACCTATTGCACCAGGCCAGATAAAAGAAC
CAAAAAGAAGTGATATAGCAAGAACTACTAGTACCACCCAAGAACAAATA
GCATAGATAACAGGCAACCCACCTATCCCAGTAGGAGACATCTATAAAAG
ATAGATAATCCTAAGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTA
GCATTTTAGATGTAAAACAAAGGCCAAAAGAACCCTTCAGAGACTATGTA
GATAGGTTCTTTAAAATTCTCAAAGCTGAGCAAGCTTCACAAGATGTAAA
AGGTTAGATGACAGAAACATTACTAGTTCAAAATGCAAATCCAGATTGTA
AGTCTATTTTAAGAGCATTAGGAGCAGGGGCTACATTAGAAGAAATGATG
ACAGCATGCCAAGGAGTAGGAGGACCCGGCCATAAAGCAAAGGTTTTGGC
TGAGGCAATGAGTCAAGT---AC---AAA---A---TA--C---A-----
-----------------AACATA---ATGATGCAGAGAAGTAATTTTAAA
GGCCAGAAA---AAGATTAAGTGTTTCAACTGTGGCAAAGAAAGACACCT
AGCCAAAAATTGCAGGGCCCCTAAGAAAAAAGGCTGTTAGAAATGTAAGA
AAAAAAGACACCAAATGAAAGACTGCACT------GAGAGACAGGCTAAT
TTTTTAAAGAGAATTTAGCCTTC---CAGCAAGAAG---AGGCCAGGAAA
TTTTCCTCAGAGCAGA---------------CCAGAACCAACAGCCCCA-
-----------------------------------CCA---GCAGAGCTC
CTTAAGATGAAAGACAAGATA---------------GCCTTCCCTCCG--
----AAGCAGGAGCAG------------AACGA---CAAAAGTCAGAAT-
-----TCA------CCTTCAGTTTCCCTCAAATCACTCTTTAGCAACGAC
CTCTTGTCACAGTAAGAATAGAAGGACAGCTAAAAGAAGCTCTATTAGAT
ACAGGAGCAGATGATACAGTATTAGAAGACATAAATTTGCCAAGAAAATA
GAAACCAAAAATGATAGGGGGAATTAGAAGTTTTATCAAAGTAAAACAGT
ATGATCAGATACTTATAGAAATTTGTAGAAAAAAGGCTATAAGTACAGTA
TTGATAAGACCTACACCTGTCAACA---TAATTAGAAGAAATATGTTGAC
TCAGATTAGTTGTACGTTAAATTTCCCAATTAGCCCTATTAAAACTGTAC
CAGTACAATTAAAGCCAAAAATAG---ACAGCCCAAAAGTTAAACAATAG
CCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACA-----
-GAAATAGAAAAAGAAAGAAAAATTTCAAAAATTAAGCCTGAAAATCCAT
ACAATACTCCAATATTTGCTATAAAGAAAAAAGACAGCACTAAATAGAGA
AAATTAGTAGATTTCAGAAAGCTCAATAAAAGAACTCAAAACTTTTAAGA
AGTTCAATTAAGAATACCGCATCC---AGCAGGCTTAAAAAAGAAAAAAT
CAGTAA---CAGTACTAGATGTAGAAGACGCATATTTTTCAGTTCCCTTA
GATGAAAGCTTTAGAAAGTATACAGCATTCACCATACCTAGTACAAACAA
TAAGACACCAAGAATCAGGTATCAGTACAATGTGCTTCCACAAAAGTAAA
AAAGATCACCAGCAATATTCCAGAGTAG---CATGACAAAAATCTTAGAG
CCCTTTAGATCAAAAAATCCAGAAATAATTATCTATCAATACATAGATGA
CTTGTATGTAAGATCTGATTTAGAGATAAAGCAGCATAGAACGAAAGTAG
AAGAGTTAAAAGATCATTTATTAAGCTAAAGATTTACTACACCAGAC---
AAAAAGCATCAGAAAGAACCTCCCTTTCTTTAGATAAGATATGAACTCCA
TCCTGATAAGTAGACTGTCCAACCTATAGAGCTGCCAGAAAAAGAAAGCT
AGACTGTCAATGATAT---ACAGAAATTAGTAAAGAAACTAAATTAGGCA
AGTCAAATTTATGCAAGAATTAAAGTAAAACAATTGTGTAGGCTCCTCAG
AGGAGCCAAAGCCCTAACAGATGTAGTAACATTAACTGAAGAAGCAGAAT
TAGAATTAGCAGAGAACA---AAGAGATCCTAAAGGACCCTGTGCATAAA
GTATATTATGACCCATCAAAAGACTTAATAGCAGAGATACAGAAGCAAAG
ACAAGACCAATAGACATATCAGATTTATCAAGAACCATTTAAAAATCTGA
AAACAAGGAAATATGCAAGAAAAAAGTCTGCTCACACTAATGATGTAAAA
CAATTAGCAGAAGTGGTGCAAAAAGTAGTCATAGAAAGCATAGTAATATG
AAGAAAGA---CTCCTAAATTTAAACTA---CCCATACAAAAAGAAACAT
AAGAAACA---TAGTAGATAGACTATTAGCAGGCTACCTAGATTCCTGAA
TAAGAGTTTGTCAATACCCCTCCTCTAGTAAAATTATAGTATCAGTTAAA
GAAAGATCCTATAGTAAGAGCAGAGACTTTCTATGTAAATGAGGCATCCA
ATAAGGAGACTAAGCTAAGAAAAGCAAAGTATGTCACTGACAGAAGAAGA
CAAAAAGTTGTTTCCCTAACTAAGA---CAACAAATCAAAAGACTAAATT
ACATGCAATCCATCTAGCCTTGCAAGATTCAAGATCAGAAGTAAACATAG
T---AACAGACTCACAGTATGCATTAAGAATCA---TTCAAGCTAAGCCA
GACAGGAGTGAAGCAGAGTTAGTCAATCAAATAATAGAAGAGCTAATAAG
AAAAGACAAAGTCTACCTA---TCATAAGTACCAGCACACAAAAGAATTA
GAAGAAATGAACAAGTAGATAAATTAGTTAGTTCTAGAATCAAGAAAGTG
CTATTTTTAGATAAGATAGATAAAGCTCAAG---AAGAACATGAAAGATA
---TCACAGCAATTAAAGAACAATAGCTAATGATTTTAATCTGCCACCTA
TAGTAGCAAAAGAAATAGTAGCCAGCTGTAATAAAT---GTCA---GCTA
AAAAAAGAAGCCATGCACAGACAAGTAGACTGTAGTCCAGAAATATGGCA
ATTAGATTGCACACATCTAGAAAGAAAAATAATTCTAGTAGCAGTCCATG
TAGCCAGTGGCTATATAGAAGCAGAAGTTATCCCAGCAGAAACAAGACAA
GAGGCAGCATACTTTCTGCTAAAGTTAGCAAAAAGATGGCCAGTAAAAGT
AGTACACACAGACAATGGCAGCAATTTCACCAGCGCTGCATTTAAAGCAG
CCTGTTAGTAGGCAAATGTCAGCCAAAAATTTAAAATCCCCTACAATCCC
CAAAGTCAAAGAGTAGTAGAATCTATGAATAAAGAATTAAAAAAAATCAT
AAGACAGGTAAAAGAGCAAGCTGAACACCTTAGAACAGCAGTACAAATAG
CAGTTTTCATTCACAATTTTAAAAGAAAA---GGGGGGATTAGAAGGTAC
AGTGCAGAGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAG
AGAATTACAAAAACAAATTACAAATATTCAAAAATTTCAAGTTTATTACA
AAGACAGCAAAGATCCAATTTAGAAAAGACCAGCAAAACTACTCTAGAAA
AGTGAAAAGGC---AGTAGTAATACAGGATAATAGTGATATAAAAGTAGT
ACCAAGAAGAAAAGCAAAGATCATTAAGGATTATAAAAAACAGATGGCAA
GTGATGATTGTGTGGCAGGTAGACAGGATGAAGATTAGA---ACATAGAA
CAGTTTAGTAAAACATCATATGTATGTCTCAAAGAAAGCTAAAAGTTAAG
TTTATAGACATCACTTTGAAAGCAGGCATCCAAAAAGAAGTTCAGAAGTA
CACATCCCACTAGAAG---ATG---CTAGAATAGTAATAAGAACATATTA
AAGTCTGCATACAGGAGAAAAAGACTGGCAGTTAGGTCATAAAGTCTCCA
TAGAATGGAGGCTAAAAGAATATAGCACACAA------ATAGATCCTGAC
CTGGCAGACCAACTAATTCATCTGCATTATTTTAACTGTTTTTCAGACTC
---TGCCATAAAGAAAGCCATATTAAGGCAAGTAGTTAGCCCTAGTTGTG
AATATCAAACAGGACACA---ACAAGGTAAGATCTCTACAATATTTAGCA
CTAAAAGCAGTAGTAACACC---AACAAAGGCAAAGCCACCTTTGCCTAG
TGTTAAGAAACTAACAGAAGATAGATGGAGCAAGCCCCAAAAGACCAGGG
GCCCCAGAAAGAGCCATACAATGAATAGATGTTAGATCTGTTAGAAGAGC
TTAAGCATAAAACTGTTAGACATTTTCCTAGGCCATGGCTCCATAGATTA
AGACAGCATATCTATGTCACTTATGAAGATACTTAAGAAAAAGTTGAAG-
--CTATAGTAAGAACTTTGCAG---CAACTACTGTTTGTTCAT---TTCA
GAATCAGGTGCC---AACACAGCAG---AATAGGCATT---ATTCAAAAA
AGAAAAGTCA----------GAGATAGATCCAGTAGATCCTAACCTAGAG
CCCTAGAACCACCCAGGAAGTCAGCCTACAACTCCTTGTA---GCAAGTG
TTACTGTAAAGCTTGTTGCTATCATTGCATA---------------GTTT
GCTTTCAGAA---AAAAAGCTTAGGCATCTCCTATGGCAAGAAGAAGCAG
AAAC------A---GCGACGAAGA------A---CTCCTCAAGGCAATAA
GGATCATCAAGATCCTATACCAAAGCAGTAAGTAC--TAGTAATT-----
-AATATATGTA---ATG---------------------------------
---------CTTCCTTTAG---------------AAATCTGTGCAATAGT
A---AGACTGATAGTAGC---GC--TAATTC-TAGCAATAGTTGTGTAGA
CTATAGTAGGTATAGAATAT---AAGA------------AATTGCTAAAG
CAA---AGAAAAATAGACAGGTTAATTAAAAGAATAAAAGAAAGAGCAGA
GGACAGTGGCAATAAGAGTGATAAAGATACAGAAGAATTGTCAGCACTT-
--ATTAAGATG------------------------AAGAACTATG---AT
CTTGAAG---ATGATAATAAT------------CTGT------AGTACTG
C---------AGA---A------------G---A------CTTG------
TAAGTTACTGTCTACTATAAAGTACCTGTGTAGAAAAACGCAA---AG--
ACCACCC-TATTTTGTGCATCAGATGCTAAGGCATATAAAACAGAAGTGC
ATAATGTCTAAGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAA
GAAATACATTTAGAAAATGTGACAGAAGAGTTTAATGTGTAGAAAAATAA
CATAGTAAAGCAGATGCATACAGACATAATCAGTTTATAAGACCAAAGCC
TAAAGCCATGTGTAAAGTTAACCCCTCTCTGCGTTACTTTAAACTATACC
A---ATG---TC--------------------------------------
----------------------------GA-AG-TTA---CC--------
-------A-ACAGCAGC---A---T-------------------------
--------------------------GAT---AG--A---AA--G-----
---------------------A-GA-AATAA-AAAACTGCTCTTACAATA
TGACCACAGAACTAAAAGATAAGAAAAAGAAAATATTTTCGC---TTTTT
TATAAACTTGATGTAGTACCAATTAATAAA--------------------
-----------------------AGTAAT---AGT---------------
---------------------A---AG--TATAGA-T-TAATAAATTGTA
-ATACCTCAGCCATTACACAGGCTTGTCCAAAAGTAACCTTTGAGCCAAT
TCCCATACATTATTGTGCCCCAGCTAGTTTTGCAATTCTAAAGTGTAAAG
ATGAAGAGTTCAATAGAACAAAGTTATGCAAGAATGTCAGCACAGTACAA
TGCACACATAGAATCAAGCCAGTAGTGTCAACTCAACTACTGTTAAATGG
CAGTCTAGCAGAA---AAAGA---GATAAGAATTAAATCTAAAAACATCT
TAGACAATGCTAAAACCATAATTGTACAACTTACCAAGCCTGTAATAATC
AATTGTACCAGACC------T------AACAACA---AT---ACAAGAAA
AAATGTACATATA---------AGACCAAGACAAGCATTCTATGCA---A
CAGATGAT------ATAATAAAAGATATAAGACAAGCATATTGTGAAGTC
AATAGAGCACAATAGAATGACACTTTAAGACAAGTAGCG---AT--ACAA
TTAAGAAAA------CACTAG---A----AC-----------ACAACA--
----ATAATCTTTAAT----AAACC---CTCAAGAGAAGATTTAGAAATT
ACAACAC------ATAGTTTTAATTGTAAAG---AAGAATTTTTTTATTG
TAATACATCAGGCCTATTTAAT---AGTACT---TA---G----------
------AAAAT--TGAA---------------------------GACACT
G---CCAGC---A-T-------A---AAT---GG-CAC---A---G----
--AG--TT--AAA---T---------------GACACTATAACT------
---CTCCCATG-CA-GAATAAAGCAAATTATAAATATGTGGCA---GAGA
ATAAGACAAGCAATGTATGCCCCTCCCATCCAAAGAGTAATAAAGTGTCA
ATCAAACATTACAAGAATACTATTAACAAGAGATGG---TAAGAA---TA
CT------AAGAATAAT---------AGC--AGTA---CA--AATGAAAC
CTTTAGACCTAGAA-GAGAAG-ATATGAAAGACAATTAAAGAAGTAAATT
ATATAAGTATAAAGTAATAAAAATTAAACCACTAAGAGTAGCACCCACCA
AGGCAAAAAGAAAAGTAGTAGA------AAAAGAAAAAAGAGCAG---TT
AGA-------CTAAGAGC---TG--T---ATTCATTAAGT---TCTTAAG
----AG-CAGCCAGAAG-CACTATAGGCGCGGCGTCAATAACGCTGACAG
TACAGGCCAGACAATTATTGTCTGGCATAGTGCAACAGCAAAACAATTTG
CTGAAGGCTATAGAAGCTCAACAGCATCTGTTGAAACTCACAGTCTAAGG
CATTAAACAGCTCCAGGCAAAAGTCCTGGCTGTAGAAAGATACCTAAAAG
ATCAACAGCTACTAAGAATTTAAGGCTGCTCTAAAAAACTCATCTGCACC
ACTAATGTGCCTTAGAACTCTAGTTGAAG---T---AAT-----------
-AAATCTTACAA---TGAGATAT---AAG---AAAACATAACCTAGCTGC
AATAAGATAAAGAAATTAACAATTACACAAAACTAATATATAGCCTAATT
AAAGAATCGCAGAACCAGCAAAAAAAGAATGAACAAGACTTATTGGCATT
AGACAAGTAAGCAAGTCTGTAGAATTAGTTTGACATATCCAACTAGCTGT
AGTATATAAAAATATTTATAATGATAGTAAGAGGCTTAATAAGATTAAAA
ATAGTTGTTGCTGTGCTTTCTGTAATAAATAGAGTTAGGCAAAGATACTC
ACCACTATC---ATTTCAGACC---CATACCC---CAAACCCAAAAGGA-
-----CTCGACAGGCCCGAAAGAATCGAAGAAGAAAGTGAAAAGCAAGAC
AGAACCAGATCGACTCGATTAGTCAGCAGATTCTTAGCACTTGCTTAAGA
CGACCTGCAGAGCCTGAGCCTTTTCCTCTACCACCGATTAAAAGACTTCA
TCTTGATTGCCGCGAAGACTGTAGAACTTCTAAGA---CACAGCAGTCTC
AAAAAGTTAAGACTAAAGTAAAAAAGACTCAAGTATCT---GTAAAATCT
C---CTGTTATATTAAGGTCAAGAACTAAAAATTAGTGCTATTAACTTGC
TCAATA---CCATAGCAATAGCAGTAGCTAGCTAGACAGATAAAGTTATA
GAAATAAGACAAAGAATTAGTAAAGCTATTCTCCACATACCTAGAAGAAT
CAGGCAAAGCTTCGAAAAGGCTTTATTATAA
'A1.KE.00.KNH1144'
------GCGAGAGCGTCAGTATTAAGTGGGGG---AAAATTAGATAGATG
GGAGAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGAATGAAAC
ATCTAGTATGGGCAAGCAGGGAGCTGGAAAGATTCGCACTTAACCCTAGC
CTTTTAGAAACAGCAGAAGGATGTCAGCAAATAATAGAACAGATACAACC
AGCTCTCAAGACAGGAACAGAAGAACTTAGATCATTATTTAATACAATAG
CAACCCTCTATTGCGTACATCAAAAGATAGATGTGAAAGACACCAAGGAA
GCTCTAG---AT--AAA-ATAGAGGAACTGCA------------AAATAA
GAGCAAG------------CAAAAGACA---------CA---ACAA----
--------------GCA---GCA---------------------GCT---
------------------------GATACAGGA-----------------
-------AGTGGCAGC------------AAGGTCAGCGTCAGCCAAAATT
ACCCTATAGTGCAAAATGCACAAGGGCAAATGATACACCAGACTTTGTCA
CCTAGGACCTTGAATGCATGGGTAAAAGTAATAGAAGAAAAGGCTTTCAG
CCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACTCCAC
AAGATTTAAATATGATGCTGAACATAGTGGGGGGACACCA---GGCAGCC
ATGCAAATGTTAAAGGATACCATCAATGAGGAAGCTGCAGAATGGGACAG
GACACATCCAGTACATGCAGGGCCTATTCCACCAGGCCAGATGAGAGAAC
CAAGGGGAAGTGACATAGCAGGAACTACTAGCACCCCTCAAGAACAAATA
GGATGGATGACAAGCAACCCACCTATCCCAGTGGGAGACATCTATAAAAG
ATGGATAATCTTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTA
GCATTTTGGATATAAAACAAGGGCCAAAAGAACCCTTCAGAGATTATGTA
GATAGGTTCTTTAAAACTCTCAGAGCTGAGCAAGCTACACAGGAGGTAAA
AGGTTGGATGACAGAAACATTACTGGTCCAAAATGCAAATCCAGATTGTA
AGTCCATTTTAAGAGCATTAGGAACAGGAGCTACATTAGAAGAAATGATG
ACAGCATGCCAGGGAGTGGGAGGACCCGGCCATAAAGCAAGGGTTTTGGC
TGAGGCAATGAGTCAAGT---AC---AAC---A---TA--C---A-----
-----------------AACATA---ATGATGCAAAGAGGCAACTTTAGG
GGCCAGAAA---AGAATTAAGTGTTTCAACTGTGGCAAAGAAGGACACCT
AGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGGA
AGGATGGACATCAAATGAAAGACTGCACT------GAAAGACAGGCTAAT
TTTTTAGGGAAAATTTGGCCTTC---CAGCAAGGGG---AGGCCAGGAAA
TTTTCCTCAGAGCAGA---------------CCGGAACCAACAGCCCCA-
-----------------------------------CCA---GCAGAGCTC
TTTGGGATGGGGGAAGAGATA---------------GCCTCCCCTCTA--
----AAGCAGGAGCAG------------AAAGG---CAAGGAACAGACT-
-----CCA------CCCTCAATCTCCCTCAAATCACTCTTTGGCAACGAC
CCCTTGTCACAGTAAAAATAGCGGGACAGCTAAGAGAAGCTCTATTAGAT
ACAGGGGCAGATGATACAGTATTAGAAGACATAGATTTGCCAGGTAAATG
GAAGCCAAAAATGATAGGGGGAATTGGAGGTTTCATCAAGGTAAAACAGT
ATGAGCAGGTACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTA
TTAGTAGGACCTACACCTGTCAACA---TAATTGGAAGAAACATGTTGAC
CCAGATTGGTTGTACTTTAAATTTCCCAATTAGTCCTATTGAGACTGTAC
CAGTAAAATTAAAGCCAGGAATGG---ATGGCCCAAAGGTTAAACAATGG
CCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGCACA-----
-GAGATGGAAAAGGAAGGAAAAATTTCACAAATTGGACCTGAAAATCCAT
ACAATACTCCAATATTTGCAATAAAGAAAAAAGATAGCACTAAATGGAGG
AAATTAGTAGATTTCAGAGAGCTCAATAAAAGAACACAAGACTTTTGGGA
AGTTCAATTAGGGATACCGCATCC---AGCGGGCCTAAAAAAGAAAAAAT
CAGTAA---CAGTGCTAGATGTGGGGGACGCATATTTCTCAGTCCCTTTA
CATGAAGACTTTAGAAAGTATACTGCATTCACCATACCTAGTACAAACAA
TGAGACACCAGGAAAAAGGTATCAGTACAATGTGCTTCCACAGGGATGGA
AAGGATCACCAGCAATATTCCAGAGTAG---TATGACAAAAATCTTAGAG
CCCTTTAGATCAAAAAATCCAGAAATAATTATCTATCAATACATGGATGA
CTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAGCAAAAATAG
AAGAATTAAGAGCTCATCTATTGAGCTGGGGATTTACTACACCAGAC---
AAGAAGCATCAGAAAGAACCTCCATTCCTTTGGATGGGATATGAGCTCCA
TCCTGACAAGTGGACAGTCCAGCCTATAGAGCTGCCAAACAAAGAAAGCT
GGACTGTCAATGATAT---ACAGAAATTAGTGGGGAAACTAAATTGGGCT
AGTCAAATTTATGCAGGAATTAAAGTAAAGCACTTGTGTAGACTTCTCAG
GGGAGCCAAAGCACTAACAGATGTAGTAACATTGACTGAGGAAGCAGAAT
TAGAGTTGGCAGAAAACA---AGGAGATTCTAAAAGAACCTGTGCATGGA
GTATATTATGACCCATCAAAAGAACTAATAGCAGAAGTACAGAAACAAGG
GCAAGACCAATGGACATACCAAATCTATCAAGAGCCATTTAAAAATCTAA
AAACAGGGAAATATGCAAGACAAAGGTCTGCTCACACTAATGATGTAAAA
CAATTAGCAGAAGTGGTACAAAAAATAGCCATGGAAGGCATAGTAATATG
GGGAAAGA---CTCCTAAATTTAGACTA---CCCATACAAAAAGAGACAT
GGGAAACA---TGGTGGAGGGACTATTGGCAGGCTACCTGGATTCCCGAA
TGGGAATTTGTCAATACCCCTCCTTTAGTAAAATTGTGGTACCAATTAGA
GAAAGACCCCATAGTAGGAGCAGAGACTTTCTATGTAGATGGAGCAGCCA
ATAGGGAGACTAAGCTAGGAAAAGCAGGGTATGTCACTGACAGGGGAAGA
CAAAAGGTTGTTTCCCTGACTGAGA---CAACAAATCAAAAAACTGAACT
ACATGCAATCTATCTAGCCTTGCAAGATTCAGGATCAGAAGTAAACATAG
T---AACAGACTCACAGTATGCATTAGGAATCA---TTCAGGCACAACCA
GACAAGAGTGAATCAGAGTTAGTCAATCAAATAATAGAGAAGCTAATAGG
AAAGGACAAAGTCTACCTG---TCATGGGTACCAGCACACAAGGGAATCG
GAGGAAATGAAAAAGTAGATAAATTAGTCAGTAACGGAATCAGGAAGGTG
CTGTTTTTAGATGGGATAGATAAAGCTCAAG---AAGAACATGAAAGATA
---TCACAGCAATTGGAGAGCAATGGCTAGTGATTTTAATCTACCACCTA
TAGTAGCAAAGGAAATAGTAGCCTGCTGTGATAAAT---GTCA---GCTA
AAAGGAGAAGCCATACATGGACAAGTAGACTGCAGTCCAGGGATATGGCA
ATTAGATTGTACACATCTAGAAGGAAAAATAATTTTGGTAGCAGTCCATG
TAGCCAGTGGCTATATAGAAGCAGAAGTTATCCCAGCAGAAACAGGACAA
GAGACAGCATACTTTATACTAAAATTAGCAGGAAGATGGCCAGTAAAAGT
AATACACACAGACAATGGCAGCAATTTCACCAGCGCTGCAGTTAAAGCAG
CCTGTTGGTGGGCAGATATCCAGCAGGAATTTGGAATTCCCTACAACCCC
CAAAGTCAAGGAGTAGTAGAATCTATGAATAAGGAATTAAAGAAAATCAT
AGGACAGGTAAGAGAGCAAGCTGAACACCTTAAAACAGCAGTACAAATGG
CAGTATTCATTCACAATTTTAAAAGAAAA---GGGGGGATTGGGGGGTAC
AGTGCAGGGGAAAGAATAATAGATATAATAGCAACAGACATACAAACTAA
AGAATTACAAAAACACATTACAAAAATTCAAAATTTTCGGGTTTATTACA
GGGACAGCAGAGATCCAGTTTGGAAAGGACCAGCAAAACTACTTTGGAAA
GGTGAAGGGGC---AGTAGTAATACAGGACAATAGTGATATAAAGGTAGT
ACCAAGAAGAAAAGCAAAAATCATCAGGGATTATGGAAAACAAATGGCAG
GTGATGATTGTGTGGCAGGTAGACAGGATGAGGATTAGA---ACATGGAA
CAGTTTAGTAAAACATCATATGTATGTATCAAAGAAAGCAAAAAATTGGG
TCTATAGGCATCACTTTGAAAGCAGAAATCCAAGAGTAAGTTCAGAAGTA
CACATCCCACTAGGGG---ATG---CTAAACTAGTAGTAAGAACATATTG
GGGTCTGCATCCAGGAGAAAATGACTGGCATTTGGGTCATGGGGTCTCCA
TAGAATGGAGGCTAAAAAGTTACAGCACACAA------GTAGATCCTGAC
CTGGCAGACCAACTAATTCATCTGTATTATTTTGACTGTTTTTCAGGCTC
---TGCCATAAGGAAAGCCATATTAGGAGAATTAGTTAGCCCTAGATGTG
AATATCAAACAGGACACA---GCAAGGTAGGATCTCTACAATATTTAGCA
CTGAAAGCATTAGTAACACC---ACAAAAGACAAAGCCACCTTTGCCTAG
TGTTAGGATATTAGCAGAGGATAGATGGAACAAGCACCAGAAGACCAGGG
GCCCCAGAGAGAGCCATACAATGAATGGATGTTAGAGCTGTTAGAAGATC
TTAAGCATGAAGCTGTTAGACACTTTCCTAGGCCATGGCTTCATGGATTA
GGACAACACATCTATGACACCTATGGGGATACTTGGGAAGGAGTTGAAG-
--CTATAATAAGAACTCTGCAA---CAACTACTGTTTGTTCAT---TTCA
GAATTGGGTGTC---AACATAGCAG---AATAGGCATT---ATTCGGGGA
AGAAGAGGCA----------GGAATGGATCCAGTAGATCCTAACCTAGAC
CCCTGGAACCACCCGGGAAGTCAGCCTACAACTCCTTGTA---ACAAGTG
TTACTGTAAAAAGTGTTGCTATCATTGCCAG---------------TATT
GCTTTTTGAA---CAAAGGCTTAGGCATCTCCTATGGCAGGAAGAAGCGG
AGAC------A---GCGACGAGGA------A---CTCCTCACAGCAGTAA
GGATCATCAAAATCCTCTACCAAAGCAGTAAGTAT--TAGTAATT-----
-AGTATATGTA---ATGTTG------------------------------
---------CCTCCTTTAC---------------ATATCTGTGCAATAGT
A---GGACTGATAGTAGC---GG--CAATCC-TAGCAATAATTGTGTGGA
CTATAGTAGGTATAGAATAT---AGGA------------AACTGTTAAAA
CAA---AGGAAAATAGACAGGTTAATTGAGAGAATAAGAGAAAGAGCAGA
GGACAGTGGCAATGAGAGTGATGGGGACACAGATGAATTGTCAGCACTT-
--ATTGAGATG------------------------GGGAACTATG---AT
CTTGGGA---TTGATAATAAT------------CTGT------AATGCTG
T---------AAACAGC------------A---A------CTTG------
TGGGTTACTGTCTATTATGGGGTACCTGTGTGGAAAGATGCAG---AG--
ACCACCT-TATTTTGTGCATCAGATGCTAAAGCATATAAAACAGAAAAGC
ATAATGTCTGGGCTACACATGCCTGTGTGCCCACAGACCCCAACCCACAA
GAAATACCTTTGGAAAATGTGACAGAAGAGTTTAACATGTGGAAAAATAA
AATGGTAGAACAAATGCATACAGATATAATCAGTCTATGGGACCAAAGCC
TACAGCCATGTGTAAAGTTAACCCCTCTCTGCGTTACTTTAAATTGTACA
G---ATG---TT--ACTAATGTT---------------------------
-----------AC--AGAT---GT---TAG-TG-GTA---CG--------
-------A-GGGGCAAC---AT--C-------------------------
--------------------------ACC---AT--C---AT--GAA--A
GAG---ATGGA------G-GGA-GA-AATAA-AAAACTGTTCTTTCAATA
TGACCACAGAAATAAGGGATAAGAAACAGAAAGTATATTCAC---TCTTT
TATAGACTTGATGTAGTACCAATAAATCAGGGTAATAGT-----------
-------AGTA---GT--AA--AAACAGT---AGT---------------
---------------------G---AG--TATAGA-T-TAATAAGTTGTA
-ATACCTCAGCCATTACACAAGCTTGCCCAAAGGTAAGCTTTGAGCCAAT
TCCCATACATTATTGTGCCCCAGCTGGTTTTGCGATCCTGAAGTGTAGGG
ATAAGGAGTTCAATGGAACAGGGGAATGCAAGAATGTCAGCACAGTCCAA
TGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTACTGTTAAATGG
CAGTCTAGCAGAA---GAAAA---GGTAAAAATCAGAACTGAAAATATCA
CAAACAATGCCAAAACTATAATAGTACAACTTGTCGAGCCTGTGAGAATT
AATTGTACTAGACC------T------AATAACA---AT---ACAAGAGA
GAGTGTGCGTATA---------GGGCCAGGACAAGCATTCTTTGCA---A
CAGGTGAC------ATAATAGGGGATATAAGACAAGCACATTGTAATGTC
AGTAGATCACAATGGAATAAGACTTTACAACAGGTAGCT---GA--ACAA
TTAAGAGAA------CACTTT---A----AA--AAC------AAAACA--
----ATAATATTTAAC----AGTTC---CTCAGGAGGGGATCTAGAAATC
ACAACAC------ATAGTTTCAATTGTGGAG---GAGAATTTTTCTATTG
TAATACATCAGGTCTGTTCAAT---AGCACC---TG---G----------
------AAT-----ACC---------------------------AGCATG
T---CAGGG---T-C-------A---AGT---AA-CAC---G---G----
--AG--AC--AAA---T---------------GACACTATAACT------
---CTCCAATG-CA-GAATAAAGCAAATTATAAATATGTGGCA---GAGA
ACAGGACAAGCAATATATGCCCCTCCCATCCAGGGAGTGATAAGGTGTGA
ATCAAACATCACAGGACTACTGTTAACAAGAGATGG---TGGGGA---GG
AG------AAG---------------AAC--AGTA---CA--AATGAAAT
CTTCAGACCTGGAG-GAGGAG-ATATGAGGGACAACTGGAGAAGTGAATT
ATATAAGTATAAAGTAGTAAAAATTGAACCACTAGGAGTAGCACCCACCA
GGGCAAGGAGAAGAGTGGTGGG------AAGAGAAAAAAGAGCAG---TT
GGA-------ATAGGAGC---TG--T---TTTCCTTGGGT---TCTTAGG
----AG-CAGCAGGAAG-CACTATGGGCGCGGCGTCAATAACGCTGACGG
TACAGGCCAGGCAATTATTGTCTGGCATAGTGCAACAGCAGAGCAATTTG
CTGAGGGCTATAGAGGCTCAACAACATATGTTGAAACTCACGGTCTGGGG
CATTAAACAGCTCCAGGCAAGAGTCCTTGCTGTGGAAAGATACCTAAGGG
ATCAACAGCTCCTAGGAATTTGGGGCTGCTCTGGAAAACTCATCTGCACC
ACTAATGTGCCCTGGAACTCTAGTTGGAG---T---AAT-----------
-AAATCTCAGGA---TGAAATAT---GGA---ACAACATGACCTGGCTGC
AATGGGATAAAGAAATTAGCAATTACACAAACCTAATATATAGTCTAATT
GAAGAATCGCAAAACCAGCAGGAAAAGAATGAACAAGACTTATTGGCATT
GGGCAAGTGGGCAAATCTGTGGACTTGGTTTGACATATCAAATTGGCTGT
GGTATATAAGAATATTTATAATGATAGTAGGAGGCTTAATAGGATTAAGA
ATAGTTTTTGCTGTGCTTGCTGTAATAAAGAGAGTTAGGCAGGGATACTC
ACCTGTGTC---ATTTCAGATC---CATGCCC---CAAACCCAGGGGGT-
-----CTCGACAGGCCCGGAAGAATCGAAGAAGAAGGTGGAGAGCCAGGC
AGAGGCAGATCGATTCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGA
CGATCTGAGGAACCTGTGCCTCTTCAGCTACCATCGCTTGAGGGACTTCG
CCTTGATTGTTGCGAGGACTGTGGAACTTCTGGGA---CACAGCAGTCTC
AAGGGGTTGAGGCTGGGGTGGGAGGGCCTCAAGTATCT---GTGGAATCT
C---CTGGTATACTGGAGTCAGGAACTAAAAACTAGTGCTATTAGTTTGG
TTGATA---CTATAGCAATAGCAGTAGCTGGCTGGACAGATAGAGCTATA
GAAATAGGACAAGGAATTGGTAGAGCTTTTCTCCACATACCTAGAAGAAT
CAGACAGGGCTTAGAAAGGGCTTTGCTGTAA
'A1.KE.00.KNH1199'
------GCGAGAGCGTCAGTATTAAGCGGGGR---AAAATTAGCTGCATG
GGAGAAGATTCGGTTAAGGCCAGGGGGAAGGAAAAGATATCGCATAAAAC
ATTTAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTCAACCCTAGC
CTTTTAGAAACAGCAGAAGGATGTCAACAAATAATGGAACAGTTACAACC
AGCTCTCAAGACAGGAACAGAAGAACTTAGATCATTATTTAATACAGTAG
CAACCATCTATTGCGTGCATCAACGAATAGATGTGAAAGACACCAAGGAA
GCTCTAG---AT--AAA-ATAGAGGAAATGCA------------AAAGAA
GAGCAAG------------CAAAAGACA---------CA---ACAG----
--------------GCA---GCA---------------------GCT---
------------------------GACACAGGA-----------------
-------CACAGCAGC------------CAG------GTCAGCCAAAATT
ACCCTATAGTACAAAATGCACAAGGGCAAATGGTACACCAGGCAGTATCA
CCTAGGACTTTGAATGCATGGGTAAAAGTAATAGAAGAAAAGGCTTTCAG
CCCAGAAGTAATACCCATGTTCTCAGCATTATCAGAAGGAGCCACCCCAC
AAGATTTAAATATGATGCTGAACATAGTGGGGGGACATCA---GGCAGCT
ATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAG
GTTACATCCAGTACATGCAGGGCCTATTCCACCAGGCCAGATGAGAGAAC
CAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCCTCAAGAACAAATA
GGGTGGATGACAGGCAACCCACCCATCCCAGTGGGAGACATCTATAAAAG
ATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTA
GCATTTTAGATATAAAACAAGGGCCAAAAGAACCCTTCAGAGATTATGTG
GATAGGTTCTTTAAAACTCTCAGAGCTGAGCAAGCTACACAGGAGGTAAA
AAATTGGATGACAGAGACATTACTGATCCAAAATTCAAATCCAGATTGTA
AGTCCATCTTAAGAGCATTAGGACCAGGGGCTACATTAGAAGAAATGATG
ACAGCATGCCAGGGAGTGGGAGGACCCGGCCATAAAGCAAGGGTTTTGGC
TGAGGCAATGAGTCAGGT---AC---AAC---A---GC--C---A-----
-----------------AACATAATGATGATGCAAAGAGGTAATTTTAGG
GGCCAGAAA---AAGATTAAGTGTTTCAACTGTGGCAAAGAAGGACACCT
AGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAA
AGGAGGGACACCAAATGAAAGACTGCACT------GAAAGACAGGCTAAT
TTTTTAGGGAGAATTTGGCCTTC---CAGCAAAGGG---AGGCCAGGGAA
TTTTCCTCAGAACAGA---------------TTGGAGCCAACAGCCCCA-
-----------------------------------CCA---GCAGAGATC
TGTGGGATGGGGGAAGAGATA---------------GCCTCCCCTCCG--
----AAGCAGGAGCAG------------AGAGA---CAAGGAACAGGCC-
-----TCA------CCTTCAGTTTCCCTCAAATCACTCTTTGGCAACGAC
CTATTGTCACAGTAAGAATAGGGGGACAGCTAAAAGAAGCTCTATTAGAT
ACAGGAGCAGATGATACAGTATTAGAAGATATAGATCTGCCAGGAAAATG
GAAGCCAAAAATGATAGGGGGAATTGGAGGATTCATCAAAGTAAGACAGT
ATGATCAGATACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTA
TTAGTAGGACCTACACCTGTCAACA---TAATTGGAAGGAACATGTTGAC
CCAGATTGGTTGTACTTTAAATTTCCCAATTAGTCCTATTGAAACTGTAC
CAGTAAAATTAAAGCCAGGTATGG---ATGGCCCAAAGGTTAAACAATGG
CCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACA-----
-GATATGGAAAAGGAAGGAAAAATTTCAAGAATTGGGCCTGAAAATCCAT
ACAATACTCCAATATTTGCAATAAAGAAAAAGGATAGCACTAAATGGAGG
AAATTAGTAGATTTCAGAGAGCTCAATAAAAGAACACAAGACTTGTGGGA
AGTTCAATTAGGAATACCACATCC---ATCGGGCCTAAAAAAGAAAAAAT
CAGTAA---CAGTACTAGATGTGGGGGACGCATATTTTTCAGTTCCTTTA
GATGAGAACTTTAGAAAATATACTGCATTCACCATACCTAGTACAAACAA
TGAGACACCAGGAATCAGATATCAGTACAATGTGCTTCCACAGGGATGGA
AAGGATCACCAGCAATATTCCAGAGTAG---CATGACAAAAATCTTAGAG
CCCTTTAGATTAAAAAATCCAGAAATAATTATTTATCAATACATGGATGA
CTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAGCAAAAATAG
AAGAGTTAAGAGCTCATCTATTGAGCTGGGGATTTACTACACCAGAC---
AAAAAGCATCAGAAAGAACCTCCATTCCTTTGGATGGGATATGAGCTCCA
TCCTGACAAGTGGACAGTCCAGCCTATAGTGCTGCCAGAAAAAGAAAGCT
GGACTGTCAATGATAT---ACAGAAATTAGTGGGAAAACTAAATTGGGCA
AGTCAAATTTATGCAGGGATTAAAGTAAGGCAGTTGTGTAAACTCCTCAG
GGGAGCCAAAGCACTAACAGATGTAGTAACATTGACTGAGGAAGCAGAAT
TAGAATTGGCAGAGAACA---GGGAGATACTAAGAGACCCTGTGCATGGA
GTATATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGG
GCAAGACCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAATCTAA
AAACAGGAAAATATGCAAGAAAAAAGTCTGCTCACACTAATGATGTAAGA
CAATTAGCAGAGGTGGTGCAAAAGGTAGTCATGGAAAGCATAGTCATATG
GGGAAAGA---CTCCTAAATTTAGACTA---CCCATACAAAAAGAGACAT
GGGAAACA---TGGTGGATGGACTATTGGCAGGCTACCTGGATTCCTGAA
TGGGAGTTTGTCAATACCCCTCCTCTAGTAAAATTGTGGTACCAATTAGA
AAAAGACCCTATAGCAGGAGCAGAGACTTTCTATGTAGATGGGGCAGCCA
ATAGGGAGACTAAGCTAGGAAAAGCAGGGTATGTCACTGACAGGGGAAGA
CAAAAGATTGTTTCCCTAACTGAAA---CAACAAATCAAAGGACTGAACT
ACATGCAATCTATCTAGCTTTGCAGGATTCAGGATCAGAAGTAAATATAG
T---AACAGACTCACAATATGCATTAGGAATCA---TTCATGCACAACCA
GACAGAAGTGACTCAGAGTTAGTCAATCAGATAATAGAGAAGCTAATAGG
AAAGGACAAAGTATACCTG---TCATGGGTTCCAGCACACAAAGGAATTG
GAGGAAATGAACAAGTAGATAAATTAGTCAGTTCCGGAATCAGAAAGGTG
CTGTTTTTAGATGGGATAGATAAAGCTCAAG---AAGAACATGAAAGATA
---TCACAGCAATTGGAGAGCAATGGCTAGTGATTTTAATTTGCCACCTA
TAGTAGCAAAGGAGATAGTAGCCAGCTGTGATAAAT---GTCA---GCTA
AAAGGGGAAGCCATGCATGGACAAGTAGACTGCAGTCCAGGGATATGGCA
ATTAGATTGCACACATCTAGAAGGAAAAGTAATACTGGTAGCAGTTCATG
TAGCCAGTGGCTATATGGAAGCAGAAGTTATCCCAGCAGAAACAGGACAA
GAGACAGCATACTTTATACTAAAACTAGCAGGAAGATGGCCAGTAAAAGT
AGTACACACAGACAATGGCAGCAATTTCACCAGTGCTGCAGTTAAAGCAG
CCTGTTGGTGGGCAAATATCAAACAGGAATTTGGGATTCCCTACAATCCC
CAAAGTCAAGGAGTAGTGGAATCTCTAAATAAGGAATTAAAGAAAATTAT
AGGACAGGTAAGAGAGCAAGCTGAACATCTTAAAACAGCAGTACAAATGG
CAGTATTCATTCACAATTTTAAAAGAAAA---AGGGGGATTGGGGGGTAC
AGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAC
AGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACA
GGGACAGCAGAGATCCAATTTGGAAAGGACCAGCAAAACTACTCTGGAAA
GGTGAAGGGGC---AGTAGTAATACAGGACAATGGTGATATAAAGGTAGT
ACCAAGAAGAAAAGTAAAAATCATTAGGGACTATGGAAAACAGATGGCAG
GTGATGATTGTGTGGCAGGTGGACAGAATGAGGATTAGA---ACATGGCA
CAGTTTAGTAAAACATCATATGTATATCTCAAAGCAAGCTAAAAATTGGT
CTTATATACATCACTTTCAAAGCAGGCATCCAAAAGTAAGTTCAGAAGTA
CACATCCCACTAAAGG---ATG---CTAGATTAGTAGTAAAAACATATTG
GGGTCTGCATACAGGAGAAAAAGACTGGCACTTGGGTCATGGGGTCTCCA
TAGAATGGAGGTTAAAAGGATATAGCACACAA------GTAGATCCTGAC
CAGGCAGACCAACTAATTCATCTGCATTATTTTGACTGTTTTTCAGACTC
---TGCCATAAGGAAAGCCATATTAGGAGAAGTAGTTAGCCCTAGGTGTG
CATATCAAACAGGACATA---ACAAGGTAGGATCTCTGCAATATTTAGCG
CTGAAAGCATTAGTAACACC---AACAAAGACAAAGCCACCTTTGCCTAG
TGTTAGGATATTAGCAGAGGATAGATGGAACAAGCCCCGGAAGACCAAGG
GCCCCAGAGAGAGCCATACAATGAATGGATGTTAGAGCTGTTAGAAGATC
TTAAGAATGAAGCCGTTAGACATTTTCCTAGAATGTGGCTTCATGGATTA
GGACAACACATCTATGAAACCTATGGGGATACTTGGGAAGGAGTTGAAG-
--CTATAGTAAGAACTCTGCAA---CAACTACTGTTTGTTCAT---TTCA
GAATTGGGTGCC---AACATAGCAG---AATAGGCATT---ATTCGAGGG
AGAAGAGGCA----------GGAATGGATCCGGTAGATCCTAACCTAGAG
CCCTGGAACCACCCGGGAAGTCAGCCTACAACACCTTGTA---GCAAGTG
TTACTGTAAAAAGTGTTGCTATCATTGTCCA---------------GTTT
GCTTTTTGAA---CAAAGGCTTAGGCATCTCCTATGGCAGGAAGAAGCGG
AGAC------A---GCGACGAAGA------A---CTCCTCCGTGCAATAA
GGATCATCAAAATCCTGTACCAAAGCAGTAAGTAA--TAGTAATT-----
-AGTATATGTA---ATGTGG------------------------------
---------CTTCCTTTGC---------------AAATTTGTGCAGTAGT
A---GGATTGATAGTAGC---AA--TAATCA-TAGCAATAGTTGTGTGGA
CTATAGTAGGTATAGAATAT---AAGA------------GATTGCTAAAG
CAA---AGAAAAATAGACAGGTTAATTGAAAGAATAAGAGAAAGAGAAGA
AGACAGTGGCAATGAGAGTGATGGAGACACAGAGGAATTGTCAACACTT-
--ATTAAGATG------------------------GGGAATTATG---AT
CTTGGGG---ATGATAATAAT------------TTGT------AGTACTA
C---------AGA---A------------A---A------CTTG------
TGGGTTACTGTCTACTATGGGGTACCTGTGTGGAAAGACACAG---AG--
ACCACCT-TATTTTGTGCATCAGATGCTAAAGCATATGAGACAGAAAAAC
ATAATGTCTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAA
GAAATATATTTGGAAAATGTGACAGAAGAGTTTAACATGTGGAAAAATAA
CATGGTAGAGCAAATGCATACAGATATAATCAGTCTATGGGACCAAAGCC
TAAAGCCATGTGTAAAGTTAACCCCTCTCTGCGTCACTTTAAATTGTAGC
A---ATG---TC--AGGGTCAATGCCTCGAGTATAGAGACCAATGCC---
-----------TC--GAGA---AG---CAA-TG-TCA---GC--------
-------A-GTATCAAT---GG--C-------------------------
--------------------------TSG---AG--T---TT--A-----
-------------------GAA-GA-AATAA-GAAACTGTTCTTTCAATA
TGACCACAGAGCTAAGGGATAAGAAAAAGCAGGTATATGCAC---TTTTT
TATAAACTTGATGTAGTACAAATTAATGAA--------------------
-------AATG---AA--AG--TAATAGT---AGT---------------
---------------------A---AG--TATAGA-T-TAATAAATTGTA
-ATACCTCAGCCATTACACAGGCTTGCCCAAAGGTAACCTTTGAACCAAT
TCCCATACATTATTGTGCCCCAGCTGGTTTTGCGATCCTAAAGTGTAGGG
ATGAAGAGTTCAATGGAACAGGGCCATGCAAGAATGTCAGCACAGTACAA
TGTACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGTTAAATGG
CAGTCTAGCAAAA---AATAC---AGTAAAAATTAGATCTGAAAATATCA
CAAACAATGTCAAAACTATAATAGCACAACTTGTCAATCCTGTAACAATT
AATTGTACCAGACC------T------AGCAACA---AT---ACAAGGAC
AAGTATACGTATA---------GGACCAGGACAAGCATTCTATGCA---A
CAGGAGAC------ATAATAGGGGACATAAGAAAAGCATATTGTAATGTC
AGTGAATCAGAATGGGAGAAAGCTTTAAAACAGGTAGCT---GG--ACAA
TTAGGAAAG------CACTTT---A----GC--AAC------AAAACA--
----ATAAAATTTACT----AACTC---CTCAGGAGGGGATCTAGAAATC
ACAACAC------ATAGTTTTAACTGTGGAG---GAGAATTCTTCTATTG
TAATACATCAGGCCTGTTTAAT---AGCTTT---TG---GA--GTTATAG
C-----AATGG--GACTTACAGCACAAATAGCACA---------AAGTCA
A---ATGGC---A-C-------A---AAT---AG-CAC---A---A----
--AG--TC--AAA---T---------------GGCACTATACAG------
---CTCCCATG-CA-GAATAAAGCAAATTATAAATATGTGGCA---GAGA
GCAGGACAAGCAATGTRTGCTCCTCCCATCCGAGGAATAATAAGGTGWGA
ATCAAACATTACAGGACTAATATTAACAAGGGATGG---TGGGAG---TA
ATGGGAATAAT---------------AGC--AATA---CA--ACAGAGAT
CTTCAGACCTGGAG-GAGGAG-ATATGAGGGACAATTGGAGAAGTGAATT
ATATAAGTATAAAGTAGTAAAAATTGAACCACTAGGAGTAGCACCCACCA
GGGCAAGGAGAAGAGTGGTGTG------GAGAGAAAAAAGAGCAG---TT
GGA-------ATAGGAGC---TG--T---ATTCCTTGGGT---TCTTAGG
----AG-CAGCAGGAAG-CACTATGGGCGCGGCGTCAATAACGCTGACGG
TACAGGCCAGACAATTATTGTCTGGCATAGTGCGACAGCAAAGCAATTTG
CTGAGGGCTATAGAGGCTCAACAACATCTGTTGAAACTCACGGTCTGGGG
CATTAAACAGCTCCAGGCAAGAGTCCTGGCTGTGGAAAGATACCTAAAGG
ATCAACAGCTCCTAGGAATTTGGGGCTGCTCTGGAAAACTCATCTGCACC
ACTAATGTGCCCTGGAACTCTAGTTGGAG---T---AAT-----------
-AAATCTCAGAC---TGAGATAT---GGA---ATAACATGACCTGGCTGC
AATGGGATAAAGAAATTACCAATTACACACAAGAAATATATAAACTAATT
GAAGAGTCGCAGAACCAGCAGGAAAAGAATGAGCAAGACTTATTGGCCTT
GGACAAGTGGGCAAGTCTGTGGAATTGGTTTGAAATATCAAATTGGCTGT
GGTACATAAAAATATTTATAATGATAGTAGGAGGCTTAATAGGATTAAGG
ATAATTTTTGCTGTGCTTTCTGTAATAAATAGAGTTAGGCAGGGCTACTC
ACCTTTGTC---ATTTCAGACC---CATACCC---CAAACCCAGGGGGT-
-----CTCGACAGGCCAGGAAGAATCGAAGAAGAAGGTGGAGAGCAAGGC
AGAGACAGATCGATTCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGA
CGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTCA
TCTTGATTGCAGCGAGGACTGTGGAACTTCTGGGA---CACAGCAGTCTC
AAGGGGTTGAGACTGGGGTGGGAAGGCCTCAAGTATCT---GTGGAATCT
C---CTGTTATACTGGGCTCGGGAACTAAAAATTAGTGCTATTAATTTGT
TTGATA---CCATAGCAATAGTAGTAGCTGGCTGGACAGATAGGGTTATA
GAACTAGGACAAAGAATTGGTAGAGCTATTCTA-----------------
------AGGCTTTGAAAAGGCTTTGCTATAA
'A1.KE.00.KNH1207'
------GCGAGAGCGTCAGTATTAAGTGGGGG---AAAATTAGATGCATG
GGAGAAAATTAATTTAAGGCCAGGGGGAAAGAAAAAATATAAAATGAAGC
ATTTAGTATGGGCAAGCAGGGAGCTGGAAAGATTCGCACTTAACCCTAGT
CTTTTAGAAACAGCAGAAGGATGTCAACAAATAATAGAACAATTACAACC
AGCTCTCAGGACAGGAACAGAAGAATTTAGATCATTATTTAATACAGTAG
CAACCCTCTATTGCGTGCATCAAAAGATTGATGTAAAAGACACCAAGGAA
GCTTTAG---AT--AAA-ATAGAAGAAATACA------------AAATAA
GAACAAG------------CAAAAGACA---------CA---GCAG----
--------------GCA---GCG---------------------GCT---
------------------------GATACAGGA-----------------
-------AACAGCAGC------------AAG------GTCAGCCAAAATT
ACCCTATAGTGCAAAATGCACAAGGGCAAATGATACACCAGCCCTTATCA
CCCAGGACTTTGAATGCCTGGGTAAAAGTAATAGAAGAAAAGGGTTTCAG
CCCAGAAGTAATACCTATGTTCTCAGCATTATCAGAAGGAGCCATCCCAC
AAGATTTAAATATGATGCTGAACATAGTGGGGGGACACCA---GGCAGCT
ATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGATAG
ATTACATCCAGTACATGCAGGGCCCATTCCACCAGGCCAAATGAGAGAAC
CAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCCTCAAGAACAAGTA
GGATGGATGACAGGCAATCCACCTATCCCAGTGGGAGACATTTATAAAAG
ATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTA
GCATTTTGGACATAAAACAAGGGCCAAAAGAACCCTTCAGAGACTATGTA
GATAGGTTCTTTAAAGTTCTCAGAGCTGAACAAGGTTCACAGGATGTAAA
AAATTGGATGACAGAAACCTTGCTGGTCCAAAATGCAAATCCAGATTGTA
AGTCTATTCTGAGAGCATTAGGACAAGGGGCTTCATTAGAAGAAATGATG
ACAGCATGCCAGGGAGTGGGAGGACCCGGCCATAAAGCAAGGGTTTTGGC
TGAGGCAATGAGTCAGGT---AC---AAC---A---TA--C---A-----
-----------------AATATA---ATGATGCAAAGAGGCAATTTTAGG
GGCCAGAAA---AGAATTAAGTGTTTCAACTGTGGCAAAGAAGGACATCT
AGCCAGAAATTGCAAGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGGA
GAGAGGGACACCAAATGAAAGACTGCACT------GAGAGACAGGCTAAT
TTTTTAGGGAAAATTTGGCCTTC---CAGCAAGGGG---AGGCCAGGAAA
TTTTCCTCAGAGCAGA---------------CCGGAGCCAACAGCCCCA-
-----------------------------------CCA---GCAGAGATC
TTTGGGATGGGGGAAGAGATA---------------ACCTCTCCTCCG--
----AAGCAGGAGCGG------------AAACA---GGACCCA-------
--------------CCCTTAGTTTCCCTCAAATCACTCTTTGGCAACGAC
CCCTTGTCACAGTAAAAATAGGAGGACAGCTAAAAGAAGCTCTATTAGAT
ACAGGAGCAGATGATACAGTATTAGAAGATATAAATTTGCCAGGGAAATG
GAAACCAAAAATGATAGGAGGAATTGGAGGTTTTATCAAGGTAAAACAGT
ATGATCAGATACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTA
TTAGTAGGACCTACACCTGTCAACA---TAATTGGAAGAAATATGCTGAC
CCAAATTGGTTGTACTTTAAATTTTCCCATAAGTCCTATTGAGACTGTAC
CAGTAAAATTGAAACCAGGAATGG---ATGGCCCAAAGGTTAAACAATGG
CCATTAACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACA-----
-GATATGGAAAAGGAAGGAAAACTTTCAAGAATTGGGCCTGAAAATCCAT
ACAATACTCCAGTGTTTGCTATAAAGAAAAAAGATAGCACTAAATGGAGG
AAATTAGTAGATTTCAGAGAGCTCAATAAAAGAACACAAGACTTTTGGGA
AGTCCAATTAGGAATACCGCATCC---AGCGGGCCTAAAAAAGAAAAAAT
CAGTGA---CAGTACTGGATGTGGGGGACGCATATTTTTCAGTTCCTTTA
GATGAAGGCTTTAGAAAGTATACTGCTTTCACCATACCTAGTATAAACAA
TGAGACACCAGGAATCAGGTATCAGTACAATGTGCTCCCACAGGGATGGA
AAGGATCACCGGCAATATTCCAGAGTAG---CATGACAAAAATCTTAGAG
CCCTTTAGATCAAAAAATCCAGAAATAATTATCTATCAATACATGGATGA
CTTGTATGTAGGATCTGATTTAGAAATAGGGCAACATAGAACAAAAATAG
AAGAGTTAAGAGCTCATTTATTGAGCTGGGGATTTACTACACCAGAC---
AAAAAGCATCAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTACA
TCCTGACAAATGGACAGTCCAGCCTATACAGCTGCCAGAAAAGGACAGCT
GGACTGTCAATGATAT---ACAGAAATTAGTGGGAAAATTAAATTGGGCA
AGTCAGATTTATGCAGGGATTAAGGTAAAGCAACTGTGTAGACTCCTTAG
GGGAACCAAAGCACTAACAGATGTAGTACCAATGACTGAGGAAGCAGAAT
TAGAATTGGCAGAAAATA---GGGAGATTTTAAAAGACCCTGTACATGGA
GTATATTATGACCCATCAAAAGACCTAATAGCAGAAATACAGAAGCAAGG
GCAAGACCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTAA
AAACAGGGAAATATGCAAAAAGGAGGTCTGCTCACACTAATGATGTAAAA
CAATTAACAGAAGTAGTGCAAAAGGTGGTCACGGAAAGCATAGTAATATG
GGGAAAGA---CTCCTAAATTTAAACTA---CCCATACAAAAAGAAACAT
GGGAAGCA---TGGTGGATGGACTATTGGCAGGCTACCTGGATCCCTGAA
TGGGAGTTTGTCAATACCCCACCTCTAGTAAAACTATGGTACCAGTTAGA
GAAAGACCCTATAGTAGGAGCAGAGACTTTCTATGTAGATGGGGCAGCCA
ATAGGGAAACTAAGTTAGGAAAAGCAGGGTATGTCATTGACAGAGGAAGA
CAAAAGGTTGTTTCCCTAACTGAGA---CAACAAACCAAAAGACTGAATT
ACATGCTATCCATCTAGCATTGCAGGATTCAGGATCAGAAGTAAATATAG
T---AACAGACTCACAGTATGCATTAGGAATTA---TTCAGGCACAACCA
GACAGGAGTGAATCGGAGTTAGTCAATCTAATAATAGAACAGCTAATAGG
AAAGGACAAGGTCTACCTG---TCATGGGTACCAGCACACAAGGGGATTG
GAGGAAATGAACAGGTAGATAAATTAGTCAGCTCTGGAATCAGGAAGGTA
CTATTTTTAGATGGGATAGATAAAGCTCAAG---AAGAACATGAAAGATA
---TCATAGTAATTGGAGAACAATGGCTAGTGATTTTAATCTGCCACCTA
TAGTAGCAAAGGAAATAGTAGCCAGCTGTGACAAAT---GTCA---ACTA
AAAGGGGAAGCCATGCATGGACAAGTAGATTGTAGTCCAGGGATATGGCA
ATTAGATTGCACACATCTAGAAGGAAAAGTAATCCTGGTAGCAGTCCATG
TAGCCAGTGGCTATATAGAAGCAGAAGTTATCCCAGCAGAAACAGGACAG
GAAACAGCATACTTTCTGTTAAAATTAGCAGGAAGATGGCCAGTAAAAGT
AGTACACACAGACAATGGCAGCAATTTCACCAGCGCTGCATTTAAAGCAG
CCTGTTGGTGGGCAAATATCCAACAGGAATTTGGAATTCCCTACAATCCC
CAAAGTCAAGGAGTAGTGGAATCTATGAATAAAGAATTAAAGAAAATCAT
AGGGCAGGTAAGAGAGCAAGCTGAACACCTTAGGACAGCAGTACAAATGG
CAGTATTCATTCACAATTTTAAAAGAAAA---GGGGGGATTGGGGGGTAC
AGTGCAGGGGAAAGAATAATAGACATAATAGCAMCAGATATACAAACTAA
AGAATTACAAAAACACATTTCAAAAATTCAAAATTTTCGGGTCTATTACA
GGGACAGCAGAGATCCCATTTGGAAAGGACCAGCAAAACTACTCTGGAAA
GGTGAAGGGGC---AGTAGTAATACAGGACAATAGTGATATAAAGGTAGT
ACCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAG
GTGATGATTGTATGGCAAGTAGACAGGATGAGGATTAGA---ACATGGAA
CAGTTTAGTAAAACATCATATGTATCTTTCAAAGAAAGCTAAAGGGTGGT
TTTATAGACATCACTATGAAAGCAGGCATCCAAAAGTAAGTTCAGAAGTA
CACATTCCACTAGGGG---ATG---CTAGATTAGTAGTAAGAACATATTG
GGGGCTGCATACAGGAGAAAAAGACTGGCACTTGGGTCATGGGGTCTCCA
TAGAATGGAGGCTAAAAAGATATAGCACACAA------ATAGATCCTGAC
CTGGCAGACCAACTAATTCATATGCATTATTTTGAATGTTTTTCAGACTC
---TGCCATAAGGAAAGCCATATTAGGACAAGTAGTTAGCCCTAGGTGTG
AATACCAAACAGGACATA---ACAAGGTAGGATCTCTACAATATTTGGCA
CTGAAAGCATTAGTAAAACC---AAAAAAGATAAAGCCACCCTTACCAAG
TGTTAGGAAATTAACAGAGGATAGATGGAACGAGCCCCAGAAGACCAGGG
GCCCCAGAGGGAGCCATACAATGAATGGATGTTAGAACTATTAGAAGACC
TTAAACATGAAGCTGTTAGACATTTTCCTAGGCCATGGCTTCATGGACTA
GGACAACATATCTATAACACCTATGGGGATACGTGGGAGGGAGTTGAAG-
--CTATAATAAGAACTTTGCAA---CAATTGCTGTTTGTTCAT---TTCA
GAATTGGGTGCC---AGCATAGCAG---AATAGGCATT---ATTCAAGGG
AGAAGAGGCA----------GGAATGGATCCGGTAGATCCTAACCTAGAG
CCCTGGAACCATCCGGGAAGTCAGCCTGCAACTCCTTGTA---GCAAGTG
TTACTGTAAAAAGTGCTGCTATCATTGTCCA---------------GTTT
GCTTTCTGAA---AAAAGGCTTAGGCATCTCCTATGGCAGGAAGAAGCGG
AGAC------C---GCGACGAAGA------G---CTCCTCAAAGCAGTAA
GGATCATCAGAATCCTATACCAAAGCAGTAAGTAT--TAGCAATT-----
-AGTATATGTA---ATG---------------------------------
---------AGTCCTTTGG---------------AAGTCTGTGCAATAGT
A---GGACTGATAGTGGC---AC--TAATCA-TAGCAATAGTTGTGTGGA
CTATAGTAGGTATAGAATAT---AGGA------------AATTGCGAAAG
CAA---AAAAGAATAGACAGGTTAATTAAGAGAATAAGTGAAAGAGCAGA
AGACAGTGGCAATGAGAGTGATGGGGATACAGATGAATTGTCAAAGCTT-
--GTGGAGATG------------------------GGGAACTATG---AT
CTTGGGA---ATGTTAATGAT------------TTGT------AGTGTTG
C---------AGG---A------------A---A------CTTG------
TGGGTTACTGTCTACTATGGGGTACCTGTGTGGAAAGAGGCAG---AC--
ACCACCT-TATTTTGTGCATCAAATGCTAGAGCATATGATACAGAAGTGC
ATAATGTCTGGGCTACACATGCCTGTGTACCTACAGACCCCAACCCACAA
GAAATAGATTTGGAGAATGTGACAGAAGAGTTTAACATGTGGAAAAATAA
CATGGTAGAGCAAATGCATACAGATATAATTAGTCTATGGGACCAAAGCC
TAAAACCATGTGTAAAGTTAACCCCTCTCTGCGTTACTTTAGATTGTGGC
T---ATA---AT--------------------------------------
----------------------GT---AAC-CA-ACT---TG--------
-------A-ATTTCACC---AG--T-------------------------
--------------------------------------------------
AAC---ATGAA------A-GGA-GA-CATAA-CAAACTGCTCTTACAATA
TGACCACAGAAATAAGGGATAGGAAACAGAAAGTGTATTCAC---TTTTT
TATAGGCTTGATATAGTACCAATTAATGAAGAAAAGAAT-----------
-------AATA---GC--AG--GGAGACT---AGT---------------
---------------------C---CG--TATAGA-T-TAATAAATTGTA
-ATACCTCAGCCATTACACAGGCTTGTCCTAAGGTATCTTTTGAACCAAT
TCCCATACATTATTGTGCCCCAGCTGGTTTTGCGATTCTAAAATGTAAGG
ATGCAGAGTTCAATGGAACAGGGCCATGCAAGAATGTCAGCACAGTACAA
TGTACACATGGAATCAGGCCAGTAATATCAACTCAACTGCTGTTAAATGG
CAGTTTAGCAGAG---AATGG---GACAAAGATTAGATCTGAAAATATCA
CAAACAATGCCAAAACCATAATAGTACAACTTAACGAGACTGTACAAATT
AATTGTACCAGACC------T------AGCAACA---AT---ACAAGAAA
AAGTGTACGTATA---------GGACCAGGACAAGCATTCTATACA---A
CAGGTGAT------ATAACAGGGGATATAAGACAAGCATATTGTAATGTC
AGTAGACAAGAATGGGAACAAGCATTAAAAGGGGTAGTT---AT--ACAA
TTAAGAAAA------CACTTT---A----AC-----------AAAACA--
----ATAATCTTTAAC----AGTTC---CTCAGGAGGGGATTTAGAAATT
ACAACAC------ATAGTTTTAATTGTGGAG---GAGAATTTTTCTATTG
TGATACATCAGGCCTGTTTAAT---AGCACC---TG---G----------
------AAC-----ACG---------------------------AACACC
A---CCGAG---C-C-------A---AAC---AA-CAC---A---A----
--CG--TC--AAA---T---------------GGCACTATCATT------
---CTCCAATG-CA-GAATAAAGCAAATTATAAATCTGTGGCA---GAGA
ACAGGACAAGCAATGTATGCCCCTCCCATCCAAGGGGTAATAAGGTGTGA
TTCCAACATTACAGGACTACTATTAACAAGAGATGG---TGGAGT---AG
TT------GATAGT------------ATA--AATG---AA--ACCGAAAT
CTTCAGACCTGGAG-GAGGAG-ATATGAGGGACAATTGGAGAAGTGAATT
ATATAAGTATAAAGTAGTAAAAATTGAACCACTAGGAGTAGCACCCACCG
GGGCAAAGAGAAGAGTGGTGGA------GAGAGAAAAAAGAGCAG---TT
GGC-------ATAGGAGC---TG--T---ATTCATTGGGT---TCTTAGG
----AG-CAGCAGGAAG-CACTATGGGCGCGGCGTCAATAACGCTGACGG
TACAGGCCAGACAATTATTGTCTGGCATAGTGCAACAGCAAAACAATTTG
CTGAGGGCTATAGAGGCTCAACAGCATATGTTGAGACTCACGGTCTGGGG
CATTAAGCAGCTCCAGGCAAGAGTCCTGGCTGTGGAAAGATACCTAAGGG
ATCAACAGCTCCTAGGAATTTGGGGCTGCTCTGGAAAACTCATCTGCACC
ACTAATGTGCCCTGGAACTCTAGTTGGAG---T---AAT-----------
-AAATCTCAGGA---GGAAATAT---GGG---GTAACATGACCTGGCTGC
AATGGGATAAAGAAATTAGCAATTACACACAAACAATATATAACCTACTT
GAAGAATCGCAGAACCAGCAGGAAAAGAATGAACAAGACTTATTGGCATT
GGACAAGTGGGCAAATTTGTGGACTTGGTTTGACATAACAAATTGGCTGT
GGTATATAAAAATATTTATAATGATAGTAGGAGGCTTAATAGGATTAAGA
ATAGTTTTTGCTGTGCTTTCTGTAATAAATAGAGTTAGGCAGGGATACTC
ACCTCTGTC---GTTTCAGACC---CATATCC---CGAGCCCAAGGGGT-
-----CTCGACAGGCCCGGAAGAATCGAAGAAGAAGGTGGAGAGCGAGAC
AGAGACAGATCGATTCGATTGGTGAGCGGATTCTTAGCACTTGCCTGGGA
CGATCTACGGAACCTGTGCCTCTTCAGCTACCACCGATTGAGAGACTTCA
TCTTGATTGCAGCGAGGACTGTGGAACTTCTGGGA---CACAGCAGTCTC
AAGGGGTTGAGACTGGGGTGGGAAGGCCTCAAGTATCT---GTGGAATCT
T---CTGATATATTGGGGTCGGGAACTAAAACTTAGTGCTATCAATTTGA
TTGATA---CCATAGCAATAGCAGTAGCTGGCTGGACAGATAGAATTATA
GAAGTAGGACAAAGACTTTGTAGAGCTATACTTAACATACCTAGAAGAAT
CAGACAGGGTGCCGAAAGGGCTTGGCTATAA
'A1.KE.00.KNH1209'
------GCGAGAGCGTCAGTATTAAGCGGGGG---AAAATTAGATGCATG
GGAGAAGATTCGGTTAAGGCCAGGGGGAAAGAAAAAATACAGAATGAAAC
ATTTAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCGGGC
CTTTTAGAAACAGCAGAAGGATGTCAACAAATATTGGAACAATTACAATC
AGCTCTCGGGACAGGAACAGAGGAACTTAAATCATTGTATAATACAGTAG
CCACCCTCTATTGCGTACATCAAAGAATAGAGGTAAAAGACACCAAGGAA
GCTCTAG---AT--AAA-ATAGAGGAACTACA------------AAATAA
GAGCAAG------------CAAAAGATA---------CA---ACAG----
--------------GCA---GCA---------------------GCA---
------------------------GCTACAGGA-----------------
-------AGCAGCAGC------------AAG------GTTAGCCAAAATT
ACCCTATAGTGCAAAATGCACAAGGGCAAATGATACACCAGTCCTTGTCA
CCTAGGACTTTGAATGCATGGGTAAAAGTAATAGAAGAAAAGGCTTTCAG
CCCAGAAGTAATACCCATGTTCTCAGCATTATCAGAGGGAGCCACCCCAC
AAGATTTAAATATGATGCTGAATATAGTGGGGGGACACCA---GGCAGCG
ATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAG
GTTACATCCAGTACATGCAGGGCCTATTCCACCAGGCCAGATGAGAGAAC
CAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCCTCAAGAACAGATA
GGGTGGATGACAAGCAACCCACCTATTCCAGTGGGAGACATCTATAAAAG
ATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTA
GCATTTTAGATATAAAACAAGGACCAAAAGAACCCTTCAGAGATTATGTA
GATAGGTTCTTTAAAACTCTCAGAGCTGAGCAAGCTACACAGGAGGTAAA
AAATTGGATGACAGACACATTGCTGGTCCAAAATGCAAATCCAGATTGCA
AGTCCATTTTAAGAGCATTAGGACCAGGAGCTACATTAGAGGAAATGATG
ACAGCATGCCAGGGAGTGGGAGGACCCAGCCATAAAGCAAGGGTTTTGGC
TGAGGCAATGAGTCAGGC---AC---AAA---A---TA--C---A-----
-----------------AACATA---ATGATGCAGAGAGGCAATTTTAGG
GGCCAGAAA---AGAATTAAGTGCTTCAATTGTGGCAAAGAAGGACACCT
AGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGGA
AAGAGGGACATCAAATGAAAGACTGCACT------GAAAGACAGGCTAAT
TTTTTAGGGAGAATCTGGCCTTC---CAGCAAGGGG---AGGCCAGGGAA
TTTTCCTCAGAACAGA---------------CTAGAGCCAACAGCCCCA-
-----------------------------------CCA---GCAGAGATC
TGTGGGATAGGGGAAGAGATA---------------GCCTCCCCTCTG--
----AAGCAGGAGCAG------------AGAGA---CAGGGAACAGACT-
-----CCA------ACTTTAATTTCCCTCAAATCACTCTTTGGCAACGAC
CCATTGTCACAGTAAGAATAGGGGGACAACTAAAAGAAGCTCTATTAGAT
ACAGGAGCAGATGATACAGTATTAGAAGACATAGATTTGCCAGGAAAATG
GAAACCAAAAATGATAGGGGGAATTGGAGGTTTCATCAAAGTAAAACAGT
ATGATCAGATACTTATAGAAATTTGTGGAAAAAGGGCTATAGGCACAGTA
TTAGTAGGACCTACACCTGTCAACA---TAATTGGCAGAAACATGTTGAC
CCAGATTGGTTGTACTTTAAATTTCCCAATTAGTCCTATTGAGACTGTGC
CAGTAGAATTAAAGCCAGGAATGG---ATGGCCCAAAGGTTAAACAATGG
CCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACA-----
-GAAATGGAAAAGGAAGGAAAAATTTCAAGAATAGGGCCTGAAAATCCAT
ACAATACTCCAATATTTGCAATAAAGAAAAAAGACAGCACTAAATGGAGG
AAATTAGTGGATTTCAGAGAGCTCAATAAAAGAACACAAGACTTTTGGGA
AGTTCAATTAGGAATACCGCATCC---AGCGGGTCTAAAAAAGAAGAAAT
CAGTAA---CAGTACTAGATGTGGGGGATGCATACTTTTCAGTTCCTTTA
CATAAAAGTTTTAGAAAATATACTGCATTCACCATACCTAGTACAAACAA
TGAGACACCAGGAATCAGATATCAATACAATGTGCTTCCACAGGGATGGA
AAGGATCACCAGCAATATTCCAGAGTAG---CATGATAAAAATCTTAGAG
CCTTTTAGATCAAAAAATCCAGAAATAATTATCTATCAATACATGGATGA
CTTGTATGTAGGATCTGATTTGGAAATAGGACAGCATAGAGCAAAAATAG
AAGAGTTGAGAGCTCATCTATTGAGCTGGGGATTTACTACACCAGAC---
AAAAAGCATCAGAAAGAACCTCCATTCCTTTGGATGGGATATGAGCTCCA
TCCTGACAAGTGGACAGTCCAGCCTATACAGTTGCCAGAAAAAGAAAGCT
GGACTGTCAATGATAT---ACAGAAATTAGTGGGGAAACTAAATTGGGCA
AGTCAAATTTATGCAGGGATTAGAATAAAGCAATTGTGTAAACTCCTCAG
GGGAGCCAAAGCTTTAACAGATATAGTAACATTGACTGAGGAAGCAGAAC
TAGAATTGGCAGAAAACA---GGGAAATTCTAAAAAACCCTGTGCATGGG
GTATATTATGACCCATCAAAAGACTTAGTAGCAGAAATACAGAAACAAGG
GCAAGAACAATGGACATACCAAATTTATCAAGAGCCATTTAAAAATTTAA
AAACAGGAAAATATGCAAGAAAAAGATCTACTCACACTAATGATGTAAAG
CAATTAGCAGAAGTGGTGCAAAAGGTAGCCATGGAAAGCATAGTAATATG
GGGAAAGA---CTCCTAAATTTAAACTA---CCCATACAAAAGGAGACAT
GGGAGACA---TGGTGGATGGACCACTGGCAGGCTACCTGGATTCCTGAA
TGGGAATTTGTCAATACCCCTCCTCTAGTAAAATTGTGGTACCAATTAGA
GAAAGACCCCATAATGGGAGCAGAGACTTTCTATGTAGATGGGGCAGCCA
ATAGACAGACCAAACTAGGAAAAGCAGGGTATGTCACTGACAGGGGAAGA
CAAAAGGTTGTTTCCCTACCTGAGA---CAACAAATCAAAAGACTGAACT
ATATGCCATCCATCTAGCCTTGCAGGATTCAGGATCAGAAGTAAACATAG
T---AACAGACTCACAGTATGCATTAGGAATCA---TTCAGGCACAACCA
GACAGAAGTGAATCAGAAATAGTTAATCAAATAATAGAGCAACTAATAGA
AAAAGACAGAGTCTACCTA---TCATGGGTACCGGCACACAAAGGAATTG
GAGGAAATGAACAAGTAGATAAATTAGTCAGTTCTGGAATCAGAAAGGTG
CTGTTTATAGATGGGATAGATAAAGCTCAAG---AGGATCATGAAAGATA
---TCACAGCAATTGGAGAACAATGGCTAGTGATTTTAATCTGCCACCTA
TAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAAT---GTCA---GCTA
AAAGGAGAAGCCATGCATGGACAAGTAGACTGCAGCCCAGGGATATGGCA
ATTAGATTGCACACATCTAGAAGGAAAAGTAATTTTGGTAGCAGTTCATG
TAGCCAGTGGCTATATAGAAGCAGAAGTTATCCCAGCAGAAACAGGACAA
GAGACAGCATACTTTCTACTAAAATTAGCAGGAAGATGGCCAGTAAAAGT
AGTACACACAGACAATGGCAGCAATTTTACCAGCGCTGCAGTCAAAGCAG
CCTGTTGGTGGGCAGGTATCCAACAGGAATTTGGGATCCCCTACAATCCC
CAAAGTCAAGGAGTAGTGGAATCTATGAATAAGGAATTAAAGAAAATCAT
AGGACAGGTAAGAGAGCAAGCTGAACACCTTAAAACAGCTGTACAAATGG
CAGTATTCATTCACAATTTTAAAAGAAAA---GGGGGGATTGGGGGGTAC
AGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAA
AGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACA
GGGACAGCAGAGATCCAGTTTGGAAAGGACCAGCAAAACTGCTCTGGAAA
GGTGAAGGGGC---AGTAGTAATACAGGACAATAGTGATATAAAGGTAGT
ACCAAGAAGAAAAGCAAAAATCATCAGGGACTATGGAAAACAGATGGCAG
GTGATGATTGTGTGGCAGGTAGACAGGATGAGGATTAGA---ACATGGCA
CAGTTTGGTAAAATATCATAAGTATATATCAAAGAAAGCTAAAAATTGGC
ATTATAGACATCACTATGAAAGTAGACATCCAAAAACATGTTCAGAAGTA
CATATCCCACTAGGGG---ATG---CTAGATTAGTAGTAAGGACATATTG
GGGTCTGCATACAGGAGAAAAAGACTGGCACTTGGGTCATGGGGTCTCCA
TAGAATGGAGGCTAAGAAGATATAGCACACAA------GTAGATCCTGAT
CAGGCAGACCAACTAATTCATCTGCATTATTTTAACTGTTTTTCAGACTC
---TGCCATAAGGAAAGCCATATTAGGACAAGTAGTTAGCCCTAGGTGTG
ACTATCAAACAGGACATA---ACAAGGTAGGATCTCTACAATATTTAGCA
CTGAAAGCATTAGTAAAACC---AGAAAAGACAAAGCCACCTTTGCCTAG
TGTTAGGATATTAGCAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGG
GCCCCAGAGAGAGCCATACAATGAATGGATGTTAGACCTGTTAGAAGAGC
TTAAGCATGAAGCCGTTAGGCATTTTCCCAGGCCATGGCTTCATGGATTA
GGACAACATATCTATAACACCTATGGGGATACTTGGGAAGGAGTTGAAG-
--CTATAATAAGAATTCTGCAA---CAACTACTGTTTGTTCAT---TTCA
GAATTGGGTGCC---AACATAGCAG---AATAGGCATT---ATTCGAGGG
AGAAGAGTTA----------GGAATGGACCCAGTAGATCCTAACCTAGAG
CCATGGAACCACCCGGGAAGTCAGCCTGCAACCCCTTGTA---ACAAATG
TTATTGTAAAAAGTGTTGCTATCATTGCCAA---------------GCTT
GCTTTTTGAA---CAAAGGCTTAGGCATCTCCTATGGCAGGAAGAAGCGG
AGAC------A---GCGACGAAGA------T---CTCCTCAGAGCAGTAA
GGATCATCAACATTCTACACAAGAGCAGTAAGTAT--TAGTAGTT-----
-GATATATGTA---ATG---------------------------------
---------CTTCCTTTGC---------------AAATCTTGGCAATAAT
A---GGACTGATAGTAGC---CC--TAATCC-TAGCAATAGTTGTATGGA
CTATAGTAGGTATAGAATGT---AAGA------------AATTTCTAAAA
CAA---AGAAAAATAGACAGGTTAATTGAGAGAATAAGAGAAAGAGCAGA
AGACAGTGGCAATGAGAGTGATGGGGATACAGAGGAATTGTCAGAACTT-
--ATTGACATG------------------------GGGAACTATG---AT
CTTGGGG---ATAATAATCTT------------CTGT------AGTGCTA
C---------AGA---C------------A---A------CTTG------
TGGGTTACTGTCTATTATGGGGTACCAGTGTGGAAAGACGCAG---AG--
ACCACCT-TATTTTGTGCATCAGATGCTAAAGCATATGCGACAGAAAAGC
ATAATGTCTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAA
GAAATACATTTGGAAAATGTGACAGAAGAATTTAACATGTGGAAAAATAA
CATGGTAGAACAGATGCATACAGATATAATCAGTCTATGGGACCAAAGCC
TAAAACCATGTGTAAAGTTAACCCCTCTCTGCGTTACTTTAAATTGTAGC
A---ATG---CC--AATGTAGGTTAT------------------------
-----------AG--CAAT---GC---CAC-TG-TTA---AC--------
-------A-ACACCATC---AA--G-------------------------
--------------------------------------------------
-------------------GAT-GA-AATAA-AAAACTGCTCTTTCAATA
CAACCACAGCACTAAGGGATAAGAGACAGAAAGTATATTCAC---TTTTT
TATAGACTTGATATAGTACAAATTGATAATAGTAGT--------------
-------AGTG---AT--AG--TAGTAGT---AGT---------------
---------------------G---AG--TATAGA-T-TAATAAATTGTA
-ATACCTCAGCCATTACACAAGCTTGTCCAAAGGTAACCTTTGAGCCAAT
TCCCATACATTATTGTGCCCCAGCTGGTTTTGCAATCCTAAAGTGTAAAG
ATGAGGAGTTCAATGGAACAGGGCCATGCAAGAATGTCAGCACAGTACAA
TGCACACATGGAATCAAGCCAGTAGTATCAACTCAACTGCTGCTAAATGG
CAGTCTAGCAAAA---AGAGA---GGTAAAAATTAGATCTGAAAATATCA
CAAACAATGCCAAAAATATAATAGTACAATTTGTTGATCCTGTGGAAATT
AATTGTACCAGACC------T------AACAACA---AT---ACAAGAAA
AAGTATACATATA---------GGACCAGGACAAGCATTCTATGCA---A
CAGGTGAC------ATAATAGGGGATATAAGACAAGCACATTGTAATGTC
AGTAGATCATCCTGGAATAGGACTTTACAACAGGTAGCT---AA--ACAA
TTAGGAACA------TACTTT---A----AG--AAC------AAAACA--
----ATAGTATTTAAT----ACATC---CTCAGGAGGGGATCCTGAAATC
ACAACAC------ATAGTTTTAACTGTGCAG---GAGAATTTTTCTATTG
TGATACATCAGGCCTGTTTAAT---AGCAGT---TG---G----------
------AATGA--TACC---------------------------ACTTGG
A---ATGAG---T-C-------A---AAT---AG-CAC---G---G----
--GG--TC--AAA---T---------------GACACTATAACT------
---CTCCTATG-CA-GAATAAAACAAATTATAAATATGTGGCA---GAGA
ACAGGACAAGCAATGTATGCCCCTCCCATCCCAGGGTTAATAAGCTGTAA
ATCAAACATTACAGGTATAATATTGACAAGAGATGG---TGGGAA---TG
GT------AAC--------------------AATA---CA--AATGAAAC
CTTCAGACCGGGAG-GAGGAG-ATATGAGGGACAATTGGAGAAGTGAACT
GTATAGGTATAAAGTAGTACAAATTGAACCACTAGGAGTAGCACCCACCA
GGGCAAGGAGAAGAGTGGTGCA------GAGAGAAAAAAGAGCAG---TA
GGA-------ATAGGAGC---TG--T---CTTCCTTGGGT---TCTTAGG
----AG-CAGCAGGAAG-CACTATGGGCGCAGCGTCAATAACGCTGACGG
TACAGGCCAGACAATTATTGTCTGGCATAGTGCAACAGCAAAGCAATTTG
CTGAGGGCTATAGAGGCTCAACAACATCTGTTGAAACTCACGGTCTGGGG
CATTAAACAGCTCCAGGCAAGAGTCCTGGCTGTGGAGAGATACCTAAGGG
ATCAACAGCTCCTAGGAATTTGGGGCTGCTCTGGAAAACTCATCTGCACC
ACTAATGTACCCTGGAACTCTAGTTGGAG---T---AAT-----------
-AAATCTTATAA---TGACATAT---GGG---ATAACATGACCTGGCTGC
AATGGGATAAAGAAATTCACAATTACACACAATTAATATATAACCTAATT
GAAGAATCGCAGAACCAGCAGGAAAAGAATGAACAAGACTTATTGGCATT
GGACAAGTGGGCAAATCTGTGGAATTGGTTTAACATAACAAATTGGCTGT
GGTATATAAAAATATTTATAATGGTAGTAGGAGGCTTAATAGGATTAAGA
ATAGTTTTTGCTGTGCTTTCGATAATAAATAGAGTTAGGCAGGGATACTC
ACCTTTGTC---GTTTCAGACC---CACCTCC---CAAACCCAAGGGAT-
-----CTCGACAGGCCCGAAAGAATCGAAGAAGAAGGTGGAGAGCAAGGC
AGAGACAGATCGATTCGCTTAGTGAGCGGATTCTTAGCGCTTGCCTGGGA
CGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTCA
TCTTGATTGCCGCGAGGACTGTGGAACTTCTGGGA---CAGAGCAGTCTC
AAGGGGTTGAGACTGGGGTGGGAAAGCCTCAAGTATCT---GTGGAATCT
C---CTAAGGTATTGGGTTCGGGAACTAAAAATTAGTGCTGTTAATTTAG
TTGATA---CCATAGCAATAGCAGTAGCTGGCTGGACAGATAGGGTTATA
GAAATAGGACAAGAAATTGGTAGAGCTATTCGCCACATACCTAGAAGAAT
CAGACAGGGTTTAGAAAGAGCTTTGCTATAA
'A1.KE.00.KNH1211'
------GCGAGAGCGTCAGTATTAAGCGGGGG---AAAATTAGATGCATG
GGAGAAGATTTATTTAAGGCCAGGGGGAAAGAAAAAATATAAACTAAAAC
ATTTAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCTAGC
CTTTTAGAAACAACAGAAGGATGTCAACAAATAATGGAACAGTTACAACC
ATCTCTCAAGACAGGATCAGAAGAACTTAGATCTTTATTTAATACAGTAG
CAACCCTCTATTGTGTACATCAAAGAATAAATGTAAAAGACACCAAGGAA
GCTCTAG---AT--AAA-ATAGAGGAAATACA------------AAATAA
GAACAAG------------CAAAAGACA---------CA---ACAG----
--------------GCA---GCA---------------------GCT---
------------------------GATACAGGA-----------------
-------AGCAGCAGC------------AAG------GTCAGCCAAAATT
ACCCTATAGTGCAAAATGCACAGGGGCAAATGATACATCAGTCCTTATCA
CCTAGGACTTTGAATGCATGGGTAAAAGTAATAGAGGAAAAGGCTTTCAG
CCCAGAAGTAATACCCATGTTCTCAGCATTATCAGACGGAGCCACCCCAC
AAGATTTAAATATGATGTTGAATATAGTAGGGGGACATCA---GGCAGCT
ATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAG
GTTACATCCAGTACATGCAGGGCCTATTCCACCAGGCCAGATGAGAGAAC
CAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCCTCAAGAACAAATA
GGATGGATGACAGGCAACCCACCTATCCCAGTGGGAGAAATCTATAAAAG
ATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTA
GCATTTTGGATATAAAGCAAGGACCAAAAGAACCCTTTAGAGATTATGTA
GATAGGTTCTTTAAAACTCTTAGAGCTGAGCAAGCCACACAGGAGGTAAA
AGGTTGGATGACAGAAACATTACTGGTCCAAAATGCAAATCCAGATTGTA
AGTCCATTTTAAGAGCATTAGGAACAGGGGCTACGTTAGAAGAAATGATG
ACAGCATGCCAGGGAGTGGGAGGACCCGGCCATAAAGCAAGGGTTTTGGC
TGAGGCAATGAGTCAGGT---AC---AGC---A---TA--C---A-----
-----------------AACATA---ATGATGCAGAGAGGCAATTTTAGG
GGCCAGAAA---AGGATTAAGTGTTTCAACTGTGGCAAAGAAGGACACCT
AGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGGA
AGGAGGGACATCAAATGAAAGACTGCACT------GAAAGGCAGGCTAAT
TTTTTAGGGAAAATTTGGCCTCC---CAACAAGGGG---AGGCCAGGAAA
TTTTCCTCAGAGCAGA---------------TTAGAGCCAACAGCCCCA-
-----------------------------------CCA---GCAGAGATC
TGTGGGATGAGGGAAGAGATA---------------GCCTCCCCTCCG--
----AAGCAGGAGCAG------------AAAGA---CAGGGAACAAACT-
-----CCA------CCTTCAATTTCCCTCAAATCACTCTTTGGCAACGAC
CCCTTGTCACAGTAAAAATAGGGGGACAGCTAAAAGAAGCCCTATTAGAT
ACAGGAGCAGATGATACAGTATTAGAAGACATAGATTTGCCAGGGAAATG
GAAACCAAGAATGATAGGGGGAATTGGAGGTTTCATCAAGGTAAAACAGT
ATGATCAGATACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTA
TTAGTAGGACCTACACCTGTCAACA---TAATTGGAAGAAACATGTTGAC
CCAGATTGGTTGTACTTTAAATTTCCCAATTAGTCCTATTGAGACTGTAC
CAGTAACATTAAAGCCAGGAATGG---ATGGCCCAAAGGTTAAACAATGG
CCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACA-----
-GAAATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCAT
ACAATACTCCAATATTTGCGATAAAGAAAAAAGATAGCACTAAATGGAGA
AAATTAGTAGATTTCAGAGAGCTCAATAAAAGAACACAAGATTTTTGGGA
AGTTCAATTAGGAATACCACATCC---AGCGGGCCTAAAAAAGAAAAAAT
CAGTAA---CAGTACTGGATGTGGGGGACGCATATTTTTCAGTTCCTTTA
CATGAAAGCTTTAGAAAATATACTGCATTCACCATACCTAGTACAAACAA
TGAGACACCAGGAATCAGGTACCAGTACAATGTGCTTCCACAGGGATGGA
AAGGATCACCGGCAATATTCCAGAGTAG---CATGACAAAAATCTTAGAG
CCCTTTAGATCAAAAAATCCAGACATAATTATCTATCAATACATGGATGA
CTTGTATGTAGGATCTGATTTAGAAATAGAGCAGCATAGAACAAAAATAG
AAGAGTTAAGAGCTCATCTATTGAGCTGGGGATTTACTACACCAGAC---
AAAAAGCATCAGAAAGAACCTCCATTCCTTTGGATGGGATATGAGCTCCA
TCCTGACAAGTGGACAGTCCAGCCTATAATGCTGCCAGAAAAAGAAAGCT
GGACTGTCAATGATAT---ACAGAAATTAGTAGGGAAACTAAATTGGGCA
AGTCAAATTTACCCAGGGATTAGAGTAAAACAATTGTGTAAACTCCTCAG
GGGAGCCAAAGCACTAACAGAGATAGTAACATTGACTGAGGAAGCAGAAT
TAGAATTGGCAGAGAACA---GGGAGATTCTAAAGGACCCTGTGCATGGG
GTATATTATGACCCCTCAAAAGACTTAATAGCAGAAATACAGAAACAAGG
GCAAGACCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTAA
AAACAGGGAAATATGCAAGAAAAAGGTCTGCTCACACTAATGATGTAAAA
CAATTAGCAGAAGTGGTGCAAAAGGTGGTCATGGAAAGCATAGTAATATG
GGGAAAGG---CTCCTAAATTTAAACTA---CCCATACAAAAGGACACAT
GGGAAACA---TGGTGGATGGACTATTGGCAGGCTACCTGGATCCCTGAA
TGGGAATTTGTCAATACCCCTCCTCTAGTAAAATTATGGTACCAATTAGA
GAAAGACCCCATAACAGGAGCAGAGACTTTCTATGTAGATGGGGCAGCCA
ATAGGGAGACTAAGCTAGGAAAAGCAGGGTATGTCACTGACAGGGGAAGA
CAAAGGGTTGTTTCCCTAACTGAGA---CAACAAATCAAAAGACTGAGCT
ACATGCAATCCATCTAGCCTTGCAGGATTCAGGATCAGAAGTAAACATAG
T---AACAGACTCACAGTATGCATTAGGAATCA---TTCATGCACAACCA
GACAGTAGTGAATCAGAGTTAGTTAATCAAATAATAGAGAAGCTAATAGA
AAAGGACAAAATCTACCTA---TCATGGGTACCGGCACACAAAGGAATTG
GAGGAAATGAACAAGTAGATAAATTAGTCAGTTCCGGAATCAGGAAGGTG
CTGTTTCTAGATGGGGTAGATAAAGCTCAAG---AAGAACATGAAAGATA
---TCACAGCAATTGGAGAGCAATGGCTAGTGATTTTAATCTGCCACCTG
TAGTAGCAAAGGAAATAGTAGCCAGCTGTGATAAAT---GTCA---GCTA
AAAGGGGAAGCCATGCATGGACAAGTAGATTGTAGTCCAGGGATATGGCA
ATTAGATTGCACACATCTAGAAGGAAAAGTAATTCTGGTAGCAGTTCATG
TAGCCAGTGGCTATATAGAAGCAGAAGTTATCCCAGCAGAAACAGGACAA
GAGACAGCATACTTTCTACTAAAATTGGCAGGAAGATGGCCAGTAAAAGT
AGTCCACACAGACAATGGCCCCAACTTTATCAGCGCTGCAGTTAAAGCAG
CCTGTTGGTGGGCAGGTATCCAACAGGAATTTGGAATTCCCTACAATCCC
CAAAGTCAAGGAGTAGTGGAATCTATGAATAAGGAATTAAAGAAAATCAT
AGGACAGGTAAGAGAGCAAGCTGAACACCTTAAAACAGCAGTACAAATGG
CAGTATTCATTCACAATTTTAAAAGAAAA---GGGGGGATTGGGGGGTAC
AGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAA
AGAATTACAAAAACAAATTATAAAAATTCAAAATTTTCGGGTTTATTACA
GGGACAGCAGAGATCCAATTTGGAAAGGACCAGCAAAACTACTCTGGAAA
GGTGAAGGGGC---AGTAGTAATACAGGACAATAGTGATATAAAGGTAGT
ACCAAGAAGAAAAGCAAAAATCATCAGGGACTATGGAAAACAGATGGCAG
GTGATGATTGTGTGGCAGGTAGACAGGATGAGGATTAGA---ACATGGCA
CAGTTTAGTAAAACATCATATGTATGTCTCAAAGAAGGCTAACAAATGGT
GGTATAGACATCACTATGAAAGCAGACATCCAAGAGTAAGTTCAGAAGTA
CACATCCCACTAGAGG---ATG---CTAGATTAGTAGTAAGAACATATTG
GGGTCTGCATACAGGAGAAAAAGACTGGCAATTGGGGCATGGAGTCTCCA
TAGAATGGAGGCTAAGAAAATATAGCACACAA------ATAGATCCTGAA
CAGGCAGACCGACTAATTCATCTACATTATTTTGACTGTTTTTCAGACTC
---TGCCATAAGGAAAGCCATATTAGGACAAGTAGTTAGACCTAGATGTG
AATATCAAACAGGACATA---ACAAGGTAGGATCTCTACAATATTTAGCA
CTGAAAGCATTAGTAGGACC---AGTAAAGACAAAGCCACCTTTGCCTAG
TGTCAGGAAATTAACAGAGGATAGATGGAACAAACCCCAGAAGACCAGGG
GCCACAGAGAGAGCCATACAATGAATGGATGTTAGATCTGTTAGAAGATC
TTAAGCATGAAGCCGTCAGACATTTTCCTAGGCCATGGCTTCATGGATTA
GGACAACATATCTATAACACCTATGGGGATACCTGGGAAGGAGTTGAAG-
--CTATAACAAGAACTCTGCAA---CAACTACTGTTTGTTCAT---TTCA
GAATTGGGTGCC---AACATAGCAG---AATAGGCATT---ATTCCRGRG
AGAAGAGGCA----------GGAATGGATCCGGTAGATCCTAACCTAGAG
CCCTGGAACCACCCGGGAAGTCAGCCTGCAACACCTTGTA---GCAAGTG
TTACTGTAAAAAATGTTGCTATCATTGTCCA---------------GCTT
GCTTTTTGAA---CAAAGGCTTAGGCATCTCCTATGGCAGGAAGAAGCGG
AGAC------A---GCGACGAGGA------A---CTTCTCAGAGCAATAA
GGATCATCAAAATCCTGTACCAAAGCAGTAAGTAT--TAGTAATT-----
-AGTATAAGTA---ATGTTG------------------------------
---------TCTCTTTTGC---------------ACATCTTTGCAATAGT
A---AGTCTGATAGTATC---GC--TAATCA-TAGCAATAATTGTGTGGA
CTATAGTAGGTATAGAATAT---AAGA------------GATTGTTAAAA
CAA---AAGAGAATAGACAGATTAATTGAGAGAATAAGAGAAAGAGCAGA
AGACAGTGGCAATGAGAGTGATGGGGATACAGAGGAATTGTCAACACTT-
--GTTAACATG------------------------GGGGACTACG---AT
CTTGGGG---ATGATATTAAT------------CTGTTAT---AGTGTTA
C---------AGA---A------------G---A------CTTG------
TGGGTTACTGTCTACTATGGGGTACCTGTGTGGAAAGATGCAG---AG--
ACCACCC-TATTTTGTGCATCAGATGCTAAAGCATATGAGACAGAAAAGC
ATAATGTATGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAA
GAAATACATTTGGAAAATGTAACAGAAGAGTTTAACATGTGGAAAAATAA
CATGGTAGAGCAGATGCATACAGATATAATCAGTTTATGGGACCAAAGCT
TAAAGCCATGTGTAAAGTTAACCCCTCTCTGTGTTACTCTAAATTGTACC
A---ATG---CC--------------------------------------
--------------------------------A-ATG---CC--------
-------A-AGAATGGC---AC--C-------------------------
--------------------------AAC---GA--T---TT--G-----
AAG---GACCA------G-GAA-GA-AATAA-AAAACTGCTCTTTCAACA
TAACCACAGAGCTAAGGGATAAGAGGAGGAAGGTATATTCAC---TTTTT
TATAAACTTGATATAGTACAGATTAATGAAAATCAAGGT-----------
-------AATA---GA--AG--TAACAAT---AGT---------------
---------------------G---AG--TATAGA-T-TAATAAATTGTA
-ATACCTCAGCAATTACACAGGCTTGCCCAAAGGTAACTTTTGAGCCAAT
TCCCATACATTATTGTGCCCCAGCTGGTTTTGCGATCCTAAAGTGTAAGG
ATGAGGAGTTCAATGGAACAGGGCCATGCAAGAATGTCAGCTCAGTCCAA
TGCACACATGGAATCAGGCCAGTAGTATCAACTCAACTGTTGTTAAATGG
TAGTCTAGCAAAA---GGAAA---GGTAAAAATTAGATCTGAAAATATCG
CAGACAATGTCAAAACTATAATAGTACAACTTACTGAGCCTGTAAACATT
ACTTGTATCAGGCC------T------AATAACA---AT---ACAAGAAC
AAGTGTACGTATA---------GGACCAGGACAAACATTCTATGCA---A
CAGGTGAC------ATAATAGGGAATATAAGACAAGCACAGTGTACTGTC
AATAGAACAAAATGGAATAGCGCTTTACACCAGGTAGTT---AC--ACAA
TTAGGACAC------TTTGTC---A----CC-----------AAAACT--
----ATAAAATTTAAT----GAATC---CTCAGGAGGGGATTTAGAAATC
ATAACAC------ATAGTTTTAATTGTGGAG---GAGAATTTTTCTATTG
TAATACATCAGGCCTGTTTAAT---AGCACT---TG---G----------
------AATAG--CACTGGGAATGACACTTGGAGT---------GGCAAT
G---CCAGC-----------------------AC-GCA---G---G----
--AG--TC--AAA---T---------------GACACTATAACT------
---CTCCCATG-CA-GAATAAAGCAAATTGTAAATATGTGGCA---GAGA
ATAGGACAAGCAATGTATGCCCCTCCCATCCAAGGAGTAATAAGGTGTGA
ATCAAACATTACAGGACTACTATTAACAAGAGATGG------TGG---GA
AC-----------------------------AATG---AA--AGTGAAAC
CTTCAGACCTGGAG-GAGGAA-ATATGAGGGACAATTGGAGAAGTGAATT
ATATAGGTACAAAGTAGTGAAAATTGAACCACTAGGAGTAGCACCCACCA
GGGCAAAAAGAAGAGTGGTGGG------GAGAGAAAAAAGAGCAG---TT
GGA-------ATAGGAGC---TG--T---GTTCCTTGGGT---TCTTAGG
----AG-CAGCAGGAAG-CACTATGGGCGCGGCGTCAGTAACGCTGACGG
TACAGGCCAGACAATTATTGTCTGGCATAGTGCAACAGCAAAGCAACTTG
CTGAGGGCTATAGAGGCTCAACAACATCTGTTGAAACTCACGGTCTGGGG
CATTAAACAGCTCCAGGCAAGAGTCCTTGCTGTGGAAAGATACCTAAGGG
ATCAACAGCTCCTAGGAATTTGGGGCTGCTCTGGAAAACTCATCTGCACC
ACTACTGTGCCCTGGAACTCTAGTTGGAG---T---AAT-----------
-AAATCTCTGGG---GGAGATAT---GGG---AAAACATGACCTGGCTGC
AATGGGAAAAAGAAATTAGCAATTATACAGACATAATATATAGCCTAATT
GAAGAATCGCAGAACCAGCAGGAAAAGAATGAACAAGACTTATTGGCATT
GGATAAGTGGGCAAGTCTGTGGAATTGGTTTGACATATCAAAGTGGCTGT
GGTATATAAGAATATTTATAATAATAGTAGGAGGCTTAATAGGATTAAGA
ATAGTTTTTGCTGTGCTTTCTATAATAAATAGAGTTAGGCAGGGGTACTC
ACCTTTGTC---GTTTCAGACC---CATACCC---CAAACCCAGGGGAT-
-----CCCGACAGGCCCGGAAGAATCGAAGAAGAAGATGGAGAGCAAGGC
AAAAACAGATCGATTCGATTAGTGAGCGGGTTCTTAGCGCTTGCCTGGGA
CGATCTTCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTAA
TCTTGATTGCCGCGAGGACTGTGGAACTTCTGGGA---CACAGCAGTCTC
AAGGGGTTGAGACTGGGGTGGGAAGGCCTCAAGTATCT---GTGGAATCT
C---TTACGATATTGGGTTCGGGAACTCAAAATTAGTGCTATTAGTTTGG
TTGATA---CCATAGCAATAGTAGTAGCTGGCTGGACAGACAGGGTACTA
GAAA------------TTGGTAGAGCTATCCTTCACATACCTAGAAGAAT
TAGACAGGGTCTTGAAAGAGCTTTGCTATAA
;
end;

begin assumptions;
  options gapmode=missing;
end;
BioPerl-1.007002/t/data/X98338_Adh-mRNA.gb000444000766000024      1313413155576321 17421 0ustar00cjfieldsstaff000000000000LOCUS       DMALCDEHP               2071 bp    mRNA    linear   INV 06-JAN-1997
DEFINITION  D.melanogaster mRNA for alcohol dehydrogenase related protein.
ACCESSION   X98338
VERSION     X98338.1  GI:1752657
KEYWORDS    ADH protein; ADHR protein.
SOURCE      Drosophila melanogaster (fruit fly)
  ORGANISM  Drosophila melanogaster
            Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota;
            Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha;
            Ephydroidea; Drosophilidae; Drosophila.
REFERENCE   1
  AUTHORS   Brogna,S. and Ashburner,M.
  TITLE     The Adh-related gene of Drosophila melangaster is expressed via a
            functional dicistronic messenger: multigenic transcription in
            higher organisms
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2071)
  AUTHORS   Brogna,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JUN-1996) S. Brogna, University of Cambridge,
            Genetics, Downing Street, Cambridge, CB2 3EH, UK
FEATURES             Location/Qualifiers
     source          1..2071
                     /organism="Drosophila melanogaster"
                     /mol_type="mRNA"
                     /strain="Canton-S"
                     /db_xref="taxon:7227"
                     /dev_stage="adult"
     gene            125..895
                     /gene="ADH"
     CDS             125..895
                     /gene="ADH"
                     /codon_start=1
                     /product="alcohol dehydrogenase protein"
                     /protein_id="CAA66981.1"
                     /db_xref="GI:1752658"
                     /db_xref="FLYBASE:FBgn0000055"
                     /db_xref="SWISS-PROT:P00334"
                     /translation="MSFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENP
                     AAIAELKAINPKVTVTFYPYDVTVPIAETTKLLKTIFAQLKTVDVLINGAGILDDHQI
                     ERTIAVNYTGLVNTTTAILDFWDKRKGGPGGIICNIGSVTGFNAIYQVPVYSGTKAAV
                     VNFTSSLAKLAPITGVTAYTVNPGITRTTLVHKFNSWLDVEPQVAEKLLAHPTQPSLA
                     CAENFVKAIELNQNGAIWKLDLGTLEAIQWTKHWDSGI"
     polyA_signal    1017..1022
     polyA_site      1066
     gene            1194..2012
                     /gene="ADHR"
     CDS             1194..2012
                     /gene="ADHR"
                     /codon_start=1
                     /product="alcohol dehydrogenase related protein"
                     /protein_id="CAA66982.1"
                     /db_xref="GI:1752659"
                     /db_xref="FLYBASE:FBgn0000056"
                     /db_xref="SWISS-PROT:P91615"
                     /translation="MFDLTGKHVCYVADCGGIALETSKVLMTKNIAKLAILQSTENPQ
                     AIAQLQSIKPSTQIFFWTYDVTMAREDMKKYFDEVMVQMDYIDVLINGATLCDENNID
                     ATINTNLTGMMNTVATVLPYMDRKMGGTGGLIVNVTSVIGLDPSPVFCAYSASKFGVI
                     GFTRSLADPLYYSQNGVAVMAVCCGPTRVFVDRELKAFLEYGQSFADRLRRAPCQSTS
                     VCGQNIVNAIERSENGQIWIADKGGLELVKLHWYWHMADQFVHYMQSNDEEDQD"
     polyA_signal    2023..2028
     polyA_site      2071
BASE COUNT      581 a    504 c    511 g    475 t
ORIGIN      
        1 attattgtct cagtgcagtt gtcagttgca gttcagcaga cgggctaacg agtacttgca
       61 tctcttcaaa tttacttaat tgatcaatat cgaaagagcc tgctaaagca aaaaagaagt
      121 caccatgtcg tttactttga ccaacaagaa cgtgattttc gttgccggtc tgggaggcat
      181 tggtctggac accagcaagg agctgctcaa gcgcgatctg aagaacctgg tgatcctcga
      241 ccgcattgag aacccggctg ccattgccga gctgaaggca atcaatccaa aggtgaccgt
      301 caccttctac ccctatgatg tgaccgtgcc cattgccgag accaccaagc tgctgaagac
      361 catcttcgcc cagctgaaga ccgtcgatgt cctgatcaac ggagctggta tcctggacga
      421 tcaccagatc gagcgcacca ttgccgtcaa ctacactggc ctggtcaaca ccacgacggc
      481 cattctggac ttctgggaca agcgcaaggg cggtcccggt ggtatcatct gcaacattgg
      541 atccgtcact ggattcaatg ccatctacca ggtgcccgtc tactccggca ccaaggccgc
      601 cgtggtcaac ttcaccagct ccctggcgaa actggccccc attaccggcg tgaccgctta
      661 caccgtgaac cccggcatca cccgcaccac cctggtgcac aagttcaact cctggttgga
      721 tgttgagccc caggttgctg agaagctcct ggctcatccc acccagccat cgttggcctg
      781 cgccgagaac ttcgtcaagg ctatcgaact gaaccagaac ggagccatct ggaaactgga
      841 cttgggcacc ctggaggcca tccagtggac caagcactgg gactccggca tctaagaagt
      901 gataatccca aaaaaaaaac ataacattag ttcatagggt tctgcgaacc acaagatatt
      961 cacgcaaggc aataaggctg attcgatgca cactcacatt cttctcctaa tacgataata
     1021 aaactttcca tgaaaaatat ggaaaaatat atgaaaattg agaaatccaa aaaactgata
     1081 aacgctctac ttaattaaaa tagataaatg ggagcggcag gaatggcgga gcatggccaa
     1141 gttcctccgc caatcagtcg taaaacagaa gtcgtggaaa gcggatagaa agaatgttcg
     1201 atttgacggg caagcatgtc tgctatgtgg cggattgcgg aggaattgca ctggagacca
     1261 gcaaggttct catgaccaag aatatagcga aactggccat tttacagagt acggaaaatc
     1321 cccaggccat cgctcagttg cagtcgataa agccgagtac ccaaatattt ttctggacct
     1381 acgacgtgac catggcaagg gaagatatga agaagtactt cgatgaggtg atggtccaaa
     1441 tggactacat cgatgtcctg atcaatggtg ctacgctgtg cgatgaaaat aacattgatg
     1501 ccaccatcaa tacaaatcta acgggaatga tgaacactgt ggccacagtg ttaccctata
     1561 tggacagaaa aatgggagga actggtgggc taattgtgaa cgtcacttcg gtcattggat
     1621 tggacccttc gccggttttc tgcgcatata gtgcatccaa attcggtgta attggattca
     1681 ccagaagtct agcggacccc ctttactatt cccaaaacgg ggtagctgtg atggcggttt
     1741 gttgtggtcc tacaagggtc tttgtggacc gggaactgaa agcgtttttg gaatacggac
     1801 aatcctttgc cgatcgcctg cggcgagcgc cctgccaatc gacatcggtt tgtggtcaga
     1861 atattgtcaa tgccatcgag agatcggaga atggtcagat atggattgcg gataagggtg
     1921 gactggagtt ggtcaaattg cattggtact ggcacatggc cgaccagttc gtgcactata
     1981 tgcagagcaa tgatgaagag gatcaagatt gaattcgaat caaataaaat aatgctttac
     2041 gcaaaaagta ggcaattcat tttcctatga t
//

BioPerl-1.007002/t/data/YP_007988852.gp000444000766000024      1113013155576321 16662 0ustar00cjfieldsstaff000000000000LOCUS       YP_007988852             205 aa            linear   CON 22-MAY-2013
DEFINITION  recombinase [Staphylococcus aureus].
ACCESSION   YP_007988852
VERSION     YP_007988852.1  GI:502045014
DBLINK      Project: 178791
            BioProject: PRJNA178791
DBSOURCE    REFSEQ: accession NC_021230.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcus.
REFERENCE   1  (residues 1 to 205)
  AUTHORS   Mendes,R.E., Deshpande,L.M., Bonilla,H.F., Huband,M.D., Jones,R.N.
            and Quinn,J.P.
  TITLE     Molecular analysis of cfr-carrying Staphylococcus aureus and
            Staphylococcus epidermidis clinical isolates recovered from two
            hospitals in Ohio
  JOURNAL   Unpublished
REFERENCE   2  (residues 1 to 205)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (16-MAY-2013) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
REFERENCE   3  (residues 1 to 205)
  AUTHORS   Mendes,R.E., Deshpande,L.M., Bonilla,H.F., Huband,M.D., Jones,R.N.
            and Quinn,J.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-JAN-2013) Molecular Studies, JMI Laboratories, 345
            Beaver Kreek Centre, North Liberty, IA 52317, USA
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence is identical to AGL42326.
            Method: conceptual translation.
FEATURES             Location/Qualifiers
     source          1..205
                     /organism="Staphylococcus aureus"
                     /strain="1"
                     /isolation_source="blood culture"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pSA8589"
                     /country="USA"
     Protein         1..205
                     /product="recombinase"
                     /calculated_mol_wt=23947
     Region          4..>155
                     /region_name="PinR"
                     /note="Site-specific recombinases, DNA invertase Pin
                     homologs [DNA replication, recombination, and repair];
                     COG1961"
                     /db_xref="CDD:224872"
     Region          5..126
                     /region_name="SR_ResInv"
                     /note="Serine Recombinase (SR) family, Resolvase and
                     Invertase subfamily, catalytic domain; members contain a
                     C-terminal DNA binding domain. Serine recombinases
                     catalyze site-specific recombination of DNA molecules by a
                     concerted, four-strand cleavage and...; cd03768"
                     /db_xref="CDD:239737"
     Site            order(10,12,69..70,73)
                     /site_type="active"
                     /note="catalytic residues [active]"
                     /db_xref="CDD:239737"
     Site            12
                     /site_type="active"
                     /note="catalytic nucleophile [active]"
                     /db_xref="CDD:239737"
     Site            order(68,121..122,124..125)
                     /site_type="other"
                     /note="Presynaptic Site I dimer interface [polypeptide
                     binding]"
                     /db_xref="CDD:239737"
     Site            order(74,79..80,117,120..121,124..125)
                     /site_type="other"
                     /note="Synaptic Antiparallel dimer interface [polypeptide
                     binding]"
                     /db_xref="CDD:239737"
     Site            order(98..100,117..118,121..122,125)
                     /site_type="other"
                     /note="Synaptic Flat tetramer interface [polypeptide
                     binding]"
                     /db_xref="CDD:239737"
     Site            order(98,122,125)
                     /site_type="other"
                     /note="Synaptic Site I dimer interface [polypeptide
                     binding]"
                     /db_xref="CDD:239737"
     CDS             1..205
                     /locus_tag="D646_p13002"
                     /coded_by="NC_021230.1:1774..2391"
                     /note="ORF1"
                     /transl_table=11
                     /db_xref="GeneID:15564138"
CONTIG      join(WP_015639704.1:1..205)
ORIGIN      
        1 menrkfgyir vsskdqnegr qleamrkigi terdiyldkq sgknferany qllkriirkg
       61 dilyihsldr fgrnkeeilq ewndltknie adivvldmpl ldttqykdsm gtfiadlvlq
      121 ilswmaeeer erirkrqreg idlalqngiq fgrspvvvsd efkevyrkwk akeltaveam
      181 qeagvkktsf yklvkahens ikvns
//

BioPerl-1.007002/t/data/ZABJ4EA7014.CH878695.1.blast.txt000444000766000024    336700213155576321 21327 0ustar00cjfieldsstaff000000000000


BLASTN 2.2.20+
Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and
Webb Miller (2000), "A greedy algorithm for aligning DNA
sequences", J Comput Biol 2000; 7(1-2):203-14.


RID: ZABJ4EA7014


Database: human build 35 genome database (reference assembly only)
           378 sequences; 2,866,055,344 total letters
Query= gi|95131563|gb|CH878695.1| Homo sapiens 211000035829648 genomic
scaffold
Length=29324



ALIGNMENTS
>gi|51458380|ref|NT_021937.17|Hs1_22093 Homo sapiens chromosome 1 genomic contig
Length=7618319

 Score = 3.427e+04 bits (18557),  Expect = 0.0
 Identities = 18608/18632 (99%), Gaps = 6/18632 (0%)
 Strand=Plus/Minus

Query  10698    GAATTCTTGACTTCTACCCTATCCCTAACACTGTCAATTTCCTGATTCATGCAATTAATA  10757
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7618319  GAATTCTTGACTTCTACCCTATCCCTAACACTGTCAATTTCCTGATTCATGCAATTAATA  7618260

Query  10758    TGGATATCTGATATGAATGGATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAAAC  10817
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7618259  TGGATATCTGATATGAATGGATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAAAC  7618200

Query  10818    CCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGG  10877
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7618199  CCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGG  7618140

Query  10878    AAGCTAGTGatccgcctgccttagtctcccaaagtgctaggattgcaggcatgagccact  10937
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7618139  AAGCTAGTGATCCGCCTGCCTTAGTCTCCCAAAGTGCTAGGATTGCAGGCATGAGCCACT  7618080

Query  10938    gcacctggccGGTATTTTCTGTTTTGTACaagatgttccagaaagaaaggcaaatatgga  10997
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7618079  GCACCTGGCCGGTATTTTCTGTTTTGTACAAGATGTTCCAGAAAGAAAGGCAAATATGGA  7618020

Query  10998    aagttgtctaattcatttcataagagagcagtaacccatattttaaaaatggctaaggat  11057
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7618019  AAGTTGTCTAATTCATTTCATAAGAGAGCAGTAACCCATATTTTAAAAATGGCTAAGGAT  7617960

Query  11058    attagaaggaaagtaaatttaaacttatttggcaaaagttttttttcttttttctttc-t  11116
                |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |
Sbjct  7617959  ATTAGAAGGAAAGTAAATTTAAACTTATTTGGCAAAAGTTTTTTTTCTTTTTTCTTTCTT  7617900

Query  11117    tttttttttttttgagacagagactcactctgtcatgcaggctggagtgcagtggcacaa  11176
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617899  TTTTTTTTTTTTTGAGACAGAGACTCACTCTGTCATGCAGGCTGGAGTGCAGTGGCACAA  7617840

Query  11177    tctcacctcactgcaacctcttactcccagattcgagcaattctcctgcctcagcctctc  11236
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617839  TCTCACCTCACTGCAACCTCTTACTCCCAGATTCGAGCAATTCTCCTGCCTCAGCCTCTC  7617780

Query  11237    tagtagctgggattagagccacatgccaccacatccagctaatttatgtagttttagaag  11296
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617779  TAGTAGCTGGGATTAGAGCCACATGCCACCACATCCAGCTAATTTATGTAGTTTTAGAAG  7617720

Query  11297    aggcagaatttctctgtgttggctagaactcctgacctcaggtgatccacttgcctcggc  11356
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617719  AGGCAGAATTTCTCTGTGTTGGCTAGAACTCCTGACCTCAGGTGATCCACTTGCCTCGGC  7617660

Query  11357    ctcccaaagtgctgggattacaggcatgagccaccacggtcagccAGAAAAAAGTACTTA  11416
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617659  CTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCACGGTCAGCCAGAAAAAAGTACTTA  7617600

Query  11417    ATAAATTATCAGTTAACTAAATGCAACACTGCATTAGAAAGTGATAGACAggccaggctc  11476
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617599  ATAAATTATCAGTTAACTAAATGCAACACTGCATTAGAAAGTGATAGACAGGCCAGGCTC  7617540

Query  11477    cgtggctcacgcctgcaatcccagcactttgagaggccgaggcaggtggatcacctcagg  11536
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617539  CGTGGCTCACGCCTGCAATCCCAGCACTTTGAGAGGCCGAGGCAGGTGGATCACCTCAGG  7617480

Query  11537    tctggagttcgagaccagcctgaccaacatggagaaaccccatccctactaaaaatacaa  11596
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617479  TCTGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCCATCCCTACTAAAAATACAA  7617420

Query  11597    aattagccaggtgtggtggcgcatgcctgtaatcccagcaactcaggaggctgaggctgg  11656
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617419  AATTAGCCAGGTGTGGTGGCGCATGCCTGTAATCCCAGCAACTCAGGAGGCTGAGGCTGG  7617360

Query  11657    agatttgcttgaaccaagaaggtggaagttgcagtgagtcgagatcatgccattgcactt  11716
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617359  AGATTTGCTTGAACCAAGAAGGTGGAAGTTGCAGTGAGTCGAGATCATGCCATTGCACTT  7617300

Query  11717    cagcttgtgcaaaaagagtgaaactccaccttaaaaagaaaaaaaaaagaaaaaaagaaa  11776
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617299  CAGCTTGTGCAAAAAGAGTGAAACTCCACCTTAAAAAGAAAAAAAAAAGAAAAAAAGAAA  7617240

Query  11777    GCAATATAGTGATATATAATGGCCATTCCAGGAATGCCAGCCAATCACAGGAAAATCTAA  11836
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617239  GCAATATAGTGATATATAATGGCCATTCCAGGAATGCCAGCCAATCACAGGAAAATCTAA  7617180

Query  11837    GTGTAATTCAGCATACTGACAAACTAAAGGGGGAAAAGCAAGGTTCCTACAAAATGCAGA  11896
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617179  GTGTAATTCAGCATACTGACAAACTAAAGGGGGAAAAGCAAGGTTCCTACAAAATGCAGA  7617120

Query  11897    AAAGAATTGCAGAAAAATCAAATTAAATTTATCATAACATATTTCGGAAACTGAAATGTT  11956
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617119  AAAGAATTGCAGAAAAATCAAATTAAATTTATCATAACATATTTCGGAAACTGAAATGTT  7617060

Query  11957    GTATGTTGAAAACTTGCATTAAACATCAGATGTAATGGATAAACATTAGCTCCCTTCCTA  12016
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7617059  GTATGTTGAAAACTTGCATTAAACATCAGATGTAATGGATAAACATTAGCTCCCTTCCTA  7617000

Query  12017    CTGAGATATGAAACAAGGTAAGAACCTCAGCACCTTAGGATTTGGACGCACGTAGGTATT  12076
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616999  CTGAGATATGAAACAAGGTAAGAACCTCAGCACCTTAGGATTTGGACGCACGTAGGTATT  7616940

Query  12077    TTGGTTAATAGTAAAGACTCCAGATCCAGCAGACCCAGACTGCTTAATTTAGGTTCAAAA  12136
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616939  TTGGTTAATAGTAAAGACTCCAGATCCAGCAGACCCAGACTGCTTAATTTAGGTTCAAAA  7616880

Query  12137    CTGGCTCAGTaccatcctggctaacacggtgaatccccgtctctactaaaaacacaaaaa  12196
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616879  CTGGCTCAGTACCATCCTGGCTAACACGGTGAATCCCCGTCTCTACTAAAAACACAAAAA  7616820

Query  12197    ttagccgggcatggtggcaggtgcctgtagccccagctactcgggaggctgaggcagcag  12256
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616819  TTAGCCGGGCATGGTGGCAGGTGCCTGTAGCCCCAGCTACTCGGGAGGCTGAGGCAGCAG  7616760

Query  12257    aatggagtgaacccgggaggcagagcttgcagtgagctgagatcgcgccactgcactcca  12316
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616759  AATGGAGTGAACCCGGGAGGCAGAGCTTGCAGTGAGCTGAGATCGCGCCACTGCACTCCA  7616700

Query  12317    gcctgagcgacagcatgagatgctgtctcagaaaaaagaaaaaaaaCTGGCTCAGTGGCC  12376
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616699  GCCTGAGCGACAGCATGAGATGCTGTCTCAGAAAAAAGAAAAAAAACTGGCTCAGTGGCC  7616640

Query  12377    AATGgctgtgtggtcttactcaacttacttaacctctctgtgccttagctcattcacata  12436
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616639  AATGGCTGTGTGGTCTTACTCAACTTACTTAACCTCTCTGTGCCTTAGCTCATTCACATA  7616580

Query  12437    taaaatgggataatagcaatattgacttcacagagtGCTATAAATTAATCTATTTAAGTA  12496
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616579  TAAAATGGGATAATAGCAATATTGACTTCACAGAGTGCTATAAATTAATCTATTTAAGTA  7616520

Query  12497    CTTCGAGCTGGATTTGACATAGGGCAAGCAAGGATATTTTTATTGTTATTATATTTGAAA  12556
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616519  CTTCGAGCTGGATTTGACATAGGGCAAGCAAGGATATTTTTATTGTTATTATATTTGAAA  7616460

Query  12557    AATATATTAGTTACAAACTTAGGTAAGAGACCAAGGCCTATGGTAAAGGTGATTATAAGC  12616
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616459  AATATATTAGTTACAAACTTAGGTAAGAGACCAAGGCCTATGGTAAAGGTGATTATAAGC  7616400

Query  12617    CTTCATACACCACTGTTGTTCTGAAAATCTTAATTATAACAAggccaggcacggtggctc  12676
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616399  CTTCATACACCACTGTTGTTCTGAAAATCTTAATTATAACAAGGCCAGGCACGGTGGCTC  7616340

Query  12677    acgtctgtaatcccagcactttgggaggccaaggtgggcagatcacctgaggtcaggagt  12736
                ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||
Sbjct  7616339  ACGTCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGCGGATCACCTGAGGTCAGGAGT  7616280

Query  12737    tcgagaccagcctcaccaacatggcgaaactatctctctactaaaaatacaaaaaatagc  12796
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616279  TCGAGACCAGCCTCACCAACATGGCGAAACTATCTCTCTACTAAAAATACAAAAAATAGC  7616220

Query  12797    tgggcatggtggtggacacctgtaatcccaggtattcggtaggttgaggcaggagaatca  12856
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616219  TGGGCATGGTGGTGGACACCTGTAATCCCAGGTATTCGGTAGGTTGAGGCAGGAGAATCA  7616160

Query  12857    cttgaatccaggaggcagagtttgcagtgagccaagattgaactattgctctccagcctg  12916
                |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Sbjct  7616159  CTTGAATCCAGGAGGCAGAGTTTGCAGTGAGCCATGATTGAACTATTGCTCTCCAGCCTG  7616100

Query  12917    gcgagagagtgagactccatctccaaaaaaaaaaaaaattataagaaCATGTCCATTCAC  12976
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616099  GCGAGAGAGTGAGACTCCATCTCCAAAAAAAAAAAAAATTATAAGAACATGTCCATTCAC  7616040

Query  12977    TCTCCAAAGTATCTAGGACTGGACAATTACTTGTCAGGCCCTCTTCTGTAGCACCATACA  13036
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7616039  TCTCCAAAGTATCTAGGACTGGACAATTACTTGTCAGGCCCTCTTCTGTAGCACCATACA  7615980

Query  13037    CTATAGCATATATGTGGATTAatataaatacacatacaaaattcaagtatatattctata  13096
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615979  CTATAGCATATATGTGGATTAATATAAATACACATACAAAATTCAAGTATATATTCTATA  7615920

Query  13097    tactttctatatatttatatTCTAAGAGGTCACATGCAAATTCAAGGCTAGGTCAAAGAG  13156
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615919  TACTTTCTATATATTTATATTCTAAGAGGTCACATGCAAATTCAAGGCTAGGTCAAAGAG  7615860

Query  13157    TAGAGTGGCTATCTATGGAAAGGGGAGTGGAAGTGAATCATGGTAATaaaaaaaGGTGTA  13216
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615859  TAGAGTGGCTATCTATGGAAAGGGGAGTGGAAGTGAATCATGGTAATAAAAAAAGGTGTA  7615800

Query  13217    GATATAGTTATGGATAGGTAGACATACACACATATAGCGGCAAGAAAAGGGAATGTCATG  13276
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615799  GATATAGTTATGGATAGGTAGACATACACACATATAGCGGCAAGAAAAGGGAATGTCATG  7615740

Query  13277    GACCAGTGATGACAGTGAGCCATGTAAAAAGGCTACAATTTTTGTGATTGTGTGTCCATT  13336
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615739  GACCAGTGATGACAGTGAGCCATGTAAAAAGGCTACAATTTTTGTGATTGTGTGTCCATT  7615680

Query  13337    TTCAGGATTGGTTGTAGCTTACCTTTTTAGAAAGGCTGATGCCATAGTCATAGTGAATAA  13396
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615679  TTCAGGATTGGTTGTAGCTTACCTTTTTAGAAAGGCTGATGCCATAGTCATAGTGAATAA  7615620

Query  13397    ATGATTATAAAATGTGTTTCCTTTCTGGCGAACCTCTGGAGAAATTTCCAATGGTAGGAG  13456
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615619  ATGATTATAAAATGTGTTTCCTTTCTGGCGAACCTCTGGAGAAATTTCCAATGGTAGGAG  7615560

Query  13457    AACTCAGTTTACTGGGCAGGCGATCACACAGATAAGATTTTACAGATCTAATGGCACTAC  13516
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615559  AACTCAGTTTACTGGGCAGGCGATCACACAGATAAGATTTTACAGATCTAATGGCACTAC  7615500

Query  13517    CATTAACTTCATTATCATTGGTATTCTACAAAGGTTGAGTGAACAAATGGTATCTTAAAA  13576
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615499  CATTAACTTCATTATCATTGGTATTCTACAAAGGTTGAGTGAACAAATGGTATCTTAAAA  7615440

Query  13577    TTAAATTAGCTAAATTAACAAAAAAGATTGGATTACtttttcttttttttgacacagagt  13636
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615439  TTAAATTAGCTAAATTAACAAAAAAGATTGGATTACTTTTTCTTTTTTTTGACACAGAGT  7615380

Query  13637    ctctgatgcccaagcgggagtacagtggtgctatgtcatctcactgcaacatctgcctcc  13696
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615379  CTCTGATGCCCAAGCGGGAGTACAGTGGTGCTATGTCATCTCACTGCAACATCTGCCTCC  7615320

Query  13697    cgggttcaagagattctcctgcctcagactcctgagtagccgggattacaggcacacacc  13756
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615319  CGGGTTCAAGAGATTCTCCTGCCTCAGACTCCTGAGTAGCCGGGATTACAGGCACACACC  7615260

Query  13757    accacacccagctgatttttgtatttttagcagaaacggggtttcaccatgttgaccagg  13816
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615259  ACCACACCCAGCTGATTTTTGTATTTTTAGCAGAAACGGGGTTTCACCATGTTGACCAGG  7615200

Query  13817    ttggtcttgaacccctgaccttgtgatctccctgcctcagcctcctgaagtgctggaatt  13876
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615199  TTGGTCTTGAACCCCTGACCTTGTGATCTCCCTGCCTCAGCCTCCTGAAGTGCTGGAATT  7615140

Query  13877    ataggcttgagccaccttgcccagcctaatctttttttcttttCTCAAAGGACTTCTATG  13936
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615139  ATAGGCTTGAGCCACCTTGCCCAGCCTAATCTTTTTTTCTTTTCTCAAAGGACTTCTATG  7615080

Query  13937    CACTTAGGAGAGTGAGCCCATCGTTCAGTAACAACATGATTCAATACTGCAAGACCTTGA  13996
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615079  CACTTAGGAGAGTGAGCCCATCGTTCAGTAACAACATGATTCAATACTGCAAGACCTTGA  7615020

Query  13997    TGCAGTATTTCAAAGTCTTTCCAGTAGGTGAGGGAGGCTTTCAGTGATGCTTAGACCTTC  14056
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7615019  TGCAGTATTTCAAAGTCTTTCCAGTAGGTGAGGGAGGCTTTCAGTGATGCTTAGACCTTC  7614960

Query  14057    ATGCCCTAGAATTTGGAGATTGCATCCTTTAGAAATGATACCAAGGGAAATCTGCCCATG  14116
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614959  ATGCCCTAGAATTTGGAGATTGCATCCTTTAGAAATGATACCAAGGGAAATCTGCCCATG  7614900

Query  14117    AGCAGCACTGGATGGGACTGTACCAGATGACTTAAAACTAAGGATAACCAAGGAAAAGCC  14176
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614899  AGCAGCACTGGATGGGACTGTACCAGATGACTTAAAACTAAGGATAACCAAGGAAAAGCC  7614840

Query  14177    TTCCTTAGAAGCAGACATCATCACATGGTAGACAGTTTTCCAAGACAATGGAACAAGACT  14236
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614839  TTCCTTAGAAGCAGACATCATCACATGGTAGACAGTTTTCCAAGACAATGGAACAAGACT  7614780

Query  14237    CCATTTGATCTTCTTCCATTGACTGAGACTTGGTTTTGTTTTGTATTAAAACAAAATGCT  14296
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614779  CCATTTGATCTTCTTCCATTGACTGAGACTTGGTTTTGTTTTGTATTAAAACAAAATGCT  7614720

Query  14297    CAAACCTATATTTTATGTTGTTAGGTACTTTCTCCACTCAAACCAAACACTTTCTAAGGT  14356
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614719  CAAACCTATATTTTATGTTGTTAGGTACTTTCTCCACTCAAACCAAACACTTTCTAAGGT  7614660

Query  14357    CTTCTGTTCAAAATGTAGCCACTCTCACTAACCAAAGCAATTGCTGGCTATGGAGTCATT  14416
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614659  CTTCTGTTCAAAATGTAGCCACTCTCACTAACCAAAGCAATTGCTGGCTATGGAGTCATT  7614600

Query  14417    TACATGAAAGGGAAGGATCACAACTAAATAGTAGAACATGCTCTCATAAACAGTTGGGTA  14476
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614599  TACATGAAAGGGAAGGATCACAACTAAATAGTAGAACATGCTCTCATAAACAGTTGGGTA  7614540

Query  14477    GCAATTGAGGATGCCAACTTCATCATAAGGTTTGTTATCCTTCCTTTGGAAGGTTGGTTA  14536
                |||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614539  GCAACTGAGGATGCCAACTTCATCATAAGGTTTGTTATCCTTCCTTTGGAAGGTTGGTTA  7614480

Query  14537    ACATTTATAATTACATGACTTGGCACTGAGAAGAAGCTATAGGTGCAAATGGGTGGCCTA  14596
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614479  ACATTTATAATTACATGACTTGGCACTGAGAAGAAGCTATAGGTGCAAATGGGTGGCCTA  7614420

Query  14597    TGACTATTATTGATTACATTACTGGCATTTTATCTCTATGCATAAAAAACATTAGTGAAA  14656
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614419  TGACTATTATTGATTACATTACTGGCATTTTATCTCTATGCATAAAAAACATTAGTGAAA  7614360

Query  14657    CTGGATCTAATCTAGGTAGTGTCGCAGATTCCCACTAGAATCAAACTCTTTGGTTTGACA  14716
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614359  CTGGATCTAATCTAGGTAGTGTCGCAGATTCCCACTAGAATCAAACTCTTTGGTTTGACA  7614300

Query  14717    CACCTTATGAAGACTGGAGTGCTATAGGTATCGACATAGACATAGAATCAGAACATGACC  14776
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614299  CACCTTATGAAGACTGGAGTGCTATAGGTATCGACATAGACATAGAATCAGAACATGACC  7614240

Query  14777    ATGTTACCCTCTGCCATTTAATCAGAGAACTTACTGAAACTAGACATTGGTTCATTGGAA  14836
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614239  ATGTTACCCTCTGCCATTTAATCAGAGAACTTACTGAAACTAGACATTGGTTCATTGGAA  7614180

Query  14837    ACTCTAGAGGCAAATAGAATGTGTCTATAGCTCTACTATGTGAAATACATAATAGTTTTA  14896
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614179  ACTCTAGAGGCAAATAGAATGTGTCTATAGCTCTACTATGTGAAATACATAATAGTTTTA  7614120

Query  14897    TTTATTGGATGCATCAATACTCAGGACATATTTGGAGAGGAACCTATTCATTCTTCAATG  14956
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614119  TTTATTGGATGCATCAATACTCAGGACATATTTGGAGAGGAACCTATTCATTCTTCAATG  7614060

Query  14957    CAGATGGCATGCAAGGATTACTTTATAAAACTCATAGAAATACTTTTTCTTCCCACCCCA  15016
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614059  CAGATGGCATGCAAGGATTACTTTATAAAACTCATAGAAATACTTTTTCTTCCCACCCCA  7614000

Query  15017    ATTCAAACCATTACCATGCAACCTGGTATCAATAgaagttaaggccattgaggtagaaat  15076
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613999  ATTCAAACCATTACCATGCAACCTGGTATCAATAGAAGTTAAGGCCATTGAGGTAGAAAT  7613940

Query  15077    aattaaataaagctttattggaagctaaatgtgagaatcgacctggaagacacacactga  15136
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613939  AATTAAATAAAGCTTTATTGGAAGCTAAATGTGAGAATCGACCTGGAAGACACACACTGA  7613880

Query  15137    caaagtgagtgttttccaaagtctgttacaagttggaatgcttttgtaagagaggttaaa  15196
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613879  CAAAGTGAGTGTTTTCCAAAGTCTGTTACAAGTTGGAATGCTTTTGTAAGAGAGGTTAAA  7613820

Query  15197    agaagggaatgggactcctcctatcaatttttttttaattttcttttgttttattgacct  15256
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613819  AGAAGGGAATGGGACTCCTCCTATCAATTTTTTTTTAATTTTCTTTTGTTTTATTGACCT  7613760

Query  15257    ggcaaggctcaaatagagttgagtttttgtttttgtttttcccattggaaggtacaagac  15316
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613759  GGCAAGGCTCAAATAGAGTTGAGTTTTTGTTTTTGTTTTTCCCATTGGAAGGTACAAGAC  7613700

Query  15317    agaggttacaatcgttagctttagatgacaacataacaggctaaaacattttccttgcaa  15376
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613699  AGAGGTTACAATCGTTAGCTTTAGATGACAACATAACAGGCTAAAACATTTTCCTTGCAA  7613640

Query  15377    gacaaccagcatgacttcatgatcagaataaaatcagtgtccttctcactgtcagcgggt  15436
                |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
Sbjct  7613639  GACAACCAGCATGACTTCATGATCAGAATAAAATCAGTGTCCTTCTCACTGTCAGCAGGT  7613580

Query  15437    gaagacttcatcagtacttgtagagtttgaggtactcatgaactcatgatcagattcttt  15496
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613579  GAAGACTTCATCAGTACTTGTAGAGTTTGAGGTACTCATGAACTCATGATCAGATTCTTT  7613520

Query  15497    actcagggacaggatgtaagccaatgctaagaccttctataggtggctaatttttaagct  15556
                ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Sbjct  7613519  ACTCAGGGACAGGATGTAAGCCAATGCTAAGACCTTCCATAGGTGGCTAATTTTTAAGCT  7613460

Query  15557    tgccccaatgagaccttcaggttttcaCTGGCAATATGCAGGTGCAGATATGACAAAGAA  15616
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613459  TGCCCCAATGAGACCTTCAGGTTTTCACTGGCAATATGCAGGTGCAGATATGACAAAGAA  7613400

Query  15617    TAACAATGACCTTCATATCACCTCCAGCTGTTGAGGAATGGGATCCTTTTCACCCTTCCT  15676
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613399  TAACAATGACCTTCATATCACCTCCAGCTGTTGAGGAATGGGATCCTTTTCACCCTTCCT  7613340

Query  15677    GTCCATAAAACCAAGTTACTCATCTTCAGTGGCAACAAAATATATGGTAAACTTAACAGA  15736
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613339  GTCCATAAAACCAAGTTACTCATCTTCAGTGGCAACAAAATATATGGTAAACTTAACAGA  7613280

Query  15737    GAAGGAGACTGTCAGaaaaaaaaaaaaaaaagatgtgtttatcctgaaatgaggaaagca  15796
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613279  GAAGGAGACTGTCAGAAAAAAAAAAAAAAAAGATGTGTTTATCCTGAAATGAGGAAAGCA  7613220

Query  15797    atgggaatagatgtgagattattttgggagaaaaaggaagacaaaggttttgaaaggaaa  15856
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613219  ATGGGAATAGATGTGAGATTATTTTGGGAGAAAAAGGAAGACAAAGGTTTTGAAAGGAAA  7613160

Query  15857    aataaggaggattatacaaattgttttgaaagactcaaccttggtcctaagaatcaaaag  15916
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613159  AATAAGGAGGATTATACAAATTGTTTTGAAAGACTCAACCTTGGTCCTAAGAATCAAAAG  7613100

Query  15917    taaaggggcatcagtgaaatgttggatagATTCCACCTCCACCCCCTCAGTAACCCCCAA  15976
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613099  TAAAGGGGCATCAGTGAAATGTTGGATAGATTCCACCTCCACCCCCTCAGTAACCCCCAA  7613040

Query  15977    CATGTTTACCAAGTCTTGGTTAACTCCCAGGATCCCATTAAAACACCCAGCTCAACCATG  16036
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7613039  CATGTTTACCAAGTCTTGGTTAACTCCCAGGATCCCATTAAAACACCCAGCTCAACCATG  7612980

Query  16037    CCCATCCTCTACCCTCACTTCTCTTTGTAATTTTGACATGATTTTAttacaggaccatca  16096
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612979  CCCATCCTCTACCCTCACTTCTCTTTGTAATTTTGACATGATTTTATTACAGGACCATCA  7612920

Query  16097    ggttcctatgcctgctgcacagtagctgaccaatattctgagacagcagtgtttgcagca  16156
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612919  GGTTCCTATGCCTGCTGCACAGTAGCTGACCAATATTCTGAGACAGCAGTGTTTGCAGCA  7612860

Query  16157    gacagtttaatgatcacagggtggctaaatgagaagctaggaggatatcctcaaattcat  16216
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612859  GACAGTTTAATGATCACAGGGTGGCTAAATGAGAAGCTAGGAGGATATCCTCAAATTCAT  7612800

Query  16217    ctccccaagtagtactgagggtttccagtggatcctggatagcaaggggctggaaagttg  16276
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612799  CTCCCCAAGTAGTACTGAGGGTTTCCAGTGGATCCTGGATAGCAAGGGGCTGGAAAGTTG  7612740

Query  16277    gtgtagaggtaagagggatgaagtcatcaggatgtcaaaactgcattctttggtgagttg  16336
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612739  GTGTAGAGGTAAGAGGGATGAAGTCATCAGGATGTCAAAACTGCATTCTTTGGTGAGTTG  7612680

Query  16337    gtgccttgcagagcccttcagatcagctggcatcagtagtttcactgacatgcagaacct  16396
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612679  GTGCCTTGCAGAGCCCTTCAGATCAGCTGGCATCAGTAGTTTCACTGACATGCAGAACCT  7612620

Query  16397    gaaagaatatctcaaatgagaaagttaatgttttacaaggcttaaattgttgtctgcagg  16456
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612619  GAAAGAATATCTCAAATGAGAAAGTTAATGTTTTACAAGGCTTAAATTGTTGTCTGCAGG  7612560

Query  16457    gtagttaaggggaactgtaagctaaggtctacttgatttggggacagtaagctgccagca  16516
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612559  GTAGTTAAGGGGAACTGTAAGCTAAGGTCTACTTGATTTGGGGACAGTAAGCTGCCAGCA  7612500

Query  16517    accatgaggaagaaggtcagagagcaagctgacctcatggtgaatgctgaatgcgctgca  16576
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612499  ACCATGAGGAAGAAGGTCAGAGAGCAAGCTGACCTCATGGTGAATGCTGAATGCGCTGCA  7612440

Query  16577    agcttggtttatttttgtttctccccctcccttcttcactgattaaacttataaagttta  16636
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612439  AGCTTGGTTTATTTTTGTTTCTCCCCCTCCCTTCTTCACTGATTAAACTTATAAAGTTTA  7612380

Query  16637    caggtatcatttcaATTTCTTCCAGAGAAGACTTAACCTAAGCCCTGAGACCACTCAAGC  16696
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612379  CAGGTATCATTTCAATTTCTTCCAGAGAAGACTTAACCTAAGCCCTGAGACCACTCAAGC  7612320

Query  16697    CCTCAGTGGCACCTCTCTTCCACCAGCACGAGTGAAGAAACTGCTACCTTAGGTGATATA  16756
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612319  CCTCAGTGGCACCTCTCTTCCACCAGCACGAGTGAAGAAACTGCTACCTTAGGTGATATA  7612260

Query  16757    AAACCCACAAGACCATTCCATACATGGAGATCTTTATTCTTATTTTGTAGGGACGACTCC  16816
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612259  AAACCCACAAGACCATTCCATACATGGAGATCTTTATTCTTATTTTGTAGGGACGACTCC  7612200

Query  16817    TCTGTGTTTATACAGCTATTTTAACTAGAAATATTTTTATAAATTTTATAATTTTGATGT  16876
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612199  TCTGTGTTTATACAGCTATTTTAACTAGAAATATTTTTATAAATTTTATAATTTTGATGT  7612140

Query  16877    GGCCAAAGATCTCCCCACAACACTACTTTCAGGTTTTATTTTTCTGTCTAATGTCTGGAA  16936
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612139  GGCCAAAGATCTCCCCACAACACTACTTTCAGGTTTTATTTTTCTGTCTAATGTCTGGAA  7612080

Query  16937    CAGATCAACCCCTTCCCTGCCTCACATCAGGACTTGAAGGCGAAATAGCAGTAAAATTCC  16996
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612079  CAGATCAACCCCTTCCCTGCCTCACATCAGGACTTGAAGGCGAAATAGCAGTAAAATTCC  7612020

Query  16997    ATCAGTGTTTGTGGATTTCATGAATGAATGCAttttttttgacaaaatctccctctgtca  17056
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612019  ATCAGTGTTTGTGGATTTCATGAATGAATGCATTTTTTTTGACAAAATCTCCCTCTGTCA  7611960

Query  17057    cccagtcaggagggcaatggtgtaatcttggctcactgcaaactcagcctccagggttca  17116
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611959  CCCAGTCAGGAGGGCAATGGTGTAATCTTGGCTCACTGCAAACTCAGCCTCCAGGGTTCA  7611900

Query  17117    agggattctcccacctcagccgcatgagtaactggactacaggcagccaccatcgtgcct  17176
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611899  AGGGATTCTCCCACCTCAGCCGCATGAGTAACTGGACTACAGGCAGCCACCATCGTGCCT  7611840

Query  17177    ggctaacttttctatttttgtagagacagggtttcaccatgtgggccaggctggtcttga  17236
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611839  GGCTAACTTTTCTATTTTTGTAGAGACAGGGTTTCACCATGTGGGCCAGGCTGGTCTTGA  7611780

Query  17237    actcctgacctcaggtgatccacctaccttggcctcccaaagtgctgggattacaagtgt  17296
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611779  ACTCCTGACCTCAGGTGATCCACCTACCTTGGCCTCCCAAAGTGCTGGGATTACAAGTGT  7611720

Query  17297    gagccacctcacctggccTTGAGTGAATGAATTCTTGATTTCCAGTCTATCCCTAACTCT  17356
                |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Sbjct  7611719  GAGCCACCTCACCTGGCCTTGAGTGAATGAATTCTTGACTTCCAGTCTATCCCTAACTCT  7611660

Query  17357    GTCAATTTCTTAATTCATGAAATGATTATGCATATGTGATATGAATGGATATCTCGTTCA  17416
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611659  GTCAATTTCTTAATTCATGAAATGATTATGCATATGTGATATGAATGGATATCTCGTTCA  7611600

Query  17417    ATCCATTAGTCTTCGGACAGTCAAAAACCCAATCAGGATTAACTGAGTGGAGCTTCAGAA  17476
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611599  ATCCATTAGTCTTCGGACAGTCAAAAACCCAATCAGGATTAACTGAGTGGAGCTTCAGAA  7611540

Query  17477    ATGCAATCAGATATCGCTTTTTGATTGGAAGCTAGCAGCGGATACGTGGAGGGGCGTGGG  17536
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611539  ATGCAATCAGATATCGCTTTTTGATTGGAAGCTAGCAGCGGATACGTGGAGGGGCGTGGG  7611480

Query  17537    TGGGAGTTGTGATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGACAAACTCAAA  17596
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611479  TGGGAGTTGTGATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGACAAACTCAAA  7611420

Query  17597    GTCTTCAAGCCTGGAGTTCCTGCTTGGCTCTTCCTGAGGTCTGAGCACCTTCTAAACTAC  17656
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611419  GTCTTCAAGCCTGGAGTTCCTGCTTGGCTCTTCCTGAGGTCTGAGCACCTTCTAAACTAC  7611360

Query  17657    AACCAGATCTGGTAAGTCACTAATTTCTGTAAGGACACTCCCATGTGACCTACAGTCAGC  17716
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611359  AACCAGATCTGGTAAGTCACTAATTTCTGTAAGGACACTCCCATGTGACCTACAGTCAGC  7611300

Query  17717    CGGTCTAGAACGGTGACAGTGCAGCCTACGATGGCATAGAACTATATCATGTCttttttt  17776
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611299  CGGTCTAGAACGGTGACAGTGCAGCCTACGATGGCATAGAACTATATCATGTCTTTTTTT  7611240

Query  17777    ctttttttcatatgaacactttgaagctttgatttttttttCTAAATGCAATTTTGTCGT  17836
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611239  CTTTTTTTCATATGAACACTTTGAAGCTTTGATTTTTTTTTCTAAATGCAATTTTGTCGT  7611180

Query  17837    GATTTCAAAAATGTTGTTGTGCTTTTCTTTACATCATTTCAGAATTCTTGTTGGCAGCCA  17896
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611179  GATTTCAAAAATGTTGTTGTGCTTTTCTTTACATCATTTCAGAATTCTTGTTGGCAGCCA  7611120

Query  17897    TTTTGTGAAGAGACGAAGACTGAGCTGTTTTGGCTGCATTTCTGGCCTCGAGCCGCAGTC  17956
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611119  TTTTGTGAAGAGACGAAGACTGAGCTGTTTTGGCTGCATTTCTGGCCTCGAGCCGCAGTC  7611060

Query  17957    AGCTTCTCCCCGTAGAACCCGGCAGTAGGAGACTTAGAATCGAATCTCTTCTCCCTCCCG  18016
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7611059  AGCTTCTCCCCGTAGAACCCGGCAGTAGGAGACTTAGAATCGAATCTCTTCTCCCTCCCG  7611000

Query  18017    CCTCCTGTTTTTGGCTTTTTGAGAAACCTTATCATCCAACACAATGGCCAGCAACGTTAC  18076
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610999  CCTCCTGTTTTTGGCTTTTTGAGAAACCTTATCATCCAACACAATGGCCAGCAACGTTAC  7610940

Query  18077    CAACAAGATGGATCCTCACTCCGTGAACTCCCGTGTGTTCATTGGGAATCTCAACACTCT  18136
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610939  CAACAAGATGGATCCTCACTCCGTGAACTCCCGTGTGTTCATTGGGAATCTCAACACTCT  7610880

Query  18137    TGTTGTCAAGAAATCTGATGTGGAGGCGATCTTTTCCAAGTATGGCAAAATTGCGGGCTG  18196
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610879  TGTTGTCAAGAAATCTGATGTGGAGGCGATCTTTTCCAAGTATGGCAAAATTGCGGGCTG  7610820

Query  18197    CTCTGTTCATAAGGGCTTTGCCTTCGTTCAATATGATAAGGAGAAAAATGCCCGGGCTGC  18256
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610819  CTCTGTTCATAAGGGCTTTGCCTTCGTTCAATATGATAAGGAGAAAAATGCCCGGGCTGC  7610760

Query  18257    TGTAGCAGGAGAGGATGGCAGAATGATTGCTAGCCAGGTTGCAGTTATTAACCTGGCTGC  18316
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610759  TGTAGCAGGAGAGGATGGCAGAATGATTGCTAGCCAGGTTGCAGTTATTAACCTGGCTGC  7610700

Query  18317    AGAGCCAAAAGTGAACCGAGGAAACGCAGGTGTGAAACGATCCGCAGCGGAGATGTACGG  18376
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610699  AGAGCCAAAAGTGAACCGAGGAAACGCAGGTGTGAAACGATCCGCAGCGGAGATGTACGG  7610640

Query  18377    CTCCTCTTTTGACTTGGACTATGGCTTTCAACGGGATTATTATGATGGGATGTACAGTTT  18436
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610639  CTCCTCTTTTGACTTGGACTATGGCTTTCAACGGGATTATTATGATGGGATGTACAGTTT  7610580

Query  18437    CCCAGCACGTGTACCTCCTCCTCCTCCCATTGCTCTGGCTGTAGTGCCCTCGAAACGCCA  18496
                |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
Sbjct  7610579  CCCAGCACGTGTACCTCCTCCTCCTCCCATTGCTCTGGCTGTAGTGCCCTCGAAACACCA  7610520

Query  18497    GCGCATATCAGGAAACACCTCACGAAGGGGCAAAAGTGGCTTCAATTCTAAGAGTGGAAA  18556
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610519  GCGCATATCAGGAAACACCTCACGAAGGGGCAAAAGTGGCTTCAATTCTAAGAGTGGAAA  7610460

Query  18557    GCGGGGATCTTCCAAGTCTGGAAAGCTGAAAGGAGATGACCTTCAGGCCATTAAGCAGGA  18616
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610459  GCGGGGATCTTCCAAGTCTGGAAAGCTGAAAGGAGATGACCTTCAGGCCATTAAGCAGGA  7610400

Query  18617    GTTGACCCAGATAAAACAGAAAGTGGATTCTCTCCTGGAAAACCTGGAAAAAATTGAAAA  18676
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610399  GTTGACCCAGATAAAACAGAAAGTGGATTCTCTCCTGGAAAACCTGGAAAAAATTGAAAA  7610340

Query  18677    GGAACAGAGCAAACAAGAGGTAGAGGTGAAAAATGCTAAGTCAGAAGAGGAGCAGAGCAG  18736
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610339  GGAACAGAGCAAACAAGAGGTAGAGGTGAAAAATGCTAAGTCAGAAGAGGAGCAGAGCAG  7610280

Query  18737    TAGCTCCATGAAGAAAGATGAGACTCATGTAAAGATGGAGTCTGAGGGGGGTGCAGAAGA  18796
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610279  TAGCTCCATGAAGAAAGATGAGACTCATGTAAAGATGGAGTCTGAGGGGGGTGCAGAAGA  7610220

Query  18797    CTCTGCTGAGGAGGGGGACCCACTGGATGATGATGATAATGAAGATCAGGGGGACAACCA  18856
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610219  CTCTGCTGAGGAGGGGGACCCACTGGATGATGATGATAATGAAGATCAGGGGGACAACCA  7610160

Query  18857    GCTTCATTTGATCAAGAATAATGAAAAAGATGCTGAGGAAGGAGAGGATAACAGAGACAG  18916
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610159  GCTTCATTTGATCAAGAATAATGAAAAAGATGCTGAGGAAGGAGAGGATAACAGAGACAG  7610100

Query  18917    CACCAATGGCCAGGATGACTCTTAAGCACATAGTGGGGTTGAGAAATCTTATCCCATTGT  18976
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610099  CACCAATGGCCAGGATGACTCTTAAGCACATAGTGGGGTTGAGAAATCTTATCCCATTGT  7610040

Query  18977    TTCTTTACCTAGGAGCTTGTCTAACAACAAATTTTTCACCAGATCCTCTCCCTTAGTATC  19036
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7610039  TTCTTTACCTAGGAGCTTGTCTAACAACAAATTTTTCACCAGATCCTCTCCCTTAGTATC  7609980

Query  19037    TTCAGCACATGCTTACTGTTCTCCCCATCCTTGTCCTTCCCACATTCATTAATTCATATT  19096
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609979  TTCAGCACATGCTTACTGTTCTCCCCATCCTTGTCCTTCCCACATTCATTAATTCATATT  7609920

Query  19097    GCCCTGTGCCTAGTCCCATTTTCACTTCCCATGACACCCCTAGTAGTTTTCCTAAGTCTT  19156
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609919  GCCCTGTGCCTAGTCCCATTTTCACTTCCCATGACACCCCTAGTAGTTTTCCTAAGTCTT  7609860

Query  19157    ACCCTGTAATTTTTGCTTTTAATTTTGACACCTCTTTATGACTTAACAGTAAAAAGGATG  19216
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609859  ACCCTGTAATTTTTGCTTTTAATTTTGACACCTCTTTATGACTTAACAGTAAAAAGGATG  7609800

Query  19217    TATGGTTTTTATCAACTGTCTCCAAAATAATCTCTTGTTATGCAGGGAATACAGTTCTTT  19276
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609799  TATGGTTTTTATCAACTGTCTCCAAAATAATCTCTTGTTATGCAGGGAATACAGTTCTTT  7609740

Query  19277    TCTTTCATACATAAGTTCAGTAGTTGCTTCCCTAACTGCAAAGGCAATCTCATTGAGTTG  19336
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609739  TCTTTCATACATAAGTTCAGTAGTTGCTTCCCTAACTGCAAAGGCAATCTCATTGAGTTG  7609680

Query  19337    AGTAGCTCCTGAAAGCAGCTTGGAGTTACAAGTATGTGTGTTACACCCCATATTAGTGTG  19396
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609679  AGTAGCTCCTGAAAGCAGCTTGGAGTTACAAGTATGTGTGTTACACCCCATATTAGTGTG  7609620

Query  19397    CTGTGTGGGGCAGTTCAACAAAAATCTAACAATGTATTTTTGTGAATGAGAGTTGGCATG  19456
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609619  CTGTGTGGGGCAGTTCAACAAAAATCTAACAATGTATTTTTGTGAATGAGAGTTGGCATG  7609560

Query  19457    TCAAATGCATCCTCAGAAACATAATTGGTGTTATAGTCTTCAAATGTGTTTTCTAAAGTT  19516
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609559  TCAAATGCATCCTCAGAAACATAATTGGTGTTATAGTCTTCAAATGTGTTTTCTAAAGTT  7609500

Query  19517    GATACCGTGGGTTATTTTTGTGAACAGCTTGATGTTTGGGACCTTTTCCCTGAAAATAAA  19576
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609499  GATACCGTGGGTTATTTTTGTGAACAGCTTGATGTTTGGGACCTTTTCCCTGAAAATAAA  7609440

Query  19577    CAACTCTTTATTAAACCAGCAATTTAAAGaaaaaaaaTTCTTGGTgggagcaatgactca  19636
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609439  CAACTCTTTATTAAACCAGCAATTTAAAGAAAAAAAATTCTTGGTGGGAGCAATGACTCA  7609380

Query  19637    tgcctgtaactacaacactttgggaggccaaggtgggaggatcgtttgagcgcaggggtt  19696
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609379  TGCCTGTAACTACAACACTTTGGGAGGCCAAGGTGGGAGGATCGTTTGAGCGCAGGGGTT  7609320

Query  19697    cgagaccaacctgggcaacatggcaaaaccctatctctacaaaacatTTGTTTTGAGGGG  19756
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609319  CGAGACCAACCTGGGCAACATGGCAAAACCCTATCTCTACAAAACATTTGTTTTGAGGGG  7609260

Query  19757    CGGGATGGagtctcactccgttacccaggctggaatggagtggcacaatctcagctcact  19816
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609259  CGGGATGGAGTCTCACTCCGTTACCCAGGCTGGAATGGAGTGGCACAATCTCAGCTCACT  7609200

Query  19817    ccaacctctgcctcccaggctcaagcgattctcatgcctcagcctcctgagtagctggga  19876
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609199  CCAACCTCTGCCTCCCAGGCTCAAGCGATTCTCATGCCTCAGCCTCCTGAGTAGCTGGGA  7609140

Query  19877    ttatagccacccacccccatgagcagctcatttttatattttggatagagacggcggttc  19936
                ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609139  TTATAGCCACCCACCACCATGAGCAGCTCATTTTTATATTTTGGATAGAGACGGCGGTTC  7609080

Query  19937    accatgttggccaggctggtctcaaactcctaacctcaagtgatccacctgctttggcct  19996
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609079  ACCATGTTGGCCAGGCTGGTCTCAAACTCCTAACCTCAAGTGATCCACCTGCTTTGGCCT  7609020

Query  19997    cccaaagggctgggattacaccagtgagccaccaatgccctgccTCTTTTTTAAAAAATT  20056
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7609019  CCCAAAGGGCTGGGATTACACCAGTGAGCCACCAATGCCCTGCCTCTTTTTTAAAAAATT  7608960

Query  20057    AGATGGGCATGGTtgaaggggagcagtctctccatacctgtgggtatatcgcatcaggtg  20116
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608959  AGATGGGCATGGTTGAAGGGGAGCAGTCTCTCCATACCTGTGGGTATATCGCATCAGGTG  7608900

Query  20117    ggatgacagactgtgaaaagaaataagacacagagacaaagtatggagaaagaacagggg  20176
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608899  GGATGACAGACTGTGAAAAGAAATAAGACACAGAGACAAAGTATGGAGAAAGAACAGGGG  7608840

Query  20177    gcccaggggaccggcgctcagcataaaacatgagcaaaggaatctgtgtcacaaatgagt  20236
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608839  GCCCAGGGGACCGGCGCTCAGCATAAAACATGAGCAAAGGAATCTGTGTCACAAATGAGT  7608780

Query  20237    tcaagggaaggtactctgcctggatgtgcatgtaggccagatgtatgcttctctccaccc  20296
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608779  TCAAGGGAAGGTACTCTGCCTGGATGTGCATGTAGGCCAGATGTATGCTTCTCTCCACCC  7608720

Query  20297    aaacatctcagtggagaaaagaataacagagcagcattgctgccaacatgtctcacctcc  20356
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608719  AAACATCTCAGTGGAGAAAAGAATAACAGAGCAGCATTGCTGCCAACATGTCTCACCTCC  7608660

Query  20357    caacacaggacagtttgtctcctatctcagaatagaacaaatctacaattgggttttata  20416
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608659  CAACACAGGACAGTTTGTCTCCTATCTCAGAATAGAACAAATCTACAATTGGGTTTTATA  7608600

Query  20417    ccgagacattccattcccagggacaggcaggagacagaggccttcctcttatctcaactg  20476
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608599  CCGAGACATTCCATTCCCAGGGACAGGCAGGAGACAGAGGCCTTCCTCTTATCTCAACTG  7608540

Query  20477    caagaggccttcctcttttactaatactcctcagcacagacccttcacgggagttgggct  20536
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608539  CAAGAGGCCTTCCTCTTTTACTAATACTCCTCAGCACAGACCCTTCACGGGAGTTGGGCT  7608480

Query  20537    gggggatggtcaggtctctcccatcccacaaggccatatctcaggctatcacatggggag  20596
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608479  GGGGGATGGTCAGGTCTCTCCCATCCCACAAGGCCATATCTCAGGCTATCACATGGGGAG  7608420

Query  20597    aaaccttagacaatacccggctttccagggcagaggtccctgtggctttccacagtgcat  20656
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608419  AAACCTTAGACAATACCCGGCTTTCCAGGGCAGAGGTCCCTGTGGCTTTCCACAGTGCAT  7608360

Query  20657    tgtgcccctggtttatcgagaatggagaatggcgatgattttaccaagcatattgcctgt  20716
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608359  TGTGCCCCTGGTTTATCGAGAATGGAGAATGGCGATGATTTTACCAAGCATATTGCCTGT  7608300

Query  20717    atacatattgttaacaaggcacatcctgcactgccctagatcccttaaaccttgattcca  20776
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608299  ATACATATTGTTAACAAGGCACATCCTGCACTGCCCTAGATCCCTTAAACCTTGATTCCA  7608240

Query  20777    tacaacacatgtttttgtgagctcaaggttggggcaaagttacagattaatagcatctca  20836
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608239  TACAACACATGTTTTTGTGAGCTCAAGGTTGGGGCAAAGTTACAGATTAATAGCATCTCA  7608180

Query  20837    gggcaaagcaattcttcagggcacaggtcaaaatggagtttcttatgtcttccttttcta  20896
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608179  GGGCAAAGCAATTCTTCAGGGCACAGGTCAAAATGGAGTTTCTTATGTCTTCCTTTTCTA  7608120

Query  20897    catagacacagtaacagtctgatctctctttcttttccctacacatggtggcatgcatct  20956
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608119  CATAGACACAGTAACAGTCTGATCTCTCTTTCTTTTCCCTACACATGGTGGCATGCATCT  7608060

Query  20957    gtagtcccagctacttgggtggctgaggtgggagaatcccttgaatccagaagattgatg  21016
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7608059  GTAGTCCCAGCTACTTGGGTGGCTGAGGTGGGAGAATCCCTTGAATCCAGAAGATTGATG  7608000

Query  21017    ctgcagtgagccatgctcacaccagtgctgtactccagcctgggcagcagagtcagactg  21076
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607999  CTGCAGTGAGCCATGCTCACACCAGTGCTGTACTCCAGCCTGGGCAGCAGAGTCAGACTG  7607940

Query  21077    ttgaaaaaaaaaaaTCTTAATCAAACAGTTAAAAAAGTGCAATTAATTGTAATCAGTAGG  21136
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607939  TTGAAAAAAAAAAATCTTAATCAAACAGTTAAAAAAGTGCAATTAATTGTAATCAGTAGG  7607880

Query  21137    CAGATCCCAAATTCCCCAAAAAAGGAGAGAAAGAGAGTTTAGAAGGCTCTACATGCTAGC  21196
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607879  CAGATCCCAAATTCCCCAAAAAAGGAGAGAAAGAGAGTTTAGAAGGCTCTACATGCTAGC  7607820

Query  21197    ATCCCATTCAGACTGTTTAATCCTACCATTGTGGTTTTGTAAGAAAAACAGTCTTAAAGA  21256
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607819  ATCCCATTCAGACTGTTTAATCCTACCATTGTGGTTTTGTAAGAAAAACAGTCTTAAAGA  7607760

Query  21257    TTTCCAATAATTCTCACTATGGCCATAAATTATCCTGGGTGTCATTTTCCCATCAACTTA  21316
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607759  TTTCCAATAATTCTCACTATGGCCATAAATTATCCTGGGTGTCATTTTCCCATCAACTTA  7607700

Query  21317    AAAAGGCACGTGAGAggccgggcacggtggctcacacctgtaattccagcactttgggaa  21376
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607699  AAAAGGCACGTGAGAGGCCGGGCACGGTGGCTCACACCTGTAATTCCAGCACTTTGGGAA  7607640

Query  21377    gccaaggcaggtggaacgcctgagatcaggagtttgagaccagcatggccaacatggaga  21436
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Sbjct  7607639  GCCAAGGCAGGTGGAACGCCTGAGATCAGGAGTTTGAGACCAGCATGGCCAACATAGAGA  7607580

Query  21437    aactccatttctactaaaaatacaaaaaatagccgggcgtggtggtaggcatctgtaatc  21496
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607579  AACTCCATTTCTACTAAAAATACAAAAAATAGCCGGGCGTGGTGGTAGGCATCTGTAATC  7607520

Query  21497    tcaggtacttgggaggctgaggcaggagaaacagttgaacccgagaggtggaggttgcat  21556
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607519  TCAGGTACTTGGGAGGCTGAGGCAGGAGAAACAGTTGAACCCGAGAGGTGGAGGTTGCAT  7607460

Query  21557    tgagccaagatagcacctttgcacaccagcctggccacagagcaagactccatctccaaa  21616
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607459  TGAGCCAAGATAGCACCTTTGCACACCAGCCTGGCCACAGAGCAAGACTCCATCTCCAAA  7607400

Query  21617    aaaTACTACTAATAATTATAACAGCATGTCCATTCACTCTCCAAAGTGTCTGGGACTGGA  21676
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607399  AAATACTACTAATAATTATAACAGCATGTCCATTCACTCTCCAAAGTGTCTGGGACTGGA  7607340

Query  21677    CAATTAATTGTGAGGCCCTCTTCTCTAGCACCCTACGCTATAGCATATATGTGGATTAAA  21736
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607339  CAATTAATTGTGAGGCCCTCTTCTCTAGCACCCTACGCTATAGCATATATGTGGATTAAA  7607280

Query  21737    ATAAATACACATAAAAATGCAAGtatatatgctatatactttccatatacttatattata  21796
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607279  ATAAATACACATAAAAATGCAAGTATATATGCTATATACTTTCCATATACTTATATTATA  7607220

Query  21797    taAGGTCACATGCAAATTCAAGGCTAGGTCAAAGAGTAGAGTGGCAATATATGGAAAGGT  21856
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607219  TAAGGTCACATGCAAATTCAAGGCTAGGTCAAAGAGTAGAGTGGCAATATATGGAAAGGT  7607160

Query  21857    GAGTGGAAGTGAATAATGGTAATAAAAGGAAACagatagatatagatatagatatgaata  21916
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607159  GAGTGGAAGTGAATAATGGTAATAAAAGGAAACAGATAGATATAGATATAGATATGAATA  7607100

Query  21917    ggtagacatacacatatatagCTGCAAGAAAGGGGGTTGTCATGGACCAATGATGACAGT  21976
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607099  GGTAGACATACACATATATAGCTGCAAGAAAGGGGGTTGTCATGGACCAATGATGACAGT  7607040

Query  21977    GAGCCGTGTAAAAAGGCTAAAATTCttgtgattgtgtttccattttcaggatgagttgta  22036
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7607039  GAGCCGTGTAAAAAGGCTAAAATTCTTGTGATTGTGTTTCCATTTTCAGGATGAGTTGTA  7606980

Query  22037    gcttacctttttagaaaggcttatgatgcagtcatagcaaataagtgattataaaatgtg  22096
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606979  GCTTACCTTTTTAGAAAGGCTTATGATGCAGTCATAGCAAATAAGTGATTATAAAATGTG  7606920

Query  22097    tttcctttctgggcaattctggagaaatctctaatggtatgagaattcagtttactgggc  22156
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606919  TTTCCTTTCTGGGCAATTCTGGAGAAATCTCTAATGGTATGAGAATTCAGTTTACTGGGC  7606860

Query  22157    aggttatcacacataaaattttacagacccaatgacactagCATTAACTTCATTATCCTT  22216
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606859  AGGTTATCACACATAAAATTTTACAGACCCAATGACACTAGCATTAACTTCATTATCCTT  7606800

Query  22217    GGTATTCTATAAAGGTTGAGTGAACAAATGGTATATTTAAACTAAAATTAGCTAAACTGA  22276
                |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Sbjct  7606799  GGTATTCTATAAAGGTTGAGTGAACAAATGGTATCTTTAAACTAAAATTAGCTAAACTGA  7606740

Query  22277    CAAAGAAAACTGGAttattattatttatttttgagacagagtctctgttgcccaggctgg  22336
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606739  CAAAGAAAACTGGATTATTATTATTTATTTTTGAGACAGAGTCTCTGTTGCCCAGGCTGG  7606680

Query  22337    agtacagtggtgctaccttggctcactgcaacctctgcctcccaggttcaaggagttttc  22396
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606679  AGTACAGTGGTGCTACCTTGGCTCACTGCAACCTCTGCCTCCCAGGTTCAAGGAGTTTTC  7606620

Query  22397    ctgcctcagccacctaagtagctgggattacaggcacacacaaccacacccagctaattt  22456
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606619  CTGCCTCAGCCACCTAAGTAGCTGGGATTACAGGCACACACAACCACACCCAGCTAATTT  7606560

Query  22457    ttgtatttttggcagaagcggggtttcaccattttggccaggttggtcttgaacccctga  22516
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606559  TTGTATTTTTGGCAGAAGCGGGGTTTCACCATTTTGGCCAGGTTGGTCTTGAACCCCTGA  7606500

Query  22517    catcgggatctgcctgcctcggtctcctaaagtgctgggattataggcgtcagccaccac  22576
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606499  CATCGGGATCTGCCTGCCTCGGTCTCCTAAAGTGCTGGGATTATAGGCGTCAGCCACCAC  7606440

Query  22577    acctggccGAATCtttttttcttttctcaaagatgttgtcatagtattgggttctatgca  22636
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606439  ACCTGGCCGAATCTTTTTTTCTTTTCTCAAAGATGTTGTCATAGTATTGGGTTCTATGCA  7606380

Query  22637    ctcaggagagtgagcccatCATTCAGTAACAATATGAATCAATACTGCAAGACCTTGATG  22696
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606379  CTCAGGAGAGTGAGCCCATCATTCAGTAACAATATGAATCAATACTGCAAGACCTTGATG  7606320

Query  22697    CAGAATTTCAAAGACTATTTCCAGTAGGTGAAGGCTTTCAGTGATGCTTAGATCTTCCTG  22756
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606319  CAGAATTTCAAAGACTATTTCCAGTAGGTGAAGGCTTTCAGTGATGCTTAGATCTTCCTG  7606260

Query  22757    CCCTAGCATTTGGAGATTGCATCCTTTGGAAATGACACCAAGGGAAATCTGCGCATGAGC  22816
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606259  CCCTAGCATTTGGAGATTGCATCCTTTGGAAATGACACCAAGGGAAATCTGCGCATGAGC  7606200

Query  22817    AGCAATGGATGGGACTGTACCAGATGACTGAAACGTAAAGATATCCGAGGAAAAGCCTTC  22876
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606199  AGCAATGGATGGGACTGTACCAGATGACTGAAACGTAAAGATATCCGAGGAAAAGCCTTC  7606140

Query  22877    CCTAGAAGCAGACATCATCACATGGTAGACAGCTTTTCCAAGACAATGGAACAAGACTCC  22936
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606139  CCTAGAAGCAGACATCATCACATGGTAGACAGCTTTTCCAAGACAATGGAACAAGACTCC  7606080

Query  22937    ATTTGATCTTCTTCCATTGACTGAGACTTGGTTTTGTTTTGTATTAACACAAAATTCTCA  22996
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606079  ATTTGATCTTCTTCCATTGACTGAGACTTGGTTTTGTTTTGTATTAACACAAAATTCTCA  7606020

Query  22997    AACCTGTATTTTATATTGTTAGGTACTTTCATCACTCAAACCAAACACTTTCTAAGGTCT  23056
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7606019  AACCTGTATTTTATATTGTTAGGTACTTTCATCACTCAAACCAAACACTTTCTAAGGTCT  7605960

Query  23057    CCTGTTCAAAATGTAGCCACTCTCACTAACCAAAGCAATTGCTGGCTATGGGGTCATTTA  23116
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605959  CCTGTTCAAAATGTAGCCACTCTCACTAACCAAAGCAATTGCTGGCTATGGGGTCATTTA  7605900

Query  23117    GATGAAAGGGAAGGATCACAGATAATAGTAGAACCTGCTCTCATACACAGTTGGGTAGCA  23176
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605899  GATGAAAGGGAAGGATCACAGATAATAGTAGAACCTGCTCTCATACACAGTTGGGTAGCA  7605840

Query  23177    ATTGAGGATGCTAACTTCATGATAAGGTTTGTTATCCTTCCTTTGGAAGGTTGGTTAATA  23236
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605839  ATTGAGGATGCTAACTTCATGATAAGGTTTGTTATCCTTCCTTTGGAAGGTTGGTTAATA  7605780

Query  23237    TTGATAATTAAATGACTTGGTACTGAGAAGAAGCTATAGGTGCAAATGGGTGGCCTATGA  23296
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605779  TTGATAATTAAATGACTTGGTACTGAGAAGAAGCTATAGGTGCAAATGGGTGGCCTATGA  7605720

Query  23297    CTATTATTGATTTCATTACTGGTAATTTATCTCTATGCCTAGAAAACATTAGTGTAACTG  23356
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605719  CTATTATTGATTTCATTACTGGTAATTTATCTCTATGCCTAGAAAACATTAGTGTAACTG  7605660

Query  23357    GGTCTAACCTAGATAGTGTTCCAGACTCCCACTAGAATCAAACTCTTTGGTTTGACATGC  23416
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605659  GGTCTAACCTAGATAGTGTTCCAGACTCCCACTAGAATCAAACTCTTTGGTTTGACATGC  7605600

Query  23417    ATTATGTAGATGGGAATGCTATAGATATCGACATAGACATAGAGTCAGAACATGACCATG  23476
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605599  ATTATGTAGATGGGAATGCTATAGATATCGACATAGACATAGAGTCAGAACATGACCATG  7605540

Query  23477    TTACCCTCTGCCATATAATCAGAGAACTTACTGAAACTAGGCATTGGTTCTTTGGAAACT  23536
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605539  TTACCCTCTGCCATATAATCAGAGAACTTACTGAAACTAGGCATTGGTTCTTTGGAAACT  7605480

Query  23537    CTAGAGGCAAATAGAATGCATCTATAGCTCTACTGTATGAAATAATAGTTTTATTTATTG  23596
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605479  CTAGAGGCAAATAGAATGCATCTATAGCTCTACTGTATGAAATAATAGTTTTATTTATTG  7605420

Query  23597    GATGCATCAATACTCAGGATATATTTGGAGAGGAAACTATTCTTTCTTCAATGGAGATGG  23656
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605419  GATGCATCAATACTCAGGATATATTTGGAGAGGAAACTATTCTTTCTTCAATGGAGATGG  7605360

Query  23657    CATGCAAGGATTACTTTATAAAACACACAGAAATATTTTTTCCTCCCACCCCAATTCCAA  23716
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605359  CATGCAAGGATTACTTTATAAAACACACAGAAATATTTTTTCCTCCCACCCCAATTCCAA  7605300

Query  23717    CCATTACCGTGCAACCTGTtgtcaatagacgttaaggcagttgaggcagaaataattaaa  23776
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605299  CCATTACCGTGCAACCTGTTGTCAATAGACGTTAAGGCAGTTGAGGCAGAAATAATTAAA  7605240

Query  23777    taaagcttcattggaagctaaatgtcaggatcgacctggaagacacacactgacaaaatg  23836
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605239  TAAAGCTTCATTGGAAGCTAAATGTCAGGATCGACCTGGAAGACACACACTGACAAAATG  7605180

Query  23837    agcgttttccaaagtctgttacaagttggaatgcttttataagaaaggttgaaagaaggg  23896
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605179  AGCGTTTTCCAAAGTCTGTTACAAGTTGGAATGCTTTTATAAGAAAGGTTGAAAGAAGGG  7605120

Query  23897    aatgggactcctcctatcagttgttttttttttttaattttcttttgttttatcctggca  23956
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605119  AATGGGACTCCTCCTATCAGTTGTTTTTTTTTTTTAATTTTCTTTTGTTTTATCCTGGCA  7605060

Query  23957    aggctctaatagagttgagcttttttgtttttgttttttccattggaagggacaatacag  24016
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7605059  AGGCTCTAATAGAGTTGAGCTTTTTTGTTTTTGTTTTTTCCATTGGAAGGGACAATACAG  7605000

Query  24017    aggttacaatcattgactttagatgacaacatgacaggcaaaaatattttccttgcaaga  24076
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604999  AGGTTACAATCATTGACTTTAGATGACAACATGACAGGCAAAAATATTTTCCTTGCAAGA  7604940

Query  24077    caaccagcaaaacttcacgatcagaatcaaatcagtgtccttctcactgtcactgggtga  24136
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604939  CAACCAGCAAAACTTCACGATCAGAATCAAATCAGTGTCCTTCTCACTGTCACTGGGTGA  7604880

Query  24137    agccttcatcagtacttgaagagtctcaggcactcatgaagtcaagatcagattctttac  24196
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604879  AGCCTTCATCAGTACTTGAAGAGTCTCAGGCACTCATGAAGTCAAGATCAGATTCTTTAC  7604820

Query  24197    tcagggacaggatgtaagccaatcataagaccttccacagatgatcaatttggaagtcta  24256
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604819  TCAGGGACAGGATGTAAGCCAATCATAAGACCTTCCACAGATGATCAATTTGGAAGTCTA  7604760

Query  24257    cctaatgtgacctgcaggttttcaCTGGCAATATGCAGGTGCAGATATGACAAAGAATAA  24316
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604759  CCTAATGTGACCTGCAGGTTTTCACTGGCAATATGCAGGTGCAGATATGACAAAGAATAA  7604700

Query  24317    TCCTGACCTTCATATCGCCCCTAGCTGATGAGGATTGGGATTCTTTTGTCCCTTTCTCTC  24376
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604699  TCCTGACCTTCATATCGCCCCTAGCTGATGAGGATTGGGATTCTTTTGTCCCTTTCTCTC  7604640

Query  24377    CATAAAACCAGGTTACTCATCTTGTGTGGCAACAAAATATATGGTctacttaacagagaa  24436
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604639  CATAAAACCAGGTTACTCATCTTGTGTGGCAACAAAATATATGGTCTACTTAACAGAGAA  7604580

Query  24437    agagactccacaggaaaaaaaaaaggatttttattatgaaatgagcaaagccatgggaat  24496
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604579  AGAGACTCCACAGGAAAAAAAAAAGGATTTTTATTATGAAATGAGCAAAGCCATGGGAAT  7604520

Query  24497    agatgtgagattattcggggaggtaaaggaagacaaaggttttgaaaggaaaaatgagga  24556
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604519  AGATGTGAGATTATTCGGGGAGGTAAAGGAAGACAAAGGTTTTGAAAGGAAAAATGAGGA  7604460

Query  24557    gaattacataaatttttttgaaagactcattcttggtcacaagtatgaaaaccaagggag  24616
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604459  GAATTACATAAATTTTTTTGAAAGACTCATTCTTGGTCACAAGTATGAAAACCAAGGGAG  7604400

Query  24617    cctcagtgcagtgttggaaagATTCCTCCTCCACCCTCTCAATAACCCCCAACACATTTA  24676
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604399  CCTCAGTGCAGTGTTGGAAAGATTCCTCCTCCACCCTCTCAATAACCCCCAACACATTTA  7604340

Query  24677    CCAAGTCTTTGTTCACTCCCAGGATTCCATTAAAACACCCAGCTCAACCCTGACCAGCCT  24736
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604339  CCAAGTCTTTGTTCACTCCCAGGATTCCATTAAAACACCCAGCTCAACCCTGACCAGCCT  7604280

Query  24737    CCACCTTCACTTCCCTTTGTAATTTTGACATAAATTtgttacaggaccatcaggttccta  24796
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604279  CCACCTTCACTTCCCTTTGTAATTTTGACATAAATTTGTTACAGGACCATCAGGTTCCTA  7604220

Query  24797    tgccggctgcacagtagcttaccaatattctgagacagcaggatttgcagcagaaagttt  24856
                ||||||||||||||||||||| ||||||| |||||||||||| |||||||||||||||||
Sbjct  7604219  TGCCGGCTGCACAGTAGCTTAGCAATATTGTGAGACAGCAGGGTTTGCAGCAGAAAGTTT  7604160

Query  24857    aatgatcacagggtggctgaatgagaagctgggaggagatcctcaaattcatctccccaa  24916
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604159  AATGATCACAGGGTGGCTGAATGAGAAGCTGGGAGGAGATCCTCAAATTCATCTCCCCAA  7604100

Query  24917    ggagtactgagggtttccagtggatcctggatagcaaggggctggaaagttggtgtagtt  24976
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604099  GGAGTACTGAGGGTTTCCAGTGGATCCTGGATAGCAAGGGGCTGGAAAGTTGGTGTAGTT  7604040

Query  24977    tgatggcaataagaggtatgaagttatcacgatgtcagaacggcattctttggtgagttg  25036
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7604039  TGATGGCAATAAGAGGTATGAAGTTATCACGATGTCAGAACGGCATTCTTTGGTGAGTTG  7603980

Query  25037    atgccttgcagggcccttcagatcagctggcatcagtagtttcactgacatgcagaacct  25096
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603979  ATGCCTTGCAGGGCCCTTCAGATCAGCTGGCATCAGTAGTTTCACTGACATGCAGAACCT  7603920

Query  25097    gaaagaatatctcaaatgaaaaacttaatgtttcacaatgcttaaattgttgtctgcagc  25156
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603919  GAAAGAATATCTCAAATGAAAAACTTAATGTTTCACAATGCTTAAATTGTTGTCTGCAGC  7603860

Query  25157    gtagttaaggggaattgtagtctaagttctacacgattttgggacagtaggctgccagca  25216
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603859  GTAGTTAAGGGGAATTGTAGTCTAAGTTCTACACGATTTTGGGACAGTAGGCTGCCAGCA  7603800

Query  25217    accatgaggaagcaggtcagagggcaagctgacctcctggtgaatgctgaatgcgtttca  25276
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603799  ACCATGAGGAAGCAGGTCAGAGGGCAAGCTGACCTCCTGGTGAATGCTGAATGCGTTTCA  7603740

Query  25277    agcttggtttgtttttgttcctccccctctctttttcaccgattaaatttataaagttta  25336
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603739  AGCTTGGTTTGTTTTTGTTCCTCCCCCTCTCTTTTTCACCGATTAAATTTATAAAGTTTA  7603680

Query  25337    gaaatacggtttcaATTTCTTCCAGACAAGCCTTAACCTAAGCCCTGAGACCACTCAAGC  25396
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603679  GAAATACGGTTTCAATTTCTTCCAGACAAGCCTTAACCTAAGCCCTGAGACCACTCAAGC  7603620

Query  25397    CCTCAGTGGCACCTCTCTTCCACCAGCATGAGCAAATAAATTGCTACCTTAGGTGATATA  25456
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603619  CCTCAGTGGCACCTCTCTTCCACCAGCATGAGCAAATAAATTGCTACCTTAGGTGATATA  7603560

Query  25457    AAACCCACAAGATGATTCGATACATGGAGttttttttCTGATTTTGTAGGGATGACTTCT  25516
                |||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603559  AAACCCACAAGACGATTCGATACATGGAGTTTTTTTTCTGATTTTGTAGGGATGACTTCT  7603500

Query  25517    TTGTTTCTATAAAGCTGTTTTAACTATAAAACAATTTTATAATTTTGATGTGGCCAAAGA  25576
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603499  TTGTTTCTATAAAGCTGTTTTAACTATAAAACAATTTTATAATTTTGATGTGGCCAAAGA  7603440

Query  25577    TCTCCCAACACTACTTTCAGGTTTTATTTTTCTGTCTACTATCCAGAACAGATCAAACCC  25636
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603439  TCTCCCAACACTACTTTCAGGTTTTATTTTTCTGTCTACTATCCAGAACAGATCAAACCC  7603380

Query  25637    TTCCCTGCCTCAAACTCAGGACTATATAGGTCATATATCAGTAAAATTCCATCAGTGTTT  25696
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603379  TTCCCTGCCTCAAACTCAGGACTATATAGGTCATATATCAGTAAAATTCCATCAGTGTTT  7603320

Query  25697    GCGGAgttcatgaatgaatgaattctttttttttttttttttttttttttttgtgacaaa  25756
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603319  GCGGAGTTCATGAATGAATGAATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTGTGACAAA  7603260

Query  25757    gtctacctctgtcacccagaacggtgtgcaatggtgcaatcttggctcactgcaaccatt  25816
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603259  GTCTACCTCTGTCACCCAGAACGGTGTGCAATGGTGCAATCTTGGCTCACTGCAACCATT  7603200

Query  25817    gccccctggattcaagcgattctcccacctcagcctcctgagtagctggattacaggcac  25876
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603199  GCCCCCTGGATTCAAGCGATTCTCCCACCTCAGCCTCCTGAGTAGCTGGATTACAGGCAC  7603140

Query  25877    ctgccatcatgccaggctaatttttgtgtttttgtagagctggggtttcatcatgttggc  25936
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603139  CTGCCATCATGCCAGGCTAATTTTTGTGTTTTTGTAGAGCTGGGGTTTCATCATGTTGGC  7603080

Query  25937    cttgcaggtcttgatcgcctgacctcaggtgatccagccaacttggactctcaaagtgca  25996
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603079  CTTGCAGGTCTTGATCGCCTGACCTCAGGTGATCCAGCCAACTTGGACTCTCAAAGTGCA  7603020

Query  25997    gggattacaggtgtgagccacctcacccggcctttaatgaGTGAATTCTTGATTTCCACC  26056
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603019  GGGATTACAGGTGTGAGCCACCTCACCCGGCCTTTAATGAGTGAATTCTTGATTTCCACC  7602960

Query  26057    CTATTCCTAACACTGTCAATTTCTTGATTCATGAACTTAATATGGATAGCTGATATGAAT  26116
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602959  CTATTCCTAACACTGTCAATTTCTTGATTCATGAACTTAATATGGATAGCTGATATGAAT  7602900

Query  26117    GGATATCTGATTCAATCCAGTAATCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGG  26176
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602899  GGATATCTGATTCAATCCAGTAATCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGG  7602840

Query  26177    GTGGAGCTTCAGAAATGCAATCAGATAGCACTTTTTGATTGGAAGCAAGCACTGGATAGA  26236
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602839  GTGGAGCTTCAGAAATGCAATCAGATAGCACTTTTTGATTGGAAGCAAGCACTGGATAGA  7602780

Query  26237    TGGAGGGGTGTGGGTGGGAGTTGTGATTAGAAAGATCGATAAAAGTTTCTGAAGGCCCAC  26296
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602779  TGGAGGGGTGTGGGTGGGAGTTGTGATTAGAAAGATCGATAAAAGTTTCTGAAGGCCCAC  7602720

Query  26297    AGGAGAGACCCAAAGTCTTCAAGTCTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTAAGC  26356
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602719  AGGAGAGACCCAAAGTCTTCAAGTCTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTAAGC  7602660

Query  26357    ACTCTGCAAACTCAGTCCAGATCTAGTAAGTCACTCATTTCTGGAAGGACACTCCCATCT  26416
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602659  ACTCTGCAAACTCAGTCCAGATCTAGTAAGTCACTCATTTCTGGAAGGACACTCCCATCT  7602600

Query  26417    GACCTATAGTCAGCCGGTCTGGGACGGGGGCAATGCAGCCTATGATGGCACCGAGCTATA  26476
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602599  GACCTATAGTCAGCCGGTCTGGGACGGGGGCAATGCAGCCTATGATGGCACCGAGCTATA  7602540

Query  26477    TCTGTCTTTtatatatatatatatGAACAATTTGAAGATTTGAATTTTTTCCTCTATATG  26536
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602539  TCTGTCTTTTATATATATATATATGAACAATTTGAAGATTTGAATTTTTTCCTCTATATG  7602480

Query  26537    CAGTTTTGTCTTTATTTCAAAAAATTGGATTGTGCTTTGGTTTATGTCATTTcaaaattc  26596
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602479  CAGTTTTGTCTTTATTTCAAAAAATTGGATTGTGCTTTGGTTTATGTCATTTCAAAATTC  7602420

Query  26597    ttgatgggagcaatgactcatgcccataacctcaacaccttgggaggccaaagcgggagg  26656
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602419  TTGATGGGAGCAATGACTCATGCCCATAACCTCAACACCTTGGGAGGCCAAAGCGGGAGG  7602360

Query  26657    atcatttgagcccaggggtttgagaccaacctgggcaacatggcaaaaatgcagctctac  26716
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602359  ATCATTTGAGCCCAGGGGTTTGAGACCAACCTGGGCAACATGGCAAAAATGCAGCTCTAC  7602300

Query  26717    aaaacattctttttttgaagcagggatggagtctcaccctgttgccaaggctggagtgca  26776
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602299  AAAACATTCTTTTTTTGAAGCAGGGATGGAGTCTCACCCTGTTGCCAAGGCTGGAGTGCA  7602240

Query  26777    gtggcaagagctcaactcactgcaacctcttcctcccaggctcaaacaattttcatgtct  26836
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602239  GTGGCAAGAGCTCAACTCACTGCAACCTCTTCCTCCCAGGCTCAAACAATTTTCATGTCT  7602180

Query  26837    cagcttcctgagtagctggtattacatccctctgccaccatgtctgcttaatttttgtat  26896
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602179  CAGCTTCCTGAGTAGCTGGTATTACATCCCTCTGCCACCATGTCTGCTTAATTTTTGTAT  7602120

Query  26897    ttttagtagtggtggggtttcaccatgctggccaggttggtctcaaactcctgacatcaa  26956
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7602119  TTTTAGTAGTGGTGGGGTTTCACCATGCTGGCCAGGTTGGTCTCAAACTCCTGACATCAA  7602060

Query  26957    gtgatcctcctgcctaggcccccaaaagtgctggaatgacggccgtgagccaATGGTGGT  27016
                ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct  7602059  GTGATCCTCCTGCCTAGGCCCCCGAAAGTGCTGGAATGACGGCCGTGAGCCAATGGTGGT  7602000

Query  27017    CAGCctctacaaaatatatatatcttttaatttgccaggcatggtagcatgcatctgtat  27076
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601999  CAGCCTCTACAAAATATATATATCTTTTAATTTGCCAGGCATGGTAGCATGCATCTGTAT  7601940

Query  27077    tcccagctatttggtttgctgacatgggagaatcacttgagcccagaagattgaggctgc  27136
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601939  TCCCAGCTATTTGGTTTGCTGACATGGGAGAATCACTTGAGCCCAGAAGATTGAGGCTGC  7601880

Query  27137    agtgagccatgctcacaccactgctgtactccagcctgggcaacagagtaagaccctgct  27196
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601879  AGTGAGCCATGCTCACACCACTGCTGTACTCCAGCCTGGGCAACAGAGTAAGACCCTGCT  7601820

Query  27197    aaaaacaaaaacgaaaacaaacaaacaaaaaacCTTAACCAAAGAGAATCTTTGACCTTA  27256
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601819  AAAAACAAAAACGAAAACAAACAAACAAAAAACCTTAACCAAAGAGAATCTTTGACCTTA  7601760

Query  27257    ATTTTAAACCAATCACATCCTCACTGTAATTCTTCCTCCCGAATGGAGACATgggtgtga  27316
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601759  ATTTTAAACCAATCACATCCTCACTGTAATTCTTCCTCCCGAATGGAGACATGGGTGTGA  7601700

Query  27317    gggtgcatgcctgtaatcccagctacatggaaggctgaagcatgagaattgcttgaatct  27376
                |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
Sbjct  7601699  GGGTGCATGCCTGTAATCCCAGCTACGTGGAAGGCTGAAGCATGAGAATTGCTTGAATCT  7601640

Query  27377    cagaggcggaagttacagtgagctgagatggagccgctgcactccagcctgggcgacaaa  27436
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601639  CAGAGGCGGAAGTTACAGTGAGCTGAGATGGAGCCGCTGCACTCCAGCCTGGGCGACAAA  7601580

Query  27437    gtgagactcagcttcacccacaccaaaaaaaaTTAGATTATACCACCCAGGTGATCACTG  27496
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601579  GTGAGACTCAGCTTCACCCACACCAAAAAAAATTAGATTATACCACCCAGGTGATCACTG  7601520

Query  27497    GATACATGAAGATTTCTATTGTGTGTTATTGGGGACTGTCAACTCCGTCTTTGAAAACTG  27556
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601519  GATACATGAAGATTTCTATTGTGTGTTATTGGGGACTGTCAACTCCGTCTTTGAAAACTG  7601460

Query  27557    TTTTAACTCTGAAATATTTTGATAAATTTGATGTGGCCAAGGATCCCTCAACAAAGATAC  27616
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601459  TTTTAACTCTGAAATATTTTGATAAATTTGATGTGGCCAAGGATCCCTCAACAAAGATAC  7601400

Query  27617    TTTCAAGTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGATTCAACACTTCCCTATCTCA  27676
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601399  TTTCAAGTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGATTCAACACTTCCCTATCTCA  7601340

Query  27677    CACTCAGGACTATGAAGGACACATATTAGTAAACCTCCATGTTTGTGGAGGGAATCAGTG  27736
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601339  CACTCAGGACTATGAAGGACACATATTAGTAAACCTCCATGTTTGTGGAGGGAATCAGTG  7601280

Query  27737    AATGAGTCCTGGACTTTCACCCTATCCCTAAATCTTTCACTTTCATGGATGAATATCTAA  27796
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601279  AATGAGTCCTGGACTTTCACCCTATCCCTAAATCTTTCACTTTCATGGATGAATATCTAA  7601220

Query  27797    TTCAATCAGTTAATCTGGAAGAAAGCCAAAAATCCAATCAGGATTAACTGGGTAGAGTTT  27856
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601219  TTCAATCAGTTAATCTGGAAGAAAGCCAAAAATCCAATCAGGATTAACTGGGTAGAGTTT  7601160

Query  27857    AAGAAGTCGAATCAAATGTAGTtctctctctctctctctctct-t-tt--cttttctttt  27912
                ||||||||||||||||||||||||||||||||||||||||||| | ||  ||||||||||
Sbjct  7601159  AAGAAGTCGAATCAAATGTAGTTCTCTCTCTCTCTCTCTCTCTCTCTTTTCTTTTCTTTT  7601100

Query  27913    ttttttttttttttttgaatctagcctatttcacaggctggagtgcagtggtgtattgtc  27972
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601099  TTTTTTTTTTTTTTTTGAATCTAGCCTATTTCACAGGCTGGAGTGCAGTGGTGTATTGTC  7601040

Query  27973    agctcactgcaacctctgcctcctgggttcaagtgatcctcctgcctcagcctccctagt  28032
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7601039  AGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGTGATCCTCCTGCCTCAGCCTCCCTAGT  7600980

Query  28033    agcttggactataggcgcagaccaccgcacctggctaatttttctaattttggtagaggt  28092
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600979  AGCTTGGACTATAGGCGCAGACCACCGCACCTGGCTAATTTTTCTAATTTTGGTAGAGGT  7600920

Query  28093    agggttttaccatgttggccaggctggtctcaaactcctgacctcagataatccacctgc  28152
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600919  AGGGTTTTACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGATAATCCACCTGC  7600860

Query  28153    ctctgcctcccagagggctgggattacaggtgtgagtcactgcacacagccAAAGTGGTT  28212
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600859  CTCTGCCTCCCAGAGGGCTGGGATTACAGGTGTGAGTCACTGCACACAGCCAAAGTGGTT  7600800

Query  28213    CATTTTGAATATGTGTGAGAGGTGTGTATTGGAAACATCTGTGTCTTGCCAATGATGCAT  28272
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600799  CATTTTGAATATGTGTGAGAGGTGTGTATTGGAAACATCTGTGTCTTGCCAATGATGCAT  7600740

Query  28273    AACACTGTCACATAGCTTTCAAAGCTTCTTGCTGAAATTTTCAATAATGAGACCAGgcag  28332
                |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Sbjct  7600739  AACACTGTCACATAGCTTTCAAAGCTTCTTGCTGAAATTTTCAATAATGACACCAGGCAG  7600680

Query  28333    aggctcatgcctgcaatcccagcactttgggaggccaaagtgggtggattgtttgagtct  28392
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600679  AGGCTCATGCCTGCAATCCCAGCACTTTGGGAGGCCAAAGTGGGTGGATTGTTTGAGTCT  7600620

Query  28393    aggagttcaagaccagcctggacaacatagtgaaacccactgtctttacaaaaagtcaaa  28452
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600619  AGGAGTTCAAGACCAGCCTGGACAACATAGTGAAACCCACTGTCTTTACAAAAAGTCAAA  7600560

Query  28453    aaataaaaGATTAGCTGGGTACGAGATCTGAGCTTCAGAGATCCTCGGTAACATTTGCCA  28512
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600559  AAATAAAAGATTAGCTGGGTACGAGATCTGAGCTTCAGAGATCCTCGGTAACATTTGCCA  7600500

Query  28513    GTGCTATGAGTTTAGTGGATCAGTGGCTAATAATTCATGGACTACGAGGGATCTTGCCTG  28572
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600499  GTGCTATGAGTTTAGTGGATCAGTGGCTAATAATTCATGGACTACGAGGGATCTTGCCTG  7600440

Query  28573    CTCTTTAGAAGTTGGGACACATTCTTCATGGTACCAGAAGGGTAGAACTATGTCTCTGTG  28632
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600439  CTCTTTAGAAGTTGGGACACATTCTTCATGGTACCAGAAGGGTAGAACTATGTCTCTGTG  7600380

Query  28633    GCCACTTATTGCAGAAAGGAACTGGAGTAAACTGAGGGCTCTTTCACACATGCTAGAGAA  28692
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600379  GCCACTTATTGCAGAAAGGAACTGGAGTAAACTGAGGGCTCTTTCACACATGCTAGAGAA  7600320

Query  28693    ATGACTTGGGCCCTGGGAGAATTGGGGGTTGCAGGGGATTGGTCGGAGGAACTTGCCTTT  28752
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600319  ATGACTTGGGCCCTGGGAGAATTGGGGGTTGCAGGGGATTGGTCGGAGGAACTTGCCTTT  7600260

Query  28753    TTGCTGGATTGTGCTGTAGAGTTTTTCCTTGTAGATTTGTCAGAATGAGCCTCCAGACCC  28812
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600259  TTGCTGGATTGTGCTGTAGAGTTTTTCCTTGTAGATTTGTCAGAATGAGCCTCCAGACCC  7600200

Query  28813    CATCCAGACTCCTGGAGCTGGCAGGGCAGAGCCTGATGAGGAAGCAGTTCTTGACTATCT  28872
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600199  CATCCAGACTCCTGGAGCTGGCAGGGCAGAGCCTGATGAGGAAGCAGTTCTTGACTATCT  7600140

Query  28873    TCACCCTGGACTAGCTGCCCAGGGAGGTCTCCCCTCTGACGTTCATGGAGGCCTTCAGCA  28932
                ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||
Sbjct  7600139  TCACCCTGGACTAGCTGCCCAGGGAGGTCTCCCCTCTGATGTTCATGGAGGCCTTCAGCA  7600080

Query  28933    TGAGATGTTGTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGTCCTCCCTTCACCTCCCTC  28992
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600079  TGAGATGTTGTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGTCCTCCCTTCACCTCCCTC  7600020

Query  28993    TGGGATCCCTGATGAAGACAACTCATCTGGAGACCTTGCAAGCTGTGCTGAAGGGACTTG  29052
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7600019  TGGGATCCCTGATGAAGACAACTCATCTGGAGACCTTGCAAGCTGTGCTGAAGGGACTTG  7599960

Query  29053    ATACACTAGTGTCCCAGAAGGTTTGCCCCAGTTGAGGTGACTCAGGTGGCCTGGTGGGAA  29112
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7599959  ATACACTAGTGTCCCAGAAGGTTTGCCCCAGTTGAGGTGACTCAGGTGGCCTGGTGGGAA  7599900

Query  29113    GGGTCCAGGCATCCAGGGAAGGGACAGCTGGCTCAGGAGGAGTGGCAGTGTGTGGGAGCT  29172
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7599899  GGGTCCAGGCATCCAGGGAAGGGACAGCTGGCTCAGGAGGAGTGGCAGTGTGTGGGAGCT  7599840

Query  29173    AGGGTGGCTCAGAGGCTTCTGATGGTACCCATGAGAGGCCTTGGCCATTGCCCAGATCCT  29232
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7599839  AGGGTGGCTCAGAGGCTTCTGATGGTACCCATGAGAGGCCTTGGCCATTGCCCAGATCCT  7599780

Query  29233    CTGGAAAAGGACTGCTCACCATACAGAGTCCACTGAGGAAACAGGAACCTGCTTCCTTCC  29292
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Sbjct  7599779  CTGGAAAAGGACTGCTCACCATACAGAGTCCACTGAGGAAACAGGAACCTGCTTCCT-CC  7599721

Query  29293    CAGTGGAAGGTAAAGGTACTAGAAGTGGGTAC  29324
                ||||||||||||||||||||||||||||||||
Sbjct  7599720  CAGTGGAAGGTAAAGGTACTAGAAGTGGGTAC  7599689


 Score = 2.185e+04 bits (11833),  Expect = 0.0
 Identities = 11907/11939 (99%), Gaps = 19/11939 (0%)
 Strand=Plus/Plus

Query  1        CCGTGCCGTTTTTTATTCCTTCCACAGGTGCTTCTACTTTAAGCTTCAAGCCTTCTCTTC  60
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7586883  CCGTGCCGTTTTTTATTCCTTCCACAGGTGCTTCTACTTTAAGCTTCAAGCCTTCTCTTC  7586942

Query  61       CATTCTGGGCCttcttgatgctttggggtgcctcccgcaggtgcaacacgcactgtgggt  120
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7586943  CATTCTGGGCCTTCTTGATGCTTTGGGGTGCCTCCCGCAGGTGCAACACGCACTGTGGGT  7587002

Query  121      gtgaaccagggatgccaggatcccccgggccctgtgcagggtctgctgggagggcacttt  180
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7587003  GTGAACCAGGGATGCCAGGATCCCCCGGGCCCTGTGCAGGGTCTGCTGGGAGGGCACTTT  7587062

Query  181      catccgtgggttgacccaggccccccttctcgactgcgccatttttttccttccacaggt  240
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7587063  CATCCGTGGGTTGACCCAGGCCCCCCTTCTCGACTGCGCCATTTTTTTCCTTCCACAGGT  7587122

Query  241      gcctctacctcccctttcaaaccttatcttcccttctgggctttcttgccccttccgggt  300
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7587123  GCCTCTACCTCCCCTTTCAAACCTTATCTTCCCTTCTGGGCTTTCTTGCCCCTTCCGGGT  7587182

Query  301      gcccccaccaccatgacaggcaacgtgggtgtgatccagggatgccagaaatcccgggga  360
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7587183  GCCCCCACCACCATGACAGGCAACGTGGGTGTGATCCAGGGATGCCAGAAATCCCGGGGA  7587242

Query  361      ctccgtaggggctgctgggaaggcacattcttctgtggggggacccaagcacccctcctc  420
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7587243  CTCCGTAGGGGCTGCTGGGAAGGCACATTCTTCTGTGGGGGGACCCAAGCACCCCTCCTC  7587302

Query  421      tacggtgcccatttttttcctccacaggtgcctctacctcccctttcaagtcttgtcttc  480
                |||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Sbjct  7587303  TACGGTGCCCATTTTTTTCCTCCACAGGTGCCTCTACCTCCCCTTTCACGTCTTGTCTTC  7587362

Query  481      ctttctgggcttgctagaagctttggggtgccccccataggtgcgatatgcagcgtgggt  540
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7587363  CTTTCTGGGCTTGCTAGAAGCTTTGGGGTGCCCCCCATAGGTGCGATATGCAGCGTGGGT  7587422

Query  541      gtgaaccagggacgccaggatccccggggcccagtgcagggtctgctaggaagggacttt  600
                |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct  7587423  GTGAACCAGGGACGCCAGGATCCCTGGGGCCCAGTGCAGGGTCTGCTAGGAAGGGACTTT  7587482

Query  601      cgtctgtgggtggacccaggccctccatctcagccccaccatttttttttttccttccac  660
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7587483  CGTCTGTGGGTGGACCCAGGCCCTCCATCTCAGCCCCACCATTTTTTTTTTTCCTTCCAC  7587542

Query  661      aggttcctctacctcccctttctagcattaactgccattatgggccttcttggaagtgct  720
                ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct  7587543  AGGTTCCTCTACCTCCCCTTTATAGCATTAACTGCCATTATGGGCCTTCTTGGAAGTGCT  7587602

Query  721      gggaactgcagaaccacaaaaagggaatcacagccctggctcaggaagctcccacgtctg  780
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7587603  GGGAACTGCAGAACCACAAAAAGGGAATCACAGCCCTGGCTCAGGAAGCTCCCACGTCTG  7587662

Query  781      ggctcctgaaaagagtagtagctcttctctttttctcttcacctacaacttggtgagcaa  840
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7587663  GGCTCCTGAAAAGAGTAGTAGCTCTTCTCTTTTTCTCTTCACCTACAACTTGGTGAGCAA  7587722

Query  841      ggggcgtgtttcagctttgtttgtgttactgcttttagccccaccattaggcgggtcttg  900
                ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7587723  GGGGCATGTTTCAGCTTTGTTTGTGTTACTGCTTTTAGCCCCACCATTAGGCGGGTCTTG  7587782

Query  901      tcctgcaaccaggaagaatgaaatatgcagacaagtggagagtgagcaagataaagagga  960
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7587783  TCCTGCAACCAGGAAGAATGAAATATGCAGACAAGTGGAGAGTGAGCAAGATAAAGAGGA  7587842

Query  961      cctttattgagcaatagaatggggaaggggggacctcctgggcCCTCGAGAGCACTAGGG  1020
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7587843  CCTTTATTGAGCAATAGAATGGGGAAGGGGGGACCTCCTGGGCCCTCGAGAGCACTAGGG  7587902

Query  1021     GACCTTGTTTGGTAACTGCAACCTGGGCAGCTTCAGTTGTGCCTTTggagctactgccct  1080
                |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
Sbjct  7587903  GACCTTGTTTGGTAACTGCAACCTGGGCAGCTTCAGTTGTGCCTTTGGAGCTACGGCCCT  7587962

Query  1081     gccaacttgggaggaccaggactccctcttgtcccaggatcccatcagctccaaagtgtg  1140
                ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7587963  GCCGACTTGGGAGGACCAGGACTCCCTCTTGTCCCAGGATCCCATCAGCTCCAAAGTGTG  7588022

Query  1141     cacagcctcagctttgcCCTCTCTCTGTTTCCGTGCAGAGGTGACAGGTGAGATGCAGGT  1200
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588023  CACAGCCTCAGCTTTGCCCTCTCTCTGTTTCCGTGCAGAGGTGACAGGTGAGATGCAGGT  7588082

Query  1201     TCACAGCAGCTCTGGTCAACCCCACAGAAACAAATCTGAAGCTCCTGGGTCCGGTTTAAT  1260
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588083  TCACAGCAGCTCTGGTCAACCCCACAGAAACAAATCTGAAGCTCCTGGGTCCGGTTTAAT  7588142

Query  1261     GAGCCCCAACTGCGCTCTGATCCAGGAGTTTGCAGGCTAACAGCACAAAGTGGGGAGTGA  1320
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588143  GAGCCCCAACTGCGCTCTGATCCAGGAGTTTGCAGGCTAACAGCACAAAGTGGGGAGTGA  7588202

Query  1321     GGTCGAGGCTGTGGTGGAGACTGCGGACCTAGGGGCAAGTCCCGTTTAGCCGTGAGAGGG  1380
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588203  GGTCGAGGCTGTGGTGGAGACTGCGGACCTAGGGGCAAGTCCCGTTTAGCCGTGAGAGGG  7588262

Query  1381     TATGGGTGGCACAGTTGGCTGCCTCAGGGACATGGGGCACAGGCCTGGCTGACAACCCAG  1440
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588263  TATGGGTGGCACAGTTGGCTGCCTCAGGGACATGGGGCACAGGCCTGGCTGACAACCCAG  7588322

Query  1441     CCAAGAGGTGGTGCCTTTAGGAGTGGATCGTGGTCCACAGGCCCAGCAATCGGAAGCATC  1500
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588323  CCAAGAGGTGGTGCCTTTAGGAGTGGATCGTGGTCCACAGGCCCAGCAATCGGAAGCATC  7588382

Query  1501     AGGCTCTGTGTTCACCCCTCTTGGGGGCAGATCTTGGAAATGCAGCCTCAGGAAGATTCA  1560
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588383  AGGCTCTGTGTTCACCCCTCTTGGGGGCAGATCTTGGAAATGCAGCCTCAGGAAGATTCA  7588442

Query  1561     CACAGAACTCCTTTTTAGACCTAGGAACTTGATACTATTAGCAGGGTGGGCACACAGTTG  1620
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588443  CACAGAACTCCTTTTTAGACCTAGGAACTTGATACTATTAGCAGGGTGGGCACACAGTTG  7588502

Query  1621     ATGCATAGCTGGCCAGGTCATTGAACTTGGTGCCATTTCTGCTTCCCAACTCGGGGCCCT  1680
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588503  ATGCATAGCTGGCCAGGTCATTGAACTTGGTGCCATTTCTGCTTCCCAACTCGGGGCCCT  7588562

Query  1681     GGAGCATGGCCCCAGCTCTGCCTTTGGAACCTGACAACCACACTTCATGTGCAAGCACGG  1740
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588563  GGAGCATGGCCCCAGCTCTGCCTTTGGAACCTGACAACCACACTTCATGTGCAAGCACGG  7588622

Query  1741     CACCACCCCAAGCCCATCTTCTCCTCATGGCCCCTTTCTGCCTGTGCCTTTGTGCCCGAC  1800
                |||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||
Sbjct  7588623  CACCACCCCAAGCCCATCTTCTCCTCATGGCCTCTTTCTGCCTGTGCCTTTGTGCCCGAC  7588682

Query  1801     CGAGCTGCTCCCCACAGTCGAAAAAGTATGAAAAAACAGATGACTAAAGAGAAGTAAAGG  1860
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588683  CGAGCTGCTCCCCACAGTCGAAAAAGTATGAAAAAACAGATGACTAAAGAGAAGTAAAGG  7588742

Query  1861     ATGGGTGCAGACCATTCGcacacctgtaatcccagcactttgggaggccaaggttggcgg  1920
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588743  ATGGGTGCAGACCATTCGCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGTTGGCGG  7588802

Query  1921     atcactcaaagccaggaactcaagaccagcctggtgaacagggtaaaaccctgtctctac  1980
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588803  ATCACTCAAAGCCAGGAACTCAAGACCAGCCTGGTGAACAGGGTAAAACCCTGTCTCTAC  7588862

Query  1981     gaaaaatacaaaaattagcaggcttggtggcacgtgcctgtactcccagctacttgagtg  2040
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588863  GAAAAATACAAAAATTAGCAGGCTTGGTGGCACGTGCCTGTACTCCCAGCTACTTGAGTG  7588922

Query  2041     gttgaggcacgagaatcacttgagccccacaggaaaggattccagtgatcccagattgca  2100
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588923  GTTGAGGCACGAGAATCACTTGAGCCCCACAGGAAAGGATTCCAGTGATCCCAGATTGCA  7588982

Query  2101     ccactacactccagcctgaatgacaaagcaatatttttgtctccaaaaataaaaaaataa  2160
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7588983  CCACTACACTCCAGCCTGAATGACAAAGCAATATTTTTGTCTCCAAAAATAAAAAAATAA  7589042

Query  2161     ataatgaaataaaaGAACAAGAATGGGTGGGAATTACTCAAAATGGTCTAATTTTATTTG  2220
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589043  ATAATGAAATAAAAGAACAAGAATGGGTGGGAATTACTCAAAATGGTCTAATTTTATTTG  7589102

Query  2221     GCTGCTATGATGTTCCGCAGCTGAACCTCAATCACAGACAAACTAGTGCCTCGTTATTTT  2280
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589103  GCTGCTATGATGTTCCGCAGCTGAACCTCAATCACAGACAAACTAGTGCCTCGTTATTTT  7589162

Query  2281     TCCATCAGTAACTCAATAACTAGAGATTTCTGATGTATAAATCCCTAAAACAAGTAAATC  2340
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589163  TCCATCAGTAACTCAATAACTAGAGATTTCTGATGTATAAATCCCTAAAACAAGTAAATC  7589222

Query  2341     AATTACAGAGGACACCAGAAAGTTTTCACTGAGGTTCTCTATTTCTGATATTTCTTGGTA  2400
                 ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct  7589223  TATTACAGAGGACACCAGAAGGTTTTCACTGAGGTTCTCTATTTCTGATATTTCTTGGTA  7589282

Query  2401     ATCATCCTTGCAGGGATAACATTCTCATCACTGAAGAATTTTAGTTTCTCTTTCTGACTC  2460
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589283  ATCATCCTTGCAGGGATAACATTCTCATCACTGAAGAATTTTAGTTTCTCTTTCTGACTC  7589342

Query  2461     TGTAGCTCTCATTGACTCCACCTCAATATTTTCCTCAAGTCTTGCCCCCTGCTCTTAGGA  2520
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589343  TGTAGCTCTCATTGACTCCACCTCAATATTTTCCTCAAGTCTTGCCCCCTGCTCTTAGGA  7589402

Query  2521     TTTTTTCCCTCGCACTGAGCACCTGTCTGAAACAGAGCTCTGTGCTTCCTTTAAGTTGCA  2580
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589403  TTTTTTCCCTCGCACTGAGCACCTGTCTGAAACAGAGCTCTGTGCTTCCTTTAAGTTGCA  7589462

Query  2581     CATGTggcctgggcacagtcgctcatgcctgtaatcccagcactttagaaggccgaggca  2640
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589463  CATGTGGCCTGGGCACAGTCGCTCATGCCTGTAATCCCAGCACTTTAGAAGGCCGAGGCA  7589522

Query  2641     ggagaatcccatgcgaccagcagtttgagacctgctggggcaacatagtgaaacactttc  2700
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589523  GGAGAATCCCATGCGACCAGCAGTTTGAGACCTGCTGGGGCAACATAGTGAAACACTTTC  7589582

Query  2701     tcaatttttttgtaataaaaatattggaattattaaaaaaggaaataagaaaagaggaaa  2760
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589583  TCAATTTTTTTGTAATAAAAATATTGGAATTATTAAAAAAGGAAATAAGAAAAGAGGAAA  7589642

Query  2761     ataaCTTGCACCTACATACTAGATTTTAGTGTCCAAGGGCCTAGAAGAGAACATTGGATT  2820
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589643  ATAACTTGCACCTACATACTAGATTTTAGTGTCCAAGGGCCTAGAAGAGAACATTGGATT  7589702

Query  2821     TCTCTACCCCGCTAGGCACGCCTTCCCTAGCAGCAAAGATGGAGCTCCAGTTCCTCAGAC  2880
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589703  TCTCTACCCCGCTAGGCACGCCTTCCCTAGCAGCAAAGATGGAGCTCCAGTTCCTCAGAC  7589762

Query  2881     GGTGATGAGCCACAGGACGGGCAGGGGGCGGGGCCAATGAAGATCCTCTTGGGCTGCCTG  2940
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589763  GGTGATGAGCCACAGGACGGGCAGGGGGCGGGGCCAATGAAGATCCTCTTGGGCTGCCTG  7589822

Query  2941     ACTTCCCTTAGTGTACACATCAACTAAGCCCGAAGTGGGGTGAAGATCTCCCAATCGACA  3000
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589823  ACTTCCCTTAGTGTACACATCAACTAAGCCCGAAGTGGGGTGAAGATCTCCCAATCGACA  7589882

Query  3001     TGAACCAAGGAATTCAAACTCTCCTCGGGGGCAGGATACATCTCCAGGCTTAACTTGCTC  3060
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589883  TGAACCAAGGAATTCAAACTCTCCTCGGGGGCAGGATACATCTCCAGGCTTAACTTGCTC  7589942

Query  3061     AGCCCACTGGTGTGGCACAGCAGGTCCTTCAGGGCTTCCATAGACATGCAATTTCTGCCA  3120
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7589943  AGCCCACTGGTGTGGCACAGCAGGTCCTTCAGGGCTTCCATAGACATGCAATTTCTGCCA  7590002

Query  3121     AAGTAGAAGGTGGTGAGCTGGGAGCAGCGGCTCAGGCCAGGCAGGATGGCACTGAGTTGG  3180
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590003  AAGTAGAAGGTGGTGAGCTGGGAGCAGCGGCTCAGGCCAGGCAGGATGGCACTGAGTTGG  7590062

Query  3181     GAGTAGTGGATCTGACAGCCCTCCAAGATGAGGGTCTTAAGAGTAATTGCTGCCTCTCTC  3240
                |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct  7590063  GAGTAGTGGATCTGACAGCCCTCCGAGATGAGGGTCTTAAGAGTAATTGCTGCCTCTCTC  7590122

Query  3241     GAGACCCTCGTGTTGGCAGAAACTTTCTCCAGCAGAGCTCCGAGGGGTTCAAGACTGATA  3300
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590123  GAGACCCTCGTGTTGGCAGAAACTTTCTCCAGCAGAGCTCCGAGGGGTTCAAGACTGATA  7590182

Query  3301     CAGAACTGCAGCATGTAGCTGAGATTCAGATGCTTTGGGTAAGCGAGGCTTGGGTACTGG  3360
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590183  CAGAACTGCAGCATGTAGCTGAGATTCAGATGCTTTGGGTAAGCGAGGCTTGGGTACTGG  7590242

Query  3361     TAGAGACACTTCAAGTCCTCTTCCAATAGGTAGCCGCAAGTTAATTCCAAGTTCTCCAAG  3420
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590243  TAGAGACACTTCAAGTCCTCTTCCAATAGGTAGCCGCAAGTTAATTCCAAGTTCTCCAAG  7590302

Query  3421     GGGTTCTAGAGGCACCTGTGGAGATCAAGAAGTTAGTTCTGGGCAATGGTACCAGTTAGA  3480
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590303  GGGTTCTAGAGGCACCTGTGGAGATCAAGAAGTTAGTTCTGGGCAATGGTACCAGTTAGA  7590362

Query  3481     TGAAGGTAGTGGGGAATGAACTCAAGGAAAATACCTGCTTCAACCAAACACAAGTTTGTT  3540
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590363  TGAAGGTAGTGGGGAATGAACTCAAGGAAAATACCTGCTTCAACCAAACACAAGTTTGTT  7590422

Query  3541     CCCACCATCTGATGATGGTCCTCATGCAAGTTGCTGCATGTTGAGGACCCTGATCATTCA  3600
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590423  CCCACCATCTGATGATGGTCCTCATGCAAGTTGCTGCATGTTGAGGACCCTGATCATTCA  7590482

Query  3601     GGGGCTGTCCCATTTTAGCCTCAGCCCTTTCACCATTTCTTGTGTGATTGGGTCAAGGCC  3660
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590483  GGGGCTGTCCCATTTTAGCCTCAGCCCTTTCACCATTTCTTGTGTGATTGGGTCAAGGCC  7590542

Query  3661     ACAAAATCTCTAAAGCCTTTTATCTTCATCTTTTAGCAGAAAACCTCATCTCTGGGCCAC  3720
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590543  ACAAAATCTCTAAAGCCTTTTATCTTCATCTTTTAGCAGAAAACCTCATCTCTGGGCCAC  7590602

Query  3721     AGGTACCCGGTGGGAGATGTGCACAAAGAACTCAACTCAGCAAGGTCTAGGGACATTAGC  3780
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590603  AGGTACCCGGTGGGAGATGTGCACAAAGAACTCAACTCAGCAAGGTCTAGGGACATTAGC  7590662

Query  3781     TGGGGCTACCTGCCGGCAGGGGCTCCCTGGCCTGCCTGCATCTGCAAACCAACTGTCACT  3840
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590663  TGGGGCTACCTGCCGGCAGGGGCTCCCTGGCCTGCCTGCATCTGCAAACCAACTGTCACT  7590722

Query  3841     TTTTACCACTCTCACTCCTACTCCTTCACCCTCCATCCCAGAAGCATGCATGTCCCATGT  3900
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590723  TTTTACCACTCTCACTCCTACTCCTTCACCCTCCATCCCAGAAGCATGCATGTCCCATGT  7590782

Query  3901     CAATTGACTTTCCTGGAGTTCAAAACAACCTTCTACAGACAGGGAATCAGAGACAGGATC  3960
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590783  CAATTGACTTTCCTGGAGTTCAAAACAACCTTCTACAGACAGGGAATCAGAGACAGGATC  7590842

Query  3961     ATTCATGATCACTAAGCTGGTGAGGACAGAGCTTCTACTGTGAAATGCACAAGTTTGATG  4020
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590843  ATTCATGATCACTAAGCTGGTGAGGACAGAGCTTCTACTGTGAAATGCACAAGTTTGATG  7590902

Query  4021     CACTGTCCCTCCTTTCATACCCTCCTTTGTTACCTCTTTTACATCATATCAACTTGAAAC  4080
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590903  CACTGTCCCTCCTTTCATACCCTCCTTTGTTACCTCTTTTACATCATATCAACTTGAAAC  7590962

Query  4081     ACACTTTGTAACAAGAAATTCACACGTGCACATGCAGTAGAGACAAAACGCCCACTAAGT  4140
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7590963  ACACTTTGTAACAAGAAATTCACACGTGCACATGCAGTAGAGACAAAACGCCCACTAAGT  7591022

Query  4141     ACCTTGTACATGATGTCCCTCTCTAGCCTCTACCCTAGGTGACCCCTCTGCCTTTATTGA  4200
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591023  ACCTTGTACATGATGTCCCTCTCTAGCCTCTACCCTAGGTGACCCCTCTGCCTTTATTGA  7591082

Query  4201     AGTGATCCTGTGATAGCCACTCCAGGACATGGAGCACTGAACGGGACAATGTGTTGACAT  4260
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591083  AGTGATCCTGTGATAGCCACTCCAGGACATGGAGCACTGAACGGGACAATGTGTTGACAT  7591142

Query  4261     TCTGGTGTCCCCTGCACTGTGCCGTCGCCACTGGCTGGCACACAGTACACGTCTTCTAGT  4320
                |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591143  TCTGGTGTTCCCTGCACTGTGCCGTCGCCACTGGCTGGCACACAGTACACGTCTTCTAGT  7591202

Query  4321     GTTTACTGTAACaaaaaaaaa-GGCTGCGCTGTGGTCTGCAGAGAAAGGGCACGATCCTT  4379
                ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct  7591203  GTTTACTGTAACAAAAAAAAAAGGCTGCGCTGTGGTCTGCAGAGAAAGGGCACGATCCTT  7591262

Query  4380     TCTCACCTGATCAGCTGTCCCAGGTGCCCTCTGTGGAAGGTGACCATATTCATTTTAAGC  4439
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591263  TCTCACCTGATCAGCTGTCCCAGGTGCCCTCTGTGGAAGGTGACCATATTCATTTTAAGC  7591322

Query  4440     AGCTGGAGGTGTTTCAGCCTGAGGAACATAGAGCTGATTTTGGCGACTGAGCATTCCTCG  4499
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591323  AGCTGGAGGTGTTTCAGCCTGAGGAACATAGAGCTGATTTTGGCGACTGAGCATTCCTCG  7591382

Query  4500     CGGTAATTGACGTGTAAGGATGGCACCTGGAGAAAAATGAGTTTGCGAAGATTCTTCATC  4559
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591383  CGGTAATTGACGTGTAAGGATGGCACCTGGAGAAAAATGAGTTTGCGAAGATTCTTCATC  7591442

Query  4560     TCCTTCAGGTAACAATGAAGCTTTCTTATCAGATGTGGCCAGGACACATAGCAAATTTCC  4619
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591443  TCCTTCAGGTAACAATGAAGCTTTCTTATCAGATGTGGCCAGGACACATAGCAAATTTCC  7591502

Query  4620     AGCTCCTGAATACTATTCAGGTGGATTATTTTCAATGATCTTCTGAGATATTCAATCGAC  4679
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591503  AGCTCCTGAATACTATTCAGGTGGATTATTTTCAATGATCTTCTGAGATATTCAATCGAC  7591562

Query  4680     GTTAGATAATTCACCAACTTACTACAGCACAGGTGTACTAAACCTCTCCTTTGGTAAACC  4739
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591563  GTTAGATAATTCACCAACTTACTACAGCACAGGTGTACTAAACCTCTCCTTTGGTAAACC  7591622

Query  4740     CACCGGAAGAGGTATCTCAGGCATTCATCCTGGGGTATTTCCTTGAGGCAGATGTCTATG  4799
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591623  CACCGGAAGAGGTATCTCAGGCATTCATCCTGGGGTATTTCCTTGAGGCAGATGTCTATG  7591682

Query  4800     AACACCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGTCTGCCTCTTA  4859
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591683  AACACCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGTCTGCCTCTTA  7591742

Query  4860     CTCATGGCCTCTGGGGAGGAGGACAGGGCCCTGGATTCAGACCATATGGCCCAGAAATTC  4919
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591743  CTCATGGCCTCTGGGGAGGAGGACAGGGCCCTGGATTCAGACCATATGGCCCAGAAATTC  7591802

Query  4920     TCATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAAAGTAAGGC  4979
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591803  TCATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAAAGTAAGGC  7591862

Query  4980     AGAGGCTCAGAACTTTGAAGGACAAATCCCTGACCTTTGCTTTCATTCTCATCCAATAAA  5039
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591863  AGAGGCTCAGAACTTTGAAGGACAAATCCCTGACCTTTGCTTTCATTCTCATCCAATAAA  7591922

Query  5040     TCAGCTGCTCCTGTCCTCGCTGCTCCCTGTTCTCTCTGAGTTTTCTTGGTCCCTTTTCTC  5099
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591923  TCAGCTGCTCCTGTCCTCGCTGCTCCCTGTTCTCTCTGAGTTTTCTTGGTCCCTTTTCTC  7591982

Query  5100     TTTCAATTCTGACTGGTCCCCACTTCTATTCCATTTACCTTCCACTGGGAATAGGCAAGT  5159
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7591983  TTTCAATTCTGACTGGTCCCCACTTCTATTCCATTTACCTTCCACTGGGAATAGGCAAGT  7592042

Query  5160     TTCTGTTCCCACAGTGGACCCTATATTGTGGGCAGTTCTTTCCCTGAGGATCTGGGCAAT  5219
                ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct  7592043  TTCTGTTCCCACAGTGGACCCTACATTGTGGGCAGTTCTTTCCCTGAGGATCTGGGCAAT  7592102

Query  5220     GGCCAAGGCATGCCTGAGCTTCGTCACCAGCACCACCAGAAGACACTGGGCCATCCTTGG  5279
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7592103  GGCCAAGGCATGCCTGAGCTTCGTCACCAGCACCACCAGAAGACACTGGGCCATCCTTGG  7592162

Query  5280     GATACTTCTTTGCCTGACCCTGCTGTTCTTTCCCTGGACACCTGAGCCCCATCTACCAGC  5339
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7592163  GATACTTCTTTGCCTGACCCTGCTGTTCTTTCCCTGGACACCTGAGCCCCATCTACCAGC  7592222

Query  5340     CTTCCTGGGTCACCTCACCTGGGGCGATCCTTCTGTGTAAGCAGCATGTGAAGCCCTTCC  5399
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7592223  CTTCCTGGGTCACCTCACCTGGGGCGATCCTTCTGTGTAAGCAGCATGTGAAGCCCTTCC  7592282

Query  5400     AGCAATGCTTTTAAGGTCTCCAGATGAAGCGTCTTCATCAGCGATCCCAGAGGGAGGCGG  5459
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7592283  AGCAATGCTTTTAAGGTCTCCAGATGAAGCGTCTTCATCAGCGATCCCAGAGGGAGGCGG  7592342

Query  5460     GTGAAGGGCCAGGCCTGCACCATCACTGTCAGAGTCTGGAAGTGTCTCCTGCTGAAGGCC  5519
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7592343  GTGAAGGGCCAGGCCTGCACCATCACTGTCAGAGTCTGGAAGTGTCTCCTGCTGAAGGCC  7592402

Query  5520     TCCAGGAAGAGTGGGAGGTAGAGCTCCCTGGGCAGCTCCTCCAGGGCAGAGATGGCCAAG  5579
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7592403  TCCAGGAAGAGTGGGAGGTAGAGCTCCCTGGGCAGCTCCTCCAGGGCAGAGATGGCCAAG  7592462

Query  5580     GGCTTGTCTCTCAGCAGACTCTGCCCCGCCAGCTCCAGGAGTCTGGGTGGGGCCTGGATG  5639
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7592463  GGCTTGTCTCTCAGCAGACTCTGCCCCGCCAGCTCCAGGAGTCTGGGTGGGGCCTGGATG  7592522

Query  5640     CTCATCCTGATGAATCTGTAAGGAAAAACTCTAGAAGACAAATCCAGAGAAAAGGCATCA  5699
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7592523  CTCATCCTGATGAATCTGTAAGGAAAAACTCTAGAAGACAAATCCAGAGAAAAGGCATCA  7592582

Query  5700     CTTTCAGGCCAAACACAATCACCTCATCTTCTCCTAAGGCCAGTAGCATTGCTCTGGTAG  5759
                |||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Sbjct  7592583  CTTTCAGGCCAAACACAATCACCTCATCTTCTCCTAAGGCCAATAGCATTGCTCTGGTAG  7592642

Query  5760     AGGTAGAAAAATTACCACTTTACCCCAATTCCACTCTGCACTTGGTGGCCACAAATCTAT  5819
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7592643  AGGTAGAAAAATTACCACTTTACCCCAATTCCACTCTGCACTTGGTGGCCACAAATCTAT  7592702

Query  5820     ATTTCTGCTTCTGCTGGTACCAGGAAGAATGTCTTCCAAACACCAAGGAGGGAGGGGTCA  5879
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7592703  ATTTCTGCTTCTGCTGGTACCAGGAAGAATGTCTTCCAAACACCAAGGAGGGAGGGGTCA  7592762

Query  5880     AAGAGACCACTGGCCCATTAATTTTCATCCATGGCTCCACTGAATCCCAGTACCACTGGA  5939
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7592763  AAGAGACCACTGGCCCATTAATTTTCATCCATGGCTCCACTGAATCCCAGTACCACTGGA  7592822

Query  5940     AAGTGTCACTGAGGATCCTGAAAGCCAAGCTCTACCTCTTTGAGGAAAATTTTCTTGTCA  5999
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7592823  AAGTGTCACTGAGGATCCTGAAAGCCAAGCTCTACCTCTTTGAGGAAAATTTTCTTGTCA  7592882

Query  6000     CTTACCGCCCTAAAGCAATGAGAATGAGAGTGTCCTGTGGCCCCAGACAGCCTCCATTCT  6059
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7592883  CTTACCGCCCTAAAGCAATGAGAATGAGAGTGTCCTGTGGCCCCAGACAGCCTCCATTCT  7592942

Query  6060     CAGTTTTCACCATGAACATGCTGGGGGAACACTAAAGGGACTCCCTAAAGTCAATGCCAT  6119
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7592943  CAGTTTTCACCATGAACATGCTGGGGGAACACTAAAGGGACTCCCTAAAGTCAATGCCAT  7593002

Query  6120     TATTTTTTATTTTGAAAAATTTCAACcagaaactgaccgggtgctgtggctcatgtctgt  6179
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593003  TATTTTTTATTTTGAAAAATTTCAACCAGAAACTGACCGGGTGCTGTGGCTCATGTCTGT  7593062

Query  6180     aatcccagcactgtgggaggccaaaacaggcagatcacttgaggttaggagttcgagaac  6239
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593063  AATCCCAGCACTGTGGGAGGCCAAAACAGGCAGATCACTTGAGGTTAGGAGTTCGAGAAC  7593122

Query  6240     agcctggcttacgtaatgaactctgtctctactaaatataaaaaaattaaaaaTCATTTG  6299
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593123  AGCCTGGCTTACGTAATGAACTCTGTCTCTACTAAATATAAAAAAATTAAAAATCATTTG  7593182

Query  6300     ACTCCAAAaggcagaggttgcagtgagccgagatcccaccactgcactccagtctggaca  6359
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593183  ACTCCAAAAGGCAGAGGTTGCAGTGAGCCGAGATCCCACCACTGCACTCCAGTCTGGACA  7593242

Query  6360     AAAGAGTTAGACTCTGTCTCAaataataataataataataataataataataataataat  6419
                |||||||||||||||||||||||||||||||||||||||||||||||||||||||||  |
Sbjct  7593243  AAAGAGTTAGACTCTGTCTCAAATAATAATAATAATAATAATAATAATAATAATAAT--T  7593300

Query  6420     taattaattaaaatGTTAGCCAGGTGTGGTGGTGCAGTCCTATAATCCTAGCTACTCTGG  6479
                 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593301  -AATTAATTAAAATGTTAGCCAGGTGTGGTGGTGCAGTCCTATAATCCTAGCTACTCTGG  7593359

Query  6480     AGGCAGAGGAAGAAGAATCACTTGAATCCCGGAGGCAGTGTTTTCAGTGAGCTGAACTCA  6539
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593360  AGGCAGAGGAAGAAGAATCACTTGAATCCCGGAGGCAGTGTTTTCAGTGAGCTGAACTCA  7593419

Query  6540     ACACCCTGCCCTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAGAGAAAAGA  6599
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593420  ACACCCTGCCCTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAGAGAAAAGA  7593479

Query  6600     ATTAACCAGAAACTAAAAGCGACGTGATGGTATTCTAGAGCATTTGGAAGGTAGGGATAG  6659
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593480  ATTAACCAGAAACTAAAAGCGACGTGATGGTATTCTAGAGCATTTGGAAGGTAGGGATAG  7593539

Query  6660     AAATACTAACTCTAGATGAggcacagtggctcactcctgtaatcccagcactttgggagt  6719
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593540  AAATACTAACTCTAGATGAGGCACAGTGGCTCACTCCTGTAATCCCAGCACTTTGGGAGT  7593599

Query  6720     ccaaggTGTGTGTTTTTATTTTGAAAAACTGTAAGAGAAATTATAAAAGCAGTGTTGCAG  6779
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593600  CCAAGGTGTGTGTTTTTATTTTGAAAAACTGTAAGAGAAATTATAAAAGCAGTGTTGCAG  7593659

Query  6780     TAGTCTAGAGCACTTGGAAGGTAGAAATGGAAACACTAAGTCTGAGGAGAAGGATCCAAT  6839
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593660  TAGTCTAGAGCACTTGGAAGGTAGAAATGGAAACACTAAGTCTGAGGAGAAGGATCCAAT  7593719

Query  6840     ACACATCCCTTCCACATACTCACAATCACACACTTAGGGACAGAGTCTAAGGGAAGAGAT  6899
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593720  ACACATCCCTTCCACATACTCACAATCACACACTTAGGGACAGAGTCTAAGGGAAGAGAT  7593779

Query  6900     AAATCCCAGGTTCGGAACAAGTCTCTTGAGAATGGTGTACGGGAGATCTAAGATTTCTGT  6959
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593780  AAATCCCAGGTTCGGAACAAGTCTCTTGAGAATGGTGTACGGGAGATCTAAGATTTCTGT  7593839

Query  6960     AAAATGAAAGCCTGACTAATAAAATCACAATACCGCTAAGTGTGTGAACTATAGCTGACA  7019
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593840  AAAATGAAAGCCTGACTAATAAAATCACAATACCGCTAAGTGTGTGAACTATAGCTGACA  7593899

Query  7020     GGCACAGAAACCAACAACTTCACATGTCAAGACATAAACATCCATCCAACTGTAAATTTT  7079
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593900  GGCACAGAAACCAACAACTTCACATGTCAAGACATAAACATCCATCCAACTGTAAATTTT  7593959

Query  7080     TAATAtttttttttttAAAAACTGCTTCAATAAGAATTTTGAAATGAGGAAAATGAAGCA  7139
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7593960  TAATATTTTTTTTTTTAAAAACTGCTTCAATAAGAATTTTGAAATGAGGAAAATGAAGCA  7594019

Query  7140     CAAATCAAAATTTGAGGGATGAAGTCAAAACTATATTTGGAGGAAAAATCAAAACCTACA  7199
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594020  CAAATCAAAATTTGAGGGATGAAGTCAAAACTATATTTGGAGGAAAAATCAAAACCTACA  7594079

Query  7200     TCTGTTTAATCTGAAAAAACAGACAGGAAATTCTCTGTGCCATTTTGGGCTGTGTGTCAC  7259
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594080  TCTGTTTAATCTGAAAAAACAGACAGGAAATTCTCTGTGCCATTTTGGGCTGTGTGTCAC  7594139

Query  7260     CATCCCTGACTGGCTGGCTGCAGATTAGACGGGCATGTTCCTAAGAAGGTGGTGACTTAC  7319
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594140  CATCCCTGACTGGCTGGCTGCAGATTAGACGGGCATGTTCCTAAGAAGGTGGTGACTTAC  7594199

Query  7320     CAGATCTGGACTCAGTTTGCAGGGTGCTGGGACCTCTCAGAGAACCAAGCAGTAGCTCCA  7379
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594200  CAGATCTGGACTCAGTTTGCAGGGTGCTGGGACCTCTCAGAGAACCAAGCAGTAGCTCCA  7594259

Query  7380     GGCACCAGGGCTTTGGGTCTGTCCTGTGCAAACTCAGGAGCTTTTGTTGATGTTTCTAAC  7439
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594260  GGCACCAGGGCTTTGGGTCTGTCCTGTGCAAACTCAGGAGCTTTTGTTGATGTTTCTAAC  7594319

Query  7440     CACACCCTCCCCTTCTCAATCACCAGCTTCCAATCAGAAAGTGATACCTGATTAGATCCT  7499
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594320  CACACCCTCCCCTTCTCAATCACCAGCTTCCAATCAGAAAGTGATACCTGATTAGATCCT  7594379

Query  7500     GAAGTTCCACCCAGTTAATCCTGATTGAGTTTCACACTTTCTTCTGATTCATTGATTAAA  7559
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594380  GAAGTTCCACCCAGTTAATCCTGATTGAGTTTCACACTTTCTTCTGATTCATTGATTAAA  7594439

Query  7560     TTAGATGTGCATTTATGAAAGTGAAAGAATAAATAACAGGGTGAAAGTCCAAAAGTCATT  7619
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594440  TTAGATGTGCATTTATGAAAGTGAAAGAATAAATAACAGGGTGAAAGTCCAAAAGTCATT  7594499

Query  7620     AATTCATTTATTCCCCAAACACTGATGAAGTTTGACTAACATGTGACCTTCATAGTGACA  7679
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594500  AATTCATTTATTCCCCAAACACTGATGAAGTTTGACTAACATGTGACCTTCATAGTGACA  7594559

Query  7680     TGGAAGGTTTAATCTGTTCCTGGCATTAGAAAGAAAAAACAAAACCTGATGATATCTTTA  7739
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594560  TGGAAGGTTTAATCTGTTCCTGGCATTAGAAAGAAAAAACAAAACCTGATGATATCTTTA  7594619

Query  7740     TGGGAGAATATTTGGCCACATTGAAATTATCCAAACGTTTCAGAGCTAAGACAGCTTTAA  7799
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594620  TGGGAGAATATTTGGCCACATTGAAATTATCCAAACGTTTCAGAGCTAAGACAGCTTTAA  7594679

Query  7800     AAAGACGGTGATGTCAACCCTAAGAAAACAGAATACAAAGCTCTGTTATCCAACAGTTAC  7859
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594680  AAAGACGGTGATGTCAACCCTAAGAAAACAGAATACAAAGCTCTGTTATCCAACAGTTAC  7594739

Query  7860     CTGGGTTTTATGCTTCCTAACGGGGCAGGTCATATGTGGGTTCAGGTTGAAGAGGGGAAC  7919
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594740  CTGGGTTTTATGCTTCCTAACGGGGCAGGTCATATGTGGGTTCAGGTTGAAGAGGGGAAC  7594799

Query  7920     CACTGAGGGTGTTATTGATCACAAGACTAAGGTCAAGGCTTCACTGCAGGAAATCAGGAC  7979
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594800  CACTGAGGGTGTTATTGATCACAAGACTAAGGTCAAGGCTTCACTGCAGGAAATCAGGAC  7594859

Query  7980     AGAATGACAAAGTGAGGTGGGGGCTGGGCAGGATGGGACCGGGTGTTCTAGTAGAACCCT  8039
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594860  AGAATGACAAAGTGAGGTGGGGGCTGGGCAGGATGGGACCGGGTGTTCTAGTAGAACCCT  7594919

Query  8040     GGGAAGGAACCAAGACAGCATAAAACATGGTGGGTATTTTGTGGGCATCTCCACAGAAGG  8099
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594920  GGGAAGGAACCAAGACAGCATAAAACATGGTGGGTATTTTGTGGGCATCTCCACAGAAGG  7594979

Query  8100     ATTGAAAGACTCTGTCTGGATTGAGTTTAAAAATTAAAAAGGGAATAGTTACAGAAGAGA  8159
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7594980  ATTGAAAGACTCTGTCTGGATTGAGTTTAAAAATTAAAAAGGGAATAGTTACAGAAGAGA  7595039

Query  8160     CAGTGCAGACTCTTCAAACACAACATTGTCTTTGAGGGCAGAGAAGGCAGAAACAGTCTT  8219
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595040  CAGTGCAGACTCTTCAAACACAACATTGTCTTTGAGGGCAGAGAAGGCAGAAACAGTCTT  7595099

Query  8220     GGCCCCTACTAGAAGGGAAAGCGTGTTTACTCCCAAAAATGATGGGCTCGCCTCAGAAAA  8279
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595100  GGCCCCTACTAGAAGGGAAAGCGTGTTTACTCCCAAAAATGATGGGCTCGCCTCAGAAAA  7595159

Query  8280     TCAGCCTGGGAAGATGGAATCTGAGAATCTGAGCTGGGGCAGATGCCAGAGAGAAGCAGT  8339
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595160  TCAGCCTGGGAAGATGGAATCTGAGAATCTGAGCTGGGGCAGATGCCAGAGAGAAGCAGT  7595219

Query  8340     GTGGCCAGACCTGGGAAGGGAGACTTTCCCAACCTGGAAGCCATCGAAGGTGGGAGCTGT  8399
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595220  GTGGCCAGACCTGGGAAGGGAGACTTTCCCAACCTGGAAGCCATCGAAGGTGGGAGCTGT  7595279

Query  8400     GGGTTTTGCAGGATGTGGGAGAAAGTGAACAAGGGTCCAAGTCTCTGTCATGGTGCTATG  8459
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595280  GGGTTTTGCAGGATGTGGGAGAAAGTGAACAAGGGTCCAAGTCTCTGTCATGGTGCTATG  7595339

Query  8460     GTCTGGAAACCTTTCTTTTAGACTCAGGGATCTTCCCACAGTGGGACATTTCCCAGCAAC  8519
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595340  GTCTGGAAACCTTTCTTTTAGACTCAGGGATCTTCCCACAGTGGGACATTTCCCAGCAAC  7595399

Query  8520     CCTCACCCACAGGTGTTTCCCAGGGCCCCTCATCCTCATCAATACCCTCGTGCCATTCCC  8579
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595400  CCTCACCCACAGGTGTTTCCCAGGGCCCCTCATCCTCATCAATACCCTCGTGCCATTCCC  7595459

Query  8580     CAGCATATTTTGATAATTAATGTTCTGCCATCCTTAAAGTCCTCCCTTGTCCCTGATATT  8639
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595460  CAGCATATTTTGATAATTAATGTTCTGCCATCCTTAAAGTCCTCCCTTGTCCCTGATATT  7595519

Query  8640     GAACAGAGAGATTCTGATTAAAGTGATACCATTAGGTATACAAAGAAAACTCAggccatg  8699
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595520  GAACAGAGAGATTCTGATTAAAGTGATACCATTAGGTATACAAAGAAAACTCAGGCCATG  7595579

Query  8700     tgtggtggctcatatctctaatttcagcactttgggaggccaaggcagatagattacttg  8759
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595580  TGTGGTGGCTCATATCTCTAATTTCAGCACTTTGGGAGGCCAAGGCAGATAGATTACTTG  7595639

Query  8760     agcgcaggagtttgagacctgcctgggcaacatggaaaattctgtctataaaaactatat  8819
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595640  AGCGCAGGAGTTTGAGACCTGCCTGGGCAACATGGAAAATTCTGTCTATAAAAACTATAT  7595699

Query  8820     acgaaaaattagccaggcatggtggtgtgcacctgtagtcccagctgcccaagaagttta  8879
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595700  ACGAAAAATTAGCCAGGCATGGTGGTGTGCACCTGTAGTCCCAGCTGCCCAAGAAGTTTA  7595759

Query  8880     gatgcgaggatcacctgagcccaggaggttgagactgcagtgagccatcattgtgccact  8939
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595760  GATGCGAGGATCACCTGAGCCCAGGAGGTTGAGACTGCAGTGAGCCATCATTGTGCCACT  7595819

Query  8940     gcactccagcctgctcaacagaatgaaaccttgcctcaaaaaaaaggaaggaaagaagga  8999
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595820  GCACTCCAGCCTGCTCAACAGAATGAAACCTTGCCTCAAAAAAAAGGAAGGAAAGAAGGA  7595879

Query  9000     aggaagggagggagggagggagggaggggagagaaaaagacagaaggaaacagaaagaaa  9059
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595880  AGGAAGGGAGGGAGGGAGGGAGGGAGGGGAGAGAAAAAGACAGAAGGAAACAGAAAGAAA  7595939

Query  9060     ggtggaaagaaagaaaaagaaagaagaaagaaagtaagaaaaagaaagaaagaaagaaaa  9119
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7595940  GGTGGAAAGAAAGAAAAAGAAAGAAGAAAGAAAGTAAGAAAAAGAAAGAAAGAAAGAAAA  7595999

Query  9120     agaaggaaagaaggaaggaaagaaaaagaaagaaagaagaaagaaagagaaagaaagaaa  9179
                |||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||
Sbjct  7596000  AGAAGGAAAGAAGGAAGGAAAGAAAAAGAAAGAAAGAAGAAAGAAAGA-AA-GAAAGAAA  7596057

Query  9180     gaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaaaagagcgagccttctt  9239
                |||||||||||||||||||||||||||||||| || ||  |        |||||||||||
Sbjct  7596058  GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA-AA-GA--G--------CGAGCCTTCTT  7596105

Query  9240     gtctttaagagcagcgcatatataCTGTTATATTGGGTGCACACCTAAAATACATTTCCC  9299
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596106  GTCTTTAAGAGCAGCGCATATATACTGTTATATTGGGTGCACACCTAAAATACATTTCCC  7596165

Query  9300     CCACAAAACCTGGAAGCTCTATTTCATGTTGAAATATCTGCTAAGTTCACGGATGGCTCC  9359
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596166  CCACAAAACCTGGAAGCTCTATTTCATGTTGAAATATCTGCTAAGTTCACGGATGGCTCC  7596225

Query  9360     CATCCTAAGAGGGATCACACAGTGATTCTTCCGATGTTTTAGGGCACAAAGTAGCAAGAA  9419
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596226  CATCCTAAGAGGGATCACACAGTGATTCTTCCGATGTTTTAGGGCACAAAGTAGCAAGAA  7596285

Query  9420     CCTCCCCTGCCTCCAGAAAGTCCTCCAGGCCTTTCTCTCCCATTCTATATGAAAACCAAA  9479
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596286  CCTCCCCTGCCTCCAGAAAGTCCTCCAGGCCTTTCTCTCCCATTCTATATGAAAACCAAA  7596345

Query  9480     CAGCTCTGAGATGCCACTGGCCTCCAAAACTGGAGTACTTTGAAGGGTGTTCTCTATCTT  9539
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596346  CAGCTCTGAGATGCCACTGGCCTCCAAAACTGGAGTACTTTGAAGGGTGTTCTCTATCTT  7596405

Query  9540     GAAATGTTTCTGTAAATGTTCTTTCTCCACATTTCTGACCTCACTGTCAATGCCCTGCTA  9599
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596406  GAAATGTTTCTGTAAATGTTCTTTCTCCACATTTCTGACCTCACTGTCAATGCCCTGCTA  7596465

Query  9600     TGTGTGCAATTGAGTTAAACTGAAATGTGTTCAGTGGGGCTTCTACTTTGCCTGCCCTCA  9659
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596466  TGTGTGCAATTGAGTTAAACTGAAATGTGTTCAGTGGGGCTTCTACTTTGCCTGCCCTCA  7596525

Query  9660     CTTTGTGAGCCTGAGGCTGAGGTTGAGCTCAGCACCAAGGGTGATCGTGAGTGTCTCTGG  9719
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596526  CTTTGTGAGCCTGAGGCTGAGGTTGAGCTCAGCACCAAGGGTGATCGTGAGTGTCTCTGG  7596585

Query  9720     TGACTGAGCATCCACGAGGCACAGCAGGGGCTGGTATCATTCATCCAAGATCTCAGCTCT  9779
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596586  TGACTGAGCATCCACGAGGCACAGCAGGGGCTGGTATCATTCATCCAAGATCTCAGCTCT  7596645

Query  9780     CCCTCACAAATAATCTAAAGCATGTTGGTGACCCTGAGATTTGGCTAGCAAGAGGAATCT  9839
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596646  CCCTCACAAATAATCTAAAGCATGTTGGTGACCCTGAGATTTGGCTAGCAAGAGGAATCT  7596705

Query  9840     GCCCATGTTCAGACAACAAATGATTGGCAGACCCCTCAGGTGAGAGGCTCAGAGGATCCC  9899
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596706  GCCCATGTTCAGACAACAAATGATTGGCAGACCCCTCAGGTGAGAGGCTCAGAGGATCCC  7596765

Query  9900     CTAAGCAGTTCAACAACCTAAATGTTGGAAAAAACTGGCTGACAGACTTTCCATTCTTTC  9959
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596766  CTAAGCAGTTCAACAACCTAAATGTTGGAAAAAACTGGCTGACAGACTTTCCATTCTTTC  7596825

Query  9960     CCAATTCAGAAGGTCCAGCAAGTAGTGGTTGGTCTCAGGAAGATGGAAAATCACAAACAA  10019
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596826  CCAATTCAGAAGGTCCAGCAAGTAGTGGTTGGTCTCAGGAAGATGGAAAATCACAAACAA  7596885

Query  10020    CAGTTaaaaaaaGAAACTAAGCAAAGGAACACTGGCAAGACACTGTGCCAGtgccccccc  10079
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596886  CAGTTAAAAAAAGAAACTAAGCAAAGGAACACTGGCAAGACACTGTGCCAGTGCCCCCCC  7596945

Query  10080    ctttcaccaagaaggaaggcctcccactcctgagcccactgcgcccaagcttccacaagg  10139
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7596946  CTTTCACCAAGAAGGAAGGCCTCCCACTCCTGAGCCCACTGCGCCCAAGCTTCCACAAGG  7597005

Query  10140    cctacatacccctaggctgcccagagtagagaagaaagggtgcaagacctcaggatgcaa  10199
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597006  CCTACATACCCCTAGGCTGCCCAGAGTAGAGAAGAAAGGGTGCAAGACCTCAGGATGCAA  7597065

Query  10200    gaccctcccttggctgcccgtatgaggcctagaactgggatacaaatgtccctgagagag  10259
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597066  GACCCTCCCTTGGCTGCCCGTATGAGGCCTAGAACTGGGATACAAATGTCCCTGAGAGAG  7597125

Query  10260    caacagtatactggagtagacgaggatgggcttatggtggaaagacgtgcctttgtgtac  10319
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597126  CAACAGTATACTGGAGTAGACGAGGATGGGCTTATGGTGGAAAGACGTGCCTTTGTGTAC  7597185

Query  10320    caacccttcacctctgcccatctcctccattggaaaacaataccccatcctataccgaaa  10379
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597186  CAACCCTTCACCTCTGCCCATCTCCTCCATTGGAAAACAATACCCCATCCTATACCGAAA  7597245

Query  10380    agcctcaagctataatttatttgctccaaactgttatccagacccacaaccccacctggg  10439
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597246  AGCCTCAAGCTATAATTTATTTGCTCCAAACTGTTATCCAGACCCACAACCCCACCTGGG  7597305

Query  10440    ctgattgccaccaggtgctcatgcacctctttaacacagatgaaaggtggagagtgctcc  10499
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597306  CTGATTGCCACCAGGTGCTCATGCACCTCTTTAACACAGATGAAAGGTGGAGAGTGCTCC  7597365

Query  10500    aagtggcaactaagtggctggaagaacatgttccagctgattacaaaatccccgagggta  10559
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597366  AAGTGGCAACTAAGTGGCTGGAAGAACATGTTCCAGCTGATTACAAAATCCCCGAGGGTA  7597425

Query  10560    tgtgaggatccaactagcaggaacagacccccagtgggacccaaatgaaagacagggtat  10619
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597426  TGTGAGGATCCAACTAGCAGGAACAGACCCCCAGTGGGACCCAAATGAAAGACAGGGTAT  7597485

Query  10620    gcaaagcctaaaccagtacagggaagtccttctggaaggattacaggcgtgagcTGCCTC  10679
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597486  GCAAAGCCTAAACCAGTACAGGGAAGTCCTTCTGGAAGGATTACAGGCGTGAGCTGCCTC  7597545

Query  10680    ACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCCTATCCCTAACACTGTCAATTTCC  10739
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597546  ACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCCTATCCCTAACACTGTCAATTTCC  7597605

Query  10740    TGATTCATGCAATTAATATGGATATCTGATATGAATGGATATCTGATTCAATCCATTAAT  10799
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597606  TGATTCATGCAATTAATATGGATATCTGATATGAATGGATATCTGATTCAATCCATTAAT  7597665

Query  10800    CTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGCAATCAG  10859
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597666  CTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGCAATCAG  7597725

Query  10860    ATATCACTTTTTGATTGGAAGCTAGTGatccgcctgccttagtctcccaaagtgctagga  10919
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597726  ATATCACTTTTTGATTGGAAGCTAGTGATCCGCCTGCCTTAGTCTCCCAAAGTGCTAGGA  7597785

Query  10920    ttgcaggcatgagccactgcacctggccGGTATTTTCTGTTTTGTACaagatgttccaga  10979
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597786  TTGCAGGCATGAGCCACTGCACCTGGCCGGTATTTTCTGTTTTGTACAAGATGTTCCAGA  7597845

Query  10980    aagaaaggcaaatatggaaagttgtctaattcatttcataagagagcagtaacccatatt  11039
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597846  AAGAAAGGCAAATATGGAAAGTTGTCTAATTCATTTCATAAGAGAGCAGTAACCCATATT  7597905

Query  11040    ttaaaaatggctaaggatattagaaggaaagtaaatttaaacttatttggcaaaagtttt  11099
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7597906  TTAAAAATGGCTAAGGATATTAGAAGGAAAGTAAATTTAAACTTATTTGGCAAAAGTTTT  7597965

Query  11100    ttttcttttttctttctttttttttttttt-gagacagagactcactctgtcatgcaggc  11158
                |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct  7597966  TTTTCTTTTTTCTTTCTTTTTTTTTTTTTTTGAGACAGAGACTCACTCTGTCATGCAGGC  7598025

Query  11159    tggagtgcagtggcacaatctcacctcactgcaacctcttactcccagattcgagcaatt  11218
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7598026  TGGAGTGCAGTGGCACAATCTCACCTCACTGCAACCTCTTACTCCCAGATTCGAGCAATT  7598085

Query  11219    ctcctgcctcagcctctctagtagctgggattagagccacatgccaccacatccagctaa  11278
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7598086  CTCCTGCCTCAGCCTCTCTAGTAGCTGGGATTAGAGCCACATGCCACCACATCCAGCTAA  7598145

Query  11279    tttatgtagttttagaagaggcagaatttctctgtgttggctagaactcctgacctcagg  11338
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7598146  TTTATGTAGTTTTAGAAGAGGCAGAATTTCTCTGTGTTGGCTAGAACTCCTGACCTCAGG  7598205

Query  11339    tgatccacttgcctcggcctcccaaagtgctgggattacaggcatgagccaccacggtca  11398
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7598206  TGATCCACTTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCACGGTCA  7598265

Query  11399    gccAGAAAAAAGTACTTAATAAATTATCAGTTAACTAAATGCAACACTGCATTAGAAAGT  11458
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7598266  GCCAGAAAAAAGTACTTAATAAATTATCAGTTAACTAAATGCAACACTGCATTAGAAAGT  7598325

Query  11459    GATAGACAggccaggctccgtggctcacgcctgcaatcccagcactttgagaggccgagg  11518
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7598326  GATAGACAGGCCAGGCTCCGTGGCTCACGCCTGCAATCCCAGCACTTTGAGAGGCCGAGG  7598385

Query  11519    caggtggatcacctcaggtctggagttcgagaccagcctgaccaacatggagaaacccca  11578
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7598386  CAGGTGGATCACCTCAGGTCTGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCCA  7598445

Query  11579    tccctactaaaaatacaaaattagccaggtgtggtggcgcatgcctgtaatcccagcaac  11638
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7598446  TCCCTACTAAAAATACAAAATTAGCCAGGTGTGGTGGCGCATGCCTGTAATCCCAGCAAC  7598505

Query  11639    tcaggaggctgaggctggagatttgcttgaaccaagaaggtggaagttgcagtgagtcga  11698
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7598506  TCAGGAGGCTGAGGCTGGAGATTTGCTTGAACCAAGAAGGTGGAAGTTGCAGTGAGTCGA  7598565

Query  11699    gatcatgccattgcacttcagcttgtgcaaaaagagtgaaactccaccttaaaaagaaaa  11758
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7598566  GATCATGCCATTGCACTTCAGCTTGTGCAAAAAGAGTGAAACTCCACCTTAAAAAGAAAA  7598625

Query  11759    aaaaaagaaaaaaagaaaGCAATATAGTGATATATAATGGCCATTCCAGGAATGCCAGCC  11818
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7598626  AAAAAAGAAAAAAAGAAAGCAATATAGTGATATATAATGGCCATTCCAGGAATGCCAGCC  7598685

Query  11819    AATCACAGGAAAATCTAAGTGTAATTCAGCATACTGACAAACTAAAGGGGGAAAAGCAAG  11878
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7598686  AATCACAGGAAAATCTAAGTGTAATTCAGCATACTGACAAACTAAAGGGGGAAAAGCAAG  7598745

Query  11879    GTTCCTACAAAATGCAGAAAAGAATTGCAGAAAAATCAAATTAAATTTATCATAACATA  11937
                |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7598746  GTTCCTACAAAATGCAGAAAAGAATTGCAGAAAAATCAAATTAAATTTATCATAACATA  7598804


 Score = 9208 bits (4986),  Expect = 0.0
 Identities = 5326/5483 (97%), Gaps = 52/5483 (0%)
 Strand=Plus/Minus

Query  23853    tgttacaagttggaatgcttttataagaaaggttgaaagaagggaatgggactcctccta  23912
                |||| ||||||||||||||||||||||||||||||||||||||| |||||||||||||||
Sbjct  7443495  TGTTGCAAGTTGGAATGCTTTTATAAGAAAGGTTGAAAGAAGGGGATGGGACTCCTCCTA  7443436

Query  23913    tcagttgttttttttttttaattttcttttgttttatcctggcaaggctctaatagagtt  23972
                |||||||  |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7443435  TCAGTTG--TTTTTTTTTTAATTTTCTTTTGTTTTATCCTGGCAAGGCTCTAATAGAGTT  7443378

Query  23973    gagcttttttgtttttgttttttccattggaagggacaatacagaggttacaatcattga  24032
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7443377  GAGCTTTTTTGTTTTTGTTTTTTCCATTGGAAGGGACAATACAGAGGTTACAATCATTGA  7443318

Query  24033    ctttagatgacaacatgacaggcaaaaatattttccttgcaagacaaccagcaaaacttc  24092
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7443317  CTTTAGATGACAACATGACAGGCAAAAATATTTTCCTTGCAAGACAACCAGCAAAACTTC  7443258

Query  24093    acgatcagaatcaaatcagtgtccttctcactgtcactgggtgaagccttcatcagtact  24152
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7443257  ACGATCAGAATCAAATCAGTGTCCTTCTCACTGTCACTGGGTGAAGCCTTCATCAGTACT  7443198

Query  24153    tgaagagtctcaggcactcatgaagtcaagatcagattctttactcagggacaggatgta  24212
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7443197  TGAAGAGTCTCAGGCACTCATGAAGTCAAGATCAGATTCTTTACTCAGGGACAGGATGTA  7443138

Query  24213    agccaatcataagaccttccacagatgatcaatttggaagtctacctaatgtgacctgca  24272
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7443137  AGCCAATCATAAGACCTTCCACAGATGATCAATTTGGAAGTCTACCTAATGTGACCTGCA  7443078

Query  24273    ggttttcaCTGGCAATATGCAGGTGCAGATATGACAAAGAATAATCCTGACCTTCATATC  24332
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7443077  GGTTTTCACTGGCAATATGCAGGTGCAGATATGACAAAGAATAATCCTGACCTTCATATC  7443018

Query  24333    GCCCCTAGCTGATGAGGATTGGGATTCTTTTGTCCCTTTCTCTCCATAAAACCAGGTTAC  24392
                 |||||||||| |||||||||||||||||||||||||||||||||||||||||||| |||
Sbjct  7443017  ACCCCTAGCTGTTGAGGATTGGGATTCTTTTGTCCCTTTCTCTCCATAAAACCAGGCTAC  7442958

Query  24393    TCATCTTGTGTGGCAACAAAATATATGGTctacttaacagagaaagagactccacagg--  24450
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  
Sbjct  7442957  TCATCTTGTGTGGCAACAAAATATATGGTCTACTTAACAGAGAAAGAGACTCCACAGGAA  7442898

Query  24451    aaaaaaaaaaggatttttattatgaaatgagcaaagccatgggaatagatgtgagattat  24510
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7442897  AAAAAAAAAAGGATTTTTATTATGAAATGAGCAAAGCCATGGGAATAGATGTGAGATTAT  7442838

Query  24511    tcggggaggtaaaggaagacaaaggttttgaaaggaaaaatgaggagaattacataaatt  24570
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7442837  TCGGGGAGGTAAAGGAAGACAAAGGTTTTGAAAGGAAAAATGAGGAGAATTACATAAATT  7442778

Query  24571    tttttgaaagactcattcttggtcacaagtatgaaaaccaagggagcctcagtgcagtgt  24630
                ||||||||||||||||||||||||||||||||||||||||||||| |||||||||| |||
Sbjct  7442777  TTTTTGAAAGACTCATTCTTGGTCACAAGTATGAAAACCAAGGGACCCTCAGTGCAATGT  7442718

Query  24631    tggaaagATTCCTCCTCCACCCTCTCAATAACCCCCAACACATTTACCAAGTCTTTGTTC  24690
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Sbjct  7442717  TGGAAAGATTCCTCCTCCACCCTCTCAATAACCCCCAACACATTTACCAAGTCTTCGTTC  7442658

Query  24691    ACTCCCAGGATTCCATTAAAACACCCAGCTCAACCCTGACCAGCCTCCACCTTCACTTCC  24750
                |||||||||||||||||||||||||||||||||||||||||||||||||  |||||||||
Sbjct  7442657  ACTCCCAGGATTCCATTAAAACACCCAGCTCAACCCTGACCAGCCTCCATTTTCACTTCC  7442598

Query  24751    CTTTGTAATTTTGACATAAATTtgttacaggaccatcaggttcctatgccggctgcacag  24810
                |||| ||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Sbjct  7442597  CTTTATAATTTTGACATAAATTTGTTACAGGACCATCAGGTTCCTATGCCTGCTGCACAG  7442538

Query  24811    tagcttaccaatattctgagacagcaggatttgcagcagaaagtttaatgatcacagggt  24870
                |||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||
Sbjct  7442537  TAGCTTACCAATATTCTGAGACAGCAGGGTTTGCAGCAGAAAGTTTAATGATCACAGGGT  7442478

Query  24871    ggctgaatgagaagctgggaggagatcctcaaattcatctccccaaggagtactgagggt  24930
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7442477  GGCTGAATGAGAAGCTGGGAGGAGATCCTCAAATTCATCTCCCCAAGGAGTACTGAGGGT  7442418

Query  24931    ttccagtggatcctggatagcaaggggctggaaagttggtgtagtttgatggcaataaga  24990
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7442417  TTCCAGTGGATCCTGGATAGCAAGGGGCTGGAAAGTTGGTGTAGTTTGATGGCAATAAGA  7442358

Query  24991    ggtatgaagttatcacgatgtcagaacggcattctttggtgagttgatgccttgcagggc  25050
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7442357  GGTATGAAGTTATCACGATGTCAGAACGGCATTCTTTGGTGAGTTGATGCCTTGCAGGGC  7442298

Query  25051    ccttcagatcagctggcatcagtagtttcactgacatgcagaacctgaaagaatatctca  25110
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7442297  CCTTCAGATCAGCTGGCATCAGTAGTTTCACTGACATGCAGAACCTGAAAGAATATCTCA  7442238

Query  25111    aatgaaaaacttaatgtttcacaatgcttaaattgttgtctgcagcgtagttaaggggaa  25170
                 |||||||| | ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7442237  GATGAAAAAGTGAATGTTTCACAATGCTTAAATTGTTGTCTGCAGCGTAGTTAAGGGGAA  7442178

Query  25171    ttgtagtctaagttctacacgattttgggacagtaggctgccagcaaccatgaggaagca  25230
                ||||||||||||||||||| |||||||||||||||||||||||| |||||||||||||||
Sbjct  7442177  TTGTAGTCTAAGTTCTACATGATTTTGGGACAGTAGGCTGCCAGGAACCATGAGGAAGCA  7442118

Query  25231    ggtcagagggcaagctgacctcctggtgaatgctgaatgcgtttcaagcttggtttgttt  25290
                ||||||||||||||||||||||||||||||||||||||||| | ||||||||||||||||
Sbjct  7442117  GGTCAGAGGGCAAGCTGACCTCCTGGTGAATGCTGAATGCGCTGCAAGCTTGGTTTGTTT  7442058

Query  25291    ttgttcctccccctctctttttcaccgattaaatttataaagtttagaaatacggtttca  25350
                ||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||
Sbjct  7442057  TTGTTCCTCCCCCTCTCTTTTTCACTGATTAAATTTATAAAGTTTAGAGATACGGTTTCA  7441998

Query  25351    ATTTCTTCCAGACAAGCCTTAACCTAAGCCCTGAGACCACTCAAGCCCTCAGTGGCACCT  25410
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7441997  ATTTCTTCCAGACAAGCCTTAACCTAAGCCCTGAGACCACTCAAGCCCTCAGTGGCACCT  7441938

Query  25411    CTCTTCCACCAGCATGAGCAAATAAATTGCTACCTTAGGTGATATAAAACCCACAAGATG  25470
                ||||||||||||| |||||||||||||||||||||||||||||||| |||||||||||  
Sbjct  7441937  CTCTTCCACCAGCGTGAGCAAATAAATTGCTACCTTAGGTGATATAGAACCCACAAGACC  7441878

Query  25471    ATTCGATACATGGAG-ttttttttCTGATTTTGTAGGGATGACTTCTTTGTTTCTATAAA  25529
                ||||||||||||||| ||||||||||||||||||||||||||||||| ||||| ||||||
Sbjct  7441877  ATTCGATACATGGAGATTTTTTTTCTGATTTTGTAGGGATGACTTCTCTGTTTTTATAAA  7441818

Query  25530    GCTGTTTTAACTATAAAACAATTTTATAATTTTGATGTGGCCAAAGATCTCCCAACACTA  25589
                ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||
Sbjct  7441817  GCTGTTTTAACTATAAAACAATTTTATAATTTTAATGTGGCCAAAGATCTCCCAACACTA  7441758

Query  25590    CTTTCAGGTTTTATTTTTCTGTCTACTATCCAGAACAGATCAAACCCTTCCCTGCCTCAA  25649
                ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||
Sbjct  7441757  CTTTCAGGTTTTATTTTTCTGTCTACTATCCGGAACAGATCAAACCCTTCCCTGCCTCAA  7441698

Query  25650    ACTCAGGACTATATAGGTCATATATCAGTAAAATTCCATCAGTGTTTGCGGAgttcatga  25709
                |||||||||||||||||||||||||||||||||||||||||||||||| |||||| ||||
Sbjct  7441697  ACTCAGGACTATATAGGTCATATATCAGTAAAATTCCATCAGTGTTTGTGGAGTTTATGA  7441638

Query  25710    atgaatgaattctttttttttttttttttttttttttttgtgacaaagtctacctctgtc  25769
                ||||||||||||||||| ||||| |||||||        |  ||||||||||||||||||
Sbjct  7441637  ATGAATGAATTCTTTTTATTTTTATTTTTTT--------G--ACAAAGTCTACCTCTGTC  7441588

Query  25770    acccagaacggtgtgcaatggtgcaatcttggctcactgcaaccattgccccctggattc  25829
                |||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||
Sbjct  7441587  ACCCAGAACGGTGTGCAATGGTGCAATCTTGGCTCACTGCAACCATTGCCTCCGGGATTC  7441528

Query  25830    aagcgattctcccacctcagcctcctgagtagctggattacaggcacctgccatcatgcc  25889
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7441527  AAGCGATTCTCCCACCTCAGCCTCCTGAGTAGCTGGATTACAGGCACCTGCCATCATGCC  7441468

Query  25890    aggctaatttttgtgtttttgtagagctggggtttcatcatgttggccttgcaggtcttg  25949
                |||||||||||||||||||||||||  |||||||||| ||||||||||||||||||||||
Sbjct  7441467  AGGCTAATTTTTGTGTTTTTGTAGAAATGGGGTTTCACCATGTTGGCCTTGCAGGTCTTG  7441408

Query  25950    atcgcctgacctcaggtgatccagccaacttggactctcaaagtgcagggattacaggtg  26009
                |||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||
Sbjct  7441407  ATCGCCTGACCTCAGGCGATCCAGCCAACTTGGACTCTCAAAGTGCAGGGATTACAGGTG  7441348

Query  26010    tgagccacctcacccggcctttaatgaGTGAATTCTTGATTTCCACCCTATTCCTAACAC  26069
                ||| ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||
Sbjct  7441347  TGACCCACCTCACCCGGCCTTTAATGAGTGAATTCTTGATTTCCAACCTATTCCTAACAC  7441288

Query  26070    TGTCAATTTCTTGATTCATGAACTTAATATGGATAGCTGATATGAATGGATATCTGATTC  26129
                |||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Sbjct  7441287  TGTCAATTTCTTGATTCATGAACTTAATATGGATAGCTGATATGAATGAATATCTGATTC  7441228

Query  26130    AATCCAGTAATCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGGGTGGAGCTTCAGA  26189
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7441227  AATCCAGTAATCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGGGTGGAGCTTCAGA  7441168

Query  26190    AATGCAATCAGATAGCACTTTTTGATTGGAAGCAAGCACTGGATAGATGGAGGGGTGTGG  26249
                ||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||
Sbjct  7441167  AATGCAATCAGATAGCACTTTTTGATTGGAAGCAAGCACTGGATACATGGAGGGGTGTGG  7441108

Query  26250    GTGGGAGTTGTGATTAGAAAGATCGATAAAAGTTTCTGAAGGCCCACAGGAGAGACCCAA  26309
                |||||||||||||||||||||||| |||||||||||||||| ||||||||||||||||||
Sbjct  7441107  GTGGGAGTTGTGATTAGAAAGATCAATAAAAGTTTCTGAAGACCCACAGGAGAGACCCAA  7441048

Query  26310    AGTCTTCAAGTCTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTAAGCACT-CTGCAAACT  26368
                |||||||||||||||||||||||||||||||||||||||||||||||| | |||||||||
Sbjct  7441047  AGTCTTCAAGTCTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTAAGCA-TGCTGCAAACT  7440989

Query  26369    CAGTCCAGATCTAGTAAGTCACTCATTTCTGGAAGGACACTCCCATCTGACCTATAGTCA  26428
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7440988  CAGTCCAGATCTAGTAAGTCACTCATTTCTGGAAGGACACTCCCATCTGACCTATAGTCA  7440929

Query  26429    GCCGGTCTGGGACGGGGGCAATGCAGCCTATGATGGCACCGAGCTATATCTGTCTTTtat  26488
                | ||||||||||| ||| || ||||||||||||||||||| |||||||||||||||||||
Sbjct  7440928  GTCGGTCTGGGACAGGGACAGTGCAGCCTATGATGGCACCAAGCTATATCTGTCTTTTAT  7440869

Query  26489    atatatatatatGAACAATTTGAAGATTTGAATTTTTTCCTCTATATGCAGTTTTGTCTT  26548
                ||||||||||  ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7440868  ATATATATAT--GAACAATTTGAAGATTTGAATTTTTTCCTCTATATGCAGTTTTGTCTT  7440811

Query  26549    TATTTCAAAAAATTGGATTGTGCTTTGGTTTATGTCATTTcaaaattcttgatgggagca  26608
                |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
Sbjct  7440810  TATTTCAAAAAATTGGATTGTGCTTTGGTTTATGTCATTTCAAAATTCTTGATGAGAGCA  7440751

Query  26609    atgactcatgcccataacctcaacaccttgggaggccaaagcgggaggatcatttgagcc  26668
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 
Sbjct  7440750  ATGACTCATGCCCATAACCTCAACACCTTGGGAGGCCAAAGCGGGAGGATCATTTGAGCT  7440691

Query  26669    caggggtttgagaccaacctgggcaacatggcaaaaatgcagctctacaaaacattcttt  26728
                ||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Sbjct  7440690  CAGCGGTTTGAGACCAACCTGGGCAACATGGCAAAAACGCAGCTCTACAAAACATTCTTT  7440631

Query  26729    ttttgaagcagggatggagtctcaccctgttgccaaggctggagtgcagtggcaagagct  26788
                ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||
Sbjct  7440630  TTTTGAAGCAGGGATGGAGCCTCACCCTGTTGCCAAGGCTGGAGTGCAGTGGCAAGAGCT  7440571

Query  26789    caactcactgcaacctcttcctcccaggctcaaacaattttcatgtctcagcttcctgag  26848
                ||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||
Sbjct  7440570  CAACTCACTGCAACCTCTTCCTCCCAGGCTCAAACAATTTTCATGCCTCAGCTTCCTGAG  7440511

Query  26849    tagctggtattacatccctctgccaccatgtctgcttaatttttgtatttttagtagtgg  26908
                |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct  7440510  TAGCTGGTATTACATCCCTCTGCCACCATGCCTGCTTAATTTTTGTATTTTTAGTAGTGG  7440451

Query  26909    tggggtttcaccatgctggccaggttggtctcaaactcctgacatcaagtgatcctcctg  26968
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7440450  TGGGGTTTCACCATGCTGGCCAGGTTGGTCTCAAACTCCTGACATCAAGTGATCCTCCTG  7440391

Query  26969    cct-aggcccccaaaagtgctggaatgacggccgtgagccaATGGTGGTCAGCctctaca  27027
                ||| || |||||||| ||||||||||||| ||| ||||||||||||||||||||||||||
Sbjct  7440390  CCTCAGCCCCCCAAA-GTGCTGGAATGACAGCCTTGAGCCAATGGTGGTCAGCCTCTACA  7440332

Query  27028    aaatatatatatcttttaatttgccaggcatggtagcatgcatctgtattcccagctatt  27087
                ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Sbjct  7440331  AAATATATATATCTTTTAATTTGCCAGGCATGGTAGCATGCGTCTGTATTCCCAGCTATT  7440272

Query  27088    tggtttgctgacatgggagaatcacttgagcccagaagattgaggctgcagtgagccatg  27147
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7440271  TGGTTTGCTGACATGGGAGAATCACTTGAGCCCAGAAGATTGAGGCTGCAGTGAGCCATG  7440212

Query  27148    ctcacaccactgctgtactccagcctgggcaacagagtaagaccctgctaaaaacaaaaa  27207
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7440211  CTCACACCACTGCTGTACTCCAGCCTGGGCAACAGAGTAAGACCCTGCTAAAAACAAAAA  7440152

Query  27208    cgaaa-a----caaacaaacaaaaaacCTTAACCAAAGAGAATCTTTGACCTTAATTTTA  27262
                | ||| |    |||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7440151  CAAAACAAAAACAAACAAACAAAAAACCTTAACCAAAGAGAATCTTTGACCTTAATTTTA  7440092

Query  27263    AACCAATCACATCCTCACTGTAATTCTTCCTCCCGAATGGAGACATgggtgtgagggtgc  27322
                ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||
Sbjct  7440091  AACCAATCACATCCTCACTGTAATTCTTCCTCCCGAATGGAGACATGGGTGTGGGGGTGC  7440032

Query  27323    atgcctgtaatcccagctacatggaaggctgaagcatgagaattgcttgaatctcagagg  27382
                |||||||||||||||||||| ||||||| |||||||||||||||||||||||||||||||
Sbjct  7440031  ATGCCTGTAATCCCAGCTACGTGGAAGGTTGAAGCATGAGAATTGCTTGAATCTCAGAGG  7439972

Query  27383    cggaagttacagtgagctgagatggagccgctgcactccagcctgggcgacaaagtgaga  27442
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7439971  CGGAAGTTACAGTGAGCTGAGATGGAGCCGCTGCACTCCAGCCTGGGCGACAAAGTGAGA  7439912

Query  27443    ctcagcttcacccacaccaaaaaaaaTTAGATTATACCACCCAGGTGATCACTGGATACA  27502
                 |||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||
Sbjct  7439911  TTCAGCTTCACCCACACCAAAAAAAATGAGATTATACCACCCAGGTGATCATTGGATACA  7439852

Query  27503    TGAAGATTTCTATTGTGTGTTATTGGGGACTGTCAACTCCGTCTTTGAAAACTGTTTTAA  27562
                |||||||||||||||||| || ||||||||||||||||||||||||||||||||||||||
Sbjct  7439851  TGAAGATTTCTATTGTGTTTTCTTGGGGACTGTCAACTCCGTCTTTGAAAACTGTTTTAA  7439792

Query  27563    CTCTGAAATATTTTGATAAATTTGATGTGGCCAAGGATCCCTCAACAAAGATACTTTCAA  27622
                |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7439791  CTCTGAAAAATTTTGATAAATTTGATGTGGCCAAGGATCCCTCAACAAAGATACTTTCAA  7439732

Query  27623    GTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGATTCAACACTTCCCTATCTCACACTCA  27682
                ||||||||||||||| |||||||||||||||||||||||| |||||||||||||||||||
Sbjct  7439731  GTTTTCTTTCTTTCTATCTAATATCAGGAAGAGATTCAACCCTTCCCTATCTCACACTCA  7439672

Query  27683    GGACTATGAAGGACACATATTAGTAAACCTCCATGTTTGTGGAGGGAATCAGTGAATGAG  27742
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7439671  GGACTATGAAGGACACATATTAGTAAACCTCCATGTTTGTGGAGGGAATCAGTGAATGAG  7439612

Query  27743    TCCTGGACTTTCACCCTATCCCTAAATCTTTCACTTTCATGGATGAATATCTAATTCAAT  27802
                ||||||||||||||||||||||||||||||||||| | ||||||||||||||||||||||
Sbjct  7439611  TCCTGGACTTTCACCCTATCCCTAAATCTTTCACTCTGATGGATGAATATCTAATTCAAT  7439552

Query  27803    CAGTTAATCTGGAAGAAAGCCAAAAATCCAATCAGGATTAACTGGGTAGAGTTTAAGAAG  27862
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7439551  CAGTTAATCTGGAAGAAAGCCAAAAATCCAATCAGGATTAACTGGGTAGAGTTTAAGAAG  7439492

Query  27863    TCGAATCAAATGTAGTtctctctctctctctctctcttttcttttctttttttttttttt  27922
                ||||||||||||||||||||||||| | | ||| | |||| |||| ||| |||       
Sbjct  7439491  TCGAATCAAATGTAGTTCTCTCTCT-T-T-TCT-T-TTTT-TTTT-TTTCTTT-------  7439446

Query  27923    ttttttgaatctagcctatttcacaggctggagtgcagtggtgtattgtcagctcactgc  27982
                      |||||||||||||||| |||||||||||||||||| ||||||||||||||||||
Sbjct  7439445  ------GAATCTAGCCTATTTCCCAGGCTGGAGTGCAGTGGAGTATTGTCAGCTCACTGC  7439392

Query  27983    aacctctgcctcctgggttcaagtgatcctcctgcctcagcctccctagtagcttggact  28042
                 |||||||||||||||||||||| || |||||||| |||||||||||||||||||||| |
Sbjct  7439391  GACCTCTGCCTCCTGGGTTCAAGCGAGCCTCCTGCATCAGCCTCCCTAGTAGCTTGGATT  7439332

Query  28043    ataggcgcagaccaccgcacctggctaatttttctaattttggtagaggtagggttttac  28102
                |||||| ||||| || |||||| |||||||||||||||||||||||||||||||||||||
Sbjct  7439331  ATAGGCACAGACAACTGCACCTTGCTAATTTTTCTAATTTTGGTAGAGGTAGGGTTTTAC  7439272

Query  28103    catgttggccaggctggtctcaaactcctgacctcagataatccacctgcctctgcctcc  28162
                ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Sbjct  7439271  CATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCGGATAATCCACCTGCCTCTGCCTCC  7439212

Query  28163    cagagggctgggattacaggtgtgagtcactgcacacagccAAAGTGGTTCATTTTGAAT  28222
                ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7439211  CAGAGTGCTGGGATTACAGGTGTGAGTCACTGCACACAGCCAAAGTGGTTCATTTTGAAT  7439152

Query  28223    ATGTGTGAGAGGTGTGTATTGGAAACATCTGTGTCTTGCCAATGATGCATAACACTGTCA  28282
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7439151  ATGTGTGAGAGGTGTGTATTGGAAACATCTGTGTCTTGCCAATGATGCATAACACTGTCA  7439092

Query  28283    CATAGCTTTCAAAGCTTCTTGCTGAAATTTTCAATAATGAGACCAGgcagaggctcatgc  28342
                ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||
Sbjct  7439091  CATAGCTTTCAAAGCTTCTCGCTGAAATTTTCAATAATGAGACCAGGCAGAGGCTCATGC  7439032

Query  28343    ctgcaatcccagcactttgggaggccaaagtgggtggattgtttgagtctaggagttcaa  28402
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7439031  CTGCAATCCCAGCACTTTGGGAGGCCAAAGTGGGTGGATTGTTTGAGTCTAGGAGTTCAA  7438972

Query  28403    gaccagcctggacaacatagtgaaacccactgtctttacaaaaagtcaaaaaataaaaGA  28462
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7438971  GACCAGCCTGGACAACATAGTGAAACCCACTGTCTTTACAAAAAGTCAAAAAATAAAAGA  7438912

Query  28463    TTAGCTGGGTACGAGATCTGAGCTTCAGAGATCCTCGGTAACATTTGCCAGTGCTATGAG  28522
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7438911  TTAGCTGGGTACGAGATCTGAGCTTCAGAGATCCTCGGTAACATTTGCCAGTGCTATGAG  7438852

Query  28523    TTTAGTGGATCAGTGGCTAATAATTCATGGACTACGAGGGATCTTGCCTGCTCTTTAGAA  28582
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7438851  TTTAGTGGATCAGTGGCTAATAATTCATGGACTACGAGGGATCTTGCCTGCTCTTTAGAA  7438792

Query  28583    GTTGGGACACATTCTTCATGGTACCAGAAGGGTAGAACTATGTCTCTGTGGCCACTTATT  28642
                ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||
Sbjct  7438791  GTTGGGACACATTCTTCATGGTACCAGAAGGGTAGAACTGTGTCTCTGTGGCCACTTATT  7438732

Query  28643    GCAGAAAGGAACTGGAGTAAACTGAGGGCTCTTTCACACATGCTAGAGAAATGACTTGGG  28702
                ||||||||||||||||||||||| |||||||||||||||| |||||||||||||||| ||
Sbjct  7438731  GCAGAAAGGAACTGGAGTAAACTAAGGGCTCTTTCACACACGCTAGAGAAATGACTTTGG  7438672

Query  28703    CCCTGGGAGAATTGGGGGTTGCAGGGGATTGGTCGGAGGAACTTGCCTTTTTGCTGGATT  28762
                |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Sbjct  7438671  CCCTGGGAGAATTGGGGGTTGCAGGGGATTGGTCTGAGGAACTTGCCTTTTTGCTGGATT  7438612

Query  28763    GTGCTGTAGAGTTTTTCCTTGTAGATTTGTCAGAATGAGCCTCCAGACCCCATCCAGACT  28822
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7438611  GTGCTGTAGAGTTTTTCCTTGTAGATTTGTCAGAATGAGCCTCCAGACCCCATCCAGACT  7438552

Query  28823    CCTGGAGCTGGCAGGGCAGAGCCTGATGAGGAAGCAGTTCTTGACTATCTTCACCCTGGA  28882
                ||||||||||||||||||||||||| ||||||| ||||||||||||||||||||||||||
Sbjct  7438551  CCTGGAGCTGGCAGGGCAGAGCCTGCTGAGGAACCAGTTCTTGACTATCTTCACCCTGGA  7438492

Query  28883    CT-AGCTGCCCAGGGAGGTCTCCCCTCTGACGTTCATGGAGGCCTTCAGCATGAGATGTT  28941
                 | ||||||||||||||||||||||||||   ||||||||||||||||||||||||||||
Sbjct  7438491  -TGAGCTGCCCAGGGAGGTCTCCCCTCTG---TTCATGGAGGCCTTCAGCATGAGATGTT  7438436

Query  28942    GTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGTCCTCCCTTCACCTCCCTCTGGGATCCC  29001
                |||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||
Sbjct  7438435  GTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGCCCTCCCTTCACCTCCCTCTGGGATCCC  7438376

Query  29002    TGATGAAGACAACTCATCTGGAGACCTTGCAAGCTGTGCTGAAGGGACTTGATACACTAG  29061
                ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7438375  TGATGAAGACACCTCATCTGGAGACCTTGCAAGCTGTGCTGAAGGGACTTGATACACTAG  7438316

Query  29062    TGTCCCAGAAGGTTTGCCCCAGTTGAGGTGACTCAGGTGGCCTGGTGGGAAGGGTCCAGG  29121
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 
Sbjct  7438315  TGTCCCAGAAGGTTTGCCCCAGTTGAGGTGACTCAGGTGGCCTGGTGGGAAGGGTCCAGA  7438256

Query  29122    CATCCAGGGAAGGGACAGCTGGCTCAGGAGGAGTGGCAGTGTGTGGGAGCTAGGGTGGCT  29181
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7438255  CATCCAGGGAAGGGACAGCTGGCTCAGGAGGAGTGGCAGTGTGTGGGAGCTAGGGTGGCT  7438196

Query  29182    CAGAGGCTTCTGATGGTACCCATGAGAGGCCTTGGCCATTGCCCAGATCCTCTGGAAAAG  29241
                ||||||||||||||||| ||||||||| ||||||||||||||||||||||||||||||||
Sbjct  7438195  CAGAGGCTTCTGATGGTGCCCATGAGAAGCCTTGGCCATTGCCCAGATCCTCTGGAAAAG  7438136

Query  29242    GACTGCTCACCATACAGAGTCCACTGAGGAAACAGGAACCTGCTTCCTTCCCAGTGGAAG  29301
                ||||||| ||||||||| |||||||||||||||||||||||||||||| |||||||||||
Sbjct  7438135  GACTGCTTACCATACAGGGTCCACTGAGGAAACAGGAACCTGCTTCCT-CCCAGTGGAAG  7438077

Query  29302    GTAAAGGTACTAGAAGTGGGTAC  29324
                |||||||||||||||||||||||
Sbjct  7438076  GTAAAGGTACTAGAAGTGGGTAC  7438054


 Score = 7313 bits (3960),  Expect = 0.0
 Identities = 5443/6146 (88%), Gaps = 153/6146 (2%)
 Strand=Plus/Minus

Query  23225    GGTTGGTTAATATTGATAATTAAATGACTTGGTACTGAGAAGAAGCTATAGGTGCAAATG  23284
                |||||||||||||||||||||||||||||||| |||||| ||||||||||| ||||||||
Sbjct  7498557  GGTTGGTTAATATTGATAATTAAATGACTTGGCACTGAGCAGAAGCTATAGATGCAAATG  7498498

Query  23285    GGTGGCCTATGACTATTATTGATTTCATTACTGGTAATTTATCTCTATGCCTAGAAAACA  23344
                ||||||||||||||||| |||||||||||||| |||| ||||||| |||| ||| |||||
Sbjct  7498497  GGTGGCCTATGACTATTGTTGATTTCATTACTTGTAACTTATCTCCATGCATAGGAAACA  7498438

Query  23345    TTAGTGTAACTGGGTCTAACCTAGATAGTGTTCCAGACTCCCACTAGAATCAAACTCTTT  23404
                |||||||||| |||||||| |||| |||||| |||||||||| |||||||||||||||||
Sbjct  7498437  TTAGTGTAACCGGGTCTAATCTAGGTAGTGTCCCAGACTCCCCCTAGAATCAAACTCTTT  7498378

Query  23405    GGTTTGACATGCATTATGTAGA-TGGGAATGCTAT-AGATATCGACATAGACATAGAGTC  23462
                  |||||||  ||||||| ||| | | |||||||| || ||| |||||||||| ||| ||
Sbjct  7498377  CATTTGACACACATTATGAAGACT-GAAATGCTATAAG-TATTGACATAGACACAGAATC  7498320

Query  23463    AGAACATGACCATGTTACCCTCTGCCATATAATCAGAGAACTTACTGAAACTAGGCATTG  23522
                ||||||||||||||||| |||||||||||||||||||||||||||||||||||| |||| 
Sbjct  7498319  AGAACATGACCATGTTATCCTCTGCCATATAATCAGAGAACTTACTGAAACTAGACATTT  7498260

Query  23523    GTTCTTTGGAAACTCTAGAGGCAAATAGAATGCATCTATAGCTCTACTGTATGAAAT---  23579
                |||| ||||||||||  ||||||||||||||||||||||||||||||| ||||||||   
Sbjct  7498259  GTTCATTGGAAACTC--GAGGCAAATAGAATGCATCTATAGCTCTACTATATGAAATAAA  7498202

Query  23580    -AATAGTTTTATTTATTGGATGCATCAATACTCAGGATATATTTGGAGAGGAAACTATTC  23638
                 |||||||| |||||||||||||||| |||||||| | ||||||||||| ||  ||||||
Sbjct  7498201  CAATAGTTTCATTTATTGGATGCATCCATACTCAGCACATATTTGGAGAAGACCCTATTC  7498142

Query  23639    TTTCTTCAATGGAGATGGCATGCAAGGATTACTTT-ATAAAACACACAGAAATATTTTTT  23697
                 |||||||||||||||| ||||||||||||| ||| ||||||  || | |||||||||||
Sbjct  7498141  ATTCTTCAATGGAGATGACATGCAAGGATTA-TTTAATAAAATTCATAAAAATATTTTTT  7498083

Query  23698    CCTCCCACCCCAATTCCAACCATTACCGTGCAACCTGTtgtcaatagacgttaaggcag-  23756
                | |||||||||| ||| |||  | ||| ||||||||| ||||| | || | |||||| | 
Sbjct  7498082  CATCCCACCCCAGTTCAAACTGTCACCATGCAACCTGGTGTCAGTGGAAGGTAAGGC-GC  7498024

Query  23757    ttgaggcagaaataattaaataaagcttcattggaagctaaatgtcaggatcgacctgga  23816
                || ||||||||||||||||||||| |||||||||||||||||||| || ||| |  ||||
Sbjct  7498023  TTAAGGCAGAAATAATTAAATAAATCTTCATTGGAAGCTAAATGTGAGAATCAATGTGGA  7497964

Query  23817    agacacacactgacaaaatgagcgttttccaaagtctgttacaagttggaatgcttttat  23876
                ||||||| ||  ||||| || | || |||||||||||||||||||||||||||||||| |
Sbjct  7497963  AGACACAGACCAACAAAGTGGGTGTGTTCCAAAGTCTGTTACAAGTTGGAATGCTTTTGT  7497904

Query  23877    aagaaaggttgaaagaagggaatgggactcctcctatcagttgttttttttttttaattt  23936
                 ||||| ||| ||||||||||||| ||||||||||||||   ||||||||||||||||||
Sbjct  7497903  GAGAAAAGTTAAAAGAAGGGAATGAGACTCCTCCTATCA---GTTTTTTTTTTTTAATTT  7497847

Query  23937    tcttttgtttta-t--cctggcaaggctctaatagagttgag--ctt-ttttgtttttgt  23990
                |||||||||||| |  ||||||||||||| ||||||||||||   || ||||||||||||
Sbjct  7497846  TCTTTTGTTTTACTGACCTGGCAAGGCTCAAATAGAGTTGAGTTTTTGTTTTGTTTTTGT  7497787

Query  23991    tttttccattggaagggacaatacagaggttacaatcattgactttagatgacaacatga  24050
                |||||||||||||||| ||||||||||||||||||||||||||||||| ||||||||| |
Sbjct  7497786  TTTTTCCATTGGAAGGTACAATACAGAGGTTACAATCATTGACTTTAGCTGACAACATAA  7497727

Query  24051    caggcaaaaatattttccttgcaagacaaccagcaaaacttcacgatcagaatcaaatca  24110
                || |   ||| ||||||||||||||||||||||  |||||||| ||||||||||||||||
Sbjct  7497726  CAAG-TTAAACATTTTCCTTGCAAGACAACCAGTGAAACTTCATGATCAGAATCAAATCA  7497668

Query  24111    gtgtccttctcactgtcactgggtgaagccttcatcagtacttgaagagtctcaggcact  24170
                |||||||||||||||| | ||||||||| |||||||| || ||| ||||| | |||||||
Sbjct  7497667  GTGTCCTTCTCACTGTAAGTGGGTGAAG-CTTCATCAATAATTGCAGAGTTTGAGGCACT  7497609

Query  24171    catgaagtcaagatcagattctttactcagggacaggatgtaagccaatcataagacctt  24230
                |||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||
Sbjct  7497608  CATGAACTCAAGATCAGATTCTTTACTCAGGGACAGAATGTAAGCCAATCATAAGACCTT  7497549

Query  24231    ccacagatgatcaatttggaagt-ct-acctaatgtgacctgcaggttttcaCTGGCAAT  24288
                |||||| || | ||||||| | | || |   ||||||||||| | |||||||||||||||
Sbjct  7497548  CCACAGGTGGTTAATTTGG-ACTCCTGA-AAAATGTGACCTGTAAGTTTTCACTGGCAAT  7497491

Query  24289    ATGCAGGTGCAGATATGACAAAGAATAATCC-TGACCTTCATATCGCCCCTAGCTGATGA  24347
                ||||||||||| |||||||||| ||||| ||  |||||| ||||| |||| | ||| || 
Sbjct  7497490  ATGCAGGTGCACATATGACAAATAATAA-CCAGGACCTTTATATCACCCCCAACTGGTGG  7497432

Query  24348    GGATTGGGATTCTTTTGTCCCTTTCTCTCCATAAAACCAGGTTACTCATCTTGTGTGGCA  24407
                ||| |||||| |||||| |||||||||||||||| |||||| ||||||||||||||||||
Sbjct  7497431  GGAATGGGATCCTTTTGACCCTTTCTCTCCATAATACCAGGCTACTCATCTTGTGTGGCA  7497372

Query  24408    ACAAAATATATGGTctacttaacagagaaagagactccacaggaaaaaaaaaaggatttt  24467
                | |||||||||||||||||| ||||||||||||| | |     |||||||||||||||||
Sbjct  7497371  ATAAAATATATGGTCTACTTCACAGAGAAAGAGA-TTCTTTTAAAAAAAAAAAGGATTTT  7497313

Query  24468    tattatgaaatgagcaaagccatgggaatagatgtgagattattcggggaggtaaaggaa  24527
                |||||||||||||||||||| |||||||||||||||||||||||| ||||||||||||||
Sbjct  7497312  TATTATGAAATGAGCAAAGCAATGGGAATAGATGTGAGATTATTCAGGGAGGTAAAGGAA  7497253

Query  24528    gacaaaggttttgaaaggaaaaatgaggagaattacataaatttttttgaaagactcatt  24587
                |||||||||||||||||||||||| |||||||||||||| | | ||||| ||||||||||
Sbjct  7497252  GACAAAGGTTTTGAAAGGAAAAATCAGGAGAATTACATACACTGTTTTGGAAGACTCATT  7497193

Query  24588    cttggtcacaagtatgaaaaccaagggagcctcagtgcagtgttggaaagATTCCTCCTC  24647
                ||||||||||||||| || |||||||| ||||||||||| ||||||||||||||||||||
Sbjct  7497192  CTTGGTCACAAGTATCAACACCAAGGGGGCCTCAGTGCAATGTTGGAAAGATTCCTCCTC  7497133

Query  24648    CAC-CCTCTCAATAACCCCCAACACATTTACCAAGTCTTTGTTCACTCCCAGGATTCCAT  24706
                ||| || |||||||||||||||||  ||||||||||||| |||||||||| |||| ||||
Sbjct  7497132  CACGCC-CTCAATAACCCCCAACATGTTTACCAAGTCTTGGTTCACTCCCCGGATCCCAT  7497074

Query  24707    TAAAACACCCAGCTCAACCCTGACCAGCCTCCACCTTCACTTCCCTTTGTAATTTTGACA  24766
                |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7497073  TAAAACACACAGCTCAACCCTGACCAGCCTCCACCTTCACTTCCCTTTGTAATTTTGACA  7497014

Query  24767    T-AAATTtgttacaggaccatcaggttcctatgccggctgcacagtagcttaccaatatt  24825
                | |  ||| |||||||||||||||||||||||||| || |||||||||| ||| ||||||
Sbjct  7497013  TGACTTTTTTTACAGGACCATCAGGTTCCTATGCCTGCAGCACAGTAGCATACTAATATT  7496954

Query  24826    ctgagacagcaggatttgcagcagaaagtttaatgatcacagggtggctgaatgagaagc  24885
                ||||||||||||| ||||||||||| ||||||| ||||||||||||||  ||||| ||||
Sbjct  7496953  CTGAGACAGCAGGGTTTGCAGCAGAGAGTTTAACGATCACAGGGTGGCAAAATGAAAAGC  7496894

Query  24886    tgggaggagatcctcaaattcatctccccaaggagtactgagggtttccagtggatcctg  24945
                |||||||||| ||||||||||||||||||||| ||||||||| |||| ||| ||||| ||
Sbjct  7496893  TGGGAGGAGACCCTCAAATTCATCTCCCCAAGAAGTACTGAGAGTTTTCAGAGGATCATG  7496834

Query  24946    gatagcaaggggctggaaagttggtgtagtttgatggcaataagaggtatgaagttatca  25005
                ||||||||| |||||||||||||||| |||||| ||||| ||||||||||||||| ||||
Sbjct  7496833  GATAGCAAGAGGCTGGAAAGTTGGTGCAGTTTGGTGGCAGTAAGAGGTATGAAGTCATCA  7496774

Query  25006    cgatgtcagaacggcattctttggtgagttgatgccttgcagggcccttcagatcagctg  25065
                 ||||||| ||| |||||| ||||||||||| |||||||||||||||||||||||| |||
Sbjct  7496773  GGATGTCAAAACTGCATTCCTTGGTGAGTTGGTGCCTTGCAGGGCCCTTCAGATCACCTG  7496714

Query  25066    gcatcagtagtttcactgacatgcagaacctgaaagaatatctcaaatgaaaaacttaat  25125
                 ||||||||| |||||||||||||||||||||||||||||| |||||||||||| |||||
Sbjct  7496713  CCATCAGTAGCTTCACTGACATGCAGAACCTGAAAGAATATGTCAAATGAAAAAGTTAAT  7496654

Query  25126    gtttcacaatgcttaaattgttgtctgcagcgtagttaaggggaattgtagtctaagttc  25185
                |||| |||| || ||||||||||||||||| | ||||||||| || |||| |||||| ||
Sbjct  7496653  GTTTTACAAGGCCTAAATTGTTGTCTGCAGGGCAGTTAAGGGCAACTGTAATCTAAGGTC  7496594

Query  25186    tacacgattttgggacagtaggctgccagcaaccatgaggaagcaggtcagagggcaagc  25245
                |||| ||||||||||||| |||||||||||||||||||||||||||||||||| ||||||
Sbjct  7496593  TACATGATTTTGGGACAGCAGGCTGCCAGCAACCATGAGGAAGCAGGTCAGAGAGCAAGC  7496534

Query  25246    tgacctcctggtgaatgctgaatgcgtttcaagcttggtttgtttttgttcctccccctc  25305
                ||||||| || ||||||||||||||  | |||||||||||| | |||||| |||||||||
Sbjct  7496533  TGACCTCATGATGAATGCTGAATGCACTGCAAGCTTGGTTTATGTTTGTTTCTCCCCCTC  7496474

Query  25306    tctttttcaccgattaaatttataaagtttagaaatacggtttcaATTTCTTCCAGACAA  25365
                 ||| ||||| |||||||||||||||||||| || || |||| ||||||||||||||  |
Sbjct  7496473  CCTTCTTCACTGATTAAATTTATAAAGTTTATAAGTATGGTTGCAATTTCTTCCAGAGTA  7496414

Query  25366    GCCTTAACCTAAGCCCTGAGACCACTCAAGCCCTCAGTGGCACCTCTCTTCCACCAGCAT  25425
                |||||||||||||||||||||||||||| | |||||||||||||||||||||||||||| 
Sbjct  7496413  GCCTTAACCTAAGCCCTGAGACCACTCAGGTCCTCAGTGGCACCTCTCTTCCACCAGCAG  7496354

Query  25426    GAG-CAAATAAATTGCTACCTTAGGTGATATAAAACCCACAAGATGATTCG-ATACATGG  25483
                |||  ||| |||||||||||||||||||||||||||||||||||  ||| | ||||||||
Sbjct  7496353  GAGTGAAA-AAATTGCTACCTTAGGTGATATAAAACCCACAAGACCATT-GAATACATGG  7496296

Query  25484    AG-ttttt-tttCTGATTTTGTAGGGATGACTTCTTTGTTTCTATAAAGCTGTTTTAACT  25541
                || ||||| ||| |||||||||||||| |||| || ||||| ||||||||| ||||||||
Sbjct  7496295  AGATTTTTATTT-TGATTTTGTAGGGACGACTCCTCTGTTTTTATAAAGCTATTTTAACT  7496237

Query  25542    ATAAAACAATTTTATAATTTTGATGTGGCCAAAGATCTCCCAAC---ACTACTTTCAGGT  25598
                |||||||| |||| | ||||||||||||||||||||||||||||   ||||||||||| |
Sbjct  7496236  ATAAAACATTTTTGTGATTTTGATGTGGCCAAAGATCTCCCAACAATACTACTTTCAGAT  7496177

Query  25599    TTTATTTTTCTGTCTACTATC-CAGAACAGATCAAACCCTTCCCTGCCTCAAACTCAGGA  25657
                |||| ||||||||||| ||||   ||| |||| | |||||||||||| ||| ||||||||
Sbjct  7496176  TTTAGTTTTCTGTCTAATATCTGGGAA-AGATTAGACCCTTCCCTGCTTCAGACTCAGGA  7496118

Query  25658    CTATATAGGTCATATATCAGTAAAATTCCATCAGTGTTTGCGGAgttcatgaatgaatga  25717
                ||||  |||||| |||| ||| |||||||||||||||||| | |||||||||||||||||
Sbjct  7496117  CTATGCAGGTCACATATTAGTGAAATTCCATCAGTGTTTGTGAAGTTCATGAATGAATGA  7496058

Query  25718    attctttttttttttttttttttttttttttgtgacaaagtctacctctgtcacccagaa  25777
                |                    ||||||||||  |||||| ||| ||||||||||||||| 
Sbjct  7496057  A--------------------TTTTTTTTTTCCGACAAATTCTCCCTCTGTCACCCAGAG  7496018

Query  25778    cggtgtgcaatggtgcaatcttggctcactgcaaccattgccccctggattcaagcgatt  25837
                 || |||||||||||||||||||| ||||||||||||||||| | ||| |||||||||||
Sbjct  7496017  TGGAGTGCAATGGTGCAATCTTGGTTCACTGCAACCATTGCCTCTTGGGTTCAAGCGATT  7495958

Query  25838    ctcccacctcagcctcctgagtagctggattacaggcacctgccatcatgccaggctaat  25897
                ||||||||||||||||||||||||||||||||||||||  ||||||| | || | |||||
Sbjct  7495957  CTCCCACCTCAGCCTCCTGAGTAGCTGGATTACAGGCATGTGCCATCGTCCCTGTCTAAT  7495898

Query  25898    ttttgtgtttttgtagag-ctggggtttcatcatgttggccttgcaggtcttg-atcgcc  25955
                | |||| ||||||||||| | ||||||||| | ||||||||| ||  |||||| || | |
Sbjct  7495897  TCTTGTATTTTTGTAGAGAC-GGGGTTTCACCTTGTTGGCCTGGCTCGTCTTGAAT-GTC  7495840

Query  25956    tgacctcaggtgatccagccaacttggactctcaaagtgcagggattacaggtgtgagcc  26015
                ||| ||||||||| ||| ||||||||  ||| |||||||| ||||||||||| |||||||
Sbjct  7495839  TGAACTCAGGTGACCCACCCAACTTGTCCTCCCAAAGTGCTGGGATTACAGGAGTGAGCC  7495780

Query  26016    acctcacccggcctttaatgaGTGAATTCTTGATTTCCACCCTATTCCTAACACTGTCAA  26075
                ||||  ||||| ||| ||||| || |||||||||| ||||||||| ||||||||||||||
Sbjct  7495779  ACCTTGCCCGGTCTTGAATGAATGCATTCTTGATTCCCACCCTATCCCTAACACTGTCAA  7495720

Query  26076    TTTCTTGATTCATGAACTTAATATGGATAGCTGATATGAATGGATATCTGATTCAATCCA  26135
                ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct  7495719  TTTCTTGATTCATGAACTTAATATGGATATCTGATATGAATGGATATCTGATTCAATCCA  7495660

Query  26136    GTAATCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGGGTGGAGCTTCAGAAATGCA  26195
                 ||||||||||| |||||||| |||||||| |||||||||||||||||||||||||||||
Sbjct  7495659  TTAATCTGGGGAGAGCCAAAACCCCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGCA  7495600

Query  26196    ATCAGATAGCACTTTTTGATTGGAAGCAAGCACTGGATA-GATGGAGGGGTGTGGGTGGG  26254
                |||||||| ||||| |||||||||||| |||| |||||| | ||||||||||||||||||
Sbjct  7495599  ATCAGATATCACTTGTTGATTGGAAGCTAGCAGTGGATACG-TGGAGGGGTGTGGGTGGG  7495541

Query  26255    AGTTGTGATTAGAAAGATCGATAAAAGTTTCTGAAGGCCCACAGGAGAGACCCAAAGTCT  26314
                |||||||||||||||| || ||||||| |||| ||| ||||||| |||||||||||||||
Sbjct  7495540  AGTTGTGATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGAAGAGACCCAAAGTCT  7495481

Query  26315    TCAAGTCTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTAAGCACTCTGCAAACTCAGTCC  26374
                ||||| ||||||||||||||| |||||||||||||||| ||||| || |||||| |||||
Sbjct  7495480  TCAAGCCTGGAGTTCCTGCTTAGTTCTTCCTGAGGTCTGAGCACCCTCCAAACTGAGTCC  7495421

Query  26375    AGATCTAGTAAGTCACTCAT-T-TCTGGAAGGACACTCCCATCTGACCTATAGTCAGCCG  26432
                |||||| |||||||||| || | |||| ||||||||||||| |||||||| ||||||| |
Sbjct  7495420  AGATCTGGTAAGTCACTAATCTCTCTGTAAGGACACTCCCAACTGACCTACAGTCAGCTG  7495361

Query  26433    GTCTGGGACGGGGGCAATGCAGCCTATGATGGCACCGAGCTATAT-CTGTCTTT-tatat  26490
                |||||||| || | || ||||||||| |||||||  ||| ||||| |||| ||| | | |
Sbjct  7495360  GTCTGGGATGGTGACAGTGCAGCCTAAGATGGCATAGAGTTATATCCTGT-TTTGT-TTT  7495303

Query  26491    atatat-atatGAACAATTTGAAGATTTGAATTTTTTCCTCTATATGCAGTTTTGTCTTT  26549
                 | | | ||||||||||||||||| |||| |||||||||| || ||||||||||||||||
Sbjct  7495302  TTTTCTCATATGAACAATTTGAAGCTTTGCATTTTTTCCTTTAAATGCAGTTTTGTCTTT  7495243

Query  26550    ATTTCAAAAAATTGGATTGTGCTTTGGTTTATGTCATTTcaaaattcttgatgggagcaa  26609
                ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| 
Sbjct  7495242  ATTTCAAAAAATTGGATTGTGCTTTGGTTTATGTCATTTCAAAATTCTTGAAGGGAGCAG  7495183

Query  26610    tgactcatgcccataacctcaacaccttgggaggccaaagcgggaggatcatttgagccc  26669
                |||||||||||  ||||| |||||| ||||||| |||| ||||||||||||||| |||||
Sbjct  7495182  TGACTCATGCCTTTAACCCCAACACTTTGGGAGACCAAGGCGGGAGGATCATTTCAGCCC  7495123

Query  26670    aggggtttgagaccaacctgggcaacatggcaaaaatgcagctctacaaaacattctttt  26729
                |||||| |||||||||||||| ||||| ||||||||  || ||||| |||| |||| |||
Sbjct  7495122  AGGGGTCTGAGACCAACCTGGACAACACGGCAAAAACCCATCTCTATAAAATATTC-TTT  7495064

Query  26730    tttgaagcagggatggagtctcaccctgttgccaaggctggagtgcagtggcaagagctc  26789
                 ||||||  ||||||||||||| | ||||| |||||||||||||||||||||| || |||
Sbjct  7495063  ATTGAAGGGGGGATGGAGTCTCGCTCTGTTTCCAAGGCTGGAGTGCAGTGGCACGATCTC  7495004

Query  26790    aactcactgcaacctcttcctcccaggctcaaacaattttcatgtctcagcttcctgagt  26849
                || ||| |||||| ||| |||||||||||||| ||||| ||||| |||||| ||||||||
Sbjct  7495003  AAATCATTGCAACTTCTGCCTCCCAGGCTCAAGCAATTCTCATGCCTCAGCCTCCTGAGT  7494944

Query  26850    agctggtattacatccctctgccaccatgtct-gcttaatttttgtatttttagtagtgg  26908
                | ||||||||||||||  |||||| | || || || ||||||||||||||||||||| ||
Sbjct  7494943  ATCTGGTATTACATCCAACTGCCAACTTGCCTGGC-TAATTTTTGTATTTTTAGTAGAGG  7494885

Query  26909    tggggtttcaccatgctggccaggttggtctcaaactcctgacatcaagtgatcctcctg  26968
                |||||||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||
Sbjct  7494884  TGGGGTTTCACCATGCTGGCCAAGTTGGTCTCAAACTCCTGACCTCAAGTGATCCACCTG  7494825

Query  26969    cctaggcc-cccaaaagtgctggaatgacggccgtgagccaATGGTGGTCAGCctctaca  27027
                ||| |||| ||| ||||||||||||| || ||| ||||||| ||||| |  |||||||||
Sbjct  7494824  CCTTGGCCTCCC-AAAGTGCTGGAATTACAGCCCTGAGCCACTGGTGCTTGGCCTCTACA  7494766

Query  27028    aaatatatatatcttttaatttgccaggcatggtagcatgcatctgtattcccagctatt  27087
                ||||||| |||| |||||||| ||| ||||||||||||||||||||| |||||| || | 
Sbjct  7494765  AAATATACATATTTTTTAATTAGCCGGGCATGGTAGCATGCATCTGTCTTCCCAACTGTA  7494706

Query  27088    tggtttgctgacatgggagaatcacttgagcccagaagattgaggctgcagtgagccatg  27147
                ||| ||||||||||||||||| || |||||||||||||||||||||||||||||||||||
Sbjct  7494705  TGGGTTGCTGACATGGGAGAAACAATTGAGCCCAGAAGATTGAGGCTGCAGTGAGCCATG  7494646

Query  27148    ctcacaccactgctgtactccagcctgggcaacagagtaagaccctgctaaaaacaaaaa  27207
                |||| |||||||||||||||||||||||||||||  |  ||  ||  || |  ||    |
Sbjct  7494645  CTCATACCACTGCTGTACTCCAGCCTGGGCAACATTGCGAG-GCC--CT-ATTAC----A  7494594

Query  27208    cgaaaacaaacaaacaaaaaacCTTAACCAAAGAGAATCTTTGACCTTAATTTTAAACCA  27267
                 |          || |||||| ||||||||||||| ||||||||||||||||||||||||
Sbjct  7494593  -G----------AA-AAAAAATCTTAACCAAAGAGGATCTTTGACCTTAATTTTAAACCA  7494546

Query  27268    ATCACATCCTCACTGTAATTCTTCCTCCCGAATGGAGACATgggtgt-gagggtgcatgc  27326
                |||||||||||| ||||| |||||| ||| || |||||||||||||| || |||||||||
Sbjct  7494545  ATCACATCCTCATTGTAACTCTTCCACCCAAACGGAGACATGGGTGTGGA-GGTGCATGC  7494487

Query  27327    ctgtaatcccagctacatggaaggctgaagcatgagaattgcttgaatctcagaggcgga  27386
                ||||||||||||||||||||||||||||||||| || ||  |||||| ||  ||||| ||
Sbjct  7494486  CTGTAATCCCAGCTACATGGAAGGCTGAAGCATAAGTATCACTTGAACCTGGGAGGCAGA  7494427

Query  27387    agttacagtgagctgagatgg-agccgctgcactccagcctgggcgacaaagtgagactc  27445
                 |||||||||||||||||||| | || ||| ||||||||||||| ||  |||||||||||
Sbjct  7494426  GGTTACAGTGAGCTGAGATGGCA-CCACTGTACTCCAGCCTGGGTGATGAAGTGAGACTC  7494368

Query  27446    agcttcaccc-acaccaaaaaaaaTTAGATTATACCACCCAGGTGATCACTGGATACATG  27504
                |||| | ||| ||| | |||||||||| ||||||||||||||||||||| ||||| ||||
Sbjct  7494367  AGCTAC-CCCGACA-CGAAAAAAATTAAATTATACCACCCAGGTGATCATTGGATTCATG  7494310

Query  27505    AAGATTTCTATTGTGTGTTATTGGGGACTGTCAACTCCGTCTTTG-AAAACTGTTTTAAC  27563
                |||||||||| ||||| || || ||||||||||  ||  |||||| ||||||||||||||
Sbjct  7494309  AAGATTTCTACTGTGTTTTCTTAGGGACTGTCATGTCTATCTTTGTAAAACTGTTTTAAC  7494250

Query  27564    TCTGAAATATTTTGATAAATTTGATGTGGCCAAGGATCCCTCAACAAAGATACTTTCAAG  27623
                |||||||||||||||||||||||||||||||||||||| |||||||||||||||||| ||
Sbjct  7494249  TCTGAAATATTTTGATAAATTTGATGTGGCCAAGGATCTCTCAACAAAGATACTTTCGAG  7494190

Query  27624    TTTTCTTTCTTTCTGTCTAATATCAGGAAGAGATTCAACACTTCCCTATCTCACACTCAG  27683
                |||| |||||||||||||||| ||||||||||||||||| ||||||||||||||||||||
Sbjct  7494189  TTTT-TTTCTTTCTGTCTAATGTCAGGAAGAGATTCAACTCTTCCCTATCTCACACTCAG  7494131

Query  27684    GACTATGAAGGACACATATTAGTAAACCTCCATGTTTGTGGAGGGAATCAGTGAATGAGT  27743
                 ||||  |||| ||||||||| ||||  |||||||||||||||  |||||||||||||||
Sbjct  7494130  AACTACAAAGGTCACATATTACTAAAATTCCATGTTTGTGGAGTAAATCAGTGAATGAGT  7494071

Query  27744    CCTGGACTTTCACCCTATCCCTAAATCTTTCACTTTCATGGATGAATATCTAATTCAATC  27803
                |||||||||||||| ||||||||||| ||||||||||||||||||||||||||||  || 
Sbjct  7494070  CCTGGACTTTCACCATATCCCTAAATATTTCACTTTCATGGATGAATATCTAATTTGAT-  7494012

Query  27804    AGTTAATCTGGAAGAAAGCCAAAAATCCAATCAGGATTAACTGGGTAGAGTTTAAGAAGT  27863
                |||||||||||||||||| |||||||||||||| |||||||||| | ||| |||||||||
Sbjct  7494011  AGTTAATCTGGAAGAAAGACAAAAATCCAATCATGATTAACTGGATGGAGCTTAAGAAGT  7493952

Query  27864    CGAATCAAATGTAGTtctctctctctctctctctcttttcttttcttttttttttttttt  27923
                | |||| |||||||     | ||||||||||||||   ||   ||              |
Sbjct  7493951  CTAATCCAATGTAG-----T-TCTCTCTCTCTCTC---TC---TC--------------T  7493918

Query  27924    tttttgaatctagcctatttcacaggctggagtgcagtggtgtattgtcagctcactgca  27983
                ||||||||||||||| ||||| ||||||||| || |||||| || | |||||| ||||||
Sbjct  7493917  TTTTTGAATCTAGCCAATTTCCCAGGCTGGATTGTAGTGGTATAATCTCAGCTAACTGCA  7493858

Query  27984    acctctgcctcctgggttcaagtgatcctcctgcctcagcctccctagtagcttggacta  28043
                |||| ||||||||||||||||| ||||||||||| |||||||||||||||||||||||||
Sbjct  7493857  ACCTATGCCTCCTGGGTTCAAGCGATCCTCCTGCTTCAGCCTCCCTAGTAGCTTGGACTA  7493798

Query  28044    taggcgcagaccaccgcacctggctaatttttctaattttggtagaggtagggttttacc  28103
                |||||||||||||| ||||||||||||||||| ||||||| |||||||||| ||||||||
Sbjct  7493797  TAGGCGCAGACCACTGCACCTGGCTAATTTTTGTAATTTTAGTAGAGGTAGTGTTTTACC  7493738

Query  28104    atgttggccaggctggtctcaaactcctgacctcagataatccacctgcctctgcctccc  28163
                |||||||||||| |||||||||||||||||||||||||||||||  ||||||||||||||
Sbjct  7493737  ATGTTGGCCAGGATGGTCTCAAACTCCTGACCTCAGATAATCCA-ATGCCTCTGCCTCCC  7493679

Query  28164    agagggctgggattacaggtgtgagtcactgcacacagccAAAGTGGTTCATTTTGAATA  28223
                | || ||||||||||||||||||||||||||| ||||||||||||||||||||||||| |
Sbjct  7493678  AAAGTGCTGGGATTACAGGTGTGAGTCACTGCGCACAGCCAAAGTGGTTCATTTTGAACA  7493619

Query  28224    TGTGTGAGAGGTGTGTATTGGAAACATCTGTGTCTTGCCAATGATGCATAACACTGTCAC  28283
                || || |||||||||||||||||||| ||||||||||| |||||||||||||||||||||
Sbjct  7493618  TGCGTAAGAGGTGTGTATTGGAAACACCTGTGTCTTGCGAATGATGCATAACACTGTCAC  7493559

Query  28284    ATAGCTTTCAAAGCTTCTTGCTGAAATTTTCAATAATGAGACCAGgcagaggctcatgcc  28343
                | |||||||||||||||||| ||||||||||||||||||| || || ||||| | | |||
Sbjct  7493558  ACAGCTTTCAAAGCTTCTTGGTGAAATTTTCAATAATGAGTCCCGGAAGAGGATTACGCC  7493499

Query  28344    tgcaatcccagcactttgggaggccaaagtgggtggattgtttgagtctaggagttcaag  28403
                || |||||||| ||||||||||||||| | ||||||| ||||||||||||||||||||||
Sbjct  7493498  TGTAATCCCAGTACTTTGGGAGGCCAAGGCGGGTGGAATGTTTGAGTCTAGGAGTTCAAG  7493439

Query  28404    accagcctggacaacatagtgaaacccactgtctttacaaaaagtcaaaaaataaaaGAT  28463
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7493438  ACCAGCCTGGACAACATAGTGAAACCCACTGTCTTTACAAAAAGTCAAAAAATAAAAGAT  7493379

Query  28464    TAGCTGGGTACGAGATCTGAGCTTCAGAGATCCTCGGTAACATTTGCCAGTGCTATGAGT  28523
                |||||||| | |||||| ||||||||||||||||||||||||||| ||||||||||||||
Sbjct  7493378  TAGCTGGGCATGAGATCCGAGCTTCAGAGATCCTCGGTAACATTTCCCAGTGCTATGAGT  7493319

Query  28524    TTAGTGGATCAGTGGCTAATAATTCATGGACTACGAGGGATCTTGCCTGCTCTTTAGAAG  28583
                ||| || | |||||||||||||||||||||||| || ||||||||||||||||||||| |
Sbjct  7493318  TTATTGCAACAGTGGCTAATAATTCATGGACTAGGAAGGATCTTGCCTGCTCTTTAGAGG  7493259

Query  28584    TTGGGACACATTCTTCATGGTACCAGAAGGGTAGAACTATGTCTCTGTGGCCACTTATTG  28643
                |||||||||| ||||| |||||||||||||| ||||| ||| |||||| |||||||||||
Sbjct  7493258  TTGGGACACACTCTTCTTGGTACCAGAAGGGCAGAACCATGCCTCTGTAGCCACTTATTG  7493199

Query  28644    CAGAAAGGAACTGGAGTAAACTGAGGGCTCTTTCACACATGCTAGAGAAATGACTTGGGC  28703
                ||||| |||| ||||||||||||||||||||||||||| ||||||||||||||||| |||
Sbjct  7493198  CAGAACGGAATTGGAGTAAACTGAGGGCTCTTTCACACGTGCTAGAGAAATGACTTTGGC  7493139

Query  28704    CCTGGGAGAATTGGGGGTTGCAGGGGATTGGTCGGAGGAACTTGCCTTTTTGCTGGATTG  28763
                ||| |||||| ||||| |||| ||||| ||| | ||| ||||||||||||  || |||||
Sbjct  7493138  CCTAGGAGAAGTGGGGCTTGCTGGGGAATGGCCCGAGAAACTTGCCTTTTCACTTGATTG  7493079

Query  28764    TGCTGTAGAGTTTTTCCTTGTAGATTTGTCAGAATGAGCCTCCAGACCCCATCCAGACTC  28823
                | || ||||||||||||| | |||||||||||||||||||||||| ||||||||||||| 
Sbjct  7493078  TCCTCTAGAGTTTTTCCTCGGAGATTTGTCAGAATGAGCCTCCAGGCCCCATCCAGACTG  7493019

Query  28824    CTGGAGCTGGCAGGGCAGAGCCTGATGAGGAAGCAGTTCTTGACTATCTTCACCCTGGAC  28883
                |||||||||||||||||||||||| ||||||| ||||||||||| |||||||||||||| 
Sbjct  7493018  CTGGAGCTGGCAGGGCAGAGCCTGCTGAGGAACCAGTTCTTGACCATCTTCACCCTGGA-  7492960

Query  28884    T-AGCTGCCCAGGGAGGTCTCCCCTCTGACGTTCATGGAGGCCTTCAGCATGAGATGTTG  28942
                | |||||||||||||||||| |||||||| ||||||||||||||||||||||||| ||| 
Sbjct  7492959  TGAGCTGCCCAGGGAGGTCTTCCCTCTGATGTTCATGGAGGCCTTCAGCATGAGACGTTT  7492900

Query  28943    TGAGGCCCTGAAGCTGATGGTGCAGGCCTGGTCCTCCCTTCA-CCTCCCTCTGGGATCCC  29001
                ||||||||||||||||||||||||||||||| ||| || ||| |||||||||||||||||
Sbjct  7492899  TGAGGCCCTGAAGCTGATGGTGCAGGCCTGGCCCTTCC-TCAGCCTCCCTCTGGGATCCC  7492841

Query  29002    TGATGAAGACAAC-TCATCTGGAGACCTTGCAAGCTGTGCTGAAGGGACTTGATACACTA  29060
                |||||||||| || |||||||||||||||||||||||| |||| ||||||||||||||| 
Sbjct  7492840  TGATGAAGAC-ACTTCATCTGGAGACCTTGCAAGCTGTCCTGAGGGGACTTGATACACTG  7492782

Query  29061    GTGTCCCAGAAGGTTTGCCCCAGTTGAGGTGACTCAGGTGGC-CTGGTGGGAAGGGTCCA  29119
                ||| ||||||||||| ||||||| ||||||||||||||||||  | | ||||||||||||
Sbjct  7492781  GTGGCCCAGAAGGTTCGCCCCAGGTGAGGTGACTCAGGTGGCTTTCG-GGGAAGGGTCCA  7492723

Query  29120    GGCATCCAGGGAAGGGACAGCTGGCTCAGGAGGAGTGGCAGTG-TGTGGGAGCTAGGGTG  29178
                ||||||||||||||||||||||||||||||||||||||  | | || |||||||||||||
Sbjct  7492722  GGCATCCAGGGAAGGGACAGCTGGCTCAGGAGGAGTGGTGGGGTTG-GGGAGCTAGGGTG  7492664

Query  29179    GCTCAGAGGCTTCTGATGGTACCCATGAGAGGCCTTGGCCATTGCCCAGATCCTCTGGAA  29238
                |||||||||||||||| ||| |||||||||||||||||||||||||||||||||||||||
Sbjct  7492663  GCTCAGAGGCTTCTGACGGTGCCCATGAGAGGCCTTGGCCATTGCCCAGATCCTCTGGAA  7492604

Query  29239    AAGGACTGCTCACCATACAGAGTCCACTGAGGAAACAGGAACCTGCTTCCTTCCCAGTGG  29298
                |||| ||||||||||||||| ||||||||||||||||||| | || ||||| |||||  |
Sbjct  7492603  AAGGTCTGCTCACCATACAGGGTCCACTGAGGAAACAGGAGCTTGTTTCCT-CCCAGCAG  7492545

Query  29299    AAGGTAAAGGTACTAGAAGTGGGTAC  29324
                || |||||||||||||||||||||||
Sbjct  7492544  AAAGTAAAGGTACTAGAAGTGGGTAC  7492519


 Score = 5662 bits (3066),  Expect = 0.0
 Identities = 3414/3576 (95%), Gaps = 48/3576 (1%)
 Strand=Plus/Minus

Query  15705    GTGGCAACAAAATATATGGTAAACTTAACAGAGAAGGAGACTGTCAG-aa-aaaaaaaaa  15762
                ||||||||||||||||||||  ||||||||||||||||||||||  | || |||||||||
Sbjct  7447872  GTGGCAACAAAATATATGGTCTACTTAACAGAGAAGGAGACTGT--GTAAGAAAAAAAAA  7447815

Query  15763    aaaaagatgtgtttatcctgaaatgaggaaagcaatgggaatagatgtgagattattttg  15822
                |||||||  |||||||||||||||||| |||||| ||||||| |||||||||||||||||
Sbjct  7447814  AAAAAGA--TGTTTATCCTGAAATGAGCAAAGCATTGGGAATGGATGTGAGATTATTTTG  7447757

Query  15823    ggagaaaaa-ggaagacaaaggttttgaaaggaaaaataaggaggattatacaaattgtt  15881
                |||||||||  |||||  ||||||||||||||||||||||||||||||||| ||||||||
Sbjct  7447756  GGAGAAAAATAGAAGATGAAGGTTTTGAAAGGAAAAATAAGGAGGATTATATAAATTGTT  7447697

Query  15882    ttgaaagactcaaccttggtcctaagaatcaaaagtaaaggggcatcagtgaaatgttgg  15941
                ||||||| |||| |||||||||||| ||||||||  ||||||||||||||||||| ||||
Sbjct  7447696  TTGAAAGGCTCATCCTTGGTCCTAATAATCAAAACCAAAGGGGCATCAGTGAAATATTGG  7447637

Query  15942    atagATTCCACCTCCACCCCCTCAGTAACCCCCAACATGTTTACCAAGTCTTGGTTAACT  16001
                ||||||||| |||||||||||||||||||||||||||||||||||||||||||||| |||
Sbjct  7447636  ATAGATTCCTCCTCCACCCCCTCAGTAACCCCCAACATGTTTACCAAGTCTTGGTTCACT  7447577

Query  16002    CCCAGGATCCCATTAAAACACCCAGCTCAACCATGCCCATCCTCTACCCTCACTT-CTCT  16060
                |||||||||||||||||||||| |||||||||| ||||||||||||||||||||| || |
Sbjct  7447576  CCCAGGATCCCATTAAAACACCAAGCTCAACCAAGCCCATCCTCTACCCTCACTTCCT-T  7447518

Query  16061    TTGTAATTTTGACATGATTTTAttacaggaccatcaggttcctatgcctgctgcacagta  16120
                ||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Sbjct  7447517  TTGCAATTTTGACATGATTTTATTACAGGACCATCAGATTCCTATGCCTGCTGCACAGTA  7447458

Query  16121    gctgaccaatattctgagacagcagtgtttgcagcagacagtttaatgatcacagggtgg  16180
                ||| ||||||||| ||||||||||| |||||||||||| |||||||||||||||||||||
Sbjct  7447457  GCTTACCAATATTTTGAGACAGCAGAGTTTGCAGCAGAGAGTTTAATGATCACAGGGTGG  7447398

Query  16181    ctaaatgagaagctaggaggatatcctcaaattcatctcccc-a--agtag-t--actga  16234
                ||||||||||||||||||||| |||||||||||||||||||| |  || || |  |||||
Sbjct  7447397  CTAAATGAGAAGCTAGGAGGAGATCCTCAAATTCATCTCCCCAAGGAGGAGATCCACTGA  7447338

Query  16235    gggtttccagtggatcctggatagcaaggggctggaaagttggtgtagaggtaagaggga  16294
                |||||||||||||||||||||||||||||||||||||||||| | ||||| |||||||||
Sbjct  7447337  GGGTTTCCAGTGGATCCTGGATAGCAAGGGGCTGGAAAGTTGATATAGAGTTAAGAGGGA  7447278

Query  16295    tgaagtcatcaggatgtcaaaactgcattctttggtgagttggtgccttgcagagccctt  16354
                ||||||||||||||||||||||||||||||||||||| |||||||||||| || ||||||
Sbjct  7447277  TGAAGTCATCAGGATGTCAAAACTGCATTCTTTGGTGCGTTGGTGCCTTGTAGGGCCCTT  7447218

Query  16355    cagatcagctggcatcagtagtttcactgacatgcagaacctgaaagaatatctcaaatg  16414
                |||||||||||||||||||| |||||||||||||||||| | | ||||||||||||||||
Sbjct  7447217  CAGATCAGCTGGCATCAGTACTTTCACTGACATGCAGAA-C-GTAAGAATATCTCAAATG  7447160

Query  16415    agaaagttaatgttttacaaggcttaaattgttgtctgcagggtagttaaggggaactgt  16474
                | ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct  7447159  AAAAAGTTAATGTTTTACAAGGCTTAAATTGTTGTCTGCAGGGCAGTTAAGGGGAACTGT  7447100

Query  16475    aagctaaggtctacttgatttggggacagtaagctgccagcaaccatgaggaagaaggtc  16534
                || ||||||||||  |||||||||||||||| ||||||||||||||||||||||||||||
Sbjct  7447099  AATCTAAGGTCTAAATGATTTGGGGACAGTAGGCTGCCAGCAACCATGAGGAAGAAGGTC  7447040

Query  16535    agagagcaagctgacctcatggtgaatgctgaatgcgctgcaagcttggtttatttttgt  16594
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7447039  AGAGAGCAAGCTGACCTCATGGTGAATGCTGAATGCGCTGCAAGCTTGGTTTATTTTTGT  7446980

Query  16595    ttctccccctcccttcttcactgattaaacttataaagtttacaggtatcatttcaATTT  16654
                ||||||||||||||||||||||||||||| |||||||||||| ||||||| |||||||||
Sbjct  7446979  TTCTCCCCCTCCCTTCTTCACTGATTAAATTTATAAAGTTTATAGGTATCGTTTCAATTT  7446920

Query  16655    CTTCCAGAGAAGACTTAACCTAAGCCCTGAGACCACTCAAGCCCTCAGTGGCACCTCTCT  16714
                |||||| ||||| |||||||||||| ||||||||||||| ||||| ||||||||||||||
Sbjct  7446919  CTTCCAAAGAAGCCTTAACCTAAGCACTGAGACCACTCACGCCCTGAGTGGCACCTCTCT  7446860

Query  16715    TCCACCAGCACGAGTGAAGAAACTGCTACCTTAGGTGATATAAAACCCACAAGACCATTC  16774
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7446859  TCCACCAGCACGAGTGAAGAAACTGCTACCTTAGGTGATATAAAACCCACAAGACCATTC  7446800

Query  16775    CATACATGGAGATCTTTATTCTTATTTTGTAGGGACGACTCCTCTGTGTTTATACAGCTA  16834
                ||||||||||||||||||||||||||||||||||| |||| | | || |||||| || | 
Sbjct  7446799  CATACATGGAGATCTTTATTCTTATTTTGTAGGGATGACT-C-C-GTTTTTATAAAGTTG  7446743

Query  16835    TTTTAACTAGAAATATTTTTATAAATTTTATAATTTTGATGTGGCCAAAGATCTCCCCAC  16894
                |||||||||| || |     ||   |||||||||||||||||||||||||||||||||||
Sbjct  7446742  TTTTAACTAG-AA-A---GCAT---TTTTATAATTTTGATGTGGCCAAAGATCTCCCCAC  7446691

Query  16895    AACACTACTTTCAGGTTTTATTTTTCTGTCTAATGTCTGGAACAGATCAACCCCTTCCCT  16954
                ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Sbjct  7446690  AACACTACTTTCAGGTTTTATTTTTCTGTCTAATGTCCGGAACAGATCAACCCCTTCCCT  7446631

Query  16955    GCCTCACA-TCAGGACTTGAAGGCGAAATAGCAGTAAAATTCCATCAGTGTTTGTGGATT  17013
                |||||||| ||||||| ||||||||| |||||||||||||||||||||||||||||||||
Sbjct  7446630  GCCTCACACTCAGGACCTGAAGGCGACATAGCAGTAAAATTCCATCAGTGTTTGTGGATT  7446571

Query  17014    TCATGAATGAATGCA--ttttttttgacaaaatctccctctgtcacccagtcaggagggc  17071
                |||||||||||||||  ||||||||||||||||||||||| |||||||||||||||||||
Sbjct  7446570  TCATGAATGAATGCATTTTTTTTTTGACAAAATCTCCCTCCGTCACCCAGTCAGGAGGGC  7446511

Query  17072    aatggtgtaatcttggctcactgcaaactcagcctccagggttcaagggattctcccacc  17131
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7446510  AATGGTGTAATCTTGGCTCACTGCAAACTCAGCCTCCAGGGTTCAAGGGATTCTCCCACC  7446451

Query  17132    tcagccgcatgagtaactggactacaggcagccaccatcgtgcctggctaacttttctat  17191
                |||||| |||||||| ||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7446450  TCAGCCACATGAGTAGCTGGACTACAGGCAGCCACCATCGTGCCTGGCTAACTTTTCTAT  7446391

Query  17192    ttttgtagagacagggtttcaccatgtgggccaggctggtcttgaactcctgacctcagg  17251
                |||||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||
Sbjct  7446390  TTTTGTAGAGACAGGGTTTCACCATGTGGGCCAGGCGGGTCTTGAACTCCTGACATCAGG  7446331

Query  17252    tgatccacctaccttggcctcccaaagtgctgggattacaagtgtgagccacctcacctg  17311
                |||||||||||||||||||||| ||||||||||||||||| ||||||||||||||| |||
Sbjct  7446330  TGATCCACCTACCTTGGCCTCCTAAAGTGCTGGGATTACAGGTGTGAGCCACCTCATCTG  7446271

Query  17312    gccTTGAGTGAATGAATTCTTGATTTCCAGTCTATCCCTAACTCTGTCAATTTCTTAATT  17371
                ||||||||||||||||||||||| ||||| |||||||||||| |||||||||||||||||
Sbjct  7446270  GCCTTGAGTGAATGAATTCTTGACTTCCACTCTATCCCTAACGCTGTCAATTTCTTAATT  7446211

Query  17372    CATGAAATGATTATGCATATGTGATATGAATGGATATCTCGTTCAATCCATTAGTCTTCG  17431
                |||||||||| ||||||||||||||||||||||||| || ||||||||||||||||||||
Sbjct  7446210  CATGAAATGAATATGCATATGTGATATGAATGGATACCTGGTTCAATCCATTAGTCTTCG  7446151

Query  17432    GACAGTCAAAAACCCAATCAGGATTAACTGAGTGGAGCTTCAGAAATGCAATCAGATATC  17491
                ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7446150  GACAGCCAAAAACCCAATCAGGATTAACTGAGTGGAGCTTCAGAAATGCAATCAGATATC  7446091

Query  17492    GCTTTTTGATTGGAAGCTAGCAGCGGATACGTGGAGGGGCGTGGGTGGGAGTTGTGATTA  17551
                ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct  7446090  GCTTTTTGATTGGAAGCTAGCAGCGGATATGTGGAGGGGCGTGGGTGGGAGTTGTGATTA  7446031

Query  17552    GAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGACAAACTCAAAGTCTTCAAGCCTGGA  17611
                ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Sbjct  7446030  GAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGACAGACTCAAAGTCTTCAAGCCTGGA  7445971

Query  17612    GTTCCTGCTTGGCTCTTCCTGAGGTCTGAGC-AC--CT-----------TCTAAACTACA  17657
                ||||||||||||||||||||||||||||||| ||  ||           |||||||||||
Sbjct  7445970  GTTCCTGCTTGGCTCTTCCTGAGGTCTGAGCTACAACTACAACCAGAGGTCTAAACTACA  7445911

Query  17658    ACCAGATCTGGTAAGTCACTAATTTCTGTAAGGACACTCCCATGTGACCTACAGTCAGCC  17717
                |||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||
Sbjct  7445910  ACCAGATCTGGTAAGTCACTAATTTCTGGAAGGACACTCCCATCTGACCTACAGTCAGCC  7445851

Query  17718    GGTCTAGAACGGTGACAGTGCAGCCTACGATGGCATAGAACTATATCATGTCtttttttc  17777
                |||||||||||||||||||||||||||||| |||| ||||||||||| ||||||||||||
Sbjct  7445850  GGTCTAGAACGGTGACAGTGCAGCCTACGACGGCACAGAACTATATCCTGTCTTTTTTTC  7445791

Query  17778    tttttttcatatgaacactttgaagctttgatttttttttCTAAATGCAATTTTGTCGTG  17837
                ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||| | 
Sbjct  7445790  TTTTTTTCATATGAACACTTTGAAGCTTTGA-TTTTTTTTCTAAATGCAATTTTGTCTTT  7445732

Query  17838    ATTTCAAAAATGTTGTTGTGCTTTTCTTTACATCATTTCAGAATTCTTGTTGGCAGCCAT  17897
                ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||
Sbjct  7445731  ATTTCAAAAATGTTGTTGTGCTTTTCTTTACATCATTTCAGAATTCTTGTTGGGAGCCAT  7445672

Query  17898    TTTGTGAAGAGACGAAGACTGAGCTGTTTTGGCTGCATTTCTGGCCTCGAGCCGCAGTCA  17957
                |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
Sbjct  7445671  TTTGTGAAGAGACGAAGACTGAGCTGGTTTGGCTGCATTTCTGGCCTCGAGCCGCAGTCA  7445612

Query  17958    GCTTCTCCCCGTAGAACCCGGCAGTAGGAGACTTAGAATCGAATCTCTTCTCCCTCCCGC  18017
                | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7445611  GTTTCTCCCCGTAGAACCCGGCAGTAGGAGACTTAGAATCGAATCTCTTCTCCCTCCCGC  7445552

Query  18018    CTCCTGTTTTTGGCTTTTTGAGAAACCTTATCATCCAACACAATGGCCAGCAACGTTACC  18077
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7445551  CTCCTGTTTTTGGCTTTTTGAGAAACCTTATCATCCAACACAATGGCCAGCAACGTTACC  7445492

Query  18078    AACAAGATGGATCCTCACTCCGTGAACTCCCGTGTGTTCATTGGGAATCTCAACACTCTT  18137
                ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct  7445491  AACAAGATGGATCCTCACTCCATGAACTCCCGTGTGTTCATTGGGAATCTCAACACTCTT  7445432

Query  18138    GTTGTCAAGAAATCTGATGTGGAGGCGATCTTTTCCAAGTATGGCAAAATTGCGGGCTGC  18197
                |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7445431  GTTGTCAAGAAATCGGATGTGGAGGCGATCTTTTCCAAGTATGGCAAAATTGCGGGCTGC  7445372

Query  18198    TCTGTTCATAAGGGCTTTGCCTTCGTTCAATATGATAAGGAGAAAAATGCCCGGGCTGCT  18257
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7445371  TCTGTTCATAAGGGCTTTGCCTTCGTTCAATATGATAAGGAGAAAAATGCCCGGGCTGCT  7445312

Query  18258    GTAGCAGGAGAGGATGGCAGAATGATTGCTAGCCAGGTTGCAGTTATTAACCTGGCTGCA  18317
                |||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||
Sbjct  7445311  GTAGCAGGAGAGGATGGCAGAATGATTGCTAGCCAGGTTGTAGATATTAACCTGGCTGCA  7445252

Query  18318    GAGCCAAAAGTGAACCGAGGAAACGCAGGTGTGAAACGATCCGCAGCGGAGATGTACGGC  18377
                ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Sbjct  7445251  GAGCCAAAAGTGAACCGAGGAAACGCAGGTGTGAAACGATCAGCAGCGGAGATGTACGGC  7445192

Query  18378    TCCTCTTTTGACTTGGACTATGGCTTTCAACGGGATTATTATGATGGGATGTACAGTTTC  18437
                ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
Sbjct  7445191  TCCTCTTTTGACTTGGACTATGGCTTTCAACGGGATTATTATGATGGAATGTACAGTTTC  7445132

Query  18438    CCAGCACGTGTACCTCCTCCTCCTCCCATTGCTCTGGCTGTAGTGCCCTCGAAACGCCAG  18497
                |||||||||||||||||||||||||||||||||||||||||||||||||||||||| || 
Sbjct  7445131  CCAGCACGTGTACCTCCTCCTCCTCCCATTGCTCTGGCTGTAGTGCCCTCGAAACGTCAA  7445072

Query  18498    CG-CATATCAGGAAACACCTCACGAAGGGGCAAAAGTGGCTTCAATTCTAAGAGTGGAAA  18556
                || | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7445071  CGTC-TATCAGGAAACACCTCACGAAGGGGCAAAAGTGGCTTCAATTCTAAGAGTGGAAA  7445013

Query  18557    GCGGGGATCTTCCAAGTCTGGAAAGCTGAAAGGAGATGACCTTCAGGCCATTAAGCAGGA  18616
                ||||||||||||||||||||||||| ||||||| ||||||||||||||||||||||||||
Sbjct  7445012  GCGGGGATCTTCCAAGTCTGGAAAGTTGAAAGGTGATGACCTTCAGGCCATTAAGCAGGA  7444953

Query  18617    GTTGACCCAGATAAAACAGAAAGTGGATTCTCTCCTGGAAAACCTGGAAAAAATTGAAAA  18676
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7444952  GTTGACCCAGATAAAACAGAAAGTGGATTCTCTCCTGGAAAACCTGGAAAAAATTGAAAA  7444893

Query  18677    GGAACAGAGCAAACAAGAGGTAGAGGTGAAAAATGCTAAGTCAGAAGAGGAGCAGAGCAG  18736
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7444892  GGAACAGAGCAAACAAGAGGTAGAGGTGAAAAATGCTAAGTCAGAAGAGGAGCAGAGCAG  7444833

Query  18737    TAGCTCCATGAAGAAAGATGAGACTCATGTAAAGATGGAGTCTGAGGGGGGTGCAGAAGA  18796
                |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct  7444832  TAGCTCCATGAAGAAAGATGAGACTCATGTGAAGATGGAGTCTGAGGGGGGTGCAGAAGA  7444773

Query  18797    CTCTGCTGAGGAGGGGGACCCACTGGATGATGATGATAATGAAGATCAGGGGGACAACCA  18856
                ||||||||||||||||||||||||||||||||||| ||||||||||||||||||  ||||
Sbjct  7444772  CTCTGCTGAGGAGGGGGACCCACTGGATGATGATGTTAATGAAGATCAGGGGGATGACCA  7444713

Query  18857    GCTTCATTTGATCAAGAATAATGAAAAAGATGCTGAGGAAGGAGAGGATAACAGAGACAG  18916
                |||  | ||||||||| || |||||||||| |||||||||||||||||| ||||||||||
Sbjct  7444712  GCTGGAGTTGATCAAGGATGATGAAAAAGAGGCTGAGGAAGGAGAGGATGACAGAGACAG  7444653

Query  18917    CACCAATGGCCAGGATGACTCTTAAGCACATAGTGGGGTTGAGAAATCTTATCCCATTGT  18976
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7444652  CACCAATGGCCAGGATGACTCTTAAGCACATAGTGGGGTTGAGAAATCTTATCCCATTGT  7444593

Query  18977    TTCTTTACCTAGGAGCTTGTCTAACAACAAATTTTTCACCAGATCCTCTCCCTTAGTATC  19036
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7444592  TTCTTTACCTAGGAGCTTGTCTAACAACAAATTTTTCACCAGATCCTCTCCCTTAGTATC  7444533

Query  19037    TTCAGCACATGCTTACTGTTCTCCCCATCCTTGTCCTTCCCACATTCATTAATTCATATT  19096
                ||||||||||||||||||||||||||||| ||||||||||||  ||||||||||||||||
Sbjct  7444532  TTCAGCACATGCTTACTGTTCTCCCCATCTTTGTCCTTCCCATGTTCATTAATTCATATT  7444473

Query  19097    GCCCTGTGCCTAGTCCCATTTTCACTTCCCATGACACCCCTAGTAGTTTTCCTAAGTCTT  19156
                |||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||
Sbjct  7444472  GCCCTGTGCCTAGTCCCATTTTCACTTCCCTTGACACCCCTAGTAGTTGTCCTAAGTCTT  7444413

Query  19157    ACCCTGTAATTTTTGCTTTTAATTTTGACACCTCTTTATGACTTAACAGTAAAAAGGATG  19216
                |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7444412  ACCCTGTAATTTTTCCTTTTAATTTTGACACCTCTTTATGACTTAACAGTAAAAAGGATG  7444353

Query  19217    TATGGTTTTTATCAACTGTCTCCAAAATAATCTCTT  19252
                ||||||||||||||||||||||||||||||| ||||
Sbjct  7444352  TATGGTTTTTATCAACTGTCTCCAAAATAATTTCTT  7444317


 Score = 5162 bits (2795),  Expect = 0.0
 Identities = 3932/4463 (88%), Gaps = 150/4463 (3%)
 Strand=Plus/Minus

Query  12658    Aggccaggcacggtggctcacgtctgtaatcccagcactttgggaggccaaggtgggcag  12717
                ||||| |||||||||||||||  ||||||| |||||||||||||| |||||||  ||  |
Sbjct  7607685  AGGCCGGGCACGGTGGCTCACACCTGTAATTCCAGCACTTTGGGAAGCCAAGGCAGGTGG  7607626

Query  12718    atcacctgaggtcaggagttcgagaccagcctcaccaacatggcgaaactatc-tctcta  12776
                | | |||||| ||||||||| ||||||||| |  ||||||| | ||||||  | | ||||
Sbjct  7607625  AACGCCTGAGATCAGGAGTTTGAGACCAGCATGGCCAACATAGAGAAACT-CCATTTCTA  7607567

Query  12777    ctaaaaatacaaaaaatagctgggcatggtggt-ggacacctgtaatcccaggta-ttcg  12834
                |||||||||||||||||||| |||| ||||||| || || |||||||| |||||| || |
Sbjct  7607566  CTAAAAATACAAAAAATAGCCGGGCGTGGTGGTAGG-CATCTGTAATCTCAGGTACTT-G  7607509

Query  12835    gtaggttgaggcaggagaatcacttgaatccag-gaggcagagtttgcagtgagccaaga  12893
                | ||| ||||||||||||| || ||||| || | ||||  ||| ||||| ||||||||||
Sbjct  7607508  GGAGGCTGAGGCAGGAGAAACAGTTGAA-CCCGAGAGGTGGAGGTTGCATTGAGCCAAGA  7607450

Query  12894    ttg-aactattgctctccagcctggcgagagagtgagactccatctccaaaaaa-a--a-  12948
                | | | || |||| | |||||||||| | ||||  ||||||||||||||||||| |  | 
Sbjct  7607449  TAGCACCT-TTGCACACCAGCCTGGCCACAGAGCAAGACTCCATCTCCAAAAAATACTAC  7607391

Query  12949    aaaaaattataagaaCATGTCCATTCACTCTCCAAAGTATCTAGGACTGGACAATTACTT  13008
                 || |||||||| | ||||||||||||||||||||||| ||| |||||||||||||| ||
Sbjct  7607390  TAATAATTATAACAGCATGTCCATTCACTCTCCAAAGTGTCTGGGACTGGACAATTAATT  7607331

Query  13009    GTCAGGCCCTCTTCTGTAGCACCATACACTATAGCATATATGTGGATTAatataaataca  13068
                || |||||||||||| ||||||| ||| |||||||||||||||||||||| |||||||||
Sbjct  7607330  GTGAGGCCCTCTTCTCTAGCACCCTACGCTATAGCATATATGTGGATTAAAATAAATACA  7607271

Query  13069    catacaaaattcaagtatatattctatatactttctatatatttatatTCTA-AGAGGTC  13127
                |||| ||||| ||||||||||| |||||||||||| ||||| ||||||| || | |||||
Sbjct  7607270  CATA-AAAATGCAAGTATATATGCTATATACTTTCCATATACTTATATTATATA-AGGTC  7607213

Query  13128    ACATGCAAATTCAAGGCTAGGTCAAAGAGTAGAGTGGCTATCTATGGAAAGGGGAGTGGA  13187
                |||||||||||||||||||||||||||||||||||||| || |||||||||| |||||||
Sbjct  7607212  ACATGCAAATTCAAGGCTAGGTCAAAGAGTAGAGTGGCAATATATGGAAAGGTGAGTGGA  7607153

Query  13188    AGTGAATCATGGTAAT-aaa--aaa-aG---G-TGTAGATATAGTTATGGATAGGTAGAC  13239
                ||||||| |||||||| |||  ||| ||   | | ||||||||| |||| ||||||||||
Sbjct  7607152  AGTGAATAATGGTAATAAAAGGAAACAGATAGATATAGATATAGATATGAATAGGTAGAC  7607093

Query  13240    ATACACACATATAGCGGCAAGAAAAGGGAATGTCATGGACCAGTGATGACAGTGAGCCAT  13299
                ||||||| ||||||| |||||||| |||  |||||||||||| ||||||||||||||| |
Sbjct  7607092  ATACACATATATAGCTGCAAGAAAGGGGGTTGTCATGGACCAATGATGACAGTGAGCCGT  7607033

Query  13300    GTAAAAAGGCTACAATTTTTGTGATTGTGTGTCCATTTTCAGGATTG-GTTGTAGCTTAC  13358
                |||||||||||| |||| |||||||||||| ||||||||||||| || ||||||||||||
Sbjct  7607032  GTAAAAAGGCTAAAATTCTTGTGATTGTGTTTCCATTTTCAGGA-TGAGTTGTAGCTTAC  7606974

Query  13359    CTTTTTAGAAAGGCTGATGCCAT--AGTCATAGTGAATAAATGATTATAAAATGTGTTTC  13416
                ||||||||||||||| |||  ||  ||||||||  ||||| |||||||||||||||||||
Sbjct  7606973  CTTTTTAGAAAGGCTTATG--ATGCAGTCATAGCAAATAAGTGATTATAAAATGTGTTTC  7606916

Query  13417    CTTTCT-GGCGAACCTCTGGAGAAATTTCCAATGGTAGGAGAACTCAGTTTACTGGGCAG  13475
                |||||| ||| ||  ||||||||||| || ||||||| ||||| ||||||||||||||||
Sbjct  7606915  CTTTCTGGGC-AA-TTCTGGAGAAATCTCTAATGGTATGAGAATTCAGTTTACTGGGCAG  7606858

Query  13476    GCGATCACACAGATAAGATTTTACAGATCTAATGGCACTACCATTAACTTCATTATCATT  13535
                |  |||||||  |||| |||||||||| | |||| ||||| |||||||||||||||| ||
Sbjct  7606857  GTTATCACAC--ATAAAATTTTACAGACCCAATGACACTAGCATTAACTTCATTATCCTT  7606800

Query  13536    GGTATTCTACAAAGGTTGAGTGAACAAATGGTATC-TTAAAATTAAATTAGCTAAATTAA  13594
                ||||||||| ||||||||||||||||||||||||| ||||| | |||||||||||| | |
Sbjct  7606799  GGTATTCTATAAAGGTTGAGTGAACAAATGGTATCTTTAAACTAAAATTAGCTAAACTGA  7606740

Query  13595    CAAA-AAAGATTGGATTACtttttcttt-tttttgacacagagtctctgatgcccaagcg  13652
                |||| ||| | ||||||| || || ||| ||||||| |||||||||||| |||||| || 
Sbjct  7606739  CAAAGAAA-ACTGGATTA-TTATTATTTATTTTTGAGACAGAGTCTCTGTTGCCCAGGCT  7606682

Query  13653    ggagtacagtggtgctatgtcatctcactgcaacatctgcctcccgggttcaa-gagatt  13711
                |||||||||||||||||  |   ||||||||||| |||||||||| ||||||| ||| ||
Sbjct  7606681  GGAGTACAGTGGTGCTACCTTGGCTCACTGCAACCTCTGCCTCCCAGGTTCAAGGAG-TT  7606623

Query  13712    ctcctgcctcagactcctgagtagccgggattacaggcacacaccaccacacccagctga  13771
                 ||||||||||| | ||| |||||| |||||||||||||||||| ||||||||||||| |
Sbjct  7606622  TTCCTGCCTCAGCCACCTAAGTAGCTGGGATTACAGGCACACACAACCACACCCAGCTAA  7606563

Query  13772    tttttgtatttttagcagaaacggggtttcaccatgttgaccaggttggtcttgaacccc  13831
                ||||||||||||| |||||| |||||||||||||| ||| ||||||||||||||||||||
Sbjct  7606562  TTTTTGTATTTTTGGCAGAAGCGGGGTTTCACCATTTTGGCCAGGTTGGTCTTGAACCCC  7606503

Query  13832    tgaccttgtgatctccctgcctcagcctcctgaagtgctggaattataggcttgagccac  13891
                |||| | | ||||| |||||||| | ||||| ||||||||| ||||||||| | ||||||
Sbjct  7606502  TGACATCGGGATCTGCCTGCCTCGGTCTCCTAAAGTGCTGGGATTATAGGCGTCAGCCAC  7606443

Query  13892    cttgcccagcctaatctttttttcttttCTC-AA-A----G-----G-A----CTTCTAT  13935
                |   ||  ||| ||||||||||||||||||| || |    |     | |     ||||||
Sbjct  7606442  CACACCTGGCCGAATCTTTTTTTCTTTTCTCAAAGATGTTGTCATAGTATTGGGTTCTAT  7606383

Query  13936    GCACTTAGGAGAGTGAGCCCATCGTTCAGTAACAACATGATTCAATACTGCAAGACCTTG  13995
                ||||| ||||||||||||||||| ||||||||||| |||| |||||||||||||||||||
Sbjct  7606382  GCACTCAGGAGAGTGAGCCCATCATTCAGTAACAATATGAATCAATACTGCAAGACCTTG  7606323

Query  13996    ATGCAGTATTTCAAAG--TCTTTCCAGTAGGTGAGGGAGGCTTTCAGTGATGCTTAGACC  14053
                |||||| |||||||||  | ||||||||||||||   ||||||||||||||||||||| |
Sbjct  7606322  ATGCAGAATTTCAAAGACTATTTCCAGTAGGTGA---AGGCTTTCAGTGATGCTTAGATC  7606266

Query  14054    TTCATGCCCTAGAATTTGGAGATTGCATCCTTTAGAAATGATACCAAGGGAAATCTGCCC  14113
                ||| |||||||| |||||||||||||||||||| ||||||| |||||||||||||||| |
Sbjct  7606265  TTCCTGCCCTAGCATTTGGAGATTGCATCCTTTGGAAATGACACCAAGGGAAATCTGCGC  7606206

Query  14114    ATGAGCAGCACTGGATGGGACTGTACCAGATGACTTAAAAC-TAAGGATAACCAAGGAAA  14172
                |||||||||| ||||||||||||||||||||||| | |||| ||| |||| || ||||||
Sbjct  7606205  ATGAGCAGCAATGGATGGGACTGTACCAGATGAC-TGAAACGTAAAGATATCCGAGGAAA  7606147

Query  14173    AGCCTTCCTTAGAAGCAGACATCATCACATGGTAGACAG-TTTTCCAAGACAATGGAACA  14231
                |||||||| |||||||||||||||||||||||||||||| ||||||||||||||||||||
Sbjct  7606146  AGCCTTCCCTAGAAGCAGACATCATCACATGGTAGACAGCTTTTCCAAGACAATGGAACA  7606087

Query  14232    AGACTCCATTTGATCTTCTTCCATTGACTGAGACTTGGTTTTGTTTTGTATTAAAACAAA  14291
                |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
Sbjct  7606086  AGACTCCATTTGATCTTCTTCCATTGACTGAGACTTGGTTTTGTTTTGTATTAACACAAA  7606027

Query  14292    ATGCTCAAACCTATATTTTATGTTGTTAGGTACTTTC-TCCACTCAAACCAAACACTTTC  14350
                || ||||||||| |||||||| ||||||||||||||| | ||||||||||||||||||||
Sbjct  7606026  ATTCTCAAACCTGTATTTTATATTGTTAGGTACTTTCAT-CACTCAAACCAAACACTTTC  7605968

Query  14351    TAAGGTCTTCTGTTCAAAATGTAGCCACTCTCACTAACCAAAGCAATTGCTGGCTATGGA  14410
                |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| 
Sbjct  7605967  TAAGGTCTCCTGTTCAAAATGTAGCCACTCTCACTAACCAAAGCAATTGCTGGCTATGGG  7605908

Query  14411    GTCATTTACATGAAAGGGAAGGATCACA-ACTAAATAGTAGAACATGCTCTCATAAACAG  14469
                |||||||| ||||||||||||||||||| | | ||||||||||| |||||||||| ||||
Sbjct  7605907  GTCATTTAGATGAAAGGGAAGGATCACAGA-T-AATAGTAGAACCTGCTCTCATACACAG  7605850

Query  14470    TTGGGTAGCAATTGAGGATGCCAACTTCATCATAAGGTTTGTTATCCTTCCTTTGGAAGG  14529
                ||||||||||||||||||||| |||||||| |||||||||||||||||||||||||||||
Sbjct  7605849  TTGGGTAGCAATTGAGGATGCTAACTTCATGATAAGGTTTGTTATCCTTCCTTTGGAAGG  7605790

Query  14530    TTGGTTAACATTTATAATTACATGACTTGGCACTGAGAAGAAGCTATAGGTGCAAATGGG  14589
                |||||||| ||| ||||||| ||||||||| |||||||||||||||||||||||||||||
Sbjct  7605789  TTGGTTAATATTGATAATTAAATGACTTGGTACTGAGAAGAAGCTATAGGTGCAAATGGG  7605730

Query  14590    TGGCCTATGACTATTATTGATTACATTACTGGCATTTTATCTCTATGCATAAAAAACATT  14649
                |||||||||||||||||||||| ||||||||| | ||||||||||||| || ||||||||
Sbjct  7605729  TGGCCTATGACTATTATTGATTTCATTACTGGTAATTTATCTCTATGCCTAGAAAACATT  7605670

Query  14650    AGTGAAACTGGATCTAATCTAGGTAGTG-TCGCAGATTCCCACTAGAATCAAACTCTTTG  14708
                |||| |||||| ||||| |||| ||||| || |||| |||||||||||||||||||||||
Sbjct  7605669  AGTGTAACTGGGTCTAACCTAGATAGTGTTC-CAGACTCCCACTAGAATCAAACTCTTTG  7605611

Query  14709    GTTTGACACACCTTATGAAGACT-GGAGTGCTATAGGTATCGACATAGACATAGAATCAG  14767
                ||||||||  | ||||| ||| | ||| |||||||| |||||||||||||||||| ||||
Sbjct  7605610  GTTTGACATGCATTATGTAGA-TGGGAATGCTATAGATATCGACATAGACATAGAGTCAG  7605552

Query  14768    AACATGACCATGTTACCCTCTGCCATTTAATCAGAGAACTTACTGAAACTAGACATTGGT  14827
                |||||||||||||||||||||||||| ||||||||||||||||||||||||| |||||||
Sbjct  7605551  AACATGACCATGTTACCCTCTGCCATATAATCAGAGAACTTACTGAAACTAGGCATTGGT  7605492

Query  14828    TCATTGGAAACTCTAGAGGCAAATAGAATGTGTCTATAGCTCTACTATGTGAAATACATA  14887
                || |||||||||||||||||||||||||||  |||||||||||||| | ||  | | |||
Sbjct  7605491  TCTTTGGAAACTCTAGAGGCAAATAGAATGCATCTATAGCTCTACTGTATG--A-A-ATA  7605436

Query  14888    ATAGTTTTATTTATTGGATGCATCAATACTCAGGACATATTTGGAGAGGAACCTATTCAT  14947
                ||||||||||||||||||||||||||||||||||| ||||||||||||||| |||||| |
Sbjct  7605435  ATAGTTTTATTTATTGGATGCATCAATACTCAGGATATATTTGGAGAGGAAACTATTCTT  7605376

Query  14948    TCTTCAATGCAGATGGCATGCAAGGATTACTTTATAAAACTCATAGAAATACTTTTTCTT  15007
                ||||||||| |||||||||||||||||||||||||||||| || ||||||| |||||| |
Sbjct  7605375  TCTTCAATGGAGATGGCATGCAAGGATTACTTTATAAAACACACAGAAATATTTTTTCCT  7605316

Query  15008    CCCACCCCAATTCAAACCATTACCATGCAACCTGGTATCAATAgaagttaaggcca-ttg  15066
                ||||||||||||| |||||||||| ||||||||| | |||||||| ||||||| || |||
Sbjct  7605315  CCCACCCCAATTCCAACCATTACCGTGCAACCTGTTGTCAATAGACGTTAAGG-CAGTTG  7605257

Query  15067    aggtagaaataattaaataaagctttattggaagctaaatgtgagaatcgacctggaaga  15126
                ||| ||||||||||||||||||||| |||||||||||||||| || ||||||||||||||
Sbjct  7605256  AGGCAGAAATAATTAAATAAAGCTTCATTGGAAGCTAAATGTCAGGATCGACCTGGAAGA  7605197

Query  15127    cacacactgacaaagtgagtgttttccaaagtctgttacaagttggaatgcttttgtaag  15186
                |||||||||||||| |||| ||||||||||||||||||||||||||||||||||| ||||
Sbjct  7605196  CACACACTGACAAAATGAGCGTTTTCCAAAGTCTGTTACAAGTTGGAATGCTTTTATAAG  7605137

Query  15187    agaggttaaaagaagggaatgggactcctcctatca------atttttttttaattttct  15240
                | ||||| ||||||||||||||||||||||||||||       |||||||||||||||||
Sbjct  7605136  AAAGGTTGAAAGAAGGGAATGGGACTCCTCCTATCAGTTGTTTTTTTTTTTTAATTTTCT  7605077

Query  15241    tttgttttattgacctggcaaggctcaaatagagttgag--tttttgtttttgtttttcc  15298
                ||||||||| |  ||||||||||||| ||||||||||||  ||||||||||||||||| |
Sbjct  7605076  TTTGTTTTA-T--CCTGGCAAGGCTCTAATAGAGTTGAGCTTTTTTGTTTTTGTTTTTTC  7605020

Query  15299    cattggaaggtacaagacagaggttacaatcgttag-ctttagatgacaacataacaggc  15357
                |||||||||| |||| ||||||||||||||| || | |||||||||||||||| ||||||
Sbjct  7605019  CATTGGAAGGGACAATACAGAGGTTACAATCATT-GACTTTAGATGACAACATGACAGGC  7604961

Query  15358    taaaacattttccttgcaagacaaccagcatgacttcatgatcagaataaaatcagtgtc  15417
                 |||| ||||||||||||||||||||||||  |||||| ||||||||| |||||||||||
Sbjct  7604960  AAAAATATTTTCCTTGCAAGACAACCAGCAAAACTTCACGATCAGAATCAAATCAGTGTC  7604901

Query  15418    cttctcactgtcagc-gggtgaagacttcatcagtacttgtagagtttgaggtactcatg  15476
                ||||||||||||| | |||||||| ||||||||||||||| ||||| | ||| |||||||
Sbjct  7604900  CTTCTCACTGTCA-CTGGGTGAAGCCTTCATCAGTACTTGAAGAGTCTCAGGCACTCATG  7604842

Query  15477    aactcatgatcagattctttactcagggacaggatgtaagccaatgc-taagaccttcta  15535
                || ||| |||||||||||||||||||||||||||||||||||||| | |||||||||| |
Sbjct  7604841  AAGTCAAGATCAGATTCTTTACTCAGGGACAGGATGTAAGCCAAT-CATAAGACCTTCCA  7604783

Query  15536    taggtggct-aatttttaagct-tgccccaatgagaccttcaggttttcaCTGGCAATAT  15593
                 || | | | |||||  ||| | |  || |||| ||||| ||||||||||||||||||||
Sbjct  7604782  CAGAT-GATCAATTTGGAAG-TCT-ACCTAATGTGACCTGCAGGTTTTCACTGGCAATAT  7604726

Query  15594    GCAGGTGCAGATATGACAAAGAATAA-CAATGACCTTCATATCACCTCC-AGCTGTTGAG  15651
                |||||||||||||||||||||||||| |  ||||||||||||| || || ||||| ||||
Sbjct  7604725  GCAGGTGCAGATATGACAAAGAATAATC-CTGACCTTCATATCGCC-CCTAGCTGATGAG  7604668

Query  15652    GAATGGGATCCTTTTCACCCTTCCTGTCCATAAAACCAAGTTACTCATCTTCAGTGGCAA  15711
                || |||||| |||||  ||||| || |||||||||||| ||||||||||||  |||||||
Sbjct  7604667  GATTGGGATTCTTTTGTCCCTTTCTCTCCATAAAACCAGGTTACTCATCTTGTGTGGCAA  7604608

Query  15712    CAAAATATATGGTAAACTTAACAGAGAAGGAGACTGTCAGaaaaaaaaaaaaaaaagatg  15771
                |||||||||||||  ||||||||||||| |||||  ||  | |  |||||||||| ||| 
Sbjct  7604607  CAAAATATATGGTCTACTTAACAGAGAAAGAGAC--TC-CACAGGAAAAAAAAAAGGAT-  7604552

Query  15772    tgtttatcctgaaatgaggaaagcaatgggaatagatgtgagattattttgggagaaaaa  15831
                | |||||  ||||||||| ||||| |||||||||||||||||||||||  |||||  |||
Sbjct  7604551  T-TTTATTATGAAATGAGCAAAGCCATGGGAATAGATGTGAGATTATTCGGGGAGGTAAA  7604493

Query  15832    ggaagacaaaggttttgaaaggaaaaataaggaggattatacaaattgttttgaaagact  15891
                |||||||||||||||||||||||||||| ||||| |||| | ||||| ||||||||||||
Sbjct  7604492  GGAAGACAAAGGTTTTGAAAGGAAAAATGAGGAGAATTACATAAATTTTTTTGAAAGACT  7604433

Query  15892    caaccttggtc-ctaagaatcaaaagtaaaggg-gcatcagtgaaatgttggatagATTC  15949
                ||  ||||||| | ||| || ||||   ||||| || |||||| | ||||||| ||||||
Sbjct  7604432  CATTCTTGGTCAC-AAGTATGAAAA-CCAAGGGAGCCTCAGTGCAGTGTTGGAAAGATTC  7604375

Query  15950    CACCTCCACCCCCTCAGTAACCCCCAACATGTTTACCAAGTCTTGGTTAACTCCCAGGAT  16009
                | ||||||||| |||| ||||||||||||  ||||||||||||| ||| |||||||||||
Sbjct  7604374  CTCCTCCACCCTCTCAATAACCCCCAACACATTTACCAAGTCTTTGTTCACTCCCAGGAT  7604315

Query  16010    CCCATTAAAACACCCAGCTCAACCATGCCCATCCTCTACCCTCACTTCTCTTTGTAATTT  16069
                 ||||||||||||||||||||||| || ||| |||| ||| ||||||| |||||||||||
Sbjct  7604314  TCCATTAAAACACCCAGCTCAACCCTGACCAGCCTCCACCTTCACTTCCCTTTGTAATTT  7604255

Query  16070    TGACATGATTTTAttacaggaccatcaggttcctatgcctgctgcacagtagctgaccaa  16129
                |||||| | ||| |||||||||||||||||||||||||| |||||||||||||| | |||
Sbjct  7604254  TGACATAAATTTGTTACAGGACCATCAGGTTCCTATGCCGGCTGCACAGTAGCTTAGCAA  7604195

Query  16130    tattctgagacagcagtgtttgcagcagacagtttaatgatcacagggtggctaaatgag  16189
                |||| ||||||||||| |||||||||||| ||||||||||||||||||||||| ||||||
Sbjct  7604194  TATTGTGAGACAGCAGGGTTTGCAGCAGAAAGTTTAATGATCACAGGGTGGCTGAATGAG  7604135

Query  16190    aagctaggaggatatcctcaaattcatctccccaagtagtactgagggtttccagtggat  16249
                ||||| |||||| ||||||||||||||||||||||| |||||||||||||||||||||||
Sbjct  7604134  AAGCTGGGAGGAGATCCTCAAATTCATCTCCCCAAGGAGTACTGAGGGTTTCCAGTGGAT  7604075

Query  16250    cctggatagcaaggggctggaaagttggtgta----ga-gg---taagagggatgaagtc  16301
                ||||||||||||||||||||||||||||||||    || ||   ||||||| ||||||| 
Sbjct  7604074  CCTGGATAGCAAGGGGCTGGAAAGTTGGTGTAGTTTGATGGCAATAAGAGGTATGAAGTT  7604015

Query  16302    atcaggatgtcaaaactgcattctttggtgagttggtgccttgcagagcccttcagatca  16361
                |||| ||||||| ||| |||||||||||||||||| |||||||||| |||||||||||||
Sbjct  7604014  ATCACGATGTCAGAACGGCATTCTTTGGTGAGTTGATGCCTTGCAGGGCCCTTCAGATCA  7603955

Query  16362    gctggcatcagtagtttcactgacatgcagaacctgaaagaatatctcaaatgagaaagt  16421
                |||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| |
Sbjct  7603954  GCTGGCATCAGTAGTTTCACTGACATGCAGAACCTGAAAGAATATCTCAAATGAAAAACT  7603895

Query  16422    taatgttttacaaggcttaaattgttgtctgcagggtagttaaggggaactgtaag-cta  16480
                |||||||| |||| |||||||||||||||||||| |||||||||||||| ||| || |||
Sbjct  7603894  TAATGTTTCACAATGCTTAAATTGTTGTCTGCAGCGTAGTTAAGGGGAATTGT-AGTCTA  7603836

Query  16481    aggtctacttgatttggggacagtaagctgccagcaaccatgaggaagaaggtcagagag  16540
                || |||||  ||||| ||||||||| |||||||||||||||||||||| ||||||||| |
Sbjct  7603835  AGTTCTACACGATTTTGGGACAGTAGGCTGCCAGCAACCATGAGGAAGCAGGTCAGAGGG  7603776

Query  16541    caagctgacctcatggtgaatgctgaatgcgctgcaagcttggtttatttttgtttctcc  16600
                |||||||||||| |||||||||||||||||| | |||||||||||| |||||||| ||||
Sbjct  7603775  CAAGCTGACCTCCTGGTGAATGCTGAATGCGTTTCAAGCTTGGTTTGTTTTTGTTCCTCC  7603716

Query  16601    ccctcccttcttcactgattaaacttataaagtttacaggtatc-atttcaATTTCTTCC  16659
                ||||| ||| ||||| ||||||| |||||||||||| |  || |  ||||||||||||||
Sbjct  7603715  CCCTCTCTTTTTCACCGATTAAATTTATAAAGTTTAGAAATA-CGGTTTCAATTTCTTCC  7603657

Query  16660    AGAGAAGACTTAACCTAAGCCCTGAGACCACTCAAGCCCTCAGTGGCACCTCTCTTCCAC  16719
                ||| ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7603656  AGACAAGCCTTAACCTAAGCCCTGAGACCACTCAAGCCCTCAGTGGCACCTCTCTTCCAC  7603597

Query  16720    CAGCACGAGTGAAGAAACTGCTACCTTAGGTGATATAAAACCCACAAGACCATTCCATAC  16779
                ||||| |||  || ||| |||||||||||||||||||||||||||||||| |||| ||||
Sbjct  7603596  CAGCATGAGCAAATAAATTGCTACCTTAGGTGATATAAAACCCACAAGACGATTCGATAC  7603537

Query  16780    ATGGAGATCTTTATTCTTATTTTGTAGGGACGACTCCTCTGTGTT-TATACAGCTATTTT  16838
                |||||| | ||| |||| |||||||||||| |||| || ||| || |||| |||| ||||
Sbjct  7603536  ATGGAG-TTTTTTTTCTGATTTTGTAGGGATGACTTCTTTGT-TTCTATAAAGCTGTTTT  7603479

Query  16839    AACTAGAAATATTTTTATAAATTTTATAATTTTGATGTGGCCAAAGATCTCCCCACAACA  16898
                |||||  || |     |  |||||||||||||||||||||||||||||||||| | | ||
Sbjct  7603478  AACTA-TAA-A-----A-CAATTTTATAATTTTGATGTGGCCAAAGATCTCCC-A-A-CA  7603430

Query  16899    CTACTTTCAGGTTTTATTTTTCTGTCTAATGTCTGGAACAGATCAACCCCTTCCCTGCCT  16958
                |||||||||||||||||||||||||||| | ||  ||||||||||| |||||||||||||
Sbjct  7603429  CTACTTTCAGGTTTTATTTTTCTGTCTACTATCCAGAACAGATCAAACCCTTCCCTGCCT  7603370

Query  16959    CACA-TCAGGACT-TGA-AGG-CGAAATAGCAGTAAAATTCCATCAGTGTTTGTGGATTT  17014
                || | |||||||| | | ||| | | ||| ||||||||||||||||||||||| ||| ||
Sbjct  7603369  CAAACTCAGGACTAT-ATAGGTC-ATATATCAGTAAAATTCCATCAGTGTTTGCGGAGTT  7603312

Query  17015    CATGAATGAATGCAtt-tttttt  17036
                |||||||||||| ||| ||||||
Sbjct  7603311  CATGAATGAATGAATTCTTTTTT  7603289


 Score = 5156 bits (2792),  Expect = 0.0
 Identities = 3933/4465 (88%), Gaps = 154/4465 (3%)
 Strand=Plus/Minus

Query  21331    Aggccgggcacggtggctcacacctgtaattccagcactttgggaagccaaggcaggtgg  21390
                ||||| |||||||||||||||  ||||||| |||||||||||||| |||||||  || ||
Sbjct  7616358  AGGCCAGGCACGGTGGCTCACGTCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGCGG  7616299

Query  21391    aacgcctgagatcaggagtttgagaccagcatggccaacatggagaaactccat-t-tct  21448
                | | |||||| ||||||||| ||||||||| |  ||||||||| ||||||  || | |||
Sbjct  7616298  ATCACCTGAGGTCAGGAGTTCGAGACCAGCCTCACCAACATGGCGAAACT--ATCTCTCT  7616241

Query  21449    actaaaaatacaaaaaatagccgggcgtggtggtagg-catctgtaatctcaggtactt-  21506
                ||||||||||||||||||||| |||| ||||||| || || |||||||| |||||| || 
Sbjct  7616240  ACTAAAAATACAAAAAATAGCTGGGCATGGTGGT-GGACACCTGTAATCCCAGGTA-TTC  7616183

Query  21507    gggaggctgaggcaggagaaacagttgaa-cccgagaggtggaggttgcattgagccaag  21565
                || ||| ||||||||||||| || ||||| || | ||||  ||| ||||| ||||||| |
Sbjct  7616182  GGTAGGTTGAGGCAGGAGAATCACTTGAATCCAG-GAGGCAGAGTTTGCAGTGAGCCATG  7616124

Query  21566    atagcacct-ttgcacaccagcctggccacagagcaagactccatctccaaaaaaTACTA  21624
                || | | || |||| | |||||||||| | ||||  ||||||||||||||||||| |  |
Sbjct  7616123  ATTG-AACTATTGCTCTCCAGCCTGGCGAGAGAGTGAGACTCCATCTCCAAAAAA-A--A  7616068

Query  21625    CTAATAATTATAACAGCATGTCCATTCACTCTCCAAAGTGTCTGGGACTGGACAATTAAT  21684
                  || |||||||| | ||||||||||||||||||||||| ||| |||||||||||||| |
Sbjct  7616067  -AAAAAATTATAAGAACATGTCCATTCACTCTCCAAAGTATCTAGGACTGGACAATTACT  7616009

Query  21685    TGTGAGGCCCTCTTCTCTAGCACCCTACGCTATAGCATATATGTGGATTAAAATAAATAC  21744
                ||| |||||||||||| ||||||| ||| |||||||||||||||||||||| ||||||||
Sbjct  7616008  TGTCAGGCCCTCTTCTGTAGCACCATACACTATAGCATATATGTGGATTAATATAAATAC  7615949

Query  21745    ACATA-AAAATGCAAGtatatatgctatatactttccatatacttatattatata-AGGT  21802
                ||||| ||||| ||||||||||| |||||||||||| ||||| ||||||| || | ||||
Sbjct  7615948  ACATACAAAATTCAAGTATATATTCTATATACTTTCTATATATTTATATTCTA-AGAGGT  7615890

Query  21803    CACATGCAAATTCAAGGCTAGGTCAAAGAGTAGAGTGGCAATATATGGAAAGGTGAGTGG  21862
                ||||||||||||||||||||||||||||||||||||||| || |||||||||| ||||||
Sbjct  7615889  CACATGCAAATTCAAGGCTAGGTCAAAGAGTAGAGTGGCTATCTATGGAAAGGGGAGTGG  7615830

Query  21863    AAGTGAATAATGGTAATAAAAGGAAACagatagatatagatatagatatgaataggtaga  21922
                |||||||| |||||||| |||  ||| ||   | | ||||||||| |||| |||||||||
Sbjct  7615829  AAGTGAATCATGGTAAT-AAA--AAA-AG---G-TGTAGATATAGTTATGGATAGGTAGA  7615778

Query  21923    catacacatatatagCTGCAAGAAAGGGGGTTGTCATGGACCAATGATGACAGTGAGCCG  21982
                |||||||| ||||||| |||||||| |||  |||||||||||| ||||||||||||||| 
Sbjct  7615777  CATACACACATATAGCGGCAAGAAAAGGGAATGTCATGGACCAGTGATGACAGTGAGCCA  7615718

Query  21983    TGTAAAAAGGCTAAAATTCttgtgattgtgtttccattttcagga-tgagttgtagctta  22041
                ||||||||||||| |||| |||||||||||| ||||||||||||| || |||||||||||
Sbjct  7615717  TGTAAAAAGGCTACAATTTTTGTGATTGTGTGTCCATTTTCAGGATTG-GTTGTAGCTTA  7615659

Query  22042    cctttttagaaaggcttatg--atgcagtcatagcaaataagtgattataaaatgtgttt  22099
                |||||||||||||||| |||  ||  ||||||||  ||||| ||||||||||||||||||
Sbjct  7615658  CCTTTTTAGAAAGGCTGATGCCAT--AGTCATAGTGAATAAATGATTATAAAATGTGTTT  7615601

Query  22100    cctttctgggc-aa-ttctggagaaatctctaatggtatgagaattcagtttactgggca  22157
                ||||||| ||| ||  ||||||||||| || ||||||| ||||| |||||||||||||||
Sbjct  7615600  CCTTTCT-GGCGAACCTCTGGAGAAATTTCCAATGGTAGGAGAACTCAGTTTACTGGGCA  7615542

Query  22158    ggttatcacac--ataaaattttacagacccaatgacactagCATTAACTTCATTATCCT  22215
                ||  |||||||  |||| |||||||||| | |||| ||||| |||||||||||||||| |
Sbjct  7615541  GGCGATCACACAGATAAGATTTTACAGATCTAATGGCACTACCATTAACTTCATTATCAT  7615482

Query  22216    TGGTATTCTATAAAGGTTGAGTGAACAAATGGTATATTTAAACTAAAATTAGCTAAACTG  22275
                |||||||||| ||||||||||||||||||||||||  ||||| | |||||||||||| | 
Sbjct  7615481  TGGTATTCTACAAAGGTTGAGTGAACAAATGGTAT-CTTAAAATTAAATTAGCTAAATTA  7615423

Query  22276    ACAAAGAAA-ACTGGAtta-ttattatttatttttgagacagagtctctgttgcccaggc  22333
                ||||| ||| | ||||||| || || ||| ||||||| |||||||||||| |||||| ||
Sbjct  7615422  ACAAA-AAAGATTGGATTACTTTTTCTTT-TTTTTGACACAGAGTCTCTGATGCCCAAGC  7615365

Query  22334    tggagtacagtggtgctaccttggctcactgcaacctctgcctcccaggttcaaggag-t  22392
                 |||||||||||||||||  |   ||||||||||| |||||||||| ||||||| ||| |
Sbjct  7615364  GGGAGTACAGTGGTGCTATGTCATCTCACTGCAACATCTGCCTCCCGGGTTCAA-GAGAT  7615306

Query  22393    tttcctgcctcagccacctaagtagctgggattacaggcacacacaaccacacccagcta  22452
                | ||||||||||| | ||| |||||| |||||||||||||||||| ||||||||||||| 
Sbjct  7615305  TCTCCTGCCTCAGACTCCTGAGTAGCCGGGATTACAGGCACACACCACCACACCCAGCTG  7615246

Query  22453    atttttgtatttttggcagaagcggggtttcaccattttggccaggttggtcttgaaccc  22512
                |||||||||||||| |||||| |||||||||||||| ||| |||||||||||||||||||
Sbjct  7615245  ATTTTTGTATTTTTAGCAGAAACGGGGTTTCACCATGTTGACCAGGTTGGTCTTGAACCC  7615186

Query  22513    ctgacatcgggatctgcctgcctcggtctcctaaagtgctgggattataggcgtcagcca  22572
                ||||| | | ||||| |||||||| | ||||| ||||||||| ||||||||| | |||||
Sbjct  7615185  CTGACCTTGTGATCTCCCTGCCTCAGCCTCCTGAAGTGCTGGAATTATAGGCTTGAGCCA  7615126

Query  22573    ccacacctggccGAATCtttttttcttttctcaaagatgttgtcatagtattgggttcta  22632
                ||   ||  ||| ||||||||||||||||||| || |    |     | |     |||||
Sbjct  7615125  CCTTGCCCAGCCTAATCTTTTTTTCTTTTCTC-AA-A----G-----G-A----CTTCTA  7615082

Query  22633    tgcactcaggagagtgagcccatCATTCAGTAACAATATGAATCAATACTGCAAGACCTT  22692
                |||||| ||||||||||||||||| ||||||||||| |||| ||||||||||||||||||
Sbjct  7615081  TGCACTTAGGAGAGTGAGCCCATCGTTCAGTAACAACATGATTCAATACTGCAAGACCTT  7615022

Query  22693    GATGCAGAATTTCAAAGACTATTTCCAGTAGGTGA---AGGCTTTCAGTGATGCTTAGAT  22749
                ||||||| |||||||||  | ||||||||||||||   ||||||||||||||||||||| 
Sbjct  7615021  GATGCAGTATTTCAAAG--TCTTTCCAGTAGGTGAGGGAGGCTTTCAGTGATGCTTAGAC  7614964

Query  22750    CTTCCTGCCCTAGCATTTGGAGATTGCATCCTTTGGAAATGACACCAAGGGAAATCTGCG  22809
                |||| |||||||| |||||||||||||||||||| ||||||| |||||||||||||||| 
Sbjct  7614963  CTTCATGCCCTAGAATTTGGAGATTGCATCCTTTAGAAATGATACCAAGGGAAATCTGCC  7614904

Query  22810    CATGAGCAGCAATGGATGGGACTGTACCAGATGAC-TGAAACGTAAAGATATCCGAGGAA  22868
                ||||||||||| ||||||||||||||||||||||| | |||| ||| |||| || |||||
Sbjct  7614903  CATGAGCAGCACTGGATGGGACTGTACCAGATGACTTAAAAC-TAAGGATAACCAAGGAA  7614845

Query  22869    AAGCCTTCCCTAGAAGCAGACATCATCACATGGTAGACAGCTTTTCCAAGACAATGGAAC  22928
                ||||||||| |||||||||||||||||||||||||||||| |||||||||||||||||||
Sbjct  7614844  AAGCCTTCCTTAGAAGCAGACATCATCACATGGTAGACAG-TTTTCCAAGACAATGGAAC  7614786

Query  22929    AAGACTCCATTTGATCTTCTTCCATTGACTGAGACTTGGTTTTGTTTTGTATTAACACAA  22988
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Sbjct  7614785  AAGACTCCATTTGATCTTCTTCCATTGACTGAGACTTGGTTTTGTTTTGTATTAAAACAA  7614726

Query  22989    AATTCTCAAACCTGTATTTTATATTGTTAGGTACTTTCAT-CACTCAAACCAAACACTTT  23047
                ||| ||||||||| |||||||| ||||||||||||||| | |||||||||||||||||||
Sbjct  7614725  AATGCTCAAACCTATATTTTATGTTGTTAGGTACTTTC-TCCACTCAAACCAAACACTTT  7614667

Query  23048    CTAAGGTCTCCTGTTCAAAATGTAGCCACTCTCACTAACCAAAGCAATTGCTGGCTATGG  23107
                ||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7614666  CTAAGGTCTTCTGTTCAAAATGTAGCCACTCTCACTAACCAAAGCAATTGCTGGCTATGG  7614607

Query  23108    GGTCATTTAGATGAAAGGGAAGGATCACAGA-T-AATAGTAGAACCTGCTCTCATACACA  23165
                 |||||||| ||||||||||||||||||| | | ||||||||||| |||||||||| |||
Sbjct  7614606  AGTCATTTACATGAAAGGGAAGGATCACA-ACTAAATAGTAGAACATGCTCTCATAAACA  7614548

Query  23166    GTTGGGTAGCAATTGAGGATGCTAACTTCATGATAAGGTTTGTTATCCTTCCTTTGGAAG  23225
                |||||||||||| ||||||||| |||||||| ||||||||||||||||||||||||||||
Sbjct  7614547  GTTGGGTAGCAACTGAGGATGCCAACTTCATCATAAGGTTTGTTATCCTTCCTTTGGAAG  7614488

Query  23226    GTTGGTTAATATTGATAATTAAATGACTTGGTACTGAGAAGAAGCTATAGGTGCAAATGG  23285
                ||||||||| ||| ||||||| ||||||||| ||||||||||||||||||||||||||||
Sbjct  7614487  GTTGGTTAACATTTATAATTACATGACTTGGCACTGAGAAGAAGCTATAGGTGCAAATGG  7614428

Query  23286    GTGGCCTATGACTATTATTGATTTCATTACTGGTAATTTATCTCTATGCCTAGAAAACAT  23345
                ||||||||||||||||||||||| ||||||||| | ||||||||||||| || |||||||
Sbjct  7614427  GTGGCCTATGACTATTATTGATTACATTACTGGCATTTTATCTCTATGCATAAAAAACAT  7614368

Query  23346    TAGTGTAACTGGGTCTAACCTAGATAGTGTTC-CAGACTCCCACTAGAATCAAACTCTTT  23404
                ||||| |||||| ||||| |||| ||||| || |||| ||||||||||||||||||||||
Sbjct  7614367  TAGTGAAACTGGATCTAATCTAGGTAGTG-TCGCAGATTCCCACTAGAATCAAACTCTTT  7614309

Query  23405    GGTTTGACATGCATTATGTAGA-TGGGAATGCTATAGATATCGACATAGACATAGAGTCA  23463
                |||||||||  | ||||| ||| | ||| |||||||| |||||||||||||||||| |||
Sbjct  7614308  GGTTTGACACACCTTATGAAGACT-GGAGTGCTATAGGTATCGACATAGACATAGAATCA  7614250

Query  23464    GAACATGACCATGTTACCCTCTGCCATATAATCAGAGAACTTACTGAAACTAGGCATTGG  23523
                ||||||||||||||||||||||||||| ||||||||||||||||||||||||| ||||||
Sbjct  7614249  GAACATGACCATGTTACCCTCTGCCATTTAATCAGAGAACTTACTGAAACTAGACATTGG  7614190

Query  23524    TTCTTTGGAAACTCTAGAGGCAAATAGAATGCATCTATAGCTCTACTGTATG--A-A-AT  23579
                ||| |||||||||||||||||||||||||||  |||||||||||||| | ||  | | ||
Sbjct  7614189  TTCATTGGAAACTCTAGAGGCAAATAGAATGTGTCTATAGCTCTACTATGTGAAATACAT  7614130

Query  23580    AATAGTTTTATTTATTGGATGCATCAATACTCAGGATATATTTGGAGAGGAAACTATTCT  23639
                |||||||||||||||||||||||||||||||||||| ||||||||||||||| |||||| 
Sbjct  7614129  AATAGTTTTATTTATTGGATGCATCAATACTCAGGACATATTTGGAGAGGAACCTATTCA  7614070

Query  23640    TTCTTCAATGGAGATGGCATGCAAGGATTACTTTATAAAACACACAGAAATATTTTTTCC  23699
                |||||||||| |||||||||||||||||||||||||||||| || ||||||| |||||| 
Sbjct  7614069  TTCTTCAATGCAGATGGCATGCAAGGATTACTTTATAAAACTCATAGAAATACTTTTTCT  7614010

Query  23700    TCCCACCCCAATTCCAACCATTACCGTGCAACCTGTtgtcaatagacgttaagg-cagtt  23758
                |||||||||||||| |||||||||| ||||||||| | |||||||| ||||||| || ||
Sbjct  7614009  TCCCACCCCAATTCAAACCATTACCATGCAACCTGGTATCAATAGAAGTTAAGGCCA-TT  7613951

Query  23759    gaggcagaaataattaaataaagcttcattggaagctaaatgtcaggatcgacctggaag  23818
                |||| ||||||||||||||||||||| |||||||||||||||| || |||||||||||||
Sbjct  7613950  GAGGTAGAAATAATTAAATAAAGCTTTATTGGAAGCTAAATGTGAGAATCGACCTGGAAG  7613891

Query  23819    acacacactgacaaaatgagcgttttccaaagtctgttacaagttggaatgcttttataa  23878
                ||||||||||||||| |||| ||||||||||||||||||||||||||||||||||| |||
Sbjct  7613890  ACACACACTGACAAAGTGAGTGTTTTCCAAAGTCTGTTACAAGTTGGAATGCTTTTGTAA  7613831

Query  23879    gaaaggttgaaagaagggaatgggactcctcctatcagttgttttttttttttaattttc  23938
                || ||||| ||||||||||||||||||||||||||||       ||||||||||||||||
Sbjct  7613830  GAGAGGTTAAAAGAAGGGAATGGGACTCCTCCTATCA------ATTTTTTTTTAATTTTC  7613777

Query  23939    ttttgtttta-t--cctggcaaggctctaatagagttgagcttttttgtttttgtttttt  23995
                |||||||||| |  ||||||||||||| ||||||||||||  ||||||||||||||||| 
Sbjct  7613776  TTTTGTTTTATTGACCTGGCAAGGCTCAAATAGAGTTGAG--TTTTTGTTTTTGTTTTTC  7613719

Query  23996    ccattggaagggacaatacagaggttacaatcattga-ctttagatgacaacatgacagg  24054
                ||||||||||| |||| ||||||||||||||| || | |||||||||||||||| |||||
Sbjct  7613718  CCATTGGAAGGTACAAGACAGAGGTTACAATCGTT-AGCTTTAGATGACAACATAACAGG  7613660

Query  24055    caaaaatattttccttgcaagacaaccagcaaaacttcacgatcagaatcaaatcagtgt  24114
                | |||| ||||||||||||||||||||||||  |||||| ||||||||| ||||||||||
Sbjct  7613659  CTAAAACATTTTCCTTGCAAGACAACCAGCATGACTTCATGATCAGAATAAAATCAGTGT  7613600

Query  24115    ccttctcactgtca-ctgggtgaagccttcatcagtacttgaagagtctcaggcactcat  24173
                |||||||||||||| |  ||||||| ||||||||||||||| ||||| | ||| ||||||
Sbjct  7613599  CCTTCTCACTGTCAGC-AGGTGAAGACTTCATCAGTACTTGTAGAGTTTGAGGTACTCAT  7613541

Query  24174    gaagtcaagatcagattctttactcagggacaggatgtaagccaat-cataagaccttcc  24232
                ||| ||| |||||||||||||||||||||||||||||||||||||| | |||||||||||
Sbjct  7613540  GAACTCATGATCAGATTCTTTACTCAGGGACAGGATGTAAGCCAATGC-TAAGACCTTCC  7613482

Query  24233    acagat-gatcaatttggaagtc-t-acctaatgtgacctgcaggttttcaCTGGCAATA  24289
                | || | | | |||||  ||| | |  || |||| ||||| |||||||||||||||||||
Sbjct  7613481  ATAGGTGGCT-AATTTTTAAG-CTTGCCCCAATGAGACCTTCAGGTTTTCACTGGCAATA  7613424

Query  24290    TGCAGGTGCAGATATGACAAAGAATAATC-CTGACCTTCATATCGCC-CCTAGCTGATGA  24347
                ||||||||||||||||||||||||||| |  ||||||||||||| || || ||||| |||
Sbjct  7613423  TGCAGGTGCAGATATGACAAAGAATAA-CAATGACCTTCATATCACCTCC-AGCTGTTGA  7613366

Query  24348    GGATTGGGATTCTTTTGTCCCTTTCTCTCCATAAAACCAGGTTACTCATCTTGTGTGGCA  24407
                ||| |||||| |||||  ||||| || |||||||||||| ||||||||||||  ||||||
Sbjct  7613365  GGAATGGGATCCTTTTCACCCTTCCTGTCCATAAAACCAAGTTACTCATCTTCAGTGGCA  7613306

Query  24408    ACAAAATATATGGTctacttaacagagaaagagac--tc-cacaggaaaaaaaaaaggat  24464
                ||||||||||||||  ||||||||||||| |||||  ||  | |  |||||||||| |||
Sbjct  7613305  ACAAAATATATGGTAAACTTAACAGAGAAGGAGACTGTCAGAAAAAAAAAAAAAAAAGAT  7613246

Query  24465    -t-tttattatgaaatgagcaaagccatgggaatagatgtgagattattcggggaggtaa  24522
                 | |||||  ||||||||| ||||| |||||||||||||||||||||||  |||||  ||
Sbjct  7613245  GTGTTTATCCTGAAATGAGGAAAGCAATGGGAATAGATGTGAGATTATTTTGGGAGAAAA  7613186

Query  24523    aggaagacaaaggttttgaaaggaaaaatgaggagaattacataaatttttttgaaagac  24582
                ||||||||||||||||||||||||||||| ||||| |||| | ||||| |||||||||||
Sbjct  7613185  AGGAAGACAAAGGTTTTGAAAGGAAAAATAAGGAGGATTATACAAATTGTTTTGAAAGAC  7613126

Query  24583    tcattcttggtcac-aagtatgaaaa-ccaagggagcctcagtgcagtgttggaaagATT  24640
                |||  ||||||| | ||| || ||||   ||||| || |||||| | ||||||| |||||
Sbjct  7613125  TCAACCTTGGTC-CTAAGAATCAAAAGTAAAGGG-GCATCAGTGAAATGTTGGATAGATT  7613068

Query  24641    CCTCCTCCACCCTCTCAATAACCCCCAACACATTTACCAAGTCTTTGTTCACTCCCAGGA  24700
                || ||||||||| |||| ||||||||||||  ||||||||||||| ||| ||||||||||
Sbjct  7613067  CCACCTCCACCCCCTCAGTAACCCCCAACATGTTTACCAAGTCTTGGTTAACTCCCAGGA  7613008

Query  24701    TTCCATTAAAACACCCAGCTCAACCCTGACCAGCCTCCACCTTCACTTCCCTTTGTAATT  24760
                | ||||||||||||||||||||||| || ||| |||| ||| ||||||| ||||||||||
Sbjct  7613007  TCCCATTAAAACACCCAGCTCAACCATGCCCATCCTCTACCCTCACTTCTCTTTGTAATT  7612948

Query  24761    TTGACATAAATTtgttacaggaccatcaggttcctatgccggctgcacagtagcttacca  24820
                ||||||| | ||| |||||||||||||||||||||||||| |||||||||||||| ||||
Sbjct  7612947  TTGACATGATTTTATTACAGGACCATCAGGTTCCTATGCCTGCTGCACAGTAGCTGACCA  7612888

Query  24821    atattctgagacagcag-gatttgcagcagaaagtttaatgatcacagggtggctgaatg  24879
                ||||||||||||||||| | ||||||||||| ||||||||||||||||||||||| ||||
Sbjct  7612887  ATATTCTGAGACAGCAGTG-TTTGCAGCAGACAGTTTAATGATCACAGGGTGGCTAAATG  7612829

Query  24880    agaagctgggaggagatcctcaaattcatctccccaaggagtactgagggtttccagtgg  24939
                ||||||| |||||| ||||||||||||||||||||||| |||||||||||||||||||||
Sbjct  7612828  AGAAGCTAGGAGGATATCCTCAAATTCATCTCCCCAAGTAGTACTGAGGGTTTCCAGTGG  7612769

Query  24940    atcctggatagcaaggggctggaaagttggtgtagtttgatggcaataagaggtatgaag  24999
                ||||||||||||||||||||||||||||||||||    || ||   ||||||| ||||||
Sbjct  7612768  ATCCTGGATAGCAAGGGGCTGGAAAGTTGGTGTA----GA-GG---TAAGAGGGATGAAG  7612717

Query  25000    ttatcacgatgtcagaacggcattctttggtgagttgatgccttgcagggcccttcagat  25059
                | |||| ||||||| ||| |||||||||||||||||| |||||||||| |||||||||||
Sbjct  7612716  TCATCAGGATGTCAAAACTGCATTCTTTGGTGAGTTGGTGCCTTGCAGAGCCCTTCAGAT  7612657

Query  25060    cagctggcatcagtagtttcactgacatgcagaacctgaaagaatatctcaaatgaaaaa  25119
                |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
Sbjct  7612656  CAGCTGGCATCAGTAGTTTCACTGACATGCAGAACCTGAAAGAATATCTCAAATGAGAAA  7612597

Query  25120    cttaatgtttcacaatgcttaaattgttgtctgcagcgtagttaaggggaattgt-agtc  25178
                 ||||||||| |||| |||||||||||||||||||| |||||||||||||| ||| || |
Sbjct  7612596  GTTAATGTTTTACAAGGCTTAAATTGTTGTCTGCAGGGTAGTTAAGGGGAACTGTAAG-C  7612538

Query  25179    taagttctacacgattttgggacagtaggctgccagcaaccatgaggaagcaggtcagag  25238
                |||| |||||  ||||| ||||||||| |||||||||||||||||||||| |||||||||
Sbjct  7612537  TAAGGTCTACTTGATTTGGGGACAGTAAGCTGCCAGCAACCATGAGGAAGAAGGTCAGAG  7612478

Query  25239    ggcaagctgacctcctggtgaatgctgaatgcgtttcaagcttggtttgtttttgttcct  25298
                 ||||||||||||| |||||||||||||||||| | |||||||||||| |||||||| ||
Sbjct  7612477  AGCAAGCTGACCTCATGGTGAATGCTGAATGCGCTGCAAGCTTGGTTTATTTTTGTTTCT  7612418

Query  25299    ccccctctctttttcaccgattaaatttataaagtttagaaata-cggtttcaATTTCTT  25357
                ||||||| ||| ||||| ||||||| |||||||||||| |  || |  ||||||||||||
Sbjct  7612417  CCCCCTCCCTTCTTCACTGATTAAACTTATAAAGTTTACAGGTATC-ATTTCAATTTCTT  7612359

Query  25358    CCAGACAAGCCTTAACCTAAGCCCTGAGACCACTCAAGCCCTCAGTGGCACCTCTCTTCC  25417
                ||||| ||| ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7612358  CCAGAGAAGACTTAACCTAAGCCCTGAGACCACTCAAGCCCTCAGTGGCACCTCTCTTCC  7612299

Query  25418    ACCAGCATGAGCAAATAAATTGCTACCTTAGGTGATATAAAACCCACAAGATGATTCGAT  25477
                ||||||| |||  || ||| |||||||||||||||||||||||||||||||  |||| ||
Sbjct  7612298  ACCAGCACGAGTGAAGAAACTGCTACCTTAGGTGATATAAAACCCACAAGACCATTCCAT  7612239

Query  25478    ACATGGAGtttttt-ttCTGATTTTGTAGGGATGACTTCTTTGT-TTCTATAAAGCTGTT  25535
                |||||||| | ||| |||| |||||||||||| |||| || ||| || |||| |||| ||
Sbjct  7612238  ACATGGAGATCTTTATTCTTATTTTGTAGGGACGACTCCTCTGTGTT-TATACAGCTATT  7612180

Query  25536    TTAACTATAAA-AC----A-A--TTTTATAATTTTGATGTGGCCAAAGATCTCCC-A-A-  25584
                ||||||| ||| |     | |  |||||||||||||||||||||||||||||||| | | 
Sbjct  7612179  TTAACTAGAAATATTTTTATAAATTTTATAATTTTGATGTGGCCAAAGATCTCCCCACAA  7612120

Query  25585    CACTACTTTCAGGTTTTATTTTTCTGTCTACTATCCAGAACAGATCAAACCCTTCCCTGC  25644
                |||||||||||||||||||||||||||||| | ||  ||||||||||| |||||||||||
Sbjct  7612119  CACTACTTTCAGGTTTTATTTTTCTGTCTAATGTCTGGAACAGATCAACCCCTTCCCTGC  7612060

Query  25645    CTCAAACTCAGGACTAT-ATAGGTC-ATATATCAGTAAAATTCCATCAGTGTTTGCGGAg  25702
                |||| | |||||||| | | ||| | | ||| ||||||||||||||||||||||| ||| 
Sbjct  7612059  CTCACA-TCAGGACT-TGA-AGG-CGAAATAGCAGTAAAATTCCATCAGTGTTTGTGGAT  7612004

Query  25703    ttcatgaatgaatgaattctttttt  25727
                |||||||||||||| ||| ||||||
Sbjct  7612003  TTCATGAATGAATGCATT-TTTTTT  7611980


 Score = 4737 bits (2565),  Expect = 0.0
 Identities = 3795/4366 (86%), Gaps = 176/4366 (4%)
 Strand=Plus/Minus

Query  23894    gggaatgggactcctcctatcagttgttttttttttttaattttcttttgtttta-t--c  23950
                ||||||||||||||||||||||     || ||||||| ||||||||||||||||| |  |
Sbjct  7547168  GGGAATGGGACTCCTCCTATCA----ATTATTTTTTTAAATTTTCTTTTGTTTTATTGAC  7547113

Query  23951    ctggcaaggctctaatagagttgagcttttttgtttttgttttttccattggaagggaca  24010
                ||| |||||||| ||||||||||||  |||||||||| ||||||||||||||||| ||||
Sbjct  7547112  CTGACAAGGCTCAAATAGAGTTGAG--TTTTTGTTTTCGTTTTTTCCATTGGAAGAGACA  7547055

Query  24011    atacagaggttacaatcattgactttagatgacaacatgacaggca-aaaatattttcct  24069
                ||||||||||||||||||||| ||||||||||||| || | | | | |||| || |||||
Sbjct  7547054  ATACAGAGGTTACAATCATTGGCTTTAGATGACAAGAT-AAAAGAATAAAACATATTCCT  7546996

Query  24070    tgcaagacaaccagcaaaacttcacgatcagaatcaaatcagtgtccttctcactgtcac  24129
                |||||||||||||||||||||||| |||||||| |||||||||| |||||||||||||| 
Sbjct  7546995  TGCAAGACAACCAGCAAAACTTCATGATCAGAAGCAAATCAGTG-CCTTCTCACTGTCAG  7546937

Query  24130    tgggt-gaagccttcatcagtacttgaagagtctcaggcactcatgaagtcaagatcaga  24188
                ||||| ||||||||||||| |||||| ||||| | ||||||||||||| |||  || |||
Sbjct  7546936  TGGGTGGAAGCCTTCATCAATACTTGCAGAGTTTGAGGCACTCATGAACTCACCATGAGA  7546877

Query  24189    ttctttactcagggacaggatgtaagccaatcataagaccttccacagatgatcaatttg  24248
                |||||||||||||||||||||||||||||| || |||||||||||||| || | ||||||
Sbjct  7546876  TTCTTTACTCAGGGACAGGATGTAAGCCAAGCAAAAGACCTTCCACAGGTGGTGAATTTG  7546817

Query  24249    gaagtctacctaatgtgacctgcaggttttcaCTGGCAATATGCAGGTGCAGATATGACA  24308
                |||| || || ||||| ||||||| |||||||||||||||||||||||||||||||||||
Sbjct  7546816  GAAGCCTGCCCAATGTAACCTGCAAGTTTTCACTGGCAATATGCAGGTGCAGATATGACA  7546757

Query  24309    AAGAATAATCC-TGACCTTCATATCGCCCCTAGCTGATGAGGATTGGGATTCTTTTGTCC  24367
                |||||||| || ||||||| | ||| |||| ||||| |||||| |||||| |||||| ||
Sbjct  7546756  AAGAATAA-CCATGACCTTTACATCACCCCCAGCTGTTGAGGAATGGGATCCTTTTGACC  7546698

Query  24368    CTTTCTCTCCATAAAACCAGGTTACTCATCTTGTGTGGCAACAAAATATATGGTctactt  24427
                |||||| |||||| ||||||||| |||||||||||||||||||| |||| ||||||||||
Sbjct  7546697  CTTTCTGTCCATAGAACCAGGTTGCTCATCTTGTGTGGCAACAACATATGTGGTCTACTT  7546638

Query  24428    aacagagaaag-agactccacaggaaaaaaaaaaggatttttattatgaaatgagcaaag  24486
                ||||||| ||| |||||   |  |   |||||||  || ||||||||| | | |||||||
Sbjct  7546637  AACAGAG-AAGAAGACT---C-TG--TAAAAAAA--ATGTTTATTATGTAGTAAGCAAAG  7546587

Query  24487    ccatgggaatagatgtgagattattcggggaggtaaaggaagacaaaggttttgaaagga  24546
                  ||||||||||||||||||||||| |||||| |||||||||   |||||||||||||||
Sbjct  7546586  AAATGGGAATAGATGTGAGATTATTTGGGGAGATAAAGGAAGTTGAAGGTTTTGAAAGGA  7546527

Query  24547    aaaatgaggagaattacataaatttttttgaaagactcattcttggtcacaagtatgaaa  24606
                ||||| ||||| |||| | ||||| ||||||||||||||| ||||||||  || || |||
Sbjct  7546526  AAAATAAGGAGGATTATACAAATTGTTTTGAAAGACTCATACTTGGTCATGAGGATTAAA  7546467

Query  24607    acc-aagggagcctcagtgcagtgttggaaagATTCCTCCTCCACCCTCTCAATAACCCC  24665
                ||| || || || |||||||| |||| || ||||||||| | ||||| ||| ||||||||
Sbjct  7546466  ACCAAAAGG-GCATCAGTGCAATGTTAGATAGATTCCTCTTACACCCACTCGATAACCCC  7546408

Query  24666    CAACACATTTACCAAGTCTTTGTTCACTCCCAGGATT-CCATTAAAACACCCAGCTCAAC  24724
                |||||  || | |||||||| ||||||||||||| || ||||||||| ||||||||||||
Sbjct  7546407  CAACATGTTCAGCAAGTCTTGGTTCACTCCCAGG-TTCCCATTAAAA-ACCCAGCTCAAC  7546350

Query  24725    CCTGACCAGCCTCCACCTTCACTTCCCTTTGTAATTTTGACATAAATTtgttacaggacc  24784
                ||||||||| ||||||| |||||||| |||||||||||||||| | ||| ||||||||||
Sbjct  7546349  CCTGACCAG-CTCCACCCTCACTTCCATTTGTAATTTTGACATGACTTTATTACAGGACC  7546291

Query  24785    atcaggttcctatgccggctgcacagtagcttaccaatattctgagacagcaggatttgc  24844
                |||||||||||||||| |||||||||||||||| |||||||||||||||||||| |||||
Sbjct  7546290  ATCAGGTTCCTATGCCTGCTGCACAGTAGCTTAGCAATATTCTGAGACAGCAGGGTTTGC  7546231

Query  24845    agcagaaagtttaatgatcacagggtggctgaatgagaagctgggaggagatcctcaaat  24904
                |||||| ||||||||||||||| ||||||||||||||||||| |||||||||||||||||
Sbjct  7546230  AGCAGAGAGTTTAATGATCACAAGGTGGCTGAATGAGAAGCTAGGAGGAGATCCTCAAAT  7546171

Query  24905    tcatctccccaaggagtactgagggtttccagtggatcctggatagcaaggggctggaaa  24964
                |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
Sbjct  7546170  TCATCTCCCCAAGGAGTACTGAGGGTTTCCAGTGGATCCTGGATAGCAAGGGGCCGGAAA  7546111

Query  24965    gttggtgtagtttgatggcaataagaggtatgaagttatcacgatgtcag-aacggcatt  25023
                ||||| |  |  | |  ||  ||||||| | ||||| | || ||||| || ||| |||||
Sbjct  7546110  GTTGG-G--G--T-A--GCGGTAAGAGGGAAGAAGTCAACAGGATGT-AGAAACTGCATT  7546060

Query  25024    ctttggtgagttgatgccttgcagggcccttcagatcagctggcatcagtagtttcactg  25083
                ||||||||||||| ||| |||||||||||||||||||||||||||||||||| |||||||
Sbjct  7546059  CTTTGGTGAGTTGGTGCATTGCAGGGCCCTTCAGATCAGCTGGCATCAGTAGATTCACTG  7546000

Query  25084    acatgcagaacctgaaagaatatctcaaatgaaaaacttaatgtttcacaatgcttaaat  25143
                ||||||||||||||||||||||||||| |||||||| ||||||||| |||||||||||||
Sbjct  7545999  ACATGCAGAACCTGAAAGAATATCTCAGATGAAAAAGTTAATGTTTTACAATGCTTAAAT  7545940

Query  25144    tgttgtctgcagcgtagttaaggggaattgtagtctaagttctacacgattttgggacag  25203
                 ||||||||||| | |||||||||||| |||| |||||| |||| | |||||||| ||||
Sbjct  7545939  GGTTGTCTGCAGGGAAGTTAAGGGGAACTGTAATCTAAGGTCTATATGATTTTGGAACAG  7545880

Query  25204    taggctgccagcaaccatgaggaagcaggtcagagggcaagctgacctcctggtgaatgc  25263
                |||| ||||||||||||||||||| |||||||||| |||||  ||||||||| |||||||
Sbjct  7545879  TAGGTTGCCAGCAACCATGAGGAACCAGGTCAGAGAGCAAGAAGACCTCCTGATGAATGC  7545820

Query  25264    tgaatgcgtttcaagcttggtttgtttttgttcctccccctctctttttcaccgattaaa  25323
                |||||| ||| |||||||||||| |||||||| ||| ||||| ||| ||||| |||||||
Sbjct  7545819  TGAATGTGTTCCAAGCTTGGTTTATTTTTGTTTCTCTCCCTCCCTTCTTCACTGATTAAA  7545760

Query  25324    tttataaagtttagaaatacggtttcaATTTCTTCCAGACAAGCCTTAACCTAAGCCCTG  25383
                |||||||||||||   ||  || |||||||||||||| | ||| ||||||||||||||||
Sbjct  7545759  TTTATAAAGTTTATCGATGTGGCTTCAATTTCTTCCAAAGAAGACTTAACCTAAGCCCTG  7545700

Query  25384    AGACCACTCAAGCCCTCAGTGGCACCTCTCTTCCACCAGCATGAGCAAATAAAT-TGCTA  25442
                |||||||||| ||||||||||||||||||| |||||||| | |||||  | ||| |||||
Sbjct  7545699  AGACCACTCACGCCCTCAGTGGCACCTCTCCTCCACCAGAACGAGCATGT-AATCTGCTA  7545641

Query  25443    CCTTAGGTGATATAAAA-CCCACAAGATGATTCGATACATGGAG-ttttttttCTGATTT  25500
                |||||||| ||| |||| |||  ||||  |||| |||| | ||| ||||| |||||||||
Sbjct  7545640  CCTTAGGTTATACAAAATCCC-GAAGACCATTCAATACGTTGAGATTTTTATTCTGATTT  7545582

Query  25501    TGTAGGGATGACTTCTTTGTTTCTATAAAGCTGTTTT-AACTATAAAACAATTTTATAAT  25559
                  |||||| |||| || ||||| ||||||||| |||| || || ||| || |||||| ||
Sbjct  7545581  CCTAGGGACGACTCCTCTGTTTTTATAAAGCT-TTTTAAAGTAGAAAGCATTTTTAT-AT  7545524

Query  25560    TTTGATGTGGCCAAAGATCTCC---CAACACTACTTTCAGGTTTTATTTTTCTGTCTACT  25616
                |||||||||||||||||| |||   ||||||||||||||| ||||||||||||||||| |
Sbjct  7545523  TTTGATGTGGCCAAAGATTTCCTAACAACACTACTTTCAGATTTTATTTTTCTGTCTAAT  7545464

Query  25617    ATCCAGAACAGATCAAACCCTTCCCTGCCTCAAACTCAGGACTAT-ATAGGTCATATATC  25675
                 |   |||||||||||| ||||||||||||   ||||| |||||| | || ||| |||| 
Sbjct  7545463  GTTGGGAACAGATCAAATCCTTCCCTGCCTGTCACTCAAGACTATGA-AGTTCACATATT  7545405

Query  25676    AGTAAAATTCCATCAGTGTTTGCGGAgttcatgaatgaatgaattctttttttttttttt  25735
                |||||||| ||||||||||||| |||||||||||||||||| |                 
Sbjct  7545404  AGTAAAATACCATCAGTGTTTGTGGAGTTCATGAATGAATG-A-----------------  7545363

Query  25736    tttttttttttttgtgaca-aagtctacctctgtcacccagaac-ggtgtgcaatggtgc  25793
                ||||||| ||||| ||||| || | | |||||||||||||| || || ||||| |||  |
Sbjct  7545362  TTTTTTTATTTTT-TGACAGAA-TGTCCCTCTGTCACCCAG-ACTGGAGTGCAGTGGCAC  7545306

Query  25794    aa-tcttggctcactgcaaccattgccccctggattcaagcgattctcccacctcagcct  25852
                || || ||||||||||||||||||||| ||||| ||||||| |||||||  |||||||||
Sbjct  7545305  AATTC-TGGCTCACTGCAACCATTGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCT  7545247

Query  25853    cctgagtagctggattacaggcacctgccatcatg-ccaggctaatttttg------tg-  25904
                ||  ||||||||| || |||||||||||||||||| ||| |||||||||||      || 
Sbjct  7545246  CCCAAGTAGCTGGGTTTCAGGCACCTGCCATCATGCCCA-GCTAATTTTTGTATTTTTGT  7545188

Query  25905    -tttttgtagag-ctggggtttcatcatgttggccttgcaggtcttgatcgcctgacctc  25962
                 ||||||||||| |  |||||||| | | ||| ||| ||  ||||||| | |||||| ||
Sbjct  7545187  ATTTTTGTAGAGAC-AGGGTTTCACCTTTTTGACCTGGCTCGTCTTGAACCCCTGACATC  7545129

Query  25963    aggtgatccagc-caacttggac-tctcaaagtgcagggattacaggtgtgagccacctc  26020
                |||||||| | | || ||||  | || |||||||| || ||||||| | ||| |||||||
Sbjct  7545128  AGGTGATCTA-CTCACCTTGTCCTTC-CAAAGTGCTGGAATTACAGCTATGAACCACCTC  7545071

Query  26021    acccggcctttaatgaGTGAATTCTTGATTTCCACCCTATTCCTAACACTGTCAATTTCT  26080
                ||||  |||| ||||| || |||||||| ||| ||||||| |||||||||||| ||||||
Sbjct  7545070  ACCCACCCTTGAATGAATGTATTCTTGACTTCTACCCTATCCCTAACACTGTCGATTTCT  7545011

Query  26081    TGATTCATGAACTTAATATGGATA-GCTGATATGAATGGATATCTGATTCAATCCAGTAA  26139
                || |||||||| | ||||| |||| | ||||||||||||| |||||||||||||| ||||
Sbjct  7545010  TGCTTCATGAAGTGAATATAGATATG-TGATATGAATGGACATCTGATTCAATCCGGTAA  7544952

Query  26140    TCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGGGTGGAGCTTCAGAAATGCAATCA  26199
                |||||||| ||||||||||||||||| ||||||||||||||||||||| |||||||||||
Sbjct  7544951  TCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCACAAATGCAATCA  7544892

Query  26200    GATAGCACTTTTTGATTGGAAGCAAGCA-CTGGATA-GATGGAGGGGTGTGGGTGGGAGT  26257
                |||| || ||||||||||||||  |||| | ||||| | || ||||| ||||||||||||
Sbjct  7544891  GATATCATTTTTTGATTGGAAGGTAGCAGC-GGATATG-TGCAGGGGCGTGGGTGGGAGT  7544834

Query  26258    TGTGATTAGAAAGATCGATAAAAGTTTCTGAAGGCCCACAGGAGAGACCCAAAGTCTTCA  26317
                ||||||||||||| || ||||||| |||| ||| ||||||||||||||||||||||||||
Sbjct  7544833  TGTGATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGAGAGACCCAAAGTCTTCA  7544774

Query  26318    AGTCTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTAAGCACTCTGC-AAACT-CAGTCCA  26375
                || ||||||||||||||||||||||||||||| || ||||| || | | ||| || ||||
Sbjct  7544773  AGCCTGGAGTTCCTGCTTGGTTCTTCCTGAGGACTGAGCAC-CTTCTAGACTACA-TCCA  7544716

Query  26376    GATCTAGTAAGTCACTCATTTCTGGAAGGACACTCCCATCTGACCTATAGTCAGCCGGTC  26435
                ||||| ||||| |||| ||||||| |||||||||||||||||||||| |||||| |||||
Sbjct  7544715  GATCTGGTAAGCCACTAATTTCTGTAAGGACACTCCCATCTGACCTACAGTCAGTCGGTC  7544656

Query  26436    TGGGACGGGGGCAATGCAGCCTATGATGGCACCGAGCTATAT-CTGT-CTTTtatatata  26493
                ||||| || | || ||||||||| |||||||| ||||||||| |||| ||||| | | | 
Sbjct  7544655  TGGGATGGTGACAGTGCAGCCTACGATGGCACAGAGCTATATCCTGTCCTTTT-T-T-T-  7544600

Query  26494    tat-atatGAACAATTTGAAGATTTGAATTTTTTCCTCTATATGCAGTTTTGTCTTTATT  26552
                | | |||||||||||||||||  |||||| |||||||||| |||||||| ||||||||||
Sbjct  7544599  TTTCATATGAACAATTTGAAG-CTTGAATGTTTTCCTCTAAATGCAGTTCTGTCTTTATT  7544541

Query  26553    TCAAAAAA-TTGGATTGTGCTTTGGTTTATGTCATTTcaaaattcttgatgggagcaatg  26611
                |||||||| || ||||||||||||||| ||| ||||| ||||||| ||| ||||||||||
Sbjct  7544540  TCAAAAAAGTT-GATTGTGCTTTGGTTGATGCCATTTTAAAATTCGTGAAGGGAGCAATG  7544482

Query  26612    actcatgcccataacctcaacaccttgggaggccaaagcgggaggatcatttgagcccag  26671
                ||||||| |  ||||| |||||| |||||||||||||| ||||||||||||| |||||||
Sbjct  7544481  ACTCATGTCTTTAACCCCAACACTTTGGGAGGCCAAAGTGGGAGGATCATTTCAGCCCAG  7544422

Query  26672    gggtttgagaccaacctgggcaacatggcaaaaatgcagctctacaaaac---attcttt  26728
                ||||||||||||||||||||||||||| |||||   |  ||||||| |||    || |||
Sbjct  7544421  GGGTTTGAGACCAACCTGGGCAACATGACAAAAGCCCTCCTCTACACAACGTTTTTTTTT  7544362

Query  26729    ttttga-agcagggatggagtctcaccctgttgccaaggctggagtgcagtggcaagagc  26787
                ||||||  |  |||||||||||||||  ||||||| || |||||||||||||||| || |
Sbjct  7544361  TTTTGAGGGTGGGGATGGAGTCTCACTGTGTTGCCCAGACTGGAGTGCAGTGGCACGATC  7544302

Query  26788    tcaactcactgcaacctctt-cctcccaggctcaaacaattttcatgtctcag-ct---t  26842
                |||| |||||||||||| || |||||| || |||| ||||| ||||| ||||| ||   |
Sbjct  7544301  TCAAATCACTGCAACCT-TTACCTCCCGGGTTCAAGCAATTCTCATGCCTCAGTCTCCAT  7544243

Query  26843    cctgagtagctggtattacatccctctgccaccatgtct-gcttaatttttgtattttta  26901
                ||| || ||||||| | |||  | ||||  |||||| || || |||||||||||||||||
Sbjct  7544242  CCTCAGAAGCTGGTGTCACAGACATCTGAAACCATGCCTGGC-TAATTTTTGTATTTTTA  7544184

Query  26902    gtagtggtggggtttcaccatgctggccaggttggtctcaaactcctgacatcaagtgat  26961
                |||| |||||||||||||||||||||||||||||||||| ||| |||||| |||||||||
Sbjct  7544183  GTAGAGGTGGGGTTTCACCATGCTGGCCAGGTTGGTCTCGAACACCTGACCTCAAGTGAT  7544124

Query  26962    cctcctgcctaggcc-cccaaaagtgctggaatgacggccgtgagccaATGGTGGTCAGC  27020
                || ||||||| |||| ||| |||||||||| || || || ||||| || ||||| |  ||
Sbjct  7544123  CCACCTGCCTTGGCCTCCC-AAAGTGCTGGGATTACAGCTGTGAGTCACTGGTGCTTGGC  7544065

Query  27021    ctctacaaaatatatatatcttttaatttgccag-gcatggtag-catgcatctgtattc  27078
                ||||||    | | | | | |||||||| ||| | ||||||| | |||||||||||| ||
Sbjct  7544064  CTCTAC----T-TTTTTTTATTTTAATTAGCC-GAGCATGGT-GACATGCATCTGTAGTC  7544012

Query  27079    ccagctatttggtttgctgacatgggagaatcacttgagcccagaagattgaggctgcag  27138
                |||||||||||| | ||||   ||||||||||||||||||||||||||||||||||||||
Sbjct  7544011  CCAGCTATTTGGGTGGCTGGTGTGGGAGAATCACTTGAGCCCAGAAGATTGAGGCTGCAG  7543952

Query  27139    tgagccatgctcacaccactgctgtactccagcctgggcaacagagta-agaccctgcta  27197
                ||||||||||||||||||||||||||||||||||||||||| |||| | |||||||| | 
Sbjct  7543951  TGAGCCATGCTCACACCACTGCTGTACTCCAGCCTGGGCAAAAGAG-AGAGACCCTG-T-  7543895

Query  27198    aaaacaaaaacgaaaacaaacaaacaaaaaacCTTAACCAAAGAGAATCTTTGACCTTAA  27257
                    |   ||  ||||| || ||||  || | |||||||||| || |||| |||||||||
Sbjct  7543894  ----C--CAA--AAAAC-AA-AAAC--AATATCTTAACCAAAAAGGATCTATGACCTTAA  7543847

Query  27258    TTTTAAACCAATCACATCCTCACTGTAATTCTTCCTCCCGAATGGAGACATgggtgtgag  27317
                ||||||||||||||| ||||||||||||||||||| | |||||||||||||||||||| |
Sbjct  7543846  TTTTAAACCAATCACGTCCTCACTGTAATTCTTCCACTCGAATGGAGACATGGGTGTGGG  7543787

Query  27318    ggtgcatgcctgtaatcccagctacatggaaggctgaagcatgagaattgcttgaatctc  27377
                ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct  7543786  GGTGCATGCCTGTAATCCCAGCTACGTGGAAGGCTGAAGCATGAGAATTGCTTGAATCTC  7543727

Query  27378    agaggcggaagttacagtgagctgagatggagccgctgcactccagcctgggcgacaaag  27437
                ||||| ||| |||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct  7543726  AGAGGTGGAGGTTACAGTGAGCTGAGATGGCGCCGCTGCACTCCAGCCTGGGCGACAAAG  7543667

Query  27438    tgagactcagcttcacccacaccaaaaaaaaTTAGATTATACCACCCAGGTGATCACTGG  27497
                |||||||||||||| ||||||||||||||||||||||||||||||||||||||||| |||
Sbjct  7543666  TGAGACTCAGCTTCCCCCACACCAAAAAAAATTAGATTATACCACCCAGGTGATCATTGG  7543607

Query  27498    ATACATGAAGATTTCTATTGTGTGTTATTGGGGACTGTCAACTCCGTCTTTGAAAACTGT  27557
                |||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||
Sbjct  7543606  ATACATGAAGATTTCTATTGTGTGTTCTTGGGGACTGTCAACTCTGTCTTTGAAAACTGT  7543547

Query  27558    TTTAACTCTGAAATATTTTGATAAATTTGATGTGGCCAAGGATCCCTCAACAAAGATACT  27617
                ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Sbjct  7543546  TTTAACTCTGAAATATTTTGATAAATTTGATGTGGCCGAGGATCCCTCAACAAAGATACT  7543487

Query  27618    TTCAAGTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGATTCAACACTTCCCTATCTCAC  27677
                |||||||||| || ||||||||||||||||||||||||||||||| ||||||||||||||
Sbjct  7543486  TTCAAGTTTT-TT-CTTTCTGTCTAATATCAGGAAGAGATTCAACCCTTCCCTATCTCAC  7543429

Query  27678    ACTCAGGACTATGAAGGACACATATTAGTAAA-CCTCCAT---GTTTGTGGAGGGAATCA  27733
                |||||||||| |||||||||||||||| |||| || ||||   ||||||| |||||||||
Sbjct  7543428  ACTCAGGACTGTGAAGGACACATATTAATAAAACC-CCATTTTGTTTGTGAAGGGAATCA  7543370

Query  27734    GTGAATGAGTCCTGGACTTTCACCCTATCCCTAAATCTTTCACTTTCATGGATGAATATC  27793
                ||||||||||||||| ||| ||||| |||||||||||||||||||| |||| ||||||||
Sbjct  7543369  GTGAATGAGTCCTGGGCTTCCACCCCATCCCTAAATCTTTCACTTTGATGGGTGAATATC  7543310

Query  27794    TAATTCAATCAGTTAATCTGGAAGAAAGCCAAAAATCCAATCAGGATTAACTGGGTAGAG  27853
                |||||| |||||| ||||||||||||||||||||||||||||||||||||||||||| | 
Sbjct  7543309  TAATTCCATCAGTAAATCTGGAAGAAAGCCAAAAATCCAATCAGGATTAACTGGGTAAA-  7543251

Query  27854    TTTAAGAAGTCGAATCAAATGTAGTtctctctctctc-tctctct----cttttcttttc  27908
                ||        |||||||||| ||| |||||||||||| | | |||    ||||| |||| 
Sbjct  7543250  TT--------CGAATCAAATCTAGCTCTCTCTCTCTCCTTTTTCTTTTTCTTTTTTTTTT  7543199

Query  27909    tttttttttttttttttttt-gaatctagcctatttcacaggctggagtgcagtggtgta  27967
                |||||||||||||||||||| |||||||||||||||| ||||||||||| ||||||||||
Sbjct  7543198  TTTTTTTTTTTTTTTTTTTTTGAATCTAGCCTATTTCCCAGGCTGGAGTTCAGTGGTGTA  7543139

Query  27968    ttgtcagctcactgcaacctctgcctcctgggttcaagtgatcctcctgcctcagcctcc  28027
                |||||||||||||||||||||||||||||||||||||| |||| ||||| ||||||||||
Sbjct  7543138  TTGTCAGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGCGATCTTCCTGTCTCAGCCTCC  7543079

Query  28028    ctagtagcttggactataggcgcagaccaccgcacctggctaatttttctaattttggta  28087
                |||||||||||||||||||||||||||||||||| ||||||||||||| ||||||| |||
Sbjct  7543078  CTAGTAGCTTGGACTATAGGCGCAGACCACCGCAACTGGCTAATTTTTGTAATTTTAGTA  7543019

Query  28088    gaggtagggttttaccatgttggccaggctggtctcaaactcctgacctcagataatcca  28147
                |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct  7543018  GAGGTAGGGTTTTACCATGTTGGCCAGGCTTGTCTCAAACTCCTGACCTCAGATAATCCA  7542959

Query  28148    cctgcctctgcctcccagagggctgggattacaggtgtgagtcact  28193
                ||| ||||||| |||||||| |||||||||||||||||||| ||||
Sbjct  7542958  CCTACCTCTGCGTCCCAGAGTGCTGGGATTACAGGTGTGAGCCACT  7542913


 Score = 4325 bits (2342),  Expect = 0.0
 Identities = 3123/3495 (89%), Gaps = 74/3495 (2%)
 Strand=Plus/Minus

Query  3255     GGCAGAAACTTTCTCCAGCAGAGCTCCGAGGGGTTCAAGACTGATACAGAACTGCAGCAT  3314
                ||||| || |||||| ||||||||||| ||||||||||||||||| | |||| |||||| 
Sbjct  7458623  GGCAGCAATTTTCTCTAGCAGAGCTCCTAGGGGTTCAAGACTGATGCGGAACAGCAGCAC  7458564

Query  3315     GTAGCTGAGATTCAGATGCTTTGGGTAAGCGAGGCTTGGGTACTGGTAGAGACACTTCAA  3374
                |||||||||||||||||||||| ||||| ||||||||||| ||||| |||||||||||||
Sbjct  7458563  GTAGCTGAGATTCAGATGCTTTAGGTAACCGAGGCTTGGGAACTGGGAGAGACACTTCAA  7458504

Query  3375     GTCCTCTTCCAATAGGTAGCCGCAAGTTAATTCCAAGTTCTCCAAGGGGTTCTAGAGGCA  3434
                ||||||||| ||||||| ||| ||||||||||||||||||||||||||||||| ||||||
Sbjct  7458503  GTCCTCTTCTAATAGGTTGCCACAAGTTAATTCCAAGTTCTCCAAGGGGTTCTGGAGGCA  7458444

Query  3435     CCTGTGGAGATCAAGAAGTTAGTTCTGGGCAATGGTACCAGTTAGATGAAGGTAGTGGGG  3494
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7458443  CCTGTGGAGATCAAGAAGTTAGTTCTGGGCAATGGTACCAGTTAGATGAAGGTAGTGGGG  7458384

Query  3495     AATGAA-CTCAAGGAAAATACCTGCTTCAACCAAACACAAGTTTGTTCCCACCATCTGAT  3553
                ||| || |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7458383  AAT-AACCTCAAGGAAAATACCTGCTTCAACCAAACACAAGTTTGTTCCCACCATCTGAT  7458325

Query  3554     GATGGTCCTCATGCAAGTTGCTGCATGTTGAGGACCCTGATCATTCAGGGGCTGTCCCAT  3613
                ||||||||||||| ||||||||||||| |||||||||||||| |||||||||||||||||
Sbjct  7458324  GATGGTCCTCATGGAAGTTGCTGCATGATGAGGACCCTGATCGTTCAGGGGCTGTCCCAT  7458265

Query  3614     TTTAGCCTCAGCCCTTTCACCATTTCTTGTGTGATTGGGTCAAGGCCACAAAATCTCTAA  3673
                |||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||
Sbjct  7458264  TTTAGCCTCAGCCCTTTCACCATTGCTTGTGTGATTGGGTCAAGGCCATAAAATCTCTAA  7458205

Query  3674     AGCC-TTTT-ATCTTCATCTTTTAGCAGAAAACCTCATCTCTGGGCCACAGGTACCCGGT  3731
                |||| ||||  | |||||||||||||||||||| |||||||||||| |||||||||| ||
Sbjct  7458204  AGCCTTTTTGTTTTTCATCTTTTAGCAGAAAACTTCATCTCTGGGCTACAGGTACCCCGT  7458145

Query  3732     GGGAGATGTGCACAAAGAACTCAACTCAGCAAGGTCTAGGGACATTAGCTGGGGCTACCT  3791
                |||||||||| |||||||||||||||||||||||||||||||||| |||| ||||||| |
Sbjct  7458144  GGGAGATGTGAACAAAGAACTCAACTCAGCAAGGTCTAGGGACATCAGCTAGGGCTACAT  7458085

Query  3792     GCCGGCAGGGGCTCCCTGGCCTGCCTGCATCTGCAAACCAACTGTCACTTTTTACCACTC  3851
                | |||||||||||||||| | |||||||||||||||||||||||||||||||||||||||
Sbjct  7458084  GTCGGCAGGGGCTCCCTGACATGCCTGCATCTGCAAACCAACTGTCACTTTTTACCACTC  7458025

Query  3852     TCACTCCTACTCCTTCACCCTCCATCCCAGAAGCATGCATGTCCCATGTCAATTGA-CTT  3910
                |||| |||||||| ||| |||||||||| |||||| |||| ||||||||||||| | |||
Sbjct  7458024  TCACGCCTACTCCCTCA-CCTCCATCCCGGAAGCACGCATTTCCCATGTCAATT-ACCTT  7457967

Query  3911     TCCTGGAGTTCAAAACAACCTTCTACAGACAGGGAATCAGAGACAGGATCATTCATGATC  3970
                ||||||||||||||||||| || | |||||||||||| | |||||||||||||| |||||
Sbjct  7457966  TCCTGGAGTTCAAAACAACGTTTTGCAGACAGGGAATTAAAGACAGGATCATTCGTGATC  7457907

Query  3971     ACTAAGCTGGTGAGGACAGAGC-TTCTACTGTGAAATGCACAAGTTTGATGCACTGTCCC  4029
                ||||||| |||||||||||| | ||||| ||||||||| ||| ||||||||| || ||||
Sbjct  7457906  ACTAAGCCGGTGAGGACAGA-CGTTCTATTGTGAAATGGACAGGTTTGATGCGCTTTCCC  7457848

Query  4030     TCCTTTCATACCCTCCTTTGTTACCTCTTTTACATCATATCAACTTGAAACACACTTTGT  4089
                ||||||||||||||||| | ||| |||||| |||||||||||||||||||||||||||||
Sbjct  7457847  TCCTTTCATACCCTCCTCTATTATCTCTTTGACATCATATCAACTTGAAACACACTTTGT  7457788

Query  4090     AACAAGAAATTCACACGTGCACATGCAGTAGAGAC-AAAACGCCCACTAAGTACCTTGTA  4148
                |||| |||||||||||||||||   || ||||| |  |||| |||||| | || ||||||
Sbjct  7457787  AACAGGAAATTCACACGTGCACCCCCAATAGAG-CTGAAACCCCCACTGACTAGCTTGTA  7457729

Query  4149     CATGATGTCCCTCTCTAGCCTCTACCCTAGGTGACCCCTCTGCCTTTATTGAAGTGATCC  4208
                ||||||||||||||||||| ||||||| |||||||||||||||| |||||| || |||||
Sbjct  7457728  CATGATGTCCCTCTCTAGCTTCTACCCCAGGTGACCCCTCTGCCCTTATTGGAGCGATCC  7457669

Query  4209     TGTGATAGCCACTCCAGGACATGGAGCACTGAACGGGACAATGTGTTGACATTCTGGTGT  4268
                ||||||||||||||||||||||||| ||||||| ||||||||||||||||||||||||||
Sbjct  7457668  TGTGATAGCCACTCCAGGACATGGAACACTGAATGGGACAATGTGTTGACATTCTGGTGT  7457609

Query  4269     CCCCTGCACTGTGCCGTCGCCACTGGCTGGCACACAGTACACGTCTTCTAGTGTTTACTG  4328
                 |||| ||||||| ||| ||||||||||||||||||||||||| |||||| ||||| |||
Sbjct  7457608  TCCCTTCACTGTGACGTTGCCACTGGCTGGCACACAGTACACGCCTTCTAATGTTTGCTG  7457549

Query  4329     TAACaaaaaaaaaGGCTGCGCTGTGGTCTGCAGAGAAAGGGCACGATCCTTTCTCACCTG  4388
                ||||  | || ||| ||| ||||||||||||| | |||| |||| |||||||||||||||
Sbjct  7457548  TAAC--AGAACAAGTCTGTGCTGTGGTCTGCATACAAAGTGCACAATCCTTTCTCACCTG  7457491

Query  4389     ATCAGCTGTCCCAGGTGCCCTCTGTGGAAGGTGA-CCATATTCATTTTAAGCAGCTGGAG  4447
                ||||||||| |||||||||| |||  |||||||| | || || |||||||||| ||||||
Sbjct  7457490  ATCAGCTGTTCCAGGTGCCCACTGAAGAAGGTGATCAAT-TTTATTTTAAGCAACTGGAG  7457432

Query  4448     GTGTTTCAGCCTGAGGAACATAGAGCTGATTTTGGCGACTGAGCATTCCTCGCGGT-A--  4504
                ||||| |||||||||||||| |||| ||| | ||| |||| | ||| ||||| | | |  
Sbjct  7457431  GTGTTCCAGCCTGAGGAACACAGAGGTGAATCTGGTGACTAACCATCCCTCGAGTTCATT  7457372

Query  4505     AT-TGACGTGTAAGGATGGCACCTGGAGAAAAATGAGTTTGCGAAGATTCTTCATCTCCT  4563
                || |||||||||| |||||||||||||| |||| |||||||| |||| ||||||||||||
Sbjct  7457371  ATCTGACGTGTAATGATGGCACCTGGAG-AAAACGAGTTTGCAAAGAGTCTTCATCTCCT  7457313

Query  4564     TCAGGTAACAATGAAGCTTTCTTATCAGATGTGGCCAGGACACATAGCAAATTTCCAGCT  4623
                |||||||||||| ||||||||||||||||||||||||| ||   | |  |||||||||||
Sbjct  7457312  TCAGGTAACAATAAAGCTTTCTTATCAGATGTGGCCAGCACGTGTTGTGAATTTCCAGCT  7457253

Query  4624     CCTGAATACTATTCAGGTGGATTATTTTCAATGATC-TTCTGAGATATTCAATCGACGTT  4682
                ||  ||||||||| | ||  |||||||||||||| | |||||||||||| ||| | ||||
Sbjct  7457252  CCCCAATACTATTAATGTATATTATTTTCAATGA-CTTTCTGAGATATTTAATTGGCGTT  7457194

Query  4683     AGATAATTCACCAACTTACTACAGCACAGGTGTACTAAACCTCTCCTTTGGTAAACCCAC  4742
                |||||||| |||| ||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7457193  AGATAATTGACCAGCTTACTACAGCACAGGTGTACTAAACCTCTCCTTTGGTAAACCCAC  7457134

Query  4743     CGGAAGAGGTATCTCAGGCATTCATCCTGGGGTATTTCCTTGAGGCAGATGTCTATGAAC  4802
                 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7457133  TGGAAGAGGTATCTCAGGCATTCATCCTGGGGTATTTCCTTGAGGCAGATGTCTATGAAC  7457074

Query  4803     ACCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGTCTGCCTCTTACTC  4862
                ||||| |||||||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct  7457073  ACCTTTAAGGGCTGGTGCTCTCCCGTCCTTGGACAGTCCTCTGCTGTCTGCCTCTTACTC  7457014

Query  4863     ATGGCCTCTGGGGAGGAGGACAGGGCCCTGGATTCAGACCATATGGCCCAGAAATTCTCA  4922
                |||||||||||| || |||||||||||| || | ||| |||| |||||||||||||||||
Sbjct  7457013  ATGGCCTCTGGGAAGCAGGACAGGGCCCAGGCTCCAGGCCATCTGGCCCAGAAATTCTCA  7456954

Query  4923     TCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAAAGTAAGGCAGA  4982
                |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
Sbjct  7456953  TCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAAAGTAAGGGAGA  7456894

Query  4983     GGCTCAGAACTTT-GAAGGACAAATCCCTGACCTTTGCTTTCATTCTCATCCAATAAATC  5041
                ||||||||| ||| || ||||  ||||||||||||||||||||||||||||| |||||||
Sbjct  7456893  GGCTCAGAA-TTTAGAGGGACTCATCCCTGACCTTTGCTTTCATTCTCATCCCATAAATC  7456835

Query  5042     AGCTGCTCCTGTCCTC-GCTGCTCCCTGTTCTCTCTGAGTTTTCTTGGTCCCTTTTCTCT  5100
                |||||||||||||||| | ||||||||||||||| ||  ||||||   ||||||||| ||
Sbjct  7456834  AGCTGCTCCTGTCCTCAG-TGCTCCCTGTTCTCTTTGTCTTTTCTCAATCCCTTTTCCCT  7456776

Query  5101     TTCAATTCTGACTGGTCCCCACTTCTATTCCATTTACCTTCCACTG-GGAATAGGCAAGT  5159
                ||  ||||||| ||||||||||||||||||| |||||||||||||| | || ||||  ||
Sbjct  7456775  TTGGATTCTGAGTGGTCCCCACTTCTATTCCCTTTACCTTCCACTGAGTAA-AGGCCGGT  7456717

Query  5160     TTCTGTTCCCACAGTGGACCCTATATTGTGGGCAGTTCTTTCCCTGAGGATCTGGGCAAT  5219
                |||||||||||||||||||||| ||| ||| ||||| ||||| |||||||||||| ||||
Sbjct  7456716  TTCTGTTCCCACAGTGGACCCTGTATGGTGAGCAGTCCTTTCTCTGAGGATCTGGACAAT  7456657

Query  5220     GGCCAAGGCATGCCTGAGCTTCGTCACCAGCACCACCAGAAGACACTGGGCCATC-CTTG  5278
                |||||| || | |||||||||| || ||| ||||| |||||||| |||||||  | ||||
Sbjct  7456656  GGCCAAAGCCTCCCTGAGCTTCCTCGCCAACACCATCAGAAGACTCTGGGCC-GCACTTG  7456598

Query  5279     GGATACTTCTTTGCCTGACCCTGCTGTTCTTTCCCTGGACACCTGAGCCCCATCTACCAG  5338
                || ||||||| ||||||||||||||||||||||||||||||||||||||| |||||| ||
Sbjct  7456597  GGTTACTTCTCTGCCTGACCCTGCTGTTCTTTCCCTGGACACCTGAGCCCTATCTACTAG  7456538

Query  5339     CCTTCCTGGGTCACCTCACCTGGGGCGATCCTTCTGTGTAAGCAGCATGTGAAGCCCTTC  5398
                || ||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Sbjct  7456537  CCCTCCTGGGTCACCTCACCTGGGGCGATCCTTCTGTGTAAGCAGCATATGAAGCCCTTC  7456478

Query  5399     CAGCAATGCTTTTAA-GGTCTCCAGATGAAGCGTCTTCATCAGCGATCCCAGAGGGAGGC  5457
                |||||||||||| || || |||||||||||||||||||||||||||| ||||||||||||
Sbjct  7456477  CAGCAATGCTTTCAATGG-CTCCAGATGAAGCGTCTTCATCAGCGATACCAGAGGGAGGC  7456419

Query  5458     GGGTGAAGGGCCAGGCCTGCACCATCACTGTCAGAGTCTGGAAGTGTCTCCTGCTGAAGG  5517
                 |||||| |||||||||||||||||||| |||||||||||||||||||||||||||||||
Sbjct  7456418  AGGTGAAAGGCCAGGCCTGCACCATCACCGTCAGAGTCTGGAAGTGTCTCCTGCTGAAGG  7456359

Query  5518     CCTCCAGGAAGAGTGGGAGGTAGAGCTCCCTGGGCAGCTCCTCCAGGGCAGAGATGGCCA  5577
                |||||  |||||||||||| |||||| |||||||||||||||||| ||||||||||| ||
Sbjct  7456358  CCTCCCTGAAGAGTGGGAGATAGAGCACCCTGGGCAGCTCCTCCATGGCAGAGATGGACA  7456299

Query  5578     AGGGCTTGTCTCTCAGCAGACTCTGCCCCGCCAGCTCCAGGAGTCTGGGTGGGGCCTGGA  5637
                ||| || |||||||||||| |||||||||||||||||||| ||||| |||||||||||||
Sbjct  7456298  AGGCCTGGTCTCTCAGCAGGCTCTGCCCCGCCAGCTCCAGTAGTCTCGGTGGGGCCTGGA  7456239

Query  5638     TGCTCATCCTGATGAATCTGTAAGGAAAAA-CTCTAGAAGACAAATCCAGAGAAAAGGCA  5696
                |||||||||||||| ||||| || |||||| ||||||||||||||||||| || || | |
Sbjct  7456238  TGCTCATCCTGATGGATCTGCAA-GAAAAATCTCTAGAAGACAAATCCAGGGAGAATGTA  7456180

Query  5697     TCACTTTCAGGCCAAACACAATCACCTCATCTTCTCCTAAGG-CCAGTAGCATTGCTCTG  5755
                ||||| ||||| |||||||||||||||||||||||||| ||| ||| || ||||||||||
Sbjct  7456179  TCACTCTCAGGGCAAACACAATCACCTCATCTTCTCCT-AGGACCAATATCATTGCTCTG  7456121

Query  5756     GTAGAGGTAGAAAAATTACCACTTTACCCCAATTCCACTCTGCACTTGGTGGCCACAAAT  5815
                ||||||||||||||||||||||||||||||||||||||| |||  ||| ||||| |||||
Sbjct  7456120  GTAGAGGTAGAAAAATTACCACTTTACCCCAATTCCACTGTGC--TTGTTGGCCTCAAAT  7456063

Query  5816     CTATATTTCTGCTTCTGCTGGTACCAGGAAGAATGTCTTCCAAACACCAAGGAGGGAGGG  5875
                ||||| |||||||||||||||||||||||||||| |||||||||||||||||||||||||
Sbjct  7456062  CTATACTTCTGCTTCTGCTGGTACCAGGAAGAATATCTTCCAAACACCAAGGAGGGAGGG  7456003

Query  5876     GTCAAAGAGACCACTGGCCCATTAATTTTCATCCATGGCTCCACTGAATCCCAGTACCAC  5935
                ||||||||||||| || ||||||||||||||||| | ||||||||||||||||| |||||
Sbjct  7456002  GTCAAAGAGACCATTGACCCATTAATTTTCATCCTTCGCTCCACTGAATCCCAGAACCAC  7455943

Query  5936     TGGAAAGTGTCACTGAGGATCCTGAAAGCCAAGCTCTACCTCTTTGAGGAAAATTTTCTT  5995
                |||| |||| ||||||||||||||||||||||||||||||||||||||||||| ||||||
Sbjct  7455942  TGGACAGTGCCACTGAGGATCCTGAAAGCCAAGCTCTACCTCTTTGAGGAAAAATTTCTT  7455883

Query  5996     GTCACTTACCGCCCTAAAGCAATGAGAATGAGAGTGTCCTGTGGCCCCAGACAGCCTCCA  6055
                |||||||||| |||||||||| ||||||||||||||||| |||| |||||||||||||||
Sbjct  7455882  GTCACTTACCACCCTAAAGCATTGAGAATGAGAGTGTCCCGTGGGCCCAGACAGCCTCCA  7455823

Query  6056     TTCTCAGTTTTCACCATGAACATGCTGGGGGAACACTAAAGGGACTCCCTAAAGTCAATG  6115
                |||||||||  |||||||||||||||||||||||||||||||||||||||||| || |||
Sbjct  7455822  TTCTCAGTTCACACCATGAACATGCTGGGGGAACACTAAAGGGACTCCCTAAAATCGATG  7455763

Query  6116     CCATTATTTTTTATTTTGAAAAATTTCAACcagaaactg-accgggtgctgtggctcatg  6174
                |||||||||||||||||||||| |||| |||||||| || ||| |||||||||||| |||
Sbjct  7455762  CCATTATTTTTTATTTTGAAAATTTTCTACCAGAAA-TGGACCAGGTGCTGTGGCTTATG  7455704

Query  6175     tctgtaatcccagcactg-tgggaggccaaaacaggcagatcacttgaggttaggagttc  6233
                |||||||||||| ||||| ||| |  ||||  ||||||||||||||||||| ||||||||
Sbjct  7455703  TCTGTAATCCCAACACTGCTGG-ACACCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTC  7455645

Query  6234     gagaacagcctgg-cttacgtaatgaa-ctc-tgtctctactaaatataaaaaaattaaa  6290
                ||||||||||||| | ||| ||||||| | | ||||||||||||||||| |||| |||| 
Sbjct  7455644  GAGAACAGCCTGGGCCTACATAATGAAAC-CATGTCTCTACTAAATATACAAAAGTTAAG  7455586

Query  6291     aaTCATTTGACTCCAAAaggcagaggttgcagtgagccgagatcccaccactgcactcca  6350
                ||||||||||||||| |||||||||||| ||||||||||| ||| |||||||||||||||
Sbjct  7455585  AATCATTTGACTCCAGAAGGCAGAGGTTTCAGTGAGCCGACATCACACCACTGCACTCCA  7455526

Query  6351     gtctggacaAAAGAGTTAGACTCTGTCTCAaataataataataataataataataataat  6410
                | ||||   | || ||| ||||||| |||||| ||||| |  || | |  | |||| | |
Sbjct  7455525  GCCTGGGTGACAGCGTTGGACTCTGACTCAAA-AATAA-AC-AA-A-T--TGATAA-A-T  7455475

Query  6411     aataataattaattaattaaaatGTTAGCCAGGTGTGGTGGTGCA-GTCCTATAATCCTA  6469
                  ||||  | ||||  | ||| | |||||||||||||||  |||| | | | ||||||||
Sbjct  7455474  --TAAT--T-AATT--T-AAA-TATTAGCCAGGTGTGGTCATGCATGAC-TGTAATCCTA  7455425

Query  6470     GCTACTCTGGAGGCAGAGGAAGAAGAATCACTTGAATCCCGGAGGCAGTGTTTTCAGTGA  6529
                |||||||||||||||||||||| ||||||||||||| ||| ||| ||| |||| ||| ||
Sbjct  7455424  GCTACTCTGGAGGCAGAGGAAGGAGAATCACTTGAAGCCCAGAGACAGAGTTTCCAGGGA  7455365

Query  6530     GCTGAACTCAACACCCTGCCCTTCAGCCTGGGTGACAG-AGTGAGACTCCATCTCAGAAC  6588
                ||  | ||||   |||||| || ||| ||||||||| | | | ||| | |||| ||||| 
Sbjct  7455364  GCCCAGCTCAGGGCCCTGCACTCCAGTCTGGGTGAC-GCACTCAGAGTACATCGCAGAAA  7455306

Query  6589     AAGAGAAAAGAATTAACCAGAAACT--AAAAGCGACGTGATGGTATTCTAGAGCATTTGG  6646
                || | |||| |||| ||  ||| ||  ||||| |  |||||||||||| | |||||||||
Sbjct  7455305  AAAACAAAATAATTCACTGGAA-CTGTAAAAGTGGTGTGATGGTATTCCACAGCATTTGG  7455247

Query  6647     AAGGTAGGGATAGAAATACTAACTCTAGATGAggcacag-tggctcactcctgtaatccc  6705
                |||||| | |||||||| |||||| ||| || ||||  | ||||| ||||||||||||||
Sbjct  7455246  AAGGTATGTATAGAAATGCTAACTGTAGCTG-GGCAT-GCTGGCTTACTCCTGTAATCCC  7455189

Query  6706     agcactttgggagtc  6720
                |||||||||||||||
Sbjct  7455188  AGCACTTTGGGAGTC  7455174


 Score = 4128 bits (2235),  Expect = 0.0
 Identities = 3489/4068 (85%), Gaps = 191/4068 (4%)
 Strand=Plus/Minus

Query  23894    gggaatgggactcctcctatcagttgttttttttttttaattttcttttgtttta-t--c  23950
                |||||||||| |||||||||||     || ||||||| ||||||||||||||||| |  |
Sbjct  7431035  GGGAATGGGATTCCTCCTATCA----ATTCTTTTTTTAAATTTTCTTTTGTTTTATTGAC  7430980

Query  23951    ctggcaaggctctaatagagttgagcttttttgtttttgttttttccattggaagggaca  24010
                ||| |||||||| ||||||||||||  |||||||||||||||||||||||||||||||||
Sbjct  7430979  CTGACAAGGCTCAAATAGAGTTGAG--TTTTTGTTTTTGTTTTTTCCATTGGAAGGGACA  7430922

Query  24011    atacagaggttacaatcattgactttagatgacaac-atgacaggca-aaaatattttcc  24068
                ||||||||||||||||||||| ||||||||||| || || | | | | |||| || ||||
Sbjct  7430921  ATACAGAGGTTACAATCATTGGCTTTAGATGAC-ACGAT-AAAAGAATAAAACATATTCC  7430864

Query  24069    ttgcaagacaaccagcaaaacttcacgatcagaatcaaatcagtgtccttctcactgtca  24128
                ||||||||||||||||||||||||| |||||| |||||||||||| ||||||||||||||
Sbjct  7430863  TTGCAAGACAACCAGCAAAACTTCATGATCAGCATCAAATCAGTG-CCTTCTCACTGTCA  7430805

Query  24129    ctgggt-gaagccttcatcagtacttgaagagtctcaggcactcatgaagtca-agatca  24186
                 ||||| ||||||||||||| |||||| ||||| | | ||||||||||| ||| | ||||
Sbjct  7430804  GTGGGTGGAAGCCTTCATCAATACTTGTAGAGTTTGAAGCACTCATGAACTCACA-ATCA  7430746

Query  24187    gattctttactcagggacaggatgtaagccaatc-ataagaccttccacagatgatcaat  24245
                || ||||||||||||||||||||||||||||||| | |||||||||||||| || | |||
Sbjct  7430745  GACTCTTTACTCAGGGACAGGATGTAAGCCAATCGA-AAGACCTTCCACAGGTGGTGAAT  7430687

Query  24246    ttggaagtctacctaatgtgacctgcaggttttcaCTGGCAATATGCAGGTGCAGATATG  24305
                |||| || || || ||||||||||||| ||||||||||||||||||||||||||||||||
Sbjct  7430686  TTGGGAGCCTGCCCAATGTGACCTGCAAGTTTTCACTGGCAATATGCAGGTGCAGATATG  7430627

Query  24306    ACAAAGAATAATCC-TGACCTTCATATCGCCCCTAGCTGATGAGGATTGGGATTCTTTTG  24364
                ||||||||||| || ||||||| | ||| |||| ||||| |||||| |||||| ||||||
Sbjct  7430626  ACAAAGAATAA-CCATGACCTTTACATCACCCCCAGCTGTTGAGGAATGGGATCCTTTTG  7430568

Query  24365    TCCCTTTCTCTCCATAAAACCAGGTTACTCATCTTGTGTGGCAACAAAATATATGGTcta  24424
                 |||||||| |||||| ||||| ||||||||||||| |||||||||||||||||||||||
Sbjct  7430567  ACCCTTTCTGTCCATAGAACCATGTTACTCATCTTGAGTGGCAACAAAATATATGGTCTA  7430508

Query  24425    cttaacagagaaag-agactccacaggaaaaaaaaaaggatttttattatgaaatgagca  24483
                |||||||||| ||| |||||   |  |  ||||||||  || ||||||||||| | ||||
Sbjct  7430507  CTTAACAGAG-AAGAAGACT---C-TG-TAAAAAAAA--ATGTTTATTATGAAGTAAGCA  7430456

Query  24484    aagcca-tgggaatagatgtgagattattcggggaggtaaaggaagacaaaggttttgaa  24542
                |||  | ||| |||||||| ||||||||| |||||| |||||||||   |||||||||||
Sbjct  7430455  AAG-AAGTGGCAATAGATGCGAGATTATTTGGGGAGATAAAGGAAGTTGAAGGTTTTGAA  7430397

Query  24543    aggaaaaatgaggagaattacataaatttttttgaaagactcattcttggtcacaagtat  24602
                ||||||||| ||||| |||| | ||||| ||||||||||||||| |||||||| ||| ||
Sbjct  7430396  AGGAAAAATAAGGAGGATTATACAAATTGTTTTGAAAGACTCATACTTGGTCATAAGGAT  7430337

Query  24603    gaaaacc-aagggagcctcagtgcagtgttggaaagATTCCTCCTCCACCCTCTCAATAA  24661
                 |||||| || || || |||||||| |||| || ||||||||| | ||||| ||||||||
Sbjct  7430336  TAAAACCAAAAGG-GCATCAGTGCAATGTTAGATAGATTCCTCTTACACCCACTCAATAA  7430278

Query  24662    CCCCCAACACATTTACCAAGTCTTTG-TTCACTCCCAGGATT-CCATTAAAACACCCAGC  24719
                |||||||||  || | |||||| ||| |||||||||||| || ||||||||| |||||||
Sbjct  7430277  CCCCCAACATGTTCAGCAAGTC-TTGCTTCACTCCCAGG-TTCCCATTAAAA-ACCCAGC  7430221

Query  24720    TCAACCCTGACCAGCCTCCACCTTCACTTCCCTTTGTAATTTTGACATAAATTtgttaca  24779
                |||||||||||||| ||||||| |||||||| |||||||||||||||| | ||| |||||
Sbjct  7430220  TCAACCCTGACCAG-CTCCACCCTCACTTCCATTTGTAATTTTGACATGACTTTATTACA  7430162

Query  24780    ggaccatcaggttcctatgccggctgcacagtagcttaccaatattctgagacagcagga  24839
                ||||||||||||||||||||| |||||||||||||||| |||||||||||||||||||| 
Sbjct  7430161  GGACCATCAGGTTCCTATGCCTGCTGCACAGTAGCTTAGCAATATTCTGAGACAGCAGGG  7430102

Query  24840    tttgcagcagaaagtttaatgatcacagggtggctgaatgagaagctgggaggagatcct  24899
                ||||||||||| ||||||||||||||| ||||||||||||||||||| ||||||||||||
Sbjct  7430101  TTTGCAGCAGAGAGTTTAATGATCACAAGGTGGCTGAATGAGAAGCTAGGAGGAGATCCT  7430042

Query  24900    caaattcatctccccaaggagtactgagggtttccagtggatcctggatagcaaggggct  24959
                ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| 
Sbjct  7430041  CAAATTCATCTCCCCAAGGAGTACTGAAGGTTTCCAGTGGATCCTGGATAGCAAGGGGCC  7429982

Query  24960    ggaaagttggtgtagtttgatggcaataagaggtatgaagttatcacgatgtcag-aacg  25018
                |||||||||| |  |  | |  ||  ||||||| | ||||| | || ||||| || ||| 
Sbjct  7429981  GGAAAGTTGG-G--G--T-A--GCGGTAAGAGGGAAGAAGTCAACAGGATGT-AGAAACT  7429931

Query  25019    gcattctttggtgagttgatgccttgcagggcccttcagatcagctggcatcagtagttt  25078
                |||||||||||||||||| ||| ||||| ||||||||||||||||||||||||| |||||
Sbjct  7429930  GCATTCTTTGGTGAGTTGGTGCATTGCATGGCCCTTCAGATCAGCTGGCATCAGCAGTTT  7429871

Query  25079    cactgacatgcagaacctgaaagaatatctcaaatgaaaaacttaatgtttcacaatgct  25138
                |||||||||||||||||||||||||||||||| |||||||| ||||||||| ||||||||
Sbjct  7429870  CACTGACATGCAGAACCTGAAAGAATATCTCAGATGAAAAAATTAATGTTTTACAATGCT  7429811

Query  25139    taaattgttgtctgcagcgtagttaaggggaattgtagtctaagttctacacgattttgg  25198
                | ||| ||||||||||| | |||||||||||| |||| |||||| |||| | ||||||||
Sbjct  7429810  TGAATCGTTGTCTGCAGGGAAGTTAAGGGGAACTGTAATCTAAGGTCTATATGATTTTGG  7429751

Query  25199    gacagtaggctgccagcaaccatgaggaagcaggtcagagggcaagctgacctcctggtg  25258
                 ||||||||||||||||||||| |||||| |||||||||| |||||  ||||||||| ||
Sbjct  7429750  AACAGTAGGCTGCCAGCAACCACGAGGAACCAGGTCAGAGAGCAAGAAGACCTCCTGATG  7429691

Query  25259    aatgctgaatgcgtttcaagcttggtttgtttttgttcctccccctctctttttcaccga  25318
                || |||||||| ||| ||||||| |||| |||||||| ||| ||||| ||| ||||| ||
Sbjct  7429690  AAGGCTGAATGTGTTGCAAGCTTCGTTTATTTTTGTTTCTCTCCCTCCCTTCTTCACTGA  7429631

Query  25319    ttaaatttataaagtttagaaatacggtttcaATTTCTTCCAGACAAGCCTTAACCTAAG  25378
                ||||||||||||| |||||| ||  ||||||||||||||||| | |||||||||||||||
Sbjct  7429630  TTAAATTTATAAACTTTAGAGATGTGGTTTCAATTTCTTCCAAAGAAGCCTTAACCTAAG  7429571

Query  25379    CCCTGAGACCACTCAAGCCCTCAGTGGCACCTCTCTTCCACCAGCATGAGCAAATAAAT-  25437
                ||||||||||||||| ||||||||||||||||||| |||||||| | |||||  | ||| 
Sbjct  7429570  CCCTGAGACCACTCACGCCCTCAGTGGCACCTCTCCTCCACCAGAACGAGCATGT-AATC  7429512

Query  25438    TGCTACCTTAGGTGATATAAAA-CCCACAAGATGATTCGATACATGGAG-ttttttttCT  25495
                ||||||||||||| | | |||| |||| || |  |||| |||||| ||| ||||| ||||
Sbjct  7429511  TGCTACCTTAGGTTACACAAAATCCCA-AAAACCATTCAATACATTGAGATTTTTATTCT  7429453

Query  25496    GATTTTGTAGGGATGACTTCTTTGTTTCTATAAAGCTGTTTT-AACTATAAAACAATTTT  25554
                ||||| |||||||||||| || ||||| ||||||||| |||| || || ||| || ||||
Sbjct  7429452  GATTTCGTAGGGATGACTCCTCTGTTTTTATAAAGCT-TTTTAAAGTAGAAAGCATTTTT  7429394

Query  25555    ATAATTTTGATGTGGCCAAAGATCTCC---CAACACTACTTTCAGGTTTTATTTTTCTGT  25611
                || ||||||||||||||||||||||||   ||||||||||||||| ||||||||||||||
Sbjct  7429393  AT-ATTTTGATGTGGCCAAAGATCTCCTAACAACACTACTTTCAGATTTTATTTTTCTGT  7429335

Query  25612    CTACTATCCAG-AACAGATCAAACCCTTCCCTGCCTCAAACTCAGGACTAT-ATAGGTCA  25669
                ||| | | | | ||||||||||| || ||||||||||| ||||| |||||| | || |||
Sbjct  7429334  CTAATGT-C-GTAACAGATCAAATCCGTCCCTGCCTCACACTCAAGACTATGA-AGTTCA  7429278

Query  25670    TATATCAGTAAAATTCCATCAGTGTTTGCGGAgttcatgaatgaatgaattctttttttt  25729
                 |||| |||||||| ||||||||||||| |||||||||||||||||| |           
Sbjct  7429277  CATATTAGTAAAATGCCATCAGTGTTTGTGGAGTTCATGAATGAATG-A-----------  7429230

Query  25730    tttttttttttttttttttgtgaca-aagtctacctctgtcacccagaac-ggtgtgcaa  25787
                      ||||||| ||||| ||||| || ||| |||||||||||||| || || ||||| 
Sbjct  7429229  ------TTTTTTTATTTTT-TGACAGAA-TCTCCCTCTGTCACCCAG-ACTGGAGTGCAG  7429179

Query  25788    tggtgcaa-tcttggctcactgcaaccattgccccctggattcaagcgattctcccacct  25846
                |||  ||| || ||||||||||||||||||||| ||||| ||||||| |||||||  |||
Sbjct  7429178  TGGCACAATTC-TGGCTCACTGCAACCATTGCCTCCTGGGTTCAAGCAATTCTCCTGCCT  7429120

Query  25847    cagcctcctga-gtagctggattacaggcacctgccatcatg-ccaggctaatttttg--  25902
                ||||||||  | |||||||| || ||||  |||||||||||| ||| |||||||||||  
Sbjct  7429119  CAGCCTCC-CATGTAGCTGGGTTTCAGGTGCCTGCCATCATGCCCA-GCTAATTTTTGTA  7429062

Query  25903    ----tg--tttttgtagag-ctggggtttcatcatgttggccttgcaggtcttgatcgcc  25955
                    ||  ||||||||||| |  |||||||| | | ||| ||| ||  ||||||| | ||
Sbjct  7429061  TTTTTGTATTTTTGTAGAGAC-AGGGTTTCACCTTTTTGACCTGGCTCGTCTTGAACCCC  7429003

Query  25956    tgacctcaggtgatccagc-caacttggac-tctcaaagtgcagggattacaggtgtgag  26013
                |||| |||||||||| | | || ||||  | || |||||||| || ||||||| | ||||
Sbjct  7429002  TGACATCAGGTGATCTA-CTCACCTTGTCCTTC-CAAAGTGCTGGAATTACAGCTATGAG  7428945

Query  26014    ccacctcacccggcctttaatgaGTGAATTCTTGATTTCCACCCTATTCCTAACACTGTC  26073
                |||||||||||  |||| ||||| || |||||||| ||| ||||||| ||||||||||||
Sbjct  7428944  CCACCTCACCCACCCTTGAATGAATGTATTCTTGACTTCTACCCTATCCCTAACACTGTC  7428885

Query  26074    AATTTCTTGATTCATGAACTTAATATGGATA-GCTGATATGAATGGATATCTGATTCAAT  26132
                ||||||||| |||| ||||| ||||| |||| | ||||||||| |||||||||| |||||
Sbjct  7428884  AATTTCTTGCTTCACGAACTGAATATAGATATG-TGATATGAACGGATATCTGACTCAAT  7428826

Query  26133    CCAGTAATCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGGGTGGAGCTTCAGAAAT  26192
                ||| ||||||||||| ||||||||||||||||| ||||||||||||||||||||| ||||
Sbjct  7428825  CCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCACAAAT  7428766

Query  26193    GCAATCAGATAGCACTTTTTGATTGGAAGCAAGCACTGGATA-GATGGAGGGGTGTGGGT  26251
                |||||||||||   |||||||||||||||| |||| || | | | |||| |||  |||||
Sbjct  7428765  GCAATCAGATATTGCTTTTTGATTGGAAGCTAGCAGTGCAAACG-TGGAAGGGCATGGGT  7428707

Query  26252    GGGAGTTGTGATTAGAAAGATCGATAAAAGT-TTCTGAAGGCCCACAGGAGAGACCCAAA  26310
                ||||||||||||||||||| || |||||| | |||| ||| |||||||||||||||||||
Sbjct  7428706  GGGAGTTGTGATTAGAAAGGTCAATAAAA-TCTTCTAAAGACCCACAGGAGAGACCCAAA  7428648

Query  26311    GTCTTCAAGTCTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTAAGCACTCTGC-AAACT-  26368
                ||||||||| |||||||||||||||||||||||||||||||| ||||| || | | ||| 
Sbjct  7428647  GTCTTCAAGCCTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTGAGCAC-CTTCTAGACTA  7428589

Query  26369    CAGTCCAGATCTAGTAAGTCACTCATTTCTGGAAGGACACTCCCATCTGACCTATAGTCA  26428
                || ||||||||| |||||||||| ||||||| |||||||||||||||||||||| |||||
Sbjct  7428588  CA-TCCAGATCTGGTAAGTCACTAATTTCTGTAAGGACACTCCCATCTGACCTACAGTCA  7428530

Query  26429    GCCGGTCTGGGACGGGGGCAATGCAGCCTATGATGGCACCGAGCTATATC-TGTC-TTTt  26486
                | | |||||||| || | || ||||||||| |||||||| |||||||||| |||| ||||
Sbjct  7428529  GTCAGTCTGGGATGGTGACAGTGCAGCCTACGATGGCACAGAGCTATATCCTGTCCTTTT  7428470

Query  26487    atatatatatatatGAACAATTTGAAGATTTGAATTTTTTCCTCTATATGCAGTTTTGTC  26546
                 | | | |  ||||||||||||||||| |||||||||||||||||| |||||||| ||||
Sbjct  7428469  TTTT-TCTC-ATATGAACAATTTGAAGCTTTGAATTTTTTCCTCTAAATGCAGTTCTGTC  7428412

Query  26547    TTTATTTCAAAAAA-TTGGATTGTGCTTTGGTTTATGTCATTTcaaaattcttgatggga  26605
                |||||||||||||| ||| |||||||||||||| ||||||||||||||||||||| ||||
Sbjct  7428411  TTTATTTCAAAAAAGTTG-ATTGTGCTTTGGTTGATGTCATTTCAAAATTCTTGAAGGGA  7428353

Query  26606    gcaatgactcatgcccataacctcaacaccttgggaggccaaagcgggaggatcatttga  26665
                ||| |||||||||||  ||||| |||||| |||||||||||||| ||||||||||||| |
Sbjct  7428352  GCAGTGACTCATGCCTTTAACCCCAACACATTGGGAGGCCAAAGTGGGAGGATCATTTCA  7428293

Query  26666    gcccaggggtttgagaccaacctgggcaacatggcaaaaatgcagctctacaaaacattc  26725
                ||||||||||||||||||||||||||||||||| |||||   |  ||||||| ||| || 
Sbjct  7428292  GCCCAGGGGTTTGAGACCAACCTGGGCAACATGACAAAAGCCCTCCTCTACACAACGTTT  7428233

Query  26726    ttttttt----gaagcaggg-atggagtctcaccctgttgccaaggctggagtgcagtgg  26780
                |||||||    || |  ||| ||||||||||||  ||||||| || ||||||||||||||
Sbjct  7428232  TTTTTTTTTTTGAGGGTGGGGATGGAGTCTCACTGTGTTGCCCAGACTGGAGTGCAGTGG  7428173

Query  26781    caagagctcaactcactgcaacctctt-cctcccaggctcaaacaattttcatgtctcag  26839
                || || |||||||||||||||||| || |||||| || |||| ||||| ||||| |||||
Sbjct  7428172  CATGATCTCAACTCACTGCAACCT-TTACCTCCCGGGTTCAAGCAATTCTCATGCCTCAG  7428114

Query  26840    -ct---tcctgagtagctggtattacatccctctgccaccatgtct-gcttaatttttgt  26894
                 ||   |||| || ||||||| | |||  | ||||  |||||| || ||| |||||||||
Sbjct  7428113  TCTCCATCCTCAGAAGCTGGTGTCACAGACATCTGAAACCATGCCTCGCT-AATTTTTGT  7428055

Query  26895    atttttagtagtggtggggtttcaccatgctggccaggttggtctcaaactcctgacatc  26954
                ||||||||||| |||||||||||||||||||||||||||||||||| ||| |||||| ||
Sbjct  7428054  ATTTTTAGTAGAGGTGGGGTTTCACCATGCTGGCCAGGTTGGTCTCGAACACCTGACCTC  7427995

Query  26955    aagtgatcctcctgcctaggcc-cccaaaagtgctggaatgacggccgtgagccaATGGT  27013
                ||||||||| ||||||| |||| |||||| ||||||| || || || ||||| || ||||
Sbjct  7427994  AAGTGATCCACCTGCCTTGGCCTCCCAAA-GTGCTGGGATTACAGCTGTGAGTCACTGGT  7427936

Query  27014    GGTCAGCctctacaaaatatatatatcttttaatttgcc-aggcatggt-agcatgcatc  27071
                | |  ||||||||    | | | | | |||||||| ||| || |||||| | ||||||||
Sbjct  7427935  GCTTGGCCTCTACTTTTT-T-T-T-T-TTTTAATTAGCCGAG-CATGGTGA-CATGCATC  7427883

Query  27072    tgtattcccagctatttggtttgctgacatgggagaatcacttgagcccagaagattgag  27131
                |||| |||||||||||||| | ||||   |||||||||||||||||||||||||||||||
Sbjct  7427882  TGTAGTCCCAGCTATTTGGGTGGCTGGTGTGGGAGAATCACTTGAGCCCAGAAGATTGAG  7427823

Query  27132    gctgcagtgagccatgctcacaccactgctgtactccagcctgggcaacagagta-agac  27190
                |||||||||||||||||||| |||||| |||||||||||||||||||| |||| | | ||
Sbjct  7427822  GCTGCAGTGAGCCATGCTCATACCACTCCTGTACTCCAGCCTGGGCAAAAGAG-AGACAC  7427764

Query  27191    cctgctaaaaacaaaaacgaaaacaaacaaacaaaaaacCTTAACCAAAGAGAATCTTTG  27250
                |||| |  ||| ||| |  |||||||| |  |||    |   ||  |||| || ||||||
Sbjct  7427763  CCTG-TCCAAA-AAACA--AAAACAAA-AT-CAAT---C---AA--AAAG-GA-TCTTTG  7427720

Query  27251    ACCTTAATTTTAAACCAATCACATCCTCACTGTAATTCTTCCTCCCGAATGGAGACATgg  27310
                ||||||||||||||||||||||||||||  | |    |  |  ||| |||||||||||||
Sbjct  7427719  ACCTTAATTTTAAACCAATCACATCCTC--T-T----C--CA-CCCAAATGGAGACATGG  7427670

Query  27311    gtgtgaggg-tgcatgcctgtaatcccagctacatggaaggctgaagcatgagaattgct  27369
                 |||| ||| |||||||||||| |||||||||| ||||||||||||||||||||||||||
Sbjct  7427669  CTGTGGGGGGTGCATGCCTGTAGTCCCAGCTACGTGGAAGGCTGAAGCATGAGAATTGCT  7427610

Query  27370    tgaatctcagaggcggaagttacagtgagctgagatgg-agccgctgcactccagcctgg  27428
                |||||||  ||||| || || ||||||||| || |||  | || |||||||| |||||||
Sbjct  7427609  TGAATCTTGGAGGCCGAGGTAACAGTGAGCCGATATGACA-CCACTGCACTCTAGCCTGG  7427551

Query  27429    gcgacaaagtgagactcagcttcacc-ca-caccaaaaaaaaTTA-GATTATACCACCCA  27485
                 |||  |||||||| |||||| | || || ||||||||| ||||| |      ||||| |
Sbjct  7427550  CCGATGAAGTGAGATTCAGCT-C-CCTCAACACCAAAAAGAATTACG------CCACCTA  7427499

Query  27486    GGTGATCACTGGATACATGAAGATTTCTATTGTGTGTTATTGGGGACTGTCAACTCCGTC  27545
                |||||||  |||||| ||||||||||||| ||||| || || |||||||||| ||| |||
Sbjct  7427498  GGTGATCTTTGGATATATGAAGATTTCTACTGTGTTTTCTTAGGGACTGTCATCTCTGTC  7427439

Query  27546    TTTGAAAACTGTTTTAACTCTGAAATATTTTGATAAATTTGATGTGGCCAAGGATCCCTC  27605
                ||||||||||||||||||||||||||||||||||||||||||  ||||||||||||||||
Sbjct  7427438  TTTGAAAACTGTTTTAACTCTGAAATATTTTGATAAATTTGACATGGCCAAGGATCCCTC  7427379

Query  27606    AACAAAGATACTTTCAAGTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGATTCAACACT  27665
                |||||||||||||||||||||||||||||||||||||||||||||||||| |||||| ||
Sbjct  7427378  AACAAAGATACTTTCAAGTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGGTTCAACCCT  7427319

Query  27666    TCCCTATCTCACACTCAGGACTATGAAGGACACATATTAGTAAACCTCCATGTTTGTGGA  27725
                |||||||||||||||||||||| ||||||||||||||||||||| ||||||||||||| |
Sbjct  7427318  TCCCTATCTCACACTCAGGACTTTGAAGGACACATATTAGTAAAACTCCATGTTTGTGAA  7427259

Query  27726    GGGAATCAGTGAATGAGTCCTGGACTTTCACCCTATCCCTAAATCTTTCACTTTCATGGA  27785
                |||||||||||||||||||||||||||||||||||||||||||||||||| ||| |||||
Sbjct  7427258  GGGAATCAGTGAATGAGTCCTGGACTTTCACCCTATCCCTAAATCTTTCATTTTGATGGA  7427199

Query  27786    TGAATATCTAATTCAATCAGTTAATCTGGAAGAAAGCCAAAAATCCAATCAGGATTAACT  27845
                |||||||||||||| |||||||||| |  ||||||| |||||||||||||||||||||||
Sbjct  7427198  TGAATATCTAATTCGATCAGTTAATATTTAAGAAAGTCAAAAATCCAATCAGGATTAACT  7427139

Query  27846    GGGTAGAGTTTAAGAAGTCGAATCAAATGTAGTtctctctctctctct  27893
                |||||||| ||||||| || |||||||||||| ||||||| |||||||
Sbjct  7427138  GGGTAGAGATTAAGAATTCTAATCAAATGTAGCTCTCTCTGTCTCTCT  7427091


 Score = 3855 bits (2087),  Expect = 0.0
 Identities = 2982/3407 (87%), Gaps = 90/3407 (2%)
 Strand=Plus/Minus

Query  14528    GGTTGGTTAACATTTATAATTACATGACTTGGCACTGAGAAGAAGCTATAGGTGCAAATG  14587
                |||||||||| ||| ||||||| |||||||||||||||| ||||||||||| ||||||||
Sbjct  7498557  GGTTGGTTAATATTGATAATTAAATGACTTGGCACTGAGCAGAAGCTATAGATGCAAATG  7498498

Query  14588    GGTGGCCTATGACTATTATTGATTACATTACTGGCATTTTATCTCTATGCATAAAAAACA  14647
                ||||||||||||||||| |||||| ||||||| | |  ||||||| |||||||  |||||
Sbjct  7498497  GGTGGCCTATGACTATTGTTGATTTCATTACTTGTAACTTATCTCCATGCATAGGAAACA  7498438

Query  14648    TTAGTGAAACTGGATCTAATCTAGGTAGTGTCGCAGATTCCCACTAGAATCAAACTCTTT  14707
                |||||| ||| || |||||||||||||||||| |||| |||| |||||||||||||||||
Sbjct  7498437  TTAGTGTAACCGGGTCTAATCTAGGTAGTGTCCCAGACTCCCCCTAGAATCAAACTCTTT  7498378

Query  14708    GGTTTGACACACCTTATGAAGACTGGAGTGCTATAGGTATCGACATAGACATAGAATCAG  14767
                  |||||||||| |||||||||||| | ||||||| |||| |||||||||| ||||||||
Sbjct  7498377  CATTTGACACACATTATGAAGACTGAAATGCTATAAGTATTGACATAGACACAGAATCAG  7498318

Query  14768    AACATGACCATGTTACCCTCTGCCATTTAATCAGAGAACTTACTGAAACTAGACATTGGT  14827
                ||||||||||||||| |||||||||| |||||||||||||||||||||||||||||| ||
Sbjct  7498317  AACATGACCATGTTATCCTCTGCCATATAATCAGAGAACTTACTGAAACTAGACATTTGT  7498258

Query  14828    TCATTGGAAACTCTAGAGGCAAATAGAATGTGTCTATAGCTCTACTATGTGAAATACATA  14887
                |||||||||||||  |||||||||||||||  |||||||||||||||| ||||||| | |
Sbjct  7498257  TCATTGGAAACTC--GAGGCAAATAGAATGCATCTATAGCTCTACTATATGAAATAAACA  7498200

Query  14888    ATAGTTTTATTTATTGGATGCATCAATACTCAGGACATATTTGGAGAGGAACCTATTCAT  14947
                ||||||| |||||||||||||||| |||||||| ||||||||||||| || |||||||||
Sbjct  7498199  ATAGTTTCATTTATTGGATGCATCCATACTCAGCACATATTTGGAGAAGACCCTATTCAT  7498140

Query  14948    TCTTCAATGCAGATGGCATGCAAGGATTACTTT-ATAAAACTCATAGAAATACTTTTTCT  15006
                ||||||||| ||||| ||||||||||||| ||| |||||| ||||| ||||| |||||| 
Sbjct  7498139  TCTTCAATGGAGATGACATGCAAGGATTA-TTTAATAAAATTCATAAAAATATTTTTTCA  7498081

Query  15007    TCCCACCCCAATTCAAACCATTACCATGCAACCTGGTATCAATAgaagttaaggc-catt  15065
                |||||||||| |||||||  | ||||||||||||||| ||| | |||| |||||| | ||
Sbjct  7498080  TCCCACCCCAGTTCAAACTGTCACCATGCAACCTGGTGTCAGTGGAAGGTAAGGCGC-TT  7498022

Query  15066    gaggtagaaataattaaataaagctttattggaagctaaatgtgagaatcgacctggaag  15125
                 ||| ||||||||||||||||| ||| ||||||||||||||||||||||| |  ||||||
Sbjct  7498021  AAGGCAGAAATAATTAAATAAATCTTCATTGGAAGCTAAATGTGAGAATCAATGTGGAAG  7497962

Query  15126    acacacactgacaaagtgagtgttttccaaagtctgttacaagttggaatgcttttgtaa  15185
                ||||| ||  |||||||| |||| |||||||||||||||||||||||||||||||||| |
Sbjct  7497961  ACACAGACCAACAAAGTGGGTGTGTTCCAAAGTCTGTTACAAGTTGGAATGCTTTTGTGA  7497902

Query  15186    gagaggttaaaagaagggaatgggactcctcctatca---atttttttttaattttcttt  15242
                || | ||||||||||||||||| ||||||||||||||    |||||||||||||||||||
Sbjct  7497901  GAAAAGTTAAAAGAAGGGAATGAGACTCCTCCTATCAGTTTTTTTTTTTTAATTTTCTTT  7497842

Query  15243    tgttttattgacctggcaaggctcaaatagagttgag----t-ttttgtttttgtttttc  15297
                ||||||| |||||||||||||||||||||||||||||    | |||||||||||||||| 
Sbjct  7497841  TGTTTTACTGACCTGGCAAGGCTCAAATAGAGTTGAGTTTTTGTTTTGTTTTTGTTTTTT  7497782

Query  15298    ccattggaaggtacaagacagaggttacaatcgttag-ctttagatgacaacataacagg  15356
                |||||||||||||||| ||||||||||||||| || | |||||| ||||||||||||| |
Sbjct  7497781  CCATTGGAAGGTACAATACAGAGGTTACAATCATT-GACTTTAGCTGACAACATAACAAG  7497723

Query  15357    ctaaaacattttccttgcaagacaaccagcatg--acttcatgatcagaataaaatcagt  15414
                 | ||||||||||||||||||||||||||  ||  |||||||||||||||| ||||||||
Sbjct  7497722  -TTAAACATTTTCCTTGCAAGACAACCAG--TGAAACTTCATGATCAGAATCAAATCAGT  7497666

Query  15415    gtccttctcactgtcagcgggtgaagacttcatcagtacttgtagagtttgaggtactca  15474
                |||||||||||||| || |||||||| |||||||| || ||| ||||||||||| |||||
Sbjct  7497665  GTCCTTCTCACTGTAAGTGGGTGAAG-CTTCATCAATAATTGCAGAGTTTGAGGCACTCA  7497607

Query  15475    tgaactcatgatcagattctttactcagggacaggatgtaagccaatgc-taagaccttc  15533
                |||||||| ||||||||||||||||||||||||| |||||||||||| | ||||||||||
Sbjct  7497606  TGAACTCAAGATCAGATTCTTTACTCAGGGACAGAATGTAAGCCAAT-CATAAGACCTTC  7497548

Query  15534    tataggtggctaatttttaagcttgccccaatgagacct-tcaggttttcaCTGGCAATA  15592
                 | |||||| ||||||  |  | ||    |||| ||||| | | ||||||||||||||||
Sbjct  7497547  CACAGGTGGTTAATTTGGACTCCTG-AAAAATGTGACCTGT-AAGTTTTCACTGGCAATA  7497490

Query  15593    TGCAGGTGCAGATATGACAAAGAATAACAATGACCTTCATATCACCTCCAGCTGTTGAGG  15652
                |||||||||| |||||||||| |||||| | |||||| |||||||| ||| ||| || ||
Sbjct  7497489  TGCAGGTGCACATATGACAAATAATAACCAGGACCTTTATATCACCCCCAACTGGTGGGG  7497430

Query  15653    AATGGGATCCTTTTCACCCTTCCTGTCCATAAAACCAAGTTACTCATCTTCAGTGGCAAC  15712
                |||||||||||||| |||||| || ||||||| |||| | ||||||||||  ||||||| 
Sbjct  7497429  AATGGGATCCTTTTGACCCTTTCTCTCCATAATACCAGGCTACTCATCTTGTGTGGCAAT  7497370

Query  15713    AAAATATATGGTAAACTTAACAGAGAAGGAGACTGTCAGaaaaaaaaaaaaaaaagatgt  15772
                ||||||||||||  |||| |||||||| |||| | ||      ||||||||||| ||| |
Sbjct  7497369  AAAATATATGGTCTACTTCACAGAGAAAGAGA-T-TC--TTTTAAAAAAAAAAAGGAT-T  7497315

Query  15773    gtttatcctgaaatgaggaaagcaatgggaatagatgtgagattattttgggagaaaaag  15832
                 |||||  ||||||||| |||||||||||||||||||||||||||||  |||||  ||||
Sbjct  7497314  -TTTATTATGAAATGAGCAAAGCAATGGGAATAGATGTGAGATTATTCAGGGAGGTAAAG  7497256

Query  15833    gaagacaaaggttttgaaaggaaaaataaggaggattatacaaattgttttgaaagactc  15892
                ||||||||||||||||||||||||||| ||||| |||| | | | ||||||| |||||||
Sbjct  7497255  GAAGACAAAGGTTTTGAAAGGAAAAATCAGGAGAATTACATACACTGTTTTGGAAGACTC  7497196

Query  15893    aaccttggtc-ctaagaatcaaaagtaaaggggcatcagtgaaatgttggatagATTCCA  15951
                |  ||||||| | ||| ||||| |  || ||||| |||||| ||||||||| ||||||| 
Sbjct  7497195  ATTCTTGGTCAC-AAGTATCAACACCAAGGGGGCCTCAGTGCAATGTTGGAAAGATTCCT  7497137

Query  15952    CCTCCACCCCCTCAGTAACCCCCAACATGTTTACCAAGTCTTGGTTAACTCCCAGGATCC  16011
                ||||||| |||||| ||||||||||||||||||||||||||||||| |||||| ||||||
Sbjct  7497136  CCTCCACGCCCTCAATAACCCCCAACATGTTTACCAAGTCTTGGTTCACTCCCCGGATCC  7497077

Query  16012    CATTAAAACACCCAGCTCAACCATGCCCATCCTCTACCCTCACTTCTCTTTGTAATTTTG  16071
                ||||||||||| |||||||||| || ||| |||| ||| ||||||| |||||||||||||
Sbjct  7497076  CATTAAAACACACAGCTCAACCCTGACCAGCCTCCACCTTCACTTCCCTTTGTAATTTTG  7497017

Query  16072    ACATGA-TTTTAttacaggaccatcaggttcctatgcctgctgcacagtagc-tgaccaa  16129
                |||||| |||| ||||||||||||||||||||||||||||| |||||||||| | || ||
Sbjct  7497016  ACATGACTTTTTTTACAGGACCATCAGGTTCCTATGCCTGCAGCACAGTAGCAT-ACTAA  7496958

Query  16130    tattctgagacagcagtgtttgcagcagacagtttaatgatcacagggtggctaaatgag  16189
                |||||||||||||||| |||||||||||| ||||||| |||||||||||||| |||||| 
Sbjct  7496957  TATTCTGAGACAGCAGGGTTTGCAGCAGAGAGTTTAACGATCACAGGGTGGCAAAATGAA  7496898

Query  16190    aagctaggaggatatcctcaaattcatctccccaagtagtactgagggtttccagtggat  16249
                ||||| |||||| | ||||||||||||||||||||| ||||||||| |||| ||| ||||
Sbjct  7496897  AAGCTGGGAGGAGACCCTCAAATTCATCTCCCCAAGAAGTACTGAGAGTTTTCAGAGGAT  7496838

Query  16250    cctggatagcaaggggctggaaagttggt---g--tag-ag--gtaagagggatgaagtc  16301
                | ||||||||||| |||||||||||||||   |  | |  |  |||||||| ||||||||
Sbjct  7496837  CATGGATAGCAAGAGGCTGGAAAGTTGGTGCAGTTTGGTGGCAGTAAGAGGTATGAAGTC  7496778

Query  16302    atcaggatgtcaaaactgcattctttggtgagttggtgccttgcagagcccttcagatca  16361
                ||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||
Sbjct  7496777  ATCAGGATGTCAAAACTGCATTCCTTGGTGAGTTGGTGCCTTGCAGGGCCCTTCAGATCA  7496718

Query  16362    gctggcatcagtagtttcactgacatgcagaacctgaaagaatatctcaaatgagaaagt  16421
                 ||| ||||||||| |||||||||||||||||||||||||||||| |||||||| |||||
Sbjct  7496717  CCTGCCATCAGTAGCTTCACTGACATGCAGAACCTGAAAGAATATGTCAAATGAAAAAGT  7496658

Query  16422    taatgttttacaaggcttaaattgttgtctgcagggtagttaaggggaactgtaagctaa  16481
                |||||||||||||||| ||||||||||||||||||| ||||||||| |||||||| ||||
Sbjct  7496657  TAATGTTTTACAAGGCCTAAATTGTTGTCTGCAGGGCAGTTAAGGGCAACTGTAATCTAA  7496598

Query  16482    ggtctacttgatttggggacagtaagctgccagcaaccatgaggaagaaggtcagagagc  16541
                ||||||| |||||| ||||||| | |||||||||||||||||||||| ||||||||||||
Sbjct  7496597  GGTCTACATGATTTTGGGACAGCAGGCTGCCAGCAACCATGAGGAAGCAGGTCAGAGAGC  7496538

Query  16542    aagctgacctcatggtgaatgctgaatgcgctgcaagcttggtttatttttgtttctccc  16601
                |||||||||||||| |||||||||||||| ||||||||||||||||| ||||||||||||
Sbjct  7496537  AAGCTGACCTCATGATGAATGCTGAATGCACTGCAAGCTTGGTTTATGTTTGTTTCTCCC  7496478

Query  16602    cctcccttcttcactgattaaacttataaagtttacaggtatcatttcaATTTCTTCCAG  16661
                |||||||||||||||||||||| |||||||||||| | ||||  || |||||||||||||
Sbjct  7496477  CCTCCCTTCTTCACTGATTAAATTTATAAAGTTTATAAGTATGGTTGCAATTTCTTCCAG  7496418

Query  16662    AGAAGACTTAACCTAAGCCCTGAGACCACTCAAGCCCTCAGTGGCACCTCTCTTCCACCA  16721
                || || |||||||||||||||||||||||||| | |||||||||||||||||||||||||
Sbjct  7496417  AGTAGCCTTAACCTAAGCCCTGAGACCACTCAGGTCCTCAGTGGCACCTCTCTTCCACCA  7496358

Query  16722    GCACGAGTGAAGAAACTGCTACCTTAGGTGATATAAAACCCACAAGACCATTCCATACAT  16781
                ||| ||||||| ||| ||||||||||||||||||||||||||||||||||||  ||||||
Sbjct  7496357  GCAGGAGTGAAAAAATTGCTACCTTAGGTGATATAAAACCCACAAGACCATTGAATACAT  7496298

Query  16782    GGAGATCTTTATTCTT-ATTTTGTAGGGACGACTCCTCTGTGTTTATACAGCTATTTTAA  16840
                |||||| |||||| || |||||||||||||||||||||||| |||||| |||||||||||
Sbjct  7496297  GGAGATTTTTATT-TTGATTTTGTAGGGACGACTCCTCTGTTTTTATAAAGCTATTTTAA  7496239

Query  16841    CTAGAAATATTTTTATAAATTTTATAATTTTGATGTGGCCAAAGATCTCCCCACAACACT  16900
                ||| ||| |     ||   |||| | ||||||||||||||||||||||||| |||| |||
Sbjct  7496238  CTATAAA-AC----AT---TTTTGTGATTTTGATGTGGCCAAAGATCTCCCAACAATACT  7496187

Query  16901    ACTTTCAGGTTTTATTTTTCTGTCTAATGTCTGG-AACAGATCA-ACCCCTTCCCTGCCT  16958
                |||||||| ||||| ||||||||||||| ||||| || |||| | |||| |||||||| |
Sbjct  7496186  ACTTTCAGATTTTAGTTTTCTGTCTAATATCTGGGAA-AGATTAGACCC-TTCCCTGCTT  7496129

Query  16959    CACA-TCAGGACT-TGAAGG-CGAAATAGCAGTAAAATTCCATCAGTGTTTGTGGATTTC  17015
                || | |||||||| || ||| | | |||  ||| |||||||||||||||||||| | |||
Sbjct  7496128  CAGACTCAGGACTATGCAGGTC-ACATATTAGTGAAATTCCATCAGTGTTTGTGAAGTTC  7496070

Query  17016    ATGAATGAATGCAtttttttt----gacaaaatctccctctgtcacccagtcaggagggc  17071
                ||||||||||| |||||||||    |||||| ||||||||||||||||||   |||| ||
Sbjct  7496069  ATGAATGAATGAATTTTTTTTTTCCGACAAATTCTCCCTCTGTCACCCAGAGTGGAGTGC  7496010

Query  17072    aatggtgtaatcttggctcactgcaaac-tcagcctccagggttcaagggattctcccac  17130
                ||||||| |||||||| ||||||||| | |  |||||  ||||||||| |||||||||||
Sbjct  7496009  AATGGTGCAATCTTGGTTCACTGCAACCATT-GCCTCTTGGGTTCAAGCGATTCTCCCAC  7495951

Query  17131    ctcagccgcatgagtaactggactacaggca-gccaccatcgtgcctggctaactt-ttc  17188
                ||||||| | |||||| ||||| |||||||| |   ||||||| |||| |||| || || 
Sbjct  7495950  CTCAGCCTCCTGAGTAGCTGGATTACAGGCATGTG-CCATCGTCCCTGTCTAA-TTCTTG  7495893

Query  17189    tatttttgtagagacagggtttcaccatgtgggccaggctggtcttgaac-tcctgacct  17247
                ||||||||||||||| |||||||||| ||| |||| |||| ||||||||  || ||| ||
Sbjct  7495892  TATTTTTGTAGAGACGGGGTTTCACCTTGTTGGCCTGGCTCGTCTTGAATGTC-TGAACT  7495834

Query  17248    caggtgatccacctaccttggcctcccaaagtgctgggattacaagtgtgagccacctca  17307
                ||||||| ||||| | |||| ||||||||||||||||||||||| | |||||||||||  
Sbjct  7495833  CAGGTGACCCACCCAACTTGTCCTCCCAAAGTGCTGGGATTACAGGAGTGAGCCACCTTG  7495774

Query  17308    cctggccTTGAGTGAATGAATTCTTGATTTCCAGTCTATCCCTAACTCTGTCAATTTCTT  17367
                || || ||||| |||||| |||||||||| |||  ||||||||||| |||||||||||||
Sbjct  7495773  CCCGGTCTTGAATGAATGCATTCTTGATTCCCACCCTATCCCTAACACTGTCAATTTCTT  7495714

Query  17368    AATTCATGAAATGATTATGCATATGTGATATGAATGGATATCTCG-TTCAATCCATTAGT  17426
                 ||||||||| | | |||| |||| |||||||||||||||||| | |||||||||||| |
Sbjct  7495713  GATTCATGAACTTAATATGGATATCTGATATGAATGGATATCT-GATTCAATCCATTAAT  7495655

Query  17427    CTTCGGACAGTCAAAAACCCAATCAGGATTAACTGAGTGGAGCTTCAGAAATGCAATCAG  17486
                ||  ||| || ||||| |||||||||||||||||| ||||||||||||||||||||||||
Sbjct  7495654  CTGGGGAGAGCCAAAACCCCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGCAATCAG  7495595

Query  17487    ATATCGCTTTTTGATTGGAAGCTAGCAGCGGATACGTGGAGGGGCGTGGGTGGGAGTTGT  17546
                ||||| ||| |||||||||||||||||| ||||||||||||||| |||||||||||||||
Sbjct  7495594  ATATCACTTGTTGATTGGAAGCTAGCAGTGGATACGTGGAGGGGTGTGGGTGGGAGTTGT  7495535

Query  17547    GATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGACAAACTCAAAGTCTTCAAGC  17606
                |||||||||||||||||||||||||||||||||||||| | | || ||||||||||||||
Sbjct  7495534  GATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGAAGAGACCCAAAGTCTTCAAGC  7495475

Query  17607    CTGGAGTTCCTGCTTGGCTCTTCCTGAGGTCTGAGCACCTTCTAAACT-ACAACCAGATC  17665
                ||||||||||||||| | ||||||||||||||||||||| || ||||| |   |||||||
Sbjct  7495474  CTGGAGTTCCTGCTTAGTTCTTCCTGAGGTCTGAGCACCCTCCAAACTGAGT-CCAGATC  7495416

Query  17666    TGGTAAGTCACTAAT-T-TCTGTAAGGACACTCCCATGTGACCTACAGTCAGCCGGTCTA  17723
                ||||||||||||||| | ||||||||||||||||||  ||||||||||||||| ||||| 
Sbjct  7495415  TGGTAAGTCACTAATCTCTCTGTAAGGACACTCCCAACTGACCTACAGTCAGCTGGTCTG  7495356

Query  17724    GAACGGTGACAGTGCAGCCTACGATGGCATAGAACTATATCATGTCtttttttctttttt  17783
                | | ||||||||||||||||| |||||||||||  |||||| ||| ||| ||| ||||| 
Sbjct  7495355  GGATGGTGACAGTGCAGCCTAAGATGGCATAGAGTTATATCCTGT-TTTGTTT-TTTTTC  7495298

Query  17784    tcatatgaacactttgaagctttg-attttttt-ttCTAAATGCAATTTTGTCGTGATTT  17841
                ||||||||||| |||||||||||| |||||||  || |||||||| ||||||| | ||||
Sbjct  7495297  TCATATGAACAATTTGAAGCTTTGCATTTTTTCCTT-TAAATGCAGTTTTGTCTTTATTT  7495239

Query  17842    CAAAAATGTTG--TTGTGCTTTTCTTTACATCATTTCAGAATTCTTG  17886
                ||||||  |||  |||||||||  ||||  |||||||| ||||||||
Sbjct  7495238  CAAAAAA-TTGGATTGTGCTTTGGTTTATGTCATTTCAAAATTCTTG  7495193


 Score = 3236 bits (1752),  Expect = 0.0
 Identities = 2713/3162 (85%), Gaps = 125/3162 (3%)
 Strand=Plus/Minus

Query  23894    gggaatgggactcctcctatcagttgttttttttttttaattttcttttgtttta-t--c  23950
                ||||| || |||||||||||||     || ||||||| ||||||||||||||||| |  |
Sbjct  7485788  GGGAAAGGAACTCCTCCTATCA----ATTATTTTTTTAAATTTTCTTTTGTTTTATTGAC  7485733

Query  23951    ctggcaaggctctaatagagttgagcttttttgtttttgttttttccattggaagggaca  24010
                ||| ||||| || ||||||||||||  ||||||||||||||||||||||||||||| |||
Sbjct  7485732  CTGACAAGGGTCAAATAGAGTTGAG--TTTTTGTTTTTGTTTTTTCCATTGGAAGGTACA  7485675

Query  24011    atacagaggttacaatcattgactttagatgacaacatgacaggca-aaaatattttcct  24069
                | ||||||||||||||||||| ||||||||||||| || | | | | |||| || |||||
Sbjct  7485674  A-ACAGAGGTTACAATCATTGGCTTTAGATGACAAGAT-AAAAGAATAAAACATATTCCT  7485617

Query  24070    tgcaagacaaccagcaaaacttcacgatcagaatcaaatcagtgtccttctcactgtcac  24129
                |||||||||||||||| ||||||| |||||| |||||||||||| |||||||||||||| 
Sbjct  7485616  TGCAAGACAACCAGCAGAACTTCATGATCAGCATCAAATCAGTG-CCTTCTCACTGTCAG  7485558

Query  24130    tgggt-gaagccttcatcagtacttgaagagtctcaggcactcatgaagtcaagatcaga  24188
                ||||| ||||||||||||| |||||| ||||| | | ||||||||||| ||| |||||||
Sbjct  7485557  TGGGTGGAAGCCTTCATCAATACTTGTAGAGTTTAAAGCACTCATGAACTCACGATCAGA  7485498

Query  24189    ttctttactcagggacaggatgtaagccaatcataagaccttccacagatgatcaatttg  24248
                 ||||||||||||||||||||||||||||| || |||||||||||||| || | ||||||
Sbjct  7485497  CTCTTTACTCAGGGACAGGATGTAAGCCAAGCAAAAGACCTTCCACAGGTGGTGAATTTG  7485438

Query  24249    gaagtctacctaatgtgacctgcaggttttcaCTGGCAATATGCAGGTGCAGATATGACA  24308
                |||| || || ||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct  7485437  GAAGCCTGCCCAATGTGACCTGCAAGTTTTCACTGGCAATATGCAGGTGCAGATATGACA  7485378

Query  24309    AAGAATAATCC-TGACCTTCATATCGCCCCTAGCTGATGAGGATTGGGATTCTTTTGTCC  24367
                |||||||| || ||||||| | ||| |||| ||||| |||||| |||||| |||||| ||
Sbjct  7485377  AAGAATAA-CCATGACCTTTACATCACCCCCAGCTGTTGAGGAATGGGATCCTTTTGACC  7485319

Query  24368    CTTTCTCTCCATAAAACCAGGTTACTCATCTTGTGTGGCAACAAAATATATGGTctactt  24427
                |||||| |||||| |||||||||| ||||||||||||||||||| ||||||||| |||||
Sbjct  7485318  CTTTCTGTCCATAGAACCAGGTTATTCATCTTGTGTGGCAACAACATATATGGTGTACTT  7485259

Query  24428    aacagagaaaga-gactccacaggaaaaaaaaaaggatttttattatgaaatgagcaaag  24486
                |||||| ||||| |||||    | |||||||||||  |||  |||||||| | |||||||
Sbjct  7485258  AACAGA-AAAGAAGACTCT---GTAAAAAAAAAAG--TTT--ATTATGAAGTAAGCAAAG  7485207

Query  24487    cca-tgggaatagatgtgagattattcggggaggtaaaggaagacaaaggttttgaaagg  24545
                  | ||| |||||||| ||||||||| |||||| |||||||||   ||||||||||||||
Sbjct  7485206  A-AGTGGCAATAGATGCGAGATTATTTGGGGAGATAAAGGAAGTTGAAGGTTTTGAAAGG  7485148

Query  24546    aaaaatgaggagaattacataaatttttttgaaagactcattcttggtcacaagtatgaa  24605
                |||||| ||||| |||| | ||||| ||||||||||||||| |||||||| ||| || ||
Sbjct  7485147  AAAAATAAGGAGGATTATACAAATTGTTTTGAAAGACTCATACTTGGTCATAAGGATTAA  7485088

Query  24606    aaccaag-ggagcctcagtgcagtgttggaaagATTCCTCCTCCACCCTCTCAATAACCC  24664
                ||||||  || || |||||||| |||| || ||||||||| | ||||| |||||||||||
Sbjct  7485087  AACCAAAAGG-GCATCAGTGCAATGTTAGATAGATTCCTCTTACACCCACTCAATAACCC  7485029

Query  24665    CCAACACATTTACCAAGTCTTTG-TTCACTCCCAGGATTCC-ATTAAAACACCCAGCTCA  24722
                ||||||  || | |||||||| | |||||||||||| |||| ||||||| ||||||||||
Sbjct  7485028  CCAACATGTTCAGCAAGTCTT-GCTTCACTCCCAGG-TTCCCATTAAAA-ACCCAGCTCA  7484972

Query  24723    ACCCTGACCAGCCTCCACCTTCACTTCCCTTTGTAATTTTGACATAAATTtgttacagga  24782
                |||||||||||| |||||| |||||||| |||||||||||||||| | ||| ||||||||
Sbjct  7484971  ACCCTGACCAGC-TCCACCCTCACTTCCATTTGTAATTTTGACATGACTTTATTACAGGA  7484913

Query  24783    ccatcaggttcctatgccggctgcacagtagcttaccaatattctgagacagcaggattt  24842
                |||||||||||||||||| |||||||||||||||| |||||||||||||||||||| |||
Sbjct  7484912  CCATCAGGTTCCTATGCCTGCTGCACAGTAGCTTAGCAATATTCTGAGACAGCAGGGTTT  7484853

Query  24843    gcagcagaaagtttaatgatcacagggtggctgaatgagaagctgggaggagatcctcaa  24902
                |||||||| ||||||||||||||| ||||||||||||||||||| |||||||||||||||
Sbjct  7484852  GCAGCAGAGAGTTTAATGATCACAAGGTGGCTGAATGAGAAGCTAGGAGGAGATCCTCAA  7484793

Query  24903    attcatctccccaaggagtactgagggtttccagtggatcctggatagcaaggggctgga  24962
                |||||||||||||||||||||||| ||||||||||||||||||||||||||||||| |||
Sbjct  7484792  ATTCATCTCCCCAAGGAGTACTGAAGGTTTCCAGTGGATCCTGGATAGCAAGGGGCCGGA  7484733

Query  24963    aagttggtgtagtttgatggcaataagaggtatgaagttatcacgatgtcagaa-cggca  25021
                ||||||| |||||  |  |    ||||||| | ||||| | || ||||| |||| | |||
Sbjct  7484732  AAGTTGGGGTAGT--G--G----TAAGAGGGAAGAAGTCAACAGGATGT-AGAAACTGCA  7484682

Query  25022    ttctttggtgagttgatgccttgcagggcccttcagatcagctggcatcagtagtttcac  25081
                ||||||||||||||| ||| ||||| ||||||||||||||||||||||||||||||||||
Sbjct  7484681  TTCTTTGGTGAGTTGGTGCATTGCATGGCCCTTCAGATCAGCTGGCATCAGTAGTTTCAC  7484622

Query  25082    tgacatgcagaacctgaaagaatatctcaaatgaaaaacttaatgtttcacaatgcttaa  25141
                ||||||||||||||||||||||||||||| |||||||| ||||||||| ||||||||| |
Sbjct  7484621  TGACATGCAGAACCTGAAAGAATATCTCAGATGAAAAAGTTAATGTTTTACAATGCTTGA  7484562

Query  25142    attgttgtctgcagcgtagttaaggggaattgtagtctaagttctacacgattttgggac  25201
                || ||||||||||| | |||||||||||| |||| |||||| |||| | |||||||| ||
Sbjct  7484561  ATCGTTGTCTGCAGGGAAGTTAAGGGGAACTGTAATCTAAGGTCTATATGATTTTGGAAC  7484502

Query  25202    agtaggctgccagcaaccatgaggaagcaggtcagagggcaagctgacctcctggtgaat  25261
                |||||||||||||||||||||||||| |||||||||| |||||  ||||||||| |||||
Sbjct  7484501  AGTAGGCTGCCAGCAACCATGAGGAACCAGGTCAGAGAGCAAGAAGACCTCCTGATGAAT  7484442

Query  25262    gctgaatgcgtttcaagcttggtttgtttttgttcctccccctctctttttcaccgatta  25321
                |||||||| ||| |||||||||||| ||||| || ||| ||||| ||| ||||| |||||
Sbjct  7484441  GCTGAATGTGTTGCAAGCTTGGTTTATTTTTCTTTCTCTCCCTCCCTTCTTCACTGATTA  7484382

Query  25322    aatttataaagtttagaaatacggtttcaATTTCTTCCAGACAAGCCTTAACCTAAGCCC  25381
                |||||||||||||||   ||  ||||||||||||||||| | |||||||||||||||| |
Sbjct  7484381  AATTTATAAAGTTTATCGATGTGGTTTCAATTTCTTCCAAAGAAGCCTTAACCTAAGCAC  7484322

Query  25382    TGAGACCACTCAAGCCCTCAGTGGCACCTCTCTTCCACCAGCATGAGCAAATAAAT-TGC  25440
                |||||||||||| ||||||||||||||||||| |||||||| | |||||  ||| | |||
Sbjct  7484321  TGAGACCACTCACGCCCTCAGTGGCACCTCTCCTCCACCAGAACGAGCATGTAA-TCTGC  7484263

Query  25441    TACCTTAGGTGATATAAAA-CCCACAAGATGATTCGATACATGGAGtttttt-ttCTGAT  25498
                |||||||||| |||||||| |||| ||||  |||| |||||| ||| ||||| |||||||
Sbjct  7484262  TACCTTAGGTTATATAAAATCCCA-AAGACCATTCAATACATTGAGATTTTTATTCTGAT  7484204

Query  25499    TTTGTAGGGATGACTTCTTTGTTTCTATAAAGCTGTTTTAAC-TATAAAACAATTTTATA  25557
                 | |||||||||||| || ||||| ||||||||| ||||||  || ||| || |||||||
Sbjct  7484203  ATCGTAGGGATGACTCCTCTGTTTTTATAAAGCT-TTTTAAAGTAGAAAGCATTTTTATA  7484145

Query  25558    ATTTTGATGTGGCCAAAGATCTCC---CAACACTACTTTCAGGTTTTATTTTTCTGTCTA  25614
                 |||||||||||||||||||||||   ||||||||||||||| |||||||||||||||||
Sbjct  7484144  -TTTTGATGTGGCCAAAGATCTCCTAACAACACTACTTTCAGATTTTATTTTTCTGTCTA  7484086

Query  25615    CTATCCAGAACAGATCAAACCCTTCCCTGCCTCAAACTCAGGACTAT-ATAGGTCATATA  25673
                 | |   |||||||||||| |||||||||||||| ||||| |||||| | || ||| |||
Sbjct  7484085  ATGTTGGGAACAGATCAAATCCTTCCCTGCCTCACACTCAAGACTATGA-AGTTCACATA  7484027

Query  25674    TCAGTAAAATTCCATCAGTGTTTGCGGAgttcatgaatgaatgaattctttttttttttt  25733
                | | |||||| ||||||||||||| ||||||||||||||||||| || ||||| ||||||
Sbjct  7484026  TTAATAAAATACCATCAGTGTTTGTGGAGTTCATGAATGAATGA-TT-TTTTTATTTTTT  7483969

Query  25734    tttttttttttttttgtgaca-aagtctacctctgtcacccagaac-ggtgtgcaatggt  25791
                               |  ||| || ||| ||||||||||||||| | || ||||| ||| 
Sbjct  7483968  ---------------G--ACAGAA-TCTCCCTCTGTCACCCAGA-CTGGAGTGCAGTGGC  7483928

Query  25792    gcaa-tcttggctcactgcaaccattgccccctggattcaagcgattctcccacctcagc  25850
                 ||| ||| |||||||||||||||||||| ||||| ||||||| |||||||  |||||||
Sbjct  7483927  ACAAATCT-GGCTCACTGCAACCATTGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGC  7483869

Query  25851    ctcctgagtagctggattacaggcacctgccatcatgcc-aggctaatttttgtgttttt  25909
                ||||  ||||||||| || ||||  |||||||||||||| || ||||||||||| |||||
Sbjct  7483868  CTCCCAAGTAGCTGGGTTTCAGGTGCCTGCCATCATGCCCAG-CTAATTTTTGTATTTTT  7483810

Query  25910    gtagag-ctggggtttcatcatgttggccttg-caggtcttgatcgcctgacctcaggtg  25967
                |||||| | ||||||||| | | ||| ||| | | |||||||| | |||||| |||||||
Sbjct  7483809  GTAGAGAC-GGGGTTTCACCTTTTTGACCT-GACTGGTCTTGAACCCCTGACATCAGGTG  7483752

Query  25968    atccagc-caacttggactctc-aaagtgcagggattacaggtgtgagccacctcacccg  26025
                ||| | | || |||   || || ||||||| || ||||||||| ||||||||||| ||| 
Sbjct  7483751  ATCTA-CTCACCTTCTCCT-TCCAAAGTGCTGGAATTACAGGTATGAGCCACCTCGCCCA  7483694

Query  26026    gcctttaatgaGTGAATTCTTGATTTCCACCCTATTCCTAACACTGTCAATTTCTTGATT  26085
                 |||| ||||| || |||||||| ||| ||||||| ||||||||||||||||||||| ||
Sbjct  7483693  CCCTTGAATGAATGTATTCTTGACTTCTACCCTATCCCTAACACTGTCAATTTCTTGCTT  7483634

Query  26086    CATGAACTTAATATGGATA-GCTGATATGAATGGATATCTGATTCAATCCAGTAATCTGG  26144
                || ||||| ||||  |||| | |||||||||||||||||||| |||||||| ||||||||
Sbjct  7483633  CACGAACTGAATACAGATATG-TGATATGAATGGATATCTGACTCAATCCATTAATCTGG  7483575

Query  26145    GGACAGCCAAAAACCCAATCAAGATTAACTGGGTGGAGCTTCAGAAATGCAATCAGATAG  26204
                ||| ||||||||||||||||| ||||||||||||||||||||| ||||||||||||||| 
Sbjct  7483574  GGAAAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCACAAATGCAATCAGATAT  7483515

Query  26205    CACTTTTTGATTGGAAGCAAGCACTGGATA-GATGGAGGGGTGTGGGTGGGAGTTGTGAT  26263
                  |||||||||||||||| |||| || ||| | |||||||| ||||||||||||||||||
Sbjct  7483514  TGCTTTTTGATTGGAAGCTAGCAGTGCATACG-TGGAGGGGCGTGGGTGGGAGTTGTGAT  7483456

Query  26264    TAGAAAGATC-GATAAAAGTTTCTGAAGG-CCCACAGGAGAGACCCAAAGTCTTCAAGTC  26321
                ||||||| || | |||||| |||| |||| |||||||||||||||||||||||||||| |
Sbjct  7483455  TAGAAAGGTCAG-TAAAAGCTTCT-AAGGACCCACAGGAGAGACCCAAAGTCTTCAAGCC  7483398

Query  26322    TGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTAAGCACTCTGCAA-ACT-CAGTCCAGATC  26379
                ||||||||||||||||||||||||||| ||| ||||| || | | ||| || ||||||||
Sbjct  7483397  TGGAGTTCCTGCTTGGTTCTTCCTGAGATCTGAGCAC-CTTCTAGACTACA-TCCAGATC  7483340

Query  26380    TAGTAAGTCACTCATTTCTGGAAGGACACTCCCATCTGACCTATAGTCAGCCGGTCTGGG  26439
                | |||||||||| ||||||| |||||||||||||||||||||| |||||| |||||||||
Sbjct  7483339  TGGTAAGTCACTAATTTCTGTAAGGACACTCCCATCTGACCTACAGTCAGTCGGTCTGGG  7483280

Query  26440    ACGGGGGCAATGCAGCCTATGATGGCACCGAGCTATATC-TGTC-TTTtatatatatat-  26496
                | || | || ||||||||| |||||||| |||||||||| |||| |||| | | | | | 
Sbjct  7483279  ATGGTGACAGTGCAGCCTACGATGGCACAGAGCTATATCCTGTCCTTTTTTTTTTTTTTT  7483220

Query  26497    ----atatGAACAATTTGAAGATTTGAATTTTTTCCTCTATATGCAGTTTTGTCTTTATT  26552
                    |||||||||||| |||| |||||||||||||||||| |||||||| ||||||||||
Sbjct  7483219  TTTTATATGAACAATTGGAAGCTTTGAATTTTTTCCTCTAAATGCAGTTCTGTCTTTATT  7483160

Query  26553    TCAAAAAA-TTGGATTGTGCTTTGGTTTATGTCATTTcaaaattcttgatgggagcaatg  26611
                |||||||| ||| |||||||||||||| ||| ||||| ||||||||||| ||||||| ||
Sbjct  7483159  TCAAAAAAGTTG-ATTGTGCTTTGGTTGATGCCATTTTAAAATTCTTGAAGGGAGCAGTG  7483101

Query  26612    actcatgcccataacctcaacaccttgggaggccaaagcgggaggatcatttgagcccag  26671
                |||||||||  ||||| |||||| |||||||||||||| ||||||||||||| |||||||
Sbjct  7483100  ACTCATGCCTTTAACCCCAACACTTTGGGAGGCCAAAGTGGGAGGATCATTTCAGCCCAG  7483041

Query  26672    gggtttgagaccaacctgggcaacatggcaaaaatgcagctctacaaaacattctttttt  26731
                || |||||||||||||||| ||||||| ||||||  |  |||| || ||| || ||||||
Sbjct  7483040  GGATTTGAGACCAACCTGGACAACATGACAAAAACCCTCCTCTGCACAACGTTTTTTTTT  7482981

Query  26732    tgaagcaggg-atggagtctcaccctgttgccaaggctggagtgcagtggcaagagctca  26790
                ||| |  ||| ||||||||||||  ||||||| || |||||||||||||||| || ||||
Sbjct  7482980  TGAGGGTGGGGATGGAGTCTCACTGTGTTGCCCAGACTGGAGTGCAGTGGCATGATCTCA  7482921

Query  26791    actcactgcaacctcttcct-cccaggctcaaacaattttcatgtctcag-ct---tcct  26845
                |||| ||||||||| || || ||| || |||| ||||| ||||| ||||| ||   ||||
Sbjct  7482920  ACTCCCTGCAACCT-TTACTTCCCGGGTTCAAGCAATTCTCATGCCTCAGTCTCCATCCT  7482862

Query  26846    gagtagctggtattacatccctctgccaccatgtctg-cttaatttttgtatttttagta  26904
                 || ||||||| | |||  | ||||  |||||| ||| || || ||||||||||||||||
Sbjct  7482861  CAGAAGCTGGTGTCACAGACATCTGAAACCATGCCTGGCT-AACTTTTGTATTTTTAGTA  7482803

Query  26905    gtggtggggtttcaccatgctggccaggttggtctcaaactcctgacatcaagtgatcct  26964
                | ||||||||||||||| |||||||||||||||||| ||| |||||| ||||||||||| 
Sbjct  7482802  GAGGTGGGGTTTCACCACGCTGGCCAGGTTGGTCTCGAACACCTGACCTCAAGTGATCCA  7482743

Query  26965    cctgcctaggcc-cccaaaagtgctggaatgacggccgtgag  27005
                ||||||| |||| |||||| ||||||| || || || |||||
Sbjct  7482742  CCTGCCTTGGCCTCCCAAA-GTGCTGGGATTACAGCTGTGAG  7482702


 Score = 3203 bits (1734),  Expect = 0.0
 Identities = 2242/2486 (90%), Gaps = 39/2486 (1%)
 Strand=Plus/Minus

Query  3255     GGCAGAAACTTTCTCCAGCAGAGCTCCGAGGGGTTCAAGACTGATACAGAACTGCAGCAT  3314
                ||||| || |||||||||||||||||||||||||||||||||||| | |||| |||||| 
Sbjct  7393134  GGCAGCAATTTTCTCCAGCAGAGCTCCGAGGGGTTCAAGACTGATGCGGAACAGCAGCAC  7393075

Query  3315     GTAGCTGAGATTCAGATGCTTTGGGTAAGCGAGGCTTGGGTACTGGTAGAGACACTTCAA  3374
                |||||||||||||||||||||| ||||| ||||||||||||||||| |||||||||||| 
Sbjct  7393074  GTAGCTGAGATTCAGATGCTTTAGGTAACCGAGGCTTGGGTACTGGGAGAGACACTTCAT  7393015

Query  3375     GTCCTCTTCCAATAGGTAGCCGCAAGTTAATTCCAAGTTCTCCAAGGGGTTCTAGAGGCA  3434
                ||| |||||||||||||||||  |||||||||||||||||||||||||||||| ||||||
Sbjct  7393014  GTCTTCTTCCAATAGGTAGCCATAAGTTAATTCCAAGTTCTCCAAGGGGTTCTGGAGGCA  7392955

Query  3435     CCTGTGGAGATCAAGAAGTTAGTTCTGGGCAATGGTACCAGTTAGATGAAGGTAGTGGGG  3494
                ||||||||||||||||||||||||||||||| || |||||||||||||||||||||   |
Sbjct  7392954  CCTGTGGAGATCAAGAAGTTAGTTCTGGGCAGTGATACCAGTTAGATGAAGGTAGT---G  7392898

Query  3495     AATGAACTCAAGGAAAATACCTGCTTCAACCAAACACAAGTTTGTTCCCACCATCTGATG  3554
                  |  | || |||||||| ||||| |||| ||||||||||||||||||||||||||||||
Sbjct  7392897  CCTTCA-TCTAGGAAAATGCCTGCGTCAAACAAACACAAGTTTGTTCCCACCATCTGATG  7392839

Query  3555     ATGGTCCTCATGCAAGTTGCTGCATGTTGAGGACCCTGATCATTCAGGGGCTGTCCCATT  3614
                |||||||||||| ||||||||||||| |||||||||||||| ||||||||||||||||||
Sbjct  7392838  ATGGTCCTCATGGAAGTTGCTGCATGATGAGGACCCTGATCGTTCAGGGGCTGTCCCATT  7392779

Query  3615     TTAGCCTCAGCCCTTTCACCATTTCTTGTGTGATTGGGTCAAGGCCACAAAATCTCTAAA  3674
                ||||||||||||||||||||||| ||||||||||||| ||||||||| ||||||||||||
Sbjct  7392778  TTAGCCTCAGCCCTTTCACCATTGCTTGTGTGATTGGTTCAAGGCCATAAAATCTCTAAA  7392719

Query  3675     GCC-TTTTATCTTCATCTTTTAGCAGAAAACCTCATCTCTGGGCCACAGGTACCCGGTGG  3733
                ||| |||| | |||||||||||||||||||| ||||||||||||||||||||||||||||
Sbjct  7392718  GCCTTTTTTTTTTCATCTTTTAGCAGAAAACTTCATCTCTGGGCCACAGGTACCCGGTGG  7392659

Query  3734     GAGATGTGCACAAAGAACTCAACTCAGCAAGGTCTAGGGACATTAGCTGGGGCTACCTGC  3793
                |||||||| ||||||||||||||| |||||||||||||||||| |||| | ||||| || 
Sbjct  7392658  GAGATGTGAACAAAGAACTCAACTGAGCAAGGTCTAGGGACATCAGCTAGAGCTACATGT  7392599

Query  3794     CGGCAGGGGCTCCCTGGCCTGCCTGCATCTGCAAACCAACTGTCACTTTTTACCACTCTC  3853
                | |||||||||||||| | |||||||||||||||||||||||||||||||||||||||||
Sbjct  7392598  CAGCAGGGGCTCCCTGACATGCCTGCATCTGCAAACCAACTGTCACTTTTTACCACTCTC  7392539

Query  3854     ACTCCTACTCCTTCACCCTCCATCCCAGAAGCATGCATGTCCCATGTCAATTGA-CTTTC  3912
                || |||||||| ||| |||||||||| |||||| |||| ||||||||||||| | |||||
Sbjct  7392538  ACGCCTACTCCCTCA-CCTCCATCCCGGAAGCACGCATTTCCCATGTCAATT-ACCTTTC  7392481

Query  3913     CTGGAGTTCAAAACAACCTTCTACAGACAGGGAATCAGAGACAGGATCATTCATGATCAC  3972
                |||||||||||||||||||| |||| |||||||||||||||||||||||||| |||||||
Sbjct  7392480  CTGGAGTTCAAAACAACCTTTTACAAACAGGGAATCAGAGACAGGATCATTCGTGATCAC  7392421

Query  3973     TAAGCTGGTGAGGACAGAGC-TTCTACTGTGAAATGCACAAGTTTGATGCACTGTCCCTC  4031
                ||||| |||||||||||| | ||||| ||||||||| ||| ||||||||| || ||||||
Sbjct  7392420  TAAGCCGGTGAGGACAGA-CGTTCTATTGTGAAATGGACAGGTTTGATGCGCTTTCCCTC  7392362

Query  4032     CTTTCATACCCTCCTTTGTTACCTCTTTTACATCATATCAACTTGAAACACACTTTGTAA  4091
                ||||||||||||||| | ||| |||||| |||||||||||||||||||||||||||||||
Sbjct  7392361  CTTTCATACCCTCCTCTATTATCTCTTTGACATCATATCAACTTGAAACACACTTTGTAA  7392302

Query  4092     CAAGAAATTCACACGTGCACATGCAGTAGAGAC-AAAACGCCCACTAAGTACCTTGTACA  4150
                || |||||||||||||||||   || ||||| |  |||| |||||||| || ||||||||
Sbjct  7392301  CAGGAAATTCACACGTGCACCCCCAATAGAG-CTGAAACCCCCACTAACTAGCTTGTACA  7392243

Query  4151     TGATGTCCCTCTCTAGCCTCTACCCTAGGTGACCCCTCTGCCTTTATTGAAGTGATCCTG  4210
                ||||||||||||||||| ||||||| ||||||||||||| || |||||| || |||||||
Sbjct  7392242  TGATGTCCCTCTCTAGCTTCTACCCCAGGTGACCCCTCTCCCCTTATTGGAGCGATCCTG  7392183

Query  4211     TGATAGCCACTCCAGGACATGGAGCACTGAACGGGACAATGTGTTGACATTCTGGTGTCC  4270
                ||||||||||||||||||||||| ||||||| |||||||||||||||||||||| |||||
Sbjct  7392182  TGATAGCCACTCCAGGACATGGAACACTGAATGGGACAATGTGTTGACATTCTGATGTCC  7392123

Query  4271     CCTGCACTGTGCCGTCGCCACTGGCTGGCACACAGTACACGTCTTCTAGTGTTTACTGTA  4330
                ||| ||||||| ||| ||||||||||||||||||||||| | |||||| ||||| |||| 
Sbjct  7392122  CCTTCACTGTGACGTTGCCACTGGCTGGCACACAGTACATGCCTTCTAATGTTTGCTGTT  7392063

Query  4331     ACaaaaaaaaaGGCTGCGCTGTGGTCTGCAGAGAAAGGGCACGATCCTTTCTCACCTGAT  4390
                ||  | || ||||||  ||||||||||||| | |||| ||| ||||||||||||||||||
Sbjct  7392062  AC--AGAACAAGGCTATGCTGTGGTCTGCATACAAAGTGCATGATCCTTTCTCACCTGAT  7392005

Query  4391     CAGCTGTCCCAGGTGCCCTCTGTGGAAGGTGA-CCATATTCATTTTAAGCAGCTGGAGGT  4449
                ||||||| |||||||||| |||  |||||||| | || || |||||||||| ||| ||||
Sbjct  7392004  CAGCTGTTCCAGGTGCCCACTGAAGAAGGTGATCAAT-TTTATTTTAAGCAACTGAAGGT  7391946

Query  4450     GTTTCAGCCTGAGGAACATAGAGCTGATTTTGGCGACTGAGCATTCC-TCGCGGT-A--A  4505
                ||| |||||||||||||| |||||||| |||||| ||| | |  ||| | | | | |  |
Sbjct  7391945  GTTCCAGCCTGAGGAACACAGAGCTGAATTTGGCAACT-AACCGTCCTTGGAGTTCATTA  7391887

Query  4506     T-TGACGTGTAAGGATGGCACCTGGAGAAAAATGAGTTTGCGAAGATTCTTCATCTCCTT  4564
                | |||||||||| |||||||||||||| |||| |||||||||||||||||||||||||||
Sbjct  7391886  TCTGACGTGTAATGATGGCACCTGGAG-AAAACGAGTTTGCGAAGATTCTTCATCTCCTT  7391828

Query  4565     CAGGTAACAATGAAGCTTTCTTATCAGATGTGGCCAGGACACATAGCAAATTTCCAGCTC  4624
                |||||||||| ||||||||||||||||| ||||||||||||  | || ||||||||||||
Sbjct  7391827  CAGGTAACAACGAAGCTTTCTTATCAGACGTGGCCAGGACATGTTGCGAATTTCCAGCTC  7391768

Query  4625     CTGAATACTATTCAGGTGGATTATTTTCAATGATC-TTCTGAGATATTCAATCGACGTTA  4683
                 ||||||||||||||||  |||||||||||||| | |||||||||||| ||||| |||||
Sbjct  7391767  TTGAATACTATTCAGGTATATTATTTTCAATGA-CTTTCTGAGATATTTAATCGGCGTTA  7391709

Query  4684     GATAATTCACCAACTTACTACAGCACAGGTGTACTAAACCTCTCCTTTGGTAAACCCACC  4743
                ||||||| |||| |||||||||||||||||||||||||||||||||||||||||||||| 
Sbjct  7391708  GATAATTGACCAGCTTACTACAGCACAGGTGTACTAAACCTCTCCTTTGGTAAACCCACT  7391649

Query  4744     GGAAGAGGTATCTCAGGCATTCATCCTGGGGTATTTCCTTGAGGCAGATGTCTATGAACA  4803
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7391648  GGAAGAGGTATCTCAGGCATTCATCCTGGGGTATTTCCTTGAGGCAGATGTCTATGAACA  7391589

Query  4804     CCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGTCTGCCTCTTACTCA  4863
                |||| |||||||||||||||||||||||||||||||||||||||||||||||||||||| 
Sbjct  7391588  CCTTTAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGTCTGCCTCTTACTCG  7391529

Query  4864     TGGCCTCTGGGGAGGAGGACAGGGCCCTGGATTCAGACCATATGGCCCAGAAATTCTCAT  4923
                ||| ||||||| || |||||||||||| || | ||| |||| |||||||||||||||| |
Sbjct  7391528  TGGTCTCTGGGAAGCAGGACAGGGCCCAGGCTCCAGGCCATCTGGCCCAGAAATTCTCGT  7391469

Query  4924     CAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAAAGTAAGGCAGAG  4983
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Sbjct  7391468  CAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAAAGTAAGGGAGAG  7391409

Query  4984     GCTCAGAACTTT-GAAGGACAAATCCCTGACCTTTGCTTTCATTCTCATCCAATAAATCA  5042
                 ||||||| ||| |||||||  |||||||||||||||||||||| |||||| ||||||||
Sbjct  7391408  ACTCAGAA-TTTAGAAGGACTCATCCCTGACCTTTGCTTTCATTGTCATCCCATAAATCA  7391350

Query  5043     GCTGCTCCTGTCCTC-GCTGCTCCCTGTTCTCTCTGAGTTTTCTTGGTCCCTTTTCTCTT  5101
                ||||||||||||||| | ||||||||||||||| ||  ||||||   ||||| ||| |||
Sbjct  7391349  GCTGCTCCTGTCCTCAG-TGCTCCCTGTTCTCTTTGTCTTTTCTCAATCCCTGTTCCCTT  7391291

Query  5102     TCAATTCTGAC---TG-GTCCCCACTTCTATTCCATTTACCTTCCACTG-GGAATAGGCA  5156
                |  ||||||||   ||  |||||||||||||||| |||||||||||||| | || |||||
Sbjct  7391290  TTGATTCTGACTTTTGATTCCCCACTTCTATTCCCTTTACCTTCCACTGAGTAA-AGGCA  7391232

Query  5157     AGTTTCTGTTCCCACAGTGGACCCTATATTGTGGGCAGTTCTTTCCCTGAGGATCTGGGC  5216
                 |||||||||||||||||||||||| ||| ||| ||||| ||||| ||||||||||||  
Sbjct  7391231  GGTTTCTGTTCCCACAGTGGACCCTGTATGGTGAGCAGTCCTTTCTCTGAGGATCTGGAA  7391172

Query  5217     AATGGCCAAGGCATGCCTGAGCTTCGTCACCAGCACCACCAGAAGACACTGGGCCATC-C  5275
                ||||||||| || | ||||| |||| || ||| ||||| |||||||| |||||||| | |
Sbjct  7391171  AATGGCCAAAGCCTCCCTGATCTTCCTCGCCAACACCATCAGAAGACTCTGGGCCA-CAC  7391113

Query  5276     TTGGGATACTTCTTTGCCTGACCCTGCTGTTCTTTCCCTGGACACCTGAGCCCCATCTAC  5335
                ||||| ||||||| ||||||||||||||||||||||||||||||||||||||| ||||||
Sbjct  7391112  TTGGGCTACTTCTCTGCCTGACCCTGCTGTTCTTTCCCTGGACACCTGAGCCCTATCTAC  7391053

Query  5336     CAGCCTTCCTGGGTCACCTCACCTGGGGCGATCCTTCTGTGTAAGCAGCATGTGAAGCCC  5395
                ||||| ||||||||||||||||||||||||||||||||||||||||||||| ||||||||
Sbjct  7391052  CAGCCCTCCTGGGTCACCTCACCTGGGGCGATCCTTCTGTGTAAGCAGCATATGAAGCCC  7390993

Query  5396     TTCCAGCAATGCTTTTAAGGTCTCCAGATGAAGCGTCTTCATCAGCGATCCCAGAGGGAG  5455
                |||||||||||||||||||||||||| |||||||||||||||||| ||||||||||||||
Sbjct  7390992  TTCCAGCAATGCTTTTAAGGTCTCCAAATGAAGCGTCTTCATCAGTGATCCCAGAGGGAG  7390933

Query  5456     GCGGGTGAAGGGCCAGGCCTGCACCATCACTGTCAGAGTCTGGAAGTGTCTCCTGCTGAA  5515
                || |||||||||||||||||| |||||||| |||||||||||||||||||||||||||||
Sbjct  7390932  GCAGGTGAAGGGCCAGGCCTGAACCATCACCGTCAGAGTCTGGAAGTGTCTCCTGCTGAA  7390873

Query  5516     GGCCTCCAGGAAGAGTGGGAGGTAGAGCTCCCTGGGCAGCTCCTCCAGGGCAGAGATGGC  5575
                |||||||| |||||||||||| |||||| |||||||||||||||||| ||||||||||| 
Sbjct  7390872  GGCCTCCATGAAGAGTGGGAGATAGAGCACCCTGGGCAGCTCCTCCATGGCAGAGATGGA  7390813

Query  5576     CAAGGGCTTGTCTCTCAGCAGACTCTGCCCCGCCAGCTCCAGGAGTCTGGGTGGGGCCTG  5635
                ||||| || |||||||||||| |||||||| ||||||||||| |||||||||||||||||
Sbjct  7390812  CAAGGCCTGGTCTCTCAGCAGGCTCTGCCCTGCCAGCTCCAGTAGTCTGGGTGGGGCCTG  7390753

Query  5636     GATGCTCATCCTGAT-GAATCTGTAAGGAAAAACTCTAGAAGACAAATCCAGAGAAAAGG  5694
                ||||||||||||||| || |||| |||||||| ||||||||||||||||||| ||||| |
Sbjct  7390752  GATGCTCATCCTGATAGA-TCTGCAAGGAAAATCTCTAGAAGACAAATCCAGGGAAAATG  7390694

Query  5695     CATCACTTTCAGGCCAAACACAATCA  5720
                  ||||| ||||| |||| |||||||
Sbjct  7390693  TGTCACTCTCAGGGCAAAGACAATCA  7390668


 Score = 3157 bits (1709),  Expect = 0.0
 Identities = 1973/2095 (94%), Gaps = 40/2095 (1%)
 Strand=Plus/Minus

Query  11376    acaggcatgagccaccacggtcagccAGAAAAAAGTACTTAATAAATTATCAGTTAACTA  11435
                ||||||||||||||||||||||||||||||||||||||||||||||||| ||| ||||||
Sbjct  7452546  ACAGGCATGAGCCACCACGGTCAGCCAGAAAAAAGTACTTAATAAATTACCAGCTAACTA  7452487

Query  11436    AATGCAACACTGCATTAGAAAGTGATAGACAggccaggctccgtggctcacgcctgcaat  11495
                ||||||||||||||| |||||||||||||||||||||||||||||||||| |||||||||
Sbjct  7452486  AATGCAACACTGCATCAGAAAGTGATAGACAGGCCAGGCTCCGTGGCTCATGCCTGCAAT  7452427

Query  11496    cccagcactttgagaggccgaggcaggtggatcacctcaggtctggagttcgagaccagc  11555
                |||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||
Sbjct  7452426  CCCAGCACTTTGAGAGGCTGAGGCAGGTGGATCACCTCAGGTCTGGAGTTCGAGACCAGC  7452367

Query  11556    ctgaccaacatggagaaaccccatccctactaaaaatacaaaattagccaggtgtggtgg  11615
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7452366  CTGACCAACATGGAGAAACCCCATCCCTACTAAAAATACAAAATTAGCCAGGTGTGGTGG  7452307

Query  11616    cgcatgcctgtaatcccagcaactcaggaggctgaggctggagatttgcttgaaccaaga  11675
                |||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||
Sbjct  7452306  CGCATGCCTGTAATCCCAGCAACTCAGGAGGCTGAGGCTGGAGATTCGCTTGAACCAAGA  7452247

Query  11676    aggtggaagttgcagtgagtcgagatcatgccattgcacttcagcttgtgcaaaaagagt  11735
                ||||||| ||||||||||||||||||| |||||||||||||| ||||| |||| ||||||
Sbjct  7452246  AGGTGGAGGTTGCAGTGAGTCGAGATCGTGCCATTGCACTTCGGCTTGGGCAACAAGAGT  7452187

Query  11736    gaaactccaccttaaaaagaaaaaaaaaagaaaaaaagaaaGCAATATAGTGATATATAA  11795
                ||||||||| || ||||| |||||||||||||| ||||||| ||||||||| ||||||||
Sbjct  7452186  GAAACTCCAGCTCAAAAAAAAAAAAAAAAGAAAGAAAGAAAACAATATAGTAATATATAA  7452127

Query  11796    TGGCCATTCCAGGAATGCCAGCCAATCACAGGAAAATCTAAGTGTAATTCAGCATACTGA  11855
                ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||
Sbjct  7452126  TGGCCATTCCAGGAATGCCAGCCAATCACAGAAAAATCTAAGTGTAATTCAGCATACTGA  7452067

Query  11856    CAAACTAAAGGGGGAAAAGCAAGGTTCCTACAAAATGCAGAAAAGAATTGCAGAAAAATC  11915
                ||||||||||||||||||||||||||||||||||||||||||| |||||| |||||||||
Sbjct  7452066  CAAACTAAAGGGGGAAAAGCAAGGTTCCTACAAAATGCAGAAAGGAATTGAAGAAAAATC  7452007

Query  11916    AAATTAAATTTATCATAACATATTTCGGAAACTGAAATGTTGTATGTTGAAAACTTGCAT  11975
                ||||||||||||||||| ||||||| ||||| ||| ||||||||||||||||||||||||
Sbjct  7452006  AAATTAAATTTATCATAGCATATTTTGGAAAATGAGATGTTGTATGTTGAAAACTTGCAT  7451947

Query  11976    TAAACATCAGATGTAATGGATAAACATTAGCTCCCTTCCTACTGAGATATGAAACAAGGT  12035
                ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Sbjct  7451946  TAAACATCAGATGTAATGGATAAACATTAGCTCCCTTCCTAGTGAGATATGAAACAAGGT  7451887

Query  12036    AAGAACCTCAGCACCTTAGGATTTGGACGCACGTAGGTATTTTGGTTAATAGTAAAGACT  12095
                |||| |||||||| ||||||||||| | |||||||||||||||||||| |||||||||||
Sbjct  7451886  AAGACCCTCAGCAACTTAGGATTTGAAGGCACGTAGGTATTTTGGTTAGTAGTAAAGACT  7451827

Query  12096    CCAGATCCAGCAGACCCAGACTGCTTAATTTAGGTTCAAAACTGGCTCAGTaccatcctg  12155
                |||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||||
Sbjct  7451826  CCAGATCCAGCAGATCCAGACTGTTTAATTTAGGTTCAAAACTGGCTCAGTACCATCCTG  7451767

Query  12156    gctaacacggtgaatccccgtctctactaaaaacacaaaaattagccgggcatggtggca  12215
                ||||||||||||||||||| ||||||||||||| ||||||||||||| | ||||||||||
Sbjct  7451766  GCTAACACGGTGAATCCCCATCTCTACTAAAAATACAAAAATTAGCCAGACATGGTGGCA  7451707

Query  12216    ggtgcctgtagccccagctactcgggaggctgaggcagcagaatggagtgaacccgggag  12275
                ||  ||||||| |||||||||||||||||||||||||| |||||||||||||||||||||
Sbjct  7451706  GGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGAGTGAACCCGGGAG  7451647

Query  12276    gcagagcttgcagtgagctgagatcgcgccactgcactccagcctgagcgacagcatgag  12335
                |||||||||||||||||| ||||||||||||||||||||||||||| ||||||||| |||
Sbjct  7451646  GCAGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGCACGAG  7451587

Query  12336    a-tgctgtctcagaaaaaagaaaaaaaaCTGGCTCAGTGGCCAATGgctgtgtggtctta  12394
                | | |  || ||||||||| ||||    ||||||||||||||||||||||||||||||||
Sbjct  7451586  ACTCCA-TCCCAGAAAAAA-AAAA----CTGGCTCAGTGGCCAATGGCTGTGTGGTCTTA  7451533

Query  12395    ctcaacttacttaacctctctgtgccttagctcattcacatataaaatgggataatagca  12454
                | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7451532  CCCAACTTACTTAACCTCTCTGTGCCTTAGCTCATTCACATATAAAATGGGATAATAGCA  7451473

Query  12455    atattgacttcacagagtGCTATAAATTAATCTATTTAAGTACTTCGAGCTGGATTTGAC  12514
                ||||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||
Sbjct  7451472  ATATTGACTTCACAGAGTGTTATAAGTTAATCTATTTAAGTACTTCGAGCTGGATTTGAC  7451413

Query  12515    ATAGGGCAAGCAAGGATATTTTTATTGTTATTATATTTGAAAAATATATTAGTTACAAAC  12574
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7451412  ATAGGGCAAGCAAGGATATTTTTATTGTTATTATATTTGAAAAATATATTAGTTACAAAC  7451353

Query  12575    TTAGGTAAGAGACCAAGGCCTATGGTAAAGGTGATTATAAGCCTTCATACACCACTGTTG  12634
                |||||| ||||||||||| |||||||||||||||||||||||||||||||||| ||||||
Sbjct  7451352  TTAGGTGAGAGACCAAGGTCTATGGTAAAGGTGATTATAAGCCTTCATACACCCCTGTTG  7451293

Query  12635    TTCTGAAAATCTTAATTATAACAAggccaggcacg-gtggctcacgtctgtaatcccagc  12693
                |||||||||||||||||||||||||||| ||   | ||||||||||||||||||||||||
Sbjct  7451292  TTCTGAAAATCTTAATTATAACAAGGCCCGGTG-GAGTGGCTCACGTCTGTAATCCCAGC  7451234

Query  12694    actttgggaggccaaggtgggcagatcacctgaggt--------c--a------g-g---  12733
                ||||||||||||  |||||||| |||||||||||||        |  |      | |   
Sbjct  7451233  ACTTTGGGAGGCTGAGGTGGGCGGATCACCTGAGGTGAGGTGGGCGGATCACCTGAGGTC  7451174

Query  12734    ag---ttcgagaccagcctcaccaaca-tggcgaaactatctctctactaaaaatacaaa  12789
                ||   |||||||||||||||||||| | |||| |||||||||||||| ||||| ||||||
Sbjct  7451173  AGGAGTTCGAGACCAGCCTCACCAA-AGTGGCAAAACTATCTCTCTATTAAAA-TACAAA  7451116

Query  12790    aaatagctgggcatggtggtggacacctgtaatcccaggtattcggtaggttgaggcagg  12849
                ||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||
Sbjct  7451115  AAATAGCTGGGCATGGTGGTGGACACCTGTAATCCCAGGTACTCGGTAGGCTGAGGCAGG  7451056

Query  12850    agaatcacttgaatccaggaggcagagtttgcagtgagccaagattgaactattgctctc  12909
                ||||||||||||||||||||||||||||||||||||| ||||||| ||||||||||||||
Sbjct  7451055  AGAATCACTTGAATCCAGGAGGCAGAGTTTGCAGTGAACCAAGATGGAACTATTGCTCTC  7450996

Query  12910    cagcctggcga-gagagtgagactccatctccaaaaaaaaaaaa--aattataagaaCAT  12966
                ||||||||||| | ||||||||||||||||||||||||||| ||  |||||||| | |||
Sbjct  7450995  CAGCCTGGCGACG-GAGTGAGACTCCATCTCCAAAAAAAAATAATTAATTATAACAGCAT  7450937

Query  12967    GTCCATTCACTCTCCAAAGTATCTAGGACTGGACAATTACTTGTCAGGCCCTCTTCTGTA  13026
                |||||||||||||||||||| |||||||||||||||||| ||||||||||||||||||||
Sbjct  7450936  GTCCATTCACTCTCCAAAGTGTCTAGGACTGGACAATTAATTGTCAGGCCCTCTTCTGTA  7450877

Query  13027    GCACCATACACTATAGCATATATGTGGATTAatataaatacacatacaaaattcaagtat  13086
                ||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||||
Sbjct  7450876  GCACCCTACACTATAGCATATATGTGGATTAATATAAATACACATACAAATTTCAAGTAT  7450817

Query  13087    atattctatatactttctatatatttatatTCTAAGAGGTCACATGCAAATTCAAGGCTA  13146
                |||||| |||||||||||||||| |||| |||||||||||||||||||||||||||||||
Sbjct  7450816  ATATTCCATATACTTTCTATATACTTATTTTCTAAGAGGTCACATGCAAATTCAAGGCTA  7450757

Query  13147    GGTCAAAGAGTAGAGTGGCTATCTATGGAAAGGGGAGTGGAAGTGAATCATGGTAATaaa  13206
                 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7450756  TGTCAAAGAGTAGAGTGGCTATCTATGGAAAGGGGAGTGGAAGTGAATCATGGTAATAAA  7450697

Query  13207    aaa-aGGTGTAGATATAGTTATGGATAGGTAGACATACACACATATAGCGGCAAGAAAAG  13265
                ||| |||||||||||||| |||| ||| ||||||||||||||||||||||||||||||||
Sbjct  7450696  AAATAGGTGTAGATATAGATATGAATATGTAGACATACACACATATAGCGGCAAGAAAAG  7450637

Query  13266    GGAATGTCATGGACCAGTGATGACAGTGAGCCATGTAAAAAGGCTACAATTTTTGTGATT  13325
                |||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||
Sbjct  7450636  GGAATGTCATGGACCAATGATGACAGTGAGCCATGTAAAAAGGCTACAATTTTTGTGATT  7450577

Query  13326    GTGTGTCCATTTTCAGGATTGGTTGTAGCTTACCTTTTTAGAAAGGCTGATGCCATAGTC  13385
                ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||
Sbjct  7450576  GTGTGTCCATTTTCAGGATGGGTTGTAGCTTACCTTTTTAGAAAGGCTGATGCCATAGTC  7450517

Query  13386    ATAGTGAATAAATGATTATAAAATGTGTTTCCTTTCTGGCGAACCTCTGGAGAAA  13440
                ||||||||||||||||||||||||||||||||||||||| | |||||||||||||
Sbjct  7450516  ATAGTGAATAAATGATTATAAAATGTGTTTCCTTTCTGGTGCACCTCTGGAGAAA  7450462


 Score = 2985 bits (1616),  Expect = 0.0
 Identities = 2370/2725 (86%), Gaps = 88/2725 (3%)
 Strand=Plus/Minus

Query  15201    gggaatgggactcctcctatcaatt-ttttttt-aattttcttttgttttattgacctgg  15258
                ||||| || |||||||||||||||| ||||||| ||||||||||||||||||||||||| 
Sbjct  7485788  GGGAAAGGAACTCCTCCTATCAATTATTTTTTTAAATTTTCTTTTGTTTTATTGACCTGA  7485729

Query  15259    caaggctcaaatagagttgagtttttgtttttgtttttcccattggaaggtacaagacag  15318
                ||||| |||||||||||||||||||||||||||||||| |||||||||||||||| ||||
Sbjct  7485728  CAAGGGTCAAATAGAGTTGAGTTTTTGTTTTTGTTTTTTCCATTGGAAGGTACAA-ACAG  7485670

Query  15319    aggttacaatcgttagctttagatgacaacataacaggctaaaacattttccttgcaaga  15378
                ||||||||||| || |||||||||||||| |||| ||  |||||||| ||||||||||||
Sbjct  7485669  AGGTTACAATCATTGGCTTTAGATGACAAGATAAAAGAATAAAACATATTCCTTGCAAGA  7485610

Query  15379    caaccagcatg-acttcatgatcagaataaaatcagtgtccttctcactgtcagcgggt-  15436
                ||||||||| | ||||||||||||| || ||||||||| ||||||||||||||| |||| 
Sbjct  7485609  CAACCAGCA-GAACTTCATGATCAGCATCAAATCAGTG-CCTTCTCACTGTCAGTGGGTG  7485552

Query  15437    gaagacttcatcagtacttgtagagtttgaggtactcatgaactcatgatcagattcttt  15496
                |||| |||||||| |||||||||||||| | | ||||||||||||| ||||||| |||||
Sbjct  7485551  GAAGCCTTCATCAATACTTGTAGAGTTTAAAGCACTCATGAACTCACGATCAGACTCTTT  7485492

Query  15497    actcagggacaggatgtaagccaatgc-taagaccttctataggtggct-aatttttaag  15554
                |||||||||||||||||||||||| ||  ||||||||| | |||||| | |||||  |||
Sbjct  7485491  ACTCAGGGACAGGATGTAAGCCAA-GCAAAAGACCTTCCACAGGTGG-TGAATTTGGAAG  7485434

Query  15555    cttgccccaatgagaccttcaggttttcaCTGGCAATATGCAGGTGCAGATATGACAAAG  15614
                | || ||||||| ||||| || ||||||||||||||||||||||||||||||||||||||
Sbjct  7485433  CCTG-CCCAATGTGACCTGCAAGTTTTCACTGGCAATATGCAGGTGCAGATATGACAAAG  7485375

Query  15615    AATAACAATGACCTTCATATCACCTCCAGCTGTTGAGGAATGGGATCCTTTTCACCCTTC  15674
                |||||| |||||||| | |||||| ||||||||||||||||||||||||||| |||||| 
Sbjct  7485374  AATAACCATGACCTTTACATCACCCCCAGCTGTTGAGGAATGGGATCCTTTTGACCCTTT  7485315

Query  15675    CTGTCCATAAAACCAAGTTACTCATCTTCAGTGGCAACAAAATATATGGTAAACTTAACA  15734
                ||||||||| ||||| |||| |||||||  |||||||||| |||||||||  ||||||||
Sbjct  7485314  CTGTCCATAGAACCAGGTTATTCATCTTGTGTGGCAACAACATATATGGTGTACTTAACA  7485255

Query  15735    GAGAAGGAGACTGTCAGaaaaaaaaaaaaaaaagatgtgtttatcctgaaatgaggaaag  15794
                || ||| ||||  || |       ||||||||| |   ||||||  |||| | || ||||
Sbjct  7485254  GAAAAGAAGAC--TCTG------TAAAAAAAAA-A---GTTTATTATGAAGTAAGCAAAG  7485207

Query  15795    caa-tgggaatagatgtgagattattttgggagaaaaaggaagacaaaggttttgaaagg  15853
                 || ||| |||||||| |||||||||| |||||| ||||||||   ||||||||||||||
Sbjct  7485206  -AAGTGGCAATAGATGCGAGATTATTTGGGGAGATAAAGGAAGTTGAAGGTTTTGAAAGG  7485148

Query  15854    aaaaataaggaggattatacaaattgttttgaaagactca-accttggtcctaagaatca  15912
                |||||||||||||||||||||||||||||||||||||||| | ||||||| |||| || |
Sbjct  7485147  AAAAATAAGGAGGATTATACAAATTGTTTTGAAAGACTCATA-CTTGGTCATAAGGATTA  7485089

Query  15913    aaagtaaaggggcatcagtgaaatgttggatagATTCCACCTCCACCCCCTCAGTAACCC  15972
                |||  ||| ||||||||||| |||||| |||||||||| | | ||||| |||| ||||||
Sbjct  7485088  AAACCAAAAGGGCATCAGTGCAATGTTAGATAGATTCCTCTTACACCCACTCAATAACCC  7485029

Query  15973    CCAACATGTTTACCAAGTCTTGGTTAACTCCCAGGATCCCATTAAAACACCCAGCTCAAC  16032
                |||||||||| | ||||||||| || ||||||||| ||||||||||| ||||||||||||
Sbjct  7485028  CCAACATGTTCAGCAAGTCTTGCTTCACTCCCAGGTTCCCATTAAAA-ACCCAGCTCAAC  7484970

Query  16033    CATGCCCATCCTCTACCCTCACTTCTC-TTTGTAATTTTGACATGATTTTAttacaggac  16091
                | || |||  ||| ||||||||||| | |||||||||||||||||| |||||||||||||
Sbjct  7484969  CCTGACCA-GCTCCACCCTCACTTC-CATTTGTAATTTTGACATGACTTTATTACAGGAC  7484912

Query  16092    catcaggttcctatgcctgctgcacagtagctgaccaatattctgagacagcagtgtttg  16151
                |||||||||||||||||||||||||||||||| | ||||||||||||||||||| |||||
Sbjct  7484911  CATCAGGTTCCTATGCCTGCTGCACAGTAGCTTAGCAATATTCTGAGACAGCAGGGTTTG  7484852

Query  16152    cagcagacagtttaatgatcacagggtggctaaatgagaagctaggaggatatcctcaaa  16211
                ||||||| ||||||||||||||| ||||||| |||||||||||||||||| |||||||||
Sbjct  7484851  CAGCAGAGAGTTTAATGATCACAAGGTGGCTGAATGAGAAGCTAGGAGGAGATCCTCAAA  7484792

Query  16212    ttcatctccccaagtagtactgagggtttccagtggatcctggatagcaaggggctggaa  16271
                |||||||||||||| |||||||| ||||||||||||||||||||||||||||||| ||||
Sbjct  7484791  TTCATCTCCCCAAGGAGTACTGAAGGTTTCCAGTGGATCCTGGATAGCAAGGGGCCGGAA  7484732

Query  16272    agttggtgtagaggtaagagggatgaagtcatcaggatgtca-aaactgcattctttggt  16330
                |||||| |||| ||||||||||| ||||||| |||||||| | |||||||||||||||||
Sbjct  7484731  AGTTGGGGTAGTGGTAAGAGGGAAGAAGTCAACAGGATGT-AGAAACTGCATTCTTTGGT  7484673

Query  16331    gagttggtgccttgca-gagcccttcagatcagctggcatcagtagtttcactgacatgc  16389
                |||||||||| ||||| | |||||||||||||||||||||||||||||||||||||||||
Sbjct  7484672  GAGTTGGTGCATTGCATG-GCCCTTCAGATCAGCTGGCATCAGTAGTTTCACTGACATGC  7484614

Query  16390    agaacctgaaagaatatctcaaatgagaaagttaatgttttacaaggcttaaattgttgt  16449
                ||||||||||||||||||||| |||| |||||||||||||||||| |||| ||| |||||
Sbjct  7484613  AGAACCTGAAAGAATATCTCAGATGAAAAAGTTAATGTTTTACAATGCTTGAATCGTTGT  7484554

Query  16450    ctgcagggtagttaaggggaactgtaagctaaggtctact-tgatttggggacagtaagc  16508
                |||||||| |||||||||||||||||| |||||||||| | |||||| || |||||| ||
Sbjct  7484553  CTGCAGGGAAGTTAAGGGGAACTGTAATCTAAGGTCTA-TATGATTTTGGAACAGTAGGC  7484495

Query  16509    tgccagcaaccatgaggaagaaggtcagagagcaagctgacctcatggtgaatgctgaat  16568
                |||||||||||||||||||  |||||||||||||||  |||||| || ||||||||||||
Sbjct  7484494  TGCCAGCAACCATGAGGAACCAGGTCAGAGAGCAAGAAGACCTCCTGATGAATGCTGAAT  7484435

Query  16569    gcgctgcaagcttggtttatttttgtttctccccctcccttcttcactgattaaacttat  16628
                | | |||||||||||||||||||| |||||| ||||||||||||||||||||||| ||||
Sbjct  7484434  GTGTTGCAAGCTTGGTTTATTTTTCTTTCTCTCCCTCCCTTCTTCACTGATTAAATTTAT  7484375

Query  16629    aaagttta-caggtatcatttcaATTTCTTCCAGAGAAGACTTAACCTAAGCCCTGAGAC  16687
                |||||||| | | | |  ||||||||||||||| ||||| |||||||||||| |||||||
Sbjct  7484374  AAAGTTTATC-GATGTGGTTTCAATTTCTTCCAAAGAAGCCTTAACCTAAGCACTGAGAC  7484316

Query  16688    CACTCAAGCCCTCAGTGGCACCTCTCTTCCACCAGCACGAGTGAAG-AAACTGCTACCTT  16746
                |||||| ||||||||||||||||||| |||||||| |||||  | | || ||||||||||
Sbjct  7484315  CACTCACGCCCTCAGTGGCACCTCTCCTCCACCAGAACGAG-CATGTAATCTGCTACCTT  7484257

Query  16747    AGGTGATATAAAA-CCCACAAGACCATTCCATACATGGAGATCTTTATTCTTATTTTGTA  16805
                |||| |||||||| |||| |||||||||| |||||| ||||| |||||||| || | |||
Sbjct  7484256  AGGTTATATAAAATCCCA-AAGACCATTCAATACATTGAGATTTTTATTCTGATATCGTA  7484198

Query  16806    GGGACGACTCCTCTGTGTTTATACAGCTATTTT-AACTAGAAATATTTTTATAAATTTTA  16864
                |||| ||||||||||| |||||| |||| |||| || ||| || |     ||   |||||
Sbjct  7484197  GGGATGACTCCTCTGTTTTTATAAAGCT-TTTTAAAGTAG-AA-A---GCAT---TTTTA  7484147

Query  16865    TAATTTTGATGTGGCCAAAGATCTCCCCACAACACTACTTTCAGGTTTTATTTTTCTGTC  16924
                | ||||||||||||||||||||||||  |||||||||||||||| |||||||||||||||
Sbjct  7484146  T-ATTTTGATGTGGCCAAAGATCTCCTAACAACACTACTTTCAGATTTTATTTTTCTGTC  7484088

Query  16925    TAATGTCT-GGAACAGATCAACCCCTTCCCTGCCTCACA-TCAGGACT-TGAAG-GCGAA  16980
                |||||| | ||||||||||||  |||||||||||||||| ||| |||| |||||  | | 
Sbjct  7484087  TAATGT-TGGGAACAGATCAAATCCTTCCCTGCCTCACACTCAAGACTATGAAGTTC-AC  7484030

Query  16981    ATAGCAGTAAAATTCCATCAGTGTTTGTGGATTTCATGAATGAATGCA-----tt-tttt  17034
                |||  | |||||| ||||||||||||||||| |||||||||||||| |     || ||||
Sbjct  7484029  ATATTAATAAAATACCATCAGTGTTTGTGGAGTTCATGAATGAATG-ATTTTTTTATTTT  7483971

Query  17035    ttgacaaaatctccctctgtcacccagtcaggagggcaatgg-tgtaatcttggctcact  17093
                |||||| |||||||||||||||||||| | |||| ||| |||    |||| |||||||||
Sbjct  7483970  TTGACAGAATCTCCCTCTGTCACCCAGACTGGAGTGCAGTGGCACAAATC-TGGCTCACT  7483912

Query  17094    gcaaactca--gcctccagggttcaagggattctcccacctcagccgcatgagtaactgg  17151
                || ||| ||  |||||| |||||||||  |||||||  |||||||| |   |||| ||||
Sbjct  7483911  GC-AAC-CATTGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCAAGTAGCTGG  7483854

Query  17152    actacaggcagcc-accatcgtgcctggctaacttttctatttttgtagagacagggttt  17210
                  | ||||  |||  ||||| ||||  ||||| |||| ||||||||||||||| ||||||
Sbjct  7483853  GTTTCAGG-TGCCTGCCATCATGCCCAGCTAATTTTTGTATTTTTGTAGAGACGGGGTTT  7483795

Query  17211    caccatgtgggccaggctggtcttgaactcctgacctcaggtgatccacct-accttggc  17269
                |||| | | | || | |||||||||||| |||||| |||||||||| | || |||||  |
Sbjct  7483794  CACCTTTTTGACCTGACTGGTCTTGAACCCCTGACATCAGGTGATCTA-CTCACCTTCTC  7483736

Query  17270    ctcccaaagtgctgggattacaagtgtgagccacctcacctggccTTGAGTGAATGAATT  17329
                || |||||||||||| |||||| || ||||||||||| ||   |||||| |||||| |||
Sbjct  7483735  CTTCCAAAGTGCTGGAATTACAGGTATGAGCCACCTCGCCCACCCTTGAATGAATGTATT  7483676

Query  17330    CTTGATTTCCAGTCTATCCCTAACTCTGTCAATTTCTTAATTCATGAAATGATTA-TGCA  17388
                ||||| ||| |  ||||||||||| |||||||||||||  |||| ||| ||| ||  | |
Sbjct  7483675  CTTGACTTCTACCCTATCCCTAACACTGTCAATTTCTTGCTTCACGAACTGAATACAG-A  7483617

Query  17389    TATGTGATATGAATGGATATCTCG-TTCAATCCATTAGTCTTCGGACAGTCAAAAACCCA  17447
                |||||||||||||||||||||| |  ||||||||||| |||  ||| || ||||||||||
Sbjct  7483616  TATGTGATATGAATGGATATCT-GACTCAATCCATTAATCTGGGGAAAGCCAAAAACCCA  7483558

Query  17448    ATCAGGATTAACTGAGTGGAGCTTCAGAAATGCAATCAGATATCGCTTTTTGATTGGAAG  17507
                |||||||||||||| ||||||||||| |||||||||||||||| ||||||||||||||||
Sbjct  7483557  ATCAGGATTAACTGGGTGGAGCTTCACAAATGCAATCAGATATTGCTTTTTGATTGGAAG  7483498

Query  17508    CTAGCAGCGGATACGTGGAGGGGCGTGGGTGGGAGTTGTGATTAGAAAGGTCAATAAAAG  17567
                ||||||| | ||||||||||||||||||||||||||||||||||||||||||| ||||||
Sbjct  7483497  CTAGCAGTGCATACGTGGAGGGGCGTGGGTGGGAGTTGTGATTAGAAAGGTCAGTAAAAG  7483438

Query  17568    CTTCTAAAGACCCACAGGACAAACTCAAAGTCTTCAAGCCTGGAGTTCCTGCTTGGCTCT  17627
                ||||||| ||||||||||| | || ||||||||||||||||||||||||||||||| |||
Sbjct  7483437  CTTCTAAGGACCCACAGGAGAGACCCAAAGTCTTCAAGCCTGGAGTTCCTGCTTGGTTCT  7483378

Query  17628    TCCTGAGGTCTGAGCACCTTCTAAACTACAACCAGATCTGGTAAGTCACTAATTTCTGTA  17687
                ||||||| ||||||||||||||| |||||| |||||||||||||||||||||||||||||
Sbjct  7483377  TCCTGAGATCTGAGCACCTTCTAGACTACATCCAGATCTGGTAAGTCACTAATTTCTGTA  7483318

Query  17688    AGGACACTCCCATGTGACCTACAGTCAGCCGGTCTAGAACGGTGACAGTGCAGCCTACGA  17747
                ||||||||||||| |||||||||||||| |||||| | | ||||||||||||||||||||
Sbjct  7483317  AGGACACTCCCATCTGACCTACAGTCAGTCGGTCTGGGATGGTGACAGTGCAGCCTACGA  7483258

Query  17748    TGGCATAGAACTATATCATGTC-tttttttctttttttc---atatgaacactttgaagc  17803
                ||||| ||| ||||||| |||| ||||||| |||||||    ||||||||| || |||||
Sbjct  7483257  TGGCACAGAGCTATATCCTGTCCTTTTTTTTTTTTTTTTTTTATATGAACAATTGGAAGC  7483198

Query  17804    tttgatttttttt-tCTAAATGCAATTTTGTCGTGATTTCAAAAATGTTG-TTGTGCTTT  17861
                ||||| ||||||  |||||||||| || |||| | |||||||||| |||| |||||||||
Sbjct  7483197  TTTGAATTTTTTCCTCTAAATGCAGTTCTGTCTTTATTTCAAAAAAGTTGATTGTGCTTT  7483138

Query  17862    TCTTTACATCATTTCAGAATTCTTG  17886
                  || |   ||||| | ||||||||
Sbjct  7483137  GGTTGATGCCATTTTAAAATTCTTG  7483113


 Score = 2977 bits (1612),  Expect = 0.0
 Identities = 2413/2786 (86%), Gaps = 109/2786 (3%)
 Strand=Plus/Minus

Query  15160    tgttacaagttggaatgcttttgtaagagaggttaaaagaagggaatgggactcctccta  15219
                |||| ||||||||||||||||| ||||| ||||| ||||||||| |||||||||||||||
Sbjct  7443495  TGTTGCAAGTTGGAATGCTTTTATAAGAAAGGTTGAAAGAAGGGGATGGGACTCCTCCTA  7443436

Query  15220    tca----atttttttttaattttcttttgttttattgacctggcaaggctcaaatagagt  15275
                |||     |||||||||||||||||||||||||| |  ||||||||||||| ||||||||
Sbjct  7443435  TCAGTTGTTTTTTTTTTAATTTTCTTTTGTTTTA-T--CCTGGCAAGGCTCTAATAGAGT  7443379

Query  15276    tgag--tttttgtttttgtttttcccattggaaggtacaagacagaggttacaatcgtta  15333
                ||||  ||||||||||||||||| ||||||||||| |||| ||||||||||||||| || 
Sbjct  7443378  TGAGCTTTTTTGTTTTTGTTTTTTCCATTGGAAGGGACAATACAGAGGTTACAATCATT-  7443320

Query  15334    g-ctttagatgacaacataacaggctaaaacattttccttgcaagacaaccagcatgact  15392
                | |||||||||||||||| |||||| |||| ||||||||||||||||||||||||  |||
Sbjct  7443319  GACTTTAGATGACAACATGACAGGCAAAAATATTTTCCTTGCAAGACAACCAGCAAAACT  7443260

Query  15393    tcatgatcagaataaaatcagtgtccttctcactgtcagc-gggtgaagacttcatcagt  15451
                ||| ||||||||| |||||||||||||||||||||||| | |||||||| ||||||||||
Sbjct  7443259  TCACGATCAGAATCAAATCAGTGTCCTTCTCACTGTCA-CTGGGTGAAGCCTTCATCAGT  7443201

Query  15452    acttgtagagtttgaggtactcatgaactcatgatcagattctttactcagggacaggat  15511
                ||||| ||||| | ||| ||||||||| ||| ||||||||||||||||||||||||||||
Sbjct  7443200  ACTTGAAGAGTCTCAGGCACTCATGAAGTCAAGATCAGATTCTTTACTCAGGGACAGGAT  7443141

Query  15512    gtaagccaatgc-taagaccttctataggtggct-aatttttaagct-tgccccaatgag  15568
                |||||||||| | |||||||||| | || | | | |||||  ||| | |  || |||| |
Sbjct  7443140  GTAAGCCAAT-CATAAGACCTTCCACAGAT-GATCAATTTGGAAG-TCT-ACCTAATGTG  7443085

Query  15569    accttcaggttttcaCTGGCAATATGCAGGTGCAGATATGACAAAGAATAA-CAATGACC  15627
                |||| |||||||||||||||||||||||||||||||||||||||||||||| |  |||||
Sbjct  7443084  ACCTGCAGGTTTTCACTGGCAATATGCAGGTGCAGATATGACAAAGAATAATC-CTGACC  7443026

Query  15628    TTCATATCACCTCC-AGCTGTTGAGGAATGGGATCCTTTTCACCCTTCCTGTCCATAAAA  15686
                ||||||||||| || |||||||||||| |||||| |||||  ||||| || |||||||||
Sbjct  7443025  TTCATATCACC-CCTAGCTGTTGAGGATTGGGATTCTTTTGTCCCTTTCTCTCCATAAAA  7442967

Query  15687    CCAAGTTACTCATCTTCAGTGGCAACAAAATATATGGTAAACTTAACAGAGAAGGAGACT  15746
                ||| | ||||||||||  ||||||||||||||||||||  ||||||||||||| ||||||
Sbjct  7442966  CCAGGCTACTCATCTTGTGTGGCAACAAAATATATGGTCTACTTAACAGAGAAAGAGACT  7442907

Query  15747    GTCAGaaaaaaaaaaaaaaaagatgtgtttatcctgaaatgaggaaagcaatgggaatag  15806
                  || |  |||||||||||| ||| | |||||  ||||||||| ||||| ||||||||||
Sbjct  7442906  -CCACAGGAAAAAAAAAAAAGGAT-T-TTTATTATGAAATGAGCAAAGCCATGGGAATAG  7442850

Query  15807    atgtgagattattttgggagaaaaaggaagacaaaggttttgaaaggaaaaataaggagg  15866
                |||||||||||||  |||||  ||||||||||||||||||||||||||||||| ||||| 
Sbjct  7442849  ATGTGAGATTATTCGGGGAGGTAAAGGAAGACAAAGGTTTTGAAAGGAAAAATGAGGAGA  7442790

Query  15867    attatacaaattgttttgaaagactcaaccttggtc-ctaagaatcaaaagtaaaggg-g  15924
                |||| | ||||| ||||||||||||||  ||||||| | ||| || ||||   |||||  
Sbjct  7442789  ATTACATAAATTTTTTTGAAAGACTCATTCTTGGTCAC-AAGTATGAAAA-CCAAGGGAC  7442732

Query  15925    catcagtgaaatgttggatagATTCCACCTCCACCCCCTCAGTAACCCCCAACATGTTTA  15984
                | |||||| ||||||||| ||||||| ||||||||| |||| ||||||||||||  ||||
Sbjct  7442731  CCTCAGTGCAATGTTGGAAAGATTCCTCCTCCACCCTCTCAATAACCCCCAACACATTTA  7442672

Query  15985    CCAAGTCTTGGTTAACTCCCAGGATCCCATTAAAACACCCAGCTCAACCATGCCCATCCT  16044
                ||||||||| ||| ||||||||||| ||||||||||||||||||||||| || ||| |||
Sbjct  7442671  CCAAGTCTTCGTTCACTCCCAGGATTCCATTAAAACACCCAGCTCAACCCTGACCAGCCT  7442612

Query  16045    CTACCCTCACTTCTCTTTGTAATTTTGACATGATTTTAttacaggaccatcaggttccta  16104
                | |   ||||||| |||| |||||||||||| | ||| ||||||||||||||||||||||
Sbjct  7442611  CCATTTTCACTTCCCTTTATAATTTTGACATAAATTTGTTACAGGACCATCAGGTTCCTA  7442552

Query  16105    tgcctgctgcacagtagctgaccaatattctgagacagcagtgtttgcagcagacagttt  16164
                ||||||||||||||||||| ||||||||||||||||||||| |||||||||||| |||||
Sbjct  7442551  TGCCTGCTGCACAGTAGCTTACCAATATTCTGAGACAGCAGGGTTTGCAGCAGAAAGTTT  7442492

Query  16165    aatgatcacagggtggctaaatgagaagctaggaggatatcctcaaattcatctccccaa  16224
                |||||||||||||||||| ||||||||||| |||||| ||||||||||||||||||||||
Sbjct  7442491  AATGATCACAGGGTGGCTGAATGAGAAGCTGGGAGGAGATCCTCAAATTCATCTCCCCAA  7442432

Query  16225    gtagtactgagggtttccagtggatcctggatagcaaggggctggaaagttggtgta---  16281
                | |||||||||||||||||||||||||||||||||||||||||||||||||||||||   
Sbjct  7442431  GGAGTACTGAGGGTTTCCAGTGGATCCTGGATAGCAAGGGGCTGGAAAGTTGGTGTAGTT  7442372

Query  16282    -ga-gg---taagagggatgaagtcatcaggatgtcaaaactgcattctttggtgagttg  16336
                 || ||   ||||||| ||||||| |||| ||||||| ||| ||||||||||||||||||
Sbjct  7442371  TGATGGCAATAAGAGGTATGAAGTTATCACGATGTCAGAACGGCATTCTTTGGTGAGTTG  7442312

Query  16337    gtgccttgcagagcccttcagatcagctggcatcagtagtttcactgacatgcagaacct  16396
                 |||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7442311  ATGCCTTGCAGGGCCCTTCAGATCAGCTGGCATCAGTAGTTTCACTGACATGCAGAACCT  7442252

Query  16397    gaaagaatatctcaaatgagaaagttaatgttttacaaggcttaaattgttgtctgcagg  16456
                |||||||||||||| |||| ||||| ||||||| |||| |||||||||||||||||||| 
Sbjct  7442251  GAAAGAATATCTCAGATGAAAAAGTGAATGTTTCACAATGCTTAAATTGTTGTCTGCAGC  7442192

Query  16457    gtagttaaggggaactgtaag-ctaaggtctacttgatttggggacagtaagctgccagc  16515
                |||||||||||||| ||| || ||||| ||||| |||||| ||||||||| |||||||| 
Sbjct  7442191  GTAGTTAAGGGGAATTGT-AGTCTAAGTTCTACATGATTTTGGGACAGTAGGCTGCCAGG  7442133

Query  16516    aaccatgaggaagaaggtcagagagcaagctgacctcatggtgaatgctgaatgcgctgc  16575
                ||||||||||||| ||||||||| ||||||||||||| ||||||||||||||||||||||
Sbjct  7442132  AACCATGAGGAAGCAGGTCAGAGGGCAAGCTGACCTCCTGGTGAATGCTGAATGCGCTGC  7442073

Query  16576    aagcttggtttatttttgtttctccccctcccttcttcactgattaaacttataaagttt  16635
                ||||||||||| |||||||| ||||||||| ||| ||||||||||||| |||||||||||
Sbjct  7442072  AAGCTTGGTTTGTTTTTGTTCCTCCCCCTCTCTTTTTCACTGATTAAATTTATAAAGTTT  7442013

Query  16636    acaggtatc-atttcaATTTCTTCCAGAGAAGACTTAACCTAAGCCCTGAGACCACTCAA  16694
                | || || |  ||||||||||||||||| ||| |||||||||||||||||||||||||||
Sbjct  7442012  AGAGATA-CGGTTTCAATTTCTTCCAGACAAGCCTTAACCTAAGCCCTGAGACCACTCAA  7441954

Query  16695    GCCCTCAGTGGCACCTCTCTTCCACCAGCACGAGTGAAGAAACTGCTACCTTAGGTGATA  16754
                |||||||||||||||||||||||||||||  |||  || ||| |||||||||||||||||
Sbjct  7441953  GCCCTCAGTGGCACCTCTCTTCCACCAGCGTGAGCAAATAAATTGCTACCTTAGGTGATA  7441894

Query  16755    TAAAACCCACAAGACCATTCCATACATGGAGATCTTTATTCTTATTTTGTAGGGACGACT  16814
                || ||||||||||||||||| |||||||||||| ||| |||| |||||||||||| ||||
Sbjct  7441893  TAGAACCCACAAGACCATTCGATACATGGAGATTTTTTTTCTGATTTTGTAGGGATGACT  7441834

Query  16815    CCTCTGTGTTTATACAGCTATTTTAACTAGAAATATTTTTATAAATTTTATAATTTTGAT  16874
                 |||||| |||||| |||| ||||||||| ||| |     | |  |||||||||||| ||
Sbjct  7441833  TCTCTGTTTTTATAAAGCTGTTTTAACTATAAA-AC----A-A--TTTTATAATTTTAAT  7441782

Query  16875    GTGGCCAAAGATCTCCCCACAACACTACTTTCAGGTTTTATTTTTCTGTCTAATGTCTGG  16934
                ||||||||||||||||| | | |||||||||||||||||||||||||||||| | || ||
Sbjct  7441781  GTGGCCAAAGATCTCCC-A-A-CACTACTTTCAGGTTTTATTTTTCTGTCTACTATCCGG  7441725

Query  16935    AACAGATCAACCCCTTCCCTGCCTCACA-TCAGGACT-TGA-AGG-CGAAATAGCAGTAA  16990
                |||||||||| ||||||||||||||| | |||||||| | | ||| | | ||| ||||||
Sbjct  7441724  AACAGATCAAACCCTTCCCTGCCTCAAACTCAGGACTAT-ATAGGTC-ATATATCAGTAA  7441667

Query  16991    AATTCCATCAGTGTTTGTGGA-TTTCATGAATGAATG----C-----Attttt-ttt---  17036
                ||||||||||||||||||||| ||| |||||||||||    |     |||||| |||   
Sbjct  7441666  AATTCCATCAGTGTTTGTGGAGTTT-ATGAATGAATGAATTCTTTTTATTTTTATTTTTT  7441608

Query  17037    -gacaaaatctccctctgtcacccagt-caggagggcaatggtgtaatcttggctcactg  17094
                 |||||| ||| ||||||||||||||  | || | ||||||||| |||||||||||||||
Sbjct  7441607  TGACAAAGTCTACCTCTGTCACCCAGAAC-GGTGTGCAATGGTGCAATCTTGGCTCACTG  7441549

Query  17095    caaac-tcagcctccaggg-ttcaagggattctcccacctcagccgcatgagtaactgga  17152
                ||| | |  |||||| ||| |||||| |||||||||||||||||| | |||||| |||||
Sbjct  7441548  CAACCATT-GCCTCC-GGGATTCAAGCGATTCTCCCACCTCAGCCTCCTGAGTAGCTGGA  7441491

Query  17153    ctacaggcagcca-ccatcgtgcctggctaacttttctatttttgtagagacagggtttc  17211
                 |||||||| ||  ||||| |||| |||||| |||| | |||||||||| |  |||||||
Sbjct  7441490  TTACAGGCA-CCTGCCATCATGCCAGGCTAATTTTTGTGTTTTTGTAGAAATGGGGTTTC  7441432

Query  17212    accatgtgggccaggctggtcttgaactcctgacctcaggtgatcca-cctaccttggcc  17270
                ||||||| ||||  || |||||||| | |||||||||||| |||||| || || |||| |
Sbjct  7441431  ACCATGTTGGCCTTGCAGGTCTTGATCGCCTGACCTCAGGCGATCCAGCCAAC-TTGGAC  7441373

Query  17271    tcccaaagtgctgggattacaagtgtgagccacctcacctggccTTGAGTGAATGAATTC  17330
                || |||||||| ||||||||| |||||| |||||||||| |||||| | ||| |||||||
Sbjct  7441372  TCTCAAAGTGCAGGGATTACAGGTGTGACCCACCTCACCCGGCCTTTAATGAGTGAATTC  7441313

Query  17331    TTGATTTCCAGTCTATCCCTAACTCTGTCAATTTCTTAATTCATGAAATGATTATGCATA  17390
                ||||||||||  |||| |||||| ||||||||||||| ||||||||| | | |||| |||
Sbjct  7441312  TTGATTTCCAACCTATTCCTAACACTGTCAATTTCTTGATTCATGAACTTAATATGGATA  7441253

Query  17391    TG-TGATATGAATGGATATCTCG-TTCAATCCATTAGTCTTCGGACAGTCAAAAACCCAA  17448
                 | ||||||||||| |||||| | ||||||||| || |||  |||||| |||||||||||
Sbjct  7441252  -GCTGATATGAATGAATATCT-GATTCAATCCAGTAATCTGGGGACAGCCAAAAACCCAA  7441195

Query  17449    TCAGGATTAACTGAGTGGAGCTTCAGAAATGCAATCAGATATCGCTTTTTGATTGGAAGC  17508
                ||| ||||||||| ||||||||||||||||||||||||||| | ||||||||||||||||
Sbjct  7441194  TCAAGATTAACTGGGTGGAGCTTCAGAAATGCAATCAGATAGCACTTTTTGATTGGAAGC  7441135

Query  17509    TAGCAGC-GGATACGTGGAGGGGCGTGGGTGGGAGTTGTGATTAGAAAGGTCAATAAAAG  17567
                 |||| | |||||| |||||||| ||||||||||||||||||||||||| ||||||||||
Sbjct  7441134  AAGCA-CTGGATACATGGAGGGGTGTGGGTGGGAGTTGTGATTAGAAAGATCAATAAAAG  7441076

Query  17568    CTTCTAAAGACCCACAGGACAAACTCAAAGTCTTCAAGCCTGGAGTTCCTGCTTGGCTCT  17627
                 |||| ||||||||||||| | || ||||||||||||| ||||||||||||||||| |||
Sbjct  7441075  TTTCTGAAGACCCACAGGAGAGACCCAAAGTCTTCAAGTCTGGAGTTCCTGCTTGGTTCT  7441016

Query  17628    TCCTGAGGTCTGAGCAC-CTTCTAAACTACAA-CCAGATCTGGTAAGTCACTAATTTCTG  17685
                ||||||||||| ||||  || | ||||| ||  |||||||| |||||||||| |||||||
Sbjct  7441015  TCCTGAGGTCTAAGCATGCTGC-AAACT-CAGTCCAGATCTAGTAAGTCACTCATTTCTG  7440958

Query  17686    TAAGGACACTCCCATGTGACCTACAGTCAGCCGGTCTAGAAC-GGTGACAGTGCAGCCTA  17744
                 |||||||||||||| ||||||| |||||| |||||| | || || ||||||||||||||
Sbjct  7440957  GAAGGACACTCCCATCTGACCTATAGTCAGTCGGTCTGGGACAGG-GACAGTGCAGCCTA  7440899

Query  17745    CGATGGCATAGAA-CTATATCATGTCtttttttctttttttcatatgaacactttgaagc  17803
                 |||||||   || ||||||| |||||||| |  | | |   ||||||||| ||||||| 
Sbjct  7440898  TGATGGCACC-AAGCTATATC-TGTCTTTTATA-TATAT---ATATGAACAATTTGAAGA  7440845

Query  17804    tttgatttttttt-tCTAAATGCAATTTTGTCGTGATTTCAAAAATGTTG--TTGTGCTT  17860
                ||||| ||||||  |||| ||||| ||||||| | ||||||||||  |||  ||||||||
Sbjct  7440844  TTTGAATTTTTTCCTCTATATGCAGTTTTGTCTTTATTTCAAAAAA-TTGGATTGTGCTT  7440786

Query  17861    TTCTTTACATCATTTCAGAATTCTTG  17886
                |  ||||  |||||||| ||||||||
Sbjct  7440785  TGGTTTATGTCATTTCAAAATTCTTG  7440760


 Score = 2946 bits (1595),  Expect = 0.0
 Identities = 2368/2730 (86%), Gaps = 97/2730 (3%)
 Strand=Plus/Minus

Query  15201    gggaatgggactcctcctatcaatt-ttttttt-aattttcttttgttttattgacctgg  15258
                |||||||||| |||||||||||||| ||||||| ||||||||||||||||||||||||| 
Sbjct  7431035  GGGAATGGGATTCCTCCTATCAATTCTTTTTTTAAATTTTCTTTTGTTTTATTGACCTGA  7430976

Query  15259    caaggctcaaatagagttgagtttttgtttttgtttttcccattggaaggtacaagacag  15318
                |||||||||||||||||||||||||||||||||||||| ||||||||||| |||| ||||
Sbjct  7430975  CAAGGCTCAAATAGAGTTGAGTTTTTGTTTTTGTTTTTTCCATTGGAAGGGACAATACAG  7430916

Query  15319    aggttacaatcgttagctttagatgacaac-ataacaggctaaaacattttccttgcaag  15377
                ||||||||||| || |||||||||||| || |||| ||  |||||||| |||||||||||
Sbjct  7430915  AGGTTACAATCATTGGCTTTAGATGAC-ACGATAAAAGAATAAAACATATTCCTTGCAAG  7430857

Query  15378    acaaccagcatgacttcatgatcagaataaaatcagtgtccttctcactgtcagcgggt-  15436
                ||||||||||  ||||||||||||| || ||||||||| ||||||||||||||| |||| 
Sbjct  7430856  ACAACCAGCAAAACTTCATGATCAGCATCAAATCAGTG-CCTTCTCACTGTCAGTGGGTG  7430798

Query  15437    gaagacttcatcagtacttgtagagtttgaggtactcatgaactcatgatcagattcttt  15496
                |||| |||||||| |||||||||||||||| | |||||||||||||  |||||| |||||
Sbjct  7430797  GAAGCCTTCATCAATACTTGTAGAGTTTGAAGCACTCATGAACTCACAATCAGACTCTTT  7430738

Query  15497    actcagggacaggatgtaagccaatgc-taagaccttctataggtggct-aatttttaag  15554
                ||||||||||||||||||||||||| |  ||||||||| | |||||| | |||||   ||
Sbjct  7430737  ACTCAGGGACAGGATGTAAGCCAAT-CGAAAGACCTTCCACAGGTGG-TGAATTTGGGAG  7430680

Query  15555    cttgccccaatgagaccttcaggttttcaCTGGCAATATGCAGGTGCAGATATGACAAAG  15614
                | || ||||||| ||||| || ||||||||||||||||||||||||||||||||||||||
Sbjct  7430679  CCTG-CCCAATGTGACCTGCAAGTTTTCACTGGCAATATGCAGGTGCAGATATGACAAAG  7430621

Query  15615    AATAACAATGACCTTCATATCACCTCCAGCTGTTGAGGAATGGGATCCTTTTCACCCTTC  15674
                |||||| |||||||| | |||||| ||||||||||||||||||||||||||| |||||| 
Sbjct  7430620  AATAACCATGACCTTTACATCACCCCCAGCTGTTGAGGAATGGGATCCTTTTGACCCTTT  7430561

Query  15675    CTGTCCATAAAACCAAGTTACTCATCTTCAGTGGCAACAAAATATATGGTAAACTTAACA  15734
                ||||||||| ||||| |||||||||||| |||||||||||||||||||||  ||||||||
Sbjct  7430560  CTGTCCATAGAACCATGTTACTCATCTTGAGTGGCAACAAAATATATGGTCTACTTAACA  7430501

Query  15735    GAGAAGGAGACTGTCAGaaaaaaaaaaaaaaaagatgtgtttatcctgaaatgaggaaag  15794
                |||||| ||||  || |        |||||||| |  |||||||  |||| | || ||||
Sbjct  7430500  GAGAAGAAGAC--TCTG-------TAAAAAAAA-A--TGTTTATTATGAAGTAAGCAAAG  7430453

Query  15795    caa-tgggaatagatgtgagattattttgggagaaaaaggaagacaaaggttttgaaagg  15853
                 || ||| |||||||| |||||||||| |||||| ||||||||   ||||||||||||||
Sbjct  7430452  -AAGTGGCAATAGATGCGAGATTATTTGGGGAGATAAAGGAAGTTGAAGGTTTTGAAAGG  7430394

Query  15854    aaaaataaggaggattatacaaattgttttgaaagactca-accttggtcctaagaatca  15912
                |||||||||||||||||||||||||||||||||||||||| | ||||||| |||| || |
Sbjct  7430393  AAAAATAAGGAGGATTATACAAATTGTTTTGAAAGACTCATA-CTTGGTCATAAGGATTA  7430335

Query  15913    aaagtaaaggggcatcagtgaaatgttggatagATTCCACCTCCACCCCCTCAGTAACCC  15972
                |||  ||| ||||||||||| |||||| |||||||||| | | ||||| |||| ||||||
Sbjct  7430334  AAACCAAAAGGGCATCAGTGCAATGTTAGATAGATTCCTCTTACACCCACTCAATAACCC  7430275

Query  15973    CCAACATGTTTACCAAGTCTTGGTTAACTCCCAGGATCCCATTAAAACACCCAGCTCAAC  16032
                |||||||||| | ||||||||| || ||||||||| ||||||||||| ||||||||||||
Sbjct  7430274  CCAACATGTTCAGCAAGTCTTGCTTCACTCCCAGGTTCCCATTAAAA-ACCCAGCTCAAC  7430216

Query  16033    CATGCCCATCCTCTACCCTCACTTCTC-TTTGTAATTTTGACATGATTTTAttacaggac  16091
                | || |||  ||| ||||||||||| | |||||||||||||||||| |||||||||||||
Sbjct  7430215  CCTGACCA-GCTCCACCCTCACTTC-CATTTGTAATTTTGACATGACTTTATTACAGGAC  7430158

Query  16092    catcaggttcctatgcctgctgcacagtagctgaccaatattctgagacagcagtgtttg  16151
                |||||||||||||||||||||||||||||||| | ||||||||||||||||||| |||||
Sbjct  7430157  CATCAGGTTCCTATGCCTGCTGCACAGTAGCTTAGCAATATTCTGAGACAGCAGGGTTTG  7430098

Query  16152    cagcagacagtttaatgatcacagggtggctaaatgagaagctaggaggatatcctcaaa  16211
                ||||||| ||||||||||||||| ||||||| |||||||||||||||||| |||||||||
Sbjct  7430097  CAGCAGAGAGTTTAATGATCACAAGGTGGCTGAATGAGAAGCTAGGAGGAGATCCTCAAA  7430038

Query  16212    ttcatctccccaagtagtactgagggtttccagtggatcctggatagcaaggggctggaa  16271
                |||||||||||||| |||||||| ||||||||||||||||||||||||||||||| ||||
Sbjct  7430037  TTCATCTCCCCAAGGAGTACTGAAGGTTTCCAGTGGATCCTGGATAGCAAGGGGCCGGAA  7429978

Query  16272    agttggtgtagaggtaagagggatgaagtcatcaggatgtca-aaactgcattctttggt  16330
                |||||| |||| ||||||||||| ||||||| |||||||| | |||||||||||||||||
Sbjct  7429977  AGTTGGGGTAGCGGTAAGAGGGAAGAAGTCAACAGGATGT-AGAAACTGCATTCTTTGGT  7429919

Query  16331    gagttggtgccttgca-gagcccttcagatcagctggcatcagtagtttcactgacatgc  16389
                |||||||||| ||||| | |||||||||||||||||||||||| ||||||||||||||||
Sbjct  7429918  GAGTTGGTGCATTGCATG-GCCCTTCAGATCAGCTGGCATCAGCAGTTTCACTGACATGC  7429860

Query  16390    agaacctgaaagaatatctcaaatgagaaagttaatgttttacaaggcttaaattgttgt  16449
                ||||||||||||||||||||| |||| ||| |||||||||||||| |||| ||| |||||
Sbjct  7429859  AGAACCTGAAAGAATATCTCAGATGAAAAAATTAATGTTTTACAATGCTTGAATCGTTGT  7429800

Query  16450    ctgcagggtagttaaggggaactgtaagctaaggtctact-tgatttggggacagtaagc  16508
                |||||||| |||||||||||||||||| |||||||||| | |||||| || |||||| ||
Sbjct  7429799  CTGCAGGGAAGTTAAGGGGAACTGTAATCTAAGGTCTA-TATGATTTTGGAACAGTAGGC  7429741

Query  16509    tgccagcaaccatgaggaagaaggtcagagagcaagctgacctcatggtgaatgctgaat  16568
                |||||||||||| ||||||  |||||||||||||||  |||||| || |||| |||||||
Sbjct  7429740  TGCCAGCAACCACGAGGAACCAGGTCAGAGAGCAAGAAGACCTCCTGATGAAGGCTGAAT  7429681

Query  16569    gcgctgcaagcttggtttatttttgtttctccccctcccttcttcactgattaaacttat  16628
                | | ||||||||| ||||||||||||||||| ||||||||||||||||||||||| ||||
Sbjct  7429680  GTGTTGCAAGCTTCGTTTATTTTTGTTTCTCTCCCTCCCTTCTTCACTGATTAAATTTAT  7429621

Query  16629    aaagtttacaggtatcatttcaATTTCTTCCAGAGAAGACTTAACCTAAGCCCTGAGACC  16688
                ||| |||| || | |  ||||||||||||||| ||||| |||||||||||||||||||||
Sbjct  7429620  AAACTTTAGAGATGTGGTTTCAATTTCTTCCAAAGAAGCCTTAACCTAAGCCCTGAGACC  7429561

Query  16689    ACTCAAGCCCTCAGTGGCACCTCTCTTCCACCAGCACGAGTGAAG-AAACTGCTACCTTA  16747
                ||||| ||||||||||||||||||| |||||||| |||||  | | || |||||||||||
Sbjct  7429560  ACTCACGCCCTCAGTGGCACCTCTCCTCCACCAGAACGAG-CATGTAATCTGCTACCTTA  7429502

Query  16748    GGTGATATAAAA-CCCACAAGACCATTCCATACATGGAGATCTTTATTCTTATTTTGTAG  16806
                ||| | | |||| |||| || ||||||| |||||| ||||| |||||||| |||| ||||
Sbjct  7429501  GGTTACACAAAATCCCA-AAAACCATTCAATACATTGAGATTTTTATTCTGATTTCGTAG  7429443

Query  16807    GGACGACTCCTCTGTGTTTATACAGCTATTTT-AACTAGAAATATTTTTATAAATTTTAT  16865
                ||| ||||||||||| |||||| |||| |||| || ||| || |     ||   ||||||
Sbjct  7429442  GGATGACTCCTCTGTTTTTATAAAGCT-TTTTAAAGTAG-AA-A---GCAT---TTTTAT  7429392

Query  16866    AATTTTGATGTGGCCAAAGATCTCCCCACAACACTACTTTCAGGTTTTATTTTTCTGTCT  16925
                 ||||||||||||||||||||||||  |||||||||||||||| ||||||||||||||||
Sbjct  7429391  -ATTTTGATGTGGCCAAAGATCTCCTAACAACACTACTTTCAGATTTTATTTTTCTGTCT  7429333

Query  16926    AATGTCTGGAACAGATCAACCCCTTCCCTGCCTCACA-TCAGGACT-TGAAG-GCGAAAT  16982
                |||||| | ||||||||||  || ||||||||||||| ||| |||| |||||  | | ||
Sbjct  7429332  AATGTC-GTAACAGATCAAATCCGTCCCTGCCTCACACTCAAGACTATGAAGTTC-ACAT  7429275

Query  16983    AGCAGTAAAATTCCATCAGTGTTTGTGGATTTCATGAATGAATGCA-----tt-tttttt  17036
                |  |||||||| ||||||||||||||||| |||||||||||||| |     || ||||||
Sbjct  7429274  ATTAGTAAAATGCCATCAGTGTTTGTGGAGTTCATGAATGAATG-ATTTTTTTATTTTTT  7429216

Query  17037    gacaaaatctccctctgtcacccagtcaggagggcaatggtgtaa-tcttggctcactgc  17095
                |||| |||||||||||||||||||| | |||| ||| |||   || || |||||||||||
Sbjct  7429215  GACAGAATCTCCCTCTGTCACCCAGACTGGAGTGCAGTGGCACAATTC-TGGCTCACTGC  7429157

Query  17096    aaactca--gcctccagggttcaagggattctcccacctcag-c-cgcatgagtaactgg  17151
                 ||| ||  |||||| |||||||||  |||||||  |||||| | | |||  ||| ||||
Sbjct  7429156  -AAC-CATTGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCAT--GTAGCTGG  7429101

Query  17152    actacaggcagcc-accatcgtgcctggct-a-------acttttctatttttgtagaga  17202
                  | ||||  |||  ||||| ||||  ||| |       | |||| ||||||||||||||
Sbjct  7429100  GTTTCAGG-TGCCTGCCATCATGCCCAGCTAATTTTTGTATTTTTGTATTTTTGTAGAGA  7429042

Query  17203    cagggtttcaccatgtgggccaggctggtcttgaactcctgacctcaggtgatccacct-  17261
                |||||||||||| | | | || |||| ||||||||| |||||| |||||||||| | || 
Sbjct  7429041  CAGGGTTTCACCTTTTTGACCTGGCTCGTCTTGAACCCCTGACATCAGGTGATCTA-CTC  7428983

Query  17262    accttggcctcccaaagtgctgggattacaag-tgtgagccacctcacctggccTTGAGT  17320
                |||||| ||| |||||||||||| ||||| || | ||||||||||||||   |||||| |
Sbjct  7428982  ACCTTGTCCTTCCAAAGTGCTGGAATTAC-AGCTATGAGCCACCTCACCCACCCTTGAAT  7428924

Query  17321    GAATGAATTCTTGATTTCCAGTCTATCCCTAACTCTGTCAATTTCTTAATTCATGAAATG  17380
                ||||| |||||||| ||| |  ||||||||||| |||||||||||||  |||| ||| ||
Sbjct  7428923  GAATGTATTCTTGACTTCTACCCTATCCCTAACACTGTCAATTTCTTGCTTCACGAACTG  7428864

Query  17381    ATTAT-GCATATGTGATATGAATGGATATCTCG-TTCAATCCATTAGTCTTCGGACAGTC  17438
                | ||| | |||||||||||||| |||||||| |  ||||||||||| |||  ||| || |
Sbjct  7428863  AATATAG-ATATGTGATATGAACGGATATCT-GACTCAATCCATTAATCTGGGGAGAGCC  7428806

Query  17439    AAAAACCCAATCAGGATTAACTGAGTGGAGCTTCAGAAATGCAATCAGATATCGCTTTTT  17498
                ||||||||||||||||||||||| ||||||||||| |||||||||||||||| |||||||
Sbjct  7428805  AAAAACCCAATCAGGATTAACTGGGTGGAGCTTCACAAATGCAATCAGATATTGCTTTTT  7428746

Query  17499    GATTGGAAGCTAGCAGCGGATACGTGGAGGGGCGTGGGTGGGAGTTGTGATTAGAAAGGT  17558
                |||||||||||||||| | | ||||||| |||| ||||||||||||||||||||||||||
Sbjct  7428745  GATTGGAAGCTAGCAGTGCAAACGTGGAAGGGCATGGGTGGGAGTTGTGATTAGAAAGGT  7428686

Query  17559    CAATAAAAGCTTCTAAAGACCCACAGGACAAACTCAAAGTCTTCAAGCCTGGAGTTCCTG  17618
                |||||||| ||||||||||||||||||| | || ||||||||||||||||||||||||||
Sbjct  7428685  CAATAAAATCTTCTAAAGACCCACAGGAGAGACCCAAAGTCTTCAAGCCTGGAGTTCCTG  7428626

Query  17619    CTTGGCTCTTCCTGAGGTCTGAGCACCTTCTAAACTACAACCAGATCTGGTAAGTCACTA  17678
                ||||| |||||||||||||||||||||||||| |||||| ||||||||||||||||||||
Sbjct  7428625  CTTGGTTCTTCCTGAGGTCTGAGCACCTTCTAGACTACATCCAGATCTGGTAAGTCACTA  7428566

Query  17679    ATTTCTGTAAGGACACTCCCATGTGACCTACAGTCAGCCGGTCTAGAACGGTGACAGTGC  17738
                |||||||||||||||||||||| |||||||||||||| | |||| | | |||||||||||
Sbjct  7428565  ATTTCTGTAAGGACACTCCCATCTGACCTACAGTCAGTCAGTCTGGGATGGTGACAGTGC  7428506

Query  17739    AGCCTACGATGGCATAGAACTATATCATGTCtttttttctttttttcatatgaacacttt  17798
                |||||||||||||| ||| ||||||| |||| |||||| ||| |  |||||||||| |||
Sbjct  7428505  AGCCTACGATGGCACAGAGCTATATCCTGTCCTTTTTT-TTTCT--CATATGAACAATTT  7428449

Query  17799    gaagctttgatttttttt-tCTAAATGCAATTTTGTCGTGATTTCAAAAATGTTG-TTGT  17856
                |||||||||| ||||||  |||||||||| || |||| | |||||||||| |||| ||||
Sbjct  7428448  GAAGCTTTGAATTTTTTCCTCTAAATGCAGTTCTGTCTTTATTTCAAAAAAGTTGATTGT  7428389

Query  17857    GCTTTTCTTTACATCATTTCAGAATTCTTG  17886
                |||||  || |  |||||||| ||||||||
Sbjct  7428388  GCTTTGGTTGATGTCATTTCAAAATTCTTG  7428359


 Score = 2915 bits (1578),  Expect = 0.0
 Identities = 2346/2705 (86%), Gaps = 99/2705 (3%)
 Strand=Plus/Minus

Query  15201    gggaatgggactcctcctatcaatt-ttttttt-aattttcttttgttttattgacctgg  15258
                ||||||||||||||||||||||||| ||||||| ||||||||||||||||||||||||| 
Sbjct  7547168  GGGAATGGGACTCCTCCTATCAATTATTTTTTTAAATTTTCTTTTGTTTTATTGACCTGA  7547109

Query  15259    caaggctcaaatagagttgagtttttgtttttgtttttcccattggaag-gtacaagaca  15317
                ||||||||||||||||||||||||||||||| |||||| |||||||||| | |||| |||
Sbjct  7547108  CAAGGCTCAAATAGAGTTGAGTTTTTGTTTTCGTTTTTTCCATTGGAAGAG-ACAATACA  7547050

Query  15318    gaggttacaatcgttagctttagatgacaacataacaggctaaaacattttccttgcaag  15377
                |||||||||||| || |||||||||||||| |||| ||  |||||||| |||||||||||
Sbjct  7547049  GAGGTTACAATCATTGGCTTTAGATGACAAGATAAAAGAATAAAACATATTCCTTGCAAG  7546990

Query  15378    acaaccagcatgacttcatgatcagaataaaatcagtgtccttctcactgtcagcgggt-  15436
                ||||||||||  |||||||||||||||  ||||||||| ||||||||||||||| |||| 
Sbjct  7546989  ACAACCAGCAAAACTTCATGATCAGAAGCAAATCAGTG-CCTTCTCACTGTCAGTGGGTG  7546931

Query  15437    gaagacttcatcagtacttgtagagtttgaggtactcatgaactcatgatcagattcttt  15496
                |||| |||||||| |||||| ||||||||||| |||||||||||||  || |||||||||
Sbjct  7546930  GAAGCCTTCATCAATACTTGCAGAGTTTGAGGCACTCATGAACTCACCATGAGATTCTTT  7546871

Query  15497    actcagggacaggatgtaagccaatgc-taagaccttctataggtggct-aatttttaag  15554
                |||||||||||||||||||||||| ||  ||||||||| | |||||| | |||||  |||
Sbjct  7546870  ACTCAGGGACAGGATGTAAGCCAA-GCAAAAGACCTTCCACAGGTGG-TGAATTTGGAAG  7546813

Query  15555    cttgccccaatg-agaccttcaggttttcaCTGGCAATATGCAGGTGCAGATATGACAAA  15613
                | || ||||||| | |||| || |||||||||||||||||||||||||||||||||||||
Sbjct  7546812  CCTG-CCCAATGTA-ACCTGCAAGTTTTCACTGGCAATATGCAGGTGCAGATATGACAAA  7546755

Query  15614    GAATAACAATGACCTTCATATCACCTCCAGCTGTTGAGGAATGGGATCCTTTTCACCCTT  15673
                ||||||| |||||||| | |||||| ||||||||||||||||||||||||||| ||||||
Sbjct  7546754  GAATAACCATGACCTTTACATCACCCCCAGCTGTTGAGGAATGGGATCCTTTTGACCCTT  7546695

Query  15674    CCTGTCCATAAAACCAAGTTACTCATCTTCAGTGGCAACAAAATATATGGTAAACTTAAC  15733
                 ||||||||| ||||| ||| ||||||||  |||||||||| |||| ||||  |||||||
Sbjct  7546694  TCTGTCCATAGAACCAGGTTGCTCATCTTGTGTGGCAACAACATATGTGGTCTACTTAAC  7546635

Query  15734    AGAGAAGGAGACTGTCAGaaaaaaaaaaaaaaaagatgtgtttatcctgaaatgaggaaa  15793
                ||||||| ||||  || |         ||||||| |  |||||||  || | | || |||
Sbjct  7546634  AGAGAAGAAGAC--TCTG--------TAAAAAAA-A--TGTTTATTATGTAGTAAGCAAA  7546588

Query  15794    gcaatgggaatagatgtgagattattttgggagaaaaaggaagacaaaggttttgaaagg  15853
                | ||||||||||||||||||||||||| |||||| ||||||||   ||||||||||||||
Sbjct  7546587  GAAATGGGAATAGATGTGAGATTATTTGGGGAGATAAAGGAAGTTGAAGGTTTTGAAAGG  7546528

Query  15854    aaaaataaggaggattatacaaattgttttgaaagactca-accttggtcctaagaatca  15912
                |||||||||||||||||||||||||||||||||||||||| | ||||||| | || || |
Sbjct  7546527  AAAAATAAGGAGGATTATACAAATTGTTTTGAAAGACTCATA-CTTGGTCATGAGGATTA  7546469

Query  15913    aaagtaaaggggcatcagtgaaatgttggatagATTCCACCTCCACCCCCTCAG-TAACC  15971
                |||  ||| ||||||||||| |||||| |||||||||| | | ||||| ||| | |||||
Sbjct  7546468  AAACCAAAAGGGCATCAGTGCAATGTTAGATAGATTCCTCTTACACCCACTC-GATAACC  7546410

Query  15972    CCCAACATGTTTACCAAGTCTTGGTTAACTCCCAGGATCCCATTAAAACACCCAGCTCAA  16031
                ||||||||||| | |||||||||||| ||||||||| ||||||||||| |||||||||||
Sbjct  7546409  CCCAACATGTTCAGCAAGTCTTGGTTCACTCCCAGGTTCCCATTAAAA-ACCCAGCTCAA  7546351

Query  16032    CCATGCCCATCCTCTACCCTCACTTCTC-TTTGTAATTTTGACATGATTTTAttacagga  16090
                || || |||  ||| ||||||||||| | |||||||||||||||||| ||||||||||||
Sbjct  7546350  CCCTGACCA-GCTCCACCCTCACTTC-CATTTGTAATTTTGACATGACTTTATTACAGGA  7546293

Query  16091    ccatcaggttcctatgcctgctgcacagtagctgaccaatattctgagacagcagtgttt  16150
                ||||||||||||||||||||||||||||||||| | ||||||||||||||||||| ||||
Sbjct  7546292  CCATCAGGTTCCTATGCCTGCTGCACAGTAGCTTAGCAATATTCTGAGACAGCAGGGTTT  7546233

Query  16151    gcagcagacagtttaatgatcacagggtggctaaatgagaagctaggaggatatcctcaa  16210
                |||||||| ||||||||||||||| ||||||| |||||||||||||||||| ||||||||
Sbjct  7546232  GCAGCAGAGAGTTTAATGATCACAAGGTGGCTGAATGAGAAGCTAGGAGGAGATCCTCAA  7546173

Query  16211    attcatctccccaagtagtactgagggtttccagtggatcctggatagcaaggggctgga  16270
                ||||||||||||||| |||||||||||||||||||||||||||||||||||||||| |||
Sbjct  7546172  ATTCATCTCCCCAAGGAGTACTGAGGGTTTCCAGTGGATCCTGGATAGCAAGGGGCCGGA  7546113

Query  16271    aagttggtgtagaggtaagagggatgaagtcatcaggatgtca-aaactgcattctttgg  16329
                ||||||| |||| ||||||||||| ||||||| |||||||| | ||||||||||||||||
Sbjct  7546112  AAGTTGGGGTAGCGGTAAGAGGGAAGAAGTCAACAGGATGT-AGAAACTGCATTCTTTGG  7546054

Query  16330    tgagttggtgccttgcagagcccttcagatcagctggcatcagtagtttcactgacatgc  16389
                ||||||||||| |||||| ||||||||||||||||||||||||||| |||||||||||||
Sbjct  7546053  TGAGTTGGTGCATTGCAGGGCCCTTCAGATCAGCTGGCATCAGTAGATTCACTGACATGC  7545994

Query  16390    agaacctgaaagaatatctcaaatgagaaagttaatgttttacaaggcttaaattgttgt  16449
                ||||||||||||||||||||| |||| |||||||||||||||||| |||||||| |||||
Sbjct  7545993  AGAACCTGAAAGAATATCTCAGATGAAAAAGTTAATGTTTTACAATGCTTAAATGGTTGT  7545934

Query  16450    ctgcagggtagttaaggggaactgtaagctaaggtctact-tgatttggggacagtaagc  16508
                |||||||| |||||||||||||||||| |||||||||| | |||||| || |||||| | 
Sbjct  7545933  CTGCAGGGAAGTTAAGGGGAACTGTAATCTAAGGTCTA-TATGATTTTGGAACAGTAGGT  7545875

Query  16509    tgccagcaaccatgaggaagaaggtcagagagcaagctgacctcatggtgaatgctgaat  16568
                |||||||||||||||||||  |||||||||||||||  |||||| || ||||||||||||
Sbjct  7545874  TGCCAGCAACCATGAGGAACCAGGTCAGAGAGCAAGAAGACCTCCTGATGAATGCTGAAT  7545815

Query  16569    gcgctgcaagcttggtttatttttgtttctccccctcccttcttcactgattaaacttat  16628
                | | | ||||||||||||||||||||||||| ||||||||||||||||||||||| ||||
Sbjct  7545814  GTGTTCCAAGCTTGGTTTATTTTTGTTTCTCTCCCTCCCTTCTTCACTGATTAAATTTAT  7545755

Query  16629    aaagttta-caggtatcatttcaATTTCTTCCAGAGAAGACTTAACCTAAGCCCTGAGAC  16687
                |||||||| | | | |   |||||||||||||| ||||||||||||||||||||||||||
Sbjct  7545754  AAAGTTTATC-GATGTGGCTTCAATTTCTTCCAAAGAAGACTTAACCTAAGCCCTGAGAC  7545696

Query  16688    CACTCAAGCCCTCAGTGGCACCTCTCTTCCACCAGCACGAGTGAAGAAA-CTGCTACCTT  16746
                |||||| ||||||||||||||||||| |||||||| |||||  | | || ||||||||||
Sbjct  7545695  CACTCACGCCCTCAGTGGCACCTCTCCTCCACCAGAACGAGC-ATGTAATCTGCTACCTT  7545637

Query  16747    AGGTGATATAAAA-CCCACAAGACCATTCCATACATGGAGATCTTTATTCTTATTTTGTA  16805
                |||| ||| |||| |||  |||||||||| |||| | ||||| |||||||| ||||  ||
Sbjct  7545636  AGGTTATACAAAATCCCG-AAGACCATTCAATACGTTGAGATTTTTATTCTGATTTCCTA  7545578

Query  16806    GGGACGACTCCTCTGTGTTTATACAGCTATTTTAAC-TAGAAATATTTTTATAAATTTTA  16864
                |||||||||||||||| |||||| |||| ||||||  ||||||       ||   |||||
Sbjct  7545577  GGGACGACTCCTCTGTTTTTATAAAGCT-TTTTAAAGTAGAAAGC-----AT---TTTTA  7545527

Query  16865    TAATTTTGATGTGGCCAAAGATCTCCCCACAACACTACTTTCAGGTTTTATTTTTCTGTC  16924
                || ||||||||||||||||||| |||  |||||||||||||||| |||||||||||||||
Sbjct  7545526  TA-TTTTGATGTGGCCAAAGATTTCCTAACAACACTACTTTCAGATTTTATTTTTCTGTC  7545468

Query  16925    TAATGTCTGG-AACAGATCAACCCCTTCCCTGCCT--CACATCAGGACT-TGAAGG-CGA  16979
                |||||| ||| ||||||||||  ||||||||||||  ||| ||| |||| |||||  | |
Sbjct  7545467  TAATGT-TGGGAACAGATCAAATCCTTCCCTGCCTGTCAC-TCAAGACTATGAAGTTC-A  7545411

Query  16980    AATAGCAGTAAAATTCCATCAGTGTTTGTGGATTTCATGAATGAATGCAttttttt-t--  17036
                 |||  |||||||| ||||||||||||||||| |||||||||||||| |||||||| |  
Sbjct  7545410  CATATTAGTAAAATACCATCAGTGTTTGTGGAGTTCATGAATGAATG-ATTTTTTTATTT  7545352

Query  17037    ---gacaaaatctccctctgtcacccagtcaggagggcaatggtgtaat-cttggctcac  17092
                   |||| ||| |||||||||||||||| | |||| ||| |||   ||| || |||||||
Sbjct  7545351  TTTGACAGAATGTCCCTCTGTCACCCAGACTGGAGTGCAGTGGCACAATTCT-GGCTCAC  7545293

Query  17093    tgcaaac-tcagcctccagggttcaagggattctcccacctcagccgcatgagtaactgg  17151
                ||||| | |  |||||| |||||||||  |||||||  |||||||| |   |||| ||||
Sbjct  7545292  TGCAACCATT-GCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCAAGTAGCTGG  7545234

Query  17152    actacaggcagcca-ccatcgtgcctggctaacttttctatttttgta-----g-aga--  17202
                  | |||||| ||  ||||| ||||  ||||| |||| ||||||||||     | |||  
Sbjct  7545233  GTTTCAGGCA-CCTGCCATCATGCCCAGCTAATTTTTGTATTTTTGTATTTTTGTAGAGA  7545175

Query  17203    cagggtttcaccatgtgggccaggctggtcttgaactcctgacctcaggtgatccac-ct  17261
                |||||||||||| | | | || |||| ||||||||| |||||| |||||||||| || | 
Sbjct  7545174  CAGGGTTTCACCTTTTTGACCTGGCTCGTCTTGAACCCCTGACATCAGGTGATCTACTC-  7545116

Query  17262    accttggcctcccaaagtgctgggattacaag-tgtgagccacctcacctggccTTGAGT  17320
                |||||| ||| |||||||||||| |||||| | | ||| ||||||||||   |||||| |
Sbjct  7545115  ACCTTGTCCTTCCAAAGTGCTGGAATTACA-GCTATGAACCACCTCACCCACCCTTGAAT  7545057

Query  17321    GAATGAATTCTTGATTTCCAGTCTATCCCTAACTCTGTCAATTTCTTAATTCATGAAATG  17380
                ||||| |||||||| ||| |  ||||||||||| ||||| |||||||  |||||||| ||
Sbjct  7545056  GAATGTATTCTTGACTTCTACCCTATCCCTAACACTGTCGATTTCTTGCTTCATGAAGTG  7544997

Query  17381    ATTAT-GCATATGTGATATGAATGGATATCTCG-TTCAATCCATTAGTCTTCGGACAGTC  17438
                | ||| | |||||||||||||||||| |||| | ||||||||  || |||  ||| || |
Sbjct  7544996  AATATAG-ATATGTGATATGAATGGACATCT-GATTCAATCCGGTAATCTGGGGAGAGCC  7544939

Query  17439    AAAAACCCAATCAGGATTAACTGAGTGGAGCTTCAGAAATGCAATCAGATATCGCTTTTT  17498
                ||||||||||||||||||||||| ||||||||||| |||||||||||||||||  |||||
Sbjct  7544938  AAAAACCCAATCAGGATTAACTGGGTGGAGCTTCACAAATGCAATCAGATATCATTTTTT  7544879

Query  17499    GATTGGAAGCTAGCAGCGGATACGTGGAGGGGCGTGGGTGGGAGTTGTGATTAGAAAGGT  17558
                ||||||||| |||||||||||| ||| |||||||||||||||||||||||||||||||||
Sbjct  7544878  GATTGGAAGGTAGCAGCGGATATGTGCAGGGGCGTGGGTGGGAGTTGTGATTAGAAAGGT  7544819

Query  17559    CAATAAAAGCTTCTAAAGACCCACAGGACAAACTCAAAGTCTTCAAGCCTGGAGTTCCTG  17618
                |||||||||||||||||||||||||||| | || ||||||||||||||||||||||||||
Sbjct  7544818  CAATAAAAGCTTCTAAAGACCCACAGGAGAGACCCAAAGTCTTCAAGCCTGGAGTTCCTG  7544759

Query  17619    CTTGGCTCTTCCTGAGGTCTGAGCACCTTCTAAACTACAACCAGATCTGGTAAGTCACTA  17678
                ||||| ||||||||||| |||||||||||||| |||||| |||||||||||||| |||||
Sbjct  7544758  CTTGGTTCTTCCTGAGGACTGAGCACCTTCTAGACTACATCCAGATCTGGTAAGCCACTA  7544699

Query  17679    ATTTCTGTAAGGACACTCCCATGTGACCTACAGTCAGCCGGTCTAGAACGGTGACAGTGC  17738
                |||||||||||||||||||||| |||||||||||||| |||||| | | |||||||||||
Sbjct  7544698  ATTTCTGTAAGGACACTCCCATCTGACCTACAGTCAGTCGGTCTGGGATGGTGACAGTGC  7544639

Query  17739    AGCCTACGATGGCATAGAACTATATCATGTCtttttttctttttttcatatgaacacttt  17798
                |||||||||||||| ||| ||||||| |||| |||||| ||||   |||||||||| |||
Sbjct  7544638  AGCCTACGATGGCACAGAGCTATATCCTGTCCTTTTTT-TTTT---CATATGAACAATTT  7544583

Query  17799    gaagctttgatttttttt-tCTAAATGCAATTTTGTCGTGATTTCAAAAATGTTG-TTGT  17856
                ||||||| || | ||||  |||||||||| || |||| | |||||||||| |||| ||||
Sbjct  7544582  GAAGCTT-GAATGTTTTCCTCTAAATGCAGTTCTGTCTTTATTTCAAAAAAGTTGATTGT  7544524

Query  17857    GCTTT  17861
                |||||
Sbjct  7544523  GCTTT  7544519


 Score = 2281 bits (1235),  Expect = 0.0
 Identities = 1786/2043 (87%), Gaps = 73/2043 (3%)
 Strand=Plus/Minus

Query  3254     TGGCAGAAACTTTCTCCAGCAGAGCTCCGAGGGGTTCAAGACTGATACAGAACTGCAGCA  3313
                |||||| || |||||| ||||||||||||||||||||||||||||| | |||| ||||||
Sbjct  7525071  TGGCAGCAATTTTCTCTAGCAGAGCTCCGAGGGGTTCAAGACTGATGCGGAACAGCAGCA  7525012

Query  3314     TGTAGCTGAGATTCAGATGCTTTGGGTAAGC-GAGGCTTGGGTACTG-GTAGAGACACTT  3371
                 |||||||||||||||||||||| ||| ||| ||||||||||||||| | | ||||||||
Sbjct  7525011  CGTAGCTGAGATTCAGATGCTTTAGGT-AGCTGAGGCTTGGGTACTGAG-ACAGACACTT  7524954

Query  3372     CAAGTCCTCTTCCAATAGGTAGCCGCAAGTTAATTCCAAGTTCTCCAAGGGGTTCTAGAG  3431
                || ||||||||||||||||||||| |||||||| |||||||||||||||||||||| |||
Sbjct  7524953  CATGTCCTCTTCCAATAGGTAGCCACAAGTTAACTCCAAGTTCTCCAAGGGGTTCTGGAG  7524894

Query  3432     GCACCTGTGGAGATCAAGAAGTTAGTTCTGGGCAATGGTACCAGTTAGATGAAGGTAGTG  3491
                |||||||||||||||||||||||||||||||||| || |||||||||||||||||| |||
Sbjct  7524893  GCACCTGTGGAGATCAAGAAGTTAGTTCTGGGCAGTGATACCAGTTAGATGAAGGTGGTG  7524834

Query  3492     GGGAATGAACT-CAAGGAAAATACCTGCTTCAACCAAACACAAGTTTGTTCCCACCATCT  3550
                |||||| ||||  |||| ||||  |||||||| |||||||||||||| |||||| ||| |
Sbjct  7524833  GGGAAT-AACTGAAAGGGAAATGTCTGCTTCACCCAAACACAAGTTTATTCCCATCATGT  7524775

Query  3551     GATGATGGTCCTCATGCAAGTTGCTGCATGT--TGAGGACCCTGATCATTCAGGGGCTGT  3608
                ||||||||||| ||||||||||||| | |||  ||||||| |||||||||||||||| ||
Sbjct  7524774  GATGATGGTCCACATGCAAGTTGCT-C-TGTGATGAGGACTCTGATCATTCAGGGGCAGT  7524717

Query  3609     CCCATTTTAGCCTCAGCCCTTTCACCATTTCTTGTGTGATTGGGTCAAGGCCACAAAAT-  3667
                || | ||||||||||  |||||||||||| ||||||||||||| ||||||||||||||| 
Sbjct  7524716  CCTAGTTTAGCCTCAATCCTTTCACCATTGCTTGTGTGATTGGTTCAAGGCCACAAAATC  7524657

Query  3668     -C-T--CTAAAGCCT-TTTATCTTCATCTTTTAGCAGAAAACCTCATCTCTGGGCCACAG  3722
                 | |  ||||||||| ||| |||||||||||||||||||||| |||||||||||||||||
Sbjct  7524656  ACATCACTAAAGCCTCTTT-TCTTCATCTTTTAGCAGAAAACTTCATCTCTGGGCCACAG  7524598

Query  3723     GTACCCGGTGGGAGATGTGCACAAAGAACTCAACTCAGCAAGGTCTAGGGACATTAGCTG  3782
                |||||||||||||||||||||  |||||||||||| |||||||||||||| ||| |||| 
Sbjct  7524597  GTACCCGGTGGGAGATGTGCATGAAGAACTCAACTGAGCAAGGTCTAGGGTCATCAGCTA  7524538

Query  3783     GGGCTACCTGCCGGCAGGGGCTCCCTGGCCTGCCTGCATCTGCAAACCAACTGTCACTTT  3842
                ||||||||| | ||||||||||||||| | ||||||||||||||||||| || |||||||
Sbjct  7524537  GGGCTACCTACTGGCAGGGGCTCCCTGACGTGCCTGCATCTGCAAACCACCTATCACTTT  7524478

Query  3843     TTACCACTCTCACTCCTACTCCTTCACCCTCCATCCCAGAAGCATGCATGTCCCATGTCA  3902
                ||||||||||||| |||||||| ||| ||||||| | |||||||  ||| ||||||||||
Sbjct  7524477  TTACCACTCTCACGCCTACTCCCTCAGCCTCCATTCAAGAAGCACACATTTCCCATGTCA  7524418

Query  3903     ATTGA-CTTTCCTGGAGTTCAAAACAACCTTCTACAGACAGGGAATCAGAGACAGGATCA  3961
                 || | ||||||||| ||||||||||||||| |||||||||||||| |||||||||||||
Sbjct  7524417  GTT-ACCTTTCCTGGGGTTCAAAACAACCTTTTACAGACAGGGAAT-AGAGACAGGATCA  7524360

Query  3962     TTCATGATCACTAAGCTGGTGAGGACAGAGCTTCTACTGTGAAATGCACAAGTTTGATGC  4021
                ||  |||||||||||||||||||||||||| ||||||||||||||||||| |||||||||
Sbjct  7524359  TTTGTGATCACTAAGCTGGTGAGGACAGAGTTTCTACTGTGAAATGCACAGGTTTGATGC  7524300

Query  4022     ACTGTCCCTCCTTTCATACCCTCCTTTGTTACCTCTTTTAC-ATCATATCAACTTGAAAC  4080
                 |||||||||||||||||||||||| | ||||||| ||| | ||||||||||||||||||
Sbjct  7524299  GCTGTCCCTCCTTTCATACCCTCCTCTATTACCTC-TTTCCTATCATATCAACTTGAAAC  7524241

Query  4081     ACACTTTGTAACAAGAAATTCACACGTGCA-CATGCAGTAGAGAC-AAAACGCCCACTAA  4138
                ||||||||||||||||||||||||  |||| |   |||||||| |  |||| ||||||| 
Sbjct  7524240  ACACTTTGTAACAAGAAATTCACATATGCACCCCCCAGTAGAG-CTGAAACCCCCACTAC  7524182

Query  4139     GTACCTTGTACATGATGTCCCTCTCTAGCCTCTACCCTAGGTGACCCCTCTGCCTTTATT  4198
                 |  ||||||||||||||  ||||||||||||||||| |||||||||| ||||| | |||
Sbjct  7524181  CTGGCTTGTACATGATGTAGCTCTCTAGCCTCTACCCCAGGTGACCCCGCTGCCCTCATT  7524122

Query  4199     GAAGTGATCCTGTGATAGCCACTCCAGGACATGGAGCACTGAACGGGACAATGTGTTGAC  4258
                | || |||||||||||||||||||||| ||||||||||||||| ||||||||||||||| 
Sbjct  7524121  GCAGAGATCCTGTGATAGCCACTCCAGAACATGGAGCACTGAATGGGACAATGTGTTGAT  7524062

Query  4259     ATTCTGGTGTCCCCTGCACTGTGCCGTCGCCACTGGCTGGCAC-ACAGTACACGTCTTCT  4317
                ||||||||||||||| |||||||  ||| |||||||||| ||| | |||  | | |||||
Sbjct  7524061  ATTCTGGTGTCCCCTTCACTGTGATGTCACCACTGGCTGACACAAAAGT-TATGCCTTCT  7524003

Query  4318     AGTGTTTACTGTAACaaaaaaaaaGGCTGCGCTGTGGTCTGCAGAGAAAGGGCACGATCC  4377
                || |||| |||||||  |||||||||||| |||||||||| ||||||||| |||||||||
Sbjct  7524002  AGCGTTTGCTGTAAC--AAAAAAAGGCTGTGCTGTGGTCTTCAGAGAAAGTGCACGATCC  7523945

Query  4378     TTTCTCACCTGATCAGCTGTCCCAGGTGCCCTCTGTGGAAGGTGA-CCATATTCATTTTA  4436
                |||||||||||||||||||| |||||||||| |||  |||||||| | || || | ||||
Sbjct  7523944  TTTCTCACCTGATCAGCTGTTCCAGGTGCCCACTGAAGAAGGTGATCAAT-TTTACTTTA  7523886

Query  4437     AGCAGCTGGAGGTGTTTCAGCCTGAGGAACATAGAGCTGATTTTGGCGACTGAGCATTCC  4496
                ||||  |||||||||| |||||||||||||| || ||||| ||||| || | | ||||||
Sbjct  7523885  AGCAATTGGAGGTGTTCCAGCCTGAGGAACACAG-GCTGAATTTGGTGAGTAACCATTCC  7523827

Query  4497     TCGCGGT-AAT-T--GACGTGTAAGGATGGCACCTGGAGAAAAATGAGTTTGCGAAGATT  4552
                ||| ||| | | |  |||| |||| |||||||||||||| |||| |||||||||||||||
Sbjct  7523826  TCGAGGTCATTGTCCGACGAGTAATGATGGCACCTGGAG-AAAACGAGTTTGCGAAGATT  7523768

Query  4553     CTTCATCTCCTTCAGGTAACAATGAAGCTTTCTTATCAGATGTGGCCAGGACACATAGCA  4612
                ||||||||||||||||||||||||||||||||||||||||||  |||||||||  | |  
Sbjct  7523767  CTTCATCTCCTTCAGGTAACAATGAAGCTTTCTTATCAGATGCAGCCAGGACATGTTGTG  7523708

Query  4613     AATTTCCAGCTCCTGAATACTATTCAGGTGGATTATTTTCAATGATC-TTCTGAGATATT  4671
                |||||||| ||||||||||||||||||||||| |||||||||||| | |||| |||||||
Sbjct  7523707  AATTTCCAACTCCTGAATACTATTCAGGTGGACTATTTTCAATGA-CTTTCTAAGATATT  7523649

Query  4672     CAATCGACGTTAGATAATTCACCAACTTACTACAGCACAGGTGTACTAAACCTCTCCTTT  4731
                 ||| |  |||||||||||||||||||||||||||||||||||||||||| |||||||||
Sbjct  7523648  TAATGGGTGTTAGATAATTCACCAACTTACTACAGCACAGGTGTACTAAAACTCTCCTTT  7523589

Query  4732     GGTAAACCCACCGGAAGAGGTATCTCAGGCATTCATCCTGGGGTATTTCCTTGAGGCAGA  4791
                ||||||||||| ||||||||||||||||||||||||| |||||| |||||||||||||||
Sbjct  7523588  GGTAAACCCACTGGAAGAGGTATCTCAGGCATTCATCTTGGGGTGTTTCCTTGAGGCAGA  7523529

Query  4792     TGTCTATGAACACCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGTCT  4851
                 ||||||||||||||| ||||||||||||||||||||||||||| |||||||||||||||
Sbjct  7523528  CGTCTATGAACACCTTTAAGGGCTGGTGCTCTCCCATCCTTGGATAGTCCTCTGCTGTCT  7523469

Query  4852     GCCTCTTACTCATGGCCTCTGGGGAGGAGGACAGGGCCCTGGATTC-AGACCATATGGCC  4910
                |||||||||||||||||||||||||||||||||||||| | |  || || ||||   |||
Sbjct  7523468  GCCTCTTACTCATGGCCTCTGGGGAGGAGGACAGGGCC-TAGCCTCCAGGCCATCCAGCC  7523410

Query  4911     CAGAAATTCTCATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTA  4970
                |||| |||||||||||||||| |||| |||||||||||||||||||||||||| | ||||
Sbjct  7523409  CAGACATTCTCATCAACATCCAGCAAGTCCAGCACTTGAAGTTTCCACCTCCTATAGGTA  7523350

Query  4971     AAGTAAGGCAGAGGCTCAGAACTTT-GAAGGACAAATCCCTGACCTTTGCTTTCATTCTC  5029
                |||||||| ||| |||||||| ||| |||||||  ||||||||| |||||||||||||||
Sbjct  7523349  AAGTAAGGGAGAAGCTCAGAA-TTTAGAAGGACCCATCCCTGACTTTTGCTTTCATTCTC  7523291

Query  5030     ATCCAATAAATCAGCTGCTCCTGTCCTCGCTGCTCCCTGTTCTCTCTGAGTTTTCTTGGT  5089
                ||    |      ||| | |||||  ||  | |||  |   ||    || ||||||  ||
Sbjct  7523290  AT----T------GCT-C-CCTGT--TC--T-CTC--T---CT----GACTTTTCTCAGT  7523257

Query  5090     CCCTTTTCTCTTTCAATTC-TGACTGGTCCCCACTTCTATTCCATTTACCTTCCACTGGG  5148
                || ||||||||||  |||| | |||| |||||||||||| ||| ||||||||||||||||
Sbjct  7523256  CCGTTTTCTCTTTTGATTCAT-ACTGCTCCCCACTTCTAGTCCCTTTACCTTCCACTGGG  7523198

Query  5149     AATAGGCAAGTTTCTGTTCCCACAGTGGACCCTATATTGTGGGCAGTTCTTTCCCTGAGG  5208
                || | ||| |||||||||||||||||||||||| ||| ||| ||||| ||||| ||||||
Sbjct  7523197  AAAAAGCAGGTTTCTGTTCCCACAGTGGACCCTGTATGGTGAGCAGTCCTTTCTCTGAGG  7523138

Query  5209     ATCTGGGCAATGGCCAAGGCATGCCT-GAGCTTCGTCACCAGCACCACCAGAAGACACTG  5267
                |||||| ||| |||||| || | ||| ||||||| |||||||||||| |||||||| |||
Sbjct  7523137  ATCTGGACAACGGCCAAAGCCT-CCTTGAGCTTCCTCACCAGCACCATCAGAAGACTCTG  7523079

Query  5268     GGC  5270
                |||
Sbjct  7523078  GGC  7523076


 Score = 2230 bits (1207),  Expect = 0.0
 Identities = 1925/2257 (85%), Gaps = 108/2257 (4%)
 Strand=Plus/Minus

Query  24401    TGTGGCAACAAAATATATGGTctacttaacagagaaagagac--t-ccacaggaaaaaaa  24457
                |||||||||||||||||||||||||||||||||||| |||||  |   | |  |||||||
Sbjct  7447873  TGTGGCAACAAAATATATGGTCTACTTAACAGAGAAGGAGACTGTGTAAGAAAAAAAAAA  7447814

Query  24458    aaaggatttttattatgaaatgagcaaagcca-tgggaatagatgtgagattattcgggg  24516
                ||| ||| |||||  |||||||||||||| || ||||||| ||||||||||||||  |||
Sbjct  7447813  AAAAGATGTTTATCCTGAAATGAGCAAAG-CATTGGGAATGGATGTGAGATTATTTTGGG  7447755

Query  24517    aggtaaa-ggaagacaaaggttttgaaaggaaaaatgaggagaattacataaattttttt  24575
                ||  |||  |||||  |||||||||||||||||||| ||||| |||| ||||||| ||||
Sbjct  7447754  AGAAAAATAGAAGATGAAGGTTTTGAAAGGAAAAATAAGGAGGATTATATAAATTGTTTT  7447695

Query  24576    gaaagactcattcttggtcac-aagt-atgaaaacc-aagggagcctcagtgcagtgttg  24632
                ||||| ||||| ||||||| | || | || |||||| ||||| || |||||| | | |||
Sbjct  7447694  GAAAGGCTCATCCTTGGTC-CTAA-TAATCAAAACCAAAGGG-GCATCAGTGAAATATTG  7447638

Query  24633    gaaagATTCCTCCTCCACCCTCTCAATAACCCCCAACACATTTACCAAGTCTTTGTTCAC  24692
                || ||||||||||||||||| |||| ||||||||||||  ||||||||||||| ||||||
Sbjct  7447637  GATAGATTCCTCCTCCACCCCCTCAGTAACCCCCAACATGTTTACCAAGTCTTGGTTCAC  7447578

Query  24693    TCCCAGGATTCCATTAAAACACCCAGCTCAACCCTGACCAGCCTCCACCTTCACTTCCCT  24752
                ||||||||| ||||||||||||| |||||||||  | ||| |||| ||| |||||||| |
Sbjct  7447577  TCCCAGGATCCCATTAAAACACCAAGCTCAACCAAGCCCATCCTCTACCCTCACTTCCTT  7447518

Query  24753    TTGTAATTTTGACATAAATTtgttacaggaccatcaggttcctatgccggctgcacagta  24812
                ||| ||||||||||| | ||| ||||||||||||||| |||||||||| |||||||||||
Sbjct  7447517  TTGCAATTTTGACATGATTTTATTACAGGACCATCAGATTCCTATGCCTGCTGCACAGTA  7447458

Query  24813    gcttaccaatattctgagacagcagga-tttgcagcagaaagtttaatgatcacagggtg  24871
                ||||||||||||| |||||||||| || ||||||||||| ||||||||||||||||||||
Sbjct  7447457  GCTTACCAATATTTTGAGACAGCA-GAGTTTGCAGCAGAGAGTTTAATGATCACAGGGTG  7447399

Query  24872    gctgaatgagaagctgggaggagatcctcaaattcatctcccc-a--aggag-t--actg  24925
                ||| ||||||||||| ||||||||||||||||||||||||||| |  ||||| |  ||||
Sbjct  7447398  GCTAAATGAGAAGCTAGGAGGAGATCCTCAAATTCATCTCCCCAAGGAGGAGATCCACTG  7447339

Query  24926    agggtttccagtggatcctggatagcaaggggctggaaagttggtgtagtttgatggcaa  24985
                |||||||||||||||||||||||||||||||||||||||||| |  ||  | ||  |   
Sbjct  7447338  AGGGTTTCCAGTGGATCCTGGATAGCAAGGGGCTGGAAAGTT-G-ATA--TAGA--G--T  7447287

Query  24986    taagaggtatgaagttatcacgatgtcagaacggcattctttggtgagttgatgccttgc  25045
                ||||||| ||||||| |||| ||||||| ||| ||||||||||||| |||| ||||||| 
Sbjct  7447286  TAAGAGGGATGAAGTCATCAGGATGTCAAAACTGCATTCTTTGGTGCGTTGGTGCCTTGT  7447227

Query  25046    agggcccttcagatcagctggcatcagtagtttcactgacatgcagaacctgaaagaata  25105
                ||||||||||||||||||||||||||||| |||||||||||||||||| | | |||||||
Sbjct  7447226  AGGGCCCTTCAGATCAGCTGGCATCAGTACTTTCACTGACATGCAGAA-C-GTAAGAATA  7447169

Query  25106    tctcaaatgaaaaacttaatgtttcacaatgcttaaattgttgtctgcagcgtagttaag  25165
                |||||||||||||| ||||||||| |||| |||||||||||||||||||| | |||||||
Sbjct  7447168  TCTCAAATGAAAAAGTTAATGTTTTACAAGGCTTAAATTGTTGTCTGCAGGGCAGTTAAG  7447109

Query  25166    gggaattgtagtctaagttctacacgattttgggacagtaggctgccagcaaccatgagg  25225
                ||||| |||| |||||| |||| | ||||| |||||||||||||||||||||||||||||
Sbjct  7447108  GGGAACTGTAATCTAAGGTCTAAATGATTTGGGGACAGTAGGCTGCCAGCAACCATGAGG  7447049

Query  25226    aagcaggtcagagggcaagctgacctcctggtgaatgctgaatgcgtttcaagcttggtt  25285
                ||| ||||||||| ||||||||||||| |||||||||||||||||| | |||||||||||
Sbjct  7447048  AAGAAGGTCAGAGAGCAAGCTGACCTCATGGTGAATGCTGAATGCGCTGCAAGCTTGGTT  7446989

Query  25286    tgtttttgttcctccccctctctttttcaccgattaaatttataaagtttagaaata-cg  25344
                | |||||||| ||||||||| ||| ||||| |||||||||||||||||||| |  || | 
Sbjct  7446988  TATTTTTGTTTCTCCCCCTCCCTTCTTCACTGATTAAATTTATAAAGTTTATAGGTATC-  7446930

Query  25345    gtttcaATTTCTTCCAGACAAGCCTTAACCTAAGCCCTGAGACCACTCAAGCCCTCAGTG  25404
                |||||||||||||||| | |||||||||||||||| ||||||||||||| ||||| ||||
Sbjct  7446929  GTTTCAATTTCTTCCAAAGAAGCCTTAACCTAAGCACTGAGACCACTCACGCCCTGAGTG  7446870

Query  25405    GCACCTCTCTTCCACCAGCATGAGCAAATAAATTGCTACCTTAGGTGATATAAAACCCAC  25464
                |||||||||||||||||||| |||  || ||| |||||||||||||||||||||||||||
Sbjct  7446869  GCACCTCTCTTCCACCAGCACGAGTGAAGAAACTGCTACCTTAGGTGATATAAAACCCAC  7446810

Query  25465    AAGATGATTCGATACATGGAGtttttt-ttCTGATTTTGTAGGGATGACTTCTTTGTTTC  25523
                ||||  |||| |||||||||| | ||| |||| ||||||||||||||||| | || ||| 
Sbjct  7446809  AAGACCATTCCATACATGGAGATCTTTATTCTTATTTTGTAGGGATGACTCCGTT-TTT-  7446752

Query  25524    TATAAAGCTGTTTTAACTATAAAACAATTTTATAATTTTGATGTGGCCAAAGATCTCCC-  25582
                 |||||| ||||||||||| ||| || |||||||||||||||||||||||||||||||| 
Sbjct  7446751  -ATAAAGTTGTTTTAACTAGAAAGCATTTTTATAATTTTGATGTGGCCAAAGATCTCCCC  7446693

Query  25583    A-A-CACTACTTTCAGGTTTTATTTTTCTGTCTACTATCCAGAACAGATCAAACCCTTCC  25640
                | | |||||||||||||||||||||||||||||| | ||| ||||||||||| |||||||
Sbjct  7446692  ACAACACTACTTTCAGGTTTTATTTTTCTGTCTAATGTCCGGAACAGATCAACCCCTTCC  7446633

Query  25641    CTGCCTCAAACTCAGGAC-TATATAGGTC-ATATATCAGTAAAATTCCATCAGTGTTTGC  25698
                |||||||| ||||||||| |  | ||| | | ||| ||||||||||||||||||||||| 
Sbjct  7446632  CTGCCTCACACTCAGGACCTG-A-AGG-CGACATAGCAGTAAAATTCCATCAGTGTTTGT  7446576

Query  25699    GGAgttcatgaatgaatgaattctttttttttttttttttttttttttttgtgacaaagt  25758
                ||| |||||||||||||| ||| ||||||||                   |  ||||| |
Sbjct  7446575  GGATTTCATGAATGAATGCATT-TTTTTTTT-------------------G--ACAAAAT  7446538

Query  25759    ctacctctgtcacccaga-acggtgtgcaatggtgcaatcttggctcactgcaa-c-cat  25815
                || |||| |||||||||  | || | ||||||||| |||||||||||||||||| | || 
Sbjct  7446537  CTCCCTCCGTCACCCAGTCA-GGAGGGCAATGGTGTAATCTTGGCTCACTGCAAACTCA-  7446480

Query  25816    tgccccctggattcaagcgattctcccacctcagcctcctgagtagctggattacaggca  25875
                 ||| || || |||||| |||||||||||||||||| | |||||||||||| ||||||||
Sbjct  7446479  -GCCTCCAGGGTTCAAGGGATTCTCCCACCTCAGCCACATGAGTAGCTGGACTACAGGCA  7446421

Query  25876    -cctgccatcatgccaggctaatttttgtgtttttgtagag-ctggggtttcatcatgtt  25933
                 ||  ||||| |||| |||||| |||| | ||||||||||| | ||| ||||| ||||| 
Sbjct  7446420  GCCA-CCATCGTGCCTGGCTAACTTTTCTATTTTTGTAGAGACAGGG-TTTCACCATGTG  7446363

Query  25934    ggccttgcaggtcttgatcgcctgacctcaggtgatccagccaac-ttggactc-tcaaa  25991
                ||||  || |||||||| | |||||| |||||||||||| || || |||| ||| | |||
Sbjct  7446362  GGCCAGGCGGGTCTTGAACTCCTGACATCAGGTGATCCA-CCTACCTTGGCCTCCT-AAA  7446305

Query  25992    gtgcagggattacaggtgtgagccacctcacccggcctttaatgaGTGAATTCTTGATTT  26051
                |||| ||||||||||||||||||||||||| | |||||| | ||| ||||||||||| ||
Sbjct  7446304  GTGCTGGGATTACAGGTGTGAGCCACCTCATCTGGCCTTGAGTGAATGAATTCTTGACTT  7446245

Query  26052    CCACCCTATTCCTAACACTGTCAATTTCTTGATTCATGAACTTAATATGGATA-GCTGAT  26110
                |||| |||| |||||| ||||||||||||| ||||||||| | |||||| ||| | ||||
Sbjct  7446244  CCACTCTATCCCTAACGCTGTCAATTTCTTAATTCATGAAATGAATATGCATATG-TGAT  7446186

Query  26111    ATGAATGGATATCTGATTCAATCCAGTAATCTGGGGACAGCCAAAAACCCAATCAAGATT  26170
                ||||||||||| ||| ||||||||| || |||  ||||||||||||||||||||| ||||
Sbjct  7446185  ATGAATGGATACCTGGTTCAATCCATTAGTCTTCGGACAGCCAAAAACCCAATCAGGATT  7446126

Query  26171    AACTGGGTGGAGCTTCAGAAATGCAATCAGATAGCACTTTTTGATTGGAAGCAAGCA-CT  26229
                ||||| ||||||||||||||||||||||||||| | |||||||||||||||| |||| | 
Sbjct  7446125  AACTGAGTGGAGCTTCAGAAATGCAATCAGATATCGCTTTTTGATTGGAAGCTAGCAGC-  7446067

Query  26230    GGATA-GATGGAGGGGTGTGGGTGGGAGTTGTGATTAGAAAGATCGATAAAAGTTTCTGA  26288
                ||||| | |||||||| ||||||||||||||||||||||||| || ||||||| |||| |
Sbjct  7446066  GGATATG-TGGAGGGGCGTGGGTGGGAGTTGTGATTAGAAAGGTCAATAAAAGCTTCTAA  7446008

Query  26289    AGGCCCACAGGAGAGACCCAAAGTCTTCAAGTCTGGAGTTCCTGCTTGGTTCTTCCTGAG  26348
                || ||||||||| |||| ||||||||||||| ||||||||||||||||| ||||||||||
Sbjct  7446007  AGACCCACAGGACAGACTCAAAGTCTTCAAGCCTGGAGTTCCTGCTTGGCTCTTCCTGAG  7445948

Query  26349    GTCTAAGC-ACT-CTGCAAAC-----TC-AG--T-C--C-AGATCTAGTAAGTCACTCAT  26394
                |||| ||| ||  || ||| |     || |   | |  | |||||| |||||||||| ||
Sbjct  7445947  GTCTGAGCTACAACTACAACCAGAGGTCTAAACTACAACCAGATCTGGTAAGTCACTAAT  7445888

Query  26395    TTCTGGAAGGACACTCCCATCTGACCTATAGTCAGCCGGTCTGGGACGGGGGCAATGCAG  26454
                |||||||||||||||||||||||||||| ||||||||||||| | |||| | || |||||
Sbjct  7445887  TTCTGGAAGGACACTCCCATCTGACCTACAGTCAGCCGGTCTAGAACGGTGACAGTGCAG  7445828

Query  26455    CCTATGATGGCACCGAGCTATATC-TGTCTTTtata-tatatat-atatGAACAATTTGA  26511
                |||| || ||||| || ||||||| |||||||| |  | | | | ||||||||| |||||
Sbjct  7445827  CCTACGACGGCACAGAACTATATCCTGTCTTTTTTTCTTTTTTTCATATGAACACTTTGA  7445768

Query  26512    AGATTTGAATTTTTTCCTCTATATGCAGTTTTGTCTTTATTTCAAAAAA-TTGGATTGTG  26570
                || ||||| ||||||  |||| ||||| ||||||||||||||||||||  |||  |||||
Sbjct  7445767  AGCTTTGATTTTTTT--TCTAAATGCAATTTTGTCTTTATTTCAAAAATGTTG--TTGTG  7445712

Query  26571    CTTTGGTTTATGTCATTTcaaaattcttgatgggagc  26607
                ||||  ||||  |||||||| |||||||| |||||||
Sbjct  7445711  CTTTTCTTTACATCATTTCAGAATTCTTGTTGGGAGC  7445675


 Score = 2026 bits (1097),  Expect = 0.0
 Identities = 1275/1360 (93%), Gaps = 16/1360 (1%)
 Strand=Plus/Minus

Query  6980     AAAATCACAATACCGCTAAGTGTGTGAACTATAGCTGACA-GGCACAGAAACCAACAACT  7038
                |||||||||||||  ||||||||||||||| ||||||| | ||||||||||| || ||||
Sbjct  7514211  AAAATCACAATACAACTAAGTGTGTGAACTGTAGCTGA-AGGGCACAGAAACAAATAACT  7514153

Query  7039     TCACATGTCAAGACATAAACATCCATCCAACTGTAAATTTTTAATAtttttttttttAAA  7098
                ||||||||||||||||||| || |||||||||||||||||||||||  | |||||| |||
Sbjct  7514152  TCACATGTCAAGACATAAAAATTCATCCAACTGTAAATTTTTAATA--TCTTTTTTAAAA  7514095

Query  7099     AACTGCTTCAATAAGAATTTTGAAATGAGGAAAATGAAGCACAAATCAAAATTTGAGGGA  7158
                ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||
Sbjct  7514094  AACTGCTTCAATAAGAATTTTGAAATGAGAAAAATGAAGCAGAAATCAAAATTTGAGGGA  7514035

Query  7159     TGAAGTCAAAACTATATTTGGAGGAAAAATCAAAACCTACATCTGTTTAATCTGAAAAAA  7218
                |||||| || ||||||||| ||||||||||||||||||||||||||| ||| ||||||||
Sbjct  7514034  TGAAGTGAATACTATATTTAGAGGAAAAATCAAAACCTACATCTGTTAAAT-TGAAAAAA  7513976

Query  7219     CAGACAGGAAATTCTCTGTGCCATTTTGGGCTGTGTGTCACCATCCCTGACTGGCTGGCT  7278
                ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct  7513975  CAGACAGGAAATTCTCTGTGCCACTTTGGGCTGTGTGTCACCATCCCTGACTGGCTGGCT  7513916

Query  7279     GCAGATTAGACGGGCATGTTCCTAAGAAGGTGGTGACTTACCAGATCTGGACTCAGTTTG  7338
                |||||| ||| ||||||||||||||| |||||||||||||||||||||||||||||||||
Sbjct  7513915  GCAGATCAGATGGGCATGTTCCTAAGGAGGTGGTGACTTACCAGATCTGGACTCAGTTTG  7513856

Query  7339     CAGGGTGCTGGGACCTCTCAGAGAACCAAGCAGTAGCTCCAGGCACCAGGGCTTTGGGTC  7398
                 |||||||||||| ||||||||||| |||||||||| |||||||||||||||||||||||
Sbjct  7513855  TAGGGTGCTGGGATCTCTCAGAGAATCAAGCAGTAGTTCCAGGCACCAGGGCTTTGGGTC  7513796

Query  7399     TGTCCTGTGCAAACTCAGGAGCTTTTGTTGATGTTTCTAACCACACCCTCCCCTTCTCAA  7458
                | |||| ||||||||||||||||||| |||||||||||||||||||||||||||||||||
Sbjct  7513795  TCTCCTTTGCAAACTCAGGAGCTTTTATTGATGTTTCTAACCACACCCTCCCCTTCTCAA  7513736

Query  7459     TCACCAGCTTCCAATCAGAAAGTGATACCTGATTAGA-TCCTGAAGTTCCACCCAGTTAA  7517
                ||||||||||||||||||||||||||||||||||||| ||| ||||||||||| ||||| 
Sbjct  7513735  TCACCAGCTTCCAATCAGAAAGTGATACCTGATTAGATTCC-GAAGTTCCACCTAGTTAG  7513677

Query  7518     TCCTGATTGAGTTTCACACTTTCTTCTGATTCATTGATTAAATTAGATGTGCATTTATGA  7577
                |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7513676  TCCTGATTGAGTTTTACACTTTCTTCTGATTCATTGATTAAATTAGATGTGCATTTATGA  7513617

Query  7578     AAGTGAAAGAATAAATAACAGGGTGAAAGTCCAAAAGTCATTAATTCATTTATTCCCCAA  7637
                |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Sbjct  7513616  AAGTGAAAGAATAAATAACAGGGTGAAAGTCCAAAACTCATTAATTCATTTATTCCCCAA  7513557

Query  7638     ACACTGATGAAGTTTGACTAACATGTGACCTTCATAGTGACATGGAAGGTTTAATCTGTT  7697
                ||||||||||| ||||||||  ||||||||||||||| ||||||||||||||||||||||
Sbjct  7513556  ACACTGATGAAATTTGACTAGTATGTGACCTTCATAGAGACATGGAAGGTTTAATCTGTT  7513497

Query  7698     CCTGGCATTAGAAAGAAAAAACAAAACCTGATGATATCTTTATGGGAGAATATTTGGCCA  7757
                |||| |||||||||||||||||||||||||||||||||||||||||| ||| | ||||||
Sbjct  7513496  CCTGACATTAGAAAGAAAAAACAAAACCTGATGATATCTTTATGGGAAAATCTGTGGCCA  7513437

Query  7758     CATTGAAATTATCCAAACGTTTC----AG--AGCTAAGACAGCTTTAAAAAGACGGTGAT  7811
                ||| ||||||||| |||||||||    ||  || ||| |||||||||||||||| |||||
Sbjct  7513436  CATCGAAATTATCAAAACGTTTCGTTAAGACAGTTAAAACAGCTTTAAAAAGACAGTGAT  7513377

Query  7812     GTCAACCCTAAGAAAACAGAATACAAAGCT-CTGTTATCCAACAGTTACCTGGGTTTTAT  7870
                ||| ||||||||||||| || || |||||| || ||||||||  || |||||||||||||
Sbjct  7513376  GTCCACCCTAAGAAAACGGATTAAAAAGCTCCT-TTATCCAATGGTCACCTGGGTTTTAT  7513318

Query  7871     GCTTCCTAACGGGGCAGGTCATATGTGGGTTCAGGTTGAAGAGGGGAACCACTGAGGGTG  7930
                | ||  |||| ||||||||||||||||||||||||||||| | ||||||||| |||||||
Sbjct  7513317  GTTTTATAACAGGGCAGGTCATATGTGGGTTCAGGTTGAA-AAGGGAACCACGGAGGGTG  7513259

Query  7931     TTATTGATCACAAGACTAAGGTCAAGGCTTCACTGCAGGAAATCAGGACAGAATGACAAA  7990
                | ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Sbjct  7513258  TGATTGATCACAAGACTAAGGTCAAGGCTTCACTGAAGGAAATCAGGACAGAATGACAAA  7513199

Query  7991     GTGAGGTGGGGGCTGGGCAGGATGGGACCGGGTGTTCTAGTAGAACCCTGGGAAGGAACC  8050
                ||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7513198  GTGAGGTGGCGGCTGGGCAGGATGGGACCGGGTGTTCTAGTAGAACCCTGGGAAGGAACC  7513139

Query  8051     AAGACAGCATAAAACATGGTGGGTATTTTGTGGGCATCTCCACAGAAGGATTGAAAGACT  8110
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7513138  AAGACAGCATAAAACATGGTGGGTATTTTGTGGGCATCTCCACAGAAGGATTGAAAGACT  7513079

Query  8111     CTGTCTGGATTGAGTTTAAAAATTAAAAAGGGAATAGTTACAGAAGAGACAGTGCAGACT  8170
                |||||| ||||||||||||||||||||||||||||| ||||| |||||||||||||||||
Sbjct  7513078  CTGTCTAGATTGAGTTTAAAAATTAAAAAGGGAATAATTACAAAAGAGACAGTGCAGACT  7513019

Query  8171     CTTCAAACACAACATTGTCTTTGAGGGCAGAGAAGGCAGAAACAGTCTTGGCCCCTACTA  8230
                |||||||||||||||||||||||||||||||| ||||||| |||||||||||| ||||||
Sbjct  7513018  CTTCAAACACAACATTGTCTTTGAGGGCAGAGGAGGCAGATACAGTCTTGGCCTCTACTA  7512959

Query  8231     GAAGGGAAAGCGTGTTTACTCCCAAAAATGATGGGCTCGCCTCAGAAAATCAGCCTGGGA  8290
                 |||||||||||||||||||||||||||||||||||||||||  ||||||||||||||||
Sbjct  7512958  CAAGGGAAAGCGTGTTTACTCCCAAAAATGATGGGCTCGCCTTGGAAAATCAGCCTGGGA  7512899

Query  8291     AGATGGAATCTGAGAATCTGAGCTGGGGCAGATGCCAGAG  8330
                ||||||||||||||||| ||||||||||||||||||||||
Sbjct  7512898  AGATGGAATCTGAGAATGTGAGCTGGGGCAGATGCCAGAG  7512859


 Score = 2023 bits (1095),  Expect = 0.0
 Identities = 1861/2216 (83%), Gaps = 111/2216 (5%)
 Strand=Plus/Minus

Query  25719    ttctttttttttttttttttttttttttttgtgacaaagtcta-cctctgtcacccagaa  25777
                |||||||||||||||||||||||||||||| |    || |||| ||| | |  |||||  
Sbjct  7543211  TTCTTTTTTTTTTTTTTTTTTTTTTTTTTT-TTTTGAA-TCTAGCCTAT-T-TCCCAG-G  7543157

Query  25778    c-ggtgtgcaatggtgcaatcttggctcactgcaaccat-tgccccctggattcaagcga  25835
                | || || || ||||| | | |  ||||||||||||| | |||| ||||| |||||||||
Sbjct  7543156  CTGGAGTTCAGTGGTGTATTGTCAGCTCACTGCAACC-TCTGCCTCCTGGGTTCAAGCGA  7543098

Query  25836    ttc-tcccacctcagcct-cctgagtagc-tggattacaggcacctg-ccatcatgc--c  25889
                 || |||   |||||||| ||| |||||| |||| || ||||  | | ||| |  ||  |
Sbjct  7543097  -TCTTCCTGTCTCAGCCTCCCT-AGTAGCTTGGACTATAGGC-GCAGACCA-C-CGCAAC  7543043

Query  25890    aggctaatttttgt-gtttttgtagagctggggtttcatcatgttggccttgcaggtctt  25948
                 |||||||||||||  |||| |||||| | |||||| | ||||||||||  ||  |||| 
Sbjct  7543042  TGGCTAATTTTTGTAATTTTAGTAGAGGTAGGGTTTTACCATGTTGGCCAGGCTTGTCTC  7542983

Query  25949    gatcgcctgacctcaggtgatccagcc-aact-tggac-tctcaaagtgcagggattaca  26005
                 | | ||||||||||| | ||||| || | || | | | || || ||||| |||||||||
Sbjct  7542982  AAACTCCTGACCTCAGATAATCCA-CCTACCTCT-G-CGTCCCAGAGTGCTGGGATTACA  7542926

Query  26006    ggtgtgagccacctcacccggcctttaatgaGTGAATTCTTGATTTCCACCCTATTCCTA  26065
                |||||||||||| ||  | |||||| ||||| || |||||||| ||| ||||||| ||||
Sbjct  7542925  GGTGTGAGCCACTTCGTCTGGCCTTGAATGAATGTATTCTTGACTTCTACCCTATCCCTA  7542866

Query  26066    ACACTGTCAATTTCTTGATTCATGAACTTAATATGGATA-GCTGATATGAATGGATATCT  26124
                |||||||| |||||||| |||||||| | ||||| |||| | ||||||||||||| ||||
Sbjct  7542865  ACACTGTCGATTTCTTGCTTCATGAAGTGAATATAGATATG-TGATATGAATGGACATCT  7542807

Query  26125    GATTCAATCCAGTAATCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGGGTGGAGCT  26184
                |||||||||| |||||||||||| ||||||||||||||||| ||||||||||||||||||
Sbjct  7542806  GATTCAATCCGGTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCT  7542747

Query  26185    TCAGAAATGCAATCAGATAGCACTTTTTGATTGGAAGCAAGCA-CTGGATA-GATGGAGG  26242
                ||| ||||||||||||||| || ||||||||||||||   ||| | ||||| | || |||
Sbjct  7542746  TCACAAATGCAATCAGATATCATTTTTTGATTGGAAGGTCGCAGC-GGATATG-TGCAGG  7542689

Query  26243    GGTGTGGGTGGGAGTTGTGATTAGAAAGATCGATAAAAGTTTCTGAAGGCCCACAGGAGA  26302
                || ||||||||||||||||||||||||| || ||||||| |||| ||| |||||||||||
Sbjct  7542688  GGCGTGGGTGGGAGTTGTGATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGAGA  7542629

Query  26303    GACCCAAAGTCTTCAAGTCTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTAAGCACTCTG  26362
                ||||||||||||||||| || |||||||||||||||||||||||||| || ||||| || 
Sbjct  7542628  GACCCAAAGTCTTCAAGCCTAGAGTTCCTGCTTGGTTCTTCCTGAGGACTGAGCAC-CTT  7542570

Query  26363    CAA-ACT-CAGTCCAGATCTAGTAAGTCACTCATTTCTGGAAGGACACTCCCATCTGACC  26420
                | | ||| || ||||||||| |||||||||| ||||||| ||||||||||||||||||||
Sbjct  7542569  CTAGACTACA-TCCAGATCTGGTAAGTCACTAATTTCTGTAAGGACACTCCCATCTGACC  7542511

Query  26421    TATAGTCAGCCGGTCTGGGACGGGGGCAATGCAGCCTATGATGGCACCGAGCTATATC-T  26479
                || |||||| |||||||||  || | || | ||||||| |||||||| |||||||||| |
Sbjct  7542510  TACAGTCAGTCGGTCTGGGGTGGTGACAGTACAGCCTACGATGGCACAGAGCTATATCCT  7542451

Query  26480    GTC-TTTtatatatatatatatGAACAATTTGAAGATTTGAATTTTTTCCTCTATATGCA  26538
                ||| |||| | | | |  ||||||||||||||||| ||||||| |||||||||| |||||
Sbjct  7542450  GTCCTTTTTTTTTT-TC-ATATGAACAATTTGAAGCTTTGAATGTTTTCCTCTAAATGCA  7542393

Query  26539    GTTTTGTCTTTATTTCAAAAAA-TTGGATTGTGCTTTGGTTTATGTCATTTcaaaattct  26597
                ||| |||||||||||||||||| ||| |||||||||||||| ||| ||||| ||||||||
Sbjct  7542392  GTTCTGTCTTTATTTCAAAAAAGTTG-ATTGTGCTTTGGTTGATGCCATTTTAAAATTCT  7542334

Query  26598    tgatgggagcaatgactcatgcccataacctcaacaccttgggaggccaaagcgggagga  26657
                ||| ||||||||| |||||||||  ||||| |||||| |||||||||||||| |||||||
Sbjct  7542333  TGAAGGGAGCAATAACTCATGCCTTTAACCCCAACACTTTGGGAGGCCAAAGTGGGAGGA  7542274

Query  26658    tcatttgagcccaggggtttgagaccaacctgggcaacatggcaaaaatgcagctctaca  26717
                |||||| |||||||||||||||||||||||||||||||||| |||||   |  |||||||
Sbjct  7542273  TCATTTCAGCCCAGGGGTTTGAGACCAACCTGGGCAACATGACAAAAGCCCTCCTCTACA  7542214

Query  26718    aaacattcttttttt--gaagcaggg-atggagtctcaccctgttgccaaggctggagtg  26774
                 ||| || |||||||  || |  ||| ||||||||||||  ||||||| || ||||||||
Sbjct  7542213  CAACGTTTTTTTTTTTTGAGGGTGGGGATGGAGTCTCACTGTGTTGCCCAGACTGGAGTG  7542154

Query  26775    cagtggcaagagctcaactcactgcaacctctt-cctcccaggctcaaacaattttcatg  26833
                |||||||| || ||||| |||||||||||| || |||||| || |||| ||||| |||||
Sbjct  7542153  CAGTGGCACGATCTCAAATCACTGCAACCT-TTACCTCCCGGGTTCAAGCAATTCTCATG  7542095

Query  26834    tctcag-ct---tcctgagtagctggtattacatccctctgccaccatgtctg-cttaat  26888
                 ||||| ||   |||| || ||||||| | |||  | ||||  |||||| ||| || |||
Sbjct  7542094  CCTCAGTCTCCATCCTCAGAAGCTGGTGTCACAGACATCTGAAACCATGCCTGGCT-AAT  7542036

Query  26889    ttttgtatttttagtagtggtggggtttcaccatgctggccaggttggtctcaaactcct  26948
                ||||||||||||||||| |||||||||||||||||||||||||||||||||| ||| |||
Sbjct  7542035  TTTTGTATTTTTAGTAGAGGTGGGGTTTCACCATGCTGGCCAGGTTGGTCTCGAACACCT  7541976

Query  26949    gacatcaagtgatcctcctgcctaggccc-ccaaaagtgctggaatgacggccgtgagcc  27007
                ||| ||||||||||| ||||||| ||||  ||||| ||||||| || || || ||||| |
Sbjct  7541975  GACCTCAAGTGATCCACCTGCCTTGGCCTTCCAAA-GTGCTGGGATTACAGCTGTGAGTC  7541917

Query  27008    aATGGTGGTCAGCctctacaaaatatatatatcttttaattt-gcc-aggcatggt-agc  27064
                | ||||| |  ||||||||    | | | | | |||||| || ||| || |||||| | |
Sbjct  7541916  ACTGGTGCTTGGCCTCTACTTT-T-T-T-T-T-TTTTAAATTAGCCGAG-CATGGTGA-C  7541865

Query  27065    atgcatctgtattcccagctatttggtt-tgctgacatgggagaatcacttgagcccaga  27123
                ||||||||||| |||||||||||||| | | |||   ||||||||||||||||| |||||
Sbjct  7541864  ATGCATCTGTAGTCCCAGCTATTTGGGTGT-CTGGTGTGGGAGAATCACTTGAGACCAGA  7541806

Query  27124    agattgaggctgcagtgagccatgctcacaccactgctgtactccagcctgggcaacaga  27183
                |||||||||||||||||||||||||||| |||||| |||||||||||||||||||| |||
Sbjct  7541805  AGATTGAGGCTGCAGTGAGCCATGCTCATACCACTCCTGTACTCCAGCCTGGGCAAAAGA  7541746

Query  27184    gta-agaccctgctaaaaacaaaaacgaaaacaaacaaacaaaaaacCTTAACCAAAGAG  27242
                | | | |||||| |  ||| ||| |  |||||||| |  |||    |   ||  |||| |
Sbjct  7541745  G-AGACACCCTG-TCCAAA-AAACA--AAAACAAA-AT-CAAT---C---AA--AAAG-G  7541702

Query  27243    AATCTTTGACCTTAATTTTAAACCAATCACATCCTCACTGTAATTCTTCCTCCCGAATGG  27302
                | ||||||||||||||||||||||||||||||||||  | |    |  |  ||| |||||
Sbjct  7541701  A-TCTTTGACCTTAATTTTAAACCAATCACATCCTC--T-T----C--CA-CCCAAATGG  7541653

Query  27303    AGACATgggtgt-gagggtgcatgcctgtaatcccagctacatggaaggctgaagcatga  27361
                |||||||| ||  | ||||||||||||||| |||||||||  ||||||||||||||||||
Sbjct  7541652  AGACATGGCTGCAGGGGGTGCATGCCTGTAGTCCCAGCTATGTGGAAGGCTGAAGCATGA  7541593

Query  27362    gaattgcttgaatctcagaggcggaagttacagtgagctgagatgg-agccgctgcactc  27420
                |||||||||||||||  ||||| || |  ||||||||| || |||  | || ||||||||
Sbjct  7541592  GAATTGCTTGAATCTTGGAGGCCGAGGCAACAGTGAGCCGAAATGACA-CCACTGCACTC  7541534

Query  27421    cagcctgggcgacaaagtgagactcagcttcacc-ca-caccaaaaaaaaTTAGATTATA  27478
                 ||||||| |||  |||||||| |||||| | || || ||||||||| | |||  |    
Sbjct  7541533  TAGCCTGGCCGATGAAGTGAGATTCAGCT-C-CCTCAACACCAAAAAGACTTA--TG---  7541481

Query  27479    CCACCCAGGTGATCACTGGATACATGAAGATTTCTATTGTGTGTTATTGGGGACTGTCAA  27538
                ||||| ||||||||| |||||| ||||||||||||||||||| || || |||||||||| 
Sbjct  7541480  CCACCTAGGTGATCATTGGATATATGAAGATTTCTATTGTGTTTTCTTAGGGACTGTCAT  7541421

Query  27539    CTCCGTCTTTGAAAACTGTTTTAACTCTGAAATATTTTGATAAATTTGATGTGGCCAAGG  27598
                ||| |||| |||||||||||||||| |||||||||||||||||| |||   |||||||||
Sbjct  7541420  CTCTGTCTCTGAAAACTGTTTTAACCCTGAAATATTTTGATAAACTTGGCATGGCCAAGG  7541361

Query  27599    ATCCCTCAACAAAGATACTTTCAAGTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGATT  27658
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Sbjct  7541360  ATCCCTCAACAAAGATACTTTCAAGTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGGTT  7541301

Query  27659    CAACACTTCCCTATCTCACACTCAGGACTATGAAGGACACATATTAGTAAA-CCTCCATG  27717
                |||| ||||||| |||||||||||||||| ||||||||||||||||||||| || |||||
Sbjct  7541300  CAACCCTTCCCTGTCTCACACTCAGGACTTTGAAGGACACATATTAGTAAAACC-CCATG  7541242

Query  27718    TTTGTGGAGGGAATCAGTGAATGAGTCCTGGACTTTCACCCTATCCCTAAATCTTTCACT  27777
                |||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| |
Sbjct  7541241  TTTGTGAAGGGAATCAGTGAATGAGTCCTGGACTTTCACCCTATCCCTAAATCTTTCATT  7541182

Query  27778    TTCATGGATGAATATCTAATTCAATCAGTTAATCTGGAAGAAAGCCAAAAATCCAATCAG  27837
                || ||| ||||||||||||||  |||||||||| |  ||||||| |||||||||||||||
Sbjct  7541181  TTGATGAATGAATATCTAATTTGATCAGTTAATATTTAAGAAAGGCAAAAATCCAATCAG  7541122

Query  27838    GATTAACTGGGTAGAGTTTAAGAAGTCGAATCAAATGTAGTtctctctctctctct  27893
                |||||||||||||||| ||||||| || |||||||||||| ||||||| |||||||
Sbjct  7541121  GATTAACTGGGTAGAGATTAAGAATTCTAATCAAATGTAGCTCTCTCTGTCTCTCT  7541066


 Score = 1973 bits (1068),  Expect = 0.0
 Identities = 1910/2296 (83%), Gaps = 139/2296 (6%)
 Strand=Plus/Minus

Query  977      gaatggggaaggggggacctcctgggcCCTCGAGAGCACTAGGGGACCT-TGTTTGGTAA  1035
                ||| || |||| ||||| ||||||||||||| |||||||| ||||||||  | |||||||
Sbjct  7395341  GAA-GGAGAAGTGGGGATCTCCTGGGCCCTCAAGAGCACTGGGGGACCTCAG-TTGGTAA  7395284

Query  1036     CTGCAACCTGGGCAGCTTCAGTTGTGCCTTTggagctactgccctgccaacttgggagga  1095
                |||  |||||||||| ||||||||  ||||||||||| |||||||||||||| | |||||
Sbjct  7395283  CTGTGACCTGGGCAGATTCAGTTGCACCTTTGGAGCTGCTGCCCTGCCAACTCGAGAGGA  7395224

Query  1096     ccaggactccctcttgtcccaggatcccatcagctccaaagtgtgcacagcctcagcttt  1155
                ||||||||||||||||||||||| ||||||||||||| |||||| | ||||||  ||| |
Sbjct  7395223  CCAGGACTCCCTCTTGTCCCAGGCTCCCATCAGCTCCGAAGTGTACGCAGCCTTGGCTGT  7395164

Query  1156     gcCCTCTCTC--TGTTTCCGTGCAGAG-GTGACAGGTGAGATGCAGGTTCACAGCAGCTC  1212
                ||||||||||  |||||||   ||||| | ||||||||||||||||||||||||||||||
Sbjct  7395163  GCCCTCTCTCTGTGTTTCCCCACAGAGAG-GACAGGTGAGATGCAGGTTCACAGCAGCTC  7395105

Query  1213     TGGTCAACCCCACAGAAACAAATCTGAA-GCTCCTGGGTCCGGTTTAATGAGCCCCAACT  1271
                ||  ||||||| || ||||||| |  || ||||||||||  |||||||  ||||||||||
Sbjct  7395104  TGACCAACCCCGCACAAACAAA-CCCAATGCTCCTGGGTGTGGTTTAACCAGCCCCAACT  7395046

Query  1272     GCGCTCTGATCCAGGAGTTTGCAGGCTAACAGCACAAAGTGGGGAGTGAGGTCGAGGCTG  1331
                || || | ||||||||| ||||||||||||||||   |||||| |||||||| |||||||
Sbjct  7395045  GCACTATCATCCAGGAGCTTGCAGGCTAACAGCAGGCAGTGGGCAGTGAGGTAGAGGCTG  7394986

Query  1332     TGGTGGAGACTGCGGACCTAGGG-GCAAGTCCCGTTTAGCCGTGAGAGGGTATGGGTGGC  1390
                ||||||||||| | ||||| |||  || || || ||| ||| ||||||||| ||||||||
Sbjct  7394985  TGGTGGAGACTCCAGACCT-GGGTCCAGGTTCCATTTTGCCATGAGAGGGTGTGGGTGGC  7394927

Query  1391     ACAGTTGGCTGCCTCAGGGACATGGGGCACAGGCCTGGCTGACAACCCAGCCAAGAGGTG  1450
                |||| |||||||||||||||||||| |||||||||||||| |  |||| |||||| || |
Sbjct  7394926  ACAGCTGGCTGCCTCAGGGACATGGAGCACAGGCCTGGCTCATGACCCTGCCAAG-GGGG  7394868

Query  1451     GTGCCTTTAGGAGTGGATCGTGG-TCCACAGGCCCAGCAATCGGAAGCATCAGGCTCTGT  1509
                | ||||  |||||||| |||||| ||| |||||||||||||| | | | ||   |  || 
Sbjct  7394867  GGGCCTCCAGGAGTGGTTCGTGGTTCC-CAGGCCCAGCAATCAG-A-C-TC---C-ATG-  7394817

Query  1510     GTTCACCCCT-CTTGGGGGCAGATCTTGGAAATGCAGCCTCAGGAAGATTCACACAGAA-  1567
                | || ||||| |  ||||||||||||||||||  ||||||  ||  ||| | ||  ||| 
Sbjct  7394816  G-TCTCCCCTAC-AGGGGGCAGATCTTGGAAAAACAGCCTGGGGTGGATCCGCATGGAAC  7394759

Query  1568     CTCCTTTTTAGACCTAGGAACTTGATACTATTAGCAGGGTGGGCACACAGTTG--ATGCA  1625
                |||| ||  ||||| |||| ||||| ||| ||| |||| ||||  |||||| |  | | |
Sbjct  7394758  CTCCCTTCAAGACCCAGGAGCTTGACACTGTTAACAGGATGGG--CACAGTGGCCA-G-A  7394703

Query  1626     TAGCTGGCCAGGTCATTGAA-CTTGGTGCCATTTCTGCTTCCCAACTC-GGGGCCCTGGA  1683
                |||||   |||| | ||||| |  ||||||| || |||||| | || | ||  |||| ||
Sbjct  7394702  TAGCTCAACAGGACCTTGAAGC-AGGTGCCACTTGTGCTTCTC-ACCCTGGCCCCCT-GA  7394646

Query  1684     -GCATGGCCCCAGCTCTGCCTT-TGGAACCTGACAACCACACTTCATGTGCAAGCACGGC  1741
                 | |||||||||||||||  || |||  |||| || ||||||||| ||||| |||  |||
Sbjct  7394645  TGGATGGCCCCAGCTCTGTTTTCTGG-GCCTGGCATCCACACTTCTTGTGCGAGCGGGGC  7394587

Query  1742     ACCACCCCAAGCCCATCTTCTCCTCATGGCCCCTTTCTGCCTGTGCCTTTGTGCCCGACC  1801
                |||||||||  || ||||||||||   ||||||| ||||||||| |||||||||| ||||
Sbjct  7394586  ACCACCCCATTCCTATCTTCTCCTTGGGGCCCCTCTCTGCCTGTCCCTTTGTGCCTGACC  7394527

Query  1802     GAGCTGCTCCCCACAGTC-GAAAAAGTATG-AAAAAACAGATGACTAAAGAGAAGTAAAG  1859
                |||||||||||  ||| |  |||||| | | ||||||| ||||||| |||||||||||||
Sbjct  7394526  GAGCTGCTCCCTGCAGGCAAAAAAAGGAAGAAAAAAACTGATGACTGAAGAGAAGTAAAG  7394467

Query  1860     GATGGGTGCAGACCATTC-Gcacacctgtaatcccagcactttgggaggccaaggttggc  1918
                 ||||||| ||| || || ||||||||||  |||||||||||||||||||||||||||| 
Sbjct  7394466  AATGGGTGGAGATCA-TCTGCACACCTGTTTTCCCAGCACTTTGGGAGGCCAAGGTTGGT  7394408

Query  1919     ggatcactcaaagccaggaactcaagaccagcctggtgaacagggtaaaa-ccctgtctc  1977
                ||||||||| ||| ||||| ||  ||||||| ||| | |||| || |||| |||  ||| 
Sbjct  7394407  GGATCACTCGAAGACAGGATCTTGAGACCAGGCTGATCAACATGGAAAAATCCC-ATCTT  7394349

Query  1978     tacgaaaaatacaaaaatta-gcaggcttggtggcacgtgcctgtactcccagctacttg  2036
                ||  |||||||||||||| |  |||||||||||| |  |||||| | ||||||| | |||
Sbjct  7394348  TATTAAAAATACAAAAATCACCCAGGCTTGGTGGAATATGCCTGCAGTCCCAGCCATTTG  7394289

Query  2037     agtggttgaggcacgagaatcacttgagccc-cacaggaaaggattccagtgatcccaga  2095
                |||||||||||||||||||||||||||||||  | |||| |||||| |||||| ||||||
Sbjct  7394288  AGTGGTTGAGGCACGAGAATCACTTGAGCCCTGA-AGGACAGGATTGCAGTGAGCCCAGA  7394230

Query  2096     ttgcaccact-acactccagcctgaatgacaaagc-aatatttttgtctccaaaaataaa  2153
                |||||||| |  ||||||||||| ||||||||| |  | | ||||||||||         
Sbjct  7394229  TTGCACCA-TCGCACTCCAGCCTAAATGACAAA-CTGAGA-TTTTGTCTCC---------  7394182

Query  2154     aaaataaataatgaaataaaaGAACAAGAATGGGTGGGAATTACTCAAAATGGTCTAA-T  2212
                   | |||  |  |||  |||||||||||||||||||||| ||||||||||| ||||| |
Sbjct  7394181  ---A-AAA-CA--AAA-CAAAGAACAAGAATGGGTGGGAAATACTCAAAATGATCTAATT  7394130

Query  2213     TTTATTTGGCTGCTATGATGTTCCGCAGCTGAACCTCAATCACAGACAAACTAGTGCCTC  2272
                ||||||||| |||| ||||||||  || ||||| |||||||||||||||| ||||   ||
Sbjct  7394129  TTTATTTGGTTGCTTTGATGTTCTACAACTGAAACTCAATCACAGACAAATTAGTATTTC  7394070

Query  2273     GTTATTTTTCCATCAGTAACTCAATAACTAGAGATTTCTGATGTATAAATCCCTAAAACA  2332
                |||||||||||||| ||||||| |||||||||||||||||||| ||||||   |      
Sbjct  7394069  GTTATTTTTCCATCCGTAACTCGATAACTAGAGATTTCTGATGGATAAAT---T------  7394019

Query  2333     AGTAAATCAATTACAGAGGACACCAGAAAGTTTTCACTGAGGT--TCTCTATTTCTGATA  2390
                 |   | | |  ||  |||     | |||||||||| | ||||  ||| |||| ||||||
Sbjct  7394018  -G--CA-C-A--AC--AGG---TTA-AAAGTTTTCATTCAGGTGCTCTTTATTGCTGATA  7393972

Query  2391     TTTCTTGGTAATCATCCTTGCAGGGATAACATTCTCATCACTGAAGAATTTTAGTTTCTC  2450
                || |||||||| ||||||||||||||||||| ||||||||||| |||| ||||| |||||
Sbjct  7393971  TTCCTTGGTAACCATCCTTGCAGGGATAACAGTCTCATCACTGTAGAACTTTAGCTTCTC  7393912

Query  2451     -TT-----TCT--G--AC---T--CTGTAGCTCTCATTGACT-CCACCTCAATATTTTCC  2494
                 ||     |||  |  ||   |  ||| || ||||| ||| |  |||||||| |||||||
Sbjct  7393911  TTTCCGACTCTAGGACACGGGTCCCTGAAGTTCTCACTGA-TGTCACCTCAACATTTTCC  7393853

Query  2495     T-CAAGTCTTGCCCCCTGCTCTTAGGATTTTTTCCCTCGCACTGAGCACCTGTCTGAAAC  2553
                | |||  ||||||||||||| ||| | ||||||||||| |||||| || |  | |     
Sbjct  7393852  TCCAA-CCTTGCCCCCTGCTGTTATG-TTTTTTCCCTCACACTGAACA-C--T-T-----  7393804

Query  2554     AGAGCTCTGTGCTTCCTTTAAGTTGCACATGTggcctgggcacagtcgctcatgcctgta  2613
                   || |||||||||||||||||||  |||||||||||| ||||||| |||||||| |||
Sbjct  7393803  ---GC-CTGTGCTTCCTTTAAGTTG--CATGTGGCCTGGACACAGTCACTCATGCCAGTA  7393750

Query  2614     atcccagcacttta-gaaggccgaggcaggagaatcccatgcgaccagcagtttgagacc  2672
                |||||||||||||| ||| || |||||||||| |||||||  | ||||||||||||||||
Sbjct  7393749  ATCCCAGCACTTTAGGAA-GCTGAGGCAGGAGGATCCCATAAGCCCAGCAGTTTGAGACC  7393691

Query  2673     tgctggggcaacatagtgaaacactttctc-aatttttttgtaataaaaatattggaatt  2731
                 ||||| |||||| || ||||| || |||| |||| | || |||||||||| ||||||||
Sbjct  7393690  AGCTGGAGCAACACAGCGAAACCCTGTCTCAAATTGTCTT-TAATAAAAATTTTGGAATT  7393632

Query  2732     attaaaaaa-g---gaaataagaaaagaggaaaataaCTTGCACCTACATACTAGATTTT  2787
                ||||||||| |    |||||||||||||| ||||||  ||||||| ||||| ||||||||
Sbjct  7393631  ATTAAAAAATGAAATAAATAAGAAAAGAGAAAAATAGTTTGCACCCACATAGTAGATTTT  7393572

Query  2788     AGTGTCCAAGGGCCTAGAAGAGAACATTGGATTTCTCTACCCCGCTAGGCACGCCTTCCC  2847
                |||||||||| |||| ||||||||| ||||||||||||||||| || |||||||||||||
Sbjct  7393571  AGTGTCCAAGTGCCTGGAAGAGAACTTTGGATTTCTCTACCCCACTGGGCACGCCTTCCC  7393512

Query  2848     TAGCAGCAAAGATGGAGCTCCAGTTCCTCAGACGGTGATGAGCCACAGGACGGGCAGGGG  2907
                |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Sbjct  7393511  TAGCAGCAAAGATGGAGCTCCAGTTCCTCAGACGGTGATGAGCCACAGGAAGGGCAGGGG  7393452

Query  2908     GCGGGGCCAATGAAGATCCTCTTGGGCTGCCTGACTTCCCTTAGTGTACACATCAACTAA  2967
                | ||||||||||||||||||||||||||||||||||||||| ||||||||||||| || |
Sbjct  7393451  GTGGGGCCAATGAAGATCCTCTTGGGCTGCCTGACTTCCCTCAGTGTACACATCAGCTCA  7393392

Query  2968     GCCCGAAGTGGGGTGAAGATCTCCCAATCGACATGAACCAAGGAATTCAAACTCTCCTCG  3027
                |||||||||||||||||||||||||||| |||| ||||||||||||||||||||||||| 
Sbjct  7393391  GCCCGAAGTGGGGTGAAGATCTCCCAATTGACACGAACCAAGGAATTCAAACTCTCCTCA  7393332

Query  3028     GGGGCAGGATACATCTCCAGGCTTAACTTGCTCAGCCCACTGGTGTGGCACAGCAGGTCC  3087
                |||||||||||| |||||||||||||||||||||||||||||||||||| ||||||||||
Sbjct  7393331  GGGGCAGGATACGTCTCCAGGCTTAACTTGCTCAGCCCACTGGTGTGGCGCAGCAGGTCC  7393272

Query  3088     TTCAGGGCTTCCATAGACATGCAATTTCTGCCAAAGTAGAAGGTGGTGAGCTGGGAGCAG  3147
                |||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| 
Sbjct  7393271  TTCAGGGCGTCAATAGACATGCAATTTCTGCCAAAGTAGAAGGTGGTGAGCTGGGAGCAC  7393212

Query  3148     CGGCTCAGGCCAGGCAGGATGGCACTGAGTTGGGAGTAGTGGATCTGACAGCCCTCCAAG  3207
                ||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7393211  CGGCTCAGGGCAGGCAGGATGGCACTGAGTTGGGAGTAGTGGATCTGACAGCCCTCCAAG  7393152

Query  3208     ATGAGGGTCTTAAGAG  3223
                |||||||| || ||||
Sbjct  7393151  ATGAGGGTTTTGAGAG  7393136


 Score = 1762 bits (954),  Expect = 0.0
 Identities = 1865/2280 (81%), Gaps = 161/2280 (7%)
 Strand=Plus/Minus

Query  984      gaaggggggacctcctgggcCCTCGAGAGCACTAGGGGACCTTGTTTGGTAACTGCAACC  1043
                |||||||||| ||||||| |||||||||| ||| ||||||||  |||||||||||  |||
Sbjct  7460795  GAAGGGGGGATCTCCTGGACCCTCGAGAGTACTGGGGGACCTCATTTGGTAACTGTGACC  7460736

Query  1044     TGGGCAGCTTCAGTTGTGCCTTTggagctactgccctgccaacttgggaggaccaggact  1103
                ||| || ||||||||| | |||||||||||||||||||||||||  ||||||||||||||
Sbjct  7460735  TGGACAACTTCAGTTGCGTCTTTGGAGCTACTGCCCTGCCAACTCAGGAGGACCAGGACT  7460676

Query  1104     ccctcttgtcccaggatcccatcagctccaaagtgtgcacagcctcagctttgcCCTCTC  1163
                ||||||||||||||| ||||||||||||  |||||| | ||||||  ||| |||||||||
Sbjct  7460675  CCCTCTTGTCCCAGGCTCCCATCAGCTCTGAAGTGTACGCAGCCTTGGCTGTGCCCTCTC  7460616

Query  1164     TC--TGTTTCCGTGCAGAGGTGACAGGTGAGATGCAGGTTCACAGCAGCTCTGGTCAACC  1221
                ||  ||||||| |||||| ||||||| ||||| |||||| |||||||||||||| |||||
Sbjct  7460615  TCTGTGTTTCCCTGCAGAAGTGACAGTTGAGAAGCAGGTACACAGCAGCTCTGGCCAACC  7460556

Query  1222     CCACAGAAACAAATCTGAA-GCTCCTGGGTCCGGTTTAATGAGCCCCAACTGCGCTCTGA  1280
                ||||| ||||||| |  || ||||||||||  |||||||  |||||||||||| || | |
Sbjct  7460555  CCACACAAACAAA-CCCAATGCTCCTGGGTGTGGTTTAACCAGCCCCAACTGCACTATCA  7460497

Query  1281     TCCAGGAGTTTGCAGGCTAACAGCACAAAGTGGGGAGTGAGGTCGAGGCTGTGGTGGAGA  1340
                |||||||| |||||||||||| |||   |||| | ||||| || ||||||||||||||||
Sbjct  7460496  TCCAGGAGCTTGCAGGCTAACGGCAGGCAGTGAGCAGTGAAGTAGAGGCTGTGGTGGAGA  7460437

Query  1341     CTGCGGACCTAGGGGCAA-GTCCCGTTTAGCCGTGAGAGGGTATGGGTGGCACAGTTGGC  1399
                || | ||||| ||| ||| || || ||| ||  ||||||||| ||||||||||||| |||
Sbjct  7460436  CTCCAGACCT-GGGACAAGGTTCCATTTTGCAATGAGAGGGTGTGGGTGGCACAGTAGGC  7460378

Query  1400     TGCCTCAGGGACATGGGGCACAGGCCTGGCTGACAACCCAGCCAAGAGGTGGTGCCTTTA  1459
                ||||||||||| |||| |||||||||||||| |  |||| | |||| || |||||||  |
Sbjct  7460377  TGCCTCAGGGAAATGGAGCACAGGCCTGGCTCATGACCCTGTCAAG-GGGGGTGCCTCCA  7460319

Query  1460     GGAGTGGATCGT-GGTCCACAGGCCCAGCAATCGGAAGCATCAGGCTCTGTGTTCACCCC  1518
                ||||||| || | | ||| ||||||||||||||    |     ||  ||| | |||| ||
Sbjct  7460318  GGAGTGGTTCATAGTTCC-CAGGCCCAGCAATC----G-----GG--CTG-G-TCACTCC  7460273

Query  1519     TCTTGGGGGCAGATCTTGGAAATGCAGCCTCAGGAAGATTCACACAGA-ACTCCTTTTTA  1577
                | | |||||| ||||| |||||  |||| |  ||  ||| | || |||  |||| ||  |
Sbjct  7460272  TATGGGGGGCGGATCTCGGAAACACAGCATGGGGTGGATCCGCATAGACCCTCCCTTCAA  7460213

Query  1578     GACCTAGGAACTTGATACTATTAGCAGGGTGGGCACACAGTTG--ATGCATAGCTGGCCA  1635
                ||||| ||| ||||| ||| |||||||| ||||  |||||| |  | | |||||||||||
Sbjct  7460212  GACCTGGGAGCTTGACACTGTTAGCAGGATGGG--CACAGTGGCCA-G-ATAGCTGGCCA  7460157

Query  1636     GGTCATTG-AACTTGGTGCCATTTCTGCTTCCCAACTC-GGGGCCCTGGA-GCATGGCCC  1692
                |||| ||| |||  ||||||||||||||||| | || | ||  |||| || | |||||||
Sbjct  7460156  GGTCCTTGAAAC-AGGTGCCATTTCTGCTTCTC-ACCCTGGCCCCCT-GATGGATGGCCC  7460100

Query  1693     CAGCTCTGCCTT-TGGAACCTGACAACCACACTTCATGTGC-AAGCACGGCACCACCCCA  1750
                ||||| |||||| |||  |||| || || ||| || ||||| || |  ||||||||||||
Sbjct  7460099  CAGCTATGCCTTCTGG-GCCTGGCATCCGCACATCTTGTGCGAA-CGTGGCACCACCCCA  7460042

Query  1751     AGCCCATCTTCTCCTCATGGCCCCTTTCTGCCTGTGCCTTTGTGCCCGACCGAGCTGCTC  1810
                  || ||||||||||   ||||||| |||||| || |||| | ||| |||||||||||||
Sbjct  7460041  TTCCTATCTTCTCCTTGGGGCCCCTCTCTGCCCGTCCCTTCGCGCCTGACCGAGCTGCTC  7459982

Query  1811     CCCACAGTCGAAAAAGTATG-AAAAAACAGATGACTAAAGAGAAGTAAAGGATGGGTGCA  1869
                |||   | | |||||||| | ||||||| ||||||| ||||||||||||| ||||||| |
Sbjct  7459981  CCCTTGGGCAAAAAAGTAAGAAAAAAACTGATGACTGAAGAGAAGTAAAGAATGGGTGGA  7459922

Query  1870     GACCATTC-Gcacacctgtaatcccagcactttgggaggccaaggttggcggatcactca  1928
                 | || || | |  |||||  ||||||| |||||||||||||||||  | ||||||||||
Sbjct  7459921  AATCA-TCTGTATGCCTGTTTTCCCAGCGCTTTGGGAGGCCAAGGTCAGTGGATCACTCA  7459863

Query  1929     aagccaggaactcaagaccagcctggtgaacagggtaaaaccct-gtctctacgaaaaat  1987
                ||||||||| ||  ||||||| ||| | |||| || |||| |||  |||| |  ||||||
Sbjct  7459862  AAGCCAGGATCTTGAGACCAGGCTGATCAACATGG-AAAAACCTCATCTCCATTAAAAAT  7459804

Query  1988     acaaaaattag-caggcttggtggcacgtgcctgtac-tcccagctacttgagtggttga  2045
                |||||||| || ||| |||||||  |||||||||  | ||||||||| ||||||||||||
Sbjct  7459803  ACAAAAATCAGCCAGTCTTGGTGAAACGTGCCTG-CCGTCCCAGCTAATTGAGTGGTTGA  7459745

Query  2046     ggcacgagaatcacttgagccc-cacaggaaaggattccagtgatcccagattgcaccac  2104
                ||||| ||||||||||||||||  | ||||||||||| || ||| |||||||||||||||
Sbjct  7459744  GGCACAAGAATCACTTGAGCCCTGA-AGGAAAGGATTGCAATGAGCCCAGATTGCACCAC  7459686

Query  2105     tacactccagcctgaatgacaaagc-aatatttttgtctccaaaaataaaaaaataaata  2163
                | ||||||||||| ||||||||| |  | | ||||||||||            | |||  
Sbjct  7459685  TGCACTCCAGCCTAAATGACAAA-CTGAGA-TTTTGTCTCC------------A-AAA-C  7459642

Query  2164     atgaaataaaaGAACAAGAATGGGTGGGAATTACTCAAAATGGTCTAATTTTATTTGGCT  2223
                |  |||  |||||||||||||||||||||| |||| |||||| || |||||||||||| |
Sbjct  7459641  A--AAA-CAAAGAACAAGAATGGGTGGGAAATACTTAAAATGATCAAATTTTATTTGGTT  7459585

Query  2224     GCTATGATGTTCCGCAGCTGAACCTCAATCACAGACAAACTAGTGCCTCGTTATTTTTCC  2283
                ||| ||||||||  |||||||| |||||||||||||||| ||||   || ||||||||||
Sbjct  7459584  GCTTTGATGTTCTACAGCTGAAACTCAATCACAGACAAAGTAGTATTTCATTATTTTTCC  7459525

Query  2284     ATCAGTAACTCAATAACTAGAGATTTCTGATGTATAAATCCCTAAAACAAGTAAATCAAT  2343
                ||||||||||||||||||||| ||||||| || ||||||  ||| |||| ||   | || 
Sbjct  7459524  ATCAGTAACTCAATAACTAGATATTTCTGGTGGATAAATTGCTACAACACGT---T-AA-  7459470

Query  2344     TACAGAGGACACCAGAAAGTTTTCACTGAGGTTCTCT--ATTTCTGATATTTCTTGGTAA  2401
                 | ||              |||||| | |||| ||||  |||||||||||| ||||||||
Sbjct  7459469  -A-AG--------------TTTTCATTCAGGTGCTCTTTATTTCTGATATTCCTTGGTAA  7459426

Query  2402     TCATCCTTGCAGGGATAACATTCTCATCACTGAAGAATTTTAGTTTCTCTTTCTGACTCT  2461
                 ||||||||||||||||||||||||||||||| |||| ||||| ||||||||| ||||||
Sbjct  7459425  CCATCCTTGCAGGGATAACATTCTCATCACTGTAGAACTTTAGCTTCTCTTTCCGACTCT  7459366

Query  2462     GTAG--C-----TC--T------C--ATTGAC-TCCACCTCAATATTTTCCTCAAGTCTT  2503
                ||||  |     ||  |      |  |||||  || ||||||| ||||||||| || |||
Sbjct  7459365  GTAGGACACGGGTCCCTGAAGTTCTCATTGATGTC-ACCTCAACATTTTCCTCCAGCCTT  7459307

Query  2504     GCCCCCTGCTCTTAGGATTTTTTCCCTCGCACTGAGCACCTGTCTGAAACAGAGCTCTGT  2563
                |||||||||| ||| | |||| || ||| |||||||||| | |  |   |    ||  ||
Sbjct  7459306  GCCCCCTGCTGTTATG-TTTTCTCTCTCACACTGAGCAC-T-T--G---C----CT--GT  7459261

Query  2564     GCTTCCTTTAAGTTGCACATGTggcctgggcacagtcgctcatgcctgtaatcccagcac  2623
                |||||||||||||||||  |||||||||| ||||||| |||||||| |||||||||||||
Sbjct  7459260  GCTTCCTTTAAGTTGCA--TGTGGCCTGGACACAGTCACTCATGCCAGTAATCCCAGCAC  7459203

Query  2624     tttag-aaggccgaggcaggagaatcccat-gcgaccagcagtttgagacctgctggggc  2681
                ||||| ||| | |||||||||| ||||||  || || | |||   || |||  |||   |
Sbjct  7459202  TTTAGGAAG-CTGAGGCAGGAGGATCCCAGAGCAAC-A-CAGA--GAAACC--CTGTCTC  7459150

Query  2682     aacatagtgaaacactttctcaatttttttgtaataaaaatattggaattattaaaaaag  2741
                || || ||    |  |||   |||        || |||  | ||||||||||||||||| 
Sbjct  7459149  AA-ATTGT----C--TTT---AAT--------AA-AAAT-T-TTGGAATTATTAAAAAAT  7459111

Query  2742     gaaataa----gaaaagaggaaaataaCTTGCACCTACATACTAGATTTTAGTGTCCAAG  2797
                |||||||    |||||||| ||||||  ||||||||||||| ||||||||||||||||||
Sbjct  7459110  GAAATAAATAAGAAAAGAGAAAAATAGTTTGCACCTACATAGTAGATTTTAGTGTCCAAG  7459051

Query  2798     GGCCTAGAAGAGAACATTGGATTTCTCTACCCCGCTAGGCACGCCTTCCCTAGCAGCAAA  2857
                 |||| ||||||||| ||||||||||||||||| || |||||||||||||||||||||||
Sbjct  7459050  TGCCTGGAAGAGAACTTTGGATTTCTCTACCCCACTGGGCACGCCTTCCCTAGCAGCAAA  7458991

Query  2858     GATGGAGCTCCAGTTCCTCAGACGGTGATGAGCCACAGGACGGGCAGGGGGCGGGGCCAA  2917
                |||||||||||||||||||||||||||||||||||||||| |||||||||| ||||||||
Sbjct  7458990  GATGGAGCTCCAGTTCCTCAGACGGTGATGAGCCACAGGAAGGGCAGGGGGTGGGGCCAA  7458931

Query  2918     TGAAGATCCTCTTGGGCTGCCTGACTTCCCTTAGTGTACACATCAACTAAGCCCGAAGTG  2977
                |||||||||||||||||||||||| |||||| ||||||||||||| || |||||||||||
Sbjct  7458930  TGAAGATCCTCTTGGGCTGCCTGAATTCCCTCAGTGTACACATCAGCTCAGCCCGAAGTG  7458871

Query  2978     GGGTGAAGATCTCCCAATCGACATGAACCAAGGAATTCAAACTCTCCTCGGGGGCAGGAT  3037
                |||||||||||||||||| |||| ||||||||||||||||||||||||| ||||||||||
Sbjct  7458870  GGGTGAAGATCTCCCAATTGACACGAACCAAGGAATTCAAACTCTCCTCAGGGGCAGGAT  7458811

Query  3038     ACATCTCCAGGCTTAACTTGCTCAGCCCACTGGTGTGGCACAGCAGGTCCTTCAGGGCTT  3097
                || |||||||||||||||||||||||||||||||||||| |||||||||||||||||| |
Sbjct  7458810  ACGTCTCCAGGCTTAACTTGCTCAGCCCACTGGTGTGGCGCAGCAGGTCCTTCAGGGCGT  7458751

Query  3098     CCATAGACATGCAATTTCTGCCAAAGTAGAAGGTGGTGAGCTGGGAGCAGCGGCTCAGGC  3157
                | |||||||||||||| |||||||||||||||||||||||||||||||||| ||||||||
Sbjct  7458750  CAATAGACATGCAATTGCTGCCAAAGTAGAAGGTGGTGAGCTGGGAGCAGCAGCTCAGGC  7458691

Query  3158     CAGGCAGGATGGCACTGAGTTGGGAGTAGTGGATCTGACAGCCCTCCAAGATGAGGGTCT  3217
                |||||||||||||||||||||||||||||||||||||||||||||| || | ||||||||
Sbjct  7458690  CAGGCAGGATGGCACTGAGTTGGGAGTAGTGGATCTGACAGCCCTCTAACACGAGGGTCT  7458631


 Score = 1640 bits (888),  Expect = 0.0
 Identities = 1660/2023 (82%), Gaps = 92/2023 (4%)
 Strand=Plus/Minus

Query  6732     TTTTTATTTTGAAAAACTGTAA-GAGAAATTATAAAAGCAGTGTTG-CAGTAG-TCTAGA  6788
                |||||||||||||||| |||||  ||||||| ||||| |||   || |||| | ||||||
Sbjct  7371930  TTTTTATTTTGAAAAATTGTAACAAGAAATTGTAAAAACAG-CATGACAGT-GTTCTAGA  7371873

Query  6789     GCACT-TGGAAGGTAGAAATGGAAACACTAAGTCTGAGGA-GAAGGATCCAATACACATC  6846
                || || || ||| |||  ||  ||||||||| ||| | || ||||| ||||||    |||
Sbjct  7371872  GC-CTGTGAAAGTTAGGGATAAAAACACTAACTCTCA-GATGAAGGTTCCAATGTTGATC  7371815

Query  6847     CCTTCCACATACTCACAATCACACACTTAGGGACAGAGTCTAAGGG-AAGAGATAAATCC  6905
                 ||| |||| ||||||||| || ||||| ||||  || |||| ||| || | ||   |||
Sbjct  7371814  TCTTACACAGACTCACAATGACCCACTTTGGGATGGAATCTAGGGGAAAAAAATGGGTCC  7371755

Query  6906     CAGGTTCGGAAC-AAG--T---CTCTTGAGAATGGTGTACGGGAGATC--TAAGAT-TTC  6956
                || |||| |||| |||  |   |||||||||||||  || || | |||  |||| | || 
Sbjct  7371754  CATGTTCAGAACAAAGACTCCACTCTTGAGAATGGCCTATGGAATATCTTTAAGGTATT-  7371696

Query  6957     TGT-AAAA-TGAAAGCCTGACTA-ATAAAATCACAATACCGCTAAGTGTGTGAACTATAG  7013
                 || |||| | || |||| || |  ||||||||| || || | |||| | ||||||||| 
Sbjct  7371695  AGTAAAAACT-AAGGCCTAAC-ATGTAAAATCACGATGCCACCAAGTCTATGAACTATAA  7371638

Query  7014     CTGACA-GGCACAGAAACCAACAACTTCACATGTCAAGACATAAACATCCATCCAACTGT  7072
                 | | | |||||| |||| ||  | |||| |||||| || ||||| || || |||  |||
Sbjct  7371637  TTTA-AGGGCACAAAAACTAATTATTTCAAATGTCACGAAATAAAAATTCAACCAGTTGT  7371579

Query  7073     AAATTTTTAATAt-t-tt-tttttttAAAAACTGCTTCAATAAGAATTTTGAAATGAGGA  7129
                || |||||||||| | || ||     |||||||||||||||||||||||||||||||  |
Sbjct  7371578  AACTTTTTAATATCTCTTGTTAAAAAAAAAACTGCTTCAATAAGAATTTTGAAATGACAA  7371519

Query  7130     AAATGAAGCACAAATCAAAATTTGAGGGATGAAGTCAAAACTATATTTGGAGGAAAAATC  7189
                |||  ||||||||||| || |||| ||||||||| |||||||| |||| |||||||||||
Sbjct  7371518  AAACCAAGCACAAATCCAATTTTGGGGGATGAAGACAAAACTACATTTAGAGGAAAAATC  7371459

Query  7190     AAAACCTACATCTGTTTAATCTGAAAAAACAGAC-AGGAAATTCTCTGTGCCATTTTGGG  7248
                ||| |||| || || ||  ||||  ||||||||| || ||||||||| |||||  |||||
Sbjct  7371458  AAAGCCTAAATTTG-TTCTTCTG--AAAACAGACAAGAAAATTCTCTCTGCCACCTTGGG  7371402

Query  7249     CTGTGTGTCACCATCCCTGA----CTGGCTGGCTGCAGATTAGACGGGCATGTTCCTAAG  7304
                |||  |||||||||||||||    |||||||||||||||| ||| |||||||  ||||||
Sbjct  7371401  CTGCATGTCACCATCCCTGACTGGCTGGCTGGCTGCAGATCAGATGGGCATGACCCTAAG  7371342

Query  7305     AAGGTGGTGACTTACCAGATCTGGACTCAGTTTGCAGGGTGCTGGGACCTCTCAGAGAAC  7364
                 |||||||||||||||||||||||||||||||||||||||||||  ||||||||||||||
Sbjct  7371341  GAGGTGGTGACTTACCAGATCTGGACTCAGTTTGCAGGGTGCTGCAACCTCTCAGAGAAC  7371282

Query  7365     CAAGCAGTAGCTCCAGGCACCAGGGCTTTGG-GTCTGTCCTGTGCAAAC-TCAGGAGCTT  7422
                | |||||||||||||||   ||| || ||||  ||| |||||||| | | || |||||||
Sbjct  7371281  CGAGCAGTAGCTCCAGGTGTCAGCGCCTTGGATTCTCTCCTGTGC-ACCTTCGGGAGCTT  7371223

Query  7423     TTGTTGATGTTTCTAACCACACCCTCCCCTTCTCAATC-ACCAGCTTCCAATCAGAAAGT  7481
                || | ||  |||||||||||||||||||| |||||| | |||| |||||||||||||| |
Sbjct  7371222  TTATGGACCTTTCTAACCACACCCTCCCCATCTCAA-CAACCAACTTCCAATCAGAAAAT  7371164

Query  7482     GATACCTGATTAGATCCTGAAGTTCCACCCAGTTAATCCTGATTGAGTTTCAC-ACTTTC  7540
                |||  |||||||||| ||||||||||||||||||||||||||||||||||  | ||||||
Sbjct  7371163  GATGTCTGATTAGATTCTGAAGTTCCACCCAGTTAATCCTGATTGAGTTT-GCGACTTTC  7371105

Query  7541     TTCTGATTCATTGATTAAATTAGATGTGCATTTATGAAAGTGAAAGA-ATAAATAACAGG  7599
                |||||||| |||||||  || |||| | | ||||||||||||||||| |||||||| |||
Sbjct  7371104  TTCTGATTAATTGATTGGATCAGATATACGTTTATGAAAGTGAAAGATATAAATAATAGG  7371045

Query  7600     GTGAAAGTCCAAAAGTCATTAATTCATTTATTCCCCAAACACTGATGAAGTTTGACTAAC  7659
                ||||||||||| || ||||| |||| |||||||| |||||||||||| ||||||||| ||
Sbjct  7371044  GTGAAAGTCCACAACTCATTCATTCCTTTATTCCACAAACACTGATGGAGTTTGACTGAC  7370985

Query  7660     ATGTGACCTTCATAGTGA--CATGG-AA-GGTTTAATCTGTTCCTGGCATTAGAAAGAAA  7715
                ||| || |||||||||||  || || || |||| |||||||| |||||||| || |||||
Sbjct  7370984  ATGAGAGCTTCATAGTGATGCA-GGAAAGGGTTGAATCTGTTTCTGGCATTTGACAGAAA  7370926

Query  7716     AAACAAAACCTGATGATATCTTT-ATGGGAGAATATTTGGCCACATTGAA-ATTATCCAA  7773
                ||||||||||||| | |||||||  |||| | || |||||||||| | || |||||| ||
Sbjct  7370925  AAACAAAACCTGAAGGTATCTTTGCTGGG-GGATCTTTGGCCACA-TAAACATTATCAAA  7370868

Query  7774     ACGTTTCAGAGCTAAGACAGCTTTAAAAAGACGGTGATGTCAACCCTAAGAAAACAGAAT  7833
                | || |||||||||| |||||| ||| ||||| || || ||| |||||||||| ||||||
Sbjct  7370867  ATGTCTCAGAGCTAAAACAGCTCTAAGAAGACAGTAATTTCATCCCTAAGAAAGCAGAAT  7370808

Query  7834     ACAA-AGCTCTG-TTATCCAACAGTTACCTGGGTTTTATGCTTCCTAACGGGGCAGGTCA  7891
                | || | |||||  ||||||   || | ||||| |||| |||| |||||  || || |||
Sbjct  7370807  A-AATATCTCTGCATATCCAGTGGTCAGCTGGGATTTACGCTTTCTAACATGGTAGATCA  7370749

Query  7892     TATGTGGGTTCAGGTTGAAGAGGGGAACCACTGAGGGTGTTATTGATCACAAGACTAAGG  7951
                ||||    ||||||| | |||||||||||||||||||||| ||||||| |||||| ||||
Sbjct  7370748  TATGCCCATTCAGGTGGCAGAGGGGAACCACTGAGGGTGTGATTGATCTCAAGACGAAGG  7370689

Query  7952     -TCAAGGCTTCACTGCAGGAAATCAGGA-CAGAATGACAAAGTGAGGTGGGGGCTGGGCA  8009
                 || ||||||| | | ||||||| |  | || ||| ||||||||||||||||||||||||
Sbjct  7370688  TTC-AGGCTTCTCCGGAGGAAATTA-AACCAAAATTACAAAGTGAGGTGGGGGCTGGGCA  7370631

Query  8010     GGATGGGACCGGGTGTTCTAGTAGAACCCTGGGAAGGAACCAAGACAGCATAAAACATGG  8069
                |||||||||||||||||||| | |||||||||||||||||||||||||||||||||||||
Sbjct  7370630  GGATGGGACCGGGTGTTCTAATGGAACCCTGGGAAGGAACCAAGACAGCATAAAACATGG  7370571

Query  8070     TGGGTATTTTGTGGGC-ATCTCCACAGAAGGATTGAAAGACTCTGTCTGGATTGAGTTTA  8128
                |||||||||||||||  |     || |||||||||||||||||  | | |||||| || |
Sbjct  7370570  TGGGTATTTTGTGGGAGAGGAG-ACGGAAGGATTGAAAGACTCCATTTAGATTGAATTCA  7370512

Query  8129     AAAATTAAAAAGGGAATAGTTACAGAAGAGACAGTGCAGACTCTTCAAACACAACATTGT  8188
                |||| | |||||| |||| ||||| |||||||| || ||||||   |||||||| |||| 
Sbjct  7370511  AAAACTGAAAAGGAAATAATTACAAAAGAGACACTGTAGACTCA--AAACACAATATTGC  7370454

Query  8189     CTTTGAGGGCA-GAGAAGGCAGAAACAGTCTTGGCC-CCTACTAGAAGGGAAAGCGTGTT  8246
                ||||||||||| | || |  ||| |||||||||| | ||| |||||||| ||||||||||
Sbjct  7370453  CTTTGAGGGCATGGGACG--AGATACAGTCTTGGTCACCT-CTAGAAGGTAAAGCGTGTT  7370397

Query  8247     TACTCCCAAAAATGATGGGCTCGCCTCAGAAAATCAGCCT-GGGAAGATGGAATCTGAGA  8305
                ||||| |||||||||||||| | |||||||||| |||| | |||| ||| ||||||||||
Sbjct  7370396  TACTCACAAAAATGATGGGCACCCCTCAGAAAACCAGCTTCGGGA-GATTGAATCTGAGA  7370338

Query  8306     ATCTGAGCTGGGGCAGATGCCAGAGAGAAGCAGTGTGGCCAGACCTGGGAAGGGAGACTT  8365
                || ||||||||| |||| |||||| |||||||  |||||||| |||  ||||||||||| 
Sbjct  7370337  ATGTGAGCTGGGACAGAGGCCAGACAGAAGCACAGTGGCCAGGCCTAAGAAGGGAGACTC  7370278

Query  8366     TCCCAACCTGGAAGCCATC-GAAGGTGGGAGCTGTGGGTTTTGCAGGA--TGTGGGAGAA  8422
                 ||||| |||||||||| | || ||||| ||||||||| | |||||||  || |||||||
Sbjct  7370277  CCCCAAGCTGGAAGCCA-CAGAGGGTGGAAGCTGTGGGCTCTGCAGGACATGGGGGAGAA  7370219

Query  8423     AGTGAACAAGGGTCCAAGTCTC--TGTCATGGTGCTATGGTCTGGAAACCTTTCTTTTAG  8480
                | || ||||||||||  |||||  |||||||| ||||||||||||||| ||||| |||||
Sbjct  7370218  A-TGCACAAGGGTCCGTGTCTCCCTGTCATGGCGCTATGGTCTGGAAATCTTTCCTTTAG  7370160

Query  8481     ACTCAGGGATCTTCCCACAGTGGGACATTTCCCAGCAACCCTCACC-CACAGGTGTTTCC  8539
                ||||||||||||||||||||||| ||||||||||||||||||||   | ||||  |||||
Sbjct  7370159  ACTCAGGGATCTTCCCACAGTGGAACATTTCCCAGCAACCCTCAGGTC-CAGGCATTTCC  7370101

Query  8540     CAGGGCCCCTCATCCTCATCAATACCC-TCGTGCCA-TTCCCCAGC-ATATTTTGATAAT  8596
                |||||||| |||||||||||||| ||| ||| |||  || || ||  |||||||||| ||
Sbjct  7370100  CAGGGCCCTTCATCCTCATCAAT-CCCATCG-GCCCCTTTCC-AGGTATATTTTGATCAT  7370044

Query  8597     TAATGTTCTGC-CATCCTTAAAGTCCTCCCTTGTCCCTGATATTGAACAGAGAGATTCTG  8655
                ||||||| | | |||||||||||||||| ||||||||| |||||||||| ||||||||||
Sbjct  7370043  TAATGTTTT-CTCATCCTTAAAGTCCTCTCTTGTCCCTAATATTGAACATAGAGATTCTG  7369985

Query  8656     ATTA-AAGTGATACCATTAGGTATACAAAGAAAACTCAggcca  8697
                || | ||   | | ||||||| |||  ||||||||||||||||
Sbjct  7369984  ATCAGAACA-ACAACATTAGGCATATGAAGAAAACTCAGGCCA  7369943


 Score = 1218 bits (659),  Expect = 0.0
 Identities = 905/1019 (88%), Gaps = 35/1019 (3%)
 Strand=Plus/Minus

Query  2229     GATGTTCCGCAGCTGAACCTCAATCACAGACAAAC-TAGTGCCTCGTTATTTTTCCATCA  2287
                ||||||  ||||||||| ||||||||||||| |||  ||| | | | || ||||||||||
Sbjct  7526077  GATGTTTTGCAGCTGAATCTCAATCACAGAC-AACAGAGTACTTTGATACTTTTCCATCA  7526019

Query  2288     GTAACTCAATAACTAGAGATTTCTGATGTATAAATCCCTAAAACAAGTAAATCAATTACA  2347
                |||||||||||||||||||||||||||||||||||| ||||||||||| |||||| ||||
Sbjct  7526018  GTAACTCAATAACTAGAGATTTCTGATGTATAAATCGCTAAAACAAGTCAATCAAATACA  7525959

Query  2348     GAGGACACCAGAAAGTTTTCACTGAGGTTCTCTATTTCTGATATTTCTTGGTAATCATCC  2407
                ||||||||||||||||||||| |||||   | |||||||||||||||||||||| | |||
Sbjct  7525958  GAGGACACCAGAAAGTTTTCATTGAGG---T-TATTTCTGATATTTCTTGGTAACCGTCC  7525903

Query  2408     TTGCAGGGATAACATTCTCATCACTGAAGAATTTTAGTTTCTCTTTCTGACTCTGT----  2463
                 ||||||||||||||||||||||||| |||| ||||| ||||||||||||||||||    
Sbjct  7525902  CTGCAGGGATAACATTCTCATCACTGTAGAACTTTAGCTTCTCTTTCTGACTCTGTAGGA  7525843

Query  2464     -A---G---C------TCTCATTGACTCCACCTCAATATTTTCCTCAAGTCTTGCCCCCT  2510
                 |   |   |      |||||||||||||||||| | ||||||||| |||||||||||||
Sbjct  7525842  CATGGGTCCCGTAAGGTCTCATTGACTCCACCTCCACATTTTCCTCCAGTCTTGCCCCCT  7525783

Query  2511     GCTCTTAGGATTTTTTCCCTCGCACTGAGCACCTGTCTGAA--ACAGAGCTCTGTGCTTC  2568
                ||| |||   |||||||||||  |||||||||||| |||||  | |||  ||||||||||
Sbjct  7525782  GCTGTTA-TCTTTTTTCCCTCATACTGAGCACCTGCCTGAAGCAAAGAATTCTGTGCTTC  7525724

Query  2569     CTTTAAGTTGCACATGTggcctgggcacagtcgctcatgcctgtaatcccagcactttag  2628
                || |||||||  |||||||||||| |||| || |||||||| |||||||  |||||||||
Sbjct  7525723  CTGTAAGTTG--CATGTGGCCTGGTCACAATCACTCATGCCAGTAATCCTGGCACTTTAG  7525666

Query  2629     aaggccgaggcaggagaatcccatgcgaccagcagtttgagacctgctggggcaacatag  2688
                 ||||| |||||||||||||||||| | |||||||||| ||||| |||||||||||| ||
Sbjct  7525665  GAGGCCAAGGCAGGAGAATCCCATGTGCCCAGCAGTTTCAGACCAGCTGGGGCAACACAG  7525606

Query  2689     tgaaacactttctc-aatttttttgtaataaaaatattggaattattaaaaaaggaaata  2747
                 ||||| || |||| ||| || || |||| ||||| || |||||||||||||||||||||
Sbjct  7525605  CGAAACCCTGTCTCAAATGTTCTT-TAAT-AAAATTTTAGAATTATTAAAAAAGGAAATA  7525548

Query  2748     agaaaagaggaaa-ataaCTTGCACCTACATACTAGATTTTAGTGTCCAAGGGCCTAGAA  2806
                |||||| |  ||| ||||||||||| ||||||||||||||||||||||||| |||| |||
Sbjct  7525547  AGAAAA-AACAAACATAACTTGCACTTACATACTAGATTTTAGTGTCCAAGTGCCTGGAA  7525489

Query  2807     GAGAACATTGGATTTCTCTACCCCGCTAGGCACGCCTTCCCTAGCAGCAAAGATGGAGCT  2866
                |||||| |||||||| || ||||| |||||||||||||||||||||||||||||||||||
Sbjct  7525488  GAGAACTTTGGATTTATCAACCCCACTAGGCACGCCTTCCCTAGCAGCAAAGATGGAGCT  7525429

Query  2867     CCAGTTCCTCAGACGGTGATGAGCCACAGGACGGGCAGGGGGCGGGGCCAATGAAGATCC  2926
                ||||||||||||||||||||||||||||||| |||||||| | ||| ||| |||||||||
Sbjct  7525428  CCAGTTCCTCAGACGGTGATGAGCCACAGGAAGGGCAGGGAGTGGGACCAGTGAAGATCC  7525369

Query  2927     TCTTGGGCTGCCTGACTTCCCTTAGTGTACACATCAACTAAGCCCGAAGTGGGGTGAAGA  2986
                |||||||||||||||||||||| ||||||||||||| || |||||||||||||| |||||
Sbjct  7525368  TCTTGGGCTGCCTGACTTCCCTCAGTGTACACATCAGCTCAGCCCGAAGTGGGGCGAAGA  7525309

Query  2987     TCTCCCAATCGACATGAACCAAGGAATTCAAACTCTCCTCGGGGGCAGGATACATCTCCA  3046
                |||||||||||||| ||||||||||||||||||||||||| |||||||||||| ||||||
Sbjct  7525308  TCTCCCAATCGACACGAACCAAGGAATTCAAACTCTCCTCAGGGGCAGGATACGTCTCCA  7525249

Query  3047     GGCTTAACTTGCTCAGCCCACTGGTGTGGCACAGCAGGTCCTTCAGGGCT-TCCATAGAC  3105
                |||||||||||||||||||||||||||||| ||||||||||||||||| | ||| |||||
Sbjct  7525248  GGCTTAACTTGCTCAGCCCACTGGTGTGGCGCAGCAGGTCCTTCAGGG-TGTCCGTAGAC  7525190

Query  3106     ATGCAATTTCTGCCAAAGTAGAAGGTGGTGAGCTGGGAGCAGCGGCTCAGGCCAGGCAGG  3165
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7525189  ATGCAATTTCTGCCAAAGTAGAAGGTGGTGAGCTGGGAGCAGCGGCTCAGGCCAGGCAGG  7525130

Query  3166     ATGGCACTGAGTTGGGAGTAGTGGATCTGACAGCCCTCCAAGATGAGGGTCTTAAGAGT  3224
                ||||| ||||||||| |||||||||||||||||||||| |||||||||||||| |||||
Sbjct  7525129  ATGGCGCTGAGTTGGCAGTAGTGGATCTGACAGCCCTCGAAGATGAGGGTCTTGAGAGT  7525071


 Score = 1170 bits (633),  Expect = 0.0
 Identities = 782/853 (91%), Gaps = 13/853 (1%)
 Strand=Plus/Minus

Query  28475    GAGATCTGAGCTTCAGAGATCCTCGGTAACATTTGCCAGTGCTATGAGTTTAGTGGAT-C  28533
                ||||||||||||||| ||||||| | ||||| || |||||||||| ||| |||| | | |
Sbjct  7553448  GAGATCTGAGCTTCAAAGATCCTTGCTAACACTTCCCAGTGCTATCAGTGTAGTAG-TGC  7553390

Query  28534    AGTGGCTAATAATTCATGGA--C--TACGAGGGATCTTGCCTGCTCTTTAGAAGTTGGGA  28589
                ||||||||||||||||||||  |  || |||||||||||||||||||||||| |||||||
Sbjct  7553389  AGTGGCTAATAATTCATGGACCCTATAGGAGGGATCTTGCCTGCTCTTTAGAGGTTGGGA  7553330

Query  28590    CACATTCTTCATGGTACCAGAAGGGTAGAACTATGTCTCTGTGGCCACTTATTGCAGAAA  28649
                |||| ||||| | |||||||||||| ||||||||| ||||||||||||||||||||||| 
Sbjct  7553329  CACACTCTTCTTAGTACCAGAAGGGCAGAACTATGCCTCTGTGGCCACTTATTGCAGAAT  7553270

Query  28650    GGAACTGGAGTAAACTGAGGGCTCTTTCACACATGCTAGAGAAATGACTTGGGCCCTGGG  28709
                |||| ||||||||||||||||||||||||||||||||||||||||||||| |||||| ||
Sbjct  7553269  GGAATTGGAGTAAACTGAGGGCTCTTTCACACATGCTAGAGAAATGACTTTGGCCCTAGG  7553210

Query  28710    AGAATTGGGGGTTGCAGGGGATTGGTCGGAGGAACTTGCCTTTTTGCTGGATTGTGCTGT  28769
                ||||  |||| |||||||||||||| | ||| ||||||||||||  ||||||||| || |
Sbjct  7553209  AGAAGCGGGGATTGCAGGGGATTGGCCTGAGAAACTTGCCTTTTCACTGGATTGTCCTCT  7553150

Query  28770    AGAGTTTTTCCTTGTAGATTTGTCAGAATGAGCCTCCAGACCCCATCCAGACTCCTGGAG  28829
                |||||||||||||| |||||||||||||||||||||||| ||||||||||||||||||||
Sbjct  7553149  AGAGTTTTTCCTTGCAGATTTGTCAGAATGAGCCTCCAGTCCCCATCCAGACTCCTGGAG  7553090

Query  28830    CTGGCAGGGCAGAGCCTGA-TGAGGAAGCAGTTCTTGACTATCTTCACCCTGGACTAGCT  28888
                ||||||||||||||||| | ||||||| ||||||||||| ||||||| ||||||| ||||
Sbjct  7553089  CTGGCAGGGCAGAGCCT-ACTGAGGAACCAGTTCTTGACCATCTTCATCCTGGACGAGCT  7553031

Query  28889    GCCCAGGGAGGTCTCCCCTCTGACGTTCATGGAGGCCTTCAGCATGAGATGTTGTGAGGC  28948
                |||||||||||||| |||||||| ||||||||||||| |||||| |||| | ||||||||
Sbjct  7553030  GCCCAGGGAGGTCTTCCCTCTGATGTTCATGGAGGCCGTCAGCAGGAGACGCTGTGAGGC  7552971

Query  28949    CCTGAAGCTGATGGTGCAGGCCTGGTCCTCCCTTCACCTCCCTCTGGGATCCCTGATGAA  29008
                ||||||||||||||||||||||||||||| ||| ||||||||||||||||||||||||||
Sbjct  7552970  CCTGAAGCTGATGGTGCAGGCCTGGTCCTTCCTCCACCTCCCTCTGGGATCCCTGATGAA  7552911

Query  29009    GACAACTCATCTGGAGACCTTGCAAGCTGTGCTGAAGGGACTTGATACACTAG-TGTCCC  29067
                |||| |||||||||||||||||||||||||||||||||||||||||||||| | || |||
Sbjct  7552910  GACACCTCATCTGGAGACCTTGCAAGCTGTGCTGAAGGGACTTGATACACT-GCTGGCCC  7552852

Query  29068    AGAAGGTTTGCCCCAGTTGAGGTGACTCAGGTGGCCTGGTGGGAAGGGTCCAGGCATCCA  29127
                |||||||||||| ||| |||||||||||||||||||||||||||||||||||||||||||
Sbjct  7552851  AGAAGGTTTGCCTCAGGTGAGGTGACTCAGGTGGCCTGGTGGGAAGGGTCCAGGCATCCA  7552792

Query  29128    GGGAAGGGACAGCTGGCTCAGGAGGAGTGGCAGTG-TGTGGGAGCTAGGGTGGCTCAGAG  29186
                ||||||||||||||||||||||||||||||  | | || |||||||||||||||||||||
Sbjct  7552791  GGGAAGGGACAGCTGGCTCAGGAGGAGTGGTGGGGTTG-GGGAGCTAGGGTGGCTCAGAG  7552733

Query  29187    GCTTCTGATGGTACCCATGAGAGGCCTTGGCCATTGCCCAGATCCTCTGGAAAAGGACTG  29246
                |||||||||||| |||||||||||||||| |||||||||||||||||||| |||||||||
Sbjct  7552732  GCTTCTGATGGTGCCCATGAGAGGCCTTGACCATTGCCCAGATCCTCTGGGAAAGGACTG  7552673

Query  29247    CTCACCATACAGAGTCCACTGAGGAAACAGGAACCTGCTTCCTTCCCAGTGGAAGGTAAA  29306
                |||||||||||| ||||||||||||||||||||||||||| | ||||||||||| |||||
Sbjct  7552672  CTCACCATACAGGGTCCACTGAGGAAACAGGAACCTGCTTTC-TCCCAGTGGAACGTAAA  7552614

Query  29307    GGTACTAGAAGTG  29319
                | | |||||||||
Sbjct  7552613  GATTCTAGAAGTG  7552601


 Score = 1016 bits (550),  Expect = 0.0
 Identities = 1084/1336 (81%), Gaps = 60/1336 (4%)
 Strand=Plus/Minus

Query  6828     GAAGGATCCAATACACATCCCTTCCACATACTCACAATCACACACTTAGGGACAGAGT-C  6886
                ||||| ||| ||| ||||| |||||||||||||||||| || |||||  ||||||| | |
Sbjct  7389487  GAAGGTTCCTATAGACATCACTTCCACATACTCACAATTACCCACTTTTGGACAGA-TCC  7389429

Query  6887     TAAGGG-AAGAGATAAATCCCAGGTTC-G-G-AACAA--G-TCTCTTGAGAATGGTGTAC  6939
                || ||| || |||| ||||||| | || | | || ||  |  ||||||||| || |||  
Sbjct  7389428  TAGGGGCAA-AGATGAATCCCATGATCTGAGCAA-AACTGCACTCTTGAGATTGCTGTGT  7389371

Query  6940     GGGAGA--TCTAA-GA-TTTCTGTAAAATGAAAGCCTGACTAATAAAATCACAATACCGC  6995
                |||| |  | ||| || ||| || ||||||||||| | |||   | |||||||||| | |
Sbjct  7389370  GGGATACCTTTAAGGATTTTATG-AAAATGAAAGCAT-ACTTGGAGAATCACAATAACAC  7389313

Query  6996     TAAGTGTGTGAACTATAGCTGACA-GGCACAGAAACCAACAACTTCACATGTCAAGACAT  7054
                 |||| | |||||| ||  ||| | |||||| |||| || ||||||| ||||||||| ||
Sbjct  7389312  CAAGTCTATGAACTGTAATTGA-AGGGCACAAAAACAAATAACTTCAAATGTCAAGAAAT  7389254

Query  7055     AAACATCCAT-CCAACTGTAAATTTTTAATAtttttttttttAAAAA-CTGCTTCAATAA  7112
                ||| || |||  | |||||||||||||||||   | ||||| ||||| ||||||| ||||
Sbjct  7389253  AAAAATTCATGTC-ACTGTAAATTTTTAATA---TATTTTTAAAAAACCTGCTTCGATAA  7389198

Query  7113     GAATTTTGAAATGAGGAAAATGAAGCACAAATCAAAATTTGAGGGATGAAGTCAAAACTA  7172
                ||||||| ||||||  ||||  |||||||||||| ||||||| |||||||| ||||||||
Sbjct  7389197  GAATTTTAAAATGACAAAAACCAAGCACAAATCACAATTTGATGGATGAAGACAAAACTA  7389138

Query  7173     TATTTGGAGGAAAAATCAAAACCTACATCTGTTTAATCTGAAAAAACAGACAG-GAAAT-  7230
                 |||| |||||||||| ||| |||| ||||| || |||| |  ||||||||||  |||| 
Sbjct  7389137  CATTTAGAGGAAAAATGAAAGCCTAAATCTG-TTCATCTCACGAAACAGACAGAAAAATA  7389079

Query  7231     TCTCTGTGCCATTTTGGGCTGTGTGTCACCATCCCTGACTGGCTGGCTGCAGATTAGACG  7290
                | | ||||||| |||||| ||||||||||| ||||||||||||||||||| ||| ||| |
Sbjct  7389078  T-TGTGTGCCACTTTGGGATGTGTGTCACCGTCCCTGACTGGCTGGCTGCTGATCAGATG  7389020

Query  7291     GGCATGTTCCTAAGAAGGTGGTGACTTACCAGATCTGGACTCAGTTTGCAGGGTGCTGGG  7350
                ||||||  |||||| |||||||||||||||||  ||||||||| || |||| || |||||
Sbjct  7389019  GGCATGACCCTAAGCAGGTGGTGACTTACCAGCGCTGGACTCACTTCGCAGAGTTCTGGG  7388960

Query  7351     ACCTCTCAGAGAACCAAGCAGTAGCTCCAGGCACCAGGGCTTTGGGTCTGTCCTGTGCAA  7410
                ||||||||| ||||||| |||||||| |||| |  || ||| ||||||| | ||| | | 
Sbjct  7388959  ACCTCTCAGGGAACCAACCAGTAGCTTCAGGAATGAGTGCTGTGGGTCTCTTCTGGGTAC  7388900

Query  7411     ACTCAGGAGCTTTTGTTGATGTTTCTAACCACACCCTCCCCTTCTCAATCACCAGCTTCC  7470
                 ||||||||||||| | ||  ||||||||| |||||| ||||||||||||||||||||||
Sbjct  7388899  CCTCAGGAGCTTTTATAGACCTTTCTAACCCCACCCTTCCCTTCTCAATCACCAGCTTCC  7388840

Query  7471     AATCAGAAAGTGATACCTGATTAGATCCTGAAGTTC-CACCCAGTTAATCCTGATTGAGT  7529
                ||||||||||||||||||||||||||| || ||| | |||||||||||||||||||||||
Sbjct  7388839  AATCAGAAAGTGATACCTGATTAGATCTTGCAGT-CACACCCAGTTAATCCTGATTGAGT  7388781

Query  7530     TT-CACACTTTCTTCTGATTCATTGATTAAATTAGATGTGCATTTATGAAAGTGAAAGAA  7588
                || ||  ||||||||||| | ||||||  ||||||||   |||||||| |||| ||||||
Sbjct  7388780  TTTCAG-CTTTCTTCTGACTAATTGATCGAATTAGATACACATTTATGGAAGTAAAAGAA  7388722

Query  7589     TAAATAACAGGGTGAAAGTCCAAAAGTCATTAATTCATTTATTCCCCAAACACTGATGAA  7648
                ||||||| ||||||||||||||||| ||||| ||||||||||||| |||| |||||||||
Sbjct  7388721  TAAATAATAGGGTGAAAGTCCAAAACTCATTCATTCATTTATTCCTCAAATACTGATGAA  7388662

Query  7649     GTTT-GACTAACATGTGACCTTCATAGTGA--CATGGAAGGT-TTAATCTGTTCCTGGCA  7704
                |||| | |||| |   ||| ||||||||||  || ||||||  ||||||||||||||  |
Sbjct  7388661  GTTTCG-CTAATACACGACTTTCATAGTGATACAGGGAAGGGATTAATCTGTTCCTGATA  7388603

Query  7705     TTAGA--AAGAAAAAACAAAACCTGATGATATCTTTATGGGAGAATATTTGGCCACATTG  7762
                |||||  || |||||| ||||||| | | | || |||| |||| || |||||||||||  
Sbjct  7388602  TTAGACCAAAAAAAAA-AAAACCTTAAGGTGTCCTTATTGGAGGATGTTTGGCCACATCA  7388544

Query  7763     AAATTATCCAAACGTTTCAGAGCTA-AGACAGCTTTAAAAAGACGGTGATGTCAA-CCCT  7820
                ||||| || ||| |||||||||||| | ||||| | || ||||  |||||||||  ||| 
Sbjct  7388543  AAATTGTCAAAATGTTTCAGAGCTACA-ACAGCCTGAAGAAGATAGTGATGTCATTCCC-  7388486

Query  7821     AAGAAAACAGAATACAAAGCTCTGT-TATCCAACAGTTACCTGGGTTTTATGCT-TCCTA  7878
                |||||||||||||| |||||| ||| |||| ||  || ||||| |||||||||| || ||
Sbjct  7388485  AAGAAAACAGAATAAAAAGCTGTGTATATCGAATGGTCACCTGTGTTTTATGCTATC-TA  7388427

Query  7879     ACGGGGCAGGTCATATGTGGGTTCAGGTTGAAGAGGGGAACCACTGAGGGTGTTAT-TGA  7937
                ||   |||| |||||||    ||||||| |||||  ||||||||||||||||| || | |
Sbjct  7388426  ACATAGCAGATCATATGCACATTCAGGTAGAAGAAAGGAACCACTGAGGGTGTGATCT-A  7388368

Query  7938     TCACAAGACTAAGGTCAAGGCTTCACTGCAGGAAATCAGGACAGAA-TGACAAAGTGAGG  7996
                || |||||||||| |||||||||||||| |||||||||||||| || |||| ||||||||
Sbjct  7388367  TCTCAAGACTAAG-TCAAGGCTTCACTGAAGGAAATCAGGACA-AAGTGACCAAGTGAGG  7388310

Query  7997     TGGGGGCTGGGCAGGA-TGGGACCGGGTGTTCTAGTAG-AACCCTGGGAAGGAACCAAGA  8054
                ||||| ||| || ||| || |||  ||||||||| | | |||| ||  |||||| |||||
Sbjct  7388309  TGGGGACTGAGC-GGAATGAGACTAGGTGTTCTAATGGGAACC-TGCAAAGGAAACAAGA  7388252

Query  8055     CAGCATAAAACATGGTGGGTATTTTGTGGGCATCTCCACAGA-AGGATTGAAAGAC-TCT  8112
                ||   |||||||||| || ||| ||||||||||||  |  |  |||| | |||| | | |
Sbjct  7388251  CAATGTAAAACATGGCGGTTATCTTGTGGGCATCTAGAT-GTCAGGACTCAAAGTCCTTT  7388193

Query  8113     GTCTGGATTGAGTTTA  8128
                |||  |||||||||||
Sbjct  7388192  GTCAAGATTGAGTTTA  7388177


 Score =  994 bits (538),  Expect = 0.0
 Identities = 1085/1342 (80%), Gaps = 65/1342 (4%)
 Strand=Plus/Minus

Query  6828     GAAGGATCCAATACACATCCCTTCCACATACTCACAATCACACAC---TT-AGGGA-CAG  6882
                ||||| ||| ||| ||||| |||||||||||||||||| || |||   || | ||| | |
Sbjct  7454870  GAAGGTTCCTATAGACATCACTTCCACATACTCACAATTACCCACTTTTTGATGGATC-G  7454812

Query  6883     AGT-CTAAGGG--AAGAGATAAATCCCAGGTTC-G-G-AACAA--G-TCTCTTGAGAATG  6933
                | | || ||||  || | ||||||||||   || | | || ||  |  ||||||||| ||
Sbjct  7454811  A-TCCT-AGGGTCAA-AAATAAATCCCACAATCTGAGCAA-AACTGCACTCTTGAGATTG  7454756

Query  6934     GTGTACGGGAGA--TCTAA-GA-TTTCTGTAAAATGAAAGCCTGACTAATAAAATCACAA  6989
                ||||  |||| |  | ||| || ||| || ||||||||||| | |||   |  |||||||
Sbjct  7454755  GTGTGTGGGATACCTTTAAGGATTTTATG-AAAATGAAAGCAT-ACTTGGAGGATCACAA  7454698

Query  6990     TACCGCTAAGTGTGTGAACTATAGCTGACAGGCACAGAAACCAACAACTTCACATGTCAA  7049
                || | | |||| | |||||| ||  ||| ||||||| |||| || ||||||| |||||||
Sbjct  7454697  TAACACCAAGTCTATGAACTGTAATTGAAAGGCACAAAAACAAATAACTTCAAATGTCAA  7454638

Query  7050     GACATAAACATCCAT-CCAACTGTAAATTTTTAATAtttttttttttAAAAA-CTGCTTC  7107
                || ||||| || |||  | |||||||| ||||||||   | ||||| ||||| |||||||
Sbjct  7454637  GAAATAAAAATTCATGTC-ACTGTAAAGTTTTAATA---TATTTTTAAAAAACCTGCTTC  7454582

Query  7108     AATAAGAATTTTGAAATGAGGAAAATGAAGCACAAATCAAAATTTGAGGGATGAAGTCAA  7167
                 ||||||||||| ||||||  ||||  |||||||||||| ||| ||| |||||||| |||
Sbjct  7454581  CATAAGAATTTTAAAATGACAAAAACCAAGCACAAATCACAATCTGATGGATGAAGACAA  7454522

Query  7168     AACTATATTTGGAGGAAAAATCAAAACCTACATCTGTTTAATCTGAAAAAACAGACAG-G  7226
                ||||| |||| |||||||||| ||| |||| ||||| || |||| | |||||||||||  
Sbjct  7454521  AACTACATTTAGAGGAAAAATGAAAGCCTAAATCTG-TTCATCTCACAAAACAGACAGAA  7454463

Query  7227     AAAT-TCTCTGTGCCATTTTGGGCTGTGTGTCACCATCCCTGACTGGCTGGCTGCAGATT  7285
                |||| | | ||||||| |||||| ||||||||||| ||||||||||||||||||| ||| 
Sbjct  7454462  AAATAT-TGTGTGCCACTTTGGGATGTGTGTCACCGTCCCTGACTGGCTGGCTGCTGATC  7454404

Query  7286     AGACGGGCATGTTCCTAAGAAGGTGGTGACTTACCAGATCTGGACTCAGTTTGCAGGGTG  7345
                ||| |||||||  ||||||||||||||||||||||||  ||||||||| ||||||| || 
Sbjct  7454403  AGATGGGCATGACCCTAAGAAGGTGGTGACTTACCAGCGCTGGACTCACTTTGCAGAGTT  7454344

Query  7346     CTGGGACCTCTCAGAGAACCAAGCAGTAGCTCCAGGCACCAGGGCTTTGGGTCTGTCCTG  7405
                |||||||||||||| ||||||| |||||||| ||||    || ||| ||||||| | |||
Sbjct  7454343  CTGGGACCTCTCAGGGAACCAACCAGTAGCTTCAGGTGTGAGTGCTGTGGGTCTCTTCTG  7454284

Query  7406     TGCAAACTCAGGAGCTTTTGTTGATGTTTCTAACCACACCCTCCCCTTCTCAATCACCAG  7465
                 | |  ||||||||||||| | ||  ||||||||| |||||| |||||||||||||||||
Sbjct  7454283  GGTACCCTCAGGAGCTTTTATAGACCTTTCTAACCCCACCCTTCCCTTCTCAATCACCAG  7454224

Query  7466     CTTCCAATCAGAAAGTGATACCTGATTAGATCCTGAAGTTC-CACCCAGTTAATCCTGAT  7524
                |||||||||||||||||||||||||||||||| || ||| | ||||||||||||||||||
Sbjct  7454223  CTTCCAATCAGAAAGTGATACCTGATTAGATCTTGCAGT-CACACCCAGTTAATCCTGAT  7454165

Query  7525     TGAGTTT-CACACTTTCTTCTGATTCATTGATTAAATTAGATGTGCATTTATGAAAGTGA  7583
                ||||||| ||  ||||||||||| | ||||||  ||||||||   |||||||| |||| |
Sbjct  7454164  TGAGTTTTCAG-CTTTCTTCTGACTAATTGATCGAATTAGATACACATTTATGGAAGTAA  7454106

Query  7584     AAGAATAAATAACAGGGTGAAAGTCCAAAAGTCATTAATTCATTTATTCCCCAAACACTG  7643
                |||||||||||| ||||||||||||||||| ||||| |||||||||||||||||| ||||
Sbjct  7454105  AAGAATAAATAATAGGGTGAAAGTCCAAAACTCATTCATTCATTTATTCCCCAAATACTG  7454046

Query  7644     ATGAAGTTTGACTAACATG-TGACCTTCATAGTGA--CATGGAAGGT-TTAATCTGTTCC  7699
                |||||||||| |||| | | |||| ||||||||||  || ||||||  ||||||||||||
Sbjct  7454045  ATGAAGTTTGGCTAATA-GATGACTTTCATAGTGATACAGGGAAGGGATTAATCTGTTCC  7453987

Query  7700     TGGCATTAGA-AAGAAAAAACAAAA---CCTGATGATATCTTTATGGGAGAATATTTGGC  7755
                ||  || ||| || |||||| ||||   ||| | | | || |||| |||| || ||||||
Sbjct  7453986  TGATATCAGACAAAAAAAAAAAAAAAAACCTTAAGGTGTCCTTATTGGAGGATGTTTGGC  7453927

Query  7756     CACATTGAAATTATCCAAACGTTTCAGAGCTA-AGACAGCTTTAAAAAGACGGTGATGTC  7814
                |||||  ||||| || ||| |||||||||||| | ||||| | || ||||  ||||||||
Sbjct  7453926  CACATCAAAATTGTCAAAATGTTTCAGAGCTACA-ACAGCCTGAAGAAGATAGTGATGTC  7453868

Query  7815     AA-CCCTAAGAAAACAGAATACAAAGCTCTGT-TATCCAACAGTTACCTGGGTTTTATGC  7872
                |  ||| |||||||||||||| |||||| ||| |||| ||  |||||||| |||||||||
Sbjct  7453867  ATTCCC-AAGAAAACAGAATAAAAAGCTGTGTATATCGAATGGTTACCTGTGTTTTATGC  7453809

Query  7873     T-TCCTAACGGGGCAGGTCATATGTGGGTTCAGGTTGAAGAGGGGAACCACTGAGGGTGT  7931
                | || ||||   |||| |||||||    ||||||| |||||  |||||||||||||||||
Sbjct  7453808  TATC-TAACATAGCAGATCATATGCACATTCAGGTAGAAGAAAGGAACCACTGAGGGTGT  7453750

Query  7932     TAT-TGATCACAAGACTAAGGTCAAGGCTTCACTGCAGGAAATCAGGACAGAATGACAAA  7990
                 || | ||| |||||||||| |||||||||||||| |||||||||||||| |||||| ||
Sbjct  7453749  GATCT-ATCTCAAGACTAAG-TCAAGGCTTCACTGAAGGAAATCAGGACAAAATGACCAA  7453692

Query  7991     GTGAGGTGGGGGCTGGGCAGGA-TGGGACCGGGTGTTCTAGTAG-AACCCTGGGAAGGAA  8048
                |||||||| || ||| |  ||| || |||  ||| ||||| | | |||| ||  ||||||
Sbjct  7453691  GTGAGGTGCGGACTGAGT-GGAATGAGACTAGGTTTTCTAATGGGAACC-TGCAAAGGAA  7453634

Query  8049     CCAAGACAGCATAAAACATGGTGGGTATTTTGTGGGCATCTCCACAGA-AGGATTGAAAG  8107
                 |||||||   ||||||||||||| ||| ||||||||||||  |  |  |||| ||||||
Sbjct  7453633  ACAAGACAATGTAAAACATGGTGGTTATCTTGTGGGCATCTAGAT-GTCAGGACTGAAAG  7453575

Query  8108     AC-TCTGTCTGGATTGAGTTTA  8128
                 | | ||||  |||||||||||
Sbjct  7453574  TCCTTTGTCAAGATTGAGTTTA  7453553


 Score =  970 bits (525),  Expect = 0.0
 Identities = 738/834 (88%), Gaps = 41/834 (4%)
 Strand=Plus/Minus

Query  27064    catgcatctgtattcccagctatttggtttgctgacatgggagaatcacttgagcccaga  27123
                |||||||||||| |||||||||||||| | ||||   |||||||||||||||||||||||
Sbjct  7482697  CATGCATCTGTAGTCCCAGCTATTTGGGTGGCTGGTGTGGGAGAATCACTTGAGCCCAGA  7482638

Query  27124    agattgaggctgcagtgagccatgctcacaccactgctgtactccagcctgggcaacaga  27183
                ||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||
Sbjct  7482637  AGATTGAGGCTGCAGTGAGCCATGCTCACACCACTACTGTACTCCAGCCTGGGCAAAAGA  7482578

Query  27184    gtaagaccctgctaaaaacaaaaacgaaaacaaacaaacaaaaaacCTTAACCAAAGAGA  27243
                |  |||| || ||     |||||||   || |||| || ||  ||  | ||  |||| | 
Sbjct  7482577  G--AGACACT-CT--GTCCAAAAAC---AA-AAAC-AA-AATCAA--TCAA--AAAG-G-  7482535

Query  27244    ATCTTTGACCTTAATTTTAAACCAATCACATCCTCACTGTAATTCTTCCTCCCGAATGGA  27303
                ||||||||||||||||||||||||||||||   || |      |||||| ||| ||||||
Sbjct  7482534  ATCTTTGACCTTAATTTTAAACCAATCACA---TC-C------TCTTCCACCCAAATGGA  7482485

Query  27304    GACATgggtgt-gagggtgcatgcctgtaatcccagctacatggaaggctgaagcatgag  27362
                | ||||| ||| | ||||||||||||||| |||||||||  |||||||||||||||||||
Sbjct  7482484  GGCATGGCTGTGGGGGGTGCATGCCTGTAGTCCCAGCTATGTGGAAGGCTGAAGCATGAG  7482425

Query  27363    aattgcttgaatctcagaggcggaagttacagtgagctga-gatggagccgctgcactcc  27421
                ||||||||||||||  |||||||| || |||||||||  | ||||| ||| |||||||||
Sbjct  7482424  AATTGCTTGAATCTTGGAGGCGGAGGTAACAGTGAGC-CATGATGGTGCCACTGCACTCC  7482366

Query  27422    agcctgggcgacaaagtgagactcagcttcacc-ca-caccaaaaaaaaTTAGATTATAC  27479
                |||||||||||| |||||||||||||| || || || ||||||||| ||||  | |||  
Sbjct  7482365  AGCCTGGGCGACGAAGTGAGACTCAGC-TC-CCTCAGCACCAAAAACAATT--A-TAT--  7482313

Query  27480    CACCCAGGTGATCACT-GGATACATGAAGATTTCTATTGTGTGTTATTGGGGACTGTCAA  27538
                 ||||||||||||| | ||||||||||||||||||||||||| || || |||||||||| 
Sbjct  7482312  GACCCAGGTGATCA-TCGGATACATGAAGATTTCTATTGTGTTTTCTTAGGGACTGTCAT  7482254

Query  27539    CTCCGTCTTTGAAAACTGTTTTAACTCTGAAATATTTTGATAAATTTGATGTGGCCAAGG  27598
                ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7482253  CTCTGTCTTTGAAAACTGTTTTAACTCTGAAATATTTTGATAAATTTGATGTGGCCAAGG  7482194

Query  27599    ATCCCTCAACAAAGATACTTTCAAGTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGATT  27658
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7482193  ATCCCTCAACAAAGATACTTTCAAGTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGATT  7482134

Query  27659    CAACACTTCCCTATCTCACACTCAGGACTATGAAGGACACATATTAGTAAACCTCCATGT  27718
                |||| ||||||| |||||||||||||||| ||||||||||||||||||||| ||||||||
Sbjct  7482133  CAACCCTTCCCTGTCTCACACTCAGGACTTTGAAGGACACATATTAGTAAAACTCCATGT  7482074

Query  27719    TTGTGGAGGGAATCAGTGAATGAGTCCTGGACTTTCACCCTATCCCTAAATCTTTCACTT  27778
                ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Sbjct  7482073  TTGTGAAGGGAATCAGTGAATGAGTCCTGGACTTTCACCCTATCCCTAAATCTTTCATTT  7482014

Query  27779    TCATGGATGAATATCTAATTCAATCAGTTAATCTGGAAGAAAGCCAAAAATCCAATCAGG  27838
                | |||||| |||||||||||| ||||||||||||  |||||||||||||||||||| |||
Sbjct  7482013  TGATGGATCAATATCTAATTCGATCAGTTAATCTTTAAGAAAGCCAAAAATCCAATAAGG  7481954

Query  27839    ATTAACTGGGTAGAGTTTAAGAAGTCGAATCAAATGTAGTtctctctctctctc  27892
                ||||||||||||||| |||||||||| | |||||||||| ||||||| ||||||
Sbjct  7481953  ATTAACTGGGTAGAGATTAAGAAGTCTAGTCAAATGTAGCTCTCTCTGTCTCTC  7481900


 Score =  965 bits (522),  Expect = 0.0
 Identities = 738/839 (87%), Gaps = 28/839 (3%)
 Strand=Plus/Minus

Query  13081    aagtatatattctatatactttctatatatttatatTCTAAGAGGTCACATGCAAATTCA  13140
                |||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||
Sbjct  7502345  AAGTATATATTCTAAATACTTTCTATATACTTATATTCTAAGAGGTCACATGCAAATTCA  7502286

Query  13141    AGGCTAGGTCAAAGAGTAGAGTGGCTATCTATGGAAAGGGGAGTGGAAGTGAATCATGGT  13200
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7502285  AGGCTAGGTCAAAGAGTAGAGTGGCTATCTATGGAAAGGGGAGTGGAAGTGAATCATGGT  7502226

Query  13201    AATaaaaa--aaGGTGTAGATATAGTTATGG-ATAGGTAGACATACACACATATAGCGGC  13257
                ||||||||  || || ||||||||| || || |||| |||||||||||||||||||| ||
Sbjct  7502225  AATAAAAATTAA-GTATAGATATAGATA-GGAATAGATAGACATACACACATATAGCTGC  7502168

Query  13258    AAGAAAAGGGAATGTCATGGACCAGTGATGACAGTGAGCCATGTAAAAAGGCTACAATTT  13317
                |||||| ||||||||||||||||| ||||| |||||||||||||||||||||||||||| 
Sbjct  7502167  AAGAAAGGGGAATGTCATGGACCAATGATGTCAGTGAGCCATGTAAAAAGGCTACAATTC  7502108

Query  13318    TTGTGATTGTGTGTCCATTTTCAGGATTGGTTGTAGCTTACCTTTTTAGAAAGGCTGATG  13377
                |||||||||||||||  |||||||||| ||||||||||||||||||||||||||||||||
Sbjct  7502107  TTGTGATTGTGTGTCTGTTTTCAGGATGGGTTGTAGCTTACCTTTTTAGAAAGGCTGATG  7502048

Query  13378    CCATAGTCATAGTGAATAAATGATTATAAAATGTGTTTCCTTTCTGGCGAACCTCTGGAG  13437
                ||| || ||||||||||||||| |||||||||||||||||||||||| | | ||||||||
Sbjct  7502047  CCACAGCCATAGTGAATAAATGGTTATAAAATGTGTTTCCTTTCTGGGGCATCTCTGGAG  7501988

Query  13438    AAATTTCCAATGGTAGGAGAACTCAGTTTACTGGGCAGGCGATCACACAGATAAGATTTT  13497
                |||| |||| |||||||||||||| |||||||||||||| ||||||||||||||||||||
Sbjct  7501987  AAATCTCCAGTGGTAGGAGAACTCCGTTTACTGGGCAGGTGATCACACAGATAAGATTTT  7501928

Query  13498    ACAGATCTAATGGCACTACCATTAACTTCATTATCATTGGTATTCTACAAAGGTTGAGTG  13557
                 |||||| ||||||||||||||||||||||||||| |||||||||||||||||| |||||
Sbjct  7501927  TCAGATCCAATGGCACTACCATTAACTTCATTATCCTTGGTATTCTACAAAGGTCGAGTG  7501868

Query  13558    AACAAATGGTATCTTAAAATTAAA-TTAGCTAAATTAACAAAAAAGATTGGATTACtttt  13616
                || |||||||||||| ||| |||| ||||||||| |||||||  ||| ||| ||| ||||
Sbjct  7501867  AAGAAATGGTATCTTGAAACTAAAATTAGCTAAACTAACAAAGGAGACTGGGTTAATTTT  7501808

Query  13617    tctttttttt--------gacacagagtctctgatgcccaagcgggagtacagtggtgct  13668
                | ||||||||        || |||||||||||| | |||| || ||||| ||||||||||
Sbjct  7501807  TTTTTTTTTTTTTTTTTTGAGACAGAGTCTCTGTTACCCAGGCTGGAGTTCAGTGGTGCT  7501748

Query  13669    atgtcatctcactgcaacatctgcctcccgggttcaagagattctcctgcctcagactcc  13728
                || ||| ||||||||||| ||||||||| ||||||||| |||| || ||||| || ||||
Sbjct  7501747  ATCTCAGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGTGATTGTCATGCCTTAGCCTCC  7501688

Query  13729    tgagtagccgggattacaggcacacaccaccacacccagctgatttttgtatttttagca  13788
                  |||||| ||||||||||||| || | ||||||||||||| |||||||||||||||| |
Sbjct  7501687  CAAGTAGCTGGGATTACAGGCATAC-C-ACCACACCCAGCTAATTTTTGTATTTTTAGTA  7501630

Query  13789    ga-aacggggtttcaccatgttgaccaggttggtcttgaacccctgacctt--gtgatct  13845
                || |||||||||||| ||||||| |||| ||| ||   ||| |||| |||   |||||| 
Sbjct  7501629  GATAACGGGGTTTCAACATGTTGCCCAGATTGCTC---AACTCCTGGCCTCAAGTGATC-  7501574

Query  13846    c-cctgcctcagcctcctgaagtgctg-gaattataggct-tgagccaccttgcccagc  13901
                | || ||||| ||||||  |||||||| || ||| ||| | ||||||| | || |||||
Sbjct  7501573  CACCAGCCTCGGCCTCCCAAAGTGCTGAGA-TTACAGG-TGTGAGCCATCATGTCCAGC  7501517


 Score =  929 bits (503),  Expect = 0.0
 Identities = 1435/1866 (76%), Gaps = 140/1866 (7%)
 Strand=Plus/Minus

Query  4063     ATCATATCAACTTGAAACACACTTTGTAACAAGAAATT-C--ACACG--TGCA-CATGCA  4116
                ||||||| ||||| ||||||||||  ||||||| |||| |  | | |  | || | | ||
Sbjct  7569113  ATCATATTAACTTTAAACACACTTCCTAACAAGGAATTCCTAAAAGGAATTCACCCT-CA  7569055

Query  4117     GTAGAGACAAAACGC-CCACTAAGTACCT-TGTACATGATGTCCCTCTC--TAGCCTCTA  4172
                 ||||| |  ||| | |||||||  | ||   |||| ||||||||||||  |||| ||||
Sbjct  7569054  CTAGAG-CTGAACCCTCCACTAACCAGCTCCCTACACGATGTCCCTCTCTGTAGCTTCTA  7568996

Query  4173     CCCTAGGTGACCCCTCTGCCTTTATTGAAGTGATCCTGTGATAGCCACTCCAGGACATGG  4232
                ||| |||| | ||||||||| ||| || || |||||||||||| ||||| ||||| || |
Sbjct  7568995  CCCCAGGTCATCCCTCTGCCCTTACTGGAGCGATCCTGTGATACCCACTTCAGGATATAG  7568936

Query  4233     AGCACTGAACGGGACAATGTGTTGACATTCTGGTGTCCCCTGCACTGTGCCGTCGCCACT  4292
                |||||  ||| |||| |   | || |||||| ||||||||| | ||  | | || ||| |
Sbjct  7568935  AGCACCAAACAGGAC-A---G-TG-CATTCTAGTGTCCCCTTCCCT-AGACATCTCCAGT  7568883

Query  4293     GGCTGGCACACAGTACACGTCT--TCTAGTGTTTACTGTAACaaaaaaaaaGGCTGCGCT  4350
                ||||||||||||||| | | ||  | | ||||||| ||||||  |||||||||||| |||
Sbjct  7568882  GGCTGGCACACAGTAGATG-CTGAT-TGGTGTTTATTGTAAC--AAAAAAAGGCTGTGCT  7568827

Query  4351     GTGGTCTGCAGAGAAAGGGCACGATCCTTTCTCACCTGATCAGCT-GTCCCAGGTGCCCT  4409
                 ||| |  |||||||||  ||| |||||| ||||||||||||||| || ||||||| |||
Sbjct  7568826  ATGGCCCCCAGAGAAAGCTCACCATCCTTCCTCACCTGATCAGCTGGT-CCAGGTGGCCT  7568768

Query  4410     CTGTGGAAGGTGA-CCATATTCATTTTAAGCAGCTGGAGGTGT-TTCAGCCTGAGGAACA  4467
                |||  ||||  || || | || |  | ||||| |||||||| | | ||||||||||| ||
Sbjct  7568767  CTGAAGAAGCAGACCCTTCTT-ACATAAAGCATCTGGAGGT-TCTCCAGCCTGAGGAGCA  7568710

Query  4468     TAGAGCTGATTTTGGCGACTGAGC-ATTCCTCGCGGT-A-A--TTGA-C-GTGTAAGGA-  4519
                 |||||||| ||  || ||| | |  ||| | || || | |  || | | | |||| || 
Sbjct  7568709  CAGAGCTGAATTCAGCAACT-AACTGTTCTTGGCTGTCAGAGCTT-AGCAG-GTAACGAC  7568653

Query  4520     TGGCACCTGGAGAAAAATGAGTTTGCGAAGATTCTTCATCT-CCTTCAGGTAA-CAATGA  4577
                 | || | |||||  || |||||||||||||||| ||||||  | ||||||||    | |
Sbjct  7568652  AGCCATC-GGAGATGAA-GAGTTTGCGAAGATTCCTCATCTGGC-TCAGGTAAGGGCT-A  7568597

Query  4578     AGCT-TTCTTATCAGATGTGGCCAGGACACATAGCAAATTTCCAGCTCCTGAATACTATT  4636
                | || | | ||||| |   |||||| |||  |  |||||||||| | | || |||||  |
Sbjct  7568596  AACTCTAC-TATCATACACGGCCAGCACATGTTCCAAATTTCCAACACTTGGATACT-GT  7568539

Query  4637     C-AGGTGGATTATTTTCAATGAT-CTTCTGAGATATT-CAATCG-ACGTTAG-ATAATTC  4691
                |  |||  | | ||| |||| ||  |||||| || ||  ||| |  | || | |||||||
Sbjct  7568538  CTGGGTATACTGTTTCCAAT-ATGTTTCTGAAAT-TTAGAAT-GCTCATT-GAATAATTC  7568483

Query  4692     ACCAACTTACTACAGCACAGGTGTACTAAACCTCTCCTTTGGTAAACCCA-CCGGAAGAG  4750
                |||| |||| ||||||||||||||||| ||||||| || || |  ||||| || | ||| 
Sbjct  7568482  ACCACCTTAGTACAGCACAGGTGTACTGAACCTCTTCTGTGCTGGACCCACCCAG-AGAA  7568424

Query  4751     GTATCTCAG-GCATTCATCC-TGGGGTATTTCCTTGAGGCAGATGTCTATGAACACCTTC  4808
                | | |||||  | ||||||| | |  | ||||||||||||| |  || ||||||||||||
Sbjct  7568423  GAAGCTCAGATC-TTCATCCAT-GAATTTTTCCTTGAGGCAAACATCCATGAACACCTTC  7568366

Query  4809     AAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGTCTGCCTCTTACTCATGGCC  4868
                |||||||| | ||||||  ||||||||||||||||  |||||||||||||||||||||||
Sbjct  7568365  AAGGGCTGCTTCTCTCCTGTCCTTGGACAGTCCTCCACTGTCTGCCTCTTACTCATGGCC  7568306

Query  4869     TCTGGGGAGGAGGACAGGGCCCTGGATTCAGACCATATGGCCCAGAAATTCTCATCAACA  4928
                ||||||||| ||||||||| ||||| | |||||||||||| ||| |||||||||||||||
Sbjct  7568305  TCTGGGGAGCAGGACAGGGGCCTGGCTCCAGACCATATGGTCCAAAAATTCTCATCAACA  7568246

Query  4929     TCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAA-AGTAAGGCAGAGGCTC  4987
                |||||||| ||||||||||||||||||| ||||||||| |||| | || || | | ||||
Sbjct  7568245  TCCCGCAATTCCAGCACTTGAAGTTTCCGCCTCCTGTGAGTAACA-TAGGGGAAAAGCTC  7568187

Query  4988     AGAACTTTGA-A-GGACAAATCCCTGACCTTTGCTTTCATTCT-CATCCAATAAAT-CAG  5043
                ||||| | || | ||||  | |||||||||  ||||||| ||  |||| ||  | | |||
Sbjct  7568186  AGAACGTAGACAAGGACCCACCCCTGACCTGGGCTTTCACTCCACATC-AAGGACTTCAG  7568128

Query  5044     CTGCTCCTGTCCTC-GCTGCTCCCTGTTCTCTCTGAGTTTTCTTGGTCCCTTTTCTCTTT  5102
                |||||  | ||||| || || ||||   || ||||  | ||||   ||||||| | | ||
Sbjct  7568127  CTGCTTTTTTCCTCAGC-GC-CCCTC--CT-TCTGTCTCTTCTCCATCCCTTTCCCCCTT  7568073

Query  5103     CAATTCTGACTGGTCCCCACTTCTATT-CCATTTACCTTCCACTGGGAATAGGCAAGTTT  5161
                  |||||| ||||| |||||||||| | || |||||||||||||||||  ||||| ||| 
Sbjct  7568072  GGATTCTGCCTGGTACCCACTTCTAGTGCC-TTTACCTTCCACTGGGAGCAGGCAGGTTC  7568014

Query  5162     CTGTTCCCACAGTGGACCCTATATTGTGGGCAGTTCTTTCCCTGAGGATCTGGGCAATGG  5221
                ||||| || ||||||||||| ||| ||| ||||| ||||||| ||||| ||||||||| |
Sbjct  7568013  CTGTTTCCTCAGTGGACCCTGTATGGTGAGCAGTCCTTTCCCAGAGGAGCTGGGCAATAG  7567954

Query  5222     CCAAGG-CATGCCTGAGCTT-CGTCACCAGCACCACCAGAAGACACTGGGCCATCCTTGG  5279
                |||||  | | ||  ||||| | ||||  |||||| |||||| | |||||||| ||  ||
Sbjct  7567953  CCAAGAACGTTCCC-AGCTTTC-TCACTGGCACCATCAGAAGCCCCTGGGCCACCCC-GG  7567897

Query  5280     GATACTTCTTTGCCTGACCCTGCTGTTCTT-TCCCTGGACACCTGAGCCCCATCTACCAG  5338
                | | |   |||| ||||||| |||||| |  |||||||||||||| ||||  ||  ||| 
Sbjct  7567896  GTTCCCAATTTGTCTGACCCAGCTGTT-TAGTCCCTGGACACCTGGGCCC--TCC-CCA-  7567842

Query  5339     CCTTCCTGGGTCACCTCACCTGGGGCGATCCTTCTGTGTAAGCAG-CATGTGAAGCCCTT  5397
                |||    ||||||||||||||||||||| |||| || | |||||| ||  | || ||| |
Sbjct  7567841  CCT----GGGTCACCTCACCTGGGGCGAACCTTTTGGGCAAGCAGGCAA-TCAATCCCAT  7567787

Query  5398     CCAGC-A-ATGCTTTTAAGGTCTCCAGATGAAGCGTCTTCATCAGCGATCCCAGAGGGAG  5455
                ||| | | ||  | | ||| ||||||||| | ||||||||||||| || |||||||||||
Sbjct  7567786  CCA-CTACATAATGT-AAGATCTCCAGATCAGGCGTCTTCATCAGGGACCCCAGAGGGAG  7567729

Query  5456     GC-GGGTGAAGGGCCAGGCCTGCACCATCAC-TGTCAGAGTCTGGAAGTGTCTCCT-GCT  5512
                || ||| |||||||||||||||||||||||| | |||||  || | || |||| || | |
Sbjct  7567728  GCAGGG-GAAGGGCCAGGCCTGCACCATCACCT-TCAGAACCTCGCAGCGTCTGCTAG-T  7567672

Query  5513     GAAGGCCTCCAGGAAGAGTGGGAGGTAGAGCTCCCTGGGCAGCTCCTCCAGGGCAGAGAT  5572
                ||||||||||| ||| |||||| || ||||||||||||||||||| |||| |   |||||
Sbjct  7567671  GAAGGCCTCCACGAACAGTGGGGGGAAGAGCTCCCTGGGCAGCTCATCCAAGATGGAGAT  7567612

Query  5573     GGCCAAGGGCTTGTCTCTCAGCAGACTCTGCCCCGCCAGCTCCAGGAGTCTGGGTGGGGC  5632
                |||||||| || ||| | |||||| |||||||| |||||||||||||||||| |||||||
Sbjct  7567611  GGCCAAGGCCTGGTCCCCCAGCAGGCTCTGCCCTGCCAGCTCCAGGAGTCTGCGTGGGGC  7567552

Query  5633     CTGGATGCTCATCCTGATGAATCTGTAAGGAAAAACTCTAGAAGACAAATCCAGAGAAAA  5692
                ||| | ||||||||| || |||||| ||| |||| |   | ||      |||||||||||
Sbjct  7567551  CTGTAGGCTCATCCTCATAAATCTGCAAG-AAAA-C---A-AA------TCCAGAGAAAA  7567504

Query  5693     GGCATCACTT-TCAGGCCAAACACAATCAC-CTC--ATCTTCTCCTAAGGCCAGTAG-CA  5747
                | ||  |||| ||||||||  | |  |||| | |  | ||||||||  |||||  || ||
Sbjct  7567503  GACAA-ACTTATCAGGCCAGTC-CTCTCACACCCTGA-CTTCTCCTG-GGCCAAAAGTCA  7567448

Query  5748     TTGCTCTGGTAGAGGTAGAAAAATTACC-AC-TTTACCCCAATTCCACTCTGCACTTGGT  5805
                 | |||||| ||| || |||| | | || |  ||||||||||||| |||||||| |   |
Sbjct  7567447  CTACTCTGGCAGATGT-GAAAGAGT-CCTAAGTTTACCCCAATTCGACTCTGCAATAATT  7567390

Query  5806     GGCCACA-A-ATCTATATTTCTGCTTCTGCTGGTACCAGGAAGAATGTCTTCCAAACA-C  5862
                ||||||| | | | ||| ||||||  || ||||||||| ||||| ||||| || |||  |
Sbjct  7567389  GGCCACACAGA-C-ATAGTTCTGCC-CTTCTGGTACCAAGAAGAGTGTCT-CCTAACCTC  7567334

Query  5863     CAAGGA  5868
                ||||||
Sbjct  7567333  CAAGGA  7567328


 Score =  922 bits (499),  Expect = 0.0
 Identities = 740/851 (86%), Gaps = 37/851 (4%)
 Strand=Plus/Minus

Query  9160     aagaaagagaaa-gaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaa  9218
                ||| ||| |||| |||||||||||||||||||||||||||||||||||||||||||||| 
Sbjct  7512744  AAGGAAG-GAAATGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAG  7512686

Query  9219     agaaaaag-agc-gagccttcttgtctttaagagcagcgcatatataCT-GTTATATTGG  9275
                ||| | || | |  ||||||| ||||||||||| | | ||| | || || ||| ||||| 
Sbjct  7512685  AGAGAGAGAAACTCAGCCTTCCTGTCTTTAAGAACGGTGCACACAT-CTGGTTGTATTGT  7512627

Query  9276     GTGCACACCTAAAATACATTTCCCCCACAAAACCTGGAAGCTCTATTTCATGTTGAAATA  9335
                ||||| |  || ||||||||||||| |||||||||||||||||||||||||||| ||| |
Sbjct  7512626  GTGCAAATGTACAATACATTTCCCCAACAAAACCTGGAAGCTCTATTTCATGTTAAAAGA  7512567

Query  9336     TCTGCTAAGTTCACGGATGGCTCCCATCCTAAG-AGGGATCACACAGTGATTCTTCCGAT  9394
                ||||||||||||| ||||||||||||||||||| | |||||||||||| ||||||| | |
Sbjct  7512566  TCTGCTAAGTTCAGGGATGGCTCCCATCCTAAGCA-GGATCACACAGTCATTCTTCTGCT  7512508

Query  9395     GTTTTAGGGCACAAAGTAGCAAGAACCTCCCCTGCCTCCAGAAAGTCCTCCAGGCCTTTC  9454
                 ||||||||||||||||||||||||| ||||| |||||||||||||||||||||||||||
Sbjct  7512507  ATTTTAGGGCACAAAGTAGCAAGAACGTCCCCCGCCTCCAGAAAGTCCTCCAGGCCTTTC  7512448

Query  9455     TCTCCCATTCTATATGAAAACCAAACAGCTCTGAGATGCCACTGGCCTCCAAAACTGGAG  9514
                |||||||||| |||||||| ||||||||| | |||||||||||||| |||||||||| ||
Sbjct  7512447  TCTCCCATTCCATATGAAACCCAAACAGCCCGGAGATGCCACTGGCTTCCAAAACTGAAG  7512388

Query  9515     TACTTTGAAGGGTGTTCTCTATCTTGAAATGTTTCTGTAAATGTTCTTTCTCCACATTTC  9574
                ||||||||||| ||||||| ||| || ||| |||||||||||||||||||||||||||||
Sbjct  7512387  TACTTTGAAGGATGTTCTCCATCATGGAATATTTCTGTAAATGTTCTTTCTCCACATTTC  7512328

Query  9575     TGACCTCACTGTCAATGCCCTGCTATGTGTGCAATTGAGTTAAACTGAAATGTGTTCAGT  9634
                |||||||||| |||||||||||||||||||||||| |||||||||||||| ||| |||||
Sbjct  7512327  TGACCTCACTATCAATGCCCTGCTATGTGTGCAATCGAGTTAAACTGAAACGTGCTCAGT  7512268

Query  9635     GGGGCTTCTACTTTGCCTGCCCTCACTTTGTGAGCCTGAGGCTGAGGTTGAGCTCAGCAC  9694
                | |||||||||||  |||||||||||||||||||||||||||||||| ||||||||||||
Sbjct  7512267  GCGGCTTCTACTTCACCTGCCCTCACTTTGTGAGCCTGAGGCTGAGGGTGAGCTCAGCAC  7512208

Query  9695     CAAGGGTGATCGTGAGTGTCTCTGGTGACTGAGCATCCACGAGGCACAGCAGGGGCTGGT  9754
                ||| ||||||| |||||||||||| ||| ||||||| ||| ||||||||||||| |||||
Sbjct  7512207  CAAAGGTGATCCTGAGTGTCTCTGTTGATTGAGCATGCACAAGGCACAGCAGGGACTGGT  7512148

Query  9755     ATCATTCATCCAAGATCTCAGCTCTCCCTCAC-A--AAT--AA----T----CTAAAG-C  9800
                | |||||||||||||||||||||||||||||| |  |||  ||    |    ||| |  |
Sbjct  7512147  ACCATTCATCCAAGATCTCAGCTCTCCCTCACGAGGAATCTAAGGCATGTTGCTATATTC  7512088

Query  9801     ---ATGTT----G-G-TGACCCTGAGATTTGGCTAGCAAGAGGAATCTGCCCATGTTCAG  9851
                   || ||    | | ||||||||||| ||||||||  ||||||| |||||| |||||||
Sbjct  7512087  CTCATTTTTAAAGTGGTGACCCTGAGACTTGGCTAGGGAGAGGAACCTGCCCGTGTTCAG  7512028

Query  9852     ACAACAAATGATTGG-CAGACCCCTCAGGTGAG-AGGCTCAGAGGATCCCCTAAGCAGTT  9909
                 || |||||||| || |||||||||| |||||| || |||||||||||||||||| ||||
Sbjct  7512027  GCAGCAAATGAT-GGACAGACCCCTCTGGTGAGGAG-CTCAGAGGATCCCCTAAGGAGTT  7511970

Query  9910     CAACAACCTAAATGTTGGAAAA-AACTGGCTGACAGACTTTCCATTCTTTCCCAATTCAG  9968
                ||| || |||||||||| |||| |||||  ||||||||||||| ||| | ||||||||||
Sbjct  7511969  CAATAATCTAAATGTTG-AAAAGAACTGATTGACAGACTTTCCCTTCCTGCCCAATTCAG  7511911

Query  9969     AAGGTCCAGCA  9979
                |||||||||||
Sbjct  7511910  AAGGTCCAGCA  7511900


 Score =  915 bits (495),  Expect = 0.0
 Identities = 780/913 (85%), Gaps = 37/913 (4%)
 Strand=Plus/Minus

Query  5823     TCTGCTTCTGCTGGTACCAGGAAGAATGTCTTCCAAACACCAAGGAGGGAGGGGTCAAAG  5882
                ||||||||| |||||||||||||||||||||||||||||||||||||||||||||||  |
Sbjct  7390667  TCTGCTTCTACTGGTACCAGGAAGAATGTCTTCCAAACACCAAGGAGGGAGGGGTCATGG  7390608

Query  5883     AGACCACTGGCCCATTAATTTTCATCCATGGCTCCACTGAATCCCAGTACCACTGGAAAG  5942
                ||||||||| |  |||||||||| ||||| ||||||||||||||||| ||||| ||| ||
Sbjct  7390607  AGACCACTGACTTATTAATTTTCTTCCATTGCTCCACTGAATCCCAGAACCACCGGACAG  7390548

Query  5943     TGTCACTGAGGATCCTGAAAGCCAAGCTCTACCTCTTTGAGGAAAATTTTCTTGTCACTT  6002
                || ||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||
Sbjct  7390547  TGCCACTGAGGATCCTGAAAGCCAAGCTCTACCTCTTTGAAGAAAAATTTCTTGTCACTT  7390488

Query  6003     ACCGCCCTAAAGCAATGAGAATGAGAGTGTCCTGTGGCCCCAGACAGCCTCCATTCTCAG  6062
                ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7390487  ACCACCCTAAAGCAATGAGAATGAGAGTGTCCTGTGGCCCCAGACAGCCTCCATTCTCAG  7390428

Query  6063     TTTTCACCATGAACATGCTGGGGGAACACTAAAGGGACTCCCTAAAGTCAATGCCATTAT  6122
                ||| |||||| ||||||||||||||||||||||||||||||||||| || ||||||||||
Sbjct  7390427  TTTACACCATAAACATGCTGGGGGAACACTAAAGGGACTCCCTAAAATCGATGCCATTAT  7390368

Query  6123     TTTTTATTTTGAAAAATTTCAACcagaaactg-accgggtgctgtggctcatgtctgtaa  6181
                ||||||||||||||| |||| |||||||| || ||| |||||||||||||||||||||||
Sbjct  7390367  TTTTTATTTTGAAAATTTTCTACCAGAAA-TGGACCAGGTGCTGTGGCTCATGTCTGTAA  7390309

Query  6182     tcccagcactg-tgggaggccaaaacaggcagatcacttgaggttaggagttcgagaaca  6240
                ||||| ||||| ||| |  ||||   ||||||||||||||||||  | | || |||||||
Sbjct  7390308  TCCCAACACTGCTGG-ACACCAAGG-AGGCAGATCACTTGAGGTCCGTAATTTGAGAACA  7390251

Query  6241     gcctggcttacgtaatgaa-ctc-tgtctctactaaatataaaaaaattaaaaaTCATTT  6298
                ||||||| ||||||||||| | | ||||||||||||||||||||||||||| ||||||||
Sbjct  7390250  GCCTGGCCTACGTAATGAAAC-CATGTCTCTACTAAATATAAAAAAATTAAGAATCATTT  7390192

Query  6299     GACTCCAAAaggcagaggttgcagtgagccgagatcccaccactgcactccagtctggac  6358
                ||||||| |||||||| |||||| |||||| ||||| ||||||||| |||||| ||||  
Sbjct  7390191  GACTCCAGAAGGCAGAAGTTGCAATGAGCCAAGATCGCACCACTGCTCTCCAGCCTGGGT  7390132

Query  6359     aAAAGAGTTAGACTCTGTCTCAaataataataataataataataataataataataataa  6418
                 | ||| || ||||||| |||||| || || |  || | |  | |||| | |||   |  
Sbjct  7390131  GACAGACTTGGACTCTGACTCAAACAA-AA-AC-AA-A-T--TGATAA-A-TAAG--T--  7390085

Query  6419     ttaattaattaaaatGTTAGCCAGGTGTGGTGGTGCA-GTCCTATAATCCTAGCTACTCT  6477
                | ||||||  ||  |||||||||||||||||  |||| | | | ||||||||||||||||
Sbjct  7390084  T-AATTAA--AA--TGTTAGCCAGGTGTGGTCATGCATGAC-TGTAATCCTAGCTACTCT  7390031

Query  6478     GGAGGCAGAGGAAGAAGAATCACTTGAATCCCGGAGGCAGTGTTTTCAGTGAGCTGAACT  6537
                |||||||||| ||| ||||||||||||| ||| ||||||| |||| ||| ||||  | ||
Sbjct  7390030  GGAGGCAGAGAAAGGAGAATCACTTGAAGCCCAGAGGCAGAGTTTCCAGGGAGCCCAGCT  7389971

Query  6538     CAACACCCTGCCCTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAGAGAA-A  6596
                ||   |||||| || ||| |||||||||| | | ||| | |||| ||||| || | || |
Sbjct  7389970  CAGGGCCCTGCACTCCAGTCTGGGTGACACACTCAGAGTACATCACAGAA-AA-A-AACA  7389914

Query  6597     AGAATTAACCAGAAACT--AAAAGCGACGTGATGGTATTCTAGAGCATTTGGAAGGTAGG  6654
                | |||| ||  ||| ||  ||||| |  |||||||||||| | ||||||||||||||| |
Sbjct  7389913  A-AATTCACTGGAA-CTGTAAAAGTGGTGTGATGGTATTCCACAGCATTTGGAAGGTATG  7389856

Query  6655     GATAGAAATACTAACTCTAGATGAggcacagtggctcactcctgtaatcccagcactttg  6714
                 |||||||| |||||| ||| || ||| | ||||||||||| ||||||||||||||||||
Sbjct  7389855  TATAGAAATGCTAACTGTAGCTG-GGCGCGGTGGCTCACTCATGTAATCCCAGCACTTTG  7389797

Query  6715     ggagtccaaggTG  6727
                ||||||  |||||
Sbjct  7389796  GGAGTCTGAGGTG  7389784


 Score =  874 bits (473),  Expect = 0.0
 Identities = 1127/1430 (78%), Gaps = 95/1430 (6%)
 Strand=Plus/Minus

Query  4758     AGGCATTCATCCTGGGGT-AT-TTCCTTGAGGCAGATGTCTATGAACACCTTCAAGGGCT  4815
                |||||||||| || | ||  | || |||||| || | ||||||||||||| | || ||||
Sbjct  7515746  AGGCATTCAT-CTAGTGTCCTGTT-CTTGAGACAAAGGTCTATGAACACCATGAATGGCT  7515689

Query  4816     GGTGCTCT-CCCATCCTTGGACAGTCCTCTGCTGTCTGCCTCTTACTCATG-GCCTCTGG  4873
                | ||| || ||  ||| ||||||||  |||||||| ||| ||| ||||| | ||||| ||
Sbjct  7515688  GCTGC-CTGCCTGTCCCTGGACAGTTATCTGCTGTTTGCTTCTGACTCA-GAGCCTCCGG  7515631

Query  4874     GGAGGAGGACAGGGCCCTGGATTCAGACCATATGGCCCAGAAATTCTCATCAACATCCCG  4933
                | |||| | ||  |   | | | ||||  ||||| | ||||| |||||||| |||| || 
Sbjct  7515630  GAAGGATG-CA--G---TAGCTCCAGAAAATATGTCGCAGAAGTTCTCATCCACATTCCT  7515577

Query  4934     CAAATCCAGCACTTGAAGTTTCCACCT-CCTGTGGGTAAAGTA-AGGCAGAGGCT-CAGA  4990
                ||| |||||||||||||||||  | || ||||||||||||| | | | ||||||| || |
Sbjct  7515576  CAAGTCCAGCACTTGAAGTTTTGA-CTGCCTGTGGGTAAAGGAGAAG-AGAGGCTCCA-A  7515520

Query  4991     ACTTTGAAGGACAAATCCCTGACCTTTGCTTTCATTCT-CATCCAATAAATCAGCTGCTC  5049
                ||  | |||| | ||     |||||  ||||| ||| | ||||| | | |||||||| | 
Sbjct  7515519  AC--T-AAGG-C-AA----GGACCTGAGCTTTTATT-TACATCCCAGACATCAGCTG-T-  7515472

Query  5050     CTGTCCTCGCTGCTCCCTGTT--CTCTCTGAGTTTTCT-TGGTCCCTTTTCTCTTTC-AA  5105
                 | ||||| |||| | || ||  |||||||| |||| |     |||||||| | | |  |
Sbjct  7515471  -TCTCCTCTCTGC-CACTTTTCCCTCTCTGA-TTTTGTCCAACCCCTTTTC-CCTCCGGA  7515416

Query  5106     TTCTGACTGGTCCCCACTT--CTATTCCATTTAC-CTTCCACTGGGAATAGGCAAGTTTC  5162
                || || ||  |||||| ||  || |  | ||| |    |||||  ||| | | |||||||
Sbjct  7515415  TTTTGCCTCATCCCCA-TTGCCTGTAGC-TTT-CAGAGCCACT-AGAAGA-G-AAGTTTC  7515362

Query  5163     TGTTCCCACAGTGGACCCTATATTGTGGGCAGTTCTTTCCCTGAGGATCTGGGCAATGGC  5222
                |||| || |||||||||||  || ||| ||||| ||||||| ||||  ||||||||||||
Sbjct  7515361  TGTTTCCTCAGTGGACCCTGCATGGTGAGCAGTCCTTTCCCAGAGGGGCTGGGCAATGGC  7515302

Query  5223     CAAGGCATGCCTGAGCTTCGTCACCAGCACCACCAGAAGA-CACTGGGCCATCCTTGG-G  5280
                |||||| | |||||||||| ||||  |||||| ||||| | | ||||||| ||| ||| |
Sbjct  7515301  CAAGGCCTTCCTGAGCTTCCTCACTGGCACCATCAGAA-ACCTCTGGGCC-TCCATGGTG  7515244

Query  5281     ATACTTCT-TTGCCTGACCCTGCTGTTCTTTCCCTGGACACCTGAGCCC-CATCTACC-A  5337
                   || ||  | |||||  | ||||| | | |||||||||   | |||| |  | |||  
Sbjct  7515243  CCCCTCCTCCT-CCTGAAACAGCTGTCCCTACCCTGGACAAAAGGGCCCTC-CCCACCTG  7515186

Query  5338     GCCTTCCTGGGTCACCTCACCTGGGGCGATCCTTC-TGTGT-AAGCAGCATGTGAAGCCC  5395
                | |  |||||||||||||||||||||||| || || || || || |||||  | || |||
Sbjct  7515185  GAC-ACCTGGGTCACCTCACCTGGGGCGAACC-TCTTGGGTCAA-CAGCACATCAACCCC  7515129

Query  5396     TTCCAGCA-ATGCTTTTAAGGTCTCCAGATGAAGCGTCTTCATCAGCGATCCC-AGAGGG  5453
                |||||||| | | |||||| | |||||||||| ||| ||||||||| || ||| ||||||
Sbjct  7515128  TTCCAGCACA-GATTTTAATGACTCCAGATGAGGCGACTTCATCAGGGA-CCCTAGAGGG  7515071

Query  5454     AGGCGGGTGAAGGGCCAGGCCTGCACCATCACTGTCAGAGTCTGGA-AGTGTCTCCTGCT  5512
                ||||||||||| |||||||||||||||||   | |||| || |  | || ||||||||||
Sbjct  7515070  AGGCGGGTGAAAGGCCAGGCCTGCACCATTGTTTTCAGGGT-TTCACAGCGTCTCCTGCT  7515012

Query  5513     GAAGGCCTCCAGGAAGAGTG-GGAGGTAGAGCTCCCTGGGCAGCTCCTCCAGGGCAGAGA  5571
                ||||||||||| ||| |||| || || |||||||||||||||||||||||| ||  ||||
Sbjct  7515011  GAAGGCCTCCATGAACAGTGTGG-GGAAGAGCTCCCTGGGCAGCTCCTCCATGGTGGAGA  7514953

Query  5572     TGGCCAAGGGCTTGTCTCTCAGCAGACTCTGCCCCGCCAGCTCCAGGAGTCTGGGTGGGG  5631
                ||||||||| || ||| |||||||| |||||||  |||||||||||||||||||||||||
Sbjct  7514952  TGGCCAAGGCCTGGTCCCTCAGCAGCCTCTGCCTTGCCAGCTCCAGGAGTCTGGGTGGGG  7514893

Query  5632     -CCTGGATGCTCATCCTGATGAATCTGTAAGGAAAAACTCTAGAAGACAAATCCAGAGAA  5690
                 ||| |||||||||| ||||||||||| |||| ||||||||||| |||||||||||||||
Sbjct  7514892  CCCT-GATGCTCATCTTGATGAATCTGCAAGGGAAAACTCTAGAGGACAAATCCAGAGAA  7514834

Query  5691     AAGGCATCACTTTCAGGCCAAACACAATCACCTCATCTTCTCCTAAGGCCAGTAGCATTG  5750
                ||||||||||| |||||||||| |  |||||||||||||||||||  || | |  |||||
Sbjct  7514833  AAGGCATCACTCTCAGGCCAAATATGATCACCTCATCTTCTCCTATTGCTAATCTCATTG  7514774

Query  5751     CTCTGGTAGAGGTAGAAAAATTAC-CACTTTACCCCAATTCCACTCTGCACTTGGTGGCC  5809
                ||||||| ||||| | ||||   | || ||  ||||| ||||| ||||||||||||||||
Sbjct  7514773  CTCTGGTGGAGGT-GGAAAAGCCCTCAATTCCCCCCAGTTCCATTCTGCACTTGGTGGCC  7514715

Query  5810     ACAAATCTATATTTCTGCTTCTGCTG-GTACCAGGAAGAATGTCTTCCAAACACCAAGGA  5868
                |||||||| ||| | |||  ||| ||  |||||  |||||||||||||||||||||||||
Sbjct  7514714  ACAAATCTGTATCTGTGCCCCTG-TGACTACCACAAAGAATGTCTTCCAAACACCAAGGA  7514656

Query  5869     GGG-AGG-GGTCAAAGAGACCACTGGCCCATTAATTT-TCATCCATGGCTCCACTGAATC  5925
                ||| | | |||    | | ||| |||||||||||||| | || ||| ||||||||||| |
Sbjct  7514655  GGGGACGAGGT----G-G-CCAGTGGCCCATTAATTTCT-ATACATTGCTCCACTGAAAC  7514603

Query  5926     CCAGTACCACTGGAAAGTGTCACTGAGGATCCTGAAAGCCAAGCTCTACCTCTTTGAGGA  5985
                 ||| |  ||||| |  ||||||| |||||||||||||| |||||| |||| ||||||| 
Sbjct  7514602  TCAGGATTACTGGGATCTGTCACTCAGGATCCTGAAAGCTAAGCTCCACCTTTTTGAGGG  7514543

Query  5986     AAATTTTCTTGTCACTTACCGCCCTAAAGCAATGAGAATGAGAGTGTCCTGTGGCCCCAG  6045
                ||||||| |||| ||||||| ||| ||| ||||||||||||   ||||||||||||||| 
Sbjct  7514542  AAATTTTTTTGTTACTTACCACCCAAAAACAATGAGAATGAC--TGTCCTGTGGCCCCAC  7514485

Query  6046     ACAGCCTCCATTCTCAGTTTTCACCATGAACATGCTGGGGGAACACTAAAGGGACTCCCT  6105
                ||||||| |||||||||||| ||| || | |||||| |||||| ||| ||| |||||| |
Sbjct  7514484  ACAGCCTGCATTCTCAGTTTACACAATTAGCATGCTTGGGGAAGACTGAAGTGACTCCTT  7514425

Query  6106     AAAGTCAATGCCA-TTATTTTTTATTTTGAAAAATT-TCAACcagaaact  6153
                ||| ||||||||| || ||||| ||||||||||||| | ||  |||||||
Sbjct  7514424  AAAATCAATGCCACTTGTTTTT-ATTTTGAAAAATTAT-AAG-AGAAACT  7514378


 Score =  845 bits (457),  Expect = 0.0
 Identities = 713/833 (85%), Gaps = 32/833 (3%)
 Strand=Plus/Minus

Query  21757    AAGtatatatgctatatactttccatatacttatattatata-AGGTCACATGCAAATTC  21815
                |||||||||| ||| |||||||| ||||||||||||| || | |||||||||||||||||
Sbjct  7502345  AAGTATATATTCTAAATACTTTCTATATACTTATATTCTA-AGAGGTCACATGCAAATTC  7502287

Query  21816    AAGGCTAGGTCAAAGAGTAGAGTGGCAATATATGGAAAGGTGAGTGGAAGTGAATAATGG  21875
                |||||||||||||||||||||||||| || |||||||||| |||||||||||||| ||||
Sbjct  7502286  AAGGCTAGGTCAAAGAGTAGAGTGGCTATCTATGGAAAGGGGAGTGGAAGTGAATCATGG  7502227

Query  21876    TAATAAAAGGAAACagatagatatagatatagatatgaataggtagacatacacatatat  21935
                ||||||||  |   | |  | |||||||||||||| |||||| |||||||||||| ||||
Sbjct  7502226  TAATAAAA--ATT-A-A--G-TATAGATATAGATAGGAATAGATAGACATACACACATAT  7502174

Query  21936    agCTGCAAGAAAGGGGGTTGTCATGGACCAATGATGACAGTGAGCCGTGTAAAAAGGCTA  21995
                ||||||||||||||||  |||||||||||||||||| ||||||||| |||||||||||||
Sbjct  7502173  AGCTGCAAGAAAGGGGAATGTCATGGACCAATGATGTCAGTGAGCCATGTAAAAAGGCTA  7502114

Query  21996    AAATTCttgtgattgtgtttccattttcaggatgagttgtagcttacctttttagaaagg  22055
                 ||||||||||||||||| ||  ||||||||||| |||||||||||||||||||||||||
Sbjct  7502113  CAATTCTTGTGATTGTGTGTCTGTTTTCAGGATGGGTTGTAGCTTACCTTTTTAGAAAGG  7502054

Query  22056    cttatgatgcagtcatagcaaataagtgattataaaatgtgtttcctttctggg-caat-  22113
                || |||   ||| |||||  ||||| || ||||||||||||||||||||||||| || | 
Sbjct  7502053  CTGATGCCACAGCCATAGTGAATAAATGGTTATAAAATGTGTTTCCTTTCTGGGGCA-TC  7501995

Query  22114    tctggagaaatctctaatggtatgagaattcagtttactgggcaggttatcacacata-a  22172
                |||||||||||||| | ||||| ||||| || ||||||||||||||| |||||||| | |
Sbjct  7501994  TCTGGAGAAATCTCCAGTGGTAGGAGAACTCCGTTTACTGGGCAGGTGATCACACAGATA  7501935

Query  22173    a-attttacagacccaatgacactagCATTAACTTCATTATCCTTGGTATTCTATAAAGG  22231
                | ||||| |||| |||||| ||||| |||||||||||||||||||||||||||| |||||
Sbjct  7501934  AGATTTTTCAGATCCAATGGCACTACCATTAACTTCATTATCCTTGGTATTCTACAAAGG  7501875

Query  22232    TTGAGTGAACAAATGGTATATTTAAACTAAAATTAGCTAAACTGACAAAGAAAACTGGAt  22291
                | ||||||| ||||||||| || |||||||||||||||||||| |||||| | ||||| |
Sbjct  7501874  TCGAGTGAAGAAATGGTATCTTGAAACTAAAATTAGCTAAACTAACAAAGGAGACTGGGT  7501815

Query  22292    ta-ttattatttattttt-------gagacagagtctctgttgcccaggctggagtacag  22343
                || || || ||| |||||       ||||||||||||||||| ||||||||||||| |||
Sbjct  7501814  TAATTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTCTGTTACCCAGGCTGGAGTTCAG  7501755

Query  22344    tggtgctaccttggctcactgcaacctctgcctcccaggttcaag-gagttttcctgcct  22402
                |||||||| ||  ||||||||||||||||||||||  |||||||| || || || |||||
Sbjct  7501754  TGGTGCTATCTCAGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGTGA-TTGTCATGCCT  7501696

Query  22403    cagccacctaagtagctgggattacaggcacacacaaccacacccagctaatttttgtat  22462
                 |||| || ||||||||||||||||||||| || || |||||||||||||||||||||||
Sbjct  7501695  TAGCCTCCCAAGTAGCTGGGATTACAGGCATAC-CA-CCACACCCAGCTAATTTTTGTAT  7501638

Query  22463    ttttggcaga-agcggggtttcaccattttggccaggttggtcttgaacccctgacatcg  22521
                |||| | ||| | |||||||||| ||| ||| |||| ||| ||   ||| |||| | || 
Sbjct  7501637  TTTTAGTAGATAACGGGGTTTCAACATGTTGCCCAGATTGCTC---AACTCCTGGCCTCA  7501581

Query  22522    -g-gatctgcctgcctcggtctcctaaagtgctgggattataggcgtcagcca  22572
                 | ||||  || ||||||| |||| ||||||||| ||||| ||| || |||||
Sbjct  7501580  AGTGATCCACCAGCCTCGGCCTCCCAAAGTGCTGAGATTACAGGTGTGAGCCA  7501528


 Score =  835 bits (452),  Expect = 0.0
 Identities = 714/840 (85%), Gaps = 19/840 (2%)
 Strand=Plus/Minus

Query  17057    cccagtcaggagggcaatggtgtaatcttggctcactgcaaactcagcctccagggttca  17116
                ||||| | ||||  || ||||||| | |  ||||||||||| ||| |||||| |||||||
Sbjct  7543162  CCCAGGCTGGAGTTCAGTGGTGTATTGTCAGCTCACTGCAACCTCTGCCTCCTGGGTTCA  7543103

Query  17117    agggattc-tcccacctcagcc-gcatgagtaac-tggactacaggcagc-caccatcgt  17172
                || || || |||   |||||||  | | |||| | ||||||| |||| ||  |||| || 
Sbjct  7543102  AGCGA-TCTTCCTGTCTCAGCCTCCCT-AGTAGCTTGGACTATAGGC-GCAGACCACCGC  7543046

Query  17173    gcctggctaacttttct-atttttgtagagacagggtttcaccatgtgggccaggctggt  17231
                  |||||||| |||| | ||||| ||||||  ||||||| ||||||| ||||||||| ||
Sbjct  7543045  AACTGGCTAATTTTTGTAATTTTAGTAGAGGTAGGGTTTTACCATGTTGGCCAGGCTTGT  7542986

Query  17232    cttgaactcctgacctcaggtgatccacctacct-tggcctcccaaagtgctgggattac  17290
                ||  ||||||||||||||| | |||||||||||| | || ||||| ||||||||||||||
Sbjct  7542985  CTCAAACTCCTGACCTCAGATAATCCACCTACCTCT-GCGTCCCAGAGTGCTGGGATTAC  7542927

Query  17291    aagtgtgagccacctcacctggccTTGAGTGAATGAATTCTTGATTTCCAGTCTATCCCT  17350
                | ||||||||||| ||  |||||||||| |||||| |||||||| ||| |  ||||||||
Sbjct  7542926  AGGTGTGAGCCACTTCGTCTGGCCTTGAATGAATGTATTCTTGACTTCTACCCTATCCCT  7542867

Query  17351    AACTCTGTCAATTTCTTAATTCATGAAATGATTAT-GCATATGTGATATGAATGGATATC  17409
                ||| ||||| |||||||  |||||||| ||| ||| | |||||||||||||||||| |||
Sbjct  7542866  AACACTGTCGATTTCTTGCTTCATGAAGTGAATATAG-ATATGTGATATGAATGGACATC  7542808

Query  17410    TCG-TTCAATCCATTAGTCTTCGGACAGTCAAAAACCCAATCAGGATTAACTGAGTGGAG  17468
                | | ||||||||  || |||  ||| || |||||||||||||||||||||||| ||||||
Sbjct  7542807  T-GATTCAATCCGGTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAG  7542749

Query  17469    CTTCAGAAATGCAATCAGATATCGCTTTTTGATTGGAAGCTAGCAGCGGATACGTGGAGG  17528
                ||||| |||||||||||||||||  |||||||||||||| | |||||||||| ||| |||
Sbjct  7542748  CTTCACAAATGCAATCAGATATCATTTTTTGATTGGAAGGTCGCAGCGGATATGTGCAGG  7542689

Query  17529    GGCGTGGGTGGGAGTTGTGATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGACA  17588
                |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |
Sbjct  7542688  GGCGTGGGTGGGAGTTGTGATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGAGA  7542629

Query  17589    AACTCAAAGTCTTCAAGCCTGGAGTTCCTGCTTGGCTCTTCCTGAGGTCTGAGCACCTTC  17648
                 || |||||||||||||||| |||||||||||||| ||||||||||| ||||||||||||
Sbjct  7542628  GACCCAAAGTCTTCAAGCCTAGAGTTCCTGCTTGGTTCTTCCTGAGGACTGAGCACCTTC  7542569

Query  17649    TAAACTACAACCAGATCTGGTAAGTCACTAATTTCTGTAAGGACACTCCCATGTGACCTA  17708
                || |||||| |||||||||||||||||||||||||||||||||||||||||| |||||||
Sbjct  7542568  TAGACTACATCCAGATCTGGTAAGTCACTAATTTCTGTAAGGACACTCCCATCTGACCTA  7542509

Query  17709    CAGTCAGCCGGTCTAGAACGGTGACAGTGCAGCCTACGATGGCATAGAACTATATCATGT  17768
                ||||||| |||||| |   ||||||||| ||||||||||||||| ||| ||||||| |||
Sbjct  7542508  CAGTCAGTCGGTCTGGGGTGGTGACAGTACAGCCTACGATGGCACAGAGCTATATCCTGT  7542449

Query  17769    Ctttttttctttttttcatatgaacactttgaagctttgatttttttt-tCTAAATGCAA  17827
                | |||||| |||||  |||||||||| ||||||||||||| | ||||  |||||||||| 
Sbjct  7542448  CCTTTTTT-TTTTT--CATATGAACAATTTGAAGCTTTGAATGTTTTCCTCTAAATGCAG  7542392

Query  17828    TTTTGTCGTGATTTCAAAAATGTTG-TTGTGCTTTTCTTTACATCATTTCAGAATTCTTG  17886
                || |||| | |||||||||| |||| |||||||||  || |   ||||| | ||||||||
Sbjct  7542391  TTCTGTCTTTATTTCAAAAAAGTTGATTGTGCTTTGGTTGATGCCATTTTAAAATTCTTG  7542332


 Score =  791 bits (428),  Expect = 0.0
 Identities = 643/742 (86%), Gaps = 34/742 (4%)
 Strand=Plus/Minus

Query  21395    cctgagatcaggagtttgagaccagcatggccaaca-tgg-agaaactccat-t-tctac  21450
                |||||| ||||||||| ||||||||| |  |||| | ||| | |||||  || | |||| 
Sbjct  7451182  CCTGAGGTCAGGAGTTCGAGACCAGCCTCACCAA-AGTGGCA-AAACT--ATCTCTCTA-  7451128

Query  21451    taaaaatacaaaaaatagccgggcgtggtggtagg-catctgtaatctcaggtacttggg  21509
                | ||||||||||||||||| |||| ||||||| || || |||||||| |||||||| || 
Sbjct  7451127  TTAAAATACAAAAAATAGCTGGGCATGGTGGT-GGACACCTGTAATCCCAGGTACTCGGT  7451069

Query  21510    aggctgaggcaggagaaacagttgaa-cccgagaggtggaggttgcattgagccaagata  21568
                ||||||||||||||||| || ||||| || | ||||  ||| ||||| ||| ||||||| 
Sbjct  7451068  AGGCTGAGGCAGGAGAATCACTTGAATCCAG-GAGGCAGAGTTTGCAGTGAACCAAGAT-  7451011

Query  21569    gcacct-ttgcacaccagcctggccacagagcaagactccatctccaaaaaaTACTACTA  21627
                | | || |||| | |||||||||| || |||  ||||||||||||||||||| |  | ||
Sbjct  7451010  GGAACTATTGCTCTCCAGCCTGGCGACGGAGTGAGACTCCATCTCCAAAAAA-A--AATA  7450954

Query  21628    A-TAATTATAACAGCATGTCCATTCACTCTCCAAAGTGTCTGGGACTGGACAATTAATTG  21686
                | ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Sbjct  7450953  ATTAATTATAACAGCATGTCCATTCACTCTCCAAAGTGTCTAGGACTGGACAATTAATTG  7450894

Query  21687    TGAGGCCCTCTTCTCTAGCACCCTACGCTATAGCATATATGTGGATTAAAATAAATACAC  21746
                | |||||||||||| ||||||||||| |||||||||||||||||||||| ||||||||||
Sbjct  7450893  TCAGGCCCTCTTCTGTAGCACCCTACACTATAGCATATATGTGGATTAATATAAATACAC  7450834

Query  21747    ATA-AAAATGCAAGtatatatgctatatactttccatatacttatattatata-AGGTCA  21804
                ||| ||| | ||||||||||| | |||||||||| |||||||||| || || | ||||||
Sbjct  7450833  ATACAAATTTCAAGTATATATTCCATATACTTTCTATATACTTATTTTCTA-AGAGGTCA  7450775

Query  21805    CATGCAAATTCAAGGCTAGGTCAAAGAGTAGAGTGGCAATATATGGAAAGGTGAGTGGAA  21864
                |||||||||||||||||| |||||||||||||||||| || |||||||||| ||||||||
Sbjct  7450774  CATGCAAATTCAAGGCTATGTCAAAGAGTAGAGTGGCTATCTATGGAAAGGGGAGTGGAA  7450715

Query  21865    GTGAATAATGGTAATAAAAGGAAACagatagatatagatatagatatgaataggtagaca  21924
                |||||| ||||||||   |  ||| | |||| | |||||||||||||||||| |||||||
Sbjct  7450714  GTGAATCATGGTAAT---A--AAA-A-ATAGGTGTAGATATAGATATGAATATGTAGACA  7450662

Query  21925    tacacatatatagCTGCAAGAAAGGGGGTTGTCATGGACCAATGATGACAGTGAGCCGTG  21984
                |||||| ||||||| |||||||| |||  |||||||||||||||||||||||||||| ||
Sbjct  7450661  TACACACATATAGCGGCAAGAAAAGGGAATGTCATGGACCAATGATGACAGTGAGCCATG  7450602

Query  21985    TAAAAAGGCTAAAATTCttgtgattgtgtttccattttcaggatgagttgtagcttacct  22044
                ||||||||||| |||| |||||||||||| ||||||||||||||| ||||||||||||||
Sbjct  7450601  TAAAAAGGCTACAATTTTTGTGATTGTGTGTCCATTTTCAGGATGGGTTGTAGCTTACCT  7450542

Query  22045    ttttagaaaggcttatg--atgcagtcatagcaaataagtgattataaaatgtgtttcct  22102
                ||||||||||||| |||  ||  ||||||||  ||||| |||||||||||||||||||||
Sbjct  7450541  TTTTAGAAAGGCTGATGCCAT--AGTCATAGTGAATAAATGATTATAAAATGTGTTTCCT  7450484

Query  22103    ttctgg-gcaattctggagaaa  22123
                |||||| |||  ||||||||||
Sbjct  7450483  TTCTGGTGCACCTCTGGAGAAA  7450462


 Score =  756 bits (409),  Expect = 0.0
 Identities = 721/865 (83%), Gaps = 48/865 (5%)
 Strand=Plus/Minus

Query  22327    cccaggctggagtacagtggtgctaccttggctcactgcaacctctgcctcccaggttca  22386
                ||||||||||| | ||| ||||| | ||  |||||||||||||||||||||||||| |||
Sbjct  7449398  CCCAGGCTGGACTGCAGAGGTGCAATCTCAGCTCACTGCAACCTCTGCCTCCCAGGATCA  7449339

Query  22387    ag-gagtt-ttcctgcctcagccaccta-agtagctgggattacaggcacaca-caacca  22442
                 |  | || || ||| ||||||| || | ||||||||||||||||||||   | | ||||
Sbjct  7449338  TGCCA-TTCTT-CTGACTCAGCCTCC-AGAGTAGCTGGGATTACAGGCATGGATC-ACCA  7449283

Query  22443    cacccagctaatttttgtatttttggcagaag-c-ggggtttcaccattttggccaggtt  22500
                |||||||||||||| ||||||||| | || || | ||| |||| |||| ||| |||||  
Sbjct  7449282  CACCCAGCTAATTTGTGTATTTTTAGTAG-AGACAGGGTTTTC-CCATGTTGTCCAGG-C  7449226

Query  22501    ggtcttgaacccctgacatcgggatctgcctgcctcggtctcctaaagtgctgggattat  22560
                |||||  |||||||||| | | |||||| || |||||| ||||||||||||||| |||||
Sbjct  7449225  GGTCTCAAACCCCTGACCTTGTGATCTGACTCCCTCGGCCTCCTAAAGTGCTGGTATTAT  7449166

Query  22561    aggcgtcagccaccacacctggccGAATCtttttttcttttctcaaa-gat-gttgtcat  22618
                |||| | ||   |||| | | ||| |  ||||||| |||||||||||  || || ||  |
Sbjct  7449165  AGGCATGAG---CCAC-CGT-GCCCAGCCTTTTTTGCTTTTCTCAAACCATGGTGGT-GT  7449112

Query  22619    agtattgggttctatgcactcaggagagtgagcccatCATTCAGTAACAATATGAATCAA  22678
                |||||||||||||||||||| |||||||||||| ||||||||||||||||||||| ||| 
Sbjct  7449111  AGTATTGGGTTCTATGCACTTAGGAGAGTGAGCTCATCATTCAGTAACAATATGACTCAG  7449052

Query  22679    TACTGCAAGACCTTGATGCAGAATTTCAAAGACTATTTCCAGTAGGTG-A--AGGCTTTC  22735
                |||  |   | |  || | |   ||||||||||||||||||||||||| |  ||||||| 
Sbjct  7449051  TAC--C---A-C--GA-G-A-CCTTTCAAAGACTATTTCCAGTAGGTGAAGGAGGCTTTT  7449003

Query  22736    AGTGATGCTTAGATCTTCCTGCCCTAGCATTTGGAGATTGCATCCTTTGGAAATGACACC  22795
                | ||||| || || |||| ||||||| |||||||||||||  | ||||  ||||| | ||
Sbjct  7449002  AATGATGATTGGACCTTCATGCCCTACCATTTGGAGATTGTGT-CTTTTAAAATGGC-CC  7448945

Query  22796    -AAGGGAAATCTGCGCATGAGCAGCAATGGATGGGACTGTACCAGATGACTGAAACGTAA  22854
                 ||||||||||||| ||||||||||| |||||| |||  |||||| ||||| |||  |||
Sbjct  7448944  TAAGGGAAATCTGCCCATGAGCAGCATTGGATGAGACCATACCAGGTGACTTAAAATTAA  7448885

Query  22855    AGATATCCGAGG--AAAAGCCTTCCCTAGAAGCAGACATCATCACATGGTAGACAGCT-T  22911
                 |||| || |||  ||||||||| | || ||||||||||||||||||||||||||||| |
Sbjct  7448884  GGATAACCAAGGAAAAAAGCCTTTCTTACAAGCAGACATCATCACATGGTAGACAGCTGT  7448825

Query  22912    TTCCAAGACAATGGAACAAGACTCCATT-TGATCTTCTTCCATTGACTGAGACTTGGTTT  22970
                ||  |||| |||||||||| |||||||| | |||| ||||||||||||||||||||||||
Sbjct  7448824  TT-TAAGAAAATGGAACAAAACTCCATTCT-ATCTCCTTCCATTGACTGAGACTTGGTTT  7448767

Query  22971    TGTTTTGTATTAACACAAAATTCTCAAACCTGTATTTTATATTGTTAGGTACTTTCATCA  23030
                ||||||||| |||||||||||  |||| |||  ||||||| |||||| ||||||||| ||
Sbjct  7448766  TGTTTTGTACTAACACAAAATGATCAAGCCTACATTTTATTTTGTTACGTACTTTCACCA  7448707

Query  23031    CTCAAACCAAACACTTTCTAAGGTCTCCTGTTCAAAATGTAGCCACTCTCACTAACCAAA  23090
                 ||||| |||||||||||||||||||||| |||||||| |||||||| ||||||||||||
Sbjct  7448706  GTCAAAGCAAACACTTTCTAAGGTCTCCTCTTCAAAATTTAGCCACTATCACTAACCAAA  7448647

Query  23091    GCAATTGCTGGCTATGGGGTCATTTAGATGAA-AGGGAAGGATCACAGA-TAATAGTAGA  23148
                |||||||||| |||||| |||||||||||||| ||| |||||||||| | ||||||||||
Sbjct  7448646  GCAATTGCTGCCTATGGAGTCATTTAGATGAATAGG-AAGGATCACA-ACTAATAGTAGA  7448589

Query  23149    ACCTGCTCTCATACACAGTTGGGTA  23173
                ||||||||||| |||| ||||||||
Sbjct  7448588  ACCTGCTCTCACACACGGTTGGGTA  7448564


 Score =  743 bits (402),  Expect = 0.0
 Identities = 702/840 (83%), Gaps = 47/840 (5%)
 Strand=Plus/Minus

Query  13645    cccaagcgggagtacagtggtgctatgtc-atctcactgcaacatctgcctcccgggttc  13703
                |||| || ||||| ||| ||||| || || | ||||||||||| |||||||| | || ||
Sbjct  7499355  CCCAGGCTGGAGTGCAGAGGTGCAATCTCGA-CTCACTGCAACCTCTGCCTCACAGGATC  7499297

Query  13704    aagagattctcctgcctcagactcctgagtagccgggattacaggcacacaccaccacac  13763
                ||| |||||| ||||||||| ||||| |||||| |||||||||| ||     || |||||
Sbjct  7499296  AAGTGATTCTTCTGCCTCAGCCTCCTAAGTAGCTGGGATTACAGACATGGGTCATCACAC  7499237

Query  13764    ccagctgatttttgtattttt-agcagaaacggggtttcaccatgttgaccaggttggtc  13822
                |||||| |||| ||||||||| |  ||| || |||||||||||| ||| ||||| |||  
Sbjct  7499236  CCAGCTAATTTGTGTATTTTTCA-TAGAGACAGGGTTTCACCATATTGGCCAGGCTGG-A  7499179

Query  13823    tt-gaacccctgaccttgtgatctc-cctgcctcagcctcctgaa-gtgctggaattata  13879
                || |||||||||||||||||||| | ||| |||  ||||||| || |||||| || ||||
Sbjct  7499178  TTCGAACCCCTGACCTTGTGATC-CGCCTACCTTGGCCTCCT-AATGTGCTGCAAATATA  7499121

Query  13880    ggct-tgagccaccttgcccagcctaatctttttttcttttCTCAAAGGACTTCTATGCA  13938
                || | | ||||||| ||||||| |    ||||||| |   | |        |||||||||
Sbjct  7499120  GG-TGTCAGCCACCATGCCCAG-C----CTTTTTTGC---T-T--------TTCTATGCA  7499079

Query  13939    CTTAGGAGAGTGAGCCCATCGTTCAGTAACAACATGATTCAATACTGCAAGACCTTGATG  13998
                |||||||||||||||||||||||||||||||| |||| ||| ||||||||||||||  | 
Sbjct  7499078  CTTAGGAGAGTGAGCCCATCGTTCAGTAACAATATGACTCAGTACTGCAAGACCTT--T-  7499022

Query  13999    CAGTATTTCAAAGTCTTTCCAGTAGGTGAGGGAGGCTTTCAG-TGATGC-TTAGACCTTC  14056
                ||  |    |   | |||||||| ||||| ||||| |||| | |||| |  | |||||||
Sbjct  7499021  CA--A----AGCCTATTTCCAGTTGGTGAAGGAGGGTTTC-GATGAT-CACTGGACCTTC  7498970

Query  14057    ATGCCCTAGAATTTGGAGATTGCATCCTTTAGAAATGATACCAAGGGAAATCTGCCCATG  14116
                ||||||||  ||||||||| |||||| |||| |||||| |||||||||||||||||||||
Sbjct  7498969  ATGCCCTACCATTTGGAGACTGCATCTTTTA-AAATGACACCAAGGGAAATCTGCCCATG  7498911

Query  14117    AGCAGCACTGGATGGGACTGTACCAGATGACTTAAAACTAAGGATAACCAAGG-A-AAAG  14174
                ||||||| ||||||||||  |||||| |||||||||| ||||||||||||||| | ||||
Sbjct  7498910  AGCAGCATTGGATGGGACCATACCAGGTGACTTAAAATTAAGGATAACCAAGGAACAAAG  7498851

Query  14175    CCTTCCTTAGAAGCAGACATCATCACATGGTAGACAG-TTTTCCAAGACAATGGAACAAG  14233
                 ||| |||||||||||||||||||||||||||||||| ||||  |||| ||||| |||| 
Sbjct  7498850  TCTTTCTTAGAAGCAGACATCATCACATGGTAGACAGCTTTTTTAAGAAAATGGGACAAA  7498791

Query  14234    ACTCCATTTGATCTTCTTCCATTGACTGAGACTTGGTTTTGTTTTGTATTAAAACAAAAT  14293
                |||||||||||||| ||||||||||||||||||||||||||||||||||||| ||||| |
Sbjct  7498790  ACTCCATTTGATCTCCTTCCATTGACTGAGACTTGGTTTTGTTTTGTATTAACACAAAGT  7498731

Query  14294    GCTCAAACCTATATTTTATGTTGTTAGGTACTTTCTCCACTCAAACCAAACACTTTCTAA  14353
                | |||| |||| ||||||| |||||| |||||||| ||| ||||| ||||||||||||||
Sbjct  7498730  GATCAAGCCTACATTTTATTTTGTTACGTACTTTCACCAGTCAAAGCAAACACTTTCTAA  7498671

Query  14354    GGTCTTCTGTTCAAAATGTAGCCACTCTCACTAACCAAAGCAATTGCTGGCTATGGAGTC  14413
                | ||| || |||||||| |||||| |||||||||||||||||||| ||||||||||||||
Sbjct  7498670  GTTCTCCTATTCAAAATTTAGCCATTCTCACTAACCAAAGCAATTACTGGCTATGGAGTC  7498611

Query  14414    ATTTACATGAAAGGGAAGGATCACAACTAAATAGTAGAACATGCTCTCATAAACAGTTGG  14473
                ||||| ||||| |||||||||||||||||| ||||||||| |||||||| | || |||||
Sbjct  7498610  ATTTAGATGAATGGGAAGGATCACAACTAA-TAGTAGAACCTGCTCTCACACACGGTTGG  7498552


 Score =  741 bits (401),  Expect = 0.0
 Identities = 713/857 (83%), Gaps = 47/857 (5%)
 Strand=Plus/Minus

Query  13645    cccaagcgggagtacagtggtgctatgtcatctcactgcaacatctgcctcccgggttca  13704
                |||| || ||| | ||| ||||| || ||| ||||||||||| |||||||||| || |||
Sbjct  7449398  CCCAGGCTGGACTGCAGAGGTGCAATCTCAGCTCACTGCAACCTCTGCCTCCCAGGATCA  7449339

Query  13705    agagattctcctgcctcagactcctgagtagccgggattacaggcacacaccaccacacc  13764
                 |  ||||| ||| ||||| |||| ||||||| |||||||||||||   | |||||||||
Sbjct  7449338  TGCCATTCTTCTGACTCAGCCTCCAGAGTAGCTGGGATTACAGGCATGGATCACCACACC  7449279

Query  13765    cagctgatttttgtatttttagcagaaac-ggggtttcaccatgttgaccaggttggtct  13823
                ||||| |||| ||||||||||| ||| || ||| |||| |||||||| |||||  |||||
Sbjct  7449278  CAGCTAATTTGTGTATTTTTAGTAGAGACAGGGTTTTC-CCATGTTGTCCAGG-CGGTCT  7449221

Query  13824    tgaacccctgaccttgtgatctccctgcctcagcctcctgaagtgctggaattataggct  13883
                  ||||||||||||||||||||  || |||| ||||||| ||||||||| ||||||||| 
Sbjct  7449220  CAAACCCCTGACCTTGTGATCTGACTCCCTCGGCCTCCTAAAGTGCTGGTATTATAGGCA  7449161

Query  13884    tgagccaccttgcccagcctaatctttttttcttttCTC-AA--A-------G--G-A--  13928
                ||||||||| ||||||| |    ||||||| |||||||| ||  |       |  | |  
Sbjct  7449160  TGAGCCACCGTGCCCAG-C----CTTTTTTGCTTTTCTCAAACCATGGTGGTGTAGTATT  7449106

Query  13929    --CTTCTATGCACTTAGGAGAGTGAGCCCATCGTTCAGTAACAACATGATTCAATACTGC  13986
                   |||||||||||||||||||||||| |||| ||||||||||| |||| ||| |||  |
Sbjct  7449105  GGGTTCTATGCACTTAGGAGAGTGAGCTCATCATTCAGTAACAATATGACTCAGTACCAC  7449046

Query  13987    AAGACCTTGATGCAGTATTTCAAAGTCTTTCCAGTAGGTGAGGGAGGCTTTCAGTGATGC  14046
                 |||||||  | ||  |    | | | |||||||||||||| ||||||||| | ||||| 
Sbjct  7449045  GAGACCTT--T-CA--A----AGACTATTTCCAGTAGGTGAAGGAGGCTTTTAATGATGA  7448995

Query  14047    TTAGACCTTCATGCCCTAGAATTTGGAGATTGCATCCTTTAGAAATGATACC-AAGGGAA  14105
                || |||||||||||||||  ||||||||||||  || |||| |||||   || |||||||
Sbjct  7448994  TTGGACCTTCATGCCCTACCATTTGGAGATTGTGTCTTTTA-AAATG-GCCCTAAGGGAA  7448937

Query  14106    ATCTGCCCATGAGCAGCACTGGATGGGACTGTACCAGATGACTTAAAACTAAGGATAACC  14165
                |||||||||||||||||| |||||| |||  |||||| |||||||||| |||||||||||
Sbjct  7448936  ATCTGCCCATGAGCAGCATTGGATGAGACCATACCAGGTGACTTAAAATTAAGGATAACC  7448877

Query  14166    AAGG--AAAAGCCTTCCTTAGAAGCAGACATCATCACATGGTAGACAG-T-TTTCCAAGA  14221
                ||||  ||||||||| |||| ||||||||||||||||||||||||||| | |||  ||||
Sbjct  7448876  AAGGAAAAAAGCCTTTCTTACAAGCAGACATCATCACATGGTAGACAGCTGTTT-TAAGA  7448818

Query  14222    CAATGGAACAAGACTCCATT-TGATCTTCTTCCATTGACTGAGACTTGGTTTTGTTTTGT  14280
                 |||||||||| |||||||| | |||| ||||||||||||||||||||||||||||||||
Sbjct  7448817  AAATGGAACAAAACTCCATTCT-ATCTCCTTCCATTGACTGAGACTTGGTTTTGTTTTGT  7448759

Query  14281    ATTAAAACAAAATGCTCAAACCTATATTTTATGTTGTTAGGTACTTTCTCCACTCAAACC  14340
                | ||| |||||||| |||| |||| ||||||| |||||| |||||||| ||| ||||| |
Sbjct  7448758  ACTAACACAAAATGATCAAGCCTACATTTTATTTTGTTACGTACTTTCACCAGTCAAAGC  7448699

Query  14341    AAACACTTTCTAAGGTCTTCTGTTCAAAATGTAGCCACTCTCACTAACCAAAGCAATTGC  14400
                |||||||||||||||||| || |||||||| |||||||| ||||||||||||||||||||
Sbjct  7448698  AAACACTTTCTAAGGTCTCCTCTTCAAAATTTAGCCACTATCACTAACCAAAGCAATTGC  7448639

Query  14401    TGGCTATGGAGTCATTTACATGAA-AGGGAAGGATCACAACTAAATAGTAGAACATGCTC  14459
                || ||||||||||||||| ||||| ||| ||||||||||||||| ||||||||| |||||
Sbjct  7448638  TGCCTATGGAGTCATTTAGATGAATAGG-AAGGATCACAACTAA-TAGTAGAACCTGCTC  7448581

Query  14460    TCATAAACAGTTGGGTA  14476
                ||| | || ||||||||
Sbjct  7448580  TCACACACGGTTGGGTA  7448564


 Score =  682 bits (369),  Expect = 0.0
 Identities = 995/1286 (77%), Gaps = 87/1286 (6%)
 Strand=Plus/Plus

Query  4616     TTCCAGCTCCTGAATACTATTC-AGGTGGATTATTTTCAAT-GATCTTCTGAGATA-TTC  4672
                ||||| |||||| |||||  ||  |||  ||  ||| |||| ||| |||||| | | || 
Sbjct  7492017  TTCCAACTCCTGGATACT-GTCTGGGTATATCCTTTCCAATAGAT-TTCTGA-A-ACTTG  7492072

Query  4673     AA-TCGACGTTAGA-TAATTCACCAACTTACTACAGCACAGGTGTACTAAACCTCTCCTT  4730
                || | | | || || ||||||  || ||||||||| |||||||| ||||  ||||| || 
Sbjct  7492073  AAGTGGGCATT-GAGTAATTCTGCACCTTACTACAACACAGGTGCACTAGGCCTCTTCTG  7492131

Query  4731     TGGTAAACCCACCGGAAGAGGTATCTCAGGCATTCATCCTGGGGTA-TTTCCTTGAGGCA  4789
                | ||  | |||||  || ||||| |||||||||||||||  | ||| ||||||| |||||
Sbjct  7492132  TAGTGGATCCACCCAAAAAGGTAGCTCAGGCATTCATCC-AGTGTACTTTCCTTTAGGCA  7492190

Query  4790     GATGTCTATGAACACCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGT  4849
                || |||||||||||||||||||||||||||||||||||||||||||||||||||  ||||
Sbjct  7492191  GAGGTCTATGAACACCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCCACTGT  7492250

Query  4850     CTGCCTCTTACTCATGGCCTCTGGGGAGGAGGACAGGGCCCTGGATTCAGACCATATGGC  4909
                |||||||||||||||||||||||||||| |||| ||| |||||| | |||||||||||| 
Sbjct  7492251  CTGCCTCTTACTCATGGCCTCTGGGGAGCAGGAGAGGACCCTGGCTCCAGACCATATGGT  7492310

Query  4910     CCAGAAATTCTCATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGT  4969
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Sbjct  7492311  CCAGAAATTCTCATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGAGT  7492370

Query  4970     AA-AGTAAGGCAGAGGCTCAGAACTTT-G--AAGGACAAATCCCTGACCTTTGCTTTCAT  5025
                || | || || | | |||||||| | | |  ||||||  | |||||||||  ||||||| 
Sbjct  7492371  AACA-TAGGGGAAAAGCTCAGAA-TGTAGGCAAGGACCCACCCCTGACCTGAGCTTTCAC  7492428

Query  5026     TCT-CATCCAATA-A--A-TCAGCTGCTCCTGTCCTC-GCTGCTCCCTGTTCTCTCTGAG  5079
                ||  ||||||  | |  | |||||||||||||||||| | |||||| |   || ||||  
Sbjct  7492429  TCCACATCCAGGACATCAGTCAGCTGCTCCTGTCCTCAG-TGCTCC-TC--CT-TCTGTC  7492483

Query  5080     TTTTCTTGGTCCCTTTTCTCT-TTCAATTCTGACTGGTCCCCACTTCTATT-CCATTTAC  5137
                | ||||   ||| |  || || ||  |||||| ||||| |||||||||| | || |||||
Sbjct  7492484  TCTTCTCCATCC-TGCTCCCTCTTGGATTCTGCCTGGTACCCACTTCTAGTACC-TTTAC  7492541

Query  5138     CTTCCACTGGGAATAGGCAAGTTTCTGTTCCCACAGTGGACCCTATATTGTGGGCAGTTC  5197
                 |||  ||||||  |  |||| | ||||| || ||||||||||| ||| ||| ||||  |
Sbjct  7492542  TTTCTGCTGGGAGGAAACAAGCTCCTGTTTCCTCAGTGGACCCTGTATGGTGAGCAGACC  7492601

Query  5198     TTTCCCTGAGGATCTGGGCAATGGCCAAGGCATGC-C-TGAGCTTCGTCACCAGCACCAC  5255
                ||| || |||||||||||||||||||||||| | | | || ||  |||||  ||| |  |
Sbjct  7492602  TTTTCCAGAGGATCTGGGCAATGGCCAAGGCCT-CTCATGGGCACCGTCAGAAGC-CT-C  7492658

Query  5256     CAGAAGACAC--TGGG-CC--ATCCTTGGGATACTTCTTTGCCTGACCCTGCTGTTCTTT  5310
                  || | |||  | |  ||  | ||     |  || ||   ||||| || ||||| | ||
Sbjct  7492659  T-GA-GCCACCCTAGCTCCCCAACCCCACCA--CTCCT---CCTGAGCCAGCTGTCCCTT  7492711

Query  5311     CCCTGGACACCTGAGCCCCATCTACC-A--GCCTTCCTGGGTCACCTCACCTGGGGCGAT  5367
                |||||||  |||| | ||| ||  || |  |||  |||| ||||||||||||||||||| 
Sbjct  7492712  CCCTGGATGCCTG-GACCCTTCC-CCGAAAGCCA-CCTGAGTCACCTCACCTGGGGCGAA  7492768

Query  5368     CCTTCTGTGTAAGCAGCATGTGAAG-CCCTTCCAGCA-ATGCTTTTAAGGTCTCCAGATG  5425
                ||||||| |  | |||  | | ||| ||| || || | | ||||  ||||||||||||||
Sbjct  7492769  CCTTCTGGGCCACCAGTGTATCAAGTCCCCTC-AGGACA-GCTTGCAAGGTCTCCAGATG  7492826

Query  5426     AAGCGTCTTCATCAGCGATCCCAGAGGGAGGCGG-GTGAAGGGCCAGGCCTGCACCATCA  5484
                ||| ||||||||||| |||||||||||||||| | | |||||||||||||||||||||||
Sbjct  7492827  AAGTGTCTTCATCAGGGATCCCAGAGGGAGGCTGAG-GAAGGGCCAGGCCTGCACCATCA  7492885

Query  5485     -CTGTCAGAGTCTGGAAGTGTCTCCTGCTGAAGGCCTCCAGGAAGAGTGGGAGGTA-GAG  5542
                 || |||| | ||  ||  ||||| ||||||||||||||| ||| | |  |||| | || 
Sbjct  7492886  GCT-TCAGGGCCTCAAAACGTCTCATGCTGAAGGCCTCCATGAACA-TCAGAGGGAAGAC  7492943

Query  5543     CTCCCTGGGCAGCTCCTCCAGGGCAGA-GATGGCCAAGGGCTTGTCTC-TCAGCAGACTC  5600
                ||||||||||||||| |||||||  || ||||| ||||  || || || ||||||| |||
Sbjct  7492944  CTCCCTGGGCAGCTCATCCAGGGT-GAAGATGGTCAAGAACTGGT-TCCTCAGCAGGCTC  7493001

Query  5601     TGCCCCGCCAGCTCCAGGAGTCTGGGTGGGGCCTGGATGCTCATCCTGATGAATCTGTAA  5660
                ||||| ||||||||||| ||||||| ||||||||||| |||||| ||||  |||||   |
Sbjct  7493002  TGCCCTGCCAGCTCCAGCAGTCTGGATGGGGCCTGGAGGCTCATTCTGACAAATCTCCGA  7493061

Query  5661     GGAAAAACTCTAGAAGACAAATCCAGAGAAAAGGCATCACTTTCA-GG-CCAAACACAAT  5718
                |||||||||||||| ||||| || || |||||||||  | ||||  || |||  | | | 
Sbjct  7493062  GGAAAAACTCTAGAGGACAA-TCAAGTGAAAAGGCA--AGTTTCTCGGGCCATTCCCCAG  7493118

Query  5719     CA--CCTCATCTTCTCCTAAGGCCAGTAG-CATTGCTCTGGTA-GAGGTAGAAAAATTAC  5774
                ||  || || ||||||||| |||||  || |||| |||| | | | | | |||| |   |
Sbjct  7493119  CAAGCCCCA-CTTCTCCTAGGGCCAA-AGTCATTTCTCTAGCACGTG-T-GAAAGAGCCC  7493174

Query  5775     -CACTTTACCCCAATTCCACTCTGCACTTGGTGGCCACAAAT-CTATATTTCTGCTTCTG  5832
                 || ||||| ||||||||  |||||| |  ||||| ||| |  | ||  ||||||  || 
Sbjct  7493175  TCAGTTTACTCCAATTCCGTTCTGCAATAAGTGGCTACAGAGGC-ATGGTTCTGCC-CTT  7493232

Query  5833     CTGGTACCAGGAAGAATGTCTTCCAA  5858
                ||||||||| ||||| ||| | ||||
Sbjct  7493233  CTGGTACCAAGAAGAGTGTGTCCCAA  7493258


 Score =  675 bits (365),  Expect = 0.0
 Identities = 614/732 (83%), Gaps = 25/732 (3%)
 Strand=Plus/Minus

Query  984      gaaggggggacctcctgggcCCTCGAGAGCACTAGGGGACCTTGTTTGGTAACTGCAACC  1043
                ||||||| ||||||||| |||||| |||||||| |||||||||| |||| |||||| |||
Sbjct  7527262  GAAGGGGAGACCTCCTGAGCCCTCAAGAGCACTGGGGGACCTTGGTTGG-AACTGCGACC  7527204

Query  1044     TGGGCAGCTTCAGTTGTGCCTTTggagctactgccctgccaacttgggaggaccaggact  1103
                ||||||||||||||||||||||||||||||||| |||||||||| |||||| ||||||||
Sbjct  7527203  TGGGCAGCTTCAGTTGTGCCTTTGGAGCTACTGTCCTGCCAACTCGGGAGGGCCAGGACT  7527144

Query  1104     ccctcttgtcccaggatcccatcagctccaaagtgtgcacagcctcagctt-tgcCCTCT  1162
                ||||||||||||||||||||||||| | ||||||||    |||||||| || ||||||||
Sbjct  7527143  CCCTCTTGTCCCAGGATCCCATCAGGTTCAAAGTGTATGTAGCCTCAG-TTATGCCCTCT  7527085

Query  1163     CTCTGT-TTCCGTGCA--GAGGTGACAGGTGAGATGCAGGTTCACAGCAGCTCTGGTCAA  1219
                |||||| || | | ||  |||||||||||||||||||||||||||||||||||||| |||
Sbjct  7527084  CTCTGTGTTTC-TCCACAGAGGTGACAGGTGAGATGCAGGTTCACAGCAGCTCTGGCCAA  7527026

Query  1220     CCCCACAGAAACAAATCTGAA-GCTCCTGGGTCCGGTTTAATGAGCCCCAACTGCGCTCT  1278
                |||  || ||||||| |  || ||| ||||||| |||| |||||||||||||||| ||||
Sbjct  7527025  CCCTGCAAAAACAAACCC-AATGCTTCTGGGTCTGGTTGAATGAGCCCCAACTGCACTCT  7526967

Query  1279     -GATCCAGGAGT-TTGCAGGCTAACAGCACAAAGTGGGGAGTGAGGTCGAGGCTGTGGTG  1336
                 | |  || | | ||||||||||||||||    ||| |||||||| | |||||| || | 
Sbjct  7526966  AGTTA-AGAA-TATTGCAGGCTAACAGCAGGCCGTGAGGAGTGAGTTTGAGGCTTTG-TA  7526910

Query  1337     GAGACTGCGGACCTAGGG-GCAAGTCCCGTTTAGCCGTGAGAGGGTATGGGTGGCACAGT  1395
                ||| || | ||||  ||| ||  ||| | || |||| ||||||||| |||||||||||| 
Sbjct  7526909  GAGGCTCCAGACCC-GGGAGCGGGTCTCATTAAGCCATGAGAGGGTGTGGGTGGCACAGC  7526851

Query  1396     TGGCTGCCTCAGGGACATGGGGCACAGGCCTGGCTGACAACCCAGCCAAGA-GGTGGTGC  1454
                || |||||||||| ||| |||||| |||||||||| ||||||| ||||||  || |||||
Sbjct  7526850  TGTCTGCCTCAGGAACACGGGGCAGAGGCCTGGCTCACAACCCTGCCAAGGTGG-GGTGC  7526792

Query  1455     CTTTAGGAGTGGATCGTGGTCCACAGGCCCAGCAATC-GGAAGCATCAGGCTCTGTGTTC  1513
                ||  ||| ||||| |||||||| ||| |||||||||  |||| | |||| ||||||| ||
Sbjct  7526791  CTCCAGGGGTGGACCGTGGTCCCCAGACCCAGCAATTAGGAA-CGTCAGTCTCTGTGGTC  7526733

Query  1514     ACCCCTCTTGGGGGCAGATCTTGGAAATGCAGCCTCAGGAAGATTCA-CACAGAAC-TCC  1571
                |||||| | ||||||||||||||||||||||||| ||||| |||| | |||||||| |||
Sbjct  7526732  ACCCCTGTGGGGGGCAGATCTTGGAAATGCAGCCCCAGGAGGATT-AGCACAGAACCTCC  7526674

Query  1572     TTTTTAGACCTAGGAACTTGATACTATTAGCAGGGTGGGCACACAGTTGATGCATAGCTG  1631
                 ||  | ||| |||||||||  ||| |||||||||||||||||  || |   ||||||||
Sbjct  7526673  CTTCGACACCCAGGAACTTGGCACTGTTAGCAGGGTGGGCACA--GTGGCCCCATAGCTG  7526616

Query  1632     GCCAGGTCATTGAACTTGGTGCCATTTCTGCTTCCCAACTCGGGGCCCTGGAGCATGGCC  1691
                |||||||||||||||| ||||||||||||||||||||||   || ||||| ||| ||  |
Sbjct  7526615  GCCAGGTCATTGAACTAGGTGCCATTTCTGCTTCCCAACAAAGGCCCCTGTAGCTTGATC  7526556

Query  1692     CCAGCTCTGCCT  1703
                ||||||||||||
Sbjct  7526555  CCAGCTCTGCCT  7526544


 Score =  664 bits (359),  Expect = 0.0
 Identities = 737/915 (80%), Gaps = 44/915 (4%)
 Strand=Plus/Plus

Query  3514     CCTGCTTCAACCAAACACAAGTTTGTTCCCACCATCTGATGATGGTCCT-CATGCAAGTT  3572
                |||| |||| ||||||||||||||||||||| |||| ||||||||| ||   |||||| |
Sbjct  7550988  CCTGTTTCACCCAAACACAAGTTTGTTCCCATCATCAGATGATGGT-CTGTGTGCAAGGT  7551046

Query  3573     GCTGCATGTTGAGGACCCTGATCATTCAGGGGCTGTC-CCATTTTAGCCTCAGCCCTTTC  3631
                ||||| || ||| ||| | |||||||||||||| | | ||||||||| ||||| ||||||
Sbjct  7551047  GCTGCCTGATGAAGACTCAGATCATTCAGGGGCAG-CTCCATTTTAGGCTCAGTCCTTTC  7551105

Query  3632     A-CCATTTCTTGTGTGATTGGGTCAAGGCCACAAAATCTCTAAAGCCT-TTTATCTTCAT  3689
                | || || ||||||||||||| ||||||||||||||||| |||||||| |||| || |||
Sbjct  7551106  AGCC-TTGCTTGTGTGATTGGTTCAAGGCCACAAAATCTTTAAAGCCTCTTTA-CTGCAT  7551163

Query  3690     CTTTTAGCAGAAAACCTCATCTCTGGGCCACAGGTA-CCCGGTGGGAGATGTGCACAAAG  3748
                |||| |||||| |||||||||||||||||| ||| | ||| |||||||||||||||||||
Sbjct  7551164  CTTTCAGCAGACAACCTCATCTCTGGGCCAGAGG-AGCCCAGTGGGAGATGTGCACAAAG  7551222

Query  3749     AACTCAACTCAGCAAGGTCTAGGGACATTAGCTGGGGCTACCTGCCGGCAGGGGCTCCCT  3808
                ||||||||| |||||||||||||||||| |||| |||| ||||||| |||  || |||||
Sbjct  7551223  AACTCAACTGAGCAAGGTCTAGGGACATCAGCTAGGGCCACCTGCCTGCAAAGGTTCCCT  7551282

Query  3809     GGCCTGCCTGCATCTGCAAACCAACTGTCACTTTTTACCACTCTCACT-CCTACTCCTTC  3867
                | | |||| || ||||||||||| || ||||||| |||||||||| || |||||||| ||
Sbjct  7551283  GACGTGCCCGCGTCTGCAAACCACCTATCACTTTATACCACTCTC-CTGCCTACTCCCTC  7551341

Query  3868     ACCCTCCATCCCAGAAGCATGCATGTCCCATGTCAATTGACTTT-CCTGGAGTTCAAAAC  3926
                ||| ||  ||| |||||||||| | || |||||||| | ||||| ||||| |||||||| 
Sbjct  7551342  ACC-TCTGTCCAAGAAGCATGCTTTTCTCATGTCAACT-ACTTTTCCTGGGGTTCAAAAG  7551399

Query  3927     AACCTTCTACAGACAGGGAATCAGAGACAGGATCATTCATGATCACTAAGCTGGTGAGGA  3986
                |||||| ||||||||| |||| |||| ||||||||||  || | ||||||||| ||||||
Sbjct  7551400  AACCTTTTACAGACAGAGAATTAGAGGCAGGATCATTGGTGTTTACTAAGCTG-TGAGGA  7551458

Query  3987     CAGAGCTTCTACTGTGAAATGCACAAGTTTGATGCACTGTCCCTCCTTTCATACCCTCCT  4046
                | ||||||||||||||||| ||||| |||||||||||| ||||| ||||||||| |||||
Sbjct  7551459  CGGAGCTTCTACTGTGAAACGCACAGGTTTGATGCACTTTCCCTTCTTTCATACTCTCCT  7551518

Query  4047     TTGT-T-ACCTCT---TTTACATCATATCAACTTGAAACACACTTTGTAACAAGAAATTC  4101
                 | | | |    |   ||| |||||||| ||||| |||| |||||  ||| ||| |||||
Sbjct  7551519  CTATATGAAGAGTAAGTTT-CATCATATTAACTTCAAACGCACTTCCTAAAAAGGAATTC  7551577

Query  4102     ACACGTGCACA-TGCAGTAGAGACAAAACGCCCACTAAGTACCTTG-TACATG-ATGTCC  4158
                |||  |||||  | |  ||||  |  ||| |||  | | || || | | | || ||||| 
Sbjct  7551578  ACAAATGCACCCTCCC-TAGAT-CTGAAC-CCC--TGACTAACTAGATCCCTGCATGTCT  7551632

Query  4159     CTCTCT--AGCCTCTA-CCCTAGGTGACCCCTCTGCCTTTATT-GAA-GTGATCCTGTGA  4213
                ||||||  ||| |||  |||  ||  | ||||||||| ||||| ||  | | |  |||||
Sbjct  7551633  CTCTCTGTAGCATCTGGCCCG-GGCCATCCCTCTGCCCTTATTTGAGCGGGTT--TGTGA  7551689

Query  4214     TAGCCACTCCAGGACATGGAGCACTGAACGGGACAATGTGTTGACATTCTGGTGTCCCCT  4273
                || ||||| ||||| || ||||||||||| | | |||| ||||||||||| | ||||| |
Sbjct  7551690  TACCCACTTCAGGATATAGAGCACTGAACAGCATAATGAGTTGACATTCTAGCGTCCCAT  7551749

Query  4274     GCACTGTGCCGTCGCCACTGGCTGGCACACAGTACACGTCTTCTAGTGTTTACTGT-AAC  4332
                 | ||||| | || ||| |||||||||||||||| | | |  |||| ||||||||| || 
Sbjct  7551750  TCCCTGTGACATCACCAGTGGCTGGCACACAGTAGATGCCCACTAGCGTTTACTGTGAA-  7551808

Query  4333     aaa-aa-aaaaGGCTGCGCTGTGGTCTGCAGAGAAAGGGCACGATCCTTTCTCACCTGAT  4390
                ||| || ||||| ||| | | ||||| ||||||||||  ||| ||||||||| |||||| 
Sbjct  7551809  AAAGAACAAAAGTCTGTGGTATGGTCCGCAGAGAAAGCTCACCATCCTTTCTTACCTGAG  7551868

Query  4391     CAGCTG-TCCCAGGT  4404
                ||| || ||| ||||
Sbjct  7551869  CAGGTGCTCC-AGGT  7551882


 Score =  647 bits (350),  Expect = 0.0
 Identities = 944/1218 (77%), Gaps = 91/1218 (7%)
 Strand=Plus/Plus

Query  4686     TAATTCACCAACTTACTACAGCACAGGTGTACTAAACCTCTCCT-T--TGG-TAAACCCA  4741
                ||||||  || |||| ||||||||||||| |||| |||||| || |  ||| |  |||||
Sbjct  7552164  TAATTCTGCACCTTATTACAGCACAGGTGCACTAGACCTCTTCTGTAGTGGATCTACCCA  7552223

Query  4742     CCGGAAGAGGTATCTCAGGCATTCATCCTGGGGTA-TTTCCTTGAGGCAGATGTCTATGA  4800
                 |  || ||||| |||||||||||||||  | ||| ||| ||| ||||||  ||||||||
Sbjct  7552224  -C--AA-AGGTAGCTCAGGCATTCATCC-AGTGTACTTTTCTTTAGGCAGCGGTCTATGA  7552278

Query  4801     ACACCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGTCTGCCTCTTAC  4860
                |||||||||||||||||  ||||||||||||||||||||||||  |||||||||| ||||
Sbjct  7552279  ACACCTTCAAGGGCTGGCACTCTCCCATCCTTGGACAGTCCTCCACTGTCTGCCTTTTAC  7552338

Query  4861     TCATGGCCTCTGGGGAGGAGGACAGGGCCCTGGATTCAGACCATATGGCCCAGAAATTCT  4920
                ||||||||||||||||| |||| ||| || ||| | |||||||||||| |||||||||| 
Sbjct  7552339  TCATGGCCTCTGGGGAGCAGGAGAGGACCTTGGCTCCAGACCATATGGTCCAGAAATTCC  7552398

Query  4921     CATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAA-AGTAAGGC  4979
                |||||||||||||||||||||||||||||||||||||||||||||| |||| |  | || 
Sbjct  7552399  CATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGAGTAACAC-AGGGG  7552457

Query  4980     AGAGGCTCAGAACTTT-G--AAGGACAAATCCCTGACCTTTGCTTTCATTCT-CATCCAA  5035
                | | |||||||| | | |  ||||||  | |||||||||  ||||||| ||  |||||| 
Sbjct  7552458  AAAAGCTCAGAA-TGTAGGCAAGGACCCACCCCTGACCTGAGCTTTCACTCCACATCCAG  7552516

Query  5036     TA-A--A-TCAGCTGCTCCTGTCCTC-GCTGCTCCCTGTTCTCTCTGAGTTTTCTTGGTC  5090
                 | |  | |||||||||||||||||| | |||||| |   || ||||  | ||||   ||
Sbjct  7552517  GACATCAGTCAGCTGCTCCTGTCCTCAG-TGCTCC-TC--CT-TCTGTCTCTTCTCCATC  7552571

Query  5091     CCTTTTCTCTTTCAATTCTGACTGGTCCCCACTTCTAT--TCCATTTACCTTCCACTGGG  5148
                ||  | | | ||   ||||| ||||| | ||||||||   ||  ||||| ||||||||||
Sbjct  7552572  CCGCTCCCCCTTGGGTTCTGCCTGGTTCTCACTTCTAGAATC--TTTACGTTCCACTGGG  7552629

Query  5149     A-ATAGGCAAGTTTCTGTTCCCACAGTGGACCCTATATTGTGGGCAGTTCTTTCCCTGAG  5207
                | | || || ||| ||||| || ||||||||||| ||| ||| ||||| ||||||| |||
Sbjct  7552630  AGAAAG-CAGGTTCCTGTTTCCTCAGTGGACCCTGTATGGTGAGCAGTCCTTTCCCAGAG  7552688

Query  5208     GATCTGGGCAATGGCCAAGGCATGC-C-TGAGCTTCGTCACCAGCACCACCAGAAGACAC  5265
                |||||||||||||| |||||| | | | || ||  | |||  ||| |  |  || | |||
Sbjct  7552689  GATCTGGGCAATGGTCAAGGCCT-CTCATGGGCACCATCAGAAGC-CT-CT-GA-GCCAC  7552743

Query  5266     --TGGG-CC--ATCCTTGGGATACTTCTTTGCCTGACCCTGCTGTTCTTTCCCTGGACAC  5320
                  | |  ||  | ||     |  || ||   ||||| || ||||| | |||||||||  |
Sbjct  7552744  CCTAGCTCCCCAACCCCACCA--CTCCT---CCTGAGCCAGCTGTCCCTTCCCTGGATGC  7552798

Query  5321     CTGAGCCCCATCT-ACCAG-CCTTCCTGGGTCACCTCACCTGGGGCGATCCTTCTGTGTA  5378
                ||| | ||| ||  ||||| ||  |||| ||||||||||||| ||| | ||||||| |  
Sbjct  7552799  CTG-GACCCTTCCCACCAGGCCA-CCTGAGTCACCTCACCTGAGGCAAACCTTCTGGGCC  7552856

Query  5379     AGCAGCATGTGAAG-CCCTTCCAGCA-ATGCTTTTAAGGTCTCCAGATGAAGCGTCTTCA  5436
                |||||  | | ||| |||||| |||| | ||||  ||||||||||||||| | |||||||
Sbjct  7552857  AGCAGTGTATCAAGTCCCTTC-AGCACA-GCTTGCAAGGTCTCCAGATGAGGTGTCTTCA  7552914

Query  5437     TCAGCGATCCCAGAGGGAGGCGG-GTGAAGGGCCAGGCCTGCACCATCA-CTGTCAGAGT  5494
                |||| ||||||||||||||| || | ||||| ||||||||||||||||| || |||| | 
Sbjct  7552915  TCAGGGATCCCAGAGGGAGGTGGAG-GAAGGACCAGGCCTGCACCATCAGCT-TCAGGGC  7552972

Query  5495     CTGGA-AGTGTCTCCTGCTGAAGGCCTCCAGGAAGAGTGGGAGGTA-GAGCTCCCTGGGC  5552
                ||  | || |||||||||||| |||||||| ||| | |  |||| | || ||||||||||
Sbjct  7552973  CTC-ACAGCGTCTCCTGCTGACGGCCTCCATGAACA-TCAGAGGGAAGACCTCCCTGGGC  7553030

Query  5553     AGCTCCTCCAGGGCAGA-GATGGCCAAGGGCTTGTCTC-TCAGCAGACTCTGCCCCGCCA  5610
                ||||| ||||||   || ||||| ||||  || || || |||| || |||||||| ||||
Sbjct  7553031  AGCTCGTCCAGGAT-GAAGATGGTCAAGAACTGGT-TCCTCAGTAGGCTCTGCCCTGCCA  7553088

Query  5611     GCTCCAGGAGTCTGGGTGGGGCCTGGATGCTCATCCTGATGAATCTGTAAGGAAAAACTC  5670
                ||||||||||||||| ||||| ||||| |||||| ||||  |||||| ||||||||||||
Sbjct  7553089  GCTCCAGGAGTCTGGATGGGGACTGGAGGCTCATTCTGACAAATCTGCAAGGAAAAACTC  7553148

Query  5671     TAGAAGACAAATCCAGAGAAAAGGCATCACTTTC--AGGCCAAACAC----AATCACCTC  5724
                |||| ||||| ||||| |||||||||  | ||||  ||||||| | |    |||| || |
Sbjct  7553149  TAGAGGACAA-TCCAGTGAAAAGGCA--AGTTTCTCAGGCCAATCCCCTGCAATC-CC-C  7553203

Query  5725     ATCTTCTCCTAAGGCCAGTAG-CATTGCTCTGGTA-GAGGTAGAAAAATTAC-CACTTTA  5781
                  ||||||||| |||||  || |||| |||| | | | | | |||| |   | || ||||
Sbjct  7553204  G-CTTCTCCTAGGGCCAA-AGTCATTTCTCTAGCATGTG-T-GAAAGAGCCCTCAGTTTA  7553259

Query  5782     CCCCAATTCCACTCTGCACTTGGTGGCCACAAAT-CTATATTTCTGCTTCTGCTGGTACC  5840
                | ||||||||| |||||| |  ||||||||| |  | ||| ||||||  || ||||||| 
Sbjct  7553260  CTCCAATTCCATTCTGCAATAAGTGGCCACAGAGGC-ATAGTTCTGCC-CTTCTGGTACT  7553317

Query  5841     AGGAAGAATGTCTTCCAA  5858
                | ||||| ||| | ||||
Sbjct  7553318  AAGAAGAGTGTGTCCCAA  7553335


 Score =  612 bits (331),  Expect = 4e-171
 Identities = 875/1124 (77%), Gaps = 91/1124 (8%)
 Strand=Plus/Plus

Query  4616     TTCCAGCTCCTGAATACTATTC-AGGTGGATTATTTTCAAT-GATCTTCTGAGATA-TTC  4672
                ||||| |||||| |||||| ||  |||  ||  ||| |||| ||| |||||| | | || 
Sbjct  7437553  TTCCAACTCCTGGATACTA-TCTGGGTATATCCTTTCCAATAGAT-TTCTGA-A-ACTTG  7437608

Query  4673     AA-TCGACGTTAGA-TAATTCACCAACTTACTACAGCACAGGTGTACTAAACCTCTCCTT  4730
                || | | | || || ||||||  || ||||||||| |||||||| ||||  ||||| || 
Sbjct  7437609  AAGTGGGCATT-GAGTAATTCTGCACCTTACTACAACACAGGTGCACTAGGCCTCTTCTG  7437667

Query  4731     TGGTAAACCCACCGGAAGAGGTATCTCAGGCATTCATCCTGGGGTA-TTTCCTTGAGGCA  4789
                | ||  | |||||   ||||||| ||||||||||||| |  | ||| ||||||| |||||
Sbjct  7437668  TAGTGGATCCACCTTCAGAGGTAGCTCAGGCATTCATGC-AGTGTACTTTCCTTCAGGCA  7437726

Query  4790     GATGTCTATGAACACCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGT  4849
                || |||||||||||||||||||||||||  |||||||||||||||||||| |||  ||||
Sbjct  7437727  GAGGTCTATGAACACCTTCAAGGGCTGGCACTCTCCCATCCTTGGACAGTTCTCCACTGT  7437786

Query  4850     CTGCCTCTTACTCATGGCCTCTGGGGAGGAGGACAGGGCCCTGGATTC-AGACCATATGG  4908
                |||||||||||||||||||||||||||| |||  ||| ||||| | || |||||||||||
Sbjct  7437787  CTGCCTCTTACTCATGGCCTCTGGGGAGCAGGGGAGGACCCTG-ACTCCAGACCATATGG  7437845

Query  4909     CCCAGAAATTCTCATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGG  4968
                 ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| |
Sbjct  7437846  TCCAGAAATTCTCATCAACATCCCTCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGAG  7437905

Query  4969     TAA-AGTAAGGCAGAGGCTCAGAACTTT-G--AAGGACAAATCCCT-GACCTTTGCTTTC  5023
                ||| | ||||| | | |||||||| | | |  ||||||  | |||| |||||   |||||
Sbjct  7437906  TAACA-TAAGGGAAAAGCTCAGAA-TGTAGGCAAGGACCGA-CCCTTGACCTGAACTTTC  7437962

Query  5024     ATTCT-CATCCAATA-A--A-TCAGCTGCTCCTGTCCTC-GCTGCTCCCTGTTCTCTCTG  5077
                | ||  ||||||  | |  | |||||||||||||||| | | |||||| |   || ||||
Sbjct  7437963  ACTCCGCATCCAGGACATGAGTCAGCTGCTCCTGTCC-CAG-TGCTCC-TC--CT-TCTG  7438016

Query  5078     AGTTTTCTTGGTCCCTTTTCTCT-TTCAATTCTG-ACTGGTCCCCACTTCTATT-CCATT  5134
                  ||||||   ||| | ||| |  ||  |||||| | |||| |||||||||| | || ||
Sbjct  7438017  TCTTTTCTCCATCC-TGTTCCCCCTTGGATTCTGCA-TGGTACCCACTTCTAGTACC-TT  7438073

Query  5135     TACCTTCCACTGGGAATAGGCAAGTTTCTGTTCCCACAGTGGACCCTATATTGTGGGCAG  5194
                |||||||||||||||  | ||| ||| ||||| || ||||||||||| ||| ||  ||||
Sbjct  7438074  TACCTTCCACTGGGAGGAAGCAGGTTCCTGTTTCCTCAGTGGACCCTGTATGGTAAGCAG  7438133

Query  5195     TTCTTTCCCTGAGGATCTGGGCAATGGCCAAGGCATGCCTGAGCTTCGTCACCAGCACCA  5254
                | |||| || |||||||||||||||||||||||| | | | |  |  |      ||||||
Sbjct  7438134  TCCTTTTCCAGAGGATCTGGGCAATGGCCAAGGCTT-C-TCA--TG-G------GCACCA  7438182

Query  5255     CCAGAAGACACTGGGCCATCCTTGGG---ATACT-T-CTT-TGC-C-TGACCCTGCTGTT  5306
                 |||||| | ||| |||| ||| |     | ||  | |   | | | ||| || ||||| 
Sbjct  7438183  TCAGAAGCCTCTGAGCCACCCTAGCTCCCACACACTGCCACTCCTCCTGAGCCAGCTGTC  7438242

Query  5307     CTTTCCCTGGACACCTGAGCCCCATCT-ACCAG-CCTTCCTGGGTCACCTCACCTGGGGC  5364
                | |||||||||   ||| | ||| ||  ||||| ||  |||| ||||||||| |||||||
Sbjct  7438243  CCTTCCCTGGATGTCTG-GACCCTTCCCACCAGGCCA-CCTGAGTCACCTCAACTGGGGC  7438300

Query  5365     GATCCTTCTGTGTA-AGC-AGCATGTGAAG-CCCTTCCAGCA-ATGCTTTTAAGGTCTCC  5420
                 | ||||||| | | | | ||  | | ||| |||||| |||| | ||||  |||||||||
Sbjct  7438301  AAACCTTCTGGG-ACA-CTAGTGTATCAAGTCCCTTC-AGCACA-GCTTGCAAGGTCTCC  7438356

Query  5421     AGATGAAGCGTCTTCATCAGCGATCCCAGAGGGAGGCG--GGTGAAGGGCCAGGCCTGCA  5478
                |||||| | ||||||||||| ||||||||||||||| |  || || ||||||||||||||
Sbjct  7438357  AGATGAGGTGTCTTCATCAGGGATCCCAGAGGGAGGTGAAGG-GA-GGGCCAGGCCTGCA  7438414

Query  5479     CCATCA-CTGTCAGAGTCTGG-AAGTGTCTCCTGCTGAAGGCCTCCAGGAAGAGTGGGAG  5536
                |||||| || |||| | ||   ||   |||| ||||||||||||||| ||| || ||| |
Sbjct  7438415  CCATCAGCT-TCAGGGCCTCACAACA-TCTCATGCTGAAGGCCTCCATGAACAGAGGG-G  7438471

Query  5537     GTAGAGCTCCCTGGGCAGCTCCTCCAGGGCAGA-GATGGCCAAGGGCTTGTCTC-TCAGC  5594
                  ||| ||||||||||||||| |||||||  || ||| | ||||  || || || |||||
Sbjct  7438472  --AGACCTCCCTGGGCAGCTCATCCAGGGT-GAAGATAGTCAAGAACTGGT-TCCTCAGC  7438527

Query  5595     AGACTCTGCCCCGCCAGCTCCAGGAGTCTGGGTGGGGCCTGGATGCTCATCCTGATGAAT  5654
                || |||||||| ||||||||||||||||||| ||||| ||||| |||||| ||||  |||
Sbjct  7438528  AGGCTCTGCCCTGCCAGCTCCAGGAGTCTGGATGGGGTCTGGAGGCTCATTCTGACAAAT  7438587

Query  5655     CTGTAAGGAAAAACTCTAGAAG-ACAAATCCAG-AGAAAAGGCA  5696
                ||  |||||||||||||| | | |||| ||||| | ||||||||
Sbjct  7438588  CTACAAGGAAAAACTCTACA-GCACAA-TCCAGCA-AAAAGGCA  7438628


 Score =  588 bits (318),  Expect = 6e-164
 Identities = 874/1128 (77%), Gaps = 96/1128 (8%)
 Strand=Plus/Plus

Query  4616     TTCCAGCTCCTGAATACTATTC-AGGTGGATTATTTTCAAT-GATCTTCTGAGATA-TTC  4672
                ||||| |||||| |||||  ||  |||  ||  ||| |||| ||| |||||| | | || 
Sbjct  7599188  TTCCAACTCCTGGATACT-GTCTGGGTATATCCTTTCCAATAGAT-TTCTGA-A-ACTTG  7599243

Query  4673     AA-TCGACGTTAGA-TAATTCACCAACTTACTACAGCACAGGTGTACTAAACCTCTCCTT  4730
                || | | | || || ||||||  || ||||||||| |||||||| ||||  ||||| || 
Sbjct  7599244  AAGTGGGCATT-GAGTAATTCTGCACCTTACTACAACACAGGTGCACTAGGCCTCTTCTG  7599302

Query  4731     TGGTAAACCCACCGGAAGAGGTATCTCAGGCATTCATCCTGGGGTA-TTTCCTTGAGGCA  4789
                | ||  | |||||   ||||||| |||||||||||||||  | ||| ||||||| |||||
Sbjct  7599303  TAGTGGATCCACCTTCAGAGGTAGCTCAGGCATTCATCC-AGTGTACTTTCCTTCAGGCA  7599361

Query  4790     GATGTCTATGAACACCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGT  4849
                || |||||||||||||||||||||||||  ||||||||||||||||||||||||  ||||
Sbjct  7599362  GAGGTCTATGAACACCTTCAAGGGCTGGCACTCTCCCATCCTTGGACAGTCCTCCACTGT  7599421

Query  4850     CTGCCTCTTACTCATGGCCTCTGGGGAGGAGGACAGGGCCCTGGATTC-AGACCATATGG  4908
                |||||||||||||||||||||||||||| |||  ||| ||||| | || |||||||||||
Sbjct  7599422  CTGCCTCTTACTCATGGCCTCTGGGGAGCAGGGGAGGACCCTG-ACTCCAGACCATATGG  7599480

Query  4909     CCCAGAAATTCTCATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGG  4968
                 ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| |
Sbjct  7599481  TCCAGAAATTCTCATCAACATCCCTCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGAG  7599540

Query  4969     TAA-AGTAAGGCAGAGGCTCAGAACTTT-GA--AGGACAAATCCCT-GACCTTTGCTTTC  5023
                ||| | ||||| | | |||||||| | | |   |||||  | |||| |||||   |||||
Sbjct  7599541  TAACA-TAAGGGAAAAGCTCAGAA-TGTAGGCGAGGACCGA-CCCTTGACCTGAACTTTC  7599597

Query  5024     ATTCT-CATCCAATA-A--A-TCAGCTGCTCCTGTCCTC-GCTGCTCCCTGTTCTCTCTG  5077
                | ||  ||||||  | |  | |||||||||||||||| | | |||||| |   || ||||
Sbjct  7599598  ACTCCACATCCAGGACATGAGTCAGCTGCTCCTGTCC-CAG-TGCTCC-TC--CT-TCTG  7599651

Query  5078     AGTTTTCTTGGTCCCTTTTCTCT-TTCAATTCTG-ACTGGTCCCCACTTCTATT-CCATT  5134
                  ||||||   ||| | ||| |  ||  |||||| | |||| |||||||||| | || ||
Sbjct  7599652  TCTTTTCTCCATCC-TGTTCCCCCTTGGATTCTGCA-TGGTACCCACTTCTAGTACC-TT  7599708

Query  5135     TACCTTCCACTGGGAATAGGCAAGTTTCTGTTCCCACAGTGGACCCTATATTGTGGGCAG  5194
                |||||||||||||||  | ||| ||| ||||| || |||||||| || ||| ||| ||||
Sbjct  7599709  TACCTTCCACTGGGAGGAAGCAGGTTCCTGTTTCCTCAGTGGACTCTGTATGGTGAGCAG  7599768

Query  5195     TTCTTTCCCTGAGGATCTGGGCAATGGCCAAGGCATGC-C-TGAGCTTCGTCACCAGCA-  5251
                | |||| || |||||||||||||||||||||||| | | | || | | |  || ||| | 
Sbjct  7599769  TCCTTTTCCAGAGGATCTGGGCAATGGCCAAGGCCT-CTCATGGG-TAC--CATCAGAAG  7599824

Query  5252     CCACCAGAAGACAC--TGGG-CC-AT-C-CTTGGGATACTTCTTTGCCTGACCCTGCTGT  5305
                || |  || | |||  | |  || |  | || |  |  || ||   ||||| || |||||
Sbjct  7599825  CCTCT-GA-GCCACCCTAGCTCCCACACACT-GCCA--CTCCT---CCTGAGCCAGCTGT  7599876

Query  5306     TCTTTCCCTGGACACCTGAGCCCCATCT-ACCAG-CCTTCCTGGGTCACCTCACCTGGGG  5363
                 | |||||||||  |||| | ||| ||  ||||| ||  |||| ||||||||| ||||||
Sbjct  7599877  CCCTTCCCTGGATGCCTG-GACCCTTCCCACCAGGCCA-CCTGAGTCACCTCAACTGGGG  7599934

Query  5364     CGATCCTTCTGTGTA-AGC-AGCATGTGAAG-CCCTTCCAGCA-ATGCTTTTAAGGTCTC  5419
                | | ||||||| | | | | ||  | | ||| |||||| |||| | ||||  ||||||||
Sbjct  7599935  CAAACCTTCTGGG-ACA-CTAGTGTATCAAGTCCCTTC-AGCACA-GCTTGCAAGGTCTC  7599990

Query  5420     CAGATGAAGC-GTCTTCATCAGCGATCCCAGAGGGAGGCG--GGTGAAGGGCCAGGCCTG  5476
                ||||||| |  ||||||||||| ||||||||||||||| |  || || || |||||||||
Sbjct  7599991  CAGATGA-GTTGTCTTCATCAGGGATCCCAGAGGGAGGTGAAGG-GA-GGACCAGGCCTG  7600047

Query  5477     CACCATCA-CTGTCAGAGTCTGG-AAGTGTCTCCTGCTGAAGGCCTCCAGGAAGAGTGGG  5534
                |||||||| || |||| | ||   ||   |||| ||||||||||||||| ||| | |  |
Sbjct  7600048  CACCATCAGCT-TCAGGGCCTCACAACA-TCTCATGCTGAAGGCCTCCATGAACA-TCAG  7600104

Query  5535     AGGT-AGAGCTCCCTGGGCAGCTCCTCCAGGGCAGA-GATGGCCAAGGGCTTGTCT-C-T  5590
                |||  ||| ||||||||||||||  |||||||  || ||| | ||||  || | || | |
Sbjct  7600105  AGGGGAGACCTCCCTGGGCAGCTAGTCCAGGGT-GAAGATAGTCAAGAACT-G-CTTCCT  7600161

Query  5591     CAGCAGACTCTGCCCCGCCAGCTCCAGGAGTCTGGGTGGGGCCTGGATGCTCATCCTGAT  5650
                || ||| |||||||| ||||||||||||||||||| ||||| ||||| |||||| |||| 
Sbjct  7600162  CATCAGGCTCTGCCCTGCCAGCTCCAGGAGTCTGGATGGGGTCTGGAGGCTCATTCTGAC  7600221

Query  5651     GAATCTGTAAGGAAAAACTCTAGAAG-ACAAATCCAG-AGAAAAGGCA  5696
                 |||||  |||||||||||||| | | |||| ||||| | ||||||||
Sbjct  7600222  AAATCTACAAGGAAAAACTCTACA-GCACAA-TCCAGCA-AAAAGGCA  7600266


 Score =  564 bits (305),  Expect = 1e-156
 Identities = 473/551 (85%), Gaps = 23/551 (4%)
 Strand=Plus/Minus

Query  22628    ttctatgcactcaggagagtgagcccatCATTCAGTAACAATATGAATCAATACTGCAAG  22687
                ||||||||||| ||||||||||||||||| |||||||||||||||| ||| |||||||||
Sbjct  7499087  TTCTATGCACTTAGGAGAGTGAGCCCATCGTTCAGTAACAATATGACTCAGTACTGCAAG  7499028

Query  22688    ACCTTGATGCAGAATTTCAAAGACTATTTCCAGTAGGTG-A--AGGCTTTCAG-TGATGC  22743
                | |      |    |||||||| ||||||||||| |||| |  ||| |||| | |||| |
Sbjct  7499027  A-C------C----TTTCAAAGCCTATTTCCAGTTGGTGAAGGAGGGTTTC-GATGAT-C  7498981

Query  22744    -TTAGATCTTCCTGCCCTAGCATTTGGAGATTGCATCCTTTGGAAATGACACCAAGGGAA  22802
                  | || |||| ||||||| |||||||||| ||||| ||||  |||||||||||||||||
Sbjct  7498980  ACTGGACCTTCATGCCCTACCATTTGGAGACTGCAT-CTTTTAAAATGACACCAAGGGAA  7498922

Query  22803    ATCTGCGCATGAGCAGCAATGGATGGGACTGTACCAGATGACTGAAACGTAAAGATATCC  22862
                |||||| ||||||||||| ||||||||||  |||||| ||||| |||  ||| |||| ||
Sbjct  7498921  ATCTGCCCATGAGCAGCATTGGATGGGACCATACCAGGTGACTTAAAATTAAGGATAACC  7498862

Query  22863    GAGG-A-AAAGCCTTCCCTAGAAGCAGACATCATCACATGGTAGACAGCTTTTCCAAGAC  22920
                 ||| | |||| ||| | |||||||||||||||||||||||||||||||||||  |||| 
Sbjct  7498861  AAGGAACAAAGTCTTTCTTAGAAGCAGACATCATCACATGGTAGACAGCTTTTTTAAGAA  7498802

Query  22921    AATGGAACAAGACTCCATTTGATCTTCTTCCATTGACTGAGACTTGGTTTTGTTTTGTAT  22980
                ||||| |||| |||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct  7498801  AATGGGACAAAACTCCATTTGATCTCCTTCCATTGACTGAGACTTGGTTTTGTTTTGTAT  7498742

Query  22981    TAACACAAAATTCTCAAACCTGTATTTTATATTGTTAGGTACTTTCATCACTCAAACCAA  23040
                ||||||||| |  |||| |||  ||||||| |||||| ||||||||| || ||||| |||
Sbjct  7498741  TAACACAAAGTGATCAAGCCTACATTTTATTTTGTTACGTACTTTCACCAGTCAAAGCAA  7498682

Query  23041    ACACTTTCTAAGGTCTCCTGTTCAAAATGTAGCCACTCTCACTAACCAAAGCAATTGCTG  23100
                |||||||||||| |||||| |||||||| |||||| |||||||||||||||||||| |||
Sbjct  7498681  ACACTTTCTAAGTTCTCCTATTCAAAATTTAGCCATTCTCACTAACCAAAGCAATTACTG  7498622

Query  23101    GCTATGGGGTCATTTAGATGAAAGGGAAGGATCACAGA-TAATAGTAGAACCTGCTCTCA  23159
                ||||||| |||||||||||||| ||||||||||||| | |||||||||||||||||||||
Sbjct  7498621  GCTATGGAGTCATTTAGATGAATGGGAAGGATCACA-ACTAATAGTAGAACCTGCTCTCA  7498563

Query  23160    TACACAGTTGG  23170
                 |||| |||||
Sbjct  7498562  CACACGGTTGG  7498552


 Score =  446 bits (241),  Expect = 4e-121
 Identities = 400/474 (84%), Gaps = 21/474 (4%)
 Strand=Plus/Minus

Query  9290     TACATTTCCCCCACAAAACCTGGAAGCTCTATTTCATGTTGAAATATCTGCTAAG-TTCA  9348
                ||||||| ||||||||||||  | |||||  | ||| | || ||  | || |||| || |
Sbjct  7369607  TACATTT-CCCCACAAAACCCAG-AGCTCCGTATCACGCTGCAAGCTTTG-TAAGCTT-A  7369552

Query  9349     CGGATGGCTCCCATCCTAAG-AGGGATCACACAGTGATTCTTCCGATGTTTTAGGG-CAC  9406
                 || |||||||||||||  | | | ||||||| |||||||||| |||||||| |||  ||
Sbjct  7369551  GGGGTGGCTCCCATCCTGGGCA-GAATCACACCGTGATTCTTCTGATGTTTT-GGGATAC  7369494

Query  9407     AAAGTAGCAAGAACCTCCCCTGCCTCCAGA-AAGTCCTCCAGGCCTTTCTCTCCCATTCT  9465
                |||||||||||| |||||||  || ||||| || |||||||||||||||||||||||| |
Sbjct  7369493  AAAGTAGCAAGAGCCTCCCCCACC-CCAGAGAA-TCCTCCAGGCCTTTCTCTCCCATTTT  7369436

Query  9466     ATATGAAAACCAAACAGCTCTGAGATGCCACTGG-CCTCCAAAACTGGAGTACTTTGAAG  9524
                 ||||| | ||||||||||||||||||||||||| || ||||| ||||||| ||| ||||
Sbjct  7369435  TTATGACACCCAAACAGCTCTGAGATGCCACTGGCCCACCAAAGCTGGAGTTCTTCGAAG  7369376

Query  9525     GGTGTTCTCTATCTTGAAATGTTTCTGTAAATGTTCTT-TCTCCACATTTCTGACCTCAC  9583
                | ||||||| |||| | ||| |||||| ||||||| || |||||||||||||||||||||
Sbjct  7369375  GATGTTCTCCATCTCGGAATCTTTCTGGAAATGTT-TTCTCTCCACATTTCTGACCTCAC  7369317

Query  9584     TGTCAATGCCCTGCTATGTGTGCAATTGAGTTAAACTGAAATGTGTTCAGTGGGGCTTCT  9643
                | |||||| |||  ||||||||||||  ||||||||||||||||  |||||| |||||||
Sbjct  7369316  TATCAATG-CCT--TATGTGTGCAATCAAGTTAAACTGAAATGTACTCAGTGAGGCTTCT  7369260

Query  9644     ACTTTGCCTG-CCCTCACTTTGTGAGCCTGAGGCTGAGGTTGAGCTCAGCACCAAGGGTG  9702
                || || || | ||||  |||||||| ||||||||||||| ||||||||||||||||| ||
Sbjct  7369259  AC-TTCCCAGCCCCTTGCTTTGTGAACCTGAGGCTGAGGGTGAGCTCAGCACCAAGGATG  7369201

Query  9703     ATCGTGAGTGTCTCTGGTGACTGAGCATCCACGAGGCACAGCAGGGGCTG-GTA  9755
                 |||||||  |||||| ||||||||||||||||||||||||||||||||| |||
Sbjct  7369200  GTCGTGAGCATCTCTGTTGACTGAGCATCCACGAGGCACAGCAGGGGCTGAGTA  7369147


 Score =  427 bits (231),  Expect = 1e-115
 Identities = 677/879 (77%), Gaps = 84/879 (9%)
 Strand=Plus/Plus

Query  28480    CTGAGC-TTCAGAGATC-CTCGGTAACATTTGCCAGTGCT-AT-GAGTTTAGTGGATCAG  28535
                |||||| || | ||| | || ||||||| || |||| ||| || |||||  ||||| || 
Sbjct  7567232  CTGAGCTTTGA-AGA-CTCTTGGTAACACTTCCCAGAGCTAATAGAGTTGGGTGGAGCAA  7567289

Query  28536    TGGCT-AATAATTCATGGACTACGAGGGATCTTGCCTGCTCTTTAGAAGTTGGGACACAT  28594
                |   | || |||||||||| || ||| ||| ||||| | || || || ||| ||| ||| 
Sbjct  7567290  TTAATGAA-AATTCATGGAGTAGGAGTGATTTTGCCCGTTCCTTGGAGGTTAGGAGACAC  7567348

Query  28595    TCTTCATGGTACCAGAAGGGTAGAACTATGTCTCTGTGGCCACTTATTGCAGAAAGGAAC  28654
                ||||| |||||||||||||| |||||||||||| |||||||| ||||||||||   ||| 
Sbjct  7567349  TCTTCTTGGTACCAGAAGGGCAGAACTATGTCTGTGTGGCCAATTATTGCAGAGTCGAAT  7567408

Query  28655    TGGAGTAAACTGAGGGCTCTTTCACA-CATGCTAGAGAAATGAC-TTGGGCCCTGGGAGA  28712
                ||| ||||||| ||| |||||||||| | ||| |||| | |||| || |||||  |||||
Sbjct  7567409  TGGGGTAAACTTAGGACTCTTTCACATC-TGCCAGAGTAGTGACTTTTGGCCC-AGGAGA  7567466

Query  28713    ATTGGGGGT-TGCAGGGGATTGGTCGGAGGAA-CTTGCCTTTT-TGCTGGATTGTGCTGT  28769
                | |  |||| || || ||| ||| | ||  ||  ||| ||||| | |||||   |  | |
Sbjct  7567467  AGTCAGGGTGTG-AGAGGACTGGCCTGA-TAAGTTTGTCTTTTCT-CTGGA---T--T-T  7567517

Query  28770    AGAGTTTTTCCTTGTAGATTTGTCAGAATGAGCCTCCAGACCCCATC-CAGACTCCTGGA  28828
                   | |||| |||| |||||| | || |||||||| ||| ||||| | ||||||||||||
Sbjct  7567518  ---G-TTTT-CTTGCAGATTTATGAGGATGAGCCTACAGGCCCCA-CGCAGACTCCTGGA  7567571

Query  28829    GCTGGCAGGGCAGAGCCTGATGAGGAAGCAGTTCTTGACTATCTTCACCCTGGACT-AGC  28887
                ||||||||||||||||||| || || | |||  |||| | |||| || | |||| | |||
Sbjct  7567572  GCTGGCAGGGCAGAGCCTGCTGGGGGACCAGGCCTTGGCCATCTCCATCTTGGA-TGAGC  7567630

Query  28888    TGCCCAGGGAGGTCT-CCCCTCTGAC-GTTCATGGAGGCCTTCAGC-ATG-AGATGTTGT  28943
                ||||||||||| ||| |||| |  || |||| |||||||||||| | | | ||| | || 
Sbjct  7567631  TGCCCAGGGAGCTCTTCCCCCC--ACTGTTCGTGGAGGCCTTCA-CTA-GCAGACGCTGC  7567686

Query  28944    GAGGCCCTGAAGCTGATGGTGCAGGCCTGGTCCT-CCCTTCACCTCCCTCTGGGATCCCT  29002
                ||||  |||||| ||||||||||||||||| ||| ||| |  |||||||||||| |||||
Sbjct  7567687  GAGGTTCTGAAGGTGATGGTGCAGGCCTGGCCCTTCCCCTG-CCTCCCTCTGGGGTCCCT  7567745

Query  29003    GATGAAGACAACTCATCTGGAGACCTTGCAAGCTGT-GCTGAA-GGGACTTGATA-CACT  29059
                |||||||||  || ||||||||| ||| ||   ||| | || | |||| |||||  | ||
Sbjct  7567746  GATGAAGACGCCTGATCTGGAGATCTTACATTATGTAG-TGGATGGGA-TTGATTGC-CT  7567802

Query  29060    AG-T-GTCCCAGAAGGTTTGCCCCAGTTGAGGTGACTCAGGTGGCCTGGTGGGAAGGGTC  29117
                 | | | |||| |||||| ||||||| ||||||||| |||||||   ||    | ||| |
Sbjct  7567803  -GCTTG-CCCAAAAGGTTCGCCCCAGGTGAGGTGACCCAGGTGG---GG----A-GGGCC  7567852

Query  29118    CAGGCATCCAGGGAAGGGACAGCTGGCTCAGGAGGAGTGGCAGTGTGTGGGAGCTAGGGT  29177
                ||||  ||||||||    |||||||| |||| |  |     | | || || | |  ||||
Sbjct  7567853  CAGGTGTCCAGGGACTAAACAGCTGGGTCAG-ACAA-----A-T-TG-GGAACCCGGGGT  7567903

Query  29178    GGCTCAGAGGCTTCTGATGGTACCCA-TGAGA--G--G----C---CTTGGCCATTGCCC  29225
                ||| ||| ||||||||||||| || | |||||  |  |    |   |||||| |||||||
Sbjct  7567904  GGCCCAGGGGCTTCTGATGGTGCC-AGTGAGAAAGCTGGGAACGTTCTTGGCTATTGCCC  7567962

Query  29226    AGATCCTCTGGAAAAGGACTGCTCACCATACAGAGTCCACTGAGGAAACAGGAACCTGCT  29285
                || |||||||| ||||||||||||||||||||| ||||||||||||||||||||||||| 
Sbjct  7567963  AGCTCCTCTGGGAAAGGACTGCTCACCATACAGGGTCCACTGAGGAAACAGGAACCTGCC  7568022

Query  29286    TCCTTCCCAGTGGAAGGTAAAGGTACTAGAAGTGGGTAC  29324
                | || |||||||||||||||||| |||||||||||||||
Sbjct  7568023  TGCT-CCCAGTGGAAGGTAAAGGCACTAGAAGTGGGTAC  7568060


 Score =  348 bits (188),  Expect = 1e-91
 Identities = 375/460 (81%), Gaps = 33/460 (7%)
 Strand=Plus/Plus

Query  2779     CTAGATTTTAGTGTCCAAGGG-CCTAGAAGAGAACATTGGATTTCTCTACCCCGCTAGGC  2837
                ||||||||||||| ||||||| || |||||| || |   | | || | | ||| |||| |
Sbjct  7550221  CTAGATTTTAGTGCCCAAGGGTCC-AGAAGA-AA-A--CG-TGTC-C-ATCCCACTAGCC  7550272

Query  2838     ACGCCTTCCCT-AGCAGCAAAGATGGAGCTCCAGTTCCTCAGACGGTGATGAGCCACAGG  2896
                | ||||||||| || ||||||||||||| |||| || |||||| ||  ||||||||||||
Sbjct  7550273  AGGCCTTCCCTAAG-AGCAAAGATGGAGGTCCACTTTCTCAGATGGCCATGAGCCACAGG  7550331

Query  2897     ACGGGCAGGGGGCGGGGCCAATGAAGATCCTCTTGGGCTGCCTGACTTCCCTTAGTGTAC  2956
                | ||||||||| |||| ||||  ||||||||||||||||||||||||||||| |||||||
Sbjct  7550332  AAGGGCAGGGGACGGGACCAAAAAAGATCCTCTTGGGCTGCCTGACTTCCCTGAGTGTAC  7550391

Query  2957     ACATCAACTAAGCCCGAAGTGGGGTGAAG-ATCTCCCAATCGACATGAACCAAGGAATTC  3015
                |||||| || |||||||| |||||  ||| |||||||||| | ||||| ||  |   | |
Sbjct  7550392  ACATCAGCTCAGCCCGAATTGGGGC-AAGGATCTCCCAATTGGCATGACCCCTGTTGT-C  7550449

Query  3016     AA-ACTCTCCTCGG-GGGCAGGATACATCTCCAGGCTTAACTTGCTCAGCCCAC-TGGTG  3072
                || |||||||  |  ||| |||||||| |||||||| ||||||||||||||||| || ||
Sbjct  7550450  AAGACTCTCCA-GACGGGAAGGATACAACTCCAGGCCTAACTTGCTCAGCCCACCTG-TG  7550507

Query  3073     TGGCACAGCAGGTCCTTCAGGGC-TTCCATAGACA-TG-CAATTTC-T-GCCAAAGTAGA  3127
                || ||||| ||||| ||||| || ||| || || | |  |  |||| | |  ||||||||
Sbjct  7550508  TGACACAGAAGGTCTTTCAGAGCATTC-ATGGA-AGTCTCG-TTTCCTTG--AAAGTAGA  7550562

Query  3128     AGGTGGTGAGCTGGGAGCAGCGGCTCAGGCCAGGCAGGATGG-CACTGAGTTGGGAGTAG  3186
                |||||||||||||||||||| |||||||| ||||||||| || | |||||||||||||  
Sbjct  7550563  AGGTGGTGAGCTGGGAGCAGTGGCTCAGGGCAGGCAGGA-GGACCCTGAGTTGGGAGTCC  7550621

Query  3187     TGGATCTGACAGCCCTCCAA-GATGAGGGTCTTAAGAGTA  3225
                |||||||||||| |||  || | ||||||||| |||||||
Sbjct  7550622  TGGATCTGACAGTCCTTTAACG-TGAGGGTCTCAAGAGTA  7550660


 Score =  333 bits (180),  Expect = 3e-87
 Identities = 214/230 (93%), Gaps = 4/230 (1%)
 Strand=Plus/Minus

Query  10657    ggattacaggcgtgagcTGCCTCACCCGGCCTTGAATGAGTGAATTCTTGACTT-CTACC  10715
                |||||||||| ||||||  |||  ||||| ||||||||| || |||||||| || | |||
Sbjct  7495797  GGATTACAGGAGTGAGCCACCTTGCCCGGTCTTGAATGAATGCATTCTTGA-TTCCCACC  7495739

Query  10716    CTATCCCTAACACTGTCAATTTCCTGATTCATGCAA-TTAATATGGATATCTGATATGAA  10774
                ||||||||||||||||||||||| ||||||||| || |||||||||||||||||||||||
Sbjct  7495738  CTATCCCTAACACTGTCAATTTCTTGATTCATG-AACTTAATATGGATATCTGATATGAA  7495680

Query  10775    TGGATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTG  10834
                ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Sbjct  7495679  TGGATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAACCCCAATCAGGATTAACTG  7495620

Query  10835    GGTGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGGAAGCTAG  10884
                |||||||||||||||||||||||||||||||||| |||||||||||||||
Sbjct  7495619  GGTGGAGCTTCAGAAATGCAATCAGATATCACTTGTTGATTGGAAGCTAG  7495570


 Score =  333 bits (180),  Expect = 3e-87
 Identities = 211/226 (93%), Gaps = 2/226 (0%)
 Strand=Plus/Plus

Query  25998    ggattacaggtgtgagccacctcacccggcctttaatgaGTGAATTCTTGATTTCCACCC  26057
                |||||||||| ||||||  |||||||||||||| ||||||||||||||||| ||| ||||
Sbjct  7597523  GGATTACAGGCGTGAGCTGCCTCACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCC  7597582

Query  26058    TATTCCTAACACTGTCAATTTCTTGATTCATG-AACTTAATATGGATAGCTGATATGAAT  26116
                ||| |||||||||||||||||| ||||||||| || |||||||||||| |||||||||||
Sbjct  7597583  TATCCCTAACACTGTCAATTTCCTGATTCATGCAA-TTAATATGGATATCTGATATGAAT  7597641

Query  26117    GGATATCTGATTCAATCCAGTAATCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGG  26176
                ||||||||||||||||||| ||||||||||| ||||||||||||||||| ||||||||||
Sbjct  7597642  GGATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGG  7597701

Query  26177    GTGGAGCTTCAGAAATGCAATCAGATAGCACTTTTTGATTGGAAGC  26222
                ||||||||||||||||||||||||||| ||||||||||||||||||
Sbjct  7597702  GTGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGGAAGC  7597747


 Score =  333 bits (180),  Expect = 3e-87
 Identities = 211/226 (93%), Gaps = 2/226 (0%)
 Strand=Plus/Minus

Query  10657    ggattacaggcgtgagcTGCCTCACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCC  10716
                |||||||||| ||||||  |||||||||||||| ||||||||||||||||| ||| ||||
Sbjct  7603018  GGATTACAGGTGTGAGCCACCTCACCCGGCCTTTAATGAGTGAATTCTTGATTTCCACCC  7602959

Query  10717    TATCCCTAACACTGTCAATTTCCTGATTCATGCAA-TTAATATGGATATCTGATATGAAT  10775
                ||| |||||||||||||||||| ||||||||| || |||||||||||| |||||||||||
Sbjct  7602958  TATTCCTAACACTGTCAATTTCTTGATTCATG-AACTTAATATGGATAGCTGATATGAAT  7602900

Query  10776    GGATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGG  10835
                ||||||||||||||||||| ||||||||||| ||||||||||||||||| ||||||||||
Sbjct  7602899  GGATATCTGATTCAATCCAGTAATCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGG  7602840

Query  10836    GTGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGGAAGC  10881
                ||||||||||||||||||||||||||| ||||||||||||||||||
Sbjct  7602839  GTGGAGCTTCAGAAATGCAATCAGATAGCACTTTTTGATTGGAAGC  7602794


 Score =  331 bits (179),  Expect = 1e-86
 Identities = 327/396 (82%), Gaps = 20/396 (5%)
 Strand=Plus/Plus

Query  2840     GCCTTCCCTAGCAGCAAAGATGG-AGCTCCAGTTCCTCAGACGGTGATGAGCCACAG-GA  2897
                ||||||||||| ||||||||||| || |||| || |||||| ||  |||||||||||  |
Sbjct  7490107  GCCTTCCCTAGGAGCAAAGATGGAAG-TCCACTTTCTCAGATGGCCATGAGCCACAGTTA  7490165

Query  2898     CGGGCAGGGGGCGGGGCCAATGAAGATCCTCTTGGGCTGCCTGACTTCCCTTAGTGTACA  2957
                 ||||| ||| |||| |||| |||||||||||||||||||||||||||||| ||||||| 
Sbjct  7490166  -GGGCAAGGGACGGGACCAAAGAAGATCCTCTTGGGCTGCCTGACTTCCCTGAGTGTACG  7490224

Query  2958     CATCAACTAAGCCCGAAGTGGGGTGAAGATCTCCCAATCGACATGAACCAAGGAATTCAA  3017
                ||||| || |||||||| |||||||| ||||||||||| ||||||| ||  | | | |||
Sbjct  7490225  CATCAGCTCAGCCCGAATTGGGGTGAGGATCTCCCAATTGACATGACCCTTGTAGT-CAA  7490283

Query  3018     -ACTCTCCTCG-GGGGCAGGATACATCTCCAGGCTTAACTTGCTCAGCCCAC-TGGTGTG  3074
                 |||||||  | ||||||||||||| |||||||| ||||||||||||||| | || ||||
Sbjct  7490284  GACTCTCCA-GAGGGGCAGGATACAACTCCAGGCCTAACTTGCTCAGCCCGCCTG-TGTG  7490341

Query  3075     GCACAGCAGGTCCTTCAGGGC-TTCCATAGACATG-CAATTTC--TGCCAAAGTAGAAGG  3130
                 | ||||||||| ||||| || ||| || ||  |  || ||||  ||  ||||| |||||
Sbjct  7490342  ACGCAGCAGGTCTTTCAGAGCATTC-ATGGAGGTCTCA-TTTCCATG--AAAGTTGAAGG  7490397

Query  3131     TGGTGAGCTGGGAGCAGCGGCTCAGGCCAGGCAGGATGG-CACTGAGTTGGGAGTAGTGG  3189
                ||||||||||||| ||| |||||||| ||||||||| || | |||||||||| ||  |||
Sbjct  7490398  TGGTGAGCTGGGAACAGTGGCTCAGGGCAGGCAGGA-GGACCCTGAGTTGGGGGTCCTGG  7490456

Query  3190     ATCTGACAGCCCTCCAAGATGAGGGTCTTAAGAGTA  3225
                ||| ||||| |||  |||| ||||||||| ||||||
Sbjct  7490457  ATCCGACAGTCCTTTAAGACGAGGGTCTTGAGAGTA  7490492


 Score =  316 bits (171),  Expect = 3e-82
 Identities = 208/226 (92%), Gaps = 2/226 (0%)
 Strand=Plus/Minus

Query  10657    ggattacaggcgtgagcTGCCTCACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCC  10716
                |||||||||| |||| |  |||||||||||||| ||||||||||||||||| ||| | ||
Sbjct  7441359  GGATTACAGGTGTGACCCACCTCACCCGGCCTTTAATGAGTGAATTCTTGATTTCCAACC  7441300

Query  10717    TATCCCTAACACTGTCAATTTCCTGATTCATGCAA-TTAATATGGATATCTGATATGAAT  10775
                ||| |||||||||||||||||| ||||||||| || |||||||||||| |||||||||||
Sbjct  7441299  TATTCCTAACACTGTCAATTTCTTGATTCATG-AACTTAATATGGATAGCTGATATGAAT  7441241

Query  10776    GGATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGG  10835
                | ||||||||||||||||| ||||||||||| ||||||||||||||||| ||||||||||
Sbjct  7441240  GAATATCTGATTCAATCCAGTAATCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGG  7441181

Query  10836    GTGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGGAAGC  10881
                ||||||||||||||||||||||||||| ||||||||||||||||||
Sbjct  7441180  GTGGAGCTTCAGAAATGCAATCAGATAGCACTTTTTGATTGGAAGC  7441135


 Score =  313 bits (169),  Expect = 4e-81
 Identities = 517/676 (76%), Gaps = 59/676 (8%)
 Strand=Plus/Minus

Query  28631    TGGCCACTTATTGCAGA-AAGGAACTGGAGTAAACTGAGGGCTCTTTCACACA-TGCTAG  28688
                |||||||| | | ||||  | ||| |||||||||||||||||| |||||| || ||| ||
Sbjct  7426176  TGGCCACTGAGTACAGAGTA-GAATTGGAGTAAACTGAGGGCTGTTTCAC-CATTGCCAG  7426119

Query  28689    AGAAATGACTTGGGCCCTGGGAGAA-TTGGGGGTTGCAGGGGATTGGTC-G-GAG-GAAC  28744
                || | |||||| |||||||||||||  | | | ||||| ||| |||| | | ||| | | 
Sbjct  7426118  AGCAGTGACTTTGGCCCTGGGAGAAGAT-GAGATTGCATGGGCTTGGCCTGAGAGTG-A-  7426062

Query  28745    TTGCCTTTT-TGCT-GGATTGTGCTGTAG-AGTTTTTCCTTGTAGATT--TGTCAGAATG  28799
                 |||||||| | || || |||| || | | || |||||| || |||||  ||  || |||
Sbjct  7426061  -TGCCTTTTCT-CTGGGTTTGTCCTCTGGAAG-TTTTCCCTGCAGATTCATG-AAG-ATG  7426007

Query  28800    AGCCTCCAGACCCCATCCAGACTCCTGGAGCTGGCAGGGCAGAGCCTGATGAGGAAGC-A  28858
                ||| ||| ||  ||| |||||||||||||||| || |||| ||||||| ||||| | | |
Sbjct  7426006  AGCATCCGGATTCCACCCAGACTCCTGGAGCTTGC-GGGCGGAGCCTGCTGAGGGACCAA  7425948

Query  28859    GTTCTTGACTATCTTCACCCTGGACTAGCTGCCCA-GGGAGGTCTCCCCTCTGAC-GTTC  28916
                |  |||| |  ||| |||||||||  ||||||||| || |  | ||||| |  || ||||
Sbjct  7425947  G-CCTTGGCCGTCTCCACCCTGGAGGAGCTGCCCACGGAACTTTTCCCC-C-CACTGTTC  7425891

Query  28917    ATGGAGGCCTTCAGCATGAGATGTTGTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGTCC  28976
                |||||||||||||||| |||| | ||||||||||||||||||||||||||||||||| ||
Sbjct  7425890  ATGGAGGCCTTCAGCAGGAGACGCTGTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGCCC  7425831

Query  28977    TCCCTTCACCTCCCTCTG-GGATCC-CTGATGAAGACAACTCATCTGGAGACCTTGCAAG  29034
                | ||  | |||||||||| ||  || ||||| ||||   ||  ||||||| |||| ||||
Sbjct  7425830  TTCCGCCGCCTCCCTCTGAGG--CCTCTGATAAAGATGCCTTGTCTGGAGGCCTTCCAAG  7425773

Query  29035    CTGTGCT-GAAGGGACTTGATACACTAG-TGT-CCCAGAAGGTTT-GCCCCAGTTGAGGT  29090
                ||||||| || ||| |||||| |||| | | | |||| | || || | ||||| ||||||
Sbjct  7425772  CTGTGCTCGATGGG-CTTGATGCACT-GCT-TACCCA-AGGGGTTCGTCCCAGGTGAGGT  7425717

Query  29091    GACTCAGGTGGCCTGGTGGGAAGGGTCCAGGCATCCAGG-GAAGGGACAGCTGGCTCAGG  29149
                | | ||||||| |||||||| |||| |||||  ||||   ||||| |||||||| ||| |
Sbjct  7425716  GGCCCAGGTGGGCTGGTGGGGAGGGCCCAGGTGTCCAACTGAAGGAACAGCTGGGTCATG  7425657

Query  29150    AGGAGTGGCAGTGTGTGGGAGCTAGGGTGGCTCAGAGGCTTCTGATGGTACCCATGAGAG  29209
                 | ||||  || | | |    | |||| || |  | || |  ||| || | ||  |||||
Sbjct  7425656  TGAAGTG--AG-GAG-GCC--CAAGGG-GGATG-GTGG-TGGTGA-GGAAGCC--GAGAG  7425609

Query  29210    GCCTTGGCCATTGC-CCAGATCCTCTGGAAAAGGACTGCTCACCATACAGAG-TCCACT-  29266
                | |||||||||| | |||| ||||| || |||| |||||||||||  || || |||| | 
Sbjct  7425608  GACTTGGCCATT-CACCAGCTCCTCAGGGAAAGCACTGCTCACCAGGCA-AGGTCCA-TA  7425552

Query  29267    GAGGAAACAGGAACCT  29282
                |||| |||||||||||
Sbjct  7425551  GAGGTAACAGGAACCT  7425536


 Score =  296 bits (160),  Expect = 4e-76
 Identities = 206/228 (90%), Gaps = 4/228 (1%)
 Strand=Plus/Minus

Query  10659    attacaggc-gtgagcTGCCTCACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCCT  10717
                |||||| ||  |||||  ||||||||  |||||||||| || ||||||||||||||||||
Sbjct  7428958  ATTACA-GCTATGAGCCACCTCACCCACCCTTGAATGAATGTATTCTTGACTTCTACCCT  7428900

Query  10718    ATCCCTAACACTGTCAATTTCCTGATTCATGCAA-TTAATATGGATATCTGATATGAATG  10776
                ||||||||||||||||||||| || |||| | || | ||||| ||||| ||||||||| |
Sbjct  7428899  ATCCCTAACACTGTCAATTTCTTGCTTCACG-AACTGAATATAGATATGTGATATGAACG  7428841

Query  10777    GATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGG  10836
                ||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  7428840  GATATCTGACTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGG  7428781

Query  10837    TGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGGAAGCTAG  10884
                |||||||||| ||||||||||||||||  |||||||||||||||||||
Sbjct  7428780  TGGAGCTTCACAAATGCAATCAGATATTGCTTTTTGATTGGAAGCTAG  7428733


 Score =  292 bits (158),  Expect = 6e-75
 Identities = 203/225 (90%), Gaps = 2/225 (0%)
 Strand=Plus/Minus

Query  10657    ggattacaggcgtgagcTGCCTCACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCC  10716
                |||||||||| ||||||  | ||  | |||||||||||| || |||||||||||||||||
Sbjct  7542933  GGATTACAGGTGTGAGCCACTTCGTCTGGCCTTGAATGAATGTATTCTTGACTTCTACCC  7542874

Query  10717    TATCCCTAACACTGTCAATTTCCTGATTCATGCAA-TTAATATGGATATCTGATATGAAT  10775
                |||||||||||||||| ||||| || |||||| || | ||||| ||||| ||||||||||
Sbjct  7542873  TATCCCTAACACTGTCGATTTCTTGCTTCATG-AAGTGAATATAGATATGTGATATGAAT  7542815

Query  10776    GGATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGG  10835
                ||| ||||||||||||||  ||||||||||||||||||||||||||||||||||||||||
Sbjct  7542814  GGACATCTGATTCAATCCGGTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGG  7542755

Query  10836    GTGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGGAAG  10880
                ||||||||||| |||||||||||||||||| ||||||||||||||
Sbjct  7542754  GTGGAGCTTCACAAATGCAATCAGATATCATTTTTTGATTGGAAG  7542710


 Score =  291 bits (157),  Expect = 2e-74
 Identities = 204/227 (89%), Gaps = 2/227 (0%)
 Strand=Plus/Minus

Query  10659    attacaggcgtgagcTGCCTCACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCCTA  10718
                ||||||||  |||||  |||| |||  |||||||||| || |||||||||||||||||||
Sbjct  7483719  ATTACAGGTATGAGCCACCTCGCCCACCCTTGAATGAATGTATTCTTGACTTCTACCCTA  7483660

Query  10719    TCCCTAACACTGTCAATTTCCTGATTCATGCAA-TTAATATGGATATCTGATATGAATGG  10777
                |||||||||||||||||||| || |||| | || | ||||  ||||| ||||||||||||
Sbjct  7483659  TCCCTAACACTGTCAATTTCTTGCTTCACG-AACTGAATACAGATATGTGATATGAATGG  7483601

Query  10778    ATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGT  10837
                |||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct  7483600  ATATCTGACTCAATCCATTAATCTGGGGAAAGCCAAAAACCCAATCAGGATTAACTGGGT  7483541

Query  10838    GGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGGAAGCTAG  10884
                ||||||||| ||||||||||||||||  |||||||||||||||||||
Sbjct  7483540  GGAGCTTCACAAATGCAATCAGATATTGCTTTTTGATTGGAAGCTAG  7483494


 Score =  289 bits (156),  Expect = 7e-74
 Identities = 204/228 (89%), Gaps = 0/228 (0%)
 Strand=Plus/Minus

Query  10657    ggattacaggcgtgagcTGCCTCACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCC  10716
                |||||||||| ||||||  ||||| | |||||||| ||| ||||||||||||||| || |
Sbjct  7446298  GGATTACAGGTGTGAGCCACCTCATCTGGCCTTGAGTGAATGAATTCTTGACTTCCACTC  7446239

Query  10717    TATCCCTAACACTGTCAATTTCCTGATTCATGCAATTAATATGGATATCTGATATGAATG  10776
                |||||||||| ||||||||||| | ||||||| ||| |||||| |||| |||||||||||
Sbjct  7446238  TATCCCTAACGCTGTCAATTTCTTAATTCATGAAATGAATATGCATATGTGATATGAATG  7446179

Query  10777    GATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGG  10836
                |||| ||| |||||||||||| |||  ||| ||||||||||||||||||||||||||| |
Sbjct  7446178  GATACCTGGTTCAATCCATTAGTCTTCGGACAGCCAAAAACCCAATCAGGATTAACTGAG  7446119

Query  10837    TGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGGAAGCTAG  10884
                |||||||||||||||||||||||||||| |||||||||||||||||||
Sbjct  7446118  TGGAGCTTCAGAAATGCAATCAGATATCGCTTTTTGATTGGAAGCTAG  7446071


 Score =  289 bits (156),  Expect = 7e-74
 Identities = 499/656 (76%), Gaps = 58/656 (8%)
 Strand=Plus/Minus

Query  28651    GAACTGGAGTAAACTGAGGGCTCTTTCACACA-TGCTAGAGAAATGACTTGGGCCCTGGG  28709
                ||| |||||||||||||||||| |||||| || ||| |||| | |||||| |||| ||||
Sbjct  7539862  GAATTGGAGTAAACTGAGGGCTGTTTCAC-CATTGCCAGAGCAGTGACTTTGGCCTTGGG  7539804

Query  28710    AGAA-TTGGGGGTTGCAGGGGATTGGTC-G-GAG-GAACTTGCCTTTT-TGCT-GGATTG  28763
                ||||  |   | ||||| ||| |||| | | ||| | |  |||||||| | || || |||
Sbjct  7539803  AGAAGAT-AAGATTGCATGGGCTTGGCCTGAGAGTG-A--TGCCTTTTCT-CTGGGTTTG  7539749

Query  28764    TGCTGTAG-AGTTTTTCCTTGTAGATTTGT-CAGAATGAGCCTCCAGACCCCATCCAGAC  28821
                | || | | || |||||| || ||||| ||  || |||||| ||| ||| ||| ||||||
Sbjct  7539748  TCCTCTGGAAG-TTTTCCCTGCAGATTCGTGAAG-ATGAGCATCCGGACTCCACCCAGAC  7539691

Query  28822    TCCTGGAGCTGGCAGGGCAGAGCCTGATGAGGAAGC-AGTTCTTGACTATCTTCACCCTG  28880
                |||||||||| ||||||| ||||||| ||||| | | ||  |||| | || | |||||||
Sbjct  7539690  TCCTGGAGCTTGCAGGGCGGAGCCTGCTGAGGGACCAAG-CCTTGGCCATGTCCACCCTG  7539632

Query  28881    GACTAGCTGCCCA-GGGAGGTCTCCCCTCTGAC-GTTCATGGAGGCCTTCAGCATGAGAT  28938
                ||  |||||||||  | |  | ||||| |  || |||||||||||||||||||| |||| 
Sbjct  7539631  GAGGAGCTGCCCACAGAACTTTTCCCC-C-CACTGTTCATGGAGGCCTTCAGCAGGAGAC  7539574

Query  28939    GTTGTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGTCCTCCCTTCACCTCCCTCTG-GGA  28997
                | ||||||||||||||||||||||||||||||||| ||| ||  | |||||||||| || 
Sbjct  7539573  GCTGTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGCCCTTCCGCCGCCTCCCTCTGAGG-  7539515

Query  28998    TCC-CTGATGAAGACAACTCATCTGGAGACCTTGCAAGCTGTGCT-GAAGGGACTTGATA  29055
                 || ||||| ||||   ||  ||||||| |||| ||||||||||| || ||| || ||| 
Sbjct  7539514  -CCTCTGATAAAGATGCCTTGTCTGGAGGCCTTCCAAGCTGTGCTCGATGGG-CTGGATG  7539457

Query  29056    CACTAG-TGT-CCCAGAAGGTTTGC--CCCAGTTGAGGTGACTCAGGTGGCCTGGTGGGA  29111
                |||| | | | |||| | || || |  ||||| ||||||| | ||||||| |||||||| 
Sbjct  7539456  CACT-GCT-TACCCA-AGGGGTT-CATCCCAGGTGAGGTGGCCCAGGTGGGCTGGTGGGG  7539401

Query  29112    AGGGTCCAGGCATCCAGGGAAGGGAC-AGCTG-GCTCAGGAGGAGTGGCAGTGTGTGGGA  29169
                |||| ||||| |||||   || |||  ||||| | ||| ||  ||||  || | | |   
Sbjct  7539400  AGGGCCCAGGTATCCAACCAAAGGAAGAGCTGTG-TCATGACAAGTG--AG-GAG-GCC-  7539347

Query  29170    GCTAGGGTGGCTCAGAGGCTTCTGATGGTACCCATGAGAGGCCTTGGCCATTGC-CCAGA  29228
                 | |||| || |  | || |  ||| || | ||  |||||| |||||||||| | |||| 
Sbjct  7539346  -CAAGGG-GGATG-GTGG-TGGTGA-GGAAGCC--GAGAGGACTTGGCCATT-CACCAGC  7539295

Query  29229    TCCTCTGGAAAAGGACTGCTCACCATACAGAG-TCCACTG-AGGAAACAGGAACCT  29282
                ||||| || |||| |||||||||||  || || |||| || ||| |||||||||||
Sbjct  7539294  TCCTCAGGGAAAGCACTGCTCACCACGCA-AGGTCCA-TGGAGGTAACAGGAACCT  7539241


 Score =  287 bits (155),  Expect = 3e-73
 Identities = 192/210 (91%), Gaps = 2/210 (0%)
 Strand=Plus/Minus

Query  10676    CCTCACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCCTATCCCTAACACTGTCAAT  10735
                ||||||||  |||||||||| || ||||||||||||||||||||||||||||||||| ||
Sbjct  7545074  CCTCACCCACCCTTGAATGAATGTATTCTTGACTTCTACCCTATCCCTAACACTGTCGAT  7545015

Query  10736    TTCCTGATTCATGCAA-TTAATATGGATATCTGATATGAATGGATATCTGATTCAATCCA  10794
                ||| || |||||| || | ||||| ||||| ||||||||||||| |||||||||||||| 
Sbjct  7545014  TTCTTGCTTCATG-AAGTGAATATAGATATGTGATATGAATGGACATCTGATTCAATCCG  7544956

Query  10795    TTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGCA  10854
                 ||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Sbjct  7544955  GTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCACAAATGCA  7544896

Query  10855    ATCAGATATCACTTTTTGATTGGAAGCTAG  10884
                ||||||||||| |||||||||||||| |||
Sbjct  7544895  ATCAGATATCATTTTTTGATTGGAAGGTAG  7544866


 Score =  279 bits (151),  Expect = 4e-71
 Identities = 174/185 (94%), Gaps = 2/185 (1%)
 Strand=Plus/Minus

Query  26039    GAATTCTTGATTTCCACCCTATTCCTAACACTGTCAATTTCTTGATTCATG-AACTTAAT  26097
                |||||||||| ||| ||||||| |||||||||||||||||| ||||||||| || |||||
Sbjct  7618319  GAATTCTTGACTTCTACCCTATCCCTAACACTGTCAATTTCCTGATTCATGCAA-TTAAT  7618261

Query  26098    ATGGATAGCTGATATGAATGGATATCTGATTCAATCCAGTAATCTGGGGACAGCCAAAAA  26157
                ||||||| |||||||||||||||||||||||||||||| ||||||||||| |||||||||
Sbjct  7618260  ATGGATATCTGATATGAATGGATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAAA  7618201

Query  26158    CCCAATCAAGATTAACTGGGTGGAGCTTCAGAAATGCAATCAGATAGCACTTTTTGATTG  26217
                |||||||| ||||||||||||||||||||||||||||||||||||| |||||||||||||
Sbjct  7618200  CCCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTG  7618141

Query  26218    GAAGC  26222
                |||||
Sbjct  7618140  GAAGC  7618136


 Score =  272 bits (147),  Expect = 7e-69
 Identities = 202/229 (88%), Gaps = 2/229 (0%)
 Strand=Plus/Minus

Query  10657    ggattacaggcgtgagcTGCCTCACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCC  10716
                |||||||| | ||||||  ||||||| |||||||| ||| ||||||||||||||| |  |
Sbjct  7611732  GGATTACAAGTGTGAGCCACCTCACCTGGCCTTGAGTGAATGAATTCTTGACTTCCAGTC  7611673

Query  10717    TATCCCTAACACTGTCAATTTCCTGATTCATGCAATTAATATGGATATCTGATATGAATG  10776
                |||||||||| ||||||||||| | ||||||| ||| | |||| |||| |||||||||||
Sbjct  7611672  TATCCCTAACTCTGTCAATTTCTTAATTCATGAAATGATTATGCATATGTGATATGAATG  7611613

Query  10777    GATATCT-GATTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGG  10835
                ||||||| | |||||||||||| |||  ||| || |||||||||||||||||||||||| 
Sbjct  7611612  GATATCTCG-TTCAATCCATTAGTCTTCGGACAGTCAAAAACCCAATCAGGATTAACTGA  7611554

Query  10836    GTGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGGAAGCTAG  10884
                ||||||||||||||||||||||||||||| |||||||||||||||||||
Sbjct  7611553  GTGGAGCTTCAGAAATGCAATCAGATATCGCTTTTTGATTGGAAGCTAG  7611505


 Score =  267 bits (144),  Expect = 3e-67
 Identities = 201/229 (87%), Gaps = 2/229 (0%)
 Strand=Plus/Plus

Query  17284    ggattacaagtgtgagccacctcacctggccTTGAGTGAATGAATTCTTGATTTCCAGTC  17343
                |||||||| | ||||||  ||||||| |||||||| ||| ||||||||||| ||| |  |
Sbjct  7597523  GGATTACAGGCGTGAGCTGCCTCACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCC  7597582

Query  17344    TATCCCTAACTCTGTCAATTTCTTAATTCATGAAATGATTATGCATATGTGATATGAATG  17403
                |||||||||| ||||||||||| | ||||||| ||| | |||| |||| |||||||||||
Sbjct  7597583  TATCCCTAACACTGTCAATTTCCTGATTCATGCAATTAATATGGATATCTGATATGAATG  7597642

Query  17404    GATATCTCG-TTCAATCCATTAGTCTTCGGACAGTCAAAAACCCAATCAGGATTAACTGA  17462
                ||||||| | |||||||||||| |||  ||| || |||||||||||||||||||||||| 
Sbjct  7597643  GATATCT-GATTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGG  7597701

Query  17463    GTGGAGCTTCAGAAATGCAATCAGATATCGCTTTTTGATTGGAAGCTAG  17511
                ||||||||||||||||||||||||||||| |||||||||||||||||||
Sbjct  7597702  GTGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGGAAGCTAG  7597750


 Score =  265 bits (143),  Expect = 1e-66
 Identities = 186/206 (90%), Gaps = 5/206 (2%)
 Strand=Plus/Minus

Query  12892    gattgaactattgctctccagcctggcgagagagtgagactccatctccaaaaaaaaa--  12949
                ||| |||| |||||||||||||||||| | ||||||||||||||||||||||||||||  
Sbjct  7507942  GATCGAACCATTGCTCTCCAGCCTGGCAACAGAGTGAGACTCCATCTCCAAAAAAAAAGC  7507883

Query  12950    aa-aaattataagaaCATGTC-CATTCACTCTCCAAAGTATCTAGGACTGGACAATTACT  13007
                ||  |||||||| |||| ||| | ||||||||||||||| ||| |||||||||||||| |
Sbjct  7507882  AATTAATTATAACAACACGTCTC-TTCACTCTCCAAAGTGTCTGGGACTGGACAATTAAT  7507824

Query  13008    TGTCAGGCCCTCTTCTGTAGCACCATACACTATAGCATATATGTGGATTAatataaatac  13067
                |||||||||||||||||||||||||||||||| |||||||| ||||||||| ||||||||
Sbjct  7507823  TGTCAGGCCCTCTTCTGTAGCACCATACACTAGAGCATATACGTGGATTAAAATAAATAC  7507764

Query  13068    acatacaaaattcaagtatatattct  13093
                ||| ||||||| ||||||||||||||
Sbjct  7507763  ACACACAAAATGCAAGTATATATTCT  7507738


 Score =  230 bits (124),  Expect = 5e-56
 Identities = 176/200 (88%), Gaps = 8/200 (4%)
 Strand=Plus/Minus

Query  21571    acctttgcacaccagcctggccacagagcaagactccatctccaaaaaaTACTA-CTAA-  21628
                ||| |||| | |||||||||| ||||||  ||||||||||||||||||| |  | | || 
Sbjct  7507936  ACCATTGCTCTCCAGCCTGGCAACAGAGTGAGACTCCATCTCCAAAAAA-A-AAGC-AAT  7507880

Query  21629    TAATTATAACAGCATGTC-CATTCACTCTCCAAAGTGTCTGGGACTGGACAATTAATTGT  21687
                ||||||||||| || ||| | |||||||||||||||||||||||||||||||||||||||
Sbjct  7507879  TAATTATAACAACACGTCTC-TTCACTCTCCAAAGTGTCTGGGACTGGACAATTAATTGT  7507821

Query  21688    GAGGCCCTCTTCTCTAGCACCCTACGCTATAGCATATATGTGGATTAAAATAAATACACA  21747
                 |||||||||||| ||||||| ||| ||| |||||||| |||||||||||||||||||||
Sbjct  7507820  CAGGCCCTCTTCTGTAGCACCATACACTAGAGCATATACGTGGATTAAAATAAATACACA  7507761

Query  21748    TA-AAAATGCAAGtatatat  21766
                 | |||||||||||||||||
Sbjct  7507760  CACAAAATGCAAGTATATAT  7507741


 Score =  230 bits (124),  Expect = 5e-56
 Identities = 167/188 (88%), Gaps = 2/188 (1%)
 Strand=Plus/Minus

Query  17325    GAATTCTTGATTTCCAGTCTATCCCTAACTCTGTCAATTTCTTAATTCATGAAATGATTA  17384
                |||||||||| ||| |  ||||||||||| ||||||||||| | ||||||| ||| | ||
Sbjct  7618319  GAATTCTTGACTTCTACCCTATCCCTAACACTGTCAATTTCCTGATTCATGCAATTAATA  7618260

Query  17385    TGCATATGTGATATGAATGGATATCTCG-TTCAATCCATTAGTCTTCGGACAGTCAAAAA  17443
                || |||| |||||||||||||||||| | |||||||||||| |||  ||| || ||||||
Sbjct  7618259  TGGATATCTGATATGAATGGATATCT-GATTCAATCCATTAATCTGGGGAGAGCCAAAAA  7618201

Query  17444    CCCAATCAGGATTAACTGAGTGGAGCTTCAGAAATGCAATCAGATATCGCTTTTTGATTG  17503
                |||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||
Sbjct  7618200  CCCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTG  7618141

Query  17504    GAAGCTAG  17511
                ||||||||
Sbjct  7618140  GAAGCTAG  7618133


 Score =  224 bits (121),  Expect = 2e-54
 Identities = 147/160 (91%), Gaps = 0/160 (0%)
 Strand=Plus/Minus

Query  23225    GGTTGGTTAATATTGATAATTAAATGACTTGGTACTGAGAAGAAGCTATAGGTGCAAATG  23284
                |||||| ||||||| || ||||||||||| || |||||||||||||||||| ||||||||
Sbjct  7448572  GGTTGGGTAATATTTATGATTAAATGACTCGGCACTGAGAAGAAGCTATAGATGCAAATG  7448513

Query  23285    GGTGGCCTATGACTATTATTGATTTCATTACTGGTAATTTATCTCTATGCCTAGAAAACA  23344
                ||||||||||||||||||||||||||||||||||||| |||||||||||| ||| |||||
Sbjct  7448512  GGTGGCCTATGACTATTATTGATTTCATTACTGGTAACTTATCTCTATGCATAGGAAACA  7448453

Query  23345    TTAGTGTAACTGGGTCTAACCTAGATAGTGTTCCAGACTC  23384
                ||||||||||||||||||| |||| | |||| ||||||||
Sbjct  7448452  TTAGTGTAACTGGGTCTAATCTAGGTGGTGTCCCAGACTC  7448413


 Score =  202 bits (109),  Expect = 1e-47
 Identities = 141/157 (89%), Gaps = 0/157 (0%)
 Strand=Plus/Minus

Query  14528    GGTTGGTTAACATTTATAATTACATGACTTGGCACTGAGAAGAAGCTATAGGTGCAAATG  14587
                |||||| ||| |||||| |||| |||||| ||||||||||||||||||||| ||||||||
Sbjct  7448572  GGTTGGGTAATATTTATGATTAAATGACTCGGCACTGAGAAGAAGCTATAGATGCAAATG  7448513

Query  14588    GGTGGCCTATGACTATTATTGATTACATTACTGGCATTTTATCTCTATGCATAAAAAACA  14647
                |||||||||||||||||||||||| ||||||||| |  |||||||||||||||  |||||
Sbjct  7448512  GGTGGCCTATGACTATTATTGATTTCATTACTGGTAACTTATCTCTATGCATAGGAAACA  7448453

Query  14648    TTAGTGAAACTGGATCTAATCTAGGTAGTGTCGCAGA  14684
                |||||| |||||| |||||||||||| ||||| ||||
Sbjct  7448452  TTAGTGTAACTGGGTCTAATCTAGGTGGTGTCCCAGA  7448416


 Score =  161 bits (87),  Expect = 2e-35
 Identities = 338/452 (74%), Gaps = 46/452 (10%)
 Strand=Plus/Plus

Query  7111     AAGAATTTTGAAATGAGGA-AAA-TGAAGCACAAATCAAAATTTGAGGGATGAAGTCAAA  7168
                ||||||||||||||||  | |||   |||||| |||| || |||  |  || ||| ||||
Sbjct  7495194  AAGAATTTTGAAATGA-CATAAACCAAAGCAC-AATCCAATTTTTTGAAATAAAGACAAA  7495251

Query  7169     ACTATATTTGGAGG-AAAAAT-CAAAACCT-ACATCTGTTTA-ATCTG--AAAAAAC-AG  7221
                |||  ||||  ||| |||||| |||| | | | || |||| | ||  |  ||||||| | 
Sbjct  7495252  ACTGCATTTAAAGGAAAAAATGCAAAGCTTCAAAT-TGTTCATATGAGAAAAAAAACAAA  7495310

Query  7222     ACAGGAAAT-TCTCTGTGCCATTTTGGGCTG-TGTGTCACCATCCCTGACTGGCTGGCTG  7279
                |||||| ||  |||| |||||| || |||||   |||||||||||| |||  |||| |||
Sbjct  7495311  ACAGGATATAACTCTATGCCATCTTAGGCTGCACTGTCACCATCCCAGACCAGCTGACTG  7495370

Query  7280     CAGATTAGACGGGCATGT-TCC-TA-AGA-AG-GTGGTGACTTACCAGATCTGGACTCAG  7334
                 || | ||  ||| | || ||| || ||| ||  | ||||||||||||||||||||||||
Sbjct  7495371  TAGGTCAGTTGGG-A-GTGTCCTTACAGAGAGATTAGTGACTTACCAGATCTGGACTCAG  7495428

Query  7335     TTTGCAGGGTGCTGGGACCTCTCAG-A-GAACCAAGCAGTAGCTCCAGGCACCAGGGCTT  7392
                |||| ||||||||  ||||||  || | |||| |||||| | ||||||||   | | |||
Sbjct  7495429  TTTGGAGGGTGCTCAGACCTC--AGGAAGAACTAAGCAGGAACTCCAGGCTTGAAGACTT  7495486

Query  7393     TGGGTCTGTCCTGTGCAAACTC-AGGAGCTTTTGTTGATGTTTCTAACCACA-C-CCT-C  7448
                ||||||| | |||||    ||  || ||||||| ||||  ||||||| |||| | ||  |
Sbjct  7495487  TGGGTCTCTTCTGTGGGT-CTTTAGAAGCTTTTATTGACCTTTCTAATCACAACTCCCAC  7495545

Query  7449     CC-CTTC--TC-A---ATC-AC--C-AGCTTCCAATCAGA-AAGTGATACCTGATTAG-A  7495
                || |  |  || |   ||| ||  | |||||||||||| | |||||||| |||||| | |
Sbjct  7495546  CCACACCCCTCCACGTATCCACTGCTAGCTTCCAATCA-ACAAGTGATATCTGATT-GCA  7495603

Query  7496     TC-CTGAAGTTCCACCCAGTTAATCCTGATTG  7526
                |  |||||| ||||||||||||||||||||||
Sbjct  7495604  TTTCTGAAGCTCCACCCAGTTAATCCTGATTG  7495635


 Score =  130 bits (70),  Expect = 5e-26
 Identities = 138/169 (81%), Gaps = 12/169 (7%)
 Strand=Plus/Minus

Query  6435    TTAGCCAGGTGTGGTGGTGCA-GT-CCTATAATCCTAGCTACTCTGGAGGCAGAGGAAGA  6492
               ||||||||||||||| | ||| || ||| || ||| |||||||| |||||| |||| || 
Sbjct  271062  TTAGCCAGGTGTGGT-G-GCATGTGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGC  271005

Query  6493    AGAATCACTTGAATCCCGGA-GGCAGTGTTTTCAGTGAGCTGA-ACTC-AACACCCTGCC  6549
               |||||| |||||| || ||| ||  | | || ||||||||||| | || ||| | |||| 
Sbjct  271004  AGAATCGCTTGAA-CCAGGAGGGGGGAGGTTGCAGTGAGCTGAGA-TCGAAC-CACTGCA  270948

Query  6550    CTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAGAGAAAAG  6598
               || |||||||||||||||||||||||||||||||| || || | |||||
Sbjct  270947  CTCCAGCCTGGGTGACAGAGTGAGACTCCATCTCAAAAAAA-A-AAAAG  270901


 Score =  126 bits (68),  Expect = 6e-25
 Identities = 139/171 (81%), Gaps = 13/171 (7%)
 Strand=Plus/Minus

Query  6435     TTAGCCAGGTGTGGTGGTGCA-G-TCCTATAATCCTAGCTACTCTGGAGGCAGAGGAAGA  6492
                |||||||||  |||| | ||| |  ||| |||||| |||||||| |||||| |||| || 
Sbjct  6830596  TTAGCCAGGCATGGT-G-GCAGGCACCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGG  6830539

Query  6493     AGAATCACTTGAATCCC-GGAGGCAGTGTTTTCAGTGAGCTGAA-CTCAACACC-CTGCC  6549
                |||||| |||||| ||| |||||||| | || ||||||||  ||  || ||||| | || 
Sbjct  6830538  AGAATCCCTTGAA-CCCGGGAGGCAGAGGTTGCAGTGAGC-CAAGATC-ACACCACCGCA  6830482

Query  6550     CTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAGAGAAAAGAA  6600
                || |||||||||||||||||||||||||||||||| || || | |||||||
Sbjct  6830481  CTCCAGCCTGGGTGACAGAGTGAGACTCCATCTCAAAA-AA-A-AAAAGAA  6830434


 Score =  126 bits (68),  Expect = 6e-25
 Identities = 230/305 (75%), Gaps = 24/305 (7%)
 Strand=Plus/Plus

Query  4702     TACAGCACAGGTGTACTAAACCTCTCCTTTGGTAAACCCACCGGAA-GAGGTATCTCAGG  4760
                ||||||||||||||| |||| || |||| || |  |||||   ||| |||| |  | |||
Sbjct  7479364  TACAGCACAGGTGTAGTAAATCTTTCCTCTGCTTGACCCA-TAGAAGGAGGCAGGTGAGG  7479422

Query  4761     CATTCATCCTGGGGT-AT-TTCCTTGAGGCAGATG-TCTATGAACACCTTCAAGGGCTG-  4816
                 ||||||||  | ||  | || |||||| || | | |||| ||||||  |||||||||| 
Sbjct  7479423  TATTCATCC-AGAGTCCTGTT-CTTGAGCCA-AAGTTCTACGAACACAGTCAAGGGCTGC  7479479

Query  4817     -GTGCTCTCCCATCCTTGGACAGTCCTCTGCT-GTCTGCCTCTTACTCATGGCCTCTG-G  4873
                 || | ||| ||||||||||||||||||  || || |   | || ||| |||| | || |
Sbjct  7479480  CGT-C-CTCTCATCCTTGGACAGTCCTCCACTGGT-TTTTTGTTCCTCTTGGCAT-TGAG  7479535

Query  4874     GGAGGAGGACA-GGGCCCTGGATTCAGACCATATGGCCCAGAAATTCTCATCA-ACATCC  4931
                | || |   || ||||| | | ||||||||| |    |||||| |||||| || ||||||
Sbjct  7479536  GAAGCA-CCCATGGGCCATAGCTTCAGACCAAACCATCCAGAAGTTCTCA-CAGACATCC  7479593

Query  4932     CGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAAAGTA-AGGCAGAGGCTCAGA  4990
                 | |||||||||||||||||||||||||||||||||| ||| || |||  ||| || |||
Sbjct  7479594  TGTAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGAAAA-TAGAGGT-GAGACTGAGA  7479651

Query  4991     ACTTT  4995
                | |||
Sbjct  7479652  A-TTT  7479655


 Score =  126 bits (68),  Expect = 6e-25
 Identities = 231/306 (75%), Gaps = 26/306 (8%)
 Strand=Plus/Plus

Query  4702     TACAGCACAGGTGTACTAAACCTCTCCTTTGGTAAACCCACCGGAA-GAGGTATCTCAGG  4760
                ||||||||||||||| |||| || |||| || |  |||||   ||| |||| |  | |||
Sbjct  7538503  TACAGCACAGGTGTAGTAAATCTTTCCTCTGCTTGACCCA-TAGAAGGAGGCAGGTGAGG  7538561

Query  4761     CATTCATCCTGGGGT-AT-TTCCTTGAGGCAGATG-TCTATGAACACCTTCAAGGGCTGG  4817
                 ||||||||  | ||  | || |||||| || | | |||| ||||||  |||||||||| 
Sbjct  7538562  TATTCATCC-AGAGTCCTGTT-CTTGAGCCA-AAGTTCTACGAACACAGTCAAGGGCTGC  7538618

Query  4818     TGCT-CTCCCATCCTTGGACAGTCCT---CTGCTGTCTGCCTCTTACTCATGGCCTCTG-  4872
                || | ||| |||||||||||||||||   ||| ||| |   | || ||| |||| | || 
Sbjct  7538619  TG-TCCTCTCATCCTTGGACAGTCCTGCACTGGTGT-T--TTGTTCCTCTTGGCAT-TGA  7538673

Query  4873     GGGAGGAGGACA-GGGCCCTGGATTCAGACCATATGGCCCAGAAATTCTCATCA-ACATC  4930
                || || |   || ||||| | | ||||||||| |    |||||| |||||| || |||||
Sbjct  7538674  GGAAGCA-CCCACGGGCCATAGCTTCAGACCAAACCATCCAGAAGTTCTCA-CAGACATC  7538731

Query  4931     CCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAAAGTA-AGGCAGAGGCTCAG  4989
                | | |||||||||||||||||||||||||||||||||| ||| || |||  ||| || ||
Sbjct  7538732  CTGTAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGAAAA-TAGAGGT-GAGACTGAG  7538789

Query  4990     AACTTT  4995
                || |||
Sbjct  7538790  AA-TTT  7538794


 Score =  115 bits (62),  Expect = 1e-21
 Identities = 135/168 (80%), Gaps = 14/168 (8%)
 Strand=Plus/Minus

Query  6429     aaaatGTTAGCCAGGTGTGGTGG--TGCAGTCCTATAATCCTAGCTACTCT-GGAGGCAG  6485
                ||||||  |||||||||||||||  ||| | ||| |||||| ||||||| | |||||| |
Sbjct  5399447  AAAATG--AGCCAGGTGTGGTGGTATGC-G-CCTGTAATCCCAGCTACT-TGGGAGGCTG  5399393

Query  6486     AGGAAGAAGAATCACTTGAATCCC-GGAGGCAGTGTTTTCAGTGAGCTGAA-CTCAACAC  6543
                ||| || |||||| |||||| ||| |||||| | | || ||||||||  ||  |   | |
Sbjct  5399392  AGGCAGGAGAATCGCTTGAA-CCCGGGAGGCGGAGGTTGCAGTGAGC-CAAGGT-TGCGC  5399336

Query  6544     C-CTGCCCTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAA  6590
                |  ||| || |||||||||||||||||||||||||||||||| |||||
Sbjct  5399335  CATTGCACTCCAGCCTGGGTGACAGAGTGAGACTCCATCTCAAAACAA  5399288


 Score =  111 bits (60),  Expect = 2e-20
 Identities = 107/129 (82%), Gaps = 6/129 (4%)
 Strand=Plus/Plus

Query  6459     CTATAATCCTAGCTACTCTGGAGGCAGAGGAAGAAGAATCACTTGAATCC-CGGAGGCAG  6517
                ||||||||| |||||||| |||||| || | || |||||| |||||| ||  ||||||||
Sbjct  1324670  CTATAATCCCAGCTACTCAGGAGGCTGAAGCAGGAGAATCGCTTGAA-CCTGGGAGGCAG  1324728

Query  6518     TGTTTTCAGTGAGCTGA-ACTCAACACC-CTGCCCTTCAGCCTGGGTGACAGAGTGAGAC  6575
                 | || |||||||| || | || || || || | || |||||||||||||||||||||||
Sbjct  1324729  AGCTTGCAGTGAGCCGAGA-TC-ACGCCACTACACTGCAGCCTGGGTGACAGAGTGAGAC  1324786

Query  6576     TCCATCTCA  6584
                |||||||||
Sbjct  1324787  TCCATCTCA  1324795


 Score =  110 bits (59),  Expect = 6e-20
 Identities = 136/171 (79%), Gaps = 14/171 (8%)
 Strand=Plus/Plus

Query  6435     TTAGCCAGGTGTGGT-G-GTGCAGTCCTATAATCCTAGCTACTCTGGAGGCAGAGGAAGA  6492
                |||||| |||||||| | | |||  ||| |||||| |||||||| || ||| |||| || 
Sbjct  4113378  TTAGCCGGGTGTGGTGGCGGGCA--CCTGTAATCCCAGCTACTCAGGGGGCTGAGGCAGG  4113435

Query  6493     AGAATCACTTGAATCCC-GGAGGCAGTGTTTTCAGTGAGCTGA-ACTCAACACC-CTGCC  6549
                ||||||||||||| ||| |||||| | | || |||||| |  | || |    ||  ||||
Sbjct  4113436  AGAATCACTTGAA-CCCGGGAGGCGGAGGTTGCAGTGAACCCAGAC-C-GTGCCATTGCC  4113492

Query  6550     CTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAGAGAAA-AGA  6599
                || |||||||||||||||||||||||||||||||| || || ||||| |||
Sbjct  4113493  CTCCAGCCTGGGTGACAGAGTGAGACTCCATCTCA-AA-AA-AGAAAGAGA  4113540


 Score =  110 bits (59),  Expect = 6e-20
 Identities = 129/161 (80%), Gaps = 11/161 (6%)
 Strand=Plus/Plus

Query  6435     TTAGCCAGGTGTGGTGGTGCAGT-CCTATAATCCTAGCTACTCTG-GAGGCAGAGGAAGA  6492
                |||||||||  |||||| ||  | |||||||||| ||| |||| | ||||| |||| || 
Sbjct  5355063  TTAGCCAGGCATGGTGGCGC-TTGCCTATAATCCCAGCCACTC-GAGAGGCTGAGGCAGG  5355120

Query  6493     AGAATCACTTGAATCCC-GGAGGCAGTGTTTTCAGTGAGCTGAA-CTCAACAC-CCTGCC  6549
                |||||||| |||| ||| |||||| | | || ||||||||  ||  |   |||  |||| 
Sbjct  5355121  AGAATCACCTGAA-CCCGGGAGGCGGAGGTTGCAGTGAGC-CAAGAT-TGCACTGCTGCA  5355177

Query  6550     CTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAA  6590
                || |||||||||||||||||||||||||||||||| |||||
Sbjct  5355178  CTCCAGCCTGGGTGACAGAGTGAGACTCCATCTCA-AACAA  5355217


 Score =  108 bits (58),  Expect = 2e-19
 Identities = 134/169 (79%), Gaps = 12/169 (7%)
 Strand=Plus/Plus

Query  6435     TTAGCCAGGTGTGGTGGT--GCAGTCCTATAATCCTAGCTACTCT-GGAGGCAGAGGAAG  6491
                ||||||||||||||||||  |||  ||| |  ||| ||||||| | |||||| |||| ||
Sbjct  1114585  TTAGCCAGGTGTGGTGGTGGGCA--CCTGTGGTCCCAGCTACT-TGGGAGGCTGAGGCAG  1114641

Query  6492     AAGAATCACTTGAATCCCG-GAGGCAGTGTTTTCAGTGAGCTGA-ACTCAACACC-CTGC  6548
                ||||||  | |||| || | ||||| | | || |||||||| || | ||  | || ||||
Sbjct  1114642  AAGAATGGCATGAA-CCTGAGAGGCGGAGGTTACAGTGAGCCGAGA-TC-GCGCCACTGC  1114698

Query  6549     CCTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAGAGAAAA  6597
                 || |||||||||||||||||||||||||||||||| || || | ||||
Sbjct  1114699  ACTCCAGCCTGGGTGACAGAGTGAGACTCCATCTCAAAAAAAAAAAAAA  1114747


 Score =  108 bits (58),  Expect = 2e-19
 Identities = 135/171 (78%), Gaps = 10/171 (5%)
 Strand=Plus/Plus

Query  6435     TTAGCCAGGTGTGGTGGTGCAGTCCTATAATCCT-AGCTACTCT-GGAGGCAGAGGAAGA  6492
                |||||  || |||||||||||  ||| |||| || ||||||| | |||||| |||| || 
Sbjct  3709247  TTAGCTGGGCGTGGTGGTGCACACCTGTAAT-CTCAGCTACT-TGGGAGGCTGAGGCAGG  3709304

Query  6493     AGAATCACTTGAATCCC-GGAGGCAGTGTTTTCAGTGAGCTGA-ACTCAACACCCTGCCC  6550
                ||||||| ||||| ||| |||||  | | || ||||||||||| | |   | |  || | 
Sbjct  3709305  AGAATCATTTGAA-CCCAGGAGGTGGAGGTTGCAGTGAGCTGAGATTGTGC-CATTG-CG  3709361

Query  6551     TT-CAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAGAGAAAAGAA  6600
                || | |||||||||||||||||||||||||||||| || |||| |||||||
Sbjct  3709362  TTCCCGCCTGGGTGACAGAGTGAGACTCCATCTCAAAAAAAGAAAAAAGAA  3709412


 Score =  106 bits (57),  Expect = 8e-19
 Identities = 133/169 (78%), Gaps = 7/169 (4%)
 Strand=Plus/Plus

Query  6435     TTAGCCAGGTGTGGTGGTGCAGTCCTATAATCCTAGCTACTCTGGAGGCAGAGG-AAGAA  6493
                |||||  || ||||||| ||| |||| ||| || |||||||| |||||  |||| | |||
Sbjct  4225578  TTAGCTGGGCGTGGTGGCGCATTCCTGTAACCCCAGCTACTCGGGAGGTTGAGGCAGGAA  4225637

Query  6494     GAATCACTTGAATCCCGGAGGCAGTGTTTTCAGTGAGCTGA-ACTCAACACCCTGCCCTT  6552
                 |||| ||||||||  |||||| | | || ||||||||  | | |   | | |||| || 
Sbjct  4225638  -AATCGCTTGAATCTGGGAGGCGGAGGTTGCAGTGAGCCAAGATTGTGC-CACTGCGCTC  4225695

Query  6553     CAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAGAGA-AAAGAA  6600
                |||||||||||||||||||||||||||||||| || |||| | ||||||
Sbjct  4225696  CAGCCTGGGTGACAGAGTGAGACTCCATCTCA-AA-AAGAAAGAAAGAA  4225742


 Score =  104 bits (56),  Expect = 3e-18
 Identities = 129/162 (79%), Gaps = 13/162 (8%)
 Strand=Plus/Plus

Query  6442     GGTGTGGTGGTGC-AGTCCTATAATCCTAGCTACTCTGGAGGCAGAGG-AAGAAGAATCA  6499
                ||| ||||||  | || |||||||||| ||||| || |||||| |||| | | |||||||
Sbjct  6732599  GGT-TGGTGGCACGAG-CCTATAATCCCAGCTATTCGGGAGGCTGAGGCATG-AGAATCA  6732655

Query  6500     CTTGAATCCC-GGAGGCAGTGTTTTCAGTGAGCTGA-ACTCAACACC-CTGCCCTTC-AG  6555
                |||||| ||| |||||| | | || || ||||| || | || |  || |||| | || ||
Sbjct  6732656  CTTGAA-CCCAGGAGGCGGAGGTTACATTGAGCCGAGA-TC-ATGCCACTGCAC-TCTAG  6732711

Query  6556     CCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAGAGAAAA  6597
                ||||||||||||||||||||||||||||| || || | ||||
Sbjct  6732712  CCTGGGTGACAGAGTGAGACTCCATCTCAAAAAAAAAAAAAA  6732753


 Score = 99.0 bits (53),  Expect = 1e-16
 Identities = 133/170 (78%), Gaps = 12/170 (7%)
 Strand=Plus/Plus

Query  6435     TTAGCCAGGTGTGGTGGTGCA-GT-CCTATAATCCTAGCTACTCTGGAGGCAGAGGAAGA  6492
                ||||||||| |  || | ||| || ||| || ||| |||||||| |||||| |||| || 
Sbjct  7118242  TTAGCCAGGCGCAGT-G-GCAGGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGG  7118299

Query  6493     AGAATCACTTGAATCCCGG-AGGCAGTGTTTTCAGTGAGCTGA-ACTCAACACC-CTGCC  6549
                ||||| || |||| ||||| |||  | | || |||||||| || | || |  || |||  
Sbjct  7118300  AGAATGACGTGAA-CCCGGAAGGTGGAGCTTGCAGTGAGCCGAGA-TC-ATGCCACTGTA  7118356

Query  6550     CTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAGAGAAAAGA  6599
                || |||||||||||||||||||||||||||||||| || || | ||||||
Sbjct  7118357  CTCCAGCCTGGGTGACAGAGTGAGACTCCATCTCAAAAAAA-A-AAAAGA  7118404


 Score = 97.1 bits (52),  Expect = 5e-16
 Identities = 113/141 (80%), Gaps = 10/141 (7%)
 Strand=Plus/Plus

Query  6445     GTGGTGGTGCAGTCCTATAATCCTAGCTACTCTGGAGGCAGAGGAAGAAGAATCACTTGA  6504
                ||||||| || | ||| |||||| |||||||| |||||| |||| || |||||| | |||
Sbjct  2518960  GTGGTGG-GC-G-CCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAG-AGAATCGCCTGA  2519015

Query  6505     ATCC-CGGAGGCAGTGTTTTCAGTGAGCTGA-ACTCAACACC-CTGCCCTTCAGCCTGGG  6561
                | ||  |||||  | | || ||||||||||| | |   | || |||| || |||||||||
Sbjct  2519016  A-CCTGGGAGGTGGAGGTTGCAGTGAGCTGAGA-T-TGCGCCACTGCACTCCAGCCTGGG  2519072

Query  6562     TGACAGAGTGAGACTCCATCT  6582
                |||||||||||||||||||||
Sbjct  2519073  TGACAGAGTGAGACTCCATCT  2519093


 Score = 95.3 bits (51),  Expect = 2e-15
 Identities = 125/158 (79%), Gaps = 16/158 (10%)
 Strand=Plus/Plus

Query  6435     TTAGCCAGG--T-GTGGTGGTGCAGTCCTATAATCCTAGCTACTCTGGAGGCAGAGGAAG  6491
                |||||||||  | |||| || |||  ||| |||||| |||| ||  |||||| |||| ||
Sbjct  5434073  TTAGCCAGGCCTGGTGGCGG-GCA--CCTGTAATCCCAGCTGCTAGGGAGGCTGAGGCAG  5434129

Query  6492     AAGAATCACTTGAATCCCGGAGGCAGT---GTTTTCAGTGAGCTGA-ACTCAACACC-CT  6546
                 |||||| |||||| | |  |||||||   | || |||||||| || | || ||||| ||
Sbjct  5434130  GAGAATCGCTTGAA-CTC--AGGCAGTGGAGATTGCAGTGAGCCGAGA-TC-ACACCACT  5434184

Query  6547     GCCCTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCA  6584
                || || ||| ||||||||||||||||||||||||||||
Sbjct  5434185  GCACTCCAGTCTGGGTGACAGAGTGAGACTCCATCTCA  5434222


 Score = 93.5 bits (50),  Expect = 6e-15
 Identities = 113/142 (79%), Gaps = 10/142 (7%)
 Strand=Plus/Plus

Query  6447    GGTGGTGCA-GTCCTATAATCCTAGCTACTCTGGAGGCAGAGGA-AGAAGAATCACTTGA  6504
               ||||||||| | ||| || ||| |||||||| |||||| || || || ||||||||||||
Sbjct  987862  GGTGGTGCACG-CCTGTAGTCCCAGCTACTCGGGAGGCTGA-GACAGGAGAATCACTTGA  987919

Query  6505    ATC-CCGGAGGCAGTGTTTTCAGTGAGCTGA-ACT-CAACACCCTGCCCTTCAGCCTGGG  6561
               | |   |||||||| | || |||| ||| || | |    || || || || |||||||||
Sbjct  987920  A-CAAAGGAGGCAGAGGTTGCAGTTAGCCGAGAGTGTGTCA-CC-GCACTCCAGCCTGGG  987976

Query  6562    TGACAGAGTGAGACTCCATCTC  6583
               ||||||||||||||||||||||
Sbjct  987977  TGACAGAGTGAGACTCCATCTC  987998


 Score = 91.6 bits (49),  Expect = 2e-14
 Identities = 115/145 (79%), Gaps = 11/145 (7%)
 Strand=Plus/Minus

Query  6458    CCTATAATCCTAGCTACTCTGG-AGGCAGAGGAAGAAGAATCACTTGAATCC-CGGAGGC  6515
               ||| || |||| |||||| ||| |||| |||| || ||||||||||||| ||  ||||| 
Sbjct  612602  CCTGTAGTCCTGGCTACT-TGGTAGGCTGAGGCAGGAGAATCACTTGAA-CCTGGGAGGT  612545

Query  6516    AG-TGTTTTCAGTGAGCTGA-ACTCAACACC-CTGCCCTTCAGCCTGGGTGACAGAGTGA  6572
                |  ||| |  ||||||||| | ||  | || |||| || ||||||||||||||||||||
Sbjct  612544  GGAAGTTGT-GGTGAGCTGAGA-TC-CCGCCACTGCACTCCAGCCTGGGTGACAGAGTGA  612488

Query  6573    GACTCCATCTCAGAACAAGAGAAAA  6597
               |||||||||||| || || | ||||
Sbjct  612487  GACTCCATCTCAAAA-AACAAAAAA  612464


 Score = 91.6 bits (49),  Expect = 2e-14
 Identities = 106/133 (79%), Gaps = 6/133 (4%)
 Strand=Plus/Minus

Query  6458     CCTATAATCCTAGCTACTCTGGAGGCAGAGGAAGAAGAATCACTTGAATCCC-GGAGGCA  6516
                ||| || ||| |||||||| ||| || |||| ||  ||||  | |||| ||| |||||| 
Sbjct  2876673  CCTGTAGTCCCAGCTACTCAGGAAGCTGAGGCAGGGGAATGGCGTGAA-CCCAGGAGGCG  2876615

Query  6517     GTGTTTTCAGTGAGCTGAA-CTCAACACC-CTGCCCTTCAGCCTGGGTGACAGAGTGAGA  6574
                | | || ||||||||  ||  ||  |||| |||| || ||||||||||||||||||||||
Sbjct  2876614  GAGCTTGCAGTGAGC-CAAGATC-GCACCACTGCACTCCAGCCTGGGTGACAGAGTGAGA  2876557

Query  6575     CTCCATCTCAGAA  6587
                |||||||||||||
Sbjct  2876556  CTCCATCTCAGAA  2876544


 Score = 91.6 bits (49),  Expect = 2e-14
 Identities = 122/156 (78%), Gaps = 9/156 (5%)
 Strand=Plus/Plus

Query  6445     GTGGTGGTGCAGTCCTATAATCCTAGCTACTCTGGAGGCAGAGGAAGAAGAATCACTTGA  6504
                ||||||| |||  |||||| |||  ||| ||| |||||| |||| || |||||  | |||
Sbjct  5144157  GTGGTGG-GCA--CCTATAGTCCCCGCTGCTCAGGAGGCTGAGGCAGGAGAATGGCGTGA  5144213

Query  6505     ATCCC-GGAGGCAGTGTTTTCAGTGAGCTGA-ACTCAACACC-CTGCCCTTCAGCCTGGG  6561
                | ||| |||||| | | || |||||||| || | |   | || |||| || |||||||||
Sbjct  5144214  A-CCCGGGAGGCGGAGGTTGCAGTGAGCCGAGA-T-TGCGCCACTGCACTCCAGCCTGGG  5144270

Query  6562     TGACAGAGTGAGACTCCATCTCAGAACAAGAGAAAA  6597
                ||||||||||||||||||||||| || || | ||||
Sbjct  5144271  TGACAGAGTGAGACTCCATCTCAAAAAAAAACAAAA  5144306


 Score = 91.6 bits (49),  Expect = 2e-14
 Identities = 109/137 (79%), Gaps = 8/137 (5%)
 Strand=Plus/Plus

Query  6465     TCCTAGCTACTCT-GGAGGCAGAGGAAGAAGAATCACTTGAATCC-CGGAGGCAGTGTTT  6522
                ||| ||||||| | |||||| ||||  | || ||| |||||| ||  |||||||| |  |
Sbjct  6628080  TCCCAGCTACT-TGGGAGGCTGAGGTGGGAGGATCGCTTGAA-CCTGGGAGGCAGAGGCT  6628137

Query  6523     TCAGTGAGCTGA-ACTCAACACC-CTGCCCTTCAGCCTGGGTGACAGAGTGAGACTCCAT  6580
                 ||||||||||| | ||  | || |||| || ||||||||||||||||||||||||||||
Sbjct  6628138  GCAGTGAGCTGAGA-TC-TCGCCACTGCACTGCAGCCTGGGTGACAGAGTGAGACTCCAT  6628195

Query  6581     CTCAGAACAAGAGAAAA  6597
                |||| || || | ||||
Sbjct  6628196  CTCAAAAAAAAAAAAAA  6628212


 Score = 89.8 bits (48),  Expect = 8e-14
 Identities = 122/156 (78%), Gaps = 12/156 (7%)
 Strand=Plus/Plus

Query  6435     TTAGCCAGGTGTGGTGGTGCAGT-CCTATAATCCTAGCTACTCT-GGAGGCAGAGGAAGA  6492
                |||||| || ||||||||||| | ||| |||||| ||||||| | |||||| ||||  | 
Sbjct  1458190  TTAGCCTGGCGTGGTGGTGCA-TGCCTGTAATCCCAGCTACT-TGGGAGGCTGAGGTGGG  1458247

Query  6493     AGAATC-ACTTGAATCCC-GGAGGCAG-TGTTTTCAGTGAGCTGA-ACTCAACACCCTGC  6548
                |||| |  |||||| ||| ||||||||  ||| | ||||| |  | | |     |  |||
Sbjct  1458248  AGAA-CTGCTTGAA-CCCGGGAGGCAGAAGTTGT-AGTGACCCCAGA-TTGTGTCATTGC  1458303

Query  6549     CCTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCA  6584
                ||| ||||||||||||||||||||||||||||||||
Sbjct  1458304  CCTCCAGCCTGGGTGACAGAGTGAGACTCCATCTCA  1458339


 Score = 89.8 bits (48),  Expect = 8e-14
 Identities = 125/161 (77%), Gaps = 9/161 (5%)
 Strand=Plus/Minus

Query  6435     TTAGCCAGGTGTGGTGGTGCAGT-CCTATAATCCTAGCTACTCT-GGAGGCAGAGGAAGA  6492
                ||||||||||||| ||| ||| | ||| |||||| |||| || | |||||| |||| || 
Sbjct  7562246  TTAGCCAGGTGTGTTGGGGCA-TGCCTGTAATCCCAGCTGCT-TGGGAGGCTGAGGCAGG  7562189

Query  6493     AGAATCACTTGAATC-CCGGAGGCAGTGTTTTCAGTGAGCTGAACTCAACACC-CTGCCC  6550
                |||||  |||||| |   |||||| |   || ||||||||  ||  |  ||||  ||| |
Sbjct  7562188  AGAATTGCTTGAA-CAAGGGAGGCGGACATTGCAGTGAGC-CAAGACTGCACCATTGCAC  7562131

Query  6551     TTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAG  6591
                | || ||||||||||||||||||||||||||||| || |||
Sbjct  7562130  TCCACCCTGGGTGACAGAGTGAGACTCCATCTCAAAA-AAG  7562091


 Score = 87.9 bits (47),  Expect = 3e-13
 Identities = 126/162 (77%), Gaps = 13/162 (8%)
 Strand=Plus/Plus

Query  6436     TAGCCAGGTGTGGT-G-GTGCAGTCCTATAATCCTAGCTACTCT-GGAGGCAGAGGA-AG  6491
                |||||||||||||| | |||||  ||| || ||| |||| || | ||| || || || ||
Sbjct  1564520  TAGCCAGGTGTGGTGGTGTGCA--CCTGTAGTCCCAGCTGCT-TGGGAAGCTGA-GACAG  1564575

Query  6492     AAGAATCACTTGAATCCC-GGAGGCAGTGTTTTCAGTGAGCTGA-ACTCAACACCCTGCC  6549
                 |||||  |||||| ||| |||||  | | || |||||||| || |||   | | |||| 
Sbjct  1564576  GAGAATTGCTTGAA-CCCAGGAGGTGGAGGTTGCAGTGAGCCGAGACTGTGC-CACTGCA  1564633

Query  6550     CTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAA-CAA  6590
                || |||||||||||||||||||||||||||| ||| || |||
Sbjct  1564634  CTCCAGCCTGGGTGACAGAGTGAGACTCCATTTCAAAAACAA  1564675


 Score = 87.9 bits (47),  Expect = 3e-13
 Identities = 112/142 (78%), Gaps = 10/142 (7%)
 Strand=Plus/Plus

Query  6461     ATAATCCTAGCTACTCTGGAGGCAGAGGAAGAAGAATCACTTGAATCC-CGGAGGCAGTG  6519
                ||| ||| || ||||| |||||| |||| || ||| |  | |||| ||  |||||||| |
Sbjct  4930994  ATAGTCCCAGGTACTCGGGAGGCTGAGGCAGGAGAGTGGCGTGAA-CCTGGGAGGCAGAG  4931052

Query  6520     TTTTCAGTGAGCTGA-ACTCAACACC-CTGCCCTT-CAGCCTGGGTGACAGAGTGAGACT  6576
                 || |||||||| || |||   |||| ||| | || ||||||||||||||||||||||||
Sbjct  4931053  CTTGCAGTGAGCCGAGACT--GCACCACTG-CATTCCAGCCTGGGTGACAGAGTGAGACT  4931109

Query  6577     CCATCTCAGAA-CAAGAGAAAA  6597
                |||||||| || || || ||||
Sbjct  4931110  CCATCTCAAAATCA-GACAAAA  4931130


 Score = 86.1 bits (46),  Expect = 1e-12
 Identities = 111/141 (78%), Gaps = 9/141 (6%)
 Strand=Plus/Minus

Query  6445    GTGGTGGTGCAGTCCTATAATCCTAGCTACTCTGGAGGCAGAGGAAGAAGAATCACTTGA  6504
               ||||||| || || || |||||| |||| ||| |||||| |||| || |||||  |||||
Sbjct  182426  GTGGTGG-GC-GT-CTCTAATCCCAGCTGCTCCGGAGGCTGAGGCAGGAGAATTGCTTGA  182370

Query  6505    ATCC-CGGAGGCAGTGTTTTCAGTGAGCTGA-ACTCAACACC-CTGCCCTTCAGCCTGGG  6561
               | ||  |||| | | |||| |||||||| || | |    ||| | || || |||||||||
Sbjct  182369  A-CCTGGGAGTCGGAGTTTGCAGTGAGCCGAGA-T-GGTACCACAGCACTCCAGCCTGGG  182313

Query  6562    TGACAGAGTGAGACTCCATCT  6582
               |||||||||||||||||||||
Sbjct  182312  TGACAGAGTGAGACTCCATCT  182292


 Score = 86.1 bits (46),  Expect = 1e-12
 Identities = 120/153 (78%), Gaps = 16/153 (10%)
 Strand=Plus/Minus

Query  6442     GGT-GTGGTGGTGCAGTCCTATAATCCTAGCTACTCTGGAGGCAGAGG-AAGAAGAATCA  6499
                ||| ||||| |||| | ||| || ||| | |||||| |||||| |||| | | |||||  
Sbjct  3549720  GGTGGTGGT-GTGC-G-CCTGTAGTCCCATCTACTCAGGAGGCTGAGGCATG-AGAATTG  3549665

Query  6500     CTTGAATCCC--GGAGGCAGTGTTTTCAGTGAGCTGAA-CTCAACACC-CTGCCCTT-CA  6554
                |||| | |||  |||||||| | || ||||||||  ||  || |  || ||| | || ||
Sbjct  3549664  CTTG-A-CCCTAGGAGGCAGAGGTTGCAGTGAGC-CAAGATC-ATGCCACTG-CATTCCA  3549610

Query  6555     GCCTGGGTGACAGAGTGAGACTCCATCTCAGAA  6587
                |||||||||||||||||||||||||||||||||
Sbjct  3549609  GCCTGGGTGACAGAGTGAGACTCCATCTCAGAA  3549577


 Score = 80.5 bits (43),  Expect = 5e-11
 Identities = 109/140 (77%), Gaps = 8/140 (5%)
 Strand=Plus/Minus

Query  6462    TAATCCTAGCTACTCTGGAGGCAGAGGAAGAAGAATCACTTGAATCC-CGGAGGCAGTGT  6520
               |||||| |||| ||| |||||| || | || |||||  |||||| ||  |||||  | | 
Sbjct  426467  TAATCCCAGCTCCTCAGGAGGCTGAAGTAGGAGAATTGCTTGAA-CCTGGGAGGTGGAGG  426409

Query  6521    TTTCAGTGAG-CTGAACTCAACACC-CTGCCCTTC-AGCCTGGGTGACAGAGTGAGACTC  6577
               || ||||||| | | | || |  || |||| | || ||||||||||||||||||||||||
Sbjct  426408  TTGCAGTGAGCCAGGA-TC-ATGCCACTGCAC-TCTAGCCTGGGTGACAGAGTGAGACTC  426352

Query  6578    CATCTCAGAACAAGAGAAAA  6597
               ||||||| ||||| | ||||
Sbjct  426351  CATCTCAAAACAAAACAAAA  426332


 Score = 76.8 bits (41),  Expect = 6e-10
 Identities = 113/146 (77%), Gaps = 11/146 (7%)
 Strand=Plus/Plus

Query  6462     TAATCCTAGCTACTCTGGAGGCAGAGGAAGAAGAATCACTTGAATCCCGGAGGCA-GTGT  6520
                |||||| |||||||| |||||| |||| || |||||  |||||||||| ||   | | | 
Sbjct  4825488  TAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATTGCTTGAATCCC-GAAAAAGGAGG  4825546

Query  6521     TTTCAGTGAGCTGAA-CTCAACACC-CTGCCCTTCA----G-CCTGGGTGACAGAGTGAG  6573
                || ||||||||  ||  || |  || |||| || ||    | ||||||||||||||||||
Sbjct  4825547  TTGCAGTGAGC-CAAGATC-ATGCCACTGCACTCCAGCCTGACCTGGGTGACAGAGTGAG  4825604

Query  6574     ACTCCATCTCAGAACAAGAGAAAAGA  6599
                ||||||||||| || || ||||||||
Sbjct  4825605  ACTCCATCTCAAAAAAAAAGAAAAGA  4825630


 Score = 75.0 bits (40),  Expect = 2e-09
 Identities = 123/160 (76%), Gaps = 18/160 (11%)
 Strand=Plus/Plus

Query  6435     TTAGCCAGGTGTGGTGGTGCA-GT-CCTATAATCCT-AGCTACTCTGGAGGCAGAGGA-A  6490
                |||||||||| |||| | ||| || ||| |||| || ||||| || |||||| || || |
Sbjct  4746216  TTAGCCAGGTATGGT-G-GCACGTGCCTGTAAT-CTCAGCTATTCGGGAGGCTGA-GACA  4746271

Query  6491     -GAAGAATC-ACTTGAATC-CCGGAGGCAGTGTTTTCAGTGAGCTGAA-CTCAACACC-C  6545
                 | | |||| | ||||| |   |||||  | | || ||||||||  ||  |   |||| |
Sbjct  4746272  TG-ATAATCGA-TTGAA-CTGGGGAGGTGGAGGTTGCAGTGAGC-CAAGAT-TGCACCAC  4746326

Query  6546     TGCCCTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAG  6585
                ||| || |||||||||||||||||||||||||||||||||
Sbjct  4746327  TGCACTCCAGCCTGGGTGACAGAGTGAGACTCCATCTCAG  4746366


 Score = 71.3 bits (38),  Expect = 3e-08
 Identities = 113/147 (76%), Gaps = 14/147 (9%)
 Strand=Plus/Plus

Query  6458     CCTATAATCCTAGCTACTCTG-GAGGCAGAGG-AAGAAGAATCACTTGAATCCC-GGA-G  6513
                ||| |||||| |||||||| |  |||| |||| |||  ||||| |||||| ||| ||| |
Sbjct  4111386  CCTGTAATCCCAGCTACTC-GAAAGGCTGAGGCAAG-TGAATCTCTTGAA-CCCGGGAGG  4111442

Query  6514     -GCAGTGTTTTCAGTGAGCTGAA-CTCAACACC-CTGCCCTTCAGCCTGGGTGACAGAGT  6570
                 | || | || ||||||||  ||  ||    ||  ||| || ||||||||||||||||||
Sbjct  4111443  TGAAG-G-TTGCAGTGAGC-CAAGATC-GTGCCATTGCACTCCAGCCTGGGTGACAGAGT  4111498

Query  6571     GAGACTCCATCTCAGAACAAGAGAAAA  6597
                |||||||||||||| || || | ||||
Sbjct  4111499  GAGACTCCATCTCAAAAAAAAAAAAAA  4111525


 Score = 69.4 bits (37),  Expect = 1e-07
 Identities = 60/70 (85%), Gaps = 5/70 (7%)
 Strand=Plus/Minus

Query  6524     CAGTGAGCTGAAC-TCAACACC-CTGCCCTTCAGCCTGGGTGACAGAGTGAGACTCCATC  6581
                ||||||||||  | ||  |||| |||| || |||||||||||||||||||||||||||||
Sbjct  4037509  CAGTGAGCTG-TCATC-CCACCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCCATC  4037452

Query  6582     TCAGAA-CAA  6590
                ||| || |||
Sbjct  4037451  TCAAAAACAA  4037442


 Score = 69.4 bits (37),  Expect = 1e-07
 Identities = 48/53 (90%), Gaps = 1/53 (1%)
 Strand=Plus/Minus

Query  6545     CTGCCCTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAGAGAAAA  6597
                |||| || |||||||||||||||||||||||||||||||| || |||| ||||
Sbjct  4831195  CTGCACTCCAGCCTGGGTGACAGAGTGAGACTCCATCTCAAAA-AAGAAAAAA  4831144


 Score = 56.5 bits (30),  Expect = 8e-04
 Identities = 30/30 (100%), Gaps = 0/30 (0%)
 Strand=Plus/Plus

Query  3225     AATTGCTGCCTCTCTCGAGACCCTCGTGTT  3254
                ||||||||||||||||||||||||||||||
Sbjct  7458614  AATTGCTGCCTCTCTCGAGACCCTCGTGTT  7458643


 Score = 54.7 bits (29),  Expect = 0.003
 Identities = 29/29 (100%), Gaps = 0/29 (0%)
 Strand=Plus/Minus

Query  6556     CCTGGGTGACAGAGTGAGACTCCATCTCA  6584
                |||||||||||||||||||||||||||||
Sbjct  6953042  CCTGGGTGACAGAGTGAGACTCCATCTCA  6953014


>gi|51459264|ref|NT_077382.3|Hs1_77431 Homo sapiens chromosome 1 genomic contig
Length=237250

 Features flanking this part of subject sequence:
   16338 bp at 5' side: PRAME family member 8
   11926 bp at 3' side: PRAME family member 9

 Score = 7286 bits (3945),  Expect = 0.0
 Identities = 5437/6145 (88%), Gaps = 152/6145 (2%)
 Strand=Plus/Plus

Query  23225  GGTTGGTTAATATTGATAATTAAATGACTTGGTACTGAGAAGAAGCTATAGGTGCAAATG  23284
              |||||||||||||||||||||||||||||||| |||||| ||||||||||| ||||||||
Sbjct  86128  GGTTGGTTAATATTGATAATTAAATGACTTGGCACTGAGCAGAAGCTATAGATGCAAATG  86187

Query  23285  GGTGGCCTATGACTATTATTGATTTCATTACTGGTAATTTATCTCTATGCCTAGAAAACA  23344
              ||||||||||||||||| |||||||||||||| |||| ||||||| |||| ||| |||||
Sbjct  86188  GGTGGCCTATGACTATTGTTGATTTCATTACTTGTAACTTATCTCCATGCATAGGAAACA  86247

Query  23345  TTAGTGTAACTGGGTCTAACCTAGATAGTGTTCCAGACTCCCAC-TAGAATCAAACTCTT  23403
              |||||||||| |||||||| |||| |||||| |||||||||| | | |||||||||||||
Sbjct  86248  TTAGTGTAACCGGGTCTAATCTAGGTAGTGTCCCAGACTCCC-CTTGGAATCAAACTCTT  86306

Query  23404  TGGTTTGACATGCATTATGTAGA-TGGGAATGCTAT-AGATATCGACATAGACATAGAGT  23461
              |  |||||||  ||||||| ||| | | |||||||| || ||| |||||||||| ||| |
Sbjct  86307  TCATTTGACACACATTATGAAGACT-GAAATGCTATAAG-TATTGACATAGACACAGAAT  86364

Query  23462  CAGAACATGACCATGTTACCCTCTGCCATATAATCAGAGAACTTACTGAAACTAGGCATT  23521
              |||||||||||||||||| |||||||||||||||||||||||||||||||||||| ||||
Sbjct  86365  CAGAACATGACCATGTTATCCTCTGCCATATAATCAGAGAACTTACTGAAACTAGACATT  86424

Query  23522  GGTTCTTTGGAAACTCTAGAGGCAAATAGAATGCATCTATAGCTCTACTGTATGAAAT--  23579
               |||| ||||||||||  ||||||||||||||||||||||||||||||  ||||||||  
Sbjct  86425  TGTTCATTGGAAACTC--GAGGCAAATAGAATGCATCTATAGCTCTACCATATGAAATAA  86482

Query  23580  --AATAGTTTTATTTATTGGATGCATCAATACTCAGGATATATTTGGAGAGGAAACTATT  23637
                |||||||| |||||||||||||||| |||||||| | ||||||||||| ||  |||||
Sbjct  86483  ACAATAGTTTCATTTATTGGATGCATCCATACTCAGCACATATTTGGAGAAGACCCTATT  86542

Query  23638  CTTTCTTCAATGGAGATGGCATGCAAGGATTACT-TTATAAAACACACAGAAATATTTTT  23696
              | |||||||||||||||| ||||||||||||| | | ||||||  || | ||||||||||
Sbjct  86543  CATTCTTCAATGGAGATGACATGCAAGGATTA-TATAATAAAATTCATAAAAATATTTTT  86601

Query  23697  TCCTCCCACCCCAATTCCAACCATTACCGTGCAACCTGTtgtcaatagacgttaaggcag  23756
              || |||||||||| ||| |||  | ||| ||||||||| ||||| | || | |||||| |
Sbjct  86602  TCATCCCACCCCAGTTCAAACTGTCACCATGCAACCTGGTGTCAGTGGAAGGTAAGGC-G  86660

Query  23757  -ttgaggcagaaataattaaataaagcttcattggaagctaaatgtcaggatcgacctgg  23815
               || ||||||||||||||||||||| |||||||||||||||||||| || ||| |  |||
Sbjct  86661  CTTAAGGCAGAAATAATTAAATAAATCTTCATTGGAAGCTAAATGTGAGAATCAATGTGG  86720

Query  23816  aagacacacactgacaaaatgagcgttttccaaagtctgttacaagttggaatgctttta  23875
              |||||||| ||  ||||| || | || |||||||||||||||||||||||||||||||| 
Sbjct  86721  AAGACACAGACCAACAAAGTGGGTGTGTTCCAAAGTCTGTTACAAGTTGGAATGCTTTTG  86780

Query  23876  taagaaaggttgaaagaagggaatgggactcctcctatcagttgttttttttttttaatt  23935
              | ||||| ||| ||||||||||||| ||||||||||||||   |  ||||||||||||||
Sbjct  86781  TGAGAAAAGTTAAAAGAAGGGAATGAGACTCCTCCTATCA---G-CTTTTTTTTTTAATT  86836

Query  23936  ttcttttgtttta-t--cctggcaaggctctaatagagttgag--ctt-ttttgtttttg  23989
              ||||||||||||| |  ||||||||||||| ||||||||||||   || |||||||||||
Sbjct  86837  TTCTTTTGTTTTACTGACCTGGCAAGGCTCAAATAGAGTTGAGTTTTTGTTTTGTTTTTG  86896

Query  23990  ttttttccattggaagggacaatacagaggttacaatcattgactttagatgacaacatg  24049
              ||||||||||||||||| ||||||||||||||||||||||||||||||| ||||||||| 
Sbjct  86897  TTTTTTCCATTGGAAGGTACAATACAGAGGTTACAATCATTGACTTTAGCTGACAACATA  86956

Query  24050  acaggcaaaaatattttccttgcaagacaaccagcaaaacttcacgatcagaatcaaatc  24109
              ||| |   ||| ||||||||||||||||||||||  |||||||| |||||||||||||||
Sbjct  86957  ACAAG-TTAAACATTTTCCTTGCAAGACAACCAGTGAAACTTCATGATCAGAATCAAATC  87015

Query  24110  agtgtccttctcactgtcactgggtgaagccttcatcagtacttgaagagtctcaggcac  24169
              ||||||||||||||||| | ||||||||| |||||||| || ||| ||||| | ||||||
Sbjct  87016  AGTGTCCTTCTCACTGTAAGTGGGTGAAG-CTTCATCAATAATTGCAGAGTTTGAGGCAC  87074

Query  24170  tcatgaagtcaagatcagattctttactcagggacaggatgtaagccaatcataagacct  24229
              ||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||
Sbjct  87075  TCATGAACTCAAGATCAGATTCTTTACTCAGGGACAGAATGTAAGCCAATCATAAGACCT  87134

Query  24230  tccacagatgatcaatttggaagt-ct-acctaatgtgacctgcaggttttcaCTGGCAA  24287
              ||||||| || | ||||||| | | || |   ||||||||||| | ||||||||||||||
Sbjct  87135  TCCACAGGTGGTTAATTTGG-ACTCCTGA-AAAATGTGACCTGTAAGTTTTCACTGGCAA  87192

Query  24288  TATGCAGGTGCAGATATGACAAAGAATAATCC-TGACCTTCATATCGCCCCTAGCTGATG  24346
              |||||||||||| |||||||||| ||||| ||  |||||| ||||| |||| ||||| ||
Sbjct  87193  TATGCAGGTGCACATATGACAAATAATAA-CCAGGACCTTTATATCACCCCCAGCTGGTG  87251

Query  24347  AGGATTGGGATTCTTTTGTCCCTTTCTCTCCATAAAACCAGGTTACTCATCTTGTGTGGC  24406
               ||| |||||| |||||| |||||||||||||||| |||||| ||||||| |||||||||
Sbjct  87252  GGGAATGGGATCCTTTTGACCCTTTCTCTCCATAATACCAGGCTACTCATGTTGTGTGGC  87311

Query  24407  AACAAAATATATGGTctacttaacagagaaagagactccacaggaaaaaaaaaaggattt  24466
              || |||||||||||||||||| ||||||||||||| | |     ||||||||||||||||
Sbjct  87312  AATAAAATATATGGTCTACTTCACAGAGAAAGAGA-TTCTTTTAAAAAAAAAAAGGATTT  87370

Query  24467  ttattatgaaatgagcaaagccatgggaatagatgtgagattattcggggaggtaaagga  24526
              ||||||||||||||||||||| |||||||||||||||||||||||| |||||||||||||
Sbjct  87371  TTATTATGAAATGAGCAAAGCAATGGGAATAGATGTGAGATTATTCAGGGAGGTAAAGGA  87430

Query  24527  agacaaaggttttgaaaggaaaaatgaggagaattacataaatttttttgaaagactcat  24586
              ||||||||||||||||||||||||| |||||||||||||| | | ||||| |||||||||
Sbjct  87431  AGACAAAGGTTTTGAAAGGAAAAATCAGGAGAATTACATACACTGTTTTGGAAGACTCAT  87490

Query  24587  tcttggtcacaagtatgaaaaccaagggagcctcagtgcagtgttggaaagATTCCTCCT  24646
              |||||||||||||||| || |||||||| ||||||||||| |||||||||||||||||||
Sbjct  87491  TCTTGGTCACAAGTATCAACACCAAGGGGGCCTCAGTGCAATGTTGGAAAGATTCCTCCT  87550

Query  24647  CCAC-CCTCTCAATAACCCCCAACACATTTACCAAGTCTTTGTTCACTCCCAGGATTCCA  24705
              |||| || |||||||||||||||||  ||||||||||||| |||||||||| |||| |||
Sbjct  87551  CCACGCC-CTCAATAACCCCCAACATGTTTACCAAGTCTTGGTTCACTCCCCGGATCCCA  87609

Query  24706  TTAAAACACCCAGCTCAACCCTGACCAGCCTCCACCTTCACTTCCCTTTGTAATTTTGAC  24765
              ||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  87610  TTAAAACACACAGCTCAACCCTGACCAGCCTCCACCTTCACTTCCCTTTGTAATTTTGAC  87669

Query  24766  AT-AAATTtgttacaggaccatcaggttcctatgccggctgcacagtagcttaccaatat  24824
              || |  ||| |||||||||||||||||||||||||| || |||||||||| ||| |||||
Sbjct  87670  ATGACTTTTTTTACAGGACCATCAGGTTCCTATGCCTGCAGCACAGTAGCATACTAATAT  87729

Query  24825  tctgagacagcaggatttgcagcagaaagtttaatgatcacagggtggctgaatgagaag  24884
              |||||||||||||| ||||||||||| ||||||| ||||||||||||||  ||||| |||
Sbjct  87730  TCTGAGACAGCAGGGTTTGCAGCAGAGAGTTTAACGATCACAGGGTGGCAAAATGAAAAG  87789

Query  24885  ctgggaggagatcctcaaattcatctccccaaggagtactgagggtttccagtggatcct  24944
              ||||||||||| ||||||||||||||||||||| ||||||||| |||| ||| ||||| |
Sbjct  87790  CTGGGAGGAGACCCTCAAATTCATCTCCCCAAGAAGTACTGAGAGTTTTCAGAGGATCAT  87849

Query  24945  ggatagcaaggggctggaaagttggtgtagtttgatggcaataagaggtatgaagttatc  25004
              |||||||||| |||||||||||||||| |||||| ||||| ||||||||||||||| |||
Sbjct  87850  GGATAGCAAGAGGCTGGAAAGTTGGTGCAGTTTGGTGGCAGTAAGAGGTATGAAGTCATC  87909

Query  25005  acgatgtcagaacggcattctttggtgagttgatgccttgcagggcccttcagatcagct  25064
              | ||||||| ||| |||||| ||||||||||| |||||||||||||||||||||||| ||
Sbjct  87910  AGGATGTCAAAACTGCATTCCTTGGTGAGTTGGTGCCTTGCAGGGCCCTTCAGATCACCT  87969

Query  25065  ggcatcagtagtttcactgacatgcagaacctgaaagaatatctcaaatgaaaaacttaa  25124
              | ||||||||| |||||||||||||||||||||||||||||| |||||||||||| ||||
Sbjct  87970  GCCATCAGTAGCTTCACTGACATGCAGAACCTGAAAGAATATGTCAAATGAAAAAGTTAA  88029

Query  25125  tgtttcacaatgcttaaattgttgtctgcagcgtagttaaggggaattgtagtctaagtt  25184
              ||||| |||| || ||||||||||||||||| | ||||||||| || |||| |||||| |
Sbjct  88030  TGTTTTACAAGGCCTAAATTGTTGTCTGCAGGGCAGTTAAGGGCAACTGTAATCTAAGGT  88089

Query  25185  ctacacgattttgggacagtaggctgccagcaaccatgaggaagcaggtcagagggcaag  25244
              ||||| ||||||||||||| |||||||||||||||||||||||||||||||||| |||||
Sbjct  88090  CTACATGATTTTGGGACAGCAGGCTGCCAGCAACCATGAGGAAGCAGGTCAGAGAGCAAG  88149

Query  25245  ctgacctcctggtgaatgctgaatgcgtttcaagcttggtttgtttttgttcctccccct  25304
              |||||||| || ||||||||||||||  | |||||||||||| | | |||| ||||||||
Sbjct  88150  CTGACCTCATGATGAATGCTGAATGCACTGCAAGCTTGGTTTATGTCTGTTTCTCCCCCT  88209

Query  25305  ctctttttcaccgattaaatttataaagtttagaaatacggtttcaATTTCTTCCAGACA  25364
              | ||| ||||| |||||||||||||||||||| || || |||| ||||||||||||||  
Sbjct  88210  CCCTTCTTCACTGATTAAATTTATAAAGTTTATAAGTATGGTTGCAATTTCTTCCAGAGT  88269

Query  25365  AGCCTTAACCTAAGCCCTGAGACCACTCAAGCCCTCAGTGGCACCTCTCTTCCACCAGCA  25424
              ||||||||||||||||||||||||||||| | ||||||||||||||||||||||||||||
Sbjct  88270  AGCCTTAACCTAAGCCCTGAGACCACTCAGGTCCTCAGTGGCACCTCTCTTCCACCAGCA  88329

Query  25425  TGAG-CAAATAAATTGCTACCTTAGGTGATATAAAACCCACAAGATGATTCGATACATGG  25483
               |||  ||| |||||||||||||||||||||||||||||||||||  |||| ||||||||
Sbjct  88330  GGAGTGAAA-AAATTGCTACCTTAGGTGATATAAAACCCACAAGACCATTCAATACATGG  88388

Query  25484  AG-ttttt-tttCTGATTTTGTAGGGATGACTTCTTTGTTTCTATAAAGCTGTTTTAACT  25541
              || ||||| ||| |||||||||||||| |||| || ||||| ||||||||| ||||||||
Sbjct  88389  AGATTTTTATTT-TGATTTTGTAGGGACGACTCCTCTGTTTTTATAAAGCTATTTTAACT  88447

Query  25542  ATAAAACAATTTTATAATTTTGATGTGGCCAAAGATCTCCCAAC---ACTACTTTCAGGT  25598
              |||||||| |||| | ||||||||||||||||||||||||||||   ||||||||||| |
Sbjct  88448  ATAAAACATTTTTGTGATTTTGATGTGGCCAAAGATCTCCCAACAATACTACTTTCAGAT  88507

Query  25599  TTTATTTTTCTGTCTACTATC-CAGAACAGATCAAACCCTTCCCTGCCTCAAACTCAGGA  25657
              |||| ||||||||||| ||||   ||| |||| | |||||||||||| ||| ||||||||
Sbjct  88508  TTTAGTTTTCTGTCTAATATCTGGGAA-AGATTAGACCCTTCCCTGCTTCAGACTCAGGA  88566

Query  25658  CTATATAGGTCATATATCAGTAAAATTCCATCAGTGTTTGCGGAgttcatgaatgaatga  25717
              ||||  |||||| |||| ||| |||||||||||||||||| | |||||| ||||||||||
Sbjct  88567  CTATGCAGGTCACATATTAGTGAAATTCCATCAGTGTTTGTGAAGTTCACGAATGAATGA  88626

Query  25718  attctttttttttttttttttttttttttttgtgacaaagtctacctctgtcacccagaa  25777
              |                    ||||||||||  |||||| ||| ||||||||||||||| 
Sbjct  88627  A--------------------TTTTTTTTTTCCGACAAATTCTCCCTCTGTCACCCAGAG  88666

Query  25778  cggtgtgcaatggtgcaatcttggctcactgcaaccattgccccctggattcaagcgatt  25837
               || |||||||||||||||||||| ||||||||||||||||| | ||| |||||||||||
Sbjct  88667  TGGAGTGCAATGGTGCAATCTTGGTTCACTGCAACCATTGCCTCTTGGGTTCAAGCGATT  88726

Query  25838  ctcccacctcagcctcctgagtagctggattacaggcacctgccatcatgccaggctaat  25897
              ||||||||||||||||||||||||||||||||||||||  ||||||| | || | |||||
Sbjct  88727  CTCCCACCTCAGCCTCCTGAGTAGCTGGATTACAGGCATGTGCCATCGTCCCTGCCTAAT  88786

Query  25898  ttttgtgtttttgtagag-ctggggtttcatcatgttggccttgcaggtcttg-atcgcc  25955
              | |||| ||||||||||| | ||||||||| | ||||||||| ||  |||||| || | |
Sbjct  88787  TCTTGTATTTTTGTAGAGAC-GGGGTTTCACCTTGTTGGCCTGGCTCGTCTTGAAT-GTC  88844

Query  25956  tgacctcaggtgatccagccaacttggac-tctcaaagtgcagggattacaggtgtgagc  26014
              ||| ||||||||| ||| ||||||| | | || |||||||| ||||||||||| ||||||
Sbjct  88845  TGAACTCAGGTGACCCACCCAACTT-GTCTTCCCAAAGTGCTGGGATTACAGGAGTGAGC  88903

Query  26015  cacctcacccggcctttaatgaGTGAATTCTTGATTTCCACCCTATTCCTAACACTGTCA  26074
              |||||  ||||| ||| ||||| || |||||||||| ||||||||| |||||||||||||
Sbjct  88904  CACCTTGCCCGGTCTTGAATGAATGCATTCTTGATTCCCACCCTATCCCTAACACTGTCA  88963

Query  26075  ATTTCTTGATTCATGAACTTAATATGGATAGCTGATATGAATGGATATCTGATTCAATCC  26134
              |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct  88964  ATTTCTTGATTCATGAACTTAATATGGATATCTGATATGAATGGATATCTGATTCAATCC  89023

Query  26135  AGTAATCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGGGTGGAGCTTCAGAAATGC  26194
              | ||||||||||| |||||||| |||||||| ||||||||||||||||||||||||||||
Sbjct  89024  ATTAATCTGGGGAGAGCCAAAACCCCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGC  89083

Query  26195  AATCAGATAGCACTTTTTGATTGGAAGCAAGCACTGGATA-GATGGAGGGGTGTGGGTGG  26253
              ||||||||| ||||| |||||||||||| |||| |||||| | |||||||||||||||||
Sbjct  89084  AATCAGATATCACTTGTTGATTGGAAGCTAGCAGTGGATACG-TGGAGGGGTGTGGGTGG  89142

Query  26254  GAGTTGTGATTAGAAAGATCGATAAAAGTTTCTGAAGGCCCACAGGAGAGACCCAAAGTC  26313
              ||||||||||||||||| || ||||||| |||| ||| ||||||| ||||||||||||||
Sbjct  89143  GAGTTGTGATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGAAGAGACCCAAAGTC  89202

Query  26314  TTCAAGTCTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTAAGCACTCTGCAAACTCAGTC  26373
              |||||| |||||||||||||||  ||||||||||||||| ||||| || |||||| ||||
Sbjct  89203  TTCAAGCCTGGAGTTCCTGCTTATTTCTTCCTGAGGTCTGAGCACCCTCCAAACTGAGTC  89262

Query  26374  CAGATCTAGTAAGTCACTCAT-T-TCTGGAAGGACACTCCCATCTGACCTATAGTCAGCC  26431
              ||||||| |||||||||| || | |||| ||||||||||||| |||||||| ||||||| 
Sbjct  89263  CAGATCTGGTAAGTCACTAATCTCTCTGTAAGGACACTCCCAACTGACCTACAGTCAGCT  89322

Query  26432  GGTCTGGGACGGGGGCAATGCAGCCTATGATGGCACCGAGCTATAT-CTGTCTTT-tata  26489
              ||||||||| || | || ||||||||| |||||||  ||| ||||| |||| ||| | | 
Sbjct  89323  GGTCTGGGATGGTGACAGTGCAGCCTAAGATGGCATAGAGTTATATCCTGT-TTTGT-TT  89380

Query  26490  tatatat-atatGAACAATTTGAAGATTTGAATTTTTTCCTCTATATGCAGTTTTGTCTT  26548
              | | | | ||||||||||||||||| |||| ||||||||||||| |||||||||||||||
Sbjct  89381  TTTTTCTCATATGAACAATTTGAAGCTTTGCATTTTTTCCTCTAAATGCAGTTTTGTCTT  89440

Query  26549  TATTTCAAAAAATTGGATTGTGCTTTGGTTTATGTCATTTcaaaattcttgatgggagca  26608
              |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Sbjct  89441  TATTTCAAAAAATTGGATTGTGCTTTGGTTTATGTCATTTCAAAATTCTTGAAGGGAGCA  89500

Query  26609  atgactcatgcccataacctcaacaccttgggaggccaaagcgggaggatcatttgagcc  26668
               |||||||||||  ||||| |||||| ||||||| |||| ||||||||||||||| ||||
Sbjct  89501  GTGACTCATGCCTTTAACCCCAACACTTTGGGAGACCAAGGCGGGAGGATCATTTCAGCC  89560

Query  26669  caggggtttgagaccaacctgggcaacatggcaaaaatgcagctctacaaaacattcttt  26728
              ||||||| |||||||||||||| ||||| ||||||||  || ||||| |||| |||| ||
Sbjct  89561  CAGGGGTCTGAGACCAACCTGGACAACACGGCAAAAACCCATCTCTATAAAATATTC-TT  89619

Query  26729  ttttgaagcagggatggagtctcaccctgttgccaaggctggagtgcagtggcaagagct  26788
              | ||||||  ||||||||||||| | ||||| |||||||||||||||||||||| || ||
Sbjct  89620  TATTGAAGGGGGGATGGAGTCTCGCTCTGTTTCCAAGGCTGGAGTGCAGTGGCACGATCT  89679

Query  26789  caactcactgcaacctcttcctcccaggctcaaacaattttcatgtctcagcttcctgag  26848
              ||| ||| |||||||||| |||||||||||||| ||||| ||||| |||||| |||||||
Sbjct  89680  CAAATCATTGCAACCTCTGCCTCCCAGGCTCAAGCAATTCTCATGCCTCAGCCTCCTGAG  89739

Query  26849  tagctggtattacatccctctgccaccatgtct-gcttaatttttgtatttttagtagtg  26907
              || ||||||||||||||  |||||| | || || || || |||||||||||||||||| |
Sbjct  89740  TATCTGGTATTACATCCAACTGCCAACTTGCCTGGC-TACTTTTTGTATTTTTAGTAGAG  89798

Query  26908  gtggggtttcaccatgctggccaggttggtctcaaactcctgacatcaagtgatcctcct  26967
              ||||||||||||||||||||||| |||||||||||||||||||| ||||||||||| |||
Sbjct  89799  GTGGGGTTTCACCATGCTGGCCAAGTTGGTCTCAAACTCCTGACCTCAAGTGATCCACCT  89858

Query  26968  gcctaggcc-cccaaaagtgctggaatgacggccgtgagccaATGGTGGTCAGCctctac  27026
              |||| |||| ||| |||||||||| || || ||| ||||||| ||||| |  ||||||||
Sbjct  89859  GCCTTGGCCTCCC-AAAGTGCTGGGATTACAGCCATGAGCCACTGGTGCTTGGCCTCTAC  89917

Query  27027  aaaatatatatatcttttaatttgccaggcatggtagcatgcatctgtattcccagctat  27086
              |||||||| |||| |||||||| ||| ||||||||||||||||||||| |||||| || |
Sbjct  89918  AAAATATACATATTTTTTAATTAGCCGGGCATGGTAGCATGCATCTGTCTTCCCAACTGT  89977

Query  27087  ttggtttgctgacatgggagaatcacttgagcccagaagattgaggctgcagtgagccat  27146
               ||| ||||||||||||||||| || ||||||||||||||||||||||||||||||||||
Sbjct  89978  ATGGGTTGCTGACATGGGAGAAACAATTGAGCCCAGAAGATTGAGGCTGCAGTGAGCCAT  90037

Query  27147  gctcacaccactgctgtactccagcctgggcaacagagtaagaccctgctaaaaacaaaa  27206
              ||||| |||||||||||||||||||||||||||||  |  ||  ||  ||    |   ||
Sbjct  90038  GCTCATACCACTGCTGTACTCCAGCCTGGGCAACATTGCGAG-GCC--CT----A-TTAA  90089

Query  27207  acgaaaacaaacaaacaaaaaacCTTAACCAAAGAGAATCTTTGACCTTAATTTTAAACC  27266
              | |          || |||||| ||||||||||||| |||||||||||||||||||||||
Sbjct  90090  A-G----------AA-AAAAAATCTTAACCAAAGAGGATCTTTGACCTTAATTTTAAACC  90137

Query  27267  AATCACATCCTCACTGTAATTCTTCCTCCCGAATGGAGACATgggtgt-gagggtgcatg  27325
              ||||||||||||| ||||| |||||| ||| || |||||||||||||| || ||||||||
Sbjct  90138  AATCACATCCTCATTGTAACTCTTCCACCCAAACGGAGACATGGGTGTGGA-GGTGCATG  90196

Query  27326  cctgtaatcccagctacatggaaggctgaagcatgagaattgcttgaatctcagaggcgg  27385
              |||||||||||||||||||||||||||||||||| || ||  |||||| ||  ||||| |
Sbjct  90197  CCTGTAATCCCAGCTACATGGAAGGCTGAAGCATAAGTATCACTTGAACCTGGGAGGCAG  90256

Query  27386  aagttacagtgagctgagatgg-agccgctgcactccagcctgggcgacaaagtgagact  27444
              | |||||||||||||||||||| | || ||| ||||||||||||| ||  ||||||||||
Sbjct  90257  AGGTTACAGTGAGCTGAGATGGCA-CCACTGTACTCCAGCCTGGGTGATGAAGTGAGACT  90315

Query  27445  cagcttcaccc-acaccaaaaaaaaTTAGATTATACCACCCAGGTGATCACTGGATACAT  27503
              ||||| | ||| ||| | |||||||||| ||||||||||||||||||||| ||||| |||
Sbjct  90316  CAGCTAC-CCCGACA-CGAAAAAAATTAAATTATACCACCCAGGTGATCATTGGATTCAT  90373

Query  27504  GAAGATTTCTATTGTGTGTTATTGGGGACTGTCAACTCCGTCTTTG-AAAACTGTTTTAA  27562
              ||||||||||| ||||| || || ||||||||||  ||  |||||| |||||||||||||
Sbjct  90374  GAAGATTTCTACTGTGTTTTCTTAGGGACTGTCATGTCTATCTTTGTAAAACTGTTTTAA  90433

Query  27563  CTCTGAAATATTTTGATAAATTTGATGTGGCCAAGGATCCCTCAACAAAGATACTTTCAA  27622
              ||||||||||||||||||||||||||||||||||||||| |||||||||||||||||| |
Sbjct  90434  CTCTGAAATATTTTGATAAATTTGATGTGGCCAAGGATCTCTCAACAAAGATACTTTCGA  90493

Query  27623  GTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGATTCAACACTTCCCTATCTCACACTCA  27682
              ||||| |||||||||||||||| ||||||||||||||||| |||||||||||||||||||
Sbjct  90494  GTTTT-TTTCTTTCTGTCTAATGTCAGGAAGAGATTCAACTCTTCCCTATCTCACACTCA  90552

Query  27683  GGACTATGAAGGACACATATTAGTAAACCTCCATGTTTGTGGAGGGAATCAGTGAATGAG  27742
              | ||||  |||| ||||||||| ||||  |||||||||||||||  ||||||||||||||
Sbjct  90553  GAACTACAAAGGTCACATATTACTAAAATTCCATGTTTGTGGAGTAAATCAGTGAATGAG  90612

Query  27743  TCCTGGACTTTCACCCTATCCCTAAATCTTTCACTTTCATGGATGAATATCTAATTCAAT  27802
              ||||||||||||||| ||||||| ||| ||||||||||||||||||||||||||||  ||
Sbjct  90613  TCCTGGACTTTCACCATATCCCTGAATATTTCACTTTCATGGATGAATATCTAATTTGAT  90672

Query  27803  CAGTTAATCTGGAAGAAAGCCAAAAATCCAATCAGGATTAACTGGGTAGAGTTTAAGAAG  27862
               |||||||||||||||||| |||||||||||||| |||||||||| | ||| ||||||||
Sbjct  90673  -AGTTAATCTGGAAGAAAGACAAAAATCCAATCATGATTAACTGGATGGAGCTTAAGAAG  90731

Query  27863  TCGAATCAAATGTAGTtctctctctctctctctctcttttcttttctttttttttttttt  27922
              || |||| |||||||     | ||||||||||||||   ||   ||              
Sbjct  90732  TCTAATCCAATGTAG-----T-TCTCTCTCTCTCTC---TC---TC--------------  90765

Query  27923  ttttttgaatctagcctatttcacaggctggagtgcagtggtgtattgtcagctcactgc  27982
              |||||||||||||||| ||||| ||||||||| || |||||| || | |||||| |||||
Sbjct  90766  TTTTTTGAATCTAGCCAATTTCCCAGGCTGGATTGTAGTGGTATAATCTCAGCTAACTGC  90825

Query  27983  aacctctgcctcctgggttcaagtgatcctcctgcctcagcctccctagtagcttggact  28042
              ||||| ||||||||||||||||| ||||||||||| ||||||||||||||||||||||||
Sbjct  90826  AACCTATGCCTCCTGGGTTCAAGCGATCCTCCTGCTTCAGCCTCCCTAGTAGCTTGGACT  90885

Query  28043  ataggcgcagaccaccgcacctggctaatttttctaattttggtagaggtagggttttac  28102
              ||||||||||||||| ||||||||||||||||| ||||||| |||||||||| |||||||
Sbjct  90886  ATAGGCGCAGACCACTGCACCTGGCTAATTTTTGTAATTTTAGTAGAGGTAGTGTTTTAC  90945

Query  28103  catgttggccaggctggtctcaaactcctgacctcagataatccacctgcctctgcctcc  28162
              ||||||||||||| |||||||||||||||||||||||||||||||  |||||||||||||
Sbjct  90946  CATGTTGGCCAGGATGGTCTCAAACTCCTGACCTCAGATAATCCA-ATGCCTCTGCCTCC  91004

Query  28163  cagagggctgggattacaggtgtgagtcactgcacacagccAAAGTGGTTCATTTTGAAT  28222
              || || ||||||||||||||||||||||||||| ||||||||||||||||||||||||| 
Sbjct  91005  CAAAGTGCTGGGATTACAGGTGTGAGTCACTGCGCACAGCCAAAGTGGTTCATTTTGAAC  91064

Query  28223  ATGTGTGAGAGGTGTGTATTGGAAACATCTGTGTCTTGCCAATGATGCATAACACTGTCA  28282
              ||| || |||||||||||||||||||||||||||||||| ||||||||||||||||||||
Sbjct  91065  ATGCGTAAGAGGTGTGTATTGGAAACATCTGTGTCTTGCGAATGATGCATAACACTGTCA  91124

Query  28283  CATAGCTTTCAAAGCTTCTTGCTGAAATTTTCAATAATGAGACCAGgcagaggctcatgc  28342
              || |||||||||||||||||| ||||||||||||||||||| || || ||||| | | ||
Sbjct  91125  CACAGCTTTCAAAGCTTCTTGGTGAAATTTTCAATAATGAGTCCGGGAAGAGGATTACGC  91184

Query  28343  ctgcaatcccagcactttgggaggccaaagtgggtggattgtttgagtctaggagttcaa  28402
              ||| |||||||| ||||||||||||||| | ||||||| |||||||||||||||||||||
Sbjct  91185  CTGTAATCCCAGTACTTTGGGAGGCCAAGGCGGGTGGAATGTTTGAGTCTAGGAGTTCAA  91244

Query  28403  gaccagcctggacaacatagtgaaacccactgtctttacaaaaagtcaaaaaataaaaGA  28462
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  91245  GACCAGCCTGGACAACATAGTGAAACCCACTGTCTTTACAAAAAGTCAAAAAATAAAAGA  91304

Query  28463  TTAGCTGGGTACGAGATCTGAGCTTCAGAGATCCTCGGTAACATTTGCCAGTGCTATGAG  28522
              ||||||||| | |||||| ||||||||||||||||||||||||||| |||||||||||||
Sbjct  91305  TTAGCTGGGCATGAGATCCGAGCTTCAGAGATCCTCGGTAACATTTCCCAGTGCTATGAG  91364

Query  28523  TTTAGTGGATCAGTGGCTAATAATTCATGGACTACGAGGGATCTTGCCTGCTCTTTAGAA  28582
              |||| || | |||||||||||||||||||||||| |||||||||||||||||||||||| 
Sbjct  91365  TTTATTGCAACAGTGGCTAATAATTCATGGACTAGGAGGGATCTTGCCTGCTCTTTAGAG  91424

Query  28583  GTTGGGACACATTCTTCATGGTACCAGAAGGGTAGAACTATGTCTCTGTGGCCACTTATT  28642
              ||||||||||| ||||| |||||||||||||| ||||| ||| |||||| ||||||||||
Sbjct  91425  GTTGGGACACACTCTTCTTGGTACCAGAAGGGCAGAACCATGCCTCTGTAGCCACTTATT  91484

Query  28643  GCAGAAAGGAACTGGAGTAAACTGAGGGCTCTTTCACACATGCTAGAGAAATGACTTGGG  28702
              |||||| |||| ||||||||||||||||||||||||||| ||||||||||||||||| ||
Sbjct  91485  GCAGAACGGAATTGGAGTAAACTGAGGGCTCTTTCACACGTGCTAGAGAAATGACTTTGG  91544

Query  28703  CCCTGGGAGAATTGGGGGTTGCAGGGGATTGGTCGGAGGAACTTGCCTTTTTGCTGGATT  28762
              |||| |||||| ||||| |||| ||||| ||| | ||| ||||||||||||  || ||||
Sbjct  91545  CCCTAGGAGAAGTGGGGCTTGCTGGGGAATGGCCCGAGAAACTTGCCTTTTCACTTGATT  91604

Query  28763  GTGCTGTAGAGTTTTTCCTTGTAGATTTGTCAGAATGAGCCTCCAGACCCCATCCAGACT  28822
              || || ||||||||||||| | |||||||||||||||||||||||| |||||||||||||
Sbjct  91605  GTCCTCTAGAGTTTTTCCTCGGAGATTTGTCAGAATGAGCCTCCAGGCCCCATCCAGACT  91664

Query  28823  CCTGGAGCTGGCAGGGCAGAGCCTGATGAGGAAGCAGTTCTTGACTATCTTCACCCTGGA  28882
               |||||||||||||||||||||||| ||||||| ||||||||||| ||||||||||||||
Sbjct  91665  GCTGGAGCTGGCAGGGCAGAGCCTGCTGAGGAACCAGTTCTTGACCATCTTCACCCTGGA  91724

Query  28883  CT-AGCTGCCCAGGGAGGTCTCCCCTCTGACGTTCATGGAGGCCTTCAGCATGAGATGTT  28941
               | |||||||||||||||||| |||||||| ||||||||||||||||||||||||| |||
Sbjct  91725  -TGAGCTGCCCAGGGAGGTCTTCCCTCTGATGTTCATGGAGGCCTTCAGCATGAGACGTT  91783

Query  28942  GTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGTCCTCCCTTCACCTCCCTCTGGGATCCC  29001
               ||||||||||||||||||||||||||||||| ||| ||| | |||||||||||||||||
Sbjct  91784  TTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGCCCTTCCTCCGCCTCCCTCTGGGATCCC  91843

Query  29002  TGATGAAGACAACTCATCTGGAGACCTTGCAAGCTGTGCTGAAGGGACTTGATACACTAG  29061
              ||||||||||| ||||||||||||||||||||||||| |||| ||||||||||||||| |
Sbjct  91844  TGATGAAGACACCTCATCTGGAGACCTTGCAAGCTGTCCTGAGGGGACTTGATACACTGG  91903

Query  29062  TGTCCCAGAAGGTTTGCCCCAGTTGAGGTGACTCAGGTGGCCTG-GTGGGAAGGGTCCAG  29120
              || ||||||||||| ||||||| |||||||||||||||||| |  | |||||||||||||
Sbjct  91904  TGGCCCAGAAGGTTCGCCCCAGGTGAGGTGACTCAGGTGGCTTTCG-GGGAAGGGTCCAG  91962

Query  29121  GCATCCAGGGAAGGGACAGCTGGCTCAGGAGGAGTGGCAGTGTGTGGG-AGCTAGGGTGG  29179
              |||||||||||||||||||||||||||||||||||||  | || |||| |||||||||||
Sbjct  91963  GCATCCAGGGAAGGGACAGCTGGCTCAGGAGGAGTGGTGGGGT-TGGGGAGCTAGGGTGG  92021

Query  29180  CTCAGAGGCTTCTGATGGTACCCATGAGAGGCCTTGGCCATTGCCCAGATCCTCTGGAAA  29239
              ||||||||||||||| ||| ||||||||||||||||||||||||||||||||||||||||
Sbjct  92022  CTCAGAGGCTTCTGACGGTGCCCATGAGAGGCCTTGGCCATTGCCCAGATCCTCTGGAAA  92081

Query  29240  AGGACTGCTCACCATACAGAGTCCACTGAGGAAACAGGAACCTGCTTCCTTCCCAGTGGA  29299
              ||| ||||||||||||||| ||||||||||||||||||| |||||||||| |||||  ||
Sbjct  92082  AGGTCTGCTCACCATACAGGGTCCACTGAGGAAACAGGAGCCTGCTTCCT-CCCAGCAGA  92140

Query  29300  AGGTAAAGGTACTAGAAGTGGGTAC  29324
              | |||||||||||||||||||||||
Sbjct  92141  AAGTAAAGGTACTAGAAGTGGGTAC  92165


 Features flanking this part of subject sequence:
   25773 bp at 5' side: PRAME family member 3
   3198 bp at 3' side: PRAME family member 5

 Score = 4732 bits (2562),  Expect = 0.0
 Identities = 3795/4367 (86%), Gaps = 178/4367 (4%)
 Strand=Plus/Plus

Query  23894  gggaatgggactcctcctatcagttgttttttttttttaattttcttttgtttta-t--c  23950
              |||||||||| |||||||||||     || ||||||| ||||||||||||||||| |  |
Sbjct  37526  GGGAATGGGATTCCTCCTATCA----ATTATTTTTTTAAATTTTCTTTTGTTTTATTGAC  37581

Query  23951  ctggcaaggctctaatagagttgagcttttttgtttttgttttttccattggaagggaca  24010
              ||| |||||||| ||||||||||||  |||||||||| ||||||||||||||||| ||||
Sbjct  37582  CTGACAAGGCTCAAATAGAGTTGAG--TTTTTGTTTTCGTTTTTTCCATTGGAAGAGACA  37639

Query  24011  atacagaggttacaatcattgactttagatgacaacatgacaggca-aaaatattttcct  24069
              ||||||||||||||||||||| ||||||||||||| || | | | | |||| || |||||
Sbjct  37640  ATACAGAGGTTACAATCATTGGCTTTAGATGACAAGAT-AAAAGAATAAAACATATTCCT  37698

Query  24070  tgcaagacaaccagcaaaacttcacgatcagaatcaaatcagtgtccttctcactgtcac  24129
              |||||||||||||||||||||||| |||||  |||||||||||| |||||||||||||| 
Sbjct  37699  TGCAAGACAACCAGCAAAACTTCATGATCACCATCAAATCAGTG-CCTTCTCACTGTCAG  37757

Query  24130  tgggt-gaagccttcatcagtacttgaagagtctcaggcactcatgaagtcaagatcaga  24188
              ||||| ||||||||||||| |||||| ||||| | ||||||||||||| |||  || |||
Sbjct  37758  TGGGTGGAAGCCTTCATCAATACTTGCAGAGTTTGAGGCACTCATGAACTCACCATGAGA  37817

Query  24189  ttctttactcagggacaggatgtaagccaatcataagaccttccacagatgatcaatttg  24248
              |||||||||||||||||||||||||||||| || |||||||||||||| || | ||||||
Sbjct  37818  TTCTTTACTCAGGGACAGGATGTAAGCCAAGCAAAAGACCTTCCACAGGTGGTGAATTTG  37877

Query  24249  gaagtctacctaatgtgacctgcaggttttcaCTGGCAATATGCAGGTGCAGATATGACA  24308
              |||| || || ||||| ||||||| |||||||||||||||||||||||||||||||||||
Sbjct  37878  GAAGCCTGCCCAATGTAACCTGCAAGTTTTCACTGGCAATATGCAGGTGCAGATATGACA  37937

Query  24309  AAGAATAATCC-TGACCTTCATATCGCCCCTAGCTGATGAGGATTGGGATTCTTTTGTCC  24367
              |||||||| || ||||||| | ||| |||| ||||| |||||| |||||| |||||| ||
Sbjct  37938  AAGAATAA-CCATGACCTTTACATCACCCCCAGCTGTTGAGGAATGGGATCCTTTTGACC  37996

Query  24368  CTTTCTCTCCATAAAACCAGGTTACTCATCTTGTGTGGCAACAAAATATATGGTctactt  24427
              |||||| |||||| ||||||||| |||||||||||||||||||| |||| ||||||||||
Sbjct  37997  CTTTCTGTCCATAGAACCAGGTTGCTCATCTTGTGTGGCAACAACATATGTGGTCTACTT  38056

Query  24428  aacagagaaag-agactccacaggaaaaaaaaaaggatttttattatgaaatgagcaaag  24486
              ||||||| ||| |||||   |  |   |||||||  || ||||||||| | | |||||||
Sbjct  38057  AACAGAG-AAGAAGACT---C-TG--TAAAAAAA--ATGTTTATTATGTAGTAAGCAAAG  38107

Query  24487  ccatgggaatagatgtgagattattcggggaggtaaaggaagacaaaggttttgaaagga  24546
                ||||||||||||||||||||||| |||||| |||||||||   |||||||||||||||
Sbjct  38108  AAATGGGAATAGATGTGAGATTATTTGGGGAGATAAAGGAAGTTGAAGGTTTTGAAAGGA  38167

Query  24547  aaaatgaggagaattacataaatttttttgaaagactcattcttggtcacaagtatgaaa  24606
              ||||| ||||| |||| | ||||| ||||||||||||||| ||||||||  || || |||
Sbjct  38168  AAAATAAGGAGGATTATACAAATTGTTTTGAAAGACTCATACTTGGTCATGAGGATTAAA  38227

Query  24607  acc-aagggagcctcagtgcagtgttggaaagATTCCTCCTCCACCCTCTCAATAACCCC  24665
              ||| || || || |||||||| |||| || ||||||||| | ||||| ||| ||||||||
Sbjct  38228  ACCAAAAGG-GCATCAGTGCAATGTTAGATAGATTCCTCTTACACCCACTCGATAACCCC  38286

Query  24666  CAACACATTTACCAAGTCTTTGTTCACTCCCAGGATT-CCATTAAAACACCCAGCTCAAC  24724
              |||||  || | |||||||| ||||||||||||| || ||||||||| ||||||||||||
Sbjct  38287  CAACATGTTCAGCAAGTCTTGGTTCACTCCCAGG-TTCCCATTAAAA-ACCCAGCTCAAC  38344

Query  24725  CCTGACCAGCCTCCACCTTCACTTCCCTTTGTAATTTTGACATAAATTtgttacaggacc  24784
              ||||||||| ||||||| |||||||| |||||||||||||||| | ||| ||||||||||
Sbjct  38345  CCTGACCAG-CTCCACCCTCACTTCCATTTGTAATTTTGACATGACTTTATTACAGGACC  38403

Query  24785  atcaggttcctatgccggctgcacagtagcttaccaatattctgagacagcaggatttgc  24844
              |||||||||||||||| |||||||||||||||| |||||||||||||||||||| |||||
Sbjct  38404  ATCAGGTTCCTATGCCTGCTGCACAGTAGCTTAGCAATATTCTGAGACAGCAGGGTTTGC  38463

Query  24845  agcagaaagtttaatgatcacagggtggctgaatgagaagctgggaggagatcctcaaat  24904
              |||||| ||||||||||||||| ||||||||||||||||||| |||||||||||||||||
Sbjct  38464  AGCAGAGAGTTTAATGATCACAAGGTGGCTGAATGAGAAGCTAGGAGGAGATCCTCAAAT  38523

Query  24905  tcatctccccaaggagtactgagggtttccagtggatcctggatagcaaggggctggaaa  24964
              |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
Sbjct  38524  TCATCTCCCCAAGGAGTACTGAGGGTTTCCAGTGGATCCTGGATAGCAAGGGGCCGGAAA  38583

Query  24965  gttggtgtagtttgatggcaataagaggtatgaagttatcacgatgtcag-aacggcatt  25023
              ||||| |  |  | |  ||  ||||||| | ||||| | || ||||| || ||| |||||
Sbjct  38584  GTTGG-G--G--T-A--GCGGTAAGAGGGAAGAAGTCAACAGGATGT-AGAAACTGCATT  38634

Query  25024  ctttggtgagttgatgccttgcagggcccttcagatcagctggcatcagtagtttcactg  25083
              ||||||||||||| ||| |||||||||||||||||||||||||||||||||| |||||||
Sbjct  38635  CTTTGGTGAGTTGGTGCATTGCAGGGCCCTTCAGATCAGCTGGCATCAGTAGATTCACTG  38694

Query  25084  acatgcagaacctgaaagaatatctcaaatgaaaaacttaatgtttcacaatgcttaaat  25143
              ||||||||||||||||||||||||||| |||||||| ||||||||| |||||||||||||
Sbjct  38695  ACATGCAGAACCTGAAAGAATATCTCAGATGAAAAAGTTAATGTTTTACAATGCTTAAAT  38754

Query  25144  tgttgtctgcagcgtagttaaggggaattgtagtctaagttctacacgattttgggacag  25203
               ||||||||||| | |||||||||||| |||| |||||| |||| | |||||||| ||||
Sbjct  38755  GGTTGTCTGCAGGGAAGTTAAGGGGAACTGTAATCTAAGGTCTATATGATTTTGGAACAG  38814

Query  25204  taggctgccagcaaccatgaggaagcaggtcagagggcaagctgacctcctggtgaatgc  25263
              |||| ||||||||||||||||||| |||||||||| |||||  ||||||||| |||||||
Sbjct  38815  TAGGTTGCCAGCAACCATGAGGAACCAGGTCAGAGAGCAAGAAGACCTCCTGATGAATGC  38874

Query  25264  tgaatgcgtttcaagcttggtttgtttttgttcctccccctctctttttcaccgattaaa  25323
              |||||| ||| |||||||||||| |||||||| ||| ||||| ||| ||||| |||||||
Sbjct  38875  TGAATGTGTTCCAAGCTTGGTTTATTTTTGTTTCTCTCCCTCCCTTCTTCACTGATTAAA  38934

Query  25324  tttataaagtttagaaatacggtttcaATTTCTTCCAGACAAGCCTTAACCTAAGCCCTG  25383
              |||||||||||||   ||  || |||||||||||||| | ||| ||||||||||||||||
Sbjct  38935  TTTATAAAGTTTATCGATGTGGCTTCAATTTCTTCCAAAGAAGACTTAACCTAAGCCCTG  38994

Query  25384  AGACCACTCAAGCCCTCAGTGGCACCTCTCTTCCACCAGCATGAGCAAATAAAT-TGCTA  25442
              |||||||||| ||||||||||||||||||| |||||||| | |||||  | ||| |||||
Sbjct  38995  AGACCACTCACGCCCTCAGTGGCACCTCTCCTCCACCAGAACGAGCATGT-AATCTGCTA  39053

Query  25443  CCTTAGGTGATATAAAA-CCCACAAGATGATTCGA-TACATGGAG-ttttttttCTGATT  25499
              |||||||| ||| |||| |||  ||||  |||| | ||||| ||| ||||| ||||||||
Sbjct  39054  CCTTAGGTTATACAAAATCCC-GAAGACCATTC-AGTACATTGAGATTTTTATTCTGATT  39111

Query  25500  TTGTAGGGATGACTTCTTTGTTTCTATAAAGCTGTTTT-AACTATAAAACAATTTTATAA  25558
              |  |||||| |||| || ||||| ||||||||| |||| || || ||| || |||||| |
Sbjct  39112  TCCTAGGGACGACTCCTCTGTTTTTATAAAGCT-TTTTAAAGTAGAAAGCATTTTTAT-A  39169

Query  25559  TTTTGATGTGGCCAAAGATCTCC---CAACACTACTTTCAGGTTTTATTTTTCTGTCTAC  25615
              |||||||||||||||||||||||   ||||||||||||||| ||||||||||||||||| 
Sbjct  39170  TTTTGATGTGGCCAAAGATCTCCTAACAACACTACTTTCAGATTTTATTTTTCTGTCTAA  39229

Query  25616  TATCCAGAACAGATCAAACCCTTCCCTGCCTCAAACTCAGGACTAT-ATAGGTCATATAT  25674
              | |   |||||||||||| ||||||||||||   ||||| |||||| | || ||| ||||
Sbjct  39230  TGTTGGGAACAGATCAAATCCTTCCCTGCCTGTCACTCAAGACTATGA-AGTTCACATAT  39288

Query  25675  CAGTAAAATTCCATCAGTGTTTGCGGAgttcatgaatgaatgaattcttttttttttttt  25734
               |||||||| ||||||||||||| |||||||||||||||||| |                
Sbjct  39289  TAGTAAAATACCATCAGTGTTTGTGGAGTTCATGAATGAATG-A----------------  39331

Query  25735  ttttttttttttttgtgaca-aagtctacctctgtcacccagaac-ggtgtgcaatggtg  25792
               ||||||| ||||| ||||| || | | |||||||||||||| || || ||||| |||  
Sbjct  39332  -TTTTTTTATTTTT-TGACAGAA-TGTCCCTCTGTCACCCAG-ACTGGAGTGCAGTGGCA  39387

Query  25793  caa-tcttggctcactgcaaccattgccccctggattcaagcgattctcccacctcagcc  25851
              ||| || ||||||||||||||||||||| ||||| ||||||| |||||||  ||||||||
Sbjct  39388  CAATTC-TGGCTCACTGCAACCATTGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCC  39446

Query  25852  tcctgagtagctggattacaggcacctgccatcatg-ccaggctaatttttg------tg  25904
              |||  ||||||||| || |||||||||||||||||| ||||| |||||||||      ||
Sbjct  39447  TCCCAAGTAGCTGGGTTTCAGGCACCTGCCATCATGCCCAGG-TAATTTTTGTATTTTTG  39505

Query  25905  --tttttgtagag-ctggggtttcatcatgttggccttgcaggtcttgatcgcctgacct  25961
                ||||||||||| |  |||||||| | | ||| ||| ||  ||||||| | |||||| |
Sbjct  39506  TATTTTTGTAGAGAC-AGGGTTTCACCTTTTTGACCTGGCTCGTCTTGAACCCCTGACAT  39564

Query  25962  caggtgatccagc-caacttggac-tctcaaagtgcagggattacaggtgtgagccacct  26019
              ||||||||| | | || ||||  | || |||||||| || ||||||| | ||| ||||||
Sbjct  39565  CAGGTGATCTA-CTCACCTTGTCCTTC-CAAAGTGCTGGAATTACAGCTATGAACCACCT  39622

Query  26020  cacccggcctttaatgaGTGAATTCTTGATTTCCACCCTATTCCTAACACTGTCAATTTC  26079
              |||||  |||| ||||| || |||||||| ||| ||||||| |||| ||||||| |||||
Sbjct  39623  CACCCACCCTTGAATGAATGTATTCTTGACTTCTACCCTATCCCTACCACTGTCGATTTC  39682

Query  26080  TTGATTCATGAACTTAATATGGATA-GCTGATATGAATGGATATCTGATTCAATCCAGTA  26138
              ||| |||||||| | ||||| |||| | ||||||||||||| |||||||||||||| |||
Sbjct  39683  TTGCTTCATGAAGTGAATATAGATATG-TGATATGAATGGACATCTGATTCAATCCGGTA  39741

Query  26139  ATCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGGGTGGAGCTTCAGAAATGCAATC  26198
              ||||||||| ||||||||||||||||| ||||||||||||||||||||| ||||||||||
Sbjct  39742  ATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCACAAATGCAATC  39801

Query  26199  AGATAGCACTTTTTGATTGGAAGCAAGCA-CTGGATA-GATGGAGGGGTGTGGGTGGGAG  26256
              ||||| || ||||||||||||||  |||| | ||||| | || ||||| |||||||||||
Sbjct  39802  AGATATCATTTTTTGATTGGAAGGTAGCAGC-GGATATG-TGCAGGGGCGTGGGTGGGAG  39859

Query  26257  TTGTGATTAGAAAGATCGATAAAAGTTTCTGAAGGCCCACAGGAGAGACCCAAAGTCTTC  26316
              |||||||||||||| || ||||||| |||| ||| |||||||||||||||||||||||||
Sbjct  39860  TTGTGATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGAGAGACCCAAAGTCTTC  39919

Query  26317  AAGTCTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTAAGCACTCTGC-AAACT-CAGTCC  26374
              ||| ||||||||||||||||||||||||||||| || ||||| || | | ||| || |||
Sbjct  39920  AAGCCTGGAGTTCCTGCTTGGTTCTTCCTGAGGACTGAGCAC-CTTCTAGACTACA-TCC  39977

Query  26375  AGATCTAGTAAGTCACTCATTTCTGGAAGGACACTCCCATCTGACCTATAGTCAGCCGGT  26434
              |||||| ||||| |||| ||||||| |||||||||||||||||||||| |||||| ||||
Sbjct  39978  AGATCTGGTAAGCCACTAATTTCTGTAAGGACACTCCCATCTGACCTACAGTCAGTCGGT  40037

Query  26435  CTGGGACGGGGGCAATGCAGCCTATGATGGCACCGAGCTATAT-CTGT-CTTTtatatat  26492
              |||||| || | || ||||||||| |||||||| ||||||||| |||| ||||| | | |
Sbjct  40038  CTGGGATGGTGACAGTGCAGCCTACGATGGCACAGAGCTATATCCTGTCCTTTT-T-T-T  40094

Query  26493  atat-atatGAACAATTTGAAGATTTGAATTTTTTCCTCTATATGCAGTTTTGTCTTTAT  26551
               | | |||||||||||||||||  |||||| |||||||||| |||||||| |||||||||
Sbjct  40095  -TTTCATATGAACAATTTGAAG-CTTGAATGTTTTCCTCTAAATGCAGTTCTGTCTTTAT  40152

Query  26552  TTCAAAAAA-TTGGATTGTGCTTTGGTTTATGTCATTTcaaaattcttgatgggagcaat  26610
              ||||||||| || ||||||||||||||| ||| ||||| ||||||| ||| |||||||||
Sbjct  40153  TTCAAAAAAGTT-GATTGTGCTTTGGTTGATGCCATTTTAAAATTCGTGAAGGGAGCAAT  40211

Query  26611  gactcatgcccataacctcaacaccttgggaggccaaagcgggaggatcatttgagccca  26670
              |||||||| |  ||||| |||||| |||||||||||||| ||||||||||||| ||||||
Sbjct  40212  GACTCATGTCTTTAACCCCAACACTTTGGGAGGCCAAAGTGGGAGGATCATTTCAGCCCA  40271

Query  26671  ggggtttgagaccaacctgggcaacatggcaaaaatgcagctctacaaaac---attctt  26727
              |||||||||||||||||||||||||||| |||||   |  ||||||| |||    || ||
Sbjct  40272  GGGGTTTGAGACCAACCTGGGCAACATGACAAAAGCCCTCCTCTACACAACGTTTTTTTT  40331

Query  26728  tttttga-agcagggatggagtctcaccctgttgccaaggctggagtgcagtggcaagag  26786
              |||||||  |  |||||||||||||||  ||||||| || |||||||||||||||| || 
Sbjct  40332  TTTTTGAGGGTGGGGATGGAGTCTCACTGTGTTGCCCAGACTGGAGTGCAGTGGCACGAT  40391

Query  26787  ctcaactcactgcaacctctt-cctcccaggctcaaacaattttcatgtctcag-ct---  26841
              ||||| |||||||||||| || |||||| || |||| ||||||||||| ||||| ||   
Sbjct  40392  CTCAAATCACTGCAACCT-TTACCTCCCGGGTTCAAGCAATTTTCATGCCTCAGTCTCCA  40450

Query  26842  tcctgagtagctggtattacatccctctgccaccatgtct-gcttaatttttgtattttt  26900
              |||| || ||||||| | |||  | ||||  |||||| || || ||||||||||||||||
Sbjct  40451  TCCTCAGAAGCTGGTGTCACAGACATCTGAAACCATGCCTGGC-TAATTTTTGTATTTTT  40509

Query  26901  agtagtggtggggtttcaccatgctggccaggttggtctcaaactcctgacatcaagtga  26960
              ||||| |||||||||||||||||||||||||||||||||| ||| |||||| ||||||||
Sbjct  40510  AGTAGAGGTGGGGTTTCACCATGCTGGCCAGGTTGGTCTCGAACACCTGACCTCAAGTGA  40569

Query  26961  tcctcctgcctaggcc-cccaaaagtgctggaatgacggccgtgagccaATGGTGGTCAG  27019
              ||| ||||||| |||| ||| |||||||||| || || || ||||| || ||||| |  |
Sbjct  40570  TCCACCTGCCTTGGCCTCCC-AAAGTGCTGGGATTACAGCTGTGAGTCACTGGTGCTTGG  40628

Query  27020  Cctctacaaaatatatatatcttttaatttgccag-gcatggtag-catgcatctgtatt  27077
              |||||||    | | | | | |||||||| ||| | ||||||| | |||||||||||| |
Sbjct  40629  CCTCTAC----T-TTTTTTTATTTTAATTAGCC-GAGCATGGT-GACATGCATCTGTAGT  40681

Query  27078  cccagctatttggtttgctgacatgggagaatcacttgagcccagaagattgaggctgca  27137
              ||||||||||||| | ||||   |||||||||||||||||||||||||||||||||||||
Sbjct  40682  CCCAGCTATTTGGGTGGCTGGTGTGGGAGAATCACTTGAGCCCAGAAGATTGAGGCTGCA  40741

Query  27138  gtgagccatgctcacaccactgctgtactccagcctgggcaacagagta-agaccctgct  27196
              |||||||||||||||||||||||||||||||||||||||||| |||| | |||||||| |
Sbjct  40742  GTGAGCCATGCTCACACCACTGCTGTACTCCAGCCTGGGCAAAAGAG-AGAGACCCTG-T  40799

Query  27197  aaaaacaaaaacgaaaacaaacaaacaaaaaacCTTAACCAAAGAGAATCTTTGACCTTA  27256
                   |   ||  ||||| || ||||  || | |||||||||| || |||| ||||||||
Sbjct  40800  -----C--CAA--AAAAC-AA-AAAC--AATATCTTAACCAAAAAGGATCTATGACCTTA  40846

Query  27257  ATTTTAAACCAATCACATCCTCACTGTAATTCTTCCTCCCGAATGGAGACATgggtgtga  27316
              |||||||||||||||| ||||||||||||||||||| | |||||||||||||||||||| 
Sbjct  40847  ATTTTAAACCAATCACGTCCTCACTGTAATTCTTCCACTCGAATGGAGACATGGGTGTGG  40906

Query  27317  gggtgcatgcctgtaatcccagctacatggaaggctgaagcatgagaattgcttgaatct  27376
              |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
Sbjct  40907  GGGTGCATGCCTGTAATCCCAGCTACGTGGAAGGCTGAAGCATGAGAATTGCTTGAATCT  40966

Query  27377  cagaggcggaagttacagtgagctgagatggagccgctgcactccagcctgggcgacaaa  27436
              |||||| ||| |||||||||||||||||||| ||||||||||||||||||||||||||||
Sbjct  40967  CAGAGGTGGAGGTTACAGTGAGCTGAGATGGCGCCGCTGCACTCCAGCCTGGGCGACAAA  41026

Query  27437  gtgagactcagcttcacccacaccaaaaaaaaTTAGATTATACCACCCAGGTGATCACTG  27496
              ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||
Sbjct  41027  GTGAGACTCAGCTTCCCCCACACCAAAAAAAATTAGATTATACCACCCAGGTGATCATTG  41086

Query  27497  GATACATGAAGATTTCTATTGTGTGTTATTGGGGACTGTCAACTCCGTCTTTGAAAACTG  27556
              ||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||
Sbjct  41087  GATACATGAAGATTTCTATTGTGTGTTCTTGGGGACTGTCAACTCTGTCTTTGAAAACTG  41146

Query  27557  TTTTAACTCTGAAATATTTTGATAAATTTGATGTGGCCAAGGATCCCTCAACAAAGATAC  27616
              |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Sbjct  41147  TTTTAACTCTGAAATATTTTGATAAATTTGATGTGGCCGAGGATCCCTCAACAAAGATAC  41206

Query  27617  TTTCAAGTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGATTCAACACTTCCCTATCTCA  27676
              ||||||||||| || ||||||||||||||||||||||||||||||| |||||||||||||
Sbjct  41207  TTTCAAGTTTT-TT-CTTTCTGTCTAATATCAGGAAGAGATTCAACCCTTCCCTATCTCA  41264

Query  27677  CACTCAGGACTATGAAGGACACATATTAGTAAA-CCTCCAT---GTTTGTGGAGGGAATC  27732
              ||||||||||| |||||||||||||||| |||| || ||||   ||||||| ||||||||
Sbjct  41265  CACTCAGGACTGTGAAGGACACATATTAATAAAACC-CCATTTTGTTTGTGAAGGGAATC  41323

Query  27733  AGTGAATGAGTCCTGGACTTTCACCCTATCCCTAAATCTTTCACTTTCATGGATGAATAT  27792
              |||||||||||||||| ||| ||||| |||||||||||||||||||| |||| |||||||
Sbjct  41324  AGTGAATGAGTCCTGGGCTTCCACCCCATCCCTAAATCTTTCACTTTGATGGGTGAATAT  41383

Query  27793  CTAATTCAATCAGTTAATCTGGAAGAAAGCCAAAAATCCAATCAGGATTAACTGGGTAGA  27852
              ||||||| |||||| ||||||||||||||||||||||||||||||||||||||||||| |
Sbjct  41384  CTAATTCCATCAGTAAATCTGGAAGAAAGCCAAAAATCCAATCAGGATTAACTGGGTAAA  41443

Query  27853  GTTTAAGAAGTCGAATCAAATGTAGTtctctctctctc-tctctct----cttttctttt  27907
               ||        |||||||||| ||| |||||||||||| | | |||    ||||| ||||
Sbjct  41444  -TT--------CGAATCAAATCTAGCTCTCTCTCTCTCCTTTTTCTTTTTCTTTTTTTTT  41494

Query  27908  ctttttttttttttttttttt-gaatctagcctatttcacaggctggagtgcagtggtgt  27966
               |||||||||||||||||||| |||||||||||||||| ||||||||||| |||||||||
Sbjct  41495  TTTTTTTTTTTTTTTTTTTTTTGAATCTAGCCTATTTCCCAGGCTGGAGTTCAGTGGTGT  41554

Query  27967  attgtcagctcactgcaacctctgcctcctgggttcaagtgatcctcctgcctcagcctc  28026
              ||||||||||||||||||||||||||||||||||||||| |||| ||||| |||||||||
Sbjct  41555  ATTGTCAGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGCGATCTTCCTGTCTCAGCCTC  41614

Query  28027  cctagtagcttggactataggcgcagaccaccgcacctggctaatttttctaattttggt  28086
              ||||||||||||||||||||||||||||||||||| ||||||||||||| ||||||| ||
Sbjct  41615  CCTAGTAGCTTGGACTATAGGCGCAGACCACCGCAACTGGCTAATTTTTGTAATTTTAGT  41674

Query  28087  agaggtagggttttaccatgttggccaggctggtctcaaactcctgacctcagataatcc  28146
              ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||
Sbjct  41675  AGAGGTAGGGTTTTACCATGTTGGCCAGGCTTGTCTCAAACTCCTGACCTCAGATAATCC  41734

Query  28147  acctgcctctgcctcccagagggctgggattacaggtgtgagtcact  28193
              |||| ||||||| |||||||| |||||||||||||||||||| ||||
Sbjct  41735  ACCTACCTCTGCGTCCCAGAGTGCTGGGATTACAGGTGTGAGCCACT  41781


 Features flanking this part of subject sequence:
   16338 bp at 5' side: PRAME family member 8
   14600 bp at 3' side: PRAME family member 9

 Score = 3825 bits (2071),  Expect = 0.0
 Identities = 2976/3406 (87%), Gaps = 89/3406 (2%)
 Strand=Plus/Plus

Query  14528  GGTTGGTTAACATTTATAATTACATGACTTGGCACTGAGAAGAAGCTATAGGTGCAAATG  14587
              |||||||||| ||| ||||||| |||||||||||||||| ||||||||||| ||||||||
Sbjct  86128  GGTTGGTTAATATTGATAATTAAATGACTTGGCACTGAGCAGAAGCTATAGATGCAAATG  86187

Query  14588  GGTGGCCTATGACTATTATTGATTACATTACTGGCATTTTATCTCTATGCATAAAAAACA  14647
              ||||||||||||||||| |||||| ||||||| | |  ||||||| |||||||  |||||
Sbjct  86188  GGTGGCCTATGACTATTGTTGATTTCATTACTTGTAACTTATCTCCATGCATAGGAAACA  86247

Query  14648  TTAGTGAAACTGGATCTAATCTAGGTAGTGTCGCAGATTCCCAC-TAGAATCAAACTCTT  14706
              |||||| ||| || |||||||||||||||||| |||| |||| | | |||||||||||||
Sbjct  86248  TTAGTGTAACCGGGTCTAATCTAGGTAGTGTCCCAGACTCCC-CTTGGAATCAAACTCTT  86306

Query  14707  TGGTTTGACACACCTTATGAAGACTGGAGTGCTATAGGTATCGACATAGACATAGAATCA  14766
              |  |||||||||| |||||||||||| | ||||||| |||| |||||||||| |||||||
Sbjct  86307  TCATTTGACACACATTATGAAGACTGAAATGCTATAAGTATTGACATAGACACAGAATCA  86366

Query  14767  GAACATGACCATGTTACCCTCTGCCATTTAATCAGAGAACTTACTGAAACTAGACATTGG  14826
              |||||||||||||||| |||||||||| |||||||||||||||||||||||||||||| |
Sbjct  86367  GAACATGACCATGTTATCCTCTGCCATATAATCAGAGAACTTACTGAAACTAGACATTTG  86426

Query  14827  TTCATTGGAAACTCTAGAGGCAAATAGAATGTGTCTATAGCTCTACTATGTGAAATACAT  14886
              ||||||||||||||  |||||||||||||||  ||||||||||||| || ||||||| | 
Sbjct  86427  TTCATTGGAAACTC--GAGGCAAATAGAATGCATCTATAGCTCTACCATATGAAATAAAC  86484

Query  14887  AATAGTTTTATTTATTGGATGCATCAATACTCAGGACATATTTGGAGAGGAACCTATTCA  14946
              |||||||| |||||||||||||||| |||||||| ||||||||||||| || ||||||||
Sbjct  86485  AATAGTTTCATTTATTGGATGCATCCATACTCAGCACATATTTGGAGAAGACCCTATTCA  86544

Query  14947  TTCTTCAATGCAGATGGCATGCAAGGATTACT-TTATAAAACTCATAGAAATACTTTTTC  15005
              |||||||||| ||||| ||||||||||||| | | |||||| ||||| ||||| ||||||
Sbjct  86545  TTCTTCAATGGAGATGACATGCAAGGATTA-TATAATAAAATTCATAAAAATATTTTTTC  86603

Query  15006  TTCCCACCCCAATTCAAACCATTACCATGCAACCTGGTATCAATAgaagttaaggc-cat  15064
               |||||||||| |||||||  | ||||||||||||||| ||| | |||| |||||| | |
Sbjct  86604  ATCCCACCCCAGTTCAAACTGTCACCATGCAACCTGGTGTCAGTGGAAGGTAAGGCGC-T  86662

Query  15065  tgaggtagaaataattaaataaagctttattggaagctaaatgtgagaatcgacctggaa  15124
              | ||| ||||||||||||||||| ||| ||||||||||||||||||||||| |  |||||
Sbjct  86663  TAAGGCAGAAATAATTAAATAAATCTTCATTGGAAGCTAAATGTGAGAATCAATGTGGAA  86722

Query  15125  gacacacactgacaaagtgagtgttttccaaagtctgttacaagttggaatgcttttgta  15184
              |||||| ||  |||||||| |||| |||||||||||||||||||||||||||||||||| 
Sbjct  86723  GACACAGACCAACAAAGTGGGTGTGTTCCAAAGTCTGTTACAAGTTGGAATGCTTTTGTG  86782

Query  15185  agagaggttaaaagaagggaatgggactcctcctatca--atttttttttaattttcttt  15242
              ||| | ||||||||||||||||| ||||||||||||||   |||||||||||||||||||
Sbjct  86783  AGAAAAGTTAAAAGAAGGGAATGAGACTCCTCCTATCAGCTTTTTTTTTTAATTTTCTTT  86842

Query  15243  tgttttattgacctggcaaggctcaaatagagttgag----t-ttttgtttttgtttttc  15297
              ||||||| |||||||||||||||||||||||||||||    | |||||||||||||||| 
Sbjct  86843  TGTTTTACTGACCTGGCAAGGCTCAAATAGAGTTGAGTTTTTGTTTTGTTTTTGTTTTTT  86902

Query  15298  ccattggaaggtacaagacagaggttacaatcgttag-ctttagatgacaacataacagg  15356
              |||||||||||||||| ||||||||||||||| || | |||||| ||||||||||||| |
Sbjct  86903  CCATTGGAAGGTACAATACAGAGGTTACAATCATT-GACTTTAGCTGACAACATAACAAG  86961

Query  15357  ctaaaacattttccttgcaagacaaccagcatg--acttcatgatcagaataaaatcagt  15414
               | ||||||||||||||||||||||||||  ||  |||||||||||||||| ||||||||
Sbjct  86962  -TTAAACATTTTCCTTGCAAGACAACCAG--TGAAACTTCATGATCAGAATCAAATCAGT  87018

Query  15415  gtccttctcactgtcagcgggtgaagacttcatcagtacttgtagagtttgaggtactca  15474
              |||||||||||||| || |||||||| |||||||| || ||| ||||||||||| |||||
Sbjct  87019  GTCCTTCTCACTGTAAGTGGGTGAAG-CTTCATCAATAATTGCAGAGTTTGAGGCACTCA  87077

Query  15475  tgaactcatgatcagattctttactcagggacaggatgtaagccaatgc-taagaccttc  15533
              |||||||| ||||||||||||||||||||||||| |||||||||||| | ||||||||||
Sbjct  87078  TGAACTCAAGATCAGATTCTTTACTCAGGGACAGAATGTAAGCCAAT-CATAAGACCTTC  87136

Query  15534  tataggtggctaatttttaagcttgccccaatgagacct-tcaggttttcaCTGGCAATA  15592
               | |||||| ||||||  |  | ||    |||| ||||| | | ||||||||||||||||
Sbjct  87137  CACAGGTGGTTAATTTGGACTCCTG-AAAAATGTGACCTGT-AAGTTTTCACTGGCAATA  87194

Query  15593  TGCAGGTGCAGATATGACAAAGAATAACAATGACCTTCATATCACCTCCAGCTGTTGAGG  15652
              |||||||||| |||||||||| |||||| | |||||| |||||||| ||||||| || ||
Sbjct  87195  TGCAGGTGCACATATGACAAATAATAACCAGGACCTTTATATCACCCCCAGCTGGTGGGG  87254

Query  15653  AATGGGATCCTTTTCACCCTTCCTGTCCATAAAACCAAGTTACTCATCTTCAGTGGCAAC  15712
              |||||||||||||| |||||| || ||||||| |||| | ||||||| ||  ||||||| 
Sbjct  87255  AATGGGATCCTTTTGACCCTTTCTCTCCATAATACCAGGCTACTCATGTTGTGTGGCAAT  87314

Query  15713  AAAATATATGGTAAACTTAACAGAGAAGGAGACTGTCAGaaaaaaaaaaaaaaaagatgt  15772
              ||||||||||||  |||| |||||||| |||| | ||      ||||||||||| ||| |
Sbjct  87315  AAAATATATGGTCTACTTCACAGAGAAAGAGA-T-TC--TTTTAAAAAAAAAAAGGAT-T  87369

Query  15773  gtttatcctgaaatgaggaaagcaatgggaatagatgtgagattattttgggagaaaaag  15832
               |||||  ||||||||| |||||||||||||||||||||||||||||  |||||  ||||
Sbjct  87370  -TTTATTATGAAATGAGCAAAGCAATGGGAATAGATGTGAGATTATTCAGGGAGGTAAAG  87428

Query  15833  gaagacaaaggttttgaaaggaaaaataaggaggattatacaaattgttttgaaagactc  15892
              ||||||||||||||||||||||||||| ||||| |||| | | | ||||||| |||||||
Sbjct  87429  GAAGACAAAGGTTTTGAAAGGAAAAATCAGGAGAATTACATACACTGTTTTGGAAGACTC  87488

Query  15893  aaccttggtc-ctaagaatcaaaagtaaaggggcatcagtgaaatgttggatagATTCCA  15951
              |  ||||||| | ||| ||||| |  || ||||| |||||| ||||||||| ||||||| 
Sbjct  87489  ATTCTTGGTCAC-AAGTATCAACACCAAGGGGGCCTCAGTGCAATGTTGGAAAGATTCCT  87547

Query  15952  CCTCCACCCCCTCAGTAACCCCCAACATGTTTACCAAGTCTTGGTTAACTCCCAGGATCC  16011
              ||||||| |||||| ||||||||||||||||||||||||||||||| |||||| ||||||
Sbjct  87548  CCTCCACGCCCTCAATAACCCCCAACATGTTTACCAAGTCTTGGTTCACTCCCCGGATCC  87607

Query  16012  CATTAAAACACCCAGCTCAACCATGCCCATCCTCTACCCTCACTTCTCTTTGTAATTTTG  16071
              ||||||||||| |||||||||| || ||| |||| ||| ||||||| |||||||||||||
Sbjct  87608  CATTAAAACACACAGCTCAACCCTGACCAGCCTCCACCTTCACTTCCCTTTGTAATTTTG  87667

Query  16072  ACATGA-TTTTAttacaggaccatcaggttcctatgcctgctgcacagtagc-tgaccaa  16129
              |||||| |||| ||||||||||||||||||||||||||||| |||||||||| | || ||
Sbjct  87668  ACATGACTTTTTTTACAGGACCATCAGGTTCCTATGCCTGCAGCACAGTAGCAT-ACTAA  87726

Query  16130  tattctgagacagcagtgtttgcagcagacagtttaatgatcacagggtggctaaatgag  16189
              |||||||||||||||| |||||||||||| ||||||| |||||||||||||| |||||| 
Sbjct  87727  TATTCTGAGACAGCAGGGTTTGCAGCAGAGAGTTTAACGATCACAGGGTGGCAAAATGAA  87786

Query  16190  aagctaggaggatatcctcaaattcatctccccaagtagtactgagggtttccagtggat  16249
              ||||| |||||| | ||||||||||||||||||||| ||||||||| |||| ||| ||||
Sbjct  87787  AAGCTGGGAGGAGACCCTCAAATTCATCTCCCCAAGAAGTACTGAGAGTTTTCAGAGGAT  87846

Query  16250  cctggatagcaaggggctggaaagttggt---g--tag-ag--gtaagagggatgaagtc  16301
              | ||||||||||| |||||||||||||||   |  | |  |  |||||||| ||||||||
Sbjct  87847  CATGGATAGCAAGAGGCTGGAAAGTTGGTGCAGTTTGGTGGCAGTAAGAGGTATGAAGTC  87906

Query  16302  atcaggatgtcaaaactgcattctttggtgagttggtgccttgcagagcccttcagatca  16361
              ||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||
Sbjct  87907  ATCAGGATGTCAAAACTGCATTCCTTGGTGAGTTGGTGCCTTGCAGGGCCCTTCAGATCA  87966

Query  16362  gctggcatcagtagtttcactgacatgcagaacctgaaagaatatctcaaatgagaaagt  16421
               ||| ||||||||| |||||||||||||||||||||||||||||| |||||||| |||||
Sbjct  87967  CCTGCCATCAGTAGCTTCACTGACATGCAGAACCTGAAAGAATATGTCAAATGAAAAAGT  88026

Query  16422  taatgttttacaaggcttaaattgttgtctgcagggtagttaaggggaactgtaagctaa  16481
              |||||||||||||||| ||||||||||||||||||| ||||||||| |||||||| ||||
Sbjct  88027  TAATGTTTTACAAGGCCTAAATTGTTGTCTGCAGGGCAGTTAAGGGCAACTGTAATCTAA  88086

Query  16482  ggtctacttgatttggggacagtaagctgccagcaaccatgaggaagaaggtcagagagc  16541
              ||||||| |||||| ||||||| | |||||||||||||||||||||| ||||||||||||
Sbjct  88087  GGTCTACATGATTTTGGGACAGCAGGCTGCCAGCAACCATGAGGAAGCAGGTCAGAGAGC  88146

Query  16542  aagctgacctcatggtgaatgctgaatgcgctgcaagcttggtttatttttgtttctccc  16601
              |||||||||||||| |||||||||||||| ||||||||||||||||| | ||||||||||
Sbjct  88147  AAGCTGACCTCATGATGAATGCTGAATGCACTGCAAGCTTGGTTTATGTCTGTTTCTCCC  88206

Query  16602  cctcccttcttcactgattaaacttataaagtttacaggtatcatttcaATTTCTTCCAG  16661
              |||||||||||||||||||||| |||||||||||| | ||||  || |||||||||||||
Sbjct  88207  CCTCCCTTCTTCACTGATTAAATTTATAAAGTTTATAAGTATGGTTGCAATTTCTTCCAG  88266

Query  16662  AGAAGACTTAACCTAAGCCCTGAGACCACTCAAGCCCTCAGTGGCACCTCTCTTCCACCA  16721
              || || |||||||||||||||||||||||||| | |||||||||||||||||||||||||
Sbjct  88267  AGTAGCCTTAACCTAAGCCCTGAGACCACTCAGGTCCTCAGTGGCACCTCTCTTCCACCA  88326

Query  16722  GCACGAGTGAAGAAACTGCTACCTTAGGTGATATAAAACCCACAAGACCATTCCATACAT  16781
              ||| ||||||| ||| ||||||||||||||||||||||||||||||||||||| ||||||
Sbjct  88327  GCAGGAGTGAAAAAATTGCTACCTTAGGTGATATAAAACCCACAAGACCATTCAATACAT  88386

Query  16782  GGAGATCTTTATTCTT-ATTTTGTAGGGACGACTCCTCTGTGTTTATACAGCTATTTTAA  16840
              |||||| |||||| || |||||||||||||||||||||||| |||||| |||||||||||
Sbjct  88387  GGAGATTTTTATT-TTGATTTTGTAGGGACGACTCCTCTGTTTTTATAAAGCTATTTTAA  88445

Query  16841  CTAGAAATATTTTTATAAATTTTATAATTTTGATGTGGCCAAAGATCTCCCCACAACACT  16900
              ||| ||| |     ||   |||| | ||||||||||||||||||||||||| |||| |||
Sbjct  88446  CTATAAA-AC----AT---TTTTGTGATTTTGATGTGGCCAAAGATCTCCCAACAATACT  88497

Query  16901  ACTTTCAGGTTTTATTTTTCTGTCTAATGTCTGG-AACAGATCA-ACCCCTTCCCTGCCT  16958
              |||||||| ||||| ||||||||||||| ||||| || |||| | |||| |||||||| |
Sbjct  88498  ACTTTCAGATTTTAGTTTTCTGTCTAATATCTGGGAA-AGATTAGACCC-TTCCCTGCTT  88555

Query  16959  CACA-TCAGGACT-TGAAGG-CGAAATAGCAGTAAAATTCCATCAGTGTTTGTGGATTTC  17015
              || | |||||||| || ||| | | |||  ||| |||||||||||||||||||| | |||
Sbjct  88556  CAGACTCAGGACTATGCAGGTC-ACATATTAGTGAAATTCCATCAGTGTTTGTGAAGTTC  88614

Query  17016  ATGAATGAATGCAtttttttt----gacaaaatctccctctgtcacccagtcaggagggc  17071
              | ||||||||| |||||||||    |||||| ||||||||||||||||||   |||| ||
Sbjct  88615  ACGAATGAATGAATTTTTTTTTTCCGACAAATTCTCCCTCTGTCACCCAGAGTGGAGTGC  88674

Query  17072  aatggtgtaatcttggctcactgcaaac-tcagcctccagggttcaagggattctcccac  17130
              ||||||| |||||||| ||||||||| | |  |||||  ||||||||| |||||||||||
Sbjct  88675  AATGGTGCAATCTTGGTTCACTGCAACCATT-GCCTCTTGGGTTCAAGCGATTCTCCCAC  88733

Query  17131  ctcagccgcatgagtaactggactacaggca-gccaccatcgtgcctggctaactt-ttc  17188
              ||||||| | |||||| ||||| |||||||| |   ||||||| |||| |||| || || 
Sbjct  88734  CTCAGCCTCCTGAGTAGCTGGATTACAGGCATGTG-CCATCGTCCCTGCCTAA-TTCTTG  88791

Query  17189  tatttttgtagagacagggtttcaccatgtgggccaggctggtcttgaac-tcctgacct  17247
              ||||||||||||||| |||||||||| ||| |||| |||| ||||||||  || ||| ||
Sbjct  88792  TATTTTTGTAGAGACGGGGTTTCACCTTGTTGGCCTGGCTCGTCTTGAATGTC-TGAACT  88850

Query  17248  caggtgatccacctaccttggcctcccaaagtgctgggattacaagtgtgagccacctca  17307
              ||||||| ||||| | |||| | ||||||||||||||||||||| | |||||||||||  
Sbjct  88851  CAGGTGACCCACCCAACTTGTCTTCCCAAAGTGCTGGGATTACAGGAGTGAGCCACCTTG  88910

Query  17308  cctggccTTGAGTGAATGAATTCTTGATTTCCAGTCTATCCCTAACTCTGTCAATTTCTT  17367
              || || ||||| |||||| |||||||||| |||  ||||||||||| |||||||||||||
Sbjct  88911  CCCGGTCTTGAATGAATGCATTCTTGATTCCCACCCTATCCCTAACACTGTCAATTTCTT  88970

Query  17368  AATTCATGAAATGATTATGCATATGTGATATGAATGGATATCTCG-TTCAATCCATTAGT  17426
               ||||||||| | | |||| |||| |||||||||||||||||| | |||||||||||| |
Sbjct  88971  GATTCATGAACTTAATATGGATATCTGATATGAATGGATATCT-GATTCAATCCATTAAT  89029

Query  17427  CTTCGGACAGTCAAAAACCCAATCAGGATTAACTGAGTGGAGCTTCAGAAATGCAATCAG  17486
              ||  ||| || ||||| |||||||||||||||||| ||||||||||||||||||||||||
Sbjct  89030  CTGGGGAGAGCCAAAACCCCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGCAATCAG  89089

Query  17487  ATATCGCTTTTTGATTGGAAGCTAGCAGCGGATACGTGGAGGGGCGTGGGTGGGAGTTGT  17546
              ||||| ||| |||||||||||||||||| ||||||||||||||| |||||||||||||||
Sbjct  89090  ATATCACTTGTTGATTGGAAGCTAGCAGTGGATACGTGGAGGGGTGTGGGTGGGAGTTGT  89149

Query  17547  GATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGACAAACTCAAAGTCTTCAAGC  17606
              |||||||||||||||||||||||||||||||||||||| | | || ||||||||||||||
Sbjct  89150  GATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGAAGAGACCCAAAGTCTTCAAGC  89209

Query  17607  CTGGAGTTCCTGCTTGGCTCTTCCTGAGGTCTGAGCACCTTCTAAACT-ACAACCAGATC  17665
              |||||||||||||||   ||||||||||||||||||||| || ||||| |   |||||||
Sbjct  89210  CTGGAGTTCCTGCTTATTTCTTCCTGAGGTCTGAGCACCCTCCAAACTGAGT-CCAGATC  89268

Query  17666  TGGTAAGTCACTAAT-T-TCTGTAAGGACACTCCCATGTGACCTACAGTCAGCCGGTCTA  17723
              ||||||||||||||| | ||||||||||||||||||  ||||||||||||||| ||||| 
Sbjct  89269  TGGTAAGTCACTAATCTCTCTGTAAGGACACTCCCAACTGACCTACAGTCAGCTGGTCTG  89328

Query  17724  GAACGGTGACAGTGCAGCCTACGATGGCATAGAACTATATCATGTCtttttttctttttt  17783
              | | ||||||||||||||||| |||||||||||  |||||| ||| ||| ||| ||||| 
Sbjct  89329  GGATGGTGACAGTGCAGCCTAAGATGGCATAGAGTTATATCCTGT-TTTGTTT-TTTTTC  89386

Query  17784  tcatatgaacactttgaagctttg-atttttttttCTAAATGCAATTTTGTCGTGATTTC  17842
              ||||||||||| |||||||||||| |||||||  |||||||||| ||||||| | |||||
Sbjct  89387  TCATATGAACAATTTGAAGCTTTGCATTTTTTCCTCTAAATGCAGTTTTGTCTTTATTTC  89446

Query  17843  AAAAATGTTG--TTGTGCTTTTCTTTACATCATTTCAGAATTCTTG  17886
              |||||  |||  |||||||||  ||||  |||||||| ||||||||
Sbjct  89447  AAAAAA-TTGGATTGTGCTTTGGTTTATGTCATTTCAAAATTCTTG  89491


 Features flanking this part of subject sequence:
   29101 bp at 5' side: PRAME family member 8
   2120 bp at 3' side: PRAME family member 9

 Score = 3241 bits (1755),  Expect = 0.0
 Identities = 2711/3158 (85%), Gaps = 123/3158 (3%)
 Strand=Plus/Plus

Query  23894   gggaatgggactcctcctatcagttgttttttttttttaattttcttttgtttta-t--c  23950
               ||||| ||||||||||||||||     || ||||||| ||||||||||||||||| |  |
Sbjct  98891   GGGAAAGGGACTCCTCCTATCA----ATTATTTTTTTAAATTTTCTTTTGTTTTATTGAC  98946

Query  23951   ctggcaaggctctaatagagttgagcttttttgtttttgttttttccattggaagggaca  24010
               ||| ||||| || ||||||||||||  |||||||||||||||||||||||||||||||||
Sbjct  98947   CTGACAAGGGTCAAATAGAGTTGAG--TTTTTGTTTTTGTTTTTTCCATTGGAAGGGACA  99004

Query  24011   atacagaggttacaatcattgactttagatgacaacatgacaggca-aaaatattttcct  24069
               | ||| ||||||||||||||| ||||||||||||| || | | | | |||| || |||||
Sbjct  99005   A-ACACAGGTTACAATCATTGGCTTTAGATGACAAGAT-AAAAGAATAAAACATATTCCT  99062

Query  24070   tgcaagacaaccagcaaaacttcacgatcagaatcaaatcagtgtccttctcactgtcac  24129
               || ||||||||||||| ||||||| |||||| |||||||||||| |||||||||||||| 
Sbjct  99063   TGAAAGACAACCAGCAGAACTTCATGATCAGCATCAAATCAGTG-CCTTCTCACTGTCAG  99121

Query  24130   tgggt-gaagccttcatcagtacttgaagagtctcaggcactcatgaagtcaagatcaga  24188
               ||||| ||||||||||||| |||||| ||||| | | ||||||||||| ||| |||||||
Sbjct  99122   TGGGTGGAAGCCTTCATCAATACTTGTAGAGTTTGAAGCACTCATGAACTCACGATCAGA  99181

Query  24189   ttctttactcagggacaggatgtaagccaatc-ataagaccttccacagatgatcaattt  24247
                |||||||||||||||| |||||||||||| | | |||||||||||||| || | |||||
Sbjct  99182   CTCTTTACTCAGGGACAAGATGTAAGCCAAGCGA-AAGACCTTCCACAGGTGGTGAATTT  99240

Query  24248   ggaagtctacctaatgtgacctgcaggttttcaCTGGCAATATGCAGGTGCAGATATGAC  24307
               ||||| || || ||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct  99241   GGAAGCCTGCCCAATGTGACCTGCAAGTTTTCACTGGCAATATGCAGGTGCAGATATGAC  99300

Query  24308   AAAGAATAATCC-TGACCTTCATATCGC-CCCTAGCTGATGAGGATTGGGATTCTTTTGT  24365
               ||||||||| || ||||||| | ||| | ||| ||||| |||||| |||||| |||||| 
Sbjct  99301   AAAGAATAA-CCATGACCTTTACATCACTCCC-AGCTGTTGAGGAATGGGATCCTTTTGA  99358

Query  24366   CCCTTTCTCTCCATAAAACCAGGTTACTCATCTTGTGTGGCAACAAAATATATGGTctac  24425
               |||||||| |||||| |||||||||||||||||||||||||||||| |||||||||||||
Sbjct  99359   CCCTTTCTGTCCATAGAACCAGGTTACTCATCTTGTGTGGCAACAACATATATGGTCTAC  99418

Query  24426   ttaacagagaaaga-gactccacaggaaaaaaaaaaggatttttattatgaaatgagcaa  24484
               ||||||||||| || |||||    | |||||||||||  |||  |||||||| | |||||
Sbjct  99419   TTAACAGAGAA-GAAGACTCT---GTAAAAAAAAAAG--TTT--ATTATGAAGTAAGCAA  99470

Query  24485   agcca-tgggaatagatgtgagattattcggggaggtaaaggaagacaaaggttttgaaa  24543
               ||  | ||| |||||||| ||||||||| |||||| |||||||||   |||| |||||||
Sbjct  99471   AGA-AGTGGCAATAGATGCGAGATTATTTGGGGAGATAAAGGAAGTTGAAGGGTTTGAAA  99529

Query  24544   ggaaaaatgaggagaattacataaatttttttgaaagactcattcttggtcacaagtatg  24603
               |||||||| ||||| |||| | ||||| ||||||||||||||| |||||||| ||| || 
Sbjct  99530   GGAAAAATAAGGAGGATTATACAAATTGTTTTGAAAGACTCATACTTGGTCATAAGGATT  99589

Query  24604   aaaaccaag-ggagcctcagtgcagtgttggaaagATTCCTCCTCCACCCTCTCAATAAC  24662
               ||||||||  || || |||||||| |||| || ||||||||| | ||||| |||||||||
Sbjct  99590   AAAACCAAAAGG-GCATCAGTGCAATGTTAGATAGATTCCTCTTACACCCACTCAATAAC  99648

Query  24663   CCCCAACACATTTACCAAGTCTTTGTTCACTCCCAGGATTCC-ATTAAAACACCCAGCTC  24721
               ||||||||  || | |||||||| ||||||||||||| |||| ||||||| |||||||||
Sbjct  99649   CCCCAACATGTTCAGCAAGTCTTGGTTCACTCCCAGG-TTCCCATTAAAA-ACCCAGCTC  99706

Query  24722   AACCCTGACCAGCCTCCACCTTCACTTCCCTTTGTAATTTTGACATAAATTtgttacagg  24781
               ||||||||||||| |||||| |||||||| |||||||||||||||| | ||| |||||||
Sbjct  99707   AACCCTGACCAGC-TCCACCCTCACTTCCATTTGTAATTTTGACATGACTTTATTACAGG  99765

Query  24782   accatcaggttcctatgccggctgcacagtagcttaccaatattctgagacagcaggatt  24841
               ||||||||||||||||||| |||||||||||||||| |||||||||||||||||||| ||
Sbjct  99766   ACCATCAGGTTCCTATGCCTGCTGCACAGTAGCTTAGCAATATTCTGAGACAGCAGGGTT  99825

Query  24842   tgcagcagaaagtttaatgatcacagggtggctgaatgagaagctgggaggagatcctca  24901
               ||||||||| ||||||||||||||| ||||||||||||||||||| ||||||||||||||
Sbjct  99826   TGCAGCAGAGAGTTTAATGATCACAAGGTGGCTGAATGAGAAGCTAGGAGGAGATCCTCA  99885

Query  24902   aattcatctccccaaggagtactgagggtttccagtggatcctggatagcaaggggctgg  24961
               ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| ||
Sbjct  99886   AATTCATCTCCCCAAGGAGTACTGAAGGTTTCCAGTGGATCCTGGATAGCAAGGGGCCGG  99945

Query  24962   aaagttggtgtagtttgatggcaataagaggtatgaagttatcacgatgtcagaa-cggc  25020
               |||||||| ||||   |  |    ||||||| | ||||| | || ||||| |||| | ||
Sbjct  99946   AAAGTTGGGGTAGC--G--G----TAAGAGGGAAGAAGTCAACAGGATGT-AGAAACTGC  99996

Query  25021   attctttggtgagttgatgccttgcagggcccttcagatcagctggcatcagtagtttca  25080
               |||||||||||||||| ||| |||||||||||||||||||||||||||||||||||||||
Sbjct  99997   ATTCTTTGGTGAGTTGGTGCATTGCAGGGCCCTTCAGATCAGCTGGCATCAGTAGTTTCA  100056

Query  25081   ctgacatgcagaacctgaaagaatatctcaaatgaaaaacttaatgtttcacaatgctta  25140
               |||||||||||||||||||||||||||||| |||||||| ||||||||| ||||||||||
Sbjct  100057  CTGACATGCAGAACCTGAAAGAATATCTCACATGAAAAAGTTAATGTTTTACAATGCTTA  100116

Query  25141   aattgttgtctgcagcgtagttaaggggaattgtagtctaagttctacacgattttggga  25200
               ||| ||||||||||| | |||||||||||| |||| |||||| |||| | |||||||| |
Sbjct  100117  AATCGTTGTCTGCAGGGAAGTTAAGGGGAACTGTAATCTAAGGTCTATATGATTTTGGAA  100176

Query  25201   cagtaggctgccagcaaccatgaggaagcaggtcagagggcaagctgacctcctggtgaa  25260
               ||||||||||||||||||||||||||| |||||||||| |||||  ||||||||| ||||
Sbjct  100177  CAGTAGGCTGCCAGCAACCATGAGGAACCAGGTCAGAGAGCAAGAAGACCTCCTGATGAA  100236

Query  25261   tgctgaatgcgtttcaagcttggtttgtttttgttcctccccctctctttttcaccgatt  25320
               ||||||||| ||| |||||||||||| |||||||| ||| ||||| ||| ||||| ||||
Sbjct  100237  TGCTGAATGTGTTGCAAGCTTGGTTTATTTTTGTTTCTCTCCCTCCCTTCTTCACTGATT  100296

Query  25321   aaatttataaagtttagaaatacggtttcaATTTCTTCCAGACAAGCCTTAACCTAAGCC  25380
               ||||||||||||||||   ||  ||||||||||||||||| | |||||||||||||||| 
Sbjct  100297  AAATTTATAAAGTTTATCGATGTGGTTTCAATTTCTTCCAAAGAAGCCTTAACCTAAGCA  100356

Query  25381   CTGAGACCACTCAAGCCCTCAGTGGCACCTCTCTTCCACCAGCATGAGCAAATAAAT-TG  25439
               ||||||||||||| ||||||||| ||||||||| |||||||| | |||||  ||| | ||
Sbjct  100357  CTGAGACCACTCACGCCCTCAGTAGCACCTCTCCTCCACCAGAACGAGCATGTAA-TCTG  100415

Query  25440   CTACCTTAGGTGATATAAAA-CCCACAAGATGATTCGA-TACATGGAGtttttt-ttCTG  25496
               ||||||||||| |||||||| |||| ||||  ||| || ||||| ||| ||||| |||||
Sbjct  100416  CTACCTTAGGTTATATAAAATCCCA-AAGACCATT-GAATACATTGAGATTTTTATTCTG  100473

Query  25497   ATTTTGTAGGGATGACTTCTTTGTTTCTATAAAGCTGTTTTAAC-TATAAAACAATTTTA  25555
               || | |||| ||||||| || ||||| ||||||||| ||||||  || ||| || |||||
Sbjct  100474  ATATCGTAGTGATGACTCCTCTGTTTTTATAAAGCT-TTTTAAAGTAGAAAGCATTTTTA  100532

Query  25556   TAATTTTGATGTGGCCAAAGATCTCC---CAACACTACTTTCAGGTTTTATTTTTCTGTC  25612
               || |||||||||||||||||||| ||   ||||||||||||||| |||||||||||||||
Sbjct  100533  TA-TTTTGATGTGGCCAAAGATCCCCTAACAACACTACTTTCAGATTTTATTTTTCTGTC  100591

Query  25613   TACTATCCAGAACAGATCAAACCCTTCCCTGCCTCAAACTCAGGACTAT-ATAGGTCATA  25671
               || | ||  |||||||||||| |||||||||||||| ||||| |||||| | || ||| |
Sbjct  100592  TAATGTCGGGAACAGATCAAATCCTTCCCTGCCTCACACTCAAGACTATGA-AGTTCACA  100650

Query  25672   TATCAGTAAAATTCCATCAGTGTTTGCGGAgttcatgaatgaatgaattctttttttttt  25731
               ||| | |||||| ||||||||||||| ||||||||||||||||||| || ||||| ||||
Sbjct  100651  TATTAATAAAATACCATCAGTGTTTGTGGAGTTCATGAATGAATGA-TT-TTTTTATTTT  100708

Query  25732   tttttttttttttttttgtgaca-aagtctacctctgtcacccagaac-ggtgtgcaatg  25789
               ||               |  ||| || ||| ||||||||||||||| | || ||| | ||
Sbjct  100709  TT---------------G--ACAGAA-TCTCCCTCTGTCACCCAGA-CTGGAGTGGAGTG  100749

Query  25790   gtgcaat-cttggctcactgcaaccattgccccctggattcaagcgattctcccacctca  25848
               |  |||| || |||||||||||||||||||| ||||| ||||||| |||||||  |||||
Sbjct  100750  GCACAATTCT-GGCTCACTGCAACCATTGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCA  100808

Query  25849   gcctcctgagtagctggattacaggcacctgccatcatgcc-aggctaatttttgtgttt  25907
               ||||||  ||||||||| || ||||  |||||||||||||| || ||||||||||| |||
Sbjct  100809  GCCTCCCAAGTAGCTGGGTTTCAGGTGCCTGCCATCATGCCCAG-CTAATTTTTGTATTT  100867

Query  25908   ttgtagag-ctggggtttcatcatgttggccttg-caggtcttgatcgc-ctgacctcag  25964
               |||||||| | ||||||||| | | ||| ||| | | |||||||| | | ||||| ||||
Sbjct  100868  TTGTAGAGAC-GGGGTTTCACCTTTTTGACCT-GACTGGTCTTGAAC-CACTGACATCAG  100924

Query  25965   gtgatccagc-caacttggactctc-aaagtgcagggattacaggtgtgagccacctcac  26022
               |||||| | | || |||   || || ||||||| || ||||||||| |||||||||||||
Sbjct  100925  GTGATCTA-CTCACCTTCTCCT-TCCAAAGTGCTGGAATTACAGGTATGAGCCACCTCAC  100982

Query  26023   ccggcctttaatgaGTGAATTCTTGATTTCCACCCTATTCCTAACACTGTCAATTTCTTG  26082
               ||  |||| ||||| || |||||||| ||| ||||||| |||||||||||||||||||||
Sbjct  100983  CCACCCTTGAATGAATGTATTCTTGACTTCTACCCTATCCCTAACACTGTCAATTTCTTG  101042

Query  26083   ATTCATGAACTTAATATGGATA-GCTGATATGAATGGATATCTGATTCAATCCAGTAATC  26141
                |||| ||||| ||||  |||| | |||||||||||||||||||| |||||||| |||||
Sbjct  101043  CTTCACGAACTGAATACAGATATG-TGATATGAATGGATATCTGACTCAATCCATTAATC  101101

Query  26142   TGGGGACAGCCAAAAACCCAATCAAGATTAACTGGGTGGAGCTTCAGAAATGCAATCAGA  26201
               |||||| ||||||||||||||||| ||||||||||||||||||||| |||||||||||||
Sbjct  101102  TGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCACAAATGCAATCAGA  101161

Query  26202   TAGCACTTTTTGATTGGAAGCAAGCACTGGATA-GATGGAGGGGTGTGGGTGGGAGTTGT  26260
               ||   |||||||||||||||| |||| || ||| | |||||||| |||||||||||||||
Sbjct  101162  TATTGCTTTTTGATTGGAAGCTAGCAGTGCATACG-TGGAGGGGCGTGGGTGGGAGTTGT  101220

Query  26261   GATTAGAAAGATCGATAAAAGTTTCTGAAGGCCCACAGGAGAGACCCAAAGTCTTCAAGT  26320
               |||||||||| || ||||||| |||| ||| |||||||||||||||||||||||||||| 
Sbjct  101221  GATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGAGAGACCCAAAGTCTTCAAGC  101280

Query  26321   CTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTAAGCACTCTGCAA-ACT-CAGTCCAGAT  26378
               |||||||||||||||||||||||||||||||| ||||| || | | ||| || |||||||
Sbjct  101281  CTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTGAGCAC-CTTCTAGACTACA-TCCAGAT  101338

Query  26379   CTAGTAAGTCACTCATTTCTGGAAGGACACTCCCATCTGACCTATAGTCAGCCGGTCTGG  26438
               || |||||||||| ||||||| |||||||||||||||||||||| |||||| ||||||||
Sbjct  101339  CTGGTAAGTCACTAATTTCTGTAAGGACACTCCCATCTGACCTACAGTCAGTCGGTCTGG  101398

Query  26439   GACGGGGGCAATGCAGCCTATGATGGCACCGAGCTATATC-TGTC-TTTtatatatatat  26496
               || || | || ||||||||| |||||||| |||||||||| |||| |||| | | | | |
Sbjct  101399  GATGGTGACAGTGCAGCCTACGATGGCACAGAGCTATATCCTGTCCTTTTTTTTTTTTTT  101458

Query  26497   -atatGAACAATTTGAAGATTTGAATTTTTTCCTCTATATGCAGTTTTGTCTTTATTTCA  26555
                |||||||||||| |||| |||||||||||||||||| |||||||| |||||||||||||
Sbjct  101459  TATATGAACAATTGGAAGCTTTGAATTTTTTCCTCTAAATGCAGTTCTGTCTTTATTTCA  101518

Query  26556   AAAAA-TTGGATTGTGCTTTGGTTTATGTCATTTcaaaattcttgatgggagcaatgact  26614
               ||||| ||| |||||||||||||| ||| ||||| ||||||||||| ||||||| |||||
Sbjct  101519  AAAAAGTTG-ATTGTGCTTTGGTTGATGCCATTTTAAAATTCTTGAAGGGAGCAGTGACT  101577

Query  26615   catgcccataacctcaacaccttgggaggccaaagcgggaggatcatttgagcccagggg  26674
               ||||||  ||||| |||||| |||||||||||||| ||||||||||||| ||||||||| 
Sbjct  101578  CATGCCTTTAACCCCAACACTTTGGGAGGCCAAAGTGGGAGGATCATTTCAGCCCAGGGA  101637

Query  26675   tttgagaccaacctgggcaacatggcaaaaatgcagctctacaaaacattctttttttga  26734
               |||||||||||||||| ||||||| ||||||  |  |||| || ||| || |||||| | 
Sbjct  101638  TTTGAGACCAACCTGGACAACATGACAAAAACCCTCCTCTGCACAACGTT-TTTTTTGGG  101696

Query  26735   agcagggatggagtctcaccctgttgccaaggctggagtgcagtggcaagagctcaactc  26794
                |  |||||||||||||||  ||||||| || |||||||||||||||| || ||||||||
Sbjct  101697  GGTGGGGATGGAGTCTCACTGTGTTGCCCAGACTGGAGTGCAGTGGCACGATCTCAACTC  101756

Query  26795   actgcaacctcttcct-cccaggctcaaacaattttcatgtctcag-ct---tcctgagt  26849
                ||||||||| || || ||| || |||| ||||| ||||| ||||| ||   |||| || 
Sbjct  101757  CCTGCAACCT-TTACTTCCCGGGTTCAAGCAATTCTCATGCCTCAGTCTCCATCCTCAGA  101815

Query  26850   agctggtattacatccctctgccaccatgtctg-cttaatttttgtatttttagtagtgg  26908
               ||||||| | |||  | ||||  |||||| ||| || || ||||||||||||||||| ||
Sbjct  101816  AGCTGGTGTCACAGACATCTGAAACCATGCCTGGCT-AAGTTTTGTATTTTTAGTAGAGG  101874

Query  26909   tggggtttcaccatgctggccaggttggtctcaaactcctgacatcaagtgatcctcctg  26968
               ||||||||||||| |||||||||||||||||| ||| |||||| ||||||||||| ||||
Sbjct  101875  TGGGGTTTCACCACGCTGGCCAGGTTGGTCTCGAACACCTGACCTCAAGTGATCCACCTG  101934

Query  26969   cctaggcc-cccaaaagtgctggaatgacggccgtgag  27005
               ||| |||| |||||| ||||||| || || || |||||
Sbjct  101935  CCTTGGCCTCCCAAA-GTGCTGGGATTACAGCTGTGAG  101971


 Features in this part of subject sequence:
   PRAME family member 13

 Score = 3142 bits (1701),  Expect = 0.0
 Identities = 2249/2507 (89%), Gaps = 63/2507 (2%)
 Strand=Plus/Plus

Query  3255    GGCAGAAACTTTCTCCAGCAGAGCTCCGAGGGGTTCAAGACTGATACAGAACTGCAGCAT  3314
               ||||| || |||||| ||||||||||||||||||||||||||||| | |||| |||||| 
Sbjct  128516  GGCAGCAATTTTCTCTAGCAGAGCTCCGAGGGGTTCAAGACTGATGCGGAACAGCAGCAC  128575

Query  3315    GTAGCTGAGATTCAGATGCTTTGGGTAAGCGAGGCTTGGGTACTGGTAGAGACACTTCAA  3374
               |||||||||||||||||||||| ||||| ||||||||||||||||| |||||||||||| 
Sbjct  128576  GTAGCTGAGATTCAGATGCTTTAGGTAACCGAGGCTTGGGTACTGGGAGAGACACTTCAT  128635

Query  3375    GTCCTCTTCCAATAGGTAGCCGCAAGTTAATTCCAAGTTCTCCAAGGGGTTCTAGAGGCA  3434
               ||| |||||||||||||||||  |||||||||||||||||||||||||||||| ||||||
Sbjct  128636  GTCTTCTTCCAATAGGTAGCCATAAGTTAATTCCAAGTTCTCCAAGGGGTTCTGGAGGCA  128695

Query  3435    CCTGTGGAGATCAAGAAGTTAGTTCTGGGCAATGGTACCAGTTAGATGAAGGTAGTGGGG  3494
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||   |
Sbjct  128696  CCTGTGGAGATCAAGAAGTTAGTTCTGGGCAATGGTACCAGTTAGATGAAGGTAGT---G  128752

Query  3495    AATGAACTCAAGGAAAATACCTGCTTCAACCAAACACAAGTTTGTTCCCACCATCTGATG  3554
                 |  | || |||||||| ||||| |||| ||||||||||||||||||||||||||||||
Sbjct  128753  CCTTCA-TCTAGGAAAATGCCTGCGTCAAACAAACACAAGTTTGTTCCCACCATCTGATG  128811

Query  3555    ATGGTCCTCATGCAAGTTGCTGCATGTTGAGGACCCTGATCATTCAGGGGCTGTCCCATT  3614
               |||||||||||| ||||||||||||| |||||||||||||| ||||||||||||||||||
Sbjct  128812  ATGGTCCTCATGGAAGTTGCTGCATGATGAGGACCCTGATCGTTCAGGGGCTGTCCCATT  128871

Query  3615    TTAGCCTCAGCCCTTTCACCATTTCTTGTGTGATTGGGTCAAGGCCACAAAATCTCTAAA  3674
               |||||||||||||||||| |||| ||||||||||||| ||||||||| ||||||||||||
Sbjct  128872  TTAGCCTCAGCCCTTTCAACATTGCTTGTGTGATTGGTTCAAGGCCATAAAATCTCTAAA  128931

Query  3675    GCC--------TTTTATCTTCATCTTTTAGCAGAAAACCTCATCTCTGGGCCACAGGTAC  3726
               |||        |||| | |||||||||||||||||||| | |||||||||| ||||||||
Sbjct  128932  GCCTTTTTTTTTTTTTTTTTCATCTTTTAGCAGAAAACTTTATCTCTGGGCTACAGGTAC  128991

Query  3727    CCGGTGGGAGATGTGCACAAAGAACTCAACTCAGCAAGGTCTAGGGACATTAGCTGGGGC  3786
               ||||||||||||||| |||||||||||||||||||||||||||||||||| |||| ||||
Sbjct  128992  CCGGTGGGAGATGTGAACAAAGAACTCAACTCAGCAAGGTCTAGGGACATCAGCTAGGGC  129051

Query  3787    TACCTGCCGGCAGGGGCTCCCTGGCCTGCCTGCATCTGCAAACCAACTGTCACTTTTTAC  3846
               ||| || |||||||||||||||| | ||||||||||||||||||||||||||||||||||
Sbjct  129052  TACATGTCGGCAGGGGCTCCCTGACATGCCTGCATCTGCAAACCAACTGTCACTTTTTAC  129111

Query  3847    CACTCTCACTCCTACTCCTTCACCCTCCATCCCAGAAGCATGCATGTCCCATGTCAATTG  3906
               ||||||||| |||||||| ||| |||||||||||||||||  ||| |||||||||| || 
Sbjct  129112  CACTCTCACGCCTACTCCCTCA-CCTCCATCCCAGAAGCACACATTTCCCATGTCAGTT-  129169

Query  3907    A-CTTTCCTGGAGTTCAAAACAACCTTCTACAGACAGGGAATCAGAGACAGGATCATTCA  3965
               | ||||||||||||||||||||||||| |||| |||||||||||||||||||||||||| 
Sbjct  129170  ACCTTTCCTGGAGTTCAAAACAACCTTTTACAAACAGGGAATCAGAGACAGGATCATTCG  129229

Query  3966    TGATCACTAAGCTGGTGAGGACAGAGC-TTCTACTGTGAAATGCACAAGTTTGATGCACT  4024
               |||||||||||| |||||||||||| | ||||| ||||||||| ||| ||||||||| ||
Sbjct  129230  TGATCACTAAGCCGGTGAGGACAGA-CGTTCTATTGTGAAATGGACAGGTTTGATGCGCT  129288

Query  4025    GTCCCTCCTTTCATACCCTCCTTTGTTACCTCTTTTACATCATATCAACTTGAAACACAC  4084
                ||||||||||||||||||||| | ||| |||||| ||||||||||||||||||||||||
Sbjct  129289  TTCCCTCCTTTCATACCCTCCTCTATTATCTCTTTGACATCATATCAACTTGAAACACAC  129348

Query  4085    TTTGTAACAAGAAATTCACACGTGCACATGCAGTAGAGAC-AAAACGCCCACTAAGTACC  4143
               ||||||||| |||||||||||||||||   || ||||| |  |||| |||||||| || |
Sbjct  129349  TTTGTAACAGGAAATTCACACGTGCACCCCCAATAGAG-CTGAAACCCCCACTAACTAGC  129407

Query  4144    TTGTACATGATGTCCCTCTCTAGCCTCTACCCTAGGTGACCCCTCTGCCTTTATTGAAGT  4203
               |||||||||||||| ||||||||| ||||||| |||||||||||||||| |||||| || 
Sbjct  129408  TTGTACATGATGTCTCTCTCTAGCTTCTACCCCAGGTGACCCCTCTGCCCTTATTGGAGC  129467

Query  4204    GATCCTGTGATAGCCACTCCAGGACATGGAGCACTGAACGGGACAATGTGTTGACATTCT  4263
               | |||||||||||||||||||||||||||| ||||||| |||||||||||||||||||||
Sbjct  129468  GTTCCTGTGATAGCCACTCCAGGACATGGAACACTGAATGGGACAATGTGTTGACATTCT  129527

Query  4264    GGTGTCCCCTGCACTGTGCCGTCGCCACTGGCTGGCACACAGTACACGTCTTCTAGTGTT  4323
               |||||||||| ||||||| ||| ||||||||||||||||||||||||| |||||| ||||
Sbjct  129528  GGTGTCCCCTTCACTGTGACGTTGCCACTGGCTGGCACACAGTACACGCCTTCTAATGTT  129587

Query  4324    TACTGTAACaaaaaaaaaGGCTGCGCTGTGGTCTGCAGAGAAAGGGCACGATCCTTTCTC  4383
               | |||||||  | || ||||||  ||||||||||||| | |||| ||| ||||||| |||
Sbjct  129588  TGCTGTAAC--AGAACAAGGCTATGCTGTGGTCTGCATATAAAGTGCATGATCCTTCCTC  129645

Query  4384    ACCTGATCAGCTGTCCCAGGTGCCCTCTGTGGAAGGTGA-CCATATTCATTTTAAGCAGC  4442
               |||||||||||||| |||||||||| |||  |||||||| | || || |||||||||| |
Sbjct  129646  ACCTGATCAGCTGTTCCAGGTGCCCACTGAAGAAGGTGATCAAT-TTTATTTTAAGCAAC  129704

Query  4443    TGGAGGTGTTTCAGCCTGAGGAACATAGAGCTGATTTTGGCGACTGAGCATTCC-TCGCG  4501
               |||||||||| |||||||||||||| |||||||| ||||| |||| | |  ||| ||| |
Sbjct  129705  TGGAGGTGTTCCAGCCTGAGGAACACAGAGCTGAATTTGGTGACT-AACCGTCCTTCGAG  129763

Query  4502    GT-A--AT-TGACGTGTAAGGATGGCACCTGGAGAAAAATGAGTTTGCGAAGATTCTTCA  4557
                | |  || |||| || || |||||||||||||| |||| ||||||||||||||||||||
Sbjct  129764  TTCATTATCTGACATGGAATGATGGCACCTGGAG-AAAACGAGTTTGCGAAGATTCTTCA  129822

Query  4558    TCTCCTTCAGGTAACAATGAAGCTTTCTTATCAGATGTGGCCAGGACACATAGCAAATTT  4617
               ||||||||||||||||| ||||||||||||||||| ||||||||||||  | || |||||
Sbjct  129823  TCTCCTTCAGGTAACAACGAAGCTTTCTTATCAGACGTGGCCAGGACATGTTGCGAATTT  129882

Query  4618    CCAGCTCCTGAATACTATTCAGGTGGATTATTTTCAATGATC-TTCTGAGATATTCAATC  4676
               ||||||  ||||||||||||||||  |||||||||||||| | ||||||||| || ||||
Sbjct  129883  CCAGCTGTTGAATACTATTCAGGTATATTATTTTCAATGA-CTTTCTGAGATGTTTAATC  129941

Query  4677    GACGTTAGATAATTCACCAACTTACTACAGCACAGGTGTACTAAACCTCTCCTTTGGTAA  4736
               | |||||||||||| |||| ||||||||||||||||||||||||||||||||||||||||
Sbjct  129942  GGCGTTAGATAATTGACCAGCTTACTACAGCACAGGTGTACTAAACCTCTCCTTTGGTAA  130001

Query  4737    ACCCACCGGAAGAGGTATCTCAGGCATTCATCCTGGGGTATTTCCTTGAGGCAGATGTCT  4796
               |||||| | |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  130002  ACCCACTGAAAGAGGTATCTCAGGCATTCATCCTGGGGTATTTCCTTGAGGCAGATGTCT  130061

Query  4797    ATGAACACCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGTCTGCCTC  4856
               ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  130062  ATGAACACCTTTAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGTCTGCCTC  130121

Query  4857    TTACTCATGGCCTCTGGGGAGGAGGACAGGGCCCTGGATTCAGACCATATGGCCCAGAAA  4916
               |||||||||| ||||||| || |||||||||||| || | ||| |||| |||||||||||
Sbjct  130122  TTACTCATGGTCTCTGGGAAGCAGGACAGGGCCCAGGCTCCAGGCCATCTGGCCCAGAAA  130181

Query  4917    TTCTCATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAAAGTAA  4976
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  130182  TTCTCATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAAAGTAA  130241

Query  4977    GGCAGAGGCTCAGAACTTT-GAAGGACAAATCCCTGACCTTTGCTTTCATTCTCATCCAA  5035
               || |||| ||||||| ||| |||||||  ||||||||||||||||||||||||||||| |
Sbjct  130242  GGGAGAGACTCAGAA-TTTAGAAGGACTCATCCCTGACCTTTGCTTTCATTCTCATCCCA  130300

Query  5036    TAAATCAGCTGCTCCTGTCCTC-GCTGCTCCCTGTTCTCTCTG-AGTTT-TC--T---TG  5087
               |||||||||||||||||||||| | ||||||||||||||| ||   ||| ||  |   ||
Sbjct  130301  TAAATCAGCTGCTCCTGTCCTCAG-TGCTCCCTGTTCTCTTTGTCTTTTCTCAATCCCTG  130359

Query  5088    GTCCC--TT--TTCTCTTTCAATTCTGAC---TG-GTCCCCACTTCTATTCCATTTACCT  5139
                ||||  ||  ||| ||||  ||||||||   ||  |||||||||||||||| |||||||
Sbjct  130360  TTCCCTTTTGATTCCCTTTTGATTCTGACTTTTGATTCCCCACTTCTATTCCCTTTACCT  130419

Query  5140    TCCACTG-GGAATAGGCAAGTTTCTGTTCCCACAGTGGACCCTATATTGTGGGCAGTTCT  5198
               ||||||| | || ||||| |||||||||||||||||||||||| ||| ||| ||| | ||
Sbjct  130420  TCCACTGAGTAA-AGGCAGGTTTCTGTTCCCACAGTGGACCCTGTATGGTGAGCACTCCT  130478

Query  5199    TTCCCTGAGGATCTGGGCAATGGCC-AAGGCATGCCTGAGCTTCGTCACCAGCACCACCA  5257
               ||| |||||||||||| |||||||| ||| | | ||||| |||| || ||| ||||| ||
Sbjct  130479  TTCTCTGAGGATCTGGACAATGGCCAAAGTC-TCCCTGATCTTCCTCGCCAACACCATCA  130537

Query  5258    GAAGACACTGGGCCATC-CTTGGGATACTTCTTTGCCTGACCCTGCTGTTCTTTCCCTGG  5316
               |||||| |||||||| | |||||| ||||||| |||||||||||||||||||||||||||
Sbjct  130538  GAAGACTCTGGGCCA-CACTTGGGCTACTTCTCTGCCTGACCCTGCTGTTCTTTCCCTGG  130596

Query  5317    ACACCTGAGCCCCATCTACCAGCCTTCCTGGGTCACCTCACCTGGGGCGATCCTTCTGTG  5376
               |||||||||||| ||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct  130597  ACACCTGAGCCCTATCTACCAGCCCTCCTGGGTCACCTCACCTGGGGCGATCCTTCTGTG  130656

Query  5377    TAAGCAGCATGTGAAGCCCTTCCAGCAATGCTTTTAAGGTCTCCAGATGAAGCGTCTTCA  5436
               |||||||||| |||||||||||||||||||||||||||||||||| ||||||||||||||
Sbjct  130657  TAAGCAGCATATGAAGCCCTTCCAGCAATGCTTTTAAGGTCTCCAAATGAAGCGTCTTCA  130716

Query  5437    TCAGCGATCCCAGAGGGAGGCGGGTGAAGGGCCAGGCCTGCACCATCACTGTCAGAGTCT  5496
               |||| |||||||||||||||| ||||||||||||||||||||||||||| ||||||||||
Sbjct  130717  TCAGTGATCCCAGAGGGAGGCAGGTGAAGGGCCAGGCCTGCACCATCACCGTCAGAGTCT  130776

Query  5497    GGAAGTGTCTCCTGCTGAAGGCCTCCAGGAAGAGTGGGAGGTAGAGCTCCCTGGGCAGCT  5556
               ||||||||||||||| ||||||||||| |||||||||||| |||||| ||||||||||||
Sbjct  130777  GGAAGTGTCTCCTGCGGAAGGCCTCCATGAAGAGTGGGAGATAGAGCACCCTGGGCAGCT  130836

Query  5557    CCTCCAGGGCAGAGATGGCCAAGGGCTTGTCTCTCAGCAGACTCTGCCCCGCCAGCTCCA  5616
               |||||| ||||||||||| ||||| || |||||||||||| |||||||| ||||||||||
Sbjct  130837  CCTCCATGGCAGAGATGGACAAGGCCTGGTCTCTCAGCAGGCTCTGCCCTGCCAGCTCCA  130896

Query  5617    GGAGTCTGGGTGGGGCCTGGATGCTCATCCTGAT-GAATCTGTAAGGAAAAA-CTCTAGA  5674
               |||||||||||||||||||||||||||||||||| || |||| ||| ||||| |||||||
Sbjct  130897  GGAGTCTGGGTGGGGCCTGGATGCTCATCCTGATAGA-TCTGCAAG-AAAAATCTCTAGA  130954

Query  5675    AGACAAATCCAGAGAAAAGGCATCACTTTCA-GGCCAAACACAATCA  5720
               |||||||||||| ||||| | |||||| ||| ||| |||||||||||
Sbjct  130955  AGACAAATCCAGGGAAAATGTATCACTCTCATGGC-AAACACAATCA  131000


 Features flanking this part of subject sequence:
   29101 bp at 5' side: PRAME family member 8
   2529 bp at 3' side: PRAME family member 9

 Score = 3003 bits (1626),  Expect = 0.0
 Identities = 2373/2724 (87%), Gaps = 90/2724 (3%)
 Strand=Plus/Plus

Query  15201   gggaatgggactcctcctatcaatt-ttttttt-aattttcttttgttttattgacctgg  15258
               ||||| ||||||||||||||||||| ||||||| ||||||||||||||||||||||||| 
Sbjct  98891   GGGAAAGGGACTCCTCCTATCAATTATTTTTTTAAATTTTCTTTTGTTTTATTGACCTGA  98950

Query  15259   caaggctcaaatagagttgagtttttgtttttgtttttcccattggaaggtacaagacag  15318
               ||||| |||||||||||||||||||||||||||||||| ||||||||||| |||| ||| 
Sbjct  98951   CAAGGGTCAAATAGAGTTGAGTTTTTGTTTTTGTTTTTTCCATTGGAAGGGACAA-ACAC  99009

Query  15319   aggttacaatcgttagctttagatgacaacataacaggctaaaacattttccttgcaaga  15378
               ||||||||||| || |||||||||||||| |||| ||  |||||||| ||||||| ||||
Sbjct  99010   AGGTTACAATCATTGGCTTTAGATGACAAGATAAAAGAATAAAACATATTCCTTGAAAGA  99069

Query  15379   caaccagcatg-acttcatgatcagaataaaatcagtgtccttctcactgtcagcgggt-  15436
               ||||||||| | ||||||||||||| || ||||||||| ||||||||||||||| |||| 
Sbjct  99070   CAACCAGCA-GAACTTCATGATCAGCATCAAATCAGTG-CCTTCTCACTGTCAGTGGGTG  99127

Query  15437   gaagacttcatcagtacttgtagagtttgaggtactcatgaactcatgatcagattcttt  15496
               |||| |||||||| |||||||||||||||| | ||||||||||||| ||||||| |||||
Sbjct  99128   GAAGCCTTCATCAATACTTGTAGAGTTTGAAGCACTCATGAACTCACGATCAGACTCTTT  99187

Query  15497   actcagggacaggatgtaagccaatgc-taagaccttctataggtggct-aatttttaag  15554
               ||||||||||| |||||||||||| ||  ||||||||| | |||||| | |||||  |||
Sbjct  99188   ACTCAGGGACAAGATGTAAGCCAA-GCGAAAGACCTTCCACAGGTGG-TGAATTTGGAAG  99245

Query  15555   cttgccccaatgagaccttcaggttttcaCTGGCAATATGCAGGTGCAGATATGACAAAG  15614
               | || ||||||| ||||| || ||||||||||||||||||||||||||||||||||||||
Sbjct  99246   CCTG-CCCAATGTGACCTGCAAGTTTTCACTGGCAATATGCAGGTGCAGATATGACAAAG  99304

Query  15615   AATAACAATGACCTTCATATCACCT-CCAGCTGTTGAGGAATGGGATCCTTTTCACCCTT  15673
               |||||| |||||||| | |||| || ||||||||||||||||||||||||||| ||||||
Sbjct  99305   AATAACCATGACCTTTACATCA-CTCCCAGCTGTTGAGGAATGGGATCCTTTTGACCCTT  99363

Query  15674   CCTGTCCATAAAACCAAGTTACTCATCTTCAGTGGCAACAAAATATATGGTAAACTTAAC  15733
                ||||||||| ||||| ||||||||||||  |||||||||| |||||||||  |||||||
Sbjct  99364   TCTGTCCATAGAACCAGGTTACTCATCTTGTGTGGCAACAACATATATGGTCTACTTAAC  99423

Query  15734   AGAGAAGGAGACTGTCAGaaaaaaaaaaaaaaaagatgtgtttatcctgaaatgaggaaa  15793
               ||||||| ||||  || |       ||||||||| |   ||||||  |||| | || |||
Sbjct  99424   AGAGAAGAAGAC--TCTG------TAAAAAAAAA-A---GTTTATTATGAAGTAAGCAAA  99471

Query  15794   gcaa-tgggaatagatgtgagattattttgggagaaaaaggaagacaaaggttttgaaag  15852
               | || ||| |||||||| |||||||||| |||||| ||||||||   |||| ||||||||
Sbjct  99472   G-AAGTGGCAATAGATGCGAGATTATTTGGGGAGATAAAGGAAGTTGAAGGGTTTGAAAG  99530

Query  15853   gaaaaataaggaggattatacaaattgttttgaaagactca-accttggtcctaagaatc  15911
               ||||||||||||||||||||||||||||||||||||||||| | ||||||| |||| || 
Sbjct  99531   GAAAAATAAGGAGGATTATACAAATTGTTTTGAAAGACTCATA-CTTGGTCATAAGGATT  99589

Query  15912   aaaagtaaaggggcatcagtgaaatgttggatagATTCCACCTCCACCCCCTCAGTAACC  15971
               ||||  ||| ||||||||||| |||||| |||||||||| | | ||||| |||| |||||
Sbjct  99590   AAAACCAAAAGGGCATCAGTGCAATGTTAGATAGATTCCTCTTACACCCACTCAATAACC  99649

Query  15972   CCCAACATGTTTACCAAGTCTTGGTTAACTCCCAGGATCCCATTAAAACACCCAGCTCAA  16031
               ||||||||||| | |||||||||||| ||||||||| ||||||||||| |||||||||||
Sbjct  99650   CCCAACATGTTCAGCAAGTCTTGGTTCACTCCCAGGTTCCCATTAAAA-ACCCAGCTCAA  99708

Query  16032   CCATGCCCATCCTCTACCCTCACTTCTC-TTTGTAATTTTGACATGATTTTAttacagga  16090
               || || |||  ||| ||||||||||| | |||||||||||||||||| ||||||||||||
Sbjct  99709   CCCTGACCA-GCTCCACCCTCACTTC-CATTTGTAATTTTGACATGACTTTATTACAGGA  99766

Query  16091   ccatcaggttcctatgcctgctgcacagtagctgaccaatattctgagacagcagtgttt  16150
               ||||||||||||||||||||||||||||||||| | ||||||||||||||||||| ||||
Sbjct  99767   CCATCAGGTTCCTATGCCTGCTGCACAGTAGCTTAGCAATATTCTGAGACAGCAGGGTTT  99826

Query  16151   gcagcagacagtttaatgatcacagggtggctaaatgagaagctaggaggatatcctcaa  16210
               |||||||| ||||||||||||||| ||||||| |||||||||||||||||| ||||||||
Sbjct  99827   GCAGCAGAGAGTTTAATGATCACAAGGTGGCTGAATGAGAAGCTAGGAGGAGATCCTCAA  99886

Query  16211   attcatctccccaagtagtactgagggtttccagtggatcctggatagcaaggggctgga  16270
               ||||||||||||||| |||||||| ||||||||||||||||||||||||||||||| |||
Sbjct  99887   ATTCATCTCCCCAAGGAGTACTGAAGGTTTCCAGTGGATCCTGGATAGCAAGGGGCCGGA  99946

Query  16271   aagttggtgtagaggtaagagggatgaagtcatcaggatgtca-aaactgcattctttgg  16329
               ||||||| |||| ||||||||||| ||||||| |||||||| | ||||||||||||||||
Sbjct  99947   AAGTTGGGGTAGCGGTAAGAGGGAAGAAGTCAACAGGATGT-AGAAACTGCATTCTTTGG  100005

Query  16330   tgagttggtgccttgcagagcccttcagatcagctggcatcagtagtttcactgacatgc  16389
               ||||||||||| |||||| |||||||||||||||||||||||||||||||||||||||||
Sbjct  100006  TGAGTTGGTGCATTGCAGGGCCCTTCAGATCAGCTGGCATCAGTAGTTTCACTGACATGC  100065

Query  16390   agaacctgaaagaatatctcaaatgagaaagttaatgttttacaaggcttaaattgttgt  16449
               ||||||||||||||||||||| |||| |||||||||||||||||| |||||||| |||||
Sbjct  100066  AGAACCTGAAAGAATATCTCACATGAAAAAGTTAATGTTTTACAATGCTTAAATCGTTGT  100125

Query  16450   ctgcagggtagttaaggggaactgtaagctaaggtctact-tgatttggggacagtaagc  16508
               |||||||| |||||||||||||||||| |||||||||| | |||||| || |||||| ||
Sbjct  100126  CTGCAGGGAAGTTAAGGGGAACTGTAATCTAAGGTCTA-TATGATTTTGGAACAGTAGGC  100184

Query  16509   tgccagcaaccatgaggaagaaggtcagagagcaagctgacctcatggtgaatgctgaat  16568
               |||||||||||||||||||  |||||||||||||||  |||||| || ||||||||||||
Sbjct  100185  TGCCAGCAACCATGAGGAACCAGGTCAGAGAGCAAGAAGACCTCCTGATGAATGCTGAAT  100244

Query  16569   gcgctgcaagcttggtttatttttgtttctccccctcccttcttcactgattaaacttat  16628
               | | ||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||
Sbjct  100245  GTGTTGCAAGCTTGGTTTATTTTTGTTTCTCTCCCTCCCTTCTTCACTGATTAAATTTAT  100304

Query  16629   aaagttta-caggtatcatttcaATTTCTTCCAGAGAAGACTTAACCTAAGCCCTGAGAC  16687
               |||||||| | | | |  ||||||||||||||| ||||| |||||||||||| |||||||
Sbjct  100305  AAAGTTTATC-GATGTGGTTTCAATTTCTTCCAAAGAAGCCTTAACCTAAGCACTGAGAC  100363

Query  16688   CACTCAAGCCCTCAGTGGCACCTCTCTTCCACCAGCACGAGTGAAG-AAACTGCTACCTT  16746
               |||||| ||||||||| ||||||||| |||||||| |||||  | | || ||||||||||
Sbjct  100364  CACTCACGCCCTCAGTAGCACCTCTCCTCCACCAGAACGAG-CATGTAATCTGCTACCTT  100422

Query  16747   AGGTGATATAAAA-CCCACAAGACCATTCCATACATGGAGATCTTTATTCTTATTTTGTA  16805
               |||| |||||||| |||| |||||||||  |||||| ||||| |||||||| || | |||
Sbjct  100423  AGGTTATATAAAATCCCA-AAGACCATTGAATACATTGAGATTTTTATTCTGATATCGTA  100481

Query  16806   GGGACGACTCCTCTGTGTTTATACAGCTATTTT-AACTAGAAATATTTTTATAAATTTTA  16864
               | || ||||||||||| |||||| |||| |||| || ||| || |     ||   |||||
Sbjct  100482  GTGATGACTCCTCTGTTTTTATAAAGCT-TTTTAAAGTAG-AA-A---GCAT---TTTTA  100532

Query  16865   TAATTTTGATGTGGCCAAAGATCTCCC-CACAACACTACTTTCAGGTTTTATTTTTCTGT  16923
               | ||||||||||||||||||||| |||  |||||||||||||||| ||||||||||||||
Sbjct  100533  T-ATTTTGATGTGGCCAAAGATC-CCCTAACAACACTACTTTCAGATTTTATTTTTCTGT  100590

Query  16924   CTAATGTCTGGAACAGATCAACCCCTTCCCTGCCTCACA-TCAGGACT-TGAAG-GCGAA  16980
               |||||||| ||||||||||||  |||||||||||||||| ||| |||| |||||  | | 
Sbjct  100591  CTAATGTCGGGAACAGATCAAATCCTTCCCTGCCTCACACTCAAGACTATGAAGTTC-AC  100649

Query  16981   ATAGCAGTAAAATTCCATCAGTGTTTGTGGATTTCATGAATGAATGCA-----tt-tttt  17034
               |||  | |||||| ||||||||||||||||| |||||||||||||| |     || ||||
Sbjct  100650  ATATTAATAAAATACCATCAGTGTTTGTGGAGTTCATGAATGAATG-ATTTTTTTATTTT  100708

Query  17035   ttgacaaaatctccctctgtcacccagtcaggag-ggcaatggtgtaa-tcttggctcac  17092
               |||||| |||||||||||||||||||| | |||| || | |||   || || ||||||||
Sbjct  100709  TTGACAGAATCTCCCTCTGTCACCCAGACTGGAGTGG-AGTGGCACAATTC-TGGCTCAC  100766

Query  17093   tgcaaactca--gcctccagggttcaagggattctcccacctcagccgcatgagtaactg  17150
               ||| ||| ||  |||||| |||||||||  |||||||  |||||||| |   |||| |||
Sbjct  100767  TGC-AAC-CATTGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCAAGTAGCTG  100824

Query  17151   gactacaggcagcc-accatcgtgcctggctaacttttctatttttgtagagacagggtt  17209
               |  | ||||  |||  ||||| ||||  ||||| |||| ||||||||||||||| |||||
Sbjct  100825  GGTTTCAGG-TGCCTGCCATCATGCCCAGCTAATTTTTGTATTTTTGTAGAGACGGGGTT  100883

Query  17210   tcaccatgtgggccaggctggtcttgaactc-ctgacctcaggtgatccacct-accttg  17267
               ||||| | | | || | |||||||||||| | ||||| |||||||||| | || ||||| 
Sbjct  100884  TCACCTTTTTGACCTGACTGGTCTTGAAC-CACTGACATCAGGTGATCTA-CTCACCTTC  100941

Query  17268   gcctcccaaagtgctgggattacaagtgtgagccacctcacctggccTTGAGTGAATGAA  17327
                ||| |||||||||||| |||||| || ||||||||||||||   |||||| |||||| |
Sbjct  100942  TCCTTCCAAAGTGCTGGAATTACAGGTATGAGCCACCTCACCCACCCTTGAATGAATGTA  101001

Query  17328   TTCTTGATTTCCAGTCTATCCCTAACTCTGTCAATTTCTTAATTCATGAAATGATTA-TG  17386
               ||||||| ||| |  ||||||||||| |||||||||||||  |||| ||| ||| ||  |
Sbjct  101002  TTCTTGACTTCTACCCTATCCCTAACACTGTCAATTTCTTGCTTCACGAACTGAATACAG  101061

Query  17387   CATATGTGATATGAATGGATATCTCG-TTCAATCCATTAGTCTTCGGACAGTCAAAAACC  17445
                ||||||||||||||||||||||| |  ||||||||||| |||  ||| || ||||||||
Sbjct  101062  -ATATGTGATATGAATGGATATCT-GACTCAATCCATTAATCTGGGGAGAGCCAAAAACC  101119

Query  17446   CAATCAGGATTAACTGAGTGGAGCTTCAGAAATGCAATCAGATATCGCTTTTTGATTGGA  17505
               |||||||||||||||| ||||||||||| |||||||||||||||| ||||||||||||||
Sbjct  101120  CAATCAGGATTAACTGGGTGGAGCTTCACAAATGCAATCAGATATTGCTTTTTGATTGGA  101179

Query  17506   AGCTAGCAGCGGATACGTGGAGGGGCGTGGGTGGGAGTTGTGATTAGAAAGGTCAATAAA  17565
               ||||||||| | ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  101180  AGCTAGCAGTGCATACGTGGAGGGGCGTGGGTGGGAGTTGTGATTAGAAAGGTCAATAAA  101239

Query  17566   AGCTTCTAAAGACCCACAGGACAAACTCAAAGTCTTCAAGCCTGGAGTTCCTGCTTGGCT  17625
               ||||||||||||||||||||| | || ||||||||||||||||||||||||||||||| |
Sbjct  101240  AGCTTCTAAAGACCCACAGGAGAGACCCAAAGTCTTCAAGCCTGGAGTTCCTGCTTGGTT  101299

Query  17626   CTTCCTGAGGTCTGAGCACCTTCTAAACTACAACCAGATCTGGTAAGTCACTAATTTCTG  17685
               ||||||||||||||||||||||||| |||||| |||||||||||||||||||||||||||
Sbjct  101300  CTTCCTGAGGTCTGAGCACCTTCTAGACTACATCCAGATCTGGTAAGTCACTAATTTCTG  101359

Query  17686   TAAGGACACTCCCATGTGACCTACAGTCAGCCGGTCTAGAACGGTGACAGTGCAGCCTAC  17745
               ||||||||||||||| |||||||||||||| |||||| | | ||||||||||||||||||
Sbjct  101360  TAAGGACACTCCCATCTGACCTACAGTCAGTCGGTCTGGGATGGTGACAGTGCAGCCTAC  101419

Query  17746   GATGGCATAGAACTATATCATGTC-tttttttctttttttcatatgaacactttgaagct  17804
               ||||||| ||| ||||||| |||| ||||||| ||||||| ||||||||| || ||||||
Sbjct  101420  GATGGCACAGAGCTATATCCTGTCCTTTTTTTTTTTTTTT-ATATGAACAATTGGAAGCT  101478

Query  17805   ttgatttttttt-tCTAAATGCAATTTTGTCGTGATTTCAAAAATGTTG-TTGTGCTTTT  17862
               |||| ||||||  |||||||||| || |||| | |||||||||| |||| ||||||||| 
Sbjct  101479  TTGAATTTTTTCCTCTAAATGCAGTTCTGTCTTTATTTCAAAAAAGTTGATTGTGCTTTG  101538

Query  17863   CTTTACATCATTTCAGAATTCTTG  17886
                || |   ||||| | ||||||||
Sbjct  101539  GTTGATGCCATTTTAAAATTCTTG  101562


 Features flanking this part of subject sequence:
   25773 bp at 5' side: PRAME family member 3
   4804 bp at 3' side: PRAME family member 5

 Score = 2898 bits (1569),  Expect = 0.0
 Identities = 2345/2707 (86%), Gaps = 103/2707 (3%)
 Strand=Plus/Plus

Query  15201  gggaatgggactcctcctatcaatt-ttttttt-aattttcttttgttttattgacctgg  15258
              |||||||||| |||||||||||||| ||||||| ||||||||||||||||||||||||| 
Sbjct  37526  GGGAATGGGATTCCTCCTATCAATTATTTTTTTAAATTTTCTTTTGTTTTATTGACCTGA  37585

Query  15259  caaggctcaaatagagttgagtttttgtttttgtttttcccattggaag-gtacaagaca  15317
              ||||||||||||||||||||||||||||||| |||||| |||||||||| | |||| |||
Sbjct  37586  CAAGGCTCAAATAGAGTTGAGTTTTTGTTTTCGTTTTTTCCATTGGAAGAG-ACAATACA  37644

Query  15318  gaggttacaatcgttagctttagatgacaacataacaggctaaaacattttccttgcaag  15377
              |||||||||||| || |||||||||||||| |||| ||  |||||||| |||||||||||
Sbjct  37645  GAGGTTACAATCATTGGCTTTAGATGACAAGATAAAAGAATAAAACATATTCCTTGCAAG  37704

Query  15378  acaaccagcatgacttcatgatcagaataaaatcagtgtccttctcactgtcagcgggt-  15436
              ||||||||||  ||||||||||||  || ||||||||| ||||||||||||||| |||| 
Sbjct  37705  ACAACCAGCAAAACTTCATGATCACCATCAAATCAGTG-CCTTCTCACTGTCAGTGGGTG  37763

Query  15437  gaagacttcatcagtacttgtagagtttgaggtactcatgaactcatgatcagattcttt  15496
              |||| |||||||| |||||| ||||||||||| |||||||||||||  || |||||||||
Sbjct  37764  GAAGCCTTCATCAATACTTGCAGAGTTTGAGGCACTCATGAACTCACCATGAGATTCTTT  37823

Query  15497  actcagggacaggatgtaagccaatgc-taagaccttctataggtggct-aatttttaag  15554
              |||||||||||||||||||||||| ||  ||||||||| | |||||| | |||||  |||
Sbjct  37824  ACTCAGGGACAGGATGTAAGCCAA-GCAAAAGACCTTCCACAGGTGG-TGAATTTGGAAG  37881

Query  15555  cttgccccaatg-agaccttcaggttttcaCTGGCAATATGCAGGTGCAGATATGACAAA  15613
              | || ||||||| | |||| || |||||||||||||||||||||||||||||||||||||
Sbjct  37882  CCTG-CCCAATGTA-ACCTGCAAGTTTTCACTGGCAATATGCAGGTGCAGATATGACAAA  37939

Query  15614  GAATAACAATGACCTTCATATCACCTCCAGCTGTTGAGGAATGGGATCCTTTTCACCCTT  15673
              ||||||| |||||||| | |||||| ||||||||||||||||||||||||||| ||||||
Sbjct  37940  GAATAACCATGACCTTTACATCACCCCCAGCTGTTGAGGAATGGGATCCTTTTGACCCTT  37999

Query  15674  CCTGTCCATAAAACCAAGTTACTCATCTTCAGTGGCAACAAAATATATGGTAAACTTAAC  15733
               ||||||||| ||||| ||| ||||||||  |||||||||| |||| ||||  |||||||
Sbjct  38000  TCTGTCCATAGAACCAGGTTGCTCATCTTGTGTGGCAACAACATATGTGGTCTACTTAAC  38059

Query  15734  AGAGAAGGAGACTGTCAGaaaaaaaaaaaaaaaagatgtgtttatcctgaaatgaggaaa  15793
              ||||||| ||||  || |         ||||||| |  |||||||  || | | || |||
Sbjct  38060  AGAGAAGAAGAC--TCTG--------TAAAAAAA-A--TGTTTATTATGTAGTAAGCAAA  38106

Query  15794  gcaatgggaatagatgtgagattattttgggagaaaaaggaagacaaaggttttgaaagg  15853
              | ||||||||||||||||||||||||| |||||| ||||||||   ||||||||||||||
Sbjct  38107  GAAATGGGAATAGATGTGAGATTATTTGGGGAGATAAAGGAAGTTGAAGGTTTTGAAAGG  38166

Query  15854  aaaaataaggaggattatacaaattgttttgaaagactca-accttggtcctaagaatca  15912
              |||||||||||||||||||||||||||||||||||||||| | ||||||| | || || |
Sbjct  38167  AAAAATAAGGAGGATTATACAAATTGTTTTGAAAGACTCATA-CTTGGTCATGAGGATTA  38225

Query  15913  aaagtaaaggggcatcagtgaaatgttggatagATTCCACCTCCACCCCCTCAG-TAACC  15971
              |||  ||| ||||||||||| |||||| |||||||||| | | ||||| ||| | |||||
Sbjct  38226  AAACCAAAAGGGCATCAGTGCAATGTTAGATAGATTCCTCTTACACCCACTC-GATAACC  38284

Query  15972  CCCAACATGTTTACCAAGTCTTGGTTAACTCCCAGGATCCCATTAAAACACCCAGCTCAA  16031
              ||||||||||| | |||||||||||| ||||||||| ||||||||||| |||||||||||
Sbjct  38285  CCCAACATGTTCAGCAAGTCTTGGTTCACTCCCAGGTTCCCATTAAAA-ACCCAGCTCAA  38343

Query  16032  CCATGCCCATCCTCTACCCTCACTTCTC-TTTGTAATTTTGACATGATTTTAttacagga  16090
              || || |||  ||| ||||||||||| | |||||||||||||||||| ||||||||||||
Sbjct  38344  CCCTGACCA-GCTCCACCCTCACTTC-CATTTGTAATTTTGACATGACTTTATTACAGGA  38401

Query  16091  ccatcaggttcctatgcctgctgcacagtagctgaccaatattctgagacagcagtgttt  16150
              ||||||||||||||||||||||||||||||||| | ||||||||||||||||||| ||||
Sbjct  38402  CCATCAGGTTCCTATGCCTGCTGCACAGTAGCTTAGCAATATTCTGAGACAGCAGGGTTT  38461

Query  16151  gcagcagacagtttaatgatcacagggtggctaaatgagaagctaggaggatatcctcaa  16210
              |||||||| ||||||||||||||| ||||||| |||||||||||||||||| ||||||||
Sbjct  38462  GCAGCAGAGAGTTTAATGATCACAAGGTGGCTGAATGAGAAGCTAGGAGGAGATCCTCAA  38521

Query  16211  attcatctccccaagtagtactgagggtttccagtggatcctggatagcaaggggctgga  16270
              ||||||||||||||| |||||||||||||||||||||||||||||||||||||||| |||
Sbjct  38522  ATTCATCTCCCCAAGGAGTACTGAGGGTTTCCAGTGGATCCTGGATAGCAAGGGGCCGGA  38581

Query  16271  aagttggtgtagaggtaagagggatgaagtcatcaggatgtca-aaactgcattctttgg  16329
              ||||||| |||| ||||||||||| ||||||| |||||||| | ||||||||||||||||
Sbjct  38582  AAGTTGGGGTAGCGGTAAGAGGGAAGAAGTCAACAGGATGT-AGAAACTGCATTCTTTGG  38640

Query  16330  tgagttggtgccttgcagagcccttcagatcagctggcatcagtagtttcactgacatgc  16389
              ||||||||||| |||||| ||||||||||||||||||||||||||| |||||||||||||
Sbjct  38641  TGAGTTGGTGCATTGCAGGGCCCTTCAGATCAGCTGGCATCAGTAGATTCACTGACATGC  38700

Query  16390  agaacctgaaagaatatctcaaatgagaaagttaatgttttacaaggcttaaattgttgt  16449
              ||||||||||||||||||||| |||| |||||||||||||||||| |||||||| |||||
Sbjct  38701  AGAACCTGAAAGAATATCTCAGATGAAAAAGTTAATGTTTTACAATGCTTAAATGGTTGT  38760

Query  16450  ctgcagggtagttaaggggaactgtaagctaaggtctact-tgatttggggacagtaagc  16508
              |||||||| |||||||||||||||||| |||||||||| | |||||| || |||||| | 
Sbjct  38761  CTGCAGGGAAGTTAAGGGGAACTGTAATCTAAGGTCTA-TATGATTTTGGAACAGTAGGT  38819

Query  16509  tgccagcaaccatgaggaagaaggtcagagagcaagctgacctcatggtgaatgctgaat  16568
              |||||||||||||||||||  |||||||||||||||  |||||| || ||||||||||||
Sbjct  38820  TGCCAGCAACCATGAGGAACCAGGTCAGAGAGCAAGAAGACCTCCTGATGAATGCTGAAT  38879

Query  16569  gcgctgcaagcttggtttatttttgtttctccccctcccttcttcactgattaaacttat  16628
              | | | ||||||||||||||||||||||||| ||||||||||||||||||||||| ||||
Sbjct  38880  GTGTTCCAAGCTTGGTTTATTTTTGTTTCTCTCCCTCCCTTCTTCACTGATTAAATTTAT  38939

Query  16629  aaagttta-caggtatcatttcaATTTCTTCCAGAGAAGACTTAACCTAAGCCCTGAGAC  16687
              |||||||| | | | |   |||||||||||||| ||||||||||||||||||||||||||
Sbjct  38940  AAAGTTTATC-GATGTGGCTTCAATTTCTTCCAAAGAAGACTTAACCTAAGCCCTGAGAC  38998

Query  16688  CACTCAAGCCCTCAGTGGCACCTCTCTTCCACCAGCACGAGTGAAGAAA-CTGCTACCTT  16746
              |||||| ||||||||||||||||||| |||||||| |||||  | | || ||||||||||
Sbjct  38999  CACTCACGCCCTCAGTGGCACCTCTCCTCCACCAGAACGAGC-ATGTAATCTGCTACCTT  39057

Query  16747  AGGTGATATAAAA-CCCACAAGACCATTCCA-TACATGGAGATCTTTATTCTTATTTTGT  16804
              |||| ||| |||| |||  |||||||||| | ||||| ||||| |||||||| ||||  |
Sbjct  39058  AGGTTATACAAAATCCCG-AAGACCATTC-AGTACATTGAGATTTTTATTCTGATTTCCT  39115

Query  16805  AGGGACGACTCCTCTGTGTTTATACAGCTATTTTAAC-TAGAAATATTTTTATAAATTTT  16863
              ||||||||||||||||| |||||| |||| ||||||  ||||||       ||   ||||
Sbjct  39116  AGGGACGACTCCTCTGTTTTTATAAAGCT-TTTTAAAGTAGAAAGC-----AT---TTTT  39166

Query  16864  ATAATTTTGATGTGGCCAAAGATCTCCCCACAACACTACTTTCAGGTTTTATTTTTCTGT  16923
              ||| |||||||||||||||||||||||  |||||||||||||||| ||||||||||||||
Sbjct  39167  ATA-TTTTGATGTGGCCAAAGATCTCCTAACAACACTACTTTCAGATTTTATTTTTCTGT  39225

Query  16924  CTAATGTCTGG-AACAGATCAACCCCTTCCCTGCCT--CACATCAGGACT-TGAAGG-CG  16978
              ||||||| ||| ||||||||||  ||||||||||||  ||| ||| |||| |||||  | 
Sbjct  39226  CTAATGT-TGGGAACAGATCAAATCCTTCCCTGCCTGTCAC-TCAAGACTATGAAGTTC-  39282

Query  16979  AAATAGCAGTAAAATTCCATCAGTGTTTGTGGATTTCATGAATGAATGCAttttttt-t-  17036
              | |||  |||||||| ||||||||||||||||| |||||||||||||| |||||||| | 
Sbjct  39283  ACATATTAGTAAAATACCATCAGTGTTTGTGGAGTTCATGAATGAATG-ATTTTTTTATT  39341

Query  17037  ----gacaaaatctccctctgtcacccagtcaggagggcaatggtgtaat-cttggctca  17091
                  |||| ||| |||||||||||||||| | |||| ||| |||   ||| || ||||||
Sbjct  39342  TTTTGACAGAATGTCCCTCTGTCACCCAGACTGGAGTGCAGTGGCACAATTCT-GGCTCA  39400

Query  17092  ctgcaaac-tcagcctccagggttcaagggattctcccacctcagccgcatgagtaactg  17150
              |||||| | |  |||||| |||||||||  |||||||  |||||||| |   |||| |||
Sbjct  39401  CTGCAACCATT-GCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCAAGTAGCTG  39459

Query  17151  gactacaggcagcca-ccatcgtgcct-ggctaacttttctatttttgta-----g-aga  17202
              |  | |||||| ||  ||||| ||||  || ||| |||| ||||||||||     | |||
Sbjct  39460  GGTTTCAGGCA-CCTGCCATCATGCCCAGG-TAATTTTTGTATTTTTGTATTTTTGTAGA  39517

Query  17203  --cagggtttcaccatgtgggccaggctggtcttgaactcctgacctcaggtgatccac-  17259
                |||||||||||| | | | || |||| ||||||||| |||||| |||||||||| || 
Sbjct  39518  GACAGGGTTTCACCTTTTTGACCTGGCTCGTCTTGAACCCCTGACATCAGGTGATCTACT  39577

Query  17260  ctaccttggcctcccaaagtgctgggattacaag-tgtgagccacctcacctggccTTGA  17318
              | |||||| ||| |||||||||||| |||||| | | ||| ||||||||||   ||||||
Sbjct  39578  C-ACCTTGTCCTTCCAAAGTGCTGGAATTACA-GCTATGAACCACCTCACCCACCCTTGA  39635

Query  17319  GTGAATGAATTCTTGATTTCCAGTCTATCCCTAACTCTGTCAATTTCTTAATTCATGAAA  17378
               |||||| |||||||| ||| |  ||||||||| | ||||| |||||||  |||||||| 
Sbjct  39636  ATGAATGTATTCTTGACTTCTACCCTATCCCTACCACTGTCGATTTCTTGCTTCATGAAG  39695

Query  17379  TGATTAT-GCATATGTGATATGAATGGATATCTCG-TTCAATCCATTAGTCTTCGGACAG  17436
              ||| ||| | |||||||||||||||||| |||| | ||||||||  || |||  ||| ||
Sbjct  39696  TGAATATAG-ATATGTGATATGAATGGACATCT-GATTCAATCCGGTAATCTGGGGAGAG  39753

Query  17437  TCAAAAACCCAATCAGGATTAACTGAGTGGAGCTTCAGAAATGCAATCAGATATCGCTTT  17496
               |||||||||||||||||||||||| ||||||||||| |||||||||||||||||  |||
Sbjct  39754  CCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCACAAATGCAATCAGATATCATTTT  39813

Query  17497  TTGATTGGAAGCTAGCAGCGGATACGTGGAGGGGCGTGGGTGGGAGTTGTGATTAGAAAG  17556
              ||||||||||| |||||||||||| ||| |||||||||||||||||||||||||||||||
Sbjct  39814  TTGATTGGAAGGTAGCAGCGGATATGTGCAGGGGCGTGGGTGGGAGTTGTGATTAGAAAG  39873

Query  17557  GTCAATAAAAGCTTCTAAAGACCCACAGGACAAACTCAAAGTCTTCAAGCCTGGAGTTCC  17616
              |||||||||||||||||||||||||||||| | || ||||||||||||||||||||||||
Sbjct  39874  GTCAATAAAAGCTTCTAAAGACCCACAGGAGAGACCCAAAGTCTTCAAGCCTGGAGTTCC  39933

Query  17617  TGCTTGGCTCTTCCTGAGGTCTGAGCACCTTCTAAACTACAACCAGATCTGGTAAGTCAC  17676
              ||||||| ||||||||||| |||||||||||||| |||||| |||||||||||||| |||
Sbjct  39934  TGCTTGGTTCTTCCTGAGGACTGAGCACCTTCTAGACTACATCCAGATCTGGTAAGCCAC  39993

Query  17677  TAATTTCTGTAAGGACACTCCCATGTGACCTACAGTCAGCCGGTCTAGAACGGTGACAGT  17736
              |||||||||||||||||||||||| |||||||||||||| |||||| | | |||||||||
Sbjct  39994  TAATTTCTGTAAGGACACTCCCATCTGACCTACAGTCAGTCGGTCTGGGATGGTGACAGT  40053

Query  17737  GCAGCCTACGATGGCATAGAACTATATCATGTCtttttttctttttttcatatgaacact  17796
              |||||||||||||||| ||| ||||||| |||| |||||| ||||   |||||||||| |
Sbjct  40054  GCAGCCTACGATGGCACAGAGCTATATCCTGTCCTTTTTT-TTTT---CATATGAACAAT  40109

Query  17797  ttgaagctttgatttttttt-tCTAAATGCAATTTTGTCGTGATTTCAAAAATGTTG-TT  17854
              ||||||||| || | ||||  |||||||||| || |||| | |||||||||| |||| ||
Sbjct  40110  TTGAAGCTT-GAATGTTTTCCTCTAAATGCAGTTCTGTCTTTATTTCAAAAAAGTTGATT  40168

Query  17855  GTGCTTT  17861
              |||||||
Sbjct  40169  GTGCTTT  40175


 Features flanking this part of subject sequence:
   14881 bp at 5' side: PRAME family member 16
   7025 bp at 3' side: PRAME family member 21

 Score = 2385 bits (1291),  Expect = 0.0
 Identities = 1744/1959 (89%), Gaps = 46/1959 (2%)
 Strand=Plus/Plus

Query  23633   CTATTCTTTCTTCAATGGAGATGGCATGCAAGGATTACTTTATAAAACACACAGAAATAT  23692
               |||||| ||||||| ||||||||||||||  ||||||||||||||||  || ||||||||
Sbjct  193097  CTATTCATTCTTCAGTGGAGATGGCATGCGGGGATTACTTTATAAAATTCATAGAAATAT  193156

Query  23693   TTTTTCCTCCCACCCCAATTC-CAACCATTACCGTGCAACCTGTtgtcaatagacgttaa  23751
               |||||| || |||||||| ||  |||||||||| |||| |||| ||||||| || |||| 
Sbjct  193157  TTTTTCTTCTCACCCCAA-TCTAAACCATTACCATGCAGCCTGGTGTCAATGGAAGTTAG  193215

Query  23752   ggcagttgaggcagaaataattaaataaagcttcattggaagctaaatgtcaggatcgac  23811
               |||  ||||||||||||||||| ||||||||||||||||||||||||||| |||||||||
Sbjct  193216  GGCTCTTGAGGCAGAAATAATT-AATAAAGCTTCATTGGAAGCTAAATGTGAGGATCGAC  193274

Query  23812   ctggaagacacacactgacaaaatgagcgttttccaaagtctgttacaagttggaatgct  23871
               |||||||||||||||||||||| || | || | ||||||||||||||||||||||||| |
Sbjct  193275  CTGGAAGACACACACTGACAAAGTGGGTGTGTCCCAAAGTCTGTTACAAGTTGGAATGTT  193334

Query  23872   tttataagaaaggttgaaagaagggaatgggactcctcctatcag-ttgttttttttttt  23930
               ||| | ||||| ||| ||||||||||||||| ||||||||||||| |||||| ||| |||
Sbjct  193335  TTTGTGAGAAATGTTAAAAGAAGGGAATGGGGCTCCTCCTATCAGTTTGTTTGTTTGTTT  193394

Query  23931   taattttcttttg-tt-tt-atcctggcaaggctctaatagagttgagcttttttgtttt  23987
               |||||| ||| || || || || |||||||| ||| |||||||||  | ||||||   | 
Sbjct  193395  TAATTTGCTTCTGTTTCTTGAT-CTGGCAAGCCTCAAATAGAGTT--G-TTTTTTCAGTG  193450

Query  23988   tgttttttccattggaagggacaatacagaggttacaatcattgactttagatgacaaca  24047
               ||| ||||||||||||| | | |||||||||| ||||||||||| |||||||||||||||
Sbjct  193451  TGTCTTTTCCATTGGAA-GTATAATACAGAGGCTACAATCATTGGCTTTAGATGACAACA  193509

Query  24048   tgacaggcaaaaatattttccttgcaagacaaccagcaaaacttcacgatcagaatcaaa  24107
               | ||||||    | |||||||||||||||||||||||||||||||| |||||||||||||
Sbjct  193510  TAACAGGC--TTACATTTTCCTTGCAAGACAACCAGCAAAACTTCATGATCAGAATCAAA  193567

Query  24108   tcagtgtccttctcactgtcactgggtgaagccttcatcagtacttgaagagtctcaggc  24167
               |||||||||||||||| |||  | ||||||||||||||||||||||||||||| | || |
Sbjct  193568  TCAGTGTCCTTCTCACCGTCTGTAGGTGAAGCCTTCATCAGTACTTGAAGAGTTTGAGTC  193627

Query  24168   actcatgaagtcaagatcagattctttactcagggacaggatgtaagccaatcataagac  24227
               ||||||||| ||| ||||||||||||||||||||||||||||||||||||||| ||||||
Sbjct  193628  ACTCATGAACTCATGATCAGATTCTTTACTCAGGGACAGGATGTAAGCCAATCGTAAGAC  193687

Query  24228   cttccacagatgatcaatttggaagtctacctaatgtgacctgcaggttttcaCTGGCAA  24287
               ||||| ||| || | |||||||||| || || ||||||||||||||||||||||||||||
Sbjct  193688  CTTCCGCAGGTGGTTAATTTGGAAGCCTGCCCAATGTGACCTGCAGGTTTTCACTGGCAA  193747

Query  24288   TATGCAGGTGCAGATATGACAAAGAATAATCC-TGACCTTCATATCGCCCCTAGCTGATG  24346
               ||||||||||||||||||||||||||||| || ||||||||||||| |||| ||||| | 
Sbjct  193748  TATGCAGGTGCAGATATGACAAAGAATAA-CCATGACCTTCATATCACCCCCAGCTGGTT  193806

Query  24347   AGGATTGGGATTCTTTTGTCCCTTTCTCTCCATAAAACCAGGTTACTCATCTTGTGTGGC  24406
               |||| |||||| |||||| ||||||||||||||||||||||||||| |||||||||||||
Sbjct  193807  AGGAATGGGATCCTTTTGACCCTTTCTCTCCATAAAACCAGGTTACACATCTTGTGTGGC  193866

Query  24407   AACAAAATATATGGTctacttaacagagaaagagactc--------ca-cagga-aaaaa  24456
                |||||||||||||||| ||||||||||||||||||||         |  |  | |||||
Sbjct  193867  GACAAAATATATGGTCTGCTTAACAGAGAAAGAGACTCTGTAAAAAAATAAAAATAAAAA  193926

Query  24457   aa-aaggatttttattatgaaatgagcaaagccatgggaatagatgtgagattattcggg  24515
               || ||||||||||||||||||||||||||||| ||||||||| |||||||||||| | ||
Sbjct  193927  AATAAGGATTTTTATTATGAAATGAGCAAAGCAATGGGAATAAATGTGAGATTATCCAGG  193986

Query  24516   gaggtaaaggaagacaaaggttttgaaaggaaaaatgagg-agaattacataaatttttt  24574
               |||||||||||||||||| | ||||||||||||||| ||| || |||||||||| | |||
Sbjct  193987  GAGGTAAAGGAAGACAAA-GATTTGAAAGGAAAAATAAGGAAG-ATTACATAAACTGTTT  194044

Query  24575   tgaaagactcattcttggtcacaa-gtatgaaaaccaagggag-cct-cagtgcagtgtt  24631
               |||||||||||| |||| ||| || || | ||||||||||| | | | ||||||| ||||
Sbjct  194045  TGAAAGACTCATCCTTGCTCATAAGGT-TCAAAACCAAGGG-GTCATCCAGTGCAATGTT  194102

Query  24632   ggaaagATTCCTCCTCCACC-CTCTCAATAACCCCCAACACATTTACCAAGTCTTTGTTC  24690
               ||| |||||||||||||||| | ||||||||||| |||||  ||||||||||||| ||||
Sbjct  194103  GGATAGATTCCTCCTCCACCAC-CTCAATAACCCACAACATGTTTACCAAGTCTTGGTTC  194161

Query  24691   ACTCCCAGGATTCC-ATTAAAACACCCAGCTCAACCCTGACCAGCCTCCACCTTCACTTC  24749
               |||||||||| ||| |||||||||||||||||||||||| |||||| ||||| |||||||
Sbjct  194162  ACTCCCAGGA-TCCAATTAAAACACCCAGCTCAACCCTGCCCAGCCCCCACCCTCACTTC  194220

Query  24750   CCTTTGTAATTTTGACATAAATTtgttacaggaccatcaggttcctatgccggctgcaca  24809
               |||| ||||||||||||| | ||| |||||||||||||||||||||||||| ||||||||
Sbjct  194221  CCTTCGTAATTTTGACATGACTTTATTACAGGACCATCAGGTTCCTATGCCTGCTGCACA  194280

Query  24810   gtagcttaccaatattctgagacagcaggatttgcagcagaaagtttaatgatcacaggg  24869
               |||||| | |||||||||||||||||||| ||||||||||| |||||||||||||||| |
Sbjct  194281  GTAGCTGAGCAATATTCTGAGACAGCAGGGTTTGCAGCAGAGAGTTTAATGATCACAGAG  194340

Query  24870   tggctgaatgagaagctgggaggagatcctcaaattcatctccccaaggagtactgaggg  24929
               ||||||||||| ||||| |||||||||||||||||||||||||||||||| |||| ||||
Sbjct  194341  TGGCTGAATGATAAGCTAGGAGGAGATCCTCAAATTCATCTCCCCAAGGATTACTCAGGG  194400

Query  24930   tttccagtggatcctggatag-caaggggctggaaagttggtgtagtttgatggcaataa  24988
               ||| ||| ||||| ||||| | |||| ||||||||||||||||||||||| ||||| |||
Sbjct  194401  TTTTCAGGGGATCATGGAT-GACAAGCGGCTGGAAAGTTGGTGTAGTTTGGTGGCAGTAA  194459

Query  24989   gaggtatgaagttatcacgatgtcagaacggcattctttggtgagttgatgccttgcagg  25048
               |||||||||||| |||| ||||||| ||| |||||||||||||||||| |||||||||| 
Sbjct  194460  GAGGTATGAAGTCATCAGGATGTCAAAACTGCATTCTTTGGTGAGTTGGTGCCTTGCAGA  194519

Query  25049   gcccttcagatcagctggcatcagtagtttcactgacatgcagaacctgaaagaatatct  25108
               |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |
Sbjct  194520  GCCCTTCAGATCAGCTGGCATCAGTAGTTTCACTGACATGCAGAACCTGAAAGAATATGT  194579

Query  25109   caaatgaaaaa-cttaatgtttcacaatgcttaaattgttgtctgcagcgtagttaaggg  25167
               ||||||||||| | |||||||| |||||||||||||||| |||||||| | |||||||||
Sbjct  194580  CAAATGAAAAAGC-TAATGTTTTACAATGCTTAAATTGTCGTCTGCAGGGCAGTTAAGGG  194638

Query  25168   gaattgtagtctaagttctacacgattttgggacagtaggctgccagcaaccatgaggaa  25227
               ||| |||| |||||| |||||| |||||||||||||||||||||||||||||||||||||
Sbjct  194639  GAACTGTAATCTAAGGTCTACATGATTTTGGGACAGTAGGCTGCCAGCAACCATGAGGAA  194698

Query  25228   gcaggtcagagggcaagctgacctcctggtgaatgctgaatgcgtttcaagcttggtttg  25287
               ||||||||||| |||||||||||||||| ||||||||||||||  | |||||||||||||
Sbjct  194699  GCAGGTCAGAGAGCAAGCTGACCTCCTGATGAATGCTGAATGCACTGCAAGCTTGGTTTG  194758

Query  25288   tttttgttcctccccctctctttttcaccgattaaatttataaagtttagaaatacggtt  25347
               |||| ||| ||||||||| ||| ||||| |||||||||||||||||||||||||||||||
Sbjct  194759  TTTTGGTTTCTCCCCCTCCCTTCTTCACTGATTAAATTTATAAAGTTTAGAAATACGGTT  194818

Query  25348   tcaATTTCTTCCAGACAAGCCTTAACCTAAGCCCTGAGACCACTCAAGCCCTCAGTGGCA  25407
               |||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||
Sbjct  194819  TCAATTTCTTCCAGACAAGCCTTAACCTAAGCCCTGAGACCACTCACGCCCTCAGTGGCA  194878

Query  25408   CCTCTCTTCCACCAGCATGAGCAAATAAAT-TGCTACCTTAGGTGATATAAAACCCACAA  25466
               ||||||||||||||| |  |||  |||| | |||||| ||||||||||||||||||||||
Sbjct  194879  CCTCTCTTCCACCAGAACAAGCGTATAA-TCTGCTACATTAGGTGATATAAAACCCACAA  194937

Query  25467   GATGATTCGATACATGGAGtttttt-ttCTGATTTTGTAGGGATGACTTCTTTGTTTCTA  25525
               ||  |||||||||| |||| ||||| |||| ||||||||||||||||  |||||||| ||
Sbjct  194938  GACCATTCGATACAAGGAGATTTTTATTCTTATTTTGTAGGGATGACACCTTTGTTTTTA  194997

Query  25526   TAAAGCTGTTTTAACTATAAAACAATTTTATAATTTTGA  25564
               ||||||| ||||||||||||| || |||| |  ||||||
Sbjct  194998  TAAAGCTATTTTAACTATAAAGCATTTTTTTTTTTTTGA  195036


 Features flanking this part of subject sequence:
   14880 bp at 5' side: PRAME family member 16
   7035 bp at 3' side: PRAME family member 21

 Score = 2350 bits (1272),  Expect = 0.0
 Identities = 1731/1948 (88%), Gaps = 49/1948 (2%)
 Strand=Plus/Plus

Query  14939   CCTATTCATTCTTCAATGCAGATGGCATGCAAGGATTACTTTATAAAACTCATAGAAATA  14998
               ||||||||||||||| || |||||||||||  |||||||||||||||| |||||||||||
Sbjct  193096  CCTATTCATTCTTCAGTGGAGATGGCATGCGGGGATTACTTTATAAAATTCATAGAAATA  193155

Query  14999   CTTTTTCTTCCCACCCCAAT-TCAAACCATTACCATGCAACCTGGTATCAATAgaagtta  15057
                ||||||||| ||||||||| | |||||||||||||||| |||||| ||||| |||||||
Sbjct  193156  TTTTTTCTTCTCACCCCAATCT-AAACCATTACCATGCAGCCTGGTGTCAATGGAAGTTA  193214

Query  15058   aggc-cattgaggtagaaataattaaataaagctttattggaagctaaatgtgagaatcg  15116
                ||| | |||||| |||||||||||| |||||||| ||||||||||||||||||| ||||
Sbjct  193215  GGGCTC-TTGAGGCAGAAATAATTAA-TAAAGCTTCATTGGAAGCTAAATGTGAGGATCG  193272

Query  15117   acctggaagacacacactgacaaagtgagtgttttccaaagtctgttacaagttggaatg  15176
               ||||||||||||||||||||||||||| |||| | |||||||||||||||||||||||||
Sbjct  193273  ACCTGGAAGACACACACTGACAAAGTGGGTGTGTCCCAAAGTCTGTTACAAGTTGGAATG  193332

Query  15177   cttttgtaagagaggttaaaagaagggaatgggactcctcctatcaattt-ttt-ttt--  15232
                |||||| ||| | ||||||||||||||||||| |||||||||||| ||| ||| |||  
Sbjct  193333  TTTTTGTGAGAAATGTTAAAAGAAGGGAATGGGGCTCCTCCTATCAGTTTGTTTGTTTGT  193392

Query  15233   ---aattttcttttgttttattgacctggcaaggctcaaatagagttgagtttttgtttt  15289
                  ||||| ||| |||||  |||| |||||||| ||||||||||||||  |||||   | 
Sbjct  193393  TTTAATTTGCTTCTGTTTC-TTGATCTGGCAAGCCTCAAATAGAGTTGT-TTTTTCAGTG  193450

Query  15290   tgt-ttttcccattggaaggtacaagacagaggttacaatcgttagctttagatgacaac  15348
               ||| |||||| |||||||| || || ||||||| ||||||| || |||||||||||||||
Sbjct  193451  TGTCTTTTCC-ATTGGAAG-TATAATACAGAGGCTACAATCATTGGCTTTAGATGACAAC  193508

Query  15349   ataacaggctaaaacattttccttgcaagacaaccagcatgacttcatgatcagaataaa  15408
               |||||||||| |  |||||||||||||||||||||||||  |||||||||||||||| ||
Sbjct  193509  ATAACAGGCTTA--CATTTTCCTTGCAAGACAACCAGCAAAACTTCATGATCAGAATCAA  193566

Query  15409   atcagtgtccttctcactgtcagcgggtgaagacttcatcagtacttgtagagtttgagg  15468
               ||||||||||||||||| ||| |  ||||||| ||||||||||||||| |||||||||| 
Sbjct  193567  ATCAGTGTCCTTCTCACCGTCTGTAGGTGAAGCCTTCATCAGTACTTGAAGAGTTTGAG-  193625

Query  15469   t-actcatgaactcatgatcagattctttactcagggacaggatgtaagccaat-gctaa  15526
               | |||||||||||||||||||||||||||||||||||||||||||||||||||| | |||
Sbjct  193626  TCACTCATGAACTCATGATCAGATTCTTTACTCAGGGACAGGATGTAAGCCAATCG-TAA  193684

Query  15527   gaccttctataggtggctaatttttaagcttgccccaatgagaccttcaggttttcaCTG  15586
               |||||||   |||||| ||||||  |||| ||||| |||| ||||| |||||||||||||
Sbjct  193685  GACCTTCCGCAGGTGGTTAATTTGGAAGCCTGCCC-AATGTGACCTGCAGGTTTTCACTG  193743

Query  15587   GCAATATGCAGGTGCAGATATGACAAAGAATAACAATGACCTTCATATCACCTCCAGCTG  15646
               |||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||
Sbjct  193744  GCAATATGCAGGTGCAGATATGACAAAGAATAACCATGACCTTCATATCACCCCCAGCTG  193803

Query  15647   -TTGAGGAATGGGATCCTTTTCACCCTTCCTGTCCATAAAACCAAGTTACTCATCTTCAG  15705
                || ||||||||||||||||| |||||| || |||||||||||| ||||| ||||||  |
Sbjct  193804  GTT-AGGAATGGGATCCTTTTGACCCTTTCTCTCCATAAAACCAGGTTACACATCTTGTG  193862

Query  15706   TGGCAACAAAATATATGGTAAACTTAACAGAGAAGGAGACT--GTCAGaaaa-aaaaa-a  15761
               |||| ||||||||||||||   |||||||||||| ||||||  || | |||| ||||| |
Sbjct  193863  TGGCGACAAAATATATGGTCTGCTTAACAGAGAAAGAGACTCTGTAAAAAAATAAAAATA  193922

Query  15762   aaaaaagatg--tgtttatcctgaaatgaggaaagcaatgggaatagatgtgagattatt  15819
               |||||| | |  | |||||  ||||||||| ||||||||||||||| |||||||||||| 
Sbjct  193923  AAAAAATAAGGATTTTTATTATGAAATGAGCAAAGCAATGGGAATAAATGTGAGATTATC  193982

Query  15820   ttgggagaaaaaggaagacaaaggttttgaaaggaaaaataaggaggattatacaaattg  15879
                 |||||  |||||||||||||| ||| ||||||||||||||||| ||||| | ||| ||
Sbjct  193983  CAGGGAGGTAAAGGAAGACAAAGATTT-GAAAGGAAAAATAAGGAAGATTACATAAACTG  194041

Query  15880   ttttgaaagactcaaccttggtcctaagaatcaaaagtaaagggg-catc-agtgaaatg  15937
               |||||||||||||| ||||| || ||||  ||||||  || |||| |||| |||| ||||
Sbjct  194042  TTTTGAAAGACTCATCCTTGCTCATAAGGTTCAAAACCAA-GGGGTCATCCAGTGCAATG  194100

Query  15938   ttggatagATTCCACCTCCACCCCCTCAGTAACCCCCAACATGTTTACCAAGTCTTGGTT  15997
               ||||||||||||| |||||||| ||||| |||||| ||||||||||||||||||||||||
Sbjct  194101  TTGGATAGATTCCTCCTCCACCACCTCAATAACCCACAACATGTTTACCAAGTCTTGGTT  194160

Query  15998   AACTCCCAGGATCCCATTAAAACACCCAGCTCAACCATGCCCATCCTCTACCCTCACTTC  16057
                ||||||||||||| ||||||||||||||||||||| |||||| || | |||||||||||
Sbjct  194161  CACTCCCAGGATCCAATTAAAACACCCAGCTCAACCCTGCCCAGCCCCCACCCTCACTTC  194220

Query  16058   TCTTTGTAATTTTGACATGATTTTAttacaggaccatcaggttcctatgcctgctgcaca  16117
                ||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct  194221  CCTTCGTAATTTTGACATGACTTTATTACAGGACCATCAGGTTCCTATGCCTGCTGCACA  194280

Query  16118   gtagctgaccaatattctgagacagcagtgtttgcagcagacagtttaatgatcacaggg  16177
               |||||||| ||||||||||||||||||| |||||||||||| |||||||||||||||| |
Sbjct  194281  GTAGCTGAGCAATATTCTGAGACAGCAGGGTTTGCAGCAGAGAGTTTAATGATCACAGAG  194340

Query  16178   tggctaaatgagaagctaggaggatatcctcaaattcatctccccaagtagtactgaggg  16237
               ||||| ||||| |||||||||||| ||||||||||||||||||||||| | |||| ||||
Sbjct  194341  TGGCTGAATGATAAGCTAGGAGGAGATCCTCAAATTCATCTCCCCAAGGATTACTCAGGG  194400

Query  16238   tttccagtggatcctggat-agcaaggggctggaaagttggtgtaga--ggta--ag-a-  16290
               ||| ||| ||||| ||||| | |||| |||||||||||||||||||   |||   || | 
Sbjct  194401  TTTTCAGGGGATCATGGATGA-CAAGCGGCTGGAAAGTTGGTGTAGTTTGGTGGCAGTAA  194459

Query  16291   g-gg-atgaagtcatcaggatgtcaaaactgcattctttggtgagttggtgccttgcaga  16348
               | || |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  194460  GAGGTATGAAGTCATCAGGATGTCAAAACTGCATTCTTTGGTGAGTTGGTGCCTTGCAGA  194519

Query  16349   gcccttcagatcagctggcatcagtagtttcactgacatgcagaacctgaaagaatatct  16408
               |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |
Sbjct  194520  GCCCTTCAGATCAGCTGGCATCAGTAGTTTCACTGACATGCAGAACCTGAAAGAATATGT  194579

Query  16409   caaatgagaaagttaatgttttacaaggcttaaattgttgtctgcagggtagttaagggg  16468
               ||||||| |||| ||||||||||||| ||||||||||| |||||||||| ||||||||||
Sbjct  194580  CAAATGAAAAAGCTAATGTTTTACAATGCTTAAATTGTCGTCTGCAGGGCAGTTAAGGGG  194639

Query  16469   aactgtaagctaaggtctacttgatttggggacagtaagctgccagcaaccatgaggaag  16528
               |||||||| ||||||||||| |||||| ||||||||| ||||||||||||||||||||||
Sbjct  194640  AACTGTAATCTAAGGTCTACATGATTTTGGGACAGTAGGCTGCCAGCAACCATGAGGAAG  194699

Query  16529   aaggtcagagagcaagctgacctcatggtgaatgctgaatgcgctgcaagcttggtttat  16588
                ||||||||||||||||||||||| || |||||||||||||| ||||||||||||||| |
Sbjct  194700  CAGGTCAGAGAGCAAGCTGACCTCCTGATGAATGCTGAATGCACTGCAAGCTTGGTTTGT  194759

Query  16589   ttttgtttctccccctcccttcttcactgattaaacttataaagtttacaggtatca-tt  16647
               ||| ||||||||||||||||||||||||||||||| |||||||||||| |  || |  ||
Sbjct  194760  TTTGGTTTCTCCCCCTCCCTTCTTCACTGATTAAATTTATAAAGTTTAGAAATA-CGGTT  194818

Query  16648   tcaATTTCTTCCAGAGAAGACTTAACCTAAGCCCTGAGACCACTCAAGCCCTCAGTGGCA  16707
               ||||||||||||||| ||| |||||||||||||||||||||||||| |||||||||||||
Sbjct  194819  TCAATTTCTTCCAGACAAGCCTTAACCTAAGCCCTGAGACCACTCACGCCCTCAGTGGCA  194878

Query  16708   CCTCTCTTCCACCAGCACGAGTGAAGAAACTGCTACCTTAGGTGATATAAAACCCACAAG  16767
               ||||||||||||||| || || | | || ||||||| |||||||||||||||||||||||
Sbjct  194879  CCTCTCTTCCACCAGAACAAGCGTATAATCTGCTACATTAGGTGATATAAAACCCACAAG  194938

Query  16768   ACCATTCCATACATGGAGATCTTTATTCTTATTTTGTAGGGACGACTCCTCTGTGTTTAT  16827
               ||||||| ||||| |||||| ||||||||||||||||||||| ||| ||| ||| |||||
Sbjct  194939  ACCATTCGATACAAGGAGATTTTTATTCTTATTTTGTAGGGATGACACCTTTGTTTTTAT  194998

Query  16828   ACAGCTATTTTAACTAGAAAT-ATTTTT  16854
               | |||||||||||||| |||  ||||||
Sbjct  194999  AAAGCTATTTTAACTATAAAGCATTTTT  195026


 Features flanking this part of subject sequence:
   10790 bp at 5' side: PRAME family member 5
   5464 bp at 3' side: PRAME family member 8

 Score = 2265 bits (1226),  Expect = 0.0
 Identities = 1784/2044 (87%), Gaps = 75/2044 (3%)
 Strand=Plus/Plus

Query  3254   TGGCAGAAACTTTCTCCAGCAGAGCTCCGAGGGGTTCAAGACTGATACAGAACTGCAGCA  3313
              |||||| || |||||| ||||||||||||||||||||||||||||| | |||| ||||||
Sbjct  59611  TGGCAGCAATTTTCTCTAGCAGAGCTCCGAGGGGTTCAAGACTGATGCGGAACAGCAGCA  59670

Query  3314   TGTAGCTGAGATTCAGATGCTTTGGGTAAGC-GAGGCTTGGGTACTG-GTAGAGACACTT  3371
               |||||||||||||||||||||| ||| ||| ||||||||||||||| | | ||||||||
Sbjct  59671  CGTAGCTGAGATTCAGATGCTTTAGGT-AGCTGAGGCTTGGGTACTGAG-ACAGACACTT  59728

Query  3372   CAAGTCCTCTTCCAATAGGTAGCCGCAAGTTAATTCCAAGTTCTCCAAGGGGTTCTAGAG  3431
              || ||| ||||||||||||||||| |||||||| |||||||||||||||||||||| |||
Sbjct  59729  CATGTCTTCTTCCAATAGGTAGCCACAAGTTAACTCCAAGTTCTCCAAGGGGTTCTGGAG  59788

Query  3432   GCACCTGTGGAGATCAAGAAGTTAGTTCTGGGCAATGGTACCAGTTAGATGAAGGTAGTG  3491
              |||||||||||||||||||||||||||||||||| || |||||||||||||||||| |||
Sbjct  59789  GCACCTGTGGAGATCAAGAAGTTAGTTCTGGGCAGTGATACCAGTTAGATGAAGGTGGTG  59848

Query  3492   GGGAATGAACT-CAAGGAAAATACCTGCTTCAACCAAACACAAGTTTGTTCCCACCATCT  3550
              |||||| ||||  |||| ||||  |||||||| |||||||||||||| |||||| ||| |
Sbjct  59849  GGGAAT-AACTGAAAGGGAAATGTCTGCTTCACCCAAACACAAGTTTATTCCCATCATGT  59907

Query  3551   GATGATGGTCCTCATGCAAGTTGCTGCATGT--TGAGGACCCTGATCATTCAGGGGCTGT  3608
              ||||||||||| ||||||||||||| | |||  ||||||| |||||||||| ||||| ||
Sbjct  59908  GATGATGGTCCACATGCAAGTTGCT-C-TGTGATGAGGACTCTGATCATTCCGGGGCAGT  59965

Query  3609   CCCATTTTAGCCTCAGCCCTTTCACCATTTCTTGTGTGATTGGGTCAAGGCCACAAAAT-  3667
              || | ||||||||||  |||||||||||| ||||||||||||| ||||||||||||||| 
Sbjct  59966  CCTAGTTTAGCCTCAATCCTTTCACCATTGCTTGTGTGATTGGTTCAAGGCCACAAAATC  60025

Query  3668   -C-T--CTAAAGCCT-TTTATCTTCATCTTTTAGCAGAAAACCTCATCTCTGGGCCACAG  3722
               | |  ||||||||| ||| |||||||||||||||||||||| |||||||||||||||||
Sbjct  60026  ACATCACTAAAGCCTCTTT-TCTTCATCTTTTAGCAGAAAACTTCATCTCTGGGCCACAG  60084

Query  3723   GTACCCGGTGGGAGATGTGCACAAAGAACTCAACTCAGCAAGGTCTAGGGACATTAGCTG  3782
              |||||||||||||||||||||  |||||||||||| |||||||||||||| ||| |||| 
Sbjct  60085  GTACCCGGTGGGAGATGTGCATGAAGAACTCAACTGAGCAAGGTCTAGGGTCATCAGCTA  60144

Query  3783   GGGCTACCTGCCGGCAGGGGCTCCCTGGCCTGCCTGCATCTGCAAACCAACTGTCACTTT  3842
              ||||||||| | ||||||||||||||| | ||||||||||||||||||| || |||||||
Sbjct  60145  GGGCTACCTACTGGCAGGGGCTCCCTGACGTGCCTGCATCTGCAAACCACCTATCACTTT  60204

Query  3843   TTACCACTCTCACTCCTACTCCTTCACCCTCCATCCCAGAAGCATGCATGTCCCATGTCA  3902
              ||||||||||||| |||||||| ||| ||||||| | |||||||  ||| ||||||||||
Sbjct  60205  TTACCACTCTCACGCCTACTCCCTCAGCCTCCATTCAAGAAGCACACATTTCCCATGTCA  60264

Query  3903   ATTGA-CTTTCCTGGAGTTCAAAACAACCTTCTACAGACAGGGAATCAGAGACAGGATCA  3961
               || | ||||||||| ||||||||||||||| |||||||||||||| |||||||||||||
Sbjct  60265  GTT-ACCTTTCCTGGGGTTCAAAACAACCTTTTACAGACAGGGAAT-AGAGACAGGATCA  60322

Query  3962   TTCATGATCACTAAGCTGGTGAGGACAGAGCTTCTACTGTGAAATGCACAAGTTTGATGC  4021
              ||  |||||||||||||||||||||||||| ||||||||||||||||||| |||||||||
Sbjct  60323  TTTGTGATCACTAAGCTGGTGAGGACAGAGTTTCTACTGTGAAATGCACAGGTTTGATGC  60382

Query  4022   ACTGTCCCTCCTTTCATACCCTCCTTTGTTACCTCTTTTAC-ATCATATCAACTTGAAAC  4080
               |||||||||||||||||||||||| | ||||||| ||| | ||||||||||||||||||
Sbjct  60383  GCTGTCCCTCCTTTCATACCCTCCTCTATTACCTC-TTTCCTATCATATCAACTTGAAAC  60441

Query  4081   ACACTTTGTAACAAGAAATTCACACGTGCA-CATGCAGTAGAGAC-AAAACGCCCACTAA  4138
              ||||||||||||||||||||||||  |||| |   |||||||| |  |||| ||||||| 
Sbjct  60442  ACACTTTGTAACAAGAAATTCACATATGCACCCCCCAGTAGAG-CTGAAACCCCCACTAC  60500

Query  4139   GTACCTTGTACATGATGTCCCTCTCTAGCCTCTACCCTAGGTGACCCCTCTGCCTTTATT  4198
               |  ||||||||||||||  ||||||||||||||||| |||||||||| ||||| | |||
Sbjct  60501  CTGGCTTGTACATGATGTAGCTCTCTAGCCTCTACCCCAGGTGACCCCGCTGCCCTCATT  60560

Query  4199   GAAGTGATCCTGTGATAGCCACTCCAGG-ACATGGAGCACTGAACGGGACAATGTGTTGA  4257
              | || |||||||||||||||||||| || ||||||||||||||| |||||||||||||||
Sbjct  60561  GCAGAGATCCTGTGATAGCCACTCC-GGAACATGGAGCACTGAATGGGACAATGTGTTGA  60619

Query  4258   CATTCTGGTGTCCCCTGCACTGTGCCGTCGCCACTGGCTGGCAC-ACAGTACACGTCTTC  4316
               ||||||||||||||| |||||||  ||| |||||||||| ||| | |||  | | ||||
Sbjct  60620  TATTCTGGTGTCCCCTTCACTGTGATGTCACCACTGGCTGACACAAAAGT-TATGCCTTC  60678

Query  4317   TAGTGTTTACTGTAACaaaaaaaaaGGCTGCGCTGTGGTCTGCAGAGAAAGGGCACGATC  4376
              ||| |||| |||||||  |||||||||||| |||||||||| ||||||||| ||||||||
Sbjct  60679  TAGCGTTTGCTGTAAC--AAAAAAAGGCTGTGCTGTGGTCTTCAGAGAAAGTGCACGATC  60736

Query  4377   CTTTCTCACCTGATCAGCTGTCCCAGGTGCCCTCTGTGGAAGGTGA-CCATATTCATTTT  4435
              ||||||||||||||||||||| |||||||||| |||  |||||||| | || || | |||
Sbjct  60737  CTTTCTCACCTGATCAGCTGTTCCAGGTGCCCACTGAAGAAGGTGATCAAT-TTTACTTT  60795

Query  4436   AAGCAGCTGGAGGTGTTTCAGCCTGAGGAACATAGAGCTGATTTTGGCGACTGAGCATTC  4495
              |||||  |||||||||| |||||||||||||| || ||||| ||||| || | | |||||
Sbjct  60796  AAGCAATTGGAGGTGTTCCAGCCTGAGGAACACAG-GCTGAATTTGGTGAGTAACCATTC  60854

Query  4496   CTCGCGGT-AAT-T--GACGTGTAAGGATGGCACCTGGAGAAAAATGAGTTTGCGAAGAT  4551
              |||| ||| | | |  || | |||| |||||||||||||| |||| ||||||||||||||
Sbjct  60855  CTCGAGGTCATTGTCCGAAGAGTAATGATGGCACCTGGAG-AAAACGAGTTTGCGAAGAT  60913

Query  4552   TCTTCATCTCCTTCAGGTAACAATGAAGCTTTCTTATCAGATGTGGCCAGGACACATAGC  4611
              |||||||||||||||||||||||||||||||||||||||||||  |||||||||  | | 
Sbjct  60914  TCTTCATCTCCTTCAGGTAACAATGAAGCTTTCTTATCAGATGCAGCCAGGACATGTTGT  60973

Query  4612   AAATTTCCAGCTCCTGAATACTATTCAGGTGGATTATTTTCAATGATCTT-CTGAGATAT  4670
               |||||||| ||||||||||||||||||||||| |||||||||||| ||| || ||||||
Sbjct  60974  GAATTTCCAACTCCTGAATACTATTCAGGTGGACTATTTTCAATGA-CTTTCTAAGATAT  61032

Query  4671   TCAATCGACGTTAGATAATTCACCAACTTACTACAGCACAGGTGTACTAAACCTCTCCTT  4730
              | ||| |  |||||||||||||||||||||||||||||||||||||||||| ||||||||
Sbjct  61033  TTAATGGGTGTTAGATAATTCACCAACTTACTACAGCACAGGTGTACTAAAACTCTCCTT  61092

Query  4731   TGGTAAACCCACCGGAAGAGGTATCTCAGGCATTCATCCTGGGGTATTTCCTTGAGGCAG  4790
              |||||||||||| ||||||||||||||||||||||||| |||||| ||||||||||||||
Sbjct  61093  TGGTAAACCCACTGGAAGAGGTATCTCAGGCATTCATCTTGGGGTGTTTCCTTGAGGCAG  61152

Query  4791   ATGTCTATGAACACCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGTC  4850
              | ||||||||||||||| ||||||||||||||||||||||||||| ||||||||||||||
Sbjct  61153  ACGTCTATGAACACCTTTAAGGGCTGGTGCTCTCCCATCCTTGGATAGTCCTCTGCTGTC  61212

Query  4851   TGCCTCTTACTCATGGCCTCTGGGGAGGAGGACAGGGCCCTGGATTC-AGACCATATGGC  4909
              ||||||||||||||||||||||||||||||||||||||| | |  || || ||||   ||
Sbjct  61213  TGCCTCTTACTCATGGCCTCTGGGGAGGAGGACAGGGCC-TAGCCTCCAGGCCATCCAGC  61271

Query  4910   CCAGAAATTCTCATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGT  4969
              ||||| |||||||||||||||| |||| |||||||||||||||||||||||||| | |||
Sbjct  61272  CCAGACATTCTCATCAACATCCAGCAAGTCCAGCACTTGAAGTTTCCACCTCCTATAGGT  61331

Query  4970   AAAGTAAGGCAGAGGCTCAGAACTTT-GAAGGACAAATCCCTGACCTTTGCTTTCATTCT  5028
              ||||||||| ||| |||||||| ||| |||||||  ||||||||| ||||||||||||||
Sbjct  61332  AAAGTAAGGGAGAAGCTCAGAA-TTTAGAAGGACCCATCCCTGACTTTTGCTTTCATTCT  61390

Query  5029   CATCCAATAAATCAGCTGCTCCTGTCCTCGCTGCTCCCTGTTCTCTCTGAGTTTTCTTGG  5088
              |||    |      ||| | |||||  ||  | |||  |   ||    || ||||||  |
Sbjct  61391  CAT----T------GCT-C-CCTGT--TC--T-CTC--T---CT----GACTTTTCTCAG  61424

Query  5089   TCCCTTTTCTCTTTCAATTC-TGACTGGTCCCCACTTCTATTCCATTTACCTTCCACTGG  5147
              ||| ||||||||||  |||| | |||| |||||||||||| ||| |||||||||||||||
Sbjct  61425  TCCGTTTTCTCTTTTGATTCAT-ACTGCTCCCCACTTCTAGTCCCTTTACCTTCCACTGG  61483

Query  5148   GAATAGGCAAGTTTCTGTTCCCACAGTGGACCCTATATTGTGGGCAGTTCTTTCCCTGAG  5207
              ||| | ||| |||||||||||||||||||||||| ||| ||| ||||| ||||| |||||
Sbjct  61484  GAAAAAGCAGGTTTCTGTTCCCACAGTGGACCCTGTATGGTGAGCAGTCCTTTCTCTGAG  61543

Query  5208   GATCTGGGCAATGGCCAAGGCATGCCT-GAGCTTCGTCACCAGCACCACCAGAAGACACT  5266
              ||||||| |||||||||| || | ||| ||||||| |||||||||||| |||||||| ||
Sbjct  61544  GATCTGGACAATGGCCAAAGCCT-CCTTGAGCTTCCTCACCAGCACCATCAGAAGACTCT  61602

Query  5267   GGGC  5270
              ||||
Sbjct  61603  GGGC  61606


 Features flanking this part of subject sequence:
   669 bp at 5' side: PRAME family member 8
   32276 bp at 3' side: PRAME family member 9

 Score = 2034 bits (1101),  Expect = 0.0
 Identities = 1280/1365 (93%), Gaps = 17/1365 (1%)
 Strand=Plus/Plus

Query  6980   AAAATCACAATACCGCTAAGTGTGTGAACTATAGCTGACA-GGCACAGAAACCAACAACT  7038
              |||||||||||||  ||||||||||||||| ||||||| | ||||||||||| || ||||
Sbjct  70459  AAAATCACAATACAACTAAGTGTGTGAACTGTAGCTGA-AGGGCACAGAAACAAAGAACT  70517

Query  7039   TCACATGTCAAGACATAAACATCCATCCAACTGTAAATTTTTAATAtttttttttttAAA  7098
              ||||||||||||||||||| || |||||||||||||||||||||||  | |||||| |||
Sbjct  70518  TCACATGTCAAGACATAAAAATTCATCCAACTGTAAATTTTTAATA--TCTTTTTTAAAA  70575

Query  7099   AACTGCTTCAATAAGAATTTTGAAATGAGGAAAATGAAGCACAAATCAAAATTTGAGGGA  7158
              ||||||||||||||||||||||||||||| ||||||||||| |||||||||| |||||||
Sbjct  70576  AACTGCTTCAATAAGAATTTTGAAATGAGAAAAATGAAGCAGAAATCAAAATCTGAGGGA  70635

Query  7159   TGAAGTCAAAACTATATTTGGAGGAAAAATCAAAACCTACATCTGTTTAATCTGAAAAAA  7218
              |||||| || ||||||||| ||||||||||||||||||||||||||| ||| ||||||||
Sbjct  70636  TGAAGTGAATACTATATTTAGAGGAAAAATCAAAACCTACATCTGTTAAAT-TGAAAAAA  70694

Query  7219   CAGACAGGAAATTCTCTGTGCCATTTTGGGCTGTGTGTCACCATCCCTGACTGGCTGGCT  7278
              ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct  70695  CAGACAGGAAATTCTCTGTGCCACTTTGGGCTGTGTGTCACCATCCCTGACTGGCTGGCT  70754

Query  7279   GCAGATTAGACGGGCATGTTCCTAAGAAGGTGGTGACTTACCAGATCTGGACTCAGTTTG  7338
              |||||| ||| |||| |||||||||| |||||||||||||||||||||||||||||||||
Sbjct  70755  GCAGATCAGATGGGCGTGTTCCTAAGGAGGTGGTGACTTACCAGATCTGGACTCAGTTTG  70814

Query  7339   CAGGGTGCTGGGACCTCTCAGAGAACCAAGCAGTAGCTCCAGGCACCAGGGCTTTGGGTC  7398
               |||||||||||| ||||||||||| |||||||||| |||||||||||||||||||||||
Sbjct  70815  TAGGGTGCTGGGATCTCTCAGAGAATCAAGCAGTAGTTCCAGGCACCAGGGCTTTGGGTC  70874

Query  7399   TGTCCTGTGCAAACTCAGGAGCTTTTGTTGATGTTTCTAACCACACCCTCCCCTTCTCAA  7458
              | |||| ||||||||||||||||||| |||||||||||||||||||||||||||||||||
Sbjct  70875  TCTCCTTTGCAAACTCAGGAGCTTTTATTGATGTTTCTAACCACACCCTCCCCTTCTCAA  70934

Query  7459   TCACCAGCTTCCAATCAGAAAGTGATACCTGATTAGAT-CCTGAAGTTCCACCCAGTTAA  7517
              |||||||||||||||||||||||||||||||||||||| || ||||||||||| ||||| 
Sbjct  70935  TCACCAGCTTCCAATCAGAAAGTGATACCTGATTAGATTCC-GAAGTTCCACCTAGTTAG  70993

Query  7518   TCCTGATTGAGTTTCACACTTTCTTCTGATTCATTGATTAAATTAGATGTGCATTTATGA  7577
              |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Sbjct  70994  TCCTGATTGAGTTTTACACTTTCTTCTGATTCATTGATTAAATTAGATGTGCATTTATGA  71053

Query  7578   AAGTGAAAGAATAAATAACAGGGTGAAAGTCCAAAAGTCATTAATTCATTTATTCCCCAA  7637
              |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Sbjct  71054  AAGTGAAAGAATAAATAACAGGGTGAAAGTCCAAAACTCATTAATTCATTTATTCCCCAA  71113

Query  7638   ACACTGATGAAGTTTGACTAACATGTGACCTTCATAGTGACATGGAAGGTTTAATCTGTT  7697
              ||||||||||||||||||||| ||||||||||||||| ||||||||||||||||||||||
Sbjct  71114  ACACTGATGAAGTTTGACTAATATGTGACCTTCATAGAGACATGGAAGGTTTAATCTGTT  71173

Query  7698   CCTGGCATTAGAAAGAAAAAACAAAACCTGATGATATCTTTATGGGAGAATATTTGGCCA  7757
              |||| |||||||||||||||||||||||||||||||||||||||||| ||| | ||||||
Sbjct  71174  CCTGACATTAGAAAGAAAAAACAAAACCTGATGATATCTTTATGGGAAAATCTGTGGCCA  71233

Query  7758   CATTGAAATTATCCAAACGTTTC---A-GA--GCTAAGACAGCTTTAAAAAGACGGTGAT  7811
              ||| ||||||||| |||||||||   | ||  | ||| |||||||||||||||| |||||
Sbjct  71234  CATCGAAATTATCAAAACGTTTCGTTAAGACAGTTAAAACAGCTTTAAAAAGACAGTGAT  71293

Query  7812   GTCAACCCTAAGAAAACAGAATACAAAGCTC-TGTTATCCAACAGTTACCTGGGTTTTAT  7870
              ||| ||||||||||||| || || ||||||| | ||||||||  || |||||||||||||
Sbjct  71294  GTCCACCCTAAGAAAACGGATTAAAAAGCTCCT-TTATCCAATGGTCACCTGGGTTTTAT  71352

Query  7871   GCTTCCTAACGGGGCAGGTCATATGTGGGTTCAGGTTGAAGAGGGGAACCACTGAGGGTG  7930
              | ||  |||| ||||||||||||||||||||||||||||| |||| |||||| |||||||
Sbjct  71353  GTTTTATAACAGGGCAGGTCATATGTGGGTTCAGGTTGAAAAGGG-AACCACGGAGGGTG  71411

Query  7931   TTATTGATCACAAGACTAAGGTCAAGGCTTCACTGCAGGAAATCAGGACAGAATGACAAA  7990
              | ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Sbjct  71412  TGATTGATCACAAGACTAAGGTCAAGGCTTCACTGAAGGAAATCAGGACAGAATGACAAA  71471

Query  7991   GTGAGGTGGGGGCTGGGCAGGATGGGACCGGGTGTTCTAGTAGAACCCTGGGAAGGAACC  8050
              ||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  71472  GTGAGGTGGCGGCTGGGCAGGATGGGACCGGGTGTTCTAGTAGAACCCTGGGAAGGAACC  71531

Query  8051   AAGACAGCATAAAACATGGTGGGTATTTTGTGGGCATCTCCACAGAAGGATTGAAAGACT  8110
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  71532  AAGACAGCATAAAACATGGTGGGTATTTTGTGGGCATCTCCACAGAAGGATTGAAAGACT  71591

Query  8111   CTGTCTGGATTGAGTTTAAAAATTAAAAAGGGAATAGTTACAGAAGAGACAGTGCAGACT  8170
              |||||| ||||||||||||||||||||||||||||| ||||| |||||||||||||||||
Sbjct  71592  CTGTCTAGATTGAGTTTAAAAATTAAAAAGGGAATAATTACAAAAGAGACAGTGCAGACT  71651

Query  8171   CTTCAAACACAACATTGTCTTTGAGGGCAGAGAAGGCAGAAACAGTCTTGGCCCCTACTA  8230
              |||||||||||||||||||||||||||||||| ||||||| |||||||||||| ||||||
Sbjct  71652  CTTCAAACACAACATTGTCTTTGAGGGCAGAGGAGGCAGATACAGTCTTGGCCTCTACTA  71711

Query  8231   GAAGGGAAAGCGTGTTTACTCCCAAAAATGATGGGCTCGCCTCAGAAAATCAGCCTGGGA  8290
               |||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct  71712  CAAGGGAAAGCGTGTTTACTCCCAAAAATGATGGGCTCGCCTCGGAAAATCAGCCTGGGA  71771

Query  8291   AGATGGAATCTGAGAATCTGAGCTGGGGCAGATGCCAGAGAGAAG  8335
              ||||||||||||||||| |||||||||||||||||||||| ||||
Sbjct  71772  AGATGGAATCTGAGAATGTGAGCTGGGGCAGATGCCAGAG-GAAG  71815


 Features flanking this part of subject sequence:
   29730 bp at 5' side: PRAME family member 3
   1351 bp at 3' side: PRAME family member 5

 Score = 2028 bits (1098),  Expect = 0.0
 Identities = 1863/2217 (84%), Gaps = 113/2217 (5%)
 Strand=Plus/Plus

Query  25719  ttctttttttttttttttttttttttttttgtgacaaagtcta-cctctgtcacccagaa  25777
              |||||||||||||||||||||||||||||| |    || |||| ||| | |  |||||  
Sbjct  41483  TTCTTTTTTTTTTTTTTTTTTTTTTTTTTT-TTTTGAA-TCTAGCCTAT-T-TCCCAG-G  41537

Query  25778  c-ggtgtgcaatggtgcaatcttggctcactgcaaccat-tgccccctggattcaagcga  25835
              | || || || ||||| | | |  ||||||||||||| | |||| ||||| |||||||||
Sbjct  41538  CTGGAGTTCAGTGGTGTATTGTCAGCTCACTGCAACC-TCTGCCTCCTGGGTTCAAGCGA  41596

Query  25836  ttc-tcccacctcagcct-cctgagtagc-tggattacaggcacctg-ccatcatgc--c  25889
               || |||   |||||||| ||| |||||| |||| || ||||  | | ||| |  ||  |
Sbjct  41597  -TCTTCCTGTCTCAGCCTCCCT-AGTAGCTTGGACTATAGGC-GCAGACCA-C-CGCAAC  41651

Query  25890  aggctaatttttgt-gtttttgtagagctggggtttcatcatgttggccttgcaggtctt  25948
               |||||||||||||  |||| |||||| | |||||| | ||||||||||  ||  |||| 
Sbjct  41652  TGGCTAATTTTTGTAATTTTAGTAGAGGTAGGGTTTTACCATGTTGGCCAGGCTTGTCTC  41711

Query  25949  gatcgcctgacctcaggtgatccagcc-aact-tggac-tctcaaagtgcagggattaca  26005
               | | ||||||||||| | ||||| || | || | | | || || ||||| |||||||||
Sbjct  41712  AAACTCCTGACCTCAGATAATCCA-CCTACCTCT-G-CGTCCCAGAGTGCTGGGATTACA  41768

Query  26006  ggtgtgagccacctcacccggcctttaatgaGTGAATTCTTGATTTCCACCCTATTCCTA  26065
              |||||||||||| ||  | |||||| ||||| || |||||||| ||| ||||||| ||||
Sbjct  41769  GGTGTGAGCCACTTCGTCTGGCCTTGAATGAATGTATTCTTGACTTCTACCCTATCCCTA  41828

Query  26066  ACACTGTCAATTTCTTGATTCATGAACTTAATATGGATA-GCTGATATGAATGGATATCT  26124
              |||||||| |||||||| |||||||| | ||||| |||| | ||||||||||||| ||||
Sbjct  41829  ACACTGTCGATTTCTTGCTTCATGAAGTGAATATAGATATG-TGATATGAATGGACATCT  41887

Query  26125  GATTCAATCCAGTAATCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGGGTGGAGCT  26184
              |||||||||| |||||||||||| ||||||||||||||||| ||||||||||||||||||
Sbjct  41888  GATTCAATCCGGTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCT  41947

Query  26185  TCAGAAATGCAATCAGATAGCACTTTTTGATTGGAAGCAAGCA-CTGGATA-GATGGAGG  26242
              ||| ||||||||||||||| || ||||||||||||||  |||| | ||||| | || |||
Sbjct  41948  TCACAAATGCAATCAGATATCATTTTTTGATTGGAAGGTAGCAGC-GGATATG-TGCAGG  42005

Query  26243  GGTGTGGGTGGGAGTTGTGATTAGAAAGATCGATAAAAGTTTCTGAAGGCCCACAGGAGA  26302
              || ||||||||||||||||||||||||| || ||||||| |||| ||| |||||||||||
Sbjct  42006  GGCGTGGGTGGGAGTTGTGATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGAGA  42065

Query  26303  GACCCAAAGTCTTCAAGTCTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTAAGCACTCTG  26362
              ||||||||||||||||| || |||||||||||||||||||||||||| || ||||| || 
Sbjct  42066  GACCCAAAGTCTTCAAGCCTAGAGTTCCTGCTTGGTTCTTCCTGAGGACTGAGCAC-CTT  42124

Query  26363  C-AAACT-CAGTCCAGATCTAGTAAGTCACTCATTTCTGGAAGGACACTCCCATCTGACC  26420
              | | ||| || ||||||||| |||||||||| ||||||| ||||||||||||||||||||
Sbjct  42125  CTAGACTACA-TCCAGATCTGGTAAGTCACTAATTTCTGTAAGGACACTCCCATCTGACC  42183

Query  26421  TATAGTCAGCCGGTCTGGGACGGGGGCAATGCAGCCTATGATGGCACCGAGCTATAT-CT  26479
              || |||||| |||||||||  || | || | ||||||| |||||||| ||||||||| ||
Sbjct  42184  TACAGTCAGTCGGTCTGGGGTGGTGACAGTACAGCCTACGATGGCACAGAGCTATATCCT  42243

Query  26480  GT-CTTTtatatatatat-atatGAACAATTTGAAGATTTGAATTTTTTCCTCTATATGC  26537
              || ||||| | | | | | ||||||||||||||||| ||||||| |||||||||| ||||
Sbjct  42244  GTCCTTTT-T-T-TTTTTCATATGAACAATTTGAAGCTTTGAATGTTTTCCTCTAAATGC  42300

Query  26538  AGTTTTGTCTTTATTTCAAAAAA-TTGGATTGTGCTTTGGTTTATGTCATTTcaaaattc  26596
              |||| |||||||||||||||||| || ||||||||||||||| ||| ||||| |||||||
Sbjct  42301  AGTTCTGTCTTTATTTCAAAAAAGTT-GATTGTGCTTTGGTTGATGCCATTTTAAAATTC  42359

Query  26597  ttgatgggagcaatgactcatgcccataacctcaacaccttgggaggccaaagcgggagg  26656
              |||| ||||||||| |||||||||  ||||| |||||| |||||||||||||| ||||||
Sbjct  42360  TTGAAGGGAGCAATAACTCATGCCTTTAACCCCAACACTTTGGGAGGCCAAAGTGGGAGG  42419

Query  26657  atcatttgagcccaggggtttgagaccaacctgggcaacatggcaaaaatgcagctctac  26716
              ||||||| |||||||||||||||||||||||||||||||||| |||||   |  ||||||
Sbjct  42420  ATCATTTCAGCCCAGGGGTTTGAGACCAACCTGGGCAACATGACAAAAGCCCTCCTCTAC  42479

Query  26717  aaaac--attctttttttga-agcagggatggagtctcaccctgttgccaaggctggagt  26773
              | |||   || |||||||||  |  |||||||||||||||  ||||||| || |||||||
Sbjct  42480  ACAACGTTTTTTTTTTTTGAGGGTGGGGATGGAGTCTCACTGTGTTGCCCAGACTGGAGT  42539

Query  26774  gcagtggcaagagctcaactcactgcaacctctt-cctcccaggctcaaacaattttcat  26832
              ||||||||| || ||||| |||||||||||| || |||||| || |||| ||||| ||||
Sbjct  42540  GCAGTGGCACGATCTCAAATCACTGCAACCT-TTACCTCCCGGGTTCAAGCAATTCTCAT  42598

Query  26833  gtctcag-ct---tcctgagtagctggtattacatccctctgccaccatgtct-gcttaa  26887
              | ||||| ||   |||| || ||||||| | |||  | ||||  |||||| || || |||
Sbjct  42599  GCCTCAGTCTCCATCCTCAGAAGCTGGTGTCACAGACATCTGAAACCATGCCTGGC-TAA  42657

Query  26888  tttttgtatttttagtagtggtggggtttcaccatgctggccaggttggtctcaaactcc  26947
              |||||||||||||||||| |||||||||||||||||||||||||||||||||| ||| ||
Sbjct  42658  TTTTTGTATTTTTAGTAGAGGTGGGGTTTCACCATGCTGGCCAGGTTGGTCTCGAACACC  42717

Query  26948  tgacatcaagtgatcctcctgcctaggcc-cccaaaagtgctggaatgacggccgtgagc  27006
              |||| ||||||||||| ||||||| ||||  || |||||||||| || || || ||||| 
Sbjct  42718  TGACCTCAAGTGATCCACCTGCCTTGGCCTTCC-AAAGTGCTGGGATTACAGCTGTGAGT  42776

Query  27007  caATGGTGGTCAGCctctacaaaatatatatatctttt-aatttgccag-gcatggtag-  27063
              || ||||| |  ||||||||    | | | | | |||| |||| ||| | ||||||| | 
Sbjct  42777  CACTGGTGCTTGGCCTCTAC----T-T-TTTTTTTTTTAAATTAGCC-GAGCATGGT-GA  42828

Query  27064  catgcatctgtattcccagctattt-ggtttgctgacatgggagaatcacttgagcccag  27122
              |||||||||||| |||||||||||| ||| | |||   ||||||||||||||||| ||||
Sbjct  42829  CATGCATCTGTAGTCCCAGCTATTTGGGTGT-CTGGTGTGGGAGAATCACTTGAGACCAG  42887

Query  27123  aagattgaggctgcagtgagccatgctcacaccactgctgtactccagcctgggcaacag  27182
              ||||||||||||||||||||||||||||| |||||| |||||||||||||||||||| ||
Sbjct  42888  AAGATTGAGGCTGCAGTGAGCCATGCTCATACCACTCCTGTACTCCAGCCTGGGCAAAAG  42947

Query  27183  agta-agaccctgctaaaaacaaaaacgaaaacaaacaaacaa-aaaacCTTAACCAAAG  27240
              || | | |||||| |     |     |  ||| ||||||| || ||||  | || |||| 
Sbjct  42948  AG-AGACACCCTG-T-----C-----C--AAA-AAACAAA-AAGAAAA--TCAATCAAAA  42989

Query  27241  AGAATCTTTGACCTTAATTTTAAACCAATCACATCCTCACTGTAATTCTTCCTCCCGAAT  27300
              || ||||||||||||||||||||||||||||||   || |      |||||| ||| |||
Sbjct  42990  AGGATCTTTGACCTTAATTTTAAACCAATCACA---TC-C------TCTTCCACCCAAAT  43039

Query  27301  GGAGACATgggtg-tgagggtgcatgcctgtaatcccagctacatggaaggctgaagcat  27359
              |||||||||| ||  | ||||||||||||||| |||||||||  ||||||||||||||||
Sbjct  43040  GGAGACATGGCTGCAGGGGGTGCATGCCTGTAGTCCCAGCTATGTGGAAGGCTGAAGCAT  43099

Query  27360  gagaattgcttgaatctcagaggcggaagttacagtgagctgagatgga-gccgctgcac  27418
              |||||||||||||||||  ||||| || |  ||||||||| || || ||  || ||||||
Sbjct  43100  GAGAATTGCTTGAATCTTGGAGGCCGAGGCAACAGTGAGCCGAAAT-GACACCACTGCAC  43158

Query  27419  tccagcctgggcgacaaagtgagactcagcttcacccacaccaaaaaaaaTTAGA-TTAT  27477
              || ||||||| |||  |||||||| ||||| |  ||| || | |  ||||  ||| ||||
Sbjct  43159  TCTAGCCTGGCCGATGAAGTGAGATTCAGC-T--CCCTCAAC-ACCAAAA--AGACTTAT  43212

Query  27478  ACCACCCAGGTGATCACTGGATACATGAAGATTTCTATTGTGTGTTATTGGGGACTGTCA  27537
               ||||| ||||||||| |||||| ||||||||||||||||||| || || ||||||||||
Sbjct  43213  GCCACCTAGGTGATCATTGGATATATGAAGATTTCTATTGTGTTTTCTTAGGGACTGTCA  43272

Query  27538  ACTCCGTCTTTGAAAACTGTTTTAACTCTGAAATATTTTGATAAATTTGATGTGGCCAAG  27597
               ||| ||||||||||||||||||||| |||||||||||||||||| |||   ||||||||
Sbjct  43273  TCTCTGTCTTTGAAAACTGTTTTAACCCTGAAATATTTTGATAAACTTGGCATGGCCAAG  43332

Query  27598  GATCCCTCAACAAAGATACTTTCAAGTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGAT  27657
              |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |
Sbjct  43333  GATCCCTCAACAAAGATACTTTCAAGTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGGT  43392

Query  27658  TCAACACTTCCCTATCTCACACTCAGGACTATGAAGGACACATATTAGTAAA-CCTCCAT  27716
              ||||| ||||||| |||||||||||||||| ||||||||||||||||||||| || ||||
Sbjct  43393  TCAACCCTTCCCTGTCTCACACTCAGGACTTTGAAGGACACATATTAGTAAAACC-CCAT  43451

Query  27717  GTTTGTGGAGGGAATCAGTGAATGAGTCCTGGACTTTCACCCTATCCCTAAATCTTTCAC  27776
              ||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| 
Sbjct  43452  GTTTGTGAAGGGAATCAGTGAATGAGTCCTGGACTTTCACCCTATCCCTAAATCTTTCAT  43511

Query  27777  TTTCATGGATGAATATCTAATTCAATCAGTTAATCTGGAAGAAAGCCAAAAATCCAATCA  27836
              ||| ||| ||||||||||||||  |||||||||| |  ||||||| ||||||||||||||
Sbjct  43512  TTTGATGAATGAATATCTAATTTGATCAGTTAATATTTAAGAAAGGCAAAAATCCAATCA  43571

Query  27837  GGATTAACTGGGTAGAGTTTAAGAAGTCGAATCAAATGTAGTtctctctctctctct  27893
              ||||||||||||||||| ||||||| || |||||||||||| ||||||| |||||||
Sbjct  43572  GGATTAACTGGGTAGAGATTAAGAATTCTAATCAAATGTAGCTCTCTCTGTCTCTCT  43628


 Features in this part of subject sequence:
   PRAME family member 13

 Score = 1892 bits (1024),  Expect = 0.0
 Identities = 1886/2282 (82%), Gaps = 140/2282 (6%)
 Strand=Plus/Plus

Query  984     gaaggggggacctcctgggcCCTCGAGAGCACTAGGGGACCTTGTTTGGTAACTGCAACC  1043
               |||||||||| ||||||| |||||||||| ||| ||||||||  |||||||||||  |||
Sbjct  126315  GAAGGGGGGATCTCCTGGACCCTCGAGAGTACTGGGGGACCTCATTTGGTAACTGTGACC  126374

Query  1044    TGGGCAGCTTCAGTTGTGCCTTTggagctactgccctgccaacttgggaggaccaggact  1103
               ||| || ||||||||| | |||||||||||||||||||||||||  ||||||||||||||
Sbjct  126375  TGGACAACTTCAGTTGCGTCTTTGGAGCTACTGCCCTGCCAACTCAGGAGGACCAGGACT  126434

Query  1104    ccctcttgtcccaggatcccatcagctccaaagtgtgcacagcctcagctttgcCC--TC  1161
               ||||||||||||||| ||||||||||||  |||||| | ||||||  ||| |||||  ||
Sbjct  126435  CCCTCTTGTCCCAGGCTCCCATCAGCTCTGAAGTGTACGCAGCCTTGGCTGTGCCCTTTC  126494

Query  1162    TCTCTGTTTCCGTGCAGAGGTGACAGGTGAGATGCAGGTTCACAGCAGCTCTGGTCAACC  1221
               ||| ||||||| |||||| ||||||| ||||| |||||| |||||||||||||  |||||
Sbjct  126495  TCTGTGTTTCCCTGCAGAAGTGACAGTTGAGAAGCAGGTACACAGCAGCTCTGACCAACC  126554

Query  1222    CCACAGAAACAAATCTGAA-GCTCCTGGGTCCGGTTTAATGAGCCCCAACTGCGCTCTGA  1280
               || || ||||||| |  || ||||||||||  |||||||  |||||||||||| || | |
Sbjct  126555  CCGCACAAACAAA-CCCAATGCTCCTGGGTGTGGTTTAACCAGCCCCAACTGCACTATCA  126613

Query  1281    TCCAGGAGTTTGCAGGCTAACAGCACAAAGTGGGGAGTGAGGTCGAGGCTGTGGTGGAGA  1340
               |||||||| ||||||||||||||||   |||| | ||||| || ||||||||||||||||
Sbjct  126614  TCCAGGAGCTTGCAGGCTAACAGCAGGCAGTGAGCAGTGAAGTAGAGGCTGTGGTGGAGA  126673

Query  1341    CTGCGGACCTAGGGGCAA-GTCCCGTTTAGCCG-TGAGAGGGTATGGGTGGCACAGTTGG  1398
               || | ||||| ||| ||| || || ||| | || ||||||||| ||||||||||||||||
Sbjct  126674  CTCCAGACCT-GGGACAAGGTTCCATTTTG-CGATGAGAGGGTGTGGGTGGCACAGTTGG  126731

Query  1399    CTGCCTCAGGGACATGGGGCACAGGCCTGGCTGACAACCCAGCCAAGAGGTG-GTGCCTT  1457
                ||||||||||| |||| |||||||||||||| |  |||||| |||| || | |||||| 
Sbjct  126732  GTGCCTCAGGGAAATGGAGCACAGGCCTGGCTCATGACCCAGTCAAG-GG-GAGTGCCTC  126789

Query  1458    TAGGAGTGGATCGTGG-TCCACAGGCCCAGCAATCGGAAGCATCAGGCTCTGTGTTCACC  1516
                |||||||| || ||| ||| ||||||||||||||    |     ||  ||| | |||||
Sbjct  126790  CAGGAGTGGTTCATGGTTCC-CAGGCCCAGCAATC----G-----GG--CTG-G-TCACC  126835

Query  1517    CCTCTTGGGGGCAGATCTTGGAAATGCAGCCTCAGGAAGATTCACACAGA-ACTCCTTTT  1575
               ||| | |||||| ||||| |||||  ||||||  ||  ||| | || |||  |||| || 
Sbjct  126836  CCTATGGGGGGCGGATCTCGGAAACACAGCCTGGGGTGGATCCGCATAGACCCTCCCTTC  126895

Query  1576    TAGACCTAGGAACTTGATACTATTAGCAGGGTGGGCACACAGTTG--ATGCATAGCTGGC  1633
                |||||| ||| ||||| ||| |||||||| ||||  |||||| |  | | |||||||||
Sbjct  126896  AAGACCTGGGAGCTTGACACTGTTAGCAGGATGGG--CACAGTGGCCA-G-ATAGCTGGC  126951

Query  1634    CAGGTCATTGAA-CTTGGTGCCATTTCTGCTTCCCAACTC-GGGGCCCTGGA-GCATGGC  1690
               |||||| ||||| |  ||||||||||||||||| | || | ||  |||| || | |||||
Sbjct  126952  CAGGTCCTTGAAGC-AGGTGCCATTTCTGCTTCTC-ACCCTGGCCCCCT-GATGGATGGC  127008

Query  1691    CCCAGCTCTGCCTT-TGGAACCTGACAACCACACTTCATGTGC-AAGCACGGCACCACCC  1748
               ||||||| |||||| |||  |||| || || ||| || ||||| || |  ||||||||||
Sbjct  127009  CCCAGCTATGCCTTCTGG-GCCTGGCATCCGCACATCTTGTGCGAA-CGTGGCACCACCC  127066

Query  1749    CAAGCCCATCTTCTCCTCATGGCCCCTTTCTGCCTGTGCCTTTGTGCCCGACCGAGCTGC  1808
               ||  || ||||||||||   ||||||| |||||| || |||| | ||| |||||||||||
Sbjct  127067  CATTCCTATCTTCTCCTTGGGGCCCCTCTCTGCCCGTCCCTTCGCGCCTGACCGAGCTGC  127126

Query  1809    TCCCCACAGTCGAAAAAGTATG-AAAAAACAGATGACTAAAGAGAAGTAAAGGATGGGTG  1867
               |||||   | | |||||||| | ||||||| ||||||| ||||||||||||| |||||||
Sbjct  127127  TCCCCTTGGGCAAAAAAGTAAGAAAAAAACTGATGACTGAAGAGAAGTAAAGAATGGGTG  127186

Query  1868    CAGACCATTC-Gcacacctgtaatcccagcactttgggaggccaaggttggcggatcact  1926
                ||| || || | |  |||||  ||||||| |||||||||||||||||  | ||||||||
Sbjct  127187  GAGATCA-TCTGTATGCCTGTTTTCCCAGCGCTTTGGGAGGCCAAGGTCAGTGGATCACT  127245

Query  1927    caaagccaggaactcaagaccagcctggtgaacagggtaaaaccctgtctctacgaaaaa  1986
                 ||||||||| ||  ||||||| ||| | |||| || |||||||  ||||||  |||||
Sbjct  127246  TGAAGCCAGGATCTTGAGACCAGGCTGATCAACATGGAAAAACCCCATCTCTATTAAAAA  127305

Query  1987    tacaaaaattag-caggcttggtggcacgtgcctgtactcccagctacttgagtggttga  2045
               ||||||||| || ||| |||||||| ||||||||| | ||||||||| ||||||||||||
Sbjct  127306  TACAAAAATCAGCCAGTCTTGGTGGAACGTGCCTGCAGTCCCAGCTATTTGAGTGGTTGA  127365

Query  2046    ggcacgagaatcacttgagccc-cacaggaaaggattccagtgatcccagattgcaccac  2104
               ||||| ||||||||||||||||  | ||||||||||| || ||| |||||||||||||||
Sbjct  127366  GGCACAAGAATCACTTGAGCCCTGA-AGGAAAGGATTACAATGAGCCCAGATTGCACCAC  127424

Query  2105    tacactccagcctgaatgacaaagc-aatatttttgtctccaaaaataaaaaaataaata  2163
               | ||||||||||| ||||||||| |  | | ||||||||||            | |||  
Sbjct  127425  TGCACTCCAGCCTAAATGACAAA-CTGAGA-TTTTGTCTCC------------A-AAA-C  127468

Query  2164    atgaaataaaaGAACAAGAATGGGTGGGAATTACTCAAAATGGTCTAATTTTATTTGGCT  2223
               |  |||  |||||||||||| ||||||||| |||| |||||| || |||| ||||||| |
Sbjct  127469  A--AAA-CAAAGAACAAGAACGGGTGGGAAATACTTAAAATGATCAAATTCTATTTGGTT  127525

Query  2224    GCTATGATGTTCCGCAGCTGAACCTCAATCACAGACAAACTAGTGCCTCGTTATTTTTCC  2283
               ||| ||||||||  |||||||| |||||||||||||||| ||||   || ||||||||||
Sbjct  127526  GCTTTGATGTTCTACAGCTGAAACTCAATCACAGACAAAGTAGTATTTCATTATTTTTCC  127585

Query  2284    ATCAGTAACTCAATAACTAGAGATTTCTGATGTATAAATCCCTAAAACAAGTAAATCAAT  2343
               ||||||||||||||||||||| ||||||| || ||||||   |    |   |  | | | 
Sbjct  127586  ATCAGTAACTCAATAACTAGATATTTCTGGTGGATAAAT---T---GC---T--A-C-A-  127631

Query  2344    TACAGAGGACACCAGAAAGTTTTCACTGAGGT--TCTCTATTTCTGATATTTCTTGGTAA  2401
                ||  |||     | |||||||||| | ||||  ||| ||||||||||||| ||||||||
Sbjct  127632  -AC--AGG---TTA-AAAGTTTTCATTCAGGTGCTCTTTATTTCTGATATTCCTTGGTAA  127684

Query  2402    TCATCCTTGCAGGGATAACATTCTCATCACTGAAGAATTTTAGTTTCTCTTTCTGACTCT  2461
                ||||||||||||||||||||||||||||||| |||| ||||| ||||||||| ||||||
Sbjct  127685  CCATCCTTGCAGGGATAACATTCTCATCACTGTAGAACTTTAGCTTCTCTTTCCGACTCT  127744

Query  2462    GT-----A---G---C------TCTCATTGACT-CCACCTCAATATTTTCCTCAAGTCTT  2503
               ||     |   |   |      ||||||||| |  |||||||| ||||||||| || |||
Sbjct  127745  GTAGGACACGGGTCCCTGAAGTTCTCATTGA-TGTCACCTCAACATTTTCCTCCAGCCTT  127803

Query  2504    GCCCCCTGCTCTTAGGATTTTTTCCCTCGCACTGAGCACCTGTCTGAAACAGAGCTCTGT  2563
               |||||||||| ||| | ||||||||||| ||||||||| |  | |    |    | ||||
Sbjct  127804  GCCCCCTGCTGTTATGTTTTTTTCCCTCACACTGAGCA-C--T-T----C----C-CTGT  127850

Query  2564    GCTTCCTTTAAGTTGCACATGTggcctgggcacagtcgctcatgcctgtaatcccagcac  2623
               |||||||||||||||  |||||||||||| ||||||| |||||||| |||||||||||||
Sbjct  127851  GCTTCCTTTAAGTTG--CATGTGGCCTGGACACAGTCACTCATGCCAGTAATCCCAGCAC  127908

Query  2624    ttta-gaaggccgaggcaggagaatcccatgcgaccagc--a-gtttga-gacctgctgg  2678
               |||| ||| || |||||||||| |||||||  | |||||  | |   || ||  | |  |
Sbjct  127909  TTTAGGAA-GCTGAGGCAGGAGGATCCCATAAGCCCAGCTGAGGCAGGAGGA--TCCCAG  127965

Query  2679    ggcaacatagtgaaacactttctc-aatttttttgtaataaaaatattggaattattaaa  2737
                |||||| || ||||| || |||| |||| | || |||||||||| ||||||||||||||
Sbjct  127966  AGCAACACAGAGAAACCCTGTCTCAAATTGTCTT-TAATAAAAATTTTGGAATTATTAAA  128024

Query  2738    aaa-g---gaaataagaaaagaggaaaataaCTTGCACCTACATACTAGATTTTAGTGTC  2793
               ||| |    |||||||||||||| ||||||  ||||||||||||| ||||||||||||||
Sbjct  128025  AAATGAAATAAATAAGAAAAGAGAAAAATAGTTTGCACCTACATAGTAGATTTTAGTGTC  128084

Query  2794    CAAGGGCCTAGAAGAGAACATTGGATTTCTCTACCCCGCTAGGCACGCCTTCCCTAGCAG  2853
               | || |||| ||||||||| ||||||||||||||||||||||||||||||||||||||||
Sbjct  128085  CCAGTGCCTGGAAGAGAACTTTGGATTTCTCTACCCCGCTAGGCACGCCTTCCCTAGCAG  128144

Query  2854    CAAAGATGGAGCTCCAGTTCCTCAGACGGTGATGAGCCACAGGACGGGCAGGGGGCGGGG  2913
               |||||||||||||||||||||||||||||||||||||||||||| |||||||||| ||| 
Sbjct  128145  CAAAGATGGAGCTCCAGTTCCTCAGACGGTGATGAGCCACAGGAAGGGCAGGGGGTGGGA  128204

Query  2914    CCAATGAAGATCCTCTTGGGCTGCCTGACTTCCCTTAGTGTACACATCAACTAAGCCCGA  2973
               ||||||||||||||||||||||||||||||||||| ||||||||||||| || |||||||
Sbjct  128205  CCAATGAAGATCCTCTTGGGCTGCCTGACTTCCCTCAGTGTACACATCAGCTCAGCCCGA  128264

Query  2974    AGTGGGGTGAAGATCTCCCAATCGACATGAACCAAGGAATTCAAACTCTCCTCGGGGGCA  3033
               ||| ||| ||||||||||||||||||| ||||||||||||||||||||||||| ||||||
Sbjct  128265  AGTAGGGCGAAGATCTCCCAATCGACACGAACCAAGGAATTCAAACTCTCCTCAGGGGCA  128324

Query  3034    GGATACATCTCCAGGCTTAACTTGCTCAGCCCACTGGTGTGGCACAGCAGGTCCTTCAGG  3093
               |||||| |||||||||||||||||||||||||||||||||||| || |||||||||||||
Sbjct  128325  GGATACGTCTCCAGGCTTAACTTGCTCAGCCCACTGGTGTGGCGCAACAGGTCCTTCAGG  128384

Query  3094    GCTTCCATAGACATGCAATTTCTGCCAAAGTAGAAGGTGGTGAGCTGGGAGCAGCGGCTC  3153
               ||  |||||||||| ||||||||||||||||||||||||||||||||||||||| |||||
Sbjct  128385  GCACCCATAGACATACAATTTCTGCCAAAGTAGAAGGTGGTGAGCTGGGAGCAGTGGCTC  128444

Query  3154    AGGCCAGGCAGGATGGCACTGAGTTGGGAGTAGTGGATCTGACAGCCCTCCAAGATGAGG  3213
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  128445  AGGCCAGGCAGGATGGCACTGAGTTGGGAGTAGTGGATCTGACAGCCCTCCAAGATGAGG  128504

Query  3214    GT  3215
               ||
Sbjct  128505  GT  128506


 Features flanking this part of subject sequence:
   17476 bp at 5' side: PRAME family member 16
   5030 bp at 3' side: PRAME family member 21

 Score = 1280 bits (693),  Expect = 0.0
 Identities = 1155/1373 (84%), Gaps = 51/1373 (3%)
 Strand=Plus/Plus

Query  25840   cccacctcagcctcctga-gtagct-ggattacaggcacctg--ccatcatgccagg-c-  25893
               ||||||| || ||||  | || ||| ||||||||||  | ||  ||| |||||| || | 
Sbjct  195692  CCCACCTTAGTCTCCCAACGT-GCTGGGATTACAGG--CGTGATCCACCATGCCTGGCCT  195748

Query  25894   taatttttgtgtttttgtagag-ctggggtttcatcatgttggccttgcaggtcttgatc  25952
               |||||||| | | ||||||||| |  |||||||| | ||| ||||  || |||||||| |
Sbjct  195749  TAATTTTTCTATATTTGTAGAGAC-AGGGTTTCACCCTGTCGGCCAGGCTGGTCTTGAAC  195807

Query  25953   gcctgacctcaggtgatccagcc-aacttggactctcaaagtgcagggattacaggtgtg  26011
                |||||||||| |||||||| ||   ||||| ||| |||||||| || | ||||||  ||
Sbjct  195808  TCCTGACCTCAAGTGATCCA-CCTGCCTTGGCCTCCCAAAGTGCTGGTAATACAGGCATG  195866

Query  26012   agccacctcacccggcctttaatgaGTGAATTCTTGATTTCCACCCTATTCCTAACACTG  26071
               |||||||  |    ||||| ||||| ||||||||||| |||||| |||| ||||| ||||
Sbjct  195867  AGCCACC-GA----GCCTTGAATGAATGAATTCTTGACTTCCACTCTATCCCTAATACTG  195921

Query  26072   TCAATTTCTTGATTCATGAACTTAATATGGATAGCTGATATGAATGGATATCTGATTCAA  26131
               ||| |||||||||||||||| | |||||||||| ||| ||||||||||||||||||||||
Sbjct  195922  TCACTTTCTTGATTCATGAAATGAATATGGATATCTGGTATGAATGGATATCTGATTCAA  195981

Query  26132   TCCAGTAATCTGGGGACAGCCAAAAACCCAATCAAGATTAACTGGGTGGAGCTTCAGAAA  26191
               |||| ||||||||||| ||||||||||||||||| |||||||||||||||||||||||||
Sbjct  195982  TCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCAGAAA  196041

Query  26192   TGCAATCAGATAGCACTTTTTGATTGGAAGCAAGCA-CTGGATA-GATGGAGGGGTGTGG  26249
               |||||||||||| |||||||||| ||||||| |||| | ||||| | |||||||| ||||
Sbjct  196042  TGCAATCAGATACCACTTTTTGACTGGAAGCTAGCAGC-GGATACG-TGGAGGGGCGTGG  196099

Query  26250   GTGGGAGTTGTGATTAGAAAGATCGATAAAAGTTTCTGAAGGCCCACAGGAGAGACCCAA  26309
               ||||||||||||||||||||| || ||||||| |||| ||| ||||||||||||||||||
Sbjct  196100  GTGGGAGTTGTGATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGAGAGACCCAA  196159

Query  26310   AGTCTTCAAGTCTGGAGTTCCTGCTTGGTTCTTCCTGAGGTCTAAGCACTCTGCAAACTC  26369
               |||||||||| |||||||| |||||||||| |||||||||||| ||||| ||||||||| 
Sbjct  196160  AGTCTTCAAGCCTGGAGTTTCTGCTTGGTTTTTCCTGAGGTCTGAGCACCCTGCAAACTG  196219

Query  26370   AGTCCAGATCTAGTAAGTCACTCATTTCTGGAAGGACACTCCCATCTGACCTATAGTCAG  26429
               ||||||||||| ||||||| || || |||| |||||||||||||||||||||| ||||||
Sbjct  196220  AGTCCAGATCTGGTAAGTCCCTAATCTCTGTAAGGACACTCCCATCTGACCTACAGTCAG  196279

Query  26430   CCGGTCTGGGACGGGGGCAATGCAGCCTATGATGGCACCGAGCTATATC-TGTCTTTtat  26488
               ||||||||||| || | || ||||| | |      ||  ||| |||||| |||||||| |
Sbjct  196280  CCGGTCTGGGATGGTGACAGTGCAGGC-A------CA--GAGTTATATCCTGTCTTTTTT  196330

Query  26489   atatatata-tatGAACAATTTGAAGATTTGAATTTTTTCCTCTATATGCAGTTTTGTCT  26547
                | | | |  |||||||||||||||| ||||| ||||| ||| || ||||||||||||||
Sbjct  196331  TTTTTTTTTGTATGAACAATTTGAAGCTTTGACTTTTT-CCTTTAAATGCAGTTTTGTCT  196389

Query  26548   TTATTTCAAAAAATTGGATT-GTGCTTTGGTTTATGTCATTTcaaaattcttgatgggag  26606
               | ||||||||||||| |||| |||||||||||||| || ||||| |||||||| ||||||
Sbjct  196390  TCATTTCAAAAAATTTGATTTGTGCTTTGGTTTATATCCTTTCAGAATTCTTGGTGGGAG  196449

Query  26607   caatgactcatgcccataa-cctcaacaccttgggaggccaaagcgggaggatcatttga  26665
                | |||| |||||| | || || |||||| || ||||||||| | |||||||||||||||
Sbjct  196450  TAGTGACCCATGCCTACAATCC-CAACACTTTCGGAGGCCAATGTGGGAGGATCATTTGA  196508

Query  26666   gcccaggggtttgagaccaacctgggcaacatggcaaaaatgcagctctacaaaacattc  26725
               ||||| |||||  ||||||| |||||||||||||||||| | || |||||||||| ||| 
Sbjct  196509  GCCCACGGGTTCAAGACCAATCTGGGCAACATGGCAAAACTCCATCTCTACAAAATATT-  196567

Query  26726   tttttttgaagcagggatggagtctcaccctgttg-ccaaggctggagtgcagtggcaag  26784
               ||||||||  |  ||||| ||||||  | |||||| ||| ||||| |||||||||||| |
Sbjct  196568  TTTTTTTGGTGG-GGGATAGAGTCTTGCTCTGTTGGCCA-GGCTGCAGTGCAGTGGCATG  196625

Query  26785   agctcaactcactgcaacctcttcctcccaggctcaaacaattttcatgtctcagcttcc  26844
               | |||  | ||||||||||||  |||||||||||||| ||||| ||||| |||||| |||
Sbjct  196626  ATCTCGGCCCACTGCAACCTCCGCCTCCCAGGCTCAAGCAATTCTCATGCCTCAGCCTCC  196685

Query  26845   tgagtagctggtattacatcc-ctctgccaccatgtctg-cttaatttttgtatttttag  26902
               ||||||||||| |||||| || | ||||||| ||| ||| || |||||||||||||||||
Sbjct  196686  TGAGTAGCTGGGATTACAGCCGC-CTGCCACTATGCCTGGCT-AATTTTTGTATTTTTAG  196743

Query  26903   tagtggtggggtttcaccatgctggccaggttggtctcaaactcctgacatcaagtgatc  26962
               ||| ||||||||||||| ||| |||||||| ||||||| |||||||||| ||||||||||
Sbjct  196744  TAGAGGTGGGGTTTCACTATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAAGTGATC  196803

Query  26963   ctcctgcctaggcc-cccaaaagtgctggaatgacggccgtgagccaATGGTGGTCAGCc  27021
               | ||  ||| |||| |||||| ||||||| || || ||| | | |||   ||   |||||
Sbjct  196804  CACCCACCTTGGCCTCCCAAA-GTGCTGGGATTACAGCCATCAACCACCAGTCCCCAGCC  196862

Query  27022   tctacaaaatatatatatcttttaatttgccaggcatggtagcatgcatctgtattccca  27081
               |||||| || | || | | ||| |||| ||| |||||||| ||||||||||||| |||||
Sbjct  196863  TCTACATAA-A-ATGT-T-TTTAAATTAGCCGGGCATGGTGGCATGCATCTGTAGTCCCA  196918

Query  27082   gctatttggtttgctgacatgggagaatcacttgagcccagaagattgaggctgcagtga  27141
               ||||||||| | |||||  |||||||||| ||||||||| |||| ||||||||||| |||
Sbjct  196919  GCTATTTGGGTGGCTGAGGTGGGAGAATCCCTTGAGCCCGGAAGTTTGAGGCTGCAATGA  196978

Query  27142   gccatgctcacaccactgctgtactccagcctgggcaacagagtaagaccctg  27194
               ||| |||||||||||||||||||||||||||||||||||||||| |||| |||
Sbjct  196979  GCCGTGCTCACACCACTGCTGTACTCCAGCCTGGGCAACAGAGTGAGACTCTG  197031


 Features flanking this part of subject sequence:
   9784 bp at 5' side: PRAME family member 5
   7459 bp at 3' side: PRAME family member 8

 Score = 1212 bits (656),  Expect = 0.0
 Identities = 904/1019 (88%), Gaps = 35/1019 (3%)
 Strand=Plus/Plus

Query  2229   GATGTTCCGCAGCTGAACCTCAATCACAGACAAAC-TAGTGCCTCGTTATTTTTCCATCA  2287
              ||||||  ||||||||| ||||||||||||| |||  ||| | | | || ||||||||||
Sbjct  58605  GATGTTTTGCAGCTGAATCTCAATCACAGAC-AACAGAGTACTTTGATACTTTTCCATCA  58663

Query  2288   GTAACTCAATAACTAGAGATTTCTGATGTATAAATCCCTAAAACAAGTAAATCAATTACA  2347
              |||||||||||||||||||||||||||||||||||| ||||||||||| |||||| ||||
Sbjct  58664  GTAACTCAATAACTAGAGATTTCTGATGTATAAATCGCTAAAACAAGTCAATCAAATACA  58723

Query  2348   GAGGACACCAGAAAGTTTTCACTGAGGTTCTCTATTTCTGATATTTCTTGGTAATCATCC  2407
              ||||||||||||||||||||| |||||   | |||||||||||||||||||||| | |||
Sbjct  58724  GAGGACACCAGAAAGTTTTCATTGAGG---T-TATTTCTGATATTTCTTGGTAACCGTCC  58779

Query  2408   TTGCAGGGATAACATTCTCATCACTGAAGAATTTTAGTTTCTCTTTCTGACTCTGT----  2463
               ||||||||||||||||||||||||| |||| ||||| ||||||||||||||||||    
Sbjct  58780  CTGCAGGGATAACATTCTCATCACTGTAGAACTTTAGCTTCTCTTTCTGACTCTGTAGGA  58839

Query  2464   -A---G---C------TCTCATTGACTCCACCTCAATATTTTCCTCAAGTCTTGCCCCCT  2510
               |   |   |      |||||||||||||||||| | ||||||||| |||||||||||||
Sbjct  58840  CATGGGTCCCGTAAGGTCTCATTGACTCCACCTCCACATTTTCCTCCAGTCTTGCCCCCT  58899

Query  2511   GCTCTTAGGATTTTTTCCCTCGCACTGAGCACCTGTCTGAA--ACAGAGCTCTGTGCTTC  2568
              ||| |||   |||||||||||  |||||||||||| |||||  | |||  ||||||||||
Sbjct  58900  GCTGTTA-TCTTTTTTCCCTCATACTGAGCACCTGCCTGAAGCAAAGAATTCTGTGCTTC  58958

Query  2569   CTTTAAGTTGCACATGTggcctgggcacagtcgctcatgcctgtaatcccagcactttag  2628
              || |||||||  |||||||||||| |||| || |||||||| |||||||  |||||||||
Sbjct  58959  CTGTAAGTTG--CATGTGGCCTGGTCACAATCACTCATGCCAGTAATCCTGGCACTTTAG  59016

Query  2629   aaggccgaggcaggagaatcccatgcgaccagcagtttgagacctgctggggcaacatag  2688
               ||||| |||||||||||||||||| | |||||||||| ||||| |||||||||||| ||
Sbjct  59017  GAGGCCAAGGCAGGAGAATCCCATGTGCCCAGCAGTTTCAGACCAGCTGGGGCAACACAG  59076

Query  2689   tgaaacactttctc-aatttttttgtaataaaaatattggaattattaaaaaaggaaata  2747
               ||||| || |||| ||| || || |||| ||||| || |||||||||||||||||||||
Sbjct  59077  CGAAACCCTGTCTCAAATGTTCTT-TAAT-AAAATTTTAGAATTATTAAAAAAGGAAATA  59134

Query  2748   agaaaagaggaaa-ataaCTTGCACCTACATACTAGATTTTAGTGTCCAAGGGCCTAGAA  2806
              |||||| |  ||| ||||||||||| ||||||||||||||||||||||||| |||| |||
Sbjct  59135  AGAAAA-AACAAACATAACTTGCACTTACATACTAGATTTTAGTGTCCAAGTGCCTGGAA  59193

Query  2807   GAGAACATTGGATTTCTCTACCCCGCTAGGCACGCCTTCCCTAGCAGCAAAGATGGAGCT  2866
              |||||| |||||||| || ||||| |||||||||||||||||||||||||||||||||||
Sbjct  59194  GAGAACTTTGGATTTATCAACCCCACTAGGCACGCCTTCCCTAGCAGCAAAGATGGAGCT  59253

Query  2867   CCAGTTCCTCAGACGGTGATGAGCCACAGGACGGGCAGGGGGCGGGGCCAATGAAGATCC  2926
              ||||||||||||||||||||||||||||||| |||||||| | ||| ||| |||||||||
Sbjct  59254  CCAGTTCCTCAGACGGTGATGAGCCACAGGAAGGGCAGGGAGTGGGACCAGTGAAGATCC  59313

Query  2927   TCTTGGGCTGCCTGACTTCCCTTAGTGTACACATCAACTAAGCCCGAAGTGGGGTGAAGA  2986
              |||||||||||||||||||||| ||||||||||||| || ||||| |||||||| |||||
Sbjct  59314  TCTTGGGCTGCCTGACTTCCCTCAGTGTACACATCAGCTCAGCCCAAAGTGGGGCGAAGA  59373

Query  2987   TCTCCCAATCGACATGAACCAAGGAATTCAAACTCTCCTCGGGGGCAGGATACATCTCCA  3046
              |||||||||||||| ||||||||||||||||||||||||| |||||||||||| ||||||
Sbjct  59374  TCTCCCAATCGACACGAACCAAGGAATTCAAACTCTCCTCAGGGGCAGGATACGTCTCCA  59433

Query  3047   GGCTTAACTTGCTCAGCCCACTGGTGTGGCACAGCAGGTCCTTCAGGGCT-TCCATAGAC  3105
              |||||||||||||||||||||||||||||| ||||||||||||||||| | ||| |||||
Sbjct  59434  GGCTTAACTTGCTCAGCCCACTGGTGTGGCGCAGCAGGTCCTTCAGGG-TGTCCGTAGAC  59492

Query  3106   ATGCAATTTCTGCCAAAGTAGAAGGTGGTGAGCTGGGAGCAGCGGCTCAGGCCAGGCAGG  3165
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  59493  ATGCAATTTCTGCCAAAGTAGAAGGTGGTGAGCTGGGAGCAGCGGCTCAGGCCAGGCAGG  59552

Query  3166   ATGGCACTGAGTTGGGAGTAGTGGATCTGACAGCCCTCCAAGATGAGGGTCTTAAGAGT  3224
              ||||| ||||||||| |||||||||||||||||||||| |||||||||||||| |||||
Sbjct  59553  ATGGCGCTGAGTTGGCAGTAGTGGATCTGACAGCCCTCGAAGATGAGGGTCTTGAGAGT  59611


 Features in this part of subject sequence:
   PRAME family member 16

 Score = 1175 bits (636),  Expect = 0.0
 Identities = 783/853 (91%), Gaps = 13/853 (1%)
 Strand=Plus/Plus

Query  28475   GAGATCTGAGCTTCAGAGATCCTCGGTAACATTTGCCAGTGCTATGAGTTTAGTGGAT-C  28533
               ||||||||||||||| ||||||| ||||||| || |||||||||| ||| |||||| | |
Sbjct  175046  GAGATCTGAGCTTCAAAGATCCTTGGTAACACTTCCCAGTGCTATCAGTGTAGTGG-TGC  175104

Query  28534   AGTGGCTAATAATTCATGGA--C--TACGAGGGATCTTGCCTGCTCTTTAGAAGTTGGGA  28589
               ||||||||||||||||||||  |  || |||||||||||||||||||||||| |||||||
Sbjct  175105  AGTGGCTAATAATTCATGGACCCTATAGGAGGGATCTTGCCTGCTCTTTAGAGGTTGGGA  175164

Query  28590   CACATTCTTCATGGTACCAGAAGGGTAGAACTATGTCTCTGTGGCCACTTATTGCAGAAA  28649
               |||| ||||| |||||||||||||| ||||||||| ||||||||||||||||||||||| 
Sbjct  175165  CACACTCTTCTTGGTACCAGAAGGGCAGAACTATGCCTCTGTGGCCACTTATTGCAGAAT  175224

Query  28650   GGAACTGGAGTAAACTGAGGGCTCTTTCACACATGCTAGAGAAATGACTTGGGCCCTGGG  28709
               |||| ||||||||||||||||| |||||||||||||||||||| |||||| |||||| ||
Sbjct  175225  GGAATTGGAGTAAACTGAGGGCCCTTTCACACATGCTAGAGAACTGACTTTGGCCCTAGG  175284

Query  28710   AGAATTGGGGGTTGCAGGGGATTGGTCGGAGGAACTTGCCTTTTTGCTGGATTGTGCTGT  28769
               |||| |||||||||||||||||||| | ||| ||||||||||||  ||||||||| || |
Sbjct  175285  AGAAGTGGGGGTTGCAGGGGATTGGCCTGAGAAACTTGCCTTTTCACTGGATTGTCCTCT  175344

Query  28770   AGAGTTTTTC-CTTGTAGATTTGTCAGAATGAGCCTCCAGACCCCATCCAGACTCCTGGA  28828
               |||||||||| | || |||||||||||||||||||||||| |||||||||||||||||||
Sbjct  175345  AGAGTTTTTCAC-TGGAGATTTGTCAGAATGAGCCTCCAGTCCCCATCCAGACTCCTGGA  175403

Query  28829   GCTGGCAGGGCAGAGCCTGATGAGGAAGCAGTTCTTGACTATCTTCACCCTGGACTAGCT  28888
               ||||||||| ||||||||| ||||||| ||||||||||| ||||||| ||||||| ||||
Sbjct  175404  GCTGGCAGGCCAGAGCCTGCTGAGGAACCAGTTCTTGACCATCTTCATCCTGGACGAGCT  175463

Query  28889   GCCCAGGGAGGTCTCCCCTCTGACGTTCATGGAGGCCTTCAGCATGAGATGTTGTGAGGC  28948
               |||||||||||||| |||||||| |||||||||||||| ||||||||||  || ||||||
Sbjct  175464  GCCCAGGGAGGTCTTCCCTCTGATGTTCATGGAGGCCTCCAGCATGAGACATTTTGAGGC  175523

Query  28949   CCTGAAGCTGATGGTGCAGGCCTGGTCCTCCCTTCACCTCCCTCTGGGATCCCTGATGAA  29008
               ||||||||||||||||||||||||| ||| ||| | ||||||||||||||||||||||||
Sbjct  175524  CCTGAAGCTGATGGTGCAGGCCTGGCCCTTCCTCCGCCTCCCTCTGGGATCCCTGATGAA  175583

Query  29009   GACAACTCATCTGGAGACCTTGCAAGCTGTGCTGAAGGGACTTGATACACTAG-TGTCCC  29067
               |||| |||||||||||||||||||||||||||||||||||||||||||||| | || |||
Sbjct  175584  GACACCTCATCTGGAGACCTTGCAAGCTGTGCTGAAGGGACTTGATACACT-GCTGGCCC  175642

Query  29068   AGAAGGTTTGCCCCAGTTGAGGTGACTCAGGTGGCCTGGTGGGAAGGGTCCAGGCATCCA  29127
               ||||| || ||||||| |||||||||||||||||||||||||||||||||||||||||||
Sbjct  175643  AGAAGCTTCGCCCCAGGTGAGGTGACTCAGGTGGCCTGGTGGGAAGGGTCCAGGCATCCA  175702

Query  29128   GGGAAGGGACAGCTGGCTCAGGAGGAGTGGCAGTGTGTGGG-AGCTAGGGTGGCTCAGAG  29186
               ||||||||||||||||||||||||||||||  | || |||| ||||||||||||||||||
Sbjct  175703  GGGAAGGGACAGCTGGCTCAGGAGGAGTGGTGGGGT-TGGGGAGCTAGGGTGGCTCAGAG  175761

Query  29187   GCTTCTGATGGTACCCATGAGAGGCCTTGGCCATTGCCCAGATCCTCTGGAAAAGGACTG  29246
               |||||||||||| |||||||||| ||||| ||||||||||||||||||||||||||||||
Sbjct  175762  GCTTCTGATGGTGCCCATGAGAGACCTTGACCATTGCCCAGATCCTCTGGAAAAGGACTG  175821

Query  29247   CTCACCATACAGAGTCCACTGAGGAAACAGGAACCTGCTTCCTTCCCAGTGGAAGGTAAA  29306
               |||||||||||| |||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct  175822  CTCACCATACAGGGTCCACTGAGGAAACAGGAACCTGCTTCCT-CCCAGTGGAAGGTAAA  175880

Query  29307   GGTACTAGAAGTG  29319
               ||| |||||||||
Sbjct  175881  GGTTCTAGAAGTG  175893


 Features flanking this part of subject sequence:
   19491 bp at 5' side: PRAME family member 3
   12888 bp at 3' side: PRAME family member 5

 Score = 1164 bits (630),  Expect = 0.0
 Identities = 781/853 (91%), Gaps = 13/853 (1%)
 Strand=Plus/Plus

Query  28475  GAGATCTGAGCTTCAGAGATCCTCGGTAACATTTGCCAGTGCTATGAGTTTAGTGGAT-C  28533
              ||||||||||||||| ||||||| | ||||| || |||||||||| ||| |||| | | |
Sbjct  31244  GAGATCTGAGCTTCAAAGATCCTTGCTAACACTTCCCAGTGCTATCAGTGTAGTAG-TGC  31302

Query  28534  AGTGGCTAATAATTCATGGA--C--TACGAGGGATCTTGCCTGCTCTTTAGAAGTTGGGA  28589
              ||||||||||||||||||||  |  || |||||||||||||||||||||||| |||||||
Sbjct  31303  AGTGGCTAATAATTCATGGACCCTATAGGAGGGATCTTGCCTGCTCTTTAGAGGTTGGGA  31362

Query  28590  CACATTCTTCATGGTACCAGAAGGGTAGAACTATGTCTCTGTGGCCACTTATTGCAGAAA  28649
              |||| ||||| | |||||||||||| ||||||||| ||||||||||||||||||||||| 
Sbjct  31363  CACACTCTTCTTAGTACCAGAAGGGCAGAACTATGCCTCTGTGGCCACTTATTGCAGAAT  31422

Query  28650  GGAACTGGAGTAAACTGAGGGCTCTTTCACACATGCTAGAGAAATGACTTGGGCCCTGGG  28709
              |||| ||||||||||||||||||||||||||||||||||||||||||||| |||||| ||
Sbjct  31423  GGAATTGGAGTAAACTGAGGGCTCTTTCACACATGCTAGAGAAATGACTTTGGCCCTAGG  31482

Query  28710  AGAATTGGGGGTTGCAGGGGATTGGTCGGAGGAACTTGCCTTTTTGCTGGATTGTGCTGT  28769
              ||||  |||| |||||||||||||| | ||| ||||||||||||  ||||||||| || |
Sbjct  31483  AGAAGCGGGGATTGCAGGGGATTGGCCTGAGAAACTTGCCTTTTCACTGGATTGTCCTCT  31542

Query  28770  AGAGTTTTTCCTTGTAGATTTGTCAGAATGAGCCTCCAGACCCCATCCAGACTCCTGGAG  28829
              |||||||||||||| ||||||||||||||||| |||||| ||||||||||||||||||||
Sbjct  31543  AGAGTTTTTCCTTGCAGATTTGTCAGAATGAGTCTCCAGTCCCCATCCAGACTCCTGGAG  31602

Query  28830  CTGGCAGGGCAGAGCCTGA-TGAGGAAGCAGTTCTTGACTATCTTCACCCTGGACTAGCT  28888
              ||||||||||||||||| | ||||||| ||||||||||| ||||||| ||||||| ||||
Sbjct  31603  CTGGCAGGGCAGAGCCT-ACTGAGGAACCAGTTCTTGACCATCTTCATCCTGGACGAGCT  31661

Query  28889  GCCCAGGGAGGTCTCCCCTCTGACGTTCATGGAGGCCTTCAGCATGAGATGTTGTGAGGC  28948
              |||||||||||||| |||||||| ||||||||||||| |||||| |||| | ||||||||
Sbjct  31662  GCCCAGGGAGGTCTTCCCTCTGATGTTCATGGAGGCCGTCAGCAGGAGAAGCTGTGAGGC  31721

Query  28949  CCTGAAGCTGATGGTGCAGGCCTGGTCCTCCCTTCACCTCCCTCTGGGATCCCTGATGAA  29008
              ||||||||||||||||||||||||||||| ||| ||||||||||||||||||||||||||
Sbjct  31722  CCTGAAGCTGATGGTGCAGGCCTGGTCCTTCCTCCACCTCCCTCTGGGATCCCTGATGAA  31781

Query  29009  GACAACTCATCTGGAGACCTTGCAAGCTGTGCTGAAGGGACTTGATACACTAG-TGTCCC  29067
              |||| |||||||||||||||||||||||||||||||||||||||||||||| | || |||
Sbjct  31782  GACACCTCATCTGGAGACCTTGCAAGCTGTGCTGAAGGGACTTGATACACT-GCTGGCCC  31840

Query  29068  AGAAGGTTTGCCCCAGTTGAGGTGACTCAGGTGGCCTGGTGGGAAGGGTCCAGGCATCCA  29127
              |||||||||||| ||| |||||||||||||||||||||||||||||||||||||||||||
Sbjct  31841  AGAAGGTTTGCCTCAGGTGAGGTGACTCAGGTGGCCTGGTGGGAAGGGTCCAGGCATCCA  31900

Query  29128  GGGAAGGGACAGCTGGCTCAGGAGGAGTGGCAGTGTGTGGG-AGCTAGGGTGGCTCAGAG  29186
              ||||||||||||||||||||||||||||||  | || |||| ||||||||||||||||||
Sbjct  31901  GGGAAGGGACAGCTGGCTCAGGAGGAGTGGTGGGGT-TGGGGAGCTAGGGTGGCTCAGAG  31959

Query  29187  GCTTCTGATGGTACCCATGAGAGGCCTTGGCCATTGCCCAGATCCTCTGGAAAAGGACTG  29246
              |||||||||||| |||||||||||||||| |||||||||||||||||||| |||||||||
Sbjct  31960  GCTTCTGATGGTGCCCATGAGAGGCCTTGACCATTGCCCAGATCCTCTGGGAAAGGACTG  32019

Query  29247  CTCACCATACAGAGTCCACTGAGGAAACAGGAACCTGCTTCCTTCCCAGTGGAAGGTAAA  29306
              |||||||||||| ||||||||||||||||||||||||||| || |||||||||| |||||
Sbjct  32020  CTCACCATACAGGGTCCACTGAGGAAACAGGAACCTGCTTTCT-CCCAGTGGAACGTAAA  32078

Query  29307  GGTACTAGAAGTG  29319
              | | |||||||||
Sbjct  32079  GATTCTAGAAGTG  32091


 Features flanking this part of subject sequence:
   20199 bp at 5' side: PRAME family member 16
   2702 bp at 3' side: PRAME family member 21

 Score = 1118 bits (605),  Expect = 0.0
 Identities = 853/968 (88%), Gaps = 35/968 (3%)
 Strand=Plus/Plus

Query  27239   AGAGAATCTTTGACCTTAATTTTAAACCAATCACATCCTCACTGTAATTCTTCCTCCCGA  27298
               ||||||||||||| ||||||||||||||||||||||||||| ||||| |||||| |||||
Sbjct  198415  AGAGAATCTTTGAGCTTAATTTTAAACCAATCACATCCTCATTGTAACTCTTCCACCCGA  198474

Query  27299   ATGGAGACATgggtgtgagggtgcatgcctgtaatcccagctacatggaaggctgaagca  27358
               ||||||||||||||| | ||||||||||||||||||||||||||||||||||||||||||
Sbjct  198475  ATGGAGACATGGGTGCGGGGGTGCATGCCTGTAATCCCAGCTACATGGAAGGCTGAAGCA  198534

Query  27359   tgagaattgc-ttgaatctcagaggcggaagttacagtgagctgagatgga-gccgctgc  27416
               |||||| | | ||||| ||  |||| ||| ||||||||||||  | || ||  || ||||
Sbjct  198535  TGAGAA-TCCATTGAACCTGGGAGGTGGAGGTTACAGTGAGCCAAAAT-GACACCACTGC  198592

Query  27417   actccagcctgggcga-caaagtgagactcag--cttca-cc--c-acaccaaaaaaaaT  27469
               |||||||||||||| |  ||| ||||||||||  |  || ||  | ||||||||||||||
Sbjct  198593  ACTCCAGCCTGGGCTAGGAAA-TGAGACTCAGCCCCCCACCCTGCAACACCAAAAAAAAT  198651

Query  27470   TAGATTATACCACCCAGGTGATCACTGGATACATGAAGATTTCTATTGTGTGTTATTGGG  27529
               || |||||||||||||||| |||||||||||||||| |||||||||||||| || || ||
Sbjct  198652  TAAATTATACCACCCAGGTAATCACTGGATACATGATGATTTCTATTGTGTTTTCTTAGG  198711

Query  27530   GACTGTCAACTCCGTCTTTGAAAACTGTTTTAACTCTGAAATATTTTGATAAATTTGATG  27589
               |||||||| ||| ||||||| |||||||||||||||||||||||| ||||||| ||  ||
Sbjct  198712  GACTGTCATCTCTGTCTTTGTAAACTGTTTTAACTCTGAAATATTCTGATAAA-TT--TG  198768

Query  27590   TGGCCAAGGATCCCTCAACAAAGATACTTTCAAGTTTTCTTTCTTTCTGTCTAATATCAG  27649
               || ||||||||||||||||||||||||||||||| ||| |||||||||||||||| ||||
Sbjct  198769  TGACCAAGGATCCCTCAACAAAGATACTTTCAAG-TTT-TTTCTTTCTGTCTAATGTCAG  198826

Query  27650   GAAGAGATTCAACACTTCCCTATCTCACACTCAGGACTATGAAGGACACATATTAGTAAA  27709
               ||||||||||||| |||||||||||||||||||||||||||||||||| |||||||||||
Sbjct  198827  GAAGAGATTCAACCCTTCCCTATCTCACACTCAGGACTATGAAGGACATATATTAGTAAA  198886

Query  27710   CCTCCATGTTTGTGGAGGGAATCAGTGAATGAGTCCTGGACTTTCACCCTATCCCTAAAT  27769
                 ||||||||||||||| ||||||||||||||||| |||||||||||||||| |||||||
Sbjct  198887  ATTCCATGTTTGTGGAGTGAATCAGTGAATGAGTCATGGACTTTCACCCTATACCTAAAT  198946

Query  27770   CTTTCACTTTCATGGATGAATATCTAATTCAATCAGTTAATCTGGAAGAAAGCCAAAAAT  27829
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  198947  CTTTCACTTTCATGGATGAATATCTAATTCAATCAGTTAATCTGGAAGAAAGCCAAAAAT  199006

Query  27830   CCAATCAGGATTAACTGGGTAGAGTTTAAGAAGTCGAATCAAATGTAGTtctctctctct  27889
               ||| |||||||||||||||| ||| |||||| |   | | |||||||||| | ||| | |
Sbjct  199007  CCAGTCAGGATTAACTGGGTGGAGCTTAAGA-G---ATTTAAATGTAGTT-T-TCT-T-T  199058

Query  27890   ctctctctcttttcttttcttttttttttttttttttt-tgaatctagcctatttcacag  27948
                | | | | | || || | |||| ||||| |||||    ||||||||||||||||| |||
Sbjct  199059  -T-T-TGT-TGTTGTTGT-TTTTGTTTTTGTTTTTGAGATGAATCTAGCCTATTTCTCAG  199113

Query  27949   gctggagtgcagtggtgtattgtcagctcactgcaacctctgcctcctgggttcaagtga  28008
               ||||||||||||||||  | | ||||||||||||||||||  ||||||||||||||||||
Sbjct  199114  GCTGGAGTGCAGTGGTACAATCTCAGCTCACTGCAACCTCCACCTCCTGGGTTCAAGTGA  199173

Query  28009   tcctcctgcctcagcctccctagtagcttggactataggcgcagaccaccgcacctggct  28068
               |||||||||||||||||||||||||||| |||||| |||| || ||||| ||||||||||
Sbjct  199174  TCCTCCTGCCTCAGCCTCCCTAGTAGCTGGGACTACAGGCACACACCACTGCACCTGGCT  199233

Query  28069   aatttttctaattttggtagaggtagggttttaccatgttggccaggctggtctcaaact  28128
               ||||||| || |||||||| || |||||||||||||||||||||| ||||||||||||||
Sbjct  199234  AATTTTTGTATTTTTGGTACAGATAGGGTTTTACCATGTTGGCCAAGCTGGTCTCAAACT  199293

Query  28129   cctgacctc-agataatccacc-tgcctctgcctcccagagggctgggattacaggtgtg  28186
               ||||||||| ||  | |||||| | | || ||| |||| || |||| |||||||||||||
Sbjct  199294  CCTGACCTCTAGGCA-TCCACCCTTC-TCAGCCCCCCAAAGTGCTGAGATTACAGGTGTG  199351

Query  28187   agtcactg  28194
               || |||||
Sbjct  199352  AGCCACTG  199359


 Features flanking this part of subject sequence:
   12539 bp at 5' side: PRAME family member 16
   10240 bp at 3' side: PRAME family member 21

 Score = 1109 bits (600),  Expect = 0.0
 Identities = 930/1082 (85%), Gaps = 51/1082 (4%)
 Strand=Plus/Plus

Query  12359   aaaaCTGGCTCAGTGGCCAATGgctgtgtggtcttactcaacttacttaacctctctgtg  12418
               ||||||||||||||||||||||||  ||| | | | | |||||| |||||||||||||||
Sbjct  190755  AAAACTGGCTCAGTGGCCAATGGCCATGT-GACCT-C-CAACTTCCTTAACCTCTCTGTG  190811

Query  12419   ccttagctcattcacatataaaatgggataat-agcaatattgacttcacagagtGCTAT  12477
               ||| |||||| ||||  ||||||||||||||| | |||||||||||||||||||||||||
Sbjct  190812  CCTCAGCTCACTCACCCATAAAATGGGATAATCA-CAATATTGACTTCACAGAGTGCTAT  190870

Query  12478   AAATTAATCTATTTAAGTACTTCGAGCTGGATTTGACATAGGGCAAGCAAGGA-TATTTT  12536
                | || ||||||||||||||||| || ||||||||||||| | |||||||  | ||||||
Sbjct  190871  GAGTTCATCTATTTAAGTACTTCAAGGTGGATTTGACATAAGACAAGCAA-TAGTATTTT  190929

Query  12537   TATTGTTATTATATTTGAAAAATATATTAGTTACAAACTTAGGT-AAGAGACCAAGGCCT  12595
               ||||||||||||||||||||||||||||||||| |||||||||| || | ||||||| ||
Sbjct  190930  TATTGTTATTATATTTGAAAAATATATTAGTTAAAAACTTAGGTTAAAA-ACCAAGGTCT  190988

Query  12596   ATGGTAAAGGTGATTATAAGCCTTCATACACCACTGTTGTTCTGAAAATCTTAATTATAA  12655
               || || |||||||||||||||||  ||||||| |||||||||||||||||||||||||||
Sbjct  190989  ATAGTTAAGGTGATTATAAGCCTAAATACACCCCTGTTGTTCTGAAAATCTTAATTATAA  191048

Query  12656   CAAggccaggc-acggtggctcacgtctgtaatcccagcactttgggaggccaaggtggg  12714
               ||||||  ||  | ||||||||| | |  ||||||||||||||||||||||| |||||||
Sbjct  191049  CAAGGCTGGGTGA-GGTGGCTCATGCCCATAATCCCAGCACTTTGGGAGGCCGAGGTGGG  191107

Query  12715   cagatcacctgaggtcaggagttcgagaccagcctcaccaacatggcgaaactatc-tct  12773
                 |||||||||||||||||||||| ||||||||||  |||||||||||||||   | |||
Sbjct  191108  TGGATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGCGAAACCC-CATCT  191166

Query  12774   ctactaaaaatacaaaaaatagctgggcatggtg-gtg-gacacctgtaatcccaggta-  12830
               |||||||||||||||||| || |  ||  || |  |   | |||||||||||||||||| 
Sbjct  191167  CTACTAAAAATACAAAAAGTAACCAGGTGTG-TCAGCAAG-CACCTGTAATCCCAGGTAC  191224

Query  12831   ttcggtaggttgaggcaggagaatcacttgaatccaggaggcagagtttgcagtgagcca  12890
               || || ||| | || ||||||||||||||||| || |||||  ||| ||||||||||   
Sbjct  191225  TTGGG-AGGCTAAGACAGGAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGTGG  191283

Query  12891   agattg-a---actattgctctccagc--c-tggcgagagagtgagactccatctcca-a  12942
               |||||| |   || ||||| |||||||  | ||| || |||| ||||||||||||||| |
Sbjct  191284  AGATTGCATGCAC-ATTGCACTCCAGCAGCCTGGTGACAGAGCGAGACTCCATCTCCACA  191342

Query  12943   -a-a-a-aaaaaa-aa-a-ttataagaaCATGTCCATTCACTCTCCAAAGTATCTAGGAC  12995
                | | | |||||| || | |||||| | ||||||||||||||||||||||| ||| ||||
Sbjct  191343  CACACACAAAAAATAATAATTATAACAGCATGTCCATTCACTCTCCAAAGTGTCTGGGAC  191402

Query  12996   TGGACAATTACTTGTCAGGCCCTCTTCTGTAGCACCATACACTATAGCATATATGTGGAT  13055
               ||||| |||| |||| ||||||||||||||||||||||||||||||||||||| ||||||
Sbjct  191403  TGGACGATTAATTGTGAGGCCCTCTTCTGTAGCACCATACACTATAGCATATACGTGGAT  191462

Query  13056   TAatataaataca-catacaaaattcaagtatatattctatatactttctatatatttat  13114
               ||| ||||||||| | |||||||| |||||||||||||||||||||||| ||||| ||||
Sbjct  191463  TAAAATAAATACAAC-TACAAAATGCAAGTATATATTCTATATACTTTCCATATACTTAT  191521

Query  13115   atTCTAAGAGGTCACATGCAAATTCAAGGCTAGGTCAAAGAGTAGAGTGGCTATCTATGG  13174
               ||| || |||||||||||||||||||||| |||||||||||||||||||||| |||||||
Sbjct  191522  ATTTTATGAGGTCACATGCAAATTCAAGGTTAGGTCAAAGAGTAGAGTGGCTGTCTATGG  191581

Query  13175   AAAGGGGAGTGGAAGTGAATCATGGTAATaaaa--aaaG-G-T---G-TAGA--TATAGT  13224
               |||||||||||||||||||||||||||||||||  |||  | |   | || |  ||||| 
Sbjct  191582  AAAGGGGAGTGGAAGTGAATCATGGTAATAAAAGGAAATAGATACAGATATAAATATAGA  191641

Query  13225   TATGGATAGGTAGACATACACACATATAGCGGCAAGAAAAGGGAAT-GTCATGGACCAGT  13283
               |||| |||| |||||||||||| ||||||| |||| ||||||| || ||||||||||| |
Sbjct  191642  TATGAATAGATAGACATACACATATATAGCTGCAA-AAAAGGGGATTGTCATGGACCAAT  191700

Query  13284   GATGACAGTGAGCCATGTAAAAAGGCTACAATTTTTGTGATTGTGTGTCCATTTTCAGGA  13343
               ||||||||||||||||| ||||||||||||||| |||||||||||||||  ||| |||||
Sbjct  191701  GATGACAGTGAGCCATGAAAAAAGGCTACAATTCTTGTGATTGTGTGTCTGTTTGCAGGA  191760

Query  13344   TTGGTTGTAGCTTACCTTTTT-AGAAAGGCTGATGCCATAGTCATAGTGAATAAATGATT  13402
               | |||| |||||| ||||||| |||||||||||| ||| ||||||||  |||||||||||
Sbjct  191761  TGGGTTATAGCTT-CCTTTTTTAGAAAGGCTGATACCACAGTCATAGCAAATAAATGATT  191819

Query  13403   AT  13404
               ||
Sbjct  191820  AT  191821


 Features flanking this part of subject sequence:
   1234 bp at 5' side: PRAME family member 13
   21297 bp at 3' side: PRAME family member 18

 Score = 1000 bits (541),  Expect = 0.0
 Identities = 1092/1351 (80%), Gaps = 66/1351 (4%)
 Strand=Plus/Plus

Query  6816    TAAGTCTGAGGA-GAAGGATCCAATACACATCCCTTCCACATACTCACAATCACACACTT  6874
               ||| ||||| || ||||| ||| ||| ||||| |||||||||||||||||| || |||||
Sbjct  132158  TAACTCTGA-GATGAAGGTTCCTATAGACATCACTTCCACATACTCACAATTACCCACTT  132216

Query  6875    AGGGACAGAGT-CTAAGGG-AAGAGATAAATCCCAGGTTC-G-G-AACAA--G-TCTCTT  6926
                  ||  || | ||| ||| || |||||||||||| | || | | || ||  |  |||||
Sbjct  132217  TTTGATGGA-TCCTAGGGGCAA-AGATAAATCCCATGATCTGAGCAA-AACTGCACTCTT  132273

Query  6927    GAGAATGGTGTACGGGAGA--TCTAA-GA-TTTCTGTAAAATGAAAGCCTGACTAATAAA  6982
               |||| ||||||  |||| |  | ||| || ||| || ||||||||||| | |||   | |
Sbjct  132274  GAGATTGGTGTGTGGGATACCTTTAAGGATTTTATG-AAAATGAAAGCAT-ACTTGGAGA  132331

Query  6983    ATCACAATACCGCTAAGTGTGTGAACTATAGCTGACA-GGCACAGAAACCA-ACAACTTC  7040
               ||||||||| | | |||| | |||||| ||  ||| | |||||| ||| || | ||||||
Sbjct  132332  ATCACAATAACACCAAGTCTATGAACTGTAATTGA-AGGGCACA-AAAACAGATAACTTC  132389

Query  7041    ACATGTCAAGACATAAACATCCAT-CCAACTGTAAATTTTTAATAtttttttttttAAAA  7099
               | ||||||||| ||||| || |||  | |||||||||||||||||   | ||||| ||||
Sbjct  132390  AAATGTCAAGAAATAAAAATTCATGTC-ACTGTAAATTTTTAATA---TATTTTTAAAAA  132445

Query  7100    A-CTGCTTCAATAAGAATTTTGAAATGAGGAAAA-TGAAGCACAAATCAAAATTTGAGGG  7157
               | ||||||| ||||||||||| ||||||  |||| | |||||||||||| ||||||| ||
Sbjct  132446  ACCTGCTTCGATAAGAATTTTAAAATGACAAAAACT-AAGCACAAATCACAATTTGATGG  132504

Query  7158    ATGAAGTCAAAACTATATTTGGAGGAAAAATCAAAACCTACATCTGTTTAATCTGAAAAA  7217
               |||||| |||||||| |||| |||||||||| ||| |||| ||||| || |||| |  ||
Sbjct  132505  ATGAAGACAAAACTACATTTAGAGGAAAAATGAAAGCCTAAATCTG-TTCATCTCACGAA  132563

Query  7218    ACAGACAG-GAAAT-TCTCTGTGCCATTTTGGGCTGTGTGTCACCATCCCTGACTGGCTG  7275
               ||||||||  |||| | | ||||||| |||||| ||||||||||| ||||||||||||||
Sbjct  132564  ACAGACAGAAAAATAT-TGTGTGCCACTTTGGGATGTGTGTCACCGTCCCTGACTGGCTG  132622

Query  7276    GCTGCAGATTAGACGGGCATGTTCCTAAGAAGGTGGTGACTTACCAGATCTGGACTCAGT  7335
               ||||| ||| ||| |||||||  ||||||||||||||||||||||||  ||||||||| |
Sbjct  132623  GCTGCTGATCAGATGGGCATGACCCTAAGAAGGTGGTGACTTACCAGCGCTGGACTCACT  132682

Query  7336    TTGCAGGGTGCTGGGACCTCTCAGAGAACCAAGCAGTAGCTCCAGGCACCAGGGCTTTGG  7395
               |||||| || |||||||||||||| ||||||||||||||||||||| |  || ||| |||
Sbjct  132683  TTGCAGAGTTCTGGGACCTCTCAGGGAACCAAGCAGTAGCTCCAGGAATGAGTGCTGTGG  132742

Query  7396    GTCTGTCCTGTGCAAACTCAGGAGCTTTTGTTGATGTTTCTAACCACACCCTCCCCTTCT  7455
               |||| | ||| | |  ||||||||||||| | ||  ||||||||| |||||| |||||||
Sbjct  132743  GTCTCTTCTGGGTACCCTCAGGAGCTTTTATGGACCTTTCTAACCCCACCCTTCCCTTCT  132802

Query  7456    CAATCACCAGCTTCCAATCAGAAAGTGATACCTGATTAGATCCTGAAGTTC-CACCCAGT  7514
               |||||||||||||||||||||||| ||||||||||||||||| || ||| | ||||||||
Sbjct  132803  CAATCACCAGCTTCCAATCAGAAACTGATACCTGATTAGATCTTGCAGT-CACACCCAGT  132861

Query  7515    TAATCCTGATTGAGTTT-CACACTTTCTTCTGATTCATTGATTAAATTAGATGTGCATTT  7573
               ||||||||||||||||| ||  ||||||||||| | ||||||  ||||||||   |||||
Sbjct  132862  TAATCCTGATTGAGTTTTCAG-CTTTCTTCTGACTAATTGATCGAATTAGATACACATTT  132920

Query  7574    ATGAAAGTGAAAGAATAAATAACAGGGTGAAAGTCCAAAAGTCATTAATTCATTTATTCC  7633
               ||| |||| ||||||||||||| ||||||||||||||||| |||||  ||||||||||||
Sbjct  132921  ATGGAAGTAAAAGAATAAATAATAGGGTGAAAGTCCAAAACTCATTCGTTCATTTATTCC  132980

Query  7634    CCAAACACTGATGAAGTTTGACTAACATGTGACCTTCATAGTGACAT-GG-AAGGT-TTA  7690
               | ||| |||||||||||||| |||| |   ||| ||| ||||||  | || ||||  |||
Sbjct  132981  CGAAATACTGATGAAGTTTGGCTAATACACGACTTTCGTAGTGATGTAGGGAAGGGATTA  133040

Query  7691    ATCTGTTCCTGGCATTAG---AAAGAAAAAACAAAACCTGATGATATCTTTATGGGAGAA  7747
               |||||||||||  |||||   ||| |||||| ||||||| | | | || |||| |||| |
Sbjct  133041  ATCTGTTCCTGATATTAGGCCAAA-AAAAAA-AAAACCTTAAGGTGTCCTTATTGGAGGA  133098

Query  7748    TATTTGGCCACATTGAAATTATCCAAACGTTTCAGAGCTA-AGACAGCTTTAAAAAGACG  7806
               | |||||||||||  ||||| || ||| |||||||||||| | ||||| | || ||||  
Sbjct  133099  TGTTTGGCCACATCAAAATTGTCAAAATGTTTCAGAGCTACA-ACAGCCTGAAGAAGATA  133157

Query  7807    GTGATGTCAA-CCCTAAGAAAACAGAATACAAAGCTCTGT-TATCCAACAGTTACCTGGG  7864
               |||||||||  ||| |||||||||||||| |||||| ||| |||| ||  || ||||| |
Sbjct  133158  GTGATGTCATTCCC-AAGAAAACAGAATAAAAAGCTGTGTATATCGAATGGTCACCTGTG  133216

Query  7865    TTTTATGCT-TCCTAACGGGGCAGGTCATATGTGGGTTCAGGTTGAAGAGGGGAACCACT  7923
               ||||||||| || ||||   |||| |||||||    ||||||| |||||  |||||||||
Sbjct  133217  TTTTATGCTATC-TAACATAGCAGATCATATGCACATTCAGGTAGAAGAAAGGAACCACT  133275

Query  7924    GAGGGTGTTAT-TGATCACAAGACTAAGGTCAAGGCTTCACTGCAGGAAATCAGGACAGA  7982
               ||| |||| || | ||| |||||||||| |||||||||||| | |||||||||||||| |
Sbjct  133276  GAGAGTGTGATCT-ATCTCAAGACTAAG-TCAAGGCTTCACCGAAGGAAATCAGGACA-A  133332

Query  7983    A-TGACAAAGTGAGGTGGGGGCTGGGCAGGA-TGGGACCGGGTGTTCTAGTAG-AACCCT  8039
               | |||| ||||||||||||| ||| || ||| || |||  ||||||||| | | |||| |
Sbjct  133333  AGTGACCAAGTGAGGTGGGGACTGAGC-GGAATGAGACTAGGTGTTCTAATGGGAACC-T  133390

Query  8040    GGGAAGGAACCAAGACAGCATAAAACATGGTGGGTATTTTGTGGGCATCTCCACAGA-AG  8098
               |  |||||| |||||||   |||||||||| || ||| ||||||||||||  |  |  ||
Sbjct  133391  GCAAAGGAAACAAGACAATGTAAAACATGGCGGTTATCTTGTGGGCATCTAGAT-GTCAG  133449

Query  8099    GATTGAAAGACTCT-GTCTGGATTGAGTTTA  8128
               || | |||| || | |||  |||||||||||
Sbjct  133450  GACTCAAAGTCTTTTGTCAAGATTGAGTTTA  133480


 Features flanking this part of subject sequence:
   12551 bp at 5' side: PRAME family member 8
   20923 bp at 3' side: PRAME family member 9

 Score =  974 bits (527),  Expect = 0.0
 Identities = 739/838 (88%), Gaps = 27/838 (3%)
 Strand=Plus/Plus

Query  13081  aagtatatattctatatactttctatatatttatatTCTAAGAGGTCACATGCAAATTCA  13140
              |||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||
Sbjct  82341  AAGTATATATTCTAAATACTTTCTATATACTTATATTCTAAGAGGTCACATGCAAATTCA  82400

Query  13141  AGGCTAGGTCAAAGAGTAGAGTGGCTATCTATGGAAAGGGGAGTGGAAGTGAATCATGGT  13200
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  82401  AGGCTAGGTCAAAGAGTAGAGTGGCTATCTATGGAAAGGGGAGTGGAAGTGAATCATGGT  82460

Query  13201  AATaaaaa--aaGGTGTAGATATAGTTATGG-ATAGGTAGACATACACACATATAGCGGC  13257
              ||||||||  || || ||||||||| || || |||| |||||||||||||||||||| ||
Sbjct  82461  AATAAAAATTAA-GTATAGATATAGATA-GGAATAGATAGACATACACACATATAGCTGC  82518

Query  13258  AAGAAAAGGGAATGTCATGGACCAGTGATGACAGTGAGCCATGTAAAAAGGCTACAATTT  13317
              |||||| ||||||||||||||||| ||||| |||||||||||||||||||||||||||| 
Sbjct  82519  AAGAAAGGGGAATGTCATGGACCAATGATGTCAGTGAGCCATGTAAAAAGGCTACAATTC  82578

Query  13318  TTGTGATTGTGTGTCCATTTTCAGGATTGGTTGTAGCTTACCTTTTTAGAAAGGCTGATG  13377
              |||||||||||||||  |||||||||| ||||||||||||||||||||||||||||||||
Sbjct  82579  TTGTGATTGTGTGTCTGTTTTCAGGATGGGTTGTAGCTTACCTTTTTAGAAAGGCTGATG  82638

Query  13378  CCATAGTCATAGTGAATAAATGATTATAAAATGTGTTTCCTTTCTGGCGAACCTCTGGAG  13437
              ||| || ||||||||||||||| |||||||||||||||||||||||| | | ||||||||
Sbjct  82639  CCACAGCCATAGTGAATAAATGGTTATAAAATGTGTTTCCTTTCTGGGGCATCTCTGGAG  82698

Query  13438  AAATTTCCAATGGTAGGAGAACTCAGTTTACTGGGCAGGCGATCACACAGATAAGATTTT  13497
              |||| |||| |||||||||||||| |||||||||||||| ||||||||||||||||||||
Sbjct  82699  AAATCTCCAGTGGTAGGAGAACTCCGTTTACTGGGCAGGTGATCACACAGATAAGATTTT  82758

Query  13498  ACAGATCTAATGGCACTACCATTAACTTCATTATCATTGGTATTCTACAAAGGTTGAGTG  13557
               |||||| ||||||||||||||||||||||||||| |||||||||||||||||| |||||
Sbjct  82759  TCAGATCCAATGGCACTACCATTAACTTCATTATCCTTGGTATTCTACAAAGGTCGAGTG  82818

Query  13558  AACAAATGGTATCTTAAAATTAAA-TTAGCTAAATTAACAAAAAAGATTGGATTACtttt  13616
              || |||||||||||| ||| |||| ||||||||| |||||||  ||| ||| ||| ||||
Sbjct  82819  AAGAAATGGTATCTTGAAACTAAAATTAGCTAAACTAACAAAGGAGACTGGGTTAATTTT  82878

Query  13617  tctttttttt-------gacacagagtctctgatgcccaagcgggagtacagtggtgcta  13669
              | ||||||||       || |||||||||||| | |||| || ||||| |||||||||||
Sbjct  82879  TTTTTTTTTTTTTTTTTGAGACAGAGTCTCTGTTACCCAGGCTGGAGTTCAGTGGTGCTA  82938

Query  13670  tgtcatctcactgcaacatctgcctcccgggttcaagagattctcctgcctcagactcct  13729
              | ||| ||||||||||| ||||||||| ||||||||| |||| || ||||| || |||| 
Sbjct  82939  TCTCAGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGTGATTGTCATGCCTTAGCCTCCC  82998

Query  13730  gagtagccgggattacaggcacacaccaccacacccagctgatttttgtatttttagcag  13789
               |||||| ||||||||||||| || | ||||||||||||| |||||||||||||||| ||
Sbjct  82999  AAGTAGCTGGGATTACAGGCATAC-C-ACCACACCCAGCTAATTTTTGTATTTTTAGTAG  83056

Query  13790  a-aacggggtttcaccatgttgaccaggttggtcttgaacccctgacctt--gtgatctc  13846
              | |||||||||||||||||||| |||| ||| ||   ||| |||| |||   |||||| |
Sbjct  83057  ATAACGGGGTTTCACCATGTTGCCCAGATTGCTC---AACTCCTGGCCTCAAGTGATC-C  83112

Query  13847  -cctgcctcagcctcctgaagtgctg-gaattataggct-tgagccaccttgcccagc  13901
               || ||||| ||||||  |||||||| || ||| ||| | ||||||| | || |||||
Sbjct  83113  ACCAGCCTCGGCCTCCCAAAGTGCTGAGA-TTACAGG-TGTGAGCCATCATGTCCAGC  83168


 Features flanking this part of subject sequence:
   77 bp at 5' side: PRAME family member 13
   22888 bp at 3' side: PRAME family member 18

 Score =  948 bits (513),  Expect = 0.0
 Identities = 784/912 (85%), Gaps = 30/912 (3%)
 Strand=Plus/Plus

Query  5823    TCTGCTTCTGCTGGTACCAGGAAGAATGTCTTCCAAACACCAAGGAGGGAGGGGTCAAAG  5882
               ||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| |
Sbjct  131001  TCTGCTTCTACTGGTACCAGGAAGAATGTCTTCCAAACACCAAGGAGGGAGGGGTCAAGG  131060

Query  5883    AGACCACTGGCCCATTAATTTTCATCCATGGCTCCACTGAATCCCAGTACCACTGGAAAG  5942
               |||||||||||  |||||||||||||| |   ||||||||||||||| ||||| ||| | 
Sbjct  131061  AGACCACTGGCTTATTAATTTTCATCCTTCATTCCACTGAATCCCAGAACCACCGGACAC  131120

Query  5943    TGTCACTGAGGATCCTGAAAGCCAAGCTCTACCTCTTTGAGGAAAATTTTCTTGTCACTT  6002
               || ||||||||||||||||||||||||||||||||||||||||||| |||||||||||||
Sbjct  131121  TGCCACTGAGGATCCTGAAAGCCAAGCTCTACCTCTTTGAGGAAAAATTTCTTGTCACTT  131180

Query  6003    ACCGCCCTAAAGCAATGAGAATGAGAGTGTCCTGTGGCCCCAGACAGCCTCCATTCTCAG  6062
               ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  131181  ACCACCCTAAAGCAATGAGAATGAGAGTGTCCTGTGGCCCCAGACAGCCTCCATTCTCAG  131240

Query  6063    TTTTCACCATGAACATGCTGGGGGAACACTAAAGGGACTCCCTAAAGTCAATGCCATTAT  6122
               ||  |||||| ||| ||||||||||||||||||||||||||||||| || ||||||||||
Sbjct  131241  TTCACACCATAAACGTGCTGGGGGAACACTAAAGGGACTCCCTAAAATCGATGCCATTAT  131300

Query  6123    TTTTTATTTTGAAAAATTTCAACcagaaactg-accgggtgctgtggctcatgtctgtaa  6181
               ||||||||||||||| |||| |||||||| || ||| |||||||||||||||||||||||
Sbjct  131301  TTTTTATTTTGAAAATTTTCTACCAGAAA-TGGACCAGGTGCTGTGGCTCATGTCTGTAA  131359

Query  6182    tcccagcactg-tgggaggccaaaacaggcagatcacttgaggttaggagttcgagaaca  6240
               ||||| ||||| ||| |  ||||  ||||||||||||||||||| |||||||||||||||
Sbjct  131360  TCCCAACACTGCTGG-ACACCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTCGAGAACA  131418

Query  6241    gcctggcttacgtaatgaa-ctctgtctctactaaatataaaaaaattaaaaaTCATTTG  6299
               ||||||| ||| ||||||| |  ||||||||||||||| ||||||||||| |||||||||
Sbjct  131419  GCCTGGCCTACATAATGAAACGATGTCTCTACTAAATACAAAAAAATTAAGAATCATTTG  131478

Query  6300    ACTCCAAAaggcagaggttgcagtgagccgagatcccaccactgcactccagtctggaca  6359
               |||||| |||||||||||||||||||||| ||||| ||||||||| |||||| ||||   
Sbjct  131479  ACTCCAGAAGGCAGAGGTTGCAGTGAGCCAAGATCTCACCACTGCTCTCCAGCCTGGGTG  131538

Query  6360    AAAGAGTTAGACTCTGTCTCAaataataataataataataataataataataataataat  6419
               | |||||| ||||| | |||||| || || |  || | | |||| | |  ||||  ||||
Sbjct  131539  ACAGAGTTGGACTCCGACTCAAACAA-AA-AC-AA-ACTGATAA-A-T--TAAT--TAAT  131588

Query  6420    taattaattaaaatGTTAGCCAGGTGTGGTGGTGCA-GTCCTATAATCCTAGCTACTCTG  6478
               |||  |||      ||||||||||||||||  |||| | | | |||||||||||||||||
Sbjct  131589  TAA--AAT------GTTAGCCAGGTGTGGTCATGCATGAC-TGTAATCCTAGCTACTCTG  131639

Query  6479    GAGGCAGAGGAAGAAGAATCACTTGAATCCCGGAGGCAGTGTTTTCAGTGAGCTGAACTC  6538
               ||||||||||||| ||||||||||||| ||| ||||||| |||| ||| ||||  | |||
Sbjct  131640  GAGGCAGAGGAAGGAGAATCACTTGAAGCCCAGAGGCAGAGTTTCCAGGGAGCCCAGCTC  131699

Query  6539    AACACCCTGCCCTTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAGAG-AAAA  6597
               |   |||||| || ||| |||||||||| | | ||| | |||| ||||| || |  ||||
Sbjct  131700  AGGGCCCTGCACTCCAGTCTGGGTGACACACTCAGAGTACATCGCAGAAAAAAAACAAAA  131759

Query  6598    GAATTAACCAGAAACT--AAAAGCGACGTGATGGTATTCTAGAGCATTTGGAAGGTAGGG  6655
                |||| ||  ||| ||  ||||| |  |||||||||||| | ||||||||||||||| | 
Sbjct  131760  TAATTCACTGGAA-CTGTAAAAGTGGTGTGATGGTATTCCACAGCATTTGGAAGGTATGT  131818

Query  6656    ATAGAAATACTAACTCTAGATGAggcacagtggctcactcctgtaatcccagcactttgg  6715
               |||||||| |||||| ||| || ||| | |||||||||||||||||||||||||||||||
Sbjct  131819  ATAGAAATGCTAACTGTAGCTG-GGCGCGGTGGCTCACTCCTGTAATCCCAGCACTTTGG  131877

Query  6716    gagtccaaggTG  6727
               |||||  |||||
Sbjct  131878  GAGTCTGAGGTG  131889


 Features in this part of subject sequence:
   PRAME family member 3

 Score =  939 bits (508),  Expect = 0.0
 Identities = 1529/2001 (76%), Gaps = 154/2001 (7%)
 Strand=Plus/Plus

Query  4063   ATCATATCAACTTGAAACACACTTTGTAACAAGAAATT-C--ACACG--TGCA-CATGCA  4116
              ||||||| ||||| ||||||||||  ||||||| |||| |  | | |  | || | | ||
Sbjct  10180  ATCATATTAACTTTAAACACACTTCCTAACAAGGAATTCCTAAAAGGAATTCACCCT-CA  10238

Query  4117   GTAGAGACAAAACGC-CCACTAAGTACCT-TGTACATGATGTCCCTCTC--TAGCCTCTA  4172
               ||||| |  ||| | |||||||  | ||   |||| ||||||||||||  |||| ||||
Sbjct  10239  CTAGAG-CTGAACCCTCCACTAACCAGCTCCCTACACGATGTCCCTCTCTGTAGCTTCTA  10297

Query  4173   CCCTAGGTGACCCCTCTGCCTTTATTGAAGTGATCCTGTGATAGCCACTCCAGGACATGG  4232
              ||| |||| | ||||||||| ||| || || |||||||||||| ||||| ||||| || |
Sbjct  10298  CCCCAGGTCATCCCTCTGCCCTTACTGGAGCGATCCTGTGATACCCACTTCAGGATATAG  10357

Query  4233   AGCACTGAACGGGACAATGTGTTGACATTCTGGTGTCCCCTGCACTGTGCCGTCGCCACT  4292
              |||||  ||| |||| |   | || ||||||  |||||||| | ||  | | || ||| |
Sbjct  10358  AGCACCAAACAGGAC-A---G-TG-CATTCTACTGTCCCCTTCCCT-AGACATCTCCAGT  10410

Query  4293   GGCTGGCACACAGTACACGTCT--TCTAGTGTTTACTGTAACaaaaaaaaaGGCTGCGCT  4350
              ||||||||||||||| | | ||  | | ||||||| ||||||  |||||||||||| |||
Sbjct  10411  GGCTGGCACACAGTAGATG-CTGAT-TGGTGTTTATTGTAAC--AAAAAAAGGCTGTGCT  10466

Query  4351   GTGGTCTGCAGAGAAAGGGCACGATCCTTTCTCACCTGATCAGCT-GTCCCAGGTGCCCT  4409
               ||| |  |||||||||  ||| |||||| ||||||||||||||| || ||||||| |||
Sbjct  10467  ATGGCCCCCAGAGAAAGCTCACCATCCTTCCTCACCTGATCAGCTGGT-CCAGGTGGCCT  10525

Query  4410   CTGTGGAAGGTGA-CCATATTCATTTTAAGCAGCTGGAGGTGTTTCAGCCTGAGGAACAT  4468
              |||  ||||  || || | || |  | ||||| ||||||||  | ||||||||||| || 
Sbjct  10526  CTGAAGAAGCAGACCCTTCTT-ACATAAAGCATCTGGAGGTACTCCAGCCTGAGGAGCAC  10584

Query  4469   AGAGCTGATTTTGGCGACTGAGC-ATTCCTCGCGGT-A-A--TTGA-C-GTGTAAGGA-T  4520
              |||||||| ||  || ||| | |  ||| | || || | |  || | | | |||| ||  
Sbjct  10585  AGAGCTGAATTCAGCAACT-AACTGTTCTTGGCTGTCAGAGCTT-AGCAG-GTAACGACA  10641

Query  4521   GGCACCTGGAGAAAAATGAGTTTGCGAAGATTCTTCATCT-CCTTCAGGTAAC-AATGAA  4578
              | || | |||||  || |||||||||||||||| ||||||  | |||||||||  || ||
Sbjct  10642  GCCATC-GGAGATGAA-GAGTTTGCGAAGATTCCTCATCTGGC-TCAGGTAACGGAT-AA  10697

Query  4579   GCT-TTCTTATCAGATGTGGCCAGGACACATAGCAAATTTCCAGCTCCTGAATACTATTC  4637
               || | | ||||| |   |||||| |||  |  |||||||||| | | || |||||  ||
Sbjct  10698  ACTCTAC-TATCATACACGGCCAGCACATGTTCCAAATTTCCAACACTTGGATACT-GTC  10755

Query  4638   -AGGTGGATTATTTTCAATGAT-CTTCTGAGATATT-CAATCG-ACGTTAG-ATAATTCA  4692
                |||  | | ||| |||| ||  |||||| || ||  ||| |  | || | ||||||||
Sbjct  10756  TGGGTATACTGTTTCCAAT-ATGTTTCTGAAAT-TTAGAAT-GCTCATT-GAATAATTCA  10811

Query  4693   CCAACTTACTACAGCACAGGTGTACTAAACCTCTCCTTTGGTAAACCCA-CCGGAAGAGG  4751
              ||| |||| ||||||||||||||||| ||||||| || || |  ||||| || | ||| |
Sbjct  10812  CCACCTTAGTACAGCACAGGTGTACTGAACCTCTTCTGTGCTGGACCCACCCAG-AGAAG  10870

Query  4752   TATCTCAG-GCATTCATCC-TGGGGTATTTCCTTGAGGCAGATGTCTATGAACACCTTCA  4809
               | |||||  | ||||||| | |  | ||||||||||||| |  || |||||||||||||
Sbjct  10871  AAGCTCAGATC-TTCATCCAT-GAATTTTTCCTTGAGGCAAACATCCATGAACACCTTCA  10928

Query  4810   AGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGTCTGCCTCTTACTCATGGCCT  4869
              ||||||| | ||||||  ||||||||||||||||  ||||||||||||||||||||||||
Sbjct  10929  AGGGCTGCTTCTCTCCTGTCCTTGGACAGTCCTCCACTGTCTGCCTCTTACTCATGGCCT  10988

Query  4870   CTGGGGAGGAGGACAGGGCCCTGGATTCAGACCATATGGCCCAGAAATTCTCATCAACAT  4929
              |||||||| ||||||||| ||||| | |||||||||||| ||| ||||||||||||||||
Sbjct  10989  CTGGGGAGCAGGACAGGGGCCTGGCTCCAGACCATATGGTCCAAAAATTCTCATCAACAT  11048

Query  4930   CCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAA-AGTAAGGCAGAGGCTCA  4988
              ||||||| ||||||||||||||||||| ||||||||| |||| | || || | | |||||
Sbjct  11049  CCCGCAATTCCAGCACTTGAAGTTTCCGCCTCCTGTGAGTAACA-TAGGGGAAAAGCTCA  11107

Query  4989   GAACTTTGA-A-GGACAAATCCCTGACCTTTGCTTTCATTCT-CATCCAATAAAT-CAGC  5044
              |||| | || | ||||  | |||||||||  ||||||| ||  |||| ||  | | ||||
Sbjct  11108  GAACGTAGACAAGGACCCACCCCTGACCTGGGCTTTCACTCCACATC-AAGGACTTCAGC  11166

Query  5045   TGCTCCTGTCCTC-GCTGCTCCCTGTTCTCTCTGAGTTTTCTTGGTCCCTTTTCTCTTTC  5103
              ||||  | ||||| || || ||||   || ||||  | ||||   ||||||| | | || 
Sbjct  11167  TGCTTTTTTCCTCAGC-GC-CCCTC--CT-TCTGTCTCTTCTCCATCCCTTTCCCCCTTG  11221

Query  5104   AATTCTGACTGGTCCCCACTTCTATT-CCATTTACCTTCCACTGGGAATAGGCAAGTTTC  5162
               |||||| ||||| |||||||||| | || |||||||||||||||||  ||||| ||| |
Sbjct  11222  GATTCTGCCTGGTACCCACTTCTAGTGCC-TTTACCTTCCACTGGGAGCAGGCAGGTTCC  11280

Query  5163   TGTTCCCACAGTGGACCCTATATTGTGGGCAGTTCTTTCCCTGAGGATCTGGGCAATGGC  5222
              |||| || ||||||||||| ||| ||| ||||| ||||||| ||||| ||||||||| ||
Sbjct  11281  TGTTTCCTCAGTGGACCCTGTATGGTGAGCAGTCCTTTCCCAGAGGAGCTGGGCAATAGC  11340

Query  5223   CAAGG-CATGCCTGAGCTT-CGTCACCAGCACCACCAGAAGACACTGGGCCATCCTTGGG  5280
              ||||  | | ||  ||||| | ||||  |||||| |||||| | |||||||| ||  |||
Sbjct  11341  CAAGAACGTTCCC-AGCTTTC-TCACTGGCACCATCAGAAGCCCCTGGGCCACCCC-GGG  11397

Query  5281   ATACTTCTTTGCCTGACCCTGCTGTTCTT-TCCCTGGACACCTGAGCCCCATCTACCAGC  5339
               | |   |||| ||||||| |||||| |  |||||||||||||| ||||  ||  ||| |
Sbjct  11398  TTCCCAATTTGTCTGACCCAGCTGTT-TAGTCCCTGGACACCTGGGCCC--TCC-CCA-C  11452

Query  5340   CTTCCTGGGTCACCTCACCTGGGGCGATCCTTCTGTGTAAGCAG-CATGTGAAGCCCTTC  5398
              ||    ||||||||||||||||||||| |||| || | |||||| ||  | || ||| ||
Sbjct  11453  CT----GGGTCACCTCACCTGGGGCGAACCTTTTGGGCAAGCAGGCAA-TCAATCCCATC  11507

Query  5399   CAGC-A-ATGCTTTTAAGGTCTCCAGATGAAGCGTCTTCATCAGCGATCCCAGAGGGAGG  5456
              || | | ||  | | ||| ||||||||| | ||||||||||||| || ||||||||||||
Sbjct  11508  CA-CTACATAATGT-AAGATCTCCAGATCAGGCGTCTTCATCAGGGACCCCAGAGGGAGG  11565

Query  5457   C-GGGTGAAGGGCCAGGCCTGCACCATCAC-TGTCAGAGTCTGGAAGTGTCTCCT-GCTG  5513
              | ||| |||||||||||||||||||||||| | |||||  || | || |||| || | ||
Sbjct  11566  CAGGG-GAAGGGCCAGGCCTGCACCATCACCT-TCAGAACCTCGCAGCGTCTGCTAG-TG  11622

Query  5514   AAGGCCTCCAGGAAGAGTGGGAGGTAGAGCTCCCTGGGCAGCTCCTCCAGGGCAGAGATG  5573
              |||||||||| ||| |||||| || ||||||||||||||||||| |||| |   ||||||
Sbjct  11623  AAGGCCTCCACGAACAGTGGGGGGAAGAGCTCCCTGGGCAGCTCATCCAAGATGGAGATG  11682

Query  5574   GCCAAGGGCTTGTCTCTCAGCAGACTCTGCCCCGCCAGCTCCAGGAGTCTGGGTGGGGCC  5633
              ||||||| || ||| | |||||| |||||||| |||||||||||||||||| ||||||||
Sbjct  11683  GCCAAGGCCTGGTCCCCCAGCAGGCTCTGCCCTGCCAGCTCCAGGAGTCTGCGTGGGGCC  11742

Query  5634   TGGATGCTCATCCTGATGAATCTGTAAGGAAAAACTCTAGAAGACAAATCCAGAGAAAAG  5693
              || | ||||||||| || |||||| ||| |||| |   | ||      ||||||||||||
Sbjct  11743  TGTAGGCTCATCCTCATAAATCTGCAAG-AAAA-C---A-AA------TCCAGAGAAAAG  11790

Query  5694   GCATCACTT-TCAGGCCAAACACAATCAC-CTC--ATCTTCTCCTAAGGCCAGTAG-CAT  5748
               ||  |||| ||||||||  | |  |||| | |  | ||||||||  |||||  || || 
Sbjct  11791  ACAA-ACTTATCAGGCCAGTC-CTCTCACACCCTGA-CTTCTCCTG-GGCCAAAAGTCAC  11846

Query  5749   TGCTCTGGTAGAGGTAGAAAAATTACC-AC-TTTACCCCAATTCCACTCTGCACTTGGTG  5806
              | |||||| ||| || |||| | | || |  ||||||||||||| |||||||| |   ||
Sbjct  11847  TACTCTGGCAGATGT-GAAAGAGT-CCTAAGTTTACCCCAATTCGACTCTGCAATAATTG  11904

Query  5807   GCCACA-A-ATCTATATTTCTGCTTCTGCTGGTACCAGGAAGAATGTCTTCCAAACA-CC  5863
              |||||| | | | ||| ||||||  || ||||||||| ||||| ||||| || |||  ||
Sbjct  11905  GCCACACAGA-C-ATAGTTCTGCC-CTTCTGGTACCAAGAAGAGTGTCT-CCTAACCTCC  11960

Query  5864   AAGGAGGGAGGGGTCAAAGAG-AC-CACTGGC-CCATTAATTTTCATCCATGGCTCCACT  5920
              |||||   | ||| |||| |  || | ||  | |||| |||||||||  || ||||||| 
Sbjct  11961  AAGGA---ACGGG-CAAA-ATCACTC-CTA-CTCCATGAATTTTCATTAATTGCTCCACC  12013

Query  5921   GAA-TCCCAGTACCACTGGAAAGTGTCACTGAGGATCCTGAAAGC-CAAGCTCTACCTCT  5978
               || ||  | || | |||| |||||| ||  || ||| | ||||| || ||||  | | |
Sbjct  12014  CAACTCT-ATTAGCTCTGGGAAGTGTTACCAAGAATCTTCAAAGCTCA-GCTC--CTTTT  12069

Query  5979   TTGAGGAAAATTTTCTTGTCA  5999
              ||||| |||| | |||| |||
Sbjct  12070  TTGAGAAAAAATGTCTTCTCA  12090


 Features flanking this part of subject sequence:
   2102 bp at 5' side: PRAME family member 8
   31332 bp at 3' side: PRAME family member 9

 Score =  937 bits (507),  Expect = 0.0
 Identities = 760/877 (86%), Gaps = 38/877 (4%)
 Strand=Plus/Plus

Query  9132   ggaaggaaagaaaaagaaagaaag-aagaaagaaagagaaagaaagaaagaaagaaagaa  9190
              |||||| ||| ||| ||||||||| ||||||| || ||||||||||||||||||||||||
Sbjct  71892  GGAAGG-AAGGAAATGAAAGAAAGAAAGAAAGGAA-AGAAAGAAAGAAAGAAAGAAAGAA  71949

Query  9191   agaaagaaagaaagaaagaaagaaagaaagaaaaagagcgagccttcttgtctttaagag  9250
              ||||||||||||||||||||||| ||| ||| |||   | ||||||| ||||||||||| 
Sbjct  71950  AGAAAGAAAGAAAGAAAGAAAGAGAGAGAGAGAAA-CTC-AGCCTTCCTGTCTTTAAGAA  72007

Query  9251   cagcgcatatataCT-GTTATATTGGGTGCACACCTAAAATACATTTCCCCCACAAAACC  9309
                | ||| | || || ||| ||||| ||||| |  || ||||||||||||| ||||||||
Sbjct  72008  TGGTGCACACAT-CTGGTTGTATTGTGTGCAAATGTACAATACATTTCCCCAACAAAACC  72066

Query  9310   TGGAAGCTCTATTTCATGTTGAAATATCTGCTAAGTTCACGGATGGCTCCCATCCTAAG-  9368
              |||||||||||||||||||| ||| |||||||||||||| ||||||||||||||||||| 
Sbjct  72067  TGGAAGCTCTATTTCATGTTAAAAGATCTGCTAAGTTCAGGGATGGCTCCCATCCTAAGC  72126

Query  9369   AGGGATCACACAGTGATTCTTCCGATGTTTTAGGGCACAAAGTAGCAAGAACCTCCCCTG  9428
              ||| |||||||||| ||||||| | | ||||||||||||||||||||||||| ||||| |
Sbjct  72127  AGG-ATCACACAGTCATTCTTCTGCTATTTTAGGGCACAAAGTAGCAAGAACGTCCCCCG  72185

Query  9429   CCTCCAGAAAGTCCTCCAGGCCTTTCTCTCCCATTCTATATGAAAACCAAACAGCTCTGA  9488
              |||||||||||||||||||||||||||||||||||| |||||||| ||||||||| | ||
Sbjct  72186  CCTCCAGAAAGTCCTCCAGGCCTTTCTCTCCCATTCCATATGAAACCCAAACAGCCCGGA  72245

Query  9489   GATGCCACTGGCCTCCAAAACTGGAGTACTTTGAAGGGTGTTCTCTATCTTGAAATGTTT  9548
              |||||||||||| |||||||||| ||||||||||||| ||||||| ||| || ||| |||
Sbjct  72246  GATGCCACTGGCTTCCAAAACTGAAGTACTTTGAAGGATGTTCTCCATCATGGAATATTT  72305

Query  9549   CTGTAAATGTTCTTTCTCCACATTTCTGACCTCACTGTCAATGCCCTGCTATGTGTGCAA  9608
              ||||||||||||||||||||| |||||||||||||| |||||||||||||||||||||||
Sbjct  72306  CTGTAAATGTTCTTTCTCCACGTTTCTGACCTCACTATCAATGCCCTGCTATGTGTGCAA  72365

Query  9609   TTGAGTTAAACTGAAATGTGTTCAGTGGGGCTTCTACTTTGCCTGCCCTCACTTTGTGAG  9668
              | |||||||||||||| ||| |||||| |||||||||||  |||||||||||||||||||
Sbjct  72366  TCGAGTTAAACTGAAACGTGCTCAGTGCGGCTTCTACTTCACCTGCCCTCACTTTGTGAG  72425

Query  9669   CCTGAGGCTGAGGTTGAGCTCAGCACCAAGGGTGATCGTGAGTGTCTCTGGTGACTGAGC  9728
              ||||||||||||| ||||||||||||||| ||||||| |||||||||||| ||| |||||
Sbjct  72426  CCTGAGGCTGAGGGTGAGCTCAGCACCAAAGGTGATCCTGAGTGTCTCTGTTGATTGAGC  72485

Query  9729   ATCCACGAGGCACAGCAGGGGCTGGTATCATTCATCCAAGATCTCAGCTCTCCCTCAC-A  9787
              || ||| ||||||||||||| |||||| |||||||||||||||||||||||||||||| |
Sbjct  72486  ATGCACAAGGCACAGCAGGGACTGGTACCATTCATCCAAGATCTCAGCTCTCCCTCACGA  72545

Query  9788   --AAT--AA----T----CTAAAG-C---ATGTT----G-G-TGACCCTGAGATTTGGCT  9825
                |||  ||    |    ||| |  |   || ||    | | ||||||||||| ||||||
Sbjct  72546  GGAATCTAAGGCATGTTGCTATATTCCTCATTTTTAAAGTGGTGACCCTGAGACTTGGCT  72605

Query  9826   AGCAAGAGGAATCTGCCCATGTTCAGACAACAAATGATTGG-CAGACCCCTCAGGTGAG-  9883
              ||  ||||||| |||||| ||||||| || |||||||| || |||||||||| |||||| 
Sbjct  72606  AGGGAGAGGAACCTGCCCGTGTTCAGGCAGCAAATGAT-GGACAGACCCCTCTGGTGAGG  72664

Query  9884   AGGCTCAGAGGATCCCCTAAGCAGTTCAACAACCTAAATGTTGGAAAA-AACTGGCTGAC  9942
              || |||||||||||||||||| ||||||| |  |||||||||| |||| |||||  ||||
Sbjct  72665  AG-CTCAGAGGATCCCCTAAGGAGTTCAATAGTCTAAATGTTG-AAAAGAACTGTTTGAC  72722

Query  9943   AGACTTTCCATTCTTTCCCAATTCAGAAGGTCCAGCA  9979
              ||||||||| ||| | |||||||||||||||||||||
Sbjct  72723  AGACTTTCCCTTCCTGCCCAATTCAGAAGGTCCAGCA  72759


 Features flanking this part of subject sequence:
   32186 bp at 5' side: PRAME family member 8
   1318 bp at 3' side: PRAME family member 9

 Score =  931 bits (504),  Expect = 0.0
 Identities = 730/833 (87%), Gaps = 39/833 (4%)
 Strand=Plus/Plus

Query  27064   catgcatctgtattcccagctatttggtttgctgacatgggagaatcacttgagcccaga  27123
               |||||||||||| |||||||||||||| | ||||   |||||||||||||||||| ||||
Sbjct  101976  CATGCATCTGTAGTCCCAGCTATTTGGGTGGCTGGTGTGGGAGAATCACTTGAGCACAGA  102035

Query  27124   agattgaggctgcagtgagccatgctcacaccactgctgtactccagcctgggcaacaga  27183
               |||||||||||||||||||||||||||| ||||||||||||||||||||||||||| |||
Sbjct  102036  AGATTGAGGCTGCAGTGAGCCATGCTCATACCACTGCTGTACTCCAGCCTGGGCAAAAGA  102095

Query  27184   gtaagaccctgctaaaaacaaaaacgaaaacaaacaaacaaaaaacCTTAACCAAAGAGA  27243
               |  |||| || ||     |||||||   || |||| || ||  ||  | ||  |||| | 
Sbjct  102096  G--AGACACT-CT--GTCCAAAAAC---AA-AAAC-AA-AATCAA--TCAA--AAAG-G-  102138

Query  27244   ATCTTTGACCTTAATTTTAAACCAATCACATCCTCACTGTAATTCTTCCTCCCGAATGGA  27303
               |||||||||| |||||||||||||||||||   || |      |||||| ||| ||||||
Sbjct  102139  ATCTTTGACCGTAATTTTAAACCAATCACA---TC-C------TCTTCCACCCAAATGGA  102188

Query  27304   GACATgggtgt-gagggtgcatgcctgtaatcccagctacatggaaggctgaagcatgag  27362
               ||||||| ||| | ||||||||||||||| |||||||||  |||||||||||||||||||
Sbjct  102189  GACATGGCTGTGGGGGGTGCATGCCTGTAGTCCCAGCTATGTGGAAGGCTGAAGCATGAG  102248

Query  27363   aattgcttgaatctcagaggcggaagttacagtgagctgagatggagccgctgcactcca  27422
               ||||||||||||||  ||||| || || |||||||||  |||||| ||| ||||| ||||
Sbjct  102249  AATTGCTTGAATCTTGGAGGCCGAGGTAACAGTGAGCCAAGATGGTGCCACTGCATTCCA  102308

Query  27423   gcctgggcgacaaagtgagactcagcttcacc-ca-caccaaaaaaaaTTAGATTATACC  27480
               || |||||||| | |||||||||||| || || || ||||||||||||||  | |||   
Sbjct  102309  GCTTGGGCGACGATGTGAGACTCAGC-TC-CCTCAGCACCAAAAAAAATT--A-TAT--G  102361

Query  27481   ACCCAGGTGATCACT-GGATACATGAAGATTTCTATTGTGTGTTATTGGGGACTGTCAAC  27539
               ||||||||||||| | || |||||||||||||||||||||| || || |||||||||| |
Sbjct  102362  ACCCAGGTGATCA-TGGGTTACATGAAGATTTCTATTGTGTTTTCTTAGGGACTGTCATC  102420

Query  27540   TCCGTCTTTGAAAACTGTTTTAACTCTGAAATATTTTGATAAATTTGATGTGGCCAAGGA  27599
               || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  102421  TCTGTCTTTGAAAACTGTTTTAACTCTGAAATATTTTGATAAATTTGATGTGGCCAAGGA  102480

Query  27600   TCCCTCAACAAAGATACTTTCAAGTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGATTC  27659
               ||||||||||| |||| |||||||||||||||||||||||||||||||||||||||||||
Sbjct  102481  TCCCTCAACAAGGATAATTTCAAGTTTTCTTTCTTTCTGTCTAATATCAGGAAGAGATTC  102540

Query  27660   AACACTTCCCTATCTCACACTCAGGACTATGAAGGACACATATTAGTAAACCTCCATGTT  27719
               ||| ||||||| |||||||||||||||| ||||||||||||||||||||| |||||||||
Sbjct  102541  AACCCTTCCCTGTCTCACACTCAGGACTTTGAAGGACACATATTAGTAAAACTCCATGTT  102600

Query  27720   TGTGGAGGGAATCAGTGAATGAGTCCTGGACTTTCACCCTATCCCTAAATCTTTCACTTT  27779
               |||| ||||||||||||||||||||||||||||||||||||||||||||||||||| |||
Sbjct  102601  TGTGAAGGGAATCAGTGAATGAGTCCTGGACTTTCACCCTATCCCTAAATCTTTCATTTT  102660

Query  27780   CATGGATGAATATCTAATTCAATCAGTTAATCTGGAAGAAAGCCAAAAATCCAATCAGGA  27839
                |||||| |||||||||||| |||||||| |||  |||||||||||||||||||| ||||
Sbjct  102661  GATGGATTAATATCTAATTCGATCAGTTATTCTTTAAGAAAGCCAAAAATCCAATAAGGA  102720

Query  27840   TTAACTGGGTAGAGTTTAAGAAGTCGAATCAAATGTAGTtctctctctctctc  27892
               |||||||||||||| |||||||||| | |||||||||| ||||||| ||||||
Sbjct  102721  TTAACTGGGTAGAGATTAAGAAGTCTAGTCAAATGTAGCTCTCTCTGTCTCTC  102773


 Features in this part of subject sequence:
   PRAME family member 18

 Score =  905 bits (490),  Expect = 0.0
 Identities = 1410/1832 (76%), Gaps = 151/1832 (8%)
 Strand=Plus/Plus

Query  4147    TACATGATGTCCCTCTC--TAGCCTCTA-CCCTAGGTGACCCCTCTGCCTTTATTGAAGT  4203
               |||| ||||||||||||  |||| ||||  || |||| | ||||||||| ||| || || 
Sbjct  156127  TACACGATGTCCCTCTCTGTAGCGTCTATGCC-AGGTCATCCCTCTGCCCTTACTGGAGC  156185

Query  4204    GATCCTGTGATAGCCACTCCAGGACATGGAGCACTGAACGGGACAATGTGTTGACATTCT  4263
               |||||||||||| ||||| ||||| || ||||||  ||| ||||||     || ||||||
Sbjct  156186  GATCCTGTGATACCCACTTCAGGATATAGAGCACCAAACAGGACAA-----TG-CATTCT  156239

Query  4264    GGTGTCCCCTGCACTGTGCCGTCGCCACTGGCTGGCACACAGTACACGTCT-TCTAGTGT  4322
                || |||||| | ||| | | || ||| |||||||||||||||| | | ||  |||||||
Sbjct  156240  AGTATCCCCTTCCCTG-GACATCTCCAGTGGCTGGCACACAGTAGATG-CTGACTAGTGT  156297

Query  4323    TTACTGTAACaaaaaaaaaGGCTGCGCTGTGGT-CTGCAGAGAAAGGGCACGATCCTTT-  4380
               ||||||||||  |||||||||||| ||||| || |  |||||||||  ||| || |||| 
Sbjct  156298  TTACTGTAAC--AAAAAAAGGCTGTGCTGT-GTCCCCCAGAGAAAGCTCACCAT-CTTTC  156353

Query  4381    CTCACCTGATCAGCT-GTCCCAGGT-GCCCTCTGTGGAAG-GTGA-CCATAT-TCATTTT  4435
               ||||||||||||||| || |||||| ||| || |  |||| | || || | | |||| | 
Sbjct  156354  CTCACCTGATCAGCTGGT-CCAGGTAGCCTTC-GAAGAAGCG-GATCC-T-TCTCATATA  156408

Query  4436    AAGCAGCTGGAGGTGTTTCAGCCTGAGGAACATAGAGCTGATTTTGGCGACTGAGCAT-T  4494
               ||||| ||||||||  | |||||||||||||| |||||||| ||  || ||| | | | |
Sbjct  156409  AAGCATCTGGAGGTACTCCAGCCTGAGGAACACAGAGCTGAATTCAGCAACT-AAC-TGT  156466

Query  4495    CC-TCGCGGT--AA--TTGAC-GTGTAAGGA-TGGCACCTGGAGAAAAATGAGTTTGCGA  4547
               || | ||  |  ||  ||| | | ||||  |  | || | |||||  || |||||| |||
Sbjct  156467  CCTTGGCTCTCAAAGCTTGGCAG-GTAACCACAGCCATC-GGAGATGAA-GAGTTTTCGA  156523

Query  4548    AGATTCTTCATCT-CCTTCAGGTAAC-AATGAAGCT-TTCTTATCAGATGTGGCCAGGAC  4604
               |||||||||||||  | |||||||||   | || || | | || || |   |||||| ||
Sbjct  156524  AGATTCTTCATCTGGC-TCAGGTAACGGCT-AACCTCTGC-TACCATACACGGCCAGCAC  156580

Query  4605    ACATAGCAAATTTCCAGCT-CCTGAATACTATTCAGGTGGATTA-T-TTTC-AATGAT-C  4659
               |  |  ||||||||||  | | || |||||  || || | | || | |||| ||| ||  
Sbjct  156581  ATGTTCCAAATTTCCA-ATACTTGGATACT-GTCTGG-GTA-TACTGTTTCTAAT-ATGT  156635

Query  4660    TTCTGAGATATT-CAATCG-ACGTTAG-ATAATTCACCAACTTACTACAGCACAGGTGTA  4716
               |||||| || ||  ||| |  | || | |||||| |||| |||| |||||||||||||||
Sbjct  156636  TTCTGAAAT-TTAGAAT-GTTCATT-GAATAATTTACCACCTTAGTACAGCACAGGTGTA  156692

Query  4717    CTAAACCTCTCCTTTGGTAAACCCA-CCGGAAGAGGTATCTCAG-GCATTCATCCTGGGG  4774
               || ||| ||| || || |  ||||| || | ||| | | |||||  | |||||||  || 
Sbjct  156693  CTGAACGTCTTCTGTGCTGCACCCACCCAG-AGAAGAAGCTCAGATC-TTCATCCACGGA  156750

Query  4775    TATTTCCTTGAGGCAGATGTCTATGAACACCTTCAAGGGCTGGTGCTCTCCCATCCTTGG  4834
               | ||||||||||||| |  || |||||||||||||||||||| | ||||||  |||||||
Sbjct  156751  TTTTTCCTTGAGGCAAACATCCATGAACACCTTCAAGGGCTGCTTCTCTCCTGTCCTTGG  156810

Query  4835    ACAGTCCTCTGCTGTCTGCCTCTTACTCATGGCCTCTGGGGAGGAGGACAGGGCCCTGGA  4894
               |||||||||  ||||||| |||||||||||||||||||||||| ||||||||| ||||| 
Sbjct  156811  ACAGTCCTCCACTGTCTGTCTCTTACTCATGGCCTCTGGGGAGCAGGACAGGGGCCTGGC  156870

Query  4895    TTCAGACCATATGGCCCAGAAATTCTCATCAACATCCCGCAAATCCAGCACTTGAAGTTT  4954
               | |||||||||||| ||| ||||||||||||||||||||||  |||||||||||||||||
Sbjct  156871  TCCAGACCATATGGTCCAAAAATTCTCATCAACATCCCGCATTTCCAGCACTTGAAGTTT  156930

Query  4955    CCACCTCCTGTGGGTAA-AGTAAGGCAGAGGCTCAGAACTTTGA-A-GGACAAATCCCTG  5011
               |||||||||||| |||| | || || | | ||||||||| | || | ||||  | |||||
Sbjct  156931  CCACCTCCTGTGAGTAACA-TAGGGGAAAAGCTCAGAACGTAGACAAGGACCCACCCCTG  156989

Query  5012    ACCTTTGCTTTCATTCT-CATCCAATAAAT-CAGCTGCTCCTGTCCTC-GCTGCTCCCTG  5068
               ||||  ||||||| ||  |||| ||  | | ||||||||  | ||||| || || |||| 
Sbjct  156990  ACCTGGGCTTTCACTCCACATC-AAGGACTTCAGCTGCTTTTTTCCTCAGC-GC-CCCTC  157046

Query  5069    TTCTCTCTGAGTTTTCTTGGTCCCTTTTCTCTTTCAATTCTGACTGGTCCCCACTTCTAT  5128
                 || ||||  | ||||   ||||||| | | ||  |||||| ||||| |||||||||| 
Sbjct  157047  --CT-TCTGTCTCTTCTCCATCCCTTTCCCCCTTGGATTCTGCCTGGTACCCACTTCTAG  157103

Query  5129    T-CCATTTACCTTCCACTGGGAATAGGCAAGTTTCTGTTCCCACAGTGGACCCTATATTG  5187
               | || |||||||||||||||||  ||||| ||| ||||| || ||||||||||| ||| |
Sbjct  157104  TGCC-TTTACCTTCCACTGGGAGCAGGCAGGTTCCTGTTTCCTCAGTGGACCCTGTATGG  157162

Query  5188    TGGGCAGTTCTTTCCCTGAGGATCTGGGCAATGGCCAAGG-CATGCCTGAGCTT-CGTCA  5245
               || ||||| ||||||| ||||| ||||||||| ||||||  | | ||  ||||| | |||
Sbjct  157163  TGAGCAGTCCTTTCCCAGAGGAGCTGGGCAATAGCCAAGAACGTTCCC-AGCTTTC-TCA  157220

Query  5246    CCAGCACCACCAGAAGACACTGGGCCATCCTTGGGATACTTCTTTGCCTGACCCTGCTG-  5304
               |  |||||| |||||| | |||||||| ||  ||  | |   |||| ||||||| |||| 
Sbjct  157221  CTGGCACCATCAGAAGCCCCTGGGCCACCCCAGGT-TCCCAATTTGTCTGACCCAGCTGC  157279

Query  5305    TTCTTTCCCTGGACACCTGAGCCCCATCTACCAGCCTTCCTGGGTCACCTCACCTGGGGC  5364
               ||  | ||||||||||||| ||||  ||  ||| |||    |||||||||||||||||||
Sbjct  157280  TTAGT-CCCTGGACACCTGGGCCC--TCC-CCA-CCT----GGGTCACCTCACCTGGGGC  157330

Query  5365    GATCCTTCTGTGTAAGCAG-CATGTGAAGCCCTTCCAGC-A-ATGCTTTTAAGGTCTCCA  5421
               || |||| || | |||||| ||  | || ||| |||| | | ||  | | ||| ||||||
Sbjct  157331  GAACCTTTTGGGCAAGCAGGCAA-TCAATCCCATCCA-CTACATAATGT-AAGATCTCCA  157387

Query  5422    GATGAAGCGTCTTCATCAGCGATCCCAGAGGGAGGC-GGGTGAAGGGCCAGGCCTGCACC  5480
               ||| | ||||||||||||| || ||||||||||||| ||| |||||||||||||||||||
Sbjct  157388  GATCAGGCGTCTTCATCAGGGACCCCAGAGGGAGGCAGGG-GAAGGGCCAGGCCTGCACC  157446

Query  5481    ATCAC-TGTCAGAGTCTGGAAGTGTCTCCT-GCTGAAGGCCTCCAGGAAGAGT-GGGAGG  5537
               ||||| | |||||  || | || |||| || | |||||||||||| ||| ||| ||| ||
Sbjct  157447  ATCACCT-TCAGAACCTCGCAGCGTCTGCTAG-TGAAGGCCTCCACGAACAGTCGGG-GG  157503

Query  5538    TAGAGCTCCCTGGGCAGCTCCTCCAGGGCAGAGATGGCCAAGGGCTTGTCTCTCAGCAGA  5597
                ||||||||||||||||||| |||||| | ||||||||||||| || ||| |||||||| 
Sbjct  157504  AAGAGCTCCCTGGGCAGCTCATCCAGGACGGAGATGGCCAAGGCCTGGTCCCTCAGCAGG  157563

Query  5598    CTCTGCCCCGCCAGCTCCAGGAGTCTGGGTGGGGCCTGGATGCTCATCCTGATGAATCTG  5657
               |||||||| |||||||||||||||||| |||||||||||| |||||||||||| ||||||
Sbjct  157564  CTCTGCCCTGCCAGCTCCAGGAGTCTGCGTGGGGCCTGGAAGCTCATCCTGATAAATCTG  157623

Query  5658    TAAGGAAAAACTCTAGAAGACAAATCCAGAGAAAAGGCATCACTTTCAGGCCAAACACAA  5717
                ||| ||||| || ||| || |||    || |||    ||||    ||| ||   |||| 
Sbjct  157624  CAAG-AAAAA-TCCAGA-GA-AAA----GACAAACTT-ATCAGGC-CAGTCCTCTCACA-  157672

Query  5718    TCACCTCATCTTCTCCTAAGGCCAGTAG-CATTGCTCTGGT-AGAG-GTAGAAAAATTAC  5774
                | ||| | ||||||||  |||||  || || | ||||| | || | || |||| | | |
Sbjct  157673  -C-CCTGA-CTTCTCCTC-GGCCAAAAGTCACTACTCTG-TCAG-GTGT-GAAAGAGT-C  157724

Query  5775    C--ACTTTACCCCAATTCCACTCTGCACTTGGTGGCCACA-A-ATCTATATTTCTGCTTC  5830
               |  | ||||||||||||| |||||||| |   |||||||| | | | ||| ||||||  |
Sbjct  157725  CTTAGTTTACCCCAATTCGACTCTGCAATAATTGGCCACAGAGA-C-ATAGTTCTGCC-C  157781

Query  5831    TGCTGGTACCAGGAAGAATGTCTTCCAAACACCAAGGAGGGAGGGGTCAAAGAG-AC-CA  5888
               | ||||||||| ||||| ||||| |||| | |||||||| | ||   ||| ||  || | 
Sbjct  157782  TTCTGGTACCAAGAAGAGTGTCTCCCAACCTCCAAGGAGCG-GG---CAA-GATCACTC-  157835

Query  5889    CTGGC-CCATTAATTTTCATCCATGGCTCCAC  5919
               ||  | |||| ||||||||||||| |||||||
Sbjct  157836  CTA-CTCCATGAATTTTCATCCATTGCTCCAC  157866


 Features in this part of subject sequence:
   PRAME family member 8

 Score =  874 bits (473),  Expect = 0.0
 Identities = 1127/1430 (78%), Gaps = 95/1430 (6%)
 Strand=Plus/Plus

Query  4758   AGGCATTCATCCTGGGGT-AT-TTCCTTGAGGCAGATGTCTATGAACACCTTCAAGGGCT  4815
              |||||||||| || | ||  | || |||||| || | ||||||||||||| | || ||||
Sbjct  68924  AGGCATTCAT-CTAGTGTCCTGTT-CTTGAGACAAAGGTCTATGAACACCATGAATGGCT  68981

Query  4816   GGTGCTCT-CCCATCCTTGGACAGTCCTCTGCTGTCTGCCTCTTACTCATG-GCCTCTGG  4873
              | ||| || ||  ||| ||||||||  |||||||| ||| ||| ||||| | ||||| ||
Sbjct  68982  GCTGC-CTGCCTGTCCCTGGACAGTTATCTGCTGTTTGCTTCTGACTCA-GAGCCTCCGG  69039

Query  4874   GGAGGAGGACAGGGCCCTGGATTCAGACCATATGGCCCAGAAATTCTCATCAACATCCCG  4933
              | |||| | ||  |   | | | ||||  ||||| | ||||| |||||||| |||| || 
Sbjct  69040  GAAGGATG-CA--G---TAGCTCCAGAAAATATGTCGCAGAAGTTCTCATCCACATTCCT  69093

Query  4934   CAAATCCAGCACTTGAAGTTTCCACCT-CCTGTGGGTAAAGTA-AGGCAGAGGCT-CAGA  4990
              ||| |||||||||||||||||  | || ||||||||||||| | | | ||||||| || |
Sbjct  69094  CAAGTCCAGCACTTGAAGTTTTGA-CTGCCTGTGGGTAAAGGAGAAG-AGAGGCTCCA-A  69150

Query  4991   ACTTTGAAGGACAAATCCCTGACCTTTGCTTTCATTCT-CATCCAATAAATCAGCTGCTC  5049
              ||  | |||| | ||     |||||  ||||| ||| | ||||| | | |||||||| | 
Sbjct  69151  AC--T-AAGG-C-AA----GGACCTGAGCTTTTATT-TACATCCCAGACATCAGCTG-T-  69198

Query  5050   CTGTCCTCGCTGCTCCCTGTT--CTCTCTGAGTTTTCT-TGGTCCCTTTTCTCTTTC-AA  5105
               | ||||| |||| | || ||  |||||||| |||| |     |||||||| | | |  |
Sbjct  69199  -TCTCCTCTCTGC-CACTTTTCCCTCTCTGA-TTTTGTCCAACCCCTTTTC-CCTCCGGA  69254

Query  5106   TTCTGACTGGTCCCCACTT--CTATTCCATTTAC-CTTCCACTGGGAATAGGCAAGTTTC  5162
              || || ||  |||||| ||  || |  | ||| |    |||||  ||| | | |||||||
Sbjct  69255  TTTTGCCTCATCCCCA-TTGCCTGTAGC-TTT-CAGAGCCACT-AGAAGA-G-AAGTTTC  69308

Query  5163   TGTTCCCACAGTGGACCCTATATTGTGGGCAGTTCTTTCCCTGAGGATCTGGGCAATGGC  5222
              |||| || |||||||||||  || ||| ||||| ||||||| ||||  ||||||||||||
Sbjct  69309  TGTTTCCTCAGTGGACCCTGCATGGTGAGCAGTCCTTTCCCAGAGGGGCTGGGCAATGGC  69368

Query  5223   CAAGGCATGCCTGAGCTTCGTCACCAGCACCACCAGAAGA-CACTGGGCCATCCTTGG-G  5280
              |||||| | |||||||||| ||||  |||||| ||||| | | ||||||| ||| ||| |
Sbjct  69369  CAAGGCCTTCCTGAGCTTCCTCACTGGCACCATCAGAA-ACCTCTGGGCC-TCCATGGTG  69426

Query  5281   ATACTTCT-TTGCCTGACCCTGCTGTTCTTTCCCTGGACACCTGAGCCC-CATCTACC-A  5337
                 || ||  | |||||  | ||||| | | |||||||||   | |||| |  | |||  
Sbjct  69427  CCCCTCCTCCT-CCTGAAACAGCTGTCCCTACCCTGGACAAAAGGGCCCTC-CCCACCTG  69484

Query  5338   GCCTTCCTGGGTCACCTCACCTGGGGCGATCCTTC-TGTGT-AAGCAGCATGTGAAGCCC  5395
              | |  |||||||||||||||||||||||| || || || || || |||||  | || |||
Sbjct  69485  GAC-ACCTGGGTCACCTCACCTGGGGCGAACC-TCTTGGGTCAA-CAGCACATCAACCCC  69541

Query  5396   TTCCAGCA-ATGCTTTTAAGGTCTCCAGATGAAGCGTCTTCATCAGCGATCCC-AGAGGG  5453
              |||||||| | | |||||| | |||||||||| ||| ||||||||| || ||| ||||||
Sbjct  69542  TTCCAGCACA-GATTTTAATGACTCCAGATGAGGCGACTTCATCAGGGA-CCCTAGAGGG  69599

Query  5454   AGGCGGGTGAAGGGCCAGGCCTGCACCATCACTGTCAGAGTCTGGA-AGTGTCTCCTGCT  5512
              ||||||||||| |||||||||||||||||   | |||| || |  | || ||||||||||
Sbjct  69600  AGGCGGGTGAAAGGCCAGGCCTGCACCATTGTTTTCAGGGT-TTCACAGCGTCTCCTGCT  69658

Query  5513   GAAGGCCTCCAGGAAGAGTG-GGAGGTAGAGCTCCCTGGGCAGCTCCTCCAGGGCAGAGA  5571
              ||||||||||| ||| |||| || || |||||||||||||||||||||||| ||  ||||
Sbjct  69659  GAAGGCCTCCATGAACAGTGTGG-GGAAGAGCTCCCTGGGCAGCTCCTCCATGGTGGAGA  69717

Query  5572   TGGCCAAGGGCTTGTCTCTCAGCAGACTCTGCCCCGCCAGCTCCAGGAGTCTGGGTGGGG  5631
              ||||||||| || ||| |||||||| |||||||  |||||||||||||||||||||||||
Sbjct  69718  TGGCCAAGGCCTGGTCCCTCAGCAGCCTCTGCCTTGCCAGCTCCAGGAGTCTGGGTGGGG  69777

Query  5632   -CCTGGATGCTCATCCTGATGAATCTGTAAGGAAAAACTCTAGAAGACAAATCCAGAGAA  5690
               ||| |||||||||| ||||||||||| |||| ||||||||||| |||||||||||||||
Sbjct  69778  CCCT-GATGCTCATCTTGATGAATCTGCAAGGGAAAACTCTAGAGGACAAATCCAGAGAA  69836

Query  5691   AAGGCATCACTTTCAGGCCAAACACAATCACCTCATCTTCTCCTAAGGCCAGTAGCATTG  5750
              ||||||||||| |||||||||| |  |||||||||||||||||||  || | |  |||||
Sbjct  69837  AAGGCATCACTCTCAGGCCAAATATGATCACCTCATCTTCTCCTATTGCTAATCTCATTG  69896

Query  5751   CTCTGGTAGAGGTAGAAAAATTAC-CACTTTACCCCAATTCCACTCTGCACTTGGTGGCC  5809
              ||||||| ||||| | ||||   | || ||  ||||| ||||| ||||||||||||||||
Sbjct  69897  CTCTGGTGGAGGT-GGAAAAGCCCTCAATTCCCCCCAGTTCCATTCTGCACTTGGTGGCC  69955

Query  5810   ACAAATCTATATTTCTGCTTCTGCTG-GTACCAGGAAGAATGTCTTCCAAACACCAAGGA  5868
              |||||||| ||| | |||  ||| ||  |||||  |||||||||||||||||||||||||
Sbjct  69956  ACAAATCTGTATCTGTGCCCCTG-TGACTACCACAAAGAATGTCTTCCAAACACCAAGGA  70014

Query  5869   GGG-AGG-GGTCAAAGAGACCACTGGCCCATTAATTT-TCATCCATGGCTCCACTGAATC  5925
              ||| | | |||    | | ||| |||||||||||||| | || ||| ||||||||||| |
Sbjct  70015  GGGGACGAGGT----G-G-CCAGTGGCCCATTAATTTCT-ATACATTGCTCCACTGAAAC  70067

Query  5926   CCAGTACCACTGGAAAGTGTCACTGAGGATCCTGAAAGCCAAGCTCTACCTCTTTGAGGA  5985
               ||| |  ||||| |  ||||||| |||||||||||||| |||||| |||| ||||||| 
Sbjct  70068  TCAGGATTACTGGGATCTGTCACTCAGGATCCTGAAAGCTAAGCTCCACCTTTTTGAGGG  70127

Query  5986   AAATTTTCTTGTCACTTACCGCCCTAAAGCAATGAGAATGAGAGTGTCCTGTGGCCCCAG  6045
              ||||||| |||| ||||||| ||| ||| ||||||||||||   ||||||||||||||| 
Sbjct  70128  AAATTTTTTTGTTACTTACCACCCAAAAACAATGAGAATGAC--TGTCCTGTGGCCCCAC  70185

Query  6046   ACAGCCTCCATTCTCAGTTTTCACCATGAACATGCTGGGGGAACACTAAAGGGACTCCCT  6105
              ||||||| |||||||||||| ||| || | |||||| |||||| ||| ||| |||||| |
Sbjct  70186  ACAGCCTGCATTCTCAGTTTACACAATTAGCATGCTTGGGGAAGACTGAAGTGACTCCTT  70245

Query  6106   AAAGTCAATGCCA-TTATTTTTTATTTTGAAAAATT-TCAACcagaaact  6153
              ||| ||||||||| || ||||| ||||||||||||| | ||  |||||||
Sbjct  70246  AAAATCAATGCCACTTGTTTTT-ATTTTGAAAAATTAT-AAG-AGAAACT  70292


 Features flanking this part of subject sequence:
   12551 bp at 5' side: PRAME family member 8
   20934 bp at 3' side: PRAME family member 9

 Score =  854 bits (462),  Expect = 0.0
 Identities = 714/832 (85%), Gaps = 31/832 (3%)
 Strand=Plus/Plus

Query  21757  AAGtatatatgctatatactttccatatacttatattatata-AGGTCACATGCAAATTC  21815
              |||||||||| ||| |||||||| ||||||||||||| || | |||||||||||||||||
Sbjct  82341  AAGTATATATTCTAAATACTTTCTATATACTTATATTCTA-AGAGGTCACATGCAAATTC  82399

Query  21816  AAGGCTAGGTCAAAGAGTAGAGTGGCAATATATGGAAAGGTGAGTGGAAGTGAATAATGG  21875
              |||||||||||||||||||||||||| || |||||||||| |||||||||||||| ||||
Sbjct  82400  AAGGCTAGGTCAAAGAGTAGAGTGGCTATCTATGGAAAGGGGAGTGGAAGTGAATCATGG  82459

Query  21876  TAATAAAAGGAAACagatagatatagatatagatatgaataggtagacatacacatatat  21935
              ||||||||  |   | |  | |||||||||||||| |||||| |||||||||||| ||||
Sbjct  82460  TAATAAAA--ATT-A-A--G-TATAGATATAGATAGGAATAGATAGACATACACACATAT  82512

Query  21936  agCTGCAAGAAAGGGGGTTGTCATGGACCAATGATGACAGTGAGCCGTGTAAAAAGGCTA  21995
              ||||||||||||||||  |||||||||||||||||| ||||||||| |||||||||||||
Sbjct  82513  AGCTGCAAGAAAGGGGAATGTCATGGACCAATGATGTCAGTGAGCCATGTAAAAAGGCTA  82572

Query  21996  AAATTCttgtgattgtgtttccattttcaggatgagttgtagcttacctttttagaaagg  22055
               ||||||||||||||||| ||  ||||||||||| |||||||||||||||||||||||||
Sbjct  82573  CAATTCTTGTGATTGTGTGTCTGTTTTCAGGATGGGTTGTAGCTTACCTTTTTAGAAAGG  82632

Query  22056  cttatgatgcagtcatagcaaataagtgattataaaatgtgtttcctttctggg-caat-  22113
              || |||   ||| |||||  ||||| || ||||||||||||||||||||||||| || | 
Sbjct  82633  CTGATGCCACAGCCATAGTGAATAAATGGTTATAAAATGTGTTTCCTTTCTGGGGCA-TC  82691

Query  22114  tctggagaaatctctaatggtatgagaattcagtttactgggcaggttatcacacata-a  22172
              |||||||||||||| | ||||| ||||| || ||||||||||||||| |||||||| | |
Sbjct  82692  TCTGGAGAAATCTCCAGTGGTAGGAGAACTCCGTTTACTGGGCAGGTGATCACACAGATA  82751

Query  22173  a-attttacagacccaatgacactagCATTAACTTCATTATCCTTGGTATTCTATAAAGG  22231
              | ||||| |||| |||||| ||||| |||||||||||||||||||||||||||| |||||
Sbjct  82752  AGATTTTTCAGATCCAATGGCACTACCATTAACTTCATTATCCTTGGTATTCTACAAAGG  82811

Query  22232  TTGAGTGAACAAATGGTATATTTAAACTAAAATTAGCTAAACTGACAAAGAAAACTGGAt  22291
              | ||||||| ||||||||| || |||||||||||||||||||| |||||| | ||||| |
Sbjct  82812  TCGAGTGAAGAAATGGTATCTTGAAACTAAAATTAGCTAAACTAACAAAGGAGACTGGGT  82871

Query  22292  ta-ttattatttattttt------gagacagagtctctgttgcccaggctggagtacagt  22344
              || || || ||| |||||      ||||||||||||||||| ||||||||||||| ||||
Sbjct  82872  TAATTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTCTGTTACCCAGGCTGGAGTTCAGT  82931

Query  22345  ggtgctaccttggctcactgcaacctctgcctcccaggttcaag-gagttttcctgcctc  22403
              ||||||| ||  ||||||||||||||||||||||  |||||||| || || || ||||| 
Sbjct  82932  GGTGCTATCTCAGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGTGA-TTGTCATGCCTT  82990

Query  22404  agccacctaagtagctgggattacaggcacacacaaccacacccagctaatttttgtatt  22463
              |||| || ||||||||||||||||||||| || || ||||||||||||||||||||||||
Sbjct  82991  AGCCTCCCAAGTAGCTGGGATTACAGGCATAC-CA-CCACACCCAGCTAATTTTTGTATT  83048

Query  22464  tttggcaga-agcggggtttcaccattttggccaggttggtcttgaacccctgacatcg-  22521
              ||| | ||| | |||||||||||||| ||| |||| ||| ||   ||| |||| | ||  
Sbjct  83049  TTTAGTAGATAACGGGGTTTCACCATGTTGCCCAGATTGCTC---AACTCCTGGCCTCAA  83105

Query  22522  g-gatctgcctgcctcggtctcctaaagtgctgggattataggcgtcagcca  22572
              | ||||  || ||||||| |||| ||||||||| ||||| ||| || |||||
Sbjct  83106  GTGATCCACCAGCCTCGGCCTCCCAAAGTGCTGAGATTACAGGTGTGAGCCA  83157


 Features flanking this part of subject sequence:
   29779 bp at 5' side: PRAME family member 3
   2617 bp at 3' side: PRAME family member 5

 Score =  841 bits (455),  Expect = 0.0
 Identities = 715/840 (85%), Gaps = 19/840 (2%)
 Strand=Plus/Plus

Query  17057  cccagtcaggagggcaatggtgtaatcttggctcactgcaaactcagcctccagggttca  17116
              ||||| | ||||  || ||||||| | |  ||||||||||| ||| |||||| |||||||
Sbjct  41532  CCCAGGCTGGAGTTCAGTGGTGTATTGTCAGCTCACTGCAACCTCTGCCTCCTGGGTTCA  41591

Query  17117  agggattc-tcccacctcagcc-gcatgagtaac-tggactacaggcagc-caccatcgt  17172
              || || || |||   |||||||  | | |||| | ||||||| |||| ||  |||| || 
Sbjct  41592  AGCGA-TCTTCCTGTCTCAGCCTCCCT-AGTAGCTTGGACTATAGGC-GCAGACCACCGC  41648

Query  17173  gcctggctaacttttct-atttttgtagagacagggtttcaccatgtgggccaggctggt  17231
                |||||||| |||| | ||||| ||||||  ||||||| ||||||| ||||||||| ||
Sbjct  41649  AACTGGCTAATTTTTGTAATTTTAGTAGAGGTAGGGTTTTACCATGTTGGCCAGGCTTGT  41708

Query  17232  cttgaactcctgacctcaggtgatccacctacct-tggcctcccaaagtgctgggattac  17290
              ||  ||||||||||||||| | |||||||||||| | || ||||| ||||||||||||||
Sbjct  41709  CTCAAACTCCTGACCTCAGATAATCCACCTACCTCT-GCGTCCCAGAGTGCTGGGATTAC  41767

Query  17291  aagtgtgagccacctcacctggccTTGAGTGAATGAATTCTTGATTTCCAGTCTATCCCT  17350
              | ||||||||||| ||  |||||||||| |||||| |||||||| ||| |  ||||||||
Sbjct  41768  AGGTGTGAGCCACTTCGTCTGGCCTTGAATGAATGTATTCTTGACTTCTACCCTATCCCT  41827

Query  17351  AACTCTGTCAATTTCTTAATTCATGAAATGATTAT-GCATATGTGATATGAATGGATATC  17409
              ||| ||||| |||||||  |||||||| ||| ||| | |||||||||||||||||| |||
Sbjct  41828  AACACTGTCGATTTCTTGCTTCATGAAGTGAATATAG-ATATGTGATATGAATGGACATC  41886

Query  17410  TCG-TTCAATCCATTAGTCTTCGGACAGTCAAAAACCCAATCAGGATTAACTGAGTGGAG  17468
              | | ||||||||  || |||  ||| || |||||||||||||||||||||||| ||||||
Sbjct  41887  T-GATTCAATCCGGTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAG  41945

Query  17469  CTTCAGAAATGCAATCAGATATCGCTTTTTGATTGGAAGCTAGCAGCGGATACGTGGAGG  17528
              ||||| |||||||||||||||||  |||||||||||||| |||||||||||| ||| |||
Sbjct  41946  CTTCACAAATGCAATCAGATATCATTTTTTGATTGGAAGGTAGCAGCGGATATGTGCAGG  42005

Query  17529  GGCGTGGGTGGGAGTTGTGATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGACA  17588
              |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |
Sbjct  42006  GGCGTGGGTGGGAGTTGTGATTAGAAAGGTCAATAAAAGCTTCTAAAGACCCACAGGAGA  42065

Query  17589  AACTCAAAGTCTTCAAGCCTGGAGTTCCTGCTTGGCTCTTCCTGAGGTCTGAGCACCTTC  17648
               || |||||||||||||||| |||||||||||||| ||||||||||| ||||||||||||
Sbjct  42066  GACCCAAAGTCTTCAAGCCTAGAGTTCCTGCTTGGTTCTTCCTGAGGACTGAGCACCTTC  42125

Query  17649  TAAACTACAACCAGATCTGGTAAGTCACTAATTTCTGTAAGGACACTCCCATGTGACCTA  17708
              || |||||| |||||||||||||||||||||||||||||||||||||||||| |||||||
Sbjct  42126  TAGACTACATCCAGATCTGGTAAGTCACTAATTTCTGTAAGGACACTCCCATCTGACCTA  42185

Query  17709  CAGTCAGCCGGTCTAGAACGGTGACAGTGCAGCCTACGATGGCATAGAACTATATCATGT  17768
              ||||||| |||||| |   ||||||||| ||||||||||||||| ||| ||||||| |||
Sbjct  42186  CAGTCAGTCGGTCTGGGGTGGTGACAGTACAGCCTACGATGGCACAGAGCTATATCCTGT  42245

Query  17769  Ctttttttctttttttcatatgaacactttgaagctttgatttttttt-tCTAAATGCAA  17827
              | |||||| |||||  |||||||||| ||||||||||||| | ||||  |||||||||| 
Sbjct  42246  CCTTTTTT-TTTTT--CATATGAACAATTTGAAGCTTTGAATGTTTTCCTCTAAATGCAG  42302

Query  17828  TTTTGTCGTGATTTCAAAAATGTTG-TTGTGCTTTTCTTTACATCATTTCAGAATTCTTG  17886
              || |||| | |||||||||| |||| |||||||||  || |   ||||| | ||||||||
Sbjct  42303  TTCTGTCTTTATTTCAAAAAAGTTGATTGTGCTTTGGTTGATGCCATTTTAAAATTCTTG  42362


 Features flanking this part of subject sequence:
   12846 bp at 5' side: PRAME family member 16
   10240 bp at 3' side: PRAME family member 21

 Score =  837 bits (453),  Expect = 0.0
 Identities = 665/765 (86%), Gaps = 23/765 (3%)
 Strand=Plus/Plus

Query  21342   ggtggctcacacctgtaattccagcactttgggaagccaaggcaggtggaacgcctgaga  21401
               |||||||||  ||  |||| |||||||||||||| ||| |||  |||||| | |||||| 
Sbjct  191062  GGTGGCTCATGCCCATAATCCCAGCACTTTGGGAGGCCGAGGTGGGTGGATCACCTGAGG  191121

Query  21402   tcaggagtttgagaccagcatggccaacatggagaaactccatttctactaaaaatacaa  21461
               |||||||||  |||||||| |||||||||||| ||||| |||| ||||||||||||||||
Sbjct  191122  TCAGGAGTTCAAGACCAGCCTGGCCAACATGGCGAAACCCCATCTCTACTAAAAATACAA  191181

Query  21462   aaaatagccgggcgtggt-ggtaggcatctgtaatctcaggtacttgggaggctgaggca  21520
               ||| || || || || ||  | | ||| |||||||| ||||||||||||||||| || ||
Sbjct  191182  AAAGTAACCAGGTGT-GTCAGCAAGCACCTGTAATCCCAGGTACTTGGGAGGCTAAGACA  191240

Query  21521   ggagaaacagttgaacccgagaggtggaggttgcattgagccaagatagca--c-ctttg  21577
               |||||| || ||||||||| ||||||||||||||| ||||   |||| |||  | | |||
Sbjct  191241  GGAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGTGGAGATTGCATGCACATTG  191300

Query  21578   ca---caccagcctggccacagagcaagactccatctcca-a-a-a-a-aTACTACTAAT  21629
               ||   || ||||||||  ||||||| |||||||||||||| | | | | | |  | ||||
Sbjct  191301  CACTCCAGCAGCCTGGTGACAGAGCGAGACTCCATCTCCACACACACACA-AAAAATAAT  191359

Query  21630   AATTATAACAGCATGTCCATTCACTCTCCAAAGTGTCTGGGACTGGACAATTAATTGTGA  21689
               |||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Sbjct  191360  AATTATAACAGCATGTCCATTCACTCTCCAAAGTGTCTGGGACTGGACGATTAATTGTGA  191419

Query  21690   GGCCCTCTTCTCTAGCACCCTACGCTATAGCATATATGTGGATTAAAATAAATAC-ACAT  21748
               ||||||||||| ||||||| ||| |||||||||||| |||||||||||||||||| || |
Sbjct  191420  GGCCCTCTTCTGTAGCACCATACACTATAGCATATACGTGGATTAAAATAAATACAAC-T  191478

Query  21749   A-AAAATGCAAGtatatatgctatatactttccatatacttatattatataAGGTCACAT  21807
               | ||||||||||||||||| |||||||||||||||||||||||||| ||| |||||||||
Sbjct  191479  ACAAAATGCAAGTATATATTCTATATACTTTCCATATACTTATATTTTATGAGGTCACAT  191538

Query  21808   GCAAATTCAAGGCTAGGTCAAAGAGTAGAGTGGCAATATATGGAAAGGTGAGTGGAAGTG  21867
               |||||||||||| |||||||||||||||||||||  | |||||||||| |||||||||||
Sbjct  191539  GCAAATTCAAGGTTAGGTCAAAGAGTAGAGTGGCTGTCTATGGAAAGGGGAGTGGAAGTG  191598

Query  21868   AATAATGGTAATAAAAGGAAACagat--agatatagatatagatatgaataggtagacat  21925
               ||| ||||||||||||||||| ||||  ||||||| |||||||||||||||| |||||||
Sbjct  191599  AATCATGGTAATAAAAGGAAATAGATACAGATATAAATATAGATATGAATAGATAGACAT  191658

Query  21926   acacatatatagCTGCAAGAAAGGGGGTTGTCATGGACCAATGATGACAGTGAGCCGTGT  21985
               |||||||||||||||||| ||||||| ||||||||||||||||||||||||||||| || 
Sbjct  191659  ACACATATATAGCTGCAAAAAAGGGGATTGTCATGGACCAATGATGACAGTGAGCCATGA  191718

Query  21986   AAAAAGGCTAAAATTCttgtgattgtgtttccattttcaggatgagttgtagcttacctt  22045
               |||||||||| ||||||||||||||||| ||  ||| ||||||| ||| |||||| ||||
Sbjct  191719  AAAAAGGCTACAATTCTTGTGATTGTGTGTCTGTTTGCAGGATGGGTTATAGCTT-CCTT  191777

Query  22046   ttt-agaaaggcttatgatg-cagtcatagcaaataagtgattat  22088
               ||| ||||||||| || |   |||||||||||||||| |||||||
Sbjct  191778  TTTTAGAAAGGCTGAT-ACCACAGTCATAGCAAATAAATGATTAT  191821


 Features flanking this part of subject sequence:
   17501 bp at 5' side: PRAME family member 16
   5615 bp at 3' side: PRAME family member 21

 Score =  809 bits (438),  Expect = 0.0
 Identities = 653/752 (86%), Gaps = 33/752 (4%)
 Strand=Plus/Plus

Query  17150   ggactacaggcagcca-ccatcgtgcctgg-c-taacttttctatttttgtagagacagg  17206
               ||| ||||||| |  | ||| | ||||||| | ||| |||||||| ||||||||||||||
Sbjct  195717  GGATTACAGGC-GTGATCCACCATGCCTGGCCTTAATTTTTCTATATTTGTAGAGACAGG  195775

Query  17207   gtttcaccatgtgggccaggctggtcttgaactcctgacctcaggtgatccacctacctt  17266
               |||||||| ||| |||||||||||||||||||||||||||||| ||||||||||| ||||
Sbjct  195776  GTTTCACCCTGTCGGCCAGGCTGGTCTTGAACTCCTGACCTCAAGTGATCCACCTGCCTT  195835

Query  17267   ggcctcccaaagtgctgggattacaagtgtgagccacctcacctggccTTGAGTGAATGA  17326
               |||||||||||||||||| | |||| |  |||||||||  |    ||||||| |||||||
Sbjct  195836  GGCCTCCCAAAGTGCTGGTAATACAGGCATGAGCCACC-GA----GCCTTGAATGAATGA  195890

Query  17327   ATTCTTGATTTCCAGTCTATCCCTAACT-CTGTCAATTTCTTAATTCATGAAATGATTAT  17385
               |||||||| ||||| ||||||||||| | |||||| |||||| ||||||||||||| |||
Sbjct  195891  ATTCTTGACTTCCACTCTATCCCTAA-TACTGTCACTTTCTTGATTCATGAAATGAATAT  195949

Query  17386   GCATATGTGATATGAATGGATATCTCG-TTCAATCCATTAGTCTTCGGACAGTCAAAAAC  17444
               | |||| || ||||||||||||||| | |||||||||||| |||  ||| || |||||||
Sbjct  195950  GGATATCTGGTATGAATGGATATCT-GATTCAATCCATTAATCTGGGGAGAGCCAAAAAC  196008

Query  17445   CCAATCAGGATTAACTGAGTGGAGCTTCAGAAATGCAATCAGATATCGCTTTTTGATTGG  17504
               ||||||||||||||||| ||||||||||||||||||||||||||| | |||||||| |||
Sbjct  196009  CCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGCAATCAGATACCACTTTTTGACTGG  196068

Query  17505   AAGCTAGCAGCGGATACGTGGAGGGGCGTGGGTGGGAGTTGTGATTAGAAAGGTCAATAA  17564
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  196069  AAGCTAGCAGCGGATACGTGGAGGGGCGTGGGTGGGAGTTGTGATTAGAAAGGTCAATAA  196128

Query  17565   AAGCTTCTAAAGACCCACAGGACAAACTCAAAGTCTTCAAGCCTGGAGTTCCTGCTTGGC  17624
               |||||||||||||||||||||| | || |||||||||||||||||||||| |||||||| 
Sbjct  196129  AAGCTTCTAAAGACCCACAGGAGAGACCCAAAGTCTTCAAGCCTGGAGTTTCTGCTTGGT  196188

Query  17625   TCTTCCTGAGGTCTGAGCACCTT-CTAAACT-ACAACCAGATCTGGTAAGTCACTAATTT  17682
               | ||||||||||||||||||| | | ||||| |   |||||||||||||||| ||||| |
Sbjct  196189  TTTTCCTGAGGTCTGAGCACCCTGC-AAACTGAGT-CCAGATCTGGTAAGTCCCTAATCT  196246

Query  17683   CTGTAAGGACACTCCCATGTGACCTACAGTCAGCCGGTCTAGAACGGTGACAGTGCAGCC  17742
               |||||||||||||||||| ||||||||||||||||||||| | | ||||||||||||| |
Sbjct  196247  CTGTAAGGACACTCCCATCTGACCTACAGTCAGCCGGTCTGGGATGGTGACAGTGCAGGC  196306

Query  17743   TACGATGGCATAGAACTATATCATGTCtttttttctttttttcatatgaacactttgaag  17802
                || | |  |  |   |||||| ||||||||||| |||||||  |||||||| |||||||
Sbjct  196307  -AC-A-G--A--GT--TATATCCTGTCTTTTTTTTTTTTTTTG-TATGAACAATTTGAAG  196356

Query  17803   ctttgattttttt-ttCTAAATGCAATTTTGTCGTGATTTCAAAAA-TGTTG-TT-GTGC  17858
               |||||| |||||  || |||||||| ||||||| | |||||||||| | ||| || ||||
Sbjct  196357  CTTTGACTTTTTCCTT-TAAATGCAGTTTTGTCTTCATTTCAAAAAAT-TTGATTTGTGC  196414

Query  17859   TTTTCTTTACATCATTTCAGAATTCTTGTTGG  17890
               |||  |||| ||| |||||||||||||| |||
Sbjct  196415  TTTGGTTTATATCCTTTCAGAATTCTTGGTGG  196446


 Features flanking this part of subject sequence:
   15540 bp at 5' side: PRAME family member 8
   17958 bp at 3' side: PRAME family member 9

 Score =  754 bits (408),  Expect = 0.0
 Identities = 702/838 (83%), Gaps = 43/838 (5%)
 Strand=Plus/Plus

Query  13645  cccaagcgggagtacagtggtgctatgtcatctcactgcaacatctgcctcccgggttca  13704
              |||| || ||||| ||| ||||| || ||  ||||||||||| |||||||| | || |||
Sbjct  85330  CCCAGGCTGGAGTGCAGAGGTGCAATCTCGGCTCACTGCAACCTCTGCCTCACAGGATCA  85389

Query  13705  agagattctcctgcctcagactcctgagtagccgggattacaggcacacaccaccacacc  13764
              || |||||| ||||||||| ||||| |||||| |||||||||| ||     || ||||||
Sbjct  85390  AGTGATTCTTCTGCCTCAGCCTCCTAAGTAGCTGGGATTACAGACATGGGTCATCACACC  85449

Query  13765  cagctgatttttgtattttt-agcagaaacggggtttcaccatgttgaccaggttggtct  13823
              ||||| |||| ||||||||| |  ||| || |||||||||||| ||| ||||| |||  |
Sbjct  85450  CAGCTAATTTGTGTATTTTTCA-TAGAGACAGGGTTTCACCATATTGGCCAGGCTGG-AT  85507

Query  13824  t-gaacccctgaccttgtgatctc-cctgcctcagcctcctgaagtgctggaattatagg  13881
              | |||||||||||||||||||| | ||| |||  ||||||| |||||||| || ||||||
Sbjct  85508  TCGAACCCCTGACCTTGTGATC-CGCCTACCTTGGCCTCCTAAAGTGCTGCAAATATAGG  85566

Query  13882  ct-tgagccaccttgcccagcctaatctttttttcttttCTCAAAGGACTTCTATGCACT  13940
               | | ||||||| ||||||| |    ||||||| |   | |        |||||||||||
Sbjct  85567  -TGTCAGCCACCATGCCCAG-C----CTTTTTTGC---T-T--------TTCTATGCACT  85608

Query  13941  TAGGAGAGTGAGCCCATCGTTCAGTAACAACATGATTCAATACTGCAAGACCTTGATGCA  14000
              |||||||||||||||||||||||||||||| |||| ||| ||||||||||||||  | ||
Sbjct  85609  TAGGAGAGTGAGCCCATCGTTCAGTAACAATATGACTCAGTACTGCAAGACCTT--T-CA  85665

Query  14001  GTATTTCAAAGTCTTTCCAGTAGGTGAGGGAGGCTTTCAG-TGATGC-TTAGACCTTCAT  14058
                |    |   | |||||||| ||||| ||||| |||| | |||| |  | |||||||||
Sbjct  85666  --A----AGCCTATTTCCAGTTGGTGAAGGAGGGTTTC-GATGAT-CACTGGACCTTCAT  85717

Query  14059  GCCCTAGAATTTGGAGATTGCATCCTTTAGAAATGATACCAAGGGAAATCTGCCCATGAG  14118
              ||||||  ||||||||| |||||| |||| |||||| |||||||||||||||||||||||
Sbjct  85718  GCCCTACCATTTGGAGACTGCATCTTTTA-AAATGACACCAAGGGAAATCTGCCCATGAG  85776

Query  14119  CAGCACTGGATGGGACTGTACCAGATGACTTAAAACTAAGGATAACCAAGG-A-AAAGCC  14176
              ||||| ||||||||||  |||||| |||||||||| ||||||||||||||| | |||| |
Sbjct  85777  CAGCATTGGATGGGACCATACCAGGTGACTTAAAATTAAGGATAACCAAGGAACAAAGTC  85836

Query  14177  TTCCTTAGAAGCAGACATCATCACATGGTAGACAG-TTTTCCAAGACAATGGAACAAGAC  14235
              || |||||||||||||||||||||||||||||||| ||||  |||| ||||| |||| ||
Sbjct  85837  TTTCTTAGAAGCAGACATCATCACATGGTAGACAGCTTTTTTAAGAAAATGGGACAAAAC  85896

Query  14236  TCCATTTGATCTTCTTCCATTGACTGAGACTTGGTTTTGTTTTGTATTAAAACAAAATGC  14295
              |||||||||||| |||||| |||||||||||||||||||||||||||||| |||||||| 
Sbjct  85897  TCCATTTGATCTCCTTCCACTGACTGAGACTTGGTTTTGTTTTGTATTAACACAAAATGA  85956

Query  14296  TCAAACCTATATTTTATGTTGTTAGGTACTTTCTCCACTCAAACCAAACACTTTCTAAGG  14355
              |||| |||| ||||||| |||||| |||||||| ||| ||||| ||||||||||||||| 
Sbjct  85957  TCAAGCCTACATTTTATTTTGTTACGTACTTTCACCAGTCAAAGCAAACACTTTCTAAGT  86016

Query  14356  TCTTCTGTTCAAAATGTAGCCACTCTCACTAACCAAAGCAATTGCTGGCTATGGAGTCAT  14415
              ||| || |||||||| ||||||||||||||||||||||||||| ||||||||||||||||
Sbjct  86017  TCTCCTATTCAAAATTTAGCCACTCTCACTAACCAAAGCAATTACTGGCTATGGAGTCAT  86076

Query  14416  TTACATGAAAGGGAAGGATCACAACTAAATAGTAGAACATGCTCTCATAAACAGTTGG  14473
              ||| ||||| |||||||||||||||||| ||||||||| |||||||| | || |||||
Sbjct  86077  TTAGATGAATGGGAAGGATCACAACTAA-TAGTAGAACCTGCTCTCACACACGGTTGG  86133


 Features flanking this part of subject sequence:
   8602 bp at 5' side: PRAME family member 5
   8929 bp at 3' side: PRAME family member 8

 Score =  686 bits (371),  Expect = 0.0
 Identities = 616/732 (84%), Gaps = 25/732 (3%)
 Strand=Plus/Plus

Query  984    gaaggggggacctcctgggcCCTCGAGAGCACTAGGGGACCTTGTTTGGTAACTGCAACC  1043
              ||||||| ||||||||| |||||| |||||||| |||||||||| |||| |||||| |||
Sbjct  57423  GAAGGGGAGACCTCCTGAGCCCTCAAGAGCACTGGGGGACCTTGGTTGG-AACTGCGACC  57481

Query  1044   TGGGCAGCTTCAGTTGTGCCTTTggagctactgccctgccaacttgggaggaccaggact  1103
              ||||||||||||||||||||||||||||||||| |||||||||| |||||| ||||||||
Sbjct  57482  TGGGCAGCTTCAGTTGTGCCTTTGGAGCTACTGTCCTGCCAACTCGGGAGGGCCAGGACT  57541

Query  1104   ccctcttgtcccaggatcccatcagctccaaagtgtgcacagcctcagctt-tgcCCTCT  1162
              ||||||||||||||||||||||||| | ||||||||    |||||||| || ||||||||
Sbjct  57542  CCCTCTTGTCCCAGGATCCCATCAGGTTCAAAGTGTATGTAGCCTCAG-TTATGCCCTCT  57600

Query  1163   CTCTGT-TTCCGTGCA--GAGGTGACAGGTGAGATGCAGGTTCACAGCAGCTCTGGTCAA  1219
              |||||| || | | ||  |||||||||||||||||||||||||||||||||||||| |||
Sbjct  57601  CTCTGTGTTTC-TCCACAGAGGTGACAGGTGAGATGCAGGTTCACAGCAGCTCTGGCCAA  57659

Query  1220   CCCCACAGAAACAAATCTGAA-GCTCCTGGGTCCGGTTTAATGAGCCCCAACTGCGCTCT  1278
              |||  || ||||||| |  || ||| ||||||| |||| |||||||||||||||| ||||
Sbjct  57660  CCCTGCAAAAACAAACCC-AATGCTTCTGGGTCTGGTTGAATGAGCCCCAACTGCACTCT  57718

Query  1279   -GATCCAGGAGT-TTGCAGGCTAACAGCACAAAGTGGGGAGTGAGGTCGAGGCTGTGGTG  1336
               | |  || | | ||||||||||||||||    ||| |||||||| | |||||| || | 
Sbjct  57719  AGTTA-AGAA-TATTGCAGGCTAACAGCAGGCCGTGAGGAGTGAGTTTGAGGCTTTG-TA  57775

Query  1337   GAGACTGCGGACCTAGGG-GCAAGTCCCGTTTAGCCGTGAGAGGGTATGGGTGGCACAGT  1395
              ||| || | ||||  ||| ||  ||| | || |||| ||||||||| |||||||||||| 
Sbjct  57776  GAGGCTCCAGACCC-GGGAGCGGGTCTCATTAAGCCATGAGAGGGTGTGGGTGGCACAGC  57834

Query  1396   TGGCTGCCTCAGGGACATGGGGCACAGGCCTGGCTGACAACCCAGCCAAGA-GGTGGTGC  1454
              || |||||||||| ||| ||||||||||||||||| ||||||| ||||||  || |||||
Sbjct  57835  TGTCTGCCTCAGGAACACGGGGCACAGGCCTGGCTCACAACCCTGCCAAGGTGG-GGTGC  57893

Query  1455   CTTTAGGAGTGGATCGTGGTCCACAGGCCCAGCAATC-GGAAGCATCAGGCTCTGTGTTC  1513
              ||  ||||||||| |||||||| ||| |||||||||  |||| | |||| ||||||| ||
Sbjct  57894  CTCCAGGAGTGGACCGTGGTCCCCAGACCCAGCAATTAGGAA-CGTCAGTCTCTGTGGTC  57952

Query  1514   ACCCCTCTTGGGGGCAGATCTTGGAAATGCAGCCTCAGGAAGATTCA-CACAGAAC-TCC  1571
              |||||| | ||||||||||||||||||||||||| ||||| |||| | |||||||| |||
Sbjct  57953  ACCCCTGTGGGGGGCAGATCTTGGAAATGCAGCCCCAGGAGGATT-AGCACAGAACCTCC  58011

Query  1572   TTTTTAGACCTAGGAACTTGATACTATTAGCAGGGTGGGCACACAGTTGATGCATAGCTG  1631
               ||  | ||| |||||||||  ||| |||||||||||||||||  || |   ||||||||
Sbjct  58012  CTTCGACACCCAGGAACTTGGCACTGTTAGCAGGGTGGGCACA--GTGGCCCCATAGCTG  58069

Query  1632   GCCAGGTCATTGAACTTGGTGCCATTTCTGCTTCCCAACTCGGGGCCCTGGAGCATGGCC  1691
              |||||||||||||||| ||||||||||||||||||||||   || ||||| ||| ||  |
Sbjct  58070  GCCAGGTCATTGAACTAGGTGCCATTTCTGCTTCCCAACAAAGGCCCCTGTAGCTTGATC  58129

Query  1692   CCAGCTCTGCCT  1703
              ||||||||||||
Sbjct  58130  CCAGCTCTGCCT  58141


 Features in this part of subject sequence:
   PRAME family member 16

 Score =  682 bits (369),  Expect = 0.0
 Identities = 1000/1292 (77%), Gaps = 93/1292 (7%)
 Strand=Plus/Minus

Query  4613    AATTTCCAGCTCCTGAATACTATTC-AGGTGGATTATTTTCAAT-GATCTTCTGAGATA-  4669
               |||||||| |||||| |||||  ||  |||  |   ||||||||  || |||||| | | 
Sbjct  176403  AATTTCCAACTCCTGGATACT-GTCTGGGTATACCCTTTTCAATAAAT-TTCTGA-A-AC  176348

Query  4670    TTCAA-TCGACGTTAGA-TAATTCACCAACTTACTACAGCACAGGTGTACTAAACCTCTC  4727
               || || | | | || || ||||||  || |||| |||| |||||||| |||| |||||| 
Sbjct  176347  TTGAAGTGGGCATT-GAGTAATTCTGCACCTTATTACAACACAGGTGCACTAGACCTCTT  176289

Query  4728    CTTTGGTAAACCCACCGGAAGAGGTATCTCAGGCATTCATCCTGGGGTA-TTTCCTTGAG  4786
               || | ||  | ||||| | ||||||| |||||||||||||||  | ||| |||||||  |
Sbjct  176288  CTGTAGTGGATCCACCTGCAGAGGTAGCTCAGGCATTCATCC-AGTGTACTTTCCTTTTG  176230

Query  4787    GCAGATGTCTATGAACACCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGC  4846
               ||||| |||||||||||||||||||||||||||||||||| |||||||| |||||||  |
Sbjct  176229  GCAGAGGTCTATGAACACCTTCAAGGGCTGGTGCTCTCCCGTCCTTGGATAGTCCTCCAC  176170

Query  4847    TGTCTGCCTCTTACTCATGGCCTCTGGGGAGGAGGACAGGGCCCTGGATTCAGACCATAT  4906
               |||||||||||| |||||||||||||||||| |||| |||||||||| | ||||||||||
Sbjct  176169  TGTCTGCCTCTTTCTCATGGCCTCTGGGGAGCAGGAGAGGGCCCTGGCTCCAGACCATAT  176110

Query  4907    GGCCCAGAAATTCTCATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTG  4966
                | |||||||||| ||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  176109  AGTCCAGAAATTCCCATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTG  176050

Query  4967    GGTAA-AGTAAGGCAGAGGCTCAGAACTTT-G--AAGGACAAATCCCTGACCTTTGCTTT  5022
                |||| | || || | | |||||||| | | |  || |||  | |||||||||  |||||
Sbjct  176049  AGTAACA-TAGGGGAAAAGCTCAGAA-TGTAGGCAAAGACCCACCCCTGACCTGAGCTTT  175992

Query  5023    CATTCT-CATCCAATA-A--A-TCAGCTGCTCCTGTCCTC-GCTGCTCCCTGTTCTCTCT  5076
               || ||  ||||||  | |  | |||||||||||||||||| | |||||| |   || |||
Sbjct  175991  CACTCAACATCCAGGACATCAGTCAGCTGCTCCTGTCCTCAG-TGCTCC-TC--CT-TCT  175937

Query  5077    GAGTTTTCTTGGTCCCTTTTCTCTTTCAATTCTGACTGGTCCCCACTTCTATT-CCATTT  5135
               |  | ||||   ||||  | | | ||  |||||| ||||| | ||||||||   || |||
Sbjct  175936  GTCTCTTCTCCATCCCGCTCCCCCTTGGATTCTGCCTGGTTCTCACTTCTAGAACC-TTT  175878

Query  5136    ACCTTCCACTGGGAATAGGCAAGTTTCTGTTCCCACAGTGGACCCTATATTGTGGGCAGT  5195
               ||||||||||||||  | ||| ||| ||||| || ||||||||||| ||| ||| |||||
Sbjct  175877  ACCTTCCACTGGGAGGAAGCAGGTTCCTGTTTCCTCAGTGGACCCTGTATGGTGAGCAGT  175818

Query  5196    TCTTTCCCTGAGGATCTGGGCAATGGCCAAGGCATGCCTGAGCTTCGTCACCAGCACCAC  5255
                |||| || ||||||||||||||||| |||||  | | |   || | |     |||||| 
Sbjct  175817  CCTTTTCCAGAGGATCTGGGCAATGGTCAAGG--T-C-T---CT-CATGG---GCACCAT  175769

Query  5256    CAGAAGACACTGGGCCATCCTTGGG----AT----ACTTCTT-TGCCTGACCCTGCTGTT  5306
               |||||| | ||| |||| ||| |      |     ||  ||  | ||||| || ||||| 
Sbjct  175768  CAGAAGCCTCTGAGCCACCCTAGCTCCCCAACCCCACCACTCCT-CCTGAGCCAGCTGTC  175710

Query  5307    CTTTCCCTGGACACCTGAGCCCCATCT-ACCAG-CCTTCCTGGGTCACCTCACCTGGGGC  5364
               | |||||||||  |||| | ||| ||  ||||| ||  |||| |||||||||||||||||
Sbjct  175709  CCTTCCCTGGATGCCTG-GACCCTTCCCACCAGGCCA-CCTGAGTCACCTCACCTGGGGC  175652

Query  5365    GATCCTTCTGTGTAAGCAGCATGTGAAG-CCCTTCCAGCA-ATGCTTTTAAGGTCTCCAG  5422
               ||  |||||| |  |||||  | | ||| |||||| |||| | ||||  |||||||||||
Sbjct  175651  GAAGCTTCTGGGCCAGCAGTGTATCAAGTCCCTTC-AGCACA-GCTTGCAAGGTCTCCAG  175594

Query  5423    ATGAAGCGTCTTCATCAGCGATCCCAGAGGGAGGCGG-GTGAAGGGCCAGGCCTGCACCA  5481
               |||| | ||||||||||| |||||||||||||||||| | ||||||||||||||||||||
Sbjct  175593  ATGAGGTGTCTTCATCAGGGATCCCAGAGGGAGGCGGAG-GAAGGGCCAGGCCTGCACCA  175535

Query  5482    TCA-CTGTCAGAGTCTGGAAGTGTCTCCTGCTGAAGGCCTCCAGGAAGAGTGGGAGGTA-  5539
               ||| || |||| | ||  || |||||| ||||| ||||||||| ||| | |  |||| | 
Sbjct  175534  TCAGCT-TCAGGGCCTCAAAATGTCTCATGCTGGAGGCCTCCATGAACA-TCAGAGGGAA  175477

Query  5540    GAGCTCCCTGGGCAGCTCCTCCAGGGCAGA-GATGGCCAAGGGCTTGTCTC-TCAGCAGA  5597
               || ||||||||||||||| ||||||   || ||||| ||||  || || || ||||||| 
Sbjct  175476  GACCTCCCTGGGCAGCTCGTCCAGGAT-GAAGATGGTCAAGAACTGGT-TCCTCAGCAGG  175419

Query  5598    CTCTGCCCCGCCAGCTCCAGGAGTCTGGGTGGGGCCTGGATGCTCATCCTGATGAATCTG  5657
               ||||| || ||||||||||||||||||| ||||| ||||| |||||| ||||  ||||| 
Sbjct  175418  CTCTGGCCTGCCAGCTCCAGGAGTCTGGATGGGGACTGGAGGCTCATTCTGACAAATCTC  175359

Query  5658    TAAG-GAAAAACTCTAGAAGACAAATCCAGAGAAAAGGCATCACTTTC--AGGCCAAACA  5714
                | | ||||||||||||| ||||| ||||| |||||||||  | ||||  ||||||| | 
Sbjct  175358  CA-GTGAAAAACTCTAGAGGACAA-TCCAGTGAAAAGGCA--AGTTTCTCAGGCCAATCC  175303

Query  5715    CAAT-CA-CCTC-ATCTTCTCCTAAGGCCAGTAG-CA-TTGCTCTGGTA-GAGGTAGAAA  5768
               |  | || || | | ||||||||| |||||  || || || |||| | | | | | ||||
Sbjct  175302  CC-TGCAACCCCCA-CTTCTCCTAGGGCCAA-AGTCAGTT-CTCTAGCATGTG-T-GAAA  175249

Query  5769    AATTAC-CACTTTACCCCAATTCCACTCTGCACTTGGTGGCCACAAAT-CTATATTTCTG  5826
                    | || ||||| ||||||||| |||||| |  ||||||||| |  | ||| |||||
Sbjct  175248  GGGCCCTCAGTTTACTCCAATTCCATTCTGCAATAAGTGGCCACAGAGGC-ATAGTTCTG  175190

Query  5827    CTTCTGCTGGTACCAGGAAGAATGTCTTCCAA  5858
               |  || ||||||||| ||||| ||| | ||||
Sbjct  175189  CC-CTTCTGGTACCAAGAAGAGTGTGTCCCAA  175159


 Features flanking this part of subject sequence:
   21057 bp at 5' side: PRAME family member 3
   11274 bp at 3' side: PRAME family member 5

 Score =  675 bits (365),  Expect = 0.0
 Identities = 739/915 (80%), Gaps = 43/915 (4%)
 Strand=Plus/Minus

Query  3514   CCTGCTTCAACCAAACACAAGTTTGTTCCCACCATCTGATGATGGTCCT-CATGCAAGTT  3572
              |||| |||| ||||||||||||||||||||| |||| ||||||||| ||   |||||| |
Sbjct  33705  CCTGTTTCACCCAAACACAAGTTTGTTCCCATCATCAGATGATGGT-CTGTGTGCAAGGT  33647

Query  3573   GCTGCATGTTGAGGACCCTGATCATTCAGGGGCTGTC-CCATTTTAGCCTCAGCCCTTTC  3631
              ||||| || ||| ||| | |||||||||||||| | | ||||||||| ||||| ||||||
Sbjct  33646  GCTGCCTGATGAAGACTCAGATCATTCAGGGGCAG-CTCCATTTTAGGCTCAGTCCTTTC  33588

Query  3632   A-CCATTTCTTGTGTGATTGGGTCAAGGCC-ACAAAATCTCTAAAGCCT-TTTATCTTCA  3688
              | || || ||||||||||||| |||||||| ||||||||| ||||| || |||| || ||
Sbjct  33587  AGCC-TTGCTTGTGTGATTGGTTCAAGGCCAACAAAATCTTTAAAGTCTCTTTA-CTGCA  33530

Query  3689   TCTTTTAGCAGAAAACCTCATCTCTGGGCCACAGGTA-CCCGGTGGGAGATGTGCACAAA  3747
              ||||| |||||| |||||||||||||||||| ||| | ||| ||||||||||||||||||
Sbjct  33529  TCTTTCAGCAGACAACCTCATCTCTGGGCCAGAGG-AGCCCAGTGGGAGATGTGCACAAA  33471

Query  3748   GAACTCAACTCAGCAAGGTCTAGGGACATTAGCTGGGGCTACCTGCCGGCAGGGGCTCCC  3807
              |||||||||| |||||||||||||||||| |||| |||| ||||||| |||  || ||||
Sbjct  33470  GAACTCAACTGAGCAAGGTCTAGGGACATCAGCTAGGGCCACCTGCCTGCAAAGGTTCCC  33411

Query  3808   TGGCCTGCCTGCATCTGCAAACCAACTGTCACTTTTTACCACTCTCACT-CCTACTCCTT  3866
              || | |||| || ||||||||||| || ||||||| |||||||||| || |||||||| |
Sbjct  33410  TGACGTGCCCGCGTCTGCAAACCACCTATCACTTTATACCACTCTC-CTGCCTACTCCCT  33352

Query  3867   CACCCTCCATCCCAGAAGCATGCATGTCCCATGTCAATTGACTTT-CCTGGAGTTCAAAA  3925
              |||| ||  ||| |||||||||| | || |||||||| | ||||| ||||| ||||||||
Sbjct  33351  CACC-TCTGTCCAAGAAGCATGCTTTTCTCATGTCAACT-ACTTTTCCTGGGGTTCAAAA  33294

Query  3926   CAACCTTCTACAGACAGGGAATCAGAGACAGGATCATTCATGATCACTAAGCTGGTGAGG  3985
               |||||| ||||||||| |||| |||||||||||||||  || | ||||||||| |||||
Sbjct  33293  GAACCTTTTACAGACAGAGAATTAGAGACAGGATCATTGGTGTTTACTAAGCTG-TGAGG  33235

Query  3986   ACAGAGCTTCTACTGTGAAATGCACAAGTTTGATGCACTGTCCCTCCTTTCATACCCTCC  4045
              || ||||||||||||||||||||||| |||||||||||| ||||| ||||||||| ||||
Sbjct  33234  ACGGAGCTTCTACTGTGAAATGCACAGGTTTGATGCACTTTCCCTTCTTTCATACTCTCC  33175

Query  4046   TTTGT-T-ACCTCT---TTTACATCATATCAACTTGAAACACACTTTGTAACAAGAAATT  4100
              | | | | |    |   ||| |||||||| ||||| |||| |||||  ||| ||| ||||
Sbjct  33174  TCTATATGAAGAGTAAGTTT-CATCATATTAACTTCAAACGCACTTCCTAAAAAGGAATT  33116

Query  4101   CACACGTGCACA-TGCAGTAGAGACAAAACGCCCACTAAGTACCTTG-TACATG-ATGTC  4157
              ||||  |||||  | |  ||||  |  ||| |||  | | || || | | | || |||||
Sbjct  33115  CACAAATGCACCCTCCC-TAGAT-CTGAAC-CCC--TGACTAACTAGATCCCTGCATGTC  33061

Query  4158   CCTCTCT--AGCCTCTACCCTAGGTGACCCCTCTGCCTTTATT-GAA-GTGATCCTGTGA  4213
               ||||||  ||| ||| |||  ||  | ||||||||| ||||| ||  | | |  |||||
Sbjct  33060  TCTCTCTGTAGCATCTGCCCCGGGCCATCCCTCTGCCCTTATTTGAGCGGGTT--TGTGA  33003

Query  4214   TAGCCACTCCAGGACATGGAGCACTGAACGGGACAATGTGTTGACATTCTGGTGTCCCCT  4273
              || ||||| ||||| || ||||||||||| | | |||| ||||||||||| | ||||| |
Sbjct  33002  TACCCACTTCAGGATATAGAGCACTGAACAGCATAATGAGTTGACATTCTAGCGTCCCAT  32943

Query  4274   GCACTGTGCCGTCGCCACTGGCTGGCACACAGTACACGTCTTCTAGTGTTTACTGT-AAC  4332
               | ||||| | || ||| |||||||||||||||| ||| |  |||| ||||||||| || 
Sbjct  32942  TCCCTGTGACATCACCAGTGGCTGGCACACAGTAGACGCCCACTAGCGTTTACTGTGAA-  32884

Query  4333   aaa-aa-aaaaGGCTGCGCTGTGGTCTGCAGAGAAAGGGCACGATCCTTTCTCACCTGAT  4390
              ||| || ||||| ||| | | ||||| ||||||||||  ||| ||||||||| |||||| 
Sbjct  32883  AAAGAACAAAAGTCTGTGGTATGGTCCGCAGAGAAAGCTCACCATCCTTTCTTACCTGAG  32824

Query  4391   CAGCTG-TCCCAGGT  4404
              ||| || ||| ||||
Sbjct  32823  CAGGTGCTCC-AGGT  32810


 Features flanking this part of subject sequence:
   21636 bp at 5' side: PRAME family member 8
   11424 bp at 3' side: PRAME family member 9

 Score =  671 bits (363),  Expect = 0.0
 Identities = 993/1286 (77%), Gaps = 87/1286 (6%)
 Strand=Plus/Minus

Query  4616   TTCCAGCTCCTGAATACTATTC-AGGTGGATTATTTTCAAT-GATCTTCTGAGATA-TTC  4672
              ||||| |||||| |||||  ||  |||  ||  ||| |||| ||| |||||| | | || 
Sbjct  92667  TTCCAACTCCTGGATACT-GTCTGGGTATATCCTTTCCAATAGAT-TTCTGA-A-ACTTG  92612

Query  4673   AA-TCGACGTTAGA-TAATTCACCAACTTACTACAGCACAGGTGTACTAAACCTCTCCTT  4730
              || | | | || || ||||||  || ||||||||| |||||||| ||||  ||||| || 
Sbjct  92611  AAGTGGGCATT-GAGTAATTCTGCACCTTACTACAACACAGGTGCACTAGGCCTCTTCTG  92553

Query  4731   TGGTAAACCCACCGGAAGAGGTATCTCAGGCATTCATCCTGGGGTA-TTTCCTTGAGGCA  4789
              | ||  | |||||  || ||||| |||||||||||||||  | ||| ||||||| |||||
Sbjct  92552  TAGTGGATCCACCCAAAAAGGTAGCTCAGGCATTCATCC-AGTGTACTTTCCTTTAGGCA  92494

Query  4790   GATGTCTATGAACACCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGT  4849
              || ||||||||||||||||||||||||| |||||||||||||||||||||||||  ||||
Sbjct  92493  GAGGTCTATGAACACCTTCAAGGGCTGGCGCTCTCCCATCCTTGGACAGTCCTCCACTGT  92434

Query  4850   CTGCCTCTTACTCATGGCCTCTGGGGAGGAGGACAGGGCCCTGGATTCAGACCATATGGC  4909
              |||||||||||||||||||||||||||| |||| ||| |||||| | |||||||||||| 
Sbjct  92433  CTGCCTCTTACTCATGGCCTCTGGGGAGCAGGAGAGGACCCTGGCTCCAGACCATATGGT  92374

Query  4910   CCAGAAATTCTCATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGT  4969
              |||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||
Sbjct  92373  CCAGAAATTCTCATCAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTATGAGT  92314

Query  4970   AA-AGTAAGGCAGAGGCTCAGAACTTT-G--AAGGACAAATCCCTGACCTTTGCTTTCAT  5025
              || | || || | | |||||||| | | |  ||||||  | |||||||||  ||||||| 
Sbjct  92313  AACA-TAGGGGAAAAGCTCAGAA-TGTAGGCAAGGACCCACCCCTGACCTGAGCTTTCAC  92256

Query  5026   TCT-CATCCAATA-A--A-TCAGCTGCTCCTGTCCTC-GCTGCTCCCTGTTCTCTCTGAG  5079
              ||  ||||||  | |  | |||||||||||||||||| | |||||| |   || ||||  
Sbjct  92255  TCCACATCCAGGACATCAGTCAGCTGCTCCTGTCCTCAG-TGCTCC-TC--CT-TCTGTC  92201

Query  5080   TTTTCTTGGTCCCTTTTCTCT-TTCAATTCTGACTGGTCCCCACTTCTATT-CCATTTAC  5137
              | ||||   ||| |  || || ||  |||||| ||||| |||||||||| | || |||||
Sbjct  92200  TCTTCTCCATCC-TGCTCCCTCTTGGATTCTGCCTGGTACCCACTTCTAGTACC-TTTAC  92143

Query  5138   CTTCCACTGGGAATAGGCAAGTTTCTGTTCCCACAGTGGACCCTATATTGTGGGCAGTTC  5197
               |||  ||||||  | ||| | | ||||| || ||||||||||| ||| ||| ||||  |
Sbjct  92142  TTTCTGCTGGGAGGAAGCAGGCTCCTGTTTCCTCAGTGGACCCTGTATGGTGAGCAGACC  92083

Query  5198   TTTCCCTGAGGATCTGGGCAATGGCCAAGGCATGC-C-TGAGCTTCGTCACCAGCACCAC  5255
              ||| || |||||||||||||||||||||||| | | | || ||  |||||  ||| |  |
Sbjct  92082  TTTTCCAGAGGATCTGGGCAATGGCCAAGGCCT-CTCATGGGCACCGTCAGAAGC-CT-C  92026

Query  5256   CAGAAGACAC--TGGG-CC--ATCCTTGGGATACTTCTTTGCCTGACCCTGCTGTTCTTT  5310
                || | |||  | |  ||  | ||     |  || ||   ||||| || ||||| | ||
Sbjct  92025  T-GA-GCCACCCTAGCTCCCCAACCCCACCA--CTCCT---CCTGAGCCAGCTGTCCCTT  91973

Query  5311   CCCTGGACACCTGAGCCCCATCTACC-A--GCCTTCCTGGGTCACCTCACCTGGGGCGAT  5367
              |||||||  |||| | ||| ||  || |  |||  |||| ||||||||||||||||||| 
Sbjct  91972  CCCTGGATGCCTG-GACCCTTCC-CCGAAAGCCA-CCTGAGTCACCTCACCTGGGGCGAA  91916

Query  5368   CCTTCTGTGTAAGCAGCATGTGAAG-CCCTTCCAGCA-ATGCTTTTAAGGTCTCCAGATG  5425
              ||||||| |  | |||  | | ||| ||| || || | | ||||  ||||||||||||||
Sbjct  91915  CCTTCTGGGCCACCAGTGTATCAAGTCCCCTC-AGGACA-GCTTGCAAGGTCTCCAGATG  91858

Query  5426   AAGCGTCTTCATCAGCGATCCCAGAGGGAGGCGG-GTGAAGGGCCAGGCCTGCACCATCA  5484
              | | ||||||||||| |||||||||||||||||| | |||||||||||||||||||||||
Sbjct  91857  AGGTGTCTTCATCAGGGATCCCAGAGGGAGGCGGAG-GAAGGGCCAGGCCTGCACCATCA  91799

Query  5485   -CTGTCAGAGTCTGGAAGTGTCTCCTGCTGAAGGCCTCCAGGAAGAGTGGGAGGTA-GAG  5542
               || |||| | ||  ||  ||||| ||||||||||||||| ||| | |  |||| | || 
Sbjct  91798  GCT-TCAGGGCCTCAAAACGTCTCATGCTGAAGGCCTCCATGAACA-TCAGAGGGAAGAC  91741

Query  5543   CTCCCTGGGCAGCTCCTCCAGGGCAGA-GATGGCCAAGGGCTTGTCTC-TCAGCAGACTC  5600
              ||||||||||||||| |||||||  || ||||| ||||  || || || ||||||| |||
Sbjct  91740  CTCCCTGGGCAGCTCATCCAGGGT-GAAGATGGTCAAGAACTGGT-TCCTCAGCAGGCTC  91683

Query  5601   TGCCCCGCCAGCTCCAGGAGTCTGGGTGGGGCCTGGATGCTCATCCTGATGAATCTGTAA  5660
              ||||| ||||||||||| ||||||| ||||||||||| |||||| ||||  |||||   |
Sbjct  91682  TGCCCTGCCAGCTCCAGCAGTCTGGATGGGGCCTGGAGGCTCATTCTGACAAATCTCCGA  91623

Query  5661   GGAAAAACTCTAGAAGACAAATCCAGAGAAAAGGCATCACTTTCA-GG-CCAAACACAAT  5718
              |||||||||||||| ||||| || || |||||||||  | ||||  || |||  | | | 
Sbjct  91622  GGAAAAACTCTAGAGGACAA-TCAAGTGAAAAGGCA--AGTTTCTCGGGCCATTCCCCAG  91566

Query  5719   CA--CCTCATCTTCTCCTAAGGCCAGTAG-CATTGCTCTGGTA-GAGGTAGAAAAATTAC  5774
              ||  || || ||||||||| |||||  || |||| |||| | | | | | |||| |   |
Sbjct  91565  CAAGCCCCA-CTTCTCCTAGGGCCAA-AGTCATTTCTCTAGCACGTG-T-GAAAGAGCCC  91510

Query  5775   -CACTTTACCCCAATTCCACTCTGCACTTGGTGGCCACAAAT-CTATATTTCTGCTTCTG  5832
               || ||||| ||||||||  |||||| |  ||||| ||| |  | ||  ||||||  || 
Sbjct  91509  TCAGTTTACTCCAATTCCGTTCTGCAATAAGTGGCTACAGAGGC-ATGGTTCTGCC-CTT  91452

Query  5833   CTGGTACCAGGAAGAATGTCTTCCAA  5858
              ||||||||| ||||| ||| | ||||
Sbjct  91451  CTGGTACCAAGAAGAGTGTGTCCCAA  91426


 Features flanking this part of subject sequence:
   19604 bp at 5' side: PRAME family member 3
   12451 bp at 3' side: PRAME family member 5

 Score =  641 bits (347),  Expect = 5e-180
 Identities = 942/1217 (77%), Gaps = 89/1217 (7%)
 Strand=Plus/Minus

Query  4686   TAATTCACCAACTTACTACAGCACAGGTGTACTAAACCTCTCCTTTGGTAAACCCACCGG  4745
              ||||||  || |||| ||||||||||||| |||| |||||| || | ||  | | |||  
Sbjct  32528  TAATTCTGCACCTTATTACAGCACAGGTGCACTAGACCTCTTCTGTAGTGGATCTACC-C  32470

Query  4746   A-AGAGGTATCTCAGGCATTCATCCTGGGGTA-TTTCCTTGAGGCAGATGTCTATGAACA  4803
              | ||||||| |||||||||||||||  | ||| ||| ||| ||||||  |||||||||||
Sbjct  32469  ACAGAGGTAGCTCAGGCATTCATCC-AGTGTACTTTTCTTTAGGCAGCGGTCTATGAACA  32411

Query  4804   CCTTCAAGGGCTGGTGCTCTCCCATCCTTGGACAGTCCTCTGCTGTCTGCCTCTTACTCA  4863
              ||||||||||||||  ||||||||||||||||||||||||  |||||||||| |||||||
Sbjct  32410  CCTTCAAGGGCTGGCACTCTCCCATCCTTGGACAGTCCTCCACTGTCTGCCTTTTACTCA  32351

Query  4864   TGGCCTCTGGGGAGGAGGACAGGGCCCTGGATTCAGACCATATGGCCCAGAAATTCTCAT  4923
              |||||||||||||| |||| ||| || ||| | |||||||||||| |||||||||| |||
Sbjct  32350  TGGCCTCTGGGGAGCAGGAGAGGACCTTGGCTCCAGACCATATGGTCCAGAAATTCCCAT  32291

Query  4924   CAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAA-AGTAAGGCAGA  4982
              ||||||||||||||||||||||||||||||||||||||||||| |||| |  | || | |
Sbjct  32290  CAACATCCCGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGAGTAACAC-AGGGGAAA  32232

Query  4983   GGCTCAGAACTTT-G--AAGGACAAATCCCTGACCTTTGCTTTCATTCT-CATCCAATA-  5037
               |||||||| | | |  ||||||  | |||||||||  ||||||| ||  ||||||  | 
Sbjct  32231  AGCTCAGAA-TGTAGGCAAGGACCCACCCCTGACCTGAGCTTTCACTCCACATCCAGGAC  32173

Query  5038   A--A-TCAGCTGCTCCTGTCCTC-GCTGCTCCCTGTTCTCTCTGAGTTTTCTTGGTCCCT  5093
              |  | |||||||||||||||||| | |||||| |   || ||||  | ||||   |||| 
Sbjct  32172  ATCAGTCAGCTGCTCCTGTCCTCAG-TGCTCC-TC--CT-TCTGTCTCTTCTCCATCCCG  32118

Query  5094   TTTCTCTTTCAATTCTGACTGGTCCCCACTTCTAT--TCCATTTACCTTCCACTGGGA-A  5150
               | | | ||   ||||| ||||| | ||||||||   ||  ||||| ||||||||||| |
Sbjct  32117  CTCCCCCTTGGGTTCTGCCTGGTTCTCACTTCTAGAATC--TTTACGTTCCACTGGGAGA  32060

Query  5151   TAGGCAAGTTTCTGTTCCCACAGTGGACCCTATATTGTGGGCAGTTCTTTCCCTGAGGAT  5210
               || || ||| ||||| || ||||||||||| ||| ||| ||||| ||||||| ||||||
Sbjct  32059  AAG-CAGGTTCCTGTTTCCTCAGTGGACCCTGTATGGTGAGCAGTCCTTTCCCAGAGGAT  32001

Query  5211   CTGGGCAATGGCCAAGGCATGC-C-TGAGCTTCGTCACCAGCACCACCAGAAGACAC--T  5266
              ||||||||||| |||||| | | | || ||  | |||  ||| |  |  || | |||  |
Sbjct  32000  CTGGGCAATGGTCAAGGCCT-CTCATGGGCACCATCAGAAGC-CT-CT-GA-GCCACCCT  31946

Query  5267   GGG-CC--ATCCTTGGGATACTTCTTTGCCTGACCCTGCTGTTCTTTCCCTGGACACCTG  5323
               |  ||  | ||     |  || ||   ||||| || ||||| | |||||||||  ||||
Sbjct  31945  AGCTCCCCAACCCCACCA--CTCCT---CCTGAGCCAGCTGTCCCTTCCCTGGATGCCTG  31891

Query  5324   AGCCCCATCT-ACCAG-CCTTCCTGGGTCACCTCACCTGGGGCGATCCTTCTGTGTAAGC  5381
               | ||| ||  ||||| ||  |||| ||||||||||||| ||| | ||||||| |  |||
Sbjct  31890  -GACCCTTCCCACCAGGCCA-CCTGAGTCACCTCACCTGAGGCAAACCTTCTGGGCCAGC  31833

Query  5382   AGCATGTGAAG-CCCTTCCAGCA-ATGCTTTTAAGGTCTCCAGATGAAGCGTCTTCATCA  5439
              ||  | | ||| |||||| |||| | ||||  ||||||||||||||| | ||||||||||
Sbjct  31832  AGTGTATCAAGTCCCTTC-AGCACA-GCTTGCAAGGTCTCCAGATGAGGTGTCTTCATCA  31775

Query  5440   GCGATCCCAGAGGGAGGCGG-GTGAAGGGCCAGGCCTGCACCATCA-CTGTCAGAGTCTG  5497
              | ||||||||||||||| || | ||||| ||||||||||||||||| || |||| | || 
Sbjct  31774  GGGATCCCAGAGGGAGGTGGAG-GAAGGACCAGGCCTGCACCATCAGCT-TCAGGGCCTC  31717

Query  5498   GA-AG-TGTCTCCTGCTGAAGGCCTCCAGGAAGAGTGGGAGGTA-GAGCTCCCTGGGCAG  5554
               | || | ||||||||||| |||||||| ||| | |  |||| | || ||||||||||||
Sbjct  31716  -ACAGCT-TCTCCTGCTGACGGCCTCCATGAACA-TCAGAGGGAAGACCTCCCTGGGCAG  31660

Query  5555   CTCCTCCAGGGCAGA-GATGGCCAAGGGCTTGTCTC-TCAGCAGACTCTGCCCCGCCAGC  5612
              ||| ||||||   || ||||| ||||  || || || |||| || |||||||| ||||||
Sbjct  31659  CTCGTCCAGGAT-GAAGATGGTCAAGAACTGGT-TCCTCAGTAGGCTCTGCCCTGCCAGC  31602

Query  5613   TCCAGGAGTCTGGGTGGGGCCTGGATG-CTCATCCTGATGAATCTGTAAGGAAAAACTCT  5671
              ||||||||||||| ||||| ||||| | ||||| ||||  |||||| |||||||||||||
Sbjct  31601  TCCAGGAGTCTGGATGGGGACTGGA-GACTCATTCTGACAAATCTGCAAGGAAAAACTCT  31543

Query  5672   AGAAGACAAATCCAGAGAAAAGGCATCACTTTC--AGGCCAAACAC----AATCACCTCA  5725
              ||| ||||| ||||| |||||||||  | ||||  ||||||| | |    |||| || | 
Sbjct  31542  AGAGGACAA-TCCAGTGAAAAGGCA--AGTTTCTCAGGCCAATCCCCTGCAATC-CC-CG  31488

Query  5726   TCTTCTCCTAAGGCCAGTAG-CATTGCTCTGGTA-GAGGTAGAAAAATTAC-CACTTTAC  5782
               ||||||||| |||||  || |||| |||| | | | | | |||| |   | || |||||
Sbjct  31487  -CTTCTCCTAGGGCCAA-AGTCATTTCTCTAGCATGTG-T-GAAAGAGCCCTCAGTTTAC  31432

Query  5783   CCCAATTCCACTCTGCACTTGGTGGCCACAAAT-CTATATTTCTGCTTCTGCTGGTACCA  5841
               ||||||||| |||||| |  ||||||||| |  | ||| ||||||  || ||||||| |
Sbjct  31431  TCCAATTCCATTCTGCAATAAGTGGCCACAGAGGC-ATAGTTCTGCC-CTTCTGGTACTA  31374

Query  5842   GGAAGAATGTCTTCCAA  5858
               ||||| ||| | ||||
Sbjct  31373  AGAAGAGTGTGTCCCAA  31357


 Features flanking this part of subject sequence:
   15808 bp at 5' side: PRAME family member 8
   17958 bp at 3' side: PRAME family member 9

 Score =  569 bits (308),  Expect = 2e-158
 Identities = 474/551 (86%), Gaps = 23/551 (4%)
 Strand=Plus/Plus

Query  22628  ttctatgcactcaggagagtgagcccatCATTCAGTAACAATATGAATCAATACTGCAAG  22687
              ||||||||||| ||||||||||||||||| |||||||||||||||| ||| |||||||||
Sbjct  85598  TTCTATGCACTTAGGAGAGTGAGCCCATCGTTCAGTAACAATATGACTCAGTACTGCAAG  85657

Query  22688  ACCTTGATGCAGAATTTCAAAGACTATTTCCAGTAGGTG-A--AGGCTTTCAG-TGATGC  22743
              | |      |    |||||||| ||||||||||| |||| |  ||| |||| | |||| |
Sbjct  85658  A-C------C----TTTCAAAGCCTATTTCCAGTTGGTGAAGGAGGGTTTC-GATGAT-C  85704

Query  22744  -TTAGATCTTCCTGCCCTAGCATTTGGAGATTGCATCCTTTGGAAATGACACCAAGGGAA  22802
                | || |||| ||||||| |||||||||| ||||| ||||  |||||||||||||||||
Sbjct  85705  ACTGGACCTTCATGCCCTACCATTTGGAGACTGCAT-CTTTTAAAATGACACCAAGGGAA  85763

Query  22803  ATCTGCGCATGAGCAGCAATGGATGGGACTGTACCAGATGACTGAAACGTAAAGATATCC  22862
              |||||| ||||||||||| ||||||||||  |||||| ||||| |||  ||| |||| ||
Sbjct  85764  ATCTGCCCATGAGCAGCATTGGATGGGACCATACCAGGTGACTTAAAATTAAGGATAACC  85823

Query  22863  GAGG-A-AAAGCCTTCCCTAGAAGCAGACATCATCACATGGTAGACAGCTTTTCCAAGAC  22920
               ||| | |||| ||| | |||||||||||||||||||||||||||||||||||  |||| 
Sbjct  85824  AAGGAACAAAGTCTTTCTTAGAAGCAGACATCATCACATGGTAGACAGCTTTTTTAAGAA  85883

Query  22921  AATGGAACAAGACTCCATTTGATCTTCTTCCATTGACTGAGACTTGGTTTTGTTTTGTAT  22980
              ||||| |||| |||||||||||||| |||||| |||||||||||||||||||||||||||
Sbjct  85884  AATGGGACAAAACTCCATTTGATCTCCTTCCACTGACTGAGACTTGGTTTTGTTTTGTAT  85943

Query  22981  TAACACAAAATTCTCAAACCTGTATTTTATATTGTTAGGTACTTTCATCACTCAAACCAA  23040
              |||||||||||  |||| |||  ||||||| |||||| ||||||||| || ||||| |||
Sbjct  85944  TAACACAAAATGATCAAGCCTACATTTTATTTTGTTACGTACTTTCACCAGTCAAAGCAA  86003

Query  23041  ACACTTTCTAAGGTCTCCTGTTCAAAATGTAGCCACTCTCACTAACCAAAGCAATTGCTG  23100
              |||||||||||| |||||| |||||||| ||||||||||||||||||||||||||| |||
Sbjct  86004  ACACTTTCTAAGTTCTCCTATTCAAAATTTAGCCACTCTCACTAACCAAAGCAATTACTG  86063

Query  23101  GCTATGGGGTCATTTAGATGAAAGGGAAGGATCACAGA-TAATAGTAGAACCTGCTCTCA  23159
              ||||||| |||||||||||||| ||||||||||||| | |||||||||||||||||||||
Sbjct  86064  GCTATGGAGTCATTTAGATGAATGGGAAGGATCACA-ACTAATAGTAGAACCTGCTCTCA  86122

Query  23160  TACACAGTTGG  23170
               |||| |||||
Sbjct  86123  CACACGGTTGG  86133


 Features flanking this part of subject sequence:
   13632 bp at 5' side: PRAME family member 16
   9708 bp at 3' side: PRAME family member 21

 Score =  488 bits (264),  Expect = 7e-134
 Identities = 437/518 (84%), Gaps = 21/518 (4%)
 Strand=Plus/Plus

Query  13393   ATAAATGATTATAAAATGTGTTTCCTTTCTGGCGAACCTCTGGAGAAATTTCCAATGGTA  13452
               |||||||| |||||||| |||||||||||||| | | ||| |||||| | ||||||||||
Sbjct  191848  ATAAATGAGTATAAAATATGTTTCCTTTCTGGGGCATCTCCGGAGAAGTCTCCAATGGTA  191907

Query  13453   GGAGAACTCAGTTTACTGGGCAGGCGATCACACAGATAAGATTTTACAGATCTAATGGCA  13512
               |||||||||||| |||||||||||  |||||||||||||||| ||||||||| |||||| 
Sbjct  191908  GGAGAACTCAGTGTACTGGGCAGGTTATCACACAGATAAGATCTTACAGATCCAATGGCC  191967

Query  13513   CTACCATTAACTTCATTATCATTGGTATTCTACAAAGGTTGAGTGAACAAATGGTATCTT  13572
               |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct  191968  CTACCATTAACTTCATTATCCTTGGTATTCTACAAAGGTTGAGTGAACAAATGGTATCTT  192027

Query  13573   AAAATTAAA-TTAGCTAAATTAACAAAAAAGATTGGATTACtttttctttttttt--gac  13629
                ||| |||| ||||||||| ||||||| |||| ||||||||||||| ||||||||  || 
Sbjct  192028  GAAACTAAAATTAGCTAAACTAACAAAGAAGACTGGATTACTTTTTTTTTTTTTTTTGAG  192087

Query  13630   acagagtctctgatgccca-agcgggagtacagtggtgctatgtcat--ctcactgcaac  13686
               |||||||||||| |||||| | | ||||||||||||||||  ||| |  ||||||| |||
Sbjct  192088  ACAGAGTCTCTGTTGCCCAGA-CAGGAGTACAGTGGTGCT--GTCTTGGCTCACTGAAAC  192144

Query  13687   atctgcctcccgggttcaagagattctcctgcctcagactcctgagtagccgggattaca  13746
                ||||||||| ||||||||| ||||||| |||||||| ||||  ||| || || ||||||
Sbjct  192145  CTCTGCCTCCTGGGTTCAAGTGATTCTCATGCCTCAGCCTCCCAAGTGGCAGGAATTACA  192204

Query  13747   ggcacacaccaccacacccagctgatttttgtatttttagcagaaacggggtttcaccat  13806
               ||    | | ||||||||||||| |||||||||||||||| |||||| | ||||||||||
Sbjct  192205  GGTGTGC-C-ACCACACCCAGCTAATTTTTGTATTTTTAGTAGAAACCGTGTTTCACCAT  192262

Query  13807   gttgaccaggttggtcttgaacccctgacctt--gtgatctc-cctgcctcagcctcctg  13863
               |||| ||||| || ||   |||   || |||   |||||| | || ||||  ||||||  
Sbjct  192263  GTTGGCCAGGCTGATC---AACT--TG-CCTCAAGTGATC-CGCCAGCCTTGGCCTCCCA  192315

Query  13864   aagtgctggaattataggcttgagccaccttgcccagc  13901
               || |||||| |||| |||| |||||||||  |||||||
Sbjct  192316  AATTGCTGGGATTACAGGCGTGAGCCACCACGCCCAGC  192353


 Features flanking this part of subject sequence:
   13632 bp at 5' side: PRAME family member 16
   9715 bp at 3' side: PRAME family member 21

 Score =  484 bits (262),  Expect = 9e-133
 Identities = 430/509 (84%), Gaps = 19/509 (3%)
 Strand=Plus/Plus

Query  22077   ataagtgattataaaatgtgtttcctttct-gggcaat-tctggagaaatctctaatggt  22134
               |||| ||| |||||||| |||||||||||| |||| || || |||||| |||| ||||||
Sbjct  191848  ATAAATGAGTATAAAATATGTTTCCTTTCTGGGGC-ATCTCCGGAGAAGTCTCCAATGGT  191906

Query  22135   atgagaattcagtttactgggcaggttatcacac--ataaaattttacagacccaatgac  22192
               | ||||| ||||| ||||||||||||||||||||  |||| || ||||||| |||||| |
Sbjct  191907  AGGAGAACTCAGTGTACTGGGCAGGTTATCACACAGATAAGATCTTACAGATCCAATGGC  191966

Query  22193   actagCATTAACTTCATTATCCTTGGTATTCTATAAAGGTTGAGTGAACAAATGGTATAT  22252
                ||| |||||||||||||||||||||||||||| |||||||||||||||||||||||| |
Sbjct  191967  CCTACCATTAACTTCATTATCCTTGGTATTCTACAAAGGTTGAGTGAACAAATGGTATCT  192026

Query  22253   TTAAACTAAAATTAGCTAAACTGACAAAGAAAACTGGAtta-ttattatttattttt-ga  22310
               | |||||||||||||||||||| |||||||| ||||||||| || || ||| ||||| ||
Sbjct  192027  TGAAACTAAAATTAGCTAAACTAACAAAGAAGACTGGATTACTTTTTTTTTTTTTTTTGA  192086

Query  22311   gacagagtctctgttgcccaggctggagtacagtggtgctaccttggctcactgcaacct  22370
               ||||||||||||||||||||| | ||||||||||||||||  |||||||||||| |||||
Sbjct  192087  GACAGAGTCTCTGTTGCCCAGACAGGAGTACAGTGGTGCTGTCTTGGCTCACTGAAACCT  192146

Query  22371   ctgcctcccaggttcaag-gagttttcctgcctcagccacctaagtagctgggattacag  22429
               ||||||||  |||||||| || || || |||||||||| || |||| || || |||||||
Sbjct  192147  CTGCCTCCTGGGTTCAAGTGA-TTCTCATGCCTCAGCCTCCCAAGTGGCAGGAATTACAG  192205

Query  22430   gcacacacaaccacacccagctaatttttgtatttttggcagaagcggggtttcaccatt  22489
               |    | || ||||||||||||||||||||||||||| | |||| | | |||||||||| 
Sbjct  192206  GTGTGC-CA-CCACACCCAGCTAATTTTTGTATTTTTAGTAGAAACCGTGTTTCACCATG  192263

Query  22490   ttggccaggttggtcttgaacccctgacatcg-g-gatctgcctgcctcggtctcctaaa  22547
               ||||||||| || ||   |||   || | ||  | |||| ||| |||| || |||| |||
Sbjct  192264  TTGGCCAGGCTGATC---AACT--TGCC-TCAAGTGATCCGCCAGCCTTGGCCTCCCAAA  192317

Query  22548   gtgctgggattataggcgtcagccaccac  22576
                ||||||||||| |||||| |||||||||
Sbjct  192318  TTGCTGGGATTACAGGCGTGAGCCACCAC  192346


 Features in this part of subject sequence:
   PRAME family member 18

 Score =  451 bits (244),  Expect = 9e-123
 Identities = 648/829 (78%), Gaps = 83/829 (10%)
 Strand=Plus/Minus

Query  28527   GTGGATCAGTGGCT-AATAATTCATGGACTACGAGGGATCTTGCCTGCTCTTTAGAAGTT  28585
               ||||| || ||| | || |||||||||| || ||| ||||||||| |||| || || |||
Sbjct  157866  GTGGAGCAATGGATGAA-AATTCATGGAGTAGGAGTGATCTTGCCCGCTCCTTGGAGGTT  157808

Query  28586   GGGACACATTCTTCATGGTACCAGAAGGGTAGAACTATGTCTCTGTGGCCACTTATTGCA  28645
               |||| ||| ||||| |||||||||||||| ||||||||||||||||||||| ||||||||
Sbjct  157807  GGGAGACACTCTTCTTGGTACCAGAAGGGCAGAACTATGTCTCTGTGGCCAATTATTGCA  157748

Query  28646   GAAAGGAACTGGAGTAAACTGAGGGCTCTTTCACACATG-CTAGAGAAATGAC-TTGGGC  28703
               ||   ||| ||| ||||||| ||| ||||||||||| || | |||| | |||| || || 
Sbjct  157747  GAGTCGAATTGGGGTAAACTAAGGACTCTTTCACACCTGAC-AGAGTAGTGACTTTTGG-  157690

Query  28704   CCTG-GGAGAATTGGGGGT-TGCAGGGGATTGGTCGGAGGAACTTGCCTTTTTGCTGGAT  28761
               || | |||||| |  |||| || || ||| ||| | ||  ||   |  ||| | ||   |
Sbjct  157689  CC-GAGGAGAAGTCAGGGTGTG-AGAGGACTGGCCTGA-TAA---G--TTTGT-CT---T  157642

Query  28762   TGTGCTGTAGAGTTTTTCCTTGTAGATTTGTCAGAATGAGCCTCCAGACCCCATC-CAGA  28820
               | | || | || ||||| |||| |||||| |||| |||||| ||||| ||||| | ||||
Sbjct  157641  T-T-CTCTGGA-TTTTT-CTTGCAGATTTATCAGGATGAGCTTCCAGGCCCCA-CGCAGA  157587

Query  28821   CTCCTGGAGCTGGCAGGGCAGAGCCTGATGAGGAAGCAGTTCTTGACTATCTTCACCCTG  28880
               ||||||||||||||||||||||||||| ||||| | |||  |||| | |||| |  ||||
Sbjct  157586  CTCCTGGAGCTGGCAGGGCAGAGCCTGCTGAGGGACCAGGCCTTGGCCATCTCCGTCCTG  157527

Query  28881   GACT-AGCTGCCCAGGGAGGTCT-CCCCTCTGAC-GTTCATGGAGGCCTTCAGC-ATG-A  28935
               || | |||||||||||||| ||| |||| | ||| |||| |||||||||||| | | | |
Sbjct  157526  GA-TGAGCTGCCCAGGGAGCTCTTCCCC-C-GACTGTTCGTGGAGGCCTTCA-CTA-GCA  157472

Query  28936   GATGTTGTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGTCCT-CCCTTCACCTCCCTCTG  28994
               || | || ||||  |||||| ||||||||||||||||| ||| ||| |  ||||||||||
Sbjct  157471  GACGCTGCGAGGTTCTGAAGGTGATGGTGCAGGCCTGGCCCTTCCCCTG-CCTCCCTCTG  157413

Query  28995   GGATCCCTGATGAAGACAACTCATCTGGAGACCTTGCAAGCTGT-GCTGAA-GGGACTTG  29052
               || ||||||||||||||  || ||||||||| ||| ||   ||| | || | |||| |||
Sbjct  157412  GGGTCCCTGATGAAGACGCCTGATCTGGAGATCTTACATTATGTAG-TGGATGGGA-TTG  157355

Query  29053   ATA-CACTAG-T-GTCCCAGAAGGTTTGCCCCAGTTGAGGTGACTCAGGTGGCCTGGTGG  29109
               ||  | || | | | |||| |||||| ||||||| ||||||||| |||||||   ||   
Sbjct  157354  ATTGC-CT-GCTTG-CCCAAAAGGTTCGCCCCAGGTGAGGTGACCCAGGTGG---GG---  157304

Query  29110   GAAGGGTCCAGGCATCCAGGGA--AGGGACAGCTGGCTCAGGAGGAGTGGCAGTGTGTGG  29167
                | ||| |||||  ||||||||  | |  ||||||| |||| |  |     | | || ||
Sbjct  157303  -A-GGGCCCAGGTGTCCAGGGACTAAG--CAGCTGGGTCAG-ACAA-----A-T-TG-GG  157257

Query  29168   GAGCTAGGGTGGCTCAGAGGCTTCTGATGGTACCCA-TGAGA--G--G----C---CTTG  29215
                | || ||||||| ||| ||||||||||||| || | |||||  |  |    |   ||||
Sbjct  157256  AACCTGGGGTGGCCCAGGGGCTTCTGATGGTGCC-AGTGAGAAAGCTGGGAACGTTCTTG  157198

Query  29216   GCCATTGCCCAGATCCTCTGGAAAAGGACTGCTCACCATACAGAGTCCACTGAGGAAACA  29275
               || ||||||||| |||||||| ||||||||||||||||||||| ||||||||||||||||
Sbjct  157197  GCTATTGCCCAGCTCCTCTGGGAAAGGACTGCTCACCATACAGGGTCCACTGAGGAAACA  157138

Query  29276   GGAACCTGCTTCCTTCCCAGTGGAAGGTAAAGGTACTAGAAGTGGGTAC  29324
               ||||||||| | || |||||||||||||||||| |||||||||||||||
Sbjct  157137  GGAACCTGCCTGCT-CCCAGTGGAAGGTAAAGGCACTAGAAGTGGGTAC  157090


 Features in this part of subject sequence:
   PRAME family member 3

 Score =  433 bits (234),  Expect = 3e-117
 Identities = 677/878 (77%), Gaps = 82/878 (9%)
 Strand=Plus/Minus

Query  28480  CTGAGC-TTCAGAGATCCTCGGTAACATTTGCCAGTGCT-AT-GAGTTTAGTGGATCAGT  28536
              |||||| || | |||| || ||||||| || |||| ||| || |||||  ||||| || |
Sbjct  12061  CTGAGCTTTGA-AGATTCTTGGTAACACTTCCCAGAGCTAATAGAGTTGGGTGGAGCAAT  12003

Query  28537  GGCT-AATAATTCATGGACTACGAGGGATCTTGCCTGCTCTTTAGAAGTTGGGACACATT  28595
                 | || |||||||||| || ||| ||| ||||| | || || || ||| ||| ||| |
Sbjct  12002  TAATGAA-AATTCATGGAGTAGGAGTGATTTTGCCCGTTCCTTGGAGGTTAGGAGACACT  11944

Query  28596  CTTCATGGTACCAGAAGGGTAGAACTATGTCTCTGTGGCCACTTATTGCAGAAAGGAACT  28655
              |||| |||||||||||||| |||||||||||| |||||||| ||||||||||   ||| |
Sbjct  11943  CTTCTTGGTACCAGAAGGGCAGAACTATGTCTGTGTGGCCAATTATTGCAGAGTCGAATT  11884

Query  28656  GGAGTAAACTGAGGGCTCTTTCACA-CATGCTAGAGAAATGAC-TTGGGCCCTGGGAGAA  28713
              || ||||||| ||| |||||||||| | ||| |||| | |||| || |||||  ||||||
Sbjct  11883  GGGGTAAACTTAGGACTCTTTCACATC-TGCCAGAGTAGTGACTTTTGGCCC-AGGAGAA  11826

Query  28714  TTGGGGGT-TGCAGGGGATTGGTCGGAGGAA-CTTGCCTTTT-TGCTGGATTGTGCTGTA  28770
               |  |||| || || ||| ||| | ||  ||  ||| ||||| | |||||   |  | | 
Sbjct  11825  GTCAGGGTGTG-AGAGGACTGGCCTGA-TAAGTTTGTCTTTTCT-CTGGA---T--T-T-  11776

Query  28771  GAGTTTTTCCTTGTAGATTTGTCAGAATGAGCCTCCAGACCCCATC-CAGACTCCTGGAG  28829
                | |||| |||| |||||| | || |||||||| ||| ||||| | |||||||||||||
Sbjct  11775  --G-TTTT-CTTGCAGATTTATGAGGATGAGCCTACAGGCCCCA-CGCAGACTCCTGGAG  11721

Query  28830  CTGGCAGGGCAGAGCCTGATGAGGAAGCAGTTCTTGACTATCTTCACCCTGGACT-AGCT  28888
              |||||||||||||||||| || || | |||  |||| | |||| || | |||| | ||||
Sbjct  11720  CTGGCAGGGCAGAGCCTGCTGGGGGACCAGGCCTTGGCCATCTCCATCTTGGA-TGAGCT  11662

Query  28889  GCCCAGGGAGGTCT-CCCCTCTGAC-GTTCATGGAGGCCTTCAGC-ATG-AGATGTTGTG  28944
              |||||||||| ||| |||| |  || |||| |||||||||||| | | | ||| | || |
Sbjct  11661  GCCCAGGGAGCTCTTCCCCCC--ACTGTTCGTGGAGGCCTTCA-CTA-GCAGACGCTGCG  11606

Query  28945  AGGCCCTGAAGCTGATGGTGCAGGCCTGGTCCT-CCCTTCACCTCCCTCTGGGATCCCTG  29003
              |||  |||||| ||||||||||||||||| ||| ||| |  |||||||||||| ||||||
Sbjct  11605  AGGTTCTGAAGGTGATGGTGCAGGCCTGGCCCTTCCCCTG-CCTCCCTCTGGGGTCCCTG  11547

Query  29004  ATGAAGACAACTCATCTGGAGACCTTGCAAGCTGT-GCTGAA-GGGACTTGATA-CACTA  29060
              ||||||||  || ||||||||| ||| ||   ||| | || | |||| |||||  | || 
Sbjct  11546  ATGAAGACGCCTGATCTGGAGATCTTACATTATGTAG-TGGATGGGA-TTGATTGC-CT-  11491

Query  29061  G-T-GTCCCAGAAGGTTTGCCCCAGTTGAGGTGACTCAGGTGGCCTGGTGGGAAGGGTCC  29118
              | | | |||| |||||| ||||||| ||||||||| |||||||   ||    | ||| ||
Sbjct  11490  GCTTG-CCCAAAAGGTTCGCCCCAGGTGAGGTGACCCAGGTGG---GG----A-GGGCCC  11440

Query  29119  AGGCATCCAGGGAAGGGACAGCTGGCTCAGGAGGAGTGGCAGTGTGTGGGAGCTAGGGTG  29178
              |||  ||||||||    |||||||| |||| |  |     | | || || | |  |||||
Sbjct  11439  AGGTGTCCAGGGACTAAACAGCTGGGTCAG-ACAA-----A-T-TG-GGAACCCGGGGTG  11389

Query  29179  GCTCAGAGGCTTCTGATGGTACCCA-TGAGA--G--G----C---CTTGGCCATTGCCCA  29226
              || ||| ||||||||||||| || | |||||  |  |    |   |||||| ||||||||
Sbjct  11388  GCCCAGGGGCTTCTGATGGTGCC-AGTGAGAAAGCTGGGAACGTTCTTGGCTATTGCCCA  11330

Query  29227  GATCCTCTGGAAAAGGACTGCTCACCATACAGAGTCCACTGAGGAAACAGGAACCTGCTT  29286
              | |||||||| ||||||||||||||||||||| ||||||||||||||||||||||||| |
Sbjct  11329  GCTCCTCTGGGAAAGGACTGCTCACCATACAGGGTCCACTGAGGAAACAGGAACCTGCCT  11270

Query  29287  CCTTCCCAGTGGAAGGTAAAGGTACTAGAAGTGGGTAC  29324
               || |||||||||||||||||| |||||||||||||||
Sbjct  11269  GCT-CCCAGTGGAAGGTAAAGGCACTAGAAGTGGGTAC  11233


 Features flanking this part of subject sequence:
   12192 bp at 5' side: PRAME family member 16
   11293 bp at 3' side: PRAME family member 21

 Score =  431 bits (233),  Expect = 1e-116
 Identities = 334/379 (88%), Gaps = 22/379 (5%)
 Strand=Plus/Plus

Query  11772   agaaaG-CAATATAGTGAT--ATATAATGGCCATTCCAGGAATGCCAGCCAATCACAGGA  11828
               |||||| | |||| || ||  ||||||| |||||||  ||||| |||| ||||||||| |
Sbjct  190408  AGAAAGTC-ATAT-GTAATGGATATAATAGCCATTCTGGGAATTCCAGACAATCACAGAA  190465

Query  11829   AAATCTAAGTGTAATTCAGCATACTGACAAACTAAAGGGGGAAAAGCAAGGTTCCTACAA  11888
               |||||||||||||||||| || |||| |||||||||||||||||||||||||||||||||
Sbjct  190466  AAATCTAAGTGTAATTCACCACACTGGCAAACTAAAGGGGGAAAAGCAAGGTTCCTACAA  190525

Query  11889   AATGCAGAAAAGAATTGCAGAAAAATCAAATTAAATTTATCATAACATA-TTTCGGAAAC  11947
               ||||||||||||||| ||||||||||||||||||| || | |||||||| ||| ||||| 
Sbjct  190526  AATGCAGAAAAGAATAGCAGAAAAATCAAATTAAA-TT-T-ATAACATATTTTGGGAAA-  190581

Query  11948   TGAAATGTTGTATGTTGAAAACTTGCATTAAACATCAGATGTAATGGATAAACATTAGCT  12007
               |||||   |||||||| |||||||||||||||||||||||||||||||||||||||||||
Sbjct  190582  TGAAA---TGTATGTTAAAAACTTGCATTAAACATCAGATGTAATGGATAAACATTAGCT  190638

Query  12008   CCCTTCCTACTGAGATATGAAACAAGGTAAGAACCTCAGCACCTTAGGATTTGGACGCAC  12067
               |||||||||||||||||||||||||||||||| |||||||| |||||||||| || || |
Sbjct  190639  CCCTTCCTACTGAGATATGAAACAAGGTAAGACCCTCAGCAACTTAGGATTTAGAGGCCC  190698

Query  12068   GTAGGTATTTTGGTTAATAGTAAAGACTCCAGATCCAGCAGACCCAGACTGCTTAATTTA  12127
                ||||||||||||| | ||||||||||| ||||||||| |  |   || |  | ||||||
Sbjct  190699  ATAGGTATTTTGGTCAGTAGTAAAGACTTCAGATCCAG-A--CT--GA-T--T-AATTTA  190749

Query  12128   GGTTCAAAACTGGCTCAGT  12146
               |||||||||||||||||||
Sbjct  190750  GGTTCAAAACTGGCTCAGT  190768


 Features in this part of subject sequence:
   PRAME family member 21

 Score =  416 bits (225),  Expect = 3e-112
 Identities = 527/667 (79%), Gaps = 43/667 (6%)
 Strand=Plus/Minus

Query  5191    GCAGTTCTTTCCCTGAGGATCTGGGCAATGGCCAAGGCATGC-CTGAGCTTCGTCACCAG  5249
               ||||| ||||||||||||| |||||||||||||||||| | | || |||||| |||||| 
Sbjct  202517  GCAGTCCTTTCCCTGAGGAGCTGGGCAATGGCCAAGGCCT-CTCTAAGCTTCCTCACCAA  202459

Query  5250    CACCACCAGAAGACACTGGGCCATCCTTGGGATACT--TCTTTGC-C-TGACCCTGCTGT  5305
                ||||  ||||| |  |||||| ||||| |||  ||  ||  | | | |||||| |||||
Sbjct  202458  AACCATTAGAAGCCTGTGGGCCCTCCTT-GGA-CCTCCTCACTCCTCATGACCCAGCTGT  202401

Query  5306    TCTTTC-CCTGGACACCTGAGCCC-CATCTACCAGCCTTCCTGGGTCACCTCACCTGGGG  5363
               || |||   |||||||||| |||| |  | |||||||  | |||| ||||||||||| | 
Sbjct  202400  TCCTTCTGTTGGACACCTGGGCCCTC-CCCACCAGCCCACTTGGGCCACCTCACCTGAGA  202342

Query  5364    CGATCCTTCTGTGTAAGCA--GCATGTGAAGCCCTTCCAGCA-ATGCTTTTAAGGTCTCC  5420
               ||| || | || |||||||  |||  | |||||| || |||| | ||||  ||||||| |
Sbjct  202341  CGAACCCTGTGGGTAAGCAGTGCA--TCAAGCCCATCAAGCACA-GCTTGGAAGGTCT-C  202286

Query  5421    AGATG-AA-GCGTCTTCATCAGCGATCCCAGAGGGAGGCGG-GTGAAGGGCCAGGCCTGC  5477
                |  | || || | |||||||| || |||||||| |||||| | ||| ||||||||||||
Sbjct  202285  TG-GGCAAGGCCTTTTCATCAGAGACCCCAGAGGAAGGCGGAG-GAAAGGCCAGGCCTGC  202228

Query  5478    ACCATCA-CTGTCAGAGTCTGGA-AGTGTCTCCTGCTGAAGGCCTCCAGGAAGAGTGGGA  5535
               ||||||| || |||| | ||  | |||||||||||||||||||||||| ||| | |||| 
Sbjct  202227  ACCATCAGCT-TCAGGGCCT-CACAGTGTCTCCTGCTGAAGGCCTCCATGAACAATGGG-  202171

Query  5536    GG-TAGAGCTCCCTGGGCAGCTCCTCCAGGGCAGAGATGGCCAAGGGCTTGTCTCTCAGC  5594
               ||  | || ||| ||||||||||||||||||  ||||||||||||| || ||| ||||||
Sbjct  202170  GGAAAAAGTTCCGTGGGCAGCTCCTCCAGGGTGGAGATGGCCAAGGCCTCGTCCCTCAGC  202111

Query  5595    AGACTCTGCCCCGCCAGCTCCAGGAGTCTGGGTGGGG-CCTGGATGCTCATCCTGATGAA  5653
               || ||| |||||||||||||||||||||||||||| | || ||||||||||| |  ||||
Sbjct  202110  AGGCTCCGCCCCGCCAGCTCCAGGAGTCTGGGTGGAGTCC-GGATGCTCATCTTCCTGAA  202052

Query  5654    TCTGTAAGGAAAAACTCTAGAAGACAAATCCAGAGAAAAGGCATCACTTTCAGGCCAAAC  5713
               |||| || |||||  || ||| |||||||||||||||||||||||||| ||||||||| |
Sbjct  202051  TCTGCAAAGAAAAGTTCCAGAGGACAAATCCAGAGAAAAGGCATCACTCTCAGGCCAAGC  201992

Query  5714    ACAAT-CAC-CTCATCTTCTCCTAAGGCCAGTAG-CATTGCTCTGGTAGA-GGTAGAAAA  5769
                || | ||  ||||||| | || | |||||  || ||||||||||| | | ||| |||| 
Sbjct  201991  CCA-TGCAATCTCATCT-C-CC-AGGGCCAA-AGTCATTGCTCTGGCA-ATGGT-GAAAG  201939

Query  5770    ATTAC-CACTTTACCCCAATTCCACTCTGCACTTGGTGGCCACAAATCTATATTTCTGCT  5828
               |   | || ||||| ||||||| |||||| |||  ||||||||||| | |   |||||| 
Sbjct  201938  AGCCCTCAGTTTACTCCAATTCTACTCTGTACTCAGTGGCCACAAAGCCAGGCTTCTGCC  201879

Query  5829    TCTGCTG  5835
               |||||||
Sbjct  201878  TCTGCTG  201872


 Features flanking this part of subject sequence:
   18677 bp at 5' side: PRAME family member 16
   4751 bp at 3' side: PRAME family member 21

 Score =  372 bits (201),  Expect = 7e-99
 Identities = 354/422 (83%), Gaps = 34/422 (8%)
 Strand=Plus/Plus

Query  20940   catggtggcatgcatctgtagtcccagctacttgggtggctgaggtgggagaatcccttg  20999
               |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct  196893  CATGGTGGCATGCATCTGTAGTCCCAGCTATTTGGGTGGCTGAGGTGGGAGAATCCCTTG  196952

Query  21000   aatccagaagattgatgctgcagtgagccatgctcacaccagtgctgtactccagcctgg  21059
               |  || |||| |||| |||||| |||||| ||||||||||| ||||||||||||||||||
Sbjct  196953  AGCCCGGAAGTTTGAGGCTGCAATGAGCCGTGCTCACACCACTGCTGTACTCCAGCCTGG  197012

Query  21060   gcagcagagtcaga--ct-g-----t-----tga---aaaaaaaaaaTCTTAAT-CAAAC  21102
               ||| |||||| |||  || |     |       |     |||| | ||||| || |||||
Sbjct  197013  GCAACAGAGTGAGACTCTGGCCCCCTCCCCCCCACCGCCAAAATATATCTT-ATGCAAAC  197071

Query  21103   AG-TTAAA-AA-AGTGCAATTAATTGTAATCAGTAGGCAGATCCCAA---A-TTCCC--C  21153
               || ||||| || | | |||||||||| ||||||||||||||||||||   |   |||  |
Sbjct  197072  AGTTTAAACAATA-TCCAATTAATTGAAATCAGTAGGCAGATCCCAACCCACCCCCCTTC  197130

Query  21154   AAAAAAGGAGAGAAAGAGAGTTTAGAAGGCTCTACATGCTAGCATCCCATTCAGACTGTT  21213
               |||||||||||| || |||||||||||| |||||||||||||||| ||||||||||||||
Sbjct  197131  AAAAAAGGAGAG-AA-AGAGTTTAGAAGTCTCTACATGCTAGCATTCCATTCAGACTGTT  197188

Query  21214   TAATCCTACCATTGTGGTTTTGTAAGAAAAACAGTCTTAAAGATTTCCAATAATTCTCAC  21273
               ||||||||| |||| ||||||||||||||||||||||||||||||||||||||||| |||
Sbjct  197189  TAATCCTACAATTGCGGTTTTGTAAGAAAAACAGTCTTAAAGATTTCCAATAATTCCCAC  197248

Query  21274   TATGGCCATAA----ATTATCCTGGGTGTCATTTTCCCATCAACTTAAAAAGGCACGTGA  21329
                |||||| ||     |||||||||||||| ||||||||||||  ||||||| |||| |||
Sbjct  197249  AATGGCCTTATGGTCATTATCCTGGGTGTAATTTTCCCATCAGTTTAAAAATGCACATGA  197308

Query  21330   GA  21331
               ||
Sbjct  197309  GA  197310


 Features flanking this part of subject sequence:
   17052 bp at 5' side: PRAME family member 16
   6312 bp at 3' side: PRAME family member 21

 Score =  368 bits (199),  Expect = 9e-98
 Identities = 394/484 (81%), Gaps = 29/484 (5%)
 Strand=Plus/Plus

Query  16860   TTTTATAATTTTGATGTGGCCAAAGATCTCCCCACAACACTACTTTCAGGTTTTATTTTT  16919
               |||||||||||||||||||||||||||||||  |||| ||| ||||||| ||||||||||
Sbjct  195268  TTTTATAATTTTGATGTGGCCAAAGATCTCCTAACAATACTCCTTTCAGATTTTATTTTT  195327

Query  16920   CTGTCTAATGTCTGGAACAGATCAACCCCTTCCCTGCCTCACA-TCAGGACT-TGAAGG-  16976
               || | |||||||| ||||||||||| || |||||||||||||| |||||||| || ||| 
Sbjct  195328  CTCTTTAATGTCTAGAACAGATCAAACCGTTCCCTGCCTCACACTCAGGACTATGCAGGT  195387

Query  16977   CGAAATAGCAGTAAAATTCCATCAGTGTTTGTGGATTTCATGAATGAATGCAtttttttt  17036
               | | |||  |||||||||||||||||||||||||| |||||||||||||| |||||||||
Sbjct  195388  C-ACATATTAGTAAAATTCCATCAGTGTTTGTGGAGTTCATGAATGAATGAATTTTTTTT  195446

Query  17037   ------gacaaaatctccctctgtcacccagtcaggagggcaatggtgtaatcttggctc  17090
                     |||| | ||||| || ||  ||||| | |||| |||||||   |||||   |||
Sbjct  195447  TTTTTTGACAGAGTCTCCTTCAGTTGCCCAGGCTGGAGTGCAATGGCACAATCTCCACTC  195506

Query  17091   actgcaaactcagcctccagggttcaagggattctcccacctcagccgcatgagtaactg  17150
               |||| || ||| |||||| |||||||||  ||||||||||||||||| |   |||| |||
Sbjct  195507  ACTGTAACCTCTGCCTCCTGGGTTCAAGCAATTCTCCCACCTCAGCCTCCCAAGTAGCTG  195566

Query  17151   gactacaggcagccaccatcgtgcctggctaacttttctatttt-tgt-a---------g  17199
               || |||||||  |||||||| ||||  || || |||| |||||| | | |         |
Sbjct  195567  GATTACAGGCCCCCACCATCATGCCCAGCCAATTTTTGTATTTTATTTTATTTTATTTTG  195626

Query  17200   agacag-g---g--tttcaccatgtgggccaggctggtcttgaactcctgacctcaggtg  17253
               |||||| |   |  ||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct  195627  AGACAGAGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAGGTG  195686

Query  17254   atccacctaccttggcctcccaaagtgctgggattacaagtgtgagccacc-tcacctgg  17312
               ||||||| ||||| | ||||||| |||||||||||||| | |||| ||||| |  |||||
Sbjct  195687  ATCCACCCACCTTAGTCTCCCAACGTGCTGGGATTACAGGCGTGATCCACCATG-CCTGG  195745

Query  17313   ccTT  17316
               ||||
Sbjct  195746  CCTT  195749


 Features flanking this part of subject sequence:
   22280 bp at 5' side: PRAME family member 3
   10507 bp at 3' side: PRAME family member 5

 Score =  342 bits (185),  Expect = 6e-90
 Identities = 375/461 (81%), Gaps = 35/461 (7%)
 Strand=Plus/Minus

Query  2779   CTAGATTTTAGTGTCCAAGGG-CCTAGAAGAGAACATTGGATTTCTCTACCCCGCTAGGC  2837
              ||||||||||||| ||||||| || |||||| || |   | | || | | ||| |||| |
Sbjct  34472  CTAGATTTTAGTGCCCAAGGGTCC-AGAAGA-AA-A--CG-TGTC-C-ATCCCACTAGCC  34421

Query  2838   ACGCCTTCCCT-AGCAGCAAAGATGGAGCTCCAGTTCCTCAGACGGTGATGAGCCACAGG  2896
              | ||||||||| || ||||||||||||| |||| || |||||| ||  ||||||||||||
Sbjct  34420  AGGCCTTCCCTAAG-AGCAAAGATGGAGGTCCACTTTCTCAGATGGCCATGAGCCACAGG  34362

Query  2897   ACGGGCAGGGGGCGGGGCCAATGAAGATCCTCTTGGGCTGCCTGACTTCCCTTAGTGTAC  2956
              | ||||||||| |||| ||||  ||||||||||||||||||||||||||||| |||||||
Sbjct  34361  AAGGGCAGGGGACGGGACCAAAAAAGATCCTCTTGGGCTGCCTGACTTCCCTGAGTGTAC  34302

Query  2957   ACATCAACTAAGCCCGAAGTGGGGTGAA-GATCTCCCAATCGACATGAACCAAGGAAT-T  3014
              |||||| || |||||||| |||||  || ||||||||||| | |||| |||   |  | |
Sbjct  34301  ACATCAGCTCAGCCCGAATTGGGG-CAAGGATCTCCCAATTGGCATG-ACCCCTG-TTGT  34245

Query  3015   CAA-ACTCTCCTCG-GGGGCAGGATACATCTCCAGGCTTAACTTGCTCAGCCC-ACTGGT  3071
              ||| |||||||  |  ||| |||||||| |||||||| |||||||||||||||  || ||
Sbjct  34244  CAAGACTCTCC-AGACGGGAAGGATACAACTCCAGGCCTAACTTGCTCAGCCCGCCT-GT  34187

Query  3072   GTGGCACAGCAGGTCCTTCAGGGC-TTCCATAGACATG-C-AATTT-C-TGCCAAAGTAG  3126
              ||| ||||| ||||| ||||| || || ||| || | | |   ||| | ||  |||||||
Sbjct  34186  GTGACACAGAAGGTCTTTCAGAGCATT-CATGGA-A-GTCTCGTTTCCTTG--AAAGTAG  34132

Query  3127   AAGGTGGTGAGCTGGGAGCAGCGGCTCAGGCCAGGCAGGATGG-CACTGAGTTGGGAGTA  3185
              ||||||||||||||||||||| |||||||| ||||||||| || | ||||||||||||| 
Sbjct  34131  AAGGTGGTGAGCTGGGAGCAGTGGCTCAGGGCAGGCAGGA-GGACCCTGAGTTGGGAGTC  34073

Query  3186   GTGGATCTGACAGCCCTCCAA-GATGAGGGTCTTAAGAGTA  3225
               |||||||||||| |||  || | ||||||||| |||||||
Sbjct  34072  CTGGATCTGACAGTCCTTTAACG-TGAGGGTCTCAAGAGTA  34033


 Features flanking this part of subject sequence:
   24402 bp at 5' side: PRAME family member 8
   9514 bp at 3' side: PRAME family member 9

 Score =  342 bits (185),  Expect = 6e-90
 Identities = 329/396 (83%), Gaps = 20/396 (5%)
 Strand=Plus/Minus

Query  2840   GCCTTCCCTAGCAGCAAAGATGG-AGCTCCAGTTCCTCAGACGGTGATGAGCCACAGG-A  2897
              ||||||||||| ||||||||||| || |||| || |||||| ||  |||||||||||| |
Sbjct  94577  GCCTTCCCTAGGAGCAAAGATGGAAG-TCCACTTTCTCAGATGGCCATGAGCCACAGGTA  94519

Query  2898   CGGGCAGGGGGCGGGGCCAATGAAGATCCTCTTGGGCTGCCTGACTTCCCTTAGTGTACA  2957
               ||||| ||| |||| |||| |||||||||||||||||||||||||||||| ||||||| 
Sbjct  94518  -GGGCAAGGGACGGGACCAAAGAAGATCCTCTTGGGCTGCCTGACTTCCCTGAGTGTACG  94460

Query  2958   CATCAACTAAGCCCGAAGTGGGGTGAAGATCTCCCAATCGACATGAACCAAGGAATTCAA  3017
              ||||| || |||||||| |||||||| ||||||||||| ||||||| ||  | | | |||
Sbjct  94459  CATCAGCTCAGCCCGAATTGGGGTGAGGATCTCCCAATTGACATGACCCTTGTAGT-CAA  94401

Query  3018   -ACTCTCCTCG-GGGGCAGGATACATCTCCAGGCTTAACTTGCTCAGCCCAC-TGGTGTG  3074
               |||||||  | ||||||||||||| |||||||| ||||||||||||||||| || ||||
Sbjct  94400  GACTCTCCA-GAGGGGCAGGATACAACTCCAGGCCTAACTTGCTCAGCCCACGTG-TGTG  94343

Query  3075   GCACAGCAGGTCCTTCAGGGC-TTCCATAGACATG-CAATTTC--TGCCAAAGTAGAAGG  3130
               | ||||||||| ||||| || ||| || ||  |  || ||||  ||  ||||| |||||
Sbjct  94342  ACGCAGCAGGTCTTTCAGAGCATTC-ATGGAGGTCTCA-TTTCCATG--AAAGTTGAAGG  94287

Query  3131   TGGTGAGCTGGGAGCAGCGGCTCAGGCCAGGCAGGATGG-CACTGAGTTGGGAGTAGTGG  3189
              ||||||||||||| ||| |||||||| ||||||||| || | |||||||||| ||  |||
Sbjct  94286  TGGTGAGCTGGGAACAGTGGCTCAGGGCAGGCAGGA-GGACCCTGAGTTGGGGGTCCTGG  94228

Query  3190   ATCTGACAGCCCTCCAAGATGAGGGTCTTAAGAGTA  3225
              ||| ||||| |||  |||| ||||||||| ||||||
Sbjct  94227  ATCCGACAGTCCTTTAAGACGAGGGTCTTGAGAGTA  94192


 Features in this part of subject sequence:
   PRAME family member 21

 Score =  342 bits (185),  Expect = 6e-90
 Identities = 523/680 (76%), Gaps = 48/680 (7%)
 Strand=Plus/Plus

Query  28629   TGTGGCCACTTATTGCAGA-AAGGAACTGGAGTAAACTGAGGGCTCTTTCACACA-TGCT  28686
               |||||||||| | | ||||  | ||| ||||||||||||||||||||||||| || ||| 
Sbjct  201895  TGTGGCCACTGAGTACAGAGTA-GAATTGGAGTAAACTGAGGGCTCTTTCAC-CATTGCC  201952

Query  28687   AGAGAAATGACTTGGGCCCTGGGAGAATTGGGGGTTGCAGGGGATTGGTC-G-GAG-GAA  28743
               |||| |||||||| ||||||||||| | | | | ||||| ||| |||| | | ||| | |
Sbjct  201953  AGAGCAATGACTTTGGCCCTGGGAG-A-T-GAGATTGCATGGGCTTGGCCTGAGAGTG-A  202008

Query  28744   CTTGCCTTTT-TGCTGGA-TTGTGCTGTAGAGTTTTTCCTTGTAGATT-TGTCAGAATGA  28800
                 |||||||| | ||||| |||| || | ||  ||||| ||| |||||  |  || ||||
Sbjct  202009  --TGCCTTTTCT-CTGGATTTGTCCTCTGGAACTTTTCTTTGCAGATTCAGGAAG-ATGA  202064

Query  28801   GCCTCCAGACCCCATCCAGACTCCTGGAGCTGGCAGGGCAGAGCCTGATGA-GGAAGCAG  28859
               || ||| ||| ||| ||||||||||||||||||| |||| ||||||| ||| ||| | ||
Sbjct  202065  GCATCCGGACTCCACCCAGACTCCTGGAGCTGGCGGGGCGGAGCCTGCTGAGGGACG-AG  202123

Query  28860   TTCTTGACTATCTTCACCCTGGACTAGCTGCCCA-GGGA-GGTCTCCCCTCTGA-CGTTC  28916
                 |||| | |||| |||||||||  ||||||||| || |   | ||||| |  |  ||||
Sbjct  202124  GCCTTGGCCATCTCCACCCTGGAGGAGCTGCCCACGGAACTTTTTCCCC-C--ATTGTTC  202180

Query  28917   ATGGAGGCCTTCAGCATGAGATGTTGTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGTCC  28976
               |||||||||||||||| ||||   ||||||||||||||||||||||||||||||||| ||
Sbjct  202181  ATGGAGGCCTTCAGCAGGAGACACTGTGAGGCCCTGAAGCTGATGGTGCAGGCCTGG-CC  202239

Query  28977   TC-CCTTCACCTCCCTCTGGGATCCCTGATGAAGACAACTCATCTGGAGACCTTGCAAGC  29035
               |  ||| | ||| |||||||| || |||||||| |   ||   |  |||||||| |||||
Sbjct  202240  TTTCCTCCGCCTTCCTCTGGGGTCTCTGATGAAAAGGCCTTGCCCAGAGACCTTCCAAGC  202299

Query  29036   TGTGCT-GAAGGGACTTGATACACTAG-TGT-CCCAGAAGGTTTGCCCCAGTTGAGGTGA  29092
               |||||| || ||| |||||| |||| | | | |||| | |||| | | ||| ||||||| 
Sbjct  202300  TGTGCTTGATGGG-CTTGATGCACT-GCT-TACCCACAGGGTTCGTCTCAGGTGAGGTGG  202356

Query  29093   CTCAGGTGGCCTGGTGGGAAGGGTCCAGGCATCCAGG-GAAGGGACAGCTGGCTCAGGAG  29151
               | || |||| |||||||| |||| |||||  ||||   ||||| |||||||| ||| |||
Sbjct  202357  CCCAAGTGGGCTGGTGGGGAGGGCCCAGGTGTCCAACAGAAGGAACAGCTGGGTCATGAG  202416

Query  29152   GAGTG-GCAGTGTGTG-GGAG--CT-AG-GG-TGGCTCAGAGGCTTCTGATG-GTACCCA  29203
               ||||| | || ||    ||||  |  |  || |  || |  || || || || | |  | 
Sbjct  202417  GAGTGAGGAG-GTCCAAGGAGGGCCCACAGGCTT-CTAAT-GGTTT-TGGTGAGGAAGCT  202472

Query  29204   T-GAGAGGCCTTGGCCATTGCCCAGATCCTCTGGAAAAGGACTGCTCACCATACAGAGTC  29262
               | ||||||||||||||||||||||| ||||| || ||||||||||||| ||  | | |||
Sbjct  202473  TAGAGAGGCCTTGGCCATTGCCCAGCTCCTCAGGGAAAGGACTGCTCATCACCCGGGGTC  202532

Query  29263   CACTGAGGAAACAGGAACCT  29282
               ||| |||| |||||||||||
Sbjct  202533  CACCGAGGTAACAGGAACCT  202552


 Features in this part of subject sequence:
   PRAME family member 16

 Score =  337 bits (182),  Expect = 3e-88
 Identities = 372/459 (81%), Gaps = 31/459 (6%)
 Strand=Plus/Minus

Query  2779    CTAGATTTTAGTGTCC-AAGGG-CCTAGAAGAGAACATTGGATTTCTCTACCCCGCTAGG  2836
               ||||||||||||| || ||||| ||| | | |||| |  | || || | | ||| |||  
Sbjct  178277  CTAGATTTTAGTG-CCTAAGGGTCCT-G-A-AGAA-A--GCATATC-C-ATCCCACTAAT  178227

Query  2837    CACGCCTTCCCT-AGCAGCAAAGATGG-AGCTCCAGTTCCTCAGACGGTGATGAGCCACA  2894
               || |||||| || || ||||||||||| || |||| || |||||| ||  ||||||||||
Sbjct  178226  CAGGCCTTCACTAAG-AGCAAAGATGGAAG-TCCACTTTCTCAGATGGCCATGAGCCACA  178169

Query  2895    GGACGGGCAGGGGGCGGGGCCAATGAAGATCCTCTTGGGCTGCCTGACTTCCCTTAGTGT  2954
               ||| |||||||||  ||| ||||  ||||||||||||||||||||||||||||| |||||
Sbjct  178168  GGAAGGGCAGGGGATGGGACCAAAAAAGATCCTCTTGGGCTGCCTGACTTCCCTGAGTGT  178109

Query  2955    ACACATCAACTAAGCCCGAAGTGGGGTGAAGATCTCCCAATCGACATGAACCAAGGAAT-  3013
               |||||||| || |||||||| ||||| || ||||||||||| |||||| |||   |  | 
Sbjct  178108  ACACATCAGCTCAGCCCGAATTGGGGCGAGGATCTCCCAATTGACATG-ACCCCTG-TTG  178051

Query  3014    TCAA-ACTCTCCTCG-GGGGCAGGATACATCTCCAGGCTTAACTTGCTCAGCCCA-CTGG  3070
               |||| || ||||  | ||||||||||||| |||||| | |||||||||||||||| || |
Sbjct  178050  TCAAGACACTCC-AGAGGGGCAGGATACAACTCCAGACCTAACTTGCTCAGCCCACCT-G  177993

Query  3071    TGTGGCACAGCAGGTCCTTCAGGGC-TTCCATAGACATGC-AATTTCTGCCAAAGTAGAA  3128
               |||| ||||||||||| ||||| || || | | ||  | |  ||||| || |||||||||
Sbjct  177992  TGTGACACAGCAGGTCTTTCAGAGCATT-CGTGGAGGT-CTCATTTCCGCGAAAGTAGAA  177935

Query  3129    GGTGGTGAGCTGGGAGCAGCGGCTCAGGCCAGGCAGGATGG-CACTGAGTTGGGAGTAGT  3187
               |||||||||||||||||||||||||||| ||||||||| || | ||||| |||||||  |
Sbjct  177934  GGTGGTGAGCTGGGAGCAGCGGCTCAGGGCAGGCAGGA-GGACCCTGAGCTGGGAGTCCT  177876

Query  3188    GGATCTGACAGCCCTCCAA-GATGAGGGTCTTAAGAGTA  3225
               ||||||||||| |||  || | ||||| |||  ||||||
Sbjct  177875  GGATCTGACAGTCCTTTAACG-TGAGGATCTCGAGAGTA  177838


 Features flanking this part of subject sequence:
   19097 bp at 5' side: PRAME family member 8
   14977 bp at 3' side: PRAME family member 9

 Score =  333 bits (180),  Expect = 3e-87
 Identities = 214/230 (93%), Gaps = 4/230 (1%)
 Strand=Plus/Plus

Query  10657  ggattacaggcgtgagcTGCCTCACCCGGCCTTGAATGAGTGAATTCTTGACTT-CTACC  10715
              |||||||||| ||||||  |||  ||||| ||||||||| || |||||||| || | |||
Sbjct  88887  GGATTACAGGAGTGAGCCACCTTGCCCGGTCTTGAATGAATGCATTCTTGA-TTCCCACC  88945

Query  10716  CTATCCCTAACACTGTCAATTTCCTGATTCATGCAA-TTAATATGGATATCTGATATGAA  10774
              ||||||||||||||||||||||| ||||||||| || |||||||||||||||||||||||
Sbjct  88946  CTATCCCTAACACTGTCAATTTCTTGATTCATG-AACTTAATATGGATATCTGATATGAA  89004

Query  10775  TGGATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTG  10834
              ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Sbjct  89005  TGGATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAACCCCAATCAGGATTAACTG  89064

Query  10835  GGTGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGGAAGCTAG  10884
              |||||||||||||||||||||||||||||||||| |||||||||||||||
Sbjct  89065  GGTGGAGCTTCAGAAATGCAATCAGATATCACTTGTTGATTGGAAGCTAG  89114


 Features flanking this part of subject sequence:
   17040 bp at 5' side: PRAME family member 16
   6309 bp at 3' side: PRAME family member 21

 Score =  318 bits (172),  Expect = 9e-83
 Identities = 413/521 (79%), Gaps = 49/521 (9%)
 Strand=Plus/Plus

Query  25539   ACTATAAAACAATTTTATAATTTTGATGTGGCCAAAGATCTCCCAACACTACT--TT-CA  25595
               ||||||||  | ||||||||||||||||||||||||||||||| |||| ||||  || ||
Sbjct  195256  ACTATAAAGTATTTTTATAATTTTGATGTGGCCAAAGATCTCCTAACAATACTCCTTTCA  195315

Query  25596   GGTTTTATTTTTCTGTCTACTATCCAGAACAGATCAAACCCTTCCCTGCCTCAAACTCAG  25655
               | |||||||||||| | || | || ||||||||||||||| |||||||||||| ||||||
Sbjct  195316  GATTTTATTTTTCTCTTTAATGTCTAGAACAGATCAAACCGTTCCCTGCCTCACACTCAG  195375

Query  25656   GACTATATAGGTCATATATCAGTAAAATTCCATCAGTGTTTGCGGAgttcatgaatgaat  25715
               ||||||  |||||| |||| |||||||||||||||||||||| |||||||||||||||||
Sbjct  195376  GACTATGCAGGTCACATATTAGTAAAATTCCATCAGTGTTTGTGGAGTTCATGAATGAAT  195435

Query  25716   gaattctttttttttttttttttttttttttttgtgacaaagtctacct-ctgtcaccca  25774
               ||||| ||||||||||||               |  ||| ||||| ||| | ||  ||||
Sbjct  195436  GAATT-TTTTTTTTTTTT---------------G--ACAGAGTCT-CCTTCAGTTGCCCA  195476

Query  25775   gaac-ggtgtgcaatggtgcaatcttggctcactgcaaccat-tgccccctggattcaag  25832
               |  | || |||||||||  ||||||   ||||||| |||| | |||| ||||| ||||||
Sbjct  195477  GG-CTGGAGTGCAATGGCACAATCTCCACTCACTGTAACC-TCTGCCTCCTGGGTTCAAG  195534

Query  25833   cgattctcccacctcagcctcctgagtagctggattacaggcacctgccatcatgcc-ag  25891
               | ||||||||||||||||||||  |||||||||||||||||| ||  |||||||||| ||
Sbjct  195535  CAATTCTCCCACCTCAGCCTCCCAAGTAGCTGGATTACAGGCCCCCACCATCATGCCCAG  195594

Query  25892   gctaatttttgtgtttt-tgt-a---------gag-ctg-g---gg-tttcatcatgttg  25934
                | ||||||||| |||| | | |         ||| | | |   || ||||| |||||||
Sbjct  195595  CC-AATTTTTGTATTTTATTTTATTTTATTTTGAGACAGAGACAGGGTTTCACCATGTTG  195653

Query  25935   gccttgcaggtcttgatcgcctgacctcaggtgatccagccaacttggactctcaaagtg  25994
               |||  || |||||||| | ||||||||||||||||||| ||| ||| | ||| ||| |||
Sbjct  195654  GCCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCCACCCACCTTAGTCTCCCAACGTG  195713

Query  25995   cagggattacaggtgtgagccacc-tcacccggcctttaat  26034
               | ||||||||||| |||| ||||| |  || |||||| |||
Sbjct  195714  CTGGGATTACAGGCGTGATCCACCATG-CCTGGCCTT-AAT  195752


 Features flanking this part of subject sequence:
   17656 bp at 5' side: PRAME family member 16
   5986 bp at 3' side: PRAME family member 21

 Score =  309 bits (167),  Expect = 6e-80
 Identities = 192/204 (94%), Gaps = 1/204 (0%)
 Strand=Plus/Plus

Query  10682   CCG-GCCTTGAATGAGTGAATTCTTGACTTCTACCCTATCCCTAACACTGTCAATTTCCT  10740
               ||| ||||||||||| ||||||||||||||| || |||||||||| ||||||| |||| |
Sbjct  195872  CCGAGCCTTGAATGAATGAATTCTTGACTTCCACTCTATCCCTAATACTGTCACTTTCTT  195931

Query  10741   GATTCATGCAATTAATATGGATATCTGATATGAATGGATATCTGATTCAATCCATTAATC  10800
               |||||||| ||| |||||||||||||| ||||||||||||||||||||||||||||||||
Sbjct  195932  GATTCATGAAATGAATATGGATATCTGGTATGAATGGATATCTGATTCAATCCATTAATC  195991

Query  10801   TGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGCAATCAGA  10860
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  195992  TGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGCAATCAGA  196051

Query  10861   TATCACTTTTTGATTGGAAGCTAG  10884
               || |||||||||| ||||||||||
Sbjct  196052  TACCACTTTTTGACTGGAAGCTAG  196075


 Features in this part of subject sequence:
   PRAME family member 9

 Score =  303 bits (164),  Expect = 3e-78
 Identities = 515/676 (76%), Gaps = 58/676 (8%)
 Strand=Plus/Plus

Query  28631   TGGCCACTTATTGCAGA-AAGGAACTGGAGTAAACTGAGGGCTCTTTCACACA-TGCTAG  28688
               |||||||| | | ||||  | ||| ||||||||||||||| ||||||||| || ||| ||
Sbjct  103930  TGGCCACTGAGTACAGAGTA-GAATTGGAGTAAACTGAGGACTCTTTCAC-CATTGCCAG  103987

Query  28689   AGAAATGACTTGGGCCCTGGGAGAA-TTGGGGGTTGCAGGGGATTGGTC-G-GAG-GAAC  28744
               || | ||| || |||| | ||||||  | | | ||||| ||| |||| | | ||| | | 
Sbjct  103988  AGCAGTGAGTTTGGCCATAGGAGAAGAT-GAGATTGCATGGGCTTGGCCTGAGAGTG-A-  104044

Query  28745   TTGCCTTTT-TGCT-GGATTGTGCTGTAG-AGTTTTTCCTTGTAGATT--TGTCAGAATG  28799
                |||||||| | || || |||| || | | || |||||| || |||||  ||  || |||
Sbjct  104045  -TGCCTTTTCT-CTGGGTTTGTCCTCTGGAAG-TTTTCCCTGCAGATTCATG-AAG-ATG  104099

Query  28800   AGCCTCCAGACCCCATCCAGACTCCTGGAGCTGGCAGGGCAGAGCCTGATGAGGAAGC-A  28858
               ||| ||| ||| ||| |||||||||||||||| ||||||| ||||||| ||||| | | |
Sbjct  104100  AGCATCCGGACTCCACCCAGACTCCTGGAGCTTGCAGGGCGGAGCCTGCTGAGGGACCAA  104159

Query  28859   GTTCTTGACTATCTTCACCCTGGACTAGCTGCCCA-GGGAGGTCTCCCCTCTGAC-GTTC  28916
               | | ||| | || | |||||||||  |||||||||  | |  | ||||| |  || ||||
Sbjct  104160  GCT-TTGGCCATGTCCACCCTGGAGGAGCTGCCCACAGAACTTTTCCCC-C-CACTGTTC  104216

Query  28917   ATGGAGGCCTTCAGCATGAGATGTTGTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGTCC  28976
               |||||||||||||||| |||| | ||||||||||||||||||||||||||||||||| ||
Sbjct  104217  ATGGAGGCCTTCAGCAGGAGACGCTGTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGCCC  104276

Query  28977   TCCCTTCACCTCCCTCTG-GGATCC-CTGATGAAGACAACTCATCTGGAGACCTTGCAAG  29034
               | ||  | |||||||||| ||  || ||||| ||||   ||  ||||||| |||| ||||
Sbjct  104277  TTCCGCCGCCTCCCTCTGAGG--CCTCTGATAAAGATGCCTTGTCTGGAGGCCTTCCAAG  104334

Query  29035   CTGTGCT-GAAGGGACTTGATACACTAG-TGT-CCCAGAAGGTTT-GCCCCAGTTGAGGT  29090
               ||||||| || ||| |||||| |||| | | | |||| | || || | ||||| ||||||
Sbjct  104335  CTGTGCTCGATGGG-CTTGATGCACT-GCT-TACCCA-AGGGGTTCGTCCCAGGTGAGGT  104390

Query  29091   GACTCAGGTGGCCTGGTGGGAAGGGTCCAGGCATCCAGG-GAAGGGACAGCTGGCTCAGG  29149
               | | ||||||| |||||||| |||| |||||  ||||   ||||| |||||||| ||| |
Sbjct  104391  GGCCCAGGTGGGCTGGTGGGGAGGGCCCAGGTGTCCAACTGAAGGAACAGCTGGGTCATG  104450

Query  29150   AGGAGTGGCAGTGTGTGGGAGCTAGGGTGGCTCAGAGGCTTCTGATGGTACCCATGAGAG  29209
                | ||||  || | | |    | |||| || |  | || |  ||| || | ||  |||||
Sbjct  104451  TGAAGTG--AG-GAG-GCC--CAAGGG-GGATG-GTGG-TGGTGA-GGAAGCC--GAGAG  104498

Query  29210   GCCTTGGCCATTGC-CCAGATCCTCTGGAAAAGGACTGCTCACCATACAGAG-TCCACTG  29267
               | |||||||||| | |||| ||||| || |||| |||||||||||  || || |||| ||
Sbjct  104499  GACTTGGCCATT-CACCAGCTCCTCAGGGAAAGCACTGCTCACCACGCA-AGGTCCA-TG  104555

Query  29268   -AGGAAACAGGAACCT  29282
                ||| |||||||||||
Sbjct  104556  GAGGTAACAGGAACCT  104571


 Features flanking this part of subject sequence:
   31170 bp at 5' side: PRAME family member 8
   2906 bp at 3' side: PRAME family member 9

 Score =  302 bits (163),  Expect = 9e-78
 Identities = 206/227 (90%), Gaps = 2/227 (0%)
 Strand=Plus/Plus

Query  10659   attacaggcgtgagcTGCCTCACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCCTA  10718
               ||||||||  |||||  ||||||||  |||||||||| || |||||||||||||||||||
Sbjct  100960  ATTACAGGTATGAGCCACCTCACCCACCCTTGAATGAATGTATTCTTGACTTCTACCCTA  101019

Query  10719   TCCCTAACACTGTCAATTTCCTGATTCATGCAATT-AATATGGATATCTGATATGAATGG  10777
               |||||||||||||||||||| || |||| | || | ||||  ||||| ||||||||||||
Sbjct  101020  TCCCTAACACTGTCAATTTCTTGCTTCACG-AACTGAATACAGATATGTGATATGAATGG  101078

Query  10778   ATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGT  10837
               |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  101079  ATATCTGACTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGT  101138

Query  10838   GGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGGAAGCTAG  10884
               ||||||||| ||||||||||||||||  |||||||||||||||||||
Sbjct  101139  GGAGCTTCACAAATGCAATCAGATATTGCTTTTTGATTGGAAGCTAG  101185


 Features flanking this part of subject sequence:
   30008 bp at 5' side: PRAME family member 3
   2991 bp at 3' side: PRAME family member 5

 Score =  294 bits (159),  Expect = 2e-75
 Identities = 206/229 (89%), Gaps = 2/229 (0%)
 Strand=Plus/Plus

Query  10657  ggattacaggcgtgagcTGCCTCACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCC  10716
              |||||||||| ||||||  | ||  | |||||||||||| || |||||||||||||||||
Sbjct  41761  GGATTACAGGTGTGAGCCACTTCGTCTGGCCTTGAATGAATGTATTCTTGACTTCTACCC  41820

Query  10717  TATCCCTAACACTGTCAATTTCCTGATTCATGCAATT-AATATGGATATCTGATATGAAT  10775
              |||||||||||||||| ||||| || |||||| || | ||||| ||||| ||||||||||
Sbjct  41821  TATCCCTAACACTGTCGATTTCTTGCTTCATG-AAGTGAATATAGATATGTGATATGAAT  41879

Query  10776  GGATATCTGATTCAATCCATTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGG  10835
              ||| ||||||||||||||  ||||||||||||||||||||||||||||||||||||||||
Sbjct  41880  GGACATCTGATTCAATCCGGTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGG  41939

Query  10836  GTGGAGCTTCAGAAATGCAATCAGATATCACTTTTTGATTGGAAGCTAG  10884
              ||||||||||| |||||||||||||||||| |||||||||||||| |||
Sbjct  41940  GTGGAGCTTCACAAATGCAATCAGATATCATTTTTTGATTGGAAGGTAG  41988


 Features in this part of subject sequence:
   PRAME family member 5

 Score =  289 bits (156),  Expect = 7e-74
 Identities = 499/656 (76%), Gaps = 58/656 (8%)
 Strand=Plus/Plus

Query  28651  GAACTGGAGTAAACTGAGGGCTCTTTCACACA-TGCTAGAGAAATGACTTGGGCCCTGGG  28709
              ||| |||||||||||||||||| |||||| || ||| |||| | |||||| |||| ||||
Sbjct  44832  GAATTGGAGTAAACTGAGGGCTGTTTCAC-CATTGCCAGAGCAGTGACTTTGGCCTTGGG  44890

Query  28710  AGAA-TTGGGGGTTGCAGGGGATTGGTC-G-GAG-GAACTTGCCTTTT-TGCT-GGATTG  28763
              ||||  |   | ||||| ||| |||| | | ||| | |  |||||||| | || || |||
Sbjct  44891  AGAAGAT-AAGATTGCATGGGCTTGGCCTGAGAGTG-A--TGCCTTTTCT-CTGGGTTTG  44945

Query  28764  TGCTGTAG-AGTTTTTCCTTGTAGATTTGT-CAGAATGAGCCTCCAGACCCCATCCAGAC  28821
              | || | | || |||||| || ||||| ||  || |||||| ||| ||| ||| ||||||
Sbjct  44946  TCCTCTGGAAG-TTTTCCCTGCAGATTCGTGAAG-ATGAGCATCCGGACTCCACCCAGAC  45003

Query  28822  TCCTGGAGCTGGCAGGGCAGAGCCTGATGAGGAAGC-AGTTCTTGACTATCTTCACCCTG  28880
              |||||||||| ||||||| ||||||| ||||| | | ||  |||| | || | |||||||
Sbjct  45004  TCCTGGAGCTTGCAGGGCGGAGCCTGCTGAGGGACCAAG-CCTTGGCCATGTCCACCCTG  45062

Query  28881  GACTAGCTGCCCA-GGGAGGTCTCCCCTCTGAC-GTTCATGGAGGCCTTCAGCATGAGAT  28938
              ||  |||||||||  | |  | ||||| |  || |||||||||||||||||||| |||| 
Sbjct  45063  GAGGAGCTGCCCACAGAACTTTTCCCC-C-CACTGTTCATGGAGGCCTTCAGCAGGAGAC  45120

Query  28939  GTTGTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGTCCTCCCTTCACCTCCCTCTG-GGA  28997
              | ||||||||||||||||||||||||||||||||| ||| ||  | |||||||||| || 
Sbjct  45121  GCTGTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGCCCTTCCGCCGCCTCCCTCTGAGG-  45179

Query  28998  TCC-CTGATGAAGACAACTCATCTGGAGACCTTGCAAGCTGTGCT-GAAGGGACTTGATA  29055
               || ||||| ||||   ||  ||||||| |||| ||||||||||| || ||| || ||| 
Sbjct  45180  -CCTCTGATAAAGATGCCTTGTCTGGAGGCCTTCCAAGCTGTGCTCGATGGG-CTGGATG  45237

Query  29056  CACTAG-TGT-CCCAGAAGGTTTGC--CCCAGTTGAGGTGACTCAGGTGGCCTGGTGGGA  29111
              |||| | | | |||| | || || |  ||||| ||||||| | ||||||| |||||||| 
Sbjct  45238  CACT-GCT-TACCCA-AGGGGTT-CATCCCAGGTGAGGTGGCCCAGGTGGGCTGGTGGGG  45293

Query  29112  AGGGTCCAGGCATCCAGGGAAGGGAC-AGCTG-GCTCAGGAGGAGTGGCAGTGTGTGGGA  29169
              |||| ||||| |||||   || |||  ||||| | ||| ||  ||||  || | | |   
Sbjct  45294  AGGGCCCAGGTATCCAACCAAAGGAAGAGCTGTG-TCATGACAAGTG--AG-GAG-GCC-  45347

Query  29170  GCTAGGGTGGCTCAGAGGCTTCTGATGGTACCCATGAGAGGCCTTGGCCATTGC-CCAGA  29228
               | |||| || |  | || |  ||| || | ||  |||||| |||||||||| | |||| 
Sbjct  45348  -CAAGGG-GGATG-GTGG-TGGTGA-GGAAGCC--GAGAGGACTTGGCCATT-CACCAGC  45399

Query  29229  TCCTCTGGAAAAGGACTGCTCACCATACAGAG-TCCACTG-AGGAAACAGGAACCT  29282
              ||||| || |||| |||||||||||  || || |||| || ||| |||||||||||
Sbjct  45400  TCCTCAGGGAAAGCACTGCTCACCACGCA-AGGTCCA-TGGAGGTAACAGGAACCT  45453


 Features in this part of subject sequence:
   PRAME family member 13

 Score =  283 bits (153),  Expect = 3e-72
 Identities = 459/597 (76%), Gaps = 59/597 (9%)
 Strand=Plus/Minus

Query  28756   CTGGA-TTGTGC-TGTAGAG-TTTTTCCTTGTAGATTTGTCAGAATGAGCCTCCAGACCC  28812
               ||||| |||| | | ||||| ||||| |||| |||| | |||| |||||| ||||| |||
Sbjct  130966  CTGGATTTGT-CTTCTAGAGATTTTT-CTTGCAGATCTATCAGGATGAGCATCCAGGCCC  130909

Query  28813   CATCCAGACTCCTGGAGCTGGCAGGGCAGAGCCTGATGAG-GAAGCAGTTCTTGACTATC  28871
               || |||||||||||||||||||||||||||||||| |||| ||  |||  |||| | |||
Sbjct  130908  CACCCAGACTCCTGGAGCTGGCAGGGCAGAGCCTGCTGAGAGAC-CAGGCCTTGTCCATC  130850

Query  28872   TTCACCC-TGGACTAGCTGCCCAGGGAGGTCT--C-CCCTCTGACGTTCATGGAGGCCTT  28927
               | |  || ||||  |||||||||||| | |||  | ||| ||  | ||||||||||||||
Sbjct  130849  T-CTGCCATGGAGGAGCTGCCCAGGGTGCTCTATCTCCCACT--C-TTCATGGAGGCCTT  130794

Query  28928   CAGCATGAGATG-TTGTGAGGCCCTGAAGCTGATGGTGCAGGCCTGGTCCT-C-CCTTCA  28984
               | ||| ||||   ||   || | |||| | ||||||||||||||||| ||| | ||| | 
Sbjct  130793  CCGCAGGAGACACTTCC-AGACTCTGACGGTGATGGTGCAGGCCTGGCCCTTCACCTGC-  130736

Query  28985   CCTCCCTCTGGGATCCCTGATGAAGACAACT-CATCTGGAGACCTTGCAAGC-TGTGCTG  29042
               | ||||||||||||| |||||||||||  || ||| ||||||||||  |||| | |||||
Sbjct  130735  C-TCCCTCTGGGATCACTGATGAAGACG-CTTCATTTGGAGACCTTAAAAGCAT-TGCTG  130679

Query  29043   -AAGGGACTTGATACACTAG-TGTCC-CAGAAGGTTTGCCCCAGTTGAGGTGACTCAGGT  29099
                ||||| ||| |||  || | | | | ||||||| | ||||||| ||||||||| |||| 
Sbjct  130678  GAAGGG-CTTCATATGCT-GCT-TACACAGAAGGATCGCCCCAGGTGAGGTGACCCAGGA  130622

Query  29100   GGCCTGGTGGGA-AGGG-TCCAGGCATCCAGGGAAGGGACAGCTGGCTCAGG-AG-GA-G  29154
               || ||||| | | |||| || |||  ||||||||| | ||||| || ||||| || || |
Sbjct  130621  GGGCTGGTAG-ATAGGGCTC-AGGTGTCCAGGGAAAGAACAGCAGGGTCAGGCAGAGAAG  130564

Query  29155   TGGC--AGTGTGTGGGAGCTAGGGTGGCT-CAGA-GGC-TT--CTGATGGTACC-CATGA  29206
               | ||  |  ||||||   | || ||  || | || ||  ||  | || || |   || | 
Sbjct  130563  TAGCCCAA-GTGTGGCC-C-AGAGT--CTTCTGATGGTGTTGGC-GA-GGAAGATCAGG-  130512

Query  29207   GAGGCCTTGGCCATTGCCCAGATCCTCTG-GAAAAGGACTGCTCACCATACAGAGTCCAC  29265
               ||| | |||||||||| |||||||||| | |||| ||| |||||||||||||| ||||||
Sbjct  130511  GAGACTTTGGCCATTGTCCAGATCCTCAGAGAAA-GGAGTGCTCACCATACAGGGTCCAC  130453

Query  29266   TGAGGAAACAGGAACCTGCTTCCTTCC-CAGTGGAAGGTAAAGGTACTAGAAGTGGG  29321
               || || ||||| ||||||| |  || | |||||||||||||||| | ||||||||||
Sbjct  130452  TGTGGGAACAGAAACCTGCCT--TTACTCAGTGGAAGGTAAAGGGAATAGAAGTGGG  130398


 Features flanking this part of subject sequence:
   27867 bp at 5' side: PRAME family member 3
   5151 bp at 3' side: PRAME family member 5

 Score =  281 bits (152),  Expect = 1e-71
 Identities = 191/210 (90%), Gaps = 2/210 (0%)
 Strand=Plus/Plus

Query  10676  CCTCACCCGGCCTTGAATGAGTGAATTCTTGACTTCTACCCTATCCCTAACACTGTCAAT  10735
              ||||||||  |||||||||| || ||||||||||||||||||||||||| ||||||| ||
Sbjct  39620  CCTCACCCACCCTTGAATGAATGTATTCTTGACTTCTACCCTATCCCTACCACTGTCGAT  39679

Query  10736  TTCCTGATTCATGCAA-TTAATATGGATATCTGATATGAATGGATATCTGATTCAATCCA  10794
              ||| || |||||| || | ||||| ||||| ||||||||||||| |||||||||||||| 
Sbjct  39680  TTCTTGCTTCATG-AAGTGAATATAGATATGTGATATGAATGGACATCTGATTCAATCCG  39738

Query  10795  TTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCAGAAATGCA  10854
               ||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Sbjct  39739  GTAATCTGGGGAGAGCCAAAAACCCAATCAGGATTAACTGGGTGGAGCTTCACAAATGCA  39798

Query  10855  ATCAGATATCACTTTTTGATTGGAAGCTAG  10884
              ||||||||||| |||||||||||||| |||
Sbjct  39799  ATCAGATATCATTTTTTGATTGGAAGGTAG  39828


 Features flanking this part of subject sequence:
   6945 bp at 5' side: PRAME family member 8
   27151 bp at 3' side: PRAME family member 9

 Score =  272 bits (147),  Expect = 7e-69
 Identities = 187/206 (90%), Gaps = 4/206 (1%)
 Strand=Plus/Plus

Query  12892  gattgaactattgctctccagcctggcgagagagtgagactccatctccaaaaaaaaaa-  12950
              ||| |||| |||||||||||||||||| | ||||||||||||||||||||||||||||| 
Sbjct  76735  GATCGAACCATTGCTCTCCAGCCTGGCAACAGAGTGAGACTCCATCTCCAAAAAAAAAAG  76794

Query  12951  -aa--aattataagaaCATGTCCATTCACTCTCCAAAGTATCTAGGACTGGACAATTACT  13007
               ||  |||||||| |||| |||||||||||||||||||| ||| |||||||||||||| |
Sbjct  76795  CAATTAATTATAACAACACGTCCATTCACTCTCCAAAGTGTCTGGGACTGGACAATTAAT  76854

Query  13008  TGTCAGGCCCTCTTCTGTAGCACCATACACTATAGCATATATGTGGATTAatataaatac  13067
              |||||||||||||||||||||||||||||||| |||||||| ||||||||| ||||||||
Sbjct  76855  TGTCAGGCCCTCTTCTGTAGCACCATACACTAGAGCATATACGTGGATTAAAATAAATAC  76914

Query  13068  acatacaaaattcaagtatatattct  13093
              ||| ||||||| ||||||| ||||||
Sbjct  76915  ACACACAAAATGCAAGTATGTATTCT  76940


 Features flanking this part of subject sequence:
   6951 bp at 5' side: PRAME family member 8
   27154 bp at 3' side: PRAME family member 9

 Score =  235 bits (127),  Expect = 1e-57
 Identities = 176/199 (88%), Gaps = 5/199 (2%)
 Strand=Plus/Plus

Query  21571  acctttgcacaccagcctggccacagagcaagactccatctccaaaaaaTACTA-CTAA-  21628
              ||| |||| | |||||||||| ||||||  ||||||||||||||||||| |  | | || 
Sbjct  76741  ACCATTGCTCTCCAGCCTGGCAACAGAGTGAGACTCCATCTCCAAAAAA-AAAAGC-AAT  76798

Query  21629  TAATTATAACAGCATGTCCATTCACTCTCCAAAGTGTCTGGGACTGGACAATTAATTGTG  21688
              ||||||||||| || |||||||||||||||||||||||||||||||||||||||||||| 
Sbjct  76799  TAATTATAACAACACGTCCATTCACTCTCCAAAGTGTCTGGGACTGGACAATTAATTGTC  76858

Query  21689  AGGCCCTCTTCTCTAGCACCCTACGCTATAGCATATATGTGGATTAAAATAAATACACAT  21748
              |||||||||||| ||||||| ||| ||| |||||||| ||||||||||||||||||||| 
Sbjct  76859  AGGCCCTCTTCTGTAGCACCATACACTAGAGCATATACGTGGATTAAAATAAATACACAC  76918

Query  21749  A-AAAATGCAAGtatatat  21766
              | ||||||||||||| |||
Sbjct  76919  ACAAAATGCAAGTATGTAT  76937


 Features flanking this part of subject sequence:
   19259 bp at 5' side: PRAME family member 8
   14601 bp at 3' side: PRAME family member 9

 Score =  161 bits (87),  Expect = 2e-35
 Identities = 338/452 (74%), Gaps = 46/452 (10%)
 Strand=Plus/Minus

Query  7111   AAGAATTTTGAAATGAGGA-AAA-TGAAGCACAAATCAAAATTTGAGGGATGAAGTCAAA  7168
              ||||||||||||||||  | |||   |||||| |||| || |||  |  || ||| ||||
Sbjct  89490  AAGAATTTTGAAATGA-CATAAACCAAAGCAC-AATCCAATTTTTTGAAATAAAGACAAA  89433

Query  7169   ACTATATTTGGAGG-AAAAAT-CAAAACCT-ACATCTGTTTA-ATCTG--AAAAAAC-AG  7221
              |||  |||| |||| |||||| |||| | | | || |||| | ||  |  ||||||| | 
Sbjct  89432  ACTGCATTTAGAGGAAAAAATGCAAAGCTTCAAAT-TGTTCATATGAGAAAAAAAACAAA  89374

Query  7222   ACAGGAAAT-TCTCTGTGCCATTTTGGGCTG-TGTGTCACCATCCCTGACTGGCTGGCTG  7279
              |||||| ||  |||| |||||| || |||||   |||||||||||| |||  |||| |||
Sbjct  89373  ACAGGATATAACTCTATGCCATCTTAGGCTGCACTGTCACCATCCCAGACCAGCTGACTG  89314

Query  7280   CAGATTAGACGGGCATGT-TCC-TA-AGA-AG-GTGGTGACTTACCAGATCTGGACTCAG  7334
               || | ||  ||| | || ||| || ||| ||  | ||||||||||||||||||||||||
Sbjct  89313  TAGGTCAGTTGGG-A-GTGTCCTTACAGAGAGATTAGTGACTTACCAGATCTGGACTCAG  89256

Query  7335   TTTGCAGGGTGCTGGGACCTCTCAG-A-GAACCAAGCAGTAGCTCCAGGCACCAGGGCTT  7392
              |||| ||||||||  ||||||  || | |||  |||||| | ||||||||   | | |||
Sbjct  89255  TTTGGAGGGTGCTCAGACCTC--AGGAAGAAATAAGCAGGAACTCCAGGCTTGAAGACTT  89198

Query  7393   TGGGTCTGTCCTGTGCAAACTC-AGGAGCTTTTGTTGATGTTTCTAACCACA-C-CCT-C  7448
              ||||||| | |||||    ||  || ||||||| ||||  ||||||| |||| | ||  |
Sbjct  89197  TGGGTCTCTTCTGTGGGT-CTTTAGAAGCTTTTATTGACCTTTCTAATCACAACTCCCAC  89139

Query  7449   CC-CTTC--TC-A---ATC-AC--C-AGCTTCCAATCAGA-AAGTGATACCTGATTAG-A  7495
              || |  |  || |   ||| ||  | |||||||||||| | |||||||| |||||| | |
Sbjct  89138  CCACACCCCTCCACGTATCCACTGCTAGCTTCCAATCA-ACAAGTGATATCTGATT-GCA  89081

Query  7496   TC-CTGAAGTTCCACCCAGTTAATCCTGATTG  7526
              |  |||||| ||||||||||||||||||||||
Sbjct  89080  TTTCTGAAGCTCCACCCAGTTAATCCTGATTG  89049


 Features in this part of subject sequence:
   PRAME family member 21

 Score =  154 bits (83),  Expect = 3e-33
 Identities = 239/311 (76%), Gaps = 23/311 (7%)
 Strand=Plus/Minus

Query  4702    TACAGCACAGGTGTACTAAACC-TCTCCTTTGGTAAACCCACCGGAAGAGGTATCTCAGG  4760
               |||||||||||||||||||||| || ||| || |  |||||  | |||||| |  | | |
Sbjct  204084  TACAGCACAGGTGTACTAAACCTTC-CCTCTGCTTGACCCATAGAAAGAGGCAGGTGAAG  204026

Query  4761    CATTCATCCTGGGGT-AT-TTCCTTGAGGCAGATGTCTATGAACACCTTCAAGGGCTGGT  4818
                ||||||||  | ||  | || ||||||||| | ||||||||||||  |||||||||| |
Sbjct  204025  TATTCATCC-AGAGTCCTGTT-CTTGAGGCAAAGGTCTATGAACACAGTCAAGGGCTGCT  203968

Query  4819    GCT-CTCCCATCCTTGGACAGTCCT-CTGCT-GTCTGCCTCTTAC-TCATGGCCTCTGGG  4874
               | | ||| ||||||||||||||||| |  || || |  || || | ||||||| | ||| 
Sbjct  203967  G-TCCTCTCATCCTTGGACAGTCCTGC-ACTGGT-TTTCTGTT-CATCATGGCATTTGGT  203912

Query  4875    GAGGA-GGACAGGGCCCTGGATTCAGACCATATGGCCCAGAAATTCTCATC-AACATCCC  4932
                || |   || ||||| ||| ||||||||| |    |||||| |||||| |  |||||| 
Sbjct  203911  AAGCACCTAC-GGGCCATGGCTTCAGACCAAACCATCCAGAAGTTCTCA-CTGACATCCT  203854

Query  4933    GCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAAAGTA-AGGCAGAGGCTCAGAA  4991
               | |||||||||||||||||||||||||||||| ||  ||| || | | ||||||| ||||
Sbjct  203853  GTAAATCCAGCACTTGAAGTTTCCACCTCCTGAGGAAAAA-TAGAAG-AGAGGCTGAGAA  203796

Query  4992    CTTTGAAGGAC  5002
                ||| ||||||
Sbjct  203795  -TTT-AAGGAC  203787


 Features flanking this part of subject sequence:
   17789 bp at 5' side: PRAME family member 16
   5620 bp at 3' side: PRAME family member 21

 Score =  139 bits (75),  Expect = 8e-29
 Identities = 337/455 (74%), Gaps = 52/455 (11%)
 Strand=Plus/Minus

Query  7111    AAGAATTTTGAAATGAGGA-AAA-TGAAGCACAAATCAAAATTTGAGGGATGAAGTCAAA  7168
               ||||||| ||||| ||  | |||   |||||||||||||| |||  |  |||||| ||||
Sbjct  196441  AAGAATTCTGAAAGGA-TATAAACCAAAGCACAAATCAAATTTTTTGAAATGAAGACAAA  196383

Query  7169    ACTATATTTGGAGGAAAAA-TCAAAACCT-ACATCTGTT--T---AATCTGAAAAAACAG  7221
               |||  ||||  |||||||| ||||| | | | || ||||  |   ||    |||||| ||
Sbjct  196382  ACTGCATTTAAAGGAAAAAGTCAAAGCTTCAAAT-TGTTCATACAAAAAAAAAAAAAAAG  196324

Query  7222    ACAGGAAAT-TCTCTGTGCCATTTTGGGCTGTGTGTCACCATCCCTGACTGGCTGGCTGC  7280
               |||||| ||  |||||||||    |  ||    |||||||||||| ||| ||||| ||| 
Sbjct  196323  ACAGGATATAACTCTGTGCC----T--GC--ACTGTCACCATCCCAGACCGGCTGACTGT  196272

Query  7281    AGATTAGACGGGCATGT-TCC-TA-AGAAG-GT-GGTGACTTACCAGATCTGGACTCAGT  7335
               || | ||| ||| | || ||| || || ||  | || |||||||||||||||||||||||
Sbjct  196271  AGGTCAGATGGG-A-GTGTCCTTACAG-AGATTAGG-GACTTACCAGATCTGGACTCAGT  196216

Query  7336    TTGCAGGGTGCTGGGACCTCTCAG-AGAA-CCAAGCAGTAGCTCCAGGCACCAGGGCTTT  7393
               ||||||||||||  ||||||  || | || |||||||| | ||||||||   | | ||||
Sbjct  196215  TTGCAGGGTGCTCAGACCTC--AGGAAAAACCAAGCAGAAACTCCAGGCTTGAAGACTTT  196158

Query  7394    GGGTCTGTCCTGTGCAAACTC-AGGAGCTTTTGTTGATGTTTCTAACCACA-C-CCT-CC  7449
               |||||| |||||||    ||  || ||||||| ||||  ||||||| |||| | ||  ||
Sbjct  196157  GGGTCTCTCCTGTGGGT-CTTTAGAAGCTTTTATTGACCTTTCTAATCACAACTCCCACC  196099

Query  7450    C-CTTC--TC-A---ATCA-C--C-AGCTTCCAATCAGAAAGTGATACCTGATTAG-ATC  7497
               | |  |  || |   |||  |  | |||||||| ||| |||||| || |||||| | || 
Sbjct  196098  CACGCCCCTCCACGTATCCGCTGCTAGCTTCCAGTCAAAAAGTGGTATCTGATT-GCATT  196040

Query  7498    -CTGAAGTTCCACCCAGTTAATCCTGATTGAGTTT  7531
                |||||| |||||||||||||||||||||| ||||
Sbjct  196039  TCTGAAGCTCCACCCAGTTAATCCTGATTGGGTTT  196005


 Features in this part of subject sequence:
   PRAME family member 5

 Score =  124 bits (67),  Expect = 2e-24
 Identities = 213/281 (75%), Gaps = 20/281 (7%)
 Strand=Plus/Minus

Query  4702   TACAGCACAGGTGTACTAAACCTCTCCTTTGGTAAACCCACCGGAA-GAGGTATCTCAGG  4760
              ||||||||||||||| |||| || |||| || |  |||||   ||| |||| |  | |||
Sbjct  46191  TACAGCACAGGTGTAGTAAATCTTTCCTCTGCTTGACCCA-TAGAAGGAGGCAGGTGAGG  46133

Query  4761   CATTCATCCTGGGGT-AT-TTCCTTGAGGCAGATG-TCTATGAACACCTTCAAGGGCTGG  4817
               ||||||||  | ||  | || |||||| || | | |||| ||||||  |||||||||| 
Sbjct  46132  TATTCATCC-AGAGTCCTGTT-CTTGAGCCA-AAGTTCTACGAACACAGTCAAGGGCTGC  46076

Query  4818   TGCT-CTCCCATCCTTGGACAGTCCT-CTGCT-GTCTGCCTCTTACTCATGGCCTCTG-G  4873
              || | ||| ||||||||||||||||| |  || || |   | || ||| |||| | || |
Sbjct  46075  TG-TCCTCTCATCCTTGGACAGTCCTGC-ACTGGT-TTTTTGTTCCTCTTGGCAT-TGAG  46020

Query  4874   GGAGGAGGACA-GGGCCCTGGATTCAGACCATATGGCCCAGAAATTCTCATCA-ACATCC  4931
              | || |   || ||||| | | ||||||||| |    |||||| |||||| || ||||||
Sbjct  46019  GAAGCA-CCCATGGGCCATAGCTTCAGACCAAACCATCCAGAAGTTCTCA-CAGACATCC  45962

Query  4932   CGCAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGTAAA  4972
               | |||||||||||||||||||||||||||||||||| |||
Sbjct  45961  TGTAAATCCAGCACTTGAAGTTTCCACCTCCTGTGGGAAAA  45921


 Features flanking this part of subject sequence:
   30011 bp at 5' side: PRAME family member 21

 Score =  111 bits (60),  Expect = 2e-20
 Identities = 107/129 (82%), Gaps = 6/129 (4%)
 Strand=Plus/Minus

Query  6458    CCTATAATCCTAGCTACTCTGGAGGCAGAGGAAGAAGAATCACTTGAATCCC-GGAGGCA  6516
               ||| |||||| ||||||| ||||||| |||| || ||||||||||||| ||| || ||||
Sbjct  237097  CCTGTAATCCCAGCTACTATGGAGGCTGAGGCAGGAGAATCACTTGAA-CCCAGGGGGCA  237039

Query  6517    GTGTTTTCAGTGAGCTGAA-CTCA-ACACCCTGCCCTTCAGCCTGGGTGACAGAGTGAGA  6574
               | | || ||||| ||  ||  |||  | |||||| || ||||||||||||||||||||||
Sbjct  237038  GAGGTTGCAGTGGGC-CAAGATCATGC-CCCTGCACTCCAGCCTGGGTGACAGAGTGAGA  236981

Query  6575    CTCCATCTC  6583
               |||||||||
Sbjct  236980  CTCCATCTC  236972


 Features flanking this part of subject sequence:
   5292 bp at 5' side: PRAME family member 3
   27779 bp at 3' side: PRAME family member 5

 Score = 89.8 bits (48),  Expect = 8e-14
 Identities = 125/161 (77%), Gaps = 9/161 (5%)
 Strand=Plus/Plus

Query  6435   TTAGCCAGGTGTGGTGGTGCAGT-CCTATAATCCTAGCTACTCT-GGAGGCAGAGGAAGA  6492
              ||||||||||||| ||| ||| | ||| |||||| |||| || | |||||| |||| || 
Sbjct  17045  TTAGCCAGGTGTGTTGGGGCA-TGCCTGTAATCCCAGCTGCT-TGGGAGGCTGAGGCAGG  17102

Query  6493   AGAATCACTTGAATC-CCGGAGGCAGTGTTTTCAGTGAGCTGAACTCAACACC-CTGCCC  6550
              |||||  |||||| |   |||||| |   || ||||||||  ||  |  ||||  ||| |
Sbjct  17103  AGAATTGCTTGAA-CAAGGGAGGCGGACATTGCAGTGAGC-CAAGACTGCACCATTGCAC  17160

Query  6551   TTCAGCCTGGGTGACAGAGTGAGACTCCATCTCAGAACAAG  6591
              | || ||||||||||||||||||||||||||||| || |||
Sbjct  17161  TCCACCCTGGGTGACAGAGTGAGACTCCATCTCAAAA-AAG  17200


>gi|37549741|ref|NT_079483.1|Hs1_79548 Homo sapiens chromosome 1 genomic contig
Length=172789

 Score =  130 bits (70),  Expect = 5e-26
 Identities = 111/130 (85%), Gaps = 6/130 (4%)
 Strand=Plus/Plus

Query  6458   CCTATAATCCTAGCTACTCTGGAGGCAGAGGAAGAAGAATCACTTGAATCCCGG-AGGCA  6516
              |||||||||| |||||||| |||||| |||| || ||||||||||||| ||||| || | 
Sbjct  36212  CCTATAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAA-CCCGGAAGACG  36270

Query  6517   GTGTTTTCAGTGAGCTGA-ACTCAACACC-CTGCCCTTCAGCCTGGGTGACAGAGTGAGA  6574
              | | || ||||||||||| | || ||||| || | || ||||||||||||||||||||||
Sbjct  36271  GAGGTTGCAGTGAGCTGAGA-TC-ACACCACTACACTCCAGCCTGGGTGACAGAGTGAGA  36328

Query  6575   CTCCATCTCA  6584
              ||||||||||
Sbjct  36329  CTCCATCTCA  36338



  Database: human build 35 genome database (reference assembly only)
    Posted date:  Jul 26, 2007  3:20 PM
  Number of letters in database: -1,428,911,948
  Number of sequences in database:  378

Lambda     K      H
    1.33    0.621     1.12 
Gapped
Lambda     K      H
    1.28    0.460    0.850 
Matrix: blastn matrix:1 -2
Gap Penalties: Existence: 0, Extension: 0
Number of Sequences: 378
Number of Hits to DB: 121892
Number of extensions: 216
Number of successful extensions: 216
Number of sequences better than 0.01: 10
Number of HSP's better than 0.01 without gapping: 0
Number of HSP's gapped: 216
Number of HSP's successfully gapped: 212
Length of query: 29324
Length of database: 2866055344
Length adjustment: 34
Effective length of query: 29290
Effective length of database: 2866042492
Effective search space: 83946384590680
Effective search space used: 83946384590680
A: 0
X1: 23 (44.2 bits)
X2: 32 (59.1 bits)
X3: 54 (99.7 bits)
S1: 23 (43.6 bits)
S2: 29 (54.7 bits)




BioPerl-1.007002/t/data/a_thaliana.blastn000444000766000024      3641613155576321 20210 0ustar00cjfieldsstaff000000000000BLASTN 2.2.1 [Apr-13-2001]

Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.
RID: 1012577175-3730-28291
Query= 
         (60 letters)

Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
or phase 0, 1 or 2 HTGS sequences) 
           1,083,200 sequences; 4,677,375,331 total letters




                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gb|AY052359.1| Arabidopsis thaliana At2g17400 mRNA, complete cds       96   3e-18
gb|AC002329.2|AC002329 Arabidopsis thaliana chromosome II sectio...    96   3e-18
gb|AF132318.1|AF132318 Buchnera aphidicola phosphoribosyl anthra...    42   0.040
gb|AC024791.1| Caenorhabditis elegans cosmid Y47G6A, complete se...    36   2.5  
gb|AC017078.8| Homo sapiens BAC clone RP11-457N9 from 2, complet...    36   2.5  
gb|AC005046.3|AC005046 Homo sapiens BAC clone CTB-13F3 from 7q22...    36   2.5  
gb|AC006017.2|AC006017 Homo sapiens PAC clone RP5-981O7 from 7q3...    36   2.5  
dbj|AP001519.1|AP001519 Bacillus halodurans genomic DNA, section...    36   2.5  
gb|AC095064.3| Homo sapiens chromosome 4 clone RP11-620C21, comp...    34   9.7  
gb|AC003029.3| Homo sapiens Chromosome 12q24 PAC RP3-462E2 (Rosw...    34   9.7  
gb|AC079248.5| Homo sapiens BAC clone RP11-24J11 from 2, complet...    34   9.7  
gb|AC093865.2| Homo sapiens chromosome 2 clone RP11-560C24, comp...    34   9.7  
gb|AC010202.6|AC010202 Homo sapiens 12q BAC RP11-210L7 (Roswell ...    34   9.7  
gb|AC017118.3|AC017118 Genomic sequence for Arabidopsis thaliana...    34   9.7  
emb|AL355520.8|AL355520 Human DNA sequence from clone RP4-595C2 ...    34   9.7  
emb|AL137879.15|AL137879 Human DNA sequence from clone RP11-153O...    34   9.7  
gb|AC006395.1|AC006395 Homo sapiens PAC clone RP3-394H4 from Xq2...    34   9.7  
gb|AE000650.1|AE000650 Helicobacter pylori 26695 section 128 of ...    34   9.7  
gb|AC006924.3|AC006924 Homo sapiens, clone hRPK.32_A_1, complete...    34   9.7  
gb|AC006266.1|AC006266 Arabidopsis thaliana BAC F1K3 from chromo...    34   9.7  
gb|U32797.1|U32797 Haemophilus influenzae Rd section 112 of 163 ...    34   9.7  
emb|AJ286341.1|HIM286341 Human immunodeficiency virus type 1 pro...    34   9.7  
emb|AL161561.2|ATCHRIV61 Arabidopsis thaliana DNA chromosome 4, ...    34   9.7  
emb|AL161508.2|ATCHRIV20 Arabidopsis thaliana DNA chromosome 4, ...    34   9.7  
emb|AL035356.1|ATF22K18 Arabidopsis thaliana DNA chromosome 4, B...    34   9.7  
emb|AJ132676.1|MMU132676 Mus musculus IgVk gh33r pseudogene            34   9.7  
emb|AJ132673.1|MMU132673 Mus musculus IgVk gd33r pseudogene            34   9.7  
emb|AJ132672.1|MMU132672 Mus musculus IgVk gc33r pseudogene            34   9.7  
emb|Z74955.1|SCYOR047C S.cerevisiae chromosome XV reading frame ...    34   9.7  
emb|Z74954.1|SCYOR046C S.cerevisiae chromosome XV reading frame ...    34   9.7  
gb|U28135.1|SCU28135 Saccharomyces cerevisiae DEAD-Box Protein 5...    34   9.7  

ALIGNMENTS
>gb|AY052359.1| Arabidopsis thaliana At2g17400 mRNA, complete cds
          Length = 2826

 Score = 95.6 bits (48), Expect = 3e-18
 Identities = 58/60 (96%), Gaps = 1/60 (1%)
 Strand = Plus / Plus

                                                                       
Query: 1   aggaatgctgtttaattggaatcgtacaatggagaatttgacggaaatagaatcaacgat 60
           |||||||||||||||||||||||  |||||||||||||||||||||||||||||||||||
Sbjct: 154 aggaatgctgtttaattggaatca-acaatggagaatttgacggaaatagaatcaacgat 212


>gb|AC002329.2|AC002329 Arabidopsis thaliana chromosome II section 100 of 255 of the complete
             sequence. Sequence from clones T23A1, F5J6, MJB20
          Length = 76170

 Score = 95.6 bits (48), Expect = 3e-18
 Identities = 58/60 (96%), Gaps = 1/60 (1%)
 Strand = Plus / Plus

                                                                         
Query: 1     aggaatgctgtttaattggaatcgtacaatggagaatttgacggaaatagaatcaacgat 60
             |||||||||||||||||||||||  |||||||||||||||||||||||||||||||||||
Sbjct: 60659 aggaatgctgtttaattggaatca-acaatggagaatttgacggaaatagaatcaacgat 60717


>gb|AF132318.1|AF132318 Buchnera aphidicola phosphoribosyl anthranilate transferase (trpD),
           phosphoribosyl anthranilate isomerase/indoleglycerol
           phosphate synthetase fusion (trpC/F), beta subunit of
           tryptophan synthetase (trpB), and alpha subunit of
           tryptophan synthetase (trp>
          Length = 5383

 Score = 42.1 bits (21), Expect = 0.040
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                
Query: 35  aatttgacggaaatagaatca 55
           |||||||||||||||||||||
Sbjct: 536 aatttgacggaaatagaatca 556


>gb|AC024791.1| Caenorhabditis elegans cosmid Y47G6A, complete sequence
          Length = 194322

 Score = 36.2 bits (18), Expect = 2.5
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                                
Query: 34     gaatttgacggaaataga 51
              ||||||||||||||||||
Sbjct: 193876 gaatttgacggaaataga 193859


>gb|AC017078.8| Homo sapiens BAC clone RP11-457N9 from 2, complete sequence
          Length = 193979

 Score = 36.2 bits (18), Expect = 2.5
 Identities = 24/26 (92%)
 Strand = Plus / Plus

                                        
Query: 3      gaatgctgtttaattggaatcgtaca 28
              ||||| ||||||| ||||||||||||
Sbjct: 142900 gaatgttgtttaaatggaatcgtaca 142925


>gb|AC005046.3|AC005046 Homo sapiens BAC clone CTB-13F3 from 7q22, complete sequence
          Length = 219436

 Score = 36.2 bits (18), Expect = 2.5
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                               
Query: 13    taattggaatcgtacaat 30
             ||||||||||||||||||
Sbjct: 46649 taattggaatcgtacaat 46666


>gb|AC006017.2|AC006017 Homo sapiens PAC clone RP5-981O7 from 7q34-q36, complete sequence
          Length = 162556

 Score = 36.2 bits (18), Expect = 2.5
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                                
Query: 13     taattggaatcgtacaat 30
              ||||||||||||||||||
Sbjct: 114940 taattggaatcgtacaat 114923


>dbj|AP001519.1|AP001519 Bacillus halodurans genomic DNA, section 13/14
          Length = 303650

 Score = 36.2 bits (18), Expect = 2.5
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                               
Query: 30    tggagaatttgacggaaa 47
             ||||||||||||||||||
Sbjct: 28875 tggagaatttgacggaaa 28858


>gb|AC095064.3| Homo sapiens chromosome 4 clone RP11-620C21, complete sequence
          Length = 87943

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                              
Query: 12    ttaattggaatcgtaca 28
             |||||||||||||||||
Sbjct: 42346 ttaattggaatcgtaca 42362


>gb|AC003029.3| Homo sapiens Chromosome 12q24 PAC RP3-462E2 (Roswell Park Cancer
             Institute Human PAC library) complete sequence
          Length = 137830

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                              
Query: 24    gtacaatggagaatttg 40
             |||||||||||||||||
Sbjct: 71491 gtacaatggagaatttg 71507


>gb|AC079248.5| Homo sapiens BAC clone RP11-24J11 from 2, complete sequence
          Length = 128535

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                               
Query: 6      tgctgtttaattggaat 22
              |||||||||||||||||
Sbjct: 111999 tgctgtttaattggaat 111983


>gb|AC093865.2| Homo sapiens chromosome 2 clone RP11-560C24, complete sequence
          Length = 186218

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                               
Query: 5      atgctgtttaattggaa 21
              |||||||||||||||||
Sbjct: 113514 atgctgtttaattggaa 113530


>gb|AC010202.6|AC010202 Homo sapiens 12q BAC RP11-210L7 (Roswell Park Cancer Institute Human
             BAC Library) complete sequence
          Length = 170004

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                              
Query: 4     aatgctgtttaattgga 20
             |||||||||||||||||
Sbjct: 95294 aatgctgtttaattgga 95310


>gb|AC017118.3|AC017118 Genomic sequence for Arabidopsis thaliana BAC F6N18 from chromosome I,
             complete sequence
          Length = 92219

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                              
Query: 14    aattggaatcgtacaat 30
             |||||||||||||||||
Sbjct: 84400 aattggaatcgtacaat 84416


>emb|AL355520.8|AL355520 Human DNA sequence from clone RP4-595C2 on chromosome 1q24.1-25.3
             Contains ESTs, STSs and GSSs. Contains the 3' part of the
             gene for two isoforms of the KIAA0351 protein and the gene
             for angiopoietin Y1, complete sequence [Homo sapiens]
          Length = 157575

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                              
Query: 5     atgctgtttaattggaa 21
             |||||||||||||||||
Sbjct: 80465 atgctgtttaattggaa 80481


>emb|AL137879.15|AL137879 Human DNA sequence from clone RP11-153O23 on chromosome 13, complete
             sequence [Homo sapiens]
          Length = 85149

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                              
Query: 25    tacaatggagaatttga 41
             |||||||||||||||||
Sbjct: 41783 tacaatggagaatttga 41799


>gb|AC006395.1|AC006395 Homo sapiens PAC clone RP3-394H4 from Xq23, complete sequence
          Length = 72291

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                              
Query: 1     aggaatgctgtttaatt 17
             |||||||||||||||||
Sbjct: 40047 aggaatgctgtttaatt 40063


>gb|AE000650.1|AE000650 Helicobacter pylori 26695 section 128 of 134 of the complete genome
          Length = 11043

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                             
Query: 36   atttgacggaaatagaa 52
            |||||||||||||||||
Sbjct: 1772 atttgacggaaatagaa 1756


>gb|AC006924.3|AC006924 Homo sapiens, clone hRPK.32_A_1, complete sequence
          Length = 165633

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                              
Query: 4     aatgctgtttaattgga 20
             |||||||||||||||||
Sbjct: 11360 aatgctgtttaattgga 11344


>gb|AC006266.1|AC006266 Arabidopsis thaliana BAC F1K3 from chromosome IV near 21 cM, complete
             sequence
          Length = 105680

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 20/21 (95%)
 Strand = Plus / Minus

                                  
Query: 20    aatcgtacaatggagaatttg 40
             ||||||||||||||| |||||
Sbjct: 52077 aatcgtacaatggagtatttg 52057


>gb|U32797.1|U32797 Haemophilus influenzae Rd section 112 of 163 of the complete genome
          Length = 10274

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                             
Query: 26   acaatggagaatttgac 42
            |||||||||||||||||
Sbjct: 2447 acaatggagaatttgac 2431


>emb|AJ286341.1|HIM286341 Human immunodeficiency virus type 1 proviral env gene for gp160,
            genomic RNA, isolate M2424/4, clone 1
          Length = 2586

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 20/21 (95%)
 Strand = Plus / Plus

                                 
Query: 7    gctgtttaattggaatcgtac 27
            |||||||||||||||| ||||
Sbjct: 1176 gctgtttaattggaatagtac 1196


>emb|AL161561.2|ATCHRIV61 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 61
          Length = 198402

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                               
Query: 44     gaaatagaatcaacgat 60
              |||||||||||||||||
Sbjct: 146009 gaaatagaatcaacgat 146025


>emb|AL161508.2|ATCHRIV20 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 20
          Length = 196517

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 20/21 (95%)
 Strand = Plus / Minus

                                   
Query: 20     aatcgtacaatggagaatttg 40
              ||||||||||||||| |||||
Sbjct: 180658 aatcgtacaatggagtatttg 180638


>emb|AL035356.1|ATF22K18 Arabidopsis thaliana DNA chromosome 4, BAC clone  F22K18 (ESSAII project)
          Length = 125803

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                               
Query: 44     gaaatagaatcaacgat 60
              |||||||||||||||||
Sbjct: 102901 gaaatagaatcaacgat 102885


>emb|AJ132676.1|MMU132676 Mus musculus IgVk gh33r pseudogene
          Length = 737

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                            
Query: 13  taattggaatcgtacaa 29
           |||||||||||||||||
Sbjct: 317 taattggaatcgtacaa 301


>emb|AJ132673.1|MMU132673 Mus musculus IgVk gd33r pseudogene
          Length = 813

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                            
Query: 13  taattggaatcgtacaa 29
           |||||||||||||||||
Sbjct: 318 taattggaatcgtacaa 302


>emb|AJ132672.1|MMU132672 Mus musculus IgVk gc33r pseudogene
          Length = 736

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                            
Query: 13  taattggaatcgtacaa 29
           |||||||||||||||||
Sbjct: 318 taattggaatcgtacaa 302


>emb|Z74955.1|SCYOR047C S.cerevisiae chromosome XV reading frame ORF YOR047c
          Length = 3461

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                            
Query: 24  gtacaatggagaatttg 40
           |||||||||||||||||
Sbjct: 473 gtacaatggagaatttg 489


>emb|Z74954.1|SCYOR046C S.cerevisiae chromosome XV reading frame ORF YOR046c
          Length = 2310

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                             
Query: 24   gtacaatggagaatttg 40
            |||||||||||||||||
Sbjct: 1605 gtacaatggagaatttg 1621


>gb|U28135.1|SCU28135 Saccharomyces cerevisiae DEAD-Box Protein 5 (DBP5) gene, complete cds
          Length = 3696

 Score = 34.2 bits (17), Expect = 9.7
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                             
Query: 24   gtacaatggagaatttg 40
            |||||||||||||||||
Sbjct: 1212 gtacaatggagaatttg 1196


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
  or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Jan 31, 2002 11:56 PM
  Number of letters in database: 382,408,035
  Number of sequences in database:  1,083,200
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 117,267
Number of Sequences: 1083200
Number of extensions: 117267
Number of successful extensions: 7699
Number of sequences better than 10.0: 31
length of query: 60
length of database: 4,677,375,331
effective HSP length: 19
effective length of query: 41
effective length of database: 4,656,794,531
effective search space: 190928575771
effective search space used: 190928575771
T: 0
A: 30
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 17 (34.2 bits)

BioPerl-1.007002/t/data/acefile.ace.1000555000766000024    123373413155576321 17171 0ustar00cjfieldsstaff000000000000AS 53 114

CO Contig1 796 1 1 U
atxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccacg
cgtccggcaacaagcacaccacctgttgaaGCAGAAGAGAGTAAGAATAA
GAAGCCACGATTGGCATAGAGTCAGCTGAGTGTCGCACCCACCACCGCAT
TTACTTTTCTTTTTAAAATCTTTGTTTTCATTTGCTTTCTGTCTTTTTGT
TTCCAACTTCGTATTTTAGACTCCATGTGGTGGTGCATGTTTTACTTATG
AATCCAAGTTCTTCTCTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAaggGGggxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxgggggacgggaaaaaccct
ggggttccccaacttaatcgccttgcagaaaatccccttttccccagttg
gggtaaaaccaaaaaggcccccaccgatcgcccttcccaacagttgccca
ccctgaatggcaaaggggaccccccctgtaccggcccattaagcgcgggg
ggtgtgggggttccccccagggggaccgttacatttgccagggccctagc
gcccgctcctttggtttttttcccttcttttttcgccacgttcgccggtt
ttccccgtcaagctttaaatggggggccccctatagggttccgatt

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 46 42 42 39 39 37 42 42 43 37 40 35 39 39 39 35 35 35 35 35
 35 37 37 35 39 35 35 35 35 40 40 39 39 39 35 35 35 39 39 40 39 35 35 35 35 35 39 39 40 51 51 40 35 35 35 35 35 35 40 40 40 40 40 40 35 35 38 38 38 39
 39 35 35 35 35 39 40 56 56 56 56 46 46 46 46 40 40 51 56 56 56 51 51 51 51 51 51 51 51 51 51 43 35 35 35 35 35 43 51 51 41 51 51 51 51 51 56 56 56 43
 43 43 43 43 43 43 43 43 43 43 43 43 45 56 51 51 51 51 43 43 43 43 43 43 45 51 51 51 56 56 56 56 43 43 43 43 43 43 56 56 51 51 43 43 43 43 43 43 51 51
 56 56 56 56 56 56 56 51 45 45 45 45 45 51 51 51 51 51 51 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56
 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56
 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 46 33 13 13 12 31 29 14 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2261r U 1
BS 1 796 LL2261r

RD LL2261r 796 0 6
atxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccacg
cgtccggcaacaagcacaccacctgttgaaGCAGAAGAGAGTAAGAATAA
GAAGCCACGATTGGCATAGAGTCAGCTGAGTGTCGCACCCACCACCGCAT
TTACTTTTCTTTTTAAAATCTTTGTTTTCATTTGCTTTCTGTCTTTTTGT
TTCCAACTTCGTATTTTAGACTCCATGTGGTGGTGCATGTTTTACTTATG
AATCCAAGTTCTTCTCTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAaggGGggxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxgggggacgggaaaaaccct
ggggttccccaacttaatcgccttgcagaaaatccccttttccccagttg
gggtaaaaccaaaaaggcccccaccgatcgcccttcccaacagttgccca
ccctgaatggcaaaggggaccccccctgtaccggcccattaagcgcgggg
ggtgtgggggttccccccagggggaccgttacatttgccagggccctagc
gcccgctcctttggtttttttcccttcttttttcgccacgttcgccggtt
ttccccgtcaagctttaaatggggggccccctatagggttccgatt

QA 81 571 46 796
DS CHROMAT_FILE: LL2261r PHD_FILE: LL2261r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:32 2000

RT{
LL2261r matchElsewhereLowQual phrap 710 758 000919:094547
}

RT{
LL2261r matchElsewhereLowQual phrap 664 695 000919:094547
}

RT{
LL2261r matchElsewhereLowQual phrap 599 614 000919:094547
}

RT{
LL2261r matchElsewhereLowQual phrap 572 589 000919:094547
}

RT{
LL2261r matchElsewhereLowQual phrap 529 553 000919:094547
}

RT{
LL2261r matchElsewhereLowQual phrap 492 525 000919:094547
}

CO Contig2 787 1 1 U
atxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccacgcg
tccgcccacgcgtccgcaacaaccaataaacggtttATTTCGCTCAGCAC
TCAACCGCAATGGCCGCCTCAACAATGGCTCTCTCCTCCCCTGCCTTCGC
CGGAAAGGCCGTCAAGCTTTCCCCAGCAGCATCAGAAGTCCTTGGAAGCG
GCCGTGTGACAATGAGGAAGACCGTAGCCAAGCCAAAGGGCCCATCAGGC
AGCCCATGGTACGGATCCGAGAGAGTCAAGTACTTGGGCCCATTCTCCGG
CGAGCCACCGAGCTACCTTACCGGAGAGTTCCCCGGAGACTACGGATGGG
ACACCGCAGGTCTCTCAGCCGATCCCGAGACGTTCGCGAGGAACCGTGAG
CTAGAAGTTATCCACTGCAGGTGGGCCATGCTCGGAGCCCTAGGCTGCGT
CTTCCCGGAGCTGTTGGCCAGGAACGGAGTCAAGTTCGGAGAGGCGGTTT
GGTTCAAGGCCGGTTCGCAGATCTTCAGCGAAGGAGGACTTGATTACTTG
GGAAACCCTAGCTTGGTTCACGCTCAGAGCATCTTGgCTATTTGGGCTAC
TCAAGTGATCTTGATGGGAGCCGTTGAAGGTTACAGAGTCGCAGGAGATG
GGCCGTTGGGAGAGGCCGAGGACTTGCttTACCCAGGTggCAGCTTTGAC
ccgTTGGGTTTGgctACTGACccagaggccTTCGCGGAGTTGAaggTGAA
GgAGATCaagaaacggaGattggctatgttCtctAtg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 25 29 32 34 34 34 34 34 40 46 39 39 39
 39 39 40 45 35 35 35 35 35 40 46 40 40 34 34 34 34 34 35 40 40 51 40 40 40 40 39 39 39 39 39 39 40 40 40 40 40 40 40 40 39 39 39 39 39 35 35 35 35 35
 35 35 51 51 56 46 40 39 39 39 35 40 40 51 39 39 39 39 39 39 51 51 51 51 51 51 40 40 40 40 40 40 45 45 45 51 40 40 40 40 40 40 56 51 56 51 39 39 35 35
 35 35 35 35 45 45 51 51 51 40 40 40 45 45 51 56 56 56 39 38 35 35 35 35 43 43 45 45 45 45 51 51 51 51 51 51 56 46 45 41 41 41 45 46 56 56 56 56 56 51
 45 45 45 45 45 56 56 56 56 45 45 45 45 45 45 45 45 43 43 43 43 43 43 43 45 51 56 51 51 43 43 43 43 43 43 43 51 51 51 51 51 51 51 45 45 45 45 45 43 43
 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 45 45 51 51 45 45 51 51 43 43 51 43 43 36 36 36 36 36 36 43 43 43 51 56 56 43 43
 43 43 43 43 43 43 43 43 45 51 51 51 51 51 51 56 51 51 51 51 51 51 51 45 45 45 45 43 43 43 43 43 43 43 43 43 43 43 43 43 56 56 45 45 45 45 45 45 51 45
 45 45 45 45 45 51 51 51 51 51 51 51 45 45 45 45 40 40 43 46 46 51 51 51 45 45 45 45 40 40 45 45 45 40 45 45 45 45 45 51 51 56 45 40 40 40 40 40 40 45
 45 51 51 51 51 45 45 45 45 45 45 45 51 51 51 45 45 45 45 45 45 51 45 45 45 45 45 51 45 45 45 45 45 45 45 45 45 45 45 51 51 46 46 43 42 42 46 48 56 56
 56 56 51 51 51 51 51 45 56 56 42 46 46 51 37 37 37 37 37 40 46 51 51 56 56 56 45 45 45 37 37 37 40 38 40 40 40 40 40 40 45 42 37 37 37 40 40 40 51 56
 51 56 46 46 46 40 40 40 44 40 40 40 40 34 32 25 29 32 32 32 34 34 34 33 37 35 48 40 40 40 48 48 48 48 34 26 19 25 27 27 29 39 48 46 39 31 35 35 35 35
 35 37 40 40 40 51 42 51 56 56 56 56 56 56 56 56 56 48 46 44 32 32 26 26 25 29 29 29 29 21 21 21 29 32 40 48 40 40 29 29 27 27 25 25 34 37 40 40 40 32
 34 32 32 32 25 25 25 29 29 48 40 40 27 25 22 25 27 29 25 22 22 25 25 22 24 29 29 19 19 23 27 27 27 32 25 22 22 25 19 18 24 25 27 29 25 32 20 25 21 21
 12 15 19 21 21 29 29 37 34 34 22 22 15 19 18 20 20 29 27 27 25 18 19 14 13 8 8 8 11 15 24 27 27 25 25 20 22 29 29 29 25 28 25 19 19 15 24 24 20 20
 22 19 25 26 26 29 24 19 9 10 10 9 9 9 10 18 19 22 19 15 19 18 12 17 14 13 13 16 11 16 23 17 18 14 21 18 0

AF LL2330r U 1
BS 1 787 LL2330r

RD LL2330r 787 0 0
atxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccacgcg
tccgcccacgcgtccgcaacaaccaataaacggtttATTTCGCTCAGCAC
TCAACCGCAATGGCCGCCTCAACAATGGCTCTCTCCTCCCCTGCCTTCGC
CGGAAAGGCCGTCAAGCTTTCCCCAGCAGCATCAGAAGTCCTTGGAAGCG
GCCGTGTGACAATGAGGAAGACCGTAGCCAAGCCAAAGGGCCCATCAGGC
AGCCCATGGTACGGATCCGAGAGAGTCAAGTACTTGGGCCCATTCTCCGG
CGAGCCACCGAGCTACCTTACCGGAGAGTTCCCCGGAGACTACGGATGGG
ACACCGCAGGTCTCTCAGCCGATCCCGAGACGTTCGCGAGGAACCGTGAG
CTAGAAGTTATCCACTGCAGGTGGGCCATGCTCGGAGCCCTAGGCTGCGT
CTTCCCGGAGCTGTTGGCCAGGAACGGAGTCAAGTTCGGAGAGGCGGTTT
GGTTCAAGGCCGGTTCGCAGATCTTCAGCGAAGGAGGACTTGATTACTTG
GGAAACCCTAGCTTGGTTCACGCTCAGAGCATCTTGgCTATTTGGGCTAC
TCAAGTGATCTTGATGGGAGCCGTTGAAGGTTACAGAGTCGCAGGAGATG
GGCCGTTGGGAGAGGCCGAGGACTTGCttTACCCAGGTggCAGCTTTGAC
ccgTTGGGTTTGgctACTGACccagaggccTTCGCGGAGTTGAaggTGAA
GgAGATCaagaaacggaGattggctatgttCtctAtg

QA 81 786 44 787
DS CHROMAT_FILE: LL2330r PHD_FILE: LL2330r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:21 2000

CO Contig3 770 1 1 U
atttcgagctcggtacccggggatcctctagagtcgacctgcaggcxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxGCCTGGGGTGCCTAATGAGTGAG
CTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAA
ACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGC
GGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCG
CTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAA
TACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCA
AAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTT
TTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAA
GTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCC
CCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGG
ATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGgCGCtTTCTCATAGCT
CACGCTGTAggTATCTCAGttCGGTGTAggTCGTtCGCTCCAAGCTGGGC
TGTgTGCACGAACCCCCCGt

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 41 45 45 45 51 51 56 36 36 36 36 36 36 41 41 46 56 56 42 46 42 38 36
 43 36 36 36 43 43 36 36 40 40 43 41 41 41 43 43 43 43 43 43 43 43 43 43 43 43 36 36 36 36 39 43 36 36 36 36 36 36 43 46 42 42 42 46 46 46 46 42 42 41
 41 41 45 45 45 45 45 43 43 39 40 40 36 38 43 43 43 43 40 43 41 41 41 45 43 43 41 45 39 43 36 39 38 36 36 43 43 43 43 43 43 36 40 41 41 41 38 38 43 39
 43 43 46 43 43 43 43 43 43 43 56 56 51 43 43 43 43 43 43 43 43 43 36 36 36 36 36 36 43 43 43 43 43 36 36 36 36 36 36 36 43 43 36 39 43 43 43 43 43 43
 43 43 43 43 43 45 51 51 51 51 51 51 51 45 45 45 45 43 40 40 38 38 41 45 43 43 43 51 45 45 45 45 45 40 38 38 40 40 38 41 43 46 45 45 45 45 45 45 56 56
 40 43 38 40 38 35 42 43 42 46 41 41 41 41 41 42 41 41 41 41 41 45 50 56 56 56 41 40 40 40 40 35 41 41 42 42 42 44 44 56 42 43 43 50 50 44 47 47 50 50
 56 56 50 42 45 45 40 35 35 42 50 44 44 42 40 40 40 37 37 37 35 42 40 40 40 40 40 40 50 50 43 43 44 46 40 39 35 35 35 39 39 35 35 35 39 40 45 45 45 45
 56 56 51 51 46 46 40 37 37 40 45 45 40 40 51 51 51 51 56 56 56 40 39 35 35 35 39 40 51 56 56 44 47 56 56 56 56 56 42 42 40 40 40 40 40 37 40 42 42 44
 44 42 42 45 37 37 40 45 45 40 35 35 35 35 35 37 37 40 40 45 40 40 40 40 40 37 37 35 35 35 35 42 51 45 40 35 35 35 35 35 37 40 40 40 36 34 40 40 36 40
 48 40 34 32 32 29 40 30 32 32 32 33 46 48 56 40 46 33 40 34 32 32 32 29 29 29 34 40 40 37 29 22 25 27 27 29 39 39 33 28 28 29 29 32 29 27 27 25 26 32
 34 32 32 36 34 40 40 40 33 39 29 29 29 35 46 40 40 40 40 40 32 48 31 29 25 29 31 34 29 29 40 31 29 22 19 25 25 25 19 22 29 40 40 40 40 44 40 40 40 40
 33 31 29 29 29 29 27 27 25 18 18 25 29 27 29 29 27 25 21 17 19 25 20 22 27 28 29 24 19 19 25 29 29 25 18 24 27 27 25 22 22 22 20 25 27 34 29 29 29 29
 32 24 24 18 25 20 29 25 27 24 24 25 29 40 40 40 29 29 24 16

AF pgemr U 1
BS 1 770 pgemr

RD pgemr 770 0 1
atttcgagctcggtacccggggatcctctagagtcgacctgcaggcxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxGCCTGGGGTGCCTAATGAGTGAG
CTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAA
ACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGC
GGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCG
CTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAA
TACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCA
AAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTT
TTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAA
GTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCC
CCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGG
ATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGgCGCtTTCTCATAGCT
CACGCTGTAggTATCTCAGttCGGTGTAggTCGTtCGCTCCAAGCTGGGC
TGTgTGCACGAACCCCCCGt

QA 178 770 178 770
DS CHROMAT_FILE: pgemr PHD_FILE: pgemr.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:41 2000

RT{
pgemr matchElsewhereHighQual phrap 178 318 000919:094547
}

CO Contig4 637 2 79 U
tTtttCGCATAAA*TGAAAAATA*GTTTAAAACGgc*GAAAAATAAACAA
TAATCAGGACTTCAACAATATTTATAAGAAAAAAAAAACCAAAAAAAATG
AAGCAGCGACCAAAACATAATATAATATTTTTTGCTTAAGGACAAAAAAA
CAGCATCACAAGAATCCTAAAGAGAAATAAAAGACACAGATAGAACTAAA
GTACACAGAGACTCTTGACACATCCAGAAGGTTCCAAAGAACCACATAAC
AACATATAGTTCCAATTCCCATATCAGCTAGGGAAAGAGACTTGTAAACA
GACTCACCACACCACGAAGAAGGGAGCAGAGCCCTTAGAAGCACTTCCTG
TGAACAATGGATGGACCTGACTCATCGTACTCTCCCTTTGAAATCCACAT
CTGTTGGAAAGTGCTGAGGGATGCAAGGATAGATCCTCCAATCCAGACAC
TGTATTTCCTCTCAGGAGGAGCCACCACCTTGATCTTCATGCTGCTAGGC
GCAAGCGCCGTGATCTCCTTGCTCATACGATCAGCGATTCCTGGGAACAT
GGTTGAACCACCACTGAGGACGATGTTTCCATACAGATCCTTCCTGATAT
CGACATCACACTTCCCCACGCGTCCGCGGACGCGTGG

BQ
 0 27 18 18 19 24 25 27 27 25 22 22 25 32 32 42 47 44 42 31 29 27 29 27 41 47 43 44 44 44 36 31 13 18 25 25 55 55 55 61 55 55 69 62 67 65 65 74 66 69
 69 69 75 72 72 71 69 55 50 38 35 33 36 28 43 47 55 80 86 88 82 82 82 77 77 84 84 78 82 90 90 88 75 65 62 60 64 83 87 88 90 90 80 71 71 77 77 69 69 66
 64 66 61 64 70 70 90 90 90 90 90 90 82 81 82 74 74 72 72 74 74 74 74 77 88 83 90 90 90 90 90 81 79 77 75 75 71 88 88 87 86 90 90 90 90 90 81 75 75 75
 72 72 82 88 83 83 80 90 87 82 79 77 79 82 84 85 90 90 90 90 90 90 90 90 88 88 90 90 90 90 90 88 88 88 90 90 90 90 90 88 86 86 86 86 80 77 82 82 82 82
 90 90 90 90 90 90 90 85 85 82 78 82 86 86 90 82 82 82 87 86 90 90 90 90 90 90 90 90 90 84 84 89 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 85 85 85 85 77 77 83 90 90 90 90 90 90 90 90 90 90 90 90 90 87 81 80 76 77 86 86 90 90 90 90 90 90 90 90 88 88 71 71 67 76 76 87 88 89 86 86 80 80
 77 80 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 85 84 84 84 84 84 80 85 84 84 86 74 74 74 74 73 85 78 78 71 70 82 85 90 71 71 62 69 69 77
 82 82 82 77 78 72 88 81 88 90 90 90 90 90 90 90 90 85 82 82 78 85 85 78 71 70 76 75 77 81 83 88 88 88 90 90 90 90 90 90 90 85 86 85 82 82 78 80 80 80
 88 88 90 90 87 73 73 57 57 62 72 74 82 85 90 90 90 83 83 79 79 78 78 90 87 87 87 87 87 82 88 90 90 90 90 90 90 90 90 89 87 80 80 80 74 79 67 69 57 73
 68 79 84 85 87 78 78 78 85 88 90 90 90 84 77 76 80 75 84 84 90 90 90 90 90 90 84 84 84 88 88 84 86 90 88 79 80 80 70 70 66 60 60 64 67 68 68 64 64 64
 67 64 67 62 59 59 50 50 50 67 68 83 90 90 90 82 75 71 71 71 71 75 74 80 82 82 82 81 76 72 67 64 69 70 72 77 72 72 73 79 82 82 79 79 77 72 68 70 64 62
 69 81 75 70 77 83 83 90 90 76 71 71 72 78 79 73 78 74 74 68 67 66 85 61 61 70 75 80 90 90 90 85 85 85 80 90 82 82 84 79 79 79 77 77 73 64 61 65 65 69
 71 82 74 76 59 68 63 67 61 67 73 72 66 60 55 59 59 57 54 64 58 58 57 57 56 63 75 71 49 49 49 34 34 35

AF LL2260r C -108
AF LL2260f U 0
BS 1 9 LL2260r
BS 10 10 LL2260f
BS 11 16 LL2260r
BS 17 21 LL2260f
BS 22 26 LL2260r
BS 27 35 LL2260f
BS 36 54 LL2260r
BS 55 55 LL2260f
BS 56 61 LL2260r
BS 62 68 LL2260f
BS 69 69 LL2260r
BS 70 71 LL2260f
BS 72 73 LL2260r
BS 74 76 LL2260f
BS 77 81 LL2260r
BS 82 90 LL2260f
BS 91 93 LL2260r
BS 94 98 LL2260f
BS 99 100 LL2260r
BS 101 109 LL2260f
BS 110 115 LL2260r
BS 116 126 LL2260f
BS 127 129 LL2260r
BS 130 131 LL2260f
BS 132 143 LL2260r
BS 144 144 LL2260f
BS 145 146 LL2260r
BS 147 149 LL2260f
BS 150 160 LL2260r
BS 161 164 LL2260f
BS 165 165 LL2260r
BS 166 168 LL2260f
BS 169 172 LL2260r
BS 173 175 LL2260f
BS 176 218 LL2260r
BS 219 221 LL2260f
BS 222 223 LL2260r
BS 224 224 LL2260f
BS 225 228 LL2260r
BS 229 234 LL2260f
BS 235 242 LL2260r
BS 243 248 LL2260f
BS 249 258 LL2260r
BS 259 262 LL2260f
BS 263 273 LL2260r
BS 274 274 LL2260f
BS 275 282 LL2260r
BS 283 284 LL2260f
BS 285 322 LL2260r
BS 323 323 LL2260f
BS 324 338 LL2260r
BS 339 339 LL2260f
BS 340 352 LL2260r
BS 353 353 LL2260f
BS 354 390 LL2260r
BS 391 394 LL2260f
BS 395 407 LL2260r
BS 408 410 LL2260f
BS 411 455 LL2260r
BS 456 456 LL2260f
BS 457 461 LL2260r
BS 462 463 LL2260f
BS 464 468 LL2260r
BS 469 470 LL2260f
BS 471 471 LL2260r
BS 472 473 LL2260f
BS 474 479 LL2260r
BS 480 482 LL2260f
BS 483 484 LL2260r
BS 485 486 LL2260f
BS 487 526 LL2260r
BS 527 537 LL2260f
BS 538 542 LL2260r
BS 543 548 LL2260f
BS 549 554 LL2260r
BS 555 557 LL2260f
BS 558 591 LL2260r
BS 592 596 LL2260f
BS 597 637 LL2260r

RD LL2260r 791 0 0
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxctttttttttttttttttttttttttttttttttnn
nntttnntntTtttCGCATAAA*TGAAAAATA*GTTTAAAAcggc*GAAA
AATAAACAATAATCAGGACTTcagcaATATTTATAAGAAAAAAAAAACCA
AAAAAAATGAAGCAGCGACCAAAACATAATATAATATTTTTTGCTTAAGG
ACAAAAAAACAGCATCACAAGAATCCTAAAGAGAAATAAAAGACACAGAT
AGAACTAAAGTACACAGAGACTCTTGACACATCCAGAAGGTTCCAAAGAA
CCACATAACAACATATAGTTCCAATTCCCATATCAGCTAGGGAAAGAGAC
TTGTAAACAGACTCACCACACCACGAAGAAGGGAGCAGAGCCCTTAGAAG
CACTTCCTGTGAACAATGGATGGACCTGACTCATCGTACTCTCCCTTTGA
AATCCACATCTGTTGGAAAGTGCTGAGGGATGCAAGGATAGATCCTCCAA
TCCAGACACTGTATTTCCTCTCAGGAGGAGCCACCACCTTGATCTTCATG
CTGCTAGGCGCAAGCGCCGTGATCTCCTTGCTCATACGATCAGCGATTCC
TGGGAACATGGTTGAACCACCACTGAGGACGATGTTTCCATACAGATCCT
TCCTGATATCGACATCACACTTCCCCACGCGTCCGCGGACGCGTGGxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxagt

QA 111 746 110 746
DS CHROMAT_FILE: LL2260r PHD_FILE: LL2260r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:27 2000

RD LL2260f 792 0 0
nctttccgcATaaactgAAAAAtaggtTTAAAACGgcggaAAAATAAACA
ATAATCAGGACTTCAACAATATTTATAAGAAAAAAAAAACCAAAAAAAAT
GAAGCAGCGACCAAAACATAATATAATATTTTTTGCTTAAGGACAAAAAA
ACAGCATCACAAGAATCCTAAAGAGAAATAAAAGACACAGATAGAACTAA
AGTACACAGAGACTCTTGACACATCCAGAAGGTTCCAAAGAACCACATAA
CAACATATAGTTCCAATTCCCATATCAGCTAGGGAAAGAGACTTGTAAAC
AGACTCACCACACCACGAAGAAGGGAGCAGAGCCCTTAGAAGCACTTCCT
GTGAACAATGGATGGACCTGACTCATCGTACTCTCCCTTTGAAATCCACA
TCTGTTGGAAAGTGCTGAGGGATGCAAGGATAGATCCTCCAATCCAGACA
CTGTATTTCCTCTCAGGAGGAGCCACCACCTTGATCTTCATGCTGCTAGG
CGCAAGCGCCGTGATCTCCTTGCTCATACGATCAGCGATTCCTGGGAACA
TGGTTGAACCACCACTGAGGACGATGTTTCCATACAGATCCTTCCTGATA
TCGACATCACACTTCCCCACGCGTCCGCGGACGCGTgGxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

QA 40 638 3 638
DS CHROMAT_FILE: LL2260f PHD_FILE: LL2260f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:50 2000

CO Contig5 605 2 63 U
CTtTTTTTTTTTTTTTTTTtttTtttttTTTTTTTTTTTTTTTTTTtttt
ttTTTTTTTTTTTTTTTTTTTTTTTGAGGTTAACTTGATAGATTCAAATG
GATATGAGAACTTTGATGAATCAAGACAGTGAGAGAGATGGGTGATAGAT
ACATTGTTGAGTTTATACAAGAATGGACAGAAAAAAAAAAAGAAACATGT
TCACCATTTCCAGAAAACATTGGAACCACACTTGAACTTGTCTTTGCCTT
CGCATTCCAACGCCAAGTCTTCTGAGATAAATGGGACTTTCTTTTGCTTG
GCAAGATCTTGGCAACCAGTGAAATTCTCAGGGAACTTGCAGCTTCCGAA
TTGGACAGTAAACGCTCTCGCAAAGTTTGCTCCACTTGTTGCCAATCTCT
TCTTATCATTAAGCTCTTTGTTGGCTTTGCTCTTCTCGAGGTATTCATCG
AAGACGCCAGCATTAGCAGAAGCAGAAACAGCAGCAGAGGAGAAGAGTGT
AGCGGCTAAGACAACCATTGCGGATCTTCGTCCATTAACATCATCACCAC
CAACTCTTTGAGCTGCTTTGATCACCGGAAGCGTTTGTTTCTTCCGGACG
CGTGG

BQ
 22 21 16 25 27 27 56 56 47 42 33 44 42 30 30 30 33 33 31 18 18 18 25 19 18 17 17 17 25 25 26 26 26 42 48 42 42 42 42 42 43 44 44 30 30 20 19 14 14 14
 14 18 28 29 33 42 44 47 48 48 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 45 40 40 39 39 39 44 50 55 62 57 56 55 66 67 69 66 71 76 78 76 80 80 71 70
 74 71 71 72 81 81 75 71 71 71 71 77 81 80 85 85 80 80 80 80 80 80 81 81 74 71 55 61 62 68 69 80 85 85 85 86 90 89 90 90 86 90 90 90 90 87 87 80 80 86
 90 90 90 90 90 90 90 80 82 82 82 82 82 90 90 90 90 90 90 90 90 90 90 88 81 83 81 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 82 82 85 85 90 90 90 90 90 90 90 90 86 86 86 90 86 86 86 78 78 78 83 83 83 89 90 90 90 90 80 80
 80 80 80 80 90 90 90 90 81 78 78 78 78 78 80 86 84 83 81 85 86 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 86 86
 90 86 86 85 90 90 90 90 90 84 84 89 89 88 88 90 90 90 90 90 87 90 90 90 90 90 90 87 90 90 90 90 89 90 89 83 79 86 79 79 79 79 83 83 83 88 90 90 90 90
 90 90 90 90 86 86 83 81 86 79 86 81 86 86 86 86 86 86 86 86 86 86 86 84 90 90 81 86 90 90 90 90 90 90 90 87 87 90 90 89 90 89 89 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 84 88 83 83 86 90 90 90 90 90 88 82 80 80 80 82 88 90 90 90 90 90 90 90 90 90 90 90 90 90 85 80 80 80 85 90 90 86 85 85 86
 87 83 70 70 70 70 73 74 80 90 86 86 86 81 90 85 85 77 77 71 73 71 84 71 82 90 90 85 75 75 75 75 75 75 77 77 76 88 90 90 85 85 85 70 70 62 59 56 66 63
 52 52 52 57 56 64 58 70 58 61 69 80 86 86 90 88 88 72 77 79 90 90 90 90 90 90 83 83 77 69 65 65 75 57 57 61 64 64 67 73 80 85 90 90 90 85 85 90 90 90
 90 84 84 86 86 80 80 80 82 84 82 82 80 79 90 90 79 79 82 85 80 80 76 85 83 80 79 70 57 56 62 58 57 57 53 60 60 62 62 62 59 60 64 68 69 76 76 80 83 49
 49 49 34 33 32

AF LL2263r C -139
AF LL2263f U 71
BS 1 81 LL2263r
BS 82 83 LL2263f
BS 84 144 LL2263r
BS 145 145 LL2263f
BS 146 182 LL2263r
BS 183 188 LL2263f
BS 189 265 LL2263r
BS 266 268 LL2263f
BS 269 281 LL2263r
BS 282 283 LL2263f
BS 284 290 LL2263r
BS 291 293 LL2263f
BS 294 298 LL2263r
BS 299 303 LL2263f
BS 304 304 LL2263r
BS 305 305 LL2263f
BS 306 311 LL2263r
BS 312 321 LL2263f
BS 322 322 LL2263r
BS 323 324 LL2263f
BS 325 328 LL2263r
BS 329 333 LL2263f
BS 334 337 LL2263r
BS 338 342 LL2263f
BS 343 346 LL2263r
BS 347 350 LL2263f
BS 351 354 LL2263r
BS 355 356 LL2263f
BS 357 358 LL2263r
BS 359 361 LL2263f
BS 362 362 LL2263r
BS 363 373 LL2263f
BS 374 374 LL2263r
BS 375 376 LL2263f
BS 377 377 LL2263r
BS 378 378 LL2263f
BS 379 410 LL2263r
BS 411 411 LL2263f
BS 412 414 LL2263r
BS 415 415 LL2263f
BS 416 436 LL2263r
BS 437 439 LL2263f
BS 440 446 LL2263r
BS 447 447 LL2263f
BS 448 449 LL2263r
BS 450 451 LL2263f
BS 452 452 LL2263r
BS 453 475 LL2263f
BS 476 478 LL2263r
BS 479 486 LL2263f
BS 487 507 LL2263r
BS 508 508 LL2263f
BS 509 517 LL2263r
BS 518 529 LL2263f
BS 530 540 LL2263r
BS 541 542 LL2263f
BS 543 545 LL2263r
BS 546 547 LL2263f
BS 548 558 LL2263r
BS 559 562 LL2263f
BS 563 570 LL2263r
BS 571 572 LL2263f
BS 573 605 LL2263r

RD LL2263r 791 0 0
ttaagttgggtaacgccagggttttxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxCTtTTTTTTT
TTTTTTTTTtttTtttttTTTTTTTTTTTTTTTTTTttttttTTTTTTTT
TTTTTTTTTTTTTTTGAGGTTAACTTGATAGATTCAAATGGATATGAGAA
CTTTGATGAATCAAGACAGTGAGAGAGATGGGTGATAGATACATTGTTGA
GTTTATACAAGAATGGACAGAAAAAAAAAAAGAAACATGTTCACCATTTC
CAGAAAACATTGGAACCACACTTGAACTTGTCTTTGCCTTCGCATTCCAA
CGCCAAGTCTTCTGAGATAAATGGGACTTTCTTTTGCTTGGCAAGATCTT
GGCAACCAGTGAAATTCTCAGGGAACTTGCAGCTTCCGAATTGGACAGTA
AACGCTCTCGCAAAGTTTGCTCCACTTGTTGCCAATCTCTTCTTATCATT
AAGCTCTTTGTTGGCTTTGCTCTTCTCGAGGTATTCATCGAAGACGCCAG
CATTAGCAGAAGCAGAAACAGCAGCAGAGGAGAAGAGTGTAGCGGCTAAG
ACAACCATTGCGGATCTTCGTCCATTAACATCATCACCACCAACTCTTTG
AGCTGCTTTGATCACCGGAAGCGTTTGTTTCTTCCGGACGCGTGGxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxatt

QA 141 745 141 745
DS CHROMAT_FILE: LL2263r PHD_FILE: LL2263r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:41 2000

RD LL2263f 788 0 3
nctaaaagGTTAACTTGATAGATTCAAATGGATATGAGAACTTTGATGAA
TCAAGACAGTGAGAGAGATGGGTGATAGATACATTGTTGAGTTTATACAA
GAATGGACAGAAAAAAAAAAAGAAACATGTTCACCATTTCCAGAAAACAT
TGGAACCACACTTGAACTTGTCTTTGCCTTCGCATTCCAACGCCAAGTCT
TCTGAGATAAATGGGACTTTCTTTTGCTTGGCAAGATCTTGGCAACCAGT
GAAATTCTCAGGGAACTTGCAGCTTCCGAATTGGACAGTAAACGCTCTCG
CAAAGTTTGCTCCACTTGTTGCCAATCTCTTCTTATCATTAAGCTCTTTG
TTGGCTTTGCTCTTCTCGAGGTATTCATCGAAGACGCCAGCATTAGCAGA
AGCAGAAACAGCAGCAGAGGAGAAGAGTGTAGCGGCTAAGACAACCATTG
CGGATCTTCGTCCATTAACATCATCACCACCAACTCTTTGAGCTGCTTTG
ATCACCGGAAGCGTTTGTTTCTTCCGGACGCGtgGxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxcgcatagc
ctcgggtgcctaatgagcgagccacctcacattattgcgctgcgctcact
gcccgtttccagccgggaaacccggcgtgccacctgca

QA 14 535 7 535
DS CHROMAT_FILE: LL2263f PHD_FILE: LL2263f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:04 2000

RT{
LL2263f chimera phrap 698 788 000919:094547
}

RT{
LL2263f matchElsewhereLowQual phrap 735 754 000919:094547
}

RT{
LL2263f matchElsewhereLowQual phrap 704 722 000919:094547
}

CO Contig6 1092 2 38 U
cttttatatttcaattgcataaccatatatttatgcacaccacgtacttg
cgtatgtgcacaattgcataaaagacattaCAATCCAATTTTTCTCGCAA
TTATATAAACGTACAAGAAGAAACATGATCATTGTACGTACGTCTTGTAC
ATGGTATTATTTCAAGCATGACACTCGATTGGTGGGACAGGATACCTTGA
CTTGTCGGTACAATAATCATATACCATATGGTTTACTCTAACCCAACGGT
AACGTCGAGCTTCCACGGCGTTAAGTGACTGATAAGCGTAGCCTTCCCAC
CAATTGTGAGGGTTCGATGGACAATTGGTGGGTCCAGGAACAGGACAGCC
TTCGATGTCGAAATCTTTGTAATAAGCATAAAAAGGAGCTTTGCTCCAAT
CAATTTTCTCTAATCCTCCACGTGTCGCCCAATCATCGGCTTCCCATAGT
GTTGAGTAAACTCCCATGGGTTGTGATGTTGGGTAGGCTATGTTCTTGGC
TTGGTTGTTTTTGTATTCTCTTATTGGTACATCGTCCACGTAAAAAACAA
TGTGTTTGTGTGACCAAAGGATACTGTAAGTGTGGAAATCCAAAGATGGG
TCGAACCAAAGATTAACCCTTTGTTCTCTATCTCCTTTGCCATGAGCAAA
TATGTTTGTTTGCACCGAGTAAGGTTGGCCACTTCGGTTTCCCAAGAACT
CAAAATCTAGTTCATCCCGTACGGTGTCTGTATCCGAGTTCATGTAGAAG
GCGGTGACCGTACCGGCAGAGTCGCCGGGAATGAGTTTGATCTTCATGCT
CACTTTTCCGAATAGATACTTTCTTTTGGAAGAGAATCCACATCCAGTGC
TCTGGTCAAGGACAAGTTGGATAGCTTTTCCACCGTCGACTTGACGGATG
TGAGATCCCGACCATGCGGCTTTGAAATCCTCGGCGAATGTCGTAGGCCG
TGCTGAAATCTTGATGAACATTAGCGTACAAAGAGTGACAATGCAAAGAA
AATGAGTTTTGGCCATCATGGTCGGCCTTTATAACGATGAAAAAAATATG
TTCGAGTgactacttgtgacccacgcgtccgcggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 39 39 51 40 40 40 46 46 46 51 51 51 51 51 39 39 39 39 35 35
 35 35 35 35 35 39 39 35 35 35 35 35 35 40 40 45 45 40 40 51 51 51 51 51 40 40 40 40 40 40 40 40 40 45 40 40 39 39 38 38 38 38 39 39 51 39 39 40 38 38
 43 45 43 43 40 35 43 43 43 43 43 45 51 51 51 51 51 51 51 51 51 43 43 43 43 43 43 43 45 56 56 56 56 56 43 43 43 43 43 43 51 43 43 43 43 43 43 36 36 36
 36 36 36 43 43 43 43 43 43 43 43 43 43 51 51 45 45 45 45 45 45 45 45 45 45 45 45 45 51 51 56 43 43 43 43 43 43 43 43 45 45 45 45 45 43 43 43 43 43 45
 43 43 43 43 43 43 51 45 45 43 43 43 43 43 43 43 43 43 43 43 43 43 51 51 51 51 43 43 43 43 43 43 56 56 43 43 43 43 43 43 45 45 45 45 43 43 43 43 43 43
 43 43 56 56 56 56 56 56 56 56 56 51 43 43 43 38 38 43 43 43 43 43 43 43 51 51 56 56 56 56 56 56 56 56 56 56 56 43 43 43 43 43 43 43 43 43 43 43 43 43
 43 43 43 45 45 51 45 63 70 66 61 43 51 56 56 56 56 56 56 56 51 51 70 69 69 45 51 51 56 56 56 56 56 56 56 56 45 45 45 45 55 54 43 48 48 46 47 65 68 85
 85 80 85 76 78 80 74 74 77 82 82 88 88 85 81 84 88 83 60 63 64 61 69 80 74 74 77 74 70 70 83 88 88 88 83 83 80 76 76 74 77 77 77 85 85 81 78 83 88 88
 85 85 81 81 72 78 76 73 60 64 69 77 71 74 88 90 90 88 88 88 84 84 76 82 84 86 86 76 85 81 83 73 78 80 80 66 75 75 75 75 83 78 77 77 77 75 80 64 64 66
 61 56 62 66 70 74 80 86 86 84 88 80 80 77 74 74 74 88 88 80 79 76 64 61 63 65 65 85 88 90 80 77 69 67 65 60 56 62 61 61 66 73 88 81 89 89 88 73 73 71
 90 73 90 90 90 90 90 90 90 84 77 75 74 86 84 82 81 80 76 77 80 78 88 78 75 68 62 59 69 69 80 80 90 82 74 70 73 77 80 80 76 72 72 81 85 90 90 74 70 70
 69 74 69 70 69 76 74 67 70 75 83 67 69 69 62 65 65 78 76 80 66 70 60 65 64 53 56 58 42 47 43 43 51 51 51 51 51 51 51 56 72 76 66 67 61 64 61 59 64 76
 85 80 88 79 74 71 66 71 68 64 63 62 62 61 59 68 69 65 69 72 63 59 59 58 58 58 61 59 62 62 76 75 69 61 62 55 55 55 69 70 76 73 74 74 68 63 62 64 64 61
 61 57 57 57 59 54 53 51 50 50 50 45 44 44 42 42 46 46 51 45 45 45 45 43 43 45 45 45 45 62 63 62 63 66 55 56 56 53 51 51 57 51 45 45 51 51 51 51 51 51
 51 51 51 51 51 51 45 45 45 45 45 45 51 45 45 45 45 43 43 43 43 43 43 43 45 45 51 56 56 51 51 43 43 43 43 43 43 51 56 56 56 56 56 56 56 51 51 51 51 51
 56 56 56 56 56 56 45 45 45 45 45 41 41 41 45 45 45 56 56 51 51 51 51 51 51 56 51 51 45 45 45 45 45 45 45 41 41 43 56 56 46 43 42 38 43 43 43 43 43 43
 43 43 43 43 43 43 43 43 46 43 46 46 43 43 43 43 43 43 51 51 40 43 43 43 43 45 56 56 56 56 56 51 43 43 43 43 43 43 43 45 51 51 51 51 51 46 46 41 43 43
 43 43 43 43 40 41 41 45 45 45 45 46 56 38 36 36 36 36 36 45 45 51 51 51 51 51 56 51 51 43 43 36 36 36 36 35 35 43 43 43 43 43 43 43 43 43 43 43 43 43
 43 43 43 43 43 43 43 43 56 56 51 46 46 43 43 43 46 46 51 40 38 35 35 35 35 35 35 38 46 45 45 39 39 38 38 38 38 40 40 46 37 37 37 40 40 40 51 51 51 51
 51 51 45 45 45 45 45 40 40 40 40 40 40 40 40 56 40 40 40 39 35 35 35 35 35 39 40 40 40 39 39 39 35 35 35 35 35 34 35 35 35 56 56 56 51 51 51 46 51 51
 40 40 35 35 35 35 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2264f U 1
AF LL2264r C 354
BS 1 357 LL2264f
BS 358 361 LL2264r
BS 362 372 LL2264f
BS 373 375 LL2264r
BS 376 390 LL2264f
BS 391 399 LL2264r
BS 400 461 LL2264f
BS 462 462 LL2264r
BS 463 486 LL2264f
BS 487 491 LL2264r
BS 492 497 LL2264f
BS 498 500 LL2264r
BS 501 501 LL2264f
BS 502 504 LL2264r
BS 505 506 LL2264f
BS 507 510 LL2264r
BS 511 511 LL2264f
BS 512 515 LL2264r
BS 516 517 LL2264f
BS 518 523 LL2264r
BS 524 525 LL2264f
BS 526 527 LL2264r
BS 528 530 LL2264f
BS 531 531 LL2264r
BS 532 532 LL2264f
BS 533 541 LL2264r
BS 542 544 LL2264f
BS 545 550 LL2264r
BS 551 551 LL2264f
BS 552 622 LL2264r
BS 623 628 LL2264f
BS 629 629 LL2264r
BS 630 630 LL2264f
BS 631 640 LL2264r
BS 641 711 LL2264f
BS 712 729 LL2264r
BS 730 742 LL2264f
BS 743 1092 LL2264r

RD LL2264f 762 0 0
cttttatatttcaattgcataaccatatatttatgcacaccacgtacttg
cgtatgtgcacaattgcataaaagacattaCAATCCAATTTTTCTCGCAA
TTATATAAACGTACAAGAAGAAACATGATCATTGTACGTACGTCTTGTAC
ATGGTATTATTTCAAGCATGACACTCGATTGGTGGGACAGGATACCTTGA
CTTGTCGGTACAATAATCATATACCATATGGTTTACTCTAACCCAACGGT
AACGTCGAGCTTCCACGGCGTTAAGTGACTGATAAGCGTAGCCTTCCCAC
CAATTGTGAGGGTTCGATGGACAATTGGTGGGTCCAGGAACAGGACAGCC
TTCGATGTCGAAATCTTTGTAATAAGCATAAAAAGGAGCTTTGCTCCAAT
CAATTTTCTCTAATCCTCCACGTGTCGCCCAATCATCGGCTTCCCATAGT
GTTGAGTAAACTCCCATGGGTTGTGATGTTGGGTAGGCTATGTTCTTGGC
TTGGTTGTTTTTGTATTCTCTTATTGGTACATCGTCCACGTAAAAAACAA
TGTGTTTGTGTGACCAAAGGATACTGTAAGTGTGGAAATCCAAAGATGGG
TCGAACCAAAGATTAACCCTTTGTTCTCTATCtnctTTGCCATGAGCAAA
TATGTTTGTTTGCACCGAGTAAGGTTGGCCACTTCGGTTTCCCAAGAACT
CAAAATCTAGTTCattccgtacggngtCTGTATCCGAGTTCATGtaaaag
gccgtgACCGta

QA 81 622 1 762
DS CHROMAT_FILE: LL2264f PHD_FILE: LL2264f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:31 2000

RD LL2264r 784 0 0
gATGTCGAAATctntgTAATAAGCATanaaagGAGCTTTGCTCCAATCAA
TTTTCTCTAATCCTCCACGTGTCGCCCAATCATCGGCTTCCCATAGTGTT
GAGTAAACTCCCATGGGTTGTGATGTTGGGTAGGCTATGTTCTTGGCTTG
GTTGTTTTTGTATTCTCTTATTGGTACATCGTCCACGTAAAAAACAATGT
GTTTGTGTGACCAAAGGATACTGTAAGTGTGGAAATCCAAAGATGGGTCG
AACCAAAGATTAACCCTTTGTTCTCTATCTCCTTTGCCATGAGCAAATAT
GTTTGTTTGCACCGAGTAAGGTTGGCCACTTCGGTTTCCCAAGAACTCAA
AATCTAGTTCATCCCGTACGGTGTCTGTATCCGAGTTCATGTAGAAGGCG
GTGACCGTACCGGCAGAGTCGCCGGGAATGAGTTTGATCTTCATGCTCAC
TTTTCCGAATAGATACTTTCTTTTGGAAGAGAATCCACATCCAGTGCTCT
GGTCAAGGACAAGTTGGATAGCTTTTCCACCGTCGACTTGACGGATGTGA
GATCCCGACCATGCGGCTTTGAAATCCTCGGCGAATGTCGTAGGCCGTGC
TGAAATCTTGATGAACATTAGCGTACAAAGAGTGACAATGCAAAGAAAAT
GAGTTTTGGCCATCATGGTCGGCCTTTATAACGATGAAAAAAATATGTTC
GAGTgactacttgtgacccacgcgtccgcggacgcgtggxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxagt

QA 47 704 1 739
DS CHROMAT_FILE: LL2264r PHD_FILE: LL2264r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:09 2000

CO Contig7 796 2 49 U
ctttagggaaccatagagactaggatgttaaatagagaagcattcattat
gaagagaccacatattatagagaagcccaaatcaaaccaaagcaaagtat
tcaatggcagtttttcatacagacgataacatgctctttacttataaatc
ttattcatatgtttctaaaagcttattacggtcctgaatctgccaccttt
ttcaaaacttctattttgtttttaagcacgccctttataaaatgcgttta
tgataataggaaagtggtgctcaaaatttggcgctttggaggcctatcct
cagcttcagagactctTATTTGTCTGCCgtcCAAAtcagcgccATTCAAG
gttctGaTGGCAtttctggaCcttcttgAgcagagttgtacgtcacaAAC
CcaaaacCcttggaACGgccactgtcCCTGTCgtagaTGACTCTAGCCTC
GACAACCTTTCCTTgcTCACCGAACAAACTCTCCAGAGCCATGTCATCGA
CtccCCATGAGagactgcCGACATAAACACGgcttccTGAACCAGCAGCA
GCAC*CACCACCATATCCAGAACCAGAGCTTCCAAAGCTGcttCTGGgaC
ctctgGaGAAAGagtcttccctcttcgggggaggaggaccagcattcact
ctnaagggtctaccatccaactcatagccaccgaattgctgcgcagctgc
cctaa*cttcagagaccgacgaccatagcc*cgaacccgaaccccctgcc
tcgc*cctgtccctttgtcatagatcacccca*ccatcccgaaatt

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 25 27 34 44 30 28 26 24 24 26 22 20 19 19 19 22 23 22 25 14 14 12 12 11 13 17 16 22 22 25 25 21 21 21
 19 19 11 11 13 23 19 23 23 22 22 22 13 13 13 9 10 10 18 17 22 12 12 12 12 13 16 18 22 19 19 15 15 15 14 14 12 11 11 11 14 14 15 15 15 17 19 22 22 25
 25 17 17 18 18 18 18 20 13 8 8 12 13 13 23 24 24 18 18 17 19 16 16 11 11 15 21 21 27 24 24 27 19 18 13 12 16 25 25 30 33 26 24 24 33 24 24 27 24 27
 24 24 30 31 31 29 31 31 42 33 37 33 33 27 14 14 22 23 23 28 32 33 35 39 35 42 37 37 42 30 30 24 25 22 27 22 24 27 31 30 27 27 33 24 24 24 27 33 33 24
 27 15 15 15 29 25 33 28 28 23 26 17 14 8 6 6 8 13 21 25 25 27 30 29 29 25 25 22 24 20 24 14 11 11 13 8 15 23 29 29 40 31 31 28 23 30 29 32 29 29
 29 31 31 32 29 29 33 33 29 33 30 27 22 32 27 32 28 30 25 21 25 25 31 32 29 31 38 32 32 35 35 41 48 45 38 41 27 24 20 12 11 11 24 25 25 22 19 19 23 12
 11 11 14 12 23 18 21 20 22 25 23 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2266f U 1
AF LL2266r C 438
BS 1 568 LL2266f
BS 569 569 LL2266r
BS 570 575 LL2266f
BS 576 587 LL2266r
BS 588 588 LL2266f
BS 589 589 LL2266r
BS 590 613 LL2266f
BS 614 616 LL2266r
BS 617 626 LL2266f
BS 627 631 LL2266r
BS 632 635 LL2266f
BS 636 636 LL2266r
BS 637 638 LL2266f
BS 639 644 LL2266r
BS 645 646 LL2266f
BS 647 647 LL2266r
BS 648 654 LL2266f
BS 655 661 LL2266r
BS 662 663 LL2266f
BS 664 664 LL2266r
BS 665 665 LL2266f
BS 666 668 LL2266r
BS 669 676 LL2266f
BS 677 679 LL2266r
BS 680 692 LL2266f
BS 693 693 LL2266r
BS 694 694 LL2266f
BS 695 695 LL2266r
BS 696 720 LL2266f
BS 721 722 LL2266r
BS 723 724 LL2266f
BS 725 727 LL2266r
BS 728 732 LL2266f
BS 733 733 LL2266r
BS 734 738 LL2266f
BS 739 740 LL2266r
BS 741 745 LL2266f
BS 746 748 LL2266r
BS 749 750 LL2266f
BS 751 751 LL2266r
BS 752 754 LL2266f
BS 756 762 LL2266r
BS 763 764 LL2266f
BS 765 773 LL2266r
BS 774 775 LL2266f
BS 776 776 LL2266r
BS 777 784 LL2266f
BS 785 788 LL2266r
BS 789 796 LL2266f

RD LL2266f 796 0 0
ctttagggaaccatagagactaggatgttaaatagagaagcattcattat
gaagagaccacatattatagagaagcccaaatcaaaccaaagcaaagtat
tcaatggcagtttttcatacagacgataacatgctctttacttataaatc
ttattcatatgtttctaaaagcttattacggtcctgaatctgccaccttt
ttcaaaacttctattttgtttttaagcacgccctttataaaatgcgttta
tgataataggaaagtggtgctcaaaatttggcgctttggaggcctatcct
cagcttcagagactctTATTTGTCTGCCgtcCAAAtcagcgccATTCAAG
gttctGaTGGCAtttctggaCcttcttgAgcagagttgtacgtcacaAAC
CcaaaacCcttggaACGgccactgtcCCTGTCgtagaTGACTCTAGCCTC
GACAACCTTTCCTTgcTCACCGAACAAACTCTCCAGAGCCATGTCATCGA
CtccCCATGAGagactgcCGACATAAACACGgcttccTGAACCAGCAGCA
GCAC*CACCACCATATCCAGAACCAGAGCTTCCAAAGCTGcttCTGGgaC
ctctgGaGAAAGagtcttccctcttcggnggaggaggaccagcattcact
ctnaagggtctaccatccaactcatagccaccgaattgctgcgcagctgc
cctaa*cttcagagaccgacgaccatagcc*cgaacccgaaccccctgcc
tcgc*cctgtccctttgtcatagatcacccca*ccatcccgaaatt

QA 316 613 1 796
DS CHROMAT_FILE: LL2266f PHD_FILE: LL2266f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:40 2000

RD LL2266r 816 0 0
ttttttttgcttcgacaacctttcgttggtcgcgggacaggatcccgaga
gcgggggctggaactccccatgggagggaccgggcagaagcccggcttcg
ggagccagcaggagcagtcaccgccagatCCAgacccaGAGCTTCCAAAG
CTgcgtggaggacctctgtagagagagtctacgctgttcgggggaggagg
gccagcattcactagcaagggtctagcatccaggtgaacgccattgagnt
gatgagcaga*gccctcagcatcggaggcagaagac*atagtcgcgaaac
cgaaacctctgcttcgtgcctgtcccgttgtcatagagcacctcaaccat
ctacacatctccggcgctctcgaagagctgagcgagctgagcactgtacg
cgttaaaggcaaggtgaccgactcagagtctgaggtcaccatcgaagtgt
tgctcccgcatgcggaggcggctcagcgtcatcggagataatgctgtcat
cttcttcttcttattcgctgaagtcatctgtacccgcggccgatgcgcat
aaccagaaacccggcggaggaagggaagatggagagggtaatggactggg
agttgagtttgaagtagacgaaagaatggaggaggagagtgcaacctggg
ttcggagatggagaaagggatgcatttacggcttgaaggtgcagagagcg
agggcggaagctggagcagccatgtaggccgagaagagagcggacgcgtg
ggtcgacccgggaattcccggaacggtaccgcaagttgacccgagggncg
cccaacagcttatcct

QA -1 -1 93 351
DS CHROMAT_FILE: LL2266r PHD_FILE: LL2266r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:18 2000

CO Contig8 875 2 40 U
cttttgggatacagtacaaatgatctcatgacataaactgctggcaaaac
atatgtagtctcaggaggaacaaaaacaaaAGACAAGTCAAAAACTCTTT
ATGGACTTGTAGCAAGCTTGTTGAAGGCGGCATGAACCCTCTCTTCAGTG
AACATTCTGTGATTCTCATAGAAATCTAATATCTCCATTGCGATATTCTT
CACTATGTTCATGTCCGCAGAGAGCTCTTCAAACCATGTCTTTATGTCTT
TCTCTTTGTACACAGAAGCAACGTAAATGCAAGCGATCGTGATGAGATGA
GGCGGGTGTGTAAGGATCAGGTCCATTTTGTAAGTGTCGTTGACAAGACC
CCAAGTTAAATGGGTCATGCTTGTGTCATTGAGTCCAGAGTCCTGCAAGT
ACTCAGGGAGAGAACGGTATGGGTGGAAGACAACAAGATAGAAGTTCAAA
GCTTCCAAGACCTTCATCTCCATCTCCAGAATATCCTTAATCTCATACCT
AAACTTCTCATCAGCATACAATTTCTTGATGTAGAAGACAAGAATCTTGG
CATGGACCACACTCTCCTCTGCTTTGCAAGCCAGATACAAGCAGGTGGGA
GCAACAAGACGAGGCTCATACTCTGTCAAACTCTTCCTTGTGTAAACACG
GCGCATATAGGTTACAGCAGTTGCAACAACTCTTTGCCTAATCTTAATGT
GTTGTGCCAGCTTCGATATGTAGTTAGACATATGAAGCTTAATGAGTTTG
AAATCTTCGAGAGAGATTCCTCTCTGAGCATCAAGAGGATGAACAACATT
AATCTCTTCTGGGTCCTTAAGCTCTTTGTAGTGTGTTGATgtccagaaat
tggaagccattttccggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 40 40 39 39 39 39 39 39 40 40 51 51 51 51 51 40 46 40
 40 40 40 40 40 40 40 40 45 51 51 51 51 51 40 40 40 40 40 45 40 40 40 40 40 35 35 35 35 35 35 39 39 40 40 40 40 66 60 60 60 63 63 55 58 58 65 69 61 59
 55 55 55 60 65 67 67 69 74 71 74 69 69 70 70 69 78 76 80 82 85 85 80 70 67 61 61 74 74 75 77 71 75 72 77 77 88 65 60 66 68 70 70 66 74 69 69 69 67 68
 68 75 69 74 72 72 80 80 80 74 74 85 80 73 61 58 61 61 68 83 85 85 83 83 83 74 72 65 67 69 78 76 90 81 85 85 90 90 90 90 85 85 85 80 90 90 90 90 85 83
 83 83 83 84 84 83 77 84 90 90 85 85 85 85 90 85 85 80 80 78 78 74 74 72 82 90 83 83 83 80 83 68 72 75 75 75 79 85 85 85 85 90 90 90 90 90 90 90 90 90
 76 78 78 82 76 90 90 90 90 90 90 90 90 90 90 90 90 90 90 86 86 86 90 90 90 90 90 90 90 90 90 90 90 90 90 83 83 88 83 83 83 90 83 83 90 90 90 90 90 90
 90 90 90 90 86 86 90 90 90 86 90 90 90 87 89 87 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 82 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 88
 88 88 85 90 90 90 90 90 90 90 90 90 90 90 90 90 86 90 90 90 90 90 90 90 90 90 90 90 90 89 90 90 90 90 90 90 90 90 90 85 87 90 87 87 85 85 90 89 89 85
 90 85 85 90 90 90 90 90 90 90 90 86 86 90 90 90 90 90 88 88 88 90 90 90 90 90 87 90 90 86 86 87 90 90 90 90 90 90 90 90 90 90 90 88 90 90 90 90 90 90
 90 90 90 90 89 84 81 85 85 85 80 84 90 89 73 75 80 90 84 83 78 77 77 77 78 85 86 90 90 90 82 80 72 66 75 72 71 72 75 71 71 80 70 76 82 82 79 76 66 66
 69 78 72 76 71 66 66 76 85 66 66 66 75 70 62 60 60 60 63 64 67 75 64 66 64 76 76 77 77 77 76 76 79 75 74 75 80 61 64 58 58 58 60 58 59 64 61 63 66 58
 58 43 43 43 51 51 51 51 43 43 43 43 43 45 51 51 68 73 70 80 74 51 43 43 43 43 43 43 56 51 51 51 45 45 51 51 51 43 45 43 43 43 43 43 43 65 62 65 48 42
 42 43 43 43 55 58 51 45 45 45 45 45 45 43 43 43 43 43 43 43 43 43 43 43 43 43 56 56 56 56 56 51 51 51 51 51 45 45 45 45 45 45 45 45 45 45 45 45 45 51
 51 51 51 51 51 51 43 43 43 45 45 43 43 43 43 43 43 45 43 43 43 43 43 43 43 43 43 43 45 56 56 51 51 43 43 43 43 43 43 51 51 51 43 43 43 43 43 43 51 51
 51 51 51 56 51 40 40 40 40 40 40 45 45 45 45 45 45 51 51 51 51 51 40 40 39 35 35 35 35 35 39 51 51 51 51 51 51 39 39 39 39 39 39 40 40 40 56 39 39 39
 39 40 40 51 51 51 51 51 51 51 40 40 40 40 40 40 40 35 35 35 35 45 45 51 51 51 51 45 40 40 40 40 40 46 46 51 51 51 40 35 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2268f U 1
AF LL2268r C 136
BS 1 264 LL2268f
BS 265 265 LL2268r
BS 266 291 LL2268f
BS 292 298 LL2268r
BS 299 305 LL2268f
BS 306 306 LL2268r
BS 307 315 LL2268f
BS 316 317 LL2268r
BS 318 324 LL2268f
BS 325 325 LL2268r
BS 326 326 LL2268f
BS 327 327 LL2268r
BS 328 337 LL2268f
BS 338 338 LL2268r
BS 339 341 LL2268f
BS 342 342 LL2268r
BS 343 344 LL2268f
BS 345 352 LL2268r
BS 353 354 LL2268f
BS 355 360 LL2268r
BS 361 363 LL2268f
BS 364 379 LL2268r
BS 380 386 LL2268f
BS 387 387 LL2268r
BS 388 393 LL2268f
BS 394 403 LL2268r
BS 404 404 LL2268f
BS 405 440 LL2268r
BS 441 444 LL2268f
BS 445 450 LL2268r
BS 451 451 LL2268f
BS 452 464 LL2268r
BS 465 465 LL2268f
BS 466 512 LL2268r
BS 513 513 LL2268f
BS 514 616 LL2268r
BS 617 621 LL2268f
BS 622 645 LL2268r
BS 646 656 LL2268f
BS 657 875 LL2268r

RD LL2268f 764 0 0
cttttgggatacagtacaaatgatctcatgacataaactgctggcaaaac
atatgtagtctcaggaggaacaaaaacaaaAGACAAGTCAAAAACTCTTT
ATGGACTTGTAGCAAGCTTGTTGAAGGCGGCATGAACCCTCTCTTCAGTG
AACATTCTGTGATTCTCATAGAAATCTAATATCTCCATTGCGATATTCTT
CACTATGTTCATGTCCGCAGAGAGCTCTTCAAACCATGTCTTTATGTCTT
TCTCTTTGTACACAGAAGCAACGTAAATGCAAGCGATCGTGATGAGATGA
GGCGGGTGTGTAAGGATCAGGTCCATTTTGTAAGTGTCGTTGACAAGACC
CCAAGTTAAATGGGTCATGCTTGTGTCATTGAGTCCAGAGTCCTGCAAGT
ACTCAGGGAGAGAACGGTATGGGTGGAAGACAACAAGATAGAAGTTCAAA
GCTTCCAAGACCTTCATCTCCATCTCCAGAATATCCTTAATCTCATACCT
AAACTTCTCATCAGCATACAATTTCTTGATGTAGAAGACAAGAATCTTGG
CATGGACCACACTCTCCTCTGCTTTGCAAGCCAGATACAAGCAGGTGGGA
GcaccacgaccagGCTCATACTCTgCcaacctCTTCCTtgcgtAAACACG
GCGCATATaggctaCAGcacgctgcccacctttcctccctatctcactgc
gctgcgcccacccccccccgctccctcactccccatccccaccgcccccc
ccatcccccatacg

QA 81 601 1 669
DS CHROMAT_FILE: LL2268f PHD_FILE: LL2268f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:50 2000

RD LL2268r 785 0 0
acCCTCTCTTCAGTGAACATTCTGTGATTCTCATAGAAATCTAATATCTC
CATTGCGATATTCTTCACTATGTTCATGTCCGCAGAGAGCTCTTCAAACC
ATGTCTTTATGTCTTTCTCTTTGTACACAGAAGCAACGTAAATGCAAGCG
ATCGTGATGAGATGAGGCGGGTGTGTAAGGATCAGGTCCATTTTGTAAGT
GTCGTTGACAAGACCCCAAGTTAAATGGGTCATGCTTGTGTCATTGAGTC
CAGAGTCCTGCAAGTACTCAGGGAGAGAACGGTATGGGTGGAAGACAACA
AGATAGAAGTTCAAAGCTTCCAAGACCTTCATCTCCATCTCCAGAATATC
CTTAATCTCATACCTAAACTTCTCATCAGCATACAATTTCTTGATGTAGA
AGACAAGAATCTTGGCATGGACCACACTCTCCTCTGCTTTGCAAGCCAGA
TACAAGCAGGTGGGAGCAACAAGACGAGGCTCATACTCTGTCAAACTCTT
CCTTGTGTAAACACGGCGCATATAGGTTACAGCAGTTGCAACAACTCTTT
GCCTAATCTTAATGTGTTGTGCCAGCTTCGATATGTAGTTAGACATATGA
AGCTTAATGAGTTTGAAATCTTCGAGAGAGATTCCTCTCTGAGCATCAAG
AGGATGAACAACATTAATCTCTTCTGGGTCCTTAAGCTCTTTGTAGTGTG
TTGATgtccagaaattggaagccattttccggacgcgtggxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxatt

QA 3 705 1 740
DS CHROMAT_FILE: LL2268r PHD_FILE: LL2268r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:27 2000

CO Contig9 1201 2 34 U
ccacgcgtccgtacgataaaaaaaaaaaaagaacTTACCAACTAATAACT
ACAGCATTAATAAATAACCTAAGCAACTCATTGCTTCGCATTATCTGGAT
CCAAAAAATTAGTCAAGATATGATAGGCTGATCATATCATTGGAGCAACT
GACTAAAAAAAAAGAATAAAGAAAGATGATTATTAAGTTATGAAAGGTAA
TCAAAAAGTATGCGGATAAATGGAAGGATGAAAGAAAGAGCGAAAAAATT
GAATATTAATGATATATGATTCCAATTTGGAAAATCTATGAGGTCACTGT
AAGAAAAGCAATGTAATAAAGCATCAATACAGATTCATTCATAATAATTA
GATAAATAATAATAATTAGATAAATCTGTTCCGAAAACAAAAAATTAAGA
GCCTTGAGACAATCAAAACTGAGAAAATTGCCTCAAAAAAAAAAAGAAAT
TCAAAATTTCATGTAAAAGCTCCATTGTAGAATTCAGGCCTAATGATTAA
TCAAGAAGCGATGGGAACGACGGAACCCATGAATATATAGGATTCTAGTG
AACAAGAAATCTTAGTAATTCATTGGACAGGATGGCGGAATAAACCAGAA
ACTTTATTATCTATTCTGATTTTGATTCTGAGACCTCGGGGGATAAACAG
CAAACTTAAATAGATATTGAAAGAGTAAATATTCGCCGGCGAAAAATTGG
TTTTTTTTTTTCAAATAAAAACAGTAATAAAAGATGAAAAAAACAATGAA
AAAAAAATAAGGATTTGTTATAATATTCTAACTCTAATAAAAATTACATT
TGTAATGATGATATTACGTTATTTTTAAATAAATCGAAATAAAATTGATC
TTTGATTCTATTTCAAAAAAGACATACACAAATTTAGAAGAGATAAGATG
AAATAAAAAAAAAATACCATGATTAATAGGATTAATCATTAACTACATCT
ATATCTTAATTAATCCTTTTATTCGCGAGGAGCTGGATGAGaaGAAACTC
TCACGTCCAGTtCTGCAGTAGAGATGGAATTTCTCATTTAGAAAAAACCC
ATCAACTATAACCCAAAAAGAACCAAATTTCGTAAACAACATCGAGGAaG
aCTAaAAGGAATATcCTCTCgtgggAATCGTATttGttttGGCAGaTATG
CTcttCaaACACttGAACCCGCTTGGAttAcAtctagacaaatagaagca
g

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 37 37 37 40 40 40 46 40 39 39 39
 39 39 40 56 56 46 46 46 46 46 46 46 40 40 40 39 39 39 40 40 40 40 46 51 40 40 40 40 40 40 40 39 35 39 39 35 35 35 35 35 39 39 35 35 35 51 51 45 51 46
 46 46 46 46 46 56 56 35 35 35 35 35 35 40 51 51 51 51 45 45 45 45 45 45 45 43 43 43 43 43 43 51 51 51 51 51 51 51 56 56 56 56 51 51 51 43 35 35 35 35
 35 35 35 35 35 43 43 56 56 56 56 56 56 56 51 51 51 51 51 51 56 56 56 56 56 56 56 51 43 43 43 43 43 43 43 43 43 43 43 43 43 43 45 45 51 51 51 51 51 51
 51 51 51 51 51 56 51 51 45 43 36 36 36 36 36 43 51 51 51 51 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 51 43 43 43 43 43 43 51 56 56 56 56 56
 56 56 56 51 45 45 45 45 45 45 51 51 51 56 51 51 51 51 45 45 45 45 45 51 56 56 56 56 56 56 56 56 56 51 51 51 51 51 51 56 56 56 56 43 36 36 36 36 36 45
 56 51 51 51 51 45 51 51 51 51 51 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 51 51 51 51 51 51 51 51 51 51 51 51 51 51 51 51 51 45 45 45 45
 45 45 51 56 56 56 56 56 56 56 56 56 56 51 45 45 45 45 45 45 51 51 51 51 56 51 51 51 51 43 45 45 45 45 45 56 56 56 56 56 56 56 56 45 45 45 45 45 43 56
 56 56 56 56 56 56 43 43 42 46 43 51 56 56 56 56 45 45 45 45 45 41 43 51 51 51 56 51 45 43 43 43 43 51 51 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56
 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 51 46 56 56 56 50 53 53 56 52 61 56 56 56 66 66 66 61 61 61 61 55 55 55 55 56 61 66 50 50 50 50 50
 50 53 53 52 52 66 55 55 55 50 50 50 66 66 66 50 49 49 45 45 45 55 55 50 61 61 61 61 66 66 66 56 56 56 52 52 52 52 52 52 52 66 66 52 52 52 52 52 52 52
 54 56 54 52 50 52 52 56 56 55 50 50 50 50 50 50 50 50 50 61 61 61 61 61 50 53 53 53 53 53 66 66 53 45 45 45 45 45 53 61 61 53 53 53 53 53 53 55 53 45
 45 45 45 50 53 53 53 53 53 53 53 53 53 53 55 56 55 66 55 55 66 66 66 66 61 61 61 61 61 66 53 53 53 53 53 53 61 61 61 66 66 61 61 61 61 61 55 55 55 55
 55 55 53 53 53 53 53 53 61 55 55 53 55 55 61 61 61 61 61 61 61 61 61 61 61 61 66 66 66 66 66 53 53 53 53 53 53 53 55 55 55 55 55 66 66 66 66 66 66 66
 66 66 66 66 66 66 66 66 56 56 42 42 42 44 43 51 51 61 53 50 50 50 53 48 56 42 42 56 56 56 56 56 66 56 56 56 56 56 56 56 43 38 38 38 38 38 42 42 50 56
 56 56 56 56 56 56 56 51 51 43 43 56 50 50 44 44 42 46 44 56 51 51 51 51 44 43 42 42 43 41 41 41 41 41 51 56 56 56 56 56 56 56 43 43 42 41 41 41 50 50
 42 42 46 46 42 42 50 42 56 56 56 56 56 56 43 43 43 43 43 35 40 40 40 40 40 51 51 51 51 51 51 46 40 43 42 42 42 46 56 56 56 56 56 50 42 42 42 42 43 43
 56 56 51 43 44 43 42 42 43 46 43 42 42 42 56 56 56 56 56 40 40 40 40 40 42 44 44 44 44 48 48 56 56 56 56 56 56 56 56 47 56 56 56 42 46 46 46 42 42 56
 56 44 44 44 56 56 56 56 56 56 56 56 56 56 42 42 42 46 42 42 42 40 40 45 45 45 45 51 51 51 40 40 40 40 40 40 51 45 40 40 40 40 40 40 40 35 40 40 40 46
 46 44 48 48 48 40 37 34 32 34 40 40 40 40 40 48 48 40 40 37 37 40 35 29 31 31 34 34 37 40 40 40 40 40 34 34 40 37 37 28 25 18 16 21 26 29 29 32 29 29
 32 32 32 32 29 29 24 25 29 29 25 19 24 25 29 32 33 32 37 27 27 24 33 33 35 35 40 40 40 40 48 33 33 33 26 26 29 22 22 24 24 24 48 48 32 25 25 25 25 24
 37 40 48 29 20 24 24 24 25 24 25 29 32 32 32 26 29 29 29 25 20 22 25 27 27 27 27 29 29 25 29 32 28 24 24 29 29 29 29 37 40 40 40 27 27 25 25 22 18 21
 17 22 22 22 19 24 24 24 25 22 24 25 26 25 19 25 24 23 24 21 10 10 10 17 18 25 25 29 29 29 24 24 24 19 19 21 16 16 19 19 29 25 29 21 21 18 22 22 23 29
 27 23 18 12 17 20 17 18 23 25 24 21 19 18 22 22 22 22 22 24 25 25 21 22 22 25 21 17 14 21 18 20 18 18 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0

AF LL2271r U -45
AF LL2276r U 409
BS 1 468 LL2271r
BS 469 473 LL2276r
BS 474 477 LL2271r
BS 478 481 LL2276r
BS 482 492 LL2271r
BS 493 493 LL2276r
BS 494 495 LL2271r
BS 496 501 LL2276r
BS 502 515 LL2271r
BS 516 516 LL2276r
BS 517 518 LL2271r
BS 519 521 LL2276r
BS 522 531 LL2271r
BS 532 534 LL2276r
BS 535 551 LL2271r
BS 552 552 LL2276r
BS 553 554 LL2271r
BS 555 555 LL2276r
BS 556 559 LL2271r
BS 560 603 LL2276r
BS 604 604 LL2271r
BS 605 615 LL2276r
BS 616 616 LL2271r
BS 617 617 LL2276r
BS 618 618 LL2271r
BS 619 620 LL2276r
BS 621 621 LL2271r
BS 622 623 LL2276r
BS 624 624 LL2271r
BS 625 717 LL2276r
BS 718 725 LL2271r
BS 726 732 LL2276r
BS 733 733 LL2271r
BS 734 1201 LL2276r

RD LL2271r 785 0 0
actxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccac
gcgtccgtacgataaaaaaaaaaaaagaacTTACCAACTAATAACTACAG
CATTAATAAATAACCTAAGCAACTCATTGCTTCGCATTATCTGGATCCAA
AAAATTAGTCAAGATATGATAGGCTGATCATATCATTGGAGCAACTGACT
AAAAAAAAAGAATAAAGAAAGATGATTATTAAGTTATGAAAGGTAATCAA
AAAGTATGCGGATAAATGGAAGGATGAAAGAAAGAGCGAAAAAATTGAAT
ATTAATGATATATGATTCCAATTTGGAAAATCTATGAGGTCACTGTAAGA
AAAGCAATGTAATAAAGCATCAATACAGATTCATTCATAATAATTAGATA
AATAATAATAATTAGATAAATCTGTTCCGAAAACAAAAAATTAAGAGCCT
TGAGACAATCAAAACTGAGAAAATTGCCTCAAAAAAAAAAAGAAATTCAA
AATTTCATGTAAAAGCTCCATTGTAGAATTCAGGCCTAATGATTAATCAA
GAAGCGATGGGAACGACGGAACCCATGAATATATAGGATTCTAGTGAACA
AGAAATCTTAGTAATTCATTGGACAGGATGGCGGAATAAACCAGAAACTT
TATTATCTATTCTGATTTTGATTCTGAGACCTCGGGGGATAAACAGCAAA
CTTAAATAGATATTGAAAGAGTAAATATTCGCCGGCGAAAAATTGGTTTT
TTTTTTTCAAATAAAAACAGTAATAAAAGATGAAA

QA 81 756 47 785
DS CHROMAT_FILE: LL2271r PHD_FILE: LL2271r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:42 2000

RD LL2276r 793 0 0
atxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccacg
cgtccgAAAAGCTCCATTGTAGAATTCAGGCCTAATGATTAATCAAGAAG
CGATGGGAACGACGGAACCCATGAATATATAGGATTCTAGTGAACAAGAA
ATCTTAGTAATTCATTGGACAGGATGGCGGAATAAACCAGAAACTTTATT
ATCTATTCTGATTTTGATTCTGAGACCTCGGGGGATAAACAGCAAACTTA
AATAGATATTGAAAGAGTAAATATTCGCCGGCGAAAAATTGGTTTTTTTT
TTTCAAATAAAAACAGTAATAAAAGATGAAAAAAACAATGAAAAAAAAAT
AAGGATTTGTTATAATATTCTAACTCTAATAAAAATTACATTTGTAATGA
TGATATTACGTTATTTTTAAATAAATCGAAATAAAATTGATCTTTGATTC
TATTTCAAAAAAGACATACACAAATTTAGAAGAGATAAGATGAAATAAAA
AAAAAATACCATGATTAATAGGATTAATCATTAACTACATCTATATCTTA
ATTAATCCTTTTATTCGCGAGGAGCTGGATGAGaaGAAACTCTCACGTCC
AGTtCTGCAGTAGAGATGGAATTTCTCATTTAGAAAAAACCCATCAACTA
TAACCCAAAAAGAACCAAATTTCGTAAACAACATCGAGGAaGaCTAaAAG
GAATATcCTCTCgtgggAATCGTATttGttttGGCAGaTATGCTcttCaa
ACACttGAACCCGCTTGGAttAcAtctagacaaatagaagcag

QA 57 777 57 793
DS CHROMAT_FILE: LL2276r PHD_FILE: LL2276r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:28 2000

CO Contig10 1053 2 32 U
cattgttttcttcaagaatcaagatcctttacatgataagttccaagaag
agggaacttgagcgccccccaccccccactCAAGAACCACAAAGTTACAA
ACCACTAGAGCCTTACATATTAGTCTGTCTCTTTCCACACCATTAAACAA
GCAAACAAGCAGTGTAGGAAAGATAAAGAGAAGTGGTTTTAGAAAGAAAA
ATAAGTTGTTTACTTGCGGTGTGTGTATTGTTATAGTGGGGCAAAAGGCT
CAGGGAGCAGCTCGAAACCTCCATTATCAAACATGAGTCCATGTTCTGAC
GACCTATCATCAATGCTATGCAACCAGTTTGTGTTCTTCACGTCTTCTTT
CAACAGAAACGCGTCATACCTTGAGCTCTCATACATATTCATATCGCTCG
ACTTCCCCATCAGTCTTCTTCCCTCGTTTGTTTCGTTCCCGTTCTCTGCG
CTGTTGCTGCTGATAGAATCCGAAAGGCTATTCACTGAACGGATTGGCTG
TATCTTGGACGAGGCTTGTCTGATGCTCTGAGGGAACAACGTCGTGCTTG
ATAGTGCGCAACCGTTACTCTTCCCGTTTCTTATGTCCATGTGCTTAATG
GCCATATCAAGTGAACTTTTTGATAATGACCTCCCAAGCCCGTTGTTATT
GTCCATCACAGTTGAAGAAGTCCTCACGGTTCTCCGTGAAGTTACCTCTG
AAACATTTGAAATCCTTCTCGGCTCTGGTGCATATATGTTATGTTGCTGT
CCATTACCACTCAAACGGCCTTTTCCTTGGCTCTCTATGAGTCTTCCTCT
CGTCACAACAGGAGatgnnagtTCCTTCTCGTCATGGGACCTTTGGGTTC
TGGACTTGCCTTTGCTGCAACAGGCCTAGACCTGCCAGCTGATATCGGTC
TTCCCGGGAGACTTGTTCTGAGGTTAGGTGGTGCATCAAGAGAGAAGTCT
GGTAGCACAATTGGCTGTTGTGTGTTGGTGGTGGTGGTGGTTCGGACTCT
AGGTTGTCCAGGAGAGCTcggcctagacaatgaaggtgcgggcggacgcg
tgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 35 37 37 37 35 35 37 37 40 40 42 42 37 37 37 37 37 39 43
 37 37 35 35 32 32 32 32 35 42 42 35 35 35 35 35 35 37 35 28 35 35 28 28 33 37 35 36 36 35 35 35 46 35 40 40 40 38 35 42 42 37 37 40 40 40 40 40 40 40
 40 43 45 43 56 43 45 41 41 41 41 41 35 35 40 40 37 37 43 56 56 37 37 38 43 43 43 56 56 56 50 50 44 44 44 50 50 51 46 46 42 42 42 56 56 56 56 56 56 43
 43 41 41 45 45 42 42 44 46 42 38 38 38 38 38 35 35 35 32 35 35 50 42 42 42 41 41 41 41 35 38 38 40 40 40 35 35 44 40 40 40 40 40 43 56 42 38 31 31 31
 35 35 46 56 56 56 43 40 36 32 32 32 36 36 36 36 36 32 36 31 36 35 35 42 50 50 44 44 42 43 42 42 42 42 50 44 50 50 50 44 44 44 50 42 42 42 35 36 36 36
 36 36 38 41 41 42 42 44 44 44 50 42 42 32 35 38 38 38 38 41 41 41 43 42 43 43 50 50 44 44 44 44 44 46 42 42 42 35 35 35 36 36 36 38 42 42 42 42 46 42
 42 42 42 42 41 41 44 45 40 40 40 40 38 38 35 44 42 42 42 42 42 42 42 41 41 41 41 48 48 53 52 57 56 56 56 48 48 50 49 51 49 57 41 32 35 33 37 35 37 41
 42 42 42 46 46 50 50 50 50 44 57 50 56 56 56 56 50 50 50 50 50 44 44 44 50 50 50 52 50 50 53 56 51 43 43 42 42 40 40 40 40 40 36 52 52 45 39 46 44 46
 46 48 52 47 47 51 51 51 51 51 43 48 50 62 54 57 53 60 50 48 45 45 45 48 52 45 40 45 38 42 42 51 41 41 45 49 50 43 45 45 45 45 52 55 51 43 47 53 54 54
 50 56 45 44 44 58 49 52 62 61 65 60 60 57 62 62 53 48 54 56 58 70 67 67 54 54 46 48 47 66 57 66 66 52 49 49 52 48 53 62 83 65 71 59 57 57 69 59 62 65
 65 67 69 69 58 50 50 45 44 30 34 41 49 54 57 56 59 59 61 65 53 80 61 57 61 72 64 57 53 58 48 61 58 67 67 65 64 65 69 77 74 74 74 66 57 54 57 56 49 38
 39 48 59 67 69 80 58 57 54 57 57 61 68 57 57 61 80 88 77 72 72 64 63 69 65 65 69 77 80 80 80 67 62 65 71 71 67 65 65 61 66 69 70 76 75 71 71 71 60 55
 55 55 55 55 76 75 82 64 64 66 64 58 60 69 64 64 78 59 55 57 60 47 48 47 45 46 51 61 65 64 59 64 68 61 64 61 61 61 66 64 65 58 54 50 48 48 52 54 62 71
 71 74 73 79 76 69 64 67 66 63 52 55 54 52 47 50 48 40 40 40 45 40 40 40 40 40 46 51 59 59 68 77 82 85 89 84 90 75 68 66 68 68 62 59 59 54 49 51 55 55
 54 53 66 66 70 75 66 61 65 65 65 65 62 40 40 39 39 39 39 45 51 56 56 56 56 56 56 51 51 51 51 45 45 45 45 45 45 40 34 34 34 34 34 35 51 51 51 51 40 39
 39 39 39 39 40 46 46 46 46 40 39 39 36 33 19 15 4 0 0 4 19 19 33 36 44 44 46 39 34 34 34 34 34 40 56 56 56 56 56 56 56 56 56 56 51 51 51 51 51 51
 56 56 51 51 51 45 45 45 45 45 45 45 45 45 40 40 40 40 40 40 51 45 45 45 45 45 45 45 45 45 51 56 56 56 40 39 39 39 39 39 45 45 51 40 45 35 35 35 35 35
 35 51 45 45 45 40 40 40 45 45 45 40 39 39 35 35 35 35 45 45 40 40 40 40 40 40 45 45 40 40 39 39 39 39 39 39 45 45 45 45 45 45 45 45 45 45 45 40 40 40
 35 35 35 35 35 35 39 40 56 40 40 40 40 40 40 45 51 51 51 51 51 51 51 51 51 51 40 40 40 40 40 40 40 40 40 40 40 40 40 46 40 40 40 40 40 45 51 51 51 51
 46 40 40 35 35 40 40 40 40 51 51 51 51 42 42 37 40 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0

AF LL2272f U 1
AF LL2272r C 368
BS 1 377 LL2272f
BS 378 392 LL2272r
BS 393 410 LL2272f
BS 411 411 LL2272r
BS 412 427 LL2272f
BS 428 432 LL2272r
BS 433 443 LL2272f
BS 444 539 LL2272r
BS 540 554 LL2272f
BS 555 557 LL2272r
BS 558 563 LL2272f
BS 564 564 LL2272r
BS 565 572 LL2272f
BS 573 573 LL2272r
BS 574 574 LL2272f
BS 575 575 LL2272r
BS 576 576 LL2272f
BS 577 577 LL2272r
BS 578 589 LL2272f
BS 590 594 LL2272r
BS 595 599 LL2272f
BS 600 612 LL2272r
BS 613 616 LL2272f
BS 617 618 LL2272r
BS 619 621 LL2272f
BS 622 627 LL2272r
BS 628 628 LL2272f
BS 629 671 LL2272r
BS 672 717 LL2272f
BS 718 728 LL2272r
BS 729 763 LL2272f
BS 764 1053 LL2272r

RD LL2272f 779 0 0
cattgttttcttcaagaatcaagatcctttacatgataagttccaagaag
agggaacttgagcgccccccaccccccactCAAGAACCACAAAGTTACAA
ACCACTAGAGCCTTACATATTAGTCTGTCTCTTTCCACACCATTAAACAA
GCAAACAAGCAGTGTAGGAAAGATAAAGAGAAGTGGTTTTAGAAAGAAAA
ATAAGTTGTTTACTTGCGGTGTGTGTATTGTTATAGTGGGGCAAAAGGCT
CAGGGAGCAGCTCGAAACCTCCATTATCAAACATGAGTCCATGTTCTGAC
GACCTATCATCAATGCTATGCAACCAGTTTGTGTTCTTCACGTCTTCTTT
CAACAGAAACGCGTCATACCTTGAGCTCTCATACATATTCATATCGCTCG
ACTTCCCCATCAGTCTTCTTCCCTCGTTTGTTTCGTTCCCGTTCTCTGCG
CTGTTGCTGCTGATAGAATCCGAAAGGCTATTCACTGAACGGATTGGCTG
TATCTTGGACGAGGCTTGTCTGATGCTCTGAGGGAACAACGTCGTGCTTG
ATAGTGCGCAACCGTTACTCTTCCCGTTTCTTATGTCCATGTGCTTAATG
GCCATATCAAGTGAACTTTTTGATAATGACCTCCCAAGCCCGTTGTTATT
GTCCATCACAGTTGAAGAAGTCCTCACGGTTCTCCGTGAAGTTACCTCTG
AAACATTTGAAATCCTTCTcgcttcTGGTGCATATATGTTATGTTGCTGT
CCATTACCACTCAAAcggncttTttcttg

QA 81 671 1 779
DS CHROMAT_FILE: LL2272f PHD_FILE: LL2272f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:31 2000

RD LL2272r 731 0 0
accttaagCTCTCATACATATTCATATcggtggact*cCCCATCAGTCTT
ctcccctCGTTTGTTTCgtccccgTTCTCTGCGCTGTTGCTGCTGATAGA
ATCCGAAAGGCTATTCACTGAACGGATTGGCTGTATCTTGGACGAGGCTT
GTCTGATGCTCTGAGGGAACAACGTCGTGCTTGATAGTGCGCAACCGTTA
CTCTTCCCGTTTCTTATGTCCATGTGCTTAATGGCCATATCAAGTGAACT
TTTTGATAATGACCTCCCAAGCCCGTTGTTATTGTCCATCACAGTTGAAG
AAGTCCTCACGGTTCTCCGTGAAGTTACCTCTGAAACATTTGAAATCCTT
CTCGGCTCTGGTGCATATATGTTATGTTGCTGTCCATTACCACTCAAACG
GCCTTTTCCTTGGCTCTCTATGAGTCTTCCTCTCGTCACAACAGGAGatg
nnagtTCCTTCTCGTCATGGGACCTTTGGGTTCTGGACTTGCCTTTGCTG
CAACAGGCCTAGACCTGCCAGCTGATATCGGTCTTCCCGGGAGACTTGTT
CTGAGGTTAGGTGGTGCATCAAGAGAGAAGTCTGGTAGCACAATTGGCTG
TTGTGTGTTGGTGGTGGTGGTGGTTCGGACTCTAGGTTGTCCAGGAGAGC
Tcggcctagacaatgaaggtgcgggcggacgcgtggxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxagt

QA 173 651 1 686
DS CHROMAT_FILE: LL2272r PHD_FILE: LL2272r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:09 2000

CO Contig11 735 2 105 U
ccacgcgtccgcttttttttttttttttttttttTTTTTCTCATAAAACC
TCTGTTTATatctTGAACAAAGTTACATTATAAGATGAGATGATGAGTGA
TGAGAAAGGAGAAAAAGATTTCTAAGAGGAGGAGAAGGTATCGATGATGG
TGGTGTGAAGGGGATCACTGAGGTGAGTAGCCCAATTGTTGAGTGGGCCT
TTACCAGTAGCAGCGGCTTGAACAGCGAAGCCCAAGAAGGCGACCATGGC
AAGACGAGCGTGCTTGATCTCAGCTAACTGAAGCTGAGCCATCTTCTCAG
GGTCAGACGCTAAACCAAGCGGGTCGAAGAATTTGCCGCCAGGGTACAAA
CGCTTCTCAGAGTCAAGCTCAGCGTTGCGCTGGAACTCGATGTAGCCGAT
CACTAACACCTCGATCCATATCAACGTCGAGATGGAGAAGGGTAGTGGCT
GCCCCAAGTAGGACGATCCATCCACTAGCTCCACCTTTCCGGCGTCTTGC
CAAGTGACGCCGGTGAGCCAtTcGACGGagaGAGCGCCGAGAGTGGCGAG
CATGGCCCACCGTCCGTGAATCAGCTCGCATTCTCTGAACCtCTGGATCC
CGAACACCtCGCTGTACGGCTGAAACGGAGTcgaTtTGGGGGCCgCCTCt
tcGGTACGGGttcCGATCACGtctccggctaagttcttcGccaGaTtCtg
gtcTagtgaatctatatCgaaCTggagataCTcgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 56 56 56 56 47 35 35 35 35 35 34 46 35 40 40 37
 48 50 50 50 44 42 42 34 25 4 4 4 13 20 26 42 42 42 44 43 44 44 47 44 45 45 45 45 45 45 50 50 44 45 45 45 45 45 45 45 45 45 47 50 50 47 47 47 47 47
 47 50 47 47 47 47 47 52 53 50 50 47 52 52 52 52 47 47 52 47 47 47 47 47 47 47 52 54 53 61 66 66 50 50 50 52 50 56 50 45 45 45 45 45 45 52 53 52 56 66
 54 54 52 52 45 50 50 50 50 50 58 56 53 50 50 35 35 35 35 37 47 53 45 45 45 47 45 47 45 45 45 54 54 52 52 52 66 60 52 52 53 53 61 61 50 50 50 50 50 50
 50 50 52 53 53 50 54 53 53 53 53 45 45 45 45 45 45 45 45 53 50 50 50 45 45 45 45 45 45 52 52 52 52 54 54 60 60 48 46 46 46 46 46 46 48 50 66 66 66 66
 66 48 46 48 46 46 46 55 55 48 48 48 53 50 50 55 61 61 61 61 61 53 53 53 53 46 46 46 51 51 55 55 55 51 51 51 55 53 53 55 55 51 51 51 55 55 55 53 61 61
 61 54 54 52 48 46 45 46 46 46 45 45 47 60 60 60 60 48 48 48 48 56 52 51 51 51 51 45 47 47 52 52 51 51 47 46 46 46 45 46 48 56 56 52 51 51 52 52 51 51
 46 53 46 46 45 45 45 46 45 45 45 45 52 54 60 51 48 48 42 42 41 45 51 51 51 51 47 46 46 42 42 42 47 46 45 46 43 43 45 52 52 47 54 45 45 45 60 60 52 56
 51 51 51 55 53 53 51 52 52 52 45 47 52 47 56 60 66 66 56 52 47 60 52 56 54 56 56 52 52 44 47 47 52 46 56 32 32 32 47 58 66 52 52 47 47 47 45 45 42 42
 45 45 55 50 53 52 56 56 56 56 50 45 45 45 45 45 45 52 52 54 54 52 49 50 49 49 41 43 45 48 45 45 48 47 49 48 56 52 52 53 53 52 52 42 34 34 34 42 42 56
 56 42 52 44 43 33 39 37 34 32 30 36 42 42 42 37 40 40 33 22 19 25 16 24 34 41 34 34 15 15 15 35 30 32 34 39 39 32 35 32 32 32 43 39 35 42 34 39 39 39
 40 50 50 57 57 47 43 42 39 34 33 23 28 20 20 24 26 26 31 32 31 33 21 21 21 29 25 29 29 29 30 38 38 36 36 54 43 43 50 41 31 18 20 32 27 25 34 40 29 29
 21 24 33 35 38 39 32 29 18 25 25 30 30 33 34 34 35 35 29 29 28 32 29 35 35 33 29 29 33 29 21 18 15 15 20 18 25 29 40 48 40 32 29 22 19 25 23 23 21 15
 15 17 24 27 26 29 25 24 26 22 18 15 18 23 25 25 24 23 25 24 20 17 18 18 15 15 18 11 15 10 9 8 19 15 9 12 9 11 15 21 15 18 18 21 16 23 14 20 14 15
 14 17 15 21 14 13 14 14 17 17 16 16 13 18 11 12 11 21 19 18 19 24 25 13 15 12 12 11 16 18 23 20 18 18 18

AF LL2273r U -45
AF LL2273f U 36
BS 1 50 LL2273r
BS 51 63 LL2273f
BS 64 64 LL2273r
BS 65 65 LL2273f
BS 66 68 LL2273r
BS 69 69 LL2273f
BS 70 70 LL2273r
BS 71 72 LL2273f
BS 73 73 LL2273r
BS 74 83 LL2273f
BS 84 93 LL2273r
BS 94 107 LL2273f
BS 108 108 LL2273r
BS 109 112 LL2273f
BS 113 116 LL2273r
BS 117 118 LL2273f
BS 119 119 LL2273r
BS 120 135 LL2273f
BS 136 136 LL2273r
BS 137 137 LL2273f
BS 138 138 LL2273r
BS 139 145 LL2273f
BS 146 146 LL2273r
BS 147 155 LL2273f
BS 156 161 LL2273r
BS 162 175 LL2273f
BS 176 176 LL2273r
BS 177 177 LL2273f
BS 178 178 LL2273r
BS 179 181 LL2273f
BS 182 184 LL2273r
BS 185 202 LL2273f
BS 203 203 LL2273r
BS 204 206 LL2273f
BS 207 207 LL2273r
BS 208 312 LL2273f
BS 313 317 LL2273r
BS 318 321 LL2273f
BS 322 323 LL2273r
BS 324 332 LL2273f
BS 333 335 LL2273r
BS 336 339 LL2273f
BS 340 341 LL2273r
BS 342 343 LL2273f
BS 344 344 LL2273r
BS 345 346 LL2273f
BS 347 350 LL2273r
BS 351 354 LL2273f
BS 355 356 LL2273r
BS 357 365 LL2273f
BS 366 366 LL2273r
BS 367 370 LL2273f
BS 371 377 LL2273r
BS 378 382 LL2273f
BS 383 383 LL2273r
BS 384 384 LL2273f
BS 385 385 LL2273r
BS 386 386 LL2273f
BS 387 391 LL2273r
BS 392 392 LL2273f
BS 393 393 LL2273r
BS 394 396 LL2273f
BS 397 399 LL2273r
BS 400 407 LL2273f
BS 408 414 LL2273r
BS 415 421 LL2273f
BS 422 432 LL2273r
BS 433 434 LL2273f
BS 435 435 LL2273r
BS 436 439 LL2273f
BS 440 441 LL2273r
BS 442 450 LL2273f
BS 451 451 LL2273r
BS 452 452 LL2273f
BS 453 453 LL2273r
BS 454 454 LL2273f
BS 455 466 LL2273r
BS 467 468 LL2273f
BS 469 471 LL2273r
BS 472 476 LL2273f
BS 477 483 LL2273r
BS 484 485 LL2273f
BS 486 487 LL2273r
BS 488 489 LL2273f
BS 490 507 LL2273r
BS 508 510 LL2273f
BS 511 517 LL2273r
BS 518 520 LL2273f
BS 521 528 LL2273r
BS 529 533 LL2273f
BS 534 557 LL2273r
BS 558 560 LL2273f
BS 561 581 LL2273r
BS 582 590 LL2273f
BS 591 593 LL2273r
BS 594 596 LL2273f
BS 597 602 LL2273r
BS 603 607 LL2273f
BS 608 645 LL2273r
BS 646 651 LL2273f
BS 652 663 LL2273r
BS 664 666 LL2273f
BS 667 669 LL2273r
BS 670 670 LL2273f
BS 671 735 LL2273r

RD LL2273r 781 0 0
aatxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccac
gcgtccgcttttttttttttttttttttttTTTTTCTCATAAAACCTCTG
TTTatat*tTGAACAAAGTTACATTATAAGATGAGATGATGAGTGATGAG
AAAGGAGAAAAAGATTTCTAAGAGGAGGAGAAGGTATCGATGATGGTGGT
GTGAAGGGGATcattGAGGTGAGTAGCCCAATTGTTGAGTGGGCCTTTAC
CAGTAGCAGCGGCTTGAACAGCGAAGCCCAAGAAGGCGACCATGGCAAGA
CGAGCGTGCTTGATCTCAGCTAACTGAAGCTGAGCCATCTTCTCAGGGTC
AGACGCTAAACCAAGCGGGTCGAAGAATTTGCCGCCAGGGTACAAACGCT
TCTCAGAGTCAAGCTCAGCGTTGCGCTGGAACTCGATGTAGCCGATCACT
AACACCTCGATCCATATCAACGTCGAGATGGAGAAGGGTAGTGGCTGCCC
CAAGTAGGACGATCCATCCACTAGCTCCACCTTTCCGGCGTCTTGCCAAG
TGACGCCGGTGAGCCAtTcGACGGagaGAGCGCCGAGAGTGGCGAGCATG
GCCCACCGTCCGTGAATCAGCTCGCATTCTCTGAACCtCtGGATCCCGAA
cACCtCGCTGTACGGCTGAAACGGAGTcgaTtTGGGGGCCgcctcttcGG
TACGGGttccGATCAcGtctccggctaagttcttcGccaGaTtCtggtcT
agtgaatctatatCgaaCTggagataCTcgg

QA 81 781 47 781
DS CHROMAT_FILE: LL2273r PHD_FILE: LL2273r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:14 2000

RD LL2273f 767 0 0
cttaaccggaaccccTCTGTTTATatcttGAACAAAGTTACATTATAAGA
TGAGATGATGAGTGATGAGAAAGGAGAAAAAGATTTCTAAGAGGAGGAGA
AGGTATCGATGATGGTGGTGTGAAGGGGATCACTGAGGTGAGTAGCCCAA
TTGTTGAGTGGGCCTTTACCAGTAGCAGCGGCTTGAACAGCGAAGCCCAA
GAAGGCGACCATGGCAAGACGAGCGTGCTTGATCTCAGCTAACTGAAGCT
GAGCCATCTTCTCAGGGTCAGACGCTAAACCAAGCGGGTCGAAGAATTTG
CCGCCAGGGTACAAACGCTTCTCAGAGTCAAGCTCAGCGTTGCGCTGGAA
CTCGATGTAGCCGATCACTAACACCTCGATCCATATCAACGTCGAGATGG
AGAAGGGTAGTGGCTGCCCCAAGTAGGACGATCCATCCACTAGCTCCACC
TTTCCGGCgtttTgtcaAGTGACGCcggcGAGCCAtccgACGGagaGAGC
GCCGAGAGTGGCGAGCATGGCCCACCgtncgcgaATCacctCGCATTCTC
TGAACCtCTGGattccgAACACCtccctgcacGGCTGAAACGGAgttcat
tcgcgggtcgCCTCttcGGTAcggcttcCGATCACgttctcggctccctc
ctttcccacactctgccccactcactcacatcccattcgttcattttgcc
cgcttcacctactttataggctcaatctgtctttttcccttatcgccctc
tcccctctcttgttacc

QA 28 526 14 637
DS CHROMAT_FILE: LL2273f PHD_FILE: LL2273f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:36 2000

CO Contig12 771 2 7 U
agcgcacacccaccatatgatctttaagggaatgacttaacaactgttgg
taatagttttgttgcttctcatataaCCCAATAGAAAAAAAAATTAATCA
TCCCGCTTATGGAAAATTAACATGCTTTCAGTTTTATTATAAAAAGTTTC
TAAGCATTAGCTCCAATGGGAACATTCTTGAGTCTTGATGTTCCGTAAAG
GGTTTCTTCAAAGCGGATGATCTCGTTCTTTGAGCCATAAGCAACTTGAG
TTCTATCGTCGAGGTTGACGATGGTCTTGTCGAGCACAGACTTGTATCCA
TCACTGCTGAATCCACCAGCATTCTCAATGAGTAGGCCTAAAGGAGCCAC
TTCGAACAAGAGTCTCAACTTTGCCTTAGCCGTAGGAGAAGTCACGTTTG
TGAAGATTCCTTTCTCCTTCACAATAATCTGGTTAACGTCAGGAACCATT
CCTCCTGTATATCTCAATGTGTACTTCTCTTTCACGTAGTAATCAATCAG
CTTGCTGTATTCAGAATTGTCAAACGTGGCTCTCAAGTTTCCTGGTGAGA
ACATTTTCCCTTCATTAATCTctgTGGTCTCCTTAACATGCTGCCATTTA
CCTTCATCAAGA*AGCAAGAAC*TCATGAG*TTCC*TGGAAACCCTTTAA
CAGCCAAAACATAAGTGgttcTTGGACCATagATTccCATGgCTGCAGcc
ACttGATCTcctcccgTGACTccggTtaaCTTATCACCAGGCCAAACCGg
ACgcgtGggCggacgcgtggc

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 39 37 35 35 35 37 37 40 46 51 56 56 56 56 40 40 37 40 40 35 35 35
 35 35 35 35 35 35 35 35 35 35 39 51 51 51 51 35 35 35 35 35 35 37 35 39 35 35 35 35 40 37 37 37 35 35 35 38 38 38 38 38 39 40 40 56 56 50 42 42 40 40
 40 40 40 40 42 37 37 40 35 35 35 35 35 43 40 51 51 56 56 51 51 51 51 51 43 41 45 45 45 51 51 45 45 45 45 45 43 43 43 42 42 38 43 43 40 41 45 56 56 56
 56 56 40 38 43 43 36 43 43 51 51 45 45 45 45 45 45 56 56 51 51 45 43 43 38 38 38 41 41 51 56 56 56 46 46 43 43 42 46 56 56 56 43 43 43 43 43 43 56 51
 45 43 43 43 43 43 43 45 45 45 51 51 51 56 56 43 43 43 43 43 43 43 51 56 56 56 51 51 45 45 45 45 45 43 43 43 43 43 43 43 43 43 43 45 51 51 51 51 51 51
 51 43 43 43 43 43 43 43 43 43 56 56 46 43 43 43 43 43 51 51 51 51 45 45 45 45 45 51 56 56 56 56 51 45 45 45 45 45 45 51 51 56 56 56 51 51 43 43 43 43
 43 43 43 51 51 51 56 51 51 51 51 51 51 51 51 51 45 45 45 45 45 45 56 56 56 50 50 46 46 51 51 51 51 51 51 46 46 50 50 50 56 56 45 45 45 45 45 51 56 56
 56 56 56 56 51 45 45 45 45 41 41 56 46 56 56 56 56 56 56 56 56 56 56 56 56 56 56 51 56 56 56 45 45 51 43 43 43 51 51 51 56 56 56 51 45 45 45 45 40 40
 51 51 51 51 51 56 56 56 56 56 45 45 45 45 45 45 56 56 50 50 50 45 45 40 45 40 42 56 56 56 56 56 51 51 51 51 51 51 56 56 56 56 48 56 44 44 42 43 45 45
 45 37 37 37 37 37 37 40 56 56 56 56 56 56 42 46 46 46 40 40 42 46 45 40 51 42 42 35 35 35 35 35 37 43 46 56 56 42 42 40 45 45 45 48 42 42 42 44 42 42
 42 42 42 42 42 56 56 42 46 42 40 38 35 35 38 40 40 38 42 37 48 16 16 11 21 21 40 40 40 44 40 40 40 34 32 29 34 48 32 32 29 29 25 25 27 29 33 33 34 34
 34 32 29 31 33 32 40 40 29 29 29 29 29 29 40 40 40 34 22 24 25 27 32 32 48 40 37 29 25 28 25 29 27 34 34 27 32 32 32 32 32 32 32 29 25 24 29 32 38 41
 38 38 35 42 39 37 27 26 25 20 25 24 20 15 10 10 17 44 46 50 48 70 45 42 40 24 18 18 22 24 23 18 18 27 40 29 22 19 23 25 25 25 25 24 19 15 21 23 18 18
 25 32 40 26 25 17 15 19 15 10 15 17 26 22 24 21 25 18 13 15 12 20 16 19 19 32 32 24 25 29 27 29 27 27 25 22 22 25 24 20 22 25 27 25 26 18 24 21 18 18
 18 18 22 13 13 21 18 18 17 17 13 11 19 15 0 0 0

AF LL2274f U -3
AF LL2274r C 4
BS 1 652 LL2274f
BS 653 660 LL2274r
BS 661 661 LL2274f
BS 662 663 LL2274r
BS 664 671 LL2274f
BS 672 679 LL2274r
BS 680 771 LL2274f

RD LL2274f 776 0 0
ctgnagcgcacacccaccatatgatctttaagggaatgacttaacaactg
ttggtaatagttttgttgcttctcatataaCCCAATAGAAAAAAAAATTA
ATCATCCCGCTTATGGAAAATTAACATGCTTTCAGTTTTATTATAAAAAG
TTTCTAAGCATTAGCTCCAATGGGAACATTCTTGAGTCTTGATGTTCCGT
AAAGGGTTTCTTCAAAGCGGATGATCTCGTTCTTTGAGCCATAAGCAACT
TGAGTTCTATCGTCGAGGTTGACGATGGTCTTGTCGAGCACAGACTTGTA
TCCATCACTGCTGAATCCACCAGCATTCTCAATGAGTAGGCCTAAAGGAG
CCACTTCGAACAAGAGTCTCAACTTTGCCTTAGCCGTAGGAGAAGTCACG
TTTGTGAAGATTCCTTTCTCCTTCACAATAATCTGGTTAACGTCAGGAAC
CATTCCTCCTGTATATCTCAATGTGTACTTCTCTTTCACGTAGTAATCAA
TCAGCTTGCTGTATTCAGAATTGTCAAACGTGGCTCTCAAGTTTCCTGGT
GAGAACATTTTCCCTTCATTAATCTctgTGGTCTCCTTAACATGCTGCCA
TTTACCTTCATCAAGA*AGCAAGAAC*TCATGAG*TTCC*TGGAAACCCT
TTAACAGCCAAAACATAAGTGgttcTTgGACCATagATTccCATGgCTGC
AGccACttGATCTcctcccgTGACTccggTtaaCTTATCACCAGGCCAAA
CCGgACgcgtGggCggacgcgtggcn

QA 81 772 5 775
DS CHROMAT_FILE: LL2274f PHD_FILE: LL2274f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:41 2000

RD LL2274r 866 0 0
atataactcttagaaacaacaattcagcagtacggacatggagaatcagc
atgcgctcagtcggaccatacacagagtccaatcataggctgcaatgaga
acagtatttagttgtgaagtgccgaacaagggattctcaaaacggacgat
ctcgttcttgaagccataagcagcttgagctcgatcgtcgagtgtaacga
cgctctcatcgagcgcataggtagtatccgacaccgaataagccaccacc
actcgcaaaggaagccttaaaatagccgctgatacaaagctctccactat
gcttcaccaggtagcatgaagcgcgcgctttgatgacagtcatcacgttc
ctaccttgcgagcagagtatactactagagtgtatactgtcccagcgaga
gcctatntccatacgctgtcactatgcacctaagcgtcgttacagtgctc
aatttcccaggtagctaactcaatcacagcantgtagtaatcagatgatg
tcggtcagtggctagctaaggttgtctgagagatgagcaattatctcctc
atacatctagttgtattgtggtcgccatcaacattggagacatcatacat
tcatcagaatagcaagaacgtcatgaggttccgtgtaatccgtttaACAG
CCAAAACATAagaga*tcTTGGACCATacaatgccatgggggcaagcact
*gctctcctccatgttgcaccggttaacaaaactaccagcccaatccatc
cgtgtagccggaagcgtgctcgaacgcggagacgaacgcgcgggcggacg
cgtgggtcgacccgggaatcccggaacggtaccgcaagtacccngagggn
gnnnaaaaggttatac

QA -1 -1 596 711
DS CHROMAT_FILE: LL2274r PHD_FILE: LL2274r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:19 2000

CO Contig13 319 2 1 U
cttTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTAAATTGTAAACCAAAAAATGATATTACATTACAT
GTGTTAACATATTTCTACTAGAAATGACATCACTAGAACTCGAATAGACT
TAAAATTAAAGAAAAGATGAATGACTGTTATTTACCATACAACGCAAGCG
CAAGAGAATTGTTTTCCATGTATTCATACACGAGTAGCAATTGATTCTTC
TCGACACAACATCCATAAAGCTTGACAAGGTTTGGATGGTTCAACCCTGA
GATCATTCCGGACGCGTGG

BQ
 15 15 15 36 46 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56
 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 51 51 51 51 45 45 45 45 45 45 45 56 71 71 71 71 71 71 71 71 66 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 83 83 82 83 78 83 90 85 90 90 90 90 85 84 84 84 84 84 85 85 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 85 83 83 83 83 83 83 90 85 90 90 90 90
 90 84 90 90 85 85 80 80 80 80 90 90 90 90 90 90 90 90 90 90 90 90 90 90 85 85 80 80 86 86 86 86 90 84 84 84 85 85 85 90 82 70 70 70 70 70 70 69 69 69
 69 72 75 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 78 78 78 82 82 82 83 83 83 90 83 83 83 83 78 78 78 78 78 78 78 82 83 83 83 89 89 83 90 90 89 82
 82 82 82 82 83 90 90 90 90 90 90 90 90 90 90 90 90 86 83 88 78 78 76 76 83 83 89 83 85 85 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 85 80 80 78 78 83 88 90 90 90 49 49 49 34 33 32

AF LL2275r C -406
AF LL2275f U 63
BS 1 319 LL2275r

RD LL2275r 771 0 5
aaagggagcccccgatttagagcttgacggggaaagccggcgaacgtggc
gagaaaggaagggaagaaagcgaaaggagcgggcgctagggcgctggcaa
gtgtagcggtcacgctgcgggtaaccaccacacccgccgcgcttaatgcg
ccgctacagggcgcgtcccattcgccattcagggtgcgcaactgttggga
agggcgatcggtgcgggccttttcgctattacgccagctggcgaaagggg
gatgtgctgcaaggcgattaagttgggtaacgccagggttttxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxcttTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTAAATTGTAAACCAAAAAATGATATTAC
ATTACATGTGTTAACATATTTCTACTAGAAATGACATCACTAGAACTCGA
ATAGACTTAAAATTAAAGAAAAGATGAATGACTGTTATTTACCATACAAC
GCAAGCGCAAGAGAATTGTTTTCCATGTATTCATACACGAGTAGCAATTG
ATTCTTCTCGACACAACATCCATAAAGCTTGACAAGGTTTGGATGGTTCA
ACCCTGAGATCATTCCGGACGCGTGGxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxatt

QA 1 726 408 726
DS CHROMAT_FILE: LL2275r PHD_FILE: LL2275r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:23 2000

RT{
LL2275r chimera phrap 1 292 000919:094547
}

RT{
LL2275r matchElsewhereHighQual phrap 1 119 000919:094547
}

RT{
LL2275r matchElsewhereHighQual phrap 121 183 000919:094547
}

RT{
LL2275r matchElsewhereHighQual phrap 185 236 000919:094547
}

RT{
LL2275r matchElsewhereHighQual phrap 222 292 000919:094547
}

RD LL2275f 767 0 2
ctttaaggtgacaaCCAAAAAATGATATTACATTACATGTGTTAACATAT
TTCTACTAGAAATGACATCACTAGAACTCGAATAGACTTAAAATTAAAGA
AAAGATGAATGACTGTTATTTACCATACAACGCAAGCGCAAGAGAATTGT
TTTCCATGTATTCATACACGAGTAGCAATTGATTCTTCTCGACACAACAT
CCATAAAGCTTGACAAGGTTTGGATGGTTCAACCCTGAGATCATTCCGGA
CGCGTGGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxGCCTGGGGTGCCTAATGAGTGAGCTAACTC
ACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTC
GTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGC
GTATTGGGCGCCAGGGTGGTTTTTCTTTTCACCAGTGAGACGGGCAACAG
CTGATTGCCCTTCACCGCCTGGCCCTGAGAGAGTTGCAGCAAGCGGTCcA
CGCTGGTTTGCCCCAGCAGGCGAAAATCCTGTTTGATGGTGgttaACGGC
GGGATATAACATGAGCTGTCTTCGGTATCGTCGTATCCCACTACCGAGAT
ATCCGCACCAACGCGCA

QA 15 767 13 257
DS CHROMAT_FILE: LL2275f PHD_FILE: LL2275f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:46 2000

RT{
LL2275f chimera phrap 421 767 000919:094547
}

RT{
LL2275f matchElsewhereHighQual phrap 421 767 000919:094547
}

CO Contig14 1056 2 32 U
ccttttcttagaagcatatgataaaaccattgtagtatatcaagaagatg
aagatggaagtttgttttcacagtgtcaatAGAAATTGTCATCAAACAAA
GTCTACAAAGCTCTTTAATAAACTAGAAATGGCTTAAAGTGTAGGAGCTC
TCTCAGCGGTTCCAGCTATGACGGTAAGCAAATTGTTTCCAAAAGGATCA
CTGAGATGCTTTGAAAGGTTCTCAACAGGACCTTCTCCAGTAACATAAGC
TTGGATGAAGAAACCGAGCATCGCAAACATGGCTAATCTCCCGTTCTTGA
TCTCTTTAACCTTGAGGAGAGCTCCTTGTTCGGGGTCCTTAGCAAGTCCT
AAAGGATCAAATGGACCTCCGGGGTGTAGCTTGTCCTCAAAATCCAATCC
GTTGGTGATTCTGTAGTACTCGGCTCCACCGAGGAGAACAACCTCAGCAA
CTACGGCGAGAACAAGGTTGATTGGGATGTTCTTGCCAAAGTAGTTCAAT
GTGTTTCCATCAAGAAGCAGAGCACCAGTCTTGAACCAGACGGCTTCAGG
ACCACAGTTAGCTCCGTATTTGTTTAAAGCTTCAGGGATGATGAAACCAG
CTGCTCCCAACATAGCCCATCTCGCATGGATCAGCTCAAAGGCTTGGTAT
TTAGCAAAGTTCTCAGGCTTCTTTCCAAGTCCAAATGGGTCATAGCCATA
GTCTCCAGCAACTTCACCGTTTAAGTACTCTGGGATCTCTGATCTGTCCA
AAAGACCATCCGGCAGGAAAACTCTCCTGTCAGGACCATACCACTTGGCG
AGTTCATCGTTAGCAACAGAGACGGTTTTGGCCTTGGCAGGAGCTGGCTT
TTTCTTGGAGAACAGAGCAACTGTCTTAAACGTAGCCGGGCTCGATGCCG
ATGGAGCAGACGATCTTGACACTGCCTTGAAGTTAAGTGGCTTACCAAGC
ATTTCCGAAACACCCATAGACGCCATCTTTGTACCCCAAAGTTTCAAGCT
TTAACTCTGTTTCAAAACAAtgaaatgctaagtgaaaggaaggaacggac
gcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 40 40 51 51 46 46 46 46 46 40 40 40 46 51 51 51 51 51 51
 51 39 39 39 39 39 40 51 40 39 39 39 39 35 39 39 35 35 35 39 38 35 35 35 35 35 35 40 51 39 35 35 35 35 35 35 39 39 51 43 43 43 43 43 43 43 35 35 35 35
 35 35 43 43 43 43 43 43 35 35 37 43 43 43 35 35 35 35 35 35 43 43 43 43 43 43 43 43 43 43 43 56 56 56 56 38 38 43 43 46 46 56 56 56 56 51 51 43 36 36
 36 36 36 43 51 43 35 35 35 35 35 43 56 56 56 56 56 51 45 45 45 45 45 45 51 51 51 43 43 43 43 43 43 45 45 45 45 45 51 56 56 56 51 45 45 45 45 43 43 45
 45 45 51 56 51 51 51 51 51 51 51 45 43 43 43 43 45 45 56 43 36 36 36 36 36 36 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 45 45 45 51 51 51 51 51
 51 51 51 51 45 45 45 45 45 45 45 45 51 51 56 56 56 56 71 58 58 58 58 67 65 67 78 75 73 80 80 80 77 67 69 69 60 60 60 66 69 76 74 76 69 69 69 60 60 63
 69 70 85 85 85 85 90 88 88 88 85 81 71 64 69 64 64 69 73 77 83 82 81 83 83 81 81 70 72 72 69 74 72 80 75 75 80 80 88 88 88 88 85 81 81 88 88 77 81 89
 79 74 74 85 88 83 88 85 85 85 90 90 78 80 85 88 78 76 85 81 85 90 85 79 77 90 90 90 79 79 90 85 80 80 80 80 75 75 76 76 76 80 80 80 83 83 83 77 63 63
 70 85 77 74 72 72 72 75 72 89 90 90 90 90 84 84 81 79 79 82 88 88 90 90 90 90 90 90 76 74 74 76 77 67 71 75 78 78 86 80 75 75 75 79 72 84 90 90 90 90
 90 90 90 90 85 80 90 90 90 90 90 90 90 90 90 90 90 90 90 90 83 83 78 83 77 77 76 83 88 88 90 90 77 72 72 72 72 88 88 88 90 84 84 86 88 88 90 90 90 90
 90 90 90 86 80 84 79 79 79 75 79 76 88 82 85 90 90 90 90 90 90 88 90 90 90 86 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 85 85 90 86 74 79 80
 74 72 83 83 81 78 78 90 85 85 74 75 75 75 75 79 86 90 90 90 80 69 69 69 67 70 83 85 90 90 90 83 77 77 72 72 81 81 85 90 83 83 69 65 64 66 74 69 85 83
 72 72 66 61 56 60 55 59 56 64 65 74 90 83 80 75 76 80 71 75 80 67 71 75 73 67 61 61 66 68 68 74 90 90 90 85 80 80 75 80 75 83 83 70 68 65 65 68 70 69
 76 83 72 80 70 67 72 68 65 67 69 78 74 74 77 81 77 76 72 66 66 62 60 60 64 68 68 72 68 68 64 69 74 73 74 90 90 90 90 90 90 90 90 76 77 67 71 66 71 78
 78 82 66 71 65 59 64 73 66 69 62 69 60 66 66 52 53 53 59 51 51 51 51 51 51 56 43 43 43 43 43 43 45 45 45 51 51 56 56 56 56 56 56 56 56 43 43 43 43 43
 43 43 43 43 43 51 45 45 43 43 43 43 43 43 43 43 51 51 51 51 45 45 43 43 43 43 43 43 51 51 51 51 51 51 43 43 43 43 43 43 45 45 45 45 45 56 56 56 56 56
 56 56 56 56 56 51 51 51 51 51 51 51 51 45 43 43 43 43 43 43 51 51 51 51 51 51 51 51 43 43 43 43 43 43 43 43 43 43 45 45 43 43 43 43 43 43 43 43 43 43
 43 43 43 35 35 35 35 35 35 43 43 43 43 43 51 51 51 51 51 51 51 51 51 51 51 51 51 51 43 43 43 43 43 40 40 40 40 38 39 40 40 40 40 40 46 39 39 39 39 39
 39 46 51 40 39 39 39 39 39 40 51 51 51 56 39 35 35 35 35 35 35 35 35 35 40 56 51 51 51 39 39 40 40 40 40 56 56 56 51 51 51 40 40 46 40 40 40 45 45 35
 40 40 40 40 35 51 40 40 40 40 46 46 46 46 46 51 51 51 40 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0

AF LL2277f U 1
AF LL2277r C 314
BS 1 425 LL2277f
BS 426 428 LL2277r
BS 429 430 LL2277f
BS 431 431 LL2277r
BS 432 459 LL2277f
BS 460 460 LL2277r
BS 461 482 LL2277f
BS 483 483 LL2277r
BS 484 484 LL2277f
BS 485 485 LL2277r
BS 486 486 LL2277f
BS 487 490 LL2277r
BS 491 497 LL2277f
BS 498 498 LL2277r
BS 499 503 LL2277f
BS 504 509 LL2277r
BS 510 510 LL2277f
BS 511 511 LL2277r
BS 512 537 LL2277f
BS 538 555 LL2277r
BS 556 561 LL2277f
BS 562 566 LL2277r
BS 567 569 LL2277f
BS 570 578 LL2277r
BS 579 579 LL2277f
BS 580 587 LL2277r
BS 588 593 LL2277f
BS 594 611 LL2277r
BS 612 617 LL2277f
BS 618 752 LL2277r
BS 753 769 LL2277f
BS 770 1056 LL2277r

RD LL2277f 776 0 0
ccttttcttagaagcatatgataaaaccattgtagtatatcaagaagatg
aagatggaagtttgttttcacagtgtcaatAGAAATTGTCATCAAACAAA
GTCTACAAAGCTCTTTAATAAACTAGAAATGGCTTAAAGTGTAGGAGCTC
TCTCAGCGGTTCCAGCTATGACGGTAAGCAAATTGTTTCCAAAAGGATCA
CTGAGATGCTTTGAAAGGTTCTCAACAGGACCTTCTCCAGTAACATAAGC
TTGGATGAAGAAACCGAGCATCGCAAACATGGCTAATCTCCCGTTCTTGA
TCTCTTTAACCTTGAGGAGAGCTCCTTGTTCGGGGTCCTTAGCAAGTCCT
AAAGGATCAAATGGACCTCCGGGGTGTAGCTTGTCCTCAAAATCCAATCC
GTTGGTGATTCTGTAGTACTCGGCTCCACCGAGGAGAACAACCTCAGCAA
CTACGGCGAGAACAAGGTTGATTGGGATGTTCTTGCCAAAGTAGTTCAAT
GTGTTTCCATCAAGAAGCAGAGCACCAGTCTTGAACCAGACGGCTTCAGG
ACCACAGTTAGCTCCGTATTTGTTTAAAGCTTCAGGGATGATGAAACCAG
CTGCTCCCAACATAGCCCATCTCGCATGGATCAGCTCAAAGGCTTGGTAT
TTAGCAAAGTTCTCAGGCTTCTTTCCAAGTCCAAATGGGTCATAGCCATA
GTCTCCAGCAACTTCACCGTTTAAGTACTCTGGGATCTCTGATCTGTCCA
AAAGACCATCCGGCAGGAAAACTCTC

QA 81 752 1 776
DS CHROMAT_FILE: LL2277f PHD_FILE: LL2277f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:56 2000

RD LL2277r 787 0 0
nagGAGAGCTCCTTGTTCGGGGTCCTTAGCAAGTCCTAAAGGATCAAATG
GACCTCCGGGGTGTAGCTTGTCCTCAAAATCCAATCCGTTGGTGATTCTG
TAGTACTCGGCTCCACCGAGGAGAACAACCTCAGCAACTACGGCGAGAAC
AAGGTTGATTGGGATGTTCTTGCCAAAGTAGTTCAATGTGTTTCCATCAA
GAAGCAGAGCACCAGTCTTGAACCAGACGGCTTCAGGACCACAGTTAGCT
CCGTATTTGTTTAAAGCTTCAGGGATGATGAAACCAGCTGCTCCCAACAT
AGCCCATCTCGCATGGATCAGCTCAAAGGCTTGGTATTTAGCAAAGTTCT
CAGGCTTCTTTCCAAGTCCAAATGGGTCATAGCCATAGTCTCCAGCAACT
TCACCGTTTAAGTACTCTGGGATCTCTGATCTGTCCAAAAGACCATCCGG
CAGGAAAACTCTCCTGTCAGGACCATACCACTTGGCGAGTTCATCGTTAG
CAACAGAGACGGTTTTGGCCTTGGCAGGAGCTGGCTTTTTCTTGGAGAAC
AGAGCAACTGTCTTAAACGTAGCCGGGCTCGATGCCGATGGAGCAGACGA
TCTTGACACTGCCTTGAAGTTAAGTGGCTTACCAAGCATTTCCGAAACAC
CCATAGACGCCATCTTTGTACCCCAAAGTTTCAAGCTTTAACTCTGTTTC
AAAACAAtgaaatgctaagtgaaaggaaggaacggacgcgtggxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxat

QA 6 707 2 743
DS CHROMAT_FILE: LL2277r PHD_FILE: LL2277r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:33 2000

CO Contig15 728 2 1 U
taaccccgccccaaaggaagttaagaaagggaaaggggcggggctaggtc
cctctcaagtgtgcggtttttttgacggaacaaggggggccctttgttaa
ttccccctacaggaaaagggaattcgctcaaaggggtttacatttgttag
caacgggtttttcccagggccttttggttaaaacgccggccgtgaaaaag
agtatgtgggcacacaaaaaaaagtttggtaacccacgggccttgccagt
aaattgggtgctattaaaaggcccgccccatttatttaggttggctttat
aaaagatttatttttttgcattgtttcgcgtTTTttatTTtgtTtTTTTt
ttatttttTttttTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTCAGACTCTACCAAACGTAAAATAAAACCTGCT
TGTAGCACAACTCCAGGCAACAACAACAAGCAAATTACAATCTCTAATAT
ATTTGCCTAGTGACTGACAATAGGCAAATAGGGATAGAGACCCCTTGAAG
ATGTAGTAGTAGCTAAGACTAAGATTTATGTGCTCTGTGATCAGGCCTTA
ACCTCCTCTCCACCACCACCAGATCCTCCTCCAGCTTTCTCTCTCTCTTT
CTCAGCATCCTCTTCTTCTCCTTCCTCAGCATCGGCTTCATCTGCTAGCT
TTGTGAGCTCATCTTGGCGGACGCGTGG

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 16 25 23 24 16 12 12 12 22 33 12 11 11 20 19 29 29 33 44 19
 16 11 11 11 19 12 17 17 24 19 15 15 15 21 28 48 48 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56
 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 51 51 51 51 51 56 56 56 56 71 75 82 75 72 72 77 75 75 77 70 70 70 74 76 70 71 71 74 78 90 90 77
 80 72 74 77 77 77 83 83 80 80 90 90 89 89 82 82 82 76 83 83 85 85 85 90 90 90 90 90 90 90 90 89 83 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 82 82 83 83 89 83 85 85 85 85 85 85 82 82 82 83 83 83 88 90 82 80 80 80 80 80 82 82 82 85 82 82 82 85 90 88 88 90 90 90 90 90 90 90
 90 85 80 80 78 78 78 78 78 78 78 78 78 78 86 86 86 86 86 80 80 80 80 89 82 88 90 78 78 78 73 73 78 75 73 78 78 80 86 89 88 88 81 81 86 83 76 76 75 75
 75 75 90 90 90 90 90 90 90 86 86 86 90 90 90 90 90 90 90 88 88 85 85 85 85 85 85 90 90 90 90 90 84 84 80 80 87 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 77 76 76 76 76 76 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 82 82 72 76 76 71 71 71 72 72 78 82 86 83 82 82 76 75 75 75 77 77 78
 78 78 82 81 81 79 74 89 67 66 66 69 75 75 75 75 75 75 70 70 76 75 44 44 44 29 29 34

AF LL2279r C 1
AF LL2279f U 412
BS 1 728 LL2279r

RD LL2279r 772 0 0
taaccccgccccaaaggaagttaagaaagggaaaggggcggggctaggtc
cctctcaagtgtgcggtttttttgacggaacaaggggggccctttgttaa
ttccccctacaggaaaagggaattcgctcaaaggggtttacatttgttag
caacgggtttttcccagggccttttggttaaaacgccggccgtgaaaaag
agtatgtgggcacacaaaaaaaagtttggtaacccacgggccttgccagt
aaattgggtgctattaaaaggcccgccccatttatttaggttggctttat
aaaagatttatttttttgcattgtttcgcgtTTTttatTTtgtTtTTTTt
ttatttttTttttTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTCAGACTCTACCAAACGTAAAATAAAACCTGCT
TGTAGCACAACTCCAGGCAACAACAACAAGCAAATTACAATCTCTAATAT
ATTTGCCTAGTGACTGACAATAGGCAAATAGGGATAGAGACCCCTTGAAG
ATGTAGTAGTAGCTAAGACTAAGATTTATGTGCTCTGTGATCAGGCCTTA
ACCTCCTCTCCACCACCACCAGATCCTCCTCCAGCTTTCTCTCTCTCTTT
CTCAGCATCCTCTTCTTCTCCTTCCTCAGCATCGGCTTCATCTGCTAGCT
TTGTGAGCTCATCTTGGCGGACGCGTGGxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxat

QA 330 728 1 728
DS CHROMAT_FILE: LL2279r PHD_FILE: LL2279r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:42 2000

RD LL2279f 779 0 5
ncttttaagacaactACCAAACGTAAAATAAAACCTGCTTGTAGCACAAC
TCCAGGCAACAACAACAAGCAAATTACAATCTCTAATATATTTGCCTAGT
GACTGACAATAGGCAAATAGGGATAGAGACCCCTTGAAGATGTAGTAGTA
GCTAAGACTAAGATTTATGTGCTCTGTGATCAGGCCTTAACCTCCTCTCC
ACCACCACCAGATCCTCCTCCAGCTTTCTCTCTCTCTTTCTCAGCATCCT
CTTCTTCTCCTTCCTCAGCATCGGCTTCATCTGCTAGCTTTGTGAGCTCA
TCTTGGCGGACGCGTGGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxcgtcaaagcctggggtgcctaatgag
cgagctaactcacattaattgcgctgcgctcactgcccgctttccagtcg
ggacgcctgccgtgccacctgcattaacgcactccccatcgcgcggggag
aggcggcttgcgcactgtccgccacggcggctctctttctcaccactgag
acggtcgacacccgcccgccctcttccgtctcgtcccgtcacagccgctc
cgtgccgcctcatcctcgatcgtcccggcgggctcatcgttctgcccgct
cgcgcgctcgtcccccttttccgctcccc

QA 17 545 14 317
DS CHROMAT_FILE: LL2279f PHD_FILE: LL2279f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:05 2000

RT{
LL2279f chimera phrap 481 654 000919:094547
}

RT{
LL2279f matchElsewhereHighQual phrap 590 606 000919:094547
}

RT{
LL2279f matchElsewhereHighQual phrap 525 553 000919:094547
}

RT{
LL2279f matchElsewhereHighQual phrap 502 523 000919:094547
}

RT{
LL2279f matchElsewhereHighQual phrap 482 500 000919:094547
}

CO Contig16 440 2 50 U
CCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTAAAGTAAAACCAACGAAAGACTCA*ACAGCTTG
AAAACCCCATAAAAAAAAACAGAGTTTAGAGTTTCCAAAGAAGAAAACCA
AATCATGGTCTTCTCTTTGCTTCTACAAACCTCAAATCATAATGTTTTAA
GAAACTAAAGCCAAATCCATACCATACATACTTAGAAATGTCTTGCTCGC
TCCCTTCCTCTGATCACTTCAACAACTACGCTTGTTTCCCTTCTTCAGGC
TCGTCTTTTGACGCCTCCTTGATCTCATCACCACCCACCTCATCGTTGAG
GTCAGAAGTCCAGAGGGTCAGATTGTCACGGAGAAGTTGCATTATCAGTG
TACTGTCTTTGTATGATTCTTCTCCTAATCGGACGCGTGG

BQ
 27 42 47 50 50 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56
 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 41 45 43 43 43 43 43 43 56 56 46 43 51 43 46 47 82 75 75 65 56 56 56 56 51 51 66 66 58 77 79 84 77
 79 90 90 90 90 90 79 79 79 79 85 90 90 90 90 90 90 90 90 86 80 80 80 80 82 90 90 90 90 90 90 90 90 90 90 90 86 82 90 90 90 90 90 86 82 90 90 90 90 90
 90 90 90 90 80 80 87 80 85 89 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 82 82 82 85 90 90 90 90 90 90 86 86 86 86
 90 90 86 86 86 78 71 75 76 76 76 83 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 85 90 88 88 88 88 90 90 90 90 90 88 85 88 78 90 86 78 78 78 78 78 78
 86 90 90 90 90 90 90 88 88 88 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 86 86 86 86 86 79 86 88 90 90 90 90 90 90 90 90 90 90 90 90 87 86 86 88 79
 77 77 79 79 86 90 90 90 86 78 78 78 78 78 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 83 83 83 90 84 84 84 84 84 85 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 85 85 85 90 86 86 82 90 90 90 90 90 82 82 90 90 90 90 85 85 86 84 77 74 76 76 76 76 90 90 90 90 90 90 78 76 81
 85 83 82 77 79 80 80 81 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 76 76 90 80 90 90 90 58 58 58 43 51 56

AF LL2280r C -296
AF LL2280f U 66
BS 1 82 LL2280r
BS 83 87 LL2280f
BS 88 139 LL2280r
BS 140 144 LL2280f
BS 145 157 LL2280r
BS 158 159 LL2280f
BS 160 160 LL2280r
BS 161 161 LL2280f
BS 162 162 LL2280r
BS 163 166 LL2280f
BS 167 184 LL2280r
BS 185 185 LL2280f
BS 186 191 LL2280r
BS 192 195 LL2280f
BS 196 208 LL2280r
BS 209 212 LL2280f
BS 213 215 LL2280r
BS 216 217 LL2280f
BS 218 220 LL2280r
BS 221 228 LL2280f
BS 229 229 LL2280r
BS 230 230 LL2280f
BS 231 234 LL2280r
BS 235 242 LL2280f
BS 243 257 LL2280r
BS 258 263 LL2280f
BS 264 276 LL2280r
BS 277 287 LL2280f
BS 288 288 LL2280r
BS 289 295 LL2280f
BS 296 299 LL2280r
BS 300 316 LL2280f
BS 317 319 LL2280r
BS 320 328 LL2280f
BS 329 337 LL2280r
BS 338 361 LL2280f
BS 362 364 LL2280r
BS 365 371 LL2280f
BS 372 372 LL2280r
BS 373 378 LL2280f
BS 379 382 LL2280r
BS 383 386 LL2280f
BS 387 394 LL2280r
BS 395 404 LL2280f
BS 405 405 LL2280r
BS 406 409 LL2280f
BS 410 410 LL2280r
BS 411 431 LL2280f
BS 432 434 LL2280r
BS 435 440 LL2280f

RD LL2280r 782 0 5
cacgctgcgcgtaaccaccacaccccccgcgcttaatgcgccgctacagg
gcgcgtcccattcgccattcaggctgcgcaactgttgggaagggcgatcg
gtgcgggccttttcgctattacgccaactggcgaaagggggatgtgctgc
aaggcgattaagttgggtaacgccagggttttxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxCCT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTAAAGTAAAACCAACGAAAGACTCA*ACAGCTTGAAA
ACCCCATAAAAAAAAACAGAGTTTAGAGTTTCCAAAGAAGAAAACCAAAT
CATGGTCTTCTCTTTGCTTCTACAAACCTCAAATCATAATGTTTTAAGAA
ACTAAAGCCAAATCCATACCATACATACTTAGAAATGTCTTGCTCGCTCC
CTTCCTCTGATCACTTCAACAACTACGCTTGTTTCCCTTCTTCAGGCTCG
TCTTTTGACGCCTCCTTGATCTCATCACCACCCACCTCATCGTTGAGGTC
AGAAGTCCAGAGGGTCAGATTGTCACGGAGAAGTTGCATTATCAGTGTAC
TGTCTTTGTATGATTCTTCTCCTAATCGGACGCGTGGxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxatt

QA 94 737 298 737
DS CHROMAT_FILE: LL2280r PHD_FILE: LL2280r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:10 2000

RT{
LL2280r chimera phrap 1 182 000919:094547
}

RT{
LL2280r matchElsewhereHighQual phrap 1 25 000919:094547
}

RT{
LL2280r matchElsewhereHighQual phrap 27 110 000919:094547
}

RT{
LL2280r matchElsewhereHighQual phrap 75 126 000919:094547
}

RT{
LL2280r matchElsewhereHighQual phrap 128 182 000919:094547
}

RD LL2280f 777 0 3
ctttaagtaacccaACGAAAGACTcanacAGCTTGAAAACCCCATAAAAA
AAAACAGAGTTTAGAGTTTCCAAAGAAGAAAACCAAATCATGGTCTTCTC
TTTGCTTCTACAAACCTCAAATCATAATGTTTTAAGAAACTAAAGCCAAA
TCCATACCATACATACTTAGAAATGTCTTGCTCGCTCCCTTCCTCTGATC
ACTTCAACAACTACGCTTGTTTCCCTTCTTCAGGCTCGTCTTTTGACGCC
TCCTTGATCTCATCACCACCCACCTCATCGTTGAGGTCAGAAGTCCAGAG
GGTCAGATTGTCACGGAGAAGTTGCATTATCAGTGTACTGTCTTTGTATG
ATTCTTCTCCTAATCGGACGCGTGGxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxgcctggggtgcc
taatgagtgagctaactcacattaattgcgttgcgctcactgcccgcttt
ccagtcgggaaacctgtcgtgccagctgcattaatgaatcggccaacgcg
cggggagaggcggcttgcgtattgggcgccagggtggtttttcttttcac
cagtgagacgggcaacagctgattgcccttcaccgcctggccctgagaga
gttgcagcaagcggtccacgctggttt

QA 29 755 12 375
DS CHROMAT_FILE: LL2280f PHD_FILE: LL2280f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:32 2000

RT{
LL2280f chimera phrap 539 777 000919:094547
}

RT{
LL2280f matchElsewhereHighQual phrap 665 777 000919:094547
}

RT{
LL2280f matchElsewhereHighQual phrap 539 663 000919:094547
}

CO Contig17 969 2 46 U
cttttagaaacgaggttcggtttctgataaaatcatacaaagatacgaca
aaggaagtttcacaaatatacaaacaaactCTCTTTCACATGATAATTAA
CCTTTTAACTCCTTCACTTTCCGGGGACGAAGTTGGTGGCAAAGGCCCAT
GCATTGTTGTTGACTGGATCAGCCAAATGGTCAGCAAGATTCTCCAACGG
TCCCTTTCCGGTGACGATAGCCTGAACGAAGAATCCAAACATAGAGAACA
TAGCCAACCTTCCGTTCTTGATCTCCTTCACCTTCAACTCCGCGAAAGCT
TCTGGGTCGGTAGCAAGACCCAACGGGTCAAAGCTGCCTCCTGGGTAGAG
CAAGTCCTCTGCTTCCCCCAATGGTCCTTCTCCGGCGACTCTGTAACCTT
CAACAGCTCCCATGAGGATCACCTGAGTAGCCCAAATGGCTAAGATGCTC
TGTGCGTGGACCAAGCTCGGGTTTCCCAAGTAGTCGAGCCCTCCTTCGCT
GAAGATCTGTGAACCAGCCTTGAACCAAACAGCTTCTCCGAACTTCACTC
CGTTCCTAGCCAAAAGCTCAGGGAAAACGCAGCCTAGGGCTCCAAGCATG
GCCCATCTGCAGTGGATAACTTCTAGCTCACGGTTCCTGGCGAAGGTCTC
GGGGTCAGCGGAAAGACCGGCGGTGTCCCATCCGTAGTCACCGGGGAACT
CTCCTGTGAGGTAGCTTGGGGGCTCTCCGGAGAATGGACCCAAGTACTTG
ACCCTGTCGGATCCGTACCATGGGCTGCCAGATGGACCGGTGGGTTTGAC
GGTTTTTCTCATGGTGACACGGCCGGTTCCAAAGACCTCTGAGGCTCCCG
GTGAGAGCTTCACGGCCTTTCCGGTAAAGGCAGGGGAGGACAGAGCCATG
GTTGAGGCAGCCATTAGAAATTTTCTTGATCTTttttagtttttgtgttt
tttttttcggacggcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 56 56 56 40 40 40 40 39 39 40 51 51 51 51 35 35 35 35 35
 35 45 45 40 46 46 40 40 40 45 45 45 46 46 40 40 40 40 45 45 45 45 45 51 40 39 35 35 35 35 35 35 56 56 56 56 40 40 40 40 40 40 40 40 40 40 40 40 43 43
 43 43 43 43 56 56 51 51 51 43 43 43 43 43 43 43 45 51 45 43 40 40 43 37 40 41 51 56 56 56 56 37 38 38 38 38 38 42 43 41 41 41 41 41 38 36 36 36 38 36
 40 42 42 42 41 45 40 38 38 38 41 38 38 36 36 36 36 36 40 43 43 43 51 40 36 36 36 36 51 50 71 73 79 79 79 75 85 77 74 68 73 69 74 79 83 82 70 63 60 56
 56 61 64 60 65 62 62 62 62 62 67 67 69 70 67 67 70 67 74 80 90 90 82 80 75 76 75 68 72 65 60 60 60 70 77 72 72 72 75 61 61 66 67 67 63 69 70 77 70 65
 63 66 64 60 66 62 62 74 72 68 72 83 85 85 85 83 83 80 77 69 65 60 63 67 69 61 68 78 80 78 88 73 72 75 72 72 67 69 68 83 83 72 90 74 80 82 82 78 79 85
 85 85 85 90 90 86 90 90 85 83 90 90 90 90 90 90 90 88 88 88 83 86 86 85 83 81 81 85 85 85 90 89 84 74 74 74 79 79 85 89 85 90 90 85 80 80 85 90 90 90
 90 90 89 89 85 85 85 85 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 80 80 85 80 88 88 90 90 90 90 90 90 83 83 80 81 90 90 90 90 90 90 90 85 90
 90 90 83 83 83 83 83 83 90 90 90 90 90 90 90 88 88 88 83 90 90 90 90 90 90 90 90 90 90 90 90 88 85 85 84 84 84 84 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 80 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 83 83 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 85 83 83 83 83 83 88 90 90 90 90 90 88 86 86 86 90 86 90 90 90 90 90 88 83
 80 80 82 90 90 90 90 90 87 87 87 87 90 87 90 90 90 90 90 90 90 90 87 90 87 85 85 85 85 78 79 79 85 79 83 83 83 79 71 70 71 72 74 68 67 67 72 83 83 83
 85 90 90 89 87 76 68 68 68 64 68 75 90 72 80 68 70 63 65 62 72 72 72 70 75 68 67 68 76 90 74 74 72 72 83 83 74 72 68 70 72 70 64 68 77 90 80 74 74 80
 80 76 77 64 72 74 72 63 61 65 62 68 66 70 66 60 71 71 66 60 60 70 72 68 66 66 64 64 71 69 68 66 66 66 71 74 76 79 81 76 69 63 72 72 75 75 74 70 67 70
 70 67 73 64 76 71 69 68 65 65 68 70 65 63 67 66 64 69 70 81 81 70 74 74 62 62 59 53 53 58 51 51 51 56 56 51 51 43 43 43 43 43 43 51 51 51 51 45 45 35
 35 35 35 43 43 56 56 56 56 56 56 43 43 43 43 43 43 43 43 43 43 43 43 35 35 35 35 39 40 56 56 45 45 45 45 45 51 56 46 40 40 40 40 40 40 40 39 45 35 35
 35 35 35 35 39 39 39 39 40 51 40 40 39 39 39 39 40 46 51 45 45 40 35 35 35 39 39 39 39 39 39 39 39 40 40 40 40 40 40 51 40 39 39 39 39 39 35 39 39 39
 39 39 40 40 35 35 32 32 33 33 39 39 46 46 46 46 46 46 51 51 51 51 51 51 40 40 37 40 40 40 46 46 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2281f U 1
AF LL2281r C 227
BS 1 317 LL2281f
BS 318 318 LL2281r
BS 319 360 LL2281f
BS 361 365 LL2281r
BS 366 408 LL2281f
BS 409 424 LL2281r
BS 425 441 LL2281f
BS 442 448 LL2281r
BS 449 449 LL2281f
BS 450 450 LL2281r
BS 451 458 LL2281f
BS 459 468 LL2281r
BS 469 471 LL2281f
BS 472 475 LL2281r
BS 476 476 LL2281f
BS 477 477 LL2281r
BS 478 500 LL2281f
BS 501 536 LL2281r
BS 537 540 LL2281f
BS 541 549 LL2281r
BS 550 554 LL2281f
BS 555 555 LL2281r
BS 556 558 LL2281f
BS 559 560 LL2281r
BS 561 561 LL2281f
BS 562 564 LL2281r
BS 565 568 LL2281f
BS 569 572 LL2281r
BS 573 573 LL2281f
BS 574 581 LL2281r
BS 582 582 LL2281f
BS 583 593 LL2281r
BS 594 599 LL2281f
BS 600 612 LL2281r
BS 613 613 LL2281f
BS 614 623 LL2281r
BS 624 624 LL2281f
BS 625 651 LL2281r
BS 652 653 LL2281f
BS 654 654 LL2281r
BS 655 656 LL2281f
BS 657 662 LL2281r
BS 663 663 LL2281f
BS 664 776 LL2281r
BS 777 780 LL2281f
BS 781 969 LL2281r

RD LL2281f 785 0 0
cttttagaaacgaggttcggtttctgataaaatcatacaaagatacgaca
aaggaagtttcacaaatatacaaacaaactCTCTTTCACATGATAATTAA
CCTTTTAACTCCTTCACTTTCCGGGGACGAAGTTGGTGGCAAAGGCCCAT
GCATTGTTGTTGACTGGATCAGCCAAATGGTCAGCAAGATTCTCCAACGG
TCCCTTTCCGGTGACGATAGCCTGAACGAAGAATCCAAACATAGAGAACA
TAGCCAACCTTCCGTTCTTGATCTCCTTCACCTTCAACTCCGCGAAAGCT
TCTGGGTCGGTAGCAAGACCCAACGGGTCAAAGCTGCCTCCTGGGTAGAG
CAAGTCCTCTGCTTCCCCCAATGGTCCTTCTCCGGCGACTCTGTAACCTT
CAACAGCTCCCATGAGGATCACCTGAGTAGCCCAAATGGCTAAGATGCTC
TGTGCGTGGACCAAGCTCGGGTTTCCCAAGTAGTCGAGCCCTCCTTCGCT
GAAGATCTGTGAACCAGCCTTGAACCAAACAGCTTCTCCGAACTTCACTC
CGTTCCTAGCCAAAAGCTCAGGGAAAACGCAGCCTAGGGCTCCAAGCATG
GCCCATCTGCAGTGGATAACTTCTAGCTCACGGTTCCTGGCGAAGGTCTC
GGGGTCAGCGGAAAGACCGGCGGTGTCCCATCCGTAGTCACCGGGGAACT
CTCCTGTGAGGTAGCTTGGGGGCTCTCCGGAGAATGGACCCAAGTACTTG
ACCCTGTCGGATCCGTACCATGGGCTGCCAGATgg

QA 81 776 1 785
DS CHROMAT_FILE: LL2281f PHD_FILE: LL2281f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:36 2000

RD LL2281r 787 0 0
CGAAGAATCCAAACATAGAGAACATAGCCAACCTTCCGTTCTTGATCTCC
TTCACCTTCAACTCCGCGAAAGCTTCTGGGTCGGTAGCAAGACCCAACGG
GTCAAAGCTGCCTCCTGGGTAGAGCAAGTCCTCTGCTTCCCCCAATGGTC
CTTCTCCGGCGACTCTGTAACCTTCAACAGCTCCCATGAGGATCACCTGA
GTAGCCCAAATGGCTAAGATGCTCTGTGCGTGGACCAAGCTCGGGTTTCC
CAAGTAGTCGAGCCCTCCTTCGCTGAAGATCTGTGAACCAGCCTTGAACC
AAACAGCTTCTCCGAACTTCACTCCGTTCCTAGCCAAAAGCTCAGGGAAA
ACGCAGCCTAGGGCTCCAAGCATGGCCCATCTGCAGTGGATAACTTCTAG
CTCACGGTTCCTGGCGAAGGTCTCGGGGTCAGCGGAAAGACCGGCGGTGT
CCCATCCGTAGTCACCGGGGAACTCTCCTGTGAGGTAGCTTGGGGGCTCT
CCGGAGAATGGACCCAAGTACTTGACCCTGTCGGATCCGTACCATGGGCT
GCCAGATGGACCGGTGGGTTTGACGGTTTTTCTCATGGTGACACGGCCGG
TTCCAAAGACCTCTGAGGCTCCCGGTGAGAGCTTCACGGCCTTTCCGGTA
AAGGCAGGGGAGGACAGAGCCATGGTTGAGGCAGCCATTAGAAATTTTCT
TGATCTTttttagtttttgtgttttttttttcggacggcgtggxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxat

QA 1 707 1 743
DS CHROMAT_FILE: LL2281r PHD_FILE: LL2281r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:15 2000

CO Contig18 491 2 1 U
GCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTC
ACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAA
TCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCCAGGGTGGT
TTTTCTTTTCACCAGTGAGACGGGCAACAGCTGATTGCCCTTCACCGCCT
GGCCCTGAGAGAGTTGCAGCAAGCGGTCCACGCTGGTTTGCCCCAGCAGG
CGAAAATCCTGTTTGATGGTGGTTAACGGCGGGATATAACATGAGCTGTC
TTCGGTATCGTCGTATCCCACTACCGAGATATCCGCACCAACGCGCAGCC
CGGACTCGGTAATGGCGCGCATTGCGCCCAGCGCCATCTGATCGTTGGCA
ACCAGCATCGCAGTGGGAACGATGCCCTCATTCAGCATTTGCATGgtttg
ttgaAAACCGGACATGGCActccaGTcgccttCccgttccg

BQ
 43 43 43 43 51 51 56 43 43 43 43 43 43 45 45 56 56 56 56 56 51 43 43 43 43 43 43 43 43 43 43 45 45 45 51 51 51 43 36 36 36 36 36 36 36 36 36 36 36 36
 36 36 36 36 43 45 43 43 43 43 43 45 56 51 51 51 51 56 56 51 51 51 45 45 45 45 45 56 51 51 45 45 45 45 45 43 45 43 43 43 43 45 45 51 51 51 56 56 56 51
 51 45 45 45 45 51 51 51 45 45 45 45 45 45 51 56 56 56 56 51 45 45 45 45 45 51 51 43 43 43 43 43 43 56 56 56 43 43 43 43 43 43 40 43 43 46 56 56 56 56
 56 56 56 56 56 56 56 51 51 45 45 45 45 51 51 56 56 51 45 45 45 45 45 51 56 56 56 56 45 45 51 45 45 45 45 45 45 45 45 45 51 45 45 45 40 39 35 35 35 39
 40 45 45 45 45 51 51 51 51 51 51 51 56 40 40 40 40 37 40 56 56 45 45 45 45 45 45 51 40 40 39 39 39 40 40 40 51 39 39 37 37 37 39 46 56 56 51 51 45 45
 45 45 45 45 56 51 51 51 51 51 51 56 56 56 56 51 51 51 51 51 51 35 35 35 35 35 39 46 42 42 42 51 46 56 46 46 51 51 51 51 56 56 56 51 51 45 45 35 35 35
 40 40 40 40 46 56 40 40 40 40 40 36 40 40 40 34 29 28 32 32 32 36 36 40 40 40 40 40 40 40 40 40 33 32 29 29 27 27 25 25 28 32 32 32 32 32 32 32 29 32
 32 26 25 25 27 27 29 32 44 40 40 40 34 26 25 25 27 32 32 34 40 39 37 29 29 29 29 29 29 42 35 35 29 32 29 32 40 40 40 40 40 32 32 29 24 24 29 29 29 25
 25 29 29 26 26 32 32 29 29 29 29 27 27 25 25 29 25 25 25 29 32 30 30 29 29 24 25 25 25 26 32 32 34 32 40 40 40 34 22 22 24 24 25 24 22 19 19 10 17 9
 9 9 19 16 25 24 22 25 25 26 20 23 25 27 25 25 21 25 21 19 9 10 10 19 21 22 19 15 10 11 14 17 21 12 15 0 0 0 0 0 0

AF LL2283r C 1
AF LL2283f U -303
BS 1 491 LL2283f

RD LL2283r 800 1 5
aagggcgaaaaaccgtttatcagggcgatgggcccctacgtgaaccatcc
ccctaatcaagttttttggggtcgaggtgccgtaaagcccttaattggaa
ccctaaagggagccccccatttaaaactttacggggaaaaccggcgaacg
tggcgaaaaaagaagggaaaaaaaccaaaagagcgggcgctaaggccctg
gcaaatgtaacggtccccctgggggtaaccccccccccccccgcgcttta
tgggccggttcagggggggttccctttgccatttagggtgggcaaatttt
tggaaaggcgattggttcgggccttttttttttttccccaactggggaaa
aggggatttttttcaaagcgatttaatttggtaaccccagggtttttxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxCCCCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTGGTGCAACAAACACAAAAGCATAATCTCTCA
GATTAATAAATAATAACGAGCTTTAACTCCAATCTGCAGAGAACATTTCA
AGCACATGGGAGAAGCTCTGCAGAACAAGAAAGATCATATCTTCCCGGAC
gctggxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxagt

QA 265 752 -1 -1
DS CHROMAT_FILE: LL2283r PHD_FILE: LL2283r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:24 2000

WR{
LL2283r unaligned phrap 000919:094547
}

RT{
LL2283r chimera phrap 1 397 000919:094547
}

RT{
LL2283r matchElsewhereLowQual phrap 131 179 000919:094547
}

RT{
LL2283r matchElsewhereLowQual phrap 194 225 000919:094547
}

RT{
LL2283r matchElsewhereHighQual phrap 336 360 000919:094547
}

RT{
LL2283r matchElsewhereHighQual phrap 383 397 000919:094547
}

RD LL2283f 796 0 2
ngtgnngggaacAAACACAAAAGCATAATCTCTCAGATTAATAAATAATA
ACGAGCTTTAACTCCAATCTGCAGAGAACATTTCAAGCACATGGGAGAAG
CTCTGCAGAACAAGAAAGATCATATCTTCCCGGACGCGTGGxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGC
GCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAA
TGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCCAGGG
TGGTTTTTCTTTTCACCAGTGAGACGGGCAACAGCTGATTGCCCTTCACC
GCCTGGCCCTGAGAGAGTTGCAGCAAGCGGTCCACGCTGGTTTGCCCCAG
CAGGCGAAAATCCTGTTTGATGGTGGTTAACGGCGGGATATAACATGAGC
TGTCTTCGGTATCGTCGTATCCCACTACCGAGATATCCGCACCAACGCGC
AGCCCGGACTCGGTAATGGCGCGCATTGCGCCCAGCGCCATCTGATCGTT
GGCAACCAGCATCGCAGTGGGAACGATGCCCTCATTCAGCATTTGCATGg
tttgttgaAAACCGGACATGGCActccaGTcgccttCccgttccgn

QA 11 789 305 795
DS CHROMAT_FILE: LL2283f PHD_FILE: LL2283f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:46 2000

RT{
LL2283f chimera phrap 305 651 000919:094547
}

RT{
LL2283f matchElsewhereHighQual phrap 305 512 000919:094547
}

CO Contig19 911 2 62 U
ctttaagggaacaagagttgaatataaagtcacaatatagcagacagaaa
tcatgatcaaataaacaaatatttttttaaTACAGAAAACAATACAAAAA
GACAGCTGGGCCAAGCTAATCGAGCATGTGTGTCTCTTCGCCATCATTAC
CTGTCTCCGGCACAGCCGAGCTGGAGCCAACGGCGGAGATAATGGCATTC
AAAGCACGAATCTGCATCTCCATCGCAACAATGTAATCAGTAGTTTCTTC
TAAAACCACCGGTAATGGTTGTTTCCGGCAACCGGGGATTAACCGGCTCA
GCAATTTCACTTTCCTCTGTACAGCTGTAAACCCCTTCCCCTTCAACCTC
AAAACCGTTGCTCTCTTTTTCTTTAACCGGCTATTCCCGGTTATCGAAAC
CACCGTGGGAGGAGGATTCGAAGTTCTTAACCGGTTATGTTTCCTAAACT
TGAGCTTCACTTTAACGGCTTTAGATAGTATAGCTCGGCTCCACAGTGTT
CTGCCTCTCGCCGTAACCGCCAGAGACCTGTAAGCGGCGTCACGTACGGC
TATACCTCCGCCGCGAGGAGAGAGCTTACCAGATGCATCGGTGGCGGCGC
TAATACGTAGTTCCCTTAGAGATTGAATGATGTTGGTCGAGTAGATTTGC
TGCTGCTTCTCGGATCTCCATTTCTGCACCAAAGATTGAGACGAAGAATG
CGACGGTGATGGTGACGTTGGTTTCTTCTTACGCTTACGCCGCGACTGAT
CATAACTGGAGCCAGCCGTTGGATGATTTGTCAGTGGAGAAATATACTCC
ATGTCAATTCCTCTGCTTCTCCGGTGACAGTACCTGAAGACAGAAACAGA
GAAAGGAGATTAGCAAGGTGAGACACgtatgtggaggaagaggaaaatcc
cggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 40 40 40 51 51 39 40 45 40 40 40 51 51 51 51 51 51 51 46
 46 40 40 39 39 40 40 40 40 39 39 39 39 35 35 35 35 35 35 35 39 39 39 39 46 46 46 56 56 51 51 45 45 45 45 40 40 38 38 38 38 38 40 51 51 39 39 39 39 39
 39 51 45 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 51 51 51 51 43 43 58 58 58 62 58 58 68 83 80 90 83 80 72 72 70 68 70 68 77 80
 77 68 73 72 60 65 65 68 68 76 71 76 80 80 80 83 79 85 85 89 81 75 65 68 64 62 58 58 66 74 74 80 80 80 80 82 82 90 79 72 72 70 83 76 77 74 78 75 69 72
 72 72 69 67 74 74 85 80 72 69 74 77 77 81 80 78 78 83 80 76 85 83 83 75 72 69 66 63 63 58 58 72 83 90 90 79 85 70 70 70 66 67 61 69 72 83 83 75 72 72
 74 76 79 81 90 90 83 85 89 89 90 89 83 90 90 90 90 90 83 85 80 80 88 83 83 83 83 83 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 88 80 80 80 88 89 90
 90 90 90 85 88 88 88 88 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 85 85 90 90 89 90 90 90 90 90 90 90 90 90 90 87 87 89 85 85 85 90 88 88 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 88 90 90 90 90 90 90 90 90 88 88 88 90 90 86 86 90 90 90 90 90 90 90 90 88 83 88 81 83 83 85 85 85 85 85 90 90 90 86 83 83 83 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 88 88 83 82 82 78 78 78 90 90 90 90 90 90 90 90 90 90 90 88 88 83 83 80 80 80 83 90 88 88 83 83 83 88 90 88 88
 80 90 90 90 90 90 90 90 90 90 83 83 88 88 90 90 90 90 90 90 90 90 85 86 83 83 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 85 78 78 78 78 76 76 74 78
 78 86 86 82 80 79 77 82 75 83 83 72 74 80 80 88 83 74 74 77 85 85 90 90 90 90 90 90 90 90 90 90 90 90 90 83 80 80 83 83 83 88 83 85 90 90 80 84 80 80
 80 78 78 78 78 76 76 82 83 83 83 83 77 83 83 83 76 78 78 83 90 90 90 83 83 75 75 75 80 90 90 90 90 90 90 82 80 79 74 72 70 70 70 72 72 81 85 76 72 72
 72 72 72 74 74 68 78 90 90 90 90 77 77 72 72 72 68 65 65 79 74 74 74 80 85 90 90 80 73 61 68 66 66 68 65 61 64 64 64 65 65 65 64 65 65 74 80 80 83 90
 90 90 80 80 80 80 80 72 67 68 70 70 64 61 60 58 58 62 58 61 62 78 71 71 51 45 45 43 43 43 43 43 43 43 43 43 43 45 45 45 45 45 40 40 40 40 40 40 56 56
 51 40 40 40 40 40 40 51 51 51 51 51 51 51 51 51 51 51 51 40 45 40 39 39 39 40 39 39 39 39 39 39 46 46 46 40 40 40 51 51 51 51 51 51 51 51 51 51 51 51
 51 51 51 51 51 51 51 51 40 39 39 39 39 39 51 39 39 39 39 35 40 37 51 45 40 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0

AF LL2286f U 1
AF LL2286r C 176
BS 1 283 LL2286f
BS 284 284 LL2286r
BS 285 308 LL2286f
BS 309 312 LL2286r
BS 313 322 LL2286f
BS 323 323 LL2286r
BS 324 331 LL2286f
BS 332 342 LL2286r
BS 343 343 LL2286f
BS 344 344 LL2286r
BS 345 347 LL2286f
BS 348 353 LL2286r
BS 354 354 LL2286f
BS 355 371 LL2286r
BS 372 376 LL2286f
BS 377 392 LL2286r
BS 393 395 LL2286f
BS 396 402 LL2286r
BS 403 414 LL2286f
BS 415 422 LL2286r
BS 423 425 LL2286f
BS 426 426 LL2286r
BS 427 431 LL2286f
BS 432 442 LL2286r
BS 443 446 LL2286f
BS 447 451 LL2286r
BS 452 454 LL2286f
BS 455 463 LL2286r
BS 464 466 LL2286f
BS 467 474 LL2286r
BS 475 476 LL2286f
BS 477 478 LL2286r
BS 479 479 LL2286f
BS 480 480 LL2286r
BS 481 481 LL2286f
BS 482 496 LL2286r
BS 497 498 LL2286f
BS 499 506 LL2286r
BS 507 515 LL2286f
BS 516 530 LL2286r
BS 531 534 LL2286f
BS 535 541 LL2286r
BS 542 543 LL2286f
BS 544 546 LL2286r
BS 547 547 LL2286f
BS 548 556 LL2286r
BS 557 557 LL2286f
BS 558 562 LL2286r
BS 563 565 LL2286f
BS 566 569 LL2286r
BS 570 572 LL2286f
BS 573 586 LL2286r
BS 587 591 LL2286f
BS 592 622 LL2286r
BS 623 628 LL2286f
BS 629 629 LL2286r
BS 630 635 LL2286f
BS 636 641 LL2286r
BS 642 642 LL2286f
BS 643 709 LL2286r
BS 710 711 LL2286f
BS 712 911 LL2286r

RD LL2286f 776 0 0
ctttaagggaacaagagttgaatataaagtcacaatatagcagacagaaa
tcatgatcaaataaacaaatatttttttaaTACAGAAAACAATACAAAAA
GACAGCTGGGCCAAGCTAATCGAGCATGTGTGTCTCTTCGCCATCATTAC
CTGTCTCCGGCACAGCCGAGCTGGAGCCAACGGCGGAGATAATGGCATTC
AAAGCACGAATCTGCATCTCCATCGCAACAATGTAATCAGTAGTTTCTTC
TAAAACCACCGGTAATGGTTGTTTCCGGCAACCGGGGATTAACCGGCTCA
GCAATTTCACTTTCCTCTGTACAGCTGTAAACCCCTTCCCCTTCAACCTC
AAAACCGTTGCTCTCTTTTTCTTTAACCGGCTATTCCCGGTTATCGAAAC
CACCGTGGGAGGAGGATTCGAAGTTCTTAACCGGTTATGTTTCCTAAACT
TGAGCTTCACTTTAACGGCTTTAGATAGTATAGCTCGGCTCCACAGTGTT
CTGCCTCTCGCCGTAACCGCCAGAGACCTGTAAGCGGCGTCACGTACGGC
TATACCTCCGCCGCGAGGAGAGAGCTTACCAGATGCATCGGTGGCGGCGC
TAATACGTAGTTCCCTTAGAGATTGAATGATGTTGGTCGAGTAGATTTGC
TGCTGCTTCTCGGATCTCCATTTCTGCACCAAAGATTGAGACGAAGAATG
CGACGGTGATGGTGACGTTGGTTTCTTCTTACGCTTACGCCGCGACTGAT
CATAACTGGAGCCAGCCGTTGGATga

QA 81 774 1 776
DS CHROMAT_FILE: LL2286f PHD_FILE: LL2286f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:01 2000

RD LL2286r 781 0 0
nccaACGGCGGAGATAATGGCATTCAAAGCACGAATCTGCATCTCCATCG
CAACAATGTAATCAGTAGTTTCTTCTAAAACCACCGGTAATGGTTGTTTC
CGGCAACCGGGGATTAACCGGCTCAGCAATTTCACTTTCCTCTGTACAGC
TGTAAACCCCTTCCCCTTCAACCTCAAAACCGTTGCTCTCTTTTTCTTTA
ACCGGCTATTCCCGGTTATCGAAACCACCGTGGGAGGAGGATTCGAAGTT
CTTAACCGGTTATGTTTCCTAAACTTGAGCTTCACTTTAACGGCTTTAGA
TAGTATAGCTCGGCTCCACAGTGTTCTGCCTCTCGCCGTAACCGCCAGAG
ACCTGTAAGCGGCGTCACGTACGGCTATACCTCCGCCGCGAGGAGAGAGC
TTACCAGATGCATCGGTGGCGGCGCTAATACGTAGTTCCCTTAGAGATTG
AATGATGTTGGTCGAGTAGATTTGCTGCTGCTTCTCGGATCTCCATTTCT
GCACCAAAGATTGAGACGAAGAATGCGACGGTGATGGTGACGTTGGTTTC
TTCTTACGCTTACGCCGCGACTGATCATAACTGGAGCCAGCCGTTGGATG
ATTTGTCAGTGGAGAAATATACTCCATGTCAATTCCTCTGCTTCTCCGGT
GACAGTACCTGAAGACAGAAACAGAGAAAGGAGATTAGCAAGGTGAGACA
Cgtatgtggaggaagaggaaaatcccggacgcgtggxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxat

QA 6 701 2 736
DS CHROMAT_FILE: LL2286r PHD_FILE: LL2286r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:38 2000

CO Contig20 547 2 7 U
cCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAT
TTGAAGAAACCTTTATAAAAACGATTAAGGGGCTGAATGCGAGACAAAAA
TATATTTCTGATTTGAATCAATGAAAAATATATAAATGGAAGATCTAAAA
CATTTCTCACCAATGGCGCTATAACACAACAGAGAAGATTGAATTTAAAG
GCATGACTGCTCTTGTCACTTCCAGCCTTTCTTTTATTATTGGTTTAAAT
AC*GTGAAGGTGGATGAGCTCCATCACCTTGTCAACTTTATAGCTTTGCG
ATCGCTGAAGCAGGCAAGTGTTTCCTTGGTGGAAGCTTAAGATCCTCCCA
TCCCTCCTCTTCTTCCACTCTCTTGAAGTACTTATCTACCATGTTATCTT
TCATATCCTCCAGTCTCCTTGGCTCCCACTTTGGGTTCCTATCTTTGTTT
ATCAATATGGCTCTACCCCCCTCCACAAAATCTTTGCTTATATCTCCCTT
CATCACATGTGACACCATTCTATTCTCACGGATAAGCGGACGCGTGG

BQ
 19 22 37 48 48 48 48 48 48 48 48 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 51 51 51 51 51
 51 51 51 51 51 51 56 56 56 56 56 56 56 51 51 51 51 51 51 51 51 51 51 51 56 56 56 56 51 60 60 60 60 60 66 71 60 60 45 45 45 45 56 71 71 71 73 77 78 84
 90 90 89 87 72 68 68 70 76 80 80 85 87 80 81 81 82 83 78 73 80 80 86 84 84 90 85 85 90 90 89 89 66 66 66 70 78 72 74 72 72 72 79 76 81 74 74 74 74 80
 86 89 84 71 71 71 79 75 84 81 74 66 74 61 62 60 62 62 62 58 60 60 64 68 78 89 88 88 71 71 71 56 56 56 56 56 56 60 60 60 77 83 82 77 75 73 73 70 66 75
 77 71 67 73 85 85 80 80 75 74 74 75 75 78 81 85 87 84 82 79 78 80 75 70 73 73 78 90 90 83 74 73 80 71 71 71 75 75 81 72 71 66 66 66 66 66 66 66 66 61
 43 43 43 43 58 58 58 71 72 68 66 67 73 60 60 58 58 58 68 74 83 86 84 84 84 66 66 58 43 43 43 43 43 71 71 71 71 76 76 76 71 69 62 62 51 51 51 57 58 65
 72 71 67 67 67 65 70 78 76 90 73 70 70 66 58 58 58 43 43 43 43 43 45 60 60 51 51 51 51 51 55 62 58 58 60 60 51 51 51 51 56 56 71 71 77 77 77 89 89 90
 90 84 84 78 78 78 79 79 79 89 84 90 74 74 71 79 74 78 75 74 77 77 82 74 67 58 58 62 70 74 74 84 77 74 74 81 81 84 90 78 80 66 70 74 82 82 84 87 84 78
 78 79 90 87 86 74 80 72 58 50 35 35 35 35 43 71 66 60 58 58 58 58 66 66 86 86 86 86 86 86 89 73 59 59 55 55 55 84 84 90 86 86 84 90 75 70 64 65 65 67
 73 73 86 83 72 72 69 63 55 55 55 64 67 75 81 81 90 90 89 89 72 66 69 76 78 80 86 86 86 86 86 82 82 65 61 61 76 71 80 88 87 79 79 74 79 79 88 88 74 74
 74 74 74 77 84 76 64 54 55 54 63 67 84 84 73 69 69 68 77 70 68 64 63 63 66 66 69 67 54 54 54 39 39 39 39 39 35 35 45 45 49 49 49 34 33 32

AF LL2289r C -194
AF LL2289f U 57
BS 1 310 LL2289r
BS 311 311 LL2289f
BS 312 465 LL2289r
BS 466 466 LL2289f
BS 467 489 LL2289r
BS 490 490 LL2289f
BS 491 547 LL2289r

RD LL2289r 788 0 2
gcgggcctcttcgctattacgccagctggcgaaagggggatgtgctgcaa
ggcgattaagttgggtaacgccagggttttxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxcCTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTGAA
GAAACCTTTATAAAAACGATTAAGGGGCTGAATGCGAGACAAAAATATAT
TTCTGATTTGAATCAATGAAAAATATATAAATGGAAGATCTAAAACATTT
CTCACCAATGGCGCTATAACACAACAGAGAAGATTGAATTTAAAGGCATG
ACTGCTCTTGTCACTTCCAGCCTTTCTTTTATTATTGGTTTAAATAC*GT
GAAGGTGGATGAGCTCCATCACCTTGTCAACTTTATAGCTTTGCGATCGC
TGAAGCAGGCAAGTGTTTCCTTGGTGGAAGCTTAAGATCCTCCCATCCCT
CCTCTTCTTCCACTCTCTTGAAGTACTTATCTACCATGTTATCTTTCATA
TCCTCCAGTCTCCTTGGCTCCCACTTTGGGTTCCTATCTTTGTTTATCAA
TATGGCTCTACCCCCCTCCACAAAATCTTTGCTTATATCTCCCTTCATCA
CATGTGACACCATTCTATTCTCACGGATAAGCGGACGCGTGGxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxaatt

QA 19 742 196 742
DS CHROMAT_FILE: LL2289r PHD_FILE: LL2289r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:15 2000

RT{
LL2289r chimera phrap 1 80 000919:094547
}

RT{
LL2289r matchElsewhereHighQual phrap 1 80 000919:094547
}

RD LL2289f 769 0 3
caacCTTTat*aaAaCgatgaagGGGCTGAATGccagACAAAAATATATT
TCTGATTTGAATCAATGAAAAATATATAAATGGAAGATCTAAAACATTTC
TCACCAATGGCGCTATAACACAACAGaaaAGATTGAATTTAAAGGCATGA
CTGCTCTTGTCACTTCCAGCCTTTCTTTTATTATTGGTTTAAATacagtG
AAGGTGGATGAGCTCCATCACCTTgccaACTTTATAGCTTTGCGATCGCT
GAAGCAGGCAAGTgcttcCTTGGTGGAAGCTtaacaTCCTCCCATCCCTC
CTCTTCTTCCACTCTCTTGAAGTACTTATCTACCATGTTATCTTTCATAT
CCTCCagcctCCTTGGCTCCCACTTTGGGTTCCTATCTTTGTTTATCAAT
ATGGCTCTACCCCCCTCCACAAAATCTTTGCTTATATCTCCCTTCATCAC
ATGTGACACCATTCTATTCTCACGGATAaacgcaCGCGTGgxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxgcctggcgtgcctaatgagcgagctaactcacattaattgcgttgc
gctcactgcccgctttccagtcggcaaacctgtccagccagctgcattaa
tgaatcggccaacgcgcgg

QA 23 720 2 491
DS CHROMAT_FILE: LL2289f PHD_FILE: LL2289f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:37 2000

RT{
LL2289f chimera phrap 655 769 000919:094547
}

RT{
LL2289f matchElsewhereHighQual phrap 737 769 000919:094547
}

RT{
LL2289f matchElsewhereHighQual phrap 675 724 000919:094547
}

CO Contig21 766 2 29 U
ccacgcgtccgtttttgatgtaatacAGTTTTTTCTGAATAAAATTTAAC
ATTTATTCAAAAAAAAAAAAATAATTAGATTACAAGCTTAACAAATTTAT
TATAAATCATCATACCTTGTTCATTTATAAATGAAAATCTGAAGAAAACA
AAAAATGTTTGGTAAACACCAACATGAACTGTTGTCAGGTTGGTATAACT
AATTGTGAAGCAGGAGAGGACTGGAGGAGCAGTAACCGAACTATGGAGAC
TAGCAAGATCAACTGTATCAAGAAATAGAAACTGGACTTGCATGTTTTAC
CTAACATGGCTCCACGGTTCGGTTCAGGATCTTCAGCTACAGAATGTACC
TTCTTCGGATGTTCTTTGAGTAGCGTTGAGTTCAGAGAACTTCTGAGCAT
CAAATGCTGGATTTCAGCTTCGATCTTTCGCTGGAAAACGCCTTCAAGTT
CAGCTTCAATCTTCGCGTTTTCGAGTTCTTGGATCCTGGCTTCCTTTGCG
TCGA*GATCAGCTCTCGCTTCCTCGAGTTTAACTTGGAGAAGTTTCACCT
TCTGCTTCAAG*ATCAGTACCTGTGATCCTGAATTGTCTTCATCAATATT
CGAATGTAGTGGTGGTATAGATTCCTTACTCagCTcCTGGAAACTtGTaa
cCTCtTTccaaAGAGCttCcTGCaaAGCTgcaagaCAtCTGATAGaATCt
gcaacATGATCCTtgtctgcctgataatggntgntcttcttcttatggct
ctcatctccaccatct

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 61 66 66 66 66 66 50 50 50 45 45 47 47 50 50 61 56 56 56 56 56 50
 61 50 50 50 50 49 45 49 49 50 50 61 61 66 66 66 66 66 66 57 52 52 48 47 45 45 45 45 45 45 50 52 48 48 55 55 47 47 47 47 52 52 66 61 61 50 56 50 47 47
 50 50 50 50 56 56 50 50 50 50 48 52 55 55 55 55 50 66 52 56 56 55 55 50 50 50 50 50 50 55 55 55 55 55 61 61 61 61 61 61 61 61 61 66 66 54 66 66 53 53
 53 66 66 66 66 66 66 66 66 66 61 61 61 66 66 66 66 61 61 55 55 55 55 55 55 61 55 55 55 55 53 53 61 51 55 55 55 55 55 66 66 55 55 55 55 55 53 53 53 53
 53 53 53 61 61 61 61 61 61 66 66 66 66 66 61 61 61 53 53 53 53 53 53 53 61 61 61 61 61 61 61 61 55 55 53 53 53 53 53 53 53 53 53 55 61 66 53 53 53 53
 53 53 53 55 61 61 61 61 61 55 53 53 53 53 53 53 66 66 66 61 61 61 61 61 61 61 61 61 55 53 53 53 53 53 53 53 53 53 53 53 53 53 53 66 66 61 61 55 53 53
 53 53 53 53 61 61 61 56 53 53 53 53 53 53 43 43 43 51 56 56 66 61 61 61 61 61 61 61 66 66 66 61 61 61 55 53 53 53 53 53 53 51 56 56 56 51 55 53 53 53
 50 61 61 66 66 66 66 66 66 66 66 66 66 66 66 66 56 56 56 51 51 40 40 40 40 40 40 51 56 51 51 46 46 42 42 42 46 45 45 45 45 55 55 61 61 66 66 66 66 56
 66 56 56 56 55 55 55 55 55 51 56 56 56 56 56 45 45 45 45 45 40 51 51 56 56 56 56 40 35 35 35 45 45 46 56 56 61 51 51 51 51 51 51 51 51 56 51 51 51 51
 51 45 45 40 40 40 40 45 51 56 56 51 40 40 37 37 37 40 40 40 40 40 40 40 46 56 56 56 48 48 48 48 48 48 48 48 48 29 32 32 32 32 36 36 40 39 34 29 29 29
 29 35 42 42 42 42 44 44 37 40 40 37 34 29 32 32 27 27 27 25 25 32 48 48 40 48 40 46 44 34 32 32 32 32 25 29 27 27 25 25 37 40 40 40 34 34 40 40 40 40
 33 32 32 32 32 32 29 25 25 29 29 29 29 28 28 33 33 40 33 40 36 36 36 48 48 34 34 48 48 29 29 29 40 40 40 29 34 29 29 27 32 37 29 29 29 40 29 29 29 32
 40 40 40 40 32 26 29 25 25 21 27 21 25 29 29 40 32 30 28 33 33 40 34 35 33 33 33 25 25 18 18 20 23 19 20 29 24 25 29 26 29 29 25 18 23 24 19 19 18 25
 25 25 18 22 21 18 15 19 19 23 25 25 25 21 18 18 20 16 24 21 21 14 18 29 40 27 21 15 13 8 10 11 14 20 24 19 25 32 32 29 29 26 25 19 29 29 21 19 10 10
 10 15 19 25 40 40 28 27 25 25 20 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2291r U -43
AF LL2291f U 14
BS 1 65 LL2291r
BS 66 77 LL2291f
BS 78 79 LL2291r
BS 80 80 LL2291f
BS 81 81 LL2291r
BS 82 84 LL2291f
BS 85 86 LL2291r
BS 87 93 LL2291f
BS 94 95 LL2291r
BS 96 107 LL2291f
BS 108 110 LL2291r
BS 111 112 LL2291f
BS 113 145 LL2291r
BS 146 148 LL2291f
BS 149 150 LL2291r
BS 151 151 LL2291f
BS 152 166 LL2291r
BS 167 167 LL2291f
BS 168 391 LL2291r
BS 392 399 LL2291f
BS 400 400 LL2291r
BS 401 401 LL2291f
BS 402 404 LL2291r
BS 405 409 LL2291f
BS 410 431 LL2291r
BS 432 433 LL2291f
BS 434 436 LL2291r
BS 437 437 LL2291f
BS 438 766 LL2291r

RD LL2291r 810 0 0
atxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccacgc
gtccgtttttgatgtaatacAGTTTTTTCTGAATAAAATTTAACATTTAT
TCAAAAAAAAAAAAATAATTAGATTACAAGCTTAACAAATTTATTATAAA
TCATCATACCTTGTTCATTTATAAATGAAAATCTGAAGAAAACAAAAAAT
GTTTGGTAAACACCAACATGAACTGTTGTCAGGTTGGTATAACTAATTGT
GAAGCAGGAGAGGACTGGAGGAGCAGTAACCGAACTATGGAGACTAGCAA
GATCAACTGTATCAAGAAATAGAAACTGGACTTGCATGTTTTACCTAACA
TGGCTCCACGGTTCGGTTCAGGATCTTCAGCTACAGAATGTACCTTCTTC
GGATGTTCTTTGAGTAGCGTTGAGTTCAGAGAACTTCTGAGCATCAAATG
CTGGATTTCAGCTTCGATCTTTCGCTGGAAAACGCCTTCAAGTTCAGCTT
CAATCTTCGCGTTTTCGAGTTCTTGGATCCTGGCTTCCTTTGCGTCGA*G
ATCAGCTCTCGCTTCCTCGAGTTTAACTTGGAGAAGTTTCACCTTCTGCT
TCAAG*ATCAGTACCTGTGATCCTGAATTGTCTTCATCAATATTCGAATG
TAGTGGTGGTATAGATTCCTTACTCagCTcCTGGAAACTtGTaacCTCtT
TccaaAGAGCttCcTGCaaAGCTgcaagaCAtCTGATAGaATCtgcaacA
TGATCCTtgtctgcctgataatggntgntcttcttcttatggctctcatc
tccaccatct

QA 71 758 45 810
DS CHROMAT_FILE: LL2291r PHD_FILE: LL2291r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:24 2000

RD LL2291f 810 0 0
cctttatgtatctagTTTTTTCTGAATAAAATTTAACATTTATTCAAAAA
AAAAAAAATAATTAGATTACAAGCTTAACAAATTTATTATAAATCATCAT
ACCTTGTTCATTTATAAATGAAAATCTGAAGAAAACAAAAAATGTTTGGT
AAACACCAACATGAACTGTTGTCAGGTTGGTATAACTAATTGTGAAGCAG
GAGAGGACTGGAGGAGCAGTAACCGAACTATGGAGACTAGCAAGATCAAC
TGTATCAAGAAATAGAAACTGGACTTGCATGTTTTACCTAACATGGCTCC
ACggctcGGTTCAGGATCTTCAGCTACAgactgTACCTTCTTCGGATGTT
CTTtgcgtactgccgagtttagAGAACTTCTGAGCATCAAATGCTGGATT
tccgttcctatttTtcGCTGGAAAACGCCTTCAagctcAGCTtccttctt
tccgtctccgagttcctggaccttggctttcttt*cgccctcgatcagtt
ctcgctttctcgaccctaacttgcccaagccccaccttccgcctcaagca
tcagcccctgcgattccgaattgtctccttccctccccgacagtcccgct
cgtcctctctctctctcttctcctgcacttcctctcccccgtttcccgtc
cccgcgcttccccgctcccgcctgtcgtcttcgcccctccctcctcgctc
ttcccttcccttcccttcccttcctcctttgccgcctcccttctcgtgtc
ttatccgccgatgcgctcccttctccattctccgcccggctcgcgccaat
gcgcctaccc

QA 15 354 14 576
DS CHROMAT_FILE: LL2291f PHD_FILE: LL2291f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:47 2000

CO Contig22 1048 2 38 U
ttagtttctcattcttgatttggtacgcttgatgaagtgatattgtcata
caaatcccatgtcccAAAACACTGAAAGATCTACAAACAGCTCTCTAACC
TCATCAAACGTTAACTGTTCTTCGGTTTTCTCTCAAGTCTTTATTTGACT
GGCCCTGTCCTTGTTCTTGTTCATCATCTCCATCTTCTTCCCCTTCCCCT
TCTTCATCTTCATACACCACCATAACAACATTACCATCCTCATCTACTTC
ATACTCTACATCATCCCCTTCTTCCTCTTCTTCAAACTCCTCTTCCTCTT
CCTCATCATCATCAAAGTCGTCATCCTCGTCCATACTTGCGCGAACCGAG
TGAAACTCGGGAGGGGGAGGGCAGTCTTCTGTAATAGCCTCATCACGTTT
CATCACAAGATGCCTAATAACCCTCTCATCACCATCCAACATCCCTTTGA
ACTCGTTCAAGTGTTTCGCTTCCATCTCAAAGTTCATCAGTATATAATGT
GCATTCTCCGCCTTCTGTATCTTATACGCCAGTCTACGCATTCCCCAGTC
ACTAAACCTCCACACTTTCCCCTTCTTCTCCTTCAGAAACTCTTGAACTT
TCTCATTGACGCTTTTGACCTCCTCTGCATGTTTCTCATGAATCAAGTAA
ACCACCTCATAGTGTCTCATTCTTTCTTCATTCAAGTCGCTCTGAAGCTG
AAGATCAAGAAACTCGTATAGCTCCTTTTCTTCATCATCAGCGAACTCAG
GGAGAAGATCACCTTCCTCATCAACCTTCTTCTCTTTGAGAAGAATGGAT
TCGGGAAACGGACCGGTGGCTTCGTCAGGTCTAGCGGAGAAGCTGTGATT
GTCATCTTTCTTGCTTTTCTTCTTCTTCGCGGCGGCGACCAAAGGAAGGG
ACTTTGATCCTCTGCGGCCGAGACTAGGTATGAAGCACACGCGGGGAGAG
TTGATGAACGAATCTCGGCCGTCTATTCTGGGACCGAGAGATACTAGAGA
CGAAGACGAGTGcaggattgactccattggaggaatgcggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 51 51 40 40 40 51 51 51 51 40 46 46 46 46 46 46 46 46 46 51 40 39 39 39 39 39 39 40 40 40 40 40 40
 40 40 40 46 46 46 40 40 45 35 35 35 35 35 35 40 40 40 46 42 42 43 46 46 42 44 42 46 46 51 51 40 40 40 40 40 40 46 46 37 37 37 40 40 37 37 43 43 43 43
 38 43 43 43 43 45 41 41 41 41 41 41 41 46 51 51 51 51 51 51 51 51 51 51 51 43 43 43 43 43 43 45 51 51 46 46 38 38 38 43 43 43 45 45 45 45 51 51 56 56
 56 56 51 51 51 51 51 51 43 43 43 51 51 51 56 56 51 45 45 45 45 45 51 56 56 56 56 56 51 45 45 45 45 45 45 45 45 45 51 51 51 51 45 45 43 43 43 43 43 43
 51 40 40 40 38 38 43 45 45 51 51 56 51 51 51 51 51 45 45 45 45 45 45 51 51 51 51 51 51 51 56 56 56 51 43 43 43 43 43 45 51 60 60 66 66 66 66 66 66 58
 60 60 58 66 66 71 88 88 88 88 88 88 90 81 76 75 63 67 60 58 58 58 86 75 76 65 68 66 64 64 58 76 80 72 64 55 56 53 58 62 62 60 62 58 62 62 62 66 66 74
 81 75 81 66 62 66 69 65 64 60 64 71 71 68 68 74 74 74 80 71 65 51 51 35 33 57 51 58 71 67 62 70 68 59 65 64 64 61 61 71 68 79 81 71 66 61 61 55 56 69
 73 76 79 77 80 80 64 63 78 81 81 70 63 58 61 62 72 69 57 61 61 71 71 71 77 80 80 80 82 66 66 65 69 74 79 85 85 85 87 90 83 71 74 75 68 68 64 78 81 64
 64 62 71 68 57 57 59 61 54 65 77 88 80 80 52 51 48 58 58 56 53 57 74 71 82 70 63 71 74 69 75 84 80 80 76 79 68 80 85 85 73 73 84 76 82 75 68 67 62 65
 67 67 75 81 80 75 67 67 74 70 66 66 69 76 73 88 84 84 90 88 81 76 76 74 62 57 67 67 60 49 56 49 55 55 51 58 56 60 62 76 64 83 83 87 78 78 75 69 69 64
 73 73 67 65 58 60 60 66 62 65 70 72 67 73 73 78 68 75 90 90 90 90 90 90 90 90 90 90 90 90 83 83 77 80 79 77 73 74 81 83 83 80 83 90 80 80 80 85 85 86
 88 88 88 90 90 90 90 78 75 77 77 72 74 77 71 71 66 67 66 69 76 80 83 81 78 66 83 80 81 81 81 76 79 84 81 83 83 80 80 75 75 71 75 69 56 54 54 54 54 66
 66 76 67 65 64 73 65 61 55 57 59 50 49 49 54 55 69 74 79 81 79 79 79 73 69 67 66 65 65 71 66 56 45 45 45 45 45 45 45 45 45 56 75 66 65 59 66 67 72 75
 71 71 73 73 56 56 56 56 56 56 56 56 43 43 43 54 56 59 69 67 60 55 55 66 66 71 70 70 66 66 64 64 67 69 71 74 74 57 47 46 46 50 49 36 43 45 45 45 45 45
 45 45 45 45 45 51 51 51 51 56 56 56 56 56 56 56 56 51 51 51 51 63 56 56 56 56 56 56 51 51 51 51 51 51 56 56 51 51 51 51 51 51 51 51 51 51 51 56 56 45
 45 45 43 43 43 45 43 43 45 45 45 45 45 43 43 43 43 43 43 56 45 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 45 43 43 43 43 45 45 56 51 51 51 51 45
 45 51 51 51 51 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 45 43 43 43 35 34 34 34 34 34 34 35 35 43 51 56 56 43 43 43 43 43 43 43 43
 43 43 43 51 51 51 51 51 51 51 51 35 35 35 35 35 35 43 43 43 43 43 43 45 45 45 45 45 45 40 46 39 35 35 35 35 35 35 34 34 34 34 34 35 40 40 35 35 35 39
 39 39 40 40 40 40 39 39 39 39 39 39 40 35 35 35 35 35 35 35 35 35 35 39 39 39 40 46 46 46 46 51 45 45 45 45 45 45 51 40 40 40 40 40 40 40 40 40 51 51
 51 51 51 51 46 46 42 35 35 35 35 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2292f U -14
AF LL2292r C 289
BS 1 319 LL2292f
BS 320 322 LL2292r
BS 323 373 LL2292f
BS 374 375 LL2292r
BS 376 424 LL2292f
BS 425 428 LL2292r
BS 429 452 LL2292f
BS 453 458 LL2292r
BS 459 464 LL2292f
BS 465 471 LL2292r
BS 472 475 LL2292f
BS 476 481 LL2292r
BS 482 484 LL2292f
BS 485 486 LL2292r
BS 487 490 LL2292f
BS 491 494 LL2292r
BS 495 495 LL2292f
BS 496 506 LL2292r
BS 507 518 LL2292f
BS 519 519 LL2292r
BS 520 529 LL2292f
BS 530 536 LL2292r
BS 537 539 LL2292f
BS 540 544 LL2292r
BS 545 550 LL2292f
BS 551 552 LL2292r
BS 553 558 LL2292f
BS 559 568 LL2292r
BS 569 569 LL2292f
BS 570 652 LL2292r
BS 653 681 LL2292f
BS 682 692 LL2292r
BS 693 704 LL2292f
BS 705 715 LL2292r
BS 716 743 LL2292f
BS 744 771 LL2292r
BS 772 772 LL2292f
BS 773 1048 LL2292r

RD LL2292f 802 0 0
cttaagggaacctgnttagtttctcattcttgatttggtacgcttgatga
agtgatattgtcatacaaatcccatgtcccAAAACACTGAAAGATCTACA
AACAGCTCTCTAACCTCATCAAACGTTAACTGTTCTTCGGTTTTCTCTCA
AGTCTTTATTTGACTGGCCCTGTCCTTGTTCTTGTTCATCATCTCCATCT
TCTTCCCCTTCCCCTTCTTCATCTTCATACACCACCATAACAACATTACC
ATCCTCATCTACTTCATACTCTACATCATCCCCTTCTTCCTCTTCTTCAA
ACTCCTCTTCCTCTTCCTCATCATCATCAAAGTCGTCATCCTCGTCCATA
CTTGCGCGAACCGAGTGAAACTCGGGAGGGGGAGGGCAGTCTTCTGTAAT
AGCCTCATCACGTTTCATCACAAGATGCCTAATAACCCTCTCATCACCAT
CCAACATCCCTTTGAACTCGTTCAAGTGTTTCGCTTCCATCTCAAAGTTC
ATCAGTATATAATGTGCATTCTCCGCCTTCTGTATCTTATACGCCAGTCT
ACGCATTCCCCAGTCACTAAACCTCCACACTTTCCCCTTCTTCTCCTTCA
GAAACTCTTGAACTTTCTCATTGACGCTTTTGACCTCCTCTGCATGTTTC
TCATGAATCAAGTAAACCACCTCATAGTGTCTCATTCTTTCTTCATTCAa
gccGCTCTGAAGCTGAAGATCAAgacacTCGTATAGCTCCTTTTCTTCAT
CATCAGCGAActtagGGAGAAGATCACctttctCATCAACCTTCTTCTct
tg

QA 81 667 16 801
DS CHROMAT_FILE: LL2292f PHD_FILE: LL2292f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:52 2000

RD LL2292r 804 0 0
cctCTTCCTCTTCCTCATCATCATCAAAGTCGTCATCCTCGTCCATACTT
GCGCGAACCGAGTGAAACTCGGGAGGGGGAGGGCAGTCTTCTGTAATAGC
CTCATCACGTTTCATCACAAGATGCCTAATAACCCTCTCATCACCATCCA
ACATCCCTTTGAACTCGTTCAAGTGTTTCGCTTCCATCTCAAAGTTCATC
AGTATATAATGTGCATTCTCCGCCTTCTGTATCTTATACGCCAGTCTACG
CATTCCCCAGTCACTAAACCTCCACACTTTCCCCTTCTTCTCCTTCAGAA
ACTCTTGAACTTTCTCATTGACGCTTTTGACCTCCTCTGCATGTTTCTCA
TGAATCAAGTAAACCACCTCATAGTGTCTCATTCTTTCTTCATTCAAGTC
GCTCTGAAGCTGAAGATCAAGAAACTCGTATAGCTCCTTTTCTTCATCAT
CAGCGAACTCAGGGAGAAGATCACCTTCCTCATCAACCTTCTTCTCTTTG
AGAAGAATGGATTCGGGAAACGGACCGGTGGCTTCGTCAGGTCTAGCGGA
GAAGCTGTGATTGTCATCTTTCTTGCTTTTCTTCTTCTTCGCGGCGGCGA
CCAAAGGAAGGGACTTTGATCCTCTGCGGCCGAGACTAGGTATGAAGCAC
ACGCGGGGAGAGTTGATGAACGAATCTCGGCCGTCTATTCTGGGACCGAG
AGATACTAGAGACGAAGACGAGTGcaggattgactccattggaggaatgc
ggacgcgtggxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxat

QA 3 724 1 760
DS CHROMAT_FILE: LL2292r PHD_FILE: LL2292r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:29 2000

CO Contig23 1431 2 12 U
cttttaagaacaaacactaataaaatattgaatcttctttttaacataac
attccaatccaaagtatctcccttatgagaGCTCCAAGTGGAAAATAAAA
AAATAAAACTGAATAAGGACTCTCATGTAGCTCATATTATCAAAATACAG
CAACAATACAAATATATATATATATAGTAGATGATTAAGATCATTTTTTT
AACTGGAAGTTAAAGACAAAGAAaccttcagaagATAacatgtaaCCACC
AGATGATGAAGATACTATTTGTCTCCCTggatgagCTTaaactggaGAAT
gtACCaGACAGATTCTTAAGCGTTGCAAGCGGAGACCCTGCATTTGTAAA
GTATGACGCGAGGTTGATCtCCGAGTTGTTGTCGTATTTCTTCACGAAAG
GATGTTCCATTAGTTCCCTAGCAGAGCTTCGACTGTTTGGGTCCTTTTGC
AAACAAGTGGAGATGAATGAAGATAACTCAGGGGAGAAGCttTCTGAAGG
AAGagttggTGGTGGTTGGTCCACGATTGCTTCCATCAACTCGAAAACAC
TGCTCCATGTTTCCTCTTCATCTGGTGGCAAATATGGGAACTTCCCTGTT
GCACATTCAAGCACTACTAATCCCAAGCTCCATATATCGCTTTTGTTACC
GTACTTGTTccCAACGATCCTCTCTGGAGACATATAGTTGTAAGTCCCAA
CAAATGTGtttgCTAAACCCGCGGTGTTAGTCATAACGGTACTCACACCG
AAGTCAGTGATCTTGACCTCTCCTCTGTGGTTGACCAACAGATTCGATGG
TTTCAAGTCACGGTGGATGATGTGCTTGTCATGATGAAGATAGATCAGTC
CTTGAAGCACTTGCTTAAAGATGGTAGAAAGATAGGACTCAGGGATGGTT
TTGACTGATTTGAGAAAATCTTCTAGAGATCCACCGTCCATGTACTCCAA
AATCAGCGAGATTGCGCCATTATCGTAAAACGATTGGTACGAGGTAACAA
GGTACGGACATTGTGACGACTGGTTTATTTTAAGCTCTTGTGCAATTGAC
TTGCGAATCGCTTCATCGACGTTTAGTTGAATGACCTTTAAGGCGAAGAA
TTGACCAGTCCATTTGTGTTGAACAAGCTGCACAACACCGCTGCTTCCTT
TACCAATGACTTTAACCATGTCCAAATCGGATAAGCTCAACTCATCATCC
GCTGGCTTAATCGGAGACAGAGCTTCAGGCTCAGACTGAGAGACGATTCG
AACTCCGTCTTTGTTGACTCGCAGATCTCCATCCTTGAACGTACCGCTCT
GCGTCAAGAATTTGGTGATGGATTGCTCGCCAGCAGGAGGGATTGAGAGC
TTGAGATTATTGCTGAATCCACCCTTCTTCATTTCGTCTTCTTCTtcctt
cttctcctcgtcgctttccccggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 35 35 32 29 32 33 26 30 29 36 36 42 32 29 29 32 32 32 47
 47 39 39 35 35 35 35 42 35 35 35 35 35 32 35 35 35 35 35 35 35 35 32 35 35 35 32 32 32 29 29 32 29 29 35 35 35 35 35 35 29 35 35 30 35 35 35 26 26 30
 30 30 30 29 29 29 29 31 31 32 35 35 35 35 37 37 37 37 37 37 37 37 37 35 32 32 31 31 29 27 27 35 42 42 42 42 42 35 35 33 42 37 37 42 48 48 56 40 39 37
 31 31 31 31 31 35 30 30 20 20 29 25 25 29 33 37 30 28 28 28 28 28 27 12 11 7 7 7 9 11 14 14 19 18 25 25 25 16 16 9 9 10 13 14 18 21 33 27 27 30
 26 26 28 33 33 42 42 33 42 30 28 28 29 27 29 29 29 29 39 33 33 30 28 28 28 28 28 28 16 13 6 6 6 13 13 20 22 22 19 18 13 10 10 10 16 13 21 21 23 23
 19 19 20 24 24 19 20 20 29 29 35 33 33 28 28 28 36 33 29 27 28 29 24 24 28 28 28 22 28 29 29 29 26 29 27 29 29 29 26 23 23 23 26 35 28 29 29 29 32 42
 44 37 37 35 32 29 29 32 29 29 29 32 22 22 22 24 24 24 24 19 23 23 32 35 35 32 32 28 29 30 26 29 29 29 29 35 35 39 29 29 29 29 28 28 33 33 35 35 44 47
 44 42 42 35 35 35 35 30 35 36 36 30 30 35 35 35 35 33 35 33 37 44 44 44 35 35 35 36 30 27 27 29 29 32 35 38 56 47 47 47 47 47 47 47 47 48 45 35 35 35
 35 35 42 42 39 39 37 37 42 47 42 42 42 42 42 42 42 42 42 42 37 37 37 42 35 33 42 30 30 30 33 37 40 40 40 40 40 40 31 27 16 18 21 27 27 29 40 40 40 40
 47 47 23 16 9 9 9 16 15 22 23 25 30 42 42 42 42 42 42 42 42 35 35 35 35 35 35 35 35 35 35 35 35 42 43 48 47 37 36 36 35 35 35 40 40 46 51 37 37 37
 35 32 32 32 35 35 40 45 40 37 37 37 37 37 39 45 45 45 45 37 37 37 40 45 40 42 42 42 38 38 39 39 40 40 40 40 56 51 37 40 37 35 35 35 42 44 48 42 42 42
 37 37 37 46 46 51 56 56 56 56 46 37 33 33 34 32 32 32 32 32 29 29 29 34 40 32 29 34 29 29 31 37 46 46 46 40 32 32 25 25 25 32 30 46 30 30 30 39 30 39
 33 34 34 40 32 32 24 24 21 19 19 29 25 25 29 32 32 32 40 40 40 40 40 40 37 34 34 29 29 24 28 25 32 33 37 34 33 33 41 43 43 41 42 40 44 44 37 37 30 30
 20 22 22 37 40 32 29 23 17 12 19 19 32 40 37 37 40 45 37 30 39 35 42 44 45 47 40 40 47 55 53 72 72 54 44 49 47 38 34 48 59 60 60 61 53 53 52 49 47 47
 41 44 47 52 52 63 49 49 44 61 61 63 58 48 50 54 55 63 58 61 44 37 37 40 42 48 47 44 47 44 34 37 40 42 34 41 33 33 40 46 47 48 32 29 34 32 32 29 27 30
 25 25 25 34 32 25 29 32 32 32 29 27 27 25 22 22 34 40 48 40 44 44 46 46 46 56 56 56 56 56 56 56 51 51 51 51 51 46 46 42 44 43 51 42 42 40 40 40 40 40
 40 40 46 40 40 34 40 40 40 48 34 34 48 32 32 32 32 39 39 39 31 35 35 35 35 34 40 40 44 44 40 48 40 32 32 32 32 32 32 36 44 48 48 46 40 39 39 39 35 39
 40 40 37 40 40 51 51 51 51 51 51 51 51 51 56 51 51 51 51 45 45 45 40 40 40 45 45 56 56 56 56 56 56 45 45 45 45 45 45 51 45 45 45 45 45 45 51 56 56 56
 56 56 45 39 39 39 39 39 40 56 56 45 39 39 39 39 39 39 40 45 51 40 39 39 39 39 39 45 45 51 51 51 45 45 45 45 45 45 45 45 56 51 45 45 45 45 51 51 56 45
 45 45 45 45 45 51 51 51 51 56 56 56 56 56 51 51 51 56 51 51 51 51 51 51 51 56 56 56 56 56 45 45 45 45 51 51 56 56 56 56 56 51 51 51 51 51 51 51 51 51
 43 43 43 43 43 43 45 45 45 45 45 45 56 56 56 56 56 51 45 45 45 43 43 43 43 43 43 45 56 56 56 56 56 56 56 56 56 56 56 51 45 45 45 45 45 45 56 56 56 51
 51 51 56 56 45 45 45 45 45 45 56 56 56 56 56 56 56 51 51 51 51 51 51 46 43 43 43 43 43 43 43 43 43 51 56 56 46 43 43 43 43 43 45 45 45 51 56 56 56 56
 56 56 51 51 56 51 51 51 56 56 51 45 45 45 45 45 56 43 43 43 43 43 43 56 56 45 45 45 45 45 45 43 43 43 43 43 43 56 56 56 56 56 56 56 56 56 56 43 43 43
 43 43 43 45 45 45 45 45 45 43 43 43 43 43 43 45 45 45 43 43 43 43 43 45 56 51 51 51 51 51 51 51 51 51 51 45 45 45 45 45 45 45 45 45 45 43 43 43 43 43
 43 43 51 43 43 43 43 43 43 43 51 51 51 43 43 43 43 36 31 31 31 31 31 35 43 43 51 56 56 56 56 56 56 56 51 51 51 43 43 43 43 43 43 43 43 43 43 43 43 36
 35 35 35 35 43 43 45 45 45 45 51 56 51 51 51 51 51 51 51 45 45 45 45 45 43 35 35 35 35 35 35 35 35 35 35 39 51 51 51 51 51 51 40 40 40 40 40 40 45 40
 40 40 40 40 40 39 35 35 35 35 35 40 40 40 40 40 46 40 51 51 51 51 51 51 51 51 46 46 46 46 46 40 35 35 35 35 35 35 45 44 40 40 40 40 46 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2293f U 1
AF LL2293r C 682
BS 1 685 LL2293f
BS 686 706 LL2293r
BS 707 711 LL2293f
BS 712 717 LL2293r
BS 718 718 LL2293f
BS 719 720 LL2293r
BS 721 721 LL2293f
BS 722 728 LL2293r
BS 729 737 LL2293f
BS 738 747 LL2293r
BS 748 749 LL2293f
BS 750 1431 LL2293r

RD LL2293f 794 0 0
cttttaagaacaaacactaataaaatattgaatcttctttttaacataac
attccaatccaaagtatctcccttatgagaGCTCCAAGTGGAAAATAAAA
AAATAAAACTGAATAAGGACTCTCATGTAGCTCATATTATCAAAATACAG
CAACAATACAAATATATATATATATAGTAGATGATTAAGATCATTTTTTT
AACTGGAAGTTAAAGACAAAGAAaccttcagaagATAacatgtaaCCACC
AGATGATGAAGATACTATTTGTCTCCCTggatgagCTTaaactggaGAAT
gtACCaGACAGATTCTTAAGCGTTGCAAGCGGAGACCCTGCATTTGTAAA
GTATGACGCGAGGTTGATCtCCGAGTTGTTGTCGTATTTCTTCACGAAAG
GATGTTCCATTAGTTCCCTAGCAGAGCTTCGACTGTTTGGGTCCTTTTGC
AAACAAGTGGAGATGAATGAAGATAACTCAGGGGAGAAGCttTCTGAAGG
AAGagttggTGGTGGTTGGTCCACGATTGCTTCCATCAACTCGAAAACAC
TGCTCCATGTTTCCTCTTCATCTGGTGGCAAATATGGGAACTTCCCTGTT
GCACATTCAAGCACTACTAATCCCAAGCTCCATATATCGCTTTTGTTACC
GTACTTGTTccCAACGATCCTCTCTGGAGACATATAGTTGTaAGTcCCAa
canaTGTGtttgCTAAACCCGCGGTGTTAGTCATAACGGTACTCACACCG
AAGTCAGTGATCTTGACCTCTCCTCTGTGGTTGACCAACAGATT

QA 81 794 1 794
DS CHROMAT_FILE: LL2293f PHD_FILE: LL2293f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:56 2000

RD LL2293r 794 0 0
atATAGTTGTAAGTCCCAACAAATGTGtntgCTAAACCCGCGGTGTTAGT
CATAACGGTACTCACACCGAAGTCAGTGATCTTGACCTCTCCTCTGTGGT
TGACCAACAGATTCGATGGTTTCAAGTCACGGTGGATGATGTGCTTGTCA
TGATGAAGATAGATCAGTCCTTGAAGCACTTGCTTAAAGATGGTAGAAAG
ATAGGACTCAGGGATGGTTTTGACTGATTTGAGAAAATCTTCTAGAGATC
CACCGTCCATGTACTCCAAAATCAGCGAGATTGCGCCATTATCGTAAAAC
GATTGGTACGAGGTAACAAGGTACGGACATTGTGACGACTGGTTTATTTT
AAGCTCTTGTGCAATTGACTTGCGAATCGCTTCATCGACGTTTAGTTGAA
TGACCTTTAAGGCGAAGAATTGACCAGTCCATTTGTGTTGAACAAGCTGC
ACAACACCGCTGCTTCCTTTACCAATGACTTTAACCATGTCCAAATCGGA
TAAGCTCAACTCATCATCCGCTGGCTTAATCGGAGACAGAGCTTCAGGCT
CAGACTGAGAGACGATTCGAACTCCGTCTTTGTTGACTCGCAGATCTCCA
TCCTTGAACGTACCGCTCTGCGTCAAGAATTTGGTGATGGATTGCTCGCC
AGCAGGAGGGATTGAGAGCTTGAGATTATTGCTGAATCCACCCTTCTTCA
TTTCGTCTTCTTCTtccttcttctcctcgtcgctttccccggacgcgtgg
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxaat

QA 31 714 1 750
DS CHROMAT_FILE: LL2293r PHD_FILE: LL2293r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:33 2000

CO Contig24 1039 2 38 U
agttactattacagatgtatgagacggccactaaaatgaagcagcttatT
TTGTCAAATGTAAAAAAGAAAGTAGTCATGTGGAATGATATTTTTCGATT
TGTTTTTTTTTTCTTTCTTATAAATGGCATTTTCAGATTCAGAAACTGGA
GTCGTCAGTAGATGGACGCCTCAAGAAGTACCTCAGACTATTGGCAAGAA
CCTGCTGAAGAGGCTTGATTAGGGCTTTGTTTCTGTAACTTACGTGGAAC
TTAACCTTAGCCAACAAACCCTCAGTGTCGAATTCTCCAGATTCGACAGC
GACGCTGATATCTGTAATGTTCTTCACTAGCTCAACTAATAGTCCAGGCC
TATCCGCTGTTTCTATGTATAGTAAACTGCGGTCTGGTCCATCATCTTCA
ATTTTTATATGCGTTGCTATGTCCACATCAACCTGTTCAGTTGGTGGAAG
AACACCAAAAGCTGCTCCCATTGCCAACTGAGAACTTGATTCAGGATGAA
ACTCGAGCAAATTGTTAATGACAGTGAGACGGATGGCCTCGAGCAACTCA
GGGTCTTCTACTTTTCTTCCACTATCCGCTTTAGTAATGGCAAATTTGTT
GTGCTTGCCAGAAGAATCGAGGTAGACATTAGCCTTGACAACATTCAGAC
CCAAATTTTTGAGCGCATTCATAGTGTCAAGTAGAGCTCCTAGACGATCT
CCAAATGTTACTTCAACAACGGTTGCATCAGGGTCAGAATCTTGGTCGAT
TATGACCACTGGAGTTGGGACTTCGTCAGAATCCTGCTTACCATTCTCCA
CAGCAGTAGCGTTTGCTGCTCGAGGCTTCAACCCCGATAATCTGAGTCGC
TGAAGATTTATAATAGGCTTATCGACAAATCCAAACGTGATTGTGCTAGG
AGGAAGACATAAAGCTCCAAGATCACGTCTGATTGCGGGAGAAGTAGAAG
CATCAGTGAAGCAAAGAGCAGAACCAGAAGCAGAGGCCATAGCCACCATA
GCtgacttgaacccgaagcaaaaaaaaacggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51
 40 40 39 35 35 37 37 37 51 51 51 51 51 51 51 51 51 51 51 51 40 35 35 35 35 35 37 37 37 40 56 56 56 56 46 40 40 40 40 40 40 40 51 40 35 35 35 35 35 40
 51 51 51 51 51 56 56 56 56 56 56 56 56 51 51 51 46 46 46 46 46 40 40 37 37 37 40 40 40 40 56 51 51 51 51 51 51 51 45 45 40 40 40 35 35 35 35 35 40 46
 43 43 43 43 43 43 51 51 51 51 51 43 56 43 43 43 43 43 43 43 43 43 43 43 51 51 45 45 51 40 43 43 45 45 43 43 36 43 43 43 40 41 41 45 45 45 41 41 45 45
 45 43 43 43 43 43 43 43 56 56 56 45 45 45 41 41 41 43 43 43 43 43 43 43 43 43 43 43 51 51 51 51 51 51 43 45 43 43 43 43 43 43 43 36 36 40 45 43 43 43
 43 43 43 45 45 45 45 51 51 51 51 45 45 45 45 45 45 45 43 43 43 43 45 45 56 56 38 43 43 43 43 43 51 51 51 51 51 51 51 51 51 45 45 43 43 43 43 43 43 43
 43 43 43 43 43 43 43 43 56 41 41 44 46 43 46 56 56 56 50 56 56 56 56 51 43 43 43 43 43 51 45 45 45 43 43 43 43 43 43 45 56 56 51 51 51 51 51 51 51 51
 51 51 45 43 43 43 38 38 38 46 56 56 56 51 51 51 51 51 51 51 51 51 51 56 46 46 43 43 41 49 41 45 46 56 56 56 56 51 56 56 66 71 56 56 56 56 45 45 45 51
 51 51 56 56 56 56 56 51 51 45 45 51 59 48 46 46 46 47 49 47 53 59 59 59 59 59 56 56 56 45 45 45 45 45 40 43 43 51 51 51 43 56 56 56 56 56 56 56 56 56
 56 56 45 45 53 55 54 53 64 52 49 57 61 58 52 52 52 53 58 63 46 35 35 35 35 39 40 45 45 40 40 42 40 45 45 45 45 40 40 59 58 60 64 61 61 60 63 64 64 53
 55 57 63 60 58 51 51 51 51 51 51 46 46 38 38 37 40 40 66 66 64 54 63 59 57 55 54 49 45 46 48 49 52 50 48 46 43 42 46 48 65 60 58 44 37 36 45 50 50 55
 49 47 47 58 50 58 57 49 52 56 53 45 48 48 50 46 52 55 55 46 56 59 61 59 58 59 59 54 52 47 56 52 54 56 56 49 46 46 32 27 33 33 28 29 31 29 32 27 40 40
 40 39 36 36 33 37 40 40 45 42 47 51 49 54 58 59 66 67 64 50 38 33 36 38 45 45 51 53 44 44 42 45 47 50 45 51 50 48 44 37 37 49 73 57 66 69 77 69 72 76
 56 59 59 63 82 63 68 85 63 58 56 56 48 56 56 54 55 69 70 73 77 74 69 63 61 63 68 62 71 67 70 73 60 65 60 55 53 51 40 40 48 50 52 54 55 57 61 58 57 53
 47 47 49 55 47 51 42 48 48 60 59 56 59 59 62 50 45 40 40 39 44 39 35 35 56 48 51 57 64 63 54 52 51 55 57 54 49 52 52 49 56 54 54 54 44 48 45 49 58 58
 68 70 71 76 71 69 64 74 74 70 54 54 59 57 56 56 70 73 51 45 45 40 35 35 35 35 35 39 45 45 45 51 51 51 51 51 51 51 51 51 56 56 56 51 51 51 51 51 51 46
 39 35 35 35 39 39 39 39 39 39 39 39 39 40 45 45 40 45 40 40 40 40 45 45 51 51 51 51 51 51 51 56 46 46 46 39 39 39 45 45 45 51 40 40 39 39 39 39 39 39
 40 51 51 51 56 56 51 56 51 45 45 45 45 45 51 51 51 51 51 51 43 43 43 43 43 51 56 56 56 56 56 51 51 43 43 43 43 43 43 45 43 43 43 43 43 43 51 45 45 45
 45 51 45 45 45 45 51 45 51 51 43 43 43 43 43 43 51 56 56 56 51 51 51 43 35 35 35 35 35 43 45 45 43 43 43 43 43 43 51 56 51 45 45 45 45 45 45 45 51 51
 51 51 46 40 39 39 39 39 40 40 45 45 45 56 45 39 39 39 39 39 40 51 51 51 45 51 45 40 40 40 40 40 40 51 51 51 51 39 35 35 35 35 35 40 40 56 40 40 37 37
 35 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2300f U -30
AF LL2300r C 344
BS 1 379 LL2300f
BS 380 380 LL2300r
BS 381 390 LL2300f
BS 391 392 LL2300r
BS 393 412 LL2300f
BS 413 426 LL2300r
BS 427 454 LL2300f
BS 455 471 LL2300r
BS 472 489 LL2300f
BS 490 505 LL2300r
BS 506 518 LL2300f
BS 519 593 LL2300r
BS 594 600 LL2300f
BS 601 606 LL2300r
BS 607 607 LL2300f
BS 608 611 LL2300r
BS 612 621 LL2300f
BS 622 626 LL2300r
BS 627 630 LL2300f
BS 631 632 LL2300r
BS 633 633 LL2300f
BS 634 634 LL2300r
BS 635 635 LL2300f
BS 636 637 LL2300r
BS 638 638 LL2300f
BS 639 639 LL2300r
BS 640 641 LL2300f
BS 642 643 LL2300r
BS 644 644 LL2300f
BS 645 670 LL2300r
BS 671 671 LL2300f
BS 672 679 LL2300r
BS 680 682 LL2300f
BS 683 683 LL2300r
BS 684 684 LL2300f
BS 685 706 LL2300r
BS 707 768 LL2300f
BS 769 1039 LL2300r

RD LL2300f 804 0 0
ncttttatgnatagcgttggaagtagagaanagttactattacagatgta
tgagacggccactaaaatgaagcagcttatTTTGTCAAATGTAAAAAAGA
AAGTAGTCATGTGGAATGATATTTTTCGATTTGTTTTTTTTTTCTTTCTT
ATAAATGGCATTTTCAGATTCAGAAACTGGAGTCGTCAGTAGATGGACGC
CTCAAGAAGTACCTCAGACTATTGGCAAGAACCTGCTGAAGAGGCTTGAT
TAGGGCTTTGTTTCTGTAACTTACGTGGAACTTAACCTTAGCCAACAAAC
CCTCAGTGTCGAATTCTCCAGATTCGACAGCGACGCTGATATCTGTAATG
TTCTTCACTAGCTCAACTAATAGTCCAGGCCTATCCGCTGTTTCTATGTA
TAGTAAACTGCGGTCTGGTCCATCATCTTCAATTTTTATATGCGTTGCTA
TGTCCACATCAACCTGTTCAGTTGGTGGAAGAACACCAAAAGCTGCTCCC
ATTGCCAACTGAGAACTTGATTCAGGATGAAACTCGAGCAAATTGTTAAT
GACAGTGAGACGGATGGCCTCGAGCAACTCAGGGTCTTCTACTTTTCTTC
CACTATCCGCTTTAGTAATGGCaAATTTGTTGTGCTTGCCAGAAGAATCG
AGGTAGACATTAGCCTTGACAACATTCAGACCCAAATTTTTGAGCGCATT
CATAGTGTCAAGTAGAGCTCCTAGACGATCTCCAAATGTTACTTCAACAA
CGGTTGCATCAGGGTCAGAATCTTGGTCGATTATGACCACTGGAGTTGGG
ACTT

QA 81 737 32 804
DS CHROMAT_FILE: LL2300f PHD_FILE: LL2300f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:52 2000

RD LL2300r 739 0 1
ccaggcc*atc*gctggttcaagg*atagt*aacTGCGGTctg*tCCATC
ATctccaatttt*aTATGCGTTGCTATGTCCACATcancctgtncagttg
*tgaaagAACACCAAAAGCTGCTCCCATTGCcanctgaganctTGATTCA
GGATGAAACTCGAGcanantgTTAATGACAGTGAGACGGATGGCCTCGAG
CAACTCAGGGTCTTCTACTTTTCTTCCACTATCCGCTTTAGTAATGGCAA
atntGTTGTGCTTGCCAGAAGAATCGAGGTAGACATTAGCCTTGACAACA
TTCAGACCCAAATTTTTGAGCGCATTCATAGTGTCAAGTAGAGCTCCTAG
ACGATCTCCAAATGTTACTTCAACAACGGTTGCATCAGGGTCAGAATCTT
GGTCGATTATGACCACTGGAGTTGGGACTTCGTCAGAATCCTGCTTACCA
TTCTCCACAGCAGTAGCGTTTGCTGCTCGAGGCTTCAACCCCGATAATCT
GAGTCGCTGAAGATTTATAATAGGCTTATCGACAAATCCAAACGTGATTG
TGCTAGGAGGAAGACATAAAGCTCCAAGATCACGTCTGATTGCGGGAGAA
GTAGAAGCATCAGTGAAGCAAAGAGCAGAACCAGAAGCAGAGGCCATAGC
CACCATAGCtgacttgaacccgaagcaaaaaaaaacggacgcgtggxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxat

QA 255 659 1 696
DS CHROMAT_FILE: LL2300r PHD_FILE: LL2300r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:29 2000

RT{
LL2300r compression phrap 100 102 000919:094547
}

CO Contig25 1296 2 20 U
gatggaagataacttcaATATATTACAAACTTATTAAAAGGAGTAGCTAA
TGCAAATTCAGCAGAGAAAATAAGTGATTTGACATGATAATAACAACCAT
ACTCGAAAACAAATGTAATTAAAACACTTGCTTCATCTCCTTTCACAGCA
TCTTCACCTCTTCAACATTGTTGTCTTCAGTAGGTGTAGCCTTTGACGAA
CATACCCTCCTTAGCCTCTTCAGACTCACCTTCTCCGGTGTATTTTCCGA
GCTGAGCCAACGAATTGGCCTTGGCTCGAGTCAAGAGAGTGGTCTGAGCT
GCGTTCACGTTCTCAGCTCTGCCTCCCCATGTTTTCAGGCAAGTGTTCTG
AAGAGCACGTGCGTAGGAGAAGGACACGTGCCACGGGTTTGGTGCCTGGT
TCATCGCGTTCAGGTTCAACGTTGCCTCCAACTCAGACTGTCCTCCGGAC
AAGAACATGATTCCAGGGACGGCAGGAGGGATTCTGTTGCGGAGGAGCTT
AAGGGTGTAGGAGGCAACTTGTTCAGGAGTAGCTCTGTCTTTAGACTCGG
CTCCTGGAGTCACCATGCTCGGCTTCAGGAGGATACCTTCAAACATGACA
TTGTTCTGAGCTAGGTAAAAGAAAACCTCAGCCCACACCTTCTCTGCTAC
TTCGTAAGTCCTGTCAATGTCGTGTTCTCCATCCAACAAGATCTCTGGCT
CCACTATGGGAACCAATCCACTGTCTTGTGAAATGGCAGCGTATCGAGCA
AGGCCCCAAGCAGCTTCTTTCACAGCGAGAGCAGACGGACCGTTGGGAAT
GCTCACCACAGTACGCCATTTGGCGAAACGAGCACCCTGTTGGTAGTAAG
CAGCGGTCCGAGAGGATAGACCGTCAAGTCCTTGGCACCATGACTCATTG
TTAGATCCAACAAGTGGCACCAAACCCTTGTCGACTTTGATACCGGGGAC
GATGTTCTGCTCGACTAGGACGTCGACCATTTTCTTGCCTTCGGTGGTAG
ACTGATAGAGAGTCTCCTCGAACAGGATTGCACCGGAGATGTACTGTCCG
AGACCTGGTGCAGAGACAAGCAGTGTCCGGTATGCTTGACGGTTTGCCTC
AGTGTTCTCTAGCCCTATCGAGTCCAAACGCTTCCCGCATGTGGCGTTCG
ACTCGTCCATCGCCAAGATTCCTCGTCCAGGAGACGCAATTGTTTTCGCT
GTCTTAACGAGCTCATCGGCGTAGGAAGAAGCGGCGCGGACGGTAAGGTA
GGTGGCGCGGTTGCGTAGGACGACGGCGGCGGAAGcggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 36 37 40 39 34 34 34 34 34 35 35 35 35 35 35 35 39 39 39 39 40 51 46 46 46 46 46 40 34 34 34 34 34
 35 40 40 40 46 51 46 46 46 46 46 40 40 40 40 40 40 46 46 56 37 37 40 40 40 40 46 40 35 39 39 39 39 39 40 40 40 40 39 39 39 39 39 45 51 40 40 40 40 40
 40 45 40 40 40 40 40 51 51 46 46 46 51 46 46 40 40 35 35 35 35 35 35 51 40 40 40 35 35 35 35 35 35 39 40 40 40 40 40 40 40 40 40 46 40 40 40 45 45 45
 45 45 43 43 43 43 43 43 45 43 43 43 43 46 43 51 51 51 56 56 56 51 43 45 45 45 45 45 43 43 43 43 43 40 51 56 43 43 43 43 43 43 56 43 36 36 36 36 36 43
 43 43 43 43 43 43 43 43 43 43 45 45 45 45 45 45 45 45 51 51 51 43 43 43 43 43 43 43 45 45 45 51 56 51 51 51 51 56 41 51 51 51 51 51 51 43 43 43 43 43
 43 43 43 43 43 45 45 45 43 43 43 45 45 45 56 43 43 43 43 43 43 45 43 43 43 43 43 43 45 51 56 56 51 51 51 51 51 51 51 51 56 45 45 45 45 45 45 45 36 36
 36 36 36 36 43 43 43 43 43 43 43 45 45 45 43 43 43 43 43 43 43 43 43 43 45 45 51 56 56 56 56 56 56 56 56 56 51 51 51 51 51 51 56 56 51 43 43 43 43 43
 45 56 51 45 43 43 43 43 43 43 43 43 43 43 45 51 51 56 51 56 56 51 51 51 43 43 43 43 43 43 45 43 43 43 43 43 51 56 56 56 56 51 45 45 45 45 45 56 51 56
 56 56 45 43 43 43 43 43 43 45 56 56 56 56 56 56 51 43 40 40 40 40 40 45 45 45 45 45 51 40 45 45 45 45 40 45 45 45 45 40 43 43 51 51 51 51 51 51 51 51
 51 51 51 51 51 51 51 51 51 51 51 51 51 51 56 51 45 40 40 40 40 40 45 56 56 56 56 56 56 51 51 51 51 51 51 51 45 40 40 40 40 40 45 56 56 45 45 37 37 37
 40 45 45 51 51 45 51 51 51 51 51 46 46 42 42 37 40 40 40 40 40 56 56 56 56 56 56 51 51 51 40 40 40 45 45 45 56 56 56 46 46 46 37 48 51 59 59 65 63 51
 54 54 49 42 42 44 47 44 47 52 50 49 55 59 58 71 68 68 66 65 69 57 60 60 62 60 67 55 50 52 52 48 50 54 51 51 51 46 46 50 44 46 53 72 75 75 71 61 59 58
 58 64 55 55 55 66 66 64 64 54 50 43 48 41 42 40 40 40 42 47 25 25 26 23 25 25 44 44 47 61 57 51 46 43 55 55 52 43 41 38 43 48 65 69 69 55 55 50 59 51
 44 44 52 59 54 47 54 59 65 65 62 67 62 56 54 60 57 62 47 44 47 43 43 40 44 44 58 58 63 59 76 72 44 41 37 37 50 53 57 69 67 80 80 80 69 54 51 45 51 48
 40 49 67 63 63 71 69 47 41 48 44 37 37 47 47 55 59 60 58 61 56 55 45 49 47 47 54 49 55 47 49 56 61 54 46 47 53 55 56 67 72 72 72 80 80 80 69 63 62 59
 54 47 32 32 32 32 26 29 29 30 39 39 57 52 47 51 61 59 63 58 57 61 53 53 56 56 54 62 65 75 69 63 57 40 51 51 51 51 56 45 45 45 45 45 51 40 40 40 40 40
 45 56 56 56 56 56 56 42 37 40 40 40 40 37 40 40 45 56 51 45 40 37 37 37 40 40 51 51 45 45 40 45 40 45 56 56 56 56 51 45 45 45 45 45 45 45 40 40 37 37
 37 37 37 37 40 45 45 51 45 51 51 51 51 51 45 45 45 45 45 45 51 51 51 51 51 45 45 45 45 45 45 51 56 56 56 56 56 56 51 51 51 51 51 51 56 56 56 56 56 51
 45 45 45 45 45 56 56 56 56 56 51 45 45 45 43 43 45 45 45 51 56 56 56 56 56 56 56 45 51 45 45 45 45 51 56 51 51 56 56 56 56 51 56 56 56 51 51 51 51 51
 51 45 45 51 51 51 51 56 56 51 51 51 51 51 51 51 51 51 45 45 45 45 45 45 51 51 56 56 56 56 56 56 56 51 51 51 45 45 45 43 43 43 43 43 43 43 43 43 43 43
 51 51 56 56 51 51 51 51 45 43 43 43 43 43 43 56 45 45 45 45 45 45 45 45 45 45 45 51 51 51 51 45 45 45 43 43 43 43 43 43 51 51 51 43 43 43 43 43 43 43
 43 43 45 51 56 43 43 43 43 43 43 45 45 51 51 51 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 45 51 51 56 56 56 45 45 43 43 43 43 51 45 45 45 45 43 43
 43 43 43 43 43 43 43 43 43 43 43 43 43 43 51 51 43 43 43 43 43 43 43 43 43 51 43 36 36 36 36 36 43 43 43 43 43 43 36 43 43 36 34 34 34 34 34 43 43 43
 43 43 36 36 36 36 36 43 43 43 43 43 43 43 43 45 45 45 45 51 43 35 35 35 35 35 35 43 43 43 43 43 35 35 35 35 35 35 43 45 45 45 51 43 35 35 35 35 35 38
 40 40 39 39 39 35 35 35 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 46 46 46 46 39 35 35 35 35 35 35 35 35 35 35 35 40 40 40 40 40 40 39 39 39 39 39
 39 39 39 35 35 29 29 29 35 30 35 39 39 35 35 39 39 45 46 46 46 46 46 40 40 39 35 35 35 35 35 35 35 35 35 0 0 0 0 0 0 0 0 0 0 0

AF LL2302f U 1
AF LL2302r C 539
BS 1 590 LL2302f
BS 591 591 LL2302r
BS 592 612 LL2302f
BS 613 616 LL2302r
BS 617 632 LL2302f
BS 633 636 LL2302r
BS 637 643 LL2302f
BS 644 650 LL2302r
BS 651 656 LL2302f
BS 657 684 LL2302r
BS 685 687 LL2302f
BS 688 694 LL2302r
BS 695 695 LL2302f
BS 696 708 LL2302r
BS 709 711 LL2302f
BS 712 725 LL2302r
BS 726 726 LL2302f
BS 727 760 LL2302r
BS 761 783 LL2302f
BS 784 1296 LL2302r

RD LL2302f 788 0 0
gatggaagataacttcaATATATTACAAACTTATTAAAAGGAGTAGCTAA
TGCAAATTCAGCAGAGAAAATAAGTGATTTGACATGATAATAACAACCAT
ACTCGAAAACAAATGTAATTAAAACACTTGCTTCATCTCCTTTCACAGCA
TCTTCACCTCTTCAACATTGTTGTCTTCAGTAGGTGTAGCCTTTGACGAA
CATACCCTCCTTAGCCTCTTCAGACTCACCTTCTCCGGTGTATTTTCCGA
GCTGAGCCAACGAATTGGCCTTGGCTCGAGTCAAGAGAGTGGTCTGAGCT
GCGTTCACGTTCTCAGCTCTGCCTCCCCATGTTTTCAGGCAAGTGTTCTG
AAGAGCACGTGCGTAGGAGAAGGACACGTGCCACGGGTTTGGTGCCTGGT
TCATCGCGTTCAGGTTCAACGTTGCCTCCAACTCAGACTGTCCTCCGGAC
AAGAACATGATTCCAGGGACGGCAGGAGGGATTCTGTTGCGGAGGAGCTT
AAGGGTGTAGGAGGCAACTTGTTCAGGAGTAGCTCTGTCTTTAGACTCGG
CTCCTGGAGTCACCATGCTCGGCTTCAGGAGGATACCTTCAAACATGACA
TTGTTCTGAGCTAGGTAAAAGAAAACCTCAGCCCACACCTTCTCTGCTAC
TTCGTAAGTCCTGTCAATGTCGTGTTCTCCATCCAACAAGATCTCTGGCT
CCACTATGGGAACCAATCCACTGTCTTGTGAAATGGCAGCGTATCGAGCA
AGgcccncagCAGCTTCTTTCACAGCGAGAGCAGAcgg

QA 18 752 1 788
DS CHROMAT_FILE: LL2302f PHD_FILE: LL2302f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:02 2000

RD LL2302r 801 0 0
ctTTAGACTCGGCTCCTGGAGTCACCATGCTCGGCTTCAGGAGGATACCT
TCAAACATGACATTGTTCTGAGCTAGGTAAAAGanaacCTCAGCCCACAC
CTTCTCTGCTACTTCGTAAGTCCTGTCAATGTCGTGTTCTCCATCCAACA
AGATCTCTGGCTCCACTATGGGAACCAATCCACTGTCTTGTGAAATGGCA
GCGTATCGAGCAAGGCCCCAAGCAGCTTCTTTCACAGCGAGAGCAGACGG
ACCGTTGGGAATGCTCACCACAGTACGCCATTTGGCGAAACGAGCACCCT
GTTGGTAGTAAGCAGCGGTCCGAGAGGATAGACCGTCAAGTCCTTGGCAC
CATGACTCATTGTTAGATCCAACAAGTGGCACCAAACCCTTGTCGACTTT
GATACCGGGGACGATGTTCTGCTCGACTAGGACGTCGACCATTTTCTTGC
CTTCGGTGGTAGACTGATAGAGAGTCTCCTCGAACAGGATTGCACCGGAG
ATGTACTGTCCGAGACCTGGTGCAGAGACAAGCAGTGTCCGGTATGCTTG
ACGGTTTGCCTCAGTGTTCTCTAGCCCTATCGAGTCCAAACGCTTCCCGC
ATGTGGCGTTCGACTCGTCCATCGCCAAGATTCCTCGTCCAGGAGACGCA
ATTGTTTTCGCTGTCTTAACGAGCTCATCGGCGTAGGAAGAAGCGGCGCG
GACGGTAAGGTAGGTGGCGCGGTTGCGTAGGACGACGGCGGCGGAAGcgg
acgcgtggxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxa
t

QA 6 747 1 758
DS CHROMAT_FILE: LL2302r PHD_FILE: LL2302r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:39 2000

CO Contig26 816 2 80 U
cacaatagacttcattaataacaccacaacaaaataaacaatatcgagct
ccaacctcacttttacACACAAGACAATCACAACAACAAGTACATAAACA
AACTCAACAACAACTAAGGGCAGGGATAAAAGAACATGATATGGTGATTT
TATTTAAAAAAAACGCTAGTCTCAGCTGCATTTTCAGTCTTGATACTCCA
CTTCTTCCTCCTCCTCTTCTTCATACTCTCCTTCTTCATCTGCGGTTGCG
TCTTGGTATTGCTGATACTCTGAGACCAGATCGTTCATGTTGCTCTCGGC
TTCTGTAAACTCCATCTCGTCCATCCCTTCACCTGTGTACCAATGCAAGA
AAGCTTTCCTCCTGAACATGGCTGTGAACTGCTCACTCACCCTCCTAAAC
ATCTCTTGGATCGATGTGGAGTTCCCAATAAAGGTTGAGGCCATCGAGAG
GCCTCGAGGCGCTATGTCACAGACGCTTGACTTCACGTTGTTCGGTATCC
ATTCCACAAAGTAGGATGAGTTCTTGTTCTGCACGTTTATCATCTGTTCG
TCCACTTCTTTTGTGCTCATTTTGCCACGGAACATTGCTGAGGCAGTCAA
GTATCGTCCGTGACGCGGGTCTGCGGCACACATCATGTTCTTTGAATCCC
ACATCTGTTGGGTGAGCTCAGGGACGGTGAGTGCGCGGTACTGCTGGGAG
CCACGAGAGGTGAGAGGAGCGAAACCGACCATGAAGAAGTGGAGACGAGG
GAAGGGGATGAGGTTCACTGCAAGCTTCCTcagatcagagttgagctgac
cagggcggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 51 46 51 40 40 46 48 50 40 40 40 40 51 51 56 56 56 56 51 51 40 40 40 65 67 73 68 63 59 59 59 70
 60 70 40 40 40 40 51 51 56 56 56 40 35 50 50 50 57 61 55 55 61 64 62 85 65 75 69 65 66 66 76 90 70 70 76 83 83 79 83 83 77 83 77 67 67 67 77 72 69 65
 65 66 61 61 61 66 73 73 85 82 80 61 53 56 62 58 60 64 72 68 76 76 83 89 89 75 70 78 78 89 89 90 90 90 88 88 82 88 90 90 90 85 86 83 83 83 77 70 69 83
 83 69 69 84 77 77 90 83 75 77 77 77 77 85 90 90 88 90 90 90 90 90 90 87 87 85 83 90 75 77 77 83 88 90 90 90 90 89 89 87 75 75 70 75 75 69 63 70 70 70
 72 82 79 85 85 90 90 90 89 90 90 90 90 89 89 89 83 83 83 83 79 75 68 75 75 72 75 90 85 75 79 79 82 84 84 90 90 90 90 89 90 83 83 83 83 83 90 90 90 90
 90 90 90 85 85 90 90 80 80 90 90 90 90 90 88 83 83 83 83 83 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 88 88 88 88 90 90 87 87 90 90 90 90 90
 90 88 88 88 88 89 89 90 90 90 90 90 90 90 90 90 90 90 90 83 83 83 83 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 86 86 86 86 86 89 90 90 90 90 90 90 90 90 86 83 83 83 83 83 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 88 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 84 84 82 78 78 82 83 83 83 90 90 90 90 90 90 90 90 90 90 87 81 81
 81 76 83 90 90 90 90 90 90 90 90 90 87 83 83 90 90 90 90 90 90 90 90 88 90 82 82 85 90 90 90 90 90 90 90 90 86 86 86 86 78 83 83 83 83 89 89 89 89 89
 89 83 72 75 75 70 75 68 68 72 70 70 72 72 72 72 74 82 89 83 75 68 68 69 69 72 78 78 78 86 86 90 90 90 88 90 83 90 90 90 90 90 90 90 90 90 85 90 90 90
 89 89 85 85 75 75 75 75 72 75 77 90 90 83 75 75 75 72 74 69 73 73 65 70 60 54 54 60 75 83 83 70 58 51 51 49 53 49 67 67 70 72 78 78 76 68 63 70 65 61
 61 54 56 60 68 68 74 65 73 67 69 72 80 90 69 64 56 59 61 61 61 54 54 54 63 70 64 64 60 55 57 58 57 61 62 66 58 59 65 65 74 65 65 57 56 66 66 68 73 73
 76 76 76 79 79 83 80 85 90 90 69 62 55 55 55 63 71 60 62 56 52 52 49 52 52 37 40 42 46 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2304f U 1
AF LL2304r C 67
BS 1 74 LL2304f
BS 75 76 LL2304r
BS 77 91 LL2304f
BS 92 102 LL2304r
BS 103 137 LL2304f
BS 138 138 LL2304r
BS 139 173 LL2304f
BS 174 176 LL2304r
BS 177 177 LL2304f
BS 178 182 LL2304r
BS 183 199 LL2304f
BS 200 201 LL2304r
BS 202 203 LL2304f
BS 204 204 LL2304r
BS 205 206 LL2304f
BS 207 207 LL2304r
BS 208 223 LL2304f
BS 224 225 LL2304r
BS 226 227 LL2304f
BS 228 228 LL2304r
BS 229 239 LL2304f
BS 240 240 LL2304r
BS 241 258 LL2304f
BS 259 266 LL2304r
BS 267 277 LL2304f
BS 278 278 LL2304r
BS 279 289 LL2304f
BS 290 291 LL2304r
BS 292 296 LL2304f
BS 297 303 LL2304r
BS 304 309 LL2304f
BS 310 315 LL2304r
BS 316 320 LL2304f
BS 321 323 LL2304r
BS 324 324 LL2304f
BS 325 334 LL2304r
BS 335 335 LL2304f
BS 336 343 LL2304r
BS 344 345 LL2304f
BS 346 349 LL2304r
BS 350 350 LL2304f
BS 351 357 LL2304r
BS 358 363 LL2304f
BS 364 366 LL2304r
BS 367 373 LL2304f
BS 374 375 LL2304r
BS 376 376 LL2304f
BS 377 393 LL2304r
BS 394 396 LL2304f
BS 397 402 LL2304r
BS 403 407 LL2304f
BS 408 417 LL2304r
BS 418 423 LL2304f
BS 424 426 LL2304r
BS 427 439 LL2304f
BS 440 487 LL2304r
BS 488 489 LL2304f
BS 490 490 LL2304r
BS 491 496 LL2304f
BS 497 508 LL2304r
BS 509 513 LL2304f
BS 514 516 LL2304r
BS 517 528 LL2304f
BS 529 544 LL2304r
BS 545 552 LL2304f
BS 553 558 LL2304r
BS 559 559 LL2304f
BS 560 560 LL2304r
BS 561 562 LL2304f
BS 563 595 LL2304r
BS 596 601 LL2304f
BS 602 618 LL2304r
BS 619 619 LL2304f
BS 620 642 LL2304r
BS 643 646 LL2304f
BS 647 661 LL2304r
BS 662 663 LL2304f
BS 664 678 LL2304r
BS 679 680 LL2304f
BS 681 816 LL2304r

RD LL2304f 779 0 0
cacaatagacttcattaataacaccacaacaaaataaacaatatcgagct
ccaacctcacttttacACACAAGACAATCACAACAACAAGTACATAAACA
AACTCAACAACAACTAAGGGCAGGGATAAAAGAACATGATATGGTGATTT
TATTTAAAAAAAACGCTAGTCTCAGCTGCATTTTCAGTCTTGATACTCCA
CTTCTTCCTCCTCCTCTTCTTCATACTCTCCTTCTTCATCTGCGGTTGCG
TCTTGGTATTGCTGATACTCTGAGACCAGATCGTTCATGTTGCTCTCGGC
TTCTGTAAACTCCATCTCGTCCATCCCTTCACCTGTGTACCAATGCAAGA
AAGCTTTCCTCCTGAACATGGCTGTGAACTGCTCACTCACCCTCCTAAAC
ATCTCTTGGATCGATGTGGAGTTCCCAATAAAGGTTGAGGCCATCGAGAG
GCCTCGAGGCGCTATGTCACAGACGCTTGACTTCACGTTGTTCGGTATCC
ATTCCACAAAGTAGGATGAGTTCTTGTTCTGCACGTTTATCATCTGTTCG
TCCACTTCTTTTGTGCTCATTTTGCCACGGAACATTGCTGAGGCAGTCAA
GTATCGTCCGTGACGCGGGTCTGCGGCACACATCATGTTCTTTGAATCCC
ACATCTGTTGGGTGAGCTCAGGGACGGTGAGTGCGCGGTACTGCTGGGAG
CCACGAGAGGTGAGAGGAGCGAAACCGACCATGAAGAAGTGGAGACGAGG
GAAGGGGATGAGGTTCACTGCAAGCTtcn

QA 67 775 1 778
DS CHROMAT_FILE: LL2304f PHD_FILE: LL2304f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:33 2000

RD LL2304r 794 0 0
acACAAGACAATCACAacancaAGTACATAAACAAACTcaccaACAACTA
AGGGCAGGGATAAAAGAACATGATATGGTGATTTTATTTAAAAAAAACGC
TAGTCTCAGCTGCATTTTCAGTCTTGATACTCCACTTCTTCCTCCTCCTC
TTCTTCATACTCTCCTTCTTCATCTGCGGTTGCGTCTTGGTATTGCTGAT
ACTCTGAGACCAGATCGTTCATGTTGCTCTCGGCTTCTGTAAACTCCATC
TCGTCCATCCCTTCACCTGTGTACCAATGCAAGAAAGCTTTCCTCCTGAA
CATGGCTGTGAACTGCTCACTCACCCTCCTAAACATCTCTTGGATCGATG
TGGAGTTCCCAATAAAGGTTGAGGCCATCGAGAGGCCTCGAGGCGCTATG
TCACAGACGCTTGACTTCACGTTGTTCGGTATCCATTCCACAAAGTAGGA
TGAGTTCTTGTTCTGCACGTTTATCATCTGTTCGTCCACTTCTTTTGTGC
TCATTTTGCCACGGAACATTGCTGAGGCAGTCAAGTATCGTCCGTGACGC
GGGTCTGCGGCACACATCATGTTCTTTGAATCCCACATCTGTTGGGTGAG
CTCAGGGACGGTGAGTGCGCGGTACTGCTGGGAGCCACGAGAGGTGAGAG
GAGCGAAACCGACCATGAAGAAGTGGAGACGAGGGAAGGGGATGAGGTTC
ACTGCAAGCTTCCTcagatcagagttgagctgaccagggcggacgcgtgg
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxat

QA 48 714 1 750
DS CHROMAT_FILE: LL2304r PHD_FILE: LL2304r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:11 2000

CO Contig27 547 2 10 U
CTTTTTTTTTTTTTTTTAAACGAAGAAGCAAAAACTCAAGTTAATCCAAA
AAATATTCAGAATTATTACACGATAAAAGTTTTTTAGACAAAGATAGATT
TTGTTCTATATGAAGTACAATCGATGAAGAATTTACTTTTAAGTGATCAC
TGATCTAAGTACTTCACGGGAACAAGTAGAAGCTCACTTTTCTTGCTCAC
AGTAAGCCCAGGAGCTTCCTCCATGTCGACATCTTCCACCACCATGCCTT
CAGGTAACTCCCAGTCAAAATGATACAATAGACTCGCCAGACCAAACTCC
ACCGAAGTCGTCCCCATGTATATTCCAGGACAGATTCTCCTACCACTCCC
AAACGACAACAGCTCAAAG**TTTTGTCCCTTTGCATCAATGTTATTATC
CATAAACCTCTCGGGGAAAAACATCTCTGGATCCTTCCAGGTATCCGGAT
CACGCCCAATAGCCCAGACATTCACATGAAGACGTGTCTTGACGGGAATC
GTGTAGCCGTCGATCTCAAACTCCGAGGTTACTTCGGACGCGTGGga

BQ
 46 56 56 56 56 56 56 56 56 56 56 56 56 56 46 40 40 40 40 40 45 45 45 45 39 39 35 35 35 39 40 56 56 56 56 56 51 45 45 39 39 39 40 40 40 56 56 56 56 56
 56 51 51 51 51 60 60 60 60 70 78 74 73 74 74 80 83 86 75 77 79 79 74 80 90 90 82 80 72 72 72 78 75 86 83 85 85 90 85 85 85 88 83 76 71 66 60 60 71 71
 71 56 56 56 56 56 56 56 56 56 56 45 45 45 45 45 45 51 66 66 66 66 75 69 73 86 86 71 71 71 56 51 45 45 45 45 60 66 79 71 70 74 67 70 60 72 72 77 73 68
 74 74 74 76 83 83 83 80 80 77 76 76 72 90 80 85 85 80 66 66 66 66 51 51 45 45 45 60 58 59 70 70 74 77 85 85 85 81 80 79 90 90 90 90 90 90 85 85 66 58
 43 43 43 43 43 43 60 60 83 81 80 72 68 72 62 62 66 73 75 86 90 90 87 81 67 63 62 62 65 69 80 85 85 85 85 90 90 90 90 90 90 90 90 82 80 77 77 67 64 60
 60 62 68 68 76 69 71 80 87 87 86 85 87 80 73 73 78 89 90 90 90 88 90 90 84 78 78 68 68 66 78 78 75 69 69 69 69 72 74 80 86 86 90 90 87 80 80 80 80 80
 88 83 80 74 70 62 58 58 58 58 43 43 45 56 56 45 60 60 60 60 66 56 56 56 56 56 56 71 66 76 80 80 80 90 90 89 90 81 75 60 62 65 74 76 79 79 85 85 90 90
 90 78 78 80 77 78 74 86 60 60 45 45 45 45 56 45 43 43 43 43 43 51 51 51 66 66 66 80 67 58 58 58 58 59 58 69 83 75 66 66 66 67 75 70 70 70 69 69 72 81
 84 86 80 83 74 74 74 72 72 67 72 67 72 78 88 82 90 90 71 71 56 56 56 51 51 66 66 66 78 66 66 75 77 71 66 66 45 40 40 40 40 39 54 60 61 58 55 61 50 55
 55 58 54 58 68 68 68 68 57 57 52 62 59 63 65 69 75 73 70 70 70 67 55 55 55 55 67 59 66 50 50 50 35 35 40 40 40 46 40 40 40 40 40 45 51 40 39 39 39 35
 32 32 29 29 29 32 32 35 35 35 35 40 46 46 68 68 59 62 56 56 49 54 65 64 64 57 61 39 41 40 39 39 39 51 51 51 51 39 39 34 34 33 32 0 0

AF LL2305r C -196
AF LL2305f U 36
BS 1 262 LL2305r
BS 263 263 LL2305f
BS 264 516 LL2305r
BS 517 529 LL2305f
BS 530 530 LL2305r
BS 531 531 LL2305f
BS 532 539 LL2305r
BS 540 541 LL2305f
BS 542 545 LL2305r
BS 546 547 LL2305f

RD LL2305r 787 0 2
gtgcgggcctcttcgctattacgccagctggcgaaagggggatgtgctgc
aaggcgattaagttgggtaacgccagggttttxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxCTT
TTTTTTTTTTTTTTAAACGAAGAAGCAAAAACTCAAGTTAATCCAAAAAA
TATTCAGAATTATTACACGATAAAAGTTTTTTAGACAAAGATAGATTTTG
TTCTATATGAAGTACAATCGATGAAGAATTTACTTTTAAGTGATCACTGA
TCTAAGTACTTCACGGGAACAAGTAGAAGCTCACTTTTCTTGCTCACAGT
AAGCCCAGGAGCTTCCTCCATGTCGACATCTTCCACCACCATGCCTTCAG
GTAACTCCCAGTCAAAATGATACAATAGACTCGCCAGACCAAACTCCACC
GAAGTCGTCCCCATGTATATTCCAGGACAGATTCTCCTACCACTCCCAAA
CGACAACAGCTCAAAG**TTTTGTCCCTTTGCATCAATGTTATTATCCAT
AAACCTCTCGGGGAAAAACATCTCTGGATCCTTCCAGGTATCCGGATCAC
GCCCAATAGCCCAGACATTCACATGAAGACGTGTCTTGACGGGAATCGTG
TAGCCGTCGATCTCAAACTCCGAGGTTACTTCGGACGCGTGGxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxaatt

QA 13 742 198 742
DS CHROMAT_FILE: LL2305r PHD_FILE: LL2305r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:16 2000

RT{
LL2305r chimera phrap 1 82 000919:094547
}

RT{
LL2305r matchElsewhereHighQual phrap 1 82 000919:094547
}

RD LL2305f 768 0 2
tcatgttattccAAaAactaTTCAGAATTATTACACGATAAAAGTTTTTT
AGACAAAGATAGATTTtgctctAtctGAagcaCAATCGATGAAGAATtca
cTTTTAAGTGATCACTGATCTAAGTACTTCACGGGAACacgTAGAAGCTC
ACTTTTCTTGCTCACAgcaaGCCCAGGAGCTTCCTCCATGTCGACATCTT
CCACCACCATGCCTTCAGGTAACTCCCAGTCAAAATGATACAATAGACTC
GCCAGACCAAACTCCACCGAAGTCGtcctcaTGTATAtttcaGGACAGAT
TCTCCTACCACTCCCAAACGACAACagttcaaacatttttgTCCCTTTGC
ATCAATGTTATTATCCATAAACCTCTCGGGGAAAAACatatcTGGATCCT
TCCAggcATCCGGATCACGCCCAATAGCCCAGACATTCACATGAAGACGt
gcctTGAcggcaatcgtgcaccCgttcatCTCAAACTCCGAGGTTACTta
ggaCGCGtgGgaxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxtgcgaaatcgtcatcggctcacaatcgcacacaccatac
tcacccgcacgtccaatactgtacagtctggggcgcctaatgagcgagct
aactcacattaattcgcgctgcgtccactgcccgattttcacgccggaaa
cctgttttgccacttgcg

QA 20 449 1 512
DS CHROMAT_FILE: LL2305f PHD_FILE: LL2305f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:37 2000

RT{
LL2305f chimera phrap 678 762 000919:094547
}

RT{
LL2305f matchElsewhereLowQual phrap 685 714 000919:094547
}

CO Contig28 692 2 131 U
ctttttagcgacTATAATATGTTTCAAACGAAAGGAAGACCCACAGAGGC
AGAAACAAGCAGAAGAAACAAAGATTGGTGACTAGATTGGGTAACTTGCC
ATACAAGTCAAACATATACATAAACGAGAGAGATATAGTTTGAATGAATC
AGCCAAAGAAGCTTGGATCGTAGCCATTGCTAGAAGTGGCCAAAACATAG
TAAGCAACGATGTGACCAATAGAACCCCAAGCAAGAACATCCACGATGTT
GAATCCAACAGGGTCGTTCGATTTCAAGAGGCTTACGTACTCCTTGGCAC
GATCATCTCCCGCTTCGAAGTGGGTCTTCCCGTTCTGCTCCGGCACCTGT
TTAGCCACATTCTCTCTCTGGAAGTTGAAGAAGACGAACCGGCCTAGGAA
GAGGGAGAGACCTGTGCTGAGGCTAATAACGACGGATGGGCTGAGCTCGG
CTCTCACGACGGCGGAGGAGGAAGATCTTCTTCCGGAGGTGGTGGATAGC
TTGGGTAAGGCAGATGAGGAGCCACCGAGGCGGAGAGGACGGAGGCCGTG
GAATGAGATGGAGTTCGGGTGTTTCTGGGAGATTGTAGAGGAGAAAGTTG
TGGGTGTGAGCAAAGCAGATGCGCTTGTCGCCATGTTATCTTCTTCTTCT
GTGGAGAGTTTCAGTGCAACCCACGCGTCCGCGGACGCGTGG

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 27 27 54 55 55 52 55 55 55 55 53 53 53 55 52 56 59 61 54 55 51 49 49 48 53 54 77 52 52 58 59 54 57 52 54 48 48 58
 71 67 64 51 51 63 71 66 90 86 90 84 80 80 72 64 54 54 65 69 69 88 88 79 74 74 75 71 71 70 75 75 75 75 75 69 71 74 75 71 69 65 55 57 60 75 64 67 67 75
 75 68 80 74 80 80 80 80 75 86 85 90 79 88 90 88 88 88 74 77 76 74 72 72 77 81 81 86 90 90 90 90 90 79 75 75 75 78 75 75 75 75 75 75 80 88 90 85 75 88
 75 75 75 88 90 90 90 90 88 80 80 80 80 86 88 90 75 80 70 70 70 70 72 72 80 90 90 90 87 87 87 87 76 80 90 83 77 71 83 83 83 83 90 90 90 78 77 79 81 81
 78 82 78 78 86 78 80 89 89 89 85 90 90 90 90 90 90 83 81 86 90 82 82 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 89 90 89 89 89 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 86 86 83 83 81 81 88 90 90 90 90 90 90 90 90 90 90 89 89 83 81 79 79 79 79 79 81 90 90 90 90 90 86 86 88 83 86 86
 88 88 88 90 90 90 90 90 83 81 81 80 77 81 90 90 87 85 89 90 90 90 90 90 90 90 90 90 90 86 83 84 84 84 90 90 90 90 88 88 86 86 83 83 90 87 90 90 90 81
 85 85 84 84 84 84 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 81 79 79 79 81 87 83 88 88 83 83 83 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 83 86 83 85 83 86 84 81 81 86 88 88 86 86 85 88 88 88 88 90 84 84 88 90 90 88 88 87 88 90 90 86 86 86 88 88 83 83 83 88 86 80 80
 80 88 88 90 88 88 85 85 85 83 83 83 83 83 83 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 87 88 90 90 90 90 90 90 90 90 90 86 83 78 78 78
 80 90 89 90 90 90 88 88 88 88 88 83 86 90 90 90 87 85 85 85 85 85 80 80 80 80 82 76 76 83 88 88 88 88 90 87 89 80 83 80 80 83 80 83 83 83 88 88 85 85
 90 90 90 90 90 90 90 90 90 90 90 90 77 75 75 80 88 88 90 90 90 82 82 82 90 90 90 90 90 90 85 85 90 90 86 87 87 79 75 90 90 80 80 65 69 88 77 73 73 83
 80 80 88 88 88 80 80 75 90 75 72 75 75 75 73 77 79 79 65 70 68 72 72 72 75 75 74 63 63 63 63 64 68 90 65 62 73 78 78 78 86 86 86 86 86 86 86 90 77 74
 71 74 66 80 83 90 90 90 80 80 74 69 67 64 71 60 62 63 63 85 86 72 67 67 62 62 62 59 45 45 53 53 55 63 69 69 49 49 49 34 33 32

AF LL2308r C -58
AF LL2308f U 1
BS 1 12 LL2308f
BS 13 14 LL2308r
BS 15 38 LL2308f
BS 39 39 LL2308r
BS 40 44 LL2308f
BS 45 47 LL2308r
BS 48 61 LL2308f
BS 62 62 LL2308r
BS 63 71 LL2308f
BS 72 73 LL2308r
BS 74 80 LL2308f
BS 81 85 LL2308r
BS 86 95 LL2308f
BS 96 96 LL2308r
BS 97 99 LL2308f
BS 100 101 LL2308r
BS 102 109 LL2308f
BS 110 110 LL2308r
BS 111 111 LL2308f
BS 112 118 LL2308r
BS 119 119 LL2308f
BS 120 120 LL2308r
BS 121 122 LL2308f
BS 123 147 LL2308r
BS 148 148 LL2308f
BS 149 157 LL2308r
BS 158 158 LL2308f
BS 159 168 LL2308r
BS 169 175 LL2308f
BS 176 183 LL2308r
BS 184 186 LL2308f
BS 187 187 LL2308r
BS 188 192 LL2308f
BS 193 197 LL2308r
BS 198 207 LL2308f
BS 208 211 LL2308r
BS 212 212 LL2308f
BS 213 215 LL2308r
BS 216 216 LL2308f
BS 217 217 LL2308r
BS 218 223 LL2308f
BS 224 227 LL2308r
BS 228 237 LL2308f
BS 238 254 LL2308r
BS 255 260 LL2308f
BS 261 261 LL2308r
BS 262 264 LL2308f
BS 265 270 LL2308r
BS 271 271 LL2308f
BS 272 274 LL2308r
BS 275 275 LL2308f
BS 276 298 LL2308r
BS 299 300 LL2308f
BS 301 303 LL2308r
BS 304 304 LL2308f
BS 305 318 LL2308r
BS 319 323 LL2308f
BS 324 324 LL2308r
BS 325 325 LL2308f
BS 326 329 LL2308r
BS 330 330 LL2308f
BS 331 340 LL2308r
BS 341 342 LL2308f
BS 343 360 LL2308r
BS 361 366 LL2308f
BS 367 369 LL2308r
BS 370 381 LL2308f
BS 382 395 LL2308r
BS 396 407 LL2308f
BS 408 408 LL2308r
BS 409 409 LL2308f
BS 410 412 LL2308r
BS 413 413 LL2308f
BS 414 416 LL2308r
BS 417 417 LL2308f
BS 418 426 LL2308r
BS 427 427 LL2308f
BS 428 429 LL2308r
BS 430 432 LL2308f
BS 433 436 LL2308r
BS 437 438 LL2308f
BS 439 441 LL2308r
BS 442 443 LL2308f
BS 444 446 LL2308r
BS 447 448 LL2308f
BS 449 466 LL2308r
BS 467 467 LL2308f
BS 468 468 LL2308r
BS 469 474 LL2308f
BS 475 475 LL2308r
BS 476 476 LL2308f
BS 477 483 LL2308r
BS 484 484 LL2308f
BS 485 486 LL2308r
BS 487 496 LL2308f
BS 497 502 LL2308r
BS 503 511 LL2308f
BS 512 512 LL2308r
BS 513 516 LL2308f
BS 517 527 LL2308r
BS 528 529 LL2308f
BS 530 530 LL2308r
BS 531 536 LL2308f
BS 537 546 LL2308r
BS 547 548 LL2308f
BS 549 550 LL2308r
BS 551 574 LL2308f
BS 575 576 LL2308r
BS 577 580 LL2308f
BS 581 582 LL2308r
BS 583 588 LL2308f
BS 589 595 LL2308r
BS 596 596 LL2308f
BS 597 600 LL2308r
BS 601 618 LL2308f
BS 619 619 LL2308r
BS 620 620 LL2308f
BS 621 621 LL2308r
BS 622 624 LL2308f
BS 625 625 LL2308r
BS 626 627 LL2308f
BS 628 649 LL2308r
BS 650 650 LL2308f
BS 651 652 LL2308r
BS 653 658 LL2308f
BS 659 663 LL2308r
BS 664 665 LL2308f
BS 666 674 LL2308r
BS 675 677 LL2308f
BS 678 691 LL2308r
BS 692 692 LL2308f

RD LL2308r 795 0 0
tnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnntntnntnnaccacGAAATATAATATGTTTCAAACGAAAGGAAGACC
CACAGAGGCAGAAACAAGCAGAAGAAACAAAGATTGGTGACTAGATTGGG
TAACTTGCCATACAAGTCAAACATATACATAAACGAGAGAGATATAGTTT
GAATGAATCAGCCAAAGAAGCTTGGATCGTAGCCATTGCTAGAAGTGGCC
AAAACATAGTAAGCAACGATGTGACCAATAGAACCCCAAGCAAGAACATC
CACGATGTTGAATCCAACAGGGTCGTTCGATTTCAAGAGGCTTACGTACT
CCTTGGCACGATCATCTCCCGCTTCGAAGTGGGTCTTCCCGTTCTGCTCC
GGCACCTGTTTAGCCACATTCTCTCTCTGGAAGTTGAAGAAGACGAACCG
GCCTAGGAAGAGGGAGAGACCTGTGCTGAGGCTAATAACGACGGATGGGC
TGAGCTCGGCTCTCACGACGGCGGAGGAGGAAGATCTTCTTCCGGAGGTG
GTGGATAGCTTGGGTAAGGCAGATGAGGAGCCACCGAGGCGGAGAGGACG
GAGGCCGTGGAATGAGATGGAGTTCGGGTGTTTCTGGGAGATTGTAGAGG
AGAAAGTTGTGGGTGTGAGCAAAGCAGATGCGCTTGTCGCCATGTTATCT
TCTTCTTCTGTGGAGAGTTTCAGTGCAACCCACGCGTCCGCGGACGCGTG
Gxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxat

QA 68 751 72 751
DS CHROMAT_FILE: LL2308r PHD_FILE: LL2308r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:29 2000

RD LL2308f 791 0 0
ctttttagcgactATAATATGTTTCAAACGAAAGGAAGACCCACAGAGGC
AGAAACAAGCAGAAGAAACAAAGATTGGTGACTAGATTGGGTAACTTGCC
ATACAAGTCAAACATATACATAAACGAGAGAGATATAGTTTGAATGAATC
AGCCAAAGAAGCTTGGATCGTAGCCATTGCTAGAAGTGGCCAAAACATAG
TAAGCAACGATGTGACCAATAGAACCCCAAGCAAGAACATCCACGATGTT
GAATCCAACAGGGTCGTTCGATTTCAAGAGGCTTACGTACTCCTTGGCAC
GATCATCTCCCGCTTCGAAGTGGGTCTTCCCGTTCTGCTCCGGCACCTGT
TTAGCCACATTCTCTCTCTGGAAGTTGAAGAAGACGAACCGGCCTAGGAA
GAGGGAGAGACCTGTGCTGAGGCTAATAACGACGGATGGGCTGAGCTCGG
CTCTCACGACGGCGGAGGAGGAAGATCTTCTTCCGGAGGTGGTGGATAGC
TTGGGTAAGGCAGATGAGGAGCCACCGAGGCGGAGAGGACGGAGGCCGTG
GAATGAGATGGAGTTCGGGTGTTTCTGGGAGATTGTAGAGGAGAAAGTTG
TGGGTGTGAGCAAAGCAGATGCGCTTGTCGCCATGTTATCTTCTTCTTCT
GTGGAGAGTTTCAGTGCAACCCACGCGTCCGCGGACGCGTGGxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

QA 13 692 1 692
DS CHROMAT_FILE: LL2308f PHD_FILE: LL2308f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:52 2000

CO Contig29 904 2 54 U
ctggaaatttagaaaatatgaccttaaatcataatcattcgttcgggaaa
aaagaaatacattttactcaacaaaataaaTATAAATACATTTTACCCGA
GCATAGTAAACATTTCAAAGATTGAGAAATCTTTGAAGACTCATCACTCA
TATGATTCTACACCGTCAAGTACTTTAGAACTGAAGCACGCACCTTCTCC
ATGTAATCTCCTGCTTCTTTCTGGTTTCCTCTGTATGCATTTGCTATGTT
TTCATCAAGAAGTGTCAACAAAGACCTGTTGATCTCGTTTTTCTCCACCA
TATCCAACAATGTTGCTTTTATGTCGGTTGAGGTTAATATCTTGGTTAAG
CTATTTGTAGCGGTCATAAGCTCCTTTTGCATTTTGTCATAAGCCTCTAT
TCCTTCTTCTAAGGCTTTTTGAAGTGATTCAAGCTCAATCAATCTGTCTT
CATCTTCCGCGGTTTTTGTAACCGCAAACCGGATTTGCCCGATTTCAAGT
CGAATTTGCGCAAAAAACTCGTCATTTAACCTTCCACGAAGCCTAGCGAT
TTCAAACTCAATCTCCTGAGCTTCCGTATCAAGAAAGAACTCAATGAGCT
CAGCGGAAGTGTCTGGTACAACTCTAGACTCTCTAAGAGCTTGACGACGC
TCTCTCTCTTCACGGAGTTGTTTCTGAAAAGCCTCTTTAGCCTCGGAGTC
TCTCTCTAGCCTGCGTTTGAACTCAAGGCGAGCGATATGACCAGTTTGAG
CAGGACCTAAGATACCTTTCGGATCCCATTCGCAGGAGATTTTGCCCCTT
CTTGTATTAAATCTCGGGATTGTACGGACGGTGTTAGCAAAGGCGATTCC
TATTGAGAGCGAAGCCATtgttatttttatttttttgtgggcgcggacgc
gtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 37 32 32 29 29 29 35 35 35 35 26 26 26 35 35 35 32 32 32
 32 35 35 35 35 29 23 23 25 25 42 35 39 35 35 35 35 35 35 37 37 29 29 29 29 32 32 36 36 37 37 37 37 35 35 35 35 32 35 35 35 39 35 35 32 32 35 32 35 35
 37 37 40 40 40 35 35 35 35 35 37 35 29 30 29 29 23 31 29 35 47 47 56 49 39 41 35 40 33 45 48 60 60 54 57 54 53 53 49 59 55 55 50 59 59 67 66 65 58 58
 64 77 77 79 79 71 61 68 57 59 58 50 55 51 54 47 35 35 37 35 37 48 51 52 59 52 58 67 75 75 73 90 73 75 75 82 82 86 82 71 64 64 66 72 72 61 67 74 90 90
 76 81 85 89 85 81 83 90 84 58 61 54 65 65 73 71 70 66 79 82 81 79 79 79 80 75 75 79 81 81 90 88 87 78 78 78 78 83 86 90 90 90 86 86 89 90 89 79 80 83
 90 90 90 90 90 90 82 77 86 84 87 87 90 83 79 79 83 80 83 90 86 90 80 86 73 73 67 67 67 72 73 77 66 62 68 73 79 82 90 90 86 75 73 73 67 67 73 73 70 70
 75 80 86 89 86 90 77 75 72 72 73 75 80 86 86 88 90 90 86 86 90 90 90 90 90 90 88 85 90 90 90 90 90 90 90 90 90 75 77 80 75 82 82 81 81 90 90 90 90 90
 89 90 90 90 90 90 90 86 86 86 88 86 87 90 90 90 90 90 90 90 90 87 80 78 80 85 90 90 90 89 89 86 84 86 86 90 90 90 90 90 90 88 88 80 85 85 85 87 90 90
 90 90 90 90 90 88 80 78 78 79 79 79 90 85 88 89 79 72 69 69 76 76 83 78 78 78 78 86 90 90 88 90 88 90 90 90 90 86 86 88 90 90 90 90 90 89 89 90 82 75
 75 86 84 87 89 86 72 72 72 74 75 80 89 90 90 90 85 83 83 78 78 76 78 86 86 83 83 83 86 86 90 90 88 90 90 80 83 79 76 76 72 73 72 76 65 69 69 74 74 80
 90 90 90 90 86 88 90 89 90 89 90 90 90 88 88 88 87 87 80 80 66 70 62 67 70 76 85 89 90 90 90 90 90 88 90 84 85 80 81 85 85 85 90 78 71 73 71 73 80 80
 78 75 72 72 72 78 78 85 70 70 65 65 65 76 68 61 61 70 75 85 90 90 80 80 80 79 74 69 69 63 65 65 69 70 74 65 68 68 69 69 76 88 78 85 84 82 72 68 66 68
 58 60 66 66 66 69 69 84 84 81 80 81 83 77 77 84 89 80 80 81 70 64 60 66 66 76 74 68 72 83 83 70 74 60 60 58 69 69 68 72 72 85 81 75 77 89 76 76 65 65
 61 74 68 73 65 70 73 76 73 73 72 72 72 72 65 62 66 72 72 69 70 76 83 83 76 68 61 62 64 66 66 71 71 77 72 74 88 88 85 85 72 65 63 59 58 58 58 64 71 74
 74 68 58 60 60 66 66 60 58 58 58 58 58 66 66 51 46 43 43 43 43 43 43 51 51 56 56 51 43 35 35 35 35 35 38 45 45 45 45 45 51 40 40 40 40 40 40 56 45 45
 45 45 35 35 35 35 35 35 35 39 39 40 39 39 39 39 39 40 45 40 40 40 40 40 40 45 45 45 45 45 45 45 39 35 35 35 35 35 35 35 34 31 31 31 31 31 40 51 40 40
 40 40 40 46 46 39 34 34 34 33 32 33 40 40 40 45 46 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0

AF LL2309f U 1
AF LL2309r C 168
BS 1 176 LL2309f
BS 177 179 LL2309r
BS 180 180 LL2309f
BS 181 181 LL2309r
BS 182 186 LL2309f
BS 187 189 LL2309r
BS 190 196 LL2309f
BS 197 200 LL2309r
BS 201 210 LL2309f
BS 211 211 LL2309r
BS 212 212 LL2309f
BS 213 213 LL2309r
BS 214 224 LL2309f
BS 225 225 LL2309r
BS 226 227 LL2309f
BS 228 231 LL2309r
BS 232 232 LL2309f
BS 233 235 LL2309r
BS 236 240 LL2309f
BS 241 246 LL2309r
BS 247 248 LL2309f
BS 249 250 LL2309r
BS 251 254 LL2309f
BS 255 255 LL2309r
BS 256 261 LL2309f
BS 262 262 LL2309r
BS 263 271 LL2309f
BS 272 280 LL2309r
BS 281 281 LL2309f
BS 282 300 LL2309r
BS 301 301 LL2309f
BS 302 303 LL2309r
BS 304 304 LL2309f
BS 305 337 LL2309r
BS 338 338 LL2309f
BS 339 366 LL2309r
BS 367 368 LL2309f
BS 369 391 LL2309r
BS 392 393 LL2309f
BS 394 401 LL2309r
BS 402 405 LL2309f
BS 406 420 LL2309r
BS 421 421 LL2309f
BS 422 447 LL2309r
BS 448 449 LL2309f
BS 450 462 LL2309r
BS 463 463 LL2309f
BS 464 497 LL2309r
BS 498 498 LL2309f
BS 499 512 LL2309r
BS 513 513 LL2309f
BS 514 695 LL2309r
BS 696 696 LL2309f
BS 697 904 LL2309r

RD LL2309f 768 0 0
ctggaaatttagaaaatatgaccttaaatcataatcattcgttcgggaaa
aaagaaatacattttactcaacaaaataaaTATAAATACATTTTACCCGA
GCATAGTAAACATTTCAAAGATTGAGAAATCTTTGAAGACTCATCACTCA
TATGATTCTACACCGTCAAGTACTTTAGAACTGAAGCACGCACCTTCTCC
ATGTAATCTCCTGCTTCTTTCTGGTTTCCTCTGTATGCATTTGCTATGTT
TTCATCAAGAAGTGTCAACAAAGACCTGTTGATCTCGTTTTTCTCCACCA
TATCCAACAATGTTGCTTTTATGTCGGTTGAGGTTAATATCTTGGTTAAG
CTATTTGTAGCGGTCATAAGCTCCTTTTGCATTTTGTCATAAGCCTCTAT
TCCTTCTTCTAAGGCTTTTTGAAGTGATTCAAGCTCAATCAATCTGTCTT
CATCTTCCGCGGTTTTTGTAACCGCAAACCGGATTTGCCCGATTTCAAGT
CGAATTTGCGCAAAAAACTCGTCATTTAACCTTCCACGAAGCCTAGCGAT
TTCAAACTCAATCTCCTGAGCTTCCGTATCAAGAAAGAACTCAATGAGCT
CAGCGGAAGTGTCTGGTACAACTCTAGACTCTCTAAGAGCTTGACGACGC
TCTCTCTCTTCACGGAGTTGTTTCTGAAAAGCCTCTTTAGCCTCGGAGTC
TCTCTCTAGCCTGCGTTTGAACTCAAGGCGAGCGATATGACCAGTTTGAG
CAGGACCTAAGATACcTt

QA 81 768 1 768
DS CHROMAT_FILE: LL2309f PHD_FILE: LL2309f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:57 2000

RD LL2309r 781 0 0
nagTACTTTAGAACTGAAGCACGCACCTTCTCCATGTAATCTCCTGCTTC
tntcTGGTTTCCTCTGTATGCATTTGCTATGTTTTCATCAAGAAGTGTCA
ACAAAGACCTGTTGATCTCGTTTTTCTCCACCATATCCAACAATGTTGCT
TTTATGTCGGTTGAGGTTAATATCTTGGTTAAGCTATTTGTAGCGGTCAT
AAGCTCCTTTTGCATTTTGTCATAAGCCTCTATTCCTTCTTCTAAGGCTT
TTTGAAGTGATTCAAGCTCAATCAATCTGTCTTCATCTTCCGCGGTTTTT
GTAACCGCAAACCGGATTTGCCCGATTTCAAGTCGAATTTGCGCAAAAAA
CTCGTCATTTAACCTTCCACGAAGCCTAGCGATTTCAAACTCAATCTCCT
GAGCTTCCGTATCAAGAAAGAACTCAATGAGCTCAGCGGAAGTGTCTGGT
ACAACTCTAGACTCTCTAAGAGCTTGACGACGCTCTCTCTCTTCACGGAG
TTGTTTCTGAAAAGCCTCTTTAGCCTCGGAGTCTCTCTCTAGCCTGCGTT
TGAACTCAAGGCGAGCGATATGACCAGTTTGAGCAGGACCTAAGATACCT
TTCGGATCCCATTCGCAGGAGATTTTGCCCCTTCTTGTATTAAATCTCGG
GATTGTACGGACGGTGTTAGCAAAGGCGATTCCTATTGAGAGCGAAGCCA
Ttgttatttttatttttttgtgggcgcggacgcgtggxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxat

QA 3 701 2 737
DS CHROMAT_FILE: LL2309r PHD_FILE: LL2309r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:34 2000

CO Contig30 1421 2 24 U
ttcatatattaaaggctTATTAAAAAGGAGTAGCTAATGCAAATTTAGTA
GAGAAAGTAAATGATTTGACATGATAATAACAACCAAACTCAAACAAATG
CAACCAAGACACTTGCTTCGTCTCCTTTCACAGCATCATGATCGCTTCTT
CAACATTGTTGTCTTTAATAGGTGTAGCCTTTGACGAACATACCCTCCTT
AGCCTCTTCAGACTCGCCTTCTCCGCTGTATTTTCCAAGCTGAGCCAACG
AGTTGGCCTTGGCACGAGCCAAGAGAGTGGTCTGAGCAGCGTTCACGTTC
TCAGCTCTGCCTCCCCATGTTTTCAGACAAGTGTTCTGGAGAGCACGTGC
GTAGGAGAAGGACACGTGCCATGGGTTTGGTGCCTGGTTCATCGCGTTGA
GGTTCAACGTTGCCTCCAACTCAGACTGTCCTCCAGACAAGAACATGATT
CCGGGGACGGCAGGAGGGATTCTGTTGCGGAGGAGCTTAAGGGTGTAGGC
GGCAACTTGTTCAGGAGTAGCTCTGTCTTTAGACTCGGCTCCAGGAGTCA
CCATGCTCGGCTTCAGGAGGATACCTTCAAACATGACATTGTTCTGAGCA
AGGTAAAAGAAAACCTCAGCCCAAACCTTCTCAGCTACTTCGTAAGTCCT
GTCAATGTCGTGTTCTccGTCCAACAAGATCTCTGGCTCCACAATTGGGA
CCAATCCACTGTCCTGTGAAATGGCAGCGTAGCGAGCAAGGCCCCAAGCA
GCTTCTTTCACAGCGAGCGCAGACGGGCCGTTGGGAATGCTCACGACAGT
ACGCCATttaGCGAAACGAGCACCCTGTTGGTAGTAAGCAGCAGTGCGAG
AGGATAGACCATCGAGTCCTTGACACCATGACTCATTGTTAGAGCCAACA
AGTGGCACCAAACCCTTGTCAACTTTGATACCGGGGACGATGTTCTGCTC
GACGAGGACGTCGACCATTTTCTTTCCTTCGGTGGTAGACTGATAGAGAG
TCTCCTCGAACAAGATTGCCCCGGATATGTACTGTCCGAGACCTGGTGCA
GAGACAAGCAATGTCCTGTACGCTTGACGGTTTGCCTCAGTGTTCTCTAG
CCCTATCGAGTCCAAACGCTTCCCGCAAGTCGCGTTCGACTCGTCCATCG
CCAAGATTCCACGTCCCGGAGATGCAATTGTTTTCGCTGTCTTGACAAGC
TCATCGGCGTAGGAAGAAGCGGCACGGACGGCGAGGGAGGTGGCGCGGTT
GGGGAGGACGACGGATGCGGAAGAAGGCTGACGGAAGAGAACGCTTTGGC
CCTTGACCCACTCAGATTTGTCCAACACTGGAGATGCCTTGAGGAGTGAG
GTAGATGCCATTTTTTTTTGTTAATGTTATCTcTTtctcttctctctgcc
tttggtttgtcggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 25 25 29 29 27 27 31 46 40 40 40 40 37 37 34 29 29 29 29 29 35 46 40 40 40 40 40 40 40 38 38 40 40
 40 40 46 40 40 37 37 37 37 37 37 46 40 46 40 40 40 35 35 35 37 40 46 46 40 35 35 35 35 35 40 51 35 35 35 35 35 35 37 40 37 37 40 40 40 40 40 40 40 40
 40 37 37 37 37 37 37 40 46 35 35 35 39 35 35 40 40 37 40 37 37 40 40 37 37 46 46 46 46 40 40 40 40 40 40 40 40 40 40 40 38 34 34 34 34 34 35 35 37 40
 40 51 40 43 51 46 46 44 43 40 38 35 35 35 35 35 43 43 43 43 43 43 43 43 43 43 43 43 43 43 51 43 35 35 35 35 35 36 38 43 43 43 43 43 43 43 41 41 43 45
 41 41 41 45 41 45 45 45 45 40 36 36 43 43 43 43 43 40 43 42 56 56 43 43 43 36 36 36 43 46 51 51 51 51 51 51 51 43 43 45 45 45 45 56 56 51 43 43 43 43
 43 45 56 51 45 45 45 45 45 45 41 43 38 43 38 38 38 40 43 44 42 41 41 41 41 41 41 42 56 41 41 41 43 45 45 56 51 43 43 43 43 43 43 36 36 36 36 36 43 45
 45 45 43 43 43 43 43 43 43 43 43 43 43 43 43 56 56 56 56 56 51 51 51 51 43 43 43 43 43 43 51 51 45 45 45 45 45 45 46 46 41 41 43 36 36 36 36 36 43 43
 43 38 38 56 56 56 56 56 56 51 51 51 43 43 43 43 43 43 45 45 45 51 56 56 56 56 56 56 56 51 51 41 45 45 45 51 51 45 45 45 43 43 43 43 43 43 43 45 56 56
 56 56 51 51 51 43 43 43 45 43 43 45 45 41 41 43 51 45 45 45 45 45 41 41 41 45 45 43 56 56 56 56 56 51 43 43 43 43 43 43 43 43 43 43 43 43 56 56 56 51
 51 51 51 51 45 45 45 45 45 45 51 56 56 56 56 56 56 56 56 56 56 56 56 50 40 38 39 35 35 35 40 51 51 40 45 40 40 40 40 51 51 56 56 51 51 51 51 40 40 40
 40 40 40 37 39 37 37 37 40 43 51 45 40 40 40 45 45 51 40 40 40 45 45 45 56 56 56 56 56 56 42 40 40 45 45 45 51 40 40 40 40 40 51 56 56 56 51 51 45 45
 45 45 45 45 45 51 51 46 46 42 40 38 38 38 46 46 56 56 56 51 51 40 40 45 40 40 40 43 46 51 51 56 56 56 56 56 56 56 42 40 35 30 30 35 40 43 40 40 40 47
 37 46 28 28 28 32 32 48 48 34 32 34 40 40 40 40 40 40 40 40 40 40 36 40 37 37 36 39 35 42 42 46 37 35 35 33 35 35 29 39 40 44 44 48 40 40 34 29 29 29
 29 40 40 40 40 46 34 33 33 33 31 40 31 23 27 21 17 18 21 25 24 25 25 25 29 25 24 29 40 40 40 40 40 29 47 34 45 42 34 30 45 49 45 45 61 61 57 51 49 50
 49 51 50 52 62 71 53 56 55 53 54 50 42 40 48 48 48 48 39 46 53 53 39 37 48 54 51 58 50 57 52 58 57 58 54 50 50 42 41 41 37 40 42 39 37 37 35 52 63 71
 67 58 50 50 58 49 54 54 58 60 56 58 44 43 43 28 29 29 29 32 32 28 40 29 26 24 22 20 20 25 25 25 25 25 25 29 32 32 40 48 44 33 33 33 28 28 34 39 39 33
 33 32 32 32 32 32 27 15 15 17 22 22 29 39 32 33 29 33 29 35 29 35 42 56 56 56 40 37 37 37 37 37 37 37 35 36 35 29 35 28 28 26 32 32 37 37 37 40 40 51
 51 46 40 37 40 37 37 37 51 56 51 51 51 45 45 45 40 40 51 51 51 42 40 40 40 47 46 46 46 44 44 40 48 48 48 32 32 34 40 40 36 39 32 34 34 39 37 56 40 40
 40 40 39 35 36 33 36 37 56 56 56 56 56 56 56 45 51 51 45 45 45 51 56 45 51 51 51 51 51 51 51 51 51 45 45 45 45 45 45 45 45 51 51 51 51 56 56 56 56 56
 56 56 56 51 51 51 51 45 45 40 40 40 37 40 51 56 56 56 56 56 56 56 56 56 56 56 56 51 51 51 51 51 51 45 51 51 51 51 51 56 56 51 45 45 45 45 40 40 40 40
 40 40 51 51 45 45 45 45 40 51 56 56 56 56 56 56 56 56 56 51 51 51 51 51 51 51 51 51 45 45 45 43 43 43 43 43 43 51 51 51 51 56 56 51 51 51 51 45 45 45
 45 51 51 56 51 45 45 45 45 45 45 45 45 45 45 45 45 45 43 43 43 45 45 45 56 45 45 43 43 43 43 45 45 51 51 51 45 45 45 43 43 43 51 45 45 45 43 43 43 43
 43 45 56 56 51 51 43 43 43 43 43 43 43 56 43 43 43 43 43 43 51 46 43 43 43 43 36 36 36 36 36 36 43 43 43 43 43 45 45 43 36 36 36 36 36 43 43 43 43 43
 43 43 43 43 43 43 43 45 51 43 43 43 43 43 43 43 45 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 51 56 56 45 45 45 45 45
 45 56 45 45 43 43 43 43 43 43 43 51 45 45 45 43 36 36 36 36 36 36 36 40 40 51 51 51 43 43 43 43 43 43 51 51 51 43 43 43 43 43 43 43 43 43 43 43 43 51
 51 43 43 43 43 43 43 43 43 43 43 43 43 43 34 35 35 35 35 35 43 51 45 45 43 43 43 43 43 43 45 43 43 43 43 43 43 43 43 43 43 43 43 43 43 45 43 43 40 40
 40 40 51 51 51 51 51 51 56 40 40 40 40 40 40 45 45 45 45 51 51 51 51 51 56 56 51 51 40 40 40 40 40 40 45 51 51 51 51 51 51 51 45 40 40 40 40 40 40 40
 40 40 40 40 40 40 46 46 46 46 51 51 51 56 51 51 51 51 51 40 39 39 39 39 39 39 40 37 29 30 24 30 19 30 30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2311f U 1
AF LL2311r C 683
BS 1 685 LL2311f
BS 686 690 LL2311r
BS 691 696 LL2311f
BS 697 697 LL2311r
BS 698 699 LL2311f
BS 700 700 LL2311r
BS 701 710 LL2311f
BS 711 718 LL2311r
BS 719 719 LL2311f
BS 720 720 LL2311r
BS 721 725 LL2311f
BS 726 726 LL2311r
BS 727 727 LL2311f
BS 728 728 LL2311r
BS 729 731 LL2311f
BS 732 732 LL2311r
BS 733 733 LL2311f
BS 734 747 LL2311r
BS 748 751 LL2311f
BS 752 760 LL2311r
BS 761 761 LL2311f
BS 762 763 LL2311r
BS 764 764 LL2311f
BS 765 1421 LL2311r

RD LL2311f 767 0 0
ttcatatattaaaggctTATTAAAAAGGAGTAGCTAATGCAAATTTAGTA
GAGAAAGTAAATGATTTGACATGATAATAACAACCAAACTCAAACAAATG
CAACCAAGACACTTGCTTCGTCTCCTTTCACAGCATCATGATCGCTTCTT
CAACATTGTTGTCTTTAATAGGTGTAGCCTTTGACGAACATACCCTCCTT
AGCCTCTTCAGACTCGCCTTCTCCGCTGTATTTTCCAAGCTGAGCCAACG
AGTTGGCCTTGGCACGAGCCAAGAGAGTGGTCTGAGCAGCGTTCACGTTC
TCAGCTCTGCCTCCCCATGTTTTCAGACAAGTGTTCTGGAGAGCACGTGC
GTAGGAGAAGGACACGTGCCATGGGTTTGGTGCCTGGTTCATCGCGTTGA
GGTTCAACGTTGCCTCCAACTCAGACTGTCCTCCAGACAAGAACATGATT
CCGGGGACGGCAGGAGGGATTCTGTTGCGGAGGAGCTTAAGGGTGTAGGC
GGCAACTTGTTCAGGAGTAGCTCTGTCTTTAGACTCGGCTCCAGGAGTCA
CCATGCTCGGCTTCAGGAGGATACCTTCAAACATGACATTGTTCTGAGCA
AGGTAAAAGAAAACCTCAGCCCAAACCTTCTCAGCTACTTCGTAAGTCCT
GTCAATGTCGTGTTCTccGTCCAACAAGATCTCTGGCTCCACAATTGGGA
CCAATCCACTGTCCTGTGAAATGGCAGCGTAGCGAGCAAGGCCCCAAGCA
GCTTCTTTCACAGCGAG

QA 17 767 1 767
DS CHROMAT_FILE: LL2311f PHD_FILE: LL2311f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:07 2000

RD LL2311r 783 0 0
cTGGCTCCACAATTGGGACCAATCCACTGTCCTGTGAAATGGCAGCGTAG
CGAGCAAGGCCCCAAGCAGCTTCTTTCACAGCGAGCGCAGACGGGCCGTT
GGGAATGCTCACGACAGTACGCCATttaGCGAAACGAGCACCCTGTTGGT
AGTAAGCAGCAGTGCGAGAGGATAGACCATCGAGTCCTTGACACCATGAC
TCATTGTTAGAGCCAACAAGTGGCACCAAACCCTTGTCAACTTTGATACC
GGGGACGATGTTCTGCTCGACGAGGACGTCGACCATTTTCTTTCCTTCGG
TGGTAGACTGATAGAGAGTCTCCTCGAACAAGATTGCCCCGGATATGTAC
TGTCCGAGACCTGGTGCAGAGACAAGCAATGTCCTGTACGCTTGACGGTT
TGCCTCAGTGTTCTCTAGCCCTATCGAGTCCAAACGCTTCCCGCAAGTCG
CGTTCGACTCGTCCATCGCCAAGATTCCACGTCCCGGAGATGCAATTGTT
TTCGCTGTCTTGACAAGCTCATCGGCGTAGGAAGAAGCGGCACGGACGGC
GAGGGAGGTGGCGCGGTTGGGGAGGACGACGGATGCGGAAGAAGGCTGAC
GGAAGAGAACGCTTTGGCCCTTGACCCACTCAGATTTGTCCAACACTGGA
GATGCCTTGAGGAGTGAGGTAGATGCCATTTTTTTTTGTTAATGTTATCT
cTTtctcttctctctgcctttggtttgtcggacgcgtggxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxat

QA 1 703 1 739
DS CHROMAT_FILE: LL2311r PHD_FILE: LL2311r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:44 2000

CO Contig31 788 2 46 U
ccattctttctacttttacacattgaaaatacaacaatttcaataccata
tacaatacacaaaaatataaaaatttcgttTGTATAAGTTCTACAGGGAC
GAGCCCTAAATAAAAATCATACACTTATTGTACGTAAACACTTCTCGAAT
GAAGCAATGTGACTTGAGAACAAAGGCAAATACGGAGAGAGACTTACGAA
GGGGAAGTAGAAGGTGCAGTTGCAGGGTTAAATGCCTTCTGCTCAGCGCA
GCTGAGCTCCTCGTTTGGCCCCGCGTCTTCCCTTCCAATACCCAAGAGGT
*CGAGGAAGTACAAGTAGTGCGAGACTATGTTGCTCATTGGCTCAATGTC
ACCTTGACCACATGTGTACTCACCGTACAAGACGTTCATCGTGGTACCAA
AAGTCGGGCCACGTTTGGACAAAGTATCATTCTTTGTCGGCTTCCAGTTC
CCAACAAAGATGTCGTGAGCTGACGGCTGAGCTTTCTTGATCGGTGTCAT
CCATCTCCAGATTGCAGCTTGGAAGGCAAGCGTCGCGTTCTGCTCGATGT
ACTCGGGGTGGTTCAAGAGATCGGCTTTTAGAGCATCCCCAGCTGCACCG
TAGTTGAAGTTCCAGTAGATGGGTAAAGCACCACGTCCGTAGTACTCAGC
TCCAGGGCTGCAAGGGTACTTGTATTTCCATGTCTCGTCACAGTAAGATT
GCATTGGACTCATCTCCCTGTTATAGCACAGACCCCAAGCTAAAGGCCCT
CCTGTCGCAACTCCGTATCCACaggagcggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 37 37 35 35 35 35 35 35 45 35 37 37 35 35 35 51 40 35 35 35
 35 35 35 35 40 42 42 44 35 37 37 40 40 40 56 37 35 35 35 35 35 35 35 35 35 35 35 37 37 35 35 35 35 35 35 35 40 40 43 37 37 37 40 40 40 43 40 40 37 37
 40 40 40 40 40 40 37 44 42 42 37 40 40 37 40 37 42 42 42 42 42 46 43 43 43 43 43 43 40 40 36 36 36 36 36 40 42 42 44 36 34 32 32 32 28 36 36 36 36 43
 46 56 56 56 56 43 42 42 42 42 42 50 50 38 38 38 40 43 43 40 40 43 43 43 43 56 43 43 43 43 43 38 38 38 38 46 47 49 45 43 46 44 44 36 41 36 36 35 36 35
 35 38 35 47 38 38 38 38 38 38 41 41 41 45 50 38 38 43 40 43 43 43 43 38 38 36 38 41 45 45 35 41 41 45 41 42 43 43 41 45 45 45 45 46 42 42 42 46 40 43
 43 43 43 43 56 56 56 43 38 38 46 56 52 63 71 72 56 48 49 47 48 49 47 45 44 45 60 58 58 53 54 51 54 53 54 53 57 60 53 57 56 56 58 56 68 74 63 60 56 55
 58 58 55 61 50 58 58 58 58 58 69 79 76 72 71 61 66 57 57 55 55 58 58 59 58 55 58 59 59 52 55 61 59 59 65 69 66 63 66 61 61 53 69 71 81 78 71 71 71 71
 71 71 71 75 74 71 55 55 55 60 62 64 70 64 70 62 64 67 71 72 74 74 69 80 76 80 67 69 65 60 77 77 71 71 65 83 69 69 69 69 62 66 66 71 76 90 85 85 90 73
 68 61 61 65 72 77 90 90 86 86 78 76 78 73 68 68 69 76 83 69 77 66 72 57 57 55 58 61 63 70 70 72 78 74 81 82 90 90 78 76 76 82 68 68 69 79 82 82 90 88
 86 82 82 82 76 74 72 68 66 66 75 75 69 73 71 71 72 72 75 64 74 58 60 50 54 56 72 66 74 69 69 64 71 67 67 67 72 70 73 84 86 75 75 73 75 81 83 90 87 87
 85 85 85 90 87 83 69 63 63 67 67 64 60 75 73 80 79 79 78 85 77 90 81 81 84 80 63 60 54 54 54 66 66 68 76 78 78 65 68 67 75 64 64 73 68 69 69 68 64 67
 63 83 55 59 65 65 69 69 69 69 69 69 69 72 72 66 71 77 90 88 72 69 69 64 64 69 69 70 72 83 78 64 62 62 60 55 60 64 78 74 79 71 69 73 73 72 69 69 67 64
 64 67 85 72 67 67 67 67 58 58 59 61 63 68 64 69 72 69 65 63 68 76 76 76 73 74 72 72 63 66 66 67 68 67 75 56 54 54 55 61 60 63 62 56 55 58 80 58 59 58
 58 58 59 62 65 65 65 69 66 63 62 55 71 71 71 71 71 68 61 56 55 53 53 52 53 57 59 61 66 66 71 75 71 78 75 73 73 68 68 63 63 61 60 59 56 47 60 35 37 30
 45 44 50 50 50 50 50 50 55 58 63 59 55 50 50 35 35 35 35 40 45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2314f U 1
AF LL2314r C 62
BS 1 235 LL2314f
BS 236 243 LL2314r
BS 244 253 LL2314f
BS 254 254 LL2314r
BS 255 311 LL2314f
BS 312 327 LL2314r
BS 328 424 LL2314f
BS 425 425 LL2314r
BS 426 426 LL2314f
BS 427 427 LL2314r
BS 428 457 LL2314f
BS 458 460 LL2314r
BS 461 471 LL2314f
BS 472 472 LL2314r
BS 473 476 LL2314f
BS 477 480 LL2314r
BS 481 493 LL2314f
BS 494 496 LL2314r
BS 497 499 LL2314f
BS 500 502 LL2314r
BS 503 508 LL2314f
BS 509 509 LL2314r
BS 510 515 LL2314f
BS 516 523 LL2314r
BS 524 534 LL2314f
BS 535 537 LL2314r
BS 538 538 LL2314f
BS 539 546 LL2314r
BS 547 549 LL2314f
BS 550 554 LL2314r
BS 555 557 LL2314f
BS 558 572 LL2314r
BS 573 573 LL2314f
BS 574 591 LL2314r
BS 592 592 LL2314f
BS 593 602 LL2314r
BS 603 603 LL2314f
BS 604 620 LL2314r
BS 621 621 LL2314f
BS 622 639 LL2314r
BS 640 640 LL2314f
BS 641 641 LL2314r
BS 642 642 LL2314f
BS 643 748 LL2314r
BS 749 751 LL2314f
BS 752 788 LL2314r

RD LL2314f 773 0 0
ccattctttctacttttacacattgaaaatacaacaatttcaataccata
tacaatacacaaaaatataaaaatttcgttTGTATAAGTTCTACAGGGAC
GAGCCCTAAATAAAAATCATACACTTATTGTACGTAAACACTTCTCGAAT
GAAGCAATGTGACTTGAGAACAAAGGCAAATACGGAGAGAGACTTACGAA
GGGGAAGTAGAAGGTGCAGTTGCAGGGTTAAATGCCTTCTGCTCAGCGCA
GCTGAGCTCCTCGTTTGGCCCCGCGTCTTCCCTTCCAATACCCAAGAGGT
*CGAGGAAGTACAAGTAGTGCGAGACTATGTTGCTCATTGGCTCAATGTC
ACCTTGACCACATGTGTACTCACCGTACAAGACGTTCATCGTGGTACCAA
AAGTCGGGCCACGTTTGGACAAAGTATCATTCTTTGTCGGCTTCCAGTTC
CCAACAAAGATGTCGTGAGCTGACGGCTGAGCTTTCTTGATCGGTGTCAT
CCATCTCCAGATTGCAGCTTGGAAGGCAAGCGTCGCGTTCTGCTCGATGT
ACTCGGGGTGGTTCAAGAGATCGGCTTTTAGAGCATCCCCAGCTGCACCG
TAGTTGAAGTTCCAGTAGATGGGTAAAGCACCACGTCCGTAGTACTCAGC
TCCAGGGCTGCAAGGGTACTTGTATTTCCATGTCTCGTCACAGTAAGATT
GCATTGGACTCATCTCCCTGTTATAGCACAGACCCCAAGCTAAAGGCCCT
CCTGTCGCAACTCCGTattcacn

QA 81 766 1 772
DS CHROMAT_FILE: LL2314f PHD_FILE: LL2314f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:43 2000

RD LL2314r 772 0 2
aaaat*taaaaatt*cgtttgt*taagtt*tccaggc*cgagcc*taa*t
aaaa*tcat*cact*attg*acgtaacc*ct*ctcgaatg*agcaatgt*
acttaa*aacaaa*gcaaatccg*agaaagncttcng*a*gggaAGTaga
agtt*cagt*gcagggt*aAATGCCTTCTGCTCAGcg*agCTGAGctc*t
cgtttg*cCCCGCGTCTtcctttcca*tacc**agaggtncgagnaagTA
CAAGTAGTGCGAGACTATGTTGCTCATTGGCTCAATGTCACCTTGACCAC
ATGTGTACTCACCGTACAAGACGTTCATCGTGGTACCAAAAGTCGGGCCA
CGTTTGGACAAAGTATCATTCTTTGTCGGCTTCCAGTTCCCAACAAAGAT
GTCGTGAGCTGACGGCTGAGCTTTCTTGATCGGTGTCATCCATCTCCAGA
TTGCAGCTTGGAAGGCAAGCGTCGCGTTCTGCTCGATGTACTCGGGGTGG
TTCAAGAGATCGGCTTTTAGAGCATCCCCAGCTGCACCGTAGTTGAAGTT
CCAGTAGATGGGTAAAGCACCACGTCCGTAGTACTCAGCTCCAGGGCTGC
AAGGGTACTTGTATTTCCATGTCTCGTCACAGTAAGATTGCATTGGACTC
ATCTCCCTGTTATAGCACAGACCCCAAGCTAAAGGCCCTCCTGTCGCAAC
TCCGTATCCACaggagcggacgcgtggxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxatt

QA 267 711 1 727
DS CHROMAT_FILE: LL2314r PHD_FILE: LL2314r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:21 2000

RT{
LL2314r compression phrap 206 208 000919:094547
}

RT{
LL2314r compression phrap 154 156 000919:094547
}

CO Contig32 1387 2 16 U
ccatccccagctttgttaataatgcatttacatatacagaagattctaga
gcagagtaacaatgtgagattggagatcatTCTTCATTTACTTTCTCCTA
GAGAAATCATCCCATGGGTCTTCTTGACCAAAGATCTCGTCGATGATGTT
GGAAGTTGGAAGAAAATCAATGTTCTTACTCCAACAATGATCAAATGAAT
AAAAATGATCCTCCACAAGATCATTGCAATGGCTCCAGTGATTCCCAACA
TCGGATTCCTCTCTGTTTACATTGGACTGGAAGTCATCGGACATGCACGA
ATCTTCTTCTACAATCACCTCTTCTTCTTCATCATCTCTTGAGAGGCTTT
TTCCGGTTTTATCAACTGGAGTTTCAGGACCATAAAACGTGTTGTCATAC
TCTACTTGCCACTCATCATCGTCACTATCGATGTCCAGGCTTTTAGAACG
ATTCTGAACAGCTCTTCTTCGCAGGATGAAGACGTTGAAATAATAGCTCA
CAATCTCCTTCATGGTTCGTGAAGGAAACGCAGACTTTAGGTGTTTCCAG
AAATCACGGTTCAGTGAAACAGGGTTGGAGTAAACAACCTCGTGGAATAG
ATCTTCCTCGTCCTCGGTTAGTTTACCAGCGACTTCCTCTCCCATTTCAC
CGAGACCTATGTTCAAACATCTTTCGTATCCGATAGTCTCAAACAAGCCT
TCTCGGTTTTCAATGATGTGCTGCTGCACGCATCTGATGGAACCTTTATC
CACGCAAATGCATTCTTTTCTTCCTTTACCAATTTCGAAGAACTCGGTTT
CATGGTCAGGCATTGGAATCACGCACTTGCCGATCAGTTGTTCTTCGTTG
TGATCAACAACATCACGGACTTCTTCCTTGACACAATCAGGAATATTAGC
CTGGTAATCAGACCCGATTCGAACTTGTTTTCTAGGAGAACTCTGACACC
AATCTGACTCGGGAGATTCGTGAGAAAGGGTAGACTGAGTCGTAGCATCC
TCCTCAGATGAGATCCAGGAGAAAGGTGCCTTGGTCTCAGACCCCTTCTC
AACACTATCCTCACATTCAAGCCCGTAGATATCACTCAGATCCTCTCCTA
TGACAAGACCAGACTTCTCCAGTGAAACATGATATGGAACTCCTTCGTCT
AGCTTGGCCAGCTTATTGCAATAACTAATCTCTCTTGCATGCTTCATGTT
GAGCTCTTGCACATCCTCAGCTTCAAAAGTGCGCTTAACACCCATATTTT
TTTGTACAATTGATTCGAAGATAGATCTGGAAGAAGGAAGAGATCTGAAC
ACGAATTCAAGAAAAAATAAATTTGGGGGAAATTTCGTGCTTTTCgatct
ggggaagacccggcccggattaaattcggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 39 56 40 46 40 40 40 40 40 40 40 40 45 45 51 51 46 46 40 40
 40 40 51 51 51 46 40 40 40 40 40 51 51 51 51 51 56 51 51 45 45 45 45 51 40 40 39 39 39 39 39 40 56 51 45 40 40 40 43 43 43 43 43 43 43 43 43 43 56 56
 56 56 56 56 56 56 51 51 51 51 51 51 51 51 51 51 51 45 45 45 45 45 45 45 45 43 43 43 43 43 43 43 43 43 43 43 43 51 56 56 56 56 56 56 56 56 56 51 51 51
 51 51 51 56 56 56 56 56 56 51 51 51 45 45 51 51 45 45 51 51 51 51 51 45 45 45 43 41 42 56 40 43 43 43 43 43 51 56 56 56 51 51 51 51 51 51 51 51 51 43
 43 46 46 46 43 56 51 51 51 51 51 51 51 51 51 51 43 43 43 43 43 43 56 43 43 43 43 43 43 43 51 51 51 51 51 45 45 45 36 36 36 43 43 43 45 43 43 43 43 43
 43 51 51 51 51 56 56 56 43 43 43 43 43 43 45 45 43 43 43 43 45 45 51 51 51 51 51 51 51 51 56 56 56 51 51 51 51 51 51 56 56 42 42 41 43 43 43 43 43 43
 56 51 51 51 51 56 56 56 56 56 56 56 56 43 43 43 46 46 46 56 56 56 51 45 45 45 45 45 45 45 45 43 51 42 56 51 51 51 51 51 51 56 56 56 56 56 56 45 45 45
 45 45 45 51 51 51 45 43 43 43 43 43 43 43 43 56 56 51 51 51 51 51 45 45 45 45 45 45 45 51 51 51 56 56 56 56 56 45 45 51 46 45 41 44 42 42 41 45 45 45
 45 45 51 56 56 51 51 51 51 43 43 43 43 43 40 56 50 50 40 40 45 45 45 45 51 51 56 56 56 56 45 45 45 40 40 40 46 56 51 51 40 40 45 45 40 40 40 39 39 35
 46 43 45 46 51 51 51 51 51 51 56 56 56 51 56 56 43 51 43 43 42 51 51 56 56 51 40 40 37 37 40 37 45 40 45 40 40 46 42 42 42 43 44 40 40 45 45 45 40 40
 42 56 56 56 45 45 45 45 38 38 42 46 46 56 56 44 56 56 56 56 56 56 56 47 47 47 56 56 40 37 37 37 37 40 56 51 51 51 51 43 43 42 42 42 56 42 42 42 37 37
 34 40 40 40 40 40 40 40 40 40 29 29 34 37 40 40 25 20 20 25 27 27 29 29 25 29 29 29 29 29 29 29 27 27 25 22 22 25 32 29 29 29 29 32 32 32 34 34 44 49
 52 58 56 57 50 51 48 56 63 67 69 47 47 50 42 40 41 64 66 66 69 60 65 64 65 65 56 56 50 44 40 50 48 53 65 69 54 57 56 57 52 55 55 44 41 35 50 42 42 44
 47 50 53 56 52 51 49 50 50 58 61 69 69 69 69 69 78 72 70 73 69 64 62 62 62 62 52 59 57 62 62 69 75 88 88 80 80 58 42 42 37 37 40 44 46 47 47 60 61 55
 44 49 43 46 38 44 47 51 51 53 51 47 47 49 63 63 63 49 49 63 25 25 29 32 29 32 24 29 24 32 34 40 32 32 32 34 34 31 40 40 40 46 37 40 37 37 37 37 37 37
 40 37 34 34 29 29 32 34 32 32 32 32 40 25 22 22 25 32 32 32 32 29 34 31 36 40 39 31 31 31 39 39 40 32 32 32 32 25 25 34 40 32 32 32 34 34 39 40 40 46
 46 46 51 40 46 42 42 42 42 42 42 46 56 51 51 40 45 45 45 51 51 56 56 56 56 56 56 56 56 44 44 44 42 42 46 43 51 51 56 51 51 51 51 46 40 35 35 35 39 39
 45 51 40 40 40 40 37 37 51 51 51 56 56 56 56 56 45 40 40 40 40 40 40 56 56 56 56 56 56 56 56 56 44 56 56 56 56 56 56 56 42 46 46 51 43 43 42 43 43 51
 56 56 56 56 51 51 51 51 51 51 51 51 51 56 56 56 45 40 40 40 40 40 51 56 56 56 56 45 45 45 45 45 45 45 51 45 45 45 45 45 43 43 43 43 43 43 41 51 51 51
 51 51 56 51 51 51 45 45 45 51 51 51 56 56 56 56 56 56 56 56 56 56 56 45 45 45 45 45 51 51 45 43 43 43 43 43 43 51 51 51 56 56 56 56 51 51 51 51 51 51
 51 51 51 51 51 51 51 51 51 51 51 51 56 56 56 56 56 51 51 51 51 51 45 51 45 45 45 45 45 45 56 51 51 51 51 45 45 45 45 45 45 56 56 56 56 56 56 56 51 51
 56 56 56 45 45 45 45 45 45 51 51 51 51 51 51 51 51 51 43 36 36 36 36 36 43 51 51 56 56 56 56 56 56 56 51 51 51 51 51 51 56 56 56 45 43 43 43 43 43 43
 43 43 43 43 45 45 45 43 43 43 45 43 43 51 51 43 43 43 43 43 43 43 43 43 43 45 45 45 45 51 51 51 51 51 45 45 45 46 43 43 56 56 56 56 56 51 51 51 51 43
 43 43 43 43 43 45 43 43 43 43 40 40 56 56 56 56 45 45 45 45 45 45 56 56 56 40 38 38 35 35 35 35 35 35 35 40 40 40 40 56 56 56 51 51 51 51 51 51 56 56
 56 51 51 51 51 51 51 51 51 51 51 51 51 45 45 45 45 45 45 40 40 40 40 40 40 39 39 39 39 39 40 51 51 51 40 40 40 40 40 40 45 45 45 35 35 35 35 35 39 45
 45 45 45 45 45 51 51 51 51 51 51 51 51 51 56 39 39 39 39 40 40 51 51 56 56 51 51 51 51 51 51 56 56 40 39 39 39 39 39 46 40 40 29 24 23 13 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2319f U 1
AF LL2319r C 645
BS 1 654 LL2319f
BS 655 655 LL2319r
BS 656 663 LL2319f
BS 664 664 LL2319r
BS 665 676 LL2319f
BS 677 682 LL2319r
BS 683 696 LL2319f
BS 697 697 LL2319r
BS 698 704 LL2319f
BS 705 728 LL2319r
BS 729 735 LL2319f
BS 736 738 LL2319r
BS 739 744 LL2319f
BS 745 759 LL2319r
BS 760 763 LL2319f
BS 764 1387 LL2319r

RD LL2319f 774 0 0
ccatccccagctttgttaataatgcatttacatatacagaagattctaga
gcagagtaacaatgtgagattggagatcatTCTTCATTTACTTTCTCCTA
GAGAAATCATCCCATGGGTCTTCTTGACCAAAGATCTCGTCGATGATGTT
GGAAGTTGGAAGAAAATCAATGTTCTTACTCCAACAATGATCAAATGAAT
AAAAATGATCCTCCACAAGATCATTGCAATGGCTCCAGTGATTCCCAACA
TCGGATTCCTCTCTGTTTACATTGGACTGGAAGTCATCGGACATGCACGA
ATCTTCTTCTACAATCACCTCTTCTTCTTCATCATCTCTTGAGAGGCTTT
TTCCGGTTTTATCAACTGGAGTTTCAGGACCATAAAACGTGTTGTCATAC
TCTACTTGCCACTCATCATCGTCACTATCGATGTCCAGGCTTTTAGAACG
ATTCTGAACAGCTCTTCTTCGCAGGATGAAGACGTTGAAATAATAGCTCA
CAATCTCCTTCATGGTTCGTGAAGGAAACGCAGACTTTAGGTGTTTCCAG
AAATCACGGTTCAGTGAAACAGGGTTGGAGTAAACAACCTCGTGGAATAG
ATCTTCCTCGTCCTCGGTTAGTTTACCAGCGACTTCCTCTCCCATTTCAC
CGAGACCTATGTTCAAACATCTTTCGTATCCGATAGTCTCAAACAAGCCT
TCTCGGTTTTCAATGATGTGCTGCTGCACGCATCTGATGGAACCTTTATC
CACGCAAATGCATTCTTTTCTtcc

QA 81 770 1 774
DS CHROMAT_FILE: LL2319f PHD_FILE: LL2319f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:07 2000

RD LL2319r 787 0 0
tttcACCGAGACCTATGTTCAAACATCTTTCGTATCCGATAGTCTCAAAC
AAGCCTTCTCGGTTTTCAATGATGTGCTGCTGCACGCATCTGATGGAACC
TTTATCCACGCAAATGCATTCTTTTCTTCCTTTACCAATTTCGAAGAACT
CGGTTTCATGGTCAGGCATTGGAATCACGCACTTGCCGATCAGTTGTTCT
TCGTTGTGATCAACAACATCACGGACTTCTTCCTTGACACAATCAGGAAT
ATTAGCCTGGTAATCAGACCCGATTCGAACTTGTTTTCTAGGAGAACTCT
GACACCAATCTGACTCGGGAGATTCGTGAGAAAGGGTAGACTGAGTCGTA
GCATCCTCCTCAGATGAGATCCAGGAGAAAGGTGCCTTGGTCTCAGACCC
CTTCTCAACACTATCCTCACATTCAAGCCCGTAGATATCACTCAGATCCT
CTCCTATGACAAGACCAGACTTCTCCAGTGAAACATGATATGGAACTCCT
TCGTCTAGCTTGGCCAGCTTATTGCAATAACTAATCTCTCTTGCATGCTT
CATGTTGAGCTCTTGCACATCCTCAGCTTCAAAAGTGCGCTTAACACCCA
TATTTTTTTGTACAATTGATTCGAAGATAGATCTGGAAGAAGGAAGAGAT
CTGAACACGAATTCAAGAAAAAATAAATTTGGGGGAAATTTCGTGCTTTT
Cgatctggggaagacccggcccggattaaattcggacgcgtggxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxat

QA 1 707 1 743
DS CHROMAT_FILE: LL2319r PHD_FILE: LL2319r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:44 2000

CO Contig33 558 2 92 U
CTTTTTTTTTTTTTTTTTGAGAAAAGAATAAATACATTATTATGCTTTTC
ATCTGCTCAGATAAGTGCAATGCAGAAGAAATTGCAACAATGTTGTCCAC
TGGAAGAAAAGACGCAGAATAAAAAAATAATATATAAGCTTTAAAAAGAA
AAACAACGAGAAGAGAAACTCAAAAACAATGTTTGATTGTACGATACAAA
ATACTATTGCATTTTCGGTTATTTTATTATATAGATATTCATCGGAGGAA
TTGTTTACGCAACCGTCGACCGCCGTCGGCCGTAGCTCTCTACGCCGTCT
TACCTTGCCGTTTCTCTTCTTCGATCTTGGCCTTAATGACAGAGTAGAGT
GCAACGCCAGCAATGGCTATTCCAGTTCCGATACCTGTCTGCGTCGATAT
CTTGTTTCCGAAGATAACGATGGAGAATCCGATCACGAAGACACGTTTCA
GAACGTTTCCAACAGCGTGAGTCAACGGTGCTACCCTCTCCAACGTATTA
GTAGCCAACTGATTGTAGAGATGGTAAAACATTCCAACCCAGAAGAGCGG
ACGCGTGG

BQ
 42 56 56 56 56 56 56 48 48 48 48 48 40 40 40 34 29 29 34 40 40 48 48 48 40 40 40 40 40 55 55 55 57 54 54 55 79 79 79 79 75 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 89 73 72 72 72 75 86 86 86 86 90 85 83 83 77 80 80 90 90 90 90 90 90 85 76 76 77 76 82 90 90 90 90 90 90 90 71 71 66 51 45 45
 45 45 66 66 66 90 90 90 70 70 49 47 46 57 62 74 86 77 77 77 77 77 77 90 90 90 90 86 86 86 86 88 88 88 80 80 80 80 90 80 86 86 88 90 90 90 90 90 90 90
 90 90 90 90 86 85 85 85 85 86 90 90 90 90 90 90 90 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 88 90 90 90 90 90 90 78 78 78 78 78 78 90 90 90 90 90
 90 90 90 90 90 90 86 90 90 88 88 90 90 78 78 82 81 78 78 90 90 90 90 90 90 90 88 90 90 90 85 85 90 85 85 90 90 90 90 90 88 88 88 88 88 86 90 90 90 90
 90 90 90 90 90 79 78 78 78 78 78 79 88 88 88 88 86 86 83 86 86 86 79 79 79 88 86 86 86 86 86 86 88 86 86 86 86 90 90 90 82 79 79 79 79 86 79 81 87 86
 90 90 90 90 88 90 86 86 86 86 86 86 86 90 90 90 90 90 90 90 90 90 90 90 89 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 88 90 87 89 85 85 85 83 83
 83 86 86 86 86 86 86 86 86 86 83 81 81 83 83 84 83 83 83 83 90 90 90 90 90 90 85 85 89 89 88 84 90 90 88 88 90 90 88 86 83 83 73 73 78 90 90 90 90 90
 90 90 90 90 90 90 83 85 80 83 78 80 85 90 90 83 83 88 85 85 83 90 89 90 90 90 90 83 90 90 90 90 90 90 90 90 90 85 82 87 87 75 74 74 76 74 74 80 80 80
 80 73 78 78 79 74 74 90 86 86 86 75 76 84 84 84 76 72 76 81 81 81 82 79 80 80 80 71 71 70 72 72 75 72 80 90 90 90 90 90 88 78 78 72 72 72 72 77 77 72
 70 70 77 74 79 73 76 76 76 84 84 84 86 82 82 87 69 66 63 74 74 79 83 79 82 82 87 90 90 90 90 90 88 90 90 90 90 90 90 90 90 88 85 85 82 66 66 66 68 66
 80 77 49 50 54 35 46 56

AF LL2321r C -190
AF LL2321f U 15
BS 1 33 LL2321r
BS 34 35 LL2321f
BS 36 46 LL2321r
BS 47 47 LL2321f
BS 48 64 LL2321r
BS 65 75 LL2321f
BS 76 108 LL2321r
BS 109 114 LL2321f
BS 115 153 LL2321r
BS 154 154 LL2321f
BS 155 172 LL2321r
BS 173 173 LL2321f
BS 174 179 LL2321r
BS 180 182 LL2321f
BS 183 188 LL2321r
BS 189 189 LL2321f
BS 190 196 LL2321r
BS 197 198 LL2321f
BS 199 212 LL2321r
BS 213 213 LL2321f
BS 214 219 LL2321r
BS 220 220 LL2321f
BS 221 222 LL2321r
BS 223 226 LL2321f
BS 227 227 LL2321r
BS 228 230 LL2321f
BS 231 232 LL2321r
BS 233 233 LL2321f
BS 234 245 LL2321r
BS 246 268 LL2321f
BS 269 269 LL2321r
BS 270 272 LL2321f
BS 273 275 LL2321r
BS 276 287 LL2321f
BS 288 295 LL2321r
BS 296 300 LL2321f
BS 301 305 LL2321r
BS 306 313 LL2321f
BS 314 319 LL2321r
BS 320 327 LL2321f
BS 328 331 LL2321r
BS 332 332 LL2321f
BS 333 333 LL2321r
BS 334 337 LL2321f
BS 338 340 LL2321r
BS 341 345 LL2321f
BS 346 351 LL2321r
BS 352 360 LL2321f
BS 361 371 LL2321r
BS 372 376 LL2321f
BS 377 378 LL2321r
BS 379 381 LL2321f
BS 382 384 LL2321r
BS 385 390 LL2321f
BS 391 392 LL2321r
BS 393 406 LL2321f
BS 407 413 LL2321r
BS 414 415 LL2321f
BS 416 417 LL2321r
BS 418 418 LL2321f
BS 419 421 LL2321r
BS 422 427 LL2321f
BS 428 428 LL2321r
BS 429 433 LL2321f
BS 434 434 LL2321r
BS 435 437 LL2321f
BS 438 447 LL2321r
BS 448 451 LL2321f
BS 452 452 LL2321r
BS 453 455 LL2321f
BS 456 463 LL2321r
BS 464 466 LL2321f
BS 467 467 LL2321r
BS 468 468 LL2321f
BS 469 469 LL2321r
BS 470 477 LL2321f
BS 478 479 LL2321r
BS 480 485 LL2321f
BS 486 491 LL2321r
BS 492 506 LL2321f
BS 507 509 LL2321r
BS 510 515 LL2321f
BS 516 517 LL2321r
BS 518 526 LL2321f
BS 527 527 LL2321r
BS 528 529 LL2321f
BS 530 544 LL2321r
BS 545 545 LL2321f
BS 546 548 LL2321r
BS 549 549 LL2321f
BS 550 552 LL2321r
BS 553 558 LL2321f

RD LL2321r 793 0 2
ccctcttcgctattacgccagctggcgaaagggggatgtgctgcaaggcg
attaagttgggtaacgccagggttttxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxCTTTTTTTT
TTTTTTTTTGAGAAAAGAATAAATACATTATTATGCTTTTCATCTGCTCA
GATAAGTGCAATGCAGAAGAAATTGCAACAATGTTGTCCACTGGAAGAAA
AGACGCAGAATAAAAAAATAATATATAAGCTTTAAAAAGAAAAACAACGA
GAAGAGAAACTCAAAAACAATGTTTGATTGTACGATACAAAATACTATTG
CATTTTCGGTTATTTTATTATATAGATATTCATCGGAGGAATTGTTTACG
CAACCGTCGACCGCCGTCGGCCGTAGCTCTCTACGCCGTCTTACCTTGCC
GTTTCTCTTCTTCGATCTTGGCCTTAATGACAGAGTAGAGTGCAACGCCA
GCAATGGCTATTCCAGTTCCGATACCTGTCTGCGTCGATATCTTGTTTCC
GAAGATAACGATGGAGAATCCGATCACGAAGACACGTTTCAGAACGTTTC
CAACAGCGTGAGTCAACGGTGCTACCCTCTCCAACGTATTAGTAGCCAAC
TGATTGTAGAGATGGTAAAACATTCCAACCCAGAAGAGCGGACGCGTGGx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxat

QA 7 749 192 749
DS CHROMAT_FILE: LL2321r PHD_FILE: LL2321r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:17 2000

RT{
LL2321r chimera phrap 2 76 000919:094547
}

RT{
LL2321r matchElsewhereHighQual phrap 2 76 000919:094547
}

RD LL2321f 794 0 3
cttttanggaaacatAAATACATTATTATGCTTTTCATCTGCTCAGATAA
GTGCAATGCAGAAGAAATTGCAACAATGTTGTCcagtGGAAGAAAAGACG
CAGAATAAAAAAATAATATATAAGCTTTAAAAAGAAAAACAACGAGAAGA
GAAACTCAAAAACAATGTTTGATTGTACGATACAAAATACTATTGCATTT
TCGGTTATTTTATTATATAGATATTCATCGGAGGAATTGTTTACGCAACC
GTCGACCGCCGTCGGCCGTAGCTCTCTACGCCGTCTTACCTTGCCGTTTC
TCTTCTTCGATCTTGGCCTTAATGACAGAGTAGAGTGCAACGCCAGCAAT
GGCTATTCCAGTTCCGATACCTGTCTGCGTCGATATCTTGTTTCCGAAGA
TAACGATGGAGAATCCGATCACGAAGACACGTTTCAGAACGTTTCCAACA
GCGTGAGTCAACGGTGCTACCCTCTCCAACGTATTAGTAGCCAACTGATT
GTAGAGATGGTAAAACATTCCAACCCAGAAGAGCGGACGCGTGGxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxgcctgtggtgcctactgagtgagctaactcacattaattgcgt
tgcgctcactgccccgctttccagtcggaaacctgtcgtgccag

QA 15 548 14 544
DS CHROMAT_FILE: LL2321f PHD_FILE: LL2321f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:38 2000

RT{
LL2321f chimera phrap 708 794 000919:094547
}

RT{
LL2321f matchElsewhereHighQual phrap 779 794 000919:094547
}

RT{
LL2321f matchElsewhereHighQual phrap 723 764 000919:094547
}

CO Contig34 956 2 50 U
cttggtaataagaatcacaacatgaacaaactcaggagagtacatgaaca
tgaacaagtgagtacaggtaagaaggtacaACAAGCACAGACGCAAAGAA
AAAACAATCTGAAACCAGTTTGGTAGTAACCACCTTTTTGAAACTTAAAA
ATGGAACTTTTAAGATTCAGGGACGGCTTCTACAGCAGCAGCAGCAGCAG
TAGCCGCAGCAGCGGAGCGTTTGATGGAAGCAGATTTGATGAGGTGATTG
TAACTTCCTTTCTCCTTGAAAAGCTGAGCAAAGTGGTGTTTGCAGTACAA
GATCCCTTCAAGAGCTGCGTAGTTGGATGGAGAGATAGGACAGCCTCCGT
GCGAACACTTGAAGCAAGACTTGTGGTAACACTGGCTCTCCACAGTTACC
TTCTCGATAGGGTACACTGTTTTACTGCAAGTAGCGCATTTATCTTGCGT
TCCAGAGAACATTCCAGCAACTCGGCTAGGTGTTCTTGTCAGCTCAGGTG
TTGGTTTGTCTGTTAATGGCTTTGCAGGTGATTGAAAGTTCTTGTTGAAG
CTACCAGTCTCCTTGAAGAGCTGCTCAAAGTGAGGCTTACAGTACAACAC
ACCTTCCATTGATGAATAGTTGCTCAGTTGAAGGGTGGATTTGCAGTGAG
AGCACTTGAAGCAAGACTTGTGGAAAGGGACACCATCAGCTGAGAGAAGC
TCCATAGGGTACACTGTCTTCTCACACGCCCTGCACTTCTGCTGTGTTCC
TGTAAACGACATCGTTTTAGTCTTCCTTCTTCACGATCTGTCCTTCCTCT
CCTCGCTCACTCTCCGTGGATCTGAACAGAAAATGCGGAATCAAAAAAGA
AGAAGTTAGATGTGTAGAAGACGAAGTTAAAGATGAGATGTAATGATTAT
TGAGAGCACGTTCgacacacttatgagacagatagtattctaaagcggac
gcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 44 46 42 42 37 37 39 37 35 35 35 35 35 35 35 35 35 39 36 35
 35 42 42 42 37 37 35 42 35 35 37 37 37 40 40 35 35 35 35 42 47 35 35 32 32 32 32 32 35 35 40 40 37 37 42 42 50 40 37 37 37 35 35 35 32 35 35 35 35 42
 42 40 40 40 37 37 37 37 35 35 40 40 40 37 42 42 41 41 41 41 37 35 35 35 29 29 27 24 26 26 32 35 35 38 38 41 41 41 41 41 41 40 38 35 32 32 32 35 35 30
 23 21 21 21 23 21 26 28 29 32 27 27 32 32 51 53 55 65 65 62 64 74 73 74 63 65 65 53 55 53 56 62 66 90 75 69 69 69 82 82 79 79 73 68 68 64 63 63 63 60
 66 56 58 62 58 53 62 73 71 76 71 75 75 67 71 71 81 85 75 74 76 70 70 74 71 76 73 84 86 90 89 82 75 71 71 71 68 68 65 55 53 53 54 62 60 63 70 74 78 79
 84 79 79 68 68 67 67 67 68 73 70 81 78 78 76 69 76 68 52 50 48 46 34 49 43 54 59 60 68 68 68 71 72 90 76 88 75 58 53 56 56 64 59 60 60 65 63 61 64 60
 56 61 58 58 60 59 65 61 61 57 65 79 82 76 78 82 88 75 80 75 90 75 72 73 76 76 76 71 74 75 87 76 80 81 81 81 81 85 89 90 70 70 62 73 67 67 64 75 66 70
 70 73 76 82 82 82 84 90 90 90 90 90 81 87 71 83 83 90 90 89 84 84 81 77 82 82 80 73 78 82 78 78 70 71 65 67 67 75 82 86 82 82 82 72 73 64 67 70 70 67
 75 73 79 73 81 81 81 79 79 57 63 63 56 43 39 33 29 29 47 50 77 86 78 81 78 78 70 78 78 82 90 90 88 88 90 90 90 83 74 79 72 72 72 69 72 77 90 90 90 87
 82 82 86 86 80 82 90 90 90 90 86 86 82 82 82 80 82 75 75 75 80 81 77 84 82 87 87 90 90 90 90 90 90 90 90 90 90 89 89 89 90 90 90 78 73 73 73 73 77 72
 75 68 73 68 68 72 81 77 77 74 80 90 90 90 90 90 90 87 84 84 82 80 90 90 90 90 80 76 85 83 83 83 84 90 88 78 78 90 75 65 71 70 72 72 90 90 90 90 90 87
 87 84 90 90 90 90 90 90 90 90 90 90 90 90 90 79 79 78 73 73 75 90 89 72 74 62 62 62 67 89 89 90 78 78 67 67 67 84 89 90 76 75 75 72 75 69 73 58 62 62
 71 75 68 67 70 69 70 68 67 72 76 65 67 65 68 70 70 72 72 69 69 69 68 63 59 67 59 58 55 65 67 67 81 81 85 68 70 77 80 73 75 77 71 71 66 61 61 61 58 63
 60 69 74 74 72 68 60 61 61 66 67 72 85 75 76 67 67 67 76 76 76 69 69 74 70 66 68 66 62 68 68 70 66 64 64 60 71 71 71 71 71 71 73 66 66 66 66 66 68 69
 82 72 72 68 58 65 68 62 62 58 52 52 37 40 40 43 43 43 43 43 43 43 46 56 56 56 56 56 56 56 56 45 45 45 45 45 45 40 40 40 40 40 46 56 56 56 56 56 56 56
 51 35 35 35 35 35 35 51 45 45 45 45 39 35 35 35 35 35 46 56 51 51 51 51 51 51 51 51 51 51 51 51 35 34 34 34 34 34 35 37 37 40 40 40 56 56 51 51 51 51
 51 40 40 40 39 39 39 40 40 40 45 40 40 46 46 46 46 46 51 40 40 45 45 45 45 40 40 40 40 40 40 40 40 40 40 40 40 51 39 40 39 39 39 39 39 39 39 40 40 46
 46 46 40 40 40 40 40 35 34 29 29 29 29 14 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0

AF LL2322f U 1
AF LL2322r C 213
BS 1 280 LL2322f
BS 281 281 LL2322r
BS 282 312 LL2322f
BS 313 315 LL2322r
BS 316 316 LL2322f
BS 317 317 LL2322r
BS 318 318 LL2322f
BS 319 323 LL2322r
BS 324 352 LL2322f
BS 353 353 LL2322r
BS 354 366 LL2322f
BS 367 374 LL2322r
BS 375 380 LL2322f
BS 381 381 LL2322r
BS 382 389 LL2322f
BS 390 390 LL2322r
BS 391 411 LL2322f
BS 412 412 LL2322r
BS 413 415 LL2322f
BS 416 427 LL2322r
BS 428 432 LL2322f
BS 433 433 LL2322r
BS 434 434 LL2322f
BS 435 435 LL2322r
BS 436 437 LL2322f
BS 438 440 LL2322r
BS 441 450 LL2322f
BS 451 457 LL2322r
BS 458 460 LL2322f
BS 461 479 LL2322r
BS 480 482 LL2322f
BS 483 485 LL2322r
BS 486 487 LL2322f
BS 488 489 LL2322r
BS 490 490 LL2322f
BS 491 524 LL2322r
BS 525 525 LL2322f
BS 526 534 LL2322r
BS 535 537 LL2322f
BS 538 540 LL2322r
BS 541 541 LL2322f
BS 542 556 LL2322r
BS 557 559 LL2322f
BS 560 566 LL2322r
BS 567 571 LL2322f
BS 572 578 LL2322r
BS 579 583 LL2322f
BS 584 660 LL2322r
BS 661 661 LL2322f
BS 662 956 LL2322r

RD LL2322f 780 0 0
cttggtaataagaatcacaacatgaacaaactcaggagagtacatgaaca
tgaacaagtgagtacaggtaagaaggtacaACAAGCACAGACGCAAAGAA
AAAACAATCTGAAACCAGTTTGGTAGTAACCACCTTTTTGAAACTTAAAA
ATGGAACTTTTAAGATTCAGGGACGGCTTCTACAGCAGCAGCAGCAGCAG
TAGCCGCAGCAGCGGAGCGTTTGATGGAAGCAGATTTGATGAGGTGATTG
TAACTTCCTTTCTCCTTGAAAAGCTGAGCAAAGTGGTGTTTGCAGTACAA
GATCCCTTCAAGAGCTGCGTAGTTGGATGGAGAGATAGGACAGCCTCCGT
GCGAACACTTGAAGCAAGACTTGTGGTAACACTGGCTCTCCACAGTTACC
TTCTCGATAGGGTACACTGTTTTACTGCAAGTAGCGCATTTATCTTGCGT
TCCAGAGAACATTCccgCAACTCGGCTAGGTGTTCTTGTCAGCTCAGGTG
TTGGTTTGTCTGTTAATGGCTTTGCAGGTGATTGAAAGTTCTTGTTGAAG
CTACCAGTCTCCTTGAAGAGCTGCTCAAAGTGAGGCTTACAGTACAACAC
ACCTTCCATTGATGAATAGTTGCTCAGTTGAAGGGTGGATTTGCAGTGAG
AGCACTTGAAGCAAGACTTGTGGAAAGGGACACCATCAGCTGAGAGAAGC
TCCATAGGGTACACTGTCTTCTCACACGCCCTGCACTTCTGCTGTGTTCC
TGTAAACGACATcgntctaGTCTTCCTTct

QA 81 763 1 780
DS CHROMAT_FILE: LL2322f PHD_FILE: LL2322f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:43 2000

RD LL2322r 789 0 0
cgGAGCGTTTGATGGAAGCAGATTTGATGAGGTGATTGTAACTTCCTTTC
TCCTTGAAAAGCTGAGCAAAGTGGTGTTTGCAGTACAAGATCCCTTCAAG
AGCTGCGTAGTTGGATGGAGAGATAGGACAGCCTCCGTGCGAACACTTGA
AGCAAGACTTGTGGTAACACTGGCTCTCCACAGTTACCTTCTCGATAGGG
TACACTGTTTTACTGCAAGTAGCGCATTTATCTTGCGTTCCAGAGAACAT
TCCAGCAACTCGGCTAGGTGTTCTTGTCAGCTCAGGTGTTGGTTTGTCTG
TTAATGGCTTTGCAGGTGATTGAAAGTTCTTGTTGAAGCTACCAGTCTCC
TTGAAGAGCTGCTCAAAGTGAGGCTTACAGTACAACACACCTTCCATTGA
TGAATAGTTGCTCAGTTGAAGGGTGGATTTGCAGTGAGAGCACTTGAAGC
AAGACTTGTGGAAAGGGACACCATCAGCTGAGAGAAGCTCCATAGGGTAC
ACTGTCTTCTCACACGCCCTGCACTTCTGCTGTGTTCCTGTAAACGACAT
CGTTTTAGTCTTCCTTCTTCACGATCTGTCCTTCCTCTCCTCGCTCACTC
TCCGTGGATCTGAACAGAAAATGCGGAATCAAAAAAGAAGAAGTTAGATG
TGTAGAAGACGAAGTTAAAGATGAGATGTAATGATTATTGAGAGCACGTT
Cgacacacttatgagacagatagtattctaaagcggacgcgtggxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxag

QA 1 709 1 744
DS CHROMAT_FILE: LL2322r PHD_FILE: LL2322r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:21 2000

CO Contig35 645 2 99 U
acggccgGAGAAGATTTCATTTCTTTAAATAGCAAAGAGAAAACAca*cG
ACAAGAGTTCCAAAAGCAAACTAGATAAGCCAAGACTGCGTGCTGTTGTT
GCTAAACAAAGCTCTTATAACAAACGGCAGACAATATCTGTGACTTTCTT
CTTCCCATAAAACCCCATTAATTTTGTCATAATTAACCACTACGTCCAGG
TAATCGCCACGGGACTACCCACCACGTGTTTCCCATCTGACCATTCAATG
TTCCCGAAGCTAGATCCAGACGCCTTAGAAGAGTCTACGGTAAACGTCAC
CGTATACGATTTCTTCTCATTAACTTCTTTGAAATTCAAAACCGCCGGTG
CAACCGAAATCTTGACTGCTGTACTCTCCGAAATGACTTTAACCTTGTAG
GACCCAGCTCCTCCAACGCTCGTGACAGTACGCGTGTACTTATACGCTCC
GGATCCGTCAACGTTAACGGCGAAGGACGGATAGTTTAAATCCGCGACTG
AGTGCGTTTTGGAGGGATCGCAAGTGAAATTGCGTCTCGAAACGCTTCTG
ATCTGCGACGACGTGTAGTTCAACGCGCAGAGGAAACCTAAGTAATCCAC
CGTCGttAGATCGTAAACGAGTCCTGGATTGGTGCGGACGCGTGG

BQ
 0 0 0 0 0 15 18 25 29 29 25 34 37 48 34 34 33 30 35 35 41 54 61 51 51 45 48 51 52 55 50 47 49 59 57 69 71 63 63 49 44 44 49 41 23 16 19 19 39 39
 50 60 53 64 64 64 60 65 75 80 85 73 71 71 66 61 61 55 56 60 64 64 69 69 66 41 41 25 22 26 29 48 40 46 50 50 64 64 69 64 67 75 83 83 74 80 80 69 64 60
 62 62 59 50 55 72 80 80 85 85 85 85 74 69 69 65 76 66 66 58 75 58 55 54 55 51 50 60 52 57 57 88 88 90 90 88 86 90 84 84 78 79 68 67 69 72 85 80 85 90
 90 90 86 84 79 74 80 72 78 72 88 88 90 90 90 83 80 80 80 83 83 90 90 90 88 90 85 89 89 89 82 72 72 68 68 68 89 90 90 83 75 75 75 75 75 83 83 83 75 75
 73 72 63 67 65 67 65 67 77 83 76 75 75 75 75 75 76 89 90 90 90 76 76 83 80 80 83 90 90 90 90 90 90 90 90 88 87 83 85 85 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 85 85 85 83 88 88 90 90 90 90 90 90 90 79 79 78 79 79 88 88 90 90 90 90 90 90 90 88 83 88 78 78 78 80 73 78 87 80 80 80 80 80 80 80 83 88
 81 83 81 76 76 76 81 81 88 90 90 90 90 90 88 88 90 85 90 90 83 83 83 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 83 78 78 71 71 79 79 70 70 73 75
 72 75 84 88 88 88 88 90 90 90 90 90 90 90 88 80 80 80 84 78 75 75 81 88 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 82 90 86 78 78 80 85
 86 88 90 90 88 88 88 88 90 90 90 90 90 83 83 83 80 80 80 80 83 80 80 89 89 90 90 88 83 82 78 78 78 78 78 82 82 85 85 85 85 83 83 83 83 85 83 83 88 90
 90 90 83 88 88 83 81 81 88 88 83 80 80 80 85 85 82 83 75 75 80 84 90 90 78 80 80 80 79 89 90 90 90 75 75 77 77 80 77 88 75 75 72 72 72 75 77 79 75 77
 70 69 64 64 64 64 72 90 90 90 90 87 87 87 83 69 64 64 56 56 50 57 77 80 80 90 90 90 68 64 53 52 52 57 64 75 75 73 75 75 75 75 75 75 79 85 88 90 89 89
 90 72 65 60 60 60 65 73 76 79 79 79 71 64 72 72 73 73 79 75 59 60 67 62 62 64 67 72 72 77 80 70 64 64 67 64 69 65 64 56 59 61 66 66 54 62 56 52 53 56
 40 38 23 21 15 15 24 29 47 47 44 58 58 53 56 58 68 63 63 63 63 63 59 72 65 69 69 80 67 61 51 48 50 59 63 63 69 65 45 45 45 32 33 32

AF LL2323r C -108
AF LL2323f U 13
BS 1 14 LL2323r
BS 15 19 LL2323f
BS 20 21 LL2323r
BS 22 23 LL2323f
BS 24 30 LL2323r
BS 31 36 LL2323f
BS 37 39 LL2323r
BS 40 78 LL2323f
BS 79 85 LL2323r
BS 86 92 LL2323f
BS 93 95 LL2323r
BS 96 132 LL2323f
BS 133 143 LL2323r
BS 144 154 LL2323f
BS 155 155 LL2323r
BS 156 176 LL2323f
BS 177 180 LL2323r
BS 181 187 LL2323f
BS 188 190 LL2323r
BS 191 205 LL2323f
BS 206 208 LL2323r
BS 209 211 LL2323f
BS 212 224 LL2323r
BS 225 231 LL2323f
BS 232 239 LL2323r
BS 240 241 LL2323f
BS 242 247 LL2323r
BS 248 250 LL2323f
BS 251 255 LL2323r
BS 256 259 LL2323f
BS 260 264 LL2323r
BS 265 273 LL2323f
BS 274 280 LL2323r
BS 281 282 LL2323f
BS 283 283 LL2323r
BS 284 284 LL2323f
BS 285 285 LL2323r
BS 286 289 LL2323f
BS 290 292 LL2323r
BS 293 300 LL2323f
BS 301 311 LL2323r
BS 312 314 LL2323f
BS 315 315 LL2323r
BS 316 317 LL2323f
BS 318 318 LL2323r
BS 319 324 LL2323f
BS 325 327 LL2323r
BS 328 338 LL2323f
BS 339 340 LL2323r
BS 341 345 LL2323f
BS 346 347 LL2323r
BS 348 354 LL2323f
BS 355 373 LL2323r
BS 374 374 LL2323f
BS 375 376 LL2323r
BS 377 384 LL2323f
BS 385 387 LL2323r
BS 388 400 LL2323f
BS 401 401 LL2323r
BS 402 402 LL2323f
BS 403 403 LL2323r
BS 404 409 LL2323f
BS 410 424 LL2323r
BS 425 429 LL2323f
BS 430 449 LL2323r
BS 450 453 LL2323f
BS 454 454 LL2323r
BS 455 456 LL2323f
BS 457 459 LL2323r
BS 460 461 LL2323f
BS 462 468 LL2323r
BS 469 469 LL2323f
BS 470 471 LL2323r
BS 472 473 LL2323f
BS 474 476 LL2323r
BS 477 484 LL2323f
BS 485 488 LL2323r
BS 489 502 LL2323f
BS 503 507 LL2323r
BS 508 516 LL2323f
BS 517 524 LL2323r
BS 525 526 LL2323f
BS 527 536 LL2323r
BS 537 546 LL2323f
BS 547 548 LL2323r
BS 549 549 LL2323f
BS 550 551 LL2323r
BS 552 553 LL2323f
BS 554 560 LL2323r
BS 561 570 LL2323f
BS 571 599 LL2323r
BS 600 600 LL2323f
BS 601 601 LL2323r
BS 602 612 LL2323f
BS 613 624 LL2323r
BS 625 625 LL2323f
BS 626 628 LL2323r
BS 629 630 LL2323f
BS 631 645 LL2323r

RD LL2323r 799 0 0
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxctttttnnnnnnnnnnnnnnnn
ntntntnnnacggccgGAGAAGATtTCATTTCTTTAAATAGCAAAGAGAA
AACacaacGACAAGAGTTCCAAAAGCAAACTAGATAAGCCAAGACTGCGT
GCTGTTGTTGCTAAACAAAGCTCTTATAACAAACGGCAGACAATATCTGT
GACTTTCTTCTTCCCATAAAACCCCATTAATTTTGTCATAATTAACCACT
ACGTCCAGGTAATCGCCACGGGACTACCCACCACGTGTTTCCCATCTGAC
CATTCAATGTTCCCGAAGCTAGATCCAGACGCCTTAGAAGAGTCTACGGT
AAACGTCACCGTATACGATTTCTTCTCATTAACTTCTTTGAAATTCAAAA
CCGCCGGTGCAACCGAAATCTTGACTGCTGTACTCTCCGAAATGACTTTA
ACCTTGTAGGACCCAGCTCCTCCAACGCTCGTGACAGTACGCGTGTACTT
ATACGCTCCGGATCCGTCAACGTTAACGGCGAAGGACGGATAGTTTAAAT
CCGCGACTGAGTGCGTTTTGGAGGGATCGCAAGTGAAATTGCGTCTCGAA
ACGCTTCTGATCTGCGACGACGTGTAGTTCAACGCGCAGAGGAAACCTAA
GTAATCCACCGTcgc*agATCGTAAACGAGTCCTGGATTGGTGCGGACGC
GTGGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxagt

QA 115 754 110 754
DS CHROMAT_FILE: LL2323r PHD_FILE: LL2323r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:25 2000

RD LL2323f 784 0 0
gaTTTCATTTCTTTAAATAGCAAAGAGAAAACAca*cGACAAGAGTTCCA
AAAGCAAACTAGATAAgcgaagACTGCGTGCTGTTGTTGCTAAACAAAGC
TCTTATAACAAACGGCAGACAATATCTGTGACTTTCTTCTTCCCATAAAA
CCCCATTAATTTTGTCATAATTAACCACTACGTCCAGGTAATCGCCACGG
GACTACCCACCACGTGTTTCCCATCTGACCATTCAATGTTCCCGAAGCTA
GATCCAGACGCCTTAGAAGAGTCTACGGTAAACGTCACCGTATACGATTT
CTTCTCATTAACTTCTTTGAAATTCAAAACCGCCGGTGCAACCGAAATCT
TGACTGCTGTACTCTCCGAAATGACTTTAACCTTGTAGGACCCAGCTCCT
CCAACGCTCGTGACAGTACGCGTGTACTTATACGCTCCGGATCCGTCAAC
GTTAACGGCGAAGGACGGATAGTTTAAATCCGCGACTGAGTGCGTTTTGG
AGGGATCGCAAGTGAAATTGCGTCTCGAAACGCTTCTGATCTGCGACGAC
GTGTAGTTCAACGCGCAGAGGAAACCTAAGTAATCCACCGTCGttAGATC
GTAAACGAGTCCTGGATTGGTGCGGACGCGTGGxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

QA 8 633 1 633
DS CHROMAT_FILE: LL2323f PHD_FILE: LL2323f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:49 2000

CO Contig36 742 2 113 U
TTTTTTTttTTTTTTTTTTTTATCTATGAAATCGATaaacTATAACCAGA
TACTTTGATCATCACTGTTTCATTGGATTTCCAATGAAGATCTCAACAGT
GGAGTATACTTATTTAAGAAATAACAGTACAAGAAAAAAAGAGAAGGATA
GTTTCATTTCCAAGCCGGAGATGCAAGAAACATGATGAGGATCAGTATCC
CCAGTAGTCGTTACGGATTTCGTCATCAAACTTCTTTTTGAGTTCTGGGT
GCTTCTCAAAGTACTCATCTGCAGTCATCGTGCTGAGCTTTTTGCTTATC
TCCTGGACATCAACAATTTCTTTCTCCAGCCGTTCAGACTCCTTGAGCGA
CTTCTGTTCTGCTTCTTTCAGCTCCACCAACAAAGCATCAAACTTAGGCT
TGTATTCAGGGGTAACATTGTCCACGTACTTGGGAATCTCAACGCTGTCA
TAAGCTTCCTTGTACAAGTCAACAATGCCGGATCCAATACCCTTTCTGTA
GAAATCCCAATCAATAGGTTCAGGCTCCTGGCTGAACTTGGTCTGGAGCT
GCGTGTTGACCTCGTCGAAAGCGCGACGGAGGTTAGAGAACTCTCTGCGA
GCCTCATCGGTGACGAGGACCTTAGCCATCCCTTCCCAATCTATAGTCCT
CGACGCTTTGAATGCCACATCCGCCACTTTCTTGCCTGCTCCGCTCATTT
TTCTCGATTTCGCCCAAAACACACACTGATGCGGACGCGTGG

BQ
 32 32 32 32 32 22 23 17 15 23 27 32 26 26 22 22 22 22 22 20 20 21 27 24 24 25 29 25 25 25 25 27 27 27 27 24 19 17 19 16 23 21 32 34 34 34 37 42 47 54
 54 62 58 62 55 59 63 62 62 75 66 66 62 66 61 67 60 66 62 65 74 64 55 55 53 53 59 64 61 69 65 77 66 69 66 69 71 62 66 77 77 79 72 78 66 55 58 70 59 66
 61 66 64 67 71 71 69 71 69 69 69 69 64 64 64 60 60 60 85 67 64 64 55 50 50 61 61 54 52 52 66 88 88 88 88 90 90 90 90 82 82 90 90 90 90 76 66 62 69 69
 69 69 67 75 75 75 69 67 66 66 72 69 69 69 80 74 74 75 76 88 69 77 77 75 81 81 88 88 80 77 80 85 88 90 90 90 88 80 86 86 80 73 71 76 71 76 73 69 72 77
 75 88 69 69 69 66 69 69 68 68 69 66 72 75 82 82 89 80 78 71 71 71 71 75 84 90 90 87 78 90 90 90 88 88 90 90 90 90 90 90 90 82 82 81 90 90 81 86 78 76
 76 79 90 90 90 90 90 90 82 90 82 78 78 90 90 90 90 90 84 80 77 77 78 77 89 90 86 81 85 71 71 71 86 86 87 89 90 90 90 90 90 90 87 87 81 81 88 88 90 87
 90 90 90 90 90 90 90 90 90 83 87 82 83 86 90 90 90 90 90 90 90 90 90 90 90 81 80 79 76 76 77 83 83 83 90 90 88 83 87 87 87 89 90 88 87 83 81 79 79 86
 81 90 87 83 87 88 88 90 87 90 90 90 90 90 90 90 90 90 90 85 85 80 83 88 90 90 90 90 90 90 90 86 86 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 88 88 86 90 90 90 90 90 90 87 89 85 90 87 80 80 80 90 90 90 90 90 90 90 90 90 90 90 90 86 83 81 83 83 83 85 86 89 90
 90 90 86 88 81 81 83 90 90 85 90 87 87 87 90 89 90 90 90 84 88 90 90 90 86 87 85 85 86 85 86 85 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 89
 90 89 90 90 90 90 90 90 90 88 90 90 90 90 90 86 86 86 83 83 89 90 86 86 86 84 80 80 90 82 82 82 88 90 90 90 90 90 88 90 90 90 90 90 87 82 78 78 78 78
 78 78 78 78 83 90 90 90 90 90 83 88 85 85 83 83 83 85 88 83 75 75 71 71 71 78 80 82 82 81 81 83 83 83 85 85 80 85 85 83 83 90 90 85 72 71 71 71 71 71
 85 83 83 78 86 78 83 85 85 85 73 70 73 72 77 77 72 76 82 88 76 72 79 67 64 64 65 73 76 67 67 70 74 85 85 90 85 85 83 69 79 74 71 71 71 71 71 79 80 80
 74 71 67 67 70 65 64 68 69 77 74 63 64 64 66 72 72 77 83 68 63 62 56 53 53 63 83 90 90 90 90 65 69 60 68 67 75 74 76 63 58 58 64 68 63 72 72 75 75 78
 84 71 62 59 59 66 66 64 60 54 56 56 54 58 62 75 72 72 64 69 72 72 83 83 78 79 80 79 74 74 63 61 56 56 76 73 47 44 44 32 33 34

AF LL2325r C 1
AF LL2325f U 35
BS 1 38 LL2325r
BS 39 39 LL2325f
BS 40 41 LL2325r
BS 42 42 LL2325f
BS 43 43 LL2325r
BS 44 46 LL2325f
BS 47 51 LL2325r
BS 52 59 LL2325f
BS 60 60 LL2325r
BS 61 89 LL2325f
BS 90 92 LL2325r
BS 93 118 LL2325f
BS 119 119 LL2325r
BS 120 131 LL2325f
BS 132 135 LL2325r
BS 136 137 LL2325f
BS 138 139 LL2325r
BS 140 141 LL2325f
BS 142 145 LL2325r
BS 146 153 LL2325f
BS 154 156 LL2325r
BS 157 171 LL2325f
BS 172 178 LL2325r
BS 179 179 LL2325f
BS 180 180 LL2325r
BS 181 181 LL2325f
BS 182 187 LL2325r
BS 188 188 LL2325f
BS 189 190 LL2325r
BS 191 193 LL2325f
BS 194 194 LL2325r
BS 195 208 LL2325f
BS 209 217 LL2325r
BS 218 227 LL2325f
BS 228 237 LL2325r
BS 238 244 LL2325f
BS 245 246 LL2325r
BS 247 248 LL2325f
BS 249 258 LL2325r
BS 259 261 LL2325f
BS 262 270 LL2325r
BS 271 272 LL2325f
BS 273 275 LL2325r
BS 276 276 LL2325f
BS 277 277 LL2325r
BS 278 279 LL2325f
BS 280 311 LL2325r
BS 312 315 LL2325f
BS 316 325 LL2325r
BS 326 330 LL2325f
BS 331 344 LL2325r
BS 345 345 LL2325f
BS 346 349 LL2325r
BS 350 350 LL2325f
BS 351 367 LL2325r
BS 368 369 LL2325f
BS 370 383 LL2325r
BS 384 388 LL2325f
BS 389 409 LL2325r
BS 410 411 LL2325f
BS 412 413 LL2325r
BS 414 415 LL2325f
BS 416 423 LL2325r
BS 424 424 LL2325f
BS 425 449 LL2325r
BS 450 454 LL2325f
BS 455 460 LL2325r
BS 461 469 LL2325f
BS 470 470 LL2325r
BS 471 471 LL2325f
BS 472 478 LL2325r
BS 479 479 LL2325f
BS 480 480 LL2325r
BS 481 481 LL2325f
BS 482 492 LL2325r
BS 493 494 LL2325f
BS 495 495 LL2325r
BS 496 499 LL2325f
BS 500 500 LL2325r
BS 501 501 LL2325f
BS 502 502 LL2325r
BS 503 504 LL2325f
BS 505 506 LL2325r
BS 507 509 LL2325f
BS 510 510 LL2325r
BS 511 513 LL2325f
BS 514 515 LL2325r
BS 516 518 LL2325f
BS 519 520 LL2325r
BS 521 521 LL2325f
BS 522 528 LL2325r
BS 529 529 LL2325f
BS 530 537 LL2325r
BS 538 548 LL2325f
BS 549 561 LL2325r
BS 562 562 LL2325f
BS 563 568 LL2325r
BS 569 569 LL2325f
BS 570 570 LL2325r
BS 571 572 LL2325f
BS 573 591 LL2325r
BS 592 593 LL2325f
BS 594 594 LL2325r
BS 595 600 LL2325f
BS 601 621 LL2325r
BS 622 623 LL2325f
BS 624 640 LL2325r
BS 641 650 LL2325f
BS 651 700 LL2325r
BS 701 707 LL2325f
BS 708 726 LL2325r
BS 727 730 LL2325f
BS 731 742 LL2325r

RD LL2325r 786 0 0
TTTTTTTttTTTTTTTTTTTTATCTATGAAATCGATaaacTATAACCAGA
TACTTTGATCATCACTGTTTCATTGGATTTCCAATGAAGATCTCAACAGT
GGAGTATACTTATTTAAGAAATAACAGTACAAGAAAAAAAGAGAAGGATA
GTTTCATTTCCAAGCCGGAGATGCAAGAAACATGATGAGGATCAGTATCC
CCAGTAGTCGTTACGGATTTCGTCATCAAACTTCTTTTTGAGTTCTGGGT
GCTTCTCAAAGTACTCATCTGCAGTCATCGTGCTGAGCTTTTTGCTTATC
TCCTGGACATCAACAATTTCTTTCTCCAGCCGTTCAGACTCCTTGAGCGA
CTTCTGTTCTGCTTCTTTCAGCTCCACCAACAAAGCATCAAACTTAGGCT
TGTATTCAGGGGTAACATTGTCCACGTACTTGGGAATCTCAACGCTGTCA
TAAGCTTCCTTGTACAAGTCAACAATGCCGGATCCAATACCCTTTCTGTA
GAAATCCCAATCAATAGGTTCAGGCTCCTGGCTGAACTTGGTCTGGAGCT
GCGTGTTGACCTCGTCGAAAGCGCGACGGAGGTTAGAGAACTCTCTGCGA
GCCTCATCGGTGACGAGGACCTTAGCCATCCCTTCCCAATCTATAGTCCT
CGACGCTTTGAATGCCACATCCGCCACTTTCTTGCCTGCTCCGCTCATTT
TTCTCGATTTCGCCCAAAACACACACTGATGCGGACGCGTGGxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxat

QA 1 742 1 742
DS CHROMAT_FILE: LL2325r PHD_FILE: LL2325r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:35 2000

RD LL2325f 766 0 0
agtaacTATAACCAGATACTTTGATCATCACTGTTTCATTGGATTTCCAA
TGAAGATCTCAACAGTGGAGTATACTTATTTAAGAAATAACAGTACAAGA
AAAAAAGAGAAGGATAGTTTCATTTCCAAGCCGGAGATGCAAGAAACATG
ATGAGGATCAGTATCCCCAGTAGTCGTTACGGATTTCGTCATCAAACTTC
TTTTTGAGTTCTGGGTGCTTCTCAAAGTACTCATCTGCAGTCATCGTGCT
GAGCTTTTTGCTTATCTCCTGGACATCAACAATTTCTTTCTCCAGCCGTT
CAGACTCCTTGAGCGACTTCTGTTCTGCTTCTTTCAGCTCCACCAACAAA
GCATCAAACTTAGGCTTGTATTCAGGGGTAACATTGTCCACGTACTTGGG
AATCTCAACGCTGTCATAAGCTTCCTTGTACAAGTCAACAATGCCGGATC
CAATACCCTTTCTGTAGAAATCCCAATCAATAGGTTCAGGCTCCTGGCTG
AACTTGGTCTGGAGCTGCGTGTTGACCTCGTCGAAAGCGCGACGGAGGTT
AGAGAACTCTCTGCGAGCCTCATCGGTGACGAGGACCTTAGCCATCCCTT
CCCAATCTATAGTCCTCGACGCTTTGAATGCCACATCCGCCACTTTCTTG
CCTGCTCCGCTCATTTTTCTCGATTTCGCCCAAAACACACACTGATGCGG
ACGCGTGGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxx

QA 9 708 4 708
DS CHROMAT_FILE: LL2325f PHD_FILE: LL2325f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:58 2000

CO Contig37 1093 2 34 U
tcgaaattctttacaaaataacaaaaacctaaaccttaaaaccaacaatg
gacattctctcgagctcgctTCACCTACATTACAAAAACATAAATATTTA
CATAAAAAAATAAATCAAACCGGTTTACGCTAAACCTAAAAGAAACAAAA
AAAAACCTAATCCTCCGCCTCCACCTCCTCTGTTCGCTTCCTCCGTCAAC
CCCTCTGCCTCCTCCTCCATCAAGATGTAGCAATGTCGTCATGGCTACCA
AGTCTATCAATTGTTCCATCTTTTAAATCGTACCACGGATTCTAACACCT
CGTTTCTTGCTTGGTAGAATGCTCTCATCCTCACGATCCTCAAACGTCCT
CCGTAGTTAATCTCCAACAATGAGTCAATAATAGCTTCTTGCTCCATTCT
TTCTTGACAAGAGAAGACCAAATCTCGAACCATTGCTAGACCTTTGCTAG
AATCCACCAATGAGAAGCTTCAACACTCAAAAAATGGTTCAGGAAAAACA
CAAACTGATGAATCAAGTTCTCTTTTCACTGCTGAAGACCAGCTCGAGCA
GAAGATCTGAATAGAGCTTAGAAGCAATGGACGCCATATGGGAGAGAAGC
TCGGGATCTGAGCCGTCGTCCTCTTCCTCTGTCTTCTTCGTTTCCGCTAA
TGGGATAGAAGCTCAGGATTCGCTGCCACCGCCTTTGACGCTGCTCCGCC
TTGCCACCGGAGAAGAGAGAGAGAACGAGGTGTGACGGAGATGAGGAGAT
GCGACGAACCCCTAACAAGAAGTCTCGAATGGAAACAAGTAAATctGAAC
CCTATAATCAGTAGAAGAAGAAACAAATTCTCAGAAATCGACCTGTGGAT
CAAGGCCTGTTCGAGACCCGTAACGATGACGACGAACTCAGACCGGTGGT
GATGGAGACGAACTCATACCGGTGACGATGGCACAAACTCAGACCGGTCT
CTTCTTCCTCATGCAATCTCTCATCTTTCTCTGTCTCATCTCTCTTCTCT
CTGTCGTGTTTGAGAAGAGAAATGGAGAGGACAAAACACAATCTCCCTCC
TTcccctaatgcaggaatcaagattaactttccggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 20 29 32 34 34 39 40 40 46 46 46 46 46 46 51 46 46 46 46 46 46 51 46 46 46 46 40 40 40 39
 39 39 40 40 40 46 51 51 40 40 40 39 39 39 40 40 40 40 39 40 37 37 37 35 35 29 29 31 31 31 31 34 35 39 40 40 40 40 40 40 51 56 40 40 46 40 40 40 51 51
 56 56 46 40 40 40 40 40 45 45 45 45 45 45 35 35 35 35 35 35 35 35 35 35 35 35 39 39 40 45 45 40 37 35 34 34 34 34 34 38 40 40 45 45 40 40 40 45 45 45
 45 45 51 51 45 45 51 51 51 45 45 45 45 45 45 51 51 51 51 51 51 56 56 56 56 56 50 42 42 42 45 45 45 46 41 41 37 37 43 43 45 45 43 36 36 36 36 36 43 56
 56 56 56 56 56 56 56 56 56 56 56 56 42 42 42 43 46 45 51 51 51 51 51 56 56 56 45 45 45 36 36 36 43 43 43 43 43 43 43 43 45 45 45 45 45 45 45 45 45 45
 51 51 45 45 45 45 43 43 43 43 43 43 43 43 43 42 43 43 43 43 43 43 43 43 43 45 45 45 45 45 43 43 43 43 43 43 45 51 51 51 51 43 43 43 43 36 36 38 46 46
 51 51 56 56 79 60 52 52 56 56 60 76 70 58 60 59 59 59 75 79 83 72 71 65 66 68 74 75 64 60 60 62 63 70 67 72 72 72 74 70 72 69 68 67 80 85 85 85 85 81
 81 81 88 76 71 75 75 75 73 71 85 85 85 81 72 72 72 68 72 69 81 81 83 72 72 72 67 58 59 67 73 90 85 80 66 65 62 70 65 69 63 63 68 61 61 64 64 69 77 77
 83 85 85 77 75 72 73 77 80 88 88 88 90 90 85 74 74 70 65 61 66 72 72 67 72 66 70 70 82 90 90 90 90 86 77 71 60 51 51 66 72 65 67 81 87 82 77 79 79 81
 79 90 82 88 83 86 82 82 90 90 90 83 90 90 86 86 76 85 71 79 90 90 90 90 85 90 77 88 87 90 90 83 90 90 86 88 88 88 90 90 84 80 80 80 80 72 74 80 85 88
 90 90 90 90 90 90 90 90 90 90 88 90 88 90 85 90 80 74 80 71 72 68 77 80 90 90 90 90 90 72 67 67 67 67 78 86 90 90 90 90 90 90 90 90 90 90 87 90 90 90
 90 90 90 90 90 90 90 90 83 75 75 75 81 71 67 68 66 69 66 66 78 90 88 88 88 82 81 85 77 88 68 66 69 88 90 90 79 78 78 63 60 57 64 62 71 63 65 67 80 80
 90 90 90 90 85 85 85 74 74 73 77 75 75 83 80 81 80 85 74 77 74 74 67 64 60 57 57 56 60 58 56 56 60 65 82 83 72 72 67 72 72 72 68 74 68 60 56 59 60 65
 84 80 77 73 71 76 81 79 71 82 81 81 78 73 78 78 81 81 88 88 90 77 71 59 60 65 73 69 67 67 82 85 75 68 68 63 61 62 71 82 82 88 88 81 73 73 78 82 83 72
 72 72 65 63 67 61 53 56 63 79 64 63 64 60 56 41 45 46 56 45 45 45 45 45 45 51 51 51 51 45 45 46 46 42 42 41 43 43 43 43 43 51 46 46 15 15 24 33 33 50
 46 46 45 45 45 42 42 38 36 43 43 43 43 43 56 56 51 45 45 45 45 41 42 50 56 56 51 51 51 51 51 45 45 45 45 45 43 45 43 41 41 41 43 43 43 43 43 43 56 56
 51 51 51 51 51 51 43 43 43 43 43 43 43 43 40 40 40 43 43 43 43 38 38 41 45 45 45 51 51 45 43 43 43 43 43 43 51 45 45 45 41 50 50 41 41 41 41 41 41 41
 45 46 51 45 45 45 43 43 43 43 43 43 51 51 51 51 43 40 40 39 39 39 39 38 38 39 39 39 35 38 38 38 38 38 45 51 56 56 51 45 45 40 37 37 35 35 35 35 35 35
 51 51 51 51 45 51 45 45 45 45 35 35 35 35 35 35 56 56 40 40 40 40 40 40 51 51 51 51 45 45 40 40 40 35 35 35 35 35 39 56 51 51 51 51 51 51 51 51 56 56
 51 40 35 35 35 35 35 39 51 51 51 51 51 46 51 51 51 51 51 51 39 39 39 39 40 40 51 51 46 40 40 40 40 40 51 51 51 51 51 51 46 46 40 40 48 48 40 40 40 40
 24 24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2326f U -19
AF LL2326r C 350
BS 1 354 LL2326f
BS 355 368 LL2326r
BS 369 520 LL2326f
BS 521 524 LL2326r
BS 525 527 LL2326f
BS 528 536 LL2326r
BS 537 540 LL2326f
BS 541 545 LL2326r
BS 546 551 LL2326f
BS 552 555 LL2326r
BS 556 560 LL2326f
BS 561 561 LL2326r
BS 562 562 LL2326f
BS 563 563 LL2326r
BS 564 564 LL2326f
BS 565 565 LL2326r
BS 566 566 LL2326f
BS 567 571 LL2326r
BS 572 584 LL2326f
BS 585 586 LL2326r
BS 587 594 LL2326f
BS 595 595 LL2326r
BS 596 596 LL2326f
BS 597 603 LL2326r
BS 604 605 LL2326f
BS 606 607 LL2326r
BS 608 613 LL2326f
BS 614 629 LL2326r
BS 630 630 LL2326f
BS 631 633 LL2326r
BS 634 634 LL2326f
BS 635 636 LL2326r
BS 637 639 LL2326f
BS 640 1093 LL2326r

RD LL2326f 790 0 0
nctttaggggtacgatatantcgaaattctttacaaaataacaaaaacct
aaaccttaaaaccaacaatggacattctctcgagctcgctTCACCTACAT
TACAAAAACATAAATATTTACATAAAAAAATAAATCAAACCGGTTTACGC
TAAACCTAAAAGAAACAAAAAAAAACCTAATCCTCCGCCTCCACCTCCTC
TGTTCGCTTCCTCCGTCAACCCCTCTGCCTCCTCCTCCATCAAGATGTAG
CAATGTCGTCATGGCTACCAAGTCTATCAATTGTTCCATCTTTTAAATCG
TACCACGGATTCTAACACCTCGTTTCTTGCTTGGTAGAATGCTCTCATCC
TCACGATCCTCAAACGTCCTCCGTAGTTAATCTCCAACAATGAGTCAATA
ATAGCTTCTTGCTCCATTCTTTCTTGACAAGAGAAGACCAAATCTCGAAC
CATTGCTAGACCTTTGCTAGAATCCACCAATGAGAAGCTTCAACACTCAA
AAAATGGTTCAGGAAAAACACAAACTGATGAATCAAGTTCTCTTTTCACT
GCTGAAGACCAGCTCGAGCAGAAGATCTGAATAGAGCTTAGAAGCAATGG
ACGCCATATGGGAGAGAAGCTCGGGATCTGAGCCGTCGTCCTCTTCCTCT
GTCTTCTTCGTTTCCGCTAATGGGATAGAAGCTCAGGATTCGCTGCCACC
GCCTTTGACGCTGCTCCGCCTTGCCACCGGAGAAGAGAGAGAGAACGAGG
TGTGACGGAGATGAGGAGATGCGACGAACCCCTAACAAga

QA 81 785 21 790
DS CHROMAT_FILE: LL2326f PHD_FILE: LL2326f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:03 2000

RD LL2326r 789 0 0
tcCGTAGTTAATCTCCAACAATGAGTCAATAATAGCTTCTTGCTCCATTC
TTTCTTGACAAGAGAAGACCAAATCTCGAACCATTGCTAGACCTTTGCTA
GAATCCACCAATGAGAAGCTTCAACACTCAAAAAATGGTTCAGGAAAAAC
ACAAACTGATGAATCAAGTTCTCTTTTCACTGCTGAAGACCAGCTCGAGC
AGAAGATCTGAATAGAGCTTAGAAGCAATGGACGCCATATGGGAGAGAAG
CTCGGGATCTGAGCCGTCGTCCTCTTCCTCTGTCTTCTTCGTTTCCGCTA
ATGGGATAGAAGCTCAGGATTCGCTGCCACCGCCTTTGACGCTGCTCCGC
CTTGCCACCGGAGAAGAGAGAGAGAACGAGGTGTGACGGAGATGAGGAGA
TGCGACGAACCCCTAACAAGAAGTCTCGAATGGAAACAAGTAAATctGAA
CCCTATAATCAGTAGAAGAAGAAACAAATTCTCAGAAATCGACCTGTGGA
TCAAGGCCTGTTCGAGACCCGTAACGATGACGACGAACTCAGACCGGTGG
TGATGGAGACGAACTCATACCGGTGACGATGGCACAAACTCAGACCGGTC
TCTTCTTCCTCATGCAATCTCTCATCTTTCTCTGTCTCATCTCTCTTCTC
TCTGTCGTGTTTGAGAAGAGAAATGGAGAGGACAAAACACAATCTCCCTC
CTTcccctaatgcaggaatcaagattaactttccggacgcgtggxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxaagt

QA 20 709 1 744
DS CHROMAT_FILE: LL2326r PHD_FILE: LL2326r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:40 2000

CO Contig38 894 2 66 U
cttttgacaaaccaaacataactctacaattatatgtactaaactgagta
caacattagaaatgaatgtctcatgctataGATtTGGAATCAAGTTTGTT
TATGGTTTATAAAAGAGAAAATAGCCTTTAAAGTGGCGAAACACAAACAA
ACAATGTTTCGAGAAATGAGACGATTAATTTATGAAAAGTGGACAGCTGC
AGAGTCTCTGCGACACAACCTATGTAGTGAGTTCCATGATGGCGGAAACA
ATATCTCCATCATTGGCTTTGAGAGCCTTAGTGGCTTTGGCCTTCGAAAC
ACCAGCCTGAGTCATCACGAGCTCAACATCCTTGGCTTCAACACCAGTCT
CATCCACGTCATCATCTTCGTACTCCTCTTGTGCAACCGCGGCTGCTTCA
GAAGCATCGGAGTTAGGGATCATAGAGGCAACGTCCGGCATCTTGAACCT
CTGAGCAGCTTGAGCTTGTAGCTGAGAGCTCATATCATCAATCTTGGCCT
CACCGAATATGACATAGGTCTCAGAGTTGGGACTCTTGAAGACATCCGGC
TTCGAGATGACAAACAAAACATTCTTTGATCTCTTGATAGTCACTCTGCT
AACATCAGTGACAGGTTTCATTCCAAGTTTCAGCATAGCTTTGCGGCTTT
TCTTTTCGCTTCTGCTTTGTTTAGAGCTCTCATTGTCACCAGCTCCATCG
ACGTTGTCATCGTCATCGTCATCGACGTCTTCGTCTCCGTCTTTCACATC
CTCAACGACAACATCATCTTCCTTCTCGAGCTTCATTTGCTCTTTGATGG
CTTCCTCAATCTTAACTTCTTCAGCAACAGGGCCTGGCATCTTCTTCTTC
Aaccccctatcttcttccaacaaacccttctagcggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 33 24 24 16 22 26 39 40 40 37 37 40 37 37 56 40 37 37 35 35
 35 35 35 35 40 35 35 35 35 35 35 46 46 51 56 40 40 40 40 37 32 35 35 35 35 35 35 35 40 35 32 32 44 32 30 35 35 35 35 35 37 40 40 40 39 42 42 42 42 42
 42 37 50 50 50 52 56 55 52 56 58 64 60 71 63 64 66 65 62 53 53 53 59 53 49 57 57 57 57 65 61 64 64 63 56 59 63 61 62 60 50 53 52 56 58 53 48 44 46 50
 60 59 69 73 61 59 52 52 52 56 56 51 51 51 53 55 51 50 50 50 62 69 71 78 73 65 71 71 71 71 71 66 68 69 66 90 73 71 62 57 56 56 56 56 56 53 57 57 57 61
 62 85 74 72 66 65 59 69 70 78 78 71 60 60 57 57 63 65 64 60 67 69 74 59 58 56 56 57 62 62 79 71 64 61 61 64 58 58 59 54 50 48 50 50 56 62 54 51 56 67
 67 60 69 64 64 53 54 66 71 73 76 78 76 84 82 78 73 71 73 73 75 75 72 82 78 81 81 81 64 59 59 65 67 66 70 61 68 76 70 72 70 70 72 68 69 70 88 72 75 82
 86 88 90 90 78 79 70 70 67 70 88 90 87 90 90 90 90 82 82 81 72 72 82 80 78 90 86 87 82 82 76 79 72 73 72 69 69 69 62 59 65 56 66 69 70 82 76 90 90 90
 89 74 85 72 81 79 88 90 90 82 82 86 81 82 83 88 87 90 90 90 90 90 90 90 88 78 78 78 78 75 75 81 86 86 86 86 81 81 81 87 90 90 90 87 87 82 83 81 88 84
 90 87 89 79 81 81 80 80 86 86 90 90 90 90 90 90 81 75 85 70 74 74 85 90 90 90 90 90 86 86 86 86 90 90 90 90 90 90 90 90 88 90 90 90 85 80 78 81 85 85
 82 82 82 90 90 90 90 90 90 90 90 90 90 90 90 85 85 85 86 84 83 90 89 85 85 80 80 80 90 90 90 88 88 88 82 85 87 87 87 80 90 79 84 90 81 88 90 86 86 83
 86 86 88 90 90 90 83 88 90 90 90 90 90 86 86 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 85 85 85 85 85 80 87 90 90 77 76 74 74 74
 70 72 78 90 82 82 87 85 85 71 80 83 85 85 90 85 90 90 90 90 90 90 90 90 85 85 83 83 83 83 83 76 76 76 83 90 83 83 72 68 58 73 63 61 61 64 71 82 90 90
 90 90 87 85 68 65 70 70 68 65 65 75 80 77 81 75 63 68 67 59 59 67 67 69 68 75 75 74 80 74 77 77 72 87 65 71 71 76 72 74 70 64 60 56 65 65 58 62 64 67
 65 62 60 58 58 66 66 72 72 72 72 73 68 64 64 72 75 63 59 60 68 80 74 63 67 67 63 60 63 60 57 60 63 59 52 50 50 50 54 56 60 59 78 71 77 79 76 76 72 66
 66 69 69 54 54 58 62 54 54 60 66 60 64 65 65 71 78 81 85 77 72 72 76 70 66 63 60 57 59 61 54 50 55 66 66 70 55 55 40 46 46 46 51 51 51 40 40 40 40 40
 40 40 40 40 40 40 40 40 40 45 34 34 32 32 35 35 42 46 46 46 39 33 33 33 33 33 34 51 51 40 40 40 40 40 39 39 39 39 39 40 51 56 56 56 44 46 33 33 30 24
 24 14 19 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2327f U 1
AF LL2327r C 144
BS 1 194 LL2327f
BS 195 197 LL2327r
BS 198 235 LL2327f
BS 236 236 LL2327r
BS 237 257 LL2327f
BS 258 258 LL2327r
BS 259 282 LL2327f
BS 283 283 LL2327r
BS 284 315 LL2327f
BS 316 316 LL2327r
BS 317 323 LL2327f
BS 324 325 LL2327r
BS 326 337 LL2327f
BS 338 338 LL2327r
BS 339 350 LL2327f
BS 351 355 LL2327r
BS 356 356 LL2327f
BS 357 364 LL2327r
BS 365 365 LL2327f
BS 366 366 LL2327r
BS 367 370 LL2327f
BS 371 376 LL2327r
BS 377 377 LL2327f
BS 378 378 LL2327r
BS 379 390 LL2327f
BS 391 402 LL2327r
BS 403 406 LL2327f
BS 407 409 LL2327r
BS 410 411 LL2327f
BS 412 412 LL2327r
BS 413 415 LL2327f
BS 416 425 LL2327r
BS 426 432 LL2327f
BS 433 436 LL2327r
BS 437 439 LL2327f
BS 440 445 LL2327r
BS 446 448 LL2327f
BS 449 450 LL2327r
BS 451 451 LL2327f
BS 452 452 LL2327r
BS 453 458 LL2327f
BS 459 466 LL2327r
BS 467 469 LL2327f
BS 470 507 LL2327r
BS 508 509 LL2327f
BS 510 519 LL2327r
BS 520 521 LL2327f
BS 522 562 LL2327r
BS 563 565 LL2327f
BS 566 566 LL2327r
BS 567 570 LL2327f
BS 571 577 LL2327r
BS 578 582 LL2327f
BS 583 604 LL2327r
BS 605 607 LL2327f
BS 608 610 LL2327r
BS 611 612 LL2327f
BS 613 614 LL2327r
BS 615 615 LL2327f
BS 616 635 LL2327r
BS 636 636 LL2327f
BS 637 641 LL2327r
BS 642 642 LL2327f
BS 643 683 LL2327r
BS 684 684 LL2327f
BS 685 894 LL2327r

RD LL2327f 792 0 0
cttttgacaaaccaaacataactctacaattatatgtactaaactgagta
caacattagaaatgaatgtctcatgctataGATtTGGAATCAAGTTTGTT
TATGGTTTATAAAAGAGAAAATAGCCTTTAAAGTGGCGAAACACAAACAA
ACAATGTTTCGAGAAATGAGACGATTAATTTATGAAAAGTGGACAGCTGC
AGAGTCTCTGCGACACAACCTATGTAGTGAGTTCCATGATGGCGGAAACA
ATATCTCCATCATTGGCTTTGAGAGCCTTAGTGGCTTTGGCCTTCGAAAC
ACCAGCCTGAGTCATCACGAGCTCAACATCCTTGGCTTCAACACCAGTCT
CATCCACGTCATCATCTTCGTACTCCTCTTGTGCAACCGCGGCTGCTTCA
GAAGCATCGGAGTTAGGGATCATAGAGGCAACGTCCGGCATCTTGAACCT
CTGAGCAGCTTGAGCTTGTAGCTGAGAGCTCATATCATCAATCTTGGCCT
CACCGAATATGACATAGGTCTCAGAGTTGGGACTCTTGAAGACATCCGGC
TTCGAGATGACAAACAAAACATTCTTTGATCTCTTGATAGTCACTCTGCT
AACATCAGTGACAGGTTTCATTCCAAGTTTCAGCATAGCTTTGCGGCTTT
TCTTTTCGCTTCTGCTTTGTTTAGAGCTCTCATTGTCACCAGCTCCATCG
ACGTTGTCATCGTCATCGTCATCGACGTCTTCGTCTCCGTCTTTCACATC
CTCAACGACAACATCATCTTCCTTCTCGAGCTTCATTTGctt

QA 81 788 1 791
DS CHROMAT_FILE: LL2327f PHD_FILE: LL2327f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:08 2000

RD LL2327r 795 0 0
caAACAAACAATGTTTCGAGAAATGAGACGATTAATTTATGAAAAGTGGA
CAGCTGCAGAGTCTCTGCGACACAACCTATGTAGTGAGTTCCATGATGGC
GGAAACAATATCTCCATCATTGGCTTTGAGAGCCTTAGTGGCTTTGGCCT
TCGAAACACCAGCCTGAGTCATCACGAGCTCAACATCCTTGGCTTCAACA
CCAGTCTCATCCACGTCATCATCTTCGTACTCCTCTTGTGCAACCGCGGC
TGCTTCAGAAGCATCGGAGTTAGGGATCATAGAGGCAACGTCCGGCATCT
TGAACCTCTGAGCAGCTTGAGCTTGTAGCTGAGAGCTCATATCATCAATC
TTGGCCTCACCGAATATGACATAGGTCTCAGAGTTGGGACTCTTGAAGAC
ATCCGGCTTCGAGATGACAAACAAAACATTCTTTGATCTCTTGATAGTCA
CTCTGCTAACATCAGTGACAGGTTTCATTCCAAGTTTCAGCATAGCTTTG
CGGCTTTTCTTTTCGCTTCTGCTTTGTTTAGAGCTCTCATTGTCACCAGC
TCCATCGACGTTGTCATCGTCATCGTCATCGACGTCTTCGTCTCCGTCTT
TCACATCCTCAACGACAACATCATCTTCCTTCTCGAGCTTCATTTGCTCT
TTGATGGCTTCCTCAATCTTAACTTCTTCAGCAACAGGGCCTGGCATCTT
CTTCTTCAaccccctatcttcttccaacaaacccttctagcggacgcgtg
gxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxaag

QA 10 715 1 751
DS CHROMAT_FILE: LL2327r PHD_FILE: LL2327r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:44 2000

CO Contig39 566 2 76 U
tTTTTTTTTtttaacCataacAGTTTCCTTGATTACATTAACTTCATGAG
GTTTAGTATTACACAC*ACTGGTCTGAAACAAAGCTATCTCAGCCTTATT
TATTTCATATAATTTAGCAGAAACATTTAGATTATTACCCTTTAAACAAG
TGAAATGTTCAAGAAGAAGATTCTTTAAACTCTTGTAACTGCTTGAAGTT
CATCCATGGCTTCACCCAAACTTTGGCTTCGAAGTTCTTAGCCTGGCCAC
CTTCGTTTGCTTCAAGAGTTAAGTAGTACATGGTTCCAGCAACCACCTGT
TCTCTTGCCTTTACAATCTTCTTGAACTCAAGAACCTTGTTCTCTCGGTT
GTTATGTTCTTGAATAGCGAATCGAGCGAGACTCTCGATCTCTCCACTGT
TTTGGTTTCCTCGGAGATCATGAACGCCTCCTAAAATCATCGTCTTCTCC
GTGGTTTTCTCTATTGATCTGCAACTTCTTGGTTGAATTGTTCGACAGAG
AAGGAGGGTTACGATCAAGAACGTAACAGATACGAAAGCTTTTGATTCCA
TTTTCCGGACGCGTGG

BQ
 0 27 27 48 40 40 40 40 25 17 8 9 9 11 11 22 17 19 10 10 10 24 24 29 25 25 25 22 22 22 25 27 22 22 25 24 27 27 24 21 28 43 46 57 70 87 79 79 75 80
 66 66 64 65 65 67 64 58 49 49 51 48 42 40 40 40 40 42 47 48 72 66 68 70 78 69 65 71 67 69 66 74 72 72 72 80 80 80 86 86 65 60 57 59 54 56 60 60 71 72
 79 85 79 90 90 90 77 77 80 77 75 74 68 68 66 68 68 80 82 88 82 88 79 88 86 82 84 79 85 80 80 80 80 86 80 84 80 80 90 72 72 75 81 81 86 82 86 85 85 85
 85 90 85 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 86 86 86 90 86 80 90 90 90 90 90 90 90 77 77 76 90 90 89 89 89 84 90 90 90 90 90 90
 90 90 90 90 90 88 80 80 80 80 86 90 90 90 90 90 90 90 80 80 66 61 64 74 70 88 90 90 90 90 88 90 88 88 83 90 86 86 88 88 88 90 90 90 90 90 90 90 90 90
 88 90 90 90 90 86 86 90 90 90 90 90 90 90 90 90 86 86 86 86 86 86 86 86 86 86 88 90 90 90 90 90 90 90 90 90 90 90 90 87 90 90 90 90 90 86 86 88 88 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 86 90 88 88 88 88 88 88 88 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 88 81 75 75 75 75 75 85 90 85 82 82 82 82 82 78 78 80 86 80 78 82 83 83 83 88 90 90 90 90 90 90 90 83 83 83 90 90
 90 90 90 90 83 83 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 82 78 78 78 78 78 83 88 88 90 90 90 90 90 90 90 86 86 86 90 90 90 90 90 90 90 85 84 80
 85 85 90 90 90 90 90 90 90 90 90 89 84 90 82 82 90 81 81 75 75 68 69 83 87 79 73 88 88 72 69 69 69 72 72 80 90 90 79 75 69 75 75 75 85 90 90 90 90 90
 90 90 90 90 90 90 86 86 75 72 71 74 74 74 72 68 67 67 64 67 67 67 67 61 71 70 77 77 80 77 74 77 77 77 87 86 86 86 86 80 84 84 72 72 67 71 61 61 46 40
 39 39 39 39 39 51 66 66 61 47 47 47 32 33 46

AF LL2329r C -169
AF LL2329f U 29
BS 1 37 LL2329r
BS 38 41 LL2329f
BS 42 43 LL2329r
BS 44 44 LL2329f
BS 45 48 LL2329r
BS 49 63 LL2329f
BS 64 69 LL2329r
BS 70 96 LL2329f
BS 97 99 LL2329r
BS 100 100 LL2329f
BS 101 107 LL2329r
BS 108 119 LL2329f
BS 120 122 LL2329r
BS 123 123 LL2329f
BS 124 139 LL2329r
BS 140 146 LL2329f
BS 147 152 LL2329r
BS 153 153 LL2329f
BS 154 155 LL2329r
BS 156 156 LL2329f
BS 157 183 LL2329r
BS 184 189 LL2329f
BS 190 195 LL2329r
BS 196 197 LL2329f
BS 198 203 LL2329r
BS 204 206 LL2329f
BS 207 232 LL2329r
BS 233 233 LL2329f
BS 234 235 LL2329r
BS 236 236 LL2329f
BS 237 237 LL2329r
BS 238 248 LL2329f
BS 249 251 LL2329r
BS 252 258 LL2329f
BS 259 263 LL2329r
BS 264 278 LL2329f
BS 279 280 LL2329r
BS 281 292 LL2329f
BS 293 296 LL2329r
BS 297 302 LL2329f
BS 303 303 LL2329r
BS 304 304 LL2329f
BS 305 316 LL2329r
BS 317 324 LL2329f
BS 325 330 LL2329r
BS 331 331 LL2329f
BS 332 336 LL2329r
BS 337 350 LL2329f
BS 351 356 LL2329r
BS 357 370 LL2329f
BS 371 388 LL2329r
BS 389 389 LL2329f
BS 390 396 LL2329r
BS 397 405 LL2329f
BS 406 407 LL2329r
BS 408 408 LL2329f
BS 409 409 LL2329r
BS 410 422 LL2329f
BS 423 429 LL2329r
BS 430 472 LL2329f
BS 473 478 LL2329r
BS 479 480 LL2329f
BS 481 486 LL2329r
BS 487 487 LL2329f
BS 488 489 LL2329r
BS 490 491 LL2329f
BS 492 492 LL2329r
BS 493 495 LL2329f
BS 496 496 LL2329r
BS 497 507 LL2329f
BS 508 524 LL2329r
BS 525 532 LL2329f
BS 533 540 LL2329r
BS 541 543 LL2329f
BS 544 564 LL2329r
BS 565 566 LL2329f

RD LL2329r 780 0 0
ttggtancgccagggttttxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxcttttttttttttttt
ttttnttttttttnnttnnntTTTTTTTTtttaacCataacAGTTTCCTT
GATTACAttaaCTTCATGAGGTTTAGTATTACACAC*ACTGGTCTGAAAC
AAAGCTATCTCAGCCTTATTTATTTCATATAATTTAGCAGAAACATTTAG
ATTATTACCCTTTAAACAAGTGAAATGTTCAAGAAGAAGATTCTTTAAAC
TCTTGTAACTGCTTGAAGTTCATCCATGGCTTCACCCAAACTTTGGCTTC
GAAGTTCTTAGCCTGGCCACCTTCGTTTGCTTCAAGAGTTAAGTAGTACA
TGGTTCCAGCAACCACCTGTTCTCTTGCCTTTACAATCTTCTTGAACTCA
AGAACCTTGTTCTCTCGGTTGTTATGTTCTTGAATAGCGAATCGAGCGAG
ACTCTCGATCTCTCCACTGTTTTGGTTTCCTCGGAGATCATGAACGCCTC
CTAAAATCATCGTCTTCTCCGTGGTTTTCTCTATTGATCTGCAACTTCTT
GGTTGAATTGTTCGACAGAGAAGGAGGGTTACGATCAAGAACGTAACAGA
TACGAAAGCTTTTGATTCCATTTTCCGGACGCGTGGxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxat

QA 172 736 171 736
DS CHROMAT_FILE: LL2329r PHD_FILE: LL2329r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:17 2000

RD LL2329f 759 0 2
ttgat*aCATTAACTTCATGAGGTTTAGTATTACAcaccaCTGGTCTGAA
ACAAAGCTATCTCAGCCTTATTTATTTCATATAATTTAGCAGAAACATTT
AGATTATTACCCTTTAAACAAGTGAAATGTTCAAGAAGAAGATTCTTTAA
ACTCTTGTAACTGCTTGAAGTTCATCCATGGCTTCACCCAAACTTTGGCT
TCGAAGTTCTTAGCCTGGCCACCTTCGTTTGCTTCAAGAGTTAAGTAGTA
CATGGTTCCAGCAACCACCTGTTCTCTTGCCTTTACAATCTTCTTGAACT
CAAGAACCTTGTTCTCTCGGTTGTTATGTTCTTGAATAGCGAATCGAGCG
AGACTCTCGATCTCTCCACTGTTTTGGTTTCCTCGGAGATCATGAACGCC
TCCTAAAATCATCGTCTTCTCCGTGGTTTTCTCTATTGATCTGCAACTTC
TTGGTTGAATTGTTCGACAGAGAAGGAGGGTTACGATCAAGAACGTAACA
GATACGAAAGCTTTTGATTCCATttctcgGACGCGTGGxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xgcctggngtgcctaatgagtgagctaactcacattaattgcgttgcgct
cactgcccg

QA 14 538 1 538
DS CHROMAT_FILE: LL2329f PHD_FILE: LL2329f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:39 2000

RT{
LL2329f chimera phrap 702 759 000919:094547
}

RT{
LL2329f matchElsewhereHighQual phrap 709 759 000919:094547
}

CO Contig40 338 2 1 U
CCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGAAA
AAGAGGTTCGATTTCTGATGAATCATACAAAGATACGACAAAGGAAATTG
CACAAATTTACATAGGAAAGACCACAAACAAACTTCTCTTTCTCTGGCTC
TCACTCACATAAGCTTCACTTTCCGGGGACGAAGTTGGTGGCGAAGGCCC
ATGCGTTGTTGTTGACTGGATCAGCCAAATGGTCGGCGAGATTCTCCAAC
GGTCCCTTTCCAGTGACAATAGCCTGGACAAAGAATCCAAACATAGagcc
caTAGCCAACCTTCCGTTCTTGATCTCCGGACGCGTGG

BQ
 20 27 27 50 50 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 51
 51 51 51 43 43 58 58 58 77 79 79 79 90 86 90 77 77 82 82 82 85 85 85 86 86 86 86 90 86 80 80 80 74 72 72 72 78 78 80 90 90 90 90 90 90 90 90 90 90 90
 88 90 90 90 90 90 90 90 90 90 90 90 86 85 85 90 90 90 60 66 66 66 51 51 51 51 56 56 56 71 71 71 71 71 71 90 90 90 90 90 90 90 90 90 90 85 85 85 85 90
 90 90 90 90 90 90 90 85 85 83 83 80 80 90 85 90 90 90 90 90 90 85 85 85 85 80 79 75 71 71 69 68 68 74 87 79 90 90 72 70 67 67 67 67 71 75 82 82 85 82
 77 70 70 70 70 70 80 90 83 86 86 85 85 75 86 86 86 86 77 82 76 74 74 74 74 74 77 90 90 90 90 75 75 69 69 69 69 69 69 74 74 84 90 90 88 90 88 75 75 74
 74 74 74 80 86 90 90 90 90 82 82 81 83 77 77 79 77 75 73 73 70 70 73 74 79 76 76 77 88 88 88 90 90 90 90 88 88 88 90 90 88 88 55 49 47 40 19 11 9 9
 14 16 31 44 71 79 72 77 84 86 89 89 90 84 84 80 80 80 80 80 85 90 85 79 79 79 79 79 83 76 76 76 49 49 49 35 35 35

AF LL2331r C -410
AF LL2331f U 42
BS 1 338 LL2331r

RD LL2331r 793 0 2
ccctaaagggagcccccgatttagagcttgacggggaaagccggcgaacg
tggcgagaaaggaagggaagaaagcgaaaggagcgggcgctagggcgctg
gcaagtgtagcggtcacgctgcgcgtaaccaccacacccgccgcgcttaa
tgcgccgctacagggcgcgtcccattcgccattcaggctgcgcaactgtt
gggaagggcgatcggtgcgggcctcttcgctattacgccagctggcgaaa
gggggatgtgctgcaaggcgattaagttgggtaacgccagggttttxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTGAGAAAAAGAGGTTCGATTTCTGATGAATCATACAAAGATACGAC
AAAGGAAATTGCACAAATTTACATAGGAAAGACCACAAACAAACTTCTCT
TTCTCTGGCTCTCACTCACATAAGCTTCACTTTCCGGGGACGAAGTTGGT
GGCGAAGGCCCATGCGTTGTTGTTGACTGGATCAGCCAAATGGTCGGCGA
GATTCTCCAACGGTCCCTTTCCAGTGACAATAGCCTGGACAAAGAATCCA
AACATAGagcccaTAGCCAACCTTCCGTTCTTGATCTCCGGACGCGTGGx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccagaat

QA 142 749 412 749
DS CHROMAT_FILE: LL2331r PHD_FILE: LL2331r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:26 2000

RT{
LL2331r chimera phrap 1 296 000919:094547
}

RT{
LL2331r matchElsewhereHighQual phrap 1 296 000919:094547
}

RD LL2331f 788 0 3
cttttagaaaacagGTTCGATTTCTGATGAATCATACAAAGATACGACAA
AGGAAATTGCACAAATTTACATAGGAAAGACcaggaaCAAACTTCTCTTT
CTCTGGCTCTCACTCACATAAGCTTCACTTTCCGGGGACGAAGTTGGTGG
CGAAGGCCCATGCGTTGTTGTTGACTGGATCAGCCAAATGGTCGGCGAGA
TTCTCCAACGGTCCCTTTCCAGTGACAATAGCCTGGACAAAGAATCCAAA
CATAGAGAACATAGCCAACCTTCCGTTCTTGATCTCCGGACGCGTGGxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxgcctggggtgcctaatgagtgagctaactcacattaattg
cgttgcgctcactgcccgctttccagtcgggaaacctgtcgtgccagctg
cattaatgaatcggccaacgcgcggggagaggcggtttgcgtattgggcg
ccagggtggtttttcttttcaccagtgagacgggcaacagctgattgccc
ttcaccgcctggccctgagagagttgcagcaagcggtccacgctggtttg
ccccgcaggcgaaaatcctgtttgatggtggttaacggcgggatataaca
tgagctgtcttcggtatcgtcgtatcccactaccgaga

QA 14 785 8 297
DS CHROMAT_FILE: LL2331f PHD_FILE: LL2331f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:49 2000

RT{
LL2331f chimera phrap 461 788 000919:094547
}

RT{
LL2331f matchElsewhereHighQual phrap 705 788 000919:094547
}

RT{
LL2331f matchElsewhereHighQual phrap 461 703 000919:094547
}

CO Contig41 830 2 64 U
ccacgcgtccgcggacgcgtgggttttttttttttTTTTTTTTTTTTATT
TTTATTTTTTAGAAATTGAATTATTAAATTTAGTTTTGCTATAATCTTTA
TATTTTCTGGATAATTAAATTCATCAATAAACTCTCATTTTTTAGTTTTG
CTATAATCTTGATTATGAAAATAGCTCATACACACGACTCATGATCACAC
AACTCACTCAGCTCTGGATCAGTCTGCCTGAACCGTGATTGGCTTTCCTC
TTCCCATCGAGAATCCTCTGGTCCCATCAGGCATCCTTGGTCCCGGTGGT
TGCTGTTTTGGCTACTCCATGCTGCTCATTGGATGGTTTGAAGGTGGTGT
TCCAACTTGATGTTGATGGTGATGATTATGATGATTCCCACGCTACGCCC
TTTTCTCTGCCCACCCGCTTTCTCATTCCCTTCATCCCTTGCTCCTCTCC
TACTATCACTGCCTGCTCAGGCACATTTGTATCCCATTCTCCAGAGAACT
CCTCAGCTTGTTTCTCAATTGGCTGTTGCTCAGATGTCGTGGCATCATCT
TCTTCATGTTCTACTTCTACATCATGTCCTTTTCTTCCTCGCCCTTGAAC
CTGTTTTGGTTCCTTTGTCTTGGTGCCTTGATCGAAACCTTGCAGAGGCA
AGTGTAATTATCTCTTTTCTGAAGATTTTCAGGGAAACCACCAAAGATCC
TCTCAATACAAGTGTGAATGTCTCTTTTCATAGACTTATTCCCAAATTGG
AAGAaACCTAAATTcCCAAATCagaaaatCAAAATCCCTAAATTGAGATA
ATACCCACGaAaTCaaACATGATGAagaat

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 37 30 30 30 30 33 44 48 56 40 40 37 37 40 40
 40 40 40 40 40 40 56 40 39 39 29 29 29 46 46 40 40 40 40 35 35 35 35 35 35 35 35 45 49 45 45 45 45 45 53 45 45 45 45 45 45 45 45 50 50 52 50 50 49 55
 50 50 52 52 66 56 61 61 53 53 53 50 55 50 50 50 50 50 50 61 61 61 61 61 66 50 40 40 40 35 35 37 47 47 50 56 55 61 66 66 61 56 56 52 52 52 54 45 43 44
 44 44 44 45 53 50 50 66 50 50 50 50 50 53 53 53 53 66 66 61 55 55 53 53 47 51 51 50 56 56 56 61 49 44 44 50 50 53 51 51 51 66 66 66 66 60 52 56 56 61
 49 48 53 53 53 48 49 49 49 48 50 50 48 48 48 66 66 66 61 56 53 52 52 51 53 51 51 51 53 53 50 53 49 49 45 50 50 61 66 53 48 48 48 48 53 53 51 51 51 51
 51 55 55 61 61 55 53 51 51 51 51 52 56 56 56 54 53 53 53 53 53 66 66 66 66 66 66 66 66 61 61 61 61 61 61 61 61 66 66 66 66 55 55 55 56 51 51 66 66 53
 46 46 46 46 46 53 66 66 61 53 46 46 46 46 46 46 53 55 66 61 61 53 53 50 53 50 53 53 66 66 66 66 66 66 66 66 66 61 61 61 61 61 61 66 66 66 66 60 52 52
 52 66 66 53 53 53 53 60 66 61 66 66 66 66 66 66 61 61 61 61 61 61 61 66 61 61 61 61 61 61 66 66 66 61 61 61 61 55 50 50 48 48 48 48 48 48 53 53 54 56
 66 66 66 61 61 61 53 53 53 53 53 53 53 51 53 53 46 46 46 53 55 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 61 55 55 55 55 55 55 61 66 66 66 53
 53 53 53 53 53 55 53 53 53 53 53 53 53 55 53 53 53 55 53 61 61 61 61 61 61 61 66 66 66 66 66 66 66 66 66 66 66 66 66 61 56 56 52 52 52 53 50 53 53 53
 53 53 61 66 55 55 55 55 55 55 61 61 61 61 61 61 61 61 61 61 55 55 55 55 55 53 48 53 53 53 53 47 52 66 56 55 55 55 50 50 50 56 52 61 53 61 61 61 66 66
 66 66 61 61 61 61 61 61 66 50 52 55 50 50 50 55 50 52 47 52 52 56 61 61 61 61 61 61 61 61 66 66 66 61 61 61 61 61 49 45 45 45 45 49 66 66 50 50 50 50
 50 50 54 61 61 61 61 61 47 47 47 50 50 50 66 66 66 66 66 66 66 66 50 45 45 45 45 50 66 66 61 50 50 50 50 50 50 61 61 61 61 56 53 52 52 45 47 45 47 45
 56 57 53 52 52 52 50 47 47 47 47 47 50 50 50 50 50 50 50 50 44 39 39 44 50 50 50 54 54 56 56 56 56 56 56 50 50 50 47 47 52 56 56 56 56 56 50 50 50 50
 50 50 50 44 39 44 58 58 50 50 50 50 50 37 39 39 45 42 43 47 46 46 50 50 50 44 35 35 39 39 42 42 42 42 39 41 41 45 45 44 47 36 40 44 40 40 40 34 29 29
 34 40 37 25 18 23 27 27 23 22 22 27 27 23 19 20 25 34 34 34 32 32 15 9 9 9 9 9 16 25 25 32 32 31 29 25 29 29 29 34 29 34 29 29 26 28 26 25 29 24
 24 29 32 29 32 20 20 20 22 19 25 19 25 21 17 17 25 29 32 32 40 36 28 27 25 17 0 0 0 0

AF LL2336r U -44
AF LL2336f U 67
BS 1 92 LL2336r
BS 93 95 LL2336f
BS 96 96 LL2336r
BS 97 98 LL2336f
BS 99 99 LL2336r
BS 100 105 LL2336f
BS 106 106 LL2336r
BS 107 108 LL2336f
BS 109 135 LL2336r
BS 136 136 LL2336f
BS 137 147 LL2336r
BS 148 153 LL2336f
BS 154 155 LL2336r
BS 156 161 LL2336f
BS 162 178 LL2336r
BS 179 185 LL2336f
BS 186 197 LL2336r
BS 198 201 LL2336f
BS 202 206 LL2336r
BS 207 209 LL2336f
BS 210 230 LL2336r
BS 231 231 LL2336f
BS 232 232 LL2336r
BS 233 239 LL2336f
BS 240 266 LL2336r
BS 267 271 LL2336f
BS 272 279 LL2336r
BS 280 294 LL2336f
BS 295 295 LL2336r
BS 296 308 LL2336f
BS 309 309 LL2336r
BS 310 317 LL2336f
BS 318 327 LL2336r
BS 328 328 LL2336f
BS 329 329 LL2336r
BS 330 351 LL2336f
BS 352 353 LL2336r
BS 354 357 LL2336f
BS 358 359 LL2336r
BS 360 360 LL2336f
BS 361 366 LL2336r
BS 367 373 LL2336f
BS 374 374 LL2336r
BS 375 387 LL2336f
BS 388 400 LL2336r
BS 401 401 LL2336f
BS 402 403 LL2336r
BS 404 413 LL2336f
BS 414 416 LL2336r
BS 417 419 LL2336f
BS 420 436 LL2336r
BS 437 463 LL2336f
BS 464 464 LL2336r
BS 465 467 LL2336f
BS 468 468 LL2336r
BS 469 543 LL2336f
BS 544 544 LL2336r
BS 545 560 LL2336f
BS 561 562 LL2336r
BS 563 567 LL2336f
BS 568 568 LL2336r
BS 569 569 LL2336f
BS 570 571 LL2336r
BS 572 830 LL2336f

RD LL2336r 790 0 0
actxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccacg
cgtccgcggacgcgtgggttttttttttttTTTTTTTTTTTTATTTTTAT
TTTTTAGAAATTGAATTATTAAATTTAGTTTTGCTATAATCTTTATATTT
TCTGGATAATTAAATTCATCAATAAACTCTCATTTTTTAGTTTTGCTATA
ATCTTGATTATGAAAATAGCTCATACACACGACTCATGATCACACAACTC
ACTCAGCTCTGGATCAGTCTGCCTGAACCGTGATTGGCTTTCCTCTTCCC
ATCGAGAATCCTCTGGTCCCATCAGGCATCCTTGGTCCCGGTGGTTGCTG
TTTTGGCTACTCCATGCTGCTCATTGGATGGTTTGAAGGTGGTGTTCCAA
CTTGATGTTGATGGTGATGATTATGATGATTCCCACGCTACGCCCTTTTC
TCTGCCCACCCGCTTTCTCATTCCCTTCATCCCTTGCTCCTCTCCTACTA
TCACTGCCTGCTCAGGCACATTTGTATCCCATTCTCCAGAGAACTCCTCA
GCTTGTTTCTCAATTGGCTGTTGCTCAGATGTCGTGGCATCATCTTCTTC
ATGTTCTACTTCTACATCATGTCCTTTTCTTCCTCGCCCTTGAACCTGTT
TTGGTTCCTTTGTCTTGGTGCCTTGATCGAAACCTTGCAGAGGCAAGTGT
AATTATCTCTTTTCTGAAGATTTTCAGGGAAACCACCAAAGATCCTCTCA
ATACAAGTGTGAATGTCTCTTTTCATAGACTTATTCCcan

QA 81 786 46 789
DS CHROMAT_FILE: LL2336r PHD_FILE: LL2336r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:13 2000

RD LL2336f 765 0 0
cttgatactaAATTTAGTTTTGCTATAATCTTTATATTTTCTGGATAATT
AAATTCATCAatgaaCTCTCATTTTTTAGTTTTGCTATAATCTTGATTAT
GAAAATAGCTCATACACACGACTCATGATCACACAACTCACTCAGCTCTG
GATCAGTCTGCCTGAACCGTGATTGGCTTTCCTCTTCCCATCGAGAATCC
TCTGGTCCCATCAGGCATCCTTGGTCCCGGTGGTTGCTGTTTTGGCTACT
CCATGCTGCTCATTGGATGGTTTGAAGGTGGTGTTCCAACTTGATGTTGA
TGGTGATGATTATGATGATTCCCACGCTACGCCCTTTTCTCTGCCCACCC
GCTTTCTCATTCCCTTCATCCCTTGCTCCTCTCCTACTATCACTGCCTGC
TCAGGCACATTTGTATCCCATTCTCCAGAGAACTCCTCAGCTTGTTTCTC
AATTGGCTGTTGCTCAGATGTCGTGGCATCATCTTCTTCATGTTCTACTT
CTACATCATGTCCTTTTCTTCCTCGCCCTTGAACCTGTTTTGGTTCCTTT
GTCTTGGTGCCTTGATCGAAACCTTGCAGAGGCAAGTGTAATTATCTCTT
TTCTGAAGATTTTCAGGGAAACCACCAAAGATCCTCTCAATACAAGTGTG
AATGTCTCTTTTCATAGACTTATTCCCAAATTGGAAGAaACCTAAATTcC
CAAATCagaaaatCAAAATCCCTAAATTGAGATAATACCCACGaAaTCaa
ACATGATGAagaatn

QA 12 760 9 764
DS CHROMAT_FILE: LL2336f PHD_FILE: LL2336f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:34 2000

CO Contig42 1294 2 18 U
ctttaagggaactgcttttagttaagtttattcgagtttgtaataccaaa
gataaagcaaataccatgttcaagaggtaTATGAACAAACTCAAACACAA
ACATCTAACATAGATTCGGACAAACAAACAAAAACGAAGTGTGTGTGTAA
TAAGCTCTCTCAGACATAGCTTACTCAACTTATAGACGAAACTAAAAGAT
ATGACATTTGACTCCACGCATCATTCTCCTTAATGCAGATAGGTTTCTAG
GAATGTCTACTACACATAGCTTACATATAATATCTTTTAGCCTAGATCAG
GGACAATGAAATGCTCTTCTTCATCATCCTCATCATCAACTCTGATCTCT
AACCTCGGCTTCTTGTATGACACGCTGGACTTCATTGGTCTGTACGAATG
AACATGACCTAAATGCGCAACAGAAAGCTCCGGAACTTGAGCTGCAGGAA
GAGTCTCCTGATTAATCTGATCACTGAAGAAACCCATGTCTGAAAACCAC
TCCAACTCCCCAAGATCAAGCTGTCCTTTCTGCTATACATTCAAACAAAA
AAAAAAACAAGTCAATACAAAAAAAAAACAAAGCATTAAGGATCAAACCA
ACACTTCAATCTCTACCTTATCGGTGAACTCAGGATCAGAGAAGTGGAAG
AAATCATCAACAGCCCAAGGAAGAGGAGAAGCAGAAGAAGGCTGTTGCTG
GCTTGGGATCTCCTTAGCTTTCTGTTGGTTGTTGGAAGGCTCGGACTGAT
GATTCTTGTCTGTTTCTTTACTGCAACTACTTGAGCTCAGAGCCACTTTG
ATCCCAGTGGCTAAGAACCTCTGGTGATTTGCAGATCTAGAGTTAGCCAC
GTGGATAGATTCATCACAGTCCCTGCAAAGCAGAGCTCTATCCTCCACAC
AGAAAATGAAAGCTGCCTTCTCTTGACAGATGTCGCAACGAGGGAACTTG
GTGGAGAGAGAGTTGAGATGGAGGCGTTGGTGCTTGCTGGCGAGTTTGTT
AGCTGCGTGAATCTCCACGTCGCATTTAGGACACAGAGCTGCTTCGTCGG
CGCAACATATCACCGTCGCAGGAGCATTCTCACACACATCACACTGTATC
TTCATCACAGTTCTTGATTCTTGGTTTAATAGATCAAGAACACTTGAATC
TACCTTCTGAGAGTAGCCTAGCAAAAATATAGATGAAGAGAAAGTATTTT
GAGACAGAAATCGAGAGATGTAAACAACAAAAGAGGAACAAGTAACAACT
GTGTGGTGtggaggggaagagaggagagaagatcggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 37 35 35 35 27 27 29 32 35 35 40 40 37 37 43 51 46 46 46 40 40
 42 42 42 37 37 39 37 37 37 40 40 37 40 40 40 40 40 35 35 35 40 40 40 51 51 51 51 51 51 51 51 51 40 39 39 39 39 38 37 56 50 50 44 44 46 40 40 40 38 38
 35 35 35 35 43 43 43 43 45 45 45 43 46 46 41 40 40 38 38 38 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 36 36 36 43 43 36 36 38 56 42 42 41
 41 41 43 45 45 41 41 42 38 36 36 36 35 35 36 36 43 43 36 38 42 42 42 42 46 43 43 43 41 43 43 42 42 42 46 46 42 42 42 46 46 46 42 41 38 38 38 38 40 43
 51 56 50 50 41 38 38 39 43 43 43 43 36 40 43 46 46 43 42 41 35 35 35 38 38 38 56 56 56 56 56 42 42 42 42 41 41 50 42 42 42 46 40 35 35 35 36 40 50 41
 36 36 36 36 35 35 47 50 50 56 51 43 43 43 43 43 40 42 42 50 50 50 44 44 44 50 46 56 50 50 44 44 47 50 50 50 43 43 43 43 43 38 38 43 42 56 45 45 45 38
 38 38 36 36 35 41 45 45 45 41 41 41 44 50 50 37 37 42 42 43 43 43 43 43 38 38 38 38 43 38 38 38 41 42 43 43 56 50 50 41 42 35 32 32 38 38 38 43 56 56
 56 56 56 56 56 45 41 41 41 41 42 50 50 41 38 38 38 38 35 37 42 42 42 42 41 41 41 41 41 41 41 42 41 35 35 38 38 38 41 38 40 38 40 35 38 50 50 50 50 42
 42 42 42 41 41 35 33 40 35 35 35 41 42 46 51 45 51 46 46 35 35 31 35 35 35 30 35 35 37 35 35 35 42 46 42 56 56 56 56 50 56 56 56 56 56 50 50 35 35 35
 40 40 40 40 40 37 40 40 40 56 56 56 56 56 51 51 51 51 45 45 56 46 42 42 56 56 56 56 56 56 56 42 42 42 42 42 46 56 56 56 50 56 46 46 46 42 42 42 47 56
 56 56 56 47 47 47 48 44 37 52 57 57 63 64 64 57 61 55 69 71 82 82 74 88 78 78 71 62 59 61 50 51 58 57 62 62 65 60 60 62 73 73 84 69 73 62 74 65 64 53
 53 59 70 62 54 43 42 42 56 54 63 65 80 69 69 67 67 69 71 71 82 73 67 47 42 40 46 50 60 75 69 63 66 69 74 80 72 72 74 74 71 53 48 54 50 40 43 58 53 52
 59 60 71 73 73 65 54 49 34 34 40 54 48 58 61 61 67 50 41 44 54 50 50 54 46 49 59 64 56 55 55 40 48 48 48 46 46 55 55 55 55 55 55 71 71 71 66 55 55 60
 60 68 63 68 70 70 76 90 83 69 61 57 50 50 47 47 51 51 61 63 65 61 61 58 55 55 58 59 58 62 59 51 48 41 41 40 47 47 55 59 64 63 61 61 61 64 71 67 69 70
 69 58 53 55 72 52 54 59 61 62 61 61 67 61 61 61 61 71 68 71 54 52 52 52 52 53 66 68 69 66 61 60 68 60 60 60 45 56 40 40 45 45 45 45 56 56 51 51 51 51
 51 51 56 51 45 40 40 40 40 45 40 40 51 45 45 51 40 40 45 40 40 40 40 40 40 40 45 45 40 37 37 37 40 40 51 51 56 56 45 45 45 40 40 40 40 40 40 45 40 40
 40 40 40 51 51 51 51 51 51 56 56 56 56 56 56 51 40 40 40 40 40 45 51 56 56 56 45 40 40 40 40 40 40 45 45 45 45 46 46 43 43 56 56 56 56 56 56 51 51 51
 51 51 56 56 56 56 56 56 43 43 43 43 43 43 56 56 51 51 51 51 51 45 45 45 51 45 45 56 56 51 51 45 43 43 43 43 43 45 51 51 51 51 51 51 51 51 51 51 45 45
 45 45 45 51 56 56 56 56 51 45 45 45 45 45 56 56 56 56 56 51 51 45 43 43 43 43 43 43 45 45 45 45 45 51 51 51 51 43 43 43 43 43 43 43 43 43 45 45 43 43
 43 43 43 43 36 36 36 36 36 43 45 45 51 51 51 45 43 43 43 43 43 43 43 43 51 51 51 51 51 51 51 56 51 45 43 43 43 43 43 43 45 45 43 43 43 43 43 36 35 35
 35 35 35 36 43 51 51 51 51 56 56 51 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 45 45 45 45 51 51 56
 56 56 56 56 56 56 51 43 43 43 43 43 51 51 51 51 51 51 56 56 56 56 56 56 43 43 43 43 43 43 45 45 45 51 45 43 43 43 43 43 45 51 51 45 45 51 51 51 51 56
 56 56 56 51 51 51 45 45 45 43 43 35 35 35 35 35 35 43 35 35 35 35 35 38 56 45 45 40 40 40 40 40 40 45 51 51 51 51 51 51 40 40 39 39 39 39 46 46 46 40
 40 40 40 51 40 40 40 40 40 40 51 51 51 51 51 51 51 40 39 39 39 39 39 39 40 40 40 37 40 46 56 56 56 51 51 51 51 51 45 40 40 40 40 40 40 37 51 51 40 37
 46 40 36 35 35 35 35 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2337f U 0
AF LL2337r C 553
BS 1 582 LL2337f
BS 583 583 LL2337r
BS 584 606 LL2337f
BS 607 608 LL2337r
BS 609 612 LL2337f
BS 613 613 LL2337r
BS 614 621 LL2337f
BS 622 626 LL2337r
BS 627 627 LL2337f
BS 628 628 LL2337r
BS 629 629 LL2337f
BS 630 632 LL2337r
BS 633 635 LL2337f
BS 636 644 LL2337r
BS 645 648 LL2337f
BS 649 658 LL2337r
BS 659 661 LL2337f
BS 662 1294 LL2337r

RD LL2337f 789 0 0
nctttaagggaactgcttttagttaagtttattcgagtttgtaataccaa
agataaagcaaataccatgttcaagaggtaTATGAACAAACTCAAACACA
AACATCTAACATAGATTCGGACAAACAAACAAAAACGAAGTGTGTGTGTA
ATAAGCTCTCTCAGACATAGCTTACTCAACTTATAGACGAAACTAAAAGA
TATGACATTTGACTCCACGCATCATTCTCCTTAATGCAGATAGGTTTCTA
GGAATGTCTACTACACATAGCTTACATATAATATCTTTTAGCCTAGATCA
GGGACAATGAAATGCTCTTCTTCATCATCCTCATCATCAACTCTGATCTC
TAACCTCGGCTTCTTGTATGACACGCTGGACTTCATTGGTCTGTACGAAT
GAACATGACCTAAATGCGCAACAGAAAGCTCCGGAACTTGAGCTGCAGGA
AGAGTCTCCTGATTAATCTGATCACTGAAGAAACCCATGTCTGAAAACCA
CTCCAACTCCCCAAGATCAAGCTGTCCTTTCTGCTATACATTCAAACAAA
AAAAAAAACAAGTCAATACAAAAAAAAAACAAAGCATTAAGGATCAAACC
AACACTTCAATCTCTACCTTATCGGTGAACTCAGGATCAGAGAAGTGGAA
GAAATCATCAACAGCCCAAGGAAGAGGAGAAGcacaagAAGGCTGTTGCT
GGCTTGGGATCTCCTTAGCTTTCTGTTGGTTGTTGGAAGGCTCGGACTGA
TGATTCTTGTCTGTTTCTTTACTGCAACTACTTGAGCtc

QA 81 787 2 789
DS CHROMAT_FILE: LL2337f PHD_FILE: LL2337f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:39 2000

RD LL2337r 786 0 0
aaaancaAGTCAATACAAAAAAAAAACAAAGCATTAAGGATCAAACCAAC
ACTTCAATCTCTACCTTATCGGTGAACTCAGGATCAGAGAAGTGGAAGAA
ATCATCAACAGCCCAAGGAAGAGGAGAAGCAGAAGAAGGCTGTTGCTGGC
TTGGGATCTCCTTAGCTTTCTGTTGGTTGTTGGAAGGCTCGGACTGATGA
TTCTTGTCTGTTTCTTTACTGCAACTACTTGAGCTCAGAGCCACTTTGAT
CCCAGTGGCTAAGAACCTCTGGTGATTTGCAGATCTAGAGTTAGCCACGT
GGATAGATTCATCACAGTCCCTGCAAAGCAGAGCTCTATCCTCCACACAG
AAAATGAAAGCTGCCTTCTCTTGACAGATGTCGCAACGAGGGAACTTGGT
GGAGAGAGAGTTGAGATGGAGGCGTTGGTGCTTGCTGGCGAGTTTGTTAG
CTGCGTGAATCTCCACGTCGCATTTAGGACACAGAGCTGCTTCGTCGGCG
CAACATATCACCGTCGCAGGAGCATTCTCACACACATCACACTGTATCTT
CATCACAGTTCTTGATTCTTGGTTTAATAGATCAAGAACACTTGAATCTA
CCTTCTGAGAGTAGCCTAGCAAAAATATAGATGAAGAGAAAGTATTTTGA
GACAGAAATCGAGAGATGTAAACAACAAAAGAGGAACAAGTAACAACTGT
GTGGTGtggaggggaagagaggagagaagatcggacgcgtggxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxat

QA 7 706 1 742
DS CHROMAT_FILE: LL2337r PHD_FILE: LL2337r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:17 2000

CO Contig43 512 2 76 U
tgAGCGAATTGTGTCTATGTCATTCACTTTCAAAAAATTATAGAACAACT
CTTTCAAGAAGAAGAGAAAAAAATCATCTATTAACAAGGTACAAGTCTAT
CTCTAATTAGATGAACAATATGATGGATAATCATCAATGAAGCCGAGAAG
TAACATTGATGAAAGTATCTTCAGGACAAGGGATAGTTAAGCCACCCATT
GGATGATCAAACCCAAACTCTTCTTCAGATCTGCTGAGGAGAGCTTGAAA
TAAGGGCTGGCTCAAGTATGAGATTGGCACCACATATCTCTTCTTCTGGC
TCTCTCCAACGTACACCGCAAGAAACCCTTTTGGTGGTGCCGCCATGGTT
GCTCTTTTGCTTGTAGAAGCTGTTGCTGTTACGGAACGACCAAGAATCTT
TTTTGCACCCAATAAACTTCTAACCAAAGCCATTTGTCTGAAATTTTAAA
CTCTTTGGAAGAGATGTATGAAAAGATTCAAGTTATTGGATTGCTGCTTG
CCGGACGCGTGG

BQ
 0 17 20 27 29 34 34 39 40 40 46 55 55 55 55 55 86 83 85 85 85 85 85 88 88 85 85 85 88 90 90 90 90 90 86 85 85 85 79 85 90 80 85 78 82 82 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 85 86 82 82 79 90 90 85 82 77 80 80 80 90 90 79 79 90 90 90
 90 84 84 84 84 80 80 86 86 86 86 86 86 82 82 82 81 81 86 89 90 90 85 85 85 84 84 83 89 89 89 90 90 90 90 90 90 90 90 85 85 80 88 88 90 90 88 88 78 78
 78 75 86 86 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 88 90 90 90 83 83 86 86 83 83 83 86 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 88 88 88 88 88 88 88 90 90 86 84 86 88 88 86 90 90 90 90 90
 90 90 90 88 88 88 88 88 88 90 90 90 86 86 88 88 88 88 88 90 90 90 90 90 88 88 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 88 88 90
 90 90 90 90 90 90 90 89 86 86 86 86 86 90 86 86 86 81 81 81 79 86 88 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 75 72 72 70 72 72 86 82 90 90 76 75
 75 75 75 75 90 90 90 90 90 90 85 82 86 90 90 85 89 80 80 76 80 85 83 83 83 83 83 83 88 82 82 78 78 78 78 78 78 78 78 78 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 86 86 86 90 90 90 90 90 90 84 84 90 90 74 74 90 85 79 80 90 90 84 90 90 90 90 90 90 88 90 90 90 79 84 85 85 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 66 66 51 51 51 56 56 51 51 60 60 89 89 90 86 86 86 90 86 90 90 90 90 85 85 81 81 81 86 81 81 85 81
 83 83 86 90 90 83 52 55 55 40 51 56

AF LL2340r C -231
AF LL2340f U -2
BS 1 15 LL2340r
BS 16 16 LL2340f
BS 17 41 LL2340r
BS 42 42 LL2340f
BS 43 43 LL2340r
BS 44 44 LL2340f
BS 45 46 LL2340r
BS 47 47 LL2340f
BS 48 71 LL2340r
BS 72 74 LL2340f
BS 75 76 LL2340r
BS 77 80 LL2340f
BS 81 86 LL2340r
BS 87 87 LL2340f
BS 88 90 LL2340r
BS 91 95 LL2340f
BS 96 138 LL2340r
BS 139 139 LL2340f
BS 140 154 LL2340r
BS 155 163 LL2340f
BS 164 181 LL2340r
BS 182 185 LL2340f
BS 186 187 LL2340r
BS 188 189 LL2340f
BS 190 192 LL2340r
BS 193 193 LL2340f
BS 194 197 LL2340r
BS 198 200 LL2340f
BS 201 207 LL2340r
BS 208 208 LL2340f
BS 209 221 LL2340r
BS 222 230 LL2340f
BS 231 237 LL2340r
BS 238 240 LL2340f
BS 241 241 LL2340r
BS 242 242 LL2340f
BS 243 244 LL2340r
BS 245 245 LL2340f
BS 246 247 LL2340r
BS 248 248 LL2340f
BS 249 262 LL2340r
BS 263 269 LL2340f
BS 270 274 LL2340r
BS 275 280 LL2340f
BS 281 283 LL2340r
BS 284 292 LL2340f
BS 293 293 LL2340r
BS 294 297 LL2340f
BS 298 308 LL2340r
BS 309 313 LL2340f
BS 314 314 LL2340r
BS 315 317 LL2340f
BS 318 331 LL2340r
BS 332 336 LL2340f
BS 337 345 LL2340r
BS 346 348 LL2340f
BS 349 356 LL2340r
BS 357 378 LL2340f
BS 379 379 LL2340r
BS 380 390 LL2340f
BS 391 394 LL2340r
BS 395 408 LL2340f
BS 409 410 LL2340r
BS 411 416 LL2340f
BS 417 417 LL2340r
BS 418 424 LL2340f
BS 425 425 LL2340r
BS 426 441 LL2340f
BS 442 442 LL2340r
BS 443 450 LL2340f
BS 451 451 LL2340r
BS 452 480 LL2340f
BS 481 487 LL2340r
BS 488 488 LL2340f
BS 489 506 LL2340r
BS 507 512 LL2340f

RD LL2340r 789 0 2
cgatcggtgcgggcctcttcgctattacgccagctggcgaaagggggatg
tgctgcaaggcgattaagttgggtaacgccagggttttxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxctttttttttttttttttttttttttttntgAGCGAATTGTGTCTAT
GTCATTCACTTTCAAAAAATTATAGAACAACTCTTTCAAGAAGAAGAGAA
AAAAATCATCTATTAACAAGGTACAAGTCTATCTCTAATTAGATGAACAA
TATGATGGATAATCATCAATGAAGCCGAGAAGTAACATTGATGAAAGTAT
CTTCAGGACAAGGGATAGTTAAGCCACCCATTGGATGATCAAACCCAAAC
TCTTCTTCAGATCTGCTGAGGAGAGCTTGAAATAAGGGCTGGCTCAAGTA
TGAGATTGGCACCACATATCTCTTCTTCTGGCTCTCTCCAACGTACACCG
CAAGAAACCCTTTTGGTGGTGCCGCCATGGTTGCTCTTTTGCTTGTAGAA
GCTGTTGCTGTTACGGAACGACCAAGAATCTTTTTTGCACCCAATAAACT
TCTAACCAAAGCCATTTGTCTGAAATTTTAAACTCTTTGGAAGAGATGTA
TGAaacgATTCAAGTTATTGGATTGCTGCTTGCCGGACGCGTGGxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxaag

QA 28 744 233 744
DS CHROMAT_FILE: LL2340r PHD_FILE: LL2340r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:31 2000

RT{
LL2340r chimera phrap 1 88 000919:094547
}

RT{
LL2340r matchElsewhereHighQual phrap 1 88 000919:094547
}

RD LL2340f 787 0 3
cttttagcgaactGTGTCTATGTCATTCACTTTCAAAAAATTATAGAACA
ACTCTTTCAAGAAGAAGAGAAAAAAATCATCTATTAACAAGGTACAAGTC
TATCTCTAATTAGATGAACAATATGATGGATAATCATCAATGAAGCCGAG
AAGTAACATTGATGAAAGTATCTTCAGGACAAGGGATAGTTAAGCCACCC
ATTGGATGATCAAACCCAAACTCTTCTTCAGATCTGCTGAGGAGAGCTTG
AAATAAGGGCTGGCTCAAGTATGAGATTGGCACCACATATCTCTTCTTCT
GGCTCTCTCCAACGTACACCGCAAGAAACCCTTTTGGTGGTGCCGCCATG
GTTGCTCTTTTGCTTGTAGAAGCTGTTGCTGTTACGGAACGACCAAGAAT
CTTTTTTGCACCCAATAAACTTCTAACCAAAGCCATTTGTCTGAAATTTT
AAACTCTTTGGAAGAGATGTATGAAAAGATTCAAGTTATTGGATTGCTGC
TTGCCGGACGCGTGGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxgcctggggtgcctaatgagtga
gctaactcacattaattgcgttgcgctcactggcccgctttcagtcggga
aacctgtcgtgccagctgcattaatgaatcggccacg

QA 14 781 6 515
DS CHROMAT_FILE: LL2340f PHD_FILE: LL2340f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:54 2000

RT{
LL2340f chimera phrap 679 785 000919:094547
}

RT{
LL2340f matchElsewhereHighQual phrap 743 785 000919:094547
}

RT{
LL2340f matchElsewhereHighQual phrap 679 732 000919:094547
}

CO Contig44 1230 2 30 U
ctttatgggaaacaaaaaaatatttatatatcatagacctagtgactatt
cccctgtcttctcgtctccgaatctctaataactaacatatcttcgtctc
tctttgtactttgtaatatgagactctgacttgaacatccaatctaacac
acaacatttaaaagccaatattgatttgccagtcttgtcttctctttctc
atatatttggcatactatcattatagtcttgttcaactgtgtcattagcc
tggtgagttggttgccgaacccttttctctttctctctcagctgctgctt
catcctcagttttcttggcaaaccggctctcactatctccttgcccTTTt
caTTTgcatgcttgtgtctTGACTCATGAagaTATGgctTtctGTTGATA
AGTTTTCTTTctagctcggccttgtgcgcgtgctTTttctccgccttata
attccgtggtacttgtTTcgcATTCACaTAAACAGGCTCTTGTGTCATGT
CAAGCGGTAGTGCTGTTCTTTCACCAGGCATTCCAGGATATGGACGAAAC
CCTTGCAATTGCTGATGTCCATATGCTCCCACCATTCCCCCATAATATGG
ATCCTGATATGGATTTGGGACACAAGCAATGTAGTGTCCAACAAGCTCTG
GTGGTTGTACAAGTTGCTGCTGATCATGCACGTTACCCACAGAAGCAGCA
GGATCATTCCCTTCCACTCCATGGTTATCTGAAGGGGACGAAGTAGCAGC
TTGTGTATCCTTCCAAGCGCCATCGTCTCCAGACGCTGAGTGAACATCGT
TTGATTCTAAAGAGGAGGACTTTGAAAGAACCACAGAAGGTATCTCTTGA
GGAACGACACCAAAAGAGTTATTTTTTTTCCACCATGGCTCCTCTGCATA
CATCATTGGCTGCTCACCAGAATGGTGATTGACTTCCACTTCATTCCCAC
TTCCCTTGGATTGCATCTCTTCAAAACAACACCAGAGGATATTCACGAGG
GAGTTTTTTGCAATCGTCTTCGTGTTCCTATGATGATGACTTAAAGACCC
CTGAAGTTATGTAATCGATGGAGCTCAGAGTGAGACAAAACAAAAAGAAT
CAGAATTTGAACAGAGCCAGAGAAGAATTTGGAGAAGAGAGACGAATACG
ATTGGGCAGAAGAAACCCTAATTTTTGGGGATTTTTGTttctcAAaattg
ttttttctttgtatttttgcggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 15 14 18 21 22 20 17
 17 15 29 27 21 15 12 11 11 12 13 15 17 14 15 15 17 17 18 23 23 25 25 22 22 24 24 20 25 14 14 14 25 22 22 22 19 19 16 27 17 15 15 21 21 26 30 30 28 30
 22 22 22 33 36 24 30 30 42 24 19 19 15 15 18 18 16 16 14 12 11 14 10 8 8 8 11 11 17 11 10 10 10 11 23 23 18 15 15 15 19 17 15 18 17 17 17 11 11 11
 11 10 15 12 14 11 13 14 14 13 15 10 8 10 13 18 24 21 18 18 18 24 24 25 25 23 22 19 21 34 37 38 49 45 50 42 48 49 52 39 46 47 51 54 53 61 54 56 50 53
 50 45 39 47 48 51 48 48 46 46 46 50 49 54 50 40 40 50 50 53 44 52 51 44 44 36 40 43 43 42 44 47 47 44 53 46 52 55 57 60 58 50 48 54 55 53 47 49 49 53
 54 49 48 49 54 54 61 57 55 54 47 59 43 49 44 47 47 49 50 65 64 63 63 59 61 55 55 55 63 44 52 52 55 58 68 68 68 72 77 79 68 63 62 62 59 60 60 55 49 51
 45 52 46 51 49 55 47 55 56 52 47 47 50 49 40 40 40 40 39 52 52 56 65 76 55 55 40 46 40 40 37 37 52 50 50 50 55 52 54 49 49 49 61 60 55 57 57 67 63 68
 60 67 62 58 52 50 57 57 60 68 75 78 73 62 60 67 66 60 61 65 64 80 78 80 85 83 70 73 54 52 52 59 59 50 55 59 64 73 73 65 75 63 63 55 60 58 58 58 62 62
 67 75 80 72 72 75 71 74 71 71 68 66 66 66 66 70 71 71 71 71 75 75 74 66 67 66 66 67 74 73 71 71 71 71 67 66 70 73 70 56 56 55 55 55 55 62 64 65 59 67
 54 64 64 51 51 51 45 45 45 51 51 51 56 45 43 43 68 70 68 63 63 68 64 66 70 62 60 51 58 63 66 62 59 60 61 45 45 43 43 43 43 43 51 56 56 45 45 45 45 43
 43 51 51 51 51 51 51 51 45 45 45 51 45 45 45 45 45 45 51 51 45 45 51 51 51 51 56 56 56 56 56 56 56 56 56 51 56 45 45 45 45 45 45 51 51 51 51 51 56 56
 51 45 43 43 43 40 40 41 56 56 56 56 56 56 51 45 45 45 45 45 56 56 56 56 56 56 56 56 56 56 56 56 56 56 51 45 45 45 45 45 45 51 51 45 51 51 51 51 51 56
 56 56 56 56 51 43 43 43 43 43 43 51 56 56 56 56 56 51 51 51 51 51 45 45 45 45 45 51 51 51 51 51 51 51 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56
 56 56 56 56 56 56 51 51 51 45 43 43 43 43 43 43 45 45 51 56 56 56 56 56 56 56 56 56 56 56 56 45 43 43 43 43 43 43 45 56 56 56 56 51 51 51 51 51 51 45
 43 43 43 43 43 46 56 51 51 45 45 45 43 43 43 43 43 43 43 43 43 43 43 43 51 56 56 56 56 56 56 56 56 56 51 51 51 51 51 51 51 51 45 45 45 51 51 51 56 56
 56 56 45 45 45 43 43 43 51 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43 45 45 43 43 43 43 43 43 43 45 45 45 51 51 51 51 51 51 51 56 51 51 51 43 43 43
 43 43 43 45 51 51 43 40 40 40 40 40 39 39 39 39 39 39 40 51 51 51 51 51 51 51 51 40 40 46 46 46 46 51 51 51 51 51 51 51 40 40 40 40 40 39 39 39 39 39
 39 39 46 40 39 39 39 39 39 51 51 51 51 51 51 51 35 35 35 35 35 40 51 56 56 56 56 56 56 56 56 51 51 42 40 36 39 24 16 13 11 10 12 24 24 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2343f U 0
AF LL2343r C 478
BS 1 477 LL2343f
BS 478 479 LL2343r
BS 480 484 LL2343f
BS 485 485 LL2343r
BS 486 486 LL2343f
BS 487 489 LL2343r
BS 490 491 LL2343f
BS 492 500 LL2343r
BS 501 505 LL2343f
BS 506 512 LL2343r
BS 513 514 LL2343f
BS 515 515 LL2343r
BS 516 516 LL2343f
BS 517 519 LL2343r
BS 520 531 LL2343f
BS 532 535 LL2343r
BS 536 556 LL2343f
BS 557 557 LL2343r
BS 558 558 LL2343f
BS 559 581 LL2343r
BS 582 582 LL2343f
BS 583 591 LL2343r
BS 592 600 LL2343f
BS 601 619 LL2343r
BS 620 622 LL2343f
BS 623 750 LL2343r
BS 751 753 LL2343f
BS 754 766 LL2343r
BS 767 785 LL2343f
BS 786 1230 LL2343r

RD LL2343f 809 0 0
nctttatgggaaacaaaaaaatatttatatatcatagacctagtgactat
tcccctgtcttctcgtctccgaatctctaataactaacatatcttcgtct
ctctttgtactttgtaatatgagactctgacttgaacatccaatctaaca
cacaacatttaaaagccaatattgatttgccagtcttgtcttctctttct
catatatttggcatactatcattatagtcttgttcaactgtgtcattagc
ctggtgagttggttgccgaacccttttctctttctctctcagctgctgct
tcatcctcagttttcttggcaaaccggctctcactatctccttgcccTTT
tcaTTTgcatgcttgtgtctTGACTCATGAagaTATGgctTtctGTTGAT
AAGTTTTCTTTctagctcggccttgtgcgcgtgctTTttctccgccttat
aattccgtggtacttgtTTcgcATTCACatAAACAGGCTCTTGTGTCATG
TCAAGCGGTAGTGCTGTTCTTTCACCAGGCATTCCAGGATATGGACGAAA
CCCTTGCAATTGCTGATGTCCATATGCTCCCACCATTCCCCCATAATATG
GATCCTGATATGGATTTGGGACACAAGCAacgtAGTGTCCAACAAGCTCT
GGTGGTTGTACAAGTTGCTGCTGATCATGCACGTTACCCACAGAAGCAGC
AGGATCATTCCCTTCCACTCCATGGTTATCTGAAGGGGACGAAGTAGCAG
CTTGTGTattctTCCAAGCGCCATCGTCTCCAGACGCTGAgcgAACATCg
cttgATTct

QA 343 751 2 809
DS CHROMAT_FILE: LL2343f PHD_FILE: LL2343f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:08 2000

RD LL2343r 798 0 0
aTAAACAGGCTCTTGTGTCATGTCAAGCGGTAGTGCTGTTCTTTCACCAG
GCATTCCAGGATATGGACGAAACCCTTGCAATTGCTGATGTCCATATGCT
CCCACCATTCCCCCATAATATGGATCCTGATATGGATTTGGGACACAAGC
AATGTAGTGTCCAACAAGCTCTGGTGGTTGTACAAGTTGCTGCTGATCAT
GCACGTTACCCACAGAAGCAGCAGGATCATTCCCTTCCACTCCATGGTTA
TCTGAAGGGGACGAAGTAGCAGCTTGTGTATCCTTCCAAGCGCCATCGTC
TCCAGACGCTGAGTGAACATCGTTTGATTCTAAAGAGGAGGACTTTGAAA
GAACCACAGAAGGTATCTCTTGAGGAACGACACCAAAAGAGTTATTTTTT
TTCCACCATGGCTCCTCTGCATACATCATTGGCTGCTCACCAGAATGGTG
ATTGACTTCCACTTCATTCCCACTTCCCTTGGATTGCATCTCTTCAAAAC
AACACCAGAGGATATTCACGAGGGAGTTTTTTGCAATCGTCTTCGTGTTC
CTATGATGATGACTTAAAGACCCCTGAAGTTATGTAATCGATGGAGCTCA
GAGTGAGACAAAACAAAAAGAATCAGAATTTGAACAGAGCCAGAGAAGAA
TTTGGAGAAGAGAGACGAATACGATTGGGCAGAAGAAACCCTAATTTTTG
GGGATTTTTGTttctcAAaattgttttttctttgtatttttgcggacgcg
tggxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxtgtccagaatt

QA 1 718 1 753
DS CHROMAT_FILE: LL2343r PHD_FILE: LL2343r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:45 2000

CO Contig45 867 2 66 U
ctgtaaggcgtccatctacttcaacagacaaatgtattacaaaatagctt
caagaaaatatttataacattttgaagattCCAAAATATTTTTTTTAAAT
AGCAAAAAAGACAAATGCAGCAAAAGATTTAACAAGAAAAACTTCACAAA
CTTTGATCCTGGCCAATCTCTTCCCCCCTTTCTCTATGTTCCTTGGGGAT
GCAGCAGTAGCAGTCTTTGACTATTGGAAAGGTTGTTAGTTGGCGAAAAC
GTTGAGCCTAACGCGAGCAGTGACATCAGGGTGAAGTTTGAGTTCGGCTA
TGTATTCTCCCGTTTCACGGATCTCCGGAAGAGAGACAAGGCGCTTGTCT
ATATCCCTTTGGAGCTGCGCCTTGATGATGTCAACAAGGTCTTGTGCTGT
GACAGATCCAAATATTTGTTTGCCCTTACCGCCCTTGCGTTTAACCTTGA
AAGCCCCAACGGTTTCGAATACGGTAGCCAATTGTAGCGCCTCTTCTTTC
ACCCTTTGCTTTTCTGCCTCTATCCTTTCGTTTTCCATCTTCATTTCCTT
GAGCAGAAGCGGAGTCATGAGCTGAGCCTTTCCAGTGGGCAAGAGGAAGT
TTCTGAAGAAACCGGCTTTCACGTCCAGTAATTGCCCTTGCTTGCCCAAG
TCCAACACATCCTCTTTCAAGATTACCTTGCGGAGTTTCTTGGCTTTCTT
CTGGGCAACAACCTCCAAAGTAGACCTTCGCTGGGATACTTTTAGTGTTT
CATTTCCGACGACATTGAAGGTGTGAGACGAACAAAGCGAGGAGCTCCAC
GAGAGTGACAAAGACGAAGAAGCCATTggcGAAgcttattcagtcccacg
cgtccgcggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 39 39 40 37 37 37 37 40 37 56 56 56 35 35 35 35 35 34 35
 35 35 35 40 46 51 51 51 40 40 40 40 35 35 35 35 35 35 35 35 40 40 55 61 61 71 71 54 55 55 55 60 51 65 65 80 83 80 81 67 67 72 62 62 65 72 71 72 65 79
 76 74 58 63 65 67 64 62 62 58 55 55 55 55 60 72 67 72 74 84 84 88 90 90 90 80 80 79 77 70 67 72 77 85 85 77 77 72 65 65 65 65 65 76 83 88 85 80 64 66
 66 68 66 66 73 79 69 74 80 80 80 86 78 80 79 77 77 77 79 79 75 90 72 68 68 78 78 83 83 85 88 82 68 67 64 61 61 69 74 72 77 72 73 72 77 77 77 75 75 75
 75 75 68 81 81 83 77 77 85 83 77 79 80 78 78 78 80 82 85 85 83 83 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 84 84 83 83 83 89 87 87
 83 90 90 79 77 77 90 90 85 81 81 90 85 85 89 89 87 87 89 89 87 90 90 90 90 70 68 70 70 77 77 90 90 90 90 90 90 89 83 82 71 71 75 75 76 76 83 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 80 80 78 78 80 83 85 85 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 87 90 83 88 90 90 90 90 90 90 85 85 85 85 85 85 90 90 80 80 80 83 78 78 88 82 82 85 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 85 88 88 90 90 90 90 90 90 90 90 85 85 85 87 88 88 90 90 90 90 90 90 90 88 82 82 79 79 79 84 87 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 83 83 83 83 76 78 90 90 90 90 89 90 83 83 81 83 83 83 87 87 86 83 90 90 86 84 89 85 85 90 90 90 90 90 90 90 90 90 89 82 90 90 83
 76 76 85 79 77 85 83 75 69 66 73 76 74 76 85 90 84 90 90 75 72 63 63 61 58 65 77 83 83 75 80 70 80 76 72 78 80 89 89 85 85 80 84 72 70 70 82 75 83 83
 68 65 73 76 78 83 83 75 85 85 85 85 90 90 90 89 88 83 76 76 85 73 73 74 75 80 75 78 78 76 72 70 70 83 83 72 71 76 80 77 72 63 63 68 63 63 70 74 75 83
 90 83 68 68 65 65 61 61 79 72 64 67 72 66 63 68 68 57 67 67 67 59 53 52 59 64 72 69 83 83 83 90 85 80 72 72 70 75 75 78 79 77 75 75 68 61 55 55 55 55
 60 72 74 66 62 62 58 60 61 61 62 65 69 83 90 83 68 63 60 55 55 52 52 52 54 40 40 40 40 40 40 45 43 40 35 35 35 35 35 35 35 35 35 39 39 39 46 45 45 45
 45 45 45 35 35 35 35 37 37 46 46 42 42 42 46 46 46 46 40 40 40 40 40 40 40 29 21 15 15 15 21 21 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2345f U 1
AF LL2345r C 121
BS 1 169 LL2345f
BS 170 173 LL2345r
BS 174 221 LL2345f
BS 222 222 LL2345r
BS 223 272 LL2345f
BS 273 276 LL2345r
BS 277 297 LL2345f
BS 298 300 LL2345r
BS 301 306 LL2345f
BS 307 308 LL2345r
BS 309 314 LL2345f
BS 315 325 LL2345r
BS 326 331 LL2345f
BS 332 338 LL2345r
BS 339 342 LL2345f
BS 343 346 LL2345r
BS 347 347 LL2345f
BS 348 359 LL2345r
BS 360 366 LL2345f
BS 367 367 LL2345r
BS 368 370 LL2345f
BS 371 377 LL2345r
BS 378 391 LL2345f
BS 392 400 LL2345r
BS 401 406 LL2345f
BS 407 416 LL2345r
BS 417 417 LL2345f
BS 418 418 LL2345r
BS 419 419 LL2345f
BS 420 427 LL2345r
BS 428 445 LL2345f
BS 446 448 LL2345r
BS 449 457 LL2345f
BS 458 475 LL2345r
BS 476 478 LL2345f
BS 479 482 LL2345r
BS 483 486 LL2345f
BS 487 493 LL2345r
BS 494 496 LL2345f
BS 497 519 LL2345r
BS 520 521 LL2345f
BS 522 525 LL2345r
BS 526 532 LL2345f
BS 533 549 LL2345r
BS 550 557 LL2345f
BS 558 561 LL2345r
BS 562 566 LL2345f
BS 567 567 LL2345r
BS 568 569 LL2345f
BS 570 575 LL2345r
BS 576 577 LL2345f
BS 578 581 LL2345r
BS 582 584 LL2345f
BS 585 586 LL2345r
BS 587 592 LL2345f
BS 593 594 LL2345r
BS 595 595 LL2345f
BS 596 596 LL2345r
BS 597 599 LL2345f
BS 600 637 LL2345r
BS 638 639 LL2345f
BS 640 677 LL2345r
BS 678 679 LL2345f
BS 680 731 LL2345r
BS 732 732 LL2345f
BS 733 867 LL2345r

RD LL2345f 777 0 0
ctgtaaggcgtccatctacttcaacagacaaatgtattacaaaatagctt
caagaaaatatttataacattttgaagattCCAAAATATTTTTTTTAAAT
AGCAAAAAAGACAAATGCAGCAAAAGATTTAACAAGAAAAACTTCACAAA
CTTTGATCCTGGCCAATCTCTTCCCCCCTTTCTCTATGTTCCTTGGGGAT
GCAGCAGTAGCAGTCTTTGACTATTGGAAAGGTTGTTAGTTGGCGAAAAC
GTTGAGCCTAACGCGAGCAGTGACATCAGGGTGAAGTTTGAGTTCGGCTA
TGTATTCTCCCGTTTCACGGATCTCCGGAAGAGAGACAAGGCGCTTGTCT
ATATCCCTTTGGAGCTGCGCCTTGATGATGTCAACAAGGTCTTGTGCTGT
GACAGATCCAAATATTTGTTTGCCCTTACCGCCCTTGCGTTTAACCTTGA
AAGCCCCAACGGTTTCGAATACGGTAGCCAATTGTAGCGCCTCTTCTTTC
ACCCTTTGCTTTTCTGCCTCTATCCTTTCGTTTTCCATCTTCATTTCCTT
GAGCAGAAGCGGAGTCATGAGCTGAGCCTTTCCAGTGGGCAAGAGGAAGT
TTCTGAAGAAACCGGCTTTCACGTCCAGTAATTGCCCTTGCTTGCCCAAG
TCCAACACATCCTCTTTCAAGATTACCTTGCGGAGTTTCTTGGCTTTCTT
CTGGGCAACAACCTCCAAAGTAGACCTTCGCTGGGATACTTTTAGTGTTT
CATTTCCGACGACATTGAAGGTGTGAg

QA 81 777 1 777
DS CHROMAT_FILE: LL2345f PHD_FILE: LL2345f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:39 2000

RD LL2345r 793 0 0
CAAAAGATTTAACAAGAAAAACTTCACAAACTTTGATCCTGGCCAATCTC
TTCCCCCCTTTCTCTATGTTCCTTGGGGATGCAGCAGTAGCAGTCTTTGA
CTATTGGAAAGGTTGTTAGTTGGCGAAAACGTTGAGCCTAACGCGAGCAG
TGACATCAGGGTGAAGTTTGAGTTCGGCTATGTATTCTCCCGTTTCACGG
ATCTCCGGAAGAGAGACAAGGCGCTTGTCTATATCCCTTTGGAGCTGCGC
CTTGATGATGTCAACAAGGTCTTGTGCTGTGACAGATCCAAATATTTGTT
TGCCCTTACCGCCCTTGCGTTTAACCTTGAAAGCCCCAACGGTTTCGAAT
ACGGTAGCCAATTGTAGCGCCTCTTCTTTCACCCTTTGCTTTTCTGCCTC
TATCCTTTCGTTTTCCATCTTCATTTCCTTGAGCAGAAGCGGAGTCATGA
GCTGAGCCTTTCCAGTGGGCAAGAGGAAGTTTCTGAAGAAACCGGCTTTC
ACGTCCAGTAATTGCCCTTGCTTGCCCAAGTCCAACACATCCTCTTTCAA
GATTACCTTGCGGAGTTTCTTGGCTTTCTTCTGGGCAACAACCTCCAAAG
TAGACCTTCGCTGGGATACTTTTAGTGTTTCATTTCCGACGACATTGAAG
GTGTGAGACGAACAAAGCGAGGAGCTCCACGAGAGTGACAAAGACGAAGA
AGCCATTggcGAAgcttattcagtcccacgcgtccgcggacgcgtggxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxatt

QA 1 713 1 747
DS CHROMAT_FILE: LL2345r PHD_FILE: LL2345r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:18 2000

CO Contig46 1226 2 44 U
cttttggtaacgaagaggctacagatagatgaagcttgccaagaaaaagc
ttatacaatagataaacgtgtggactgacTCTGAATTTGCTGAGTTCTAC
AGAGCGATTGACGCGGCAAGTGCTTTCATACATTaGcTgCTTTGAGGGAA
AGAAAATCagaAATCTTGCTGgtgagaAATCTGGTTGTATCTTGTTCTCA
GGGCTTTCCAACATCGAGATTGAAGTAACACCCGAGAGGACAAGCAGAGT
TTTACAACCACCATTCTGCCCAAACAAAATATCAGTGTCCAATCTATCAC
CCACCATGCATATCTGTGACTTTTCGATTCCAAATTTGTCTGCCAAATAG
TCCATCATAAAAGTTGAGGGTTTTCCAACTACAAGAggttcACgttGACA
GGATCCAACAAGAGCACCAACCATAGAGCCACCACCTGCCCATTCTTGAG
CATCGGTAAGGTGGGTGACAGCATCTCGgttTgTAGCAATGAACAGACAG
CCCGGGTTTTCGCGGATACAGAGAGTTCCATACTGAATTTTGTAGTAGTT
GAAATAGCGGTCAAATCCAACCACCACAGCTCCCACATCATTATCATGCT
CCATTAGAAACCCTGGCTTCAGTTCAATCTGTTTTTTACCATCATCCGGA
CCTCCAAGATACTGGAAACCAGCAAGGTCGAGCTCCTTCAAGATACCCTC
CTCACCAATCACATAGACCTTCTTATCTTTGGGGAAATTAATAGACTGCA
AGTATGCAGCTGCAGCAAAAGAAGAAGCAAATATTTCCTCCTCGTTAACA
TTCAGGCCAAGAGTCTCAAACTTTTTGCCATATTGTTTCCTAGATTTTGT
TGAGTTGTTTGTCACAAAAACCAACCTCTTTCCCTTGGCACGGAGCATAT
CAAGAGTCTCTGGAACTCCCTCAATCAATTTATCTCCCTTCCAAATGACT
CCGTCACAGTCGAAGATAAAAGTTTCAACGGAATCGATGAGCTGATCGGC
GTTCTCGAGCTGCTGTGCCGCCATAGCTCTCGGTGTCATATTGGGAGTCA
TCACGCGGAGAGGCTTATGATCGATTCTGCGAATGATGCCACCGGAGAAG
GAGGAAGAACGAAATCCTGAGAAAGCCTTGACGGAGAAGAAAGGTTTGGA
GTTTGGTAAGAGAGAAACTGAGGAAGAAGAAACAagcgctgttctgttca
gcatcttttcttctccggacgcgtgg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 35 35 39 37 33 42 32 29 29 35 35 35 35 37 37 35 35 35 35 32
 32 35 35 32 32 32 32 35 37 35 32 35 32 32 32 29 29 29 29 29 29 29 35 32 35 32 32 35 35 35 35 35 24 29 17 21 15 28 19 27 27 28 39 35 35 35 35 35 35 35
 32 37 37 37 37 44 27 27 15 13 13 20 24 35 35 32 35 35 32 25 21 10 10 9 9 9 10 31 23 32 32 33 33 35 37 33 35 35 36 36 36 36 36 32 35 35 38 38 38 32
 35 32 32 32 36 36 35 41 41 35 42 42 35 35 30 30 29 35 37 39 39 42 35 29 26 26 26 26 26 37 35 41 31 33 27 27 27 33 29 35 32 30 30 31 28 21 21 21 37 37
 46 46 42 42 39 35 35 35 35 35 35 36 42 42 42 35 35 35 35 37 37 35 32 32 32 32 32 35 37 42 42 35 33 28 28 26 26 29 32 33 33 37 42 42 42 43 40 40 40 40
 37 37 37 37 37 37 40 40 40 40 40 35 32 32 32 32 29 35 35 35 35 35 42 36 35 33 30 36 42 44 44 44 44 44 44 35 38 36 35 35 35 35 35 35 32 37 30 33 26 28
 33 42 42 42 47 47 47 47 47 47 42 42 37 37 42 42 34 34 34 34 34 35 35 34 34 34 33 33 33 33 33 29 32 33 33 23 19 15 10 8 17 20 23 18 19 19 23 25 37 40
 40 37 37 37 37 42 37 33 42 30 30 30 30 30 42 42 37 42 32 29 29 35 35 35 33 35 35 42 35 38 38 38 38 38 42 42 42 42 42 44 42 44 44 44 44 44 48 44 47 35
 33 35 33 33 29 26 26 26 33 31 23 22 22 23 36 33 40 40 40 35 35 29 29 24 34 34 39 27 12 9 9 21 14 29 35 40 52 64 60 50 54 41 41 41 58 46 50 50 66 61
 62 62 66 66 63 69 69 67 59 55 56 56 55 50 50 58 58 61 62 66 73 75 67 60 59 55 58 62 62 66 75 80 68 55 59 59 44 44 44 37 42 33 30 29 35 42 44 49 44 58
 58 58 59 52 52 43 52 52 61 55 54 46 51 58 71 71 72 74 69 69 69 67 63 77 72 72 66 71 73 80 78 86 83 88 85 77 77 79 80 88 73 73 62 65 64 79 72 72 80 63
 54 58 56 51 51 46 52 45 47 54 55 58 52 50 44 47 52 48 51 46 50 50 48 48 56 55 61 64 63 63 58 55 55 58 53 54 54 54 61 61 69 60 60 68 70 58 73 43 40 46
 46 46 44 40 41 54 65 68 73 67 67 55 40 40 37 40 37 45 48 49 43 47 58 53 49 44 44 44 54 57 63 59 48 47 40 40 44 47 47 58 59 58 58 66 70 75 73 71 69 73
 72 68 74 83 75 80 65 64 70 78 75 80 71 70 52 50 47 55 47 47 47 50 49 48 57 70 70 72 75 75 71 72 77 77 74 71 55 56 56 58 53 53 56 61 56 60 42 40 40 45
 45 45 45 45 42 56 53 51 48 48 52 53 57 37 37 40 45 51 56 56 56 56 56 45 40 40 40 37 40 51 51 51 51 51 45 51 51 51 51 45 40 40 40 40 40 40 51 51 51 56
 56 51 51 51 51 51 51 56 56 45 40 40 40 40 40 51 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 51 51 51 51 51 51 56 56 51 51 51 51
 40 40 45 45 45 45 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 51 51 51 56 56 56 56 56 56 56 56 56 56 56 56 51 51 51 45 45 45 45 45 45 56 56 56
 56 56 45 43 43 43 43 43 43 51 51 51 56 56 56 56 56 56 51 51 51 51 51 51 51 51 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 41 43 41 45 45 43
 43 43 43 43 43 43 43 43 43 43 43 43 51 51 45 45 45 51 43 43 43 43 43 43 43 56 45 45 43 43 43 43 43 43 45 45 43 43 43 43 43 43 43 51 45 45 43 43 43 43
 43 43 43 43 51 43 43 43 43 43 43 45 45 45 43 43 43 43 43 43 43 43 43 43 43 43 43 45 45 45 45 45 45 45 56 56 51 51 51 51 51 51 56 45 43 43 43 43 43 51
 56 45 39 39 39 39 39 40 45 45 45 45 45 45 51 51 51 51 51 39 39 39 39 39 39 45 35 34 34 34 34 34 39 51 51 40 40 40 40 40 40 51 40 40 40 40 40 40 40 40
 40 40 40 40 51 51 51 40 40 40 40 40 40 51 56 51 40 40 40 40 40 39 40 40 40 40 39 46 46 40 40 40 45 45 45 51 51 51 51 51 51 51 51 51 51 51 56 45 45 45
 45 35 35 39 39 39 39 39 40 46 51 51 51 51 51 51 51 51 51 51 56 56 51 51 46 46 46 46 46 40 40 32 27 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF LL2347f U 0
AF LL2347r C 473
BS 1 474 LL2347f
BS 475 479 LL2347r
BS 480 482 LL2347f
BS 483 485 LL2347r
BS 486 521 LL2347f
BS 522 522 LL2347r
BS 523 523 LL2347f
BS 524 524 LL2347r
BS 525 530 LL2347f
BS 531 532 LL2347r
BS 533 544 LL2347f
BS 545 549 LL2347r
BS 550 555 LL2347f
BS 556 556 LL2347r
BS 557 561 LL2347f
BS 562 562 LL2347r
BS 563 563 LL2347f
BS 564 564 LL2347r
BS 565 572 LL2347f
BS 573 576 LL2347r
BS 577 579 LL2347f
BS 580 589 LL2347r
BS 590 594 LL2347f
BS 595 602 LL2347r
BS 603 606 LL2347f
BS 607 610 LL2347r
BS 611 611 LL2347f
BS 612 612 LL2347r
BS 613 613 LL2347f
BS 614 635 LL2347r
BS 636 639 LL2347f
BS 640 646 LL2347r
BS 647 647 LL2347f
BS 648 650 LL2347r
BS 651 652 LL2347f
BS 653 657 LL2347r
BS 658 659 LL2347f
BS 660 667 LL2347r
BS 668 668 LL2347f
BS 669 740 LL2347r
BS 741 746 LL2347f
BS 747 755 LL2347r
BS 756 763 LL2347f
BS 764 1226 LL2347r

RD LL2347f 795 0 0
ncttttggtaacgaagaggctacagatagatgaagcttgccaagaaaaag
cttatacaatagataaacgtgtggactgacTCTGAATTTGCTGAGTTCTA
CAGAGCGATTGACGCGGCAAGTGCTTTCATACATTaGcTgCTTTGAGGGA
AAGAAAATCagaAATCTTGCTGgtgagaAATCTGGTTGTATCTTGTTCTC
AGGGCTTTCCAACATCGAGATTGAAGTAACACCCGAGAGGACAAGCAGAG
TTTTACAACCACCATTCTGCCCAAACAAAATATCAGTGTCCAATCTATCA
CCCACCATGCATATCTGTGACTTTTCGATTCCAAATTTGTCTGCCAAATA
GTCCATCATAAAAGTTGAGGGTTTTCCAACTACAAGAggttcACgttGAC
AGGATCCAACAAGAGCACCAACCATAGAGCCACCACCTGCCCATTCTTGA
GCATCGGTAAGGTGGGTGACAGCATCTcGgttTgTAGCAATGAACAGACA
GCCCGGGTTTTCGCGGATACAGAGAGTTCCATACTGAATTTTGTAGTAGT
TGAAATAGCGGTCAAATCCAACCACCACAGCTCCCACATCATTATCATGC
TCCATTAGAAACCCTGGCTTCAGTTCAATCTGTTTTTTACCATCATCCGG
ACCTCCAAGATACTGGAAACCAGCAAGGTCGAGCTCCTTCAAGATACCCT
CCTCACCAATCACATAGACCTTCTTATCTTTGGGGAAATTAATAGACTGc
angtATGCAGCTGCAGcacacgacgaagcacatattccctcctcg

QA 81 741 2 795
DS CHROMAT_FILE: LL2347f PHD_FILE: LL2347f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:50 2000

RD LL2347r 799 0 0
atCTCGgtntgTAGCAATGAACAGACAGCCCGGGTTTTCGCGGATACAGA
GAGTTCCATACTGAatttgntaGTAGTTGAAATAGCGGTCAAATCCAACC
ACCACAGCTCCCACATCATTATCATGCTCCATTAGAAACCCTGGCTTCAG
TTCAATCTGTTTTTTACCATCATCCGGACCTCCAAGATACTGGAAACCAG
CAAGGTCGAGCTCCTTCAAGATACCCTCCTCACCAATCACATAGACCTTC
TTATCTTTGGGGAAATTAATAGACTGCAAGTATGCAGCTGCAGCAAAAGA
AGAAGCAAATATTTCCTCCTCGTTAACATTCAGGCCAAGAGTCTCAAACT
TTTTGCCATATTGTTTCCTAGATTTTGTTGAGTTGTTTGTCACAAAAACC
AACCTCTTTCCCTTGGCACGGAGCATATCAAGAGTCTCTGGAACTCCCTC
AATCAATTTATCTCCCTTCCAAATGACTCCGTCACAGTCGAAGATAAAAG
TTTCAACGGAATCGATGAGCTGATCGGCGTTCTCGAGCTGCTGTGCCGCC
ATAGCTCTCGGTGTCATATTGGGAGTCATCACGCGGAGAGGCTTATGATC
GATTCTGCGAATGATGCCACCGGAGAAGGAGGAAGAACGAAATCCTGAGA
AAGCCTTGACGGAGAAGAAAGGTTTGGAGTTTGGTAAGAGAGAAACTGAG
GAAGAAGAAACAagcgctgttctgttcagcatcttttcttctccggacgc
gtggxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxagt

QA 11 719 1 754
DS CHROMAT_FILE: LL2347r PHD_FILE: LL2347r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:27 2000

CO Contig47 757 2 91 U
tgaatttaaATCTCAAGTTGATGTCATGAAGTCACCAATATACATTCTCA
GTTTACAATCACAAAGCTTAGTTTATGACTTTTTGGTATACAAAAAAACT
ATATAAAAATGTCACTGAAGACCATACACAAGCAGAGCTCCAACAGCTCC
AAGACCGGCCAATAAGCCAACAATAACACCGATCGGAGGCAGTCCTCCTC
CTATGGCCTTCCCTGTGTTCACATCATACCTCGCAAACCTTTTCTTTGGT
GCTATACATTGTGGACATACGTATGTATCCGGCTGTTCATCAAAAGGCTT
TGGTAAAGTGTATATGAATCCACAATCAAGACAAATGTGAGTAGCTCTTG
CCTTCTGAGTCTCGGTTAACTTTCTTCCAAACCGAGGAGGAGCCGGACGC
TTATTTAGCTTCTTCACATCAACATCCGCACCACCTCTGCTGACGACAAA
GTAGACAGAATCAGGTTTTGCCTGAATAGCTGTTTTAGTGAACCCCAACT
TATCAGCAGGCCAAAGCTCATCTCCAAAGAAGCTGCTTGTGTACAGAACT
TGATCTCCAGATTTAAGCCCAGCTTTTGCTGCGTTGCCACCTCCTTCCAC
ACCAGTGATGACAACTCCACCACCTTGCTTCTGTCCAAGAGTCAGACCCA
AAGGCTTGTCCACTTCAACCTCTATGGTCTTAGAAGCTGCTGTTCTCGCT
TTGAC*TTCGAATCTTctcgaCAGGTTTAACCCACCGATCTTTCTGCGGA
CGCGtgg

BQ
 0 0 0 0 0 0 0 0 14 20 26 31 31 29 24 29 25 39 39 45 46 44 47 57 59 60 62 58 47 51 52 52 44 52 47 49 53 75 72 71 63 63 54 52 52 55 55 52 60 60
 58 55 55 52 52 57 64 52 55 55 55 40 38 38 42 46 55 52 52 54 64 61 64 57 61 67 66 77 66 64 71 70 69 64 65 67 67 71 70 71 64 68 71 76 76 71 71 69 72 67
 67 75 75 66 69 69 66 71 73 61 64 68 63 66 75 75 75 72 74 67 65 65 67 67 65 69 66 69 67 62 61 69 71 77 71 64 59 59 57 54 54 57 53 59 64 61 61 58 60 58
 64 75 71 68 67 64 57 53 50 47 54 67 67 65 65 60 60 60 60 60 71 66 64 62 57 57 61 60 63 72 72 83 83 75 72 69 64 69 69 68 71 61 72 64 67 64 61 58 56 50
 54 60 70 64 66 66 66 62 62 79 86 81 90 84 86 86 86 84 84 84 90 90 90 90 72 74 75 75 71 71 66 64 64 64 70 72 77 80 80 80 90 90 90 84 84 90 88 80 69 69
 69 71 71 71 71 74 57 57 57 42 42 42 42 42 44 59 63 71 66 66 67 67 72 79 79 79 84 69 74 79 70 72 70 70 76 76 87 87 90 90 90 90 90 90 90 90 90 85 74 73
 78 73 75 75 81 72 75 75 78 78 90 90 90 85 82 82 82 82 89 88 69 65 65 77 77 80 85 83 79 76 79 82 82 85 90 90 90 81 79 79 79 72 63 61 55 60 67 67 83 75
 72 66 68 61 53 52 69 69 79 76 50 54 42 42 37 35 35 35 50 50 57 87 87 90 90 90 90 90 90 90 84 84 84 79 79 85 90 82 80 88 75 73 71 74 74 76 73 76 70 77
 77 87 87 78 81 83 71 74 73 81 84 90 90 90 90 90 86 88 84 90 90 90 90 90 87 80 75 72 73 70 75 75 70 72 79 69 77 75 77 77 79 72 72 74 67 71 73 75 71 69
 63 55 50 50 56 74 60 65 65 65 56 58 58 53 53 71 71 78 85 85 77 83 81 81 77 68 66 71 53 53 53 43 43 43 38 38 38 53 53 57 78 84 86 90 90 88 88 75 75 72
 68 81 61 56 54 54 68 70 74 78 75 75 71 73 73 62 63 54 73 63 72 68 65 65 65 83 72 74 64 56 54 56 54 55 62 61 56 56 56 58 61 69 73 74 68 75 78 78 82 82
 86 86 86 90 90 75 60 57 60 60 67 69 78 68 68 60 59 62 60 59 61 62 61 62 61 64 73 69 70 64 51 51 52 54 56 64 75 73 75 90 90 90 90 83 83 84 84 78 79 79
 85 66 67 69 70 78 90 87 87 84 85 83 73 71 85 87 79 79 79 78 66 66 59 62 57 63 65 90 70 67 67 72 73 72 83 66 74 56 60 50 50 54 59 55 55 57 59 57 65 77
 85 68 65 64 57 44 43 44 48 48 48 55 49 47 46 43 42 48 63 65 63 61 60 61 54 48 44 37 37 35 39 32 44 44 45 45 50 55 61 53 51 47 45 45 45 51 35 35 35 35
 39 37 35 35 29 29 24 24 24 24 29 35 40 40 22 19 9 9 11 16 31 30 53 57 49 51 52 45 50 50 69 66 75 63 54 53 54 52 50 43 43 50 41 40 47 44 41 34 40 40
 34 34 34 0 0 0

AF LL2349f U -1
AF LL2349r C 0
BS 1 17 LL2349r
BS 18 19 LL2349f
BS 20 25 LL2349r
BS 26 37 LL2349f
BS 38 38 LL2349r
BS 39 77 LL2349f
BS 78 78 LL2349r
BS 79 98 LL2349f
BS 99 99 LL2349r
BS 100 101 LL2349f
BS 102 103 LL2349r
BS 104 114 LL2349f
BS 115 119 LL2349r
BS 120 147 LL2349f
BS 148 148 LL2349r
BS 149 149 LL2349f
BS 150 150 LL2349r
BS 151 151 LL2349f
BS 152 154 LL2349r
BS 155 179 LL2349f
BS 180 185 LL2349r
BS 186 190 LL2349f
BS 191 191 LL2349r
BS 192 192 LL2349f
BS 193 194 LL2349r
BS 195 210 LL2349f
BS 211 211 LL2349r
BS 212 217 LL2349f
BS 218 224 LL2349r
BS 225 225 LL2349f
BS 226 226 LL2349r
BS 227 234 LL2349f
BS 235 241 LL2349r
BS 242 247 LL2349f
BS 248 286 LL2349r
BS 287 288 LL2349f
BS 289 304 LL2349r
BS 305 305 LL2349f
BS 306 314 LL2349r
BS 315 318 LL2349f
BS 319 320 LL2349r
BS 321 323 LL2349f
BS 324 337 LL2349r
BS 338 342 LL2349f
BS 343 352 LL2349r
BS 353 353 LL2349f
BS 354 354 LL2349r
BS 355 362 LL2349f
BS 363 369 LL2349r
BS 370 370 LL2349f
BS 371 388 LL2349r
BS 389 390 LL2349f
BS 391 399 LL2349r
BS 400 401 LL2349f
BS 402 403 LL2349r
BS 404 405 LL2349f
BS 406 408 LL2349r
BS 409 409 LL2349f
BS 410 412 LL2349r
BS 413 413 LL2349f
BS 414 414 LL2349r
BS 415 415 LL2349f
BS 416 416 LL2349r
BS 417 417 LL2349f
BS 418 419 LL2349r
BS 420 423 LL2349f
BS 424 427 LL2349r
BS 428 432 LL2349f
BS 433 441 LL2349r
BS 442 446 LL2349f
BS 447 467 LL2349r
BS 468 468 LL2349f
BS 469 492 LL2349r
BS 493 493 LL2349f
BS 494 553 LL2349r
BS 554 554 LL2349f
BS 555 562 LL2349r
BS 563 563 LL2349f
BS 564 606 LL2349r
BS 607 609 LL2349f
BS 610 611 LL2349r
BS 612 612 LL2349f
BS 613 655 LL2349r
BS 656 696 LL2349f
BS 697 715 LL2349r
BS 716 716 LL2349f
BS 717 719 LL2349r
BS 720 722 LL2349f
BS 723 723 LL2349r
BS 724 748 LL2349f
BS 749 757 LL2349r

RD LL2349f 797 0 0
cttttnagcaacccngcagTTGATGTCATGAAGTCACCAATATACATTCT
CAGTTTACAATCACAAAGCTTAGTTTATGACTTTTTGGTATACAAAAAAA
CTATATAAAAATGTCACTGAAGACCATACACAAGCAGAGCTCCAACAGCT
CCAAGACCGGCCAATAAGCCAACAATAACACCGATCGGAGGCAGTCCTCC
TCCTATGGCCTTCCCTGTGTTCACATCATACCTCGCAAACCTTTTCTTTG
GTGCTATACATtgcggaCATACGTATGTATCCGGCTGTTCATCAAAAGGC
TTTGGTAAAGTGTATATGAATCCACAATCAAGACAAATGTGAGTAGCTCT
TGCCTTCTGAGTCTCGgctAACTTTCTTCCAAACCGAGGAGGAGCCGGAC
GCTTATTTAGCTTCTTCACATCAACATCCGCACCACCTCTGCTGACGACA
AAGTAGACAGAATCAGGTTTTGCCTGAATAGCTgttctaGTGAACCCCAA
CTTATCAGCAGGCCAAAGCTCATCTCCAAAGAAGCTGCTTGTGTACAGAA
CTTGATCTCCAGATTTAAGCCCAGCTTTTGCTGCGTTGCCACCTCCTTCC
ACACCAGTGATGACAACTCCACCACCTTGCTTCTGTCCAAGAGTCAGACC
CAAAGGCTTGTCCACTTCAACCTCTATGGTCTTAGAAGCTGCTGTTCTCG
ctctgaccttccaatCTTcttgaCAGGTTTAACCCACCGATCTTTCTGCG
GACGcgcggxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxt

QA 20 657 18 756
DS CHROMAT_FILE: LL2349f PHD_FILE: LL2349f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:59 2000

RD LL2349r 803 0 0
ntgaatttaaATCTCAAGTTGATGTCATGAAGTCACCAATATACATTCTC
AGTTTACAATCACanaGCTTAGTTTATGACTTTTTGGTATACAAAAAAAC
TATATAAAAATGTCACTGAAGACCATACACAAGCAGAGCTCCAACAGCTC
CAAGACCGGCCAATAAGCCAACAATAACACCGATCGGAGGCAGTCCTCCT
CCTATGGCCTTCCCTGTGTTCACATCATACCTCGCAAACCTTTTCTTTGG
TGCTATACATTGTGGACATACGTATGTATCCGGCTGTTCATCAAAAGGCT
TTGGTAAAGTGTATATGAATCCACAATCAAGACAAATGTGAGTAGCTCTT
GCCTTCTGAGTCTCGGTTAACTTTCTTCCAAACCGAGGAGGAGCCGGACG
CTTATTTAGCTTCTTCACATCAACATCCGCACCACCTCTGCTGACGACAA
AGTAGACAGAATCAGGTTTTGCCTGAATAGCTGTTTTAGTGAACCCCAAC
TTATCAGCAGGCCAAAGCTCATCTCCAAAGAAGCTGCTTGTGTACAGAAC
TTGATCTCCAGATTTAAGCCCAGCTTTTGCTGCGTTGCCACCTCCTTCCA
CACCAGTGATGACAACTCCACCACCTTGCTTCTGTCCAAGAGTCAGACCC
AAAGGCTTGTCCACTTCAACCTCTATGGTCTTAGAAGCTGCTGTTCTCGC
TTTGAC*TTCGAATCTTctcgaCAGGTTTAACCCACCGATCTTTCTGCGG
ACGCGtggxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
aag

QA 10 755 2 758
DS CHROMAT_FILE: LL2349r PHD_FILE: LL2349r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:36 2000

CO Contig48 549 2 72 U
CTTTTTTTTTTTTTTTTTAGAGAATCATTCACGTTCATTCCATAGAAAGA
AGTACAAACTGACTCATCCGTCACACATGGCAGAGACAACTAGATATGAC
GTCAACACAAACGAAAACCATTATCGGCTAAAAGACAAAAGCCTGCAGCC
GTTATTACACCGTAAACAAAACCTAGAACATCATTAGGGTTACTTAATAT
AATTAAACTCTGATTATCTCTGCCTCCTTAGAAAGGTTCCATTATTATTC
ATTTACAGGTGCAAGGATCACACTTGCAGTCAGATCCACACTTGCATGCA
TCGTTCTCAGCGACACCCTCTCCAGAAGCCTCGTACTGGTTCTTCATCGC
CGGTGCAACGCCGAAGACAAAAGTCTCGGTCGTGGTCGACTCGCCGGAAA
AGCCCAAGTCCGGGTACATTTTGCAACCTCCGCAACCGTTGCCGCACTTG
CAGCCAGATCCACAACCACAGTTTCCACCACAGCAAGACATTTTCTCGAG
AAAGACCGAAGAAATAGCAGAGAATGTTTATCAAATTGCGGACGCGTGG

BQ
 29 37 48 48 48 48 48 48 48 48 56 56 56 56 56 46 42 42 36 46 46 48 46 42 42 42 46 46 56 40 52 50 62 54 59 60 66 70 82 85 80 72 71 65 74 75 85 85 88 73
 77 74 80 85 79 90 90 90 90 90 90 90 90 90 90 90 84 79 76 77 75 75 81 90 90 90 90 81 90 90 90 86 86 90 90 86 90 90 86 86 86 90 90 90 90 80 83 62 61 53
 55 63 63 85 86 90 90 90 90 77 77 77 80 80 80 89 90 90 90 88 88 88 80 80 80 86 75 75 75 75 75 75 90 90 90 90 90 80 82 82 82 83 78 78 75 75 75 75 75 80
 72 72 65 77 77 84 86 90 78 82 82 81 81 78 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 88 90 90 90 88 77 77 77 86 86 86 86 86 89 89 90 90
 90 89 89 89 90 87 88 90 88 88 88 90 88 88 83 85 83 88 90 88 84 79 79 81 81 87 86 89 90 90 90 90 90 90 90 85 85 85 88 90 86 86 86 85 85 85 90 90 90 90
 90 90 90 90 90 90 84 84 84 84 85 89 89 90 90 90 90 90 90 90 90 90 90 79 79 86 83 86 86 90 90 88 90 90 90 90 90 90 90 90 90 81 81 89 90 90 90 90 90 86
 79 81 81 81 79 88 88 81 79 79 74 74 79 86 90 90 85 85 83 85 85 90 90 90 90 90 90 90 90 90 90 90 83 86 86 88 86 81 88 89 90 90 90 90 90 86 78 79 82 86
 79 83 84 84 85 90 86 86 86 86 86 86 81 90 80 86 86 87 87 79 78 86 80 73 78 82 89 85 84 59 59 59 36 36 36 36 36 36 58 58 79 79 81 84 84 84 85 85 90 90
 85 86 86 90 86 77 76 76 76 76 77 85 85 85 90 90 90 90 90 90 88 78 78 75 75 75 90 90 90 79 79 85 85 85 74 82 82 81 75 70 72 72 75 75 75 75 79 72 72 72
 77 77 72 89 89 90 90 90 90 90 90 90 90 90 90 90 90 84 82 82 81 82 85 80 90 90 90 90 90 80 75 75 75 79 82 81 90 90 90 90 90 83 78 81 75 77 86 86 88 88
 88 88 82 80 82 55 60 40 42 30 30 30 42 33 40 50 54 54 66 67 84 90 84 82 82 82 75 75 75 75 75 77 90 90 90 78 71 71 71 71 71 75 75 50 50 49 34 42 42

AF LL2350r C -206
AF LL2350f U 17
BS 1 52 LL2350r
BS 53 54 LL2350f
BS 55 68 LL2350r
BS 69 70 LL2350f
BS 71 78 LL2350r
BS 79 81 LL2350f
BS 82 104 LL2350r
BS 105 105 LL2350f
BS 106 108 LL2350r
BS 109 116 LL2350f
BS 117 164 LL2350r
BS 165 166 LL2350f
BS 167 198 LL2350r
BS 199 199 LL2350f
BS 200 211 LL2350r
BS 212 212 LL2350f
BS 213 218 LL2350r
BS 219 219 LL2350f
BS 220 220 LL2350r
BS 221 221 LL2350f
BS 222 232 LL2350r
BS 233 235 LL2350f
BS 236 261 LL2350r
BS 262 267 LL2350f
BS 268 275 LL2350r
BS 276 276 LL2350f
BS 277 277 LL2350r
BS 278 285 LL2350f
BS 286 299 LL2350r
BS 300 314 LL2350f
BS 315 321 LL2350r
BS 322 332 LL2350f
BS 333 333 LL2350r
BS 334 335 LL2350f
BS 336 336 LL2350r
BS 337 337 LL2350f
BS 338 338 LL2350r
BS 339 342 LL2350f
BS 343 349 LL2350r
BS 350 350 LL2350f
BS 351 355 LL2350r
BS 356 362 LL2350f
BS 363 370 LL2350r
BS 371 377 LL2350f
BS 378 379 LL2350r
BS 380 382 LL2350f
BS 383 398 LL2350r
BS 399 400 LL2350f
BS 401 401 LL2350r
BS 402 411 LL2350f
BS 412 414 LL2350r
BS 415 418 LL2350f
BS 419 419 LL2350r
BS 420 426 LL2350f
BS 427 428 LL2350r
BS 429 456 LL2350f
BS 457 467 LL2350r
BS 468 474 LL2350f
BS 475 475 LL2350r
BS 476 476 LL2350f
BS 477 479 LL2350r
BS 480 486 LL2350f
BS 487 505 LL2350r
BS 506 515 LL2350f
BS 516 523 LL2350r
BS 524 526 LL2350f
BS 527 532 LL2350r
BS 533 541 LL2350f
BS 542 543 LL2350r
BS 544 545 LL2350f
BS 546 547 LL2350r
BS 548 549 LL2350f

RD LL2350r 801 0 2
agggcgatcggtgcgggcctcttcgctattacgccagctggcgaaagggg
gatgtgctgcaaggcgattaagttgggtaacgccagggttttxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxCTTTTTTTTTTTTTTTTTAGAGAATCATTCACGTTCATTCCAT
AGAAAGAAGTACAAACTGACTCATCCGTCACACATGGCAGAGACAACTAG
ATATGACGTCAACACAAACGAAAACCATTATCGGCTAAAAGACAAAAGCC
TGCAGCCGTTATTACACCGTAAACAAAACCTAGAACATCATTAGGGTTAC
TTAATATAATTAAACTCTGATTATCTCTGCCTCCTTAGAAAGGTTCCATT
ATTATTCATTTACAGGTGCAAGGATCACACTTGCAGTCAGATCCACACTT
GCATGCATCGTTCTCAGCGACACCCTCTCCAGAAGCCTCGTACTGGTTCT
TCATCGCCGGTGCAACGCCGAAGACAAAAGTCTCGGTCGTGGTCGACTCG
CCGGAAAAGCCCAAGTCCGGGTACATTTTGCAACCTCCGCAACCGTTGCC
GCACTTGCAGCCAGATCCACAACCACAGTTTCCACCACAGCAAGACATTT
TCTCGAGAAAGACCgaacaaATAGCAGAGAATGTTTATCAAATTGCGGAC
GCGTGGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxa
t

QA 45 756 208 756
DS CHROMAT_FILE: LL2350r PHD_FILE: LL2350r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:41 2000

RT{
LL2350r chimera phrap 1 92 000919:094547
}

RT{
LL2350r matchElsewhereHighQual phrap 1 92 000919:094547
}

RD LL2350f 798 0 2
ctttgagaaacttcACGTTCATTCCATAGAAAGAAGTACAAACTGACTCA
TCCGTCACACATGGCAGAGACAACTAGATATGACGTCAACACAAACGAAA
ACCATTATCGGCTAAAAGACAAAAGCCTGCAGCCGTTATTACACCGTAAA
CAAAACCTAGAACATCATTAGGGTTACTTAATATAATTAAACTCTGATTA
TCTCTGCCTCCTTAGAAAGGTTCCATTATTATTCATTTACAGGTGCAAGG
ATCACACTTGCAGTCAGATCCACACTTGCATGCATCGTTCTCAGCGACAC
CCTCTCCAGAAGCCTCGTACTGGTTCTTCATCGCCGGTGCAACGCCGAAG
ACAAAAGTCTCGGTCGTggccgACTCGCCGGAAAAGCCCAAGTCCGGGTA
CATTTTGCAACCTCCGCAACCGTTGCCGCACTTGCAGCCAGATCCACAAC
CACAGTTTCCACCACAGCAAGACATTTTCTCGAGAAAGACCGAAGAAATA
GCAGAGAATGTTTATCAAATTGCGGACGCGTGGxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxgcct
gcggtgcctaatgagtgagctaactcacattaattgcgttgcgctcactg
cccgctttccagtcgggaaacctgtcgtgccagctgcattactgaatn

QA 14 751 12 533
DS CHROMAT_FILE: LL2350f PHD_FILE: LL2350f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:04 2000

RT{
LL2350f chimera phrap 697 797 000919:094547
}

RT{
LL2350f matchElsewhereHighQual phrap 703 791 000919:094547
}

CO Contig49 516 2 56 U
CCCCccttTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTAAGAAAGAAATTTTGGACATTTGTGGACATCGATT
CAGTTTGGTTCTTTGGTTGGGATGGGGTTTTGGGTTAAAATGCCCATTCA
CCAAGCGGAAGAACTTGCACAGATGCAATACACGTTGATAGACATCGAAT
TCAAAAATAAACGCACTTCAAGAACAGCAACAGTCCGATTGAATTACACT
CAAGTTTGCTCAGAGAGACAAGTAAACAACCATTCTTTACCCTATGGCGA
CGGCTGCTGAGACTCCATCGGAATCCCAAGATCATTCCTCTTGAGAACAG
GAAGCGCGACGAAAGATTTGGTCTTACTGATGGGTCTGCTCTTTTCAAGC
CTCACAACGTCACCAAGCGGAAGAACTTGCACAGATGCAATACACGTTGA
TAGACCGGACGCGTGG

BQ
 22 22 27 26 12 10 10 19 33 48 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56
 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56
 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 71 71 71 71 71 90 89 89 77 75 71 71 71 72 75 75 75 70 73 66 66 51 56 51
 45 45 60 60 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 80 76 79 90 90 90 71 71 56 56 56 56 56 56 71 71 71
 90 82 75 76 76 82 76 76 83 90 90 85 85 85 83 83 83 89 83 83 85 85 82 82 82 82 82 82 90 90 80 78 82 78 78 78 90 85 85 85 85 85 90 84 82 82 82 82 82 90
 90 90 90 90 90 90 90 90 90 78 78 78 78 78 78 78 90 90 90 90 90 90 90 90 90 90 90 90 90 88 87 81 81 75 75 75 84 80 80 90 90 90 90 90 90 90 90 90 90 90
 84 83 90 90 90 78 86 90 90 90 90 90 90 90 90 89 89 89 83 81 81 83 83 83 89 89 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 83 83 83 82 82
 74 74 74 74 75 75 75 82 82 77 79 79 82 80 90 90 84 90 86 80 80 80 90 90 90 90 90 90 90 83 83 83 83 85 90 90 90 90 90 90 81 83 83 83 85 85 90 90 85 85
 90 79 77 70 70 70 70 70 78 88 88 88 85 90 90 90 82 83 82 90 82 86 81 80 83 83 83 83 90 90 90 90 90 84 84 82 75 76 76 82 82 90 90 89 90 90 90 85 85 85
 85 89 89 89 89 83 82 82 82 82 82 90 90 90 76 76 76 76 76 76 76 76 74 56 56 41 40 40 40 41 56 56 85 85 81 81 81 89 89 90 90 90 83 83 83 83 83 86 90 90
 90 85 81 90 90 90 86 80 80 83 55 55 56 42 56 56

AF LL2351r C -249
AF LL2351f U 112
BS 1 154 LL2351r
BS 155 161 LL2351f
BS 162 162 LL2351r
BS 163 169 LL2351f
BS 170 175 LL2351r
BS 176 176 LL2351f
BS 177 182 LL2351r
BS 183 183 LL2351f
BS 184 202 LL2351r
BS 203 208 LL2351f
BS 209 209 LL2351r
BS 210 211 LL2351f
BS 212 217 LL2351r
BS 218 218 LL2351f
BS 219 269 LL2351r
BS 270 286 LL2351f
BS 287 290 LL2351r
BS 291 292 LL2351f
BS 293 302 LL2351r
BS 303 305 LL2351f
BS 306 324 LL2351r
BS 325 327 LL2351f
BS 328 334 LL2351r
BS 335 335 LL2351f
BS 336 336 LL2351r
BS 337 337 LL2351f
BS 338 344 LL2351r
BS 345 350 LL2351f
BS 351 357 LL2351r
BS 358 359 LL2351f
BS 360 360 LL2351r
BS 361 364 LL2351f
BS 365 366 LL2351r
BS 367 377 LL2351f
BS 378 379 LL2351r
BS 380 385 LL2351f
BS 386 390 LL2351r
BS 391 396 LL2351f
BS 397 398 LL2351r
BS 399 409 LL2351f
BS 410 416 LL2351r
BS 417 428 LL2351f
BS 429 430 LL2351r
BS 431 436 LL2351f
BS 437 442 LL2351r
BS 443 443 LL2351f
BS 444 444 LL2351r
BS 445 451 LL2351f
BS 452 455 LL2351r
BS 456 463 LL2351f
BS 464 464 LL2351r
BS 465 482 LL2351f
BS 483 484 LL2351r
BS 485 503 LL2351f
BS 504 507 LL2351r
BS 508 516 LL2351f

RD LL2351r 812 0 4
gtacagggggcgtcccatttgccattcagggtgcgcaactgtgggaaggg
cgatcggtgcgggccttttcggtattaccccaactggcgaaaaggggatg
ttcttcaaggcgattaagttggggaaccccagggtttttxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
CCCCccttTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTAAGAAAGAAATTTTGGACATTTGTGGACATCGATT
CAGTTTGGTTCTTTGGTTGGGATGGGGTTTTGGGTTAAAATGCCCATTCA
CCAAGCGGAAGAACTTGCACAGATGCAATACACGTTGATAGACATCGAAT
TCAAAAATAAACGCACTTCAAGAACAGCAACAGTCCGATTGAATTACACT
CAAGTTTGCTCAGAGAGACAAGTAAACAACCATTCTTTACCCTATGGCGA
CGGCTGCTGAGACTCCATCGGAATCCCAAGATCATTCCTCTTGAGAACAG
GAAGCGCGACGAAAGATTTGGTCTTACTGATGGGTCTGCTCTTTTCAAGC
CTCACAACGTCACCAAGCGGAAGAActcgcACAGATGCAATACACGTTGA
TAGACCGGACGCGTGGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxaagt

QA 251 766 251 766
DS CHROMAT_FILE: LL2351r PHD_FILE: LL2351r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:46 2000

RT{
LL2351r chimera phrap 1 139 000919:094547
}

RT{
LL2351r matchElsewhereLowQual phrap 18 33 000919:094547
}

RT{
LL2351r matchElsewhereLowQual phrap 43 59 000919:094547
}

RT{
LL2351r matchElsewhereHighQual phrap 106 139 000919:094547
}

RD LL2351f 805 0 6
cctttatgaagacatTTTGGACATTTGTGGACATCGatccaGTTTGGTTC
TTTGGTTGGGATGGGGTTTTGGGTTAAAATGcggatTCACCAAGCGGAAG
AACTTGCACAGATGCAATACACGTTGATAGACATCGAATTCAAAAATAAA
CGCACTTCAAGAACAGCAACAGTCCGATTGAATTACACTCAAGTTTGCTC
AGAGAGACAAGTAAACAACCATTCTTTACCCTATGGCGACGGCTGCTGAG
ACTCCATCGGAATCCCAAGATCATTCCTCTTGAGAACAGGAAGCGCGACG
AAAGATTTGGTCTTACTGATGGGTCTGCTCTTTTCAAGCCTCACAACGTC
ACCAAGCGGAAGAACTTGCACAGATGCAATACACGTTGATAGACCGGACG
CGTGGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxgcctggggtgcctaatgagtgagctaactcac
attaattgcgttgcgctcactgcccgctttccagtcgggaaacctgtcgt
gccagctgcattaatgaatcggccaacgcgcggngagaggcggtttgcgt
attgcgcgccagggtggtttttcttttcccagtgagacgggcaacagctg
attgcccttcaccgnctgcgcctgacagagctgcaccaagcggtccacgc
tgcct

QA 15 682 9 405
DS CHROMAT_FILE: LL2351f PHD_FILE: LL2351f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:09 2000

RT{
LL2351f chimera phrap 569 802 000919:094547
}

RT{
LL2351f matchElsewhereHighQual phrap 787 802 000919:094547
}

RT{
LL2351f matchElsewhereHighQual phrap 729 764 000919:094547
}

RT{
LL2351f matchElsewhereHighQual phrap 706 727 000919:094547
}

RT{
LL2351f matchElsewhereHighQual phrap 685 704 000919:094547
}

RT{
LL2351f matchElsewhereHighQual phrap 569 683 000919:094547
}

CO Contig50 984 3 112 U
ccacgcgtccgattcattgcaacgaaatatttaagacatgtttTTTGAGT
TAATTAACAGCTTCTATTTTTTTTGTTCTTGTTCTTTATGGACCCTAAAA
TTAAAATAGAAGATTGGGGGTGAATCATAAATCCAAAGGAGGTTTCATGG
CCAAAGGTAAAGATGTTCGAGTAACAATTATTTTGGAATGTACCAGTTGT
GTTCGAAATGATATTAAGAAAGAATCGGCTGGAATTTCCAGATATATTAC
TCAAAAGAATCGGCATAACACTCCTAGTCGATTGGAATTGAGAAAATTCT
GTCCCTATTGTTATAAACATACAATTCATGGGGAAATTAAGAAATAGATA
AAATTGAGTGCTTGTATGTCAAATTTTATTTTAAGAACAGGAATAATGAG
AGTATCTACGTATTATTACATATATATAAATATAAACAAATAAAATAATA
GAAAGAAATCAAATCCTATATTCTTAATTCTATATAGAAACTCTATCCTA
TATAGAAATAGCAATCGTTTTTATTTTGATCCGATCAAAAATAGGATTTT
ATAGGTAAGGAATAAAAAATTATGAATAAATCTAAGCGACCTTTTACTAA
ATCCAAGCGATCTTTTCGTCGGCGTTTGCCCCCGATCCAATCGGGGGATC
GAATTGATTATAGAAACATGAGTTTAATTAGTCGATTTATTAGTGAACAA
GGAAAAATATTATCTAGACGGGTGAATAGAGTAACTTTAAAACAACAACG
ATTAATTACTATTGCTATAAAACAAGCTCGTATTTTATCTTTGTTACCTT
TTCTTAATAATCAGAAACAATTTGAAAGAAGTGAGTCGACCCCTAGAACT
ACTAGCCTTAGAACCAGAAAAAAATAGACTTATTCTTCAATTGAATAACT
AATCTGAAGGAATTAAAAAAGAGGTTAATATTTTGTTCGAca*aatCCA*
ATCA*AGAATCA*AAATTTGATTGTtacGTctgt

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 29 32 34 33 34 30
 35 34 34 34 34 34 34 34 40 40 40 40 37 40 37 40 40 40 56 56 56 56 40 40 37 37 37 40 51 51 42 42 42 51 37 40 35 35 35 39 51 51 40 40 40 40 40 40 46 35
 35 35 35 35 35 35 35 35 35 35 37 40 40 51 56 56 56 56 56 42 42 42 46 46 51 43 43 51 56 51 43 43 43 51 51 51 51 56 56 56 56 56 37 37 37 37 37 37 40 40
 40 40 45 51 56 51 51 51 51 51 51 56 56 56 50 40 37 40 40 40 40 42 42 42 40 42 40 40 40 40 40 45 56 56 56 56 56 56 56 51 51 51 45 45 45 42 42 42 42 42
 46 45 43 43 43 43 43 74 81 81 82 81 76 67 62 64 60 60 67 61 61 63 66 58 58 56 51 42 42 44 51 58 73 78 65 66 67 71 66 71 66 67 73 70 73 65 60 58 62 62
 67 78 78 88 86 86 86 80 74 80 80 80 82 77 75 71 70 79 71 78 80 90 71 71 80 83 77 79 80 80 84 77 81 79 83 87 89 84 85 90 90 90 90 90 90 90 90 86 86 88
 89 82 82 81 90 90 90 90 90 77 77 77 81 81 86 88 90 90 89 87 87 90 86 90 89 90 90 90 90 90 90 90 90 90 90 87 86 80 84 86 85 90 90 90 90 90 88 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 88 82 82 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 86 81 76 90 80 90 86 88 88 85 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 86 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 81 81 89 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 86 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 88 88 88 87 85 85 88 82 81 86 90 90 90 90 90 88 86 86 88 88
 90 90 90 90 86 84 84 86 86 90 90 90 90 90 90 90 90 90 90 87 88 89 89 89 88 88 88 90 90 90 85 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 85 85 90 90 90 88 90 90 90 90 90 90 90 90 90 90 90 90 90 86 86 90 87 90 90 90 90 90
 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 85 90 90 90 90 90 90 90 90 90 90 90 90 82 73 73 65 55 63 72 75 83 84 86 86 88 84 72 72 77 66 66 72 78
 64 70 78 76 69 69 75 75 75 76 81 81 81 75 74 68 78 78 82 86 83 85 83 65 63 55 63 58 61 64 58 66 80 76 82 86 86 82 82 90 85 81 69 62 59 65 74 71 77 81
 85 90 64 67 62 60 63 70 75 75 75 82 77 71 69 71 68 68 58 58 64 86 76 77 75 75 83 83 69 69 61 75 75 70 62 69 63 66 63 64 64 74 67 67 54 54 48 54 56 62
 62 64 57 56 59 68 56 61 61 55 54 51 52 44 48 48 37 37 42 42 56 56 40 40 40 55 55 55 69 69 69 69 66 69 67 64 64 64 64 64 61 75 72 64 61 58 45 40 48 51
 52 52 66 70 75 60 52 57 50 50 48 51 58 64 66 69 76 90 90 90 90 67 64 48 48 48 50 50 58 86 69 72 62 64 58 44 40 40 42 36 13 13 13 16 19 20 22 25 24 29
 29 25 25 27 29 42 33 29 25 25 26 25 27 44 41 41 39 44 43 22 20 16 17 17 21 23 18 19 9 9

AF LL2342r U -44
AF LL2317r U 194
AF LL2342f C 204
BS 1 207 LL2342r
BS 208 231 LL2342f
BS 232 267 LL2342r
BS 268 268 LL2317r
BS 269 271 LL2342r
BS 272 274 LL2317r
BS 275 283 LL2342r
BS 284 284 LL2317r
BS 285 296 LL2342r
BS 297 297 LL2317r
BS 298 315 LL2342r
BS 316 316 LL2317r
BS 317 340 LL2342r
BS 341 341 LL2342f
BS 342 342 LL2317r
BS 343 352 LL2342r
BS 353 353 LL2317r
BS 354 362 LL2342r
BS 363 363 LL2342f
BS 364 364 LL2342r
BS 365 366 LL2317r
BS 367 371 LL2342r
BS 372 377 LL2317r
BS 378 379 LL2342r
BS 380 384 LL2317r
BS 385 390 LL2342r
BS 391 400 LL2317r
BS 401 410 LL2342r
BS 411 412 LL2317r
BS 413 413 LL2342r
BS 414 414 LL2342f
BS 415 424 LL2342r
BS 425 438 LL2317r
BS 439 442 LL2342r
BS 443 463 LL2317r
BS 464 468 LL2342r
BS 469 470 LL2317r
BS 471 472 LL2342r
BS 473 485 LL2317r
BS 486 487 LL2342r
BS 488 494 LL2342f
BS 495 497 LL2317r
BS 498 501 LL2342r
BS 502 513 LL2317r
BS 514 516 LL2342r
BS 517 520 LL2317r
BS 521 526 LL2342f
BS 527 549 LL2317r
BS 550 551 LL2342f
BS 552 590 LL2317r
BS 591 592 LL2342r
BS 593 627 LL2317r
BS 628 628 LL2342f
BS 629 674 LL2317r
BS 675 677 LL2342f
BS 678 685 LL2317r
BS 686 691 LL2342f
BS 692 706 LL2317r
BS 707 710 LL2342f
BS 711 715 LL2317r
BS 716 716 LL2342f
BS 717 751 LL2317r
BS 752 752 LL2342f
BS 753 754 LL2317r
BS 755 766 LL2342f
BS 767 775 LL2317r
BS 776 776 LL2342f
BS 777 777 LL2317r
BS 778 778 LL2342f
BS 779 779 LL2317r
BS 780 780 LL2342f
BS 781 784 LL2317r
BS 785 789 LL2342f
BS 790 792 LL2317r
BS 793 795 LL2342f
BS 796 796 LL2317r
BS 797 798 LL2342f
BS 799 802 LL2317r
BS 803 808 LL2342f
BS 809 811 LL2317r
BS 812 812 LL2342f
BS 813 813 LL2317r
BS 814 822 LL2342f
BS 823 828 LL2317r
BS 829 831 LL2342f
BS 832 838 LL2317r
BS 839 841 LL2342f
BS 842 842 LL2317r
BS 843 852 LL2342f
BS 853 853 LL2317r
BS 854 854 LL2342f
BS 855 859 LL2317r
BS 860 872 LL2342f
BS 873 878 LL2317r
BS 879 891 LL2342f
BS 892 893 LL2317r
BS 894 894 LL2342f
BS 895 895 LL2317r
BS 896 904 LL2342f
BS 905 905 LL2317r
BS 906 917 LL2342f
BS 918 919 LL2317r
BS 920 938 LL2342f
BS 939 944 LL2317r
BS 945 947 LL2342f
BS 948 958 LL2317r
BS 959 960 LL2342f
BS 961 966 LL2317r
BS 967 976 LL2342f
BS 977 977 LL2317r
BS 978 978 LL2342f
BS 979 984 LL2317r

RD LL2342r 792 0 0
actaxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccacg
cgtccgattcattgcaacgaaatatttaagacatgtttTTTGAGTTAATT
AACAGCTTCTATTTTTTTTGTTCTTGTTCTTTATGGACCCTAAAATTAAA
ATAGAAGATTGGGGGTGAATCATAAATCCAAAGGAGGTTTCATGGCCAAA
GGTAAAGATGTTCGAGTAACAATTATTTTGGAATGTACCAGTTGTGTTCG
AAATGATATTAAGAAAGAATCGGCTGGAATTTCCAGATATATTACTCAAA
AGAATCGGCATAACACTCCTAGTCGATTGGAATTGAGAAAATTCTGTCCC
TATTGTTATAAACATACAATTCATGGGGAAATTAAGAAATAGATAAAATT
GAGTGCTTGTATGTCAAATTTTATTTTAAGAACAGGAATAATGAGAGTAT
CTACGTATTATTACATATATATAAATATAAACAAATAAAATAATAGAAAG
AAATCAAATCCTATATTCTTAATTCTATATAGAAACTCTATCCTATATAG
AAATAGCAATCGTTTTTATTTTGATCCGATCAAAAATAGGATTTTATAGG
TAAGGAATAAAAAATTATGAATAAATCTAAGCGACCTTTTACTAAATCCA
AGCGATCTTTTCGTCGGCGTTTGCCCCCGATCCAATCGGGGGATCGAATT
GATTATAGAAACATGAGTTTAATTAGTCGATTTATTAGTGAACAAGGAAA
AATATTATCTAGACGGGTGAATAGAGTAActnt*aaacaaca

QA 81 778 46 792
DS CHROMAT_FILE: LL2342r PHD_FILE: LL2342r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:40 2000

RD LL2317r 791 0 0
aatxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccacg
cgtccgCTCAAAAGAATCGGCATAACACTCCTAGTCGATTGGAATTGAGA
AAATTCTGTCCCTATTGTTATAAACATACAATTCATGGGGAAATTAAGAA
ATAGATAAAATTGAGTGCTTGTATGTCAAATTTTATTTTAAGAACAGGAA
TAATGAGAGTATCTACGTATTATTACATATATATAAATATAAACAAATAA
AATAATAGAAAGAAATCAAATCCTATATTCTTAATTCTATATAGAAACTC
TATCCTATATAGAAATAGCAATCGTTTTTATTTTGATCCGATCAAAAATA
GGATTTTATAGGTAAGGAATAAAAAATTATGAATAAATCTAAGCGACCTT
TTACTAAATCCAAGCGATCTTTTCGTCGGCGTTTGCCCCCGATCCAATCG
GGGGATCGAATTGATTATAGAAACATGAGTTTAATTAGTCGATTTATTAG
TGAACAAGGAAAAATATTATCTAGACGGGTGAATAGAGTAACTTTAAAAC
AACAACGATTAATTACTATTGCTATAAAACAAGCTCGTATTTTATCTTTG
TTACCTTTTCTTAATAATCAGAAACAATTTGAAAGAAGTGAGTCGACCCC
TAGAACTACTAGCCTTAGAACCAganaAAAATAGACTTATTCTTCAATTG
AATAACTAATCTGAAGGAATTAAAAAAGAGGTTAATATTTTGTTCGAca*
aatCCA*ATCA*AGAATCA*AAATTTGATtgttacGTctgt

QA 57 780 57 791
DS CHROMAT_FILE: LL2317r PHD_FILE: LL2317r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:35 2000

RD LL2342f 782 0 0
cgAAATGATATTAAGAAAGAATCGGCTGGAATTTCCAGATATATTACTCA
AAAGAATCGGCATAACACTCCTAGTCGATTGGAATTGAGAAAATTCTGTC
CCTATTGTTATAAACATACAATTCATGGGGAAATTAAGAAATAGATAAAA
TTGAGTGCTTGTATGTCAAATTTTATTTTAAGAACAGGAATAATGAGAGT
ATCTACGTATTATTACATATATATAAATATAAACAAATAAAATAATAGAA
AGAAATCAAATCCTATATTCTTAATTCTATATAGAAACTCTATCCTATAT
AGAAATAGCAATCGTTTTTATTTTGATCCGATCAAAAATAGGATTTTATA
GGTAAGGAATAAAAAATTATGAATAAATCTAAGCGACCTTTTACTAAATC
CAAGCGATCTTTTCGTCGGCGTTTGCCCCCGATCCAATCGGGGGATCGAA
TTGATTATAGAAACATGAGTTTAATTAGTCGATTTATTAGTGAACAAGGA
AAAATATTATCTAGACGGGTGAATAGAGTAACTTTAAAACAACAACGATT
AATTACTATTGCTATAAAACAAGCTCGTATTTTATCTTTGTTACCTTTTC
TTAATAATCAGAAACAATTTGAAAGAAGTGAGTCGACCCCTAGAACTACT
AGCCTTAGAACCAGAAAAAAATAGACTTATTCTTCAATTGAATAACTAAT
CTGAAGGAATTAAAAAAGAGGTTAATATTTTGTTCGAcacaatCcacatc
acagAATcacaaaTTTGATTGTtacgtctgtg

QA 29 737 1 781
DS CHROMAT_FILE: LL2342f PHD_FILE: LL2342f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:04 2000

CO Contig51 797 4 178 U
cgttTGGGATCCGTGTGGAAG*ACGATTACAACAGGTGTTGTCCTCTGAG
GACATAAAATACACA*CCGAGATTCATCAACTCAT*TGCTGGAGTTAGCA
TATCTACAATTGGGTGAAATGGGGAGCGATTTGCAGGCATTTGCTCGGCA
TGCCGGTAGAGGTGTGGTCAATAAGAGCGACCTCATGCTATACCTGAGAA
AGCAACCTGACCTACAGGAAAGAGTTACTCAAGAATAAGAATTTTCGTTT
TAAAACCTAAGAGTCACTTTAAAATTTGTATACACTTATTTTTTTTATAA
CTTATTTAATAATAAAAATCATAAATCATAAGAAATTCGCTTATTTAGAA
GTGTCAACAACGTATCTACCAACGATTTGACCCTTTTCCATCTTTTCGTA
AATTTCTGGCAAGGTAGACAAGCCGACAACCTTGATTGGAGACTTGACCA
AACCTCTGGCGAAGAAGTCCAAAGCTCCACCGCGGTGGCGGCCGTTACTT
ACTTAGAGCTCGACGTCTTACTTACTTAGCGGCCGCACTAGTAGATCTGA
ATTCCCGGGGTCGACCCACCCTCTTTTTTTGGGTTTGGTGGGGTATCTTC
ATCATCGAATAGATAGTTATATACATCATCCATTGTAGTGGTATTAAACA
TCCCTGTAGTGATTCCAAACGCGTTATACGCAGTTTGGTCCGTCCAACCA
GGTGACAGTGGTTTTGAATTATTACCATCATCAATTTtACTAGCCGTGAT
TTCATTATTCATGAAGTTATCATGAACGTTAGAGGAGGCAatTggtt

BQ
 0 8 8 12 25 33 37 36 42 42 42 44 44 44 44 44 49 49 49 44 44 44 39 39 43 43 44 44 44 45 44 49 49 49 50 50 61 50 50 50 50 50 56 56 56 45 45 45 45 45
 45 45 45 45 56 56 56 56 56 66 61 61 50 50 50 50 50 45 45 45 45 45 50 56 56 56 50 50 50 55 55 55 50 50 47 50 50 50 55 61 50 49 49 49 49 49 50 56 56 56
 56 56 56 50 50 61 61 61 66 66 50 56 56 56 56 56 66 66 66 66 56 49 45 45 45 45 45 45 45 45 45 45 45 50 50 50 50 49 45 45 45 45 45 48 53 53 53 53 49 49
 49 49 53 53 61 61 61 66 66 66 66 66 61 61 61 61 61 61 55 55 55 53 53 53 53 53 53 53 53 53 55 53 53 53 53 53 53 53 53 53 53 53 61 61 66 66 55 55 61 53
 53 53 55 55 53 53 53 53 53 53 53 53 53 53 66 66 66 66 66 66 61 61 53 53 53 53 53 53 66 66 61 61 61 61 61 61 66 66 66 66 61 61 61 61 61 55 55 55 61 61
 55 61 61 61 61 61 61 61 66 66 66 53 53 53 53 53 53 66 66 66 66 66 61 61 61 61 55 61 61 53 53 53 53 53 53 66 66 66 66 66 66 66 66 66 66 53 53 53 53 53
 53 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 55 53 53 53 53 53 53 53 61 61 61 61 66 66 66 66 66 66
 66 66 66 66 66 61 61 61 61 61 61 66 61 61 61 61 61 61 61 61 61 61 66 66 61 55 55 55 55 55 66 66 66 61 61 61 55 55 55 66 66 66 66 61 61 61 61 66 66 66
 66 66 66 66 66 66 66 66 66 61 61 61 55 55 55 55 55 55 66 66 61 61 61 61 61 61 66 66 66 61 61 66 66 66 61 66 61 55 55 55 55 55 61 55 55 55 55 61 61 66
 66 66 66 66 61 55 55 55 55 55 66 66 66 66 66 66 66 66 66 61 61 61 61 53 53 55 55 55 55 61 61 61 61 55 55 53 53 53 53 61 61 53 53 53 53 53 55 55 55 55
 55 55 66 55 55 55 55 50 50 50 50 55 55 61 56 55 55 55 55 55 61 61 61 61 55 55 50 50 47 47 47 47 45 45 49 50 50 55 66 66 66 66 66 66 66 66 66 61 61 61
 61 61 61 66 66 61 61 61 55 55 50 55 52 55 50 50 50 55 56 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 56 61 55 55 56 52 52 52 61 61 61 61
 61 61 61 61 61 61 66 66 66 66 66 61 50 50 47 50 50 50 66 66 66 66 66 66 56 56 56 43 50 50 50 50 50 50 58 58 42 39 39 35 39 39 39 44 44 58 58 47 50 50
 58 58 50 50 50 58 58 46 39 39 39 34 34 39 42 42 42 42 50 39 41 41 42 39 39 42 42 39 40 44 44 44 58 42 44 39 35 42 39 39 35 39 39 42 42 42 42 42 50 50
 50 50 50 50 42 47 35 35 35 35 39 39 39 39 30 33 37 37 39 39 44 44 44 44 39 42 50 50 44 39 32 34 27 22 17 24 37 37 36 38 42 40 34 34 34 42 39 35 35 37
 37 42 42 42 42 39 42 50 50 39 39 35 37 29 25 35 31 37 39 50 39 39 39 39 35 28 28 31 34 34 25 27 33 28 25 25 25 18 18 23 16 17 0 0

AF LL2269r U 1
AF LL2335r U 1
AF LL2312r U 1
AF LL2320r U 2
BS 1 1 LL2312r
BS 2 4 LL2320r
BS 5 5 LL2312r
BS 6 12 LL2320r
BS 13 15 LL2269r
BS 16 25 LL2320r
BS 26 26 LL2269r
BS 27 27 LL2320r
BS 28 29 LL2269r
BS 30 31 LL2335r
BS 32 35 LL2320r
BS 36 37 LL2269r
BS 38 38 LL2320r
BS 39 45 LL2269r
BS 46 60 LL2320r
BS 61 61 LL2269r
BS 62 75 LL2320r
BS 76 78 LL2269r
BS 79 81 LL2320r
BS 82 90 LL2269r
BS 91 93 LL2320r
BS 94 99 LL2269r
BS 100 100 LL2320r
BS 101 101 LL2269r
BS 102 102 LL2312r
BS 103 108 LL2269r
BS 109 124 LL2320r
BS 125 125 LL2335r
BS 126 146 LL2320r
BS 147 147 LL2269r
BS 148 151 LL2320r
BS 152 155 LL2269r
BS 156 157 LL2320r
BS 158 160 LL2312r
BS 161 196 LL2320r
BS 197 199 LL2269r
BS 200 205 LL2320r
BS 206 210 LL2312r
BS 211 223 LL2320r
BS 224 225 LL2269r
BS 226 231 LL2320r
BS 232 233 LL2269r
BS 234 239 LL2320r
BS 240 241 LL2269r
BS 242 243 LL2320r
BS 244 249 LL2312r
BS 250 261 LL2320r
BS 262 264 LL2312r
BS 265 280 LL2320r
BS 281 282 LL2312r
BS 283 288 LL2320r
BS 289 289 LL2335r
BS 290 293 LL2320r
BS 294 298 LL2312r
BS 299 304 LL2320r
BS 305 308 LL2312r
BS 309 309 LL2320r
BS 310 315 LL2312r
BS 316 330 LL2320r
BS 331 335 LL2269r
BS 336 358 LL2320r
BS 359 360 LL2312r
BS 361 364 LL2320r
BS 365 365 LL2312r
BS 366 384 LL2320r
BS 385 386 LL2312r
BS 387 395 LL2320r
BS 396 396 LL2312r
BS 397 411 LL2320r
BS 412 412 LL2312r
BS 413 422 LL2320r
BS 423 423 LL2312r
BS 424 429 LL2320r
BS 430 431 LL2269r
BS 432 434 LL2320r
BS 435 437 LL2335r
BS 438 440 LL2320r
BS 441 446 LL2312r
BS 447 450 LL2320r
BS 451 455 LL2269r
BS 456 457 LL2320r
BS 458 458 LL2269r
BS 459 472 LL2320r
BS 473 476 LL2269r
BS 477 478 LL2320r
BS 479 480 LL2335r
BS 481 485 LL2269r
BS 486 490 LL2320r
BS 491 492 LL2269r
BS 493 494 LL2312r
BS 495 499 LL2320r
BS 500 503 LL2269r
BS 504 516 LL2312r
BS 517 517 LL2269r
BS 518 518 LL2320r
BS 519 529 LL2269r
BS 530 538 LL2320r
BS 539 545 LL2312r
BS 546 557 LL2320r
BS 558 558 LL2269r
BS 559 561 LL2320r
BS 562 565 LL2312r
BS 566 566 LL2335r
BS 567 568 LL2269r
BS 569 569 LL2335r
BS 570 571 LL2269r
BS 572 574 LL2312r
BS 575 589 LL2320r
BS 590 593 LL2269r
BS 594 595 LL2320r
BS 596 596 LL2312r
BS 597 601 LL2269r
BS 602 602 LL2312r
BS 603 604 LL2320r
BS 605 613 LL2269r
BS 614 617 LL2312r
BS 618 621 LL2320r
BS 622 627 LL2269r
BS 628 637 LL2320r
BS 638 639 LL2312r
BS 640 640 LL2320r
BS 641 641 LL2312r
BS 642 646 LL2320r
BS 647 648 LL2335r
BS 649 651 LL2320r
BS 652 653 LL2335r
BS 654 654 LL2312r
BS 655 661 LL2320r
BS 662 669 LL2269r
BS 670 673 LL2320r
BS 674 676 LL2269r
BS 677 678 LL2320r
BS 679 680 LL2312r
BS 681 681 LL2335r
BS 682 682 LL2312r
BS 683 686 LL2269r
BS 687 687 LL2320r
BS 688 688 LL2312r
BS 689 690 LL2320r
BS 691 691 LL2312r
BS 692 692 LL2320r
BS 693 702 LL2312r
BS 703 703 LL2320r
BS 704 704 LL2312r
BS 705 705 LL2320r
BS 706 707 LL2312r
BS 708 709 LL2269r
BS 710 716 LL2320r
BS 717 718 LL2335r
BS 719 728 LL2312r
BS 729 731 LL2320r
BS 732 732 LL2312r
BS 733 741 LL2320r
BS 742 742 LL2312r
BS 743 744 LL2320r
BS 745 745 LL2312r
BS 746 747 LL2320r
BS 748 753 LL2312r
BS 754 754 LL2320r
BS 755 758 LL2335r
BS 759 759 LL2320r
BS 760 763 LL2312r
BS 764 764 LL2269r
BS 765 765 LL2312r
BS 766 766 LL2335r
BS 767 767 LL2312r
BS 768 768 LL2335r
BS 769 769 LL2312r
BS 770 770 LL2335r
BS 771 771 LL2320r
BS 772 774 LL2269r
BS 775 777 LL2320r
BS 778 778 LL2335r
BS 779 784 LL2320r
BS 785 787 LL2269r
BS 788 790 LL2335r
BS 791 792 LL2320r
BS 793 797 LL2335r

RD LL2269r 792 0 0
natatgGGATCCGTGTGGAAGAACGATTACAACAGGTGTTGTCCTCTGAG
GACATAAAATACACA*CCGAGATTCATCAACTCAT*TGCTGGAGTTAGCA
TATCTACAATTGGGTGAAATGGGGAGCGATTTGCAGGCATTTGCTCGGCA
TGCCGGTAGAGGTGTGGTCAATAAGAGCGACCTCATGCTATACCTGAGAA
AGCAACCTGACCTACAGGAAAGAGTTACTCAAGAATAAGAATTTTCGTTT
TAAAACCTAAGAGTCACTTTAAAATTTGTATACACTTATTTTTTTTATAA
CTTATTTAATAATAAAAATCATAAATCATAAGAAATTCGCTTATTTAGAA
GTGTCAACAACGTATCTACCAACGATTTGACCCTTTTCCATCTTTTCGTA
AATTTCTGGCAAGGTAGACAAGCCGACAACCTTGATTGGAGACTTGACCA
AACCTCTGGCGAAGAAGTCCAAAGCTCCACCGCGGTGGCGGCCGTTACTT
ACTTAGAGCTCGACGTCTTACTTACTTAGCGGCCGCACTAGTAGATCTGA
ATTCCCGGGGTCGACCCACCCTCTTTTTTTGGGTTTGGTGGGGTATCTTC
ATCATCGAATAGATAGTTATATACATCATCCATTGTAGTGGTATTAAACA
TCCCTGTAGTGATTCCAAACGCGTTATACGCAGTTTGGTCCGTCCAACCA
GGTGACAGTGGTTTTGAATTATTACCATCATCAaTtntaCTAGCCGTGAT
TTCATTATTCATGAAGTTATCATGAACGTTAGAGGAGGCAat

QA 6 792 5 792
DS CHROMAT_FILE: LL2269r PHD_FILE: LL2269r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:32 2000

RD LL2335r 797 0 0
catttGGGATCCGTGTGGAAG*ACGATTACAACAGGTGTTGTCCTCTGAG
GACATAAAATACACA*CCGAGATTCATCAACTCatgtgCTGGAGTTAGCA
TATCTACAATTGGGTGAAATGGGGAGCGATTTGCAGGCATTTGCTCGGCA
TGCCGGTAGAGGTGTGGTCAATAAGAGCGACCTCATGCTATACCTGAGAA
AGCAACCTGACCTACAGGAAAGAGTTACTCAAGAATAAGAATTTTCGTTT
TAAAACCTAAGAGTCACTTTAAAATTTGTATACACTTATTTTTTTTATAA
CTTATTTAATAATAAAAATCATAAATCATAAGAAATTCGCTTATTTAGAA
GTGTCAACAACGTATCTACCAACGATTTGACCCTTTTCCATCTTTTCGTA
AATTTCTGGCAAGGTAGACAAGCCGACAACCTTGATTGGAGACTTGACCA
AACCTCTGGCGAAGAAGTCCAAAGCTCCACCGCGGTGGCGGCCGTTACTT
ACTTAGAGCTCGACGTCTTACTTACTTAGCGGCCGCACTAGTAGATCTGA
ATTCCCGGGGTCGACCCACCCTCTTTTTTTGGGTTTGGTGGGGTATCTTC
ATCATCGAATAGATAGTTATATACATCATCCATTGTAGTGGTATTAAACA
TCCCTGTAGTGATTCCAAACGCGTTATACGCAGTTTGGTCCGTCCAACCA
GGTGACAGTGGTTTTGAATTATTACCATCATCAattctaCTAGCCGTGAT
TTCATTATTCATGAAGTTATCATGAACGTTAGAGGAGGCAatTggtt

QA 6 795 3 797
DS CHROMAT_FILE: LL2335r PHD_FILE: LL2335r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:45 2000

RD LL2312r 787 0 0
cgttTGGGATCCGTGTGGAAG*ACGATTACAACAGGTGTTGTCCTCTGAG
GACATAAAATACAcanccgAGATTCATCAACTCAT*TGCTGGAGTTAGCA
TATCTACAATTGGGTGAAATGGGGAGCGATTTGCAGGCATTTGCTCGGCA
TGCCGGTAGAGGTGTGGTCAATAAGAGCGACCTCATGCTATACCTGAGAA
AGCAACCTGACCTACAGGAAAGAGTTACTCAAGAATAAGAATTTTCGTTT
TAAAACCTAAGAGTCACTTTAAAATTTGTATACACTTATTTTTTTTATAA
CTTATTTAATAATAAAAATCATAAATCATAAGAAATTCGCTTATTTAGAA
GTGTCAACAACGTATCTACCAACGATTTGACCCTTTTCCATCTTTTCGTA
AATTTCTGGCAAGGTAGACAAGCCGACAACCTTGATTGGAGACTTGACCA
AACCTCTGGCGAAGAAGTCCAAAGCTCCACCGCGGTGGCGGCCGTTACTT
ACTTAGAGCTCGACGTCTTACTTACTTAGCGGCCGCACTAGTAGATCTGA
ATTCCCGGGGTCGACCCACCCTCTTTTTTTGGGTTTGGTGGGGTATCTTC
ATCATCGAATAGATAGTTATATACATCATCCATTGTAGTGGTATTAAACA
TCCCTGTAGTGATTCCAAACGCGTTATACGCAGTTTGGTCCGTCCAACCA
GGTGACAGTGGTTTTGAATTATTACCATCATCAaTtntaCTAGCCGTGAT
TTCATTATTCATGAAGTTATCATGAACGTTAGAGGag

QA 6 785 1 787
DS CHROMAT_FILE: LL2312r PHD_FILE: LL2312r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:11 2000

RD LL2320r 791 0 0
gtttGGGATCCGTGTGGAAG*ACGATTACAACAGGTGTTGTCCTCTGAGG
ACATAAAATACACA*CCGAGATTCATCAACTCAT*TGCTGGAGTTAGCAT
ATCTACAATTGGGTGAAATGGGGAGCGATTTGCAGGCATTTGCTCGGCAT
GCCGGTAGAGGTGTGGTCAATAAGAGCGACCTCATGCTATACCTGAGAAA
GCAACCTGACCTACAGGAAAGAGTTACTCAAGAATAAGAATTTTCGTTTT
AAAACCTAAGAGTCACTTTAAAATTTGTATACACTTATTTTTTTTATAAC
TTATTTAATAATAAAAATCATAAATCATAAGAAATTCGCTTATTTAGAAG
TGTCAACAACGTATCTACCAACGATTTGACCCTTTTCCATCTTTTCGTAA
ATTTCTGGCAAGGTAGACAAGCCGACAACCTTGATTGGAGACTTGACCAA
ACCTCTGGCGAAGAAGTCCAAAGCTCCACCGCGGTGGCGGCCGTTACTTA
CTTAGAGCTCGACGTCTTACTTACTTAGCGGCCGCACTAGTAGATCTGAA
TTCCCGGGGTCGACCCACCCTCTTTTTTTGGGTTTGGTGGGGTATCTTCA
TCATCGAATAGATAGTTATATACATCATCCATTGTAGTGGTATTAAACAT
CCCTGTAGTGATTCCAAACGCGTTATACGCAGTTTGGTCCGTCCAACCAG
GTGACAGTGGTTTTGAATTATTACCATCATCAATTTtACTAGCCGTGATT
TCATTATTCATGAAGTTATCATGAACGTTAGAGGAGGCAat

QA 4 791 1 791
DS CHROMAT_FILE: LL2320r PHD_FILE: LL2320r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:12 2000

CO Contig52 657 5 44 U
tgaggaacggtagcttggaacagtacagcggggttaatgaagggtttcca
cccTTCcTGtggtgcaggagccACATGAgaaggatgttgGggaAaGAAGA
TaatgcAaATGAGAATGAaacAGAGAGAAAGAGATGAGAGTTTGGATGAC
TAGTTCTAGATCGCGAGCGG*CCGCCCTTTTTTTTTTTTTTTTTTTTTAA
CTTTGAAAAGCTTCATTTTGAAGGAAATAATGAACAAACTCACCATATTG
GTCAGTTATTGACCTTATTACACGCAATTAGCAACATAAAAAGTTTTGGA
TCTTATTGACGATCTTCTCTTCTTTGTTTTATGCCCTTTGCTCCACGTAT
GACCCCGAGAGTCCTGAGGTTCCAAGAACGGTAACCTTTCCCCACTCTGA
ACCGAGCCCGCTGCATCTCATCTTCAAGTGGATCATCTTTGTCCCCAACT
CCATCTCAACCTTCTTCTTCAAGTAAACTTCTTCA*GGCCCAAACGCATC
TAGGTAGGTAGTATACCTATGATAAGCAAGATGCAGCGCTTTGGTTATAT
CTTGTGGTTGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAggggcg
ggccggt

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 18 18 20 20 22 18 23 20 18 11 14 15 19 16 17 10 10 10 17 12 16 24 21 27 21 27 21 18 14 14 8 10 16 16 10 13 18 18 22 15 15 15 22 19 29 25 25 25 25
 25 18 19 17 17 12 20 15 29 29 40 40 40 32 29 25 21 21 10 12 12 31 31 48 40 40 40 27 25 25 37 40 40 40 40 40 34 32 32 32 32 25 25 25 29 29 40 40 40 40
 29 43 50 56 71 71 65 81 81 83 80 80 80 76 74 73 80 75 76 68 69 70 70 77 85 85 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 86 77 76 75 75 75
 81 78 74 77 77 90 85 81 81 75 75 87 81 84 84 77 81 70 70 70 71 72 90 88 78 81 76 76 76 71 72 75 81 75 86 81 84 77 77 70 70 75 74 88 87 90 90 84 90 76
 73 75 80 76 76 76 79 72 72 73 61 61 73 73 82 79 80 73 73 61 56 56 61 61 70 73 78 76 76 79 79 75 78 78 90 90 90 90 90 90 90 88 88 85 88 90 90 90 90 90
 80 78 80 83 82 82 72 75 75 75 78 81 80 90 90 90 90 90 83 89 89 90 90 90 90 90 75 75 75 84 84 81 82 76 80 90 76 75 75 75 81 84 78 78 73 73 75 76 78 80
 76 78 70 71 72 70 61 61 59 67 67 65 65 67 74 74 86 86 86 82 88 90 86 77 76 70 75 76 79 74 74 73 75 74 80 80 89 89 90 90 84 80 80 65 51 51 57 56 55 66
 60 66 58 55 55 60 58 60 60 51 51 53 59 59 50 57 57 70 70 64 61 61 67 58 64 64 62 62 66 77 82 75 57 56 56 41 41 41 41 50 65 65 71 79 63 51 58 58 53 55
 61 66 57 57 57 57 57 61 61 65 65 59 59 62 63 78 90 81 78 57 58 42 43 43 51 51 46 46 56 59 59 50 50 56 43 42 43 43 51 45 43 43 40 55 55 56 55 57 57 66
 66 59 59 60 69 73 59 59 55 60 68 72 62 61 60 55 59 56 73 73 73 67 66 68 71 75 66 71 60 63 56 61 54 54 53 54 52 53 55 58 65 52 52 62 56 52 37 42 43 36
 36 21 21 21 37 29 35 35 28 29 32 48 48 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 44 44 56 47 47 56 44 56 44 44 44 44 47 47 47 56
 56 56 56 56 56 56 56 56 56 47 47 47 44 48 56 42 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 47 56 47 48 48 48 44 40 40 28 26 19 18 15 0 0 0 0 0
 0 0 0 0 0

AF LL2297f C -232
AF LL2296r C 1
AF LL2332r U 93
AF LL2297r U 93
AF LL2259r U 95
BS 1 150 LL2296r
BS 151 153 LL2332r
BS 154 160 LL2297r
BS 161 163 LL2297f
BS 164 164 LL2332r
BS 165 175 LL2297r
BS 176 182 LL2297f
BS 183 195 LL2297r
BS 196 203 LL2297f
BS 204 208 LL2297r
BS 209 210 LL2297f
BS 211 212 LL2297r
BS 213 216 LL2297f
BS 217 217 LL2297r
BS 218 218 LL2297f
BS 219 221 LL2297r
BS 222 222 LL2297f
BS 223 225 LL2297r
BS 226 231 LL2297f
BS 232 236 LL2297r
BS 237 240 LL2297f
BS 241 245 LL2297r
BS 246 248 LL2297f
BS 249 250 LL2297r
BS 251 253 LL2297f
BS 254 254 LL2297r
BS 255 260 LL2297f
BS 261 265 LL2297r
BS 266 268 LL2297f
BS 269 276 LL2297r
BS 277 277 LL2297f
BS 278 285 LL2297r
BS 286 287 LL2297f
BS 288 309 LL2297r
BS 310 313 LL2297f
BS 314 332 LL2297r
BS 333 333 LL2297f
BS 334 341 LL2297r
BS 342 342 LL2297f
BS 343 391 LL2297r
BS 392 394 LL2297f
BS 395 467 LL2297r
BS 468 468 LL2297f
BS 469 657 LL2297r

RD LL2297f 797 0 2
tcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtga
aaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcg
ttggccgattcattaatgcagctggcacgacaggtttcccgactggaaag
cgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggca
ccccaggcxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxCCACGCGTCCGCTAGTTTTAGATCGCGAG
CGG*CCGCCCTTTTTTTTTTTTTTTTTTTTTAACTTTGAAAAGCTTCATT
TTGAAGGAAATAATGAACAAACTCACCATATTGGTCAGTTATTGACCTTA
TTACACGCAATTAGCAACATAAAAAGTTTTGGATCTTATTGACGATCTTC
TCTTCTTTGTTTTATGCCCTTTGCTCCACGTATGACCCCGAGAGTCCTGA
GGTTCCAAGAACGGTAACCTTTCCCCACTCTGAACCGAGCCCGCTGCATC
TCATCTTCAAGTGGATCATctatGTCCCCAACTCCATCTCAACCTTCTTC
TTCAAGtgagcTTCTtcgcGgcccataCGCATCTAGGTAGGTAGTATACC
TATGATAAGCAAGATGCAGCGCTTTGGTTATATctggtggtgtaaan

QA 15 781 383 791
DS CHROMAT_FILE: LL2297f PHD_FILE: LL2297f.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:44:37 2000

RT{
LL2297f chimera phrap 1 208 000919:094547
}

RT{
LL2297f matchElsewhereHighQual phrap 1 208 000919:094547
}

RD LL2296r 799 0 0
tgaggaacggtagcttggaacagtacagcggggttaatgaagggtttcca
cccTTCcTGtggtgcaggagccACATGAgaaggatgttgGggaAaGAAGA
TaatgcAaATGAGAATGAaacAGAGAGAAAGAGATGAGAGTTTGGATGAC
TCGtTCTAGATCGCGAGcgggcCGCCCTTTTTTTTTTTTTTTtAaaCAAA
ACCCAAGGcaaCTAGGAAAATGCAATCAAATAGTACATCGTATCTCATTG
GTTTATTATTCCATCTCGGGAATTTTATTACAAAAACAAAAGAAAAACAA
GATTACCTTAACTTAAAATCATCGTCAAGGCAATAAAAACCGAACAATAT
TACAGAATCGAAGAAACAACAACATAAACACACAAAACATATTTGCTTAT
AAATATTATTGATTACGAAGAAATTATACGACATGTCTCCCGCAGAGGCT
TTTCTCACCTTTAGGCGTCGGACGTGGAAGGAGCT*GTTGCATCGTCAGT
CGTGGGAGGAGCTGTTGCATCGTCGGACGCAGGAGGAGCTGTGTCAGCGT
CGGCTGTGGCATCCTCGGAGGCTGATTTATCCTTTGATGAGTTAAGTTTG
TTGAACAATGGCTTAAACACGAACTCTACCGCCAACCATGCGACAGCTAA
AGCTCCGACAACAACTGTCGTTGTTTGTTTCTTGCCTGAAGATTTCTCCA
GTTTTGGAAAATGAATTTCtggtactttatccattgcttcttccggacgc
gtggxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxaat

QA 52 719 1 193
DS CHROMAT_FILE: LL2296r PHD_FILE: LL2296r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:11 2000

RD LL2332r 790 0 0
atxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxCCACGC
GTCCGGACTAGTTCTAGATCGCGAGCGG*CCgcgcTTTTTTTTTTTTTTT
CGAATCTTAGCGACAAAGGGCTGAATCTCAGTGGATCGTGGCAGCAAGGC
CACTCTGCCACTTACAATACCCCGTCGCGTATTTAAGTCGTCTGCAAAGG
ATTCTACCCGCCACTCGGTGGTAATTATAATTCAAGGCGGTCCGAACGGC
GCTTCCACCGAACGGACTTAGCCAACGACACGTGCCTTTGGGAGCCGAAG
CTCCTACTGAGGGTCGGCAATCGGGCGGCGGGCGCATGCGTCGCTTCTAG
CCCGGATTCTGACTTAGAGGCGTTCAGTCATAATCCAGCGCAC*GGTAGC
TTCGCGCCACTGGCTTTTCAACCAAGCGCGATGACCAATTGTGCGAATCA
ACGGTTCCTCTCGTACTAGGTTGAATTACTATTGCGACGCGGGCATCAGT
AGGGTAAAACTAACCTGTCTCACGACGGTCTAAACCCAGCTCACGTTCCC
TATTGgtGGGTGAACAATCCAACACTTGgTGAATTCTGCTTCACAATGAT
AGGAAGAGCCGACATCGAAGGATCAAAAAGCAACGTCGCtaTGAACGCtt
GGCTGCCACaaGCCAgttatcCCTgtggtAACTTTTCTGACAcCtCTAGC
TTCAAATTCCGaaggTCTaAAGGATCGATAggccacgctttCAcggttCG
TattcgtacTGaaaatcagaatcaaacGAGCtttTACcct

QA 45 790 56 100
DS CHROMAT_FILE: LL2332r PHD_FILE: LL2332r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:31 2000

RD LL2297r 800 0 4
aatxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxcCAC
GCGTCCGCTAGTTCTAGATCGCGAGCGG*CCGCCCTTTTTTTTTTTTTTT
TTTTTTAACTTTGAAAAGCTTCATTTTGAAGGAAATAATGAACAAACTCA
CCATATTGGTCAGTTATTGACCTTATTACACGCAATTAGCAACATAAAAA
GTTTTGGATCTTATTGACGATCTTCTCTTCTTTGTTTTATGCCCTTTGCT
CCACGTATGACCCCGAGAGTCCTGAGGTTCCAAGAACGGTAACCTTTCCC
CACTCTGAACCGAGCCCGCTGCATCTCATCTTCAAGTGGATCATCTTTGT
CCCCAACTCCATCTCAACCTTCTTCTTCAAGTAAACTTCTTCA*GGCCCA
AACGCATCTAGGTAGGTAGTATACCTATGATAAGCAAGATGCAGCGCTTT
GGTTATATCTTGTGGTTGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAggggcgggccggtxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxaaaaaccctggcgttacccaacttaatcgc
cttgaagaacatccccctttcgccagttggcgtaatagagaagaggcccg
acccgatcgcccttcccaacagttggcgcaactgaatgggaaatggcccc

QA 47 555 58 565
DS CHROMAT_FILE: LL2297r PHD_FILE: LL2297r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:15 2000

RT{
LL2297r chimera phrap 671 796 000919:094547
}

RT{
LL2297r matchElsewhereHighQual phrap 753 775 000919:094547
}

RT{
LL2297r matchElsewhereHighQual phrap 709 738 000919:094547
}

RT{
LL2297r matchElsewhereHighQual phrap 672 704 000919:094547
}

RD LL2259r 799 0 0
natcttxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxagctcgacccatg
cGTCCGTAGTTCTAGATCGCGAGCGG*CCGCCcTTTTTTTTTTTTTtttg
atcCAACAAATCAACTTGATCAGATCATTATAACAGTACAACCCTTAAAC
AAGTGAGTTGCTACAACTGTTGGTAATAAGAATTACAGTTTCTTGTCTAA
GAAAATGGCAATGTAAGGGAAGTAAGGACACTCGTATTCCCATCCGGTTC
CAGAGTAACGAACGCAATGCAACCAAAGAGCCTCATCATGCTCCTCGTct
TGTgggAACCagtgACAGGGAGAACTCATCAAATAAgagcgcatctAcaa
TATACAGGGcatcCCATagCGAATGACCCgctTtatctaAC*TCAACACG
gggatGATCTTgagaccaagattgtcagaagaatcgatgcacgtgagaga
aagctcgccttcccagacgactatctgcattccagcgaagaccngagcat
cgatccaatgcccacaacactgccctaagtctgctccccccagcggtctg
acggaccatgacgaggccctatcggccgtattgtgtttcgtccgccagca
ccccggatggcgcctccgcggcgcccccacctcccccgacaccgccatcc
gccgcagccacggcaaccggcatcctcccaacagccgcgggcgtgagcga
cgcaccccggagatcgggctccccncgccacccagatccgaccaagtttg
gccccctcgtctgtcacgcattccatttgtgtctcgcgttctcttttct

QA 50 412 57 99
DS CHROMAT_FILE: LL2259r PHD_FILE: LL2259r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:22 2000

CO Contig53 615 7 124 U
AAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTC
GCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACA
GTTGCGCAGCCTGAATGGCGAATGGGACGCGCCCTGTAGCGGCGCATTAA
GCGCGGCGGGTGTGGTGGTTACGCGCAGCGTGACCGCTACACTTGCCAGC
GCCCTAGCGCCCGCTCCTTTCGCTTTCTTCCCTTCCTTTCTCGCCACGTT
CGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCC
GATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTAGGGTGAT
GGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGAC
GTTGGAGTCCACGTTCTTAATAGTGGACTCTTGTTCCAAACTGGAACAAC
ACTCAACCCTATCTCGGTCTATTCTTTTGATTTATAAGGGATTTTGCCGA
TTTCGGCCTATTGgttaaAAAATGAGCTGATTTAACAAAAATTTAACGCG
AATTTTAACaaAaTATTAACGCTTACAATTTaggtGGCACTTTTCgggga
AATGTGcGCGgaacc

BQ
 56 56 51 56 51 61 61 55 53 53 53 53 45 45 55 55 55 55 55 55 53 53 53 53 56 55 55 51 51 51 55 55 60 60 53 56 61 61 61 61 66 66 66 66 66 66 66 61 55 53
 55 53 53 50 53 55 55 55 53 53 53 53 53 61 61 53 53 53 53 53 53 56 61 61 61 55 46 49 46 46 46 53 53 53 55 53 53 53 53 53 53 58 55 55 61 66 66 66 61 61
 61 55 53 53 53 53 53 53 53 53 53 53 66 66 66 61 53 53 53 53 53 53 66 66 61 53 53 53 53 53 53 53 53 53 66 61 61 53 53 53 53 53 53 53 53 53 55 61 61 53
 53 53 53 53 53 53 53 53 53 56 66 66 66 66 66 66 66 61 61 53 53 46 46 46 46 46 47 53 53 53 53 53 55 55 53 53 53 53 53 53 53 53 53 53 53 55 55 55 55 55
 55 55 55 55 61 55 53 53 53 53 53 53 53 53 53 53 55 66 66 61 53 53 53 53 53 61 66 66 66 66 66 66 66 66 66 66 66 66 66 66 61 55 55 55 55 55 55 55 55 53
 53 53 53 53 53 55 55 53 53 53 61 61 61 66 66 66 66 66 55 55 66 61 61 61 66 66 61 66 66 66 66 61 55 55 55 55 55 55 61 61 55 55 55 55 55 55 55 55 55 55
 55 61 55 61 61 61 61 50 50 55 55 50 50 55 55 55 55 55 55 55 55 55 50 50 50 50 50 50 61 66 66 66 61 55 55 55 55 55 61 55 55 55 55 55 55 61 61 66 66 66
 61 61 61 61 55 55 55 55 55 61 66 66 61 55 55 55 50 50 47 49 47 47 47 50 66 66 66 66 61 55 50 50 50 50 52 54 58 61 50 50 47 47 47 50 66 66 56 50 50 50
 43 43 50 54 58 50 50 44 36 34 35 37 37 42 42 42 42 42 40 38 37 42 42 42 44 44 44 47 46 46 44 58 50 39 35 32 32 42 42 42 42 42 42 39 42 42 44 39 42 44
 50 43 42 42 35 35 42 42 43 58 58 58 58 58 58 66 66 50 50 46 46 47 47 61 56 66 66 56 50 50 44 39 39 39 50 37 39 35 35 38 42 42 44 39 38 29 31 31 36 39
 39 35 42 37 32 29 31 35 37 39 50 39 32 15 15 15 15 15 37 58 58 50 58 50 44 43 42 42 40 42 39 39 35 35 35 35 39 39 42 42 58 35 35 35 32 32 35 39 39 39
 35 35 44 44 39 39 39 28 26 15 15 25 15 33 37 37 33 28 28 33 42 39 34 32 35 36 27 28 37 25 24 18 15 15 17 25 30 34 39 39 35 36 32 29 20 10 10 10 17 10
 25 24 25 25 24 25 17 25 25 24 18 18 18 18 18

AF LL2257r U -747
AF LL2348r U -680
AF LL2306r U -518
AF LL2303r U -433
AF LL2318r U -175
AF LL2265r U -174
AF LL2316r U -174
BS 1 1 LL2316r
BS 2 2 LL2306r
BS 3 3 LL2316r
BS 4 4 LL2303r
BS 5 8 LL2306r
BS 9 12 LL2265r
BS 13 14 LL2316r
BS 15 20 LL2306r
BS 21 24 LL2316r
BS 25 26 LL2303r
BS 27 27 LL2306r
BS 28 30 LL2303r
BS 31 32 LL2306r
BS 33 34 LL2303r
BS 35 35 LL2316r
BS 36 36 LL2306r
BS 37 40 LL2316r
BS 41 41 LL2303r
BS 42 43 LL2316r
BS 44 44 LL2265r
BS 45 46 LL2316r
BS 47 47 LL2265r
BS 48 48 LL2316r
BS 49 49 LL2303r
BS 50 50 LL2316r
BS 51 51 LL2303r
BS 52 53 LL2316r
BS 54 54 LL2303r
BS 55 55 LL2316r
BS 56 58 LL2306r
BS 59 63 LL2316r
BS 64 65 LL2306r
BS 66 71 LL2316r
BS 72 72 LL2306r
BS 73 75 LL2265r
BS 76 76 LL2303r
BS 77 77 LL2316r
BS 78 78 LL2306r
BS 79 81 LL2316r
BS 82 82 LL2265r
BS 83 91 LL2316r
BS 92 92 LL2306r
BS 93 95 LL2316r
BS 96 98 LL2303r
BS 99 101 LL2265r
BS 102 112 LL2316r
BS 113 113 LL2303r
BS 114 122 LL2316r
BS 123 123 LL2265r
BS 124 124 LL2316r
BS 125 125 LL2306r
BS 126 133 LL2265r
BS 134 134 LL2316r
BS 135 137 LL2265r
BS 138 167 LL2316r
BS 168 169 LL2265r
BS 170 176 LL2316r
BS 177 177 LL2303r
BS 178 197 LL2316r
BS 198 203 LL2265r
BS 204 239 LL2316r
BS 240 249 LL2265r
BS 250 264 LL2316r
BS 265 268 LL2265r
BS 269 277 LL2316r
BS 278 278 LL2265r
BS 279 308 LL2316r
BS 309 311 LL2265r
BS 312 351 LL2316r
BS 352 360 LL2265r
BS 361 363 LL2316r
BS 364 369 LL2265r
BS 370 370 LL2316r
BS 371 373 LL2265r
BS 374 385 LL2316r
BS 386 394 LL2265r
BS 395 404 LL2316r
BS 405 405 LL2265r
BS 406 406 LL2316r
BS 407 409 LL2265r
BS 410 418 LL2316r
BS 419 420 LL2318r
BS 421 443 LL2316r
BS 444 444 LL2318r
BS 445 467 LL2316r
BS 468 469 LL2265r
BS 470 484 LL2316r
BS 485 485 LL2265r
BS 486 493 LL2316r
BS 494 495 LL2265r
BS 496 502 LL2316r
BS 503 506 LL2265r
BS 507 508 LL2316r
BS 509 509 LL2265r
BS 510 520 LL2316r
BS 521 522 LL2265r
BS 523 524 LL2316r
BS 525 526 LL2265r
BS 527 528 LL2316r
BS 529 532 LL2265r
BS 533 557 LL2316r
BS 558 558 LL2265r
BS 559 559 LL2316r
BS 560 564 LL2265r
BS 565 571 LL2316r
BS 572 573 LL2265r
BS 574 575 LL2316r
BS 576 576 LL2265r
BS 577 579 LL2316r
BS 580 580 LL2265r
BS 581 582 LL2316r
BS 583 584 LL2318r
BS 585 585 LL2316r
BS 586 592 LL2265r
BS 593 595 LL2316r
BS 596 596 LL2265r
BS 597 600 LL2316r
BS 601 602 LL2318r
BS 603 603 LL2265r
BS 604 604 LL2318r
BS 605 606 LL2265r
BS 607 607 LL2316r
BS 608 610 LL2318r
BS 611 615 LL2316r

RD LL2257r 788 0 1
aatxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccacg
cgtccggtggtgcctacatcgttaggcaagCGGCTAAGAGTATTGTTGCC
AGTGGGCTAGCGAGGCGTTGCATTGTGCAGGTCTCGTACGCTATTGGTGT
CCCTGAGCCGTTGTCTGTGTTTGTGGACAGCTACGGAACTGGGAAGATAC
CAGACAAGGAGATTCTTGAGATTGTGAAGGAGAGTTTTGACTTCAGGCCG
GGGATGATTTCGATTAACTTGGATTTGAAGAGGGGTGGTAATGGTAGGTT
CTTGAAGACTGCTGCTTATGGTCATTTCGGAAGGGACGATGCTGACTTCA
CCTGGGAGGTTGTGAAGCCACTCAAGTCTAACAAGGTCCAAGCTTGAAGA
AAACTTGAACTAGTTTAGTTCTCTCAGGTCTTGCCTCTGTTTCAACTAAA
GAGATGGGTCTATTCTTTTTCCTTTTTCAATATAAGCAGTTGAGAATTTA
TATTATTATTATTTATTATCATATGTTATTGTTGTGGTAAGAAAGTTAAA
AGTCATATTTTGTATTTCTTGTTTCTTTTCAGAAGAGAATTTATATAAAA
GATTATATTCAATATTAAAAAAAAAAAAAAAAGxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxaa
AACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCAca

QA 81 775 749 788
DS CHROMAT_FILE: LL2257r PHD_FILE: LL2257r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:13 2000

RT{
LL2257r matchElsewhereHighQual phrap 749 788 000919:094547
}

RD LL2348r 793 0 1
aatxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccacg
cgtccgcaactgtcttggtgactcagaacaAAAATCTGAACAGACCTTCT
GAGTATCTTCTTGATGGGAAAGTAACAGACAAGAATGATGTCTACTCTTT
TGGGGTGATTCTCCTAGAACTTCTCCTGGGGAAGAGATCAGTGGAGAAAC
CATCAACTGAACCAGAATCCGTTGTCACTTGGGCTGTACCAAAGCTGAGT
GACAGAGCTAATCTGCCAAACATATTGGATCCTGCAATCAAAGGAACCAT
GGATTTGAAGCATCTTTATCAGGTAGCAGCGGTTGCGGTGTTGTGTGTGC
AGCCAGAGCCAAGTTACAGACCACTTATAACCGATGTTTTGCACTCACTC
ATCCCTCTTCTACCACTAGAACTCGGCGGATCATTGCGAATTTTATAGAA
ACACATTTTCATTTCCTTTATTGTAATCTTTTCATTTTGAATTGAATGTT
GTTGGTGATCTTGTGCAAAATTCCACTTTTTATCTGTTTTTTTTTGGTAA
AAAAAAAAAAAAAAAGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAAAACCCTGGCGTTACCCA
ACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCG
AAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCct

QA 81 793 682 793
DS CHROMAT_FILE: LL2348r PHD_FILE: LL2348r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:31 2000

RT{
LL2348r matchElsewhereHighQual phrap 682 793 000919:094547
}

RD LL2306r 814 0 2
agggtaggttttggacngcctttcgtgactgccgcaccgtttccgggttc
cacggtcgacccacgcgtccgctcactctcACTACCTTCTCTTCACCCgc
aaATGGCGACCGCTCCTCTCTCCGGCTTCTTCCTCACCTCTCTTTCTCCT
TCTCAGCCTTCTCTCCAAAAACAGACTCTTCGTTCTTCTCCCACCGTGGC
TTGCCTTCCCTCATCCTCCTCTTCCTCCTCCTCCTCCTCCTCCTCTCGTT
CCGTTCCAACACTTATCCGTAACGAGCCCGTTTTTGCCGCTCCTGCTCCT
ATCATCACCCCTTACTGGAGCGAAGAGATGGGTAGCGAAGCATACGAAGA
GGCCATTGAAGCTCTCAAGAAGCTTATTATCGAGAAGGAGGAGCTAAAGA
CTGTTxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxAAAACCCTGGCGTTACCCAACTTAATCGCCT
TGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCA
CCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGGACGCG
CCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCGCAGCGT
GACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGctntCTTCC
CTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCgg
nggCTCCCTTTagg

QA 81 742 520 814
DS CHROMAT_FILE: LL2306r PHD_FILE: LL2306r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:20 2000

RT{
LL2306r matchElsewhereHighQual phrap 745 800 000919:094547
}

RT{
LL2306r matchElsewhereHighQual phrap 520 743 000919:094547
}

RD LL2303r 793 0 1
atxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxccacg
cgtccgtagatcgcgaccggccgcccttttttttttttttaatatttgct
cttttctctcatcttcttttagttatctcttcgtttacctcttcctcctt
tatttaatgtaactttgctttcaatatcttatattaatgttctcagtgac
ataaaaaatatattgtatgcatatgattatgcatgtacatgattgaaaaa
acttaatggcttaagtgtttaaattgtaataactaaaaatatattttaat
caaaaaaaaaaaaaaaaagxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAAAACCCTGGCGTTAC
CCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATA
GCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAAT
GGCGAATGGGACGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGT
GGTTACGCGCAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTC
CTTTCGCTTTCTTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGT
CAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACG
GCACCTCGACCCCAAAAAACTTGATTAGGGTGATGGTTCACgt

QA 81 777 435 793
DS CHROMAT_FILE: LL2303r PHD_FILE: LL2303r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:43 2000

RT{
LL2303r matchElsewhereHighQual phrap 435 730 000919:094547
}

RD LL2318r 788 0 4
aatxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxAAAACCctgtcgTTACCCAACTTA
ATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAG
GCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATG
GGACGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGtggctACGC
GCAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCT
TTCTTCCCTTCCTTTCTCGCCAcggtCGCCGGCTTTCCCCgccAAGCTCT
AAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGggaCCTCG
ACCCCAAAAAACTTGATTAGGGTGATGGTTCACGTAGtggtccATCGCCC
TGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTAATAGT
GGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTcgtgctATTC
TTTTGATTTATAAGGGATTTTGCCGatctcggactATTGgtataaAAAtG
AGCTGATTTAAcagatatTTAACGCGAattgtaacaacatATTAACGCTT
ACAATTTaggtggCActgttcgtggaAATGtgcGCGga

QA 177 671 177 788
DS CHROMAT_FILE: LL2318r PHD_FILE: LL2318r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:39 2000

RT{
LL2318r matchElsewhereLowQual phrap 443 472 000919:094547
}

RT{
LL2318r matchElsewhereLowQual phrap 426 441 000919:094547
}

RT{
LL2318r matchElsewhereHighQual phrap 350 424 000919:094547
}

RT{
LL2318r matchElsewhereHighQual phrap 187 344 000919:094547
}

RD LL2265r 783 0 1
atxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxAAAACCCTGGCGTTACCCAACTTAA
TCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGG
CCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGG
GACGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCG
CAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCTT
TCTTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTA
AATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGA
CCCCAAAAAACTTGATTAGGGTGATGGTTCACGTAGTGGGCCATCGCCCT
GATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTAATAGTG
GACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGTCTATTCT
TTTGATTTATAAGGGATTTTGCCGATTTCGGCCTATTGgttaaAAAATGA
GCTGATTTAACAAAAATTTAACGCGAATTTTAAcaaAaTATTAACGCTTA
CAATTtangtGGCACTTTTcggngaAATGTGcg

QA 176 754 176 783
DS CHROMAT_FILE: LL2265r PHD_FILE: LL2265r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:14 2000

RT{
LL2265r matchElsewhereHighQual phrap 176 471 000919:094547
}

RD LL2316r 790 0 1
attxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxAAAACCCTGGCGTTACCCAACTTAA
TCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGG
CCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGG
GACGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCG
CAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCTT
TCTTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTA
AATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGA
CCCCAAAAAACTTGATTAGGGTGATGGTTCACGTAGTGGGCCATCGCCCT
GATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTAATAGTG
GACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGTCTATTCT
TTTGATTTATAAGGGATTTTGCCGATTTCGGCCTATTGgttaaAAAATGA
GCTGATTTAACAAAAATTTAACGCGAATTTTAaCaaaaTATTAACGCTTA
CAATTTaggtggcACTTTTCggggaaaTGtgcgcggaacc

QA 176 790 176 790
DS CHROMAT_FILE: LL2316r PHD_FILE: LL2316r.phd.1 CHEM: unknown DYE: unknown TIME: Tue Sep 19 09:45:30 2000

RT{
LL2316r matchElsewhereHighQual phrap 176 471 000919:094547
}


WA{
phrap_params phrap 000919:094547
/usr/local/genome/bin/phrap Run_SRC3700_2000-07-06_44+45.fasta.screen -new_ace -view 
phrap version 0.990329
}

BioPerl-1.007002/t/data/acefile.singlets000555000766000024     20377413155576321 20112 0ustar00cjfieldsstaff000000000000>RL767F  CHROMAT_FILE: RL767F PHD_FILE: RL767F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:27 2001
CCTANTGAGATACTTAACCTCAATGTGTCTTCTTTCCTACACATGGCATC
CTTATTAATGAAAAACAGAGAAAACATCAAATCAAATAGTAGCTTACACT
TGGTGAAAACTGAGAAAGCCCATGCTCGGAGAGATCACTTTAGAAAAGGT
GTCATGGTTCAGCAAAAGCATGAATAAGCCAAGTGGCTCTTCTTTGAGAT
GTAAGGAGAGATGAAATCTGTACCATGGGAAGAAGTCTCAGAGATCTCTG
CTGGAACTAGCACTTGAGGCTTACCCAAAGCTATCCTTTTCCCAACTGTG
TTTGCCTAGAACAAACCAGATATGGCTGGAACAAACACATCGCTTTTTGC
ACTTATGTACAAGTCAATAACATTTTCATACTCAGAACTCTCTGATTCAA
GGTACTCTGATCCCTTACTTGCTGGCATTACTGCCTCCTTTGTAAACGCT
CCTGGCAACACATCCTTAAGGATATTGAGGCTACTGTCCCATCTACGCTG
AGCCCCACACATGGCTGTGTCCCTCACCCCCATCCCGCTTCCTCCACAAC
ACACCATCCCCTTGTGCCTTGCAACAAGCTCTGTCCCCTCCCACACCCGT
TCGAACGCCCCCATCTTTTCTCCAGTGCTTCGATCCTACCGTCCCCAGCT
ATCCAACGGACACCCGCACACCCGTCCCGGCCCCTACCCCTCTTCGCGGT
CTCCACCACCCGCCCCATCTCACTCTCCACACCCAGGCACCCCCACCCGC
CCCCCGCCCCTGGTC
>RL767R  CHROMAT_FILE: RL767R PHD_FILE: RL767R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:52 2001
ACTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXATACCTTGTCTCTATCTGCCCCCACACCACACTCTCTTTGTTGG
ACTTTCCTTTTCTTTTTCTTTTCCTTTTCCTTCCTTCCTTCTCTCTGTTT
CAACTCTGTTTTCACAGATCCAGTTTTGTAAGAAAGTACTAGAAATGGGT
GTGGATTTGAGGCAAGTGGTTGCTGGTATTCTCACCATCACCATGTTTGT
GATGCTCGGACAGATGCTTCATCGAGATTACTATGATTCTCTTCAGGAGA
AAGCTCAGGGAGATGCACATGATATCGAATTCGAAGGATCAAGAGTATCT
GTGAAAGATAGTCTTGTTGGAGCGTTAGAAGGAAATAAAGGACCTTGGAT
GGATGATAACAATGACCTTAATCCTTGCTGGCCAACATTACTATCCGATG
AAGCGGTATCATCAAAAGGGTATGTTACATTCTCTCTAACGAATGGTCCT
GAGTACCATATCTCTCAGATCACTGATGCTGTAATGGTGGCAAAGCATCT
TGGAGCAACACTAGTGCTTCCTGATATAAGAGGAAGCAAACCTGGTGATG
AAAGGAACTTTGAAGACATTTATGATGCTGATAAACTAATCAAAAGCTTG
GACAATGTCATCAAAGTTGTCAAACAATTGCCTGAAGAAGTATCTCTAAG
AGACATCGCCATTGTTAAAGTCCCTACAAGAGTTACAGAAGACTACATCA
TAGAACACATTGGACCCATCTTCAAGTCCAAAGGAAACATTCGAGTAGCT
ACATACTTCCCTTCTGTCAACCTGAGGAAATCCTCACACGACGGCGAATC
CGATCCTGTGGCTTGTTTGGCATGTTTGGTCCTTGGAGTGCACCT
>RL769F  CHROMAT_FILE: RL769F PHD_FILE: RL769F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:33 2001
GCGGGGCGGGGCCCAGTAAGGNAGGCGGAGGGAAAAACAAAGAAAAAAGT
AAAAGGGGGGGGCTGGNGGCAGACTNGGAGGACGGGCCTAGAGGGGGGAG
GACAGACAGAGGCGCGGTGCGGCAAGAGAAGAACAAAGAAAAAACAAACA
GCAGCAACGGAGGGCAAAGCCCGCGCGCCGGCGAGCCCATAAAGACGCGA
TGAAGGACGACCGCCGTAGGAGTGGGGACCGAGGGAACCAAGAGAAAAAA
CCGAGACGAGGCGCCTGACGCCGGGCGGCGCGCCGAAACCGCCCCGCCGC
ACCCGACGAGACACAGCAGCCCNACATGCGGCAAGCGCGGAGCGCCAGCG
CCCACCAAAGGAGGACCGCGAGACCGGCGGGGGCGGAGGGAGGAGCAACG
AAGCACAAAAACAGACCAAAGAAATAAGTCGCCACGCGCGGGGCGTGGCG
TAGTGAGGAAAGCAGGGGACGAGAGCAAGGAGCAGACCGAGCGAGCGCGC
ACAGCGCGCACAGACCGCNCAAGCAGAACACATAGAACGACCCGTGCCNC
GCGCACGACCCGCGAGCCCAGGACACGCCCAGACGCAACCACACGCCGGA
ACGGAGCGGAACCCTGCGCCCACGGACCGGGGGCAACACGAGAGGGAAGG
AACGCGGAAAAAACATGCACCAACAAGACCTCGACACCGACGAGCGTGCA
AGAGGATCGGCGCGCGCGCGAGACCCCGAAGAAGAGAAACGCGCACACGT
AGACCCGGACGACAACGAGCGAGACNCAGAGCGAACAGCGACAACGACGA
CACACCAACGCAAAACAACGGATGACGGACCGCGCAACACGCGAACGAGA
GCGGAAAGCGAACGCGAGCGAGAGACGANGAGACCAGTAACCGGAAAGAA
GGACGCCATACGGCGGAACGCAGCGAACGCGCACGCCGCGACACGAAATC
GACACATTCGCCGCGACCGAAGGAACCGTACGCCCGCAGAACGACGACAG
CNAAGACACCAGCACGCACAGCNGCCCGAGCNGTAAGCAAGTCGACGGCA
GGAGCAGTGCGAGCGCGGCGACGGCGAGAAGACG
>RL769R  CHROMAT_FILE: RL769R PHD_FILE: RL769R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:59 2001
CGTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXCTTCTGGTATAATTCAAGGGCTTAAGTTCAACTCCAACAAGAAGT
CTTCTGATGTTATTGGATACAATGATGGTACTCCATTTACCCTCCAAGTT
CAAGACAAGAAGATAATTGGCTTTCATGGCTTCGCCGGAGACAATCTTAA
TTCTCTTGGAGCTTACTTTTCTCCATTAATAGCTGCCCCTCCTTCAGTTC
CCCCAAAGAAGCTTGAAGCTAAGGGTGGTGTGTCTGGAGCTGAGTGGGAC
GATGGTGCTCACGACAATGTTAAAAAGGTATCTGTAGGACAGGGCGAAGA
TGGTGTAGCAGCTGTCAAGTTTGAATACACAAATGGTTCGCAAGTGGTTA
TTGGAGCTGAACGTGGGACACCAACATTGCTTGGATACGAAGAGTTTGAG
CTTGAATCAGATGAATACATAACCATCGTGGAAGGCACCTACGACAAAAT
CTTAGGGAGTGATGGCCTGACGATGCTCACTTTTAAGACTAACAAGAGCA
GAACATATGGGCCGTATGGTCTCGAAGGTAGCACACACTTTGATCTCAAG
GAGGAAGGTCACAAGATTACAGGGTTCCATGGACGAGCTGGCGCGACTAT
TAGTGCTATTGGAGTTTACTTAGCTCCAGTAGGCACCATCCCCTTGACTC
CTGCACAACCAACCAAGAAGCTAGAAGCTAAGGGTGGTGAGGGAGGAACG
TCATGGGATGATGGTGCTTTCGACGGTGTACAAAAAGTGTCTGTAGGACA
AGCCCAAGATGGTATATCAGCGGTTAAGTTTGTGTACAACANAGGTTCTT
CTNGAATCATAGGAGATGAACATGGGAAGAGTACTCTACTTGGATTCGN
>RL770F  CHROMAT_FILE: RL770F PHD_FILE: RL770F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:36 2001
ACGGTACACATTCTTCTATCAGATACATTAATCCACATTAATCCAGATCT
CGCAACACAAACCATGACTATATTTTTTTTGTCTGCATCCTGTCTAGGAC
CATACAAGATAGGCACCAATGCCTTAAGAGACATAAACATATGGCCCTCG
GTGAACCCCTCTGTTCAACACCAAAATTGAAAGCTATCCTTTTGCATGGG
TTCCGAAATTTAAAGCGTGTATGCTTGTGGACTGGGACAAACATCAGATT
AAGCTTGCCTAGTTCTTTGCTCTATGAACTTGAGTCAATGGGAACAGATT
TTGCCGGAGAATAACCAAAGCTGTTGCTGCTACTGCTTTCTCCATTGGTT
GTAACATCGGATTGAGCTGAAGCTGAAGAGTTCATAAAACTCTGGTTGGC
ATTTGGGGATGGGGCTTGACCTTCTTTACGGAGTTTCTTAAGGAGGTTCA
TGACCGCTGGAACGAACTTGGTTGACAAGGCAAGAAGCACACCTCCCTGC
TCCATGTCGCGCATTCTCCTGAACTATTTAACTGCACTCACCCGGCCTTC
GAAAACATCTGCTCTCTCTCACCACACTACCTCCGTCCCACTGGCTTCAC
TCCCTCCTCCCCTCTACCGCCCTCACCTCACCCTCTCTATATGTCCTGGC
CTTGTCTCCGCCTCGCGCACACTCTGCTTATCATACCCCGTCTTTTATCT
TTCTTCCTACCCACTCATCTCTCCCTCACCCTCGCTCCTTTTACCTTCAT
CTGCCATTGCACTCGCATCTCTTCTT
>RL770R  CHROMAT_FILE: RL770R PHD_FILE: RL770R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:02 2001
ACTCTTGGTACNGNACATGCAGGTACCNNNGGTCCGGNAATNNTCCCGGG
NTNNCGACCCACNGCCGNNTCCGGNAGACTATCTCAAACGATGCAGGCTT
GACTATATTTGACGACAAACAGGCCTCATTAACACCTACTGTCTGCACTC
TTGGCAGGCACTTTGCCTAGCGTGAGTAGTACTGATGGATGTTGGTCTCC
GTGACCACATAGCGGTTGTGCTTTCTTATGCTGCATTAACATGATGCTGG
CTAAGTGATCAATAGACAATCATAATACTTTGTGACTCTTCCAGTCTCAC
TATGGCTGATGGTACACAACTAGTGCGATGCGACGAAATTGTCAATGAAA
ATGTTGCTGGTTCTTATTGCCAATGACAACTTGACGTGAATTGGATAAAG
CCTGTTCTTTCTGTACCTGAGCGTGAATTAGGAAATAATGTGAGCTAACT
CCTCCACCATTGCTTATTACAGTATGACACAGAGGCAACACTACTTTGAA
GAAGGCGTCATATCTTCCAAGAGACAACAGCTGAACTAAAAATTATTGCT
ACTTGTTCAACCAACTTTACTATACCTGCTTGGACATTTGAGATCTGGAC
CACTTGAAAACTTCAAGGATGCTTTTGATAAGGCGTTAAATGCCGGCGAA
ACCTCTTCACAATCAGAGGGTGTTCGCGCTCAGCCTTGCGTGTCTACATT
GGATAAACGATGTGACTATGCTGATACTGAACAACCGAACTGTGATACAT
GCTAAACTCGGAAACTGCTCCAGAGTGACATTGAAGCCCATATCTCTTCT
GCGCGTACTGCACAGCTGTCTGAACTGACTACTCTGTATGATTCAAAACT
AAGTGCAGCATCATCTGTACAGTAGGAGCTCTTCTGTATGGAGCACTGAC
GAACGATGGGCAGCATATTAAGCTACTAGACGAGATGGAGAATTGCTGCC
ATGATCTCTCGACGA
>RL773F  CHROMAT_FILE: RL773F PHD_FILE: RL773F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:45 2001
CATTCAAGTTAAAGATGGTTTAATGTGTCAACAGTGTGAGCTTTGAGTTC
AGTATGTTTACACATTGTGATAACAGCAACGGTATTCTTGATATCATCAT
CTCAATTCACCTTTTAAGACAAGTGATGCATGTCTTATAGCTCTAGACAC
TCTCCATATCTCGTGTTGAACGTGTTCCCAAGAAGCTTTGGTCTTTACTC
TCTTTGCATTGTCTATTGCATCATCCACTCCAGGAAATGATTTTGATCCG
TAGTCATCGTACTTGGATGGTCCATATACCAAATGCTTGTACCATGTTCT
TCCAGAGAGTCCATCTCTGTCTGTTAAAGCTCGCTCCGCCATCATTAATC
TGTCATTGACCTCTCTCACTCTCAAAGCTCCCTTTACTCCCTCCTCTTTC
TCTATATTAATTTCTTGTGCTGCTGTAGATAGATCTTGGATTGATTTGAT
TAACGGAGAGATATCTATGCTATGTGCTAACATCTNCTCCTCCAAATCTT
CAGCACTTTTCTTGAGTTCTGATGCATAGGAGGCATAGCTGAAAGGTAAC
AACTCATCATCTGCTAACCGAAGAGCCCCAAACCTACAACACTACCTATT
GCCACATGTCTCTGAAACATTGGGTCCCCAACTTCTCCATCCAAGTGAAC
CCATCCTACATACAGCGACTCACTGCCTATCCTCCTCCGAAAAGCCTGCC
ATCTGCCGGAATGCCTATCTGCTGCCCACATGCTCTCTCACACTACGC
>RL773R  CHROMAT_FILE: RL773R PHD_FILE: RL773R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:13 2001
AGTCTGGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXAAACCAACAGCAGTTCTCGTCTTCCTAATCGCTGCTTTCTCCTAC
TTCCTCTTCTCTCCTTCCCCAAAACCTCACTACTACCACACACTCTTCCT
CTCCTCTCCCTTCTCCGACAACGCTTCCATCGCCTCAAACCTCCGCACCC
TCACGCGCCGCCCCCACGTCGCCGGCTCATTAGCCAACGCAGAAGCTGCA
TCCCACGTCCTCTCCTCCTTCGCCTCCTCCTCCCTCAAACCCCGCGTCGC
CGCTTACAAAGTATCTCTAACGTACCCAGTTCATCGCTCACTCTCACTAC
TAACACCAAAAGCATCATCATCAAAGTCCATCATCGCTTTCTCTCTGGAG
CAAGAACACCTCGGAGACAACCCTTACGCGGACGAAGTCACGCCTACGTT
CCACGCCTACGCCAAGTCAGGCGACGTCTCCGGTCCCGCGGCGTACGCGA
ACTACGGACGAGTCGAAGACTTCGTGGGCCTAAACGTCTCCGGCGCCGTC
GTGGTCGCGAGGTACGGGAAGATCTACAGAGGGGATATAGTGAAGAACGC
GTACGAGGTGGGAGCTGTAGGCGTTGTGATATATACTGACGAGAGAGATT
ACGGCGGAGAGGAGTGTTTTCCGGAGAGTAGGTGGATGCCGCCTAGCGGG
GTTCAGGTGGGTACTGTTTACAATGGGTTGGGTGATCCGACGACTCCTGG
GTGGGCTAGTGTTGATGGGTGTGAGAGGTTGTCGGAGGAGAGTGTGGAGC
TGAGGGGAGATTCTNCGGGTATACCTTCTCTGCCTATCTCTGCGGCTGAT
GGNGAAGTGATNCTGAAGACGGTTGTTGGAGGTGTTGGGCCTG
>RL777F  CHROMAT_FILE: RL777F PHD_FILE: RL777F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:33 2001
CTTCGTAGGTTACTAGGCATGCATGAAAGGACAAAACACCTATTAACATT
GCAATGAATACAATTGACAGCTCACAGATTTAAAAATAACAATTCGACTC
TTTAAGTACATTTTTATTCAGATCACACTCAAGAGGTTTCTTGAAAAGGG
AGAAATATAGAACAGATGTTGGCACTACAAGGTAACTTCCAGATGACGAG
GTTTCGTTCCAGCCCATAAAACATGCCCTATGATCTTGCCACCGACATCG
GGGAATGTCTTGCATCCTGGAAGAGAACTTACTTTGCCTGTTCTATCGAC
TTGAACTGGATACTTTACAAGATGACTTGCCATCACTGTGACTTCCTCTG
CTGCATACTGCCTTCAGCTGAGCTCACTCAAATGCCTAACTCGCCCCACG
CATTCCATGCCACCTGGCTCCTCGAAACCCTGCTCCATAAACCCTACCAT
GCTCTGCCCACAGTGACCCCCCGCCTCCATACATCTTGCCCCTATGCCTC
CAGCTCTTCTTCACTCATGCCTCCCGCCGCCGATACCTCCCCATGGCACC
TCCAATGCCTCTACCCCTCTCACTCCTACATTGCCGCACCCTCCACACCC
CTCCACTATCCTTTCTCCTTCCCACTCTACCGACCGCATGCCCCACCTCA
CCCCACCCTCCCCTCCCTTCCCAGCCCCACTTCACCCCTGCTCCCCACCA
CCCTTTCCCCGCCCACCCCCCCATATATTCACCCCCCCCCCTCATCTTTT
T
>RL777R  CHROMAT_FILE: RL777R PHD_FILE: RL777R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:59 2001
ATTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXATAATTTGAATTCACTGTATCGTTCATACGATTTAAGTAATGTT
TTACTGAGTCTGGACCACTGTTGAAGTCTTTCATTGGCTAAAGTTTGAAA
GGTCAACAACGTACTGCTCACTGCTTTGATTCGTCTACTTATACCTCATA
GATTTATTCTGGATCTGTATCTCAAAGGTCCTCATAGATTTATTCTGGAT
CTGTATCTCAAAGGTCTCAGTGAACTTTTTCTTTGTTTTGTGGGTTTGAC
TCGAGATTTGATCCTTTTCTTATTTATTTTTTCCTCCGAATTTTTGGTGC
ATCATTCAGTTTATACCGAGACCAATGTCAATGGAAGGGTCAAGTAACGC
TTCTTTGAGGGTAGTGTTGTTACATGGTAACTTAGAAATTTGGGTGAAGG
AAGCTAAAAATCTTCCTAACATGGATCGTTTCCGGAGGTACAAGAAGAAC
AGTACAAGTGATCCTTACGTGACTGTCTCTATCGCAGATGCAAAGATTGG
CACAACTTTTGTGATCGACAATGATGAGAATCCTGTGTGGATGCAGCATT
TCTATGTACCGGTGGCTCACCATGCTACGGTGGTTAAGTTTGTGTTGAAA
GACAGTGACCGTTTTGGATCAAGGTCCATAGGAGATGTTAGAATCCCAAC
CGAGGAGTTGTGTTCAGGGAATAGGATCGAAGGGTTGTTTCCGATACTGA
ACACTAGTGGGAAGCCATGTANAAAGGGTGCTGTGTTGAGTTTGGCTATT
CATACACTCCAGTGGAAATGATGAAAATTTACCCAATGGGTGTTGGTAAT
GAGTGCGAAGGAGTNTCCGGTACGTACTTCCCTTTGAGGAA
>RL778F  CHROMAT_FILE: RL778F PHD_FILE: RL778F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:36 2001
GCTAAATGACACTTTTTATTCTGATTATTAANCTTGAAAAATCATACAGA
ATAACAACAAAAAAGACCAAGAAACCATATAATAGAAGGGAAATCAAAGT
GTATTTAAAAAGCAAATAGAAAATGAAAAGATATGCTTATTGATGTGCTA
TTAAGCCTAGATCACAAGACAAAGCCATATCAAAGAAAACAAACTGGTAC
AAAACAAGAACAGGTTCTCCATCACATGGGTTTATAGAAGAAAAGCTGGT
CCCTCCTTATTGCGGACCTCCTTTATAAGTATCTATTAGCTCCTTGAGTT
TCTCGAATCCCATGCGGGTTGTGAATTCTCCGAATGATTCTTTAGTTTCT
ATGTCCACTTTCCAGTGATAAAACAACGGCTCGAAGACTTTCTCCAAGTC
GTGAACCTTCACCTTATCCATGAAGCTGCTTGCTATCTGTGTCTGGTTCG
GTGTTCCTCCTAGCCAAACCTGATAGCTGCTGGGACCATTACCGACTAGA
CCAAGCTCAGTCATGTACGGTTTTGCACATCCGTTAGGACAACCGGTTAC
TGTTATCACAACAGACTTTTCGTACTGCAGACCAATCTTGTCAAACATCG
GTCTTACTCGCTCCACAATGCTGGGGATTTCGCGCTCTGCCTCCGTTATC
GTTTGAGGGTTTTTAGGATAACCTGGTCACTTCTTGTTGCCTGCTCTACT
GGTCCACCAACCTCCGCCGTCTCCTGCCCTCTTCACCTCTCCTGTGCCTA
TGGGCTCCTTCCTCTGCTA
>RL778R  CHROMAT_FILE: RL778R PHD_FILE: RL778R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:03 2001
CGTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXAAAAGCCTTCGTCACACACACTCCCTCTCTCTCAATCAGTGAAGT
GATGTCGTCGTCGTCGTCTTCGTTTCGATCTCCGGCGGGTGCCGCCGCCA
CTCTGTTCTCGTCTGATCAGAAGATCAGACTCGGGAGGCTCGACGTTCTG
AGATCTTCTCATTCGGCTTTCTTAGGGAGGAGAAATCCACGTGGCGTCGT
CTCGGTTCATCCATCCTCTTCCTCGTCGAGTCCTTCGCCTATCCAAGCCG
TCTCCACGCCGTCGAAGCCTGAGGCTGCGACCAAGCGGAGTAAAGTTGAA
ATAATCAAGGAGAAGAGCAACTTCATAAGGTATCCACTCAACGAGGAGCT
TTTAACCGAAGCTCCCAACGTCAACGAGTCAGCCGTGCAGCTCATCAAGT
TCCACGGTAGCTACCAGCAGTACAACAGAGAAGAGCGCGGTGGAAGATCT
TACTCCTTCATGCTCCGCACCAAGAACCCTTCCGGAAAGGTCCCTAACCA
GCTCTATTTAACTATGGACGACTTAGCAGATGAGTTCGGCATCGGTACGC
TTCGTTTGACCACTAGGCAGACGTTTCAGCTCCACGGTGTTCTCAAGCAG
AATCTCAAGACCGTGATGAGCTCGATTATTAGAAACATGGGAAGCACTTT
GGGGGCTTGTGGTGATCTGAACAGAAACGTTCTTGCTCCGGCGGCGCCTT
ATGTGAAGAAAGATTATCTCTCTGCGCCAGAGACGGCGGATAATATTGCG
GCTCTGCTNTCTCCTCAGTCGGGGTTNTATTACGATATGTGGGTTGATGG
NGAGCAGTTTATGACTGCTGAGCCTCCTGAGGTGGTGAAAGCTCGAANTG
ATAC
>RL781F  CHROMAT_FILE: RL781F PHD_FILE: RL781F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:46 2001
CTTTAAGTAAACATAACACTAAAATCTGACATAACACAATACCCTCAAAG
AGTTGATAAAACAACTAACATGAAAATTTAGCATAGCTGCGAGTTATAAA
GTTTGCAAACATTTATTCACACACCCAAGGCTTGTAGGCACCACAACACA
AAGGAAGATGATGACTCAAGTGAAAGTGCCAATAAAGCAACAAGGATTTT
ATTAAAACACCAAACACATTAGCAAATAGAAGAAGAAGAAGGATAATCAA
GCGGCAGCAACTTGAGAGTGCTTCAAAAGCTTGGCTTCGATTTCCTCCTT
CGCAGCACCAACAACCTTGTCGAGCTTCTCTTCGCCTTTCATGTAGACAA
AGGTCGGCATGGCCTGAACATCGAACTCCTTTGCAACAGTGGCCAATTCA
TCGACGTCGACCTTGAAGAAGACAACATCAAGGTGCTTCTTAGCGAGCTC
GACAAAGATGGGTGCAATGAAACGGCAAGGTGGGCACCACACTGCTGTAA
AGTCTATCACAATCAGTTTGTTGGATTCTTTGGCTGCCTTGAGCTTGTTG
TTCCAGTCCTCGACGGTGTGGCAAGCGATCACTTCTCCTGCTGGGATCAA
TTCTGCTGTTGCGGCCATTGTTCTCTCTTCGCTTCTAGATCTACTCGAAA
CCATGGCCACTATCACCGTCGTTAAGGCTAGGCAGATCTTCGACAGTCGT
GGCAACCCCACCGTCGAGGTTGATGTACACACATCAAATGGTGTCAAGGT
CACTGCTGCTGTTCCGAG
>RL781R  CHROMAT_FILE: RL781R PHD_FILE: RL781R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:13 2001
AGTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXTTTTTTTTTTAAATTAAAAGAAGCCGAAATTAGATTATAAAAGAA
GAGCTGCTGTCCTCTTTAAAGGCAGAGCTATCTCAGGTTTTTTTCTTACA
AAAATAAGCAACTTAATCCCAACAAGAGTGGTTTGGAAAATAAACCAACA
AAGGGAGAAAAAAAAAGCAAACGTAATGTTTTATTTAAAGCAAAATGACC
AAGCACAACTCAGATCTTCTTTTTCTCGTAACAAAGGAGAGCACTTCGCT
TCTACGAGCAGCACTTGTCTAGTACGGCTCCACAGGCTTGCGGAAGTTAG
CTCCAGCGTAAACTGCCTCTGATCCCAACTCCTCTTCAATACGCAAAAGC
TGGTTGTACTTGGCTAGACGCTCGGACCTGCATGGAGCTCCAGTCTTGAT
TTGTCCAGTAGACAAGCCAACAGATAGGTCAGCAATGAAGGTGTCCTCGG
TTTCACCACTTCTGTGGCTGGCCATCACTCCCCATCCTGCTCTTTTCGAC
ATCTTAACTGCCTCGATACTCTCGGTTACTGACCCGATTTGGTTAACCTT
CAAGAGAAGAGCATTGCAAGACTTCTCGGCGATTGCCTTTGCAACCCTCT
TGGGGTTGGTGACCAACAAGTCATCACCAACAATCTGAACACTGTCTCCA
CACTCGGTGGTCATCTTGGCATAGTGTTCCCAGTCATCTTGGTCAAATGG
GTCCTCAATGGACACGATTGGGTACTCAGCAACGAAGGACTTGTATAGGT
CCTTGAGTGCATCTNCAGAAATCTTCTGAGAACCATTGNTGNTCTCTTCT
TTGAAGNTCAAGTCATAGGTCTTGTCTGATGAGTAGAACTCGGAAGCGGG
CACN
>RL782F  CHROMAT_FILE: RL782F PHD_FILE: RL782F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:49 2001
CCCTTTAAGTAGACAATAAAAAGTATGTGAGATGCCAAACCGATCCTTCA
GTAGAGAAATCAAACAAGTTGGAGAACTTAAATATCTAGATAGTAAACAT
ATAANCGGGTTTAAATAACATAAGCTCCATAATGCACTTTCCTTTTAACC
CTTCCATAGCTTCAAAACTTTATCTTTACCACCAGAGACTACTTTCTCAC
CATCTGGACTCCAATCCACAGCAAAAACCTCATCTGCATGACCAGGAAGA
TCTTGTTTTAACTTTTTCGTCCTAATTTCCCAAATCTTGAGAGTAGAGTC
TTTACTGCCACTCAAGAGCAATCTACTGCCTGCAGACCAACTGACTTGAT
AAACAGGCCCAACATGGCCACGGAAAGCTGCAACGAATTGAACTGTGACA
CCGCCCCATACCCTAACTGATCTATCGAATGAAGGACTTGCGGTCCACTT
CCCATCAGGCGAGAAACACACACGATTCACCAGCTGATGCCGACCGGACA
CGCGCCCCTCTATGCTGCCCGCTCCCGCACGGTTGCCACCCGCCTCTCCC
TGGCCCCGCCCCACCTCGTCTCTCTCCTCCCCGCGGCCACCTCCACCCTC
CCTCGCCGCTCGTCTCCTCCCCCTTCCTTCCAACCCACCCAATGGACCCT
GTTGCCTCCCCCGCTCCCGGCCCGTCGACCCCGCCGCTCTTCTCCACCCC
TGCCCCGCTCCCTCCTCCACCCCTACCCCGTGTCTGGATCCCGCGCTTCC
CCCACACTCCCT
>RL782R  CHROMAT_FILE: RL782R PHD_FILE: RL782R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:17 2001
AGTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXCTCGTCGCGATGAACATGGAGACGAGCCAAGCAGGGATGGGGAAC
AACACGGTGATGTGTCTGTTAACAGACCCAGAAGGAACGAACTTAGGTTC
CGCCATGTATATTCCTCAGACCGCTGGTCCTTTGCAGCTTACTCAGCTCG
TCAACAGGTTCCTCAACAACGAGGAGATGTTGCCTTACAGTTTCTATGTA
TCAGACGAAGAGCTTCTTGTTCCTGTTGGAACTTACTTGGAGACAAACAA
CGTGTCTGTGGAGACGGTGTTGACCATAGTTTATCAACAACAAGCTGTGT
TTCGAATTCGTCCAGTTAACCGCTGCTCGCAAACTATTGCTGGTCACGCG
GAAGCTGTTCTTTGTGTTTCGTTTAGTCCTGACGGTAAGCAGCTAGCAAG
TGGCTCAGGTGATACAACTGTCCGGCTTTGGGATCTCTACACTGAGACTC
CATTGTTTACTTGCAAAGGACACAGGAACTGGGTACTCTCAATTGCTTGG
TCTCCAGATGGCAAGCATCTTGTGAGTGGTAGTAAATCAGGTGAAATCTG
TTGCTGGAATCCAAAGAAGGGAGAGTTAGACGGTACTCCACTTACAGGTC
ATAAGAAATGGATTACTGGTATCTCGTGGGAGCCAGTCCACCTTAGTTCA
CCATGCCGTCGGTTTGTAACTTCTAGCANAGATGGGGATGCAAGGATTTG
GGATGTTACTCTTAAAAAAACTTTGATTTGTCTCAGTGGACACACACTTG
CTGTGACTTGTGTCAAATGGGGCGGAGACGGGATTATCTATACAGGTTCC
CAAGATTGTACGATAAAGATGTGGGAGACTACTCAGGNGAN
>RL783F  CHROMAT_FILE: RL783F PHD_FILE: RL783F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:27 2001
TTCATCTGGAGAACTTATATATATCACTCTTTTGATCAACCTAACACAAA
GATCAAGTTGGTGCAAAATGTGCAGAGAGACCTTATTACAAAAGCATAAT
TTTAACTAAATACTAGGAGAAGCTTACACTAACCTCCAAAACAAGTTACA
ACTTTCTCAGTGAGTCTACGGTTTTACTCGTGGAGCCAATCTAAACTGAA
ACATTCGTCAGCAGCTTCAATCTTTAACCCTGGAACGGCCCTCTCAACTT
CTTCCCATATAAACGCGACGTCCTCATTGCACATCACATGGCGCTATGGA
CTCCACCGAAACACCTGCTCCTCACTCTACTATCGATGCCCCTTTCTCTC
CTGCCACTTTTTTCCAGCGCTCCCCCCCCCCCTATACTCCGCGGCTCACT
CCCCTCCCTCCCCCACCCGCCCACGTCTCTGCCCCCAAACTGCCGTTTCC
CCCCCTCTCCCCGCCCCCCCCGCCCTCCCCCCCTCCCCCCCCCCCCTCCC
TCTCCCGCCCTTNTACTTCGCCCCCGCCCCCCCCCCCGCCCCCCCTCTCC
TCTCCCGCCCTCTCCTCCTCCCTTTCTCTCTCCCCCCGTCCTTCGCCCCC
CTTCCTCTCCGCTCCTTCTCCTCCCGCTCCGCTCCCTACCGACCCTTTCT
CCCGGTCCCTGCCCGCTCCTTCGCCTCTCCTTTCCCTCCTCCCCCATCTC
CCCTTCCTCCCCTCCCTCCCGCTCCCCCCTCCTCTTCCTGTTGCTCGCCC
TCCACCACCTCCCCATCACATTACATA
>RL783R  CHROMAT_FILE: RL783R PHD_FILE: RL783R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:52 2001
ATXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXCTATCTCTCTCTTTTGTCTCTGTGCGTTTGGTCAGAAATCTCTT
CCTCCTGGTTTCGACAAAGACCTTGTTAAGAAGGTTGCTGGTGAGTGTAA
AGGTCTACCTTTGGCTCTCAAAGTTACGGGCGCTTCACTAAAAGACCGCC
CTGAAATGTATTGGCAGGGCGCATTGCAGAGGTTATCAAAAGGTGAACCT
GCTGATGAAACTCACGAGACTAGATTGCTTCATCACATGGAAGCTAGTCT
AGCAGATCTGGACGAGACAGCCAGAGAGTGTTTCTTGGATCTTGGCGCAT
TCCCTGAAGACAGGAAGATTCCTGTTGATATTCTCATCAACATGTGGATT
GAAGTACATGATCTAGACGAGGCAGTTGCTTTTGCCACTCTTGTTGATTT
GTCACACAAGAATCTCCTTACTCTTGGGAAAGATCCACGGCTTGGCTCTA
CGTATGCAAGCTACTATGATGTATTTGTGACACAGCATGATGTTCTGCGT
GACTTGGCACTTCATTTATCCAACAAAGGGAAAGTAAACAGAAGAAGGCG
ATTGCTGATGCCAAAAAGAGAGGAAGAGCTTCCGAAAACATGGGGAAAGA
ACTGTGATGAGGAATACAATGCAGAGATAGTCTCTATTCATACATGGGAA
ATGGATGACATGGATTGGTCTGACTTTGACATGGACTTCCCTAAGGCAGA
GATTCTAATATTGAATTTTTCCTCGGACAAGTATGTTTTGCCTCCTTTCC
TCAGCAAGATGACCCGGCTTAAGGTCCTCGTGATCATCAACAACGGCATG
TCCCCTGCGATTCTCCGTGACTTTTCAATGTTGCCAN
>RL785F  CHROMAT_FILE: RL785F PHD_FILE: RL785F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:33 2001
GCGCCACCCCACCCCCAACCGCGCACGAGCGCAAGGAGCACGACGNACGG
CGCGCCTGAGCGACCGCGNGCGGCGCACAGCGCGCCCAAATACACACACA
AGACACCCAGCCCTGANATCNGGNACTAAACGTGTCACTACATANACATC
TCAAGTAAGAAACACTGCTGGCGACTATCGCACAGAGCGAACATTCTAGA
CAAAGCCAACACGAAACCACAGCCACAGGGATATAGATCAGCGCGCACGC
NAAGTCAGCGGCAAGCGAGGAACCAACGGCCGCCCCACCACGTGGAGCAC
ATGTCGCGCCGCGTCGCCCCATGAGACGACACGAGAGCACCCCCCACTCC
ACACACAGAGGGCGGGCGAGAGGCACCGCCGCTGAGGCCAGTAGAGACCC
ACGATCTATAGAGAGTGTTCAGAGCTGGCGCGCCCGGCCGCGCCGCGGTA
CGCGCGCGGTCGCGGACGCGCGCCGTCCCCCGGCGCGCGCACCGCGCCGC
GCGCACCGGCACGGAGCGCGAATACCNCACCCCCGCCCCCGACTCACCTG
GCATACCACCCCCACCAGCCAATGCCCAAAACCCTCCGCCGCCGCCCATC
CCCCGTCGCCCCACACCCGACCACCCGGCCCCTGGGACAGACGGACCCAC
CGGCAGCGCCCACGACAGGGACAGCGGACACATAGGTACAGGACACCCAA
CGGCCTATGCGATGAGCGGAGGCGAGCAGCCCGACTCGTCATCGGGACGA
GAGGACTGATGCTAGCCGGCTCGCGAAGGANCGGCTAGGATTAGATATAA
CCAAAGCGCCCACGTCTCGACCGACCACCGGGACCGGCAGCCGCACGCAG
CGCGCGCCTCCAGCTGCGCGCACGCCGCGCGCCGCGCCGCACCGCAAGAC
TCGACCAGAACCAGCCGATCCGGCCGGCAACTAGCGGCTAGCCAGTCACG
GCGGGCGCGTCGCGGTTGGACGCAAGATAACGAGCGCCCGACGTGACAGC
GACNCCACAAANCGACAGCAAGACCTGGCGGCGACAGCCCACGCCTCGGA
CGCATCCGCCGCGAACGTAGCCCACGGCACGCAACTGATACGCACAGCAN
AGCGATACGTAACGGCTCACACTACGCCGTATCACCACACACACGCACTC
CCGCCCCACCGCGACACACGCACCCATGTCTATACCACAGCTATCGGGAG
GAACCGCCGCCACGAGCACCAGCGCACCGCGTCACGACGCACGCGCCTCC
ACGNTGAGAGTATAACTAGCACGCGCACACCACGCATAGAGATCGCG
>RL787F  CHROMAT_FILE: RL787F PHD_FILE: RL787F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:40 2001
CCAAGCAAGAGGCGGGGCGGGNGACGCGAAAACAAGGTGAAAAAAAAACA
AAAAAAAGTTAAAAAAAGGNGGCCCTTTTNGGGGNCCCNCAAAGAAGAGA
AGTTTAGGGGCGGGGGCCCCCGGNGCCACGGCCNCCCCAGCGCGGGCCCG
ACCGAAGGGNGGGCCGGGGNGGGCGCGGCGGCGAGGGGGGAGAGAGACGC
GCGAGCGCGCCGCGGGGCACCCGGCACCGCCGGGAGAAGCAGGCACCCGC
CGCCCAGCCCGGAGAGGGAGAGACGGGCGCGCCAGACGCCGCGNCGNGGG
GACGCGCGCGCCGGGGCGGCCCGGCGCGGCGAGCGGGGAGAGCGCCAGAG
GCCAGGGGGAGAGACAGGGGCGGAAACGCCCCGCGCGCGGACGGGCGCGG
CCCCCAGCGCGCGCAAAGCAGCAGGCGGGGAAAGGGACCACGCCCCGCGC
GCGCCCCGGCCGGCGGCGCGGCCCACCAGCCGCGCNGGCGGGAAAGGGCG
CACGGACAGGGCGCGCCGGCAAGCGAGACCGCGCGAGCGGAGGCCAAACC
GCNAGAGAGGCCAAAGCGGGGGGAGAAGGACGACCGCGGAAAGAGCGCAC
CGCCCGCACACCGCGCGCCACACCCAGAAAGCCGNGGCGCAGGCACCAAC
AGCAGCGCAGGCGGGGAGATGGCCGCGCGCACGCACGCCGGCGAAAGAGG
GCCCCGCGGTCGCGGNCGCGAGCACCGGCGGCACAGAGCAACCAACAGCG
CAGCACGCGCCAATAGACGAACGCAACAGAGAAACACAACGACCGACATC
ACAAACGACCACCGCAGGGACAACAACAACCACACATCCGCGCGGACCGA
CGCGCGAGACCCACGGAAACAAGGCCAACCCAACACGAAGCACGAACGCG
ACGCGACACGCACAGCGCGAAAAAACGCGCACCCGACACACACAACAGCG
CGAGCGCACCCGCACAGCCACGAACCCCAACAACCGAGACCGCGACCACA
AACCCAACAACAACTGAAAAGCAACGGGACCGGCCACACAACACGAGAAC
AT
>RL787R  CHROMAT_FILE: RL787R PHD_FILE: RL787R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:06 2001
ATTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXCCCACGCGTCCGATTCCTCCATAAGCTTTTTATAAAATTATCATC
CTCTGCTTTTGAACCCTAAGGAAGGAGACGAAATGGCCACGGACGCGTAC
GAAGCCGCCATCAAAGGACTTAAGGATCTTCTCAGTAAGAAGACAGATCT
AGGGAACGTGGCCGCGGAGAAGATCAAAGAGTTGACTCAGGAGCTTAAGG
AGCTTGATTCCAGCAACTCTGACGCCGTTGAACGTATCAAATCCGGTTTC
ACCCATTTCAAAACTCAGAAATACTTGAAGGACAGTGCTCGGTTCAATGA
TCTTGCCAAGGGTCAGAGCCCAAAGTTTCTGGTATTCGCTTGTTCTGATT
CTCGAGTGTGTCCATCTCACATCTTGAATTTCCAACCTGGCGAGGCCTTT
GTTGTCAGAAACATTGCAAACATGGTTCCACCTTTCGACCAGAAGAGACA
TTCTGGCGTTGGTGCCGCCGTTGAATACGCAGTTGTACATCTCAAGGTGG
AGAACATTGTGGTGATAGGCCATAGCTGTTGCGGTGGGATTAAGGGTCTC
ATGTCCATTGAAGATGATGCTGCACCAACTCAGAGTGACTTCATAGAAAA
TTGGGTGAAGATTGGTGCATCAGCAAGGAACAAGATCAAGGAGGAACATC
AAGACCTAGACTACGATGAACAATGTAACAAGTGTGAGAAGGAAGCTGTG
AATGTGTCGCTTGGAAACTTGCTTTCATACCCCTTTGTGCGAGCTGCAGT
GGTGAAGACACACTTGCATAAGAGGAGCTCACTACAAATTCGTCAAGGCA
CATTTGATCTCTGGGAGCTCGATTTCAAGACCACCCCTGCTTATGCCTTC
TCTTGACATN
>RL789F  CHROMAT_FILE: RL789F PHD_FILE: RL789F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:46 2001
NCTTGATGGTACCTGCTGTTTGACAAGGTTCAAATCATATATCTTTATTG
GTTTGTAAGTAACCAGTGAGATTCCTAATCAGCTGCTTTGAAGCACAAGA
AGAAAATGAAAAATGGTATATCATTGATGCTCATGTATAAGTGAATTAGA
GATCCTACAAATTTGTATGGATCTTCCAAGAAACCAGTCTTCTTCTTTTT
CCTATATTGTACAAGAAGGCCTACAAAAGTGTTGAACCAATGTCTTGTCT
TCGTTCTTCGTTCTTCGTTCTTCTATCTTGAACTCTCCTTCCATCTATCT
GACTCTCTTCTTACACTTGACTTCCAAGGCTGCTCAGGCTGAGACTTGTT
ACAGATGCAATCTGGTTGCGGGTTCGCATAAAAGTTCTCCTCTAGCCGAG
GGAACTCACCAGGAAGTCTAGCATAAGGAGCTCCAATCCTGGCTCCATGT
AATCTCTTCACCTCTGAAGAAAACTCATCCCAAGACATCACACCTTCGCC
TAAATGATCTATCAGCCTAACAAAATCTAACCTGTCTGGATTGATAGCTT
TATTGAACCCTTCAAACCTCCTGTGCCCTTGTACAGCCTTACCCATATTG
CTCATCATATGCACGCACCAAAACATCGCTCTATAACGCCTCGCTGTCCT
CTCCTGTAGTCTACCGGCCTCGGTTTGCTTTACTGGGCCCCTTCCTTCTC
TCACCCGTCCCAGCCGCCTGGACTAACCCTCTTGCTCTATCTTCCCTCAC
CCCCCACTCCCTCTTTTCTT
>RL789R  CHROMAT_FILE: RL789R PHD_FILE: RL789R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:13 2001
AGTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXAGAAAGCTTCGACGCCTCTCAGCTTCACCGAACATCACGGTGGC
TAATACAAAAAAAAAGGCATAACATGATCAACCACTAACCCCTCAAACAC
ACATTTTACCAAAAAAAAATAATAAAAAAAAAACCAACTCTTTTCTCCCT
CCCTCTCTAAACATGTCAGCGGCCGGCGCTAGCCCATTGGCCGTTGCACC
GATCACACGACGTCGTATCGGAGACTCCCTCGAAACCACGACAACCTCCG
AACGAGCCTCCGTTTCCTCCGAGTATTGCAACATAGTCAACATCTCCTCC
CTCTCTCCGGACTTAGACGACGTCGAGGGGACGAACGGCGCGTGTTCCTC
ACCTTCCTCGATGGGCTCCACGTCTAGCGGATCGCATTACCACCACGATC
ATCACTACCACCCGAAGATTCGTTACCTTATCCCACGTAAACTGAAATGG
CCGTTTCTATGCGACGGTGGATGGACGGCTGTGATTGGTCAAGGATTGGG
GAGAAACGTGGGACGTCGGATCTTGGGTTTCCTCATGGTTCTCGTCGTCG
TTTCTCTATTTGTCAGAGTTTCTGTTATGAGTGGGCGCGTTGCTGATCAC
GCGCACAGGAGAGATTTGAACGAGCTTGTTGTCGTTAGGGCGTTACATGA
AGATTGGTCGATGGCTCAAAACGCAATGTCGGAGAACGTTGCTGTCGAGA
AGCTTCCCATTCCAGAGATATGGCAGAAACCTGAATCCAGCAATTATCGC
CAGTGTGCGTCACGTCCCAAGAGTAGTCATTCAAGGGCACGTAGAAAAAC
CAACGTTACCTTCTAGTACACGCCAATGGCGGNTTAAATCAGATGAGACT

>RL790F  CHROMAT_FILE: RL790F PHD_FILE: RL790F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:49 2001
GCGCACCGCACAACAGACACCGCNGCGGGCGCGACGCGNNNNNACNCGAC
AACAACACNAANACAAGGAGTGAAACACAAGAAAANCAATGAGACNACAG
ACACANGNTTTACACAGCAGAAGANACAGAACNGNNNNCCCCTCNNNNTN
TNNNGGNNNNNNNNNNACTGNNGACNGNAGCANAGCAGNANANNAGNNGG
GTTAGNANACGANAGANNNGAGANANCAAAAACCCANNNNNGNGNNNGNA
GAGGGAGNNANGCGNAGNNNNAGNGANGGCAGCAGACAGAGGNGNCGCGC
GCGCCCGNGCAGCCGCGCCGGCGNGNCNGNGNGGCCGNGGCGGCGCNACG
CGGNGNNCNNCGCGCGCGGACCGAGCGCGGNCGCGAGCACGAACGAGCGA
GGCNNCNNNNNNGCGGGGCNAGAGAGAGGAGNGCGNCCNNNCNGANCGNA
GGNGCGCGCCGCGAAGCNCGAGGNGNCGCGCGGCGCGCGCGCCGCCNCGC
GCNCGGNCGNGCAGGACAGAGNAGGCGNCGCGCCGCNAGCACGCGCGAGC
ANGCACCCAGGGNCGNGCACGCGCGNGCGNCGNGNGNNAGAGCGCNGCNN
CACGACGAGGCGCGCGCCNCCCAACGCACGACGCGNACCACGCACGCGCC
ACAAGGACNCGCGCNCCNNCGCGCCGCCGGCCGCGCGGCCCGACGCANCG
NCGCGCGACGACGCACGCGNNAGAACAGCACACACNGCGCGCAGCCCCGC
GAGCNCCGGCGGNGCACCGCGCGGCNCNCNCGAANACACCACGAAGCGCG
NGCGNCNCAGGACGACGAACGCGACGCGGCGCGANCCGGCGCAGAGGACC
GCAGGCGCGCGACGCGCGGCGCACGTCGCACGAAGACGGCCCCACNGCNG
CGCCGNCGCAGACNGCCNCNGGACGCGCACGAGANACGCGCNGACAGNGN
GNCAACCNNAGCACCNNGGCGGCGGCAGGCNGNGAACGNCGCGAGCAGNC
NNNGAGGGCGAGGNCGCGGCGCCAACGCNGCGCCAACCCAGAGCGGAACG
NGACACGCGACGACACANGAACGAACAGNACGGATTTAGTAAGGATATGA
GAGACGNACTCGCTGACCTCCGTCGCCGGGCGTTCTGGGGACGCGGCGTG
CGCGACGCAGCGAGCCGCACGAGCGAGGACACGAGNCGGCGTATAACGCG
TTACTACGTCCACTCGCAGTCGTCGNGCGGACTGTGTTGCCACACTGCTG
AGGTCTGCTCCGCGNTCACGNGCACGCCCTCATCGTTCATCCAAACGTGC
CTGCGTCCGAGTGNTCTCCAGATCTTGTCACGCAGCGACGACACTTACAT
CCGGCTACTCCATACGCCGCTACAGNCACACTGTCATNTGATATGTGTTT
CAGATACTACGAANCCAAGTTACATTCATACTACACATCCATACGAGCAC
GACACNTCGCGATTGCCGTACCCCACCACACGCAATCGATAAACATCGCC
ATACGTCCATGCGAAGACGCGACACGAGAATCCGAGTCACATGACACGCG
ACCGCAAGTACAGCGCCATACTATTCACAACTTCAACATAGTCGACACGA
CACACCACGGCACGGCTCTGAAGAGATACGCTGGACAACCACATCAGGCT
CGTACACCACGAGACCGAACTTCCGAGTTATAAATAGTGTACCACCACAC
AGCAGTACCACACCATAGAGAAACTGAA
>RL790R  CHROMAT_FILE: RL790R PHD_FILE: RL790R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:17 2001
AGTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXAGGAAAGAAGGTTTATTACTCAGCAAATCTAGTTGTTACGTTAA
GTTTCTGTGAGGTTATTACTTTGAGAGACGAGACAATGTTTGGTTTGAGG
AAATCTCCAGCAAAGCTTCCCAAGCACAACTCTGCTGACCCTGGCTTTCA
CAAATCTTCCAAGCCCAATCCTTTCGATTCAGATGATGAGCTGGACAACA
ACAGCAACAAACACACACTTAACCCCTCCAAGAGGACTTCCTCTGAGCCT
TCCTTGGCTGACATGACCAACCCTTTTGACGGCGAGGATAAGGTTGAGAA
AGGGTTTACTTCGTCGTCCAAGCAGCCCTTGACTTCTAACTCCAGATACC
AGTACAAGAACAACTTCCGTGATTCCGGAGGTGTTGAGAACCAGTCTGTT
CAGGAGCTTGAGGGTTATGCTGTCTACAAGGCTGAAGAGACTACCAAATC
TGTACAAGGTTGTCTCAAGGTGGCTGAAGATATAAGGTCTGATGCTACCA
GGACTTTGGTCATGTTGCACGAGCAGGGTGAGCAGATCACCAGGACGCAC
CATAAAGCTGTTGAAATTGATCATGATCTCAGTAGAGGTGAGAAGCTTCT
TGGTAGCCTTGGAGGTATGTTTTCAAAGACTTGGAAGCCGAAGAAGACTC
GCCCTATTAATGGCCCTGTCATTACTAGAGATCACTCGCCAACGAGAAGA
ATTAACCACTTGGAGAAAAGGGAGAAACTGNGACTNGACCCAGCNACCAA
AGCACAATCAAGAAGCAGAGAACCGCTTCCTGAATCAGCTGATGCGTATC
AGAGAGTGGAGATGGAAAAGCNNCAGCAGACGATGGGCTTTCAGATTTGA
GTGATCTACT
>RL791R  CHROMAT_FILE: RL791R PHD_FILE: RL791R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:53 2001
AATXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXCCGCCCTTTTTTTTTTTTTTTACGTTTAATCTTTTGATGTGGT
CTTGAATTGCTTACGAGAATTGAAAAGGTGAATGCAAAATATAGAGACAA
GTAACAAAGAAAAACACTGAAAGGAGTATAAACAGTAAGTCGCATTGTAT
GATAAAACAATGTTTTTATGATCACAAATCTTTTTGCTTAAACCCAGAGT
TTTACTTACTGCTGTTTCGAACCATGGGTCTCGCTATTCACAGGTGTGGA
TGAGCCACTACGCTTACTAGACTGACCTGTAATTGTTCTACCCATGAATC
TCCCTGCTTTGCTCAATCCACTACCCATTGCTCCAAAACCGGTACCAACC
ATCCCGACGCCCGAGGTCACCCCGGTCCCAACCAGGCCTACTCCTGCACC
AATCCCTGTCCCAACCAATCCTACACCAGTACCGAGCCCACTTCCAACTG
CATCCATTGTGCTACCTATCATTCCTGCTTCCTTCAGTCTCTTCCGCTCT
TCCATTATTTTCTTCTCTTCTTCTAACGCAGCCATTTGCTCCTCTTTGTT
GAACTCATGATAATGTACCTTTAGGGTTATACTTCCTCTATCTTTCTTAT
CTTTTACTTTCAGAGTATCAAGTGAAGACAACAGGTTTAGCTCCATCTCC
TTTGTAACCCCGACCTCCAAACTGCTTAAAGGAAGTTTCACAAGTCCTAG
ACGCTCGTCTTGGCCTACGTCTTTATCAAATACCTCTATAGTGAGCGACT
GAGTTTCTTTGTCCTCTGCAATCAATTCAAAGGTTTGGTCCCAACAGGAC
TCAGGTTGTTCTCGATTGTCTTTGTTATATACTTG
>RL793F  CHROMAT_FILE: RL793F PHD_FILE: RL793F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:34 2001
GGCTTTTTCTGTACACAGTGAACAAAAACTGGTAGAAATCCCAAAGACAA
CATCCATAAAATAAATCAACAATATTATATAACCTAAATGCAAAATGAAA
GAGAAATTATGCTACGGAACATCTTGTTGTTATTTGATTGACAGAGTCAA
GAGAATGAAGAAAAAAGAACAAAATCCATTCAACGATCACTTAAGCAGCT
GCCTGAATCGGTGGTCCACTTGATCTGTTGAATCCACCACGGCCTCCTCC
CCTTCCACGACCTCCCCTACCACGCCCACCTCCACGGCCCTGATGAGGAG
CACCGTATCCGTAGTCTCCCCCATCATGCTCAGCTTCATAGTATTGTGGA
GGACCATTGAAACCTCCTCTTCCACGACCACCGCGAGTACCTCTTCTCCC
TCCCCCTCTTCCTCTACCAGATGGCCGCTCAGGCTCCATGCCTCCATCAT
CGTACTCATGATCACTGTGGNNNNNNNCCCCTCTCCCTCCCCCCCCCCCC
CCCCCCCCCCNCCTCCCCCNTCCCCCCGCCCCCGCCTCCTCCCCTTCCCT
CCCCCCGCTCCCCCCTTCCTCCTTCTCTCCCCTCCCACCTCCTCCTTCCC
CCCCCTCTCCGTCCCCTCTCTCACTCTTCTCCCNCGCGCCCGTCCCTTAC
CCCTCCGTTTTTCCTCCTTCTTTCCTCCCCCCTCTCTCCTCTCCATTTCT
CACCACCCGCTCTCTCTCTCTTTCTCTCTCTCCCTTCCCTCNTCCCCGCC
CCTCGTCCCCTCCCCTTTATTCCACCCGCCACCTCACAATATAATAA
>RL793R  CHROMAT_FILE: RL793R PHD_FILE: RL793R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:00 2001
AGTTTGTACGACCTGCAGTACCNNGTCTCGGATTCCCCGCTCGACCCACG
CGTCCGAGAAAGAGTACTCGCCTCCATCATCGTACTCATGATCCTGTGGA
GNACCCNCANTGNTATCATAGTGNNNTTGANGGGGTAGACTAATGTTATG
GTGTTGAATATAAAGAATGTGGAGGAGGATTTGTTAATGGAGGTTATAGT
TATGACATCAGGCAGTGCCGTCCCTTTNTGATAACTGAGCCTCCCGGTTC
TCTGCATCCTCCACCCCTCACCCCCGTCCGTCTTACCGCCCCCCCCCCAT
CAATTCCCTAGTCCCCGGTCTCCTCGCTCCTTCGTTCCATCCTTCCTCTC
ACCTCATCCCCCCATCCCTTCACCATCCTCCAACCCACTTCTCCCTACTC
CTTCAATCTTCACCACTATCCTTCCTCCCCCCCACCTCGCTTTCATCCTC
TCCCTCTCCCCCCCCCCTATTTCTTTTATCCAACCCCCCCCACATCAACT
ATCGTCTCTTATTCTTTTATCCCCCCATTGTATCGTCTGCTCTATTCCCC
CCCCCCCCCCCCCCCCACCAGTACCAACCTGCCATTCTTATTAACCCTCC
CCCCCCCCACCCCCCAGCATCCCTCTTCCCCCCTCCACTTCCTCATTCTC
CTCACCCCCTCCACCTATTTTCTTCTCCCCATATCCGCTATACAATTTAC
TTCACCCCTACTCCCTAACTCACCTCACACACCTACCCATCCTACATTAT
CTTTTCTTCCCCTATTCTTTTCACCATCTCCACCTCTTTCCCCTCTTCAC
CTCCTGTCAACTACTCCCACACCCATATTACACGTCTCCTCCTCTTCTCT
TCACTCACTCGTTCCTTCATCTTTCTTATCCATTTATCCTATCAACCTCA
TCATTATCCCTTTGTT
>RL795F  CHROMAT_FILE: RL795F PHD_FILE: RL795F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:40 2001
CCTTGGNGGGAGACAACCTTCTCGTGTTCGAAACTCAACGACAGCAACAT
CAACAGCAAAAGTTACACATCGCAAAGGAATTAAAAAAAAAAAAAGAGAA
CATGAAATGTGGAATGGTTGAAAGGTGTTAAACAAAGTTTCATGGCACGC
TTAATAAAAAGAGTTTTTGCTTTTTAAGCGAACTGTCGACCACCATCTGA
AGACGAACAAATGGTACCAACCACATGCGGTACTGACGCCATCACCCCTC
ACCGCCGCCCTCACCACCCCTAGTGAACACACTGCCTCCAATACTCGCCC
CCCCATGCCCCACCATCCCCCCCGCACCCCCCGCCTCCCCGCCCTTGCTT
ATATCCCACCTCCCCCCCCCCCCTCCCCGCACACCCCCCCCGCAAACCAA
CCACTCCCCCCTCCCCGACACCTGCCCCCCCGCCCCCTCCCCCCCACCCT
TCCCACCCAACCTCCCACACCCTCCCTACACCACCTCCCTCATGTTCTAA
CCACCTACTCCTCCTCCCGTCCTCTCTCTCCTCCCCCCCCCGACCCTTAA
CCAACCCCGCCCTCGCATCGATCCCCCTCCCTCCACACCACACACCCCCA
ACACACCCCCCACCTTCCCACCCCCACGACACACCCCACGTATCGAACCA
ACCCACTCCTTACACCCACTTCTCCCCCACACCACCCCGCACATTGCACA
CCCCCTCACCTCCCTACCCACCCCCTCGCACCCTCACCCAACCCCTCCCA
AAAACTATCCACCCCTCACCCCCGCACTTCATT
>RL795R  CHROMAT_FILE: RL795R PHD_FILE: RL795R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:07 2001
CTTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXTGGCTCGGAAGGTCTGTTTGCTCAAAAGACTCTGGAGATCACT
GATGATATACTCCAGACTTACAAAAACCAAGGTGGCTATGATTTGCTGGG
AAGAACCAAGGATCAGATCAGAACCACTGAGCAGGTTAACGCTGCTCTCA
AAGCTTGCACAGATTTGAAGCTAGATGGCCTTGTTATCATTGGAGGTGTA
ACATCAAACACAGATGCCGCTCATCTTGCTGAATTTTTCGCTGAAGCAAA
ATGCTCAACAAAGGTAGTTGGTGTTCCAGTCACTACAAATGGAGATCTCA
AGAATCAGTTTGTGGAGGCAAACGTTGGTTTTGACACCATATGCAAGGTG
AATTCTCAGCTCATTAGCAATGCCTGCACCGATGCTCTATCTGCAGAGAA
GTACTATTATTTTATCCGTCTCATGGGTCGGAAGCACTCTCATGTTGCCC
TTGAGTGTACCCTCCAGTCTCATCCAAACATGGTGATACTGGGAGAGGAG
GTCGCAGCATCTAAGCTCACCATTTTTGACATTTCTAAGCAGATCTGTGA
TGCAGTTCAAGCAAGAGCAGGACAAGACAAGAATCATGGAGTCATCCTCA
TTCCCGAAGGGATCATAGAGAGTATTCCTGAAGTTTACGCTCTGTTGAAG
GAAATTCATGGGCTACTTAGGGAGGGTGTAGCTGCTGATAAGATTTCTAC
TCAGCTCTCACCTTGGTCATCTGCTTTGTTTGAATTCCTTCCTCCATTCA
TTAAGAAACAGCTACTCCTCCATCCTGAGTCTGATGATTCTGCTCAGCTA
TCCCAAATTGAGACTGAGAAGCTTCTCGCGTATCTGGTGGAGACTGA
>RL797F  CHROMAT_FILE: RL797F PHD_FILE: RL797F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:46 2001
GGCCTTTCTATGTGACGACAAACAAAGTGTCCAATGTAAGTAACGTAGAA
ATTCAGGAATCAAATAAATAAGGGAAATCCAATTCAGACTTAGATTCAGA
TCCTTCAAGTTTCATTCAGCAAAAACAAAAAGATAAGAAAAAAAACATGA
AAAAGGAAGATTGTTTTCACCAGGTGATTCTTGTTGTATGCCTATTAATC
CTCCTCAGTGTTCTTGAGATTCATAAACAGATGACCAAGTGCAGTTTCAC
AAGCTGTTTGGCCATCTTCTCCCAAACCCTTGAGGAGAGACTTGGTGAGT
TTCAACGAAGAGACCATTCTAAACACCCTGCCACAGAACTTGCGCACCTT
AGCCCGCCTTGCTTGCTTCTCCGGCATATTTGTAACAAGCTCTTTAATAA
AATGACTCAGTTTCACCAGATGAAACTTCATTTTCTTCTTCGACTCTTCT
TGCGTCTCTTTGCCTATAGGAGCCAACGACCTTAAAGCTTCAGAGATCAA
TTCAAGAGCTTCCACTCTACGATACTCAACCTTCGGATTCACAATTTTCT
CCAGAAGAAATCCAAACAGCTGGTGTGCAATCCACGGTCTCCTTCTAAAC
ACTTCCTCAAGAAATTCTACCTTTATTTGAGACTTCTTGCTGCTATCAAA
GTACCCGACAAGGACACTCCTAAACACATCCAAGATCTTCTCCAGTTCGG
TCTCTGAGAACTTTCTCGAGTCGATTATCCTAAGACCCAGTAGGTTGAGT
TCTGGGCAGGTTAGTGATCATCTTGTGTCG
>RL797R  CHROMAT_FILE: RL797R PHD_FILE: RL797R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:14 2001
ACTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXCGGACGCGTGGGCGGACGCGTGGGCGGACGCGTGGGCAAAATCAAA
ATCGCGGCTTCTGAGTTTCATCACCAATGGGTAGTAAGAAGAGAAGCAGC
GCCGATTCATCGGAAGATGTCGAGAAGAATCACACCGATTCCTTCATGAA
GAAGAAGAAGAAATCCAAGCGTGATAAGATGAACGCTGACGATTCCGATG
CCGAGGCGGCGGCGCCTCCTCCTCCCGGCGTCGCGAGTACCGGTAAAGAC
ATGGAGAAGAAGAAGAAGAGGAGAGCTTCCGACAAGGAGAGAAAACGCGC
CGCTCTCGATAACGACGGCGGTGAGCCTCCCCGCCGCCCTAAACCCCCTG
CGGCGGTGGTGGTTTCTGATTCGAACTCCGACGGAGCCGCGGCGGCTTCT
TCGTCCTCTTCTTTGCCGGAGTTGCCTCTTAGCTATTTTAGGGATTTGGC
TTCTCCTGAGGGTTCAGTTAGAGAAGCAGCAGCTACCTCATTGGTGACGA
GGCTGCAAGAGATTCAGAAGCAGTACGAGATGTTGCCTGATAAGGGATCC
GTCGACGGAGGATTGATGCTTGAAGCTGAGAAGAACGATGGGTTGGATAG
CTGTGCGCCGCATCTCAGATACGCTCTACGGAGGCTTATTCGTGGTGTCT
CTTCTTCAAGAGAGTGTGNCAGACAAGGATTTGCTTTGGGGCTGACGTTA
CCTGTTAGCTTAATCTCTAGCATTAATGTGGAGTCGCTACTCAAGCTCAT
TTCTGATTCTTTGTCCGTTTCTTCGTCCATGAAGGGACAGGATGTNGAAG
AATGCTTATTGGGTCGGNTGTNTGCCTACGGTGCGCTAGCACGATCTGGG
AGACTTGGTGN
>RL803F  CHROMAT_FILE: RL803F PHD_FILE: RL803F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:40 2001
AGAATAACTTGGGNNCNGGCTGACTGTACTACAGCTAAAGATCAAAGAAG
GACGTAAGCTCACTTCAAAGTTAAAAGCCTCATCAACAGAAGAGAAAACA
AGGAAAGCGAAATGTGTAAAAGTATTTTAAAAGGGAAGAGTCTCTACTCA
GTGTGTAAGTGAGGCATATGTTTTAGGGAGTCTCTTCCTCCACCGTACGC
TTTGTACGGATCCCCAACTTCGCCGCCCATGGTTCCCTTGTCCTTTGTTA
TCGTACCTGTTTCCGCCCCCGCGCCGTCTTCCCCCTCCGCCTGCCGCCTG
GCCCCCCCGCCCCTCTCCCCCCCCTCCTCCTTCTCCCCCTCCCCGCCCCG
CCCTCCCGCGCTGCCCTCCTCCCCTCCCCCCCTCGTCCCTTCTTGCTTCC
CCTTCCCCCCCCCCCCCGNCCCCGCCCCCCTCTCCCCGTGCCCCCCTCTC
CCCCCCCCTCCTTCCCCTTTTCTTTCCCCTCTTTGTGTTTTCTTCCGTCC
TTTCTCTGTGCGCTTCGCGCCTCCCCTTCTCTTCCTCCTCCCCCCCTTCC
CCNTTCTTCCCTTCCTCTTCCTGTCTTCCCCGCTCCTCCTCCTCTTCCTT
CCCCCTCTCTTCCCCCCCCCCTCCCTCCCTCCCTTCCTCTCGCTTCTCTT
CCCTCTCCCTCCCTCCCCCCTCCCTCTTCTCCCCCTCCTCTCCCCTTCCT
CTCCGTCCCGTTCGTCCCCTCCTCCCTCCCCCCTCCCCCTCTTCTCCCCC
CTCCTCCCCTCTCTTCGCCCTTCTCCTCCTCTCGTCCCCTTCCGCTCCCC
CCTTCCCCTTCCCCTCCTCTCTCCCCTACCACACCATAACAAA
>RL806F  CHROMAT_FILE: RL806F PHD_FILE: RL806F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:50 2001
CTTTGGCCTATGATATGCTGGCATATACCGCAGTAAGAACAAAACATGCA
ACACCTACAAAAGAGCCAACGTCGCCCAACTTATCAGATCATTGTGCTCC
TCACGAAGACGAATGTAGTATACAAAAGAAGTGAGTCCATGTCCTTCCCC
TTCCACAAATGCATATTTACATTACCACTCATAGGTAAGTTTAAAATACA
AAGATAAACCCAACAAGACGAGTCTAGGCAACAGCAGCATGTCCTGAACA
AATCTTCGAACAAGAGACTTCTTCGTTTTAAAGGCCACCCTATTTATGTC
TTAATTACCTATTTACATTTGTAACTTTAGTGCGGAATAAGATCCGTTTA
CAATCCCTTTTTCAGTCTCAAGTGGCGAGTAGGAGAGATCCACAGGCATC
AGAAGCATGTTTGCCTTCTCCAAACACCAAGTTTCCTCTTACAAATGTTG
AAACTACTTTACCTGATAACTTTCTTCCCAAATAAGCTGAGATGCCAGGG
TGTTTGAAGTGAATAGGATGGTCTTCATCAAGATCAAACTCCACTTCAGG
TTCCCACACAACAATATCCGCATGTTTCCCAACCGCAATAGCTCCCTTAG
AGTGTAGTCCAGCGAGTTTGGAAGGCCTATCGCTCCACCAAGAAGCTACC
TGCTCGAGAGTCACTCCATACTTTCTTCCGTATGACCATGTTACTGGTAG
AACAAACTGTAAAGACGATATCCCACCCCATGCCTTCAAGAAATTACCAT
CACTCAAGAGTTTGAGTTCAGGCTTTGTTGGTGAAT
>RL806R  CHROMAT_FILE: RL806R PHD_FILE: RL806R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:18 2001
AGTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXAGAGAGATGGAGAGGTCGCTGCTTCAATGGAGATTACTGCCTCT
TCTCGCTCTCATCGCTTCTCTTCTCTCAGTCTTCTTCGCTTCTCGCTCTT
ACGAGGAGACGCAGTGCAGTCTTCTTCCTCATGATCACTATTGGATCTCG
AGCAAACGCATCCTCACACCAGATGGTCTCATCTCCGGCTCTGTGGAAGT
GAACGGAGGCGTTATTGTGTCGGTGGTGAAAGAGGAAGATTGGTATAAGA
AGCAGAGGAGCCGAGTGAAAGTGATTGACTATGGAGAAGCTGTCATCATG
CCTGGTCTTGTTGATGTGCATGCACATCTTGATGATCCTGGACGAAGTGA
ATGGGAAGGGTTTCCTTCTGGAACAAAGGCTGCTGCTGCTGGGGGTATCA
CCACGTTGATTGACATGCCCTTAAACAGTGACCCTTCAACTGTATCTCCT
GAAACTTTGAAACTCAAGATTGAAGCTGCTAAAAAGAGAGTATTTGTTGA
TGTTGGTTTCTGGGGAGGGTTGGTGCCTGATAATGCACTCAATTCAACTG
CCCTTGCCTCTCTCTTAGATGCTGGAGTTCTTGGTCTCAAGTCCTTCATG
TGTCCTTCAGGGATCAATGATTTCCCCATGACANACATCACTCACATAAA
GGAAGGTCTTTCTGTATTAGCTAAATACAAACGACCGTTGCTTGTACACG
CAGAGGTCGAAATGGATTCAGAAACTTGTTATCGGTTACCGAGAACACNA
AGGATTGGTGGTTCTGCAGAAGGAGCACATGTTCATATTGTTCATCTGTC
TGACGCCTCTTCTTCCTTGGAGATGANTAAGGAAGCGAAGGGCAAGGAGA
CAGTGNTACCGTTGAACATGCCCGN
>RL807F  CHROMAT_FILE: RL807F PHD_FILE: RL807F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:28 2001
NCCTGNGGGATACTTATTTAAAAATTGTTACAATATGTATCGTTTTTTAT
TTTTATTTTTTTTTATGTATATTTTTTTTTTTTTTTTGTTTGTTTTTTTT
TTTTTTTTTTTGTTTTTTAAATATTTTATTATTTTTTGTTTTTTGTTTTT
TTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTGTTTTGGTTTTAATGAAAT
ATATTTAATTTTATTGTTTTCTTTTATTTTTTTTTTTATTTTTTTGGTTT
TTTTTGTCTTTTCTATTGATCCGGTTTTTTTTATGTACTCTTTCATGGAG
AAAGAGTGAATTTATCCGATAATTCAAACTACTCGCCCGCAAAGCTGCTT
CCTTTTTGCCCACCTGTTTTTTCCTGCCGGTATCCGTCTCCTCCGATGGA
AGACACCCAATCGGCCGGTGCTGCACATCGACACCATTTCTATAGGGAGG
CACTCACAGGCCCGCCCCGCACCCCACCGCCCCACCCCCCAACCGGACCG
CCCACAGCCCGCGCGCCCGGCGCGCAACGCGCCCACCGCCGGCGCCGCCC
CGGGGCGGACCGCGCACGCCGGGCACCCGGTAAGGCGGCCACAGACAACA
CCCACGCCCCCCGTGCCGCGCCCCCGCACGACCGCGCGCCCGGCCGACCG
ACCGCACCGCAGACCCGCACGCCCACGCGCGGAGCCACGCCAGGCGCCGC
CCACGCACCCCCGCACCCGGGCCACGACGCCGCCCGCCCGCCGCCCACAG
GCGGGCCGAGCCCGCACAGAACCGAAAA
>RL807R  CHROMAT_FILE: RL807R PHD_FILE: RL807R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:53 2001
AGTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXCTTCCATCGCTGCTGACCTTCCTTCATCGAAGAATCTCTCTATCT
ATCTTTCTCCCTTCGCCGGAGCTCGTAGTGTTGGTGGTAGACGGCGGAGA
GATGTCTATCTTCGGTGCTATTGCTCCCTCGATCTCAAATTGGGTATCAG
CTGTGACCAAATCAGTTAACGGTTTGGTTGGGTATGAGGGAGTTGAAGTT
ATTAACCCTGAAGGAAGTAATGAAGATGCAGCTGAGGAAGCTAACAAAGG
GAGATGGAATCAAGAGGATCGAGATGGTTATTGGAAGATGATGCAGAAGT
ACATAGGATCTGATGTTACATCAATGGTGACCCTCCCTGTTATTATTTTC
GAACCGATGACTATGCTCCAGAAAATGGCTGAGTTGATGGAATACTCGCA
TCTATTGGACATGGCTGACAAAACGGATGACCCTTATATGCGCATGGTGT
ATGCTTCATCATGGGCTATATCTGTGTACTATGCTTTCCAACGTACCTGG
AAACCGTTTAACCCAATCCTCGGAGAGACTTATGAGATGGCTAATTACAA
CGGTGTTAACTTCATATCCGAACAGGTCAGCCATCACCCTCCAATGAGTG
CTGGTCATGCTGAAAATGAGCACTTCACTTATGATTGTACTTCAAAGCTG
AAAACAAAGTTTCTCGGCAATTCTATTGACGTTTACCCAGTAGGAAGGAC
ACGGGTGACACTTAAAAGAGATGGAGTAGTTCTTGACTTGGTACCTNCTC
TAAACCAAGTTCACAACCTAATCTTTGGACGAACTTGNGTCGATTCTCCT
GGGGAAATGATCATGACTAACCTCACCACTGGTGACANAGTGGGTGCTTA
CTTTCAACCGTGTGGNTGGNTCNGATCTGGT
>RL808F  CHROMAT_FILE: RL808F PHD_FILE: RL808F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:31 2001
GGTGNGGGGAACTCGGAGCCTGACCCCAACATACTTAACAGTTAATAAAA
TTACAAGAAGCTTGAAAATTAAACGCGAGGAGGAGTACAGAACGAGGGAA
AGGAGATCCAGGGTCAACTCTTTGGAGCTGAATGGCCCTGTGAGACTCAT
CATCATTATCATAGTACATATAAGCAAAACCACCGTGACGTGTCATATCC
ATACCGGCCATCTCATCCTTCTCCGATATCCTCAGCAAACCGAGCCTTTT
GAGCAATGAAGAAGAGTGTTCCCATGGTAGCACTAACCCATCCTGCAACC
ACAAGTATTTGAACTAATTGTGCTCCCAACAGCTTCCCTCCTCCACCCAT
TAACAGTCCATATGGCCTTCCAGGTGTCTCGCCGTAAACCTCGTTTAGAT
ACTTCTCCTTTGCAAAAAGCCCTACGAATATCAACCCCCACGCACCACAT
CCTCCGTGTAGTTGCGCCGCCTCAAGGGGATCATCATACTGTACGATCTC
CGCGAGCTTGTTGCAGCCGATGAGAACGAGGGCAGCCATGAATCCACATA
CGATCGCAGCCCAGGGCTCTACCACAGAGCAACCCCCTGTTATGGCGGCG
AACCCACCGAGTAGCCCGTTACATACGTCTGTCACGGCCCAGCGGCCAGA
GAGAAGACGTTTACCGAAGAGTGTGGCTAGAGCTGCGGTGGATCCAGCAA
GCGTGGTTGTAACCGCTGTCCGTCCTATTCCGTCCATTGGCCGTACTAGA
ACAGGTCCATACGGAACGAGGATCTG
>RL810F  CHROMAT_FILE: RL810F PHD_FILE: RL810F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:37 2001
NGTGANGGAAAATCAATTTATACAACCAATAGGGGGAAAATAATCCTGTA
ACTTTCAAATAATTGATACAACTATTTTAAAGCAAGACTCTTTTCTGTTC
AGATGTTTACTCTGTCAAGTGTCAACACTTTGAACGAGTATGGATAAGCA
AACAACCTTGTAAACAAAGACATGACTCCCAGTTCCTATTAACAGAACCA
GAAACTAATGAGAAAAGAGTCAGTCCAGAGGGTTACTCTGTCAACGCTTA
TATGACAAAGGCTTCTTCCTAGTTTTGGAAAACGCGCCTTTAGCTTTTGG
AGCCTGAGGGTGGCCATGTCCTCTATTTCACTAACAGATAGATCTCTACT
GAAAAGTTCTTCCGAGTACAACCCCACTGAATATAATAGCACCAAACCAC
TTGTTCGACACAAACTTTTTACTGCAGTCAGTGCGAGATGACAAGTCAGC
TGTCCCTATTTGCCATCCTAAGTGTCCTGATGCAGCGACCAGTGATGCGT
AATATTGCCACCCGAGATCTGCACTGAGTCCAGAAAGTGTAAGCAAACCC
ATGGATGCTGTGCCAAATCCAGTTAGCCAAAGCTTTGTATTATCACCGAA
TCTAAGAGCTGTTGACTTCACACCAACCTTCACATCATCTTCTTTGTCCT
GATGTGCATAGATAGTATCATACACAAGGGTCCAGCAGACTCCTGAGAGA
TAAAGAGGGAGAACAACAGCTGGTTCTAAGCTTCCTTTAACAGCAGCCCA
TCCTAACAATGCTCCCCAGTTTATGGTCAAACCT
>RL810R  CHROMAT_FILE: RL810R PHD_FILE: RL810R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:04 2001
ATTAATGTNNNCATGCTGTGACGCTGCAGTACCGGTCCGGGATCCCAGGT
CGACCACGCGTCCGCCCATGCGTCCGNNNATGTGTNNAGTTAGGGGTAAG
GTTATTNTTTTTATTAATTGTTGTTTGGTTGTGTGTGTTGTATGTTGTGT
AATGATTTGGTTTATTTTTTATGGTAATTGTNGTTGTTTGTGTTTTTATT
ATTTGGTTTTTTATTGTTTTGTTTTTTATATTTTTTAATTTTATAATAAA
TATAGTGGGGTTTTTTTTTATTTATTTTTTTATGTGTTTTTTATTATGTT
ATGATTTGATTTTAGTTTTATTTTTTTTTTTGTAATTTTTTTATTTATTG
TGTTTTTTTGATAAGATTTATTTATATTTGTTGTATAATATATTAATAAT
TATTTATATATTATTATTATTTTTATTATTATAATATATATTTATATTTA
TTTTTTTTTATTTTAGATGATATATAGTTTTATTTATATTTATTTGTATT
TGTTTTTGGATATTTATTGTTTTGTTTTTTTTTATTAATTTAATTTATAA
TTAAGATTTTTTATTTTTTTATTAAGTAATAAGATTTATGGNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNN
>RL811F  CHROMAT_FILE: RL811F PHD_FILE: RL811F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:40 2001
CGCCCCGCGCGACCCCNGGCGCGNNGCGCGCNNNCGGCGACGAGACAGCG
AGGAGCGAGAGACAATAGCATACATAGAACAGAACTTTGNGGCCCGCCGC
GCCGCGNNCCCTTTCNTCNGGGNNNNAACCTTGNACNCANCACAAAAAGA
NTTTNNNNAAGAAAGNAGANTGAACCCGGNCGNCCAGGAGCACGCGCGGA
GACCNAGCACAAGACGAGCGGGCGCGCCGCCCCGCGGGCCGCGACGCNGG
GCCGCGCAGGAGAGNAGAGACAGAGAACAGAGCACAGACACAAACAAGCA
AGCNCNGGCGCGAGACGACGTGGGCNGCGCCGAAANGCGCGGCAGCCNAG
CCGCCGGCGACGCGAGCGCCACCACCCGCGCGCAGNACGGCTGTGGTATG
CTACCTGCGTCGGTCTCTCCTCTTGCGCACGGGACTCGTCGCGCCGCGTC
AGCGCGCGCGACGCGCCCATGTCCCGGCGCTGACCAGGTGCGCTGTGGAG
GATCGGATCACGCGGGCGTGCTGCGTGATGGGCGAGGTGCACCGGTGCCC
GCCGTCGACATCGAGACAGGANGACACGNGCAGGAGACTAGTTGTCAGTC
GATGTGACTGATGCGCGGGCGCGTGTNGTGTCGTCGTATGATCATACTTA
ATGGAGATGCGTGTGAAGAATTGCCGGCGCACACTGCTACGACACAGTAA
GGCCATGATGCGGTGCCGTGCCGTGTCCAATCACCACAGCGCAGCGCGCG
TGGACAAGCNACAGACGGATGACTCGGTGGNGACACACGGCAGNACCGAG
AGGNAGNCGAAGCACAGGTGCTNATTGTGTTCTATCGTGCTCGGCCNCGC
ATCTCGAATATACATCGATTGANAGTCGCAGTTGGATAGAAAGAATAACG
GAACTCCGGGTGGCACGTTCGCACCATCGCACACTCTGCTGTGCGCGACG
CCCGTGTAANACCTACGGCGAATAGCGCACTATCACTAGCCAGAGCGTGC
GCCCCGTGCACGCGGCGTACTCGAACTCTGTCACACAAACGTAGCGTCTT
ACACGCCCGTTAAACATACAGAGGAGCAAGTCGAGATCACAAATCGAGCA
CCAGCGGTCCCGCACCTGTGGTCAATAACGTATCGTCCGACTACATCAAG
GCGAGATTGTATAGTAGGCGTATAACATCGCGCACTACATGCTAGAACGC
AGCATCGAACGTCTACCGAGGGCGTATTCGTAGGCGTCCTCACGCAACCG
AATAACTAAGTGGCTACGACGATTGAGACGACAGACACGACGACGTATGA
GCATAGCGATGGACACGACAACACCATGACATAGGCTCCGATCACACATA
CACGCAACATATCACGNGTTCGACTACGCTACAGCTGAGTGCACGCTCGT
GTACTTNACCTAGACATCACAACCTAGGACTAACGACGTCGAGCGACGCG
ACGAGGCGTGCTGCGTNGATAATANTGTTACCTCATCTCACACACATACA
CCAATCGCCAACATAATATCAATCT
>RL811R  CHROMAT_FILE: RL811R PHD_FILE: RL811R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:07 2001
NAAACAAAAAANNNNTTCNNTTNTTTTAAAAAATAAAAAAAATAAAAAAA
NAANCTACGGGGCGACTGGGAGGCACGGTCCGGGGATTCCGGGGCGGACC
CAGGCGNCCGGGGCGCGCGCGCGCGAGACGCGACGGAGGGAGCAGCCGGC
AGAAGTGAGCGTAAGAGAAGACAGGGAGGCAGGCTGCGGACCACACGCAC
ACGGAGCTCGCTGGCTAGAGTGGCAAGNGGACCGCTCAAAGAGAGACGGC
AGCCAGAAGAGGAAACCCACACCCCCCTAGCAGCAAGGCTAGCAGCCACG
GTAGCCAAACAAAGTGGAATAGAGCGGAAGACATCATCGACCCGCGAGAG
AGTGGGGAACCACGCCGCCGCTGAGGAGCGCGCTACGGAGACCAGAACAA
CAACCATAGCACCGGGGCAAAGGAGGACGATGACGTAGCCCCAACGCAGC
GCAGACCAGCCACCACACCCAACCCCGCACGAGCATAGCACACAGCCCGA
GAGTCCCCCGNCACGATGCAGAGTATCGCCCGTCCGTCGACCGCCGCGGA
ACACACCGAGATAGGGGGGAAGGGCCCCACGAAGACTCAAGCGCGGGCAG
ACGCAACAAAAGGACACACCAACAGCCCACCGCTCTCACGAGCAGACTAC
ACCAAGAAGGACGACGAGACACAGCCCGCGCGCGAGGCGGCTTAAACCAC
ACCCCACCGGAGCACGCAGAGAGAAAATTCAATAGCCACATCACTGAACC
CTAGTGGCCCGCGCGCCCCGCCCACGCATACATTCGAAACACAACGGAGC
ACACACGAGGATGGCCAGCCAACCCCCCGCACGCGCACGCACAGACACGC
AACCACCAAACCACCCCACCCCCAGTACATGCACCAGCGCAAATGCAGAT
GCAGTGGTTCGGAGACCAACAGCCACGACACAGCGCCAAACCACACGCAC
ACCCCCACAACACAGCACACCAAAGCGCCCAGCAACCACAAGAGACACGC
CACAAACGCAACGGAAACACTACACGCNGCAATACCAAATCAACACACAA
CCACAACACAAAAACA
>RL812F  CHROMAT_FILE: RL812F PHD_FILE: RL812F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:44 2001
TCTTAGTTGGAACATCAAATAACATAAGGTCATATTTCATATCCACCACA
TTTGGAAGTTCTTTTGCTCGAAAGTAACTACTTCATATAAAATAACTCGG
ACACAGAGATACAACACACAAGTCACATTTTATTCTTGATAATATCTTCT
TCTTGTTTGTTTGGACAACATGATAGGAGTTTTCTCTTAAAACATAGGAC
CAGCAGCGAGAATCTCCTCCGTGAGCTTACCATCCACACCAATCTTGTGG
CTAGCGAACGTCTCAAAGTTCTTCTTGAACAAACCTCCCAGCTTCAACAG
AGTCTCCTTGTGTGCGTTCTTATCAGACCACGAGTTGATTGGATCCAAGA
TCTCTGAAGGTATCCCTTCGATCTCAGTTGGGATTTCAAACCCAAAGATC
TCCGTCTTCTTGTAGTTCGCCTTCAACAAGCTACCTGAATGGATTGCATC
GATGATCTTCCTAGTATACGCCAGCTTGATCCTGTTTCCAACACCGTAGC
TGCCACCAGACCAGCCAGTGTTAACGAGCCATCCAGTAGCACCTTGCGTC
TTCATCTTCTCGGCTAACATAGCTGCGTACTTGGTAGGATGCAGCATTAT
GAAAGCTGCACCAAAACAAGCTGAGAATGTTGCTGTTGGCTCCTTGATAC
CGTCCTCTGTTCCAGCAACCAGAGCAGTGTAACCACTAATGAAGTGGTAC
ATGGTCTGCGCCAGGTTCAGCTTGCTCACAGGCGGGAGAACACCAAAGGC
ATCACAAGCCAGAAGTATCACGTTNTTAGG
>RL812R  CHROMAT_FILE: RL812R PHD_FILE: RL812R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:11 2001
ATXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXCCCACGCGTCCGCTCTTCCATACACTTCAAATGATCTTCTCCTCT
AATCATTAATCTCTTTGATCTCTCTCAAGTCTTCTTGTTCGTGATCTCTC
TTCCTTCCCCCGGTAACGGAAAAAGATGTCGGCAGGTAACGGAAATCCTA
ACGGTGACGGAGGCTTCAGCTTCCCGAAAGGACCAGCGATGCCGAAGATA
ACGACGGGAGCTAAGAGGGGTAGCGAAATATGCCACGATGACAGTGGTCC
GACGGTGAAGGCGACGACGATCGATGAGCTCCACTCGTTACAGAAGAAGC
GTTCTGCTCCCACCACACCTATTAACCAGAGCGGCGCCGCCGCTTTCTCC
GCCGTCTCGGAGGAGGAGCGCCAGAAGATTCAACTCCAGTCTATCAGTGC
ATCGTTAGCGTCGTTGACGAGAGAGTCTGGACCCAAAGTGGTGAGAGGAG
ATCCGGCGGAGAAGAAGGCCGACGGTTCCACTACTCCGGCCTACGCACAC
GGCCAGCATCACTCCATATTCTCTCCGGATCTAGGAGCCGTGAGTGACAG
CTCATTGAAATTCACCCACGTCCTCTACAACCTCTCCCCTGCAGAGCTCT
ACGAGCAAGCTATCAAGTACGAGAAAGGCTCGTTCATCACTTCTAATGGA
GCTTTGGCGACGCTTTCGGGGGCCAAGACTGGTCGTGCTCCGAGGGATAA
GCGTGTCGTTAGAGATGCCACGACAGAGGGCGAGCTNTGGTGGGGAAAGG
GTTCGCCTAATATCGAGATGGATGAACACACCTTCATGGTGAACAGAGAA
AGAGCCGTTGATTACTTNGACTCCTTTGGAAAGGTCTTTGTCAACGATCA
GTTCTTGAACTGGGATCCAG
>RL817F  CHROMAT_FILE: RL817F PHD_FILE: RL817F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:34 2001
CCAGAAAACGGCCCGTCNCGCCTTCTAATTTGTTTCATGTATAATATTAA
TTACAAAACACCGCCCTTTTTNGNNNNACTGNAACGAAANAGTTGAGAGA
GGGGCCGCCGCNCGGGCGGCCGGCCGCCGCCGGAGCGGCCCCGACGCCAA
AAAGCGCGGGAAGACGGCACAGCANCGGGCGCCCGCGGGCGCCGGCGCCC
GCACGCGCAGACGGCACAAGCCCCCGCCCCCGGCGCGGAGCGCCACACCA
AACCCNGAGGGACGCAGCGCGAAACCCCCGCCGACACACCGAGAGCACCG
GGCGAAAACGCAGAAAGGCCCCAGAGGGTGCCCGCGGGGGGGAGAGCCAG
AGCGAGCCGACGGGGACAGGAGACCCCGCGGGACGAGCGTCAGTGCGCGG
CGAGGGCGGGAGGCTGATTTTTTTTTTTCTTCTTTTTTTCTCTTTTCTTC
TTCTTTTTTCTTGTTCTGTTTTTTGTTATTGTTGGTCTTGTCAGCTGTTC
GCATTGTGTAGTTATACTTTTTTCATCTCTCTTTTTATATTTTATATTTT
ATTAGTATTTATTTCTTTCGTTCTATTTTTTGTTATCCATTTTTTTTTTC
TTATTTTTTTTATCCTCTTTCTTTCCTGATATTATTTTTTCTTTTTTTTA
TTAGTATGTTTTTGATTCTTCTCTTTTCGTTATTCTTATTTTTCTCTTCT
TTTTTTTTATTTTTCTTCTTTAATTTTCTTTCTTTTAATTTTTGTCGTTT
TTTTATATTAGAATTATGCCGTTCTTCTCATTTCTCTACTTGGTTATCTT
TCTATGCTGTGGTACTATTTTATCGATTTTATTTTCACTATCACCTTACA
TTCTATATCACCCTTCTATTTTCGTTTATCTTATATCGTTTTTTTGTCTT
CTCATCTTTGTTCATTTTATTATTTTCTTCACTTTTTTCATTATATTTTA
TTN
>RL819F  CHROMAT_FILE: RL819F PHD_FILE: RL819F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:41 2001
GGCAGCACGAGACGGCGCNCGNNGGAGNNNGGTCGCGGGCCGCCGAGGGG
AAGCAAAGCGTTCGGCGGGTGGGGCCTACTGGGGGAACGCGCGCCNNNCG
AGTTGCGAGGGAGCCGTCGCNCAACGCGCAGGGCGANNCAAAGAGAGCGC
CCGCGCACGGAGGAACGGGCAGAAGAGNGGGGGGGGAGAGGTACGGCGCG
TGCACGGGATACCTACGCACCCCGATCGCGCCTGCCGCCCGCCCCGCGCG
GGATGAGCGACGGCGACCAGCCNGTGGTCCGTCGTGCGGAGCCGGCGACC
CACACGCCGACAGACCGTAACGCGCGGTACGCGCGCCACGGCGATCTGCG
TGCGAGCCCTTACCCCTTCCGATACACGACAATAACCTAGTAGGATACAG
ACACGCCTGGCCACAGGTATATAACTATATATATACAANGAAGCCAAATC
CAATGAAACACTGATAACACGAGAAGCTAAATAGTTGAAGACAAGCCGGC
GAGAAGGGGGANNGAGACCGGGTGAGTGAGACAGGTACGCCGAGCCGAGA
GGGCGGTCAGAGATGGGAGCTCGCCACGGGACACGGTAAGCATCGACACG
GTGAGGAGAGGCACGCAGAAACAGAACGGGCAGAGACTAACCTATCAGAC
ATGGGAAGGGTAGCGGAATGCCACCCTGGAGACCCGCGACCGCANACGAA
ACAATCGCCAGACAACACAGAAAAGTANCGTCTCAAAACGGCAGCATCCA
GCGCCGGGGGACACGGAAGCGGACGACGCCCGGACGTGTTATAAACGAAC
GCGACCGCTAAGATGGCATCTAAGGCGGAGACAACATAACGACATAAGAG
ACAACGCGCGACGACGCGAACGTACGCGATGGATCCGAGGAACGCGCAAC
GAANACGATCGTCTATGCAAACACACAACGAGAAACACGATACGGTTATA
GGACGAAGATGGAAGTAACGTGGCGAACACATCACCAAATACTATGACGA
TACANACACGGAGAAGGAGCAGAGTGTACGCGCGGTCCGCTCATCGCGCC
ACGGCGACCCAGCGAACATGATGGAAGTGTATCGGCGGCGCGGACAACTC
GAGGAATAAAG
>RL822F  CHROMAT_FILE: RL822F PHD_FILE: RL822F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:50 2001
CCCCCCAACGGCNGGGCCGCGGCNGNTGATTTGTCGGGTGTAAGAAAAAA
TGAAATATAAAACTANAAANNAAGNNGGGCCTTCTTCGNNNNACTTGCCA
CACNCGGGNCGTTTCCGCGGGAGNCNGACCCNNCAGNGCCGGCAGCGCCN
CCCGCGCGCCGGCCCCCCCCGCCCGGGCGGCNCNNCCCGCGGGGGGGCGN
NCGGGCGCGCGNACNCCACAACCCCCCNGCAACACGNCGGCGGGCCCCGG
CGACGCCGCGGGCGGGGGCGGGCCGCGCGCCCGCGCGCGNGCCGCGGGCG
CGCGCCGGCACCGGGCCCGGCGGGCCCGCNCCGCGGCGCCCCCCGCCCCC
GCCCGCCCGCCGGGGGCGCGGGCGCGCGGCCGGGCGCGCCGCGCGCGCNG
CGCCGCGCGGCGNNCGGGCGNNGNGNGGNNNGGGCCGCGGCAGCGGCGCG
NAGGCGCGCGCGGGCGCCGACCAGAGACGCGCCCCCCGCGCNCCGCGCGC
GGCNGAGAGACGCGCGNACGCGACAACACAAAACGAGCGCGCGGCNNGCC
NGGGGGGGCGGCGGCGACGCGCCGCGCACGCCGCCGGGCCAGGCGCGNGG
ACGGCGCGCGCCNACGGANGCNCGNNNGCCNNGCGCCGCCGCGCCGGGGN
GCGCCGCGAACCCGCACCGCCGAGCGGCGCGGGCGGGNGGGGGGAGGGGG
CGGGGGAGAGCGANACGAGGGCGCGCCGCGGAAAGGGCGGAGGCGGCGAG
GACGCGCGGCGCCGGCGGCGACGCGGCNGGCGGCCCGGGCNCCAGAGCNC
AGCGAAACACGAGGGCGCANACGCGNCCAACCGNCACNCAACGCGCCNCG
AACAGAAGAAGCGCACACGNGCGCGCACGGCGCGNCGCGGCAGGCGAGCG
ANACCNAGACGAGGAGCAGGCGACGGACGGNGGAGNAGAGNGGNNGGGCC
CGAGNCGCCGGCGACGCAGACAGAGAGAAGCCGGCCGNGGNCGGCACCGA
CACGCCGACGCGCGACCGCGGNCGGGCCCGCGCGAGCGCACGCAACACGA
CGNCGGCGCGCCGNCGCGGNNCNCGCACGCGCGGACGCGAAGCGGCAAGA
GCGNGACGCGCGAGCGCAGGNGGGNGCNCAGCCGCGCGAGAGGCCGGAAG
ACGNCGAGCGNGGCNGACGACGCNGACGACGAAGACGNCGCGCGCGCACG
CGACAACACACACGACGNCGCGCCGCAGCCNGCACAACACCAACACGCAC
AGCGCACAGACGCCGGCACGAGANCNAGANCACGACGNACCNAGCAGACG
ACGCGTCNTNGCNTCTCTATGATCTATGCAGTCGTTCTCGAAAGNGTATA
TAANATGTAGTAGCTAGCTNGNACACAGANTNGNATCCTTCAGACTCATC
AGTNTGATCNNTTAT
>RL829F  CHROMAT_FILE: RL829F PHD_FILE: RL829F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:47 2001
CTTANGAGTAACTATATTTTAAAATTCTCCAAGTTGAAGAAAGTTGTTTT
ATTCTCAAGGGGACAATTTTGTATTTTCCCACTTTAGTTACAAAGAGGCA
GTGATCTTCTCAGTATTCCCCCAAATTCAAATACTTAAATCCAAAAAGCT
TAATTAAGAAAAAGAAACTGCCTAACAAACTAAACCTTGTTGTCTCCATT
CTCATAATTTCTTCATTATTATTGGGGACGCATATCTACATCAAGCTCTT
TCCCCCGGTTTTAGCCGAAATCAACGAGCTCAACATCGGACTGGAACACT
GCATGTCTTGCCCGATCAAAGCTTTGCCTGGGAATACAAGAAGGTTCCGA
GGATAGCAATGGCAGCTCCAAGAGCGTTAACGGGCTGGACAGGGGTGCGG
AAGATAATGATGGAGGAGACAATGACTGAGATACGCTTCATGGTGTTACC
GACACTAAACGTCAAGGGAGAGATTTGGTCTAAAGACATGTAAGACACTT
GGTTGTAGAGATGATAGAACACACTCTGCGCAGCCACCCACCCGACGAAT
TGAGGTCCGACGTGGGAGAGAGCCTTTTGCCAGCCATCGATCCACATCTG
AGGACCTTCAACCGCAATTGCAAAGGGGGTGAGAATCAAGAGTGATAGCA
TGGAGAGACAAGCATAGTAGTTCATTCCGCTCACAGACTTTCCCTTCATT
CCCTTCTTTGAGAAGATGTTACGGAACACAAAAGCCAAGTTCGATATCAT
CGCTCCCATGAAACCAGTCATG
>RL829R  CHROMAT_FILE: RL829R PHD_FILE: RL829R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:15 2001
CGTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXCTCTTACTTAATAACGAACGGCCTTCTCCGTGATCAAAGTTTTAA
TATTTTATTTTAATTCGACGAAAAAGTCTTTTCCTTTTCTCTTTCTCTCT
CTTTTATTCCGACGATGGTTTTAGCGGCGAAGCAGGCTCTCTCCGCTAAG
ATCGGGTTCTCCAACCCTCTTTCGCGACGGAACCCATCTTCCCCGCTCCA
ACGATCACCTCTCGCCGCCTCGTTTCCATCGACGGACCTTCGGAAACGCA
CCGTTTTAGCCGTCTCCAAGCCTCTGCACCTCTCTCCCATGAGAGCGAAG
CCTCCGGCGAGACGCGAGGCCTACGAAGCCGATAAGTCGGAGCCTCAGCC
GATCGATGATGATGCGGCGGAAACGAAGTCGGAGGCGGCGAAGAAGCTGA
AGATCGGAATCTACTTCGCGACTTGGTGGGCGTTGAACGTTGTGTTCAAC
ATCTACAACAAGAAGGTGTTGAACGCTTACCCTTATCCTTGGCTTACCTC
CACGCTCTCTCTCGCGGCTGGTTCGTTGATGATGCTCATCTCTTGGGCTG
TTGGGATCGTTGAGACTCCGAAAACTGATTTCGATTTCTGGAAAACTCTT
TTTCCGGTTGCTGTGGCACATACGATTGGTCATGTGGCTGCAACGGTGAG
TATGTCAAAGGTTGCGGTTTCCTTCACTCACATCATCAAGAGTGGTGAAC
CGGCGTTTAGCGTTCTTGTCTCGAGGTTCCTTTTGGGTGAAACCTTCCCT
ACTTCGGTTTACTTGTCCCTTATTCCGATCATTGGTGGCTGTGCTCTCTC
TGCTCTTACTGAGNCTAACTTCACATGACTGGNTCATGGGAGCGATGATA
TCGN
>RL835F  CHROMAT_FILE: RL835F PHD_FILE: RL835F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:41 2001
GCCGCCGCAGGCCGCCCCCCCCGCCCGGGCGGCGACCCACCCCACATCAA
AAGAGAAGCCTTGTGGGGACTGGTAGTAGGGTTTCAGGCAGAAGCACATA
GTGGGGGGCGGTGCGGAGGGGGCCAGAGTGATAAGGGGGGGGAGGAGGGA
GAAAACGCGCCACCGGCGCCGATCCCGGATGCCGTCGGAGTGGTTGCGCC
GAAGTAGACGTTAGAAATTAGTGGGTGGAGTGTATATAAATGAGCCTCTA
TTTGAACTCCCTTCTATCTCTCAGTCGGTGTCCGTGTGCTCCACACGCTT
TAACTATATCCATCCGCTACGCCACTACTCCGCGAGGCCGCGACAACGGA
GGTGAAACAGAGGGAGGGCGCGCGTCGCGAGAGCGGAGGGTAGGGGCACG
CGCGCCGGCGCGGCTGGTGCTGGGTTGCGGAAGATGGGGTCGCGTGCGAG
CAGAGCGCATCTGGCGATGCAAGGTTAAAGATTATGGTTAGTTTTAGAGG
TAGGGAACGAAGAGAGAGTGTAGATCTAGAGCTTGTGATACCGCCTATAT
ACTAAAGCGATTCATCCCCTCTGAGCGTGCCGACGCGCCCGCGCGTGGCA
CGGCAAAAGTGGTAGCGCATCACGGCGTACACGCGCGCATTCATGAAAGC
GGCGCGGCACGGAAGGTAAATACTATCGCGCTACGAGACCGAACCGAGCG
AGAGCATACGAAGTGTNGACAGNCGCGACCGACGACACGACGGCGCGAAC
GAGGGAGACGCACACAGAAAGACGCGNCGAGATGCGATCGCGAACCGAAC
GCGTATATGATCCGACAATATACGGCCACCGCACACAGAGAGCACGGTGA
CGGTGCACACGAGAAAGACATNATATCAGTCACATGCACAGTTCCGAGTA
GCGGCGTCCAGTTGATATGGGAGGGGAGCCGACGCAAGCGCGGATATAG
>RL835R  CHROMAT_FILE: RL835R PHD_FILE: RL835R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:08 2001
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNCTCNGGGGACAACAGCNAAGAACCGGTTCCGG
GAATTNCCGGGGNGGAACCAAACAAGCCGGGCCGGACACCAGCAACACGC
GCCCAACAAGGGGGGGAGCAGGGAGCAGAAAAAAACAGGACAACAACCGG
CCCAGCCAAGAGAGAGAACGAAAGCAGCGCGCCCAAAGAAGAGCACACAT
CGACGCGCAGACCCAAGAGAGCAAANGAGGGAGCACAGCGGAGTACCACA
CGAGACCACACAAGCCCCCCCGAACGCAAACAGCCACCAGAGCGAAACGG
CCGCGAAAAGACACAAACGCCACGCAGGACAGAAGGAGACCAAGAACCAA
CGCCCGCAAGCCCCGGCGAAAACTGAAGACCCACTAGCCCACACCCCGCN
CACCAGACACACAGAAAAGGACAGTCTACGTCCGCGGCCGCCAAAGCTCA
TAACACCCACACCAACGCCAAGCACAAAGCAAAGCGGCACAAAAAGGACC
CGTAGAGAAGCCACACTCCGCAACGCCCCACCCACACCGACCCGACCAAA
TAGCCGAGGAGACAAAGAACGCCCACCGACACAGAACCCCCAGACCGAAC
AGCAGAGAAAAGCACAAAAACCACGAACAGAACGAACACACAAAACAGAG
AAAGGATCAGAAACGCCGCAACAACAGGCCACCCAACACATAGAGCGAAG
AGTCACGAAGGAAAGCGAGCAACAGAATCCCACACACAACGAAGAGCACA
GAGCAAAAAGAGAACGCGGGCGACCACACCGCTCCCCCCCTCAGGCCGGC
AGAAAAAACACGCCACACCCACCACAAAACCCAGGAGTACAACAACAAAA
NACCAGAAAACAACAAAGCCAACGCAAGGCGCACCACAGACCACCGCAGC
ACCAAACACGCAAAGCAACATCAGAGAACGCCCGACAGCGGCAAGAAATG
AGGCACCACGCCGGACNGCACAGGAGGAAGAAAACAGCGAGCGAAGCCAA
CAGAGACACGGAGAGGAGCCAACCGCACAAACAGAACATGAGGACAAAAA
CACCAGACAACACCCCACCAACCAGCAGCCTCAAAACACAACAGCGACGC
GCCACACACACACGACCAGCTCAGAGCCACAGCGAGCACAGAGACCGACG
CGCAANCCCAACATAACACAGCCGACGACGAACGAAAAACACAGCGACAA
AAGGGACCCAGAAGAGAAAGCAAGACCATAGAAAGTAT
>RL844F  CHROMAT_FILE: RL844F PHD_FILE: RL844F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:45 2001
NTTCGACAAAGCCGAAGAGACAAAGAGAGAGAGGGATTGTATCATTTGCA
GGCCATAAGCATGGAGTTTATCACGTGCATTGTAAGTCTTGTGGCAGAGA
CGTCGCTGCCTGGTGCGTTGCGGTGGTGGTGCAGAATTTGATACACTTGC
TCAAAGATTGGGCGACCATGGACAGCTACCATCGGGTCTGATGGGTTAAT
TGCTGCAACCACATCGGTCATCCATGCAAGCTTACGGGATGAGTCCTTGC
TGATGTCGCAGGCTAGCTGTTGCAGCAGTGACAGAAGAACGCCTTGGCTC
AGAGGAAGCGGGTTCATCGCCAGTAGTCCACGCAGATCCACCTGTGAGCA
AAGCCATGATACTATGGAGACATCGCTTCTCTGTAGAGCTGAAGTAAATG
ATTCTTCATATTTGCGTTCCGATATCAACCTTGATAATTCTGTTATTGGG
TCTGCTTCAACCTTTTCAAGAAGAGCACCCAAAGGTCCACCACTTCGTTG
AGAAACCAATGTGTTTGATCCACTAGAATTTGCTCCAGCGGCTGCGAGAG
CTAAGCGATTCCTTTGGCTCTCCGCTAATTCACGGCTCAATGCTTGAGTA
ACTGACGACGCAGAAGTAATGGTTTCCTTTAAAGTATGAGCAAGTTGGGA
GTGTCCAGCGTCAAACCGTTGTTGGGCTGCGTTTGTGTGCTCGGCCATCC
CTTTCTGGAAGGCTGCGTCTACTTGCTCAAACATGGTCTTGCATGACCTC
TCAAGGAAGGTATGAGCGAGGC
>RL844R  CHROMAT_FILE: RL844R PHD_FILE: RL844R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:12 2001
ATTTTGGAAAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXAAGCTCAAGAAGCAAGGACAATGATGTTAGGCCTGATGATGATGT
GTCTGGGATGCGAACCGCACAAGCTTTCTTCAAGCATCCCACGCATCTTG
TAACTCCTTCGGAGTTTTTGATGCGCGTTCCGTCTACTGAAGCTTCCATT
ACCACTGAAGACAAAAGGGATAGAGATGCAAATATCCAGGACGTCAATAT
TGATTCAAGAGACACAGAAGTTGAGGTAAAAGAAGTAGGGGAATCAAGTT
CGACGCAGAATGGTGAAATCAATTACAGTGATGAAACTGAGCATCGCACT
TCAGTAAATACAGAAAAAACCTTTTACTCACAGACTACGAACCTGAGCAC
TGAGATGGCAAGAGACTGTTATCCTGGTACAGAGTTAGAGGAATCTAAGG
CTTATGAACAGTCTGTACAAGCTGGGGATAATCTTGACTCGAGAGATGTG
TCTGGAAAGCTTCCTGAGTCGGTTTCATCAATTGGGCTTTCACAGTCAGC
CGCTACAACCAAAGGGAAGAAGCAGAAGTCGAAAAGCTCACAGGGTCCCG
GATTGTCATCTACATCCTCAAATGTTGCCAATTTGGCTGATACCTACAAT
GAGCAAACTCAGAGTTCAAGCCAACCTATCTTAGCTTTGCAAGAAACAAT
GAATCAGATGATGGTTTCACAGAAGGAGATGCAGAGACAACTGTCCAATG
CTGTCAATGGCCCTGTTACTAAAGAAGGTAAAAGACTAGAAGTGGCTTTA
GGGAGAATGATTGAGAGATCCAGCNNAGTCAATGCTGATGCTCTNTGNGC
CCGCTTTACAGAGGAGATCGTTAAGAATGAAAGGGCATGCGTGACATTCA
CAGCAATTGT
>RL845F  CHROMAT_FILE: RL845F PHD_FILE: RL845F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:48 2001
CCTTTTGGAGACANTAAAGATCCAAACATAACAGTACGAAACACACAGCA
CACATGCTTGTGAAAGGTGAGAGTACCTCAACTTCACAAGCCATTATTCA
TTACGAAACAAAAGAAAGATTGCATAAAAACAGAAAGCTCATAAATAGTT
CTGCTAGATTCCCTCGTCCTTCTCGTCCTCGCTGCTGCAGCTATTGTTGG
CTGCTCCACTCACACTTCAAGGTAGATCTAGGCGATCCACAGTACTTGCC
AAGCTTCTCAAACGTCTGATACATAACCGTCCCACTCTCTTCCCCTAGAG
ACTCAAATGTCCTCTCTCTGCACCCATAGTCTTCCAAGTCCACACTGATC
TCTGGCTTGTACGCGTTCGATCCAACGCTCGAGTGCACGGCCACAGAGAA
TTGCTTTGGCTCAAAGCAAGACAGAACCCTTGTCACAAGCTGGCTCAGGT
CGAGGGTGTTGAAGTCGTAACCCACGGCTTCGAAGCTAGCGTAGCTAAAC
CCATCCTCAGGGGTCACATGGATAGTGGAGATCGCATCTCCTTCAATGGA
GTTCATAGAGTAGCCACAGGGCTCGAACTCAAAGTCGCAGATCTGGGACT
TGGGGAGGATCTTTCTGATTCCAGAGTTGTCGGTCATCGATCCATTCTCC
CCACCAGTTTCATTCTTGTAGAAGACAGAGGCTTTCTCCTTGTCAAGACC
AGTCATACACATCTCGAGCGTGTAGACATTGTTGTTGCAGTCGCTGGAGG
TCTGAGCAGAGGAGGCAG
>RL845R  CHROMAT_FILE: RL845R PHD_FILE: RL845R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:15 2001
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXCTCATTGGCTCATCATTACCAAATCATCATAATAAATCGTCATTT
CTCTCAAAATTAGGGTTTTCTCTTCCGGTTATCTGTATCTGGGGTTTTGA
AGGTTTCGTTTCGTATCTGGGAAGAAAGGATTCGTTAATTCGTGGTCTAG
ATCTAAAATTCATATATATAAGGCGTGAATGAGATTATGATGGAATCGAA
AGGTGGTAATAAAAAGTCGTCGTCTAGTAGTTCCTTATTTTACGAAGCTC
CCCTCGGTTACAGCATTGAAGACGTTCGCCCCAACGGTGGAATCAAGAAA
TTCAAATCTTCTGTCTACTCCAACTGCGCTAAGAGGCCATCCTGAGTTGT
AGCGTGCACCGAGTCCTCCTGCTATAGTTATAGCTTTTTATAATTTCCAG
TTTATAATTTACTTTTTTCTTTCTAAGCTCCGTTTCTGCTTGGTTCCCCA
ATCCCATCGTTCTCTCCTCCTACTACAATGGCCTTATCTGCAATCGGTTT
CGAAGGCTACGAGAAGCGCCTCGAGGTCTCTTTCTTCGAGCCTAGCTTCT
TCCAAGACTCCAAGGGACTTGGTCTCCGTGCTCTGACCAGGTCCCAGCTT
GACGAGATTCTCACTCCTGCTGCCTGCGAGATCGTTTCCTCTCTCTCCAA
CGATCACTTGGACTCTTACGTCCTCTCTGAGTCCAGCTTCTTTGTCTACC
CTTACCAAGTCATCATCAAGACCTGTGGCACCACCAAGCTCCTCCTCTCC
ATCCCGCCGCTTCTTAAGCTGGCCGGTGAGCTNTCCCTGAGTGTTAAGTC
TGTTAAATACACTCGCGGCTCCTTCCTCTGCCCTGGAGGCCAGCCTTTTT
CTN
>RL847F  CHROMAT_FILE: RL847F PHD_FILE: RL847F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:29 2001
CTTGGGGATACGTTCAAAGATGCATAACAAACAAAAAGAAGGTAAATAAA
TAAAGATCACAAAGCTAACATTCTCACCACGTGGTTGCACGAATTAAAAC
CAAAGGGGTGAAAATGCAACATACCACACCAACGACCAACTTATTAGTTC
TAAAAGTAGACACAGACACTCAGTTTATTCAAAGACAGAGAAGTTCATTG
TTAAGATATACCCAAGTGAAACCTAGGTTGTAAGGATTGGAGGCAAGTAG
TCAGATTTGGTTCCAAGGATACGAGCCTTTGTGTCAGGGAAGAACTCAAA
TCCGGGAAACTCAGTGACGTCACCTTCACAGTCTACATCAACAGGGTAGC
GTAGCAAGTGACCGGGAAGGTCATGTTCAAGTGACTCGCTCGAGTATAAG
TCCCAATACTTGTCAGAAATGCGGTTAACTTTCTCAATGCATTCCACGCT
TGATGGATCGAGGAAGGTCTCATCGAGCATTCCTAGGTGTTCGTACCAGA
GTGACATGCGGAACCCATGGATCTGTCCACGAGCTGGTTGTCTATGTGAC
AAGTGATGTGGTTGGTAGCCTCCCATTGCAATCTCAGAGTCCCTCGCACC
ATCCATCGACCTCTGGTTGATGTTAGCAGATCCAATGATGATATATTCAT
CGTCAACGATCATCATTTTGGTGTGGACGTAGATCATGAAGCGACGTGCT
TCTTGTGCCTTCATATAGCTCGAGTCAGCGTCTGGTCTCTCTGCTGGCTC
ATACTCTCCTTCTTTCTTT
>RL847R  CHROMAT_FILE: RL847R PHD_FILE: RL847R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:55 2001
CTTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXTTGTGGACAGCGAGATGCCGAGCCGAGGGGGTTCACAGATGAGGA
GGATCGTGAGTTTTGTTGGTGGGATCGATCTCTGTGATGGACGTTACGAC
ACTCCTTTCCACTCCTTGTTCAGGACGTTGGACACTGTCCACCACGACGA
CTTCCACCAGCCTAACTTCACCGGCGCCGCCATCACCAAAGGCGGGCCGA
GGGAGCCTTGGCACGACATCCACTCTCGCCTCGAAGGTCCCATCGCTTGG
GATGTTTTGTACAACTTCGAGCAGAGGTGGAGCAAGCAAGGTGGTAAAGA
CATTCTCGTTAAGCTGAGGGAGCTTAGTGATATCATCATCACACCTTCTC
CCGTTATGTTCCAAGAGGATCACGACGTGTGGAATGTGCAGCTGTTTAGA
TCCATCGACGGTGGAGCTGCTGCTGGGTTCCCCGAGTCGCCTGAAGCTGC
TGCTGAAGCTGGTCTTGTGAGTGGTAAGGATAACATCATTGATAGAAGCA
TCCAAGATGCTTACATTCACGCTATCCGTCGCGCGAAAGACTTCATCTAC
ATTGAGAATCAGTACTTCCTTGGAAGCTCTTTTGCTTGGGCAGCTGATGG
TATCACTCCTGAGGACATCAACGCTCTGCACTTGATCCCAAAAGAGCTGT
CCTTAAAGATCGTTAGCAAGATTGAGAAGGGAGAGAAGTTCAGGGTTTAT
GTTGTGGTGCCGATGTGGCCGGAAGGTCTTCCGGAGAGTGCATCAGTGCA
AGCTATATTGGATTGGCAGAGGAGGACCATGCAGATGATGTACAAGGATA
TTGTTCAAGCTCTTAGGGCTCANGGCTTAGAGGAAGATCCTAGAACTATC
TG
>RL849F  CHROMAT_FILE: RL849F PHD_FILE: RL849F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:36 2001
GCCCGTTCTCGGCCACTCATAGGCGTTCCACAATTTCATACAGTGAGTTG
GTGGGCCCTTTATTGAAGCCCATTATCTTATGAGAAAAAAAAAAAACATA
AACATATGTTCGACACTTCTCACAACAAAGCTTCGTTTTCGACTTTGATT
AAACCATTACTGTGTTCACTTCTAATCACCATTACAATCTTGGAACTTGA
GATCGTTTTCCCTCTGAGTTTCATCAAATGCGTAAGAACCTCATTCATAT
CGGGCCTATCCTCAGGTCTAGAGCTTGTACAGTACAAACAAAGCTTAAAC
AAATCTCCAACAGCCTTTTCCTGCTTCCTAGTAACAATAGATAACCCAAT
CTCCGAATCAAGAACCCTGATCATCCCTTCCACTCCATCTCCAACCGCTT
CCTCCACCAATTGACGCAGACTCACCCCTTGTGATTCTTCATCGATCACC
GAAGTCGGTCTCCGTTTCGTCATCAGCTCCATCATCACAATCCCGAAGCT
GAACACGTCCGCTTTCGTCGTCACTTTCCTCATATAAGCAAACTCTGGAG
CTAAGAACCCAATCGTCCCCTCGAAGGCTAACGTAGAAGCTGTAACGCTT
CCATCTTCTCGTAACCCTAGGATCCTCGCAGTCCCAAAATCGCTGACGTG
AGCAACTCCATCTCCGTCGAGGAGTATATTCGCCGGCTTCAGATCGCAAT
GCACGATCGGGAATCCAAATCCAGAGTGAAGGTAATCGATTCCGCTAGCG
ATATCAACGCACAGATCGATTT
>RL849R  CHROMAT_FILE: RL849R PHD_FILE: RL849R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:02 2001
AGTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXCGAATCTGGGGATTCTTACAAACCTTGGGAACCTTTCTGCACA
CGACAATCTTCTTACCGGGTCAATACCTTCTAGCATAAGTAACTGCACCA
GTCTTAAAGTCTTGGACCTGTCTTATAACCAGATGACTGGCAAGATTCCT
AGGGGTTTAGGACGGATGAATCTTACATTACTTTCTCTTGGGCCGAATCG
GTTTACTGGCGAAATTCCGGATGATATCTTTAACTGTTCAGACTTGGGAA
TTCTTAATCTGGCACAGAACAACTTCACAGGAGCAATCAAGCCATTCATT
GGGAAGCTTCAGAAGCTACGGATATTGCAGCTATCTTCTAACTCTCTCAC
TGGATCAATTCCTCGAGAGATAGGGAATCTCAGAGAGCTGAGTCTCTTGC
AACTTCACACTAATCATTTCACGGGAAGAATCCCGAGGGAGATATCAAGT
CTGACTCTACTGCAGGGGCTTGAGCTGGGTAGAAACTATCTCCAAGGTCC
AATTCCTGAAGAGATATTTGGTATGAAGCAACTCTCAGAGCTCTATCTGT
CCAACAACAACTTCTCAGGTCCAATTCCTGTCTTGTTCTCGAAGCTTGAA
TCTCTTACCTACTTGGGTCTTCGTGGAAACAAGTTCAACGGGTCTATCCC
TGCAAGCCTCAAGTCACTTTCGCATCTCAACACATTGGATATCTCCGACA
ATCTTCTCACCGGAACCATCCCTAGCGAGCTGATATCTTCGATGAGAAAC
TTGCAGCTTACCCTCAACTTCTCAAACATTTATTGTCAGGAACCATCCNN
CATGAGCTTTTGGAAGCTAGAATGGTTCAAGAGATCGACTTTTCAN
>RL855F  CHROMAT_FILE: RL855F PHD_FILE: RL855F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:30 2001
GCTTACTGCTAACCACATGACCATGTCAAGAAGAATATCAAAAAGACCGG
CAAACATTCGCTGAGCTGCTTTATTCAAACAAGGGTAATAAAACTGAAGA
AAGCTGGGAAAAAAGTGAAGAGGGTTTTCTTGGTGATTGTACACATCATC
ATAATATTTTCTAGCGAGCGTCCTTGGACAAAAGGCCATGCGATTCAACT
TTCCTTGCGTTGCGAAGCTCATCAACTCCATCTCCTCTCTCAAACACAGC
CGCTGCACCCATCCCCGTCCCAATGCACATTGAAACTACCCCAAATCGAC
AGTCTTTTCCGCGGCGTTTCATCTCATGCAACAAAGTAGCAACGCAACGT
GCTCCTGTAGCACCCAAAGGATGTCCTATGGCCATTGCGCCTCCGTTGAC
ATTGATTTTCTCTGCGTCGAGTCCCAACTTGTTACGGCAATAAACAAACT
GAGATGCAAATGCCTCGTTGATCTCAAACAAGTCAATGTCATCGAGTTCT
AAACCAGCAGCCTTAACTGCAGCAGGAATGGCAACTGCTGGACCAACTCC
CATGATTGCTGGGTCAACACCAACTGCAGCACATGTCCTGAATACACCAA
GAACGGGAAGCCCTTTCTGCGCAGCACCACTCCTTCTTATGAGAAGAACC
GCTCCAGCACCATCACTAACTTGGCTGGAGCTAACAGCTGCTGCGGCCTC
ATCCTTTTTAAACACTGGCTTCATCTCCCAACAGCACCAGGGTTGTGGCT
GGCTCGATTCCATCACTCACAAAAN
>RL855R  CHROMAT_FILE: RL855R PHD_FILE: RL855R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:55 2001
ATTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXACACAAATCCTTTGGTCAGGATGGAGGGGCAATCGAGAGACAAAG
AGTTCTTCTTGAACATCTCCGTCCTTCTTCTTCTTCTTCCTCTCACAGCT
TTGAAGGCTCTCTCTCTGCTTCAGCTTGCTTGGCTGGGGATAGTGCTGCG
TATCAGAGGACCTCTCTCTATGGAGATGATGTAGTCATTGTTGCGGCACA
TAGGACGGCACTATGCAAGTCGAAACGTGGCAATTTCAAGGATACTTATC
CGGATGATCTTCTTGCACCTGTTTTGAGGGCATTGATAGAGAAGACGAAT
CTGAACCCAAGTGATGTTGGTGACATTGTTGTCGGTACTGTTTTGGCACC
GGGATCTCAGAGGGCCAGCGAGTGCAGGATGTCTGCTTTCTACGCCGGTT
TCCCTGAAACCGTTCCCGTTAGAACCGTGAATAGACAATGCTCTTCTGGG
CTTCAGGCTGTTGCTGATGTAGCCGCCGCCATCAAAGCTGGATTTTATGA
TATTGGTATTGGGGCTGGATTGGAGTCCATGACCACTAATCCAATGGCAT
GGGAAGGGTCAGTCAACCCAGCGGTGAAGAAGTTTGAGCAAGCACAGAAC
TGTCTTCTCCCTATGGGTGTTACTTCAGAAAATGTGGCACAACGATTTGG
TGTCTCAAGGCAGGAGCAAGATCAAGCTGCTGTTGACTCGCACAGAAAGG
CAGCTGCTGCTACTGCTGCTGGTAAGTTCAAGGATGAGATCATTCCGGTT
AAAACCAAGCTTGNTGACCCAAAGACAGGAGATGAGAAACCCCATTACAG
TTCTGTGGATGATGGGATCCGACCACCACACCCTTGCTACTCTTGGAAGC
TGAGCCAGT
>RL856F  CHROMAT_FILE: RL856F PHD_FILE: RL856F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:33 2001
CCCAAAACCGCGNGGGGGNGGGCGNGGCCTGCGGGAGAAAGAAAAATGGC
CATCNGCTTCGGGNNNCNNNNCTTGNTCGTNTACTGCCACCAAANNCTNN
NNNGGGGNNAAACCNNGNGGNGNGGGGGNNGGGGGGGGGGGGGCGCCCCG
GCCNGNCGCGCCCGCGGGGCGCGNGCGCGGGGGGCGGGCGCGGCGCGGCG
CNCGCGCGCGGCCGGCGCCCGGCGGGGGCGGGCCCGCCCCCGCCGCGCGC
GGGCGGCGGCCCGGCCCGCCCGCGGCGCCGCCCGCCCCCGCGCGCGGCCG
CCGCGCGCGCGGCGGCCCCGGGCGGNGGGCCGCGGGGGGCGGGGCGCGGG
CGCGGGCGGGGNNGGCGGCCCGCGGGCGCCGGGCGCCCCGCCCCGCCCGC
CGCGCGGCGCCGCCCGGGGGCGCCGGGGGGGGCGGGGCGGGGGCCCGGGC
GGGCGCCCGGCCCCGCGGCGGCCGGCGCCGCCGCCGCCCCGCCCGCCGGC
GCGCGGCGCCCCCCGGCCCCGCGCCCCGGGGCCGGCCCGCGCGGGCCCGG
NGCGCGCCCCGGGGCCGGCGCNGCGCGGCGGNNCGCGGGCGGGGGGGCCG
GCCNCCGCGCCGCGGGCCGCCCGCCCCCCGGCGCGCGCCGCGCCGCGCCG
CGGCGCCGGCCCGCGCGCCGCGCGCGCCCGCGGGCCGNGNCGCCNCGCCC
CGGCGCCGGCCGCGGCCGCGCGGGCGCGCGCCCCGCGGGCCCCGGCGNCG
CGCGNGCCGGCGCGGCCCGGGCNCGGCGCCCGGCGGCCCNCCGCGCCGCG
CCGGCGCCGCNGCGGCGCGGCGGCGGNGCGCGAGCCGGCCCCCGCGGCGC
CGCCGCGCGCGCCGCGTGNGGCGNCGGCGCNCGCGGCCGNGCGCGTCCCG
GCGCGGGNGGCGGNCGGCGTCGCCCGCGTCGTCGCGCGTCGGCCCCGTGC
GNCCGCCGCTCGGCGTCCGTCGCCGCTCTCCGCGTTTCCGCGTGTTGCGC
GCGCGACGCGGCGNCGCGCGCGCTGGCCCCGTCGCGCGTCCCCGCGTCGT
CTGCCGTGTCCGCCGCCGCGTCGCGCGNGTCGCGGTCGTGCGCCGTCNTC
NCGCGCGGGCTCGCCGGTGCGCGCNCGTGCCGCCGCGGCGCGCTGCGTGC
GCCGCGGTCCGCTNTCCTCGCGCGCGACACACAACACGAACAATCNCCGC
AATTCCNTTA
>RL856R  CHROMAT_FILE: RL856R PHD_FILE: RL856R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:58 2001
NAACAAAATGCNGGGGCNGNTTGTTTGATGGAAAAAAAAAAAAAAAACTA
AAAANNNNNCCTTTGCGACGACTGCAGGAACCGGTCCGGAATCCAGCGTG
GACCCACGCGGCCGATGGCGGCGCCTGCTTCCCGCGCCGGCGGGGGCCCG
GCCCCGCTAGGCCGGTCCGCCCCAGACACCGAACGCCCGGGCCCCGCGGA
GGCGCCGAGCGCGCGGAGCGGGGTGACCCCACCGTGCGCCCGAGCGCGCG
CCCCCCCCCCCCCCCGCGCCCGCCGGCCCCCGCGCCCCCCCGGCCCCCCC
GCGGAGGGGGGCGCACGAGCGAGGCCCCCCCCCCCCTCCAGCCGGCGCCC
GACCCCCCCCAGGCGCCCCCACCGGCCCGCCGCGCGGCGGTGGGACCCCG
GCCCGCCGTGCGCGCCCCCGCCGCCCCCCCGCGACCCGAAAACGCACAAC
ACCAACCCGCCCTCCGCCCCCCGCGCAAGGGGCGCGGCCGCACTTCGCGT
GCCCGCCGCCGCGCCGGGCCGGCGCAAGACAAACCCGCGACGCCCCGCGG
GGAGTGAGGCACTCGGTGGGAGCCCCCCCCGGAGCCGCAGACGCAGGCAC
GAGAGACAATCCGCGCGCCAGAGCCGACCGCCGCGCAACAGCCAAACCGC
CCCGCCCGCCCCCGCCAGCGGCGAACCCGCACGACAGGGACACAGGCCAC
CCGGCAGCCAGCACAGCCGACGAGAGGGCCACCCGCCAGACCAGCCCCGC
ATGGCGCCCCCGAGCCCGACACAGAGTCGCAACAAGACACGCCGTGAGCC
CCGCCCGGAGCCAAAGAAGACCGACAAGGACGGAGCGAGCCGCACGCCCG
CCGCCACGAGCCCCGCCGCGCGGCGGCCGCCACAGAGAGAAACCACACCC
GCAGCCACGCCCCACCGTCCCCCCACTACACACGCCCCCCACACCACACA
CCCCCCAACCCCCGCCGCCCCGACGCGCCGCAACCCTCCCCCCCCACCAC
GAACGAAAAACAAAGAAAACAAACACACACG
>RL859F  CHROMAT_FILE: RL859F PHD_FILE: RL859F.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:44:42 2001
GCTTCTGAGATACATCACGAAATCCAACATTTTGGTCTTAGGAATGAAAC
AGACAACATGAGGATATCAAACTGATTTTGTGTTTAAACAGACAACATGA
AGGGAGGAAACAAGTGAGAGCGTTTGAGATGGGATAAAGACAACCAGTAC
ATCAAGTTGTTTGACTAGAGAGGAAGAGAGCTTTTCATTTTTTTCTCCAT
CATTCCTCTGCAGCACTAGCTGCGTTAAGGTCCACACTTAAATCCAGTTC
CTTGCCGGTGATAAGTTTATACATGTTCAGCACATCAACAACAGTAGTAT
CAAAGTGTGTTGTCGCATCGTAACTCGTTGAAATGAAGCAGTTGTCCAAA
GTGGGTTCGTTGACAGGCTCGTATCTATCATAGATGTCGAAGAACAGCTC
ATCAACTTGGCCAAGAAGGTCGATTCCAGGCTTCAGCTCGGTCTGTGGGT
TGTCAGTCTCTGCGTCTGTCGACACAAATGCTATGAATTTTCCCTTGGGA
GCAACGTTGTGGGAATACGAACAGCAGAAGACATACATGTCTGATTTGCG
GCCCAATTGCTTTTGAGGTAGGATGACTTGCACCGAGTGAGAATCATTGG
TGTTTGGAATAGGGTGGCTCATAATGGCAATCGCCCTAGCAACCCTCCCA
ATCTTCCTCACCTTGTTGGGCAGGTAAGAAGGATCGCAGACAACTTTCTT
GCATTTGGCAGTCTCTCCCTCAGATGTAACACCCACAACCTTACCTTCCT
CATCGAACTCCACCTTGCACTCAG
>RL859R  CHROMAT_FILE: RL859R PHD_FILE: RL859R.phd.1 CHEM: term DYE: big TIME: Thu May  3 10:45:09 2001
ATTCTGGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXCTCCTACCAAAAAATAAAAAGTCCCTCTCTTTCTTCAGCGATCAGC
CAATCATGGATGAAGAGTACGAAGTTATCGTTCTCGGTACTGGTCTCAAG
GAGTGCATCCTCAGTGGCCTCCTCTCCGTCGATGGCATCAAGGTACTTCA
CATGGACAGGAATGACTACTACGGTGGAGAGTCAACTTCACTTAATCTCA
ATCAGCTGTGGAAGAAGTTTAGGGGAGAAGACAAAGCTCCTGCTCATCTA
GGTTCTAGCAGAGACTACAATGTTGACATGATGCCCAAGTTTATGATGGC
GAATGGGAAGCTTGTTCGTGTCCTTATCCACACAGATGTGACCAAGTACT
TGTCTTTTAAAGCTGTGGATGGGAGTTACGTCTTCGTCAAAGGCAAGGTT
CAGAAGGTGCCAGCAACTCCAGTGGAGGCCCTCAAATCTTCTCTTATGGG
TATTTTTGAGAAACGTCGTGCTGGAAAGTTCTTCAGCTACGTTCAGGAAT
ACGATGAGAAGGATCCGAAAACACATGATGGAGTTGATTTGAAGAGAGTT
ACAACAAAGGAGTTGATTGCGAAATTTGGTCTGGATGAAAACACTATTGA
CTTTATTGGTCATGCGGTGGCGCTTCACAGTAATGATAGCCATCTCCATC
AACCTGCTTATGATACTGTGATGAGAATGAAGCTCTACGCAGAGTCCCTT
GCTCGTTTCCAAGGAGGTTCACCGTATATCTATCCTCTCTATGGGTTGNG
AGAATTGCCTCAGGCGTTTGCACGACTTAGTGCTGTCTATGGTGGGACTA
CATGTTGAATAACCTGAGTGCAGGTGGAGTTCGATGAGGAAGGTAAGTTG
TGGG
BioPerl-1.007002/t/data/adh.mb_tree.nexus000444000766000024      4124213155576321 20147 0ustar00cjfieldsstaff000000000000#NEXUS
begin trees;
   translate
     17 d.tsacasi,
     22 d.texana,
     54 z.tuberculatus,
     14 d.orena,
     18 d.crassifemur,
     48 d.planitibia,
     19 d.montana,
     43 d.affinidisjuncta,
     49 d.heteroneura,
     25 d.borealis,
     37 d.mulleri_2,
     53 d.hawaiiensis,
      7 d.madeirensis,
      9 d.lebanonensis,
     12 d.mauritiana,
     36 d.mulleri_1,
     32 d.hydei_1,
     21 d.buzzatii_2,
     52 d.mayaguana,
     38 d.navojoa,
     24 d.lacicola,
     39 d.virilis_1,
     28 sc.albovittata,
     23 d.lummei,
     10 d.melanogaster,
     16 d.yakuba,
     42 d.grimshawi,
     31 d.arizonae_2,
     44 d.nigra,
     45 d.mimica,
      8 d.willistoni,
     33 d.hydei_2,
     35 d.mojavensis_2,
      4 d.miranda,
      5 d.ambigua,
     13 d.teissieri,
      2 d.pseudoobscura1,
     47 d.picticornis,
     41 d.silvestris,
      6 d.subobscura,
     34 d.mojavensis_1,
     50 d.differens,
     46 d.adiastola,
     51 d.wheeleri,
     15 d.sechellia,
     11 d.simulans,
     26 d.flavomontana,
     40 d.virilis_2,
     27 d.americana,
     20 d.buzzatii_1,
     29 d.immigrans,
      3 d.pseudoobscura2,
     30 d.mettleri,
      1 d.persimilis;
   tree rep.1 = (((22:0.157963,54:0.125585):0.018579,14:0.027001):0.134996,(17:0.023317,((18:0.172811,(48:0.153690,(19:0.120099,((43:0.049425,49:0.080196):0.145571,(((25:0.014888,37:0.157056):0.020382,53:0.082720):0.110316,((((7:0.039223,9:0.129119):0.180479,12:0.167484):0.107546,(36:0.143350,32:0.037119):0.126282):0.083525,((21:0.150729,(52:0.112407,(38:0.005115,(24:0.127020,(39:0.083231,(28:0.121717,23:0.086451):0.112299):0.008499):0.120916):0.119008):0.115839):0.082094,(10:0.150963,(16:0.040991,(42:0.138176,((31:0.034408,44:0.128276):0.043900,(45:0.175700,(((8:0.047586,33:0.158794):0.065235,35:0.048337):0.029596,(4:0.000947,(5:0.050439,(13:0.174097,2:0.081204):0.149235):0.166073):0.094284):0.158802):0.012646):0.018672):0.133240):0.177054):0.014718):0.017657):0.032351):0.009559):0.070867):0.105545):0.050691):0.031521,(47:0.091158,(41:0.111627,(6:0.011247,(34:0.012016,(50:0.172260,(46:0.000766,((51:0.109803,(15:0.160931,(11:0.071819,(((26:0.075067,40:0.157040):0.113187,27:0.173541):0.018777,(20:0.074769,(29:0.074750,3:0.122801):0.079648):0.059964):0.053481):0.089055):0.139545):0.064332,30:0.012602):0.001813):0.031837):0.116060):0.160691):0.045201):0.001897):0.164978):0.077134):0.031565,1:0.014800);
   tree rep.100 = (((22:0.157963,54:0.125585):0.065002,(17:0.038858,((18:0.172811,(48:0.153690,(19:0.076261,((43:0.049425,49:0.080196):0.145571,(((25:0.014888,37:0.157056):0.104016,53:0.082720):0.027222,((36:0.139635,32:0.037119):0.204371,((21:0.150729,((24:0.127020,(39:0.083231,(28:0.121717,23:0.075231):0.112007):0.007485):0.120916,(38:0.117588,52:0.116324):0.019183):0.004655):0.030382,(10:0.150963,(16:0.050516,(42:0.138176,((31:0.034408,44:0.128276):0.043900,(45:0.175700,(((8:0.045541,(5:0.050439,(4:0.000947,(13:0.174097,2:0.081204):0.096513):0.041065):0.337782):0.068564,33:0.158794):0.069085,35:0.046885):0.062082):0.012646):0.019251):0.133240):0.129116):0.098729):0.063630):0.031512):0.008868):0.069030):0.102165):0.049377):0.030704,(47:0.091158,(41:0.111627,((6:0.011247,(34:0.047703,(46:0.000766,(50:0.081921,((51:0.042867,30:0.071396):0.059062,(15:0.160931,(11:0.071819,(((26:0.062302,27:0.173541):0.008927,40:0.157040):0.125217,(20:0.074769,(29:0.074750,3:0.174294):0.044187):0.002981):0.111490):0.086250):0.036449):0.181165):0.074995):0.116060):0.117958):0.013739,((7:0.222720,12:0.057596):0.112188,9:0.129119):0.107546):0.028495):0.001848):0.160703):0.070932):0.017780):0.030528,14:0.027001,1:0.076733);
   tree rep.200 = (4:0.140083,(10:0.046455,(((44:0.303242,3:0.046149):0.007085,(12:0.264171,(39:0.010329,(28:0.010442,((((13:0.164415,32:0.085013):0.012181,36:0.088070):0.239645,((47:0.045731,42:0.055141):0.028604,(43:0.037115,(53:0.094489,(45:0.170989,17:0.084207):0.037785):0.081498):0.028893):0.075241):0.031188,(((11:0.053767,15:0.007988):0.365837,41:0.009924):0.106798,(((14:0.020334,(16:0.003141,(52:0.009450,(31:0.065281,9:0.081911):0.025622):0.205320):0.130518):0.130135,((((20:0.069017,21:0.001805):0.095042,((22:0.000992,27:0.055347):0.028541,((33:0.048426,(37:0.055803,((((5:0.197727,35:0.126381):0.024362,7:0.110282):0.037632,48:0.012853):0.004593,49:0.069144):0.048461):0.043626):0.044665,40:0.137528):0.041607):0.174554):0.131272,25:0.119919):0.026458,(19:0.043106,(24:0.036835,26:0.141457):0.001981):0.023511):0.045316):0.004905,(30:0.164116,23:0.139063):0.051306):0.045154):0.027607):0.184355):0.092816):0.111078):0.017810):0.011860,(51:0.124000,(((((((6:0.036025,(8:0.044154,18:0.131440):0.010261):0.051278,50:0.092479):0.015989,(54:0.138965,29:0.038900):0.117072):0.019978,2:0.066155):0.055828,34:0.084369):0.007028,38:0.132118):0.116475,46:0.095168):0.081231):0.099059):0.057599):0.092299,1:0.155488);
   tree rep.300 = ((((41:0.074469,(47:0.070075,(18:0.170195,(48:0.216005,(19:0.155284,((43:0.049425,49:0.080196):0.153125,(((25:0.078322,37:0.160449):0.035496,53:0.112645):0.008125,((36:0.139635,32:0.052845):0.168416,(((24:0.127020,(28:0.121717,(39:0.083231,23:0.078065):0.115864):0.008696):0.052982,((42:0.138176,((31:0.034408,44:0.124188):0.013267,(45:0.117313,(((8:0.045541,(4:0.000947,(5:0.086055,(13:0.209025,2:0.081204):0.024175):0.011399):0.337782):0.105831,33:0.158794):0.069085,35:0.069308):0.031964):0.003124):0.025722):0.259725,(10:0.042425,16:0.110297):0.039735):0.191014):0.068713,(21:0.135116,(38:0.117588,52:0.111942):0.022356):0.011332):0.059385):0.037720):0.000909):0.014457):0.003132):0.007537):0.005212):0.020328):0.031939,(9:0.157964,(6:0.071972,((7:0.222720,12:0.057596):0.020190,(34:0.039949,(((50:0.016105,46:0.110602):0.081029,(((26:0.056793,(27:0.064620,40:0.125765):0.033330):0.043797,(20:0.074769,(29:0.074750,3:0.181634):0.046047):0.017717):0.027723,(11:0.106754,15:0.040884):0.191869):0.021053):0.006087,(51:0.042867,30:0.071396):0.058507):0.170142):0.250851):0.044118):0.046820):0.067374):0.068167,(22:0.158868,54:0.125585):0.065002):0.043176,(17:0.044466,14:0.016232):0.030029,1:0.254144);
   tree rep.400 = (((3:0.054881,((12:0.149557,(((((36:0.011361,32:0.091895):0.227251,13:0.164415):0.072047,((47:0.045731,42:0.045457):0.028604,(45:0.170989,(43:0.037115,(53:0.094489,17:0.151875):0.010276):0.036399):0.002994):0.069442):0.023635,(((11:0.053767,15:0.007291):0.341002,41:0.082941):0.018099,(((9:0.107703,(52:0.022211,31:0.065281):0.129209):0.052897,(14:0.052534,16:0.002995):0.119894):0.152800,(((37:0.055803,(33:0.048426,((49:0.069144,48:0.018638):0.011130,((5:0.203993,7:0.107996):0.003241,35:0.116375):0.033522):0.046802):0.027947):0.066914,(40:0.005572,(22:0.000992,27:0.055347):0.074961):0.262467):0.011952,(((26:0.044133,(19:0.021968,24:0.034463):0.004692):0.090414,25:0.110170):0.081060,((20:0.069017,21:0.001768):0.142084,(30:0.164116,23:0.139063):0.039907):0.003682):0.029602):0.039057):0.033620):0.024068):0.165826,(28:0.013535,39:0.149488):0.042895):0.097397):0.002867,44:0.296540):0.111579):0.011860,(51:0.124000,(((((2:0.086296,(54:0.138965,29:0.046449):0.131077):0.002123,((6:0.036862,(8:0.044154,18:0.134018):0.044121):0.029918,50:0.100654):0.002909):0.054425,34:0.064165):0.004946,38:0.012104):0.078140,46:0.095168):0.024181):0.112252):0.007356,(10:0.095486,4:0.148723):0.005218,1:0.069766);
   tree rep.500 = (((3:0.033638,(46:0.095168,(((((2:0.086296,(54:0.138965,29:0.046449):0.131077):0.002123,((6:0.036862,(8:0.044154,18:0.134018):0.075578):0.033011,50:0.104237):0.001729):0.055197,34:0.064165):0.068011,38:0.012104):0.033603,51:0.068707):0.046721):0.129746):0.016252,((44:0.300154,(28:0.013535,((((((11:0.053767,15:0.007291):0.341002,41:0.102068):0.016061,(((9:0.074116,(14:0.052534,16:0.002995):0.119929):0.086773,(52:0.022211,31:0.026627):0.084519):0.050469,(((37:0.080049,(33:0.086746,(35:0.116375,((5:0.203993,7:0.107996):0.038960,(49:0.069144,48:0.018638):0.011130):0.030953):0.018647):0.012069):0.016175,(40:0.005572,(22:0.003777,27:0.055347):0.065961):0.240988):0.011172,((20:0.069017,21:0.001768):0.142084,(23:0.139063,(30:0.145755,((26:0.044133,(19:0.021968,24:0.034463):0.004692):0.090414,25:0.110170):0.120926):0.016964):0.000632):0.034642):0.047233):0.001381):0.018795,((47:0.046981,(42:0.008165,((53:0.060089,43:0.027814):0.025023,17:0.151875):0.025364):0.041768):0.031422,45:0.085737):0.049032):0.030224,((36:0.010390,32:0.091895):0.227251,13:0.348171):0.010029):0.007993,39:0.116947):0.096577):0.017004):0.154726,12:0.149557):0.028553):0.018993,(10:0.095486,4:0.003046):0.005218,1:0.009243);
   tree rep.600 = (((10:0.095486,4:0.003046):0.005343,3:0.021494):0.009169,(((((((2:0.086296,(54:0.138965,29:0.046449):0.131077):0.002123,((6:0.089047,(8:0.044154,18:0.128126):0.075578):0.018450,50:0.104237):0.001729):0.055197,34:0.111462):0.032442,38:0.011793):0.036585,51:0.040738):0.061847,(46:0.095789,((((36:0.010390,32:0.091895):0.227251,(39:0.103153,13:0.335504):0.007758):0.003709,((((47:0.046981,(42:0.008165,((53:0.057021,43:0.027814):0.029252,17:0.151875):0.018562):0.041768):0.029268,45:0.085737):0.078836,(((((37:0.080049,(35:0.116375,(33:0.086746,((5:0.203993,7:0.107996):0.036763,(49:0.069144,48:0.010749):0.027480):0.053627):0.010414):0.002045):0.014092,(40:0.005572,(22:0.003777,27:0.055347):0.065961):0.240988):0.013061,((20:0.069017,21:0.001768):0.139885,(30:0.145755,(23:0.074823,((26:0.038522,(19:0.020894,24:0.034463):0.004692):0.007915,25:0.110170):0.103839):0.021174):0.058565):0.059773):0.038037,(52:0.022211,31:0.026627):0.037033):0.068284,(9:0.137424,(14:0.052534,16:0.002594):0.077089):0.080195):0.023779):0.009356,((11:0.053767,15:0.007291):0.341002,41:0.102068):0.016061):0.015006):0.096982,(28:0.029431,44:0.300154):0.111298):0.065358):0.013070):0.103558,12:0.149557):0.021459,1:0.010304);
   tree rep.700 = (((10:0.095486,4:0.003046):0.001620,(((((((2:0.086296,(54:0.138965,29:0.046449):0.131077):0.002123,((6:0.089047,(8:0.044154,18:0.128126):0.075578):0.018450,50:0.104237):0.001729):0.055197,34:0.111462):0.032442,38:0.011793):0.035039,51:0.040738):0.062315,((((36:0.009831,32:0.091895):0.144482,(39:0.099656,13:0.335504):0.007758):0.070347,((((47:0.046981,(42:0.008165,((17:0.151875,43:0.004931):0.021655,53:0.041322):0.054598):0.039002):0.036883,45:0.085737):0.077772,((((((33:0.086746,((5:0.101655,7:0.107996):0.036763,(49:0.069144,48:0.010749):0.029499):0.156790):0.010414,(35:0.057180,37:0.085725):0.060494):0.011283,(40:0.005572,(22:0.003777,27:0.055347):0.065961):0.240988):0.013043,((20:0.069017,21:0.001768):0.139885,((23:0.023018,(24:0.034463,(19:0.016869,(26:0.033856,25:0.110170):0.001843):0.002865):0.102246):0.103048,30:0.145755):0.029617):0.059773):0.034692,(52:0.027299,31:0.026627):0.037033):0.026735,(9:0.137424,(14:0.052534,16:0.002594):0.077089):0.080195):0.023779):0.009923,((11:0.053767,15:0.007291):0.341002,41:0.102068):0.015241):0.016285):0.002109,(46:0.104690,(28:0.117042,44:0.300154):0.090580):0.034915):0.013070):0.123724,12:0.149557):0.028839):0.003483,3:0.007190,1:0.016949);
   tree rep.800 = (((10:0.095486,4:0.003046):0.001620,(((((((2:0.086296,(54:0.206909,29:0.046449):0.053397):0.025375,((6:0.089047,(8:0.044154,18:0.128126):0.075578):0.018450,50:0.104237):0.001729):0.053655,34:0.111170):0.039514,38:0.011793):0.027790,51:0.040738):0.063963,((((32:0.121633,36:0.009831):0.107936,(39:0.099656,13:0.335504):0.007758):0.055974,((((47:0.046981,(42:0.008165,((17:0.151875,43:0.004931):0.028254,53:0.041322):0.018579):0.064401):0.027425,45:0.075355):0.031943,((((20:0.069017,21:0.001768):0.089403,(52:0.027299,31:0.024214):0.081996):0.018165,((((33:0.086746,((5:0.104794,7:0.107996):0.044540,(49:0.069144,48:0.010749):0.029499):0.154989):0.010414,(35:0.057180,37:0.085725):0.060494):0.011980,(40:0.074830,(22:0.003777,27:0.007992):0.025837):0.286798):0.013043,((23:0.022780,(24:0.001597,(19:0.016600,(26:0.033856,25:0.086776):0.001843):0.023453):0.102246):0.133695,30:0.145755):0.056725):0.005719):0.060348,(9:0.137424,(14:0.052534,16:0.002594):0.077089):0.080195):0.023779):0.009923,((11:0.053767,15:0.007291):0.341002,41:0.102068):0.015241):0.016285):0.001986,(46:0.104690,(28:0.117042,44:0.300154):0.090580):0.034915):0.013070):0.123724,12:0.161895):0.118611):0.012373,3:0.007190,1:0.008078);
   tree rep.900 = ((((((51:0.040738,38:0.039412):0.030687,((50:0.104237,(2:0.086296,((6:0.089047,(8:0.044154,18:0.128126):0.075578):0.021833,(54:0.206909,29:0.046449):0.046705):0.008497):0.028494):0.081836,34:0.111170):0.007082):0.033001,((((32:0.118685,36:0.082241):0.038003,(39:0.099656,13:0.335504):0.007758):0.056416,((((47:0.046981,(42:0.007482,((17:0.151875,43:0.004931):0.028254,53:0.045698):0.018579):0.020312):0.016615,45:0.075355):0.030191,((((((20:0.069017,21:0.021536):0.068942,(52:0.027299,31:0.024214):0.081996):0.022691,(30:0.154294,(23:0.022780,(24:0.001597,(19:0.016600,(26:0.033856,25:0.086776):0.001843):0.023453):0.102246):0.133695):0.034372):0.022434,(40:0.043656,(27:0.016136,22:0.003553):0.018409):0.041255):0.006726,((33:0.051346,(35:0.057180,37:0.085725):0.060494):0.024317,((5:0.104794,7:0.105982):0.044540,(49:0.069144,48:0.010749):0.086428):0.060317):0.012113):0.068974,(9:0.137424,(14:0.052534,16:0.002594):0.077089):0.080195):0.023779):0.009923,((11:0.053767,15:0.007291):0.341002,41:0.102068):0.008310):0.015474):0.001986,(46:0.104690,(28:0.117042,44:0.300154):0.084854):0.038572):0.006848):0.204873,(10:0.027456,12:0.056298):0.052795):0.211349,4:0.003046):0.013823,3:0.007190,1:0.008078);
   tree rep.1000 = ((((((51:0.040738,38:0.039412):0.030687,((50:0.104237,(2:0.086296,(((54:0.206909,29:0.046449):0.096613,(8:0.044154,18:0.128126):0.053092):0.028063,6:0.089047):0.000197):0.028494):0.081836,34:0.111170):0.007082):0.033001,((((32:0.118685,36:0.082241):0.038003,(39:0.099656,13:0.335504):0.007758):0.056416,((11:0.053767,15:0.007291):0.341002,((((47:0.025066,(((53:0.008946,42:0.007482):0.033860,43:0.031909):0.000497,17:0.151875):0.035837):0.016615,45:0.071141):0.026863,41:0.049708):0.006356,(((((20:0.071823,21:0.021536):0.013429,(52:0.027299,31:0.024214):0.081996):0.100193,(40:0.043656,(27:0.016136,(22:0.002140,(30:0.154294,(23:0.022780,(24:0.001467,(19:0.005589,(26:0.033856,25:0.085683):0.001772):0.012551):0.118877):0.089879):0.034372):0.003064):0.010310):0.054562):0.006438,((33:0.051346,(35:0.055085,37:0.085725):0.026366):0.047866,((5:0.087195,7:0.105982):0.058704,(49:0.069144,48:0.010749):0.086428):0.058929):0.010462):0.049444,(9:0.137424,(14:0.052534,16:0.003555):0.079087):0.083174):0.037953):0.032490):0.009204):0.006528,(46:0.073950,(28:0.117042,44:0.300154):0.084854):0.038033):0.044531):0.163318,(10:0.009874,12:0.056298):0.052795):0.068925,4:0.003046):0.013823,3:0.007190,1:0.008078);
   tree rep.1100 = ((((((50:0.107844,(2:0.086296,(((54:0.206909,29:0.046449):0.096613,(8:0.044154,18:0.128126):0.053092):0.028063,6:0.089047):0.000197):0.028494):0.044237,((51:0.040738,38:0.036842):0.035562,34:0.048777):0.067401):0.031800,((((32:0.100759,36:0.082241):0.038003,(39:0.099656,13:0.335504):0.007151):0.043657,((11:0.053767,15:0.007291):0.341002,((((47:0.025835,(((53:0.008946,42:0.007482):0.034313,43:0.031909):0.017045,17:0.151875):0.019774):0.012526,45:0.084441):0.022574,41:0.015479):0.063603,(((33:0.051346,((((5:0.087195,7:0.105982):0.058704,(49:0.069144,48:0.010749):0.086428):0.092891,(35:0.055085,37:0.085725):0.020590):0.014053,((20:0.071823,21:0.021536):0.012302,(52:0.027299,31:0.024214):0.081996):0.008775):0.057688):0.066101,(40:0.043656,((30:0.154294,(23:0.066909,(24:0.001467,(19:0.005343,(26:0.033856,25:0.059398):0.001772):0.024194):0.118877):0.045948):0.005920,(22:0.005639,27:0.009875):0.006250):0.003561):0.054562):0.009186,(9:0.137424,(14:0.052534,16:0.003555):0.079087):0.077207):0.037953):0.000861):0.009204):0.006528,(46:0.073950,(28:0.117042,44:0.300154):0.084854):0.038033):0.044531):0.163318,(10:0.009874,12:0.056298):0.052795):0.068925,4:0.003046):0.013823,3:0.007190,1:0.008078);
   tree rep.1200 = ((((((50:0.107844,(2:0.086296,(((54:0.206909,29:0.046449):0.096613,(8:0.044154,18:0.128126):0.051987):0.028063,6:0.102805):0.011867):0.028494):0.033927,((((32:0.131601,36:0.082241):0.038003,(39:0.099656,13:0.335504):0.007547):0.007449,((((47:0.059698,45:0.049145):0.013379,(((53:0.008435,42:0.006022):0.041278,43:0.028299):0.021851,17:0.151875):0.000340):0.015594,41:0.015479):0.063603,(((33:0.041632,((20:0.071823,21:0.019709):0.034885,((((5:0.087534,7:0.105982):0.111835,(49:0.069144,48:0.010749):0.086428):0.040349,(35:0.055085,37:0.082988):0.029187):0.013419,(52:0.027299,31:0.067965):0.004678):0.029692):0.029170):0.053192,(40:0.043656,((23:0.066909,(30:0.190145,(24:0.001467,(19:0.005343,(26:0.033856,25:0.059398):0.001772):0.024194):0.076242):0.036640):0.005920,(22:0.005639,27:0.009875):0.006250):0.003561):0.054562):0.018943,((11:0.053767,15:0.007291):0.392912,(9:0.137424,(14:0.052534,16:0.003555):0.079087):0.017883):0.066686):0.015733):0.007235):0.009433,(46:0.073950,(28:0.172143,44:0.300154):0.016105):0.035520):0.036868):0.012822,((51:0.040738,38:0.036244):0.035562,34:0.037424):0.045547):0.206198,(10:0.009874,12:0.056298):0.052795):0.068925,4:0.003046):0.013823,3:0.007190,1:0.008078);
BioPerl-1.007002/t/data/alleles.fas000444000766000024        25613155576321 16767 0ustar00cjfieldsstaff000000000000>testseq
GGATCCATTGCTACT
>allele1
GGATCCATTCCTACT
>allele2
GGAT--ATTCCTCCT
>allele3
GCATCCATTGCTACT
>allele4
GGATCCATTGCTACT
>allele5
GGATCCATTGCTACA
>allele6
GGATCCATTGCTAGABioPerl-1.007002/t/data/alnfile.fasta000444000766000024        44613155576321 17306 0ustar00cjfieldsstaff000000000000>BS1-fragment 7fab light chain variable region
TISCTGSSSNIGAGNHVKWYQQLPG
>BS2-fragment 2fb4 light chain variable region
VTISCTGTSSNIGSITVNWYQQLPG
>BS3-fragment 2fb4 heavy chain variable region
LRLSCSSSGFIFSSYAMYWVRQAPG
>BS4-fragment 7fab heavy chain variable region 
LSLTCTVSGTSFDDYYSTWVRQPPG

BioPerl-1.007002/t/data/amino.fa000444000766000024        67613155576321 16274 0ustar00cjfieldsstaff000000000000>CYS1_DICDI fragment
SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE

>ALEU_HORVU
MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGK
SYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRD
AAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNG
GLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAF
QVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCA
IATCASYPVVAA
BioPerl-1.007002/t/data/amphora.newick000444000766000024        30613155576321 17500 0ustar00cjfieldsstaff000000000000((REF-YP_004290029-NC_015216:0.23840847960367719804[I116],REF-YP_004520254-NC_015574:0.18701622612251170286[I117]):0.03268127637536134139[I115],REF-YP_447902-NC_007681:0.32812155226299949407[I118])
BioPerl-1.007002/t/data/ar.embl000444000766000024      1676013155576321 16165 0ustar00cjfieldsstaff000000000000ID   HSANDREC   standard; RNA; HUM; 3569 BP.
XX
AC   M20132; J03180;
XX
SV   M20132.1
XX
DT   23-NOV-1989 (Rel. 21, Created)
DT   02-JUL-1999 (Rel. 60, Last updated, Version 4)
XX
DE   Human androgen receptor (AR) mRNA, complete cds.
XX
KW   androgen receptor.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; Eutheria;
OC   Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-3569
RX   MEDLINE; 89112208.
RA   Lubahn D.B., Joseph D.R., Sar M., Tan J., Higgs H.N., Larson R.E.,
RA   French F.S., Wilson E.M.;
RT   "The human androgen receptor: complementary deoxyribonucleic acid cloning,
RT   sequence analysis and gene expression in prostate";
RL   Mol. Endocrinol. 2(12):1265-1275(1988).
XX
DR   GDB; 120556; AR.
DR   SWISS-PROT; P10275; ANDR_HUMAN.
DR   TRANSFAC; T00040; T00040.
XX
CC   Draft entry and computer readable sequence [1] kindly submitted by
CC   E.M.Wilson, 18-AUG-1988.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..3569
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
FT                   /map="Xq11.2-q12"
FT   gene            363..3122
FT                   /gene="AR"
FT   CDS             363..3122
FT                   /codon_start=1
FT                   /db_xref="SWISS-PROT:P10275"
FT                   /note="androgen receptor"
FT                   /gene="AR"
FT                   /protein_id="AAA51729.1"
FT                   /translation="MEVQLGLGRVYPRPPSKTYRGAFQNLFQSVREVIQNPGPRHPEAA
FT                   SAAPPGASLLLLQQQQQQQQQQQQQQQQQQQQQETSPRQQQQQQGEDGSPQAHRRGPTG
FT                   YLVLDEEQQPSQPQSALECHPERGCVPEPGAAVAASKGLPQQLPAPPDEDDSAAPSTLS
FT                   LLGPTFPGLSSCSADLKDILSEASTMQLLQQQQQEAVSEGSSSGRAREASGAPTSSKDN
FT                   YLGGTSTISDNAKELCKAVSVSMGLGVEALEHLSPGEQLRGDCMYAPLLGVPPAVRPTP
FT                   CAPLAECKGSLLDDSAGKSTEDTAEYSPFKGGYTKGLEGESLGCSGSAAAGSSGTLELP
FT                   STLSLYKSGALDEAAAYQSRDYYNFPLALAGPPPPPPPPHPHARIKLENPLDYGSAWAA
FT                   AAAQCRYGDLASLHGAGAAGPGSGSPSAAASSSWHTLFTAEEGQLYGPCGGGGGGGGGG
FT                   GGGGGGGGGGGGGGEAGAVAPYGYTRPPQGLAGQESDFTAPDVWYPGGMVSRVPYPSPT
FT                   CVKSEMGPWMDSYSGPYGDMRLETARDHVLPIDYYFPPQKTCLICGDEASGCHYGALTC
FT                   GSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKLG
FT                   NLKLQEEGEASSTTSPTEETTQKLTVSHIEGYECQPIFLNVLEAIEPGVVCAGHDNNQP
FT                   DSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRS
FT                   FTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLL
FT                   FSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIAR
FT                   ELHQFTFDLLIKSHMVSVDFPEMMAEIISVQVPKILSGKVKPIYFHTQ"
XX
SQ   Sequence 3569 BP; 796 A; 1009 C; 974 G; 790 T; 0 other;
     taataactca gttcttattt gcacctactt cagtggacac tgaatttgga aggtggagga        60
     ttttgttttt ttcttttaag atctgggcat cttttgaatc tacccttcaa gtattaagag       120
     acagactgtg agcctagcag ggcagatctt gtccaccgtg tgtcttcttc tgcacgagac       180
     tttgaggctg tcagagcgct ttttgcgtgg ttgctcccgc aagtttcctt ctctggagct       240
     tcccgcaggt gggcagctag ctgcagcgac taccgcatca tcacagcctg ttgaactctt       300
     ctgagcaaga gaaggggagg cggggtaagg gaagtaggtg gaagattcag ccaagctcaa       360
     ggatggaagt gcagttaggg ctgggaaggg tctaccctcg gccgccgtcc aagacctacc       420
     gaggagcttt ccagaatctg ttccagagcg tgcgcgaagt gatccagaac ccgggcccca       480
     ggcacccaga ggccgcgagc gcagcacctc ccggcgccag tttgctgctg ctgcagcagc       540
     agcagcagca gcagcagcag cagcagcagc agcagcagca gcagcagcag cagcaagaga       600
     ctagccccag gcagcagcag cagcagcagg gtgaggatgg ttctccccaa gcccatcgta       660
     gaggccccac aggctacctg gtcctggatg aggaacagca accttcacag ccgcagtcgg       720
     ccctggagtg ccaccccgag agaggttgcg tcccagagcc tggagccgcc gtggccgcca       780
     gcaaggggct gccgcagcag ctgccagcac ctccggacga ggatgactca gctgccccat       840
     ccacgttgtc cctgctgggc cccactttcc ccggcttaag cagctgctcc gctgacctta       900
     aagacatcct gagcgaggcc agcaccatgc aactccttca gcaacagcag caggaagcag       960
     tatccgaagg cagcagcagc gggagagcga gggaggcctc gggggctccc acttcctcca      1020
     aggacaatta cttagggggc acttcgacca tttctgacaa cgccaaggag ttgtgtaagg      1080
     cagtgtcggt gtccatgggc ctgggtgtgg aggcgttgga gcatctgagt ccaggggaac      1140
     agcttcgggg ggattgcatg tacgccccac ttttgggagt tccacccgct gtgcgtccca      1200
     ctccttgtgc cccattggcc gaatgcaaag gttctctgct agacgacagc gcaggcaaga      1260
     gcactgaaga tactgctgag tattcccctt tcaagggagg ttacaccaaa gggctagaag      1320
     gcgagagcct aggctgctct ggcagcgctg cagcagggag ctccgggaca cttgaactgc      1380
     cgtctaccct gtctctctac aagtccggag cactggacga ggcagctgcg taccagagtc      1440
     gcgactacta caactttcca ctggctctgg ccggaccgcc gccccctccg ccgcctcccc      1500
     atccccacgc tcgcatcaag ctggagaacc cgctggacta cggcagcgcc tgggcggctg      1560
     cggcggcgca gtgccgctat ggggacctgg cgagcctgca tggcgcgggt gcagcgggac      1620
     ccggttctgg gtcaccctca gccgccgctt cctcatcctg gcacactctc ttcacagccg      1680
     aagaaggcca gttgtatgga ccgtgtggtg gtggtggggg tggtggcggc ggcggcggcg      1740
     gcggcggcgg cggcggcggc ggcggcggcg gcggcggcga ggcgggagct gtagccccct      1800
     acggctacac tcggccccct caggggctgg cgggccagga aagcgacttc accgcacctg      1860
     atgtgtggta ccctggcggc atggtgagca gagtgcccta tcccagtccc acttgtgtca      1920
     aaagcgaaat gggcccctgg atggatagct actccggacc ttacggggac atgcgtttgg      1980
     agactgccag ggaccatgtt ttgcccattg actattactt tccaccccag aagacctgcc      2040
     tgatctgtgg agatgaagct tctgggtgtc actatggagc tctcacatgt ggaagctgca      2100
     aggtcttctt caaaagagcc gctgaaggga aacagaagta cctgtgcgcc agcagaaatg      2160
     attgcactat tgataaattc cgaaggaaaa attgtccatc ttgtcgtctt cggaaatgtt      2220
     atgaagcagg gatgactctg ggagcccgga agctgaagaa acttggtaat ctgaaactac      2280
     aggaggaagg agaggcttcc agcaccacca gccccactga ggagacaacc cagaagctga      2340
     cagtgtcaca cattgaaggc tatgaatgtc agcccatctt tctgaatgtc ctggaagcca      2400
     ttgagccagg tgtagtgtgt gctggacacg acaacaacca gcccgactcc tttgcagcct      2460
     tgctctctag cctcaatgaa ctgggagaga gacagcttgt acacgtggtc aagtgggcca      2520
     aggccttgcc tggcttccgc aacttacacg tggacgacca gatggctgtc attcagtact      2580
     cctggatggg gctcatggtg tttgccatgg gctggcgatc cttcaccaat gtcaactcca      2640
     ggatgctcta cttcgcccct gatctggttt tcaatgagta ccgcatgcac aagtcccgga      2700
     tgtacagcca gtgtgtccga atgaggcacc tctctcaaga gtttggatgg ctccaaatca      2760
     ccccccagga attcctgtgc atgaaagcac tgctactctt cagcattatt ccagtggatg      2820
     ggctgaaaaa tcaaaaattc tttgatgaac ttcgaatgaa ctacatcaag gaactcgatc      2880
     gtatcattgc atgcaaaaga aaaaatccca catcctgctc aagacgcttc taccagctca      2940
     ccaagctcct ggactccgtg cagcctattg cgagagagct gcatcagttc acttttgacc      3000
     tgctaatcaa gtcacacatg gtgagcgtgg actttccgga aatgatggca gagatcatct      3060
     ctgtgcaagt gcccaagatc ctttctggga aagtcaagcc catctatttc cacacccagt      3120
     gaagcattgg aaaccctatt tccccacccc agctcatgcc ccctttcaga tgtcttctgc      3180
     ctgttataac tctgcactac tcctctgcag tgccttgggg aatttcctct attgatgtac      3240
     agtctgtcat gaacatgttc ctgaattcta tttgctgggc tttttttttc tctttctctc      3300
     ctttcttttt cttcttccct ccctatctaa ccctcccatg gcaccttcag actttgcttc      3360
     ccattgtggc tcctatctgt gttttgaatg gtgttgtatg cctttaaatc tgtgatgatc      3420
     ctcatatggc ccagtgtcaa gttgtgcttg tttacagcac tactctgtgc cagccacaca      3480
     aacgtttact tatcttatgc cacgggaagt ttagagagct aagattatct ggggaaatca      3540
     aaacaaaaaa caagcaaaca aaaaaaaaa                                        3569
//
BioPerl-1.007002/t/data/assembly_with_singlets.ace000444000766000024      6765013155576321 22162 0ustar00cjfieldsstaff000000000000AS 36 39

CO Contig1| 131 1 1 U
gctagaaaaaaaaggactcccagtagaaatacgtacaataaagtaggttc
ctctagttaactgttacaaaataagtttcccattggtaatataatagatt
tataactgttatatccagagcaacctagggg

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5765593 U 1
BS 1 131 5765593

RD 5765593 131 0 6
gctagaaaaaaaaggactcccagtagaaatacgtacaataaagtaggttc
ctctagttaactgttacaaaataagtttcccattggtaatataatagatt
tataactgttatatccagagcaacctagggg

QA 1 131 1 131

RT{
5765593 matchElsewhereHighQual phrap 108 131 080215:162048
}

RT{
5765593 matchElsewhereHighQual phrap 98 118 080215:162048
}

RT{
5765593 matchElsewhereHighQual phrap 36 57 080215:162048
}

RT{
5765593 matchElsewhereHighQual phrap 15 34 080215:162048
}

RT{
5765593 matchElsewhereHighQual phrap 8 27 080215:162048
}

RT{
5765593 matchElsewhereHighQual phrap 6 25 080215:162048
}

CO Contig2 139 1 1 U
gtgggggcatggcggcccttggccgcccccagtaagtcaattgtcccgcg
aaggagcgggacgaagggtcccgcagggacccgagaaccgatcgggggct
cttaacacaaaatgtccttccggcgggggggccccgtac

BQ
 0 0 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5740343 U 1
BS 1 139 5740343

RD 5740343 139 0 4
gtgggggcatggcggcccttggccgcccccagtaagtcaattgtcccgcg
aaggagcgggacgaagggtcccgcagggacccgagaaccgatcgggggct
cttaacacaaaatgtccttccggcgggggggccccgtac

QA 4 139 1 139

RT{
5740343 matchElsewhereHighQual phrap 102 135 080215:162048
}

RT{
5740343 matchElsewhereHighQual phrap 89 129 080215:162048
}

RT{
5740343 matchElsewhereHighQual phrap 40 90 080215:162048
}

RT{
5740343 matchElsewhereHighQual phrap 4 45 080215:162048
}

CO Contig3 118 1 1 U
cctacgcgaggatacgaatgtttcttcgacaataataagctttttattat
tattattattattattattatttctattattattattattattattatta
ttattattattattatta

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5685889 U 1
BS 1 118 5685889

RD 5685889 118 0 2
cctacgcgaggatacgaatgtttcttcgacaataataagctttttattat
tattattattattattattatttctattattattattattattattatta
ttattattattattatta

QA 44 118 1 118

RT{
5685889 matchElsewhereHighQual phrap 75 118 080215:162048
}

RT{
5685889 matchElsewhereHighQual phrap 44 72 080215:162048
}

CO Contig4 81 1 1 U
gctctggctcactcgctctgagcaggcaatctttcagtcttacacagtct
acattcatactggacagcagtgtagacttaa

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5695780 U 1
BS 1 81 5695780

RD 5695780 81 0 2
gctctggctcactcgctctgagcaggcaatctttcagtcttacacagtct
acattcatactggacagcagtgtagacttaa

QA 1 81 1 81

RT{
5695780 matchElsewhereHighQual phrap 23 81 080215:162048
}

RT{
5695780 matchElsewhereHighQual phrap 1 67 080215:162048
}

CO Contig5 86 1 1 U
gtgtgtgcatgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtcgtccgtccgtcgtagtagtagtgtg

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5659765 U 1
BS 1 86 5659765

RD 5659765 86 0 1
gtgtgtgcatgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtcgtccgtccgtcgtagtagtagtgtg

QA 1 86 1 86

RT{
5659765 matchElsewhereHighQual phrap 10 60 080215:162048
}

CO Contig6 83 1 1 U
gaggaggtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg

BQ
 0 0 0 0 0 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5772270 U 1
BS 1 83 5772270

RD 5772270 83 0 2
gaggaggtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg

QA 7 83 1 83

RT{
5772270 matchElsewhereHighQual phrap 7 83 080215:162048
}

RT{
5772270 matchElsewhereHighQual phrap 6 81 080215:162048
}

CO Contig7 82 1 1 U
cttccttcagcaactgtgtgtgtgtgtntgtgtgtgtgtgtgtgtgtgtg
tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5717803 U 1
BS 1 82 5717803

RD 5717803 82 0 1
cttccttcagcaactgtgtgtgtgtgtntgtgtgtgtgtgtgtgtgtgtg
tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg

QA 15 82 1 82

RT{
5717803 matchElsewhereHighQual phrap 29 82 080215:162048
}

CO Contig8 139 1 1 U
attattattattattattattattattattattattattattattattat
tattattattattattatttattcaatttcgactttaattgttgtttttt
ttattaagtaaatactttaattttttttactttaaatac

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5671215 U 1
BS 1 139 5671215

RD 5671215 139 0 0
attattattattattattattattattattattattattattattattat
tattattattattattatttattcaatttcgactttaattgttgtttttt
ttattaagtaaatactttaattttttttactttaaatac

QA 70 139 1 139

CO Contig9 81 1 1 U
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5726177 U 1
BS 1 81 5726177

RD 5726177 81 0 2
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg

QA 1 81 1 81

RT{
5726177 matchElsewhereHighQual phrap 3 81 080215:162048
}

RT{
5726177 matchElsewhereHighQual phrap 1 77 080215:162048
}

CO Contig10 83 1 1 U
gtgtgtgtgcgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgtgtgtgtactac

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5741972 U 1
BS 1 83 5741972

RD 5741972 83 0 1
gtgtgtgtgcgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgtgtgtgtactac

QA 1 83 1 83

RT{
5741972 matchElsewhereHighQual phrap 11 78 080215:162048
}

CO Contig11 177 1 1 U
ttattttatttattttatttattttatttattttatttattttatttatt
ttatttattttatttattttatttattttatttattttatttattttatt
tattttatttattttatttattttatttattttatttattttatttattt
tatttattttatttatttatttattta

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5695538 U 1
BS 1 177 5695538

RD 5695538 177 0 2
ttattttatttattttatttattttatttattttatttattttatttatt
ttatttattttatttattttatttattttatttattttatttattttatt
tattttatttattttatttattttatttattttatttattttatttattt
tatttattttatttatttatttattta

QA 1 177 1 177

RT{
5695538 matchElsewhereHighQual phrap 161 177 080215:162048
}

RT{
5695538 matchElsewhereHighQual phrap 1 167 080215:162048
}

CO Contig12 121 1 1 U
atctcttgatagttgcacgctacattgaacgaaccaaatcccttttttaa
ggtgagtttggtaagattggggtaatatattcatttgataggtctcccta
aaaatggcctantttttttac

BQ
 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 0 0 0 0 0 0 0 0 0 0

AF 5732765 U 1
BS 1 121 5732765

RD 5732765 121 0 4
atctcttgatagttgcacgctacattgaacgaaccaaatcccttttttaa
ggtgagtttggtaagattggggtaatatattcatttgataggtctcccta
aaaatggcctantttttttac

QA 2 121 1 121

RT{
5732765 matchElsewhereHighQual phrap 81 110 080215:162048
}

RT{
5732765 matchElsewhereHighQual phrap 54 103 080215:162048
}

RT{
5732765 matchElsewhereHighQual phrap 53 98 080215:162048
}

RT{
5732765 matchElsewhereHighQual phrap 2 55 080215:162048
}

CO Contig13 119 1 1 U
tattattattattattattattattattattattattattattattatta
ttattattattattattattattattattattattattattattattatt
attattattattattatta

BQ
 0 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5685756 U 1
BS 1 119 5685756

RD 5685756 119 0 1
tattattattattattattattattattattattattattattattatta
ttattattattattattattattattattattattattattattattatt
attattattattattatta

QA 3 119 1 119

RT{
5685756 matchElsewhereHighQual phrap 7 86 080215:162048
}

CO Contig14 178 1 1 U
ttattttatttattttatttattttatttattttatttattttatttatt
ttatttattttatttattttatttattttatttattttatttattttatt
tattttatttattttatttattttatttattttatttattttatttattt
tatttattttatttattttatttattta

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5693041 U 1
BS 1 178 5693041

RD 5693041 178 0 1
ttattttatttattttatttattttatttattttatttattttatttatt
ttatttattttatttattttatttattttatttattttatttattttatt
tattttatttattttatttattttatttattttatttattttatttattt
tatttattttatttattttatttattta

QA 1 178 1 178

RT{
5693041 matchElsewhereHighQual phrap 1 168 080215:162048
}

CO Contig15 115 1 1 U
ttgaaggatggtagccatcctactctttttctataagttatgttccgcca
ggaagagcagccgccgttagatagggactcacaacccttcaaaatcgccc
taagacttctcaacc

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5651991 U 1
BS 1 115 5651991

RD 5651991 115 0 2
ttgaaggatggtagccatcctactctttttctataagttatgttccgcca
ggaagagcagccgccgttagatagggactcacaacccttcaaaatcgccc
taagacttctcaacc

QA 1 115 1 115

RT{
5651991 matchElsewhereHighQual phrap 47 115 080215:162048
}

RT{
5651991 matchElsewhereHighQual phrap 1 46 080215:162048
}

CO Contig16 83 1 1 U
cacacacaaacacacacacacacccacacacacacacacacacacacaca
cacacacacacacacacacacacacacacacac

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5756120 U 1
BS 1 83 5756120

RD 5756120 83 0 2
cacacacaaacacacacacacacccacacacacacacacacacacacaca
cacacacacacacacacacacacacacacacac

QA 1 83 1 83

RT{
5756120 matchElsewhereHighQual phrap 25 83 080215:162048
}

RT{
5756120 matchElsewhereHighQual phrap 9 23 080215:162048
}

CO Contig17 120 1 1 U
ttcaattttaatattattattattattattattattattattattattat
tattattattattattattattattattattattattattactactacta
ctactactactactactgtc

BQ
 0 0 0 0 0 0 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5766191 U 1
BS 1 120 5766191

RD 5766191 120 0 1
ttcaattttaatattattattattattattattattattattattattat
tattattattattattattattattattattattattattactactacta
ctactactactactactgtc

QA 8 120 1 120

RT{
5766191 matchElsewhereHighQual phrap 12 91 080215:162048
}

CO Contig18 81 1 1 U
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgtgtgtagtnt

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 0 0

AF 5701563 U 1
BS 1 81 5701563

RD 5701563 81 0 1
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgtgtgtagtnt

QA 1 81 1 81

RT{
5701563 matchElsewhereHighQual phrap 1 76 080215:162048
}

CO Contig19 85 1 1 U
gtgtgtgtgcgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgtgtagtcgtactac

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5710086 U 1
BS 1 85 5710086

RD 5710086 85 0 1
gtgtgtgtgcgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgtgtagtcgtactac

QA 1 85 1 85

RT{
5710086 matchElsewhereHighQual phrap 11 74 080215:162048
}

CO Contig20 175 1 1 U
ttattttatttattttatttattttatttattttatttattttatttatt
ttatttattttatttattttatttattttatttattttatttattttatt
tattttatttattttatttattttatttattttattattttatttatttt
atttatttatttatttatttattta

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5692289 U 1
BS 1 175 5692289

RD 5692289 175 0 3
ttattttatttattttatttattttatttattttatttattttatttatt
ttatttattttatttattttatttattttatttattttatttattttatt
tattttatttattttatttattttatttattttattattttatttatttt
atttatttatttatttatttattta

QA 1 175 1 175

RT{
5692289 matchElsewhereHighQual phrap 159 175 080215:162048
}

RT{
5692289 matchElsewhereHighQual phrap 137 157 080215:162048
}

RT{
5692289 matchElsewhereHighQual phrap 1 135 080215:162048
}

CO Contig21 122 1 1 U
agtgttattactattattattattattattattattattattattattat
tattattattattattatttccactaacaaaatatatatataatataatt
tattctaaatttttttaatcta

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5731835 U 1
BS 1 122 5731835

RD 5731835 122 0 0
agtgttattactattattattattattattattattattattattattat
tattattattattattatttccactaacaaaatatatatataatataatt
tattctaaatttttttaatcta

QA 77 122 1 122

CO Contig22 79 1 1 U
cacacacacacacacacacacacacacacacacacacacacacacacaca
cacacacacacacacacacacacacacac

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5734795 U 1
BS 1 79 5734795

RD 5734795 79 0 1
cacacacacacacacacacacacacacacacacacacacacacacacaca
cacacacacacacacacacacacacacac

QA 1 79 1 79

RT{
5734795 matchElsewhereHighQual phrap 1 79 080215:162048
}

CO Contig23 72 1 1 U
atatatatatgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgt

BQ
 0 0 0 0 0 0 0 0 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5769497 U 1
BS 1 72 5769497

RD 5769497 72 0 1
atatatatatgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgt

QA 10 72 1 72

RT{
5769497 matchElsewhereHighQual phrap 10 72 080215:162048
}

CO Contig24 71 1 1 U
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtagt

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5685312 U 1
BS 1 71 5685312

RD 5685312 71 0 1
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtagt

QA 1 71 1 71

RT{
5685312 matchElsewhereHighQual phrap 1 68 080215:162048
}

CO Contig25 79 1 1 U
catacacacacatacatacatacacaatctcacacacacacacacacaca
cacacacacacacacacacacacacacac

BQ
 0 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5654419 U 1
BS 1 79 5654419

RD 5654419 79 0 1
catacacacacatacatacatacacaatctcacacacacacacacacaca
cacacacacacacacacacacacacacac

QA 3 79 1 79

RT{
5654419 matchElsewhereHighQual phrap 31 79 080215:162048
}

CO Contig26 85 1 1 U
cgaagacccggtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg

BQ
 0 0 0 0 0 0 0 0 0 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5722605 U 1
BS 1 85 5722605

RD 5722605 85 0 1
cgaagacccggtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg

QA 11 85 1 85

RT{
5722605 matchElsewhereHighQual phrap 10 85 080215:162048
}

CO Contig27 83 1 1 U
attnatattaatacanaacacacacacacacacacacacacacacacaca
cacacacacacacacacacacacacacacacac

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5667144 U 1
BS 1 83 5667144

RD 5667144 83 0 2
attnatattaatacanaacacacacacacacacacacacacacacacaca
cacacacacacacacacacacacacacacacac

QA 12 83 1 83

RT{
5667144 matchElsewhereHighQual phrap 18 83 080215:162048
}

RT{
5667144 matchElsewhereHighQual phrap 17 31 080215:162048
}

CO Contig28 103 1 1 U
atcatttaggattgctatattttggattttggattgggaaatgcctggct
agacaaccgttctggaaattgaaatcatgcagatgtaaacaaaaatggga
tca

BQ
 0 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15

AF 5754151 U 1
BS 1 103 5754151

RD 5754151 103 0 0
atcatttaggattgctatattttggattttggattgggaaatgcctggct
agacaaccgttctggaaattgaaatcatgcagatgtaaacaaaaatggga
tca

QA 3 103 1 103

CO Contig29 79 1 1 U
natacacacacatacatacatacacaatctcacacacacacacacacaca
cacacacacacacacacacacacacacac

BQ
 0 0 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5764329 U 1
BS 1 79 5764329

RD 5764329 79 0 1
natacacacacatacatacatacacaatctcacacacacacacacacaca
cacacacacacacacacacacacacacac

QA 4 79 2 79

RT{
5764329 matchElsewhereHighQual phrap 31 79 080215:162048
}

CO Contig30 112 1 1 U
attttcagattcatttgtattttgatttggattattatcattgttgttat
tgttgttattattattattattattattattattattattattattatta
ttattattatta

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15

AF 5725479 U 1
BS 1 112 5725479

RD 5725479 112 0 1
attttcagattcatttgtattttgatttggattattatcattgttgttat
tgttgttattattattattattattattattattattattattattatta
ttattattatta

QA 33 112 1 112

RT{
5725479 matchElsewhereHighQual phrap 56 112 080215:162048
}

CO Contig31 78 1 1 U
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgtgtgtgt

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

AF 5762369 U 1
BS 1 78 5762369

RD 5762369 78 0 1
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgtgtgtgtgtgtgtgtgt

QA 1 78 1 78

RT{
5762369 matchElsewhereHighQual phrap 1 78 080215:162048
}

CO Contig32 82 1 1 U
acacacacacacacacacacacacacacacacacacacacacacacacac
acacacacacacacacacacacacgacgacnc

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 0 0

AF 5679898 U 1
BS 1 82 5679898

RD 5679898 82 0 1
acacacacacacacacacacacacacacacacacacacacacacacacac
acacacacacacacacacacacacgacgacnc

QA 1 82 1 82

RT{
5679898 matchElsewhereHighQual phrap 1 74 080215:162048
}

CO Contig33 62 1 1 U
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgt

BQ
 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
 15 15 15 15 15 15 15 15 15 15 15 15

AF 5697733 U 1
BS 1 62 5697733

RD 5697733 62 0 1
gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt
gtgtgtgtgtgt

QA 1 62 1 62

RT{
5697733 matchElsewhereHighQual phrap 1 62 080215:162048
}

CO Contig34 98 2 54 U
aagggaCTCGTCTAAGTGAAAGGCAGTAGATGTATGTAAGTCATGATGAC
ATCATCGCtaatcAAGCCtaacaGTTTGAAGACATTTCTAATTTAAta

BQ
 0 0 0 15 15 15 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25
 25 25 25 25 25 25 25 25 15 15 15 15 15 25 25 25 25 25 15 15 15 15 15 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 15 15

AF 5704073 U 2
AF 5762101 U 1
BS 1 3 5762101
BS 4 4 5704073
BS 5 5 5762101
BS 6 6 5704073
BS 7 7 5762101
BS 8 8 5704073
BS 9 9 5762101
BS 10 14 5704073
BS 15 15 5762101
BS 16 18 5704073
BS 19 20 5762101
BS 21 21 5704073
BS 22 24 5762101
BS 25 25 5704073
BS 26 26 5762101
BS 27 27 5704073
BS 28 28 5762101
BS 29 29 5704073
BS 30 30 5762101
BS 31 32 5704073
BS 33 38 5762101
BS 39 39 5704073
BS 40 46 5762101
BS 47 47 5704073
BS 48 50 5762101
BS 51 52 5704073
BS 53 54 5762101
BS 55 55 5704073
BS 56 56 5762101
BS 57 61 5704073
BS 62 63 5762101
BS 64 65 5704073
BS 66 66 5762101
BS 67 68 5704073
BS 69 69 5762101
BS 70 72 5704073
BS 73 74 5762101
BS 75 75 5704073
BS 76 77 5762101
BS 78 78 5704073
BS 79 80 5762101
BS 81 81 5704073
BS 82 82 5762101
BS 83 83 5704073
BS 84 84 5762101
BS 85 85 5704073
BS 86 88 5762101
BS 89 90 5704073
BS 91 92 5762101
BS 93 93 5704073
BS 94 94 5762101
BS 95 96 5704073
BS 97 97 5762101
BS 98 98 5704073

RD 5704073 97 0 0
aaggaCTCGTCTAAGTGAAAGGCAGTAGATGTATGTAAGTCATGATGACA
TCATCGCtaatcAAGCCtaacaGTTTGAAGACATTTCTAATTTAAta

QA 3 97 3 97

RD 5762101 98 0 0
aagggaCTCGTCTAAGTGAAAGGCAGTAGATGTATGTAAGTCATGATGAC
ATCATCGCta*tcAAGCCta*caGTTTGAAGACATTTCTAATTTAAta

QA 4 98 1 98

CO Contig35 108 2 62 U
atTTTCAATCctttacaCACGTTTCTGTACTCCGATGCATGATTCCGATC
CTATGTGCTTCATAGTCTAAAAAGATGATCTGTTAATGAAGGGAAAAAAC
TAAATTta

BQ
 15 15 25 25 25 25 25 25 25 25 15 15 15 15 15 15 15 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25
 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25
 25 25 25 25 25 25 15 15

AF 5748846 U 1
AF 5729853 U 1
BS 1 6 5748846
BS 7 8 5729853
BS 9 9 5748846
BS 10 11 5729853
BS 12 12 5748846
BS 13 13 5729853
BS 14 16 5748846
BS 17 19 5729853
BS 20 21 5748846
BS 22 22 5729853
BS 23 23 5748846
BS 24 24 5729853
BS 25 25 5748846
BS 26 26 5729853
BS 27 28 5748846
BS 29 30 5729853
BS 31 33 5748846
BS 34 35 5729853
BS 36 36 5748846
BS 37 37 5729853
BS 38 38 5748846
BS 39 39 5729853
BS 40 40 5748846
BS 41 41 5729853
BS 42 43 5748846
BS 44 44 5729853
BS 45 45 5748846
BS 46 48 5729853
BS 49 49 5748846
BS 50 51 5729853
BS 52 52 5748846
BS 53 55 5729853
BS 56 57 5748846
BS 58 58 5729853
BS 59 60 5748846
BS 61 63 5729853
BS 64 68 5748846
BS 69 72 5729853
BS 73 74 5748846
BS 75 75 5729853
BS 76 76 5748846
BS 77 77 5729853
BS 78 78 5748846
BS 79 79 5729853
BS 80 80 5748846
BS 81 81 5729853
BS 82 84 5748846
BS 85 86 5729853
BS 87 89 5748846
BS 90 90 5729853
BS 91 92 5748846
BS 93 93 5729853
BS 94 94 5748846
BS 95 95 5729853
BS 96 96 5748846
BS 97 97 5729853
BS 98 99 5748846
BS 100 101 5729853
BS 102 104 5748846
BS 105 106 5729853
BS 107 107 5748846
BS 108 108 5729853

RD 5748846 108 0 0
atTTTCAATCctttacaCACGTTTCTGTACTCCGATGCATGATTCCGATC
CTATGTGCTTCATAGTCTAAAAAGATGATCTGTTAATGAAGGGAAAAAAC
TAAATTta

QA 1 108 1 108

RD 5729853 108 0 0
atTTTCAATCcttt*caCACGTTTCTGTACTCCGATGCATGATTCCGATC
CTATGTGCTTCATAGTCTAAAAAGATGATCTGTTAATGAAGGGAAAAAAC
TAAATTta

QA 1 108 1 108

CO Contig36 111 2 63 U
taTAAAGTCGATGGGGAGGAAGATAGGGGAGCTAAAGCCATAGGGAAACC
ACGTAGTTCTGCGTCAAGCGTTgccttcCGAGGTGCTCTCCGCTTTTCCA
TGCtccaatcg

BQ
 15 15 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25
 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 15 15 15 15 15 15 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25
 25 25 25 15 15 15 15 15 15 15 15

AF 5648323 U 1
AF 5703145 U 1
BS 1 1 5648323
BS 2 2 5703145
BS 3 4 5648323
BS 5 5 5703145
BS 6 6 5648323
BS 7 8 5703145
BS 9 12 5648323
BS 13 13 5703145
BS 14 15 5648323
BS 16 16 5703145
BS 17 17 5648323
BS 18 18 5703145
BS 19 19 5648323
BS 20 20 5703145
BS 21 21 5648323
BS 22 22 5703145
BS 23 24 5648323
BS 25 25 5703145
BS 26 27 5648323
BS 28 29 5703145
BS 30 32 5648323
BS 33 34 5703145
BS 35 35 5648323
BS 36 36 5703145
BS 37 37 5648323
BS 38 38 5703145
BS 39 39 5648323
BS 40 40 5703145
BS 41 42 5648323
BS 43 43 5703145
BS 44 44 5648323
BS 45 45 5703145
BS 46 46 5648323
BS 47 50 5703145
BS 51 51 5648323
BS 52 55 5703145
BS 56 57 5648323
BS 58 60 5703145
BS 61 63 5648323
BS 64 65 5703145
BS 66 66 5648323
BS 67 67 5703145
BS 68 68 5648323
BS 69 69 5703145
BS 70 70 5648323
BS 71 72 5703145
BS 73 76 5648323
BS 77 78 5703145
BS 79 79 5648323
BS 80 82 5703145
BS 83 84 5648323
BS 85 86 5703145
BS 87 87 5648323
BS 88 90 5703145
BS 91 92 5648323
BS 93 93 5703145
BS 94 95 5648323
BS 96 96 5703145
BS 97 97 5648323
BS 98 99 5703145
BS 100 102 5648323
BS 103 104 5703145
BS 105 111 5648323

RD 5648323 111 0 0
taTAAAGTCGATGGGGAGGAAGATAGGGGAGCTAAAGCCATAGGGAAACC
ACGTAGTTCTGCGTCAAGCGTTgccttcCGAGGTGCTCTCCGCTTTTCCA
TGCtccaatcg

QA 1 111 1 111

RD 5703145 109 0 1
taTAAAGTCGATGGGGAGGAAGATAGGGGAGCTAAAGCCATAGGGAAACC
ACGTAGTTCTGCGTCAAGCGTTgc*ttcCGAGGTGCTCTCCGCTTTTCCA
TGCtcatcg

QA 1 109 1 105

RT{
5703145 compression phrap 74 76 080215:162048
}
BioPerl-1.007002/t/data/atp1.matrix000444000766000024     24134313155576321 17032 0ustar00cjfieldsstaff000000000000
Last position-specific scoring matrix computed, weighted observed percentages rounded down, information per position, and relative weight of gapless real matches to pseudocounts
           A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V   A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V
    1 M   -2 -2 -3 -4 -2 -1 -3 -4 -2  0  1 -2  8 -1 -3 -2 -1 -2 -2  0    0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0   0   0  1.01 0.28
    2 E    1 -1 -1 -1 -3  0  4 -2 -2 -3 -3  0 -3 -4 -2  3  1 -4 -3 -2   10   0   0   0   0   0  41   0   0   0   0   5   0   0   0  33   8   0   0   3  0.55 0.40
    3 L   -2 -3 -2 -3 -3 -2 -3 -4 -3  0  1 -3  8  0 -4 -3  0 -3 -3  1    1   0   2   1   0   0   1   0   0   3   8   0  66   2   0   0   7   0   0   9  1.03 0.64
    4 S    0  0  3  1 -4  3  2 -2 -2 -4 -4  2 -3 -5 -3  2  1 -5 -4 -4    9   3  13   7   0  15  12   1   0   0   0  13   0   0   0  16  10   0   0   0  0.43 0.68
    5 P   -2 -4 -5 -3 -3 -4 -4 -5 -5  6  3 -3  1  0 -1 -3 -2 -4 -3  1    2   0   0   2   0   0   0   0   0  59  25   1   2   3   3   1   1   0   0   2  0.82 0.68
    6 R   -2  4  5 -1 -4  1 -2 -3 -2 -4 -4  2 -3 -5 -3  1 -1 -5 -4 -4    0  27  36   2   0   4   0   0   0   1   0  15   0   0   1  12   2   0   0   0  0.78 0.70
    7 A    2 -4 -2 -3 -3 -3 -3 -1 -2 -2 -2 -3 -3 -4  6  1  0 -5 -4 -1   22   0   1   0   0   0   0   4   1   2   4   0   0   0  45  11   7   0   0   3  0.95 0.72
    8 A    2 -3  0  4 -3  0  2 -2 -3 -2 -4 -1 -3 -4 -3  3  1 -5 -4 -3   16   0   4  22   0   3  15   1   0   3   0   2   0   0   0  25   8   0   0   1  0.49 0.72
    9 E   -3 -2 -1  1 -5  1  7 -4 -2 -3 -4 -1 -4 -5 -3 -2 -3 -5 -4 -4    0   0   1   3   0   2  90   0   0   1   1   1   0   0   0   1   0   0   0   0  1.41 0.72
   10 L   -3 -5 -5 -5 -3 -4 -5 -5 -5  6  1 -4  0 -1 -5 -4 -2 -4 -1  3    1   0   0   0   0   1   0   0   0  68   8   0   0   1   0   0   0   0   2  19  1.06 0.72
   11 T    0  0 -1 -2 -1 -1 -2 -1 -2 -3 -4 -2 -3 -3 -2  5  2 -5 -3 -2    4   4   0   0   1   2   0   2   1   1   1   0   0   0   1  69  15   0   0   1  0.84 0.72
   12 N    2 -1  0  1 -4  1  2 -2 -2 -4 -4  3 -3 -4 -3  3  0 -5 -3 -3   15   1   4   8   0   4  13   2   0   0   1  19   0   0   0  30   3   0   1   0  0.46 0.73
   13 L   -1 -4 -5 -5 -3 -4 -5 -5 -5  6  3 -4  0 -2 -4 -3 -2 -4 -3  2    6   1   0   0   0   0   0   0   0  55  26   0   1   0   0   1   0   0   0   9  0.87 0.72
   14 F   -3 -4 -4 -5 -3 -4 -5 -6 -5  5  4 -4  0 -1 -5 -4 -2 -4 -3  0    0   0   1   0   0   0   0   0   0  50  46   0   0   1   0   0   1   0   0   0  1.01 0.74
   15 E   -2  3 -1 -2 -5  1  3 -4  0 -5 -4  6 -3 -5 -3 -2 -3 -5 -4 -4    1  17   1   1   0   4  19   0   2   0   0  55   0   0   0   1   0   0   0   0  0.96 0.74
   16 S   -1 -1  1  1 -5  5  4 -3 -2 -5 -4  2 -3 -5 -3  1 -1 -5 -3 -4    5   1   7   8   0  27  28   1   0   0   0  12   0   0   0   8   2   0   1   0  0.67 0.75
   17 R   -2  4 -2 -2 -5  6  1 -3 -2 -4 -3  2 -3 -2 -3 -2 -2 -4 -1 -2    2  26   1   0   0  44   6   1   0   0   1  11   0   1   0   0   2   0   2   4  0.84 0.76
   18 I   -3 -2 -5 -5 -3 -4 -5 -6 -5  7  1 -4  1 -1 -5 -4 -1 -4 -3  2    0   2   0   0   0   0   0   0   0  74   8   0   3   1   0   0   3   0   0   9  1.10 0.78
   19 R    1  0  1  2 -4  1  3 -2 -2 -4 -1  3 -3 -5 -3  0 -1 -5 -4 -4   12   4   6  10   0   4  24   1   0   0   6  23   0   0   0   7   3   0   0   0  0.44 0.78
   20 N   -2 -1  4  0 -4  2  0  2 -2 -5 -5  3 -4 -5 -3  2 -2 -5 -4 -4    1   2  28   4   0  10   5  15   0   0   0  20   0   0   0  14   1   0   0   0  0.61 0.79
   21 F   -1 -4 -4 -5 -4 -2 -4 -5 -1 -1  0 -2 -2  5 -5 -2 -1  0  6  0    4   0   0   0   0   1   0   0   1   3  10   2   0  30   0   2   4   1  36   5  0.91 0.78
   22 Y   -2 -2  2  3 -4  1  3  2 -2 -4 -2  0 -3 -4 -1 -1  0 -4  0 -3    2   1  10  21   0   7  18  14   0   0   4   6   0   0   3   4   7   0   4   1  0.39 0.78
   23 A    0 -1  0  1 -3  1  0 -1 -3 -1 -1  1 -2 -1  1  1  2 -4 -3  0    7   1   4   7   0   8   6   3   0   4   7   9   0   2   8   9  16   0   0   6  0.15 0.78
   24 N   -1 -1  1  1 -4  1  2  0  2 -3 -4  3 -3 -3 -2  1  1 -5 -3 -2    3   1   7   7   0   6  17   8   5   1   1  21   0   1   1  12   8   0   0   2  0.36 0.78
   25 F    3 -4 -2 -4 -1 -3 -2 -3 -4  1  1 -2  0  0 -1  1  0 -4 -3  3   25   0   1   0   1   0   2   0   0   9  13   2   1   5   3  11   6   0   0  22  0.32 0.78
   26 Q   -2 -1  2  3 -5  2  4 -2 -2 -3 -3  1 -3 -3 -2  1  0 -5 -4 -2    1   2   8  16   0  10  30   2   0   1   1   8   0   1   1   9   6   0   0   2  0.49 0.77
   27 V    0  0 -2 -3 -3  0 -2 -4 -4  1  1 -2  2 -1  1 -1  0 -4 -2  4    8   5   2   1   0   4   2   0   0   7  14   1   4   2   7   5   4   0   1  35  0.32 0.77
   28 D    0  1  0  1 -4  1  3 -2  0 -3 -3  0 -2 -1 -3  2  1 -4 -2  0    6   7   3   9   0   5  19   2   2   1   0   6   0   3   0  21   8   0   1   8  0.28 0.77
   29 E   -2 -2  4  2 -5  0  5 -3 -1 -5 -3 -1 -4 -5 -3 -1  0 -5 -4 -4    1   0  23   7   0   1  56   0   1   0   2   1   0   0   0   3   5   0   0   0  0.93 0.76
   30 I   -2 -4 -2 -3 -3 -1  1 -5 -1  3 -1 -3 -1 -3 -4 -1  2 -4 -1  4    0   0   2   0   0   2  11   0   2  18   4   1   0   0   0   2  15   0   2  40  0.52 0.77
   31 G   -2 -4 -2 -3 -4 -4 -4  7 -4 -6 -6 -3 -5 -5 -4 -2 -3 -4 -5 -5    0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0  1.92 0.77
   32 R   -2  3 -1 -3 -4  2  0 -4 -2 -1 -3  2 -3 -3 -3 -1  4 -4  0 -1    0  21   1   0   0   9   5   0   0   4   0  12   0   1   0   2  38   0   3   3  0.59 0.77
   33 V   -2 -5 -5 -5 -3 -4 -5 -5 -5  4 -1 -4 -1 -3 -4 -4 -2 -5 -3  6    0   0   0   0   0   0   0   0   0  19   0   0   0   0   0   0   0   0   0  81  1.24 0.77
   34 V   -2 -4 -3 -4 -2 -3  1 -5 -4  3  4 -1  0 -1 -4 -3  0 -4 -3  2    2   0   1   0   0   0  10   0   0  15  44   3   1   1   0   1   5   0   0  17  0.54 0.78
   35 S   -1 -1 -1 -1 -4  3  1 -2 -1 -4 -4  1 -3 -1 -3  5  1 -4  0 -3    2   2   2   2   0  16   7   1   1   0   0   7   0   3   0  49   6   0   4   0  0.60 0.79
   36 V   -1 -5 -5 -5 -3 -4 -5 -5 -5  4  0 -4 -1 -2 -5 -3 -2 -5 -2  6    3   0   0   0   0   0   0   0   0  29   4   0   0   1   0   1   1   0   1  60  1.04 0.85
   37 G    1 -3 -2 -3 -2  0 -2  6 -3 -5 -5  0 -3 -5 -4  2 -1 -4 -2 -4    9   0   1   0   1   4   1  57   0   0   0   6   0   0   0  16   4   0   2   1  0.90 0.86
   38 D   -4 -2 -1  8 -6 -2  0 -3 -2 -5 -6 -3 -5 -6 -4 -2 -1 -6 -5 -5    0   1   0  96   0   0   0   0   0   0   0   0   0   0   0   0   2   0   0   0  1.91 0.86
   39 G   -2 -4 -1 -2 -5 -4 -4  7 -4 -6 -6 -4 -5 -5 -4 -1 -3 -5 -5 -5    0   0   2   1   0   0   0  95   0   0   0   0   0   0   0   2   0   0   0   0  1.84 0.86
   40 I   -3 -5 -5 -5 -3 -5 -5 -6 -5  7  0 -5 -1 -2 -5 -4 -2 -5 -3  4    0   0   0   0   0   0   0   0   0  75   1   0   0   0   0   0   1   0   0  23  1.34 0.87
   41 A    6 -4 -4 -4  0 -3 -3 -2 -4  2 -2 -3 -2 -4 -3 -1 -2 -5 -4  1   72   0   0   0   2   0   0   0   0  14   0   0   0   0   0   0   1   0   0  11  0.96 0.87
   42 Q   -3  7 -1 -4 -5  1 -1 -4  0 -2 -2  1 -3  2 -4 -3 -3 -4 -2 -4    0  65   2   0   0   5   2   0   2   3   4   6   0   9   0   0   0   0   1   0  1.08 0.88
   43 V    0 -5 -5 -5  1 -4 -5 -5 -5  4 -1 -4 -1 -3 -4 -2 -2 -5 -3  5    9   0   0   0   3   0   0   0   0  30   1   0   0   0   0   3   0   0   0  54  0.96 0.88
   44 Y   -3 -2 -2 -3 -3 -3 -1 -3  5 -3 -3 -3 -3  1 -4  2  0 -1  7 -4    0   1   1   0   0   0   3   1  17   0   1   0   0   4   0  16   5   0  48   0  1.08 0.88
   45 G   -2 -2 -2 -3 -3 -4 -4  7 -4 -6 -6 -3 -5 -5 -4 -2 -4 -5 -5 -5    0   2   0   0   1   0   0  97   0   0   0   0   0   0   0   0   0   0   0   0  1.91 0.88
   46 L   -3 -4 -5 -6 -3 -4 -5 -6 -5  1  6 -5  2 -2 -5 -4 -3 -4 -3 -1    0   0   0   0   0   0   0   0   0   3  92   0   3   0   0   1   0   0   0   1  1.33 0.88
   47 N    0 -1  2  3 -5 -1  3  0 -3 -5 -4  2 -4 -5  1  1 -1 -5 -4 -4    6   3  12  20   0   1  20   6   0   0   2  12   0   0   8   9   3   0   0   0  0.48 0.88
   48 E   -3 -2  6  2 -5  1  2  0 -1 -5 -5  1 -4 -5 -4 -1 -2 -6 -4 -5    1   1  51  12   0   6  11   5   1   0   0   8   0   0   0   3   1   0   0   0  0.94 0.88
   49 I    2 -4 -5 -4  2 -4 -4 -4 -5  3 -1 -4 -1 -3 -4 -3 -2 -5 -3  5   22   0   0   1   4   0   0   0   0  20   1   0   0   0   0   0   0   0   0  52  0.88 0.88
   50 Q    0  1 -3 -4 -4  5 -1 -3 -3 -2 -1  1  7 -1 -4 -2 -3 -4 -3 -2    7   5   0   0   0  32   1   2   0   1   3   8  38   2   0   0   0   0   0   1  0.86 0.88
   51 A    4 -3 -2 -4 -3  1 -3 -3 -3 -1  0 -3 -1  0 -3  1 -2 -3  2  0   48   0   2   0   0   6   0   0   0   3  12   0   1   4   0  11   1   0   8   4  0.51 0.88
   52 G   -2 -4  1  0 -5 -2  1  6  2 -6 -5 -3 -2 -5 -4  0 -3 -3 -2 -5    0   0   6   3   0   1  11  63   6   0   0   0   1   0   0   8   0   0   1   0  1.05 0.87
   53 E   -3 -2 -2  0 -6  2  7 -4 -2 -5 -5 -1 -4 -5 -3 -2 -3 -5 -4 -5    0   0   0   0   0   6  94   0   0   0   0   0   0   0   0   0   0   0   0   0  1.68 0.87
   54 M   -1 -4 -5 -5 -3 -3 -4 -5 -4  0  4 -1  7 -1 -5 -4 -3 -4 -3  1    5   0   0   0   0   0   0   0   0   2  40   4  41   1   0   0   0   0   0   6  1.03 0.88
   55 V   -3 -5 -5 -5 -1 -4 -5 -6 -5  3  3 -5 -1 -2 -5 -4 -2 -5 -3  6    0   0   0   0   1   0   0   0   0  14  24   0   0   0   0   0   0   0   0  61  1.05 0.88
   56 L   -1  1 -2 -1 -3  0  6 -4 -2 -3 -1  1 -3 -3 -3 -1 -1 -5 -4 -4    3   6   0   1   1   2  67   0   0   1   6   6   0   1   0   3   3   0   0   0  0.97 0.90
   57 F   -4 -5 -5 -6 -4 -5 -5 -5 -4  0  1 -5 -2  8 -6 -4 -4 -1  1 -2    0   0   0   0   0   0   0   0   0   6  10   0   0  84   0   1   0   0   0   0  1.74 0.90
   58 A    1 -3 -1  3 -4 -1  3 -2 -1 -4 -5 -1 -4 -5  4  1 -2 -5 -4 -3   14   0   3  16   0   2  23   1   1   0   0   1   0   0  24  13   0   0   0   1  0.69 0.90
   59 N   -2 -3  4  3 -4 -2  1  3  0 -5 -5 -1 -4 -5 -4  3 -1 -5 -3 -5    0   0  20  15   0   1   9  20   2   0   0   3   0   0   0  28   2   0   1   0  0.68 0.90
   60 G   -2  0  3  1 -5 -3 -1  6 -3 -6 -6 -1 -5 -5 -4  0 -3 -5 -5 -5    0   6  13   7   0   0   3  62   0   0   0   2   0   0   0   5   0   0   0   0  1.09 0.90
   61 V   -1 -2 -3 -2 -3 -3 -3 -4  2  3  1 -3 -1 -3 -4  1  3 -5 -3  3    3   3   0   2   0   0   1   0   5  19  13   1   0   0   0  10  17   0   0  26  0.44 0.90
   62 K   -3  1 -3 -4 -5  0  0 -4 -2  0  0  4  0  3 -4 -2 -2 -3  4 -1    0   6   0   0   0   4   4   0   0   5   7  33   3  16   0   2   2   0  14   4  0.52 0.90
   63 G    0 -4 -2 -3 -5 -4 -4  7 -4 -6 -6 -4 -5 -5 -4 -2 -4 -5 -5 -5    5   0   0   0   0   0   0  95   0   0   0   0   0   0   0   0   0   0   0   0  1.88 0.89
   64 M   -3 -4 -5 -5 -3 -1 -4 -5 -4  4  2 -4  8  0 -5 -4 -3 -4 -2  1    0   0   0   0   0   3   0   0   0  26  16   0  45   2   0   0   0   0   1   8  1.08 0.91
   65 A    6 -4 -4 -4  0 -3 -3 -3 -4  0 -3 -3 -2 -4 -3 -1 -1 -5 -4  3   70   0   0   0   1   0   0   0   0   5   0   0   0   0   0   1   2   0   0  20  0.96 0.91
   66 L   -3 -4 -5 -5 -4  0 -4 -5 -2 -1  5 -4  4  2 -5 -3 -3 -3 -2  0    1   0   0   0   0   4   0   0   1   0  67   0  12   8   0   1   1   0   0   5  0.96 0.92
   67 N   -3 -3  8  0 -5 -2  0 -1 -2 -5 -6 -2 -4 -5 -4 -1 -1 -6 -4 -5    0   0  88   1   0   0   4   2   0   0   0   0   0   0   0   2   2   0   0   0  1.71 0.92
   68 L   -4 -4 -6 -6 -3 -4 -5 -6 -5  1  6 -5  0 -1 -3 -5 -3 -4 -3  0    0   0   0   0   0   0   0   0   0   4  92   0   0   1   2   0   0   0   0   2  1.32 0.92
   69 E   -3 -1  1  3 -6  0  6 -3 -2 -5 -5 -2 -4 -5 -3 -2 -3 -5 -1 -5    0   2   7  16   0   1  72   1   0   0   0   0   0   0   0   0   0   0   3   0  1.30 0.93
   70 N    0  1  2  0 -4  1  3 -4 -1 -3 -4  1 -2 -5  0  1 -1 -5 -2  0    7   9  10   4   0   7  23   0   1   1   0   8   1   0   5  12   2   0   1  10  0.35 0.93
   71 E   -3 -2  1  7 -5 -2  3 -3 -2 -5 -6  0 -5 -6 -4  0 -1 -6 -5 -5    0   1   7  62   0   0  17   1   1   0   0   4   0   0   0   5   3   0   0   0  1.22 0.93
   72 N   -2 -2  6 -1 -4  0  0 -1  0 -4 -3 -2 -4  0 -4  2  0 -5 -1 -2    2   0  49   2   0   5   5   3   2   1   1   0   0   5   0  16   5   0   2   2  0.78 0.93
   73 V   -2 -5 -5 -5 -2 -4 -5 -5 -5  3 -1 -4  0 -3 -5 -4 -1 -5 -3  6    1   0   0   0   1   0   0   0   0  13   0   0   1   0   0   0   2   0   0  83  1.30 0.93
   74 G   -2 -2 -1 -2 -5 -3 -4  7 -4 -6 -6 -3 -5 -5 -4 -1 -4 -5 -5 -5    1   3   2   1   0   1   0  91   0   0   0   0   0   0   0   3   0   0   0   0  1.75 0.95
   75 I    3 -5 -5 -5  2 -4 -4 -1 -5  4 -1 -4 -2 -3 -4 -3 -2 -5 -4  4   26   0   0   0   5   0   0   5   0  28   1   0   0   0   0   0   1   0   0  35  0.75 0.95
   76 V   -1 -5 -5 -5 -3 -4 -5 -2 -5  3  0 -4 -1 -3 -5 -3 -2 -5 -3  6    3   0   0   0   0   0   0   4   0  12   7   0   0   0   0   1   0   0   0  73  1.10 0.97
   77 V   -3 -5 -5 -6 -3 -5 -5 -4 -5  4  4 -5  1 -2 -5 -4 -3 -4 -3  4    0   0   0   0   0   0   0   1   0  27  39   0   3   0   0   0   0   0   0  29  0.95 0.97
   78 F   -3 -4 -4 -4 -3 -3 -4 -4 -3  1  4 -4  5  5 -4 -3 -3 -2  0 -1    1   1   0   1   0   0   1   1   0   7  37   1  17  29   1   1   1   0   1   1  0.87 0.89
   79 G   -2 -3  2  1 -4 -3 -3  6 -3 -5 -5 -3 -4 -4 -3 -2 -3 -4 -4 -4    1   1   9  10   0   0   1  71   0   1   1   1   0   0   1   1   1   0   0   1  1.26 0.90
   80 G   -2 -2  3  5 -4  0  2 -2 -2 -4 -4  0 -4 -3  3  1 -2 -4 -2 -4    2   1  12  32   0   3  11   2   0   1   1   5   0   1  13  11   1   0   2   1  0.62 0.90
   81 D   -2 -3 -2  4 -4 -1  1  1 -2 -2 -4  0 -3  0 -2  0  0 -3  4 -3    3   0   0  27   0   3   8  12   0   3   1   6   0   4   2   6   5   0  18   1  0.46 0.89
   82 T   -1  3  1  1 -3 -1  0 -3 -3 -2  0  1 -2 -2 -3  1  3 -4 -2  0    3  16   8   7   0   1   5   1   0   2  10   7   0   1   1  10  19   0   1   7  0.24 0.88
   83 A    1 -1  1  2 -4  0  1  2  3 -3 -1  0 -1 -2 -3  0 -1 -4 -3 -3   13   4   7  11   0   3   8  15   9   1   8   4   1   2   1   6   4   0   0   1  0.22 0.87
   84 I   -3 -4 -4 -4 -3 -4 -4 -4 -4  6  2 -4 -1 -2 -4 -3  0 -4 -3  3    1   1   0   1   0   0   1   1   0  55  14   1   0   0   1   1   6   0   0  17  0.89 0.84
   85 K   -1  1 -1 -2 -4  2  0 -3  0 -2 -1  5 -2 -3 -3  1  0 -4 -1 -2    4   5   1   1   0  11   4   1   2   2   8  37   0   0   1  13   4   0   2   3  0.45 0.86
   86 E    0 -2 -2 -1 -4  2  6 -3 -2 -4 -4 -1 -3 -4 -2  0 -2 -4 -3 -2    9   0   0   1   0   6  68   1   0   0   1   1   0   0   1   6   1   0   0   2  1.04 0.86
   87 G   -2 -4 -1 -2 -4 -3 -3  7 -3 -5 -5 -3 -4 -4 -3 -2 -3 -4 -4 -4    1   0   3   1   0   0   1  86   0   0   1   1   0   0   1   2   1   0   0   1  1.58 0.86
   88 D   -1 -3 -1  5 -4  2  0 -2 -2 -3 -3 -2  2 -3 -3  2  1 -4 -3 -2    5   0   1  38   0   9   4   2   1   0   1   1   7   1   1  14   9   0   0   3  0.57 0.86
   89 L   -2  0 -1 -2 -3 -1  0 -3  0  1  1  2  0 -2 -1  1  2 -4 -2  0    1   4   3   1   0   3   7   1   2  10  17  13   1   1   3  10  16   0   1   6  0.19 0.86
   90 V    0 -4 -4 -4  1 -3 -4 -4 -4  2 -1 -4 -1 -3 -4 -3 -2 -4 -3  6    7   0   0   1   3   0   1   1   0   9   1   1   0   0   1   1   1   0   0  74  1.01 0.82
   91 K   -2  2  0 -2 -4 -1  0 -2 -1 -3 -3  5  0 -3 -3  1 -1 -2  1 -2    1  11   3   0   0   1   4   3   1   1   2  49   3   0   0   9   3   0   5   2  0.63 0.83
   92 R    1  5 -2 -3  4 -1 -2  1 -3 -3 -3 -1 -3 -4 -1  0 -1 -4 -3 -1   12  44   0   1  10   1   1  12   0   0   1   1   0   0   2   5   4   0   0   5  0.66 0.81
   93 T   -2 -2 -2 -3  1 -2 -3 -3 -3 -2 -2 -2  1 -3 -3  1  7 -4 -3 -2    1   2   0   1   3   0   1   1   0   0   3   1   5   0   0   6  75   0   0   1  1.07 0.81
   94 G   -2 -2  1 -1 -4 -2 -1  6  0 -4 -4  0 -4 -2 -3 -1 -3 -3  2 -4    1   1   8   3   0   1   3  58   2   0   1   5   0   1   0   4   1   0   9   1  0.88 0.81
   95 S    0  4  0 -1 -4  2  0 -3  1 -3 -4  4 -3 -3 -2  2 -1 -4 -3 -3    7  21   3   3   0   8   4   1   3   1   1  24   0   1   1  18   4   0   0   1  0.49 0.81
   96 I   -3 -4 -2 -2 -3 -4 -4 -4 -4  6  2 -4 -1  1 -4 -3 -2 -4 -2  2    1   0   2   3   0   0   1   1   0  53  17   1   0   5   0   1   1   0   0  13  0.76 0.78
   97 V    3 -3 -4 -4 -3 -3 -3 -3 -4  1  2 -3  2  0 -3 -2 -2 -3 -2  4   26   0   0   0   0   0   1   1   0   7  20   1   6   5   0   1   1   0   0  30  0.51 0.78
   98 D   -1 -1 -1  4 -4  2  3 -2  0 -4 -4  1 -3 -3 -3  2 -2 -4 -1 -4    4   1   1  21   0  10  23   2   2   0   1   8   0   1   0  21   1   0   2   1  0.54 0.79
   99 V   -1 -4 -4 -4 -3 -3 -4 -4 -4  4  1 -3 -1  0 -4 -3  1 -4 -3  5    2   0   0   0   0   0   1   1   0  20   9   1   0   3   0   1   9   0   0  51  0.74 0.77
  100 P   -2 -2  0 -1 -4 -1 -2 -2 -3 -4 -2  0 -3 -3  7 -2 -3 -4  2 -3    1   1   5   3   0   3   1   2   0   0   6   5   0   0  61   1   1   0   8   1  1.33 0.78
  101 A    1 -4 -4 -4 -2 -3 -4 -4 -4  1  2 -3 -1 -2 -3 -2 -1 -4 -3  5   10   0   0   0   0   0   1   1   0   2  18   1   0   0   0   2   2   0   0  60  0.76 0.76
  102 G   -1 -4 -2 -2 -4 -3 -3  7 -3 -4 -4 -3 -4  0 -3 -1 -3 -4 -4 -4    2   0   0   2   0   0   1  81   0   0   1   0   0   5   0   4   0   0   0   1  1.37 0.77
  103 K   -1  2  0  3 -4 -1  3 -3 -1 -3 -4  3 -2 -4  0 -2 -2 -4  0 -3    5  10   4  18   0   1  24   1   1   2   1  21   1   0   4   1   0   0   4   1  0.51 0.77
  104 A    3 -3 -1 -1 -2  0  3  2 -1 -4 -3 -2 -3  0 -3 -1 -2 -3  2 -2   25   0   2   3   1   4  21  19   1   0   1   1   0   4   0   3   2   0   9   2  0.39 0.77
  105 M    0 -3 -4 -4 -3 -3 -3 -4 -3  0  4 -3  5  0 -4  0 -1 -3  0  1    6   0   0   0   0   0   0   1   0   3  43   0  16   4   0   9   2   0   3  10  0.52 0.72
  106 L   -1 -3 -4 -4 -1 -2 -3 -4 -4  2  5 -2  1 -1 -3  0 -2 -3 -3  0    5   0   0   0   1   1   1   1   0  13  58   2   2   1   1   9   1   0   0   3  0.59 0.71
  107 G   -1 -2 -2 -3 -4 -3 -3  6 -3 -4 -4 -3 -4 -4 -3  1 -3 -4 -4 -4    1   2   0   0   0   0   0  78   0   0   1   0   0   0   0  10   0   0   0   0  1.27 0.71
  108 R   -3  7 -2 -3  4 -1 -2 -4 -2 -4 -3  1 -3 -4 -3 -1 -2 -4 -3 -4    1  76   0   0   9   0   0   0   0   0   1   5   0   0   0   5   0   0   0   0  1.26 0.69
  109 V   -2 -4 -4 -4 -3 -4 -4 -5 -4  3 -1 -4 -1  2 -4 -3 -1 -4 -2  6    0   0   0   0   0   0   0   0   0  13   1   0   0   8   0   0   2   0   0  72  0.98 0.72
  110 V   -2 -4 -4 -4 -3 -4 -4 -4 -4  3  0 -4  3 -2 -4 -3 -1 -4 -3  6    2   0   0   0   0   0   0   0   0  19   3   0   9   0   0   0   2   0   0  62  0.90 0.72
  111 D   -3 -3  5  6 -4 -2  1 -3 -2 -5 -5 -2 -4 -5 -3  0 -1 -5 -4 -4    0   0  34  44   0   0   7   0   0   0   0   0   0   0   0   6   2   0   0   0  1.02 0.79
  112 A    3 -3 -3 -3 -3 -3 -3  1 -4 -4 -4 -3 -3 -4  6  1  1 -5 -4 -2   29   0   0   0   0   0   0   8   0   0   0   0   0   0  37   9   9   0   0   2  0.86 0.79
  113 M   -3 -1 -4 -5 -3 -4 -4 -5 -4  1  5 -4  1 -2 -4 -3  1 -4 -3 -1    0   4   0   0   0   0   0   0   0   5  71   0   2   0   0   0  12   0   0   2  0.86 0.81
  114 G    0 -4 -3 -3 -4 -4 -4  7 -4 -5 -5 -3  0 -5 -4 -1 -3 -5 -5 -2    7   0   0   0   0   0   0  83   0   0   0   0   3   0   0   4   0   0   0   3  1.50 0.87
  115 V   -2  1  4 -1 -5  2  2  0  3 -3 -3  2 -2 -2 -4 -2 -1 -5 -2 -2    1   6  20   1   0  11  16   8   9   1   2  12   1   1   0   1   2   0   1   3  0.43 0.96
  116 P   -1 -4 -4  1 -1 -1  0 -4 -4 -3  0 -3  3  1  6 -2 -1 -5 -4 -2    4   0   0   7   2   2   8   0   0   0   8   0   8   6  47   2   4   0   0   2  0.95 0.96
  117 I   -3 -5 -5 -6 -3 -5 -5 -6 -5  6  3 -5  2  2 -5 -5 -3 -4 -3  2    0   0   0   0   0   0   0   0   0  53  26   0   5   7   0   0   0   0   0   9  1.04 0.96
  118 D   -3 -3 -1  5 -4 -2 -1 -4 -2 -2  0 -3 -2 -2 -3 -2  2 -3  3  1    0   0   0  49   0   0   0   0   0   0  11   0   0   0   0   0  13   0  15  13  0.69 0.61
  119 G    1  2  2  2 -4 -2  2  1 -3 -4  0 -2 -3 -4 -4  1 -2 -5 -4 -3   13  13  13  13   0   0  13  12   0   0  13   0   0   0   0  13   0   0   0   0  0.33 0.78
  120 K   -2  1 -1 -1 -5  0  0 -2 -3 -4  0  6 -3 -4 -2 -1 -2 -5 -4 -3    0   6   2   2   0   1   3   2   0   0  10  68   0   0   1   3   0   0   0   2  0.88 0.77
  121 G   -2 -1 -2 -2 -4 -3 -1  7 -4 -6 -5 -2 -4 -5 -2  0 -3 -5 -5 -4    0   3   0   1   0   0   3  83   0   0   0   1   0   0   2   6   0   0   0   0  1.42 0.77
  122 A    2 -1  0  1 -4 -1  3 -3 -3 -4 -4 -2 -4 -4  5  0 -2 -5 -1 -3   23   3   3   9   0   1  19   0   0   0   1   1   0   0  30   6   1   0   2   1  0.68 0.77
  123 L   -3 -4 -5 -5 -3 -4 -2 -6 -5  6  3 -4  0 -1 -3 -4 -3 -4 -3  2    0   0   0   0   0   0   3   0   0  51  31   0   0   1   1   0   0   0   0  12  0.90 0.76
  124 S   -1 -2  2  2 -4  2  1 -1 -1 -3 -2  2 -3 -1 -1  1 -1 -5 -3 -1    4   0  12  12   0   9  10   5   1   1   4  17   0   2   3   9   4   0   0   6  0.22 0.76
  125 D    2 -3  0  1  0 -2 -1  0 -1 -3 -4  0 -3 -2  0  1  3 -4 -2 -1   17   0   4  10   2   0   3   7   2   1   0   6   0   1   4  12  23   0   1   3  0.27 0.76
  126 H   -1 -2  1  3 -4 -1  2 -1  2 -3 -3  2 -3 -4 -3  2  2 -5 -3 -2    2   0   5  16   0   2  14   5   5   1   1  15   0   0   0  16  13   0   0   4  0.33 0.76
  127 E   -1 -1 -1  1 -3  1  4 -1  1 -2 -2  2 -1 -3 -2 -1  0 -4  1 -3    6   1   2   6   0   4  31   4   3   2   3  17   1   0   1   4   5   0   6   0  0.34 0.73
  128 Q   -2  5 -1 -1 -4  0  0 -3 -1 -3 -2  1 -2  1 -4  1  2  0  1 -3    1  34   2   3   0   2   4   0   1   0   3   5   1   8   0  11  18   1   4   0  0.44 0.72
  129 R    0  5 -2 -1 -4 -1 -1 -2 -3 -3  0  0  3 -3 -4  2 -1  0 -3 -2    6  38   0   3   0   1   1   2   0   0   8   5   8   1   0  16   3   2   0   3  0.45 0.72
  130 R   -1  4 -3 -3 -4 -1 -1 -4 -2 -2 -1  0 -1 -3  6 -1 -3 -5 -4 -2    3  31   0   1   0   2   2   0   1   1   8   3   1   1  39   3   0   0   0   2  0.87 0.70
  131 V   -1 -4 -5 -5 -1 -4 -4 -5 -5  4  1 -4  0 -2 -4 -4 -2 -4 -3  5    3   0   0   0   1   0   0   0   0  32  12   0   0   0   0   0   0   0   0  49  0.86 0.69
  132 E   -3 -2 -2  2 -5  1  7 -2 -2 -5 -4 -1 -4 -1 -3 -2 -3 -4 -3 -4    0   0   0   7   0   1  83   3   0   0   0   0   0   3   0   0   0   0   0   0  1.24 0.69
  133 V    0  3 -3 -4  1 -2 -2 -4 -3  1  0  1 -1 -3 -4  0  0 -4 -3  3    8  17   0   0   3   0   1   0   0   8   8  10   1   1   0   9   6   0   0  28  0.30 0.69
  134 K   -2 -1 -2 -2 -4  1 -2 -2 -3  1 -2  5 -1 -4  3 -2 -2 -5 -3  1    1   0   1   2   0   5   0   2   0   9   1  49   2   0  15   1   0   0   0  12  0.61 0.69
  135 A    6 -3 -3 -3 -2 -2 -3 -2 -3 -3 -3 -2 -3 -4 -3  0  0 -4 -4 -2   96   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   3   0   0   0  1.19 0.69
  136 P   -1 -4 -4 -3 -4 -3 -3 -4 -3 -4 -3 -3 -4 -4  8 -2 -2 -5 -3 -4    3   0   0   0   0   0   0   0   0   0   2   0   0   0  91   0   2   0   1   0  2.33 0.67
  137 G    0 -4  0 -2 -4 -3 -4  7 -4 -5 -5 -3 -4 -5 -2  0 -2 -4 -5 -5    5   0   3   0   0   0   0  86   0   0   0   0   0   0   1   4   1   0   0   0  1.47 0.67
  138 I   -2 -4 -5 -5 -3 -4 -5 -5 -5  6  0 -4 -1 -2 -4 -4 -2 -4 -3  4    0   0   0   0   0   0   0   0   0  62   0   0   0   0   0   0   0   0   0  35  1.07 0.66
  139 L   -2 -4 -5 -5 -2 -4 -5 -5 -5  6  1 -4  5 -2 -4 -4 -2 -4 -3  2    1   0   0   0   0   0   0   0   0  65   3   0  18   0   0   0   0   0   0  11  1.01 0.68
  140 E    1 -2 -2  2 -3  1  3 -3 -2 -4 -4 -1 -3 -1  4  1  0  0 -1 -2   12   0   0  11   0   5  21   0   1   0   0   2   0   4  22  10   6   1   3   2  0.47 0.68
  141 R   -3  8 -2 -3 -5 -1 -1 -4 -2 -2 -4  1 -3 -4 -4 -2 -3 -4 -3 -4    0  96   0   0   0   0   1   0   0   3   0   0   0   0   0   0   0   0   0   0  1.63 0.66
  142 K   -1  1 -2  0 -4  4  1 -3 -1 -2 -3  5 -2 -4 -3 -1 -2 -4 -3 -3    3   6   0   6   0  26   6   0   1   3   1  41   0   0   0   4   1   0   0   1  0.67 0.67
  143 S   -1 -3 -1 -2 -3 -2 -2 -1 -3 -4 -3 -2 -2 -3  4  6  0 -5 -4 -3    0   0   0   0   0   0   0   2   0   0   2   1   1   1  19  73   1   0   0   0  0.98 0.67
  144 V   -2 -4 -5 -5 -2 -4 -4 -5 -5  2 -1 -4 -1 -2 -4 -3 -2 -5 -3  7    0   0   0   0   0   0   0   0   0   2   0   0   0   0   0   0   0   0   0  98  1.26 0.66
  145 H   -2  1  3  2  1 -2 -1 -2  6 -4 -4 -1 -3 -2 -3  1  1 -4  0 -4    2   7  18  13   4   0   1   1  26   0   0   3   0   1   0  13   9   0   3   0  0.59 0.66
  146 E   -2  0 -2 -1 -5  4  6 -4 -2 -4 -4  0 -3 -4 -3 -2 -2 -4 -1 -1    0   3   0   0   0  18  70   0   0   0   0   2   0   0   0   0   1   0   2   5  1.09 0.66
  147 P   -2 -4 -2 -3 -5 -3 -3 -4 -4 -5 -5 -3 -4 -5  8 -2 -3 -5 -5 -4    0   0   2   0   0   0   0   0   0   0   0   0   0   0  96   2   0   0   0   0  2.49 0.65
  148 M   -3 -4 -5 -5 -3 -3 -4 -5 -4  1  4 -4  7  0 -3 -4 -2 -3 -2  2    0   0   0   0   0   0   0   0   0   3  38   0  37   3   1   0   0   0   0  18  0.89 0.66
  149 Q   -1 -1 -1 -2 -4  7  1 -3 -1 -3 -1 -1 -1 -4 -2 -1 -2 -4 -2 -3    4   0   2   0   0  74   6   0   0   1   8   0   0   0   1   2   0   0   1   0  1.07 0.66
  150 T   -2 -3 -2 -3 -3 -2 -3 -3 -3 -1 -2 -2 -2 -2 -3  0  7 -4 -3 -2    0   0   0   0   0   0   0   0   0   3   1   0   0   2   0   2  92   0   0   0  1.24 0.66
  151 G   -1 -3 -2 -3 -4 -3 -4  7 -4 -6 -5 -3 -4 -5 -4 -2 -3 -4 -5 -5    0   1   0   0   0   0   0  99   0   0   0   0   0   0   0   0   0   0   0   0  1.81 0.66
  152 L   -3 -4 -5 -5 -3 -4 -5 -5 -4  5  4 -4  0  0 -5 -3 -2 -3  1  1    0   0   0   0   0   0   0   0   0  40  45   0   0   2   0   1   1   0   6   5  0.82 0.66
  153 K   -2  0  0 -3 -4 -1 -1 -3 -3 -1 -1  6 -2 -4 -3 -2  0 -5 -3 -1    2   0   4   0   0   0   0   0   0   3   7  72   0   0   0   0   4   0   0   5  0.82 0.66
  154 A    5 -3 -3 -3  1 -3 -3 -2 -3  0 -2 -2 -2 -4 -2  3 -1 -4 -3  1   61   0   0   0   3   0   0   0   0   4   1   0   0   0   1  21   1   0   0   9  0.71 0.66
  155 V   -2 -5 -5 -5 -3 -4 -5 -5 -5  6  0 -4 -1 -2 -4 -4 -2 -4 -3  5    0   0   0   0   0   0   0   0   0  57   3   0   0   0   0   0   0   0   0  40  1.08 0.66
  156 D   -3 -3  0  8 -5 -2  0 -3 -3 -5 -5 -2 -5 -5 -3 -2 -3 -6 -5 -5    0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.86 0.66
  157 S    4 -3 -2 -3  2 -2 -2 -1 -3 -3 -3 -2 -2 -4 -3  5  0 -4 -3 -2   37   0   0   0   4   0   0   1   0   0   0   0   0   0   0  53   3   0   0   1  0.80 0.66
  158 L   -3 -4 -5 -5 -3 -3 -4 -5 -4  0  4 -4  7 -1 -2 -4 -3 -3 -3 -1    0   0   0   0   0   0   0   0   0   2  49   0  47   0   2   0   0   0   0   0  1.12 0.67
  159 V   -2 -4 -5 -5 -3 -4 -4 -5 -5  5  0 -4 -1  1 -4 -3  0 -4 -2  5    0   0   0   0   0   0   0   0   0  40   1   0   0   5   0   0   6   0   0  47  0.90 0.67
  160 P   -2 -4 -4 -3 -4 -3 -3 -4 -4 -4 -4 -3 -4 -5  8 -2 -3 -5 -5 -4    2   0   0   0   0   0   0   0   0   0   1   0   0   0  96   1   0   0   0   0  2.50 0.67
  161 I   -3 -5 -5 -5 -3 -4 -5 -6 -5  7  0 -4 -1 -2 -5 -4 -2 -4 -3  3    0   0   0   0   0   0   0   0   0  80   0   0   0   0   0   0   0   0   0  20  1.24 0.69
  162 G   -1 -4 -2 -3 -2 -4 -4  7 -4 -6 -6 -3 -5 -5 -3 -2 -3 -4 -5 -5    0   0   0   0   1   0   0  99   0   0   0   0   0   0   1   0   0   0   0   0  1.82 0.70
  163 R   -3  7 -2 -3  1 -1 -2 -4 -2 -5 -3  1 -3 -5 -4 -2 -3 -5 -4 -4    0  92   0   0   3   0   0   0   0   0   2   4   0   0   0   0   0   0   0   0  1.58 0.71
  164 G   -2 -4 -2 -3 -4 -4 -4  7 -4 -6 -6 -3 -5 -5 -4 -2 -3 -4 -5 -5    0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0  1.88 0.71
  165 Q   -3 -1 -2 -2 -5  8  0 -4 -1 -5 -4  0 -2 -5 -3 -2 -2 -4 -3 -4    0   0   0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.74 0.71
  166 R   -3  8 -2 -3 -5 -1 -2 -4 -2 -5 -4  1 -3 -5 -4 -3 -3 -5 -4 -4    0 100   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.79 0.71
  167 E   -3 -2 -2  0 -6  2  7 -4 -2 -5 -5 -1 -4 -5 -3 -2 -3 -5 -4 -4    0   0   0   0   0   6  94   0   0   0   0   0   0   0   0   0   0   0   0   0  1.55 0.71
  168 L   -3 -4 -5 -5 -3 -4 -5 -6 -5  0  6 -4  0 -1 -2 -4 -3 -4 -3 -1    0   0   0   0   0   0   0   0   0   0  96   0   0   0   2   0   0   0   0   0  1.26 0.76
  169 L   -3 -5 -5 -5 -3 -5 -5 -6 -5  7  0 -5 -1 -2 -5 -4 -3 -5 -3  2    0   0   0   0   0   0   0   0   0  90   2   0   0   0   0   0   0   0   0   7  1.41 0.77
  170 I   -3 -5 -5 -5 -1 -5 -5 -6 -5  7  1 -5  0 -2 -5 -4 -3 -5 -3  1    0   0   0   0   1   0   0   0   0  92   4   0   0   0   0   0   0   0   0   2  1.41 0.78
  171 G   -2 -4 -2 -3 -5 -4 -4  7 -4 -6 -6 -3 -5 -5 -4 -2 -4 -4 -5 -5    0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0  1.94 0.79
  172 G   -4 -4  0  8 -6 -2  0 -3 -3 -5 -6 -3 -5 -6 -3 -2 -3 -6 -5 -5    0   0   2  96   0   0   1   1   0   0   0   0   0   0   0   0   0   0   0   0  1.90 0.80
  173 R   -3  8 -2 -4 -5  1 -2 -4 -2 -5 -4  1 -3 -5 -4 -3 -3 -5 -4 -5    0  96   0   0   0   3   0   0   0   0   0   1   0   0   0   0   0   0   0   0  1.79 0.81
  174 Q   -1 -1  0 -2 -5  8  0 -3 -1 -5 -4  1 -2 -5 -3 -2 -2 -4 -3 -4    3   0   3   0   0  87   0   0   0   0   0   4   0   0   0   1   1   0   0   0  1.52 0.81
  175 T   -2 -3 -2 -3 -1 -3 -3 -4 -4 -1 -3 -3 -2 -4 -3  0  7 -4 -4 -1    0   0   0   0   1   0   0   0   0   2   0   0   0   0   0   2  94   0   0   2  1.43 0.81
  176 G   -2 -4 -2 -3 -5 -4 -4  7 -4 -6 -6 -3 -5 -5 -4 -2 -4 -5 -5 -5    0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0  1.96 0.81
  177 K   -2  0 -2 -2 -5  0 -1 -3 -2 -4 -4  7 -3 -5 -3 -2 -2 -4 -3 -4    0   0   0   0   0   0   0   0   0   0   0  95   0   0   0   0   0   0   0   0  1.47 0.77
  178 T   -2 -3 -2 -3 -3 -2 -3 -3 -3 -3 -3 -2 -2 -4 -3  0  7 -4 -3 -2    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   3  93   0   0   0  1.45 0.82
  179 T    5 -2 -3 -3 -2 -1 -2 -2 -3 -3 -3 -2 -3 -4 -3  2  1 -4 -3 -2   68   1   0   0   0   2   0   0   0   0   0   0   0   0   0  18   8   0   0   0  0.92 0.82
  180 I   -3 -4 -5 -5 -3 -4 -5 -5 -5  6  1 -4  0 -2 -4 -4 -2 -4 -3  4    0   0   0   0   0   0   0   0   0  50  11   0   1   0   0   0   0   0   0  34  1.04 0.85
  181 A    6 -3 -3 -4  4 -2 -3 -1 -4 -2 -3 -3 -3 -4 -3 -1 -2 -4 -4 -2   84   0   0   0   8   1   0   3   0   2   1   0   0   0   0   0   0   0   0   0  1.15 0.85
  182 I   -3 -4 -5 -5 -3 -4 -5 -5 -5  6  2 -4  0 -2 -4 -4 -1 -4 -3  3    0   0   0   0   0   0   0   0   0  58  14   0   1   1   0   0   3   0   0  19  0.99 0.85
  183 D   -3 -3 -1  8 -5 -2  0 -3 -3 -5 -5 -3 -5 -5 -3  0 -3 -6 -5 -5    0   0   0  92   0   0   0   0   0   0   0   0   0   0   0   5   0   0   0   0  1.84 0.88
  184 T    3 -3 -3 -3  0 -3 -3 -3 -4  0 -3 -3 -1 -4 -3 -1  6 -4 -4 -2   26   0   0   0   2   0   0   0   0   7   0   0   2   0   0   1  61   0   0   0  0.96 0.88
  185 I   -3 -5 -5 -5 -3 -5 -5 -5 -5  7  0 -4  0 -1 -5 -4 -3 -4 -3  1    0   0   0   0   0   0   0   0   0  88   1   0   1   2   0   0   0   0   0   4  1.40 0.88
  186 L   -3 -4 -5 -5 -3 -4 -5 -5 -5  6  4 -4  0 -2 -4 -2 -3 -4 -3  1    0   0   0   0   0   0   0   0   0  50  38   0   0   0   1   4   0   0   0   5  0.98 0.88
  187 N   -3 -2  8 -1 -5 -2 -2 -3  1 -5 -5 -2 -4 -5 -4 -1 -2 -6 -4 -5    2   1  93   0   0   0   0   0   2   0   0   1   0   0   0   1   0   0   0   0  1.86 0.93
  188 Q   -3 -1 -2 -2 -5  8  0 -4 -1 -5 -3 -1 -2 -5 -3 -2 -3 -4 -3 -4    0   0   0   0   0  97   0   0   1   0   2   0   0   0   0   0   0   0   0   0  1.87 0.93
  189 K   -2  2 -1 -3 -5  0 -1 -3 -3 -4 -4  7 -3 -5 -3 -2 -3 -5 -4 -2    2   9   1   0   0   1   0   0   0   0   1  81   0   0   0   0   0   0   0   2  1.31 0.89
  190 Q   -1  3  1  0 -3  2  1  0  1 -2 -1  1 -2 -1 -1  0 -1 -2  2 -2    5  17   6   5   1   8   8   8   3   2   6   9   1   3   3   5   2   0   7   2  0.17 0.69
  191 I   -1 -2 -2 -2 -2 -1 -1 -2 -2  2  0  0  2  2 -1  0  2  2  0  1    4   2   2   2   1   2   3   3   1  16   8   5   5   9   2   9  14   2   3   8  0.16 0.61
  192 N   -1 -1  6 -1 -2 -1 -1 -1  4 -2 -2 -1 -2 -2 -2 -1 -1 -2  0 -2    4   2  48   2   1   2   3   3  10   2   4   2   1   2   2   3   2   1   4   3  0.70 0.56
  193 S    0 -1  1  2 -1  0  0 -1 -1 -1  0  0 -1 -1 -1  1 -1  3 -1 -1    7   3   7  14   1   5   6   5   1   3   8   4   1   2   3  13   4   4   2   5  0.10 0.35
  194 R    0  2  0  0 -1  1  2 -1 -1 -1 -1  2 -1 -1 -1  0  0 -1 -1 -1    6  11   5   3   1   6  16   4   1   3   6  13   1   2   3   5   5   1   2   4  0.13 0.40
  195 A    0 -1  0 -1 -1 -1 -1  2 -1  1 -1 -1 -1 -1  0  2  0  0 -1 -1    6   3   3   3   1   2   4  17   1   8   7   4   1   2   5  19   5   1   2   5  0.12 0.42
  196 T    0  0  1  1 -1  0 -1  1 -1 -1 -1  0 -1 -1  0  0  2  0 -1 -1    8   4   6   9   1   3   4  12   1   3   7   6   1   3   4   8  13   1   2   4  0.08 0.40
  197 S   -1  0  2  4 -2 -1  0  0 -1 -2 -1 -1 -1 -2 -1  1 -1 -2 -1 -1    5   6   9  25   1   2   6   7   1   3   5   4   1   2   3   9   4   1   2   4  0.22 0.40
  198 E    0 -1 -1  0 -2  0  4 -1  2 -2 -1  0 -1 -2  1  0  1 -2 -1 -1    7   3   3   5   1   3  27   4   6   3   6   5   1   2   6   6   9   1   2   4  0.22 0.44
  199 S   -1 -1  1  2 -2 -1 -1  3 -2 -3 -3  3 -3 -3 -2  2 -1 -3 -3 -3    4   1   6  12   1   1   2  22   0   1   2  19   0   1   1  21   3   0   1   1  0.39 0.66
  200 E   -2  0  2  1 -3  4  2 -1 -2 -3 -3  3 -3 -4 -2  1 -2 -3 -3 -3    2   2   9   8   0  20  16   3   0   2   2  21   0   1   1  11   1   0   1   1  0.45 0.71
  201 T   -1 -1  1  4 -4  0 -1  2 -3 -4 -4  3 -3 -1  0  0  0 -4 -3 -3    4   1   5  23   0   3   2  15   0   0   1  25   0   4   5   5   4   0   0   1  0.44 0.75
  202 M   -3 -4 -5 -5 -1 -4 -5 -5 -5  3  3 -4  3 -2 -5 -4 -2 -4 -3  5    0   0   0   0   1   0   0   0   0  17  30   0   6   0   0   0   1   0   0  45  0.86 0.79
  203 Y   -3 -1 -3 -4 -4 -2 -3 -5  1  3 -1  1 -2  2 -3 -3  0 -2  6  0    0   3   1   0   0   1   0   0   3  24   3  11   0   6   1   0   5   0  37   6  0.71 0.80
  204 C   -2  0 -4 -5 11 -4 -5 -3 -5 -3 -3 -4 -3 -4 -5 -1 -3 -4 -4 -2    0   6   0   0  87   0   0   2   0   0   0   0   0   0   0   4   0   0   0   1  2.31 0.78
  205 V   -3 -5 -5 -5 -3 -5 -5 -6 -5  6 -1 -5 -1  1 -5 -4 -2 -4 -3  5    0   0   0   0   0   0   0   0   0  54   0   0   0   5   0   0   0   0   0  42  1.13 0.79
  206 Y   -4 -4 -4 -5 -5 -3 -4 -5  2 -3 -3 -4 -3  1 -5 -4 -4  0  9 -3    0   0   0   0   0   0   0   0   4   0   0   0   0   0   0   0   0   0  96   0  2.18 0.83
  207 V   -2 -5 -5 -5  1 -4 -5 -3 -5  1 -1 -4 -1 -3 -4 -4 -2 -5 -3  7    1   0   0   0   3   0   0   2   0   1   2   0   0   0   0   0   1   0   0  90  1.27 0.87
  208 A    6 -4 -3 -4  0 -3 -3 -1 -4 -3 -4 -3 -3 -3 -1  0  0 -5 -4 -2   82   0   0   0   2   0   0   3   0   0   0   0   0   1   3   4   4   0   0   0  1.09 0.88
  209 I   -3 -5 -5 -5  0 -5 -5 -6 -5  7 -1 -5  1 -2 -5 -4 -3 -5 -3  3    0   0   0   0   2   0   0   0   0  78   0   0   2   0   0   0   0   0   0  18  1.36 0.90
  210 G   -2 -5 -3 -4 -5 -4 -4  7 -4 -5 -6 -4 -5 -5 -4 -2 -4 -5 -5 -2    0   0   0   0   0   0   0  96   0   0   0   0   0   0   0   0   0   0   0   4  1.91 0.93
  211 Q   -3 -1 -2 -2 -5  8  0 -4  0 -5 -3 -1 -2 -5 -3 -2 -1 -4 -3 -4    0   0   0   0   0  92   0   0   2   0   3   0   0   0   0   0   4   0   0   0  1.72 0.93
  212 K   -3  4 -2 -3 -6 -1 -2 -4 -3 -5 -5  7 -4 -5 -3 -3 -3 -5 -4 -5    0  17   0   0   0   0   0   0   0   0   0  83   0   0   0   0   0   0   0   0  1.59 1.04
  213 R    3  5 -1 -1  0  1 -1 -1 -3 -2 -3  0 -2 -3 -4  0 -2 -5 -4 -4   27  36   2   3   2   7   4   3   0   2   1   3   1   1   0   6   2   0   0   0  0.60 1.04
  214 S    1 -3 -2 -2 -3 -2 -2 -1 -3 -4 -4 -2 -3 -4 -3  6  1 -4 -4 -3    8   0   0   0   0   0   1   4   0   0   1   0   0   0   0  76   6   0   0   1  1.11 0.99
  215 T    0 -3  0 -3 -3 -1 -1 -2 -3 -3 -3 -1 -3 -4 -3  3  6 -4 -2 -3    8   0   3   0   0   1   3   2   0   0   1   3   0   0   0  22  52   0   2   1  0.82 0.99
  216 V   -2 -4 -5 -5 -3 -4 -4 -3 -5  3 -1 -4  0 -3 -4 -4 -2 -4 -3  6    2   0   0   0   0   0   0   3   0  16   3   0   2   0   0   0   0   0   0  70  1.15 1.08
  217 G    5  2 -2 -4 -3 -1 -2 -2 -3 -2 -1 -2 -1 -4 -3 -1 -2 -4 -4 -1   63  12   2   0   0   3   2   1   0   2   5   2   1   0   0   2   1   0   0   3  0.80 1.15
  218 Q    0  1  2 -1 -4  6  0 -1  1 -4 -3  0 -3 -5 -4  0 -1 -4 -4 -3    8   8   9   2   0  45   4   4   3   0   2   3   0   0   0   6   4   0   0   2  0.75 1.17
  219 L   -1 -4 -2 -5 -3 -1 -4 -5 -5  4  2 -4  0 -1 -4 -2 -1 -4 -3  4    6   0   2   0   0   3   0   0   0  24  22   0   2   2   0   3   3   0   0  31  0.65 1.16
  220 I   -2 -2 -4 -4  0 -1 -1 -5 -1  2 -1 -2 -2 -3 -4 -2 -1 -4  1  6    3   2   0   0   2   3   3   0   2   7   4   2   0   0   0   2   2   0   6  56  0.70 1.19
  221 Q   -1  1  2  0 -5  4  2 -2  0 -4 -2  3 -3 -5 -4 -1  1 -5 -4 -4    5   7   8   4   0  19  15   3   2   0   3  19   0   0   0   3   7   0   0   0  0.44 1.12
  222 T    0  0 -1 -3 -4  1 -1 -4 -4  3 -1  1  0 -4 -4  0  3 -5 -4  0    8   6   3   0   0   6   4   0   0  22   4   9   3   0   0   5  23   0   0   5  0.37 1.12
  223 L   -3 -5 -5 -5 -4 -4 -5 -6 -5  2  4 -5 -1  3  2 -4 -3 -4 -2  1    0   0   0   0   0   0   0   0   0  11  53   0   0  13  12   0   0   0   0  10  0.86 0.94
  224 E    0  3  0  0 -4  1  2 -4  2 -1 -4  0 -3 -5  2  1  0 -5 -4 -1    7  16   4   4   0   7  16   0   5   4   0   4   0   0  10  13   4   0   0   4  0.32 0.94
  225 E   -1  0  1  2 -5  2  5 -2  0 -5 -5  2 -4 -5 -4 -1 -1 -5 -4 -2    4   5   5  13   0   7  40   2   2   0   0  11   0   0   0   4   2   0   0   4  0.66 1.00
  226 A    2  0  3 -3 -4 -1  0 -2  3 -4 -2  1 -1  1 -4 -1  1 -4  2 -2   20   6  15   0   0   2   7   2   9   0   4   8   2   5   0   2   8   0   8   2  0.31 1.00
  227 N   -1 -4  2  3 -5 -1 -1  6  0 -6 -6 -1 -5 -5 -4 -1 -3 -5 -5 -5    3   0   8  16   0   3   3  57   3   0   0   3   0   0   0   4   0   0   0   0  1.04 1.00
  228 A    6 -4 -4 -4  3 -3 -3 -2 -4 -3 -4 -3 -3 -4 -3  1 -2 -5 -4  0   76   0   0   0   7   0   0   0   0   0   0   0   0   0   0  10   0   0   0   7  1.13 1.00
  229 L    0 -4 -5 -5 -4 -4 -5 -5 -4  1  3 -4  6  1  0  0 -3 -4  2  0    9   0   0   0   0   0   0   0   0   6  33   0  21   6   6   7   0   0   6   7  0.65 1.17
  230 E    0  0  0  1 -5  2  4 -1  3 -5 -2  0 -4  2  0 -1 -1 -5 -3 -4    7   4   4   8   0   9  29   4   6   0   4   5   0   9   5   4   4   0   0   0  0.41 1.17
  231 Y    1  1  0 -4 -4 -2 -3 -4  3 -3 -3  1 -3  2 -4 -2 -3 -1  7 -3   12  10   6   0   0   0   0   0   7   0   0  10   0   5   0   0   0   0  51   0  0.91 0.67
  232 S   -2 -3 -3 -3  3 -3 -3 -4 -4  1  1 -3 -2 -3  1  1  5 -4 -3  1    0   0   0   0   7   0   0   0   0   7  16   0   0   0   7  10  45   0   0   7  0.58 0.67
  233 I    1 -4 -4 -4  3 -3 -4 -4 -4  4  0 -3 -1 -3 -4  1  1 -4 -3  3   11   0   0   0   7   0   0   0   0  31   7   0   0   0   0  11  10   0   0  23  0.51 0.67
  234 L   -3 -4 -4 -4 -3 -3 -4 -4 -4  3  2 -4  4  3 -4 -3 -2 -3 -1  2    0   0   0   0   0   0   0   0   0  17  17   0  17  17   0   0   0   0   0  17  0.40 0.56
  235 V   -2 -4  2 -4 -3 -3 -4 -5 -4  3 -1 -4  4 -3 -4 -3 -2 -5 -3  5    0   0  13   0   0   0   0   0   0  15   0   0  13   0   0   0   0   0   0  60  0.87 0.72
  236 A    4 -3  0 -3  2 -3 -1 -3 -3  0 -1 -3  1  0 -3  1  0 -4 -3  1   44   0   6   0   5   0   5   0   0   5   5   0   5   5   0   9   5   0   0   8  0.40 0.72
  237 A    5 -1 -3 -3 -3 -2  0  1 -3 -3 -4 -2 -3 -4 -3  1  1 -4 -4 -2   66   3   0   0   0   0   7   7   0   0   0   0   0   0   0   9   7   0   0   0  0.76 0.70
  238 T    1 -3  1 -2 -3 -2  0  0  0 -2 -3 -2  0 -4  1  1  4 -4 -3 -2   15   0   8   0   0   0   6   8   3   2   2   0   2   0   6  10  39   0   0   0  0.47 0.70
  239 A    4 -3 -2  1 -2 -2 -2  1 -3 -3 -3 -2 -3 -4  2  1 -2 -4 -3 -2   56   0   0   9   0   0   0  10   0   0   0   0   0   0   9   9   0   0   0   0  0.54 0.56
  240 S    2 -3  3  3 -3 -2 -2  2 -2 -4 -4 -2 -3 -4 -3  2  2 -5 -4 -3   17   0  17  17   0   0   0  17   0   0   0   0   0   0   0  17  17   0   0   0  0.50 0.56
  241 D    1 -3  2  2 -4  2  1 -3 -2 -4 -4 -2 -3  2 -4  1  1 -3  3 -4   11   0  11  11   0  11  11   0   0   0   0   0   0  11   0  11  11   0  11   0  0.41 0.89
  242 P    2 -3 -3 -3  2 -2  0 -3 -3 -3 -1 -2  1 -4  5  3 -2 -5 -4 -3   16   0   0   0   5   0   5   0   0   0   7   0   5   0  32  30   0   0   0   0  0.74 0.67
  243 A    5 -3 -3  0 -2 -3 -2 -2 -3 -3 -1 -3 -2 -4  2  1 -2 -4 -4  0   64   0   0   6   0   0   0   0   0   0   6   0   0   0  11   8   0   0   0   6  0.71 0.67
  244 P    2 -3 -3 -3 -3 -3 -3  0 -4 -1 -4 -3 -3 -4  6  1  2 -5 -4 -1   16   0   0   0   0   0   0   8   0   4   0   0   0   0  43  10  15   0   0   5  0.92 0.67
  245 L    1 -4 -4 -4  4 -3  1 -4 -3  2  1 -4  4  3  2 -3 -3 -3  3 -2   11   0   0   0  11   0  11   0   0  11  11   0  11  11  11   0   0   0  11   0  0.48 0.89
  246 Q   -2  0 -1 -2 -4  7  0 -4  2 -1 -2  1 -2 -4 -2 -1 -1 -4 -3 -2    0   2   2   0   0  74   0   0   4   4   3   5   0   0   2   2   2   0   0   2  1.06 0.63
  247 F   -3 -4 -1 -5 -4 -3 -4 -5 -1 -2 -2 -4  1  5 -5 -3 -3  5  7 -1    0   0   4   0   0   0   0   0   0   0   0   0   4  28   0   0   0   7  52   6  1.26 0.63
  248 L   -3 -4 -5 -5 -3 -4 -5 -5 -4  3  4 -4  1  1 -2 -4 -3 -3  2  0    0   0   0   0   0   0   0   0   0  23  59   0   3   4   2   0   0   0   7   3  0.78 0.63
  249 A    3 -2 -1 -2 -2 -1 -1 -1 -2 -1 -2 -1 -2 -3 -2  4  2 -4 -3  1   31   0   0   0   0   0   0   0   0   0   0   0   0   0   0  44  13   0   0  13  0.44 0.28
  250 P    3 -3 -3 -3 -2 -2 -2 -2 -3  0 -1 -2 -1 -3  5 -1 -1 -4 -3  3   33   0   0   0   0   0   0   0   0   0   0   0   0   0  33   0   0   0   0  33  0.65 0.22
  251 Y   -3 -3 -3 -4 -3 -2 -3 -4  0 -1  1 -3  3  4 -4 -3 -2  1  7 -1    0   0   0   0   0   0   0   0   0   0  13   0  13  14   0   0   0   0  61   0  0.90 0.28
  252 S    1 -4 -3 -3  5 -3 -3  2 -4 -2 -3 -3 -3 -4  3  2  2 -4 -4  1   14   0   0   0  14   0   0  14   0   0   0   0   0   0  14  14  14   0   0  14  0.51 0.67
  253 G    1 -3 -2 -3 -3 -3 -3  6 -3 -4 -4 -3 -4 -4 -3  1 -2 -4 -4 -4   14   0   0   0   0   0   0  69   0   0   0   0   0   0   0   8   0   0   0   0  1.05 0.59
  254 C    1 -4 -4 -4  8 -3 -4 -4 -4  0 -2 -4  1  0 -4  0  1 -4 -3  2   12   0   0   0  42   0   0   0   0   4   0   0   4   4   0   5   7   0   0  20  0.89 0.59
  255 A    4 -3 -2 -3  2 -2 -3 -2 -3 -2  0 -2 -2 -3 -3  2  3 -4 -3  0   41   0   0   0   5   0   0   0   0   0  11   0   0   0   0  20  20   0   0   4  0.51 0.58
  256 M   -1 -3 -4 -4 -2 -3 -4 -4 -3  4  2 -3  6  1 -4 -3 -2 -3 -2  1    6   0   0   0   0   0   0   0   0  38  11   0  34   6   0   0   0   0   0   6  0.61 0.37
  257 G    2 -3 -2 -3  3 -3 -3  5 -3 -4 -4 -2 -3 -4 -3  1 -2 -4 -4 -3   23   0   0   0   8   0   0  60   0   0   0   0   0   0   0   8   0   0   0   0  0.88 0.37
  258 E   -2 -1 -1  0 -5  3  6 -3 -1 -4 -4  2 -3 -4 -2 -1 -2 -4 -3 -4    0   0   0   0   0  12  77   0   0   0   0  11   0   0   0   0   0   0   0   0  1.01 0.37
  259 Y    0 -3  2 -3 -4  2  1 -4  4 -4  0 -3 -3  2 -4  1 -3  6  3 -4   10   0  10   0   0  10  10   0  10   0  10   0   0  10   0  10   0  10  10   0  0.50 1.00
  260 F   -3 -4 -4 -5 -4 -4 -4 -4 -3  0  0 -4 -1  6  0 -1 -3  6  3  0    0   0   0   0   0   0   0   0   0   6   6   0   0  49   6   6   0  13   7   6  0.90 0.56
  261 R    2  3 -3 -3 -2 -1 -2 -3 -2 -1  2 -1  5 -2 -3 -2 -2 -3 -2 -1   25  25   0   0   0   0   0   0   0   0  25   0  25   0   0   0   0   0   0   0  0.41 0.33
  262 D   -2 -1  0  5  0 -3  0 -4  1 -4 -4  1  0  0 -4 -2 -3  3  5 -2    3   3   3  34   2   0   5   0   3   0   0   8   2   3   0   3   0   3  25   2  0.74 1.04
  263 N   -1  1  4  0 -5  3 -1 -1  1 -2 -3  2 -3 -5 -4  1  0 -5 -4 -4    6   8  24   4   0  15   3   3   3   3   3  14   0   0   0  12   4   0   0   0  0.47 1.04
  264 G   -1 -1 -3 -3 -5 -3 -1  6  0 -6 -6 -1 -5 -5  0 -1 -4 -5 -5 -5    3   4   0   0   0   0   5  73   3   0   0   3   0   0   5   3   0   0   0   0  1.30 1.04
  265 M    0  1  1  1 -5  2  1  0 -3 -4 -1  1  3 -4 -4  0  1 -5  2 -4    8   8   8   8   0   8   8   8   0   0   8   8   8   0   0   8   8   0   8   0  0.23 1.33
  266 H    1  2  2  2 -4 -2 -2 -3  4 -5 -5  2 -4 -5  3  1 -2 -5 -3 -4   13  13  13  13   0   0   0   0  13   0   0  13   0   0  13  13   0   0   0   0  0.52 0.78
  267 A    1  2 -2  2  5 -3 -3  1 -3 -3 -3 -2 -3 -4 -4  1  2 -5 -4  1   13  13   0  13  12   0   0  13   0   0   0   0   0   0   0  13  13   0   0  12  0.39 0.78
  268 L   -2 -4 -4 -4  5 -3 -4 -4 -4  2  1 -4  4  3 -4  1 -2 -3 -2  2    0   0   0   0  14   0   0   0   0  14  14   0  14  14   0  14   0   0   0  14  0.55 0.67
  269 I   -1 -4 -4 -4  1 -4 -4 -5 -4  5  1 -4  1 -2 -4 -3  2 -4 -1  2    3   0   0   0   3   0   0   0   0  53  12   0   3   0   0   0  16   0   3   9  0.69 0.62
  270 I   -1 -4 -4 -5  3 -4 -4 -3 -4  5 -1 -4  2  1 -4 -2 -2 -4 -2  4    3   0   0   0   6   0   0   2   0  38   0   0   5   6   0   2   0   0   0  36  0.66 0.62
  271 Y   -3 -2 -2 -3 -3 -2 -2 -4  6  0  0 -3 -2  2 -4 -2  0 -1  5 -2    0   0   0   0   0   0   0   0  32   7   7   0   0   9   0   0   7   0  30   0  0.66 0.39
  272 D   -3 -2  0  6 -5  4  1 -3 -2 -4 -4 -1 -3 -5 -3 -1 -2 -5 -4 -4    0   0   0  68   0  32   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.12 0.39
  273 D   -1 -2  0  5 -4 -1  0  4 -2 -4 -4 -1 -3 -4 -2 -1 -2 -4 -4 -4    0   0   0  50   0   0   0  50   0   0   0   0   0   0   0   0   0   0   0   0  0.79 0.11
  274 L   -2  3 -3 -4 -3 -2 -3 -4 -3  0  4 -2  0 -2  2 -3 -2 -3 -3  1    0  23   0   0   0   0   0   0   0   0  52   0   0   0  13   0   0   0   0  13  0.52 0.39
  275 S    1 -2 -1 -2 -2 -2 -2 -2 -2 -3 -3 -2 -3 -4  4  4  2 -4 -3 -2   10   0   0   0   0   0   0   0   0   0   0   0   0   0  23  46  12   0   0   0  0.58 0.39
  276 K   -2  3  3 -1 -4  3 -1 -2 -1 -4 -4  3 -3 -4 -3  2 -1 -4 -3 -4    0  20  20   0   0  20   0   0   0   0   0  20   0   0   0  20   0   0   0   0  0.60 0.44
  277 Q   -3  0 -1 -2 -5  6  0 -3  6 -5 -4  3 -2 -4 -3 -2 -2 -4 -2 -4    0   0   0   0   0  54   0   0  22   0   0  25   0   0   0   0   0   0   0   0  1.12 0.63
  278 A    5 -3 -2 -3 -2 -2 -2 -2  5 -3 -3 -2 -3 -4 -3  2 -2 -4 -2 -2   67   0   0   0   0   0   0   0  19   0   0   0   0   0   0  14   0   0   0   0  0.90 0.63
  279 V   -1 -1 -3 -1  1  0 -1  2 -4  0 -2 -3  0 -3 -4 -1 -1  3 -1  4    4   3   0   3   3   5   3  19   0   4   0   0   2   0   0   3   3   5   3  41  0.37 0.63
  280 A    5 -3 -3 -4  6  0 -3 -1 -3 -3 -3 -3 -3 -4 -3  0  0 -4 -4 -1   59   0   0   0  20   4   0   4   0   0   0   0   0   0   0   6   4   0   0   4  0.82 0.64
  281 Y   -3 -3 -3 -5 -4 -3 -4 -5  4  1  2 -3 -1  1 -4 -3 -3  0  7 -2    0   0   0   0   0   0   0   0  11   8  21   0   0   0   0   0   0   0  59   0  1.11 0.58
  282 R    2  4 -2 -2 -3 -1 -1 -2 -2 -3 -3  0 -2 -4  5 -1 -1 -4 -3 -2   33  33   0   0   0   0   0   0   0   0   0   0   0   0  33   0   0   0   0   0  0.74 0.22
  283 Q    0 -2 -2 -2 -3  3  1 -3  2  3 -2  0 -2 -3 -3  2  1 -4 -3 -1    7   0   0   0   0  20   9   0   6  23   0   6   0   0   0  23   7   0   0   0  0.34 0.50
  284 M   -2 -4 -4 -5  4 -3 -4 -5 -4  4  2 -4  5 -2 -4 -3  1 -4 -3  2    0   0   0   0  11   0   0   0   0  28  18   0  25   0   0   0   8   0   0   9  0.67 0.56
  285 S    1 -3 -2 -3  3 -2 -2 -2 -2 -2 -3 -2 -2 -3 -3  4  3 -3  2  0    9   0   0   0   8   0   0   0   0   0   0   0   0   0   0  49  17   0   8   9  0.58 0.56
  286 L   -3 -4 -5 -5 -3 -4 -4 -5 -4  2  5 -4  1  3 -4 -4 -3 -3 -2  0    0   0   0   0   0   0   0   0   0  10  78   0   0  11   0   0   0   0   0   0  0.92 0.52
  287 L   -3 -3 -3  1 -3 -3 -3 -4 -4  1  4 -3  0  1 -4 -2  1 -3 -2  0    0   0   0  11   0   0   0   0   0   3  64   0   0   6   0   2  10   0   0   3  0.59 0.52
  288 L   -2 -4 -4 -4 -3 -3 -4 -4 -4  0  4 -4  1  3  2 -3  0 -3 -1  0    3   0   0   0   0   0   0   0   0   3  52   0   2  18  11   0   8   0   0   3  0.59 0.52
  289 R   -3  6  1 -2 -5  0 -1 -3  2 -4 -4  3 -3 -4 -3 -2 -2 -4 -3 -4    0  66   8   0   0   0   0   0   5   0   0  22   0   0   0   0   0   0   0   0  1.09 0.52
  290 R   -3  7 -2 -2 -5  2  1 -4 -2 -4 -4  3 -3 -4 -3 -2 -2 -4 -3 -4    0  72   0   0   0   6  10   0   0   0   0  12   0   0   0   0   0   0   0   0  1.12 0.49
  291 P   -2 -3 -3 -3 -4 -2 -2 -3 -3 -4 -4 -2 -4 -5  8 -2 -2 -5 -4 -4    0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0  2.48 0.40
  292 P   -1 -3 -3 -3 -4 -2 -2 -3 -3 -4 -3 -2 -3 -5  8 -1  0 -5 -4 -3    2   0   0   0   0   0   0   0   0   0   2   0   0   0  89   2   5   0   0   0  2.07 0.38
  293 G    0 -3 -2 -2 -4 -3 -3  6 -3 -5 -5 -3 -4 -4 -3 -1 -3  2 -4 -4    2   0   0   0   0   0   0  91   0   0   0   0   0   0   0   2   0   4   0   0  1.39 0.38
  294 R   -2  7 -1 -3 -4  0 -1 -3 -1 -4 -3  2 -2 -4 -3 -2  1 -4 -3 -3    0  88   0   0   0   0   0   0   0   0   0   3   0   0   0   0   9   0   0   0  1.17 0.38
  295 E   -2  1 -1  0  3  1  6 -3 -1 -4 -4  0 -3 -4 -2 -1 -2 -4 -3 -3    0   6   0   0   8   0  84   0   0   0   0   2   0   0   0   0   0   0   0   0  1.00 0.36
  296 A    5 -3 -2 -3 -2 -2 -2  2 -3 -3 -3 -2 -2 -4  2  0 -1 -4 -3 -2   72   0   0   0   0   0   0  16   0   0   0   0   0   0   9   0   2   0   0   0  0.70 0.36
  297 F   -3 -3 -3 -4 -3 -3 -3 -4  0  1 -1 -3 -1  4 -4 -2 -2  1  7 -1    0   0   0   0   0   0   0   0   0  11   0   0   0  20   0   2   0   0  68   0  1.06 0.30
  298 P   -2 -3 -3 -2 -4 -2 -2 -3 -3 -3 -3 -2  2 -4  8 -1 -2 -4 -4 -3    0   0   0   0   0   0   0   0   0   0   0   0  11   0  86   3   0   0   0   0  1.90 0.30
  299 G   -1 -3 -1 -2 -4 -3 -3  7 -3 -5 -5 -2 -4 -4 -3 -1 -3 -3 -4 -4    0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0  1.47 0.30
  300 D   -3 -2  1  7 -5 -1  1 -2 -2 -4 -5 -1 -4 -5 -2 -1 -2 -5 -4 -4    0   0   0  95   0   0   5   0   0   0   0   0   0   0   0   0   0   0   0   0  1.36 0.30
  301 V   -1 -3 -4 -4 -2 -3 -3 -4 -4  3  0 -3  0 -2 -3 -1 -1 -4 -2  5    0   0   0   0   0   0   0   0   0  22   0   0   0   0   0   5   0   0   0  73  0.67 0.30
  302 F   -2 -3 -3 -3 -3 -3 -3 -3 -2 -1  0 -3 -1  7 -3 -3 -2  0  2 -1    1   1   1   1   0   1   1   1   0   1   4   1   0  85   1   1   1   0   0   1  0.99 0.24
  303 Y   -3 -3 -3 -4 -3 -2 -3 -4  2 -2 -2 -3 -2  3 -4 -3 -3  1  8 -2    0   0   0   0   0   0   0   0   2   0   0   0   0   6   0   0   0   0  93   0  1.40 0.30
  304 L   -2 -3 -4 -4 -1 -3 -4 -4 -4  2  5 -3  1 -1 -3 -2 -2 -3 -2  1    2   0   0   0   1   0   0   0   0   8  78   0   0   0   1   2   0   0   0   8  0.65 0.30
  305 H   -3 -1  0 -2 -4  0 -1 -3  9 -4 -4 -2 -2 -2 -3 -2 -3 -3  1 -4    0   0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0   0   0  1.57 0.28
  306 S    1 -2  0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3 -2  5  1 -4 -3 -2    8   0   0   0   0   0   0   0   0   0   0   0   0   0   0  92   0   0   0   0  0.78 0.28
  307 R   -2  7 -1 -2 -4  0 -1 -2 -1 -4 -3  2 -2 -4 -3 -1 -2 -4 -3 -3    0  92   0   0   0   1   0   2   0   0   0   1   0   0   0   4   0   0   0   0  1.10 0.28
  308 L   -2 -3 -4 -4 -2 -3 -4 -5 -4  1  5 -3  1  0 -1 -2 -2 -3 -2  0    0   0   0   0   0   0   0   0   0   0  96   0   0   0   2   2   0   0   0   0  0.77 0.28
  309 L   -2 -3 -3 -4 -2 -3 -3 -4 -3  1  5 -3  1 -1 -3  1 -1 -3 -2  0    0   0   0   0   0   0   0   0   0   0  84   0   0   0   0  16   0   0   0   0  0.61 0.27
  310 E   -2 -1 -1  1 -5  1  6  1 -1 -4 -4  0 -3 -4 -2 -1 -2 -4 -3 -4    0   0   0   0   0   0  88  11   0   0   0   1   0   0   0   0   0   0   0   0  0.97 0.29
  311 R   -2  7 -1 -3 -4  0 -1 -3 -1 -4 -3  1 -2 -4 -3 -2 -2 -4 -3 -4    0 100   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.26 0.29
  312 A    5 -2 -2 -2  0 -1  1 -1 -2 -3 -3 -1 -2 -3 -1  2 -1 -4 -3 -1   72   0   0   0   1   0  11   1   0   0   0   0   0   0   2  13   0   0   0   1  0.57 0.29
  313 A    5  1 -2 -3  1 -1 -2 -1 -2 -2 -2 -1 -2 -3 -2  1 -1 -4 -3  0   74  11   0   0   3   0   0   1   0   0   1   0   0   0   0   6   1   0   0   4  0.55 0.29
  314 K   -2  3 -1  1 -4  1  0 -3  0 -4 -3  5 -2 -4 -2 -1 -2 -4 -3 -3    0  13   0  11   0   4   0   0   2   0   0  69   1   0   0   0   0   0   0   0  0.75 0.31
  315 R   -2  1 -4 -4 -2 -2 -3 -4 -2  1  4 -2  3  0 -4 -3 -2 -2  2  2    0  11   0   0   0   0   0   0   0   3  49   0  12   0   0   0   0   0  12  13  0.45 0.31
  316 S    0 -2  4  2 -2 -1 -1 -1 -1 -2 -3 -1 -3 -3 -2  4  0 -4 -3 -3    2   1  27  11   1   0   1   1   1   2   1   1   0   0   0  49   2   0   0   0  0.54 0.33
  317 D    0 -1  0  5 -4  0  2 -2  3 -4 -4  0 -3 -4  0  0  0 -4 -2 -3    8   1   3  41   0   3  13   1  10   0   0   6   0   0   4   2   6   0   0   0  0.53 0.36
  318 Q    0  2  1  2 -4  3  4 -2 -1 -3 -3  1 -3 -4 -2  0 -1 -4 -3 -2    6  12   6  13   0  13  30   1   1   0   1   9   0   0   0   4   1   0   0   3  0.44 0.40
  319 T   -2 -1  3 -2 -2 -1 -2  0  4 -2  2  1  0  0 -3 -1  1 -3  0 -2    1   1  20   1   1   1   0   7  12   1  22  12   2   3   0   1  13   0   2   1  0.25 0.47
  320 G    0 -3 -2 -3 -4 -2 -3  6 -3 -5 -5  1 -4 -4 -3 -1 -3 -4 -4 -3    4   0   0   0   0   1   0  84   0   0   0   9   0   0   0   1   0   0   0   1  1.27 0.47
  321 A    2 -3 -1 -2 -2 -2 -1  5 -3 -4 -4 -2 -3 -4 -3  0  1 -4 -4 -3   19   0   1   0   0   1   3  62   0   0   0   1   0   0   0   4  10   0   0   0  0.89 0.47
  322 G   -1 -4 -2 -3 -4 -3 -3  7 -3 -5 -5 -3 -4 -5 -3 -1 -3 -4 -4 -5    0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0  1.65 0.46
  323 S    0 -2  0 -1 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2  6  0 -4 -3 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0  1.04 0.44
  324 L   -3 -3 -4 -5 -2 -3 -4 -5 -4  3  5 -4  3 -1 -4 -3 -1 -3 -2  0    0   0   0   0   0   0   0   0   0  21  64   0   9   0   0   1   3   0   0   1  0.74 0.44
  325 T   -1 -2 -1 -2 -2 -2 -2 -3 -3 -2 -2 -2 -2 -3 -2  0  7 -4 -3 -1    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0  1.16 0.44
  326 A    6 -3 -3 -3  2 -2 -2  0 -3 -3 -3 -2 -2 -4 -2  0 -1 -4 -3 -1   93   0   0   0   4   0   0   2   0   0   0   0   0   0   0   1   0   0   0   0  0.91 0.43
  327 L   -3 -4 -5 -5 -3 -4 -4 -5 -4  1  5 -4  1  1 -4 -4 -2 -3 -2  0    0   0   0   0   0   0   0   0   0   4  91   0   0   6   0   0   0   0   0   0  0.94 0.43
  328 P   -2 -3 -3 -3 -4 -2 -2 -3 -3 -4 -4 -2 -4 -5  8 -2 -2 -5 -4 -4    0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0  2.49 0.42
  329 V   -2 -4 -4 -4 -2 -3 -4 -4 -4  5  0 -3  1  0 -4  0 -1 -4 -2  3    0   0   0   0   0   0   0   0   0  58   0   0   4   3   0   8   0   0   0  27  0.70 0.43
  330 I   -1 -4 -4 -4 -2 -3 -4 -5  2  6  0 -4  0 -1 -4 -3 -2 -4 -2  2    5   0   0   0   0   0   0   0   8  77   0   0   1   0   0   0   0   0   0   9  0.81 0.43
  331 E   -2  1 -1  0 -5  1  6 -3 -1 -5 -4  0 -3 -5 -2 -1 -2 -4 -3 -4    0   9   0   0   0   2  88   0   0   0   0   1   0   0   0   0   0   0   0   0  1.16 0.42
  332 T   -1 -2  2 -2 -2 -2 -2 -3 -3 -1 -2 -2 -2 -3 -2  0  6 -4 -3 -1    0   0  10   0   0   0   0   0   0   2   0   0   0   0   0   0  88   0   0   0  0.96 0.41
  333 Q   -2  0 -1 -1 -4  7  1 -3 -1 -3  0  0 -1 -4 -3 -1 -2 -3 -3 -3    0   0   0   2   0  75   6   0   0   0  14   3   1   0   0   0   0   0   0   0  0.92 0.42
  334 A    5 -3 -2 -2 -2 -1 -1  1 -3 -2 -3 -2 -2 -3 -2  1 -1 -4 -3  1   69   0   1   1   0   1   4   9   0   0   0   0   0   0   0   6   0   0   0   9  0.61 0.42
  335 G   -1 -3  3  0 -4 -1 -3  6 -3 -5 -5 -2 -4 -4 -3 -1 -2 -4 -4 -4    0   0  15   4   0   2   0  77   0   0   0   0   0   0   0   1   0   0   0   0  1.18 0.43
  336 D   -3 -2  2  7 -5 -1  1 -2 -2 -4 -5  1 -4 -5 -3 -1 -2 -5 -4 -4    0   0   7  82   0   0   2   0   0   0   0   9   0   0   0   0   0   0   0   0  1.26 0.42
  337 V   -1 -4 -4 -5 -2 -4 -4 -5 -4  3  1 -4  0 -2 -4 -3 -1 -4 -2  6    0   0   0   0   0   0   0   0   0   8   8   0   0   0   0   0   0   0   0  84  0.87 0.42
  338 S    0 -2 -1 -2 -1 -1 -1 -2 -2 -3 -4  1 -3 -4 -2  5  1 -4 -3 -3    3   0   0   0   0   0   0   0   0   0   0   9   0   0   0  81   7   0   0   0  0.80 0.42
  339 A    6 -3 -3 -3 -2 -2 -2  0 -3 -3 -3 -2 -2 -3 -2  0 -1 -4 -3 -1   97   0   0   0   0   0   0   2   0   0   0   0   0   0   0   2   0   0   0   0  0.94 0.42
  340 Y   -3 -3 -4 -4 -4 -3 -3 -4  0 -2 -2 -3 -2  5 -4 -3 -3  1  8 -2    0   0   0   0   0   0   0   0   0   0   0   0   0  21   0   0   0   0  79   0  1.47 0.41
  341 I   -2 -4 -4 -4 -2 -4 -4 -5 -5  6  0 -4  0 -1 -4 -3 -1 -4 -2  3    0   0   0   0   0   0   0   0   0  88   0   0   0   0   0   0   1   0   0  11  0.97 0.41
  342 P   -1 -3 -3 -3 -4 -2 -2 -3 -3 -4 -4 -2 -4 -5  8 -1 -2 -5 -4 -3    2   0   0   0   0   0   0   0   0   0   0   0   0   0  93   3   0   0   0   1  2.23 0.41
  343 T   -1 -2 -1 -2 -2 -2 -2 -3 -3 -2 -2 -2 -2 -3 -2  0  7 -4 -3 -1    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0  1.10 0.40
  344 N   -3 -1  8  0 -4 -1 -1 -2  0 -4 -5 -1 -3 -4 -3  0 -1 -5 -3 -4    0   0  99   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0  1.39 0.39
  345 V   -1 -4 -4 -4 -2 -3 -4 -4 -4  2  1 -3  0 -2 -4 -3 -1 -4 -2  6    1   0   0   0   0   0   0   0   0   2   8   0   1   0   0   0   0   0   0  89  0.85 0.39
  346 I   -2 -4 -5 -4 -2 -4 -4 -5 -5  7  1 -4  0 -1 -4 -4 -2 -4 -2  2    0   0   0   0   0   0   0   0   0  98   2   0   0   0   0   0   0   0   0   0  1.03 0.39
  347 S    0 -2  0 -1 -2  0 -1 -1 -2 -4 -4 -1 -3 -4  0  6  0 -4 -3 -3    0   0   0   0   0   2   0   0   0   0   0   0   0   0   4  94   0   0   0   0  0.90 0.39
  348 I   -2 -4 -4 -4 -2 -4 -4 -5 -4  6  1 -4  0 -1 -4 -3 -1 -4 -2  2    0   0   1   0   0   0   0   0   0  96   2   0   0   0   0   0   1   0   0   0  0.99 0.39
  349 T   -1 -2 -1 -2 -2 -2 -2 -3 -3 -2 -1 -2 -2 -3 -2  0  6 -4 -3 -1    2   0   0   0   0   0   0   0   0   0   4   0   0   0   0   0  93   0   0   0  0.96 0.38
  350 D   -3 -3  0  7 -5 -1  0 -1 -2 -4 -4 -2 -1 -4 -3 -1 -2 -5 -4 -4    0   0   0  93   0   0   0   3   0   0   0   0   4   0   0   0   0   0   0   0  1.36 0.38
  351 G    0 -3 -1 -2 -4 -3 -3  7 -3 -5 -5 -3 -4 -4 -3 -1 -3 -4 -4 -4    4   0   0   0   0   0   1  95   0   0   0   0   0   0   0   0   0   0   0   0  1.44 0.38
  352 Q   -2  0 -1 -1 -4  7  1 -3  3 -4 -3  1 -2 -4 -2 -1 -2 -3 -2 -3    0   0   0   0   0  85   0   0   8   0   0   4   0   0   0   0   0   0   0   0  1.13 0.40
  353 I   -2  0 -4 -4 -1 -3 -4 -5 -4  6  1 -3  0 -1 -4 -3 -1 -3  0  1    0   8   0   0   1   0   0   0   0  79   5   0   0   0   0   0   1   0   4   1  0.74 0.40
  354 C   -3 -3 -4 -4  3 -4 -4 -4 -2 -1 -1 -4 -1  7 -4 -3 -3  0  5 -1    0   2   0   0   7   0   0   0   0   0   0   0   0  67   0   0   0   0  19   4  1.09 0.40
  355 L   -2 -3 -4 -4 -2 -3 -4 -4 -4  0  5 -3  1  2 -2 -2 -1 -2 -2  0    0   0   0   0   0   0   0   0   0   0  81   0   2   8   1   3   3   0   0   1  0.73 0.40
  356 E   -1 -1  1  1 -4  1  5 -2 -1 -4 -4  0 -2 -4 -2  2 -1 -4 -3 -3    0   0   8   6   0   5  58   1   0   0   1   4   0   0   0  15   1   0   0   1  0.72 0.40
  357 T    1  1 -1 -2 -2 -1 -1 -2 -2 -2 -3 -1 -2 -3  0  3  5 -4 -3 -2   11   8   0   1   0   0   1   1   0   0   0   2   0   0   4  25  45   0   0   0  0.52 0.42
  358 E    0 -2  2  4 -4  0  4 -1  0 -4 -4 -1 -3 -4 -2  0 -1 -4 -3 -3   11   0  12  34   0   1  31   2   1   0   0   1   0   0   0   5   1   0   0   0  0.65 0.42
  359 L   -2 -3 -4 -5 -2 -3 -4 -5 -4  1  5 -4  1 -1 -4 -3 -2 -3 -2  1    0   0   0   0   0   0   0   0   0   1  87   0   1   0   0   0   0   0   1   8  0.87 0.43
  360 F   -2 -4 -4 -5 -3 -4 -4 -4 -3 -1  1 -4 -1  8 -4 -3 -3  0  2 -2    2   0   0   0   0   0   0   0   0   0  13   0   0  82   0   0   0   0   1   0  1.23 0.43
  361 Y   -1 -1  5 -1 -3 -2 -1 -2  0 -3 -2 -2 -2  1 -3  1 -1 -2  4 -3    6   3  45   0   0   0   2   0   1   0   4   0   0   6   0   9   2   0  22   0  0.59 0.43
  362 R    2  2 -1 -2 -3  3 -1 -1 -2 -3 -3  1 -2 -4 -2  3 -1 -4 -3 -3   20  14   0   0   0  14   0   3   0   0   2   9   0   0   0  35   1   0   0   0  0.43 0.43
  363 G   -1 -3  1 -2 -4 -2 -3  6 -3 -5 -5 -2 -4 -4 -3 -1 -3 -4 -4 -4    0   1   6   0   0   1   0  89   0   0   0   0   0   0   0   0   0   0   0   1  1.36 0.44
  364 I   -2 -3 -3 -3 -3  2 -2 -4 -3  5  1 -3  0 -1 -3 -3 -1 -3 -2  3    0   0   1   0   0  16   0   0   0  51   5   0   0   2   0   0   1   0   0  22  0.58 0.44
  365 R   -2  7 -2 -3 -4  0 -1 -3 -1 -3 -2  2 -2 -4 -3 -2 -2 -4 -3 -3    0  86   0   0   0   0   0   0   0   1   3   7   0   0   0   0   0   0   0   0  1.21 0.44
  366 P   -2 -3 -3 -3 -4 -2 -2 -3 -3 -4 -4 -2 -4 -5  8 -2 -2 -5 -4 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0  96   0   0   0   0   0  2.34 0.43
  367 A    6 -2 -3 -3 -2 -2 -2 -1 -3 -2 -3 -2 -2 -3 -2  0 -1 -4 -3 -1   95   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0  0.93 0.43
  368 I   -2 -4 -4 -4 -2 -3 -4 -4 -4  5  0 -3  1 -1 -4 -3 -2 -4 -2  4    0   0   0   0   0   0   0   0   0  56   2   0   3   0   0   0   0   0   0  36  0.79 0.43
  369 N   -3 -2  7  3 -4 -1 -1 -2  0 -5 -5 -1 -4 -4 -3  0 -1 -5 -4 -4    0   0  77  20   0   0   0   0   1   0   0   0   0   0   0   1   0   0   0   0  1.23 0.45
  370 V    1 -4 -4 -4 -2 -3 -3 -4 -4  1 -1 -3 -1 -3  3 -2 -1 -4 -3  5   11   0   0   0   0   0   0   0   0   4   0   0   0   0  18   1   1   0   0  65  0.69 0.44
  371 G   -1 -4 -2 -3 -4 -3 -3  7 -3 -5 -5 -3 -4 -4 -3 -1 -3 -4 -4 -4    1   0   0   0   0   0   0  98   0   0   0   0   0   0   0   1   0   0   0   0  1.59 0.44
  372 L   -2 -3 -4 -4 -3 -3 -4 -5 -4  4  4 -2  0 -1 -4 -2 -2 -3 -2  1    0   1   0   0   0   1   0   0   0  32  55   2   0   1   0   2   1   0   0   5  0.67 0.45
  373 S    0 -2 -1 -1 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -1  6  0 -4 -3 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0   1  99   0   0   0   0  1.02 0.44
  374 V   -1 -4 -4 -4 -2 -3 -4 -4 -4  2  0 -4  0 -2 -4 -3 -1 -4 -2  6    1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  98  0.99 0.44
  375 S    0 -2 -1 -1 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2  6  1 -4 -3 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  96   4   0   0   0  1.00 0.44
  376 R   -3  7 -2 -3 -5  0 -1 -4 -1 -4 -3  1 -3 -4 -3 -2 -2 -4 -3 -4    0 100   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.46 0.43
  377 V   -1 -4 -4 -5 -2 -4 -4 -5 -4  2  0 -4  0 -2 -4 -3 -1 -4 -2  6    0   0   0   0   0   0   0   0   0   4   0   0   0   0   0   0   0   0   0  96  0.99 0.43
  378 G   -1 -4 -2 -3 -4 -3 -3  7 -3 -5 -5 -3 -4 -4 -3 -1 -3 -4 -4 -4    0   0   0   0   0   0   0  98   0   0   0   0   0   0   0   2   0   0   0   0  1.58 0.43
  379 S    0 -3 -1 -2 -3 -2 -2  5 -3 -4 -4 -2 -3 -4 -3  4 -1 -4 -4 -4    0   0   0   0   0   0   0  49   0   0   0   0   0   0   0  51   0   0   0   0  0.91 0.42
  380 A    4 -2  0  0 -2 -1 -1 -1 -2 -3 -3  0 -2 -4 -2  3 -1 -4 -3 -2   57   0   3   4   0   0   0   0   0   0   0   7   0   0   0  28   0   0   0   0  0.60 0.42
  381 A    6 -3 -3 -3 -2 -2 -2 -1 -3 -3 -3 -2 -2 -3 -2  0 -1 -4 -3 -1   99   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0  0.96 0.42
  382 Q   -2  0 -1 -1 -4  8  1 -3 -1 -4 -3  0 -2 -5 -2 -1 -2 -3 -3 -3    0   0   0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.36 0.42
  383 L   -2 -2 -2 -3 -1 -2 -3 -4  1  4  1 -3  0 -1 -1 -1  3  1 -1  1    1   2   1   0   1   1   0   0   4  33  16   0   1   1   3   2  29   2   2   4  0.36 0.43
  384 K   -1  1 -1  0 -4  0  0 -2 -2 -4 -4  6 -3 -4  1 -1 -1 -4 -2 -3    4   1   1   3   0   1   0   2   0   0   0  77   0   0   7   1   1   0   1   1  0.83 0.45
  385 A    5 -3 -3 -3  0 -2 -2  0 -3  1 -2 -2 -2 -3 -2  1 -1 -4 -3  0   72   0   0   0   1   1   0   3   0  12   1   0   0   0   0   5   0   0   0   4  0.62 0.45
  386 M   -2 -3 -4 -4 -3 -2 -4 -4 -3  2  1 -3  8 -1 -4 -3 -1 -3  0  0    0   0   0   0   0   0   0   0   0  15   6   0  72   0   0   0   1   0   3   3  0.99 0.45
  387 K   -2  3 -1 -2 -4  0  0 -3 -2 -4 -4  6 -3 -4 -2 -1 -2 -4 -3 -4    0  12   1   0   0   0   0   0   0   0   0  87   0   0   0   1   0   0   0   0  1.09 0.45
  388 Q   -1  0 -1 -1 -4  5  1 -2 -2 -4 -2  5 -1 -4 -2 -1 -2 -4 -3 -3    3   0   1   0   0  33   5   2   0   0   3  48   1   0   0   2   0   0   0   1  0.71 0.46
  389 V   -2 -4 -4 -5 -2 -3 -4 -5 -4  2  2 -4  0 -2 -4 -3 -1 -4 -2  5    0   0   0   0   0   1   0   0   0   5  18   0   0   0   0   0   1   0   0  75  0.81 0.46
  390 C    4 -1 -2 -3  4 -2 -2  0 -3 -3 -3 -2 -2 -4 -2  3  0 -4 -3 -2   48   3   0   0  10   0   0   6   0   0   0   0   0   0   0  30   2   0   0   0  0.60 0.46
  391 G    0 -3 -2 -3 -4 -3 -3  7 -3 -5 -5 -1 -4 -4 -3 -1 -3 -4 -4 -4    4   0   0   0   0   0   0  89   0   0   0   3   0   0   0   3   0   0   0   0  1.39 0.46
  392 S   -1  1  0 -1 -3 -1 -2  1 -2 -4 -4  1 -2 -4  2  3  2 -4 -3 -3    1   8   4   2   0   1   0  13   0   0   0  10   0   0   9  35  17   0   0   0  0.43 0.46
  393 S   -2 -3 -4 -5 -3 -3 -4 -5 -4  3  4 -4  3 -1 -4 -1 -2 -3  0  1    0   0   0   0   0   0   0   0   0  16  58   0   9   0   0   5   0   0   2   9  0.65 0.46
  394 K   -2  5 -1 -2 -4  0 -1 -3 -2 -4 -4  6 -3 -4 -3 -2 -1 -4 -3 -4    0  34   0   0   0   0   0   0   0   0   0  63   0   0   0   0   3   0   0   0  1.01 0.47
  395 L   -2 -3 -4 -5 -3 -3 -4 -2 -4  1  5 -4  1 -1 -1 -3  0 -3 -2  0    1   0   0   0   0   0   0   3   0   6  78   0   1   0   3   0   7   0   1   1  0.72 0.47
  396 E    0 -2 -1  3 -4  0  5 -3 -2 -1 -1 -1 -2 -3 -3 -1 -1 -4 -3 -3   11   0   1  20   0   2  51   0   0   4   5   0   1   1   0   2   2   0   0   0  0.63 0.47
  397 L   -3 -3 -4 -5 -3 -2 -4 -5 -2  1  5 -4  1  0 -4 -3 -2 -2  3 -1    0   0   0   0   0   2   0   0   1   2  79   0   1   0   0   1   0   0  15   0  0.82 0.48
  398 A    6 -3 -2 -3 -2 -2 -2 -1 -3 -3 -3 -2 -2 -4 -2  2 -1 -4 -3 -2   84   0   0   0   0   0   0   0   0   0   0   0   0   0   0  15   1   0   0   0  0.89 0.47
  399 Q   -1  0 -1 -2 -4  7  1 -3 -1 -4 -3  0 -1 -4 -3  0 -2 -3 -3 -3    3   0   1   0   0  89   2   0   0   0   1   0   1   0   0   4   0   0   0   0  1.23 0.47
  400 Y   -3 -3 -4 -5 -4 -3 -4 -4  0 -2 -2 -3 -2  5 -4 -3 -3  1  8 -2    0   0   0   0   0   0   0   0   0   0   0   0   0  24   0   1   0   0  75   0  1.50 0.47
  401 R   -1  6 -1 -1 -4  0  0 -3 -1 -3 -2  1 -2 -4 -3 -1 -2 -2 -3 -2    5  73   1   3   0   1   5   0   0   0   4   1   0   0   0   1   0   0   0   3  0.92 0.48
  402 E   -2 -1 -1  1 -5  1  7 -3 -1 -5 -4  0 -3 -5 -2 -1 -2 -4 -3 -4    1   0   0   2   0   0  94   0   0   0   0   1   0   0   0   1   1   0   0   0  1.29 0.48
  403 V   -2 -3 -4 -5 -3 -3 -4 -5 -4  1  5 -3  4 -1 -4 -3 -2 -3 -1  2    0   0   0   0   0   0   0   0   0   1  62   0  16   0   0   0   0   0   2  17  0.76 0.49
  404 A    4 -2 -2 -1 -3  2  4 -2 -2 -3 -2  0 -2 -4 -2  0 -2 -4 -3 -2   47   0   0   2   0  10  30   0   0   1   2   5   0   0   0   2   0   0   0   1  0.56 0.49
  405 A    5 -2 -2 -2 -2 -2 -1 -1 -3 -3 -3 -2  1 -4 -2  2  0 -4 -3 -1   71   2   0   0   0   0   3   0   0   0   0   0   4   0   0  16   3   0   0   1  0.70 0.49
  406 F   -3 -4 -4 -3 -4 -4 -4 -4 -3 -1  0 -4 -1  8 -5 -2 -3  0  2 -2    0   0   0   2   0   0   0   0   0   0   4   0   0  90   0   3   0   0   0   1  1.41 0.49
  407 A    5 -3 -2 -2 -2 -2 -1 -1 -3 -3 -2 -2 -2 -4 -2  3  0 -4 -3 -2   60   0   0   0   0   0   2   0   0   0   4   0   0   0   0  31   3   0   0   0  0.69 0.49
  408 Q   -2  1 -1  0 -4  7  1 -3 -1 -4 -3  1 -1 -5 -3 -1 -2 -4 -3 -3    2   6   0   3   0  79   1   0   0   0   0   7   1   0   0   0   1   0   0   2  1.10 0.50
  409 F   -3 -4 -4 -5 -4 -4 -5 -3 -3 -1  0 -4 -1  8 -5 -2 -3  0  2 -2    0   0   0   0   0   0   0   2   0   0   3   0   0  92   0   3   0   0   0   0  1.47 0.49
  410 G    3 -3 -2 -2 -3 -3 -3  6 -3 -4 -4 -3 -3 -4 -3  0 -2 -4 -4 -3   26   0   0   1   0   0   0  67   0   0   0   0   0   0   0   6   0   0   0   0  1.07 0.49
  411 S    0 -2  1 -2 -2 -1 -2  0 -2 -4 -4 -2 -3 -4 -2  6  1 -4 -3 -3    4   0   4   0   0   1   0   5   0   0   0   0   0   0   0  83   2   0   0   0  0.88 0.49
  412 D   -2 -2  0  7 -5  0  1 -3 -2 -4 -3 -2 -4 -2 -3 -1 -2 -5 -4 -4    3   1   1  82   0   3   4   0   0   0   2   1   0   2   0   1   0   0   0   0  1.25 0.50
  413 L   -2 -4 -5 -5 -3 -3 -4 -3 -4  1  5 -4  1 -1 -2 -4 -1 -3 -2  0    1   0   0   0   0   0   0   2   0   3  88   0   1   0   2   0   2   0   0   2  0.90 0.50
  414 D   -3 -3  0  7 -5  0  1 -1 -2 -5 -5 -2 -4 -5 -3 -2 -2 -6 -4 -5    0   0   0  93   0   2   1   3   0   0   0   0   0   0   0   0   0   0   0   0  1.53 0.50
  415 A    4 -1 -2  2 -3  1  2 -2 -2 -3 -3  2 -3 -4  0  0 -1 -4 -3 -2   42   0   0  13   0   8  15   0   0   0   0  13   0   0   4   1   2   0   0   1  0.46 0.50
  416 A    4 -2 -1  1 -2 -2  0 -1 -1 -1 -3 -2 -2 -3 -2  2  0 -4 -3  0   47   1   3   7   0   0   7   3   1   5   0   0   0   0   0  16   3   0   0   5  0.40 0.51
  417 T   -1 -3 -1 -2 -2 -2 -2 -3 -3 -2 -2 -2 -2 -3 -1  2  6 -4 -3  0    0   0   0   0   0   0   0   0   0   0   2   0   0   0   2  10  81   0   0   4  0.96 0.51
  418 Q   -1  3 -2 -2 -4  5  0 -3 -1 -3 -2  4  0 -4 -3 -2 -2 -4 -3 -3    3  17   0   0   0  43   0   0   0   0   5  27   3   0   0   0   1   0   0   0  0.73 0.50
  419 A    3  1  1  0 -3  2  0 -1 -2 -3 -3  3 -1 -4 -2  0 -2 -4 -1 -3   34   6   7   6   0  11   3   3   0   1   1  22   1   0   0   3   0   0   2   0  0.37 0.51
  420 L   -2  2 -2 -3 -3  5 -1 -4 -2  0  2  1  1 -3 -1 -2 -1 -3 -1 -1    1  12   0   0   0  34   1   0   0   4  26   6   3   0   3   1   3   0   2   3  0.42 0.51
  421 L   -3 -4 -5 -5 -3 -4 -4 -5 -4  2  5 -4  2 -1 -3 -2 -2 -2 -3  1    0   0   0   0   0   0   0   0   0   8  80   0   3   0   1   4   0   0   0   5  0.88 0.54
  422 N    2 -2  4  1 -3  0  3 -2 -1 -1 -3 -1 -3 -4 -3  0  0 -5 -3 -1   24   0  30   7   0   2  20   0   0   5   0   1   0   0   0   4   4   0   0   3  0.46 0.54
  423 R   -3  6  0 -1 -5  1 -1 -4  3 -4 -3  2 -3 -4 -3 -2 -2 -4 -2 -4    0  70   3   3   0   6   0   0   9   1   1   7   0   0   0   0   0   0   0   0  1.06 0.54
  424 G   -1 -4 -2 -3 -4 -3 -4  7 -4 -5 -5 -3 -4 -5 -4 -2 -3 -4 -5 -5    1   0   0   0   0   0   0  99   0   0   0   0   0   0   0   0   0   0   0   0  1.69 0.53
  425 A    2  2 -1 -2 -3  3  3 -3 -1 -3 -3  2 -2 -4 -3  1 -2 -4 -2 -1   25  14   2   0   0  14  19   0   1   0   1  11   0   0   0   8   0   0   1   4  0.40 0.54
  426 R   -2  7 -2 -3 -3  0 -1 -4 -1 -3 -1  3  0 -4 -3 -2 -2 -4 -3 -3    1  75   0   0   0   0   0   0   1   1   5  13   2   0   0   0   0   0   0   0  1.11 0.54
  427 L   -2 -4 -2 -5 -3 -4 -4 -5 -4  3  4 -4  2  0 -4 -3  0 -3 -2  2    1   0   2   0   0   0   0   0   0  21  52   0   6   3   0   0   5   0   0  10  0.65 0.55
  428 T   -2  2 -1 -3 -3 -2 -3 -2 -3  0 -1 -2  2 -3 -3 -1  5 -4 -2  3    1  13   2   0   0   0   0   2   0   3   1   0   6   0   0   1  44   0   1  26  0.52 0.55
  429 E    0 -2 -2  0 -5  1  6 -3 -2 -4 -4 -1 -3 -5 -3 -1 -2 -4 -3 -3    9   0   0   0   0   2  87   0   0   1   0   1   0   0   0   0   0   0   0   2  1.18 0.55
  430 V   -3 -4 -5 -5 -3 -4 -4 -5 -4  3  4 -4  2 -1 -4 -3 -2 -3 -1  3    0   0   0   0   0   0   0   0   0  20  52   0   5   0   0   0   0   0   2  20  0.75 0.54
  431 P   -3 -4 -5 -5 -3 -4 -4 -5 -4  1  5 -4  3  2  0 -4 -2 -3 -2 -1    0   0   0   0   0   0   0   0   0   5  72   0   7   9   6   0   1   0   0   0  0.82 0.55
  432 K   -1  1  0 -2 -4  0 -1 -3 -2 -3 -4  7 -3 -5 -2 -1 -1 -5 -3 -4    3   0   3   0   0   2   0   0   0   1   0  89   0   0   0   0   1   0   0   0  1.11 0.55
  433 Q   -2  0 -1 -2 -4  8  1 -3 -1 -4 -4  0 -2 -5 -3 -1 -2 -3 -3 -4    0   0   0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.54 0.55
  434 P   -1 -1  1  2 -4 -1 -1  1 -3 -4 -4  2 -3 -2  5  1 -1 -5 -4 -3    4   1   7  10   0   1   1   9   0   0   0  20   0   2  32  11   2   0   0   1  0.64 0.55
  435 Q   -2  1 -1 -2  0  7  0 -3 -1 -1 -1  1 -2 -4 -1 -2 -2 -3 -3 -2    1   5   2   0   2  66   2   0   1   4   6   5   0   0   3   0   0   0   0   2  0.83 0.54
  436 Y   -2 -2  2 -3 -4 -2 -3 -2  3 -3 -1 -3 -2  3 -4 -1 -2  0  7 -3    3   1  13   0   0   1   0   3   6   0   3   0   0  11   0   4   2   0  53   0  0.89 0.54
  437 A    1 -1  0  0 -3  1  0 -2  1 -3 -3  0 -1 -4 -1  4  1 -4 -3 -1   12   1   4   4   0   7   6   0   3   0   0   6   1   0   2  42   7   0   0   4  0.40 0.56
  438 P   -2 -4 -3 -3 -3 -3 -3 -4 -4 -4 -4 -2 -4 -5  8 -2 -1 -5 -4 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0  96   0   3   0   0   1  2.43 0.56
  439 L   -3 -3 -4 -5 -2 -2 -4 -5 -3  1  4 -3  6  0 -3 -2 -2 -3  0  1    0   1   0   0   0   1   0   0   0   5  42   0  32   3   1   3   0   0   4   8  0.72 0.57
  440 P    0  0  0  1 -3 -1 -1 -2 -3 -3 -4 -1 -3 -2  5  3  2 -4 -2 -3    6   4   5   8   0   2   1   0   0   1   0   2   0   1  27  25  14   0   1   1  0.57 0.57
  441 I   -2 -4 -3 -4 -3 -1 -4 -5 -4  3  1 -4  0  0 -2 -3  0 -2 -2  5    0   0   1   0   0   3   0   0   0  21   9   0   2   3   2   0   5   0   0  53  0.65 0.57
  442 E    2 -2 -2 -1 -4 -1  5 -2 -2 -3 -3 -1  1 -2  1  0  0  0  0 -1   20   0   1   1   0   0  47   1   0   0   0   0   5   1   6   5   4   1   4   4  0.52 0.58
  443 K   -2 -1  1  2 -2  2  4 -3  0 -4 -3  3 -3 -4 -3 -1 -1 -4 -2 -2    0   0   5  11   1   8  39   0   2   0   2  23   0   0   0   3   2   0   1   2  0.62 0.59
  444 Q   -1 -1 -2 -2 -4  7  2 -3 -1 -3 -1  0  2 -4 -3 -2 -2 -4 -3 -3    3   0   0   0   0  78   8   0   0   1   5   0   6   0   0   0   0   0   0   0  1.12 0.59
  445 I    1 -4 -4 -4 -1 -4 -4 -2 -4  4  0 -4 -1 -2 -4 -2 -1 -4 -3  5   12   0   0   0   1   0   0   3   0  26   1   0   0   0   0   2   1   0   0  54  0.71 0.59
  446 L    2 -4 -4 -4  1 -3 -4 -2 -4  3  2 -3  0 -2 -2 -2 -1 -4 -3  3   21   0   0   0   2   0   0   2   0  18  23   0   2   0   1   1   2   0   0  27  0.45 0.59
  447 V   -1 -3 -3 -4  0 -3 -3 -4 -4  4  1 -3  1 -1 -4  2  0 -4 -3  3    1   0   0   0   2   0   0   0   0  26  15   0   3   2   0  24   5   0   0  21  0.44 0.59
  448 I   -3 -4 -5 -5 -3 -4 -5 -5 -5  5  4 -4  1  0 -4 -4 -2 -2 -2  2    0   0   0   0   0   0   0   0   0  42  45   0   1   2   0   0   0   0   0   8  0.84 0.58
  449 Y   -2 -4 -4 -5 -4 -3 -4 -3 -1 -2 -1 -4 -2  5 -5 -2 -3  3  7 -2    3   0   0   0   0   0   0   1   0   1   4   0   0  29   0   3   0   3  56   1  1.23 0.59
  450 A    5 -3 -3 -3  3 -2 -3 -1 -3 -1 -1 -2 -1 -3 -3  0  1 -4 -3 -1   71   0   0   0   6   0   0   1   0   2   6   0   1   0   0   3   9   0   0   2  0.73 0.58
  451 A    3 -4 -3 -4  2 -3 -4  4 -4  0  1 -3 -1  0 -3 -2 -2 -4 -3  1   26   0   0   0   4   0   0  34   0   5  13   0   1   4   0   0   0   0   0  12  0.48 0.59
  452 V    0 -3  1 -1 -3  0 -1 -1 -3  0 -1 -1 -1 -3 -3  0  3 -4 -3  3    8   0   8   3   0   3   4   5   0   5   3   3   0   0   0   4  22   0   0  30  0.28 0.59
  453 N   -2  2  5 -1 -4  1  2 -2  2 -5 -4  3 -3 -2 -3 -1 -1 -4 -2 -4    2  10  39   0   0   5  14   1   5   0   0  18   0   2   0   3   2   0   1   0  0.66 0.59
  454 G   -1 -2  2  0 -4 -3 -2  6 -2 -5 -5  0 -4 -5 -4 -1 -3 -4 -4 -5    1   1   9   4   0   0   1  76   0   0   1   5   0   0   0   2   0   0   0   0  1.20 0.60
  455 F   -2 -3 -4 -5 -4 -3 -4 -5  3 -2  0 -3 -2  5 -5 -3 -3  0  7 -1    3   0   0   0   0   0   0   0   6   0  11   1   0  28   0   0   0   0  46   4  1.04 0.60
  456 C   -3 -4 -5 -5  2 -4 -5 -5 -4  2  5 -4  2  2 -5 -4 -3 -3 -2  0    0   0   0   0   4   0   0   0   0  11  71   0   3   7   0   0   0   0   1   3  0.87 0.61
  457 D   -2 -1  0  6 -5 -1  0 -3 -2 -4 -3  1 -1 -5 -2 -1  0 -5 -4 -4    2   3   2  67   0   1   2   0   1   0   2  11   2   0   1   1   6   0   0   0  0.99 0.61
  458 R   -1  0  2  5 -4  0  1 -2 -2 -3 -4  2 -3 -3 -1  0 -2  0 -4 -3    4   6   9  40   0   3   5   2   0   1   1  16   0   1   2   5   1   2   0   2  0.56 0.61
  459 M   -2 -3 -5 -5 -3 -4 -4 -5 -5  5  2 -4  2  0 -4 -4 -2 -4 -2  4    1   1   0   0   0   0   0   0   0  39  16   0   6   2   0   0   0   0   1  35  0.77 0.61
  460 P    0 -2 -1  2 -4 -1  3 -3 -3 -4 -4  0 -4 -5  6 -1 -2 -5 -4 -3    8   0   2  10   0   1  24   0   0   0   0   6   0   0  45   3   0   0   0   0  1.05 0.60
  461 L   -2 -3 -3 -4 -3 -2 -3 -5 -4  2  2 -3 -1 -2  1 -2 -1 -4 -3  5    2   1   1   0   0   2   1   0   0  11  25   1   0   0   7   1   2   0   0  47  0.58 0.63
  462 D    1 -1  2  3 -4  0  3 -1 -2 -4 -4  2 -3 -5 -2  1 -1 -5 -4 -3   11   1  11  20   0   3  26   4   0   0   0  12   0   0   1  11   1   0   0   1  0.50 0.63
  463 R   -2  1  1  4 -1  2  1 -3 -1 -3 -3  3 -3 -4 -3 -1 -2 -4  0 -3    1   8   7  26   2  12   4   0   1   1   3  26   0   0   0   3   0   0   5   1  0.50 0.63
  464 I   -1 -4 -5 -5 -3 -4 -4 -5 -5  5  1 -4  1 -2 -4 -3 -2 -4 -3  4    4   0   0   0   0   0   0   0   0  48   7   0   2   0   0   0   0   0   0  40  0.91 0.64
  465 S    0  3 -2 -3 -4  2 -1  0 -3 -1 -1  2 -2 -4 -1  1  1 -4 -3 -1    8  20   1   0   0  10   3   7   0   3   7  12   0   0   3  11   7   0   0   6  0.24 0.64
  466 Q    0  2  0  3 -4  1  2 -3 -2 -4 -3  2 -3 -2 -1  1 -1 -4 -2 -3   10  14   3  16   0   6  16   0   0   1   2  14   0   1   2  10   3   0   1   0  0.37 0.64
  467 Y   -2 -4 -4 -5 -2 -4 -4 -5 -2 -1 -1 -4 -2  7 -5 -4 -4  2  5 -2    3   0   0   0   1   0   1   0   0   3   3   0   0  71   0   0   0   2  17   0  1.36 0.63
  468 E   -2  0 -2 -1 -4  1  6 -3 -2 -3 -1  2 -2 -2 -3 -2 -2 -4 -3 -3    1   3   0   0   0   2  71   0   0   1   7  11   0   2   0   1   0   0   0   1  0.92 0.64
  469 K    0  1  1  0 -4  1  1  0  0 -3 -3  3 -2 -3 -3  1  1 -4  0 -2   10   7   6   3   0   5  11   5   2   1   1  25   0   0   0  10   8   0   3   3  0.28 0.64
  470 A    2 -1 -1  2 -4  1  3  1 -3 -3 -1  1  0 -3 -3  0 -2 -4 -2 -2   17   3   2  12   0   5  19  12   0   1   8  10   3   1   0   7   1   0   1   1  0.26 0.65
  471 I   -3 -4 -5 -5 -3 -4 -5 -5 -4  3  5 -4  1  3 -5 -4 -3  0  1  0    0   0   0   0   0   0   0   0   0  16  61   0   2  12   0   0   0   1   4   3  0.83 0.65
  472 P   -2  2 -2 -4 -2 -2 -4 -5  1  2  3 -2  0  3 -3 -3 -2 -2  1  0    3  12   1   0   1   2   0   0   4  14  40   0   1  12   1   0   1   0   4   4  0.43 0.64
  473 N    1 -1  2  2 -4  1  3 -2 -1 -3 -2  0 -3 -4 -2  1  0 -4 -3 -3   14   2  10  12   0   6  24   1   1   1   5   6   0   0   1  11   4   0   0   0  0.34 0.64
  474 S   -1 -1 -1 -3 -3 -1  0 -3  4 -3 -2  1 -2  4 -4 -1 -2  2  6 -3    4   2   2   1   0   2   5   1  10   0   3  10   0  17   0   5   2   2  33   1  0.62 0.63
  475 V    0 -4 -4 -5  2 -4 -4 -4 -4  2  4 -4  2  3 -4 -3 -2 -3 -2  2    8   0   0   0   5   0   0   0   0  12  40   0   6  12   0   1   0   0   0  16  0.56 0.64
  476 K   -2  3  2  3 -4  1  0 -3  3 -3 -4  4 -3 -4 -2 -1 -1 -4 -2 -3    1  16  10  21   0   4   4   1   8   2   0  27   0   0   1   2   3   0   1   2  0.52 0.63
  477 P    2  0  1 -1 -3  1  0 -1  0 -3 -3  0 -3 -4  1  3  2 -4 -2 -2   15   4   8   3   0   5   6   3   3   0   2   5   0   0   6  26  13   0   1   1  0.31 0.64
  478 E   -1 -1  4  2 -4  2  2 -2  1 -3 -4  2 -3 -4 -3  2 -1 -5 -2 -3    2   2  23   9   0   8  17   1   3   1   0  17   0   0   0  14   2   0   1   1  0.51 0.65
  479 L    0  0  0 -1 -3  0 -1 -2  6 -2  0  3 -2 -1 -4 -2 -3 -3  3 -2    8   3   3   4   0   2   2   2  29   2   9  20   0   2   0   0   0   0  13   1  0.53 0.65
  480 L    1 -2 -1 -2 -3  0 -2  1 -3 -3  0  1 -3  0  5  1 -1 -4 -3 -3   11   1   3   0   0   5   1   9   0   0  10  10   0   4  29  12   4   0   0   1  0.47 0.64
  481 Q    0 -2 -1  4 -4  2  4 -2 -2 -3 -4  0 -3 -3 -2  0 -2 -4 -3 -3    8   0   1  29   0   8  36   2   0   2   1   5   0   1   1   5   1   0   0   0  0.66 0.63
  482 A   -2 -4 -4 -2 -2 -3 -1 -4 -2  4  3 -3 -1  1 -4 -1 -1 -3  0  2    2   0   0   2   0   0   4   0   1  31  27   1   0   7   0   5   2   0   3  14  0.44 0.64
  483 L   -2 -2 -4 -4 -1 -3 -2 -2 -4  2  4 -3  4  2 -3 -3 -3  0 -1  1    2   1   0   0   1   1   3   3   0  15  43   1  13   8   1   0   0   1   1   6  0.51 0.66
  484 K    0  1  1  2 -4  1  3 -2 -2 -4 -3  3 -3 -4 -3  0  0 -4  0 -4   10   6   5  11   0   4  25   1   0   0   2  21   0   0   0   7   4   0   4   0  0.43 0.68
  485 G    0 -1  0  1 -4  1  2  2 -1 -1 -3  1 -3 -4 -3  2  1 -3 -4 -3    8   2   4   7   0   5  13  13   1   4   2  11   0   0   0  18   8   0   0   1  0.26 0.67
  486 G   -2 -2 -3 -2 -3  0 -3 -1 -4  6  0 -2  1 -2 -4 -2  1 -4 -3  2    2   2   1   2   0   4   1   5   0  55   3   2   3   0   0   2  10   0   0   8  0.57 0.66
  487 L    1  3  1 -2 -3  1  0 -2 -2  2  1  2 -1 -1 -3 -1 -2 -4 -2 -1   11  15   9   0   0   7   4   3   0  13  13  11   1   3   0   4   1   0   0   2  0.18 0.67
  488 T   -1  0  1  1 -3 -1  2 -2 -3 -3 -4  0 -3 -4 -3  2  5 -4 -3 -3    1   4   7   6   0   0  14   2   0   0   0   6   0   0   0  18  41   0   1   0  0.57 0.68
  489 N   -2 -1  3  1 -4  0  1  3 -2 -3 -3  3 -3 -4 -2 -1  0 -5 -4 -4    2   0  15   6   0   2  11  26   0   1   3  26   0   0   1   3   4   0   0   0  0.48 0.68
  490 E   -1 -1 -1  3 -2  1  3 -2 -2 -4 -4  4 -3 -5 -2 -1  0 -5 -3 -2    3   1   2  20   1   5  23   2   0   0   0  29   0   0   1   2   7   0   1   3  0.57 0.69
  491 R   -1  0 -2 -3 -3 -3 -3 -2 -1  2  3  0  1  3 -4 -3 -2  2  2 -1    4   5   1   1   0   0   1   3   1  11  39   8   3  11   0   0   1   3   7   0  0.38 0.69
  492 K   -2 -2  3  3 -4 -1  1 -2 -2 -4 -2  1 -3 -1 -3  2  3 -4 -2 -3    1   0  17  14   0   0  10   2   0   0   4   7   0   3   0  20  19   0   1   0  0.42 0.70
  493 M    1 -2 -1  4 -4 -1  2 -2 -2 -1 -1  1 -1 -2  0 -1 -2 -3 -1 -3   12   0   1  32   0   1  17   3   0   3   8   8   2   2   4   4   0   0   3   0  0.40 0.70
  494 E   -1 -2  1  4 -5  2  4 -2 -2 -4 -4  0  0 -5  0  0 -2 -5 -4 -3    3   0   5  25   0   7  36   2   0   1   1   4   3   0   4   8   1   0   0   1  0.64 0.71
  495 P    1 -3  0  0 -3 -2 -1 -4  1  3  2 -2 -1 -2 -2  0  2 -4  0  0   13   0   6   7   0   0   3   0   3  18  18   2   0   1   2   5  13   0   3   6  0.19 0.71
  496 D    0 -2 -1  2 -4  1  5 -4 -2 -3 -3  2 -3 -3 -3 -1 -1 -5 -4  0    6   0   2  12   0   4  47   0   0   0   2  12   0   1   0   1   2   0   0  10  0.63 0.70
  497 A    3 -1  2  1 -4  1  2 -1 -2 -4 -4  3 -3 -5 -3  0  0 -5 -4 -3   25   1   9   7   0   6  12   3   0   0   0  26   0   0   0   5   4   0   0   1  0.44 0.70
  498 F    2  0 -2 -1 -1  2  0 -2 -3 -1  0  3  2  1 -3  0  0 -4 -3 -1   20   2   0   2   1  13   4   1   0   3   9  19   5   6   0   5   4   0   0   4  0.22 0.70
  499 L   -3 -4 -5 -5 -1 -4 -5 -5 -4  2  5 -4  1  2 -5 -4 -2 -3 -1  0    1   0   0   0   1   0   0   0   0  12  74   0   1   9   0   0   1   0   1   1  0.96 0.70
  500 K   -1  0  2  1 -4  0  2 -3 -2 -1 -3  5 -3 -3 -3  0  0 -5 -4 -1    3   3   9   6   0   1  11   1   0   3   1  47   0   1   0   5   5   0   0   4  0.55 0.71
  501 E    1 -2  1  2 -4  0  4 -2 -2 -4 -3  2 -3 -4 -3  0 -1 -4  0 -3   16   0   7   8   0   3  35   2   0   0   1  14   0   0   0   7   2   0   3   0  0.50 0.71
  502 R    3 -3 -1 -4  0 -3 -2 -2 -3  2  0 -3 -1  1 -4  0 -1 -4 -1  3   35   0   3   0   2   0   1   2   0  14   8   0   1   7   0   4   1   0   1  20  0.38 0.71
  503 A   -1 -4 -5 -5 -2 -3 -4 -4 -5  5  2 -1  1  0 -4 -3 -1 -4 -3  2    6   0   0   0   0   1   0   0   0  48  20   4   2   3   0   0   3   0   0  12  0.68 0.71
  504 L   -1  1  1  2 -4  2  3 -3 -2 -3 -3  3 -3 -5 -3  0  1 -5 -4 -3    4   5   7  13   0   7  22   0   0   1   3  23   0   0   0   5   8   0   0   1  0.45 0.71
  505 A    0 -1  2  2 -4  0  4 -2 -2 -4 -4  1 -1  0 -1  1  0 -5 -3 -3    7   1   9  13   0   2  32   2   0   0   0   9   1   4   3  11   5   0   0   0  0.44 0.71
  506 L   -4 -4 -5 -5 -4 -5 -5 -5 -2 -2  1 -5 -1  8 -5 -4 -4 -1  4 -2    0   0   0   0   0   0   0   0   0   0   9   0   0  75   0   0   0   0  15   1  1.51 0.69
  507 I   -2 -4 -4 -5 -2 -3 -4 -5 -4  3  3 -4  3 -1 -4 -3 -2 -4 -2  4    0   0   0   0   0   0   0   0   0  21  33   0  11   0   0   0   0   0   0  35  0.67 0.45

                      K         Lambda
Standard Ungapped    0.1349     0.3178
Standard Gapped      0.0410     0.2670
PSI Ungapped         0.1840     0.3174
PSI Gapped           0.0563     0.2670
BioPerl-1.007002/t/data/ay007676.gb000444000766000024       655213155576321 16315 0ustar00cjfieldsstaff000000000000LOCUS       AY007676                1389 bp    DNA     linear   BCT 29-OCT-2001
DEFINITION  Unknown marine gamma proteobacterium NOR5 16S ribosomal RNA,
            partial sequence.
ACCESSION   AY007676
VERSION     AY007676.1  GI:12000362
KEYWORDS    .
SOURCE      unknown marine gamma proteobacterium NOR5
  ORGANISM  unknown marine gamma proteobacterium NOR5
            Bacteria; Proteobacteria; Gammaproteobacteria.
REFERENCE   1  (bases 1 to 1389)
  AUTHORS   Eilers,H., Pernthaler,J., Peplies,J., Glockner,F.O., Gerdts,G. and
            Amann,R.
  TITLE     Isolation of novel pelagic bacteria from the German bight and their
            seasonal contributions to surface picoplankton
  JOURNAL   Appl. Environ. Microbiol. 67 (11), 5134-5142 (2001)
   PUBMED   11679337
REFERENCE   2  (bases 1 to 1389)
  AUTHORS   Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., Gerdts,G.,
            Schuett,C. and Amann,R.
  TITLE     Identification and seasonal dominance of culturable marine bacteria
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 1389)
  AUTHORS   Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., Gerdts,G.,
            Schuett,C. and Amann,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-AUG-2000) Molecular Ecology, Max-Planck-Institute,
            Celsiusstrasse 1, Bremen 28359, Germany
FEATURES             Location/Qualifiers
     source          1..1389
                     /organism="unknown marine gamma proteobacterium NOR5"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:145658"
     rRNA            <1..>1389
                     /product="16S ribosomal RNA"
ORIGIN      
        1 cgcgaaagta cttcggtatg agtagagcgg cggacgggtg agtaacgcgt aggaatctat
       61 ccagtagtgg gggacaactc ggggaaactc gagctaatac cgcatacgtc ctaagggaga
      121 aagcggggga tcttcggacc tcgcgctatt ggaggagcct gcgttggatt agctagttgg
      181 tggggtaaag gcctaccaag gcgacgatcc atagctggtc tgagaggatg atcagccaca
      241 ccgggactga gacacggccc ggactcctac gggaggcagc agtggggaat attgcgcaat
      301 gggcgaaagc ctgacgcagc catgccgcgt gtgtgaagaa ggccttcggg ttgtaaagca
      361 ctttcaattg ggaagaaagg ttagtagtta ataactgcta gctgtgacat tacctttaga
      421 agaagcaccg gctaactccg tgccagcagc cgcggtaata cggaggtgcg agcgttaatc
      481 ggaattactg ggcgtaaagc gcgcgtaggc ggtctgttaa gtcggatgtg aaagccccgg
      541 gctcaacctg ggaattgcac ccgatactgg ccgactggag tgcgagagag ggaggtagaa
      601 ttccacgtgt agcggtgaaa tgcgtagata tgtggaggaa taccggtggc gaaggcggcc
      661 tcctggctcg acactgacgc tgaggtgcga aagcgtgggg agcaaacagg attagatacc
      721 ctggtagtcc acgccgtaaa cgatgtctac tagccgttgg gagacttgat ttcttggtgg
      781 cgaagttaac gcgataagta gaccgcctgg ggagtacggc cgcaaggtta aaactcaaat
      841 gaattgacgg gggcccgcac aagcggtgga gcatgtggtt taattcgatg caacgcgaag
      901 aaccttacca ggccttgaca tcctaggaat cctgtagaga tacgggagtg ccttcgggaa
      961 tctagtgaca ggtgctgcat ggctgtcgtc agctcgtgtc gtgagatgtt gggttaagtc
     1021 ccgtaacgag cgcaaccctt gtccttagtt gccagcgcgt aatggcggga actctaagga
     1081 gactgccggt gacaaaccgg aggaaggtgg ggacgacgtc aagtcatcat ggcccttacg
     1141 gcctgggcta cacacgtgct acaatggaac gcacagaggg cagcaaaccc gcgaggggga
     1201 gcgaatccca caaaacgttt cgtagtccgg atcggagtct gcaactcgac tccgtgaagt
     1261 cggaatcgct agtaatcgtg aatcagaatg tcacggtgaa tacgttcccg ggccttgtac
     1321 acaccgcccg tcacaccatg ggagtgggtt gctccagaag tggttagcct aaccttcggg
     1381 agggcgatc
//

BioPerl-1.007002/t/data/ay116458.gb000444000766000024       442713155576321 16313 0ustar00cjfieldsstaff000000000000LOCUS       AY116458                 229 bp    DNA     linear   PLN 09-APR-2003
DEFINITION  Eucalyptus globulus subsp. bicostata isolate EgRT12 Ty1-copia
            retrotransposon reverse transcriptase-like (RT) gene, partial
            sequence.
ACCESSION   AY116458
VERSION     AY116458.1  GI:22858882
KEYWORDS    .
SOURCE      Eucalyptus globulus subsp. bicostata
  ORGANISM  Eucalyptus globulus subsp. bicostata
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; Myrtales; Myrtaceae; Eucalyptus.
REFERENCE   1  (bases 1 to 229)
  AUTHORS   Diez,J., Beguiristain,T., Le Tacon,F., Casacuberta,J.M. and Tagu,D.
  TITLE     Identification of Ty1- copia retrotransposons in three
            ectomycorrhizal basidiomycetes: evolutionary relationships and use
            as molecular markers
  JOURNAL   Curr. Genet. 43 (1), 34-44 (2003)
   PUBMED   12684843
REFERENCE   2  (bases 1 to 229)
  AUTHORS   Beguiristain,T., Diez,J., Le Tacon,F., Casacuberta,J. and Tagu,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-MAY-2002) UMR 1136 IaM Interactions
            Arbres/Micro-Organismes, INRA-Nancy, Champenoux 54280, France
FEATURES             Location/Qualifiers
     source          1..229
                     /organism="Eucalyptus globulus subsp. bicostata"
                     /mol_type="genomic DNA"
                     /isolate="EgRT12"
                     /sub_species="bicostata"
                     /db_xref="taxon:71272"
     gene            <1..>229
                     /gene="RT"
                     /note="EgRT"
     misc_feature    <1..>229
                     /gene="RT"
                     /note="similar to reverse transcriptase; unknown if
                     correctly expressed due to presence of premature
                     stopcodons and frameshifts"
     repeat_region   <1..>229
                     /transposon="Ty1-copia retrotransposon"
ORIGIN      
        1 aatgggaatt tagaggaaga ggtttatatg gaccaacccg aaggctttcc agttatagga
       61 aaggaacaca tggtatgtaa attaaagaag tcaatatatg gacttaaaca agcttcccga
      121 caatggtatc ttaagttaaa cgataccata acttcatttg gatttaagga aaacactgtt
      181 gatcggtgta tatatatgaa gattagtggg agcaagttta tttttctag
//

BioPerl-1.007002/t/data/ay149291.gb000444000766000024       423613155576321 16312 0ustar00cjfieldsstaff000000000000LOCUS       AY149291                 357 bp    DNA     linear   PRI 25-FEB-2003
DEFINITION  Homo sapiens neanderthalsensis mitochondrial D-loop hypervariable
            region I, partial sequence.
ACCESSION   AY149291
VERSION     AY149291.1  GI:28557455
KEYWORDS    .
SOURCE      mitochondrion Homo sapiens neanderthalensis
  ORGANISM  Homo sapiens neanderthalensis
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 357)
  AUTHORS   Schmitz,R.W., Serre,D., Bonani,G., Feine,S., Hillgruber,F.,
            Krainitzki,H., Paabo,S. and Smith,F.H.
  TITLE     The Neandertal type site revisited: interdisciplinary
            investigations of skeletal remains from the Neander Valley, Germany
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 99 (20), 13342-13347 (2002)
   PUBMED   12232049
REFERENCE   2  (bases 1 to 357)
  AUTHORS   Serre,D. and Paabo,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-SEP-2002) Department of Evolutionary Genetics, Max
            Planck Institute for Evolutionary Anthropology, Inselstrasse,
            Leipzig D-04103, Germany
FEATURES             Location/Qualifiers
     source          1..357
                     /organism="Homo sapiens neanderthalensis"
                     /organelle="mitochondrion"
                     /mol_type="genomic DNA"
                     /isolate="Neandertal 2"
                     /sub_species="neanderthalensis"
                     /db_xref="taxon:63221"
                     /country="Germany: Neandertal"
     D-loop          <1..>357
                     /note="hypervariable region I"
ORIGIN      
        1 gttctttcat gggggagcag atttgggtac cacccaagta ttgactcacc catcagcaac
       61 cgctatgtat ttcgtacatt actgccagcc accatgaata ttgtacagta ccataattac
      121 ttgactacct gcagtacata aaaacctaat ccacatcaac cccccccccc catgcttaca
      181 agcaagcaca gcaatcaacc ttcaactgtc atacatcaac tacaactcca aagacaccct
      241 tacacccact aggatatcaa caaacctacc cacccttgac agtacatagc acataaagtc
      301 atttaccgta catagcacat tacagtcaaa tcccttctcg cccccatgga tgacccc
//

BioPerl-1.007002/t/data/badfasta.fa000444000766000024       202513155576321 16744 0ustar00cjfieldsstaff000000000000>CEESC12R
gcacgagtccatctccatatgccaccacaacantggtcctgtcgaaccaa
caaccagcttggctcaatgacaaaatgcttcgcgcgccanaatgccaaca
aatcccgtgccaccagagccaccggcgcgatatgcagatcataccgctgg
aagacgatctcgatcgagccgtgcatccgatgggagaggaactctgaatg
gcggactccatcaccggactagcggaagtcaacggtcggatagtccacct
cacacagatgtgagctatgttcagcttcactcatccgatggaactggtag
tagtaaggaaagaantngggagcggagaacaccaccgaataaa
>CEESC13F
cttgcttgaaaaatttatataaatatttaagagaagaaaaataaataatc
gcatctaatgacgtctgtccttgtatccctggtttccattgactggtgca
ctttcctgtctttgaggacatggacaatattcggcatcagttcctggctc
tccctcctctcctggtgctccagcagaaccgttctctccattatctccct
tgtctccacgtggtccacgctctcctggtgctcctggaataccttgagct
ccctcgtgccgaattcctgcagcccgggggatccactagttctagagcgg
ccgccaccgcggtgggagctccagcttttgttncctttagtgagggttaa

tttcgagcttggcgtaatcatggtcatagctgtttcctg
>CEESC13R
gcacgagggagctcaaggtattccaggagcaccaggagagcgtggaccac
gtggagacaagggagataatggagagaacggttctgctggagcaccagga

gaggagggagagccaggaactgatgccgaatattgtccatgtcctcaaag
acaggaaagtgcaccagtcaatggaaaccagggatacaagaacagacgtc
attagatgcgattatttatttttcttctcttaaatatttatataaatttt
tcaagcaag

BioPerl-1.007002/t/data/barns-combined.nex000444000766000024     17676313155576321 20353 0ustar00cjfieldsstaff000000000000#NEXUS 

[non-conforming file, fused from two files obtained from Chuck
 Delwiche.
The first has an empty PAUP block and a DATA block, with no TAXA
 block.  The second has only a TREES block.]

BEGIN PAUP;

[!
Small subunit rRNA alignment from Barns, S.M., C.F. Delwiche,
J.D. Palmer, and N.R. Pace.  1996.  Perspectives on archaeal
diversity, thermophily and monophyly from environmental rRNA
sequences.  Proc. Natl. Acad. Sci. USA. In press.
]	
ENDBLOCK;

BEGIN DATA;
DIMENSIONS  NTAX=64 NCHAR=922;
FORMAT MISSING=- GAP="  DATATYPE=RNA ;
OPTIONS  MSTAXA=UNCERTAIN ;

MATRIX
[                     10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920]
[                     .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .  ]

E.coli       UCAGAU-UGAACGCUGGCGGCA-GGC-CUAA-CACAUGCAAGUCACGUGGCGGACGGGUGAGUAAUGUCUGGGAACUGCCUGAUGGGGGGGAUAACUACUGCGGUAGCUAAUACCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCCUGAUGCAGCCAUGCCGCGCACC-GGCUA-A-CUCCGUGCCAGCAGCCGCGGUAAUACGGAG-GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGC-ACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAGACUGCCAGUACUG-GAGGAAGGUGGGGAUGACGUCAAGUCAUC-AUGGCCCUGACCAGGGCUACACACGUGCUACAAUGCGUAGUCCGGAUUGGAGUCUGCAAGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGA-AUGCCACGGUGAAUACGUUCCCGGGCCU   [922]
Aquifex_p    UCAGCG-CGAACGCUGGCGGCG-UGC-CUAA-CACAUGCAAGUCGCGCGGCAAACGGGUGAGUAACACGUGGGUCCUACCCCCAGGGGGGGAUAACCCCGGCCGGGGCUAAUACCCUGGGGAUGGGCCCGCGGCCCAUCAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCUAUGACGGGUAGCCGGCCUGAGAGGGUGGCCGGCCACAGCGGGACUGAGACACGGCCCGCACCCCUACGGGGGGCAGCAGUGGGGAAUCGUGGGCAAUGGGCGCCUGACCCCGCGACGCCGCGGGAC-GGCUA-A-CUACGUGCCAGCAGCCGCGGUAAUACGUAG-GUCCCGAGCGUUGCGCGAAGUCACUGGGCGUAAAGCGUCCGCAGCCAGGCACGCCCGGGCAGGCGGAAUUCCCGGGGUAGCGGUGAAAUGCGUAGAUCUCGGGAGGAACACCGAAGGGGAAGCCAGCCUGCUGGGGCUGUCCUGACGGUCAGGGACGAAAGCCGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCCGGCCGUAAACCAUGGGCGCUAAGCGCCCCGCCUGGGGAGUACGGGCGCAAGCCUGAAACUCAAAGGAAUUGGCGGGGGCCCGC-ACAACCGGUGGAGCGUCUGGUUCAAUUCGAUGCUAACCGAAGAACCUUACCCGGGCAGGUGGUGCAUGGCCGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUGGACCGCCGGCGCCG-GAGGAAGGGGGGGAUGACGUCAGGUCAGU-AUGCCCUUGCCCGGGGCCACACAGGCGCUACAGUGCAUGGUGCGGAUUGGGGGCUGAAAGCCCCCAUGAAGCCGGAAUCGGUAGUAACGGGGUAUCAGCGAUGUCCCCGUGAAUACGUUCUCGGGCCU   [922]
Thermotog    UCAGGG-UGAACGCUGGCGGCG-UGC-CUAA-CACAUGCAAGUCGCGCGGCGGACGGGUGAGUAACACGUGGGUCCUGCCCUCCGGGGGGGAUAACCAGGGCCCUGGCUAAUACCCGGAGGAGGGGCCCGCGGCCCAUCAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGACGACGGGUAGCCGGCCUGAGAGGGUGGUCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUGGGGAAUCUUGGACAAUGGGGCCCUGAUCCAGCGACGCCGCGCCCC-GGCUA-A-CUACGUGCCAGCAGCCGCGGUAAUACGUAG-GGGGCAAGCGUUACCCGGAUUUACUGGGCGUAAAGGGGGCGUAGGCGGGGCGGUAGAGGGAGACGGAACUGCCGGUGUAGGGGUGAAAUCCGUAGAUAUCGGCAGGAACGCCGGUGGGGAAGCCGGUCUCCUGGGCCGACCCCGACGCUGAGGCCCGAAAGCCAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAACGAUGCCCACUAAGUGGGCCGCCUGGGGAGUACGCCCGCAAGGGUGAAACUCAAAGGAAUUGACGGGGGCCCGC-ACAAGCGGUGGAGCGUGUGGUUUAAUUGGAUGCUAAGCCAAGAACCUUACCAGGGCAGGUGGUGCACGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUGGACUGCCGGCGCCG-GAGGAAGGAGGGGAUGACGUCAGGUACUC-GUGCCCCUGCCCUGGGCGACACACGCGCUACAAUGCUCAGUUCGGAUCGCAGGCUGCAAGCCUGCGUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCU   [922]
Thermomic    UCAGGG-GGAACGCUGGCGGCG-UGC-CUAA-UGCAUGCAAGUCACGUGGCGGACGGGUGCGUAACACGUGGGGCCCUCCCGGGUGGGGGGAUAACCCGGGCUCGGGCUAAUACCGCUCGGAGGGCCCUGCGGCCUAUCAGCUAGACGGUAGGGUAACGGCCUACCGUGGCGAUGACGGGUAGCUGGUCUGAGAGGAUGGCCAGCCACACGGGCACUGAGACACGGGCCCGACUCCUACGGGAGGCAGCAGCAGGGAAUCUUCCGCAAUGGGGCCCUGACGGAGCGACGCCGCGUCCC-GGCUA-A-CUACGUGCCAGCAGCCGCGGUAAGACGUAG-GGGGCGAGCGUUACCCGGAGUCACUGGGCGUAAAGGGCGUGUAGGCAGGGCGGGAGAGGCGGGUGGAAUUCCCGGUGUAGCGGUGAAAUGCGUAGAGAUCGGGAGGAACGCCGGUGGCGAAGGCGGCCCGCUGGCCCGUACCUGACGCUGAGGCGCGAAGGCGUGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCACGCAGUAAACGAUGCGGGCGAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGC-ACAAGCAGCGGAGCGUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUACCAGGGCAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGGACUGCCGGGCCCG-GAGGAAGGAGGGGAUGACGUCAAGUCAGC-AUGGCCCUGCCCUGGGCGACACACACGCUACAGUGCGUGGUGGGGAUCGCAGGCUGCAAGCCUGCGUGAACGCGGAGUUGCUAGUAACCGCCGGUCAGCCAUACGGCGGUGAAUACGUUCCCGGGCCU   [922]
Thermus_t    UCAGGG-UGAACGCUGGCGGCG-UGC-CUAA-GACAUGCAAGUCGCGCGGCGGACGGGUGAGUAACGCGUGGGUCCUACCCGGAAGGGGGGACAACCCGGGCUCGGGCUAAUCCCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCCUGACGGAGCGACGCCGCGCGCC-GGCCA-A-CUCCGUGCCAGCAGCCGCGGUAAUACGGAG-GGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGC-ACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGGACUGCCCGCGCGG-GAGGAAGGAGGGGACGACGUCUGGUCAGC-AUGGCCCUGGCCUGGGCGACACACGUGCUACAAUGCCCAGUUCGGAUUGGGGUCUGCAAGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCU   [922]
Chlamydia    UCAGAU-UGAACGCUGGCGGCG-UGG-AUGA-GGCAUGCAAGUCACGUGGCGGAAGGGUUAGUAAUACAUAGAUUCUGUCCUCAACUGGGAAUAACGGUUGCGACCGCUAAUACCUUGAGGGAGAGUCUAUGGGAUAUCAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCUUUGACGUCUAGGCGGAUUGAGAGAUUGACCGCCAACACUGGGACUGAGACACUGCCCAGACUUCUACGGAAGGCUGCAGUCGAGAAUCUUUCGCAAUGGACGUCUGACGAAGCGACGCCGCGCACC-GGCUA-A-CUCCGUGCCAGCAGCUGCGGUAAUACGGAG-GGUGCUAGCGUUAAUCGGAUUUAUUGGGCGUAAAGGGCGUGUAGGCAGGGUAGAUGGAGAAAAGGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAUAUGUGGAAGAACACCAGUGGCGAAGGCGCUUUUCUAAUUUACACCUGACGCUAAGGCGCGAAAGCAAGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCUUGCCGUAAACGAUGCAUACUUAGUAUGCCGCCUGAGGAGUACACUCGCAAGGGUGAAACUCAAAAGAAUUGACGGGGGCCCGC-ACAAGCAGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGGCAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAGACUGCCUGGCCAG-GAGGAAGGCGAGGAUGACGUCAAGUCAGC-AUGGCCCUGCCCAGGGCUACACACGUGCUACAAUGCCCAGUUCGGAUUGUAGUCUGCAAGACUACAUGAAGUCGGAAUUGCUAGUAAUGGCGUGUCAGCUAUAACGCCGUGAAUACGUUCCCGGGCCU   [922]
Planctomy    UCAGAA-UGAACGUUGGCGGCA-UGG-AUUA-GGCAUGCAAGUCGCGCGGCGAAAGGGAGAGUAAUACGUAGGACCUACCUUCGGGCUGGGAUAGCGGCGGCUGCCGGUAAUACCCUGAAGAGGGGCCUACGUCGUAUUAGCUAGUUGGUAGGGUAAUGGCCUACCAAGGCAAAGAUGCGUAUGGGGUGUGAGAGCAUGCCCCCACUCACUGGGACUGAGACACUGCCCAGACACCUACGGGUGGCUGCAGUCGAGAAUCUUCGGCAAUGGGCGCCUGACCGAGCGAUGCCGCGGGCC-GGCUA-A-UCUCGUGCCA--AGCCGCGGUAAUACGAGA-GGCCCAAACGUUAUUCGGAUUUACUGGGCUUAAAGAGUUCGUAGGCAGGGGGAUAGAGGUAAGCGGAACUGAUGGUGGAGCGGUGAAAUGCGUUGAUAUCAUCAGGAACACCGGAGGCGAAGGCGGCUUACUGGGUCCUUUCUGACGCUGAGGAACGAAAGCUAGGGGAGCAAACGGGAUUAGAUACCCCGGUAGUCCUAGCCGUAAACGAUGAGCACUGAGUGCUCCGCCUGGGGAGUAUGGUCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCUCAC-ACAAGCGGUGGAGGAUGUGGCUUAAUUCGAGGCUACGCGAAGAACCUUACCUAGUCAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUCGGGUUAAGUCCCUUAACGAGCGAAACCCUUGGACUGCCGGUACCG-GAGGAAGGUGGGGAUGACGUCAAGUCCUC-AUGGCCUUGAUUAGGGCUGCACACGUCCUACAAUGCUCAGUUCGGAUUGCAGGCUGCAAGCCUGCAUGAAGCUGGAAUCGCUAGUAAUCGCGGGUCAGC-AUACCGCGGUGAAU-UGUUCCUGAGCCU   [922]
Leptonema    UCAGAA-CUAACGCUGGCGGCG-CGU-CUUA-AACAUGCAAGUCGCGCGGCGAACGGGUGAGUAACACGUAGGUUUUGCCCACGGAGGGGGAUAACCUUUCGGAAGGCUAAUACCCUGUGGAGAAGCCUGCGUCCGAUUAGGUAGUUGGUGAGGUAACGGCUCACCAAGCCAGCGAUCGGUAGCCGGCCUGAGAGGGUGAACGGCCACACUGGAACUGGGACACGGUCCAGACUCCUACGGGAGGCAGCAGUUAAGAAUCUUGCGCAAUGGAGCUCUGACGCAGCGACGCCGCGCACC-GGCUA-A-CUACGUGCCAGCAGCCGCGGUAAUACGUAU-GGUGCAAGCGUUGUUCGGAAUCACUGGGCGUAAAGGGUGCGCAGGCAGUCCCGGAGAGGCAGGCGGAAUUCCCGGUGUAGCGGUGAAAUGCACAGAUAUCGGGAGGAACACCAAUGGCGAAGGCAGCCUGCUGGACGGAGACUGACGCUCAUGCACGAAAGCGUGGGGAUCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCCUAAACGUUGUAGACCAAGUCUACCGCCUGGGGACUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGG-CCGC-ACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAAAAACCUUACCCGGGCAGGUGCUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUAAACUGCCGGUACCG-GAGGAAGGUGGGGAUGACGUCAAAUCCUC-AUGGCCUUGUCCGGGGCUACACACGUGCUACAAUGCUCAGUUCGGAUUGGGGUCUGCAAGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGC-AUGCCGCGGUGAAUACGUUCCCGGGCCU   [922]
Chlorobiu    UCAGGA-CGAACGCUGGCGGCG-UGC-CUAA-CACAUGCAAGUCAAUUGGCGCAAGGGUGAGUAAGGCAUAGGUUCUGCCCUUUGGCUGGCAUAACCCCGAUCGGGGACAAUACCCAAAGGAUGAGCCUAUGUUCCAUCAGGUAGUUGGUAGGGUAACGGCCUACCAAGCCAACGACGGAUAGCUGGUCUGAGAGGAUGAUCAGCCACAUUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGCGCAAUGGGCGCCUGACGCAGCAACGCCGCGCCAC-GGCUA-A-CUCUGUGCCAGCAGCCGCGGUGAUACAGGG-GUGGCAAGCGUUGUCCGGAUUUACUGGGUGUAAAGGGUGCGCAGGCAGUCUCGAAGAGGAAGAUGGAAUUUCCGGUGUAACGGUGGAAUGUGUAGAUAUCGGAAAGAACACCAGUGGCGAAGGCAGUCUUCUGGUCGAGUACUGACGCUCAGGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAAUACUAAGUAUUCCACCUGGGAAGUACGCCCGCAAGGGUGAAACUCAAAGGAAUUGACG----CC-GC-ACAAGCGGUGGAUCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUAGGCAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUAAACUGCCUACGUAGAGAGGAAGGA-GGGAUGACGUCAAGUCCUC-AUGGCCCUGCCUAGGGCCACACACGUGAUACAAUGCUCAGUCCGGAUCGGAGUCUGCAAGACUCCGUGAAGUUGGAAUCGCUAGUAAUCGCGGAUCAGC-AUGCCGCGGUGAAUGUGUUCCCGGGCCU   [922]
Flavobact    UCAGGA-U-AACGCUAGCGGGA-GGC-UUAA-CACAUGCAAGCCGGCCGGCGCACGGGUGCGUAACGCGUAUGCCUUGCCCUACUGAAAGGAUAGCCCAGAUUUGGAUUAAUACUAGUAGGAUAGGCAUGCGUAAGAUUAGAUAGUUGGUGAGGUAACGGCUCACCAAGUCGACGAUCUUUAGGGGGCCUGAGAGGGUGAACCCCCACACUGGUACUGAGACACGGACCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGACAAUGGGUGCCUGAUCCAGCCAUCCCGCGCACC-GGCUA-A-CUCCGUGCCAGCAGCCGCGGUAAUACGGAG-GGUGC-AGCGUUAUCCGGAUUUAUUGGGUUUAAAGGGUCCGUAGGCAAUUAGUUUGAAGUGGCUGGAAUGUGUAGUGUAGCGGUGAAAUGCUUAGAUAUUACGCAGAACACCAAUUGCGAAGGCAGGUCACUAAGUCUAUAUUGACGCUGAUGGAC-AAAGCGU-GGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGGAUACUUAGUAUCCCACCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCC-GC-ACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUACCAAGGCAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUAGGUUAAGUCCU-CAACGAGCGCAACCCCUAGACUGCCAAUGUUGAGAGGAAGGUGGGGACGACGUCAAGUCAUC-ACGGCCCUGUCUUGGGCUACACACGUGCUACAAUGCUCAGUUCGGAUUGGAGUCUGCAAGACUCUAUGAAGCUGGAAUCGCUAGUAAUCGCAUAUCAGCCAUGAUGCGGUGAAUACGUUCCCGGGC-U   [922]
Agrobacte    UCAGAA-CGAACGCUGGCGGCA-GGC-UUAA-CACAUGCAAGUCACGUGGCAGACGGGUGAGUAACGCGUGGGAUCUACCGUGCCCGCGGAAUAGCUCCGGCUGGAAUUAAUACCGGUAUGAUGAGCCCGCGUUGGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCCAUAGCUGGUCUGAGAGGAUGAUCAGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGCCUGAUCCAGCCAUGCCGCGCCCC-GGCUA-A-CUUCGUGCCAGCAGCCGCGGUAAUACGAAG-GGGGCUAGCGUUGUUCGGAAUUACUGGGCGUAAAGCGCACGUAGGCAGUAUGGAAGAGGUAAGUGGAAUUCCGAGUGUAGAGGUGAAAUUCGUAGAUAUUCGGAGGAACGCCAGUGGCGAAGGCGGCUUACUGGUCCAUUACUGACGCUGAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAAUGUUAAACAUUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCCCGC-ACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGCAGAACCUUACCAGCUCAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGGACUGCCGGUGCCGAGAGGAAGGUGGGGAUGACGUCAAGUCCUC-AUGGCCCUGGGCUGGGCUACACACGUGCUACAAUGCUCAGUUCGGAUUGCACUCUGCAAGAGUGCAUGAAGUUGGAAUCGCUAGUAAUCGCAGAUCAGC-AUGCUGCGGUGAAUACGUUCCCGGGCCU   [922]
Flexibact    UCAGGA-U-AACGCUAGCGGCA-GGC-CUAA-UACAUGCAAGUCACGUGGCGCACGGGUGCGUAACGCGUAUGCCCUACCUUUUACGGGGGAUAGCUCGGGCUCGAAUUAAUACCUAAAAGAUGGGCAUGCGUCUGAUUAGCUAGAUGGCGGGGUAACGGCCCACCAUGGCGAUGAUCAGUAGGGGUUCUGAGAGGAUGAUCCCCCACACUGGUACUGAGACACGGACCAGACUCCUACGGGAGGCAGCAGUAGGGAAUAUUGGACAAUGGGCGCC--AUCCAGCCAUGCCGCGCACC-GGCUA-A-CUCCGUGCCAGCAGCC-C----AUACGGAG--GUGC-AGCGUUGUCCGGAUUUAUUGGGUUUAAAGGGUGCGUAGGCAGUACGGUUGAAGUAGGCGGAAUUUAUGGUGUAGCGGUGAAAUGCAUAGAUACCAUAAAGAACACCGAUAGCGUAGGCAGCUUACUAAGCCGU-ACUGACGCUGAGGCAC-AAAGCAUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCAUGCCGUAAACGAUGAUCACUCAGUGAUCCACCUGGGGAGUACGUCCGCAAGGAUGAAACUCAAAGGAAUUGACGGGGGUC-GC-ACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUACCUGGGCAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCC--AACGAGCGCAACCCC-AGACUGCCUGCGCAGAGAGGAAGGAGGGGACGACGU--AGUCAUC-AUGGCCCUGUCCAGGGCUACACACGUGCUACAAUGCUCAGUUCGGAUUGGGGUCUGCAAGACCCUAUGAAGUUGGAAUCGCUAGUAAUCGCGUAUCAGCAAUGACGCGGUGAAUACGUUCCCGGACCU   [922]
Rhodocycl    UCAGAU-UGAACGCUGGCGGCA-UGC-CUUA-CACAUGCAAGUCACGUGGCGAACGGGUGAGUAAUGCAUCGGACAUGCCCUGAAGGGGGGAUAACGUAGCGUUACGCUAAUACCUUUGGGAGUGGCCGAUGUCGGAUUAGCUAGUUGGUGGGGUAAAAGCCUACCAAGGCAACGAUCCGUAGCGGGUCUGAGAGGAUGAUCCGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGGACAAUGGGCGCCUGAUCCAGCCAUGCCGCGCACC-GGCUA-A-CUACGUGCCAGCAGCCGCGGUAAUACGUAG-GGUGC-AGCGUUAAUCGGAAUUACUGGGCGUAAAGCGUGCGCAGGCAGUACGGCAGAGGGGGGUGGAAUUCCACGUGUAGCAGUGAAAUGCGUAGAGAUGUGGAGGAACACCGAUGGCGAAGGCAGCCCCCUGGGCCAAUACUGACGCUCAUGCACG-AAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCCUAAACGAUGUCAACUAAGUUGACCGCCUGGGGAGUACGGCGGCAAGGUUAAAACUCAAAGGAAUUGACGGGGA-CCGC-ACAAGCGGUGGAUGAUGUGGAUUAAUUCGAUGCAACGCGAAAAACCUUACCUACCCAGGUGCUGCAUGGC-GUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGAACUGCCGGUACCG-GAGGAAGGUGGGGAUGACGUCAAGUCCUC-AUGGCCCUGGGUAGGGCUUCACACGUCAUACAAUGCGUAGUCCGGAUUGCAGUCUGCAAGACUGCAUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGC-AUGUCGCGGUGAAUACGUUCCCGGGUCU   [922]
Desulfovi    UCAGAU-UGAACGCUGGCGGCG-UGC-UUAA-CACAUGCAAGUCACGUGGCGCACGGGUGAGUAACGCGUGGAUUCUGCCCUUAUGUCGGGAUAACAGUUGCGGCUGCUAAUACCGUAAGGAUGAGUCCGCGUCCCAUUAGCUUGUUGGCGGGGUAACGGCCCACCAAGGCAUCGAUGGGUAGCCGAUUUGAGAGGAUGAUCGGCCACACUGGAACUGAAACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGGCGCCUGACGCAGCGACGCCGCGCACC-GGCUA-A-CUCCGUGCCAGCAGCCGCGGUAAUACGGAG-GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGUAGGCAAUCCGGGAGAGGGUGGCGGAAUUCCAGGUGUAGGAGUGAAAUCCGUAGAUAUCUGGAGGAACAUCAGUGGCGAAGGCGGCCACCUGGACCGGUAUUGACGCUGAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCUGUAAACGAUGGAUGCUAAGCAUCCCGCCUGGGGAGUACGGUCGCAAGGCUGAAACUCAAAGAAAUUGACGGGGGCCCGC-ACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUAGGUAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUAGACUGCCCGGCCGG-GAGGAAGGUGGGGACGACGUCAAGUCAUC-AUGGCCCUGCCUAGGGCUACACACGUACUACAAUGCCCAGUCCGGAUUGCAGUCUGCAAGACUGCAUGAAGUUGGAAUCGCUAGUAAUUCGAGAUCAGC-AUGCUCGGGUGAAUGCGUUCCCGGGCCU   [922]
Gloeobact    ----GA-UGAACGCUGGCGGCG-UGC-UUAA-CGCAUGCAAGUCACGUGGCGGACGGGUGAGUAACACGUGGGAUCUGCCCUCAGGGGGGGAUAACGGCCGCGGCCGCUAAUACCCUGAGGAUGAGCCCGCGUCUGAUUAGCUAGUUGGUGGGGUAAUGGCCUACCAAGGCUACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGCCURACGGAGCAACGCCGCGCAUC-GGCUA-A-CUCCGUGCCAGCAGCCGCGGUAAUACGGAG-GAUGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGUACGUAGGCAGUGCGGUAGGGGCAAGGGGAAUUCCCGGUGUAGCGGUGAAAUGUGGAGAUAUCGGGAAGAACACCAGCGGCGAAAGCGCCUUGCUGGACCGCAACUGACGCUGAGGUACGAAAGCCAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUGGCCGUAAACGAUGGACACUAAGUGUCCCGCCUGGGGAGUACGCACGCAAGUGUGAAACUCAAAGGAAUUGACGGGGGCCCGC-ACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGCAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGGACUGCCGGUACCG-GAGGAAGGUGGGGAUGACGUCAAGUCAGC-AUGGCUCUGUCCUGGGCUACACACGUGCUACAAUGCUCAGUUCGGAUUGCAGGCUGCAAGCCUGCAUGAAGUCGGAAUCGCUAGUAAUCGCAGGUCAGC-AUACUGCGGUGAAUACGUUCCCGGGCCU   [922]
Synechoco    UCAGGA-UGAACGCUGGCGGCG-UGC-UUAA-CACAUGCAAGUCACGUGGCGGACGGGUGAGUAACGCGUGAGAUCUGCCUACAGGCGGGGACAACAGUUGCGACUGCUAAUACCCUGUAGAUGAGCUCGCGUCUGAUUAGCUAGUUGGUGGGGUAAGGGCCUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGC--GACGGAGCAACGCCGCGCCUC-GGCUA-A-UUCCGUGCCAGCAGCCGCGGUAAUACGGGA-GAGGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGCCUGCAGGCAGUAUGGUAGGGGUAGCGGGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAUAUCUGGAAGAACACCAGCGGCGAAAGCGCGCUACUGGGCCAUAACUGACGCUCAUGGACGAAAGCUAGGGGAGCGAAAGGGAUUAGAUACCCCUGUAGUCCUAGCCGUAAACGAUGAACACUAAGUGUUCCGCCUGGGGAGUACGCACGCAAGUUGGAAACUCAAAGGAAUUGACGGGGGCCCGC-ACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCACGAACUGCCGGUACCG-GAGGAAGGUGUGGACGACGUCAAGUCAUC-AUGCCCCUAUCCUGGGCUACACACGUACUACAAUGCUCAGUUCAGAUUGCAGGCUGCAAGCCUGCAUGAAGGCGGAAUCGCUAGUAAUCGCAGGUCAGC-AUACUGCGGUGAAUACGUUCCCGGGCCU   [922]
Arthrobac    UCAGGA-UGAACGCUGGCGGCG-UGC-UUAA-CACAUGCAAGUCACGUGGCGAACGGGUGAGUAACACGUGAGUCCUGCCCUUGACCUGGGAUAAGCCUGGCUGGGUCUAAUACCUUUUGGAUGGACUCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGUGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCCUGAUGCAGCGACGCCGCGCGCC-GGCUA-A-CUACGUGCCAGCAGCCGCGGUAAUACGUAG-GGCGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCAGUGAUGUAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGAUGGCGAAGGCAGGUCUCUGGGCAUUAACUGACGCUGAGGAGCGAAAGCAUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCAUGCCGUAAACGUUGGGCACUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGC-ACAAGCGGCGGAGCAUGCGGAUUAAUUCGAUGCAACGCGAAGAACCUUACCAAGGCAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGGACUGCCGGGCUCG-GAGGAAGGUGGGGACGACGUCAAAUCAUC-AUGCCCCUGUCUUGGGCUUCACGCAUGCUACAAUGCUCAGUUCGGAUUGGGGUCUGCAAGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGCCU   [922]
Heliobact    UCAGGA-CGAACGCUGGCGGCA-UGC-CUAA-CACAUGCAAGUCACGUGGCGGACGGGUGAGUAACGCGUGGACCCUACCGGAGAGGGGGGAUAACAGUCCGGGCUGCUAAUACCUUUCCGAUGGGUCCGCGUCCGAUUAGCUAGUUGGUAGGGUAAAGGCCUACCAAGGCGACGAUCGGUAGCCGGCCUGAGAGGGUGAACGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUCUUCCGCAAUGGGCGCCUGACGGAGCAAUGCCGCGCCCC-GGCUA-A-CUACGUGCCAGCAGCCGCGGUAAUACGUAG-GGGGCAAGCGUUGUCCGGAAUGACUGGGCGUAAAGCGCGUGCAGGCAGAGAUGGAGAGGAUAGCGGAAUUCCCGGUGUAGCGGUGAAAUGCGUAGAUAUCGGGAGGAACACCCGUGGCGAAGGCGGCUAUCUGGACAUUAUCUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGCACUCCGCCUGGGGAGUACGGCCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGGCCCGC-ACAAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAGACUGCCCGGCCGG-GAGGAAGGCGGGGAUGACGUCAAAUCAUC-AUGCCCCUGUCUUGGGCUACACACGUGCUACAAUGCCCAGUUCGGAUUGCUCUCUGCAAGAGAGCAUGAAGGCGGAAUCGCUAGUAAUCGCGGGUCAGC-AUACCGCGGUGAAUACGUUCCCGGGCCU   [922]
Clostridi    UCAGGA-CGAACGCUGGCGGUA-UGC-UUAA-CACAUGCAAGUCACGUGGCGAACGGGUGAGUAACGCGUGGGUCCUGCCUCAUGGAAGGAAUAGCCUCGGCUGGGAGUAAAGCCCAUGAGAUGGACCCGCGUCCCAUUAGCUAGUUGGUGAGAUAACAGCCCACCAAGGCAACGAUGGGUAACCGGUCUGAGAGGGCGAACGGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGGGCCCUGACGCAGCAAUACCGCGUCCC-GGCUA-A-CUACGUGCCAGCAGCCGCGGUAAUACGUAG-GGGACAAGCGUUGUCCGGAAUCACUGGGCGUAAAGGGCGCGUAGGCAGUACUGGAGAGGCAAGUGGAAUUCCUAGUGUAGCGGUGAAAUGCGUAGAUAUUAGGAGGAACACCGGUGGCGAAGGCGGCUUGCUGGACAGAUACUGACGCUGAGGUGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAUGACUAAGUCAUCCGCCUGGGGAGUACGACCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGACCCGC-ACAAGCAGCGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGGACUGCCGUAUACG-GAGGAAGGUGGGGACGACGUCAAAUCAUC-AUGCCCCUGGCCUGGGCUACACACGUGCUACAAUGCCCAGUUCGGAUUGCAGGCUGAAAGCCUGCAUGAAGUUGGAGUUGCUAGUAAUCGCAGAUCAGA-AUGCUGCGGUGAAUGCGUUCCCGGGUCU   [922]
Bacillus     UCAGGA-CGAACGCUGGCGGCG-UGC-CUAA-UACAUGCAAGUCGCGCGGCGGACGGGUGAGUAACACGUGGGUCCUGCCUGUAAGCUGGGAUAACUCCGGCCGGGGCUAAUACCUUACAGAUGGACCCGCGGCGCAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCAACGAUGCGUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGACGUCUGACGGAGCAACGCCGCGCCAC-GGCUA-A-CUACGUGCCAGCAGCCGCGGUAAUACGUAG-GUGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGGGCUCGCAGGCAGUGCAGAAGAGGAGAGUGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAACACCAGUGGCGAAGGCGACUCUCUGGUCUGUAACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUCAAAGGAAUUGACGGGGGCCCGC-ACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGUCAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGGACUGCCGGUACCG-GAGGAAGGUGGGGAUGACGUCAAAUCAUC-AUGCCCCUGACCUGGGCUACACACGUGCUACAAUGCUCAGUUCGGAUCGCAGUCUGCAAGACUGCGUGAAGCUGGAAUCGCUAGUAAUCGCGGAUCAGC-AUGCCGCGGUGAAUACGUUCCCGGGCCU   [922]
pSL_17       GGACCC-C-ACUGCUAUCGGGGUGGGACUAA-GCCAUGCGAGUUGCGCGGCGGACGGCUCCGUAACACGUAGCCCCUACCCUCAGGCGGGAAUAACCCCGGCUGGGGCUAAUUCCCUGAGGAUGGGGCUGCGGCCGAUCAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCUAUAACCGGUACGGGCCGUGAGAGCGGGAGCCCGGAGAUGGGUACUGAGACAAGGACCCAGGCCCUACGGGG-GCAGCAGGCGCGAAAACUCCGCAAUGCGCGCGUGACGGGGCUACCCCGAGGGGAGGGCAA-GUCGG-GUGUCAGCCGCCGCGGUAAUAC-CCGCUCCCCGAGUGGUGGGGACGAUUAUUGGGCUUAAAGCGUCCGUAGCCGGGGCGGGAGAGGCCGGCGGUAUUCCCGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGAGGACCGCCGGUGGCGAAGGCGGCCGGCCAGAACGCGCCCGACGGUGAGGGACGAAAGCUGGGGGAGCGAUCCGGAUUAGAUACCCGGGUAGUCCCAGCCGUAAACGAUGCGGGCUAAGCCCGCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGAAGCUUGCGGUUCAAUUGGAGUCAACACCGGGAACCUUACCGGGGGAGGAGGUGCAUGGCCGUCGCCAGUUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGCAACGAUCGAGACCCGCGGACUGCCGCCGGCG-GAGGAAGGGGCGGGCUACGGCAGGUCAGU-AUGCCCCGCCCCCGGGCCACACGCGAGCUGCAAUGCUCAGUUGGGAUCGAGGGCUGCAAGCCCUCGUGAACAUGGAAUCCCUAGUAAUCGCGCGUCAUC-AACGCGCGGUGAAUACGUCCCCGCUCCU   [922]
pSL_22       GGACCC-G-ACUGCUAUCAGGGUGAGACUAA-GCCAUGCGAGUCACGUGGCGCACGGCUCAGUAAUACACGGUCCCUACCCUUAGGCGCGGAUAACCGCGGCUGCGGAUAAUCCGCUAAGGAUGGGACCGUGCCCGAUCAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCUAAGACCGGUGCGGGCCGUGGGAGCGGGAGCCCGGAGAUGGACCCUGAGACAAGGGUCCAGGCCCUACGGGG-GCAGCAGGCG-GAAAACUCCGCUAUGCGCGCGCGACGGGGUCACCCUGAGGGGAGGGCAA-GUCUG-GUGUCAGCCGC-G-GGUAAUAC-CAGCUCCCCGAGUGGUCGGGGCGAUUAUUGGGCCUAAAGCGUCCGUAGCCGGGGCGGGAGAGGCUGGCGGUAUUCCCGAGGGAGGGGCGAAAUCCUGAGAUCUCGGGAGGACCACCAGUGGCGAAGGCGGCCAGCUGGAACGCGCCCGACGGUGAGGGACGAAAGCCGGGGGAGCGAACCGGUUUAGAUACCCGGGUAGUCCCGGCCGUAAACGAUGCGGGCUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGAUGCUGCGGUUUAAUUGGAGUCAACCCCGGGAACCUUACCAGGGGAGGAGGUGCAUGGCCGUCGCCAGCUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGCAACGAGCGAGACCCCCGGACUGCCGCCGGCG-GAGGAAGGAGGGGGCUACGGCAGGUCAGU-AUGCCCCGCCCCUGGGCCACACGCGGCAUACAAUGCUCAGUUGGGAUCGAGGGUUGCAAACCCUCGUGAACCCGGAAUCCCUAGUAACUSCGCGUCACC-AACGCGCGGUGAAUACGUCCCUGCUCCU   [922]
pSL_50       GGACAU-G-ACCGCUGUCGGGGUGGGACUAA-GCCAUGCGAGUCACGUGGCGCACGGCUCCGUAAAACGUGGCUACUACCCCCAGGCGAGAAUAACCCCGGCUGGGGCUAAUUCUCUGGGGAUGUGGCCACGGCCUAUCAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAUGACGGGUACGGGCCCUGAGAGGGGGAGCCCGGAGAUGGCCACUGAGACAAGGGGCCAGGCCCUACGGGG-GCAGCAGGCGCGAAACCUCCGCAAUGGGCGCCCGACGGGGUCACCUCGAGCGGGGGGCAA-GUCUG-GUGUCAGCCGCCGCGGUAACAC-CAGCCCCGCGAGUGGUCAUGACGUUUAUUGGGCUUAAAGCAUCCGUAGCCGGGGUGGGAGAAGCCGGGGGUACUCCAGGGGUAGGGGCAAAAUCCUAUAAUCCCUGGAGGACCACCAGUGGCGAAGGCGCCCGGCUAGAACACGCCCGACGGUGAGGGAUGAAAGCUGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCCAGCUGUAAACGAUGCAGGCUAAGCCUGCCGCCUGGGGAGUACGGUCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGGGCACCACAAGGGGUGAAUGCUGCGGUUUAAUUGGAGUCAACGCCGGGAACCUUACCAGGGGAGGAGGUGCAUGGCCGUCGCCAGUUCGUGCCGUGAGGUGUCCGGUUAAGUCCGGAAACGAACGAGACCCCUAGACUGCCGGCGUCG-GAGGAAGGAGGGGGCUACGGCAGGUCAGU-AUGCCCCGCCCCUGGGCUACACGCGGCAUGCAAUGCUAAGUUGGAAUCGAGGGCUGCAAGCCCUCGUGAAUACGAAAUCCCUAGUAACCGCGUGUCAUC-AUCGCGCGGUGAAUACGUCCCUGCCCCU   [922]
pJP_78       GGAGGG-A-ACCCCUAUCGGGUUCAGACUAA-GCCAUGCAAGUCGCGCGGCGCACGGCUCAGUAAUACGCGGUCCCUACCCUGGGGCCGGGAUAACCUCGGCUGAGGCUAAUCCCCCCAGGAUGGGACCG-GGCCUAUCAGGUAGUAGGUGGGGUAACGGCCCACCUAGCCUACGACGGGUACGGGCCCUGAGAGGGGGA-CCCGGAGAUGGGCACUGAGACAAGGGUCUAGGCCCUAAGGGGUGCAGCAGGCGCGAAGAUUCCGCAAUGCCCGGGCGACGGAGUGAACCCGAGGGGAGGGCAA-GGCUG-GUGGCAGCCGCCGCGGUAAAAC-CAGCUCCCCGAGGGGUUCCCACGCAUACUGGGCCUAAAGCGUCCGUAGCCGGAGCGGGAGGAGCCGGGGGUAUUCCCGGGGGAGCGGUAAAAUGCGUAGAUCCCGGGAGGACCACCAGUGGCGAAGGCGCCCGGCUUGAACGCGUCCGACGGUGAGGGACGAAAGCUGGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCCAGCCGUAAACGAUGCCGGCUAAGCCGGCCGCCUGAGGAGUACGGCCGCAAGGCUGAAACUUGAAGGAAUUGACGGGGGGGCACCACAAGGGGUGAAGCCUGCGGCUUAAUUGGACUCAACGCCGGGAAUCUUACCGGGGGGGGUGGUGCAUGGCCGUCGCCAGCUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGCAACGAGCGAGACCCCCGGACCGCCUCCGGAG-GAGGAAGGUGGGGGCUACGGCAGGUCAGU-AUGCCCCUCCCCCGGGCCGCACGCGGGCUGCAAUGCGUAGUUGGGAUCGAGGGCUGCAAGCCCUCGUGAACCCGGAAUCCCUAGUAACCGCGGUUCUCC-AUACCGCGGUGAAUACGUCCCUGCCCCU   [922]
pJP_27       GGAGGG-A-ACCCCUAUCGGGCUCGCACUAA-GCCAUGCGAGUCGCGUGGCGCACGGCUCCGUAAUACACGGUCCCUGUCCUGGGGCCGGGAUAACCUCGGCUGAGGCCAAUACCCCCAGGGUGGGACCGUGGCCUAUCAGGUAGUAGGUGGGGUAACGGCCCACCUAGCCUAAGACGGGUACGGGCUCUGAGAGGAGGAGCCCGGAGAUGGGCACUGAGACAAGGGCCCAGGCCCUACGGGG-GCAGCAGGCGGGAAACUUCCCCAAUGCGCGCGUGAGGGAGUGAGCCCGAGGGGAGGGUAA-GGCUG-GUGCCAGCCGCCGCGGUAAAAC-CAGCUCCCCGAGGGGUUCCCACGCAUACUGGGCCUAAAGCGUCCGUAGCCGGAGCGGGAGGGGCCGAGGGUAUUCCGGGGGGAGCGGUAAAAUGCGUAGAUCCCCGGAGGACCACCAGUGGCGAAGGCGCUCGGCUGGAACGCGUCCGACGGUGAGGGACGAAAGCUGGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCCAGCCGUAAACGAUGCCGGCUAAGCCGGCCGCCUGAGGAGUACAGCCGCAAGGCCGAAACUUAAAGGAAUUGACGGGGGGGCACCACAAGGGGUGAAGCCUGCGGCUCAAUUGGACUCAACGCCGGGAAUCUUACCGGGGGGGGUGGUGCAUGGCCGUCGCCAGCUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGCAACGAGCGAGACCCCCGGACUGCCGGCGCCG-GAGGAAGGAGGGGGCUACGGCAGGUCAGU-AUGCCCCUCCCCCGGGCCGCACGCGGGCUGCAAUGCGUGGUUGGGAUCGAGGGUUGCAAGCCCUCGUGAACCCGGAAUCCCUAGUAACCGCGGUUCUCC-AUACCGCGGUGAAUACGUCCCUGCCCCU   [922]
pSL_4        GGACCC-C-ACUGCUAUCGGGGUGGGACUAA-GCCAUGCAAGUCAUAUGGCGUACGGCUCAGUAACACGUAGCUCCUGCCCUAGAGGGGGGAUAUCCUCGGCUGAGGGUAAACCCUCUAGGAUGGGGCUGCGGCCGAUCAGGUAGUUGGUGAGGUAACGGCUCACCAAGCCUGUGACCGGUGCGGGCCGUGAGAGCGGGAGCCCGGAGAUGGACUCUGAGACAAGAGUCCAGGCCCUACGGGG-GCAG-AGGCGCGAAACCUCCGCAAUG-GCGCGCGACGGGGUCGCCCCGAGGGGGGGGCAA-GACGG-GUGUCAGCCGCCGCGGUAAUAC-CCGCUCCCCGAGUGGUGGGGACUUUUAUUGGGCUUAAAGCGUCCGUAGCGGGGGUGGAAGAAGCCACCGGUACUCCUAGGGUAGGGGUAAAAUCCUCUGAUCCUAGGAGGACCACCAGUGGCGAAGGCGGGUGGCUAGGACACGCCCGACCGUGAGGGACGAAAGCUGGGGGAGCAAACGGGAUUAGAUACCCCGGUAGUCCCAGCUGUAAACGAUGCAGACUAAGUCUGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGAUGUUGCGGCUUAAUUGGAGUCAACGCCGGAAACCUUACCAGGGGAGGAGGUGCAUGGCCGUCGCCAGUGCGUGCCGUGAGGCGUCCUGUUAAUUCAGGCAACGGACGAGACCCCCAGACUGCCGCCGGCG-GAGGAAGGAGGGGGCCACGGCAGGUCAGU-AUGCCCCGCCCCUGGGCCGCACGCGACAUUCAAUGCUAGGUUGGGAUCGAGGGUUGCAAGCCCUCGUGAACGUGGAAUCCCUAGUAACCGCGCGUUACC-AUUGCGCGGUGAAUACGUCCCCGCUCCU   [922]
pJP_96       GGACCC-G-ACUGCUAUGGGGGUGGGACUAA-GCCAUGCGAGUCGCGCGGCGUACGGCUCAGUAAAACGUGGCUCCUACCCUAGGGUGGGGAUAACCCCGGCUGGGGAUAACCCCCCUAGGAUGGGGCCACGUCCCAUCAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCUAUAACGGGUACGGGCCGUGAAAGCGGGAGCCCGGAGAUGGGCACUGAGACAAGGGCCCAGGC--UACGGG-GGCAGCAGGCGCGAAACCUACACAAUGUGCGCACGAUGUGGUCACCCCCAGCGGGGGGCAA-GUCUG-GUGUCUGCCGCCGCGGUAAUAC-CAGCUCCGCGAGUGGUCGGGGCGUUUAUUGGGCCUAAAGCGUCCGUAGCCGGGGCGGGAGAGGCUGAGGGUACUCCUGGGGUAGGGGCGAAAUCCUAUAAUCCCAGGAGGACCACCAGUGGCGAAGGCGCUCAGCUGGAACGCGCCCGACGGUGAGGGACGAAAGCCGGGGGAGCGAAGGGGAUUAGAUACCCCCGUAGUCCCGGCUGUAAACGAUGCGGGCUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGAAGCCUGCGGUUUAAUUGGAGUCAACCCCGAGAACCUUACCGGGGGAGGAGGUGCAUGGCCGUCGCCAGUUCGUGCCGUGAGGUGUCCGGUUAAGUCCGGCAACGAACAAGACCCCCAGACUGCCGCCGGCG-GAGGAAGGAGGGGGCCACGGCAGGUCCGU-AUGCCCCGCCCCCGGGCCACACGCGGGCUGCAAUGCUCAGUUGGGAUCGAGGGCUGCAAGCCCUCGUGAACAUGGAAUCCCUAGUAACCGCGCGUCACC-AACGCGCGGUGAAUACGUCCCUGCUCCU   [922]
pSL_12       GGACCC-G-ACUGCUAUCGGAAUGGGACUAA-GCCAUGCGAGUCAUAUGGCGAACGGCUCAGUAACACGUGGCCCCUACCCUCAAGUGCGGAUAACCCCGGCUGGGACUAAUCCGUUGAGGAUGGGGCUACGGCCGAUCAGGCUGUUGGUGGGGUAACGGCCCACCAAACCUUUGACCGGUACGGGCUUUGAGAGAAGGAGCCCGGAGAUGGACACUGAGACAAGGGUCCAGGCCCUAUGGGGCCCAGCAGGCGCGAAACCUCCACAAUGGGCGCCUGAUGGGGUCAUUCCGAGGGGAGGGCAA-GUCUG-GUGUCAGCCGCCGCGGUAAUAC-CAGCUCCCCGAGUGGUCGGGACGGUUAUUGGGCCUAAAGCAUCCGUAGCCGGGGCGGGAGAGGUGGACGGUACUCCAAGGGUAGGGGUAAAAUCCUCUGAUCCUUGGAAGACCACCGGUGGCGAAGGCGGUCCACCAGAACGCGCCCGACGGUGAGGGAUGAAAGCUGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCCAGCCGUAAACGAUGCGAGCUAAGCUCGCCGCCUGGGGAGCACGGACGCAAGUCUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGAAGCCUGCGGUUCAAUUGGAGUCAACGCCGGGAACCUCACCAGGGGAGGAGGUGCAUGGCCGUCGCCAGCUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGCAACGAUCGAGACCCUCGGACUGCCGCCAGGG-CAGGAAGGAGAGGGCUACGGCAGGUCAGU-AUGCCCCGCCCCUGGGCCACACGCGGGCUGCAAUGCCCAGUUGUGAUUGAGGGUUGCAAACCCUCAUGAAUAUGGAAUCCCUAGUAACCGCGUGACACC-AUCGCGCGAUGAAUACGUCCCUGCUCCU   [922]
marineSBA    GGACCU-G-ACUGCUAUCGGAUUGAUACUAA-GCCAUGCGAGUCUGAAGGCAUACGGCUCAGUAACGCGUAGUCCCUAACCUAUGGCGGGAAUAACCUCGGCUGAGAAUAAUGCCCCGUAGAUGGGACUGCGGCCUAUCAGUUUGUUGGUGAGGUAAUGGCCCACCAAGACUAUUACAGGUACGGGCUCUGAGAGGAGUAGCCCGGAGAUGGGUACUGAGACACGGACCCAGGGCCUAUGGGGCGCAGCAGGCGAGAAAACUUUGCAAUGUGCGCACGACAAGGUUAAUCCGAGGGGUGGGCAA-GUCUG-GUGUCAGCCGCCGCGGUAAAAC-CAGCACCUCAAGUGGUCAGGAUGAUUAUUGGGCCUAAAGCAUCCGUAGCCGGAGUGGGAGAAGUAGACGGUACUCGGUAGGAAGUGGUAAAAUGCUUUGAUCUAUCGAUGACCACCUGUGGCGAAGGCGGUCUACUAGAACACGUCCGACGGUGAGGGAUGAAAGCUGGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCCAGCUGUAAACUAUGCAAACUCAGUUUGCCGCCUGGGAAGUACGUACGCAAGUAUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGAAGCUGCGGUUCAAUUGGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------   [922]
Sulfolobu    GGACCC-G-ACCGCUAUCGGGGUAGGGAUAA-GCCAUGGGAGUCACGUGGCGGACGGCUGAGUAACACGUGGCUCCUACCCUCGGGCGGGGAUAACCCCGGCUGGGGAUAAUCCCCCGAGGAUGGGGCUACGGCCCAUCAGGCUGUCGGUGGGGUAAAGGCCCACCGAACCUAUAACGGGUAGGGGCCGUGGAAGCGGGAGCCUCCAGUUGGGCACUGAGACAAGGGCCCAGGCCCUACGGGGCGCACCAGGCGCGAAACGUCCCCAAUGCGCGCGUGAGGGCGCUACCCCGAGCGGGGGGCAA-GUCUG-GUGUCAGCCGCCGCGGUAAUAC-CAGCUCCGCGAGUGGUCGGGGUGAUUACUGGGCCUAAAGCGCCUGUAGCCGGGGCGGGAGAGGCGGGGGGUACUCCCGGAGUAGGGGCGAAAUCCUUAGAUACCGGGAGGACCACCAGUGGCGGAAGCGCCCCGCUAGAACGCGCCCGACGGUGAGAGGCGAAAGCCGGGGCAGCAAACGGGAUUAGAUACCCCGGUAGUCCCGGCUGUAAACGAUGCGGGCUAAGCCCGCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGAACCUGCGGCUCAAUUGGAGUCAACGCCUGGAAUCUUACCGGGGGAGGAGGUGCAUGGCCGUCGCCAGCUCGUGUUGUGAAAUGUCCGGUUAAGUCCGGCAACGAGCGAGACCCCCAGACUGCCGGCGCCG-GAGGAAGGAGGGGGCCACGGCAGGUCAGC-AUGCCCCGCUCCCGGGCCGCACGCGGGUUACAAUGCGCAGUUGGGAUCGAGGGCUGAAAGCCCUCGUGAACGAGGAAUCCCUAGUAACCGCGGGUCAAC-AACCCGCGGUGAAUACGUCCCUGCUCCU   [922]
Pyrodicti    GGGCCC-G-ACCGCUAUCGGGGUGGGACUAA-GCCAUGGGAGUCGCGCGGCGGACGGCUGAGUAACACGUGGCCCCUACCCUCGGGCGGGGAUAACCCCGGCUGGGGCUAAUCCCCCGAGGAUGGGGCUGCGGCCCAUCAGGUAGUUGGCGGGGUAACGGCCCGCCAAGCCGAUAACGGGUAGGGGCCGUGAGAGCGGGAG-CCCCAGAUGGGCACUGAGACAAGGGCCCAGGCCCUACGGGGCGCACCAGGCGCGAAACCUCCGCAAUGCGGCCGUGACGGGGUCACCCCGAGCGGGGGGCAA-GUCUG-GUGUCAGCCGCCGCGGUAAUAC-CAGCCCCGCGAGCGGUCGGGAUGAUUACUGGGCCUAAAGCGCCCGUAGCCGGGGCGGGAGAGGCCGAGGGUACUCCCGGGGUAGGGGCGAAAUCCGAUAAUCCCGGGAGGACCACCAGUGGCGAAGGCGCUCGGCUGGAACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCCGGCUGUAAACGAUGCGGGCUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGG-AGCACCACAAGGGGUGGAGCCUGCGGCUUAAUUGGAGUCAACGCCGGGAAUCUUACCGGGGGAGGAGGUGCAUGGCCGUCGCCAGCUCGUGCCGUGAGGUGUCCGGUUAAGUCCGGCAACGAGCGAGACCCCCAGACUGCCG-CGGCG-GAGGAAGGAGGGGGCCACGGCAGGUCAGC-AUGCCCCGCCCCCGGGCUGCACGCGGGCUACAAUGCGCAGUUGGGAUCGAGGGCUGCAAGCCCUCGUGAACGCGGAAUCCCUAGUAACCGCGCGUUAGC-AUCGCGCGGUGAAUACGUCCCUGCUCCU   [922]
Desulfuro    GGUCCC-G-ACCGCUAUCGGGGUGGGGCUAA-GCCAUGGGAGUCACGUGGCGGACGGCUGAGUAACACGUGGCUCCUACCCUCGGGGGGGGAUAACACCGGCUGGUGCUAAUCCCCCGAGGAUGGGGCUACGGCCCAUUAGGUUGUUGGCGGGGUAACGGCCCGCCAAGCCGAUAAUGGGUAGGGGCCGUGAGAGCGGGAGCCCCCAGAUGGGCACUGAGACAAGGGCCCAGGCCCUACGGGGCGCACCAGGCGCGAAACCUCCGCAAUGCGGCCGUGACGGGGCCACCCCGAGCGGGGGGCAA-GUCUG-GUGUCAGCCGCCGCGGUAAUAC-CAGCCCCGCGAGUGGUCGGGACGAUUAUUGGGCCUAAAGCGCCCGUAGCCGGGGUGGGAGAGGCCGAGGGUACUCCCGGGGUAGGGGCGAAAUCCUAUAAUCCCGGGAGGACCACCAGUGGCGAAGGCGCUCGGCUGGAACACGCCCGACGGUGAGGGGCGAAAGCCGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCCGGCUGUAAACGAUGCGGGCUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGAGCCUGCGGUUCAAUUGGAGUCAACGCCGGGAAUCUCACCGGGGGAGGAGGUGCAUGGCCGUCGCCAGCUCGUGCUGUGAAGUGUCCGGUUAAGUCCGGAAACGAGCGAGACCCCCAGACUGCCGCCGGCG-GAGGAAGGAGGGGGCCACGGCAGGUCAGC-AUGCCCCGCCCCCGGGCUACACGCGGGCUACAAUGCGUGGUUGGGAUCGAGGGCUGCAAGCCCUCGUGAACGAGGAAUCCCUAGUAACCGCGCGUCAAC-AUCGCGCGGUGAAUACGUCCCUGCUCCU   [922]
Thermopro    GGACCU-G-ACCGCUAUCGGGGUGGGGCUAA-GCCAUGCGAGUCGCGCGGCGCACGGCUCAGUAACACGUACCCCCUAACCUCGGGGGGGGACAACCCCGGCUGGGGCUGAUCCCCCGAGGGUGGGGGUACGGCCCAUCAGGUUGUUGGCGGGGUAACGGCCCGCCAAGCCGAAGACGGGUAGGGGCGGUGAGAGCCGGAGCCCCGAGAUGGGCACUGAGACAAGGGCCCAGGCCCUACGGGGUGCAGCAGGCGCGAAUACUCCGCAAUGCGGCCGCGACGGGGCCACCCCGAGCGGGGGGUAA-GUCUG-GUGUCAGCCGCCGCGGUAAUAC-CAGCCCCGCGAGUGGUCAGGGUGAUUACUGGGCUUAAAGCGCCCGUAGCCGGGGCGGGAGAGGCCGCCGGUACUCCGGGGGUAGGGGCGAAAUCCUAUAAUCCCCGGAGGACCACCAGUGGCGAAAGCGGGCGGCCAGAACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGGAGCAAAGGGGAUUAGAUACCCCUGUAGUCCCGGCCGUAAACGAUGCGGGCUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGGGCACCACAAGGGGUGAAGCUUGCGGCUUAAUUGGAGUCAACGCCGGAAACCUUACCCGGGGAGGAGGUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUCCGGUUAAGUCCGGCAACGAGCGAGACCCCCAGACUGCCGGCGCCG-GAGGAAGGAGGGGGCGACGGCAGGUCAGU-AUGCCCCGCCCCGGGGCUGCACGCGAGCUGCAAUGCCCAGUAGGGAUCGAGGGCUGCAAGCCCUCGUGAACGUGGAAUCCCUAGUAACCGCGUGUCACC-AACGCGCGGUGAAUACGUCCCUGCCCCU   [922]
Thermofil    GGACCC-G-ACCGCUAUCGGGGUGGGGCUAA-CCCAUGGAAGUCGGCCGGCGGACGGCUCAGUAGCACGUGGCUCCUACCCUCGGGGGGGGAUAACCCCGGCUGGGGAUAAACCCCCGAGGAUGGGGCUGCGCCCUAUCAGGUAGUUGGCGGGGUAACGGCCCGCCAAGCCGAUAACGGGUGGGGGCCGUGAGAGCGGGAGCCCCGAGAUGGGCACUGAGACAAGGGCCCAGGCCCUACGGGGUGCACCAGGGGCGAAACUUCCGCAAUGCGGCCGUGACGGAGUCACCCCGAGCGGGGGGCAA-GCUUG-GUGUCAGCCGCCGCGGUAAUAC-CAACCCCGCGAGUGGUCGGGACGUUUAUUGGGCCUAAAGCGUCCGUAGCCGGGGCGGGAGAGGCCGGGGGUACUCCUGGGGUAGGGGCGAAAUCCUAUAAUCCCAGGAGGACCACCAGUGGCGAAGGCGCCCGGCUAGCACGCGCCCGACGGUGAGGGACGAAAGCUGGGGGAGCAAAGGGGAUUAGAUACCCCCGUAGUCCCAGCUGUAAACGAUGCGGGCUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGAAGCUUGCGGUUUAAUUGGAGUCAACGCCGGAAACCUUACCGGGGGAGGAGGUGCAUGGCCGUCGCCGGCUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGGAACGAGCGAGACCCCCGGACUGCCGGCGCCG-GAGGAAGGUGGGGGCUACGGCAGGUCAGU-AUGCCCCGCCCCCGGGCUACACGCGAGCUGCAAUGCUCAGUAGGAAUCGAGGGCUGCAAGCCCUCGUGAACGUGGAAUCCCUAGUAACCGCGUGUCACC-AACGCGCGGUGAAUACGUCCCUGCUCCU   [922]
Methanopy    GGAGGC-C-ACCGCUAUCGGGGUCCGACUAA-GCCAUGCAAGUCGGCCGGCGGACGGCUCAGUAACACGUGGGUCCUACCCUCGGGCGGGGAUAACCCCGGGUGGGGCUAAUCCCCCGAGGAUGGGCCUGCGGCCGAUUAGGUAGUUGGCGGGGUAACGGCCCGCCAAGCCGAUAAUCGGUACGGGCGGUGAGAGCCGGAGCCCGGAGACGGGGACUGAGACAAGGCCCCGGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGCCGCGACGGGGGGACCCCGAGCGGCGGGCAA-GACCG-CUGCCAGCCGCCGCGGUAAUAG-CGGCGCCGCAAGUGGUGGCCGCUUUUAUUGGGCCUAAAGGGGCCGUAGCCGGACCGGGAGAGGCCGGAGGUACCCCCGGGGUAGGGGUGAAAUCCUGUCAUCCCGGGGGGACCGCCAGUGGCGAAGGCGUCCGGCUGGAACGGGUCCGACGGUGAGGGCCGAAAGCCGGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCCGGCUGUAAACGAUGCGGACUAAGUCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAACCGGUGGAGCCUGCGGUUUAAUUGGAUUCAACGCCGGAAACCUUACCGGGGGAGGAGGUGCAUGGCCGCCGUCAGCUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGUAACGAGCGAGACCCCCGGAUCGCCGCCGGCG-GAUGAAAGUGGGGGCGACGGCAGGUCCGU-AUGCCCCGCCCCCGGGCUACACGCGGGCUACAAUGCGUAGUUCGGAUUGCGGGCUGCAAGCCCGCAUGAAGGUGGAAUCGGUAGUAACCGUGCCUCAGA-AUGGCACGGUGAAUACGUCCCUGCUCCU   [922]
Thermococ    GGAGGC-C-ACUGCUAUGGGGGUCCGACUAA-GCCAUGCGAGUCGGCCGGCGGACGGCUCAGUAACACGUCGGUCCUACCCUCGGGGGGGGAUAACCCCGGCUGGGGCUAAUCCCCCGAGGAUGGGCCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCAUGAGAGUGGGAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGCCGCGACGGGGGGACCCCCAGGGCUGGGCAA-GGCCG-GUGGCAGCCGCCGCGGUAAUAC-CGGCGGCCCGAGUGGUGGCCGCUAUUAUUGGGCCUAAAGCGUCCGUAGCCGGACCGGGAGAGGCCGGGGGUACCCCUGGGGUAGGGGUGAAAUCCUAUAAUCCCAGGGGGACCGCCAGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGACGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAAGGGGUGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCUCACCGGGGGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGGACCGCCGGCGCCG-GAGGAAGGAGCGGGCGACGGUAGGUCAGU-AUGCCCCGCCCCCGGGCUACACGCGCGCUACAAUGCCCAGUUCGGAUCGCGGGCUGCAAGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGUGUCAUC-AUCGCGCGGCGAAUACGUCCCUGCUCCU   [922]
Archaeogl    AGAGGC-C-GCUGCUAUCCGGCUGGGACUAAGCCAUGCGAGUCAGGCCGGCGGACGGCUCAGUAACACGUGGACCCUGCCCUCGGGGGGGGAUAACCCCGGCUGGGGCUAAUCCCCCGAGGAUGGGUCUGCGGCGGAUUAGGUUGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCCGUACGGGCCAUGAGAGUGGGAGCCCGGAGAUGGACCCUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGCCGCGACGGGGUCAGCCGGAGGGCCGGGCAA-GGCCG-GUGGCAGCCGCCGCGGUAAUAC-CGGCGGCCCGAGUGGCGGCCACUUUUAUUGGGCCUAAAGCGUCCGUAGCCGGACCGGGAGAGGCCGGGGGUAUUCCCGGAGUAGGGGUGAAAUCCUGUAAUCCCGGGAGGACCACCUGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGACGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAACGAUGCGGACUAAGUCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAACGGGUGGAGCCUGCGGUUUAAUUGGAUUCAACGCCGGGAAGCUUACCGGGGGAGGUGGUGCAUGGCCGCCGUCAGUUCGUACUGUGAAGCAUCCUGUUAAGUCAGGCAACGAGCGAGACCCGCGGACUGCCGGCGCCG-GAGGAAGGUGCGGGCAACGGCAGGUCCGU-AUGCCCCGCCCCCGGGCUACACGCGGGCUACAAUGCUAACCUGGGAUCGAGGGCUGCAAGCCCUCGUGAACCUGGAAUCCGUAGUAAUCGCGCCUCAAA-AUGGCGCGGUGAAUACGUCCCUGCUCCU   [922]
Thermopla    GGCGGU-C-ACUGCUAUCAGGUUCCGACUAAGCCAUGCAAGUCAGGCCGGCGAACAGCUCAGUAACACGUGGAUUUUACCCUCAGGGGGGCAUAACCUCGGCUGAGGCUAAUUCCCUGAGGAUAAGUCUGCGGCCUAUCAGGUAGUAGGUGGUGUAAAGGACCACCUAGCCUAAGACGGGUACGGGCCCUGAAAGGGGGAGCCCGGAGAUGGACUCUGAGACAACAGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAAACUGUGCAAUGCGCGCGCGACACGGGGAGCCUGAGGGCUGGGCAA-GACGG-GUGCCAGCCGCCGCGGUAACAC-CCGCAGCUCGAGUGGUGAUCACUUUUAUUGAGUCUAAAGCGUUCGUAACCGGACCGGGUGAGGUUGAAUGUACUUUCAGGGUAGGGGUAAAAUCCUGUAAUCCUGAAAGGACGACCGGUGGCGAAAGCGUUCAACUAGAACGGAUCCGACGGUGAGGGACGAAGGCUAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGCUGCCCACUUAGUGGGUCACUUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACCGCAACGGGAGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGAAAACUCACCGGGAGAGGUGGUGCAUGGCCGUCGUCAGCUCGUACCGUAGGGCGUUCACUUAAGUGUGAUAACGAGCAAGACCCCCAGACCGCCAGCGCUG-GAGGAAGGAGGGGUCGACGGCAGGUCAGU-ACGCCCCGCUCCCGGGCUACACGCGCGCUACAAAGCGUAGUCAGGACUGAGGGCUGUAAGCCCUCACGAAUGUGGAUUCCGUAGUAAUCGUAGGUCAAC-AGCCUACGGUGAAUAUGCCCCUGCUCCU   [922]
Haloferax    GGAGGU-C-AUUGCUAUUGGGGUCCGAUUUA-GCCAUGCUAGUUACGUGGCGAAAAGCUCAGUAACACGUGGCCACUACCCUACAGGAACGAUAACCUCGGCUGAGGCUAAUAGUUGUAGGAUGUGGCUGCGGCCGAUUAGGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAAGAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACGGGGCGCAGCAGGCGCGAAACCUUUACACUGCACGUGCGAUAAGGGGACCCCAAGAGCUGGGCAA-GACCG-GUGCCAGCCGCCGCGGUAAUAC-CGGCAGCUCAAGUGAUGACCGAUAUUAUUGGGCCUAAAGCGUCCGUAGCCGGACCGGAAGGCUCGAGGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCACCGAUGGCGAAAGCACCUCGAGAAGACGGAUCCGACGGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGCUCGCUAAGCGAGCCGCCUGGGAAGUACGUCCGCAAGGAUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGAGCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCUCACCAGCUCAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGCAGACUGCCGCUAGCG-GAGGAAGGAACGGGCAACGGUAGGUCAGU-AUGCCCCGGAGCUGGGCUACACGCGGGCUACAAUGCGUAGUUCGGAUUGAGGGCUGAAAGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCAUUUCAAU-AGAGUGCGGUGAAUACGUCCCUGCUCCU   [922]
Methanoba    GGAGGC-C-ACUGCUAUUGGGUUUCGAUUAA-GCCAUGCAAGUCACGUGGCGUACGGCUCAGUAACACGUGGAUCCUAACCUUAGGCUGGGAUAACCCUGGCUGGGGAUAAUACCCUAAGGAUGGAUCUGCGGCAGAUUAGGUAGUUGGCGGGGUAAAUGCCCACCAAGCCAGUAAUCUGUACGGGUUGUGAGAGCAAGAGCCCGGAGAUGGAACCUGAGACAAGGUUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCACGUGCGACGGGGGAAACCCAAGAGCUGGGCAA-GACCG-GUGCCAGCCGCCGCGGUAACAC-CGGCAGCUCAAGUGGUGGCCGUUUUUAUUGGGCCUAAAGCGUUCGUAGCCAGGCCGGGAGAGGUUAGCGGUACUCCCGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGAGGACCACCUGUGGCGAAGGCGGCUAACUGGAACGGGCCUGACGGUGAGUAACGAAAGCCAGGGGCGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCCGUAAACGAUGUGGACUUAGUCCACCGCCUGGGAAGUACGGUCGCAAGACUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAACGCGUGGAGCCUGCGGUUUAAUUGGAUUCAACGCCGGACAUCUCACCAGGGGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCACGGACCGCCAGUACUG-GAGGAAGGAGUGGACGACGGUAGGUCCGU-AUGCCCCGCCCCUGGGCUACACGCGGGCUACAAUGCUUAGUUCGGAUUGAGGGCUGUAAGCCCUCAUGAAGCUGGAAUGCGUAGUAAUCGCGUGUCAUA-ACCGCGCGGUGAAUACGUCCCUGCUCCU   [922]
Methco.va    GGAGGC-U-ACUGCUAUUGGGGUUCGACUAA-GCCAUGCGAGUCAUAUGGCGGACGGCUCAUUAACACGUGGUUCUUAACCUCAGGGGAGCAUAACCUUGGCUGAGGAUAAUUCUCCGAGGAUAGGACUGCGCUCGAUUAGGUAGUUGGUGGGGUAAUGGCCCACCAAGCCUACGAUCGAUACGGGCCUUGAGAGAGGGAGCCCGGAGAUGGGGACUGAGACACGGCCCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCACGUGCGACGGGGGGACCCCAAGGGCUGGGCAA-GUUCG-GUGCCAGCAGCCGCGGUAAUAC-CGACGGCCCGAGUGGUAGCCACUCUUAUUGGGCCUAAAGCGUCCGUAGCCGGACCGGGAGAGGACAAGGGUACUCCAGGGGUAGCGGUGAAAUGUGUUGAUCCUUGGAGGACCACCUAUGGCGAAGGCACUUGUCUGGAACGGGUCCGACGGUGAGGGACGAAAGCCAGGGGCGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCCGUAAACUCUGCGAACUAAGUUCGCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAACGGGUGGAGCCUGCGGUUUAAUUGGAUUCAACGCCGGGCAUCUCACCAGGAGAGGUGGUGCAUGGCCAUCGUCAGCUCGUACCGCGAGGCGUCCUGUUAAGUCAGGUAACGAGCGAGACCCGUGGACCGCUAGCGCUA-GAGGAAGGAGCGGGCAACGAUAGGUCCGC-AUGCCCCGCUCCUGGGCUACACGCGGGCUACAAUGCGUAGUUCGGAUCGUGGGCUGUAAGCCCACGUGAAGCUGGAAUCCGUAGUAAUCGCAGUUCAUA-AUACUGCGGUGAAUGUGUCCCUGCUCCU   [922]
Methco.ja    GGAGGC-C-ACUGCUAUCGGGGUCCGACUAA-GCCAUGCGAGUCGGCCGGCGCACGGCUCAGUAACACGUGGCUCCUACCCUCGGGGGGGGAUAACCUCGGCUGAGGCUAAUCCCCCGA--AUGGGGCUGCGGCGGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCUACGAUCCGUACGGGCCCUGAGAGGGGGAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGCGCGCGACGGGGGGACCCCGAGGGCUGGGCAA-GUCCG-GUGCCAGCAGCCGCGGUAAUAC-CGGCGGCCCAAGUGGUGGCCACUGUUAUUGGGCCUAAAGCGUCCGUAGCCG-ACCGGGAGAGGCC-GGGGUACCCCAGGGGUAGCGGUGAAAUGCGUUGAUCCCUGGGGGACCACCUGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGACGAAGGCCAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAACUCUGCGGACUAAGUCCGCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAACGGGUGG--ACCGCGGUUUAAUUGGAUUCAACGCCGGGCAUCUUACCAGGGGAGGUGGUGCAUGGCCGUCGUCAGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGUAACGAGCGAGACCCGUG-ACCG-CGGCGCCG-GAGGAAGGUGCGGGCAACGACAGGUCCGC-AUGCCCCGCCCCUGGGCUACACGCGGGCUACAAUGCGUAGUCCGGAUCGAGGGCUGUAAGCCCUCGUGAAGCCGGAAUCCGUAGUAAUCGCGCCUCACC-AUGGCGCGGUGAAUGCGUCCCUGCUCCU   [922]
Methanosp    AGAGGC-C-ACUGCUAUCGGGGUUUGACUAA-GCCAUGCGAGUCGAUCGGCGUACUGCUCAGUAACACGUGGACUCUGCCCUGAAGGGAGGAUAAUCCCGGCUGGGGGUAAUACUUUCAGGAUGAGUCUGCGGCCGAUUAGGUAGUUGUUGGGGUAACGGCCCAACAAGCCUGUCAUCGGUACGGGUUGUGGGAGCAAGAGCCCGGAGAUGGAUUCUGAGACACGAAUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAAACUUUACCAUGCGGCCGUGAUAAGGAAACCCCGAGGGCCGGGCAA-GACCG-GUGCCAGCCGCCGCGGUAAUAC-CGGCGGCUCGAGUGGUGGCCGCUAUUACUGGGCUUAAAGGGUCCGUAGCUGGACCGGGAGAGGUGAGAGGUACUGCCGGGGUAGGAGUGAAAUCCUGUAAUCCCGGUGGGACCACCUAUGGCGAAGGCAUCUCACCAGAACGGGUCCGACAGUGAGGGACGAAAGCUGGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCCAGCUGUAAACGAUGCGCGUUAAACGCGCCGCCUGGGGAGUACGGUCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAACGGGUGGAGCCUGCGGUUUAAUCGGACUCAACGCCGGAAAUCUCACCGGAUAAGGAGGUGCAUGGCCGUCGUCAGUUCGUACUGUGAAGCAUCCUGUUUAGUCAGGCAACGAGCGAGACCCACGGACCGCCUCUAGGG-GAGGAAGGAAUGGGCAACGGUAGGUCAGC-AUGCCCCGUAUCCGGGCUACACGCGGGCUACAAUGCGAAGUUCGGAUUGCGGGUUGUAAACCCGCAUGAAGCUGGAAUCCGUAGUAAUCGCGUUUCAAC-AUAGCGCGGUGAAUAUGUCCCUGCUCCU   [922]
Methanoth    GGAGGC-C-ACUGCUAUGGGGGUCCGACUAA-GCCAUGCAAGUCACGUGGCGAACGGCUCAGUAACACGUGGACCCUACCCUGGGGCCGGGAUAACCCCGGCUGGGGCUAAUCCCCCCAGGAUGGGUCUGCGGCCGAUUAGGUAGUUGGUAGGGUAACGGCCUACCAAGCCUACGAUCGGUACGGGUUGUGAGAGCAAGAGCCCGGAGACGGGGCCUGAGACAAGGCCCCGGGCCCUACGGGGCGCAGCAGGCGCGAAAACUCCGCAAUGCGCGCGCGACGGGGGGACCCCCAGGGCUGGGCAA-GACCG-GUGCCAGCCGCCGCGGUAACAC-CGGCAGCCCGAGUGGUGGCCGCGUUUAUUGGGCCUAAAGCGUCCGUAGCCGGGCCGGGAGAGGCCGGAGGUACCCCCGGGGUAGGGGUGAAAUCCUGUAAUCCCGGGGGGACCACCUGUGGCGAAGGCGUCCGGCUGGAACGGGCCCGACGGUGAGGGACGAAAGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCCGUAAACGAUGCGGACUUAGUCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAACGCGUGGAGCCUGCGGUUUAAUUGGAUUCAACGCCGGACACCUCACCGGGGGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGCGGACCGCCAGCGCUG-GAGGAAGGUGCGGGCGACGGUAGGUCCGU-AUGCCCCGCCCCCGGGCUACACGCGGGCUACAAUGCGUAGUUCGGAUCGAGGGCUGCAAGCCCUCGUGAAGCUGGAAUGCGUAGUAAUCGCGGGUCACU-AUCCCGCGGUGAAUACGUCCCUGCUCCU   [922]
Vairimorp    UGACGU-A-GACGCUAUUCCCU-AAGAUUAA-CCCAUGCAUGU-UUAAAAUGGACUGCUCAGUAAUACUCACUUUUUAAUGUAUUAUUAGUAUAACUGCGUGUGUAGCUAAGACAUAUACAGUAAGAGUGAGACCUAUCAGCU--UUGUUAAGGUAAUGGCUUAACAAGGCAAUGACGGGU-CGGUAUUACUUUUAAU-AUUCCGGAGAAGGAGCCUGAGAGACGGCUACUAAGUCUAAGGAUUGCAGCAGGGGCGAAACUUGACCUAUGGAUAUCUGAGGCAGUUAUGGGAAUUGGAGGGCAA-AUCAA-GUGCCAGCAGCCGCGGUAAUAC-UUGUUCCAAGAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCCGUAGUUAAGCAAUAUGAGGUGUACUGUAUAGUUGGGAGAGAGAUGAAAUGUGACGACCCUGACUGGACGAACAGAAGCGAAAGCUGUACACUUGUAUGUAUUUUUUGAACAAGGACGUAAGCUGGAGGAGCGAAGAUGAUUAGAUACCAUUGUAGUUCCAGCAGUAAACUAUGCCGACGAAGUUGGCUCUGGGGAUAGUAUGAUCGCAAGAUUGAAAAUUAAAGAAAUUGACGGAAGAAUACCAGAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGUAACUUACCAAUAUUAGUGGUGCAUGGCCGUUUUCAAUGGAUGCUGUGAAGU-UUUGAUUAAUUUCACCAAGACGUGAGACCCUUUGACAGACA-CG-UG-UAGGAAGGAAAGGAUUAAAACAGGUCCGUUAUGCCCUCAUUUUGGGCUGCACGCGCAAUACAAUAUCUUUAUGGGAUAAUAUUUUGUAAAGAUAUUUGAACUUGGAAUUGCUAGUAAAUUUUAUUAAAU-AAGUAGAAUUGAAUGUGUCCCUGUUCUU   [922]
Dictyoste    AGUAGUCA-UAUGCUUGUCUCA-AAGAUUAA-GCCAUGCAUGUCAGACUGCAGACGGCUCAUUACAACAGUGAUACUAAUAGACUUUUUGGAUAACCGCAGC-GGGGCUAAUACAAGUCUACUGUGUCACUGCCCUAUCAACU--AUGGUACGGUAUUGGCCUACCAUGGUUGUAACGGGU-CGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUGGCUACCACUUCUACGGAAGGCAGCAGGCGCGCAAAUUACUCAAUCCCACGGGGAAGUAGUGACAAUAAUUGGAGGGCAA-GUCUG-GUGCCAGCAGCCGCGGUAAUUC-CAGCUCCAAUAGCAUAUACUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGGAUGGAUGGGGGUGUUCAUAUUGGUGGGCGAGAGGUGAAAUUCGUUGACCCUAUCAAGAUGAACUUCUGCGAAAGCAUUCACCAAAUACCUCCCCAUUAAUCAAGAACGAAAGUUUGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCAAACUAUAAACUAUGUCGACCAAGUGGAUUCCGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACACAAUGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACUCGGGAAAACUUACCAAGCUUGGUGGUGCAUGGUCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUCAAUUCCGAUAACGGACGAGACCUCGAGACUACCUGCGCAG-GCGGAAGUCCGAGGCAAUAACAGGUCUGUGAUGCCCUUACCUUGGGCCGCACGCGCGCUACAAUGCGUAACUGGGCUUGAUCUUUGUAAUUGAUCAUAAACGAGGAAUUCCUUGUAAGCGUAAGUCAUU-ACCUUAUGCUGAAUAUGUCCCUGCCCUU   [922]
Encephali    UGACGU-A-GAUGCUAGUCUCU-GAGAUUAA-GCCAUGCAUGU-AGACGGCGAACGGCUCAGUAAUGUUGCGGUUUUGGUCUCUGUGUAAACUAACCACGGCUGUGGCUAAAA--CGGAGAAUAAGGCGCAACCCUAUCAGCU--UUGGUAGUGUAAAGGACUACCAAGGCCAUGACGGGU-CGGGAAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUG-UCCACUCCUGGGGGAGACAGUCAUGAGACUUGGAGGGCAAGCUUUG-GUGCCAGCAGCCGCGGUAACUC-CAACUCCAAGAGUGUCUAUGGUGGAUGCUGCAGUUAAAGGGUCCGUAGUCGGAACGGAUAGGGAGUGUAGUAUAGACUGGCGAAGAAUGAAAUCUCAAGACCCAGUUUGGACUAACGGAGGCGAAGGCGACACUCUUAGACGUAUCUUAGGAUCAAGGACGAAGGCAGGAGUAUCGAAAGUGAUUAGACACCGCUGUAGUUCCUGCAGUAAACUAUGCCGACAGAGUGGGCUCUGGGGAUAGUACGCUCGCAAGGGUGAAACUUAAAGAAAUUGACGGAAGGACACUACCAGGAGUGGAUUGUGCUGCUUAAUUUAACUCAACGCGGGAAAACUUACCAGGGUGAGUGGUGCAUGGCCGUUGGAAAUUGAUGGGGCGACCU-UUAGCUUAAAUGCUUAAACCAGUGAGACCUCCUGACAGGUGUUAACA-CAGGAGGGUGGAGGCUAUAACAGGUCCGUGAUGCCCUUAUCCUGGGCAGCAAGCGCAAUACAAUAU--GAGUAGGAUCUACGUUUGUAAUACGUAGUGAAUAAGGAAUUCCUAGUAACGGUGCCUCAUC-AAGGCAUGGUGAAUGUGUCCCUGUUCUU   [922]
Physarum     AGUAGU-G-UAUGCUUCUCCUA-AAGACUAA-GCCAUGCAUGUCCGUCUGCGAACGGCUCCGCAUACCAGUUGUACCAUAGCAAGCCAGGGAUAACCCUGGCUGAGGCUAAUACACUCGCUGUGUGCUUCUGACCUAUCAACU--UGGCA-GCGUAACGGACAUGCCAGGUAACAACGGGU-CAGAGGAUAAGGGUUCGAUCCUGGAGAGUGGGCCUGAGAGAUUGCUCACACUUCUAAGGAAGGCAGCAGGCGCGCAACGUUCCCAUUGGGCGCUCGAGGGCGUUAGGGGACUUAGAGGACAA-GUCUG-GUGCCAGCACCCGCGGUAAUUC-CAGCUCUAAUAGCAUACGUUAAAGUUGUUGCGGUUAAAACGCUCGUAGUCGGGAUGUUCGAGGGUGACCGAAUUGCUGGGCGAGUGGUGAAAUACGUUGACCCUAGCAAGUCGACCAAAGGCGUAAGCAGUCAUCAAGGGCAUUCCCGUUGAUCAAGAGCGAAAGUUAAGGGUUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACUAUAAAUGAUGCAGACCAAGUCGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAC-ACAAAGAGUGGAACCUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACCAGGUCUGGUGGUGCAUGGUCGUUCUUAGUUCGUGGAUUGAUUUGUCUGGUUUAUUCCGAUAACGAGCGAGACCCCGGUAUCAGAGCCGGUU-CUUGAAA--UGGGUUAAUAACAGGUCAGUCAUGCCCUUGUUCUGGGCCGCACGCGCGUUACAAUGUUUGACUGGGACAGAUCUUUGCAAUUGGUCUCAAACGAGGAAUUUUUAGUAAUCGCAGGUCAUU-AACCUGCGUUGAAUGCGUCCCUGCCCUU   [922]
Entamoeba    AGUAUU-A-UAUGCUGAUGUUA-AAGAUUAA-GCCAUGCAUGUGAGACUGCGGACGGCUCAUUAUAACAGUAAUUUUCUUUGGUUACAAGGAUAGCUUUGUAUAAAGAUAAUACUACCAAUGAGAAUUUCUGAUCUAUCAAUC--UUGGUAGUAUCGAGGACUACCAAGAUUAUAACGGAU-CGAGGAAUUGGGGUUCGACAUCGGAGAGGGAGCUUUACAGAUGGCUACCACUUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCACUUUCGUGAAGAGGUAGUGACGACACUUGGAGGGCAA-GUCUG-GUGCCAGCAGCCGCGGUAAUUC-CAGCUCCAAUAGUGUAUAUUAAAGUUGCUGUGAUUAAAACGCUCGUAGUUGGAACAAUUGGGGUGAUUCAGAAAAUAACGGGAGAGGUGAAAAUCCAUGAUCGCUAUAAGAUGCACGAGAGCGAAAGCAUUUCACUCAACUGUGUCCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACUAUAAACGAUGUCAACCAAGUUGACUUCAGGGGGAGUAUGGUCACAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAC-ACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAAGACUAGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCAGGUUAAUUCCGGUAACGAACGAGACUGAAAGACCUCUUUUGAAA-AAGGAAGCAUUCAGCAAUAACAGGUCUGUGAUGCCCUUAUCUUGGGCCGCACGCGCGCUACAAUGCAUGACAGGGAUAAAUGAUUGGAAUUUGUUUUGAACGAGGAAUUCCUUGUAAUAUCGAGUCAUU-AACUCGAGAUGAAUACGUCCCUGCCCUU   [922]
Euglena_g    AGCAGUCA-UAUGCUUUGUUCA-AGGGCUAA-GCCAUGCACGUCAGUCUGUGAAUGGCUCCUUACAUCAGCAGUUCUACGUGAUAGAUUGGACAUCCACCAUUGUGGCUAAUACAGAUCGCAAGAGCUUCUGACCUAUCAGCU--ACUGUGGUGUAUCGGACCACAGUGGCCUUGACGGGU-CGGAGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACUACCAAGGUGGGCAGCAGGCACGCAAAUUGCCCCAUGCAACUGUGAGGCAGCGACGAACACCGGAGGGCAA-GUCUG-GUGCCAGCAGCUGCGGUAAUUC-CAGCUCCGAGGGCGUAUACUAACAUUGCUGCUGUUAAAACACUUGUAGUCGGACUGUUCGGGGUGAAAGAUACGGGAGCGCCAGAGGUGAAAUUCUUAGAUCGCUGCCAGAUCCACUGCAGCGAAGGCGUUCUGCAAGUGCACGUCCGUCGAUCAAGAAUGAGAGUUCGGGGAGCAAAGAUGAUCAGACACCGUCGUAGUCCGGACUGUAAACGAUGCCGGCCAAGCCGGUUCAGGGGGGAGUACUGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAUGGCACCACAAGGCGUGGAGUAUGCGGCUUAAUUUGACUCAACGCGGGGAAUGUUACCAGGUCCGGUGGUGCAUGGCCGCUCCUGAUUGGUGGAGUGAUUUGUCUGGUUGAUUCCGAUAACGAGUGAGACAUCUGUGCUGUGUCCGGGC-AUGCAUGCUAGAGCCAACAGCAGGUCUGUGAUGCUCCCGUCCUGGGCCGCACGCGCACUACAUUGCGUACUGGGGAUAGAUGGUUGCAAUCUGCCUUGAACGUGGAAUGCCUAGUAUGCCUGGGUCAUC-AGCCCAGACCGAUUGUGUCCCUGCCAUU   [922]
Naegleria    AGUACU-A-UAUGCUUGUCUCA-AAGCCUAA-GCCAUGCAAAUGAGUCUGUGGAAGGCUCAUUAUAACAGUUAUUCCUAGCCACUGCAAGGAUACCACCGUGCAGCGAUA-UACUAGGCAGAGGAGUUUCUUACCUAUCAGCU--UUGUUUGUUUAAAGGACAAACCAGGCUUUGACGGGU-CGGGGAAUCAGUGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUCGCUACCACAUCUAAGGACGGCAGCAGGCGCGCAAAUUACCCAAUCUCACGAGGAGGUAGUGACAAGCUUUGGAGGAAAA-GUCUG-GUGCCAGCACCCGCGGUAAUUC-CAGCUCCAAGAGCGUAUAUUAAUACUGCUGUAGUUAAAACGCCCGUAGUAGCUCAGGGUGAGGCCCCGGGUACCAUGAGGCUAGAGGUGAAAUUCUGAGACCCUCAUGUGACCAACUAAGGCGAAAGCUGUGGGCCACCACAAGCUCGUCUAUCAGGGACAAAAGUUGGGGGAUCGAAGACGAUUAGAUACCGUCGUAGUCCCAACUAUAAACGAUACCAACCGAGUCGGUUCUGGGGGGAGUAUAGUCGCAAGACCGAAACUUAAAGGAAUUGACGGAAAGGCACCACCAGGAGUGGAGUCUGCGGCUUAAUUCGACUCAACACGGGGAAACUCACCAGGUCGGGUAGUGCAUGGCCGUUUCCAGUUCGUGGAGUGAUCUGUCUUGUUAAUUCAGAUAACGAACGAGACCUAAGGACUUCAUUCGGAU-GAGGAAGAUUUAGGCCAUAACAGGUCUGUGAUGCUCUUGUCCUGGGCUGCACGCGUACUACAAUAUAUGACAGGGAUCGAGGAUUGGAAAUCCUCGUGAACGAGGAAUUCCUAGUAAGCGUGGUUCAUC-AUACCACAUUGAUUACGUCCCUGCCUUU   [922]
Trypanoso    AGUAGUCA-UAUGCUUGUUUCA-AGGACUUA-GCCAUGCAUGCCAGUCUGCGCAUGGCUCAUUACAUCAGACGUUCUGCCGCCAAAACUGGAUAACUUGGCGCCAAGCUAAUACACUACUGACGAACAACUGCCCUAUCAGCC--AUGGCCGUGUAGUGGACUGCCAUGGCGUUGACGGGA-CGGGGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACUUCUACGGAGGGCAGCAGGCGCGCAAAUUGCCCAAUGUCGCGAUGAGGCAGCGAAAAGAAUUGGAGGACAA-GUCUG-GUGCCAGCACCCGCGGUAAUUC-CAGCUCCAAAAGCGUAUAUUAAUGCUGUUGCUGUUAAAGGGUUCGUAGUUGGGUAGUUCGGGGGAGAACGUACUGGUGCGUCAGAGGUGAAAUUCUUAGACCGCACCAAGACGAACUACAGCGAAGGCAUUCUUCAAGGAUACCUUCCUCAAUCAAGAACCAAAGUGUGGGGAUCAAAGAUGAUUAGAGACCAUUGUAGUCCACACUGCAAACCAUGACACCCAGAGGGUCUCAGGGGGGAGUACGUUCGCAAGAGUGAAACUUAAAGAAAUUGACGGAAUGGCACCACAAGACGUGGAGCGUGCGGUUUAAUUUGACUCAACACGGGGAACUUUACCAGAUCUGGUGGUGCAUGGCCGCUUUUGGUCGGUGGAGUGAUUUGUUUGGUUGAUUCCGUCAACGGACGAGAUCCAAGGAUUCCUUGCGCAA-GGUGAGAUUUUGGGCAACAGCAGGUCUGUGAUGCUCCUGUUCUGGGCGACACGCGCACUACAAUGCCCACUUGGGACCGAGUAUUGCAAUUGGUCGCGAACGAGGAAUGUCUCGUAGGCGCAGCUCAUC-AAACUGUGCCGAUUACGUCCCUGCCAUU   [922]
Tritricho    AAGGAA-G-CACACUUCGGUCA-UAGAUUAA-GCCAUGCAAGUGAGACUGCGAACAGCUCAUUAACACGCUCAGUCUACUUGGUGGUUUGGAUAGCAGCAGCUGGUGCUAAUACACACCAAUCGAUUGAGCGACCUAUCAGCU--UACUUAGGGUCUUUACCUAGGUAGGCUAUCACGGGU-CGGGCGGUUACCGUCGGACUCCGGAGAAGGCGCCUGAGAGAUAGCGACUAUAUCCACGGGUAGCAGCAGGCGCGAAACUUACCCACUCGAGUUCGGAGGUGGUAAUGACCAGCAGAGGGCCA-GUCUG-GUGCCAGCAGCUGCGGUAAUUC-CAGCUCUGCGAGUUUGCUCCCAUAUUGUUGCAGUUAAAACGCUCGUAGUCAGAGCCACCGGGGGUAGAUCUAUUUCAUGGCGAACGGUGGAAUGUUUUGACCCAUGAGAGAGAAACGAAGGCGAAAGCAUCUACCUAGAGGGUUUCUGUCGAUCAAGGGCGAGAGUAGGAGUAUCCAACCGGAUCAGAGACCCGGGUAGUUCCUACCUUAAACGAUGCCGACAGAGUUGGCUCUGGGGGAACUACGACCGCAAGGCUGAAACUUGAAGGAAUUGACGGAAGGGCAC-ACCAGGGGUGGAGCUUGUGGCUUAAUUUGAAUCAACACGGGGAAACUUACCAGGACUGGUGGUGCAUGGCCGUUGGUGGUGCGUGGGUUGACCUGUCGCGUUGAUUCAGAUAACGAGCGAGAUUAUCGGACUCCCUGCGCAG-GAGGAAGAGGGUAGCAAUAACAGGUCCGUGAUGUCCUUGCUCUGGGCUGCACGCGCGCUACAAUGCGUAGUUGGGAUUGAGGAUUGUAAAUUCUCAUGAACCAGGAAUCCCUUGUAAAUGCGUGUCAAC-AGCGCGCGUUGAAUACGUCCCUGCCCUU   [922]
Babesia_c    AGUAGUCA-UAUGCUUGUCUUA-AAGAUUAA-GCCAUGCAUGUCAGACUGCGAAUGGCUCAUUACAACAGUUAUUUUCUUUGGUAUUAUGGAUAACCGUGCGUAGGGCUAAUACAGCCCAUUCAAGUUUCUGACCCAUCAGCU--ACGGUAGGGUAUUGGCCUACCGAGGCAGCAACGGGU-CGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGCAGGGAGGUAGUGACAAGAAUUGGAGGGCAA-GUCUG-GUGCCAGCAGCCGCGGUAAUUC-CAGCUCCAAUAGCGUAUAUUAAACUUGUUGCAGUUAAAAAGCUCGUAGUUGGAACGGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAACGAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAAGUCGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAAGACUUUACAGCUGU-AGGGAAGUUUAAGGCAAUAACAGGUCUGUGAUGCCCUUGUCCUGGGCUGCACGCGCGCUACACUGCGUGUCGGGGAUUGAUUUUUGCAAUAAAUCAUGAACGAGGAAUGCCUAGUAUGCGCAAGUCAUC-AGCUUGUGCAGAUUACGUCCCUGCCCUU   [922]
Porphyra     AGUAGUCA-UAUGCUUGUCUCA-AAGAUUAA-GCCAUGCAUGUCAGACUGCGAAUGGCUCAUUACAACAGUUAUUUCCUUUGAGAACUUGGAUAACCGUAGCUAGAGCUAAUACAGCUCAUUCAAAUUUCUGCCCUAUCAACU--AUGGUAGAGUAUUGGUCUACCAUGGUGUCGACGGGU-CGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGCGGGGAGGUAGUGACAAAAAUUGGAGGGCAA-GUCUG-GUGCCAGCAGCCGCGGUAAUUC-CAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGGACAGUUGGGGGUAUUCGUAUUUCAUUGUCAGAGGUGAAAUUCUUGGAUUGAUGGAAGACGCACAACUGCGAAAGCAUCUGCCAUGGAUGUUUUCAUUGAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACGAUGCCGACUGAGUCGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCGUGACUAUGCGCGCGU-AUGGAAGAUUGAGGCAAUAACAGGUCUGUGAUGCCCUUGUUCUGGGCCGCACGCGCGCUACACUGCGUGCUGGGGAUAGAUCAUUGCAAUUGAUCUUGAACGAGGAAUUCCUUGUAGGCGUAGGUCAUC-ACCCUGCGCCGAAUACGUCCCUGCCCUU   [922]
Parameciu    AGAAGUCA-UAUGCUUGUCUUA-AAGAUUAA-GCCAUGCAUGUCAGACUGCGAAUGGCUCAUUAAAACAGUUAUUUUAUUUGAUAGCAUGGAUAACCGUGGCUAGAGCUAAUACAAAUCAUUCAAGUUUCUGCCCUAUCAGCU--AUGGUAGUGUAUUGGACUACCAUGGCAGUCACGGGU-CGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCCGCGGGGAGGUAGUGACAAGAAUUGGAGGGCAA-GUCUG-GUGCCAGCAGCCGCGGUAAUUC-CAGCUCCAAUAGCGUAUACUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGGACAGAUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACUAUAAACUAUACCGACUCAGUCGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUAAGACUAUGUAUGUGC-AUGGAAGUUUAAGGCAAUAACAGGUCUGUGAUGCCCCUGUCCUGGGCCGCACGCGCGCUACACUGCGUGCUGGGGAUAGAUCUUUGCAAUAGAUCUUGAACGAGGAAUUCCUUGUAAGCACAGGUCAUC-AGCCUGUGCUGAAUACGUCCCUGCCCUU   [922]
Zea_mays     AGUAGUCA-UAUGCUUGUCUCA-AAGAUUAA-GCCAUGCAUGUGAGACUGCGAAUGGCUCAUUAAAUCAGUUAUUUUGUUUGAUGGCUCGGAUAACCGUAGCUAGAGCUAAUACGCAUCAUUCAAAUUUCUGCCCUAUCAACU--AUGGUAGGAUAGGGGCCUACCAUGGUGGUGACGGGU-CGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGCGGGGAGGUAGUGACAAUAAUUGGAGGGCAA-GUCUG-GUGCCAGCAGCCGCGGUAAUUC-CAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAAGUCGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCUGGUGGUGCAUGGUCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGGACUAUGGCCGGCC-GCG-AAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUGUUCUGGGCCGCACGCGCGCUACACUGCGUGAUGGGGAUAGAUCAUUGCAAUUGGUCUUCAACGAGGAAUGCCUAGUAAGCGCGAGUCAUC-AGCUCGCGUUGACUACGUCCCUGCCCUU   [922]
Homo_sapi    AGUAG-CA-UAUGCUUGUCUCA-AAGAUUAA-GCCAUGCAUGUCAGACUGCGAAUGGCUCAUUAAAUCAGUUAUUUCCUUUGGUCGCUUGGAUAACUGUGGCUAGAGCUAAUACAACCCAUUCGAACGUCUGCCCUAUCAACU--AUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGU-CGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGCGGGGAGGUAGUGACGAAAAUUGGAGGGCAA-GUCUG-GUGCCAGCAGCCGCGGUAAUUC-CAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACCGAGUCGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGGACAAGUGGCGCCA-CCCGAGA-UUGA-GCAAUAACAGGUCUGUGAUGCCCUUGUCCGGGGCUGCACGCGCGCUACACUGCGUGAUGGGGAUCGGGGAUUGCAAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUA-AGCUUGCGUUGAUUAAGUCCCUGCCCUU   [922]
Coprinus     AGUAGUCA-UAUGCUUGUCUCA-AAGAUUAA-GCCAUGCAUGUCAGACUGCGAAUGGCUCAUUAAAUCAGUUAUUUUAUUUUAUGGCAUGGAUAACUGUGGCUAGAGCUAAUACACUUCAUUCAAAUAUCUGCCCUAUCAACU--AUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGU-CGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCC-GCGGGGAGGUAGUGACAAUAAUUGGAGGGCAA-GUCUG-GUGCCAGCAGCCGCGGUAAUUC-CAGCUCCAAUA-CGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGGAUAGUUGGGGGCAUUGGUAUUGAGUCGCUAGAGGUGAAAUUCUUGGAUUGACUCAAGACCAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAGGUUAGGGGAUCGAAAACGAUUAGAUACCGUUGUAGUCUUAACAGUAAACUAUGCCGACUAAGUCGGUUCUGGGGGG-GUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGUGUGGACGCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUAAGACUGUCAGCGCUG-ACGGAAG-UUGAGGCAAUAACAGGUCUGUGAUGCCCUUGUUCUGGGC-GCACG-GUGCUACACUGCGUGCUGGGGAUAGAGCAUUGCAAUUGCUCUUCAACGAGGAAUACCUAGUAAGCGUGAGUCAUC-AGCUCGCGUUGAUUACGUCCCUGCCCUU   [922]
Cryptomon    AGUAGUCA-UAUGCUUGUCUCA-AAGAUUAA-GCCAUGCAUGUCAGACUGCGAAUGGCUCAUUAAAUCAGUUAUUUUAUUUGAUGGCAUGGAUAACCGUAGCUAGAGCUAAUACAAUUCAUUCAAAUUUCUGCCCUAUCAACU--AUGGUAGGAUAGAGGCCUACCAUGGUUUUAACGGGU-CGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGCGGGGAGGUAGUGACAAUAAUUAGAGGGCAA-GUCUG-GUGCCAGCAGCCGCGGUAAUUC-CAGCUCUAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUCGGGACAGUUGGGGCCGUUUAUAUUUCGUUGUCAGAGGUGAAAUUCUUGGAUUUACGAAAGAUAAACUUCUGCGAAAGCAUUCGGCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAAGUUGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGGACUAUUUGUAUGA-AUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUGUUCUGGGCCGCACGCGCGCUACACUGCGUGAUGGGGAUAGAUUAUUGCAAUUAAUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUC-AGCUCGCGUUGAUUACGUCCCUGCCCUU   [922]
Achlya_bi    AGUAGUCA-UACGCUUGUCUCA-AAGAUUAA-GCCAUGCAUGUCAGACUGCGAAUGGCUCAUUAUAUCAGUUAUUCUACUUGAUAGCUUGGAUAACCGUAGCUAGAGCUAAUACACAUCAAUUGAGUUUCUGCCCUAUCAGCU--AUGGUAGGAUAUGGGCCUACCAUGGCGUUAACGGGU-CGGGGAAUUAGGGUUUGAUUCCGGAGAGGGAGCCUUAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGCAGGGAGGUAGUGACAAUAAUUGGAGGGCAA-GUCUG-GUGCCAGCAGCCGCGGUAAUUC-CAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGGACAGUUGGGGGUAUUCAUAUUUCAACGUCAGAGGUGAAAUUCUUGGAUCGUUGAAAGAUGAGCUUAGGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUCAGUCGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCCGGACUUUCAGUACUG-AAGGAAGUUGGAGGCAAUAACAGGUCUGUGAUGCCCUUGUUCUGGGCCGCACGCGCGCUACACUGCGUGCUAGGGAUAGAUUAUUGCAAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAAGUCAUC-AGCUUGCAUUGAUUACGUCCCUGCCCUU   [922]
Costaria     AGUAGUCA-UACGCUUGUCUCA-AAGAUUAA-GCCAUGCAUGUCAGACUGCGAAUGGCUCAUUAUAUCAGUCAUUUUAUUUGAAAGCAUGGAUAACCGUAGCUAGAGCUAAUACAUUUCAUUCAAGUUUCUGCCCUAUCAGCU--AUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGU-CGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGG-AGCAGGCGCGUAAAUUACCCAAUCCUGCAGGGAGGUAGUGACAAUAAUUGGAGGGCAA-GUCUG-GUGCCAGCAGCCGCGGUAAUUC-CAGCUC-AAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAACGGUUGGGGGUAUUCGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUGGAAGACGAACUACUGCGAAA-CGUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAAGUCGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUC-GUUAACGAACGAGACCCCCGGACUUUCGGUACCG-AAG-AAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUGUCCUGGGCCGCACGCGCGCUACACUGCGUGAUAGGGAUAGAUCAUUGCAAUUGAUCUUGAACGAGGAAUUCCUAGUAAACGCGAGUCAUC-AGCUCGCAUUGAUUACGUCCCUGCCCUU   [922]
Giardia_m    GGAGUA-C-UACGCUA-CCCCA-AGGACAAAAGCCAUGCAAGCGCAGUGGCGGACGGCUCGGUACAACGGUACGUCUGACCGGGGGGACGGAUACCGCUGGCCAGCGCCAAGACGGCCCGGAUGAGGUUCCGAGGUAUUACCU--UCGGUAGAGUAGUGGUCUACGGAGGGGAUGAUGCCU-CGGAGGAUCAGGGUUUGACUCCGGAGAACGGGCCUGAGAGACGGCCCGUACAUCCAAGGACGGCAGCAGGCGCGGAACUUGCCCAAUGCGUGCGUGAGGCAGCAACGGGGGGUCGAGGGAAAGGUCUG-GUGCCAGCAGCCGCGGUAAUUC-CAGCUCGGCAGGCGUCGUACGGCGCUGUUGCAGUUAAAACGUCCGGAGUCUGAAUGGGUAAGGGCAUGUGUAUUGGUGGGGGACGGGUGAAAUAGGAUGAUCCGACCAAGACAGACAAAGGCGUAGGCACUUGCCAAGACCAUAUCAGUCGAACCAGGACGAAGCCCGGGGGCGAGAAGGCGAUUAGACACCACCGUAUUCCCGGGCGUAAACGAUGCCACCGAAGGGGGCUCUGGGGGGAGUAUGGCCGCAAGGCUGGAACUUGAAGGCAUUGACGGAGGGGUACCACCAGACGUGGAGUCUGCGGCUCAAUUUGACUCAACGCGAACA-CCUUACCAGGCCUGGUGGUGCAUGGCCGUUCACAGCCCGUGGCUUGAGCCGUCUGCUUGACUGCGACAACGAGCGAGACCCUAAGACCGCCAAUAUUG-GAGGAA-GGUGGGGCGAUAACAGGUCUGUGAUGCCCUUGCCCUGGGCUGCACGCGUACUACACUGCGUGGUUGGGAUCGUGGACUGGAAGUCCUCGUGAACCUGGAAUGUCUAGUAGGCGUAGGUCAUC-AAUCUACGCCGGAUACGUCCCUGCCCCU   [922]
Hexamita     AGAAGG-G-CAAGCUAAGAUUA-AGGAUUAA-GCCAUGCAUGCCGUGUGAAACUGCGAACGGCUCAUUAAAUCAUGAAAUGUCUCGGUCGGCUAAUACGGGUCUCUUACUAAUCGGGCACGAUCAGCUUCUGACGCAUCAUUA--UAGGAGAAGUAAAGGUUAUCCUAUGAGUUCACGCGU-CGGAGAAUUAGGGUUCGACUCCGGAGAAUGAGCAUGAGAGACGGCUCAUAGUUCUAAGGGAGGCAGCAGGCGCGGAAAUUGCCCAAUGUACGUACGAGGCAGUGACGAAAAUUAGUGGGAGA-GCAUG-GUGCCAGCAGCCGCGGUAAUUC-CAUCACUGAUAGCUUUCUCUUACGUUGUUGCAGUUAAAAAGCUCGUAGCCUGGCGGCGCGGGACUGAUAGUAUUUGGUGGGGACAGGUGAAAUAGGAUGAUCCACCAAGGACUUUCAACAGCGAAGGCAGUCGGUAAGCGCCGUCCAGUUGGUCAAGAGCGAAAGUGUGAGGAUAGACGAUGAUUAGAAACCGUUUUAUUUCACGCCUUAAACGAUACCAUCUCAAGUGGUUCUGGGGGAAGUAUGAUUGCAAGAUUGAAACUUGAAGGUAUUGACGGAAAGAUACCACAAGACGUGGAGUCUGCGGCUCAAUUUGACUCAACACGCAAA-UCUUACCAGACCUGGUGGUGCAUGGCCGCUCCUAGUUCGUGGUGUAAACUGUCUGCCUUAUUGCGUUAACGAGCGAGACAACCAGAGCGCCUGCGCAG-GACGAACGUGGUUGCUCUAGCAGGUCUGUGAUGCCCUUACUCUGGGCCGCACGCGUACUACAAUGCGUGGUAGGGAUCGGAGAUUGGAAUUUCUCGUGAACGAGGAAUGUCUUGUAGGUCUGCGUUAUU-AGCGCGGGCUGACUAUGUCCCUGUCUUU   [922]
;
END;



 [from Barns et al. 1996 PNAS 93:9188]

 begin trees;
 
  utree pnas=((((Flexibact: 0.061548,Flavobact: 0.119902): 0.087037,Planctomy: 
  0.169467): 0.027312,((Desulfovi: 0.097401,((Gloeobact: 0.046858,Synechoco: 0.073425): 
  0.061168,((Leptonema: 0.125621,(Chlorobiu: 0.129472,Chlamydia: 0.150492): 0.029726): 
  0.037272,((Heliobact: 0.086575,(Bacillus_: 0.066895,Clostridi: 0.085782): 0.023452): 
  0.024500,(((Thermomic: 0.119327,Thermus_t: 0.079374): 0.029503,(Thermotog: 0.063284,(Aquifex_p: 
  0.098565,((Tritricho: 0.199512,((Giardia_m: 0.175678,Hexamita_: 0.219659): 0.080379,((Vairimorp: 
  0.213154,Encephali: 0.146264): 0.170005,(Physarum_: 0.175572,(((Dictyoste: 0.101802,((Porphyra_: 
  0.046000,(Babesia_c: 0.052891,Parameciu: 0.032407): 0.017681): 0.009800,((Costaria_: 
  0.025262,Achlya_bi: 0.027623): 0.021980,(Zea_mays: 0.032720,((Coprinus_: 0.030974,Homo_sapi: 
  0.090566): 0.020407,Cryptomon: 0.027381): 0.001796): 0.009373): 0.010101): 0.038120): 
  0.024795,(Naegleria: 0.167833,Entamoeba: 0.135045): 0.039350): 0.023652,(Trypanoso: 
  0.157718,Euglena_g: 0.151850): 0.081778): 0.024206): 0.046480): 0.037954): 0.047334): 
  0.202657,((pJP_27: 0.043872,pJP_78: 0.033809): 0.073583,((((marineSBA: 0.209428,pSL_12: 
  0.060451): 0.064360,(pSL_22: 0.085505,(pSL_4: 0.099318,pSL_17: 0.038405): 0.013970): 
  0.006916): 0.021609,(((Pyrodicti: 0.019002,(Desulfuro: 0.031971,Sulfolobu: 0.083252): 
  0.014211): 0.028489,(Thermofil: 0.043513,Thermopro: 0.080630): 0.020236): 0.017727,(pSL_50: 
  0.096937,pJP_96: 0.061339): 0.015609): 0.013605): 0.021279,(Methanopy: 0.083784,((Methanoba: 
  0.104398,Methanoth: 0.029354): 0.036693,(Thermococ: 0.067505,(((Thermopla: 0.176997,(Methanosp: 
  0.114294,Haloferax: 0.133982): 0.056133): 0.041739,Archaeogl: 0.077897): 0.016797,(Methco.va: 
  0.104705,Methco.ja: 0.022091): 0.046189): 0.015186): 0.017027): 0.013439): 0.041431): 
  0.035926): 0.036530): 0.132286): 0.042630): 0.024804): 0.066252,Arthrobac: 0.101839): 
  0.017192): 0.024545): 0.021638): 0.023967): 0.022243,Agrobacte: 0.097634): 0.010306): 
  0.030954,Rhodocycl: 0.087659,E.coli: 0.086111):0.0; 
  
end;
BioPerl-1.007002/t/data/basic-bush.nex000444000766000024        70013155576321 17401 0ustar00cjfieldsstaff000000000000#NEXUS

BEGIN TAXA;
      dimensions ntax=8;
      taxlabels A B C D E F G H;  
END;

BEGIN CHARACTERS;
      dimensions nchar=6;
      format datatype=protein missing=? gap=-;
      charlabels one two three four five six;
      matrix
A     WITH-B
B     WITH-A
C     WITH-D
D     WITH-C
E     WITH-F
F     WITH-E
G     WITH-H
H     WITH-G;
END;

BEGIN TREES;
       tree basic_bush = (((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1);
END;BioPerl-1.007002/t/data/basic-ladder.nex000444000766000024        66613155576321 17706 0ustar00cjfieldsstaff000000000000#NEXUS

BEGIN TAXA;
      dimensions ntax=8;
      taxlabels A B C D E F G H;  
END;

BEGIN CHARACTERS;
      dimensions nchar=5;
      format datatype=protein missing=? gap=-;
      charlabels one two three four five;
      matrix
A     --ONE
B     --ONE
C     TWO--
D     THREE
E     F-OUR
F     FIVE-
G     SIX--
H     SEVEN;
END;

BEGIN TREES;
       tree basic_ladder = (((((((A:1,B:1):1,C:2):1,D:3):1,E:4):1,F:5):1,G:6):1,H:7);
END;BioPerl-1.007002/t/data/biofpc.cor000444000766000024      4613013155576321 16663 0ustar00cjfieldsstaff000000000000‰ÎÔã'+qªÙÙŽŽ¥¼á/b®ä.4z²÷	)6??fÓ.rÄÆÒü+Zˆºê(m€§)3?w±ÎÎõ67di×*pšã&†ç!‡‡ËÓä&+r{©Úኤà,­,‡‡ËÔä',p{ªØቧâ-®®24h‹  ªô—0[aü-rrƒ¬º57ceùÁÞ1@‡¥ªªØ?OOÆýýAAUûý^bÙ22_âþ&Iƒøø?Xll°³_bžnƒ";\yËË5DgŠ‚áúŽŽ­!‚Œú&0}üGg›Å
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.¾Ód‚ÆåGGµµgguuÔ((¥Øå	*2Xuƒ•¶¾Ýè,h†ÜÜTT¸ÞcÉ÷ˆŸ×)1Ww—¼¼Þê-h‡ááWW“¹â Ø*1Yw–¹ÂÜç0h†ÝäVV’ßcˆÉÏù”‹ äô'-0–­¸ègÙÙÞŒŒ§ßßeyÉ÷ý.ˆ¡ä(-0˜ª¶gÚÚáàùbe¥Êú4Œ¡
*1v•¶»Üå,g…ÙÛMˆˆÛÝc}Êï,Š¢Ûáé	+0Xwƒ–·¼ÙÙè*e€„ÝÝSUŽŽµßß<ddÃÉò÷Y|™µ
J¶»»»øLii‡²µ¾ð(-;ZZŠ”²ÕÕ QX[e¤§ö8‰¢ÌÓã),0p––§³gÙÙã‹¥ºààbgg|«¬Å3ˆ¡ÌÒã((1q••©µÿfÙÙ㨹Þã,gg|¬ÉÎóú-8BioPerl-1.007002/t/data/biofpc.fpc000444000766000024     23070713155576321 16675 0ustar00cjfieldsstaff000000000000// fpc project demo
// 8.5.1  Date: 10:54 Fri 18 Aug 2006  User: will
// Contigs 10  Clones 355  Markers 15  Bands 9772
// Framework Maize Label Chromosome Abbrev Chr Genome 0 AvgBand 4096  AvgInsert 160000
// Configure 429 Tol 7 Cut 1e-13 Apx 0.100 Gel 3300 End 15 Kill -1 Bad 15 Best 10 Log 0 Std 1 Page 3000 Match 2 agarose
// CpM Off 50 1 0 0 TBL 1 1e-12 2 1e-11 3 1e-10
// Build 10/6/105 15:24 Cut 1e-13 Off 50 1 0 0 TBL 1 1e-12 2 1e-11 3 1e-10 
// Clip(0 4600) MinMax(0 65535) Precompute UseSeq DQer(5,1)
// MTP Mndtry 62 MinOlap -5 MaxOlap 10 MinShared 6 Weight 10 MinScore 400 Identity 97 MaxSeqOlap 50000 CtgRatio 3
// BES_pre 0 BES_suff 1 BES_dot 0
  
BAC : "b0297K22"
Map "ctg9" Ends Left 9.000
Map "ctg9" Ends Right 32.000 Oldctg 9
Gel_number    b1297B1
Bands  4386 24
Remark "this is a test"
Shotgun NONE SHOTGUN
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 46 
  
BAC : "b0303H17"
Map "ctg8" Ends Left 27.000
Map "ctg8" Ends Right 58.000 Oldctg 8
Gel_number    b8303C1
Bands  7476 32
Shotgun NONE TILE
Positive_STS "A07" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b0306N07"
Map "ctg2" Ends Left 8.000
Map "ctg2" Ends Right 36.000 Oldctg 2
Gel_number    b8306C1
Bands  7508 29
Exact_match_to_cosmid "c1074L23"
Shotgun NONE SENT
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0306N18"
Map "ctg3" Ends Left 78.000
Map "ctg3" Ends Right 106.000 Oldctg 3
Gel_number    b8306D1
Bands  7537 29
Approximate_match_to_cosmid "c0186L14"
Shotgun NONE READY
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b0307M15"
Map "ctg1" Ends Left 36.000
Map "ctg1" Ends Right 53.000 Oldctg 1
Gel_number    b1307A1
Bands  4410 18
Exact_match_to_cosmid "c1024E06"
Shotgun NONE CANCELLED
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0316M15"
Map "ctg2" Ends Left 33.000
Map "ctg2" Ends Right 60.000 Oldctg 2
Gel_number    b1316A1
Bands  4428 28
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0319B18"
Map "ctg5" Ends Left 30.000
Map "ctg5" Ends Right 64.000 Oldctg 5
Gel_number    b1319D1
Bands  4456 35
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0324I14"
Map "ctg9" Ends Left 7.000
Map "ctg9" Ends Right 29.000 Oldctg 9
Gel_number    b1324B1
Bands  4491 23
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0325O10"
Map "ctg4" Ends Left 72.000
Map "ctg4" Ends Right 95.000 Oldctg 4
Gel_number    b1325B1
Bands  4514 24
Exact_match_to_cosmid "H0054L03"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0326L07"
Map "ctg9" Ends Left 23.000
Map "ctg9" Ends Right 47.000 Oldctg 9
Gel_number    b1326C1
Bands  4538 25
Positive_STS "C24" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b0327I21"
Map "ctg7" Ends Left 9.000
Map "ctg7" Ends Right 29.000 Oldctg 7
Gel_number    b1327A1
Bands  4563 21
Approximate_match_to_cosmid "c1115H20"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0332M08"
Map "ctg1" Ends Left 54.000
Map "ctg1" Ends Right 89.000 Oldctg 1
Gel_number    b1332B1
Bands  4584 36
Approximate_match_to_cosmid "c1017J12"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0333F08"
Map "ctg1" Ends Left 1.000
Map "ctg1" Ends Right 29.000 Oldctg 1
Gel_number    b1333D1
Bands  4620 29
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0334C23"
Map "ctg4" Ends Left 50.000
Map "ctg4" Ends Right 72.000 Oldctg 4
Gel_number    b1334A1
Bands  4649 23
Approximate_match_to_cosmid "c1082B18"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0336D23"
Map "ctg7" Ends Left 3.000
Map "ctg7" Ends Right 26.000 Oldctg 7
Gel_number    b1336C1
Bands  4672 24
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0336J22"
Map "ctg6" Ends Left 62.000
Map "ctg6" Ends Right 83.000 Oldctg 6
Gel_number    b1336D1
Bands  4696 22
Exact_match_to_cosmid "c1085E05"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0340P21"
Map "ctg3" Ends Left 20.000
Map "ctg3" Ends Right 39.000 Oldctg 3
Gel_number    b1340C1
Bands  4718 20
Exact_match_to_cosmid "b1584L19"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b0341J19"
Map "ctg1" Ends Left 13.000
Map "ctg1" Ends Right 38.000 Oldctg 1
Gel_number    b1341C1
Bands  4776 26
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0341K22"
Map "ctg6" Ends Left 71.000
Map "ctg6" Ends Right 92.000 Oldctg 6
Gel_number    b1341B1
Bands  4754 22
Approximate_match_to_cosmid "c1085E05"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0341O09"
Map "ctg8" Ends Left 11.000
Map "ctg8" Ends Right 26.000 Oldctg 8
Gel_number    b1341A1
Bands  4738 16
Exact_match_to_cosmid "b1622G13"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0343C02"
Map "ctg2" Ends Left 36.000
Map "ctg2" Ends Right 68.000 Oldctg 2
Gel_number    b1343B1
Bands  4802 33
Positive_STS "A01" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b0343L16"
Map "ctg7" Ends Left 5.000
Map "ctg7" Ends Right 23.000 Oldctg 7
Gel_number    b1343D1
Bands  4835 19
Approximate_match_to_cosmid "b0336D23"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0347L04"
Map "ctg7" Ends Left 0.000
Map "ctg7" Ends Right 19.000 Oldctg 7
Gel_number    b1347D1
Bands  4854 20
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0368F18"
Map "ctg3" Ends Left 61.000
Map "ctg3" Ends Right 83.000 Oldctg 3
Gel_number    b1368D1
Bands  4898 23
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b0368G07"
Map "ctg3" Ends Left 109.000
Map "ctg3" Ends Right 132.000 Oldctg 3
Gel_number    b1368A1
Bands  4874 24
Approximate_match_to_cosmid "c1065C21"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b0372I14"
Map "ctg4" Ends Left 13.000
Map "ctg4" Ends Right 42.000 Oldctg 4
Gel_number    b1372B1
Bands  4921 30
Positive_STS "D57" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b0376P09"
Map "ctg9" Ends Left 6.000
Map "ctg9" Ends Right 26.000 Oldctg 9
Gel_number    b1376C1
Bands  4951 21
Approximate_match_to_cosmid "b0324I14"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0377M02"
Map "ctg2" Ends Left 69.000
Map "ctg2" Ends Right 101.000 Oldctg 2
Gel_number    b1377B1
Bands  4972 33
Approximate_match_to_cosmid "H0002F22"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0379F02"
Map "ctg6" Ends Left 26.000
Map "ctg6" Ends Right 50.000 Oldctg 6
Gel_number    b1379D1
Bands  5005 25
Approximate_match_to_cosmid "H0082F20"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0380N03"
Map "ctg6" Ends Left 8.000
Map "ctg6" Ends Right 32.000 Oldctg 6
Gel_number    b1380C1
Bands  5030 25
Approximate_match_to_cosmid "c1053I24"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0382H22"
Map "ctg3" Ends Left 121.000
Map "ctg3" Ends Right 152.000 Oldctg 3
Gel_number    b1382D1
Bands  5055 32
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b0382N02"
Map "ctg6" Ends Left 4.000
Map "ctg6" Ends Right 35.000 Oldctg 6
Gel_number    b1382D1
Bands  5087 32
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0390G23"
Map "ctg5" Ends Left 14.000
Map "ctg5" Ends Right 41.000 Oldctg 5
Gel_number    b1390A1
Bands  5119 28
Approximate_match_to_cosmid "H0005K08"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0391G06"
Map "ctg1" Ends Left 53.000
Map "ctg1" Ends Right 86.000 Oldctg 1
Gel_number    b1391B1
Bands  5147 34
Approximate_match_to_cosmid "c1017J12"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0393C16"
Map "ctg2" Ends Left 72.000
Map "ctg2" Ends Right 101.000 Oldctg 2
Gel_number    b1393B1
Bands  5181 30
Approximate_match_to_cosmid "H0002F22"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0398K02"
Map "ctg8" Ends Left 12.000
Map "ctg8" Ends Right 22.000 Oldctg 8
Gel_number    b1398B1
Bands  5211 11
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0398L18"
Map "ctg3" Ends Left 76.000
Map "ctg3" Ends Right 97.000 Oldctg 3
Gel_number    b1398D1
Bands  5222 22
Approximate_match_to_cosmid "c0186L14"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b0399D10"
Map "ctg3" Ends Left 55.000
Map "ctg3" Ends Right 77.000 Oldctg 3
Gel_number    b1399D1
Bands  5244 23
Approximate_match_to_cosmid "H0006G12"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b0406I02"
Map "ctg6" Ends Left 71.000
Map "ctg6" Ends Right 93.000 Oldctg 6
Gel_number    b1406B1
Bands  5288 23
Exact_match_to_cosmid "c1085E05"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0406I15"
Map "ctg3" Ends Left 29.000
Map "ctg3" Ends Right 49.000 Oldctg 3
Gel_number    b1406A1
Bands  5267 21
Approximate_match_to_cosmid "b1246P23"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b0407D07"
Map "ctg2" Ends Left 32.000
Map "ctg2" Ends Right 52.000 Oldctg 2
Gel_number    b1407C1
Bands  5311 21
Exact_match_to_cosmid "b1522B13"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0411C10"
Map "ctg10" Ends Left 8.000
Map "ctg10" Ends Right 30.000 Oldctg 10
Gel_number    b1411B1
Bands  5332 23
Approximate_match_to_cosmid "H0201H09"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0412E22"
Map "ctg8" Ends Left 47.000
Map "ctg8" Ends Right 71.000 Oldctg 8
Gel_number    b1412B1
Bands  5355 25
Positive_STS "A07" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b0419N02"
Map "ctg3" Ends Left 49.000
Map "ctg3" Ends Right 71.000 Oldctg 3
Gel_number    b1419D1
Bands  5380 23
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b0435L06"
Map "ctg4" Ends Left 80.000
Map "ctg4" Ends Right 107.000 Oldctg 4
Gel_number    b1435D1
Bands  9538 28
Approximate_match_to_cosmid "c1050F12"
Remark "new_add"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 46 
  
BAC : "b0439K14"
Map "ctg5" Ends Left 35.000
Map "ctg5" Ends Right 62.000 Oldctg 5
Gel_number    b1439B1
Bands  5403 28
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0441C07"
Map "ctg9" Ends Left 35.000
Map "ctg9" Ends Right 55.000 Oldctg 9
Gel_number    b1441A1
Bands  5431 21
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0443N08"
Gel_number    b1443D1
Bands  5452 30
Creation_date 105 6 6 18 22 
Modified_date 105 6 6 18 22 
  
BAC : "b0447G07"
Map "ctg9" Ends Left 20.000
Map "ctg9" Ends Right 41.000 Oldctg 9
Gel_number    b1447A1
Bands  5482 22
Positive_STS "C24" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b0449B24"
Map "ctg1" Ends Left 69.000
Map "ctg1" Ends Right 92.000 Oldctg 1
Gel_number    b1449D1
Bands  5504 24
Approximate_match_to_cosmid "c1032M05"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b0452G20"
Map "ctg2" Ends Left 57.000
Map "ctg2" Ends Right 85.000 Oldctg 2
Gel_number    b1452B1
Bands  5528 29
Positive_STS "A01" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b0461E16"
Map "ctg6" Ends Left 19.000
Map "ctg6" Ends Right 41.000 Oldctg 6
Gel_number    b1461B1
Bands  5557 23
Approximate_match_to_cosmid "b1531L10"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1004I23"
Map "ctg3" Ends Left 95.000
Map "ctg3" Ends Right 124.000 Oldctg 3
Gel_number    b1004A1
Bands  3756 30
Approximate_match_to_cosmid "c1098L12"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1046O08"
Map "ctg1" Ends Left 60.000
Map "ctg1" Ends Right 94.000 Oldctg 1
Gel_number    b1046B1
Bands  3786 35
Positive_STS "J9" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b1075H04"
Map "ctg1" Ends Left 0.000
Map "ctg1" Ends Right 29.000 Oldctg 1
Gel_number    b1075D1
Bands  3821 30
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1075N16"
Map "ctg3" Ends Left 52.000
Map "ctg3" Ends Right 72.000 Oldctg 3
Gel_number    b1075D1
Bands  3851 21
Exact_match_to_cosmid "b1503B23"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1081C22"
Map "ctg6" Ends Left 45.000
Map "ctg6" Ends Right 73.000 Oldctg 6
Gel_number    b1081B1
Bands  3872 29
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1083O09"
Map "ctg3" Ends Left 121.000
Map "ctg3" Ends Right 150.000 Oldctg 3
Gel_number    b1083A1
Bands  3901 30
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1085K18"
Map "ctg3" Ends Left 120.000
Map "ctg3" Ends Right 137.000 Oldctg 3
Gel_number    b1085B1
Bands  3931 18
Exact_match_to_cosmid "c1065C21"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1101J03"
Map "ctg2" Ends Left 14.000
Map "ctg2" Ends Right 51.000 Oldctg 2
Gel_number    b1101C1
Bands  3949 38
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1103E10"
Map "ctg9" Ends Left 7.000
Map "ctg9" Ends Right 29.000 Oldctg 9
Gel_number    b1103B1
Bands  3987 23
Exact_match_to_cosmid "b0324I14"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1153C20"
Map "ctg1" Ends Left 77.000
Map "ctg1" Ends Right 105.000 Oldctg 1
Gel_number    b1153B1
Bands  9509 29
Approximate_match_to_cosmid "c1032M05"
Remark "new_add"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 46 
  
BAC : "b1154L07"
Map "ctg6" Ends Left 4.000
Map "ctg6" Ends Right 32.000 Oldctg 6
Gel_number    b1154C1
Bands  4010 29
Exact_match_to_cosmid "c1053I24"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1158P05"
Map "ctg5" Ends Left 14.000
Map "ctg5" Ends Right 47.000 Oldctg 5
Gel_number    b1158C1
Bands  4039 34
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1177F07"
Map "ctg1" Ends Left 47.000
Map "ctg1" Ends Right 75.000 Oldctg 1
Gel_number    b1177C1
Bands  4073 29
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1245K13"
Map "ctg3" Ends Left 52.000
Map "ctg3" Ends Right 70.000 Oldctg 3
Gel_number    b1245A1
Bands  4102 19
Exact_match_to_cosmid "H0006G12"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1246P23"
Map "ctg3" Ends Left 30.000
Map "ctg3" Ends Right 52.000 Oldctg 3
Gel_number    b1246C1
Bands  4121 23
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1257O16"
Map "ctg8" Ends Left 33.000
Map "ctg8" Ends Right 69.000 Oldctg 8
Gel_number    b1257B1
Bands  4144 37
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1259M17"
Map "ctg7" Ends Left 10.000
Map "ctg7" Ends Right 30.000 Oldctg 7
Gel_number    b1259A1
Bands  4181 21
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1264H12"
Map "ctg3" Ends Left 52.000
Map "ctg3" Ends Right 78.000 Oldctg 3
Gel_number    b1264D1
Bands  4202 27
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1264N04"
Map "ctg6" Ends Left 26.000
Map "ctg6" Ends Right 50.000 Oldctg 6
Gel_number    b1264D1
Bands  4229 25
Positive_Locus "J5" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b1266K23"
Map "ctg4" Ends Left 62.000
Map "ctg4" Ends Right 81.000 Oldctg 4
Gel_number    b1266A1
Bands  4254 20
Exact_match_to_cosmid "c1082E16"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1274A11"
Map "ctg3" Ends Left 63.000
Map "ctg3" Ends Right 88.000 Oldctg 3
Gel_number    b1274A1
Bands  4303 26
Approximate_match_to_cosmid "H0198H02"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1274M03"
Map "ctg3" Ends Left 138.000
Map "ctg3" Ends Right 166.000 Oldctg 3
Gel_number    b1274A1
Bands  4274 29
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1282L07"
Map "ctg2" Ends Left 28.000
Map "ctg2" Ends Right 56.000 Oldctg 2
Gel_number    b1282C1
Bands  4329 29
Approximate_match_to_cosmid "b1522B13"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1285J21"
Map "ctg4" Ends Left 59.000
Map "ctg4" Ends Right 86.000 Oldctg 4
Gel_number    b1285C1
Bands  4358 28
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1468I11"
Map "ctg1" Ends Left 39.000
Map "ctg1" Ends Right 74.000 Oldctg 1
Gel_number    b1468A1
Bands  5580 36
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1477K21"
Map "ctg7" Ends Left 14.000
Map "ctg7" Ends Right 28.000 Oldctg 7
Gel_number    b1477A1
Bands  5616 15
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1478J02"
Map "ctg9" Ends Left 12.000
Map "ctg9" Ends Right 33.000 Oldctg 9
Gel_number    b1478D1
Bands  5631 22
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1482G15"
Map "ctg6" Ends Left 50.000
Map "ctg6" Ends Right 75.000 Oldctg 6
Gel_number    b1482A1
Bands  5653 26
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1482I12"
Map "ctg6" Ends Left 29.000
Map "ctg6" Ends Right 50.000 Oldctg 6
Gel_number    b1482B1
Bands  5679 22
Approximate_match_to_cosmid "H0082F20"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1494B06"
Map "ctg3" Ends Left 23.000
Map "ctg3" Ends Right 44.000 Oldctg 3
Gel_number    b1494D1
Bands  5701 22
Approximate_match_to_cosmid "b1584L19"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1498E10"
Map "ctg3" Ends Left 125.000
Map "ctg3" Ends Right 152.000 Oldctg 3
Gel_number    b1498B1
Bands  5723 28
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1502M06"
Map "ctg8" Ends Left 7.000
Map "ctg8" Ends Right 24.000 Oldctg 8
Gel_number    b1502B1
Bands  5751 18
Exact_match_to_cosmid "c0021L10"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1503B23"
Map "ctg3" Ends Left 50.000
Map "ctg3" Ends Right 76.000 Oldctg 3
Gel_number    b1503C1
Bands  5769 27
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1503L05"
Map "ctg2" Ends Left 61.000
Map "ctg2" Ends Right 87.000 Oldctg 2
Gel_number    b1503C1
Bands  5796 27
Exact_match_to_cosmid "b1588O10"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1505H15"
Map "ctg6" Ends Left 38.000
Map "ctg6" Ends Right 66.000 Oldctg 6
Gel_number    b1505C1
Bands  5823 29
Approximate_match_to_cosmid "c0108C20"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1509B02"
Map "ctg4" Ends Left 60.000
Map "ctg4" Ends Right 90.000 Oldctg 4
Gel_number    b1509D1
Bands  5852 31
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1511G13"
Map "ctg4" Ends Left 79.000
Map "ctg4" Ends Right 104.000 Oldctg 4
Gel_number    b1511A1
Bands  9566 26
Approximate_match_to_cosmid "c1050F12"
Remark "new_add"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 46 
  
BAC : "b1512M05"
Map "ctg9" Ends Left 13.000
Map "ctg9" Ends Right 40.000 Oldctg 9
Gel_number    b1512A1
Bands  5883 28
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1514A05"
Map "ctg2" Ends Left 20.000
Map "ctg2" Ends Right 50.000 Oldctg 2
Gel_number    b1514A1
Bands  5911 31
Exact_match_to_cosmid "b1566O10"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1520O04"
Map "ctg6" Ends Left 19.000
Map "ctg6" Ends Right 40.000 Oldctg 6
Gel_number    b1520B1
Bands  5942 22
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1522B13"
Map "ctg2" Ends Left 22.000
Map "ctg2" Ends Right 56.000 Oldctg 2
Gel_number    b1522C1
Bands  5991 35
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1522D12"
Map "ctg10" Ends Left 7.000
Map "ctg10" Ends Right 30.000 Oldctg 10
Gel_number    b1522D1
Bands  6048 24
Approximate_match_to_cosmid "H0201H09"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1522J10"
Map "ctg3" Ends Left 64.000
Map "ctg3" Ends Right 85.000 Oldctg 3
Gel_number    b1522D1
Bands  6026 22
Positive_STS "B13" New
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1522J13"
Map "ctg1" Ends Left 13.000
Map "ctg1" Ends Right 39.000 Oldctg 1
Gel_number    b1522C1
Bands  5964 27
Approximate_match_to_cosmid "c1086K04"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1529D11"
Map "ctg3" Ends Left 127.000
Map "ctg3" Ends Right 149.000 Oldctg 3
Gel_number    b1529C1
Bands  6072 23
Approximate_match_to_cosmid "b0382H22"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1529P11"
Map "ctg2" Ends Left 56.000
Map "ctg2" Ends Right 82.000 Oldctg 2
Gel_number    b1529C1
Bands  6095 27
Exact_match_to_cosmid "b1588O10"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1531L10"
Map "ctg6" Ends Left 18.000
Map "ctg6" Ends Right 42.000 Oldctg 6
Gel_number    b1531D1
Bands  6122 25
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1537B07"
Map "ctg2" Ends Left 39.000
Map "ctg2" Ends Right 73.000 Oldctg 2
Gel_number    b1537C1
Bands  6182 35
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1537E21"
Map "ctg5" Ends Left 25.000
Map "ctg5" Ends Right 59.000 Oldctg 5
Gel_number    b1537A1
Bands  6147 35
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1540A14"
Map "ctg2" Ends Left 19.000
Map "ctg2" Ends Right 44.000 Oldctg 2
Gel_number    b1540B1
Bands  6244 26
Exact_match_to_cosmid "b1101J03"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1540M20"
Map "ctg1" Ends Left 1.000
Map "ctg1" Ends Right 27.000 Oldctg 1
Gel_number    b1540B1
Bands  6217 27
Approximate_match_to_cosmid "b1075H04"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1548D16"
Map "ctg1" Ends Left 6.000
Map "ctg1" Ends Right 28.000 Oldctg 1
Gel_number    b1548D1
Bands  6270 23
Exact_match_to_cosmid "b1075H04"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1557J13"
Map "ctg2" Ends Left 68.000
Map "ctg2" Ends Right 96.000 Oldctg 2
Gel_number    b1557C1
Bands  6293 29
Approximate_match_to_cosmid "H0002F22"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1566O10"
Map "ctg2" Ends Left 18.000
Map "ctg2" Ends Right 53.000 Oldctg 2
Gel_number    b1566B1
Bands  6322 36
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1567H22"
Map "ctg8" Ends Left 24.000
Map "ctg8" Ends Right 53.000 Oldctg 8
Gel_number    b1567D1
Bands  6358 30
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1568O15"
Map "ctg3" Ends Left 77.000
Map "ctg3" Ends Right 95.000 Oldctg 3
Gel_number    b1568A1
Bands  6388 19
Approximate_match_to_cosmid "c1041H02"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1570G15"
Map "ctg4" Ends Left 61.000
Map "ctg4" Ends Right 81.000 Oldctg 4
Gel_number    b1570A1
Bands  6407 21
Exact_match_to_cosmid "c1082E16"
Positive_STS "D58" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b1573O12"
Map "ctg3" Ends Left 97.000
Map "ctg3" Ends Right 124.000 Oldctg 3
Gel_number    b1573B1
Bands  6428 28
Approximate_match_to_cosmid "c1098L12"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1577M16"
Map "ctg3" Ends Left 129.000
Map "ctg3" Ends Right 159.000 Oldctg 3
Gel_number    b1577B1
Bands  6456 31
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1584L19"
Map "ctg3" Ends Left 17.000
Map "ctg3" Ends Right 44.000 Oldctg 3
Gel_number    b1584C1
Bands  6487 28
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1585M07"
Map "ctg1" Ends Left 57.000
Map "ctg1" Ends Right 85.000 Oldctg 1
Gel_number    b1585A1
Bands  6515 29
Approximate_match_to_cosmid "c1017J12"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1586A22"
Map "ctg2" Ends Left 68.000
Map "ctg2" Ends Right 95.000 Oldctg 2
Gel_number    b1586B1
Bands  6544 28
Approximate_match_to_cosmid "H0002F22"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1588H16"
Map "ctg10" Ends Left 0.000
Map "ctg10" Ends Right 22.000 Oldctg 10
Gel_number    b1588D1
Bands  6626 23
Positive_STS "A10" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b1588K02"
Map "ctg2" Ends Left 70.000
Map "ctg2" Ends Right 89.000 Oldctg 2
Gel_number    b1588B1
Bands  6606 20
Exact_match_to_cosmid "H0016J06"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1588O10"
Map "ctg2" Ends Left 56.000
Map "ctg2" Ends Right 89.000 Oldctg 2
Gel_number    b1588B1
Bands  6572 34
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1593C11"
Map "ctg2" Ends Left 68.000
Map "ctg2" Ends Right 89.000 Oldctg 2
Gel_number    b1593A1
Bands  6649 22
Exact_match_to_cosmid "H0276H10"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1596H05"
Map "ctg8" Ends Left 16.000
Map "ctg8" Ends Right 42.000 Oldctg 8
Gel_number    b1596C1
Bands  6671 27
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1599A19"
Map "ctg4" Ends Left 57.000
Map "ctg4" Ends Right 80.000 Oldctg 4
Gel_number    b1599A1
Bands  6727 24
Approximate_match_to_cosmid "c1082E16"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1599K15"
Map "ctg4" Ends Left 23.000
Map "ctg4" Ends Right 51.000 Oldctg 4
Gel_number    b1599A1
Bands  6698 29
Approximate_match_to_cosmid "H0143J16"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1601G04"
Map "ctg1" Ends Left 36.000
Map "ctg1" Ends Right 53.000 Oldctg 1
Gel_number    b1601B1
Bands  6751 18
Exact_match_to_cosmid "c1024E06"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1601H13"
Map "ctg5" Ends Left 44.000
Map "ctg5" Ends Right 65.000 Oldctg 5
Gel_number    b1601C1
Bands  6797 22
Approximate_match_to_cosmid "b1601H14"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1601H14"
Map "ctg5" Ends Left 41.000
Map "ctg5" Ends Right 70.000 Oldctg 5
Gel_number    b1601D1
Bands  6819 30
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1601I10"
Map "ctg6" Ends Left 15.000
Map "ctg6" Ends Right 42.000 Oldctg 6
Gel_number    b1601B1
Bands  6769 28
Positive_Locus "J5" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b1604O19"
Map "ctg3" Ends Left 53.000
Map "ctg3" Ends Right 86.000 Oldctg 3
Gel_number    b1604A1
Bands  6849 34
Positive_STS "B13" New
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1607F08"
Map "ctg2" Ends Left 61.000
Map "ctg2" Ends Right 90.000 Oldctg 2
Gel_number    b1607D1
Bands  6909 30
Positive_STS "A01" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b1607I12"
Map "ctg8" Ends Left 21.000
Map "ctg8" Ends Right 46.000 Oldctg 8
Gel_number    b1607B1
Bands  6883 26
Approximate_match_to_cosmid "H0186L03"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1610I15"
Map "ctg3" Ends Left 53.000
Map "ctg3" Ends Right 75.000 Oldctg 3
Gel_number    b1610A1
Bands  6939 23
Exact_match_to_cosmid "H0006G12"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1613A17"
Map "ctg6" Ends Left 6.000
Map "ctg6" Ends Right 32.000 Oldctg 6
Gel_number    b1613A1
Bands  6962 27
Approximate_match_to_cosmid "c1053I24"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1613P20"
Map "ctg4" Ends Left 48.000
Map "ctg4" Ends Right 71.000 Oldctg 4
Gel_number    b1613D1
Bands  6989 24
Positive_STS "D58" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b1622G13"
Map "ctg8" Ends Left 11.000
Map "ctg8" Ends Right 32.000 Oldctg 8
Gel_number    b1622A1
Bands  7013 22
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1626B19"
Map "ctg6" Ends Left 45.000
Map "ctg6" Ends Right 70.000 Oldctg 6
Gel_number    b1626C1
Bands  7060 26
Approximate_match_to_cosmid "c1037B24"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1626J19"
Map "ctg6" Ends Left 46.000
Map "ctg6" Ends Right 70.000 Oldctg 6
Gel_number    b1626C1
Bands  7035 25
Exact_match_to_cosmid "c0108C20"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1628C03"
Map "ctg8" Ends Left 0.000
Map "ctg8" Ends Right 22.000 Oldctg 8
Gel_number    b1628A1
Bands  7086 23
Positive_STS "A05" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b1628F14"
Map "ctg9" Ends Left 18.000
Map "ctg9" Ends Right 50.000 Oldctg 9
Gel_number    b1628D1
Bands  7129 33
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1628J23"
Gel_number    b1628C1
Bands  7109 20
Creation_date 105 6 6 18 22 
Modified_date 105 6 6 18 22 
  
BAC : "b1630L22"
Map "ctg3" Ends Left 125.000
Map "ctg3" Ends Right 152.000 Oldctg 3
Gel_number    b1630D1
Bands  7162 28
Approximate_match_to_cosmid "b1498E10"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1631H15"
Map "ctg1" Ends Left 6.000
Map "ctg1" Ends Right 29.000 Oldctg 1
Gel_number    b1631C1
Bands  7190 24
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1632J14"
Map "ctg8" Ends Left 66.000
Map "ctg8" Ends Right 92.000 Oldctg 8
Gel_number    b1632D1
Bands  7214 27
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1633E09"
Map "ctg2" Ends Left 54.000
Map "ctg2" Ends Right 81.000 Oldctg 2
Gel_number    b1633A1
Bands  7241 28
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1633J03"
Map "ctg1" Ends Left 29.000
Map "ctg1" Ends Right 49.000 Oldctg 1
Gel_number    b1633C1
Bands  7269 21
Approximate_match_to_cosmid "c1024E06"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1634P04"
Map "ctg6" Ends Left 21.000
Map "ctg6" Ends Right 42.000 Oldctg 6
Gel_number    b1634D1
Bands  7290 22
Positive_Locus "J5" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b1642H04"
Map "ctg1" Ends Left 63.000
Map "ctg1" Ends Right 90.000 Oldctg 1
Gel_number    b1642D1
Bands  7312 28
Exact_match_to_cosmid "c1017J12"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b1644B11"
Map "ctg3" Ends Left 51.000
Map "ctg3" Ends Right 84.000 Oldctg 3
Gel_number    b1644C1
Bands  7340 34
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "b1644D20"
Map "ctg4" Ends Left 20.000
Map "ctg4" Ends Right 44.000 Oldctg 4
Gel_number    b1644D1
Bands  7374 25
Positive_STS "D57" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "b1645E04"
Map "ctg8" Ends Left 11.000
Map "ctg8" Ends Right 30.000 Oldctg 8
Gel_number    b1645B1
Bands  7399 20
Exact_match_to_cosmid "b1622G13"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b3299K19"
Map "ctg1" Ends Left 80.000
Map "ctg1" Ends Right 106.000 Oldctg 1
Gel_number    b3299A1
Bands  9592 27
Approximate_match_to_cosmid "c1032M05"
Remark "new_add"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 46 
  
BAC : "b4305E09"
Map "ctg6" Ends Left 29.000
Map "ctg6" Ends Right 49.000 Oldctg 6
Gel_number    b4305A1
Bands  7419 21
Exact_match_to_cosmid "H0082F20"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "b6294A03"
Map "ctg6" Ends Left 38.000
Map "ctg6" Ends Right 73.000 Oldctg 6
Gel_number    b6294A1
Bands  7440 36
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c0021L10"
Map "ctg8" Ends Left 1.000
Map "ctg8" Ends Right 31.000 Oldctg 8
Gel_number    c0021D1
Bands  7566 31
Positive_STS "A05" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "c0071G24"
Map "ctg3" Ends Left 102.000
Map "ctg3" Ends Right 130.000 Oldctg 3
Gel_number    c0071B1
Bands  7597 29
Approximate_match_to_cosmid "c1098L12"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c0072H16"
Map "ctg3" Ends Left 98.000
Map "ctg3" Ends Right 134.000 Oldctg 3
Gel_number    c0072D1
Bands  7626 37
Approximate_match_to_cosmid "c1098L12"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c0085G04"
Map "ctg6" Ends Left 24.000
Map "ctg6" Ends Right 81.000 Oldctg 6
Gel_number    c1085B1
Bands  8792 58
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c0105F22"
Map "ctg3" Ends Left 41.000
Map "ctg3" Ends Right 71.000 Oldctg 3
Gel_number    c1105D1
Bands  9162 31
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c0105P24"
Map "ctg1" Ends Left 24.000
Map "ctg1" Ends Right 61.000 Oldctg 1
Gel_number    c1105D1
Bands  9124 38
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c0107A18"
Map "ctg1" Ends Left 18.000
Map "ctg1" Ends Right 62.000 Oldctg 1
Gel_number    c1107B1
Bands  9193 45
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c0108C20"
Map "ctg6" Ends Left 33.000
Map "ctg6" Ends Right 73.000 Oldctg 6
Gel_number    c1108B1
Bands  9238 41
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c0109A18"
Map "ctg6" Ends Left 30.000
Map "ctg6" Ends Right 66.000 Oldctg 6
Gel_number    c1109B1
Bands  9314 37
Positive_STS "J130" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "c0109L22"
Map "ctg8" Ends Left 30.000
Map "ctg8" Ends Right 62.000 Oldctg 8
Gel_number    c1109D1
Bands  9351 33
Approximate_match_to_cosmid "c0109M22"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c0109M22"
Map "ctg8" Ends Left 30.000
Map "ctg8" Ends Right 64.000 Oldctg 8
Gel_number    c1109B1
Bands  9279 35
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c0186L14"
Map "ctg3" Ends Left 70.000
Map "ctg3" Ends Right 112.000 Oldctg 3
Gel_number    c0186D1
Bands  7663 43
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c1010O04"
Map "ctg3" Ends Left 97.000
Map "ctg3" Ends Right 133.000 Oldctg 3
Gel_number    c1010B1
Bands  7706 37
Positive_STS "B01" New
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c1017J12"
Map "ctg1" Ends Left 48.000
Map "ctg1" Ends Right 94.000 Oldctg 1
Gel_number    c1017D1
Bands  7743 47
Positive_STS "J9" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "c1021A24"
Map "ctg2" Ends Left 40.000
Map "ctg2" Ends Right 77.000 Oldctg 2
Gel_number    c1021B1
Bands  7790 38
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1024C16"
Map "ctg1" Ends Left 29.000
Map "ctg1" Ends Right 70.000 Oldctg 1
Gel_number    c1024B1
Bands  7870 42
Approximate_match_to_cosmid "c1024E06"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1024E06"
Map "ctg1" Ends Left 34.000
Map "ctg1" Ends Right 75.000 Oldctg 1
Gel_number    c1024B1
Bands  7828 42
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1025O11"
Map "ctg3" Ends Left 7.000
Map "ctg3" Ends Right 42.000 Oldctg 3
Gel_number    c1025A1
Bands  7912 36
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c1031I14"
Map "ctg3" Ends Left 0.000
Map "ctg3" Ends Right 30.000 Oldctg 3
Gel_number    c1031B1
Bands  7948 31
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c1032I23"
Map "ctg5" Ends Left 15.000
Map "ctg5" Ends Right 56.000 Oldctg 5
Gel_number    c1032A1
Bands  9658 42
Remark "new_add"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 46 
  
BAC : "c1032M05"
Map "ctg1" Ends Left 68.000
Map "ctg1" Ends Right 106.000 Oldctg 1
Gel_number    c1032A1
Bands  9619 39
Remark "new_add"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 46 
  
BAC : "c1032M10"
Gel_number    c1032B1
Bands  7979 35
Creation_date 105 6 6 18 22 
Modified_date 105 6 6 18 22 
  
BAC : "c1036J07"
Map "ctg10" Ends Left 8.000
Map "ctg10" Ends Right 32.000 Oldctg 10
Gel_number    c1036C1
Bands  8014 25
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1037B24"
Map "ctg6" Ends Left 33.000
Map "ctg6" Ends Right 73.000 Oldctg 6
Gel_number    c1037D1
Bands  8039 41
Positive_STS "J130" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "c1041H02"
Map "ctg3" Ends Left 80.000
Map "ctg3" Ends Right 115.000 Oldctg 3
Gel_number    c1041D1
Bands  8080 36
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c1042M12"
Map "ctg1" Ends Left 27.000
Map "ctg1" Ends Right 53.000 Oldctg 1
Gel_number    c1042B1
Bands  8116 27
Approximate_match_to_cosmid "c0107A18"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1043L12"
Map "ctg5" Ends Left 24.000
Map "ctg5" Ends Right 63.000 Oldctg 5
Gel_number    c1043D1
Bands  8143 40
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1047E05"
Map "ctg9" Ends Left 28.000
Map "ctg9" Ends Right 52.000 Oldctg 9
Gel_number    c1047A1
Bands  8183 25
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1050F12"
Map "ctg4" Ends Left 73.000
Map "ctg4" Ends Right 110.000 Oldctg 4
Gel_number    c1050D1
Bands  9735 38
Remark "new_add"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 46 
  
BAC : "c1050J12"
Map "ctg4" Ends Left 75.000
Map "ctg4" Ends Right 109.000 Oldctg 4
Gel_number    c1050D1
Bands  9700 35
Approximate_match_to_cosmid "c1050F12"
Remark "new_add"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 46 
  
BAC : "c1052J13"
Map "ctg6" Ends Left 33.000
Map "ctg6" Ends Right 72.000 Oldctg 6
Gel_number    c1052C1
Bands  8208 40
Positive_STS "J130" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "c1053I24"
Map "ctg6" Ends Left 0.000
Map "ctg6" Ends Right 36.000 Oldctg 6
Gel_number    c1053B1
Bands  8248 37
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1056C07"
Map "ctg3" Ends Left 2.000
Map "ctg3" Ends Right 35.000 Oldctg 3
Gel_number    c1056A1
Bands  8285 34
Approximate_match_to_cosmid "c1096G11"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c1058K17"
Map "ctg3" Ends Left 43.000
Map "ctg3" Ends Right 70.000 Oldctg 3
Gel_number    c1058A1
Bands  8319 28
Approximate_match_to_cosmid "c0105F22"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c1060H12"
Map "ctg8" Ends Left 12.000
Map "ctg8" Ends Right 32.000 Oldctg 8
Gel_number    c1060D1
Bands  8365 21
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1060I02"
Map "ctg8" Ends Left 13.000
Map "ctg8" Ends Right 30.000 Oldctg 8
Gel_number    c1060B1
Bands  8347 18
Positive_STS "A07" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "c1063E08"
Map "ctg2" Ends Left 43.000
Map "ctg2" Ends Right 80.000 Oldctg 2
Gel_number    c1063B1
Bands  8386 38
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1065C21"
Map "ctg3" Ends Left 110.000
Map "ctg3" Ends Right 143.000 Oldctg 3
Gel_number    c1065A1
Bands  8424 34
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c1067H04"
Map "ctg6" Ends Left 3.000
Map "ctg6" Ends Right 32.000 Oldctg 6
Gel_number    c1067D1
Bands  8458 30
Exact_match_to_cosmid "c1053I24"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1074L23"
Map "ctg2" Ends Left 4.000
Map "ctg2" Ends Right 45.000 Oldctg 2
Gel_number    c1074C1
Bands  8529 42
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1074P15"
Map "ctg2" Ends Left 0.000
Map "ctg2" Ends Right 40.000 Oldctg 2
Gel_number    c1074C1
Bands  8488 41
Positive_STS "A05" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "c1082B18"
Map "ctg4" Ends Left 42.000
Map "ctg4" Ends Right 81.000 Oldctg 4
Gel_number    c1082D1
Bands  8681 40
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1082E16"
Map "ctg4" Ends Left 44.000
Map "ctg4" Ends Right 81.000 Oldctg 4
Gel_number    c1082B1
Bands  8571 38
Positive_STS "D58" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "c1082F03"
Map "ctg3" Ends Left 96.000
Map "ctg3" Ends Right 132.000 Oldctg 3
Gel_number    c1082C1
Bands  8609 37
Positive_STS "B01" New
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c1082F16"
Map "ctg4" Ends Left 46.000
Map "ctg4" Ends Right 80.000 Oldctg 4
Gel_number    c1082D1
Bands  8646 35
Exact_match_to_cosmid "c1082B18"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1083A18"
Map "ctg3" Ends Left 1.000
Map "ctg3" Ends Right 34.000 Oldctg 3
Gel_number    c1083B1
Bands  8721 34
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c1085E05"
Map "ctg6" Ends Left 57.000
Map "ctg6" Ends Right 93.000 Oldctg 6
Gel_number    c1085A1
Bands  8755 37
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1086K04"
Map "ctg1" Ends Left 11.000
Map "ctg1" Ends Right 46.000 Oldctg 1
Gel_number    c1086B1
Bands  8850 36
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1091I04"
Gel_number    c1091B1
Bands  8886 49
Creation_date 105 6 6 18 22 
Modified_date 105 6 6 18 22 
  
BAC : "c1096G11"
Map "ctg3" Ends Left 0.000
Map "ctg3" Ends Right 35.000 Oldctg 3
Gel_number    c1096A1
Bands  8935 36
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c1098F02"
Map "ctg9" Ends Left 20.000
Map "ctg9" Ends Right 61.000 Oldctg 9
Gel_number    c1098D1
Bands  9010 42
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1098L12"
Map "ctg3" Ends Left 96.000
Map "ctg3" Ends Right 134.000 Oldctg 3
Gel_number    c1098D1
Bands  8971 39
Positive_STS "B01" New
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c1100K19"
Map "ctg3" Ends Left 37.000
Map "ctg3" Ends Right 63.000 Oldctg 3
Gel_number    c1100A1
Bands  9097 27
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "c1100K23"
Map "ctg5" Ends Left 17.000
Map "ctg5" Ends Right 61.000 Oldctg 5
Gel_number    c1100A1
Bands  9052 45
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1114F11"
Map "ctg8" Ends Left 44.000
Map "ctg8" Ends Right 85.000 Oldctg 8
Gel_number    c1114C1
Bands  9384 42
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "c1115H20"
Map "ctg7" Ends Left 1.000
Map "ctg7" Ends Right 31.000 Oldctg 7
Gel_number    c1115D1
Bands  9426 31
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0002F22"
Map "ctg2" Ends Left 66.000
Map "ctg2" Ends Right 104.000 Oldctg 2
Gel_number    6002D1
Bands  1255 39
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0003F14"
Map "ctg6" Ends Left 21.000
Map "ctg6" Ends Right 41.000 Oldctg 6
Gel_number    3003D1
Bands  438 21
Approximate_match_to_cosmid "H0107A17"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0003F17"
Map "ctg5" Ends Left 32.000
Map "ctg5" Ends Right 57.000 Oldctg 5
Gel_number    3003C1
Bands  412 26
Approximate_match_to_cosmid "c1100K23"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0005K08"
Map "ctg5" Ends Left 15.000
Map "ctg5" Ends Right 48.000 Oldctg 5
Gel_number    4005B1
Bands  603 34
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0005N23"
Map "ctg3" Ends Left 139.000
Map "ctg3" Ends Right 166.000 Oldctg 3
Gel_number    3005C1
Bands  459 28
Positive_STS "A10" New
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0006G12"
Map "ctg3" Ends Left 52.000
Map "ctg3" Ends Right 77.000 Oldctg 3
Gel_number    6006B1
Bands  1294 26
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0012B12"
Map "ctg3" Ends Left 20.000
Map "ctg3" Ends Right 34.000 Oldctg 3
Gel_number    6012D1
Bands  1320 15
Exact_match_to_cosmid "b1584L19"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0013D12"
Map "ctg3" Ends Left 44.000
Map "ctg3" Ends Right 64.000 Oldctg 3
Gel_number    8013D1
Bands  2911 21
Approximate_match_to_cosmid "c0105F22"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0016J06"
Map "ctg2" Ends Left 67.000
Map "ctg2" Ends Right 96.000 Oldctg 2
Gel_number    7016D1
Bands  2429 30
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0018F10"
Map "ctg4" Ends Left 43.000
Map "ctg4" Ends Right 75.000 Oldctg 4
Gel_number    4018D1
Bands  637 33
Approximate_match_to_cosmid "c1082B18"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0019P09"
Gel_number    6019C1
Bands  1335 32
Creation_date 105 6 6 18 22 
Modified_date 105 6 6 18 22 
  
BAC : "H0020I07"
Map "ctg3" Ends Left 121.000
Map "ctg3" Ends Right 138.000 Oldctg 3
Gel_number    4020A1
Bands  670 18
Exact_match_to_cosmid "c1065C21"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0022F06"
Map "ctg2" Ends Left 46.000
Map "ctg2" Ends Right 74.000 Oldctg 2
Gel_number    6022D1
Bands  1367 29
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0024E12"
Map "ctg3" Ends Left 14.000
Map "ctg3" Ends Right 32.000 Oldctg 3
Gel_number    6024B1
Bands  1396 19
Exact_match_to_cosmid "H0087N20"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0029H15"
Map "ctg10" Ends Left 1.000
Map "ctg10" Ends Right 23.000 Oldctg 10
Gel_number    4029B1
Bands  688 23
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0029M07"
Map "ctg1" Ends Left 29.000
Map "ctg1" Ends Right 46.000 Oldctg 1
Gel_number    7029A1
Bands  2459 18
Exact_match_to_cosmid "c0107A18"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0031K16"
Map "ctg1" Ends Left 43.000
Map "ctg1" Ends Right 68.000 Oldctg 1
Gel_number    4031B1
Bands  711 26
Approximate_match_to_cosmid "b1468I11"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0032K16"
Map "ctg4" Ends Left 41.000
Map "ctg4" Ends Right 65.000 Oldctg 4
Gel_number    4032B1
Bands  759 25
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0032O01"
Map "ctg3" Ends Left 25.000
Map "ctg3" Ends Right 46.000 Oldctg 3
Gel_number    4032A1
Bands  737 22
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0032P15"
Map "ctg2" Ends Left 45.000
Map "ctg2" Ends Right 67.000 Oldctg 2
Gel_number    6032C1
Bands  1415 23
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0033N07"
Map "ctg8" Ends Left 66.000
Map "ctg8" Ends Right 92.000 Oldctg 8
Gel_number    4033C1
Bands  784 27
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0034I07"
Map "ctg3" Ends Left 52.000
Map "ctg3" Ends Right 72.000 Oldctg 3
Gel_number    6034A1
Bands  1461 21
Approximate_match_to_cosmid "b1644B11"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0034O07"
Map "ctg7" Ends Left 7.000
Map "ctg7" Ends Right 29.000 Oldctg 7
Gel_number    6034A1
Bands  1438 23
Approximate_match_to_cosmid "c1115H20"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0036E07"
Map "ctg5" Ends Left 26.000
Map "ctg5" Ends Right 55.000 Oldctg 5
Gel_number    6036A1
Bands  1482 30
Approximate_match_to_cosmid "c1100K23"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0041J05"
Map "ctg4" Ends Left 60.000
Map "ctg4" Ends Right 90.000 Oldctg 4
Gel_number    3041C1
Bands  487 31
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0043D23"
Map "ctg6" Ends Left 54.000
Map "ctg6" Ends Right 76.000 Oldctg 6
Gel_number    6043C1
Bands  1512 23
Approximate_match_to_cosmid "b1081C22"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0052J20"
Map "ctg5" Ends Left 33.000
Map "ctg5" Ends Right 58.000 Oldctg 5
Gel_number    9052D1
Bands  3121 26
Approximate_match_to_cosmid "b0319B18"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0054L03"
Map "ctg4" Ends Left 67.000
Map "ctg4" Ends Right 96.000 Oldctg 4
Gel_number    3054C1
Bands  518 30
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0054L23"
Map "ctg8" Ends Left 48.000
Map "ctg8" Ends Right 77.000 Oldctg 8
Gel_number    3054C1
Bands  548 30
Approximate_match_to_cosmid "c1114F11"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0057O04"
Map "ctg4" Ends Left 72.000
Map "ctg4" Ends Right 94.000 Oldctg 4
Gel_number    7057B1
Bands  2477 23
Exact_match_to_cosmid "H0054L03"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0058L05"
Map "ctg1" Ends Left 14.000
Map "ctg1" Ends Right 44.000 Oldctg 1
Gel_number    8058C1
Bands  2932 31
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0073O01"
Gel_number    7073A1
Bands  2500 27
Creation_date 105 6 6 18 22 
Modified_date 105 6 6 18 22 
  
BAC : "H0075O08"
Map "ctg3" Ends Left 54.000
Map "ctg3" Ends Right 74.000 Oldctg 3
Gel_number    6075B1
Bands  1535 21
Exact_match_to_cosmid "H0006G12"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0078I12"
Map "ctg9" Ends Left 24.000
Map "ctg9" Ends Right 46.000 Oldctg 9
Gel_number    6078B1
Bands  1556 23
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0078L17"
Map "ctg3" Ends Left 89.000
Map "ctg3" Ends Right 117.000 Oldctg 3
Gel_number    4078C1
Bands  811 29
Approximate_match_to_cosmid "H0105A07"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0080I09"
Map "ctg2" Ends Left 12.000
Map "ctg2" Ends Right 38.000 Oldctg 2
Gel_number    6080A1
Bands  1579 27
Approximate_match_to_cosmid "c1074L23"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0082F20"
Map "ctg6" Ends Left 26.000
Map "ctg6" Ends Right 51.000 Oldctg 6
Gel_number    7082D1
Bands  2561 26
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0082I21"
Map "ctg8" Ends Left 35.000
Map "ctg8" Ends Right 68.000 Oldctg 8
Gel_number    7082A1
Bands  2527 34
Approximate_match_to_cosmid "b1257O16"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0086A08"
Map "ctg3" Ends Left 77.000
Map "ctg3" Ends Right 109.000 Oldctg 3
Gel_number    7086B1
Bands  2612 33
Positive_STS "B13" New
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0086M22"
Map "ctg3" Ends Left 78.000
Map "ctg3" Ends Right 102.000 Oldctg 3
Gel_number    7086B1
Bands  2587 25
Positive_STS "B13" New
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0086N12"
Map "ctg1" Ends Left 42.000
Map "ctg1" Ends Right 68.000 Oldctg 1
Gel_number    4086D1
Bands  840 27
Approximate_match_to_cosmid "b1468I11"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0087F20"
Map "ctg3" Ends Left 17.000
Map "ctg3" Ends Right 36.000 Oldctg 3
Gel_number    9087D1
Bands  3167 20
Exact_match_to_cosmid "b1584L19"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0087N20"
Map "ctg3" Ends Left 13.000
Map "ctg3" Ends Right 32.000 Oldctg 3
Gel_number    9087D1
Bands  3147 20
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0089H14"
Map "ctg4" Ends Left 0.000
Map "ctg4" Ends Right 27.000 Oldctg 4
Gel_number    9089D1
Bands  3187 28
Positive_STS "D57" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "H0095C16"
Map "ctg9" Ends Left 14.000
Map "ctg9" Ends Right 36.000 Oldctg 9
Gel_number    5095B1
Bands  1138 23
Exact_match_to_cosmid "b1512M05"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0097H04"
Map "ctg4" Ends Left 9.000
Map "ctg4" Ends Right 33.000 Oldctg 4
Gel_number    6097D1
Bands  1606 25
Approximate_match_to_cosmid "H0165J23"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0098A20"
Map "ctg4" Ends Left 4.000
Map "ctg4" Ends Right 26.000 Oldctg 4
Gel_number    4098B1
Bands  867 23
Approximate_match_to_cosmid "H0089H14"
Positive_STS "D57" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "H0104J07"
Map "ctg3" Ends Left 2.000
Map "ctg3" Ends Right 30.000 Oldctg 3
Gel_number    4104C1
Bands  890 29
Approximate_match_to_cosmid "c1096G11"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0105A07"
Map "ctg3" Ends Left 78.000
Map "ctg3" Ends Right 113.000 Oldctg 3
Gel_number    6105A1
Bands  1631 36
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0107A17"
Map "ctg6" Ends Left 21.000
Map "ctg6" Ends Right 48.000 Oldctg 6
Gel_number    6107A1
Bands  1667 28
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0108P07"
Map "ctg3" Ends Left 53.000
Map "ctg3" Ends Right 71.000 Oldctg 3
Gel_number    5108C1
Bands  1161 19
Exact_match_to_cosmid "b1604O19"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0109L05"
Map "ctg5" Ends Left 44.000
Map "ctg5" Ends Right 70.000 Oldctg 5
Gel_number    6109C1
Bands  1695 27
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0112D17"
Map "ctg8" Ends Left 12.000
Map "ctg8" Ends Right 30.000 Oldctg 8
Gel_number    7112C1
Bands  2645 19
Exact_match_to_cosmid "b1622G13"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0116L11"
Map "ctg7" Ends Left 4.000
Map "ctg7" Ends Right 25.000 Oldctg 7
Gel_number    6116C1
Bands  1722 22
Exact_match_to_cosmid "c1115H20"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0119D09"
Map "ctg8" Ends Left 16.000
Map "ctg8" Ends Right 31.000 Oldctg 8
Gel_number    4119C1
Bands  948 16
Exact_match_to_cosmid "b1622G13"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0119L15"
Map "ctg1" Ends Left 64.000
Map "ctg1" Ends Right 92.000 Oldctg 1
Gel_number    4119C1
Bands  919 29
Approximate_match_to_cosmid "b1046O08"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0122E03"
Map "ctg8" Ends Left 24.000
Map "ctg8" Ends Right 50.000 Oldctg 8
Gel_number    6122A1
Bands  1744 27
Positive_STS "A07" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "H0122F13"
Map "ctg1" Ends Left 54.000
Map "ctg1" Ends Right 82.000 Oldctg 1
Gel_number    6122C1
Bands  1771 29
Approximate_match_to_cosmid "c1017J12"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0122H11"
Map "ctg2" Ends Left 63.000
Map "ctg2" Ends Right 90.000 Oldctg 2
Gel_number    6122C1
Bands  1800 28
Approximate_match_to_cosmid "H0276H10"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0125D19"
Gel_number    6125C1
Bands  1828 30
Creation_date 105 6 6 18 22 
Modified_date 105 6 6 18 22 
  
BAC : "H0130C22"
Map "ctg4" Ends Left 68.000
Map "ctg4" Ends Right 93.000 Oldctg 4
Gel_number    4130B1
Bands  964 26
Exact_match_to_cosmid "H0054L03"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0133H10"
Map "ctg6" Ends Left 63.000
Map "ctg6" Ends Right 84.000 Oldctg 6
Gel_number    4133D1
Bands  990 22
Exact_match_to_cosmid "c1085E05"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0135A11"
Map "ctg6" Ends Left 63.000
Map "ctg6" Ends Right 89.000 Oldctg 6
Gel_number    6135A1
Bands  1858 27
Exact_match_to_cosmid "c1085E05"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0136F10"
Map "ctg5" Ends Left 2.000
Map "ctg5" Ends Right 27.000 Oldctg 5
Gel_number    6136D1
Bands  1915 26
Approximate_match_to_cosmid "H0136N10"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0136N10"
Map "ctg5" Ends Left 0.000
Map "ctg5" Ends Right 29.000 Oldctg 5
Gel_number    6136D1
Bands  1885 30
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0137D12"
Map "ctg5" Ends Left 9.000
Map "ctg5" Ends Right 37.000 Oldctg 5
Gel_number    6137D1
Bands  1941 29
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0140O13"
Map "ctg3" Ends Left 128.000
Map "ctg3" Ends Right 150.000 Oldctg 3
Gel_number    7140A1
Bands  2664 23
Exact_match_to_cosmid "b1498E10"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0142H08"
Map "ctg2" Ends Left 57.000
Map "ctg2" Ends Right 83.000 Oldctg 2
Gel_number    9142D1
Bands  3215 27
Exact_match_to_cosmid "b1588O10"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0143A14"
Map "ctg6" Ends Left 29.000
Map "ctg6" Ends Right 47.000 Oldctg 6
Gel_number    9143B1
Bands  3242 19
Exact_match_to_cosmid "H0082F20"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0143J16"
Map "ctg4" Ends Left 24.000
Map "ctg4" Ends Right 52.000 Oldctg 4
Gel_number    7143D1
Bands  2687 29
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0155G20"
Map "ctg8" Ends Left 59.000
Map "ctg8" Ends Right 83.000 Oldctg 8
Gel_number    6155B1
Bands  1970 25
Approximate_match_to_cosmid "c1114F11"
Positive_STS "F100" New
Positive_STS "J_z10" New
Positive_STS "J_d34" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "H0158A08"
Map "ctg4" Ends Left 72.000
Map "ctg4" Ends Right 96.000 Oldctg 4
Gel_number    0158B1
Bands  1 25
Approximate_match_to_cosmid "c1050F12"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0162A06"
Map "ctg3" Ends Left 80.000
Map "ctg3" Ends Right 98.000 Oldctg 3
Gel_number    6162B1
Bands  2023 19
Exact_match_to_cosmid "H0086M22"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0162H15"
Map "ctg1" Ends Left 73.000
Map "ctg1" Ends Right 100.000 Oldctg 1
Gel_number    5162C1
Bands  9457 28
Exact_match_to_cosmid "c1032M05"
Remark "new_add"
Remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 46 
  
BAC : "H0162K16"
Map "ctg1" Ends Left 57.000
Map "ctg1" Ends Right 84.000 Oldctg 1
Gel_number    6162B1
Bands  1995 28
Approximate_match_to_cosmid "c1017J12"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0165J23"
Map "ctg4" Ends Left 7.000
Map "ctg4" Ends Right 38.000 Oldctg 4
Gel_number    0165C1
Bands  26 32
Positive_STS "D57" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "H0171H15"
Map "ctg4" Ends Left 26.000
Map "ctg4" Ends Right 51.000 Oldctg 4
Gel_number    0171C1
Bands  58 26
Exact_match_to_cosmid "H0143J16"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0172C08"
Map "ctg10" Ends Left 5.000
Map "ctg10" Ends Right 27.000 Oldctg 10
Gel_number    6172B1
Bands  2042 23
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0173G03"
Map "ctg3" Ends Left 17.000
Map "ctg3" Ends Right 44.000 Oldctg 3
Gel_number    6173A1
Bands  2065 28
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0175M06"
Map "ctg2" Ends Left 10.000
Map "ctg2" Ends Right 35.000 Oldctg 2
Gel_number    8175B1
Bands  2963 26
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0182L09"
Map "ctg1" Ends Left 30.000
Map "ctg1" Ends Right 53.000 Oldctg 1
Gel_number    9182A1
Bands  3261 24
Exact_match_to_cosmid "c0107A18"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0184E07"
Map "ctg4" Ends Left 60.000
Map "ctg4" Ends Right 86.000 Oldctg 4
Gel_number    5184A1
Bands  1204 27
Approximate_match_to_cosmid "b1509B02"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0184K11"
Map "ctg1" Ends Left 34.000
Map "ctg1" Ends Right 57.000 Oldctg 1
Gel_number    5184A1
Bands  1180 24
Exact_match_to_cosmid "c1024E06"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0186L03"
Map "ctg8" Ends Left 20.000
Map "ctg8" Ends Right 46.000 Oldctg 8
Gel_number    8186C1
Bands  2989 27
Positive_STS "A07" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "H0190K17"
Map "ctg1" Ends Left 2.000
Map "ctg1" Ends Right 26.000 Oldctg 1
Gel_number    3190A1
Bands  578 25
Exact_match_to_cosmid "b0333F08"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0192D10"
Map "ctg3" Ends Left 88.000
Map "ctg3" Ends Right 117.000 Oldctg 3
Gel_number    8192D1
Bands  3016 30
Approximate_match_to_cosmid "c1041H02"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0192I13"
Map "ctg8" Ends Left 29.000
Map "ctg8" Ends Right 54.000 Oldctg 8
Gel_number    6192A1
Bands  2093 26
Exact_match_to_cosmid "b0303H17"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0197G20"
Map "ctg4" Ends Left 26.000
Map "ctg4" Ends Right 54.000 Oldctg 4
Gel_number    7197B1
Bands  2716 29
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0198H02"
Map "ctg3" Ends Left 61.000
Map "ctg3" Ends Right 88.000 Oldctg 3
Gel_number    4198D1
Bands  1012 28
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0201H09"
Map "ctg10" Ends Left 5.000
Map "ctg10" Ends Right 31.000 Oldctg 10
Gel_number    7201C1
Bands  2745 27
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0208L03"
Map "ctg2" Ends Left 7.000
Map "ctg2" Ends Right 38.000 Oldctg 2
Gel_number    4208C1
Bands  1040 32
Approximate_match_to_cosmid "c1074L23"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0210F04"
Map "ctg6" Ends Left 52.000
Map "ctg6" Ends Right 77.000 Oldctg 6
Gel_number    9210D1
Bands  3285 26
Positive_STS "F100" New
Positive_STS "J_z10" New
Positive_STS "J_d34" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "H0214L16"
Map "ctg4" Ends Left 35.000
Map "ctg4" Ends Right 60.000 Oldctg 4
Gel_number    7214D1
Bands  2772 26
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0215I18"
Map "ctg3" Ends Left 78.000
Map "ctg3" Ends Right 101.000 Oldctg 3
Gel_number    9215B1
Bands  3311 24
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0216G18"
Map "ctg2" Ends Left 46.000
Map "ctg2" Ends Right 73.000 Oldctg 2
Gel_number    6216B1
Bands  2119 28
Approximate_match_to_cosmid "b1537B07"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0219D08"
Map "ctg2" Ends Left 13.000
Map "ctg2" Ends Right 49.000 Oldctg 2
Gel_number    6219D1
Bands  2192 37
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0219N07"
Map "ctg2" Ends Left 9.000
Map "ctg2" Ends Right 35.000 Oldctg 2
Gel_number    6219C1
Bands  2147 27
Exact_match_to_cosmid "c1074L23"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0219P12"
Map "ctg3" Ends Left 67.000
Map "ctg3" Ends Right 84.000 Oldctg 3
Gel_number    6219D1
Bands  2174 18
Approximate_match_to_cosmid "b1604O19"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0220C13"
Map "ctg2" Ends Left 2.000
Map "ctg2" Ends Right 28.000 Oldctg 2
Gel_number    9220A1
Bands  3335 27
Exact_match_to_cosmid "c1074P15"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0226F06"
Map "ctg8" Ends Left 58.000
Map "ctg8" Ends Right 82.000 Oldctg 8
Gel_number    9226D1
Bands  3362 25
Approximate_match_to_cosmid "c1114F11"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0228N15"
Map "ctg3" Ends Left 141.000
Map "ctg3" Ends Right 165.000 Oldctg 3
Gel_number    6228C1
Bands  2229 25
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0230B18"
Map "ctg3" Ends Left 52.000
Map "ctg3" Ends Right 74.000 Oldctg 3
Gel_number    7230D1
Bands  2798 23
Exact_match_to_cosmid "b1503B23"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0232L09"
Map "ctg2" Ends Left 68.000
Map "ctg2" Ends Right 90.000 Oldctg 2
Gel_number    7232C1
Bands  2821 23
Exact_match_to_cosmid "H0276H10"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0233C08"
Map "ctg10" Ends Left 4.000
Map "ctg10" Ends Right 29.000 Oldctg 10
Gel_number    0233B1
Bands  128 26
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0233E10"
Map "ctg4" Ends Left 70.000
Map "ctg4" Ends Right 92.000 Oldctg 4
Gel_number    0233B1
Bands  105 23
Exact_match_to_cosmid "H0054L03"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0233M10"
Map "ctg4" Ends Left 70.000
Map "ctg4" Ends Right 90.000 Oldctg 4
Gel_number    0233B1
Bands  84 21
Exact_match_to_cosmid "H0054L03"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0234C20"
Map "ctg8" Ends Left 32.000
Map "ctg8" Ends Right 58.000 Oldctg 8
Gel_number    8234B1
Bands  3046 27
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0242H23"
Map "ctg1" Ends Left 47.000
Map "ctg1" Ends Right 72.000 Oldctg 1
Gel_number    6242C1
Bands  2254 26
Approximate_match_to_cosmid "c1017J12"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0244G24"
Map "ctg3" Ends Left 31.000
Map "ctg3" Ends Right 52.000 Oldctg 3
Gel_number    7244B1
Bands  2844 22
Approximate_match_to_cosmid "b1246P23"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0249G07"
Map "ctg2" Ends Left 1.000
Map "ctg2" Ends Right 28.000 Oldctg 2
Gel_number    6249A1
Bands  2280 28
Approximate_match_to_cosmid "c1074P15"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0250K02"
Map "ctg9" Ends Left 13.000
Map "ctg9" Ends Right 31.000 Oldctg 9
Gel_number    9250B1
Bands  3387 19
Exact_match_to_cosmid "b0297K22"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0252C07"
Map "ctg2" Ends Left 25.000
Map "ctg2" Ends Right 54.000 Oldctg 2
Gel_number    9252A1
Bands  3406 30
Approximate_match_to_cosmid "b1522B13"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0257L03"
Map "ctg7" Ends Left 4.000
Map "ctg7" Ends Right 20.000 Oldctg 7
Gel_number    9257C1
Bands  3436 17
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0268I13"
Map "ctg4" Ends Left 63.000
Map "ctg4" Ends Right 86.000 Oldctg 4
Gel_number    9268A1
Bands  3453 24
Exact_match_to_cosmid "H0041J05"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0269O12"
Map "ctg4" Ends Left 47.000
Map "ctg4" Ends Right 74.000 Oldctg 4
Gel_number    9269B1
Bands  3477 28
Approximate_match_to_cosmid "c1082B18"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0272M18"
Map "ctg2" Ends Left 68.000
Map "ctg2" Ends Right 101.000 Oldctg 2
Gel_number    6272B1
Bands  2308 34
Approximate_match_to_cosmid "H0002F22"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0274O10"
Map "ctg7" Ends Left 9.000
Map "ctg7" Ends Right 26.000 Oldctg 7
Gel_number    9274B1
Bands  3505 18
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0276H10"
Map "ctg2" Ends Left 59.000
Map "ctg2" Ends Right 90.000 Oldctg 2
Gel_number    6276D1
Bands  2342 32
Positive_STS "A01" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "H0278N12"
Gel_number    9278D1
Bands  3523 28
Creation_date 105 6 6 18 22 
Modified_date 105 6 6 18 22 
  
BAC : "H0309N09"
Map "ctg7" Ends Left 1.000
Map "ctg7" Ends Right 20.000 Oldctg 7
Gel_number    4309C1
Bands  1072 20
Approximate_match_to_cosmid "c1115H20"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0310J14"
Map "ctg6" Ends Left 68.000
Map "ctg6" Ends Right 98.000 Oldctg 6
Gel_number    9310D1
Bands  3551 31
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0315J01"
Map "ctg4" Ends Left 65.000
Map "ctg4" Ends Right 87.000 Oldctg 4
Gel_number    9315C1
Bands  3582 23
Exact_match_to_cosmid "H0041J05"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0315P21"
Map "ctg3" Ends Left 122.000
Map "ctg3" Ends Right 142.000 Oldctg 3
Gel_number    9315C1
Bands  3605 21
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0328F06"
Map "ctg1" Ends Left 61.000
Map "ctg1" Ends Right 94.000 Oldctg 1
Gel_number    9328D1
Bands  3626 34
Approximate_match_to_cosmid "c1017J12"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0330L10"
Map "ctg4" Ends Left 28.000
Map "ctg4" Ends Right 60.000 Oldctg 4
Gel_number    6330D1
Bands  2374 33
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0339H13"
Map "ctg1" Ends Left 54.000
Map "ctg1" Ends Right 79.000 Oldctg 1
Gel_number    7339C1
Bands  2866 26
Exact_match_to_cosmid "c1017J12"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0345A04"
Map "ctg4" Ends Left 2.000
Map "ctg4" Ends Right 28.000 Oldctg 4
Gel_number    9345B1
Bands  3660 27
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0352B08"
Map "ctg9" Ends Left 0.000
Map "ctg9" Ends Right 28.000 Oldctg 9
Gel_number    8352D1
Bands  3073 29
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0352C06"
Map "ctg1" Ends Left 76.000
Map "ctg1" Ends Right 99.000 Oldctg 1
Gel_number    9352B1
Bands  9485 24
Exact_match_to_cosmid "c1032M05"
Remark "new_add"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 46 
  
BAC : "H0352N23"
Map "ctg1" Ends Left 0.000
Map "ctg1" Ends Right 23.000 Oldctg 1
Gel_number    5352C1
Bands  1231 24
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0353F22"
Map "ctg3" Ends Left 78.000
Map "ctg3" Ends Right 96.000 Oldctg 3
Gel_number    8353D1
Bands  3102 19
Exact_match_to_cosmid "H0215I18"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0355I07"
Map "ctg3" Ends Left 35.000
Map "ctg3" Ends Right 53.000 Oldctg 3
Gel_number    7355A1
Bands  2892 19
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0364L06"
Map "ctg5" Ends Left 46.000
Map "ctg5" Ends Right 67.000 Oldctg 5
Gel_number    9364D1
Bands  3687 22
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0364N13"
Map "ctg3" Ends Left 50.000
Map "ctg3" Ends Right 73.000 Oldctg 3
Gel_number    4364C1
Bands  1114 24
Approximate_match_to_cosmid "b1503B23"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0364P05"
Map "ctg3" Ends Left 78.000
Map "ctg3" Ends Right 99.000 Oldctg 3
Gel_number    4364C1
Bands  1092 22
Approximate_match_to_cosmid "c0186L14"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0371E18"
Map "ctg6" Ends Left 49.000
Map "ctg6" Ends Right 70.000 Oldctg 6
Gel_number    6371B1
Bands  2407 22
Exact_match_to_cosmid "c1052J13"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0401L03"
Map "ctg1" Ends Left 50.000
Map "ctg1" Ends Right 73.000 Oldctg 1
Gel_number    0401C1
Bands  154 24
Exact_match_to_cosmid "c1017J12"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0406D08"
Map "ctg2" Ends Left 31.000
Map "ctg2" Ends Right 53.000 Oldctg 2
Gel_number    0406D1
Bands  178 23
Approximate_match_to_cosmid "b1566O10"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0408L06"
Map "ctg4" Ends Left 40.000
Map "ctg4" Ends Right 64.000 Oldctg 4
Gel_number    0408D1
Bands  201 25
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0416M08"
Map "ctg8" Ends Left 18.000
Map "ctg8" Ends Right 34.000 Oldctg 8
Gel_number    0416B1
Bands  226 17
Positive_STS "A07" New
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 13 45 
  
BAC : "H0424C13"
Map "ctg6" Ends Left 55.000
Map "ctg6" Ends Right 74.000 Oldctg 6
Gel_number    0424A
Bands  243 20
Approximate_match_to_cosmid "H0210F04"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0426L02"
Map "ctg3" Ends Left 97.000
Map "ctg3" Ends Right 125.000 Oldctg 3
Gel_number    0426D1
Bands  263 29
Approximate_match_to_cosmid "c1098L12"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0427E10"
Map "ctg5" Ends Left 31.000
Map "ctg5" Ends Right 53.000 Oldctg 5
Gel_number    0427B1
Bands  292 23
Approximate_match_to_cosmid "c1100K23"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0428F15"
Map "ctg8" Ends Left 50.000
Map "ctg8" Ends Right 74.000 Oldctg 8
Gel_number    0428C1
Bands  315 25
Approximate_match_to_cosmid "c1114F11"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0429F01"
Map "ctg3" Ends Left 54.000
Map "ctg3" Ends Right 75.000 Oldctg 3
Gel_number    0429C1
Bands  340 22
Exact_match_to_cosmid "H0006G12"
Fpc_remark "test"
Fpc_remark "second"
Creation_date 105 6 6 18 22 
Modified_date 106 8 10 14 22 
  
BAC : "H0446L04"
Map "ctg4" Ends Left 49.000
Map "ctg4" Ends Right 71.000 Oldctg 4
Gel_number    0446D1
Bands  362 23
Exact_match_to_cosmid "b1613P20"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0459F06"
Map "ctg1" Ends Left 48.000
Map "ctg1" Ends Right 73.000 Oldctg 1
Gel_number    9459D1
Bands  3709 26
Approximate_match_to_cosmid "c1017J12"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0495D18"
Map "ctg7" Ends Left 4.000
Map "ctg7" Ends Right 24.000 Oldctg 7
Gel_number    9495D1
Bands  3735 21
Exact_match_to_cosmid "b0336D23"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 
  
BAC : "H0501H21"
Map "ctg1" Ends Left 64.000
Map "ctg1" Ends Right 90.000 Oldctg 1
Gel_number    0501C1
Bands  385 27
Exact_match_to_cosmid "b1046O08"
Creation_date 105 6 6 18 22 
Modified_date 105 6 10 15 24 

Markerdata

Marker_STS : "A01"
Anchor_bin "X"
Anchor_pos     1.1 P
Remark "test"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 15 29 

Marker_STS : "A05"
Anchor_bin "3"
Anchor_pos     1.0 F
Remark "test"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 15 29 

Marker_STS : "A07"
Anchor_bin "3"
Anchor_pos     1.3 P
Remark "test"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 15 29 

Marker_STS : "A10"
Anchor_bin "X"
Anchor_pos     2.1 F
Remark "test"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 15 29 

Marker_STS : "B01"
Anchor_bin "X"
Anchor_pos     3.7 F
Remark "test"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 15 29 

Marker_STS : "B13"
Anchor_bin "1"
Anchor_pos     5.8 F
Remark "test"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 15 29 

Marker_STS : "C24"
Anchor_bin "1"
Anchor_pos     7.8 F
Remark "test"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 15 29 

Marker_STS : "D57"
Anchor_bin "2"
Anchor_pos     3.5 F
Remark "test"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 15 29 

Marker_STS : "D58"
Anchor_bin "2"
Anchor_pos     9.7 F
Remark "test"
Remark "test2"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 16 1 

Marker_STS : "F100"
Remark "test"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 15 29 

Marker_Locus : "J5"
Remark "test"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 16 2 

Marker_STS : "J9"
Remark "test"
Remark "foo"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 15 29 

Marker_STS : "J130"
Remark "test"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 15 29 

Marker_STS : "J_d34"
Remark "test"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 15 29 

Marker_STS : "J_z10"
Remark "test"
Creation_date 106 8 10 13 45 
Modified_date 106 8 10 15 29 


Contigdata 10

Ctg0 10/6/105 15:24 Ok  -1 # High 0 Avg 0 Low 0 
Chr_remark "" Pos   0.000  
Ctg1 10/6/105 15:24 Ok  0 # High 924 Avg 895 Low 792 
Chr_remark "" Pos  -1.000  
Ctg2 10/6/105 15:24 Ok  0 # High 932 Avg 917 Low 905 
Chr_remark "-    [ chX/1 Fw1 Pm1]" Pos  -1.000  
User_remark "test"
Trace_remark "test"
Ctg3 10/6/105 15:24 Ok  0 # High 901 Avg 881 Low 852 
Chr_remark "+    [ ch1/1 chX/2 Fw3]" Pos  -1.000  
Ctg4 10/8/106 13:46 Ok  0 # High 929 Avg 919 Low 903 
Chr_remark "Chr2 [2 Fw2]" Pos   6.600  
Ctg5 10/6/105 15:24 Ok  0 # High 914 Avg 891 Low 803 
Chr_remark "" Pos  -1.000  
Ctg6 10/6/105 15:24 Ok  8 # High 779 Avg 754 Low 715 
Chr_remark "" Pos  -1.000  
Ctg7 10/6/105 15:24 Ok  0 # High 965 Avg 947 Low 922 
Chr_remark "" Pos  -1.000  
Ctg8 10/6/105 15:24 Ok  0 # High 939 Avg 893 Low 641 
Chr_remark "Chr3 {*   [2 Fw1 Pm1]}" Pos   1.150  
Ctg9 10/6/105 15:24 Ok  0 # High 981 Avg 958 Low 939 
Chr_remark "Chr1 [1 Fw1]" Pos   7.800  
Ctg10 10/6/105 15:24 Ok  0 # High 983 Avg 959 Low 928 
Chr_remark "-    [ chX/1 Fw1]" Pos  -1.000  
BioPerl-1.007002/t/data/biorecipe.nhx000444000766000024      2015413155576321 17372 0ustar00cjfieldsstaff000000000000((((GUITH:45.260595[&&NHX:S=Guillardia_theta_nucleomorph_only:T=55529],((((((SORBI:5.5511156[&&NHX:S=Sorghum_bicolor:T=4558],ORYSA:4.3949497[&&NHX:S=Oryza_sativa:T=4530]):8.209326[&&NHX:
B=100],((POPTR:7.743716[&&NHX:S=Populus_trichocarpa:T=3694],VITVI:7.4273393[&&NHX:S=Vitis_vinifera:T=29760]):1.7993087[&&NHX:B=100],(ARALY:1.3226165[&&NHX:S=Arabidopsis_lyrata:T=59689],ARATH:1.2519382[&&
NHX:S=Arabidopsis_thaliana:T=3702]):10.38364[&&NHX:B=100]):3.0587217[&&NHX:B=100]):17.755212[&&NHX:B=100],OSTLU:34.956257[&&NHX:S=Ostreococcus_lucimarinus:T=436017]):7.0083058[&&NHX:B=100],DICDI:36.79394
8[&&NHX:S=Dictyostelium_discoideum:T=44689]):0.37800671[&&NHX:B=69],(CRYPV:31.705985[&&NHX:S=Cryptosporidium_parvum:T=5807],PLAF7:34.478153[&&NHX:S=Plasmodium_falciparum:T=36329]):7.4079384[&&NHX:B=100])
:0.60828157[&&NHX:B=58],(GIALA:47.040426[&&NHX:S=Giardia_lamblia:T=184922],((LEIBR:4.818744[&&NHX:S=Leishmania_braziliensis:T=5660],(LEIIN:0.94650628[&&NHX:S=Leishmania_infantum:T=5671],LEIMA:1.9314021[&
&NHX:S=Leishmania_major:T=5664]):3.7710558[&&NHX:B=100]):16.797883[&&NHX:B=100],TRYBB:19.911383[&&NHX:S=Trypanosoma_brucei:T=5702]):25.940805[&&NHX:B=100]):3.5294196[&&NHX:B=99]):0.73373836[&&NHX:B=52]):
0.42838058[&&NHX:B=31],(MONBE:35.257509[&&NHX:S=Monosiga_brevicollis:T=81824],((PRIPA:18.086434[&&NHX:S=Pristionchus_pacificus:T=54126],(CAEJA:6.0045163[&&NHX:S=Caenorhabditis_japonica:T=281687],((CAEEL:
5.3180217[&&NHX:S=Caenorhabditis_elegans:T=6239],(CAERE:3.6291663[&&NHX:S=Caenorhabditis_remanei:T=31234],CAEBR:4.3000153[&&NHX:S=Caenorhabditis_briggsae:T=6238]):0.41116075[&&NHX:B=98]):0.13776817[&&NHX
:B=72],CAEBE:4.2883189[&&NHX:S=Caenorhabditis_brenneri:T=135651]):1.9913751[&&NHX:B=100]):15.936087[&&NHX:B=100]):16.164887[&&NHX:B=100],((((LOTGI:23.922724[&&NHX:S=Lottia_gigantea:T=225164],(HELRO:26.34
055[&&NHX:S=Helobdella_robusta:T=6412],CAPI1:22.755934[&&NHX:S=Capitella_sp._I:T=73382]):0.85815597[&&NHX:B=89]):2.3825092[&&NHX:B=100],(NEMVE:26.477253[&&NHX:S=Nematostella_vectensis:T=45351],((CIOSA:7.
9216903[&&NHX:S=Ciona_savignyi:T=51511],CIOIN:10.00926[&&NHX:S=Ciona_intestinalis:T=7719]):21.59891[&&NHX:B=100],((((ORYLA:6.090087[&&NHX:S=Oryzias_latipes:T=8090],(GASAC:6.1152276[&&NHX:S=Gasterosteus_a
culeatus:T=69293],(TAKRU:3.0333091[&&NHX:S=Takifugu_rubripes:T=31033],TETNG:3.3887518[&&NHX:S=Tetraodon_nigroviridis:T=99883]):3.199465[&&NHX:B=100]):0.42854645[&&NHX:B=100]):3.037336[&&NHX:B=100],DANRE:
8.0442086[&&NHX:S=Danio_rerio:T=7955]):3.80391[&&NHX:B=100],(XENTR:9.8212561[&&NHX:S=Xenopus_tropicalis:T=8364],((ORNAN:5.6204266[&&NHX:S=Ornithorhynchus_anatinus:T=9258],((MACEU:3.0333255[&&NHX:S=Macrop
us_eugenii:T=9315],MONDO:2.435399[&&NHX:S=Monodelphis_domestica:T=13616]):2.833353[&&NHX:B=100],((RATNO:1.3842393[&&NHX:S=Rattus_norvegicus:T=10116],MOUSE:1.2347199[&&NHX:S=Mus_musculus:T=10090]):2.30283
32[&&NHX:B=100],((((OCHPR:2.9196125[&&NHX:S=Ochotona_princeps:T=9978],RABIT:2.0106071[&&NHX:S=Oryctolagus_cuniculus:T=9986]):0.89841649[&&NHX:B=100],((((SPETR:3.0357335[&&NHX:S=Spermophilus_tridecemlinea
tus:T=43179],((MICMU:1.9748823[&&NHX:S=Microcebus_murinus:T=30608],OTOGA:2.6116392[&&NHX:S=Otolemur_garnettii:T=30611]):0.45473502[&&NHX:B=100],(TARSY:2.4175242[&&NHX:S=Tarsius_syrichta:T=9478],(CALJA:1.
4056291[&&NHX:S=Callithrix_jacchus:T=9483],((PONAB:0.49708744[&&NHX:S=Pongo_pygmaeus_abelii:T=9601],((HUMAN:0.18782408[&&NHX:S=Homo_sapiens:T=9606],PANTR:0.22094877[&&NHX:S=Pan_troglodytes:T=9598]):0.087
77922[&&NHX:B=100],GORGO:0.41787667[&&NHX:S=Gorilla_gorilla:T=9595]):0.15069262[&&NHX:B=100]):0.17405127[&&NHX:B=100],MACMU:0.81068563[&&NHX:S=Macaca_mulatta:T=9544]):0.40572836[&&NHX:B=100]):0.90012338[
&&NHX:B=100]):0.0382438[&&NHX:B=77]):0.16073256[&&NHX:B=100]):0.0346796[&&NHX:B=75],TUPGB:2.7339007[&&NHX:S=Tupaia_belangeri:T=37347]):0.13427474[&&NHX:B=99],(((PTEVA:2.4199647[&&NHX:S=Pteropus_vampyrus:
T=132908],MYOLU:2.916452[&&NHX:S=Myotis_lucifugus:T=59463]):0.30536254[&&NHX:B=100],(((PIGXX:1.9356621[&&NHX:S=Sus_scrofa:T=9823],(TURTR:1.8706565[&&NHX:S=Tursiops_truncatus:T=9739],BOVIN:1.8671969[&&NHX
:S=Bos_taurus:T=9913]):0.14506514[&&NHX:B=100]):0.10418683[&&NHX:B=100],LAMPA:1.5909325[&&NHX:S=Lama_guanicoe_pacos:T=30538]):0.35680951[&&NHX:B=100],(HORSE:1.7973879[&&NHX:S=Equus_caballus:T=9796],(FELC
A:1.7499263[&&NHX:S=Felis_catus:T=9685],CANFA:1.4661618[&&NHX:S=Canis_familiaris:T=9615]):0.57865839[&&NHX:B=100]):0.04776824[&&NHX:B=96]):0.02540859[&&NHX:B=52]):0.17928021[&&NHX:B=100],ERIEU:4.2884946[
&&NHX:S=Erinaceus_europaeus:T=9365]):0.10507715[&&NHX:B=45]):0.09302481[&&NHX:B=41],((ECHTE:4.2107472[&&NHX:S=Echinops_telfairi:T=9371],(PROCA:2.9088459[&&NHX:S=Procavia_capensis:T=9813],LOXAF:1.7750296[
&&NHX:S=Loxodonta_africana:T=9785]):0.57104556[&&NHX:B=100]):0.3806632[&&NHX:B=73],(CHOHO:2.5356993[&&NHX:S=Choloepus_hoffmanni:T=9358],DASNO:3.0320132[&&NHX:S=Dasypus_novemcinctus:T=9361]):0.586947[&&NH
X:B=100]):0.15651023[&&NHX:B=57]):0.13791254[&&NHX:B=51]):0.06585063[&&NHX:B=36],(CAVPO:3.3526167[&&NHX:S=Cavia_porcellus:T=10141],DIPOR:3.3549741[&&NHX:S=Dipodomys_ordii:T=10020]):0.11345984[&&NHX:B=70]
):0.05227836[&&NHX:B=31],SORAR:3.5427681[&&NHX:S=Sorex_araneus:T=42254]):0.19739776[&&NHX:B=81]):2.2484555[&&NHX:B=100]):0.8115488[&&NHX:B=100]):1.925033[&&NHX:B=100],(ANOCA:6.8789277[&&NHX:S=Anolis_caro
linensis:T=28377],(TAEGU:3.0131789[&&NHX:S=Taeniopygia_guttata:T=59729],(MELGA:0.55164365[&&NHX:S=Meleagris_gallopavo:T=9103],CHICK:0.83790488[&&NHX:S=Gallus_gallus:T=9031]):1.9357516[&&NHX:B=100]):2.787
5104[&&NHX:B=100]):0.9202608[&&NHX:B=100]):2.0010926[&&NHX:B=100]):2.6931318[&&NHX:B=100]):11.078988[&&NHX:B=100],BRAFL:21.730013[&&NHX:S=Branchiostoma_floridae:T=7739]):1.9779545[&&NHX:B=100]):0.5263615
7[&&NHX:B=100]):0.55860669[&&NHX:B=100]):0.92419882[&&NHX:B=100],TRIAD:31.681815[&&NHX:S=Trichoplax_adhaerens:T=10228]):0.72889323[&&NHX:B=79],((DAPPU:25.747514[&&NHX:S=Daphnia_pulex:T=6669],(((AEDAE:9.7
762877[&&NHX:S=Aedes_aegypti:T=7159],ANOGA:9.6648339[&&NHX:S=Anopheles_gambiae:T=7165]):9.0087147[&&NHX:B=100],(DROWI:5.6411163[&&NHX:S=Drosophila_willistoni:T=7260],((DROPS:5.494109[&&NHX:S=Drosophila_p
seudoobscura:T=46245],DROME:4.9847676[&&NHX:S=Drosophila_melanogaster:T=7227]):1.0096506[&&NHX:B=100],DROVI:6.2668086[&&NHX:S=Drosophila_virilis:T=7244]):0.11597573[&&NHX:B=67]):13.350809[&&NHX:B=100]):6
.4492757[&&NHX:B=100],(APIME:18.616225[&&NHX:S=Apis_mellifera:T=7460],PEDHC:22.359785[&&NHX:S=Pediculus_humanus_corporis:T=121224]):1.7086512[&&NHX:B=98]):3.3794766[&&NHX:B=100]):2.0656827[&&NHX:B=100],I
XOSC:25.911987[&&NHX:S=Ixodes_scapularis:T=6945]):1.7730423[&&NHX:B=100]):3.3897979[&&NHX:B=100]):1.8522167[&&NHX:B=100]):2.6952513[&&NHX:B=100]):1.5835346[&&NHX:B=81],ENCCU:57.116454[&&NHX:S=Encephalito
zoon_cuniculi:T=6035]):0.3079138[&&NHX:B=100],(((LACBI:24.773942[&&NHX:S=Laccaria_bicolor:T=29883],CRYNE:23.093254[&&NHX:S=Cryptococcus_neoformans:T=5207]):2.2382142[&&NHX:B=100],USTMA:22.093731[&&NHX:S=
Ustilago_maydis:T=5270]):5.8884234[&&NHX:B=100],(SCHPO:33.58652[&&NHX:S=Schizosaccharomyces_pombe:T=4896],((YARLI:27.176259[&&NHX:S=Yarrowia_lipolytica:T=4952],(((LODEL:10.798514[&&NHX:S=Lodderomyces_elo
ngisporus:T=36914],CANAL:10.930718[&&NHX:S=Candida_albicans:T=5476]):2.2819566[&&NHX:B=100],(PICST:11.62454[&&NHX:S=Pichia_stipitis:T=4924],DEBHA:12.486821[&&NHX:S=Debaryomyces_hansenii:T=4959]):1.548869
7[&&NHX:B=100]):9.7653977[&&NHX:B=100],((CANGA:12.853514[&&NHX:S=Candida_glabrata:T=5478],YEAST:12.995237[&&NHX:S=Saccharomyces_cerevisiae:T=4932]):2.7292937[&&NHX:B=100],(KLULA:15.769021[&&NHX:S=Kluyver
omyces_lactis:T=28985],ASHGO:15.205039[&&NHX:S=Ashbya_gossypii:T=33169]):1.5031692[&&NHX:B=100]):8.385147[&&NHX:B=100]):5.2388175[&&NHX:B=100]):4.6698393[&&NHX:B=100],(((PHANO:17.796313[&&NHX:S=Phaeosphaeria_nodorum:T=13684],MYCGR:17.395458[&&NHX:S=Mycosphaerella_graminicola:T=54734]):2.2904277[&&NHX:B=100],(ASPFU:7.6395693[&&NHX:S=Aspergillus_fumigatus:T=5085],EMENI:7.6966689[&&NHX:S=Emericella_nidulans:T=162425]):10.679052[&&NHX:B=100]):0.21889651[&&NHX:B=62],(BOTFB:14.068847[&&NHX:S=Botrytis_cinerea:T=332648],(MAGGR:13.45956[&&NHX:S=Magnaporthe_grisea:T=148305],NEUCR:12.904786[&&NHX:S=Neurospora_crassa:T=5141]):3.3272798[&&NHX:B=100]):3.0611813[&&NHX:B=100]):11.080428[&&NHX:B=100]):0.54809742[&&NHX:B=99]):3.3723191[&&NHX:B=100]):5.8323612[&&NHX:B=100]):0;
BioPerl-1.007002/t/data/bl2seq+.blastn000444000766000024       557613155576321 17355 0ustar00cjfieldsstaff000000000000BLASTN 2.2.29+


Query= gi|2695846|emb|Y13255.1| Acipenser baeri mRNA for immunoglobulin
heavy chain, clone ScH 3.3

Length=606

Subject= gi|2695846|emb|Y13255.1| Acipenser baeri mRNA for immunoglobulin
heavy chain, clone ScH 3.3

Length=606


 Score =  1120 bits (606),  Expect = 0.0
 Identities = 606/606 (100%), Gaps = 0/606 (0%)
 Strand=Plus/Plus

Query  1    TGGTTACAACACTTTCTTCTTTCAATAACCACAATACTGCAGTACAATGGGGATTTTAAC  60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  1    TGGTTACAACACTTTCTTCTTTCAATAACCACAATACTGCAGTACAATGGGGATTTTAAC  60

Query  61   AGCTCTCTGTATAATAATGACAGCTCTATCAAGTGTCCGGTCTGATGTAGTGTTGACTGA  120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  61   AGCTCTCTGTATAATAATGACAGCTCTATCAAGTGTCCGGTCTGATGTAGTGTTGACTGA  120

Query  121  GTCCGGACCAGCAGTTATAAAGCCTGGAGAGTCCCATAAACTGTCCTGTAAAGCCTCTGG  180
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  121  GTCCGGACCAGCAGTTATAAAGCCTGGAGAGTCCCATAAACTGTCCTGTAAAGCCTCTGG  180

Query  181  ATTCACATTCAGCAGCGCCTACATGAGCTGGGTTCGACAAGCTCCTGGAAAGGGTCTGGA  240
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  181  ATTCACATTCAGCAGCGCCTACATGAGCTGGGTTCGACAAGCTCCTGGAAAGGGTCTGGA  240

Query  241  ATGGGTGGCTTATATTTACTCAGGTGGTAGTAGTACATACTATGCCCAGTCTGTCCAGGG  300
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  241  ATGGGTGGCTTATATTTACTCAGGTGGTAGTAGTACATACTATGCCCAGTCTGTCCAGGG  300

Query  301  AAGATTCGCCATCTCCAGAGACGATTCCAACAGCATGCTGTATTTACAAATGAACAGCCT  360
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  301  AAGATTCGCCATCTCCAGAGACGATTCCAACAGCATGCTGTATTTACAAATGAACAGCCT  360

Query  361  GAAGACTGAAGACACTGCCGTGTATTACTGTGCTCGGGGCGGGCTGGGGTGGTCCCTTGA  420
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  361  GAAGACTGAAGACACTGCCGTGTATTACTGTGCTCGGGGCGGGCTGGGGTGGTCCCTTGA  420

Query  421  CTACTGGGGGAAAGGCACAATGATCACCGTAACTTCTGCTACGCCATCACCACCGACAGT  480
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  421  CTACTGGGGGAAAGGCACAATGATCACCGTAACTTCTGCTACGCCATCACCACCGACAGT  480

Query  481  GTTTCCGCTTATGGAGTCATGTTGTTTGAGCGATATCTCGGGTCCTGTTGCTACGGGCTG  540
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  481  GTTTCCGCTTATGGAGTCATGTTGTTTGAGCGATATCTCGGGTCCTGTTGCTACGGGCTG  540

Query  541  CTTAGCAACCGGATTCTGCCTACCCCCGCGACCTTCTCGTGGACTGATCAATCTGGAAAA  600
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  541  CTTAGCAACCGGATTCTGCCTACCCCCGCGACCTTCTCGTGGACTGATCAATCTGGAAAA  600

Query  601  GCTTTT  606
            ||||||
Sbjct  601  GCTTTT  606



Lambda      K        H
    1.33    0.621     1.12 

Gapped
Lambda      K        H
    1.28    0.460    0.850 

Effective search space used: 352836




Matrix: blastn matrix 1 -2
Gap Penalties: Existence: 0, Extension: 2.5
BioPerl-1.007002/t/data/bl2seq.blastn000444000766000024       271713155576321 17274 0ustar00cjfieldsstaff000000000000Query= 
         (180 letters)

>human
          Length = 179

 Score = 54.0 bits (27), Expect = 2e-12
 Identities = 83/94 (88%), Gaps = 7/94 (7%)
 Strand = Plus / Plus

                                                                       
Query: 94  gtggctgggctc-tgaagcatttggg--tgagcccagggg-ctcagggcagggcacct-g 148
           |||||||||||| |||||||| ||||  |||||||||||| | || |||||||||||| |
Sbjct: 86  gtggctgggctcgtgaagcatgtgggggtgagcccaggggccccaaggcagggcacctgg 145

                                             
Query: 149 ccttcag-cggcctcag-cctgcctgtctcccag 180
           ||||||| | ||||||| ||||||||||||||||
Sbjct: 146 ccttcagcctgcctcagccctgcctgtctcccag 179



 Score = 36.2 bits (18), Expect = 4e-07
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                            
Query: 1  gtctgttccaagggcctt 18
          ||||||||||||||||||
Sbjct: 1  gtctgttccaagggcctt 18


Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 7
Number of Sequences: 0
Number of extensions: 7
Number of successful extensions: 7
Number of sequences better than 10.0: 1
length of query: 180
length of database: 179
effective HSP length: 6
effective length of query: 174
effective length of database: 173
effective search space:    30102
effective search space used:    30102
T: 0
A: 30
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 6 (12.4 bits)
BioPerl-1.007002/t/data/bl2seq.blastn.rev000444000766000024       236613155576321 20067 0ustar00cjfieldsstaff000000000000Query= 
         (180 letters)

>human
          Length = 179

 Score = 54.0 bits (27), Expect = 2e-12
 Identities = 83/94 (88%), Gaps = 7/94 (7%)
 Strand = Plus / Minus

                                                                       
Query: 94  gtggctgggctc-tgaagcatttggg--tgagcccagggg-ctcagggcagggcacct-g 148
           |||||||||||| |||||||| ||||  |||||||||||| | || |||||||||||| |
Sbjct: 94  gtggctgggctcgtgaagcatgtgggggtgagcccaggggccccaaggcagggcacctgg 35

                                             
Query: 149 ccttcag-cggcctcag-cctgcctgtctcccag 180
           ||||||| | ||||||| ||||||||||||||||
Sbjct: 34  ccttcagcctgcctcagccctgcctgtctcccag 1


Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 6
Number of Sequences: 0
Number of extensions: 6
Number of successful extensions: 6
Number of sequences better than 10.0: 1
length of query: 180
length of database: 179
effective HSP length: 6
effective length of query: 174
effective length of database: 173
effective search space:    30102
effective search space used:    30102
T: 0
A: 30
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 6 (12.4 bits)
BioPerl-1.007002/t/data/bl2seq.blastx.out000444000766000024       552313155576321 20112 0ustar00cjfieldsstaff000000000000Query= AE000111.1 Escherichia coli K-12 MG1655 section 1 of 400 of the
complete genome
         (720 letters)

>AK1H_ECOLI P00561 Bifunctional aspartokinase/homoserine
           dehydrogenase I (AKI-HDI) [Includes: Aspartokinase I ;
           Homoserine dehydrogenase I ]
          Length = 820

 Score =  248 bits (634), Expect = 2e-70
 Identities = 128/128 (100%), Positives = 128/128 (100%)
 Frame = -1

Query: 384 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 205
           MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
Sbjct: 1   MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60

Query: 204 LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 25
           LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
Sbjct: 61  LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 120

Query: 24  ALICRGEK 1
           ALICRGEK
Sbjct: 121 ALICRGEK 128



 Score = 19.2 bits (38), Expect = 0.29
 Identities = 15/57 (26%), Positives = 28/57 (48%)
 Frame = -1

Query: 420 LFFSTKGNEVTTMRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITN 250
           + F+T  ++V  + V+  GG   A  E+  R    L++     +V  V ++ A +TN
Sbjct: 458 MLFNT--DQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTN 512



 Score = 18.5 bits (36), Expect = 0.49
 Identities = 11/42 (26%), Positives = 18/42 (42%)
 Frame = -1

Query: 360 TSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAM 235
           T +   E+ L V   LES     +    ++A     +H+V M
Sbjct: 146 TVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLM 187



 Score = 17.7 bits (34), Expect = 0.84
 Identities = 10/35 (28%), Positives = 17/35 (48%)
 Frame = -1

Query: 267 PAKITNHLVAMIEKTISGQDALPNISDAERIFAEL 163
           P K  ++L  M   ++SG      +  A R+FA +
Sbjct: 305 PVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAM 339



 Score = 15.0 bits (27), Expect = 5.5
 Identities = 5/14 (35%), Positives = 8/14 (56%)
 Frame = -3

Query: 388 NHASVEVRRYISGK 347
           NH    + + ISG+
Sbjct: 45  NHLVAMIEKTISGQ 58



 Score = 15.0 bits (27), Expect = 5.5
 Identities = 5/7 (71%), Positives = 7/7 (99%)
 Frame = +1

Query: 640 PVQKLLS 660
           PV+KLL+
Sbjct: 150 PVEKLLA 156


Lambda     K      H
   0.318    0.135    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1264
Number of Sequences: 0
Number of extensions: 25
Number of successful extensions: 6
Number of sequences better than 10.0: 2
Number of HSP's better than 10.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 6
length of database: 820
effective HSP length: 33
effective length of database: 787
effective search space used:   162122
frameshift window, decay const: 50,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 25 (14.3 bits)
BioPerl-1.007002/t/data/bl2seq.bug940.out000444000766000024      1426713155576321 17654 0ustar00cjfieldsstaff000000000000Query= zinc finger protein 135 (clone pHZ-17) [Homo sapiens]. neo_id
RS.ctg14243-000000.6.0
         (469 letters)

>gi|4507985| zinc finger protein 135 (clone pHZ-17) [Homo sapiens].
           neo_id RS.ctg14243-000000.6.0
          Length = 469

 Score =  637 bits (1626), Expect = 0.0
 Identities = 311/469 (66%), Positives = 330/469 (70%), Gaps = 120/469 (25%)

Query: 121 MGNTWKKGEARPKCFTENCVKEKPYKCQECGKAFSHSSALIEHHRTHTGERPYECHECLK 180
           MGNTWKKGEARPKCFTENCVKEKPYKCQECGKAFSHSSALIEHHRTHTGERPYECHECLK
Sbjct: 1   MGNTWKKGEARPKCFTENCVKEKPYKCQECGKAFSHSSALIEHHRTHTGERPYECHECLK 60

Query: 181 GFRNSSALTKHQRIHTGEKPYKCTQCGRTFNQIAPLIQHQRTHTGEKPYECSECGKSFSF 240
           GFRNSSALTKHQRIHTGEKPYKCTQCGRTFNQIAPLIQHQRTHTGEKPYECSECGKSFSF
Sbjct: 61  GFRNSSALTKHQRIHTGEKPYKCTQCGRTFNQIAPLIQHQRTHTGEKPYECSECGKSFSF 120

Query: 241 RSSFSQHERTHTGEKPYECSECGKAFR--------------------------------- 267
           RSSFSQHERTHTGEKPYECSECGKAFR                                 
Sbjct: 121 RSSFSQHERTHTGEKPYECSECGKAFRQSIHLTQHLRIHTGEKPYQCGECGKAFSHSSSL 180

Query: 268 ---QSIH--------------------LTQHLRIHTGEKPYQCGECGKAFSHSSSL---- 300
              Q IH                    L QH R HTGEKPY+CGECGKAFS S+ L    
Sbjct: 181 TKHQRIHTGEKPYECHECGKAFTQITPLIQHQRTHTGEKPYECGECGKAFSQSTLLTEHR 240

Query: 301 ----GEKPYECNDCGKAFSHSSSLTKHQRIHTGEKPYECNQCGRAFSQLAPLIQHQRIHT 356
               GEKPY CN+CGK FSHSSSL++H+R HTGEKPYEC+QCG+AF Q   L QHQRIHT
Sbjct: 241 RIHTGEKPYGCNECGKTFSHSSSLSQHERTHTGEKPYECSQCGKAFRQSTHLTQHQRIHT 300

Query: 357 GEKP----------------TKHQRIHTGEKPYECHECGKAFTQITPLIQHQRTHTGEKP 400
           GEKP                TKHQRIHTGEKPYEC++CG+AF+Q+ PLIQHQR HTGEKP
Sbjct: 301 GEKPYECNDCGKAFSHSSSLTKHQRIHTGEKPYECNQCGRAFSQLAPLIQHQRIHTGEKP 360

Query: 401 YECGECGKAFSQSTLLTEHR---------------------------------------- 420
           YEC +CG+A +++TLL EH+                                        
Sbjct: 361 YECNQCGRASARATLLIEHQRIHTKEKPYGCNECGKSFSHSSSLSQHERTHTGEKPYECH 420

Query: 421 DCGKSFRQSTHLTQHRRIHTGEKPYACRDCGKAFTHSSSLTKHQRTHTG 469
           DCGKSFRQSTHLTQHRRIHTGEKPYACRDCGKAFTHSSSLTKHQRTHTG
Sbjct: 421 DCGKSFRQSTHLTQHRRIHTGEKPYACRDCGKAFTHSSSLTKHQRTHTG 469


 Score =  598 bits (1524), Expect = e-175
 Identities = 275/444 (61%), Positives = 324/444 (72%), Gaps = 30/444 (6%)

Query: 6   EKPYGCNECGKTFSHSSSLSQHERTHTGEKPYECSQCGKAFRQSTHLTQHQRIHT----Y 61
           EKPY C ECGK FSHSS+L +H RTHTGE+PYEC +C K FR S+ LT+HQRIHT    Y
Sbjct: 22  EKPYKCQECGKAFSHSSALIEHHRTHTGERPYECHECLKGFRNSSALTKHQRIHTGEKPY 81

Query: 62  ECNQCGRASARATLLIEHQRIHTKEKPYGCNECGKXXXXXXXXXQHERTHTGEKPYEC-H 120
           +C QCGR   +   LI+HQR HT EKPY C+ECGK         QHERTHTGEKPYEC  
Sbjct: 82  KCTQCGRTFNQIAPLIQHQRTHTGEKPYECSECGKSFSFRSSFSQHERTHTGEKPYECSE 141

Query: 121 MGNTWKKGEARPKCFTENCVKEKPYKCQECGKAFSHSSALIEHHRTHTGERPYECHECLK 180
            G  +++     +    +   EKPY+C ECGKAFSHSS+L +H R HTGE+PYECHEC K
Sbjct: 142 CGKAFRQSIHLTQHLRIH-TGEKPYQCGECGKAFSHSSSLTKHQRIHTGEKPYECHECGK 200

Query: 181 GFRNSSALTKHQRIHTGEKPYKCTQCGRTFNQIAPLIQHQRTHTGEKPYECSECGKSFSF 240
            F   + L +HQR HTGEKPY+C +CG+ F+Q   L +H+R HTGEKPY C+ECGK+FS 
Sbjct: 201 AFTQITPLIQHQRTHTGEKPYECGECGKAFSQSTLLTEHRRIHTGEKPYGCNECGKTFSH 260

Query: 241 RSSFSQHERTHTGEKPYECSECGKAFRQSIHLTQHLRIHTGEKPYQCGECGKAFSHSSSL 300
            SS SQHERTHTGEKPYECS+CGKAFRQS HLTQH RIHTGEKPY+C +CGKAFSHSSSL
Sbjct: 261 SSSLSQHERTHTGEKPYECSQCGKAFRQSTHLTQHQRIHTGEKPYECNDCGKAFSHSSSL 320

Query: 301 --------GEKPYECNDCGKAFSHSSSLTKHQRIHTGEKPYECNQCGRAFSQLAPLIQHQ 352
                   GEKPYECN CG+AFS  + L +HQRIHTGEKPYECNQCGRA ++   LI+HQ
Sbjct: 321 TKHQRIHTGEKPYECNQCGRAFSQLAPLIQHQRIHTGEKPYECNQCGRASARATLLIEHQ 380

Query: 353 RIHTGEKP----------------TKHQRIHTGEKPYECHECGKAFTQITPLIQHQRTHT 396
           RIHT EKP                ++H+R HTGEKPYECH+CGK+F Q T L QH+R HT
Sbjct: 381 RIHTKEKPYGCNECGKSFSHSSSLSQHERTHTGEKPYECHDCGKSFRQSTHLTQHRRIHT 440

Query: 397 GEKPYECGECGKAFSQSTLLTEHR 420
           GEKPY C +CGKAF+ S+ LT+H+
Sbjct: 441 GEKPYACRDCGKAFTHSSSLTKHQ 464


 Score =  499 bits (1270), Expect = e-145
 Identities = 226/372 (60%), Positives = 274/372 (72%), Gaps = 18/372 (4%)

Query: 1   RIHTGEKPYGCNECGKTFSHSSSLSQHERTHTGEKPYECSQCGKAFRQSTHLTQHQRIHT 60
           R HTGEKPY C+ECGK+FS  SS SQHERTHTGEKPYECS+CGKAFRQS HLTQH RIHT
Sbjct: 101 RTHTGEKPYECSECGKSFSFRSSFSQHERTHTGEKPYECSECGKAFRQSIHLTQHLRIHT 160

Query: 61  ----YECNQCGRASARATLLIEHQRIHTKEKPYGCNECGKXXXXXXXXXQHERTHTGEKP 116
               Y+C +CG+A + ++ L +HQRIHT EKPY C+ECGK         QH+RTHTGEKP
Sbjct: 161 GEKPYQCGECGKAFSHSSSLTKHQRIHTGEKPYECHECGKAFTQITPLIQHQRTHTGEKP 220

Query: 117 YECHMGNTWKKGEARPKCFTEN---CVKEKPYKCQECGKAFSHSSALIEHHRTHTGERPY 173
           YEC       K  ++    TE+      EKPY C ECGK FSHSS+L +H RTHTGE+PY
Sbjct: 221 YEC---GECGKAFSQSTLLTEHRRIHTGEKPYGCNECGKTFSHSSSLSQHERTHTGEKPY 277

Query: 174 ECHECLKGFRNSSALTKHQRIHTGEKPYKCTQCGRTFNQIAPLIQHQRTHTGEKPYECSE 233
           EC +C K FR S+ LT+HQRIHTGEKPY+C  CG+ F+  + L +HQR HTGEKPYEC++
Sbjct: 278 ECSQCGKAFRQSTHLTQHQRIHTGEKPYECNDCGKAFSHSSSLTKHQRIHTGEKPYECNQ 337

Query: 234 CGKSFSFRSSFSQHERTHTGEKPYECSECGKAFRQSIHLTQHLRIHTGEKPYQCGECGKA 293
           CG++FS  +   QH+R HTGEKPYEC++CG+A  ++  L +H RIHT EKPY C ECGK+
Sbjct: 338 CGRAFSQLAPLIQHQRIHTGEKPYECNQCGRASARATLLIEHQRIHTKEKPYGCNECGKS 397

Query: 294 FSHSSSL--------GEKPYECNDCGKAFSHSSSLTKHQRIHTGEKPYECNQCGRAFSQL 345
           FSHSSSL        GEKPYEC+DCGK+F  S+ LT+H+RIHTGEKPY C  CG+AF+  
Sbjct: 398 FSHSSSLSQHERTHTGEKPYECHDCGKSFRQSTHLTQHRRIHTGEKPYACRDCGKAFTHS 457

Query: 346 APLIQHQRIHTG 357
           + L +HQR HTG
Sbjct: 458 SSLTKHQRTHTG 469


Lambda     K      H
   0.318    0.131    0.428 

Gapped
Lambda     K      H
   0.270   0.0470    0.230 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 38599
Number of Sequences: 0
Number of extensions: 270
Number of successful extensions: 108
Number of sequences better than 10.0: 1
Number of HSP's better than 10.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 8
length of query: 469
length of database: 469
effective HSP length: 23
effective length of query: 446
effective length of database: 446
effective search space:   198916
effective search space used:   198916
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 25 (14.4 bits)
S2: 26 (14.5 bits)
BioPerl-1.007002/t/data/bl2seq.out000444000766000024       425313155576321 16615 0ustar00cjfieldsstaff000000000000>ALEU_HORVU
          Length = 362

 Score =  191 bits (481), Expect = 2e-53
 Identities = 111/322 (34%), Positives = 167/322 (51%), Gaps = 27/322 (8%)

Query: 28  QFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSD 86
           +F  F  ++ K Y S  E   RF IF  +L ++   N   + ++     G+N+F+D+S +
Sbjct: 60  RFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYR----LGINRFSDMSWE 115

Query: 87  EFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFS 146
           EF+   L    A  T    +A         ++P   DWR  G V+PVKNQ  CGSCW+FS
Sbjct: 116 EFQATRLG---AAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFS 172

Query: 147 TTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNG 206
           TTG +E  +  +  K +SLSEQ LVDC      +        GCNGGL   A+ YI  NG
Sbjct: 173 TTGALEAAYTQATGKNISLSEQQLVDCAGGFNNF--------GCNGGLPSQAFEYIKYNG 224

Query: 207 GIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN-ETVMAGYIVSTGPLAIAADAV 265
           GI TE SYPY    G  C++ + N   ++ +   I  N E  +   +    P+++A   +
Sbjct: 225 GIDTEESYPYKGVNGV-CHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVI 283

Query: 266 E-WQFYIGGVF---DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQG 321
           + ++ Y  GV+        P+ ++H +L VGY  +N      +PYW++KNSWGADWG+ G
Sbjct: 284 DGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVEN-----GVPYWLIKNSWGADWGDNG 338

Query: 322 YIYLRRGKNTCGVSNFVSTSII 343
           Y  +  GKN C ++   S  ++
Sbjct: 339 YFKMEMGKNMCAIATCASYPVV 360


Lambda     K      H
   0.316    0.135    0.414 

Gapped
Lambda     K      H
   0.270   0.0470    0.230 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 368
Number of Sequences: 0
Number of extensions: 19
Number of successful extensions: 6
Number of sequences better than 10.0: 1
Number of HSP's better than 10.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 1
length of query: 343
length of database: 362
effective HSP length: 23
effective length of query: 320
effective length of database: 339
effective search space:   108480
effective search space used:   108480
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 24 (13.8 bits)
S2: 24 (13.8 bits)
BioPerl-1.007002/t/data/bl2seq.tblastn.out000444000766000024       353613155576321 20266 0ustar00cjfieldsstaff000000000000Query= 
         (15 letters)

>WAN03UHTX_1 pSMED2_VHP_GVHS-001 Homo sapiens
          Length = 2367

 Score = 42.4 bits (98), Expect = 4e-09
 Identities = 15/15 (100%), Positives = 15/15 (100%)
 Frame = -1

Query: 1   EPKSCDKTHTCPPCP 15
           EPKSCDKTHTCPPCP
Sbjct: 990 EPKSCDKTHTCPPCP 946



 Score = 19.6 bits (39), Expect = 0.026
 Identities = 5/9 (55%), Positives = 6/9 (66%)
 Frame = -1

Query: 7   KTHTCPPCP 15
           + H C PCP
Sbjct: 390 ENHRCTPCP 364



 Score = 16.9 bits (32), Expect = 0.17
 Identities = 5/10 (50%), Positives = 6/10 (60%)
 Frame = +2

Query: 5   CDKTHTCPPC 14
           C +  TC PC
Sbjct: 542 CWRPCTCTPC 571



 Score = 16.5 bits (31), Expect = 0.22
 Identities = 6/12 (50%), Positives = 6/12 (50%)
 Frame = +3

Query: 2    PKSCDKTHTCPP 13
            P SC  T  C P
Sbjct: 2154 PDSCSCT*ECTP 2189



 Score = 15.8 bits (29), Expect = 0.37
 Identities = 5/12 (41%), Positives = 5/12 (41%)
 Frame = +1

Query: 4   SCDKTHTCPPCP 15
           SC     C P P
Sbjct: 250 SCSPAAHCSPTP 285


Lambda     K      H
   0.316    0.138    0.541 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 303
Number of Sequences: 0
Number of extensions: 5
Number of successful extensions: 5
Number of sequences better than 10.0: 2
Number of HSP's better than 10.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 5
length of query: 15
length of database: 789
effective HSP length: 0
effective length of query: 24
effective length of database: 789
effective search space:    18936
effective search space used:    18936
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 17 (10.6 bits)
S2: 17 (11.2 bits)

BioPerl-1.007002/t/data/bl2seq.tblastx.out000444000766000024      3273613155576321 20324 0ustar00cjfieldsstaff000000000000Query= Escherichia coli K-12 MG1655 section 1 of 400 of the complete
genome
         (720 letters)

>gi|1786181|gb|AE000111.1|AE000111 Escherichia coli K-12 MG1655
           section 1 of 400 of the complete genome
          Length = 720

 Score =  515 bits (1118), Expect = e-151
 Identities = 229/240 (95%), Positives = 229/240 (95%)
 Frame = +1 / +1

                                                                       
Query: 1   SFSF*LQRAICLCVD*KKSV**QLLNWLPAVSKLKFY*LRSLNTLTNIGIAHRQIKITEY 180
           SFSF*LQRAICLCVD*KKSV**QLLNWLPAVSKLKFY*LRSLNTLTNIGIAHRQIKITEY
Sbjct: 1   SFSF*LQRAICLCVD*KKSV**QLLNWLPAVSKLKFY*LRSLNTLTNIGIAHRQIKITEY 180

                                                                       
Query: 181 TTSMKRISXXXXXXXXXXXGNGAG*RVQETQKKART*QCGLFFSTKGNEVTTMRVLKFGG 360
           TTSMKRIS           GNGAG*RVQETQKKART*QCGLFFSTKGNEVTTMRVLKFGG
Sbjct: 181 TTSMKRISTTITTTITITTGNGAG*RVQETQKKART*QCGLFFSTKGNEVTTMRVLKFGG 360

                                                                       
Query: 361 TSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAE 540
           TSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAE
Sbjct: 361 TSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAE 540

                                                                       
Query: 541 RIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEK 720
           RIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEK
Sbjct: 541 RIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEK 720



 Score =  508 bits (1103), Expect = e-149
 Identities = 218/240 (90%), Positives = 218/240 (90%)
 Frame = -1 / -1

                                                                       
Query: 720 FLATANQRSVDAIRALPQQTNAMQDMFYLGKFLIDESFQLRQREPRLGGGESRQKFGKNT 541
           FLATANQRSVDAIRALPQQTNAMQDMFYLGKFLIDESFQLRQREPRLGGGESRQKFGKNT
Sbjct: 720 FLATANQRSVDAIRALPQQTNAMQDMFYLGKFLIDESFQLRQREPRLGGGESRQKFGKNT 541

                                                                       
Query: 540 FGIADIG*SILAANGFFNHRHQVVXXXXXXXXXXGHLPLPGIAFQNIGNTQKTFCICH*C 361
           FGIADIG*SILAANGFFNHRHQVV          GHLPLPGIAFQNIGNTQKTFCICH*C
Sbjct: 540 FGIADIG*SILAANGFFNHRHQVVGDFGGGREDGGHLPLPGIAFQNIGNTQKTFCICH*C 361

                                                                       
Query: 360 TAELQHSHGCYLVTFGRKKKPALSGAGFFLCFLYASARTVTCXXXXXXXXXXXXAFHGCC 181
           TAELQHSHGCYLVTFGRKKKPALSGAGFFLCFLYASARTVTC            AFHGCC
Sbjct: 360 TAELQHSHGCYLVTFGRKKKPALSGAGFFLCFLYASARTVTCGNGDGGGNGGANAFHGCC 181

                                                                       
Query: 180 VLCNFYLSVRYAYIG*SI**PKSIKF*FTHGR*PVQKLLSDTLFLIHTETYCPLQSE*KA 1
           VLCNFYLSVRYAYIG*SI**PKSIKF*FTHGR*PVQKLLSDTLFLIHTETYCPLQSE*KA
Sbjct: 180 VLCNFYLSVRYAYIG*SI**PKSIKF*FTHGR*PVQKLLSDTLFLIHTETYCPLQSE*KA 1



 Score =  416 bits (902), Expect(2) = e-160
 Identities = 161/161 (100%), Positives = 161/161 (100%)
 Frame = +3 / +3

                                                                       
Query: 237 R*RCGLTRTGNTEKSPHLTVRAFFFDQR*RGNNHASVEVRRYISGKCRTFSACCRYSGKQ 416
           R*RCGLTRTGNTEKSPHLTVRAFFFDQR*RGNNHASVEVRRYISGKCRTFSACCRYSGKQ
Sbjct: 237 R*RCGLTRTGNTEKSPHLTVRAFFFDQR*RGNNHASVEVRRYISGKCRTFSACCRYSGKQ 416

                                                                       
Query: 417 CQAGAGGHRPLCPRQNHQPPGGDD*KNH*RPGCFTQYQRCRTYFCRTFDGTRRRPAGVPA 596
           CQAGAGGHRPLCPRQNHQPPGGDD*KNH*RPGCFTQYQRCRTYFCRTFDGTRRRPAGVPA
Sbjct: 417 CQAGAGGHRPLCPRQNHQPPGGDD*KNH*RPGCFTQYQRCRTYFCRTFDGTRRRPAGVPA 596

                                                    
Query: 597 GAIENFRRSGICPNKTCPAWH*FVGAVPG*HQRCADLPWRE 719
           GAIENFRRSGICPNKTCPAWH*FVGAVPG*HQRCADLPWRE
Sbjct: 597 GAIENFRRSGICPNKTCPAWH*FVGAVPG*HQRCADLPWRE 719



 Score =  389 bits (843), Expect(2) = e-153
 Identities = 161/161 (100%), Positives = 161/161 (100%)
 Frame = -2 / -2

                                                                       
Query: 719 FSPRQISAALMLSGHCPNKLMPCRTCFIWANS*STKVFNCASGNPGWAAASPVKSSAKIR 540
           FSPRQISAALMLSGHCPNKLMPCRTCFIWANS*STKVFNCASGNPGWAAASPVKSSAKIR
Sbjct: 719 FSPRQISAALMLSGHCPNKLMPCRTCFIWANS*STKVFNCASGNPGWAAASPVKSSAKIR 540

                                                                       
Query: 539 SASLILGKASWPLMVFSIIATRWLVILAGAERTVATCPCLALLSRISATRRKRSAFATDV 360
           SASLILGKASWPLMVFSIIATRWLVILAGAERTVATCPCLALLSRISATRRKRSAFATDV
Sbjct: 539 SASLILGKASWPLMVFSIIATRWLVILAGAERTVATCPCLALLSRISATRRKRSAFATDV 360

                                                    
Query: 359 PPNFNTRMVVTSLPLVEKKSPHCQVRAFFCVSCTRQPAPLP 237
           PPNFNTRMVVTSLPLVEKKSPHCQVRAFFCVSCTRQPAPLP
Sbjct: 359 PPNFNTRMVVTSLPLVEKKSPHCQVRAFFCVSCTRQPAPLP 237



 Score =  326 bits (706), Expect(2) = e-129
 Identities = 138/161 (85%), Positives = 138/161 (85%)
 Frame = +2 / +2

                                                                       
Query: 236 QVTVRADAYRKHRKKPAPDSAGFFFRPKVTR*QPCEC*SSAVHQWQMQNVFCVLPIFWKA 415
           QVTVRADAYRKHRKKPAPDSAGFFFRPKVTR*QPCEC*SSAVHQWQMQNVFCVLPIFWKA
Sbjct: 236 QVTVRADAYRKHRKKPAPDSAGFFFRPKVTR*QPCEC*SSAVHQWQMQNVFCVLPIFWKA 415

                                                                       
Query: 416 MPGRGRWXXXXXXXXXXXTTWWR*LKKPLAARMLYPISAMPNVFLPNFXXXXXXXXXXXX 595
           MPGRGRW           TTWWR*LKKPLAARMLYPISAMPNVFLPNF            
Sbjct: 416 MPGRGRWPPSSLPPPKSPTTWWR*LKKPLAARMLYPISAMPNVFLPNF*RDSPPPSRGSR 595

                                                    
Query: 596 WRN*KLSSIRNLPK*NMSCMALVCWGSARIASTLR*FAVAR 718
           WRN*KLSSIRNLPK*NMSCMALVCWGSARIASTLR*FAVAR
Sbjct: 596 WRN*KLSSIRNLPK*NMSCMALVCWGSARIASTLR*FAVAR 718



 Score =  198 bits (427), Expect(3) = e-136
 Identities = 79/79 (100%), Positives = 79/79 (100%)
 Frame = -3 / -3

                                                                       
Query: 718 SRHGKSAQR*CYPGTAPTN*CHAGHVLFGQIPDRRKFSIAPAGTPAGRRRVPSKVRQKYV 539
           SRHGKSAQR*CYPGTAPTN*CHAGHVLFGQIPDRRKFSIAPAGTPAGRRRVPSKVRQKYV
Sbjct: 718 SRHGKSAQR*CYPGTAPTN*CHAGHVLFGQIPDRRKFSIAPAGTPAGRRRVPSKVRQKYV 539

                              
Query: 538 RHR*YWVKHPGR*WFFQSS 482
           RHR*YWVKHPGR*WFFQSS
Sbjct: 538 RHR*YWVKHPGR*WFFQSS 482



 Score =  170 bits (365), Expect(3) = e-136
 Identities = 65/65 (100%), Positives = 65/65 (100%)
 Frame = -3 / -3

                                                                       
Query: 430 APAWHCFPEYRQHAENVLHLPLMYRRTSTLAWLLPRYLWSKKKARTVRCGLFSVFPVRVS 251
           APAWHCFPEYRQHAENVLHLPLMYRRTSTLAWLLPRYLWSKKKARTVRCGLFSVFPVRVS
Sbjct: 430 APAWHCFPEYRQHAENVLHLPLMYRRTSTLAWLLPRYLWSKKKARTVRCGLFSVFPVRVS 251

                
Query: 250 PHRYL 236
           PHRYL
Sbjct: 250 PHRYL 236



 Score =  155 bits (332), Expect(2) = e-153
 Identities = 65/65 (100%), Positives = 65/65 (100%)
 Frame = -3 / -3

                                                                       
Query: 196 VSWMLCTL*FLSVCALCLYWLKYLVT*VNKILIYSRQVTSSEAAIRHSFFNPHRDILPVA 17
           VSWMLCTL*FLSVCALCLYWLKYLVT*VNKILIYSRQVTSSEAAIRHSFFNPHRDILPVA
Sbjct: 196 VSWMLCTL*FLSVCALCLYWLKYLVT*VNKILIYSRQVTSSEAAIRHSFFNPHRDILPVA 17

                
Query: 16  VRMKS 2
           VRMKS
Sbjct: 16  VRMKS 2



 Score =  154 bits (330), Expect(2) = e-160
 Identities = 65/65 (100%), Positives = 65/65 (100%)
 Frame = +3 / +3

                                                                       
Query: 3   LFILTATGNMSLCGLKKECLIAASELVTCRE*IKILLT*VTKYFNQYRHSAQTDKNYRVH 182
           LFILTATGNMSLCGLKKECLIAASELVTCRE*IKILLT*VTKYFNQYRHSAQTDKNYRVH
Sbjct: 3   LFILTATGNMSLCGLKKECLIAASELVTCRE*IKILLT*VTKYFNQYRHSAQTDKNYRVH 182

                
Query: 183 NIHET 197
           NIHET
Sbjct: 183 NIHET 197



 Score =  141 bits (302), Expect(3) = e-136
 Identities = 59/59 (100%), Positives = 59/59 (100%)
 Frame = -2 / -2

                                                                      
Query: 179 YSVIFICLCAMPILVKVFSDLSQ*NFNLLTAGNQFRSCYQTLFF*STQRHIARCSQNEK 3
           YSVIFICLCAMPILVKVFSDLSQ*NFNLLTAGNQFRSCYQTLFF*STQRHIARCSQNEK
Sbjct: 179 YSVIFICLCAMPILVKVFSDLSQ*NFNLLTAGNQFRSCYQTLFF*STQRHIARCSQNEK 3



 Score =  139 bits (298), Expect(2) = e-129
 Identities = 62/62 (100%), Positives = 62/62 (100%)
 Frame = +2 / +2

                                                                       
Query: 2   AFHSDCNGQYVSVWIKKRVSDSSF*TGYLP*VN*NFIDLGH*IL*PI*A*RTDR*KLQST 181
           AFHSDCNGQYVSVWIKKRVSDSSF*TGYLP*VN*NFIDLGH*IL*PI*A*RTDR*KLQST
Sbjct: 2   AFHSDCNGQYVSVWIKKRVSDSSF*TGYLP*VN*NFIDLGH*IL*PI*A*RTDR*KLQST 181

             
Query: 182 QH 187
           QH
Sbjct: 182 QH 187



 Score = 24.9 bits (48), Expect = 0.002
 Identities = 9/12 (75%), Positives = 10/12 (83%)
 Frame = -2 / +3

                       
Query: 308 KKSPHCQVRAFF 273
           +KSPH  VRAFF
Sbjct: 273 EKSPHLTVRAFF 308



 Score = 24.9 bits (48), Expect = 0.002
 Identities = 9/13 (69%), Positives = 12/13 (92%)
 Frame = -3 / +1

                        
Query: 313 SKKKARTVRCGLF 275
           ++KKART +CGLF
Sbjct: 268 TQKKART*QCGLF 306



 Score = 24.9 bits (48), Expect = 0.002
 Identities = 9/12 (75%), Positives = 10/12 (83%)
 Frame = +3 / -2

                       
Query: 273 EKSPHLTVRAFF 308
           +KSPH  VRAFF
Sbjct: 308 KKSPHCQVRAFF 273



 Score = 24.9 bits (48), Expect = 0.002
 Identities = 9/13 (69%), Positives = 12/13 (92%)
 Frame = +1 / -3

                        
Query: 268 TQKKART*QCGLF 306
           ++KKART +CGLF
Sbjct: 313 SKKKARTVRCGLF 275



 Score = 22.1 bits (42), Expect = 0.012
 Identities = 8/12 (66%), Positives = 9/12 (74%)
 Frame = +2 / -1

                       
Query: 272 RKKPAPDSAGFF 307
           +KKPA   AGFF
Sbjct: 309 KKKPALSGAGFF 274



 Score = 22.1 bits (42), Expect = 0.012
 Identities = 8/12 (66%), Positives = 9/12 (74%)
 Frame = -1 / +2

                       
Query: 309 KKKPALSGAGFF 274
           +KKPA   AGFF
Sbjct: 272 RKKPAPDSAGFF 307



 Score = 18.5 bits (34), Expect = 0.15
 Identities = 5/6 (83%), Positives = 5/6 (83%)
 Frame = -3 / +3

                 
Query: 598 PAGTPA 581
           PAG PA
Sbjct: 579 PAGVPA 596



 Score = 18.5 bits (34), Expect = 0.15
 Identities = 5/6 (83%), Positives = 5/6 (83%)
 Frame = +3 / -3

                 
Query: 579 PAGVPA 596
           PAG PA
Sbjct: 598 PAGTPA 581



 Score = 18.0 bits (33), Expect = 0.20
 Identities = 6/14 (42%), Positives = 6/14 (42%)
 Frame = +3 / -3

                         
Query: 243 RCGLTRTGNTEKSP 284
           RCGL        SP
Sbjct: 289 RCGLFSVFPVRVSP 248



 Score = 18.0 bits (33), Expect = 0.20
 Identities = 6/14 (42%), Positives = 6/14 (42%)
 Frame = -3 / +3

                         
Query: 289 RCGLFSVFPVRVSP 248
           RCGL        SP
Sbjct: 243 RCGLTRTGNTEKSP 284



 Score = 17.6 bits (32), Expect = 0.28
 Identities = 5/6 (83%), Positives = 5/6 (83%)
 Frame = -3 / -1

                 
Query: 301 ARTVRC 284
           ARTV C
Sbjct: 252 ARTVTC 235



 Score = 15.3 bits (27), Expect = 1.4
 Identities = 5/14 (35%), Positives = 8/14 (56%)
 Frame = +1 / +3

                         
Query: 469 NHLVAMIEKTISGQ 510
           NH    + + ISG+
Sbjct: 333 NHASVEVRRYISGK 374



 Score = 15.3 bits (27), Expect = 1.4
 Identities = 5/14 (35%), Positives = 8/14 (56%)
 Frame = +3 / +1

                         
Query: 333 NHASVEVRRYISGK 374
           NH    + + ISG+
Sbjct: 469 NHLVAMIEKTISGQ 510



 Score = 14.8 bits (26), Expect = 1.9
 Identities = 8/20 (40%), Positives = 10/20 (50%)
 Frame = +1 / -1

                               
Query: 241 NGAG*RVQETQKKART*QCG 300
           +GAG  +      ART  CG
Sbjct: 291 SGAGFFLCFLYASARTVTCG 232



 Score = 14.8 bits (26), Expect = 1.9
 Identities = 2/6 (33%), Positives = 4/6 (66%)
 Frame = +2 / -3

                 
Query: 389 CVLPIF 406
           C L ++
Sbjct: 157 CALCLY 140



 Score = 14.8 bits (26), Expect = 1.9
 Identities = 2/6 (33%), Positives = 4/6 (66%)
 Frame = -3 / +2

                 
Query: 157 CALCLY 140
           C L ++
Sbjct: 389 CVLPIF 406



 Score = 14.3 bits (25), Expect = 2.6
 Identities = 6/18 (33%), Positives = 8/18 (44%)
 Frame = -2 / +2

                             
Query: 299 PHCQVRAFFCVSCTRQPA 246
           P   VRA       ++PA
Sbjct: 233 PQVTVRADAYRKHRKKPA 286



 Score = 13.4 bits (23), Expect = 4.9
 Identities = 11/31 (35%), Positives = 11/31 (35%)
 Frame = +3 / -3

                                          
Query: 57  CLIAASELVTCRE*IKILLT*VTKYFNQYRH 149
           CL     LVT    I I    VT      RH
Sbjct: 148 CLYWLKYLVT*VNKILIYSRQVTSSEAAIRH 56



 Score = 13.4 bits (23), Expect = 4.9
 Identities = 11/31 (35%), Positives = 11/31 (35%)
 Frame = -3 / +3

                                          
Query: 148 CLYWLKYLVT*VNKILIYSRQVTSSEAAIRH 56
           CL     LVT    I I    VT      RH
Sbjct: 57  CLIAASELVTCRE*IKILLT*VTKYFNQYRH 149



 Score = 13.0 bits (22), Expect = 6.7
 Identities = 5/14 (35%), Positives = 6/14 (42%)
 Frame = -3 / -2

                         
Query: 370 PLMYRRTSTLAWLL 329
           PLM        WL+
Sbjct: 506 PLMVFSIIATRWLV 465



 Score = 13.0 bits (22), Expect = 6.7
 Identities = 5/14 (35%), Positives = 6/14 (42%)
 Frame = -2 / -3

                         
Query: 506 PLMVFSIIATRWLV 465
           PLM        WL+
Sbjct: 370 PLMYRRTSTLAWLL 329



 Score = 12.5 bits (21), Expect = 9.2
 Identities = 3/5 (60%), Positives = 5/5 (100%)
 Frame = +2 / -2

                
Query: 275 KKPAP 289
           ++PAP
Sbjct: 257 RQPAP 243


Lambda     K      H
   0.318    0.135    0.401 


Matrix: BLOSUM62
Number of Hits to DB: 2790
Number of Sequences: 0
Number of extensions: 62
Number of successful extensions: 40
Number of sequences better than 10.0: 1
length of database: 240
effective HSP length: 19
effective length of database: 221
effective search space used:    48620
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 16 ( 7.3 bits)
X2: 0 ( 0.0 bits)
S1: 41 (21.7 bits)
BioPerl-1.007002/t/data/blast.report000444000766000024      5330313155576321 17256 0ustar00cjfieldsstaff000000000000TBLASTN 2.0.4 [Feb-24-1998]

Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A.
Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman
(1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search
 programs", Nucleic Acids Res. 25:3389-3402.

Query=
gi|1401126 
         (504 letters)

Database: Non-redundant GenBank+EMBL+DDBJ+PDB sequences
           336,723 sequences; 677,679,054 total letters

Searchingdone


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gb|U49928|HSU49928 Homo sapiens TAK1 binding protein (TAB1) mRNA...  1009  0.0
emb|Z36985|PTPP2CMR P.tetraurelia mRNA for protein phosphatase t...    58  4e-07
emb|X77116|ATMRABI1 A.thaliana mRNA for ABI1 protein                   53  1e-05
gb|U12856|ATU12856 Arabidopsis thaliana Col-0 abscisic acid inse...    53  1e-05
dbj|D38109|ATHPP2CA Arabidopsis thaliana mRNA for protein phosph...    52  3e-05
emb|Y08965|ATABI2RNA A.thaliana mRNA for ABI2 protein                  47  8e-04
emb|AL010222|PFSC04009 Plasmodium falciparum DNA *** SEQUENCING ...    45  0.004
gb|AC002409|ATAC002409 Arabidopsis thaliana chromosome II BAC T2...    43  0.012
emb|Z98762|SPAC4A8 S.pombe chromosome I cosmid c4A8                    42  0.020
gb|AF006827|AF006827 Magnaporthe grisea adenylate cyclase (MAC1)...    41  0.045
emb|Y13936|HSY13936 Homo sapiens mRNA for protein phosphatase 2C...    41  0.059
gb|U81159|BTU81159 Bos taurus magnesium-dependent calcium inhibi...    40  0.077
emb|Y10438|SPFKBAD Streptomyces sp. MA6548 fkbA gene and partial...    40  0.077
gb|AF012921|AF012921 Magnaporthe grisea adenylate cyclase (mac1)...    40  0.10
gb|U42383|MMU42383 Mus musculus fibroblast growth factor inducib...    40  0.10
gb|AF023665|AF023665 Plasmodium falciparum protein phosphatase 2...    39  0.13
gb|M24942|YSPCYR1A Yeast (S.pombe) adenylate cyclase (CYR1) gene...    39  0.17
gb|M26699|YSPADC Yeast (S.pombe) cyr1 gene encoding adenylyl cyc...    39  0.17
gb|L43413|PANADCY Podospora anserina adenyl cyclase gene, exons 1-4    38  0.30
gb|M89651|HUMMMDBC Human DNA from cosmid DNA MMDB (f10080) and M...    38  0.30
emb|Z99161|SPAC11G7 S.pombe chromosome I cosmid c11G7                  38  0.30
emb|X56042|SKADECYC Saccharomyces kluyveri gene for adenylyl cyc...    37  0.88
gb|M29235|CELPOLII C.elegans RNA polymerase II largest subunit (...    36  1.1
dbj|D45132|HUMHOXY1 Human kidney mRNA for zinc-finger DNA-bindin...    36  1.1
gb|U70654|MMU70654 Mus musculus musculus sex determining protein...    36  1.1
gb|U53333|CELF36A4 Caenorhabditis elegans cosmid F36A4.                36  1.1
gb|L29028|CREWP6A Chlamydomonas eugametos WP6 mRNA, complete cds       36  1.1
gb|U70653|MMU70653 Mus musculus musculus sex determining protein...    36  1.1
gb|U17838|HSU17838 Human zinc finger protein RIZ mRNA, complete cds    36  1.1
emb|X56432|DMRUNTR D.melanogaster mRNA for runt segmentation gene      36  1.5
emb|X67204|MMSRYLOC M.musculus DNA sequence of Sry locus               36  1.5
gb|U00051|CELF42G9 Caenorhabditis elegans cosmid F42G9.                36  1.5
gb|U70655|MMU70655 Mus musculus sex determining protein (Sry) ge...    36  1.5
gb|AF019985|AF019985 Dictyostelium discoideum Spalten (spnA) mRN...    36  2.0
emb|X78886|ATABI1G A.thaliana (Landsberg erecta) ABI1 gene             36  2.0
gb|U70651|MMU70651 Mus musculus musculus sex determining protein...    36  2.0
gb|U70652|MMU70652 Mus musculus musculus sex determining protein...    36  2.0
emb|X58924|HVRPL11E H.volcanii genes for ribosomal proteins L11e...    36  2.0
emb|X05806|CHAMPER Acetabularia plastid DNA homologous to Drosop...    36  2.0
gb|U82833|OSU82833 Oryza sativa S-adenosyl-L-methionine syntheta...    35  2.6
emb|Z27084|HLHOLLI H.lanatus mRNA for allergen Hol-lI                  35  2.6
dbj|D00676|SH1RSP40 Pseudorabies virus genome, RSp40 and pk genes      35  2.6
emb|Y10421|CCATCOLE1 C.curvatus strain ATCC 20509 Ole1 gene            35  2.6
gb|L14320|HSBBICP4A Bovine herpesvirus type 1 early-intermediate...    35  2.6
emb|AJ004801|BHV1CGEN Bovine herpesvirus 1 complete genome             35  2.6
dbj|AB010074|AB010074 Arabidopsis thaliana genomic DNA, chromoso...    35  3.4
gb|AC004490|AC004490 Homo sapiens chromosome 19, cosmid R29381, ...    35  3.4
dbj|AB011474|AB011474 Arabidopsis thaliana genomic DNA, chromoso...    35  3.4
gb|U03645|MMU03645 Mus musculus domesticus Torino (Sry) gene, co...    35  3.4
gb|U70641|MMU70641 Mus musculus domesticus sex determining prote...    35  3.4
gb|U70650|MMU70650 Mus musculus domesticus sex determining prote...    35  3.4
gb|U70642|MMU70642 Mus musculus domesticus sex determining prote...    35  3.4
gb|U70647|MMU70647 Mus musculus domesticus sex determining prote...    35  3.4
emb|Y11840|ATABI2 Arabidopsis thaliana ABI2 gene                       35  3.4
emb|Y08966|ATABI2DNA A.thaliana gene encoding ABI2 protein             35  3.4
emb|X16144|SVGRA S. violaceoruber DNA for granaticin polyketide ...    35  3.4
emb|X16300|SVPKS Streptomyces violaceoruber polyketide synthase ...    35  3.4
gb|U70657|MMU70657 Mus musculus castaneus sex determining protei...    35  3.4
gb|M57417|HUMMUCCF Human (cystic fibrosis patient) mucin mRNA, p...    35  3.4
gb|L04286|DDIGP100 Dictyostelium discoideum glycoprotein gp100 (...    35  3.4
emb|Z46938|BTTESDNA B.taurus DNA (protamine gene cluster)              35  3.4
gb|L13054|DROZESTEL Drosophila melanogaster zeste (z) gene, part...    34  4.4
gb|L13058|DROZESTEP Drosophila melanogaster zeste (z) gene, part...    34  4.4
gb|M60590|YSCAAGLCS S.cerevisiae a-agglutinin core subunit (AGA1...    34  4.4
gb|AF009521|AF009521 Mus spretus sex determining protein (Sry) g...    34  4.4
emb|Z71659|SCYNR044W S.cerevisiae chromosome XIV reading frame O...    34  4.4
gb|U19361|PMU19361 Petromyzon marinus neurofilament subunit NF-1...    34  4.4
gb|U70646|MMU70646 Mus musculus domesticus sex determining prote...    34  4.4
gb|U23477|DDU23477 Dictyostelium discoideum phosphatidylinositol...    34  4.4
emb|X55695|LEEXTEN15 Tomato mRNA for a glycine-rich protein (clo...    34  4.4
emb|Z95556|MTCY07A7 Mycobacterium tuberculosis cosmid SCY07A7          34  4.4
dbj|AB007645|AB007645 Arabidopsis thaliana genomic DNA, chromoso...    34  5.8
emb|X64346|HSGEND Herpesvirus saimiri complete genome DNA              34  5.8
emb|Z95620|SPBC3D6 S.pombe chromosome II cosmid c3D6                   34  5.8
gb|U70644|MMU70644 Mus musculus domesticus sex determining prote...    34  5.8
gb|U70649|MMU70649 Mus musculus domesticus sex determining prote...    34  5.8
gb|U43491|SCU43491 Saccharomyces cerevisiae cosmid clone pEOA156...    34  5.8
dbj|D00909|NEUNAC N.crassa nac gene coding for adenylate cyclase...    34  5.8
gb|U70645|MMU70645 Mus musculus domesticus sex determining prote...    34  5.8
gb|AF009519|AF009519 Mus musculus domesticus sex determining pro...    34  5.8
gb|M77174|MUSPERPA Mouse perlecan mRNA, complete cds.                  34  5.8
emb|Z74917|SCYOR009W S.cerevisiae chromosome XV reading frame OR...    34  5.8
gb|J04054|MUSPCGBM Mouse basement membrane proteoglycan mRNA, pa...    34  5.8
emb|Z47072|CEF26C11 Caenorhabditis elegans cosmid F26C11, comple...    34  5.8
gb|U70643|MMU70643 Mus musculus sex determining protein (Sry) ge...    34  5.8
gb|AC003671|AC003671 Arabidopsis thaliana chromosome 1 BAC F17O7...    34  5.8
emb|X16481|RN11ZNBP Rat mRNA for zinc(2+) binding protein              34  5.8
gb|U46156|SSU46156 Synechococcus sp. CcmK (ccmK) gene, complete ...    34  5.8
gb|AC000098|YUP8H12 Arabidopsis thaliana chromosome 1 YAC yUP8H1...    34  5.8
emb|Z71781|SCCIVL37K S.cerevisiae chromosome IV left arm (EU) DN...    34  5.8
emb|Y13332|SSTO1AMY Streptomyces sp. TO1 amy gene                      34  5.8
gb|M30473|NEULEURSC N.crassa cytoplasmic leucyl-tRNA synthetase ...    34  5.8
emb|Z74085|SCYDL037C S.cerevisiae chromosome IV reading frame OR...    34  5.8
gb|AF029858|AF029858 Sorghum bicolor cytochrome P450 CYP71E1 (CY...    34  5.8
gb|S47414|S47414 glycine-rich protein {clone atGRP-5} [Arabidops...    34  7.6
emb|X60294|SCSEC1A S.cereale Sec1 gene for omega secalin               34  7.6
emb|Z37975|BTPLAKOPH B.taurus mRNA for plakophilin.                    34  7.6
emb|X60295|SCSEC1B S.cereale Sec1 gene for omega secalin               34  7.6
dbj|D87895|D87895 Aspergillus nidulans DNA for chitinase, comple...    34  7.6
gb|AF017789|AF017789 Homo sapiens putative transcription factor ...    34  7.6

>gb|U49928|HSU49928 Homo sapiens TAK1 binding protein (TAB1) mRNA, complete cds.
           Length = 3096
           
 Score = 1009 bits (2580), Expect = 0.0
 Identities = 504/504 (100%), Positives = 504/504 (100%)

Query: 1   MAAQRRSLLQSEQQPSWTDDLPLCHLSGVGSASNRSYSADGKGTESHPPEDSWLKFRSEN 60
           MAAQRRSLLQSEQQPSWTDDLPLCHLSGVGSASNRSYSADGKGTESHPPEDSWLKFRSEN
Sbjct: 21  MAAQRRSLLQSEQQPSWTDDLPLCHLSGVGSASNRSYSADGKGTESHPPEDSWLKFRSEN 200

Query: 61  NCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLES 120
           NCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLES
Sbjct: 201 NCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLES 380

Query: 121 IDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLLNNKLYV 180
           IDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLLNNKLYV
Sbjct: 381 IDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLLNNKLYV 560

Query: 181 ANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQVGIICGQEST 240
           ANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQVGIICGQEST
Sbjct: 561 ANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQVGIICGQEST 740

Query: 241 RRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLMSEGLYKALEAAH 300
           RRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLMSEGLYKALEAAH
Sbjct: 741 RRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLMSEGLYKALEAAH 920

Query: 301 GPGQANQEIAAMIDTEFAKQTSLDAVAQAVVDRVKRIHSDTFASGGERARFCPRHEDMTL 360
           GPGQANQEIAAMIDTEFAKQTSLDAVAQAVVDRVKRIHSDTFASGGERARFCPRHEDMTL
Sbjct: 921 GPGQANQEIAAMIDTEFAKQTSLDAVAQAVVDRVKRIHSDTFASGGERARFCPRHEDMTL 1100

Query: 361 LVRNFGYPLGEMSQPTPSPAPAAGGRVYPVSVPYSSAQSTSKTSVTLSLVMPSQGQMVNG 420
           LVRNFGYPLGEMSQPTPSPAPAAGGRVYPVSVPYSSAQSTSKTSVTLSLVMPSQGQMVNG
Sbjct: 1101LVRNFGYPLGEMSQPTPSPAPAAGGRVYPVSVPYSSAQSTSKTSVTLSLVMPSQGQMVNG 1280

Query: 421 AHSASTLDEATPTLTNQSPTLTLQSTNTHTQSSSSSSDGGLFRSRPAHSLPPGEDGRVEP 480
           AHSASTLDEATPTLTNQSPTLTLQSTNTHTQSSSSSSDGGLFRSRPAHSLPPGEDGRVEP
Sbjct: 1281AHSASTLDEATPTLTNQSPTLTLQSTNTHTQSSSSSSDGGLFRSRPAHSLPPGEDGRVEP 1460

Query: 481 YVDFAEFYRLWSVDHGEQSVVTAP 504
           YVDFAEFYRLWSVDHGEQSVVTAP
Sbjct: 1461YVDFAEFYRLWSVDHGEQSVVTAP 1532


>emb|Z36985|PTPP2CMR P.tetraurelia mRNA for protein phosphatase type 2C
           Length = 969
           
 Score = 57.8 bits (137), Expect = 4e-07
 Identities = 64/261 (24%), Positives = 112/261 (42%), Gaps = 2/261 (0%)

Query: 64  LYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLESIDD 123
           ++GVF+G+ G  V  FV +    ELL  +                  +  E+ F E++ +
Sbjct: 182 VFGVFDGHGGREVA*FVEKHFVDELLKNK------------------NFKEQKFEEALKE 307

Query: 124 ALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREIS-GGAMAVVAVLLNNKLYVAN 182
              +   L            L P+ QK L   K  + + S  G  A VA++  N LYVAN
Sbjct: 308 TFLKMDELL-----------LTPEGQKELN*YKATDTDESYAGCTANVALIYKNTLYVAN 454

Query: 183 VGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQVGIICGQESTRR 242
            G +R++LC++  +      ++VDH  +N +E  R+ + G   G +    +      +R 
Sbjct: 455 AGDSRSVLCRNNTN----HDMSVDHKPDNPEEKSRIERAG---GFVSDGRVNGNLNLSRA 613

Query: 243 IGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLMSEGLYKALEAAHGP 302
           +GD + K      D    +    IIA P++   + L     F+++  +G+++ L      
Sbjct: 614 LGDLEYKR-----DNKLRSNE*LIIALPDVKKTE-LTP*DKFILMGCDGVFETLNH*ELL 775

Query: 303 GQANQEIA-AMIDTEFAKQTSLD 324
            Q N  I  A +  E  K+ + D
Sbjct: 776 KQVNSTIG*AQVTEELLKKAAED 844


>emb|X77116|ATMRABI1 A.thaliana mRNA for ABI1 protein
            Length = 1981
            
 Score = 52.7 bits (124), Expect = 1e-05
 Identities = 59/242 (24%), Positives = 105/242 (43%), Gaps = 6/242 (2%)

Query: 55   KFRSENNCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVE 114
            +F  ++    +GV++G+ G++V N+  +R+   L      AE   A  + +L      +E
Sbjct: 918  RFDPQSAAHFFGVYDGHGGSQVANYCRERMHLAL------AEEI-AKEKPMLCDGDTWLE 1076

Query: 115  RSFLESIDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLL 174
            +      +  L   + ++S  PE V                         G+ +VVAV+ 
Sbjct: 1077 KWKKALFNSFLRVDSEIESVAPETV-------------------------GSTSVVAVVF 1181

Query: 175  NNKLYVANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQ---- 230
             + ++VAN G +RA+LC+    G     L+VDH  + EDE  R+   G   GK+ Q    
Sbjct: 1182 PSHIFVANCGDSRAVLCR----GKTALPLSVDHKPDREDEAARIEAAG---GKVIQWNGA 1340

Query: 231  --VGIICGQESTRRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLM 288
               G++     +R IGD  +K                II +PE+   + +      L+L 
Sbjct: 1341 RVFGVLA---MSRSIGDRYLK--------------PSIIPDPEVTAVKRVK-EDDCLILA 1466

Query: 289  SEGLYKAL 296
            S+G++  +
Sbjct: 1467 SDGVWDVM 1490


>gb|U12856|ATU12856 Arabidopsis thaliana Col-0 abscisic acid insensitive protein (ABI1)
            mRNA, complete cds.
            Length = 2000
            
 Score = 52.7 bits (124), Expect = 1e-05
 Identities = 59/242 (24%), Positives = 105/242 (43%), Gaps = 6/242 (2%)

Query: 55   KFRSENNCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVE 114
            +F  ++    +GV++G+ G++V N+  +R+   L      AE   A  + +L      +E
Sbjct: 918  RFDPQSAAHFFGVYDGHGGSQVANYCRERMHLAL------AEEI-AKEKPMLCDGDTWLE 1076

Query: 115  RSFLESIDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLL 174
            +      +  L   + ++S  PE V                         G+ +VVAV+ 
Sbjct: 1077 KWKKALFNSFLRVDSEIESVAPETV-------------------------GSTSVVAVVF 1181

Query: 175  NNKLYVANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQ---- 230
             + ++VAN G +RA+LC+    G     L+VDH  + EDE  R+   G   GK+ Q    
Sbjct: 1182 PSHIFVANCGDSRAVLCR----GKTALPLSVDHKPDREDEAARIEAAG---GKVIQWNGA 1340

Query: 231  --VGIICGQESTRRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLM 288
               G++     +R IGD  +K                II +PE+   + +      L+L 
Sbjct: 1341 RVFGVLA---MSRSIGDRYLK--------------PSIIPDPEVTAVKRVK-EDDCLILA 1466

Query: 289  SEGLYKAL 296
            S+G++  +
Sbjct: 1467 SDGVWDVM 1490


>dbj|D38109|ATHPP2CA Arabidopsis thaliana mRNA for protein phosphatase 2C
           Length = 1371
           
 Score = 51.5 bits (121), Expect = 3e-05
 Identities = 73/290 (25%), Positives = 132/290 (45%), Gaps = 13/290 (4%)

Query: 47  HPPEDSWLKFRSENNCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVL 106
           HP   S+L+  SEN+ F YGVF+G+  + V     +RL  +++  ++    A  +    +
Sbjct: 447 HP---SFLQRNSENHHF-YGVFDGHGCSHVAEKCRERLH-DIVKKEVEVM-ASDEWTETM 608

Query: 107 LQAFDVVERSFLESIDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGA 166
           +++F  +++   +   + +   A+    +          PQ   +             G+
Sbjct: 609 VKSFQKMDKEVSQRECNLVVNGAT--RSMKNSCRCELQSPQCDAV-------------GS 743

Query: 167 MAVVAVLLNNKLYVANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAG 226
            AVV+V+   K+ V+N G +RA+LC++ V       L+VDH  +  DEL R+ Q G   G
Sbjct: 744 TAVVSVVTPEKIIVSNCGDSRAVLCRNGV----AIPLSVDHKPDRPDELIRIQQAG---G 902

Query: 227 KI------KQVGIICGQESTRRIGD-YKVKYGYTDIDLLSAAKSKP----IIAEPEIHGA 275
           ++      + +G++     +R IGD Y   Y   D ++    ++      I+A   +   
Sbjct: 903 RVIYWDGARVLGVLA---MSRAIGDNYLKPYVIPDPEVTVTDRTDEDECLILASDGLWDV 1073

Query: 276 QPLDGVTGF--LVLMSEGLYKALEAAHGPGQANQEIAAMIDTEFAKQTSLDAVAQAVVDR 333
            P +   G   + L   G     +AAH    A  + A ++      + S D V+  VVD 
Sbjct: 1074VPNETACGVARMCLRGAGAGDDSDAAH---NACSDAALLLTKLALARQSSDNVSVVVVDL 1244

Query: 334 VKR 336
            KR
Sbjct: 1245RKR 1253


>emb|Y08965|ATABI2RNA A.thaliana mRNA for ABI2 protein
           Length = 1470
           
 Score = 46.9 bits (109), Expect = 8e-04
 Identities = 55/241 (22%), Positives = 100/241 (40%), Gaps = 7/241 (2%)

Query: 56  FRSENNCFLYGVFNGYDGNRVTNFVAQRLSAELL--LGQLNAEHAEADV-----RRVLLQ 108
           F    +   +GV++G+ G++V N+  +R+   L   + +   E  + D      ++ L  
Sbjct: 504 FNPHLSAHFFGVYDGHGGSQVANYCRERMHLALTEEIVKEKPEFCDGDTWQEKWKKALFN 683

Query: 109 AFDVVERSFLESIDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMA 168
           +F  V+ S +E++  A           PE V                         G+ +
Sbjct: 684 SFMRVD-SEIETVAHA-----------PETV-------------------------GSTS 752

Query: 169 VVAVLLNNKLYVANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKI 228
           VVAV+    ++VAN G +RA+LC+    G     L+VDH  + +DE  R+   G    + 
Sbjct: 753 VVAVVFPTHIFVANCGDSRAVLCR----GKTPLALSVDHKPDRDDEAARIEAAGGKVIRW 920

Query: 229 KQVGIICGQESTRRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLM 288
               +      +R IGD  +K                +I +PE+   + +      L+L 
Sbjct: 921 NGARVFGVLAMSRSIGDRYLK--------------PSVIPDPEVTSVRRVK-EDDCLILA 1055

Query: 289 SEGLYKAL 296
           S+GL+  +
Sbjct: 1056SDGLWDVM 1079


>emb|AL010222|PFSC04009 Plasmodium falciparum DNA *** SEQUENCING IN PROGRESS *** from contig
            4-9, complete sequence [Plasmodium falciparum]
            Length = 5332
            
 Score = 44.5 bits (103), Expect = 0.004
 Identities = 48/183 (26%), Positives = 83/183 (45%), Gaps = 15/183 (8%)

Query: 163  SGGAMAVVAVLLNNKLYVANVGTNRALLCKSTVDGLQVTQLNVDHTTE-NEDELFRLSQL 221
            S G  A V+V+  N LYVAN+G +R ++ K+     +   L VDH    N+ E  R+ + 
Sbjct: 2760 SSGTTACVSVIFKNMLYVANIGDSRCIISKNG----RAIVLTVDHRASINKKEQDRILKS 2593

Query: 222  GLDAGKIKQVGIICGQESTRRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGV 281
            G   G +   G + G     R        G+      +  K K +I EP++   +  D  
Sbjct: 2592 G---GILDDEGYLGGCLGVCR--------GFGSFHKKTKEKLKGLICEPDLFHIKLTDD- 2449

Query: 282  TGFLVLMSEGLYKALEAAHGPGQANQEIAAMIDTEFA---------KQTSLDAVAQAVV- 331
              FL++  +G++  + +          +    D + A         K+ SLD ++  VV 
Sbjct: 2448 DEFLIICCDGIFDVITSQEAVNTVKNSLIQSRDAKTAAEALCQLAYKKKSLDNLSVLVVI 2269

Query: 332  ----DRVKRIHSDTFASG 345
                D+  ++ S   +SG
Sbjct: 2268 FQNPDKNNKVSSINESSG 2215


>gb|AC002409|ATAC002409 Arabidopsis thaliana chromosome II BAC T20B5 genomic sequence, complete
             sequence [Arabidopsis thaliana]
             Length = 72839
             
 Score = 43.0 bits (99), Expect = 0.012
 Identities = 21/57 (36%), Positives = 38/57 (65%)

Query: 165   GAMAVVAVLLNNKLYVANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQL 221
             G  A+ ++L+ NKL+VANVG +RA+LC++      ++++  D+ TE+E  L+ +  L
Sbjct: 24355 GCTAIASLLVENKLFVANVGDSRAILCRAG-HPFALSKVR*DYHTESELSLYSIGAL 24188


>emb|Z98762|SPAC4A8 S.pombe chromosome I cosmid c4A8
            Length = 43895
            
 Score = 42.2 bits (97), Expect = 0.020
 Identities = 56/230 (24%), Positives = 104/230 (44%), Gaps = 20/230 (8%)

Query: 63   FLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLESID 122
            F YG+F+G+ G   + F++  L   +    LN      D  ++L +   V    ++  + 
Sbjct: 3939 FFYGLFDGHGGTECSEFLSTNLGKIIENQDLN------DTEKILKEVHSV--GGYMAGLK 3784

Query: 123  DALAEKASLQSQLPEGVPQHQLPPQY-QKILERLKTLER----EISGGAMAVVAVLLNNK 177
               + +  LQS+  + + + +L   + Q  ++ L    R        GA+  VA++ +  
Sbjct: 3783 PPFSLRTVLQSRDEDLLWRARLYYSFLQADMDYLTNYARPSPDSAVPGAVGTVAIITSKN 3604

Query: 178  -----------LYVANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGL--- 223
                       +++A+VG  RALLC S     +  +L   H   + +E  RL +  +   
Sbjct: 3603 NLSYWESDSYIIHLAHVGDTRALLCDSRTG--RAHRLTFQHHPADVEEARRLRRYNMGFS 3430

Query: 224  -DAGKIKQVGIICGQESTRRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVT 282
             D+   K+   +    +TR  GD     GY         K   ++AEP++     L    
Sbjct: 3429 RDSFGQKRFAWVA---NTRSFGD-----GY-------KLKKLGVVAEPQLTSIHSLRDDW 3295

Query: 283  GFLVLMSEGL 292
             FL L+S+G+
Sbjct: 3294 SFLTLLSDGI 3265


>gb|AF006827|AF006827 Magnaporthe grisea adenylate cyclase (MAC1) gene, complete cds
            Length = 8678
            
 Score = 41.0 bits (94), Expect = 0.045
 Identities = 63/259 (24%), Positives = 111/259 (42%), Gaps = 8/259 (3%)

Query: 14   QPSWTDDLPLCHLSGVGSASNR-SYS-ADGKGTESHPPEDSWL--KFRSENNCFLYGVFN 69
            QPS  +    C +   GS++    Y+ AD  G   H      +  +F +     L G+F+
Sbjct: 5314 QPSIPEQSEDCRVRTSGSSAGYLPYAMADTLGKNEHLSTVDLVVPRFNASETETLLGLFD 5493

Query: 70   GY----DGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLESIDDAL 125
            G      G+++  ++ +        GQ+ A    A    +     D + R+FL +++  L
Sbjct: 5494 GQALSSGGSKIAKYLHENF------GQILATELRALKTGLKETPEDALRRAFL-ALNKEL 5652

Query: 126  AEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLLNNKLYVANVGT 185
               A   S+    VP H+   Q   IL +      +++ G +A V  L    LYVANVG 
Sbjct: 5653 VTIAIQHSEDRPSVP-HRSGSQAHVILNK-----EDLNSGGVATVVYLQGQDLYVANVGD 5814

Query: 186  NRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQVGIICGQESTRRIGD 245
             +A++ +S      +T+    H      E  R+ + G   G + + G +  Q    R   
Sbjct: 5815 AQAMIIQSDQTHKMLTR---KHDPAEPTERSRIREAG---GWVSRNGKLNDQLGVSR--- 5967

Query: 246  YKVKYGYTDIDLLSAAKSKPIIAEPEI 272
                +GY  +DL+ A ++ P ++   I
Sbjct: 5968 ---AFGY--VDLMPAVQAAPHVSHVAI 6033


CPU time:    78.72 user secs.	    0.85 sys. secs	   79.57 total secs.

  Database: Non-redundant GenBank+EMBL+DDBJ+PDB sequences
    Posted date:  Apr 16, 1998  9:38 AM
  Number of letters in database: 677,679,054
  Number of sequences in database:  336,723
  
Lambda     K      H
   0.313    0.130    0.370 

Gapped
Lambda     K      H
   0.270   0.0470    0.230 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 374080624
Number of Sequences: 336723
Number of extensions: 5779396
Number of successful extensions: 37522
Number of sequences better than 10: 214
Number of HSP's better than 10.0 without gapping: 32
Number of HSP's successfully gapped in prelim test: 85
Number of HSP's that attempted gapping in prelim test: 35679
Number of HSP's gapped (non-prelim): 445
length of query: 504
length of database: 225893018
effective HSP length: 62
effective length of query: 442
effective length of database: 205016192
effective search space: 90617156864
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 42 (21.9 bits)
S2: 74 (33.2 bits)
BioPerl-1.007002/t/data/blast_no_hit_desc.txt000444000766000024       244613155576321 21102 0ustar00cjfieldsstaff000000000000BLASTN 2.2.16 [Mar-25-2007]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= Callithrix_jacchus Callithrix jacchus clone CH259-179B5,
WORKING DRAFT SEQUENCE, 15 ordered pieces.
         (38,526 letters)

Database: blast1 
           1 sequences; 247,249,719 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

chr1                                                                 3971   0.0  

>chr1
          Length = 247249719

 Score = 3971 bits (2039), Expect = 0.0
 Identities = 2927/3229 (90%), Gaps = 63/3229 (1%)
 Strand = Plus / Plus

                                                                            
Query: 29757    acaaacacatccaggtgaaccccaacccccagcccaaaaaggtaagtctgttgtatttac 29816
                |||| ||||||||||||||| ||| ||||||||||||||||||||||||||||| |||||
Sbjct: 27202976 acaagcacatccaggtgaactccaccccccagcccaaaaaggtaagtctgttgtgtttac 27203035

(truncated, not supposed to parse fully)

BioPerl-1.007002/t/data/blast_plus.blastp000444000766000024       567213155576321 20261 0ustar00cjfieldsstaff000000000000BLASTP 2.2.23+


Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.



Reference for composition-based statistics: Alejandro A. Schaffer,
L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri
I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001),
"Improving the accuracy of PSI-BLAST protein database searches with
composition-based statistics and other refinements", Nucleic Acids
Res. 29:2994-3005.



Database: subject.fa
           1 sequences; 311 total letters



Query=  query
Length=220
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

  subject                                                              162    4e-45


> subject
Length=311

 Score =  162 bits (411),  Expect = 4e-45, Method: Compositional matrix adjust.
 Identities = 110/308 (35%), Positives = 145/308 (47%), Gaps = 94/308 (30%)

Query  5    NNTQISGFLLMGLSNKPELQLPIFGLFLSMYLITVFGNLLIILDISSDSHLHTPMYFF--  62
            N + IS F L G+S  PE Q  +FG+FL MYL+T+ GNLLIIL I SD HLHTPMYFF  
Sbjct  3    NQSSISEFFLRGISAPPEQQQSLFGIFLCMYLVTLTGNLLIILAIGSDLHLHTPMYFFLA  62

Query       ------------------------------------------------------------  
                                                                        
Sbjct  63   NLSFVDMGLTSSTVTKMLVNIQTRHHTISYTGCLTQMYFFLMFGDLDSFFLAAMAYDRYV  122

Query  63   --------------------------LANLXV--QSLMLLQLSFCSEVEIPHFFCELHQM  94
                                      L N+     + ++ +LSFC   EI HFFC++  +
Sbjct  123  AICHPLCYSTVMRPQVCALMLALCWVLTNIVALTHTFLMARLSFCVTGEIAHFFCDITPV  182

Query  95   IQLACSDTFLNDTVIYV--STVLLACGPLTGILYSYSKIVSSICRISSAQGKYKAFSTCA  152
            ++L+CSDT +N+ +++V   TVL+   P   I+ SY  IV +I R+ +  G  KAFSTC+
Sbjct  183  LKLSCSDTHINEMMVFVLGGTVLIV--PFLCIVTSYIHIVPAILRVRTRGGVGKAFSTCS  240

Query  153  SHLSVVSLFYCTVLGVYLSCAATQSSHGSAVASVMYTVVTPMLNPFIYSLRNKDIKEALI  212
            SHL VV +FY T+   YL   +  S      A+ MYT+VTPMLNPFIYSLRNKD+K AL 
Sbjct  241  SHLCVVCVFYGTLFSAYLCPPSIASEEKDIAAAAMYTIVTPMLNPFIYSLRNKDMKGALK  300

Query  213  RFLRRVTI  220
            R     +I
Sbjct  301  RLFSHRSI  308


 Score = 15.0 bits (27),  Expect = 1.9, Method: Compositional matrix adjust.
 Identities = 6/10 (60%), Positives = 8/10 (80%), Gaps = 0/10 (0%)

Query  125  LYSYSKIVSS  134
            L+S+  IVSS
Sbjct  302  LFSHRSIVSS  311



Lambda     K      H
   0.328    0.139    0.412 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 

Effective search space used: 55770


  Database: subject.fa
    Posted date:  Apr 26, 2010  2:49 PM
  Number of letters in database: 311
  Number of sequences in database:  1



Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Neighboring words threshold: 11
Window for multiple hits: 40
BioPerl-1.007002/t/data/blastp2215.blast000444000766000024      1560213155576321 17542 0ustar00cjfieldsstaff000000000000BLASTP 2.2.15 [Oct-15-2006]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman 
(1997), "Gapped BLAST and PSI-BLAST: a new generation of 
protein database search programs", Nucleic Acids Res. 25:3389-3402.

Reference: Schäffer, Alejandro A., L. Aravind, Thomas L. Madden, Sergei 
Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and 
Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST 
protein database searches with composition-based statistics 
and other refinements", Nucleic Acids Res. 29:2994-3005.

RID: 1169055516-21385-22799250964.BLASTQ4


Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
           4,460,989 sequences; 1,533,424,333 total letters
Query= gi|15608519|ref|NP_215895.1| pyrimidine regulatory protein PyrR [Mycobacterium 
tuberculosis H37Rv]
Length=193


                                                                   Score     E
Sequences producing significant alignments:                       (Bits)  Value

gi|15608519|ref|NP_215895.1|  pyrimidine regulatory protein Py...   332    8e-90
gi|55670580|pdb|1W30|A  Chain A, Pyrr Of Mycobacterium Tubercu...   331    1e-89
gi|41407212|ref|NP_960048.1|  pyrimidine regulatory protein Py...   286    5e-76
gi|118464931|ref|YP_882576.1|  PyrR bifunctional protein [Myco...   285    1e-75
gi|118617395|ref|YP_905727.1|  pyrimidine operon regulatory pr...   273    2e-72
gi|118473305|ref|YP_887358.1|  PyrR bifunctional protein [Myco...   258    1e-67
gi|89341207|ref|ZP_01193452.1|  Phosphoribosyltransferase [Myc...   254    1e-66
gi|120403643|ref|YP_953472.1|  Uracil phosphoribosyltransferas...   254    2e-66
gi|92907430|ref|ZP_01276210.1|  Uracil phosphoribosyltransfera...   244    2e-63
gi|111024097|ref|YP_707069.1|  probable uracil phosphoribosylt...   238    8e-62
Query= gi|15595598|ref|NP_249092.1| dihydroorotase [Pseudomonas aeruginosa PAO1]
Length=423


                                                                   Score     E
Sequences producing significant alignments:                       (Bits)  Value

gi|15595598|ref|NP_249092.1|  dihydroorotase [Pseudomonas aeru...   775    0.0   
gi|84324488|ref|ZP_00972546.1|  COG0044: Dihydroorotase and re...   771    0.0   
gi|116054132|ref|YP_788575.1|  noncatalytic dihydroorotase-lik...   770    0.0   
gi|309886|gb|AAA25977.1|  dihydroorotase-like                       768    0.0   
gi|94415759|ref|ZP_01295595.1|  hypothetical protein PaerP_010...   744    0.0   
gi|26991676|ref|NP_747101.1|  dihydroorotase [Pseudomonas puti...   628    4e-179
gi|82736201|ref|ZP_00899061.1|  Dihydroorotase multifunctional...   627    7e-179
gi|77461536|ref|YP_351043.1|  dihydroorotase [Pseudomonas fluo...   624    7e-178
gi|66043748|ref|YP_233589.1|  dihydroorotase [Pseudomonas syri...   622    4e-177
gi|118056991|ref|ZP_01525457.1|  dihydroorotase, multifunction...   621    5e-177
Query= gi|15595600|ref|NP_249094.1| pyrimidine regulatory protein PyrR [Pseudomonas 
aeruginosa PAO1]
Length=170


                                                                   Score     E
Sequences producing significant alignments:                       (Bits)  Value

gi|15595600|ref|NP_249094.1|  pyrimidine regulatory protein Py...   320    2e-86
gi|49081516|gb|AAT50158.1|  PA0403 [synthetic construct]            317    2e-85
gi|94415757|ref|ZP_01295593.1|  hypothetical protein PaerP_010...   310    3e-83
gi|119856461|ref|ZP_01637894.1|  Uracil phosphoribosyltransfer...   262    8e-69
gi|67154890|ref|ZP_00416635.1|  Uracil phosphoribosyltransfera...   261    2e-68
gi|26991674|ref|NP_747099.1|  pyrimidine regulatory protein Py...   260    3e-68
gi|28872153|ref|NP_794772.1|  pyrimidine regulatory protein Py...   258    9e-68
gi|104783978|ref|YP_610476.1|  transcriptional regulator PyrR ...   256    3e-67
gi|71736513|ref|YP_272777.1|  pyrimidine operon regulatory pro...   256    5e-67
gi|70733117|ref|YP_262890.1|  pyrimidine regulatory protein Py...   256    5e-67
Query= gi|15598723|ref|NP_252217.1| dihydroorotase [Pseudomonas aeruginosa PAO1]
Length=348


                                                                   Score     E
Sequences producing significant alignments:                       (Bits)  Value

gi|15598723|ref|NP_252217.1|  dihydroorotase [Pseudomonas aeru...   690    0.0   
gi|84319753|ref|ZP_00968143.1|  COG0418: Dihydroorotase [Pseud...   687    0.0   
gi|116051526|ref|YP_789638.1|  dihydroorotase, homodimeric typ...   686    0.0   
gi|94415333|ref|ZP_01295177.1|  hypothetical protein PaerP_010...   677    0.0   
gi|104780416|ref|YP_606914.1|  dihydroorotase [Pseudomonas ent...   618    5e-176
gi|77460740|ref|YP_350247.1|  dihydroorotase [Pseudomonas fluo...   617    1e-175
gi|26987822|ref|NP_743247.1|  dihydroorotase [Pseudomonas puti...   616    2e-175
gi|70732180|ref|YP_261936.1|  dihydroorotase [Pseudomonas fluo...   614    8e-175
gi|118058820|ref|ZP_01527280.1|  dihydroorotase, homodimeric t...   613    1e-174
gi|82737454|ref|ZP_00900303.1|  Dihydroorotase homodimeric typ...   613    2e-174
Query= gi|15600734|ref|NP_254228.1| dihydroorotase [Pseudomonas aeruginosa PAO1]
Length=445


                                                                   Score     E
Sequences producing significant alignments:                       (Bits)  Value

gi|15600734|ref|NP_254228.1|  dihydroorotase [Pseudomonas aeru...   871    0.0   
gi|116053692|ref|YP_794019.1|  dihydroorotase [Pseudomonas aer...   870    0.0   
gi|84318214|ref|ZP_00966642.1|  COG0044: Dihydroorotase and re...   869    0.0   
gi|94417254|ref|ZP_01297073.1|  hypothetical protein PaerP_010...   831    0.0   
gi|77461883|ref|YP_351390.1|  dihydroorotase [Pseudomonas fluo...   658    0.0   
gi|104782179|ref|YP_608677.1|  dihydroorotase [Pseudomonas ent...   634    0.0   
gi|70733466|ref|YP_263241.1|  dihydroorotase [Pseudomonas fluo...   622    2e-177
gi|118059665|ref|ZP_01528121.1|  amidohydrolase [Pseudomonas m...   606    2e-172
gi|50084596|ref|YP_046106.1|  dihydroorotase [Acinetobacter sp...   562    3e-159
gi|117621557|ref|YP_857112.1|  dihydroorotase [Aeromonas hydro...   482    3e-135

  Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding 
environmental samples
    Posted date:  Jan 16, 2007  5:53 PM
  Number of letters in database: 1,533,424,333
  Number of sequences in database:  4,460,989
Lambda     K      H
   0.319    0.139    0.394 
Gapped
Lambda     K      H
   0.267   0.0410    0.140 
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4460989
Number of Hits to DB: 469576580
Number of extensions: 20639621
Number of successful extensions: 52293
Number of sequences better than 10: 358
Number of HSP's better than 10 without gapping: 0
Number of HSP's gapped: 52059
Number of HSP's successfully gapped: 644
Length of database: 1533424333
T: 11
A: 40
X1: 16 (7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (20.4 bits)


BioPerl-1.007002/t/data/blat.psLayout3000444000766000024       117513155576321 17443 0ustar00cjfieldsstaff000000000000psLayout version 3

match	mis- 	rep. 	N's	Q gap	Q gap	T gap	T gap	strand	Q        	Q   	Q    	Q  	T        	T   	T    	T  	block	blockSizes 	qStarts	 tStarts
     	match	match	   	count	bases	count	bases	      	name     	size	start	end	name     	size	start	end	count
---------------------------------------------------------------------------------------------------------------------------------------------------------------
1775	0	0	0	0	0	0	0	+	sequence_10	1775	0	1775	sequence_10	1775	0	1775	1	1775,	0,	0,
70	0	0	0	3	334	3	334	-	sequence_10	1775	840	1244	sequence_10	1775	840	1244	4	14,21,21,14,	531,623,652,921,	840,1102,1131,1230,
BioPerl-1.007002/t/data/blosum62.bla000444000766000024       403013155576321 17016 0ustar00cjfieldsstaff000000000000#  Matrix made by matblas from blosum62.iij
#  * column uses minimum score
#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 62
#  Entropy =   0.6979, Expected =  -0.5209
 A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
 4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1  0 -4 
-1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1  0 -1 -4 
-2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  3  0 -1 -4 
-2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4  1 -1 -4 
 0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 
-1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0  3 -1 -4 
-1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
 0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -4 
-2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0  0 -1 -4 
-1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3 -3 -1 -4 
-1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4 -3 -1 -4 
-1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1 -4 
-1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3 -1 -1 -4 
-2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3 -3 -1 -4 
-1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -1 -2 -4 
 1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0  0 -4 
 0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1  0 -4 
-3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -3 -2 -4 
-2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -2 -1 -4 
 0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3 -2 -1 -4 
-2 -1  3  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1 -4 
-1  0  0  1 -3  3  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2  0  0 -2 -1 -1 -1 -1 -1 -4 
-4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1 
BioPerl-1.007002/t/data/bootstrap.tre000444000766000024         5213155576321 17356 0ustar00cjfieldsstaff000000000000((((A:5,B:5)90:2,C:4)25:3,D:10)0:4,E:11);
BioPerl-1.007002/t/data/brassica_ATH.WUBLASTN000444000766000024      2127513155576321 20363 0ustar00cjfieldsstaff000000000000BLASTN 2.0MP-WashU [22-Aug-2004] [linux24-i686-ILP32F64 2004-08-22T21:42:14]

Copyright (C) 1996-2004 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2004) http://blast.wustl.edu

Notice:  this program and its default parameter settings are optimized to find
nearly identical sequences rapidly.  To identify weak protein similarities
encoded in nucleic acid, use BLASTX, TBLASTN or TBLASTX.

Query=  e15_99na_plate_1as gi|21844367|gb|BQ704948.1|BQ704948 Bn01_02k05_A
    Bn01_AAFC_ECORC_transgenic_Brassica_napus_overexpressing_BNCBF17_constituti
    vely_frost_tolerant Brassica napus cDNA clone Bn01_02k05, mRNA sequence
        (598 letters)

Database:  ATH1_chr_all.5con
           5 sequences; 119,186,497 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done

                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

CHR1v01212004                                                  932  1.3e-79   3
CHR5v01212004                                                 1035  6.9e-71   2



>CHR1v01212004
        Length = 30,432,563

  Plus Strand HSPs:

 Score = 932 (145.9 bits), Expect = 1.3e-79, Sum P(3) = 1.3e-79, Group = 1
 Identities = 230/282 (81%), Positives = 240/282 (85%), Strand = Plus / Plus
 Links = (1)-3-2

Query:       23 AAAGGARATTAAGCACCGGSTGAAGCTTGGTGGCTTGTAGGCGATGAAGACTGATGCRCT 82
                || |||+|||||   |||| |||||||||||||||||||||| ||||| ||||||||+||
Sbjct: 25052120 AAGGGAAATTAA---CCGG-TGAAGCTTGGTGGCTTGTAGGCAATGAA-ACTGATGCACT 25052174

Query:       83 GGACCTGRCGCGTTGTTGTCGAATCCAATGATTCTAATAAAGGCGKTAGGGKACTCCGTT 142
                |||| ||+|| || |||||||||||| ||||| ||||| ||||| +| |||+||||| ||
Sbjct: 25052175 GGACTTGACGGGT-GTTGTCGAATCCGATGATCCTAATGAAGGCATTGGGGTACTCC-TT 25052232

Query:      143 CTTGSACTCTTGCACTTCCTTCAACACTTGAGARGRGTCGGKGCATCCGARCAAAGGAAG 202
                ||||+|||||| |||||||||||||||||||| +|+|||||+||| ||||+||| |||||
Sbjct: 25052233 CTTGCACTCTTCCACTTCCTTCAACACTTGAGCGGAGTCGGTGCAACCGAACAAGGGAAG 25052292

Query:      203 CTTCCACATTGTCCAATAACGGCCATCGTAGTATCCAGGTGTGCTTCCATGCTCACGGTA 262
                ||||||||||||||| || || ||||| |||||||| |||| | | || |||||||||||
Sbjct: 25052293 CTTCCACATTGTCCAGTACCGTCCATCATAGTATCCGGGTGAGTTACCGTGCTCACGGTA 25052352

Query:      263 CACAAATCCGTGCTC--CAACTCAAATTCAACACAAGGAATC 302
                ||||||||||||||   |||  || ||   ||| ||  | ||
Sbjct: 25052353 CACAAATCCGTGCTATACAAACCACATGTTACA-AACCACTC 25052393

 Score = 580 (93.1 bits), Expect = 1.3e-79, Sum P(3) = 1.3e-79, Group = 1
 Identities = 153/192 (79%), Positives = 158/192 (82%), Strand = Plus / Plus
 Links = 1-3-(2)

Query:      410 ACCTTCATGCAGCTAACTCTTCCTCCGTTGCTTGCAATGGAAGTAATATCAGTGTT-GCT 468
                |||| ||||||| |||||||||| ||||||||||  ||||||||||| ||  |||| || 
Sbjct: 25052740 ACCTGCATGCAGTTAACTCTTCCGCCGTTGCTTGTGATGGAAGTAATGTCGTTGTTAGCC 25052799

Query:      469 TTTGCGGGTGASTGGGAATGCRGCGGATGACTTCAAG-CCGGTRAAKWGGAGC-ACCATG 526
                || ||||||| +|||||| ||+||||| ||||| ||| ||| |+|| +||||| ||||| 
Sbjct: 25052800 TT-GCGGGTGGCTGGGAAGGCAGCGGAGGACTT-AAGTCCGTTGAA-AGGAGCGACCATA 25052856

Query:      527 GTGGCTTGAGCCGGTGAGGTAGCCACAGCGGCGGGAGGAGAGCATAGRAGGWAGCCATTA 586
                ||||| |||||||| |||| | ||| ||  |||| || ||||||||| |||+||||||| 
Sbjct: 25052857 GTGGCCTGAGCCGGAGAGGCAACCATAGTAGCGGAAG-AGAGCATAG-AGGAAGCCATTG 25052914

Query:      587 CTACTTCTTTTC 598
                 | ||||||| |
Sbjct: 25052915 TT-CTTCTTTAC 25052925

 Score = 512 (82.9 bits), Expect = 1.3e-79, Sum P(3) = 1.3e-79, Group = 1
 Identities = 118/139 (84%), Positives = 121/139 (87%), Strand = Plus / Plus
 Links = 1-(3)-2

Query:      275 CTCCAACTCAAATTCAACACAAGGAATCCACTCTGTTGCGGAGAAGGTAGTCAACTTCTT 334
                ||||||||| |||||||||||||||||||||| ||||||||| ||||||||||||||| |
Sbjct: 25052501 CTCCAACTCGAATTCAACACAAGGAATCCACT-TGTTGCGGATAAGGTAGTCAACTTCCT 25052559

Query:      335 TGGCCAATTCAACGTCAGTRAGGTCAGGRAGATAAGAGAGAGTCTCAGHACTTCTTCTTT 394
                | ||||||||    || ||+||||||||+|| |||||||||||||||  |||||||||||
Sbjct: 25052560 TAGCCAATTCGGAATCGGTAAGGTCAGGAAGGTAAGAGAGAGTCTCA-AACTTCTTCTTT 25052618

Query:      395 SCGACTGGKGGGCACACCT 413
                +| |  || || |||||||
Sbjct: 25052619 CCAATCGGAGGCCACACCT 25052637


>CHR5v01212004
        Length = 26,992,728

  Plus Strand HSPs:

 Score = 1035 (161.3 bits), Expect = 6.9e-71, Sum P(2) = 6.9e-71, Group = 1
 Identities = 272/348 (78%), Positives = 281/348 (80%), Strand = Plus / Plus
 Links = (1)-2

Query:        1 GATTATT-ATATGATTGTTTTAGAAAGGARATTAAGCACCGGSTGAAGCTTGGTGGCTTG 59
                ||| ||| ||| || ||||||||||| ||+|||||||  ||| |||||||||| ||||||
Sbjct: 15394700 GATAATTCATAAGAATGTTTTAGAAAAGAAATTAAGCTTCGG-TGAAGCTTGGGGGCTTG 15394758

Query:       60 TAGGCGATGAAGACTGATGCRCTGGACCTGRCGCGTTGTTGTCGAATCCAATGATTCTAA 119
                ||||| ||||| ||||||||+ ||||| ||+|| || |||||||||||| ||||| ||||
Sbjct: 15394759 TAGGCAATGAA-ACTGATGCATTGGACTTGACGGGT-GTTGTCGAATCCGATGATCCTAA 15394816

Query:      120 TAAAGGCGKTAGGGKACTCCGTTCTTGSACTCTTGCACTTCCTTCAACACTTGAGARGRG 179
                | ||||||   |||+||||| ||||||+| ||||  ||||||||||||||||||| +|+|
Sbjct: 15394817 TGAAGGCGCCCGGGTACTCC-TTCTTGCATTCTTCAACTTCCTTCAACACTTGAGCGGAG 15394875

Query:      180 TCGGKGCATCCGARCAAAGGAAGCTTCCACATTGTCCAATAACGGCCATCGTAGTATCCA 239
                ||||+||||||||+||| |||||||||||||||||||| || || |||||||||||||| 
Sbjct: 15394876 TCGGTGCATCCGAACAATGGAAGCTTCCACATTGTCCAGTACCGTCCATCGTAGTATCCG 15394935

Query:      240 GGTGTGCTTCCATGCTCACGGTACACAAATCCGTGCTCCAA-CTCA-AATTCAACACAAG 297
                || ||| |||| |||||||||||||||||||||||||  || | || ||   ||| ||  
Sbjct: 15394936 GGAGTGTTTCCGTGCTCACGGTACACAAATCCGTGCTATAAACACATAAGAAAAC-CATT 15394994

Query:      298 GAATCCACTCTGTTGC-GGAGAAGGTAGTCAACTTCTT-TGGCCAATT 343
                 ||| || | || |   |||| |  |   |||  |  | | | | |||
Sbjct: 15394995 CAATACAAT-TGATATTGGAGGATATGCACAAGGTGATATAGTCTATT 15395041

 Score = 739 (116.9 bits), Expect = 6.9e-71, Sum P(2) = 6.9e-71, Group = 1
 Identities = 166/189 (87%), Positives = 171/189 (90%), Strand = Plus / Plus
 Links = 1-(2)

Query:      410 ACCTTCATGCAGCTAACTCTTCCTCCGTTGCTTGCAATGGAAGTAATATCAGTGTTGCTT 469
                ||||||||||||||||||||||| ||||||||||| |||||||| || ||  ||||| | 
Sbjct: 15395364 ACCTTCATGCAGCTAACTCTTCCCCCGTTGCTTGCGATGGAAGTGATGTCCTTGTTGGTC 15395423

Query:      470 TTGCGGGTGASTGGGAATGCRGCGGATGACTTCAAGCCGGTRAAKWGGAGC-ACCATGGT 528
                ||||||||||+ ||||||||+||||||||||||||||||||+||+ ||||| ||||||||
Sbjct: 15395424 TTGCGGGTGACCGGGAATGCAGCGGATGACTTCAAGCCGGTGAAT-GGAGCGACCATGGT 15395482

Query:      529 GGCTTGAGCCGGTGAGGTAGCCACAGCGGCGGGAGGAGAGCATAGRAGGWAGCCATTACT 588
                ||| |||||||| || ||| |||||||||||| |||||||||||| |||+||||||||||
Sbjct: 15395483 GGCCTGAGCCGGGGATGTAACCACAGCGGCGG-AGGAGAGCATAG-AGGAAGCCATTACT 15395540

Query:      589 ACTTCTTTT 597
                ||||||| |
Sbjct: 15395541 ACTTCTTGT 15395549


Parameters:
  -i /home/jasons/pubbrassica/pub_brassica.4
  -d /home/jasons/pubbrassica/ATH1_chr_all.5con
  E=1e-5
  topcomboE=10
  wordmask=seg
  hspsepsmax=1000
  links

  ctxfactor=2.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Strand MatID Matrix name     Lambda    K       H      Lambda    K       H
   +1      0   +5,-4           0.195   0.175   0.361    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a
   -1      0   +5,-4           0.195   0.175   0.361    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a

  Query
  Strand MatID  Length  Eff.Length     E     S  W   T   X   E2      S2
   +1      0      598       598   1.0e-05  299 11 n/a  72  0.023    78
                                                      134  0.025   117
   -1      0      598       598   1.0e-05  299 11 n/a  72  0.023    78
                                                      134  0.025   117


Statistics:

  Database:  /home/jasons/pubbrassica/ATH1_chr_all.5con
   Title:  ATH1_chr_all.5con
   Posted:  11:14:54 AM EST Sep 1, 2004
   Created:  12:14:50 PM EETDT Sep 01, 2004
   Format:  XDF-1
   # of letters in database:  119,186,497
   # of sequences in database:  5
   # of database sequences satisfying E:  2
  No. of states in DFA:  233 (233 KB)
  Total size of DFA:  254 KB (2059 KB)
  Time to generate neighborhood:  0.00u 0.01s 0.01t  Elapsed: 00:00:00
  No. of threads or processors used:  2
  Search cpu time:  0.58u 0.06s 0.64t  Elapsed: 00:00:00
  Total cpu time:  0.66u 0.29s 0.95t  Elapsed: 00:00:01
  Start:  Wed Sep  1 13:19:06 2004   End:  Wed Sep  1 13:19:07 2004
BioPerl-1.007002/t/data/bug1986.blast2000444000766000024     13512013155576321 17150 0ustar00cjfieldsstaff000000000000BLASTN 2.2.13 [Nov-27-2005]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= Input_seq
         (1001 letters)

Database: traces_cjacchus 
           27,983,570 sequences; 24,049,266,895 total letters

Searching...................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

152308237                                                             377   e-101
CXAF-axf41d10.b1                                                      357   6e-95
CXAF-avn84b03.g1                                                      357   6e-95
162139183                                                             357   6e-95
143740441                                                             355   2e-94
167001817                                                             349   2e-92
159735978                                                             349   2e-92
CXAF-atf04d09.b1                                                      341   4e-90
CXAF-bgg82g03.g1                                                      333   9e-88
161278691                                                             333   9e-88
154743524                                                             333   9e-88
CXAF-bgn29h06.b1                                                      329   1e-86
CXAF-bba65f10.g1                                                      313   8e-82
164264264                                                             293   8e-76
143396124                                                             293   8e-76
164628323                                                             291   3e-75
151211459                                                             274   7e-70
CXAF-aji44c06.b1                                                      268   4e-68
CXAF-bar11h09.b1                                                      256   2e-64
142939483                                                             246   2e-61
CXAF-aqm89a09.b3                                                      244   6e-61
CXAF-aqm89a09.b1                                                      244   6e-61
CXAF-aqd56f09.g1                                                      244   6e-61
CXAF-aci24h05.b1                                                      244   6e-61
ghk08c09.x1                                                           244   6e-61
ghk03a07.x1                                                           244   6e-61
CXAF-aji06g03.b1                                                      240   1e-59
164665260                                                             240   1e-59
158291235                                                             240   1e-59
145910632                                                             240   1e-59
CXAF-bdq45h09.b1                                                      236   2e-58
CXAF-bbt24h07.g1                                                      236   2e-58
167006973                                                             236   2e-58
158780303                                                             236   2e-58
CXAF-azh09h04.b1                                                      230   1e-56
CXAF-ahk90a04.b1                                                      228   4e-56
CXAF-aha05c10.b1                                                      228   4e-56
CXAF-alg97f12.g1                                                      226   2e-55
CXAF-afr50d11.g1                                                      224   6e-55
162081134                                                             222   2e-54
CXAF-bdu78d08.b1                                                      218   4e-53
CXAF-are42d04.g1                                                      218   4e-53
CXAF-ajy47b06.b4                                                      218   4e-53
CXAF-ajy47b06.b3                                                      218   4e-53
CXAF-ajy47b06.b2                                                      218   4e-53
CXAF-ajy47b06.b1                                                      218   4e-53
151417246                                                             218   4e-53
146892060                                                             218   4e-53
CXAF-azn75g06.b1                                                      216   1e-52
CXAF-aaz81f04.b1                                                      216   1e-52
158732430                                                             216   1e-52
CXAF-bcf17f10.b1                                                      214   6e-52
CXAF-awa11c11.b1                                                      214   6e-52
CXAF-ajv90f07.b1                                                      214   6e-52
163442888                                                             214   6e-52
144295636                                                             214   6e-52
148071533                                                             212   2e-51
144996081                                                             212   2e-51
CXAF-bhc76e10.b1                                                      210   9e-51
162033953                                                             210   9e-51
157397944                                                             210   9e-51
153795963                                                             210   9e-51
143014334                                                             210   9e-51
142984270                                                             210   9e-51
143029116                                                             210   9e-51
CXAF-auu80c03.g1                                                      208   4e-50
CXAF-ars37h07.g1                                                      208   4e-50
CXAF-anu89d02.b1                                                      208   4e-50
CXAF-amr12h11.g1                                                      208   4e-50
CXAF-agq32b02.g1                                                      208   4e-50
CXAG-1109C24.b1                                                       208   4e-50
166764764                                                             208   4e-50
161213869                                                             208   4e-50
160225376                                                             208   4e-50
156960499                                                             208   4e-50
151634543                                                             208   4e-50
142067436                                                             208   4e-50
149077037                                                             208   4e-50
CXAF-bcq89g05.b1                                                      206   1e-49
CXAF-auo65e07.b1                                                      206   1e-49
CXAF-atm35c08.b1                                                      206   1e-49
166615728                                                             206   1e-49
164475729                                                             206   1e-49
162158949                                                             206   1e-49
159439494                                                             206   1e-49
143739179                                                             206   1e-49
163208263                                                             204   6e-49
162191260                                                             204   6e-49
157979251                                                             202   2e-48
146408814                                                             202   2e-48
CXAF-ajh70d02.g1                                                      200   9e-48
CXAG-0953J21.g1                                                       200   9e-48
165615767                                                             200   9e-48
162357935                                                             200   9e-48
158169353                                                             200   9e-48
147785807                                                             200   9e-48
147630354                                                             200   9e-48
146137770                                                             200   9e-48
143233524                                                             200   9e-48
143703367                                                             200   9e-48
CXAF-bhz55f03.g1                                                      198   3e-47
CXAF-bfv75d10.b1                                                      198   3e-47
CXAF-bep25c06.g1                                                      198   3e-47
CXAF-aun95d03.g1                                                      198   3e-47
CXAF-atr22b03.b1                                                      198   3e-47
CXAF-asa76f10.b1                                                      198   3e-47
CXAF-anf10b10.b1                                                      198   3e-47
CXAF-aho18f04.b1                                                      198   3e-47
145734697                                                             198   3e-47
151273839                                                             198   3e-47
150266590                                                             198   3e-47
CXAF-beq04g01.g1                                                      196   1e-46
CXAF-aqm53b04.g1                                                      196   1e-46
CXAF-aga18c10.b1                                                      196   1e-46
CXAF-abm48g04.b1                                                      196   1e-46
163395941                                                             196   1e-46
164326013                                                             196   1e-46
163856230                                                             196   1e-46
145024552                                                             196   1e-46
CXAF-ase07b08.g1                                                      194   5e-46
CXAF-ajw90h11.b1                                                      194   5e-46
CXAG-1510K05.g1                                                       194   5e-46
150060626                                                             194   5e-46
CXAF-bhc74d03.b1                                                      192   2e-45
CXAF-bhd25c02.b1                                                      192   2e-45
CXAF-baw19d06.g1                                                      192   2e-45
CXAF-bax70a06.b1                                                      192   2e-45
CXAF-azr62e11.b1                                                      192   2e-45
CXAF-afq18g03.b1                                                      192   2e-45
163680421                                                             192   2e-45
166175575                                                             192   2e-45
164723429                                                             192   2e-45
160240273                                                             192   2e-45
160662255                                                             192   2e-45
160662246                                                             192   2e-45
160240273                                                             192   2e-45
160308323                                                             192   2e-45
159697031                                                             192   2e-45
148535694                                                             192   2e-45
144085160                                                             192   2e-45
CXAF-bdv25h11.g1                                                      190   8e-45
CXAF-arv86b05.b1                                                      190   8e-45
CXAF-agu31f04.b1                                                      190   8e-45
162630351                                                             190   8e-45
159935201                                                             190   8e-45
156867822                                                             190   8e-45
156844674                                                             190   8e-45
147690974                                                             190   8e-45
147409936                                                             190   8e-45
146949800                                                             190   8e-45
143210016                                                             190   8e-45
167400543                                                             188   3e-44
167445353                                                             188   3e-44
CXAF-awm90a06.b1                                                      186   1e-43
CXAF-adm75d10.b1                                                      186   1e-43
162936895                                                             186   1e-43
144718378                                                             186   1e-43
152451999                                                             184   5e-43
CXAF-bft81c09.b1                                                      182   2e-42
CXAF-baf63c11.b1                                                      182   2e-42
CXAF-avg21c12.g1                                                      182   2e-42
CXAF-asc44g01.g1                                                      182   2e-42
CXAF-ama14f01.b1                                                      182   2e-42
CXAF-amu79g06.g1                                                      182   2e-42
CXAF-ahi08d03.g1                                                      182   2e-42
CXAF-agc25f01.b1                                                      182   2e-42
CXAF-aeu69h11.b1                                                      182   2e-42
CXAF-acr86f07.b1                                                      182   2e-42
CXAF-aar46h05.g1                                                      182   2e-42
CXAG-1235J20.g1                                                       182   2e-42
CXAG-1461H08.b1                                                       182   2e-42
CXAG-0221P12.g1                                                       182   2e-42
167729668                                                             182   2e-42
166645160                                                             182   2e-42
165405553                                                             182   2e-42
160807607                                                             182   2e-42
162328608                                                             182   2e-42
160057611                                                             182   2e-42
155596978                                                             182   2e-42
149380213                                                             182   2e-42
147393821                                                             182   2e-42
145081395                                                             182   2e-42
CXAF-bfk43e10.b1                                                      180   8e-42
CXAF-bfe51d09.b1                                                      180   8e-42
CXAF-bfi28g06.b1                                                      180   8e-42
CXAF-anc10c04.b4                                                      180   8e-42
CXAF-anc10c04.b1                                                      180   8e-42
CXAF-anc10c04.b3                                                      180   8e-42
CXAF-aln34a11.b1                                                      180   8e-42
CXAF-ahu50c09.b1                                                      180   8e-42
CXAF-acx25g09.g1                                                      180   8e-42
CXAG-1208F14.b1                                                       180   8e-42
CXAG-1629G19.g1                                                       180   8e-42
160382429                                                             180   8e-42
160181093                                                             180   8e-42
160124187                                                             180   8e-42
155272187                                                             180   8e-42
145423121                                                             180   8e-42
CXAF-bib28b01.g1                                                      178   3e-41
CXAF-ati93c10.b1                                                      178   3e-41
CXAF-akm83f02.b1                                                      178   3e-41
163472243                                                             178   3e-41
165077400                                                             178   3e-41
160011683                                                             178   3e-41
142796532                                                             178   3e-41
CXAF-bgz51d01.b1                                                      176   1e-40
CXAF-bap55e10.g1                                                      176   1e-40
CXAF-asm07e03.g1                                                      176   1e-40
CXAF-arj54d05.g1                                                      176   1e-40
CXAF-aqt53e06.g1                                                      176   1e-40
CXAF-aqq65b05.g1                                                      176   1e-40
CXAF-amp34c06.g1                                                      176   1e-40
CXAF-aci97a03.g1                                                      176   1e-40
165374357                                                             176   1e-40
164457070                                                             176   1e-40
160542098                                                             176   1e-40
160529975                                                             176   1e-40
158767952                                                             176   1e-40
155834584                                                             176   1e-40
149547208                                                             176   1e-40
156351542                                                             176   1e-40
156473351                                                             176   1e-40
150842736                                                             176   1e-40
146294986                                                             176   1e-40
146001439                                                             176   1e-40
CXAF-bdn55a03.b1                                                      174   5e-40
CXAF-bdz15c08.g1                                                      174   5e-40
CXAF-bar42c06.b1                                                      174   5e-40
CXAF-axm56c04.b1                                                      174   5e-40
CXAF-arb81e09.g1                                                      174   5e-40
CXAF-aow18f10.g1                                                      174   5e-40
CXAF-aoi87d02.b1                                                      174   5e-40
CXAF-aiy67f07.g1                                                      174   5e-40
CXAF-ahl17d02.b1                                                      174   5e-40
CXAF-acg98b08.b1                                                      174   5e-40
CXAG-1279A14.g1                                                       174   5e-40
167709416                                                             174   5e-40
167648482                                                             174   5e-40
165120487                                                             174   5e-40
161284966                                                             174   5e-40
162657555                                                             174   5e-40
158075771                                                             174   5e-40
151747072                                                             174   5e-40
154417935                                                             174   5e-40
151421789                                                             174   5e-40
145031571                                                             174   5e-40
146515029                                                             174   5e-40
CXAF-bef41e11.g1                                                      172   2e-39
CXAF-azc04f03.b1                                                      172   2e-39
CXAF-asf90c12.g1                                                      172   2e-39
CXAF-asm58c08.b1                                                      172   2e-39
CXAF-anc10c04.b2                                                      172   2e-39
CXAF-alg23a03.g1                                                      172   2e-39
CXAF-agj40h05.b1                                                      172   2e-39
CXAF-abp54d06.g1                                                      172   2e-39
ghk12a02.y1                                                           172   2e-39
158455730                                                             172   2e-39
148938727                                                             172   2e-39
142910763                                                             172   2e-39
CXAF-bhl16h10.b1                                                      170   8e-39
CXAF-bbd03c10.b1                                                      170   8e-39
CXAF-aww10b07.g1                                                      170   8e-39
CXAF-ati09c04.g1                                                      170   8e-39
CXAF-atd91d10.g1                                                      170   8e-39
CXAF-asz01a05.g1                                                      170   8e-39
CXAF-ape12g03.g1                                                      170   8e-39
CXAF-apm95f08.g1                                                      170   8e-39
CXAF-amx06f09.b1                                                      170   8e-39
CXAF-ahg63c03.b1                                                      170   8e-39
CXAF-aci08a01.g1                                                      170   8e-39
167323889                                                             170   8e-39
166197110                                                             170   8e-39
163252469                                                             170   8e-39
165637675                                                             170   8e-39
162843389                                                             170   8e-39
161868536                                                             170   8e-39
160353586                                                             170   8e-39
158444277                                                             170   8e-39
158423150                                                             170   8e-39
157328606                                                             170   8e-39
145663732                                                             170   8e-39
147469092                                                             170   8e-39
153092519                                                             170   8e-39
152695689                                                             170   8e-39
151537462                                                             170   8e-39
143408168                                                             170   8e-39
CXAF-bdk78h03.b1                                                      168   3e-38
CXAF-bat88e02.g1                                                      168   3e-38
CXAF-ava92f11.g1                                                      168   3e-38
CXAF-atg76c09.g1                                                      168   3e-38
CXAF-arr37g09.g1                                                      168   3e-38
CXAF-arj41e04.g1                                                      168   3e-38
CXAF-aqu80b03.b1                                                      168   3e-38
CXAF-ahp26b11.g1                                                      168   3e-38
CXAF-ahx73e12.b1                                                      168   3e-38
CXAF-ahp26b11.g1                                                      168   3e-38
CXAF-aah73b11.g1                                                      168   3e-38
CXAG-2031K01.b1                                                       168   3e-38
166593988                                                             168   3e-38
166524877                                                             168   3e-38
166500081                                                             168   3e-38
166112172                                                             168   3e-38
162040212                                                             168   3e-38
160229376                                                             168   3e-38
155506362                                                             168   3e-38
155847422                                                             168   3e-38
149607429                                                             168   3e-38
144241820                                                             168   3e-38
143561247                                                             168   3e-38
CXAF-bgk87b04.g1                                                      167   1e-37
CXAF-bgn10b10.g1                                                      167   1e-37
CXAF-bdi40f05.g1                                                      167   1e-37
CXAF-baa60b11.b1                                                      167   1e-37
CXAF-bbm35d05.b1                                                      167   1e-37
CXAF-axy00d03.g1                                                      167   1e-37
CXAF-azh43d10.g1                                                      167   1e-37
CXAF-azn11d01.b1                                                      167   1e-37
CXAF-auq78d03.b1                                                      167   1e-37
CXAF-atr41g05.b1                                                      167   1e-37
CXAF-arx85e04.b1                                                      167   1e-37
CXAF-arg15b07.g1                                                      167   1e-37
CXAF-art10c11.g1                                                      167   1e-37
CXAF-aqo94c07.g1                                                      167   1e-37
CXAF-apn74f11.b1                                                      167   1e-37
CXAF-apy51g08.b1                                                      167   1e-37
CXAF-aos41c08.b1                                                      167   1e-37
CXAF-alt68e05.b1                                                      167   1e-37
CXAF-ajx89e04.g1                                                      167   1e-37
CXAF-aic06d05.g1                                                      167   1e-37
CXAF-ahd71f01.b1                                                      167   1e-37
CXAF-aif98h08.b1                                                      167   1e-37
CXAF-aiu02f01.g1                                                      167   1e-37
CXAF-ahd71f01.b1                                                      167   1e-37
CXAF-aic06d05.g1                                                      167   1e-37
CXAF-aho37d07.b1                                                      167   1e-37
CXAF-agh89a12.g1                                                      167   1e-37
CXAF-afv34e12.g1                                                      167   1e-37
CXAF-aey21f08.b1                                                      167   1e-37
CXAF-afv51h12.b1                                                      167   1e-37
CXAF-adc97g07.b1                                                      167   1e-37
CXAF-abm70e02.b1                                                      167   1e-37
CXAF-aaf45c03.g1                                                      167   1e-37
CXAF-abo95d03.g1                                                      167   1e-37
CXAF-aab10e02.b1                                                      167   1e-37
CXAG-1524C04.g1                                                       167   1e-37
CXAG-0410P07.g1                                                       167   1e-37
CXAG-0520F01.g1                                                       167   1e-37
CXAG-0167E19.g1                                                       167   1e-37
168531737                                                             167   1e-37
166734452                                                             167   1e-37
163633202                                                             167   1e-37
163379199                                                             167   1e-37
163763163                                                             167   1e-37
165597462                                                             167   1e-37
166014684                                                             167   1e-37
165903989                                                             167   1e-37
165496388                                                             167   1e-37
165136919                                                             167   1e-37
165141067                                                             167   1e-37
164915848                                                             167   1e-37
164883233                                                             167   1e-37
164417712                                                             167   1e-37
160275027                                                             167   1e-37
163066594                                                             167   1e-37
160522423                                                             167   1e-37
162491209                                                             167   1e-37
157891314                                                             167   1e-37
157556763                                                             167   1e-37
149844405                                                             167   1e-37
147760001                                                             167   1e-37
144502404                                                             167   1e-37
144237941                                                             167   1e-37
154980843                                                             167   1e-37
153818331                                                             167   1e-37
153935465                                                             167   1e-37
149433619                                                             167   1e-37
153386450                                                             167   1e-37
153208079                                                             167   1e-37
152275918                                                             167   1e-37
152221611                                                             167   1e-37
150637700                                                             167   1e-37
145461697                                                             167   1e-37
143730363                                                             167   1e-37
CXAF-bgu50c01.g1                                                      165   5e-37
CXAF-bfz12g08.g1                                                      165   5e-37
CXAF-bek73h12.b1                                                      165   5e-37
CXAF-bco17g06.g1                                                      165   5e-37
CXAF-ayq35f06.b1                                                      165   5e-37
CXAF-ayo11g09.b1                                                      165   5e-37
CXAF-asr02g03.g1                                                      165   5e-37
CXAF-arx65f10.b1                                                      165   5e-37
CXAF-arx65f06.b1                                                      165   5e-37
CXAF-aqn58g03.b4                                                      165   5e-37
CXAF-aon21a01.b1                                                      165   5e-37
CXAF-akb46h02.b1                                                      165   5e-37
CXAF-aii43g02.g1                                                      165   5e-37
CXAF-agu27h05.b1                                                      165   5e-37
CXAF-aic25d01.b1                                                      165   5e-37
CXAG-2015A19.b1                                                       165   5e-37
CXAG-0523N16.g1                                                       165   5e-37
166371682                                                             165   5e-37
163798751                                                             165   5e-37
165810530                                                             165   5e-37
164473486                                                             165   5e-37
164895142                                                             165   5e-37
164838455                                                             165   5e-37
161482077                                                             165   5e-37
160503765                                                             165   5e-37
162496034                                                             165   5e-37
160394093                                                             165   5e-37
159887243                                                             165   5e-37
155431165                                                             165   5e-37
159583227                                                             165   5e-37
157592797                                                             165   5e-37
156296735                                                             165   5e-37
156346326                                                             165   5e-37
157114978                                                             165   5e-37
147596960                                                             165   5e-37
153304584                                                             165   5e-37
144718320                                                             165   5e-37
144878936                                                             165   5e-37
CXAF-bhu90d04.g1                                                      163   2e-36
CXAF-bfg30g05.b1                                                      163   2e-36
CXAF-bdg06g12.g1                                                      163   2e-36
CXAF-bea06c12.b1                                                      163   2e-36
CXAF-bcr68e11.b1                                                      163   2e-36
CXAF-bde20h11.g1                                                      163   2e-36
CXAF-bda01c05.b1                                                      163   2e-36
CXAF-bax80e02.b1                                                      163   2e-36
CXAF-bcs19f10.g1                                                      163   2e-36
CXAF-ayr10c06.g1                                                      163   2e-36
CXAF-ayt49h06.b1                                                      163   2e-36
CXAF-ays19d03.g1                                                      163   2e-36
CXAF-axy72f08.g1                                                      163   2e-36
CXAF-atd42a09.b1                                                      163   2e-36
CXAF-atr38a05.b1                                                      163   2e-36
CXAF-asn20c10.b1                                                      163   2e-36
CXAF-aqc60f05.b1                                                      163   2e-36
CXAF-asd41d09.g1                                                      163   2e-36
CXAF-are20b11.b1                                                      163   2e-36
CXAF-ano36b12.g1                                                      163   2e-36
CXAF-aob93g03.b1                                                      163   2e-36
CXAF-ano78d03.b1                                                      163   2e-36
CXAF-amt41h07.b1                                                      163   2e-36
CXAF-amr50b05.b1                                                      163   2e-36
CXAF-ajj30e08.b1                                                      163   2e-36
CXAF-akv57h09.g1                                                      163   2e-36
CXAF-ajz38h12.g1                                                      163   2e-36
CXAF-akp62f03.g1                                                      163   2e-36
CXAF-ajg64d02.b1                                                      163   2e-36
CXAF-ajl20g03.g1                                                      163   2e-36
CXAF-alo38h10.b1                                                      163   2e-36
CXAF-ajg30b01.b1                                                      163   2e-36
CXAF-ail45e09.g1                                                      163   2e-36
CXAF-acp49a10.b1                                                      163   2e-36
CXAF-aai04g09.b1                                                      163   2e-36
CXAF-aba43c05.g1                                                      163   2e-36
CXAF-aao24c02.b1                                                      163   2e-36
CXAF-aah33f05.g1                                                      163   2e-36
CXAF-aaa01h07.b1                                                      163   2e-36
CXAG-1896P01.b1                                                       163   2e-36
CXAG-2095N21.g1                                                       163   2e-36
CXAG-0934N07.b1                                                       163   2e-36
167331901                                                             163   2e-36
165712612                                                             163   2e-36
166892813                                                             163   2e-36
166834018                                                             163   2e-36
166874487                                                             163   2e-36
167085899                                                             163   2e-36
163710257                                                             163   2e-36
166148571                                                             163   2e-36
163760359                                                             163   2e-36
161736861                                                             163   2e-36
163034044                                                             163   2e-36
162837927                                                             163   2e-36
162295658                                                             163   2e-36
158510817                                                             163   2e-36
158506098                                                             163   2e-36
158114971                                                             163   2e-36
157400396                                                             163   2e-36
156015837                                                             163   2e-36
156972840                                                             163   2e-36
156966353                                                             163   2e-36
156052575                                                             163   2e-36
148543548                                                             163   2e-36
147940150                                                             163   2e-36
147576749                                                             163   2e-36
145809921                                                             163   2e-36
142070855                                                             163   2e-36
149489495                                                             163   2e-36
151223248                                                             163   2e-36
151017009                                                             163   2e-36
150921030                                                             163   2e-36
146666997                                                             163   2e-36

>152308237 
          Length = 1272

 Score =  377 bits (190), Expect = e-101
 Identities = 386/447 (86%), Gaps = 7/447 (1%)
 Strand = Plus / Minus

                                                                       
Query: 524 gcacctccccagaagccgggcttcccgccccaccg-gcccgcgaggtgccgcagggaggg 582
           |||||||||||| ||||||||| |||||||  ||| |||| |||||||||  || |||||
Sbjct: 803 gcacctccccagcagccgggctccccgccctgccgagccctcgaggtgccagagagaggg 744

                                                                       
Query: 583 tgcggtttggcttgtcagcacccaggggcgtcacaaaccctttgttgaacaggggattta 642
           || | |||||||||||||| ||||| ||||||||||||||| ||||||||||||||||| 
Sbjct: 743 tgtgatttggcttgtcagctcccagaggcgtcacaaaccctctgttgaacaggggatttt 684

                                                                       
Query: 643 cccct--ttgtgtggcgtcacttgatcaatagttcagtttcagtgtggctaatagtgtta 700
           |  ||  ||||||||| |||||||| |||||||||||||||||||||||||||   ||||
Sbjct: 683 ctgctccttgtgtggcttcacttgaccaatagttcagtttcagtgtggctaat---gtta 627

                                                                       
Query: 701 aaaactggccgggcgcggtggctcacgcctgtaatcccaacactttgggaggccgagg-c 759
           |||||||||  |||| ||||| |||| ||||||||||||||||||||||||||| ||| |
Sbjct: 626 aaaactggcttggcgtggtggttcacacctgtaatcccaacactttgggaggccaagggc 567

                                                                       
Query: 760 gggcggatcacctcaggtcaggagttcaacaccagcttagccaacatggtgaaaccttgt 819
           |||| |||||| | ||||||||||||| | || ||| | ||||| |||||||||||||||
Sbjct: 566 gggcagatcacttgaggtcaggagttcgagactagccttgccaaaatggtgaaaccttgt 507

                                                                       
Query: 820 ctctactgatacaaaaattagccgggagtggtgatgcgcgcctgtaatcccaggagactg 879
           ||||||||||||||||| | |  ||||  |||| ||||| ||||  ||||||||||||||
Sbjct: 506 ctctactgatacaaaaagttgttgggaaaggtggtgcgctcctgatatcccaggagactg 447

                                                                       
Query: 880 aggcatgagaatcgcttgaacctgggagacagaggttgcagtgagccgagatcgcaccac 939
           || ||||||||||||||||||||||||||  ||||||||||||||  ||| || | ||||
Sbjct: 446 agacatgagaatcgcttgaacctgggagagggaggttgcagtgaggtgaggtcacgccac 387

                                      
Query: 940 tgcactccagcctgggtgacagagtga 966
           |  ||||||||||||||| ||||||||
Sbjct: 386 ttaactccagcctgggtgtcagagtga 360



 Score =  115 bits (58), Expect = 4e-22
 Identities = 138/158 (87%), Gaps = 5/158 (3%)
 Strand = Plus / Minus

                                                                        
Query: 308  tgtacaaatcaaagaacccggccgtcctgcgggtggggcacgctggcgcagaaccagagg 367
            |||| |||||||||||||| ||| |||||||| ||| |||||||||||||||||||||||
Sbjct: 1047 tgtagaaatcaaagaacccagccatcctgcggatggagcacgctggcgcagaaccagagg 988

                                                                        
Query: 368  taaccggctctgcggccacctacgggtctaggaattacttgctggatgaccctgcaggga 427
            | ||| |||||| |  || |||||||||||||||||| || || ||||| ||||||| ||
Sbjct: 987  t-acctgctctgtgagca-ctacgggtctaggaattattttctagatga-cctgcagaga 931

                                                  
Query: 428  gtggcacgtggagt-cctatcga-cctcagaggcacta 463
            |||||||| ||||| |||||| | ||||||||||||||
Sbjct: 930  gtggcacggggagtccctatcaaccctcagaggcacta 893



 Score = 56.0 bits (28), Expect = 3e-04
 Identities = 68/76 (89%), Gaps = 4/76 (5%)
 Strand = Plus / Minus

                                                                        
Query: 194  cccagacagagcgttcttgtaaacttctcttcagtagaaacggtcctgctctcgaatatt 253
            |||||||||||| |||||||||  |||| |||||||| |||| ||| ||||||||||| |
Sbjct: 1161 cccagacagagcattcttgtaactttct-ttcagtag-aacgatcc-gctctcgaata-t 1106

                            
Query: 254  tcagggcatccccacc 269
            ||||||||||||||||
Sbjct: 1105 tcagggcatccccacc 1090



 Score = 48.1 bits (24), Expect = 0.078
 Identities = 40/44 (90%), Gaps = 1/44 (2%)
 Strand = Plus / Minus

                                                       
Query: 464 tcagattagccctaggaggtccgtctgggggtctcggcggcctg 507
           |||||||||||||||||||||| ||  ||||||||||| |||||
Sbjct: 878 tcagattagccctaggaggtccatc-cggggtctcggctgcctg 836



  Database: traces_cjacchus
    Posted date:  Apr 18, 2006  9:06 AM
  Number of letters in database: 3,989,705,459
  Number of sequences in database:  4,116,926
  
  Database: /data/public/DNA/Traces/Current/cjacchus/traces_cjacchus.0
  1
    Posted date:  Apr 18, 2006  9:14 AM
  Number of letters in database: 3,982,324,570
  Number of sequences in database:  4,352,299
  
  Database: /data/public/DNA/Traces/Current/cjacchus/traces_cjacchus.0
  2
    Posted date:  Apr 18, 2006  9:22 AM
  Number of letters in database: 3,920,139,351
  Number of sequences in database:  4,087,461
  
  Database: /data/public/DNA/Traces/Current/cjacchus/traces_cjacchus.0
  3
    Posted date:  Apr 18, 2006  9:31 AM
  Number of letters in database: 3,987,269,224
  Number of sequences in database:  5,092,493
  
  Database: /data/public/DNA/Traces/Current/cjacchus/traces_cjacchus.0
  4
    Posted date:  Apr 18, 2006  9:40 AM
  Number of letters in database: 3,987,395,141
  Number of sequences in database:  5,041,942
  
  Database: /data/public/DNA/Traces/Current/cjacchus/traces_cjacchus.0
  5
    Posted date:  Apr 18, 2006  9:49 AM
  Number of letters in database: 3,987,395,015
  Number of sequences in database:  5,042,820
  
  Database: /data/public/DNA/Traces/Current/cjacchus/traces_cjacchus.0
  6
    Posted date:  Apr 18, 2006  9:50 AM
  Number of letters in database: 195,038,135
  Number of sequences in database:  249,629
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 35,912,672
Number of Sequences: 27983570
Number of extensions: 35912672
Number of successful extensions: 24562055
Number of sequences better than  1.0: 5755765
Number of HSP's better than  1.0 without gapping: 5583706
Number of HSP's successfully gapped in prelim test: 172065
Number of HSP's that attempted gapping in prelim test: 3844134
Number of HSP's gapped (non-prelim): 19045195
length of query: 1001
length of database: 24,049,266,895
effective HSP length: 23
effective length of query: 978
effective length of database: 23,405,644,785
effective search space: 22890720599730
effective search space used: 22890720599730
T: 0
A: 0
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 23 (46.1 bits)
BioPerl-1.007002/t/data/bug1986.blastp000444000766000024      1170313155576321 17226 0ustar00cjfieldsstaff000000000000BLASTP 2.2.11 [Jun-05-2005]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= NP_006065
         (442 letters)

Database: Homo_sapiens.NCBI36.apr.pep.fa 
           48,851 sequences; 23,910,368 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ENSP00000350182 pep:novel clone::BX322644.8:4905:15090:-1 gene:E...   120   3e-27
ENSP00000350182 pep:novel clone::BX322644.8:4905:15090:-1 gene:E...   120   3e-27
ENSP00000327738 pep:known-ccds chromosome:NCBI36:4:189297592:189...   115   8e-26

>ENSP00000350182 pep:novel clone::BX322644.8:4905:15090:-1 gene:ENSG00000137397
           transcript:ENST00000357569 
          Length = 425

 Score =  120 bits (301), Expect = 3e-27
 Identities = 76/261 (29%), Positives = 140/261 (53%), Gaps = 21/261 (8%)

Query: 9   IEKEVTCPICLELLTEPLSLDCGHSFCQACITAKIKESVIISRGESSCPVCQTRFQPGNL 68
           +++EV CPICL++L +P+++DCGH+FC  CIT +I E+   S G   CP+C+T  +   +
Sbjct: 10  LQEEVICPICLDILQKPVTIDCGHNFCLKCIT-QIGET---SCGFFKCPLCKTSVRKNAI 65

Query: 69  RPNRHLANIVERVKEVKMSP-QEGQKRDVCEHHGKKLQIFCKEDGKVICWVCELSQEHQG 127
           R N  L N+VE+++ ++ S  Q  +K   C  H +    FC++DGK +C+VC  S++H+ 
Sbjct: 66  RFNSLLRNLVEKIQALQASEVQSKRKEATCPRHQEMFHYFCEDDGKFLCFVCCESKDHKS 125

Query: 128 HQTFRINEVVKECQEKLQVALQRLIKEDQEAEKLED------DIRQERTAWKIERQKILK 181
           H    I E  +  Q ++Q  +Q L ++++E  +++       D+  ++   + E+Q+IL 
Sbjct: 126 HNVSLIEEAAQNYQGQIQEQIQVLQQKEKETVQVKAQGVHRVDVFTDQV--EHEKQRILT 183

Query: 182 GFNEMRVILDNEEQRELQKL----EEGEVNVLDNLAAATDQLVQQRQDASTLISDLQRRL 237
            F  +  +L+ E+   L ++     EG       +A+   QL     D   L+  L+ + 
Sbjct: 184 EFELLHQVLEEEKNFLLSRIYWLGHEGTEAGKHYVASTEPQL----NDLKKLVDSLKTKQ 239

Query: 238 TGSSVEMLQDVIDVMKRSESW 258
                ++L+     + RSE +
Sbjct: 240 NMPPRQLLEVTQPHLPRSEEF 260


>ENSP00000327738 pep:known-ccds chromosome:NCBI36:4:189297592:189305643:1
           gene:ENSG00000184108 transcript:ENST00000332517
           CCDS3851.1
          Length = 468

 Score =  115 bits (289), Expect = 8e-26
 Identities = 101/410 (24%), Positives = 180/410 (43%), Gaps = 39/410 (9%)

Query: 8   DIEKEVTCPICLELLTEPLSLDCGHSFCQACITAKIKESVIISRGESSCPVCQTRFQPGN 67
           ++ +E+TC ICL+  + P++ +CGHSFC  C+    +E         SCP C    +  +
Sbjct: 9   NLREELTCFICLDYFSSPVTTECGHSFCLVCLLRSWEE----HNTPLSCPECWRTLEGPH 64

Query: 68  LRPNRHLANIVERVKEVKMSPQEGQKRDVCEHHGK-----KLQIFCKEDGKVICWVCELS 122
            + N  L  +    ++++   Q  Q  D    +G+     K     ++ G        ++
Sbjct: 65  FQSNERLGRLASIARQLR--SQVLQSEDEQGSYGRMPTTAKALSDDEQGGSAF-----VA 117

Query: 123 QEHQGHQTFRINEVVKECQEKLQVALQRLIKEDQEA------EKLEDDIRQERTAWKIER 176
           Q H  ++    +E  +  +EKLQ  L  L    +EA      EK    + QE T  K  +
Sbjct: 118 QSHGANRVHLSSEAEEHHREKLQEILNLLRVRRKEAQAVLTHEKERVKLCQEET--KTCK 175

Query: 177 QKILKGFNEMRVILDNEEQRELQKLEEGEVNVLDNLAAATDQLVQQRQDASTLISDLQRR 236
           Q ++  + +M   L  EEQ +LQ LE+ E   +  L     +L QQ +  S +I+ ++  
Sbjct: 176 QVVVSEYMKMHQFLKEEEQLQLQLLEQEEKENMRKLRNNEIKLTQQIRSLSKMIAQIESS 235

Query: 237 LTGSSVEMLQDVIDVMKRSESWTXXXXXXXXXXXXXXFRVPDLSGMLQVLKELTDVQYYW 296
              S+ E L++V   ++RSE                   +  ++GM ++L++ +      
Sbjct: 236 SQSSAFESLEEVRGALERSE----PLLLQCPEATTTELSLCRITGMKEMLRKFS------ 285

Query: 297 VDVMLNPGSATSNVAISVDQRQVKTVRTCTFKNSNPCDF-SAFGVFGCQYFSSGKYYWEV 355
            ++ L+P +A + + +S D + VK   +      NP  F  +  V G Q F+SG++YWEV
Sbjct: 286 TEITLDPATANAYLVLSEDLKSVKYGGSRQQLPDNPERFDQSATVLGTQIFTSGRHYWEV 345

Query: 356 DVSGKIAWILGVHSKISSLNKRKSSGFAFDPSVNYSKVYSRYRPQYGYWV 405
           +V  K  W +G+     S    +       P   +S +  +    Y  WV
Sbjct: 346 EVGNKTEWEVGICKDSVS----RKGNLPKPPGDLFSLIGLKIGDDYSLWV 391


  Database: Homo_sapiens.NCBI36.apr.pep.fa
    Posted date:  Jun 15, 2006  8:56 PM
  Number of letters in database: 23,910,368
  Number of sequences in database:  48,851
  
Lambda     K      H
   0.319    0.133    0.398 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,900,506
Number of Sequences: 48851
Number of extensions: 899179
Number of successful extensions: 6075
Number of sequences better than 1.0e-25: 105
Number of HSP's better than  0.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 87
Number of HSP's that attempted gapping in prelim test: 5632
Number of HSP's gapped (non-prelim): 157
length of query: 442
length of database: 23,910,368
effective HSP length: 107
effective length of query: 335
effective length of database: 18,683,311
effective search space: 6258909185
effective search space used: 6258909185
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 289 (115.9 bits)
BioPerl-1.007002/t/data/bug2120.phd000444000766000024      3324013155576321 16471 0ustar00cjfieldsstaff000000000000BEGIN_SEQUENCE HEX1549K12_01_A01.b_015-1516

BEGIN_COMMENT

CHROMAT_FILE: HEX1549K12_01_A01.b_015-1516
ABI_THUMBPRINT: 0
PHRED_VERSION: 0.020425.c
CALL_METHOD: phred
QUALITY_LEVELS: 99
TIME: Sun Oct  8 12:48:40 2006
TRACE_ARRAY_MIN_INDEX: 0
TRACE_ARRAY_MAX_INDEX: 16302
TRIM: 34 849 0.0500
TRACE_PEAK_AREA_RATIO: 0.0020
CHEM: term
DYE: big

END_COMMENT

BEGIN_DNA
g 6 14
c 6 25
g 6 39
c 6 42
c 6 60
g 6 63
t 6 79
g 6 90
t 9 106
g 9 113
g 9 121
g 12 130
g 12 145
g 8 153
c 8 169
c 9 177
t 8 203
t 8 210
a 8 218
t 9 234
g 8 244
c 6 257
t 6 270
a 8 275
g 8 285
c 8 304
g 8 316
a 8 333
a 10 339
t 8 350
c 9 359
g 9 370
c 9 378
c 10 392
t 17 408
t 12 421
c 14 429
t 18 444
t 24 457
c 28 467
t 24 479
c 24 486
c 22 499
c 23 516
c 23 526
t 19 540
a 24 548
a 24 559
g 37 570
t 44 582
c 47 592
t 47 604
t 37 616
g 37 628
t 39 641
a 41 650
c 41 659
g 47 672
t 47 684
c 57 696
g 57 707
t 57 721
c 57 732
t 57 744
t 59 757
g 59 769
t 59 781
g 59 793
g 48 807
g 48 819
a 48 831
g 48 841
a 48 853
g 57 864
t 57 874
t 57 886
g 68 898
a 68 909
a 68 920
t 68 930
c 68 942
a 68 951
t 68 963
c 68 975
c 68 987
c 50 999
a 50 1007
a 50 1019
t 50 1032
c 68 1044
c 68 1056
t 68 1068
g 68 1081
g 68 1094
a 68 1107
g 57 1118
c 57 1129
a 57 1139
a 57 1149
a 57 1160
g 57 1172
t 59 1184
t 68 1195
c 68 1207
g 68 1220
a 68 1232
g 68 1243
g 68 1256
a 68 1268
a 68 1279
c 68 1289
t 68 1301
t 68 1313
g 68 1325
a 68 1338
c 68 1348
c 68 1360
c 68 1372
t 68 1384
c 68 1396
c 68 1407
c 68 1419
a 57 1428
a 57 1439
g 57 1451
g 59 1463
g 59 1476
g 68 1488
c 68 1500
t 68 1513
t 68 1525
g 68 1536
g 68 1549
t 68 1562
g 68 1574
a 68 1586
g 68 1597
c 68 1608
a 68 1619
g 68 1632
g 68 1644
t 68 1656
c 68 1667
t 68 1679
g 68 1692
c 68 1703
g 68 1716
a 68 1728
g 68 1739
c 68 1751
t 68 1764
g 68 1776
a 68 1788
t 68 1799
c 68 1810
c 68 1822
t 68 1835
t 68 1847
g 68 1859
g 68 1872
t 68 1884
g 68 1896
t 68 1908
t 68 1920
g 68 1932
a 68 1943
t 68 1954
g 68 1966
t 68 1978
a 68 1989
g 68 2001
c 68 2013
t 59 2026
c 59 2038
g 68 2050
c 68 2062
c 68 2074
t 68 2087
c 68 2098
g 68 2110
a 68 2123
t 68 2134
g 68 2146
c 68 2157
t 68 2170
c 68 2182
c 68 2193
c 68 2205
t 68 2218
t 68 2230
c 68 2242
t 68 2254
t 68 2266
c 68 2277
c 68 2289
a 68 2299
c 68 2310
a 68 2320
c 68 2332
a 68 2343
g 68 2356
c 68 2369
t 68 2382
g 68 2393
c 68 2406
g 68 2418
g 68 2432
a 68 2444
t 68 2455
g 68 2467
a 68 2479
a 68 2491
g 68 2503
t 68 2514
g 68 2526
a 68 2539
t 68 2549
a 68 2561
c 68 2572
c 68 2584
t 62 2597
c 62 2609
a 62 2620
g 62 2633
t 62 2646
c 62 2657
g 62 2670
g 52 2683
a 62 2695
t 62 2706
g 62 2718
t 62 2730
g 68 2742
c 68 2753
t 68 2766
t 68 2778
g 68 2790
c 68 2802
t 68 2815
c 68 2826
c 68 2838
g 68 2850
t 68 2863
t 68 2875
c 68 2886
g 68 2898
t 68 2910
g 68 2922
g 68 2934
a 68 2947
a 68 2958
c 68 2969
a 68 2979
c 68 2990
g 68 3003
g 68 3016
g 68 3028
g 68 3040
t 68 3053
t 68 3065
c 68 3077
t 68 3089
t 68 3101
t 68 3113
g 68 3125
c 68 3137
c 68 3149
a 68 3159
g 68 3171
g 68 3184
g 68 3195
c 68 3208
c 68 3220
a 68 3231
g 68 3243
g 68 3255
g 68 3267
c 68 3280
g 68 3292
g 68 3305
a 68 3318
c 68 3328
t 68 3340
t 68 3352
g 68 3364
c 68 3376
t 68 3389
g 68 3401
t 68 3413
c 68 3425
c 68 3436
a 68 3447
c 68 3458
c 68 3470
a 68 3481
g 68 3494
g 68 3506
a 68 3519
g 68 3531
c 68 3543
t 68 3555
g 68 3567
c 68 3579
a 68 3590
c 68 3601
c 68 3613
g 68 3625
t 68 3638
t 68 3651
c 68 3663
t 68 3675
g 68 3687
g 68 3700
t 68 3711
g 68 3723
t 68 3735
c 68 3746
t 68 3758
t 68 3770
g 68 3782
a 68 3795
a 68 3806
c 62 3817
g 62 3830
a 62 3841
g 62 3853
a 62 3866
a 62 3877
g 62 3889
a 68 3901
t 68 3911
c 68 3923
a 68 3934
c 68 3946
c 68 3958
a 68 3969
a 68 3981
g 68 3994
t 68 4006
a 68 4018
g 62 4030
t 62 4042
c 62 4054
g 62 4067
a 62 4079
g 62 4091
c 62 4103
a 68 4114
a 68 4126
g 68 4138
c 68 4149
c 68 4161
a 68 4173
g 68 4185
a 68 4198
g 68 4209
c 68 4221
g 68 4234
c 68 4245
c 68 4257
t 68 4270
g 68 4282
a 68 4294
g 68 4305
t 68 4318
a 68 4329
c 68 4340
a 68 4351
g 68 4364
g 68 4376
c 68 4388
g 68 4401
g 68 4414
t 68 4426
g 68 4437
g 68 4450
a 68 4463
g 68 4474
g 68 4487
c 68 4498
c 68 4510
g 68 4522
c 68 4534
t 68 4547
a 68 4558
t 68 4569
g 68 4581
t 68 4594
a 68 4605
c 68 4616
t 68 4628
c 68 4640
a 68 4651
g 68 4664
c 68 4676
c 68 4688
t 68 4701
c 68 4713
a 68 4724
c 68 4735
a 68 4746
g 68 4758
c 68 4771
t 68 4783
g 68 4795
g 68 4808
a 68 4821
c 68 4831
a 68 4843
g 68 4855
g 68 4867
g 68 4878
c 68 4891
c 68 4903
a 68 4914
c 68 4926
c 68 4938
a 68 4949
c 68 4961
c 68 4973
t 68 4986
g 68 4998
c 68 5011
t 68 5023
g 68 5035
c 68 5047
t 68 5059
t 68 5071
g 68 5083
a 68 5096
c 68 5106
t 68 5119
g 68 5131
a 68 5143
t 68 5154
t 68 5166
g 68 5179
c 62 5190
c 62 5202
a 62 5213
g 62 5225
c 62 5238
t 62 5250
c 62 5262
a 62 5273
c 68 5284
g 68 5297
a 62 5309
g 62 5321
a 62 5334
c 62 5345
a 62 5356
c 68 5367
t 68 5380
t 68 5392
g 68 5404
c 68 5417
c 68 5429
g 68 5442
a 68 5454
g 68 5465
g 62 5477
a 68 5490
a 68 5502
g 68 5513
a 68 5525
g 68 5537
g 68 5549
a 68 5562
g 62 5573
g 62 5585
a 62 5598
t 62 5608
c 68 5620
c 68 5632
c 68 5644
g 68 5657
c 68 5669
t 68 5682
c 68 5694
g 68 5706
t 68 5718
g 68 5730
c 68 5742
t 68 5754
c 68 5765
t 68 5777
t 68 5790
g 68 5802
c 68 5813
t 68 5826
g 68 5837
g 68 5849
t 68 5862
g 62 5874
t 62 5886
c 62 5897
g 62 5910
a 62 5922
t 62 5933
g 62 5945
t 68 5956
c 68 5968
g 68 5981
c 68 5992
c 68 6005
g 68 6017
g 68 6030
c 68 6042
g 68 6054
t 68 6067
g 68 6078
g 68 6091
t 68 6103
c 68 6115
g 68 6127
c 68 6138
t 68 6152
g 57 6164
t 57 6176
c 59 6187
g 59 6200
c 59 6212
t 59 6224
g 57 6236
t 68 6248
a 68 6260
c 68 6270
c 68 6282
c 68 6294
g 59 6307
a 59 6320
c 57 6331
g 57 6343
a 57 6356
a 59 6368
g 59 6380
t 59 6391
g 59 6404
t 59 6415
g 68 6428
c 68 6439
c 68 6452
g 68 6464
c 68 6476
c 68 6488
c 59 6500
c 59 6512
a 59 6523
g 59 6535
g 59 6547
a 59 6560
c 59 6571
a 59 6582
c 59 6593
c 59 6606
t 59 6618
a 59 6630
g 59 6642
g 68 6655
g 68 6667
t 68 6680
a 68 6691
g 68 6703
t 68 6715
g 68 6727
g 68 6741
a 68 6752
g 68 6764
g 68 6777
c 68 6788
c 68 6800
g 68 6813
t 68 6825
g 68 6837
g 68 6849
t 68 6862
c 68 6874
g 68 6886
a 68 6899
g 68 6910
g 68 6923
g 68 6935
t 68 6946
c 68 6958
c 68 6970
c 68 6981
t 68 6994
g 68 7006
c 68 7018
t 68 7031
a 68 7042
t 68 7054
g 59 7066
t 59 7078
a 59 7090
g 59 7102
c 59 7114
g 57 7127
g 57 7140
a 57 7152
c 57 7162
g 57 7175
a 57 7187
t 59 7198
c 59 7210
c 68 7223
t 68 7235
c 68 7247
t 57 7259
t 57 7272
c 57 7284
a 57 7294
c 57 7305
t 57 7318
g 68 7330
c 68 7342
c 68 7355
t 68 7367
g 68 7379
c 68 7391
t 68 7404
g 68 7415
g 68 7429
t 68 7439
g 68 7451
t 68 7463
t 59 7475
c 59 7487
c 59 7499
g 59 7512
a 59 7524
c 59 7535
g 59 7547
t 57 7560
t 57 7572
g 68 7583
g 68 7598
t 68 7609
c 68 7621
g 59 7633
c 57 7645
t 54 7657
c 54 7668
c 54 7682
a 54 7692
t 54 7704
g 57 7716
a 59 7729
a 68 7741
c 68 7752
c 68 7764
g 68 7777
a 68 7789
c 68 7801
t 59 7813
g 59 7825
a 59 7838
c 57 7849
a 57 7861
t 59 7872
a 59 7884
g 59 7897
c 59 7909
c 59 7922
g 59 7934
a 48 7946
c 48 7958
g 43 7969
g 43 7983
a 40 7996
g 40 8006
a 41 8019
a 43 8031
t 43 8041
g 48 8054
c 48 8065
c 46 8078
a 47 8089
a 47 8101
g 59 8113
t 59 8125
c 59 8137
c 43 8149
g 41 8161
g 37 8175
c 41 8186
c 41 8199
g 47 8211
t 47 8223
g 47 8235
t 59 8248
g 47 8260
t 47 8271
g 47 8284
a 47 8297
g 47 8309
t 47 8320
g 59 8333
a 41 8344
g 37 8355
g 37 8368
t 41 8381
a 41 8393
g 44 8405
c 47 8416
g 39 8430
a 39 8442
a 35 8454
g 31 8464
g 31 8478
c 39 8489
t 39 8501
c 47 8513
c 47 8525
c 59 8536
c 47 8548
a 41 8560
c 38 8571
a 34 8582
a 34 8596
g 35 8606
g 32 8620
c 39 8632
g 41 8644
t 37 8656
t 37 8669
g 44 8680
g 44 8694
t 44 8706
a 47 8717
c 47 8728
t 59 8740
g 43 8753
c 41 8765
g 37 8778
t 41 8790
a 37 8802
g 41 8814
c 37 8826
a 59 8838
t 39 8849
c 37 8860
c 37 8873
a 41 8884
c 37 8895
t 36 8907
t 31 8921
c 32 8931
c 32 8945
t 39 8958
c 31 8968
c 32 8982
g 39 8993
t 39 9006
c 43 9017
g 39 9030
t 40 9042
g 40 9054
c 40 9066
t 46 9078
g 47 9091
t 47 9102
c 37 9114
g 37 9127
c 37 9138
g 35 9151
g 32 9163
c 41 9175
t 34 9188
c 34 9200
a 28 9211
g 31 9223
t 24 9234
t 32 9247
t 32 9259
c 35 9271
a 35 9282
g 31 9295
c 29 9305
c 29 9318
t 34 9331
c 41 9343
t 41 9356
c 32 9366
c 37 9378
t 37 9391
c 30 9402
c 25 9414
a 32 9426
t 32 9438
c 25 9449
g 19 9460
g 19 9477
a 22 9487
g 22 9499
t 28 9512
g 34 9524
a 32 9535
g 35 9547
a 35 9560
g 37 9572
c 37 9582
t 41 9595
g 31 9607
g 34 9620
a 35 9633
t 33 9643
g 28 9656
g 25 9669
c 32 9681
a 31 9693
g 37 9706
t 37 9717
c 32 9729
g 27 9741
g 25 9755
t 31 9767
g 31 9779
a 30 9792
g 30 9804
c 25 9816
c 34 9826
c 27 9838
a 32 9851
g 35 9864
c 37 9875
t 39 9888
a 39 9900
g 39 9913
c 35 9924
t 37 9937
c 32 9948
a 25 9960
a 27 9969
c 30 9982
g 34 9995
a 28 10008
t 33 10019
g 33 10031
c 28 10043
g 28 10055
c 28 10069
t 30 10081
t 26 10092
g 29 10106
g 29 10116
c 32 10131
g 17 10143
t 15 10155
a 9 10166
g 9 10174
g 9 10191
c 13 10203
g 14 10215
g 19 10229
a 26 10240
c 13 10252
t 13 10264
g 12 10276
t 18 10289
c 12 10299
g 12 10312
a 12 10326
a 12 10335
g 12 10346
c 12 10360
g 19 10374
c 18 10384
g 28 10397
a 13 10408
t 11 10420
c 9 10431
c 10 10449
c 8 10456
g 8 10467
g 10 10482
a 14 10497
g 11 10507
t 8 10520
g 8 10535
t 8 10552
t 8 10559
c 8 10566
c 8 10575
t 8 10593
g 12 10607
g 12 10617
t 16 10632
g 16 10644
c 10 10654
a 10 10666
c 10 10681
c 8 10689
t 10 10703
c 8 10716
a 8 10721
a 8 10731
t 13 10751
c 14 10762
c 20 10774
c 15 10785
t 19 10796
a 11 10810
g 11 10823
a 8 10835
t 8 10846
a 6 10862
g 6 10866
a 6 10886
a 6 10894
g 8 10905
g 10 10919
a 11 10930
g 11 10945
a 10 10956
g 10 10965
g 10 10977
a 10 10994
g 10 11007
c 8 11016
c 13 11029
c 16 11045
c 11 11052
a 10 11066
g 12 11073
g 9 11088
t 14 11103
c 10 11116
a 11 11127
c 10 11140
t 12 11147
c 10 11161
a 9 11170
t 10 11184
c 13 11197
t 13 11213
g 12 11223
g 10 11232
a 11 11245
a 11 11256
c 15 11271
g 10 11283
t 10 11294
g 10 11305
g 9 11313
c 9 11329
c 10 11342
t 18 11360
t 12 11370
c 10 11382
a 13 11396
t 12 11406
g 19 11418
t 19 11431
c 23 11443
t 22 11455
t 22 11465
c 18 11480
c 12 11492
t 11 11504
t 10 11512
t 8 11518
g 10 11528
a 8 11545
c 10 11563
g 10 11577
c 10 11588
c 12 11598
g 12 11613
c 12 11624
c 12 11634
a 12 11646
c 11 11658
c 12 11668
t 16 11681
c 15 11697
t 10 11707
g 10 11720
c 10 11736
a 9 11744
t 9 11757
c 10 11767
t 8 11784
t 8 11792
t 8 11802
g 8 11822
g 9 11831
t 8 11841
g 8 11857
c 8 11871
c 8 11879
g 10 11900
g 8 11909
t 9 11921
g 11 11931
a 16 11946
t 10 11958
c 10 11967
a 10 11981
c 10 11997
c 10 12005
a 10 12020
g 11 12032
g 11 12042
t 9 12053
c 9 12070
g 9 12085
t 9 12093
c 9 12105
a 9 12113
a 9 12128
c 9 12146
g 9 12154
t 9 12171
a 9 12179
g 7 12195
a 7 12204
a 8 12212
c 8 12232
c 10 12248
c 11 12258
c 9 12267
a 9 12275
c 9 12293
c 9 12301
a 9 12313
g 8 12324
c 8 12341
a 8 12349
g 8 12369
g 9 12378
g 8 12387
g 8 12397
c 8 12404
t 8 12423
t 9 12434
t 10 12442
t 10 12451
c 8 12466
t 8 12484
t 8 12491
c 7 12503
a 8 12521
c 10 12535
t 10 12549
c 12 12559
c 16 12571
c 17 12580
c 10 12591
c 9 12605
g 10 12623
t 10 12635
c 10 12650
g 14 12662
g 12 12672
t 12 12687
a 11 12699
g 11 12711
a 11 12723
c 11 12734
g 8 12746
a 6 12759
c 7 12771
a 6 12775
g 10 12794
c 9 12803
c 10 12816
t 13 12835
c 11 12849
a 11 12863
t 12 12874
g 13 12885
c 12 12897
g 9 12908
g 9 12916
g 9 12928
c 9 12946
t 10 12964
c 10 12973
t 10 12983
g 12 12996
c 12 13007
t 12 13021
c 9 13033
g 10 13047
a 10 13063
a 10 13071
a 10 13080
a 8 13089
c 9 13101
c 9 13111
a 9 13130
t 8 13143
c 8 13154
t 6 13174
t 6 13178
c 6 13189
c 6 13199
t 10 13218
t 10 13233
a 9 13246
g 10 13260
c 10 13271
g 10 13281
t 10 13300
g 9 13312
g 7 13322
a 8 13335
a 8 13344
g 8 13348
t 8 13362
c 6 13378
c 8 13388
g 8 13407
g 8 13415
t 8 13433
t 9 13441
t 9 13450
t 8 13459
g 8 13474
g 8 13484
c 8 13490
g 8 13504
t 8 13522
t 10 13531
c 10 13548
c 10 13559
c 11 13574
c 11 13585
a 11 13594
c 11 13607
c 16 13616
c 16 13627
c 16 13640
g 16 13654
g 12 13668
g 15 13676
g 8 13686
g 8 13695
g 9 13714
g 9 13723
c 9 13742
t 9 13760
g 9 13772
c 11 13781
c 12 13790
c 10 13806
c 10 13816
c 9 13834
a 8 13842
g 8 13856
g 8 13868
g 8 13873
c 8 13890
a 8 13911
a 8 13927
a 10 13940
a 13 13956
a 8 13964
a 12 13972
a 8 13984
a 8 14008
c 8 14017
c 8 14029
t 8 14045
t 8 14053
t 8 14060
g 8 14078
c 8 14093
c 9 14102
c 9 14113
c 8 14122
g 8 14142
g 9 14158
g 9 14166
g 14 14180
g 22 14192
g 22 14204
a 15 14215
a 12 14229
c 11 14244
c 10 14258
a 10 14268
c 10 14279
c 8 14289
t 8 14304
t 8 14320
g 8 14326
c 8 14347
c 8 14357
c 7 14366
c 8 14377
c 8 14389
t 6 14393
c 6 14405
c 6 14415
t 10 14433
g 10 14442
g 10 14453
g 10 14468
c 10 14486
g 9 14495
g 9 14508
a 9 14521
a 18 14541
a 11 14552
a 8 14563
a 6 14577
t 6 14584
c 6 14603
t 6 14607
c 6 14611
a 6 14631
a 6 14646
a 8 14651
a 8 14670
c 8 14684
c 8 14698
c 11 14705
c 9 14721
c 10 14731
g 16 14743
g 13 14754
g 12 14764
g 15 14777
g 15 14796
g 10 14805
g 7 14823
g 7 14834
t 6 14842
g 6 14843
g 8 14864
a 6 14875
t 10 14887
g 8 14906
g 8 14920
c 8 14939
c 6 14946
a 6 14956
t 6 14978
a 6 14981
a 6 14993
a 6 15002
a 12 15019
a 12 15029
a 11 15039
c 11 15051
c 11 15064
c 10 15077
t 10 15088
t 6 15099
c 6 15119
c 6 15130
t 6 15132
c 6 15146
c 8 15157
c 10 15166
c 10 15184
c 10 15196
t 10 15213
t 10 15224
c 10 15233
c 9 15250
g 10 15263
a 11 15274
t 11 15287
c 9 15301
g 9 15313
c 9 15323
g 9 15332
c 6 15343
c 8 15362
c 8 15375
g 8 15381
g 8 15398
t 8 15415
t 8 15420
g 8 15437
a 8 15451
a 11 15465
a 11 15483
a 10 15494
a 11 15505
a 15 15520
a 11 15529
a 10 15539
a 10 15548
g 8 15566
g 8 15577
c 8 15594
g 8 15600
c 8 15605
c 8 15624
c 8 15639
c 8 15654
a 8 15659
c 8 15674
t 8 15690
t 8 15697
t 8 15707
a 8 15719
a 10 15738
a 10 15748
c 10 15758
a 10 15776
c 10 15786
t 8 15800
c 8 15811
c 8 15826
a 8 15833
c 8 15838
c 8 15847
t 8 15860
c 8 15867
a 8 15887
t 7 15901
g 9 15918
g 10 15930
t 10 15939
g 10 15957
g 10 15973
g 13 15985
g 21 15995
g 28 16005
g 13 16020
g 10 16034
g 8 16045
g 8 16052
g 8 16069
a 8 16086
a 8 16096
g 8 16103
a 8 16118
g 8 16140
c 8 16148
a 8 16167
c 8 16177
a 8 16182
c 8 16197
c 8 16214
c 8 16221
c 8 16238
c 13 16253
c 9 16270
c 9 16276
c 9 16297
END_DNA

END_SEQUENCE
BioPerl-1.007002/t/data/bug2246.blast000444000766000024       340113155576321 17010 0ustar00cjfieldsstaff000000000000BLASTP 2.2.16 [Mar-11-2007]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman 
(1997), "Gapped BLAST and PSI-BLAST: a new generation of 
protein database search programs", Nucleic Acids Res. 25:3389-3402.

RID: 1174495466-9867-19326456169.BLASTQ4


Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
           4,750,295 sequences; 1,639,169,463 total letters
Query=  foo
Length=193


                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

UniRef50_Q9X0H5 Cluster: Histidyl-tRNA synthetase; n=4; Thermoto...    23    650

  Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding 
environmental samples
    Posted date:  Mar 20, 2007  6:13 PM
  Number of letters in database: 1,639,169,463
  Number of sequences in database:  4,750,295
Lambda     K      H
   0.319    0.139    0.394 
Gapped
Lambda     K      H
   0.267   0.0410    0.140 
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4750295
Number of Hits to DB: 61915690
Number of extensions: 2579181
Number of successful extensions: 7099
Number of sequences better than 0.01: 55
Number of HSP's better than 0.01 without gapping: 0
Number of HSP's gapped: 7049
Number of HSP's successfully gapped: 55
Length of query: 193
Length of database: 1639169463
Length adjustment: 125
Effective length of query: 68
Effective length of database: 1045382588
Effective search space: 71086015984
Effective search space used: 71086015984
T: 11
A: 40
X1: 16 (7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (20.4 bits)
S2: 99 (42.7 bits)



BioPerl-1.007002/t/data/bug2391.megablast000444000766000024       235513155576321 17652 0ustar00cjfieldsstaff000000000000MEGABLAST 2.2.17 [Aug-26-2007]


Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000),
"A greedy algorithm for aligning DNA sequences",
J Comput Biol 2000; 7(1-2):203-14.

Database: hsapiens
           21,314 sequences; 59,699,290 total letters

Searching..................................................done

Query= c6_COX;c6_QBL;6|31508172;31503325;31478402|rs36223351|1|dbSNP|C
/G
         (101 letters)

 ***** No hits found ******


  Database: hsapiens
    Posted date:  Oct 16, 2007 10:46 AM
  Number of letters in database: 59,699,290
  Number of sequences in database:  21,314

Lambda     K      H
    1.37    0.711     1.31

Gapped
Lambda     K      H
    1.37    0.711     1.31


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 0, Extension: 0
Number of Sequences: 21314
Number of Hits to DB: 11,376
Number of sequences better than 10.0: 0
Number of HSP's gapped: 0
Number of HSP's successfully gapped: 0
Length of query: 101
Length of database: 59,699,290
Length adjustment: 16
Effective length of query: 85
Effective length of database: 59,358,266
Effective search space: 5045452610
Effective search space used: 5045452610
X1: 11 (21.8 bits)
X2: 20 (39.6 bits)
X3: 51 (101.1 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)BioPerl-1.007002/t/data/bug2399.tblastn000444000766000024     12144713155576321 17436 0ustar00cjfieldsstaff000000000000TBLASTN 2.2.16 [Mar-25-2007]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= ENSP00000349467 pep:known-ccds
chromosome:NCBI36:14:89933126:89944148:1 gene:ENSG00000198668
transcript:ENST00000356978 CCDS9892.1
         (149 letters)

Database: Human genomic DNA 
           24 sequences; 3,080,419,480 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

10 dna:chromosome chromosome:NCBI36:10:1:135374737:1                  263   2e-69
13 dna:chromosome chromosome:NCBI36:13:1:114142980:1                  239   5e-65
17 dna:chromosome chromosome:NCBI36:17:1:78774742:1                   229   4e-59
7 dna:chromosome chromosome:NCBI36:7:1:158821424:1                    140   1e-55
18 dna:chromosome chromosome:NCBI36:18:1:76117153:1                   155   6e-37
2 dna:chromosome chromosome:NCBI36:2:1:242951149:1                    150   2e-35
19 dna:chromosome chromosome:NCBI36:19:1:63811651:1                   147   1e-34
X dna:chromosome chromosome:NCBI36:X:1:154913754:1                    135   4e-31
4 dna:chromosome chromosome:NCBI36:4:1:191273063:1                    116   3e-25
6 dna:chromosome chromosome:NCBI36:6:1:170899992:1                    112   5e-24
15 dna:chromosome chromosome:NCBI36:15:1:100338915:1                  109   4e-23
14 dna:chromosome chromosome:NCBI36:14:1:106368585:1                  101   1e-20
20 dna:chromosome chromosome:NCBI36:20:1:62435964:1                    69   9e-20
8 dna:chromosome chromosome:NCBI36:8:1:146274826:1                     79   4e-14
9 dna:chromosome chromosome:NCBI36:9:1:140273252:1                     77   2e-13
12 dna:chromosome chromosome:NCBI36:12:1:132349534:1                   72   7e-12
5 dna:chromosome chromosome:NCBI36:5:1:180857866:1                     67   2e-10
21 dna:chromosome chromosome:NCBI36:21:1:46944323:1                    66   4e-10
3 dna:chromosome chromosome:NCBI36:3:1:199501827:1                     63   4e-09
22 dna:chromosome chromosome:NCBI36:22:1:49691432:1                    60   3e-08
1 dna:chromosome chromosome:NCBI36:1:1:247249719:1                     57   3e-07
16 dna:chromosome chromosome:NCBI36:16:1:88827254:1                    55   1e-06
11 dna:chromosome chromosome:NCBI36:11:1:134452384:1                   55   1e-06

>10 dna:chromosome chromosome:NCBI36:10:1:135374737:1
          Length = 135374737

 Score =  263 bits (671), Expect = 2e-69
 Identities = 126/149 (84%), Positives = 141/149 (94%)
 Frame = +2

Query: 1       MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
               MADQLTEEQ+ EFKEAFSLFDKDGDG ITT+ELGTVMRSLGQNPTEAEL+DM++E+D DG
Sbjct: 5557049 MADQLTEEQVTEFKEAFSLFDKDGDGCITTRELGTVMRSLGQNPTEAELRDMMSEIDRDG 5557228

Query: 61      NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
               NGT+DFPEFL MMARKMKDTD+EEEIREAFRVFDKDGNG++SAAELRHVMT LGEKL+DE
Sbjct: 5557229 NGTVDFPEFLGMMARKMKDTDNEEEIREAFRVFDKDGNGFVSAAELRHVMTRLGEKLSDE 5557408

Query: 121     EVDEMIREADIDGDGQVNYEEFVQMMTAK 149
               EVDEMIR AD DGDGQVNYEEFV+++ +K
Sbjct: 5557409 EVDEMIRAADTDGDGQVNYEEFVRVLVSK 5557495



 Score =  192 bits (487), Expect(2) = 5e-64
 Identities = 99/109 (90%), Positives = 99/109 (90%)
 Frame = +2

Query: 40       LGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNG 99
                L QNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIRE F VFDKDGNG
Sbjct: 71593562 LRQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIRETFCVFDKDGNG 71593741

Query: 100      YISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA 148
                YIS  EL HVMTNLG KLTDEEVD MIREAD DGDGQVNY EFVQMMTA
Sbjct: 71593742 YISGVELHHVMTNLGVKLTDEEVD*MIREADPDGDGQVNY-EFVQMMTA 71593885



 Score = 75.1 bits (183), Expect(2) = 5e-64
 Identities = 36/43 (83%), Positives = 39/43 (90%)
 Frame = +1

Query: 1        MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQN 43
                MADQLTEEQI EFKE FSLFDKDGDGTITTK+LGTVMRS  ++
Sbjct: 71593447 MADQLTEEQIVEFKEVFSLFDKDGDGTITTKKLGTVMRSQAES 71593575



 Score =  150 bits (378), Expect = 2e-35
 Identities = 75/146 (51%), Positives = 108/146 (73%)
 Frame = -1

Query: 1       MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
               MA +LT E+ A++K+AFS  D DG+GTI  +ELG  +++ G+N +EA+L+ +I+EVD+DG
Sbjct: 5531401 MAGELTPEEEAQYKKAFSAVDTDGNGTINAQELGAALKATGKNLSEAQLRKLISEVDSDG 5531222

Query: 61      NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
               +G I F EFLT  A+K +     E+++ AFR FD+DG+G+I+  ELR  M  LG+ L  E
Sbjct: 5531221 DGEISFQEFLTA-AKKARA--GLEDLQVAFRAFDQDGDGHITVDELRRAMAGLGQPLPQE 5531051

Query: 121     EVDEMIREADIDGDGQVNYEEFVQMM 146
               E+D MIREAD+D DG+VNYEEF +M+
Sbjct: 5531050 ELDAMIREADVDQDGRVNYEEFARML 5530973



 Score = 57.8 bits (138), Expect = 1e-07
 Identities = 28/67 (41%), Positives = 40/67 (59%)
 Frame = -1

Query: 10      IAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEF 69
               + + + AF  FD+DGDG IT  EL   M  LGQ   + EL  MI E D D +G +++ EF
Sbjct: 5531164 LEDLQVAFRAFDQDGDGHITVDELRRAMAGLGQPLPQEELDAMIREADVDQDGRVNYEEF 5530985

Query: 70      LTMMARK 76
                 M+A++
Sbjct: 5530984 ARMLAQE 5530964



 Score = 57.0 bits (136), Expect = 2e-07
 Identities = 33/73 (45%), Positives = 47/73 (64%)
 Frame = +2

Query: 1        MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
                M D  +EE+I   +E F +FDKDG+G I+  EL  VM +LG   T+ E+  MI E D DG
Sbjct: 71593673 MKDTDSEEEI---RETFCVFDKDGNGYISGVELHHVMTNLGVKLTDEEVD*MIREADPDG 71593843

Query: 61       NGTIDFPEFLTMM 73
                +G +++ EF+ MM
Sbjct: 71593844 DGQVNY-EFVQMM 71593879



 Score = 53.1 bits (126), Expect = 3e-06
 Identities = 26/55 (47%), Positives = 37/55 (67%)
 Frame = -1

Query: 92       VFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMM 146
                VFDK+GNG +  AE+ H++  LGEK+T+EEVD M+     D  G +N EE + M+
Sbjct: 66599371 VFDKEGNGTVMGAEIWHILVTLGEKMTEEEVD-MLGAGHEDNIGCIN*EELICMV 66599210


>13 dna:chromosome chromosome:NCBI36:13:1:114142980:1
          Length = 114142980

 Score =  212 bits (540), Expect(2) = 5e-65
 Identities = 106/119 (89%), Positives = 110/119 (92%)
 Frame = -2

Query: 31       KELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAF 90
                KE GTVMRSLGQNPTEAELQDMINEVDADGNGT+DFPEFLTMMARKMKDTDSEEEIR+AF
Sbjct: 40643195 KESGTVMRSLGQNPTEAELQDMINEVDADGNGTVDFPEFLTMMARKMKDTDSEEEIRDAF 40643016

Query: 91       RVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 149
                 VFDKDGNGYISA EL HVMTNLGE LTD+EVDEMIR   IDGDGQ+ YEEFVQMMTAK
Sbjct: 40643015 CVFDKDGNGYISATELHHVMTNLGENLTDDEVDEMIR*PHIDGDGQMIYEEFVQMMTAK 40642839



 Score = 57.8 bits (138), Expect(2) = 5e-65
 Identities = 27/31 (87%), Positives = 29/31 (93%)
 Frame = -3

Query: 1        MADQLTEEQIAEFKEAFSLFDKDGDGTITTK 31
                MADQLTE Q AEFKEAFSLF+KDGDGTITT+
Sbjct: 40643284 MADQLTERQTAEFKEAFSLFNKDGDGTITTR 40643192



 Score =  239 bits (609), Expect = 3e-62
 Identities = 121/144 (84%), Positives = 127/144 (88%)
 Frame = -2

Query: 1        MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
                MADQLT EQI EFK A+ LFDKDGDGTITTKELGT MRSL ++PTEAELQDMI EVDAD 
Sbjct: 98091494 MADQLTGEQIVEFK*AYLLFDKDGDGTITTKELGTEMRSLRRHPTEAELQDMIYEVDADS 98091315

Query: 61       NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
                NG + FPEF+TM ARKMKD  SEEE+REAFRVFDKDGNGYISAAEL H MTNLGEKLTDE
Sbjct: 98091314 NGRVGFPEFVTMRARKMKDAGSEEEMREAFRVFDKDGNGYISAAELHHAMTNLGEKLTDE 98091135

Query: 121      EVDEMIREADIDGDGQVNYEEFVQ 144
                EVDEMIREADIDGDGQVN EEF Q
Sbjct: 98091134 EVDEMIREADIDGDGQVNCEEFAQ 98091063



 Score = 60.8 bits (146), Expect = 2e-08
 Identities = 33/76 (43%), Positives = 49/76 (64%)
 Frame = -2

Query: 1        MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
                M D  +EE+I   ++AF +FDKDG+G I+  EL  VM +LG+N T+ E+ +MI     DG
Sbjct: 40643057 MKDTDSEEEI---RDAFCVFDKDGNGYISATELHHVMTNLGENLTDDEVDEMIR*PHIDG 40642887

Query: 61       NGTIDFPEFLTMMARK 76
                +G + + EF+ MM  K
Sbjct: 40642886 DGQMIYEEFVQMMTAK 40642839



 Score = 53.9 bits (128), Expect = 2e-06
 Identities = 33/82 (40%), Positives = 46/82 (56%), Gaps = 3/82 (3%)
 Frame = -2

Query: 71       TMMARKMKDTDSEEEIRE---AFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIR 127
                T  A  M D  + E+I E   A+ +FDKDG+G I+  EL   M +L    T+ E+ +MI 
Sbjct: 98091512 TGSAFSMADQLTGEQIVEFK*AYLLFDKDGDGTITTKELGTEMRSLRRHPTEAELQDMIY 98091333

Query: 128      EADIDGDGQVNYEEFVQMMTAK 149
                E D D +G+V + EFV M   K
Sbjct: 98091332 EVDADSNGRVGFPEFVTMRARK 98091267


>17 dna:chromosome chromosome:NCBI36:17:1:78774742:1
          Length = 78774742

 Score =  229 bits (583), Expect = 4e-59
 Identities = 121/146 (82%), Positives = 128/146 (87%)
 Frame = +1

Query: 4        QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGT 63
                +LTEEQI EF EAFSLFD+D DGTITTKE+ T+MRSLG NP +A L DMINEVDADGN T
Sbjct: 65749060 KLTEEQIPEFIEAFSLFDRDNDGTITTKEVETIMRSLG*NPMKAGLPDMINEVDADGNRT 65749239

Query: 64       IDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVD 123
                 D PEFLTMMARKMKDT SEEEIREAF VFDKDGNGYISAAEL HVMTN GEKLTD++VD
Sbjct: 65749240 -DSPEFLTMMARKMKDTQSEEEIREAFLVFDKDGNGYISAAELCHVMTNPGEKLTDDKVD 65749416

Query: 124      EMIREADIDGDGQVNYEEFVQMMTAK 149
                EMIREA IDGDGQVN EEFVQ MTAK
Sbjct: 65749417 EMIREAGIDGDGQVN*EEFVQTMTAK 65749494



 Score =  112 bits (281), Expect = 4e-24
 Identities = 64/148 (43%), Positives = 87/148 (58%), Gaps = 4/148 (2%)
 Frame = +3

Query: 1        MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
                M    TE+Q  EFKEAF LFD+ GDG I   + G VMR LGQNPT  E+  ++    ++ 
Sbjct: 67128714 MMCDFTEDQTTEFKEAFQLFDRTGDGKILYNQCGDVMRPLGQNPTNTEVVKVLRNPKSNE 67128893

Query: 61       NGT--IDFPEFLTM--MARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEK 116
                     +DF  FL M  M  K KD  + E+  E  +VFDK+GNG I   E  HV+  LGEK
Sbjct: 67128894 MNVKLLDFEHFLPMLQMVAKNKDQGTYEDYVEGLQVFDKEGNGTIMGVEFWHVLVTLGEK 67129073

Query: 117      LTDEEVDEMIREADIDGDGQVNYEEFVQ 144
                +T+EEV E++   +   +G ++YE FV+
Sbjct: 67129074 ITEEEV-EVLVAGNEGSNGCIDYEAFVR 67129154


>7 dna:chromosome chromosome:NCBI36:7:1:158821424:1
          Length = 158821424

 Score =  140 bits (352), Expect(2) = 1e-55
 Identities = 72/86 (83%), Positives = 78/86 (90%)
 Frame = -2

Query: 1        MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
                MADQLT+EQIAEF+EAFSL  KD +GTITTKELGT+MRSLGQNP E+ELQDMINEVD+DG
Sbjct: 55295443 MADQLTKEQIAEFEEAFSLSYKDSNGTITTKELGTIMRSLGQNPAESELQDMINEVDSDG 55295264

Query: 61       NGTIDFPEFLTMMARKMKDTDSEEEI 86
                N TI F EFLTMMARKMKDT SEEEI
Sbjct: 55295263 NDTI*FLEFLTMMARKMKDTYSEEEI 55295186



 Score = 99.0 bits (245), Expect(2) = 1e-55
 Identities = 48/58 (82%), Positives = 51/58 (87%)
 Frame = -3

Query: 92       VFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 149
                VFD  G GYISAAELRHVMTNLGEKL DEEVDEM+ EADIDGD QV+YEE +QMMTAK
Sbjct: 55295172 VFDDSGKGYISAAELRHVMTNLGEKLIDEEVDEMMTEADIDGDRQVDYEELIQMMTAK 55294999



 Score = 63.2 bits (152), Expect(2) = 1e-15
 Identities = 35/78 (44%), Positives = 45/78 (57%), Gaps = 2/78 (2%)
 Frame = +1

Query: 6         TEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNG--T 63
                 TE+Q  EFKE F LFD  GDG I   + G VMR LGQNPT+AE+  ++    +D      
Sbjct: 141158086 TEDQTTEFKEVF*LFD*TGDGKILYSQCGDVMRVLGQNPTDAEVMQVLEIPKSDEMNVTV 141158265

Query: 64        IDFPEFLTMMARKMKDTD 81
                 +DF  FL M+    K+ D
Sbjct: 141158266 LDFGHFLPMLQAVAKNRD 141158319



 Score = 41.2 bits (95), Expect(2) = 1e-15
 Identities = 20/48 (41%), Positives = 29/48 (60%)
 Frame = +2

Query: 80        TDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIR 127
                 T + E+  E   VFDK GNG I   E+  V+  LGEK+ +EEV  +++
Sbjct: 141158318 TRAYEDYVEGLWVFDKKGNGTIMGTEI*QVLVTLGEKMIEEEVKMLVQ 141158461



 Score = 55.5 bits (132), Expect = 7e-07
 Identities = 31/64 (48%), Positives = 42/64 (65%), Gaps = 2/64 (3%)
 Frame = +3

Query: 63       TIDFPEFLTMMARKMKDTDSEEEIREAFRVFDK--DGNGYISAAELRHVMTNLGEKLTDE 120
                TIDF EFLT+  RKM++T +E + R    +     +  G++ AA + H MT LGEKLTDE
Sbjct: 56416236 TIDFLEFLTIKVRKMQNTKTESKKRN*ESILHV**EDTGHVRAAAVCHDMTYLGEKLTDE 56416415

Query: 121      EVDE 124
                EVD+
Sbjct: 56416416 EVDK 56416427



 Score = 55.5 bits (132), Expect = 7e-07
 Identities = 31/64 (48%), Positives = 42/64 (65%), Gaps = 2/64 (3%)
 Frame = -2

Query: 63       TIDFPEFLTMMARKMKDTDSEEEIREAFRVFDK--DGNGYISAAELRHVMTNLGEKLTDE 120
                TIDF EFLT+  RKM++T +E + R    +     +  G++ AA + H MT LGEKLTDE
Sbjct: 39795358 TIDFLEFLTIKVRKMQNTKTESKKRN*ESILHV**EDTGHVRAAAVCHDMTYLGEKLTDE 39795179

Query: 121      EVDE 124
                EVD+
Sbjct: 39795178 EVDK 39795167



 Score = 54.7 bits (130), Expect = 1e-06
 Identities = 31/64 (48%), Positives = 43/64 (67%), Gaps = 2/64 (3%)
 Frame = +2

Query: 63    TIDFPEFLTMMARKMKDTDSEEEIR--EAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
             TIDF EFLT+  RKM++T +E + R  E+    + +  G++ AA +   MT LGEKLTDE
Sbjct: 67877 TIDFLEFLTIKVRKMQNTKTESKKRN*ESILHVE*EDTGHVRAAAVCRDMTYLGEKLTDE 68056

Query: 121   EVDE 124
             EVD+
Sbjct: 68057 EVDK 68068



 Score = 54.7 bits (130), Expect = 1e-06
 Identities = 31/64 (48%), Positives = 43/64 (67%), Gaps = 2/64 (3%)
 Frame = -2

Query: 63        TIDFPEFLTMMARKMKDTDSEEEIR--EAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
                 TIDF EFLT+  RKM++T +E + R  E+    + +  G++ AA +   MT LGEKLTDE
Sbjct: 128075968 TIDFLEFLTIKVRKMQNTKTESKKRN*ESILHVE*EDTGHVRAAAVCRDMTYLGEKLTDE 128075789

Query: 121       EVDE 124
                 EVD+
Sbjct: 128075788 EVDK 128075777



 Score = 54.3 bits (129), Expect = 2e-06
 Identities = 25/51 (49%), Positives = 35/51 (68%)
 Frame = -2

Query: 10       IAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
                I E +EAF + D+DG+G I+ +ELG  MRSLG  P+E EL  ++  +D DG
Sbjct: 71209222 IVEIREAFRVLDRDGNGFISKQELGMAMRSLGYMPSEVELAIIMQRLDMDG 71209070



 Score = 53.9 bits (128), Expect = 2e-06
 Identities = 30/64 (46%), Positives = 41/64 (64%), Gaps = 2/64 (3%)
 Frame = +2

Query: 63       TIDFPEFLTMMARKMKDTDSEEEIREAFRVFDK--DGNGYISAAELRHVMTNLGEKLTDE 120
                TIDF EFLT+  RKM++T +E + R    +     +  G++ A  + H MT LGEKLTDE
Sbjct: 51430415 TIDFLEFLTIKVRKMQNTKTESKKRN*ESILHV**EDTGHVRAVAVCHDMTYLGEKLTDE 51430594

Query: 121      EVDE 124
                EVD+
Sbjct: 51430595 EVDK 51430606



 Score = 53.9 bits (128), Expect = 2e-06
 Identities = 33/64 (51%), Positives = 43/64 (67%), Gaps = 3/64 (4%)
 Frame = -1

Query: 64       IDFPEFLTMMARKMKDTDSEEEIRE---AFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
                IDF EFLT+  RKM++T++E + R      RV   D  G++ AA + H MT LGEKLTDE
Sbjct: 64938065 IDFLEFLTIKVRKMQNTETEGKKRN**SILRV**ND-TGHVRAAAVCHDMTYLGEKLTDE 64937889

Query: 121      EVDE 124
                EVD+
Sbjct: 64937888 EVDK 64937877



 Score = 53.5 bits (127), Expect = 3e-06
 Identities = 30/63 (47%), Positives = 41/63 (65%), Gaps = 2/63 (3%)
 Frame = -2

Query: 64       IDFPEFLTMMARKMKDTDSEEEIREAFRVFDK--DGNGYISAAELRHVMTNLGEKLTDEE 121
                IDF EFLT+  RKM++T +E + R    +     +  G++ AA + H MT LGEKLTDEE
Sbjct: 45811102 IDFLEFLTIKVRKMQNTKTESKKRN*ESILHV**EDTGHVRAAAVCHDMTYLGEKLTDEE 45810923

Query: 122      VDE 124
                VD+
Sbjct: 45810922 VDK 45810914



 Score = 53.1 bits (126), Expect = 3e-06
 Identities = 30/64 (46%), Positives = 41/64 (64%), Gaps = 2/64 (3%)
 Frame = +2

Query: 63       TIDFPEFLTMMARKMKDTDSEEEIREAFRVFDK--DGNGYISAAELRHVMTNLGEKLTDE 120
                TIDF EFLT+  RKM++ ++E +     R+     D  G++ AA + H MT LGEKL DE
Sbjct: 65484968 TIDFLEFLTIRVRKMQNKETEGKKTN*GRILHV**DDTGHVRAAAVCHNMTYLGEKLADE 65485147

Query: 121      EVDE 124
                EVD+
Sbjct: 65485148 EVDK 65485159



 Score = 52.4 bits (124), Expect = 6e-06
 Identities = 30/64 (46%), Positives = 41/64 (64%), Gaps = 2/64 (3%)
 Frame = +3

Query: 63       TIDFPEFLTMMARKMKDTDSEEEIREAFRVFDK--DGNGYISAAELRHVMTNLGEKLTDE 120
                TIDF EFLT+  RKM++T +E + R    +     +  G++ AA + H MT L EKLTDE
Sbjct: 55786080 TIDFLEFLTIKVRKMQNTKTESKKRN*ESILHV**EDTGHVRAAAVCHDMTYLEEKLTDE 55786259

Query: 121      EVDE 124
                EVD+
Sbjct: 55786260 EVDK 55786271


>18 dna:chromosome chromosome:NCBI36:18:1:76117153:1
          Length = 76117153

 Score =  155 bits (391), Expect = 6e-37
 Identities = 78/143 (54%), Positives = 101/143 (70%)
 Frame = +1

Query: 4      QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGT 63
              +LTE+Q  E +EAF LFD DG GTI  KEL   MR+LG  P + E++ MI+EVD +G G 
Sbjct: 570478 ELTEDQKQEVREAFDLFDVDGSGTIDAKELKVAMRALGFEPRKEEMKKMISEVDREGTGK 570657

Query: 64     IDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVD 123
              I F +FL +M +KM + D++EEI +AFR+FD D  G IS   L+ V   LGE LTDEE+ 
Sbjct: 570658 ISFNDFLAVMTQKMSEKDTKEEILKAFRLFDDDETGKISFKNLKRVANELGENLTDEELQ 570837

Query: 124    EMIREADIDGDGQVNYEEFVQMM 146
              EMI EAD DGDG+VN EEF+++M
Sbjct: 570838 EMIDEADRDGDGEVNEEEFLRIM 570906



 Score = 63.9 bits (154), Expect = 2e-09
 Identities = 30/69 (43%), Positives = 47/69 (68%)
 Frame = +1

Query: 81     DSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE 140
              D ++E+REAF +FD DG+G I A EL+  M  LG +   EE+ +MI E D +G G++++ 
Sbjct: 570490 DQKQEVREAFDLFDVDGSGTIDAKELKVAMRALGFEPRKEEMKKMISEVDREGTGKISFN 570669

Query: 141    EFVQMMTAK 149
              +F+ +MT K
Sbjct: 570670 DFLAVMTQK 570696



 Score = 61.6 bits (148), Expect = 1e-08
 Identities = 33/75 (44%), Positives = 49/75 (65%)
 Frame = +1

Query: 1      MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
              M+++ T+E+I +   AF LFD D  G I+ K L  V   LG+N T+ ELQ+MI+E D DG
Sbjct: 570697 MSEKDTKEEILK---AFRLFDDDETGKISFKNLKRVANELGENLTDEELQEMIDEADRDG 570867

Query: 61     NGTIDFPEFLTMMAR 75
              +G ++  EFL +M +
Sbjct: 570868 DGEVNEEEFLRIMKK 570912



 Score = 54.3 bits (129), Expect = 2e-06
 Identities = 28/65 (43%), Positives = 38/65 (58%)
 Frame = +1

Query: 35      TVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFD 94
               T  ++LG+NPT+  L  M+NE      G I+F  FLTM   K+  TD E+ IR AF  FD
Sbjct: 3243868 TPFKNLGKNPTDEYLDAMMNEAP----GPINFTMFLTMFGEKLNGTDPEDVIRNAFACFD 3244035

Query: 95      KDGNG 99
               ++  G
Sbjct: 3244036 EEATG 3244050



 Score = 52.4 bits (124), Expect = 6e-06
 Identities = 27/59 (45%), Positives = 35/59 (59%)
 Frame = +1

Query: 41      GQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNG 99
               G+NPT+A L  M+NE      G I+F  FLTM   K+  TD E+ IR AF  FD++  G
Sbjct: 3267250 GKNPTDAYLDAMMNEAP----GPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEATG 3267414


>2 dna:chromosome chromosome:NCBI36:2:1:242951149:1
          Length = 242951149

 Score =  150 bits (378), Expect = 2e-35
 Identities = 85/130 (65%), Positives = 85/130 (65%), Gaps = 42/130 (32%)
 Frame = -3

Query: 12       EFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDAD------------ 59
                EFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDAD            
Sbjct: 47243306 EFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGKSSILWGWEGL 47243127

Query: 60       ------------------------------GNGTIDFPEFLTMMARKMKDTDSEEEIREA 89
                                              GNGTIDFPEFLTMMARKMKDTDSEEEIREA
Sbjct: 47243126 KK*YLDVSTKPLLFAYMFPLKL*CFH*TISGNGTIDFPEFLTMMARKMKDTDSEEEIREA 47242947

Query: 90       FRVFDKDGNG 99
                FRVFDK   G
Sbjct: 47242946 FRVFDKVRQG 47242917



 Score = 95.1 bits (235), Expect = 8e-19
 Identities = 46/49 (93%), Positives = 47/49 (95%)
 Frame = -1

Query: 92       VFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE 140
                +F  DGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE
Sbjct: 47242513 IFC*DGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE 47242367



 Score = 79.0 bits (193), Expect = 6e-14
 Identities = 44/127 (34%), Positives = 74/127 (58%), Gaps = 4/127 (3%)
 Frame = -3

Query: 4         QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG--N 61
                 +  ++Q+ EFK AF LF+  GDG I   + G +M +L QN T A++  ++    +D   +
Sbjct: 208842749 KFNKDQLEEFKVAFKLFN*VGDGKIPYSQFGDMMGALDQNLTSAKVMKVLGNPKSDDLKS 208842570

Query: 62        GTIDFPEFLTMM--ARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTD 119
                   +DF  FL M+  A K ++  + E+  E   V  K+GN  ++ AELR V+T LG K+ +
Sbjct: 208842569 RHVDFKTFLPMLQAAAKKQNQGTYEDYLEGLHVLVKEGNSKVTGAELRQVLTTLGGKMAE 208842390

Query: 120       EEVDEMI 126
                 EE++ ++
Sbjct: 208842389 EEMETVL 208842369



 Score = 59.7 bits (143), Expect = 4e-08
 Identities = 29/57 (50%), Positives = 40/57 (70%)
 Frame = -2

Query: 11        AEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFP 67
                 AEFKEAF LFD+ GD  IT  ++G V+R+LG NPT AE++ ++     +GN +I FP
Sbjct: 210871536 AEFKEAFLLFDRTGDSKITLSQVGDVLRALGTNPTNAEVRKVLGNPSNEGNPSI-FP 210871369



 Score = 55.1 bits (131), Expect = 9e-07
 Identities = 25/55 (45%), Positives = 36/55 (65%)
 Frame = -3

Query: 83       EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQV 137
                + E +EAF +FDKDG+G I+  EL  VM +LG+  T+ E+ +MI E D DG   +
Sbjct: 47243312 QTEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGKSSI 47243148


>19 dna:chromosome chromosome:NCBI36:19:1:63811651:1
          Length = 63811651

 Score =  147 bits (372), Expect = 1e-34
 Identities = 84/131 (64%), Positives = 84/131 (64%), Gaps = 47/131 (35%)
 Frame = +1

Query: 12       EFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDAD------------ 59
                EFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDAD            
Sbjct: 51803293 EFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGEPHRARGQPCS 51803472

Query: 60       -----------------------------------GNGTIDFPEFLTMMARKMKDTDSEE 84
                                                   GNGTIDFPEFLTMMARKMKDTDSEE
Sbjct: 51803473 WSPRVTAGSLSQGDG*ARVSQGPGQEHSPSFPHLPGNGTIDFPEFLTMMARKMKDTDSEE 51803652

Query: 85       EIREAFRVFDK 95
                EIREAFRVFDK
Sbjct: 51803653 EIREAFRVFDK 51803685



 Score = 94.7 bits (234), Expect = 1e-18
 Identities = 45/46 (97%), Positives = 46/46 (100%)
 Frame = +3

Query: 95       KDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE 140
                +DGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE
Sbjct: 51803940 QDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE 51804077



 Score = 54.7 bits (130), Expect = 1e-06
 Identities = 31/64 (48%), Positives = 43/64 (67%), Gaps = 2/64 (3%)
 Frame = +1

Query: 63     TIDFPEFLTMMARKMKDTDSEEEIR--EAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
              TIDF EFLT+  RKM++T +E + R  E+    + +  G++ AA +   MT LGEKLTDE
Sbjct: 155185 TIDFLEFLTIKVRKMQNTKTESKKRN*ESILHVE*EDTGHVRAAAVCRDMTYLGEKLTDE 155364

Query: 121    EVDE 124
              EVD+
Sbjct: 155365 EVDK 155376



 Score = 54.7 bits (130), Expect = 1e-06
 Identities = 25/50 (50%), Positives = 35/50 (70%)
 Frame = +1

Query: 85       EIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGD 134
                E +EAF +FDKDG+G I+  EL  VM +LG+  T+ E+ +MI E D DG+
Sbjct: 51803293 EFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGE 51803442



 Score = 52.8 bits (125), Expect = 4e-06
 Identities = 24/49 (48%), Positives = 36/49 (73%), Gaps = 1/49 (2%)
 Frame = -3

Query: 93       FDKDGNGYISAAELRHVMTNL-GEKLTDEEVDEMIREADIDGDGQVNYE 140
                FD +G+G I+  EL+  M  L GE+LT  E+ E++READ++GDG V++E
Sbjct: 53229431 FDTNGDGEITLVELQQAMQRLLGERLTPREISEVVREADVNGDGTVDFE 53229285


>X dna:chromosome chromosome:NCBI36:X:1:154913754:1
          Length = 154913754

 Score =  135 bits (341), Expect = 4e-31
 Identities = 76/117 (64%), Positives = 86/117 (73%), Gaps = 5/117 (4%)
 Frame = +1

Query: 1        MADQLTEEQIAEFKEAFSL-----FDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINE 55
                M+DQLTEEQIAEF+EAFS+     +     GT    E+           +EAEL+DMINE
Sbjct: 94641259 MSDQLTEEQIAEFREAFSIG*RWRWHHHNKGTWNCHEV---------TGSEAELRDMINE 94641411

Query: 56       VDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTN 112
                VDA+GN TIDFPEFL M+ARKMKDTDS+EEI EAF VFDK GNGYISAAEL HVMTN
Sbjct: 94641412 VDANGNDTIDFPEFLAMIARKMKDTDSKEEIHEAF*VFDKGGNGYISAAELCHVMTN 94641582



 Score = 89.4 bits (220), Expect = 4e-17
 Identities = 64/136 (47%), Positives = 74/136 (54%), Gaps = 4/136 (2%)
 Frame = +2

Query: 18       SLFDKDGDGTITTKELGTVMRSLGQNPT----EAELQDMINEVDADGNGTIDFPEFLTMM 73
                SL DKDGDGTITTKE GTVMRSLGQ P       +   M+       N  +   E   + 
Sbjct: 94641308 SLLDKDGDGTITTKEPGTVMRSLGQKPNYGI*STKWMPMVTTPLTSPNFWL**LEK*KIQ 94641487

Query: 74       ARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDG 133
                  K K     E +     V     N Y+++ +        GEKLTDEEVDEMIREADID 
Sbjct: 94641488 IVKKKSMRHSESLTRVAMVTSVQQN-YVTS*Q-------TGEKLTDEEVDEMIREADIDR 94641643

Query: 134      DGQVNYEEFVQMMTAK 149
                  QVNYEEF+Q MTAK
Sbjct: 94641644 G*QVNYEEFIQ-MTAK 94641688


>4 dna:chromosome chromosome:NCBI36:4:1:191273063:1
          Length = 191273063

 Score =  116 bits (290), Expect = 3e-25
 Identities = 60/140 (42%), Positives = 88/140 (62%)
 Frame = -1

Query: 7         EEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDF 66
                 + QI EFKEAF++ D++ DG I+ ++L  ++ SLG+NPT+A L  ++NE      G I+F
Sbjct: 185457713 QSQIQEFKEAFNMIDQNRDGFISKEDLHGMLASLGKNPTDACLDAVMNEAP----GPINF 185457546

Query: 67        PEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMI 126
                    L M  +K+  TD E+ IR AF  FD++  G I    LR ++T +G++ TDEEVDE+ 
Sbjct: 185457545 TMLLAMFGKKLNGTDPEDVIRNAFACFDEEATGTIQEDYLRELLTTVGDQFTDEEVDELY 185457366

Query: 127       READIDGDGQVNYEEFVQMM 146
                  EA ID  G  NY EF  ++
Sbjct: 185457365 TEAPIDKKGNFNYIEFTSIL 185457306



 Score = 59.7 bits (143), Expect = 4e-08
 Identities = 33/108 (30%), Positives = 63/108 (58%), Gaps = 5/108 (4%)
 Frame = +3

Query: 5         LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPT-----EAELQDMINEVDAD 59
                 +++EQ+ +F+ +F+ FDKD  G +  +     + SLG +       EAE   +++ VD +
Sbjct: 117739764 ISQEQMQQFRASFNHFDKDHGGVLGPEGFKACLISLGYDVENDRQGEAEFNRIMSLVDPN 117739943

Query: 60        GNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELR 107
                  +G + F  F+  M+++  DTD  +++  +F+V  +D N +I+A ELR
Sbjct: 117739944 HSGLVTFQAFIDFMSQETTDTDMADQVIASFKVLARDKN-FITAEELR 117740084


>6 dna:chromosome chromosome:NCBI36:6:1:170899992:1
          Length = 170899992

 Score =  112 bits (280), Expect = 5e-24
 Identities = 59/136 (43%), Positives = 84/136 (61%)
 Frame = +3

Query: 7        EEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDF 66
                + QI EFKEAF++ D++ DG I  ++L  ++ SLG+NPT+A L  ++NE      G IDF
Sbjct: 33414813 QSQIQEFKEAFNMIDQNRDGFINKEDLHDMLVSLGKNPTDAYLDAIMNEAP----GPIDF 33414980

Query: 67       PEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMI 126
                  FLT+   K+  TD E+ I  AF  FD++  G I    LR ++  + ++ TDEEVDE+ 
Sbjct: 33414981 TMFLTIFGEKLNGTDPEDVIGNAFACFDEEATGIIQEDYLRELLITMWDRFTDEEVDELY 33415160

Query: 127      READIDGDGQVNYEEF 142
                REA I+  G  NY EF
Sbjct: 33415161 REAPINKKGNFNYIEF 33415208


>15 dna:chromosome chromosome:NCBI36:15:1:100338915:1
          Length = 100338915

 Score =  109 bits (272), Expect = 4e-23
 Identities = 61/140 (43%), Positives = 84/140 (60%)
 Frame = +1

Query: 7        EEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDF 66
                + QI EFKEAF++ D + DG I  ++L  ++ SLG+NPT+A L   +NE      G I+F
Sbjct: 40651498 QSQIQEFKEAFNMID*NRDGFINKEDLHDMLASLGKNPTDAYLDATMNEAP----GPINF 40651665

Query: 67       PEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMI 126
                    TM   K+  TD E+ IR A   FD++  G I    LR +MT +G++ TDEEVDE+ 
Sbjct: 40651666 ----TMFGEKLNGTDPEDVIRNASACFDEEATGTIQEDYLRELMTTMGDQFTDEEVDELH 40651833

Query: 127      READIDGDGQVNYEEFVQMM 146
                REA ID  G  NY EF  ++
Sbjct: 40651834 REAPIDKKGNFNYIEFTSIL 40651893



 Score = 63.5 bits (153), Expect = 3e-09
 Identities = 30/63 (47%), Positives = 44/63 (69%)
 Frame = -3

Query: 59       DGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLT 118
                DGNG +DF  FLT+M  ++K  D ++EI  A  + DK+  GY+ A++LR  +T+LGEKLT
Sbjct: 66277021 DGNGELDFSTFLTIMHMQIKQEDPKKEILLAMLMVDKEKKGYVMASDLRSKLTSLGEKLT 66276842

Query: 119      DEE 121
                 +E
Sbjct: 66276841 HKE 66276833


>14 dna:chromosome chromosome:NCBI36:14:1:106368585:1
          Length = 106368585

 Score =  101 bits (251), Expect = 1e-20
 Identities = 49/50 (98%), Positives = 50/50 (100%)
 Frame = +1

Query: 11       AEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
                +EFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
Sbjct: 89937352 SEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 89937501



 Score = 94.7 bits (234), Expect = 1e-18
 Identities = 45/46 (97%), Positives = 46/46 (100%)
 Frame = +2

Query: 95       KDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE 140
                +DGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE
Sbjct: 89940473 QDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE 89940610



 Score = 76.3 bits (186), Expect = 4e-13
 Identities = 36/36 (100%), Positives = 36/36 (100%)
 Frame = +3

Query: 60       GNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDK 95
                GNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDK
Sbjct: 89939958 GNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDK 89940065



 Score = 53.9 bits (128), Expect = 2e-06
 Identities = 25/49 (51%), Positives = 34/49 (69%)
 Frame = +1

Query: 85       EIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDG 133
                E +EAF +FDKDG+G I+  EL  VM +LG+  T+ E+ +MI E D DG
Sbjct: 89937355 EFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 89937501


>20 dna:chromosome chromosome:NCBI36:20:1:62435964:1
          Length = 62435964

 Score = 69.3 bits (168), Expect(2) = 9e-20
 Identities = 33/51 (64%), Positives = 38/51 (74%)
 Frame = -1

Query: 10       IAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
                +AEFK AF +FD DG G I+ KELGTVMR LGQ PT+ EL  +I EVD DG
Sbjct: 43886691 LAEFKAAFDMFDADGGGDISVKELGTVMRMLGQTPTKEELDAIIEEVDEDG 43886539



 Score = 49.3 bits (116), Expect(2) = 9e-20
 Identities = 24/43 (55%), Positives = 30/43 (69%), Gaps = 3/43 (6%)
 Frame = -2

Query: 60       GNGTIDFPEFLTMMARKMKDT---DSEEEIREAFRVFDKDGNG 99
                G+GTIDF EFL MM R+MK+     SEEE+ E FR+FD+   G
Sbjct: 43886453 GSGTIDFEEFLVMMVRQMKEDAKGKSEEELAECFRIFDRCAGG 43886325



 Score = 54.3 bits (129), Expect = 2e-06
 Identities = 24/48 (50%), Positives = 33/48 (68%)
 Frame = +1

Query: 99       GYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMM 146
                G+I    LR ++T +G++ TDEEVDEM REA ID  G  NY EF +++
Sbjct: 34610893 GFIHEDHLRELLTTMGDRFTDEEVDEMYREAPIDKKGNFNYVEFTRIL 34611036


>8 dna:chromosome chromosome:NCBI36:8:1:146274826:1
          Length = 146274826

 Score = 79.3 bits (194), Expect = 4e-14
 Identities = 43/108 (39%), Positives = 63/108 (58%)
 Frame = +3

Query: 7        EEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDF 66
                + QI EFKEAF++ D++ DG I  ++L  ++ S G++PT+  L  M+NE      G I F
Sbjct: 94931046 QSQIQEFKEAFNMIDQNRDGFIDKEDLQDMLASSGKSPTDWYLDAMMNEAP----GPISF 94931213

Query: 67       PEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLG 114
                  FLTM   K+  TD E+ IR AF  FD++  G I    L  ++T +G
Sbjct: 94931214 TVFLTMFGEKLNGTDPEDVIRHAFACFDEEATGTIQEDYL*ELLTTMG 94931357


>9 dna:chromosome chromosome:NCBI36:9:1:140273252:1
          Length = 140273252

 Score = 77.0 bits (188), Expect = 2e-13
 Identities = 48/147 (32%), Positives = 79/147 (53%), Gaps = 5/147 (3%)
 Frame = -1

Query: 1         MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
                 M      ++I      F   D D  G+++ +E  + +  L  NP    ++ +I+  D DG
Sbjct: 103396994 MCSHFDNDEIKRLGRRFKKLDLDKSGSLSVEEFMS-LPELRHNPL---VRRVIDVFDTDG 103396827

Query: 61        NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNL-GEKLTD 119
                 +G +DF EF+   ++     D E+++R AF ++D D +GYIS  EL  V+  + G  LTD
Sbjct: 103396826 DGEVDFKEFILGTSQFSVKGDEEQKLRFAFSIYDMDKDGYISNGELFQVLKMMVGNNLTD 103396647

Query: 120       ----EEVDEMIREADIDGDGQVNYEEF 142
                     + VD+ I   D DGDG++++EEF
Sbjct: 103396646 WQLQQLVDKTIIILDKDGDGKISFEEF 103396566


>12 dna:chromosome chromosome:NCBI36:12:1:132349534:1
          Length = 132349534

 Score = 72.0 bits (175), Expect = 7e-12
 Identities = 38/96 (39%), Positives = 57/96 (59%)
 Frame = +2

Query: 42      QNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI 101
               +NP +  LQ M++E      G I+F   LTM   K+  TD ++ I+ AF  F+++ +G+I
Sbjct: 7914905 KNPMDEYLQGMMSEAP----GPINFTTSLTMFGEKLNGTDPQDVIQNAFTCFNEESSGFI 7915072

Query: 102     SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQV 137
                   L+ ++T +G+  TDEEVDEM  EA ID   QV
Sbjct: 7915073 HEDHLQELLTTMGDSFTDEEVDEMYWEAPIDKKRQV 7915180



 Score = 63.5 bits (153), Expect = 3e-09
 Identities = 31/60 (51%), Positives = 39/60 (65%)
 Frame = +1

Query: 5        LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTI 64
                LT     EFKEAF LFD+ GDG I   + G VMR+LGQNPT AE+  ++    +DG GT+
Sbjct: 54835084 LTLPYTLEFKEAFELFDRVGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDGEGTL 54835263



 Score = 61.2 bits (147), Expect = 1e-08
 Identities = 28/52 (53%), Positives = 36/52 (69%)
 Frame = +3

Query: 11       AEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNG 62
                +EFKEAF LFD+ GDG I   + G VMR+LGQNPT AE+  ++    +DG G
Sbjct: 54839634 SEFKEAFQLFDRTGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDGEG 54839789



 Score = 54.3 bits (129), Expect = 2e-06
 Identities = 27/54 (50%), Positives = 35/54 (64%), Gaps = 2/54 (3%)
 Frame = +2

Query: 64       IDFPEFLTMM--ARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGE 115
                +DF  FL M+    K +   + E+  E FRVFDK+GNG +  AELRHV+T LGE
Sbjct: 54835487 VDFETFLPMLQAVAKNRGQGTYEDYLEGFRVFDKEGNGKVMGAELRHVLTTLGE 54835648



 Score = 52.0 bits (123), Expect = 8e-06
 Identities = 26/56 (46%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
 Frame = +1

Query: 64       IDFPEFLTMM--ARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKL 117
                +DF  FL M+    K KD  + E+  E  RVFDK+GNG +  AE+RHV+  LG+ L
Sbjct: 54840043 LDFEHFLPMLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLVTLGKVL 54840210


>5 dna:chromosome chromosome:NCBI36:5:1:180857866:1
          Length = 180857866

 Score = 67.4 bits (163), Expect = 2e-10
 Identities = 37/91 (40%), Positives = 52/91 (57%)
 Frame = -1

Query: 49       LQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRH 108
                L D  NE   D  G + +  F T++   + + D  EEI +AF++FD D +G IS   LR 
Sbjct: 89731195 LVDFTNECLCDYAGLLKYICF*TVVTDWILERDPHEEILKAFKLFDDDDSGKISLRNLRR 89731016

Query: 109      VMTNLGEKLTDEEVDEMIREADIDGDGQVNY 139
                V   LGE ++DEE+  MI E D DGDG+  +
Sbjct: 89731015 VARELGENMSDEELRAMIEEFDKDGDGESKF 89730923



 Score = 54.7 bits (130), Expect = 1e-06
 Identities = 31/64 (48%), Positives = 43/64 (67%), Gaps = 2/64 (3%)
 Frame = -2

Query: 63        TIDFPEFLTMMARKMKDTDSEEEIR--EAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
                 TIDF EFLT+  RKM++T +E + R  E+    + +  G++ AA +   MT LGEKLTDE
Sbjct: 180681144 TIDFLEFLTIKVRKMQNTKTESKKRN*ESILHVE*EDTGHVRAAAVCRDMTYLGEKLTDE 180680965

Query: 121       EVDE 124
                 EVD+
Sbjct: 180680964 EVDK 180680953


>21 dna:chromosome chromosome:NCBI36:21:1:46944323:1
          Length = 46944323

 Score = 66.2 bits (160), Expect = 4e-10
 Identities = 40/117 (34%), Positives = 66/117 (56%), Gaps = 4/117 (3%)
 Frame = -3

Query: 34       GTVMRSLGQNPTEAELQDMINEVDADGNGT--IDFPEFLTMMARKM--KDTDSEEEIREA 89
                G VMR+LGQNPT A   +++    +D      +DF  FL ++      +D  + E+  E 
Sbjct: 44100558 GGVMRALGQNPTNATALEVLGNPKSDEMNVKVLDFEHFLPLLQTVAGNRDQGT*EDYVER 44100379

Query: 90       FRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMM 146
                 +VFDK+ NG + +AE++HV+ +LGE++T E   EM+     D  G ++ E  V+ +
Sbjct: 44100378 LQVFDKEENGTVMSAEIQHVLVSLGEEMT-ERGGEMLVAGHEDSSGCIDSEVLVRRL 44100211


>3 dna:chromosome chromosome:NCBI36:3:1:199501827:1
          Length = 199501827

 Score = 62.8 bits (151), Expect = 4e-09
 Identities = 33/50 (66%), Positives = 37/50 (74%), Gaps = 1/50 (2%)
 Frame = -1

Query: 12       EFKEAFSLFDKDG-DGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
                EFK AF +F     DG I+TKELG VMR LGQNPT  ELQ+MI+EVD DG
Sbjct: 52461309 EFKAAFDIFVLGAEDGCISTKELGKVMRMLGQNPTPEELQEMIDEVDEDG 52461160



 Score = 55.5 bits (132), Expect = 7e-07
 Identities = 28/54 (51%), Positives = 35/54 (64%), Gaps = 2/54 (3%)
 Frame = -1

Query: 64       IDFPEFLTMMAR--KMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGE 115
                +DF  FL M+    K KDT + E+  E  RVFDK+GNG +  AELRHV+  LGE
Sbjct: 46876125 MDFETFLPMLQHISKNKDTGTYEDFVEGLRVFDKEGNGTVMGAELRHVLATLGE 46875964



 Score = 54.7 bits (130), Expect = 1e-06
 Identities = 31/64 (48%), Positives = 43/64 (67%), Gaps = 2/64 (3%)
 Frame = -1

Query: 63        TIDFPEFLTMMARKMKDTDSEEEIR--EAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
                 TIDF EFLT+  RKM++T +E + R  E+    + +  G++ AA +   MT LGEKLTDE
Sbjct: 199427220 TIDFLEFLTIKVRKMQNTKTESKKRN*ESILHVE*EDTGHVRAAAVCRDMTYLGEKLTDE 199427041

Query: 121       EVDE 124
                 EVD+
Sbjct: 199427040 EVDK 199427029


>22 dna:chromosome chromosome:NCBI36:22:1:49691432:1
          Length = 49691432

 Score = 60.1 bits (144), Expect = 3e-08
 Identities = 27/50 (54%), Positives = 37/50 (74%)
 Frame = +3

Query: 11       AEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
                +E +EAF +FD+DG+G I+ +ELGT MRSLG  P E EL+ +I  +D DG
Sbjct: 28453647 SEIREAFKVFDRDGNGFISKQELGTAMRSLGYMPNEVELEVIIQRLDMDG 28453796



 Score = 53.9 bits (128), Expect = 2e-06
 Identities = 25/50 (50%), Positives = 36/50 (72%)
 Frame = +3

Query: 85       EIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGD 134
                EIREAF+VFD+DGNG+IS  EL   M +LG    + E++ +I+  D+DG+
Sbjct: 28453650 EIREAFKVFDRDGNGFISKQELGTAMRSLGYMPNEVELEVIIQRLDMDGE 28453799


>1 dna:chromosome chromosome:NCBI36:1:1:247249719:1
          Length = 247249719

 Score = 56.6 bits (135), Expect = 3e-07
 Identities = 26/57 (45%), Positives = 39/57 (68%)
 Frame = +3

Query: 3       DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDAD 59
               ++L+ EQI E+K  F +FD++G+G + T EL  +M  LG NPT++EL  M  +VD D
Sbjct: 1837743 ERLSAEQIKEYKGVFEMFDEEGNGEVKTGELEWLMSLLGINPTKSELASMAKDVDRD 1837913



 Score = 54.7 bits (130), Expect = 1e-06
 Identities = 31/64 (48%), Positives = 43/64 (67%), Gaps = 2/64 (3%)
 Frame = +1

Query: 63     TIDFPEFLTMMARKMKDTDSEEEIR--EAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
              TIDF EFLT+  RKM++T +E + R  E+    + +  G++ AA +   MT LGEKLTDE
Sbjct: 657565 TIDFLEFLTIKVRKMQNTKTESKKRN*ESILHVE*EDTGHVRAAAVCRDMTYLGEKLTDE 657744

Query: 121    EVDE 124
              EVD+
Sbjct: 657745 EVDK 657756



 Score = 54.7 bits (130), Expect = 1e-06
 Identities = 31/64 (48%), Positives = 43/64 (67%), Gaps = 2/64 (3%)
 Frame = -2

Query: 63     TIDFPEFLTMMARKMKDTDSEEEIR--EAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
              TIDF EFLT+  RKM++T +E + R  E+    + +  G++ AA +   MT LGEKLTDE
Sbjct: 311786 TIDFLEFLTIKVRKMQNTKTESKKRN*ESILHVE*EDTGHVRAAAVCRDMTYLGEKLTDE 311607

Query: 121    EVDE 124
              EVD+
Sbjct: 311606 EVDK 311595



 Score = 52.4 bits (124), Expect = 6e-06
 Identities = 32/65 (49%), Positives = 42/65 (64%), Gaps = 3/65 (4%)
 Frame = +1

Query: 63        TIDFPEFLTMMARKMKDTDSEEEIRE---AFRVFDKDGNGYISAAELRHVMTNLGEKLTD 119
                 TIDF EFLT+  RKM++T ++ + R       V  KD  G++ A  + H MT LGEKLTD
Sbjct: 241289707 TIDFLEFLTIKVRKMQNTKTDSKKRN*ESILHV**KD-TGHVRAEAVCHDMTYLGEKLTD 241289883

Query: 120       EEVDE 124
                 EEVD+
Sbjct: 241289884 EEVDK 241289898



 Score = 52.0 bits (123), Expect = 8e-06
 Identities = 30/64 (46%), Positives = 42/64 (65%), Gaps = 2/64 (3%)
 Frame = +2

Query: 63     TIDFPEFLTMMARKMKDTDSEEEIR--EAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
              TI F EFLT+  RKM++T +E + R  E+    + +  G++ AA +   MT LGEKLTDE
Sbjct: 660971 TIGFLEFLTIKVRKMQNTKTESKKRN*ESILHVE*EDTGHVRAAAVCRDMTYLGEKLTDE 661150

Query: 121    EVDE 124
              EVD+
Sbjct: 661151 EVDK 661162



 Score = 52.0 bits (123), Expect = 8e-06
 Identities = 30/64 (46%), Positives = 42/64 (65%), Gaps = 2/64 (3%)
 Frame = +1

Query: 63     TIDFPEFLTMMARKMKDTDSEEEIR--EAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
              TI F EFLT+  RKM++T +E + R  E+    + +  G++ AA +   MT LGEKLTDE
Sbjct: 664387 TIGFLEFLTIKVRKMQNTKTESKKRN*ESILHVE*EDTGHVRAAAVCRDMTYLGEKLTDE 664566

Query: 121    EVDE 124
              EVD+
Sbjct: 664567 EVDK 664578


>16 dna:chromosome chromosome:NCBI36:16:1:88827254:1
          Length = 88827254

 Score = 54.7 bits (130), Expect = 1e-06
 Identities = 31/64 (48%), Positives = 43/64 (67%), Gaps = 2/64 (3%)
 Frame = -1

Query: 63       TIDFPEFLTMMARKMKDTDSEEEIR--EAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
                TIDF EFLT+  RKM++T +E + R  E+    + +  G++ AA +   MT LGEKLTDE
Sbjct: 88757546 TIDFLEFLTIKVRKMQNTKTESKKRN*ESILHVE*EDTGHVRAAAVCRDMTYLGEKLTDE 88757367

Query: 121      EVDE 124
                EVD+
Sbjct: 88757366 EVDK 88757355


>11 dna:chromosome chromosome:NCBI36:11:1:134452384:1
          Length = 134452384

 Score = 54.7 bits (130), Expect = 1e-06
 Identities = 31/64 (48%), Positives = 43/64 (67%), Gaps = 2/64 (3%)
 Frame = +2

Query: 63     TIDFPEFLTMMARKMKDTDSEEEIR--EAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE 120
              TIDF EFLT+  RKM++T +E + R  E+    + +  G++ AA +   MT LGEKLTDE
Sbjct: 123905 TIDFLEFLTIKVRKMQNTKTESKKRN*ESILHVE*EDTGHVRAAAVCRDMTYLGEKLTDE 124084

Query: 121    EVDE 124
              EVD+
Sbjct: 124085 EVDK 124096


BioPerl-1.007002/t/data/bug2453.maf000444000766000024       216013155576321 16447 0ustar00cjfieldsstaff000000000000##maf version=1 scoring=tba.v8 
# tba.v8 (((human chimp) baboon) (mouse rat)) 
# multiz.v7
# maf_project.v5 _tba_right.maf3 mouse _tba_C
# single_cov2.v4 single_cov2 /dev/stdin
                   
a score=23262.0     
s hg16.chr7    27578828 38 + 158545518 AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG
s panTro1.chr6 28741140 38 + 161576975 AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG
s baboon         116834 38 +   4622798 AAA-GGGAATGTTAACCAAATGA---GTTGTCTCTTATGGTG
s mm4.chr6     53215344 38 + 151104725 -AATGGGAATGTTAAGCAAACGA---ATTGTCTCTCAGTGTG
s rn3.chr4     81344243 40 + 187371129 -AA-GGGGATGCTAAGCCAATGAGTTGTTGTCTCTCAATGTG
                   
a score=5062.0                    
s hg16.chr7    27699739 6 + 158545518 TAAAGA
s panTro1.chr6 28862317 6 + 161576975 TAAAGA
s baboon         241163 6 +   4622798 TAAAGA 
s mm4.chr6     53303881 6 + 151104725 TAAAGA
s rn3.chr4     81444246 6 + 187371129 taagga

a score=6636.0
s hg16.chr7    27707221 13 + 158545518 gcagctgaaaaca
s panTro1.chr6 28869787 13 + 161576975 gcagctgaaaaca
s baboon         249182 13 +   4622798 gcagctgaaaaca
s mm4.chr6     53310102 13 + 151104725 ACAGCTGAAAATABioPerl-1.007002/t/data/bug2473.fasta000444000766000024       423613155576321 17012 0ustar00cjfieldsstaff000000000000# fasta34 -Q -H -E 10 -m 9 -b 1 -d 1 -r 15/-10 -g -12 -n -U ../testfiles/NAC_miRNA.fasta ../databases/cotton/CGI8.fasta
FASTA searches a protein or DNA sequence data bank
 version 3.4t25 Sept 2, 2005
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query library ../testfiles/NAC_miRNA.fasta vs ../databases/cotton/CGI8.fasta library
searching ../databases/cotton/CGI8.fasta library

  1>>>total:39860_L:12096_-3:12346_0:617_+3:14801 - 22 nt (forward-only)
 vs  ../databases/cotton/CGI8.fasta library

43526801 residues in 55673 sequences
  Expectation_n fit: rho(ln(x))= 23.6457+/-0.000561; mu= -11.6380+/- 0.037
 mean_var=607.0983+/-151.124, 0's: 0 Z-trim: 2  B-trim: 0 in 0/43
 Lambda= 0.052053

FASTA (3.47 Mar 2004) function [optimized, 15/-10 matrix (15:-10)] ktup: 2
 join: 213, opt: 198, open/ext: -12/-12, width:  16
 Scan time:  2.700
The best scores are:                                      opt bits E(55673)	%_id  %_sim   bs  alen  an0  ax0  pn0  px0  an1  ax1 pn1 px1 gapq gapl  fs 
BE054209 similar to PRF|NP_974632.1|42573071|N ( 510) [f]  286  25.6      19	0.762 0.952  286   21    1   21    1   22  471  491    1  510   0   0   0

>>>total:39860_L:12096_-3:12346_0:617_+3:14801, 22 nt vs ../databases/cotton/CGI8.fasta library

>>BE054209 similar to PRF|NP_974632.1|42573071|NP_974632 pfkB-type carbohydrate kinase family pr  (510 nt)
 initn: 286 init1: 286 opt: 286  Z-score: 111.0  bits: 25.6 E():   19
banded Smith-Waterman score: 286;  76.190% identity (95.238% similar) in 21 nt overlap (1-21:471-491)

                                             10        20                    
total:                               UUGGACAGAGUAAUCACGGUCG                  
                                     :::::..:::::: .:.::::                   
BE0542 GAACUNUCUCAGUCAAGUUUAUUAUCUGCAUUGGAUGGAGUAAAUAUGGUCUACUUUGAUGGAAGACAUC
              450       460       470       480       490       500       510



22 residues in 1 query   sequences
43526801 residues in 55673 library sequences
 Scomplib [34t25]
 start: Sat Mar 22 16:31:47 2008 done: Sat Mar 22 16:31:49 2008
 Total Scan time:  2.700 Total Display time:  0.000

Function used was FASTA [version 3.4t25 Sept 2, 2005]
BioPerl-1.007002/t/data/bug2862.pmr000444000766000024      2663413155576321 16542 0ustar00cjfieldsstaff000000000000SEQUENCE=atgNaggtgacttttatttacatcctagttattacatgttacgaaaacgacgtaaacgtttaccatattttttttcagatgtctctttggctgcctagtgaggccactgtctacttgcctcctgtcccagtatctaaNgttgtaagcacggatgaatatgttgcacgcacaaacatatattatcatgcaggaacatccagactacttgcagttggacatccctattttcctattaaaaaacctaacaataacaaaatattagttcctaaagtatcaggattacaatacagggtatttagaataNatttacctgaccccttagtgaataagtttggttttcctgacacctcattttaNaatccagatacacagcggctggtttgggcctgtgtaggtgttgaggtaggNcgtggtcagccattaggtgtgggcattagtggccatcctttattaaataaattggatgacacagaaaatgctagtgcttatgcagcaaatgcaggtgtggataatagagaatgtatatctatggattacaaacaaacacaattgtgtttaattggttgcaaaccacctataggggaacactggggcaaaggatccccatgtaNcaatgttgcagtaaNtccaggtgattgtccaccattagagttaataaacacagttattcaggatggtgatatggttgatacNggctttggtgctatggactttactacattacaggctaacaaaagtgaagttccactggatatttgtacNtctatttgcaaatatccagattatattaaaatggtgtcagaaccatatggcgacagcttatttttttatttacgaagggaacaaatgtttgttagacatttatttaatagggctggtNctgttggtgaaaatgtaccagacgatttatacattaaaggctctgggtctactgcaaatttagccagttcaaattattttcctacacctagtggttctatggttacctctgatgcccaaatattNaataaaccttattggttacaacgagcacagggccacaataatggcatttgttggggtaaccaactatttgttactgtNgtNgatactacacgcagtacaaatatgtcattatgtgctgccatatctacttcagaaNctacatataaaaaatactaactttaaNgagtacctacgacatggggaggaatatgatttacagtttatttttcaactgtgcaaaataaccttaactgcagacgttatgacatacatacattctatgaattccactattttggaggactggaattttggtNtacaacctccNccaggaggcacactagaagatacttataggtttgtaacatcccaggcaattgcttgtcaaaaacatacacctccagcacctaaagaagatgatccccttaaaaaataNactttttgggaagtaaatttaaaNgaaaagttttctgcagacctagatcagtttcctttaggacgcaaatttttactacaagcaggattNaaggccaaaccaaaatttacattaggaaaacgaaaagctacacccaccacctcatctacctctacaactgctaaacgcaaaaaacgtaagctgtaa
PRIMER_PRODUCT_SIZE_RANGE=200-1200
PRIMER_OPT_SIZE=23
PRIMER_MIN_SIZE=22
PRIMER_MAX_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_NUM_RETURN=10
PRIMER_MISPRIMING_LIBRARY=mispriming.fasta
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
PRIMER_EXPLAIN_FLAG=1
PRIMER_OPT_TM=60
PRIMER_MIN_TM=59
PRIMER_MAX_TM=61
PRIMER_LEFT_EXPLAIN=considered 4449, too many Ns 373, GC content failed 127, low tm 2109, high tm 1284, high any compl 6, high end compl 27, high repeat similarity 31, long poly-x seq 61, ok 431
PRIMER_RIGHT_EXPLAIN=considered 4370, too many Ns 400, GC content failed 120, low tm 2106, high tm 1190, high any compl 2, high end compl 6, high repeat similarity 6, long poly-x seq 58, ok 482
PRIMER_PAIR_EXPLAIN=considered 343, unacceptable product size 320, ok 23
PRIMER_PAIR_PENALTY=0.1407
PRIMER_LEFT_PENALTY=0.081493
PRIMER_RIGHT_PENALTY=0.059210
PRIMER_LEFT_SEQUENCE=tgtgctgccatatctacttcaga
PRIMER_RIGHT_SEQUENCE=taggtgctggaggtgtatgtttt
PRIMER_LEFT=1116,23
PRIMER_RIGHT=1393,23
PRIMER_LEFT_TM=59.919
PRIMER_RIGHT_TM=59.941
PRIMER_LEFT_GC_PERCENT=43.478
PRIMER_RIGHT_GC_PERCENT=43.478
PRIMER_LEFT_SELF_ANY=4.00
PRIMER_RIGHT_SELF_ANY=2.00
PRIMER_LEFT_SELF_END=3.00
PRIMER_RIGHT_SELF_END=0.00
PRIMER_LEFT_MISPRIMING_SCORE=11.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
PRIMER_RIGHT_MISPRIMING_SCORE=12.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.
PRIMER_PAIR_MISPRIMING_SCORE=20.00, reverse EF177179 Human papillomavirus type 56 clone Qv22608, complete genome.
PRIMER_LEFT_END_STABILITY=6.7000
PRIMER_RIGHT_END_STABILITY=7.0000
PRIMER_PAIR_COMPL_ANY=5.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=278
PRIMER_PAIR_PENALTY_1=0.1407
PRIMER_LEFT_1_PENALTY=0.081493
PRIMER_RIGHT_1_PENALTY=0.059210
PRIMER_LEFT_1_SEQUENCE=tgtgctgccatatctacttcaga
PRIMER_RIGHT_1_SEQUENCE=ttaggtgctggaggtgtatgttt
PRIMER_LEFT_1=1116,23
PRIMER_RIGHT_1=1394,23
PRIMER_LEFT_1_TM=59.919
PRIMER_RIGHT_1_TM=59.941
PRIMER_LEFT_1_GC_PERCENT=43.478
PRIMER_RIGHT_1_GC_PERCENT=43.478
PRIMER_LEFT_1_SELF_ANY=4.00
PRIMER_RIGHT_1_SELF_ANY=2.00
PRIMER_LEFT_1_SELF_END=3.00
PRIMER_RIGHT_1_SELF_END=0.00
PRIMER_LEFT_1_MISPRIMING_SCORE=11.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
PRIMER_RIGHT_1_MISPRIMING_SCORE=11.00, EF202156 Human papillomavirus type 45 isolate Qv20214, complete genome.
PRIMER_PAIR_1_MISPRIMING_SCORE=20.00, EF202156 Human papillomavirus type 45 isolate Qv20214, complete genome.
PRIMER_LEFT_1_END_STABILITY=6.7000
PRIMER_RIGHT_1_END_STABILITY=7.0000
PRIMER_PAIR_1_COMPL_ANY=5.00
PRIMER_PAIR_1_COMPL_END=1.00
PRIMER_PRODUCT_SIZE_1=279
PRIMER_PAIR_PENALTY_2=0.1407
PRIMER_LEFT_2_PENALTY=0.081493
PRIMER_RIGHT_2_PENALTY=0.059210
PRIMER_LEFT_2_SEQUENCE=tgtgctgccatatctacttcaga
PRIMER_RIGHT_2_SEQUENCE=tttaggtgctggaggtgtatgtt
PRIMER_LEFT_2=1116,23
PRIMER_RIGHT_2=1395,23
PRIMER_LEFT_2_TM=59.919
PRIMER_RIGHT_2_TM=59.941
PRIMER_LEFT_2_GC_PERCENT=43.478
PRIMER_RIGHT_2_GC_PERCENT=43.478
PRIMER_LEFT_2_SELF_ANY=4.00
PRIMER_RIGHT_2_SELF_ANY=2.00
PRIMER_LEFT_2_SELF_END=3.00
PRIMER_RIGHT_2_SELF_END=0.00
PRIMER_LEFT_2_MISPRIMING_SCORE=11.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
PRIMER_RIGHT_2_MISPRIMING_SCORE=11.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.
PRIMER_PAIR_2_MISPRIMING_SCORE=20.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
PRIMER_LEFT_2_END_STABILITY=6.7000
PRIMER_RIGHT_2_END_STABILITY=6.6000
PRIMER_PAIR_2_COMPL_ANY=5.00
PRIMER_PAIR_2_COMPL_END=2.00
PRIMER_PRODUCT_SIZE_2=280
PRIMER_PAIR_PENALTY_3=0.2276
PRIMER_LEFT_3_PENALTY=0.081493
PRIMER_RIGHT_3_PENALTY=0.146140
PRIMER_LEFT_3_SEQUENCE=tgtgctgccatatctacttcaga
PRIMER_RIGHT_3_SEQUENCE=aaggggatcatcttctttaggtg
PRIMER_LEFT_3=1116,23
PRIMER_RIGHT_3=1410,23
PRIMER_LEFT_3_TM=59.919
PRIMER_RIGHT_3_TM=59.854
PRIMER_LEFT_3_GC_PERCENT=43.478
PRIMER_RIGHT_3_GC_PERCENT=43.478
PRIMER_LEFT_3_SELF_ANY=4.00
PRIMER_RIGHT_3_SELF_ANY=7.00
PRIMER_LEFT_3_SELF_END=3.00
PRIMER_RIGHT_3_SELF_END=1.00
PRIMER_LEFT_3_MISPRIMING_SCORE=11.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
PRIMER_RIGHT_3_MISPRIMING_SCORE=11.00, X74481 Human papillomavirus type 52 genomic DNA.
PRIMER_PAIR_3_MISPRIMING_SCORE=20.00, DQ057317 Human papillomavirus type 52 isolate HK1151 L1 protein (L1) gene, partial cds.
PRIMER_LEFT_3_END_STABILITY=6.7000
PRIMER_RIGHT_3_END_STABILITY=7.9000
PRIMER_PAIR_3_COMPL_ANY=4.00
PRIMER_PAIR_3_COMPL_END=2.00
PRIMER_PRODUCT_SIZE_3=295
PRIMER_PAIR_PENALTY_4=0.2322
PRIMER_LEFT_4_PENALTY=0.173020
PRIMER_RIGHT_4_PENALTY=0.059210
PRIMER_LEFT_4_SEQUENCE=actgcaaatttagccagttcaaa
PRIMER_RIGHT_4_SEQUENCE=tttaggtgctggaggtgtatgtt
PRIMER_LEFT_4=930,23
PRIMER_RIGHT_4=1395,23
PRIMER_LEFT_4_TM=60.173
PRIMER_RIGHT_4_TM=59.941
PRIMER_LEFT_4_GC_PERCENT=34.783
PRIMER_RIGHT_4_GC_PERCENT=43.478
PRIMER_LEFT_4_SELF_ANY=8.00
PRIMER_RIGHT_4_SELF_ANY=2.00
PRIMER_LEFT_4_SELF_END=2.00
PRIMER_RIGHT_4_SELF_END=0.00
PRIMER_LEFT_4_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
PRIMER_RIGHT_4_MISPRIMING_SCORE=11.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.
PRIMER_PAIR_4_MISPRIMING_SCORE=19.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
PRIMER_LEFT_4_END_STABILITY=7.3000
PRIMER_RIGHT_4_END_STABILITY=6.6000
PRIMER_PAIR_4_COMPL_ANY=4.00
PRIMER_PAIR_4_COMPL_END=2.00
PRIMER_PRODUCT_SIZE_4=466
PRIMER_PAIR_PENALTY_5=0.2322
PRIMER_LEFT_5_PENALTY=0.173020
PRIMER_RIGHT_5_PENALTY=0.059210
PRIMER_LEFT_5_SEQUENCE=actgcaaatttagccagttcaaa
PRIMER_RIGHT_5_SEQUENCE=taggtgctggaggtgtatgtttt
PRIMER_LEFT_5=930,23
PRIMER_RIGHT_5=1393,23
PRIMER_LEFT_5_TM=60.173
PRIMER_RIGHT_5_TM=59.941
PRIMER_LEFT_5_GC_PERCENT=34.783
PRIMER_RIGHT_5_GC_PERCENT=43.478
PRIMER_LEFT_5_SELF_ANY=8.00
PRIMER_RIGHT_5_SELF_ANY=2.00
PRIMER_LEFT_5_SELF_END=2.00
PRIMER_RIGHT_5_SELF_END=0.00
PRIMER_LEFT_5_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
PRIMER_RIGHT_5_MISPRIMING_SCORE=12.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.
PRIMER_PAIR_5_MISPRIMING_SCORE=21.00, reverse PPHT39 Human papillomavirus ORFs.
PRIMER_LEFT_5_END_STABILITY=7.3000
PRIMER_RIGHT_5_END_STABILITY=7.0000
PRIMER_PAIR_5_COMPL_ANY=4.00
PRIMER_PAIR_5_COMPL_END=3.00
PRIMER_PRODUCT_SIZE_5=464
PRIMER_PAIR_PENALTY_6=0.2322
PRIMER_LEFT_6_PENALTY=0.173020
PRIMER_RIGHT_6_PENALTY=0.059210
PRIMER_LEFT_6_SEQUENCE=actgcaaatttagccagttcaaa
PRIMER_RIGHT_6_SEQUENCE=ttaggtgctggaggtgtatgttt
PRIMER_LEFT_6=930,23
PRIMER_RIGHT_6=1394,23
PRIMER_LEFT_6_TM=60.173
PRIMER_RIGHT_6_TM=59.941
PRIMER_LEFT_6_GC_PERCENT=34.783
PRIMER_RIGHT_6_GC_PERCENT=43.478
PRIMER_LEFT_6_SELF_ANY=8.00
PRIMER_RIGHT_6_SELF_ANY=2.00
PRIMER_LEFT_6_SELF_END=2.00
PRIMER_RIGHT_6_SELF_END=0.00
PRIMER_LEFT_6_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
PRIMER_RIGHT_6_MISPRIMING_SCORE=11.00, EF202156 Human papillomavirus type 45 isolate Qv20214, complete genome.
PRIMER_PAIR_6_MISPRIMING_SCORE=20.00, reverse PPHT39 Human papillomavirus ORFs.
PRIMER_LEFT_6_END_STABILITY=7.3000
PRIMER_RIGHT_6_END_STABILITY=7.0000
PRIMER_PAIR_6_COMPL_ANY=4.00
PRIMER_PAIR_6_COMPL_END=3.00
PRIMER_PRODUCT_SIZE_6=465
PRIMER_PAIR_PENALTY_7=0.2545
PRIMER_LEFT_7_PENALTY=0.173020
PRIMER_RIGHT_7_PENALTY=0.081493
PRIMER_LEFT_7_SEQUENCE=actgcaaatttagccagttcaaa
PRIMER_RIGHT_7_SEQUENCE=tctgaagtagatatggcagcaca
PRIMER_LEFT_7=930,23
PRIMER_RIGHT_7=1138,23
PRIMER_LEFT_7_TM=60.173
PRIMER_RIGHT_7_TM=59.919
PRIMER_LEFT_7_GC_PERCENT=34.783
PRIMER_RIGHT_7_GC_PERCENT=43.478
PRIMER_LEFT_7_SELF_ANY=8.00
PRIMER_RIGHT_7_SELF_ANY=4.00
PRIMER_LEFT_7_SELF_END=2.00
PRIMER_RIGHT_7_SELF_END=3.00
PRIMER_LEFT_7_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
PRIMER_RIGHT_7_MISPRIMING_SCORE=12.00, reverse FJ385268 Human papillomavirus type 58 isolate HPV58sc78, complete genome.
PRIMER_PAIR_7_MISPRIMING_SCORE=19.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
PRIMER_LEFT_7_END_STABILITY=7.3000
PRIMER_RIGHT_7_END_STABILITY=8.2000
PRIMER_PAIR_7_COMPL_ANY=5.00
PRIMER_PAIR_7_COMPL_END=2.00
PRIMER_PRODUCT_SIZE_7=209
PRIMER_PAIR_PENALTY_8=0.3192
PRIMER_LEFT_8_PENALTY=0.173020
PRIMER_RIGHT_8_PENALTY=0.146140
PRIMER_LEFT_8_SEQUENCE=actgcaaatttagccagttcaaa
PRIMER_RIGHT_8_SEQUENCE=aaggggatcatcttctttaggtg
PRIMER_LEFT_8=930,23
PRIMER_RIGHT_8=1410,23
PRIMER_LEFT_8_TM=60.173
PRIMER_RIGHT_8_TM=59.854
PRIMER_LEFT_8_GC_PERCENT=34.783
PRIMER_RIGHT_8_GC_PERCENT=43.478
PRIMER_LEFT_8_SELF_ANY=8.00
PRIMER_RIGHT_8_SELF_ANY=7.00
PRIMER_LEFT_8_SELF_END=2.00
PRIMER_RIGHT_8_SELF_END=1.00
PRIMER_LEFT_8_MISPRIMING_SCORE=10.00, J04353 Human papillomavirus type 31 (HPV-31) complete genome.
PRIMER_RIGHT_8_MISPRIMING_SCORE=11.00, X74481 Human papillomavirus type 52 genomic DNA.
PRIMER_PAIR_8_MISPRIMING_SCORE=19.00, X74481 Human papillomavirus type 52 genomic DNA.
PRIMER_LEFT_8_END_STABILITY=7.3000
PRIMER_RIGHT_8_END_STABILITY=7.9000
PRIMER_PAIR_8_COMPL_ANY=3.00
PRIMER_PAIR_8_COMPL_END=2.00
PRIMER_PRODUCT_SIZE_8=481
PRIMER_PAIR_PENALTY_9=0.3690
PRIMER_LEFT_9_PENALTY=0.309788
PRIMER_RIGHT_9_PENALTY=0.059210
PRIMER_LEFT_9_SEQUENCE=atgctagtgcttatgcagcaaat
PRIMER_RIGHT_9_SEQUENCE=taggtgctggaggtgtatgtttt
PRIMER_LEFT_9=475,23
PRIMER_RIGHT_9=1393,23
PRIMER_LEFT_9_TM=60.310
PRIMER_RIGHT_9_TM=59.941
PRIMER_LEFT_9_GC_PERCENT=39.130
PRIMER_RIGHT_9_GC_PERCENT=43.478
PRIMER_LEFT_9_SELF_ANY=6.00
PRIMER_RIGHT_9_SELF_ANY=2.00
PRIMER_LEFT_9_SELF_END=3.00
PRIMER_RIGHT_9_SELF_END=0.00
PRIMER_LEFT_9_MISPRIMING_SCORE=12.00, EU918766 Human papillomavirus type 33 isolate LZcc12-33, complete genome.
PRIMER_RIGHT_9_MISPRIMING_SCORE=12.00, U45909 Human papillomavirus type 45, isolate IS252, major capsid protein L1 (L1) gene, partial cds.
PRIMER_PAIR_9_MISPRIMING_SCORE=22.00, reverse PPHT39 Human papillomavirus ORFs.
PRIMER_LEFT_9_END_STABILITY=7.2000
PRIMER_RIGHT_9_END_STABILITY=7.0000
PRIMER_PAIR_9_COMPL_ANY=5.00
PRIMER_PAIR_9_COMPL_END=2.00
PRIMER_PRODUCT_SIZE_9=919
=
BioPerl-1.007002/t/data/bug2869.tree000444000766000024       565713155576321 16674 0ustar00cjfieldsstaff000000000000((((((((EMBOSS_045:-0.50000,EMBOSS_025:-0.50000):1.79848,
((EMBOSS_027:-0.50000,EMBOSS_047:-0.50000):0.99824,EMBOSS_034:0.49824):0.80024):0.34147,
EMBOSS_028:1.63995):0.22536,(((EMBOSS_092:-0.50000,EMBOSS_056:-0.50000):1.34396,
EMBOSS_023:0.84396):0.80613,((EMBOSS_013:-0.50000,EMBOSS_082:-0.50000):0.00000,
EMBOSS_094:-0.50000):2.15010):0.21521):0.06350,(((((EMBOSS_074:-0.50000,
EMBOSS_091:-0.50000):1.31318,EMBOSS_029:0.81318):0.71221,
((EMBOSS_100:-0.50000,EMBOSS_003:-0.50000):1.23223,EMBOSS_057:0.73223):0.79316):0.12013,
((EMBOSS_039:-0.50000,EMBOSS_070:-0.50000):1.87273,((EMBOSS_066:-0.50000,
EMBOSS_033:-0.50000):0.98761,EMBOSS_058:0.48761):0.88512):0.27280):0.23680,
(((((EMBOSS_041:-0.50000,EMBOSS_032:-0.50000):0.00000,EMBOSS_044:-0.50000):1.48759,
EMBOSS_018:0.98759):0.33203,(EMBOSS_048:-0.50000,EMBOSS_086:-0.50000):1.81961):0.41964,
(EMBOSS_012:-0.50000,EMBOSS_073:-0.50000):2.23925):0.14308):0.04648):0.02893,
(((((EMBOSS_055:1.46450,EMBOSS_008:1.46450):0.08397,EMBOSS_036:1.54848):0.17955,
(EMBOSS_076:-0.50000,EMBOSS_038:-0.50000):2.22802):0.04384,
EMBOSS_005:1.77186):0.12747,((((EMBOSS_075:-0.50000,EMBOSS_096:-0.50000):1.25986,
EMBOSS_022:0.75986):0.82110,((EMBOSS_019:-0.50000,EMBOSS_031:-0.50000):1.19971,
EMBOSS_098:0.69971):0.88125):0.23169,(((EMBOSS_097:-0.50000,
EMBOSS_014:-0.50000):1.10683,EMBOSS_042:0.60683):0.57915,
EMBOSS_009:1.18599):0.62667):0.08668):0.05840):0.00595,(((((EMBOSS_001:1.42164,
EMBOSS_089:1.42164):0.15376,EMBOSS_093:1.57540):0.15734,
(((EMBOSS_037:-0.50000,EMBOSS_004:-0.50000):0.00000,EMBOSS_067:-0.50000):1.63853,
(EMBOSS_071:-0.50000,EMBOSS_015:-0.50000):1.63853):0.59421):0.17397,
(((((EMBOSS_054:-0.50000,EMBOSS_026:-0.50000):1.22934,EMBOSS_052:0.72934):0.95330,
EMBOSS_095:1.68264):0.15887,((EMBOSS_068:1.44021,EMBOSS_072:1.44021):0.17219,
((((EMBOSS_065:-0.50000,EMBOSS_062:-0.50000):0.00000,EMBOSS_059:-0.50000):1.53425,
EMBOSS_046:1.03425):0.27633,EMBOSS_087:1.31058):0.30183):0.22910):0.02311,
(((EMBOSS_080:-0.50000,EMBOSS_002:-0.50000):0.98801,EMBOSS_021:0.48801):1.00237,
((EMBOSS_035:-0.50000,EMBOSS_088:-0.50000):1.31447,EMBOSS_010:0.81447):0.67592):0.37423):0.04210):0.04173,
((((EMBOSS_078:-0.50000,EMBOSS_063:-0.50000):0.97078,EMBOSS_053:0.47078):1.01179,
(EMBOSS_049:-0.50000,EMBOSS_030:-0.50000):1.98257):0.35719,
(((EMBOSS_079:-0.50000,EMBOSS_060:-0.50000):1.03209,EMBOSS_007:0.53209):1.08158,
((EMBOSS_040:-0.50000,EMBOSS_077:-0.50000):1.91905,(EMBOSS_017:-0.50000,
EMBOSS_016:-0.50000):1.91905):0.19462):0.22610):0.10868):0.01525):0.01135,
((((((EMBOSS_011:-0.50000,EMBOSS_043:-0.50000):0.00000,EMBOSS_064:-0.50000):1.93262,
(EMBOSS_090:-0.50000,EMBOSS_006:-0.50000):1.93262):0.13110,
((EMBOSS_051:-0.50000,EMBOSS_069:-0.50000):1.20725,EMBOSS_085:0.70725):0.85647):0.22219,
((EMBOSS_050:-0.50000,EMBOSS_024:-0.50000):1.28332,(EMBOSS_083:-0.50000,
EMBOSS_084:-0.50000):1.28332):1.00259):0.12842,(((EMBOSS_099:-0.50000,
EMBOSS_061:-0.50000):1.27575,EMBOSS_020:0.77575):1.03830,
EMBOSS_081:1.81405):0.10028):0.06072);
BioPerl-1.007002/t/data/bug2901.fa000444000766000024        35713155576321 16256 0ustar00cjfieldsstaff000000000000>seq1
GGTACCAGCAGGTGGGCCGCCTACTGCGCACGCGCGGGTTTGCGGGCAGCCGC
>seq2
GGTACCAGCTGGTGGGCCGCCTACTGCGCACGCGCGGGTTTGCGGGCAGCCGC
>seq3
GGTACCAGCAGGTGGTCCGCCTA------------------------------
>seq4
--------------------------CGCACGCGCGTGTTTGCGGGCAGCCGCBioPerl-1.007002/t/data/bug2937.fasta000444000766000024       764613155576321 17027 0ustar00cjfieldsstaff000000000000 /usr/local/fasta3/bin/fasta35 -O test_revcomp.fasta35 test_revcomp.fa clusters.fasta
FASTA searches a protein or DNA sequence data bank version 35.04 Mar. 26, 2009
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query: ILTV-miR1, 70 nt
  1>>>ILTV-miR1  - 70 nt - 70 nt
Library: clusters.fasta 3924656 residues in 179575 sequences

       opt      E()
< 20  8261     0:==============================
  22    16     0:=          one = represents 279 library sequences
  24     5     0:=
  26    38     4:*
  28   262    41:*
  30   712   247:*==
  32  1499   956:===*==
  34  4618  2593:=========*=======
  36  5199  5325:===================*
  38  7360  8800:===========================    *
  40  9090 12276:=================================          *
  42 15194 15005:=====================================================*=
  44 16710 16552:===========================================================*
  46 14217 16859:===================================================        *
  48 11294 16141:=========================================                *
  50 13398 14728:=================================================   *
  52 14142 12949:==============================================*====
  54 10605 11060:=======================================*
  56  6654  9239:========================         *
  58  7042  7585:========================== *
  60  7276  6144:======================*====
  62  9388  4926:=================*================
  64  3357  3918:============= *
  66  3240  3096:===========*
  68  3655  2435:========*=====
  70  1842  1909:======*
  72  1001  1491:==== *
  74   718  1163:=== *
  76   747   905:===*
  78   478   703:==*
  80   334   546:=*
  82   284   418:=*
  84   196   331:=*
  86   156   256:*
  88   126   198:*          inset = represents 2 library sequences
  90    96   153:*
  92    79   119:*         :=======================================*
  94    47    92:*         :========================               *
  96    40    71:*         :====================               *
  98    33    55:*         :=================          *
 100    24    43:*         :============         *
 102    12    33:*         :======          *
 104    15    25:*         :========    *
 106     9    20:*         :=====    *
 108     6    15:*         :===    *
 110     0    12:*         :     *
 112     0     9:*         :    *
 114     1     7:*         :=  *
 116     1     5:*         := *
 118     1     4:*         :=*
>120    94     3:*         :=*======================================
3924656 residues in 179575 sequences
Statistics:  Expectation_n fit: rho(ln(x))= 6.7921+/-0.000406; mu= 7.9651+/- 0.013
 mean_var=36.4967+/-12.281, 0's: 2734 Z-trim: 2761  B-trim: 0 in 0/14
 Lambda= 0.212299
 statistics sampled from 60000 to 179478 sequences
 Kolmogorov-Smirnov  statistic: 0.0718 (N=29) at  58
Algorithm: FASTA (3.5 Sept 2006) [optimized]
Parameters: +5/-4 matrix (5:-4) ktup: 3
 join: 60, opt: 45, open/ext: -12/-4, width:  16

The best scores are:                                      opt bits E(179572)
cluster_79238:1                                (  27) [r]  126 41.0 0.00012


>>cluster_79238:1                                         (27 nt)
rev-comp initn: 125 init1: 125 opt: 126  Z-score: 208.3  bits: 41.0 E(): 0.00012
banded Smith-Waterman score: 126; 96.3% identity (96.3% similar) in 27 nt overlap (29-3:1-27)

     60        50        40        30        20        10         
ILTV-- TGATTGGGGAATGATTGGGAAGCTTGTGCCAATTCCATTCCTCTTTCTGTCTCCACCGC
                                     ::::::::::::::::::::::::: :  
cluste                               AATTCCATTCCTCTTTCTGTCTCCAAC  
                                             10        20         



70 residues in 1 query   sequences
3924656 residues in 179575 library sequences
 Scomplib [35.04]
 start: Tue Oct 27 08:58:20 2009 done: Tue Oct 27 08:58:25 2009
 Total Scan time:  1.360 Total Display time:  0.000

Function used was FASTA [version 35.04 Mar. 26, 2009]
BioPerl-1.007002/t/data/bug2942.blastx000555000766000024      4522513155576321 17240 0ustar00cjfieldsstaff000000000000BLASTX 2.0MP-WashU [04-May-2006] [linux26-x64-I32LPF64 2006-05-10T17:22:28]

Copyright (C) 1996-2006 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2006) http://blast.wustl.edu
Gish, Warren and David J. States (1993).  Identification of protein coding
regions by database similarity search.  Nat. Genet. 3:266-72.

Query=  MySampleSeq
        (14,601 letters)

  Translating both strands of query sequence in all 6 reading frames

Database:  UNIPROT_B9GCX0
           1 sequences; 3829 total letters.
Searching done

                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

UNIPROT:B9GCX0 |B9GCX0|B9GCX0|SubName: Full=Putative unch...  7596  0.       11


>UNIPROT:B9GCX0 |B9GCX0|B9GCX0|SubName: Full=Putative uncharacterized protein;
            |Oryza sativa subsp japonica (Rice) |AA|3829
        Length = 3829

  Minus Strand HSPs:

 Score = 7596 (2679.0 bits), Expect = 0., Sum P(11) = 0., Group = 1
 Identities = 1533/2058 (74%), Positives = 1675/2058 (81%), Frame = -2

Query: 10205 PGQTSDKGKSSNLCVIHIPDMHLQKEDDLSILKQCVDKFNVPPEHRFALLTRIRYARAFN 10026
             P Q+SDK K SNLCVIHIPD+HLQKEDDLSILKQCVDKFNVP EHRF+L TRIRYA AFN
Sbjct:   435 PDQSSDKAKPSNLCVIHIPDLHLQKEDDLSILKQCVDKFNVPSEHRFSLFTRIRYAHAFN 494

Query: 10025 SARTCRIYSRISLLSFIVLVQSSDAHDELTYFFTNEPEYINELIRLVRSEDSVPGSIRXX 9846
             S RTCR+YSRISLL+FIVLVQSSDAHDELT FFTNEPEYINELIRLVRSE+ VPG IR  
Sbjct:   495 SPRTCRLYSRISLLAFIVLVQSSDAHDELTSFFTNEPEYINELIRLVRSEEFVPGPIRAL 554

Query:  9845 XXXXXXXXXXXXXSSHERARXXXXXXXXXXXXNRMVLLSVLQKAISSLNSLNDTSSPLIV 9666
                          SSHERAR            NRMVLLSVLQKAISSL+S NDTSSPLIV
Sbjct:   555 AMLALGAQLAAYASSHERARILSGSSIISAGGNRMVLLSVLQKAISSLSSPNDTSSPLIV 614

Query:  9665 DAXXXXXXXXXXXXXXXGTTVRGSGMVXXXXXXXRDNDPSHMHLVCLAVKTLQKLMEYSS 9486
             DA               GTTVRGSGMV       +DNDPSHMHLVCLAVKTLQKLMEYSS
Sbjct:   615 DALLQFFLLHVLSSSSSGTTVRGSGMVPPLLPLLQDNDPSHMHLVCLAVKTLQKLMEYSS 674

Query:  9485 PAVSLFKDLGGVELLSQRLHVEVQRVIGTADGHNSMVT-DAVKSDDNHMYSQKRLIKALL 9309
             PAVSLFKDLGGVELLSQRLHVEVQRVIG  D HNSMVT DA+KS+++H+YSQKRLIKALL
Sbjct:   675 PAVSLFKDLGGVELLSQRLHVEVQRVIGV-DSHNSMVTSDALKSEEDHLYSQKRLIKALL 733

Query:  9308 KALGSATYSPGNPARSQSSQDNSLPVSLSLIFQNVDKFGGDIYFSAVTVMSEIIHKDPTC 9129
             KALGSATYSP NPARSQSS DNSLP+SLSLIFQNVDKFGGDIYFSAVTVMSEIIHKDPTC
Sbjct:   734 KALGSATYSPANPARSQSSNDNSLPISLSLIFQNVDKFGGDIYFSAVTVMSEIIHKDPTC 793

Query:  9128 FITLKELGVPDAFISSVTAGVIPSCKALICVPNGLGAICLNNQGLEAVRETSALRFLVDT 8949
             F +LKELG+PDAF+SSV+AGVIPSCKALICVPNGLGAICLNNQGLEAVRETSALRFLVDT
Sbjct:   794 FPSLKELGLPDAFLSSVSAGVIPSCKALICVPNGLGAICLNNQGLEAVRETSALRFLVDT 853

Query:  8948 FTSRKYLIPMNEGXXXXXXXXXXXXRHVQSLRSIGVDIIIEIINKLSSSQEYKNNE-TAT 8772
             FTSRKYLIPMNEG            RHVQSLRS GVDIIIEIINKLSS +E K+NE  A+
Sbjct:   854 FTSRKYLIPMNEGVVLLANAVEELLRHVQSLRSTGVDIIIEIINKLSSPREDKSNEPAAS 913

Query:  8771 LQEKTDMETDVEGRDLVSAMDSSVDGSNDEQFSHLSIFHVMVLVHRTMENSETCRLFVEK 8592
               E+T+METD EGRDLVSAMDSS DG+NDEQFSHLSIFHVMVLVHRTMENSETCRLFVEK
Sbjct:   914 SDERTEMETDAEGRDLVSAMDSSEDGTNDEQFSHLSIFHVMVLVHRTMENSETCRLFVEK 973

Query:  8591 GGXXXXXXXXXRPSITQSSGGMPIALHSTMVFKGFTQHHSTPLARAFCSSLKEHLKSALK 8412
             GG         RPSITQSSGGMPIALHSTMVFKGFTQHHSTPLARAFCSSLKEHLK+AL+
Sbjct:   974 GGLQALLTLLLRPSITQSSGGMPIALHSTMVFKGFTQHHSTPLARAFCSSLKEHLKNALQ 1033

Query:  8411 ELDKVSNSFDMTKIEKGAIPSXXXXXXXXXXAASKDNRWMNALLSEFGDASREVLEDVGQ 8232
             ELD V++S ++ K+EKGAIPS          AASKDNRWMNALLSEFGD+SR+VLED+G+
Sbjct:  1034 ELDTVASSGEVAKLEKGAIPSLFVVEFLLFLAASKDNRWMNALLSEFGDSSRDVLEDIGR 1093

Query:  8231 VHREVLWKISLFEKNKIVXXXXXXXXXXXXXXPDMSASDIGDSRYTSFRQYLDPILRRRG 8052
             VHREVLW+ISLFE+ K+                D +  D+ DSRYTSFRQYLDP+LRRRG
Sbjct:  1094 VHREVLWQISLFEEKKV--EPETSSPLANDSQQDAAVGDVDDSRYTSFRQYLDPLLRRRG 1151

Query:  8051 SGWNIESQVSDLINMYRDIGRAASDSQRVGSDRYSSLGLPXXXXXXXX-XXXXXXXXTRX 7875
             SGWNIESQVSDLIN+YRDIGRAA DSQR     Y S GLP                 T+ 
Sbjct:  1152 SGWNIESQVSDLINIYRDIGRAAGDSQR-----YPSAGLPSSSSQDQPPSSSDASASTKS 1206

Query:  7874 XXXXXXXXXXXCFDMMRSLSYHINHLFLELGKAMLFASRRENSPVNLSPAVISVANNIAS 7695
                        C DMMRSLSYHINHLF+ELGKAML  SRRENSPVNLS +++SVA+NIAS
Sbjct:  1207 EEDKKRSEHSSCCDMMRSLSYHINHLFMELGKAMLLTSRRENSPVNLSASIVSVASNIAS 1266

Query:  7694 IVLEHLNFEGHSVSFERDMTVTTKCRYLGKVVEFVDGMLLDRPESCNSIMVNSFYCRGVI 7515
             IVLEHLNFEGH++S ER+ TV+TKCRYLGKVVEF+DG+LLDRPESCN IM+NSFYCRGVI
Sbjct:  1267 IVLEHLNFEGHTISSERETTVSTKCRYLGKVVEFIDGILLDRPESCNPIMLNSFYCRGVI 1326

Query:  7514 QAILTTFQATSELLFTMSRPPSSPMETDSKTGKDGKEMDSSWIYGPLTSYGAIMDHLVTS 7335
             QAILTTF+ATSELLF+M+R PSSPMETDSK+ K+ +E DSSWIYGPL+SYGAI+DHLVTS
Sbjct:  1327 QAILTTFEATSELLFSMNRLPSSPMETDSKSVKEDRETDSSWIYGPLSSYGAILDHLVTS 1386

Query:  7334 SFILSSSTRQLLEQPIFNGSVRFPQDAETFMKLLQSKVLKTVLPIWAHPQFPECNIELIS 7155
             SFILSSSTRQLLEQPIF+G++RFPQDAE FMKLLQS+VLKTVLPIW HPQFPECN+ELIS
Sbjct:  1387 SFILSSSTRQLLEQPIFSGNIRFPQDAEKFMKLLQSRVLKTVLPIWTHPQFPECNVELIS 1446

Query:  7154 SVMSIMRHVCSGVEVKDTVGNGGARLAGPPPDESAISLIVEMGFSRARAEEALRQVGTNS 6975
             SV SIMRHV SGVEVK+T  N GARLAGPPPDE+AISLIVEMGFSRARAEEALRQVGTNS
Sbjct:  1447 SVTSIMRHVYSGVEVKNTAINTGARLAGPPPDENAISLIVEMGFSRARAEEALRQVGTNS 1506

Query:  6974 VEIATDWLFAHPEEPQEEDDELARALAMSLGNSVTPAQEGDSRSNDLELEEATVQPPPID 6795
             VEIATDWLF+HPEEPQE DDELARALAMSLGNS T AQE D +SNDLELEE TVQ PPID
Sbjct:  1507 VEIATDWLFSHPEEPQE-DDELARALAMSLGNSDTSAQEEDGKSNDLELEEETVQLPPID 1565

Query:  6794 EMLRSCLQLLQRKEALAFSVRDMLVTISSQNDGQNRVKVLTYLIDNLKQCVVASEPSNDT 6615
             E+L SCL+LLQ KE+LAF VRDML+T+SSQNDGQNRVKVLTYLID+LK C+++S+P   T
Sbjct:  1566 EVLSSCLRLLQTKESLAFPVRDMLLTMSSQNDGQNRVKVLTYLIDHLKNCLMSSDPLKST 1625

Query:  6614 XXXXXXXXXXXXXHGDTAAREVASKAGLVKVALDLLCSWEVQIRESSMIEVPNWVISCFL 6435
                          HGDTAAREVASKAGLVKVAL+LLCSWE++ R+  + +VPNWV SCFL
Sbjct:  1626 ALSALFHVLALILHGDTAAREVASKAGLVKVALNLLCSWELEPRQGEISDVPNWVPSCFL 1685

Query:  6434 SVDQMLQLEPKLPDVTELHVLKRDNSNIKTSLVIDDSKRKDSESLPNVGLLDMEDQFQLL 6255
             S+D+MLQL+PKLPDVTEL VLK+DNSN +TS+VIDDSK+KDSE+  + GLLD+EDQ QLL
Sbjct:  1686 SIDRMLQLDPKLPDVTELDVLKKDNSNTQTSVVIDDSKKKDSEASSSTGLLDLEDQKQLL 1745

Query:  6254 KICCKCIGKQLPSASMHAILQLSATLTKVHAAAICFLESGGLNALLSLPTSSLFSGFNNM 6075
             KICCKCI KQLPSA+MHAILQL ATLTK+HAAAICFLESGGL+ALLSLPTSSLFSGFN++
Sbjct:  1746 KICCKCIQKQLPSATMHAILQLCATLTKLHAAAICFLESGGLHALLSLPTSSLFSGFNSV 1805

Query:  6074 ASTIIRHILEDPHTLQQAMELEIRHSLVTAANRHANPRVTPRNFIQNLAFVVYRDPVIFM 5895
             ASTIIRHILEDPHTLQQAMELEIRHSLVTAANRHANPRVTPRNF+QNLAFVVYRDPVIFM
Sbjct:  1806 ASTIIRHILEDPHTLQQAMELEIRHSLVTAANRHANPRVTPRNFVQNLAFVVYRDPVIFM 1865

Query:  5894 KAAQSVCQIEMVGDRPYVVLLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSGDTAAGSP 5715
             KAAQ+VCQIEMVGDRPYVVLL                              SGD A GSP
Sbjct:  1866 KAAQAVCQIEMVGDRPYVVLLKDREKEKNKEKEKDKPADKDKTSGAATKMTSGDMALGSP 1925

Query:  5714 ANSHGKQSDLNSRNVKSHRKPPQSFVTVIEHLLDLLMSFVPPPRPEDQVD-VSGTALSSD 5538
              +S GKQ+DLN+RNVKS+RKPPQSFVTVIE+LLDL+MSF+PPPR ED+ D  S TA S+D
Sbjct:  1926 ESSQGKQTDLNTRNVKSNRKPPQSFVTVIEYLLDLVMSFIPPPRAEDRPDGESSTASSTD 1985

Query:  5537 MDIDCSSAKGKGKAVSVPPEESKHAIQESTASLAKTAFFLKLLTDVLLTYASSIHVVLRH 5358
             MDID SSAKGKGKAV+V PEESKHAIQE+TASLAK+AF LKLLTDVLLTYASSI VVLRH
Sbjct:  1986 MDID-SSAKGKGKAVAVTPEESKHAIQEATASLAKSAFVLKLLTDVLLTYASSIQVVLRH 2044

Query:  5357 DAELSNMHGPNRTSARLTSGGIFNHILQHFLPHATRQKKERKNDGDWMYKLATRANQFLV 5178
             DA+LSN  GPNR    ++SGG+F+HILQHFLPH+T+QKKERK DGDW YKLATRANQFLV
Sbjct:  2045 DADLSNARGPNRIG--ISSGGVFSHILQHFLPHSTKQKKERKADGDWRYKLATRANQFLV 2102

Query:  5177 ASSIRSAEARKRIFSEICSIFLDFTDSSAGYNAPVPRMNVYVDLLNDILSARSPTGSSLS 4998
             ASSIRSAE RKRIFSEICSIF+DFTDS AG   P+ RMN YVDLLNDILSARSPTGSSLS
Sbjct:  2103 ASSIRSAEGRKRIFSEICSIFVDFTDSPAGCKPPILRMNAYVDLLNDILSARSPTGSSLS 2162

Query:  4997 AESAVIFVEAGLVHSLSTMLQVLDLDHPDSAKIVTAVVKALELVSKEHIHSAD-NAKGVN 4821
             AESAV FVE GLV  LS  LQV+DLDHPDSAKIVTA+VKALE+V+KEH+HSAD NAKG N
Sbjct:  2163 AESAVTFVEVGLVQYLSKTLQVIDLDHPDSAKIVTAIVKALEVVTKEHVHSADLNAKGEN 2222

Query:  4820 SSKIAXXXXXXXXXXXRFQALDMTSQPTEMVTDHRETFNAVRTSQISDSVADEMDHDRDM 4641
             SSK+            RFQALD T+QPTEMVTDHRE FNAV+TSQ SDSVADEMDHDRD+
Sbjct:  2223 SSKVVSDQSNLDPSSNRFQALD-TTQPTEMVTDHREAFNAVQTSQSSDSVADEMDHDRDL 2281

Query:  4640 DGGFARDGEDDFMHEMAEDGTGDGSTMEIRIEIPRNREDDMAPAADDTXXXXXXXXXXXX 4461
             DGGFARDGEDDFMHE+AEDGT + STMEIR EIPRNREDDMA   +D+            
Sbjct:  2282 DGGFARDGEDDFMHEIAEDGTPNESTMEIRFEIPRNREDDMADDDEDSDEDMSADDGEEV 2341

Query:  4460 XXXXXXXXXXXXXX-----AHRMSHPXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-GVIL 4299
                                AH+MSHP                              GVIL
Sbjct:  2342 DEDEDEDEDEENNNLEEDDAHQMSHPDTDQEDREMDEEEFDEDLLEEDDDEDEDEEGVIL 2401

Query:  4298 RLEEGINGINVLDHVEVFGGSNNLSGDTLRVMPLDIFGTRRQGRSTSIYNLLGRASDHGV 4119
             RLEEGINGINV DH+EVFGGSNNLSGDTLRVMPLDIFGTRRQGRSTSIYNLLGRA DHGV
Sbjct:  2402 RLEEGINGINVFDHIEVFGGSNNLSGDTLRVMPLDIFGTRRQGRSTSIYNLLGRAGDHGV 2461

Query:  4118 LDHPLLEEPSSTTNFSDQ 4065
              DHPLLEEPSS  +   Q
Sbjct:  2462 FDHPLLEEPSSVLHLPQQ 2479

 Score = 1665 (591.2 bits), Expect = 0., Sum P(11) = 0., Group = 1
 Identities = 326/371 (87%), Positives = 342/371 (92%), Frame = -1

Query:  1119 LSDSAYLLVGEVLKKIVALAPFFCCHFINELARSMQNLTLRAMKELHLYENSEKALLSSS 940
             LSD+AYLLV EVLKKIVALAPFFCCHFINELA SMQNLTL AMKELHLYE+SEKALLS+S
Sbjct:  3194 LSDNAYLLVAEVLKKIVALAPFFCCHFINELAHSMQNLTLCAMKELHLYEDSEKALLSTS 3253

Query:   939 SANGTAVLRVVQALSSLVNTLQERKDPEQPAEKDHSDAVSQISEINTALDSLWLELSNCI 760
             SANGTA+LRVVQALSSLV TLQE+KDP+ PAEKDHSDA+SQISEINTALD+LWLELSNCI
Sbjct:  3254 SANGTAILRVVQALSSLVTTLQEKKDPDHPAEKDHSDALSQISEINTALDALWLELSNCI 3313

Query:   759 SKIESSSEYXXXXXXXXXXXXMLTTGVAPPLPAGTQNLLPYIESFFVTCEKLRPGQPDAV 580
             SKIESSSEY             LTTGVAPPLPAGTQN+LPYIESFFVTCEKLRPGQPDA+
Sbjct:  3314 SKIESSSEYASNLSPASANAATLTTGVAPPLPAGTQNILPYIESFFVTCEKLRPGQPDAI 3373

Query:   579 QDASTSDMEDASTSSGGQRSSACQASLDEKQNAFVKFSEKHRRLLNAFIRQNSGLLEKSF 400
             Q+ASTSDMEDASTSSGGQ+SS   A+LDEK NAFVKFSEKHRRLLNAFIRQN GLLEKSF
Sbjct:  3374 QEASTSDMEDASTSSGGQKSSGSHANLDEKHNAFVKFSEKHRRLLNAFIRQNPGLLEKSF 3433

Query:   399 SLMLKIPRLIDFDNKRAYFRSKIKHQYDHHHHSPVRISVRRPYILEDSYNQLRMRSPQDL 220
             SLMLKIPRLI+FDNKRAYFRSKIKHQ+DHHH SPVRISVRR YILEDSYNQLRMRSPQDL
Sbjct:  3434 SLMLKIPRLIEFDNKRAYFRSKIKHQHDHHH-SPVRISVRRAYILEDSYNQLRMRSPQDL 3492

Query:   219 KGRLTVQFQGEEGIDAGGLTREWYQSISRVIVDKSALLFTTVGNDLTFQPNPNSVYQTEH 40
             KGRLTV FQGEEGIDAGGLTREWYQ +SRVI DK ALLFTTVGNDLTFQPNPNSVYQTEH
Sbjct:  3493 KGRLTVHFQGEEGIDAGGLTREWYQLLSRVIFDKGALLFTTVGNDLTFQPNPNSVYQTEH 3552

Query:    39 LSYFKFVGRVV 7
             LSYFKFVGRVV
Sbjct:  3553 LSYFKFVGRVV 3563

 Score = 1356 (482.4 bits), Expect = 0., Sum P(11) = 0., Group = 1
 Identities = 284/370 (76%), Positives = 307/370 (82%), Frame = -1

Query:  3882 ENLVEMAFSDRNHESSSSRLDAIFRSLRSGRNGHRFNMWLDDGPQRNGSAAPAVPEGIEE 3703
             ENLVEMAFSDRNH++SSSRLDAIFRSLRSGR+GHRFNMWLDD PQR GSAAPAVPEGIEE
Sbjct:  2483 ENLVEMAFSDRNHDNSSSRLDAIFRSLRSGRSGHRFNMWLDDSPQRTGSAAPAVPEGIEE 2542

Query:  3702 LLISHLRRPTP-QPDGQRTPVGGAQENDQPN----HGSDAEAREVAPAQQNENSESTLNP 3538
             LL+S LRRPTP QPD Q TP GGA+ENDQ N    H S+ EA   AP +QNEN+++ + P
Sbjct:  2543 LLVSQLRRPTPEQPDEQSTPAGGAEENDQSNQQHLHQSETEAGGDAPTEQNENNDNAVTP 2602

Query:  3537 -----LDLSECAGPAPPDSDALQRDVSNASELATEMQYERSDAITRDVEAVSQASSGSGA 3373
                  LD SE A PAPP S+ALQR+VS ASE ATEMQYERSDA+ RDVEAVSQASSGSGA
Sbjct:  2603 AARSELDGSESADPAPP-SNALQREVSGASEHATEMQYERSDAVVRDVEAVSQASSGSGA 2661

Query:  3372 TLGESLRSLEVEIGSVEGHDDGDRHGTSGTSERLPLGDIQAAARSRRPSGNAVPVSSRDM 3193
             TLGESLRSLEVEIGSVEGHDDGDRHG S   +RLPLGD+QAA+RSRRP G+ V  SSRD+
Sbjct:  2662 TLGESLRSLEVEIGSVEGHDDGDRHGAS---DRLPLGDLQAASRSRRPPGSVVLGSSRDI 2718

Query:  3192 SLESVSEVPQNPDQEPDQNASEGNQEPTRAAGADSIDPTFLEALPEDLRAEVLSSRQNQV 3013
             SLESVSEVPQN +QE DQNA EG+QEP RAA  DSIDPTFLEALPEDLRAEVLSSRQNQV
Sbjct:  2719 SLESVSEVPQNQNQESDQNADEGDQEPNRAADTDSIDPTFLEALPEDLRAEVLSSRQNQV 2778

Query:  3012 TQTSNDQPQDDGDIDPEFLAALPPDIREEVLAXXXXXXXXXXXXXXXXXPVEMDAVSIIA 2833
             TQTSN+QPQ+DGDIDPEFLAALPPDIREEVLA                 PVEMDAVSIIA
Sbjct:  2779 TQTSNEQPQNDGDIDPEFLAALPPDIREEVLAQQRAQRLQQSQELEGQ-PVEMDAVSIIA 2837

Query:  2832 TFPSEIREEV 2803
             TFPSEIREEV
Sbjct:  2838 TFPSEIREEV 2847

 Score = 323 (118.8 bits), Expect = 0., Sum P(11) = 0., Group = 1
 Identities = 61/72 (84%), Positives = 67/72 (93%), Frame = -2

Query:  2351 LQPLYKGQLQKLLVNLCTHRGSRQALVQILVDMLMLDLQGFSKKSIDAPEPPFRLYGCHA 2172
             +QPLYKGQLQ+LL+NLC HR SR++LVQILVDMLMLDLQG SKKSIDA EPPFRLYGCHA
Sbjct:  2945 VQPLYKGQLQRLLLNLCAHRESRKSLVQILVDMLMLDLQGSSKKSIDATEPPFRLYGCHA 3004

Query:  2171 NIAYSRPQSSDG 2136
             NI YSRPQS+DG
Sbjct:  3005 NITYSRPQSTDG 3016

 Score = 314 (115.6 bits), Expect = 0., Sum P(11) = 0., Group = 1
 Identities = 55/70 (78%), Positives = 64/70 (91%), Frame = -2

Query: 10865 WKQGNFHHWRPLFIHFDTYFKTYISSRKDLLLSDDMTEADPMPKNAILKILRVMQIILEN 10686
             + +GNFHHW+PLF+HFDTYFKT ISSRKDLLLSDDM E DP+PKN IL+ILRVMQI+LEN
Sbjct:   303 FNKGNFHHWKPLFMHFDTYFKTQISSRKDLLLSDDMAEGDPLPKNTILQILRVMQIVLEN 362

Query: 10685 CQNRSSFTGL 10656
             CQN++SF GL
Sbjct:   363 CQNKTSFAGL 372

 Score = 310 (114.2 bits), Expect = 0., Sum P(11) = 0., Group = 1
 Identities = 64/93 (68%), Positives = 74/93 (79%), Frame = -1

Query:  1698 QLLNLLDVVMHNAENEIKQAKLEASSEKPSAPDNAVQDGKNNSDISVSYGSELNPEDGSK 1519
             QLLNLL+VVM NAENEI QAKLEA+SEKPS P+NA QD +  ++ + S GS+ N ED SK
Sbjct:  3101 QLLNLLEVVMLNAENEITQAKLEAASEKPSGPENATQDAQEGANAAGSSGSKSNAEDSSK 3160

Query:  1518 APAVDNRSNLQAVLRSLPQPELRLLCSLLAHDG 1420
              P VD  S+LQ VL+SLPQ ELRLLCSLLAHDG
Sbjct:  3161 LPPVDGESSLQKVLQSLPQAELRLLCSLLAHDG 3193

 Score = 274 (101.5 bits), Expect = 0., Sum P(11) = 0., Group = 1
 Identities = 55/87 (63%), Positives = 61/87 (70%), Frame = -2

Query:  2030 GLPPLVSRRVLETLTNLARSHPNVAKLLLFLEFPCPSRCFPEAHDHRHGKAVLLDDGEEQ 1851
             G+PPLVSRRVLETLT LAR+HPNVAKLLLFLEFPCP  C  E  D R GKAVL++   EQ
Sbjct:  3016 GVPPLVSRRVLETLTYLARNHPNVAKLLLFLEFPCPPTCHAETSDQRRGKAVLMEGDSEQ 3075

Query:  1850 KTFAXXXXXXXXXXXXYMRSVAHLEQV 1770
               +A            YMRSVAHLEQ+
Sbjct:  3076 NAYALVLLLTLLNQPLYMRSVAHLEQL 3102

 Score = 231 (86.4 bits), Expect = 0., Sum P(11) = 0., Group = 1
 Identities = 46/71 (64%), Positives = 50/71 (70%), Frame = -2

Query: 10571 CVNSLPFL-CQHLKLLLASSDPEIXXXXXXXXXXXXKINPSKLHMNGKLISCGPINTHLL 10395
             C N   F   +H +LLLASSDPEI            KINPSKLHMNGKLI+CG IN+HLL
Sbjct:   363 CQNKTSFAGLEHFRLLLASSDPEIVVAALETLAALVKINPSKLHMNGKLINCGAINSHLL 422

Query: 10394 SLAQGWGSKEE 10362
             SLAQGWGSKEE
Sbjct:   423 SLAQGWGSKEE 433

 Score = 217 (81.4 bits), Expect = 0., Sum P(11) = 0., Group = 1
 Identities = 46/70 (65%), Positives = 50/70 (71%), Frame = -3

Query:  2665 NMLRERFAHRYHSSSLFGMXXXXXXXXXXXX-DIMAAGLDRNTGDPSRS-TSKPIETEGA 2492
             NMLRERFAHRYHS SLFGM             DI+ +GLDRN GD SR  TSKPIETEG+
Sbjct:  2868 NMLRERFAHRYHSGSLFGMNSRGRRGESSRRGDIIGSGLDRNAGDSSRQPTSKPIETEGS 2927

Query:  2491 PLVDEDGLKA 2462
             PLVD+D LKA
Sbjct:  2928 PLVDKDALKA 2937

 Score = 159 (61.0 bits), Expect = 0., Sum P(11) = 0., Group = 1
 Identities = 29/35 (82%), Positives = 32/35 (91%), Frame = -1

Query: 11037 PANIKAFIDRVVNIPLHDIAIPLSGFCWEFNKVNF 10933
             PA +KAFIDRV++IPLHDIAIPLSGF WEFNK NF
Sbjct:   274 PAKVKAFIDRVISIPLHDIAIPLSGFRWEFNKGNF 308

 Score = 125 (49.1 bits), Expect = 0., Sum P(11) = 0., Group = 1
 Identities = 27/41 (65%), Positives = 30/41 (73%), Frame = -3

Query: 14599 GFRSEXXXXXXXXXXHRASFPLRLQQILAGSRAVSPAIKIE 14477
             G RSE          HRASFPLRLQQIL+GSRAVSP+IK+E
Sbjct:   231 GSRSEMAAAAAMAA-HRASFPLRLQQILSGSRAVSPSIKVE 270


Parameters:
  B=1000000
  V=1000000
  W=5
  S2=65
  X=10
  cpus=8
  filter=seg
  hspsepqmax=10000
  hspmax=0
  topcomboN=1

  ctxfactor=5.77
  E=10

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +3      0   BLOSUM62        0.318   0.134   0.401    0.350   0.152   0.535  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   +2      0   BLOSUM62        0.318   0.134   0.401    0.346   0.150   0.530  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   +1      0   BLOSUM62        0.318   0.134   0.401    0.345   0.148   0.496  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   -1      0   BLOSUM62        0.318   0.134   0.401    0.351   0.155   0.580  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   -2      0   BLOSUM62        0.318   0.134   0.401    0.337   0.145   0.465  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a
   -3      0   BLOSUM62        0.318   0.134   0.401    0.358   0.157   0.604  
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E    S W   T  X   E2     S2
   +3      0     4866      4532       8.3  48 5 n/a 10  0.0044  48
                                                    44  0.21    40
   +2      0     4866      4399       8.0  48 5 n/a 10  0.0044  48
                                                    44  0.21    40
   +1      0     4867      4373       8.0  48 5 n/a 10  0.0044  48
                                                    44  0.21    40
   -1      0     4867      4371       8.0  48 5 n/a 10  0.0044  48
                                                    44  0.21    40
   -2      0     4866      4254       9.9  47 5 n/a 10  0.0061  47
                                                    44  0.21    40
   -3      0     4866      4240       9.9  47 5 n/a 10  0.0061  47
                                                    44  0.21    40


Statistics:

  Database:  UNIPROT_B9GCX0
   Title:  UNIPROT_B9GCX0
   Posted:  3:30:56 PM CET Oct 29, 2009
   Created:  3:30:56 PM CET Oct 29, 2009
   Format:  XDF-1
   # of letters in database:  3829
   # of sequences in database:  1
   # of database sequences satisfying E:  1
  No. of states in DFA:  32,067 (6765 KB)
  Total size of DFA:  7905 KB (8709 KB)
  Time to generate neighborhood:  0.03u 0.01s 0.04t   Elapsed:  00:00:00
  No. of threads or processors used:  1
  Search cpu time:  0.00u 0.01s 0.01t   Elapsed:  00:00:00
  Total cpu time:  0.03u 0.03s 0.06t   Elapsed:  00:00:00
  Start:  Fri Oct 30 09:12:00 2009   End:  Fri Oct 30 09:12:00 2009BioPerl-1.007002/t/data/bug2982.embl000444000766000024     11055513155576321 16702 0ustar00cjfieldsstaff000000000000ID   AJ229040; SV 1; linear; genomic DNA; CON; HUM; 958952 BP.
XX
AC   AJ229040;
XX
DT   22-JAN-2004 (Rel. 78, Created)
DT   24-MAR-2007 (Rel. 91, Last updated, Version 2)
XX
DE   Homo sapiens 959 kb contig between AML1 and CBR1 on chromosome 21q22
XX
KW   .
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   897811-898239
RX   DOI; 10.1093/nar/23.14.2762.
RX   PUBMED; 7651838.
RA   Miyoshi H., Ohira M., Shimizu K., Mitani K., Hirai H., Imai T.,
RA   Yokoyama K., Soeda E., Ohki M.;
RT   "Alternative splicing and genomic structure of the AML1 gene involved in
RT   acute myeloid leukemia";
RL   Nucleic Acids Res. 23(14):2762-2769(1995).
XX
RN   [2]
RP   897811-898239
RX   DOI; 10.1089/dna.1996.15.175.
RX   PUBMED; 8634147.
RA   Levanon D., Bernstein Y., Negreanu V., Ghozi M.C., Bar-Am I., Aloya R.,
RA   Goldenberg D., Lotem J., Groner Y.;
RT   "A large variety of alternatively spliced and differentially expressed
RT   mRNAs are encoded by the human acute myeloid leukemia gene AML1";
RL   DNA Cell Biol. 15(3):175-185(1996).
XX
RN   [3]
RP   896685-897802
RX   DOI; 10.1073/pnas.93.5.1935.
RX   PUBMED; 8700862.
RA   Ghozi M.C., Bernstein Y., Negreanu V., Levanon D., Groner Y.;
RT   "Expression of the human acute myeloid leukemia gene AML1 is regulated by
RT   two promoter regions";
RL   Proc. Natl. Acad. Sci. U.S.A. 93(5):1935-1940(1996).
XX
RN   [4]
RP   1-958952
RA   Blechschmidt K., Rump A., Nordsiek G., Drescher B., Weber J., Rosenthal A.;
RT   "Sequencing and Analysis of 960 kb between AML1 and CBR1 on Chromosome
RT   21q22.2";
RL   Unpublished.
XX
RN   [5]
RP   1-958952
RA   Blechschmidt K., Rump A., Nordsiek G., Drescher B., Weber J.,
RA   Schattevoy R., Rosenthal A., Yaspo M.L., Osoegawa K., Soeda E.;
RT   ;
RL   Submitted (07-MAY-1998) to the EMBL/GenBank/DDBJ databases.
RL   Karin Blechschmidt, Institute of Molecular Biotechnology, Dept. of Genome
RL   Analysis, Beutenbergstrasse 11, 07745 Jena, GERMANY
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..958952
FT                   /organism="Homo sapiens"
FT                   /chromosome="21"
FT                   /map="q22"
FT                   /mol_type="genomic DNA"
FT                   /db_xref="taxon:9606"
XX
CO   join(AJ229041.1:1..323000,AJ229042.1:51..348050,AJ229043.1:51..288002)
//
ID   AL954800; SV 2; linear; genomic DNA; CON; HUM; 87191216 BP.
XX
AC   AL954800;
XX
DT   28-JAN-2003 (Rel. 74, Created)
DT   14-APR-2004 (Rel. 79, Last updated, Version 5)
XX
DE   Human chromosome 14 complete sequence
XX
KW   complete genome.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RC   In collaboration with Kyoto University Graduate School of Medicine,
RC   Institute for Systems Biology, Seattle and Washington University Genome
RC   Sequencing Center.
RP   1-87191216
RA   Genoscope;
RT   ;
RL   Submitted (24-JAN-2003) to the EMBL/GenBank/DDBJ databases.
RL   Genoscope - Centre National de Sequencage BP 191 91006 EVRY cedex. FRANCE
XX
RN   [2]
RP   1-87191216
RX   DOI; 10.1038/nature01348.
RX   PUBMED; 12508121.
RA   Heilig R., Eckenberg R., Petit J.L., Fonknechten N., Da Silva C.,
RA   Cattolico L., Levy M., Barbe V., de Berardinis V., Ureta-Vidal A.,
RA   Pelletier E., Vico V., Anthouard V., Rowen L., Madan A., Qin S., Sun H.,
RA   Du H., Pepin K., Artiguenave F., Robert C., Cruaud C., Bruls T.,
RA   Jaillon O., Friedlander L., Samson G., Brottier P., Cure S., Segurens B.,
RA   Aniere F., Samain S., Crespeau H., Abbasi N., Aiach N., Boscus D.,
RA   Dickhoff R., Dors M., Dubois I., Friedman C., Gouyvenoux M., James R.,
RA   Madan A., Mairey-Estrada B., Mangenot S., Martins N., Menard M., Oztas S.,
RA   Ratcliffe A., Shaffer T., Trask B., Vacherie B., Bellemere C., Belser C.,
RA   Besnard-Gonnet M., Bartol-Mavel D., Boutard M., Briez-Silla S.,
RA   Combette S., Dufosse-Laurent V., Ferron C., Lechaplais C., Louesse C.,
RA   Muselet D., Magdelenat G., Pateau E., Petit E., Sirvain-Trukniewicz P.,
RA   Trybou A., Vega-Czarny N., Bataille E., Bluet E., Bordelais I., Dubois M.,
RA   Dumont C., Guerin T., Haffray S., Hammadi R., Muanga J., Pellouin V.,
RA   Robert D., Wunderle E., Gauguet G., Roy A., Sainte-Marthe L., Verdier J.,
RA   Verdier-Discalla C., Hillier L., Fulton L., McPherson J., Matsuda F.,
RA   Wilson R., Scarpelli C., Gyapay G., Wincker P., Saurin W., Quetier F.,
RA   Waterston R., Hood L., Weissenbach J.;
RT   "The DNA sequence and analysis of human chromosome 14";
RL   Nature 421(6923):601-607(2003).
XX
CC   Annotation is available here : http://www.genoscope.cns.fr/cgi-bin/ggb/ggb
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..87191216
FT                   /organism="Homo sapiens"
FT                   /chromosome="14"
FT                   /mol_type="genomic DNA"
FT                   /db_xref="taxon:9606"
XX
CO   join(complement(AL512310.3:2094..185605),
CO   complement(AL391156.3:116..136599),complement(AL359218.4:329..156319),
CO   AL163152.4:54909..158201,AL356019.5:51149..176114,
CO   complement(AL355075.6:1..204005),complement(AL163195.5:1..114969),
CO   AL163636.7:67022..202337,AL133371.3:22302..160471,
CO   complement(AL355922.4:1992..95036),AL161668.6:54801..202193,
CO   AL157687.6:139001..196377,AL135744.4:7175..193768,AL161747.5:9066..110538,
CO   AE000658.1:105..250472,AE000659.1:2..251142,AE000660.1:2..251067,
CO   AE000661.1:2..247820,AE000662.1:2..69153,AL160314.7:32033..208920,
CO   complement(AL135998.6:408..165498),AL132780.5:8574..191946,
CO   complement(AL117258.4:25866..156931),AL049829.4:1274..194296,
CO   AL132855.4:46251..155912,AL135999.4:19191..196311,
CO   complement(AL160237.4:1..165160),AL136419.3:332..169476,
CO   complement(AL136295.3:1..176705),complement(AL096870.5:1..179920),
CO   complement(AL132800.4:1..177786),AL136018.4:11095..171414,
CO   AL161663.4:2691..169539,complement(AL137164.3:2002..118674),
CO   AL161666.4:2341..165438,complement(AL163052.4:1791..126816),
CO   AL132827.2:653..118925,complement(AL079352.3:2052..175251),
CO   AL132715.3:22001..197337,complement(AL359396.5:7349..156039),
CO   AL132633.2:2..84580,complement(AL049831.2:1..218406),
CO   complement(AL121841.5:558..194413),complement(AL133316.5:139424..157126),
CO   complement(AL132716.6:2680..152403),complement(AL079343.4:2006..171481),
CO   AL132718.5:19161..128000,AL110292.4:9..177427,
CO   complement(AL136522.6:553..170744),complement(AL356015.3:2001..128566),
CO   AL390334.4:25901..168011,complement(AL391748.3:13230..137037),
CO   complement(AL390894.2:691..175037),AL391158.5:991..202437,
CO   complement(AL445384.3:100433..122879),AL163194.5:1094..161813,
CO   complement(AL163639.3:1..68131),complement(AL139023.6:4382..151180),
CO   AL133162.4:1..196431,complement(AL121766.5:20241..126302),
CO   AL049777.5:1..168313,complement(AL122126.4:26722..148909),
CO   AL138974.4:2..32228,complement(AL135878.4:2006..143693),
CO   AL117693.5:31322..172938,AL133166.3:401..103590,AL158058.5:19871..125338,
CO   complement(AL135858.3:1..163722),complement(AL356756.4:660..164090),
CO   complement(AL445884.4:33300..47979),complement(AL355053.4:1..124077),
CO   AL133372.4:356..190470,complement(AL121840.4:1810..83535),
CO   AL079305.3:2003..188736,complement(AL132985.4:4200..76347),
CO   AL117355.5:2000..137548,complement(AL121852.3:754..165136),
CO   complement(AL513133.6:715..27714),AL049830.3:2..212559,
CO   complement(AL121808.4:1..99259),complement(AL136418.4:1..191213),
CO   AL139353.3:32858..169772,AL163973.1:2181..115463,AL390798.3:2771..152139,
CO   AL359400.4:54341..173676,AL355112.4:14701..126371,AL352984.4:41971..157133,
CO   complement(AL161665.5:1..161106),complement(AL136298.5:1..178278),
CO   AL132988.4:11495..146615,AL117672.5:2..164431,
CO   complement(AL049781.5:2..188164),complement(AL109769.5:970..113373),
CO   AL355886.4:36293..164606,complement(AL139296.4:1..178149),
CO   complement(AL158802.1:2000..95921),AL133305.3:7971..157528,
CO   AL161851.4:2..185732,AL157689.3:27171..214457,AL358340.6:41992..199163,
CO   AL358274.3:33761..144617,AL162191.6:5194..204662,
CO   complement(AL356806.4:1..91833),AL445363.7:55024..181350,
CO   complement(AL445883.3:80200..161151),AL355885.4:1982..116066,
CO   AL121603.4:2..118657,AL049776.3:2..194380,complement(AL121594.6:1..183519),
CO   AL133163.3:885..181496,AL160231.4:38601..194173,
CO   complement(AL137818.4:27480..161167),complement(AL162311.5:1..167127),
CO   complement(AL133304.4:2005..141396),AL162511.5:2841..163399,
CO   AL356803.2:61030..66254,AL137226.3:687..177925,
CO   complement(AL132857.4:13991..166862),AL079303.3:11000..197948,
CO   complement(AL162464.5:16270..168567),complement(AL121775.3:605..170576),
CO   AL079304.3:2219..161225,AL121857.6:113628..150200,
CO   complement(AL109759.4:8522..201771),AL121790.4:2..202240,
CO   AL136296.3:53807..192404,complement(AL163151.1:607..136552),
CO   complement(AL359233.5:2977..153326),complement(AL392023.3:1..108999),
CO   AL450109.3:63787..96734,AL161751.3:2..87743,AL355835.3:51580..172374,
CO   complement(AL499608.3:1..28000),complement(AL357094.4:2176..157828),
CO   AL359950.4:24001..194191,AL391694.4:2..7823,
CO   complement(AL132994.4:794..179329),complement(AL109628.5:22098..190016),
CO   AL132639.4:2..194543,complement(AL157791.4:2742..80074),
CO   AL049875.2:538..161119,AL117191.6:10964..155188,
CO   complement(AL355052.3:1..135259),complement(AL133233.2:656..129943),
CO   complement(AL121767.6:24204..184869),complement(AL049828.3:1146..203079),
CO   AL352977.4:2..173149,complement(AL355889.1:1999..154110),
CO   AL390800.4:13181..167872,complement(AL451071.3:1819..129825),
CO   AL390815.5:55176..147140,complement(AL390801.4:90990..166214),
CO   AL391516.4:2..165171,AL390335.3:119496..176502,
CO   complement(AL356596.3:414..172769),AL121821.7:8710..126746,
CO   AL109662.3:2..166180,complement(AL138498.5:706..146439),
CO   AL355839.4:438..158864,complement(AL391397.4:287..139949),
CO   AL583864.3:2..282,AL445074.4:2..142537,AL450442.2:6951..143035,
CO   AL442163.5:21095..167027,complement(AL389914.3:11003..76031),
CO   complement(AL356800.4:20129..157812),complement(AL163153.4:1..166562),
CO   AL390097.2:6877..91231,AL445383.5:25619..170914,AL583809.3:69492..169712,
CO   AL442183.4:44001..151033,complement(AL358913.4:1893..179861),
CO   AL133239.4:3183..129637,AL160211.2:44506..164513,
CO   complement(AL135961.4:38520..117179),complement(AL109766.5:1999..182447),
CO   AL355888.3:17231..212852,complement(AL161752.4:991..135786),
CO   AL356022.3:42536..135726,AL358293.4:8261..197927,
CO   complement(AL160233.3:13890..78284),AL049870.3:2001..205003,
CO   complement(AL121809.6:1..206369),complement(AL133501.6:64930..158397),
CO   complement(AL162632.4:1..159416),AL139354.6:21392..199538,
CO   AL359398.2:70461..174399,AL158111.5:72339..171424,AL133449.5:84247..123840,
CO   complement(AL133224.4:51367..176945),AL161664.8:1..170521,
CO   AL358341.3:56489..136105,AL512342.2:45..838,
CO   complement(AL355099.5:116..155826),complement(AL512414.2:1..101079),
CO   AL591768.2:52166..157502,AL591769.3:39501..170856,AL591771.1:40243..154205,
CO   complement(AL359951.4:1..175834),AL157792.3:8413..193038,
CO   AL358832.3:3751..176098,complement(AL079306.3:12833..181521),
CO   AL162551.4:1124..180960,AL121576.5:140439..190918,
CO   complement(AL161415.2:1..159442),complement(AL359212.2:2000..116077),
CO   AL359332.2:79981..162487,AL512358.2:36451..144551,
CO   complement(AL358335.4:1..143099),AL512359.2:34667..156865,
CO   AL583762.1:2..3583,complement(AL358336.4:1996..177161),
CO   AL512360.2:48221..190972,AL358338.3:9393..121786,
CO   complement(AL110505.5:1..196440),complement(AL358339.2:2001..73407),
CO   AL512361.3:62201..156305,AL163612.5:34354..171345,
CO   complement(AL139099.3:1..148139),AL591767.2:43974..187435,
CO   AL627171.1:63401..172074,AL117692.5:11326..157400,AL109758.3:2..207512,
CO   AL359397.3:17582..154136,AL118556.4:262..168599,
CO   complement(AL606834.1:1738..166769),AL133485.3:15379..133980,
CO   complement(AL358334.3:1997..172999),AL591770.3:5131..158392,
CO   complement(AL591807.1:1059..142790),AL358332.3:3143..159264,
CO   complement(AL122125.4:1171..187209),AL079307.7:2..188548,
CO   complement(AL358333.4:2002..166899),AL118557.5:25781..191132,
CO   complement(AL365475.1:418..187946),complement(AL355833.4:1..56941),
CO   complement(AL157971.4:2003..158614),AL133453.3:48071..211127,
CO   AL139317.5:5860..190646,complement(AL352979.4:1..139729),
CO   complement(AL356020.3:1..150470),complement(AL390799.4:1..152375),
CO   AL365295.4:27814..192059,complement(AL445886.3:117180..142997),
CO   complement(AL163953.3:2009..160985),AL162759.4:9751..172275,
CO   AL138479.4:11511..165226,complement(AL136297.3:485..144739),
CO   AL356802.5:81918..112125,AL049778.3:2..205001,
CO   complement(AL359792.3:31684..180352),AL138994.5:2..83427,
CO   AL133444.4:1001..191200,complement(AL160471.5:1161..191558),
CO   AL352982.3:135073..138227,complement(AL139316.5:1..190439),
CO   complement(AL158801.4:1..153599),complement(AL356801.5:685..133539),
CO   AL138499.4:11979..185713,complement(AL355773.4:1..205075),
CO   complement(AL163952.5:2000..186743),AL138995.5:39601..161525,
CO   AL355073.5:2..174986,complement(AL162633.3:691..39837),
CO   AL359234.4:33176..114847,complement(AL355103.3:1..131915),
CO   complement(AL161757.4:95..239559),complement(AL162831.6:1..97299),
CO   AL137100.4:42356..165389,complement(AL391152.3:1..129109),
CO   AL139195.4:13522..86352,AL355834.4:17101..220292,
CO   complement(AL161804.4:1451..100043),AL136520.3:25124..169746,
CO   complement(AL132668.4:30460..149499),AL049838.3:2..210930,
CO   AL121579.4:16023..156232,AL132989.5:27..144806,AL139021.6:12769..175179,
CO   complement(AL135752.6:1..98592),AL133312.3:95445..153072,
CO   AL121819.6:23451..142695,AL049873.3:739..147539,
CO   complement(AL117356.5:1..153457),complement(AL359219.4:976..113123),
CO   AL133502.4:1305..172046,AL159140.4:33905..164085,
CO   complement(AL162471.3:24000..26314),complement(AL121694.4:1993..173206),
CO   AL139194.7:571..157120,AL133299.4:30891..162939,AL157911.4:21681..174561,
CO   AL163853.4:84112..157570,complement(AL157756.3:1..104542),
CO   AL132778.6:7317..169268,AL122057.4:105275..158823,AL049874.3:2..193047,
CO   complement(AL132777.4:1..159423),complement(AL160236.4:1..157634),
CO   complement(AL160234.3:1..155293),AL359220.4:48358..194695,
CO   AL138996.4:1921..182267,complement(AL355916.2:2002..170999),
CO   AL137129.4:59161..186110,complement(AL137918.4:1658..160309),
CO   AL356018.5:27076..107424,AL390816.4:1..206404,
CO   complement(AL391154.4:1..162399),complement(AL391155.3:2001..105721),
CO   AL389895.3:21071..164054,complement(AL355101.2:1..156276),
CO   complement(AL109985.5:14361..155961),complement(AL132666.8:1..143426),
CO   complement(AL137191.5:56670..133019),AL049871.4:1993..167587,
CO   complement(AL118555.6:47030..96140),AL132992.4:1698..133186,
CO   complement(AL136038.5:726..149549),complement(AL161670.4:2004..148991),
CO   AL162832.6:5331..156928,AL359235.3:19311..149635,
CO   complement(AL355094.3:1..139046),complement(AL161756.6:1538..144357),
CO   complement(AL122035.6:1299..111809),complement(AL049869.6:1..194546),
CO   complement(AL121774.5:1..154083),complement(AL135745.5:806..84550),
CO   complement(AL139022.4:1..188472),AL355076.5:11755..213081,
CO   AL359236.4:69001..179874,AL355840.2:40881..179937,
CO   complement(AL161871.6:40600..81861),AL109847.5:2001..184774,
CO   AL513142.3:2..9520,complement(AL928655.1:726..22205),AL928760.1:734..9995,
CO   AL928766.1:2..22955,AL589183.2:600..17576,
CO   complement(AL391261.3:2003..157710),AL356021.4:66041..182663,
CO   AL157997.5:15001..168075,AL359232.4:38491..150544,
CO   complement(AL355093.3:8..142045),complement(AL139295.6:16230..142099),
CO   AL133241.3:2000..157347,AL117667.4:2..90331,
CO   complement(AL049835.3:1996..187563),AL159179.3:44061..106736,
CO   complement(AL135978.4:2001..172995),AL139785.5:20581..154246,
CO   complement(AL132640.4:16811..177687),AL049779.6:2..186608,
CO   complement(AL121595.5:1940..163986),complement(AL133370.4:1..153888),
CO   complement(AL157915.3:52459..121485),AL136294.4:2..88026,
CO   complement(AL122013.5:46..173009),complement(AL589168.3:15793..134499),
CO   complement(AL121820.4:154..116160),complement(AL133313.2:162226..179463),
CO   complement(AL132986.4:19254..182129),AL117694.5:413..164284,
CO   complement(AL391262.3:1424..121889),AL359317.3:33746..207092,
CO   complement(AL157996.8:1987..187098),AL133445.4:32351..189924,
CO   complement(AL355837.6:2647..91514),AL157789.6:60001..223844,
CO   complement(AL135747.4:897..150824),complement(AL160191.3:655..186922),
CO   AL356804.4:6389..184109,AL391223.4:2..17677,AL357153.4:2..203186,
CO   complement(AC004816.1:1..165628),complement(AC004818.1:1..21425),
CO   complement(AC004825.2:1..124021),complement(AL445903.3:23081..49040),
CO   complement(AC005230.1:1..111498),complement(AC004817.2:1..128198),
CO   complement(AC005476.4:310..107531),complement(AL391735.2:240..966),
CO   complement(AC005994.2:1..90770),complement(AC004968.1:1..108622),
CO   complement(AC004974.1:1..112631),complement(AC004900.2:15202..113050),
CO   complement(AL391749.4:106912..155299),complement(AC005993.2:1..141759),
CO   complement(AC005477.1:1..106060),complement(AC005227.2:60880..99850),
CO   complement(AC005857.1:2..100459),complement(AC005226.1:1..68766),
CO   complement(AC005157.1:1..164075),complement(AC005533.2:1..82147),
CO   complement(AC004828.2:81..183049),AL392024.3:111013..139439,
CO   complement(AC006360.2:1..136851),complement(AC007160.3:176..87400),
CO   complement(AL442663.3:26000..162999),complement(AC004858.2:1..123139),
CO   complement(AC004846.2:583..154416),complement(AL391733.3:1..667),
CO   complement(AC005280.3:1..136748),complement(AC005225.2:1..166574),
CO   complement(AC006146.2:1..103948),complement(AC005520.2:1..150923),
CO   complement(AC005480.3:1..94108),complement(AC005484.2:1..131743),
CO   complement(AC006349.3:1..111737),complement(AC005519.3:20108..163783),
CO   complement(AC005479.2:1..138424),AC013451.8:23015..105123,
CO   AC007956.5:2..232647,AC006530.4:84..117603,
CO   complement(AL049780.4:757..194552),complement(AL691403.2:29915..124711),
CO   AF111167.2:781..200267,AC009363.4:11932..44312,AC007182.3:239..190959,
CO   AC009399.5:4243..144171,AF107885.2:1154..190126,AC008015.5:6219..116006,
CO   AC016526.6:222..179234,AC016543.6:1980..191159,AC008050.6:504..174975,
CO   AC007376.9:60484..171453,AF111169.2:2..181916,AC007686.5:15408..179628,
CO   AC007375.6:2..178331,AC007954.7:82514..184385,AF111168.2:2..229730,
CO   AC008044.4:19300..102033,AC008372.6:981..266238,
CO   complement(AL049832.3:116842..161874),AC007955.4:2..161312,
CO   AF099810.1:23608..170589,AC007056.4:2..180481,AC008045.5:8782..183640,
CO   AC009396.5:2..162427,AC011440.5:5936..89643,AC026888.6:2..207681,
CO   AC022469.5:26897..153812,AC018514.7:127..155144,AC012099.4:8966..153594,
CO   AC008056.6:408..161584,AC007058.2:15039..94599,AF123462.1:342..178104,
CO   AC007514.5:6136..176831,AC007372.4:2..152796,
CO   complement(AL049837.4:20361..22355),AC010849.3:2..149659,
CO   AC018513.5:13250..183488,AC022404.7:2..231060,AC010072.5:7108..109619,
CO   AC007262.4:2..159737,AC010582.6:2..2618,complement(AL136040.5:260..197419),
CO   complement(AL121769.4:1995..166503),AL136039.4:4371..173852,
CO   AL160192.3:1..185228,complement(AL355838.3:1..146009),
CO   AL358275.4:15970..178614,complement(AL162811.6:186..158499),
CO   complement(AL357095.4:1993..155871),AL356799.3:29181..158955,
CO   complement(AL390076.4:2002..89476),AL163171.4:44571..146582,
CO   AL355095.4:64121..151193,AL359238.4:12286..165668,AL162872.4:32988..171880,
CO   complement(AL163613.2:1..139447),AL355072.3:10926..167003,
CO   AL356032.4:29877..167936,AL355887.4:72914..159182,
CO   complement(AL161713.4:1..147829),AL391732.3:475..1308,
CO   complement(AL162891.4:1..162612),complement(AL356807.3:1810..110460),
CO   AL390802.2:30354..109783,AL583743.3:30193..161991,
CO   complement(AL583742.2:1..83199),complement(AL512311.3:2002..129791),
CO   AL445385.4:13681..162501,complement(AL513143.3:120541..155001),
CO   AL157690.7:213..162528,complement(AL163642.4:1..184036),
CO   complement(AL357172.3:657..197550),complement(AL157957.4:23060..134864),
CO   complement(AL133369.4:25748..101601),AL049775.2:1702..181433,
CO   complement(AL132641.3:26..119421),complement(AL137228.4:140..121358),
CO   complement(AL357092.4:1..176089),complement(AL445593.3:1..109678),
CO   complement(AL359239.4:1..141816),AL161753.4:54806..163933,
CO   complement(AL359333.6:1..109249),complement(AL359680.4:2000..77590),
CO   AL356016.2:36751..154292,complement(AL365294.4:1804..145749),
CO   AL391517.3:5916..125242,AL358292.4:2..180211,
CO   complement(AL352955.7:970..146726),AL157688.4:29088..189917,
CO   complement(AL135746.3:1..127819),complement(AL158059.3:1993..114725),
CO   AL359237.4:45171..160230,AL136501.4:10306..178584,AL157955.5:16031..145390,
CO   AL133279.7:243..196743,AL049834.3:2..171405,
CO   complement(AL162171.4:1419..181119),AL121768.4:25842..211240,
CO   complement(AL133238.3:1275..171709),AL137785.6:16043..153730,
CO   complement(AL138478.3:75..75669),complement(AL357093.4:1..155099),
CO   complement(AL157736.3:87480..89442),AL356805.5:2..157157,
CO   AL163032.3:44931..120467,complement(AL137230.3:684..196215),
CO   complement(AL163011.3:1993..89641),AL137128.4:19101..226656,
CO   AL355074.5:7431..181635,AL161662.6:85251..195369,AL512791.3:47382..89068,
CO   complement(AL096869.8:367..227284),AL139193.4:90242..141396,
CO   complement(AL122020.5:714..148122),AL159191.4:60248..105885,
CO   AL133454.6:2..163176,complement(AL121784.5:10165..170529),
CO   AL135818.3:706..88440,AL133153.3:7..231490,
CO   complement(AL133373.5:644..141113),complement(AL121839.3:1561..179597),
CO   complement(AL590328.2:35676..105579),AL049872.3:1868..170669,
CO   AL121773.5:13121..158489,complement(AL133240.4:1..74439),
CO   complement(AL118559.6:1..191792),AL159141.5:28493..174318,
CO   complement(AL136332.5:34450..101876),complement(AL132987.4:1..167509),
CO   complement(AL117192.5:1..204505),complement(AL110118.7:831..132850),
CO   AL132838.4:4285..58790,AL122023.3:2..170429,
CO   complement(AL136338.4:1..141176),complement(AL157858.5:1594..179993),
CO   AL132642.4:2..180643,AL079302.7:32452..196082,AL121838.4:2..98377,
CO   complement(AL117259.6:19505..181441),complement(AL132708.3:1..145585),
CO   AL132990.4:105808..144053,AL049839.3:2..212527,AL121612.5:26541..180914,
CO   complement(AL391542.2:381..778),complement(AL390254.6:1..177792),
CO   AL356017.3:22744..118900,complement(AL117187.7:841..152932),
CO   AL138539.7:1..148355,AL133467.4:7781..208793,AL139020.5:34211..164609,
CO   complement(AL133167.4:1..163095),complement(AL137190.5:1..155056),
CO   complement(AL355102.5:2001..157206),AL359240.4:6621..168761,
CO   AL163051.5:38805..160867,complement(AL137786.3:1..197689),
CO   complement(AL133168.6:1..179113),AL049833.5:31058..192406,
CO   complement(AL158800.6:1..163979),complement(AL352976.3:806..163215),
CO   complement(AL445885.1:76203..90809),AL355098.3:2..151095,
CO   AL163872.2:86211..167898,AL391015.3:5..2759,
CO   complement(AL355097.5:1289..164522),AL445594.3:57389..81891,
CO   AL352981.4:76..157670,complement(AL163932.5:1..159904),
CO   complement(AL391153.3:1306..120388),AL163760.4:23906..173004,
CO   AL132719.4:8044..169507,AL096821.3:17951..169086,AL132796.4:2..159803,
CO   AL162151.5:2..230568,AL359681.5:32793..100000,
CO   complement(AL109767.7:115149..175332),complement(AL132819.6:1..140073),
CO   complement(AL110504.6:103330..206733),complement(AL160313.4:1993..164184),
CO   AL136000.4:9831..199592,complement(AL133368.6:1564..132229),
CO   AL157912.5:64883..117912,AL133523.5:20681..171053,AL157871.5:41501..178689,
CO   complement(AL135838.6:1511..83209),AL845552.2:2..128569,
CO   complement(AL163974.7:2002..72697),AL132711.5:67171..175375,
CO   AL117190.6:2..165045,complement(AL132709.5:1..196669),
CO   complement(AL355836.3:1080..142978),complement(AL359682.4:1..60830),
CO   complement(AL355096.4:64330..185480),AL049836.3:2..205774,
CO   complement(AL355032.6:1..86128),complement(AL137779.6:1..141674),
CO   AL118558.6:6885..192127,complement(AL133223.5:1..116259),
CO   AL359402.3:62672..117291,AL352978.6:37781..139455,AL137229.4:10231..123780,
CO   AL136293.5:29141..224035,complement(AL132801.5:2008..154098),
CO   AL117209.7:13601..157604,AL133455.4:18991..137833,
CO   complement(AL161669.5:928..180185),AL138976.5:52018..167357,
CO   complement(AL133367.4:1..181458),complement(AL139300.6:1..145044),
CO   complement(AL049840.8:1..165471),complement(AL132712.4:11633..99672),
CO   AL136001.6:847..184780,complement(AL359399.3:310..80288),
CO   complement(AL590079.3:3700..62642),complement(AL512790.1:282..18582),
CO   complement(AL512357.4:1..173320),complement(AL512362.4:36499..161862),
CO   AL583722.6:1..193000,complement(AL590327.3:10857..38088),
CO   AL590326.3:382..29282,AL583810.5:6120..93029,AL512802.2:10401..96567,
CO   AL512356.6:2..156461,AL512355.6:31161..196273,AL928654.1:15252..211420,
CO   complement(AL928742.3:574..124699),complement(AL928761.2:1..12040),
CO   complement(AL928769.1:1501..11357),complement(AL928765.1:2..7340),
CO   complement(AL928767.1:25..10609),complement(AL928762.2:14..2395),
CO   complement(AL928768.1:1..8825),complement(AL901608.1:13168..34978),
CO   AL122127.6:2..168209,complement(AB019441.1:1..125028),
CO   complement(AB019440.1:1..200000),complement(AB019439.1:1..200000),
CO   complement(AB019438.1:1..200000),complement(AB019437.1:1..200000))
//
ID   BA000005; SV 3; linear; genomic DNA; CON; HUM; 33543332 BP.
XX
AC   BA000005;
XX
DT   23-JAN-2003 (Rel. 74, Created)
DT   16-JUL-2008 (Rel. 96, Last updated, Version 5)
XX
DE   Homo sapiens genomic DNA, chromosome 21q.
XX
KW   .
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-33543332
RG   The Chromosome 21 Mapping and Sequencing Consortium
RA   Hattori M., Fujiyama A., Taylor T.D., Watanabe H., Yada T., Park H.S.,
RA   Toyoda A., Ishii K., Totoki Y., Choi D.K., Soeda E., Ohki M., Takagi T.,
RA   Sakaki Y., Taudien S., Blechschmidt K., Polley A., Menzel U., Delabar J.,
RA   Kumpf K., Lehmann R., Patterson D., Reichwald K., Rump A., Schillhabel M.,
RA   Schudy A., Zimmermann W., Rosenthal A., Kudoh J., Shibuya K., Kawasaki K.,
RA   Asakawa S., Shintani A., Sasaki T., Nagamine K., Mitsuyama S.,
RA   Antonarakis S.E., Minoshima S., Shimizu N., Nordsiek G., Hornischer K.,
RA   Barandt P., Scharfe M., Schoen O., Desario A., Reichelt J., Kauer G.,
RA   Bloecker H., Ramser J., Beck A., Klages S., Hennig S., Riesselmann L.,
RA   Dagand E., Wehrmaeyer S., Borzym K., Gardiner K., Nizetic D., Francis F.,
RA   Lehrach H., Reinhardt R., Yaspo M.L.;
RT   ;
RL   Submitted (09-MAY-2000) to the EMBL/GenBank/DDBJ databases.
RL   * RIKEN Genomic Sciences Center Human Genome Research Group * Institute of
RL   Molecular Biotechnology Genome Analysis * Keio University School of
RL   Medicine, Dept. of Molecular Biology * GBF, Dept. of Genome Analysis *
RL   Max-Planck Institute for Molecular Genetics (addresses see below)
XX
RN   [2]
RX   DOI; 10.1038/35012518.
RX   PUBMED; 10830953.
RA   Hattori M., Fujiyama A., Taylor T.D., Watanabe H., Yada T., Park H.S.,
RA   Toyoda A., Ishii K., Totoki Y., Choi D.K., Soeda E., Ohki M., Takagi T.,
RA   Sakaki Y., Taudien S., Blechschmidt K., Polley A., Menzel U., Delabar J.,
RA   Kumpf K., Lehmann R., Patterson D., Reichwald K., Rump A., Schillhabel M.,
RA   Schudy A., Zimmermann W., Rosenthal A., Kudoh J., Shibuya K., Kawasaki K.,
RA   Asakawa S., Shintani A., Sasaki K., Nagamine K., Mitsuyama S.,
RA   Antonarakis S.E., Minoshima S., Shimizu N., Nordsiek G., Hornischer K.,
RA   Barandt P., Scharfe M., Schoen O., Desario A., Reichelt J., Kauer G.,
RA   Bloecker H., Ramser J., Beck A., Klages S., Hennig S., Riesselmann L.,
RA   Dagand E., Wehrmeyer S., Borzym K., Gardiner K., Nizetic D., Francis F.,
RA   Lehrach H., Reinhardt R., Yaspo M.L.;
RT   "The DNA sequence of human chromosome 21";
RL   Nature 405(6784):311-319(2000).
XX
CC   The chromosome 21 mapping and sequencing consortium
CC   consisting of
CC   * RIKEN Genomic Sciences Center, Human Genome Research Group,
CC   * Sagamihara 228-8555, Japan,
CC   * e.mail: hattori@gsc.riken.go.jp
CC   * URL: http://hgp.gsc.riken.go.jp/
CC   and
CC   * Institute of Molecular Biotechnology, Genome Analysis,
CC   * Beutenbergstrasse 11, D-07745 Jena, Germany,
CC   * e.mail: gscj-submit@genome.imb-jena.de
CC   * URL: http://genome.imb-jena.de/
CC   and
CC   * Keio University School of Medicine, Molecular Biology,
CC   * Tokyo 160-8582, Japan,
CC   * e.mail: nshimizu@dmb-med.keio.ac.jp
CC   * URL: http://www.dmb.med.keio.ac.jp/
CC   and
CC   * GBF, Dept. of Genome Analysis,
CC   * Mascheroder Weg 1, D-38124 Braunschweig, Germany,
CC   * e.mail: info.genome@gbf.de
CC   * URL: http://genome.gbf.de/
CC   and
CC   * Max-Planck Institute for Molecular Genetics,
CC   * Ihnestrasse 73, D-14195 Berlin, Germany,
CC   * e.mail: info-chr21@molgen.mpg.de
CC   * URL: http://chr21.rz-berlin.mpg.de/
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..33543332
FT                   /organism="Homo sapiens"
FT                   /chromosome="21"
FT                   /map="21q"
FT                   /mol_type="genomic DNA"
FT                   /db_xref="taxon:9606"
XX
CO   join(AL163202.2:1..340000,AL163203.2:1001..340000,AL163204.2:1001..340000,
CO   AP001660.1:1001..340000,AL163206.2:1001..340000,AL163207.2:1001..340000,
CO   AL163208.2:1001..340000,AL163209.2:1001..340000,AL163210.2:1001..340000,
CO   AP001666.1:1001..340000,AP001667.1:1001..340000,AL163213.2:1001..340000,
CO   AP001669.1:1001..340000,AP001670.1:1001..340000,AP001671.1:1001..340000,
CO   AL163217.2:1001..340000,AL163218.2:1001..340000,AP001674.1:1001..340000,
CO   AP001675.1:1001..340000,AP001676.1:1001..340000,AP001677.1:1001..340000,
CO   AP001678.1:1001..340000,AP001679.1:1001..340000,AP001680.1:1001..340000,
CO   AP001681.1:1001..340000,AL163227.2:1001..340000,AP001683.1:1001..340000,
CO   AP001684.1:1001..340000,AP001685.1:1001..340000,AP001686.1:1001..340000,
CO   AP001687.1:1001..340000,AP001688.1:1001..340000,AP001689.1:1001..340000,
CO   AP001690.1:1001..340000,AP001691.1:1001..340000,AP001692.1:1001..340000,
CO   AP001693.1:1001..340000,AP001694.1:1001..340000,AP001695.1:1001..340000,
CO   AP001696.1:1001..340000,AP001697.1:1001..340000,AP001698.1:1001..340000,
CO   AP001699.1:1001..340000,AP001700.1:1001..340000,AL163246.2:1001..340000,
CO   AL163247.2:1001..340000,AL163248.2:1001..340000,AL163249.2:1001..340000,
CO   AP001705.1:1001..340000,AP001706.1:1001..340000,AP001707.1:1001..340000,
CO   AP001708.1:1001..340000,AP001709.1:1001..340000,AP001710.1:1001..340000,
CO   AP001711.1:1001..340000,AP001712.1:1001..340000,AP001713.1:1001..340000,
CO   AP001714.1:1001..340000,AP001715.1:1001..340000,AP001716.1:1001..340000,
CO   AP001717.1:1001..340000,AP001718.1:1001..340000,AP001719.1:1001..340000,
CO   AP001720.1:1001..340000,AP001721.1:1001..340000,AL163267.2:1001..340000,
CO   AL163268.2:1001..340000,AP001724.1:1001..340000,AP001725.1:1001..340000,
CO   AP001726.1:1001..340000,AP001727.1:1001..340000,AP001728.1:1001..340000,
CO   AP001729.1:1001..340000,AP001730.1:1001..340000,AP001731.1:1001..340000,
CO   AP001732.1:1001..340000,AL163278.2:1001..340000,AL163279.2:1001..340000,
CO   AL163280.2:1001..340000,AL163281.2:1001..340000,AL163282.2:1001..340000,
CO   AL163283.2:1001..340000,AL163284.2:1001..340000,AL163285.2:1001..340000,
CO   AP001741.1:1001..39322,gap(unk100),AP001743.1:1..219256,gap(unk100),
CO   AP001745.1:1..336578,AP001746.1:1001..340000,AP001747.1:1001..340000,
CO   AP001748.1:1001..340000,AP001749.1:1001..26076,gap(unk100),
CO   AP001751.1:1..340000,AP001752.1:1001..340000,AP001753.1:1001..340000,
CO   AP001754.1:1001..340000,AL163300.2:1001..340000,AL163301.2:1001..340000,
CO   AL163302.2:1001..340000,AL163303.2:1001..340000,AP001759.1:1001..340000,
CO   AP001760.1:1001..340000,AP001761.1:1001..39800)
//
ID   BA000006; SV 2; linear; genomic DNA; CON; HUM; 962365 BP.
XX
AC   BA000006;
XX
DT   23-JAN-2003 (Rel. 74, Created)
DT   24-MAR-2007 (Rel. 91, Last updated, Version 3)
XX
DE   Homo sapiens genomic DNA, chromosome 22q11.2, Cat Eye Syndrome region.
XX
KW   .
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-962365
RA   Shimizu N.;
RT   ;
RL   Submitted (05-JUN-2000) to the EMBL/GenBank/DDBJ databases.
RL   Nobuyoshi Shimizu, Keio University, School of Medicine, Molecular Biology;
RL   35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
RL   (E-mail:nshimizu@dmb.med.keio.ac.jp, Tel:81-3-3351-2370,
RL   Fax:81-3-3351-2370)
XX
RN   [2]
RX   DOI; 10.1038/990031.
RX   PUBMED; 10591208.
RA   Dunham I., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M., Clamp M.,
RA   Smink L.J., Ainscough R., Almeida J.P., Babbage A., Bagguley C., Bailey J.,
RA   Barlow K., Bates K.N., Beasley O., Bird C.P., Blakey S., Bridgeman A.M.,
RA   Buck D., Burgess J., Burrill W.D., Burton J., Carder C., Carter N.P.,
RA   Chen Y., Clark G., Clegg S.M., Cobley V., Cole C.G., Collier R.E.,
RA   Connor R.E., Conroy D., Corby N., Coville G.J., Cox A.V., Davis J.,
RA   Dawson E., Dhami P.D., Dockree C., Dodsworth S.J., Durbin R.M.,
RA   Ellington A., Evans K.L., Fey J.M., Fleming K., French L., Garner A.A.,
RA   Gilbert J.G.R., Goward M.E., Grafham D., Griffiths M.N., Hall C., Hall R.,
RA   Hall-Tamlyn G., Heathcott R.W., Ho S., Holmes S., Hunt S.E., Jones M.C.,
RA   Kershaw J., Kimberley A., King A., Laird G.K., Langford C.F.,
RA   Leversha M.A., Lloyd C., Lloyd D.M., Martyn I.D., Mashreghi-Mohammadi M.,
RA   Matthews L., McCann O.T., McClay J., McLaren S., McMurray A.A., Milne S.A.,
RA   Mortimore B.J., Odell C.N., Pavitt R., Pearce A.V., Pearson D.,
RA   Phillimore B.J., Phillips S.H., Plumb R.W., Ramsay H., Ramsey Y.,
RA   Rogers L., Ross M.T., Scott C.E., Sehra H.K., Skuce C.D., Smalley S.,
RA   Smith M.L., Soderlund C., Spragon L., Steward C.A., Sulston J.E.,
RA   Swann R.M., Vaudin M., Wall M., Wallis J.M., Whiteley M.N., Willey D.,
RA   Williams L., Williams S., Williamson H., Wilmer T.E., Wilming L.,
RA   Wright C.L., Hubbard T., Bentley D.R., Beck S., Rogers J., Shimizu N.,
RA   Minoshima S., Kawasaki K., Sasaki T., Asakawa S., Kudoh J., Shintani A.,
RA   Shibuya K., Yoshizaki Y., Aoki N., Mitsuyama S., Roe B.A., Chen F., Chu L.,
RA   Crabtree J., Deschamps S., Do A., Do T., Dorman A., Fang F., Fu Y., Hu P.,
RA   Hua A., Kenton S., Lai H., Lao H.I., Lewis J., Lewis S., Lin S.-P., Loh P.,
RA   Malaj E., Nguyen T., Pan H., Phan S., Qi S., Qian Y., Ray L., Ren Q.,
RA   Shaull S., Sloan D., Song L., Wang Q., Wang Y., Wang Z., White J.,
RA   Willingham D., Wu H., Yao Z., Zhan M., Zhang G., Chissoe S., Murray J.,
RA   Miller N., Minx P., Fulton R., Johnson D., Bemis G., Bentley D.,
RA   Bradshaw H., Bourne S., Cordes M., Du Z., Fulton L., Goela D., Graves T.,
RA   Hawkins J., Hinds K., Kemp K., Latreille P., Layman D., Ozersky P.,
RA   Rohlfing T., Scheet P., Walker C., Wamsley A., Wohldmann P., Pepin K.,
RA   Nelson J., Korf I., Bedell J.A., Hillier L., Mardis E., Waterston R.,
RA   Wilson R., Emanuel B.S., Shaikh T., Kurahashi H., Saitta S., Budarf M.L.,
RA   McDermid H.E., Johnson A., Wong A.C.C., Morrow B.E., Edelmann L., Kim U.J.,
RA   Shizuya H., Simon M.I., Dumanski J.P., Peyrard M., Kedra D., Seroussi E.,
RA   Fransson I., Tapia I., Bruder C.E., O'Brien K.P.;
RT   "The DNA sequence of human chromosome 22";
RL   Nature 402(6761):489-495(1999).
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..962365
FT                   /organism="Homo sapiens"
FT                   /chromosome="22"
FT                   /map="22q11.2"
FT                   /mol_type="genomic DNA"
FT                   /db_xref="taxon:9606"
XX
CO   join(AP000522.1:1..37693,AP000523.1:2273..41306,AP000524.1:474..4455,
CO   AP000525.1:846..39301,AP000526.1:22650..36885,AP000527.1:7214..40562,
CO   AP000528.1:6429..42301,AP000529.1:6550..37981,gap(unk100),
CO   AP000530.1:1..32968,AP000531.1:12539..34029,AP000532.1:7998..37599,
CO   AP000533.1:2490..45597,AP000534.1:2502..37769,AP000535.1:4727..39151,
CO   AP000536.1:5212..39668,AP000537.1:6785..43734,AP000538.1:15492..33760,
CO   AP000539.1:10187..42207,AP000540.2:18532..41100,AP000541.1:2678..34987,
CO   AP000542.1:8603..41389,gap(unk100),AP000543.1:1..36955,
CO   AP000544.1:19046..38993,AP000545.1:4338..37247,AP000546.1:4243..39984,
CO   AP000547.1:4740..123288,AP000365.1:33343..111123)
BioPerl-1.007002/t/data/bug2982.gb000555000766000024       650213155576321 16312 0ustar00cjfieldsstaff000000000000LOCUS       NT_019265 1250660 bp    DNA             CON       16-OCT-2001
DEFINITION  Homo sapiens chromosome 1 working draft sequence segment.
ACCESSION   NT_019265
VERSION     NT_019265.6  GI:16156830
KEYWORDS    .
SOURCE      human.
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1250660)
  AUTHORS   NCBI Annotation Project.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-OCT-2001) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
COMMENT     GENOME ANNOTATION REFSEQ:  NCBI contigs are derived from assembled
            genomic sequence data. They may include both draft and finished
            sequence.
            On Oct 16, 2001 this sequence version replaced gi:15294341.
            COMPLETENESS: not full length.
FEATURES             Location/Qualifiers
     source          1..1250660
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /chromosome="1"
     source          1..3290
                     /note="Accession AL391218 sequenced by The Sanger Centre"
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /clone="RP11-13G5"
     misc_feature    215902..365470
                     /standard_name="RP11-242F24"
                     /note="FISH-mapped clone"
     variation       217508
                     /allele="T"
                     /allele="C"
                     /db_xref="dbSNP:811400"
     mRNA            join(342430..342515,363171..363300,365741..365814,
                     376398..376499,390169..390297,391257..391379,
                     392606..392679,398230..398419,399082..399167,
                     399534..399650,405844..405913,406704..406761,
                     406868..407010,407962..408091,408508..409092)
                     /gene="FLJ10737"
                     /product="hypothetical protein FLJ10737"
                     /transcript_id="XM_057697.1"
                     /db_xref="LocusID:55735"
CONTIG      join(AL391218.9:105173..108462,gap(100),
            complement(AL512330.12:1..182490),
            complement(AL590128.4:9034..81287),gap(100),
            AL591163.7:85799..94832,gap(100),AL591163.7:94933..113245,gap(100),
            AL591163.7:42173..44897,complement(AL590128.4:1..6208),
            AL591163.7:51307..52779,gap(100),AL591163.7:52880..85698,gap(100),
            AL591163.7:113346..126143,complement(AL159177.12:184729..186047),
            AL031447.4:1..112158,complement(AL159177.12:1..72671),
            complement(AL591866.12:23507..86371),AL031848.11:1..142965,
            AL031847.17:1..166418,AL035406.25:1..161651,
            complement(AL356261.20:94599..98345),
            complement(AC026968.3:54432..54579),gap(100),
            complement(AC062024.2:98529..107911),gap(100),
            AC062024.2:7713..11594,gap(100),complement(AL356261.20:1..94498),
            complement(AL356693.18:19988..70853),gap(100),
            AL356693.18:17351..19887,gap(100),
            complement(AL356693.18:3037..17250),gap(100),
            complement(AL356693.18:1..2936),gap(100),AC026968.3:675..2393,
            gap(100),AC026968.3:1..574,gap(100),AL356261.20:179029..182233)
//
BioPerl-1.007002/t/data/bug3021.gmap000444000766000024       324713155576321 16627 0ustar00cjfieldsstaff000000000000>NM_004448 
0	1 A	-17:41277408 2541449272 A	
0	2 A	-17:41277407 2541449271 A	
0	3 A	-17:41277406 2541449270 A	
0	4 A	-17:41277405 2541449269 A	
0	5 C	-17:41277404 2541449268 C	
0	6 T	-17:41277403 2541449267 T	
0	7 G	-17:41277402 2541449266 G	
0	8 C	-17:41277401 2541449265 C	
0	9 G	-17:41277400 2541449264 G	
0	10 A	-17:41277399 2541449263 A	
0	11 C	-17:41277398 2541449262 C	
0	12 T	-17:41277397 2541449261 T	
0	13 G	-17:41277396 2541449260 G	
0	14 C	-17:41277395 2541449259 C	
0	15 G	-17:41277394 2541449258 G	
0	16 C	-17:41277393 2541449257 C	
0	17 G	-17:41277392 2541449256 G	
0	18 G	-17:41277391 2541449255 G	
0	19 C	-17:41277390 2541449254 C	
0	20 G	-17:41277389 2541449253 G	
0	21 T	-17:41277388 2541449252 T	
0	22 G	-17:41277387 2541449251 G	
0	23 A	-17:41277386 2541449250 A	
0	24 G	-17:41277385 2541449249 G	
0	25 C	-17:41277384 2541449248 C	
0	26 T	-17:41277383 2541449247 T	
0	27 C	-17:41277382 2541449246 C	
0	28 G	-17:41277381 2541449245 G	
0	29 C	-17:41277380 2541449244 C	
0	30 T	-17:41277379 2541449243 T	
0	31 G	-17:41277378 2541449242 G	
0	32 A	-17:41277377 2541449241 A	
0	33 G	-17:41277376 2541449240 G	
0	34 A	-17:41277375 2541449239 A	
0	35 C	-17:41277374 2541449238 C	
0	36 T	-17:41277373 2541449237 T	
0	37 T	-17:41277372 2541449236 T	
0	38 C	-17:41277371 2541449235 C	
0	39 C	-17:41277370 2541449234 C	
0	40 T	-17:41277369 2541449233 T	
0	41 G	-17:41277368 2541449232 G	
0	42 G	-17:41277367 2541449231 G	
0	43 A	-17:41277366 2541449230 A	
0	44 C	-17:41277365 2541449229 C	
0	45 C	-17:41277364 2541449228 G	
0	46 C	-17:41277363 2541449227 G	
0	47 C	-17:41277362 2541449226 G	
0	48 G	-17:41277361 2541449225 G	
0	49 C	-17:41277360 2541449224 G	
0	50 A	-17:41277359 2541449223 A	
BioPerl-1.007002/t/data/bug3086.embl000444000766000024       772613155576321 16643 0ustar00cjfieldsstaff000000000000ID   NC_003888; SV 3; linear; unassigned DNA; STD; UNC; 8667507 BP.
XX
AC   NC_003888;
XX
DT   03-MAR-2010
XX
DE   Streptomyces coelicolor A3(2), complete genome.
XX
KW   complete genome
XX
OS   Streptomyces coelicolor A3(2) (2)
OC   Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales;
OC   Streptomycineae; Streptomycetaceae; Streptomyces.
XX
RN   [1]
RP   1-8667507
RX   PUBMED; 12000953.
RA   Bentley,S.D., Chater,K.F., Cerdeno-Tarraga,A.M., Challis,G.L.,
RA   Thomson,N.R., James,K.D., Harris,D.E., Quail,M.A., Kieser,H., Harper,D.,
RA   Bateman,A., Brown,S., Chandra,G., Chen,C.W., Collins,M., Cronin,A.,
RA   Fraser,A., Goble,A., Hidalgo,J., Hornsby,T., Howarth,S., Huang,C.H.,
RA   Kieser,T., Larke,L., Murphy,L., Oliver,K., O'Neil,S., Rabbinowitsch,E.,
RA   Rajandream,M.A., Rutherford,K., Rutter,S., Seeger,K., Saunders,D.,
RA   Sharp,S., Squares,R., Squares,S., Taylor,K., Warren,T., Wietzorrek,A.,
RA   Woodward,J., Barrell,B.G., Parkhill,J. and Hopwood,D.A.;
RT   Complete genome sequence of the model actinomycete Streptomyces coelicolor
RT   A3(2);
RL   Nature 417 (6885), 141-147 (2002)
XX
RN   [2]
RP   1-8667507
RX   PUBMED; 8843436.
RA   Redenbach,M., Kieser,H.M., Denapaite,D., Eichner,A., Cullum,J.,
RA   Kinashi,H. and Hopwood,D.A.;
RT   A set of ordered cosmids and a detailed genetic and physical map for the 8
RT   Mb Streptomyces coelicolor A3(2) chromosome;
RL   Mol. Microbiol. 21 (1), 77-96 (1996)
XX
RN   [3]
RP   1-8667507
RA   ;
RT   Direct Submission;
RL   Submitted (28-MAY-2002) National Center for Biotechnology Information,
RL   NIH, Bethesda, MD 20894, USA
XX
RN   [4]
RP   1-8667507
RA   Bentley,S.D.;
RT   Direct Submission;
RL   Submitted (09-MAY-2002) Sanger Institute, Wellcome Trust Genome Campus,
RL   Hinxton, Cambridge CB10 1SA, United Kingdom
XX
CC   PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI
CC   review. The reference sequence was derived from AL645882. On Jun 22, 2003
CC   this sequence version replaced gi:31340543. COMPLETENESS: full length.
XX
FH   Key             Location/Qualifiers
FH
FT   gene            5241975..5243546
FT                   /locus_tag="SCO4814"
FT                   /db_xref="GeneID:1100255"
FT                   /gene_synonym="SCD63A.25"
FT                   /gene="purH"
FT   CDS             5241975..5243546
FT                   /locus_tag="SCO4814"
FT                   /gene_synonym="SCD63A.25"
FT                   /protein_id="NP_628971.1"
FT                   /gene="purH"
FT                   /transl_table=11
FT                   /note="involved in de novo purine biosynthesis"
FT                   /db_xref="GI:21223192"
FT                   /db_xref="GeneID:1100255"
FT                   /codon_start=1
FT                   /translation="MTATAGSNKRAIRRALVSVYDKTGLEDLARGLHEAGVELVSTGST
FT                   AGRIAAAGVPVTKVEELTGFPECLDGRVKTLHPKVHAGILADLRLESHRQQLDELGVAP
FT                   FDLVVVNLYPFRETVASGATPDECVEQIDIGGPSMVRAAAKNHPSVAVVTSPARYADVL
FT                   LAVEGGGFDLAARKRLAAEAFQHTAAYDVAVASWFAAEYAPVDESGFPDFLGATYERAN
FT                   TLRYGENPHQPAALYTSPEGGGLAQAEQLHGKEMSYNNYTDTDAARRAAYDHAEPCVAI
FT                   IKHANPCGIAIGADVAEAHRKAHDCDPVSAYGGVIAVNRPVSKEMAERVAGIFTEVIVA
FT                   PDYEDGALEALTKKKNIRVLRAPAAPAAPVEVKPIDGGALLQVTDRLQAEGDDPATWTL
FT                   ATGEALSEAELAELAFAWRACRAVKSNAILLAKDGASVGVGMGQVNRVDSAKLAVERAG
FT                   AERAQGAYAASDAFFPFPDGLEILTGAGVKAVVQPGGSVRDELVVEAAKKAGVTMYFTG
FT                   TRHFFH"
FT                   /product="bifunctional
FT                   phosphoribosylaminoimidazolecarboxamide
FT                   formyltransferase/IMP cyclohydrolase"
FT                   /EC_number="3.5.4.10"
FT                   /EC_number="2.1.2.3"
FT   misc_feature    5242401..5243345
FT                   /locus_tag="SCO4814"
FT                   /gene_synonym="SCD63A.25"
FT                   /gene="purH"
FT                   /note="Pfam match to entry PF01808 AICARFT_IMPCHas,
FT                   AICARFT/IMPCHase bienzyme, score 508.80, E-value 4.2e-149"
//
BioPerl-1.007002/t/data/c200-vs-yeast.BLASTN000444000766000024      5200313155576321 20032 0ustar00cjfieldsstaff000000000000BLASTN 2.2.4 [Aug-26-2002]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= contig_200
         (5116 letters)

Database: /data/blast/yeast.nt 
           17 sequences; 12,155,026 total letters

Searching.done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|6323989|ref|NC_001146.1| Saccharomyces cerevisiae chromosome ...   648.7   0.0  

>gi|6323989|ref|NC_001146.1| Saccharomyces cerevisiae chromosome XIV,
              complete chromosome sequence
          Length = 784328

 Score =  648.7 bits (327), Expect = 0.0
 Identities = 830/1000 (83%)
 Strand = Plus / Minus

                                                                          
Query: 2697   ataggccaaaatcttcacatgattcaaaatttcaagaaaatgccccaatatttctcccat 2756
              ||||| ||||||||||| ||||||||||| ||||| ||||||||||| |||||||| |||
Sbjct: 133942 atagggcaaaatcttcatatgattcaaaacttcaaaaaaatgccccagtatttctctcat 133883

                                                                          
Query: 2757   ctaacccttgaaagtcacttgaaaatcattcaagcttggttatttgctgtggaacaaaca 2816
               ||||| | |||||||| |||||||| |||||||| ||||||||||| || |||||||| 
Sbjct: 133882 ttaaccttggaaagtcatttgaaaattattcaagcctggttatttgccgttgaacaaact 133823

                                                                          
Query: 2817   ctagatggaagaggcaaaatgggttccttggtaggggcctctgatgaatttaaaaacggt 2876
               ||||||||||||| |||||||||||||| ||||| || || |||||||||||||| |||
Sbjct: 133822 ttagatggaagaggaaaaatgggttccttagtaggcgcgtcggatgaatttaaaaatggt 133763

                                                                          
Query: 2877   ggaggtgaaaatgccattttagaatattgtcaatggaccatggtctttatcaatcacttg 2936
              || ||||||||||| ||| ||||||| || |||||||| ||||| ||||||||||| || 
Sbjct: 133762 gggggtgaaaatgcgattctagaatactgccaatggacaatggtttttatcaatcattta 133703

                                                                          
Query: 2937   tgttcttgttctgataatgttaatcaaagaatgcttttgagaacaaagctagaaaattgt 2996
              || ||||| ||||||||  | |||||||||||||| || || || || ||||||||||||
Sbjct: 133702 tgctcttgctctgataacataaatcaaagaatgctattaaggacgaaactagaaaattgt 133643

                                                                          
Query: 2997   ggtattctacgaatcatgaataaaataaaattgctagattatgacaaagtgattgatcaa 3056
              || ||| ||||||| ||||| ||||||||| |||||||||| ||||| || ||||| |||
Sbjct: 133642 ggaattttacgaattatgaacaaaataaaactgctagattacgacaaggtaattgaccaa 133583

                                                                          
Query: 3057   attgaattatatgacaataataaactcgatgactttaacgtaaagttggaggcaagtaac 3116
              ||||| |||||||||||||||||||| || || |||||||| || || ||||| |  || 
Sbjct: 133582 attgagttatatgacaataataaacttgacgattttaacgttaaattagaggccaacaat 133523

                                                                          
Query: 3117   aaagcatttaatgtggatttaaaagatccactatcgttgttgaagaatctttgggaaata 3176
              || || |||||||| |||||| | ||||||||||| || || || || |||||||| |||
Sbjct: 133522 aaggcttttaatgtagatttacacgatccactatcattattaaaaaacctttgggatata 133463

                                                                          
Query: 3177   tgtaaaggcacggataatgagaaactgttggtgtctttagtacaacatcttttcctttcc 3236
              |||||||| || || ||||| || || || || |||||||| ||||||||||||||||| 
Sbjct: 133462 tgtaaaggtaccgagaatgaaaagcttttagtatctttagttcaacatcttttcctttct 133403

                                                                          
Query: 3237   agctcgaaattaatcgaagagaatcagaatccctccaaactatccaaacagttgaaatta 3296
              || || || ||||| ||||| || || ||| |||| |||||  | || || |||||| | 
Sbjct: 133402 agttcaaagttaatagaagaaaaccaaaattcctctaaacttactaagcaattgaaactt 133343

                                                                          
Query: 3297   atggattctttagtgactaatgttagtgttgcctcaacagccgacgaagaatcgaatatg 3356
              ||||||||||| ||||||||||||||||||||||||||  | || |||||| | ||||||
Sbjct: 133342 atggattctttggtgactaatgttagtgttgcctcaacttctgatgaagaaactaatatg 133283

                                                                          
Query: 3357   aacatggccattcagcggctttatgatgctatgcaaactgatgaagtagcacgtcgtgca 3416
              || ||||| || ||||||||||| ||||| ||||| ||||||||||| |||||||| || 
Sbjct: 133282 aatatggctatccagcggctttacgatgccatgcagactgatgaagttgcacgtcgagct 133223

                                                                          
Query: 3417   atacttgaaagtagaactctgacnnnnnnnttagaagaaattcaagcggagagggattcc 3476
              ||| | ||||||||| |||| ||       || ||||||||||| || || |||||||| 
Sbjct: 133222 atattagaaagtagagctctaacgaagaaattggaagaaattcaggcagaaagggattct 133163

                                                                          
Query: 3477   ctaagtgaaaagctaggtaaagcagagcacgggctcgttgggcaattagagaacgagcta 3536
               ||||||||||| || | || || |||||||| |||||||| || |||||  | ||| | 
Sbjct: 133162 ttaagtgaaaagttaagcaaggcggagcacggactcgttggacagttagaagatgagttg 133103

                                                                          
Query: 3537   cacggaagagatcgtatactggccaagaaccaaagggttatgcaacagctggaatccgaa 3596
              || |  |||||||||||  | || ||||| || || |||||||| ||||||||| | || 
Sbjct: 133102 catgagagagatcgtattttagctaagaatcagagagttatgcagcagctggaagctgag 133043

                                                                          
Query: 3597   ctagaagaactgaaaaagaaacatcttctggaaaagcatcagcaagaagttgaactgaga 3656
               |||||||  |||||||||| |||||| ||||||||||||||||||| || ||| |||||
Sbjct: 133042 ttagaagagttgaaaaagaagcatcttttggaaaagcatcagcaagaggtagaattgaga 132983

                                                      
Query: 3657   aaaatgttaaccatattaaattccaggcctgaagaaagct 3696
              |||||||| || ||||| ||||| ||||||||||||||||
Sbjct: 132982 aaaatgttgactatattgaattcgaggcctgaagaaagct 132943



 Score =  317 bits (160), Expect = 1e-85
 Identities = 388/464 (83%)
 Strand = Plus / Minus

                                                                          
Query: 2170   gtttgaaaaagcaaccatctctaaacagcatttatcgaggtgggcctgaaattaatacaa 2229
              ||||||||||||| |||||||||||||  |||||| |||||||| |||| |  ||||| |
Sbjct: 134469 gtttgaaaaagcagccatctctaaacaatatttatagaggtggggctgagaacaatacga 134410

                                                                          
Query: 2230   gcgcgtccactcttccaggagacagaactaatagaccgccaatacactatgtgcaacgca 2289
              | || || |||||||||||||||||||| || ||||| || ||||| ||||||||||| |
Sbjct: 134409 gtgcatctactcttccaggagacagaacaaacagaccaccgatacattatgtgcaacgaa 134350

                                                                          
Query: 2290   tcctggccgataagcttacgaccgacgaaatgaaagatttatgggttaccttgaggacag 2349
              ||||||| || || ||||| | ||| || ||||||||||||||||| || || || || |
Sbjct: 134349 tcctggcagacaaacttactagcgatgagatgaaagatttatgggtaactttaagaactg 134290

                                                                          
Query: 2350   aacaattagactgggtagacgcctttatagaccatcagggtcacattgccatggctaacg 2409
              |||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||| |
Sbjct: 134289 aacagttagactgggtagacgcttttatagaccatcagggtcacattgctatggctaatg 134230

                                                                          
Query: 2410   tattgatgaactcaatatacaagacggcgcctcgggaacatttgacgaaggagttattgg 2469
              || | |||||||| || || ||||| || || || ||| | ||||| || || ||||| |
Sbjct: 134229 tactaatgaactctatttataagactgcaccccgagaaaacttgactaaagaattattag 134170

                                                                          
Query: 2470   aaaaggaaaattccttttttaaatgttttagagttttatcgatgctttcacaaggtttat 2529
              | || |||||||| ||||||||||| || ||||| ||||| ||||| ||||||||||| |
Sbjct: 134169 agaaagaaaattcattttttaaatgcttcagagtcttatcaatgctctcacaaggtttgt 134110

                                                                          
Query: 2530   atgaattcagcacgcatagactgatgaccgatactgtcgcagaaggtttgttctccacga 2589
              |||| ||||| || |||||  | ||||| |||||||| ||||||||||| ||||| ||||
Sbjct: 134109 atgagttcagtacacataggttaatgactgatactgttgcagaaggtttattctctacga 134050

                                                          
Query: 2590   agttggttaccaggaaaatggctactgaaattttcgtctgtatg 2633
              |  |||  || ||||||||||| ||||||||||| || ||||||
Sbjct: 134049 aactggccacaaggaaaatggccactgaaatttttgtttgtatg 134006



 Score =  289 bits (146), Expect = 3e-77
 Identities = 701/886 (79%)
 Strand = Plus / Minus

                                                                          
Query: 1246   aaatgttgaagaattcaggttccaagaattcgaattcgaaggaaagtaactccagttcaa 1305
              ||||||||||||||||||| |||||  ||||||| || ||||||||| | || | ||| |
Sbjct: 135384 aaatgttgaagaattcaggctccaaacattcgaactcaaaggaaagtcattcgaattcga 135325

                                                                          
Query: 1306   gttccggtcttttccaaaacttgaagcgtttggctaattcaagcgcatcgaataataatg 1365
              |||| ||| | |||||||| ||||||||||||||||| ||||  ||| ||||||  ||| 
Sbjct: 135324 gttctggtatattccaaaatttgaagcgtttggctaactcaaatgcaacgaatagcaata 135265

                                                                          
Query: 1366   ccacctctccgaacaatgcatcagaacaccagcatcctcccgttggacaggaaacatcca 1425
              |    ||||||| | |||||||  |||| |||||  |||| || ||| | |||   ||||
Sbjct: 135264 cgggttctccgacctatgcatcccaacaacagcactctccagtgggaaacgaagtgtcca 135205

                                                                          
Query: 1426   cttcatctgcatcgtcctcgtcttttagaaggctaaatggaccctccaggtctacatcca 1485
              ||||| ||||||| || || ||||||||||  || |||| ||| || ||||||||||| |
Sbjct: 135204 cttcacctgcatcttcgtcatcttttagaaaactgaatgcaccttctaggtctacatcta 135145

                                                                          
Query: 1486   ctgaagcaaggccgctgaacaagaaagcgacactcaacactcaaaatctgtctcagtaca 1545
              |||| || |||||| |||| || ||| ||||| | ||||| |||||  ||||||| || |
Sbjct: 135144 ctgaggcgaggccgttgaataaaaaatcgacattaaacacacaaaacttgtctcaatata 135085

                                                                          
Query: 1546   tgaacggcaagataagtaccgatgcgccaacatcgtcccagcatgcaaggtcgcattcag 1605
              |||| || ||  |||||   ||||  ||   ||| || ||||| ||||||||||||||| 
Sbjct: 135084 tgaatggtaaattaagtggagatgttcccgtatcctcacagcacgcaaggtcgcattcaa 135025

                                                                          
Query: 1606   tacagtccaaatattcgtactccaagaggacttcctctcaggcgtctaacaagctaacga 1665
              | || || ||||||||||| |||||||||| ||| || |||||||| || |||||||| |
Sbjct: 135024 tgcaatcgaaatattcgtattccaagaggaattcttcacaggcgtccaataagctaacaa 134965

                                                                          
Query: 1666   ggcaacacactgggcagagtcattctgcgacaagtcttttatccctcggctctttaacaa 1725
              |||| || || ||||| ||||| || ||  |||||||| | || |  || ||  |||| |
Sbjct: 134964 ggcagcataccgggcaaagtcactccgcatcaagtcttctctctcaaggttcgctaacta 134905

                                                                          
Query: 1726   acttaagcaaattcaccactcctgatggcaaaatccatctagagatgccctcggacccat 1785
              |||| ||||||||||| || || ||||| |||||  || |||| ||||| ||||||||||
Sbjct: 134904 acttgagcaaattcactacacccgatggtaaaatttatttagaaatgccgtcggacccat 134845

                                                                          
Query: 1786   acgaagtggaagttttgttcgaggacattatgtacaaaagaaacattttccaatctctat 1845
              |||| |||||||||||||| || || |||||||| |||||||| ||||| || ||| |||
Sbjct: 134844 acgaggtggaagttttgtttgaagatattatgtataaaagaaatatttttcagtctttat 134785

                                                                          
Query: 1846   caggtgacaaacaagaagagctaatgagctacagtacggaaaagaaatggttgattgtga 1905
              |||  |||||||||||||  || ||| ||||||| |  || ||||||||| ||||||| |
Sbjct: 134784 cagaggacaaacaagaagctctgatgggctacagcattgagaagaaatggctgattgtta 134725

                                                                          
Query: 1906   aacaagatttacagaacgaattgaaaaagattagagcaaacacgacttcttcttccgctg 1965
              | || |||||||| || ||  | ||||| ||  |||||||||| || ||||||||| |||
Sbjct: 134724 agcaggatttacaaaatgagctaaaaaaaatgcgagcaaacactacatcttcttccactg 134665

                                                                          
Query: 1966   cttctcgtacttcgatagcatcggatcaacatcccatactcacggctaattcaacacttt 2025
              | ||  | |||||||| || ||||| || ||||| || || |||||||||||| | ||||
Sbjct: 134664 cctccagaacttcgatggcgtcggaccatcatcctatccttacggctaattcatctcttt 134605

                                                                          
Query: 2026   catcgcctaaatctgctctgatgacgagtgcttcttctccgacttctactgtatatagta 2085
              | || || ||||||| | ||||||| || || |||||||| || || |||||||| || |
Sbjct: 134604 cgtctcccaaatctgttttgatgacaagcgcctcttctcccacctcaactgtatacagca 134545

                                                            
Query: 2086   acaccctaaaccattccaccactctttcatctgtgggcacgtcaac 2131
              |||   |||| ||||| || ||||||||||| || || ||||||||
Sbjct: 134544 acagtttaaatcattctactactctttcatcggtaggtacgtcaac 134499



 Score =  200 bits (101), Expect = 2e-50
 Identities = 512/649 (78%)
 Strand = Plus / Minus

                                                                          
Query: 35     catcccccttcatgatcagcatcgagaattccggcaccaaggtcctcccagacatattca 94
              |||| ||||| ||||| ||||| |||||||| ||||| || || |||||||| ||||| |
Sbjct: 136636 catcgccctttatgataagcattgagaattcaggcacaaaagttctcccagatatattta 136577

                                                                          
Query: 95     acgcggtcgtgctgatcaccatagtctccgcgggcaactccaacgtgtacatcggctcaa 154
              ||||||||||||| ||||||||  | ||||| || ||||| || |||||||| |||||||
Sbjct: 136576 acgcggtcgtgctaatcaccattctttccgcaggtaactctaatgtgtacattggctcaa 136517

                                                                          
Query: 155    gggtcctgtacagtctatccaaaaacgacttggcgccccggttcctgtcgatcgtgacca 214
              | || ||||| ||||| || |||||   |||||||||  ||||| |||| | ||||||||
Sbjct: 136516 gagtactgtatagtctgtctaaaaatagcttggcgccaaggttcttgtctaacgtgacca 136457

                                                                          
Query: 215    agggcggggtcccctactttgccgttctggcaacatctgtattcgggttcctggccttct 274
                || || || || |||||| | |||||  | ||||| || ||||| ||  |||| ||||
Sbjct: 136456 gaggtggtgttccatacttttctgttctatctacatccgtgttcggatttttggctttct 136397

                                                                          
Query: 275    tggaaacctccgcaggtagtggcaaggctttcaactggctgttaaacattactggtgtgg 334
              | ||    || ||||| || |||||||| || |||||| | || ||||| ||||||||||
Sbjct: 136396 tagaggtttctgcaggcagcggcaaggcctttaactggttattgaacataactggtgtgg 136337

                                                                          
Query: 335    caggatttttcgcatggctgctgatttcattttcgcacatccgctttatgcaagcgataa 394
              | || || || || |||||  ||||||||||||| || ||||| || |||||||| ||||
Sbjct: 136336 ccggtttctttgcctggcttttgatttcattttctcatatccgtttcatgcaagccataa 136277

                                                                          
Query: 395    gcaaacgcggaatatcgaggaacgatctgccttacaaggctcgcatgatgccttatctag 454
              | ||||| || ||||||||| | ||  | ||||| || ||||  |||||||||| | | |
Sbjct: 136276 ggaaacgtggtatatcgagggatgacttaccttataaagctcaaatgatgccttttttgg 136217

                                                                          
Query: 455    cctactacgcatcctttttcatcgccctgatagtcctgatccagggcttcactgcatttg 514
              | || || ||||| ||||||||||| || || || ||||||||||||||||| || || |
Sbjct: 136216 catattatgcatcttttttcatcgctctaattgttctgatccagggcttcaccgctttcg 136157

                                                                          
Query: 515    cgcccagtttccagcctgtagatttcgttgccgcatacatatccgtcttcctatttgttg 574
              | || | ||| |||||| |||| || || || ||||| |||||  | ||||||||| | |
Sbjct: 136156 cacctacttttcagcctatagactttgtcgctgcatatatatcaatattcctatttttgg 136097

                                                                          
Query: 575    caatctggttttcattccagctttggttcaagtgtcccataatcttgaagttgcaggacg 634
              | || ||||| ||||||||  ||||||| ||||| | | || ||| |||| |||||||  
Sbjct: 136096 ccatatggttatcattccaagtttggtttaagtgccgcttactctggaagctgcaggata 136037

                                                               
Query: 635    tcgacatagattccgaccgccgcgaaatagaggagcaggtatggataga 683
              |||| || ||||| ||||||||  |||||||||||  ||||||||||||
Sbjct: 136036 tcgatatcgattctgaccgccggcaaatagaggagttggtatggataga 135988



 Score =  174 bits (88), Expect = 1e-42
 Identities = 154/176 (87%)
 Strand = Plus / Minus

                                                                          
Query: 4041   aaactaaatgatttaaggagggccttggctgaaattcaaatggaaagtaatgatatttcc 4100
              |||||||||||  ||||| |||| ||| ||||||| ||||||||||||||||||||||||
Sbjct: 132598 aaactaaatgacctaaggcgggctttgactgaaatccaaatggaaagtaatgatatttcc 132539

                                                                          
Query: 4101   aagttcaatgtcgaagaacgtgttaatgagctatttaacgaaaagaagtctttggctttg 4160
              || || || ||||||||||||||||||||||||||||| |||||||| ||| ||||||| 
Sbjct: 132538 aaatttaacgtcgaagaacgtgttaatgagctatttaatgaaaagaaatctctggcttta 132479

                                                                      
Query: 4161   aagaggttaaaggaactagaaaccaaatataagggattcggtattgattttaatgt 4216
              |||||  | || ||||||||||| ||||| || ||||| |||||||| ||||||||
Sbjct: 132478 aagagactgaaagaactagaaacaaaatacaaaggatttggtattgactttaatgt 132423



 Score =  151 bits (76), Expect = 2e-35
 Identities = 169/200 (84%)
 Strand = Plus / Minus

                                                                          
Query: 3756   aatattcagaaggtattacaggacggattgtcgagagcgaagaaagattataaagatgac 3815
              ||||| || ||||| |||||||||||||| || ||||| || || ||||| || ||||| 
Sbjct: 132883 aatatccaaaaggtgttacaggacggattatcaagagcaaaaaaggattacaaggatgat 132824

                                                                          
Query: 3816   tcgaaaaaattcggtatgacacttcaacctaataaaaggctaaagatgctaagaatgcaa 3875
              || ||||||||||| |||||||||||||||||||| ||  |||| ||| |||||||||||
Sbjct: 132823 tcaaaaaaattcggcatgacacttcaacctaataagagattaaaaatgttaagaatgcaa 132764

                                                                          
Query: 3876   atggaaaatattgaaaatgaagcaagacagttggaaatgacaaactttgctgagtttgaa 3935
              ||||||||||||||||||||||| || ||  | || |||||||| |||||||| ||||| 
Sbjct: 132763 atggaaaatattgaaaatgaagccaggcaactagagatgacaaattttgctgaatttgag 132704

                                  
Query: 3936   aaggaacgcctcgaacctcc 3955
              || || || || ||||||||
Sbjct: 132703 aaagatcgtcttgaacctcc 132684



 Score =  129 bits (65), Expect = 7e-29
 Identities = 119/137 (86%)
 Strand = Plus / Minus

                                                                          
Query: 4437   gaaatataccaagatgcttctccaagtcaagaaagaagaggcgagtactcagagctatct 4496
              |||||||||||||| || ||||||| |||||||  |||  ||||  ||||||||||||||
Sbjct: 132196 gaaatataccaagacgcatctccaactcaagaactaaggagcgaacactcagagctatct 132137

                                                                          
Query: 4497   gcaggatcaggtcccggatcttttcttgatgccttatcccaaaaatatggcactggtcaa 4556
               ||||||||||||| || |||||||| ||||||||||| ||||||||||| |||||||||
Sbjct: 132136 tcaggatcaggtcctgggtcttttctcgatgccttatctcaaaaatatggtactggtcaa 132077

                               
Query: 4557   aacgtcaccgcatcggc 4573
              || || || ||||||||
Sbjct: 132076 aatgttactgcatcggc 132060



 Score = 85.7 bits (43), Expect = 1e-15
 Identities = 101/119 (84%), Gaps = 1/119 (0%)
 Strand = Plus / Minus

                                                                          
Query: 890    tttttgacatggaagaggcaagaagagaaaaaacagatgtgg-aaactataatccctttt 948
              |||||||| ||||||||| ||  | ||||||||||||||||| |||||| ||||||||||
Sbjct: 135742 tttttgacgtggaagagggaaagaaagaaaaaacagatgtggaaaactagaatccctttt 135683

                                                                         
Query: 949    acaaacaatagcacggacgctttccggagacaacaagacactgacggctgtgtggtaat 1007
              |  ||||||||||||||| ||| |   ||| || | |||||||||||||||||| ||||
Sbjct: 135682 aagaacaatagcacggacccttcctacagataagaggacactgacggctgtgtgttaat 135624


  Database: /data/blast/yeast.nt
    Posted date:  Aug 12, 2003 12:35 PM
  Number of letters in database: 12,155,026
  Number of sequences in database:  17
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 45,084
Number of Sequences: 17
Number of extensions: 45084
Number of successful extensions: 26
Number of sequences better than 1.0e-10: 1
length of query: 5116
length of database: 12,155,026
effective HSP length: 18
effective length of query: 5098
effective length of database: 12,154,720
effective search space: 61964762560
effective search space used: 61964762560
T: 0
A: 0
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 35 (69.9 bits)
BioPerl-1.007002/t/data/c200-vs-yeast.BLASTN.m8000444000766000024       133413155576321 20336 0ustar00cjfieldsstaff000000000000contig_200	gi|6323989|ref|NC_001146.1|	83.50	1000	165	0	2697	3696	133942	132943	0.0	648.7
contig_200	gi|6323989|ref|NC_001146.1|	83.62	464	76	0	2170	2633	134469	134006	1.5e-85	317.7
contig_200	gi|6323989|ref|NC_001146.1|	79.12	886	185	0	1246	2131	135384	134499	3.3e-77	289.9
contig_200	gi|6323989|ref|NC_001146.1|	78.89	649	137	0	35	683	136636	135988	2.4e-50	200.7
contig_200	gi|6323989|ref|NC_001146.1|	87.50	176	22	0	4041	4216	132598	132423	1.3e-42	174.9
contig_200	gi|6323989|ref|NC_001146.1|	84.50	200	31	0	3756	3955	132883	132684	2.0e-35	151.2
contig_200	gi|6323989|ref|NC_001146.1|	86.86	137	18	0	4437	4573	132196	132060	7.2e-29	129.3
contig_200	gi|6323989|ref|NC_001146.1|	84.87	119	17	1	890	1007	135742	135624	9.6e-16	85.73
BioPerl-1.007002/t/data/calm.swiss000444000766000024      3050313155576321 16717 0ustar00cjfieldsstaff000000000000ID   CALM_HUMAN     STANDARD;      PRT;   148 AA.
AC   P62158; P02593; P70667; P99014; Q61379; Q61380;
DT   21-JUL-1986 (Rel. 01, Created)
DT   21-JUL-1986 (Rel. 01, Last sequence update)
DT   01-OCT-2004 (Rel. 45, Last annotation update)
DE   Calmodulin (CaM).
GN   Name=CALM1; Synonyms=CAM1, CALM, CAM;
GN   and
GN   Name=CALM2; Synonyms=CAM2, CAMB;
GN   and
GN   Name=CALM3; Synonyms=CAM3, CAMC;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   SEQUENCE, ACETYLATION SITE ALA-1, AND METHYLATION SITE LYS-115.
RC   TISSUE=Brain;
RX   MEDLINE=82231946; PubMed=7093203;
RA   Sasagawa T., Ericsson L.H., Walsh K.A., Schreiber W.E., Fischer E.H.,
RA   Titani K.;
RT   "Complete amino acid sequence of human brain calmodulin.";
RL   Biochemistry 21:2565-2569(1982).
RN   [2]
RP   SEQUENCE FROM N.A.
RX   MEDLINE=89034207; PubMed=3182832;
RA   Fischer R., Koller M., Flura M., Mathews S., Strehler-Page M.A.,
RA   Krebs J., Penniston J.T., Carafoli E., Strehler E.E.;
RT   "Multiple divergent mRNAs code for a single human calmodulin.";
RL   J. Biol. Chem. 263:17055-17062(1988).
RN   [3]
RP   SEQUENCE FROM N.A.
RX   MEDLINE=88059053; PubMed=2445749;
RA   Sengupta B., Friedberg F., Detera-Wadleigh S.D.;
RT   "Molecular analysis of human and rat calmodulin complementary DNA
RT   clones. Evidence for additional active genes in these species.";
RL   J. Biol. Chem. 262:16663-16670(1987).
RN   [4]
RP   SEQUENCE FROM N.A.
RX   MEDLINE=85022688; PubMed=6385987;
RA   Wawrzynczak E.J., Perham R.N.;
RT   "Isolation and nucleotide sequence of a cDNA encoding human
RT   calmodulin.";
RL   Biochem. Int. 9:177-185(1984).
RN   [5]
RP   SEQUENCE FROM N.A. (CALM1).
RC   TISSUE=Blood;
RX   MEDLINE=95010144; PubMed=7925473;
RA   Rhyner J.A., Ottiger M., Wicki R., Greenwood T.M., Strehler E.E.;
RT   "Structure of the human CALM1 calmodulin gene and identification of
RT   two CALM1-related pseudogenes CALM1P1 and CALM1P2.";
RL   Eur. J. Biochem. 225:71-82(1994).
RN   [6]
RP   SEQUENCE FROM N.A.
RC   TISSUE=Lymphoma;
RA   Kato S.;
RL   Submitted (FEB-1995) to the EMBL/GenBank/DDBJ databases.
RN   [7]
RP   SEQUENCE FROM N.A. (CALM2).
RX   MEDLINE=98346173; PubMed=9681195;
RA   Toutenhoofd S.L., Foletti D., Wicki R., Rhyner J.A., Garcia F.,
RA   Tolon R., Strehler E.E.;
RT   "Characterization of the human CALM2 calmodulin gene and comparison of
RT   the transcriptional activity of CALM1, CALM2 and CALM3.";
RL   Cell Calcium 23:323-338(1998).
RN   [8]
RP   SEQUENCE FROM N.A.
RA   Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S.,
RA   Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y.,
RA   Phelan M., Farmer A.;
RT   "Cloning of human full-length CDSs in BD Creator(TM) system donor
RT   vector.";
RL   Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases.
RN   [9]
RP   SEQUENCE FROM N.A. (CALM1).
RX   MEDLINE=22459283; PubMed=12508121; DOI=10.1038/nature01348;
RA   Heilig R., Eckenberg R., Petit J.-L., Fonknechten N., Da Silva C.,
RA   Cattolico L., Levy M., Barbe V., De Berardinis V., Ureta-Vidal A.,
RA   Pelletier E., Vico V., Anthouard V., Rowen L., Madan A., Qin S.,
RA   Sun H., Du H., Pepin K., Artiguenave F., Robert C., Cruaud C.,
RA   Bruels T., Jaillon O., Friedlander L., Samson G., Brottier P.,
RA   Cure S., Segurens B., Aniere F., Samain S., Crespeau H., Abbasi N.,
RA   Aiach N., Boscus D., Dickhoff R., Dors M., Dubois I., Friedman C.,
RA   Gouyvenoux M., James R., Madan A., Mairey-Estrada B., Mangenot S.,
RA   Martins N., Menard M., Oztas S., Ratcliffe A., Shaffer T., Trask B.,
RA   Vacherie B., Bellemere C., Belser C., Besnard-Gonnet M.,
RA   Bartol-Mavel D., Boutard M., Briez-Silla S., Combette S.,
RA   Dufosse-Laurent V., Ferron C., Lechaplais C., Louesse C., Muselet D.,
RA   Magdelenat G., Pateau E., Petit E., Sirvain-Trukniewicz P., Trybou A.,
RA   Vega-Czarny N., Bataille E., Bluet E., Bordelais I., Dubois M.,
RA   Dumont C., Guerin T., Haffray S., Hammadi R., Muanga J., Pellouin V.,
RA   Robert D., Wunderle E., Gauguet G., Roy A., Sainte-Marthe L.,
RA   Verdier J., Verdier-Discala C., Hillier L.W., Fulton L., McPherson J.,
RA   Matsuda F., Wilson R., Scarpelli C., Gyapay G., Wincker P., Saurin W.,
RA   Quetier F., Waterston R., Hood L., Weissenbach J.;
RT   "The DNA sequence and analysis of human chromosome 14.";
RL   Nature 421:601-607(2003).
RN   [10]
RP   SEQUENCE FROM N.A.
RC   TISSUE=Brain, Lung, Lymph, Placenta, and Urinary bladder;
RX   MEDLINE=22388257; PubMed=12477932; DOI=10.1073/pnas.242603899;
RA   Strausberg R.L., Feingold E.A., Grouse L.H., Derge J.G.,
RA   Klausner R.D., Collins F.S., Wagner L., Shenmen C.M., Schuler G.D.,
RA   Altschul S.F., Zeeberg B., Buetow K.H., Schaefer C.F., Bhat N.K.,
RA   Hopkins R.F., Jordan H., Moore T., Max S.I., Wang J., Hsieh F.,
RA   Diatchenko L., Marusina K., Farmer A.A., Rubin G.M., Hong L.,
RA   Stapleton M., Soares M.B., Bonaldo M.F., Casavant T.L., Scheetz T.E.,
RA   Brownstein M.J., Usdin T.B., Toshiyuki S., Carninci P., Prange C.,
RA   Raha S.S., Loquellano N.A., Peters G.J., Abramson R.D., Mullahy S.J.,
RA   Bosak S.A., McEwan P.J., McKernan K.J., Malek J.A., Gunaratne P.H.,
RA   Richards S., Worley K.C., Hale S., Garcia A.M., Gay L.J., Hulyk S.W.,
RA   Villalon D.K., Muzny D.M., Sodergren E.J., Lu X., Gibbs R.A.,
RA   Fahey J., Helton E., Ketteman M., Madan A., Rodrigues S., Sanchez A.,
RA   Whiting M., Madan A., Young A.C., Shevchenko Y., Bouffard G.G.,
RA   Blakesley R.W., Touchman J.W., Green E.D., Dickson M.C.,
RA   Rodriguez A.C., Grimwood J., Schmutz J., Myers R.M.,
RA   Butterfield Y.S.N., Krzywinski M.I., Skalska U., Smailus D.E.,
RA   Schnerch A., Schein J.E., Jones S.J.M., Marra M.A.;
RT   "Generation and initial analysis of more than 15,000 full-length human
RT   and mouse cDNA sequences.";
RL   Proc. Natl. Acad. Sci. U.S.A. 99:16899-16903(2002).
RN   [11]
RP   STRUCTURE BY NMR OF 94-103.
RX   PubMed=9927666;
RA   Siedlecka M., Goch G., Ejchart A., Sticht H., Bierzyski A.;
RT   "Alpha-helix nucleation by a calcium-binding peptide loop.";
RL   Proc. Natl. Acad. Sci. U.S.A. 96:903-908(1999).
RN   [12]
RP   STRUCTURE BY NMR OF 1-76 AND 82-148.
RX   PubMed=11685248; DOI=10.1038/nsb1101-990;
RA   Chou J.J., Li S., Klee C.B., Bax A.;
RT   "Solution structure of Ca(2+)-calmodulin reveals flexible hand-like
RT   properties of its domains.";
RL   Nat. Struct. Biol. 8:990-997(2001).
RN   [13]
RP   X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
RX   PubMed=1474585;
RA   Chattopadhyaya R., Meador W.E., Means A.R., Quiocho F.A.;
RT   "Calmodulin structure refined at 1.7 A resolution.";
RL   J. Mol. Biol. 228:1177-1192(1992).
RN   [14]
RP   X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS).
RX   PubMed=7803388;
RA   Cook W.J., Walter L.J., Walter M.R.;
RT   "Drug binding by calmodulin: crystal structure of a calmodulin-
RT   trifluoperazine complex.";
RL   Biochemistry 33:15259-15265(1994).
RN   [15]
RP   X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) OF 5-148.
RX   MEDLINE=21666515; PubMed=11807546; DOI=10.1038/415396a;
RA   Drum C.L., Yan S.-Z., Bard J., Shen Y.Q., Lu D., Soelaiman S.,
RA   Grabarek Z., Bohm A., Tang W.-J.;
RT   "Structural basis for the activation of anthrax adenylyl cyclase
RT   exotoxin by calmodulin.";
RL   Nature 415:396-402(2002).
RN   [16]
RP   X-RAY CRYSTALLOGRAPHY (3.6 ANGSTROMS) OF 1-148.
RX   PubMed=12485993;
RA   Shen Y., Lee Y.-S., Soelaiman S., Bergson P., Lu D., Chen A.,
RA   Beckingham K., Grabarek Z., Mrksich M., Tang W.-J.;
RT   "Physiological calcium concentrations regulate calmodulin binding and
RT   catalysis of adenylyl cyclase exotoxins.";
RL   EMBO J. 21:6721-6732(2002).
RN   [17]
RP   X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
RX   PubMed=12577052; DOI=10.1038/nsb900;
RA   Yamauchi E., Nakatsu T., Matsubara M., Kato H., Taniguchi H.;
RT   "Crystal structure of a MARCKS peptide containing the calmodulin-
RT   binding domain in complex with Ca2+-calmodulin.";
RL   Nat. Struct. Biol. 10:226-231(2003).
CC   -!- FUNCTION: Calmodulin mediates the control of a large number of
CC       enzymes by Ca(2+). Among the enzymes to be stimulated by the
CC       calmodulin-Ca(2+) complex are a number of protein kinases and
CC       phosphatases.
CC   -!- PTM: Ubiquitylation results in a strongly decreased activity (By
CC       similarity).
CC   -!- PTM: Phosphorylation results in a decreased activity (By
CC       similarity).
CC   -!- MISCELLANEOUS: This protein has four functional calcium-binding
CC       sites.
CC   -!- SIMILARITY: Contains 4 EF-hand calcium-binding domains.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; J04046; AAA51918.1; -.
DR   EMBL; M19311; AAA35641.1; -.
DR   EMBL; M27319; AAA35635.1; -.
DR   EMBL; U12022; AAB60644.1; -.
DR   EMBL; U11886; AAB60644.1; JOINED.
DR   EMBL; D45887; BAA08302.1; -.
DR   EMBL; U94728; AAC83174.1; -.
DR   EMBL; U94725; AAC83174.1; JOINED.
DR   EMBL; U94726; AAC83174.1; JOINED.
DR   EMBL; BT006818; AAP35464.1; -.
DR   EMBL; BT006855; AAP35501.1; -.
DR   EMBL; BT009916; AAP88918.1; -.
DR   EMBL; AC006536; AAD45181.1; -.
DR   EMBL; BC000454; AAH00454.1; -.
DR   EMBL; BC003354; AAH03354.1; -.
DR   EMBL; BC005137; AAH05137.1; -.
DR   EMBL; BC006464; AAH06464.1; -.
DR   EMBL; BC008597; AAH08597.1; -.
DR   EMBL; BC011834; AAH11834.1; -.
DR   EMBL; BC017385; AAH17385.1; -.
DR   EMBL; BC018677; AAH18677.1; -.
DR   EMBL; BC026065; AAH26065.1; -.
DR   EMBL; BC047523; AAH47523.1; -.
DR   PIR; S48728; MCHU.
DR   PDB; 1AJI; 17-SEP-97.
DR   PDB; 1CLL; 31-OCT-93.
DR   PDB; 1CTR; 20-DEC-94.
DR   PDB; 1IWQ; 11-MAR-03.
DR   PDB; 1J7O; 07-NOV-01.
DR   PDB; 1J7P; 07-NOV-01.
DR   PDB; 1K90; 23-JAN-02.
DR   PDB; 1K93; 23-JAN-02.
DR   PDB; 1LVC; 04-DEC-02.
DR   PDB; 1NKF; 23-MAR-99.
DR   SWISS-2DPAGE; P62158; HUMAN.
DR   Aarhus/Ghent-2DPAGE; 9048; IEF.
DR   OGP; P02593; -.
DR   Genew; HGNC:1442; CALM1.
DR   Genew; HGNC:1445; CALM2.
DR   Genew; HGNC:1449; CALM3.
DR   Reactome; P62158; -.
DR   MIM; 114180; -.
DR   MIM; 114182; -.
DR   MIM; 114183; -.
DR   GO; GO:0005737; C:cytoplasm; TAS.
DR   GO; GO:0005886; C:plasma membrane; TAS.
DR   GO; GO:0005509; F:calcium ion binding; TAS.
DR   GO; GO:0005515; F:protein binding; NAS.
DR   GO; GO:0007186; P:G-protein coupled receptor protein signalin...; TAS.
DR   InterPro; IPR002048; EF-hand.
DR   Pfam; PF00036; efhand; 4.
DR   PRINTS; PR00450; RECOVERIN.
DR   ProDom; PD000012; EF-hand; 2.
DR   PROSITE; PS00018; EF_HAND; 4.
KW   3D-structure; Acetylation; Calcium-binding; Direct protein sequencing;
KW   Methylation; Phosphorylation; Repeat; Ubl conjugation.
FT   INIT_MET      0      0
FT   MOD_RES       1      1       N-acetylalanine.
FT   CA_BIND      20     31       EF-hand 1.
FT   CA_BIND      56     67       EF-hand 2.
FT   CA_BIND      93    104       EF-hand 3.
FT   CA_BIND     129    140       EF-hand 4.
FT   BINDING      21     21       Ubiquitin (multi-) (By similarity).
FT   MOD_RES      44     44       Phosphothreonine (by CaMK4) (By
FT                                similarity).
FT   MOD_RES     115    115       N6,N6,N6-trimethyllysine.
FT   HELIX         6     18
FT   TURN         21     22
FT   TURN         29     30
FT   HELIX        33     36
FT   TURN         37     40
FT   TURN         45     46
FT   HELIX        47     54
FT   TURN         55     55
FT   HELIX        66     72
FT   TURN         73     74
FT   HELIX        75     77
FT   TURN         78     78
FT   TURN         81     81
FT   HELIX        82     92
FT   TURN         94     95
FT   STRAND       99    100
FT   HELIX       102    111
FT   TURN        112    113
FT   HELIX       118    128
FT   STRAND      136    137
FT   HELIX       138    146
SQ   SEQUENCE   148 AA;  16706 MW;  464B8A287475A1CA CRC64;
     ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN
     GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE
     VDEMIREADI DGDGQVNYEE FVQMMTAK
//
BioPerl-1.007002/t/data/catalase-webblast.BLASTP000444000766000024      5272013155576321 21203 0ustar00cjfieldsstaff000000000000BLASTP 2.2.10 [Oct-19-2004]

Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman 
(1997), "Gapped BLAST and PSI-BLAST: a new generation of 
protein database search programs",  Nucleic Acids Res. 25:3389-3402.
RID: 1118324516-16598-103707467515.BLASTQ1
Query= anid_AN8553.1 hypothetical protein 51885 54086 +
          (528 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples 
           2,506,223 sequences; 849,940,114 total letters

                                                                   Score     E
Sequences producing significant alignments:                        (Bits)  Value

gi|40747822|gb|EAA66978.1|  hypothetical protein AN8553.2 [Asp...  1085    0.0   
gi|66846787|gb|EAL87118.1|  catalase, putative [Aspergillus fumig   785    0.0   
gi|38326687|gb|AAR17472.1|  catalase [Cochliobolus heterostrophus   716    0.0   
gi|42553486|gb|EAA76329.1|  hypothetical protein FG06596.1 [Gi...   584    2e-166
gi|2776|emb|CAA39856.1|  catalase [Pichia angusta] >gi|231690|...   336    1e-91 
gi|49651945|emb|CAG78888.1|  unnamed protein product [Yarrowia...   331    3e-90 
gi|56541435|dbj|BAD77826.1|  catalase [Candida dubliniensis]        323    7e-88 
gi|40738591|gb|EAA57781.1|  hypothetical protein AN5918.2 [Asp...   323    9e-88 
gi|46440608|gb|EAK99912.1|  hypothetical protein CaO19.6229 [C...   323    9e-88 
gi|56541439|dbj|BAD77828.1|  catalase [Candida tropicalis]          321    3e-87 
ALIGNMENTS
>gi|40747822|gb|EAA66978.1| hypothetical protein AN8553.2 [Aspergillus nidulans FGSC A4]
 gi|49125822|ref|XP_412690.1| hypothetical protein AN8553.2 [Aspergillus nidulans FGSC A4]
          Length=528

 Score = 1085 bits (2807),  Expect = 0.0
 Identities = 528/528 (100%), Positives = 528/528 (100%), Gaps = 0/528 (0%)

Query  1    MVTTAQSQCRHATEVRPPEACLWPQTRFFFRNSSTSTGRSCWSAWFILANSSGGSGAFGH  60
            MVTTAQSQCRHATEVRPPEACLWPQTRFFFRNSSTSTGRSCWSAWFILANSSGGSGAFGH
Sbjct  1    MVTTAQSQCRHATEVRPPEACLWPQTRFFFRNSSTSTGRSCWSAWFILANSSGGSGAFGH  60

Query  61   FEVTKDVSDLTKAHFLRSPGIKTPVFIRFSTVTLGREYPDLARNPRGFAVKFYTGEGNYD  120
            FEVTKDVSDLTKAHFLRSPGIKTPVFIRFSTVTLGREYPDLARNPRGFAVKFYTGEGNYD
Sbjct  61   FEVTKDVSDLTKAHFLRSPGIKTPVFIRFSTVTLGREYPDLARNPRGFAVKFYTGEGNYD  120

Query  121  IVGLNFPVFFCRDPIQGPDVIRSQYRNPQNFLLDHNSLFDLLANTPEGNHAGMMFFSDHG  180
            IVGLNFPVFFCRDPIQGPDVIRSQYRNPQNFLLDHNSLFDLLANTPEGNHAGMMFFSDHG
Sbjct  121  IVGLNFPVFFCRDPIQGPDVIRSQYRNPQNFLLDHNSLFDLLANTPEGNHAGMMFFSDHG  180

Query  181  TPAGWQNIHGYGCHTFKWVNAEGKFVYIKYHFLADHGQKQFNADEALRYGGEDPDYSKRE  240
            TPAGWQNIHGYGCHTFKWVNAEGKFVYIKYHFLADHGQKQFNADEALRYGGEDPDYSKRE
Sbjct  181  TPAGWQNIHGYGCHTFKWVNAEGKFVYIKYHFLADHGQKQFNADEALRYGGEDPDYSKRE  240

Query  241  LWRTIENGKELSWTAYVQVMKPEDADPEKLGFDPFDVTKVWPKKQFPLQEFGKLTLNKNP  300
            LWRTIENGKELSWTAYVQVMKPEDADPEKLGFDPFDVTKVWPKKQFPLQEFGKLTLNKNP
Sbjct  241  LWRTIENGKELSWTAYVQVMKPEDADPEKLGFDPFDVTKVWPKKQFPLQEFGKLTLNKNP  300

Query  301  ENFHRDVEQAAFSPGSMVPGIEDSPDPLLQFRMFFYRDAQYHRIGVNLHQVPVNCPFMAS  360
            ENFHRDVEQAAFSPGSMVPGIEDSPDPLLQFRMFFYRDAQYHRIGVNLHQVPVNCPFMAS
Sbjct  301  ENFHRDVEQAAFSPGSMVPGIEDSPDPLLQFRMFFYRDAQYHRIGVNLHQVPVNCPFMAS  360

Query  361  SYSSLNFDGQLRVDANHAMNPQYAPNSFVHKFRTDTAEAPYQLADGTVSRKSHFFHEGKA  420
            SYSSLNFDGQLRVDANHAMNPQYAPNSFVHKFRTDTAEAPYQLADGTVSRKSHFFHEGKA
Sbjct  361  SYSSLNFDGQLRVDANHAMNPQYAPNSFVHKFRTDTAEAPYQLADGTVSRKSHFFHEGKA  420

Query  421  SEYDQPRELYERVMDEKARQHLHTNTARLLKLVEYPKIQAKYLGQLLRISEKYARGVYDL  480
            SEYDQPRELYERVMDEKARQHLHTNTARLLKLVEYPKIQAKYLGQLLRISEKYARGVYDL
Sbjct  421  SEYDQPRELYERVMDEKARQHLHTNTARLLKLVEYPKIQAKYLGQLLRISEKYARGVYDL  480

Query  481  LPEKKFGFDEVQSFakgaevagkeakFRPNMPTDKLLGLCPAMAVYGP  528
            LPEKKFGFDEVQSFAKGAEVAGKEAKFRPNMPTDKLLGLCPAMAVYGP
Sbjct  481  LPEKKFGFDEVQSFAKGAEVAGKEAKFRPNMPTDKLLGLCPAMAVYGP  528


>gi|66846787|gb|EAL87118.1| catalase, putative [Aspergillus fumigatus Af293]
          Length=573

 Score =  785 bits (2027),  Expect = 0.0
 Identities = 383/473 (80%), Positives = 421/473 (89%), Gaps = 9/473 (1%)

Query  54   GSGAFGHFEVTKDVSDLTKAHFLRSPGIKTPVFIRFSTVTLGREYPDLARNPRGFAVKFY  113
            GSGAFG+FE TKDVS LTKAHFLRS G++TPVF RFSTVTLGRE+PD ARNPRGFAVKFY
Sbjct  108  GSGAFGYFETTKDVSSLTKAHFLRSVGVRTPVFARFSTVTLGREFPDEARNPRGFAVKFY  167

Query  114  TGEGNYDIVGLNFPVFFCRDPIQGPDVIRSQYRNPQNFLLDHNSLFDLLANTPEGNHAGM  173
            TGEGNYDIVGLNFPVFFCRDPIQGPDVIRSQYRNPQNFLLDHNSLFDLLANTPEGNHAGM
Sbjct  168  TGEGNYDIVGLNFPVFFCRDPIQGPDVIRSQYRNPQNFLLDHNSLFDLLANTPEGNHAGM  227

Query  174  MFFSDHGTPAGWQNIHGYGCHTFKWVNAEGKFVYIKYHFLADHGQKQFNADEALRYGGED  233
            MFFSDHGTP GW+N+HGYGCHTFK VN  G+FVYIKYHF+AD GQKQ  ADEA++  GED
Sbjct  228  MFFSDHGTPVGWRNLHGYGCHTFK-VNKRGEFVYIKYHFIADRGQKQSTADEAIQMCGED  286

Query  234  PDYSKRELWRTIENGKELSWTAYVQVMKPEDADPEKLGFDPFDVTKVWPKKQFPLQEFGK  293
            PD+SKR+L++ IE G+++SWTA+VQ+MKPE+ADP KLGFDPFDVTK        L EFGK
Sbjct  287  PDFSKRDLYQAIEKGEKISWTAHVQIMKPEEADPTKLGFDPFDVTK--------LHEFGK  338

Query  294  LTLNKNPENFHRDVEQAAFSPGSMVPGIEDSPDPLLQFRMFFYRDAQYHRIGVNLHQVPV  353
            L LNKNPENFHRDVEQAAFSPGSMVPGIEDSPDPLLQFRMFFYRDAQYHRIGVNLHQ+PV
Sbjct  339  LVLNKNPENFHRDVEQAAFSPGSMVPGIEDSPDPLLQFRMFFYRDAQYHRIGVNLHQIPV  398

Query  354  NCPFMASSYSSLNFDGQLRVDANHAMNPQYAPNSFVHKFRTDTAEAPYQLADGTVSRKSH  413
            NCPFMASSYSSLNFDG LRVDANHAMNPQYAPNSFVHKFR DTAEAPYQLAD TVSRKSH
Sbjct  399  NCPFMASSYSSLNFDGPLRVDANHAMNPQYAPNSFVHKFRPDTAEAPYQLADNTVSRKSH  458

Query  414  FFHEGKASEYDQPRELYERVMDEKARQHLHTNTARLLKLVEYPKIQAKYLGQLLRISEKY  473
            F+HEGK SEYDQPR LY++VMD + R+HLH NTAR+LK+VEYP+IQ +YL QL  I+ +Y
Sbjct  459  FYHEGKLSEYDQPRALYQKVMDARGREHLHCNTARMLKVVEYPEIQLRYLTQLYCIAPEY  518

Query  474  ARGVYDLLPEKKFGFDEVQSFakgaevagkeakFRPNMPTDKLLGLCPAMAVY  526
            ARGVYDLLPE+KF F +V++ A+GAE  GKEAKFRP+  TD L G CPA  VY
Sbjct  519  ARGVYDLLPEQKFDFSQVKAQAQGAERVGKEAKFRPSKDTDILAGKCPATPVY  571


>gi|38326687|gb|AAR17472.1| catalase [Cochliobolus heterostrophus]
          Length=547

 Score =  716 bits (1849),  Expect = 0.0
 Identities = 339/473 (71%), Positives = 398/473 (84%), Gaps = 7/473 (1%)

Query  54   GSGAFGHFEVTKDVSDLTKAHFLRSPGIKTPVFIRFSTVTLGREYPDLARNPRGFAVKFY  113
            GSGAFG+FE TKDV+ LTKA FL++ G KTP+FIRFSTVT GREYPD ARNPRGFA+KFY
Sbjct  80   GSGAFGYFETTKDVTHLTKADFLKTVGEKTPIFIRFSTVTPGREYPDEARNPRGFAIKFY  139

Query  114  TGEGNYDIVGLNFPVFFCRDPIQGPDVIRSQYRNPQNFLLDHNSLFDLLANTPEGNHAGM  173
            TGEGNYDIVGLNFPVFFCRDPIQGPDVIRSQ+RNP+NFL D++++FDLLANTPEGNHAG+
Sbjct  140  TGEGNYDIVGLNFPVFFCRDPIQGPDVIRSQWRNPKNFLFDYDAIFDLLANTPEGNHAGL  199

Query  174  MFFSDHGTPAGWQNIHGYGCHTFKWVNAEGKFVYIKYHFLADHGQKQFNADEALRYGGED  233
            MFFSDHGTP GW+  HGYGCHTFKWVN +G+FVYIKYHF+A+HGQKQF  ++A +  GED
Sbjct  200  MFFSDHGTPQGWRFNHGYGCHTFKWVNKDGQFVYIKYHFVAEHGQKQFTQEQATQMCGED  259

Query  234  PDYSKRELWRTIENGKELSWTAYVQVMKPEDADPEKLGFDPFDVTKVWPKKQFPLQEFGK  293
            PDYSKR+L+ TIENG+E+ W A+VQVM PE+ADP+KLGFDPFDVTKVWP+KQFP+QEFG+
Sbjct  260  PDYSKRDLYETIENGEEVVWKAHVQVMSPEEADPDKLGFDPFDVTKVWPRKQFPMQEFGR  319

Query  294  LTLNKNPENFHRDVEQAAFSPGSMVPGIEDSPDPLLQFRMFFYRDAQYHRIGVNLHQVPV  353
            L LNKNPENFHRDVEQAAFSPGSMVPG+EDSPDPLLQFRMFFYRDAQYHRIGVNLHQ+PV
Sbjct  320  LVLNKNPENFHRDVEQAAFSPGSMVPGVEDSPDPLLQFRMFFYRDAQYHRIGVNLHQIPV  379

Query  354  NCPFMASSYSSLNFDGQLRVDANHAMNPQYAPNSFVHKFRTDTAEAPYQLADGTVSRKSH  413
            NCPFMA S++SLNFDGQ+RVDANHA N  YAPNSF HKFR D AEAPYQ+ D  +SRKSH
Sbjct  380  NCPFMAKSFASLNFDGQMRVDANHAGNKPYAPNSFAHKFRPDVAEAPYQVNDNIMSRKSH  439

Query  414  FFHEGKASEYDQPRELYERVMDEKARQHLHTNTARLLKLVEYPKIQAKYLGQLLRISEKY  473
            ++HEGK +EYDQ +EL+ RVM  + +Q+   NTA +LK V YP+IQ   +G  L      
Sbjct  440  YWHEGKKNEYDQAKELWSRVMSVQEKQNTIKNTANMLKFVRYPEIQQYNIGTDL------  493

Query  474  ARGVYDLLPEKKFGFDEVQSFakgaevagkeakFRPNMPTDKLLGLCPAMAVY  526
            +RG+YDLLP+  F F EV+  +  A    KE KFR ++  ++L G  P+M VY
Sbjct  494  SRGIYDLLPKPAFDFSEVEELSHTAHEWYKEKKFR-SIDGERLTGFPPSMPVY  545


>gi|42553486|gb|EAA76329.1| hypothetical protein FG06596.1 [Gibberella zeae PH-1]
 gi|46124437|ref|XP_386772.1| hypothetical protein FG06596.1 [Gibberella zeae PH-1]
          Length=539

 Score =  584 bits (1506),  Expect = 2e-166
 Identities = 281/481 (58%), Positives = 338/481 (70%), Gaps = 57/481 (11%)

Query  52   SGGSGAFGHFEVTKDVSDLTKAHFLRSPGIKTPVFIRFSTVTLGREYPDLARNPRGFAVK  111
            S G+GAFG+FE T+DV++LTKA+FL S G KTPVF+RFST TLGRE+PD +RNPRGFA+K
Sbjct  112  SCGAGAFGYFECTRDVTELTKANFLSSVGEKTPVFVRFSTATLGREFPDASRNPRGFAIK  171

Query  112  FYTGEGNYDIVGLNFPVFFCRDPIQGPDVIRSQYRNPQNFLLDHNSLFDLLANTPEGNHA  171
            FYT EGNYDIVGLNFPVFFCRDPIQGPDVIRSQ RNP NFLLDH++LFD LAN PE NHA
Sbjct  172  FYTKEGNYDIVGLNFPVFFCRDPIQGPDVIRSQSRNPSNFLLDHDALFDFLANNPEANHA  231

Query  172  GMMFFSDHGTPAGWQNIHGYGCHTFKWVNAEGKFVYIKYHFLADHGQKQFNADEALRYGG  231
            G+M FSDHGTP GW+  HGYGCHTFKWVNA+G+F+Y+KYHF+A HGQKQF   EA++  G
Sbjct  232  GIMLFSDHGTPQGWRFSHGYGCHTFKWVNADGEFMYVKYHFIAKHGQKQFADSEAMQMCG  291

Query  232  EDPDYSKRELWRTIENGKELSWTAYVQVMKPEDADPEKLGFDPFDVTKVWPKKQFPLQEF  291
            EDPDYSKR+LW  IE G+++ W  +VQ+M P  ADP+ LGFDPFD TK+WP+ +F ++E 
Sbjct  292  EDPDYSKRDLWEAIEKGEDIEWMVHVQIMDPRQADPDTLGFDPFDATKIWPRSEFRMKEL  351

Query  292  GKLTLNKNPENFHRDVEQAAFSPGSMVPGIEDSPDPLLQFRMFFYRDAQYHRIGVNLHQV  351
            G+L LNKNPENFHRDVEQA FSPGSMVPGIEDSPDPLLQFRMF YRDAQYHR+G NLHQ+
Sbjct  352  GRLVLNKNPENFHRDVEQAVFSPGSMVPGIEDSPDPLLQFRMFLYRDAQYHRVGTNLHQI  411

Query  352  PVNCPFMASSYSSLNFDGQLRVDANHAMNPQYAPNSFVHKFRTDTAEAPYQLADGTVSRK  411
            PVNCPFMA SY+S  FDG + VD + A + QY  NSF HKFR DT EAPY++ D  +   
Sbjct  412  PVNCPFMAKSYAS-PFDGPMHVDTDRAGSKQYPLNSFAHKFRPDTDEAPYEVNDNFI---  467

Query  412  SHFFHEGKASEYDQPRELYERVMDEKARQHLHTNTARLLKLVEYPKIQAKYLGQLLRISE  471
                                                             KYL Q+  IS 
Sbjct  468  -------------------------------------------------KYLAQVYIISV  478

Query  472  KYARGVYDLLPEKKFGFDEVQSFakgaevagkeakFRP----NMPTDKLLGLCPAMAVYG  527
             YA+G+Y+LL E +F F +V+   +       +  ++     + P  KL+G  P +AVY 
Sbjct  479  DYAQGIYNLLDEPRFEFSKVKKLGETKFAEAADDWYKEPKFRDKPGSKLVGYPPEIAVYQ  538

Query  528  P  528
            P
Sbjct  539  P  539


>gi|2776|emb|CAA39856.1| catalase [Pichia angusta]
 gi|231690|sp|P30263|CATA_PICAN Peroxisomal catalase
 gi|228770|prf||1811225A catalase
          Length=507

 Score =  336 bits (862),  Expect = 1e-91
 Identities = 163/331 (49%), Positives = 216/331 (65%), Gaps = 2/331 (0%)

Query  54   GSGAFGHFEVTKDVSDLTKAHFLRSPGIKTPVFIRFSTVTLGREYPDLARNPRGFAVKFY  113
            G+GA+G FEVT D++D+  A FL + G KT +F RFSTV   +   D AR+PRGFA KFY
Sbjct  68   GAGAYGVFEVTDDITDVCSAKFLDTVGKKTRIFTRFSTVGGEKGSADTARDPRGFATKFY  127

Query  114  TGEGNYDIVGLNFPVFFCRDPIQGPDVIRSQYRNPQNFLLDHNSLFDLLANTPEGNHAGM  173
            T +GN D+V  N P+FF RDPI+ P  I +Q RNP   L D N  +D L    E  H  M
Sbjct  128  TEDGNLDLVYNNTPIFFIRDPIKFPHFIHTQKRNPATNLKDPNMFWDYLTANDESLHQVM  187

Query  174  MFFSDHGTPAGWQNIHGYGCHTFKWVNAEGKFVYIKYHFLADHGQKQFNADEALRYGGED  233
              FS+ GTPA ++ ++GY  HT+KW N++G++VY++ HF+A+ G      +EA R  GED
Sbjct  188  YLFSNRGTPASYRTMNGYSGHTYKWYNSKGEWVYVQVHFIANQGVHNLLDEEAGRLAGED  247

Query  234  PDYSKRELWRTIENGKELSWTAYVQVMKPEDADPEKLGFDPFDVTKVWPKKQFPLQEFGK  293
            PD+S R+LW  IE G   SW  Y+Q M  E +  +KL F  FD+TKVWP K FPL+ FG+
Sbjct  248  PDHSTRDLWEAIEKGDYPSWECYIQTMTLEQS--KKLPFSVFDLTKVWPHKDFPLRHFGR  305

Query  294  LTLNKNPENFHRDVEQAAFSPGSMVPGIEDSPDPLLQFRMFFYRDAQYHRIGVNLHQVPV  353
             TLN+NP+N++ + EQ AFSP   VPG+E S DP+LQ R+F Y D   HR+G N HQ+PV
Sbjct  306  FTLNENPKNYYAETEQIAFSPSHTVPGMEPSNDPVLQSRLFSYPDTHRHRLGPNYHQIPV  365

Query  354  NCPFMASSYSSLNFDGQLRVDANHAMNPQYA  384
            NCP  + S++ +N DG + VD N    P YA
Sbjct  366  NCPLKSGSFNPINRDGPMCVDGNLGGTPNYA  396


>gi|49651945|emb|CAG78888.1| unnamed protein product [Yarrowia lipolytica CLIB99]
 gi|50557334|ref|XP_506075.1| hypothetical protein [Yarrowia lipolytica]
          Length=492

 Score =  331 bits (849),  Expect = 3e-90
 Identities = 189/438 (43%), Positives = 251/438 (57%), Gaps = 28/438 (6%)

Query  54   GSGAFGHFEVTKDVSDLTKAHFLRSPGIKTPVFIRFSTVTLGREYPDLARNPRGFAVKFY  113
            GSGA+G FEVT D++DL  A FL   G KT  F RFSTV   +   D AR+PRGFA KFY
Sbjct  60   GSGAYGEFEVTDDITDLNCADFLSKIGKKTKTFTRFSTVGGEKGSADAARDPRGFATKFY  119

Query  114  TGEGNYDIVGLNFPVFFCRDPIQGPDVIRSQYRNPQNFLLDHNSLFDLLANTPEGNHAGM  173
            T EGN D V  N PVFF RDP + P  I +Q RNP+  L D   ++D +AN  E  H  M
Sbjct  120  TDEGNIDWVYNNTPVFFIRDPSKFPVFIHTQKRNPETNLKDATMMWDYIANNQECCHQIM  179

Query  174  MFFSDHGTPAGWQNIHGYGCHTFKWVNAEGKFVYIKYHFLADHGQKQFNADEALRYGGED  233
            + FSD GTPA ++ ++GY  HT+KW+  +G F Y++ H   D G K    DEA+   G +
Sbjct  180  VLFSDRGTPANYRQMNGYSGHTYKWIKKDGSFNYVQIHMKTDQGIKNLTNDEAVALSGTN  239

Query  234  PDYSKRELWRTIENGKELSWTAYVQVMKPEDADPEKLGFDPFDVTKVWPKKQFPLQEFGK  293
            PD+++ +L+ +I++G   SWT YVQV  PE A  EKL +  FD+TKVWP  QFPL+ FGK
Sbjct  240  PDHAQEDLFNSIKSGSFPSWTCYVQVCTPEQA--EKLKWSVFDLTKVWPHDQFPLRRFGK  297

Query  294  LTLNKNPENFHRDVEQAAFSPGSMVPGIEDSPDPLLQFRMFFYRDAQYHRIGVNLHQVPV  353
            LTLNKN +N+  + EQAAFSP + VPG E S DP+LQ R+F Y D Q HR+G N  Q+PV
Sbjct  298  LTLNKNVQNYFAETEQAAFSPSNTVPGWETSADPVLQSRLFSYPDTQRHRLGTNFAQIPV  357

Query  354  NCPFMASSYSSLNFDGQLRVDANHAMNPQYAPNSFVHKFRTDTAEAPYQLADGTVSRKSH  413
            NCP+ A  ++  + DGQ+ V+ N    P Y P+SF           P Q        + H
Sbjct  358  NCPYHA--HTPYHRDGQMAVNGNSGSLPNY-PSSF----------EPLQYRQDINLHEKH  404

Query  414  FFHEGKASEY-----------DQPRELYERV-MDEKARQHLHTNTARLLKLVEYPKIQAK  461
                G+A  Y            QP EL++ +      ++HL  N A  L     P++Q K
Sbjct  405  EKWVGEAVAYQWVVGTDGVDFQQPAELWKVLGKTPDQQEHLVYNIAVSLSGAR-PEVQDK  463

Query  462  YLGQLLRISEKYARGVYD  479
              G   ++   + + V D
Sbjct  464  TFGMFDKVDAHFGKLVRD  481


>gi|56541435|dbj|BAD77826.1| catalase [Candida dubliniensis]
          Length=485

 Score =  323 bits (829),  Expect = 7e-88
 Identities = 166/390 (42%), Positives = 239/390 (61%), Gaps = 6/390 (1%)

Query  54   GSGAFGHFEVTKDVSDLTKAHFLRSPGIKTPVFIRFSTVTLGREYPDLARNPRGFAVKFY  113
            GSGA+G FEVT D++D+  A FL + G KT VF RFSTV       D AR+PRGFA KFY
Sbjct  56   GSGAYGVFEVTDDITDVCAAKFLDTVGKKTRVFTRFSTVGGELGSADTARDPRGFATKFY  115

Query  114  TGEGNYDIVGLNFPVFFCRDPIQGPDVIRSQYRNPQNFLLDHNSLFDLLANTPEGNHAGM  173
            T EGN D+V  N PVFF RDP + P  I +Q RNP+  L D N  +D L +  E  H  M
Sbjct  116  TEEGNLDLVYNNTPVFFIRDPSKFPHFIHTQKRNPETHLKDANMFWDYLTSNEESIHQVM  175

Query  174  MFFSDHGTPAGWQNIHGYGCHTFKWVNAEGKFVYIKYHFLADHGQKQFNADEALRYGGED  233
            + FSD GTPA ++ ++GY  HT+KW N +G++ Y++ HF++D G K    +EA    G +
Sbjct  176  ILFSDRGTPASYREMNGYSGHTYKWSNKKGEWFYVQVHFISDQGIKTLTNEEAGALAGSN  235

Query  234  PDYSKRELWRTIENGKELSWTAYVQVMKPEDADPEKLGFDPFDVTKVWPKKQFPLQEFGK  293
            PDY++ +L++ I  G   SWTAY+Q M   +A+ ++  F  FD+TKVWP K++PL+ FGK
Sbjct  236  PDYAQEDLFKNIAAGNYPSWTAYIQTM--TEAEAKEADFSVFDLTKVWPHKKYPLRRFGK  293

Query  294  LTLNKNPENFHRDVEQAAFSPGSMVPGIEDSPDPLLQFRMFFYRDAQYHRIGVNLHQVPV  353
             TLN+NP+N+  +VEQAAFSP   VP +E S DP+LQ R+F Y D   HR+G N  Q+PV
Sbjct  294  FTLNENPKNYFAEVEQAAFSPAHTVPYMEPSADPVLQSRLFSYADTHRHRLGTNYTQIPV  353

Query  354  NCPFMASSYSSLNFDGQLRVDANHAMNPQYAPNSFVHKFRTDTAEAPYQLADGTVSRKSH  413
            NCP   + ++    DG + V+ N   +P Y  +    +F+  + +   ++ +G     + 
Sbjct  354  NCPVTGAVFNPHMRDGAMTVNGNLGSHPNYLASDKPVEFKQFSLQEDQEVWNGAA---TP  410

Query  414  FFHEGKASEYDQPRELYERVMDEKARQHLH  443
            F  +   +++ Q +EL+ +V+     Q  H
Sbjct  411  FHWKATPADFKQAQELW-KVLKRYPNQQEH  439


>gi|40738591|gb|EAA57781.1| hypothetical protein AN5918.2 [Aspergillus nidulans FGSC A4]
 gi|49097190|ref|XP_410055.1| hypothetical protein AN5918.2 [Aspergillus nidulans FGSC A4]
          Length=501

 Score =  323 bits (828),  Expect = 9e-88
 Identities = 162/336 (48%), Positives = 214/336 (63%), Gaps = 6/336 (1%)

Query  54   GSGAFGHFEVTKDVSDLTKAHFLRSPGIKTPVFIRFSTVTLGREYPDLARNPRGFAVKFY  113
            G+GA+G FEVT D+SD+T    L+  G KT  F+RFSTV   +  PD AR+PRGFA KFY
Sbjct  69   GAGAYGEFEVTDDISDITVIDMLKGVGKKTKTFVRFSTVGGEKGSPDSARDPRGFACKFY  128

Query  114  TGEGNYDIVGLNFPVFFCRDPIQGPDVIRSQYRNPQNFLLDHNSLFDLLANTPEGNHAGM  173
            T EGN+D V  N PVFF RDP + P  I +Q RNPQ  L D    +D L+   E  H  M
Sbjct  129  TEEGNWDWVFNNTPVFFLRDPSKFPMFIHTQKRNPQTNLKDATMFWDYLSTHQEAVHQVM  188

Query  174  MFFSDHGTPAGWQNIHGYGCHTFKWVNAEGKFVYIKYHFLADHGQKQFNADEALRYGGED  233
              FSD GTP  +++++GY  HT+KW+  +G F Y++ H   D G K F   EA R   E+
Sbjct  189  HLFSDRGTPYSYRHMNGYSGHTYKWIKPDGTFNYVQLHLKTDQGNKTFTDAEATRLAAEN  248

Query  234  PDYSKRELWRTIENGKELSWTAYVQVMKPEDADPEKLGFDPFDVTKVWPKKQFPLQEFGK  293
            PD+  ++L+  I  G+  SWT YVQ + PE A  EK  ++ FD+TKVWP+ + PL+ FG+
Sbjct  249  PDWHTQDLFNAIARGEYPSWTCYVQTLSPEQA--EKFRWNIFDLTKVWPQSEVPLRRFGR  306

Query  294  LTLNKNPENFHRDVEQAAFSPGSMVPGIEDSPDPLLQFRMFFYRDAQYHRIGV-NLHQVP  352
             TLNKNPEN+  +VEQAAFSP  +VPG+E S DP+LQ R+F Y D   HR+G  N   +P
Sbjct  307  FTLNKNPENYFAEVEQAAFSPSHLVPGVEPSADPVLQARLFSYPDTHRHRLGTSNYQSIP  366

Query  353  VNCPFMASSYSSLNFDGQLRVDANHAMNPQYAPNSF  388
            VNCP  A  ++  + DG + V+ NH  NP Y P++F
Sbjct  367  VNCPLRA--FTPFHRDGAMSVNGNHGANPNY-PSTF  399


>gi|46440608|gb|EAK99912.1| hypothetical protein CaO19.6229 [Candida albicans SC5314]
 gi|46440519|gb|EAK99824.1| hypothetical protein CaO19.13609 [Candida albicans SC5314]
 gi|2317282|dbj|BAA21767.1| catalase [Candida albicans]
          Length=485

 Score =  323 bits (828),  Expect = 9e-88
 Identities = 165/390 (42%), Positives = 239/390 (61%), Gaps = 6/390 (1%)

Query  54   GSGAFGHFEVTKDVSDLTKAHFLRSPGIKTPVFIRFSTVTLGREYPDLARNPRGFAVKFY  113
            GSGA+G FEVT D++D+  A FL + G KT +F RFSTV       D AR+PRGFA KFY
Sbjct  56   GSGAYGVFEVTDDITDICAAKFLDTVGKKTRIFTRFSTVGGELGSADTARDPRGFATKFY  115

Query  114  TGEGNYDIVGLNFPVFFCRDPIQGPDVIRSQYRNPQNFLLDHNSLFDLLANTPEGNHAGM  173
            T EGN D+V  N PVFF RDP + P  I +Q RNP+  L D N  +D L +  E  H  M
Sbjct  116  TEEGNLDLVYNNTPVFFIRDPSKFPHFIHTQKRNPETHLKDANMFWDYLTSNEESIHQVM  175

Query  174  MFFSDHGTPAGWQNIHGYGCHTFKWVNAEGKFVYIKYHFLADHGQKQFNADEALRYGGED  233
            + FSD GTPA ++ ++GY  HT+KW N +G++ Y++ HF++D G K    +EA    G +
Sbjct  176  VLFSDRGTPASYREMNGYSGHTYKWSNKKGEWFYVQVHFISDQGIKTLTNEEAGALAGSN  235

Query  234  PDYSKRELWRTIENGKELSWTAYVQVMKPEDADPEKLGFDPFDVTKVWPKKQFPLQEFGK  293
            PDY++ +L++ I  G   SWTAY+Q M   +A+ ++  F  FD+TKVWP K++PL+ FGK
Sbjct  236  PDYAQEDLFKNIAAGNYPSWTAYIQTM--TEAEAKEAEFSVFDLTKVWPHKKYPLRRFGK  293

Query  294  LTLNKNPENFHRDVEQAAFSPGSMVPGIEDSPDPLLQFRMFFYRDAQYHRIGVNLHQVPV  353
             TLN+NP+N+  +VEQAAFSP   VP +E S DP+LQ R+F Y D   HR+G N  Q+PV
Sbjct  294  FTLNENPKNYFAEVEQAAFSPAHTVPYMEPSADPVLQSRLFSYADTHRHRLGTNYTQIPV  353

Query  354  NCPFMASSYSSLNFDGQLRVDANHAMNPQYAPNSFVHKFRTDTAEAPYQLADGTVSRKSH  413
            NCP   + ++    DG + V+ N   +P Y  +    +F+  + +   ++ +G     + 
Sbjct  354  NCPVTGAVFNPHMRDGAMTVNGNLGSHPNYLASDKPVEFKQFSLQEDQEVWNGAA---TP  410

Query  414  FFHEGKASEYDQPRELYERVMDEKARQHLH  443
            F  +   +++ Q +EL+ +V+     Q  H
Sbjct  411  FHWKATPADFKQAQELW-KVLKRYPNQQEH  439


>gi|56541439|dbj|BAD77828.1| catalase [Candida tropicalis]
          Length=485

 Score =  321 bits (823),  Expect = 3e-87
 Identities = 171/436 (39%), Positives = 254/436 (58%), Gaps = 11/436 (2%)

Query  54   GSGAFGHFEVTKDVSDLTKAHFLRSPGIKTPVFIRFSTVTLGREYPDLARNPRGFAVKFY  113
            GSGA+G FEVT D++D+  A FL + G KT +F RFSTV       D AR+PRGFA KFY
Sbjct  56   GSGAYGVFEVTDDITDICAAKFLDTVGKKTRIFTRFSTVGGEAGSADTARDPRGFATKFY  115

Query  114  TGEGNYDIVGLNFPVFFCRDPIQGPDVIRSQYRNPQNFLLDHNSLFDLLANTPEGNHAGM  173
            T EGN D+V  N PVFF RDP + P  I +Q RN +  L D N  +D L +  E NH  M
Sbjct  116  TEEGNLDLVYNNTPVFFIRDPSKFPHFIHTQKRNSETHLKDANMFWDYLTSNEESNHQVM  175

Query  174  MFFSDHGTPAGWQNIHGYGCHTFKWVNAEGKFVYIKYHFLADHGQKQFNADEALRYGGED  233
            + FSD GTPA ++ ++GY  HT+KW N +G++ Y++ HF+ D G K    +EA    G +
Sbjct  176  ILFSDRGTPASYREMNGYSGHTYKWSNKKGEWHYVQVHFITDQGNKTLTNEEAGSLAGSN  235

Query  234  PDYSKRELWRTIENGKELSWTAYVQVMKPEDADPEKLGFDPFDVTKVWPKKQFPLQEFGK  293
            PDY++ +L++ +  G   SWT Y+Q M   +A  ++  F  FD+TKVWP  ++PL+ FGK
Sbjct  236  PDYAQEDLFKNMLAGNYPSWTCYIQTM--TEAQAKEADFSVFDLTKVWPHGKYPLRRFGK  293

Query  294  LTLNKNPENFHRDVEQAAFSPGSMVPGIEDSPDPLLQFRMFFYRDAQYHRIGVNLHQVPV  353
             TLN+NP+N+  +VEQAAFSP   VP +E S DP+LQ R+F Y D   HR+G N  Q+PV
Sbjct  294  FTLNENPKNYFAEVEQAAFSPAHTVPYMEPSADPVLQSRLFSYSDTHRHRLGTNYTQIPV  353

Query  354  NCPFMASSYSSLNFDGQLRVDANHAMNPQYAPNSFVHKFRTDTAEAPYQLADGTVSRKSH  413
            NCP   + ++    DG + V+ N   +P Y  +    +F+  + +   ++  G     + 
Sbjct  354  NCPVTGAVFNPHMRDGAMNVNGNLGSHPNYLASDKPIEFKQFSLQEDQEVWHGAA---TP  410

Query  414  FFHEGKASEYDQPRELYERVMD-EKARQHLHTNTARLLKLVEYPKIQAKYLGQLLRISEK  472
            F  +   +++ Q +EL++ +      ++HL  N A      + P IQ K +    ++S +
Sbjct  411  FHWKATPADFKQSQELWKVLKRYPNQQEHLAHNVAVHASAADAP-IQDKVIAYFAKVSPE  469

Query  473  YA----RGVYDLLPEK  484
             +    + + +L P K
Sbjct  470  LSNLIKKEILELSPRK  485


Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding 
environmental samples
  Posted date:  Jun 8, 2005  3:44 AM
Number of letters in database: 849940114
Number of sequences in database:  2506223
Lambda     K      H
   0.321    0.138    0.437 
Gapped
Lambda     K      H
   0.267   0.0410    0.140 
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 147123
Number of Hits to DB: 13821951
Number of extensions: 654954
Number of successful extensions: 1258
Number of sequences better than 10: 15
Number of HSP's better than 10 without gapping: 14
Number of HSP's gapped: 1225
Number of HSP's successfully gapped: 15
Number of extra gapped extensions for HSPs above 10: 1206
Length of query: 528
Length of database: 849940114
Length adjustment: 116
Effective length of query: 412
Effective length of database: 69377587
Effective search space: 28583565844
Effective search space used: 21552263428
T: 11
A: 40
X1: 16 (7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (20.4 bits)
S2: 69 (31.2 bits)
BioPerl-1.007002/t/data/cds-266.fas000444000766000024      3602113155576321 16471 0ustar00cjfieldsstaff000000000000>183.m01790 |||similar to unknown protein||chr_13|chr13|183
ATGGACGACAAAGAACTCGAAATACCGGTAGAACATTCCACGGCTTTCGGTCAGCTCGTG
ACGGGTCCCCCGGGAGCGGGTAAATCGACCTATTGTCATGGCTTACATCAGTTCCTTACA
GCCATCGGTAGACCAGTGCATATCATCAACCTCGATCCTGCAGTCCCAAACCCTCCGTAT
CCATGCTCTATAAACATCACGGAACTCATCACACTCGAAAGTGTTATGGAGGAATACAAT
CTAGGACCGAATGGGGCGATGCTTTATTGTATAGAATTCTTAGAGGCCAATTTTGACTGG
CTAGTGGAGAGGCTGGATGAGGTCTTGGCTGAAGAGGGGGGGAATGGATATGTGGTGTTT
GATACGCCGGGTCAAGCAGAGTTATGGACGAACCATGATAGTTTGAAGAACGTGGTCGAA
AAGTTGGTCAAGATGGACTATAGACTAGCGGCTGTGCATCTCAGCGACGCGCACTACATA
ACAGATGCCTCAAAATTCATCTCTGTAGTTTTGCTAGCTCTTCGGGCGATGCTGCAAATG
GAAATGCCGCATTTGAATGTGCTCAGCAAAATAGATTTGATATCAACTTATGGAGAGCTC
CCGTTCGACTTGAGCTATTACACAGAAGTCCAAGATCTGTCATACTTACTGGGCAGTCTG
GATTCAGACCCTCGAACAGCAAAGTACCACAAGTTAAATAAAGCGTTGGTAGAGCTTATA
GAAGGCTTTTCATTAGTCGGATTTCAAACCCTCGCTGTTGAGGACAAAGAATCAATGCTT
AATATCGTCCGTCTTGTCGATAAGATGACGGGCTACATATTTATTCCGTCTGGCGACCTC
GAAGGAACCAACGCCATCAATACCCAAGCTCTGTTTGGTAGTGCCATGTCGTCGGCGAAG
CTTACAGGAAGAGCAGGCGGGGACGTAAGAGATGTTCAGGAGAGATGGATGGATAACAAG
GAGGCTTGGGATGAATGGGAGAAGAAAGAATGGAAGAGAGAAGCAGAGATAAGAGCCCAG
ATGGGCACTGGAATACCAGAAGGGATGAAAGGCGGTGAAGATGCGGAAAGTACAGGTATA
>AAL117C location=AgChr1:complement(140329..141372)
ATGGCGTATGGACAGATTGTGATAGGTCCACCGGGGTCTGGGAAGTCGACATACTGTAAT
GGGTGCAGCCAGTTCTTTAATGCCATCGGCAGACACGCTCGGATCGTGAACATGGACCCT
GCAAACGACTCGCTGCCCTACCAATGCGATGTAGACATTCGAGACTTTATTACTCTGGAG
GAAATCATGAACGAGCAGCACCTGGGGCCCAACGGAGGGCTGGTGTATGCGTTTGAGTCG
GTGGAGCACTCACTGTCGCTGTTTGCGCTGCAGATCAAGACGCTGGTCAAGGATGAGAAC
GCATATCTCGTCTTTGACTGCCCCGGTCAGGTGGAGCTGTTCACGCATCACTCGGCGCTC
TCCAAGATATTCCAGCAGCTGGTGCGCGACTTGGACCTACGAGTGTGCGTGGTGAACTTG
ATGGACAGCATCTACATTACATCGCCGTCGCAGTATGTCTCGGTACTGCTGCTGGCGCTG
CGCTCAATGTTGATGATGGACCTGCCCCATATTAACGTTCTCTCTAAGATCGATATGCTG
AGCTCGTACGGCGACCTGCCGTTCCGGCTCGACTACTATACCGAGGTGCAAGACTTGGAG
TATCTGCAACCGCATATTGAACGCGAACACAAGGGAGCCAAGGCGTTGAGGTACCGCCGA
CTAACGGAGGCCATAGGAGAGGTGGTTTCGGACTTCAACCTGGTCGCCTTCGAGGTGCTT
TGCGTCGATGACAAACAGAGCATGATCAACTTGCAAAGCGCAATCGACAAGGCCAATGGT
TATATTTTTGGTGCCTCCGAAGTTGGTGGCGATACTGTGTGGGCGGAGGCAACCCGCCAG
GGCACTGCTGCAATTGAATATGACATTCAGGACAGATGGATCGACAACAAGGACTTTTAT
GACAAGGAGGAAGAGGCTAGGCGCAAGAAGTTACTTGAGGAGCATGAGCTTCTGGAGAAA
GAAGTTGATGTCAACCAGGATGATGAATGGGAACGCGCAGTGAAGGAATGGGAGTCCCAG
CACTCTGTGAACTTCGTTAAA
>AN2438.1 hypothetical protein (53856 - 52862)
ATGAGTGAGGATCAATTGGGTCCGAACGGCGGTGTTTTGTATGCGTTGGAAGAGCTAGAG
GAGAACTTTGACTTCTTGGAGGAAGGGTTGAAAGAGCTCGGAGAGGACTATATTATCTTC
GATTGTCCCGGCCAGGTAGAAATTTTCACTCACCATTCGTCCTTACGGAATATCTTCTTC
AAGATCCAGAAGATGGGCTATAGACTAATAGTACTACACCTAATCGACTCCTACAACCTC
ACCCTGCCATCGATGTACATCTCCTCTCTTATTCTATGCTTGCGTGCCATGCTCCAAATG
GACCTTCCACATCTCAACGTCCTAACAAAAATCGATAATTTGTCCAATTATACTTCGCTG
CCTTTCAACCTAGATTTCTACACCGAGGTTCAGGACCTTACATACCTCCTCCCCCACTTA
GAGGCAGAGTCCTCCCGGCTATCGCACGAGAAGTTCGGAGCACTGAACAACGCCATCATC
ACACTGATTGAGGAGTTTGGACTCGTGGGCTTCGAAACACTGGCTGTAGAAGATAAAAAG
AGCATGATGAATTTGCTCCGGGCCATTGACCGCGCAAGTGGATACGTGTTTGGGCCTGCA
GAAGGCGCAAATGACTCCGTTTGGCAAGTGGCTGTTCGGGAAGGAATGGGGTCCATGGAT
ATCCGTGATATTCAAGAGCGTTGGATAGATGCCAAAGACGAGTACGATGAGTTGGAACGA
CGGCAGCGAGAGGAGGAGATAAAAAATCACCAGCAAGCTGCAACCTACCAGGCAGGGAAC
GAGGACGACGACGATGATAACGATTACGAATTCGGGCGCAGGATGCCTGTACCAGACAGT
GGAGTGAAAGTGATGCGGAAG
>FG05298.1 hypothetical protein (258181 - 259340)
ATGCCTTTCGCGCAACTCGTTCTCGGTAGTCCGGGCTGCGGAAAGAGTACATACTGTGAT
GGCATACAGCTGACCGGTCAAGTGCATCAGTTCCTAGGCGCCATCGGGCGAGCCTGTTCA
GTCGTCAATCTCGATCCTGCCAACGATCATACCAACTACCCTGCAGCTCTCGACATTCGC
AGTTTGATTAAGCTCGAGGAGATTATGAAAGATGATAAATTAGGACCTAATGGCGGCATC
CTGTATGCCCTCGAAGAGTTGGAACACAATTTCGAGTGGTTGGAAGAAGGACTGAAAGAA
TTCAGCGAAGACTATATTCTTTTCGACTGTCCGGGACAAGTGGAACTATATACACACCAC
AACTCCTTGCGAAACATATTCTACAAGCTCCAGAAGATTGGATTCAGGCTTGTTTCCGTC
CACCTCTCCGACTCCTTCTGCCTCACGCAACCGTCGTTATACGTATCGAACGTCCTCCTC
TCCCTTCGTGCGATGATCCAGATGGATATGCCACACATAAATATTCTCTCCAAGATCGAC
AAAGTTGCCGACTACGACGAACTCCCTTTCAACCTCGATTACTACACAGACGTGGACGAC
CTTACATATTTGACACCCCATCTTGAGACAGAGTCGCCCGCTCTGAGGAGTGAGAAATTC
GGCAAGCTCAACGAGGCGATTGCGAATCTGATCGAGAGCTACGGTCTGGTGCGCTATGAA
GTCCTGGCTGTCGAGAACAAGAAAAGCATGATGCATATCCTCCGTGTCATTGACCGTGCT
GGTGGATACGTCTTTGGTAGTGCTGAAGGAGCCAATGATACAGTCTGGTCAGTTGCCATG
AGGAACGAGTCGTCCATGTTGGGGGTGCAGGACATCCAAGAGCGTTGGATCGACCAAAAG
GTGGAATATGATCAAATGGAGCGTGAGGCCGAAGAAGAACAGGCGCGCATCCAAGAAGAA
CAAGCCATGGAGATGGAACAATCACAGCCACCTCCTGCGCCGACAGGTGGCATGGATCCT
GATTTTGGTGACATGACGGTGCCCAAAGATAGTGGGATCAAAGTAGTTAGAAAG
>MG06110.4 hypothetical protein similar to (NCU09745.1) hypothetical protein (25629 - 24026)
ATGGGATTTCTAGGCGCAATAGGGAGAGCATGTTCCGTAGTAAACCTTGACCCGGCCAAT
GACCATACGAGCTATCCATGTGCCCTCGACATACGAAATCTTGTCACGCTGGAGGAAATC
ATGGGAGACGACAATTTGGGGCCAAACGGTGGCATCCTCTACGCTATTGAAGAGCTGGAG
CATAACTTTGAGTGGTTGGAAGATGGTCTGAAAGAGCTTGGGGACGACTACATACTATTC
GACTGCCCGGGCCAGGTCGAGCTGTACACACATCACAATTCATTGCGCAATATCTTCTTC
AAGTTACAAAAGCTCGGCTACAGACTTGTGGTTGTTCACCTCTCGGACAGCATTTGCCTC
ACTCAACCATCGTTGTACATCTCGAATCTCCTCCTCGCTTTGCGCGCCATGCTCCAGATG
GATCTTTCCCATGTCAATGTCCTCACCAAAATCGACAAGGTGTCTTCATATGACAGACTA
GCCTTCAACCTCGACTTTTATACCGAGGTCCACGATCTTTCGTACCTCCTCCCCGAGCTC
GAAGCCGAGAATCCGTCGCTACGCAGCGAAAAGTTCGCCAAGCTAAACCGAGCCGTCGCA
AACTTGATTGAAGACTTTGGGCTCGTCCGGTTCGAAGTCTTGGCTGTCGAGAATAAGAAA
AGTATGATGCATTTGCTCCGGGTCCTCGATCGTGCCAACGGGTACGTTTTTGGTGGGGCC
GAGGGAGCCAACGACACCGTTTGGCAAGTAGCCATGCGCAACGAGGGCTCCCTGATGGGG
GTCCAAGATATCCAGGAGCGCTGGATCGATAACAAAGAGGCTTATGACGAGATGGAGCAG
CGTGAATGGGAGGAACAGGTCAAGGCACAAGAAGCCATGGCCGAAGCCGATGCAGCAGCT
GCTGAAGAGGGCGACGATGACTTGATGGGAGGCCCAGGTGCTCGA
>NCU09745.1 (NCU09745.1) hypothetical protein (81475 - 83184)
ATGACCTCCCCACTGCCAGTGCAGCAGTTTATGGGCGCCATCGGGCGACAATGCTCGGTA
GTCAACCTCGACCCTGCGAACGACCACACCAACTACCCATGCGCGCTCGACATTCGCGAC
CTTGTCACTTTGGAGGAGATTATGGCAGACGACAAATTGGGTCCCAATGGCGGTATTCTG
TACGCACTTGAAGAGCTGGAAAATAACATGGAATGGCTCGAGAACGGCCTCAAGGAGCTT
GGAGAAGACTATGTGCTTTTTGACTGCCCTGGTCAAGTCGAGCTCTACACCCACCACAAC
TCGTTACGCAACATCTTTTACCGGTTACAGAAGCTGGGCTACAGGCTGGTAGTTGTCCAC
CTTTCCGACTGCTTCTGCCTCACACAACCATCGCTCTACATTTCCAACGTCCTCCTCTCT
TTGCGCGCCATGTTGCAAATGGACCTTCCCCACATCAACGTCCTGACCAAGATTGACAAG
ATCTCGTCCTACGATCCTCTTCCATTCAACCTCGACTATTACACCGAAGTACAAGACCTA
CGGTACCTCATGCCGTCCCTCGACGCGGAATCGCCTGCCCTGAAGAAAGGCAAGTTCACC
AAGCTTAACGAGGCCGTTGCGAACATGGTTGAGCAGTTCGGCCTTGTCAGCTTCGAGGTG
CTGGCAGTCGAGAACAAGAAGAGTATGATGCATCTGTTGCGCGTGATTGACCGTGCAAGT
GGGTACGTCTTTGGCGGCGCTGAGGGAACGAACGACACCGTCTGGCAGGTTGCCATGCGC
AACGAGTCATCATTGCCCGATGCTCTTGATATTCAAGAGAGGTGGATCGATAGCAAAGAA
GAGTATGACGAGATGGAGCGGAAGGAGGAGGAAGAACAAGAAAAACTGCGGGCGGAGCAG
GCACGGGCCGCTGAAGAAGCAGGTCTCGGTGACGGCTCGGTCCCTGGAGTGGCGCCACAG
TTCACCAGTGGCTCGGGAATCCGTGTGACGCTTAGCCTAGTGGCCGCTTTTACCAAATAT
AGCGATCTT
>SPAC144.07c SPAC144.07c conserved eukaryotic protein; ATP-binding protein; similar to S. cerevisiae YOR262W
ATGCCATTTTGTCAAGTGGTCGTTGGACCTCCGGGTTCTGGGAAATCAACTTACTGTTTC
GGAATGTACCAATTATTATCTGCCATAGGAAGGAGTAGTATTATCGTCAATCTTGACCCA
GCAAATGACTTTATCAAATACCCATGCGCAATTGATATTCGTAAAGTTCTCGATGTTGAG
ATGATCCAAAAAGACTATGATTTAGGACCAAATGGAGCACTTATTTATGCTATGGAAGCA
ATTGAATATCACGTTGAATGGTTGCTTAAGGAGCTAAAAAAGCATCGAGATTCATATGTG
ATATTTGATTGCCCTGGTCAAGTTGAGTTATTTACAAACCATAATTCCTTACAAAAAATA
ATCAAAACTTTGGAAAAGGAACTGGATTATAGACCTGTGTCCGTACAACTTGTAGATGCA
TATTGCTGCACGAATCCTTCTGCATATGTTAGTGCACTGCTTGTTTGCCTAAAGGGGATG
CTTCAGCTGGACATGCCACATGTAAATATTTTGTCGAAGGCTGATTTGCTTTGTACGTAT
GGAACTTTACCAATGAAACTAGATTTTTTTACCGAAGTACAAGACCTTTCATATTTGGCG
CCTTTGCTTGATAGAGATAAACGTCTTCAGCGCTATAGTGATTTAAACAAAGCTATTTGT
GAACTTGTTGAAGATTTTAATCTTGTTTCTTTTGAAGTTGTTGCAGTAGAAAATAAAGCC
AGTATGTTACGTGTTCTTCGAAAAATCGATCAAGCAGGTGGATATGCATATGGATCTACA
GAAATTGGTGGTGATGCCGTTTGGGTGAATGCCGTTCGTCAAGGTGGAGACCCTCTTCAA
GGTATTTCGCCTCAGGAAAGATGGATTGACAAGAAAGAGGAATATGACAAATATGAATGG
GAATTAGAGCAAAAATCGACCATGGACGAAGATGAAAATGAAGGG
>Sbay_Contig635.43 YOR262W, Contig c635 67551-68594
ATGCCTTTTGCTCAGATTGTTATTGGACCCCCGGGTTCAGGGAAGTCTACGTATTGTAAC
GGATGTTCACAATTTTTTAATGCTATTGGGAGACATTCTCAGGTGGTAAATATGGATCCC
GCCAATGATGCCTTACCTTATCCGTGTGCTGTGGATATCAGAGATTTTATAACTTTGGAA
GAGATCATGAAAGAGCAACACTTGGGCCCTAATGGTGGTTTGATGTATGCCGTTGAATCT
CTAGATAAGTCCATTGATTTATTTATACTACAGATCAAATCACTTGTAGAAGAAGAGAAG
GCATATGTTGTGTTTGACTGCCCGGGACAAGTTGAGCTGTTTACGCATCATTCTTCATTA
TTCAGCATTTTCAAGAAATTAGAAAAAGAACTAGATATGAGATTCTGTGTGGTGAATTTG
ATTGATTGTTTTTACATGACATCTCCTTCACAATATGTCTCGATTTTGCTCCTGGCATTA
AGGTCTATGCTGATGATGGACCTGCCCCATATCAACGTCTTTTCGAAGATAGATAAGTTG
AAATCATATGGAGAATTGCCATTTAGATTAGATTATTATACAGAAGTTCAAGATTTGGAT
TATTTGGAGCCGTATATTGAAAAAGAAGGTTCTGGTGCACTGGGAAAAAGATATAGCAAA
TTGACTGAAACGATTAGTGAGCTGGTTTCTGATTTTAACCTGGTTTCCTTTGAAGTTTTG
GCTGTGGATGACAAAGAAAGTATGATAAATCTCCAGGGTGTTATTGATAAAGCCAATGGT
TACATATTTGGTGCATCTGAAGTGGGCGGCGACACGGTATGGGCCGAGGCCTCGAGAGAA
GGTGCATTGCTAGCAAGCTATGATATTCAAGATAGGTGGATAGATAATAAAGAAAAATAT
GATAAAGAAGAACAAGAGAAACGGGCTGCAATGGTGAAAGAGCAGGAACTGCAAAATAAA
GAGGTTAATGTAGACGAAGAAGACGAGTGGGAAAATGCACTAAACGACTGGGAAGAAAAA
CAAGGCACAGATTTTGTCAGG
>Scas_Contig692.20 YOR262W, Contig c692 40768-41811
ATGCCATTTGCCCAAATTGTTATCGGACCCCCCGGTTCAGGAAAATCAACATACTGTAAC
GGGTGTTCTCAATTTTTCAACGCCATCGGCAGGCATGGCCAAATAGTGAACATGGATCCA
GCTAATGATGCTCTACCATATCCATGTGCAGTAGACATTCGAGATTTTGTGACTCTGGAG
GAGATTATGCAAGAGCAACAACTGGGCCCCAATGGAGGGTTGATGTATGCTGTGGAATCG
TTAGATGAATCCATCGATCTTTTCATACTACAAATAAAATCTCTAGTTCAAGAGGAGAAG
GCATATTTAGTCTTTGATTGTCCTGGACAAGTAGAGTTGTTTACTCATCATTCATCTCTG
TTCAAAATCTTCAAAAAATTGGAAAAGGAACTAGATATGCGATTTTGTGTGGTGAATTTG
ATTGATTCTTTCTATATTACCTCCCCATCACAGTATGTTTCCATTTTGCTGTTGGCTTTG
AGATCTATGTTAATGATGGACCTACCGCAAATCAATGTTTTCTCCAAGATTGATATGCTG
AAATCCTATGGAGAACTACCTTTTAGATTGGATTATTACACAGAAGTGCAAGATTTAGAT
TATTTACAGCCATTTATTGAGAAGGAGAGTTCCAGTGTTTTGGGTAGAAGATATAGCAAG
TTAACAGAAACGATTAGTGAATTGGTTTCCGATTTTAATTTGGTCTCATTTGAAGTCTTA
GCTGTAGATGATAAACAAAGCATGATTAATTTACAAAGTGTAGTAGACAAGGCTAATGGA
TATATATTTGGAGCATCTGAAGTAGGTGGTGATACTGTTTGGGCAGAAGCCACGCGAGAA
GGTGCAATGATGGTAAATTATGATATACAGGACAGATGGATAGATAACAAAGAAAAGTAC
GATGAAGAGGAGAGAAAAAGACAAGAGGAACAAGCCAAAGAGCAGAACATGCAAGAAAAG
GAGGTAGACGTGGATAATGAGGACGAATGGGAAAAGGCATTGAAGGATTGGGAAGAAAAA
CAAGGAACAGGCTATGTAAGG
>Sklu_Contig2277.4 YOR262W, Contig c2277 4093-5136
ATGCCCTTTGGTCAGATTGTTATCGGCCCTCCTGGTTCAGGAAAGTCTACCTATTGTAAT
GGTTGCTCCCAGTTTTTTAATGCTGTCGGTAGACATGCCCAAGTAATCAACATGGATCCA
GCAAATGATTCGTTACCTTACCCATGTGCCGTTGACATTCGAGATTTCATCACCTTAGAG
GAAATTATGACAGAACAGCAGCTGGGGCCTAATGGTGGATTGATGTACGCCCTAGAATCT
TTGGATAAATCAATCGACTTATTTGTTTTGCAGATCAAATCACTAGTTCAGGATGAACAT
GCTTACGTAGTATTTGATTGTCCGGGGCAAGTGGAGCTTTTTACGCACCATTCGTCCTTG
TTCCGCATATTCAAGAAGTTGGAAAGAGAACTAGATATGAGGTTATGCGTGGTTAATTTA
ATCGATTGTTTTTACATCACCTCTCCTTCACAGTATGTCTCTATTCTTTTGCTAGCTTTG
AGGTCGATGCTGATGATGGACTTACCACACATTAATGTCTTTTCTAAAATTGATTTGTTG
AAATCCTACGGTGAGCTGCCATTCCGACTAGATTATTATACCGAAGTTCAAGAGCTAGAT
TACTTGAAGCCACATATTGACAAGGAAGGGAGCAGCGTCCTTGGAAGGAAATATAGTAGG
TTGACAGAAACCATTAGTGAACTGGTTTCTGACTTTAATCTGGTTTCCTTTGAAGTTTTG
TGTGTTGATGATAAGCAGAGCATGATCAATTTGCAAAGTATTGTGGATAAAGCAAATGGT
TACATATTTGGTGTTTCTGAGATCGGTGGAGATACGGTATGGGCAGAGGCAACGCGACAA
GGCAGTGCAATTGCTAATTACGACATTCAAGAGAGATGGATAGATAATAAAGATATGTAC
GACAGAGAGGAACAGGAAAAACGTGAACAGTTGCTCAAAGAAGAAGAGCTACAGAATAAA
GAAGTAGACGTGGATAAAGGTGATGAGTGGGAAAATGCTTTAAAAGAATGGGAAGAAAAG
CAAGGCATGAGTTATGTAAAA
>Skud_Contig1703.7 YOR262W, Contig c1703 9292-10335 reverse complement
ATGCCATTTGCTCAAATTGTTATCGGCCCACCAGGCTCGGGAAAGTCAACGTATTGTAAC
GGGTGTTCGCAGTTCTTCAACGCCATTGGAAGACATTCTCAAGTGGTGAATATGGATCCC
GCTAATGATGCTTTGCCTTATCCGTGTGCTGTAGATATTAGAGATTTTATAACTTTGGAA
GAGGTTATGCAGGAGCAACAGTTGGGTCCTAATGGTGGTTTAATGTATGCCGTTGAATCC
CTAGATAACTCCATTGATCTATTCATATTACAGATCAAGTCACTTGTAGAAGAAGAAAAG
GCCTACCTTGTGTTTGACTGTCCTGGACAAGTTGAGCTATTCACGCACCATTCATCTTTA
TTTAGCATTTTCAAGAAAATGGAGAAAGAATTGGATATGAGATTCTGTGTCGTAAACTTG
ATTGATTGCTTTTATATGACATCTCCTTCTCAGTATGTTTCAATTTTGCTACTGGCATTA
AGGTCCATGCTAATGATGGATTTGCCTCACATAAACGTTTTTTCCAAAATAGATATGTTA
AAATCATATGGGGAATTACCCTTCAGATTGGATTATTATACAGAGGTCCAGGAGCTAGAT
CATTTGGAGCCATATATTGAAAAGGAAGGCTCTAGCGTTCTAGGAAAAAAATATAGTAAG
TTGACTGAAACGATCAAAGAATTAGTCTCCGATTTTAACTTAGTTTCTTTTGAGGTTCTG
TCCGTGGATGACAAAGAAAGTATGATAAATCTCCAGGGTGTTATTGATAAAGCGAATGGC
TACATATTCGGAGCATCCGAAGTTGGAGGTGATACAGTGTGGGCCGAAGCTTCGAGAGAA
GGTGCATTGTTAGAAAACTACGACATACAGGATAGGTGGATAGATAATAAAGAAACGTAT
GATAAAGAAGAACAAGAGAAGCGTGCATCGCTGTTAAAAGAACAAGAACTGCAGAATAAA
ACGGTTGATGTGAAAGAAGAAGATGAATGGGAAAATGCATTAAAGGAGTGGGAAGAAAAG
CAAGATACGGAGTTTGTCAGA
>Smik_Contig1103.1 YOR262W, Contig c1103 447-1490 reverse complement
ATGCCGTTTGCTCAGATTGTTATTGGCCCACCGGGTTCAGGCAAGTCCACTTATTGTAAC
GGCTGCTCACAGTTCTTCAATGCCATTGGGAGACATTCTCAGGTGGTGAACATGGATCCC
GCTAATGATGCTTTGCCTTATCCTTGTGCTGTGGATATCAGAGATTTTATAACGTTGGAA
GAGATTATGCAAGAGCAACAGTTAGGCCCCAATGGTGGTTTAATGTATGCAGTCGAATCC
TTGGATAAGTCTATTGATTTGTTTTTATTACAGATCAAATCGCTTGTAGAAGAAGAAAAA
GCCTATCTTGTATTCGACTGTCCAGGCCAGGTCGAGTTATTTACTCATCACTCATCCTTA
TTCAATATATTTAAGAAAATGGAGAAAGAATTGGACATGAGGTTCTGTGTAATAAACTTG
ATTGACTGTTTTTACATGACGTCACCCTCACAATATGTCTCAATTTTACTGCTTGCACTA
AGATCCATGTTGATGATGGATCTGCCCCACATAAATGTTTTTTCTAAGATAGATATGTTG
AAATCATATGGAGAACTACCATTTAGACTAGATTATTATACAGAGGTACAGGATCTAGAT
TATTTGGAACCGTATATTGAAAAAGAAGGCTCTAGTGTATTAGGAAAGAAATACAATAAG
TTGACCGACGCAATCAAAGAGCTTGTTTCTGATTTTAACTTGGTTTCCTTTGAGGTTTTG
TCCGTGGATGACAAAGAAAGTATGATAAATCTCCAGGGTGTGATTGATAAAGCAAATGGC
TACATATTTGGTGCGTCTGAGGTTGGTGGTGATACAGTGTGGGCAGAGGCTTCTAGGGAA
GGTGCTCTTTTAACAAGTTACGATATTCAAGATAGGTGGATAGATAATAAGGAAAAGTAT
GACAAAGAAGAAGAAGAGAAACGTGTAATCTTGTTAAAAGAGCAAGAGCTGCAAAATAAA
GCAGTTGACGTGAATGAAGACGATGAGTGGGAAAGTGCGCTCAAGGAATGGGAAGAAAAA
CAAGGTATGGATTTTGTTAGA
>Spar_21273 YOR262W, Contig c261 8817-9860
ATGCCCTTTGCTCAAATTGTTATTGGCCCACCGGGTTCAGGAAAATCAACCTATTGCAAC
GGCTGTTCACAGTTTTTCAATGCCATTGGAAGACATTCTCAGGTAGTAAATATGGACCCT
GCTAATGATGCGTTACCTTACCCATGTGCTGTGGATATTCGAGATTTTATAACTTTGGAG
GAGATTATGCAAGAGCAACAGTTAGGCCCCAATGGTGGTTTGGTGTATGCTGTTGAATCC
TTGGATAAGTCCATTGACTTGTTCATATTACAAATCAAGTCGCTTGTAGAAGAAGAAAAG
GCATATCTCGTATTTGACTGTCCCGGACAAGTGGAGTTATTTACTCATCACTCATCTTTA
TTCAGCATTTTTAAGAAAATGGAAAAAGAATTGGACATGAGATTCTGTGTAGTAAATTTG
ATAGACTGTTTTTACATGACTTCTCCTTCACAATACATCTCCATTTTGCTACTCGCATTA
AGGTCTATGTTAATGATGGATCTACCCCACATTAACGTTTTTTCTAAGATAGATATGTTG
AAATCCTACGGGGAATTACCCTTTAGATTAGATTATTATACAGAGGTTCAGGATCTAGAT
TATTTGGAGCCATATATCGAAAAGGAAGGCTCTAGTGTACTGGGAAAGAAATATAGCAAG
TTAACTGAGACAATCAAAGAGCTTGTTTCAGATTTCAATCTGGTTTCATTTGAGGTCCTG
TCTGTGGATGATAAAGAAAGTATGATAAATCTTCAAGGTGTTATAGATAAAGCAAATGGC
TACATATTCGGCGCATCTGAAGTTGGCGGTGATACAGTTTGGGCTGAGGCCTCTAGAGAA
GGTGCATTACTAGCAAATTACGACATTCAGGACAGATGGATAGACAATAAAGAGAAGTAC
GATAAAGAGGAAGAAGAGAAACGCGCGGCGTTGCTAAAAGAACAAGAGTTGCAAAATAAA
GCCGTTGATGTGAATGAAGAGGATGAGTGGGAAAATGCGCTGAAGGAATGGGAAGAAAAA
CAGGGTACGGATTTCGTTAGA
>YOR262W YOR262W SGDID:S0005788, Chr XV from 817289-818332
ATGCCCTTCGCTCAGATTGTTATTGGTCCACCAGGTTCAGGGAAGTCAACCTATTGCAAC
GGCTGCTCACAGTTCTTCAATGCCATCGGAAGACATTCCCAGGTAGTGAATATGGATCCT
GCTAATGATGCCTTACCTTACCCATGCGCTGTGGATATTCGTGATTTTATAACATTAGAG
GAGATCATGCAAGAGCAACAGTTAGGCCCTAATGGAGGTTTGATGTATGCTGTTGAATCA
TTGGATAATTCTATTGATTTGTTCATTTTACAGATCAAGTCACTTGTAGAAGAAGAAAAA
GCATATCTTGTATTCGACTGTCCGGGCCAAGTGGAGCTATTTACTCATCACTCATCTTTG
TTCAACATCTTTAAAAAAATGGAAAAGGAATTGGACATTAGGTTTTGTGTTGTAAATTTG
ATTGACTGTTTTTACATGACATCCCCTTCACAATATATCTCGATTTTGTTACTTGCATTG
AGGTCTATGTTAATGATGGATCTCCCTCACATCAACGTTTTTTCTAAAATAGATATGCTG
AAATCATACGGAGAATTACCCTTTAGATTAGACTATTATACAGAGGTCCAGGATCTGGAT
TATTTGGAGCCATATATTGAAAAGGAAGGCTCTAGTGTACTGGGAAAGAAATATAGCAAG
TTAACTGAAACAATCAAAGAGCTAGTCTCAGATTTCAACTTAGTATCATTTGAGGTTTTG
TCCGTGGATGACAAAGAAAGTATGATAAATCTTCAAGGTGTTATAGATAAAGCAAATGGC
TACATATTCGGCGCATCCGAAGTTGGTGGTGATACCGTGTGGGCTGAGGCTTCGCGAGAA
GGTGCATTAATAGCGAATTACGACATTCAAGACAGGTGGATAGACAATAAAGAGAAGTAT
GATAAAGAAGAAGAAGAAAAACGTACGGCGTTGTTAAAAGAACAAGAATTGCAAAATAAA
GCTGTTGATGTGAATGAAGAAGATGAGTGGGAAAATGCGCTGAAGGAGTGGGAAGAGAAA
CAAGGAATGGATTTTGTTAGG
BioPerl-1.007002/t/data/cds_sample.embl000444000766000024       275613155576321 17655 0ustar00cjfieldsstaff000000000000ID   EAL24309; SV 1; linear; genomic DNA; ANN; HUM; 192 BP.
XX
PA   CH236947.1
XX
DE   Homo sapiens (human) hypoxia-inducible protein 2
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
OX   NCBI_TaxID=9606;
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..192
FT                   /organism="Homo sapiens"
FT                   /chromosome="7"
FT                   /mol_type="genomic DNA"
FT   CDS             complement(CH236947.1:5840..6031)
FT                   /codon_start=1
FT                   /gene="HIG2"
FT                   /locus_tag="tcag7.897"
FT                   /product="hypoxia-inducible protein 2"
FT                   /note="NP_037464.1"
FT                   /db_xref="UniProtKB/Swiss-Prot:Q9Y5L2"
FT                   /db_xref="UniProtKB/TrEMBL:A4D0Z5"
FT                   /protein_id="EAL24309.1"
FT                   /translation="MKHVLNLYLLGVVLTLLSIFVRVMESLEGLLESPSPGTSWTTRSQ
FT                   LANTEPTKGLPDHPSRSM"
XX
SQ   Sequence 192 BP; 49 A; 58 C; 45 G; 40 T; 0 other; 1039264518 CRC32;
     atgaagcatg tgttgaacct ctacctgtta ggtgtggtac tgaccctact ctccatcttc        60
     gttagagtga tggagtccct agagggctta ctagagagcc catcgcctgg gacctcctgg       120
     accaccagaa gccaactagc caacacagag cccaccaagg gccttccaga ccatccatcc       180
     agaagcatgt ga                                                           192
//
BioPerl-1.007002/t/data/chad100.scf000444000766000024     23533613155576321 16561 0ustar00cjfieldsstaff000000000000.scf"½€ùhÊ:2.00še()
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+T+C#+G,+C:+CE+AQ3A\3Gj3Tv3Gƒ3G8Tš8A¦8T³8GÀ8GÌ3T×3Cä3Cò+Tÿ+G
+A
+C
!+A
-+G
:8G
G8A
S8G
`8A
k8A
w8T
ƒ3T
3T
œ-T
¦-C
²+C
À+T
Í+G
Ö+C
ã+C
ñ+G
ý3G
3A8T!8G-3G:3TE3CS3T_3Tk8Tw8T„+G+Gœ+A¥+C±+A¾+GË8AÖ8Tá8Cí8Aú8G8A3G3A*3T43CA3CM-CY-Ae-Gs-A}+GŠ+T•+Až+C®+Tº+TÄ+AÐ+AÜ+Aæ+Cõ+G+G-T8G&8A28A>8GK3TW+Tc+Gm+C|+Tˆ+G”-G¡3A¬-G¹+AÃ+CÑ+TÚ+Aç+Tô+G+G+C+T#+A0+T=+GH8AS8C`8Cl3Cx3Aƒ3T‘3T3T©+Gµ+GÂ+AË+CÙ+Tæ+Tò3Gþ8G	8C8A 8A,8G98AE3AP3G[3Ci3Cv3T‚3GŽ8A™3G¦-A±-A»-CÉ-TÕ-Tá-Tî+Gø+C(T(A(A(+A43T>3AI3CV3Ca8Am3Ay3G…8C“8CŸ8T¬8T¸8TÄ8GÐ-AÛ-Gæ-Cõ-T-G-A3T"3C/3C93AF+TR+G]-Cl-Gw-Aƒ-G8A›8T§3G³'GÀ&GÊ&CÚ&Tã&Að&Tü(G8T8T!8G-8G:8GF8AR8G]3Ci(Av(G€(C(T›(G§3G³8TÀ3TÌ3T×3Cá3Aí3Tù3C-A-T-C)3C53CA3TN8GY8Ad3Ao3G{3C‰(T”(T¡(Tª(Aµ(AÂ(AÌ3CØ3Aã3Að3Aü-T-A-C-G,3G8-AD#GO#C^#Tf#As#A}#CŒ'T˜(G¤3T°8G½8GÉ8TÔ8Cà8Cí8Tú8G8A8A3G'3C43CB*GM*TX*Ce8Tq8G}8G‰3T–3T¡3C«3A·3AÃ-GÐ(AÚ-Cè-Tó-Gÿ3G-G(G#(C2%T<(CI(TU(G_(Cm(Tz-T„-C3Tœ3T¨8G´8A¿8TË8G×8Gã3Aî3Aú3A3C3A-C&(A2(T@3TL(GW(Ad%An'C|%T…%A%Cž(Tª.T·(TÂ,GÏ(GÙ(Cå(Að(Aý G	AA C* A6 TA(CN(C["Ce AqA| Tˆ C‘ Až A¨"C¶(CÃ(TÐ.TÛ(Gæ(Tó(Tý.C
(T(C"%G+%C9%CF(GQ.T\(Ag(Gt!T€TŒG•C¤T°G»AÅGÓGßTìTøG T T(C&"T0(C=(CI(TU0C`"Gm"Gx0Tƒ0G0G›(A¦(G±(C¿(CÍ(G×(Aá(GïTøACT A&C1(A=0GJ"AU Aa"Tl Cv A€$CŽ$C˜ A¤ A®"Cº GÇGÓ AÞ Tì TöGG"A0T&0T10T=(TI GTA^GlGxA‚CŒA˜A¥G°C¾TÇAÑCÜ Aæ(Có(Cÿ(C 0C G #G 0A 7G EG RT ZC gC rA }(T ‹ T ˜ T £ G ­(A ¸T ÃC Ï"C Û"T çT ôT þA!
G!
G!A!)C!7T!CT!OG!YC!fT!oA!{A!„G!‘G!žA!¦C!³C!¾C!ËC!ØG!ãA!ïA!÷C"A"
A"G"#G"0A";G"EC"ST"]C"jT"sC"C"‹T"•C"žA"©A"»GSIGN=A=587,C=301,G=615,T=409
SPAC= 11.91
PRIM=0
MACH=SRC3700
DYEP=DT3700POP6{BD}v5.mob
NAME=ML4942R
LANE=89
GELN=
PROC=
RTRK=
CONV=phred version=0.980904.e
COMM=MeristemLib_DH12075
SRCE=ABI 373A or 377BioPerl-1.007002/t/data/char-interleave.nex000444000766000024       104413155576321 20454 0ustar00cjfieldsstaff000000000000#NEXUS

BEGIN TAXA;
      dimensions ntax=8;
      taxlabels A B C D E F G H;  
END;

BEGIN CHARACTERS;
      dimensions nchar=6;
      format interleave datatype=protein missing=? gap=-;
      charlabels one two three four five six;
      matrix
A     W I T
B     W I T
C     W I T
D     W I T
E     W I T
F     W I T
G     W I T
H     W I T

A     H - B
B     H - A
C     H - D
D     H - C
E     H - F
F     H - E
G     H - H
H     H - G;
END;

BEGIN TREES;
       tree basic_bush = (((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1);
END;BioPerl-1.007002/t/data/char-matrix-spaces.nex000444000766000024        76013155576321 21062 0ustar00cjfieldsstaff000000000000#NEXUS

BEGIN TAXA;
      dimensions ntax=8;
      taxlabels A B C D E F G H;  
END;

BEGIN CHARACTERS;
      dimensions nchar=6;
      format datatype=protein missing=? gap=-;
      charlabels one two three four five six;
      matrix
A     W I T  H - B
B     W I T  H - A
C     W I T  H - D
D     W I T  H - C
E     W I T  H - F
F     W I T  H - E
G     W I T  H - H
H     W I T  H - G;
END;

BEGIN TREES;
       tree basic_bush = (((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1);
END;BioPerl-1.007002/t/data/characters+trees.nexml.xml000444000766000024      5627613155576321 22031 0ustar00cjfieldsstaff000000000000


         
    
        
    
        
        
        
        
        
    
    
		
		
		
		
		
	
    
    
    	
	      
	        
	        
	      
	      
	      
	      
	      
        
        
                
            
            
                
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                A C G C T C G C A T C G C A T C
            
            
                A C G C T C G C A T C G C A T T
            
            
                A C G C T C G C A T C G C A T G
            
        
    
    
    
    
      
        
        
        
        
        
          
          
        
        
          
          
        
        
          
          
        
        
          
          
        
        
          
          
        
        
          
          
        
        
          
          
          
        
        
          
          
          
        
        
          
          
          
        
        
          
          
          
        
        
          
          
          
          
        
        
          
          
          
          
        
        
        
          
          
          
          
          
          
          
          
          
          
          
          
          
          
          
          
          
        
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
          
      
        
            
                ACGCUCGCAUCGCAUC
            
            
                ACGCUCGCAUCGCAUC
            
            
                ACGCUCGCAUCGCAUC
            
        
    
    
    
	    
	      
	      
	      
	      
	      	      	      
	        
        
            
                -1.545414144070023 -2.3905621575431044 -2.9610221833467265 0.7868662069161243 0.22968509237534918
            
            
                -1.6259836379710066 3.649352410850134 1.778885099660406 -1.2580877968480846 0.22335354995610862
            
            
                -1.5798979984134964 2.9548251411133157 1.522005675256233 -0.8642016921755289 -0.938129801832388
            
            
                2.7436692306788086 -0.7151148143399818 4.592207937774776 -0.6898841440534845 0.5769509574453064
            
            
                3.1060827493657683 -1.0453787389160105 2.67416332763427 -1.4045634106692808 0.019890469925520196
            
        
    
    
    
        
            
            
                                                
                                
                                 
                                    
                    
                                        
                
                
                    
                    
                      
            
            
            
            
            
        
            
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BioPerl-1.007002/t/data/characters.nexml.old.xml000444000766000024      5143113155576321 21454 0ustar00cjfieldsstaff000000000000



    
    
    
        $Author: rvos $
        $Date: 2009-03-13 01:57:49 -0400 (Fri, 13 Mar 2009) $
        $Header: $
        $Id: characters.xml 970 2009-03-13 05:57:49Z rvos $
        $Rev: 970 $
        $URL: http://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/examples/characters.xml $
              
    
        
    
        
        
        
        
        
    
    
    
    	
	      
	        
	        
	      
	      
	      
	      
	      
        
        
                
            
            
                
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                A C G C T C G C A T C G C A T C
            
            
                A C G C T C G C A T C G C A T T
            
            
                A C G C T C G C A T C G C A T G
            
        
    
    
    
    
      
        
        
        
        
        
          
          
        
        
          
          
        
        
          
          
        
        
          
          
        
        
          
          
        
        
          
          
        
        
          
          
          
        
        
          
          
          
        
        
          
          
          
        
        
          
          
          
        
        
          
          
          
          
        
        
          
          
          
          
        
        
        
          
          
          
          
          
          
          
          
          
          
          
          
          
          
          
          
          
        
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
          
      
        
            
                ACGCUCGCAUCGCAUC
            
            
                ACGCUCGCAUCGCAUC
            
            
                ACGCUCGCAUCGCAUC
            
        
    
    
    
	    
	      
	      
	      
	      
	      	      	      
	        
        
            
                -1.545414144070023 -2.3905621575431044 -2.9610221833467265 0.7868662069161243 0.22968509237534918
            
            
                -1.6259836379710066 3.649352410850134 1.778885099660406 -1.2580877968480846 0.22335354995610862
            
            
                -1.5798979984134964 2.9548251411133157 1.522005675256233 -0.8642016921755289 -0.938129801832388
            
            
                2.7436692306788086 -0.7151148143399818 4.592207937774776 -0.6898841440534845 0.5769509574453064
            
            
                3.1060827493657683 -1.0453787389160105 2.67416332763427 -1.4045634106692808 0.019890469925520196
            
        
    
    
    
        
            
            
                                                
                                
                                 
                                    
                    
                                        
                
                
                    
                    
                      
            
            
            
            
            
        
            
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BioPerl-1.007002/t/data/cmsearch.multi.out000444000766000024      4150313155576321 20362 0ustar00cjfieldsstaff000000000000# cmsearch :: search CM(s) against a sequence database
# INFERNAL 1.1.1 (July 2014)
# Copyright (C) 2014 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query CM file:                         multimodel.c.cm
# target sequence database:              multiseqs.fa
# number of worker threads:              4
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       tRNA5  [CLEN=72]
Hit scores:
 rank     E-value  score  bias  sequence        start    end   mdl trunc   gc  description
 ----   --------- ------ -----  -------------- ------ ------   --- ----- ----  -----------
  (1) !   2.9e-21   71.5   0.0  mrum-tRNA.1         1     72 +  cm    no 0.50  -
  (2) !     2e-20   68.8   0.0  mrum-tRNA.2         1     73 +  cm    no 0.67  -
  (3) !   6.1e-19   64.1   0.0  mrum-tRNA.3         1     74 +  cm    no 0.59  -
  (4) !     2e-18   62.5   0.0  mrum-tRNA.4         1     75 +  cm    no 0.61  -
  (5) !   2.1e-18   62.4   0.0  AAGA01015927.1    229    302 +  cm    no 0.62  Metagenome sequence AHAI1002.g1, whole genome shotgun sequence
  (6) !   3.6e-18   61.7   0.0  mrum-tRNA.5         1     74 +  cm    no 0.53  -
  (7) !   2.2e-17   59.2   0.0  mrum-tRNA.6         1     73 +  cm    no 0.51  -
  (8) !   2.2e-17   59.2   0.0  mrum-tRNA.7         1     75 +  cm    no 0.60  -
  (9) !   2.4e-17   59.1   0.0  mrum-tRNA.8         1     74 +  cm    no 0.59  -
 (10) !   2.7e-17   58.9   0.0  mrum-tRNA.9         1    110 +  cm    no 0.61  -
 (11) !   8.7e-17   57.3   0.0  mrum-tRNA.10        1     72 +  cm    no 0.42  -
 (12) !   1.4e-15   53.5   0.0  AAGA01015927.1    314    386 +  cm    no 0.59  Metagenome sequence AHAI1002.g1, whole genome shotgun sequence


Hit alignments:
>> mrum-tRNA.1  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (1) !   2.9e-21   71.5   0.0  cm        1       72 []           1          72 + [] 1.00    no 0.50

                   v                                             v             v     v    NC
                 (((((((,,<<<<_______>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgUGGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 G: G::AUAGC:CA+UGG AG:GCG:::G:CUG+CA :C:::AGGU : GGGUUCGAUUCCC :U::C :CA
  mrum-tRNA.1  1 GGAGCUAUAGCUCAAUGGCAGAGCGUUUGGCUGACAUCCAAAAGGUUAUGGGUUCGAUUCCCUUUAGCCCCA 72
                 ************************************************************************ PP

>> mrum-tRNA.2  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (2) !     2e-20   68.8   0.0  cm        1       72 []           1          73 + [] 1.00    no 0.67

                                                                                           NC
                 (((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 G::::C UAGC:CAGU GG AG:GCGC:::CCU+ CAAG:::GAGG CC:GGGUUC A UCCC:G G::::CA
  mrum-tRNA.2  1 GGGCCCGUAGCUCAGUuGGGAGAGCGCUGCCCUUGCAAGGCAGAGGCCCCGGGUUCAAAUCCCGGUGGGUCCA 73
                 ************************************************************************* PP

>> mrum-tRNA.3  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (3) !   6.1e-19   64.1   0.0  cm        1       72 []           1          74 + [] 1.00    no 0.59

                                                                                            NC
                 (((((((,,<<<<___..____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgU..GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 G::::CAUAGC::AG   GGUA::GCGC :G:CU + AA:C: GA GUC::GGGUUCGA UCCC::UG::::CA
  mrum-tRNA.3  1 GGGCCCAUAGCUUAGCcaGGUAGAGCGCUCGGCUCAUAACCGGGAUGUCAUGGGUUCGAAUCCCAUUGGGCCCA 74
                 ************************************************************************** PP

>> mrum-tRNA.4  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (4) !     2e-18   62.5   0.0  cm        1       72 []           1          75 + [] 1.00    no 0.61

                            v            v                                                   NC
                 (((((((,,<<<<___..___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgU..GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 :::::::U+GC CAG   GGU AG GCGC::G:CUG+ AA:C::GAGGUCC:GGGUUCGA UCCC:G:::::::A
  mrum-tRNA.4  1 AGGCUAGUGGCACAGCcuGGUcAGCGCGCACGGCUGAUAACCGUGAGGUCCUGGGUUCGAAUCCCAGCUAGCCUA 75
                 ***************999********************************************************* PP

>> AAGA01015927.1  Metagenome sequence AHAI1002.g1, whole genome shotgun sequence
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (5) !   2.1e-18   62.4   0.0  cm        1       72 []         229         302 + .. 1.00    no 0.62

                                                                                                NC
                     (((((((,,<<<<___.___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
           tRNA5   1 gCcggcAUAGcgcAgU.GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72 
                     G::::::UA:::CAGU GGU AG:::+CC:GCCUGUCA+GC:GG GGU  :GGGUUCGA UCCC: ::::::C+
  AAGA01015927.1 229 GGAGCGGUAGUUCAGUcGGUuAGAAUACCUGCCUGUCACGCAGGGGGUUGCGGGUUCGAGUCCCGUCCGUUCCG 302
                     ************************************************************************** PP

>> mrum-tRNA.5  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (6) !   3.6e-18   61.7   0.0  cm        1       72 []           1          74 + [] 1.00    no 0.53

                                                                                            NC
                 (((((((,,<<<<___..____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgU..GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 :CCG:C:UAGC:CA+U  GG AG:GCG:::G:CUGU++A:C:::A GU :::GGUUC A UCC::::G:CGG:A
  mrum-tRNA.5  1 CCCGACUUAGCUCAAUuuGGCAGAGCGUUGGACUGUAGAUCCAAAUGUUGCUGGUUCAAGUCCGGCAGUCGGGA 74
                 ************************************************************************** PP

>> mrum-tRNA.6  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (7) !   2.2e-17   59.2   0.0  cm        1       72 []           1          73 + [] 1.00    no 0.51

                                                                                            NC
                 (((((((,,<<<<___.___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgU.GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 GC::::AU+G G:A+U GG  A:C C+:C:G:CU+UC+A:C:G:  +  C:GGGUUC A UCCC:GU::::GCA
  mrum-tRNA.6  1 GCUUCUAUGGGGUAAUcGGCaAACCCAUCGGACUUUCGAUCCGAUAA-UCCGGGUUCAAAUCCCGGUAGAAGCA 73
                 ***********************************************.9************************* PP

>> mrum-tRNA.7  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (8) !   2.2e-17   59.2   0.0  cm        1       72 []           1          75 + [] 0.99    no 0.60

                                                                                              NC
                 (((((((,,<<<<___..___.._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgU..GGu..AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 GC::::AU+::G:AGU  GG   A:C:: :C:GCCU+UC+AGC:G:AG+ C :GGGUUCGA UCCC: U::::GCA
  mrum-tRNA.7  1 GCUCCGAUGGUGUAGUccGGCcaAUCAUUUCGGCCUUUCGAGCCGAAGA-CUCGGGUUCGAAUCCCGGUCGGAGCA 75
                 ********************9999*************************.************************** PP

>> mrum-tRNA.8  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (9) !   2.4e-17   59.1   0.0  cm        1       72 []           1          74 + [] 1.00    no 0.59

                             v          v                                                    NC
                 (((((((,,<<<<___..___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgU..GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 GC:G:::UAG:: AG   GGU A ::C C:A:CCUG CA+G:U:GAG+ CC:GGGUUC A UCCC:G:::C:GCA
  mrum-tRNA.8  1 GCGGUGUUAGUCCAGCcuGGUuAAGACUCUAGCCUGCCACGUUAGAGA-CCCGGGUUCAAAUCCCGGACGCCGCA 74
                 ***************999******************************.************************** PP

>> mrum-tRNA.9  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
 (10) !   2.7e-17   58.9   0.0  cm        1       72 []           1         110 + [] 0.98    no 0.61

                                                                                               NC
                  (((((((,,<<<<___.___._>>>>,<<<<<___~~~~~~>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5   1 gCcggcAUAGcgcAgU.GGu.AgcgCgccagccUg*[ 4]*gcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72 
                  GCCGG::U+GC:CAG  GGU AG:GCGC::G:CU       :C::GAG+UC::GGGUUCGA UCCC::::CCGGCA
  mrum-tRNA.9   1 GCCGGGGUGGCUCAGCuGGUuAGAGCGCACGGCUC*[40]*CCGUGAGAUCGCGGGUUCGAAUCCCGCCCCCGGCA 110
                  ********************************995...*..*********************************** PP

>> mrum-tRNA.10  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
 (11) !   8.7e-17   57.3   0.0  cm        1       72 []           1          72 + [] 1.00    no 0.42

                                            v               v                               NC
                  (((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
         tRNA5  1 gCcggcAUAGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                  G:::::AUAG:::A+  GGUA:::C+ C G:CUGU AA:C G AG+  :G :GUUCGA UC: C:U:::::C+
  mrum-tRNA.10  1 GGUUCUAUAGUUUAACaGGUAAAACAACUGGCUGUUAACCGGCAGA-UAGGAGUUCGAAUCUUCUUAGAACCG 72
                  **********************************************.9************************* PP

>> AAGA01015927.1  Metagenome sequence AHAI1002.g1, whole genome shotgun sequence
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
 (12) !   1.4e-15   53.5   0.0  cm        1       72 []         314         386 + .. 1.00    no 0.59

                                                                                               NC
                     (((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
           tRNA5   1 gCcggcAUAGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72 
                     :::GGC:UAG :CA+U GGUAG: C+CC:G:CU  +AA:C:GG  GU : G:GUUCGA UC:C ::GCC:::+
  AAGA01015927.1 314 AGGGGCGUAGUUCAAUuGGUAGAGCACCGGUCUCCAAAACCGGGUGUUGGGAGUUCGAGUCUCUCCGCCCCUG 386
                     ************************************************************************* PP



Internal CM pipeline statistics summary:
----------------------------------------
Query model(s):                                                  1  (72 consensus positions)
Target sequences:                                               13  (12958 residues searched)
Target sequences re-searched for truncated hits:                13  (5412 residues re-searched)
Windows   passing  local HMM SSV           filter:              81  (0.3848); expected (0.35)
Windows   passing  local HMM Viterbi       filter:                  (off)
Windows   passing  local HMM Viterbi  bias filter:                  (off)
Windows   passing  local HMM Forward       filter:              50  (0.2035); expected (0.02)
Windows   passing  local HMM Forward  bias filter:              48  (0.195); expected (0.02)
Windows   passing glocal HMM Forward       filter:              42  (0.1794); expected (0.02)
Windows   passing glocal HMM Forward  bias filter:              42  (0.1794); expected (0.02)
Envelopes passing glocal HMM envelope defn filter:              43  (0.1724); expected (0.02)
Envelopes passing  local CM  CYK           filter:              40  (0.1612); expected (0.0001)
Total CM hits reported:                                         12  (0.05003); includes 0 truncated hit(s)

# CPU time: 0.42u 0.01s 00:00:00.43 Elapsed: 00:00:00.44
//
Query:       Cobalamin  [CLEN=191]
Accession:   RF00174
Description: Cobalamin riboswitch
Hit scores:
 rank     E-value  score  bias  sequence        start    end   mdl trunc   gc  description
 ----   --------- ------ -----  -------------- ------ ------   --- ----- ----  -----------
  (1) !   1.4e-08   30.0   0.0  AAFY01022046.1    934    832 -  cm    5' 0.48  Metagenome sequence AGZO15064.g2, whole genome shotgun sequence


Hit alignments:
>> AAFY01022046.1  Metagenome sequence AGZO15064.g2, whole genome shotgun sequence
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (1) !   1.4e-08   30.0   0.0  cm       32      191 ~]         934         832 - ~. 0.92    5' 0.48

                                 ???              v           v      v    v                                     ???? NC
                     ~~~~~~______>>>,,,,,(((,,,<.<<<<_______>>>>>,,<<<____>>>,<<<---<<<<~~~~~~>>>>---->>>,,,,)))]]]] CS
       Cobalamin   1 <[31]*agugaaggguuAAaaGGGAAc.ccGGUGaaAaUCCgggGCuGcCCCCgCaACuGUAAgcGg*[61]*cCgcgAGcCaGGAGACCuGCCa 174
                             +G+     + AA: GGAA: : GGUG AAAUCC ::+C:G CCC  C:ACUGUAA:C:        :G:+AG+CAG A AC :  C 
  AAFY01022046.1 934 <[ 0]*GUAGGCAAAAGGAAGAGGAAGgAUGGUGGAAAUCCUUCACGGGCCCGGCCACUGUAACCAG*[ 4]*UUGGAAGUCAG-AUACUCUUCU 849
                     ......44455566666899******989************************************97...7..79*********.9********* PP

                     ??                NC
                     ]]::::::::::::::: CS
       Cobalamin 175 ucaguuuuugaaucucc 191
                       ++++   GAA+CU C
  AAFY01022046.1 848 AUUAAGGCGGAAACUAC 832
                     ***************** PP



Internal CM pipeline statistics summary:
----------------------------------------
Query model(s):                                                  1  (191 consensus positions)
Target sequences:                                               13  (12958 residues searched)
Target sequences re-searched for truncated hits:                13  (10152 residues re-searched)
Windows   passing  local HMM SSV           filter:              10  (0.207); expected (0.35)
Windows   passing  local HMM Viterbi       filter:                  (off)
Windows   passing  local HMM Viterbi  bias filter:                  (off)
Windows   passing  local HMM Forward       filter:               2  (0.03116); expected (0.02)
Windows   passing  local HMM Forward  bias filter:               2  (0.03116); expected (0.02)
Windows   passing glocal HMM Forward       filter:               1  (0.01558); expected (0.02)
Windows   passing glocal HMM Forward  bias filter:               1  (0.01558); expected (0.02)
Envelopes passing glocal HMM envelope defn filter:               1  (0.008784); expected (0.02)
Envelopes passing  local CM  CYK           filter:               1  (0.005712); expected (0.0001)
Total CM hits reported:                                          1  (0.008914); includes 1 truncated hit(s)

# CPU time: 0.16u 0.01s 00:00:00.17 Elapsed: 00:00:00.17
//
[ok]
BioPerl-1.007002/t/data/cmsearch.nohit.out000444000766000024       426313155576321 20333 0ustar00cjfieldsstaff000000000000# cmsearch :: search CM(s) against a sequence database
# INFERNAL 1.1.1 (July 2014)
# Copyright (C) 2014 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query CM file:                         Cobalamin.c.cm
# target sequence database:              mrum-tRNAs10.fa
# number of worker threads:              4
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       Cobalamin  [CLEN=191]
Accession:   RF00174
Description: Cobalamin riboswitch
Hit scores:
 rank     E-value  score  bias  sequence  start    end   mdl trunc   gc  description
 ----   --------- ------ -----  -------- ------ ------   --- ----- ----  -----------

   [No hits detected that satisfy reporting thresholds]


Hit alignments:

   [No hits detected that satisfy reporting thresholds]


Internal CM pipeline statistics summary:
----------------------------------------
Query model(s):                                                  1  (191 consensus positions)
Target sequences:                                               10  (1544 residues searched)
Target sequences re-searched for truncated hits:                10  (4632 residues re-searched)
Windows   passing  local HMM SSV           filter:               1  (0.01198); expected (0.35)
Windows   passing  local HMM Viterbi       filter:                  (off)
Windows   passing  local HMM Viterbi  bias filter:                  (off)
Windows   passing  local HMM Forward       filter:               0  (0); expected (0.02)
Windows   passing  local HMM Forward  bias filter:               0  (0); expected (0.02)
Windows   passing glocal HMM Forward       filter:               0  (0); expected (0.02)
Windows   passing glocal HMM Forward  bias filter:               0  (0); expected (0.02)
Envelopes passing glocal HMM envelope defn filter:               0  (0); expected (0.02)
Envelopes passing  local CM  CYK           filter:               0  (0); expected (0.0001)
Total CM hits reported:                                          0  (0); includes 0 truncated hit(s)

# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.03
//
[ok]
BioPerl-1.007002/t/data/cmsearch_output.txt000444000766000024      1754113155576321 20666 0ustar00cjfieldsstaff000000000000# cmsearch :: search CM(s) against a sequence database
# INFERNAL 1.1.1 (July 2014)
# Copyright (C) 2014 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query CM file:                         RF00174.cm
# target sequence database:              NC_000913.fna
# CM configuration:                      glocal
# number of worker threads:              16
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       Cobalamin  [CLEN=191]
Accession:   RF00174
Hit scores:
 rank     E-value  score  bias  sequence                        start     end   mdl trunc   gc  description
 ----   --------- ------ -----  ----------------------------- ------- -------   --- ----- ----  -----------
  (1) !   8.7e-16   98.2   0.0  gi|556503834|ref|NC_000913.3| 4163384 4163574 +  cm    no 0.54  Escherichia coli str. K-12 substr. MG1655, com
 ------ inclusion threshold ------
  (2) ?      0.63    8.4   0.0  gi|556503834|ref|NC_000913.3| 4593356 4593565 +  cm    no 0.53  Escherichia coli str. K-12 substr. MG1655, com


Hit alignments:
>> gi|556503834|ref|NC_000913.3|  Escherichia coli str. K-12 substr. MG1655, complete genome
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (1) !   8.7e-16   98.2   0.0  cm        1      191 []     4163384     4163574 + .. 0.98    no 0.54

                                                               v              v                                  NC
                                        :::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_______>>>>>,,<< CS
                      Cobalamin       1 uuaaauugaaacgaugauGGUuccccuuuaaagugaaggguuAAaaGGGAAcccGGUGaaAaUCCgggGCuG 72     
                                         U +A  ++ +   UG::GGU C : U          : GUUAA AGGGAA:CC:GUG++AAUC:GG:GCUG
  gi|556503834|ref|NC_000913.3| 4163384 CUGUAGCAUCCACUUGCCGGU-CCUGU----------GAGUUAAUAGGGAAUCCAGUGCGAAUCUGGAGCUG 4163444
                                        *********************.98888..........99********************************* PP

                                        v    v            v                                                      NC
                                        <____>>>,<<<---<<<<------<<<<<<-----......<<<-<<<<<<______>>>>>>--->>>>> CS
                      Cobalamin      73 cCCCCgCaACuGUAAgcGgagagcaccccccAauAa......GCCACUggcccgcaagggccGGGAAGGCgg 138    
                                          C C CA+C:GUAAG:: AG+ ++::::::  + +      G:CACU::C   +++  G::GGGAAG:C::
  gi|556503834|ref|NC_000913.3| 4163445 A-CGCGCAGCGGUAAGGAAAGGUGCGAUGAUUGCGUuaugcgGACACUGCC--AUUC--GGUGGGAAGUCAU 4163511
                                        *.*********************************9***************..5555..************* PP

                                                                v                                       NC
                                        >>>>----------..........>>>>---->>>,,,,)))]]]]]]::::::::::::::: CS
                      Cobalamin     139 ggggaaggaaugac..........cCgcgAGcCaGGAGACCuGCCaucaguuuuugaaucucc 191    
                                        ::::   +A+U+ C           ::C+AGCC:G+AGACCUGCC::C ++  U G AUCU  
  gi|556503834|ref|NC_000913.3| 4163512 CAUCUCUUAGUAUCuuagauacccCUCCAAGCCCGAAGACCUGCCGGCCAACGUCGCAUCUGG 4163574
                                        **********9998************************************************* PP

>> gi|556503834|ref|NC_000913.3|  Escherichia coli str. K-12 substr. MG1655, complete genome
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (2) ?      0.63    8.4   0.0  cm        1      191 []     4593356     4593565 + .. 0.72    no 0.53

                                                       v                                    v             v   v  NC
                                        :::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_______>>>>>,,<< CS
                      Cobalamin       1 uuaaauugaaacgaugauGGUuccccuuuaaagugaaggguuAAaaGGGAAcccGGUGaaAaUCCgggGCuG 72     
                                          A AUU+A+++    :UGG  :C +U ++  G     G: +AA : GGAA:  G         C  :+  G
  gi|556503834|ref|NC_000913.3| 4593356 GGAGAUUAAUCUUUACGUGGG-UCGUUGAUCGG---CUGACGAACCAGGAAGAUGU-------ACGCCAGUG 4593416
                                        *********************.88877554444...5777779*********9996.......7999***** PP

                                               v       v  v       vvvvvv     vvv    vvv                          NC
                                        <____>>>,<<<---<<<<.------<<<<<<-----<<<-<<<<<<_____.................... CS
                      Cobalamin      73 cCCCCgCaACuGUAAgcGg.agagcaccccccAauAaGCCACUggcccgcaa.................... 123    
                                        CCCCCGC +C GU+A ::     GCA ++ ++ A   GCCA   G+C G                       
  gi|556503834|ref|NC_000913.3| 4593417 CCCCCGCUGCGGUGACGCAa-CCGCAGAUGAUUAGU-GCCA---GACGG---aaugagugggugguaucaac 4593480
                                        ***************88873.333333333333333.4544...33333...44566655444444444444 PP

                                                  vvv      vvvvvvvvv                                             NC
                                        ........._>>>>>>--->>>>>>>>>----------.................................. CS
                      Cobalamin     124 .........gggccGGGAAGGCggggggaaggaaugac.................................. 152    
                                                                                                                
  gi|556503834|ref|NC_000913.3| 4593481 aauaaaacc-----------------------------aguaaugaucggcgcaaaagaggcgcagaugaag 4593523
                                        444444444.............................5666666666666666666666666777777777 PP

                                          v  v                    v                NC
                                        ..>>>>----.>>>,,,,)))]]]]]]::::::::::::::: CS
                      Cobalamin     153 ..cCgcgAGc.CaGGAGACCuGCCaucaguuuuugaaucucc 191    
                                           :: +AG+ C GGA AC : CCA:  + + + + AU    
  gi|556503834|ref|NC_000913.3| 4593524 cuGGCAAAGUuCUGGAUACUGCCCACCGACGCAGUCAUGCGA 4593565
                                        76788899966******************************* PP



Internal CM pipeline statistics summary:
----------------------------------------
Query model(s):                                                  1  (191 consensus positions)
Target sequences:                                                1  (9283304 residues searched)
Target sequences re-searched for truncated hits:                 1  (1840 residues re-searched)
Windows   passing  local HMM SSV           filter:            7160  (0.4322); expected (0.35)
Windows   passing  local HMM Viterbi       filter:                  (off)
Windows   passing  local HMM Viterbi  bias filter:                  (off)
Windows   passing  local HMM Forward       filter:             171  (0.01188); expected (0.005)
Windows   passing  local HMM Forward  bias filter:             139  (0.0095); expected (0.005)
Windows   passing glocal HMM Forward       filter:              76  (0.005795); expected (0.005)
Windows   passing glocal HMM Forward  bias filter:              69  (0.005313); expected (0.005)
Envelopes passing glocal HMM envelope defn filter:              70  (0.002021); expected (0.005)
Envelopes passing glocal CM  CYK           filter:               2  (4.534e-05); expected (0.0001)
Total CM hits reported:                                          2  (4.319e-05); includes 0 truncated hit(s)

# CPU time: 11.74u 1.00s 00:00:12.74 Elapsed: 00:00:02.27
//
[ok]
BioPerl-1.007002/t/data/codeml45b.mlc000444000766000024     11035013155576321 17203 0ustar00cjfieldsstaff000000000000      9   1425

Pdel181_DNA2  ATG TCA CCA CAA ACA GAG ACT AAA ACA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAG TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT ACT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATG CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG
Pfre186_DNA2  ATG TCA CCA CAA ACA GAG ACT AAA ACA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAG TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT ACT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATG CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT ATT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG
Pgra187_DNA2  ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT ACT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG ACT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATG AAA AGG GCT ATA TTT GCC AGA GAA TTG GGA GTT CCT ATT GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCT GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATA AAA TTT GAA TTC GAA GCA ATG GAT ACG TTG
Phet26_DNA21  ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTA CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG
Pmex37_DNA21  ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT ACT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATG CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT ATT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG
Ptre197_DNA2  ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT ACT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG ACT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATG AAA AGG GCT ATA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCT GGT GCT GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC GAA GCA ATG GAT ACG TTG
WHR1_DNA225  ATG TCA CCA CAA ACA GAG ACT AAA GCG GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAG TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCC GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT ACT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATG AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTG CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG
YALD273_DNA5  ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTA CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG
Pop_trich_ch  ATG TCA CCA CAA ACA GAG ACT AAA GCA GGT GTT GGA TTC AAG GCT GGT GTT AAA GAT TAT AAA TTG ACT TAT TAT ACT CCT GAC TAT GAA ACC AAA GAT ACT GAT ATC TTG GCA GCA TTC CGA GTA ACT CCT CAA CCT GGA GTT CCG CCC GAG GAA GCA GGG GCC GCA GTA GCT GCT GAA TCT TCT ACT GGT ACA TGG ACA ACT GTG TGG ACC GAC GGG CTT ACC AGT CTT GAT CGT TAT AAG GGA CGA TGC TAC GAC ATC GAG CCC GTT GCT GGA GAA GAA AAT CAA TTT ATT GCT TAT GTA GCT TAC CCC TTA GAC CTT TTT GAA GAA GGT TCT GTT ACT AAC ATG TTT ACT TCC ATT GTG GGT AAT GTA TTT GGG TTC AAA GCC CTA CGC GCT CTA CGT CTG GAG GAT TTG CGA ATT CCT CCT GCT TAT GTT AAA ACT TTT CAA GGC CCA CCT CAT GGT ATC CAA GTT GAA AGA GAT AAA TTG AAC AAG TAT GGT CGC CCC CTA TTG GGC TGT ACT ATT AAA CCT AAA TTG GGG TTA TCC GCT AAG AAT TAC GGT AGA GCA GTT TAT GAA TGT CTA CGC GGT GGA CTT GAT TTT ACC AAA GAT GAT GAG AAC GTG AAC TCC CAA CCA TTT ATG CGT TGG AGA GAT CGT TTC TTA TTT TGT GCC GAA GCA CTT TAT AAA GCA CAG GCT GAA ACC GGT GAA ATC AAA GGG CAT TAT TTA AAC GCT ACT GCA GGT ACA TGC GAA GAA ATG ATC AAA AGG GCT GTA TTT GCC AGA GAA TTG GGA GTT CCT ATC GTA ATG CAT GAC TAC TTA ACA GGG GGA TTC ACC GCA AAC ACT AGT TTG GCT CAT TAT TGC CGA GAT AAT GGT TTA CTT CTT CAC ATC CAT CGC GCA ATG CAT GCA GTT ATT GAT AGA CAG AAA AAT CAT GGT ATA CAC TTT CGT GTA CTA GCT AAG GCA TTA CGT ATG TCT GGT GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA GGT AAA CTT GAA GGG GAA AGA GAC ATA ACT TTG GGT TTT GTT GAT TTA CTG CGT GAT GAT TTT GTT GAA AAA GAT CGA AGC CGC GGT ATT TAT TTC ACT CAA GAT TGG GTC TCT CTA CCG GGT GTT CTA CCC GTG GCT TCG GGG GGT ATT CAC GTT TGG CAT ATG CCT GCT CTG ACC GAG ATC TTT GGA GAT GAT TCC GTA CTA CAA TTC GGT GGA GGA ACT TTA GGG CAC CCT TGG GGA AAT GCA CCC GGT GCC GTT GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA CAA GCT CGT AAT GAG GGA CGT GAT CTT GCT CGT GAG GGT AAT GAA ATT ATC CGT GAA GCT AGC AAA TGG AGC CCT GAA CTA GCT GCT GCT TGT GAA GTA TGG AAG GAG ATT AAA TTT GAA TTC CAA GCA ATG GAT ACG TTG



Printing out site pattern counts


         9        225  P

Pdel181_DNA2          AAA AAC AAG AAT ACA ACA ACC ACG ACT ACT AGA AGC AGG AGT ATA ATC ATC ATC ATG ATG ATT ATT CAA CAA CAC CAG CAT CCA CCC CCC CCG CCT CCT CGA CGC CGT CTA CTG CTG CTT GAA GAC GAG GAG GAT GCA GCC GCC GCT GCT GGA GGC GGG GGT GTA GTA GTC GTG GTT GTT GTT TAC TAT TCA TCC TCG TCT TCT TGC TGG TGT TTA TTC TTG TTT
Pfre186_DNA2          ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
Pgra187_DNA2          ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ..G ..T ..A ... ..A ... ... G.. ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... A.. ... ... ... ... ... A.. ... ... ... ... AC. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
Phet26_DNA21          ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
Pmex37_DNA21          ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
Ptre197_DNA2          ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ..G ... ..A ... ... ... ... G.. ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ..T A.. ... ... ... ... ... A.. ... ... ... ... AC. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
WHR1_DNA225           ... ... ... ... ... G.G ... ... ... .G. ... ... ... ... ... ... ..G ... ..A ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ...
YALD273_DNA5          ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
Pop_trich_ch          ... ... ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...

   18    6    6    9    5    1    8    1   16    1    6    3    1    1    1
    7    1    1    1    9    1    9    9    1    5    2    9    3    5    1
    2    1   10    6    5   11    9    1    3    9   24    5    1    9   22
   15    4    1    1   23   13    2    9   23    1   12    1    4    1    1
   13    4   13    1    4    1    1    5    3    8    5    9    8   10   14


CODONML (in paml version 4.5, December 2011)  examples/small_taxon_set.nuc
Model: One dN/dS ratio for branches
Codon frequency model: F3x4
ns =   9  ls = 475

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 14 14 14 14 14 14 | Ser TCT  6  6  6  6  6  6 | Tyr TAT 13 13 13 13 13 13 | Cys TGT  5  5  5  5  5  5
    TTC  8  8  8  8  8  8 |     TCC  4  4  4  4  4  4 |     TAC  4  4  4  4  4  4 |     TGC  3  3  3  3  3  3
Leu TTA  9  9  9  9  9  9 |     TCA  1  1  1  1  1  1 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG 10 10 10 10 10 10 |     TCG  1  1  1  1  1  1 |     TAG  0  0  0  0  0  0 | Trp TGG  8  8  8  8  8  8
--------------------------------------------------------------------------------------------------------------
Leu CTT  9  9  9  9  9  9 | Pro CCT 11 11 12 11 10 12 | His CAT  9  9  9  9  9  9 | Arg CGT 11 11 11 11 11 11
    CTC  0  0  0  0  0  0 |     CCC  6  6  5  6  6  5 |     CAC  5  5  5  5  5  5 |     CGC  5  5  5  5  5  5
    CTA  9  9  9 10  9  9 |     CCA  3  3  3  3  3  3 | Gln CAA 10 10  9 10 10  9 |     CGA  6  6  6  6  6  6
    CTG  4  4  4  3  4  4 |     CCG  2  2  2  2  2  2 |     CAG  2  2  2  2  2  2 |     CGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Ile ATT 10 11 10 10 11 10 | Thr ACT 17 17 18 16 17 18 | Asn AAT  9  9  9  9  9  9 | Ser AGT  1  1  2  2  2  2
    ATC  9  9  7  9  9  8 |     ACC  8  8  8  8  8  8 |     AAC  6  6  6  6  6  6 |     AGC  3  3  3  3  3  3
    ATA  1  1  4  2  1  3 |     ACA  6  6  5  5  5  5 | Lys AAA 18 18 18 18 18 18 | Arg AGA  6  6  6  6  6  6
Met ATG 10 10 10  9 10 10 |     ACG  1  1  1  1  1  1 |     AAG  6  6  6  6  6  6 |     AGG  1  1  1  1  1  1
--------------------------------------------------------------------------------------------------------------
Val GTT 15 14 14 15 14 14 | Ala GCT 24 24 23 24 24 24 | Asp GAT 22 22 22 22 22 22 | Gly GGT 23 23 23 23 23 23
    GTC  1  1  1  1  1  1 |     GCC  5  5  5  5  5  4 |     GAC  5  5  6  6  6  6 |     GGC  2  2  2  2  2  2
    GTA 13 13 12 13 13 12 |     GCA 15 15 16 16 16 16 | Glu GAA 24 24 25 24 24 25 |     GGA 13 13 13 13 13 13
    GTG  4  4  4  4  4  4 |     GCG  0  0  0  0  0  0 |     GAG 10 10  9  9  9  9 |     GGG  9  9  9  9  9  9
--------------------------------------------------------------------------------------------------------------

--------------------------------------------------------------------------
Phe TTT 14 14 14 | Ser TCT  5  6  6 | Tyr TAT 13 13 13 | Cys TGT  5  5  5
    TTC  8  8  8 |     TCC  5  4  4 |     TAC  4  4  4 |     TGC  3  3  3
Leu TTA  9  9  9 |     TCA  1  1  1 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG 10 10 10 |     TCG  1  1  1 |     TAG  0  0  0 | Trp TGG  8  8  8
--------------------------------------------------------------------------
Leu CTT  9  9  9 | Pro CCT 10 11 11 | His CAT  9  9  9 | Arg CGT 11 11 11
    CTC  0  0  0 |     CCC  6  6  6 |     CAC  5  5  5 |     CGC  5  5  5
    CTA  9 10 10 |     CCA  3  3  3 | Gln CAA 10 10 10 |     CGA  6  6  6
    CTG  4  3  3 |     CCG  2  2  2 |     CAG  2  2  2 |     CGG  0  0  0
--------------------------------------------------------------------------
Ile ATT 10 10 10 | Thr ACT 17 16 16 | Asn AAT  9  9  9 | Ser AGT  2  2  2
    ATC  8  9  9 |     ACC  8  8  8 |     AAC  6  6  6 |     AGC  3  3  3
    ATA  2  2  2 |     ACA  5  5  5 | Lys AAA 18 18 18 | Arg AGA  6  6  6
Met ATG 10  9  9 |     ACG  1  1  1 |     AAG  6  6  6 |     AGG  1  1  1
--------------------------------------------------------------------------
Val GTT 15 15 15 | Ala GCT 24 24 24 | Asp GAT 22 22 22 | Gly GGT 23 23 23
    GTC  1  1  1 |     GCC  5  5  5 |     GAC  5  6  6 |     GGC  2  2  2
    GTA 13 13 13 |     GCA 15 16 16 | Glu GAA 24 24 24 |     GGA 13 13 13
    GTG  4  4  4 |     GCG  1  0  0 |     GAG 10  9  9 |     GGG  9  9  9
--------------------------------------------------------------------------

Codon position x base (3x4) table for each sequence.

#1: Pdel181_DNA2
position  1:    T:0.18105    C:0.19368    A:0.23579    G:0.38947
position  2:    T:0.26526    C:0.23158    A:0.30105    G:0.20211
position  3:    T:0.41895    C:0.15579    A:0.28211    G:0.14316
Average         T:0.28842    C:0.19368    A:0.27298    G:0.24491

#2: Pfre186_DNA2
position  1:    T:0.18105    C:0.19368    A:0.23789    G:0.38737
position  2:    T:0.26526    C:0.23158    A:0.30105    G:0.20211
position  3:    T:0.41895    C:0.15579    A:0.28211    G:0.14316
Average         T:0.28842    C:0.19368    A:0.27368    G:0.24421

#3: Pgra187_DNA2
position  1:    T:0.18105    C:0.19158    A:0.24000    G:0.38737
position  2:    T:0.26316    C:0.23158    A:0.30105    G:0.20421
position  3:    T:0.42105    C:0.15158    A:0.28632    G:0.14105
Average         T:0.28842    C:0.19158    A:0.27579    G:0.24421

#4: Phet26_DNA21
position  1:    T:0.18105    C:0.19368    A:0.23368    G:0.39158
position  2:    T:0.26526    C:0.22947    A:0.30105    G:0.20421
position  3:    T:0.41895    C:0.15789    A:0.28632    G:0.13684
Average         T:0.28842    C:0.19368    A:0.27368    G:0.24421

#5: Pmex37_DNA21
position  1:    T:0.18105    C:0.19158    A:0.23789    G:0.38947
position  2:    T:0.26526    C:0.22947    A:0.30105    G:0.20421
position  3:    T:0.41895    C:0.15789    A:0.28211    G:0.14105
Average         T:0.28842    C:0.19298    A:0.27368    G:0.24491

#6: Ptre197_DNA2
position  1:    T:0.18105    C:0.19158    A:0.24000    G:0.38737
position  2:    T:0.26316    C:0.23158    A:0.30105    G:0.20421
position  3:    T:0.42316    C:0.15158    A:0.28421    G:0.14105
Average         T:0.28912    C:0.19158    A:0.27509    G:0.24421

#7: WHR1_DNA225
position  1:    T:0.18105    C:0.19158    A:0.23579    G:0.39158
position  2:    T:0.26526    C:0.22947    A:0.30105    G:0.20421
position  3:    T:0.41684    C:0.15579    A:0.28211    G:0.14526
Average         T:0.28772    C:0.19228    A:0.27298    G:0.24702

#8: YALD273_DNA5
position  1:    T:0.18105    C:0.19368    A:0.23368    G:0.39158
position  2:    T:0.26526    C:0.22947    A:0.30105    G:0.20421
position  3:    T:0.41895    C:0.15789    A:0.28632    G:0.13684
Average         T:0.28842    C:0.19368    A:0.27368    G:0.24421

#9: Pop_trich_ch
position  1:    T:0.18105    C:0.19368    A:0.23368    G:0.39158
position  2:    T:0.26526    C:0.22947    A:0.30105    G:0.20421
position  3:    T:0.41895    C:0.15789    A:0.28632    G:0.13684
Average         T:0.28842    C:0.19368    A:0.27368    G:0.24421

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT     126 | Ser S TCT      53 | Tyr Y TAT     117 | Cys C TGT      45
      TTC      72 |       TCC      37 |       TAC      36 |       TGC      27
Leu L TTA      81 |       TCA       9 | *** * TAA       0 | *** * TGA       0
      TTG      90 |       TCG       9 |       TAG       0 | Trp W TGG      72
------------------------------------------------------------------------------
Leu L CTT      81 | Pro P CCT      99 | His H CAT      81 | Arg R CGT      99
      CTC       0 |       CCC      52 |       CAC      45 |       CGC      45
      CTA      84 |       CCA      27 | Gln Q CAA      88 |       CGA      54
      CTG      33 |       CCG      18 |       CAG      18 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      92 | Thr T ACT     152 | Asn N AAT      81 | Ser S AGT      16
      ATC      77 |       ACC      72 |       AAC      54 |       AGC      27
      ATA      18 |       ACA      47 | Lys K AAA     162 | Arg R AGA      54
Met M ATG      87 |       ACG       9 |       AAG      54 |       AGG       9
------------------------------------------------------------------------------
Val V GTT     131 | Ala A GCT     215 | Asp D GAT     198 | Gly G GGT     207
      GTC       9 |       GCC      44 |       GAC      51 |       GGC      18
      GTA     115 |       GCA     141 | Glu E GAA     218 |       GGA     117
      GTG      36 |       GCG       1 |       GAG      84 |       GGG      81
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.18105    C:0.19275    A:0.23649    G:0.38971
position  2:    T:0.26480    C:0.23041    A:0.30105    G:0.20374
position  3:    T:0.41942    C:0.15579    A:0.28421    G:0.14058
Average         T:0.28842    C:0.19298    A:0.27392    G:0.24468

Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
  0.02080748  0.00772882  0.01409988  0.00697451
  0.01810545  0.00672517  0.01226889  0.00606881
  0.02365656  0.00878710  0.00000000  0.00000000
  0.01601000  0.00594683  0.00000000  0.00536643
  0.02215163  0.00822810  0.01501073  0.00742506
  0.01927505  0.00715961  0.01306145  0.00646085
  0.02518476  0.00935474  0.01706608  0.00844174
  0.01704423  0.00633099  0.01154977  0.00571310
  0.02717876  0.01009540  0.01841729  0.00911012
  0.02364937  0.00878443  0.01602564  0.00792709
  0.03090024  0.01147772  0.02093909  0.01035753
  0.02091228  0.00776775  0.01417090  0.00700964
  0.04478716  0.01663594  0.03034936  0.01501232
  0.03897116  0.01447562  0.02640823  0.01306284
  0.05091968  0.01891383  0.03450497  0.01706789
  0.03446079  0.01280027  0.02335185  0.01155100



Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later ML. analysis.
Use runmode = -2 for ML pairwise comparison.)

Pdel181_DNA2
Pfre186_DNA2aaaaaaaa-1.0300 (0.0009 0.0000)
Pgra187_DNA2         1.0623 (0.0093 0.0088) 1.1684 (0.0102 0.0088)
Phet26_DNA21         1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117)
Pmex37_DNA21        -1.0000 (0.0046 0.0000)-1.0000 (0.0037 0.0000) 0.9534 (0.0084 0.0088) 0.9555 (0.0028 0.0029)
Ptre197_DNA2         1.5965 (0.0093 0.0058) 1.7561 (0.0102 0.0058) 0.0000 (0.0000 0.0088) 0.6357 (0.0056 0.0088) 1.4328 (0.0084 0.0058)
WHR1_DNA225          0.7964 (0.0046 0.0058) 0.9557 (0.0056 0.0058) 0.4430 (0.0065 0.0147) 0.3175 (0.0028 0.0088) 0.6354 (0.0037 0.0058) 0.5548 (0.0065 0.0117)
YALD273_DNA5         1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117)-1.0000 (0.0000 0.0000) 0.9555 (0.0028 0.0029) 0.6357 (0.0056 0.0088) 0.3175 (0.0028 0.0088)
Pop_trich_ch         1.2775 (0.0037 0.0029) 1.5968 (0.0046 0.0029) 0.4758 (0.0056 0.0117)-1.0000 (0.0000 0.0000) 0.9555 (0.0028 0.0029) 0.6357 (0.0056 0.0088) 0.3175 (0.0028 0.0088)-1.0000 (0.0000 0.0000)

pairwise comparison, codon frequencies: F3x4.


2 (Pfre186_DNA2) ... 1 (Pdel181_DNA2)
lnL =-1891.391969
  0.00214 999.00000 99.00000

t= 0.0021  S=   396.3  N=  1028.7  dN/dS= 99.0000  dN = 0.0010  dS = 0.0000


3 (Pgra187_DNA2) ... 1 (Pdel181_DNA2)
lnL =-1968.029688
  0.02808  3.26389  0.98370

t= 0.0281  S=   341.7  N=  1083.3  dN/dS=  0.9837  dN = 0.0093  dS = 0.0095


3 (Pgra187_DNA2) ... 2 (Pfre186_DNA2)
lnL =-1972.711786
  0.03025  3.71696  1.10191

t= 0.0302  S=   345.4  N=  1079.6  dN/dS=  1.1019  dN = 0.0103  dS = 0.0094


4 (Phet26_DNA21) ... 1 (Pdel181_DNA2)
lnL =-1921.561815
  0.01073  3.11375  1.18654

t= 0.0107  S=   342.5  N=  1082.5  dN/dS=  1.1865  dN = 0.0037  dS = 0.0031


4 (Phet26_DNA21) ... 2 (Pfre186_DNA2)
lnL =-1927.106138
  0.01287  4.25522  1.54964

t= 0.0129  S=   352.0  N=  1073.0  dN/dS=  1.5496  dN = 0.0047  dS = 0.0030


4 (Phet26_DNA21) ... 3 (Pgra187_DNA2)
lnL =-1948.501568
  0.02179  4.30601  0.45869

t= 0.0218  S=   349.8  N=  1075.2  dN/dS=  0.4587  dN = 0.0056  dS = 0.0123


5 (Pmex37_DNA21) ... 1 (Pdel181_DNA2)
lnL =-1920.298777
  0.01053  1.55733 99.00000

t= 0.0105  S=   318.9  N=  1106.1  dN/dS= 99.0000  dN = 0.0045  dS = 0.0000


5 (Pmex37_DNA21) ... 2 (Pfre186_DNA2)
lnL =-1914.616800
  0.00838  0.77696 99.00000

t= 0.0084  S=   296.5  N=  1128.5  dN/dS= 99.0000  dN = 0.0035  dS = 0.0000


5 (Pmex37_DNA21) ... 3 (Pgra187_DNA2)
lnL =-1960.971487
  0.02594  4.03558  0.91514

t= 0.0259  S=   348.1  N=  1076.9  dN/dS=  0.9151  dN = 0.0085  dS = 0.0092


5 (Pmex37_DNA21) ... 4 (Phet26_DNA21)
lnL =-1913.389962
  0.00862  6.08298  0.97563

t= 0.0086  S=   362.3  N=  1062.7  dN/dS=  0.9756  dN = 0.0029  dS = 0.0029


6 (Ptre197_DNA2) ... 1 (Pdel181_DNA2)
lnL =-1961.098136
  0.02585  4.25957  1.53161

t= 0.0258  S=   349.5  N=  1075.5  dN/dS=  1.5316  dN = 0.0094  dS = 0.0061


6 (Ptre197_DNA2) ... 2 (Pfre186_DNA2)
lnL =-1965.694050
  0.02802  4.83643  1.71212

t= 0.0280  S=   352.8  N=  1072.2  dN/dS=  1.7121  dN = 0.0104  dS = 0.0061


6 (Ptre197_DNA2) ... 3 (Pgra187_DNA2)
lnL =-1901.130192
  0.00676  4.05781  0.00100

t= 0.0068  S=   345.2  N=  1079.8  dN/dS=  0.0010  dN = 0.0000  dS = 0.0093


6 (Ptre197_DNA2) ... 4 (Phet26_DNA21)
lnL =-1941.618065
  0.01954  6.78012  0.64571

t= 0.0195  S=   361.6  N=  1063.4  dN/dS=  0.6457  dN = 0.0057  dS = 0.0089


6 (Ptre197_DNA2) ... 5 (Pmex37_DNA21)
lnL =-1953.852896
  0.02372  5.63419  1.43296

t= 0.0237  S=   357.2  N=  1067.8  dN/dS=  1.4330  dN = 0.0086  dS = 0.0060


7 (WHR1_DNA225) ... 1 (Pdel181_DNA2)
lnL =-1936.561781
  0.01511  2.61161  0.72506

t= 0.0151  S=   337.6  N=  1087.4  dN/dS=  0.7251  dN = 0.0046  dS = 0.0064


7 (WHR1_DNA225) ... 2 (Pfre186_DNA2)
lnL =-1941.975543
  0.01725  3.35589  0.90347

t= 0.0172  S=   345.7  N=  1079.3  dN/dS=  0.9035  dN = 0.0056  dS = 0.0062


7 (WHR1_DNA225) ... 3 (Pgra187_DNA2)
lnL =-1960.455637
  0.02624  3.64066  0.41889

t= 0.0262  S=   345.9  N=  1079.1  dN/dS=  0.4189  dN = 0.0065  dS = 0.0156


7 (WHR1_DNA225) ... 4 (Phet26_DNA21)
lnL =-1928.593448
  0.01318  1.68562  0.26826

t= 0.0132  S=   322.2  N=  1102.8  dN/dS=  0.2683  dN = 0.0027  dS = 0.0101


7 (WHR1_DNA225) ... 5 (Pmex37_DNA21)
lnL =-1928.718524
  0.01300  3.82266  0.60956

t= 0.0130  S=   350.1  N=  1074.9  dN/dS=  0.6096  dN = 0.0037  dS = 0.0061


7 (WHR1_DNA225) ... 6 (Ptre197_DNA2)
lnL =-1954.005346
  0.02397  5.04975  0.54692

t= 0.0240  S=   355.1  N=  1069.9  dN/dS=  0.5469  dN = 0.0066  dS = 0.0121


8 (YALD273_DNA5) ... 1 (Pdel181_DNA2)
lnL =-1921.561815
  0.01073  3.11377  1.18654

t= 0.0107  S=   342.5  N=  1082.5  dN/dS=  1.1865  dN = 0.0037  dS = 0.0031


8 (YALD273_DNA5) ... 2 (Pfre186_DNA2)
lnL =-1927.106138
  0.01287  4.25516  1.54964

t= 0.0129  S=   352.0  N=  1073.0  dN/dS=  1.5496  dN = 0.0047  dS = 0.0030


8 (YALD273_DNA5) ... 3 (Pgra187_DNA2)
lnL =-1948.501568
  0.02179  4.30601  0.45869

t= 0.0218  S=   349.8  N=  1075.2  dN/dS=  0.4587  dN = 0.0056  dS = 0.0123


8 (YALD273_DNA5) ... 4 (Phet26_DNA21)
lnL =-1881.846112
  0.00001  8.33165  0.18598

t= 0.0000  S=   369.5  N=  1055.5  dN/dS=  0.1860  dN = 0.0000  dS = 0.0000


8 (YALD273_DNA5) ... 5 (Pmex37_DNA21)
lnL =-1913.389962
  0.00862  6.08296  0.97563

t= 0.0086  S=   362.3  N=  1062.7  dN/dS=  0.9756  dN = 0.0029  dS = 0.0029


8 (YALD273_DNA5) ... 6 (Ptre197_DNA2)
lnL =-1941.618065
  0.01954  6.78014  0.64571

t= 0.0195  S=   361.6  N=  1063.4  dN/dS=  0.6457  dN = 0.0057  dS = 0.0089


8 (YALD273_DNA5) ... 7 (WHR1_DNA225)
lnL =-1928.593448
  0.01318  1.68561  0.26826

t= 0.0132  S=   322.2  N=  1102.8  dN/dS=  0.2683  dN = 0.0027  dS = 0.0101


9 (Pop_trich_ch) ... 1 (Pdel181_DNA2)
lnL =-1921.561815
  0.01073  3.11378  1.18654

t= 0.0107  S=   342.5  N=  1082.5  dN/dS=  1.1865  dN = 0.0037  dS = 0.0031


9 (Pop_trich_ch) ... 2 (Pfre186_DNA2)
lnL =-1927.106138
  0.01287  4.25517  1.54964

t= 0.0129  S=   352.0  N=  1073.0  dN/dS=  1.5496  dN = 0.0047  dS = 0.0030


9 (Pop_trich_ch) ... 3 (Pgra187_DNA2)
lnL =-1948.501568
  0.02179  4.30599  0.45869

t= 0.0218  S=   349.8  N=  1075.2  dN/dS=  0.4587  dN = 0.0056  dS = 0.0123


9 (Pop_trich_ch) ... 4 (Phet26_DNA21)
lnL =-1881.845859
  0.00001  0.40000  0.00100

t= 0.0000  S=   281.0  N=  1144.0  dN/dS=  0.0010  dN = 0.0000  dS = 0.0000


9 (Pop_trich_ch) ... 5 (Pmex37_DNA21)
lnL =-1913.389962
  0.00862  6.08299  0.97562

t= 0.0086  S=   362.3  N=  1062.7  dN/dS=  0.9756  dN = 0.0029  dS = 0.0029


9 (Pop_trich_ch) ... 6 (Ptre197_DNA2)
lnL =-1941.618065
  0.01954  6.78013  0.64571

t= 0.0195  S=   361.6  N=  1063.4  dN/dS=  0.6457  dN = 0.0057  dS = 0.0089


9 (Pop_trich_ch) ... 7 (WHR1_DNA225)
lnL =-1928.593448
  0.01318  1.68561  0.26826

t= 0.0132  S=   322.2  N=  1102.8  dN/dS=  0.2683  dN = 0.0027  dS = 0.0101


9 (Pop_trich_ch) ... 8 (YALD273_DNA5)
lnL =-1881.846052
  0.00001  0.40000  0.16519

t= 0.0000  S=   281.0  N=  1144.0  dN/dS=  0.1652  dN = 0.0000  dS = 0.0000
BioPerl-1.007002/t/data/compLD_missingtest.prettybase000444000766000024       152313155576321 22604 0ustar00cjfieldsstaff000000000000ProcR2973EA	01	C	T
ProcR2973EA	02	N	N
ProcR2973EA	03	C	C
ProcR2973EA	04	C	T
ProcR2973EA	05	C	C
ProcR2973EA	06	C	T
ProcR2973EA	07	C	C
ProcR2973EA	08	C	C
ProcR2973EA	09	C	T
ProcR2973EA	10	N	N
ProcR2973EA	11	C	C
ProcR2973EA	12	C	C
ProcR2973EA	13	C	T
ProcR2973EA	14	T	T
ProcR2973EA	15	T	T
ProcR2973EA	16	C	T
ProcR2973EA	17	C	T
ProcR2973EA	18	C	T
ProcR2973EA	19	C	T
ProcR2973EA	20	C	C
ProcR2973EA	21	T	T
ProcR2973EA	22	C	C
ProcR2973EA	23	C	C
ProC9198EA	01	A	A
ProC9198EA	02	A	A
ProC9198EA	03	A	A
ProC9198EA	04	A	A
ProC9198EA	05	A	A
ProC9198EA	06	A	A
ProC9198EA	07	A	A
ProC9198EA	08	A	A
ProC9198EA	09	A	A
ProC9198EA	10	A	A
ProC9198EA	11	A	C
ProC9198EA	12	A	A
ProC9198EA	13	A	A
ProC9198EA	14	A	A
ProC9198EA	15	A	A
ProC9198EA	16	A	A
ProC9198EA	17	A	A
ProC9198EA	18	A	A
ProC9198EA	19	A	A
ProC9198EA	20	N	N
ProC9198EA	21	A	A
ProC9198EA	22	A	C
ProC9198EA	23	A	A
BioPerl-1.007002/t/data/compLD_test.prettybase000555000766000024        45613155576321 21201 0ustar00cjfieldsstaff00000000000001	i1	A	A
01	i2	A	A
01	i3	A	A
01	i4	G	G
01	i5	G	G
01	i6	G	G
01	i7	A	G
01	i8	A	G
01	i9	A	G
01	i10	A	G
02	i1	C	C
02	i2	C	C
02	i3	C	C
02	i4	T	T
02	i5	T	T
02	i6	T	T
02	i7	C	T
02	i8	C	T
02	i9	C	T
02	i10	C	T
03	i1	A	G
03	i2	G	G
03	i3	A	A
03	i4	A	G
03	i5	G	G
03	i6	A	A
03	i7	A	G
03	i8	G	G
03	i9	A	A
03	i10	A	ABioPerl-1.007002/t/data/component.ontology.test000444000766000024       503713155576321 21451 0ustar00cjfieldsstaff000000000000!autogenerated-by:     DAG-Edit version 1.311
!saved-by:             hjd
!date:                 Thu Sep 12 11:05:43 EDT 2002
!version: $Revision: 1.1 $
!note:     file automatically generated by GO-Editor
$Gene_Ontology ; GO:0003673
 gb|AAC76922.1| (AE000468) aspartokinase II (contig by hand) 

        Length = 810

 Score = 999 (999.9 bits), Expect = 0.0e-00, P = 0.0e-00
 Identities = 250/810 (31%), Positives = 413/810 (51%)


Query:     5 KFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNI 64
             KFGG+S+A+ + +LRVA I+   ++   +  V+SA    TN L+  ++ + + + +   +
Sbjct:    16 KFGGSSLADVKCYLRVAGIMAEYSQPDDMM-VVSAAGSTTNQLINWLKLSQTDRLSAHQV 74

Query:    65 SDAERIF-AELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLH-GISLLGQCPDSINAAL 122
                 R +  +L++GL  A+    L  +  FV  +  ++  +L  GI+      D++ A +
Sbjct:    75 QQTLRRYQCDLISGLLPAEEADSL--ISAFVS-DLERLAALLDSGIN------DAVYAEV 125

Query:   123 ICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRI--P 180
             +  GE  S  +M+ VL  +G     +D  E L A     +  VD   S   +    +  P
Sbjct:   126 VGHGEVWSARLMSAVLNQQGLPAAWLDAREFLRAE-RAAQPQVDEGLSYPLLQQLLVQHP 184

Query:   181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240
                +V+  GF + N  GE V+LGRNGSDYSA  + A        IW+DV GVY+ DPR+V
Sbjct:   185 GKRLVV-TGFISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADPRKV 243

Query:   241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300
              DA LL  +   EA EL+   A VLH RT+ P++  +I   ++ +  P    T I     
Sbjct:   244 KDACLLPLLRLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIERVLA 303

Query:   301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360
                   + +++ +++ +     P  +        +   + RA++  + +   +    + F
Sbjct:   304 SGT-GARIVTSHDDVCLIEFQVPASQDFKLAHKEIDQILKRAQVRPLAVGVHNDRQLLQF 362

Query:   361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGIS 413
             C        A + + E        GL   L + + LA++++VG G+ T   + 
Sbjct:   363 CYTSEVADSALKILDEA-------GLPGELRLRQGLALVAMVGAGV-TRNPLH 407

Query:   414 A-KFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIG 472
               +F+  L    +      Q     S+  V+      + ++  HQ +F  ++ I + + G
Sbjct:   408 CHRFWQQLKGQPVEFTW--QSDDGISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFG 465

Query:   473 VGGVGGALLEQLKRQQSWLKNKH-IDLRVCGVANSKALLTNVHGLN----LENWQEELAQ 527
              G +G   LE   R+QS L  +   +  + GV +S+  L +  GL+    L  + +E  +
Sbjct:   466 KGNIGSRWLELFAREQSTLSARTGFEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVE 525

Query:   528 AKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMD 587
               E      L   ++ +   + V++D T+SQ +ADQY DF   GFHV++ NK A  S  +
Sbjct:   526 QDEE----SLFLWMRAHPYDDLVVLDVTASQQLADQYLDFASHGFHVISANKLAGASDSN 581

Query:   588 YYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKL 647
              Y Q+  A EK+ R +LY+  VGAGLP+   +++L+++GD ++  SGI SG+LS++F + 
Sbjct:   582 KYRQIHDAFEKTGRHWLYNATVGAGLPINHTVRDLIDSGDTILSISGIFSGTLSWLFLQF 641

Query:   648 DEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPA 707
             D  + F+E    A + G TEPDPRDDLSG DV RKL+ILARE G  +E   + +E ++PA
Sbjct:   642 DGSVPFTELVDQAWQQGLTEPDPRDDLSGKDVMRKLVILAREAGYNIEPDQVRVESLVPA 701

Query:   708 EFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDP 767
                  G +  F  N  +L++    R+  AR+ G VLRYV   D +G  RV +  V  + P
Sbjct:   702 HCEG-GSIDHFFENGDELNEQMVQRLEAAREMGLVLRYVARFDANGKARVGVEAVREDHP 760

Query:   768 LFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLR 812
             L  +   +N  A  S +Y+  PLV+RG GAG DVTA  + +D+ R
Sbjct:   761 LASLLPCDNVFAIESRWYRDNPLVIRGPGAGRDVTAGAIQSDINR 805


Parameters:
  E=0.01

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.319   0.136   0.384    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E    S W   T  X   E2     S2
   +0      0      820       820     0.010  93 3  11 22  0.19    34
                                                    37  0.22    37


Statistics:

  Database:  /home/jes12/db/ecoli.aa
   Title:  ecoli.aa
   Posted:  2:52:35 PM EST Nov 18, 2001
   Created:  9:46:47 AM EST Nov 18, 2001
   Format:  XDF-1
   # of letters in database:  1,358,990
   # of sequences in database:  4289
   # of database sequences satisfying E:  4
  No. of states in DFA:  573 (61 KB)
  Total size of DFA:  281 KB (1149 KB)
  Time to generate neighborhood:  0.00u 0.02s 0.02t  Elapsed: 00:00:00
  No. of threads or processors used:  1
  Search cpu time:  1.58u 0.00s 1.58t  Elapsed: 00:00:01
  Total cpu time:  1.59u 0.02s 1.61t  Elapsed: 00:00:01
  Start:  Thu Dec  6 11:09:14 2001   End:  Thu Dec  6 11:09:15 2001
BioPerl-1.007002/t/data/contigspectrumtest.tigr000444000766000024      6214613155576321 21556 0ustar00cjfieldsstaff000000000000sequence	TTCCTTGGCCGCTCTGGTCAGCCCTCGCGATATCCGTATCTCTCCCCGCAGCCAGTCTACATCCCmCCATTCTACCGCGATGAGTTCGCTGGTCCGCAGCCCGGTCCACATGGCGAACTGCAACAGGTTCCGGTACTGGCCATCGGTGCCGGCCAGArTCAGTCGCTGCTCTTCCGGCGAGAACGGATCArTCTCGTCCTCGGTCyTCGGCTTCTCCCTGACCGAGTACGTCCAGCCCGCCAGCGGGTTGATCTCGAyCAGTTCGTCATGCACGGCATCATCTAGCGCCGACCGTAGGCAGCTCTGTACGTTCGACAGGCGCTTGTTCGAGGCGTCCATGCTCGCCATAGCCTCCTTGATCATCTTGCGACTGAGCAGCACCAGGGGATGATCGCCCAGCyTCGGCACCAGTACCCCGTCGATGATCTTCCGATAGCCATCGATGGTGCTTGCCTTCAGGACCTTCTCTTTCTTCTCCCGCCAGCTTGCGAGGTATTTCGACAACGGTACTTGCCCGGTCTGGTATCCAAGCCGATTGGCTCGCTTGGACTTGGGGAAGGTGGCCAGATAGTCGAACGTGCCGTTGTAGATCGTCAGTTCGATAGCGGCCTTGTGCTGCTCGACGCGTTTCAGGTTAGCGGGGCTGGGCTCAAGTGGGATGCGTTCGCGGCACTGCTCACCATCGAACATGAAGCTGATTTCAATACTACTTTTCGACGCCGCTCTGAcGCCGCTGCGCTTTCCACCCATTCCGCATACCCATCCACACTTATTAGAGGTTTGTTGTCCGGCGCATGCCTCCATACGAGCCCCTTGGGCCATGTGCCGTCAGCGATCTTGGCTCTGATCGCGGCCTCAGTGTAGCCACTTTCGATGGCGAACTGGCTGATCGTCTTGTATTTGACCATCTCAACCCTCCTTGCTCATGGCTTCACGGAATGCAGCGGTGTATTCCTCGACGATCTTTTCAAGTGGgTCGCTGCCGGCCGGATCGCAAAGCCGGTCGATATATTTGATTGCCATTCGGCCAAGAGCTGCATCCTTGCGCAGAGCCTCGGCTTCAGCCATGArGCAGGCGTCGCACGGcTCAGACTTGCTCGCCGCCCCATCCCTGAACCCGTCCCGCGAAGCATTGGCCATGTCTACGGCGGTGTAGAGCGGAGTAGGGCCGCCGCGCAGGTGTTCGATCATCTTGGCCTGCTGAGCGACTGTGGCTTCCAGGGCGATAATTTTGTAGTCCTGCTCG
lsequence	TTCCTTGGCCGCTCTGGTCAGCCCTCGCGATATCCGTATCTCTCCCCGCAGCCAGTCTACATCCCmCCATTCTACCGCGATGAGTTCGCTGGTCCGCAGCCCGGTCCACATGGCGAACTGCAACAGGTTCCGGTACTGGCCATCGGTGCCGGCCAGArTCAGTCGCTGCTCTTCCGGCGAGAACGGATCArTCTCGTCCTCGGTCyTCGGCTTCTCCCTGACCGAGTACGTCCAGCCCGCCAGCGGGTTGATCTCGAyCAGTTCGTCATGCACGGCATCATCTAGCGCCGACCGTAGGCAGCTCTGTACGTTCGACAGGCGCTTGTTCGAGGCGTCCATGCTCGCCATAGCCTCCTTGATCATCTTGCGACTGAGCAGCACCAGGGGATGATCGCCCAGCyTCGGCACCAGTACCCCGTCGATGATCTTCCGATAGCCATCGATGGTGCTTGCCTTCAGGACCTTCTCTTTCTTCTCCCGCCAGCTTGCGAGGTATTTCGACAACGGTACTTGCCCGGTCTGGTATCCAAGCCGATTGGCTCGCTTGGACTTGGGGAAGGTGGCCAGATAGTCGAACGTGCCGTTGTAGATCGTCAGTTCGATAGCGGCCTTGTGCTGCTCGACGCGTTTCAGGTTAGCGGGGCTGGGCTCAAGTGGGATGCGTTCGCGGCACTGCTCACCATCGAACATGAAGCTGATTTCAATACTACTTTTCGACGCCGCTCTGA-cGCCGCTGCGCTTTCCACCCATTCCGCATACCCATCCACACTTATTAGAGGTTTGTTGTCCGGCGCATGCCTCCATACGAGCCCCTTGGGCCATGTGCCGTCAGCGATCTTGGCTCTGATCGCGGCCTCAGTGTAGCCACTTTCGATGGCGAACTGGCTGATCGTCTTGTATTTGACCATCTCAACCCTCCTTGCTCATGGCTTCACGGAATGCAGCGGTGTATTCCTCGACGATCTTTTCAAGTGGgTCGCTGCCGGCCGGATCGCAAAGCCGGTCGATATATTTGATTGCCATTCGGCCAAGAGCTGCATCCTTGCGCAGAGCCTCGGCTTCAGCCATGArGCAGGCGTCGCACGGcTCAGACTTGCTCGCCGCCCCATCCCTGAACCCGTCCCGCGAAGCATTGGCCATGTCTACGGCGGTGTAGAGCGGAGTAGGGCCGCCGCGCAGGTGTTCGATCATCTTGGCCTGCTGAGCGACTGTGGCTTCCAGGGCGATAATTTTGTAGTCCTGCTCG
quality	0x0B0B0B0B0B0B0B0B0B0404040404040404040404040404040E04040404040404040404040404040402020202020202020202020202020202020202020202020202160202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020404040404040404040404040404040404040416040404040404040404040404040404040404040404040404040404040404040416040404040404040404040404040416040404040404040404040404040404040402020202020202020202020202020202020202020202020202020202020202020202160202020202020202020202020202020202020909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090202020D02020D02020202020202020202020202020202020202020202020202020202020202020201010101010101010101010101010102020216020202020202020202020202020202020202020202020202020202020202020202020202090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303080303030303110303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303080303030303030303030303030303030303030303030303030303030303030303030303030803030303030303030303030303030303030303030303030303030303030303030303030303030303030313030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303050505050505050505050505050505050505050C0505050505050505050505160505050505050505050505050505050E050505050505050505050505050505050505050E050505050505050505050505050505050B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	2
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	2.13
perc_N	0.80
seq#	6
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_013_C07.x01.phd.1
asm_lend	1
asm_rend	276
seq_lend	1
seq_rend	276
best	0
comment	
db	sdsu
offset	0
lsequence	TTCCTTGGCCGCTCTGGTCAGCCCTCGCGATATCCGTATCTCTCCCCGCAGCCAGTCTACATCCCCCCATTCTACCGCGATGAGTTCGCTGGTCCGCAGCCCGGTCCACATGGCGAACTGCAACAGGTTCCGGTACTGGCCATCGGTGCCGGCCAGAATCAGTCGCTGCTCTTCCGGCGAGAACGGATCAATCTCGTCCTCGGTCTTCGGCTTCTCCCTGACCGAGTACGTCCAGCCCGCCAGCGGGTTGATCTCGACCAGTTCGTCATGCACGGC

seq_name	SDSU_RFPERU_013_G10.x01.phd.1
asm_lend	10
asm_rend	437
seq_lend	428
seq_rend	1
best	0
comment	
db	sdsu
offset	9
lsequence	CGCTCTGGTCAGCCCCCGCGATATCCGTATCTCTCCCCGCAGCCAGTCTACATCCCACCATTCTACCGCGATGAGTTCGCTGGTCCGCAGCCCGGTCCACATGGCGAACTGCAACAGGTTCCGGTACTGGCCATCGGTGCCGGCCAGAGTCAGTCGCTGCTCTTCCGGCGAGAACGGATCAGTCTCGTCCTCGGTCCTCGGCTTCTCCCTGACCGAGTACGTCCAGCCCGCCAGCGGGTTGATCTCGATCAGTTCGTCATGCACGGCATCATCTAGCGCCGACCGTAGGCAGCTCTGTACGTTCGACAGGCGCTTGTTCGAGGCGTCCATGCTCGCCATAGCCTCCTTGATCATCTTGCGACTGAGCAGCACCAGGGGATGATCGCCCAGCTTCGGCACCAGTACCCCGTCGATGATCTTCCGATAGC

seq_name	SDSU1_RFPERU_001_A09.x01.phd.1
asm_lend	343
asm_rend	839
seq_lend	2
seq_rend	496
best	0
comment	
db	sdsu
offset	342
lsequence	CGC-ATCGCCTCCTTGATCATCTTGCGACTGAGCAGCACCAGGGGATGATCGCCCAGCCTCGGCACCAGTACCCCGTCGATGATCTTCCGATAGCCATCGATGGTGCTTGCCTTCAGGACCTTCTCTTTCTTCTCCCGCCAGCTTGCGAGGTATTTCGACAACGGTACTTGCCCGGTCTGGTATCCAAGCCGATTGGCTCGCTTGGACTTGGGGAAGGTGGCCAGATAGTCGAACGTGCCGTTGTAGATCGTCAGTTCGATAGCGGCCTTGTGCTGCTCGACGCGTTTCAGGTTAGCGGGGCTGGGCTCAAGTGGGATGCGTTCGCGGCACTGCTCACCATCGAACATGAAGCTGATTTCAATACTACTTTTCGACGCCG-TCTGA-CGCCGCTGCGCTTTCCACCCATTCCGCATACCCATCCACACTTATTAGAGGTTTGTTGTCCGGCGCATGCCTCCATACGAGCCCCTTGGGCCATGTGCCGTCAGCGATCTT

seq_name	SDSU1_RFPERU_001_B04.x01.phd.1
asm_lend	498
asm_rend	1123
seq_lend	1
seq_rend	623
best	0
comment	
db	sdsu
offset	497
lsequence	TCGACAACGGTACTTGCCCGGTCTGGTATCCAAGCCGATTGGCTCGCTTGGACTTGGGGAAGGTGGCCAGATAGTCGAACGTGCCGTTGTAGATCGTCAGTTCGATAGCGGCCTTGTGCTGCTCGACGCGTTTCAGGTTAGCGGGGCTGGGCTCAAGTGGGATGCGTTCGCGGCACTGCTCACCATCGAACATGAAGCTGATTTCAATACTACTTTTCGACGCCGCTCTGA-CGCCGCTGCGCTTTCCACCCATTCCGCATACCCATCCACACTTATTAGAGGTTTGTTGTCCGGCGCATGCCTCCATACGAGCCCCTTGGGCCATGTGCCGTCAGCGATCTTGGCTCTGATCGCGGCCTCAGTGTAGCCACTTTCGATGGCGAACTGGCTGATCGTCTCGTATTTGACCATCTCAACCCTCCTTGCTCATGGCTTCACGGAATGCAGCGGTGTATTCCTCGACGATCTTTTCAAGTGGGTCGCTGCCGGCCGGATCGCAAAGCCGGTCGATATATTTGATTGCCATTCGGCCAAGAGCTGCATCCTTGCGCAGAGCCTCGG-TTCAGCCATGAGGCAGGCGTCGCACGG-TCAGACTTGCTCGCCGCCC-ATCCCTGAACCCGTCC

seq_name	SDSU_RFPERU_015_G04.x01.phd.1
asm_lend	668
asm_rend	1082
seq_lend	1
seq_rend	416
best	0
comment	
db	sdsu
offset	667
lsequence	CGGCACTGCTCACCATCGAACATGAAGCTGATTTCAATACTACTTTTCGACGCCGCTCTGAACGCCGCTGCGCTTTCCACCCATTCCGCATACCCATCCACACTTATTAGAGGTTTGTTGTCCGGCGCATGCCTCCATACGAGCCCCTTGGGCCATGTGCCGTCAGCGATCTTGGCTCTGATCGCGGCCTCAGTGTAGCCACTTTCGATGGCGAACTGGCTGATCGTCTTGTATTTGACCATCTCAACCCTCCTTGCTCATGGCTTAACGGAATGCAGCGGTGTATTCCTCGACGATCTTTTCAAGTGGGTCGCTGCCGGCCGGATCGCAAAGCCGGTCGATATATTTGATTGCCATTCGGCCAAGAGCTGCATCCTTGCGCAGAGCCTCGGCTTCAGCCATGAAGCAGGCGTCGC

seq_name	SDSU_RFPERU_014_H06.x01.phd.1
asm_lend	833
asm_rend	1246
seq_lend	1
seq_rend	413
best	0
comment	
db	sdsu
offset	833
lsequence	CGATCTTGGCTCTGATCGCGGCCTCAGTGTAGCCACTTTCGATGGCGAACTGGCTGATCGTCTTGTATTTGACCATCTCAACCCTCCTTGCTCATGGCTTCACGGAATGCAGCGGTGTATTCCTCGACGATCTTTTCAAGTGG-TCGCTGCCGGCCGGATCGCAAAGCCGGTCGATATATTTGATTGCCATTCGGCCAAGAGCTGCATCCTTGCGCAGAGCCTCGGCTTCAGCCATGAAGCAGGCGTCGCACGGCTCAGACTTGCTCGCCGCCCCATCCCTGAACCCGTCCCGCGAAGCATTGGCCATGTCTACGGCGGTGTAGAGCGGAGTAGGGCCGCCGCGCAGGTGTTCGATCATCTTGGCCTGCTGAGCGACTGTGGCTTCCAGGGCGATAATTTTGTAGTCCTGCTCG
|
sequence	TAGGATTGGATTATTTGGAAAGGGTTTTTGCGCGCTTCTTCGACCACGCAATCACGTCAAGCACCGCGCTTTTGCTGAACACGCTGCGCTGCTTGTAGTAGTCGATCGAGTCCCGGGCTACGCTGAAGCAAATGCCCTCTGGATACTTCAGCTTGCGCAGTTCGTCGTGAACGTTTTTTCGATGAACTCAAACGGAGTCATATCGCCACCCATTCGTTTTTGCCGTTGTAGAAGCCTCGCCAyTCCCCGAGCCTGAACACCAAGGTCCCAGGGtGCAGAGCCATGCGCGAGAGATTGGCCAGCCATCGAGCCGGAAGCTTTTCTTGATCGCGCTCAGACGGCGCTTGCGGATTCGCGTTCGTGACAGATCGATCCGCCGGATTCGGATTAGAGCCATGTTGAATTCCAGyCAGGCGCCGCCCTCCGGGTTCCGGATGCAGCAGGTTGGATGGGGTTACTGCTTCGGCGCTTTCGGGAAGAACGCAGGGCGTGGGCCGCCGCGCTTCGATTTTGGATAGTCGATTTCGAACTTGGTGAGGATGCGAGTGAAGGCTGTAAAAGAGATTCCGGCCTTTTCCATAGCCTGGTTTCGCGTCAAGCCAAGCTCCTTGAACGCCTTGATGCGTGCTGCGTCTTGCGCATCTTTTGCTTCATCGACAGTGGCCGGTTTCAGATTCTTGCGCGCATAATAGGATGCTGACTGAAAACTGAATCCTCCTTCTTTGGCCAGAGAA
lsequence	TAGGATTGGATTATTTGGAAAGGGTTTTTGCGCGCTTCTTCGACCACGCAATCACGTCAAGCACCGCGCTTTTGCTGAACACGCTGCGCTGCTTGTAGTAGTCGATCGAGTCCCGGGCTACGCTGAAGCAAATGCCCTCTGGATACTTCAGCTTGCGCAGTTCGTCGTGAACGTTTTTTCGATGAACTCAAACGGAGTCATATCGCCACCCATTCGTTTTTGCCGTTGTAGAAGCCTCGCCAyTCCCCGAGCCTGAACACCAAGGTCCCAGGG-tGCAGAGCCATGCGCGAGAGATTGGCCAGCCATCGAGCCGGAAGCTTTTCTTGATCGCGCTCAGACGGCGCTTGCGGATTCGCGTTCGTGACAGATCGATCCGCCGGATTCGGATTAGAGCCATGTTGAATTCCAGyCAGGCGCCGCCCTCCGGGTTCCGGATGCAGCAGGTTGGATGGGGTTACTGCTTCGGCGCTTTCGGGAAGAACGCAGGGCGTGGGCCGCCGCGCTTCGATTTTGGATAGTCGATTTCGAACTTGGTGAGGATGCGAGTGAAGGCTGTAAAAGAGATTCCGGCCTTTTCCATAGCCTGGTTTCGCGTCAAGCCAAGCTCCTTGAACGCCTTGATGCGTGCTGCGTCTTGCGCATCTTTTGCTTCATCGACAGTGGCCGGTTTCAGATTCTTGCGCGCATAATAGGATGCTGACTGAAAACTGAATCCTCCTTCTTTGGCCAGAGAA
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090903030D030303030303030303030303030303030303030303030303030303030303030303030303030303030303160303030303030303030303030303030303030303030303030303030303030D0303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030316030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030305050505050505050505050505050505050505050505050505050B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	17
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.43
perc_N	0.41
seq#	2
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU1_RFPERU_001_E04.x01.phd.1
asm_lend	1
asm_rend	510
seq_lend	1
seq_rend	511
best	0
comment	
db	ZZZ
offset	0
lsequence	TAGGATTGGATTATTTGGAAAGGGTTTTTGCGCGCTTCTTCGACCACGCAATCACGTCAAGCACCGCGCTTTTGCTGAACACGCTGCGCTGCTTGTAGTAGTCGATCGAGTCCCGGGCTACGCTGAAGCAAATGCCCTCTGGATACTTCAGCTTGCGCAGTTCGTCGTGAACGTTTTTTCGATGAACTCAAACGGAGTCATATCGCCACCCATTCGTTTTTGCCGTTGTAGAAGCCTCGCCATTCCCCGAGCCTGAACACCAAGGTCCCAGGGGTGCAGAGCCATGCGCGAGAGATTGGCCAGCCATCGAGCCGGAAGCTTTTCTTGATCGCGCTCAGACGGCGCTTGCGGATTCGCGTTCGTGACAGATCGATCCGCCGGATTCGGATTAGAGCCATGTTGAATTCCAGTCAGGCGCCGCCCTCCGGGTTCCGGATGCAGCAGGTTGGATGGGGTTACTGCTTCGGCGCTTTCGGGAAGAACGCAGGGCGTGGGCCGCCGCGCTTCGATT

seq_name	SDSU_RFPERU_006_E05.x01.phd.1
asm_lend	198
asm_rend	734
seq_lend	3
seq_rend	538
best	0
comment	
db	ZZZ
offset	197
lsequence	TC-TATCGCCACCCATTCGTTTTTGCCGTTGTAGAAGCCTCGCCACTCCCCGAGCCTGAACACCAAGGTCCCAGGG-TGCAGAGCCATGCGCGAGAGATTGGCCAGCCATCGAGCCGGAAGCTTTTCTTGATCGCGCTCAGACGGCGCTTGCGGATTCGCGTTCGTGACAGATCGATCCGCCGGATTCGGATTAGAGCCATGTTGAATTCCAGCCAGGCGCCGCCCTCCGGGTTCCGGATGCAGCAGGTTGGATGGGGTTACTGCTTCGGCGCTTTCGGGAAGAACGCAGGGCGTGGGCCGCCGCGCTTCGATTTTGGATAGTCGATTTCGAACTTGGTGAGGATGCGAGTGAAGGCTGTAAAAGAGATTCCGGCCTTTTCCATAGCCTGGTTTCGCGTCAAGCCAAGCTCCTTGAACGCCTTGATGCGTGCTGCGTCTTGCGCATCTTTTGCTTCATCGACAGTGGCCGGTTTCAGATTCTTGCGCGCATAATAGGATGCTGACTGAAAACTGAATCCTCCTTCTTTGGCCAGAGAA
|
sequence	CCGTTCAAGCAGGAGATCAGCGCCTGCCATCTGCAACAGAGCATGGGGCGTCAAACCTCTGCGGCGTAGATCCTATATTCACAGGGGAGCCAAAAGCATTTGACCAACTGAGGGGAAGTGCCTCGGTGCCAAATTCAGAGCCTCGCCATCGTGCGGGGCTTTTTTGTTTCCTTCTTCCACTGCTCCCCAGCAGTTTGGCCGCCAACTGACGGCCTTTTTTATTCCTGGAGTCACGCCATGGCCGAACCCGCGAGCACCACTGCCGCCGGTGTCCTGCTCGCGAAGTACGGCATCATCATCGCTGGCTTCGCTGGAGCAATCCTTTCGCTGACCTTCCTTCAnGGGCCTGACCCGCAAGCAGGCCATTTGGGCATTCTTCACCGGGTTCGGCTCTGCGATCTTCTGCACGCCGCTGGCGATCAGCTTCTTCAAGCTGGAGCCTGGTGGCGAAACTCAATACGGCGTCGCATTCCTGATCGGCCTGCTGGCCATGAACATCATTCCCCTGTTGAAGAaAGCAATGCCGGGAGTGTTTGGCGTCTCGGGAGGTGCaGTAATGCAAACCATCCTGCAAGTCCTTGACGCTTTCCTGTGTGtgCTGGTGGTGCTAGCCGCTGCTGAGTACCT
lsequence	CCGTTCAAGCAGGAGATCAGCGCCTGCCATCTGCAACAGAGCATGGGGCGTCAAACCTCTGCGGCGTAGATCCTATATTCACAGGGGAGCCAAAAGCATTTGACCAACTGAGGGGAAGTGCCTCGGTGCCAAATTCAGAGCCTCGCCATCGTGCGGGGCTTTTTTGTTTCCTTCTTCCACTGCTCCCCAGCAGTTTGGCCGCCAACTGACGGCCTTTTTTATTCCTGGAGTCACGCCATGGCCGAACCCGCGAGCACCACTGCCGCCGGTGTCCTGCTCGCGAAGTACGGCATCATCATCGCTGGCTTCGCTGGAGCAATCCTTTCGCTGACCTTCCTTCAnGGGCCTGACCCGCAAGCAGGCCATTTGGGCATTCTTCACCGGGTTCGGCTCTGCGATCTTCTGCACGCCGCTGGCGATCAGCTTCTTCAAGCTGGAGCCTGGTGGCGAAACTCAATACGGCGTCGCATTCCTGATCGGCCTGCTGGCCATGAACATCATTCCCCTGTTGAAGA-aAGCAATGCCGGGAGTGTTTGGCGTCTCGGGAGGTGCaGTAATGCAAACCATCCTGCAAGTCCTTGACGCTTTCCTGTGTGtgCTGGTGGTGCTAGCCGCTGCTGAGTACCT
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B150B0B0B0B0B0B0B0B0B0B0B0B0B0B0B090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B04040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040E040404040404040404040404040402020202020202020202020202020202020202020202020D020202020202040404040404040404040404040404040404040404040404040404040404040404040404040E0E0404040B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	106
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.23
perc_N	0.80
seq#	2
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_006_E04.x01.phd.1
asm_lend	1
asm_rend	627
seq_lend	1
seq_rend	626
best	0
comment	
db	sdsu
offset	0
lsequence	CCGTTCAAGCAGGAGATCAGCGCCTGCCATCTGCAACAGAGCATGGGGCGTCAAACCTCTGCGGCGTAGATCCTATATTCACAGGGGAGCCAAAAGCATTTGACCAACTGAGGGGAAGTGCCTCGGTGCCAAATTCAGAGCCTCGCCATCGTGCGGGGCTTTTTTGTTTCCTTCTTCCACTGCTCCCCAGCAGTTTGGCCGCCAACTGACGGCCTTTTTTATTCCTGGAGTCACGCCATGGCCGAACCCGCGAGCACCACTGCCGCCGGTGTCCTGCTCGCGAAGTACGGCATCATCATCGCTGGCTTCGCTGGAGCAATCCTTTCGCTGACCTTCCTTCANGGGCCTGACCCGCAAGCAGGCCATTTGGGCATTCTTCACCGGGTTCGGCTCTGCGATCTTCTGCACGCCGCTGGCGATCAGCTTCTTCAAGCTGGAGCCTGGTGGCGAAACTCAATACGGCGTCGCATTCCTGATCGGCCTGCTGGCCATGAACATCATTCCCCTGTTGAAGA-AAGCAATGCCGGGAGTGTTTGGCGTCTCGGGAGGTGC-GTAATGCAAACCATCCTGCAAGTCCTTGACGCTTTCCTGTGTGTGCTGGTGGTGCTAGCCGCTGCTGAGTACCT

seq_name	SDSU_RFPERU_010_B05.x01.phd.1
asm_lend	460
asm_rend	601
seq_lend	141
seq_rend	1
best	0
comment	
db	ZZZ
offset	459
lsequence	CGGCGTCGCATTCCTGATCGGCCTGCTGGCCATGAACATCATTCCCCTGTTGAAGAGAAGCAATGCCGGGAGTGTTTGGCGTCTCGGGAGGTGCAGTAATGCAAACCATCCTGCAAGTCCTTGACGCTTTCCTGTGTG--CTG
|
sequence	AGCGCCGATACACATGCTCAAACCGCGCATCGAAGTCTTCGATCAAGACGCTGAAGTAGTAGCCGTCCATGTTGAAGTTGAGCGGCTGACCGGCGTCACGCAGCGTCTCCAGCTCCGTGACGCGGTCACCAGCTGTCGCGCCAGTGATCCAGCCAGACCACTGGATGTTCTTGTAATCCAGACCGAGAACATCGACAACACGCTTGCCGCCTACCAGTTTGTGCACCACGAGCTTCTGTTTGGCGCCGATCGATACTGACTCTGGGACTTCCAGGCCGGTGAACTCGACATCTCCAACGATCAACCGCGTGGCAAACGGATCCCCGCCCGGAGCGAAGTTGTCCAGGAAGCTCGTAAAGCTCATCGTTTATCCCCTTGGATAGGCTGCGCTCGGGGTTCCTGGCATCAGCATGCTGCGGTTCGGATCGAAGCCCTGCGTCCCTGTCCGTGGCTTCGCGGCTTCCTTCGCCATCCGCTGGATTACCACGTCGCTGACTTGTTTGCCGTCGATGTACAGGTTGATGTTCTGTTGGCCATCGGCGCcAGACTTGCCCGGGACCGGAGCCACCAGCGGAGACCATGCTGGCTTTTTCTCCCCGCTTCCACGGAAATCATCGGCGAATGTAGGTTTTTGAGATCTGCATCGATGCTGGAAGAATCAGGTTTGCGCCAGCGATCAGCGTGTTGAAGATCGTCTGCCAGCCGGTCAAGAAGACCAGAGCAAATGACTTGAATGCGCCGCCGATATCGCCCTGAAAGAGTTTTACAAACCCGGTCTTCATGTCGTTCCACATGAGCTTCAATGCTCCGCTGATCTCCTTCCAGTTGTTCCATAGTAGGAAGGCCGCCGCCGCGATCGCCAGATCACTAGGCCAATTGGATTCATGAGGAGTGCACGGCCAAGATTGACCACAGTCATCACAAGATAAGTTCCCATACGCGCTATCCATGGGATCAGCGGTG
lsequence	AGCGCCGATACACATGCTCAAACCGCGCATCGAAGTCTTCGATCAAGACGCTGAAGTAGTAGCCGTCCATGTTGAAGTTGAGCGGCTGACCGGCGTCACGCAGCGTCTCCAGCTCCGTGACGCGGTCACCAGCTGTCGCGCCAGTGATCCAGCCAGACCACTGGATGTTCTTGTAATCCAGACCGAGAACATCGACAACACGCTTGCCGCCTACCAGTTTGTGCACCACGAGCTTCTGTTTGGCGCCGATCGATACTGACTCTGGGACTTCCAGGCCGGTGAACTCGACATCTCCAACGATCAACCGCGTGGCAAACGGATCCCCGCCCGGAGCGAAGTTGTCCAGGAAGCTCGTAAAGCTCATCGTTTATCCCCTTGGATAGGCTGCGCTCGGGGTTCCTGGCATCAGCATGCTGCGGTTCGGATCGAAGCCCTGCGTCCCTGTCCGTGGCTTCGCGGCTTCCTTCGCCATCCGCTGGATTACCACGTCGCTGACTTGTTTGCCGTCGATGTACAGGTTGATGTTCTGTTGGCCATCGGCGCcAGACTTGCCCGGGACCGGAGCCACCAGCGGAGACCATGCTGGCTTTTTCTCCCCGCTTCCACGGAAATCATCGGCGAATGTAGGTTTTTGAGATCTGCATCGATGCTGGAAGAATCAGGTTTGCGCCAGCGATCAGCGTGTTGAAGATCGTCTGCCAGCCGGTCAAGAAGACCAGAGCAAATGACTTGAATGCGCCGCCGATATCGCCCTGAAAGAGTTTTACAAACCCGGTCTTCATGTCGTTCCACATGAGCTTCAATGCTCCGCTGATCTCCTTCCAGTTGTTCCATAGTAGGAAGGCCGCCGCCGCGATCGCCAGATCACTAGGCCAATTGGATTCATGAGGAGTGCACGGCCAAGATTGACCACAGTCATCACAAGATAAGTTCCCATACGCGCTATCCATGGGATCAGCGGTG
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B09090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B05050505050E0505050505050505050505050505050505050505050505050505050505050505050505030303030303030303030909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	144
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.05
perc_N	0.10
seq#	2
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_013_H05.x01.phd.1
asm_lend	1
asm_rend	589
seq_lend	1
seq_rend	589
best	0
comment	
db	sdsu
offset	0
lsequence	AGCGCCGATACACATGCTCAAACCGCGCATCGAAGTCTTCGATCAAGACGCTGAAGTAGTAGCCGTCCATGTTGAAGTTGAGCGGCTGACCGGCGTCACGCAGCGTCTCCAGCTCCGTGACGCGGTCACCAGCTGTCGCGCCAGTGATCCAGCCAGACCACTGGATGTTCTTGTAATCCAGACCGAGAACATCGACAACACGCTTGCCGCCTACCAGTTTGTGCACCACGAGCTTCTGTTTGGCGCCGATCGATACTGACTCTGGGACTTCCAGGCCGGTGAACTCGACATCTCCAACGATCAACCGCGTGGCAAACGGATCCCCGCCCGGAGCGAAGTTGTCCAGGAAGCTCGTAAAGCTCATCGTTTATCCCCTTGGATAGGCTGCGCTCGGGGTTCCTGGCATCAGCATGCTGCGGTTCGGATCGAAGCCCTGCGTCCCTGTCCGTGGCTTCGCGGCTTCCTTCGCCATCCGCTGGATTACCACGTCGCTGACTTGTTTGCCGTCGATGTACAGGTTGATGTTCTGTTGGCCATCGGCGCCAGACTTGCCCGGGACCGGAGCCACCAGCGGAGACCATGCTGGCTT

seq_name	SDSU_RFPERU_005_F02.x01.phd.1
asm_lend	539
asm_rend	963
seq_lend	1
seq_rend	424
best	0
comment	
db	ABC
offset	538
lsequence	GGCGC-AGACTTGCCCGGGACCGGAGCCACCAGCGGAGACCATGCTGGCTTTTTCTCCCCGCTTCCACGGAAATCATCGGCGAATGTAGGTTTTTGAGATCTGCATCGATGCTGGAAGAATCAGGTTTGCGCCAGCGATCAGCGTGTTGAAGATCGTCTGCCAGCCGGTCAAGAAGACCAGAGCAAATGACTTGAATGCGCCGCCGATATCGCCCTGAAAGAGTTTTACAAACCCGGTCTTCATGTCGTTCCACATGAGCTTCAATGCTCCGCTGATCTCCTTCCAGTTGTTCCATAGTAGGAAGGCCGCCGCCGCGATCGCCAGATCACTAGGCCAATTGGATTCATGAGGAGTGCACGGCCAAGATTGACCACAGTCATCACAAGATAAGTTCCCATACGCGCTATCCATGGGATCAGCGGTG
|
sequence	ATTGCCATTCTTTCGAAGCGCATTCCCTCTCGTGGCGCTGGCTTCCAGGATCTTTTGGAAGCGCATTCGACGCAACACACCTGCCCGTTTGGGCCGGCCCAACTGGTTCGCAGTGGTAGTGATAGAGGTACTGGTCAATCTGCTTTAATCGACATGAAGATGACGCGAAAAGCGCCCTCCTGCGGATCCGGATCCGTCGCTCACCTGGTCTTGAATGACCTGATGTTCGCAGCCATGGAAGCCGGTTACCGGCTTGCGCCAATCAAGGCAGCATGCACTGCTGAGCAAAAAGCGAGCCAAACTTGTGACCTGATGGCCTTACGCAAT
lsequence	ATTGCCATTCTTTCGAAGCGCATTCCCTCTCGTGGCGCTGGCTTCCAGGATCTTTTGGAAGCGCATTCGACGCAACACACCTGCCCGTTT-GGG-CCGGCCC-AACTGGTTCGCAGTGGTAGTGATAGAGGTACTGGTCAATCTGCTTTAATCGACATGAAGATGACGCGAAAAGCGCCCTCCTGCGGATCCGGATCCGTCGCTCACCTGGTCTTGAATGACCTGATGTTCGCAGCCATGGAAGCCGGTTACCGGCTTGCGCCAATCAAGGCAGCATGCACTGCTGAGCAAAAAGCGAGCCAAACTTGTGACCTGATGGCCTTACGCAAT
quality	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
asmbl_id	652
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	2.75
perc_N	0.00
seq#	9
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/27/07 18:38:59
comment	
frameshift	

seq_name	9986984
asm_lend	1
asm_rend	102
seq_lend	1
seq_rend	105
best	0
comment	
db	sdsu
offset	0
lsequence	ATTGCCATTCTTTCGAAGCGCATTCCCTCTCGTGGCGCTGGCTTCCAGGATCTTTTGGAAGCGCATTCGACGCAACACACCTGCCCGTTTCGGGTCCGGCCCGAA

seq_name	9944760
asm_lend	2
asm_rend	109
seq_lend	108
seq_rend	1
best	0
comment	
db	ABC
offset	1
lsequence	TTGCCATTCTTTCGAAGCGCATTCCCTCTCGTGGCGCTGGCTTCCAGGATCTTTTGGAAGCGCATTCGACGCAACACACCTGCCCGTTT-GGG-CCGGCCC-AACTGGTTC

seq_name	9980040
asm_lend	48
asm_rend	154
seq_lend	1
seq_rend	107
best	0
comment	
db	ABC
offset	47
lsequence	GGATCTTTTGGAAGCGCATTCGACGCAACACACCTGCCCGTTT-GGG-CCGGCCC-AACTGGTTCGCAGTGGTAGTGATAGAGGTACTGGTCAATCTGCTTTAATCGACA

seq_name	9956706
asm_lend	50
asm_rend	146
seq_lend	97
seq_rend	1
best	0
comment	
db	ABC
offset	49
lsequence	ATCTTTTGGAAGCGCATTCGACGCAACACACCTGCCCGTTT-GGG-CCGGCCC-AACTGGTTCGCAGTGGTAGTGATAGAGGTACTGGTCAATCTGCTTT

seq_name	9937790
asm_lend	84
asm_rend	191
seq_lend	1
seq_rend	108
best	0
comment	
db	ABC
offset	83
lsequence	CCCGTTT-GGG-CCGGCCC-AACTGGTTCGCAGTGGTAGTGATAGAGGTACTGGTCAATCTGCTTTAATCGACATGAAGATGACGCGAAAAGCGCCCTCCTGCGGATCCGG

seq_name	9976538
asm_lend	120
asm_rend	215
seq_lend	1
seq_rend	96
best	0
comment	
db	ABC
offset	122
lsequence	TGATAGAGGTACTGGTCAATCTGCTTTAATCGACATGAAGATGACGCGAAAAGCGCCCTCCTGCGGATCCGGATCCGTCGCTCACCTGGTCTTGAA

seq_name	9960711
asm_lend	134
asm_rend	229
seq_lend	1
seq_rend	96
best	0
comment	
db	ABC
offset	136
lsequence	GTCAATCTGCTTTAATCGACATGAAGATGACGCGAAAAGCGCCCTCCTGCGGATCCGGATCCGTCGCTCACCTGGTCTTGAATGACCTGATGTTCG

seq_name	9962187
asm_lend	178
asm_rend	273
seq_lend	1
seq_rend	96
best	0
comment	
db	ZZZ
offset	180
lsequence	TCCTGCGGATCCGGATCCGTCGCTCACCTGGTCTTGAATGACCTGATGTTCGCAGCCATGGAAGCCGGTTACCGGCTTGCGCCAATCAAGGCAGCA

seq_name	9970175
asm_lend	239
asm_rend	327
seq_lend	1
seq_rend	89
best	0
comment	
db	ABC
offset	241
lsequence	AAGCCGGTTACCGGCTTGCGCCAATCAAGGCAGCATGCACTGCTGAGCAAAAAGCGAGCCAAACTTGTGACCTGATGGCCTTACGCAAT
BioPerl-1.007002/t/data/crab.dat.cn000444000766000024       167713155576321 16703 0ustar00cjfieldsstaff000000000000 13 sequences
1 A-salina
2 C-vittat
3 C-sp.
4 L-aequit
5 P-camtsc
6 E-tenuim
7 L-splend
8 P-bernha
9 P-acadia
10 P-p(NE)
11 P-p(GU)
12 P-l(NE)
13 P-l(GU)
 14 and   2        0.097855
 14 and   3        0.097855
 15 and  20        0.063651
 15 and  14        0.013271
 15 and   1        0.155362
 16 and  10        0.008043
 16 and  11        0.008043
 17 and  12        0.001340
 17 and  13        0.001340
 18 and  16        0.010389
 18 and  17        0.017091
 19 and   4        0.006702
 19 and   5        0.006702
 20 and  23        0.017147
 20 and  18        0.029044
 21 and   8        0.002681
 21 and   9        0.002681
 22 and   6        0.012064
 22 and  21        0.009383
 23 and  24        0.005306
 23 and  19        0.023626
 24 and  22        0.012958
 24 and   7        0.025022

file:crab.dat  constant rate for NJ (negative branches allowed)
 p-distance was used.
Number of nucleotide sites compared 373 (nsite=421)
outgroup:  1 A-salina
BioPerl-1.007002/t/data/crab.nj000444000766000024       161413155576321 16132 0ustar00cjfieldsstaff000000000000 13 sequences
1 A-salina
2 C-vittat
3 C-sp.
4 L-aequit
5 P-camtsc
6 E-tenuim
7 L-splend
8 P-bernha
9 P-acadia
10 P-p(NE)
11 P-p(GU)
12 P-l(NE)
13 P-l(GU)
 14 and   2        0.087619
 14 and   3        0.108092
 15 and   1        0.155362
 15 and  14        0.020241
 16 and  10        0.011208
 16 and  11        0.004878
 17 and  12        0.002136
 17 and  13        0.000545
 18 and  16        0.016086
 18 and  17        0.011394
 19 and   4        0.006423
 19 and   5        0.006982
 20 and  15        0.056669
 20 and  18        0.028117
 21 and   8        0.003267
 21 and   9        0.002095
 22 and   6        0.011003
 22 and  21        0.010445
 23 and  20        0.018557
 23 and  19        0.020149
 24 and  22        0.012944
 24 and   7        0.024589
 24 and  23        0.007331

file:crab.dat   NJ tree   p-distance was used.
Number of nucleotide sites compared 373 (nsite=421)
seed=1850
BioPerl-1.007002/t/data/crab.njb000444000766000024       217213155576321 16274 0ustar00cjfieldsstaff000000000000   13 sequences     1000 bootstraping
1 A-salina
2 C-vittat
3 C-sp.
4 L-aequit
5 P-camtsc
6 E-tenuim
7 L-splend
8 P-bernha
9 P-acadia
10 P-p(NE)
11 P-p(GU)
12 P-l(NE)
13 P-l(GU)
 14 and   2        0.098857      1000
 14 and   3        0.127932      1000
 15 and   1        0.197471      1000
 15 and  14        0.029273       874
 16 and  10        0.011732      1000
 16 and  11        0.004529      1000
 17 and  12        0.002258      1000
 17 and  13        0.000428      1000
 18 and  16        0.017512      1000
 18 and  17        0.010824       998
 19 and   4        0.006534      1000
 19 and   5        0.006992      1000
 20 and  15        0.070461      1000
 20 and  18        0.030579       998
 21 and   8        0.003339      1000
 21 and   9        0.002042      1000
 22 and   6        0.011142      1000
 22 and  21        0.010693       983
 23 and  20        0.020714       996
 23 and  19        0.020350      1000
 24 and  23        0.008665       826
 24 and  22        0.013457       972
 24 and   7        0.025598      1000

JC distance was used

Number of nucleotide sites compared 373 (nsite=421)
seed=27165 ninap=0
BioPerl-1.007002/t/data/crypto.sim4-0000444000766000024        16513155576321 17125 0ustar00cjfieldsstaff000000000000
seq1 = cn416, 630 bp
seq2 = Contig147.fa (>Contig147), 1086 bp

36-132  (191-286)   89% <-
133-191  (343-401)   93%
BioPerl-1.007002/t/data/crypto.sim4-3000444000766000024       164213155576321 17151 0ustar00cjfieldsstaff000000000000
seq1 = cn416, 630 bp
seq2 = Contig147.fa (>Contig147), 1086 bp


36-132  (191-286)   89% <-
133-191  (343-401)   93%

      0     .    :    .    :    .    :    .    :    .    :
     36 AAAGCCATGCAATGCATCCCATGATACCAAAGATAAAATATCCAAAAATC
        |||||||||||||||||||-||||||||||||| || |||||||||||||
    191 AAAGCCATGCAATGCATCC ATGATACCAAAGACAATATATCCAAAAATC

     50     .    :    .    :    .    :    .    :    .    :
     86 CATGACCGATCCTGATGCAATAACCAAGAGACCGTTTATCCCGGGAA   
         | ||  |||| | ||||||||||||||||||| |||||||||||||<<<
    240 TAAGATTGATCATCATGCAATAACCAAGAGACCCTTTATCCCGGGAACTA

    100     .    :    .    :    .    :    .    :    .    :
    133       TGCCACAACGTAGTCCTTCTGTACATCCTGAACATTTCCATCAT
        ...<<<|||||||||||||||||| |||||||||||||||||||||||||
    290 ...CACTGCCACAACGTAGTCCTTTTGTACATCCTGAACATTTCCATCAT

    150     .    :    .
    177 CATCAACGAA AAGTA
        |||| |||||-||-||
    387 CATCTACGAACAA TA

BioPerl-1.007002/t/data/crypto.sim4-4000444000766000024       220013155576321 17141 0ustar00cjfieldsstaff000000000000
seq1 = cn416, 630 bp
seq2 = Contig147.fa (>Contig147), 1086 bp

>cn416 lastmodified=[2002-10-29 11:40:27] project=[B3501] length=[630] clusterid=[371] coverage=[1] crawid=[1] sequencecount=[2] longestsequence=[k9k11j2.f1] sequences=[k9k11j2.f1|k9k11j2.f1C] clone=[|k9k11j2] 
>Contig147

36-132  (191-286)   89% <-
133-191  (343-401)   93%

      0     .    :    .    :    .    :    .    :    .    :
     36 AAAGCCATGCAATGCATCCCATGATACCAAAGATAAAATATCCAAAAATC
        |||||||||||||||||||-||||||||||||| || |||||||||||||
    191 AAAGCCATGCAATGCATCC ATGATACCAAAGACAATATATCCAAAAATC

     50     .    :    .    :    .    :    .    :    .    :
     86 CATGACCGATCCTGATGCAATAACCAAGAGACCGTTTATCCCGGGAA   
         | ||  |||| | ||||||||||||||||||| |||||||||||||<<<
    240 TAAGATTGATCATCATGCAATAACCAAGAGACCCTTTATCCCGGGAACTA

    100     .    :    .    :    .    :    .    :    .    :
    133       TGCCACAACGTAGTCCTTCTGTACATCCTGAACATTTCCATCAT
        ...<<<|||||||||||||||||| |||||||||||||||||||||||||
    290 ...CACTGCCACAACGTAGTCCTTTTGTACATCCTGAACATTTCCATCAT

    150     .    :    .
    177 CATCAACGAA AAGTA
        |||| |||||-||-||
    387 CATCTACGAACAA TA

BioPerl-1.007002/t/data/ctgdemo.fpc000444000766000024     55132413155576321 17056 0ustar00cjfieldsstaff000000000000// fpc project v7demo
// 7.2  Date: 18:13 Fri 09 Apr 2004  User: cari
// Contigs 0  Clones 618  Markers 150  Bands 2028946
// Framework Demo Label Chromosome Abbrev Chr Genome 50 AvgBand 4096  AvgInsert 150000
// Configure 429 Tol 7 Cut 1e-10 Apx 0.100 Gel 3300 Min 0 End 15 Kill -1 Bad 15 Best 10 Log 0 Std 1 Page 3000 Match 2
// CpM Off 50 1 0 0 TBL 1 1e-09 2 1e-08 3 1e-07
// Build 1/1/70 0:0 Cut 1e-10 Off 50 1 0 0 TBL 1 1e-09 2 1e-08 3 1e-07 
// Clip(0 4600) MinMax(0 65535)  DQer(5,1)
  
Clone : "a0001B07"
Map "ctg1" Ends Left 457.000
Map "ctg1" Ends Right 485.000 Oldctg 2
Fp_number "01B07"
Gel_number    100131
Bands  836 29
Positive_STS "OJ000214_13" 
Positive_STS "OJ000310_29" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ990820_14" 
Positive_STS "OJ990923_08" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0001G11"
Map "ctg1" Ends Left 484.000
Map "ctg1" Ends Right 507.000 Oldctg 2
Fp_number "01G11"
Gel_number    100112
Bands  4102 24
Creation_date 99 11 12 9 2 
Modified_date 101 4 27 16 50 
  
Clone : "a0001I05"
Map "ctg1" Ends Left 548.000
Map "ctg1" Ends Right 579.000 Oldctg 2
Fp_number "01I05"
Gel_number    100113
Bands  5201 32
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0001J19"
Map "ctg1" Ends Left 162.000
Map "ctg1" Ends Right 199.000 Oldctg 2
Fp_number "01J19"
Gel_number    100133
Bands  6171 38
Positive_STS "OJ000301_13" 
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0001M01"
Map "ctg1" Ends Left 46.000
Map "ctg1" Ends Right 82.000 Oldctg 2
Fp_number "01M01"
Gel_number    100114
Bands  7729 37
Positive_STS "OJ990412_10" 
Positive_STS "OJ990605_38" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0001O24"
Map "ctg1" Ends Left 493.000
Map "ctg1" Ends Right 515.000 Oldctg 2
Fp_number "01O24"
Gel_number    100124
Bands  9590 23
Approximate_match_to_cosmid "a0014I02"
Creation_date 99 11 12 9 2 
Modified_date 101 4 11 16 57 
  
Clone : "a0002G06"
Map "ctg1" Ends Left 553.000
Map "ctg1" Ends Right 586.000 Oldctg 2
Fp_number "02G06"
Gel_number    100222
Bands  14248 34
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Positive_STS "OJ000303_09" 
Positive_STS "OJ000303_17" 
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0002I06"
Map "ctg1" Ends Left 579.000
Map "ctg1" Ends Right 607.000 Oldctg 2
Fp_number "02I06"
Gel_number    100223
Bands  15562 29
Approximate_match_to_cosmid "a0037I23"
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Positive_STS "OJ000321_15" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0002J07"
Map "ctg1" Ends Left 378.000
Map "ctg1" Ends Right 417.000 Oldctg 2
Fp_number "02J07"
Gel_number    100233
Bands  16169 39
Pseudo_match_to_cosmid "a0023C14"
Positive_OVERGO "SOG0223" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0002N24"
Map "ctg1" Ends Left 205.000
Map "ctg1" Ends Right 237.000 Oldctg 2
Fp_number "02N24"
Gel_number    100244
Bands  19147 33
Positive_OVERGO "SOG1774" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0002O22"
Map "ctg1" Ends Left 84.000
Map "ctg1" Ends Right 113.000 Oldctg 2
Fp_number "02O22"
Gel_number    100224
Bands  19717 30
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0003C15"
Map "ctg1" Ends Left 516.000
Map "ctg1" Ends Right 548.000 Oldctg 2
Fp_number "03C15"
Gel_number    100311
Bands  21818 33
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0003I09"
Map "ctg1" Ends Left 260.000
Map "ctg1" Ends Right 289.000 Oldctg 2
Fp_number "03I09"
Gel_number    100313
Bands  25078 30
Creation_date 99 11 12 9 2 
Modified_date 101 4 11 16 57 
  
Clone : "a0003K20"
Map "ctg1" Ends Left 271.000
Map "ctg1" Ends Right 300.000 Oldctg 2
Fp_number "03K20"
Gel_number    100323
Bands  26667 30
Positive_STS "OJ000317_34" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0004D12"
Map "ctg1" Ends Left 110.000
Map "ctg1" Ends Right 145.000 Oldctg 2
Fp_number "04D12"
Gel_number    100441
Bands  31925 36
Approximate_match_to_cosmid "a0038D13"
Positive_OVERGO "SOG1055" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0004G07"
Map "ctg1" Ends Left 181.000
Map "ctg1" Ends Right 219.000 Oldctg 2
Fp_number "04G07"
Gel_number    100412
Bands  33802 39
Positive_STS "OJ000207_10" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0004I02"
Map "ctg1" Ends Left 227.000
Map "ctg1" Ends Right 259.000 Oldctg 2
Fp_number "04I02"
Gel_number    100423
Bands  35015 33
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0004L12"
Map "ctg1" Ends Left 518.000
Map "ctg1" Ends Right 546.000 Oldctg 2
Fp_number "04L12"
Gel_number    100443
Bands  37433 29
Approximate_match_to_cosmid "a0003C15"
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0005D14"
Map "ctg1" Ends Left 48.000
Map "ctg1" Ends Right 84.000 Oldctg 2
Fp_number "05D14"
Gel_number    100541
Bands  42236 37
Positive_STS "42D18r" 
Positive_STS "OJ990412_10" 
Positive_STS "OJ990605_38" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0005K03"
Map "ctg1" Ends Left 108.000
Map "ctg1" Ends Right 145.000 Oldctg 2
Fp_number "05K03"
Gel_number    100513
Bands  46610 38
Approximate_match_to_cosmid "a0038D13"
Positive_STS "C1679" 
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0005L07"
Map "ctg1" Ends Left 447.000
Map "ctg1" Ends Right 481.000 Oldctg 2
Fp_number "05L07"
Gel_number    100533
Bands  47296 35
Positive_STS "OJ000214_13" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ990923_08" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Positive_Probe "CSU469" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0006B21"
Map "ctg1" Ends Left 589.000
Map "ctg1" Ends Right 614.000 Oldctg 2
Fp_number "06B21"
Gel_number    100631
Bands  51617 26
Approximate_match_to_cosmid "a0041C20"
Positive_STS "chlor" 
Positive_STS "OJ000251_05" 
Positive_STS "OJ000321_15" 
Positive_STS "OJ000330_31" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0006G06"
Map "ctg1" Ends Left 569.000
Map "ctg1" Ends Right 600.000 Oldctg 2
Fp_number "06G06"
Gel_number    100622
Bands  54655 32
Positive_STS "C953" 
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0006I10"
Map "ctg1" Ends Left 163.000
Map "ctg1" Ends Right 179.000 Oldctg 2
Fp_number "06I10"
Gel_number    100623
Bands  56103 17
Exact_match_to_cosmid "a0021N13"
Positive_STS "OJ000301_13" 
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0006N03"
Map "ctg1" Ends Left 473.000
Map "ctg1" Ends Right 501.000 Oldctg 2
Fp_number "06N03"
Gel_number    100634
Bands  59123 29
Positive_STS "OJ000310_29" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991210_12" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Positive_OVERGO "SOG1346" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0007A20"
Map "ctg1" Ends Left 371.000
Map "ctg1" Ends Right 400.000 Oldctg 2
Fp_number "07A20"
Gel_number    100721
Bands  61489 30
Approximate_match_to_cosmid "a0049H15"
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0009A16"
Map "ctg1" Ends Left 378.000
Map "ctg1" Ends Right 416.000 Oldctg 2
Fp_number "09A16"
Gel_number    100921
Bands  81626 38
Pseudo_match_to_cosmid "a0025E13"
Creation_date 99 11 12 9 2 
Modified_date 103 2 5 13 55 
  
Clone : "a0009E22"
Map "ctg1" Ends Left 173.000
Map "ctg1" Ends Right 210.000 Oldctg 2
Fp_number "09E22"
Gel_number    100922
Bands  84566 38
Positive_STS "OJ000301_13" 
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0009F12"
Map "ctg1" Ends Left 10.000
Map "ctg1" Ends Right 40.000 Oldctg 2
Fp_number "09F12"
Gel_number    100942
Bands  84962 31
Approximate_match_to_cosmid "a0070F12"
Creation_date 99 11 12 9 2 
Modified_date 101 4 11 16 57 
  
Clone : "a0009K24"
Map "ctg1" Ends Left 297.000
Map "ctg1" Ends Right 320.000 Oldctg 2
Fp_number "09K24"
Gel_number    100923
Bands  88864 24
Positive_STS "OJ990503_27" 
Positive_STS "OJ991021_17" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0010G19"
Map "ctg1" Ends Left 0.000
Map "ctg1" Ends Right 32.000 Oldctg 2
Fp_number "10G19"
Gel_number    101012
Bands  96669 33
Shotgun Full_X SHOTGUN
Positive_STS "OJ990915_01" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0010H08"
Map "ctg1" Ends Left 245.000
Map "ctg1" Ends Right 273.000 Oldctg 2
Fp_number "10H08"
Gel_number    101042
Bands  97048 29
Positive_STS "OJ000317_34" 
Positive_STS "OJ990325_01" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0010M06"
Map "ctg1" Ends Left 568.000
Map "ctg1" Ends Right 600.000 Oldctg 2
Fp_number "10M06"
Gel_number    101024
Bands  100422 33
Positive_STS "C953" 
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0010N22"
Map "ctg1" Ends Left 106.000
Map "ctg1" Ends Right 141.000 Oldctg 2
Fp_number "10N22"
Gel_number    101044
Bands  101569 36
Approximate_match_to_cosmid "a0038D13"
Creation_date 99 11 12 9 2 
Modified_date 101 4 11 16 57 
  
Clone : "a0011A23"
Map "ctg1" Ends Left 163.000
Map "ctg1" Ends Right 198.000 Oldctg 2
Fp_number "11A23"
Gel_number    101111
Bands  103591 36
Creation_date 99 11 12 9 2 
Modified_date 99 11 12 14 45 
  
Clone : "a0011L22"
Map "ctg1" Ends Left 156.000
Map "ctg1" Ends Right 190.000 Oldctg 2
Fp_number "11L22"
Gel_number    101143
Bands  110824 35
Positive_STS "G107" 
Positive_STS "OJ000301_13" 
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0011M14"
Map "ctg1" Ends Left 152.000
Map "ctg1" Ends Right 178.000 Oldctg 2
Fp_number "11M14"
Gel_number    101124
Bands  111251 27
Approximate_match_to_cosmid "a0011L22"
Positive_STS "OJ000301_13" 
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0012B02"
Map "ctg1" Ends Left 42.000
Map "ctg1" Ends Right 79.000 Oldctg 2
Fp_number "12B02"
Gel_number    101241
Bands  113921 38
Creation_date 99 11 12 9 2 
Modified_date 99 11 12 14 28 
  
Clone : "a0012O15"
Map "ctg1" Ends Left 209.000
Map "ctg1" Ends Right 235.000 Oldctg 2
Fp_number "12O15"
Gel_number    101214
Bands  122792 27
Approximate_match_to_cosmid "a0002N24"
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Positive_OVERGO "SOG1774" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0013N10"
Map "ctg1" Ends Left 115.000
Map "ctg1" Ends Right 144.000 Oldctg 2
Fp_number "13N10"
Gel_number    101344
Bands  131584 30
Exact_match_to_cosmid "a0038D13"
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0013P03"
Map "ctg1" Ends Left 217.000
Map "ctg1" Ends Right 244.000 Oldctg 2
Fp_number "13P03"
Gel_number    101334
Bands  132571 28
Approximate_match_to_cosmid "a0022E11"
Positive_STS "OJ000207_10" 
Positive_STS "OJ990325_01" 
Positive_OVERGO "SOG1774" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0014I02"
Map "ctg1" Ends Left 493.000
Map "ctg1" Ends Right 515.000 Oldctg 2
Fp_number "14I02"
Gel_number    101423
Bands  137990 23
Positive_STS "OJ000310_29" 
Positive_STS "OJ990820_14" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0014N06"
Map "ctg1" Ends Left 122.000
Map "ctg1" Ends Right 148.000 Oldctg 2
Fp_number "14N06"
Gel_number    101444
Bands  141136 27
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0015D20"
Map "ctg1" Ends Left 5.000
Map "ctg1" Ends Right 35.000 Oldctg 2
Fp_number "15D20"
Gel_number    101541
Bands  144994 31
Positive_STS "OJ990915_01" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0015J18"
Map "ctg1" Ends Left 3.000
Map "ctg1" Ends Right 33.000 Oldctg 2
Fp_number "15J18"
Gel_number    101543
Bands  148482 31
Approximate_match_to_cosmid "a0015D20"
Positive_STS "OJ990915_01" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0015K07"
Map "ctg1" Ends Left 335.000
Map "ctg1" Ends Right 368.000 Oldctg 2
Fp_number "15K07"
Gel_number    101513
Bands  148811 34
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0015N05"
Map "ctg1" Ends Left 8.000
Map "ctg1" Ends Right 35.000 Oldctg 2
Fp_number "15N05"
Gel_number    101534
Bands  150464 28
Approximate_match_to_cosmid "a0020E12"
Positive_STS "OJ990915_01" 
Positive_OVERGO "SOG1204" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0016B10"
Map "ctg1" Ends Left 396.000
Map "ctg1" Ends Right 430.000 Oldctg 2
Fp_number "16B10"
Gel_number    101641
Bands  153073 35
Positive_STS "OJ000214_10" 
Positive_STS "OJ000214_13" 
Positive_OVERGO "SOG0223" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0016J14"
Map "ctg1" Ends Left 546.000
Map "ctg1" Ends Right 571.000 Oldctg 2
Fp_number "16J14"
Gel_number    101643
Bands  158373 26
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0017B08"
Map "ctg1" Ends Left 227.000
Map "ctg1" Ends Right 240.000 Oldctg 2
Fp_number "17B08"
Gel_number    101741
Bands  163070 14
Exact_match_to_cosmid "a0004I02"
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0017C04"
Map "ctg1" Ends Left 486.000
Map "ctg1" Ends Right 506.000 Oldctg 2
Fp_number "17C04"
Gel_number    101721
Bands  163629 21
Approximate_match_to_cosmid "a0096O08"
Positive_OVERGO "SOG1745" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0017J17"
Map "ctg1" Ends Left 116.000
Map "ctg1" Ends Right 145.000 Oldctg 2
Fp_number "17J17"
Gel_number    101733
Bands  168664 30
Approximate_match_to_cosmid "a0038D13"
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Positive_OVERGO "SOG0980" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0017K20"
Map "ctg1" Ends Left 502.000
Map "ctg1" Ends Right 531.000 Oldctg 2
Fp_number "17K20"
Gel_number    101723
Bands  169460 30
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0018B18"
Map "ctg1" Ends Left 107.000
Map "ctg1" Ends Right 145.000 Oldctg 2
Fp_number "18B18"
Gel_number    101841
Bands  174269 39
Creation_date 99 11 12 9 2 
Modified_date 99 11 12 14 28 
  
Clone : "a0018B22"
Map "ctg1" Ends Left 99.000
Map "ctg1" Ends Right 143.000 Oldctg 2
Fp_number "18B22"
Gel_number    101841
Bands  174398 45
Positive_STS "OJ990412_10" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0018K01"
Map "ctg1" Ends Left 452.000
Map "ctg1" Ends Right 474.000 Oldctg 2
Fp_number "18K01"
Gel_number    101813
Bands  180202 23
Approximate_match_to_cosmid "a0005L07"
Positive_STS "OJ000214_13" 
Positive_STS "OJ000310_29" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ990923_08" 
Positive_STS "OJ991210_12" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Positive_Probe "CSU469" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0019D09"
Map "ctg1" Ends Left 230.000
Map "ctg1" Ends Right 261.000 Oldctg 2
Fp_number "19D09"
Gel_number    101931
Bands  186844 32
Positive_STS "OJ000207_10" 
Positive_STS "OJ990325_01" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0019K24"
Map "ctg1" Ends Left 492.000
Map "ctg1" Ends Right 512.000 Oldctg 2
Fp_number "19K24"
Gel_number    101923
Bands  192161 21
Creation_date 99 11 12 9 2 
Modified_date 101 4 11 16 57 
  
Clone : "a0019N07"
Map "ctg1" Ends Left 337.000
Map "ctg1" Ends Right 368.000 Oldctg 2
Fp_number "19N07"
Gel_number    101934
Bands  193716 32
Approximate_match_to_cosmid "a0015K07"
Creation_date 99 11 12 9 2 
Modified_date 101 4 11 16 57 
  
Clone : "a0020E12"
Map "ctg1" Ends Left 6.000
Map "ctg1" Ends Right 36.000 Oldctg 2
Fp_number "20E12"
Gel_number    102022
Bands  198227 31
Positive_STS "OJ990915_01" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0020G09"
Map "ctg1" Ends Left 523.000
Map "ctg1" Ends Right 548.000 Oldctg 2
Fp_number "20G09"
Gel_number    102012
Bands  199480 26
Exact_match_to_cosmid "a0003C15"
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0021G13"
Map "ctg1" Ends Left 492.000
Map "ctg1" Ends Right 510.000 Oldctg 2
Fp_number "21G13"
Gel_number    102112
Bands  210084 19
Approximate_match_to_cosmid "a0019K24"
Creation_date 99 11 12 9 2 
Modified_date 101 4 11 16 57 
  
Clone : "a0021N13"
Map "ctg1" Ends Left 152.000
Map "ctg1" Ends Right 184.000 Oldctg 2
Fp_number "21N13"
Gel_number    102134
Bands  214583 33
Positive_STS "OJ000301_13" 
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0021O04"
Map "ctg1" Ends Left 315.000
Map "ctg1" Ends Right 343.000 Oldctg 2
Fp_number "21O04"
Gel_number    102124
Bands  214946 29
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0022E11"
Map "ctg1" Ends Left 209.000
Map "ctg1" Ends Right 245.000 Oldctg 2
Fp_number "22E11"
Gel_number    102212
Bands  219203 37
Positive_OVERGO "SOG1774" 
Positive_OVERGO "SOG1816" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0023C14"
Map "ctg1" Ends Left 394.000
Map "ctg1" Ends Right 422.000 Oldctg 2
Fp_number "23C14"
Gel_number    102321
Bands  228846 29
Positive_STS "OJ000214_10" 
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Positive_OVERGO "SOG0223" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0023I04"
Map "ctg1" Ends Left 14.000
Map "ctg1" Ends Right 44.000 Oldctg 2
Fp_number "23I04"
Gel_number    102323
Bands  232493 31
Creation_date 99 11 12 9 2 
Modified_date 101 4 11 16 55 
  
Clone : "a0023L13"
Map "ctg1" Ends Left 80.000
Map "ctg1" Ends Right 93.000 Oldctg 2
Fp_number "23L13"
Gel_number    102333
Bands  234671 14
Creation_date 99 11 12 9 2 
Modified_date 99 11 12 14 28 
  
Clone : "a0023L15"
Map "ctg1" Ends Left 320.000
Map "ctg1" Ends Right 355.000 Oldctg 2
Fp_number "23L15"
Gel_number    102333
Bands  234718 36
Creation_date 99 11 12 9 2 
Modified_date 101 4 11 16 57 
  
Clone : "a0023M15"
Map "ctg1" Ends Left 250.000
Map "ctg1" Ends Right 275.000 Oldctg 2
Fp_number "23M15"
Gel_number    102314
Bands  235396 26
Positive_STS "OJ000317_34" 
Positive_OVERGO "SOG1450" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0024D10"
Map "ctg1" Ends Left 348.000
Map "ctg1" Ends Right 384.000 Oldctg 2
Fp_number "24D10"
Gel_number    102441
Bands  239966 37
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 9 2 
Modified_date 102 2 1 22 47 
  
Clone : "a0024D14"
Map "ctg1" Ends Left 45.000
Map "ctg1" Ends Right 80.000 Oldctg 2
Fp_number "24D14"
Gel_number    102441
Bands  240080 36
Positive_STS "42D18r" 
Positive_OVERGO "SOG1344" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0024L22"
Map "ctg1" Ends Left 474.000
Map "ctg1" Ends Right 495.000 Oldctg 2
Fp_number "24L22"
Gel_number    102443
Bands  245679 22
Approximate_match_to_cosmid "a0040L18"
Positive_STS "OJ000310_29" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991210_12" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0024M12"
Map "ctg1" Ends Left 3.000
Map "ctg1" Ends Right 33.000 Oldctg 2
Fp_number "24M12"
Gel_number    102424
Bands  246050 31
Approximate_match_to_cosmid "a0010G19"
Positive_STS "OJ990915_01" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0025A11"
Map "ctg1" Ends Left 208.000
Map "ctg1" Ends Right 240.000 Oldctg 2
Fp_number "25A11"
Gel_number    102511
Bands  248526 33
Positive_OVERGO "SOG1774" 
Positive_OVERGO "SOG1816" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0025B18"
Map "ctg1" Ends Left 265.000
Map "ctg1" Ends Right 279.000 Oldctg 2
Fp_number "25B18"
Gel_number    102541
Bands  249366 15
Exact_match_to_cosmid "a0003I09"
Positive_STS "OJ000317_34" 
Positive_OVERGO "SOG1450" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0025E13"
Map "ctg1" Ends Left 389.000
Map "ctg1" Ends Right 425.000 Oldctg 2
Fp_number "25E13"
Gel_number    102512
Bands  251114 37
Positive_STS "OJ000214_10" 
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Positive_OVERGO "SOG0223" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0025O08"
Map "ctg1" Ends Left 614.000
Map "ctg1" Ends Right 643.000 Oldctg 2
Fp_number "25O08"
Gel_number    102524
Bands  257565 30
Positive_STS "chlor" 
Creation_date 99 11 12 9 2 
Modified_date 101 5 9 11 19 
  
Clone : "a0025O10"
Map "ctg1" Ends Left 69.000
Map "ctg1" Ends Right 102.000 Oldctg 2
Fp_number "25O10"
Gel_number    102524
Bands  257625 34
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Positive_OVERGO "SOG1344" 
Creation_date 99 11 12 9 2 
Modified_date 103 4 22 10 21 
  
Clone : "a0026E03"
Map "ctg1" Ends Left 137.000
Map "ctg1" Ends Right 160.000 Oldctg 2
Fp_number "26E03"
Gel_number    102612
Bands  261382 24
Approximate_match_to_cosmid "a0032C10"
Positive_STS "PIB1" 
Creation_date 99 11 12 9 3 
Modified_date 101 5 9 11 19 
  
Clone : "a0026N04"
Map "ctg1" Ends Left 394.000
Map "ctg1" Ends Right 425.000 Oldctg 2
Fp_number "26N04"
Gel_number    102644
Bands  267367 31
Pseudo_match_to_cosmid "a0023C14"
Positive_OVERGO "SOG0223" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0026P24"
Map "ctg1" Ends Left 213.000
Map "ctg1" Ends Right 240.000 Oldctg 2
Fp_number "26P24"
Gel_number    102644
Bands  269209 28
Approximate_match_to_cosmid "a0022E11"
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 57 
  
Clone : "a0027M09"
Map "ctg1" Ends Left 396.000
Map "ctg1" Ends Right 431.000 Oldctg 2
Fp_number "27M09"
Gel_number    102714
Bands  277492 36
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Positive_OVERGO "SOG0223" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0028A11"
Map "ctg1" Ends Left 569.000
Map "ctg1" Ends Right 598.000 Oldctg 2
Fp_number "28A11"
Gel_number    102811
Bands  280452 30
Positive_STS "OJ000251_05" 
Positive_STS "OJ000303_09" 
Positive_STS "OJ000303_17" 
Positive_STS "OJ000321_15" 
Positive_STS "OJ000330_31" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0028D16"
Map "ctg1" Ends Left 389.000
Map "ctg1" Ends Right 427.000 Oldctg 2
Fp_number "28D16"
Gel_number    102841
Bands  282500 39
Positive_STS "OJ000214_10" 
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Positive_OVERGO "SOG0223" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0028F17"
Map "ctg1" Ends Left 484.000
Map "ctg1" Ends Right 501.000 Oldctg 2
Fp_number "28F17"
Gel_number    102832
Bands  283734 18
Exact_match_to_cosmid "a0006N03"
Positive_STS "OJ990820_14" 
Positive_STS "OJ990923_08" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0028G23"
Map "ctg1" Ends Left 486.000
Map "ctg1" Ends Right 505.000 Oldctg 2
Fp_number "28G23"
Gel_number    102812
Bands  284513 20
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 56 
  
Clone : "a0029L17"
Map "ctg1" Ends Left 553.000
Map "ctg1" Ends Right 586.000 Oldctg 2
Fp_number "29L17"
Gel_number    102933
Bands  297482 34
Approximate_match_to_cosmid "a0053D17"
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Positive_STS "OJ000303_09" 
Positive_STS "OJ000303_17" 
Positive_OVERGO "SOG0313" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0030A14"
Map "ctg1" Ends Left 186.000
Map "ctg1" Ends Right 216.000 Oldctg 2
Fp_number "30A14"
Gel_number    103021
Bands  300707 31
Approximate_match_to_cosmid "a0040B22"
Positive_STS "OJ000207_10" 
Positive_STS "OJ000301_13" 
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0030P03"
Map "ctg1" Ends Left 3.000
Map "ctg1" Ends Right 32.000 Oldctg 2
Fp_number "30P03"
Gel_number    103034
Bands  309539 30
Positive_STS "10E20fA" 
Creation_date 99 11 12 9 3 
Modified_date 101 5 9 11 19 
  
Clone : "a0032A01"
Map "ctg1" Ends Left 49.000
Map "ctg1" Ends Right 78.000 Oldctg 2
Fp_number "32A01"
Gel_number    103211
Bands  320804 30
Exact_match_to_cosmid "a0001M01"
Positive_STS "OJ990412_10" 
Positive_STS "OJ990605_38" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0032C02"
Map "ctg1" Ends Left 29.000
Map "ctg1" Ends Right 70.000 Oldctg 2
Fp_number "32C02"
Gel_number    103221
Bands  322181 42
Creation_date 99 11 12 9 3 
Modified_date 101 1 5 17 55 
  
Clone : "a0032C10"
Map "ctg1" Ends Left 126.000
Map "ctg1" Ends Right 161.000 Oldctg 2
Fp_number "32C10"
Gel_number    103221
Bands  322444 36
Positive_STS "PIB1" 
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0032J18"
Map "ctg1" Ends Left 348.000
Map "ctg1" Ends Right 384.000 Oldctg 2
Fp_number "32J18"
Gel_number    103243
Bands  327168 37
Positive_STS "OJ000221_13" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0033A10"
Map "ctg1" Ends Left 88.000
Map "ctg1" Ends Right 118.000 Oldctg 2
Fp_number "33A10"
Gel_number    103321
Bands  331591 31
Positive_STS "OJ990412_10" 
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0033H13"
Map "ctg1" Ends Left 485.000
Map "ctg1" Ends Right 506.000 Oldctg 2
Fp_number "33H13"
Gel_number    103332
Bands  335911 22
Exact_match_to_cosmid "a0001G11"
Positive_STS "10E20fA" 
Creation_date 99 11 12 9 3 
Modified_date 101 5 9 11 19 
  
Clone : "a0034C08"
Map "ctg1" Ends Left 355.000
Map "ctg1" Ends Right 392.000 Oldctg 2
Fp_number "34C08"
Gel_number    103421
Bands  342512 38
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0034D15"
Map "ctg1" Ends Left 588.000
Map "ctg1" Ends Right 602.000 Oldctg 2
Fp_number "34D15"
Gel_number    103431
Bands  343338 15
Exact_match_to_cosmid "a0091B10"
Positive_STS "OJ000251_05" 
Positive_STS "OJ000321_15" 
Positive_STS "OJ000330_31" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0034I17"
Map "ctg1" Ends Left 317.000
Map "ctg1" Ends Right 339.000 Oldctg 2
Fp_number "34I17"
Gel_number    103413
Bands  346746 23
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 56 
  
Clone : "a0034N02"
Map "ctg1" Ends Left 40.000
Map "ctg1" Ends Right 81.000 Oldctg 2
Fp_number "34N02"
Gel_number    103444
Bands  349688 42
Creation_date 99 11 12 9 3 
Modified_date 99 11 12 14 28 
  
Clone : "a0034P17"
Map "ctg1" Ends Left 483.000
Map "ctg1" Ends Right 504.000 Oldctg 2
Fp_number "34P17"
Gel_number    103434
Bands  351379 22
Approximate_match_to_cosmid "b0001O16"
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 57 
  
Clone : "a0035D22"
Map "ctg1" Ends Left 549.000
Map "ctg1" Ends Right 578.000 Oldctg 2
Fp_number "35D22"
Gel_number    103541
Bands  354048 30
Positive_STS "OJ000251_05" 
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0035O09"
Map "ctg1" Ends Left 597.000
Map "ctg1" Ends Right 635.000 Oldctg 2
Fp_number "35O09"
Gel_number    103514
Bands  361213 39
Positive_STS "OJ000321_15" 
Positive_STS "OJ000330_31" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0036C08"
Map "ctg1" Ends Left 245.000
Map "ctg1" Ends Right 274.000 Oldctg 2
Fp_number "36C08"
Gel_number    103621
Bands  363882 30
Approximate_match_to_cosmid "a0083M16"
Positive_STS "OJ000317_34" 
Positive_STS "OJ990325_01" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0036K03"
Map "ctg1" Ends Left 131.000
Map "ctg1" Ends Right 153.000 Oldctg 2
Fp_number "36K03"
Gel_number    103613
Bands  368992 23
Approximate_match_to_cosmid "a0032C10"
Positive_OVERGO "SOG0961" 
Positive_OVERGO "SOG1225" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0037C05"
Map "ctg1" Ends Left 220.000
Map "ctg1" Ends Right 250.000 Oldctg 2
Fp_number "37C05"
Gel_number    103711
Bands  374413 31
Positive_OVERGO "SOG1774" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0037G06"
Map "ctg1" Ends Left 594.000
Map "ctg1" Ends Right 625.000 Oldctg 2
Fp_number "37G06"
Gel_number    103722
Bands  376973 32
Approximate_match_to_cosmid "a0091H17"
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 57 
  
Clone : "a0037I23"
Map "ctg1" Ends Left 578.000
Map "ctg1" Ends Right 614.000 Oldctg 2
Fp_number "37I23"
Gel_number    103713
Bands  378650 37
Positive_OVERGO "SOG0279" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0038D13"
Map "ctg1" Ends Left 106.000
Map "ctg1" Ends Right 147.000 Oldctg 2
Fp_number "38D13"
Gel_number    103831
Bands  385536 42
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0038H05"
Map "ctg1" Ends Left 493.000
Map "ctg1" Ends Right 511.000 Oldctg 2
Fp_number "38H05"
Gel_number    103832
Bands  387956 19
Exact_match_to_cosmid "a0019K24"
Positive_STS "OJ000310_29" 
Positive_STS "OJ990820_14" 
Positive_STS "OJ990923_08" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0038P04"
Map "ctg1" Ends Left 123.000
Map "ctg1" Ends Right 151.000 Oldctg 2
Fp_number "38P04"
Gel_number    103844
Bands  393147 29
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0039B13"
Map "ctg1" Ends Left 136.000
Map "ctg1" Ends Right 163.000 Oldctg 2
Fp_number "39B13"
Gel_number    103931
Bands  394642 28
Positive_OVERGO "SOG0961" 
Positive_OVERGO "SOG1225" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0039K03"
Map "ctg1" Ends Left 404.000
Map "ctg1" Ends Right 440.000 Oldctg 2
Fp_number "39K03"
Gel_number    103913
Bands  400166 37
Positive_STS "10E20fA" 
Positive_STS "C51175" 
Positive_STS "OJ000214_10" 
Positive_STS "OJ000214_13" 
Positive_OVERGO "SOG0223" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0039N09"
Map "ctg1" Ends Left 592.000
Map "ctg1" Ends Right 614.000 Oldctg 2
Fp_number "39N09"
Gel_number    103934
Bands  402278 23
Pseudo_match_to_cosmid "a0094G11"
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 57 
  
Clone : "a0040B22"
Map "ctg1" Ends Left 178.000
Map "ctg1" Ends Right 221.000 Oldctg 2
Fp_number "40B22"
Gel_number    104041
Bands  405224 44
Positive_STS "OJ000207_10" 
Positive_STS "OJ000301_13" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Positive_STS "OJ990407_02" 
Positive_OVERGO "SOG1774" 
Positive_OVERGO "SOG1790" 
Positive_OVERGO "SOG1816" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0040H03"
Map "ctg1" Ends Left 220.000
Map "ctg1" Ends Right 244.000 Oldctg 2
Fp_number "40H03"
Gel_number    104032
Bands  408862 25
Approximate_match_to_cosmid "a0022E11"
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Positive_OVERGO "SOG1774" 
Positive_OVERGO "SOG1790" 
Positive_OVERGO "SOG1816" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0040J06"
Map "ctg1" Ends Left 415.000
Map "ctg1" Ends Right 447.000 Oldctg 2
Fp_number "40J06"
Gel_number    104043
Bands  410276 33
Positive_OVERGO "SOG0223" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0040L18"
Map "ctg1" Ends Left 470.000
Map "ctg1" Ends Right 498.000 Oldctg 2
Fp_number "40L18"
Gel_number    104043
Bands  412090 29
Positive_STS "OJ000310_29" 
Positive_STS "OJ990820_14" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0041C20"
Map "ctg1" Ends Left 578.000
Map "ctg1" Ends Right 616.000 Oldctg 2
Fp_number "41C20"
Gel_number    104121
Bands  417019 39
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Positive_OVERGO "SOG0279" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0042G06"
Map "ctg1" Ends Left 485.000
Map "ctg1" Ends Right 501.000 Oldctg 2
Fp_number "42G06"
Gel_number    104222
Bands  430096 17
Exact_match_to_cosmid "a0006N03"
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 57 
  
Clone : "a0042K01"
Map "ctg1" Ends Left 163.000
Map "ctg1" Ends Right 180.000 Oldctg 2
Fp_number "42K01"
Gel_number    104213
Bands  432631 18
Exact_match_to_cosmid "a0001J19"
Positive_STS "OJ000301_13" 
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0043C05"
Map "ctg1" Ends Left 115.000
Map "ctg1" Ends Right 145.000 Oldctg 2
Fp_number "43C05"
Gel_number    104311
Bands  438364 31
Approximate_match_to_cosmid "a0038D13"
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0043F13"
Map "ctg1" Ends Left 5.000
Map "ctg1" Ends Right 34.000 Oldctg 2
Fp_number "43F13"
Gel_number    104332
Bands  440357 30
Approximate_match_to_cosmid "a0070F12"
Positive_STS "OJ990915_01" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0043O12"
Map "ctg1" Ends Left 431.000
Map "ctg1" Ends Right 466.000 Oldctg 2
Fp_number "43O12"
Gel_number    104324
Bands  445832 36
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0044D22"
Map "ctg1" Ends Left 394.000
Map "ctg1" Ends Right 425.000 Oldctg 2
Fp_number "44D22"
Gel_number    104441
Bands  449244 32
Positive_STS "OJ000214_10" 
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Positive_OVERGO "SOG0223" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0044F13"
Map "ctg1" Ends Left 40.000
Map "ctg1" Ends Right 77.000 Oldctg 2
Fp_number "44F13"
Gel_number    104432
Bands  450453 38
Positive_STS "42D18r" 
Creation_date 99 11 12 9 3 
Modified_date 101 5 9 11 19 
  
Clone : "a0045F08"
Map "ctg1" Ends Left 483.000
Map "ctg1" Ends Right 506.000 Oldctg 2
Fp_number "45F08"
Gel_number    104542
Bands  461042 24
Positive_STS "OJ990923_08" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0045G04"
Map "ctg1" Ends Left 141.000
Map "ctg1" Ends Right 162.000 Oldctg 2
Fp_number "45G04"
Gel_number    104522
Bands  461583 22
Creation_date 99 11 12 9 3 
Modified_date 99 11 12 14 28 
  
Clone : "a0045M07"
Map "ctg1" Ends Left 227.000
Map "ctg1" Ends Right 250.000 Oldctg 2
Fp_number "45M07"
Gel_number    104514
Bands  465482 24
Exact_match_to_cosmid "a0004I02"
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0045P15"
Map "ctg1" Ends Left 476.000
Map "ctg1" Ends Right 501.000 Oldctg 2
Fp_number "45P15"
Gel_number    104534
Bands  467587 26
Exact_match_to_cosmid "a0006N03"
Positive_STS "OJ000310_29" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991210_12" 
Positive_STS "OJ991215_12" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0046B03"
Map "ctg1" Ends Left 259.000
Map "ctg1" Ends Right 286.000 Oldctg 2
Fp_number "46B03"
Gel_number    104631
Bands  468434 28
Exact_match_to_cosmid "a0048L02"
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 57 
  
Clone : "a0046C18"
Map "ctg1" Ends Left 493.000
Map "ctg1" Ends Right 511.000 Oldctg 2
Fp_number "46C18"
Gel_number    104621
Bands  469569 19
Exact_match_to_cosmid "a0019K24"
Positive_STS "OJ000310_29" 
Positive_STS "OJ990820_14" 
Positive_STS "OJ990923_08" 
Positive_OVERGO "SOG1745" 
Positive_OVERGO "SOG2238" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0046K10"
Map "ctg1" Ends Left 167.000
Map "ctg1" Ends Right 199.000 Oldctg 2
Fp_number "46K10"
Gel_number    104623
Bands  474577 33
Creation_date 99 11 12 9 3 
Modified_date 99 11 12 14 45 
  
Clone : "a0047E16"
Map "ctg1" Ends Left 476.000
Map "ctg1" Ends Right 501.000 Oldctg 2
Fp_number "47E16"
Gel_number    104722
Bands  481492 26
Approximate_match_to_cosmid "a0006N03"
Positive_STS "OJ000310_29" 
Positive_STS "OJ990923_08" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0047M08"
Map "ctg1" Ends Left 299.000
Map "ctg1" Ends Right 328.000 Oldctg 2
Fp_number "47M08"
Gel_number    104724
Bands  486469 30
Positive_STS "OJ990503_27" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 47 
  
Clone : "a0047O06"
Map "ctg1" Ends Left 245.000
Map "ctg1" Ends Right 265.000 Oldctg 2
Fp_number "47O06"
Gel_number    104724
Bands  487629 21
Positive_STS "R753" 
Positive_STS "OJ000317_34" 
Positive_STS "OJ990325_01" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0048K04"
Map "ctg1" Ends Left 34.000
Map "ctg1" Ends Right 71.000 Oldctg 2
Fp_number "48K04"
Gel_number    104823
Bands  495678 38
Positive_STS "42D18r" 
Creation_date 99 11 12 9 3 
Modified_date 101 5 9 11 19 
  
Clone : "a0048L02"
Map "ctg1" Ends Left 258.000
Map "ctg1" Ends Right 294.000 Oldctg 2
Fp_number "48L02"
Gel_number    104843
Bands  496288 37
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0049A12"
Map "ctg1" Ends Left 555.000
Map "ctg1" Ends Right 585.000 Oldctg 2
Fp_number "0049A12"
Gel_number    104921
Bands  499969 31
Approximate_match_to_cosmid "a0053D17"
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Positive_STS "OJ000303_09" 
Positive_STS "OJ000303_17" 
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0049D09"
Map "ctg1" Ends Left 491.000
Map "ctg1" Ends Right 510.000 Oldctg 2
Fp_number "0049D09"
Gel_number    104931
Bands  501959 20
Exact_match_to_cosmid "a0063D20"
Positive_STS "OJ000310_29" 
Positive_STS "OJ990820_14" 
Positive_STS "OJ990923_08" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0049E12"
Map "ctg1" Ends Left 101.000
Map "ctg1" Ends Right 137.000 Oldctg 2
Fp_number "0049E12"
Gel_number    104922
Bands  502745 37
Approximate_match_to_cosmid "b0091A24"
Positive_STS "OJ990412_10" 
Creation_date 99 11 12 9 3 
Modified_date 104 4 9 18 13 
  
Clone : "a0049F06"
Map "ctg1" Ends Left 104.000
Map "ctg1" Ends Right 143.000 Oldctg 2
Fp_number "0049F06"
Gel_number    104942
Bands  503272 40
Positive_STS "C1679" 
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0049H15"
Map "ctg1" Ends Left 360.000
Map "ctg1" Ends Right 400.000 Oldctg 2
Fp_number "0049H15"
Gel_number    104932
Bands  504985 41
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0049J04"
Map "ctg1" Ends Left 407.000
Map "ctg1" Ends Right 435.000 Oldctg 2
Fp_number "0049J04"
Gel_number    104943
Bands  506062 29
Approximate_match_to_cosmid "a0050I18"
Positive_STS "C146" 
Positive_STS "OJ000214_10" 
Positive_STS "OJ000214_13" 
Positive_OVERGO "SOG0223" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0049O05"
Map "ctg1" Ends Left 114.000
Map "ctg1" Ends Right 144.000 Oldctg 2
Fp_number "0049O05"
Gel_number    104914
Bands  509510 31
Exact_match_to_cosmid "a0051O20"
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0050I02"
Map "ctg1" Ends Left 42.000
Map "ctg1" Ends Right 81.000 Oldctg 2
Fp_number "0050I02"
Gel_number    105023
Bands  516137 40
Creation_date 99 11 12 9 3 
Modified_date 99 11 12 14 28 
  
Clone : "a0050I18"
Map "ctg1" Ends Left 396.000
Map "ctg1" Ends Right 431.000 Oldctg 2
Fp_number "0050I18"
Gel_number    105023
Bands  516598 36
Positive_STS "OJ000214_10" 
Positive_STS "OJ000214_13" 
Positive_OVERGO "SOG0223" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0050L04"
Map "ctg1" Ends Left 111.000
Map "ctg1" Ends Right 146.000 Oldctg 2
Fp_number "0050L04"
Gel_number    105043
Bands  518213 36
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0051E17"
Map "ctg1" Ends Left 503.000
Map "ctg1" Ends Right 527.000 Oldctg 2
Fp_number "0051E17"
Gel_number    605112
Bands  524104 25
Approximate_match_to_cosmid "b0002J03"
Creation_date 99 11 13 0 58 
Modified_date 101 4 11 16 57 
  
Clone : "a0051F10"
Map "ctg1" Ends Left 486.000
Map "ctg1" Ends Right 501.000 Oldctg 2
Fp_number "0051F10"
Gel_number    105142
Bands  524513 16
Approximate_match_to_cosmid "b0081N07"
Positive_STS "OJ000310_29" 
Positive_STS "OJ990820_14" 
Positive_STS "OJ990923_08" 
Positive_Probe "PRC0214" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0051I19"
Map "ctg1" Ends Left 12.000
Map "ctg1" Ends Right 46.000 Oldctg 2
Fp_number "0051I19"
Gel_number    105113
Bands  526482 35
Exact_match_to_cosmid "a0060C20"
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 57 
  
Clone : "a0051O20"
Map "ctg1" Ends Left 106.000
Map "ctg1" Ends Right 145.000 Oldctg 2
Fp_number "0051O20"
Gel_number    105124
Bands  530100 40
Positive_STS "OJ991015_10" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0052E04"
Map "ctg1" Ends Left 206.000
Map "ctg1" Ends Right 240.000 Oldctg 2
Fp_number "0052E04"
Gel_number    105222
Bands  533610 35
Positive_STS "OJ990325_01" 
Positive_OVERGO "SOG1774" 
Positive_OVERGO "SOG1790" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0052N06"
Map "ctg1" Ends Left 206.000
Map "ctg1" Ends Right 236.000 Oldctg 2
Fp_number "0052N06"
Gel_number    105244
Bands  539950 31
Positive_STS "OJ000207_10" 
Positive_STS "OJ000301_13" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0053B14"
Map "ctg1" Ends Left 57.000
Map "ctg1" Ends Right 91.000 Oldctg 2
Fp_number "0053B14"
Gel_number    105341
Bands  543015 35
Approximate_match_to_cosmid "a0053J14"
Positive_STS "OJ990412_10" 
Positive_STS "OJ990605_38" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0053D17"
Map "ctg1" Ends Left 550.000
Map "ctg1" Ends Right 585.000 Oldctg 2
Fp_number "0053D17"
Gel_number    105331
Bands  544532 36
Positive_STS "OJ000301_05" 
Positive_STS "OJ000303_09" 
Positive_STS "OJ000303_17" 
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0053F20"
Map "ctg1" Ends Left 498.000
Map "ctg1" Ends Right 516.000 Oldctg 2
Fp_number "0053F20"
Gel_number    105342
Bands  546031 19
Approximate_match_to_cosmid "a0067L02"
Positive_STS "OJ990820_14" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0053G14"
Map "ctg1" Ends Left 486.000
Map "ctg1" Ends Right 505.000 Oldctg 2
Fp_number "0053G14"
Gel_number    105322
Bands  546524 20
Exact_match_to_cosmid "a0096O08"
Positive_STS "OJ000310_29" 
Positive_STS "OJ990820_14" 
Positive_STS "OJ990923_08" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0053J14"
Map "ctg1" Ends Left 54.000
Map "ctg1" Ends Right 92.000 Oldctg 2
Fp_number "0053J14"
Gel_number    105343
Bands  548609 39
Positive_STS "OJ990412_10" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0054G21"
Map "ctg1" Ends Left 293.000
Map "ctg1" Ends Right 317.000 Oldctg 2
Fp_number "0054G21"
Gel_number    105412
Bands  557668 25
Positive_STS "OJ990503_27" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0054P14"
Map "ctg1" Ends Left 85.000
Map "ctg1" Ends Right 119.000 Oldctg 2
Fp_number "0054P14"
Gel_number    105444
Bands  563712 35
Approximate_match_to_cosmid "a0082D09"
Positive_STS "OJ990412_10" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0055N23"
Map "ctg1" Ends Left 78.000
Map "ctg1" Ends Right 93.000 Oldctg 2
Fp_number "0055N23"
Gel_number    105534
Bands  574301 16
Exact_match_to_cosmid "a0091K03"
Positive_STS "OJ990412_10" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0056K12"
Map "ctg1" Ends Left 441.000
Map "ctg1" Ends Right 473.000 Oldctg 2
Fp_number "0056K12"
Gel_number    105623
Bands  583074 33
Positive_STS "OJ000214_10" 
Positive_STS "OJ000310_29" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991210_12" 
Positive_STS "OJ991215_12" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0056M10"
Map "ctg1" Ends Left 45.000
Map "ctg1" Ends Right 81.000 Oldctg 2
Fp_number "0056M10"
Gel_number    105624
Bands  584323 37
Positive_STS "OJ990605_38" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0057C14"
Map "ctg1" Ends Left 569.000
Map "ctg1" Ends Right 602.000 Oldctg 2
Fp_number "0057C14"
Gel_number    105721
Bands  588475 34
Approximate_match_to_cosmid "a0074A09"
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Positive_STS "OJ000321_15" 
Positive_STS "OJ000330_31" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0057C18"
Map "ctg1" Ends Left 346.000
Map "ctg1" Ends Right 375.000 Oldctg 2
Fp_number "0057C18"
Gel_number    105721
Bands  588610 30
Approximate_match_to_cosmid "a0089D17"
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 57 
  
Clone : "a0057K18"
Map "ctg1" Ends Left 261.000
Map "ctg1" Ends Right 289.000 Oldctg 2
Fp_number "0057K18"
Gel_number    105723
Bands  594185 29
Approximate_match_to_cosmid "a0085N03"
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 57 
  
Clone : "a0057M22"
Map "ctg1" Ends Left 408.000
Map "ctg1" Ends Right 440.000 Oldctg 2
Fp_number "0057M22"
Gel_number    105724
Bands  595649 33
Approximate_match_to_cosmid "a0087L03"
Positive_STS "OJ000214_10" 
Positive_STS "OJ000214_13" 
Positive_OVERGO "SOG0223" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0058C01"
Map "ctg1" Ends Left 308.000
Map "ctg1" Ends Right 336.000 Oldctg 2
Fp_number "0058C01"
Gel_number    105811
Bands  599096 29
Positive_STS "OJ990503_27" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0059H02"
Map "ctg1" Ends Left 402.000
Map "ctg1" Ends Right 435.000 Oldctg 2
Fp_number "0059H02"
Gel_number    105942
Bands  613169 34
Approximate_match_to_cosmid "a0050I18"
Positive_STS "C146" 
Positive_STS "OJ000214_10" 
Positive_STS "OJ000214_13" 
Positive_STS "OJ000350_20" 
Positive_OVERGO "SOG1200" 
Positive_Probe "CSU455" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0060C20"
Map "ctg1" Ends Left 11.000
Map "ctg1" Ends Right 49.000 Oldctg 2
Fp_number "0060C20"
Gel_number    106021
Bands  620760 39
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 57 
  
Clone : "a0060H05"
Map "ctg1" Ends Left 315.000
Map "ctg1" Ends Right 344.000 Oldctg 2
Fp_number "0060H05"
Gel_number    106032
Bands  623976 30
Positive_STS "OJ991021_17" 
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0061B08"
Map "ctg1" Ends Left 494.000
Map "ctg1" Ends Right 515.000 Oldctg 2
Fp_number "0061B08"
Gel_number    106141
Bands  631128 22
Approximate_match_to_cosmid "a0063D20"
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 57 
  
Clone : "a0061C05"
Map "ctg1" Ends Left 154.000
Map "ctg1" Ends Right 196.000 Oldctg 2
Fp_number "0061C05"
Gel_number    106111
Bands  631753 43
Creation_date 99 11 12 9 3 
Modified_date 101 4 27 15 58 
  
Clone : "a0061G09"
Map "ctg1" Ends Left 326.000
Map "ctg1" Ends Right 361.000 Oldctg 2
Fp_number "0061G09"
Gel_number    106112
Bands  634431 36
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0061L15"
Map "ctg1" Ends Left 415.000
Map "ctg1" Ends Right 452.000 Oldctg 2
Fp_number "0061L15"
Gel_number    106133
Bands  637716 38
Positive_STS "C30" 
Positive_STS "C146" 
Positive_OVERGO "SOG0223" 
Positive_OVERGO "SOG1200" 
Positive_OVERGO "SOG1508" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0061M11"
Map "ctg1" Ends Left 133.000
Map "ctg1" Ends Right 158.000 Oldctg 2
Fp_number "0061M11"
Gel_number    106114
Bands  638266 26
Approximate_match_to_cosmid "a0079E17"
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 57 
  
Clone : "a0062B16"
Map "ctg1" Ends Left 103.000
Map "ctg1" Ends Right 127.000 Oldctg 2
Fp_number "0062B16"
Gel_number    106241
Bands  641789 25
Exact_match_to_cosmid "a0079O15"
Positive_STS "OJ990412_10" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0062P11"
Map "ctg1" Ends Left 463.000
Map "ctg1" Ends Right 494.000 Oldctg 2
Fp_number "0062P11"
Gel_number    106234
Bands  650251 32
Positive_STS "OJ000310_29" 
Positive_STS "OJ990820_14" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 9 3 
Modified_date 103 4 22 10 21 
  
Clone : "a0063A17"
Map "ctg1" Ends Left 557.000
Map "ctg1" Ends Right 594.000 Oldctg 2
Fp_number "0063A17"
Gel_number    106311
Bands  650862 38
Positive_STS "OJ000301_05" 
Positive_STS "OJ000303_09" 
Positive_STS "OJ000303_17" 
Positive_STS "OJ000321_15" 
Positive_STS "OJ000330_31" 
Creation_date 99 11 12 9 3 
Modified_date 102 2 1 22 48 
  
Clone : "a0063D17"
Map "ctg1" Ends Left 151.000
Map "ctg1" Ends Right 179.000 Oldctg 2
Fp_number "0063D17"
Gel_number    106331
Bands  652674 29
Positive_STS "OJ000301_13" 
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0063D20"
Map "ctg1" Ends Left 491.000
Map "ctg1" Ends Right 513.000 Oldctg 2
Fp_number "0063D20"
Gel_number    106341
Bands  652754 23
Positive_STS "OJ000310_29" 
Positive_STS "OJ990820_14" 
Positive_STS "OJ990923_08" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0063H14"
Map "ctg1" Ends Left 535.000
Map "ctg1" Ends Right 573.000 Oldctg 2
Fp_number "0063H14"
Gel_number    106342
Bands  655000 39
Creation_date 99 11 12 9 4 
Modified_date 101 4 11 16 57 
  
Clone : "a0063J07"
Map "ctg1" Ends Left 324.000
Map "ctg1" Ends Right 361.000 Oldctg 2
Fp_number "0063J07"
Gel_number    106333
Bands  655927 38
Positive_STS "S13984" 
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0063N13"
Map "ctg1" Ends Left 68.000
Map "ctg1" Ends Right 96.000 Oldctg 2
Fp_number "0063N13"
Gel_number    106334
Bands  658483 29
Exact_match_to_cosmid "a0082H14"
Positive_STS "OJ990412_10" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0064C11"
Map "ctg1" Ends Left 330.000
Map "ctg1" Ends Right 362.000 Oldctg 2
Fp_number "0064C11"
Gel_number    106411
Bands  661396 33
Approximate_match_to_cosmid "a0063J07"
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0064D11"
Map "ctg1" Ends Left 184.000
Map "ctg1" Ends Right 221.000 Oldctg 2
Fp_number "0064D11"
Gel_number    106431
Bands  661929 38
Approximate_match_to_cosmid "b0074P13"
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Positive_OVERGO "SOG1774" 
Positive_OVERGO "SOG1790" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0064G05"
Map "ctg1" Ends Left 491.000
Map "ctg1" Ends Right 510.000 Oldctg 2
Fp_number "0064G05"
Gel_number    106412
Bands  663578 20
Exact_match_to_cosmid "a0063D20"
Positive_STS "OJ000310_29" 
Positive_STS "OJ990820_14" 
Positive_STS "OJ990923_08" 
Positive_OVERGO "SOG1745" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0064N11"
Map "ctg1" Ends Left 465.000
Map "ctg1" Ends Right 491.000 Oldctg 2
Fp_number "0064N11"
Gel_number    106434
Bands  668130 27
Approximate_match_to_cosmid "a0062P11"
Positive_STS "OJ000214_13" 
Positive_STS "OJ000310_29" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ990820_14" 
Positive_STS "OJ990923_08" 
Positive_STS "OJ991210_12" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0065C23"
Map "ctg1" Ends Left 425.000
Map "ctg1" Ends Right 463.000 Oldctg 2
Fp_number "0065C23"
Gel_number    106511
Bands  671263 39
Positive_STS "OJ000214_10" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1855" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0065H04"
Map "ctg1" Ends Left 485.000
Map "ctg1" Ends Right 507.000 Oldctg 2
Fp_number "0065H04"
Gel_number    106542
Bands  673361 23
Approximate_match_to_cosmid "a0096O08"
Positive_STS "OJ000310_29" 
Positive_STS "OJ990820_14" 
Positive_STS "OJ990923_08" 
Positive_OVERGO "SOG1745" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0065J18"
Map "ctg1" Ends Left 70.000
Map "ctg1" Ends Right 104.000 Oldctg 2
Fp_number "0065J18"
Gel_number    106543
Bands  674896 35
Positive_STS "G1082x" 
Creation_date 99 11 12 9 4 
Modified_date 101 5 4 8 42 
  
Clone : "a0065K05"
Map "ctg1" Ends Left 296.000
Map "ctg1" Ends Right 319.000 Oldctg 2
Fp_number "0065K05"
Gel_number    106513
Bands  675155 24
Approximate_match_to_cosmid "b0062F24"
Positive_STS "OJ990503_27" 
Positive_Probe "AEST036" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0065M09"
Map "ctg1" Ends Left 175.000
Map "ctg1" Ends Right 215.000 Oldctg 2
Fp_number "0065M09"
Gel_number    106514
Bands  676344 41
Positive_STS "OJ000207_10" 
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0066I06"
Map "ctg1" Ends Left 114.000
Map "ctg1" Ends Right 149.000 Oldctg 2
Fp_number "0066I06"
Gel_number    106623
Bands  683312 36
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0067C11"
Map "ctg1" Ends Left 15.000
Map "ctg1" Ends Right 46.000 Oldctg 2
Fp_number "0067C11"
Gel_number    106711
Bands  689496 32
Approximate_match_to_cosmid "a0060C20"
Creation_date 99 11 12 9 4 
Modified_date 101 4 11 16 57 
  
Clone : "a0067J18"
Map "ctg1" Ends Left 521.000
Map "ctg1" Ends Right 553.000 Oldctg 2
Fp_number "0067J18"
Gel_number    106743
Bands  693669 33
Positive_STS "OJ000301_05" 
Positive_STS "OJ000303_09" 
Positive_STS "OJ000303_17" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0067L02"
Map "ctg1" Ends Left 494.000
Map "ctg1" Ends Right 515.000 Oldctg 2
Fp_number "0067L02"
Gel_number    106743
Bands  694511 22
Positive_STS "OJ990820_14" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0068E14"
Map "ctg1" Ends Left 341.000
Map "ctg1" Ends Right 369.000 Oldctg 2
Fp_number "0068E14"
Gel_number    106822
Bands  699734 29
Approximate_match_to_cosmid "a0089D17"
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0068F21"
Map "ctg1" Ends Left 239.000
Map "ctg1" Ends Right 271.000 Oldctg 2
Fp_number "0068F21"
Gel_number    106832
Bands  700580 33
Positive_STS "OJ990325_01" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0068G16"
Map "ctg1" Ends Left 553.000
Map "ctg1" Ends Right 581.000 Oldctg 2
Fp_number "0068G16"
Gel_number    106822
Bands  701067 29
Approximate_match_to_cosmid "a0053D17"
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Positive_STS "OJ000303_09" 
Positive_STS "OJ000303_17" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0069J07"
Map "ctg1" Ends Left 325.000
Map "ctg1" Ends Right 360.000 Oldctg 2
Fp_number "0069J07"
Gel_number    106933
Bands  711537 36
Approximate_match_to_cosmid "a0063J07"
Creation_date 99 11 12 9 4 
Modified_date 101 4 11 16 57 
  
Clone : "a0069N10"
Map "ctg1" Ends Left 226.000
Map "ctg1" Ends Right 257.000 Oldctg 2
Fp_number "0069N10"
Gel_number    106944
Bands  713838 32
Approximate_match_to_cosmid "a0070K16"
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0070D12"
Map "ctg1" Ends Left 122.000
Map "ctg1" Ends Right 151.000 Oldctg 2
Fp_number "0070D12"
Gel_number    107041
Bands  717387 30
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Positive_OVERGO "SOG0961" 
Positive_OVERGO "SOG1225" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0070F12"
Map "ctg1" Ends Left 7.000
Map "ctg1" Ends Right 43.000 Oldctg 2
Fp_number "0070F12"
Gel_number    107042
Bands  718551 37
Positive_STS "OJ990915_01" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0070K16"
Map "ctg1" Ends Left 226.000
Map "ctg1" Ends Right 257.000 Oldctg 2
Fp_number "0070K16"
Gel_number    107023
Bands  721422 32
Creation_date 99 11 12 9 4 
Modified_date 101 4 11 16 57 
  
Clone : "a0071F13"
Map "ctg1" Ends Left 18.000
Map "ctg1" Ends Right 45.000 Oldctg 2
Fp_number "0071F13"
Gel_number    107132
Bands  727932 28
Exact_match_to_cosmid "a0060C20"
Positive_STS "OJ990915_01" 
Positive_Probe "AEST171" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0071K15"
Map "ctg1" Ends Left 79.000
Map "ctg1" Ends Right 105.000 Oldctg 2
Fp_number "0071K15"
Gel_number    107113
Bands  730964 27
Approximate_match_to_cosmid "a0079P13"
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0071O23"
Map "ctg1" Ends Left 158.000
Map "ctg1" Ends Right 179.000 Oldctg 2
Fp_number "0071O23"
Gel_number    107114
Bands  733623 22
Approximate_match_to_cosmid "a0061C05"
Positive_STS "OJ000301_13" 
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0072A19"
Map "ctg1" Ends Left 250.000
Map "ctg1" Ends Right 278.000 Oldctg 2
Fp_number "0072A19"
Gel_number    107211
Bands  734553 29
Positive_STS "OJ000317_34" 
Positive_STS "OJ990325_01" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0072C01"
Map "ctg1" Ends Left 222.000
Map "ctg1" Ends Right 256.000 Oldctg 2
Fp_number "0072C01"
Gel_number    107211
Bands  735275 35
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0072L19"
Map "ctg1" Ends Left 366.000
Map "ctg1" Ends Right 400.000 Oldctg 2
Fp_number "0072L19"
Gel_number    107233
Bands  741565 35
Exact_match_to_cosmid "a0049H15"
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0072P22"
Map "ctg1" Ends Left 35.000
Map "ctg1" Ends Right 77.000 Oldctg 2
Fp_number "0072P22"
Gel_number    107244
Bands  744042 43
Approximate_match_to_cosmid "b0065P01"
Positive_STS "RG472" 
Creation_date 99 11 12 9 4 
Modified_date 101 5 4 8 42 
  
Clone : "a0073B01"
Map "ctg1" Ends Left 459.000
Map "ctg1" Ends Right 487.000 Oldctg 2
Fp_number "0073B01"
Gel_number    107331
Bands  744756 29
Positive_STS "OJ000214_13" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0073L24"
Map "ctg1" Ends Left 349.000
Map "ctg1" Ends Right 391.000 Oldctg 2
Fp_number "0073L24"
Gel_number    107343
Bands  751893 43
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0074A09"
Map "ctg1" Ends Left 568.000
Map "ctg1" Ends Right 603.000 Oldctg 2
Fp_number "0074A09"
Gel_number    107411
Bands  754480 36
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Positive_OVERGO "SOG0279" 
Positive_OVERGO "SOG0948" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0074B21"
Map "ctg1" Ends Left 294.000
Map "ctg1" Ends Right 320.000 Oldctg 2
Fp_number "0074B21"
Gel_number    107431
Bands  755414 27
Positive_STS "OJ990503_27" 
Positive_OVERGO "SOG0307" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0074N21"
Map "ctg1" Ends Left 579.000
Map "ctg1" Ends Right 614.000 Oldctg 2
Fp_number "0074N21"
Gel_number    107434
Bands  762877 36
Approximate_match_to_cosmid "a0041C20"
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0075E09"
Map "ctg1" Ends Left 329.000
Map "ctg1" Ends Right 361.000 Oldctg 2
Fp_number "0075E09"
Gel_number    107512
Bands  766285 33
Exact_match_to_cosmid "a0061G09"
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0075K10"
Map "ctg1" Ends Left 477.000
Map "ctg1" Ends Right 501.000 Oldctg 2
Fp_number "0075K10"
Gel_number    107523
Bands  770100 25
Approximate_match_to_cosmid "b0001O16"
Positive_STS "OJ000310_29" 
Positive_STS "OJ990820_14" 
Positive_STS "OJ990923_08" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0075L11"
Map "ctg1" Ends Left 293.000
Map "ctg1" Ends Right 317.000 Oldctg 2
Fp_number "0075L11"
Gel_number    107533
Bands  770678 25
Exact_match_to_cosmid "a0054G21"
Positive_STS "OJ990503_27" 
Positive_OVERGO "SOG0307" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0076J03"
Map "ctg1" Ends Left 126.000
Map "ctg1" Ends Right 154.000 Oldctg 2
Fp_number "0076J03"
Gel_number    107633
Bands  778564 29
Approximate_match_to_cosmid "a0079E17"
Positive_OVERGO "SOG0961" 
Positive_OVERGO "SOG1225" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0076O03"
Map "ctg1" Ends Left 501.000
Map "ctg1" Ends Right 526.000 Oldctg 2
Fp_number "0076O03"
Gel_number    107614
Bands  781611 26
Creation_date 99 11 12 9 4 
Modified_date 101 4 11 16 56 
  
Clone : "a0076O24"
Map "ctg1" Ends Left 315.000
Map "ctg1" Ends Right 341.000 Oldctg 2
Fp_number "0076O24"
Gel_number    107624
Bands  782192 27
Approximate_match_to_cosmid "a0060H05"
Creation_date 99 11 12 9 4 
Modified_date 101 4 11 16 57 
  
Clone : "a0077F13"
Map "ctg1" Ends Left 502.000
Map "ctg1" Ends Right 527.000 Oldctg 2
Fp_number "0077F13"
Gel_number    107732
Bands  786257 26
Positive_STS "OJ990820_14" 
Positive_OVERGO "SOG1044" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0077N20"
Map "ctg1" Ends Left 251.000
Map "ctg1" Ends Right 276.000 Oldctg 2
Fp_number "0077N20"
Gel_number    107744
Bands  791340 26
Approximate_match_to_cosmid "a0087A15"
Positive_STS "OJ000317_34" 
Positive_STS "OJ990325_01" 
Positive_OVERGO "SOG1077" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0078C10"
Map "ctg1" Ends Left 447.000
Map "ctg1" Ends Right 477.000 Oldctg 2
Fp_number "0078C10"
Gel_number    107821
Bands  794339 31
Approximate_match_to_cosmid "b0006L19"
Positive_STS "OJ000214_13" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0078G15"
Map "ctg1" Ends Left 569.000
Map "ctg1" Ends Right 590.000 Oldctg 2
Fp_number "0078G15"
Gel_number    107812
Bands  797064 22
Approximate_match_to_cosmid "a0074A09"
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Positive_OVERGO "SOG0313" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0079E17"
Map "ctg1" Ends Left 123.000
Map "ctg1" Ends Right 154.000 Oldctg 2
Fp_number "0079E17"
Gel_number    107912
Bands  805806 32
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Positive_OVERGO "SOG0961" 
Positive_OVERGO "SOG1225" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0079F12"
Map "ctg1" Ends Left 110.000
Map "ctg1" Ends Right 146.000 Oldctg 2
Fp_number "0079F12"
Gel_number    107942
Bands  806343 37
Approximate_match_to_cosmid "a0051O20"
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0079K21"
Map "ctg1" Ends Left 3.000
Map "ctg1" Ends Right 38.000 Oldctg 2
Fp_number "0079K21"
Gel_number    107913
Bands  809646 36
Approximate_match_to_cosmid "a0070F12"
Positive_STS "OJ990915_01" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0079O15"
Map "ctg1" Ends Left 103.000
Map "ctg1" Ends Right 141.000 Oldctg 2
Fp_number "0079O15"
Gel_number    107914
Bands  811657 39
Creation_date 99 11 12 9 4 
Modified_date 101 4 11 16 57 
  
Clone : "a0079P13"
Map "ctg1" Ends Left 80.000
Map "ctg1" Ends Right 112.000 Oldctg 2
Fp_number "0079P13"
Gel_number    107934
Bands  812191 33
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0080B02"
Map "ctg1" Ends Left 13.000
Map "ctg1" Ends Right 46.000 Oldctg 2
Fp_number "0080B02"
Gel_number    108041
Bands  813147 34
Approximate_match_to_cosmid "a0060C20"
Positive_STS "OJ990915_01" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0080B11"
Map "ctg1" Ends Left 11.000
Map "ctg1" Ends Right 45.000 Oldctg 2
Fp_number "0080B11"
Gel_number    108031
Bands  813400 35
Approximate_match_to_cosmid "a0060C20"
Positive_STS "OJ990915_01" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0081A12"
Map "ctg1" Ends Left 133.000
Map "ctg1" Ends Right 148.000 Oldctg 2
Fp_number "0081A12"
Gel_number    108121
Bands  822515 16
Approximate_match_to_cosmid "a0038P04"
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0082D01"
Map "ctg1" Ends Left 108.000
Map "ctg1" Ends Right 144.000 Oldctg 2
Fp_number "0082D01"
Gel_number    108231
Bands  833550 37
Approximate_match_to_cosmid "a0038D13"
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0082D09"
Map "ctg1" Ends Left 85.000
Map "ctg1" Ends Right 122.000 Oldctg 2
Fp_number "0082D09"
Gel_number    108231
Bands  833754 38
Positive_STS "OJ990412_10" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0082H14"
Map "ctg1" Ends Left 63.000
Map "ctg1" Ends Right 97.000 Oldctg 2
Fp_number "0082H14"
Gel_number    108242
Bands  836034 35
Positive_STS "OJ990412_10" 
Positive_OVERGO "SOG1344" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0082K03"
Map "ctg1" Ends Left 227.000
Map "ctg1" Ends Right 256.000 Oldctg 2
Fp_number "0082K03"
Gel_number    108213
Bands  837447 30
Approximate_match_to_cosmid "a0070K16"
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Positive_OVERGO "SOG1177" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0083A16"
Map "ctg1" Ends Left 548.000
Map "ctg1" Ends Right 581.000 Oldctg 2
Fp_number "0083A16"
Gel_number    108321
Bands  840681 34
Positive_STS "OJ000251_05" 
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0083C24"
Map "ctg1" Ends Left 443.000
Map "ctg1" Ends Right 474.000 Oldctg 2
Fp_number "0083C24"
Gel_number    108321
Bands  841901 32
Positive_STS "OJ000214_10" 
Positive_STS "OJ990923_08" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0083K23"
Map "ctg1" Ends Left 344.000
Map "ctg1" Ends Right 377.000 Oldctg 2
Fp_number "0083K23"
Gel_number    108313
Bands  846502 34
Creation_date 99 11 12 9 4 
Modified_date 101 5 9 11 19 
  
Clone : "a0083M05"
Map "ctg1" Ends Left 219.000
Map "ctg1" Ends Right 244.000 Oldctg 2
Fp_number "0083M05"
Gel_number    108314
Bands  847190 26
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Positive_OVERGO "SOG1774" 
Positive_OVERGO "SOG1790" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0083M16"
Map "ctg1" Ends Left 240.000
Map "ctg1" Ends Right 277.000 Oldctg 2
Fp_number "0083M16"
Gel_number    108324
Bands  847407 38
Shotgun Full_X SHOTGUN
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ000317_34" 
Positive_STS "OJ990325_01" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0084E08"
Map "ctg1" Ends Left 256.000
Map "ctg1" Ends Right 289.000 Oldctg 2
Fp_number "0084E08"
Gel_number    108422
Bands  851864 34
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0085A07"
Map "ctg1" Ends Left 495.000
Map "ctg1" Ends Right 520.000 Oldctg 2
Fp_number "0085A07"
Gel_number    108511
Bands  859081 26
Approximate_match_to_cosmid "b0005M11"
Positive_OVERGO "SOG2276" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0085B05"
Map "ctg1" Ends Left 295.000
Map "ctg1" Ends Right 319.000 Oldctg 2
Fp_number "0085B05"
Gel_number    108531
Bands  859629 25
Approximate_match_to_cosmid "b0062F24"
Positive_OVERGO "SOG0307" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0085L10"
Map "ctg1" Ends Left 592.000
Map "ctg1" Ends Right 626.000 Oldctg 2
Fp_number "0085L10"
Gel_number    108543
Bands  865367 35
Approximate_match_to_cosmid "a0091H17"
Positive_STS "OJ000321_15" 
Positive_OVERGO "SOG0948" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0085N03"
Map "ctg1" Ends Left 257.000
Map "ctg1" Ends Right 288.000 Oldctg 2
Fp_number "0085N03"
Gel_number    108534
Bands  866260 32
Creation_date 99 11 12 9 4 
Modified_date 101 5 9 11 19 
  
Clone : "a0085O04"
Map "ctg1" Ends Left 465.000
Map "ctg1" Ends Right 497.000 Oldctg 2
Fp_number "0085O04"
Gel_number    108524
Bands  866752 33
Positive_STS "OJ990428_07" 
Positive_STS "OJ990820_14" 
Positive_STS "OJ991210_12" 
Positive_STS "OJ991215_12" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0086E10"
Map "ctg1" Ends Left 578.000
Map "ctg1" Ends Right 613.000 Oldctg 2
Fp_number "0086E10"
Gel_number    108622
Bands  870151 36
Positive_STS "chlor" 
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Positive_OVERGO "SOG0313" 
Positive_OVERGO "SOG0948" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0086K13"
Map "ctg1" Ends Left 7.000
Map "ctg1" Ends Right 32.000 Oldctg 2
Fp_number "0086K13"
Gel_number    108613
Bands  873705 26
Approximate_match_to_cosmid "a0070F12"
Positive_STS "OJ000323_02" 
Positive_STS "OJ990915_01" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0087A15"
Map "ctg1" Ends Left 245.000
Map "ctg1" Ends Right 274.000 Oldctg 2
Fp_number "0087A15"
Gel_number    108711
Bands  877048 30
Creation_date 99 11 12 9 4 
Modified_date 101 4 11 16 57 
  
Clone : "a0087D14"
Map "ctg1" Ends Left 589.000
Map "ctg1" Ends Right 614.000 Oldctg 2
Fp_number "0087D14"
Gel_number    108741
Bands  878833 26
Approximate_match_to_cosmid "a0041C20"
Positive_STS "OJ000251_05" 
Positive_STS "OJ000321_15" 
Positive_STS "OJ000330_31" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0087L03"
Map "ctg1" Ends Left 405.000
Map "ctg1" Ends Right 445.000 Oldctg 2
Fp_number "0087L03"
Gel_number    108733
Bands  883623 41
Positive_STS "OJ000214_13" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG0223" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0087M11"
Map "ctg1" Ends Left 85.000
Map "ctg1" Ends Right 110.000 Oldctg 2
Fp_number "0087M11"
Gel_number    108714
Bands  884372 26
Approximate_match_to_cosmid "a0079P13"
Positive_STS "G1082x" 
Positive_STS "OJ990412_10" 
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0088C05"
Map "ctg1" Ends Left 108.000
Map "ctg1" Ends Right 143.000 Oldctg 2
Fp_number "0088C05"
Gel_number    108811
Bands  888056 36
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0089D17"
Map "ctg1" Ends Left 340.000
Map "ctg1" Ends Right 375.000 Oldctg 2
Fp_number "0089D17"
Gel_number    108931
Bands  898465 36
Positive_STS "OJ991201_11" 
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0089G07"
Map "ctg1" Ends Left 247.000
Map "ctg1" Ends Right 270.000 Oldctg 2
Fp_number "0089G07"
Gel_number    108912
Bands  899812 24
Approximate_match_to_cosmid "a0083M16"
Positive_STS "OJ000317_34" 
Positive_STS "OJ990325_01" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0089J14"
Map "ctg1" Ends Left 330.000
Map "ctg1" Ends Right 365.000 Oldctg 2
Fp_number "0089J14"
Gel_number    108943
Bands  901768 36
Approximate_match_to_cosmid "a0063J07"
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0089L15"
Map "ctg1" Ends Left 34.000
Map "ctg1" Ends Right 47.000 Oldctg 2
Fp_number "0089L15"
Gel_number    108933
Bands  902817 14
Exact_match_to_cosmid "b0026K13"
Positive_STS "OJ990605_38" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0089N07"
Map "ctg1" Ends Left 327.000
Map "ctg1" Ends Right 360.000 Oldctg 2
Fp_number "0089N07"
Gel_number    108934
Bands  903702 34
Approximate_match_to_cosmid "a0061G09"
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0090A16"
Map "ctg1" Ends Left 291.000
Map "ctg1" Ends Right 313.000 Oldctg 2
Fp_number "0090A16"
Gel_number    109021
Bands  905234 23
Approximate_match_to_cosmid "b0008B04"
Positive_STS "OJ990503_27" 
Positive_STS "OJ991021_17" 
Positive_OVERGO "SOG0307" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0091B10"
Map "ctg1" Ends Left 577.000
Map "ctg1" Ends Right 608.000 Oldctg 2
Fp_number "0091B10"
Gel_number    109141
Bands  914843 32
Positive_STS "OJ000251_05" 
Positive_STS "OJ000321_15" 
Positive_OVERGO "SOG0279" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0091H17"
Map "ctg1" Ends Left 593.000
Map "ctg1" Ends Right 627.000 Oldctg 2
Fp_number "0091H17"
Gel_number    109132
Bands  918695 35
Positive_STS "OJ000321_15" 
Positive_STS "OJ000330_31" 
Positive_OVERGO "SOG0948" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0091J17"
Map "ctg1" Ends Left 330.000
Map "ctg1" Ends Right 361.000 Oldctg 2
Fp_number "0091J17"
Gel_number    109133
Bands  920035 32
Exact_match_to_cosmid "a0093K20"
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 9 4 
Modified_date 103 4 22 10 21 
  
Clone : "a0091K03"
Map "ctg1" Ends Left 64.000
Map "ctg1" Ends Right 97.000 Oldctg 2
Fp_number "0091K03"
Gel_number    109113
Bands  920297 34
Positive_STS "OJ990412_10" 
Creation_date 99 11 12 9 4 
Modified_date 102 2 1 22 48 
  
Clone : "a0092B07"
Map "ctg1" Ends Left 109.000
Map "ctg1" Ends Right 146.000 Oldctg 2
Fp_number "0092B07"
Gel_number    109231
Bands  924800 38
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 5 
Modified_date 103 4 22 10 21 
  
Clone : "a0093C23"
Map "ctg1" Ends Left 473.000
Map "ctg1" Ends Right 497.000 Oldctg 2
Fp_number "0093C23"
Gel_number    109311
Bands  935783 25
Exact_match_to_cosmid "a0085O04"
Positive_STS "OJ000310_29" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ990820_14" 
Positive_STS "OJ991210_12" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 9 5 
Modified_date 103 4 22 10 21 
  
Clone : "a0093K20"
Map "ctg1" Ends Left 329.000
Map "ctg1" Ends Right 365.000 Oldctg 2
Fp_number "0093K20"
Gel_number    109323
Bands  941078 37
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 9 5 
Modified_date 103 4 22 10 21 
  
Clone : "a0093L07"
Map "ctg1" Ends Left 296.000
Map "ctg1" Ends Right 321.000 Oldctg 2
Fp_number "0093L07"
Gel_number    109333
Bands  941412 26
Positive_STS "OJ990503_27" 
Positive_STS "OJ991021_17" 
Positive_OVERGO "SOG0307" 
Creation_date 99 11 12 9 5 
Modified_date 103 4 22 10 21 
  
Clone : "a0093M03"
Map "ctg1" Ends Left 240.000
Map "ctg1" Ends Right 270.000 Oldctg 2
Fp_number "0093M03"
Gel_number    109314
Bands  941852 31
Approximate_match_to_cosmid "a0083M16"
Creation_date 99 11 12 9 5 
Modified_date 101 5 9 11 19 
  
Clone : "a0094G11"
Map "ctg1" Ends Left 582.000
Map "ctg1" Ends Right 620.000 Oldctg 2
Fp_number "0094G11"
Gel_number    109412
Bands  947953 39
Positive_STS "OJ000251_05" 
Positive_STS "OJ000321_15" 
Positive_STS "OJ000330_31" 
Positive_OVERGO "SOG0279" 
Positive_OVERGO "SOG0948" 
Creation_date 99 11 12 9 5 
Modified_date 103 4 22 10 21 
  
Clone : "a0094G23"
Map "ctg1" Ends Left 10.000
Map "ctg1" Ends Right 30.000 Oldctg 2
Fp_number "0094G23"
Gel_number    109412
Bands  948280 21
Approximate_match_to_cosmid "a0060C20"
Positive_STS "OJ990915_01" 
Creation_date 99 11 12 9 5 
Modified_date 102 2 1 22 48 
  
Clone : "a0094M18"
Map "ctg1" Ends Left 437.000
Map "ctg1" Ends Right 469.000 Oldctg 2
Fp_number "0094M18"
Gel_number    109424
Bands  951995 33
Positive_STS "OJ000214_10" 
Positive_STS "OJ000214_13" 
Positive_STS "OJ000310_29" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991210_12" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 9 5 
Modified_date 103 4 22 10 21 
  
Clone : "a0094O11"
Map "ctg1" Ends Left 147.000
Map "ctg1" Ends Right 172.000 Oldctg 2
Fp_number "0094O11"
Gel_number    109414
Bands  953170 26
Positive_STS "OJ990407_02" 
Positive_STS "OJ990412_10" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 5 
Modified_date 103 4 22 10 21 
  
Clone : "a0094P02"
Map "ctg1" Ends Left 546.000
Map "ctg1" Ends Right 577.000 Oldctg 2
Fp_number "0094P02"
Gel_number    109444
Bands  953509 32
Approximate_match_to_cosmid "a0063H14"
Positive_STS "OJ000251_05" 
Positive_STS "OJ000301_05" 
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 9 5 
Modified_date 102 2 1 22 48 
  
Clone : "a0095F06"
Map "ctg1" Ends Left 15.000
Map "ctg1" Ends Right 47.000 Oldctg 2
Fp_number "0095F06"
Gel_number    109542
Bands  957133 33
Approximate_match_to_cosmid "a0060C20"
Positive_STS "OJ990915_01" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 9 5 
Modified_date 103 4 22 10 21 
  
Clone : "a0095M19"
Map "ctg1" Ends Left 333.000
Map "ctg1" Ends Right 367.000 Oldctg 2
Fp_number "0095M19"
Gel_number    109514
Bands  961454 35
Approximate_match_to_cosmid "a0093K20"
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 9 5 
Modified_date 103 4 22 10 21 
  
Clone : "a0095O20"
Map "ctg1" Ends Left 144.000
Map "ctg1" Ends Right 171.000 Oldctg 2
Fp_number "0095O20"
Gel_number    109524
Bands  962710 28
Positive_OVERGO "SOG0961" 
Positive_OVERGO "SOG1225" 
Positive_OVERGO "SOG1231" 
Creation_date 99 11 12 9 5 
Modified_date 103 4 22 10 21 
  
Clone : "a0096B09"
Map "ctg1" Ends Left 165.000
Map "ctg1" Ends Right 195.000 Oldctg 2
Fp_number "0096B09"
Gel_number    109631
Bands  964428 31
Approximate_match_to_cosmid "a0061C05"
Creation_date 99 11 12 9 5 
Modified_date 101 4 11 16 57 
  
Clone : "a0096E08"
Map "ctg1" Ends Left 293.000
Map "ctg1" Ends Right 317.000 Oldctg 2
Fp_number "0096E08"
Gel_number    109622
Bands  966093 25
Exact_match_to_cosmid "a0054G21"
Positive_STS "OJ990503_27" 
Positive_OVERGO "SOG0307" 
Creation_date 99 11 12 9 5 
Modified_date 103 4 22 10 21 
  
Clone : "a0096I09"
Map "ctg1" Ends Left 443.000
Map "ctg1" Ends Right 473.000 Oldctg 2
Fp_number "0096I09"
Gel_number    109613
Bands  968385 31
Approximate_match_to_cosmid "b0079F11"
Positive_STS "OJ000214_10" 
Positive_STS "OJ000214_13" 
Positive_STS "OJ000310_29" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991210_12" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Positive_OVERGO "SOG1508" 
Positive_Probe "BCD1424" 
Creation_date 99 11 12 9 5 
Modified_date 103 4 22 10 21 
  
Clone : "a0096N24"
Map "ctg1" Ends Left 337.000
Map "ctg1" Ends Right 362.000 Oldctg 2
Fp_number "0096N24"
Gel_number    109644
Bands  971298 26
Exact_match_to_cosmid "a0093K20"
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 9 5 
Modified_date 103 4 22 10 21 
  
Clone : "a0096O08"
Map "ctg1" Ends Left 482.000
Map "ctg1" Ends Right 508.000 Oldctg 2
Fp_number "0096O08"
Gel_number    109624
Bands  971452 27
Positive_STS "OJ000310_29" 
Positive_STS "OJ990820_14" 
Positive_STS "OJ990923_08" 
Positive_OVERGO "SOG1746" 
Creation_date 99 11 12 9 5 
Modified_date 103 4 22 10 21 
  
Clone : "a0557J22"
Map "ctg1" Ends Left 334.000
Map "ctg1" Ends Right 371.000 Oldctg 2
Fp_number "0557J22"
Gel_number    105743
Bands  976724 38
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 56 
  
Clone : "a0557K12"
Map "ctg1" Ends Left 413.000
Map "ctg1" Ends Right 440.000 Oldctg 2
Fp_number "0557K12"
Gel_number    105723
Bands  977095 28
Approximate_match_to_cosmid "a0039K03"
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 57 
  
Clone : "a0557K23"
Map "ctg1" Ends Left 255.000
Map "ctg1" Ends Right 292.000 Oldctg 2
Fp_number "0557K23"
Gel_number    105713
Bands  977342 38
Creation_date 99 11 12 9 3 
Modified_date 101 4 11 16 57 
  
BAC : "AC091086sd1"
Map "ctg1" Ends Left 8.000
Map "ctg1" Ends Right 40.000 Oldctg 2
Gel_number    20030428
Bands  2020512 33
Remark "a0010G19, Chr1 - Hahn,J.-H., Eun"
Remark "eMRK by Gramene (S13157S)"
Shotgun Full_X FINISHED
Positive_eMRK "S13157S" 
Creation_date 103 4 28 17 3 
Modified_date 103 6 11 23 19 
  
BAC : "AL662937sd1"
Map "ctg1" Ends Left 590.000
Map "ctg1" Ends Right 616.000 Oldctg 2
Gel_number    20030428
Bands  1971368 27
Remark "a0027G07, Chr4 - Fu,G., Wang,S.Y."
Remark "eMRK by Gramene (RZ889)"
Remark "eMRK by Gramene (RM177)"
Shotgun Full_X FINISHED
Positive_eMRK "RM177" 
Positive_eMRK "RZ889" 
Creation_date 103 4 28 16 50 
Modified_date 103 6 11 23 19 
  
BAC : "AP002483sd1"
Map "ctg1" Ends Left 322.000
Map "ctg1" Ends Right 360.000 Oldctg 2
Gel_number    20030428
Bands  2022839 39
Remark "P0019D06, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (S20154S)"
Remark "eMRK by Gramene (S5853)"
Remark "eMRK by Gramene (RM6324)"
Shotgun Full_X FINISHED
Positive_eMRK "RM6324" 
Positive_eMRK "S5853" 
Positive_eMRK "S20154S" 
Creation_date 103 4 28 17 4 
Modified_date 103 6 11 23 19 
  
BAC : "AP002487sd1"
Map "ctg1" Ends Left 102.000
Map "ctg1" Ends Right 124.000 Oldctg 2
Gel_number    20030428
Bands  2021324 22
Remark "P0684C01, Chr1 - Sasaki,T."
Remark "electronic by Gramene (C1679)"
Shotgun Full_X FINISHED
Positive_STS "C1679" 
Creation_date 103 4 28 17 4 
Modified_date 103 6 11 23 19 
  
BAC : "AP002521sd1"
Map "ctg1" Ends Left 510.000
Map "ctg1" Ends Right 540.000 Oldctg 2
Gel_number    20030428
Bands  2020761 31
Remark "P0041E11, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (C804)"
Shotgun Full_X FINISHED
Positive_eMRK "C804" 
Creation_date 103 4 28 17 3 
Modified_date 103 6 11 23 19 
  
BAC : "AP002522sd1"
Map "ctg1" Ends Left 441.000
Map "ctg1" Ends Right 477.000 Oldctg 2
Gel_number    20030428
Bands  2020227 37
Remark "P0009G03, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (C1127)"
Remark "eMRK by Gramene (R106)"
Remark "eMRK by Gramene (R1841)"
Remark "eMRK by Gramene (S20229S)"
Remark "eMRK by Gramene (RM3740)"
Remark "eMRK by Gramene (RM1869)"
Shotgun Full_X FINISHED
Positive_eMRK "RM1869" 
Positive_eMRK "RM3740" 
Positive_eMRK "S20229S" 
Positive_eMRK "R1841" 
Positive_eMRK "R106" 
Positive_eMRK "C1127" 
Creation_date 103 4 28 17 3 
Modified_date 103 6 11 23 19 
  
BAC : "AP002526sd1"
Map "ctg1" Ends Left 217.000
Map "ctg1" Ends Right 247.000 Oldctg 2
Gel_number    20030428
Bands  2019208 30
Remark "P0504H10, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (S13048)"
Remark "eMRK by Gramene (RM6236)"
Remark "eMRK by Gramene (RM7536)"
Remark "eMRK by Gramene (RM8068)"
Remark "eMRK by Gramene (RM1247)"
Remark "eMRK by Gramene (RM6045)"
Remark "eMRK by Gramene (RM1331)"
Remark "eMRK by Gramene (RM7278)"
Shotgun Full_X FINISHED
Positive_eMRK "RM7278" 
Positive_eMRK "RM1331" 
Positive_eMRK "RM6045" 
Positive_eMRK "RM1247" 
Positive_eMRK "RM8068" 
Positive_eMRK "RM7536" 
Positive_eMRK "RM6236" 
Positive_eMRK "S13048" 
Creation_date 103 4 28 17 3 
Modified_date 103 6 11 23 19 
  
BAC : "AP002538sd1"
Map "ctg1" Ends Left 188.000
Map "ctg1" Ends Right 226.000 Oldctg 2
Gel_number    20030428
Bands  2017615 39
Remark "P0408F06, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (C749)"
Remark "eMRK by Gramene (S13048)"
Remark "eMRK by Gramene (RM6236)"
Remark "eMRK by Gramene (RM7536)"
Remark "eMRK by Gramene (RM8068)"
Remark "eMRK by Gramene (RM8069)"
Remark "eMRK by Gramene (RM1247)"
Remark "eMRK by Gramene (RM6470)"
Remark "eMRK by Gramene (RM1141)"
Remark "eMRK by Gramene (RM1331)"
Shotgun Full_X FINISHED
Positive_eMRK "RM1331" 
Positive_eMRK "RM1141" 
Positive_eMRK "RM6470" 
Positive_eMRK "RM1247" 
Positive_eMRK "RM8069" 
Positive_eMRK "RM8068" 
Positive_eMRK "RM7536" 
Positive_eMRK "RM6236" 
Positive_eMRK "S13048" 
Positive_eMRK "C749" 
Creation_date 103 4 28 17 3 
Modified_date 103 6 11 23 19 
  
BAC : "AP002539sd1"
Map "ctg1" Ends Left 505.000
Map "ctg1" Ends Right 535.000 Oldctg 2
Gel_number    20030428
Bands  2004290 30
Remark "P0433F09, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (C804)"
Remark "eMRK by Gramene (RZ288)"
Shotgun Full_X FINISHED
Positive_eMRK "RZ288" 
Positive_eMRK "C804" 
Creation_date 103 4 28 17 0 
Modified_date 103 6 11 23 19 
  
BAC : "AP002540sd1"
Map "ctg1" Ends Left 408.000
Map "ctg1" Ends Right 448.000 Oldctg 2
Gel_number    20030428
Bands  1988092 40
Remark "P0434B04, Chr1 - Sasaki,T."
Remark "electronic by Gramene (C146)"
Remark "electronic by Gramene (C30)"
Remark "eMRK by Gramene (C936)"
Remark "eMRK by Gramene (R106)"
Remark "eMRK by Gramene (R1841)"
Remark "eMRK by Gramene (RM1869)"
Shotgun Full_X FINISHED
Positive_eMRK "RM1869" 
Positive_eMRK "R1841" 
Positive_eMRK "R106" 
Positive_eMRK "C936" 
Positive_STS "C30" 
Positive_STS "C146" 
Creation_date 103 4 28 16 55 
Modified_date 103 6 11 23 19 
  
BAC : "AP002541sd1"
Map "ctg1" Ends Left 54.000
Map "ctg1" Ends Right 88.000 Oldctg 2
Gel_number    20030428
Bands  1985566 35
Remark "P0494A10, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (S1543)"
Remark "eMRK by Gramene (RM6340)"
Shotgun Full_X FINISHED
Positive_eMRK "RM6340" 
Positive_eMRK "S1543" 
Creation_date 103 4 28 16 54 
Modified_date 103 6 11 23 19 
  
BAC : "AP002747sd1"
Map "ctg1" Ends Left 37.000
Map "ctg1" Ends Right 71.000 Oldctg 2
Gel_number    20030428
Bands  2007710 35
Remark "P0698G03, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (S13157S)"
Remark "eMRK by Gramene (S1543)"
Shotgun Full_X FINISHED
Positive_eMRK "S1543" 
Positive_eMRK "S13157S" 
Creation_date 103 4 28 17 1 
Modified_date 103 6 11 23 19 
  
BAC : "AP002860sd1"
Map "ctg1" Ends Left 161.000
Map "ctg1" Ends Right 189.000 Oldctg 2
Gel_number    20030428
Bands  2013899 29
Remark "P0409B08, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (L451)"
Remark "eMRK by Gramene (RM8069)"
Shotgun Full_X FINISHED
Positive_eMRK "RM8069" 
Positive_eMRK "L451" 
Creation_date 103 4 28 17 2 
Modified_date 103 6 11 23 19 
  
BAC : "AP002867sd1"
Map "ctg1" Ends Left 9.000
Map "ctg1" Ends Right 39.000 Oldctg 2
Gel_number    20030428
Bands  2012147 30
Remark "P0463F06, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (S13157S)"
Shotgun Full_X FINISHED
Positive_eMRK "S13157S" 
Creation_date 103 4 28 17 2 
Modified_date 103 6 11 23 19 
  
BAC : "AP002868sd1"
Map "ctg1" Ends Left 67.000
Map "ctg1" Ends Right 99.000 Oldctg 2
Gel_number    20030428
Bands  2011674 33
Remark "P0698A04, Chr1 - Sasaki,T."
Remark "electronic by Gramene (C1679)"
Remark "eMRK by Gramene (S10623)"
Remark "eMRK by Gramene (RM6340)"
Shotgun Full_X FINISHED
Positive_eMRK "RM6340" 
Positive_eMRK "S10623" 
Positive_STS "C1679" 
Creation_date 103 4 28 17 2 
Modified_date 103 6 11 23 19 
  
BAC : "AP002872sd1"
Map "ctg1" Ends Left 379.000
Map "ctg1" Ends Right 421.000 Oldctg 2
Gel_number    20030428
Bands  2003929 43
Remark "P0416D03, Chr1 - Sasaki,T."
Remark "electronic by Gramene (C30)"
Shotgun Full_X FINISHED
Positive_STS "C30" 
Creation_date 103 4 28 17 0 
Modified_date 103 6 11 23 19 
  
BAC : "AP002909sd1"
Map "ctg1" Ends Left 138.000
Map "ctg1" Ends Right 166.000 Oldctg 2
Gel_number    20030428
Bands  2003848 29
Remark "P0044F08, Chr1 - Sasaki,T."
Remark "electronic by Gramene (G107)"
Remark "eMRK by Gramene (L451)"
Remark "eMRK by Gramene (RZ543)"
Shotgun Full_X FINISHED
Positive_eMRK "RZ543" 
Positive_eMRK "L451" 
Positive_STS "G107" 
Creation_date 103 4 28 17 0 
Modified_date 103 6 11 23 19 
  
BAC : "AP002912sd1"
Map "ctg1" Ends Left 581.000
Map "ctg1" Ends Right 609.000 Oldctg 2
Gel_number    20030428
Bands  1940366 28
Remark "P0028E10, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (R1613)"
Remark "eMRK by Gramene (RG246)"
Remark "eMRK by Gramene (RM7383)"
Shotgun Full_X FINISHED
Positive_eMRK "RM7383" 
Positive_eMRK "RG246" 
Positive_eMRK "R1613" 
Creation_date 103 4 28 16 41 
Modified_date 103 6 11 23 19 
  
BAC : "AP002913sd1"
Map "ctg1" Ends Left 301.000
Map "ctg1" Ends Right 327.000 Oldctg 2
Gel_number    20030428
Bands  2006651 26
Remark "P0480E02, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (C50986S)"
Remark "eMRK by Gramene (E30207S)"
Remark "eMRK by Gramene (RM1320)"
Remark "eMRK by Gramene (RM1254)"
Remark "eMRK by Gramene (RM5423)"
Shotgun Full_X FINISHED
Positive_eMRK "RM5423" 
Positive_eMRK "RM1254" 
Positive_eMRK "RM1320" 
Positive_eMRK "E30207S" 
Positive_eMRK "C50986S" 
Creation_date 103 4 28 17 0 
Modified_date 103 6 11 23 19 
  
BAC : "AP003045sd1"
Map "ctg1" Ends Left 463.000
Map "ctg1" Ends Right 495.000 Oldctg 2
Gel_number    20030428
Bands  1987104 32
Remark "P0030H07, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (C1127)"
Remark "eMRK by Gramene (RM3740)"
Shotgun Full_X FINISHED
Positive_eMRK "RM3740" 
Positive_eMRK "C1127" 
Creation_date 103 4 28 16 54 
Modified_date 103 6 11 23 19 
  
BAC : "AP003046sd1"
Map "ctg1" Ends Left 107.000
Map "ctg1" Ends Right 141.000 Oldctg 2
Gel_number    20030428
Bands  1992652 35
Remark "P0445D12, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (R87)"
Remark "eMRK by Gramene (RM6515)"
Shotgun Full_X FINISHED
Positive_eMRK "RM6515" 
Positive_eMRK "R87" 
Creation_date 103 4 28 16 56 
Modified_date 103 6 11 23 19 
  
BAC : "AP003209sd1"
Map "ctg1" Ends Left 532.000
Map "ctg1" Ends Right 568.000 Oldctg 2
Gel_number    20030428
Bands  1918448 36
Remark "B1189A09, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (RM6873)"
Remark "eMRK by Gramene (RM1177)"
Shotgun Full_X FINISHED
Positive_eMRK "RM1177" 
Positive_eMRK "RM6873" 
Creation_date 103 4 28 16 35 
Modified_date 103 6 11 23 19 
  
BAC : "AP003214sd1"
Map "ctg1" Ends Left 241.000
Map "ctg1" Ends Right 279.000 Oldctg 2
Gel_number    20030428
Bands  1946333 39
Remark "a0083M16, Chr1 - Sasaki,T."
Remark "electronic by Gramene (R753)"
Remark "eMRK by Gramene (RM6045)"
Remark "eMRK by Gramene (RM7278)"
Shotgun Full_X FINISHED
Positive_eMRK "RM7278" 
Positive_eMRK "RM6045" 
Positive_STS "R753" 
Creation_date 103 4 28 16 43 
Modified_date 103 6 11 23 19 
  
BAC : "AP003225sd1"
Map "ctg1" Ends Left 490.000
Map "ctg1" Ends Right 508.000 Oldctg 2
Gel_number    20030428
Bands  1946935 19
Remark "P0011G08, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (RZ288)"
Remark "eMRK by Gramene (RM6433)"
Shotgun Full_X FINISHED
Positive_eMRK "RM6433" 
Positive_eMRK "RZ288" 
Creation_date 103 4 28 16 43 
Modified_date 103 6 11 23 19 
  
BAC : "AP003233sd1"
Map "ctg1" Ends Left 132.000
Map "ctg1" Ends Right 160.000 Oldctg 2
Gel_number    20030428
Bands  1933893 28
Remark "P0037C04, Chr1 - Sasaki,T."
Remark "electronic by Gramene (G107)"
Remark "eMRK by Gramene (R87)"
Remark "eMRK by Gramene (RZ543)"
Shotgun Full_X FINISHED
Positive_eMRK "RZ543" 
Positive_eMRK "R87" 
Positive_STS "G107" 
Creation_date 103 4 28 16 39 
Modified_date 103 6 11 23 19 
  
BAC : "AP003250sd1"
Map "ctg1" Ends Left 266.000
Map "ctg1" Ends Right 294.000 Oldctg 2
Gel_number    20030428
Bands  1941929 28
Remark "P0443D08, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (C50986S)"
Remark "eMRK by Gramene (C90)"
Shotgun Full_X FINISHED
Positive_eMRK "C90" 
Positive_eMRK "C50986S" 
Creation_date 103 4 28 16 41 
Modified_date 103 6 11 23 19 
  
BAC : "AP003301sd1"
Map "ctg1" Ends Left 565.000
Map "ctg1" Ends Right 601.000 Oldctg 2
Gel_number    20030428
Bands  1949025 37
Remark "P0701D05, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (R1613)"
Remark "eMRK by Gramene (RM6873)"
Remark "eMRK by Gramene (RM7383)"
Remark "eMRK by Gramene (RM5336)"
Shotgun Full_X FINISHED
Positive_eMRK "RM5336" 
Positive_eMRK "RM7383" 
Positive_eMRK "RM6873" 
Positive_eMRK "R1613" 
Creation_date 103 4 28 16 44 
Modified_date 103 6 11 23 19 
  
BAC : "AP003311sd1"
Map "ctg1" Ends Left 340.000
Map "ctg1" Ends Right 380.000 Oldctg 2
Gel_number    20030428
Bands  1991148 41
Remark "P0024G09, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (S20154S)"
Remark "eMRK by Gramene (S5853)"
Remark "eMRK by Gramene (RM6324)"
Shotgun Full_X FINISHED
Positive_eMRK "RM6324" 
Positive_eMRK "S5853" 
Positive_eMRK "S20154S" 
Creation_date 103 4 28 16 56 
Modified_date 103 6 11 23 19 
  
BAC : "AP003338sd1"
Map "ctg1" Ends Left 10.000
Map "ctg1" Ends Right 38.000 Oldctg 2
Gel_number    20030428
Bands  1919025 29
Remark "OJ1212_B09, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (C51033)"
Remark "eMRK by Gramene (S13157S)"
Remark "eMRK by Gramene (RM3148)"
Shotgun Full_X FINISHED
Positive_eMRK "RM3148" 
Positive_eMRK "S13157S" 
Positive_eMRK "C51033" 
Creation_date 103 4 28 16 35 
Modified_date 103 6 11 23 19 
  
BAC : "AP003339sd1"
Map "ctg1" Ends Left 588.000
Map "ctg1" Ends Right 628.000 Oldctg 2
Gel_number    20030428
Bands  1942963 41
Remark "OJ1276_B06, Chr1 - Sasaki,T."
Remark "eMRK by Gramene (E222S)"
Remark "eMRK by Gramene (R1613)"
Remark "eMRK by Gramene (RG246)"
Remark "eMRK by Gramene (RM3652)"
Remark "eMRK by Gramene (RM7383)"
Shotgun Full_X FINISHED
Positive_eMRK "RM7383" 
Positive_eMRK "RM3652" 
Positive_eMRK "RG246" 
Positive_eMRK "R1613" 
Positive_eMRK "E222S" 
Creation_date 103 4 28 16 42 
Modified_date 103 6 11 23 19 
  
Clone : "b0001E17"
Map "ctg1" Ends Left 147.000
Map "ctg1" Ends Right 177.000 Oldctg 2
Fp_number "E001E17"
Gel_number    200112
Bands  981466 31
Positive_OVERGO "SOG0961" 
Positive_OVERGO "SOG1225" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0001O16"
Map "ctg1" Ends Left 476.000
Map "ctg1" Ends Right 504.000 Oldctg 2
Fp_number "E001O16"
Gel_number    200124
Bands  986315 29
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0002B22"
Map "ctg1" Ends Left 414.000
Map "ctg1" Ends Right 449.000 Oldctg 2
Fp_number "E002B22"
Gel_number    200241
Bands  987868 36
Approximate_match_to_cosmid "a0061L15"
Positive_STS "OJ000214_13" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG0223" 
Positive_OVERGO "SOG1200" 
Positive_OVERGO "SOG1508" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0002E04"
Map "ctg1" Ends Left 320.000
Map "ctg1" Ends Right 354.000 Oldctg 2
Fp_number "E002E04"
Gel_number    200222
Bands  988826 35
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0002J03"
Map "ctg1" Ends Left 504.000
Map "ctg1" Ends Right 532.000 Oldctg 2
Fp_number "E002J03"
Gel_number    200233
Bands  990602 29
Positive_STS "OJ990713_06" 
Positive_OVERGO "SOG2238" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0002P19"
Map "ctg1" Ends Left 122.000
Map "ctg1" Ends Right 146.000 Oldctg 2
Fp_number "E002P19"
Gel_number    200234
Bands  993311 25
Exact_match_to_cosmid "a0066I06"
Positive_STS "OJ991015_10" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0002P23"
Map "ctg1" Ends Left 185.000
Map "ctg1" Ends Right 219.000 Oldctg 2
Fp_number "E002P23"
Gel_number    200234
Bands  993375 35
Approximate_match_to_cosmid "b0074P13"
Positive_OVERGO "SOG1774" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0003D11"
Map "ctg1" Ends Left 125.000
Map "ctg1" Ends Right 145.000 Oldctg 2
Fp_number "E003D11"
Gel_number    200331
Bands  995012 21
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Positive_OVERGO "SOG1231" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0003G18"
Map "ctg1" Ends Left 249.000
Map "ctg1" Ends Right 278.000 Oldctg 2
Fp_number "E003G18"
Gel_number    200322
Bands  996383 30
Positive_STS "OJ000317_34" 
Creation_date 99 11 12 16 20 
Modified_date 102 2 1 22 48 
  
Clone : "b0004I04"
Map "ctg1" Ends Left 278.000
Map "ctg1" Ends Right 297.000 Oldctg 2
Fp_number "E004I04"
Gel_number    200423
Bands  1005389 20
Approximate_match_to_cosmid "b0007H05"
Positive_STS "OJ990503_27" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0005A09"
Map "ctg1" Ends Left 347.000
Map "ctg1" Ends Right 384.000 Oldctg 2
Fp_number "E005A09"
Gel_number    200511
Bands  1009115 38
Approximate_match_to_cosmid "a0073L24"
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 16 20 
Modified_date 102 2 1 22 48 
  
Clone : "b0005C01"
Map "ctg1" Ends Left 1.000
Map "ctg1" Ends Right 37.000 Oldctg 2
Fp_number "E005C01"
Gel_number    200511
Bands  1009851 37
Positive_STS "0057C09f" 
Positive_STS "OJ990915_01" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0005L08"
Map "ctg1" Ends Left 610.000
Map "ctg1" Ends Right 643.000 Oldctg 2
Fp_number "E005L08"
Gel_number    200543
Bands  1013669 34
Positive_STS "OJ000321_15" 
Positive_STS "OJ000330_31" 
Creation_date 99 11 12 16 20 
Modified_date 102 2 1 22 48 
  
Clone : "b0005M11"
Map "ctg1" Ends Left 494.000
Map "ctg1" Ends Right 520.000 Oldctg 2
Fp_number "E005M11"
Gel_number    200514
Bands  1014245 27
Positive_OVERGO "SOG2238" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0006A09"
Map "ctg1" Ends Left 376.000
Map "ctg1" Ends Right 405.000 Oldctg 2
Fp_number "E006A09"
Gel_number    200611
Bands  1015969 30
Approximate_match_to_cosmid "a0049H15"
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 16 20 
Modified_date 102 2 1 22 48 
  
Clone : "b0006H11"
Map "ctg1" Ends Left 56.000
Map "ctg1" Ends Right 86.000 Oldctg 2
Fp_number "E006H11"
Gel_number    200632
Bands  1019531 31
Approximate_match_to_cosmid "b0096N17"
Positive_STS "OJ990605_38" 
Positive_OVERGO "SOG1344" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0006K10"
Map "ctg1" Ends Left 89.000
Map "ctg1" Ends Right 124.000 Oldctg 2
Fp_number "E006K10"
Gel_number    200623
Bands  1021291 36
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 16 20 
Modified_date 102 2 1 22 48 
  
Clone : "b0006L19"
Map "ctg1" Ends Left 446.000
Map "ctg1" Ends Right 480.000 Oldctg 2
Fp_number "E006L19"
Gel_number    200633
Bands  1021995 35
Positive_STS "RG353" 
Positive_STS "OJ000214_13" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Positive_OVERGO "SOG2203" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0006M06"
Map "ctg1" Ends Left 256.000
Map "ctg1" Ends Right 282.000 Oldctg 2
Fp_number "E006M06"
Gel_number    200624
Bands  1022212 27
Positive_STS "OJ000317_34" 
Positive_OVERGO "SOG1450" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0007C14"
Map "ctg1" Ends Left 567.000
Map "ctg1" Ends Right 596.000 Oldctg 2
Fp_number "E007C14"
Gel_number    200721
Bands  1025914 30
Positive_OVERGO "SOG0313" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0007H05"
Map "ctg1" Ends Left 280.000
Map "ctg1" Ends Right 309.000 Oldctg 2
Fp_number "E007H05"
Gel_number    200732
Bands  1028432 30
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0007P11"
Map "ctg1" Ends Left 588.000
Map "ctg1" Ends Right 616.000 Oldctg 2
Fp_number "E007P11"
Gel_number    200734
Bands  1033249 29
Creation_date 99 11 12 16 20 
Modified_date 101 4 11 16 56 
  
Clone : "b0008A04"
Map "ctg1" Ends Left 296.000
Map "ctg1" Ends Right 321.000 Oldctg 2
Fp_number "E008A04"
Gel_number    200821
Bands  1033512 26
Creation_date 99 11 12 16 20 
Modified_date 101 4 11 16 56 
  
Clone : "b0008B04"
Map "ctg1" Ends Left 281.000
Map "ctg1" Ends Right 314.000 Oldctg 2
Fp_number "E008B04"
Gel_number    200841
Bands  1034058 34
Creation_date 99 11 12 16 20 
Modified_date 101 4 27 15 58 
  
Clone : "b0008E06"
Map "ctg1" Ends Left 154.000
Map "ctg1" Ends Right 183.000 Oldctg 2
Fp_number "E008E06"
Gel_number    200822
Bands  1035911 30
Approximate_match_to_cosmid "a0061C05"
Creation_date 99 11 12 16 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0008G08"
Map "ctg1" Ends Left 57.000
Map "ctg1" Ends Right 94.000 Oldctg 2
Fp_number "E008G08"
Gel_number    200822
Bands  1037121 38
Positive_OVERGO "SOG2244" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0008J05"
Map "ctg1" Ends Left 288.000
Map "ctg1" Ends Right 310.000 Oldctg 2
Fp_number "E008J05"
Gel_number    200833
Bands  1038669 23
Approximate_match_to_cosmid "b0008B04"
Creation_date 99 11 12 16 20 
Modified_date 101 4 27 15 58 
  
Clone : "b0009H13"
Map "ctg1" Ends Left 137.000
Map "ctg1" Ends Right 160.000 Oldctg 2
Fp_number "E009H13"
Gel_number    200932
Bands  1046593 24
Positive_OVERGO "SOG1225" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0009I24"
Map "ctg1" Ends Left 484.000
Map "ctg1" Ends Right 506.000 Oldctg 2
Fp_number "E009I24"
Gel_number    200923
Bands  1047390 23
Positive_OVERGO "SOG1745" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0009K15"
Map "ctg1" Ends Left 224.000
Map "ctg1" Ends Right 253.000 Oldctg 2
Fp_number "E009K15"
Gel_number    200913
Bands  1048124 30
Approximate_match_to_cosmid "b0066J19"
Positive_STS "40C03f" 
Positive_OVERGO "SOG1774" 
Positive_OVERGO "SOG1790" 
Creation_date 99 11 12 16 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0011E18"
Map "ctg1" Ends Left 504.000
Map "ctg1" Ends Right 528.000 Oldctg 2
Fp_number "E011E18"
Gel_number    201122
Bands  1053853 25
Approximate_match_to_cosmid "b0002J03"
Creation_date 99 11 12 17 9 
Modified_date 101 4 11 16 57 
  
Clone : "b0011F05"
Map "ctg1" Ends Left 617.000
Map "ctg1" Ends Right 645.000 Oldctg 2
Fp_number "E011F05"
Gel_number    201132
Bands  1054097 29
Creation_date 99 11 12 17 9 
Modified_date 101 4 11 16 56 
  
Clone : "b0011F06"
Map "ctg1" Ends Left 616.000
Map "ctg1" Ends Right 642.000 Oldctg 2
Fp_number "E011F06"
Gel_number    201142
Bands  1054126 27
Approximate_match_to_cosmid "b0005L08"
Creation_date 99 11 12 17 9 
Modified_date 101 4 11 16 57 
  
Clone : "b0011F07"
Map "ctg1" Ends Left 482.000
Map "ctg1" Ends Right 502.000 Oldctg 2
Fp_number "E011F07"
Gel_number    201132
Bands  1054153 21
Approximate_match_to_cosmid "b0001O16"
Positive_STS "OJ000310_29" 
Positive_STS "OJ990923_08" 
Positive_OVERGO "SOG1745" 
Creation_date 99 11 12 17 9 
Modified_date 103 4 22 10 21 
  
Clone : "b0011I10"
Map "ctg1" Ends Left 416.000
Map "ctg1" Ends Right 448.000 Oldctg 2
Fp_number "E011I10"
Gel_number    201123
Bands  1055784 33
Positive_STS "C30" 
Positive_OVERGO "SOG1200" 
Positive_OVERGO "SOG1508" 
Creation_date 99 11 12 17 9 
Modified_date 103 4 22 10 21 
  
Clone : "b0011M11"
Map "ctg1" Ends Left 219.000
Map "ctg1" Ends Right 238.000 Oldctg 2
Fp_number "E011M11"
Gel_number    201114
Bands  1057930 20
Positive_STS "43L01f" 
Positive_STS "51J01r" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Positive_OVERGO "SOG1774" 
Positive_OVERGO "SOG1790" 
Positive_OVERGO "SOG1816" 
Creation_date 99 11 12 17 9 
Modified_date 103 4 22 10 21 
  
Clone : "b0011P06"
Map "ctg1" Ends Left 612.000
Map "ctg1" Ends Right 643.000 Oldctg 2
Fp_number "E011P06"
Gel_number    201144
Bands  1059487 32
Creation_date 99 11 12 17 9 
Modified_date 101 4 11 16 56 
  
Clone : "b0012C02"
Map "ctg1" Ends Left 486.000
Map "ctg1" Ends Right 505.000 Oldctg 2
Fp_number "E012C02"
Gel_number    201221
Bands  1060985 20
Exact_match_to_cosmid "b0039P22"
Creation_date 99 11 12 17 9 
Modified_date 101 4 11 16 57 
  
Clone : "b0012C07"
Map "ctg1" Ends Left 507.000
Map "ctg1" Ends Right 534.000 Oldctg 2
Fp_number "E012C07"
Gel_number    201211
Bands  1061097 28
Creation_date 99 11 12 17 9 
Modified_date 101 4 11 16 57 
  
Clone : "b0012F17"
Map "ctg1" Ends Left 369.000
Map "ctg1" Ends Right 403.000 Oldctg 2
Fp_number "E012F17"
Gel_number    201232
Bands  1063025 35
Approximate_match_to_cosmid "a0049H15"
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 17 9 
Modified_date 102 2 1 22 48 
  
Clone : "b0012O04"
Map "ctg1" Ends Left 489.000
Map "ctg1" Ends Right 506.000 Oldctg 2
Fp_number "E012O04"
Gel_number    201224
Bands  1067525 18
Positive_OVERGO "SOG1745" 
Positive_OVERGO "SOG2238" 
Creation_date 100 2 18 18 17 
Modified_date 103 4 22 10 21 
  
Clone : "b0012P23"
Map "ctg1" Ends Left 335.000
Map "ctg1" Ends Right 355.000 Oldctg 2
Fp_number "E012P23"
Gel_number    201234
Bands  1068462 21
Approximate_match_to_cosmid "a0063J07"
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_OVERGO "SOG0657" 
Creation_date 99 11 12 17 9 
Modified_date 103 4 22 10 21 
  
Clone : "b0013H20"
Map "ctg1" Ends Left 582.000
Map "ctg1" Ends Right 608.000 Oldctg 2
Fp_number "E013H20"
Gel_number    201342
Bands  1072717 27
Positive_STS "OJ000321_15" 
Positive_STS "OJ000330_31" 
Creation_date 99 11 12 17 9 
Modified_date 102 2 1 22 48 
  
Clone : "b0013H23"
Map "ctg1" Ends Left 27.000
Map "ctg1" Ends Right 59.000 Oldctg 2
Fp_number "E013H23"
Gel_number    201332
Bands  1072808 33
Approximate_match_to_cosmid "b0095L23"
Positive_STS "42D18r" 
Creation_date 99 11 12 17 9 
Modified_date 101 5 9 11 19 
  
Clone : "b0013I14"
Map "ctg1" Ends Left 318.000
Map "ctg1" Ends Right 343.000 Oldctg 2
Fp_number "E013I14"
Gel_number    201323
Bands  1073197 26
Creation_date 99 11 12 17 9 
Modified_date 101 4 11 16 56 
  
Clone : "b0013L08"
Map "ctg1" Ends Left 30.000
Map "ctg1" Ends Right 59.000 Oldctg 2
Fp_number "E013L08"
Gel_number    201343
Bands  1074624 30
Approximate_match_to_cosmid "b0026K13"
Positive_STS "42D18r" 
Creation_date 99 11 12 17 9 
Modified_date 101 5 9 11 19 
  
Clone : "b0014G12"
Map "ctg1" Ends Left 120.000
Map "ctg1" Ends Right 147.000 Oldctg 2
Fp_number "E014G12"
Gel_number    201422
Bands  1080878 28
Approximate_match_to_cosmid "a0066I06"
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 17 9 
Modified_date 103 4 22 10 21 
  
Clone : "b0014H14"
Map "ctg1" Ends Left 112.000
Map "ctg1" Ends Right 146.000 Oldctg 2
Fp_number "E014H14"
Gel_number    201442
Bands  1081530 35
Creation_date 99 11 12 17 9 
Modified_date 99 11 12 17 40 
  
Clone : "b0015C03"
Map "ctg1" Ends Left 259.000
Map "ctg1" Ends Right 275.000 Oldctg 2
Fp_number "E015C03"
Gel_number    201511
Bands  1087253 17
Positive_STS "OJ000317_34" 
Creation_date 99 11 12 17 9 
Modified_date 102 2 1 22 48 
  
Clone : "b0015D07"
Map "ctg1" Ends Left 369.000
Map "ctg1" Ends Right 401.000 Oldctg 2
Fp_number "E015D07"
Gel_number    201531
Bands  1087836 33
Approximate_match_to_cosmid "a0049H15"
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 17 9 
Modified_date 102 2 1 22 48 
  
Clone : "b0015L12"
Map "ctg1" Ends Left 149.000
Map "ctg1" Ends Right 174.000 Oldctg 2
Fp_number "E015L12"
Gel_number    201543
Bands  1092399 26
Approximate_match_to_cosmid "b0001E17"
Positive_STS "OJ990407_02" 
Positive_OVERGO "SOG1225" 
Creation_date 99 11 12 17 9 
Modified_date 103 4 22 10 21 
  
Clone : "b0017D13"
Map "ctg1" Ends Left 482.000
Map "ctg1" Ends Right 502.000 Oldctg 2
Fp_number "E017D13"
Gel_number    201731
Bands  1104900 21
Creation_date 99 11 12 17 9 
Modified_date 101 4 11 16 56 
  
Clone : "b0017G05"
Map "ctg1" Ends Left 284.000
Map "ctg1" Ends Right 310.000 Oldctg 2
Fp_number "E017G05"
Gel_number    201712
Bands  1105962 27
Approximate_match_to_cosmid "b0007H05"
Positive_STS "OJ990503_27" 
Positive_STS "OJ991021_17" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 17 9 
Modified_date 103 4 22 10 21 
  
Clone : "b0017I16"
Map "ctg1" Ends Left 371.000
Map "ctg1" Ends Right 405.000 Oldctg 2
Fp_number "E017I16"
Gel_number    201723
Bands  1106949 35
Creation_date 99 11 12 17 9 
Modified_date 101 4 11 16 56 
  
Clone : "b0017M11"
Map "ctg1" Ends Left 602.000
Map "ctg1" Ends Right 635.000 Oldctg 2
Fp_number "E017M11"
Gel_number    201714
Bands  1108435 34
Positive_OVERGO "SOG2111" 
Creation_date 100 2 18 18 17 
Modified_date 103 4 22 10 21 
  
Clone : "b0018O01"
Map "ctg1" Ends Left 152.000
Map "ctg1" Ends Right 179.000 Oldctg 2
Fp_number "E018O01"
Gel_number    201814
Bands  1117553 28
Approximate_match_to_cosmid "b0087J21"
Positive_STS "OJ000301_13" 
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 17 9 
Modified_date 102 2 1 22 48 
  
Clone : "b0018O08"
Map "ctg1" Ends Left 338.000
Map "ctg1" Ends Right 363.000 Oldctg 2
Fp_number "E018O08"
Gel_number    201824
Bands  1117698 26
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Creation_date 99 11 12 17 9 
Modified_date 102 2 1 22 48 
  
Clone : "b0019B19"
Map "ctg1" Ends Left 369.000
Map "ctg1" Ends Right 404.000 Oldctg 2
Fp_number "E019B19"
Gel_number    201931
Bands  1119742 36
Approximate_match_to_cosmid "a0049H15"
Creation_date 99 11 12 17 9 
Modified_date 101 4 11 16 57 
  
Clone : "b0019P13"
Map "ctg1" Ends Left 464.000
Map "ctg1" Ends Right 487.000 Oldctg 2
Fp_number "E019P13"
Gel_number    201934
Bands  1127272 24
Approximate_match_to_cosmid "a0062P11"
Positive_STS "OJ000214_13" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991210_12" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 17 9 
Modified_date 103 4 22 10 21 
  
Clone : "b0020J05"
Map "ctg1" Ends Left 35.000
Map "ctg1" Ends Right 65.000 Oldctg 2
Fp_number "E020J05"
Gel_number    202033
Bands  1132122 31
Approximate_match_to_cosmid "b0065P01"
Positive_STS "42D18r" 
Positive_STS "OJ990605_38" 
Creation_date 99 11 12 17 9 
Modified_date 103 4 22 10 21 
  
Clone : "b0020L08"
Map "ctg1" Ends Left 369.000
Map "ctg1" Ends Right 401.000 Oldctg 2
Fp_number "E020L08"
Gel_number    202043
Bands  1133341 33
Approximate_match_to_cosmid "a0049H15"
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 17 9 
Modified_date 102 2 1 22 48 
  
Clone : "b0021C19"
Map "ctg1" Ends Left 279.000
Map "ctg1" Ends Right 301.000 Oldctg 2
Fp_number "E021C19"
Gel_number    202111
Bands  1137332 23
Approximate_match_to_cosmid "b0007H05"
Positive_STS "OJ990503_27" 
Positive_OVERGO "SOG0307" 
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 17 9 
Modified_date 103 4 22 10 21 
  
Clone : "b0021D08"
Map "ctg1" Ends Left 75.000
Map "ctg1" Ends Right 103.000 Oldctg 2
Fp_number "E021D08"
Gel_number    202141
Bands  1137640 29
Positive_STS "OJ990412_10" 
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Positive_OVERGO "SOG1344" 
Creation_date 99 11 12 17 9 
Modified_date 103 4 22 10 21 
  
Clone : "b0021G21"
Map "ctg1" Ends Left 436.000
Map "ctg1" Ends Right 465.000 Oldctg 2
Fp_number "E021G21"
Gel_number    202112
Bands  1139669 30
Approximate_match_to_cosmid "a0065C23"
Positive_STS "OJ000214_10" 
Positive_STS "OJ000214_13" 
Positive_OVERGO "SOG1200" 
Positive_OVERGO "SOG1508" 
Creation_date 99 11 12 17 9 
Modified_date 103 4 22 10 21 
  
Clone : "b0021H16"
Map "ctg1" Ends Left 119.000
Map "ctg1" Ends Right 145.000 Oldctg 2
Fp_number "E021H16"
Gel_number    202142
Bands  1140135 27
Approximate_match_to_cosmid "a0066I06"
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 17 9 
Modified_date 102 2 1 22 48 
  
Clone : "b0021O16"
Map "ctg1" Ends Left 371.000
Map "ctg1" Ends Right 403.000 Oldctg 2
Fp_number "E021O16"
Gel_number    202124
Bands  1144139 33
Approximate_match_to_cosmid "a0049H15"
Creation_date 99 11 12 17 9 
Modified_date 101 4 11 16 57 
  
Clone : "b0022B22"
Map "ctg1" Ends Left 3.000
Map "ctg1" Ends Right 29.000 Oldctg 2
Fp_number "E022B22"
Gel_number    202241
Bands  1145870 27
Approximate_match_to_cosmid "a0070F12"
Creation_date 99 11 12 17 9 
Modified_date 101 4 11 16 57 
  
Clone : "b0022I18"
Map "ctg1" Ends Left 410.000
Map "ctg1" Ends Right 437.000 Oldctg 2
Fp_number "E022I18"
Gel_number    202223
Bands  1149866 28
Positive_STS "OJ000214_10" 
Positive_STS "OJ000214_13" 
Positive_OVERGO "SOG0223" 
Positive_OVERGO "SOG1508" 
Creation_date 99 11 12 17 9 
Modified_date 103 4 22 10 21 
  
Clone : "b0026K13"
Map "ctg1" Ends Left 28.000
Map "ctg1" Ends Right 59.000 Oldctg 2
Fp_number "E026K13"
Gel_number    202613
Bands  1177062 32
Positive_STS "42D18r" 
Positive_OVERGO "SOG0961" 
Positive_OVERGO "SOG2244" 
Creation_date 99 11 12 17 9 
Modified_date 103 4 22 10 21 
  
Clone : "b0027A06"
Map "ctg1" Ends Left 147.000
Map "ctg1" Ends Right 175.000 Oldctg 2
Fp_number "E027A06"
Gel_number    202721
Bands  1180292 29
Creation_date 100 2 18 18 17 
Modified_date 100 2 23 10 44 
  
Clone : "b0027A18"
Map "ctg1" Ends Left 19.000
Map "ctg1" Ends Right 46.000 Oldctg 2
Fp_number "E027A18"
Gel_number    202721
Bands  1180564 28
Creation_date 100 2 18 18 17 
Modified_date 101 4 11 16 55 
  
Clone : "b0027C05"
Map "ctg1" Ends Left 545.000
Map "ctg1" Ends Right 570.000 Oldctg 2
Fp_number "E027C05"
Gel_number    202711
Bands  1181322 26
Approximate_match_to_cosmid "b0095I21"
Creation_date 100 2 18 18 17 
Modified_date 101 4 11 16 57 
  
Clone : "b0027F23"
Map "ctg1" Ends Left 331.000
Map "ctg1" Ends Right 360.000 Oldctg 2
Fp_number "E027F23"
Gel_number    202732
Bands  1183196 30
Approximate_match_to_cosmid "a0093K20"
Positive_OVERGO "SOG0657" 
Creation_date 100 2 18 18 18 
Modified_date 103 4 22 10 21 
  
Clone : "b0028E05"
Map "ctg1" Ends Left 90.000
Map "ctg1" Ends Right 124.000 Oldctg 2
Fp_number "E028E05"
Gel_number    202812
Bands  1190321 35
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 17 9 
Modified_date 102 2 1 22 48 
  
Clone : "b0029A01"
Map "ctg1" Ends Left 50.000
Map "ctg1" Ends Right 85.000 Oldctg 2
Fp_number "E029A01"
Gel_number    202911
Bands  1196563 36
Approximate_match_to_cosmid "a0053J14"
Positive_STS "OJ990412_10" 
Positive_STS "OJ990605_38" 
Creation_date 99 11 12 17 10 
Modified_date 102 2 1 22 48 
  
Clone : "b0029A21"
Map "ctg1" Ends Left 1.000
Map "ctg1" Ends Right 30.000 Oldctg 2
Fp_number "E029A21"
Gel_number    202911
Bands  1197081 30
Creation_date 99 11 12 17 10 
Modified_date 101 4 11 16 55 
  
Clone : "b0029B04"
Map "ctg1" Ends Left 362.000
Map "ctg1" Ends Right 395.000 Oldctg 2
Fp_number "E029B04"
Gel_number    202941
Bands  1197254 34
Approximate_match_to_cosmid "a0049H15"
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 17 10 
Modified_date 102 2 1 22 48 
  
Clone : "b0029B16"
Map "ctg1" Ends Left 227.000
Map "ctg1" Ends Right 254.000 Oldctg 2
Fp_number "E029B16"
Gel_number    202941
Bands  1197573 28
Creation_date 99 11 12 17 10 
Modified_date 101 4 11 16 56 
  
Clone : "b0029D12"
Map "ctg1" Ends Left 521.000
Map "ctg1" Ends Right 547.000 Oldctg 2
Fp_number "E029D12"
Gel_number    202941
Bands  1198598 27
Creation_date 99 11 12 17 10 
Modified_date 101 4 11 16 56 
  
Clone : "b0029E05"
Map "ctg1" Ends Left 264.000
Map "ctg1" Ends Right 283.000 Oldctg 2
Fp_number "E029E05"
Gel_number    202912
Bands  1198979 20
Approximate_match_to_cosmid "a0085N03"
Positive_STS "OJ000317_34" 
Creation_date 99 11 12 17 10 
Modified_date 102 2 1 22 48 
  
Clone : "b0029F18"
Map "ctg1" Ends Left 315.000
Map "ctg1" Ends Right 338.000 Oldctg 2
Fp_number "E029F18"
Gel_number    202942
Bands  1199758 24
Positive_STS "OJ991021_17" 
Creation_date 99 11 12 17 10 
Modified_date 102 2 1 22 48 
  
Clone : "b0030B05"
Map "ctg1" Ends Left 484.000
Map "ctg1" Ends Right 503.000 Oldctg 2
Fp_number "E030B05"
Gel_number    203031
Bands  1205762 20
Exact_match_to_cosmid "b0087O07"
Positive_OVERGO "SOG1745" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0030E04"
Map "ctg1" Ends Left 508.000
Map "ctg1" Ends Right 533.000 Oldctg 2
Fp_number "E030E04"
Gel_number    203022
Bands  1207382 26
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 19 29 
Modified_date 102 2 1 22 48 
  
Clone : "b0031K18"
Map "ctg1" Ends Left 437.000
Map "ctg1" Ends Right 467.000 Oldctg 2
Fp_number "E031K18"
Gel_number    203123
Bands  1219990 31
Positive_STS "OJ000214_10" 
Positive_STS "OJ000214_13" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0031L04"
Map "ctg1" Ends Left 19.000
Map "ctg1" Ends Right 46.000 Oldctg 2
Fp_number "E031L04"
Gel_number    203143
Bands  1220257 28
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0032A21"
Map "ctg1" Ends Left 506.000
Map "ctg1" Ends Right 534.000 Oldctg 2
Fp_number "E032A21"
Gel_number    203211
Bands  1223262 29
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0032A22"
Map "ctg1" Ends Left 506.000
Map "ctg1" Ends Right 534.000 Oldctg 2
Fp_number "E032A22"
Gel_number    203221
Bands  1223291 29
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 56 
  
Clone : "b0032B06"
Map "ctg1" Ends Left 604.000
Map "ctg1" Ends Right 634.000 Oldctg 2
Fp_number "E032B06"
Gel_number    203241
Bands  1223493 31
Approximate_match_to_cosmid "b0033I06"
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0032B10"
Map "ctg1" Ends Left 559.000
Map "ctg1" Ends Right 592.000 Oldctg 2
Fp_number "E032B10"
Gel_number    203241
Bands  1223593 34
Positive_OVERGO "SOG0279" 
Positive_OVERGO "SOG0313" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0032E14"
Map "ctg1" Ends Left 114.000
Map "ctg1" Ends Right 143.000 Oldctg 2
Fp_number "E032E14"
Gel_number    203222
Bands  1225535 30
Exact_match_to_cosmid "b0048H24"
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 19 29 
Modified_date 102 2 1 22 48 
  
Clone : "b0032J19"
Map "ctg1" Ends Left 430.000
Map "ctg1" Ends Right 463.000 Oldctg 2
Fp_number "E032J19"
Gel_number    203233
Bands  1228438 34
Positive_STS "OJ000214_10" 
Positive_OVERGO "SOG0389" 
Positive_OVERGO "SOG1200" 
Positive_OVERGO "SOG1508" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0032O15"
Map "ctg1" Ends Left 514.000
Map "ctg1" Ends Right 540.000 Oldctg 2
Fp_number "E032O15"
Gel_number    203214
Bands  1231029 27
Positive_OVERGO "SOG1383" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0032P10"
Map "ctg1" Ends Left 509.000
Map "ctg1" Ends Right 533.000 Oldctg 2
Fp_number "E032P10"
Gel_number    203244
Bands  1231495 25
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 19 29 
Modified_date 102 2 1 22 48 
  
Clone : "b0033I06"
Map "ctg1" Ends Left 601.000
Map "ctg1" Ends Right 636.000 Oldctg 2
Fp_number "E033I06"
Gel_number    203323
Bands  1236328 36
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0033L05"
Map "ctg1" Ends Left 534.000
Map "ctg1" Ends Right 563.000 Oldctg 2
Fp_number "E033L05"
Gel_number    203333
Bands  1238077 30
Approximate_match_to_cosmid "b0088P23"
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0033O02"
Map "ctg1" Ends Left 28.000
Map "ctg1" Ends Right 58.000 Oldctg 2
Fp_number "E033O02"
Gel_number    203324
Bands  1239771 31
Exact_match_to_cosmid "b0026K13"
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0033O15"
Map "ctg1" Ends Left 149.000
Map "ctg1" Ends Right 171.000 Oldctg 2
Fp_number "E033O15"
Gel_number    203314
Bands  1240083 23
Exact_match_to_cosmid "b0096L16"
Positive_OVERGO "SOG1225" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0034B22"
Map "ctg1" Ends Left 216.000
Map "ctg1" Ends Right 239.000 Oldctg 2
Fp_number "E034B22"
Gel_number    203441
Bands  1241989 24
Approximate_match_to_cosmid "a0083M05"
Positive_STS "OJ000207_10" 
Positive_OVERGO "SOG1176" 
Positive_OVERGO "SOG1774" 
Positive_OVERGO "SOG1816" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0035D11"
Map "ctg1" Ends Left 254.000
Map "ctg1" Ends Right 279.000 Oldctg 2
Fp_number "E035D11"
Gel_number    203531
Bands  1251090 26
Approximate_match_to_cosmid "b0006M06"
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0035E17"
Map "ctg1" Ends Left 484.000
Map "ctg1" Ends Right 503.000 Oldctg 2
Fp_number "E035E17"
Gel_number    203512
Bands  1251790 20
Approximate_match_to_cosmid "b0001O16"
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0035G22"
Map "ctg1" Ends Left 238.000
Map "ctg1" Ends Right 268.000 Oldctg 2
Fp_number "E035G22"
Gel_number    203522
Bands  1252956 31
Approximate_match_to_cosmid "a0083M16"
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0036D04"
Map "ctg1" Ends Left 515.000
Map "ctg1" Ends Right 536.000 Oldctg 2
Fp_number "E036D04"
Gel_number    203641
Bands  1259441 22
Approximate_match_to_cosmid "b0032A21"
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 19 29 
Modified_date 102 2 1 22 48 
  
Clone : "b0036O09"
Map "ctg1" Ends Left 374.000
Map "ctg1" Ends Right 402.000 Oldctg 2
Fp_number "E036O09"
Gel_number    203614
Bands  1265631 29
Approximate_match_to_cosmid "b0093C15"
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0037K01"
Map "ctg1" Ends Left 388.000
Map "ctg1" Ends Right 403.000 Oldctg 2
Fp_number "E037K01"
Gel_number    203713
Bands  1271360 16
Approximate_match_to_cosmid "b0093C15"
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0037K04"
Map "ctg1" Ends Left 218.000
Map "ctg1" Ends Right 247.000 Oldctg 2
Fp_number "E037K04"
Gel_number    203723
Bands  1271428 30
Positive_STS "S1001" 
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0038B06"
Map "ctg1" Ends Left 159.000
Map "ctg1" Ends Right 180.000 Oldctg 2
Fp_number "E038B06"
Gel_number    203841
Bands  1274951 22
Approximate_match_to_cosmid "a0061C05"
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 19 29 
Modified_date 102 2 1 22 48 
  
Clone : "b0039F01"
Map "ctg1" Ends Left 250.000
Map "ctg1" Ends Right 277.000 Oldctg 2
Fp_number "E039F01"
Gel_number    203932
Bands  1285003 28
Creation_date 100 2 18 18 18 
Modified_date 101 4 11 16 56 
  
Clone : "b0039P22"
Map "ctg1" Ends Left 485.000
Map "ctg1" Ends Right 505.000 Oldctg 2
Fp_number "E039P22"
Gel_number    203944
Bands  1291198 21
Positive_OVERGO "SOG1745" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0040B06"
Map "ctg1" Ends Left 544.000
Map "ctg1" Ends Right 569.000 Oldctg 2
Fp_number "E040B06"
Gel_number    204041
Bands  1291886 26
Approximate_match_to_cosmid "a0063H14"
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0040F18"
Map "ctg1" Ends Left 4.000
Map "ctg1" Ends Right 36.000 Oldctg 2
Fp_number "E040F18"
Gel_number    204042
Bands  1294331 33
Positive_STS "OJ000323_02" 
Positive_STS "OJ990915_01" 
Creation_date 99 11 12 19 29 
Modified_date 102 2 1 22 48 
  
Clone : "b0040H01"
Map "ctg1" Ends Left 484.000
Map "ctg1" Ends Right 504.000 Oldctg 2
Fp_number "E040H01"
Gel_number    204032
Bands  1295099 21
Approximate_match_to_cosmid "b0001O16"
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0040I02"
Map "ctg1" Ends Left 33.000
Map "ctg1" Ends Right 65.000 Oldctg 2
Fp_number "E040I02"
Gel_number    204023
Bands  1295698 33
Approximate_match_to_cosmid "b0065P01"
Positive_STS "42D18r" 
Creation_date 99 11 12 19 29 
Modified_date 101 5 9 11 19 
  
Clone : "b0040M10"
Map "ctg1" Ends Left 506.000
Map "ctg1" Ends Right 533.000 Oldctg 2
Fp_number "E040M10"
Gel_number    204024
Bands  1298080 28
Approximate_match_to_cosmid "b0002J03"
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 19 29 
Modified_date 102 2 1 22 48 
  
Clone : "b0041L18"
Map "ctg1" Ends Left 159.000
Map "ctg1" Ends Right 180.000 Oldctg 2
Fp_number "E041L18"
Gel_number    204143
Bands  1305398 22
Approximate_match_to_cosmid "a0061C05"
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0043I08"
Map "ctg1" Ends Left 238.000
Map "ctg1" Ends Right 269.000 Oldctg 2
Fp_number "E043I08"
Gel_number    204323
Bands  1319806 32
Approximate_match_to_cosmid "a0083M16"
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Creation_date 99 11 12 19 29 
Modified_date 102 2 1 22 48 
  
Clone : "b0044E16"
Map "ctg1" Ends Left 19.000
Map "ctg1" Ends Right 46.000 Oldctg 2
Fp_number "E044E16"
Gel_number    204422
Bands  1326029 28
Positive_STS "OJ990915_01" 
Creation_date 99 11 12 19 29 
Modified_date 102 2 1 22 48 
  
Clone : "b0044G05"
Map "ctg1" Ends Left 102.000
Map "ctg1" Ends Right 138.000 Oldctg 2
Fp_number "E044G05"
Gel_number    204412
Bands  1326890 37
Approximate_match_to_cosmid "b0091A24"
Positive_STS "OJ990412_10" 
Positive_STS "OJ991015_10" 
Positive_STS "OJ991018_02" 
Creation_date 99 11 12 19 29 
Modified_date 104 4 9 18 13 
  
Clone : "b0044H22"
Map "ctg1" Ends Left 89.000
Map "ctg1" Ends Right 123.000 Oldctg 2
Fp_number "E044H22"
Gel_number    204442
Bands  1327815 35
Positive_STS "OJ990412_10" 
Creation_date 99 11 12 19 29 
Modified_date 102 2 1 22 48 
  
Clone : "b0044K15"
Map "ctg1" Ends Left 422.000
Map "ctg1" Ends Right 456.000 Oldctg 2
Fp_number "E044K15"
Gel_number    204413
Bands  1329090 35
Approximate_match_to_cosmid "a0061L15"
Positive_STS "OJ000214_10" 
Positive_STS "OJ000214_13" 
Positive_STS "OJ990428_07" 
Positive_OVERGO "SOG1508" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0044M05"
Map "ctg1" Ends Left 32.000
Map "ctg1" Ends Right 62.000 Oldctg 2
Fp_number "E044M05"
Gel_number    204414
Bands  1329947 31
Approximate_match_to_cosmid "b0065P01"
Positive_STS "42D18r" 
Positive_STS "OJ990605_38" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0044N09"
Map "ctg1" Ends Left 543.000
Map "ctg1" Ends Right 569.000 Oldctg 2
Fp_number "E044N09"
Gel_number    204434
Bands  1330491 27
Approximate_match_to_cosmid "b0083H05"
Positive_STS "OJ000251_05" 
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 19 29 
Modified_date 102 2 1 22 48 
  
Clone : "b0044P03"
Map "ctg1" Ends Left 463.000
Map "ctg1" Ends Right 490.000 Oldctg 2
Fp_number "E044P03"
Gel_number    204434
Bands  1331453 28
Positive_STS "OJ990428_07" 
Positive_STS "OJ991210_12" 
Positive_STS "OJ991215_12" 
Creation_date 99 11 12 19 29 
Modified_date 102 2 1 22 48 
  
Clone : "b0044P13"
Map "ctg1" Ends Left 372.000
Map "ctg1" Ends Right 402.000 Oldctg 2
Fp_number "E044P13"
Gel_number    204434
Bands  1331670 31
Approximate_match_to_cosmid "a0049H15"
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0045F08"
Map "ctg1" Ends Left 369.000
Map "ctg1" Ends Right 404.000 Oldctg 2
Fp_number "E045F08"
Gel_number    204542
Bands  1334453 36
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 56 
  
Clone : "b0045P08"
Map "ctg1" Ends Left 26.000
Map "ctg1" Ends Right 60.000 Oldctg 2
Fp_number "E045P08"
Gel_number    204544
Bands  1339300 35
Positive_OVERGO "SOG2244" 
Positive_STS "42D18r" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 28 17 14 
  
Clone : "b0046G04"
Map "ctg1" Ends Left 284.000
Map "ctg1" Ends Right 310.000 Oldctg 2
Fp_number "E046G04"
Gel_number    204622
Bands  1342953 27
Approximate_match_to_cosmid "b0007H05"
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0046K18"
Map "ctg1" Ends Left 317.000
Map "ctg1" Ends Right 347.000 Oldctg 2
Fp_number "E046K18"
Gel_number    204623
Bands  1345696 31
Positive_OVERGO "SOG0657" 
Creation_date 100 2 18 18 18 
Modified_date 103 4 22 10 21 
  
Clone : "b0046O20"
Map "ctg1" Ends Left 600.000
Map "ctg1" Ends Right 630.000 Oldctg 2
Fp_number "E046O20"
Gel_number    204624
Bands  1347881 31
Approximate_match_to_cosmid "b0033I06"
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0047A11"
Map "ctg1" Ends Left 278.000
Map "ctg1" Ends Right 301.000 Oldctg 2
Fp_number "E047A11"
Gel_number    204711
Bands  1348820 24
Positive_OVERGO "SOG0307" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0048G11"
Map "ctg1" Ends Left 484.000
Map "ctg1" Ends Right 502.000 Oldctg 2
Fp_number "E048G11"
Gel_number    204812
Bands  1360797 19
Positive_OVERGO "SOG1745" 
Positive_Probe "PRC0214" 
Creation_date 99 11 12 19 29 
Modified_date 103 4 22 10 21 
  
Clone : "b0048H12"
Map "ctg1" Ends Left 300.000
Map "ctg1" Ends Right 321.000 Oldctg 2
Fp_number "E048H12"
Gel_number    204842
Bands  1361434 22
Approximate_match_to_cosmid "b0062F24"
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0048H24"
Map "ctg1" Ends Left 112.000
Map "ctg1" Ends Right 143.000 Oldctg 2
Fp_number "E048H24"
Gel_number    204842
Bands  1361692 32
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0049H13"
Map "ctg1" Ends Left 260.000
Map "ctg1" Ends Right 282.000 Oldctg 2
Fp_number "E049H13"
Gel_number    204932
Bands  1370309 23
Creation_date 99 11 12 19 29 
Modified_date 101 4 11 16 57 
  
Clone : "b0050B15"
Map "ctg1" Ends Left 370.000
Map "ctg1" Ends Right 401.000 Oldctg 2
Fp_number "E050B15"
Gel_number    205031
Bands  1376001 32
Approximate_match_to_cosmid "a0049H15"
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 12 22 57 
Modified_date 102 2 1 22 48 
  
Clone : "b0050H04"
Map "ctg1" Ends Left 425.000
Map "ctg1" Ends Right 456.000 Oldctg 2
Fp_number "E050H04"
Gel_number    205042
Bands  1378959 32
Approximate_match_to_cosmid "b0057J05"
Positive_STS "OJ000214_10" 
Positive_STS "OJ000214_13" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991210_12" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG0389" 
Positive_OVERGO "SOG1508" 
Creation_date 99 11 12 22 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0051D10"
Map "ctg1" Ends Left 497.000
Map "ctg1" Ends Right 514.000 Oldctg 2
Fp_number "E051D10"
Gel_number    205141
Bands  1385709 18
Positive_STS "OJ990820_14" 
Positive_OVERGO "SOG2238" 
Creation_date 99 11 12 22 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0051N14"
Map "ctg1" Ends Left 254.000
Map "ctg1" Ends Right 279.000 Oldctg 2
Fp_number "E051N14"
Gel_number    205144
Bands  1390764 26
Positive_OVERGO "SOG1401" 
Creation_date 99 11 12 22 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0052B16"
Map "ctg1" Ends Left 515.000
Map "ctg1" Ends Right 533.000 Oldctg 2
Fp_number "E052B16"
Gel_number    205241
Bands  1392594 19
Exact_match_to_cosmid "b0030E04"
Creation_date 100 2 18 18 18 
Modified_date 101 4 11 16 57 
  
Clone : "b0052K20"
Map "ctg1" Ends Left 147.000
Map "ctg1" Ends Right 175.000 Oldctg 2
Fp_number "E052K20"
Gel_number    205223
Bands  1397544 29
Positive_OVERGO "SOG0127" 
Positive_OVERGO "SOG1225" 
Creation_date 100 2 18 18 18 
Modified_date 103 4 22 10 21 
  
Clone : "b0053P10"
Map "ctg1" Ends Left 219.000
Map "ctg1" Ends Right 236.000 Oldctg 2
Fp_number "E053P10"
Gel_number    205344
Bands  1408007 18
Exact_match_to_cosmid "b0037K04"
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Positive_OVERGO "SOG1774" 
Creation_date 99 11 12 22 58 
Modified_date 103 4 22 10 21 
  
Clone : "b0053P12"
Map "ctg1" Ends Left 369.000
Map "ctg1" Ends Right 406.000 Oldctg 2
Fp_number "E053P12"
Gel_number    205344
Bands  1408049 38
Positive_STS "OJ000221_13" 
Positive_STS "OJ000350_20" 
Creation_date 99 11 12 22 58 
Modified_date 102 2 1 22 48 
  
Clone : "b0054A15"
Map "ctg1" Ends Left 484.000
Map "ctg1" Ends Right 504.000 Oldctg 2
Fp_number "E054A15"
Gel_number    205411
Bands  1408710 21
Exact_match_to_cosmid "b0001O16"
Creation_date 99 11 12 22 58 
Modified_date 101 4 11 16 57 
  
Clone : "b0057E10"
Map "ctg1" Ends Left 604.000
Map "ctg1" Ends Right 639.000 Oldctg 2
Fp_number "E057E10"
Gel_number    205722
Bands  1432200 36
Positive_OVERGO "SOG0252" 
Creation_date 99 11 12 22 58 
Modified_date 103 4 22 10 21 
  
Clone : "b0057J05"
Map "ctg1" Ends Left 414.000
Map "ctg1" Ends Right 452.000 Oldctg 2
Fp_number "E057J05"
Gel_number    205733
Bands  1434710 39
Positive_OVERGO "SOG0389" 
Positive_OVERGO "SOG1508" 
Creation_date 99 11 12 22 58 
Modified_date 103 4 22 10 21 
  
Clone : "b0057P12"
Map "ctg1" Ends Left 96.000
Map "ctg1" Ends Right 121.000 Oldctg 2
Fp_number "E057P12"
Gel_number    205744
Bands  1437870 26
Approximate_match_to_cosmid "b0044H22"
Positive_STS "OJ991015_10" 
Creation_date 99 11 12 22 58 
Modified_date 102 2 1 22 48 
  
Clone : "b0058B12"
Map "ctg1" Ends Left 508.000
Map "ctg1" Ends Right 533.000 Oldctg 2
Fp_number "E058B12"
Gel_number    205841
Bands  1438797 26
Approximate_match_to_cosmid "b0002J03"
Positive_STS "OJ990713_06" 
Creation_date 99 11 12 22 58 
Modified_date 102 2 1 22 48 
  
Clone : "b0058D05"
Map "ctg1" Ends Left 426.000
Map "ctg1" Ends Right 461.000 Oldctg 2
Fp_number "E058D05"
Gel_number    205831
Bands  1439861 36
Creation_date 99 11 12 22 58 
Modified_date 101 4 11 16 56 
  
Clone : "b0058N15"
Map "ctg1" Ends Left 109.000
Map "ctg1" Ends Right 138.000 Oldctg 2
Fp_number "E058N15"
Gel_number    205834
Bands  1444949 30
Approximate_match_to_cosmid "a0018B22"
Positive_STS "OJ990412_10" 
Creation_date 99 11 12 22 58 
Modified_date 102 2 1 22 48 
  
Clone : "b0059H03"
Map "ctg1" Ends Left 284.000
Map "ctg1" Ends Right 301.000 Oldctg 2
Fp_number "E059H03"
Gel_number    205932
Bands  1449650 18
Creation_date 99 11 12 22 58 
Modified_date 101 4 11 16 56 
  
Clone : "b0059I06"
Map "ctg1" Ends Left 117.000
Map "ctg1" Ends Right 147.000 Oldctg 2
Fp_number "E059I06"
Gel_number    205923
Bands  1449993 31
Creation_date 99 11 12 22 58 
Modified_date 99 11 12 23 38 
  
Clone : "b0060G19"
Map "ctg1" Ends Left 155.000
Map "ctg1" Ends Right 180.000 Oldctg 2
Fp_number "E060G19"
Gel_number    206012
Bands  1456508 26
Approximate_match_to_cosmid "a0061C05"
Creation_date 99 11 12 22 58 
Modified_date 101 4 11 16 57 
  
Clone : "b0060I06"
Map "ctg1" Ends Left 149.000
Map "ctg1" Ends Right 176.000 Oldctg 2
Fp_number "E060I06"
Gel_number    206023
Bands  1457190 28
Positive_STS "OJ000301_13" 
Positive_STS "OJ990407_02" 
Positive_OVERGO "SOG1670" 
Creation_date 99 11 12 22 58 
Modified_date 103 4 22 10 21 
  
Clone : "b0062F24"
Map "ctg1" Ends Left 292.000
Map "ctg1" Ends Right 320.000 Oldctg 2
Fp_number "E062F24"
Gel_number    206242
Bands  1472133 29
Creation_date 99 11 12 22 58 
Modified_date 101 4 11 16 57 
  
Clone : "b0062O20"
Map "ctg1" Ends Left 453.000
Map "ctg1" Ends Right 484.000 Oldctg 2
Fp_number "E062O20"
Gel_number    206224
Bands  1477118 32
Approximate_match_to_cosmid "b0006L19"
Creation_date 99 11 12 22 58 
Modified_date 101 4 11 16 57 
  
Clone : "b0063D23"
Map "ctg1" Ends Left 615.000
Map "ctg1" Ends Right 643.000 Oldctg 2
Fp_number "E063D23"
Gel_number    206331
Bands  1479687 29
Exact_match_to_cosmid "b0005L08"
Creation_date 99 11 12 22 58 
Modified_date 101 4 11 16 57 
  
Clone : "b0063E10"
Map "ctg1" Ends Left 161.000
Map "ctg1" Ends Right 179.000 Oldctg 2
Fp_number "E063E10"
Gel_number    206322
Bands  1479942 19
Approximate_match_to_cosmid "a0061C05"
Positive_STS "OJ990407_02" 
Creation_date 99 11 12 22 58 
Modified_date 102 2 1 22 48 
  
Clone : "b0063H06"
Map "ctg1" Ends Left 515.000
Map "ctg1" Ends Right 536.000 Oldctg 2
Fp_number "E063H06"
Gel_number    206342
Bands  1481490 22
Exact_match_to_cosmid "b0032O15"
Creation_date 99 11 12 22 58 
Modified_date 101 4 11 16 57 
  
Clone : "b0063M13"
Map "ctg1" Ends Left 62.000
Map "ctg1" Ends Right 89.000 Oldctg 2
Fp_number "E063M13"
Gel_number    206314
Bands  1484095 28
Approximate_match_to_cosmid "a0082H14"
Positive_STS "OJ990605_38" 
Positive_OVERGO "SOG1344" 
Creation_date 99 11 12 22 58 
Modified_date 103 4 22 10 21 
  
Clone : "b0064G15"
Map "ctg1" Ends Left 602.000
Map "ctg1" Ends Right 639.000 Oldctg 2
Fp_number "E064G15"
Gel_number    206412
Bands  1489389 38
Creation_date 100 2 18 18 19 
Modified_date 101 4 11 16 56 
  
Clone : "b0065E14"
Map "ctg1" Ends Left 107.000
Map "ctg1" Ends Right 144.000 Oldctg 2
Fp_number "E065E14"
Gel_number    206522
Bands  1496264 38
Approximate_match_to_cosmid "a0051O20"
Positive_OVERGO "SOG0961" 
Creation_date 99 11 12 22 58 
Modified_date 103 4 22 10 21 
  
Clone : "b0065F10"
Map "ctg1" Ends Left 319.000
Map "ctg1" Ends Right 339.000 Oldctg 2
Fp_number "E065F10"
Gel_number    206542
Bands  1496711 21
Approximate_match_to_cosmid "a0060H05"
Creation_date 99 11 12 22 58 
Modified_date 101 4 11 16 57 
  
Clone : "b0065H04"
Map "ctg1" Ends Left 53.000
Map "ctg1" Ends Right 84.000 Oldctg 2
Fp_number "E065H04"
Gel_number    206542
Bands  1497505 32
Approximate_match_to_cosmid "b0008G08"
Creation_date 99 11 12 22 58 
Modified_date 101 4 11 16 57 
  
Clone : "b0065P01"
Map "ctg1" Ends Left 32.000
Map "ctg1" Ends Right 76.000 Oldctg 2
Fp_number "E065P01"
Gel_number    206534
Bands  1501474 45
Positive_OVERGO "SOG2244" 
Creation_date 100 2 18 18 19 
Modified_date 103 4 22 10 21 
  
Clone : "b0066F04"
Map "ctg1" Ends Left 473.000
Map "ctg1" Ends Right 501.000 Oldctg 2
Fp_number "E066F04"
Gel_number    206642
Bands  1504476 29
Positive_STS "OJ990428_07" 
Positive_STS "OJ991210_12" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 12 22 58 
Modified_date 103 4 22 10 21 
  
Clone : "b0066J19"
Map "ctg1" Ends Left 222.000
Map "ctg1" Ends Right 255.000 Oldctg 2
Fp_number "E066J19"
Gel_number    206633
Bands  1506843 34
Positive_OVERGO "SOG1774" 
Creation_date 99 11 12 22 58 
Modified_date 103 4 22 10 21 
  
Clone : "b0068A07"
Map "ctg1" Ends Left 463.000
Map "ctg1" Ends Right 490.000 Oldctg 2
Fp_number "E068A07"
Gel_number    206811
Bands  1517437 28
Approximate_match_to_cosmid "b0044P03"
Positive_OVERGO "SOG1200" 
Creation_date 100 7 8 18 35 
Modified_date 103 4 22 10 21 
  
Clone : "b0069J02"
Map "ctg1" Ends Left 515.000
Map "ctg1" Ends Right 534.000 Oldctg 2
Fp_number "E069J02"
Gel_number    206943
Bands  1529281 20
Approximate_match_to_cosmid "a0003C15"
Creation_date 100 2 18 18 19 
Modified_date 101 4 11 16 57 
  
Clone : "b0069M06"
Map "ctg1" Ends Left 387.000
Map "ctg1" Ends Right 420.000 Oldctg 2
Fp_number "E069M06"
Gel_number    206924
Bands  1530818 34
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Positive_OVERGO "SOG0223" 
Creation_date 99 11 12 22 58 
Modified_date 103 4 22 10 21 
  
Clone : "b0070B17"
Map "ctg1" Ends Left 4.000
Map "ctg1" Ends Right 37.000 Oldctg 2
Fp_number "E070B17"
Gel_number    207031
Bands  1533535 34
Creation_date 100 2 18 18 19 
Modified_date 101 4 11 16 55 
  
Clone : "b0070C06"
Map "ctg1" Ends Left 201.000
Map "ctg1" Ends Right 218.000 Oldctg 2
Fp_number "E070C06"
Gel_number    207021
Bands  1533806 18
Approximate_match_to_cosmid "a0002N24"
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Creation_date 99 11 13 0 57 
Modified_date 102 2 1 22 48 
  
Clone : "b0071G06"
Map "ctg1" Ends Left 251.000
Map "ctg1" Ends Right 277.000 Oldctg 2
Fp_number "E071G06"
Gel_number    207122
Bands  1544433 27
Approximate_match_to_cosmid "b0003G18"
Creation_date 100 2 18 18 19 
Modified_date 101 4 11 16 57 
  
Clone : "b0072A10"
Map "ctg1" Ends Left 232.000
Map "ctg1" Ends Right 257.000 Oldctg 2
Fp_number "E072A10"
Gel_number    207221
Bands  1549409 26
Positive_OVERGO "SOG1176" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0072G05"
Map "ctg1" Ends Left 354.000
Map "ctg1" Ends Right 386.000 Oldctg 2
Fp_number "E072G05"
Gel_number    207212
Bands  1552101 33
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 13 0 57 
Modified_date 102 2 1 22 48 
  
Clone : "b0072N12"
Map "ctg1" Ends Left 504.000
Map "ctg1" Ends Right 529.000 Oldctg 2
Fp_number "E072N12"
Gel_number    207244
Bands  1556347 26
Approximate_match_to_cosmid "b0002J03"
Creation_date 99 11 13 0 57 
Modified_date 101 4 11 16 57 
  
Clone : "b0073F02"
Map "ctg1" Ends Left 569.000
Map "ctg1" Ends Right 599.000 Oldctg 2
Fp_number "E073F02"
Gel_number    207342
Bands  1558329 31
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0073N09"
Map "ctg1" Ends Left 238.000
Map "ctg1" Ends Right 262.000 Oldctg 2
Fp_number "E073N09"
Gel_number    207334
Bands  1562579 25
Approximate_match_to_cosmid "a0083M16"
Creation_date 99 11 13 0 57 
Modified_date 101 4 11 16 57 
  
Clone : "b0074B19"
Map "ctg1" Ends Left 29.000
Map "ctg1" Ends Right 59.000 Oldctg 2
Fp_number "E074B19"
Gel_number    207431
Bands  1565322 31
Approximate_match_to_cosmid "b0095L23"
Positive_OVERGO "SOG0961" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0074F15"
Map "ctg1" Ends Left 18.000
Map "ctg1" Ends Right 48.000 Oldctg 2
Fp_number "E074F15"
Gel_number    207432
Bands  1567753 31
Approximate_match_to_cosmid "a0060C20"
Creation_date 99 11 13 0 57 
Modified_date 101 4 11 16 57 
  
Clone : "b0074I20"
Map "ctg1" Ends Left 344.000
Map "ctg1" Ends Right 369.000 Oldctg 2
Fp_number "E074I20"
Gel_number    207423
Bands  1569785 26
Exact_match_to_cosmid "a0089D17"
Positive_OVERGO "SOG0657" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0074P13"
Map "ctg1" Ends Left 179.000
Map "ctg1" Ends Right 221.000 Oldctg 2
Fp_number "E074P13"
Gel_number    207434
Bands  1574002 43
Positive_STS "OJ990407_02" 
Creation_date 99 11 13 0 57 
Modified_date 102 2 1 22 48 
  
Clone : "b0074P17"
Map "ctg1" Ends Left 317.000
Map "ctg1" Ends Right 346.000 Oldctg 2
Fp_number "E074P17"
Gel_number    207434
Bands  1574133 30
Approximate_match_to_cosmid "b0046K18"
Creation_date 99 11 13 0 57 
Modified_date 101 5 9 11 19 
  
Clone : "b0076P03"
Map "ctg1" Ends Left 93.000
Map "ctg1" Ends Right 127.000 Oldctg 2
Fp_number "E076P03"
Gel_number    207634
Bands  1590425 35
Creation_date 100 2 18 18 20 
Modified_date 100 2 23 12 7 
  
Clone : "b0077L14"
Map "ctg1" Ends Left 484.000
Map "ctg1" Ends Right 503.000 Oldctg 2
Fp_number "E077L14"
Gel_number    207743
Bands  1596644 20
Approximate_match_to_cosmid "b0001O16"
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0078C03"
Map "ctg1" Ends Left 534.000
Map "ctg1" Ends Right 563.000 Oldctg 2
Fp_number "E078C03"
Gel_number    207811
Bands  1599910 30
Approximate_match_to_cosmid "b0088P23"
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0078C04"
Map "ctg1" Ends Left 356.000
Map "ctg1" Ends Right 388.000 Oldctg 2
Fp_number "E078C04"
Gel_number    207821
Bands  1599940 33
Approximate_match_to_cosmid "a0073L24"
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0078G10"
Map "ctg1" Ends Left 1.000
Map "ctg1" Ends Right 31.000 Oldctg 2
Fp_number "E078G10"
Gel_number    207822
Bands  1602367 31
Exact_match_to_cosmid "b0081H12"
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0079E11"
Map "ctg1" Ends Left 117.000
Map "ctg1" Ends Right 146.000 Oldctg 2
Fp_number "E079E11"
Gel_number    207912
Bands  1609875 30
Approximate_match_to_cosmid "a0066I06"
Positive_OVERGO "SOG0961" 
Creation_date 100 2 18 18 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0079F04"
Map "ctg1" Ends Left 439.000
Map "ctg1" Ends Right 465.000 Oldctg 2
Fp_number "E079F04"
Gel_number    207942
Bands  1610280 27
Approximate_match_to_cosmid "b0031K18"
Positive_OVERGO "SOG1200" 
Positive_OVERGO "SOG1508" 
Creation_date 100 2 18 18 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0079F11"
Map "ctg1" Ends Left 439.000
Map "ctg1" Ends Right 471.000 Oldctg 2
Fp_number "E079F11"
Gel_number    207932
Bands  1610420 33
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0079K07"
Map "ctg1" Ends Left 312.000
Map "ctg1" Ends Right 334.000 Oldctg 2
Fp_number "E079K07"
Gel_number    207913
Bands  1613317 23
Approximate_match_to_cosmid "a0058C01"
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0079L02"
Map "ctg1" Ends Left 320.000
Map "ctg1" Ends Right 350.000 Oldctg 2
Fp_number "E079L02"
Gel_number    207943
Bands  1613837 31
Approximate_match_to_cosmid "a0023L15"
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0080E04"
Map "ctg1" Ends Left 362.000
Map "ctg1" Ends Right 395.000 Oldctg 2
Fp_number "E080E04"
Gel_number    208022
Bands  1618991 34
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 56 
  
Clone : "b0080J15"
Map "ctg1" Ends Left 483.000
Map "ctg1" Ends Right 504.000 Oldctg 2
Fp_number "E080J15"
Gel_number    208033
Bands  1622338 22
Positive_OVERGO "SOG1745" 
Creation_date 100 2 18 18 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0080M24"
Map "ctg1" Ends Left 251.000
Map "ctg1" Ends Right 277.000 Oldctg 2
Fp_number "E080M24"
Gel_number    208024
Bands  1624239 27
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 56 
  
Clone : "b0080P18"
Map "ctg1" Ends Left 169.000
Map "ctg1" Ends Right 201.000 Oldctg 2
Fp_number "E080P18"
Gel_number    208044
Bands  1625931 33
Creation_date 100 2 18 18 20 
Modified_date 101 5 9 11 19 
  
Clone : "b0081E09"
Map "ctg1" Ends Left 484.000
Map "ctg1" Ends Right 500.000 Oldctg 2
Fp_number "E081E09"
Gel_number    208112
Bands  1628690 17
Exact_match_to_cosmid "b0081N07"
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0081F15"
Map "ctg1" Ends Left 175.000
Map "ctg1" Ends Right 211.000 Oldctg 2
Fp_number "E081F15"
Gel_number    208132
Bands  1629477 37
Approximate_match_to_cosmid "b0074P13"
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0081G19"
Map "ctg1" Ends Left 3.000
Map "ctg1" Ends Right 31.000 Oldctg 2
Fp_number "E081G19"
Gel_number    208112
Bands  1630233 29
Approximate_match_to_cosmid "b0092L16"
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0081H12"
Map "ctg1" Ends Left 0.000
Map "ctg1" Ends Right 32.000 Oldctg 2
Fp_number "E081H12"
Gel_number    208142
Bands  1630647 33
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0081J21"
Map "ctg1" Ends Left 119.000
Map "ctg1" Ends Right 146.000 Oldctg 2
Fp_number "E081J21"
Gel_number    208133
Bands  1632152 28
Approximate_match_to_cosmid "a0088C05"
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0081M20"
Map "ctg1" Ends Left 560.000
Map "ctg1" Ends Right 592.000 Oldctg 2
Fp_number "E081M20"
Gel_number    208124
Bands  1634059 33
Positive_OVERGO "SOG0313" 
Positive_OVERGO "SOG0316" 
Creation_date 100 2 18 18 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0081M22"
Map "ctg1" Ends Left 476.000
Map "ctg1" Ends Right 499.000 Oldctg 2
Fp_number "E081M22"
Gel_number    208124
Bands  1634092 24
Approximate_match_to_cosmid "b0066F04"
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 57 
  
Clone : "b0081N07"
Map "ctg1" Ends Left 481.000
Map "ctg1" Ends Right 504.000 Oldctg 2
Fp_number "E081N07"
Gel_number    208134
Bands  1634301 24
Positive_OVERGO "SOG1200" 
Creation_date 100 2 18 18 20 
Modified_date 103 4 22 10 21 
  
Clone : "b0082F04"
Map "ctg1" Ends Left 4.000
Map "ctg1" Ends Right 34.000 Oldctg 2
Fp_number "E082F04"
Gel_number    208242
Bands  1638867 31
Approximate_match_to_cosmid "a0070F12"
Positive_OVERGO "SOG0961" 
Creation_date 100 2 18 18 21 
Modified_date 103 4 22 10 21 
  
Clone : "b0082H15"
Map "ctg1" Ends Left 523.000
Map "ctg1" Ends Right 551.000 Oldctg 2
Fp_number "E082H15"
Gel_number    208232
Bands  1640439 29
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 57 
  
Clone : "b0082I08"
Map "ctg1" Ends Left 576.000
Map "ctg1" Ends Right 604.000 Oldctg 2
Fp_number "E082I08"
Gel_number    208223
Bands  1640796 29
Creation_date 100 2 18 18 20 
Modified_date 101 4 11 16 56 
  
Clone : "b0083C17"
Map "ctg1" Ends Left 237.000
Map "ctg1" Ends Right 268.000 Oldctg 2
Fp_number "E083C17"
Gel_number    208311
Bands  1646756 32
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 56 
  
Clone : "b0083F19"
Map "ctg1" Ends Left 44.000
Map "ctg1" Ends Right 73.000 Oldctg 2
Fp_number "E083F19"
Gel_number    208332
Bands  1648183 30
Approximate_match_to_cosmid "b0065P01"
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 57 
  
Clone : "b0083H05"
Map "ctg1" Ends Left 543.000
Map "ctg1" Ends Right 569.000 Oldctg 2
Fp_number "E083H05"
Gel_number    208332
Bands  1648896 27
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 57 
  
Clone : "b0083L21"
Map "ctg1" Ends Left 305.000
Map "ctg1" Ends Right 333.000 Oldctg 2
Fp_number "E083L21"
Gel_number    208333
Bands  1651488 29
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 56 
  
Clone : "b0083O07"
Map "ctg1" Ends Left 37.000
Map "ctg1" Ends Right 67.000 Oldctg 2
Fp_number "E083O07"
Gel_number    208314
Bands  1653039 31
Approximate_match_to_cosmid "b0065P01"
Positive_OVERGO "SOG2244" 
Creation_date 100 2 18 18 21 
Modified_date 103 4 22 10 21 
  
Clone : "b0084D17"
Map "ctg1" Ends Left 318.000
Map "ctg1" Ends Right 345.000 Oldctg 2
Fp_number "E084D17"
Gel_number    208431
Bands  1656246 28
Approximate_match_to_cosmid "b0046K18"
Positive_OVERGO "SOG0657" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0084E17"
Map "ctg1" Ends Left 175.000
Map "ctg1" Ends Right 212.000 Oldctg 2
Fp_number "E084E17"
Gel_number    208412
Bands  1656869 38
Positive_STS "OJ000301_13" 
Creation_date 99 11 13 0 57 
Modified_date 102 2 1 22 48 
  
Clone : "b0084G04"
Map "ctg1" Ends Left 300.000
Map "ctg1" Ends Right 322.000 Oldctg 2
Fp_number "E084G04"
Gel_number    208422
Bands  1657728 23
Approximate_match_to_cosmid "a0093L07"
Positive_STS "OJ990503_27" 
Positive_STS "OJ991021_17" 
Creation_date 99 11 13 0 57 
Modified_date 102 2 1 22 48 
  
Clone : "b0084N19"
Map "ctg1" Ends Left 37.000
Map "ctg1" Ends Right 66.000 Oldctg 2
Fp_number "E084N19"
Gel_number    208434
Bands  1662416 30
Approximate_match_to_cosmid "b0095L23"
Positive_OVERGO "SOG2232" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0084N21"
Map "ctg1" Ends Left 427.000
Map "ctg1" Ends Right 456.000 Oldctg 2
Fp_number "E084N21"
Gel_number    208434
Bands  1662471 30
Approximate_match_to_cosmid "b0057J05"
Positive_STS "OJ000214_13" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1508" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0085B18"
Map "ctg1" Ends Left 447.000
Map "ctg1" Ends Right 474.000 Oldctg 2
Fp_number "E085B18"
Gel_number    208541
Bands  1664826 28
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 56 
  
Clone : "b0085C01"
Map "ctg1" Ends Left 555.000
Map "ctg1" Ends Right 577.000 Oldctg 2
Fp_number "E085C01"
Gel_number    208511
Bands  1664999 23
Approximate_match_to_cosmid "a0063H14"
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 57 
  
Clone : "b0085E02"
Map "ctg1" Ends Left 87.000
Map "ctg1" Ends Right 118.000 Oldctg 2
Fp_number "E085E02"
Gel_number    208522
Bands  1666285 32
Approximate_match_to_cosmid "a0082D09"
Positive_STS "OJ990412_10" 
Creation_date 99 11 13 0 57 
Modified_date 102 2 1 22 48 
  
Clone : "b0085J15"
Map "ctg1" Ends Left 577.000
Map "ctg1" Ends Right 604.000 Oldctg 2
Fp_number "E085J15"
Gel_number    208533
Bands  1669707 28
Positive_STS "OJ000301_05" 
Positive_OVERGO "SOG0279" 
Positive_OVERGO "SOG0948" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0086F12"
Map "ctg1" Ends Left 610.000
Map "ctg1" Ends Right 640.000 Oldctg 2
Fp_number "E086F12"
Gel_number    208642
Bands  1675115 31
Approximate_match_to_cosmid "b0005L08"
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 57 
  
Clone : "b0086F17"
Map "ctg1" Ends Left 150.000
Map "ctg1" Ends Right 177.000 Oldctg 2
Fp_number "E086F17"
Gel_number    208632
Bands  1675235 28
Positive_OVERGO "SOG1225" 
Creation_date 100 2 18 18 21 
Modified_date 103 4 22 10 21 
  
Clone : "b0087C20"
Map "ctg1" Ends Left 592.000
Map "ctg1" Ends Right 623.000 Oldctg 2
Fp_number "E087C20"
Gel_number    208721
Bands  1682563 32
Approximate_match_to_cosmid "a0091H17"
Positive_STS "OJ000321_15" 
Positive_STS "OJ000330_31" 
Creation_date 99 11 13 0 57 
Modified_date 102 2 1 22 48 
  
Clone : "b0087C23"
Map "ctg1" Ends Left 210.000
Map "ctg1" Ends Right 235.000 Oldctg 2
Fp_number "E087C23"
Gel_number    208711
Bands  1682645 26
Exact_match_to_cosmid "a0052N06"
Positive_OVERGO "SOG1816" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0087G24"
Map "ctg1" Ends Left 226.000
Map "ctg1" Ends Right 257.000 Oldctg 2
Fp_number "E087G24"
Gel_number    208722
Bands  1685217 32
Approximate_match_to_cosmid "a0070K16"
Creation_date 99 11 13 0 57 
Modified_date 101 4 11 16 57 
  
Clone : "b0087J21"
Map "ctg1" Ends Left 151.000
Map "ctg1" Ends Right 181.000 Oldctg 2
Fp_number "E087J21"
Gel_number    208733
Bands  1686952 31
Positive_STS "OJ990407_02" 
Positive_OVERGO "SOG1225" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0087M11"
Map "ctg1" Ends Left 460.000
Map "ctg1" Ends Right 487.000 Oldctg 2
Fp_number "E087M11"
Gel_number    208714
Bands  1688588 28
Positive_STS "OJ000214_13" 
Positive_STS "OJ990428_07" 
Positive_STS "OJ991215_12" 
Positive_OVERGO "SOG1200" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0087O07"
Map "ctg1" Ends Left 483.000
Map "ctg1" Ends Right 505.000 Oldctg 2
Fp_number "E087O07"
Gel_number    208714
Bands  1689706 23
Creation_date 99 11 13 0 57 
Modified_date 101 4 11 16 57 
  
Clone : "b0087O21"
Map "ctg1" Ends Left 415.000
Map "ctg1" Ends Right 449.000 Oldctg 2
Fp_number "E087O21"
Gel_number    208714
Bands  1690037 35
Approximate_match_to_cosmid "a0087L03"
Positive_OVERGO "SOG0223" 
Positive_OVERGO "SOG1508" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0088M23"
Map "ctg1" Ends Left 318.000
Map "ctg1" Ends Right 347.000 Oldctg 2
Fp_number "E088M23"
Gel_number    208814
Bands  1698762 30
Approximate_match_to_cosmid "b0046K18"
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 57 
  
Clone : "b0088P23"
Map "ctg1" Ends Left 534.000
Map "ctg1" Ends Right 567.000 Oldctg 2
Fp_number "E088P23"
Gel_number    208834
Bands  1700725 34
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 57 
  
Clone : "b0089C07"
Map "ctg1" Ends Left 36.000
Map "ctg1" Ends Right 66.000 Oldctg 2
Fp_number "E089C07"
Gel_number    208911
Bands  1702298 31
Approximate_match_to_cosmid "b0065P01"
Positive_OVERGO "SOG2244" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0090I01"
Map "ctg1" Ends Left 272.000
Map "ctg1" Ends Right 297.000 Oldctg 2
Fp_number "E090I01"
Gel_number    209013
Bands  1715433 26
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 56 
  
Clone : "b0090K10"
Map "ctg1" Ends Left 368.000
Map "ctg1" Ends Right 404.000 Oldctg 2
Fp_number "E090K10"
Gel_number    209023
Bands  1716859 37
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 56 
  
Clone : "b0090O14"
Map "ctg1" Ends Left 369.000
Map "ctg1" Ends Right 403.000 Oldctg 2
Fp_number "E090O14"
Gel_number    209024
Bands  1719367 35
Approximate_match_to_cosmid "a0049H15"
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 57 
  
Clone : "b0091A24"
Map "ctg1" Ends Left 99.000
Map "ctg1" Ends Right 139.000 Oldctg 2
Fp_number "E091A24"
Gel_number    209121
Bands  1720701 41
Positive_STS "OJ990412_10" 
Creation_date 99 11 13 0 57 
Modified_date 104 4 9 18 13 
  
Clone : "b0091B14"
Map "ctg1" Ends Left 103.000
Map "ctg1" Ends Right 140.000 Oldctg 2
Fp_number "E091B14"
Gel_number    209141
Bands  1721107 38
Approximate_match_to_cosmid "b0091A24"
Creation_date 99 11 13 0 57 
Modified_date 104 4 9 18 13 
  
Clone : "b0091L22"
Map "ctg1" Ends Left 229.000
Map "ctg1" Ends Right 261.000 Oldctg 2
Fp_number "E091L22"
Gel_number    209143
Bands  1727635 33
Creation_date 99 11 13 0 57 
Modified_date 101 4 11 16 57 
  
Clone : "b0092A02"
Map "ctg1" Ends Left 515.000
Map "ctg1" Ends Right 540.000 Oldctg 2
Fp_number "E092A02"
Gel_number    209221
Bands  1730275 26
Approximate_match_to_cosmid "b0032O15"
Creation_date 99 11 13 0 57 
Modified_date 101 4 11 16 57 
  
Clone : "b0092C14"
Map "ctg1" Ends Left 250.000
Map "ctg1" Ends Right 271.000 Oldctg 2
Fp_number "E092C14"
Gel_number    209221
Bands  1731811 22
Approximate_match_to_cosmid "a0087A15"
Positive_STS "OJ000317_34" 
Positive_STS "OJ990325_01" 
Creation_date 99 11 13 0 57 
Modified_date 102 2 1 22 48 
  
Clone : "b0092H03"
Map "ctg1" Ends Left 591.000
Map "ctg1" Ends Right 623.000 Oldctg 2
Fp_number "E092H03"
Gel_number    209232
Bands  1734730 33
Approximate_match_to_cosmid "a0091H17"
Positive_STS "OJ000321_15" 
Positive_STS "OJ000330_31" 
Creation_date 99 11 13 0 57 
Modified_date 102 2 1 22 48 
  
Clone : "b0092L16"
Map "ctg1" Ends Left 0.000
Map "ctg1" Ends Right 34.000 Oldctg 2
Fp_number "E092L16"
Gel_number    209243
Bands  1737668 35
Creation_date 99 11 13 0 57 
Modified_date 101 4 11 16 57 
  
Clone : "b0092L22"
Map "ctg1" Ends Left 371.000
Map "ctg1" Ends Right 404.000 Oldctg 2
Fp_number "E092L22"
Gel_number    209243
Bands  1737824 34
Approximate_match_to_cosmid "b0053P12"
Positive_STS "OJ000350_20" 
Positive_STS "OJ991201_11" 
Creation_date 99 11 13 0 57 
Modified_date 102 2 1 22 48 
  
Clone : "b0092N13"
Map "ctg1" Ends Left 146.000
Map "ctg1" Ends Right 173.000 Oldctg 2
Fp_number "E092N13"
Gel_number    209234
Bands  1738815 28
Positive_STS "OJ990407_02" 
Positive_OVERGO "SOG1225" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0093C15"
Map "ctg1" Ends Left 370.000
Map "ctg1" Ends Right 408.000 Oldctg 2
Fp_number "E093C15"
Gel_number    209311
Bands  1742105 39
Creation_date 99 11 13 0 57 
Modified_date 101 4 11 16 57 
  
Clone : "b0093I19"
Map "ctg1" Ends Left 306.000
Map "ctg1" Ends Right 333.000 Oldctg 2
Fp_number "E093I19"
Gel_number    209313
Bands  1746161 28
Positive_STS "OJ990503_27" 
Creation_date 99 11 13 0 57 
Modified_date 102 2 1 22 48 
  
Clone : "b0094A14"
Map "ctg1" Ends Left 229.000
Map "ctg1" Ends Right 260.000 Oldctg 2
Fp_number "E094A14"
Gel_number    209421
Bands  1751276 32
Approximate_match_to_cosmid "b0091L22"
Positive_STS "OJ000207_10" 
Positive_STS "OJ000306_03" 
Positive_STS "OJ990325_01" 
Creation_date 99 11 13 0 57 
Modified_date 102 2 1 22 48 
  
Clone : "b0094B10"
Map "ctg1" Ends Left 276.000
Map "ctg1" Ends Right 301.000 Oldctg 2
Fp_number "E094B10"
Gel_number    209441
Bands  1751777 26
Positive_OVERGO "SOG0307" 
Positive_OVERGO "SOG0961" 
Creation_date 100 2 18 18 21 
Modified_date 103 4 22 10 21 
  
Clone : "b0094D11"
Map "ctg1" Ends Left 256.000
Map "ctg1" Ends Right 281.000 Oldctg 2
Fp_number "E094D11"
Gel_number    209431
Bands  1753106 26
Positive_OVERGO "SOG1077" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0094L15"
Map "ctg1" Ends Left 178.000
Map "ctg1" Ends Right 218.000 Oldctg 2
Fp_number "E094L15"
Gel_number    209433
Bands  1758047 41
Approximate_match_to_cosmid "b0074P13"
Creation_date 99 11 13 0 57 
Modified_date 101 4 11 16 57 
  
Clone : "b0094O09"
Map "ctg1" Ends Left 150.000
Map "ctg1" Ends Right 175.000 Oldctg 2
Fp_number "E094O09"
Gel_number    209414
Bands  1759895 26
Approximate_match_to_cosmid "b0060I06"
Positive_OVERGO "SOG1225" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0095I21"
Map "ctg1" Ends Left 545.000
Map "ctg1" Ends Right 570.000 Oldctg 2
Fp_number "E095I21"
Gel_number    209513
Bands  1766183 26
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 57 
  
Clone : "b0095K22"
Map "ctg1" Ends Left 595.000
Map "ctg1" Ends Right 628.000 Oldctg 2
Fp_number "E095K22"
Gel_number    209523
Bands  1767469 34
Approximate_match_to_cosmid "a0091H17"
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 57 
  
Clone : "b0095L23"
Map "ctg1" Ends Left 28.000
Map "ctg1" Ends Right 62.000 Oldctg 2
Fp_number "E095L23"
Gel_number    209533
Bands  1768027 35
Creation_date 100 2 18 18 21 
Modified_date 101 4 11 16 57 
  
Clone : "b0096D16"
Map "ctg1" Ends Left 264.000
Map "ctg1" Ends Right 287.000 Oldctg 2
Fp_number "E096D16"
Gel_number    209641
Bands  1772858 24
Positive_OVERGO "SOG1450" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0096I21"
Map "ctg1" Ends Left 156.000
Map "ctg1" Ends Right 185.000 Oldctg 2
Fp_number "E096I21"
Gel_number    209613
Bands  1776037 30
Approximate_match_to_cosmid "a0061C05"
Creation_date 99 11 13 0 57 
Modified_date 101 4 11 16 57 
  
Clone : "b0096L08"
Map "ctg1" Ends Left 141.000
Map "ctg1" Ends Right 163.000 Oldctg 2
Fp_number "E096L08"
Gel_number    209643
Bands  1777565 23
Approximate_match_to_cosmid "a0095O20"
Positive_OVERGO "SOG0127" 
Positive_OVERGO "SOG1225" 
Positive_OVERGO "SOG1231" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0096L16"
Map "ctg1" Ends Left 148.000
Map "ctg1" Ends Right 172.000 Oldctg 2
Fp_number "E096L16"
Gel_number    209643
Bands  1777770 25
Positive_STS "OJ990407_02" 
Positive_OVERGO "SOG0127" 
Positive_OVERGO "SOG1225" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0096N17"
Map "ctg1" Ends Left 55.000
Map "ctg1" Ends Right 87.000 Oldctg 2
Fp_number "E096N17"
Gel_number    209634
Bands  1779108 33
Positive_OVERGO "SOG1344" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0096P10"
Map "ctg1" Ends Left 206.000
Map "ctg1" Ends Right 237.000 Oldctg 2
Fp_number "E096P10"
Gel_number    209644
Bands  1780284 32
Approximate_match_to_cosmid "a0052E04"
Positive_OVERGO "SOG1816" 
Creation_date 99 11 13 0 57 
Modified_date 103 4 22 10 21 
  
Clone : "b0097K12"
Map "ctg1" Ends Left 528.000
Map "ctg1" Ends Right 548.000 Oldctg 2
Gel_number    b1097B2
Bands  1787375 22
Creation_date 100 2 18 18 21 
Modified_date 101 8 24 13 54 
  
BAC : "b0099P02"
Map "ctg1" Ends Left 508.000
Map "ctg1" Ends Right 534.000 Oldctg 2
Gel_number    b1099D2
Bands  1805108 26
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 14 46 
  
BAC : "b0099P14"
Map "ctg1" Ends Left 15.000
Map "ctg1" Ends Right 46.000 Oldctg 2
Gel_number    b1099D2
Bands  1805281 31
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 14 46 
  
BAC : "b0101B08"
Map "ctg1" Ends Left 237.000
Map "ctg1" Ends Right 268.000 Oldctg 2
Gel_number    b1101D1
Bands  1808303 31
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 14 47 
  
BAC : "b0101C07"
Map "ctg1" Ends Left 506.000
Map "ctg1" Ends Right 535.000 Oldctg 2
Gel_number    b1101A1
Bands  1808754 29
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 14 48 
  
BAC : "b0101F04"
Map "ctg1" Ends Left 272.000
Map "ctg1" Ends Right 300.000 Oldctg 2
Gel_number    b1101D1
Bands  1810388 28
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 14 48 
  
BAC : "b0101H21"
Map "ctg1" Ends Left 85.000
Map "ctg1" Ends Right 121.000 Oldctg 2
Gel_number    b1101C1
Bands  1811808 36
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 14 49 
  
BAC : "b0101I17"
Map "ctg1" Ends Left 514.000
Map "ctg1" Ends Right 542.000 Oldctg 2
Gel_number    b1101A2
Bands  1812317 28
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 14 49 
  
BAC : "b0101K21"
Map "ctg1" Ends Left 55.000
Map "ctg1" Ends Right 86.000 Oldctg 2
Gel_number    b1101A2
Bands  1813574 31
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 14 50 
  
BAC : "b0101L23"
Map "ctg1" Ends Left 19.000
Map "ctg1" Ends Right 47.000 Oldctg 2
Gel_number    b1101C2
Bands  1814112 28
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 14 50 
  
BAC : "b0103I21"
Map "ctg1" Ends Left 264.000
Map "ctg1" Ends Right 288.000 Oldctg 2
Gel_number    b1103A2
Bands  1823739 24
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 14 55 
  
BAC : "b0104K09"
Map "ctg1" Ends Left 407.000
Map "ctg1" Ends Right 439.000 Oldctg 2
Gel_number    b1104A2
Bands  1829559 32
Positive_OVERGO "SOG0223" 
Creation_date 101 8 24 13 54 
Modified_date 103 4 22 10 21 
  
BAC : "b0105G23"
Map "ctg1" Ends Left 179.000
Map "ctg1" Ends Right 221.000 Oldctg 2
Gel_number    b1105A1
Bands  1834073 42
Creation_date 101 10 3 11 41 
Modified_date 101 10 3 11 45 
  
BAC : "b0105K06"
Map "ctg1" Ends Left 463.000
Map "ctg1" Ends Right 487.000 Oldctg 2
Gel_number    b1105B2
Bands  1835240 24
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 14 59 
  
BAC : "b0106B21"
Map "ctg1" Ends Left 415.000
Map "ctg1" Ends Right 445.000 Oldctg 2
Gel_number    b1106C1
Bands  1837649 30
Positive_OVERGO "SOG0223" 
Positive_OVERGO "SOG0389" 
Creation_date 101 8 24 13 54 
Modified_date 103 4 22 10 21 
  
BAC : "b0108A10"
Map "ctg1" Ends Left 281.000
Map "ctg1" Ends Right 307.000 Oldctg 2
Gel_number    b1108B1
Bands  1842276 26
Creation_date 101 10 3 11 41 
Modified_date 101 10 3 11 46 
  
BAC : "b0108A22"
Map "ctg1" Ends Left 55.000
Map "ctg1" Ends Right 85.000 Oldctg 2
Gel_number    b1108B1
Bands  1842507 30
Creation_date 101 10 3 11 41 
Modified_date 101 10 3 11 46 
  
BAC : "b0108J15"
Map "ctg1" Ends Left 337.000
Map "ctg1" Ends Right 365.000 Oldctg 2
Gel_number    b1108C2
Bands  1846051 28
Positive_OVERGO "SOG0657" 
Creation_date 101 10 3 11 41 
Modified_date 103 4 22 10 21 
  
BAC : "b0108O23"
Map "ctg1" Ends Left 356.000
Map "ctg1" Ends Right 388.000 Oldctg 2
Gel_number    b1108A2
Bands  1848410 32
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 15 4 
  
BAC : "b0109D22"
Map "ctg1" Ends Left 414.000
Map "ctg1" Ends Right 443.000 Oldctg 2
Gel_number    b1109D1
Bands  1850230 29
Positive_OVERGO "SOG0389" 
Creation_date 101 8 24 13 54 
Modified_date 103 4 22 10 21 
  
BAC : "b0109M07"
Map "ctg1" Ends Left 35.000
Map "ctg1" Ends Right 66.000 Oldctg 2
Gel_number    b1109A2
Bands  1854093 31
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 15 6 
  
BAC : "b0111D13"
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Map "ctg1" Ends Right 318.000 Oldctg 2
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Bands  1859629 25
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 15 9 
  
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Gel_number    b1111A1
Bands  1860028 22
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 15 9 
  
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Map "ctg1" Ends Left 560.000
Map "ctg1" Ends Right 590.000 Oldctg 2
Gel_number    b1111D1
Bands  1860827 30
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 15 9 
  
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Bands  1863245 31
Creation_date 101 10 3 11 41 
Modified_date 101 10 3 11 49 
  
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Map "ctg1" Ends Right 530.000 Oldctg 2
Gel_number    b1112A2
Bands  1869880 26
Creation_date 101 10 3 11 41 
Modified_date 101 10 3 11 51 
  
BAC : "b0113L10"
Map "ctg1" Ends Left 504.000
Map "ctg1" Ends Right 528.000 Oldctg 2
Gel_number    b1113D2
Bands  1872623 24
Creation_date 101 10 3 11 41 
Modified_date 101 10 3 11 53 
  
BAC : "b0114E16"
Map "ctg1" Ends Left 89.000
Map "ctg1" Ends Right 126.000 Oldctg 2
Gel_number    b1114B1
Bands  1874416 37
Creation_date 101 10 3 11 41 
Modified_date 101 10 3 11 54 
  
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Map "ctg1" Ends Left 50.000
Map "ctg1" Ends Right 81.000 Oldctg 2
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Bands  1876064 31
Creation_date 101 10 3 11 41 
Modified_date 101 10 3 11 54 
  
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Map "ctg1" Ends Right 301.000 Oldctg 2
Gel_number    b1115A2
Bands  1877734 22
Creation_date 101 10 3 11 41 
Modified_date 101 10 3 11 55 
  
BAC : "b0115K18"
Map "ctg1" Ends Left 589.000
Map "ctg1" Ends Right 615.000 Oldctg 2
Gel_number    b1115B2
Bands  1878435 26
Creation_date 101 10 3 11 41 
Modified_date 101 10 3 11 55 
  
BAC : "b0116D19"
Map "ctg1" Ends Left 369.000
Map "ctg1" Ends Right 401.000 Oldctg 2
Gel_number    b1116C1
Bands  1881304 32
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 15 12 
  
BAC : "b0116E14"
Map "ctg1" Ends Left 568.000
Map "ctg1" Ends Right 598.000 Oldctg 2
Gel_number    b1116B1
Bands  1881484 30
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 15 12 
  
BAC : "b0117O21"
Map "ctg1" Ends Left 486.000
Map "ctg1" Ends Right 507.000 Oldctg 2
Gel_number    b1117A2
Bands  1888012 21
Creation_date 101 10 3 11 41 
Modified_date 101 10 3 11 57 
  
BAC : "b0118F12"
Map "ctg1" Ends Left 507.000
Map "ctg1" Ends Right 535.000 Oldctg 2
Gel_number    b1118D1
Bands  1889133 28
Creation_date 101 10 3 11 41 
Modified_date 101 10 3 11 58 
  
BAC : "b0118H07"
Map "ctg1" Ends Left 226.000
Map "ctg1" Ends Right 256.000 Oldctg 2
Gel_number    b1118C1
Bands  1889496 30
Creation_date 101 10 3 11 41 
Modified_date 101 10 3 11 58 
  
BAC : "b0119I21"
Map "ctg1" Ends Left 612.000
Map "ctg1" Ends Right 643.000 Oldctg 2
Gel_number    b1119A2
Bands  1895188 31
Creation_date 101 8 24 13 54 
Modified_date 101 8 24 15 17 
  
BAC : "b0119N16"
Map "ctg1" Ends Left 85.000
Map "ctg1" Ends Right 110.000 Oldctg 2
Gel_number    b1119D2
Bands  1896877 25
Creation_date 101 10 3 11 41 
Modified_date 101 10 3 11 59 
  
BAC : "b0122H16"
Map "ctg1" Ends Left 147.000
Map "ctg1" Ends Right 175.000 Oldctg 2
Gel_number    b1122D1
Bands  1898823 28
Positive_OVERGO "SOG0460" 
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Modified_date 103 4 22 10 21 

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Modified_date 103 4 28 17 57 

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Modified_date 103 4 22 10 21 

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Modified_date 103 4 22 10 21 

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Modified_date 102 2 1 22 47 

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Anchor_bin "1"
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Modified_date 103 4 22 10 21 

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Modified_date 102 2 1 22 47 

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Anchor_bin "1"
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Modified_date 103 4 22 10 21 

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Anchor_bin "1"
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Modified_date 103 4 22 10 21 

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Modified_date 102 2 1 22 48 

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Modified_date 103 4 22 10 21 

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Modified_date 103 4 22 10 21 

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Anchor_bin "1"
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Creation_date 102 2 1 22 47 
Modified_date 103 4 22 10 21 

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Modified_date 103 4 22 10 21 

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Modified_date 103 4 22 10 21 

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Modified_date 102 2 1 22 47 

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Creation_date 102 2 1 22 47 
Modified_date 103 4 22 10 21 

Marker_STS : "OJ990713_06"
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Modified_date 102 2 1 22 47 

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Modified_date 102 2 1 22 47 

Marker_STS : "OJ990915_01"
Anchor_bin "1"
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Modified_date 103 4 22 10 21 

Marker_STS : "OJ990923_08"
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Modified_date 102 2 1 22 47 

Marker_STS : "OJ991015_10"
Anchor_bin "1"
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Creation_date 102 2 1 22 47 
Modified_date 103 4 22 10 21 

Marker_STS : "OJ991018_02"
Anchor_bin "1"
Anchor_pos     7.0 P
Creation_date 102 2 1 22 47 
Modified_date 103 4 22 10 21 

Marker_STS : "OJ991021_17"
Anchor_bin "1"
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Creation_date 102 2 1 22 47 
Modified_date 102 2 1 22 47 

Marker_STS : "OJ991201_11"
Creation_date 102 2 1 22 47 
Modified_date 103 4 22 10 21 

Marker_STS : "OJ991210_12"
Creation_date 102 2 1 22 47 
Modified_date 102 2 1 22 47 

Marker_STS : "OJ991215_12"
Anchor_bin "1"
Anchor_pos    12.3 P
Creation_date 102 2 1 22 47 
Modified_date 103 4 22 10 21 

Marker_STS : "PIB1"
Creation_date 101 5 9 11 19 
Modified_date 103 4 28 17 14 

Marker_Probe : "PRC0214"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 24 

Marker_eMRK : "R87"
Anchor_bin "1"
Anchor_pos     8.4 F
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 59 

Marker_eMRK : "R106"
Anchor_bin "1"
Anchor_pos    12.2 F
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 56 

Marker_STS : "R753"
Anchor_bin "1"
Anchor_pos    10.9 F
Creation_date 100 4 6 15 17 
Modified_date 103 4 28 17 58 

Marker_eMRK : "R1613"
Anchor_bin "1"
Anchor_pos    16.1 F
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 18 1 

Marker_eMRK : "R1841"
Anchor_bin "1"
Anchor_pos    12.2 F
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 56 

Marker_eMRK : "RG246"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 18 1 

Marker_STS : "RG353"
Creation_date 101 1 2 17 56 
Modified_date 101 7 13 16 45 

Marker_STS : "RG472"
Creation_date 100 3 13 22 58 
Modified_date 100 8 2 11 45 

Marker_eMRK : "RM177"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 45 

Marker_eMRK : "RM1141"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 56 

Marker_eMRK : "RM1177"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 58 

Marker_eMRK : "RM1247"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 56 

Marker_eMRK : "RM1254"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 57 

Marker_eMRK : "RM1320"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 57 

Marker_eMRK : "RM1331"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 56 

Marker_eMRK : "RM1869"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 18 37 

Marker_eMRK : "RM3148"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 18 1 

Marker_eMRK : "RM3652"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 18 1 

Marker_eMRK : "RM3740"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 58 

Marker_eMRK : "RM5336"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 18 1 

Marker_eMRK : "RM5423"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 57 

Marker_eMRK : "RM6045"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 58 

Marker_eMRK : "RM6236"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 56 

Marker_eMRK : "RM6324"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 18 1 

Marker_eMRK : "RM6340"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 57 

Marker_eMRK : "RM6433"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 18 42 

Marker_eMRK : "RM6470"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 56 

Marker_eMRK : "RM6515"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 58 

Marker_eMRK : "RM6873"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 18 1 

Marker_eMRK : "RM7278"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 58 

Marker_eMRK : "RM7383"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 18 1 

Marker_eMRK : "RM7536"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 56 

Marker_eMRK : "RM8068"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 56 

Marker_eMRK : "RM8069"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 56 

Marker_eMRK : "RZ288"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 59 

Marker_eMRK : "RZ543"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 59 

Marker_eMRK : "RZ889"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 45 

Marker_STS : "S1001"
Creation_date 101 6 21 21 25 
Modified_date 101 6 21 21 25 

Marker_eMRK : "S1543"
Anchor_bin "1"
Anchor_pos     5.6 F
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 56 

Marker_eMRK : "S5853"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 18 1 

Marker_eMRK : "S10623"
Anchor_bin "1"
Anchor_pos     7.0 F
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 57 

Marker_eMRK : "S13048"
Anchor_bin "1"
Anchor_pos     9.5 F
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 56 

Marker_eMRK : "S13157S"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 18 1 

Marker_STS : "S13984"
Anchor_bin "2"
Anchor_pos   103.9 F
Creation_date 100 3 9 21 3 
Modified_date 103 4 28 18 36 

Marker_eMRK : "S20154S"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 18 1 

Marker_eMRK : "S20229S"
Creation_date 103 4 28 17 13 
Modified_date 103 4 28 17 56 

Marker_OVERGO : "SOG0127"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG0223"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG0252"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG0279"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG0307"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG0313"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG0316"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG0389"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG0460"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG0657"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG0948"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG0961"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG0980"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1044"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1055"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1077"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1176"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1177"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1200"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1204"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1225"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1231"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1344"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1346"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1383"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1401"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1450"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1508"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1670"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1745"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1746"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1774"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1790"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1816"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG1855"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG2111"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG2203"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG2232"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG2238"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG2244"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 

Marker_OVERGO : "SOG2276"
Remark "by Paterson lab"
Creation_date 103 4 22 10 21 
Modified_date 103 4 22 10 23 


Contigdata 1

Ctg1 9/4/104 18:13 Ok  -1 #
Chr_remark "Chr1" Pos   0.000  
User_remark "This is FPC V7!!!"
BioPerl-1.007002/t/data/cys1_dicdi.water000444000766000024      1352513155576321 17775 0ustar00cjfieldsstaff000000000000########################################
# Program:  water
# Rundate:  Tue Feb 12 21:31:03 2002
# Report_file: cys1_dicdi.water
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: CYS1_DICDI
# 2: CYS1_DICDI
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 343
# Identity:     343/343 (100.0%)
# Similarity:   343/343 (100.0%)
# Gaps:           0/343 ( 0.0%)
# Score: 1841.0
# 
#
#=======================================

CYS1_DICDI         1 MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFE     50
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
CYS1_DICDI         1 MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFE     50

CYS1_DICDI        51 IFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIF    100
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
CYS1_DICDI        51 IFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIF    100

CYS1_DICDI       101 TDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGN    150
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
CYS1_DICDI       101 TDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGN    150

CYS1_DICDI       151 VEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYN    200
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
CYS1_DICDI       151 VEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYN    200

CYS1_DICDI       201 YIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAG    250
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
CYS1_DICDI       201 YIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAG    250

CYS1_DICDI       251 YIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIF    300
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
CYS1_DICDI       251 YIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIF    300

CYS1_DICDI       301 RKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII    343
                     |||||||||||||||||||||||||||||||||||||||||||
CYS1_DICDI       301 RKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII    343

#=======================================
#
# Aligned_sequences: 2
# 1: CYS1_DICDI
# 2: ALEU_HORVU
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 339
# Identity:     112/339 (33.0%)
# Similarity:   169/339 (49.9%)
# Gaps:          63/339 (18.6%)
# Score: 510.5
# 
#
#=======================================

CYS1_DICDI        29 FLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGV     77
                     |..|..::.|.| |..|...||.||..:|.::...|...:.:    :.|:
ALEU_HORVU        61 FARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPY----RLGI    106

CYS1_DICDI        78 NKFADLSSDEFK----------------NYYLNNKEAIFTDDLPVADYLD    111
                     |:|:|:|.:||:                |:.:.:..|             
ALEU_HORVU       107 NRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRDAAA-------------    143

CYS1_DICDI       112 DEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNK    161
                           :|...|||..|.|:|||||..|||||:|||||.:|..:..:..|
ALEU_HORVU       144 ------LPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGK    187

CYS1_DICDI       162 LVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTE    211
                     .:|||||.||||......:        ||||||...|:.||..||||.||
ALEU_HORVU       188 NISLSEQQLVDCAGGFNNF--------GCNGGLPSQAFEYIKYNGGIDTE    229

CYS1_DICDI       212 SSYPYTAETGTQCNFNSANIGAKI---SNFTMIPKNETVMAGYIVSTGPL    258
                     .||||....|. |::.:.|...::   .|.|:..::|...|..:|.  |:
ALEU_HORVU       230 ESYPYKGVNGV-CHYKAENAAVQVLDSVNITLNAEDELKNAVGLVR--PV    276

CYS1_DICDI       259 AIAADAVE-WQFYIGGVFDIP-C--NPNSLDHGILIVGYSAKNTIFRKNM    304
                     ::|...:: ::.|..||:... |  .|:.::|.:|.|||..:|     .:
ALEU_HORVU       277 SVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVEN-----GV    321

CYS1_DICDI       305 PYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII    343
                     |||::|||||||||:.||..:..|||.|.::...|..::
ALEU_HORVU       322 PYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVV    360

#=======================================
#
# Aligned_sequences: 2
# 1: CYS1_DICDI
# 2: CATH_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 323
# Identity:     122/323 (37.8%)
# Similarity:   165/323 (51.1%)
# Gaps:          40/323 (12.4%)
# Score: 511.0
# 
#
#=======================================

CYS1_DICDI        32 FQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFA     81
                     :..|..|.||.|||..|.:.|.||..||...|    |.....|..:|:|:
CATH_HUMAN        38 WMSKHRKTYSTEEYHHRLQTFASNWRKINAHN----NGNHTFKMALNQFS     83

CYS1_DICDI        82 DLSSDEFKNYYL----NNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTR    127
                     |:|..|.|:.||    .|..|      ..::||  ......|.:.|||.:
CATH_HUMAN        84 DMSFAEIKHKYLWSEPQNCSA------TKSNYL--RGTGPYPPSVDWRKK    125

CYS1_DICDI       128 G-AVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE    176
                     | .|:||||||.|||||:|||||.:|....|:..|::||:||.||||..:
CATH_HUMAN       126 GNFVSPVKNQGACGSCWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQD    175

CYS1_DICDI       177 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNF    226
                     ...|        ||.|||...|:.||:.|.||..|.:|||..:.| .|.|
CATH_HUMAN       176 FNNY--------GCQGGLPSQAFEYILYNKGIMGEDTYPYQGKDG-YCKF    216

CYS1_DICDI       227 NSAN-IG--AKISNFTMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIG    272
                     .... ||  ..::|.|:.  :|..|...:....|::.|.:.. ::..|..
CATH_HUMAN       217 QPGKAIGFVKDVANITIY--DEEAMVEAVALYNPVSFAFEVTQDFMMYRT    264

CYS1_DICDI       273 GVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGE    319
                     |:: ...|:  |:.::|.:|.|||..||.|     ||||||||||..||.
CATH_HUMAN       265 GIYSSTSCHKTPDKVNHAVLAVGYGEKNGI-----PYWIVKNSWGPQWGM    309

CYS1_DICDI       320 QGYIYLRRGKNTCGVSNFVSTSI    342
                     .||..:.||||.||::...|..|
CATH_HUMAN       310 NGYFLIERGKNMCGLAACASYPI    332


#---------------------------------------
#---------------------------------------
BioPerl-1.007002/t/data/cysprot.fa000555000766000024       472413155576321 16715 0ustar00cjfieldsstaff000000000000>CYS1_DICDI
MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHK
ADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCG
SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQT
ESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCN
PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII


>ALEU_HORVU
MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGK
SYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRD
AAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNG
GLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAF
QVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCA
IATCASYPVVAA


>CATH_HUMAN
MWATLPLLCAGAWLLGVPVCGAAELSVNSLEKFHFKSWMSKHRKTYSTEEYHHRLQTFASNWRKINAHNN
GNHTFKMALNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPPSVDWRKKGNFVSPVKNQGACGS
CWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNYGCQGGLPSQAFEYILYNKGIMGEDTYPYQGK
DGYCKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVN
HAVLAVGYGEKNGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV


>CATH_RAT
MWTALPLLCAGAWLLSAGATAELTVNAIEKFHFTSWMKQHQKTYSSREYSHRLQVFANNWRKIQAHNQRN
HTFKMGLNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPSSMDWRKKGNVVSPVKNQGACGSCW
TFSTTGALESAVAIASGKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIGKNG
QCKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHA
VLAVGYGEQNGLLYWIVKNSWGSNWGNNGYFLIERGKNMCGLAACASYPIPQV


>CATL_HUMAN
MNPTLILAAFCLGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGK
HSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSCWA
FSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEES
CKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLV
VGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV


>CATL_RAT
MTPLLLLAVLCLGTALATPKFDQTFNAQWHQWKSTHRRLYGTNEEEWRRAVWEKNMRMIQLHNGEYSNGK
HGFTMEMNAFGDMTNEEFRQIVNGYRHQKHKKGRLFQEPLMLQIPKTVDWREKGCVTPVKNQGQCGSCWA
FSASGCLEGQMFLKTGKLISLSEQNLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGS
CKYRAEYAVANDTGFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCSSKDLDHGVLV
VGYGYEGTDSNKDKYWLVKNSWGKEWGMDGYIKIAKDRNNHCGLATAASYPIVN


>PAPA_CARPA
MAMIPSISKLLFVAICLFVYMGLSFGDFSIVGYSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFE
IFKDNLKYIDETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDW
RQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQ
YGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGG
IFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN



BioPerl-1.007002/t/data/cysprot.msf000444000766000024      1057413155576321 17131 0ustar00cjfieldsstaff000000000000PileUp



   MSF:  393  Type: P    Check:  3400   .. 

 Name: CATH_HUMAN oo  Len:  393  Check:  4989  Weight:  10.0
 Name: CATH_RAT oo  Len:  393  Check:  6434  Weight:  10.6
 Name: ALEU_HORVU oo  Len:  393  Check:  5288  Weight:  16.7
 Name: PAPA_CARPA oo  Len:  393  Check:  3242  Weight:  18.9
 Name: CATL_HUMAN oo  Len:  393  Check:  4708  Weight:  12.2
 Name: CATL_RAT oo  Len:  393  Check:  6797  Weight:  12.2
 Name: CYS1_DICDI oo  Len:  393  Check:  1942  Weight:  18.9

//



CATH_HUMAN      ....MWATLP LLCAGAWLLG VPVCGAAELS VN........ .......... 
CATH_RAT        ....MWTALP LLCAGAWLLS AGAT..AELT VN........ .......... 
ALEU_HORVU      ....MAHARV LLLALAVLAT AAVAVASSSS FADSNPIRPV TDRAASTLES 
PAPA_CARPA      MAMIPSISKL LFVAICLFVY MGLSFGDFSI VG........ .........Y 
CATL_HUMAN      ......MNPT LILAAFCLGI ASATLTFDHS LE........ .......... 
CATL_RAT        ......MTPL LLLAVLCLGT ALATPKFDQT FN........ .......... 
CYS1_DICDI      ......MKVI LLFVLAVFTV FVSSRGIPPE EQ........ .......... 


CATH_HUMAN      ........SL EKFHFKSWMS KHRKTYS.TE EYHHRLQTFA SNWRKINAHN 
CATH_RAT        ........AI EKFHFTSWMK QHQKTYS.SR EYSHRLQVFA NNWRKIQAHN 
ALEU_HORVU      AVLGALGRTR HALRFARFAV RYGKSYESAA EVRRRFRIFS ESLEEVRSTN 
PAPA_CARPA      SQNDLTSTER LIQLFESWML KHNKIYKNID EKIYRFEIFK DNLKYIDETN 
CATL_HUMAN      .......... ..AQWTKWKA MHNRLYG.MN EEGWRRAVWE KNMKMIELHN 
CATL_RAT        .......... ..AQWHQWKS THRRLYG.TN EEEWRRAVWE KNMRMIQLHN 
CYS1_DICDI      .......... ..SQFLEFQD KFNKKYS.HE EYLERFEIFK SNLGKIEELN 


CATH_HUMAN      ....NGNHTF KMALNQFSDM SFAEIKHKYL WSEPQNCSAT KS..NYLRGT 
CATH_RAT        ....QRNHTF KMGLNQFSDM SFAEIKHKYL WSEPQNCSAT KS..NYLRGT 
ALEU_HORVU      ....RKGLPY RLGINRFSDM SWEEFQATRL G.AAQTCSAT LAGNHLMRDA 
PAPA_CARPA      ....KKNNSY WLGLNVFADM SNDEFKEKYT GSIAGNYTTT ELSYEEVLND 
CATL_HUMAN      QEYREGKHSF TMAMNAFGDM TSEEFRQVMN GFQ....NRK PRKGKVFQEP 
CATL_RAT        GEYSNGKHGF TMEMNAFGDM TNEEFRQIVN GYR....HQK HKKGRLFQEP 
CYS1_DICDI      LIAINHKADT KFGVNKFADL SSDEFKNYYL NNKEAIFTDD LPVADYLDDE 


CATH_HUMAN      G..PYPPSVD WRKKGNFVSP VKNQGACGSC WTFSTTGALE SAIAIATGKM 
CATH_RAT        G..PYPSSMD WRKKGNVVSP VKNQGACGSC WTFSTTGALE SAVAIASGKM 
ALEU_HORVU      A..ALPETKD WREDG.IVSP VKNQAHCGSC WTFSTTGALE AAYTQATGKN 
PAPA_CARPA      GDVNIPEYVD WRQKG.AVTP VKNQGSCGSC WAFSAVVTIE GIIKIRTGNL 
CATL_HUMAN      LFYEAPRSVD WREKG.YVTP VKNQGQCGSC WAFSATGALE GQMFRKTGRL 
CATL_RAT        LMLQIPKTVD WREKG.CVTP VKNQGQCGSC WAFSASGCLE GQMFLKTGKL 
CYS1_DICDI      FINSIPTAFD WRTRG.AVTP VKNQGQCGSC WSFSTTGNVE GQHFISQNKL 


CATH_HUMAN      LSLAEQQLVD CAQDF..... ...NNYGCQG GLPSQAFEYI LYNKGIMGED 
CATH_RAT        MTLAEQQLVD CAQNF..... ...NNHGCQG GLPSQAFEYI LYNKGIMGED 
ALEU_HORVU      ISLSEQQLVD CAGGF..... ...NNFGCNG GLPSQAFEYI KYNGGIDTEE 
PAPA_CARPA      NEYSEQELLD CDR....... ...RSYGCNG GYPWSALQLV AQYG.IHYRN 
CATL_HUMAN      ISLSEQNLVD CSGP....QG ....NEGCNG GLMDYAFQYV QDNGGLDSEE 
CATL_RAT        ISLSEQNLVD CSHD....QG ....NQGCNG GLMDFAFQYI KENGGLDSEE 
CYS1_DICDI      VSLSEQNLVD CDHECMEYEG EEACDEGCNG GLQPNAYNYI IKNGGIQTES 


CATH_HUMAN      TYPYQGKDGY .CKFQPGKAI GFVKDVANIT IYDEEAMVEA VALYNPVSFA 
CATH_RAT        SYPYIGKNGQ .CKFNPEKAV AFVKNVVNIT LNDEAAMVEA VALYNPVSFA 
ALEU_HORVU      SYPYKGVNGV .CHYKAENAA VQVLDSVNIT LNAEDELKNA VGLVRPVSVA 
PAPA_CARPA      TYPYEGVQRY .CRSREKGPY AAKTDGVRQV QPYNEGALLY SIANQPVSVV 
CATL_HUMAN      SYPYEATEES .CKYNPKYSV ANDTGFVDIP K.QEKALMKA VATVGPISVA 
CATL_RAT        SYPYEAKDGS .CKYRAEYAV ANDTGFVDIP Q.QEKALMKA VATVGPISVA 
CYS1_DICDI      SYPYTAETGT QCNFNSANIG AKISNFTMIP K.NETVMAGY IVSTGPLAIA 


CATH_HUMAN      FEVT.QDFMM YRTGIYSSTS CHKTPDKVNH AVLAVGYGEK NG.....IPY 
CATH_RAT        FEVT.EDFMM YKSGVYSSNS CHKTPDKVNH AVLAVGYGEQ NG.....LLY 
ALEU_HORVU      FQVI.DGFRQ YKSGVYTSDH CGTTPDDVNH AVLAVGYGVE NG.....VPY 
PAPA_CARPA      LEAAGKDFQL YRGGIFVG.. ..PCGNKVDH AVAAVGYGPN .........Y 
CATL_HUMAN      IDAGHESFLF YKEGIYFEPD ..CSSEDMDH GVLVVGYGFE STESDNNK.Y 
CATL_RAT        MDASHPSLQF YSSGIYYEPN ..CSSKDLDH GVLVVGYGYE GTDSNKDK.Y 
CYS1_DICDI      ADA..VEWQF YIGGVFDIP. ..CNPNSLDH GILIVGYSAK NTIFRKNMPY 


CATH_HUMAN      WIVKNSWGPQ WGMNGYFLIE RGK....NMC GLAACASYPI PLV
CATH_RAT        WIVKNSWGSN WGNNGYFLIE RGK....NMC GLAACASYPI PQV
ALEU_HORVU      WLIKNSWGAD WGDNGYFKME MGK....NMC AIATCASYPV VAA
PAPA_CARPA      ILIKNSWGTG WGENGYIRIK RGTGNSYGVC GLYTSSFYPV KN.
CATL_HUMAN      WLVKNSWGEE WGMGGYVKMA KDRR...NHC GIASAASYPT V..
CATL_RAT        WLVKNSWGKE WGMDGYIKIA KDRN...NHC GLATAASYPI VN.
CYS1_DICDI      WIVKNSWGAD WGEQGYIYLR RGK....NTC GVSNFVSTSI I..

BioPerl-1.007002/t/data/cysprot.needle000444000766000024       420713155576321 17554 0ustar00cjfieldsstaff000000000000Global: PAPA_CARPA vs CATL_HUMAN
Score: 499.50

PAPA_CARPA      1        MAMIPSISKLLFVAICLFVYMGLSFGDFSIVGYSQNDLTSTERLI 45      
                           | |:   |:  | ||              | :   ||    | 
CATL_HUMAN      1          MNPT...LILAAFCL..............GIASATLTFDHSLE 26      

PAPA_CARPA      46       QLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKK....N 86      
                           :  |   ||::|  ::|: :|  ::: |:| |:  |::     
CATL_HUMAN      27       AQWTKWKAMHNRLY.GMNEEGWRRAVWEKNMKMIELHNQEYREGK 70      

PAPA_CARPA      87       NSYWLGLNVFADMSNDEFKEKYTG.....SIAGNYTTTELSYEEV 126     
                         :|: : :| | ||:::||::   |        |      | ||  
CATL_HUMAN      71       HSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFYE.. 113     

PAPA_CARPA      127      LNDGDVNIPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGII 171     
                                 |  ||||:|| |||||||| |||||||||   :|| :
CATL_HUMAN      114      .......APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQM 151     

PAPA_CARPA      172      KIRTGNLNEYSEQELLDCD..RRSYGCNGGYPWSALQLVAQY.GI 213     
                           :|| |   ||| |:||   : : |||||    | | |    |:
CATL_HUMAN      152      FRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGL 196     

PAPA_CARPA      214      HYRNTYPYEGVQRYCRSREKGPYAAKTD.GVRQVQPYNEGALLYS 257     
                             :||||  :  |:   |  |:   | |   : |  | ||: :
CATL_HUMAN      197      DSEESYPYEATEESCKYNPK..YSVANDTGFVDI.PKQEKALMKA 238     

PAPA_CARPA      258      IAN.QPVSVVLEAAGKDFQLYRGGIFVGP.CGNK.VDHAVAAVGY 299     
                         :|   |:|| ::|  : |  |: ||:  | | :: :|| |  |||
CATL_HUMAN      239      VATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGY 283     

PAPA_CARPA      300      G........PNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLY 336     
                         |          | |:|||||  ||  ||::: :   |    ||: 
CATL_HUMAN      284      GFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNH...CGIA 325     

PAPA_CARPA      337      TSSFYPVKN                                     345     
                         ::: ||   
CATL_HUMAN      326      SAASYPTV                                      333     

%id = 39.81			%similarity = 59.22
Overall %id = 35.65		Overall %similarity = 53.04
BioPerl-1.007002/t/data/cysprot.tblastn000444000766000024      5503213155576321 20011 0ustar00cjfieldsstaff000000000000TBLASTN 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= CYS1_DICDI
         (343 letters)

Database: alu.n
           327 sequences; 80,506 total letters

Searching......................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gnl|alu|L13391_HSAL003871 (Alu-J)                                      23  0.64
gnl|alu|M30798_HSAL001637 (Alu-J)                                      20  5.6
gnl|alu|M64231_HSAL003023 (Alu-Sb)                                     20  5.6
gnl|alu|Y00326_HSAL000959 (Alu-J)                                      19  9.5
gnl|alu|X69908_HSAL000290 (Alu-J)                                      19  9.5
gnl|alu|M65235_HSAL002711 (Alu-Sx)                                     19  9.5
gnl|alu|M80812_HSAL001801 (Alu-J)                                      19  9.5

>gnl|alu|L13391_HSAL003871 (Alu-J)
          Length = 193

 Score = 23.1 bits (48), Expect = 0.64
 Identities = 11/32 (34%), Positives = 15/32 (46%)
 Frame = +1

Query: 137 GQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQ 168
           G CGSCW        + QHF    ++  LS +
Sbjct: 19  GYCGSCW--------KSQHFGRLRQVEGLSSE 90


>gnl|alu|M30798_HSAL001637 (Alu-J)
          Length = 331

 Score = 20.0 bits (40), Expect = 5.6
 Identities = 6/7 (85%), Positives = 7/7 (99%)
 Frame = +3

Query: 278 PCNPNSL 284
           PCNPN+L
Sbjct: 12  PCNPNTL 32


>gnl|alu|M64231_HSAL003023 (Alu-Sb)
          Length = 257

 Score = 20.0 bits (40), Expect = 5.6
 Identities = 8/14 (57%), Positives = 9/14 (64%)
 Frame = +3

Query: 294 SAKNTIFRKNMPYW 307
           S KNT  +KN P W
Sbjct: 72  STKNTKKKKNGPAW 113


>gnl|alu|Y00326_HSAL000959 (Alu-J)
          Length = 260

 Score = 19.2 bits (38), Expect = 9.5
 Identities = 6/10 (60%), Positives = 6/10 (60%)
 Frame = -2

Query: 177 CMEYEGEEAC 186
           C EY GE  C
Sbjct: 34  CWEYRGEPPC 5


>gnl|alu|X69908_HSAL000290 (Alu-J)
          Length = 292

 Score = 19.2 bits (38), Expect = 9.5
 Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 3/30 (10%)
 Frame = -1

Query: 118 IPTAFDWRTRGAVTPVK---NQGQCGSCWS 144
           +P   +WR   ++ P      Q  C S WS
Sbjct: 256 LPILDNWRDHSSLKPPAPGFKQSSCLSFWS 167


>gnl|alu|M65235_HSAL002711 (Alu-Sx)
          Length = 325

 Score = 19.2 bits (38), Expect = 9.5
 Identities = 5/7 (71%), Positives = 5/7 (71%)
 Frame = -1

Query: 137 GQCGSCW 143
           G C SCW
Sbjct: 115 GACSSCW 95


>gnl|alu|M80812_HSAL001801 (Alu-J)
          Length = 202

 Score = 19.2 bits (38), Expect = 9.5
 Identities = 5/10 (50%), Positives = 7/10 (70%)
 Frame = +2

Query: 168 QNLVDCDHEC 177
           + +V CDH C
Sbjct: 113 ETIVHCDHTC 142


  Database: alu.n
    Posted date:  Feb 26, 2001  4:36 AM
  Number of letters in database: 80,506
  Number of sequences in database:  327
  
Lambda     K      H
   0.316    0.135    0.414 

Gapped
Lambda     K      H
   0.270   0.0470    0.230 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 35241
Number of Sequences: 327
Number of extensions: 483
Number of successful extensions: 7
Number of sequences better than 10.0: 14
Number of HSP's better than 10.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1
Number of HSP's gapped (non-prelim): 7
length of query: 343
length of database: 26,835
effective HSP length: 31
effective length of query: 312
effective length of database: 16,698
effective search space:  5209776
effective search space used:  5209776
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 36 (19.3 bits)
S2: 38 (19.2 bits)
TBLASTN 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= ALEU_HORVU
         (362 letters)

Database: alu.n
           327 sequences; 80,506 total letters

Searching......................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gnl|alu|L13391_HSAL003871 (Alu-J)                                      23  0.51
gnl|alu|M59213_HSAL001809 (Alu-J)                                      20  7.5
gnl|alu|M19889_HSAL002725 (Alu-J)                                      19  9.9
gnl|alu|X05322_HSAL000874 (Alu-Sx)                                     19  9.9

>gnl|alu|L13391_HSAL003871 (Alu-J)
          Length = 193

 Score = 23.5 bits (49), Expect = 0.51
 Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
 Frame = +1

Query: 164 HCGSCWTFSTTGAL---EAAYTQATGKNISLSEQQLVDCA 200
           +CGSCW     G L   E   ++  G +I ++     DCA
Sbjct: 22  YCGSCWKSQHFGRLRQVEGLSSEVRGSSIQVTVS--YDCA 135


>gnl|alu|M59213_HSAL001809 (Alu-J)
          Length = 339

 Score = 19.6 bits (39), Expect = 7.5
 Identities = 7/12 (58%), Positives = 7/12 (58%)
 Frame = +2

Query: 164 HCGSCWTFSTTG 175
           HCGSC  F   G
Sbjct: 8   HCGSCL*FQQFG 43


>gnl|alu|M19889_HSAL002725 (Alu-J)
          Length = 183

 Score = 19.2 bits (38), Expect = 9.9
 Identities = 5/8 (62%), Positives = 7/8 (87%)
 Frame = -1

Query: 236 GVNGVCHY 243
           G NG+CH+
Sbjct: 54  GTNGMCHH 31


>gnl|alu|X05322_HSAL000874 (Alu-Sx)
          Length = 225

 Score = 19.2 bits (38), Expect = 9.9
 Identities = 6/11 (54%), Positives = 7/11 (63%)
 Frame = -3

Query: 237 VNGVCHYKAEN 247
           + GVCHY   N
Sbjct: 163 ITGVCHYAQLN 131


  Database: alu.n
    Posted date:  Feb 26, 2001  4:36 AM
  Number of letters in database: 80,506
  Number of sequences in database:  327
  
Lambda     K      H
   0.318    0.132    0.400 

Gapped
Lambda     K      H
   0.270   0.0470    0.230 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 31527
Number of Sequences: 327
Number of extensions: 291
Number of successful extensions: 6
Number of sequences better than 10.0: 8
Number of HSP's better than 10.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 2
Number of HSP's gapped (non-prelim): 4
length of query: 362
length of database: 26,835
effective HSP length: 32
effective length of query: 330
effective length of database: 16,371
effective search space:  5402430
effective search space used:  5402430
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 36 (19.4 bits)
S2: 38 (19.2 bits)
TBLASTN 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= CATH_HUMAN
         (335 letters)

Database: alu.n
           327 sequences; 80,506 total letters

Searching......................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gnl|alu|M63796_HSAL002417 (Alu-J)                                      23  0.85
gnl|alu|L13391_HSAL003871 (Alu-J)                                      22  1.1
gnl|alu|M65235_HSAL002711 (Alu-Sx)                                     21  2.5
gnl|alu|M88005_HSAL001281 (Alu-Sx)                                     21  3.3
gnl|alu|M64231_HSAL003024 (Alu-J)                                      20  4.3

>gnl|alu|M63796_HSAL002417 (Alu-J)
          Length = 322

 Score = 22.7 bits (47), Expect = 0.85
 Identities = 11/34 (32%), Positives = 15/34 (43%)
 Frame = +1

Query: 302 SWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV 335
           SW P W        +  KN  G+   A Y +P+V
Sbjct: 76  SWRPAWASGHLIFTKNKKN*LGMVV*ACY-VPVV 174


>gnl|alu|L13391_HSAL003871 (Alu-J)
          Length = 193

 Score = 22.3 bits (46), Expect = 1.1
 Identities = 8/23 (34%), Positives = 11/23 (47%)
 Frame = +1

Query: 136 GACGSCWTFSTTGALESAIAIAT 158
           G CGSCW     G L     +++
Sbjct: 19  GYCGSCWKSQHFGRLRQVEGLSS 87


>gnl|alu|M65235_HSAL002711 (Alu-Sx)
          Length = 325

 Score = 21.2 bits (43), Expect = 2.5
 Identities = 6/7 (85%), Positives = 6/7 (85%)
 Frame = -1

Query: 136 GACGSCW 142
           GAC SCW
Sbjct: 115 GACSSCW 95


>gnl|alu|M88005_HSAL001281 (Alu-Sx)
          Length = 225

 Score = 20.8 bits (42), Expect = 3.3
 Identities = 9/29 (31%), Positives = 16/29 (55%)
 Frame = -1

Query: 118 PSVDWRKKGNFVSPVKNQGACGSCWTFST 146
           P++      NFV  VKN+ +C   W+ ++
Sbjct: 165 PTIPNASLTNFVFFVKNRVSCWPGWSLNS 79


>gnl|alu|M64231_HSAL003024 (Alu-J)
          Length = 287

 Score = 20.4 bits (41), Expect = 4.3
 Identities = 10/24 (41%), Positives = 13/24 (53%)
 Frame = -2

Query: 96  WSEPQNCSATKSNYLRGTGPYPPS 119
           WS   +  A  +  LRG+G  PPS
Sbjct: 232 WSAVASIMAHYTLGLRGSGDPPPS 161


  Database: alu.n
    Posted date:  Feb 26, 2001  4:36 AM
  Number of letters in database: 80,506
  Number of sequences in database:  327
  
Lambda     K      H
   0.319    0.134    0.436 

Gapped
Lambda     K      H
   0.270   0.0470    0.230 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 44068
Number of Sequences: 327
Number of extensions: 498
Number of successful extensions: 7
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 2
Number of HSP's gapped (non-prelim): 5
length of query: 335
length of database: 26,835
effective HSP length: 29
effective length of query: 306
effective length of database: 17,352
effective search space:  5309712
effective search space used:  5309712
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 36 (19.5 bits)
S2: 38 (19.2 bits)
TBLASTN 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= CATH_RAT
         (333 letters)

Database: alu.n
           327 sequences; 80,506 total letters

Searching......................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gnl|alu|L13391_HSAL003871 (Alu-J)                                      24  0.36
gnl|alu|M65235_HSAL002711 (Alu-Sx)                                     21  2.4
gnl|alu|L11016_HSAL003845 (Alu-J)                                      19  9.2

>gnl|alu|L13391_HSAL003871 (Alu-J)
          Length = 193

 Score = 23.9 bits (50), Expect = 0.36
 Identities = 9/23 (39%), Positives = 11/23 (47%)
 Frame = +1

Query: 134 GACGSCWTFSTTGALESAVAIAS 156
           G CGSCW     G L     ++S
Sbjct: 19  GYCGSCWKSQHFGRLRQVEGLSS 87


>gnl|alu|M65235_HSAL002711 (Alu-Sx)
          Length = 325

 Score = 21.2 bits (43), Expect = 2.4
 Identities = 6/7 (85%), Positives = 6/7 (85%)
 Frame = -1

Query: 134 GACGSCW 140
           GAC SCW
Sbjct: 115 GACSSCW 95


>gnl|alu|L11016_HSAL003845 (Alu-J)
          Length = 197

 Score = 19.2 bits (38), Expect = 9.2
 Identities = 7/15 (46%), Positives = 10/15 (66%)
 Frame = +3

Query: 124 GNVVSPVKNQGACGS 138
           GN+V P   + +CGS
Sbjct: 93  GNIVRPHFYKASCGS 137


  Database: alu.n
    Posted date:  Feb 26, 2001  4:36 AM
  Number of letters in database: 80,506
  Number of sequences in database:  327
  
Lambda     K      H
   0.319    0.131    0.412 

Gapped
Lambda     K      H
   0.270   0.0470    0.230 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 35152
Number of Sequences: 327
Number of extensions: 361
Number of successful extensions: 10
Number of sequences better than 10.0: 6
Number of HSP's better than 10.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 7
Number of HSP's gapped (non-prelim): 3
length of query: 333
length of database: 26,835
effective HSP length: 31
effective length of query: 302
effective length of database: 16,698
effective search space:  5042796
effective search space used:  5042796
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 35 (19.0 bits)
S2: 38 (19.2 bits)
TBLASTN 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= CATL_HUMAN
         (333 letters)

Database: alu.n
           327 sequences; 80,506 total letters

Searching......................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gnl|alu|L13391_HSAL003871 (Alu-J)                                      22  1.1
gnl|alu|M63544_HSAL002045 (Alu-J)                                      21  3.1
gnl|alu|Z17809_HSAL003365 (Alu-Sx)                                     20  7.0
gnl|alu|X16277_HSAL000821 (Alu-J)                                      19  9.2
gnl|alu|M65235_HSAL002711 (Alu-Sx)                                     19  9.2

>gnl|alu|L13391_HSAL003871 (Alu-J)
          Length = 193

 Score = 22.3 bits (46), Expect = 1.1
 Identities = 8/15 (53%), Positives = 8/15 (53%)
 Frame = +1

Query: 133 GQCGSCWAFSATGAL 147
           G CGSCW     G L
Sbjct: 19  GYCGSCWKSQHFGRL 63


>gnl|alu|M63544_HSAL002045 (Alu-J)
          Length = 265

 Score = 20.8 bits (42), Expect = 3.1
 Identities = 9/22 (40%), Positives = 14/22 (62%), Gaps = 2/22 (9%)
 Frame = -2

Query: 260 KEGIYFEP--DCSSEDMDHGVL 279
           ++G+   P  +CSS  MDH +L
Sbjct: 252 RQGLALSPRLECSSAIMDHCIL 187


>gnl|alu|Z17809_HSAL003365 (Alu-Sx)
          Length = 207

 Score = 19.6 bits (39), Expect = 7.0
 Identities = 6/14 (42%), Positives = 10/14 (70%)
 Frame = -3

Query: 174 GNEGCNGGLMDYAF 187
           G +GC  GLM +++
Sbjct: 172 GVQGCGHGLMGFSY 131


>gnl|alu|X16277_HSAL000821 (Alu-J)
          Length = 287

 Score = 19.2 bits (38), Expect = 9.2
 Identities = 6/14 (42%), Positives = 11/14 (77%)
 Frame = +3

Query: 64 QEYREGKHSFTMAM 77
          QE+  G+HS T+++
Sbjct: 72 QEFEPGQHSETLSL 113


>gnl|alu|M65235_HSAL002711 (Alu-Sx)
          Length = 325

 Score = 19.2 bits (38), Expect = 9.2
 Identities = 5/7 (71%), Positives = 5/7 (71%)
 Frame = -1

Query: 133 GQCGSCW 139
           G C SCW
Sbjct: 115 GACSSCW 95


  Database: alu.n
    Posted date:  Feb 26, 2001  4:36 AM
  Number of letters in database: 80,506
  Number of sequences in database:  327
  
Lambda     K      H
   0.317    0.133    0.417 

Gapped
Lambda     K      H
   0.270   0.0470    0.230 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 39061
Number of Sequences: 327
Number of extensions: 451
Number of successful extensions: 9
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 4
Number of HSP's gapped (non-prelim): 5
length of query: 333
length of database: 26,835
effective HSP length: 31
effective length of query: 302
effective length of database: 16,698
effective search space:  5042796
effective search space used:  5042796
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 36 (19.3 bits)
S2: 38 (19.2 bits)
TBLASTN 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= CATL_RAT
         (334 letters)

Database: alu.n
           327 sequences; 80,506 total letters

Searching......................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gnl|alu|Z17809_HSAL003365 (Alu-Sx)                                     22  1.4
gnl|alu|L13391_HSAL003871 (Alu-J)                                      22  1.9
gnl|alu|Z30166_HSAL006097 (Alu-J)                                      21  2.5
gnl|alu|L26953_HSAL004755 (Alu-Sx)                                     20  4.2
gnl|alu|M65235_HSAL002711 (Alu-Sx)                                     19  9.5

>gnl|alu|Z17809_HSAL003365 (Alu-Sx)
          Length = 207

 Score = 21.9 bits (45), Expect = 1.4
 Identities = 8/14 (57%), Positives = 10/14 (71%)
 Frame = -3

Query: 174 GNQGCNGGLMDFAF 187
           G QGC  GLM F++
Sbjct: 172 GVQGCGHGLMGFSY 131


>gnl|alu|L13391_HSAL003871 (Alu-J)
          Length = 193

 Score = 21.6 bits (44), Expect = 1.9
 Identities = 6/7 (85%), Positives = 6/7 (85%)
 Frame = +1

Query: 133 GQCGSCW 139
           G CGSCW
Sbjct: 19  GYCGSCW 39


>gnl|alu|Z30166_HSAL006097 (Alu-J)
          Length = 168

 Score = 21.2 bits (43), Expect = 2.5
 Identities = 8/22 (36%), Positives = 12/22 (54%)
 Frame = -2

Query: 108 EPLMLQIPKTVDWREKGCVTPV 129
           +P  L +PK  D+R   C  P+
Sbjct: 77  DPAHLSLPKCWDYRLSHCAWPL 12


>gnl|alu|L26953_HSAL004755 (Alu-Sx)
          Length = 337

 Score = 20.4 bits (41), Expect = 4.2
 Identities = 6/9 (66%), Positives = 7/9 (77%)
 Frame = +1

Query: 171 HDQGNQGCN 179
           HD G +GCN
Sbjct: 223 HDPGGRGCN 249


>gnl|alu|M65235_HSAL002711 (Alu-Sx)
          Length = 325

 Score = 19.2 bits (38), Expect = 9.5
 Identities = 5/7 (71%), Positives = 5/7 (71%)
 Frame = -1

Query: 133 GQCGSCW 139
           G C SCW
Sbjct: 115 GACSSCW 95


  Database: alu.n
    Posted date:  Feb 26, 2001  4:36 AM
  Number of letters in database: 80,506
  Number of sequences in database:  327
  
Lambda     K      H
   0.317    0.134    0.426 

Gapped
Lambda     K      H
   0.270   0.0470    0.230 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 36291
Number of Sequences: 327
Number of extensions: 428
Number of successful extensions: 8
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 3
Number of HSP's gapped (non-prelim): 5
length of query: 334
length of database: 26,835
effective HSP length: 30
effective length of query: 304
effective length of database: 17,025
effective search space:  5175600
effective search space used:  5175600
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 36 (19.4 bits)
S2: 38 (19.2 bits)
TBLASTN 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= PAPA_CARPA
         (345 letters)

Database: alu.n
           327 sequences; 80,506 total letters

Searching......................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gnl|alu|L13391_HSAL003871 (Alu-J)                                      22  1.1
gnl|alu|X68486_HSAL004968 (Alu-J)                                      20  5.7
gnl|alu|M65235_HSAL002711 (Alu-Sx)                                     20  5.7
gnl|alu|M78078_HSAL003530 (Alu-Sc)                                     19  9.8
gnl|alu|M63322_HSAL001805 (Alu-J)                                      19  9.8

>gnl|alu|L13391_HSAL003871 (Alu-J)
          Length = 193

 Score = 22.3 bits (46), Expect = 1.1
 Identities = 9/21 (42%), Positives = 12/21 (56%), Gaps = 3/21 (14%)
 Frame = +1

Query: 153 GSCGSCWA---FSAVVTIEGI 170
           G CGSCW    F  +  +EG+
Sbjct: 19  GYCGSCWKSQHFGRLRQVEGL 81


>gnl|alu|X68486_HSAL004968 (Alu-J)
          Length = 249

 Score = 20.0 bits (40), Expect = 5.7
 Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 10/49 (20%)
 Frame = -2

Query: 14  AICLFVYMGLSFGDFSIVGYS----------QNDLTSTERLIQLFESWM 52
           A+CLF++    FG   +  +            N L    + + + ESW+
Sbjct: 149 AVCLFIFSFFFFGRNGLFAHVAQAGLALLG*SNPLALASQSLGITESWV 3


>gnl|alu|M65235_HSAL002711 (Alu-Sx)
          Length = 325

 Score = 20.0 bits (40), Expect = 5.7
 Identities = 5/7 (71%), Positives = 6/7 (85%)
 Frame = -1

Query: 153 GSCGSCW 159
           G+C SCW
Sbjct: 115 GACSSCW 95


>gnl|alu|M78078_HSAL003530 (Alu-Sc)
          Length = 158

 Score = 19.2 bits (38), Expect = 9.8
 Identities = 7/14 (50%), Positives = 10/14 (71%)
 Frame = -1

Query: 204 ALQLVAQYGIHYRN 217
           +  LVAQ G+ +RN
Sbjct: 104 SFNLVAQAGVQWRN 63


>gnl|alu|M63322_HSAL001805 (Alu-J)
          Length = 345

 Score = 19.2 bits (38), Expect = 9.8
 Identities = 6/15 (40%), Positives = 11/15 (73%)
 Frame = +2

Query: 73  KDNLKYIDETNKKNN 87
           K+ +KY+ + NKK +
Sbjct: 284 KNKIKYVFKNNKKKS 328


  Database: alu.n
    Posted date:  Feb 26, 2001  4:36 AM
  Number of letters in database: 80,506
  Number of sequences in database:  327
  
Lambda     K      H
   0.318    0.138    0.428 

Gapped
Lambda     K      H
   0.270   0.0470    0.230 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 33866
Number of Sequences: 327
Number of extensions: 356
Number of successful extensions: 7
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 2
Number of HSP's gapped (non-prelim): 5
length of query: 345
length of database: 26,835
effective HSP length: 30
effective length of query: 315
effective length of database: 17,025
effective search space:  5362875
effective search space used:  5362875
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 36 (19.4 bits)
S2: 38 (19.2 bits)
BioPerl-1.007002/t/data/cysprot.water000444000766000024       420113155576321 17434 0ustar00cjfieldsstaff000000000000Local: PAPA_CARPA vs CATL_HUMAN
Score: 501.50

PAPA_CARPA      3        MIPSISKLLFVAICLFVYMGLSFGDFSIVGYSQNDLTSTERLIQL 47      
                         | |:   |:  | ||              | :   ||    |   
CATL_HUMAN      1        MNPT...LILAAFCL..............GIASATLTFDHSLEAQ 28      

PAPA_CARPA      48       FESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKK....NNS 88      
                         :  |   ||::|  ::|: :|  ::: |:| |:  |::     :|
CATL_HUMAN      29       WTKWKAMHNRLY.GMNEEGWRRAVWEKNMKMIELHNQEYREGKHS 72      

PAPA_CARPA      89       YWLGLNVFADMSNDEFKEKYTG.....SIAGNYTTTELSYEEVLN 128     
                         : : :| | ||:::||::   |        |      | ||    
CATL_HUMAN      73       FTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFYE.... 113     

PAPA_CARPA      129      DGDVNIPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKI 173     
                               |  ||||:|| |||||||| |||||||||   :|| :  
CATL_HUMAN      114      .....APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFR 153     

PAPA_CARPA      174      RTGNLNEYSEQELLDCD..RRSYGCNGGYPWSALQLVAQY.GIHY 215     
                         :|| |   ||| |:||   : : |||||    | | |    |:  
CATL_HUMAN      154      KTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDS 198     

PAPA_CARPA      216      RNTYPYEGVQRYCRSREKGPYAAKTD.GVRQVQPYNEGALLYSIA 259     
                           :||||  :  |:   |  |:   | |   : |  | ||: ::|
CATL_HUMAN      199      EESYPYEATEESCKYNPK..YSVANDTGFVDI.PKQEKALMKAVA 240     

PAPA_CARPA      260      N.QPVSVVLEAAGKDFQLYRGGIFVGP.CGNK.VDHAVAAVGYG. 300     
                            |:|| ::|  : |  |: ||:  | | :: :|| |  |||| 
CATL_HUMAN      241      TVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGF 285     

PAPA_CARPA      301      .......PNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTS 338     
                                  | |:|||||  ||  ||::: :   |    ||: ::
CATL_HUMAN      286      ESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNH...CGIASA 327     

PAPA_CARPA      339      SFYP                                          342     
                         : ||
CATL_HUMAN      328      ASYP                                          331     

%id = 40.07			%similarity = 59.61
Overall %id = 35.65		Overall %similarity = 53.04
BioPerl-1.007002/t/data/cysprot1.FASTA000444000766000024      3305613155576321 17263 0ustar00cjfieldsstaff000000000000 FASTA searches a protein or DNA sequence data bank
 version 3.3t08 Jan. 17, 2001
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

t/data/cysprot1.fa: 343 aa
 >CYS1_DICDI
 vs  /data_2/jason/blastdb/ecoli.aa library
searching /data_2/jason/blastdb/ecoli.aa library

       opt      E()
< 20     0     0:
  22     0     0:           one = represents 7 library sequences
  24     0     0:
  26     0     0:
  28     0     1:*
  30     4     6:*
  32    13    23:== *
  34    62    62:========*
  36   130   127:==================*
  38   252   210:=============================*======
  40   310   293:=========================================*===
  42   405   359:===================================================*======
  44   401   396:========================================================*=
  46   386   403:======================================================== *
  48   348   386:==================================================     *
  50   360   352:==================================================*=
  52   290   309:==========================================  *
  54   264   264:=====================================*
  56   215   221:===============================*
  58   145   181:=====================    *
  60   144   147:====================*
  62   119   118:================*
  64    96    94:=============*
  66    72    74:==========*
  68    65    58:========*=
  70    54    46:======*=
  72    30    36:=====*
  74    19    28:===*
  76    26    22:===*
  78    18    17:==*
  80    19    13:=*=
  82    14    10:=*
  84     8     8:=*
  86     4     6:*
  88     2     5:*          inset = represents 1 library sequences
  90     4     4:*
  92     3     3:*         :==*
  94     2     2:*         :=*
  96     1     2:*         :=*
  98     1     1:*         :*
 100     0     1:*         :*
 102     0     1:*         :*
 104     2     1:*         :*=
 106     0     0:          *
 108     1     0:=         *=
 110     0     0:          *
 112     0     0:          *
 114     0     0:          *
 116     0     0:          *
 118     0     0:          *
>120     0     0:          *
1358987 residues in  4289 sequences
  Expectation_n fit: rho(ln(x))= 5.9493+/-0.00202; mu= 2.7408+/- 0.115
 mean_var=77.5610+/-17.011, 0's: 0 Z-trim: 0  B-trim: 2 in 1/41
 Lambda= 0.1456
 Kolmogorov-Smirnov  statistic: 0.0234 (N=29) at  44

FASTA (3.36 June 2000) function [optimized, BL50 matrix (15:-5)] ktup: 2
 join: 37, opt: 25, gap-pen: -12/ -2, width:  16
 Scan time:  1.110
The best scores are:                                       opt bits E(4289)
gi|1787478|gb|AAC74309.1| (AE000221) nitrate redu  ( 512)   92   29     1.2
gi|1790635|gb|AAC77148.1| (AE000491) putative DEO  ( 251)   84   27     2.1
gi|1786590|gb|AAC73494.1| (AE000145) orf, hypothe  (  94)   78   26     2.1
gi|1790853|gb|AAC77345.1| (AE000509) soluble lyti  ( 654)   84   28     4.8
gi|1789307|gb|AAC75975.1| (AE000377) biosynthetic  ( 658)   83   27     5.6
gi|1788174|gb|AAC74937.1| (AE000280) orf, hypothe  ( 199)   74   25     7.4
gi|1789138|gb|AAC75818.1| (AE000361) putative kin  ( 492)   79   26     7.8
gi|1789427|gb|AAC76084.1| (AE000386) orf, hypothe  ( 354)   76   26     9.1

>>gi|1787478|gb|AAC74309.1| (AE000221) nitrate reductase  (512 aa)
 initn:  35 init1:  35 opt:  92  Z-score: 109.2  bits: 29.2 E():  1.2
Smith-Waterman score: 92;  23.936% identity (26.012% ungapped) in 188 aa overlap (125-305:2-181)

          100       110       120       130       140        150   
CYS1_D NKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTT-GNV--
                                     . :. :  : :  .: .: . :.:  ::  
gi|178                              MKIRSQVGMVLNLDKCIGCHTCSVTCKNVWT
                                            10        20        30 

               160       170        180       190       200        
CYS1_D --EGQHFISQNKLVSLSEQNLVDCDHECME-YEGEEACDEGCNGGLQPNAYNYIIKNGGI
         :: ..   :.. .   :..   : : .: :.:     .  :: :::   :  .  : :
gi|178 SREGVEYAWFNNVETKPGQGF-PTDWENQEKYKGGWI--RKINGKLQPRMGNRAMLLGKI
              40        50         60          70        80        

      210       220       230       240       250        260       
CYS1_D QTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGP-LAIAADAVEW
        ..   :   .     .:.  :. .   .     :.. .     . ::  .:    . .:
gi|178 FANPHLPGIDDYYEPFDFDYQNLHTAPEG----SKSQPIARPRSLITGERMAKIEKGPNW
       90       100       110           120       130       140    

       270       280       290       300       310       320       
CYS1_D QFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRR
       .  .:: ::   . ...:. :  . ::  .. :   .:                      
gi|178 EDDLGGEFDKLAKDKNFDN-IQKAMYSQFENTFMMYLPRLCEHCLNPACVATCPSGAIYK
          150       160        170       180       190       200   

       330       340                                               
CYS1_D GKNTCGVSNFVSTSII                                            
                                                                   
gi|178 REEDGIVLIDQDKCRGWRMCITGCPYKKIYFNWKSGKSEKCIFCYPRIEAGQPTVCSETC
           210       220       230       240       250       260   

>>gi|1790635|gb|AAC77148.1| (AE000491) putative DEOR-typ  (251 aa)
 initn:  46 init1:  46 opt:  84  Z-score: 104.9  bits: 27.4 E():  2.1
Smith-Waterman score: 84;  22.078% identity (23.288% ungapped) in 77 aa overlap (99-171:119-195)

       70        80        90       100       110       120        
CYS1_D HKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG
                                     :.:. ::.:.:: :.  .:.       ...
gi|179 QLVNPGESVVINCGSTAFLLGREMCGKPVQIITNYLPLANYLIDQEHDSVIIMGGQYNKS
       90       100       110       120       130       140        

      130       140           150       160       170       180    
CYS1_D AVTPVKNQGQCGSC----WSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEE
           .. ::. .:     : :..  .. .. . . . :....::....            
gi|179 QSITLSPQGSENSLYAGHWMFTSGKGLTAEGLYKTDMLTAMAEQKMLSVVGKLVVLVDSS
      150       160       170       180       190       200        

          190       200       210       220       230       240    
CYS1_D ACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN
                                                                   
gi|179 KIGERAGMLFSRADQIDMLITGKNANPEILQQLEAQGVSILRV                 
      210       220       230       240       250                  

>>gi|1786590|gb|AAC73494.1| (AE000145) orf, hypothetical  (94 aa)
 initn:  37 init1:  37 opt:  78  Z-score: 104.8  bits: 25.9 E():  2.1
Smith-Waterman score: 78;  36.842% identity (43.750% ungapped) in 38 aa overlap (242-278:42-74)

             220       230       240       250       260       270 
CYS1_D SSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFY-
                                     :.. ::..: .    :     ::..:: : 
gi|178 VKSIGFSSSSTGRASVGVMVEGEYTFSTAEPEEMTVISGALNVLLP-----DATDWQVYE
              20        30        40        50             60      

              280       290       300       310       320       330
CYS1_D IGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKN
        :.::..:                                                    
gi|178 AGSVFNVPGHSEFHLQVAEPTSYLCRYL                                
         70        80        90                                    

>>gi|1790853|gb|AAC77345.1| (AE000509) soluble lytic mur  (654 aa)
 initn:  61 init1:  61 opt:  84  Z-score: 98.5  bits: 27.6 E():  4.8
Smith-Waterman score: 84;  32.692% identity (34.694% ungapped) in 52 aa overlap (104-152:104-155)

            80        90       100       110       120       130   
CYS1_D KFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPV
                                     :: :  :...:.: .    :::   : .: 
gi|179 YPYLEYRQITDDLMNQPAVTVTNFVRANPTLPPARTLQSRFVNELARREDWRGLLAFSPE
            80        90       100       110       120       130   

              140       150       160       170       180       190
CYS1_D K---NQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGC
       :   ...::.  ..  .::. :                                      
gi|179 KPGTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTGKSQPNACDKLFSVWRASGKQDPLAY
           140       150       160       170       180       190   

>>gi|1789307|gb|AAC75975.1| (AE000377) biosynthetic argi  (658 aa)
 initn:  41 init1:  41 opt:  83  Z-score: 97.3  bits: 27.4 E():  5.6
Smith-Waterman score: 83;  23.913% identity (24.176% ungapped) in 92 aa overlap (178-268:315-406)

       150       160       170       180        190       200      
CYS1_D TGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEA-CDEGCNGGLQPNAYNYIIKNG
                                     ..::: ..  : . : ::.  : : :   :
gi|178 TGVRESARFYVELHKLGVNIQCFDVGGGLGVDYEGTRSQSDCSVNYGLNEYANNIIWAIG
          290       300       310       320       330       340    

        210       220       230       240       250       260      
CYS1_D GIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVE
           :.. :. .    .    .:.  . .::.  . .:: ..    .  .: :. .    
gi|178 DACEENGLPHPTVITESGRAVTAHHTVLVSNIIGVERNEYTVPTAPAEDAPRALQSMWET
          350       360       370       380       390       400    

        270       280       290       300       310       320      
CYS1_D WQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLR
       ::                                                          
gi|178 WQEMHEPGTRRSLREWLHDSQMDLHDIHIGYSSGIFSLQERAWAEQLYLSMCHEVQKQLD
          410       420       430       440       450       460    

>>gi|1788174|gb|AAC74937.1| (AE000280) orf, hypothetical  (199 aa)
 initn:  46 init1:  46 opt:  74  Z-score: 95.2  bits: 25.2 E():  7.4
Smith-Waterman score: 74;  43.750% identity (50.000% ungapped) in 32 aa overlap (308-335:110-141)

       280       290       300       310       320        330      
CYS1_D PCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRR-GKNT---CG
                                     :.: .::: .: .  . ::: : .:   ::
gi|178 PVDAPSPAKVLPENWWQHPAALGATDSDIEIIKRQWGAFYGTDLELQLRRRGIDTIVLCG
      80        90       100       110       120       130         

           340                                                     
CYS1_D VSNFVSTSII                                                  
       .:.                                                         
gi|178 ISTNIGVESTARNAWELGFNLVIAEDACSAASAEQHNNSINHIYPRIARVRSVEEILNAL
     140       150       160       170       180       190         

>>gi|1789138|gb|AAC75818.1| (AE000361) putative kinase [  (492 aa)
 initn:  36 init1:  36 opt:  79  Z-score: 94.7  bits: 26.5 E():  7.8
Smith-Waterman score: 84;  19.136% identity (21.233% ungapped) in 162 aa overlap (34-192:165-313)

            10        20        30        40        50        60   
CYS1_D ILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELN
                                     ::::     ...:   ..  . ::.:    
gi|178 GEFKDNIANYFGQWPVDYKSWAWSEDAAVMDKFNIP---RHMLFDVQMPGTVLGHITPQA
          140       150       160       170          180       190 

            70        80        90       100       110       120   
CYS1_D LIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFD
        .: .  :     :   .:   . .    :... :...    .: ... . . . :.:. 
gi|178 ALATHFPAGLPV-VCTTSDKPVEALGAGLLDDETAVISLGTYIALMMNGKALPKDPVAY-
             200        210       220       230       240          

           130          140       150       160       170       180
CYS1_D WRTRGAVTPV---KNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY
       :   ...  .   .. :   . :. :   .. :. .:.. .  .:: ..:..    :.  
gi|178 WPIMSSIPQTLLYEGYGIRKGMWTVSWLRDMLGESLIQDARAQDLSPEDLLNKKASCVP-
     250       260       270       280       290       300         

              190       200       210       220       230       240
CYS1_D EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTM
               ::::                                                
gi|178 -------PGCNGLMTVLDWLTNPWEPYKRGIMIGFDSSMDYAWIYRSILESVALTLKNNY
             310       320       330       340       350       360 

>>gi|1789427|gb|AAC76084.1| (AE000386) orf, hypothetical  (354 aa)
 initn:  65 init1:  40 opt:  76  Z-score: 93.5  bits: 25.8 E():  9.1
Smith-Waterman score: 76;  22.619% identity (23.899% ungapped) in 168 aa overlap (141-303:81-244)

              120       130       140       150       160       170
CYS1_D DDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNL
                                     : :.      . :: : .::. .     : 
gi|178 GDKIWQSSEYFMNVFCNNALPGPSPGEEYPSAWANIMMLLASGQDFYNQNSYTFGVTYNG
               60        70        80        90       100       110

              180       190       200        210       220         
CYS1_D VDCDHECMEYEGEEACDEGCNGGLQPNAYNY-IIKNGGIQTESSYPYTAETGTQCNFNSA
       :: :       .  .: .  ..:   :.:.   . .:: . . :  . ...  :  .. :
gi|178 VDYDSTSPLPIAAPVCIDIKGAGTFGNGYKKPAVCSGGPEPQLSVTFPVRV--QLYIKLA
              120       130       140       150       160          

     230       240       250       260       270          280      
CYS1_D NIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDI---PCNPN-SLD
       . . :...  ..: .: .   .   .:  :: .:  .  : : :. .:    :  : .:.
gi|178 KNANKVNKKLVLP-DEYIALEFKGMSGAGAIEVDK-NLTFRIRGLNNIHVLDCFVNVDLE
      170       180        190       200        210       220      

         290       300       310       320       330       340     
CYS1_D HGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII  
        .  .: ..  :.   ::                                          
gi|178 PADGVVDFGKINSRTIKNTSVSETFSVVMTKDPGAACTEQFNILGSFFTTDILSDYSHLD
        230       240       250       260       270       280      



343 residues in 1 query   sequences
1358987 residues in 4289 library sequences
 Scomplib [33t08]
 start: Sat Dec  8 11:43:36 2001 done: Sat Dec  8 11:43:37 2001
 Scan time:  1.110 Display time:  0.090

Function used was FASTA [version 3.3t08 Jan. 17, 2001]
BioPerl-1.007002/t/data/cysprot1.fa000444000766000024        55013155576321 16744 0ustar00cjfieldsstaff000000000000>CYS1_DICDI
MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHK
ADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCG
SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQT
ESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCN
PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII
BioPerl-1.007002/t/data/cysprot1a.fa000444000766000024       211113155576321 17120 0ustar00cjfieldsstaff000000000000>CYS1_DICDI
MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHK
ADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCG
SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQT
ESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCN
PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII


>ALEU_HORVU
MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGK
SYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRD
AAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNG
GLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAF
QVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCA
IATCASYPVVAA


>CATH_HUMAN
MWATLPLLCAGAWLLGVPVCGAAELSVNSLEKFHFKSWMSKHRKTYSTEEYHHRLQTFASNWRKINAHNN
GNHTFKMALNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPPSVDWRKKGNFVSPVKNQGACGS
CWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNYGCQGGLPSQAFEYILYNKGIMGEDTYPYQGK
DGYCKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVN
HAVLAVGYGEKNGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV

BioPerl-1.007002/t/data/cysprot1a.msf000444000766000024       361313155576321 17327 0ustar00cjfieldsstaff000000000000PileUp



   MSF:  383  Type: P    Check:  3696   .. 

 Name: ALEU_HORVU oo  Len:  383  Check:  9840  Weight:  34.4
 Name: CATH_HUMAN oo  Len:  383  Check:  7134  Weight:  30.1
 Name: CYS1_DICDI oo  Len:  383  Check:  6722  Weight:  35.4

//



ALEU_HORVU      MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG 
CATH_HUMAN      ......MWAT LPLLCAGAWL LG........ VPVCGAAELS VNSLEK.... 
CYS1_DICDI      .....MKVIL LFVLAVFTVF VS........ .......SRG IPPEEQ.... 


ALEU_HORVU      ALGRTRHALR FARFAVRYGK SYESAAEVRR RFRIFSESLE EVRSTN.... 
CATH_HUMAN      ........FH FKSWMSKHRK TYS.TEEYHH RLQTFASNWR KINAHN.... 
CYS1_DICDI      ........SQ FLEFQDKFNK KYS.HEEYLE RFEIFKSNLG KIEELNLIAI 


ALEU_HORVU      RKGLPYRLGI NRFSDMSWEE FQATRLG.AA QTCSATLAGN HLMRDAAA.. 
CATH_HUMAN      NGNHTFKMAL NQFSDMSFAE IKHKYLWSEP QNCSATKS.. NYLRGTGP.. 
CYS1_DICDI      NHKADTKFGV NKFADLSSDE FKNYYLNNKE AIFTDDLPVA DYLDDEFINS 


ALEU_HORVU      LPETKDWRED G.IVSPVKNQ AHCGSCWTFS TTGALEAAYT QATGKNISLS 
CATH_HUMAN      YPPSVDWRKK GNFVSPVKNQ GACGSCWTFS TTGALESAIA IATGKMLSLA 
CYS1_DICDI      IPTAFDWRTR G.AVTPVKNQ GQCGSCWSFS TTGNVEGQHF ISQNKLVSLS 


ALEU_HORVU      EQQLVDCAGG FNNF...... ..GCNGGLPS QAFEYIKYNG GIDTEESYPY 
CATH_HUMAN      EQQLVDCAQD FNNY...... ..GCQGGLPS QAFEYILYNK GIMGEDTYPY 
CYS1_DICDI      EQNLVDCDHE CMEYEGEEAC DEGCNGGLQP NAYNYIIKNG GIQTESSYPY 


ALEU_HORVU      KGVNGVCHYK AENAAVQVLD SVNITLNAED ELKNAVGLVR PVSVAFQVID 
CATH_HUMAN      QGKDGYCKFQ PGKAIGFVKD VANITIYDEE AMVEAVALYN PVSFAFEVTQ 
CYS1_DICDI      TAETGTQCNF NSANIGAKIS NFTMIPKNET VMAGYIVSTG PLAIAADAVE 


ALEU_HORVU      GFRQYKSGVY TSDHCGTTPD DVNHAVLAVG YGVEN..... GVPYWLIKNS 
CATH_HUMAN      DFMMYRTGIY SSTSCHKTPD KVNHAVLAVG YGEKN..... GIPYWIVKNS 
CYS1_DICDI      .WQFYIGGVF DIPCN...PN SLDHGILIVG YSAKNTIFRK NMPYWIVKNS 


ALEU_HORVU      WGADWGDNGY FKMEMGKNMC AIATCASYPV VAA
CATH_HUMAN      WGPQWGMNGY FLIERGKNMC GLAACASYPI PLV
CYS1_DICDI      WGADWGEQGY IYLRRGKNTC GVSNFVSTSI I..

BioPerl-1.007002/t/data/cysprot1b.fa000444000766000024       261213155576321 17127 0ustar00cjfieldsstaff000000000000>CATH_RAT
MWTALPLLCAGAWLLSAGATAELTVNAIEKFHFTSWMKQHQKTYSSREYSHRLQVFANNWRKIQAHNQRN
HTFKMGLNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPSSMDWRKKGNVVSPVKNQGACGSCW
TFSTTGALESAVAIASGKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIGKNG
QCKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHA
VLAVGYGEQNGLLYWIVKNSWGSNWGNNGYFLIERGKNMCGLAACASYPIPQV


>CATL_HUMAN
MNPTLILAAFCLGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGK
HSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSCWA
FSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEES
CKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLV
VGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV


>CATL_RAT
MTPLLLLAVLCLGTALATPKFDQTFNAQWHQWKSTHRRLYGTNEEEWRRAVWEKNMRMIQLHNGEYSNGK
HGFTMEMNAFGDMTNEEFRQIVNGYRHQKHKKGRLFQEPLMLQIPKTVDWREKGCVTPVKNQGQCGSCWA
FSASGCLEGQMFLKTGKLISLSEQNLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGS
CKYRAEYAVANDTGFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCSSKDLDHGVLV
VGYGYEGTDSNKDKYWLVKNSWGKEWGMDGYIKIAKDRNNHCGLATAASYPIVN


>PAPA_CARPA
MAMIPSISKLLFVAICLFVYMGLSFGDFSIVGYSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFE
IFKDNLKYIDETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDW
RQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQ
YGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGG
IFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN



BioPerl-1.007002/t/data/cysprot1b.hmmsearch000444000766000024      2066313155576321 20536 0ustar00cjfieldsstaff000000000000hmmsearch - search a sequence database with a profile HMM
HMMER 2.2g (August 2001)
Copyright (C) 1992-2001 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:                   Peptidase_C1.hmm [Peptidase_C1]
Sequence database:          cysprot1b.fa
per-sequence score cutoff:  [none]
per-domain score cutoff:    [none]
per-sequence Eval cutoff:   <= 10        
per-domain Eval cutoff:     [none]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query HMM:   Peptidase_C1
Accession:   PF00112
Description: Papain family cysteine protease
  [HMM has been calibrated; E-values are empirical estimates]

Scores for complete sequences (score includes all domains):
Sequence   Description                                  Score    E-value  N 
--------   -----------                                  -----    ------- ---
CATL_RAT                                                449.4     2e-135   1
CATL_HUMAN                                              444.5   6.1e-134   1
CATH_RAT                                                381.8   4.8e-115   1
PAPA_CARPA                                              337.7     9e-102   1

Parsed for domains:
Sequence   Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------   ------- ----- -----    ----- -----      -----  -------
CATL_RAT     1/1     114   332 ..     1   337 []   449.4   2e-135
CATL_HUMAN   1/1     114   332 ..     1   337 []   444.5 6.1e-134
CATH_RAT     1/1     114   330 ..     1   337 []   381.8 4.8e-115
PAPA_CARPA   1/1     134   343 ..     1   337 []   337.7   9e-102

Alignments of top-scoring domains:
CATL_RAT: domain 1 of 1, from 114 to 332: score 449.4, E = 2e-135
                   *->lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgryciktgt
                      +P+++DWRe kg  VtpVK+QG qCGSCWAFSa g lEg+ ++kt  
    CATL_RAT   114    IPKTVDWRE-KG-CVTPVKNQG-QCGSCWAFSASGCLEGQMFLKT-- 155  

                   kawggklvsLSEQqLvDCdgedygnngesCGyGCnGGGlmdnAfeYikke
                       gkl+sLSEQ+LvDC++ d gn+      GCnG Glmd Af+Yik+ 
    CATL_RAT   156 ----GKLISLSEQNLVDCSH-DQGNQ------GCNG-GLMDFAFQYIKE- 192  

                   qIsnNgGlvtEsdYekgCkPYtdfPCgkdggndtyypCpgkaydpndTgt
                       NgGl++E++Y     PY+    +kd                   g+
    CATL_RAT   193 ----NGGLDSEESY-----PYE----AKD-------------------GS 210  

                   CkynckknskypktyakikgygdvpynvsTydEealqkalaknGPvsVai
                   Cky+  + ++     a+++g++d+p++     E+al+ka+a++GP+sVa+
    CATL_RAT   211 CKYR-AEYAV-----ANDTGFVDIPQQ-----EKALMKAVATVGPISVAM 249  

                   dasedskgDFqlYksGendvgyGvYkhtsageCggtpfteLdHAVliVGY
                   das+ s    q+Y+sG       +Y+++    C+++   +LdH+Vl+VGY
    CATL_RAT   250 DASHPS---LQFYSSG-------IYYEP---NCSSK---DLDHGVLVVGY 283  

                   GteneggtfdetssskksesgiqvssgsngssgSSgssgapiedkgkdYW
                   G e+                                      ++++ +YW
    CATL_RAT   284 GYEG-T------------------------------------DSNKDKYW 296  

                   IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi<-*
                   +VKNSWG++WG++GY++ia+++n    n+CG+a+ asypi   
    CATL_RAT   297 LVKNSWGKEWGMDGYIKIAKDRN----NHCGLATAASYPI    332  

CATL_HUMAN: domain 1 of 1, from 114 to 332: score 444.5, E = 6.1e-134
                   *->lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgryciktgt
                      +P s+DWRe kg +VtpVK+QG qCGSCWAFSa+galEg+ ++kt  
  CATL_HUMAN   114    APRSVDWRE-KG-YVTPVKNQG-QCGSCWAFSATGALEGQMFRKT-- 155  

                   kawggklvsLSEQqLvDCdgedygnngesCGyGCnGGGlmdnAfeYikke
                       g l+sLSEQ+LvDC+g + gn+      GCnG Glmd+Af+Y+++ 
  CATL_HUMAN   156 ----GRLISLSEQNLVDCSG-PQGNE------GCNG-GLMDYAFQYVQD- 192  

                   qIsnNgGlvtEsdYekgCkPYtdfPCgkdggndtyypCpgkaydpndTgt
                       NgGl++E++Y     PY+    +++                    +
  CATL_HUMAN   193 ----NGGLDSEESY-----PYE----ATE-------------------ES 210  

                   CkynckknskypktyakikgygdvpynvsTydEealqkalaknGPvsVai
                   Ckyn +k s+     a+++g++d+p +     E+al+ka+a++GP+sVai
  CATL_HUMAN   211 CKYN-PKYSV-----ANDTGFVDIPKQ-----EKALMKAVATVGPISVAI 249  

                   dasedskgDFqlYksGendvgyGvYkhtsageCggtpfteLdHAVliVGY
                   da++ s   F +Yk G       +Y ++   +C+++   + dH+Vl+VGY
  CATL_HUMAN   250 DAGHES---FLFYKEG-------IYFEP---DCSSE---DMDHGVLVVGY 283  

                   GteneggtfdetssskksesgiqvssgsngssgSSgssgapiedkgkdYW
                   G e+                                      e+++ +YW
  CATL_HUMAN   284 GFES-T------------------------------------ESDNNKYW 296  

                   IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi<-*
                   +VKNSWG++WG+ GY+++a+++     n+CGIas asyp+   
  CATL_HUMAN   297 LVKNSWGEEWGMGGYVKMAKDRR----NHCGIASAASYPT    332  

CATH_RAT: domain 1 of 1, from 114 to 330: score 381.8, E = 4.8e-115
                   *->lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgryciktgt
                       P s+DWR+ kg  V+pVK+QG  CGSCW FS++galE++ +i++  
    CATH_RAT   114    YPSSMDWRK-KGNVVSPVKNQG-ACGSCWTFSTTGALESAVAIAS-- 156  

                   kawggklvsLSEQqLvDCdgedygnngesCGyGCnGGGlmdnAfeYikke
                       gk   L EQqLvDC   +++n+      GC+G Gl+++AfeYi++ 
    CATH_RAT   157 ----GKMMTLAEQQLVDCAQ-NFNNH------GCQG-GLPSQAFEYILY- 193  

                   qIsnNgGlvtEsdYekgCkPYtdfPCgkdggndtyypCpgkaydpndTgt
                       N+G++ E++Y     PY     gk+                   g+
    CATH_RAT   194 ----NKGIMGEDSY-----PYI----GKN-------------------GQ 211  

                   CkynckknskypktyakikgygdvpynvsTydEealqkalaknGPvsVai
                   Ck+n +++++     a++k+ ++++ n    dE+a+ +a+a + Pvs a+
    CATH_RAT   212 CKFN-PEKAV-----AFVKNVVNITLN----DEAAMVEAVALYNPVSFAF 251  

                   dasedskgDFqlYksGendvgyGvYkhtsageCggtpfteLdHAVliVGY
                   +++e    DF++YksG       vY++    +C +tp + ++HAVl+VGY
    CATH_RAT   252 EVTE----DFMMYKSG-------VYSSN---SCHKTP-DKVNHAVLAVGY 286  

                   GteneggtfdetssskksesgiqvssgsngssgSSgssgapiedkgkdYW
                   G +n g                                          YW
    CATH_RAT   287 GEQN-GLL----------------------------------------YW 295  

                   IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi<-*
                   IVKNSWG++WG nGYf i+Rgkn     +CG+a +asypi   
    CATH_RAT   296 IVKNSWGSNWGNNGYFLIERGKN-----MCGLAACASYPI    330  

PAPA_CARPA: domain 1 of 1, from 134 to 343: score 337.7, E = 9e-102
                   *->lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgryciktgt
                      +Pe +DWR+ kg aVtpVK+QG +CGSCWAFSav ++Eg+++i+t  
  PAPA_CARPA   134    IPEYVDWRQ-KG-AVTPVKNQG-SCGSCWAFSAVVTIEGIIKIRT-- 175  

                   kawggklvsLSEQqLvDCdgedygnngesCGyGCnGGGlmdnAfeYikke
                       g+l  +SEQ+L+DCd+    ++      GCnG G+++ A++ + + 
  PAPA_CARPA   176 ----GNLNEYSEQELLDCDR---RSY------GCNG-GYPWSALQLVAQ- 210  

                   qIsnNgGlvtEsdYekgCkPYtdfPCgkdggndtyypCpgkaydpndTgt
                         G++    Y     PY+    g++                     
  PAPA_CARPA   211 -----YGIHYRNTY-----PYE----GVQ-------------------RY 227  

                   CkynckknskypktyakikgygdvpynvsTydEealqkalaknGPvsVai
                   C+++ +k+ +    +ak +g ++v+++    +E al + +a+ +PvsV  
  PAPA_CARPA   228 CRSR-EKGPY----AAKTDGVRQVQPY----NEGALLYSIAN-QPVSVVL 267  

                   dasedskgDFqlYksGendvgyGvYkhtsageCggtpfteLdHAVliVGY
                   +a +    DFqlY++G       ++++    +Cg+     +dHAV++VGY
  PAPA_CARPA   268 EAAGK---DFQLYRGG-------IFVG----PCGN----KVDHAVAAVGY 299  

                   GteneggtfdetssskksesgiqvssgsngssgSSgssgapiedkgkdYW
                   G                                              +Y 
  PAPA_CARPA   300 G---------------------------------------------PNYI 304  

                   IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi<-*
                   ++KNSWGt WGEnGY+ri+Rg+++s ++ CG+ ++  yp+   
  PAPA_CARPA   305 LIKNSWGTGWGENGYIRIKRGTGNS-YGVCGLYTSSFYPV    343  


Histogram of all scores:
score    obs    exp  (one = represents 1 sequences)
-----    ---    ---
> 337      4      -|====                                                       


% Statistical details of theoretical EVD fit:
              mu =  -195.8384
          lambda =     0.1423
chi-sq statistic =     0.0000
  P(chi-square)  =          0

Total sequences searched: 4

Whole sequence top hits:
tophits_s report:
     Total hits:           4
     Satisfying E cutoff:  4
     Total memory:         16K

Domain top hits:
tophits_s report:
     Total hits:           4
     Satisfying E cutoff:  4
     Total memory:         20K
BioPerl-1.007002/t/data/cysprot1b.msf000444000766000024       464513155576321 17336 0ustar00cjfieldsstaff000000000000PileUp



   MSF:  366  Type: P    Check:  8252   .. 

 Name: CATL_HUMAN oo  Len:  366  Check:  9087  Weight:  21.6
 Name: CATL_RAT oo  Len:  366  Check:   271  Weight:  20.7
 Name: CATH_RAT oo  Len:  366  Check:  8974  Weight:  27.9
 Name: PAPA_CARPA oo  Len:  366  Check:  9920  Weight:  29.7

//



CATL_HUMAN      ......MNPT LILAAFCLGI .......... ...ASATLTF DHSLEAQWTK 
CATL_RAT        ......MTPL LLLAVLCLGT .......... ...ALATPKF DQTFNAQWHQ 
CATH_RAT        ...MWTALPL LCAGAWLLSA G......... ...ATAELTV NAIEKFHFTS 
PAPA_CARPA      MAMIPSISKL LFVAICLFVY MGLSFGDFSI VGYSQNDLTS TERLIQLFES 


CATL_HUMAN      WKAMHNRLYG .MNEEGWRRA VWEKNMKMIE LHNQEYREGK HSFTMAMNAF 
CATL_RAT        WKSTHRRLYG .TNEEEWRRA VWEKNMRMIQ LHNGEYSNGK HGFTMEMNAF 
CATH_RAT        WMKQHQKTYS .SREYSHRLQ VFANNWRKIQ AHNQRN.... HTFKMGLNQF 
PAPA_CARPA      WMLKHNKIYK NIDEKIYRFE IFKDNLKYID ETNKKN.... NSYWLGLNVF 


CATL_HUMAN      GDMTSEEFRQ VMNGFQNRKP RKGKVFQEPL FY....EAPR SVDWREKG.Y 
CATL_RAT        GDMTNEEFRQ IVNGYRHQKH KKGRLFQEPL ML....QIPK TVDWREKG.C 
CATH_RAT        SDMSFAEIKH KYLWSEPQNC SATKSNYLRG TG....PYPS SMDWRKKGNV 
PAPA_CARPA      ADMSNDEFKE KYTGSIAGNY TTTELSYEEV LNDGDVNIPE YVDWRQKG.A 


CATL_HUMAN      VTPVKNQGQC GSCWAFSATG ALEGQMFRKT GRLISLSEQN LVDCSGPQGN 
CATL_RAT        VTPVKNQGQC GSCWAFSASG CLEGQMFLKT GKLISLSEQN LVDCSHDQGN 
CATH_RAT        VSPVKNQGAC GSCWTFSTTG ALESAVAIAS GKMMTLAEQQ LVDCAQNFNN 
PAPA_CARPA      VTPVKNQGSC GSCWAFSAVV TIEGIIKIRT GNLNEYSEQE LLDCDRR..S 


CATL_HUMAN      EGCNGGLMDY AFQYVQDNGG LDSEESYPYE ATEESCKYNP KYSVANDTGF 
CATL_RAT        QGCNGGLMDF AFQYIKENGG LDSEESYPYE AKDGSCKYRA EYAVANDTGF 
CATH_RAT        HGCQGGLPSQ AFEYILYNKG IMGEDSYPYI GKNGQCKFNP EKAVAFVKNV 
PAPA_CARPA      YGCNGGYPWS ALQLVAQYG. IHYRNTYPYE GVQRYCRSRE KGPYAAKTDG 


CATL_HUMAN      VDIPK.QEKA LMKAVATVGP ISVAIDAGHE SFLFYKEGIY FEPDCSS..E 
CATL_RAT        VDIPQ.QEKA LMKAVATVGP ISVAMDASHP SLQFYSSGIY YEPNCSS..K 
CATH_RAT        VNITLNDEAA MVEAVALYNP VSFAFEVT.E DFMMYKSGVY SSNSCHKTPD 
PAPA_CARPA      VRQVQPYNEG ALLYSIANQP VSVVLEAAGK DFQLYRGGIF VGP.CGN... 


CATL_HUMAN      DMDHGVLVVG YGFESTESDN NKYWLVKNSW GEEWGMGGYV KMAKDRR... 
CATL_RAT        DLDHGVLVVG YGYEGTDSNK DKYWLVKNSW GKEWGMDGYI KIAKDRN... 
CATH_RAT        KVNHAVLAVG YG....EQNG LLYWIVKNSW GSNWGNNGYF LIERGK.... 
PAPA_CARPA      KVDHAVAAVG YG........ PNYILIKNSW GTGWGENGYI RIKRGTGNSY 


CATL_HUMAN      NHCGIASAAS YPTV..
CATL_RAT        NHCGLATAAS YPIVN.
CATH_RAT        NMCGLAACAS YPIPQV
PAPA_CARPA      GVCGLYTSSF YPVKN.

BioPerl-1.007002/t/data/cysprot1b.newick000444000766000024        13513155576321 17777 0ustar00cjfieldsstaff000000000000(
CATH_RAT:0.31356,
(
CATL_HUMAN:0.13938,
CATL_RAT:0.12788)
95:0.18794,
PAPA_CARPA:0.34410);
BioPerl-1.007002/t/data/cysprot_vs_gadfly.FASTA000444000766000024     12363513155576321 21263 0ustar00cjfieldsstaff000000000000 FASTA searches a protein or DNA sequence data bank
 version 3.3t08 Jan. 17, 2001
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

 cysprot.fa, 2385 aa
 vs /data_2/jason/blastdb/gadflypep2 library

7177762 residues in 14334 sequences
  Expectation_n fit: rho(ln(x))= 4.9846+/-0.000606; mu= 15.4125+/- 0.036
 mean_var=84.2366+/-16.296, 0's: 5 Z-trim: 12  B-trim: 404 in 1/54
 Lambda= 0.1397

FASTA (3.36 June 2000) function [optimized, BL50 matrix (15:-5)] ktup: 2
 join: 43, opt: 31, gap-pen: -12/ -2, width:  16
The best scores are:                                       opt bits E(14315)
Cp1|FBgn0013770|pp-CT20780|FBan0006692 GO:[cathep  ( 341) 1073  228 3.1e-59
CG11459|FBgn0037396|pp-CT28891|FBan0011459 GO:[ca  ( 336)  771  167 6.4e-41
CG4847|FBgn0034229|pp-CT15577|FBan0004847 GO:[end  ( 390)  762  165 2.5e-40
26/29kD-proteinase|FBgn0028967|pp-CT25694|FBan000  ( 549)  712  155 3.5e-37
CG12163|FBgn0037303|pp-CT8855|FBan0012163 GO:[] m  ( 475)  558  124 6.9e-28
CG1075|FBgn0037397|pp-CT1381|FBan0001075 GO:[cath  ( 274)  413   95   3e-19
CG6347|FBgn0033874|pp-CT19836|FBan0006347 GO:[cat  ( 235)  311   74 4.1e-13
CG6337|FBgn0033873|pp-CT19824|FBan0006337 GO:[end  ( 340)  265   65 3.3e-10
CG5367|FBgn0032228|pp-CT17056|FBan0005367 GO:[end  ( 228)  249   62 2.4e-09
CG3074|FBgn0034709|pp-CT10308|FBan0003074 GO:[cat  ( 441)  252   62 2.4e-09
CG10992|FBgn0030521|pp-CT30795|FBan0010992 GO:[ca  ( 340)  235   59 2.2e-08
CG10460|FBgn0034443|pp-CT29364|FBan0010460 GO:[en  (  79)  131   37   0.016
Ddx1|FBgn0015075|pp-CT25986|FBan0009054 GO:[helic  ( 727)  107   33     2.2
CPTI|FBgn0027842|pp-CT32036|FBan0012891 GO:[carni  ( 780)  105   33       3
CG4393|FBgn0039075|pp-CT14338|FBan0004393 GO:[cyt  ( 968)  105   33     3.5
CG4392|FBgn0036283|pp-CT14260|FBan0004392 GO:[mit  ( 370)  100   32     3.6
CG14034|FBgn0031691|pp-CT33593|FBan0014034 GO:[ph  ( 223)   93   30     6.8
CG6357|FBgn0033875|pp-CT19866|FBan0006357 GO:[end  ( 439)   96   31     7.2
CG11288|FBgn0039895|pp-CT31491|FBan0011288 GO:[ce  ( 202)   91   30     8.4
CG13155|FBgn0033723|pp-CT32396|FBan0013155 GO:[]   ( 236)   91   30     9.3
CG4810|FBgn0037994|pp-CT15451|FBan0004810 GO:[tra  ( 551)   95   31     9.6


>>Cp1|FBgn0013770|pp-CT20780|FBan0006692 GO:[cathepsin L  (341 aa)
 initn: 829 init1: 615 opt: 1073  Z-score: 1170.6  bits: 227.8 E(): 3.1e-59
Smith-Waterman score: 1219;  53.043% identity (56.135% ungapped) in 345 aa overlap (1373-1706:5-341)

           1350      1360      1370      1380      1390      1400  
PAPA_C SNWGNNGYFLIERGKNMCGLAACASYPIPQVMNPTLILAAFCLGIASATLTFDHSLEAQW
                                     :. : : :    :..:.: ..:   .  .:
Cp1|FB                           MRTAVLLPLLAL----LAVAQA-VSFADVVMEEW
                                         10             20         

           1410       1420      1430      1440      1450      1460 
PAPA_C TKWKAMHNRLY-GMNEEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEF
         .:  : . :   .:: .:  ....: . :  :::.. ::: :: .:.: ..:.  .::
Cp1|FB HTFKLEHRKNYQDETEERFRLKIFNENKHKIAKHNQRFAEGKVSFKLAVNKYADLLHHEF
      30        40        50        60        70        80         

               1470            1480      1490      1500      1510  
PAPA_C RQVMNGFQ---NRKPR------KGKVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSCW
       ::.::::.   ... :      :: .:  :     :.::::: :: :: ::.::.:::::
Cp1|FB RQLMNGFNYTLHKQLRAADESFKGVTFISPAHVTLPKSVDWRTKGAVTAVKDQGHCGSCW
      90       100       110       120       130       140         

           1520      1530      1540      1550      1560      1570  
PAPA_C AFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSE
       :::.::::::: :::.: :.:::::::::::   ::.:::::::: ::.:..::::.:.:
Cp1|FB AFSSTGALEGQHFRKSGVLVSLSEQNLVDCSTKYGNNGCNGGLMDNAFRYIKDNGGIDTE
     150       160       170       180       190       200         

           1580      1590      1600       1610      1620      1630 
PAPA_C ESYPYEATEESCKYNPKYSVANDTGFVDIPK-QEKALMKAVATVGPISVAIDAGHESFLF
       .:::::: ..::..:     :.: ::.:::. .:: . .:::::::.::::::.:::: :
Cp1|FB KSYPYEAIDDSCHFNKGTVGATDRGFTDIPQGDEKKMAEAVATVGPVSVAIDASHESFQF
     210       220       230       240       250       260         

            1640      1650      1660      1670      1680      1690 
PAPA_C YKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDR
       :.::.: ::.:.....::::::::.: . .  :   :::::::::  ::  :..:: ...
Cp1|FB YSEGVYNEPQCDAQNLDHGVLVVGFGTDESGED---YWLVKNSWGTTWGDKGFIKMLRNK
     270       280       290       300          310       320      

            1700      1710      1720      1730      1740      1750 
PAPA_C RNHCGIASAASYPTVMTPLLLLAVLCLGTALATPKFDQTFNAQWHQWKSTHRRLYGTNEE
       .:.::::::.::: :                                             
Cp1|FB ENQCGIASASSYPLV                                             
        330       340                                              

>>CG11459|FBgn0037396|pp-CT28891|FBan0011459 GO:[catheps  (336 aa)
 initn: 350 init1: 191 opt: 771  Z-score: 841.7  bits: 166.9 E(): 6.4e-41
Smith-Waterman score: 771;  37.143% identity (38.870% ungapped) in 315 aa overlap (1399-1705:27-335)

     1370      1380      1390      1400      1410      1420        
PAPA_C PIPQVMNPTLILAAFCLGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKN
                                     ...: ..:: .:. :  :.. ..::..:. 
CG1145     MGTPRLTVVHGLILLLLVELGLTAVSDTEWDQYKAKYNKQY-RNRDKYHRALYEQR
                   10        20        30        40         50     

     1430      1440      1450      1460      1470      1480        
PAPA_C MKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFY---
       .  .: ::: : .:: .: :..: :.:  .. . .  ...      . ... : . :   
CG1145 VLAVESHNQLYLQGKVAFKMGLNKFSDTDQRILFNYRSSIPAPLETSTNALTETVNYKRY
          60        70        80        90       100       110     

         1490      1500       1510      1520      1530      1540   
PAPA_C -EAPRSVDWREKGYVTPVKNQG-QCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCS
        .  ...:::. ::..:: .:: .: ::::::..:.::..: .: : :. :: ..:::: 
CG1145 DQITEGIDWRQYGYISPVGDQGTECLSCWAFSTSGVLEAHMAKKYGNLVPLSPKHLVDCV
         120       130       140       150       160       170     

          1550      1560      1570      1580      1590      1600   
PAPA_C GPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPK
        :  :.::.:: .. ::.:..:.: . ..:::::: .   : ..   :... .:.: . .
CG1145 -PYPNNGCSGGWVSVAFNYTRDHG-IATKESYPYEPVSGECLWKSDRSAGTLSGYVTLGN
          180       190        200       210       220       230   

           1610      1620      1630      1640        1650      1660
PAPA_C -QEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSS--EDMDHGVLVVGYGFES
        .:. : ..: ..::..:.::  :: :  :. :.   : : :  .:. :.::.::.: . 
CG1145 YDERELAEVVYNIGPVAVSIDHLHEEFDQYSGGVLSIPACRSKRQDLTHSVLLVGFGTHR
           240       250       260       270       280       290   

             1670      1680      1690      1700      1710      1720
PAPA_C TESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTVMTPLLLLAVLCLGT
         .:   ::..:::.: .:: .::.:.:..  : ::.::  .:::               
CG1145 KWGD---YWIIKNSYGTDWGESGYLKLARNANNMCGVASLPQYPTF              
              300       310       320       330                    

             1730      1740      1750      1760      1770      1780
PAPA_C ALATPKFDQTFNAQWHQWKSTHRRLYGTNEEEWRRAVWEKNMRMIQLHNGEYSNGKHGFT

>>CG4847|FBgn0034229|pp-CT15577|FBan0004847 GO:[endopept  (390 aa)
 initn: 499 init1: 281 opt: 762  Z-score: 831.0  bits: 165.2 E(): 2.5e-40
Smith-Waterman score: 762;  42.857% identity (45.896% ungapped) in 287 aa overlap (1431-1706:112-390)

             1410      1420      1430      1440      1450      1460
PAPA_C QWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEE
                                     ..:  :  . .: :.: .:.:::.:.:  :
CG4847 FGDFLSQSGKTYLSAADRALHEGAFASTKNLVEAGNAAFAQGVHTFKQAVNAFADLTHSE
              90       100       110       120       130       140 

             1470            1480      1490      1500      1510    
PAPA_C FRQVMNGFQNRKPRKG------KVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSCWAF
       : . ..:..     :.      :. . :     : . ::::.: ::::: :: :::::::
CG4847 FLSQLTGLKRSPEAKARAAASLKLVNLPA-KPIPDAFDWREHGGVTPVKFQGTCGSCWAF
             150       160       170        180       190       200

         1520      1530      1540         1550      1560       1570
PAPA_C SATGALEGQMFRKTGRLISLSEQNLVDCSGPQ---GNEGCNGGLMDYAFQYVQD-NGGLD
       ..:::.::. ::::: : .::::::::: ::    : .::.::... :: .... . :..
CG4847 ATTGAIEGHTFRKTGSLPNLSEQNLVDC-GPVEDFGLNGCDGGFQEAAFCFIDEVQKGVS
              210       220        230       240       250         

             1580      1590      1600       1610      1620         
PAPA_C SEESYPYEATEESCKYNPKYSVANDTGFVDIP-KQEKALMKAVATVGPISVAIDAGHESF
       .: .:::  .. .:::. . : :.  ::. :: :.:. : :.:::.::.. ... : :..
CG4847 QEGAYPYIDNKGTCKYDGSKSGATLQGFAAIPPKDEEQLKKVVATLGPVACSVN-GLETL
     260       270       280       290       300       310         

    1630      1640      1650      1660      1670      1680         
PAPA_C LFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAK
         :  ::: . .:.. . .:..:::::: :. ..    ::.::::: . ::  :: .. .
CG4847 KNYAGGIYNDDECNKGEPNHSILVVGYGSEKGQD----YWIVKNSWDDTWGEKGYFRLPR
      320       330       340       350           360       370    

    1690      1700      1710      1720      1730      1740         
PAPA_C DRRNHCGIASAASYPTVMTPLLLLAVLCLGTALATPKFDQTFNAQWHQWKSTHRRLYGTN
        . :.: ::   :::.:                                           
CG4847 GK-NYCFIAEECSYPVV                                           
           380       390                                           

>>26/29kD-proteinase|FBgn0028967|pp-CT25694|FBan0008947   (549 aa)
 initn: 428 init1: 244 opt: 712  Z-score: 774.7  bits: 155.2 E(): 3.5e-37
Smith-Waterman score: 769;  40.625% identity (43.624% ungapped) in 320 aa overlap (1728-2036:238-546)

      1700      1710      1720      1730      1740       1750      
PAPA_C ASAASYPTVMTPLLLLAVLCLGTALATPKFDQTFNAQWHQWKSTHRRLYGTN-EEEWRRA
                                     :.  .  .:..:  :   : .. :.: :. 
26/29k DDSLQCVGFPGPGTGHYATFNPMQEFISGTDEHVDKAFHHFKRKHGVAYHSDTEHEHRKN
       210       220       230       240       250       260       

       1760      1770      1780      1790      1800       1810     
PAPA_C VWEKNMRMIQLHNGEYSNGKHGFTMEMNAFGDMTNEEFRQIVNGYRHQK-HKKGRLFQEP
       ....:.:.:. .:     .:  .:. .: ..: :.::..    ::. .  .. :. :   
26/29k IFRQNLRYIHSKN----RAKLTYTLAVNHLADKTEEELKA-RRGYKSSGIYNTGKPFPYD
       270       280           290       300        310       320  

           1820      1830      1840      1850      1860       1870 
PAPA_C LML---QIPKTVDWREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLKTG-KLISLSEQN
       .     .::   :::  : :::::.:. :::::.:.. : ::: .:::.: .:. ::.: 
26/29k VPKYKDEIPDQYDWRLYGAVTPVKDQSVCGSCWSFGTIGHLEGAFFLKNGGNLVRLSQQA
            330       340       350       360       370       380  

            1880      1890       1900       1910      1920         
PAPA_C LVDCSHDQGNQGCNGGLMDF-AFQYIKENGGLDSEESY-PYEAKDGSCKYRAEYAVANDT
       :.:::   ::.::.::  :: ..:.. ..::. .:: : :: ..:: :.      ::   
26/29k LIDCSWAYGNNGCDGG-EDFRVYQWMLQSGGVPTEEEYGPYLGQDGYCHVNNVTLVAPIK
            390        400       410       420       430       440 

    1930      1940       1950      1960      1970        1980      
PAPA_C GFVDIPQQEKALMK-AVATVGPISVAMDASHPSLQFYSSGIYYEPNCSS--KDLDHGVLV
       :::.. ...   .: :.   ::.:::.:::  ...::: :.::::.:..    :::.::.
26/29k GFVNVTSNDPNAFKLALLKHGPLSVAIDASPKTFSFYSHGVYYEPTCKNDVDGLDHAVLA
             450       460       470       480       490       500 

       1990      2000      2010      2020      2030      2040      
PAPA_C VGYGYEGTDSNKDKYWLVKNSWGKEWGMDGYIKIAKDRNNHCGLATAASYPIVNMAMIPS
       ::::    . : . ::::::::.  :: :::: ..  .:: ::. :  .:          
26/29k VGYG----SINGEDYWLVKNSWSTYWGNDGYILMSAKKNN-CGVMTMPTYVEM       
                 510       520       530        540                

       2050      2060      2070      2080      2090      2100      
PAPA_C ISKLLFVAICLFVYMGLSFGDFSIVGYSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKI

>>CG12163|FBgn0037303|pp-CT8855|FBan0012163 GO:[] mol_we  (475 aa)
 initn: 356 init1: 356 opt: 558  Z-score: 607.7  bits: 124.1 E(): 6.9e-28
Smith-Waterman score: 847;  41.615% identity (44.816% ungapped) in 322 aa overlap (29-343:169-474)

                 10        20        30        40         50       
PAPA_C   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKY-SHEEYLERFEIFKSNLG
                                     : .:: .:...: :  :   :..::..:: 
CG1216 VQARHTRSVEWAEKKTHKKHSHRFDKVDHLFYKFQVRFGRRYVSTAERQMRLRIFRQNLK
      140       150       160       170       180       190        

        60        70        80        90        100       110      
PAPA_C KIEELNLIAINHKADTKFGVNKFADLSSDEFKNYY-LNNKEAIFTDDLPVADYLDDEFIN
        :::::    :. ...:.:...:::..:.:.:.   : ...   .    .:  .   . .
CG1216 TIEELN---ANEMGSAKYGITEFADMTSSEYKERTGLWQRDEAKATGGSAA--VVPAYHG
      200          210       220       230       240         250   

        120       130       140       150       160       170      
PAPA_C SIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE
        .:  :::: . ::: :::::.:::::.::.:::.:: . .. ..:  .:::.:.:::  
CG1216 ELPKEFDWRQKDAVTQVKNQGSCGSCWAFSVTGNIEGLYAVKTGELKEFSEQELLDCD--
           260       270       280       290       300       310   

        180       190       200       210       220       230      
PAPA_C CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKIS
               . : .:::::. :::. :   ::.. :. ::: :. . ::.:: .   ....
CG1216 --------TTDSACNGGLMDNAYKAIKDIGGLEYEAEYPYKAKKN-QCHFNRTLSHVQVA
                     320       330       340        350       360  

        240        250       260       270          280       290  
PAPA_C NFTMIPK-NETVMAGYIVSTGPLAIAADAVEWQFYIGGV---FDIPCNPNSLDHGILIVG
       .:. .:: :::.:  .....::..:. .:   ::: :::   .   :. ..::::.:.::
CG1216 GFVDLPKGNETAMQEWLLANGPISIGINANAMQFYRGGVSHPWKALCSKKNLDHGVLVVG
            370       380       390       400       410       420  

             300       310       320       330       340       350 
PAPA_C YSAKN-TIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSIIMAHARVLL
       :....   :.:..::::::::::  ::::::  . :: ::::::........        
CG1216 YGVSDYPNFHKTLPYWIVKNSWGPRWGEQGYYRVYRGDNTCGVSEMATSAVLA       
            430       440       450       460       470            

             360       370       380       390       400       410 
PAPA_C LALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRY

>>CG1075|FBgn0037397|pp-CT1381|FBan0001075 GO:[cathepsin  (274 aa)
 initn: 233 init1: 148 opt: 413  Z-score: 452.7  bits: 94.7 E(): 3e-19
Smith-Waterman score: 413;  36.548% identity (39.130% ungapped) in 197 aa overlap (1522-1715:87-273)

            1500      1510      1520      1530      1540      1550 
PAPA_C DWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGC
                                     :.  ::.:   .:: ..::::  :  :.::
CG1075 QAVANHNGLYSQGRSGFRMGLNQLYIASASGEEVRKVG---DLSPKHLVDCF-PYPNQGC
         60        70        80        90          100        110  

            1560      1570      1580      1590      1600       1610
PAPA_C NGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQ-EKALMK
       :.: .. ::.. .: : . :.:::::.  .  :... . :...   .: . .. :. : :
CG1075 NAGWVSVAFNFKRDYG-IASKESYPYKPENGECRWDRRKSTGTLREYVTLTSNDERELAK
            120        130       140       150       160       170 

             1620      1630      1640        1650      1660        
PAPA_C AVATVGPISVAIDAGHESFLFYKEGIYFEPDC--SSEDMDHGVLVVGYGFESTESDNNKY
       .:  .::. :.::  :: :  :  ::   :.:  .. :. :.::.::.  .   .:   :
CG1075 VVYKIGPVEVSIDHLHEEFDQYFGGILRTPSCRNTNYDLKHSVLLVGFETHPKWGD---Y
             180       190       200       210       220           

     1670      1680      1690      1700      1710      1720        
PAPA_C WLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTVMTPLLLLAVLCLGTALATPKFD
       :..:::.: ::: .:: :.:.. ..:  . : .:   .. : :  :.             
CG1075 WIIKNSYGTEWGESGYFKLARNCEQH--VISMTSIAKLVLPCLTEALN            
      230       240       250         260       270                

     1730      1740      1750      1760      1770      1780        
PAPA_C QTFNAQWHQWKSTHRRLYGTNEEEWRRAVWEKNMRMIQLHNGEYSNGKHGFTMEMNAFGD

>>CG6347|FBgn0033874|pp-CT19836|FBan0006347 GO:[cathepsi  (235 aa)
 initn: 273 init1: 273 opt: 311  Z-score: 342.4  bits: 74.0 E(): 4.1e-13
Smith-Waterman score: 436;  37.000% identity (39.785% ungapped) in 200 aa overlap (1710-1899:15-210)

    1680      1690      1700      1710      1720        1730       
PAPA_C GMGGYVKMAKDRRNHCGIASAASYPTVMTPLLLLAVLCLGTALATPKF-D-QTFNAQWHQ
                                     : ::... :    . ::. : :.:.   .:
CG6347                 MRMCSTMWLQMTLGLALLGAVSLQQLQSFPKLCDVQNFDDFLRQ
                               10        20        30        40    

      1740      1750      1760      1770      1780      1790       
PAPA_C WKSTHRRLYGTNEEEWRRAVWEKNMRMIQLHNGEYSNGKHGFTMEMNAFGDMTNEEFRQI
             ..:. .:. .:....  .: .: : : . .::  :: . .:...::: .:.  .
CG6347 TG----KVYSDEERVYRESIFAAKMSLITLSNKNADNGVSGFRLGVNTLADMTRKEIATL
               50        60        70        80        90       100

            1800       1810      1820      1830       1840         
PAPA_C VN------GYRHQK-HKKGRLFQEPLMLQIPKTVDWREKGCVTPVKNQG-QCGSCWAFSA
       ..      : :. . : .    ..:   ..:.  :::::: :::   ::  ::.::.:..
CG6347 LGSKISEFGERYTNGHINFVTARNPASANLPEMFDWREKGGVTPPGFQGVGCGACWSFAT
              110       120       130       140       150       160

    1850      1860      1870      1880      1890      1900         
PAPA_C SGCLEGQMFLKTGKLISLSEQNLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLDSEESYP
       .: :::..: .:: : :::.::::::. : ::.::.::.....:.::...          
CG6347 TGALEGHLFRRTGVLASLSQQNLVDCADDYGNMGCDGGFQEYGFEYIRDHERNRRTSTAR
              170       180       190       200       210       220

    1910      1920      1930      1940      1950      1960         
PAPA_C YEAKDGSCKYRAEYAVANDTGFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGI
                                                                   
CG6347 ESGENSRLCHHYSRG                                             
              230                                                  

>>CG6337|FBgn0033873|pp-CT19824|FBan0006337 GO:[endopept  (340 aa)
 initn: 191 init1: 112 opt: 265  Z-score: 290.3  bits: 64.9 E(): 3.3e-10
Smith-Waterman score: 346;  28.707% identity (31.488% ungapped) in 317 aa overlap (1073-1369:28-336)

           1050      1060      1070      1080         1090         
PAPA_C TALPLLCAGAWLLSAGATAELTVNAIEKFHFTSWMKQHQKTYSS---REYSHRLQVFANN
                                     : ..  . .:::.:   :....   ..  :
CG6337    MFKLLLCCLLLTIDSGWAFNHGQDLVDFQTYEDNFNKTYASTSARNFANYYFIYNRN
                  10        20        30        40        50       

    1100         1110       1120      1130      1140      1150     
PAPA_C WRKIQAHN---QRNHT-FKMGLNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYP
         ..  ::   .::.: .. ..:::::. .  :.   :  .  :  .. ..   ..    
CG6337 --QVAQHNAQADRNRTTYREAVNQFSDIRL--IQFAALLPKAVNTVTSAASDPPASQAAS
          60        70        80          90       100       110   

        1160      1170       1180        1190      1200      1210  
PAPA_C SSMDWRKKGNVVSPVKNQGA-CGSCWTFSTTGALE--SAVAIASGKMMTLAEQQLVDCAQ
       .:.:     ...  :..::. :.: :...:. :.:  .::  :.    .:. :::.::: 
CG6337 ASFDIITDFGLTVAVEDQGVNCSSSWAYATAKAVEIMNAVQTANPLPSSLSAQQLLDCAG
           120       130       140       150       160       170   

           1220      1230        1240         1250      1260       
PAPA_C NFNNHGCQGGLPSQAFEYI--LYNKGIMGEDSYPY---IGKNGQCKFNPEKAVAFVK--N
          . ::.   :  :..:.  : .  .. : .::    .   :.:.  : .. . ::  .
CG6337 M--GTGCSTQTPLAALNYLTQLTDAYLYPEVDYPNNNSLKTPGMCQ-PPSSVSVGVKLAG
             180       190       200       210        220       230

        1270      1280      1290       1300      1310      1320    
PAPA_C VVNITLNDEAAMVEAVALYNPVSFAFE-VTEDFMMYKSGVYSSNSCHKTPDKVNHAVLAV
         ... ::.::... :.   ::   .. .:  ::.:.:::: ...   :  : .. ...:
CG6337 YSTVADNDDAAVMRYVSNGFPVIVEYNPATFGFMQYSSGVYVQETRALTNPKSSQFLVVV
              240       250       260       270       280       290

           1330      1340      1350      1360      1370      1380  
PAPA_C GYGEQ--NGLLYWIVKNSWGSNWGNNGYFLIERGKNMCGLAACASYPIPQVMNPTLILAA
       :: ..  ..: ::   ::.:..::..::. : : .:.  .:  : .:             
CG6337 GYDHDVDSNLDYWRCLNSFGDTWGEEGYIRIVRRSNQ-PIAKNAVFPSALA         
              300       310       320        330       340         

           1390      1400      1410      1420      1430      1440  
PAPA_C FCLGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREG

>>CG5367|FBgn0032228|pp-CT17056|FBan0005367 GO:[endopept  (228 aa)
 initn: 309 init1: 173 opt: 249  Z-score: 275.0  bits: 61.5 E(): 2.4e-09
Smith-Waterman score: 493;  30.556% identity (40.741% ungapped) in 288 aa overlap (1425-1706:7-228)

         1400      1410      1420      1430      1440      1450    
PAPA_C DHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFG
                                     .:.:.:.:: :::.:.::. :: .  : :.
CG5367                         MRSYKAFEENFKVIEEHNQNYKEGQTSFRLKPNIFA
                                       10        20        30      

         1460           1470      1480      1490      1500         
PAPA_C DMTSEEF-----RQVMNGFQNRKPRKGKVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCG
       ::... .     : . .....     ...   ::. ..:.:.::: ::..::  :: .::
CG5367 DMSTDGYLKGFLRLLKSNIEDSADNMAEIVGSPLMANVPESLDWRSKGFITPPYNQLSCG
         40        50        60        70        80        90      

    1510      1520      1530      1540      1550      1560         
PAPA_C SCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGL
       ::.::: . .. ::     :.                                       
CG5367 SCYAFSIAESIMGQ----KGK---------------------------------------
        100       110                                              

    1570      1580      1590      1600       1610      1620        
PAPA_C DSEESYPYEATEESCKYNPKYSVANDTGFVDIP-KQEKALMKAVATVGPISVAIDAGHES
                     :.. :  ::.: :... .: ..:.:.. ::. .::....:.:. ..
CG5367 --------------CQFVPDLSVVNVTSWAILPVRDEQAIQAAVTHIGPVAISINASPKT
                         120       130       140       150         

     1630      1640      1650      1660      1670      1680        
PAPA_C FLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMA
       : .:..::: .: ::: ...:...:.:.:        . ::..:: ::..:: .::... 
CG5367 FQLYSDGIYDDPLCSSASVNHAMVVIGFG--------KDYWILKNWWGQNWGENGYIRIR
     160       170       180               190       200       210 

     1690      1700      1710      1720      1730      1740        
PAPA_C KDRRNHCGIASAASYPTVMTPLLLLAVLCLGTALATPKFDQTFNAQWHQWKSTHRRLYGT
       :   : ::::. :.:  :                                          
CG5367 KGV-NMCGIANYAAYAIV                                          
              220                                                  

>>CG3074|FBgn0034709|pp-CT10308|FBan0003074 GO:[cathepsi  (441 aa)
 initn: 288 init1: 124 opt: 252  Z-score: 274.7  bits: 62.4 E(): 2.4e-09
Smith-Waterman score: 411;  35.124% identity (39.352% ungapped) in 242 aa overlap (1151-1369:184-422)

             1130      1140      1150       1160      1170         
PAPA_C SDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPSSMD-WRKKGNVVSPVKNQGACGSC
                                     :   :::..   : .. .: : .:: ::. 
CG3074 GRKYSEGLKLRLGTKEPTYRVKAMTRLKNPTDGLPSSFNALDKWSSYISEVPDQGWCGAS
           160       170       180       190       200       210   

    1180      1190        1200      1210      1220      1230       
PAPA_C WTFSTTGALESAVAIAS-GKM-MTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKGI
       :..:::..  .  :: : ::  . :. :....:..   ..::.::  . :..: :..::.
CG3074 WVLSTTSVASDRFAIQSKGKENVQLSAQNILSCTRR--QQGCEGGHLDAAWRY-LHKKGV
           220       230       240         250       260        270

      1240      1250        1260                   1270      1280  
PAPA_C MGEDSYPYIGKNGQCKF--NPEKAVAF-VKNVVNI------------TLNDEAAMVEAVA
       . :. :::  .   ::.  : ..  :   .. ::.            .:: :: ..  . 
CG3074 VDENCYPYTQHRDTCKIRHNSRSLRANGCQKPVNVDRDSLYTVGPAYSLNREADIMAEIF
              280       290       300       310       320       330

           1290      1300      1310      1320       1330           
PAPA_C LYNPVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYGEQ-NGLLYW--IVKN
         .::. ...:..::. :..:::  .. ..      :.:  ::.::. ::  ::  :. :
CG3074 HSGPVQATMRVNRDFFAYSGGVYRETAANRKAPTGFHSVKLVGWGEEHNGEKYWVSIAAN
              340       350       360       370       380       390

    1340      1350      1360        1370      1380      1390       
PAPA_C SWGSNWGNNGYFLIERGKNMCGLA--ACASYPIPQVMNPTLILAAFCLGIASATLTFDHS
       :::: ::..::: : ::.: ::.   . ::.:                            
CG3074 SWGSWWGEHGYFRILRGSNECGIEEYVLASWPYVYSYYNVKPMEISRLIYF         
              400       410       420       430       440          

      1400      1410      1420      1430      1440      1450       
PAPA_C LEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMT

>>CG10992|FBgn0030521|pp-CT30795|FBan0010992 GO:[catheps  (340 aa)
 initn: 193 init1: 146 opt: 235  Z-score: 257.6  bits: 58.9 E(): 2.2e-08
Smith-Waterman score: 370;  24.620% identity (29.889% ungapped) in 329 aa overlap (753-1038:25-338)

            730       740       750       760          770         
PAPA_C PVCGAAELSVNSLEKFHFKSWMSKHRKTYSTEEYHHRLQTFASNW---RKINAHNNGNHT
                                     ..:. . ... :..:   :...:  . .: 
CG1099       MNLLLLVATAASVAALTSGEPSLLSDEFIEVVRSKAKTWTVGRNFDASVTEGHI
                     10        20        30        40        50    

     780       790       800       810       820       830         
PAPA_C FKMALNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPPSVDWRKKGN---FVSP
        ..       :.     ::.  . :..  .  . :. ..   :   : ::.      .. 
CG1099 RRL-------MGVHPDAHKF--ALPDKREVLGDLYVNSVDELPEEFDSRKQWPNCPTIGE
                  60          70        80        90       100     

        840       850       860         870       880       890    
PAPA_C VKNQGACGSCWTFSTTGALESAIAIATGKMLSL--AEQQLVDCAQDFNNYGCQGGLPSQA
       ...::.:::::.:... :. . . : .:  ...  . ..::.: .  . .::.::.:. :
CG1099 IRDQGSCGSCWAFGAVEAMSDRVCIHSGGKVNFHFSADDLVSCCHTCG-FGCNGGFPGAA
         110       120       130       140       150        160    

          900       910                                920         
PAPA_C FEYILYNKGIMGEDTY-------PYQ------------------GKDGYCKF--QPGKAI
       . :    :::..   :       ::.                  :.   :.   : : ..
CG1099 WSYWTR-KGIVSGGPYGSNQGCRPYEISPCEHHVNGTRPPCAHGGRTPKCSHVCQSGYTV
          170        180       190       200       210       220   

       930            940       950       960       970       980  
PAPA_C GFVKD----VANITIY-DEEAMVEAVALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPD
        ..::      . ..  . . . : .   .::  :: : .:...:. :.:.    :.   
CG1099 DYAKDKHFGSKSYSVRRNVREIQEEIMTNGPVEGAFTVYEDLILYKDGVYQ----HEHGK
           230       240       250       260       270             

             990        1000      1010      1020      1030         
PAPA_C KVN-HAVLAVGYG--EKNGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPL
       ... ::.  .:.:   .. ::::.. :::. .:: .:.: : ::.. ::. .  :  .: 
CG1099 ELGGHAIRILGWGVWGEEKIPYWLIGNSWNTDWGDHGFFRILRGQDHCGIESSISAGLPK
     280       290       300       310       320       330         

    1040      1050      1060      1070      1080      1090         
PAPA_C VMWTALPLLCAGAWLLSAGATAELTVNAIEKFHFTSWMKQHQKTYSSREYSHRLQVFANN
                                                                   
CG1099 L                                                           
     340                                                           

>>CG10460|FBgn0034443|pp-CT29364|FBan0010460 GO:[endopep  (79 aa)
 initn: 115 init1: 115 opt: 131  Z-score: 152.2  bits: 37.3 E(): 0.016
Smith-Waterman score: 141;  29.231% identity (29.231% ungapped) in 65 aa overlap (1399-1463:6-70)

     1370      1380      1390      1400      1410      1420        
PAPA_C PIPQVMNPTLILAAFCLGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKN
                                     . .:...:.  .. :  .:.  :: .. ..
CG1046                          MSLVSDEEWVEYKSKFDKNYEAEEDLMRRRIYAES
                                        10        20        30     

     1430      1440      1450      1460      1470      1480        
PAPA_C MKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFYEAP
          :: ::.....:. .. :..: ..:.: ::: :                         
CG1046 KARIEEHNRKFEKGEVTWKMGINHLADLTPEEFAQRCGKKVPPN                
          40        50        60        70                         

     1490      1500      1510      1520      1530      1540        
PAPA_C RSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGN

>>Ddx1|FBgn0015075|pp-CT25986|FBan0009054 GO:[helicase (  (727 aa)
 initn:  64 init1:  64 opt: 107  Z-score: 114.0  bits: 33.4 E():  2.2
Smith-Waterman score: 107;  25.581% identity (29.412% ungapped) in 215 aa overlap (2142-2341:72-273)

            2120      2130      2140      2150      2160           
PAPA_C FKDNLKYIDETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEE------
                                     .: :    :.:.:  :   .:. .      
Ddx1|F VLMAAETGSGKTGAFCLPILQIVWETLRDLEEGKAGKGGAIGGAVTPWTMSFFDRGNALA
              50        60        70        80        90       100 

        2170       2180      2190      2200      2210      2220    
PAPA_C VLNDG-DVNIPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQ
       :  ::   .  :. .:.   :.: :...:.    . : :.:: ::. ..  :  .. .. 
Ddx1|F VTPDGLRCQSREFKEWHGCRATTGVRGKGK----FYFEATVTDEGLCRV--GWSTQQANL
             110       120       130           140         150     

         2230      2240      2250      2260      2270       2280   
PAPA_C ELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKG-PYAAKTDGV
       .:  : : ..: .:    :  .   .::  . ..    :     ...: .    ... ::
Ddx1|F DLGTC-RMGFGFGGTGKKSNNRQFDDYGEAFGKA-DVIGCLLDLKNQEVSFTKNGQNLGV
         160        170       180        190       200       210   

          2290      2300      2310             2320      2330      
PAPA_C RQVQPYNEGALLYSIANQPVSVVLEAA------GK-DFQLYRGGIFVGPCGNKVDHAVAA
           : : .   .  :     :::. :      :: ::.   :. ::: :    .:. : 
Ddx1|F AFRLPDNLAKETFYPA-----VVLKNAEMQFNFGKTDFKYAPGNGFVGACQAGPEHSKAN
           220            230       240       250       260        

       2340      2350      2360      2370      2380                
PAPA_C VGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN           
          ::                                                       
Ddx1|F PITGPAAGAPSAKPAPNAPQAIIMEPSRELAEQTYNQIEKFKYHLSNPEVRSLLLIGGVR
      270       280       290       300       310       320        

>>CPTI|FBgn0027842|pp-CT32036|FBan0012891 GO:[carnitine   (780 aa)
 initn:  63 init1:  63 opt: 105  Z-score: 111.4  bits: 33.0 E():    3
Smith-Waterman score: 105;  27.551% identity (30.000% ungapped) in 98 aa overlap (904-998:486-578)

           880       890       900       910          920       930
PAPA_C LVDCAQDFNNYGCQGGLPSQAFEYILYNKGIMGEDTYPYQ---GKDGYCKFQPGKAIGFV
                                     :.:.: : :.   .  :   :::     ..
CPTI|F TVCVGTNGRVGFNAEHTWADAPVLGHLWEYIFGDDIYGYDETGNTKGTPAFQPPTPTRLT
         460       470       480       490       500       510     

              940       950       960       970       980       990
PAPA_C KDVANITIYDEEAMVEAVALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVNHAVLA
        :.       ::: .... : : :.. . : ::   :  :....  :. .::   . .: 
CPTI|F WDLKPCLAQIEEATIDVTKLINEVNLRILVHQD---YGKGFMKK--CRISPDAYIQMALQ
         520       530       540          550         560       570

             1000      1010      1020      1030      1040      1050
PAPA_C VGYGEKNGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLVMWTALPLLCA
       ..: .  :                                                    
CPTI|F LAYYRDAGRFSLTYEASMTRLFREGRTETVRPCTIESSAWVKAMQNPNTTNDERVKMMQA
              580       590       600       610       620       630

>>CG4393|FBgn0039075|pp-CT14338|FBan0004393 GO:[cytoskel  (968 aa)
 initn:  40 init1:  40 opt: 105  Z-score: 110.3  bits: 33.1 E():  3.5
Smith-Waterman score: 105;  23.973% identity (25.547% ungapped) in 146 aa overlap (412-555:373-511)

             390       400       410       420       430       440 
PAPA_C RAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRK
                                     ::: .:: . . ::    ..   ..: :. 
CG4393 NHLLNHSHSMQQSGYSKQRLSAGNGGPYNGGKSLDSALQPEDRFYQDLNAHSPLHSQNEM
            350       360       370       380       390       400  

             450       460       470         480       490         
PAPA_C GLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGN--HLMRDAAALPETKDWREDGIV
       :  :  ...  :..:   :. . ..  . ::.   :.  :.   : : :  :  :..  :
CG4393 GGGY--SVSPSSSLS--SFEPASVSPRSRCSTGGLGQPMHMSTFAPAGPPKKPPRRNLSV
              410         420       430       440       450        

     500       510       520       530       540       550         
PAPA_C SPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNGGLPSQA
       ::.  .:  :. ...:. ..   . ... :.: .. .:   .   . .. :  ::.    
CG4393 SPT--HAGPGQQFSYSSPSSQSQSQSHGHGQN-QVRRQPASESPYSHQSHGSVGGMSFDE
      460         470       480        490       500       510     

     560       570       580       590       600       610         
PAPA_C FEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPV
                                                                   
CG4393 TQLRERQRNDRLYASARQSTRSAIAGGMSLSSSNDMLDRQCSSSELNSETSVPNSSGDSP
         520       530       540       550       560       570     

>>CG4392|FBgn0036283|pp-CT14260|FBan0004392 GO:[mitochon  (370 aa)
 initn:  55 init1:  55 opt: 100  Z-score: 110.0  bits: 31.7 E():  3.6
Smith-Waterman score: 104;  20.426% identity (22.642% ungapped) in 235 aa overlap (2099-2317:15-242)

     2070      2080      2090      2100      2110      2120        
PAPA_C SIVGYSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKKNNS
                                     :.::..     ....: .  . .   .  .
CG4392                 MLRNSTYQYNLPVDYHNIQQMAVAGDMMEDFVVIFRDMMGRYLD
                               10        20        30        40    

     2130      2140            2150      2160       2170      2180 
PAPA_C YWLGLNVFADMSNDE------FKEKYTGSIAGNYTTTELS-YEEVLNDGDVNIPEYVDWR
           .::  :... :      ...  .:.:::  . :  .  ...    .:: :.:.   
CG4392 IGEDMNVPDDFTQKEMQTGLWWRHLVAGGIAGAVSRTCTAPLDRIKVYLQVNQPRYTVQT
           50        60        70        80        90       100    

                2190      2200      2210      2220      2230       
PAPA_C QKGAVTP----VKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCN
       :. ...     . :.:.  : :  ...    ...::   .  ...  : .   :   : .
CG4392 QRMGISECMHIMLNEGGSRSMWRGNGI----NVLKIAPETAFKFAAYEQMK--RLIRGDD
          110       120       130           140       150          

      2240          2250      2260      2270      2280      2290   
PAPA_C GGYPWSALQL----VAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGA
       :.   : ..     .:  ::     ::.: ..     :. : ::. .:.. ..   .::.
CG4392 GSRQMSIVERFYAGAAAGGISQTIIYPMEVLKTRLALRRTGQYAGIADAAVKIYK-QEGV
      160       170       180       190       200       210        

          2300       2310      2320      2330      2340      2350  
PAPA_C LLYSIANQP-VSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGT
         .  .  : .  .:  :: :. .:.                                  
CG4392 RSFYRGYVPNILGILPYAGIDLAVYETLKRRYIANHDNNEQPSFLVLLACGSTSSTLGQL
       220       230       240       250       260       270       

>>CG14034|FBgn0031691|pp-CT33593|FBan0014034 GO:[phospho  (223 aa)
 initn:  60 init1:  60 opt:  93  Z-score: 105.2  bits: 30.1 E():  6.8
Smith-Waterman score: 93;  18.719% identity (21.965% ungapped) in 203 aa overlap (1434-1625:28-211)

          1410      1420      1430      1440      1450      1460   
PAPA_C KWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQ
                                     :...: .:: .  .. .: :  .  . .. 
CG1403    MLVAGLDDMNCFSLQNEICPNANISFWLYTKENQEGTKLSVFELNRFEFYHHKPLKV
                  10        20        30        40        50       

          1470      1480         1490          1500      1510      
PAPA_C VMNGFQNRKPRKGKVFQEPLFYEAPR---SVDW----REKGYVTPVKNQGQCGSCWAFSA
       ...::....  . ..  .:::        :.:.     :  :.  :.:    . : :   
CG1403 LIHGFNGHRDFSPNTQLRPLFLTQDYNLISLDYPKLAYEPCYTEAVHNAKYVARCTA---
        60        70        80        90       100       110       

       1520         1530      1540      1550       1560      1570  
PAPA_C TGALEGQMFR---KTGRLISLSEQNLVDCSGPQGNEGCNGGLM-DYAFQYVQDNGGLDSE
             :..:   ..: :... . .:.  .      :  : .. .. ....    .::  
CG1403 ------QLLRVLLESG-LVKIEDLHLIGLGLGAHVAGFIGQFLPEHKLEHIT---ALDPA
                120        130       140       150          160    

           1580      1590      1600      1610      1620      1630  
PAPA_C ESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFY
       . . : . . . : .:     .:. :::. . . ...  . .:: ..  .. :       
CG1403 KPF-YMVKDPALKLDP-----TDAKFVDVVHTDVTMLGLLDAVGHVDFYLNMGVSQPNCG
           170            180       190       200       210        

           1640      1650      1660      1670      1680      1690  
PAPA_C KEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRR
                                                                   
CG1403 PINKS                                                       
      220                                                          

>>CG6357|FBgn0033875|pp-CT19866|FBan0006357 GO:[endopept  (439 aa)
 initn: 174 init1:  92 opt:  96  Z-score: 104.8  bits: 31.0 E():  7.2
Smith-Waterman score: 136;  31.852% identity (37.069% ungapped) in 135 aa overlap (344-461:1-133)

           320       330       340       350          360       370
PAPA_C GADWGEQGYIYLRRGKNTCGVSNFVSTSIIMAHARVLL---LALAVLATAAVAVASSSSF
                                     :. ::.::   : : ....:  . .:.:: 
CG6357                               MTSARILLGVPLLLYLMGVALGVPVSTSSP
                                             10        20        30

                380             390       400         410       420
PAPA_C ADS--NPIRPVT------DRAASTLESAVLGALGRTRHALRFA--RFAVRYGKSYESAAE
       : .  ::   ::      : .. :.: .  ..:.. ..  .::  :: : .   :..  :
CG6357 ATQKINPEIGVTTGKSDADSSTPTIEHT--SGLSEFEEECQFAWQRFLVDFDVHYDNDYE
               40        50          60        70        80        

              430       440           450       460       470      
PAPA_C VRRRFRIFSESLEEVRSTNRK---GL-PYRLGINRFSDMSWEEFQATRLGAAQTCSATLA
        ..:  :: :. ..::. : :   :.  .. :::..::...::..               
CG6357 RQKRRDIFCENWQKVRDHNLKYDLGVVSFKKGINQWSDLTFEEWKEKQTPKVMPEIASES
       90       100       110       120       130       140        

        480       490       500       510       520       530      
PAPA_C GNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSE
                                                                   
CG6357 SKEERDKVNCQAAWEKFLIDFGAQYKNANETEKRRNVFCANWRAIVEHNVQYEKWAEPFK
      150       160       170       180       190       200        

>>CG11288|FBgn0039895|pp-CT31491|FBan0011288 GO:[cell ad  (202 aa)
 initn:  61 init1:  61 opt:  91  Z-score: 103.5  bits: 29.6 E():  8.4
Smith-Waterman score: 91;  24.731% identity (25.843% ungapped) in 93 aa overlap (1843-1931:48-140)

           1820      1830      1840      1850      1860            
PAPA_C QEPLMLQIPKTVDWREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLKT-GKLISLSE--
                                     .:  .... :  :  . :  .: :...:  
CG1128 ENLCAHICENTFDAYQCKCHPGFMLDNNNVTCSPMKTQICPSGYNLDKLDNKCIDIDECR
        20        30        40        50        60        70       

    1870      1880      1890      1900      1910      1920         
PAPA_C QNLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGSCKYRAEYAVAN-D
       ..: ::. .:  .. :::   .  .  .   :.  ...:     : .:: :    . . :
CG1128 EDLHDCKSSQYCHNTNGGYHCLNVKEKECPPGFHYDHDYDACKDDYKCKDRKCVKIQSCD
        80        90       100       110       120       130       

     1930      1940      1950      1960      1970      1980        
PAPA_C TGFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCSSKDLDHGVLVVG
        ::                                                         
CG1128 KGFSLHNGTCSDIDECSHKSLNNCHVNSNQECVNTVGSYSCNCLPGFNLDATLNKCVGKY
       140       150       160       170       180       190       

>>CG13155|FBgn0033723|pp-CT32396|FBan0013155 GO:[] mol_w  (236 aa)
 initn:  67 init1:  67 opt:  91  Z-score: 102.7  bits: 29.7 E():  9.3
Smith-Waterman score: 91;  27.397% identity (28.986% ungapped) in 73 aa overlap (165-237:146-214)

          140       150       160       170       180       190    
PAPA_C NQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGL
                                     :.:..: : :.    :  .:  :.::. . 
CG1315 NFNGTGWQIIQFQWVRDGDESHPDTKEYSYLTENKLWDSDQA---YAYQEP-DDGCHINC
         120       130       140       150          160        170 

          200       210       220       230       240       250    
PAPA_C QPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVS
       ::..  : ...  .:     :   .  .. :.:: .  .:: .                 
CG1315 QPETAVYPLQSEPVQEPVVQPTQEQQQSRTNINSEQDPGKIHDTINEVLEYIQQRILPTL
             180       190       200       210       220       230 

          260       270       280       290       300       310    
PAPA_C TGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWG
                                                                   
CG1315 PIKGE                                                       
                                                                   

>>CG4810|FBgn0037994|pp-CT15451|FBan0004810 GO:[translat  (551 aa)
 initn:  60 init1:  60 opt:  95  Z-score: 102.4  bits: 30.9 E():  9.6
Smith-Waterman score: 95;  25.000% identity (28.409% ungapped) in 100 aa overlap (2138-2227:368-465)

      2110      2120      2130      2140         2150      2160    
PAPA_C RFEIFKDNLKYIDETNKKNNSYWLGLNVFADMSNDEF---KEKYTGSIAGNYTTTELSYE
                                     :..::     . :..: : :    ...   
CG4810 QEPRFMFEEPNPFEEPGVDLASIGYRYRQWDLGNDVVLIARCKHNGVIQGPNGDVQFLSI
       340       350       360       370       380       390       

         2170      2180             2190      2200      2210       
PAPA_C EVLNDGDVNIPEYVDWRQK-----GAV--TPVKNQGSCGSCWAFSAVVTIEGIIKIRTGN
       ..::. : .. . :.::::     :::  . ..:..   . :.  ::..  :  ... : 
CG4810 KALNEWDSKVTNSVEWRQKLDTQRGAVLASELRNNACKLARWTVEAVLA--GSDQLKLGY
       400       410       420       430       440         450     

      2220      2230      2240      2250      2260      2270       
PAPA_C LNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYA
       ..... .. :                                                  
CG4810 VSRMNPRDHLRHVILGTQQFKPQEFATQINLNMDNAWGVLRCLIDLVMRQPDGKYLIMKD
         460       470       480       490       500       510     




2385 residues in 1 query   sequences
7177762 residues in 14334 library sequences
 Scomplib [33t08]
 start: Tue May 21 16:24:31 2002 done: Tue May 21 16:24:44 2002
 Scan time: 11.240 Display time:  1.580

Function used was FASTA [version 3.3t08 Jan. 17, 2001]
BioPerl-1.007002/t/data/dcr1_sp.WUBLASTP000444000766000024     36363113155576321 17462 0ustar00cjfieldsstaff000000000000BLASTP 2.0MP-WashU [04-May-2006] [linux26-x64-I32LPF64 2006-05-10T17:22:28]

Copyright (C) 1996-2006 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2006) http://blast.wustl.edu

Query=  Celegans_dcr1
        (1845 letters)

Database:  swissprot
           353,658 sequences; 132,868,552 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done

                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

sp|P34529.2|DCR1_CAEEL RecName: Full=Endoribonuclease dcr-1   9560  0.        1
sp|Q9VCU9.1|DCR1_DROME RecName: Full=Endoribonuclease Dcr...  1792  1.5e-232  3
sp|Q9UPY3.2|DICER_HUMAN RecName: Full=Endoribonuclease Di...  2152  6.4e-223  1
sp|Q8R418.2|DICER_MOUSE RecName: Full=Endoribonuclease Di...  2120  1.6e-219  1
sp|P84634.1|DCL4_ARATH RecName: Full=Dicer-like protein 4      471  8.6e-72   5
sp|Q7S8J7.1|DCL1_NEUCR RecName: Full=Dicer-like protein 1...   505  3.0e-69   6
sp|A4RKC3.2|DCL1_MAGGR RecName: Full=Dicer-like protein 1...   481  3.5e-69   6
sp|Q0CW42.2|DCL1_ASPTN RecName: Full=Dicer-like protein 1...   464  4.8e-65   6
sp|Q1DKI1.2|DCL1_COCIM RecName: Full=Dicer-like protein 1...   498  8.4e-64   6
sp|A2RAF3.2|DCL1_ASPNC RecName: Full=Dicer-like protein 1...   466  5.3e-62   5
sp|Q09884.1|DCR1_SCHPO RecName: Full=Protein Dicer; AltNa...   415  7.7e-61   4
sp|A1CBC9.2|DCL1_ASPCL RecName: Full=Dicer-like protein 1...   428  1.2e-60   6
sp|A1DE13.1|DCL1_NEOFI RecName: Full=Dicer-like protein 1...   457  1.6e-60   6
sp|Q2VF19.1|DCL1_CRYPA RecName: Full=Dicer-like protein 1...   465  4.2e-60   4
sp|Q0UI93.2|DCL1_PHANO RecName: Full=Dicer-like protein 1...   490  3.8e-59   5
sp|Q4WVE3.3|DCL1_ASPFU RecName: Full=Dicer-like protein 1...   466  4.8e-59   6
sp|Q2U6C4.2|DCL1_ASPOR RecName: Full=Dicer-like protein 1...   474  8.5e-58   4
sp|Q2UNX5.1|DCL2_ASPOR RecName: Full=Dicer-like protein 2...   396  1.0e-53   5
sp|Q4WA22.2|DCL2_ASPFU RecName: Full=Dicer-like protein 2...   369  1.7e-51   5


>sp|P34529.2|DCR1_CAEEL RecName: Full=Endoribonuclease dcr-1
        Length = 1845

 Score = 9560 (3370.3 bits), Expect = 0., P = 0.
 Identities = 1845/1845 (100%), Positives = 1845/1845 (100%)
 Links = (1)

Query:     1 MVRVRADLQCFNPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQ 60
             MVRVRADLQCFNPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQ
Sbjct:     1 MVRVRADLQCFNPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQ 60

Query:    61 GGKRAFFVVEKVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVI 120
             GGKRAFFVVEKVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVI
Sbjct:    61 GGKRAFFVVEKVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVI 120

Query:   121 TAQCLLDLIRHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPVPRVLGLT 180
             TAQCLLDLIRHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPVPRVLGLT
Sbjct:   121 TAQCLLDLIRHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPVPRVLGLT 180

Query:   181 ASLIKAKVAPEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLG 240
             ASLIKAKVAPEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLG
Sbjct:   181 ASLIKAKVAPEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLG 240

Query:   241 IPNFDTVIEIFDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQ 300
             IPNFDTVIEIFDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQ
Sbjct:   241 IPNFDTVIEIFDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQ 300

Query:   301 VWEKELGKIIKSQVLPDKTLRFLNMAKTSMITIKRLLEPEMKKIKSIEALRPYVPQRVIR 360
             VWEKELGKIIKSQVLPDKTLRFLNMAKTSMITIKRLLEPEMKKIKSIEALRPYVPQRVIR
Sbjct:   301 VWEKELGKIIKSQVLPDKTLRFLNMAKTSMITIKRLLEPEMKKIKSIEALRPYVPQRVIR 360

Query:   361 LFEILETFNPEFQKERMKLEKAEHLSAIIFVDQRYIAYSLLLMMRHIKSWEPKFKFVNPD 420
             LFEILETFNPEFQKERMKLEKAEHLSAIIFVDQRYIAYSLLLMMRHIKSWEPKFKFVNPD
Sbjct:   361 LFEILETFNPEFQKERMKLEKAEHLSAIIFVDQRYIAYSLLLMMRHIKSWEPKFKFVNPD 420

Query:   421 YVVGASGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDR 480
             YVVGASGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDR
Sbjct:   421 YVVGASGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDR 480

Query:   481 PLDMRSYVQSKGRARRAGSRYVITVEEKDTAAYCSKLPSDIFTRLVPHNQIIPIEENGVT 540
             PLDMRSYVQSKGRARRAGSRYVITVEEKDTAAYCSKLPSDIFTRLVPHNQIIPIEENGVT
Sbjct:   481 PLDMRSYVQSKGRARRAGSRYVITVEEKDTAAYCSKLPSDIFTRLVPHNQIIPIEENGVT 540

Query:   541 KYCAELLLPINSPIKHAIVLKNPMPNKKTAQMAVALEACRQLHLEGELDDNLLPKGRESI 600
             KYCAELLLPINSPIKHAIVLKNPMPNKKTAQMAVALEACRQLHLEGELDDNLLPKGRESI
Sbjct:   541 KYCAELLLPINSPIKHAIVLKNPMPNKKTAQMAVALEACRQLHLEGELDDNLLPKGRESI 600

Query:   601 AKLLEHIDEEPDEYAPGIAAKVGSSKRKQLYDKKIARALNESFVEADKECFIYAFELERF 660
             AKLLEHIDEEPDEYAPGIAAKVGSSKRKQLYDKKIARALNESFVEADKECFIYAFELERF
Sbjct:   601 AKLLEHIDEEPDEYAPGIAAKVGSSKRKQLYDKKIARALNESFVEADKECFIYAFELERF 660

Query:   661 REAELTLNPKRRKFEDPFNYEYCFGFLSAKEIPKIPPFPVFLRQGNMKVRLIVAPKKTTV 720
             REAELTLNPKRRKFEDPFNYEYCFGFLSAKEIPKIPPFPVFLRQGNMKVRLIVAPKKTTV
Sbjct:   661 REAELTLNPKRRKFEDPFNYEYCFGFLSAKEIPKIPPFPVFLRQGNMKVRLIVAPKKTTV 720

Query:   721 TAAQLQEIQLFHNYLFTQVLQMCKTGNLEFDGTSNAPLNTLIVPLNKRKDDMSYTINMKY 780
             TAAQLQEIQLFHNYLFTQVLQMCKTGNLEFDGTSNAPLNTLIVPLNKRKDDMSYTINMKY
Sbjct:   721 TAAQLQEIQLFHNYLFTQVLQMCKTGNLEFDGTSNAPLNTLIVPLNKRKDDMSYTINMKY 780

Query:   781 VSEVVANMENMPRIPKDEVRRQYKFNAEDYKDAIVMPWYRNLEQPVFYYVAEILPEWRPS 840
             VSEVVANMENMPRIPKDEVRRQYKFNAEDYKDAIVMPWYRNLEQPVFYYVAEILPEWRPS
Sbjct:   781 VSEVVANMENMPRIPKDEVRRQYKFNAEDYKDAIVMPWYRNLEQPVFYYVAEILPEWRPS 840

Query:   841 SKFPDTHFETFNEYFIKKYKLEIYDQNQSLLDVDFTSTRLNLLQPRIQNQPRRSRTVSNS 900
             SKFPDTHFETFNEYFIKKYKLEIYDQNQSLLDVDFTSTRLNLLQPRIQNQPRRSRTVSNS
Sbjct:   841 SKFPDTHFETFNEYFIKKYKLEIYDQNQSLLDVDFTSTRLNLLQPRIQNQPRRSRTVSNS 900

Query:   901 STSNIPQASASDSKESNTSVPHSSQRQILVPELMDIHPISATLWNVIAALPSIFYRVNQL 960
             STSNIPQASASDSKESNTSVPHSSQRQILVPELMDIHPISATLWNVIAALPSIFYRVNQL
Sbjct:   901 STSNIPQASASDSKESNTSVPHSSQRQILVPELMDIHPISATLWNVIAALPSIFYRVNQL 960

Query:   961 LLTDELRETILVKAFGKEKTKLDDNVEWNSLAYATEYEEKQTIIVKKIQQLRDLNQKSIE 1020
             LLTDELRETILVKAFGKEKTKLDDNVEWNSLAYATEYEEKQTIIVKKIQQLRDLNQKSIE
Sbjct:   961 LLTDELRETILVKAFGKEKTKLDDNVEWNSLAYATEYEEKQTIIVKKIQQLRDLNQKSIE 1020

Query:  1021 DQERETRENDKIDDGEELFNIGVWDPEEAVRIGVEISSRDDRMDGEDQDTVGLTQGLHDG 1080
             DQERETRENDKIDDGEELFNIGVWDPEEAVRIGVEISSRDDRMDGEDQDTVGLTQGLHDG
Sbjct:  1021 DQERETRENDKIDDGEELFNIGVWDPEEAVRIGVEISSRDDRMDGEDQDTVGLTQGLHDG 1080

Query:  1081 NISDEDDELPFVMHDYTARLTSNRNGIGAWSGSESIVPSGWGDWDGPEPDNSPMPFQILG 1140
             NISDEDDELPFVMHDYTARLTSNRNGIGAWSGSESIVPSGWGDWDGPEPDNSPMPFQILG
Sbjct:  1081 NISDEDDELPFVMHDYTARLTSNRNGIGAWSGSESIVPSGWGDWDGPEPDNSPMPFQILG 1140

Query:  1141 GPGGLNVQALMADVGRVFDPSTASSSLSQTVQESTVSPPKQLTKEEEQFKKLQNDLLKQA 1200
             GPGGLNVQALMADVGRVFDPSTASSSLSQTVQESTVSPPKQLTKEEEQFKKLQNDLLKQA
Sbjct:  1141 GPGGLNVQALMADVGRVFDPSTASSSLSQTVQESTVSPPKQLTKEEEQFKKLQNDLLKQA 1200

Query:  1201 KERLEALEMSEDMEKPRRLEDTVNLEDYGDDQENQEDENTPTNFPKTIDEEIEELSIGAR 1260
             KERLEALEMSEDMEKPRRLEDTVNLEDYGDDQENQEDENTPTNFPKTIDEEIEELSIGAR
Sbjct:  1201 KERLEALEMSEDMEKPRRLEDTVNLEDYGDDQENQEDENTPTNFPKTIDEEIEELSIGAR 1260

Query:  1261 KKQEIDDNAAKTDVLERENCEVLPVAINEKSRSFSFEKESKAINGRLIRQRSEEYVSHID 1320
             KKQEIDDNAAKTDVLERENCEVLPVAINEKSRSFSFEKESKAINGRLIRQRSEEYVSHID
Sbjct:  1261 KKQEIDDNAAKTDVLERENCEVLPVAINEKSRSFSFEKESKAINGRLIRQRSEEYVSHID 1320

Query:  1321 SDIGLGVSPCLLLTALTTSNAADGMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSF 1380
             SDIGLGVSPCLLLTALTTSNAADGMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSF
Sbjct:  1321 SDIGLGVSPCLLLTALTTSNAADGMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSF 1380

Query:  1381 ARSKEVSNCNLYRLGKKLGIPQLIVANKFDAHDSWLPPCYIPTCDFKAPNTDDAEEKDNE 1440
             ARSKEVSNCNLYRLGKKLGIPQLIVANKFDAHDSWLPPCYIPTCDFKAPNTDDAEEKDNE
Sbjct:  1381 ARSKEVSNCNLYRLGKKLGIPQLIVANKFDAHDSWLPPCYIPTCDFKAPNTDDAEEKDNE 1440

Query:  1441 IERILDGQVIEEKPENKTGWDIGGDVSKSTTDGIETITFPKQARVGNDDISPLPYNLLTQ 1500
             IERILDGQVIEEKPENKTGWDIGGDVSKSTTDGIETITFPKQARVGNDDISPLPYNLLTQ
Sbjct:  1441 IERILDGQVIEEKPENKTGWDIGGDVSKSTTDGIETITFPKQARVGNDDISPLPYNLLTQ 1500

Query:  1501 QHISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQKDQKSDVPSPLLRFIDTPT 1560
             QHISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQKDQKSDVPSPLLRFIDTPT
Sbjct:  1501 QHISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQKDQKSDVPSPLLRFIDTPT 1560

Query:  1561 NPNASLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHASYINNRVTGCYQRLEFLG 1620
             NPNASLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHASYINNRVTGCYQRLEFLG
Sbjct:  1561 NPNASLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHASYINNRVTGCYQRLEFLG 1620

Query:  1621 DAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIAMCPGLYHM 1680
             DAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIAMCPGLYHM
Sbjct:  1621 DAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIAMCPGLYHM 1680

Query:  1681 IEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDIEVPKAMGDIFESVAGAIYLDSG 1740
             IEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDIEVPKAMGDIFESVAGAIYLDSG
Sbjct:  1681 IEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDIEVPKAMGDIFESVAGAIYLDSG 1740

Query:  1741 RNLDTTWQVIFHMMRGTIELCCANPPRSPIRELMEFEQSKVRFSKMERILESGKVRVTVE 1800
             RNLDTTWQVIFHMMRGTIELCCANPPRSPIRELMEFEQSKVRFSKMERILESGKVRVTVE
Sbjct:  1741 RNLDTTWQVIFHMMRGTIELCCANPPRSPIRELMEFEQSKVRFSKMERILESGKVRVTVE 1800

Query:  1801 VVNNMRFTGMGRNYRIAKATAAKRALKYLHQIEQQRRQSPSLTTV 1845
             VVNNMRFTGMGRNYRIAKATAAKRALKYLHQIEQQRRQSPSLTTV
Sbjct:  1801 VVNNMRFTGMGRNYRIAKATAAKRALKYLHQIEQQRRQSPSLTTV 1845


>sp|Q9VCU9.1|DCR1_DROME RecName: Full=Endoribonuclease Dcr-1; Short=Protein
            dicer-1
        Length = 2249

 Score = 1792 (635.9 bits), Expect = 1.5e-232, Sum P(3) = 1.5e-232
 Identities = 522/1454 (35%), Positives = 748/1454 (51%)
 Links = 2-3-(1)

Query:   513 YCSKLPSDIFTRLVPHNQIIPIEENGVTKYCAELLLPINSPIKHAIVLKNPMPNKKTAQM 572
             YC++LPSD FT+L    +    E  GVT +   L LPINSP+KH IV   PMP +  A+ 
Sbjct:   832 YCARLPSDTFTKLTALWRCTRNERAGVTLFQYTLRLPINSPLKHDIV-GLPMPTQTLARR 890

Query:   573 AVALEACRQLHLEGELDDNLLPKGRESIAKL---LEHIDEEP-DEYAPGIA--AKVGSSK 626
               AL+AC +LH  GELDD L P G+E    L    E  + EP DE    ++   + G++K
Sbjct:   891 LAALQACVELHRIGELDDQLQPIGKEGFRALEPDWECFELEPEDEQIVQLSDEPRPGTTK 950

Query:   627 RKQLYDKKIARALNESFVEADKECFIYAFELERFREAELTLNPKRRKFEDPFNYEYCFGF 686
             R+Q Y K+IA    +    A   C++Y  +L          N + RK   P + +  FG 
Sbjct:   951 RRQYYYKRIASEFCDCRPVAGAPCYLYFIQLTLQCPIPEEQNTRGRKIYPPEDAQQGFGI 1010

Query:   687 LSAKEIPKIPPFPVFLRQGNMKVRLIVAPKKTTVTAAQLQEIQLFHNYLFTQVLQMCKTG 746
             L+ K IPK+  F +F R G +KV L +A ++  +T+ Q+  I  F NY FT VL++ K  
Sbjct:  1011 LTTKRIPKLSAFSIFTRSGEVKVSLELAKERVILTSEQIVCINGFLNYTFTNVLRLQKFL 1070

Query:   747 NL-EFDGTSNAPLNTLIVPLNKRKDDMSYTINMKYVSEVVANMENMPRIPKDEVRRQYKF 805
              L + D T N      IVP  K      + I+ +++  + AN   MPR   DE R+   F
Sbjct:  1071 MLFDPDSTENC---VFIVPTVKAPAGGKH-IDWQFLELIQANGNTMPRAVPDEERQAQPF 1126

Query:   806 NAEDYKDAIVMPWYRNLEQPVFYYVAEILPEWRPSSKFPDTHFETFNEYFIKKYKLEIYD 865
             + + ++DA+VMPWYRN +QP ++YVAEI P   P S FP  ++ TF  Y++ KY L I +
Sbjct:  1127 DPQRFQDAVVMPWYRNQDQPQYFYVAEICPHLSPLSCFPGDNYRTFKHYYLVKYGLTIQN 1186

Query:   866 QNQSLLDVDFTSTRLNLLQPRIQNQPRRSRTVSNSSTSNIPQASASDSKESNTSVPHSSQ 925
              +Q LLDVD TS RLN L PR  N+   +   S+  T          +K  N       Q
Sbjct:  1187 TSQPLLDVDHTSARLNFLTPRYVNRKGVALPTSSEETKR--------AKRENLE-----Q 1233

Query:   926 RQILVPELMDIHPISATLWNVIAALPSIFYRVNQLLLTDELRETILVK-AFGKEKTKLDD 984
             +QILVPEL  +HP  A+LW     LP I YR+N LLL D++R+ +      G+++ + D+
Sbjct:  1234 KQILVPELCTVHPFPASLWRTAVCLPCILYRINGLLLADDIRKQVSADLGLGRQQIE-DE 1292

Query:   985 NVEWNSLAYATEYEE--KQTIIVKKIQQLRD--LNQKSIEDQERE-TRENDKID-DGEEL 1038
             + EW  L +     E  K++   K+ + L+D  +N K + D E++ T E  ++D D ++ 
Sbjct:  1293 DFEWPMLDFGWSLSEVLKKSRESKQKESLKDDTINGKDLADVEKKPTSEETQLDKDSKD- 1351

Query:  1039 FNIGVWDPEEAVRIGVEISSRDDRMDGEDQDTVGL-TQGLHDGNIS------DEDD--EL 1089
                   D  E   I + I   +   + +D   +G  +  + D   S      DEDD   L
Sbjct:  1352 ------DKVEKSAIELIIEGEEKLQEADDFIEIGTWSNDMADDIASFNQEDDDEDDAFHL 1405

Query:  1090 PFV-----MHDYTARLTSNR-----NGIGAWSGSESIV--PSGWGDWDGP-EP------- 1129
             P +       D   R  S       NG   + G +S      G G   GP +P       
Sbjct:  1406 PVLPANVKFCDQQTRYGSPTFWDVSNGESGFKGPKSSQNKQGGKGKAKGPAKPTFNYYDS 1465

Query:  1130 DNS-PMPFQILGGPGGLNVQA--LMADVGRVFDPSTASSSLSQTVQES-TVSPPKQLTKE 1185
             DNS    +      G LN       +D   V D   A      +  E+ T+   +++ K 
Sbjct:  1466 DNSLGSSYDDDDNAGPLNYMHHNYSSDDDDVADDIDAGRIAFTSKNEAETIETAQEVEKR 1525

Query:  1186 EEQFKKLQ----NDL-LKQAKERLEALEMS-EDMEKPR--RLEDTV-----NLEDYG--- 1229
             ++Q   +Q    N+   +Q K  L       ED ++P   R E+++      +E  G   
Sbjct:  1526 QKQLSIIQATNANERQYQQTKNLLIGFNFKHEDQKEPATIRYEESIAKLKTEIESGGMLV 1585

Query:  1230 -DDQEN--QEDENTPTNFPKT------------IDEEIEELSIGARKKQEIDD----NAA 1270
               DQ+   +  +       K             ++E++    +G R++  + D    NA 
Sbjct:  1586 PHDQQLVLKRSDAAEAQVAKVSMMELLKQLLPYVNEDVLAKKLGDRRELLLSDLVELNAD 1645

Query:  1271 KTDVLERENCEVLPVA-------------INEKSRSFSFEK-------ESKAINGRLIR- 1309
                  E+E   V+                ++EK     +E+        +KAI   ++  
Sbjct:  1646 WVARHEQETYNVMGCGDSFDNYNDHHRLNLDEKQLKLQYERIEIEPPTSTKAITSAILPA 1705

Query:  1310 ----QRSEEYVSHIDSDIGLGVSPCLLLTALTTSNAADGMSLERFETIGDSFLKFATTDY 1365
                  R  + V H       G SP ++L ALT SNA DG++LER ETIGDSFLK+A T Y
Sbjct:  1706 GFSFDRQPDLVGHP------GPSPSIILQALTMSNANDGINLERLETIGDSFLKYAITTY 1759

Query:  1366 LYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQLIVANKFDAHDSWLPPCY-IPT- 1423
             LY T  + HEGKLS  RSK+V+N NLYRLG++  + + ++A KF+ HD+WLPPCY +P  
Sbjct:  1760 LYITYENVHEGKLSHLRSKQVANLNLYRLGRRKRLGEYMIATKFEPHDNWLPPCYYVPKE 1819

Query:  1424 -----CDFKAPNTDDAEEKDN-EIERILDGQVIEEKPE--NKTGWDIGGDVSKSTTDGIE 1475
                   + K P T   +  D  +I+ +   Q+ E   E  +  G +  G       D   
Sbjct:  1820 LEKALIEAKIP-THHWKLADLLDIKNLSSVQICEMVREKADALGLEQNGGAQNGQLDDSN 1878

Query:  1476 TITFPKQARVGNDDISPLPYNLLTQQHISDKSIADAVEALIGVHLLTLGPNPTLKVMNWM 1535
                        ND    +PYNL++Q  I DKSIAD VEALIG +L+  GP   L  M W+
Sbjct:  1879 DSC--------NDFSCFIPYNLVSQHSIPDKSIADCVEALIGAYLIECGPRGALLFMAWL 1930

Query:  1536 GLKVI----QKD---QKSDVPS---PLLRFIDT-----PTNPNASLNFLNNLWQQFQ--- 1577
             G++V+    Q D   Q+  +P    P    + T     PT  +  L+F  N  ++     
Sbjct:  1931 GVRVLPITRQLDGGNQEQRIPGSTKPNAENVVTVYGAWPTPRSPLLHFAPNATEELDQLL 1990

Query:  1578 --FTQLEEKIGYRFKERAYLVQAFTHASYINNRVTGCYQRLEFLGDAVLDYMITRYLFED 1635
               F + EE +GY+F++R+YL+QA THASY  NR+T CYQRLEFLGDAVLDY+ITR+L+ED
Sbjct:  1991 SGFEEFEESLGYKFRDRSYLLQAMTHASYTPNRLTDCYQRLEFLGDAVLDYLITRHLYED 2050

Query:  1636 SRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIAMCPGLYHMIEKFVKLCSERNFDT 1695
              RQ+SPG LTDLRSALVNNTIFASLAV+  F K F  + PGL  +I++FV++  E     
Sbjct:  2051 PRQHSPGALTDLRSALVNNTIFASLAVRHGFHKFFRHLSPGLNDVIDRFVRIQQENG--- 2107

Query:  1696 NFNAEMYMVTTEEEIDEGQEEDIEVPKAMGDIFESVAGAIYLDSGRNLDTTWQVIFHMMR 1755
             +  +E Y + +EEE D+   ED+EVPKA+GD+FES+AGAI+LDS  +LD  W V  +MM 
Sbjct:  2108 HCISEEYYLLSEEECDDA--EDVEVPKALGDVFESIAGAIFLDSNMSLDVVWHVYSNMMS 2165

Query:  1756 GTIELCCANPPRSPIRELMEFEQSKVRFSKMERILESGKVRVTVEVVNNMRFTGMGRNYR 1815
               IE    + P+SPIREL+E E    +F K E++ +  +VRVTV+V     F G+GRNYR
Sbjct:  2166 PEIEQFSNSVPKSPIRELLELEPETAKFGKPEKLADGRRVRVTVDVFCKGTFRGIGRNYR 2225

Query:  1816 IAKATAAKRALKYL 1829
             IAK TAAK AL+ L
Sbjct:  2226 IAKCTAAKCALRQL 2239

 Score = 253 (94.1 bits), Expect = 1.5e-232, Sum P(3) = 1.5e-232
 Identities = 95/376 (25%), Positives = 169/376 (44%)
 Links = (2)-3-1

Query:    11 FNPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQGGKRAFFVVE 70
             F PRD+QVELL  A ++NTI+ LG  S K FIA+ LL+E   +       G    +   E
Sbjct:    15 FTPRDFQVELLATAYERNTIICLGHRSSKEFIALKLLQELSRRARR---HGRVSVYLSCE 71

Query:    71 KVNLVEQQAIHIEV-H-TSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLDL 128
                  E  +I+  + H T  +V Q          D +   D     +HV ++  +  L L
Sbjct:    72 VGTSTEPCSIYTMLTHLTDLRVWQEQP-------DMQIPFDHCWTDYHVSILRPEGFLYL 124

Query:   129 IRHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPVPRVLGLTASLIKAKV 188
             +    L +  + +++ ++CH +   Q   R +  ++ +       PR+LGL   L  A  
Sbjct:   125 LETRELLLSSVELIVLEDCHDSAVYQR-IRPLFENHIMPAPPADRPRILGLAGPLHSAGC 183

Query:   189 APEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNFDTVI 248
               ++L   L  LE ++   IETASD+V++ +Y ++P+E ++ C  FE+  L +   D + 
Sbjct:   184 ELQQLSAMLATLEQSVLCQIETASDIVTVLRYCSRPHEYIVQCAPFEMDELSLVLADVLN 243

Query:   249 E----IFDETVA--FVNTTTEFHPDL-DL-DPRRPIKDSLKTTRAVFRQLGPWAAWRTAQ 300
                  + D       +  T +F  +L D+ DP+    + + +   V  ++GPW   R A 
Sbjct:   244 THKSFLLDHRYDPYEIYGTDQFMDELKDIPDPKVDPLNVINSLLVVLHEMGPWCTQRAAH 303

Query:   301 VWEKELGKIIKSQVLPDKTLRFLNMAKTSMITIKRLLEPEMKK-----IKSIEALRPYVP 355
              +  +  + +K +   ++      +  T++I +  L E    +       S + +  Y  
Sbjct:   304 HFY-QCNEKLKVKTPHERHYLLYCLVSTALIQLYSLCEHAFHRHLGSGSDSRQTIERYSS 362

Query:   356 QRVIRLFEILETFNPE 371
              +V RL + L  F PE
Sbjct:   363 PKVRRLLQTLRCFKPE 378

 Score = 238 (88.8 bits), Expect = 1.5e-232, Sum P(3) = 1.5e-232
 Identities = 51/125 (40%), Positives = 76/125 (60%)
 Links = 2-(3)-1

Query:   382 AEHLSAIIFVDQRYIAYSLLLMMRHIKSWEPKFKFVNPDYVVG-ASGRNLASSDSQGLHK 440
             ++ L A+I+ +Q + A  L  ++  I   +P  KF+   Y     +       +++  H+
Sbjct:   490 SDTLCALIYCNQNHTARVLFELLAEISRRDPDLKFLRCQYTTDRVADPTTEPKEAELEHR 549

Query:   441 RQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSR 500
             RQ EVL+RF  ++ N LI TSVLEEG+DV +CNLV+++D P   RSYVQ KGRAR A + 
Sbjct:   550 RQEEVLKRFRMHDCNVLIGTSVLEEGIDVPKCNLVVRWDPPTTYRSYVQCKGRARAAPAY 609

Query:   501 YVITV 505
             +VI V
Sbjct:   610 HVILV 614

 Score = 44 (20.5 bits), Expect = 4.4e-212, Sum P(3) = 4.4e-212
 Identities = 10/34 (29%), Positives = 17/34 (50%)
 Links = 2-(4)-1

Query:   580 RQLHLEGELDDNLLPKGRESIAKLLEHIDEEPDE 613
             R  H   + D N L    ES  ++++ +D+ P E
Sbjct:   389 RMRHQVDQADFNRLSHTLESKCRMVDQMDQPPTE 422


>sp|Q9UPY3.2|DICER_HUMAN RecName: Full=Endoribonuclease Dicer; AltName:
            Full=Helicase with RNase motif; Short=Helicase MOI
        Length = 1912

 Score = 2152 (762.6 bits), Expect = 6.4e-223, P = 6.4e-223
 Identities = 706/2058 (34%), Positives = 1011/2058 (49%)
 Links = (1)

Query:    11 FNPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQGGKRAFFVVE 70
             + PR YQVELL+ A   NTIV L TGSGKTFIAVLL KE   Q+     + GKR  F+V 
Sbjct:    32 YTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELSYQIRGDFSRNGKRTVFLVN 91

Query:    71 KVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLDLIR 130
               N V QQ   +  H+  KVG+      +  W +KE+ +Q   +H V+++T    L++++
Sbjct:    92 SANQVAQQVSAVRTHSDLKVGEYSNLEVNASW-TKERWNQEFTKHQVLIMTCYVALNVLK 150

Query:   131 HAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPVPRVLGLTASLIKAKVAP 190
             + YL + D+ +L+FDECH A+   HPYR IM   KL +     PR+LGLTAS++  K  P
Sbjct:   151 NGYLSLSDINLLVFDECHLAI-LDHPYREIM---KLCENCPSCPRILGLTASILNGKCDP 206

Query:   191 EKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNFDTVIEI 250
             E+L E+++KLE  + S  ETA+DLV L +Y ++P E+V+ C  F     G+  ++ ++  
Sbjct:   207 EELEEKIQKLEKILKSNAETATDLVVLDRYTSQPCEIVVDCGPFTDRS-GL--YERLLME 263

Query:   251 FDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEKELGKII 310
              +E + F+N         + D     K  L   RAV   LGPW A + A +  +EL K I
Sbjct:   264 LEEALNFINDCNISVHSKERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYI 323

Query:   311 KSQVLPDKTLRFLNMAKTSMITIKRLLEPEM------------KKIKSIEALRPYVPQRV 358
             K +   +   +FL    T +  I  L E               K IK +E LR Y P   
Sbjct:   324 KHEQ-EELHRKFLLFTDTFLRKIHALCEEHFSPASLDLKFVTPKVIKLLEILRKYKPYER 382

Query:   359 IRLFEILETFN------------PEFQKERMKLEKAEH------------LSAIIFVDQR 394
              + FE +E +N             E   E  ++E+ E             L  IIFV++R
Sbjct:   383 -QQFESVEWYNNRNQDNYVSWSDSEDDDEDEEIEEKEKPETNFPSPFTNILCGIIFVERR 441

Query:   395 YIAYSLLLMMRHIKSWEPKFKFVNPDYVVGAS-GRNLA-SSDSQGLHKRQTEVLRRFHRN 452
             Y A  L  +++     +P+  +++ +++ G   G+N   +   +   ++Q EVLR+F  +
Sbjct:   442 YTAVVLNRLIKEAGKQDPELAYISSNFITGHGIGKNQPRNKQMEAEFRKQEEVLRKFRAH 501

Query:   453 EINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSRYVITVE------ 506
             E N LIATS++EEGVD+ +CNLV++FD P + RSYVQSKGRAR   S Y++  +      
Sbjct:   502 ETNLLIATSIVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRARAPISNYIMLADTDKIKS 561

Query:   507 -EKD-----------------------------------------------------TAA 512
              E+D                                                     TA 
Sbjct:   562 FEEDLKTYKAIEKILRNKCSKSVDTGETDIDPVMDDDDVFPPYVLRPDDGGPRVTINTAI 621

Query:   513 -----YCSKLPSDIFTRLVPHNQIIPIEENGVTKYCAELLLPINSPIKHAIVLKNPMPNK 567
                  YC++LPSD FT L P  +   + +   T Y + L LPINSP++ +IV   PM   
Sbjct:   622 GHINRYCARLPSDPFTHLAPKCRTRELPDG--TFY-STLYLPINSPLRASIV-GPPMSCV 677

Query:   568 KTAQMAVALEACRQLHLEGELDDNLLPKGRESIAKLLEHIDEEPDEYAPGIAAKVGSSKR 627
             + A+  VAL  C +LH  GELDD+L+P G+E++ K  E +D   DE    +  + GS+KR
Sbjct:   678 RLAERVVALICCEKLHKIGELDDHLMPVGKETV-KYEEELDLH-DEEETSVPGRPGSTKR 735

Query:   628 KQLYDKKIARALNESFVEADKECFIYAFELERFREAELTLNPKRRKFEDPFNYEYCFGFL 687
             +Q Y K I   L +S+   D+ C++Y   +         LN +RRK   P +   CFG L
Sbjct:   736 RQCYPKAIPECLRDSYPRPDQPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGIL 795

Query:   688 SAKEIPKIPPFPVFLRQGNMKVRLIVAPKKTTVTAAQLQEIQLFHNYLFTQVLQMCKTGN 747
             +AK IP+IP FPV+ R G + + + +      ++   L+ I   H Y+F+ +L++ K   
Sbjct:   796 TAKPIPQIPHFPVYTRSGEVTISIELKKSGFMLSLQMLELITRLHQYIFSHILRLEKPA- 854

Query:   748 LEFDGTSNAPLNTLIVPLNKRKDDMSYTINMKYVSEVVANMENMPRIPKDEVRRQ--YKF 805
             LEF  T +A     ++PLN   D  +  I+ K++ ++  + E    IP  +  ++  + F
Sbjct:   855 LEFKPT-DADSAYCVLPLNVVNDSSTLDIDFKFMEDIEKS-EARIGIPSTKYTKETPFVF 912

Query:   806 NAEDYKDAIVMPWYRNLEQPVFYYVAEILPEWRPSSKFPDTHFETFNEYFIKKYKLEIYD 865
               EDY+DA+++P YRN +QP  +YVA++  +  P SKFP   +ETF EY+  KY L++ +
Sbjct:   913 KLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTN 972

Query:   866 QNQSLLDVDFTSTRLNLLQPRIQNQPRRSRTVSNSSTSNIPQASASDSKESNTSVPHSSQ 925
              NQ LLDVD TS+RLNLL PR  NQ  ++          +P +SA   K    S+ +   
Sbjct:   973 LNQPLLDVDHTSSRLNLLTPRHLNQKGKA----------LPLSSAEKRKAKWESLQN--- 1019

Query:   926 RQILVPELMDIHPISATLWNVIAALPSIFYRVNQLLLTDELRETILVKAFGKEKTKLDDN 985
             +QILVPEL  IHPI A+LW     LPSI YR++ LL  +ELR           +T  D  
Sbjct:  1020 KQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLLTAEELRA----------QTASDAG 1069

Query:   986 VEWNSLAYATEYEEKQTIIVKKIQQLRDLNQKSIEDQERETRENDKIDDGEELFNIGVWD 1045
             V   SL     Y        K I      ++  I      + END       +       
Sbjct:  1070 VGVRSLPADFRYPNLDFGWKKSID-----SKSFISISNSSSAENDNYCKHSTIV------ 1118

Query:  1046 PEEAVRIGVEISSRDDRMDGEDQDTVGLTQGLHDGNISDEDDELPFVMHDYTARLTSNRN 1105
             PE A   G   ++R   ++  DQ +V     L                            
Sbjct:  1119 PENAAHQG---ANRTSSLENHDQMSVNCRTLL---------------------------- 1147

Query:  1106 GIGAWSGSESIVPSGWGDWDGPEPDNSPMPFQILGGPGGLNVQALMADVGRVFDPSTASS 1165
                    SES                          PG L+V+ + AD+       TA +
Sbjct:  1148 -------SES--------------------------PGKLHVE-VSADL-------TAIN 1166

Query:  1166 SLSQTVQESTVSPPKQLTKEEEQFKKLQNDLLKQAKERLEALEMSEDMEKPRRLEDTVNL 1225
              LS    ++  +    L   +  F   Q + L   K+ +          +P       NL
Sbjct:  1167 GLSYN--QNLANGSYDLANRD--F--CQGNQLNYYKQEIPV--------QPTTSYSIQNL 1212

Query:  1226 EDYGDDQENQEDENTPTNFPKTIDEEIEELSIGARKKQEIDDNAAKTDVLERENCEVLPV 1285
               Y    ENQ         P+  DE     ++ + K   +D NA K+         V+P 
Sbjct:  1213 YSY----ENQ---------PQPSDE----CTLLSNKY--LDGNANKSTSDGSPVMAVMPG 1253

Query:  1286 AINEKSRSFSFEKESKAINGRLIRQRSEEYVSHIDSDIGLGVSPCLLLTALTTSNAADGM 1345
               +            + + GR+  ++S   + +  S   LG +P L+L ALT SNA+DG 
Sbjct:  1254 TTDT----------IQVLKGRMDSEQSPS-IGY--SSRTLGPNPGLILQALTLSNASDGF 1300

Query:  1346 SLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQLIV 1405
             +LER E +GDSFLK A T YL+ T  D HEG+LS+ RSK+VSNCNLYRLGKK G+P  +V
Sbjct:  1301 NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMV 1360

Query:  1406 ANKFDAHDSWLPPCYIPTCDFKAPNTD--------------------DAEEKDNEIERIL 1445
              + FD   +WLPP Y+   D K+ NTD                    D EE+D E E ++
Sbjct:  1361 VSIFDPPVNWLPPGYVVNQD-KS-NTDKWEKDEMTKDCMLANGKLDEDYEEEDEEEESLM 1418

Query:  1446 ----------DGQVIEEKPENKTGWD-----IGGDVSK------STTDGIETITFPKQAR 1484
                       +   +E   E+    D      G  V K      STTD       PK++ 
Sbjct:  1419 WRAPKEEADYEDDFLEYDQEHIRFIDNMLMGSGAFVKKISLSPFSTTDSAYEWKMPKKSS 1478

Query:  1485 VGN-----------------------------DDI-----SP-------------LPYNL 1497
             +G+                             DD      +P             + Y+L
Sbjct:  1479 LGSMPFSSDFEDFDYSSWDAMCYLDPSKAVEEDDFVVGFWNPSEENCGVDTGKQSISYDL 1538

Query:  1498 LTQQHISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQKDQKSD-----VP--- 1549
              T+Q I+DKSIAD VEAL+G +L + G       +  +GLKV+   +++D      P   
Sbjct:  1539 HTEQCIADKSIADCVEALLGCYLTSCGERAAQLFLCSLGLKVLPVIKRTDREKALCPTRE 1598

Query:  1550 ----------------------SPLLR-----FIDTPT-----NPNASLNFLNNLWQQFQ 1577
                                   S +L+      +  P      +P+A    LN+L   F+
Sbjct:  1599 NFNSQQKNLSVSCAAASVASSRSSVLKDSEYGCLKIPPRCMFDHPDADKT-LNHLISGFE 1657

Query:  1578 FTQLEEKIGYRFKERAYLVQAFTHASYINNRVTGCYQRLEFLGDAVLDYMITRYLFEDSR 1637
                 E+KI YRFK +AYL+QAFTHASY  N +T CYQRLEFLGDA+LDY+IT++L+ED R
Sbjct:  1658 --NFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPR 1715

Query:  1638 QYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIAMCPGLYHMIEKFVKLCSERNFDTNF 1697
             Q+SPGVLTDLRSALVNNTIFASLAVK+++ K+F A+ P L+H+I+ FV+   E+N     
Sbjct:  1716 QHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEKNEMQGM 1775

Query:  1698 NAEMYMVTTEEEIDEGQEEDIEVPKAMGDIFESVAGAIYLDSGRNLDTTWQVIFHMMRGT 1757
             ++E+    +EE  DE +EEDIEVPKAMGDIFES+AGAIY+DSG +L+T WQV + MMR  
Sbjct:  1776 DSELRR--SEE--DEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLETVWQVYYPMMRPL 1831

Query:  1758 IELCCANPPRSPIRELMEFEQSKVRFSKMERILESGKVRVTVEVVNNMRFTGMGRNYRIA 1817
             IE   AN PRSP+REL+E E    +FS  ER  + GKVRVTVEVV   +F G+GR+YRIA
Sbjct:  1832 IEKFSANVPRSPVRELLEMEPETAKFSPAERTYD-GKVRVTVEVVGKGKFKGVGRSYRIA 1890

Query:  1818 KATAAKRALKYLHQIEQQ 1835
             K+ AA+RAL+ L   + Q
Sbjct:  1891 KSAAARRALRSLKANQPQ 1908


>sp|Q8R418.2|DICER_MOUSE RecName: Full=Endoribonuclease Dicer; AltName:
            Full=Double-strand-specific ribonuclease mDCR-1
        Length = 1906

 Score = 2120 (751.3 bits), Expect = 1.6e-219, P = 1.6e-219
 Identities = 698/2050 (34%), Positives = 1005/2050 (49%)
 Links = (1)

Query:    11 FNPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQGGKRAFFVVE 70
             + PR YQVELL+ A   NTIV L TGSGKTFIAVLL KE   Q+   L+   KR  F+V 
Sbjct:    32 YTPRKYQVELLEAALDHNTIVCLNTGSGKTFIAVLLTKELAHQIRGDLNPHAKRTVFLVN 91

Query:    71 KVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLDLIR 130
               N V QQ   +  H+  KVG+      +  W +KE+  Q   +H V+++T    L +++
Sbjct:    92 SANQVAQQVSAVRTHSDLKVGEYSDLEVNASW-TKERWSQEFTKHQVLIMTCYVALTVLK 150

Query:   131 HAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPVPRVLGLTASLIKAKVAP 190
             + YL + D+ +L+FDECH A+   HPYR IM   KL +     PR+LGLTAS++  K  P
Sbjct:   151 NGYLSLSDINLLVFDECHLAI-LDHPYREIM---KLCESCPSCPRILGLTASILNGKCDP 206

Query:   191 EKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNFDTVIEI 250
             E+L E+++KLE  + S  ETA+DLV L +Y ++P E+V+ C  F     G+  ++ ++  
Sbjct:   207 EELEEKIQKLERILRSDAETATDLVVLDRYTSQPCEIVVDCGPFTDRS-GL--YERLLME 263

Query:   251 FDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEKELGKII 310
              +  + F+N         + D     K  L   RAV   LGPW A + A +  +EL K I
Sbjct:   264 LEAALDFINDCNVAVHSKERDSTLISKQILSDCRAVLVVLGPWCADKVAGMMVRELQKYI 323

Query:   311 KSQVLPDKTLRFLNMAKTSMITIKRLLE----P---EMKKI-----KSIEALRPYVPQRV 358
             K +   +   +FL    T +  I  L E    P   ++K +     K +E LR Y P   
Sbjct:   324 KHEQ-EELHRKFLLFTDTLLRKIHALCEEYFSPASLDLKYVTPKVMKLLEILRKYKPYER 382

Query:   359 IRLFEILETFNPEFQ---------------KERMKLEKAEH---------LSAIIFVDQR 394
              + FE +E +N   Q               +E  + EK E          L  IIFV++R
Sbjct:   383 -QQFESVEWYNNRNQDNYVSWSDSEDDDDDEEIEEKEKPETNFPSPFTNILCGIIFVERR 441

Query:   395 YIAYSLLLMMRHIKSWEPKFKFVNPDYVVGAS-GRNLA-SSDSQGLHKRQTEVLRRFHRN 452
             Y A  L  +++     +P+  +++ +++ G   G+N   S   +   ++Q EVLR+F  +
Sbjct:   442 YTAVVLNRLIKEAGKQDPELAYISSNFITGHGIGKNQPRSKQMEAEFRKQEEVLRKFRAH 501

Query:   453 EINCLIATSVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSRYVIT-------- 504
             E N LIATSV+EEGVD+ +CNLV++FD P + RSYVQSKGRAR   S YV+         
Sbjct:   502 ETNLLIATSVVEEGVDIPKCNLVVRFDLPTEYRSYVQSKGRARAPISNYVMLADTDKIKS 561

Query:   505 ---------------------------------VEEKD-------------------TAA 512
                                              V+++D                   TA 
Sbjct:   562 FEEDLKTYKAIEKILRNKCSKSADGAEADVHAGVDDEDAFPPYVLRPDDGGPRVTINTAI 621

Query:   513 -----YCSKLPSDIFTRLVPHNQIIPIEENGVTKYCAELLLPINSPIKHAIVLKNPMPNK 567
                  YC++LPSD FT L P  +   + +   T Y + L LPINSP++ +IV   PM + 
Sbjct:   622 GHINRYCARLPSDPFTHLAPKCRTRELPDG--TFY-STLYLPINSPLRASIV-GPPMDSV 677

Query:   568 KTAQMAVALEACRQLHLEGELDDNLLPKGRESIAKLLEHIDEEPDEYAPGIAAKVGSSKR 627
             + A+  VAL  C +LH  GELD++L+P G+E++ K  E +D   DE    +  + GS+KR
Sbjct:   678 RLAERVVALICCEKLHKIGELDEHLMPVGKETV-KYEEELDLH-DEEETSVPGRPGSTKR 735

Query:   628 KQLYDKKIARALNESFVEADKECFIYAFELERFREAELTLNPKRRKFEDPFNYEYCFGFL 687
             +Q Y K I   L ES+ + D+ C++Y   +         LN +RRK   P +   CFG L
Sbjct:   736 RQCYPKAIPECLRESYPKPDQPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGIL 795

Query:   688 SAKEIPKIPPFPVFLRQGNMKVRLIVAPKKTTVTAAQLQEIQLFHNYLFTQVLQMCKTGN 747
             +AK IP+IP FPV+ R G + + + +     T++   L+ I   H Y+F+ +L++ K   
Sbjct:   796 TAKPIPQIPHFPVYTRSGEVTISIELKKSGFTLSQQMLELITRLHQYIFSHILRLEKPA- 854

Query:   748 LEFDGTSNAPLNTLIVPLNKRKDDMSYTINMKYVSEVVANMENMPRIPKDEVRRQ--YKF 805
             LEF  T  A     ++PLN   D  +  I+ K++ ++  + E    IP  +  ++  + F
Sbjct:   855 LEFKPTG-AESAYCVLPLNVVNDSGTLDIDFKFMEDIEKS-EARIGIPSTKYSKETPFVF 912

Query:   806 NAEDYKDAIVMPWYRNLEQPVFYYVAEILPEWRPSSKFPDTHFETFNEYFIKKYKLEIYD 865
               EDY+DA+++P YRN +QP  +YVA++  +  P SKFP   +ETF EY+  KY L++ +
Sbjct:   913 KLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTN 972

Query:   866 QNQSLLDVDFTSTRLNLLQPRIQNQPRRSRTVSNSSTSNIPQASASDSKESNTSVPHSSQ 925
              NQ LLDVD TS+RLNLL PR  NQ  ++          +P +SA   K    S+ +   
Sbjct:   973 LNQPLLDVDHTSSRLNLLTPRHLNQKGKA----------LPLSSAEKRKAKWESLQN--- 1019

Query:   926 RQILVPELMDIHPISATLWNVIAALPSIFYRVNQLLLTDELRETILVKAFGKEKTKLDDN 985
             +QILVPEL  IHPI A+LW     LPSI YR++ LL  +ELR      A G     L  +
Sbjct:  1020 KQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLLTAEELRAQTASDA-GVGVRSLPVD 1078

Query:   986 VEWNSLAYATEYEEKQTIIVKKIQQLRDLNQKSIEDQERETRENDKIDDGEELFNIGVWD 1045
               + +L    ++  K++I  K    +   N  S+ + +   + +  +             
Sbjct:  1079 FRYPNL----DFGWKKSIDSKSF--ISTCNS-SLAESDNYCKHSTTVV------------ 1119

Query:  1046 PEEAVRIGVEISSRDDRMDGEDQDTVGLTQGLHDGNISDEDDELPFVMHDYTARLTSNRN 1105
             PE A   G    S    ++  DQ +V                           RL     
Sbjct:  1120 PEHAAHQGATRPS----LENHDQMSVNCK------------------------RL----- 1146

Query:  1106 GIGAWSGSESIVPSGWGDWDGPEPDNSPMPFQILGGPGGLNVQALMADVGRVFDPSTASS 1165
                                    P  SP   Q            +  D+       TA +
Sbjct:  1147 -----------------------PAESPAKLQ----------SEVSTDL-------TAIN 1166

Query:  1166 SLSQTVQESTVSPPKQLTKEEEQFKKLQNDLLKQAKERLEALEMSEDMEKPRRLEDTVNL 1225
              LS    ++  +    L   +  F   Q + L   K+ +          +P       NL
Sbjct:  1167 GLSYN--KNLANGSYDLVNRD--F--CQGNQLNYFKQEIPV--------QPTTSYPIQNL 1212

Query:  1226 EDYGDDQENQEDENTPTNFPKTIDEEIEELSIGARKKQEIDDNAAKTDVLERENCEVLPV 1285
              +Y    ENQ     P+N       E   LS        +D NA  +          +P 
Sbjct:  1213 YNY----ENQPK---PSN-------ECPLLS-----NTYLDGNANTSTSDGSPAVSTMPA 1253

Query:  1286 AINEKSRSFSFEKESKAINGRLIRQRSEEYVSHIDSDIGLGVSPCLLLTALTTSNAADGM 1345
              +N            KA+  R+  ++S   V +  S   LG +P L+L ALT SNA+DG 
Sbjct:  1254 MMNAV----------KALKDRMDSEQSPS-VGY--SSRTLGPNPGLILQALTLSNASDGF 1300

Query:  1346 SLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQLIV 1405
             +LER E +GDSFLK A T YL+ T  D HEG+LS+ RSK+VSNCNLYRLGKK G+P  +V
Sbjct:  1301 NLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMV 1360

Query:  1406 ANKFDAHDSWLPPCYI----------------------------PTCD------FKAPNT 1431
              + FD   +WLPP Y+                              C+      ++AP  
Sbjct:  1361 VSIFDPPVNWLPPGYVVNQDKSNSEKWEKDEMTKDCLLANGKLGEACEEEEDLTWRAPK- 1419

Query:  1432 DDAEEKDNEIE------RILDGQVI---------------------EEKPENK------- 1457
             ++AE++D+ +E      + +D  ++                     E K   K       
Sbjct:  1420 EEAEDEDDFLEYDQEHIQFIDSMLMGSGAFVRKISLSPFSASDSAYEWKMPKKASLGSMP 1479

Query:  1458 ----------TGWDIGG--DVSKSTTDGIETITF--PKQARVGNDD-ISPLPYNLLTQQH 1502
                       + WD     D SK+  +    + F  P +   G D     + Y+L T+Q 
Sbjct:  1480 FASGLEDFDYSSWDAMCYLDPSKAVEEDDFVVGFWNPSEENCGVDTGKQSISYDLHTEQC 1539

Query:  1503 ISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKV---IQKDQKSDVPSP-------- 1551
             I+DKSIAD VEAL+G +L + G       +  +GLKV   I++  +     P        
Sbjct:  1540 IADKSIADCVEALLGCYLTSCGERAAQLFLCSLGLKVLPVIKRTSREKALDPAQENGSSQ 1599

Query:  1552 ---LLRFIDTPTNPNAS----LNF-------------------LNNLWQQFQFTQLEEKI 1585
                L      P  P +S    L +                   LN+L   F+    E+KI
Sbjct:  1600 QKSLSGSCAAPVGPRSSAGKDLEYGCLKIPPRCMFDHPDAEKTLNHLISGFE--TFEKKI 1657

Query:  1586 GYRFKERAYLVQAFTHASYINNRVTGCYQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLT 1645
              YRFK +AYL+QAFTHASY  N +T CYQRLEFLGDA+LDY+IT++L+ED RQ+SPGVLT
Sbjct:  1658 NYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLT 1717

Query:  1646 DLRSALVNNTIFASLAVKFEFQKHFIAMCPGLYHMIEKFVKLCSERNFDTNFNAEMYMVT 1705
             DLRSALVNNTIFASLAVK+++ K+F A+ P L+H+I+ FVK   E+N     ++E+    
Sbjct:  1718 DLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVKFQLEKNEMQGMDSELRR-- 1775

Query:  1706 TEEEIDEGQEEDIEVPKAMGDIFESVAGAIYLDSGRNLDTTWQVIFHMMRGTIELCCANP 1765
             +EE  DE +EEDIEVPKAMGDIFES+AGAIY+DSG +L+  WQV + MM+  IE   AN 
Sbjct:  1776 SEE--DEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLEVVWQVYYPMMQPLIEKFSANV 1833

Query:  1766 PRSPIRELMEFEQSKVRFSKMERILESGKVRVTVEVVNNMRFTGMGRNYRIAKATAAKRA 1825
             PRSP+REL+E E    +FS  ER  + GKVRVTVEVV   +F G+GR+YRIAK+ AA+RA
Sbjct:  1834 PRSPVRELLEMEPETAKFSPAERTYD-GKVRVTVEVVGKGKFKGVGRSYRIAKSAAARRA 1892

Query:  1826 LKYLHQIEQQ 1835
             L+ L   + Q
Sbjct:  1893 LRSLKANQPQ 1902


>sp|P84634.1|DCL4_ARATH RecName: Full=Dicer-like protein 4
        Length = 1589

 Score = 471 (170.9 bits), Expect = 8.6e-72, Sum P(5) = 8.6e-72
 Identities = 201/689 (29%), Positives = 323/689 (46%)
 Links = (1)-4-3-2-5

Query:    14 RDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQGGKRAFFVVEKVN 73
             R YQVEL  KAT++N IV LGTG GKT IAV+L+ E G  + +P         F+   V 
Sbjct:   125 RRYQVELCKKATEENVIVYLGTGCGKTHIAVMLIYELGHLVLSPKKSV---CIFLAPTVA 181

Query:    74 LVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLDLIRHAY 133
             LVEQQA  I    +FKV  +H      +  S  + ++ +  + V+V+T Q LL  ++H +
Sbjct:   182 LVEQQAKVIADSVNFKVA-IHCG-GKRIVKSHSEWEREIAANEVLVMTPQILLHNLQHCF 239

Query:   134 LKIEDMCVLIFDECHHALG-SQHPYRSIM-VDYKLLKKDKPVPRVLGLTASLIKAKVAPE 191
             +K+E + +LIFDECHHA   S HPY  IM V YK     +P  R+ G+TAS +  K  P 
Sbjct:   240 IKMECISLLIFDECHHAQQQSNHPYAEIMKVFYKSESLQRP--RIFGMTASPVVGKDGPP 297

Query:   192 KLMEQLKKLESAMDSVIETASDLVSLSKY-GAKPYEVVIICKDFEIGCLGIPNFDTV-IE 249
               ++       +  S    +  + SL     AK Y V     +  +   G  +   V + 
Sbjct:   298 --LDSFTYFSGSFQSE-NLSKSINSLENLLNAKVYSV-----ESNVQLDGFVSSPLVKVY 349

Query:   250 IFDETVAFVNTTTEFHPDL--DLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEKELG 307
              +   ++  + +T  + ++  D+  RR     L+   A   QL          V ++ +G
Sbjct:   350 YYRSALSDASQSTIRYENMLEDIKQRRANVYCLRFLEAAKIQLNS-----DHNVQDEPVG 404

Query:   308 KIIKSQVLPDKTLRFLNMAKTSMIT-IKRLLEPEMKKIKSIEALR-PYVPQRVIRLFEIL 365
             K  KS++       +L+MA  ++ + + +  +     + S+ AL+ P   +++++L +IL
Sbjct:   405 KNPKSKICDT----YLSMAAEALSSGVAK--DENASDLLSLAALKEPLFSRKLVQLIKIL 458

Query:   366 ETFNPEFQKERMKLEKAEHLSAIIFVDQRYIAYSLLLMMRHI---KSWEPKFKFVNPDYV 422
               F         +LE   H+  IIFV++   A +L  ++ ++   +SW+        D++
Sbjct:   459 SVF---------RLEP--HMKCIIFVNRIVTARTLSCILNNLELLRSWKS-------DFL 500

Query:   423 VGASGRNLASSDSQGLHKRQTE-VLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRP 481
             VG S      S  + + +R  E +L+RF   E+N L+AT V EEG+D++ C LVI++D P
Sbjct:   501 VGLS------SGLKSMSRRSMETILKRFQSKELNLLVATKVGEEGLDIQTCCLVIRYDLP 554

Query:   482 LDMRSYVQSKGRARRAGSRYVITVE---EKD----------------------------- 509
               + S++QS+GRAR   S Y   V+   EK+                             
Sbjct:   555 ETVTSFIQSRGRARMPQSEYAFLVDSGNEKEMDLIENFKVNEDRMNLEITYRSSEETCPR 614

Query:   510 ----------TAA-------------YCSKLPSDIFTRLVPHNQIIPIEENGVTKYCAEL 546
                       T A             YCS+LP D F +  P  Q  P++E G T  C  +
Sbjct:   615 LDEELYKVHETGACISGGSSISLLYKYCSRLPHDEFFQPKPEFQFKPVDEFGGT-IC-RI 672

Query:   547 LLPINSPIKHAIVLKNPMPNKKTAQMAVALEACRQLHLEGELDDNLLPKGRESIAKLLEH 606
              LP N+PI    +  + +P+ + A+    L+A  +LH  G L+D LLP  ++ I   L  
Sbjct:   673 TLPANAPISE--IESSLLPSTEAAKKDACLKAVHELHNLGVLNDFLLPDSKDEIEDELS- 729

Query:   607 IDEEPDEYAPGIAAKVGSSKRKQLYDKKI 635
              D+E D     I  + G S R  LY+ ++
Sbjct:   730 -DDEFD--FDNIKGE-GCS-RGDLYEMRV 753

 Score = 290 (107.1 bits), Expect = 8.6e-72, Sum P(5) = 8.6e-72
 Identities = 76/182 (41%), Positives = 99/182 (54%)
 Links = 1-4-3-(2)-5

Query:  1506 KSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKV-IQKDQKSDVPSPLLRFIDTPTNPNA 1564
             K+IAD VEAL+G  L+  G    +K + W+G+ V  +  Q  D      R++   T    
Sbjct:  1162 KTIADVVEALVGAFLVDSGFKGAVKFLKWIGVNVDFESLQVQDACIASRRYLPLTTR--- 1218

Query:  1565 SLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHASYINNRVTGCYQRLEFLGDAVL 1624
                  NNL        LE ++ Y+F  +  LVQAF H SY N    GCYQRLEFLGDAVL
Sbjct:  1219 -----NNL------ETLENQLDYKFLHKGLLVQAFIHPSY-NRHGGGCYQRLEFLGDAVL 1266

Query:  1625 DYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIAMCPGLY-H-MIE 1682
             DY++T Y F    +  PG LTDLRS  VNN   A++AV F   K F+  C  +Y H +IE
Sbjct:  1267 DYLMTSYFFTVFPKLKPGQLTDLRSLSVNNEALANVAVSFSL-KRFL-FCESIYLHEVIE 1324

Query:  1683 KF 1684
              +
Sbjct:  1325 DY 1326

 Score = 109 (43.4 bits), Expect = 8.6e-72, Sum P(5) = 8.6e-72
 Identities = 28/59 (47%), Positives = 38/59 (64%)
 Links = 1-4-(3)-2-5

Query:  1327 VSPCLLLTALTTSNAADGMSLERFETIGDSFLKFATTDYLY--HTLLDQHEGKLSFARS 1383
             VS   +L ALTT    + +SLER E +GD+FLKFA + +L+  H  LD  EG+L+  RS
Sbjct:  1044 VSGHRVLEALTTEKCHERLSLERLEVLGDAFLKFAVSRHLFLHHDSLD--EGELTRRRS 1100

 Score = 58 (25.5 bits), Expect = 8.6e-72, Sum P(5) = 8.6e-72
 Identities = 14/42 (33%), Positives = 25/42 (59%)
 Links = 1-(4)-3-2-5

Query:   931 PEL--MDIHPISATLWNVIAALPSIFYRVNQLLLTDELRETI 970
             PEL  + I  +S  + + ++ LPSI +R+  LL+  EL+  +
Sbjct:   993 PELSHLKIKGLSKDIGSSLSLLPSIMHRMENLLVAIELKHVL 1034

 Score = 57 (25.1 bits), Expect = 8.6e-72, Sum P(5) = 8.6e-72
 Identities = 22/79 (27%), Positives = 33/79 (41%)
 Links = 1-4-3-2-(5)

Query:  1765 PPRSPIRELMEFEQSKVRFSKMERILESGKVRVTVEVVNN---MRFTGMGRNYRIAKATA 1821
             P  SPI+EL+E  QS     ++    + G   V ++V  N   +  +  GRN R     A
Sbjct:  1346 PKISPIKELIELCQSYKWDREISATKKDGAFTVELKVTKNGCCLTVSATGRNKREGTKKA 1405

Query:  1822 AKRALKYLHQIEQQRRQSP 1840
             A+  +  L   E      P
Sbjct:  1406 AQLMITNLKAHENITTSHP 1424


>sp|Q7S8J7.1|DCL1_NEUCR RecName: Full=Dicer-like protein 1; Includes: RecName:
            Full=Endoribonuclease dcl-1; Includes: RecName: Full=ATP-dependent
            helicase dcl-1
        Length = 1584

 Score = 505 (182.8 bits), Expect = 3.0e-69, Sum P(6) = 3.0e-69
 Identities = 164/507 (32%), Positives = 269/507 (53%)
 Links = (1)-4-6-3-2-8

Query:    12 NPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQGGKR--AFFVV 69
             +PR+YQVEL ++A ++NTI  L TGSGKT IA +LL+          ++G  R  AFF+V
Sbjct:   121 SPREYQVELFERAKQQNTIAVLDTGSGKTLIAAMLLRWVITGELEDREKGLPRRIAFFLV 180

Query:    70 EKVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLDLI 129
             +KV LV QQ   +  +  F + ++ G+   G+ +SK    + ++++ VVV TA+ L   +
Sbjct:   181 DKVALVFQQHSFLTKNLDFPMEKLCGEMVEGV-ESKAFWKEALEQNEVVVCTAEILSTAL 239

Query:   130 RHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPVPRVLGLTASLIKAKVA 189
              H++++++ + +LIFDE HH     HPY  I+ ++ + ++ +  PR+LGLTAS + AKV 
Sbjct:   240 HHSWIRMDQINLLIFDEAHHTK-KDHPYARIIKNFYIDEQLERRPRILGLTASPVDAKVD 298

Query:   190 PEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNFDTVIE 249
             P +   +L   E+ + S I TA+D  +L     KP   +++  ++     G P+ +TV+ 
Sbjct:   299 PRRAAAEL---EALLHSQIATAADPAALQHTICKPKTELVV--EY---VRGRPDSETVLN 350

Query:   250 IFDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEKELGKI 309
                +    V     F        ++P+     TT A  + LG W A R  Q++ K+   I
Sbjct:   351 --KQLRKLVGGQELF--------KKPLNF---TTSAASK-LGTWCADRYWQLFFKQ-EDI 395

Query:   310 IKSQVLPDKTLRFLNMAKTSMIT---IKRLLEP-EMKKIKSIE--ALRP-YVPQRVIRLF 362
             +K +   ++ L  + +A    IT   +K++ E  E+    +    AL P  +  +VI L 
Sbjct:   396 VKLESRTERDL--MKVAALDEITEKHVKQVREAHELVNAHTFSPAALDPTMLSSKVIMLV 453

Query:   363 EILETFNPEFQKERMKLEKAEHLSAIIFVDQRYIAYSL--LLMMRHIKSWEPKFKFVNPD 420
              IL     +F++       A+    IIFV QR  A  L  LL    IKS  P    +  +
Sbjct:   454 RILRD---QFERG----VGAQR--CIIFVRQRNTAMLLADLLQQPEIKSHIPS---IAAE 501

Query:   421 YVVGASGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDR 480
              +VG      +  +++   ++Q  ++R+F   EINCL ATSV EEG+D+  CN+VI+FD 
Sbjct:   502 VLVGGGTTGSSYVNAKINFQQQNRIIRKFKLGEINCLFATSVAEEGLDIPDCNIVIRFDL 561

Query:   481 PLDMRSYVQSKGRARRAGSRYVITVEE 507
                +   +QS+GRARR  SRY+  +E+
Sbjct:   562 YDTLIQCIQSRGRARRPDSRYIQMIEK 588

 Score = 233 (87.1 bits), Expect = 3.0e-69, Sum P(6) = 3.0e-69
 Identities = 81/263 (30%), Positives = 117/263 (44%)
 Links = 1-4-6-3-(2)-8

Query:  1500 QQHI-SDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQKDQKSDVPS--PLLRFI 1556
             Q+H+ +DKSIAD  EALIG   LT G       M    +  + KD+K  + S        
Sbjct:  1182 QRHVLADKSIADVCEALIGAAYLT-GQEKGSFDMAIKAVTAMVKDKKHRMISYGDYYAVY 1240

Query:  1557 DTPTNPNASLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHASY--INNRVTGCYQ 1614
               PT    S N      Q+    +  E++GY+FK    L  AF H +Y  +  R+   YQ
Sbjct:  1241 QKPTWQTESANSA----QRDMAKKFSERMGYKFKHPRLLRAAFQHPTYPSLYERLPS-YQ 1295

Query:  1615 RLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIAMC 1674
             RLEFLGDA+ D +   YLF       P  LT+ + A+V+N     L+    F K    M 
Sbjct:  1296 RLEFLGDALFDMVAVDYLFRKFPAADPQWLTEHKMAMVSNQFLCCLSFHLGFNKCIATMS 1355

Query:  1675 PGLYHMIEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDI----EVPKAMGDIFES 1730
             P +   I ++V    E   +T     +    T +E        I     +PK + D+ E+
Sbjct:  1356 PSILKDIAEYVTEIEEA-LETAKQEAINAGKTADEYSRDYWVHITHASRLPKCLSDVVEA 1414

Query:  1731 VAGAIYLDSGRNLDTTWQVIFHM 1753
               GAI++DS  +     Q  F+M
Sbjct:  1415 YIGAIFVDSEYDYSVV-QNFFNM 1436

 Score = 109 (43.4 bits), Expect = 3.0e-69, Sum P(6) = 3.0e-69
 Identities = 49/187 (26%), Positives = 86/187 (45%)
 Links = 1-4-6-(3)-2-8

Query:  1249 DEEIEELSIGARKKQEIDDNAAKTDVLERENCEVL--PVAINEKSRSFSFEKESKAINGR 1306
             D+ + E ++ + ++  +DD     DV E + C ++  P+ I+        +  +  +   
Sbjct:   987 DQPVVEAALISTRRDFLDDTLRDEDV-EPQQCFLILEPMRISP----IPADVVAMLLCFP 1041

Query:  1307 LIRQRSEEYVSHIDSD--IGLGVSPCLLLTALTT-SNAAD-----------GM--SLERF 1350
              I  R E  +  +D+   +GL + P L L A T  S+ +D           GM  + ER 
Sbjct:  1042 SIIHRVESNLVALDACKLLGLDLRPDLALEAFTKDSDNSDEHDAEKENFQTGMGDNYERL 1101

Query:  1351 ETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQLIVANKFD 1410
             E +GDSFLK ATT  +Y  + D+ E +    R   + N NL+    ++G+ + I +  F+
Sbjct:  1102 EFLGDSFLKMATTIAIYTLIPDKGEFEYHVERMLLICNKNLFNNALEIGLEEYIRSMSFN 1161

Query:  1411 AHDSWLP 1417
                 W P
Sbjct:  1162 RRQ-WYP 1167

 Score = 69 (29.3 bits), Expect = 3.0e-69, Sum P(6) = 3.0e-69
 Identities = 28/82 (34%), Positives = 40/82 (48%)
 Links = 1-(4)-6-3-2-8

Query:   511 AAYCSKLPSDIFTRLVPHNQIIPIEENGVTKYCAELLLPINSPIKHAIVLKNPMPNKKTA 570
             A + + LP    T L P   I  +   G    C E+++P  SPIK A+  K  + +K  A
Sbjct:   659 ANFTATLPHPPETSLSPEYYITTVP-GGFQ--C-EVVMPDASPIKSAVG-KVHL-SKGVA 712

Query:   571 QMAVALEACRQLHLEGELDDNL 592
             + A A E C  L   G LD++L
Sbjct:   713 KCAAAFELCLALLKAGHLDNHL 734

 Score = 65 (27.9 bits), Expect = 1.0e-64, Sum P(6) = 1.0e-64
 Identities = 21/69 (30%), Positives = 36/69 (52%)
 Links = 1-4-6-(5)-2-8

Query:   925 QRQILVPELMDIHPISATLWNVIAALPSIFYRV-NQLLLTD-------ELRETILVKAFG 976
             Q+  L+ E M I PI A +  ++   PSI +RV + L+  D       +LR  + ++AF 
Sbjct:  1015 QQCFLILEPMRISPIPADVVAMLLCFPSIIHRVESNLVALDACKLLGLDLRPDLALEAFT 1074

Query:   977 KEKTKLDDN 985
             K+    D++
Sbjct:  1075 KDSDNSDEH 1083

 Score = 49 (22.3 bits), Expect = 3.0e-69, Sum P(6) = 3.0e-69
 Identities = 44/220 (20%), Positives = 84/220 (38%)
 Links = 1-4-(6)-3-2-8

Query:   687 LSAKEIPKIPPFPVFLRQGNM-KVRLIVAPKKTTVTAAQLQEIQLFHNYLFTQVLQMCKT 745
             LS   +P++  FP+F       KVR +  P         ++++  F    F  V      
Sbjct:   801 LSRSALPEVASFPLFFGTKRFSKVRCVPIPGSVQADDTLVEQLTRFTLKAFMDVFSK--- 857

Query:   746 GNLEFDGTS-NAPLNTLIVPLN-------KRKDDMSYTINMKYVSEVVANMENMPR--IP 795
                E++ T+ N P    + P++       +     ++ I+ K ++ V  N E +P   + 
Sbjct:   858 ---EYEATAVNLPY--FLSPMDGGHGFDFRLAKSPAHLIDRKALAYVSEN-EKVPYTFLE 911

Query:   796 KDEVRRQYKFNAEDYKDAI-VMPWYRNLEQPVFYYVAE--ILPEWRPSSKFPDTH--FET 850
              D+   Q KF  + Y  A      +R  +      V +  + P  R       TH     
Sbjct:   912 PDDFF-QDKFVVDPYDGARKFFTHHRRHDMKPTDPVPDGIVAPNHRAWRGLGTTHDILNY 970

Query:   851 FNEYFIKKYKLEIYDQNQSLLDVDFTSTRLNLLQPRIQNQ 890
              N  + K     I+  +Q +++    STR + L   ++++
Sbjct:   971 SNSLWSKSRGFMIFQADQPVVEAALISTRRDFLDDTLRDE 1010

 Score = 45 (20.9 bits), Expect = 4.1e-60, Sum P(4) = 4.1e-60
 Identities = 25/88 (28%), Positives = 41/88 (46%)
 Links = 1-(7)-2-8

Query:   535 EENGVTKYCAELLLPIN-SPIKH---AIVLKNPMPNKKTAQMAVALEACRQLHLEGELDD 590
             +E+   + C  +L P+  SPI     A++L  P    +     VAL+AC+ L L+   D 
Sbjct:  1009 DEDVEPQQCFLILEPMRISPIPADVVAMLLCFPSIIHRVESNLVALDACKLLGLDLRPDL 1068

Query:   591 NLLPKGRESIAKLLEHIDEEPDEYAPGI 618
              L    ++S     EH D E + +  G+
Sbjct:  1069 ALEAFTKDS-DNSDEH-DAEKENFQTGM 1094

 Score = 40 (19.1 bits), Expect = 3.0e-69, Sum P(6) = 3.0e-69
 Identities = 10/26 (38%), Positives = 16/26 (61%)
 Links = 1-4-6-3-2-(8)

Query:  1815 RIAKATAAKRALKYLH--QIEQQRRQ 1838
             R AK+  AK+A+K L    +E+ R +
Sbjct:  1529 RYAKSAMAKKAIKLLEGMSVEEFRER 1554


>sp|A4RKC3.2|DCL1_MAGGR RecName: Full=Dicer-like protein 1; Includes: RecName:
            Full=Endoribonuclease DCL1; Includes: RecName: Full=ATP-dependent
            helicase DCL1
        Length = 1591

 Score = 481 (174.4 bits), Expect = 3.5e-69, Sum P(6) = 3.5e-69
 Identities = 152/502 (30%), Positives = 238/502 (47%)
 Links = (1)-4-5-7-3-2

Query:    13 PRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEY-GVQLFAPLDQGGKR-AFFVVE 70
             PR+YQ+EL ++A +KNTI  L TG+GKT IA+LL++    ++L A      KR  FF+V+
Sbjct:   108 PREYQIELFERAKQKNTIAVLDTGTGKTLIAILLIRHIIELELGARWQGREKRITFFLVD 167

Query:    71 KVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLDLIR 130
             KV LV QQ  HI  +  F V  +HG T   LW SKE  ++ ++   VVV TA+ L   + 
Sbjct:   168 KVALVRQQTDHIRANLDFPVTGLHGDTVRNLWYSKEYFEKLLQEQEVVVCTAEILYRCLH 227

Query:   131 HAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKD-KPVPRVLGLTASLIKAKVA 189
              +YL I  + +++FDE HHA    H Y  I+ D+ L+++D +  PR+ G+TAS I  K  
Sbjct:   228 RSYLNISQVSLVVFDEAHHAK-KNHVYARIIKDFYLMEEDCQKRPRIFGMTASPIDTKDT 286

Query:   190 PEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNFDTVIE 249
                      +LES + S I T SD   L   G++P EV               ++  V+ 
Sbjct:   287 CISYERATHELESLLHSEIATISDRDLLKVIGSRPQEVR-------------KSYARVLR 333

Query:   250 IFDETVAFVNTTTEFHPDLDLDPRRPI-KDSLKTTRAVFRQLGPWAAWRTAQV-WEKELG 307
                E     N   E      L    P+ K +  +      +LG W A +  ++ + +E  
Sbjct:   334 --QENTELCNQLRE------LVGNHPLFKQTFDSAEFAVTELGAWCADKLWELCFREEAV 385

Query:   308 KIIKSQVLPDKTLRFLNMAKTSMITIKRLLEPEMKKIKSIEALRPYVPQRVIRLFEILET 367
               +  +V   +  R  +    S   +    E  +  ++      P       +  +++E 
Sbjct:   386 STLDGRVEGSRA-RDPDEVGESSHEVSNAREA-LSLVQQWSFSPPEDGSLSTKTHKLIEI 443

Query:   368 FNPEFQKERMKLEKAEHLSAIIFVDQRYIAYSL--LLMMRHIKSWEPKFKFVNPDYVVGA 425
                 F +          +  I+FV +R  A  L  L     I++  P  K     +++GA
Sbjct:   444 LAECFSQA----SAGNAIQCIVFVKRRDTAVLLNALCEQAEIRTKIPDLKGA---FLIGA 496

Query:   426 S-GRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDM 484
               G N A + +    ++Q + + RF   EINCL ATS+ EEG+D+  CN+VI+FD     
Sbjct:   497 GRGGNAAFTTT----RQQEQTVSRFRDGEINCLFATSIAEEGLDIPGCNVVIRFDLHGTT 552

Query:   485 RSYVQSKGRARRAGSRYVITVE 506
               Y+QS+GRAR   S ++   E
Sbjct:   553 IQYIQSRGRARMRNSWFIHMTE 574

 Score = 251 (93.4 bits), Expect = 3.5e-69, Sum P(6) = 3.5e-69
 Identities = 83/256 (32%), Positives = 125/256 (48%)
 Links = 1-4-5-7-3-(2)

Query:  1501 QH-ISDKSIADAVEALIGVHLLTL----GPN-----PTLKVMNWMGLKVIQ--KDQKSDV 1548
             +H + DKSIAD  EALIG   LT      PN       + VM       +Q   D  +  
Sbjct:  1166 EHALGDKSIADVCEALIGAAYLTAQAQSSPNFDLAVKAVTVMTHSKTHTMQAWSDYYASY 1225

Query:  1549 PSPLLRFIDTPTNPNASLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHASYINNR 1608
               P   ++ TP  P+ +        Q    +Q++ K+GYRFK    L  AF H SY    
Sbjct:  1226 QCP--EWLSTP--PSQT--------QLELCSQIKNKMGYRFKNPRLLRCAFMHPSYPRQY 1273

Query:  1609 VT-GCYQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQ 1667
                  YQRLEFLGD++LD +   YLF+      P  LT+ + A+V+N  F  +AV   F 
Sbjct:  1274 ENIPSYQRLEFLGDSLLDMVCVDYLFKKHPDKDPQWLTEHKMAMVSNQFFGCVAVGLGFH 1333

Query:  1668 KHFIAMCPGLYHMIEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDIEV---PKAM 1724
             +H I M P L   I ++ +L +++  +     ++ +   + E D  ++  IEV   PK +
Sbjct:  1334 RHLIHMQPALGGSITEWAELVTKKREEAR---QLAVRRGQREEDYARDFWIEVHHPPKCL 1390

Query:  1725 GDIFESVAGAIYLDSG 1740
              DI E+  GA+++D+G
Sbjct:  1391 PDILEAYVGALFVDTG 1406

 Score = 99 (39.9 bits), Expect = 3.5e-69, Sum P(6) = 3.5e-69
 Identities = 25/75 (33%), Positives = 39/75 (52%)
 Links = 1-4-5-7-(3)-2

Query:  1344 GMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQL 1403
             G + ER E +GD FLK AT+  LY TL++  E +    R  ++ N NL     +  + + 
Sbjct:  1079 GQNYERLEFLGDCFLKMATSIALY-TLVEGDEFEYHVERMLDICNKNLLNWALESNLQEH 1137

Query:  1404 IVANKFDAHDSWLPP 1418
             I +  F+   +W PP
Sbjct:  1138 IRSKSFNRR-TWYPP 1151

 Score = 70 (29.7 bits), Expect = 3.5e-69, Sum P(6) = 3.5e-69
 Identities = 20/60 (33%), Positives = 34/60 (56%)
 Links = 1-(4)-5-7-3-2

Query:   545 ELLLPINSPIKHAIVLKNPMPNKKTAQMAVALEACRQLHLEGELDDNLLPKGRESIAKLL 604
             E+ LP +SP++ A  +     +K+ A+ A A   C QL+    LDD+L    + ++AK+L
Sbjct:   674 EVYLPASSPLRSA--MGGVYRSKQLAKCAAAYAMCIQLYNSNYLDDHL----KSTLAKVL 727

 Score = 65 (27.9 bits), Expect = 3.5e-69, Sum P(6) = 3.5e-69
 Identities = 35/168 (20%), Positives = 70/168 (41%)
 Links = 1-4-(5)-7-3-2

Query:   687 LSAKEIPKIPPFPVFLRQGNMK---VRLIVAPKKTTVTAAQLQEIQLFHNYLFTQVLQMC 743
             L+ K +P+I  FP+F  +G+ +   VR I      + T  Q++ I  F   +F  +    
Sbjct:   786 LTRKPLPEIAQFPLFFGKGSSRRSNVRCIPLAHPWSPTTTQVEGICAFTLCIFRDIFSK- 844

Query:   744 KTGNLEFDGTSNAPLNTLIVPLN--KRKDDMSYTINMKYVSE--VVANMENMPRIPKDEV 799
                + +  GT + P    + P    +   D+S  +N + + +   V       R+P    
Sbjct:   845 ---DFQASGT-DMPY--FLAPSTGIEHGTDLSSLVNPERIIDWATVHRTTTTDRVP---- 894

Query:   800 RRQYKFNAED--YKDAIVMPWYRNLEQPVFYYVAEILPEWRPSSKFPD 845
                Y FN  D  ++D  V   +    +   +++ ++  + +P  K P+
Sbjct:   895 ---YNFNEPDEFFQDKYVSDPFDGSRK---FFMRKVRRDLKPQDKVPE 936

 Score = 51 (23.0 bits), Expect = 3.9e-66, Sum P(4) = 3.9e-66
 Identities = 33/139 (23%), Positives = 58/139 (41%)
 Links = 1-(6)-3-2

Query:   490 SKGRA-RRAGSRYVITVEEKDTAAYCSKLPSDIF-TRLVPHNQIIPIEENGV------TK 541
             SK RA       Y +++ +K  A + S+    +    L P  + +  E +G       T 
Sbjct:   942 SKWRAVEHTILNYSVSLWKKSRAGHNSRQDQPVVEAELAPLRRNLLDETDGENSTGPQTC 1001

Query:   542 YCA-ELLLPINSPIKHAIVLKN-PMPNKKTAQMAVALEACRQLHLEGELDDNLLPKGRES 599
             Y   E LL    P+   ++    P    +     ++LEAC+ L L+  +D  L+   ++S
Sbjct:  1002 YLVLETLLISQIPVDTVVMAYTFPAIIYRLENSLISLEACQNLGLDIPIDIALIAMTKDS 1061

Query:   600 IAKLLEHIDEEPDEYAPGI 618
                  +H DE P  +  G+
Sbjct:  1062 -DNSDDH-DEAPINFQSGM 1078

 Score = 40 (19.1 bits), Expect = 3.5e-69, Sum P(6) = 3.5e-69
 Identities = 8/26 (30%), Positives = 13/26 (50%)
 Links = 1-4-5-(7)-3-2

Query:  1231 DQENQED-ENTPTNFPKTIDEEIEEL 1255
             D +N +D +  P NF   + +  E L
Sbjct:  1060 DSDNSDDHDEAPINFQSGMGQNYERL 1085


>sp|Q0CW42.2|DCL1_ASPTN RecName: Full=Dicer-like protein 1; Includes: RecName:
            Full=Endoribonuclease dcl1; Includes: RecName: Full=ATP-dependent
            helicase dcl1
        Length = 1519

 Score = 464 (168.4 bits), Expect = 4.8e-65, Sum P(6) = 4.8e-65
 Identities = 159/512 (31%), Positives = 242/512 (47%)
 Links = (1)-4-5-9-3-2

Query:    12 NPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEY-GVQLFAPLDQGGKR-AFFVV 69
             NPR+YQ+EL ++A  +NTI  L TGSGKT IAVLLLK     +L    +    R +FF+V
Sbjct:   108 NPREYQIELFERAKVQNTIAVLDTGSGKTLIAVLLLKHVIQTELIDRANGNPPRISFFLV 167

Query:    70 EKVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLDLI 129
             + V LV QQA  +  +    V    G     LW+ +   + F K + V+V TA+ L   +
Sbjct:   168 DSVTLVYQQASVLRNNLDQNVAHFFGAMGVDLWNKQTWAEHFEK-NMVIVCTAEILNQCL 226

Query:   130 RHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPVPRVLGLTASLIKAKVA 189
              +AY+ ++ + +L+FDE HH     HPY  I+ D  L       PR+ G+TAS +  K  
Sbjct:   227 LNAYITMQQINLLVFDEAHHTK-KDHPYARIIRDSYLRVPPSSRPRIFGMTASPVDTK-- 283

Query:   190 PEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNFDTVIE 249
                ++E  + LE+ +DS I T S L  L +   +P E V I    +      P F + + 
Sbjct:   284 -GDVLEAARNLEALLDSKIATTSKLTILRQVVNRPNEEVWIYDKLQ------PTFTSDLY 336

Query:   250 IFDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEKELGKI 309
                E+         F     L+P        +  R    +LG W A R   VW   L   
Sbjct:   337 KLMES--------RFGDISHLEPM------FRFARHATSELGTWCADR---VWVSALADD 379

Query:   310 IKSQVLPDKTLRFLNMAKTSMITIKRLLEPEMKKIKSIEALRPYVPQRVIRLFEILETFN 369
             +  +V  + ++     + T +  + + +  ++ +IK    L    P       E L +  
Sbjct:   380 VLPKV--EGSIGGKRQS-TGLGQLPKDVHRDITRIKEASELVESHPPNDPGAPEALSSKV 436

Query:   370 PEFQKERMKLEKAE-HLSAIIFVDQRYIAYSLLLMMRHIKSWEPKFKFVNPDYVVGASGR 428
                 KE  +    E +   I+F ++RY A  L  +   +    P  +   P  ++G    
Sbjct:   437 RVLWKEISQCFGQETNTKCIVFTEKRYTAKVLFDLFTVLNV--PGLR---PGVLIG---- 487

Query:   429 NLASSDSQGLH---KRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMR 485
              + SSD  G++   ++Q   + RF   EINCL AT+V EEG+D+  CNLV++FD    + 
Sbjct:   488 -VRSSDRIGMNVTFRQQILTMVRFRTGEINCLFATAVAEEGLDIPDCNLVVRFDLYKTLI 546

Query:   486 SYVQSKGRARRAGSRYVITVEEKDTAAYCSKL 517
              YVQS+GRAR A S Y   +E KD A + S L
Sbjct:   547 QYVQSRGRARHADSTYASMIE-KDNADHESIL 577

 Score = 208 (78.3 bits), Expect = 4.8e-65, Sum P(6) = 4.8e-65
 Identities = 91/350 (26%), Positives = 148/350 (42%)
 Links = 1-4-5-9-3-(2)

Query:  1503 ISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQK--DQKSDVPSPLLRFIDTPT 1560
             +++K+IAD  EALIG  LLT GP         MG++ +    D      +    +I   +
Sbjct:  1163 LAEKTIADVCEALIGAALLTPGPQHRFD----MGVRAVSAVVDSNEHNAASWRDYISLYS 1218

Query:  1561 NPNASLNFLNNLWQQFQFTQ-LEEKIGYRFKERAYLVQAFTHASYINN--RVTGCYQRLE 1617
              P       +    +    + +EEK+GY F+    L  AFTH SY +   RV  CYQ LE
Sbjct:  1219 IPKYQEQAPDG--SEIDLCRRVEEKLGYHFRYPRLLHSAFTHPSYPSAWARVP-CYQSLE 1275

Query:  1618 FLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIAMCPGL 1677
             FLGDA+LD +    LF       P  LT+ + A+V+N    +LAVK     H       L
Sbjct:  1276 FLGDALLDMVCVEDLFRRFPDRDPQWLTEHKMAMVSNKFLGALAVKLGLHTHLSYFSSAL 1335

Query:  1678 YHMIEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDIEVPKA-MGDIFESVAGAIY 1736
                I  + +        ++   + + +T +             PK  + D+ E+  GA++
Sbjct:  1336 QSQITHYAEEAQAAASQSDVAVDYWTLTQDP------------PKVCLPDMVEAYLGAVF 1383

Query:  1737 LDSG---RNLDTTWQV----IFHMMRGTIELCCANPPRSPIRELMEFEQSKVRFS-KMER 1788
             +DS      ++  +Q      FH M    +      P + +   +  E   + +  K   
Sbjct:  1384 VDSNFRFEEVEVFFQQHIKPYFHDM-AIYDTFANRHPTTFLHNKLTNEYGCLNYCLKAGE 1442

Query:  1789 IL----ESGKVRVTVEVVNNMRFTGMGRNYRIAKATAAKRALKYLHQIEQ 1834
             I     ++  V   V V + +  TG+  + R AK  A++ AL  L  I++
Sbjct:  1443 IPGADGDASTVLAAVIVHDTILTTGVASSGRYAKVKASENALTELLHIDR 1492

 Score = 94 (38.1 bits), Expect = 4.8e-65, Sum P(6) = 4.8e-65
 Identities = 25/74 (33%), Positives = 37/74 (50%)
 Links = 1-4-5-9-(3)-2

Query:  1344 GMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQL 1403
             G + ER E +GD FLK AT+  L++   D +E      R   + N NL+    K  + Q 
Sbjct:  1068 GKNYERLEFLGDCFLKMATSISLFNQHPDDNEFDYHVNRMCLICNRNLFNSAVKKELYQF 1127

Query:  1404 IVANKFDAHDSWLP 1417
             I +  F + D+W P
Sbjct:  1128 IRSRGF-SRDTWYP 1140

 Score = 85 (35.0 bits), Expect = 4.8e-65, Sum P(6) = 4.8e-65
 Identities = 27/82 (32%), Positives = 38/82 (46%)
 Links = 1-(4)-5-9-3-2

Query:   511 AAYCSKLPSDIFTRLVPHNQIIPIEENGVTKYCAELLLPINSPIKHAIVLKNPMPNKKTA 570
             A Y S L  +  T       ++P+ +     Y  E++LP  SPI+ A  +  P   K TA
Sbjct:   639 ARYASSLQYENDTSAQVTYVVLPVND----AYVCEVILPEKSPIRGATGM--PAMKKSTA 692

Query:   571 QMAVALEACRQLHLEGELDDNL 592
             +   A EACR L     LD+ L
Sbjct:   693 KRYAAFEACRLLRKHRLLDEYL 714

 Score = 76 (31.8 bits), Expect = 4.8e-65, Sum P(6) = 4.8e-65
 Identities = 50/220 (22%), Positives = 88/220 (40%)
 Links = 1-4-(5)-9-3-2

Query:   692 IPKIPPFPVFLRQGNMKVRLIVAPKKTTV--TAAQLQEIQLFHNYLFTQVLQMCKTGNLE 749
             +P+ P FP+FL + +++  ++  P    +  +A +L  +  F   +F  V +  KT + E
Sbjct:   788 LPQFPTFPIFLGE-DVETIVLTVPVNMELQPSADELDYMTTFTLRIFRDVFR--KTYDKE 844

Query:   750 FDGTSNAPLNTLIVPLNKRKDDMSYTINMKYVSEVVANMENMPRIPKDEVRRQYKFNAED 809
              +      L  +  P N+  D     +N + +S V           +D++  Q     E 
Sbjct:   845 PEKLPYWLLPAISFPCNQEADPRD-VVNWEILSSVHE---------RDDIEYQADMPPEM 894

Query:   810 YKDAIVMPWYRNLEQPVFYYVAEILPEWRPSSKFPD-----THFETFNEYFIKKYK---- 860
               D  V   Y + +    Y+   +    +PSS  P       H +T   Y I   K    
Sbjct:   895 LVDRFV---YDHWDGRYRYFTLAVDENLQPSSPPPSHVARRRHMDTIMNYSISLSKNSRA 951

Query:   861 --LEIYDQNQSLLDVDFTSTRLNLLQPRIQNQPRRSRTVS 898
               L   + NQ +L  +    R NLL  R+ ++ R+  T S
Sbjct:   952 KFLSRCNWNQPVLHAELVRLRRNLLD-RMTDKERKLETRS 990

 Score = 49 (22.3 bits), Expect = 3.5e-58, Sum P(5) = 3.5e-58
 Identities = 20/74 (27%), Positives = 31/74 (41%)
 Links = 1-(6)-10-3-2

Query:  1028 ENDKIDDGEELFNIGVWDPEEAVRIGVEISSRDDRMDGEDQDTVGLTQGLHDGNISDEDD 1087
             E D  D   E   + V D E+ ++   ++   D  + G D DT        D  +  E+ 
Sbjct:   567 EKDNAD--HESILVQVNDAEKIMQSFCQLLPEDRILHGNDDDT--------DAVLDREEW 616

Query:  1088 ELPFVMHDYTARLT 1101
             E P+ +    ARLT
Sbjct:   617 EEPYTLPSTAARLT 630

 Score = 41 (19.5 bits), Expect = 2.2e-58, Sum P(4) = 2.2e-58
 Identities = 8/16 (50%), Positives = 12/16 (75%)
 Links = 1-(7)-3-2

Query:   574 VALEACRQLHLEGELD 589
             + LEAC++L LE  L+
Sbjct:  1025 IGLEACKKLGLEISLE 1040

 Score = 39 (18.8 bits), Expect = 3.8e-57, Sum P(5) = 3.8e-57
 Identities = 15/79 (18%), Positives = 35/79 (44%)
 Links = 1-(8)-9-3-2

Query:   729 QLFHNYLFTQVLQMCKTGNLEFDGTSNAPLNTLIVPLNKRKDDMSYTINMKYVSEVVANM 788
             +L H+   T + +   +  L+++  ++A +  +++P+N   D     + +   S +    
Sbjct:   628 RLTHHSAITVLARYASS--LQYENDTSAQVTYVVLPVN---DAYVCEVILPEKSPI-RGA 681

Query:   789 ENMPRIPKDEVRRQYKFNA 807
               MP + K   +R   F A
Sbjct:   682 TGMPAMKKSTAKRYAAFEA 700

 Score = 38 (18.4 bits), Expect = 4.8e-65, Sum P(6) = 4.8e-65
 Identities = 10/37 (27%), Positives = 18/37 (48%)
 Links = 1-4-5-(9)-3-2

Query:   926 RQILVPELMDIHPISATLWNVIAALPSIFYRVNQLLL 962
             R ++  E + I  I A +     A P+I  R++  L+
Sbjct:   989 RSVICIEPLKISAIPAAIAATCLAFPAIISRLDAYLI 1025

 Score = 38 (18.4 bits), Expect = 6.7e-62, Sum P(5) = 6.7e-62
 Identities = 9/35 (25%), Positives = 18/35 (51%)
 Links = 1-4-(10)-3-2

Query:  1241 PTNFPKTIDEEIEELSIGARKKQEIDDNAAKTDVL 1275
             PT FP  + E++E + +      E+  +A + D +
Sbjct:   792 PT-FPIFLGEDVETIVLTVPVNMELQPSADELDYM 825


>sp|Q1DKI1.2|DCL1_COCIM RecName: Full=Dicer-like protein 1; Includes: RecName:
            Full=Endoribonuclease DCL1; Includes: RecName: Full=ATP-dependent
            helicase DCL1
        Length = 1464

 Score = 498 (180.4 bits), Expect = 8.4e-64, Sum P(6) = 8.4e-64
 Identities = 159/507 (31%), Positives = 260/507 (51%)
 Links = (1)-3-5-8-4-2

Query:    12 NPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQGGKR----AFF 67
             +PR+YQVEL +KA K N I  L TGSGKT IAVLLLK    Q    +D+  ++    +FF
Sbjct:    98 DPREYQVELFEKAKKDNIIAVLDTGSGKTLIAVLLLKHIIEQEL--IDRSAEKPHRVSFF 155

Query:    68 VVEKVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLD 127
             +V+ V LV QQA  ++ + + +V +  G   + LW+  E  ++ + ++ V+V TA+ L  
Sbjct:   156 LVDSVTLVFQQAAVLQNNINQRVDKFCGAMETDLWNG-ETWERHLAKNMVIVCTAEVLYQ 214

Query:   128 LIRHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPVPRVLGLTASLIKAK 187
              + HA++K+E++ +LIFDE H+A    HPY  I+ D+ L   +   P++ G+TAS + AK
Sbjct:   215 CLLHAFVKMENINLLIFDEAHNAK-KDHPYARIVKDFYLKDGNAKRPKIFGMTASPVDAK 273

Query:   188 VAPEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNFDTV 247
             +    +++  + LE+ ++S I TAS+L  L +   +P E V              ++D +
Sbjct:   274 M---DVVKAARNLETLLNSQIATASNLSLLRQSVPRPNEEVW-------------SYDRL 317

Query:   248 IEIFDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAA-WRTAQVWEKEL 306
              + F ET  +    + F  DL     R ++     +      LG W A W    VW   L
Sbjct:   318 DQPF-ETRLYKELRSRFG-DL-----RALEKLFTFSLKASSNLGAWCADW----VWSYAL 366

Query:   307 GKIIKSQVLPDKTLRFLNMAKTSM--ITIKRLLEPE--MKKIKSI-EALRPY-VPQRVIR 360
              +    + LP    R    A+T+M  + I +++ PE  +++I+   E +R +      +R
Sbjct:   367 TE----ESLPKLEGR---AARTAMGNLPIAKIVRPEAEIQRIREASEIIRSHKFGDPAVR 419

Query:   361 LFEILETFNPEFQKERMK-LEKAEHLSAIIFVDQRYIAYSLLLMMRHIKSWEPKFKFVNP 419
               E+L         E +K  E+      I+F +QR+ A  L  +   I +     K + P
Sbjct:   420 P-ELLSPKVRRLHHELLKYFERHTDTKCIVFTEQRHTARILCDLFSRIGT-----KHLRP 473

Query:   420 DYVVGASGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFD 479
               ++G   R+ AS       ++Q   +  F + E+NCL ATSV EEG+D+  CNL+++FD
Sbjct:   474 GVLIGV--RSDASGGMNISFRQQVLAVVSFRKGEVNCLFATSVAEEGLDIPDCNLIVRFD 531

Query:   480 RPLDMRSYVQSKGRARRAGSRYVITVE 506
                 +  Y+QS+GRAR   S +   VE
Sbjct:   532 LASTLTQYIQSRGRARHMNSTFAHLVE 558

 Score = 218 (81.8 bits), Expect = 8.4e-64, Sum P(6) = 8.4e-64
 Identities = 68/241 (28%), Positives = 108/241 (44%)
 Links = 1-3-5-8-4-(2)

Query:  1503 ISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQKDQKSDVP-SPLLRFIDTPTN 1561
             ++DK+IAD  EALIG   L    N    +       ++  D  + +      R    P  
Sbjct:  1115 LADKTIADVCEALIGACCLLASKNHRFDIAVKAVTALVSSDDHNVLNWEQYSRLYSIPKY 1174

Query:  1562 PNASLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHASYINN--RVTGCYQRLEFL 1619
               A ++      +     Q+++K+GY FK    L  AFTH SY +   RV  CYQRLEFL
Sbjct:  1175 QTAVVDAA----ELDLAAQVKKKLGYDFKYPKLLRSAFTHPSYPSAWARVP-CYQRLEFL 1229

Query:  1620 GDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIAMCPGLYH 1679
             GDA+LD     +++       P  LT+ + A+V+N    S+AV+     H       L  
Sbjct:  1230 GDALLDMACVEHIYHKHPDKDPQWLTEHKMAMVSNKFLGSVAVRLGLHSHLNHFSTSLQS 1289

Query:  1680 MIEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDIEVPKAMGDIFESVAGAIYLDS 1739
              I  +V+       ++    + + +T++             PK + D+ E+  GAI++DS
Sbjct:  1290 QITNYVEEIEAAELESGDPPDAWTLTSDP------------PKCLPDMVEAYIGAIFIDS 1337

Query:  1740 G 1740
             G
Sbjct:  1338 G 1338

 Score = 75 (31.5 bits), Expect = 8.4e-64, Sum P(6) = 8.4e-64
 Identities = 20/52 (38%), Positives = 28/52 (53%)
 Links = 1-(3)-5-8-4-2

Query:   542 YCAELLLPINSPIKHAIVLKNPMPNKKTAQMAVALEACRQLHLEGELDDNLL 593
             +  E++LP  SPI+  IV K P   K  A+ + A E C  L   G LDD+ +
Sbjct:   655 FVCEVVLPEKSPIR-GIVGK-PASKKLIAKQSAAFETCLLLRKHGLLDDHFV 704

 Score = 66 (28.3 bits), Expect = 8.4e-64, Sum P(6) = 8.4e-64
 Identities = 28/84 (33%), Positives = 40/84 (47%)
 Links = 1-3-5-8-(4)-2

Query:  1308 IRQRSEEYVSHIDS--DIGLGVSPCLLLTALTT-SNAAD-------------GMSLERFE 1351
             I  R E Y+  +++  ++ L +SP L L ALT  S+  D             G + ER E
Sbjct:  1005 IISRIESYLIALEACQELDLPISPELALEALTKDSDNTDEHRAQQIHFQRGMGKNYERLE 1064

Query:  1352 TIGDSFLKFATTDYLYHTLLDQHE 1375
              +GD FLK AT+  L+    D  E
Sbjct:  1065 FLGDCFLKMATSISLFAMNPDNDE 1088

 Score = 55 (24.4 bits), Expect = 8.4e-64, Sum P(6) = 8.4e-64
 Identities = 44/218 (20%), Positives = 88/218 (40%)
 Links = 1-3-(5)-8-4-2

Query:   687 LSAKEIPKIPPFPVFLRQGNMKVRLIVAPKKT--TVTAAQLQEIQLFHNYLFTQVLQMCK 744
             L+ +++P  P FP++L + +++  +I +   +   V++  L+ +  F   +F  +     
Sbjct:   772 LTREKLPHFPEFPLYL-EDDIECDVICSSISSGFQVSSHDLEVLTTFTLRIFQDIFHKVY 830

Query:   745 TGNLEFDGTSNAPLN-TLIVPLNKRKDDMSYTINMKYVSEVVANMENMPRIPKDEVRRQY 803
               ++       APLN +  +  +  +D + + I +++V       +N P IP        
Sbjct:   831 DRDVGMMTYWLAPLNLSCDISSSASRDLLDWGI-LQFV------FDN-PEIPWSSSN--- 879

Query:   804 KFNAEDYKDAIVMPWYRNLEQPVFYYVAEILPEWRPSSKFPDT-----HFETFNEYFIKK 858
               +A  + +  V   Y   +    Y+   I P  RPS   P +     H     +Y +  
Sbjct:   880 --SAAFFANRFV---YDRWDGRYRYFTHGIDPSLRPSDPPPSSMARRRHMGNIMDYCLSL 934

Query:   859 YK------LEIYDQNQSLLDVDFTSTRLNLLQPRIQNQ 890
             +K      LE  D  Q ++  +    R NLL  R   +
Sbjct:   935 FKNARKKFLENCDWTQPVIKAEIIQLRRNLLDKRTNKE 972

 Score = 39 (18.8 bits), Expect = 4.1e-60, Sum P(4) = 4.1e-60
 Identities = 12/49 (24%), Positives = 24/49 (48%)
 Links = 1-(6)-4-2

Query:   957 VNQLLLTDELRETILVKAFGKEKTKLDDNVEWNSLAYATEYEEKQTIIV 1005
             V+ L  +D  R++  V+  G + T     V     A + +YE++ + +V
Sbjct:   596 VDALYESDRNRKSYTVQTTGAKLTYSSSLVVLAHFANSLQYEKETSTVV 644

 Score = 39 (18.8 bits), Expect = 2.0e-58, Sum P(3) = 2.0e-58
 Identities = 7/11 (63%), Positives = 10/11 (90%)
 Links = 1-(7)-2

Query:   574 VALEACRQLHL 584
             +ALEAC++L L
Sbjct:  1014 IALEACQELDL 1024

 Score = 37 (18.1 bits), Expect = 8.4e-64, Sum P(6) = 8.4e-64
 Identities = 9/20 (45%), Positives = 11/20 (55%)
 Links = 1-3-5-(8)-4-2

Query:   965 ELRETILVKAFGKEKTKLDD 984
             +LR  +L K   KEK K  D
Sbjct:   959 QLRRNLLDKRTNKEKIKEGD 978


>sp|A2RAF3.2|DCL1_ASPNC RecName: Full=Dicer-like protein 1; Includes: RecName:
            Full=Endoribonuclease dcl1; Includes: RecName: Full=ATP-dependent
            helicase dcl1
        Length = 1525

 Score = 466 (169.1 bits), Expect = 5.3e-62, Sum P(5) = 5.3e-62
 Identities = 154/501 (30%), Positives = 233/501 (46%)
 Links = (1)-4-5-3-2

Query:    12 NPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKE-YGVQLFAPLDQGGKR-AFFVV 69
             +PR+YQ+EL ++A  +NTI  L TGSGKT IAVLLLK     +L   ++    R AFF+V
Sbjct:   116 DPREYQLELFERAKVQNTIAVLDTGSGKTLIAVLLLKHTLEKELNDRMEGKPHRIAFFLV 175

Query:    70 EKVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLDLI 129
             + V L  QQA  +  +    VG   G   + LW SK   DQ  +++ V+V TA+ L   +
Sbjct:   176 DSVTLAYQQAAVLRNNLDQSVGHFFGAMGTDLW-SKSVWDQHFQKNMVIVCTAEILNQCL 234

Query:   130 RHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPVPRVLGLTASLIKAKVA 189
              ++Y+K+  + +LIFDE HH     HPY  I+ D  L +     PR+ G+TAS I  K  
Sbjct:   235 LNSYIKMSQINILIFDEAHHTK-KDHPYARIIRDSYLEEVYSKRPRIFGMTASPIDTK-- 291

Query:   190 PEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNFDTVIE 249
                ++++  +LE  +DS I T S++  L +   +P E V              +F+ + +
Sbjct:   292 -GDIVDEATRLEKLLDSRIATTSNMSLLRQVARRPVERVW-------------SFNKLEQ 337

Query:   250 IFDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEKELGKI 309
              F  T  + +    F  D+       ++   +       +LG W + R    W + L   
Sbjct:   338 PF-ATSLYKHLEDRFG-DMAC-----LEGIFRFAWQASSELGRWCSDRA---WARALA-- 385

Query:   310 IKSQVLPDKTLRFLNMAKTSMITIKRLLEPEMKKIKSIEALRPYVPQRVIRLFEILETFN 369
                 VLP         A +   T   + E   K+I  I      V        E     +
Sbjct:   386 --DDVLPKLEGSVRKTANSE--TSSNVPESAYKEILRITEASEIVKSYAFSSPETFGQLS 441

Query:   370 PEFQKERMKLEK----AEHLSAIIFVDQRYIAYSLLLMMRHIKSWEPKFKFVNPDYVVGA 425
             P+ Q  R +L +          I+F  +RY A  L  + + +        F+ P  ++G 
Sbjct:   442 PKVQVLREELARYFGRQTETKCIVFTQKRYTALILAELFQTLN-----IPFLRPGVLIGV 496

Query:   426 SGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMR 485
                +LA  +     ++Q   L +F   EINCL ATSV EEG+D+  CNLV++FD    + 
Sbjct:   497 RSGDLAGMNIT--FRQQFISLVKFRTGEINCLFATSVAEEGLDIPDCNLVVRFDLYQTLI 554

Query:   486 SYVQSKGRARRAGSRYVITVE 506
              YVQS+GRAR   S Y   VE
Sbjct:   555 QYVQSRGRARHFNSTYASMVE 575

 Score = 220 (82.5 bits), Expect = 5.3e-62, Sum P(5) = 5.3e-62
 Identities = 67/244 (27%), Positives = 112/244 (45%)
 Links = 1-4-5-3-(2)

Query:  1503 ISDKSIADAVEALIGVHLLTLGPNPTLKV-MNWMGLKVIQKDQKSDVPSPLLRFIDTPTN 1561
             +++K+IAD  EALIG  LL+ GP+    + +  +   V     K++     + F   P  
Sbjct:  1171 LAEKTIADVCEALIGAALLSGGPDHRFDMAVKAVTTLVNSPSHKAERWKDYISFYTIPKY 1230

Query:  1562 PNASLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHASYINNRV-TGCYQRLEFLG 1620
                + +      + +   ++EEK+ YRF+    L  AFTH SY +      CYQRLEFLG
Sbjct:  1231 QRRAADGA----ELYLSRKIEEKLSYRFRYPTLLGSAFTHPSYPSAWAKVPCYQRLEFLG 1286

Query:  1621 DAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIAMCPGLYHM 1680
             D+++D +    LF       P  LT+ + A+V+N    +LAVK     H       L   
Sbjct:  1287 DSLIDMVCVEDLFARFPDRDPQWLTEHKMAMVSNKFLGALAVKLGLHTHLKYFSAPLQSQ 1346

Query:  1681 IEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDIEVPKAMGDIFESVAGAIYLDSG 1740
             I ++ +       ++    + + VT +             PK + D+ E+  GA+++DS 
Sbjct:  1347 ITQYAEEIQTAEGESEGAVDYWTVTKDP------------PKCLPDMVEAYVGAVFVDSD 1394

Query:  1741 RNLD 1744
              N +
Sbjct:  1395 FNFE 1398

 Score = 81 (33.6 bits), Expect = 5.3e-62, Sum P(5) = 5.3e-62
 Identities = 24/74 (32%), Positives = 33/74 (44%)
 Links = 1-4-5-(3)-2

Query:  1344 GMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQL 1403
             G + ER E +GD FLK AT+  L+    D  E      R   + N NL+       I + 
Sbjct:  1076 GRNYERLEFLGDCFLKMATSIALFTQNPDDDEFDYHVNRMCLICNKNLFNAAVDKEIYKY 1135

Query:  1404 IVANKFDAHDSWLP 1417
             I +  F  H +W P
Sbjct:  1136 IRSRGFSRH-TWYP 1148

 Score = 71 (30.1 bits), Expect = 5.3e-62, Sum P(5) = 5.3e-62
 Identities = 32/122 (26%), Positives = 52/122 (42%)
 Links = 1-(4)-5-3-2

Query:   474 LVIKFDRPLD---MRSYVQSKGRARRAGSRYVITVEEKDTAAYCSKLPSDI-FTRLVPHN 529
             L+  FD  LD    +       R +  G++          A Y S L  +  F+  V + 
Sbjct:   606 LLYGFDHDLDTVLQKDEGNRTFRIKSTGAKLTYHSATAILARYASSLQYEKEFSAQVTY- 664

Query:   530 QIIPIEENGVTKYCAELLLPINSPIKHAIVLKNPMPNKKTAQMAVALEACRQLHLEGELD 589
              ++PI  NG   +  E++LP  SPI+   +  +P   K  A+ + A + C  L     LD
Sbjct:   665 VVLPI--NGA--FVCEVILPEKSPIRG--LTGSPAMKKSIAKRSAAFDTCLLLRKNKLLD 718

Query:   590 DN 591
             D+
Sbjct:   719 DH 720

 Score = 52 (23.4 bits), Expect = 5.3e-62, Sum P(5) = 5.3e-62
 Identities = 12/52 (23%), Positives = 27/52 (51%)
 Links = 1-4-(5)-3-2

Query:   690 KEIPKIPPFPVFLRQGNMKVRLIVAP--KKTTVTAAQLQEIQLFHNYLFTQV 739
             + +P  P FP+FL   +++  +I  P  K+  ++  ++  + +F   +F  V
Sbjct:   793 ERLPHFPEFPIFL-DDDVETTIITTPLEKQLLLSEKEVDALTVFTLRVFRDV 843


>sp|Q09884.1|DCR1_SCHPO RecName: Full=Protein Dicer; AltName: Full=Cell cycle
            control protein dcr1; AltName: Full=RNA interference pathway
            protein dcr1; Includes: RecName: Full=Endoribonuclease dcr1;
            Includes: RecName: Full=ATP-dependent helicase dcr1
        Length = 1374

 Score = 415 (151.1 bits), Expect = 7.7e-61, Sum P(4) = 7.7e-61
 Identities = 147/509 (28%), Positives = 247/509 (48%)
 Links = (1)-4-3-2

Query:    14 RDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKE-YGVQLFAPLD--QGGKRAFFVVE 70
             R YQ ++ + A+K+NT++ + TG+GKT +AV L+K+    Q+       +  K + F+V 
Sbjct:    13 RKYQQDVYNIASKQNTLLVMRTGAGKTLLAVKLIKQKLEEQILIQESNLEHKKISVFLVN 72

Query:    71 KVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLDLIR 130
             KV LV QQA +I      KVG  +G+ S  +  S++     + +++V+VITA      + 
Sbjct:    73 KVPLVFQQAEYIRSQLPAKVGMFYGELSIEM--SEQLLTNIILKYNVIVITADLFYLFLA 130

Query:   131 HAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYK------LLKKDKPVPRVLGLTASLI 184
               +L I D+ ++IFDECHHA+G+   Y  IM D+       L KK   +PR+ G+TAS  
Sbjct:   131 RGFLSINDLNLIIFDECHHAIGND-AYARIMNDFYHRAKAVLSKKHFTLPRIFGMTASPF 189

Query:   185 KAKVAPEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNF 244
               K     L  +L + E   DS     S+   L+ Y   P E  ++  +     L +P  
Sbjct:   190 TGKKG--NLYHRLYQWEQLFDSKAHVVSEN-ELADYFCLPEESYVMYSNK----LVVPPS 242

Query:   245 DTVIEIFDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEK 304
             D++I+  +ET               L   + I  ++KT  A    +G W      QVW  
Sbjct:   243 DSIIKKCEET---------------LQGCKLISRAVKTALAETIDMGLWFG---EQVW-L 283

Query:   305 ELGKIIKSQVLPDKTLRFLNMAKTSMITIKRL-LEPEMKKIKSIEALRPYVPQRVIRLFE 363
              L   ++++ L  K L    ++    + I RL +  E  K        P +P     +F+
Sbjct:   284 YLVDFVETKRLKKKALG-KQLSDDEELAIDRLKIFVEDWKNNKYSDNGPRIP-----VFD 337

Query:   364 ILETFNPEFQK-ERMKL--EKAEHLSAIIFVDQRYIAYSLLLMMRHIKSWEPKFKFVNPD 420
               +  +  F+  E +K    K++ +  +IFV+++  A++L L M+ +    P    +   
Sbjct:   338 STDVTDKVFKLLELLKATYRKSDSVRTVIFVERKATAFTLSLFMKTLNL--PN---IRAH 392

Query:   421 YVVGASGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDR 480
               +G    +    +     +RQ + L +F   + N LIAT+V EEG+DV  CNLVI+F+ 
Sbjct:   393 SFIGHGPSD--QGEFSMTFRRQKDTLHKFKTGKYNVLIATAVAEEGIDVPSCNLVIRFNI 450

Query:   481 PLDMRSYVQSKGRARRAGSRYVITVEEKD 509
                +  YVQS+GRAR   S+++I +  ++
Sbjct:   451 CRTVTQYVQSRGRARAMASKFLIFLNTEE 479

 Score = 224 (83.9 bits), Expect = 7.7e-61, Sum P(4) = 7.7e-61
 Identities = 81/254 (31%), Positives = 123/254 (48%)
 Links = 1-4-3-(2)

Query:  1501 QHISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQKDQKSDVPSPLLRFIDTPT 1560
             Q +S K IAD VEA IG  LL  G +  LK+   + + ++      +  +    + D  T
Sbjct:  1015 QKLSVKRIADMVEASIGACLLDSGLDSALKICKSLSVGLLDISNWDEWNN----YFDLNT 1070

Query:  1561 NPNASLNFLNNLWQQFQFTQ-LEEKIGYRFKERAYLVQAFTHASYINNR-VTGCYQRLEF 1618
               ++    L N+  QF ++  +EE IGY FK +  L  AF H S ++ + +   YQ+LEF
Sbjct:  1071 YADS----LRNV--QFPYSSYIEETIGYSFKNKKLLHLAFIHPSMMSQQGIYENYQQLEF 1124

Query:  1619 LGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHF----IAMC 1674
             LGDAVLDY+I +YL++     + G LTD +S  V N   + +       K+      AMC
Sbjct:  1125 LGDAVLDYIIVQYLYKKYPNATSGELTDYKSFYVCNKSLSYIGFVLNLHKYIQHESAAMC 1184

Query:  1675 PGLYH---MIEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDIEVPKAMGDIFESV 1731
               ++    +IE F +  SE       N   +      EID         PK + D  E++
Sbjct:  1185 DAIFEYQELIEAFRETASE-------NPWFWF-----EIDS--------PKFISDTLEAM 1224

Query:  1732 AGAIYLDSGRNLDT 1745
               AI+LDSG +L +
Sbjct:  1225 ICAIFLDSGFSLQS 1238

 Score = 118 (46.6 bits), Expect = 7.7e-61, Sum P(4) = 7.7e-61
 Identities = 34/136 (25%), Positives = 61/136 (44%)
 Links = 1-4-(3)-2

Query:  1282 VLPVAINEKSRSFSFEKESKAINGRLIRQRSEEYVSHIDSDIGLGVSPCLLLTALTTSNA 1341
             +LPV+ + K+ +         I   L+   +  ++ H   D  +  + C    ALT++ +
Sbjct:   871 ILPVSRHLKNSALLIPSILYHIENLLV---ASSFIEHFRLDCKIDTA-C---QALTSAES 923

Query:  1342 ADGMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIP 1401
                   +R E  GD FLK   +  ++    D  E +L F R K +SNCNLY++     +P
Sbjct:   924 QLNFDYDRLEFYGDCFLKLGASITVFLKFPDTQEYQLHFNRKKIISNCNLYKVAIDCELP 983

Query:  1402 QLIVANKFDAHDSWLP 1417
             +  ++   +    W P
Sbjct:   984 KYALSTPLEIRH-WCP 998

 Score = 73 (30.8 bits), Expect = 7.7e-61, Sum P(4) = 7.7e-61
 Identities = 32/104 (30%), Positives = 43/104 (41%)
 Links = 1-(4)-3-2

Query:   513 YCSKLPSDIFTRLVPHNQIIPIEENGVTKYCAELLLPINSPIKHAIVLKNPMPNKKTAQM 572
             +C+ L  D++TR  P     P        YC E+ LP     K      +P  + + A+ 
Sbjct:   544 FCNTLSRDVYTRYYPTFTAQPCLSGW---YCFEVELP--KACKVPAAQGSPAKSIRKAKQ 598

Query:   573 AVALEACRQLHLEGELDDNLLPKG-RESIAKL--LEHIDEEPDE 613
               A   C  L   G +D +L P   R  IA L  LE  DE  DE
Sbjct:   599 NAAFIMCLDLIRMGLIDKHLKPLDFRRKIADLETLEE-DELKDE 641

 Score = 66 (28.3 bits), Expect = 1.9e-55, Sum P(4) = 1.9e-55
 Identities = 18/51 (35%), Positives = 25/51 (49%)
 Links = 1-4-(5)-2

Query:   919 SVPHSSQ-RQILVPELMDIHPISATLWNVIAALPSIFYRVNQLLLTDELRE 968
             S+P S Q R   + +L  I P+S  L N    +PSI Y +  LL+     E
Sbjct:   854 SIPKSQQVRSFYINDLY-ILPVSRHLKNSALLIPSILYHIENLLVASSFIE 903

 Score = 57 (25.1 bits), Expect = 4.2e-52, Sum P(3) = 4.2e-52
 Identities = 21/72 (29%), Positives = 29/72 (40%)
 Links = 1-(6)-2

Query:  1324 GLGVSPCLLLTALTTSNAADG--MSLERFETIGDSFLKFATTD-YLYHTLLDQHEGKLSF 1380
             G+ V  C L+              S  R   +   FL F  T+  L H  +   E  L F
Sbjct:   436 GIDVPSCNLVIRFNICRTVTQYVQSRGRARAMASKFLIFLNTEELLIHERILHEEKNLKF 495

Query:  1381 ARSKEVSNCNLY 1392
             A S E+SN N++
Sbjct:   496 ALS-ELSNSNIF 506

 Score = 56 (24.8 bits), Expect = 4.5e-59, Sum P(4) = 4.5e-59
 Identities = 19/66 (28%), Positives = 36/66 (54%)
 Links = 1-(7)-3-2

Query:   499 SRYVITVEEKDTA--AYCSKLPSDIFTRLVPHN-QIIPIEENGVTKYCAEL-LLPINSPI 554
             S ++I  ++KD A  A C KLP  +   L  +  + IP  +   + Y  +L +LP++  +
Sbjct:   819 SEFMIPAKKKDKAPSALCKKLPLRLNYSLWGNRAKSIPKSQQVRSFYINDLYILPVSRHL 878

Query:   555 KHAIVL 560
             K++ +L
Sbjct:   879 KNSALL 884


>sp|A1CBC9.2|DCL1_ASPCL RecName: Full=Dicer-like protein 1; Includes: RecName:
            Full=Endoribonuclease dcl1; Includes: RecName: Full=ATP-dependent
            helicase dcl1
        Length = 1534

 Score = 428 (155.7 bits), Expect = 1.2e-60, Sum P(6) = 1.2e-60
 Identities = 151/514 (29%), Positives = 241/514 (46%)
 Links = (1)-4-5-7-3-2

Query:    12 NPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQGGKR---AFFV 68
             +PR+YQ+EL ++A  +NTI  L TGSGKT IAVLLL+   +Q        GK    +FF+
Sbjct:   122 DPREYQIELFERAKAQNTIAVLDTGSGKTLIAVLLLRHV-LQNELNDRANGKPHRVSFFL 180

Query:    69 VEKVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLDL 128
             V+ V L  QQA  +  +    V    G   + LWD ++  ++ ++++ V+V TA+ L   
Sbjct:   181 VDSVTLAYQQAAVLRNNIDQNVAHFFGAMGTDLWD-RQVWEEHLQQNMVIVCTAEILNQC 239

Query:   129 IRHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPV-PRVLGLTASLIKAK 187
             + ++++++  + +LIFDE HH     HPY  I+ D    K   P  PR+ G+TAS I  K
Sbjct:   240 LLNSHVRMNQINLLIFDEAHHTK-KDHPYARIIRD-SYFKASPPQRPRIFGMTASPIDTK 297

Query:   188 VAPEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNFDTV 247
                  ++    +LE+ +DS I T S +  L +  ++P E V     +    L  P F T 
Sbjct:   298 ---GDIIAAATRLETLLDSRIATTSKITLLRQVVSRPIEKV-----WAYDRLESP-FKTN 348

Query:   248 IEIFDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEKELG 307
             +    E   F N              + ++   +       +LG W + R    W   L 
Sbjct:   349 LHKLMEN-RFGNV-------------KALEGVFRFAWYASSELGRWCSDRA---WLYALA 391

Query:   308 KIIKSQVLPDKTLRFLNMAKTSMITIKRLLEPEMKKIKSIEALRPYVPQRVIRLFEILET 367
                   VLP        +A+++    +R  +   K+I  I+     V        E    
Sbjct:   392 ----DDVLPKLEGHVNKLAESTAAATER--DMAFKEITLIKEASNIVKAHTFNDPEFPGE 445

Query:   368 FNPEFQKERMKLEK----AEHLSAIIFVDQRYIAYSLLLMMRHIKSWEPKFKFVNPDYVV 423
              +P+ +  + +L K    A     IIF  +RY A +L  +   +    P  +   P  ++
Sbjct:   446 LSPKVRLLQTELSKHFSHAPETKCIIFTQKRYTAKTLHELFTILSI--PHLR---PGVLI 500

Query:   424 GASGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLD 483
             G    ++   +     ++Q   L +F + EINCL ATSV EEG+D+  CNLV++FD    
Sbjct:   501 GVRSGDIGGMNIT--FRQQFLALVKFRKGEINCLFATSVAEEGLDIPDCNLVVRFDLYHT 558

Query:   484 MRSYVQSKGRARRAGSRYVITVEEKDTAAYCSKL 517
             +  YVQS+GRAR   S Y   VE KD + + ++L
Sbjct:   559 LIQYVQSRGRARHYHSTYASMVE-KDNSDHEARL 591

 Score = 244 (91.0 bits), Expect = 1.2e-60, Sum P(6) = 1.2e-60
 Identities = 85/261 (32%), Positives = 122/261 (46%)
 Links = 1-4-5-7-3-(2)

Query:  1497 LLTQ-QH-ISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQK--DQKSDVPSPL 1552
             +L+Q +H + +K+IAD  EALIG  LL+ GP         MG+K +    D  S   S  
Sbjct:  1170 MLSQAKHALGEKTIADVCEALIGACLLSGGPEHRFD----MGVKAVSVFVDSPSHAVSRW 1225

Query:  1553 LRFIDTPTNPNASLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHASYINN---RV 1609
               +I     PN  +             Q+EEK+GY F+    L  A TH S  +    RV
Sbjct:  1226 KEYIGLYKPPNYQVRKAEGAETNLAL-QVEEKLGYHFRYPRLLCSAVTHPSTPSTWYFRV 1284

Query:  1610 TGCYQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKH 1669
               CYQRLEFLGD++LD +    LF       P  LT+ + A+V+N    +LAVK  F KH
Sbjct:  1285 P-CYQRLEFLGDSLLDMVCVEDLFHRFPDRDPQWLTEHKMAMVSNKFLGALAVKLGFHKH 1343

Query:  1670 FIAMCPGLYHMIEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDIEVPKAMGDIFE 1729
               A    L   I  +V+       ++   A  Y V  ++            PK + D+ E
Sbjct:  1344 IKAFSNPLQAQITYYVEEIETAEAESE-GAVDYWVVAKDP-----------PKCLPDMVE 1391

Query:  1730 SVAGAIYLDSGRNLDTTWQVI 1750
             +  GAI++DS    D +++VI
Sbjct:  1392 AYLGAIFVDS----DFSFEVI 1408

 Score = 93 (37.8 bits), Expect = 1.2e-60, Sum P(6) = 1.2e-60
 Identities = 26/74 (35%), Positives = 34/74 (45%)
 Links = 1-4-5-7-(3)-2

Query:  1344 GMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQL 1403
             G + ER E +GD FLK AT+  L+    D  E      R   + N NL+   KK  I + 
Sbjct:  1083 GKNYERLEFLGDCFLKMATSIALFTQNPDDDEFDYHVNRMCLICNKNLFNTAKKRQIYRY 1142

Query:  1404 IVANKFDAHDSWLP 1417
             I +  F  H  W P
Sbjct:  1143 IRSRSFSRH-VWYP 1155

 Score = 66 (28.3 bits), Expect = 1.2e-60, Sum P(6) = 1.2e-60
 Identities = 31/113 (27%), Positives = 48/113 (42%)
 Links = 1-(4)-5-7-3-2

Query:   483 DMRSYVQ-SKGR----ARRAGSRYVITVEEKDTAAYCSKLPSDIFTRLVPHNQIIPIEEN 537
             D+ S +Q  +GR     +  G+R          A Y S L  +  T   P    + ++  
Sbjct:   620 DLDSLLQHEEGRRTFTVKSTGARLTYHSAIAILARYASSLQYEKET--TPQATYV-VQSV 676

Query:   538 GVTKYCAELLLPINSPIKHAIVLKNPMPNKKTAQMAVALEACRQLHLEGELDD 590
             G T  C E++LP  SPI+   +  +P   K  A+ + A + C  L     LDD
Sbjct:   677 GNTYVC-EVILPEKSPIRG--LTGSPAIRKSIAKQSAAFDTCLLLRRHKLLDD 726

 Score = 50 (22.7 bits), Expect = 1.2e-60, Sum P(6) = 1.2e-60
 Identities = 12/55 (21%), Positives = 31/55 (56%)
 Links = 1-4-(5)-7-3-2

Query:   687 LSAKEIPKIPPFPVFLRQGNMKVRLIVAPKKT--TVTAAQLQEIQLFHNYLFTQV 739
             L+ +++P  P FP++L + +++ +++     T   ++A +L+ +  F   +F  V
Sbjct:   797 LTREKLPDFPAFPIYLDE-DIETKVVPRSLDTGMELSAEELRALTTFTLRIFRDV 850

 Score = 45 (20.9 bits), Expect = 4.1e-54, Sum P(3) = 4.1e-54
 Identities = 39/168 (23%), Positives = 66/168 (39%)
 Links = 1-(6)-2

Query:  1232 QENQEDENTPTNFPKTIDEEIEELSIGARKKQEID-----DNAAKTDVLERENCEVL--- 1283
             +E +E E T  NF +T+ E+   +  G     ++D     +   +T  ++     +    
Sbjct:   592 REVREAEKTMQNFCETLPED--RILHG--NDHDLDSLLQHEEGRRTFTVKSTGARLTYHS 647

Query:  1284 PVAINEK-SRSFSFEKESKAINGRLIRQRSEEYVSHI----DSDI-GLGVSPCLLLTALT 1337
              +AI  + + S  +EKE+      +++     YV  +     S I GL  SP +  +   
Sbjct:   648 AIAILARYASSLQYEKETTPQATYVVQSVGNTYVCEVILPEKSPIRGLTGSPAIRKSIAK 707

Query:  1338 TSNAADGMSLERFETIGDSFLKFATTDYLYHTLLD-QHEGKLSFARSK 1384
              S A D   L R   + D F K      +YH  L      KL+    K
Sbjct:   708 QSAAFDTCLLLRRHKLLDDFFKS-----IYHKRLPAMRNAKLAITSKK 750

 Score = 44 (20.5 bits), Expect = 1.2e-60, Sum P(6) = 1.2e-60
 Identities = 17/61 (27%), Positives = 30/61 (49%)
 Links = 1-4-5-(7)-3-2

Query:   932 ELMDIHPISATLWNVIAALPSIFYRVNQLLLT----DELRETILVKAFGKEK-TKLDDNV 986
             E + I  I  ++ +   A P+I  R++  L++    DEL + ++   +  E  TK  DN 
Sbjct:  1010 EPLKISAIPPSIASTCLAFPAIITRLDSYLISIEACDEL-DLVIRSDYALEAVTKDSDNT 1068

Query:   987 E 987
             E
Sbjct:  1069 E 1069

 Score = 39 (18.8 bits), Expect = 6.9e-58, Sum P(4) = 6.9e-58
 Identities = 19/76 (25%), Positives = 31/76 (40%)
 Links = 1-(8)-3-2

Query:   933 LMDIHPISATLWNVIAALPS--IFYR----VNQLLLTDELRETILVKAFGKEKTKLDDNV 986
             L ++     T+ N    LP   I +     ++ LL  +E R T  VK+ G   T      
Sbjct:   591 LREVREAEKTMQNFCETLPEDRILHGNDHDLDSLLQHEEGRRTFTVKSTGARLTYHSAIA 650

Query:   987 EWNSLAYATEYEEKQT 1002
                  A + +YE++ T
Sbjct:   651 ILARYASSLQYEKETT 666


>sp|A1DE13.1|DCL1_NEOFI RecName: Full=Dicer-like protein 1; Includes: RecName:
            Full=Endoribonuclease dcl1; Includes: RecName: Full=ATP-dependent
            helicase dcl1
        Length = 1538

 Score = 457 (165.9 bits), Expect = 1.6e-60, Sum P(6) = 1.6e-60
 Identities = 157/517 (30%), Positives = 237/517 (45%)
 Links = (1)-4-6-5-3-2

Query:    12 NPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQ--GGKR---AF 66
             +PR+YQ+EL ++A  +NTI  L TGSGKT IAVLLL+     +   LD    GK    +F
Sbjct:   126 DPREYQIELFERAKTQNTIAVLDTGSGKTLIAVLLLRH---TILNELDNRANGKPHRVSF 182

Query:    67 FVVEKVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLL 126
             F+V+ V L  QQA  +  +    V    G   + LWD K   D+ ++R+ V+V TA+ L 
Sbjct:   183 FLVDSVTLAYQQAAVLRNNIDQNVAHFFGAMGTDLWD-KRTWDEHLQRNMVIVCTAEILN 241

Query:   127 DLIRHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPVPRVLGLTASLIKA 186
               + ++Y+K++ + +LIFDE HHA    HPY  I+ D     +    PRV G+TAS I  
Sbjct:   242 QCLLNSYVKMDQINLLIFDEAHHAK-KDHPYARIIRDSYFKAQPSQRPRVFGMTASPIDT 300

Query:   187 KVAPEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNFDT 246
             K     + E   +LE+ +DS I T S +  L +  ++P E V     +    L  P    
Sbjct:   301 K---GDITEAATRLETLLDSRIATTSKITLLREVVSRPIEKV-----WAYNRLESPFATE 352

Query:   247 VIEIFDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEKEL 306
             + ++ D     +                 ++   +       +LG W + R    W   L
Sbjct:   353 LYKLMDTRYGNIKV---------------LEGVYRFAWHASSELGKWCSDRA---WWHAL 394

Query:   307 GKIIKSQVLPDKTLRFLNMAKTSMITIKRLLEPEMKKIKSIEALRPYVPQRVIRLFEILE 366
                    VLP        + +++ +  +       K I  I      V        E+  
Sbjct:   395 A----DDVLPKLEGNISKLVESNTLNAEH--GAVFKDIIRIREASETVKNYSFADPELPG 448

Query:   367 TFNPEFQKERMKLEKAEHLS------AIIFVDQRYIAYSLLLMMRHIKSWEPKFKFVNPD 420
               +P+ Q  RM+L K  H S       I+F  +RY A  L  +   +    P  +   P 
Sbjct:   449 ELSPKVQLLRMELSK--HFSDTTGTKCIVFTQKRYTAKILNELFTVLNI--PHLR---PG 501

Query:   421 YVVGASGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDR 480
              ++G    ++   +     ++Q   L +F   EINCL ATSV EEG+D+  CNLV++FD 
Sbjct:   502 VLIGVRPGDIGGMNVT--FRQQFLALVKFRTGEINCLFATSVAEEGLDIPDCNLVVRFDL 559

Query:   481 PLDMRSYVQSKGRARRAGSRYVITVEEKDTAAYCSKL 517
                +  YVQS+GRAR   S Y I VE KD A +  +L
Sbjct:   560 YRTLIQYVQSRGRARHCTSTYAIMVE-KDNAEHEGRL 595

 Score = 210 (79.0 bits), Expect = 1.6e-60, Sum P(6) = 1.6e-60
 Identities = 74/248 (29%), Positives = 111/248 (44%)
 Links = 1-4-6-5-3-(2)

Query:  1497 LLTQ-QH-ISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQKDQKSDVPSPLLR 1554
             LL++ +H + +K+IAD  EALIG  LL+ GP     +       ++  D  S   S    
Sbjct:  1174 LLSEGKHALGEKTIADVCEALIGASLLSGGPENRFDMATKAVTALV--DSPSHRVSCWKE 1231

Query:  1555 FIDTPTNPNASLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHASYINN---RVTG 1611
             +I   T P                  +EE++GY F     L  A TH S  +    RV  
Sbjct:  1232 YITLYTMPKYQTEKPRGSEDDLA-RHVEEELGYHFTYPRLLASAITHPSLPSTWGYRVP- 1289

Query:  1612 CYQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFI 1671
             CYQRLEFLGD++LD +    LF       P  LT+ + A+V+N    +L+VK  F +  +
Sbjct:  1290 CYQRLEFLGDSLLDMVCVEDLFRRFPDRDPQWLTEHKMAMVSNKFLGALSVKLGFHRRIM 1349

Query:  1672 AMCPGLYHMIEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDIEVPKAMGDIFESV 1731
             A    L   I  +V+       ++   A  Y V  ++            PK + D+ E+ 
Sbjct:  1350 AFSNPLQAQITHYVEEIESAQAESR-GAVDYWVVAKDP-----------PKCLPDMVEAY 1397

Query:  1732 AGAIYLDS 1739
              GAI++DS
Sbjct:  1398 LGAIFVDS 1405

 Score = 87 (35.7 bits), Expect = 1.6e-60, Sum P(6) = 1.6e-60
 Identities = 26/74 (35%), Positives = 33/74 (44%)
 Links = 1-4-6-5-(3)-2

Query:  1344 GMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQL 1403
             G + ER E +GD FLK AT+  LY    D  E      R   + N NL+    K  I + 
Sbjct:  1087 GKNYERLEFLGDCFLKMATSIALYTQNPDDDEFDYHVNRMCLICNKNLFNTAIKKQIYRY 1146

Query:  1404 IVANKFDAHDSWLP 1417
             I +  F  H  W P
Sbjct:  1147 IRSRGFSRH-IWYP 1159

 Score = 65 (27.9 bits), Expect = 1.6e-60, Sum P(6) = 1.6e-60
 Identities = 24/80 (30%), Positives = 36/80 (45%)
 Links = 1-(4)-6-5-3-2

Query:   511 AAYCSKLPSDIFTRLVPHNQIIPIEENGVTKYCAELLLPINSPIKHAIVLKNPMPNKKTA 570
             A Y S L  +  T  VP  Q+  +  +    Y  E++LP  SPI+   +  +P   K  A
Sbjct:   657 ARYASSLQYEKET--VP--QVTYVVGHVSNAYVCEVILPEKSPIRG--LTGSPAIRKAVA 710

Query:   571 QMAVALEACRQLHLEGELDD 590
             + + A + C  L     LDD
Sbjct:   711 KQSAAFDTCLLLRKHRLLDD 730

 Score = 52 (23.4 bits), Expect = 1.6e-60, Sum P(6) = 1.6e-60
 Identities = 35/136 (25%), Positives = 48/136 (35%)
 Links = 1-4-6-(5)-3-2

Query:  1108 GAWSGSESIVPSGWGDWDGPE--PDNSPMPFQILGGPGGLNVQALMADV--GRVFDPSTA 1163
             G  SG+    P  W DWD      +N  +PF     P  L V   + D   GR F   T 
Sbjct:   878 GPGSGTN---PRDWTDWDTVSFVHNNDEIPFTRDLNPDSL-VNRFIFDNWDGR-FRYFTV 932

Query:  1164 SSSLSQTVQESTVSPPKQLTKEEEQFKKLQNDLLKQAKERLEALEMSEDMEKPRRLEDTV 1223
             +  ++ T+Q S   PP            + N  L  +K          D  +P    + V
Sbjct:   933 A--VADTLQPSDPPPPS--VPRRRHMNNIMNYTLSLSKNSRARFFSGCDWNQPVLQAELV 988

Query:  1224 NLE-DYGDDQENQEDE 1238
              L  +  D    QE E
Sbjct:   989 RLRRNLLDKMTTQEKE 1004

 Score = 51 (23.0 bits), Expect = 1.6e-60, Sum P(6) = 1.6e-60
 Identities = 11/55 (20%), Positives = 31/55 (56%)
 Links = 1-4-(6)-5-3-2

Query:   687 LSAKEIPKIPPFPVFLRQGNMKVRLIVAPKK--TTVTAAQLQEIQLFHNYLFTQV 739
             L+ +++P+ P F ++L + +++ +++  P K    ++  +LQ +  F   +F  +
Sbjct:   801 LTREKLPEFPAFSIYLDE-DVETKVLSYPLKHGLQISVDELQSLTTFTLRIFRDI 854

 Score = 46 (21.3 bits), Expect = 5.2e-60, Sum P(6) = 5.2e-60
 Identities = 16/48 (33%), Positives = 24/48 (50%)
 Links = 1-4-(7)-5-3-2

Query:   824 QPVFYYVAEILPEWRPSSKFPDTHFETFNEYFIKKYKLEI-YDQNQSL 870
             +P+     E LPE+   S + D   ET    +  K+ L+I  D+ QSL
Sbjct:   796 RPILLLTREKLPEFPAFSIYLDEDVETKVLSYPLKHGLQISVDELQSL 843

 Score = 39 (18.8 bits), Expect = 7.3e-57, Sum P(4) = 7.3e-57
 Identities = 17/46 (36%), Positives = 22/46 (47%)
 Links = 1-(8)-3-2

Query:   543 CAELLLPIN-SPIKHAIV---LKNPMPNKKTAQMAVALEACRQLHL 584
             CAE   P+  S I  +IV   L  P    +     +ALEAC +L L
Sbjct:  1012 CAE---PLRISAIPTSIVSTCLAFPAIISRLDSYLIALEACDELEL 1054


>sp|Q2VF19.1|DCL1_CRYPA RecName: Full=Dicer-like protein 1; Includes: RecName:
            Full=Endoribonuclease DCL-1; Includes: RecName: Full=ATP-dependent
            helicase DCL-1
        Length = 1548

 Score = 465 (168.7 bits), Expect = 4.2e-60, Sum P(4) = 4.2e-60
 Identities = 146/501 (29%), Positives = 246/501 (49%)
 Links = (1)-4-3-2

Query:    12 NPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQGGKR--AFFVV 69
             +PRDYQ+EL ++A ++NTI  L TGSGKT IA LLL     Q      +G  R  AFF+V
Sbjct:    98 SPRDYQMELFERAKQQNTIAVLDTGSGKTLIAALLLDHTVNQELEDRAKGLPRRIAFFLV 157

Query:    70 EKVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLDLI 129
             EKV L  QQ   +E + +  V    G++    W +K   +  +  H V+V TA+ L   +
Sbjct:   158 EKVALAFQQHAVLECNLAHSVAVFSGESIKNTW-TKGFWETQLADHEVIVCTAEILNQCL 216

Query:   130 RHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPV--PRVLGLTASLIKAK 187
             ++AY++I+ + +L+FDE HH     HPY  I+ DY    KD+ +  PR+ G+TAS + A 
Sbjct:   217 QYAYIRIDQINLLVFDEAHHTK-KNHPYARIIKDYYASGKDRGLRLPRIFGMTASPVDAL 275

Query:   188 VAPEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNFDTV 247
             +    + +   +LE  + S I T +D  +L +   +P + +I              ++ +
Sbjct:   276 I---DVRQAAIELEGLLHSRIATTADPDALRRAVGRPKKEIIY------------KYNPL 320

Query:   248 IEIFDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEKELG 307
             ++     + F     +  P L +   +    +   + A  R+LG W   R  Q++ ++  
Sbjct:   321 VKPIQTMLTF-----KLRP-L-IANNKQFSKAFAFSEAAARELGTWFVDRMWQLFLED-E 372

Query:   308 KIIKSQVLPDKTLRFLNMAKTSMITIKR-LLEPEMKKIKSIEALRPYVPQRVIRLFEILE 366
             +++K +   +++L   +MA   ++   R  +    + I+S E  +P  P  +    + L 
Sbjct:   373 ELLKLEAKTERSLS-KDMAAPEVVEKHRNAVRSARELIRSHEFPKPE-PGLLSSKLKTLS 430

Query:   367 TFNPEFQKERMKLEKAEHLSAIIFVDQRYIAYSLLLMMRHIKSWEPKFKFVNPDYVVGA- 425
                 E+  +         +  I+FV++R+ A    L+    +S   +     P   VG+ 
Sbjct:   431 KLLEEYFTD-------SSIRCIVFVERRWTAK---LLTDFFESHAAEI----PGLKVGSL 476

Query:   426 SGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPLDMR 485
              G N     SQ   + Q   +  F +   NC+ ATSV EEG+D+  CNL+I+FD    M 
Sbjct:   477 MGANAEGGSSQTSFREQIRTILSFKKGNTNCIFATSVAEEGLDIPDCNLIIRFDICKTMI 536

Query:   486 SYVQSKGRARRAGSRYVITVE 506
              Y+QS+GRAR+A S Y+  +E
Sbjct:   537 QYIQSRGRARQADSTYIHLIE 557

 Score = 204 (76.9 bits), Expect = 4.2e-60, Sum P(4) = 4.2e-60
 Identities = 72/260 (27%), Positives = 111/260 (42%)
 Links = 1-4-3-(2)

Query:  1498 LTQQHISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQKDQKSDVPSPLLRFID 1557
             + +  ++DKSIAD  EALIG   +T   +    +      +++   Q      P+ ++ D
Sbjct:  1171 MDEHRLADKSIADVCEALIGAAYMTTRKHDDYDLAVRAVTRLVNHKQH-----PMTKWDD 1225

Query:  1558 ---TPTNPNASLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHAS--YINNRVTGC 1612
                    P        N  +     ++ E  GY+FK    L  AF H S  Y+ ++V   
Sbjct:  1226 YHAAYVMPGWQ-TMPANAAELDMAQKIHEATGYQFKHPRVLRSAFRHPSRPYVFDKVPH- 1283

Query:  1613 YQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIA 1672
             YQRLEFLGDA+ D     YLF  +    P  LT+ + A+V+N     LAV   F K  + 
Sbjct:  1284 YQRLEFLGDALFDMACVDYLFHIAPDEGPQWLTEHKMAMVSNQFLGCLAVSLGFHKFILH 1343

Query:  1673 MCPGLYHMIEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDIEVPKAMGDIFESVA 1732
                 +   I ++V   +E        AE           +   E  + PK + D+ E+  
Sbjct:  1344 HHASIGSQIHEYVTEITEARRAAEDAAEAAGKPRSAYSRDYWVEAPQPPKCIPDVLEAYV 1403

Query:  1733 GAIYLDSGRNLDTTWQVIFH 1752
             GAI++DS  +     Q  FH
Sbjct:  1404 GAIFVDSKYDYSVVQQ-FFH 1422

 Score = 90 (36.7 bits), Expect = 4.2e-60, Sum P(4) = 4.2e-60
 Identities = 24/76 (31%), Positives = 39/76 (51%)
 Links = 1-4-(3)-2

Query:  1344 GMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKK--LGIP 1401
             G + ER E +GDSFLK ATT  ++  + ++ E      R   + N NL+ + K   L + 
Sbjct:  1080 GANYERLELLGDSFLKMATTIAVFTLIPNKDEFDYHCERMVMICNQNLFGVAKSDDLKLH 1139

Query:  1402 QLIVANKFDAHDSWLP 1417
             + I +  F+   +W P
Sbjct:  1140 EYIRSKSFE-RGTWYP 1154

 Score = 65 (27.9 bits), Expect = 4.2e-60, Sum P(4) = 4.2e-60
 Identities = 28/102 (27%), Positives = 48/102 (47%)
 Links = 1-(4)-3-2

Query:   529 NQIIPIEENGVTKYCAELLLPIN-SPIKHAIV-LKNPMPN--KKTAQMAVALEACR--QL 582
             N +  I E     +C  +L P+  SP+   +V +   +P+   +  Q  +AL+ACR  QL
Sbjct:   981 NFLADINETSKNPFCYFVLEPMRISPLPVDVVAMAYLLPSIIHRIEQNLIALDACRLLQL 1040

Query:   583 HLEGELDDNLLPKGRESIAKLLEHIDE----EPDEYAPGIAA 620
              +  +L    L K  ++  +  E +D     EP  + PG+ A
Sbjct:  1041 DIHPDLALEALTKDSDNQGED-ERMDSIQAFEPVNFQPGMGA 1081

 Score = 64 (27.6 bits), Expect = 7.1e-60, Sum P(5) = 7.1e-60
 Identities = 18/54 (33%), Positives = 28/54 (51%)
 Links = 1-(5)-6-3-2

Query:   542 YCAELLLPINSPIKHAIVLKNPMPNKKTAQMAVALEACRQLHLEGELDDNLLPK 595
             +  E+++P  SP+  AI        K+ A+ + A E C QL  +  LDD+L  K
Sbjct:   660 FICEVMMPPLSPVTSAI--GKVYSTKQVAKCSAAFELCFQLIQKKFLDDHLRSK 711

 Score = 47 (21.6 bits), Expect = 7.1e-60, Sum P(5) = 7.1e-60
 Identities = 14/39 (35%), Positives = 20/39 (51%)
 Links = 1-5-(6)-3-2

Query:   930 VPELMDIHPISATLWNVIAALPSIFYRVNQ-LLLTDELR 967
             V E M I P+   +  +   LPSI +R+ Q L+  D  R
Sbjct:   998 VLEPMRISPLPVDVVAMAYLLPSIIHRIEQNLIALDACR 1036


>sp|Q0UI93.2|DCL1_PHANO RecName: Full=Dicer-like protein 1; Includes: RecName:
            Full=Endoribonuclease DCL1; Includes: RecName: Full=ATP-dependent
            helicase DCL1
        Length = 1522

 Score = 490 (177.5 bits), Expect = 3.8e-59, Sum P(5) = 3.8e-59
 Identities = 162/507 (31%), Positives = 253/507 (49%)
 Links = (1)-4-5-3-2

Query:    12 NPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQG--GKRAFFVV 69
             NPRDYQ+EL  +A  +NTI  L TG+GKT IA LLL+    +      +G   K AFF+V
Sbjct:    68 NPRDYQMELFLRAKMQNTIAVLDTGTGKTHIATLLLRHVLEEELENRAKGCAHKMAFFLV 127

Query:    70 EKVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLDLI 129
             + VNLV QQA  +       V  + G     L+  K+  D+    + V+V TAQ L+D +
Sbjct:   128 DSVNLVFQQANVLRCGLDQGVEGISGAMGQSLFQ-KQTWDKLFAVNMVIVCTAQVLVDCM 186

Query:   130 RHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPV-PRVLGLTASLIKAK- 187
              H+++ I  M +LIFDE HHA  S HPY  +M DY   + D    PR+  +TAS +  K 
Sbjct:   187 MHSFMSISRMNLLIFDEAHHAK-SNHPYARVMKDYYAHELDTSKRPRIFAMTASPVDVKG 245

Query:   188 VAPEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNFDTV 247
              + E + E  ++LE+ + S I T SD         +P E V +             +  +
Sbjct:   246 QSAEHVREAARELETLLHSRIATTSDSALARNSITRPEEEVAV-------------YTRL 292

Query:   248 IEIFDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAA---WRTAQVWEK 304
                F ET        ++    D+ P R +     T +    +LG WA+   W  A   E+
Sbjct:   293 RNEF-ETPLHQKVKAKYG---DVAPFRKL---FITAKLHASELGRWASDMYWSFAFADEQ 345

Query:   305 ELGKIIKSQVLPDKTLRFLNMAKTSMITIKRLLEPEMKKIKSIEALRPYVPQRVI--RLF 362
                  I+ ++  +++ R  + A+     + RL E     ++  E   P + ++ +  ++ 
Sbjct:   346 SRKLQIREELKYNRSKRDWSAAELDA-QMARLKEATAF-VQQYEIGAPTLSEQDLSSKVM 403

Query:   363 EILETFNPEFQKERMKLEKAEHLSAIIFVDQRYIAYSLLLMMRHIKSWEPKFKFVNPDYV 422
             ++    N  +  ER  L +      I+FV++R+ A  L L+  HI    P    ++ D +
Sbjct:   404 KLQYWLNLYY--ERTTLARC-----IVFVEKRHTAQLLKLIFDHIGG--PN---LHCDVL 451

Query:   423 VGASGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPL 482
             VG + R  A  ++  L + Q   L++F R E+NCL ATSV EEG+D+ QCNLV++FD   
Sbjct:   452 VGINNR--AGEENVSL-RSQILTLQKFRRGELNCLFATSVAEEGLDIPQCNLVVRFDLYR 508

Query:   483 DMRSYVQSKGRARRAGSRYVITVEEKD 509
              M  YVQS+GRAR   S+Y+  +E ++
Sbjct:   509 TMIGYVQSRGRARHRNSKYLHMLEAEN 535

 Score = 183 (69.5 bits), Expect = 3.8e-59, Sum P(5) = 3.8e-59
 Identities = 86/348 (24%), Positives = 140/348 (40%)
 Links = 1-4-5-3-(2)

Query:  1502 HISDKSIADAVEALIGVHLLTLGPNPTLKVMNW-MGLKVIQKDQKSD--VPSPLLRFIDT 1558
             ++ DKS+AD  EA IG   +           +W   +K ++    SD  +      +   
Sbjct:  1144 NLGDKSVADVCEAFIGAAFMQHHKGGQWTPNDWDEAVKAVKLFANSDDHLMEKWTDYYAA 1203

Query:  1559 PTNPNASLNFLNNLWQQFQFT-QLEEKIGYRFKERAYLVQAFTHAS--YINNRVTGCYQR 1615
              T P            Q     ++E K  YRF+    L  AF H S  ++   +   YQR
Sbjct:  1204 YTKPKYQT--AGATATQLDLAHKIEMKHPYRFRYPRLLRSAFIHPSQPFMWENIPS-YQR 1260

Query:  1616 LEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIAMCP 1675
             LEFLGD++LD     +LF       P  LT+ ++ +V+N    ++ VK  +  H      
Sbjct:  1261 LEFLGDSLLDMAFIMHLFYKYPDKDPQWLTEHKTPMVSNKFLGAVCVKLGWHTHMKQNTA 1320

Query:  1676 GLYHMIEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDIEVPKAMGDIFESVAGAI 1735
              L   I  +V    E   + N  A  Y V+  E            PK + D+ E+   AI
Sbjct:  1321 ILSSQIRDYVYEVEEAEREAN-GAVDYWVSVSEP-----------PKCLADVIEAFVAAI 1368

Query:  1736 YLDSGRNLDTTWQVI-FH-------MMRGTIELCCANPPRSPIRELME--FEQSKVRFSK 1785
             ++DS  + +   +    H       M     E   +N P + +  L+   F  S+ R   
Sbjct:  1369 FVDSEFDFNVVQKFFDLHLKPFFLDMTLDAYENFASNHPTTRLSRLLSINFGCSEWRMGA 1428

Query:  1786 ME-RILESGK---VRVTVEVVNNMRFTGMGRNYRIAKATAAKRALKYL 1829
             +E   L  GK   +   V + + + F  +G++ R A+  A+  AL+ L
Sbjct:  1429 LETETLIPGKGKAIAAMVMIHDKVHFHSLGQSGRYARVRASHAALEKL 1476

 Score = 83 (34.3 bits), Expect = 3.8e-59, Sum P(5) = 3.8e-59
 Identities = 39/128 (30%), Positives = 59/128 (46%)
 Links = 1-4-5-(3)-2

Query:  1308 IRQRSEEYVSHIDS-DI-GLGVSPCLLLTALTTS------------NAADGM--SLERFE 1351
             I  R E Y+  +D+ D+  L VSP L L ALT              N   GM  + ER E
Sbjct:   995 IIHRFESYLIALDACDVLDLKVSPALALEALTKDSDNSEEHGEEKINFKSGMGPNYERLE 1054

Query:  1352 TIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYR--LGKKLGIPQLIVANKF 1409
              +GD FLK AT+  ++    +++E +    R   + N NL    +GKK  + + +  + F
Sbjct:  1055 FLGDCFLKVATSLSVFVQQPEENEFEFHVRRMLMLCNQNLMETAVGKKK-LYKYVRTDAF 1113

Query:  1410 DAHDSWLP 1417
                + W P
Sbjct:  1114 SRRN-WYP 1120

 Score = 59 (25.8 bits), Expect = 3.8e-59, Sum P(5) = 3.8e-59
 Identities = 25/115 (21%), Positives = 56/115 (48%)
 Links = 1-(4)-5-3-2

Query:   535 EENGVTKYCAELLLPINSPIKHAIVLKNPMPNKKT-AQMAVALEACRQLHLEGELDDNLL 593
             + NG   +  E++LP + PI   I +   + ++KT A+ + A + C +L  +  L++ LL
Sbjct:   638 QRNG---FVCEVILPEHCPI---ISMVGQVYSRKTIAKCSAAFKMCIELRRKDHLNEFLL 691

Query:   594 PKGRESIAKLLEHIDEEPDEYAPGIAAKVGSSKRKQLYDKKIARALNESFVEADK 648
             P   + +  +   +    ++     A  +  +  KQ  D  +  +L+ + ++AD+
Sbjct:   692 PTISKYLPAMRNALLAVSEKKKGNYAMVIKPTFWKQDRDT-VPESLHLTIIDADR 745

 Score = 46 (21.3 bits), Expect = 3.8e-59, Sum P(5) = 3.8e-59
 Identities = 40/219 (18%), Positives = 97/219 (44%)
 Links = 1-4-(5)-3-2

Query:   687 LSAKEIPKIPPFPVFL---RQGNMKVRLIVAPKKTTVTAAQLQEIQLFHNYLFTQVLQMC 743
             L+ +  P++P FP++L   R  N+  + +  P   ++T   L+    F   +F  +    
Sbjct:   757 LTRRPFPQLPSFPIYLTDCRPSNIVSQSLHIP--ISLTPELLEMFTRFTLRIFEDIYNKV 814

Query:   744 KTGNLEFDGTSNAPLNTLIVPLNKRKDDMSYTINMKYVSEVVANMENMPRIPKDEVRRQY 803
                  ++D +    ++  ++P+ + +  ++   +M    EV+ +M+ + ++  +     +
Sbjct:   815 ----YDYDVSK---MSYWMLPVIEHR--VASVRSMSNPQEVL-DMDQIRKVYNEPF---W 861

Query:   804 KFNAEDYKDAIVMPWYRN-LEQPVFYYVAEILPEWRPSSKFPDTHFETFNEYFIKKYKLE 862
             K++ +   D ++  ++ + +     YY   + P  +P    P  +    N  F+K   L+
Sbjct:   862 KWSPQSRTDDLIDRYFVDPMNGGRRYYSDRLAPHLKPQDPVP-ANVPRQNHKFMKNI-LD 919

Query:   863 IYDQNQSLLDVDFTSTRLNLLQPRIQNQ--PRRSRTVSN 899
               D ++ +   D T  R +  QP +Q +  P R   ++N
Sbjct:   920 FSD-SKWMKSRDIT--RWHQDQPVLQVEKIPFRRNHLAN 955

 Score = 42 (19.8 bits), Expect = 9.7e-59, Sum P(5) = 9.7e-59
 Identities = 14/53 (26%), Positives = 28/53 (52%)
 Links = 1-4-(6)-3-2

Query:   979 KTKLD-DNVEWNSLAYATEYEEKQTII-VKKIQQLRDLNQKSIEDQERETREN 1029
             K  LD  + +W      T + + Q ++ V+KI   R+ +  ++ED+E++   N
Sbjct:   915 KNILDFSDSKWMKSRDITRWHQDQPVLQVEKIPFRRN-HLANVEDKEKKELAN 966


>sp|Q4WVE3.3|DCL1_ASPFU RecName: Full=Dicer-like protein 1; Includes: RecName:
            Full=Endoribonuclease dcl1; Includes: RecName: Full=ATP-dependent
            helicase dcl1
        Length = 1537

 Score = 466 (169.1 bits), Expect = 4.8e-59, Sum P(6) = 4.8e-59
 Identities = 160/515 (31%), Positives = 241/515 (46%)
 Links = (1)-4-5-7-3-2

Query:    12 NPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQ--GGKR---AF 66
             +PR+YQ+EL ++A  +NTI  L TGSGKT IAVLLL+     +   LD    GK    +F
Sbjct:   125 DPREYQIELFERAKTQNTIAVLDTGSGKTLIAVLLLRH---TILNELDDRANGKTHRVSF 181

Query:    67 FVVEKVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLL 126
             F+V+ V L  QQA  +  +    V    G   + LWD K   D+ ++R+ V+V TA+ L 
Sbjct:   182 FLVDSVTLAYQQAAVLRNNIDQNVAHFFGAMGTDLWD-KRTWDKHLQRNMVIVCTAEILN 240

Query:   127 DLIRHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPVPRVLGLTASLIKA 186
               + ++Y++++ + +LIFDE HHA    HPY  I+ D     +    PRV G+TAS I  
Sbjct:   241 QCLLNSYVRMDQINLLIFDEAHHAK-KDHPYARIIRDSYFKAQPSQRPRVFGMTASPIDT 299

Query:   187 KVAPEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNFDT 246
             K     + E   +LE+ +DS I T S +  L +  ++P E V      E      P F T
Sbjct:   300 K---GDITEAATRLETFLDSRIATTSKITLLREVVSRPIEKVWAYNRLE------PPFAT 350

Query:   247 VIEIFDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEKEL 306
                   E    ++T    + ++ +     ++   +       +LG W + R    W   L
Sbjct:   351 ------ELYKLMDTR---YGNIKV-----LEGVYRFAWNASSELGKWCSDRA---WWHAL 393

Query:   307 GKIIKSQVLPDKTLRFLNMAKTSMITIKRLLEPEMKKIKSIEALRPYVPQRVIRLFEILE 366
                    VLP        + +++  T+K       K I  I      V        E+  
Sbjct:   394 A----DDVLPKLEGNINKLIESN--TMKAEHGAVFKDIIRIREASETVKNYFFTDPELPG 447

Query:   367 TFNPEFQKERMKLEK----AEHLSAIIFVDQRYIAYSLLLMMRHIKSWEPKFKFVNPDYV 422
               +P+ Q+ RM+L K          I+F  +RY A  L  +   +    P  +   P  +
Sbjct:   448 ELSPKVQRLRMELSKHFNDTTGTKCIVFTQKRYTAKILNELFTVLNI--PNLR---PGVL 502

Query:   423 VGASGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPL 482
             +G    ++   +     ++Q   L +F   EINCL ATSV EEG+D+  CNLVI+FD   
Sbjct:   503 IGVRPGDIGGMNIT--FRQQFLALVKFRTGEINCLFATSVAEEGLDIPDCNLVIRFDLYR 560

Query:   483 DMRSYVQSKGRARRAGSRYVITVEEKDTAAYCSKL 517
              +  YVQS+GRAR   S Y I VE KD A +  +L
Sbjct:   561 TLIQYVQSRGRARHCTSTYAIMVE-KDNAEHEGRL 594

 Score = 205 (77.2 bits), Expect = 4.8e-59, Sum P(6) = 4.8e-59
 Identities = 75/250 (30%), Positives = 111/250 (44%)
 Links = 1-4-5-7-3-(2)

Query:  1497 LLTQ-QH-ISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQK--DQKSDVPSPL 1552
             LL++ +H + +K+IAD  EALIG  LL+ GP         M  K +    D  S   S  
Sbjct:  1173 LLSEGKHALGEKTIADVCEALIGASLLSGGPEHRFD----MATKAVSALVDSPSHRVSCW 1228

Query:  1553 LRFIDTPTNPNASLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHASYINN---RV 1609
               +I   T P                  +EE++GY F     L  A TH S  +    RV
Sbjct:  1229 KEYITLYTLPKYQTEKHRGSEDDLA-RHVEEELGYHFTYPRLLASAITHPSLPSTWGYRV 1287

Query:  1610 TGCYQRLEFLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKH 1669
               CYQRLEFLGD++LD +    LF       P  L++ + A+V+N    +L+VK  F + 
Sbjct:  1288 P-CYQRLEFLGDSLLDMVCVEDLFRRFPDRDPQWLSEHKMAMVSNKFLGALSVKLGFHRR 1346

Query:  1670 FIAMCPGLYHMIEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDIEVPKAMGDIFE 1729
              +A    L   I  +V+       ++   A  Y V  ++            PK + D+ E
Sbjct:  1347 IMAFSNPLQAQITHYVEEIETAQAESQ-GAVDYWVVAKDP-----------PKCLPDMVE 1394

Query:  1730 SVAGAIYLDS 1739
             +  GAI++DS
Sbjct:  1395 AYLGAIFVDS 1404

 Score = 79 (32.9 bits), Expect = 4.8e-59, Sum P(6) = 4.8e-59
 Identities = 24/74 (32%), Positives = 33/74 (44%)
 Links = 1-4-5-7-(3)-2

Query:  1344 GMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQL 1403
             G + ER E +GD FLK AT+  L+    +  E      R   + N NL+    K  I + 
Sbjct:  1086 GKNYERLEFLGDCFLKMATSIALFSQNPNDDEFDYHVNRMCLICNKNLFNTAIKKQIYRY 1145

Query:  1404 IVANKFDAHDSWLP 1417
             I +  F  H  W P
Sbjct:  1146 IRSRGFSRH-IWYP 1158

 Score = 65 (27.9 bits), Expect = 4.8e-59, Sum P(6) = 4.8e-59
 Identities = 30/113 (26%), Positives = 48/113 (42%)
 Links = 1-(4)-5-7-3-2

Query:   483 DMRSYVQSK-GR----ARRAGSRYVITVEEKDTAAYCSKLPSDIFTRLVPH-NQIIPIEE 536
             D+ S++Q + GR     +  G++          A Y S L  +  T  VP    ++ I  
Sbjct:   623 DLDSFLQEEEGRRTFTVKSTGAKLTYHSAIAILARYASSLQYEKET--VPQVTYVVTIAS 680

Query:   537 NGVTKYCAELLLPINSPIKHAIVLKNPMPNKKTAQMAVALEACRQLHLEGELD 589
             N    Y  E++LP  SPI+   +  +P   K  A+ + A + C  L     LD
Sbjct:   681 NA---YVCEVILPEKSPIRG--LTGSPAMRKAVAKRSAAFDTCLLLRKNRLLD 728

 Score = 52 (23.4 bits), Expect = 4.8e-59, Sum P(6) = 4.8e-59
 Identities = 11/55 (20%), Positives = 32/55 (58%)
 Links = 1-4-(5)-7-3-2

Query:   687 LSAKEIPKIPPFPVFLRQGNMKVRLIVAPKK--TTVTAAQLQEIQLFHNYLFTQV 739
             L+ +++P+ P F ++L + +++ +++  P K    ++  +LQ + +F   +F  +
Sbjct:   800 LTREKLPEFPAFSIYLDE-DVETKVLSYPLKHGLQISVDKLQSLTVFTLRIFRDI 853

 Score = 45 (20.9 bits), Expect = 2.5e-58, Sum P(6) = 2.5e-58
 Identities = 16/48 (33%), Positives = 24/48 (50%)
 Links = 1-4-(6)-7-3-2

Query:   824 QPVFYYVAEILPEWRPSSKFPDTHFETFNEYFIKKYKLEI-YDQNQSL 870
             +P+     E LPE+   S + D   ET    +  K+ L+I  D+ QSL
Sbjct:   795 RPILLLTREKLPEFPAFSIYLDEDVETKVLSYPLKHGLQISVDKLQSL 842

 Score = 40 (19.1 bits), Expect = 4.8e-59, Sum P(6) = 4.8e-59
 Identities = 10/32 (31%), Positives = 16/32 (50%)
 Links = 1-4-5-(7)-3-2

Query:   865 DQNQSLLDVDFTSTRLNLLQPRIQNQPRRSRT 896
             D NQ +L  +    R NLL  ++  Q +  +T
Sbjct:   976 DWNQPVLQAELVRLRRNLLD-KMTTQEKEMQT 1006

 Score = 39 (18.8 bits), Expect = 1.7e-56, Sum P(4) = 1.7e-56
 Identities = 14/43 (32%), Positives = 19/43 (44%)
 Links = 1-(8)-3-2

Query:   543 CAE-LLLPINSPIKHAIVLKNPMPNKKTAQMAVALEACRQLHL 584
             CAE L +    P   +  L  P    +     +ALEAC +L L
Sbjct:  1011 CAEPLRISALPPSIVSTCLAFPAIISRLDSYLIALEACDELEL 1053


>sp|Q2U6C4.2|DCL1_ASPOR RecName: Full=Dicer-like protein 1; Includes: RecName:
            Full=Endoribonuclease dcl1; Includes: RecName: Full=ATP-dependent
            helicase dcl1
        Length = 1523

 Score = 474 (171.9 bits), Expect = 8.5e-58, Sum P(4) = 8.5e-58
 Identities = 196/684 (28%), Positives = 307/684 (44%)
 Links = (1)-4-3-2

Query:    12 NPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQG-GKR---AFF 67
             +PR+YQVEL ++A  +NTI  L TGSGKT IAVLLLK   +Q    +D+  GK    +FF
Sbjct:   115 DPREYQVELFERAKSQNTIAVLDTGSGKTLIAVLLLKHI-IQNEL-IDRANGKPPRISFF 172

Query:    68 VVEKVNLVEQQAIHIEVHTSFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLD 127
             +V+ V L  QQA  +  +    V Q  G   + LW SK+  D   + + V+V TA+ L  
Sbjct:   173 LVDSVTLAFQQAAVLRNNLDQNVAQFFGAMGTDLW-SKQTWDHQFENNMVIVCTAEILNQ 231

Query:   128 LIRHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDYKLLKKDKPV-PRVLGLTASLIKA 186
              + ++Y++++ + +LIFDE HH     HPY  I+ +   LK D    PR+ G+TAS I  
Sbjct:   232 CLLNSYIRMDQINLLIFDEAHHTK-KDHPYARIIRE-SYLKADPTKRPRIFGMTASPIDT 289

Query:   187 KVAPEKLMEQLKKLESAMDSVIETASDLVSLSKYGAKPYEVVIICKDFEIGCLGIPNFDT 246
             K     ++E   KLE  +DS I T S    L +   +P E     + +E   L  P F T
Sbjct:   290 K---GDIIESATKLEVLLDSKIATTSKPNLLREVVRRPIE-----ESWEYDKLD-PPFAT 340

Query:   247 VIEIFDETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFRQLGPWAAWRTAQVWEKEL 306
               +++    A       F    D+   +P+    + T     +LGP  A R    W   L
Sbjct:   341 --KLYQILQA------RFG---DISSLQPV---FRFTLQASSELGPCCADRA---WAYAL 383

Query:   307 GKIIKSQVLPDKTLRFLNMAKTSMITIKRLLEPEMKKIKSIEALRPYVPQRVIRLFEILE 366
                    VLP   L   N+ K +      + +  +K+I  I+     V         +  
Sbjct:   384 A----DDVLPK--LEG-NVRKLAQSISSPIPQCALKEISRIQEASDIVKNHSFNSPNVPG 436

Query:   367 TFNPEFQKERMKLEKA-EH---LSAIIFVDQRYIAYSLLLMMRHIKSWEPKFKFVNPDYV 422
               +P+ Q  R KL K  EH      I+F  +RY A  L  +   ++       ++ P  +
Sbjct:   437 ELSPKVQLLRQKLIKYFEHPTKTKCIVFTQKRYTAKMLFDLFSTLE-----IPYLRPGVL 491

Query:   423 VGASGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLEEGVDVKQCNLVIKFDRPL 482
             +G    ++   +     ++Q   L +F   EINCL ATSV EEG+D+  CNLV++FD   
Sbjct:   492 IGVRSGDIVGMNVS--FRQQFLALVKFRSGEINCLFATSVAEEGLDIPDCNLVVRFDLYN 549

Query:   483 DMRSYVQSKGRARRAGSRYVITVEE--KDTAAY------CSKLPSDIFTRLVPHNQIIPI 534
              +  YVQS+GRAR + S Y   +E    D AA         KL    F   +P ++I+  
Sbjct:   550 TLIQYVQSRGRARHSSSTYASMIERYNADHAARLVEVREAEKLMQS-FCETLPEDRIL-- 606

Query:   535 EENGVTKYCAELLLPINSPIKHAIVLKNPMPNKKTAQMAVALEA--CRQLHLEGELDDN- 591
               +G+      +L       K   +++     K T   A+A+ A     L  E E     
Sbjct:   607 --HGIDSEIDSILQ--GEEEKRTFIIR-ATGAKLTYHSALAILARYASSLQYEKETSAQA 661

Query:   592 ---LLPKGRESIAKLLEHIDEEPDEYAPGI-AAKVGSSKRKQLYDKKIARALNESFVEAD 647
                +LP+    + +++   ++ P     G+ A+K  ++K+   +D  +   L +  +  D
Sbjct:   662 TYVVLPQNNSFVCEVILP-EKSPVRGLTGVPASKKSAAKQSAAFDTCVL--LRKHKLLDD 718

Query:   648 KECFIYAFELERFREAELTLNPKR 671
                 +Y   L   R A L +   R
Sbjct:   719 HFNSVYHRRLPAMRNARLAITSSR 742

 Score = 204 (76.9 bits), Expect = 8.5e-58, Sum P(4) = 8.5e-58
 Identities = 95/348 (27%), Positives = 153/348 (43%)
 Links = 1-4-3-(2)

Query:  1503 ISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQKDQKSDVPS-PLLRFIDTPTN 1561
             + +K++AD  EALIG  LL+ G +        M +K +      D P+   L + D  ++
Sbjct:  1169 LREKTVADVCEALIGASLLSGGLHNQFD----MAVKAVTA--VVDSPNHKALCWADYTSS 1222

Query:  1562 ---PNASLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHASYINNRV-TGCYQRLE 1617
                P       +  ++     ++EEK+GYRFK    L  AFTH SY +      CYQRLE
Sbjct:  1223 YMLPKYQTQSPDG-YELDLGRKVEEKLGYRFKYPRLLHSAFTHPSYPSTWAKVPCYQRLE 1281

Query:  1618 FLGDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQKHFIAMCPGL 1677
             FLGD++LD +    LF       P  LT+ + A+V+N    +LAVK     H       L
Sbjct:  1282 FLGDSLLDMVCVDDLFYRYPDKDPQWLTEHKMAMVSNKFLGALAVKLGLHTHLRHFSNPL 1341

Query:  1678 YHMIEKFVKLCSERNFDTNFNAEMYMVTTEEEIDEGQEEDIEVPKAMGDIFESVAGAIYL 1737
                I  + +       ++    + ++VT +             PK + D+ E+  GA ++
Sbjct:  1342 QSQITHYAEEIQAAENESQGAVDYWLVTKDP------------PKCLPDMVEAYLGAAFV 1389

Query:  1738 DSG---RNLDTTWQ----VIFHMMRGTIELCCANP-PRSPIRELMEFEQSKVRFS-KMER 1788
             DS    R ++  +Q      FH M  TI    AN  P + ++  +  E     +  K   
Sbjct:  1390 DSDFQFRVVEDFFQRHVKSYFHDM--TIYDTFANKHPTTFLQNRLTNEYGCTNYCLKAGE 1447

Query:  1789 I--LESGKVRVTVEVVNN--MRFTGMGRNYRIAKATAAKRALKYLHQI 1832
             I  ++ G V V   V+ +  +   G   + R AK  A+++AL  L  +
Sbjct:  1448 IPVVDGGTVSVLAAVIVHEVVIAEGTASSGRYAKVKASEKALSVLENM 1495

 Score = 84 (34.6 bits), Expect = 8.5e-58, Sum P(4) = 8.5e-58
 Identities = 24/74 (32%), Positives = 33/74 (44%)
 Links = 1-4-(3)-2

Query:  1344 GMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARSKEVSNCNLYRLGKKLGIPQL 1403
             G + ER E +GD FLK AT+  L+    D  E      R   + N NL+    K  + Q 
Sbjct:  1074 GKNYERLEFLGDCFLKMATSISLFVQNPDDDEFDFHVNRMCLICNKNLFNTALKKELYQY 1133

Query:  1404 IVANKFDAHDSWLP 1417
               +  F  H +W P
Sbjct:  1134 TRSRGFSRH-TWYP 1146

 Score = 39 (18.8 bits), Expect = 8.5e-58, Sum P(4) = 8.5e-58
 Identities = 10/50 (20%), Positives = 22/50 (44%)
 Links = 1-(4)-3-2

Query:   687 LSAKEIPKIPPFPVFLRQGNMKVRLIVAPKKTTVTAAQLQEIQLFHNYLF 736
             L+ + +P  P F +FL   +++  ++V            QE++    + F
Sbjct:   789 LTRERLPDFPSFTIFL-DDDIET-IVVTESVEEALHISSQELEYLSTFTF 836


>sp|Q2UNX5.1|DCL2_ASPOR RecName: Full=Dicer-like protein 2; Includes: RecName:
            Full=Endoribonuclease dcl2; Includes: RecName: Full=ATP-dependent
            helicase dcl2
        Length = 1377

 Score = 396 (144.5 bits), Expect = 1.0e-53, Sum P(5) = 1.0e-53
 Identities = 144/525 (27%), Positives = 243/525 (46%)
 Links = (1)-5-3-2-4

Query:    11 FNPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQGGKR--AFFV 68
             + PR YQ E+ + + K+N IV + TG+GKT IA+L +          L+ GG R   +F+
Sbjct:    14 YKPRQYQYEMFEASLKENIIVAMDTGTGKTQIALLRIAHQ-------LEGGGPRKLTWFL 66

Query:    69 VEKVNLVEQQAIHIEVHT-SFKVGQVHGQTSSGLWDSKEQCDQFMKRHHVVVITAQCLLD 127
                V L  QQ   I  H  + +   + G      W S+   D+ +K   VVV T   L +
Sbjct:    67 TPTVALCLQQYEVIRSHLPAVRACTITGLDKVERWKSQYIWDELLKDKQVVVSTHAVLFE 126

Query:   128 LIRHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDY--KLLKKD--KPVPRVLGLTAS- 182
              + H +++I  + +LIFDE HH +  +HP   IM+D+    L+K     VP +LGLTAS 
Sbjct:   127 ALTHGFVRISQLGLLIFDEAHHCM-RRHPANMIMLDFYHPTLRKHGRDSVPCILGLTASP 185

Query:   183 LIKAKVAPEKLMEQLKKLESAMDSVIETAS-DLVSLSKYGAKPYEVVIICKDFEIGCLG- 240
             ++++K       +++K LES +DS+ +T       L+ Y  +P  + IICK  + G  G 
Sbjct:   186 VVRSK------SQEMKTLESNLDSICKTPQVHKQELTTYAHRPELLPIICKAIDEGPGGR 239

Query:   241 ----------IPNFDTVIEIFDETVAFVNTTTEFHPDLDLDP--RRPIKDSLKTTRAVFR 288
                         + D   +   +  + +N + E+   +         IK  +  +R +F 
Sbjct:   240 ALQALEHAWDTADIDGDPDAIPQNGSLLNGSGEYKALMVRKTLCNEQIKRFVDRSRHIFA 299

Query:   289 QLGPWAAWRTAQVWEKELGKIIKSQVLPDKTLRFLNMAKTSMITIKRLLEPEMKKIKSIE 348
             +LG WAA        ++L   I+ Q L   T+ + +  +  +      L     +    +
Sbjct:   300 ELGEWAADYYICTSVEQLRTTIRDQSL---TMDWEDEERAYLSNFLSKLPVAEVQANLAD 356

Query:   349 ALRPYVPQRVIRLFEILETFN-PEFQKERMKLEKAEHLSAIIFVDQRYIAYSLLLMMRHI 407
                  +  ++  L   L+ F+ PEF             S +IFV QR +  S+L  +  +
Sbjct:   357 PNNFTMSPKLAALINFLDKFDDPEF-------------SGLIFVKQR-VTVSVLARLLSL 402

Query:   408 KSWEPKFKFVNPDYV---VGASGRNLASSDSQGLHKRQTEVLRRFHRNEINCLIATSVLE 464
                + + +F    YV   VG+  +++         K+Q   +  F     N ++ TSVLE
Sbjct:   403 HP-QTRDRFRCAAYVGMSVGSCRQDMVGDWHNA--KKQRGTMDDFRSGRKNLIVTTSVLE 459

Query:   465 EGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSRYVITVEEKD 509
             EG+DV  C +V+ FD+P +++S++Q +GRAR+  S Y I     D
Sbjct:   460 EGIDVTACRVVVCFDKPANLKSFIQRRGRARQQKSTYAIMFSTAD 504

 Score = 196 (74.1 bits), Expect = 1.0e-53, Sum P(5) = 1.0e-53
 Identities = 52/169 (30%), Positives = 88/169 (52%)
 Links = 1-5-3-(2)-4

Query:  1500 QQHISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQKDQKSDVPSPLLRFIDTP 1559
             ++ +S K +AD +EALIG   L  G +   ++     L  + + Q  D+PS +     T 
Sbjct:  1028 KRQMSAKVLADVIEALIGAAYLD-GGHSKAQICTHCFLPEVNR-QPLDIPSLI-----TQ 1080

Query:  1560 TNPNASLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHASYINNRVTGCYQRLEFL 1619
             T    +   + +         L+  +GY FK    L++A TH S  +++ T  YQRLEFL
Sbjct:  1081 TEHGRTARHIID-------GDLQRHLGYTFKNEDLLIEALTHPSCQHDQTTQSYQRLEFL 1133

Query:  1620 GDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKFEFQK 1668
             GDA+LD +I   +F+ S + SPG +T ++ A+VN  +     ++F  ++
Sbjct:  1134 GDAILDMVIVPIIFQYSNKISPGDMTLIKHAVVNANLLGFFCMEFSIEQ 1182

 Score = 99 (39.9 bits), Expect = 1.0e-53, Sum P(5) = 1.0e-53
 Identities = 36/155 (23%), Positives = 64/155 (41%)
 Links = 1-5-(3)-2-4

Query:  1264 EIDDNAAKTDVLERENCEVLPVAINEKSRSFSFEKESKAINGRLIRQRSEEYVSHIDSDI 1323
             E +  +AK  ++  E+C V  + ++              +   LI  R     + I  D+
Sbjct:   867 ESEHGSAKVHMVAAESCTVDKLPVSTAIFGLFIPHIVDRLESTLIANR---LCATILCDV 923

Query:  1324 GLGVSPCLLLTALTTSNAADGMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSFARS 1383
             G      ++ TA+   +A    + +R+E +GDS LK+  +  L+   L+  EG L+  R+
Sbjct:   924 GFADIQHVI-TAIMAPSAQGVTNYQRYEFLGDSILKYIVSCQLFFQNLNWPEGFLTEGRT 982

Query:  1384 KEVSNCNLYRLGKKLGIPQLIVANKFDAHDSWLPP 1418
               V N  L R     G+   I+         W+ P
Sbjct:   983 TIVQNPRLTRAALDAGLDSFIITKALTPR-RWIAP 1016

 Score = 65 (27.9 bits), Expect = 1.0e-53, Sum P(5) = 1.0e-53
 Identities = 14/22 (63%), Positives = 16/22 (72%)
 Links = 1-5-3-2-(4)

Query:  1722 KAMGDIFESVAGAIYLDSGRNL 1743
             K   DI ESV GAIY+DSG +L
Sbjct:  1257 KFFSDIVESVLGAIYVDSGGDL 1278

 Score = 54 (24.1 bits), Expect = 1.0e-53, Sum P(5) = 1.0e-53
 Identities = 29/111 (26%), Positives = 52/111 (46%)
 Links = 1-(5)-3-2-4

Query:   502 VITVEEKDTAAY--CSKLPSDIFTRLVPHNQIIPIEEN--GVTKYCAELLLP--INSPIK 555
             VIT +   T  Y  C+ LP +   R V +      E++  G+ K    ++LP  ++  ++
Sbjct:   555 VITPDSVVTHLYHFCAVLPEE---RYVDNRPEFSFEKDRQGLIK--GTVILPSCVHPKVR 609

Query:   556 HAIVLKNPMPNKKTAQMAVALEACRQLHLEGELDDNLLPKGRESIAKLLEH 606
               I  K    +++ A    A +A R L+  G L+D+LLP  +    +  +H
Sbjct:   610 R-IQGKLWWKSERAAVKETAFQAYRALYEFGLLNDHLLPLTKNPEMRPTDH 659

 Score = 41 (19.5 bits), Expect = 2.2e-52, Sum P(5) = 2.2e-52
 Identities = 10/30 (33%), Positives = 14/30 (46%)
 Links = 1-(6)-3-2-4

Query:   828 YYVAEILPEWRPSSKFPDTHFETFNEYFIK 857
             Y+   +LPE R     P+  FE   +  IK
Sbjct:   566 YHFCAVLPEERYVDNRPEFSFEKDRQGLIK 595


>sp|Q4WA22.2|DCL2_ASPFU RecName: Full=Dicer-like protein 2; Includes: RecName:
            Full=Endoribonuclease dcl2; Includes: RecName: Full=ATP-dependent
            helicase dcl2
        Length = 1388

 Score = 369 (135.0 bits), Expect = 1.7e-51, Sum P(5) = 1.7e-51
 Identities = 156/536 (29%), Positives = 255/536 (47%)
 Links = (1)-5-3-2-4

Query:     7 DLQCFNPRDYQVELLDKATKKNTIVQLGTGSGKTFIAVLLLKEYGVQLFAPLDQGGKRAF 66
             D   + PR+YQ+E+L+ + K+N IV + TGSGKT IAVL +K   + + +P     K  +
Sbjct:    10 DASPYQPRNYQLEMLEASMKENIIVAMDTGSGKTHIAVLRIKAE-LDICSP----DKVVW 64

Query:    67 FVVEKVNLVEQQAIHIEVHTSFKVGQVHGQTSSGL-----WDSKEQCDQFMKRHHVVVIT 121
             F+   V L  QQ  H EV  S  +  V  +T +GL     W  +   D  +  + V+V T
Sbjct:    65 FLAPTVALCIQQ--H-EVIAS-NLPAVRTRTLTGLDKVELWTDQSIWDAVLNGYRVIVST 120

Query:   122 AQCLLDLIRHAYLKIEDMCVLIFDECHHALGSQHPYRSIMVDY--KLLKKDKP--VPRVL 177
                L D + H ++K+  + +LIFDE HH    +H    IM D+    L K  P  VPR++
Sbjct:   121 HAVLADALSHGFVKMSQLALLIFDEAHHCT-RRHAANKIMQDFYHPTLTKSGPAAVPRIM 179

Query:   178 GLTASLIKAKVAPEKLMEQLKKLESAMDSVIETAS-DLVSLSKYGAKPY--EVVIICKD- 233
             GLTAS +      E LM     +ES +D+V  T       L K+  +P+  ++     D 
Sbjct:   180 GLTASPVVRSNHQELLM-----VESNLDAVCRTPRLHRQELLKFTHRPHLQQIWYTPTDP 234

Query:   234 --FEIGCLGIPNFDTVIEIFD-ETVAFVNTTTEFHPDLDLDPRRPIKDSLKTTRAVFR-Q 289
               F    L +       E  D     ++    +  P   LD R  +K +L T +   R Q
Sbjct:   235 AGFRSASLTLGALYHAWENLDIGDDPYIQRLRK-SP---LDDRA-LKKALLTGKTYCREQ 289

Query:   290 LGPWAAWRTAQVWEKELGKIIKSQVLPDKTLRFLNMAKTSMITIKRLLEPEMKKIKSIEA 349
             L  +   R+  ++E ELG+      +     +  +  + S ++       E +K   ++ 
Sbjct:   290 LRRFVD-RSRHIFE-ELGEWAAEYYIYASIKQLRDRVRDSYMSGDW---DEAEKAYLVDF 344

Query:   350 LRPYVPQRVIRLFEILET----FNPEFQKERMKLEKAEH--LSAIIFVDQRYIAYSLLLM 403
             L   +P   I  F + +      +P+F+     L+ ++    S +IFV QR +  S +  
Sbjct:   345 LSK-IPTSDIH-FALNDPDGFRISPKFESLLNFLDSSDQREFSGLIFVKQR-VTVSAMTS 401

Query:   404 MRHIKSWEPKFKFVNPDYVVGASGRNLASSDSQG--LHKR-QTEVLRRFHRNEINCLIAT 460
             +  +  +  + +F    YV G S  + AS D  G  L+ + Q + L  F     N +IAT
Sbjct:   402 LLSVHPYTRE-RFRCAAYV-GWSNSS-ASKDILGDLLNMQLQRDTLDDFRSGRKNLIIAT 458

Query:   461 SVLEEGVDVKQCNLVIKFDRPLDMRSYVQSKGRARRAGSRYVITVEEKDTAAYCSK 516
              VLEEG+D+  C++V+ +D+P +++S++Q +GRARR  S + I     DT+A  S+
Sbjct:   459 DVLEEGIDLSACSVVVCYDKPPNLKSFIQRRGRARRKQSTFAIMFPTDDTSADVSR 514

 Score = 178 (67.7 bits), Expect = 1.7e-51, Sum P(5) = 1.7e-51
 Identities = 54/165 (32%), Positives = 86/165 (52%)
 Links = 1-5-3-(2)-4

Query:  1500 QQHISDKSIADAVEALIGVHLLTLGPNPTLKVMNWMGLKVIQKDQKSDVPSPLLRFIDTP 1559
             ++ +S K +AD VEALIG   +  G + T +         I++     +P   L  +DT 
Sbjct:  1035 KRQMSTKVLADVVEALIGAAYVD-GGHSTAQAC-------IRRF----LPEINLHAVDTR 1082

Query:  1560 TNPNASLNFLNNLWQQFQFTQLEEKIGYRFKERAYLVQAFTHASYINNRVTGCYQRLEFL 1619
             T   A+ +      +     +L++ IGY F++ + LV+A TH S   +  T  YQRLE+L
Sbjct:  1083 T---AARSVAPESARHMMNDRLKDHIGYTFEDESLLVEALTHPSCDYDSTTQSYQRLEYL 1139

Query:  1620 GDAVLDYMITRYLFEDSRQYSPGVLTDLRSALVNNTIFASLAVKF 1664
             GDAVLD +I   +F    Q   G +T ++ A+VN  + A L ++F
Sbjct:  1140 GDAVLDMVIVSAIFNHRIQRPQGDMTKIKHAVVNANLLAFLCMEF 1184

 Score = 116 (45.9 bits), Expect = 1.7e-51, Sum P(5) = 1.7e-51
 Identities = 45/158 (28%), Positives = 69/158 (43%)
 Links = 1-5-(3)-2-4

Query:  1263 QEIDDNAAKTDVLERENCEV--LPVAINEKSRSFSFEKESKAINGRLIRQRSEEYVSHID 1320
             + I D+AAK  ++  E C +  LP  +       S   E   I   LI  R  + +    
Sbjct:   873 EAIPDSAAKNPIVAAEACTIDRLPFTMAIFGLFISAIVEQLEIE--LIATRLRDTILR-- 928

Query:  1321 SDIGLGVSPCLLLTALTTSNAADGMSLERFETIGDSFLKFATTDYLYHTLLDQHEGKLSF 1380
              D+    S   ++TA++T  A    + +R+E +GDS LKF+ +  L+    + HEG LS 
Sbjct:   929 -DVSFK-STDHIITAISTPLAHRLTNYQRYEFLGDSILKFSVSCQLFFQHPNWHEGYLSE 986

Query:  1381 ARSKEVSNCNLYRLGKKLGIPQLIVANKFDAHDSWLPP 1418
              R   V N  L +     G+   IV  +  A   W  P
Sbjct:   987 GRDMIVQNPRLAKAALDTGLDAYIVTKRL-ASRKWSAP 1023

 Score = 74 (31.1 bits), Expect = 1.7e-51, Sum P(5) = 1.7e-51
 Identities = 35/126 (27%), Positives = 61/126 (48%)
 Links = 1-5-3-2-(4)

Query:  1718 IEVPKAMGDIFESVAGAIYLDSGRNLDT----TWQV-IFHMMRGTIELCC-ANPPRSPIR 1771
             +   K   DI ESV GAI++DSG NL        Q+ +   +R  ++       PRS ++
Sbjct:  1259 LNADKFFSDIIESVLGAIFVDSGGNLAPCEVFVEQIGLMAYLRRILDHGIDVRHPRSVVQ 1318

Query:  1772 ELMEFEQSKVRFSKMERI-LESG--KVRVTVEVVNNMRFTGMG-RNYRIAKATAAKRALK 1827
             +L +   + ++F  ++R+  E G    + +V++     F   G      A+ TAA  A+K
Sbjct:  1319 QLAK---TNIQFV-LQRVPTEEGGASYQCSVQMEQAELFVVTGCLTAEEAEVTAAVEAIK 1374

Query:  1828 YLHQIE 1833
             +L + E
Sbjct:  1375 FLTRDE 1380

 Score = 53 (23.7 bits), Expect = 1.7e-51, Sum P(5) = 1.7e-51
 Identities = 30/145 (20%), Positives = 61/145 (42%)
 Links = 1-(5)-3-2-4

Query:   513 YCSKLPSDIFTRLVPHNQIIPIEENGVTKYCAELLLP--INSPIKHAIVLKNPMPNKKTA 570
             +C+ LP   +  + P        E+G+ K    ++LP  ++  ++     +     ++ A
Sbjct:   571 FCAVLPPQPYVDMRPVFSF-ETNEDGLLK--GTVILPSCVHPKVRRTEG-RRWWRTERAA 626

Query:   571 QMAVALEACRQLHLEGELDDNLLPKGRESIAKL-----LEHIDEEPDEYAPGIAAKVGSS 625
                 A +A + L+  G ++D+LLP  ++   K      +  I E  ++Y P I      S
Sbjct:   627 MKETAFQAYKSLYEFGLVNDHLLPLTKKPELKTHDLGSMPSILETSEQYDPWIEWAYSWS 686

Query:   626 KRKQLYDKKIARALNESFVEADKEC 650
                 ++  +I   +NE     D+ C
Sbjct:   687 S-PDIHQSRIVVKMNEG--RGDELC 708


Parameters:
  links
  postsw
  -i cele_dcr1.fa
  -i cele_dcr1.fa
  wordmask=seg+xnu
  -d /data/databases/BLAST/swissprot
  -o celedcr1-vs-swissprot.BLASTP
  E=1e-50

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.134   0.390    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0     1845      1845   9.0e-51  566 3  11 22  0.41    34
                                                     40  0.45    37


Statistics:

  Database:  /data/databases/BLAST/swissprot
   Title:  swissprot
   Posted:  9:42:51 AM PST Dec 14, 2008
   Created:  9:42:51 AM PST Dec 14, 2008
   Format:  XDF-1
   # of letters in database:  132,868,552
   # of sequences in database:  353,658
   # of database sequences satisfying E:  19
  No. of states in DFA:  634 (134 KB)
  Total size of DFA:  1250 KB (2395 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  4
  Search cpu time:  109.05u 0.35s 109.40t   Elapsed:  00:00:27
  Total cpu time:  109.26u 0.35s 109.61t   Elapsed:  00:00:27
  Start:  Sun Dec 14 09:52:50 2008   End:  Sun Dec 14 09:53:17 2008
BioPerl-1.007002/t/data/dmel_2Lchunk.gb000444000766000024      6757213155576321 17552 0ustar00cjfieldsstaff000000000000LOCUS       2L:14000-19000          5001 bp    dna     linear   UNK 
DEFINITION  THIS IS TEST DATA FOR THE UNFLATTENER - ERRONEOUS CDS RECORDS
ACCESSION   unknown
KEYWORDS    .
SOURCE      fruit fly
  ORGANISM  Drosophila melanogaster
            Eukaryota; Metazoa; Arthropoda; Insecta; Pterygota; Neoptera;
            Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
            Drosophilidae; Drosophila.
FEATURES             Location/Qualifiers
     source          1..5001
                     /location="14000..19000"
                     /chromosome="2L"
                     /type="tile"
                     /organism="Drosophila melanogaster"
                     /mol_type="genomic dna"
                     /md5checksum="d53c791f329d9bb3953522c37087626e"
     gene            complement(-4163..7373)
                     /gene="l(2)gl"
                     /comment="person=bmatthew; date=Tue May 14 09:00:55 PDT
                     2002; text=Only one EST supports this alternative
                     transcript"
                     /dbxref="GO:0007391"
                     /dbxref="GO:0005918"
                     /dbxref="GO:0016082"
                     /dbxref="GO:0005938"
                     /dbxref="GO:0005578"
                     /dbxref="GO:0017022"
                     /dbxref="GO:0016327"
                     /dbxref="GO:0045200"
                     /dbxref="GO:0007559"
                     /dbxref="GO:0008021"
                     /dbxref="GO:0030154"
                     /dbxref="GO:0007179"
                     /dbxref="GO:0005856"
                     /dbxref="GO:0002009"
                     /dbxref="GO:0045184"
                     /dbxref="GO:0005737"
                     /dbxref="GO:0007269"
                     /dbxref="GO:0008360"
                     /dbxref="FlyBase:FBgn0002121"
                     /dbxref="GO:0019991"
                     /dbxref="GO:0016336"
                     /dbxref="GO:0016335"
                     /dbxref="GO:0016334"
                     /dbxref="GO:0016333"
                     /dbxref="flybase:FBan0002671"
                     /dbxref="GO:0016332"
                     /dbxref="GO:0005829"
                     /dbxref="GO:0008283"
                     /dbxref="GO:0045159"
                     /dbxref="GO:0007399"
                     /dbxref="GO:0005614"
                     /dbxref="GO:0005886"
                     /dbxref="GO:0045197"
                     /dbxref="GO:0045175"
                     /dbxref="GO:0045196"
                     /dbxref="GO:0042127"
                     /gbunit="AE003590"
                     /sp_status="Perfect match to SwissProt real
                     (computational)"
                     /cyto_range="21A2-21A2"
                     /standard_name="CG2671"
     mRNA            complement(-4163..7373)
                     /gene="l(2)gl"
                     /standard_name="CG2671-RB"
                     /product_desc="CG2671-RB transcript from_gene[CG2671
                     l(2)gl FBgn0002121] seq_release:3 mRNA_length:5154
                     transcript_boundaries:(2L:9,836..21,372[-])
                     cyto:21A2-21A2 gene_info:[CG2671 gene symbol:l(2)gl
                     FBgn0002121 (0 ""reduction of virulence"")]"
     CDS             complement(join(-2781..-2655,-2589..-2481,-2220..-1778,
                     -1713..-1071,-479..-374,-316..875,934..1712,5886..5945))
                     /translation="MLKFIRGKGQQPSADRQRYITAQHGFPHKPSALAYDPVLKLMAI
                     GTQTGALKVFGQPGVELYGQHTLLNNSASELNVQLLEWVYGTGRILSLTAANQLILWE
                     PVGATLLPIKTLPFDGKLKKVSSLCCSLSKDLLWIGTEGGNIYQLDLHTFTIKEPVIY
                     HDVVLEQVPPAYKLNPGAIESIRQLPNSPSKLLVAYNRGLCVLWDFESASVQRAYIAP
                     GHGQSVGLTVNFEGSEFTWYHADGSYATWSIDNPEPPSNVNYVPYGPDPCKSINRLYK
                     GKRRSNDVIVFSGGMPRSAYGDHNCVSVHASDGHKVCLDFTSKVIDFFVTFENNRDVA
                     EVLVVLLEEELCAYDLTDPNICAIKAPYLHSVHASAVTCNYLASEVVQSVYESILRAG
                     DEQDIDYSNISWPITGGTLPDNLEESVEEDATKLYEILLTGHEDGSVKFWDCTGVLLK
                     PIYNFKTSSIFGSESDFRDDAAADMSAEQVDEGEPPFRKSGLFDPYSDDPRLAVKKIA
                     FCPKTGQLIVGGTAGQIVIADFIDLPEKVSLKYISMNLVSDRDGFVWKGHDQLNVRSN
                     LLDGEAIPTTERGVNISGVLQVLPPASITCMALEASWGLVSGGTAHGLVLFDFKNFVP
                     VFHRCTLNPNDLTGAGEQLSRRKSFKKSLRESFRKLRKGRSTRTNQSNQVPTTLEARP
                     VERQIEARCADDGLGSMVRCLLFAKTYVTNVNITSPTLWSATNASTVSVFLLHLPPAQ
                     TAATAVPSASGNAPPHMPRRISAQLAKEIQLKHRAPVVGISIFDQAGSPVDQLNAGEN
                     GSPPHRVLIASEEQFKVFSLPQLKPINKYKLTANEGARIRRIHFGSFSCRISPETLQS
                     MHGCSPTKSTRSHGDGEADPNISGSLAVSRGDVYNETALICLTNMGDIMVLSVPELKR
                     QLNAAAVRREDINGVSSLCFTNSGEALYMMSSSELQRIALATSRVVQPTGVVPVEPLE
                     NEESVLEENDAENNKETYACDEVVNTYEIKNPSGISICTRPAEENVGRNSVQQVNGVN
                     ISNSPNQANETISSSIGDITVDSVRDHLNMTTTTLCSINTEETIGRLSVLSTQTNKAS
                     TTVNMSEIPNINISNLEDLESKRNTTETSTSSVVIKSIITNISHEKTNGDNKIGTPKT
                     APEESQF"
                     /status="all done"
                     /gene="l(2)gl"
                     /product="CG2671-PB"
                     /sp_comment="Imperfect match to REAL SP with
                     corresponding FBgn"
                     /author="bmatthew"
                     /date="Tue May 14 09:05:05 PDT 2002"
                     /protein_id="AAG22256"
                     /codon_start=5943
                     /timestamp="1021392305000"
                     /standard_name="CG2671-RB"
                     /product_desc="CG2671-PB translation from_gene[CG2671
                     l(2)gl FBgn0002121] seq_release:3  mol_weight=125897
                     cds_boundaries:(2L:11218..19944[-])  aa_length:1153
                     transcript_info:[CG2671-RB  seq_release:3]
                     gene_info:[gene symbol:l(2)gl FBgn0002121
                     gene_boundaries:(2L:9836..21372[-])  (0 ""reduction of
                     virulence"")]"
     mRNA            complement(-4163..7373)
                     /gene="l(2)gl"
                     /standard_name="CG2671-RD"
                     /product_desc="CG2671-RD transcript from_gene[CG2671
                     l(2)gl FBgn0002121] seq_release:3 mRNA_length:5229
                     transcript_boundaries:(2L:9,836..21,372[-])
                     cyto:21A2-21A2 gene_info:[CG2671 gene symbol:l(2)gl
                     FBgn0002121 (0 ""reduction of virulence"")]"
     CDS             complement(join(-2781..-2655,-2589..-2481,-2220..-1778,
                     -1713..-1071,-479..-374,-316..875,934..1649))
                     /translation="MAIGTQTGALKVFGQPGVELYGQHTLLNNSASELNVQLLEWVYG
                     TGRILSLTAANQLILWEPVGATLLPIKTLPFDGKLKKVSSLCCSLSKDLLWIGTEGGN
                     IYQLDLHTFTIKEPVIYHDVVLEQVPPAYKLNPGAIESIRQLPNSPSKLLVAYNRGLC
                     VLWDFESASVQRAYIAPGHGQSVGLTVNFEGSEFTWYHADGSYATWSIDNPEPPSNVN
                     YVPYGPDPCKSINRLYKGKRRSNDVIVFSGGMPRSAYGDHNCVSVHASDGHKVCLDFT
                     SKVIDFFVTFENNRDVAEVLVVLLEEELCAYDLTDPNICAIKAPYLHSVHASAVTCNY
                     LASEVVQSVYESILRAGDEQDIDYSNISWPITGGTLPDNLEESVEEDATKLYEILLTG
                     HEDGSVKFWDCTGVLLKPIYNFKTSSIFGSESDFRDDAAADMSAEQVDEGEPPFRKSG
                     LFDPYSDDPRLAVKKIAFCPKTGQLIVGGTAGQIVIADFIDLPEKVSLKYISMNLVSD
                     RDGFVWKGHDQLNVRSNLLDGEAIPTTERGVNISGVLQVLPPASITCMALEASWGLVS
                     GGTAHGLVLFDFKNFVPVFHRCTLNPNDLTGAGEQLSRRKSFKKSLRESFRKLRKGRS
                     TRTNQSNQVPTTLEARPVERQIEARCADDGLGSMVRCLLFAKTYVTNVNITSPTLWSA
                     TNASTVSVFLLHLPPAQTAATAVPSASGNAPPHMPRRISAQLAKEIQLKHRAPVVGIS
                     IFDQAGSPVDQLNAGENGSPPHRVLIASEEQFKVFSLPQLKPINKYKLTANEGARIRR
                     IHFGSFSCRISPETLQSMHGCSPTKSTRSHGDGEADPNISGSLAVSRGDVYNETALIC
                     LTNMGDIMVLSVPELKRQLNAAAVRREDINGVSSLCFTNSGEALYMMSSSELQRIALA
                     TSRVVQPTGVVPVEPLENEESVLEENDAENNKETYACDEVVNTYEIKNPSGISICTRP
                     AEENVGRNSVQQVNGVNISNSPNQANETISSSIGDITVDSVRDHLNMTTTTLCSINTE
                     ETIGRLSVLSTQTNKASTTVNMSEIPNINISNLEDLESKRNTTETSTSSVVIKSIITN
                     ISHEKTNGDNKIGTPKTAPEESQF"
                     /status="all done"
                     /gene="l(2)gl"
                     /product="CG2671-PD"
                     /sp_comment="Imperfect match to REAL SP with
                     corresponding FBgn"
                     /author="bmatthew"
                     /date="Tue May 14 09:06:14 PDT 2002"
                     /protein_id="AAN10501"
                     /codon_start=1647
                     /timestamp="1021392374000"
                     /standard_name="CG2671-RD"
                     /product_desc="CG2671-PD translation from_gene[CG2671
                     l(2)gl FBgn0002121] seq_release:3  mol_weight=121250
                     cds_boundaries:(2L:11218..15648[-])  aa_length:1112
                     transcript_info:[CG2671-RD  seq_release:3]
                     gene_info:[gene symbol:l(2)gl FBgn0002121
                     gene_boundaries:(2L:9836..21372[-])  (0 ""reduction of
                     virulence"")]"
     mRNA            complement(-4163..7373)
                     /gene="l(2)gl"
                     /standard_name="CG2671-RE"
                     /product_desc="CG2671-RE transcript from_gene[CG2671
                     l(2)gl FBgn0002121] seq_release:3 mRNA_length:5224
                     transcript_boundaries:(2L:9,836..21,372[-])
                     cyto:21A2-21A2 gene_info:[CG2671 gene symbol:l(2)gl
                     FBgn0002121 (0 ""reduction of virulence"")]"
     CDS             complement(join(-2781..-2655,-2589..-2481,-2220..-1778,
                     -1713..-1071,-479..-374,-316..875,934..1649))
                     /translation="MAIGTQTGALKVFGQPGVELYGQHTLLNNSASELNVQLLEWVYG
                     TGRILSLTAANQLILWEPVGATLLPIKTLPFDGKLKKVSSLCCSLSKDLLWIGTEGGN
                     IYQLDLHTFTIKEPVIYHDVVLEQVPPAYKLNPGAIESIRQLPNSPSKLLVAYNRGLC
                     VLWDFESASVQRAYIAPGHGQSVGLTVNFEGSEFTWYHADGSYATWSIDNPEPPSNVN
                     YVPYGPDPCKSINRLYKGKRRSNDVIVFSGGMPRSAYGDHNCVSVHASDGHKVCLDFT
                     SKVIDFFVTFENNRDVAEVLVVLLEEELCAYDLTDPNICAIKAPYLHSVHASAVTCNY
                     LASEVVQSVYESILRAGDEQDIDYSNISWPITGGTLPDNLEESVEEDATKLYEILLTG
                     HEDGSVKFWDCTGVLLKPIYNFKTSSIFGSESDFRDDAAADMSAEQVDEGEPPFRKSG
                     LFDPYSDDPRLAVKKIAFCPKTGQLIVGGTAGQIVIADFIDLPEKVSLKYISMNLVSD
                     RDGFVWKGHDQLNVRSNLLDGEAIPTTERGVNISGVLQVLPPASITCMALEASWGLVS
                     GGTAHGLVLFDFKNFVPVFHRCTLNPNDLTGAGEQLSRRKSFKKSLRESFRKLRKGRS
                     TRTNQSNQVPTTLEARPVERQIEARCADDGLGSMVRCLLFAKTYVTNVNITSPTLWSA
                     TNASTVSVFLLHLPPAQTAATAVPSASGNAPPHMPRRISAQLAKEIQLKHRAPVVGIS
                     IFDQAGSPVDQLNAGENGSPPHRVLIASEEQFKVFSLPQLKPINKYKLTANEGARIRR
                     IHFGSFSCRISPETLQSMHGCSPTKSTRSHGDGEADPNISGSLAVSRGDVYNETALIC
                     LTNMGDIMVLSVPELKRQLNAAAVRREDINGVSSLCFTNSGEALYMMSSSELQRIALA
                     TSRVVQPTGVVPVEPLENEESVLEENDAENNKETYACDEVVNTYEIKNPSGISICTRP
                     AEENVGRNSVQQVNGVNISNSPNQANETISSSIGDITVDSVRDHLNMTTTTLCSINTE
                     ETIGRLSVLSTQTNKASTTVNMSEIPNINISNLEDLESKRNTTETSTSSVVIKSIITN
                     ISHEKTNGDNKIGTPKTAPEESQF"
                     /status="all done"
                     /gene="l(2)gl"
                     /product="CG2671-PE"
                     /sp_comment="Imperfect match to REAL SP with
                     corresponding FBgn"
                     /author="bmatthew"
                     /date="Tue May 14 09:02:48 PDT 2002"
                     /protein_id="AAN10502"
                     /codon_start=1647
                     /timestamp="1021392168000"
                     /standard_name="CG2671-RE"
                     /product_desc="CG2671-PE translation from_gene[CG2671
                     l(2)gl FBgn0002121] seq_release:3  mol_weight=121250
                     cds_boundaries:(2L:11218..15648[-])  aa_length:1112
                     transcript_info:[CG2671-RE  seq_release:3]
                     gene_info:[gene symbol:l(2)gl FBgn0002121
                     gene_boundaries:(2L:9836..21372[-])  (0 ""reduction of
                     virulence"")]"
     mRNA            complement(-4163..7373)
                     /gene="l(2)gl"
                     /standard_name="CG2671-RF"
                     /product_desc="CG2671-RF transcript from_gene[CG2671
                     l(2)gl FBgn0002121] seq_release:3 mRNA_length:5081
                     transcript_boundaries:(2L:9,836..21,372[-])
                     cyto:21A2-21A2 gene_info:[CG2671 gene symbol:l(2)gl
                     FBgn0002121 (0 ""reduction of virulence"")]"
     CDS             complement(join(-2781..-2655,-2589..-2481,-2220..-1778,
                     -1713..-1071,-479..-374,-316..875,934..1649))
                     /translation="MAIGTQTGALKVFGQPGVELYGQHTLLNNSASELNVQLLEWVYG
                     TGRILSLTAANQLILWEPVGATLLPIKTLPFDGKLKKVSSLCCSLSKDLLWIGTEGGN
                     IYQLDLHTFTIKEPVIYHDVVLEQVPPAYKLNPGAIESIRQLPNSPSKLLVAYNRGLC
                     VLWDFESASVQRAYIAPGHGQSVGLTVNFEGSEFTWYHADGSYATWSIDNPEPPSNVN
                     YVPYGPDPCKSINRLYKGKRRSNDVIVFSGGMPRSAYGDHNCVSVHASDGHKVCLDFT
                     SKVIDFFVTFENNRDVAEVLVVLLEEELCAYDLTDPNICAIKAPYLHSVHASAVTCNY
                     LASEVVQSVYESILRAGDEQDIDYSNISWPITGGTLPDNLEESVEEDATKLYEILLTG
                     HEDGSVKFWDCTGVLLKPIYNFKTSSIFGSESDFRDDAAADMSAEQVDEGEPPFRKSG
                     LFDPYSDDPRLAVKKIAFCPKTGQLIVGGTAGQIVIADFIDLPEKVSLKYISMNLVSD
                     RDGFVWKGHDQLNVRSNLLDGEAIPTTERGVNISGVLQVLPPASITCMALEASWGLVS
                     GGTAHGLVLFDFKNFVPVFHRCTLNPNDLTGAGEQLSRRKSFKKSLRESFRKLRKGRS
                     TRTNQSNQVPTTLEARPVERQIEARCADDGLGSMVRCLLFAKTYVTNVNITSPTLWSA
                     TNASTVSVFLLHLPPAQTAATAVPSASGNAPPHMPRRISAQLAKEIQLKHRAPVVGIS
                     IFDQAGSPVDQLNAGENGSPPHRVLIASEEQFKVFSLPQLKPINKYKLTANEGARIRR
                     IHFGSFSCRISPETLQSMHGCSPTKSTRSHGDGEADPNISGSLAVSRGDVYNETALIC
                     LTNMGDIMVLSVPELKRQLNAAAVRREDINGVSSLCFTNSGEALYMMSSSELQRIALA
                     TSRVVQPTGVVPVEPLENEESVLEENDAENNKETYACDEVVNTYEIKNPSGISICTRP
                     AEENVGRNSVQQVNGVNISNSPNQANETISSSIGDITVDSVRDHLNMTTTTLCSINTE
                     ETIGRLSVLSTQTNKASTTVNMSEIPNINISNLEDLESKRNTTETSTSSVVIKSIITN
                     ISHEKTNGDNKIGTPKTAPEESQF"
                     /status="all done"
                     /gene="l(2)gl"
                     /product="CG2671-PF"
                     /sp_comment="Imperfect match to REAL SP with
                     corresponding FBgn"
                     /author="bmatthew"
                     /date="Tue May 14 09:02:52 PDT 2002"
                     /protein_id="AAN10503"
                     /codon_start=1647
                     /timestamp="1021392172000"
                     /standard_name="CG2671-RF"
                     /product_desc="CG2671-PF translation from_gene[CG2671
                     l(2)gl FBgn0002121] seq_release:3  mol_weight=121250
                     cds_boundaries:(2L:11218..15648[-])  aa_length:1112
                     transcript_info:[CG2671-RF  seq_release:3]
                     gene_info:[gene symbol:l(2)gl FBgn0002121
                     gene_boundaries:(2L:9836..21372[-])  (0 ""reduction of
                     virulence"")]"
     mRNA            complement(-4163..4584)
                     /gene="l(2)gl"
                     /standard_name="CG2671-RC"
                     /product_desc="CG2671-RC transcript from_gene[CG2671
                     l(2)gl FBgn0002121] seq_release:3 mRNA_length:5264
                     transcript_boundaries:(2L:9,836..18,583[-])
                     cyto:21A2-21A2 gene_info:[CG2671 gene symbol:l(2)gl
                     FBgn0002121 (0 ""reduction of virulence"")]"
     CDS             complement(join(-2781..-2655,-2589..-2481,-2220..-1778,
                     -1713..-1071,-479..-374,-316..875,934..1712,3054..3137))
                     /translation="MLKFIRGKGQQPSADRHRLQKDLFAYRKTAQHGFPHKPSALAYD
                     PVLKLMAIGTQTGALKVFGQPGVELYGQHTLLNNSASELNVQLLEWVYGTGRILSLTA
                     ANQLILWEPVGATLLPIKTLPFDGKLKKVSSLCCSLSKDLLWIGTEGGNIYQLDLHTF
                     TIKEPVIYHDVVLEQVPPAYKLNPGAIESIRQLPNSPSKLLVAYNRGLCVLWDFESAS
                     VQRAYIAPGHGQSVGLTVNFEGSEFTWYHADGSYATWSIDNPEPPSNVNYVPYGPDPC
                     KSINRLYKGKRRSNDVIVFSGGMPRSAYGDHNCVSVHASDGHKVCLDFTSKVIDFFVT
                     FENNRDVAEVLVVLLEEELCAYDLTDPNICAIKAPYLHSVHASAVTCNYLASEVVQSV
                     YESILRAGDEQDIDYSNISWPITGGTLPDNLEESVEEDATKLYEILLTGHEDGSVKFW
                     DCTGVLLKPIYNFKTSSIFGSESDFRDDAAADMSAEQVDEGEPPFRKSGLFDPYSDDP
                     RLAVKKIAFCPKTGQLIVGGTAGQIVIADFIDLPEKVSLKYISMNLVSDRDGFVWKGH
                     DQLNVRSNLLDGEAIPTTERGVNISGVLQVLPPASITCMALEASWGLVSGGTAHGLVL
                     FDFKNFVPVFHRCTLNPNDLTGAGEQLSRRKSFKKSLRESFRKLRKGRSTRTNQSNQV
                     PTTLEARPVERQIEARCADDGLGSMVRCLLFAKTYVTNVNITSPTLWSATNASTVSVF
                     LLHLPPAQTAATAVPSASGNAPPHMPRRISAQLAKEIQLKHRAPVVGISIFDQAGSPV
                     DQLNAGENGSPPHRVLIASEEQFKVFSLPQLKPINKYKLTANEGARIRRIHFGSFSCR
                     ISPETLQSMHGCSPTKSTRSHGDGEADPNISGSLAVSRGDVYNETALICLTNMGDIMV
                     LSVPELKRQLNAAAVRREDINGVSSLCFTNSGEALYMMSSSELQRIALATSRVVQPTG
                     VVPVEPLENEESVLEENDAENNKETYACDEVVNTYEIKNPSGISICTRPAEENVGRNS
                     VQQVNGVNISNSPNQANETISSSIGDITVDSVRDHLNMTTTTLCSINTEETIGRLSVL
                     STQTNKASTTVNMSEIPNINISNLEDLESKRNTTETSTSSVVIKSIITNISHEKTNGD
                     NKIGTPKTAPEESQF"
                     /status="all done"
                     /gene="l(2)gl"
                     /product="CG2671-PC"
                     /sp_comment="Perfect match to REAL SP with corresponding
                     FBgn"
                     /author="bmatthew"
                     /date="Tue May 14 09:02:56 PDT 2002"
                     /protein_id="AAF51570"
                     /codon_start=3135
                     /timestamp="1021392176000"
                     /standard_name="CG2671-RC"
                     /product_desc="CG2671-PC translation from_gene[CG2671
                     l(2)gl FBgn0002121] seq_release:3  mol_weight=126893
                     cds_boundaries:(2L:11218..17136[-])  aa_length:1161
                     transcript_info:[CG2671-RC  seq_release:3]
                     gene_info:[gene symbol:l(2)gl FBgn0002121
                     gene_boundaries:(2L:9836..21372[-])  (0 ""reduction of
                     virulence"")]"
     mRNA            complement(-4163..4584)
                     /gene="l(2)gl"
                     /standard_name="CG2671-RA"
                     /product_desc="CG2671-RA transcript from_gene[CG2671
                     l(2)gl FBgn0002121] seq_release:3 mRNA_length:5407
                     transcript_boundaries:(2L:9,836..18,583[-])
                     cyto:21A2-21A2 gene_info:[CG2671 gene symbol:l(2)gl
                     FBgn0002121 (0 ""reduction of virulence"")]"
     CDS             complement(join(-2781..-2655,-2589..-2481,-2220..-1778,
                     -1713..-1071,-479..-374,-316..875,934..1712,3054..3137))
                     /translation="MLKFIRGKGQQPSADRHRLQKDLFAYRKTAQHGFPHKPSALAYD
                     PVLKLMAIGTQTGALKVFGQPGVELYGQHTLLNNSASELNVQLLEWVYGTGRILSLTA
                     ANQLILWEPVGATLLPIKTLPFDGKLKKVSSLCCSLSKDLLWIGTEGGNIYQLDLHTF
                     TIKEPVIYHDVVLEQVPPAYKLNPGAIESIRQLPNSPSKLLVAYNRGLCVLWDFESAS
                     VQRAYIAPGHGQSVGLTVNFEGSEFTWYHADGSYATWSIDNPEPPSNVNYVPYGPDPC
                     KSINRLYKGKRRSNDVIVFSGGMPRSAYGDHNCVSVHASDGHKVCLDFTSKVIDFFVT
                     FENNRDVAEVLVVLLEEELCAYDLTDPNICAIKAPYLHSVHASAVTCNYLASEVVQSV
                     YESILRAGDEQDIDYSNISWPITGGTLPDNLEESVEEDATKLYEILLTGHEDGSVKFW
                     DCTGVLLKPIYNFKTSSIFGSESDFRDDAAADMSAEQVDEGEPPFRKSGLFDPYSDDP
                     RLAVKKIAFCPKTGQLIVGGTAGQIVIADFIDLPEKVSLKYISMNLVSDRDGFVWKGH
                     DQLNVRSNLLDGEAIPTTERGVNISGVLQVLPPASITCMALEASWGLVSGGTAHGLVL
                     FDFKNFVPVFHRCTLNPNDLTGAGEQLSRRKSFKKSLRESFRKLRKGRSTRTNQSNQV
                     PTTLEARPVERQIEARCADDGLGSMVRCLLFAKTYVTNVNITSPTLWSATNASTVSVF
                     LLHLPPAQTAATAVPSASGNAPPHMPRRISAQLAKEIQLKHRAPVVGISIFDQAGSPV
                     DQLNAGENGSPPHRVLIASEEQFKVFSLPQLKPINKYKLTANEGARIRRIHFGSFSCR
                     ISPETLQSMHGCSPTKSTRSHGDGEADPNISGSLAVSRGDVYNETALICLTNMGDIMV
                     LSVPELKRQLNAAAVRREDINGVSSLCFTNSGEALYMMSSSELQRIALATSRVVQPTG
                     VVPVEPLENEESVLEENDAENNKETYACDEVVNTYEIKNPSGISICTRPAEENVGRNS
                     VQQVNGVNISNSPNQANETISSSIGDITVDSVRDHLNMTTTTLCSINTEETIGRLSVL
                     STQTNKASTTVNMSEIPNINISNLEDLESKRNTTETSTSSVVIKSIITNISHEKTNGD
                     NKIGTPKTAPEESQF"
                     /status="all done"
                     /gene="l(2)gl"
                     /product="CG2671-PA"
                     /sp_comment="Perfect match to REAL SP with corresponding
                     FBgn"
                     /comment="person=bmatthew; date=Tue May 14 08:53:50 PDT
                     2002; text=Only one EST supports this alternative
                     transcript"
                     /author="bmatthew"
                     /date="Tue May 14 09:03:00 PDT 2002"
                     /protein_id="AAG22255"
                     /codon_start=3135
                     /timestamp="1021392180000"
                     /standard_name="CG2671-RA"
                     /product_desc="CG2671-PA translation from_gene[CG2671
                     l(2)gl FBgn0002121]seq_release:3  mol_weight=126893
                     cds_boundaries:(2L:11218..17136[-])  aa_length:1161
                     transcript_info:[CG2671-RA  seq_release:3]
                     gene_info:[gene symbol:l(2)gl FBgn0002121
                     gene_boundaries:(2L:9836..21372[-]) (0 ""reduction of
                     virulence"")]"
BASE COUNT     1613 a    930 c    879 g   1579 t
ORIGIN
        1 cttctccgtc taataagttc gatcgcacgt ttaactgatc gtgacccttc cacacaaatc
       61 catcacgatc gctgaccaaa ttcattgaaa tgtattttaa agacactttt tcgggtaagt
      121 ctatgaagtc ggctataact atttggcccg ctgtgccacc aacaataagt tgtccggttt
      181 ttgggcagaa tgctattttc ttcactgcta aacgagggtc atctgaataa ggatcaaaaa
      241 gtcctgattt ccgaaatggc ggttctcctt catcgacttg ttccgcactc atatctgcag
      301 ctgcgtcatc tcggaagtct gactcacttc caaaaatgct gctagtttta aaattataaa
      361 ttggtttaag caacactcca gtgcagtccc aaaatttaac agaaccatct tcgtgaccag
      421 ttaacaaaat ctcataaagc ttagtcgcgt cctcttctac agattcttct aagttatccg
      481 ggagagtacc gccagtgata ggccagctaa tattgctata gtcaatgtct tgttcatctc
      541 cagctcttaa aatactttca tataccgact gtacgacttc agaagcaagg taattgcaag
      601 tgacagctga tgcatggaca gagtgaagat atggcgcttt gatagcacaa atattagggt
      661 cagtaagatc gtaagcgcag agttcctctt caagtagtac aacaagaact tcagcgacat
      721 ctctattatt ttcaaaggtc acaaaaaagt caatcacttt agacgtaaag tcaagacaca
      781 ctttgtgtcc atcgctggcg tgaacggaca cacaattgtg atcaccatat gctgaccgtg
      841 gcatgccgcc ggaaaaaaca attacatcgt tggatctaaa agaacgagaa attagtacac
      901 atctaaaaaa ctttgtgttt aagttatatt aaccttcgct tgcctttgta cagtcgattt
      961 atgcttttgc atggatcagg tccataaggc acataattaa cattcgacgg cggttctggg
     1021 ttatctatgc tccaagtggc gtatgaacca tcagcgtggt accaggtaaa ttcagatcct
     1081 tcgaagttca ctgtaagacc aacgctctgt ccatgtccag gggctatgta tgctcgctgg
     1141 acagatgcgc tttcaaaatc ccacaaaaca caaaggccgc gattgtatgc aactagaagt
     1201 ttgctagggg agtttggaag ttggcggatt gactcaattg caccaggatt tagcttgtag
     1261 gctggtggca cctgctctag cacaacgtca tggtaaatta caggctcctt aatggtaaat
     1321 gtatgtaaat ccagttgata gatgtttcca ccttctgttc caatccatag cagatcctta
     1381 ctgagagaac agcacagcga tgaaactttt ttaagtttgc cgtcaaacgg tagtgttttg
     1441 attggcagca acgttgctcc aactggctcc catagaatta attgattcgc tgccgtcaac
     1501 gaaagtatgc gaccagttcc atacacccat tcaagtaatt gtacattaag ctccgatgct
     1561 gaattgttta acaaagtatg ctgaccgtac aattcaactc cgggttgacc gaaaactttt
     1621 aaagcccctg tttgcgtccc tattgccata agtttcaaaa ctggatcata cgcaagagcc
     1681 gaaggcttat gaggaaagcc atgctgtgcc gtctaaaaga aaaaaatatt aaaaagtttc
     1741 aaaaagcaat tacagattct taataattca aaattgtttg gttcatttct taattgtaaa
     1801 agggttttcc aaaacattct agttttttca gttcccaaga tctggtaaat cgtcagatta
     1861 cttgccactt tatagagtcg ggaacgcttt cttaaaccat ttacatactt ttaccgaatc
     1921 taatacagca tttttcttta caattaacgg gaataaaaac ctcaataaat attgaggttt
     1981 gaatttaaat taagttcaaa aagcgcccaa agctttaaat gctgctctta agtatgtctc
     2041 ttataaacat cactgtagac agcagtccct actatcatac tatatttaca ttgatcgaaa
     2101 aaaggtttgg taaatcttat ctaattgtat aaattgtatt tttatacaaa aaaagtttta
     2161 agaagttgct atcagatctc gttatgagtt gattttgttt gattcatatt gcaggtgtat
     2221 ttggatttct aacgcagtta caggcgaata aattcttttt cttttgactt taaaatctta
     2281 tcaattttac gccgtctatg acatacttat tttgtgcctg aaataagggt gtttgtgaaa
     2341 ccaagccatt tacccaaccc attaagcaca taaaagcaat cttatcagct cccccctctt
     2401 tctggagctg gatggcgatt acctctgacc tacttttatt tgtttaataa catgtttata
     2461 ctaacatggg ataaaaaaaa ttcttataaa atttcatata cgtatattta ttaaactatt
     2521 atggtaatag ggaaacatct atggtatatt taattcgaaa atatttaaaa ggaatggaca
     2581 acattacgag cacaacgata taatagaatt tttaaagtag ccaaaaacag gcggtggaaa
     2641 aagacactca caaaatcaac aaagcttcag gtacctcctc atatttggca ccgcatagaa
     2701 ggagtgcaca aaagaaacga gcaaaaaagc accgtaacct tttttatgcg gtgctttgtg
     2761 gcgcgagtct acaaaatact gtgtgtgtat gcggtttact tgtagttgcg gtggaaaaaa
     2821 tttacctaaa tgttaatgcc caaaagtatg cacataggag aagacataac aaaagattga
     2881 aaaggaggta tttatttatt cttaataaat tataagcttt cttctaactt ccataaaaat
     2941 gtatttacca cccaggatca aaataaatga caccccacaa aatataccaa tcggctacat
     3001 atacgaaaaa aaaaaaataa aatagaatgg aaagagaaaa ttgtttgttg taccttacga
     3061 taagcaaaaa ggtccttctg taggcggtgt ctgtcagcac tgggctgctg cccttttcct
     3121 ctgataaact ttaacataat tggttatgct cttgtggtgg gttggtttcg atgaataaat
     3181 atgtatacta attgtggccg tatttattct aaactgaaaa taataaataa aaattaatca
     3241 cattttcaat aagtaaaaaa ttaaaaagga acttgtatat tttttcactc ttatgaataa
     3301 aaccgagaaa ttaaatttag gtaatactat taataccttt tatagatacg gacgatacgt
     3361 ttaatattat tctggtatac tttaatcaaa atttgtttaa caaaaagggt tttacattct
     3421 tggtcatagg aaattcagtg gacagataga tcttggctcc caagattttc caaactagtt
     3481 gtgcttattt tcttaaaact tcaaagattt gcatgtaggc agtttaataa acatgtttgt
     3541 acatatgtat atgtacatta ggaaaaatga gatgcaagat gagcgatctg tactctttgc
     3601 aatgtgtatg tatgtacata tgtacctccc tttaatgaac tagcaattcc gtcacgcaca
     3661 cgaaatattt ttttatttgt aaatcttttt ttaagtttgt ttaaacaatt tagttactat
     3721 taaagctctg aaattcataa ataaataata ataaatgtat taattatgac aaaaaacaac
     3781 ttaaaacata tacgtttatt tttgtaaaag cgttttaggc aaacgctagc tggtcggtac
     3841 taatattttt tcgaagactg tataccgtat acatacattt atgtacgtag gtatgtatcc
     3901 gtgagtaagc tgaggtgcaa aaccgtatca ccatttgctt ttcggctgat aaccaatacc
     3961 aagtaagtca actgtttccc aaatgtatct gcataacaag gtgatgacct aattttgagt
     4021 acataccgat ctttacagtt gaccagcttt gcgattgcat accggtatct gtttattcac
     4081 atatacacac acaaattgcg tgttagacag acagcaaaat gacgactgtt aactgttggc
     4141 gtggctgact caccgactac gcctctatgc taagaacata catatttgtg gacactttat
     4201 ttaagaagtt tgaaatataa atcaattgcc taatcagtaa tactgttgtt gagcccttta
     4261 cctttatgta tttccgtttg tacggttaag gcggtggccg agtaattttt tgaactattt
     4321 tatttgctca ccaacacgca taagtttgta tgtattctta tgttgagaaa cgcccgcact
     4381 gttcttcaca tcgttgcttt aaatgagaat aaatgaaata aacgtgtcaa ccaagaacac
     4441 acagataata atacgaccgg tcagagctta accgtgtatc tgttttataa aacgtgaaca
     4501 atattattag cccaaaacga tatgcgcgtc attttaacac acacaaagtc gcgatcggtg
     4561 ggtctagtgt gcccgtgtat ctctatcgaa aaaatcatat attttttaga aggtatattt
     4621 tccatgactg actggaatgg gtggagaaca tcgctttggg agtgaaactc cgctataaat
     4681 tgtcatttgt ttttatagca acctttttga tatggtcgcc aacttttata taattataat
     4741 aataattttt gtaattaatc accgctgtcg cacgaaaaat ttaggaaatg tgccaacgag
     4801 cggaattttt cggaacgatc gatgttttac cataacctgc tatataaatt gtgaaccaca
     4861 ttttcaacac aaaactagat gtgcttcatt tataacgcaa tgtcgtgatt ttgtgggcag
     4921 tgtgaccatg tccaatctgc gttcaagtaa aaccatattt agtgacacaa actttccatt
     4981 acaaaatacc aaacaacttt a
//
BioPerl-1.007002/t/data/dna1.fa000444000766000024        33413155576321 16003 0ustar00cjfieldsstaff000000000000>Test1
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
BioPerl-1.007002/t/data/dna2.fa000444000766000024       110513155576321 16021 0ustar00cjfieldsstaff000000000000>Test1
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
>Test2
CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTBioPerl-1.007002/t/data/dnaE-bsub-prot.fa000444000766000024       121213155576321 17756 0ustar00cjfieldsstaff000000000000>gi|142865|gb|AAA22406.1| DNA primase
MGNRIPDEIVDQVQKSADIVEVIGDYVQLKKQGRNYFGLCPFHGESTPSFSVSPDKQIFHCFGCGAGGNV
FSFLRQMEGYSFAESVSHLADKYQIDFPDDITVHSGARPESSGEQKMAEAHELLKKFYHHLLINTKEGQE
ALDYLLSRGFTKELINEFQIGYALDSWDFITKFLVKRGFSEAQMEKAGLLIRREDGSGYFDRFRNRVMFP
IHDHHGAVVAFSGRALGSQQPKYMNSPETPLFHKSKLLYNFYKARLHIRKQERAVLFEGFADVYTAVSSD
VKESIATMGTSLTDDHVKILRRNVEEIILCYDSDKAGYEATLKASELLQKKGCKVRVAMIPDGLDPDDYI
KKFGGEKFKNDIIDASVTVMAFKMQYFRKGKNLSDEGDRLAYIKDVLKEISTLSGSLEQEVYVKQLASEF
SLSQESLTEQLSVFSKQNKPADNSGETKTRRAHLTTKARQKRLRPAYENAERLLLAHMLRDRSVIKKVID
RVGFQFNIDEHRALAAYLYAFYEEGAELTPQHLMARVTDDHISQLLSDILMLQVNQELSEAELSDYVKKV
LNQRNWSMIKEKEAERAEAERQKDFLRAASLAQEIVTLNRSLK
BioPerl-1.007002/t/data/dnaE-bsub.fa000444000766000024       410513155576321 17000 0ustar00cjfieldsstaff000000000000>gi|142864|gb|M10040.1|BACDNAE B.subtilis dnaE gene encoding DNA primase, complete cds
GTACGACGGAGTGTTATAAGATGGGAAATCGGATACCAGATGAAATTGTGGATCAGGTGCAAAAGTCGGC
AGATATCGTTGAAGTCATAGGTGATTATGTTCAATTAAAGAAGCAAGGCCGAAACTACTTTGGACTCTGT
CCTTTTCATGGAGAAAGCACACCTTCGTTTTCCGTATCGCCCGACAAACAGATTTTTCATTGCTTTGGCT
GCGGAGCGGGCGGCAATGTTTTCTCTTTTTTAAGGCAGATGGAAGGCTATTCTTTTGCCGAGTCGGTTTC
TCACCTTGCTGACAAATACCAAATTGATTTTCCAGATGATATAACAGTCCATTCCGGAGCCCGGCCAGAG
TCTTCTGGAGAACAAAAAATGGCTGAGGCACATGAGCTCCTGAAGAAATTTTACCATCATTTGTTAATAA
ATACAAAAGAAGGTCAAGAGGCACTGGATTATCTGCTTTCTAGGGGCTTTACGAAAGAGCTGATTAATGA
ATTTCAGATTGGCTATGCTCTTGATTCTTGGGACTTTATCACGAAATTCCTTGTAAAGAGGGGATTTAGT
GAGGCGCAAATGGAAAAAGCGGGTCTCCTGATCAGACGCGAAGACGGAAGCGGATATTTCGACCGCTTCA
GAAACCGTGTCATGTTTCCGATCCATGATCATCACGGGGCTGTTGTTGCTTTCTCAGGCAGGGCTCTTGG
CAGCCAGCAGCCTAAGTATATGAACAGTCCTGAAACCCCGCTCTTTCATAAAAGCAAACTGCTTTACAAT
TTTTATAAGGCCCGCCTTCATATCAGAAAGCAGGAAAGAGCAGTCTTATTTGAAGGGTTTGCTGATGTCT
ATACGGCCGTAAGCTCGGATGTAAAGGAAAGCATAGCCACGATGGGAACGTCTCTTACAGATGATCATGT
CAAGATCCTGAGAAGAAACGTCGAAGAAATCATTCTTTGCTATGACTCTGATAAAGCCGGTTATGAAGCC
ACCTTAAAAGCTTCGGAGCTTCTGCAAAAAAAAGGCTGCAAAGTCAGAGTTGCAATGATTCCTGACGGAT
TGGACCCTGATGATTACATCAAAAAATTCGGCGGGGAAAAATTTAAAAACGACATTATTGACGCAAGTGT
CACCGTAATGGCGTTCAAAATGCAATATTTCCGAAAAGGAAAGAACCTGTCCGATGAAGGCGACCGCCTA
GCTTACATTAAAGACGTACTGAAAGAAATCAGCACGCTTTCAGGGTCTCTAGAGCAGGAAGTCTATGTAA
AGCAGCTTGCTTCAGAGTTTTCGCTTTCACAGGAGTCTTTAACTGAGCAGCTGTCTGTTTTCAGCAAGCA
AAACAAACCTGCTGACAATAGCGGTGAAACTAAAACGCGGCGAGCGCATCTGACGACAAAAGCAAGGCAA
AAACGTTTGCGTCCGGCGTATGAAAATGCAGAAAGGCTGTTACTCGCTCACATGCTTCGAGATCGGAGCG
TCATCAAAAAAGTGATTGACCGGGTAGGGTTTCAATTTAATATTGATGAGCACCGGGCATTAGCCGCTTA
TCTTTATGCTTTTTATGAAGAGGGAGCCGAGCTGACGCCTCAGCATCTGATGGCCAGGGTGACGGATGAT
CATATAAGCCAGCTCTTGTCCGATATATTAATGCTTCAGGTTAATCAAGAGCTTAGCGAAGCCGAGTTAT
CAGATTATGTAAAAAAAGTGTTGAATCAAAGAAATTGGTCAATGATAAAAGAAAAAGAGGCGGAAAGAGC
CGAAGCAGAAAGGCAAAAAGATTTTTTAAGAGCTGCTTCTTTGGCTCAAGAAATCGTTACATTGAACCGA
TCTTTAAAATAACTGGAGAACTGATGAGGAGCATTTATTGGCAATGATTCCTTGCGGAGGAGCAAATAGA
TCGCTTAACCTCATCATGAATTGTCATTTCATTATTCGCACATTGTTAAAGGCAGTTCACATAGAAAACG
CCTGAATGGACCGAATAAGAATCATACCGCTTATAGAATTC
BioPerl-1.007002/t/data/dnaEbsub_ecoli.wublastx000444000766000024      1375713155576321 21416 0ustar00cjfieldsstaff000000000000BLASTX 2.0MP-WashU [12-Feb-2001] [linux-i686 01:36:08 31-Jan-2001]

Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2000) http://blast.wustl.edu
Gish, Warren and David J. States (1993).  Identification of protein coding
regions by database similarity search.  Nat. Genet. 3:266-72.

Notice:  statistical significance is estimated under the assumption that the
equivalent of one entire reading frame in the query sequence codes for protein
and that significant alignments will involve only coding reading frames.

Query=  gi|142864|gb|M10040.1|BACDNAE B.subtilis dnaE gene encoding DNA
    primase, complete cds
        (2001 letters)

  Translating both strands of query sequence in all 6 reading frames

Database:  ecoli.aa
           4289 sequences; 1,358,990 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done

                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

gi|1789447|gb|AAC76102.1| (AE000388) DNA biosynthesis; DN...   671  1.1e-74   1



>gi|1789447|gb|AAC76102.1| (AE000388) DNA biosynthesis; DNA primase
            [Escherichia coli]
        Length = 581

  Plus Strand HSPs:

 Score = 671 (265.8 bits), Expect = 1.1e-74, P = 1.1e-74
 Identities = 151/421 (35%), Positives = 223/421 (52%), Frame = +3

Query:    21 MGNRIPDEIVDQVQKSADIVEVIGDYVQLKKQGRNYFGLCPFHGESTPSFSVSPDKQIFH 200
             M  RIP   ++ +    DIV++I   V+LKKQG+N+   CPFH E TPSF+V+ +KQ +H
Sbjct:     1 MAGRIPRVFINDLLARTDIVDLIDARVKLKKQGKNFHACCPFHNEKTPSFTVNGEKQFYH 60

Query:   201 CFGCGAGGNVFSFLRQMEGYSFAESVSHLADKYQIDFPDDITVHSGARP---ESSGEQKM 371
             CFGCGA GN   FL   +   F E+V  LA  + ++ P +    +G+ P   E    Q +
Sbjct:    61 CFGCGAHGNAIDFLMNYDKLEFVETVEELAAMHNLEVPFE----AGSGPSQIERHQRQTL 116

Query:   372 AEAHELLKKFYHHLLINTKEGQEALDYLLSRGFTKELINEFQIGYALDSWDFITKFLVKR 551
              +  + L  FY   L        A  YL  RG + E+I  F IG+A   WD + K     
Sbjct:   117 YQLMDGLNTFYQQSL-QQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGN 175

Query:   552 GFSEAQMEKAGLLIRREDGSGYFDRFRNRVMFPIHDHHGAVVAFSGRALGSQQPKYMNSP 731
               +   +  AG+L+  + G  Y DRFR RVMFPI D  G V+ F GR LG+  PKY+NSP
Sbjct:   176 PENRQSLIDAGMLVTNDQGRSY-DRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSP 234

Query:   732 ETPLFHKSKLLYNFYKARLHIRKQERAVLFEGFADVYTAVSSDVKESIATMGTSLTDDHV 911
             ET +FHK + LY  Y+A+    +  R ++ EG+ DV       +  ++A++GTS T DH+
Sbjct:   235 ETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHI 294

Query:   912 KILRRNVEEIILCYDSDKAGYEATLKASELL---QKKGCKVRVAMIPDGLDPDDYIKKFG 1082
             ++L R    +I CYD D+AG +A  +A E        G ++R   +PDG DPD  ++K G
Sbjct:   295 QLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEG 354

Query:  1083 GEKFKNDIIDASVTVMAFKMQYFRKGKNLSDEGDRLAYIKDVLKEISTLSGSLEQEVYVK 1262
              E F+  + + ++ + AF         +LS    R       L  IS + G   + +Y++
Sbjct:   355 KEAFEARM-EQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLR-IYLR 412

Query:  1263 Q 1265
             Q
Sbjct:   413 Q 413


Parameters:
  novalidctxok
  nonnegok
  gapall
  Q=12
  R=1
  cpus=1
  filter=seg
  matrix=blosum62
  W=3
  S2=41
  gapS2=68
  X=16
  gapX=38
  hitdist=40
  gi
  gapL=0.27
  gapK=0.047
  gapH=0.23

  ctxfactor=5.99
  E=10

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +3      0   blosum62        0.318   0.135   0.401    0.324   0.139   0.405  
               Q=12,R=1        0.270   0.0470  0.230     n/a     n/a     n/a
   +2      0   blosum62        0.318   0.135   0.401    0.365   0.163   0.618  
               Q=12,R=1        0.270   0.0470  0.230     n/a     n/a     n/a
   +1      0   blosum62        0.318   0.135   0.401    0.356   0.155   0.528  
               Q=12,R=1        0.270   0.0470  0.230     n/a     n/a     n/a
   -1      0   blosum62        0.318   0.135   0.401    0.350   0.155   0.543  
               Q=12,R=1        0.270   0.0470  0.230     n/a     n/a     n/a
   -2      0   blosum62        0.318   0.135   0.401    0.350   0.155   0.505  
               Q=12,R=1        0.270   0.0470  0.230     n/a     n/a     n/a
   -3      0   blosum62        0.318   0.135   0.401    0.358   0.157   0.543  
               Q=12,R=1        0.270   0.0470  0.230     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E    S W   T  X   E2     S2
   +3      0      666       666       10.  59 3  12 16  0.021   41
                                                    38  0.0     59
   +2      0      666       666       10.  59 3  12 16  0.021   41
                                                    38  0.0     59
   +1      0      667       667       10.  59 3  12 16  0.021   41
                                                    38  0.0     59
   -1      0      667       667       10.  59 3  12 16  0.021   41
                                                    38  0.0     59
   -2      0      666       666       10.  59 3  12 16  0.021   41
                                                    38  0.0     59
   -3      0      666       666       10.  59 3  12 16  0.021   41
                                                    38  0.0     59


Statistics:

  Database:  /home/jes12/db/ecoli.aa
   Title:  ecoli.aa
   Posted:  2:52:35 PM EST Nov 18, 2001
   Created:  9:46:47 AM EST Nov 18, 2001
   Format:  XDF-1
   # of letters in database:  1,358,990
   # of sequences in database:  4289
   # of database sequences satisfying E:  1
  No. of states in DFA:  600 (64 KB)
  Total size of DFA:  655 KB (1283 KB)
  Time to generate neighborhood:  0.04u 0.01s 0.05t  Elapsed: 00:00:00
  No. of threads or processors used:  1
  Search cpu time:  0.44u 0.01s 0.45t  Elapsed: 00:00:01
  Total cpu time:  0.48u 0.02s 0.50t  Elapsed: 00:00:01
  Start:  Sat Apr 20 14:39:05 2002   End:  Sat Apr 20 14:39:06 2002
BioPerl-1.007002/t/data/dnaEbsub_ecoli.wutblastn000444000766000024      1051413155576321 21554 0ustar00cjfieldsstaff000000000000TBLASTN 2.0MP-WashU [12-Feb-2001] [linux-i686 01:36:08 31-Jan-2001]

Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2000) http://blast.wustl.edu

Notice:  statistical significance is estimated under the assumption that the
equivalent of one entire reading frame of the database codes for protein and
that significant alignments will involve only coding reading frames.

Query=  gi|142865|gb|AAA22406.1| DNA primase
        (603 letters)

Database:  ecoli.nt
           400 sequences; 4,662,239 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done

                                                                     Smallest
                                                                       Sum
                                                     Reading  High  Probability
Sequences producing High-scoring Segment Pairs:        Frame Score  P(N)      N

gi|1789441|gb|AE000388.1|AE000388 Escherichia coli K-1... +2   671  1.4e-73   1



>gi|1789441|gb|AE000388.1|AE000388 Escherichia coli K-12 MG1655 section 278 of
            400 of the complete genome
        Length = 10,334

  Plus Strand HSPs:

 Score = 671 (265.8 bits), Expect = 1.4e-73, P = 1.4e-73
 Identities = 151/421 (35%), Positives = 223/421 (52%), Frame = +2

Query:     1 MGNRIPDEIVDQVQKSADIVEVIGDYVQLKKQGRNYFGLCPFHGESTPSFSVSPDKQIFH 60
             M  RIP   ++ +    DIV++I   V+LKKQG+N+   CPFH E TPSF+V+ +KQ +H
Sbjct:  4778 MAGRIPRVFINDLLARTDIVDLIDARVKLKKQGKNFHACCPFHNEKTPSFTVNGEKQFYH 4957

Query:    61 CFGCGAGGNVFSFLRQMEGYSFAESVSHLADKYQIDFPDDITVHSGARP---ESSGEQKM 117
             CFGCGA GN   FL   +   F E+V  LA  + ++ P +    +G+ P   E    Q +
Sbjct:  4958 CFGCGAHGNAIDFLMNYDKLEFVETVEELAAMHNLEVPFE----AGSGPSQIERHQRQTL 5125

Query:   118 AEAHELLKKFYHHLLINTKEGQEALDYLLSRGFTKELINEFQIGYALDSWDFITKFLVKR 177
              +  + L  FY   L        A  YL  RG + E+I  F IG+A   WD + K     
Sbjct:  5126 YQLMDGLNTFYQQSL-QQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGN 5302

Query:   178 GFSEAQMEKAGLLIRREDGSGYFDRFRNRVMFPIHDHHGAVVAFSGRALGSQQPKYMNSP 237
               +   +  AG+L+  + G  Y DRFR RVMFPI D  G V+ F GR LG+  PKY+NSP
Sbjct:  5303 PENRQSLIDAGMLVTNDQGRSY-DRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSP 5479

Query:   238 ETPLFHKSKLLYNFYKARLHIRKQERAVLFEGFADVYTAVSSDVKESIATMGTSLTDDHV 297
             ET +FHK + LY  Y+A+    +  R ++ EG+ DV       +  ++A++GTS T DH+
Sbjct:  5480 ETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHI 5659

Query:   298 KILRRNVEEIILCYDSDKAGYEATLKASELL---QKKGCKVRVAMIPDGLDPDDYIKKFG 354
             ++L R    +I CYD D+AG +A  +A E        G ++R   +PDG DPD  ++K G
Sbjct:  5660 QLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEG 5839

Query:   355 GEKFKNDIIDASVTVMAFKMQYFRKGKNLSDEGDRLAYIKDVLKEISTLSGSLEQEVYVK 414
              E F+  + + ++ + AF         +LS    R       L  IS + G   + +Y++
Sbjct:  5840 KEAFEARM-EQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLR-IYLR 6013

Query:   415 Q 415
             Q
Sbjct:  6014 Q 6016


Parameters:
  novalidctxok
  nonnegok
  gapall
  Q=12
  R=1
  cpus=1
  filter=seg
  matrix=blosum62
  W=3
  S2=41
  gapS2=68
  X=16
  gapX=38
  hitdist=40
  gi
  gapL=0.27
  gapK=0.047
  gapH=0.23

  ctxfactor=6.00
  E=10

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   blosum62        0.320   0.136   0.387    same    same    same
               Q=12,R=1        0.270   0.0470  0.230     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E    S W   T  X   E2     S2
   +0      0      603       603       10.  59 3  13 16  0.020   41
                                                    38  0.0     59


Statistics:

  Database:  /home/jes12/db/ecoli.nt
   Title:  ecoli.nt
   Posted:  3:16:20 PM EST Nov 18, 2001
   Created:  10:10:31 AM EST Nov 18, 2001
   Format:  XDF-1
   # of letters in database:  4,662,239
   # of sequences in database:  400
   # of database sequences satisfying E:  1
  No. of states in DFA:  538 (57 KB)
  Total size of DFA:  76 KB (1061 KB)
  Time to generate neighborhood:  0.00u 0.01s 0.01t  Elapsed: 00:00:00
  No. of threads or processors used:  1
  Search cpu time:  0.46u 0.01s 0.47t  Elapsed: 00:00:01
  Total cpu time:  0.46u 0.03s 0.49t  Elapsed: 00:00:03
  Start:  Sat Apr 20 18:21:51 2002   End:  Sat Apr 20 18:21:54 2002
BioPerl-1.007002/t/data/dnaEbsub_ecoli.wutblastx000444000766000024      2044713155576321 21574 0ustar00cjfieldsstaff000000000000TBLASTX 2.0MP-WashU [12-Feb-2001] [linux-i686 01:36:08 31-Jan-2001]

Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2000) http://blast.wustl.edu

Notice:  statistical significance is estimated under the assumption that the
equivalent of one entire reading frame of the query sequence and one entire
reading frame of the database code for protein and that significant alignments
will only involve coding reading frames.

Query=  gi|142864|gb|M10040.1|BACDNAE B.subtilis dnaE gene encoding DNA
    primase, complete cds
        (2001 letters)

  Translating both strands of query sequence in all 6 reading frames

Database:  ecoli.nt
           400 sequences; 4,662,239 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done

                                                                     Smallest
                                                                       Sum
                                                     Reading  High  Probability
Sequences producing High-scoring Segment Pairs:        Frame Score  P(N)      N

gi|1789441|gb|AE000388.1|AE000388 Escherichia coli K-1... +2   318  6.4e-70   5
gi|2367383|gb|AE000509.1|AE000509 Escherichia coli K-1... -3    59  0.9992    2



>gi|1789441|gb|AE000388.1|AE000388 Escherichia coli K-12 MG1655 section 278 of
            400 of the complete genome
        Length = 10,334

  Plus Strand HSPs:

 Score = 318 (148.6 bits), Expect = 6.4e-70, Sum P(5) = 6.4e-70
 Identities = 57/127 (44%), Positives = 81/127 (63%), Frame = +3 / +2

Query:   618 FDRFRNRVMFPIHDHHGAVVAFSGRALGSQQPKYMNSPETPLFHKSKLLYNFYKARLHIR 797
             +DRFR RVMFPI D  G V+ F GR LG+  PKY+NSPET +FHK + LY  Y+A+    
Sbjct:  5366 YDRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNA 5545

Query:   798 KQERAVLFEGFADVYTAVSSDVKESIATMGTSLTDDHVKILRRNVEEIILCYDSDKAGYE 977
             +  R ++ EG+ DV       +  ++A++GTS T DH+++L R    +I CYD D+AG +
Sbjct:  5546 EPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRD 5725

Query:   978 ATLKASE 998
             A  +A E
Sbjct:  5726 AAWRALE 5746

 Score = 247 (116.1 bits), Expect = 6.4e-70, Sum P(5) = 6.4e-70
 Identities = 44/98 (44%), Positives = 61/98 (62%), Frame = +3 / +2

Query:    21 MGNRIPDEIVDQVQKSADIVEVIGDYVQLKKQGRNYFGLCPFHGESTPSFSVSPDKQIFH 200
             M  RIP   ++ +    DIV++I   V+LKKQG+N+   CPFH E TPSF+V+ +KQ +H
Sbjct:  4778 MAGRIPRVFINDLLARTDIVDLIDARVKLKKQGKNFHACCPFHNEKTPSFTVNGEKQFYH 4957

Query:   201 CFGCGAGGNVFSFLRQMEGYSFAESVSHLADKYQIDFP 314
             CFGCGA GN   FL   +   F E+V  LA  + ++ P
Sbjct:  4958 CFGCGAHGNAIDFLMNYDKLEFVETVEELAAMHNLEVP 5071

 Score = 85 (41.8 bits), Expect = 6.4e-70, Sum P(5) = 6.4e-70
 Identities = 19/59 (32%), Positives = 28/59 (47%), Frame = +3 / +2

Query:   441 ALDYLLSRGFTKELINEFQIGYALDSWDFITKFLVKRGFSEAQMEKAGLLIRREDGSGY 617
             A  YL  RG + E+I  F IG+A   WD + K       +   +  AG+L+  + G  Y
Sbjct:  5192 ARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSY 5368

 Score = 65 (32.7 bits), Expect = 6.4e-70, Sum P(5) = 6.4e-70
 Identities = 12/28 (42%), Positives = 18/28 (64%), Frame = +3 / +2

Query:  1014 GCKVRVAMIPDGLDPDDYIKKFGGEKFK 1097
             G ++R   +PDG DPD  ++K G E F+
Sbjct:  5771 GRQLRFMFLPDGEDPDTLVRKEGKEAFE 5854

 Score = 48 (24.9 bits), Expect = 0.89, Sum P(4) = 0.59
 Identities = 15/49 (30%), Positives = 21/49 (42%), Frame = +3 / +2

Query:   639 VMFPIHDHHGAVVAFSGRALGSQQPKYMNSPETPLFHKSKLLYNFYKAR 785
             V F  HD    V A   R+  +  P Y     T LFH+ K    F++ +
Sbjct:  4046 VRFYAHDRGRPVQARRRRSQRAISPDYTIGWLTNLFHRRKWRCRFHRRK 4192

 Score = 46 (24.0 bits), Expect = 1.5, Sum P(4) = 0.78
 Identities = 8/17 (47%), Positives = 10/17 (58%), Frame = +3 / +2

Query:   150 GESTPSFSVSPDKQIFH 200
             G  TP +  SP+  IFH
Sbjct:  5447 GNDTPKYLNSPETDIFH 5497

 Score = 42 (22.1 bits), Expect = 6.4e-70, Sum P(5) = 6.4e-70
 Identities = 6/16 (37%), Positives = 10/16 (62%), Frame = +1 / +2

Query:  1129 WRSKCNISEKERTCPM 1176
             W S   + +K+R CP+
Sbjct:  7151 WNSTIVLKQKKRVCPI 7198

 Score = 42 (22.1 bits), Expect = 2.0e-42, Sum P(5) = 2.0e-42
 Identities = 6/18 (33%), Positives = 14/18 (77%), Frame = +3 / +2

Query:    21 MGNRIPDEIVDQVQKSAD 74
             +  R+PD++VD++++  D
Sbjct:   206 ISTRMPDDVVDKLKQLKD 259

  Minus Strand HSPs:

 Score = 102 (49.6 bits), Expect = 4.9e-08, Sum P(3) = 4.9e-08
 Identities = 32/83 (38%), Positives = 42/83 (50%), Frame = -3 / -3

Query:   319 SSGKSIWYLSAR*ETDSAKE*PSICLKKEKTLPPAPQPKQ*KICLSGDTENEGVLSP*KG 140
             S+G S   ++A   T S     S  ++K   LP AP PKQ   C S  T  +GV S   G
Sbjct:  5076 SNGTSRLCIAASSSTVSTNSSLS*FIRKSIALPCAPHPKQW*NCFSPLTVKDGVFSLWNG 4897

Query:   139 QSPK*FRPCFFN*T*SPMTSTIS 71
             Q    F PCFF+ T + + ST+S
Sbjct:  4896 QHAWKFLPCFFSFTRASIRSTMS 4828

 Score = 71 (35.4 bits), Expect = 4.9e-08, Sum P(3) = 4.9e-08
 Identities = 18/35 (51%), Positives = 20/35 (57%), Frame = -3 / -3

Query:   724 FIYLGCWLPRALPEKATTAP**SWIGNMTRFLKRS 620
             F YLG  LP   P K  T P  S +GN+TR  KRS
Sbjct:  5472 FRYLGVSLPSTRPPKPITRPRLSRMGNITRSRKRS 5368

 Score = 65 (32.7 bits), Expect = 0.0034, Sum P(3) = 0.0034
 Identities = 18/71 (25%), Positives = 34/71 (47%), Frame = -2 / -2

Query:   233 ENIAARSAAKAMKNLFVGRYGKRRCAFSMKRTESKVVSALLL*LNIITYDFNDICRLLHL 54
             + +A R+ +KA+  LF+   G+ R    ++ T    + ALL  L+      +D+     +
Sbjct:  4990 DRVAVRATSKAVVKLFLTVNGEGRGFLVVEWTTRVEILALLFQLHTGIDQIDDVSACQQI 4811

Query:    53 IHNFIWYPISH 21
             I+ + W   SH
Sbjct:  4810 INEYAWDSSSH 4778

 Score = 42 (22.1 bits), Expect = 4.9e-08, Sum P(3) = 4.9e-08
 Identities = 10/18 (55%), Positives = 12/18 (66%), Frame = -3 / -3

Query:  1093 NFSPPNFLM*SSGSNPSG 1040
             N S P+F    SGS+PSG
Sbjct:  5850 NASLPSFRTSVSGSSPSG 5797


>gi|2367383|gb|AE000509.1|AE000509 Escherichia coli K-12 MG1655 section 399 of
            400 of the complete genome
        Length = 10,589

  Minus Strand HSPs:

 Score = 59 (29.9 bits), Expect = 7.1, Sum P(2) = 1.00
 Identities = 15/40 (37%), Positives = 19/40 (47%), Frame = -3 / -3

Query:   706 WLPRALPEKATTAP**SWIGNMTRFLKRSKYPLPSSRLIR 587
             WL R     +T +P   WI  M   L  SK  LPS++  R
Sbjct:  4227 WLSRTTVGSSTVSPRTFWITRMKVKLSSSKVTLPSTKSTR 4108

 Score = 51 (26.3 bits), Expect = 7.1, Sum P(2) = 1.00
 Identities = 8/15 (53%), Positives = 10/15 (66%), Frame = -3 / -1

Query:   382 CASAIFCSPEDSGRA 338
             C S + C P+D GRA
Sbjct:  1097 CTSLMLCRPQDGGRA 1053


Parameters:
  novalidctxok
  nonnegok
  gapall
  Q=12
  R=1
  cpus=1
  filter=seg
  nogaps
  matrix=blosum62
  W=3
  S2=41
  gapS2=68
  X=16
  gapX=38
  hitdist=40
  gi
  gapL=0.27
  gapK=0.047
  gapH=0.23

  ctxfactor=36.0
  E=10

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +3      0   blosum62        0.318   0.135   0.401    0.324   0.139   0.405  
   +2      0   blosum62        0.318   0.135   0.401    0.365   0.163   0.618  
   +1      0   blosum62        0.318   0.135   0.401    0.356   0.155   0.528  
   -1      0   blosum62        0.318   0.135   0.401    0.350   0.155   0.543  
   -2      0   blosum62        0.318   0.135   0.401    0.350   0.155   0.505  
   -3      0   blosum62        0.318   0.135   0.401    0.358   0.157   0.543  

  Query
  Frame  MatID  Length  Eff.Length     E    S W   T  X   E2     S2
   +3      0      666       666       10.  54 3  13 16  0.021   41
   +2      0      666       666       10.  54 3  13 16  0.021   41
   +1      0      667       667       10.  54 3  13 16  0.021   41
   -1      0      667       667       10.  54 3  13 16  0.021   41
   -2      0      666       666       10.  54 3  13 16  0.021   41
   -3      0      666       666       10.  54 3  13 16  0.021   41


Statistics:

  Database:  /home/jes12/db/ecoli.nt
   Title:  ecoli.nt
   Posted:  3:16:20 PM EST Nov 18, 2001
   Created:  10:10:31 AM EST Nov 18, 2001
   Format:  XDF-1
   # of letters in database:  4,662,239
   # of sequences in database:  400
   # of database sequences satisfying E:  2
  No. of states in DFA:  598 (64 KB)
  Total size of DFA:  416 KB (1196 KB)
  Time to generate neighborhood:  0.02u 0.02s 0.04t  Elapsed: 00:00:00
  No. of threads or processors used:  1
  Search cpu time:  2.41u 0.01s 2.42t  Elapsed: 00:00:05
  Total cpu time:  2.44u 0.03s 2.47t  Elapsed: 00:00:07
  Start:  Sat Apr 20 18:19:43 2002   End:  Sat Apr 20 18:19:50 2002
BioPerl-1.007002/t/data/dq519393.gb000444000766000024       447413155576321 16315 0ustar00cjfieldsstaff000000000000LOCUS       DQ519393                 748 bp    RNA     linear   VRL 04-JUL-2006
DEFINITION  Hepatitis delta virus genotype I delta antigen gene, complete cds.
ACCESSION   DQ519393
VERSION     DQ519393.1  GI:109726906
KEYWORDS    .
SOURCE      Hepatitis delta virus
  ORGANISM  Hepatitis delta virus
            Viruses; Deltavirus.
REFERENCE   1  (bases 1 to 748)
  AUTHORS   Wang,T.-C. and Chao,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-APR-2006) Microbiology and Immunology, Chang Gung
            Unversity, 259, Wen-Hwa 1st Road, Kwei-Shan, Tao-Yuan 333, Taiwan
FEATURES             Location/Qualifiers
     source          1..748
                     /organism="Hepatitis delta virus"
                     /mol_type="genomic RNA"
                     /db_xref="taxon:12475"
                     /country="Taiwan"
                     /note="genotype: I"
     CDS             34..675
                     /codon_start=1
                     /product="delta antigen"
                     /protein_id="ABG45868.1"
                     /db_xref="GI:109726907"
                     /translation="MSQPDPRRPRKGREETLGKWIDARRRKEELERDLRKVNKTIKRL
                     EEDNPWLGNIRGIIRKDKDGDGAPPAKRARTDQMEVDSGPRKRKHPGGFTEQERRDHR
                     RRKALENKKKQLSSGGKSLSREEEEELRRLTEEDERRERRVAGPRVGDVNPLDGGPRG
                     APGGGFVPSMLGVPESPFTRRGDGLDTMGTQEFPWVSPQPPPPRLPLLECTPQ"
ORIGIN      
        1 aagagttctg aggaccgccg cccgcaatcg aggatgagcc agcccgatcc gaggagaccc
       61 cggaagggga gagaagagac actcggaaag tggatcgatg caagaagaag aaaggaggag
      121 ctcgagaggg acctccggaa ggtcaacaag actatcaaga gacttgagga ggacaacccc
      181 tggctgggaa acatccgagg aataataaga aaagacaagg acggggatgg agctcccccg
      241 gcgaagagag ccaggacgga tcagatggag gtcgactccg gacctaggaa gaggaaacac
      301 ccgggagggt tcaccgaaca ggagagacgg gatcaccgaa ggaggaaggc cctggagaac
      361 aagaagaagc aactctcctc gggagggaag agcctcagca gggaggaaga agaggaactt
      421 cgaaggttga ccgaggaaga cgagagaagg gaaagaagag tagccggccc gcgggttggg
      481 gatgtgaacc ccctcgacgg aggtccgagg ggagcgcccg gaggcgggtt cgtccccagc
      541 atgctaggag tcccggagtc tcccttcact cggagagggg acggcctgga caccatggga
      601 actcaggaat ttccgtgggt tagccctcag ccccctcctc cccgccttcc actcctcgag
      661 tgtacccccc aataaaggat cgagggttcc actcacggtt cgcgtccgtg tccttccttt
      721 cctcttcggg tcggcatggc ataagggc
//

BioPerl-1.007002/t/data/echofilter.wublastn000444000766000024      3376013155576321 20626 0ustar00cjfieldsstaff000000000000BLASTN 2.0MP-WashU [04-May-2006] [macosx-10.2-g4-ILP32F64 2006-05-07T21:56:24]

Copyright (C) 1996-2006 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2006) http://blast.wustl.edu

Notice:  this program and its default parameter settings are optimized to find
nearly identical sequences rapidly.  To identify weak protein similarities
encoded in nucleic acid, use BLASTX, TBLASTN or TBLASTX.

Query=  ref|NM_003201.1| Homo sapiens transcription factor A, mitochondrial
    (TFAM), mRNA
        (1936 letters)
>Unfiltered+1
CCTCGCTAGTGGCGGGCATGATAACACACGCCGGAGGGTCGCACGCGGGTTCCAGTTGTG
ATTGCTGGAGTTGTGTATTGCCAGGAGGCTCTCCGAGATTGGGGTCGGGTCACTGCCTCA
TCCACCGGAGCGATGGCGTTTCTCCGAAGCATGTGGGGCGTGCTGAGTGCCCTGGGAAGG
TCTGGAGCAGAGCTGTGCACCGGCTGTGGAAGTCGACTGCGCTCCCCCTTCAGTTTTGTG
TATTTACCGAGGTGGTTTTCATCTGTCTTGGCAAGTTGTCCAAAGAAACCTGTAAGTTCT
TACCTTCGATTTTCTAAAGAACAACTACCCATATTTAAAGCTCAGAACCCAGATGCAAAA
ACTACAGAACTAATTAGAAGAATTGCCCAGCGTTGGAGGGAACTTCCTGATTCAAAGAAA
AAAATATATCAAGATGCTTATAGGGCGGAGTGGCAGGTATATAAAGAAGAGATAAGCAGA
TTTAAAGAACAGCTAACTCCAAGTCAGATTATGTCTTTGGAAAAAGAAATCATGGACAAA
CATTTAAAAAGGAAAGCTATGACAAAAAAAAAAGAGTTAACACTGCTTGGAAAACCAAAA
AGACCTCGTTCAGCTTATAACGTTTATGTAGCTGAAAGATTCCAAGAAGCTAAGGGTGAT
TCACCGCAGGAAAAGCTGAAGACTGTAAAGGAAAACTGGAAAAATCTGTCTGACTCTGAA
AAGGAATTATATATTCAGCATGCTAAAGAGGACGAAACTCGTTATCATAATGAAATGAAG
TCTTGGGAAGAACAAATGATTGAAGTTGGACGAAAGGATCTTCTACGTCGCACAATAAAG
AAACAACGAAAATATGGTGCTGAGGAGTGTTAAAAGTAGAAGATTGAGATGTGTTCACAA
TGGATAGGCACAGGAAACCAGTTAGGTCTCAATACCTGAAGCTATCGTAAAATTAAGAAA
GGATAAAGTTGGTAAACCTTTTATATTTAGTATCTTTTTATTCAGCTCATGGACTTCTGC
CAGCATAATACTTGCTTTGGAAAACCCAGATAAAGGTTCATGCAAACTTTATTTTGTGTT
TAGGAACTACTGAGGATCAGAGTAATCCAAGCAAATGTGAATCATTTTACCTTTGACAAA
GGTAAATCAGACTATGAAGTTTTTTTTATACAGGATGATGACTATGGAAAGAGTACTCTT
GTTTCCTTATATTATGGAGGCAGGAGTTTCGTTTTCAAAATTGTTACAAATTGTAGAAGC
CACGGTGTTCTGTGATATAAGTGTGTGTTTTTCATAAAGCAGGCAGAACTCATCTAGGTA
AATTACAGTTCCTAGGTATAATTCACATTGTATTCAGAGTTGATGGTTGTACATATAAGT
GATTGCTGGTTTTAGTTGCAACTTTGTATAAAAGGGACTGAGAAATTTATAAACTTTTTT
CTTACTGTCTTTTTTCTAAAGTAAAAACAAAGAAATTATGTGCCAGATTTATGCATATTA
TTTTATGTTGCATAGAATAAAATTTTTAATCTTTAATTTTACATTTCCTAAATATATTTT
AAGACGAAACATTTGTTCTATAGCTTTTCCCTTTTTTTAAGTAAGGAATTTTATTTTTTT
CTGAATTATTTTCTCTCGTGAGTATATTGATCCAGAAAGAAAACTTGTATTATGTGTGTT
TTAAAATGAGAAATCTAAAAAACGAAAAGTCTCCAAAGTCTCTGGAATTTGAAACACTTT
GCATAACGTATAAAAGCCTGTTTAAGAGACAGCCAACTATGGCCTGTGGATCAAATCCAG
CCTGCTGCCTGCTTTTTATGGCCTGTGAGCTAGGAATTGTGTTTATAATTTTAAATGTTT
TTTTTTAAAGACTTTTATGATACTTGAAAATTAACATGAATATTTAGTGTTCATAAATAA
AGTTTGTTGAAACACA
>Unfiltered-1
TGTGTTTCAACAAACTTTATTTATGAACACTAAATATTCATGTTAATTTTCAAGTATCAT
AAAAGTCTTTAAAAAAAAACATTTAAAATTATAAACACAATTCCTAGCTCACAGGCCATA
AAAAGCAGGCAGCAGGCTGGATTTGATCCACAGGCCATAGTTGGCTGTCTCTTAAACAGG
CTTTTATACGTTATGCAAAGTGTTTCAAATTCCAGAGACTTTGGAGACTTTTCGTTTTTT
AGATTTCTCATTTTAAAACACACATAATACAAGTTTTCTTTCTGGATCAATATACTCACG
AGAGAAAATAATTCAGAAAAAAATAAAATTCCTTACTTAAAAAAAGGGAAAAGCTATAGA
ACAAATGTTTCGTCTTAAAATATATTTAGGAAATGTAAAATTAAAGATTAAAAATTTTAT
TCTATGCAACATAAAATAATATGCATAAATCTGGCACATAATTTCTTTGTTTTTACTTTA
GAAAAAAGACAGTAAGAAAAAAGTTTATAAATTTCTCAGTCCCTTTTATACAAAGTTGCA
ACTAAAACCAGCAATCACTTATATGTACAACCATCAACTCTGAATACAATGTGAATTATA
CCTAGGAACTGTAATTTACCTAGATGAGTTCTGCCTGCTTTATGAAAAACACACACTTAT
ATCACAGAACACCGTGGCTTCTACAATTTGTAACAATTTTGAAAACGAAACTCCTGCCTC
CATAATATAAGGAAACAAGAGTACTCTTTCCATAGTCATCATCCTGTATAAAAAAAACTT
CATAGTCTGATTTACCTTTGTCAAAGGTAAAATGATTCACATTTGCTTGGATTACTCTGA
TCCTCAGTAGTTCCTAAACACAAAATAAAGTTTGCATGAACCTTTATCTGGGTTTTCCAA
AGCAAGTATTATGCTGGCAGAAGTCCATGAGCTGAATAAAAAGATACTAAATATAAAAGG
TTTACCAACTTTATCCTTTCTTAATTTTACGATAGCTTCAGGTATTGAGACCTAACTGGT
TTCCTGTGCCTATCCATTGTGAACACATCTCAATCTTCTACTTTTAACACTCCTCAGCAC
CATATTTTCGTTGTTTCTTTATTGTGCGACGTAGAAGATCCTTTCGTCCAACTTCAATCA
TTTGTTCTTCCCAAGACTTCATTTCATTATGATAACGAGTTTCGTCCTCTTTAGCATGCT
GAATATATAATTCCTTTTCAGAGTCAGACAGATTTTTCCAGTTTTCCTTTACAGTCTTCA
GCTTTTCCTGCGGTGAATCACCCTTAGCTTCTTGGAATCTTTCAGCTACATAAACGTTAT
AAGCTGAACGAGGTCTTTTTGGTTTTCCAAGCAGTGTTAACTCTTTTTTTTTTGTCATAG
CTTTCCTTTTTAAATGTTTGTCCATGATTTCTTTTTCCAAAGACATAATCTGACTTGGAG
TTAGCTGTTCTTTAAATCTGCTTATCTCTTCTTTATATACCTGCCACTCCGCCCTATAAG
CATCTTGATATATTTTTTTCTTTGAATCAGGAAGTTCCCTCCAACGCTGGGCAATTCTTC
TAATTAGTTCTGTAGTTTTTGCATCTGGGTTCTGAGCTTTAAATATGGGTAGTTGTTCTT
TAGAAAATCGAAGGTAAGAACTTACAGGTTTCTTTGGACAACTTGCCAAGACAGATGAAA
ACCACCTCGGTAAATACACAAAACTGAAGGGGGAGCGCAGTCGACTTCCACAGCCGGTGC
ACAGCTCTGCTCCAGACCTTCCCAGGGCACTCAGCACGCCCCACATGCTTCGGAGAAACG
CCATCGCTCCGGTGGATGAGGCAGTGACCCGACCCCAATCTCGGAGAGCCTCCTGGCAAT
ACACAACTCCAGCAATCACAACTGGAACCCGCGTGCGACCCTCCGGCGTGTGTTATCATG
CCCGCCACTAGCGAGG

Database:  NM_003201.fa
           1 sequences; 1936 total letters.
Searching done

                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

ref|NM_003201.1| Homo sapiens transcription factor A, mit...  9680  0.        1


>ref|NM_003201.1| Homo sapiens transcription factor A, mitochondrial (TFAM),
            mRNA
        Length = 1936

  Plus Strand HSPs:

 Score = 9680 (1458.4 bits), Expect = 0., P = 0.
 Identities = 1936/1936 (100%), Positives = 1936/1936 (100%), Strand = Plus / Plus

Query:     1 CCTCGCTAGTGGCGGGCATGATAACACACGCCGGAGGGTCGCACGCGGGTTCCAGTTGTG 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 CCTCGCTAGTGGCGGGCATGATAACACACGCCGGAGGGTCGCACGCGGGTTCCAGTTGTG 60

Query:    61 ATTGCTGGAGTTGTGTATTGCCAGGAGGCTCTCCGAGATTGGGGTCGGGTCACTGCCTCA 120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 ATTGCTGGAGTTGTGTATTGCCAGGAGGCTCTCCGAGATTGGGGTCGGGTCACTGCCTCA 120

Query:   121 TCCACCGGAGCGATGGCGTTTCTCCGAAGCATGTGGGGCGTGCTGAGTGCCCTGGGAAGG 180
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 TCCACCGGAGCGATGGCGTTTCTCCGAAGCATGTGGGGCGTGCTGAGTGCCCTGGGAAGG 180

Query:   181 TCTGGAGCAGAGCTGTGCACCGGCTGTGGAAGTCGACTGCGCTCCCCCTTCAGTTTTGTG 240
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 TCTGGAGCAGAGCTGTGCACCGGCTGTGGAAGTCGACTGCGCTCCCCCTTCAGTTTTGTG 240

Query:   241 TATTTACCGAGGTGGTTTTCATCTGTCTTGGCAAGTTGTCCAAAGAAACCTGTAAGTTCT 300
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 TATTTACCGAGGTGGTTTTCATCTGTCTTGGCAAGTTGTCCAAAGAAACCTGTAAGTTCT 300

Query:   301 TACCTTCGATTTTCTAAAGAACAACTACCCATATTTAAAGCTCAGAACCCAGATGCAAAA 360
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 TACCTTCGATTTTCTAAAGAACAACTACCCATATTTAAAGCTCAGAACCCAGATGCAAAA 360

Query:   361 ACTACAGAACTAATTAGAAGAATTGCCCAGCGTTGGAGGGAACTTCCTGATTCAAAGAAA 420
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 ACTACAGAACTAATTAGAAGAATTGCCCAGCGTTGGAGGGAACTTCCTGATTCAAAGAAA 420

Query:   421 AAAATATATCAAGATGCTTATAGGGCGGAGTGGCAGGTATATAAAGAAGAGATAAGCAGA 480
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 AAAATATATCAAGATGCTTATAGGGCGGAGTGGCAGGTATATAAAGAAGAGATAAGCAGA 480

Query:   481 TTTAAAGAACAGCTAACTCCAAGTCAGATTATGTCTTTGGAAAAAGAAATCATGGACAAA 540
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 TTTAAAGAACAGCTAACTCCAAGTCAGATTATGTCTTTGGAAAAAGAAATCATGGACAAA 540

Query:   541 CATTTAAAAAGGAAAGCTATGACAAAAAAAAAAGAGTTAACACTGCTTGGAAAACCAAAA 600
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   541 CATTTAAAAAGGAAAGCTATGACAAAAAAAAAAGAGTTAACACTGCTTGGAAAACCAAAA 600

Query:   601 AGACCTCGTTCAGCTTATAACGTTTATGTAGCTGAAAGATTCCAAGAAGCTAAGGGTGAT 660
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   601 AGACCTCGTTCAGCTTATAACGTTTATGTAGCTGAAAGATTCCAAGAAGCTAAGGGTGAT 660

Query:   661 TCACCGCAGGAAAAGCTGAAGACTGTAAAGGAAAACTGGAAAAATCTGTCTGACTCTGAA 720
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   661 TCACCGCAGGAAAAGCTGAAGACTGTAAAGGAAAACTGGAAAAATCTGTCTGACTCTGAA 720

Query:   721 AAGGAATTATATATTCAGCATGCTAAAGAGGACGAAACTCGTTATCATAATGAAATGAAG 780
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   721 AAGGAATTATATATTCAGCATGCTAAAGAGGACGAAACTCGTTATCATAATGAAATGAAG 780

Query:   781 TCTTGGGAAGAACAAATGATTGAAGTTGGACGAAAGGATCTTCTACGTCGCACAATAAAG 840
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   781 TCTTGGGAAGAACAAATGATTGAAGTTGGACGAAAGGATCTTCTACGTCGCACAATAAAG 840

Query:   841 AAACAACGAAAATATGGTGCTGAGGAGTGTTAAAAGTAGAAGATTGAGATGTGTTCACAA 900
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   841 AAACAACGAAAATATGGTGCTGAGGAGTGTTAAAAGTAGAAGATTGAGATGTGTTCACAA 900

Query:   901 TGGATAGGCACAGGAAACCAGTTAGGTCTCAATACCTGAAGCTATCGTAAAATTAAGAAA 960
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   901 TGGATAGGCACAGGAAACCAGTTAGGTCTCAATACCTGAAGCTATCGTAAAATTAAGAAA 960

Query:   961 GGATAAAGTTGGTAAACCTTTTATATTTAGTATCTTTTTATTCAGCTCATGGACTTCTGC 1020
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   961 GGATAAAGTTGGTAAACCTTTTATATTTAGTATCTTTTTATTCAGCTCATGGACTTCTGC 1020

Query:  1021 CAGCATAATACTTGCTTTGGAAAACCCAGATAAAGGTTCATGCAAACTTTATTTTGTGTT 1080
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1021 CAGCATAATACTTGCTTTGGAAAACCCAGATAAAGGTTCATGCAAACTTTATTTTGTGTT 1080

Query:  1081 TAGGAACTACTGAGGATCAGAGTAATCCAAGCAAATGTGAATCATTTTACCTTTGACAAA 1140
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1081 TAGGAACTACTGAGGATCAGAGTAATCCAAGCAAATGTGAATCATTTTACCTTTGACAAA 1140

Query:  1141 GGTAAATCAGACTATGAAGTTTTTTTTATACAGGATGATGACTATGGAAAGAGTACTCTT 1200
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1141 GGTAAATCAGACTATGAAGTTTTTTTTATACAGGATGATGACTATGGAAAGAGTACTCTT 1200

Query:  1201 GTTTCCTTATATTATGGAGGCAGGAGTTTCGTTTTCAAAATTGTTACAAATTGTAGAAGC 1260
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1201 GTTTCCTTATATTATGGAGGCAGGAGTTTCGTTTTCAAAATTGTTACAAATTGTAGAAGC 1260

Query:  1261 CACGGTGTTCTGTGATATAAGTGTGTGTTTTTCATAAAGCAGGCAGAACTCATCTAGGTA 1320
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1261 CACGGTGTTCTGTGATATAAGTGTGTGTTTTTCATAAAGCAGGCAGAACTCATCTAGGTA 1320

Query:  1321 AATTACAGTTCCTAGGTATAATTCACATTGTATTCAGAGTTGATGGTTGTACATATAAGT 1380
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1321 AATTACAGTTCCTAGGTATAATTCACATTGTATTCAGAGTTGATGGTTGTACATATAAGT 1380

Query:  1381 GATTGCTGGTTTTAGTTGCAACTTTGTATAAAAGGGACTGAGAAATTTATAAACTTTTTT 1440
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1381 GATTGCTGGTTTTAGTTGCAACTTTGTATAAAAGGGACTGAGAAATTTATAAACTTTTTT 1440

Query:  1441 CTTACTGTCTTTTTTCTAAAGTAAAAACAAAGAAATTATGTGCCAGATTTATGCATATTA 1500
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1441 CTTACTGTCTTTTTTCTAAAGTAAAAACAAAGAAATTATGTGCCAGATTTATGCATATTA 1500

Query:  1501 TTTTATGTTGCATAGAATAAAATTTTTAATCTTTAATTTTACATTTCCTAAATATATTTT 1560
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1501 TTTTATGTTGCATAGAATAAAATTTTTAATCTTTAATTTTACATTTCCTAAATATATTTT 1560

Query:  1561 AAGACGAAACATTTGTTCTATAGCTTTTCCCTTTTTTTAAGTAAGGAATTTTATTTTTTT 1620
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1561 AAGACGAAACATTTGTTCTATAGCTTTTCCCTTTTTTTAAGTAAGGAATTTTATTTTTTT 1620

Query:  1621 CTGAATTATTTTCTCTCGTGAGTATATTGATCCAGAAAGAAAACTTGTATTATGTGTGTT 1680
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1621 CTGAATTATTTTCTCTCGTGAGTATATTGATCCAGAAAGAAAACTTGTATTATGTGTGTT 1680

Query:  1681 TTAAAATGAGAAATCTAAAAAACGAAAAGTCTCCAAAGTCTCTGGAATTTGAAACACTTT 1740
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1681 TTAAAATGAGAAATCTAAAAAACGAAAAGTCTCCAAAGTCTCTGGAATTTGAAACACTTT 1740

Query:  1741 GCATAACGTATAAAAGCCTGTTTAAGAGACAGCCAACTATGGCCTGTGGATCAAATCCAG 1800
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1741 GCATAACGTATAAAAGCCTGTTTAAGAGACAGCCAACTATGGCCTGTGGATCAAATCCAG 1800

Query:  1801 CCTGCTGCCTGCTTTTTATGGCCTGTGAGCTAGGAATTGTGTTTATAATTTTAAATGTTT 1860
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1801 CCTGCTGCCTGCTTTTTATGGCCTGTGAGCTAGGAATTGTGTTTATAATTTTAAATGTTT 1860

Query:  1861 TTTTTTAAAGACTTTTATGATACTTGAAAATTAACATGAATATTTAGTGTTCATAAATAA 1920
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1861 TTTTTTAAAGACTTTTATGATACTTGAAAATTAACATGAATATTTAGTGTTCATAAATAA 1920

Query:  1921 AGTTTGTTGAAACACA 1936
             ||||||||||||||||
Sbjct:  1921 AGTTTGTTGAAACACA 1936


Parameters:
  echofilter

  ctxfactor=2.00
  E=10

  Query                        -----  As Used  -----    -----  Computed  ----
  Strand MatID Matrix name     Lambda    K       H      Lambda    K       H
   +1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a
   -1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a

  Query
  Strand MatID  Length  Eff.Length     E    S  W   T   X   E2     S2
   +1      0     1936      1936       9.2  89 11 n/a  73  0.042   83
                                                     134  2.1     89
   -1      0     1936      1936       9.2  89 11 n/a  73  0.042   83
                                                     134  2.1     89


Statistics:

  Database:  NM_003201.fa
   Title:  NM_003201.fa
   Posted:  7:39:50 PM CET Nov 2, 2007
   Created:  7:39:50 PM CET Nov 2, 2007
   Format:  XDF-1
   # of letters in database:  1936
   # of sequences in database:  1
   # of database sequences satisfying E:  1
  No. of states in DFA:  257 (257 KB)
  Total size of DFA:  344 KB (2092 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  1
  Search cpu time:  0.00u 0.01s 0.01t   Elapsed:  00:00:00
  Total cpu time:  0.00u 0.01s 0.01t   Elapsed:  00:00:00
  Start:  Fri Nov  2 19:42:26 2007   End:  Fri Nov  2 19:42:26 2007
BioPerl-1.007002/t/data/ecoli-trna-qrna.out000444000766000024      6306513155576321 20447 0ustar00cjfieldsstaff000000000000#---------------------------------------------------------------------------------
#      qrna 1.2b (Tue Dec 18 15:04:38 CST 2001) using squid 1.5m (Sept 1997)
#---------------------------------------------------------------------------------
#      PAM model =  BLOSUM62 scaled by 1.000
#---------------------------------------------------------------------------------
#      RNA model =  /mix_tied_linux.cfg
#---------------------------------------------------------------------------------
#      seq file  =  ecoli-trna.blast.q
#                   #seqs: 94 (max_len = 78)
#---------------------------------------------------------------------------------
#      full length version:  -- length range = [0,1000]
#---------------------------------------------------------------------------------
# 1  [+ strand] 
>DA0780-1- (76)
>ECOLI-225501- (76)

length alignment: 76 (id=77.63)
posX: 0-75 [0-72](73) -- (0.18 0.30 0.36 0.16) 
posY: 0-75 [0-71](72) -- (0.17 0.29 0.33 0.21) 
 21.414226 -10.515196 16.075247
 19.988807 -3.972533 12.698167
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 75
COD  ends = 74 0
RNA  ends = 0 12
              OTH =       20.871             COD =       -4.957             RNA =       15.208 
   logoddspostOTH =        0.000  logoddspostCOD =      -25.828  logoddspostRNA =       -5.663 

# 2  [+ strand] 
>DA0780-1- (76)
>ECOLI-4034592- (76)

length alignment: 76 (id=77.63)
posX: 0-75 [0-72](73) -- (0.18 0.30 0.36 0.16) 
posY: 0-75 [0-71](72) -- (0.17 0.29 0.33 0.21) 
 21.414226 -10.515196 16.075247
 19.988807 -3.972533 12.698167
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 75
COD  ends = 74 0
RNA  ends = 0 12
              OTH =       20.871             COD =       -4.957             RNA =       15.208 
   logoddspostOTH =        0.000  logoddspostCOD =      -25.828  logoddspostRNA =       -5.663 

# 3  [+ strand] 
>DA0780-1- (70)
>ECOLI-3979754- (70)

length alignment: 70 (id=72.86)
posX: 0-69 [0-68](69) -- (0.17 0.29 0.38 0.16) 
posY: 0-69 [0-69](70) -- (0.16 0.30 0.36 0.19) 
 21.384909 12.463364 22.249356
 21.249381 17.921616 22.037246
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 69
COD  ends = 68 1
RNA  ends = 3 69
              OTH =       21.319             COD =       16.954             RNA =       22.147 
   logoddspostOTH =        0.000  logoddspostCOD =       -4.365  logoddspostRNA =        0.828 

# 4  [+ strand] 
>DA0780-8- (56)
>ECOLI-779995- (56)

length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18) 
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18) 
 14.761275 -0.369781 17.076846
 14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 55 0
COD  ends = 54 0
RNA  ends = 35 19
              OTH =       14.801             COD =        9.226             RNA =       20.928 
   logoddspostOTH =        0.000  logoddspostCOD =       -5.574  logoddspostRNA =        6.127 

# 5  [+ strand] 
>DA0780-8- (56)
>ECOLI-780298- (56)

length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18) 
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18) 
 14.761275 -0.369781 17.076846
 14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 55 0
COD  ends = 54 0
RNA  ends = 35 19
              OTH =       14.801             COD =        9.226             RNA =       20.928 
   logoddspostOTH =        0.000  logoddspostCOD =       -5.574  logoddspostRNA =        6.127 

# 6  [+ strand] 
>DA0780-8- (56)
>ECOLI-2518730- (56)

length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18) 
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18) 
 14.761275 -0.369781 17.076846
 14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 55 0
COD  ends = 54 0
RNA  ends = 35 19
              OTH =       14.801             COD =        9.226             RNA =       20.928 
   logoddspostOTH =        0.000  logoddspostCOD =       -5.574  logoddspostRNA =        6.127 

# 7  [+ strand] 
>DA0780-8- (56)
>ECOLI-2518850- (56)

length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18) 
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18) 
 14.761275 -0.369781 17.076846
 14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 55 0
COD  ends = 54 0
RNA  ends = 35 19
              OTH =       14.801             COD =        9.226             RNA =       20.928 
   logoddspostOTH =        0.000  logoddspostCOD =       -5.574  logoddspostRNA =        6.127 

# 8  [+ strand] 
>DA0780-8- (56)
>ECOLI-2518972- (56)

length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18) 
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18) 
 14.761275 -0.369781 17.076846
 14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 55 0
COD  ends = 54 0
RNA  ends = 35 19
              OTH =       14.801             COD =        9.226             RNA =       20.928 
   logoddspostOTH =        0.000  logoddspostCOD =       -5.574  logoddspostRNA =        6.127 

# 9  [+ strand] 
>DA0780-2- (73)
>ECOLI-2284230- (73)

length alignment: 73 (id=64.38)
posX: 0-72 [0-71](72) -- (0.18 0.31 0.35 0.17) 
posY: 0-72 [0-72](73) -- (0.15 0.27 0.38 0.19) 
 13.918545 -8.608490 24.007519
 15.073192 7.016852 12.344431
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 72 0
COD  ends = 72 0
RNA  ends = 0 70
              OTH =       14.608             COD =        6.017             RNA =       23.008 
   logoddspostOTH =        0.000  logoddspostCOD =       -8.592  logoddspostRNA =        8.400 

# 10  [+ strand] 
>DA0780-7- (59)
>ECOLI-2945191- (59)

length alignment: 59 (id=67.80)
posX: 0-58 [0-55](56) -- (0.20 0.27 0.36 0.18) 
posY: 0-58 [0-56](57) -- (0.19 0.28 0.32 0.21) 
 7.994668 -17.443195 7.730549
 8.785962 -9.672509 13.155362
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 58 0
COD  ends = 58 1
RNA  ends = 39 21
              OTH =        8.444             COD =      -10.666             RNA =       12.189 
   logoddspostOTH =        0.000  logoddspostCOD =      -19.110  logoddspostRNA =        3.745 

# 11  [+ strand] 
>DA0780-7- (59)
>ECOLI-2945301- (59)

length alignment: 59 (id=67.80)
posX: 0-58 [0-55](56) -- (0.20 0.27 0.36 0.18) 
posY: 0-58 [0-56](57) -- (0.19 0.28 0.32 0.21) 
 7.994668 -17.443195 7.730549
 8.785962 -9.672509 13.155362
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 58 0
COD  ends = 58 1
RNA  ends = 39 21
              OTH =        8.444             COD =      -10.666             RNA =       12.189 
   logoddspostOTH =        0.000  logoddspostCOD =      -19.110  logoddspostRNA =        3.745 

# 12  [+ strand] 
>DA0780-7- (59)
>ECOLI-2945411- (59)

length alignment: 59 (id=67.80)
posX: 0-58 [0-55](56) -- (0.20 0.27 0.36 0.18) 
posY: 0-58 [0-56](57) -- (0.19 0.28 0.32 0.21) 
 7.994668 -17.443195 7.730549
 8.785962 -9.672509 13.155362
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 58 0
COD  ends = 58 1
RNA  ends = 39 21
              OTH =        8.444             COD =      -10.666             RNA =       12.189 
   logoddspostOTH =        0.000  logoddspostCOD =      -19.110  logoddspostRNA =        3.745 

# 13  [+ strand] 
>DA0780-1- (76)
>ECOLI-3424373- (76)

length alignment: 76 (id=77.63)
posX: 0-75 [0-72](73) -- (0.16 0.36 0.30 0.18) 
posY: 0-75 [0-71](72) -- (0.21 0.33 0.29 0.17) 
 20.682006 -9.755632 13.248665
 21.241284 -22.237923 16.258281
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 75 0
COD  ends = 1 68
RNA  ends = 75 63
              OTH =       20.989             COD =      -10.755             RNA =       15.427 
   logoddspostOTH =        0.000  logoddspostCOD =      -31.744  logoddspostRNA =       -5.561 

# 14  [+ strand] 
>DA0780-6- (71)
>ECOLI-2815582- (71)

length alignment: 71 (id=71.83)
posX: 0-70 [0-67](68) -- (0.16 0.34 0.31 0.19) 
posY: 0-70 [0-68](69) -- (0.19 0.32 0.28 0.22) 
 16.431838 -14.269383 12.463979
 16.326307 -7.331733 13.720289
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 70
COD  ends = 70 1
RNA  ends = 24 8
              OTH =       16.380             COD =       -8.320             RNA =       13.225 
   logoddspostOTH =        0.000  logoddspostCOD =      -24.700  logoddspostRNA =       -3.155 

# 15  [+ strand] 
>DA0780-6- (71)
>ECOLI-2815857- (71)

length alignment: 71 (id=71.83)
posX: 0-70 [0-67](68) -- (0.16 0.34 0.31 0.19) 
posY: 0-70 [0-68](69) -- (0.19 0.32 0.28 0.22) 
 16.431838 -14.269383 12.463979
 16.326307 -7.331733 13.720289
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 70
COD  ends = 70 1
RNA  ends = 24 8
              OTH =       16.380             COD =       -8.320             RNA =       13.225 
   logoddspostOTH =        0.000  logoddspostCOD =      -24.700  logoddspostRNA =       -3.155 

# 16  [+ strand] 
>DA0780-6- (71)
>ECOLI-2815996- (71)

length alignment: 71 (id=71.83)
posX: 0-70 [0-67](68) -- (0.16 0.34 0.31 0.19) 
posY: 0-70 [0-68](69) -- (0.19 0.32 0.28 0.22) 
 16.431838 -14.269383 12.463979
 16.326307 -7.331733 13.720289
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 70
COD  ends = 70 1
RNA  ends = 24 8
              OTH =       16.380             COD =       -8.320             RNA =       13.225 
   logoddspostOTH =        0.000  logoddspostCOD =      -24.700  logoddspostRNA =       -3.155 

# 17  [+ strand] 
>DA0780-6- (71)
>ECOLI-2816271- (71)

length alignment: 71 (id=71.83)
posX: 0-70 [0-67](68) -- (0.16 0.34 0.31 0.19) 
posY: 0-70 [0-68](69) -- (0.19 0.32 0.28 0.22) 
 16.431838 -14.269383 12.463979
 16.326307 -7.331733 13.720289
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 70
COD  ends = 70 1
RNA  ends = 24 8
              OTH =       16.380             COD =       -8.320             RNA =       13.225 
   logoddspostOTH =        0.000  logoddspostCOD =      -24.700  logoddspostRNA =       -3.155 

# 18  [+ strand] 
>DA0780-1- (76)
>ECOLI-2515836- (76)

length alignment: 76 (id=71.05)
posX: 0-75 [0-72](73) -- (0.16 0.36 0.30 0.18) 
posY: 0-75 [0-71](72) -- (0.21 0.33 0.26 0.19) 
 14.736984 -14.375325 8.884532
 14.851236 -24.156886 9.868232
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 75 0
COD  ends = 1 75
RNA  ends = 75 63
              OTH =       14.795             COD =      -15.374             RNA =        9.459 
   logoddspostOTH =        0.000  logoddspostCOD =      -30.169  logoddspostRNA =       -5.337 

# 19  [+ strand] 
>DA0780-1- (76)
>ECOLI-2515951- (76)

length alignment: 76 (id=71.05)
posX: 0-75 [0-72](73) -- (0.16 0.36 0.30 0.18) 
posY: 0-75 [0-71](72) -- (0.21 0.33 0.26 0.19) 
 14.736984 -14.375325 8.884532
 14.851236 -24.156886 9.868232
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 75 0
COD  ends = 1 75
RNA  ends = 75 63
              OTH =       14.795             COD =      -15.374             RNA =        9.459 
   logoddspostOTH =        0.000  logoddspostCOD =      -30.169  logoddspostRNA =       -5.337 

# 20  [+ strand] 
>DA0780-6- (52)
>ECOLI-2155594- (52)

length alignment: 52 (id=71.15)
posX: 0-51 [0-48](49) -- (0.16 0.41 0.27 0.16) 
posY: 0-51 [0-48](49) -- (0.18 0.41 0.29 0.12) 
 5.862400 -19.930995 -1.194701
 7.783836 -15.355771 0.726735
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 51 0
COD  ends = 50 0
RNA  ends = 52 52
              OTH =        7.122             COD =      -16.296             RNA =        0.065 
   logoddspostOTH =        0.000  logoddspostCOD =      -23.418  logoddspostRNA =       -7.057 

# 21  [+ strand] 
>DA0780-7- (59)
>ECOLI-3315645- (59)

length alignment: 59 (id=66.10)
posX: 0-58 [0-55](56) -- (0.18 0.36 0.27 0.20) 
posY: 0-58 [0-56](57) -- (0.21 0.30 0.28 0.21) 
 7.886726 -12.920042 12.597060
 6.999592 -16.997763 6.986972
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 58
COD  ends = 0 58
RNA  ends = 20 36
              OTH =        7.510             COD =      -13.837             RNA =       11.626 
   logoddspostOTH =        0.000  logoddspostCOD =      -21.347  logoddspostRNA =        4.116 

# 22  [+ strand] 
>DA0940-1- (77)
>ECOLI-225500- (77)

length alignment: 77 (id=75.32)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.16 0.31 0.33 0.20) 
 24.181055 -0.353323 26.401988
 23.109013 11.590026 23.929123
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 76
COD  ends = 76 0
RNA  ends = 0 73
              OTH =       23.742             COD =       10.590             RNA =       25.641 
   logoddspostOTH =        0.000  logoddspostCOD =      -13.152  logoddspostRNA =        1.899 

# 23  [+ strand] 
>DA0940-1- (77)
>ECOLI-4034591- (77)

length alignment: 77 (id=75.32)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.16 0.31 0.33 0.20) 
 24.181055 -0.353323 26.401988
 23.109013 11.590026 23.929123
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 76
COD  ends = 76 0
RNA  ends = 0 73
              OTH =       23.742             COD =       10.590             RNA =       25.641 
   logoddspostOTH =        0.000  logoddspostCOD =      -13.152  logoddspostRNA =        1.899 

# 24  [+ strand] 
>DA0940-1- (77)
>ECOLI-779777- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28) 
 19.326669 -6.735706 19.727199
 19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 76 0
COD  ends = 74 1
RNA  ends = 0 73
              OTH =       19.344             COD =       -2.948             RNA =       18.779 
   logoddspostOTH =        0.000  logoddspostCOD =      -22.291  logoddspostRNA =       -0.564 

# 25  [+ strand] 
>DA0940-1- (77)
>ECOLI-780066- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28) 
 19.326669 -6.735706 19.727199
 19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 76 0
COD  ends = 74 1
RNA  ends = 0 73
              OTH =       19.344             COD =       -2.948             RNA =       18.779 
   logoddspostOTH =        0.000  logoddspostCOD =      -22.291  logoddspostRNA =       -0.564 

# 26  [+ strand] 
>DA0940-1- (77)
>ECOLI-780370- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28) 
 19.326669 -6.735706 19.727199
 19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 76 0
COD  ends = 74 1
RNA  ends = 0 73
              OTH =       19.344             COD =       -2.948             RNA =       18.779 
   logoddspostOTH =        0.000  logoddspostCOD =      -22.291  logoddspostRNA =       -0.564 

# 27  [+ strand] 
>DA0940-1- (77)
>ECOLI-780592- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28) 
 19.326669 -6.735706 19.727199
 19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 76 0
COD  ends = 74 1
RNA  ends = 0 73
              OTH =       19.344             COD =       -2.948             RNA =       18.779 
   logoddspostOTH =        0.000  logoddspostCOD =      -22.291  logoddspostRNA =       -0.564 

# 28  [+ strand] 
>DA0940-1- (77)
>ECOLI-780800- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28) 
 19.326669 -6.735706 19.727199
 19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 76 0
COD  ends = 74 1
RNA  ends = 0 73
              OTH =       19.344             COD =       -2.948             RNA =       18.779 
   logoddspostOTH =        0.000  logoddspostCOD =      -22.291  logoddspostRNA =       -0.564 

# 29  [+ strand] 
>DA0940-1- (77)
>ECOLI-2519045- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28) 
 19.326669 -6.735706 19.727199
 19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 76 0
COD  ends = 74 1
RNA  ends = 0 73
              OTH =       19.344             COD =       -2.948             RNA =       18.779 
   logoddspostOTH =        0.000  logoddspostCOD =      -22.291  logoddspostRNA =       -0.564 

# 30  [+ strand] 
>DA0940-1- (78)
>ECOLI-563946- (78)

length alignment: 78 (id=69.23)
posX: 0-77 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-77 [0-75](76) -- (0.18 0.30 0.32 0.20) 
 17.963663 -9.269558 17.104482
 18.280556 -6.326426 22.143566
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 77 0
COD  ends = 72 1
RNA  ends = 44 28
              OTH =       18.131             COD =       -7.150             RNA =       21.187 
   logoddspostOTH =        0.000  logoddspostCOD =      -25.281  logoddspostRNA =        3.056 

# 31  [+ strand] 
>DA0940-1- (78)
>ECOLI-3979754- (78)

length alignment: 78 (id=69.23)
posX: 0-77 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-77 [0-75](76) -- (0.14 0.33 0.36 0.17) 
 18.718315 -12.877073 20.514241
 18.551819 -5.649083 11.109117
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 77
COD  ends = 76 1
RNA  ends = 0 74
              OTH =       18.637             COD =       -6.639             RNA =       19.516 
   logoddspostOTH =        0.000  logoddspostCOD =      -25.277  logoddspostRNA =        0.879 

# 32  [+ strand] 
>DA0940-2- (75)
>ECOLI-3980115- (75)

length alignment: 75 (id=64.00)
posX: 0-74 [0-74](75) -- (0.15 0.35 0.36 0.15) 
posY: 0-74 [0-74](75) -- (0.16 0.27 0.36 0.21) 
 16.673417 5.650160 34.947176
 16.791520 4.389619 18.597200
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 74 0
COD  ends = 2 73
RNA  ends = 0 70
              OTH =       16.734             COD =        5.153             RNA =       33.947 
   logoddspostOTH =        0.000  logoddspostCOD =      -11.580  logoddspostRNA =       17.214 

# 33  [+ strand] 
>DA0940-8- (58)
>ECOLI-3979896- (58)

length alignment: 58 (id=68.97)
posX: 0-57 [0-56](57) -- (0.18 0.32 0.33 0.18) 
posY: 0-57 [0-55](56) -- (0.16 0.21 0.30 0.32) 
 11.514323 -1.612738 9.963681
 11.181613 -0.641287 8.426787
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 57
COD  ends = 57 0
RNA  ends = 20 37
              OTH =       11.358             COD =       -1.047             RNA =        9.391 
   logoddspostOTH =        0.000  logoddspostCOD =      -12.404  logoddspostRNA =       -1.967 

# 34  [+ strand] 
>DA0940-1- (77)
>ECOLI-3424371- (77)

length alignment: 77 (id=75.32)
posX: 0-76 [0-75](76) -- (0.14 0.37 0.34 0.14) 
posY: 0-76 [0-74](75) -- (0.20 0.33 0.31 0.16) 
 23.109013 5.520843 24.913393
 24.181055 9.917873 33.181724
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 76 0
COD  ends = 76 2
RNA  ends = 76 3
              OTH =       23.742             COD =        8.985             RNA =       32.186 
   logoddspostOTH =        0.000  logoddspostCOD =      -14.758  logoddspostRNA =        8.444 

# 35  [+ strand] 
>DA0940-1- (77)
>ECOLI-2515834- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.37 0.34 0.14) 
posY: 0-76 [0-74](75) -- (0.20 0.33 0.28 0.19) 
 18.645991 3.152473 25.533618
 18.627918 3.690656 29.967242
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 76
COD  ends = 76 2
RNA  ends = 76 3
              OTH =       18.637             COD =        3.447             RNA =       29.033 
   logoddspostOTH =        0.000  logoddspostCOD =      -15.190  logoddspostRNA =       10.396 

# 36  [+ strand] 
>DA0940-1- (77)
>ECOLI-2515949- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.37 0.34 0.14) 
posY: 0-76 [0-74](75) -- (0.20 0.33 0.28 0.19) 
 18.645991 3.152473 25.533618
 18.627918 3.690656 29.967242
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 76
COD  ends = 76 2
RNA  ends = 76 3
              OTH =       18.637             COD =        3.447             RNA =       29.033 
   logoddspostOTH =        0.000  logoddspostCOD =      -15.190  logoddspostRNA =       10.396 

# 37  [+ strand] 
>DA0940-5- (76)
>ECOLI-2815580- (76)

length alignment: 76 (id=71.05)
posX: 0-75 [0-71](72) -- (0.15 0.35 0.35 0.15) 
posY: 0-75 [0-71](72) -- (0.18 0.31 0.31 0.21) 
 13.333636 -36.156781 13.057277
 13.159042 -36.377514 9.144681
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 75
COD  ends = 0 73
RNA  ends = 32 52
              OTH =       13.249             COD =      -36.263             RNA =       12.150 
   logoddspostOTH =        0.000  logoddspostCOD =      -49.512  logoddspostRNA =       -1.099 

# 38  [+ strand] 
>DA0940-5- (76)
>ECOLI-2815855- (76)

length alignment: 76 (id=71.05)
posX: 0-75 [0-71](72) -- (0.15 0.35 0.35 0.15) 
posY: 0-75 [0-71](72) -- (0.18 0.31 0.31 0.21) 
 13.333636 -36.156781 13.057277
 13.159042 -36.377514 9.144681
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 75
COD  ends = 0 73
RNA  ends = 32 52
              OTH =       13.249             COD =      -36.263             RNA =       12.150 
   logoddspostOTH =        0.000  logoddspostCOD =      -49.512  logoddspostRNA =       -1.099 

# 39  [+ strand] 
>DA0940-5- (76)
>ECOLI-2815994- (76)

length alignment: 76 (id=71.05)
posX: 0-75 [0-71](72) -- (0.15 0.35 0.35 0.15) 
posY: 0-75 [0-71](72) -- (0.18 0.31 0.31 0.21) 
 13.333636 -36.156781 13.057277
 13.159042 -36.377514 9.144681
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 75
COD  ends = 0 73
RNA  ends = 32 52
              OTH =       13.249             COD =      -36.263             RNA =       12.150 
   logoddspostOTH =        0.000  logoddspostCOD =      -49.512  logoddspostRNA =       -1.099 

# 40  [+ strand] 
>DA0940-5- (76)
>ECOLI-2816269- (76)

length alignment: 76 (id=71.05)
posX: 0-75 [0-71](72) -- (0.15 0.35 0.35 0.15) 
posY: 0-75 [0-71](72) -- (0.18 0.31 0.31 0.21) 
 13.333636 -36.156781 13.057277
 13.159042 -36.377514 9.144681
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 75
COD  ends = 0 73
RNA  ends = 32 52
              OTH =       13.249             COD =      -36.263             RNA =       12.150 
   logoddspostOTH =        0.000  logoddspostCOD =      -49.512  logoddspostRNA =       -1.099 

# 41  [+ strand] 
>DA0940-9- (69)
>ECOLI-1804478- (69)

length alignment: 69 (id=66.67)
posX: 0-68 [0-67](68) -- (0.15 0.34 0.35 0.16) 
posY: 0-68 [0-66](67) -- (0.13 0.39 0.31 0.16) 
 10.953909 -9.639667 10.662024
 12.823044 -5.075973 10.777964
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 68 0
COD  ends = 66 1
RNA  ends = 51 31
              OTH =       12.172             COD =       -6.016             RNA =       10.721 
   logoddspostOTH =        0.000  logoddspostCOD =      -18.188  logoddspostRNA =       -1.451 

# 42  [+ strand] 
>DA0940-8- (58)
>ECOLI-3706024- (58)

length alignment: 58 (id=68.97)
posX: 0-57 [0-55](56) -- (0.18 0.34 0.30 0.18) 
posY: 0-57 [0-55](56) -- (0.20 0.39 0.25 0.16) 
 9.771742 -15.688073 2.357499
 9.187335 -13.325765 1.773092
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 57
COD  ends = 55 1
RNA  ends = -1 -1
              OTH =        9.509             COD =      -14.069             RNA =        2.095 
   logoddspostOTH =        0.000  logoddspostCOD =      -23.578  logoddspostRNA =       -7.414 

# 43  [+ strand] 
>DA0940-7- (73)
>ECOLI-695888- (73)

length alignment: 73 (id=64.38)
posX: 0-72 [0-69](70) -- (0.16 0.34 0.34 0.16) 
posY: 0-72 [0-69](70) -- (0.24 0.26 0.26 0.24) 
 10.281468 -22.207847 3.873799
 9.636380 -19.716135 1.831177
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 72
COD  ends = 72 1
RNA  ends = 10 26
              OTH =        9.995             COD =      -20.480             RNA =        3.187 
   logoddspostOTH =        0.000  logoddspostCOD =      -30.475  logoddspostRNA =       -6.807 

# 44  [+ strand] 
>DA0940-7- (73)
>ECOLI-696281- (73)

length alignment: 73 (id=64.38)
posX: 0-72 [0-69](70) -- (0.16 0.34 0.34 0.16) 
posY: 0-72 [0-69](70) -- (0.24 0.26 0.26 0.24) 
 10.281468 -22.207847 3.873799
 9.636380 -19.716135 1.831177
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 72
COD  ends = 72 1
RNA  ends = 10 26
              OTH =        9.995             COD =      -20.480             RNA =        3.187 
   logoddspostOTH =        0.000  logoddspostCOD =      -30.475  logoddspostRNA =       -6.807 

# 45  [+ strand] 
>DA0940-6- (62)
>ECOLI-695990- (62)

length alignment: 62 (id=62.90)
posX: 0-61 [0-60](61) -- (0.16 0.38 0.30 0.16) 
posY: 0-61 [0-60](61) -- (0.25 0.30 0.26 0.20) 
 10.452429 5.015902 10.936383
 9.772183 2.186248 11.450894
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 61
COD  ends = 0 61
RNA  ends = 38 22
              OTH =       10.152             COD =        4.206             RNA =       11.216 
   logoddspostOTH =        0.000  logoddspostCOD =       -5.946  logoddspostRNA =        1.064 

# 46  [+ strand] 
>DA0940-6- (62)
>ECOLI-696099- (62)

length alignment: 62 (id=62.90)
posX: 0-61 [0-60](61) -- (0.16 0.38 0.30 0.16) 
posY: 0-61 [0-60](61) -- (0.25 0.30 0.26 0.20) 
 10.452429 5.015902 10.936383
 9.772183 2.186248 11.450894
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 61
COD  ends = 0 61
RNA  ends = 38 22
              OTH =       10.152             COD =        4.206             RNA =       11.216 
   logoddspostOTH =        0.000  logoddspostCOD =       -5.946  logoddspostRNA =        1.064 

# 47  [+ strand] 
>DA0940-10- (69)
>ECOLI-2816349- (69)

length alignment: 69 (id=63.77)
posX: 0-68 [0-66](67) -- (0.15 0.34 0.36 0.15) 
posY: 0-68 [0-65](66) -- (0.18 0.27 0.36 0.18) 
 9.155278 -17.238488 5.252253
 9.115589 -17.289968 6.575597
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 68
COD  ends = 0 56
RNA  ends = 26 10
              OTH =        9.136             COD =      -17.264             RNA =        6.061 
   logoddspostOTH =        0.000  logoddspostCOD =      -26.400  logoddspostRNA =       -3.075 

BioPerl-1.007002/t/data/ecoli_domains.rpsblast000444000766000024      1332013155576321 21270 0ustar00cjfieldsstaff000000000000RPS-BLAST 2.2.4 [Aug-26-2002]

Query= gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I,
homoserine dehydrogenase I [Escherichia coli]
         (820 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gnl|CDD|3919 smart00483, POLXc, DNA polymerase X family; include...    28   0.064
gnl|CDD|7379 smart00533, MUTSd, DNA-binding domain of DNA mismat...    26   0.47 
gnl|CDD|178 smart00202, SR, Scavenger receptor Cys-rich; The sea...    22   4.5  
gnl|CDD|8977 smart00359, PUA, Putative RNA-binding Domain in Pse...    22   7.0  
gnl|CDD|7370 smart00486, POLBc, DNA polymerase type-B family; DN...    22   7.6  
gnl|CDD|28 smart00035, CLa, CLUSTERIN alpha chain;                     21   7.6  
gnl|CDD|8994 smart00450, RHOD, Rhodanese Homology Domain; An alp...    22   8.0  

>gnl|CDD|3919 smart00483, POLXc, DNA polymerase X family; includes vertebrate
           polymerase beta and terminal
           deoxynucleotidyltransferases
          Length = 335

 Score = 28.3 bits (63), Expect = 0.064
 Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 3/57 (5%)

Query: 599 SRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSE 655
           ++RK  Y         V+++L   +N+  +L    GI       I   ++ G     
Sbjct: 23  NKRKCSY---FRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGKLSKA 76


>gnl|CDD|7379 smart00533, MUTSd, DNA-binding domain of DNA mismatch repair MUTS
           family;
          Length = 310

 Score = 25.7 bits (56), Expect = 0.47
 Identities = 19/107 (17%), Positives = 36/107 (32%), Gaps = 21/107 (19%)

Query: 9   TSVANAERFLR------VADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALP 62
                 +R LR      + D+ E N R                 L+   E     +  L 
Sbjct: 13  CKTPMGKRLLRRWLLQPLTDLKEINERL-----------DAVEELLENPELRQDLRGLLK 61

Query: 63  NISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGIS 109
            I D ER+ + +    A+ +    L +L   ++    +I+ +L  + 
Sbjct: 62  RIPDLERLLSRIKLSRASPR---DLLRLYDSLEG-LKEIRKLLESLE 104


>gnl|CDD|178 smart00202, SR, Scavenger receptor Cys-rich; The sea urchin egg
           peptide speract contains 4 repeats of SR domains that
           contain 6 conserved cysteines. May bind bacterial
           antigens in the protein MARCO
          Length = 101

 Score = 22.2 bits (47), Expect = 4.5
 Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 2/53 (3%)

Query: 648 DEGMSFSEATTLAREMGYTEP--DPRDDLSGMDVARKLLILARETGRELELAD 698
           D+G    +A  + R++G+            G       L   R TG E  L+D
Sbjct: 27  DDGWDLRDANVVCRQLGFGGAVSASGSAYFGPGSGPIWLDNVRCTGTEASLSD 79


>gnl|CDD|8977 smart00359, PUA, Putative RNA-binding Domain in PseudoUridine
           synthase and Archaeosine transglycosylase;
          Length = 78

 Score = 21.8 bits (46), Expect = 7.0
 Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 5/40 (12%)

Query: 135 AGVLEARGH-----NVTVIDPVEKLLAVGHYLESTVDIAE 169
            GV+   G       V ++D   + L +G    S+ +IA 
Sbjct: 22  PGVVRVDGDIKEGDVVVIVDEKGEPLGIGLANMSSEEIAR 61


>gnl|CDD|7370 smart00486, POLBc, DNA polymerase type-B family; DNA polymerase
           alpha, delta, epsilon and zeta chain (eukaryota), DNA
           polymerases in archaea, DNA polymerase II in e. coli,
           mitochondrial DNA polymerases and and virus DNA
           polymerases
          Length = 475

 Score = 21.7 bits (45), Expect = 7.6
 Identities = 8/33 (24%), Positives = 14/33 (42%), Gaps = 3/33 (9%)

Query: 247 KSMSYQEAMELSYFGAKVLHPRTI---TPIAQF 276
           K +  +   ++ Y G KVL P+      P+   
Sbjct: 275 KGLEPELKKKVKYEGGKVLEPKKGFYENPVLVL 307


>gnl|CDD|28 smart00035, CLa, CLUSTERIN alpha chain;
          Length = 215

 Score = 21.5 bits (45), Expect = 7.6
 Identities = 7/13 (53%), Positives = 9/13 (68%)

Query: 479 ALLEQLKRQQSWL 491
           +LLEQL  Q  W+
Sbjct: 129 SLLEQLNEQFGWV 141


>gnl|CDD|8994 smart00450, RHOD, Rhodanese Homology Domain; An alpha beta fold
           found duplicated in the Rhodanese protein. The the
           Cysteine containing enzymatically active version of the
           domain is also found in the CDC25 class of protein
           phosphatases and a variety of proteins such as sulfide
           dehydrogenases and stress proteins such as Senesence
           specific protein 1 in plants, PspE and GlpE in bacteria
           and cyanide and arsenate resistance proteins. Inactive
           versions with a loss of the cysteine are also seen in
           Dual specificity phosphatases, ubiquitin hydrolases from
           yeast and in sulfuryltransferases. These are likely to
           play a role in protein interactions
          Length = 109

 Score = 21.7 bits (45), Expect = 8.0
 Identities = 14/56 (25%), Positives = 17/56 (30%)

Query: 520 NWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVV 575
              E L +  E  +L   +          PVIV C S    A         GF  V
Sbjct: 38  PLSELLDRRGETDSLFEELLGSLGLDKDKPVIVYCRSGNRSAKAAWLLRELGFKNV 93


Lambda     K      H
   0.319    0.136    0.384 

Gapped
Lambda     K      H
   0.267   0.0574    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 1100, Extension: 100
Number of Hits to DB: 194,372
Number of Sequences: 0
Number of extensions: 14001
Number of successful extensions: 17
Number of sequences better than 10.0: 1
Number of HSP's better than 10.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 17
length of query: 438
length of database: 75,508
effective HSP length: 68
effective length of query: 438
effective length of database: 31,988
effective search space: 14010744
effective search space used: 24054976
T: 11
A: 40
X1: 1600 (737.2 bits)
X2: 3800 (1463.8 bits)
X3: 6400 (2465.3 bits)
S1: 4100 (1892.0 bits)
S2: 43 (20.7 bits)
BioPerl-1.007002/t/data/ecolitst.bls000444000766000024      2601313155576321 17242 0ustar00cjfieldsstaff000000000000BLASTP 2.1.3 [Apr-11-2001]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I,
homoserine dehydrogenase I [Escherichia coli]
         (820 letters)

Database: ecoli.aa
           4289 sequences; 1,358,990 total letters

Searching..................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gb|AAC73113.1| (AE000111) aspartokinase I, homoserine dehydrogen...  1567  0.0
gb|AAC76922.1| (AE000468) aspartokinase II and homoserine dehydr...   332  1e-91
gb|AAC76994.1| (AE000475) aspartokinase III, lysine sensitive [E...   184  3e-47
gb|AAC73282.1| (AE000126) uridylate kinase [Escherichia coli]          42  3e-04

>gb|AAC73113.1| (AE000111) aspartokinase I, homoserine dehydrogenase I [Escherichia
           coli]
          Length = 820

 Score = 1567 bits (4058), Expect = 0.0
 Identities = 806/820 (98%), Positives = 806/820 (98%)

Query: 1   MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
           MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
Sbjct: 1   MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60

Query: 61  LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 120
           LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
Sbjct: 61  LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 120

Query: 121 ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP 180
           ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP
Sbjct: 121 ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP 180

Query: 181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240
           ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV
Sbjct: 181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240

Query: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300
           PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD
Sbjct: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300

Query: 301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360
           EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF
Sbjct: 301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360

Query: 361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420
           CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL
Sbjct: 361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420

Query: 421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQXXXXXXXXXXXXXXAL 480
           ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQ              AL
Sbjct: 421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL 480

Query: 481 LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL 540
           LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL
Sbjct: 481 LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL 540

Query: 541 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR 600
           VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR
Sbjct: 541 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR 600

Query: 601 RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA 660
           RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA
Sbjct: 601 RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA 660

Query: 661 REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA 720
           REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA
Sbjct: 661 REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA 720

Query: 721 NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF 780
           NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF
Sbjct: 721 NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF 780

Query: 781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820
           YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV
Sbjct: 781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820


>gb|AAC76922.1| (AE000468) aspartokinase II and homoserine dehydrogenase II
           [Escherichia coli]
          Length = 810

 Score =  332 bits (850), Expect = 1e-91
 Identities = 243/821 (29%), Positives = 403/821 (48%), Gaps = 44/821 (5%)

Query: 5   KFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNI 64
           KFGG+S+A+ + +LRVA I+   ++   +  V+SA    TN L+  ++ + + + +   +
Sbjct: 16  KFGGSSLADVKCYLRVAGIMAEYSQPDDMM-VVSAAGSTTNQLINWLKLSQTDRLSAHQV 74

Query: 65  SDAERIF-AELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALI 123
               R +  +L++GL  A+    L  +  FV         +  GI+      D++ A ++
Sbjct: 75  QQTLRRYQCDLISGLLPAEEADSL--ISAFVSDLERLAALLDSGIN------DAVYAEVV 126

Query: 124 CRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADH 183
             GE  S  +M+ VL  +G     +D  E L A      +   + E        ++   H
Sbjct: 127 GHGEVWSARLMSAVLNQQGLPAAWLDAREFLRAER---AAQPQVDEGLSYPLLQQLLVQH 183

Query: 184 ---MVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240
               +++ GF + N  GE V+LGRNGSDYSA  + A        IW+DV GVY+ DPR+V
Sbjct: 184 PGKRLVVTGFISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADPRKV 243

Query: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300
            DA LL  +   EA EL+   A VLH RT+ P++  +I   ++ +  P       G++R 
Sbjct: 244 KDACLLPLLRLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQ-----GSTRI 298

Query: 301 EDELP----VKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEY 356
           E  L      + +++ +++ +     P  +        +   + RA++  + +   +   
Sbjct: 299 ERVLASGTGARIVTSHDDVCLIEFQVPASQDFKLAHKEIDQILKRAQVRPLAVGVHNDRQ 358

Query: 357 SISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKF 416
            + FC        A + + E        GL   L + + LA++++VG G+        +F
Sbjct: 359 LLQFCYTSEVADSALKILDEA-------GLPGELRLRQGLALVAMVGAGVTRNPLHCHRF 411

Query: 417 FAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQXXXXXXXXXXXX 476
           +  L    +      Q     S+  V+      + ++  HQ +F  ++            
Sbjct: 412 WQQLKGQPVEFTW--QSDDGISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFGKGNI 469

Query: 477 XXALLEQLKRQQSWLKNKH-IDLRVCGVANSKALLTNVHGLN----LENWQEELAQAKEP 531
               LE   R+QS L  +   +  + GV +S+  L +  GL+    L  + +E  +  E 
Sbjct: 470 GSRWLELFAREQSTLSARTGFEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVEQDEE 529

Query: 532 FNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQ 591
                L   ++ +   + V++D T+SQ +ADQY DF   GFHV++ NK A  S  + Y Q
Sbjct: 530 ----SLFLWMRAHPYDDLVVLDVTASQQLADQYLDFASHGFHVISANKLAGASDSNKYRQ 585

Query: 592 LRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGM 651
           +  A EK+ R +LY+  VGAGLP+   +++L+++GD ++  SGI SG+LS++F + D  +
Sbjct: 586 IHDAFEKTGRHWLYNATVGAGLPINHTVRDLIDSGDTILSISGIFSGTLSWLFLQFDGSV 645

Query: 652 SFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNA 711
            F+E    A + G TEPDPRDDLSG DV RKL+ILARE G  +E   + +E ++PA    
Sbjct: 646 PFTELVDQAWQQGLTEPDPRDDLSGKDVMRKLVILAREAGYNIEPDQVRVESLVPAHCEG 705

Query: 712 EGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKV 771
            G +  F  N  +L++    R+  AR+ G VLRYV   D +G  RV +  V  + PL  +
Sbjct: 706 -GSIDHFFENGDELNEQMVQRLEAAREMGLVLRYVARFDANGKARVGVEAVREDHPLASL 764

Query: 772 KNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLR 812
              +N  A  S +Y+  PLV+RG GAG DVTA  + +D+ R
Sbjct: 765 LPCDNVFAIESRWYRDNPLVIRGPGAGRDVTAGAIQSDINR 805


>gb|AAC76994.1| (AE000475) aspartokinase III, lysine sensitive [Escherichia coli]
          Length = 449

 Score =  184 bits (467), Expect = 3e-47
 Identities = 142/471 (30%), Positives = 228/471 (48%), Gaps = 41/471 (8%)

Query: 3   VLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQ---- 58
           V KFGGTSVA+ +   R ADI+ S+A    V  VLSA A ITN LVA+ E    G+    
Sbjct: 6   VSKFGGTSVADFDAMNRSADIVLSDANVRLV--VLSASAGITNLLVALAEGLEPGERFEK 63

Query: 59  -DALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCP-- 115
            DA+ NI                    F + +   + +    +I+ +L  I++L +    
Sbjct: 64  LDAIRNIQ-------------------FAILERLRYPNVIREEIERLLENITVLAEAAAL 104

Query: 116 ---DSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTR 172
               ++   L+  GE MS  +   +L  R       D  + +     +  +  DIA    
Sbjct: 105 ATSPALTDELVSHGELMSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAE 164

Query: 173 RIAASRIPA--DHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVD 230
             A   +P   + +V+  GF     KG    LGR GSDY+AA+LA  L A   +IWTDV 
Sbjct: 165 LAALQLLPRLNEGLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVP 224

Query: 231 GVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQA 290
           G+YT DPR V  A+ +  +++ EA E++ FGAKVLHP T+ P  +  IP  + ++ +P+A
Sbjct: 225 GIYTTDPRVVSAAKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRA 284

Query: 291 PGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLIT 350
            GTL+  ++ E+    + ++   N  + ++    M    G  A VF  ++R  ISV LIT
Sbjct: 285 GGTLV-CNKTENPPLFRALALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLIT 343

Query: 351 QSSSEYSISFCVPQSDCV-RAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTL 409
             +SE S++  +  +      +  + +   +EL    L  + V E LA+++++G+ +   
Sbjct: 344 --TSEVSVALTLDTTGSTSTGDTLLTQSLLMEL--SALCRVEVEEGLALVALIGNDLSKA 399

Query: 410 RGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLF 460
            G+  + F  L   NI +  I  G+S  ++  +V  +DA   V+  H  LF
Sbjct: 400 CGVGKEVFGVLEPFNIRM--ICYGASSHNLCFLVPGEDAEQVVQKLHSNLF 448


>gb|AAC73282.1| (AE000126) uridylate kinase [Escherichia coli]
          Length = 241

 Score = 41.6 bits (96), Expect = 3e-04
 Identities = 28/97 (28%), Positives = 44/97 (44%), Gaps = 8/97 (8%)

Query: 199 LVVLGRNGSDYSAAVLAACLR-----ADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQE 253
           +++    G+ +     AACLR     AD     T VDGV+T DP + P A + + ++Y E
Sbjct: 132 VILSAGTGNPFFTTDSAACLRGIEIEADVVLKATKVDGVFTADPAKDPTATMYEQLTYSE 191

Query: 254 AMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQA 290
            +E      KV+     T     ++P  + N   P A
Sbjct: 192 VLEKE---LKVMDLAAFTLARDHKLPIRVFNMNKPGA 225


  Database: ecoli.aa
    Posted date:  Dec 6, 2001  1:58 PM
  Number of letters in database: 1,358,990
  Number of sequences in database:  4289
  
Lambda     K      H
   0.319    0.135    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2022122
Number of Sequences: 4289
Number of extensions: 82424
Number of successful extensions: 256
Number of sequences better than 1.0e-03: 4
Number of HSP's better than  0.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 243
Number of HSP's gapped (non-prelim): 4
length of query: 820
length of database: 1,358,990
effective HSP length: 47
effective length of query: 773
effective length of database: 1,157,407
effective search space: 894675611
effective search space used: 894675611
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 92 (40.0 bits)
BioPerl-1.007002/t/data/ecolitst.fa000444000766000024       164413155576321 17033 0ustar00cjfieldsstaff000000000000>gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I, homoserine dehydrogenase I [Escherichia coli]
MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAA
AQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHY
LESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV
PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSV
SGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIIS
VVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL
LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAV
ADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSL
SYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA
NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGND
VTAAGVFADLLRTLSWKLGV
BioPerl-1.007002/t/data/ecolitst.noseqs.wublastp000444000766000024       611713155576321 21615 0ustar00cjfieldsstaff000000000000BLASTP 2.0MP-WashU [18-Mar-2004] [linux26-ILP32F64 2004-03-13T04:13:13]

Copyright (C) 1996-2004 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2004) http://blast.wustl.edu

Query=  gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I, homoserine
    dehydrogenase I [Escherichia coli]
        (820 letters)

Database:  ecoli.aa
           4289 sequences; 1,358,990 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done

                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

gb|AAC73113.1| (AE000111) aspartokinase I, homoserine deh...  4141  0.        1
gb|AAC76922.1| (AE000468) aspartokinase II and homoserine...   907  6.6e-93   1
gb|AAC76994.1| (AE000475) aspartokinase III, lysine sensi...   483  2.8e-47   1



>gb|AAC73113.1| (AE000111) aspartokinase I, homoserine dehydrogenase I
            [Escherichia coli]
        Length = 820

 Score = 4141 (1462.8 bits), Expect = 0., P = 0.
 Identities = 820/820 (100%), Positives = 820/820 (100%)

Query: 1 - 820
Sbjct: 1 - 820


>gb|AAC76922.1| (AE000468) aspartokinase II and homoserine dehydrogenase II
            [Escherichia coli]
        Length = 810

 Score = 907 (324.3 bits), Expect = 6.6e-93, P = 6.6e-93
 Identities = 250/818 (30%), Positives = 413/818 (50%)

Query: 5 - 812
Sbjct: 16 - 805


>gb|AAC76994.1| (AE000475) aspartokinase III, lysine sensitive [Escherichia
            coli]
        Length = 449

 Score = 483 (175.1 bits), Expect = 2.8e-47, P = 2.8e-47
 Identities = 149/467 (31%), Positives = 233/467 (49%)

Query: 3 - 460
Sbjct: 6 - 448


Parameters:
  -i t/data/ecolitst.fa
  -d /data/blast/ecoli.aa
  noseqs
  E=1e-5
  postsw

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.319   0.135   0.384    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      820       820   1.0e-05  121 3  11 22  0.19    34
                                                     37  0.22    37


Statistics:

  Database:  /data/blast/ecoli.aa
   Title:  ecoli.aa
   Posted:  1:55:19 PM EDT Jun 3, 2004
   Created:  1:55:19 PM EDT Jun 3, 2004
   Format:  XDF-1
   # of letters in database:  1,358,990
   # of sequences in database:  4289
   # of database sequences satisfying E:  3
  No. of states in DFA:  618 (66 KB)
  Total size of DFA:  358 KB (2179 KB)
  Time to generate neighborhood:  0.00u 0.01s 0.01t  Elapsed: 00:00:00
  No. of threads or processors used:  2
  Search cpu time:  1.54u 0.03s 1.57t  Elapsed: 00:00:01
  Total cpu time:  1.58u 0.04s 1.62t  Elapsed: 00:00:01
  Start:  Thu Jun  3 14:00:59 2004   End:  Thu Jun  3 14:01:00 2004
BioPerl-1.007002/t/data/ecolitst.wublastp000444000766000024      3136713155576321 20333 0ustar00cjfieldsstaff000000000000BLASTP 2.0MP-WashU [12-Feb-2001] [linux-i686 01:36:08 31-Jan-2001]

Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2000) http://blast.wustl.edu

Query=  gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I, homoserine
    dehydrogenase I [Escherichia coli]
        (820 letters)

Database:  ecoli.aa
           4289 sequences; 1,358,990 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done

                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

gb|AAC73113.1| (AE000111) aspartokinase I, homoserine deh...  4141  0.0       1
gb|AAC76922.1| (AE000468) aspartokinase II and homoserine...   844  3.1e-86   1
gb|AAC76994.1| (AE000475) aspartokinase III, lysine sensi...   483  2.8e-47   1
gb|AAC73282.1| (AE000126) uridylate kinase [Escherichia c...    97  0.0010    1



>gb|AAC73113.1| (AE000111) aspartokinase I, homoserine dehydrogenase I
            [Escherichia coli]
        Length = 820

 Score = 4141 (1462.8 bits), Expect = 0.0, P = 0.0
 Identities = 820/820 (100%), Positives = 820/820 (100%)

Query:     1 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
             MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
Sbjct:     1 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60

Query:    61 LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 120
             LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
Sbjct:    61 LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 120

Query:   121 ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP 180
             ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP
Sbjct:   121 ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP 180

Query:   181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240
             ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV
Sbjct:   181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240

Query:   241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300
             PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD
Sbjct:   241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300

Query:   301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360
             EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF
Sbjct:   301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360

Query:   361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420
             CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL
Sbjct:   361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420

Query:   421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL 480
             ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL
Sbjct:   421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL 480

Query:   481 LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL 540
             LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL
Sbjct:   481 LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL 540

Query:   541 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR 600
             VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR
Sbjct:   541 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR 600

Query:   601 RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA 660
             RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA
Sbjct:   601 RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA 660

Query:   661 REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA 720
             REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA
Sbjct:   661 REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA 720

Query:   721 NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF 780
             NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF
Sbjct:   721 NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF 780

Query:   781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820
             YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV
Sbjct:   781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820


>gb|AAC76922.1| (AE000468) aspartokinase II and homoserine dehydrogenase II
            [Escherichia coli]
        Length = 810

 Score = 844 (302.2 bits), Expect = 3.1e-86, P = 3.1e-86
 Identities = 222/705 (31%), Positives = 356/705 (50%)

Query:   116 DSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIA 175
             D++ A ++  GE  S  +M+ VL  +G     +D  E L A     +  VD   S   + 
Sbjct:   119 DAVYAEVVGHGEVWSARLMSAVLNQQGLPAAWLDAREFLRAE-RAAQPQVDEGLSYPLLQ 177

Query:   176 ASRI--PADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVY 233
                +  P   +V+  GF + N  GE V+LGRNGSDYSA  + A        IW+DV GVY
Sbjct:   178 QLLVQHPGKRLVV-TGFISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVY 236

Query:   234 TCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGT 293
             + DPR+V DA LL  +   EA EL+   A VLH RT+ P++  +I   ++ +  P    T
Sbjct:   237 SADPRKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGST 296

Query:   294 LIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSS 353
              I           + +++ +++ +     P  +        +   + RA++  + +   +
Sbjct:   297 RIERVLASGT-GARIVTSHDDVCLIEFQVPASQDFKLAHKEIDQILKRAQVRPLAVGVHN 355

Query:   354 SEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGIS 413
                 + FC        A + + E        GL   L + + LA++++VG G+ T   + 
Sbjct:   356 DRQLLQFCYTSEVADSALKILDEA-------GLPGELRLRQGLALVAMVGAGV-TRNPLH 407

Query:   414 A-KFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIG 472
               +F+  L    +      Q     S+  V+      + ++  HQ +F  ++ I + + G
Sbjct:   408 CHRFWQQLKGQPVEFTW--QSDDGISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFG 465

Query:   473 VGGVGGALLEQLKRQQSWLKNKH-IDLRVCGVANSKALLTNVHGLN----LENWQEELAQ 527
              G +G   LE   R+QS L  +   +  + GV +S+  L +  GL+    L  + +E  +
Sbjct:   466 KGNIGSRWLELFAREQSTLSARTGFEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVE 525

Query:   528 AKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMD 587
               E      L   ++ +   + V++D T+SQ +ADQY DF   GFHV++ NK A  S  +
Sbjct:   526 QDEE----SLFLWMRAHPYDDLVVLDVTASQQLADQYLDFASHGFHVISANKLAGASDSN 581

Query:   588 YYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKL 647
              Y Q+  A EK+ R +LY+  VGAGLP+   +++L+++GD ++  SGI SG+LS++F + 
Sbjct:   582 KYRQIHDAFEKTGRHWLYNATVGAGLPINHTVRDLIDSGDTILSISGIFSGTLSWLFLQF 641

Query:   648 DEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPA 707
             D  + F+E    A + G TEPDPRDDLSG DV RKL+ILARE G  +E   + +E ++PA
Sbjct:   642 DGSVPFTELVDQAWQQGLTEPDPRDDLSGKDVMRKLVILAREAGYNIEPDQVRVESLVPA 701

Query:   708 EFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDP 767
                  G +  F  N  +L++    R+  AR+ G VLRYV   D +G  RV +  V  + P
Sbjct:   702 HCEG-GSIDHFFENGDELNEQMVQRLEAAREMGLVLRYVARFDANGKARVGVEAVREDHP 760

Query:   768 LFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLR 812
             L  +   +N  A  S +Y+  PLV+RG GAG DVTA  + +D+ R
Sbjct:   761 LASLLPCDNVFAIESRWYRDNPLVIRGPGAGRDVTAGAIQSDINR 805

 Score = 321 (118.1 bits), Expect = 3.6e-27, P = 3.6e-27
 Identities = 108/406 (26%), Positives = 191/406 (47%)

Query:     5 KFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNI 64
             KFGG+S+A+ + +LRVA I+   ++   +  V+SA    TN L+  ++ + + + +   +
Sbjct:    16 KFGGSSLADVKCYLRVAGIMAEYSQPDDMM-VVSAAGSTTNQLINWLKLSQTDRLSAHQV 74

Query:    65 SDAERIF-AELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLH-GISLLGQCPDSINAAL 122
                 R +  +L++GL  A+    L  +  FV  +  ++  +L  GI+      D++ A +
Sbjct:    75 QQTLRRYQCDLISGLLPAEEADSL--ISAFVS-DLERLAALLDSGIN------DAVYAEV 125

Query:   123 ICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRI--P 180
             +  GE  S  +M+ VL  +G     +D  E L A     +  VD   S   +    +  P
Sbjct:   126 VGHGEVWSARLMSAVLNQQGLPAAWLDAREFLRAE-RAAQPQVDEGLSYPLLQQLLVQHP 184

Query:   181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240
                +V+  GF + N  GE V+LGRNGSDYSA  + A        IW+DV GVY+ DPR+V
Sbjct:   185 GKRLVV-TGFISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADPRKV 243

Query:   241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300
              DA LL  +   EA EL+   A VLH RT+ P++  +I   ++ +  P    T I     
Sbjct:   244 KDACLLPLLRLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIERVLA 303

Query:   301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360
                   + +++ +++ +     P  +        +   + RA++  + +   +    + F
Sbjct:   304 SGT-GARIVTSHDDVCLIEFQVPASQDFKLAHKEIDQILKRAQVRPLAVGVHNDRQLLQF 362

Query:   361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGM 406
             C        A + + E        GL   L + + LA++++VG G+
Sbjct:   363 CYTSEVADSALKILDEA-------GLPGELRLRQGLALVAMVGAGV 401


>gb|AAC76994.1| (AE000475) aspartokinase III, lysine sensitive [Escherichia
            coli]
        Length = 449

 Score = 483 (175.1 bits), Expect = 2.8e-47, P = 2.8e-47
 Identities = 149/467 (31%), Positives = 233/467 (49%)

Query:     3 VLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQ---- 58
             V KFGGTSVA+ +   R ADI+ S+A    V  VLSA A ITN LVA+ E    G+    
Sbjct:     6 VSKFGGTSVADFDAMNRSADIVLSDANVRLV--VLSASAGITNLLVALAEGLEPGERFEK 63

Query:    59 -DALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDS 117
              DA+ NI      FA +L  L      +P   ++  +++    I  VL   + L   P +
Sbjct:    64 LDAIRNIQ-----FA-ILERLR-----YPNV-IREEIERLLENIT-VLAEAAALATSP-A 109

Query:   118 INAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVG-HYLESTVDIAESTRRIAA 176
             +   L+  GE MS  +   +L  R       D V K++     +  +  DIA      A 
Sbjct:   110 LTDELVSHGELMSTLLFVEILRERDVQAQWFD-VRKVMRTNDRFGRAEPDIAALAELAAL 168

Query:   177 SRIPA--DHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYT 234
               +P   + +V+  GF     KG    LGR GSDY+AA+LA  L A   +IWTDV G+YT
Sbjct:   169 QLLPRLNEGLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYT 228

Query:   235 CDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTL 294
              DPR V  A+ +  +++ EA E++ FGAKVLHP T+ P  +  IP  + ++ +P+A GTL
Sbjct:   229 TDPRVVSAAKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTL 288

Query:   295 IGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSS 354
             +  ++ E+    + ++   N  + ++    M    G  A VF  ++R  ISV LIT  +S
Sbjct:   289 V-CNKTENPPLFRALALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLIT--TS 345

Query:   355 EYSISFCVPQSDCVRA-ERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGIS 413
             E S++  +  +      +  + +   +EL    L  + V E LA+++++G+ +    G+ 
Sbjct:   346 EVSVALTLDTTGSTSTGDTLLTQSLLMELSA--LCRVEVEEGLALVALIGNDLSKACGVG 403

Query:   414 AKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLF 460
              + F  L   NI +  I  G+S  ++  +V  +DA   V+  H  LF
Sbjct:   404 KEVFGVLEPFNIRM--ICYGASSHNLCFLVPGEDAEQVVQKLHSNLF 448


>gb|AAC73282.1| (AE000126) uridylate kinase [Escherichia coli]
        Length = 241

 Score = 97 (39.2 bits), Expect = 0.0010, P = 0.0010
 Identities = 30/98 (30%), Positives = 45/98 (45%)

Query:   199 LVVLGRN-GSDYSAAVLAACLR-----ADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQ 252
             +V+L    G+ +     AACLR     AD     T VDGV+T DP + P A + + ++Y 
Sbjct:   131 VVILSAGTGNPFFTTDSAACLRGIEIEADVVLKATKVDGVFTADPAKDPTATMYEQLTYS 190

Query:   253 EAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQA 290
             E +E      KV+     T     ++P  + N   P A
Sbjct:   191 EVLEKEL---KVMDLAAFTLARDHKLPIRVFNMNKPGA 225


Parameters:
  E=0.01

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.319   0.136   0.384    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E    S W   T  X   E2     S2
   +0      0      820       820     0.010  93 3  11 22  0.19    34
                                                    37  0.22    37


Statistics:

  Database:  /home/jes12/db/ecoli.aa
   Title:  ecoli.aa
   Posted:  2:52:35 PM EST Nov 18, 2001
   Created:  9:46:47 AM EST Nov 18, 2001
   Format:  XDF-1
   # of letters in database:  1,358,990
   # of sequences in database:  4289
   # of database sequences satisfying E:  4
  No. of states in DFA:  573 (61 KB)
  Total size of DFA:  281 KB (1149 KB)
  Time to generate neighborhood:  0.00u 0.02s 0.02t  Elapsed: 00:00:00
  No. of threads or processors used:  1
  Search cpu time:  1.58u 0.00s 1.58t  Elapsed: 00:00:01
  Total cpu time:  1.59u 0.02s 1.61t  Elapsed: 00:00:01
  Start:  Thu Dec  6 11:09:14 2001   End:  Thu Dec  6 11:09:15 2001
BioPerl-1.007002/t/data/empty.bl2seq000444000766000024       120513155576321 17136 0ustar00cjfieldsstaff000000000000Query= 
         (468 letters)

Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 0
Number of Sequences: 0
Number of extensions: 0
Number of successful extensions: 0
Number of sequences better than 10.0: 0
length of query: 468
length of database: 2400
effective HSP length: 9
effective length of query: 459
effective length of database: 2355
effective search space:  1080945
effective search space used:  1080945
T: 0
A: 30
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 9 (18.3 bits)
BioPerl-1.007002/t/data/entrezgene.dat000444000766000024    265314213155576321 17625 0ustar00cjfieldsstaff000000000000Entrezgene ::= {
  track-info {
    geneid 1 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 20 ,
        minute 30 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 4 ,
        day 14 ,
        hour 13 ,
        minute 15 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Homo sapiens" ,
      common "human" ,
      db {
        {
          db "taxon" ,
          tag
            id 9606 } } ,
      syn {
        "man" } ,
      orgname {
        name
          binomial {
            genus "Homo" ,
            species "sapiens" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini;
 Hominidae; Homo" ,
        gcode 1 ,
        mgcode 2 ,
        div "PRI" } } ,
    subtype {
      {
        subtype chromosome ,
        name "19" } } } ,
  gene {
    locus "A1BG" ,
    desc "alpha-1-B glycoprotein" ,
    maploc "19q13.4" ,
    db {
      {
        db "MIM" ,
        tag
          id 138670 } } ,
    syn {
      "A1B" ,
      "ABG" ,
      "GAB" ,
      "HYST2477" ,
      "DKFZp686F0970" } ,
    locus-tag "HGNC:5" } ,
  prot {
    name {
      "alpha 1B-glycoprotein" ,
      "alpha-1B-glycoprotein" } } ,
  summary "The protein encoded by this gene is a plasma glycoprotein of
 unknown function. The protein shows sequence similarity to the variable
 regions of some immunoglobulin supergene family member proteins." ,
  location {
    {
      display-str "19q13.4" ,
      method
        map-type cyto } } ,
  gene-source {
    src "LocusLink" ,
    src-int 1 ,
    src-str2 "1" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000019" ,
      version 8 ,
      seqs {
        int {
          from 63548355 ,
          to 63556668 ,
          strand minus ,
          id
            gi 42406306 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_130786" ,
          version 2 ,
          genomic-coords {
            mix {
              int {
                from 63548355 ,
                to 63550206 ,
                strand minus ,
                id
                  gi 42406306 } ,
              int {
                from 63550530 ,
                to 63550817 ,
                strand minus ,
                id
                  gi 42406306 } ,
              int {
                from 63553547 ,
                to 63553828 ,
                strand minus ,
                id
                  gi 42406306 } ,
              int {
                from 63554568 ,
                to 63554864 ,
                strand minus ,
                id
                  gi 42406306 } ,
              int {
                from 63555460 ,
                to 63555732 ,
                strand minus ,
                id
                  gi 42406306 } ,
              int {
                from 63556105 ,
                to 63556374 ,
                strand minus ,
                id
                  gi 42406306 } ,
              int {
                from 63556469 ,
                to 63556504 ,
                strand minus ,
                id
                  gi 42406306 } ,
              int {
                from 63556581 ,
                to 63556668 ,
                strand minus ,
                id
                  gi 42406306 } } } ,
          seqs {
            whole
              gi 21071029 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_570602" ,
              version 2 ,
              genomic-coords {
                packed-int {
                  {
                    from 63550199 ,
                    to 63550206 ,
                    strand minus ,
                    id
                      gi 42406306 } ,
                  {
                    from 63550530 ,
                    to 63550817 ,
                    strand minus ,
                    id
                      gi 42406306 } ,
                  {
                    from 63553547 ,
                    to 63553828 ,
                    strand minus ,
                    id
                      gi 42406306 } ,
                  {
                    from 63554568 ,
                    to 63554864 ,
                    strand minus ,
                    id
                      gi 42406306 } ,
                  {
                    from 63555460 ,
                    to 63555732 ,
                    strand minus ,
                    id
                      gi 42406306 } ,
                  {
                    from 63556105 ,
                    to 63556374 ,
                    strand minus ,
                    id
                      gi 42406306 } ,
                  {
                    from 63556469 ,
                    to 63556504 ,
                    strand minus ,
                    id
                      gi 42406306 } ,
                  {
                    from 63556581 ,
                    to 63556614 ,
                    strand minus ,
                    id
                      gi 42406306 } } } ,
              seqs {
                whole
                  gi 21071030 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_011109" ,
      version 15 ,
      seqs {
        int {
          from 31124733 ,
          to 31133046 ,
          strand minus ,
          id
            gi 29800594 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_130786" ,
          version 2 ,
          genomic-coords {
            mix {
              int {
                from 31124733 ,
                to 31126584 ,
                strand minus ,
                id
                  gi 29800594 } ,
              int {
                from 31126908 ,
                to 31127195 ,
                strand minus ,
                id
                  gi 29800594 } ,
              int {
                from 31129925 ,
                to 31130206 ,
                strand minus ,
                id
                  gi 29800594 } ,
              int {
                from 31130946 ,
                to 31131242 ,
                strand minus ,
                id
                  gi 29800594 } ,
              int {
                from 31131838 ,
                to 31132110 ,
                strand minus ,
                id
                  gi 29800594 } ,
              int {
                from 31132483 ,
                to 31132752 ,
                strand minus ,
                id
                  gi 29800594 } ,
              int {
                from 31132847 ,
                to 31132882 ,
                strand minus ,
                id
                  gi 29800594 } ,
              int {
                from 31132959 ,
                to 31133046 ,
                strand minus ,
                id
                  gi 29800594 } } } ,
          seqs {
            whole
              gi 21071029 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_570602" ,
              version 2 ,
              genomic-coords {
                packed-int {
                  {
                    from 31126577 ,
                    to 31126584 ,
                    strand minus ,
                    id
                      gi 29800594 } ,
                  {
                    from 31126908 ,
                    to 31127195 ,
                    strand minus ,
                    id
                      gi 29800594 } ,
                  {
                    from 31129925 ,
                    to 31130206 ,
                    strand minus ,
                    id
                      gi 29800594 } ,
                  {
                    from 31130946 ,
                    to 31131242 ,
                    strand minus ,
                    id
                      gi 29800594 } ,
                  {
                    from 31131838 ,
                    to 31132110 ,
                    strand minus ,
                    id
                      gi 29800594 } ,
                  {
                    from 31132483 ,
                    to 31132752 ,
                    strand minus ,
                    id
                      gi 29800594 } ,
                  {
                    from 31132847 ,
                    to 31132882 ,
                    strand minus ,
                    id
                      gi 29800594 } ,
                  {
                    from 31132959 ,
                    to 31132992 ,
                    strand minus ,
                    id
                      gi 29800594 } } } ,
              seqs {
                whole
                  gi 21071030 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_086907" ,
      version 1 ,
      seqs {
        int {
          from 8163589 ,
          to 8172398 ,
          strand minus ,
          id
            gi 51475048 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_130786" ,
          version 2 ,
          genomic-coords {
            mix {
              int {
                from 8163589 ,
                to 8165440 ,
                strand minus ,
                id
                  gi 51475048 } ,
              int {
                from 8165763 ,
                to 8166050 ,
                strand minus ,
                id
                  gi 51475048 } ,
              int {
                from 8169274 ,
                to 8169555 ,
                strand minus ,
                id
                  gi 51475048 } ,
              int {
                from 8170297 ,
                to 8170593 ,
                strand minus ,
                id
                  gi 51475048 } ,
              int {
                from 8171190 ,
                to 8171462 ,
                strand minus ,
                id
                  gi 51475048 } ,
              int {
                from 8171835 ,
                to 8172104 ,
                strand minus ,
                id
                  gi 51475048 } ,
              int {
                from 8172199 ,
                to 8172234 ,
                strand minus ,
                id
                  gi 51475048 } ,
              int {
                from 8172311 ,
                to 8172398 ,
                strand minus ,
                id
                  gi 51475048 } } } ,
          seqs {
            whole
              gi 21071029 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_570602" ,
              version 2 ,
              genomic-coords {
                packed-int {
                  {
                    from 8165433 ,
                    to 8165440 ,
                    strand minus ,
                    id
                      gi 51475048 } ,
                  {
                    from 8165763 ,
                    to 8166050 ,
                    strand minus ,
                    id
                      gi 51475048 } ,
                  {
                    from 8169274 ,
                    to 8169555 ,
                    strand minus ,
                    id
                      gi 51475048 } ,
                  {
                    from 8170297 ,
                    to 8170593 ,
                    strand minus ,
                    id
                      gi 51475048 } ,
                  {
                    from 8171190 ,
                    to 8171462 ,
                    strand minus ,
                    id
                      gi 51475048 } ,
                  {
                    from 8171835 ,
                    to 8172104 ,
                    strand minus ,
                    id
                      gi 51475048 } ,
                  {
                    from 8172199 ,
                    to 8172234 ,
                    strand minus ,
                    id
                      gi 51475048 } ,
                  {
                    from 8172311 ,
                    to 8172344 ,
                    strand minus ,
                    id
                      gi 51475048 } } } ,
              seqs {
                whole
                  gi 21071030 } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "HUGO Gene Nomenclature Committee" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "A1BG" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "alpha-1-B glycoprotein" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "GOA" ,
          url "http://www.ebi.ac.uk/GOA/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 3458201 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5554 } ,
                  anchor "molecular_function unknown" ,
                  post-text "evidence: ND" } } } } } ,
        {
          type comment ,
          label "Process" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 4 } ,
                  anchor "biological_process unknown" ,
                  post-text "evidence: ND" } } } } } ,
        {
          type comment ,
          label "Component" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 3458201 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5576 } ,
                  anchor "extracellular region" ,
                  post-text "evidence: IDA" } } } } } } } } ,
  homology {
    {
      type comment ,
      heading "Mouse, Rat" ,
      version 0 ,
      source {
        {
          src {
            db "HomoloGene" ,
            tag
              id 11167 } ,
          anchor "Map Viewer" ,
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=19&
MAPS=genes-r-org/rat-chr/human%3A19,genes-r-org/mouse-chr/human%3A19,genes-r-o
rg/human-chr19&query=e%3A1[id]+AND+gene[obj_type]&QSTR=a1bg&cmd=focus&fill=10" } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "HGNC" ,
            tag
              id 5 } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "REVIEWED" ,
      version 0 } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 15461460 ,
        pmid 15221005 ,
        pmid 14702039 ,
        pmid 12477932 ,
        pmid 8889549 ,
        pmid 3610142 ,
        pmid 3458201 ,
        pmid 2591067 } } ,
    {
      type comment ,
      heading "Markers (Sequence Tagged Sites/STS)" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 89991 } ,
              anchor "SHGC-67307" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "RH80032" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "RH86145" ,
              version 0 } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 152074 } ,
              anchor "D11S2921" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "GDB:461809" ,
              version 0 } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 155756 } ,
              anchor "D10S16" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "D10S23" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "GDB:193809" ,
              version 0 } } } } } ,
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_130786" ,
          version 2 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 21071029 } ,
              anchor "NM_130786" } } ,
          seqs {
            whole
              gi 21071029 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_570602" ,
              version 2 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 21071030 } ,
                  anchor "NP_570602" ,
                  post-text "alpha 1B-glycoprotein" } } ,
              seqs {
                whole
                  gi 21071030 } ,
              comment {
                {
                  type other ,
                  heading "Consensus CDS (CCDS)" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "CCDS" ,
                        tag
                          str "CCDS12976.1" } ,
                      anchor "CCDS12976.1" } } } ,
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 21071030 } ,
                      pre-text "(1)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 365 } ,
                          anchor "smart00408: IGc2; Immunoglobulin C-2 Type" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 223 - 282  Blast Score: 103" ,
                          version 0 } } } } } } } } ,
          comment {
            {
              type other ,
              heading "Source Sequence" ,
              version 0 ,
              source {
                {
                  src {
                    db "Nucleotide" ,
                    tag
                      str "AF414429,AK055885,AK056201" } ,
                  anchor "AF414429,AK055885,AK056201" } } ,
              comment {
                {
                  type other ,
                  version 0 } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type genomic ,
          heading "Genomic" ,
          accession "AC010642" ,
          version 5 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 9929687 } ,
              anchor "AC010642" } } ,
          seqs {
            int {
              from 41119 ,
              to 43581 ,
              strand plus ,
              id
                gi 9929687 } } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AB073611" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 51555784 } ,
              anchor "AB073611" } } ,
          seqs {
            whole
              gi 51555784 } ,
          products {
            {
              type peptide ,
              accession "BAD38648" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 51555785 } ,
                  anchor "BAD38648" } } ,
              seqs {
                whole
                  gi 51555785 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AF414429" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 15778555 } ,
              anchor "AF414429" } } ,
          seqs {
            whole
              gi 15778555 } ,
          products {
            {
              type peptide ,
              accession "AAL07469" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 15778556 } ,
                  anchor "AAL07469" } } ,
              seqs {
                whole
                  gi 15778556 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AK055885" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 16550723 } ,
              anchor "AK055885" } } ,
          seqs {
            whole
              gi 16550723 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AK056201" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 16551539 } ,
              anchor "AK056201" } } ,
          seqs {
            whole
              gi 16551539 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC035719" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 23273475 } ,
              anchor "BC035719" } } ,
          seqs {
            whole
              gi 23273475 } ,
          products {
            {
              type peptide ,
              accession "AAH35719" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 23273476 } ,
                  anchor "AAH35719" } } ,
              seqs {
                whole
                  gi 23273476 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BX537419" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 31873339 } ,
              anchor "BX537419" } } ,
          seqs {
            whole
              gi 31873339 } ,
          products {
            {
              type peptide ,
              accession "CAD97661" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 31873340 } ,
                  anchor "CAD97661" } } ,
              seqs {
                whole
                  gi 31873340 } } } } ,
        {
          type other ,
          text "None" ,
          version 0 ,
          products {
            {
              type peptide ,
              accession "P04217" ,
              version 0 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 46577680 } ,
                  anchor "P04217" } } ,
              seqs {
                whole
                  gi 46577680 } } } } } } ,
    {
      type comment ,
      heading "Additional Links" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Evidence Viewer" ,
                tag
                  str "1" } ,
              anchor "Evidence Viewer" ,
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti
g=NT_011109.15&gene=A1BG&lid=1&from=31124734&to=31133047" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "ModelMaker" ,
                tag
                  str "1" } ,
              anchor "ModelMaker" ,
              url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96
06&contig=NT_011109.15&gene=A1BG&lid=1" } } } ,
        {
          type comment ,
          text "UniGene" ,
          version 0 ,
          xtra-properties {
            {
              tag "UNIGENE" ,
              value "Hs.529161" } } ,
          source {
            {
              src {
                db "UniGene" ,
                tag
                  str "Hs.529161" } ,
              anchor "Hs.529161" ,
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=52
9161" } } } ,
        {
          type comment ,
          text "MIM" ,
          version 0 ,
          source {
            {
              src {
                db "MIM" ,
                tag
                  str "138670" } ,
              anchor "138670" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "HomoloGene" ,
                tag
                  str "1" } ,
              anchor "HomoloGene" ,
              url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=
1[loc]&TAXID=9606" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "AceView" ,
                tag
                  id 1 } ,
              anchor "AceView" ,
              url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l
ocusid&org=9606&l=1" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "GDB" ,
                tag
                  str "GDB:119638" } } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Ensembl" ,
                tag
                  str "" } ,
              url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=AK055
885" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UCSC" ,
                tag
                  str "" } ,
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=
AK055885" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGC" ,
                tag
                  str "BC035719" } ,
              anchor "MGC" ,
              url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC035719" } } } } } ,
    {
      type generif ,
      text "A1BG-cysteine-rich secretory protein 3 complex displays a similar
 function in protecting the circulation from a potentially harmful effect of
 free CRISP-3" ,
      version 0 ,
      refs {
        pmid 15461460 } ,
      create-date
        str "Nov  6 2004 10:01AM" ,
      update-date
        str "Nov  6 2004  3:27PM" } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 1 } ,
    {
      db "MIM" ,
      tag
        id 138670 } } ,
  xtra-index-terms {
    "LOC1" } }
Entrezgene ::= {
  track-info {
    geneid 2 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 20 ,
        minute 30 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 4 ,
        day 14 ,
        hour 13 ,
        minute 15 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Homo sapiens" ,
      common "human" ,
      db {
        {
          db "taxon" ,
          tag
            id 9606 } } ,
      syn {
        "man" } ,
      orgname {
        name
          binomial {
            genus "Homo" ,
            species "sapiens" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini;
 Hominidae; Homo" ,
        gcode 1 ,
        mgcode 2 ,
        div "PRI" } } ,
    subtype {
      {
        subtype chromosome ,
        name "12" } } } ,
  gene {
    locus "A2M" ,
    desc "alpha-2-macroglobulin" ,
    maploc "12p13.3-p12.3" ,
    db {
      {
        db "MIM" ,
        tag
          id 103950 } } ,
    syn {
      "FWP007" ,
      "S863-7" ,
      "DKFZp779B086" } ,
    locus-tag "HGNC:7" } ,
  prot {
    name {
      "alpha-2-macroglobulin" } } ,
  summary "Alpha-2-macroglobulin is a protease inhibitor and cytokine
 transporter. It inhibits many proteases, including trypsin, thrombin and
 collagenase. A2M is implicated in Alzheimer disease (AD) due to its ability
 to mediate the clearance and degradation of A-beta, the major component of
 beta-amyloid deposits." ,
  location {
    {
      display-str "12p13.3-p12.3" ,
      method
        map-type cyto } } ,
  gene-source {
    src "LocusLink" ,
    src-int 2 ,
    src-str2 "2" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000012" ,
      version 9 ,
      seqs {
        int {
          from 9111576 ,
          to 9159755 ,
          strand minus ,
          id
            gi 51511728 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_000014" ,
          version 3 ,
          genomic-coords {
            mix {
              int {
                from 9111576 ,
                to 9111701 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9112045 ,
                to 9112086 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9112602 ,
                to 9112704 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9113607 ,
                to 9113675 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9114350 ,
                to 9114440 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9116221 ,
                to 9116348 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9116515 ,
                to 9116733 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9118422 ,
                to 9118645 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9120618 ,
                to 9120798 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9121208 ,
                to 9121282 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9121563 ,
                to 9121719 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9123106 ,
                to 9123193 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9123501 ,
                to 9123677 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9123956 ,
                to 9124039 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9133062 ,
                to 9133113 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9133764 ,
                to 9133885 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9134218 ,
                to 9134344 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9135063 ,
                to 9135291 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9137327 ,
                to 9137441 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9138835 ,
                to 9138946 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9139401 ,
                to 9139562 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9142469 ,
                to 9142618 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9143243 ,
                to 9143385 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9145006 ,
                to 9145069 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9145309 ,
                to 9145536 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9148101 ,
                to 9148262 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9150098 ,
                to 9150207 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9150353 ,
                to 9150467 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9151386 ,
                to 9151506 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9153183 ,
                to 9153267 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9153729 ,
                to 9153897 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9154176 ,
                to 9154196 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9156021 ,
                to 9156073 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9156239 ,
                to 9156398 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9157222 ,
                to 9157405 ,
                strand minus ,
                id
                  gi 51511728 } ,
              int {
                from 9159626 ,
                to 9159755 ,
                strand minus ,
                id
                  gi 51511728 } } } ,
          seqs {
            whole
              gi 6226959 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              label "precursor" ,
              accession "NP_000005" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 9111685 ,
                    to 9111701 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9112045 ,
                    to 9112086 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9112602 ,
                    to 9112704 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9113607 ,
                    to 9113675 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9114350 ,
                    to 9114440 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9116221 ,
                    to 9116348 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9116515 ,
                    to 9116733 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9118422 ,
                    to 9118645 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9120618 ,
                    to 9120798 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9121208 ,
                    to 9121282 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9121563 ,
                    to 9121719 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9123106 ,
                    to 9123193 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9123501 ,
                    to 9123677 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9123956 ,
                    to 9124039 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9133062 ,
                    to 9133113 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9133764 ,
                    to 9133885 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9134218 ,
                    to 9134344 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9135063 ,
                    to 9135291 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9137327 ,
                    to 9137441 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9138835 ,
                    to 9138946 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9139401 ,
                    to 9139562 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9142469 ,
                    to 9142618 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9143243 ,
                    to 9143385 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9145006 ,
                    to 9145069 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9145309 ,
                    to 9145536 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9148101 ,
                    to 9148262 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9150098 ,
                    to 9150207 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9150353 ,
                    to 9150467 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9151386 ,
                    to 9151506 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9153183 ,
                    to 9153267 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9153729 ,
                    to 9153897 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9154176 ,
                    to 9154196 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9156021 ,
                    to 9156073 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9156239 ,
                    to 9156398 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9157222 ,
                    to 9157405 ,
                    strand minus ,
                    id
                      gi 51511728 } ,
                  {
                    from 9159626 ,
                    to 9159711 ,
                    strand minus ,
                    id
                      gi 51511728 } } } ,
              seqs {
                whole
                  gi 4557225 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_009714" ,
      version 16 ,
      seqs {
        int {
          from 1979283 ,
          to 2027462 ,
          strand minus ,
          id
            gi 37543832 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_000014" ,
          version 3 ,
          genomic-coords {
            mix {
              int {
                from 1979283 ,
                to 1979408 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 1979752 ,
                to 1979793 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 1980309 ,
                to 1980411 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 1981314 ,
                to 1981382 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 1982057 ,
                to 1982147 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 1983928 ,
                to 1984055 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 1984222 ,
                to 1984440 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 1986129 ,
                to 1986352 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 1988325 ,
                to 1988505 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 1988915 ,
                to 1988989 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 1989270 ,
                to 1989426 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 1990813 ,
                to 1990900 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 1991208 ,
                to 1991384 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 1991663 ,
                to 1991746 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2000769 ,
                to 2000820 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2001471 ,
                to 2001592 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2001925 ,
                to 2002051 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2002770 ,
                to 2002998 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2005034 ,
                to 2005148 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2006542 ,
                to 2006653 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2007108 ,
                to 2007269 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2010176 ,
                to 2010325 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2010950 ,
                to 2011092 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2012713 ,
                to 2012776 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2013016 ,
                to 2013243 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2015808 ,
                to 2015969 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2017805 ,
                to 2017914 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2018060 ,
                to 2018174 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2019093 ,
                to 2019213 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2020890 ,
                to 2020974 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2021436 ,
                to 2021604 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2021883 ,
                to 2021903 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2023728 ,
                to 2023780 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2023946 ,
                to 2024105 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2024929 ,
                to 2025112 ,
                strand minus ,
                id
                  gi 37543832 } ,
              int {
                from 2027333 ,
                to 2027462 ,
                strand minus ,
                id
                  gi 37543832 } } } ,
          seqs {
            whole
              gi 6226959 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              label "precursor" ,
              accession "NP_000005" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 1979392 ,
                    to 1979408 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 1979752 ,
                    to 1979793 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 1980309 ,
                    to 1980411 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 1981314 ,
                    to 1981382 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 1982057 ,
                    to 1982147 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 1983928 ,
                    to 1984055 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 1984222 ,
                    to 1984440 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 1986129 ,
                    to 1986352 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 1988325 ,
                    to 1988505 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 1988915 ,
                    to 1988989 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 1989270 ,
                    to 1989426 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 1990813 ,
                    to 1990900 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 1991208 ,
                    to 1991384 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 1991663 ,
                    to 1991746 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2000769 ,
                    to 2000820 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2001471 ,
                    to 2001592 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2001925 ,
                    to 2002051 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2002770 ,
                    to 2002998 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2005034 ,
                    to 2005148 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2006542 ,
                    to 2006653 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2007108 ,
                    to 2007269 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2010176 ,
                    to 2010325 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2010950 ,
                    to 2011092 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2012713 ,
                    to 2012776 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2013016 ,
                    to 2013243 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2015808 ,
                    to 2015969 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2017805 ,
                    to 2017914 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2018060 ,
                    to 2018174 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2019093 ,
                    to 2019213 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2020890 ,
                    to 2020974 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2021436 ,
                    to 2021604 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2021883 ,
                    to 2021903 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2023728 ,
                    to 2023780 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2023946 ,
                    to 2024105 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2024929 ,
                    to 2025112 ,
                    strand minus ,
                    id
                      gi 37543832 } ,
                  {
                    from 2027333 ,
                    to 2027418 ,
                    strand minus ,
                    id
                      gi 37543832 } } } ,
              seqs {
                whole
                  gi 4557225 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_086792" ,
      version 1 ,
      seqs {
        int {
          from 4173171 ,
          to 4221277 ,
          strand minus ,
          id
            gi 51471135 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_000014" ,
          version 3 ,
          genomic-coords {
            mix {
              int {
                from 4173171 ,
                to 4173296 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4173640 ,
                to 4173681 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4174197 ,
                to 4174299 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4175201 ,
                to 4175269 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4175944 ,
                to 4176034 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4177816 ,
                to 4177943 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4178110 ,
                to 4178328 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4180017 ,
                to 4180240 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4182213 ,
                to 4182393 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4182803 ,
                to 4182877 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4183158 ,
                to 4183314 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4184702 ,
                to 4184789 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4185097 ,
                to 4185273 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4185552 ,
                to 4185635 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4194661 ,
                to 4194712 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4195363 ,
                to 4195484 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4195817 ,
                to 4195943 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4196662 ,
                to 4196890 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4198926 ,
                to 4199040 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4200364 ,
                to 4200475 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4200930 ,
                to 4201091 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4203997 ,
                to 4204146 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4204771 ,
                to 4204913 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4206534 ,
                to 4206597 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4206837 ,
                to 4207064 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4209629 ,
                to 4209790 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4211627 ,
                to 4211736 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4211882 ,
                to 4211996 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4212916 ,
                to 4213036 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4214705 ,
                to 4214789 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4215251 ,
                to 4215419 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4215698 ,
                to 4215718 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4217543 ,
                to 4217595 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4217761 ,
                to 4217920 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4218744 ,
                to 4218927 ,
                strand minus ,
                id
                  gi 51471135 } ,
              int {
                from 4221148 ,
                to 4221277 ,
                strand minus ,
                id
                  gi 51471135 } } } ,
          seqs {
            whole
              gi 6226959 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              label "precursor" ,
              accession "NP_000005" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 4173280 ,
                    to 4173296 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4173640 ,
                    to 4173681 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4174197 ,
                    to 4174299 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4175201 ,
                    to 4175269 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4175944 ,
                    to 4176034 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4177816 ,
                    to 4177943 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4178110 ,
                    to 4178328 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4180017 ,
                    to 4180240 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4182213 ,
                    to 4182393 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4182803 ,
                    to 4182877 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4183158 ,
                    to 4183314 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4184702 ,
                    to 4184789 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4185097 ,
                    to 4185273 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4185552 ,
                    to 4185635 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4194661 ,
                    to 4194712 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4195363 ,
                    to 4195484 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4195817 ,
                    to 4195943 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4196662 ,
                    to 4196890 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4198926 ,
                    to 4199040 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4200364 ,
                    to 4200475 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4200930 ,
                    to 4201091 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4203997 ,
                    to 4204146 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4204771 ,
                    to 4204913 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4206534 ,
                    to 4206597 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4206837 ,
                    to 4207064 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4209629 ,
                    to 4209790 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4211627 ,
                    to 4211736 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4211882 ,
                    to 4211996 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4212916 ,
                    to 4213036 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4214705 ,
                    to 4214789 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4215251 ,
                    to 4215419 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4215698 ,
                    to 4215718 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4217543 ,
                    to 4217595 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4217761 ,
                    to 4217920 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4218744 ,
                    to 4218927 ,
                    strand minus ,
                    id
                      gi 51471135 } ,
                  {
                    from 4221148 ,
                    to 4221233 ,
                    strand minus ,
                    id
                      gi 51471135 } } } ,
              seqs {
                whole
                  gi 4557225 } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "HUGO Gene Nomenclature Committee" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "A2M" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "alpha-2-macroglobulin" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "GOA" ,
          url "http://www.ebi.ac.uk/GOA/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 11435418 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 19899 } ,
                  anchor "enzyme binding" ,
                  post-text "evidence: IPI" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 9714181 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 19966 } ,
                  anchor "interleukin-1 binding" ,
                  post-text "evidence: IDA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 10880251 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 19959 } ,
                  anchor "interleukin-8 binding" ,
                  post-text "evidence: IPI" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 8320 } ,
                  anchor "protein carrier activity" ,
                  post-text "evidence: NR" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 4867 } ,
                  anchor "serine-type endopeptidase inhibitor activity" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 9714181 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 43120 } ,
                  anchor "tumor necrosis factor binding" ,
                  post-text "evidence: IDA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 17114 } ,
                  anchor "wide-spectrum protease inhibitor activity" ,
                  post-text "evidence: IEA" } } } } } ,
        {
          type comment ,
          label "Process" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 6886 } ,
                  anchor "intracellular protein transport" ,
                  post-text "evidence: NR" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 51260 } ,
                  anchor "protein homooligomerization" ,
                  post-text "evidence: NAS" } } } } } ,
        {
          type comment ,
          label "Component" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 14718574 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5576 } ,
                  anchor "extracellular region" ,
                  post-text "evidence: NAS" } } } } } } } } ,
  homology {
    {
      type comment ,
      heading "Mouse, Rat" ,
      version 0 ,
      source {
        {
          src {
            db "HomoloGene" ,
            tag
              id 37248 } ,
          anchor "Map Viewer" ,
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=12&
MAPS=genes-r-org/rat-chr/human%3A12,genes-r-org/mouse-chr/human%3A12,genes-r-o
rg/human-chr12&query=e%3A2[id]+AND+gene[obj_type]&QSTR=a2m&cmd=focus&fill=10" } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "HGNC" ,
            tag
              id 7 } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "REVIEWED" ,
      version 0 } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 15511627 ,
        pmid 15023809 ,
        pmid 14760718 ,
        pmid 14718574 ,
        pmid 14715656 ,
        pmid 14678766 ,
        pmid 14675603 ,
        pmid 14637088 ,
        pmid 14506912 ,
        pmid 12966032 ,
        pmid 12755687 ,
        pmid 12755614 ,
        pmid 12631277 ,
        pmid 12477932 ,
        pmid 12221172 ,
        pmid 12194978 ,
        pmid 12175343 ,
        pmid 12062545 ,
        pmid 12042276 ,
        pmid 12015318 ,
        pmid 11916201 ,
        pmid 11910179 ,
        pmid 11901360 ,
        pmid 11823454 ,
        pmid 11811950 ,
        pmid 11435418 ,
        pmid 11162584 ,
        pmid 11100124 ,
        pmid 11023837 ,
        pmid 10880251 ,
        pmid 10731476 ,
        pmid 10714547 ,
        pmid 10652313 ,
        pmid 10373500 ,
        pmid 9831625 ,
        pmid 9724081 ,
        pmid 9714181 ,
        pmid 8583572 ,
        pmid 7680268 ,
        pmid 7533769 ,
        pmid 7533162 ,
        pmid 7519849 ,
        pmid 6191979 ,
        pmid 6153632 ,
        pmid 3289986 ,
        pmid 2581245 ,
        pmid 2476070 ,
        pmid 2460294 ,
        pmid 2459995 ,
        pmid 2408344 ,
        pmid 1707161 ,
        pmid 1697852 ,
        pmid 1370808 ,
        pmid 1281457 ,
        pmid 89758 } } ,
    {
      type comment ,
      heading "Phenotypes" ,
      version 0 ,
      comment {
        {
          type phenotype ,
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                db "MIM" ,
                tag
                  id 103950 } ,
              anchor "MIM: 103950" } } } ,
        {
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            {
              src {
                db "MIM" ,
                tag
                  id 103950 } ,
              anchor "MIM: 103950" } } } } } ,
    {
      type comment ,
      heading "Markers (Sequence Tagged Sites/STS)" ,
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          type comment ,
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                tag
                  id 25036 } ,
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              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
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        {
          type comment ,
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            {
              src {
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                tag
                  id 40245 } ,
              anchor "SGC31674" ,
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          comment {
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              type other ,
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              text "EST130345" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "RH52474" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "WI-219" ,
              version 0 } } } ,
        {
          type comment ,
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            {
              src {
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                tag
                  id 46849 } ,
              anchor "RH11157" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "RH44108" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
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        {
          type comment ,
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                  id 95143 } ,
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          comment {
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              type other ,
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              text "WIAF-1430-STS" ,
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        {
          type comment ,
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                tag
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        {
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    {
      type comment ,
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          version 3 ,
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              src {
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                  anchor "NP_000005" ,
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              comment {
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                            tag
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                          anchor "pfam00207: A2M; Alpha-2-macroglobulin family" } } ,
                      comment {
                        {
                          type other ,
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                              id 25832 } ,
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                      comment {
                        {
                          type other ,
                          text "Location: 21 - 628  Blast Score: 1948" ,
                          version 0 } } } } } } } } ,
          comment {
            {
              type other ,
              heading "Source Sequence" ,
              version 0 ,
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                {
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                      str "M11313" } ,
                  anchor "M11313" } } ,
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      type comment ,
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                      id 13661816 } ,
                  anchor "AAK38110" } } ,
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                  gi 13661816 } } } } ,
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        {
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        {
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          products {
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              type peptide ,
              text "None" ,
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        {
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                tag
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              gi 51476395 } ,
          products {
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                  anchor "CAH18188" } } ,
              seqs {
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        {
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          accession "M11313" ,
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          source {
            {
              src {
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                  id 177869 } ,
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          products {
            {
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                {
                  src {
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              seqs {
                whole
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        {
          type mRNA ,
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                  anchor "AAA51552" } } ,
              seqs {
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        {
          type other ,
          text "None" ,
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          products {
            {
              type peptide ,
              accession "P01023" ,
              version 0 ,
              source {
                {
                  src {
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                      id 112911 } ,
                  anchor "P01023" } } ,
              seqs {
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    {
      type comment ,
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          type comment ,
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                  str "2" } ,
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        {
          type comment ,
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              tag "UNIGENE" ,
              value "Hs.212838" } } ,
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              src {
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              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=21
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        {
          type comment ,
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              src {
                db "MIM" ,
                tag
                  str "103950" } ,
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                  str "2" } ,
              anchor "HomoloGene" ,
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        {
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                  id 2 } ,
              anchor "AceView" ,
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        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "GDB" ,
                tag
                  str "GDB:119639" } } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "HGMD" ,
                tag
                  str "" } ,
              url "http://www.uwcm.ac.uk/uwcm/mg/search/119639.html" } } } ,
        {
          type comment ,
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          source {
            {
              src {
                db "Ensembl" ,
                tag
                  str "" } ,
              url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=CR749
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        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UCSC" ,
                tag
                  str "" } ,
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=
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        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "KEGG" ,
                tag
                  str "" } ,
              url "http://www.genome.ad.jp/dbget-bin/www_bget?hsa:2" } } } ,
        {
          type comment ,
          text "PharmGKB" ,
          version 0 ,
          source {
            {
              src {
                db "PharmGKB" ,
                tag
                  str "PA24357" } ,
              anchor "PA24357" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGC" ,
                tag
                  str "BC040071" } ,
              anchor "MGC" ,
              url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC040071" } } } } } ,
    {
      type comment ,
      heading "Pathways" ,
      version 0 ,
      comment {
        {
          type comment ,
          text "KEGG pathway: Alzheimer's disease" ,
          version 0 ,
          source {
            {
              src {
                db "05010" ,
                tag
                  str "05010" } ,
              anchor "05010" ,
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa05010+2" } } } ,
        {
          type comment ,
          text "KEGG pathway: Coagulation cascade" ,
          version 0 ,
          source {
            {
              src {
                db "04610" ,
                tag
                  str "04610" } ,
              anchor "04610" ,
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa04610+2" } } } ,
        {
          type comment ,
          text "KEGG pathway: Complement and coagulation cascades" ,
          version 0 ,
          source {
            {
              src {
                db "04610" ,
                tag
                  str "04610" } ,
              anchor "04610" ,
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa04610+2" } } } ,
        {
          type comment ,
          text "Reactome: Hemostasis" ,
          version 0 ,
          source {
            {
              anchor "49292" ,
              url "http://www.reactome.org/cgi-bin/link?SOURCE=UniProt&ID=P010
23" } } } } } ,
    {
      type generif ,
      text "an important involvement of alpha2M in regulation of increased
 proteolytic activity occurring in multiple sclerosis disease" ,
      version 0 ,
      refs {
        pmid 15511627 } ,
      create-date
        str "Dec 18 2004 10:01AM" ,
      update-date
        str "Dec 18 2004  1:19PM" } ,
    {
      type generif ,
      text "alpha2-macroglobulin inhibits human pepsin and gastricsin" ,
      version 0 ,
      refs {
        pmid 14506912 } ,
      create-date
        str "Oct  7 2003 12:00AM" ,
      update-date
        str "Jul  7 2004  1:36PM" } ,
    {
      type generif ,
      text "There is a significant genetic association of the 5 bp deletion
 and two novel polymorphisms in alpha-2-macroglobulin alpha-2-macroglobulin
 precursor with AD" ,
      version 0 ,
      refs {
        pmid 12966032 } ,
      create-date
        str "Jun 27 2004  5:41PM" ,
      update-date
        str "Jun 27 2004  6:18PM" } ,
    {
      type generif ,
      text "Alpha2-macroglobulin is a substrate and an endogenous inhibitor
 for ADAMTS-4 and ADAMTS-5" ,
      version 0 ,
      refs {
        pmid 14715656 } ,
      create-date
        str "Jun 14 2004  4:41PM" ,
      update-date
        str "Jun 14 2004  5:44PM" } ,
    {
      type generif ,
      text "A2M-D allele played a weak Alzheimer disease protective role, and
 APOE-E4 and A2M-G alleles might act synergistically in Alzheimer disease risk
 for mainland Han Chinese." ,
      version 0 ,
      refs {
        pmid 14675603 } ,
      create-date
        str "Feb 17 2004 12:00AM" ,
      update-date
        str "Apr 13 2004  1:35PM" } ,
    {
      type generif ,
      text "Plasma from patients homozygous for the intronic deletion (DD)
 showed normal alpha(2)M subunit size, conformation, and proteinase inhibitory
 activity. Plasma alpha(2)M from two DD patients showed markedly increased
 TGF-beta1 binding." ,
      version 0 ,
      refs {
        pmid 14678766 } ,
      create-date
        str "Jan 20 2004 12:00AM" ,
      update-date
        str "Mar  7 2004  7:01AM" } ,
    {
      type generif ,
      text "The presence of MPO-G/G and A2M-Val/Val genotypes synergistically
 increased the risk of AD (OR, 25.5; 95% CI, 4.65-139.75)." ,
      version 0 ,
      refs {
        pmid 15023809 } ,
      create-date
        str "Mar 25 2004 12:00AM" ,
      update-date
        str "Apr 18 2004  7:02AM" } ,
    {
      type generif ,
      text "alpha2-M deletion polymorphism is probably not associated with
 functional deficiencies important in Alzheimer's disease pathology" ,
      version 0 ,
      refs {
        pmid 14637088 } ,
      create-date
        str "Dec 31 2003 12:00AM" ,
      update-date
        str "Jan 11 2004  7:02AM" } ,
    {
      type generif ,
      text "FGF-2 and this protein interact at specific binding sites,
 involving different FGF-2 sequences." ,
      version 0 ,
      refs {
        pmid 12755687 } ,
      create-date
        str "Sep  7 2003 12:00AM" ,
      update-date
        str "Sep 28 2003  7:01AM" } ,
    {
      type generif ,
      text "alpha(2)M-derived peptides target the receptor-binding sequence in
 TGF-beta" ,
      version 0 ,
      refs {
        pmid 12755614 } ,
      create-date
        str "Jun 25 2003 12:00AM" ,
      update-date
        str "Jul  6 2003  7:01AM" } ,
    {
      type generif ,
      text "These results suggest the possible involvement of cathepsin E in
 disruption of the structural and functional integrity of alpha
 2-macroglobulin in the endolysosome system." ,
      version 0 ,
      refs {
        pmid 12631277 } ,
      create-date
        str "May  8 2003 12:00AM" ,
      update-date
        str "May 11 2003  7:01AM" } ,
    {
      type generif ,
      text "Alpha 2-macroglobulin enhances prothrombin activation and thrombin
 potential by inhibiting the anticoagulant protein C/protein S system in cord
 and adult plasma." ,
      version 0 ,
      refs {
        pmid 12062545 } ,
      create-date
        str "Feb  6 2003 12:00AM" ,
      update-date
        str "Aug 17 2003  7:01AM" } ,
    {
      type generif ,
      text "relationship between serum VEGF levels, alpha(2)M levels and the
 development of OHSS in hyperstimulated subjects undergoing IVF" ,
      version 0 ,
      refs {
        pmid 12042276 } ,
      create-date
        str "Dec 16 2002 12:00AM" ,
      update-date
        str "Feb  2 2003  7:00AM" } ,
    {
      type generif ,
      text "Genetic association of alpha2-macroglobulin polymorphisms with
 Alzheimer's disease" ,
      version 0 ,
      refs {
        pmid 12221172 } ,
      create-date
        str "Sep 27 2002 12:00AM" ,
      update-date
        str "Oct  7 2002  8:10AM" } ,
    {
      type generif ,
      text "Genetic association of argyrophilic grain disease with
 polymorphisms in alpha-2 macroglobulin." ,
      version 0 ,
      refs {
        pmid 12175343 } ,
      create-date
        str "Sep 24 2002 12:00AM" ,
      update-date
        str "Oct  7 2002  8:10AM" } ,
    {
      type generif ,
      text "The three-dimensional structure of the dimer reveals its
 structural organization in the tetrameric native and chymotrypsin alpha
 2-macroglobulin complexes." ,
      version 0 ,
      refs {
        pmid 12015318 } ,
      create-date
        str "Sep  5 2002 12:00AM" ,
      update-date
        str "Sep 23 2002  6:27AM" } ,
    {
      type generif ,
      text "has an important role in the AD-specific neurodegenerative process
 but its exon 24 Val-1000-Ile polymorphism is not likely to be associated with
 late-onset sporadic AD in the Hungarian population" ,
      version 0 ,
      refs {
        pmid 11901360 } ,
      create-date
        str "Aug  6 2002 12:00AM" ,
      update-date
        str "Aug 28 2002  6:15PM" } ,
    {
      type generif ,
      text "REVIEW: binds and neutralizes alfimeprase, which has direct
 proteolytic activity against the fibrinogen Aalpha chain" ,
      version 0 ,
      refs {
        pmid 11910179 } ,
      create-date
        str "Jun 12 2002 12:00AM" ,
      update-date
        str "Sep  7 2003  7:01AM" } ,
    {
      type generif ,
      text "distinct binding sites mediate interaction with beta-amyloid
 peptide and growth factors" ,
      version 0 ,
      refs {
        pmid 11823454 } ,
      create-date
        str "May  4 2002 12:00AM" ,
      update-date
        str "May 18 2002  6:08AM" } ,
    {
      type generif ,
      text "Differential binding to ldl receptor related protein" ,
      version 0 ,
      refs {
        pmid 11811950 } ,
      create-date
        str "Feb 14 2002 12:00AM" ,
      update-date
        str "Mar  4 2002  7:46AM" } ,
    {
      type generif ,
      heading "HIV-1 protein interactions" ,
      version 0 ,
      comment {
        {
          type generif ,
          text "Binding of HIV-1 Tat to LRP inhibits neuronal binding, uptake
 and degradation of physiological ligands for LRP, including
 alpha2-macroglobulin, apolipoprotein E4, amyloid precursor and amyloid
 beta-protein" ,
          version 0 ,
          refs {
            pmid 11100124 } ,
          comment {
            {
              type comment ,
              label "Tat" ,
              accession "NP_057853" ,
              version 1 ,
              source {
                {
                  src {
                    db "GeneID" ,
                    tag
                      id 155871 } } } } ,
            {
              type comment ,
              accession "NP_000005" ,
              version 1 } } ,
          create-date
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          update-date
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      db "LocusID" ,
      tag
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      db "MIM" ,
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      tag "PROP" ,
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      type comment ,
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              type peptide ,
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              src {
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Entrezgene ::= {
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    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 20 ,
        minute 30 ,
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    update-date
      std {
        year 2005 ,
        month 2 ,
        day 17 ,
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          type property ,
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            {
              type other ,
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              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "RH31202" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "RH73986" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "SHGC-2070" ,
              version 0 } } } } } ,
    {
      type comment ,
      heading "Additional Links" ,
      version 0 ,
      comment {
        {
          type comment ,
          text "MIM" ,
          version 0 ,
          source {
            {
              src {
                db "MIM" ,
                tag
                  str "108985" } ,
              anchor "108985" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "GDB" ,
                tag
                  str "GDB:568984" } } } } } } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 8 } ,
    {
      db "MIM" ,
      tag
        id 108985 } } ,
  xtra-index-terms {
    "LOC8" } ,
  xtra-properties {
    {
      tag "PROP" ,
      value "phenotype" } ,
    {
      tag "PROP" ,
      value "phenotype only" } } }
Entrezgene ::= {
  track-info {
    geneid 9 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 20 ,
        minute 30 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 4 ,
        day 15 ,
        hour 9 ,
        minute 40 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Homo sapiens" ,
      common "human" ,
      db {
        {
          db "taxon" ,
          tag
            id 9606 } } ,
      syn {
        "man" } ,
      orgname {
        name
          binomial {
            genus "Homo" ,
            species "sapiens" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini;
 Hominidae; Homo" ,
        gcode 1 ,
        mgcode 2 ,
        div "PRI" } } ,
    subtype {
      {
        subtype chromosome ,
        name "8" } } } ,
  gene {
    locus "NAT1" ,
    desc "N-acetyltransferase 1 (arylamine N-acetyltransferase)" ,
    maploc "8p23.1-p21.3" ,
    db {
      {
        db "MIM" ,
        tag
          id 108345 } } ,
    syn {
      "AAC1" } ,
    locus-tag "HGNC:7645" } ,
  prot {
    name {
      "N-acetyltransferase 1" ,
      "arylamine N-acetyltransferase 1" ,
      "arylamide acetylase 1 (N-acetyltransferase 1)" } } ,
  location {
    {
      display-str "8p23.1-p21.3" ,
      method
        map-type cyto } } ,
  gene-source {
    src "LocusLink" ,
    src-int 9 ,
    src-str2 "9" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000008" ,
      version 9 ,
      seqs {
        int {
          from 18111894 ,
          to 18125099 ,
          strand plus ,
          id
            gi 51511724 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_000662" ,
          version 4 ,
          genomic-coords {
            mix {
              int {
                from 18111894 ,
                to 18111968 ,
                strand plus ,
                id
                  gi 51511724 } ,
              int {
                from 18121199 ,
                to 18121277 ,
                strand plus ,
                id
                  gi 51511724 } ,
              int {
                from 18123830 ,
                to 18125099 ,
                strand plus ,
                id
                  gi 51511724 } } } ,
          seqs {
            whole
              gi 42741670 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_000653" ,
              version 3 ,
              genomic-coords {
                int {
                  from 18123836 ,
                  to 18124708 ,
                  strand plus ,
                  id
                    gi 51511724 } } ,
              seqs {
                whole
                  gi 42741671 } ,
              comment {
                {
                  type property ,
                  label "EC" ,
                  text "2.3.1.5" ,
                  version 0 ,
                  xtra-properties {
                    {
                      tag "EC" ,
                      value "2.3.1.5" } } } } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_030737" ,
      version 9 ,
      seqs {
        int {
          from 5912542 ,
          to 5925747 ,
          strand plus ,
          id
            gi 51466871 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_000662" ,
          version 4 ,
          genomic-coords {
            mix {
              int {
                from 5912542 ,
                to 5912616 ,
                strand plus ,
                id
                  gi 51466871 } ,
              int {
                from 5921847 ,
                to 5921925 ,
                strand plus ,
                id
                  gi 51466871 } ,
              int {
                from 5924478 ,
                to 5925747 ,
                strand plus ,
                id
                  gi 51466871 } } } ,
          seqs {
            whole
              gi 42741670 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_000653" ,
              version 3 ,
              genomic-coords {
                int {
                  from 5924484 ,
                  to 5925356 ,
                  strand plus ,
                  id
                    gi 51466871 } } ,
              seqs {
                whole
                  gi 42741671 } ,
              comment {
                {
                  type property ,
                  label "EC" ,
                  text "2.3.1.5" ,
                  version 0 ,
                  xtra-properties {
                    {
                      tag "EC" ,
                      value "2.3.1.5" } } } } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_086740" ,
      version 1 ,
      seqs {
        int {
          from 5593338 ,
          to 5606579 ,
          strand plus ,
          id
            gi 51467159 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_000662" ,
          version 4 ,
          genomic-coords {
            mix {
              int {
                from 5593338 ,
                to 5593412 ,
                strand plus ,
                id
                  gi 51467159 } ,
              int {
                from 5602680 ,
                to 5602758 ,
                strand plus ,
                id
                  gi 51467159 } ,
              int {
                from 5605310 ,
                to 5606579 ,
                strand plus ,
                id
                  gi 51467159 } } } ,
          seqs {
            whole
              gi 42741670 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_000653" ,
              version 3 ,
              genomic-coords {
                int {
                  from 5605316 ,
                  to 5606188 ,
                  strand plus ,
                  id
                    gi 51467159 } } ,
              seqs {
                whole
                  gi 42741671 } ,
              comment {
                {
                  type property ,
                  label "EC" ,
                  text "2.3.1.5" ,
                  version 0 ,
                  xtra-properties {
                    {
                      tag "EC" ,
                      value "2.3.1.5" } } } } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "HUGO Gene Nomenclature Committee" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "NAT1" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "N-acetyltransferase 1 (arylamine N-acetyltransferase)" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "GOA" ,
          url "http://www.ebi.ac.uk/GOA/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16407 } ,
                  anchor "acetyltransferase activity" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 10908296 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 4060 } ,
                  anchor "arylamine N-acetyltransferase activity" ,
                  post-text "evidence: TAS" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16740 } ,
                  anchor "transferase activity" ,
                  post-text "evidence: IEA" } } } } } ,
        {
          type comment ,
          label "Process" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 8152 } ,
                  anchor "metabolism" ,
                  post-text "evidence: IEA" } } } } } } } } ,
  homology {
    {
      type comment ,
      heading "Mouse, Rat" ,
      version 0 ,
      source {
        {
          src {
            db "HomoloGene" ,
            tag
              id 37329 } ,
          anchor "Map Viewer" ,
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=8&M
APS=genes-r-org/rat-chr/human%3A8,genes-r-org/mouse-chr/human%3A8,genes-r-org/
human-chr8&query=e%3A9[id]+AND+gene[obj_type]&QSTR=nat1&cmd=focus&fill=10" } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "HGNC" ,
            tag
              id 7645 } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "VALIDATED" ,
      version 0 } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 15487985 ,
        pmid 15320760 ,
        pmid 15226672 ,
        pmid 15039438 ,
        pmid 14705222 ,
        pmid 14672957 ,
        pmid 14608357 ,
        pmid 14517345 ,
        pmid 12946272 ,
        pmid 12902152 ,
        pmid 12888564 ,
        pmid 12860276 ,
        pmid 12832400 ,
        pmid 12692115 ,
        pmid 12682333 ,
        pmid 12485520 ,
        pmid 12477932 ,
        pmid 12355549 ,
        pmid 12052143 ,
        pmid 12037388 ,
        pmid 11955677 ,
        pmid 11955676 ,
        pmid 11927838 ,
        pmid 11470991 ,
        pmid 10908296 ,
        pmid 10862520 ,
        pmid 10767335 ,
        pmid 9168895 ,
        pmid 8110178 ,
        pmid 7773298 ,
        pmid 2340091 ,
        pmid 1968463 } } ,
    {
      type comment ,
      heading "Markers (Sequence Tagged Sites/STS)" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 24445 } ,
              anchor "STS-R79401" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "RH40594" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "sts-R79401" ,
              version 0 } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 57372 } ,
              anchor "STS-D90041" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "RH75822" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "sts-D90041" ,
              version 0 } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 63787 } ,
              anchor "RH70671" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "U52007" ,
              version 0 } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 271536 } ,
              anchor "PMC165273P2" ,
              post-text "(e-PCR)" } } } } } ,
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_000662" ,
          version 4 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 42741670 } ,
              anchor "NM_000662" } } ,
          seqs {
            whole
              gi 42741670 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_000653" ,
              version 3 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 42741671 } ,
                  anchor "NP_000653" ,
                  post-text "N-acetyltransferase 1" } } ,
              seqs {
                whole
                  gi 42741671 } ,
              comment {
                {
                  type other ,
                  heading "Consensus CDS (CCDS)" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "CCDS" ,
                        tag
                          str "CCDS6007.1" } ,
                      anchor "CCDS6007.1" } } } ,
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 42741671 } ,
                      pre-text "(1)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 1353 } ,
                          anchor "pfam00797: Acetyltransf_2;
 N-acetyltransferase" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 20 - 280  Blast Score: 1195" ,
                          version 0 } } } } } } } } ,
          comment {
            {
              type other ,
              heading "Source Sequence" ,
              version 0 ,
              source {
                {
                  src {
                    db "Nucleotide" ,
                    tag
                      str "AV754344,BC047666,BQ024509" } ,
                  anchor "AV754344,BC047666,BQ024509" } } ,
              comment {
                {
                  type other ,
                  version 0 } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type genomic ,
          heading "Genomic" ,
          accession "AF008204" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 2618821 } ,
              anchor "AF008204" } } ,
          seqs {
            whole
              gi 2618821 } ,
          products {
            {
              type peptide ,
              accession "AAB84384" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 2258431 } ,
                  anchor "AAB84384" } } ,
              seqs {
                whole
                  gi 2258431 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AF032677" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 2641552 } ,
              anchor "AF032677" } } ,
          seqs {
            whole
              gi 2641552 } ,
          products {
            {
              type peptide ,
              accession "AAB86878" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 2641553 } ,
                  anchor "AAB86878" } } ,
              seqs {
                whole
                  gi 2641553 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AF032678" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 2641554 } ,
              anchor "AF032678" } } ,
          seqs {
            whole
              gi 2641554 } ,
          products {
            {
              type peptide ,
              accession "AAB86879" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 2641555 } ,
                  anchor "AAB86879" } } ,
              seqs {
                whole
                  gi 2641555 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AF067408" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 3265061 } ,
              anchor "AF067408" } } ,
          seqs {
            whole
              gi 3265061 } ,
          products {
            {
              type peptide ,
              accession "AAC24707" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 3265062 } ,
                  anchor "AAC24707" } } ,
              seqs {
                whole
                  gi 3265062 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AF071552" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 3265151 } ,
              anchor "AF071552" } } ,
          seqs {
            whole
              gi 3265151 } ,
          products {
            {
              type peptide ,
              accession "AAC24712" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 3265152 } ,
                  anchor "AAC24712" } } ,
              seqs {
                whole
                  gi 3265152 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AF082903" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 3435297 } ,
              anchor "AF082903" } } ,
          seqs {
            whole
              gi 3435297 } ,
          products {
            {
              type peptide ,
              accession "AAD13343" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 3435298 } ,
                  anchor "AAD13343" } } ,
              seqs {
                whole
                  gi 3435298 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AF082904" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 3435299 } ,
              anchor "AF082904" } } ,
          seqs {
            whole
              gi 3435299 } ,
          products {
            {
              type peptide ,
              accession "AAC32388" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 3435300 } ,
                  anchor "AAC32388" } } ,
              seqs {
                whole
                  gi 3435300 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AF308866" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 10834832 } ,
              anchor "AF308866" } } ,
          seqs {
            whole
              gi 10834832 } ,
          products {
            {
              type peptide ,
              accession "AAG23842" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 10834833 } ,
                  anchor "AAG23842" } } ,
              seqs {
                whole
                  gi 10834833 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AJ278017" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 9663144 } ,
              anchor "AJ278017" } } ,
          seqs {
            whole
              gi 9663144 } ,
          products {
            {
              type peptide ,
              accession "CAC01128" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 9663145 } ,
                  anchor "CAC01128" } } ,
              seqs {
                whole
                  gi 9663145 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AJ307007" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 14018355 } ,
              anchor "AJ307007" } } ,
          seqs {
            whole
              gi 14018355 } ,
          products {
            {
              type peptide ,
              accession "CAC38345" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 14018356 } ,
                  anchor "CAC38345" } } ,
              seqs {
                whole
                  gi 14018356 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AY338489" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 32815075 } ,
              anchor "AY338489" } } ,
          seqs {
            whole
              gi 32815075 } ,
          products {
            {
              type peptide ,
              accession "AAP88036" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 32815076 } ,
                  anchor "AAP88036" } } ,
              seqs {
                whole
                  gi 32815076 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AY376850" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 34555772 } ,
              anchor "AY376850" } } ,
          seqs {
            whole
              gi 34555772 } ,
          products {
            {
              type peptide ,
              accession "AAQ74989" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 34555773 } ,
                  anchor "AAQ74989" } } ,
              seqs {
                whole
                  gi 34555773 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "U80835" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 2245375 } ,
              anchor "U80835" } } ,
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            whole
              gi 2245375 } ,
          products {
            {
              type peptide ,
              accession "AAB62398" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 2245376 } ,
                  anchor "AAB62398" } } ,
              seqs {
                whole
                  gi 2245376 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "X17059" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 34993 } ,
              anchor "X17059" } } ,
          seqs {
            whole
              gi 34993 } ,
          products {
            {
              type peptide ,
              accession "CAA34905" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 34994 } ,
                  anchor "CAA34905" } } ,
              seqs {
                whole
                  gi 34994 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AV754344" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 10912192 } ,
              anchor "AV754344" } } ,
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            whole
              gi 10912192 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } } ,
        {
          type mRNA ,
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          accession "BC013732" ,
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              src {
                db "Nucleotide" ,
                tag
                  id 16975545 } ,
              anchor "BC013732" } } ,
          seqs {
            whole
              gi 16975545 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC047666" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 28838335 } ,
              anchor "BC047666" } } ,
          seqs {
            whole
              gi 28838335 } ,
          products {
            {
              type peptide ,
              accession "AAH47666" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 28838336 } ,
                  anchor "AAH47666" } } ,
              seqs {
                whole
                  gi 28838336 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BQ024509" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 19759788 } ,
              anchor "BQ024509" } } ,
          seqs {
            whole
              gi 19759788 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BX647521" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 34366678 } ,
              anchor "BX647521" } } ,
          seqs {
            whole
              gi 34366678 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "D90041" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 219413 } ,
              anchor "D90041" } } ,
          seqs {
            whole
              gi 219413 } ,
          products {
            {
              type peptide ,
              accession "BAA14095" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 219414 } ,
                  anchor "BAA14095" } } ,
              seqs {
                whole
                  gi 219414 } } } } ,
        {
          type other ,
          text "None" ,
          version 0 ,
          products {
            {
              type peptide ,
              accession "P18440" ,
              version 0 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 114234 } ,
                  anchor "P18440" } } ,
              seqs {
                whole
                  gi 114234 } } } } } } ,
    {
      type comment ,
      heading "Additional Links" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Evidence Viewer" ,
                tag
                  str "9" } ,
              anchor "Evidence Viewer" ,
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti
g=NT_030737.9&gene=NAT1&lid=9&from=5912543&to=5925748" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "ModelMaker" ,
                tag
                  str "9" } ,
              anchor "ModelMaker" ,
              url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96
06&contig=NT_030737.9&gene=NAT1&lid=9" } } } ,
        {
          type comment ,
          text "UniGene" ,
          version 0 ,
          xtra-properties {
            {
              tag "UNIGENE" ,
              value "Hs.155956" } } ,
          source {
            {
              src {
                db "UniGene" ,
                tag
                  str "Hs.155956" } ,
              anchor "Hs.155956" ,
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=15
5956" } } } ,
        {
          type comment ,
          text "MIM" ,
          version 0 ,
          source {
            {
              src {
                db "MIM" ,
                tag
                  str "108345" } ,
              anchor "108345" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "HomoloGene" ,
                tag
                  str "9" } ,
              anchor "HomoloGene" ,
              url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=
9[loc]&TAXID=9606" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "AceView" ,
                tag
                  id 9 } ,
              anchor "AceView" ,
              url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l
ocusid&org=9606&l=9" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "GDB" ,
                tag
                  str "GDB:125364" } } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Ensembl" ,
                tag
                  str "" } ,
              url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=BC013
732" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UCSC" ,
                tag
                  str "" } ,
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=
BC013732" } } } ,
        {
          type comment ,
          text "PharmGKB" ,
          version 0 ,
          source {
            {
              src {
                db "PharmGKB" ,
                tag
                  str "PA17" } ,
              anchor "PA17" } } } ,
        {
          type comment ,
          text "Arylamine N-Acetyltransferase Nomenclature" ,
          version 0 ,
          source {
            {
              src {
                db "Arylamine N-Acetyltransferase Nomenclature" ,
                tag
                  str "Arylamine N-Acetyltransferase Nomenclature" } ,
              anchor "Arylamine N-Acetyltransferase Nomenclature" ,
              url "http://www.louisville.edu/medschool/pharmacology/NAT.html" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGC" ,
                tag
                  str "BC047666" } ,
              anchor "MGC" ,
              url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC047666" } } } } } ,
    {
      type generif ,
      text "In breast, NAT1 mRNA is transcribed from a strong promoter located
 11.8 kb upstream of the translated exon, and the mature spliced mRNA includes
 at least one additional non-coding exon." ,
      version 0 ,
      refs {
        pmid 15226672 } ,
      create-date
        str "Mar 26 2005 10:01AM" ,
      update-date
        str "Mar 26 2005  1:53PM" } ,
    {
      type generif ,
      text "Polymorphism at the NAT1 locus has been associated with the
 existence of at least 26 allelic variants, generating phenotypic variations
 in terms NAT-1 catalytic activity. This genetic variation affects the
 acetylator status of individuals." ,
      version 0 ,
      refs {
        pmid 15320760 } ,
      create-date
        str "Dec 18 2004 10:01AM" ,
      update-date
        str "Mar 17 2005  6:52AM" } ,
    {
      type generif ,
      text "NAT1 exists in the cell in either a stable acetylated state or an
 unstable non-acetylated state and mutations in the NAT1 gene that prevent
 protein acetylation produce a slow acetylator phenotype" ,
      version 0 ,
      refs {
        pmid 15039438 } ,
      create-date
        str "Jul  6 2004 11:50AM" ,
      update-date
        str "Jul  6 2004 12:11PM" } ,
    {
      type generif ,
      text "Analysis of the effect of active NAT-1 overexpression in a normal
 luminal epithelial-derived cell line demonstrated enhanced growth properties
 and etoposide resistance relative to control cells." ,
      version 0 ,
      refs {
        pmid 14517345 } ,
      create-date
        str "Jun 23 2004  4:43PM" ,
      update-date
        str "Jun 23 2004  5:16PM" } ,
    {
      type generif ,
      text "cellular generation of peroxynitrite may contribute to
 carcinogenesis and tumor progression by weakening key cellular defense
 enzymes such as arylamine N-acetyltransferase 1 (NAT1)" ,
      version 0 ,
      refs {
        pmid 14672957 } ,
      create-date
        str "Mar 24 2004 12:00AM" ,
      update-date
        str "May  9 2004  7:01AM" } ,
    {
      type generif ,
      text "although there is little overall association between NAT genotypes
 and risk of developing systemic lupus erythematosus, the interaction between
 NAT1 and NAT2 and specific exposures such as hair dyes may be important." ,
      version 0 ,
      refs {
        pmid 14705222 } ,
      create-date
        str "Apr 16 2004 12:00AM" ,
      update-date
        str "May  2 2004  7:01AM" } ,
    {
      type generif ,
      text "A putative RUNX1 binding site variant of NAT9 is associated with
 susceptibility to psoriasis" ,
      version 0 ,
      refs {
        pmid 14608357 } ,
      create-date
        str "Dec 18 2003 12:00AM" ,
      update-date
        str "Jan 11 2004  7:03AM" } ,
    {
      type generif ,
      text "Identification of minimal promoter sequences for transcription
 factor binding sites in the human N-acetyltransferase Type I gene. that binds" ,
      version 0 ,
      refs {
        pmid 12946272 } ,
      create-date
        str "Nov 24 2003 12:00AM" ,
      update-date
        str "Dec  7 2003  7:02AM" } ,
    {
      type generif ,
      text "Oxidative stress and cellular redox status may regulate NAT1
 activity and have important consequences with regard to drug
 biotransformation and cancer risk." ,
      version 0 ,
      refs {
        pmid 12832400 } ,
      create-date
        str "Oct  7 2003 12:00AM" ,
      update-date
        str "Nov 16 2003  7:02AM" } ,
    {
      type generif ,
      text "Variation in capacity for acetylation of 4ABP and PABA resulting
 from human NAT1 transgene is insufficient to affect 4ABP genotoxicity in
 mouse liver." ,
      version 0 ,
      refs {
        pmid 12902152 } ,
      create-date
        str "Sep  6 2003 12:00AM" ,
      update-date
        str "Sep 14 2003  7:01AM" } ,
    {
      type generif ,
      text "It is unlikely that the NAT1*10 or NAT2 rapid/intermediate
 genotypes are related to stomach cancer risk." ,
      version 0 ,
      refs {
        pmid 12692115 } ,
      create-date
        str "Sep  4 2003 12:00AM" ,
      update-date
        str "Sep 28 2003  7:01AM" } ,
    {
      type generif ,
      text "genetic polymorphisms of NAT1 and NAT2 have no independent effect
 on breast cancer risk, but they modulate breast cancer risk in the presence
 of GSTM1 and GSTT1 null genotypes." ,
      version 0 ,
      refs {
        pmid 12860276 } ,
      create-date
        str "Aug 18 2003 12:00AM" ,
      update-date
        str "Aug 24 2003  7:01AM" } ,
    {
      type generif ,
      text "NAT1 * 10 has increased risk of sporadic colorectal adenocarcinoma
 and significantly related to the later stage tumors, is not significantly
 related to the tumor location" ,
      version 0 ,
      refs {
        pmid 12485520 } ,
      create-date
        str "Jun 25 2003 12:00AM" ,
      update-date
        str "Jul 13 2003  7:01AM" } ,
    {
      type generif ,
      text "Single nucleotide polymorphisms of NAT1 and NAT2, and acetylation
 haplotype were not associated with increased risk for Parkinson disease" ,
      version 0 ,
      refs {
        pmid 12682333 } ,
      create-date
        str "Apr 11 2003 12:00AM" ,
      update-date
        str "Apr 27 2003  7:01AM" } ,
    {
      type generif ,
      text "NAT1 polymorphism (NAT1*10) indicates increased susceptibility to
 prostate cancer" ,
      version 0 ,
      refs {
        pmid 12355549 } ,
      create-date
        str "Oct 31 2002 12:00AM" ,
      update-date
        str "Feb  2 2003  7:01AM" } ,
    {
      type generif ,
      text "susceptibility gene for multifactorial adverse effects and
 xenobiotic-related diseases (review)" ,
      version 0 ,
      refs {
        pmid 12052143 } ,
      create-date
        str "Sep 12 2002 12:00AM" ,
      update-date
        str "Sep 16 2002  5:48AM" } ,
    {
      type generif ,
      text "NAT1 genotype acts as a modifier of diisothionate
 exposure-associated asthma risk" ,
      version 0 ,
      refs {
        pmid 11927838 } ,
      create-date
        str "Aug 30 2002 12:00AM" ,
      update-date
        str "Sep 16 2002  5:48AM" } ,
    {
      type generif ,
      text "NAT1 polymorphisms may be correlated with an increased risk of
 larynx cancer" ,
      version 0 ,
      refs {
        pmid 12037388 } ,
      create-date
        str "Aug 19 2002 12:00AM" ,
      update-date
        str "Aug 28 2002  6:15PM" } ,
    {
      type generif ,
      text "paclitaxel affected human leukemia HL-60 cells arylamine
 N-acetyltransferase (NAT) activity and DNA-2-aminofluorene adduct formation." ,
      version 0 ,
      refs {
        pmid 11955677 } ,
      create-date
        str "Jun 19 2002 12:00AM" ,
      update-date
        str "Jun 24 2002  6:31AM" } ,
    {
      type generif ,
      text "paclitaxel is an uncompetitive inhibitor to arylamine
 N-acetyltransferase (NAT) enzyme" ,
      version 0 ,
      refs {
        pmid 11955676 } ,
      create-date
        str "Jun 19 2002 12:00AM" ,
      update-date
        str "Jun 24 2002  6:31AM" } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 9 } ,
    {
      db "MIM" ,
      tag
        id 108345 } } ,
  xtra-index-terms {
    "LOC9" } }
Entrezgene ::= {
  track-info {
    geneid 10 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 20 ,
        minute 30 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 4 ,
        day 17 ,
        hour 11 ,
        minute 9 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Homo sapiens" ,
      common "human" ,
      db {
        {
          db "taxon" ,
          tag
            id 9606 } } ,
      syn {
        "man" } ,
      orgname {
        name
          binomial {
            genus "Homo" ,
            species "sapiens" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini;
 Hominidae; Homo" ,
        gcode 1 ,
        mgcode 2 ,
        div "PRI" } } ,
    subtype {
      {
        subtype chromosome ,
        name "8" } } } ,
  gene {
    locus "NAT2" ,
    desc "N-acetyltransferase 2 (arylamine N-acetyltransferase)" ,
    maploc "8p22" ,
    db {
      {
        db "MIM" ,
        tag
          id 243400 } } ,
    syn {
      "AAC2" } ,
    locus-tag "HGNC:7646" } ,
  prot {
    name {
      "arylamide acetylase 2" ,
      "Arylamine N-acetyltransferase-2" ,
      "arylamide acetylase 2 (N-acetyltransferase 2, isoniazid inactivation)" } } ,
  summary "The intronless NAT2 gene encodes N-acetyltransferase 2 (arylamine
 N-acetyltransferase 2). This enzyme functions to both activate and deactivate
 arylamine and hydrazine drugs and carcinogens. Polymorphisms in this gene are
 reponsible for the N-acetylation polymorphism in which human populations
 segregate into rapid,intermediate, and slow acetylator phenotypes.
 Polymorphisms in NAT2 are also associated with higher incidences of cancer
 and drug toxicity.A second arylamine N-acetyltransferase gene (NAT1) is
 located near NAT2." ,
  location {
    {
      display-str "8p22" ,
      method
        map-type cyto } } ,
  gene-source {
    src "LocusLink" ,
    src-int 10 ,
    src-str2 "10" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000008" ,
      version 9 ,
      seqs {
        int {
          from 18293034 ,
          to 18302961 ,
          strand plus ,
          id
            gi 51511724 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_000015" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 18293034 ,
                to 18293134 ,
                strand plus ,
                id
                  gi 51511724 } ,
              int {
                from 18301787 ,
                to 18302961 ,
                strand plus ,
                id
                  gi 51511724 } } } ,
          seqs {
            whole
              gi 4557782 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_000006" ,
              version 1 ,
              genomic-coords {
                int {
                  from 18301793 ,
                  to 18302665 ,
                  strand plus ,
                  id
                    gi 51511724 } } ,
              seqs {
                whole
                  gi 4557783 } ,
              comment {
                {
                  type property ,
                  label "EC" ,
                  text "2.3.1.5" ,
                  version 0 ,
                  xtra-properties {
                    {
                      tag "EC" ,
                      value "2.3.1.5" } } } } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_030737" ,
      version 9 ,
      seqs {
        int {
          from 6093682 ,
          to 6103609 ,
          strand plus ,
          id
            gi 51466871 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_000015" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 6093682 ,
                to 6093782 ,
                strand plus ,
                id
                  gi 51466871 } ,
              int {
                from 6102435 ,
                to 6103609 ,
                strand plus ,
                id
                  gi 51466871 } } } ,
          seqs {
            whole
              gi 4557782 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_000006" ,
              version 1 ,
              genomic-coords {
                int {
                  from 6102441 ,
                  to 6103313 ,
                  strand plus ,
                  id
                    gi 51466871 } } ,
              seqs {
                whole
                  gi 4557783 } ,
              comment {
                {
                  type property ,
                  label "EC" ,
                  text "2.3.1.5" ,
                  version 0 ,
                  xtra-properties {
                    {
                      tag "EC" ,
                      value "2.3.1.5" } } } } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_086740" ,
      version 1 ,
      seqs {
        int {
          from 5773920 ,
          to 5783845 ,
          strand plus ,
          id
            gi 51467159 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_000015" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 5773920 ,
                to 5774020 ,
                strand plus ,
                id
                  gi 51467159 } ,
              int {
                from 5782671 ,
                to 5783845 ,
                strand plus ,
                id
                  gi 51467159 } } } ,
          seqs {
            whole
              gi 4557782 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_000006" ,
              version 1 ,
              genomic-coords {
                int {
                  from 5782677 ,
                  to 5783549 ,
                  strand plus ,
                  id
                    gi 51467159 } } ,
              seqs {
                whole
                  gi 4557783 } ,
              comment {
                {
                  type property ,
                  label "EC" ,
                  text "2.3.1.5" ,
                  version 0 ,
                  xtra-properties {
                    {
                      tag "EC" ,
                      value "2.3.1.5" } } } } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "HUGO Gene Nomenclature Committee" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "NAT2" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "N-acetyltransferase 2 (arylamine N-acetyltransferase)" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "GOA" ,
          url "http://www.ebi.ac.uk/GOA/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16407 } ,
                  anchor "acetyltransferase activity" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 2340091 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 4060 } ,
                  anchor "arylamine N-acetyltransferase activity" ,
                  post-text "evidence: TAS" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16740 } ,
                  anchor "transferase activity" ,
                  post-text "evidence: IEA" } } } } } ,
        {
          type comment ,
          label "Process" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 8152 } ,
                  anchor "metabolism" ,
                  post-text "evidence: IEA" } } } } } } } } ,
  homology {
    {
      type comment ,
      heading "Mouse, Rat" ,
      version 0 ,
      source {
        {
          src {
            db "HomoloGene" ,
            tag
              id 32047 } ,
          anchor "Map Viewer" ,
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=8&M
APS=genes-r-org/rat-chr/human%3A8,genes-r-org/mouse-chr/human%3A8,genes-r-org/
human-chr8&query=e%3A10[id]+AND+gene[obj_type]&QSTR=nat2&cmd=focus&fill=10" } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "HGNC" ,
            tag
              id 7646 } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "REVIEWED" ,
      version 0 } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 15671210 ,
        pmid 15637738 ,
        pmid 15609332 ,
        pmid 15588473 ,
        pmid 15225898 ,
        pmid 15162844 ,
        pmid 15005011 ,
        pmid 14747882 ,
        pmid 14705222 ,
        pmid 14648207 ,
        pmid 14618622 ,
        pmid 14528063 ,
        pmid 12884528 ,
        pmid 12877350 ,
        pmid 12860276 ,
        pmid 12835615 ,
        pmid 12773763 ,
        pmid 12760253 ,
        pmid 12724621 ,
        pmid 12692115 ,
        pmid 12682333 ,
        pmid 12654968 ,
        pmid 12622714 ,
        pmid 12611196 ,
        pmid 12477932 ,
        pmid 12474054 ,
        pmid 12469231 ,
        pmid 12465141 ,
        pmid 12430181 ,
        pmid 12397635 ,
        pmid 12360107 ,
        pmid 12355549 ,
        pmid 12235453 ,
        pmid 12222688 ,
        pmid 12163321 ,
        pmid 12037388 ,
        pmid 12016157 ,
        pmid 12015038 ,
        pmid 11915035 ,
        pmid 11872636 ,
        pmid 11846845 ,
        pmid 11470991 ,
        pmid 9202751 ,
        pmid 8460648 ,
        pmid 8110178 ,
        pmid 8102597 ,
        pmid 7915226 ,
        pmid 7902079 ,
        pmid 7773298 ,
        pmid 2734109 ,
        pmid 2340091 ,
        pmid 2068113 ,
        pmid 1996083 ,
        pmid 1968463 ,
        pmid 1676262 ,
        pmid 1441598 ,
        pmid 1381364 ,
        pmid 1306121 } } ,
    {
      type comment ,
      heading "Markers (Sequence Tagged Sites/STS)" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
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    {
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        {
          type comment ,
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              tag "UNIGENE" ,
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                  str "Hs.2" } ,
              anchor "Hs.2" ,
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                  str "243400" } ,
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                  id 10 } ,
              anchor "AceView" ,
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              src {
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        {
          type comment ,
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              src {
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                  str "" } ,
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          type comment ,
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            {
              src {
                db "PharmGKB" ,
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                  str "PA18" } ,
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        {
          type comment ,
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                tag
                  str "Arylamine N-Acetyltransferase Nomenclature" } ,
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        {
          type comment ,
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              src {
                db "MGC" ,
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                  str "BC015878,BC067218" } ,
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    {
      type generif ,
      text "there is no association between endometriosis and NAT2 in South
 Indian women" ,
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        pmid 15588473 } ,
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        str "Mar 19 2005 10:01AM" ,
      update-date
        str "Mar 19 2005 11:47AM" } ,
    {
      type generif ,
      text "Risks for colorectal cancer are significantly associated with the
 genetic polymorphisms of GSTT1 deletion, NAT2-rapid acetylator phenotype and
 genotye and NAT2-rapid acetylator phenotype." ,
      version 0 ,
      refs {
        pmid 15637738 } ,
      create-date
        str "Mar  7 2005  7:07PM" ,
      update-date
        str "Mar  8 2005 12:10AM" } ,
    {
      type generif ,
      text "Cigarette smoking is associated with increased risk of breast
 cancer in women with the NAT2 slow acetylator genotype." ,
      version 0 ,
      refs {
        pmid 15225898 } ,
      create-date
        str "Nov 13 2004 10:01AM" ,
      update-date
        str "Nov 13 2004 10:50AM" } ,
    {
      type generif ,
      text "N-acetyltransferase 2 polymorphism does not play an important role
 in breast cancer risk of Turkish women by altering the capacity in
 deactivation of environmental carcinogens" ,
      version 0 ,
      refs {
        pmid 15162844 } ,
      create-date
        str "Oct  4 2004 10:33AM" ,
      update-date
        str "Oct  4 2004 11:19AM" } ,
    {
      type generif ,
      text "NAT2 slow acetylator genotypes might modulate the effect of
 carcinogenic arylamines contained in tobacco smoke." ,
      version 0 ,
      refs {
        pmid 14648207 } ,
      create-date
        str "Sep 27 2004  4:34PM" ,
      update-date
        str "Sep 27 2004  5:11PM" } ,
    {
      type generif ,
      text "Arylamine N-acetyltransferase 2 is a genetically polymorphic phase
 II enzyme with a role in the metabolism of many xenobiotics." ,
      version 0 ,
      refs {
        pmid 14747882 } ,
      create-date
        str "Aug  2 2004  1:09PM" ,
      update-date
        str "Aug  2 2004  1:38PM" } ,
    {
      type generif ,
      text "although there is little overall association between NAT genotypes
 and risk of developing systemic lupus erythematosus, the interaction between
 NAT1 and NAT2 and specific exposures such as hair dyes may be important" ,
      version 0 ,
      refs {
        pmid 14705222 } ,
      create-date
        str "Apr 16 2004 12:00AM" ,
      update-date
        str "May  2 2004  7:01AM" } ,
    {
      type generif ,
      text "The NAT2 acetylator genotype may modify esophageal cancer risk in
 humans from exposure to barbecued/grilled meat." ,
      version 0 ,
      refs {
        pmid 12773763 } ,
      create-date
        str "Feb 13 2004 12:00AM" ,
      update-date
        str "Feb 22 2004  7:01AM" } ,
    {
      type generif ,
      text "N-acetyltransferase 2 polymorphism does not differ between
 patients suffering from atopic dermatitis and healthy subjects" ,
      version 0 ,
      refs {
        pmid 14528063 } ,
      create-date
        str "Feb  5 2004 12:00AM" ,
      update-date
        str "Feb 15 2004  6:33PM" } ,
    {
      type generif ,
      text "Genetic NAT2 polymorphism may play a role in lifestyle
 factors-related hepato- carcinogenesis, particulary critical in smoking
 related hepatocarcinogenesis." ,
      version 0 ,
      refs {
        pmid 12877350 } ,
      create-date
        str "Feb  4 2004 12:00AM" ,
      update-date
        str "Feb 15 2004  6:32PM" } ,
    {
      type generif ,
      text "Slow acetylation activity is associated with age-related cataract
 formation." ,
      version 0 ,
      refs {
        pmid 12724621 } ,
      create-date
        str "Jan  6 2004 12:00AM" ,
      update-date
        str "Feb 22 2004  7:01AM" } ,
    {
      type generif ,
      text "A significant association between Parkinson disease & the slow
 acetylator genotype for N-acetyltransferase 2 in Hong Kong Chinesed provides
 evidence for a possible functional relationship between NAT2 slow acetylator
 genotype & PD in both racial groups." ,
      version 0 ,
      refs {
        pmid 12654968 } ,
      create-date
        str "Dec 23 2003 12:00AM" ,
      update-date
        str "Jan 18 2004  7:01AM" } ,
    {
      type generif ,
      text "RFLP of the gene coding for N-acetyltransferase 2 (NAT2) was typed
 in populations of the Volga-Ural region (Bashkirs, Tatars, Chuvashes,
 Udmurts, and Russians) and in patients with chronic obstructive pulmonary
 disease (COPD) and in healthy individuals" ,
      version 0 ,
      refs {
        pmid 12884528 } ,
      create-date
        str "Dec 18 2003 12:00AM" ,
      update-date
        str "Jan 25 2004  7:01AM" } ,
    {
      type generif ,
      text "We conclude that smoking increases risk of colorectal adenomas and
 that SULT1A1 and NAT2 only modestly modify this association." ,
      version 0 ,
      refs {
        pmid 14618622 } ,
      create-date
        str "Dec 11 2003 12:00AM" ,
      update-date
        str "Dec 21 2003  7:01AM" } ,
    {
      type generif ,
      text "In human, NAT2 polymorphism may be a genetic risk factor for joint
 destruction." ,
      version 0 ,
      refs {
        pmid 15005011 } ,
      create-date
        str "May  7 2004 12:00AM" ,
      update-date
        str "May 16 2004  7:01AM" } ,
    {
      type generif ,
      text "It is unlikely that the NAT1*10 or NAT2 rapid/intermediate
 genotypes are related to stomach cancer risk." ,
      version 0 ,
      refs {
        pmid 12692115 } ,
      create-date
        str "Sep  4 2003 12:00AM" ,
      update-date
        str "Sep 28 2003  7:01AM" } ,
    {
      type generif ,
      text "genetic polymorphisms of NAT1 and NAT2 have no independent effect
 on breast cancer risk, but they modulate breast cancer risk in the presence
 of GSTM1 and GSTT1 null genotypes." ,
      version 0 ,
      refs {
        pmid 12860276 } ,
      create-date
        str "Aug 18 2003 12:00AM" ,
      update-date
        str "Aug 24 2003  7:01AM" } ,
    {
      type generif ,
      text "NAT2 slow acetylator genotype plays an important role in
 determining the risk of developing prostate cancer in Japanese men and is
 also associated with more clinically advanced and pathologically aggressive
 disease." ,
      version 0 ,
      refs {
        pmid 12622714 } ,
      create-date
        str "Aug  9 2003 12:00AM" ,
      update-date
        str "Aug 24 2003  7:01AM" } ,
    {
      type generif ,
      text "Polymorphism of Nat2 encoding phase 2 xenobiotic detoxication
 enzyme was studied." ,
      version 0 ,
      refs {
        pmid 12760253 } ,
      create-date
        str "Jun 26 2003 12:00AM" ,
      update-date
        str "Aug 10 2003  7:01AM" } ,
    {
      type generif ,
      text "This enzyme is polymorphic in various ethnic populations of South
 India." ,
      version 0 ,
      refs {
        pmid 12469231 } ,
      create-date
        str "May 24 2003 12:00AM" ,
      update-date
        str "Jul 27 2003  7:01AM" } ,
    {
      type generif ,
      text "Maternal NAT2 acetylator status seems not to be an important
 factor in the etiology of orofacial clefts." ,
      version 0 ,
      refs {
        pmid 12397635 } ,
      create-date
        str "May  7 2003 12:00AM" ,
      update-date
        str "Jun  1 2003  7:01AM" } ,
    {
      type generif ,
      text "Genotyping the NAT2 gene and estimating diplotype configuration
 before administration of SSZ may reduce the frequency of adverse effects in
 Japanese patients with RA." ,
      version 0 ,
      refs {
        pmid 12465141 } ,
      create-date
        str "May  2 2003 12:00AM" ,
      update-date
        str "May 11 2003  7:01AM" } ,
    {
      type generif ,
      text "Single nucleotide polymorphisms of NAT1 and NAT2, and acetylation
 haplotype were not associated with increased risk for Parkinson disease" ,
      version 0 ,
      refs {
        pmid 12682333 } ,
      create-date
        str "Apr 11 2003 12:00AM" ,
      update-date
        str "Apr 27 2003  7:01AM" } ,
    {
      type generif ,
      text "lack of association between polymorphism of this gene and systemic
 lupus erythematosus" ,
      version 0 ,
      refs {
        pmid 12360107 } ,
      create-date
        str "Apr  9 2003 12:00AM" ,
      update-date
        str "Apr 27 2003  7:01AM" } ,
    {
      type generif ,
      text "Polymorphic N-acetyltransferase (NAT2) is involved in the
 metabolism of several compounds relevant in pharmacology or toxicology, with
 diverse clinical consequences--review" ,
      version 0 ,
      refs {
        pmid 12611196 } ,
      create-date
        str "Mar 24 2003 12:00AM" ,
      update-date
        str "Mar 31 2003  6:30AM" } ,
    {
      type generif ,
      text "N-acetyltransferase 2*19 possessing the C190T (R64W) single
 nucleotide polymorphisms encodes a slow acetylator phenotype for both N- and
 O-acetylation, due to a reduction in the amount and stability of the NAT2 19
 allozyme" ,
      version 0 ,
      refs {
        pmid 12222688 } ,
      create-date
        str "Mar 10 2003 12:00AM" ,
      update-date
        str "Apr 13 2003  7:01AM" } ,
    {
      type generif ,
      text "NAT2 slow acetylation and GSTM1 null genotypes may increase
 postmenopausal breast cancer risk in long-term smoking women." ,
      version 0 ,
      refs {
        pmid 12835615 } ,
      create-date
        str "Mar  7 2004 12:00AM" ,
      update-date
        str "Apr 18 2004  7:02AM" } ,
    {
      type generif ,
      text "A slow acetylator genotype of this enzyme is associated with an
 increased risk of advanced cervical cancer." ,
      version 0 ,
      refs {
        pmid 12474054 } ,
      create-date
        str "Feb 27 2003 12:00AM" ,
      update-date
        str "Apr 13 2003  7:01AM" } ,
    {
      type generif ,
      text "Women with the GSTT1 null genotype were found to have a
 significant 3.15-fold increased risk of breast cancer (95% CI = 1.7-5.8),
 while GSTM1 and NAT2 genotypes were not associated with breast cancer risk." ,
      version 0 ,
      refs {
        pmid 12430181 } ,
      create-date
        str "Nov 25 2002 12:00AM" ,
      update-date
        str "Feb  2 2003  7:01AM" } ,
    {
      type generif ,
      text "NAT2 slow genotype with NAT1 polymorphism indicates increased
 susceptibility to prostate cancer" ,
      version 0 ,
      refs {
        pmid 12355549 } ,
      create-date
        str "Oct 31 2002 12:00AM" ,
      update-date
        str "Feb  2 2003  7:01AM" } ,
    {
      type generif ,
      text "NAT2 slow acetylation genotype may be a risk factor of individual
 susceptibility to rheumatoid arthritis." ,
      version 0 ,
      refs {
        pmid 12235453 } ,
      create-date
        str "Oct  7 2002 12:00AM" ,
      update-date
        str "Feb  2 2003  7:01AM" } ,
    {
      type generif ,
      text "NAT2 acetylator status can influence susceptibility to breast
 cancer after exposure to tobacco smoke carcinogens; effect appears to be
 differential for active and passive smoke exposure" ,
      version 0 ,
      refs {
        pmid 12163321 } ,
      create-date
        str "Sep  7 2002 12:00AM" ,
      update-date
        str "Sep 16 2002  5:48AM" } ,
    {
      type generif ,
      text "NAT2 polymorphisms may be correlated with an increased risk of
 larynx cancer" ,
      version 0 ,
      refs {
        pmid 12037388 } ,
      create-date
        str "Aug 19 2002 12:00AM" ,
      update-date
        str "Aug 28 2002  6:15PM" } ,
    {
      type generif ,
      text "The combined effect of N-acetyltransferase 2 (NAT2) slow genotype
 and exposure to smoking is observed during the development of laryngeal
 cancer." ,
      version 0 ,
      refs {
        pmid 12015038 } ,
      create-date
        str "Aug  9 2002 12:00AM" ,
      update-date
        str "Sep 16 2002  5:48AM" } ,
    {
      type generif ,
      text "urinary excretion of
 N(2)-(beta-1-glucos-iduronyl)-2-hydroxyamino-1-methyl-6-phenylimidazo[4,5-b]p
yridine relationship to activity levels of NAT2" ,
      version 0 ,
      refs {
        pmid 12016157 } ,
      create-date
        str "Jun 12 2002 12:00AM" ,
      update-date
        str "Jun 24 2002  6:31AM" } ,
    {
      type generif ,
      text "Polymorphism of the N-acetyltransferase 2 gene as a susceptibility
 risk factor for antituberculosis drug-induced hepatitis." ,
      version 0 ,
      refs {
        pmid 11915035 } ,
      create-date
        str "Apr 15 2002 12:00AM" ,
      update-date
        str "Apr 28 2002  6:17PM" } ,
    {
      type generif ,
      text "Association between bone loss in periodontal disease and
 polymorphism of N-acetyltransferase (NAT2)" ,
      version 0 ,
      refs {
        pmid 11846845 } ,
      create-date
        str "Apr  9 2002 12:00AM" ,
      update-date
        str "May 14 2002  5:48AM" } ,
    {
      type generif ,
      text "we investigated the relationship between the levels of aromatic
 DNA adducts in breast tissues and polymorphisms of the drug-metabolizing
 genes CYP1A1, NAT2, and GSTM1 in 166 women having breast cancer" ,
      version 0 ,
      refs {
        pmid 11872636 } ,
      create-date
        str "Apr  2 2002 12:00AM" ,
      update-date
        str "Apr  8 2002  3:24PM" } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 10 } ,
    {
      db "MIM" ,
      tag
        id 243400 } } ,
  xtra-index-terms {
    "LOC10" } }
Entrezgene ::= {
  track-info {
    geneid 11 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 20 ,
        minute 30 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 3 ,
        day 5 ,
        hour 11 ,
        minute 30 ,
        second 0 } } ,
  type pseudo ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Homo sapiens" ,
      common "human" ,
      db {
        {
          db "taxon" ,
          tag
            id 9606 } } ,
      syn {
        "man" } ,
      orgname {
        name
          binomial {
            genus "Homo" ,
            species "sapiens" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini;
 Hominidae; Homo" ,
        gcode 1 ,
        mgcode 2 ,
        div "PRI" } } ,
    subtype {
      {
        subtype chromosome ,
        name "8" } } } ,
  gene {
    locus "AACP" ,
    desc "arylamide acetylase pseudogene" ,
    maploc "8p22" ,
    syn {
      "NATP" } ,
    locus-tag "HGNC:15" } ,
  location {
    {
      display-str "8p22" ,
      method
        map-type cyto } } ,
  gene-source {
    src "LocusLink" ,
    src-int 11 ,
    src-str2 "11" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      version 0 } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "HUGO Gene Nomenclature Committee" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "AACP" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "arylamide acetylase pseudogene" ,
          version 0 } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "HGNC" ,
            tag
              id 15 } } } } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 2340091 } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type genomic ,
          heading "Genomic" ,
          accession "X17060" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 34995 } ,
              anchor "X17060" } } ,
          seqs {
            whole
              gi 34995 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } } } } ,
    {
      type comment ,
      heading "Additional Links" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "GDB" ,
                tag
                  str "GDB:132838" } } } } } } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11 } } ,
  xtra-index-terms {
    "LOC11" } }
Entrezgene ::= {
  track-info {
    geneid 12 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 20 ,
        minute 30 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 4 ,
        day 14 ,
        hour 13 ,
        minute 15 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Homo sapiens" ,
      common "human" ,
      db {
        {
          db "taxon" ,
          tag
            id 9606 } } ,
      syn {
        "man" } ,
      orgname {
        name
          binomial {
            genus "Homo" ,
            species "sapiens" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini;
 Hominidae; Homo" ,
        gcode 1 ,
        mgcode 2 ,
        div "PRI" } } ,
    subtype {
      {
        subtype chromosome ,
        name "14" } } } ,
  gene {
    locus "SERPINA3" ,
    desc "serine (or cysteine) proteinase inhibitor, clade A (alpha-1
 antiproteinase, antitrypsin), member 3" ,
    maploc "14q32.1" ,
    db {
      {
        db "MIM" ,
        tag
          id 107280 } } ,
    syn {
      "ACT" ,
      "AACT" ,
      "MGC88254" } ,
    locus-tag "HGNC:16" } ,
  prot {
    name {
      "serine (or cysteine) proteinase inhibitor, clade A, member 3" ,
      "antichymotrypsin" ,
      "alpha-1-antichymotrypsin" ,
      "serine (or cysteine) proteinase inhibitor, clade A, member 3" } } ,
  summary "The protein encoded by this gene is a plasma protease inhibitor and
 member of the serine protease inhibitor class.  Polymorphisms in this protein
 appear to be tissue specific and influence protease targeting.  Variation in
 this protein's sequence have been implicated in Alzheimer's disease, and
 deficiency of this protein has been associated with liver disease.  Mutations
 have been identified in patients with Parkinson disease and chronic
 obstructive pulmonary disease." ,
  location {
    {
      display-str "14q32.1" ,
      method
        map-type cyto } } ,
  gene-source {
    src "LocusLink" ,
    src-int 12 ,
    src-str2 "12" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000014" ,
      version 7 ,
      seqs {
        int {
          from 94150523 ,
          to 94160143 ,
          strand plus ,
          id
            gi 51511730 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_001085" ,
          version 2 ,
          genomic-coords {
            mix {
              int {
                from 94150523 ,
                to 94151173 ,
                strand plus ,
                id
                  gi 51511730 } ,
              int {
                from 94155284 ,
                to 94155557 ,
                strand plus ,
                id
                  gi 51511730 } ,
              int {
                from 94158430 ,
                to 94158580 ,
                strand plus ,
                id
                  gi 51511730 } ,
              int {
                from 94159700 ,
                to 94160143 ,
                strand plus ,
                id
                  gi 51511730 } } } ,
          seqs {
            whole
              gi 9665246 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              label "precursor" ,
              accession "NP_001076" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 94150531 ,
                    to 94151173 ,
                    strand plus ,
                    id
                      gi 51511730 } ,
                  {
                    from 94155284 ,
                    to 94155557 ,
                    strand plus ,
                    id
                      gi 51511730 } ,
                  {
                    from 94158430 ,
                    to 94158580 ,
                    strand plus ,
                    id
                      gi 51511730 } ,
                  {
                    from 94159700 ,
                    to 94159935 ,
                    strand plus ,
                    id
                      gi 51511730 } } } ,
              seqs {
                whole
                  gi 4501843 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_026437" ,
      version 11 ,
      seqs {
        int {
          from 76080523 ,
          to 76090143 ,
          strand plus ,
          id
            gi 51493278 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_001085" ,
          version 2 ,
          genomic-coords {
            mix {
              int {
                from 76080523 ,
                to 76081173 ,
                strand plus ,
                id
                  gi 51493278 } ,
              int {
                from 76085284 ,
                to 76085557 ,
                strand plus ,
                id
                  gi 51493278 } ,
              int {
                from 76088430 ,
                to 76088580 ,
                strand plus ,
                id
                  gi 51493278 } ,
              int {
                from 76089700 ,
                to 76090143 ,
                strand plus ,
                id
                  gi 51493278 } } } ,
          seqs {
            whole
              gi 9665246 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              label "precursor" ,
              accession "NP_001076" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 76080531 ,
                    to 76081173 ,
                    strand plus ,
                    id
                      gi 51493278 } ,
                  {
                    from 76085284 ,
                    to 76085557 ,
                    strand plus ,
                    id
                      gi 51493278 } ,
                  {
                    from 76088430 ,
                    to 76088580 ,
                    strand plus ,
                    id
                      gi 51493278 } ,
                  {
                    from 76089700 ,
                    to 76089935 ,
                    strand plus ,
                    id
                      gi 51493278 } } } ,
              seqs {
                whole
                  gi 4501843 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_086807" ,
      version 1 ,
      seqs {
        int {
          from 23153523 ,
          to 23163143 ,
          strand plus ,
          id
            gi 51472322 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_001085" ,
          version 2 ,
          genomic-coords {
            mix {
              int {
                from 23153523 ,
                to 23154173 ,
                strand plus ,
                id
                  gi 51472322 } ,
              int {
                from 23158284 ,
                to 23158557 ,
                strand plus ,
                id
                  gi 51472322 } ,
              int {
                from 23161430 ,
                to 23161580 ,
                strand plus ,
                id
                  gi 51472322 } ,
              int {
                from 23162700 ,
                to 23163143 ,
                strand plus ,
                id
                  gi 51472322 } } } ,
          seqs {
            whole
              gi 9665246 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              label "precursor" ,
              accession "NP_001076" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 23153531 ,
                    to 23154173 ,
                    strand plus ,
                    id
                      gi 51472322 } ,
                  {
                    from 23158284 ,
                    to 23158557 ,
                    strand plus ,
                    id
                      gi 51472322 } ,
                  {
                    from 23161430 ,
                    to 23161580 ,
                    strand plus ,
                    id
                      gi 51472322 } ,
                  {
                    from 23162700 ,
                    to 23162935 ,
                    strand plus ,
                    id
                      gi 51472322 } } } ,
              seqs {
                whole
                  gi 4501843 } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "HUGO Gene Nomenclature Committee" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "SERPINA3" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "serine (or cysteine) proteinase inhibitor, clade A (alpha-1
 antiproteinase, antitrypsin), member 3" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "GOA" ,
          url "http://www.ebi.ac.uk/GOA/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 9880565 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 3677 } ,
                  anchor "DNA binding" ,
                  post-text "evidence: IC" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 9880565 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 30569 } ,
                  anchor "chymotrypsin inhibitor activity" ,
                  post-text "evidence: NAS" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 12709365 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5515 } ,
                  anchor "protein binding" ,
                  post-text "evidence: IPI" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 4867 } ,
                  anchor "serine-type endopeptidase inhibitor activity" ,
                  post-text "evidence: IEA" } } } } } ,
        {
          type comment ,
          label "Process" ,
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                      id 6953 } ,
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                      id 6954 } ,
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                  src {
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                  anchor "regulation of lipid metabolism" ,
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                  src {
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              type comment ,
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                      id 5576 } ,
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          src {
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    {
      type comment ,
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    {
      type comment ,
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            {
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            {
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            {
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        {
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          version 0 ,
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            {
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            {
              type other ,
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              text "SHGC-19718" ,
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        {
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            {
              src {
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                tag
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              anchor "RH78280" ,
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            {
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              text "stSG41027" ,
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        {
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          version 0 ,
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            {
              src {
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                tag
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              anchor "RH91507" ,
              post-text "(e-PCR)" } } ,
          comment {
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              type other ,
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        {
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              src {
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              anchor "PMC27764P1" ,
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    {
      type comment ,
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                        {
                          type other ,
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            {
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                  src {
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                    tag
                      str "BC003559,BG565041" } ,
                  anchor "BC003559,BG565041" } } ,
              comment {
                {
                  type other ,
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    {
      type comment ,
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        {
          type genomic ,
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            {
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              gi 47124537 } ,
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        {
          type mRNA ,
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            {
              src {
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                tag
                  id 13572694 } ,
              anchor "BG565041" } } ,
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              gi 13572694 } ,
          products {
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              type peptide ,
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        {
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            {
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        {
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                  id 177808 } ,
              anchor "K01500" } } ,
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    {
      type comment ,
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        {
          type comment ,
          version 0 ,
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              src {
                db "Evidence Viewer" ,
                tag
                  str "12" } ,
              anchor "Evidence Viewer" ,
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                  str "12" } ,
              anchor "ModelMaker" ,
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06&contig=NT_026437.11&gene=SERPINA3&lid=12" } } } ,
        {
          type comment ,
          text "UniGene" ,
          version 0 ,
          xtra-properties {
            {
              tag "UNIGENE" ,
              value "Hs.534293" } } ,
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            {
              src {
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              anchor "Hs.534293" ,
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=53
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          type comment ,
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            {
              src {
                db "MIM" ,
                tag
                  str "107280" } ,
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                  str "12" } ,
              anchor "HomoloGene" ,
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12[loc]&TAXID=9606" } } } ,
        {
          type comment ,
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          source {
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              src {
                db "AceView" ,
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                  id 12 } ,
              anchor "AceView" ,
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        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "GDB" ,
                tag
                  str "GDB:118955" } } } } ,
        {
          type comment ,
          version 0 ,
          source {
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              src {
                db "Ensembl" ,
                tag
                  str "" } ,
              url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=AK093
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        {
          type comment ,
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              src {
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                  str "" } ,
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=
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        {
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              src {
                db "KEGG" ,
                tag
                  str "" } ,
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        {
          type comment ,
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              src {
                db "MGC" ,
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                  str "BC003559,BC010530,BC034554" } ,
              anchor "MGC" ,
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    {
      type comment ,
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          type comment ,
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              anchor "05010" ,
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa05010+12" } } } } } ,
    {
      type generif ,
      text "overexpression of ACT by astrocytes could thus contribute to
 increased beta-amyloid fibril formation in Alzheimer's disease" ,
      version 0 ,
      refs {
        pmid 15530656 } ,
      create-date
        str "Jan 29 2005 10:01AM" ,
      update-date
        str "Jan 29 2005  1:54PM" } ,
    {
      type generif ,
      text "Multivariate analysis showed that ACT mRNA level, but not STC2
 mRNA level, in HR-positive patients, was a significant prognostic factor (P =
 0.042), which was independent of tumor size and lymph node metastases." ,
      version 0 ,
      refs {
        pmid 15546506 } ,
      create-date
        str "Jan 15 2005 10:01AM" ,
      update-date
        str "Jan 15 2005  4:35PM" } ,
    {
      type generif ,
      text "Alpha1-antichymotrypsin-AA may confer a modest protection against
 developing early-onset Parkinson disease in women" ,
      version 0 ,
      refs {
        pmid 15542006 } ,
      create-date
        str "Jan 15 2005 10:01AM" ,
      update-date
        str "Jan 15 2005  1:01PM" } ,
    {
      type generif ,
      text "Polymeric AACT specifically seeds the polymerization of native
 protein by a serpin-dependent process that occurs under physiological
 conditions and may be important in the deposition of AACT in plaques in
 patients with Alzheimer's disease." ,
      version 0 ,
      refs {
        pmid 12600202 } ,
      create-date
        str "May 26 2003 12:00AM" ,
      update-date
        str "Jun  1 2003  7:01AM" } ,
    {
      type generif ,
      text "alpha(1)-antichymotrypsin polymorphism: a risk factor for
 hemorrhagic stroke in normotensive subjects." ,
      version 0 ,
      refs {
        pmid 11692021 } ,
      create-date
        str "Mar  5 2003 12:00AM" ,
      update-date
        str "Mar 23 2003  7:01AM" } ,
    {
      type generif ,
      text "alpha(1)-antitrypsin and antichymotrypsin are produced by the
 mammary gland and are present in milk in relatively high amounts in early
 lactation" ,
      version 0 ,
      refs {
        pmid 12324297 } ,
      create-date
        str "Oct 11 2002 12:00AM" ,
      update-date
        str "Feb  2 2003  7:01AM" } ,
    {
      type generif ,
      text "Gene regulation of the serine proteinase inhibitors
 alpha1-antitrypsin and alpha1-antichymotrypsin." ,
      version 0 ,
      refs {
        pmid 12023832 } ,
      create-date
        str "Oct  9 2002 12:00AM" ,
      update-date
        str "Feb  2 2003  7:01AM" } ,
    {
      type generif ,
      text "data suggested that the ApoE epsilon2/epsilon4 genotype might be a
 susceptibility variant of moderate effect for sporadic idiopathic Parkinson
 disease in our samples, whereas the ACT gene signal peptide polymorphism
 might not" ,
      version 0 ,
      refs {
        pmid 11992569 } ,
      create-date
        str "Sep 26 2002 12:00AM" ,
      update-date
        str "Oct  7 2002  8:10AM" } ,
    {
      type generif ,
      text "no association seen between alpha 1-antichymotrypsin and time to
 psychosis in Alzheimer's disease" ,
      version 0 ,
      refs {
        pmid 11936240 } ,
      create-date
        str "Aug 28 2002 12:00AM" ,
      update-date
        str "Sep 16 2002  5:48AM" } ,
    {
      type generif ,
      text "significantly higher in plasma of Alzheimer patients compared to
 controls" ,
      version 0 ,
      refs {
        pmid 11959399 } ,
      create-date
        str "Jul 22 2002 12:00AM" ,
      update-date
        str "Jul 29 2002  6:27PM" } ,
    {
      type generif ,
      text "A25G and G39A substitutions in the AACT gene are probably one of
 the risk factors to Alzheimer's disease (AD) in Han Chinese." ,
      version 0 ,
      refs {
        pmid 11798857 } ,
      create-date
        str "Apr  7 2002 12:00AM" ,
      update-date
        str "Apr 13 2002  5:25PM" } ,
    {
      type generif ,
      heading "Interactions" ,
      version 0 ,
      comment {
        {
          type generif ,
          text "Alpha-1 ACT interacts with and inhibits cathepsin G." ,
          version 0 ,
          refs {
            pmid 15131125 } ,
          source {
            {
              src {
                db "BIND" ,
                tag
                  id 149291 } ,
              anchor "BIND" } } ,
          comment {
            {
              type comment ,
              label "SERPINA3" ,
              accession "NP_001076" ,
              version 1 } ,
            {
              type comment ,
              label "CTSG" ,
              accession "NP_001902" ,
              version 1 ,
              source {
                {
                  src {
                    db "GeneID" ,
                    tag
                      id 1511 } } } } } ,
          create-date
            str "2005-01-21 20:10 EDT" ,
          update-date
            str "2005-01-21 20:19 EDT" } ,
        {
          type generif ,
          text "LRP interacts with alpha-1-ACT." ,
          version 0 ,
          refs {
            pmid 15131125 } ,
          source {
            {
              src {
                db "BIND" ,
                tag
                  id 149296 } ,
              anchor "BIND" } } ,
          comment {
            {
              type comment ,
              label "SERPINA3" ,
              accession "NP_001076" ,
              version 1 } ,
            {
              type comment ,
              label "LRP1" ,
              accession "NP_002323" ,
              version 1 ,
              source {
                {
                  src {
                    db "GeneID" ,
                    tag
                      id 4035 } } } } } ,
          create-date
            str "2005-01-21 20:10 EDT" ,
          update-date
            str "2005-01-21 20:19 EDT" } } } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 12 } ,
    {
      db "MIM" ,
      tag
        id 107280 } } ,
  xtra-index-terms {
    "LOC12" } ,
  xtra-properties {
    {
      tag "PROP" ,
      value "phenotype" } } }
Entrezgene ::= {
  track-info {
    geneid 13 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 20 ,
        minute 30 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 3 ,
        day 5 ,
        hour 11 ,
        minute 30 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Homo sapiens" ,
      common "human" ,
      db {
        {
          db "taxon" ,
          tag
            id 9606 } } ,
      syn {
        "man" } ,
      orgname {
        name
          binomial {
            genus "Homo" ,
            species "sapiens" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini;
 Hominidae; Homo" ,
        gcode 1 ,
        mgcode 2 ,
        div "PRI" } } ,
    subtype {
      {
        subtype chromosome ,
        name "3" } } } ,
  gene {
    locus "AADAC" ,
    desc "arylacetamide deacetylase (esterase)" ,
    maploc "3q21.3-q25.2" ,
    db {
      {
        db "MIM" ,
        tag
          id 600338 } } ,
    syn {
      "DAC" } ,
    locus-tag "HGNC:17" } ,
  prot {
    name {
      "arylacetamide deacetylase" } } ,
  summary "Microsomal arylacetamide deacetylase competes against the activity
 of cytosolic arylamine N-acetyltransferase, which catalyzes one of the
 initial biotransformation pathways for arylamine and heterocyclic amine
 carcinogens" ,
  location {
    {
      display-str "3q21.3-q25.2" ,
      method
        map-type cyto } } ,
  gene-source {
    src "LocusLink" ,
    src-int 13 ,
    src-str2 "13" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000003" ,
      version 9 ,
      seqs {
        int {
          from 153014563 ,
          to 153028971 ,
          strand plus ,
          id
            gi 51511463 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_001086" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 153014563 ,
                to 153014785 ,
                strand plus ,
                id
                  gi 51511463 } ,
              int {
                from 153017851 ,
                to 153018073 ,
                strand plus ,
                id
                  gi 51511463 } ,
              int {
                from 153020868 ,
                to 153020937 ,
                strand plus ,
                id
                  gi 51511463 } ,
              int {
                from 153025148 ,
                to 153025319 ,
                strand plus ,
                id
                  gi 51511463 } ,
              int {
                from 153028061 ,
                to 153028971 ,
                strand plus ,
                id
                  gi 51511463 } } } ,
          seqs {
            whole
              gi 4557226 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_001077" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 153014648 ,
                    to 153014785 ,
                    strand plus ,
                    id
                      gi 51511463 } ,
                  {
                    from 153017851 ,
                    to 153018073 ,
                    strand plus ,
                    id
                      gi 51511463 } ,
                  {
                    from 153020868 ,
                    to 153020937 ,
                    strand plus ,
                    id
                      gi 51511463 } ,
                  {
                    from 153025148 ,
                    to 153025319 ,
                    strand plus ,
                    id
                      gi 51511463 } ,
                  {
                    from 153028061 ,
                    to 153028657 ,
                    strand plus ,
                    id
                      gi 51511463 } } } ,
              seqs {
                whole
                  gi 4557227 } ,
              comment {
                {
                  type property ,
                  label "EC" ,
                  text "3.1.1.-" ,
                  version 0 ,
                  xtra-properties {
                    {
                      tag "EC" ,
                      value "3.1.1.-" } } } } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_005612" ,
      version 14 ,
      seqs {
        int {
          from 58027019 ,
          to 58041427 ,
          strand plus ,
          id
            gi 37550867 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_001086" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 58027019 ,
                to 58027241 ,
                strand plus ,
                id
                  gi 37550867 } ,
              int {
                from 58030307 ,
                to 58030529 ,
                strand plus ,
                id
                  gi 37550867 } ,
              int {
                from 58033324 ,
                to 58033393 ,
                strand plus ,
                id
                  gi 37550867 } ,
              int {
                from 58037604 ,
                to 58037775 ,
                strand plus ,
                id
                  gi 37550867 } ,
              int {
                from 58040517 ,
                to 58041427 ,
                strand plus ,
                id
                  gi 37550867 } } } ,
          seqs {
            whole
              gi 4557226 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_001077" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 58027104 ,
                    to 58027241 ,
                    strand plus ,
                    id
                      gi 37550867 } ,
                  {
                    from 58030307 ,
                    to 58030529 ,
                    strand plus ,
                    id
                      gi 37550867 } ,
                  {
                    from 58033324 ,
                    to 58033393 ,
                    strand plus ,
                    id
                      gi 37550867 } ,
                  {
                    from 58037604 ,
                    to 58037775 ,
                    strand plus ,
                    id
                      gi 37550867 } ,
                  {
                    from 58040517 ,
                    to 58041113 ,
                    strand plus ,
                    id
                      gi 37550867 } } } ,
              seqs {
                whole
                  gi 4557227 } ,
              comment {
                {
                  type property ,
                  label "EC" ,
                  text "3.1.1.-" ,
                  version 0 ,
                  xtra-properties {
                    {
                      tag "EC" ,
                      value "3.1.1.-" } } } } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_086641" ,
      version 1 ,
      seqs {
        int {
          from 24339789 ,
          to 24354221 ,
          strand plus ,
          id
            gi 51464125 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_001086" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 24339789 ,
                to 24340011 ,
                strand plus ,
                id
                  gi 51464125 } ,
              int {
                from 24343078 ,
                to 24343300 ,
                strand plus ,
                id
                  gi 51464125 } ,
              int {
                from 24346094 ,
                to 24346163 ,
                strand plus ,
                id
                  gi 51464125 } ,
              int {
                from 24350369 ,
                to 24350540 ,
                strand plus ,
                id
                  gi 51464125 } ,
              int {
                from 24353311 ,
                to 24354221 ,
                strand plus ,
                id
                  gi 51464125 } } } ,
          seqs {
            whole
              gi 4557226 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_001077" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 24339874 ,
                    to 24340011 ,
                    strand plus ,
                    id
                      gi 51464125 } ,
                  {
                    from 24343078 ,
                    to 24343300 ,
                    strand plus ,
                    id
                      gi 51464125 } ,
                  {
                    from 24346094 ,
                    to 24346163 ,
                    strand plus ,
                    id
                      gi 51464125 } ,
                  {
                    from 24350369 ,
                    to 24350540 ,
                    strand plus ,
                    id
                      gi 51464125 } ,
                  {
                    from 24353311 ,
                    to 24353907 ,
                    strand plus ,
                    id
                      gi 51464125 } } } ,
              seqs {
                whole
                  gi 4557227 } ,
              comment {
                {
                  type property ,
                  label "EC" ,
                  text "3.1.1.-" ,
                  version 0 ,
                  xtra-properties {
                    {
                      tag "EC" ,
                      value "3.1.1.-" } } } } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "HUGO Gene Nomenclature Committee" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "AADAC" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "arylacetamide deacetylase (esterase)" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "GOA" ,
          url "http://www.ebi.ac.uk/GOA/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 9665742 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 19213 } ,
                  anchor "deacetylase activity" ,
                  post-text "evidence: IDA" } } } } } ,
        {
          type comment ,
          label "Process" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 8152 } ,
                  anchor "metabolism" ,
                  post-text "evidence: IEA" } } } } } ,
        {
          type comment ,
          label "Component" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 10318829 ,
                pmid 15152005 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5789 } ,
                  anchor "endoplasmic reticulum membrane" ,
                  post-text "evidence: IDA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16021 } ,
                  anchor "integral to membrane" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 8063807 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5792 } ,
                  anchor "microsome" ,
                  post-text "evidence: TAS" } } } } } } } } ,
  homology {
    {
      type comment ,
      heading "Mouse, Rat" ,
      version 0 ,
      source {
        {
          src {
            db "HomoloGene" ,
            tag
              id 37436 } ,
          anchor "Map Viewer" ,
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=3&M
APS=genes-r-org/rat-chr/human%3A3,genes-r-org/mouse-chr/human%3A3,genes-r-org/
human-chr3&query=e%3A13[id]+AND+gene[obj_type]&QSTR=aadac&cmd=focus&fill=10" } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "HGNC" ,
            tag
              id 17 } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "REVIEWED" ,
      version 0 } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 15152005 ,
        pmid 12721789 ,
        pmid 12477932 ,
        pmid 10318829 ,
        pmid 9665742 ,
        pmid 9299245 ,
        pmid 8063807 } } ,
    {
      type comment ,
      heading "Markers (Sequence Tagged Sites/STS)" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 13170 } ,
              anchor "STS-L32179" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "RH41545" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "sts-L32179" ,
              version 0 } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 18863 } ,
              anchor "D3S4189" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "SHGC-9733" ,
              version 0 } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 24707 } ,
              anchor "RH36344" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "stSG13141" ,
              version 0 } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 136046 } ,
              anchor "RH124029" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "SHGC-105511" ,
              version 0 } } } } } ,
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_001086" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 4557226 } ,
              anchor "NM_001086" } } ,
          seqs {
            whole
              gi 4557226 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_001077" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 4557227 } ,
                  anchor "NP_001077" ,
                  post-text "arylacetamide deacetylase" } } ,
              seqs {
                whole
                  gi 4557227 } ,
              comment {
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 4557227 } ,
                      pre-text "(2)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 10527 } ,
                          anchor "COG0657: Aes; Esterase/lipase [Lipid
 metabolism]" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 33 - 399  Blast Score: 380" ,
                          version 0 } } } ,
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 16555 } ,
                          anchor "cd00312: Esterase_lipase; Esterases and
 lipases (includes fungal lipases, cholinesterases, etc" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 91 - 203  Blast Score: 144" ,
                          version 0 } } } } } } } } ,
          comment {
            {
              type other ,
              heading "Source Sequence" ,
              version 0 ,
              source {
                {
                  src {
                    db "Nucleotide" ,
                    tag
                      str "L32179" } ,
                  anchor "L32179" } } ,
              comment {
                {
                  type other ,
                  version 0 } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC020706" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 18088402 } ,
              anchor "BC020706" } } ,
          seqs {
            whole
              gi 18088402 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC032309" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 21595550 } ,
              anchor "BC032309" } } ,
          seqs {
            whole
              gi 21595550 } ,
          products {
            {
              type peptide ,
              accession "AAH32309" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 21595551 } ,
                  anchor "AAH32309" } } ,
              seqs {
                whole
                  gi 21595551 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "L32179" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 537513 } ,
              anchor "L32179" } } ,
          seqs {
            whole
              gi 537513 } ,
          products {
            {
              type peptide ,
              accession "AAA35551" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 537514 } ,
                  anchor "AAA35551" } } ,
              seqs {
                whole
                  gi 537514 } } } } ,
        {
          type other ,
          text "None" ,
          version 0 ,
          products {
            {
              type peptide ,
              accession "P22760" ,
              version 0 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 57015294 } ,
                  anchor "P22760" } } ,
              seqs {
                whole
                  gi 57015294 } } } } } } ,
    {
      type comment ,
      heading "Additional Links" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Evidence Viewer" ,
                tag
                  str "13" } ,
              anchor "Evidence Viewer" ,
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti
g=NT_005612.14&gene=AADAC&lid=13&from=58027020&to=58041428" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "ModelMaker" ,
                tag
                  str "13" } ,
              anchor "ModelMaker" ,
              url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96
06&contig=NT_005612.14&gene=AADAC&lid=13" } } } ,
        {
          type comment ,
          text "UniGene" ,
          version 0 ,
          xtra-properties {
            {
              tag "UNIGENE" ,
              value "Hs.506908" } } ,
          source {
            {
              src {
                db "UniGene" ,
                tag
                  str "Hs.506908" } ,
              anchor "Hs.506908" ,
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=50
6908" } } } ,
        {
          type comment ,
          text "MIM" ,
          version 0 ,
          source {
            {
              src {
                db "MIM" ,
                tag
                  str "600338" } ,
              anchor "600338" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "HomoloGene" ,
                tag
                  str "13" } ,
              anchor "HomoloGene" ,
              url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=
13[loc]&TAXID=9606" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "AceView" ,
                tag
                  id 13 } ,
              anchor "AceView" ,
              url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l
ocusid&org=9606&l=13" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "GDB" ,
                tag
                  str "GDB:392587" } } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Ensembl" ,
                tag
                  str "" } ,
              url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=BC032
309" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UCSC" ,
                tag
                  str "" } ,
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=
BC032309" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "KEGG" ,
                tag
                  str "" } ,
              url "http://www.genome.ad.jp/dbget-bin/www_bget?hsa:13" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGC" ,
                tag
                  str "BC032309" } ,
              anchor "MGC" ,
              url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC032309" } } } } } ,
    {
      type comment ,
      heading "Pathways" ,
      version 0 ,
      comment {
        {
          type comment ,
          text "KEGG pathway: Butanoate metabolism" ,
          version 0 ,
          source {
            {
              src {
                db "00650" ,
                tag
                  str "00650" } ,
              anchor "00650" ,
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa00650+13" } } } ,
        {
          type comment ,
          text "KEGG pathway: Alkaloid biosynthesis II" ,
          version 0 ,
          source {
            {
              src {
                db "00960" ,
                tag
                  str "00960" } ,
              anchor "00960" ,
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa00960+13" } } } ,
        {
          type comment ,
          text "KEGG pathway: 2,4-Dichlorobenzoate degradation" ,
          version 0 ,
          source {
            {
              src {
                db "00623" ,
                tag
                  str "00623" } ,
              anchor "00623" ,
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa00623+13" } } } ,
        {
          type comment ,
          text "KEGG pathway: Pentose and glucuronate interconversions" ,
          version 0 ,
          source {
            {
              src {
                db "00040" ,
                tag
                  str "00040" } ,
              anchor "00040" ,
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa00040+13" } } } ,
        {
          type comment ,
          text "KEGG pathway: Glycosylphosphatidylinositol(GPI)-anchor
 biosynthesis" ,
          version 0 ,
          source {
            {
              src {
                db "00563" ,
                tag
                  str "00563" } ,
              anchor "00563" ,
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa00563+13" } } } } } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 13 } ,
    {
      db "MIM" ,
      tag
        id 600338 } } ,
  xtra-index-terms {
    "LOC13" } }
Entrezgene ::= {
  track-info {
    geneid 14 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 20 ,
        minute 30 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 4 ,
        day 14 ,
        hour 13 ,
        minute 15 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Homo sapiens" ,
      common "human" ,
      db {
        {
          db "taxon" ,
          tag
            id 9606 } } ,
      syn {
        "man" } ,
      orgname {
        name
          binomial {
            genus "Homo" ,
            species "sapiens" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini;
 Hominidae; Homo" ,
        gcode 1 ,
        mgcode 2 ,
        div "PRI" } } ,
    subtype {
      {
        subtype chromosome ,
        name "2" } } } ,
  gene {
    locus "AAMP" ,
    desc "angio-associated, migratory cell protein" ,
    maploc "2q35" ,
    db {
      {
        db "MIM" ,
        tag
          id 603488 } } ,
    locus-tag "HGNC:18" } ,
  prot {
    name {
      "angio-associated, migratory cell protein" } } ,
  summary "The gene product is an immunoglobulin-type protein. It is found to
 be expressed strongly in endothelial cells, cytotrophoblasts, and poorly
 differentiated colon adenocarcinoma cells found in lymphatics. The protein
 contains a heparin-binding domain and mediates heparin-sensitive cell
 adhesion." ,
  location {
    {
      display-str "2q35" ,
      method
        map-type cyto } } ,
  gene-source {
    src "LocusLink" ,
    src-int 14 ,
    src-str2 "14" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000002" ,
      version 9 ,
      seqs {
        int {
          from 218954357 ,
          to 218960364 ,
          strand minus ,
          id
            gi 51511462 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_001087" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 218954357 ,
                to 218954835 ,
                strand minus ,
                id
                  gi 51511462 } ,
              int {
                from 218955247 ,
                to 218955401 ,
                strand minus ,
                id
                  gi 51511462 } ,
              int {
                from 218955598 ,
                to 218955688 ,
                strand minus ,
                id
                  gi 51511462 } ,
              int {
                from 218955806 ,
                to 218955909 ,
                strand minus ,
                id
                  gi 51511462 } ,
              int {
                from 218956058 ,
                to 218956173 ,
                strand minus ,
                id
                  gi 51511462 } ,
              int {
                from 218956291 ,
                to 218956374 ,
                strand minus ,
                id
                  gi 51511462 } ,
              int {
                from 218956670 ,
                to 218956814 ,
                strand minus ,
                id
                  gi 51511462 } ,
              int {
                from 218957074 ,
                to 218957213 ,
                strand minus ,
                id
                  gi 51511462 } ,
              int {
                from 218957721 ,
                to 218957840 ,
                strand minus ,
                id
                  gi 51511462 } ,
              int {
                from 218959609 ,
                to 218959761 ,
                strand minus ,
                id
                  gi 51511462 } ,
              int {
                from 218960193 ,
                to 218960364 ,
                strand minus ,
                id
                  gi 51511462 } } } ,
          seqs {
            whole
              gi 4557228 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_001078" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 218954760 ,
                    to 218954835 ,
                    strand minus ,
                    id
                      gi 51511462 } ,
                  {
                    from 218955247 ,
                    to 218955401 ,
                    strand minus ,
                    id
                      gi 51511462 } ,
                  {
                    from 218955598 ,
                    to 218955688 ,
                    strand minus ,
                    id
                      gi 51511462 } ,
                  {
                    from 218955806 ,
                    to 218955909 ,
                    strand minus ,
                    id
                      gi 51511462 } ,
                  {
                    from 218956058 ,
                    to 218956173 ,
                    strand minus ,
                    id
                      gi 51511462 } ,
                  {
                    from 218956291 ,
                    to 218956374 ,
                    strand minus ,
                    id
                      gi 51511462 } ,
                  {
                    from 218956670 ,
                    to 218956814 ,
                    strand minus ,
                    id
                      gi 51511462 } ,
                  {
                    from 218957074 ,
                    to 218957213 ,
                    strand minus ,
                    id
                      gi 51511462 } ,
                  {
                    from 218957721 ,
                    to 218957840 ,
                    strand minus ,
                    id
                      gi 51511462 } ,
                  {
                    from 218959609 ,
                    to 218959761 ,
                    strand minus ,
                    id
                      gi 51511462 } ,
                  {
                    from 218960193 ,
                    to 218960364 ,
                    strand minus ,
                    id
                      gi 51511462 } } } ,
              seqs {
                whole
                  gi 4557229 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_005403" ,
      version 15 ,
      seqs {
        int {
          from 69338267 ,
          to 69344274 ,
          strand minus ,
          id
            gi 51461028 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_001087" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 69338267 ,
                to 69338745 ,
                strand minus ,
                id
                  gi 51461028 } ,
              int {
                from 69339157 ,
                to 69339311 ,
                strand minus ,
                id
                  gi 51461028 } ,
              int {
                from 69339508 ,
                to 69339598 ,
                strand minus ,
                id
                  gi 51461028 } ,
              int {
                from 69339716 ,
                to 69339819 ,
                strand minus ,
                id
                  gi 51461028 } ,
              int {
                from 69339968 ,
                to 69340083 ,
                strand minus ,
                id
                  gi 51461028 } ,
              int {
                from 69340201 ,
                to 69340284 ,
                strand minus ,
                id
                  gi 51461028 } ,
              int {
                from 69340580 ,
                to 69340724 ,
                strand minus ,
                id
                  gi 51461028 } ,
              int {
                from 69340984 ,
                to 69341123 ,
                strand minus ,
                id
                  gi 51461028 } ,
              int {
                from 69341631 ,
                to 69341750 ,
                strand minus ,
                id
                  gi 51461028 } ,
              int {
                from 69343519 ,
                to 69343671 ,
                strand minus ,
                id
                  gi 51461028 } ,
              int {
                from 69344103 ,
                to 69344274 ,
                strand minus ,
                id
                  gi 51461028 } } } ,
          seqs {
            whole
              gi 4557228 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_001078" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 69338670 ,
                    to 69338745 ,
                    strand minus ,
                    id
                      gi 51461028 } ,
                  {
                    from 69339157 ,
                    to 69339311 ,
                    strand minus ,
                    id
                      gi 51461028 } ,
                  {
                    from 69339508 ,
                    to 69339598 ,
                    strand minus ,
                    id
                      gi 51461028 } ,
                  {
                    from 69339716 ,
                    to 69339819 ,
                    strand minus ,
                    id
                      gi 51461028 } ,
                  {
                    from 69339968 ,
                    to 69340083 ,
                    strand minus ,
                    id
                      gi 51461028 } ,
                  {
                    from 69340201 ,
                    to 69340284 ,
                    strand minus ,
                    id
                      gi 51461028 } ,
                  {
                    from 69340580 ,
                    to 69340724 ,
                    strand minus ,
                    id
                      gi 51461028 } ,
                  {
                    from 69340984 ,
                    to 69341123 ,
                    strand minus ,
                    id
                      gi 51461028 } ,
                  {
                    from 69341631 ,
                    to 69341750 ,
                    strand minus ,
                    id
                      gi 51461028 } ,
                  {
                    from 69343519 ,
                    to 69343671 ,
                    strand minus ,
                    id
                      gi 51461028 } ,
                  {
                    from 69344103 ,
                    to 69344274 ,
                    strand minus ,
                    id
                      gi 51461028 } } } ,
              seqs {
                whole
                  gi 4557229 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_086634" ,
      version 1 ,
      seqs {
        int {
          from 23772483 ,
          to 23778490 ,
          strand minus ,
          id
            gi 51463854 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_001087" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 23772483 ,
                to 23772961 ,
                strand minus ,
                id
                  gi 51463854 } ,
              int {
                from 23773373 ,
                to 23773527 ,
                strand minus ,
                id
                  gi 51463854 } ,
              int {
                from 23773724 ,
                to 23773814 ,
                strand minus ,
                id
                  gi 51463854 } ,
              int {
                from 23773932 ,
                to 23774035 ,
                strand minus ,
                id
                  gi 51463854 } ,
              int {
                from 23774184 ,
                to 23774299 ,
                strand minus ,
                id
                  gi 51463854 } ,
              int {
                from 23774417 ,
                to 23774500 ,
                strand minus ,
                id
                  gi 51463854 } ,
              int {
                from 23774796 ,
                to 23774940 ,
                strand minus ,
                id
                  gi 51463854 } ,
              int {
                from 23775200 ,
                to 23775339 ,
                strand minus ,
                id
                  gi 51463854 } ,
              int {
                from 23775847 ,
                to 23775966 ,
                strand minus ,
                id
                  gi 51463854 } ,
              int {
                from 23777735 ,
                to 23777887 ,
                strand minus ,
                id
                  gi 51463854 } ,
              int {
                from 23778319 ,
                to 23778490 ,
                strand minus ,
                id
                  gi 51463854 } } } ,
          seqs {
            whole
              gi 4557228 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_001078" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 23772886 ,
                    to 23772961 ,
                    strand minus ,
                    id
                      gi 51463854 } ,
                  {
                    from 23773373 ,
                    to 23773527 ,
                    strand minus ,
                    id
                      gi 51463854 } ,
                  {
                    from 23773724 ,
                    to 23773814 ,
                    strand minus ,
                    id
                      gi 51463854 } ,
                  {
                    from 23773932 ,
                    to 23774035 ,
                    strand minus ,
                    id
                      gi 51463854 } ,
                  {
                    from 23774184 ,
                    to 23774299 ,
                    strand minus ,
                    id
                      gi 51463854 } ,
                  {
                    from 23774417 ,
                    to 23774500 ,
                    strand minus ,
                    id
                      gi 51463854 } ,
                  {
                    from 23774796 ,
                    to 23774940 ,
                    strand minus ,
                    id
                      gi 51463854 } ,
                  {
                    from 23775200 ,
                    to 23775339 ,
                    strand minus ,
                    id
                      gi 51463854 } ,
                  {
                    from 23775847 ,
                    to 23775966 ,
                    strand minus ,
                    id
                      gi 51463854 } ,
                  {
                    from 23777735 ,
                    to 23777887 ,
                    strand minus ,
                    id
                      gi 51463854 } ,
                  {
                    from 23778319 ,
                    to 23778490 ,
                    strand minus ,
                    id
                      gi 51463854 } } } ,
              seqs {
                whole
                  gi 4557229 } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "HUGO Gene Nomenclature Committee" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "AAMP" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "angio-associated, migratory cell protein" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "GOA" ,
          url "http://www.ebi.ac.uk/GOA/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 7743515 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 8201 } ,
                  anchor "heparin binding" ,
                  post-text "evidence: TAS" } } } } } ,
        {
          type comment ,
          label "Process" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 6928 } ,
                  anchor "cell motility" ,
                  post-text "evidence: NR" } } } } } } } } ,
  homology {
    {
      type comment ,
      heading "Mouse, Rat" ,
      version 0 ,
      source {
        {
          src {
            db "HomoloGene" ,
            tag
              id 846 } ,
          anchor "Map Viewer" ,
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=2&M
APS=genes-r-org/rat-chr/human%3A2,genes-r-org/mouse-chr/human%3A2,genes-r-org/
human-chr2&query=e%3A14[id]+AND+gene[obj_type]&QSTR=aamp&cmd=focus&fill=10" } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "HGNC" ,
            tag
              id 18 } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "REVIEWED" ,
      version 0 } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 12477932 ,
        pmid 11969303 ,
        pmid 10329261 ,
        pmid 8660919 ,
        pmid 7743515 } } ,
    {
      type comment ,
      heading "Markers (Sequence Tagged Sites/STS)" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 52581 } ,
              anchor "SGC31591" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "CM4.18" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "GC" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "RH23156" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "STS4-18" ,
              version 0 } } } } } ,
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_001087" ,
          version 2 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 55743074 } ,
              anchor "NM_001087" } } ,
          seqs {
            whole
              gi 55743074 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_001078" ,
              version 2 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 55743075 } ,
                  anchor "NP_001078" ,
                  post-text "angio-associated, migratory cell protein" } } ,
              seqs {
                whole
                  gi 55743075 } ,
              comment {
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 55743075 } ,
                      pre-text "(2)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 5398 } ,
                          anchor "cd00200: WD40; WD40 domain, found in a
 number of eukaryotic proteins that cover a wide variety of functions
 including adaptor/regulatory modules in signal transduction, pre-mRNA
 processing and cytoskeleton assembly" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 86 - 386  Blast Score: 457" ,
                          version 0 } ,
                        {
                          type other ,
                          text "Location: 325 - 430  Blast Score: 176" ,
                          version 0 } } } } } } } } ,
          comment {
            {
              type other ,
              heading "Source Sequence" ,
              version 0 ,
              source {
                {
                  src {
                    db "Nucleotide" ,
                    tag
                      str "BG534787,CN277005,M95627" } ,
                  anchor "BG534787,CN277005,M95627" } } ,
              comment {
                {
                  type other ,
                  version 0 } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AB209790" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 62089165 } ,
              anchor "AB209790" } } ,
          seqs {
            whole
              gi 62089165 } ,
          products {
            {
              type peptide ,
              accession "BAD93027" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 62089166 } ,
                  anchor "BAD93027" } } ,
              seqs {
                whole
                  gi 62089166 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AK131047" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 34528300 } ,
              anchor "AK131047" } } ,
          seqs {
            whole
              gi 34528300 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC008809" ,
          version 2 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 39644831 } ,
              anchor "BC008809" } } ,
          seqs {
            whole
              gi 39644831 } ,
          products {
            {
              type peptide ,
              accession "AAH08809" ,
              version 2 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 39644832 } ,
                  anchor "AAH08809" } } ,
              seqs {
                whole
                  gi 39644832 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC014122" ,
          version 2 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 33874729 } ,
              anchor "BC014122" } } ,
          seqs {
            whole
              gi 33874729 } ,
          products {
            {
              type peptide ,
              accession "AAH14122" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 33874730 } ,
                  anchor "AAH14122" } } ,
              seqs {
                whole
                  gi 33874730 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC020244" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 18044383 } ,
              anchor "BC020244" } } ,
          seqs {
            whole
              gi 18044383 } ,
          products {
            {
              type peptide ,
              accession "AAH20244" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 18044384 } ,
                  anchor "AAH20244" } } ,
              seqs {
                whole
                  gi 18044384 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC039866" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 25123215 } ,
              anchor "BC039866" } } ,
          seqs {
            whole
              gi 25123215 } ,
          products {
            {
              type peptide ,
              accession "AAH39866" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 56200511 } ,
                  anchor "AAH39866" } } ,
              seqs {
                whole
                  gi 56200511 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "CR456755" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 48145626 } ,
              anchor "CR456755" } } ,
          seqs {
            whole
              gi 48145626 } ,
          products {
            {
              type peptide ,
              accession "CAG33036" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 48145627 } ,
                  anchor "CAG33036" } } ,
              seqs {
                whole
                  gi 48145627 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "M95627" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 870802 } ,
              anchor "M95627" } } ,
          seqs {
            whole
              gi 870802 } ,
          products {
            {
              type peptide ,
              accession "AAA68889" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 870803 } ,
                  anchor "AAA68889" } } ,
              seqs {
                whole
                  gi 870803 } } } } ,
        {
          type other ,
          text "None" ,
          version 0 ,
          products {
            {
              type peptide ,
              accession "Q13685" ,
              version 0 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 3121739 } ,
                  anchor "Q13685" } } ,
              seqs {
                whole
                  gi 3121739 } } } } } } ,
    {
      type comment ,
      heading "Additional Links" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Evidence Viewer" ,
                tag
                  str "14" } ,
              anchor "Evidence Viewer" ,
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti
g=NT_005403.15&gene=AAMP&lid=14&from=69338268&to=69344275" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "ModelMaker" ,
                tag
                  str "14" } ,
              anchor "ModelMaker" ,
              url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96
06&contig=NT_005403.15&gene=AAMP&lid=14" } } } ,
        {
          type comment ,
          text "UniGene" ,
          version 0 ,
          xtra-properties {
            {
              tag "UNIGENE" ,
              value "Hs.83347" } } ,
          source {
            {
              src {
                db "UniGene" ,
                tag
                  str "Hs.83347" } ,
              anchor "Hs.83347" ,
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=83
347" } } } ,
        {
          type comment ,
          text "MIM" ,
          version 0 ,
          source {
            {
              src {
                db "MIM" ,
                tag
                  str "603488" } ,
              anchor "603488" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "HomoloGene" ,
                tag
                  str "14" } ,
              anchor "HomoloGene" ,
              url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=
14[loc]&TAXID=9606" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "AceView" ,
                tag
                  id 14 } ,
              anchor "AceView" ,
              url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l
ocusid&org=9606&l=14" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "GDB" ,
                tag
                  str "GDB:4573993" } } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Ensembl" ,
                tag
                  str "" } ,
              url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=AB209
790" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UCSC" ,
                tag
                  str "" } ,
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=
AB209790" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGC" ,
                tag
                  str "BC014122" } ,
              anchor "MGC" ,
              url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC014122" } } } } } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 14 } ,
    {
      db "MIM" ,
      tag
        id 603488 } } ,
  xtra-index-terms {
    "LOC14" } }
Entrezgene ::= {
  track-info {
    geneid 15 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 20 ,
        minute 30 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 4 ,
        day 14 ,
        hour 13 ,
        minute 15 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Homo sapiens" ,
      common "human" ,
      db {
        {
          db "taxon" ,
          tag
            id 9606 } } ,
      syn {
        "man" } ,
      orgname {
        name
          binomial {
            genus "Homo" ,
            species "sapiens" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini;
 Hominidae; Homo" ,
        gcode 1 ,
        mgcode 2 ,
        div "PRI" } } ,
    subtype {
      {
        subtype chromosome ,
        name "17" } } } ,
  gene {
    locus "AANAT" ,
    desc "arylalkylamine N-acetyltransferase" ,
    maploc "17q25" ,
    db {
      {
        db "MIM" ,
        tag
          id 600950 } } ,
    syn {
      "SNAT" ,
      "AA-NAT" } ,
    locus-tag "HGNC:19" } ,
  prot {
    name {
      "arylalkylamine N-acetyltransferase" ,
      "serotonin N-acetyltransferase" } } ,
  summary "Arylalkylamine N-acetyltransferase belongs to the superfamily of
 acetyltransferases. It is the penultimate enzyme in melatonin synthesis and
 controls the night/day rhythm in melatonin production in the vertebrate
 pineal gland. Melatonin is essential for seasonal reproduction, modulates the
 function of the circadian clock in the suprachiasmatic nucleus, and
 influences activity and sleep. This enzyme is rapidly inactivated when
 animals are exposed to light at night. This protein is 80% identical to sheep
 and rat AA-NAT. Arylalkylamine N-acetyltransferase may contribute a
 multifactorial genetic diseases such as altered behavior in sleep/wake cycle." ,
  location {
    {
      display-str "17q25" ,
      method
        map-type cyto } } ,
  gene-source {
    src "LocusLink" ,
    src-int 15 ,
    src-str2 "15" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000017" ,
      version 9 ,
      seqs {
        int {
          from 71975245 ,
          to 71977793 ,
          strand plus ,
          id
            gi 51511734 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_001088" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 71975245 ,
                to 71975403 ,
                strand plus ,
                id
                  gi 51511734 } ,
              int {
                from 71976348 ,
                to 71976585 ,
                strand plus ,
                id
                  gi 51511734 } ,
              int {
                from 71976849 ,
                to 71977003 ,
                strand plus ,
                id
                  gi 51511734 } ,
              int {
                from 71977341 ,
                to 71977793 ,
                strand plus ,
                id
                  gi 51511734 } } } ,
          seqs {
            whole
              gi 4501844 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_001079" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 71976423 ,
                    to 71976585 ,
                    strand plus ,
                    id
                      gi 51511734 } ,
                  {
                    from 71976849 ,
                    to 71977003 ,
                    strand plus ,
                    id
                      gi 51511734 } ,
                  {
                    from 71977341 ,
                    to 71977646 ,
                    strand plus ,
                    id
                      gi 51511734 } } } ,
              seqs {
                whole
                  gi 4501845 } ,
              comment {
                {
                  type property ,
                  label "EC" ,
                  text "2.3.1.87" ,
                  version 0 ,
                  xtra-properties {
                    {
                      tag "EC" ,
                      value "2.3.1.87" } } } } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_010641" ,
      version 15 ,
      seqs {
        int {
          from 8389922 ,
          to 8392470 ,
          strand plus ,
          id
            gi 51474120 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_001088" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 8389922 ,
                to 8390080 ,
                strand plus ,
                id
                  gi 51474120 } ,
              int {
                from 8391025 ,
                to 8391262 ,
                strand plus ,
                id
                  gi 51474120 } ,
              int {
                from 8391526 ,
                to 8391680 ,
                strand plus ,
                id
                  gi 51474120 } ,
              int {
                from 8392018 ,
                to 8392470 ,
                strand plus ,
                id
                  gi 51474120 } } } ,
          seqs {
            whole
              gi 4501844 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_001079" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 8391100 ,
                    to 8391262 ,
                    strand plus ,
                    id
                      gi 51474120 } ,
                  {
                    from 8391526 ,
                    to 8391680 ,
                    strand plus ,
                    id
                      gi 51474120 } ,
                  {
                    from 8392018 ,
                    to 8392323 ,
                    strand plus ,
                    id
                      gi 51474120 } } } ,
              seqs {
                whole
                  gi 4501845 } ,
              comment {
                {
                  type property ,
                  label "EC" ,
                  text "2.3.1.87" ,
                  version 0 ,
                  xtra-properties {
                    {
                      tag "EC" ,
                      value "2.3.1.87" } } } } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_086886" ,
      version 1 ,
      seqs {
        int {
          from 11539555 ,
          to 11542103 ,
          strand plus ,
          id
            gi 51474508 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_001088" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 11539555 ,
                to 11539713 ,
                strand plus ,
                id
                  gi 51474508 } ,
              int {
                from 11540658 ,
                to 11540895 ,
                strand plus ,
                id
                  gi 51474508 } ,
              int {
                from 11541159 ,
                to 11541313 ,
                strand plus ,
                id
                  gi 51474508 } ,
              int {
                from 11541651 ,
                to 11542103 ,
                strand plus ,
                id
                  gi 51474508 } } } ,
          seqs {
            whole
              gi 4501844 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_001079" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 11540733 ,
                    to 11540895 ,
                    strand plus ,
                    id
                      gi 51474508 } ,
                  {
                    from 11541159 ,
                    to 11541313 ,
                    strand plus ,
                    id
                      gi 51474508 } ,
                  {
                    from 11541651 ,
                    to 11541956 ,
                    strand plus ,
                    id
                      gi 51474508 } } } ,
              seqs {
                whole
                  gi 4501845 } ,
              comment {
                {
                  type property ,
                  label "EC" ,
                  text "2.3.1.87" ,
                  version 0 ,
                  xtra-properties {
                    {
                      tag "EC" ,
                      value "2.3.1.87" } } } } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "HUGO Gene Nomenclature Committee" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "AANAT" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "arylalkylamine N-acetyltransferase" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "GOA" ,
          url "http://www.ebi.ac.uk/GOA/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 8415 } ,
                  anchor "acyltransferase activity" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 8661026 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 4059 } ,
                  anchor "aralkylamine N-acetyltransferase activity" ,
                  post-text "evidence: TAS" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16740 } ,
                  anchor "transferase activity" ,
                  post-text "evidence: IEA" } } } } } ,
        {
          type comment ,
          label "Process" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 8661026 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 7623 } ,
                  anchor "circadian rhythm" ,
                  post-text "evidence: TAS" } } } } } } } } ,
  homology {
    {
      type comment ,
      heading "Mouse, Rat" ,
      version 0 ,
      source {
        {
          src {
            db "HomoloGene" ,
            tag
              id 31013 } ,
          anchor "Map Viewer" ,
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=17&
MAPS=genes-r-org/rat-chr/human%3A17,genes-r-org/mouse-chr/human%3A17,genes-r-o
rg/human-chr17&query=e%3A15[id]+AND+gene[obj_type]&QSTR=aanat&cmd=focus&fill=1
0" } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "HGNC" ,
            tag
              id 19 } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "REVIEWED" ,
      version 0 } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 15332344 ,
        pmid 12736803 ,
        pmid 12552951 ,
        pmid 12477932 ,
        pmid 12039872 ,
        pmid 11934439 ,
        pmid 11427721 ,
        pmid 11336675 ,
        pmid 11313340 ,
        pmid 9238858 ,
        pmid 8661026 ,
        pmid 7502081 ,
        pmid 2181999 } } ,
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_001088" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 4501844 } ,
              anchor "NM_001088" } } ,
          seqs {
            whole
              gi 4501844 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_001079" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 4501845 } ,
                  anchor "NP_001079" ,
                  post-text "arylalkylamine N-acetyltransferase" } } ,
              seqs {
                whole
                  gi 4501845 } ,
              comment {
                {
                  type other ,
                  heading "Consensus CDS (CCDS)" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "CCDS" ,
                        tag
                          str "CCDS11745.1" } ,
                      anchor "CCDS11745.1" } } } ,
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 4501845 } ,
                      pre-text "(1)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 25558 } ,
                          anchor "pfam00583: Acetyltransf_1; Acetyltransferase
 (GNAT) family" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 82 - 174  Blast Score: 94" ,
                          version 0 } } } } } } } } ,
          comment {
            {
              type other ,
              heading "Source Sequence" ,
              version 0 ,
              source {
                {
                  src {
                    db "Nucleotide" ,
                    tag
                      str "U40347" } ,
                  anchor "U40347" } } ,
              comment {
                {
                  type other ,
                  version 0 } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type genomic ,
          heading "Genomic" ,
          accession "AB023793" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 12248880 } ,
              anchor "AB023793" } } ,
          seqs {
            whole
              gi 12248880 } ,
          products {
            {
              type peptide ,
              accession "BAB20312" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 12248881 } ,
                  anchor "BAB20312" } } ,
              seqs {
                whole
                  gi 12248881 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AB023794" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 12248882 } ,
              anchor "AB023794" } } ,
          seqs {
            whole
              gi 12248882 } ,
          products {
            {
              type peptide ,
              accession "BAB20313" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 12248883 } ,
                  anchor "BAB20313" } } ,
              seqs {
                whole
                  gi 12248883 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AB023795" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 12248884 } ,
              anchor "AB023795" } } ,
          seqs {
            whole
              gi 12248884 } ,
          products {
            {
              type peptide ,
              accession "BAB20314" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 12248885 } ,
                  anchor "BAB20314" } } ,
              seqs {
                whole
                  gi 12248885 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AB023796" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 12248886 } ,
              anchor "AB023796" } } ,
          seqs {
            whole
              gi 12248886 } ,
          products {
            {
              type peptide ,
              accession "BAB20315" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 12248887 } ,
                  anchor "BAB20315" } } ,
              seqs {
                whole
                  gi 12248887 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AB023797" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 12248888 } ,
              anchor "AB023797" } } ,
          seqs {
            whole
              gi 12248888 } ,
          products {
            {
              type peptide ,
              accession "BAB20316" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 12248889 } ,
                  anchor "BAB20316" } } ,
              seqs {
                whole
                  gi 12248889 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AF360979" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 13936890 } ,
              anchor "AF360979" } } ,
          seqs {
            whole
              gi 13936890 } ,
          products {
            {
              type peptide ,
              accession "AAK49981" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 13936891 } ,
                  anchor "AAK49981" } } ,
              seqs {
                whole
                  gi 13936891 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "U40391" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 1389593 } ,
              anchor "U40391" } } ,
          seqs {
            whole
              gi 1389593 } ,
          products {
            {
              type peptide ,
              accession "AAC50555" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 1389594 } ,
                  anchor "AAC50555" } } ,
              seqs {
                whole
                  gi 1389594 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC069434" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 46854803 } ,
              anchor "BC069434" } } ,
          seqs {
            whole
              gi 46854803 } ,
          products {
            {
              type peptide ,
              accession "AAH69434" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 46854804 } ,
                  anchor "AAH69434" } } ,
              seqs {
                whole
                  gi 46854804 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "U40347" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 1389591 } ,
              anchor "U40347" } } ,
          seqs {
            whole
              gi 1389591 } ,
          products {
            {
              type peptide ,
              accession "AAC50554" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 1389592 } ,
                  anchor "AAC50554" } } ,
              seqs {
                whole
                  gi 1389592 } } } } ,
        {
          type other ,
          text "None" ,
          version 0 ,
          products {
            {
              type peptide ,
              accession "Q16613" ,
              version 0 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 11387096 } ,
                  anchor "Q16613" } } ,
              seqs {
                whole
                  gi 11387096 } } } } } } ,
    {
      type comment ,
      heading "Additional Links" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Evidence Viewer" ,
                tag
                  str "15" } ,
              anchor "Evidence Viewer" ,
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti
g=NT_010641.15&gene=AANAT&lid=15&from=8389923&to=8392471" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "ModelMaker" ,
                tag
                  str "15" } ,
              anchor "ModelMaker" ,
              url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=96
06&contig=NT_010641.15&gene=AANAT&lid=15" } } } ,
        {
          type comment ,
          text "UniGene" ,
          version 0 ,
          xtra-properties {
            {
              tag "UNIGENE" ,
              value "Hs.431417" } } ,
          source {
            {
              src {
                db "UniGene" ,
                tag
                  str "Hs.431417" } ,
              anchor "Hs.431417" ,
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=43
1417" } } } ,
        {
          type comment ,
          text "MIM" ,
          version 0 ,
          source {
            {
              src {
                db "MIM" ,
                tag
                  str "600950" } ,
              anchor "600950" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "HomoloGene" ,
                tag
                  str "15" } ,
              anchor "HomoloGene" ,
              url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=
15[loc]&TAXID=9606" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "AceView" ,
                tag
                  id 15 } ,
              anchor "AceView" ,
              url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=l
ocusid&org=9606&l=15" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "GDB" ,
                tag
                  str "GDB:700076" } } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Ensembl" ,
                tag
                  str "" } ,
              url "http://www.ensembl.org/Homo_sapiens/contigview?geneid=U4034
7" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UCSC" ,
                tag
                  str "" } ,
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=
U40347" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "KEGG" ,
                tag
                  str "" } ,
              url "http://www.genome.ad.jp/dbget-bin/www_bget?hsa:15" } } } ,
        {
          type comment ,
          text "PharmGKB" ,
          version 0 ,
          source {
            {
              src {
                db "PharmGKB" ,
                tag
                  str "PA24366" } ,
              anchor "PA24366" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGC" ,
                tag
                  str "BC069434" } ,
              anchor "MGC" ,
              url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC069434" } } } } } ,
    {
      type comment ,
      heading "Pathways" ,
      version 0 ,
      comment {
        {
          type comment ,
          text "KEGG pathway: Tryptophan metabolism" ,
          version 0 ,
          source {
            {
              src {
                db "00380" ,
                tag
                  str "00380" } ,
              anchor "00380" ,
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa00380+15" } } } } } ,
    {
      type generif ,
      text "Data suggest that the -263G/C single nucleotide polymorphism of
 arylalkylamine-N-acetyl-transferase (AA-NAT) may be an important determinant
 of the late/short sleep pattern." ,
      version 0 ,
      refs {
        pmid 15332344 } ,
      create-date
        str "Sep 27 2004  4:34PM" ,
      update-date
        str "Sep 27 2004  7:00PM" } ,
    {
      type generif ,
      text "There is a significant increase in AANAT allele positivity at the
 single nucleotide polymorphism (alanine 129--> threonine) at between patients
 with DSPS & controls.  AA-NAT could be a susceptibility gene for DSPS." ,
      version 0 ,
      refs {
        pmid 12736803 } ,
      create-date
        str "Jul 10 2003 12:00AM" ,
      update-date
        str "May 30 2004  7:11AM" } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 15 } ,
    {
      db "MIM" ,
      tag
        id 600950 } } ,
  xtra-index-terms {
    "LOC15" } }
Entrezgene ::= {
  track-info {
    geneid 9996 ,
    status secondary ,
    current-id {
      {
        db "LocusID" ,
        tag
          id 320632 } ,
      {
        db "GeneID" ,
        tag
          id 320632 } } ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 2 ,
        day 17 ,
        hour 12 ,
        minute 54 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } } ,
  gene {
     } ,
  gene-source {
    src "LocusLink" ,
    src-int 9996 ,
    src-str2 "9996" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 9996 } } ,
  xtra-index-terms {
    "LOC320632" } }
Entrezgene ::= {
  track-info {
    geneid 11286 ,
    status secondary ,
    current-id {
      {
        db "LocusID" ,
        tag
          id 50518 } ,
      {
        db "GeneID" ,
        tag
          id 50518 } } ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 2 ,
        day 17 ,
        hour 12 ,
        minute 54 ,
        second 0 } } ,
  type unknown ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } } ,
  gene {
     } ,
  gene-source {
    src "LocusLink" ,
    src-int 11286 ,
    src-str2 "11286" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      version 0 } } ,
  properties {
    {
      type property ,
      label "Property" ,
      text "phenotype only" ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11286 } } ,
  xtra-index-terms {
    "LOC50518" } ,
  xtra-properties {
    {
      tag "PROP" ,
      value "phenotype only" } } }
Entrezgene ::= {
  track-info {
    geneid 11287 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 4 ,
        day 19 ,
        hour 12 ,
        minute 12 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } ,
    subtype {
      {
        subtype chromosome ,
        name "6" } } } ,
  gene {
    locus "Pzp" ,
    desc "pregnancy zone protein" ,
    maploc "6 62.0 cM" ,
    syn {
      "A1m" ,
      "A2m" ,
      "MAM" } ,
    locus-tag "MGI:87854" } ,
  prot {
    name {
      "pregnancy zone protein" ,
      "alpha 1 macroglobulin" } } ,
  location {
    {
      display-str "6 F1-G3" ,
      method
        map-type cyto } ,
    {
      display-str "6 62.0 cM" ,
      method
        map-type cM } } ,
  gene-source {
    src "LocusLink" ,
    src-int 11287 ,
    src-str2 "11287" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000072" ,
      version 1 ,
      seqs {
        int {
          from 129138521 ,
          to 129181660 ,
          strand minus ,
          id
            gi 51863714 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_007376" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 129138521 ,
                to 129138673 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129139811 ,
                to 129139852 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129140505 ,
                to 129140607 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129141065 ,
                to 129141133 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129141840 ,
                to 129141930 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129142350 ,
                to 129142480 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129142828 ,
                to 129143046 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129143853 ,
                to 129144094 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129144629 ,
                to 129144806 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129144966 ,
                to 129145040 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129145470 ,
                to 129145626 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129146112 ,
                to 129146202 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129146443 ,
                to 129146619 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129147104 ,
                to 129147187 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129149375 ,
                to 129149426 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129149655 ,
                to 129149776 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129150140 ,
                to 129150266 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129150847 ,
                to 129151075 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129151526 ,
                to 129151700 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129153906 ,
                to 129153993 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129157123 ,
                to 129157287 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129158420 ,
                to 129158569 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129161683 ,
                to 129161825 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129165292 ,
                to 129165355 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129167103 ,
                to 129167330 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129168683 ,
                to 129168844 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129171020 ,
                to 129171129 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129171763 ,
                to 129171877 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129174339 ,
                to 129174462 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129176048 ,
                to 129176132 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129176963 ,
                to 129177131 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129177687 ,
                to 129177707 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129178724 ,
                to 129178776 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129178917 ,
                to 129179070 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129180062 ,
                to 129180245 ,
                strand minus ,
                id
                  gi 51863714 } ,
              int {
                from 129181526 ,
                to 129181660 ,
                strand minus ,
                id
                  gi 51863714 } } } ,
          seqs {
            whole
              gi 6680607 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_031402" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 129138651 ,
                    to 129138673 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129139811 ,
                    to 129139852 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129140505 ,
                    to 129140607 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129141065 ,
                    to 129141133 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129141840 ,
                    to 129141930 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129142350 ,
                    to 129142480 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129142828 ,
                    to 129143046 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129143853 ,
                    to 129144094 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129144629 ,
                    to 129144806 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129144966 ,
                    to 129145040 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129145470 ,
                    to 129145626 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129146112 ,
                    to 129146202 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129146443 ,
                    to 129146619 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129147104 ,
                    to 129147187 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129149375 ,
                    to 129149426 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129149655 ,
                    to 129149776 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129150140 ,
                    to 129150266 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129150847 ,
                    to 129151075 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129151526 ,
                    to 129151700 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129153906 ,
                    to 129153993 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129157123 ,
                    to 129157287 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129158420 ,
                    to 129158569 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129161683 ,
                    to 129161825 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129165292 ,
                    to 129165355 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129167103 ,
                    to 129167330 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129168683 ,
                    to 129168844 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129171020 ,
                    to 129171129 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129171763 ,
                    to 129171877 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129174339 ,
                    to 129174462 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129176048 ,
                    to 129176132 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129176963 ,
                    to 129177131 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129177687 ,
                    to 129177707 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129178724 ,
                    to 129178776 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129178917 ,
                    to 129179070 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129180062 ,
                    to 129180245 ,
                    strand minus ,
                    id
                      gi 51863714 } ,
                  {
                    from 129181526 ,
                    to 129181611 ,
                    strand minus ,
                    id
                      gi 51863714 } } } ,
              seqs {
                whole
                  gi 6680608 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_039356" ,
      version 3 ,
      seqs {
        int {
          from 3999237 ,
          to 4042376 ,
          strand minus ,
          id
            gi 51712708 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_007376" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 3999237 ,
                to 3999389 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4000527 ,
                to 4000568 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4001221 ,
                to 4001323 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4001781 ,
                to 4001849 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4002556 ,
                to 4002646 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4003066 ,
                to 4003196 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4003544 ,
                to 4003762 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4004569 ,
                to 4004810 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4005345 ,
                to 4005522 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4005682 ,
                to 4005756 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4006186 ,
                to 4006342 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4006828 ,
                to 4006918 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4007159 ,
                to 4007335 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4007820 ,
                to 4007903 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4010091 ,
                to 4010142 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4010371 ,
                to 4010492 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4010856 ,
                to 4010982 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4011563 ,
                to 4011791 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4012242 ,
                to 4012416 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4014622 ,
                to 4014709 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4017839 ,
                to 4018003 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4019136 ,
                to 4019285 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4022399 ,
                to 4022541 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4026008 ,
                to 4026071 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4027819 ,
                to 4028046 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4029399 ,
                to 4029560 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4031736 ,
                to 4031845 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4032479 ,
                to 4032593 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4035055 ,
                to 4035178 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4036764 ,
                to 4036848 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4037679 ,
                to 4037847 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4038403 ,
                to 4038423 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4039440 ,
                to 4039492 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4039633 ,
                to 4039786 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4040778 ,
                to 4040961 ,
                strand minus ,
                id
                  gi 51712708 } ,
              int {
                from 4042242 ,
                to 4042376 ,
                strand minus ,
                id
                  gi 51712708 } } } ,
          seqs {
            whole
              gi 6680607 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_031402" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 3999367 ,
                    to 3999389 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4000527 ,
                    to 4000568 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4001221 ,
                    to 4001323 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4001781 ,
                    to 4001849 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4002556 ,
                    to 4002646 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4003066 ,
                    to 4003196 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4003544 ,
                    to 4003762 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4004569 ,
                    to 4004810 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4005345 ,
                    to 4005522 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4005682 ,
                    to 4005756 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4006186 ,
                    to 4006342 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4006828 ,
                    to 4006918 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4007159 ,
                    to 4007335 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4007820 ,
                    to 4007903 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4010091 ,
                    to 4010142 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4010371 ,
                    to 4010492 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4010856 ,
                    to 4010982 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4011563 ,
                    to 4011791 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4012242 ,
                    to 4012416 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4014622 ,
                    to 4014709 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4017839 ,
                    to 4018003 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4019136 ,
                    to 4019285 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4022399 ,
                    to 4022541 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4026008 ,
                    to 4026071 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4027819 ,
                    to 4028046 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4029399 ,
                    to 4029560 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4031736 ,
                    to 4031845 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4032479 ,
                    to 4032593 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4035055 ,
                    to 4035178 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4036764 ,
                    to 4036848 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4037679 ,
                    to 4037847 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4038403 ,
                    to 4038423 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4039440 ,
                    to 4039492 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4039633 ,
                    to 4039786 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4040778 ,
                    to 4040961 ,
                    strand minus ,
                    id
                      gi 51712708 } ,
                  {
                    from 4042242 ,
                    to 4042327 ,
                    strand minus ,
                    id
                      gi 51712708 } } } ,
              seqs {
                whole
                  gi 6680608 } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "Mouse Genome Informatics" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "Pzp" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "pregnancy zone protein" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "MGI" ,
          url "http://www.informatics.jax.org/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 5559967 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 4866 } ,
                  anchor "endopeptidase inhibitor activity" ,
                  post-text "evidence: IDA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 4867 } ,
                  anchor "serine-type endopeptidase inhibitor activity" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 17114 } ,
                  anchor "wide-spectrum protease inhibitor activity" ,
                  post-text "evidence: IEA" } } } } } ,
        {
          type comment ,
          label "Component" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 5559967 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5576 } ,
                  anchor "extracellular region" ,
                  post-text "evidence: TAS" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 12466851 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5615 } ,
                  anchor "extracellular space" ,
                  post-text "evidence: TAS" } } } } } } } } ,
  homology {
    {
      type comment ,
      heading "Rat" ,
      version 0 ,
      source {
        {
          src {
            db "HomoloGene" ,
            tag
              id 56378 } ,
          anchor "Map Viewer" ,
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&chr=6&
MAPS=genes-r-org/rat-chr/mouse%3A6,genes-r-org/mouse-chr6&query=e%3A11287[id]+
AND+gene[obj_type]&QSTR=pzp&cmd=focus&fill=10" } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "MGI" ,
            tag
              id 87854 } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "PROVISIONAL" ,
      version 0 } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 12477932 ,
        pmid 12466851 ,
        pmid 7528166 ,
        pmid 5559967 ,
        pmid 1280217 } } ,
    {
      type comment ,
      heading "Markers (Sequence Tagged Sites/STS)" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 140992 } ,
              anchor "A2m" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "D6Uwa7" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "MGI:893149" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "Pzp" ,
              version 0 } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 179416 } ,
              anchor "AI838740" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "659717" ,
              version 0 } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 179477 } ,
              anchor "AI893533" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "681710" ,
              version 0 } } } } } ,
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_007376" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 6680607 } ,
              anchor "NM_007376" } } ,
          seqs {
            whole
              gi 6680607 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_031402" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 6680608 } ,
                  anchor "NP_031402" ,
                  post-text "pregnancy zone protein" } } ,
              seqs {
                whole
                  gi 6680608 } ,
              comment {
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 6680608 } ,
                      pre-text "(2)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 5952 } ,
                          anchor "pfam00207: A2M; Alpha-2-macroglobulin family" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 738 - 1482  Blast Score: 1820" ,
                          version 0 } } } ,
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 25832 } ,
                          anchor "pfam01835: A2M_N; Alpha-2-macroglobulin
 family N-terminal region" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 22 - 622  Blast Score: 1231" ,
                          version 0 } } } } } } } } ,
          comment {
            {
              type other ,
              heading "Source Sequence" ,
              version 0 ,
              source {
                {
                  src {
                    db "Nucleotide" ,
                    tag
                      str "M93264" } ,
                  anchor "M93264" } } ,
              comment {
                {
                  type other ,
                  version 0 } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type genomic ,
          heading "Genomic" ,
          accession "U06977" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 463883 } ,
              anchor "U06977" } } ,
          seqs {
            whole
              gi 463883 } ,
          products {
            {
              type peptide ,
              accession "AAA87890" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 463884 } ,
                  anchor "AAA87890" } } ,
              seqs {
                whole
                  gi 463884 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC057983" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 34785995 } ,
              anchor "BC057983" } } ,
          seqs {
            whole
              gi 34785995 } ,
          products {
            {
              type peptide ,
              accession "AAH57983" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 34785996 } ,
                  anchor "AAH57983" } } ,
              seqs {
                whole
                  gi 34785996 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "FVB/N" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "M93264" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 199085 } ,
              anchor "M93264" } } ,
          seqs {
            whole
              gi 199085 } ,
          products {
            {
              type peptide ,
              accession "AAA39508" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 199086 } ,
                  anchor "AAA39508" } } ,
              seqs {
                whole
                  gi 199086 } } } } ,
        {
          type other ,
          text "None" ,
          version 0 ,
          products {
            {
              type peptide ,
              accession "Q61838" ,
              version 0 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 2492496 } ,
                  anchor "Q61838" } } ,
              seqs {
                whole
                  gi 2492496 } } } } } } ,
    {
      type comment ,
      heading "Additional Links" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Evidence Viewer" ,
                tag
                  str "11287" } ,
              anchor "Evidence Viewer" ,
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=10090&cont
ig=NT_039356.3&gene=Pzp&lid=11287&from=3999238&to=4042377" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "ModelMaker" ,
                tag
                  str "11287" } ,
              anchor "ModelMaker" ,
              url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=10
090&contig=NT_039356.3&gene=Pzp&lid=11287" } } } ,
        {
          type comment ,
          text "UniGene" ,
          version 0 ,
          xtra-properties {
            {
              tag "UNIGENE" ,
              value "Mm.260144" } } ,
          source {
            {
              src {
                db "UniGene" ,
                tag
                  str "Mm.260144" } ,
              anchor "Mm.260144" ,
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&CID=26
0144" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "HomoloGene" ,
                tag
                  str "11287" } ,
              anchor "HomoloGene" ,
              url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=
11287[loc]&TAXID=10090" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGI" ,
                tag
                  id 87854 } ,
              anchor "MGI" ,
              url "http://www.informatics.jax.org/searches/accession_report.cg
i?id=MGI:87854" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Ensembl" ,
                tag
                  str "" } ,
              url "http://www.ensembl.org/Mus_musculus/contigview?geneid=BC057
983" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UCSC" ,
                tag
                  str "" } ,
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position=
BC057983" } } } ,
        {
          type comment ,
          text "Gene Expression Database (GXD) at MGI" ,
          version 0 ,
          source {
            {
              src {
                db "Gene Expression Database (GXD) at MGI" ,
                tag
                  str "MGI:87854" } ,
              anchor "MGI:87854" ,
              url "http://www.informatics.jax.org/searches/expression_report.c
gi?id=MGI:87854" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGC" ,
                tag
                  str "BC057983" } ,
              anchor "MGC" ,
              url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Mm&LIST=BC057983" } } } } } ,
    {
      type comment ,
      heading "Alleles" ,
      version 0 ,
      comment {
        {
          type comment ,
          text "The following allele types are documented at Mouse Genome
 Informatics" ,
          version 0 ,
          source {
            {
              anchor "(MGI)" ,
              url "http://www.informatics.jax.org/searches/allele_report.cgi?m
arkerID=MGI:87854" } } } ,
        {
          type comment ,
          heading "Targeted (knock-out) (1)" ,
          version 0 ,
          refs {
            pmid 7544347 } } } } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11287 } ,
    {
      db "MGI" ,
      tag
        id 87854 } } ,
  xtra-index-terms {
    "LOC11287" } }
Entrezgene ::= {
  track-info {
    geneid 11288 ,
    status secondary ,
    current-id {
      {
        db "LocusID" ,
        tag
          id 112131 } ,
      {
        db "GeneID" ,
        tag
          id 112131 } } ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 2 ,
        day 17 ,
        hour 12 ,
        minute 54 ,
        second 0 } } ,
  type unknown ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } } ,
  gene {
     } ,
  gene-source {
    src "LocusLink" ,
    src-int 11288 ,
    src-str2 "11288" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      version 0 } } ,
  properties {
    {
      type property ,
      label "Property" ,
      text "phenotype only" ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11288 } } ,
  xtra-index-terms {
    "LOC112131" } ,
  xtra-properties {
    {
      tag "PROP" ,
      value "phenotype only" } } }
Entrezgene ::= {
  track-info {
    geneid 11289 ,
    status secondary ,
    current-id {
      {
        db "LocusID" ,
        tag
          id 107417 } ,
      {
        db "GeneID" ,
        tag
          id 107417 } } ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 2 ,
        day 17 ,
        hour 12 ,
        minute 54 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } } ,
  gene {
     } ,
  gene-source {
    src "LocusLink" ,
    src-int 11289 ,
    src-str2 "11289" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11289 } } ,
  xtra-index-terms {
    "LOC107417" } }
Entrezgene ::= {
  track-info {
    geneid 11293 ,
    status secondary ,
    current-id {
      {
        db "LocusID" ,
        tag
          id 112132 } ,
      {
        db "GeneID" ,
        tag
          id 112132 } } ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 2 ,
        day 17 ,
        hour 12 ,
        minute 54 ,
        second 0 } } ,
  type unknown ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } } ,
  gene {
     } ,
  gene-source {
    src "LocusLink" ,
    src-int 11293 ,
    src-str2 "11293" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      version 0 } } ,
  properties {
    {
      type property ,
      label "Property" ,
      text "phenotype only" ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11293 } } ,
  xtra-index-terms {
    "LOC112132" } ,
  xtra-properties {
    {
      tag "PROP" ,
      value "phenotype only" } } }
Entrezgene ::= {
  track-info {
    geneid 11294 ,
    status secondary ,
    current-id {
      {
        db "LocusID" ,
        tag
          id 109413 } ,
      {
        db "GeneID" ,
        tag
          id 109413 } } ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 2 ,
        day 17 ,
        hour 12 ,
        minute 54 ,
        second 0 } } ,
  type unknown ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } } ,
  gene {
     } ,
  gene-source {
    src "LocusLink" ,
    src-int 11294 ,
    src-str2 "11294" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      version 0 } } ,
  properties {
    {
      type property ,
      label "Property" ,
      text "phenotype only" ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11294 } } ,
  xtra-index-terms {
    "LOC109413" } ,
  xtra-properties {
    {
      tag "PROP" ,
      value "phenotype only" } } }
Entrezgene ::= {
  track-info {
    geneid 11295 ,
    status secondary ,
    current-id {
      {
        db "LocusID" ,
        tag
          id 109414 } ,
      {
        db "GeneID" ,
        tag
          id 109414 } } ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 2 ,
        day 17 ,
        hour 12 ,
        minute 54 ,
        second 0 } } ,
  type unknown ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } } ,
  gene {
     } ,
  gene-source {
    src "LocusLink" ,
    src-int 11295 ,
    src-str2 "11295" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      version 0 } } ,
  properties {
    {
      type property ,
      label "Property" ,
      text "phenotype only" ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11295 } } ,
  xtra-index-terms {
    "LOC109414" } ,
  xtra-properties {
    {
      tag "PROP" ,
      value "phenotype only" } } }
Entrezgene ::= {
  track-info {
    geneid 11296 ,
    status secondary ,
    current-id {
      {
        db "LocusID" ,
        tag
          id 104236 } ,
      {
        db "GeneID" ,
        tag
          id 104236 } } ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 2 ,
        day 17 ,
        hour 12 ,
        minute 54 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } } ,
  gene {
     } ,
  gene-source {
    src "LocusLink" ,
    src-int 11296 ,
    src-str2 "11296" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11296 } } ,
  xtra-index-terms {
    "LOC104236" } }
Entrezgene ::= {
  track-info {
    geneid 11297 ,
    status secondary ,
    current-id {
      {
        db "LocusID" ,
        tag
          id 227290 } ,
      {
        db "GeneID" ,
        tag
          id 227290 } } ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 2 ,
        day 17 ,
        hour 12 ,
        minute 54 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } } ,
  gene {
     } ,
  gene-source {
    src "LocusLink" ,
    src-int 11297 ,
    src-str2 "11297" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11297 } } ,
  xtra-index-terms {
    "LOC227290" } }
Entrezgene ::= {
  track-info {
    geneid 11298 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 3 ,
        day 16 ,
        hour 16 ,
        minute 48 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } ,
    subtype {
      {
        subtype chromosome ,
        name "11" } } } ,
  gene {
    locus "Aanat" ,
    desc "arylalkylamine N-acetyltransferase" ,
    maploc "11 70.0 cM" ,
    syn {
      "Nat4" ,
      "SNAT" ,
      "Nat-2" } ,
    locus-tag "MGI:1328365" } ,
  prot {
    name {
      "arylalkylamine N-acetyltransferase" } } ,
  location {
    {
      display-str "11 E2" ,
      method
        map-type cyto } ,
    {
      display-str "11 70.0 cM" ,
      method
        map-type cM } } ,
  gene-source {
    src "LocusLink" ,
    src-int 11298 ,
    src-str2 "11298" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000077" ,
      version 1 ,
      seqs {
        int {
          from 116264815 ,
          to 116268672 ,
          strand plus ,
          id
            gi 51868608 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_009591" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 116264815 ,
                to 116264902 ,
                strand plus ,
                id
                  gi 51868608 } ,
              int {
                from 116266704 ,
                to 116266921 ,
                strand plus ,
                id
                  gi 51868608 } ,
              int {
                from 116267254 ,
                to 116267408 ,
                strand plus ,
                id
                  gi 51868608 } ,
              int {
                from 116267917 ,
                to 116268672 ,
                strand plus ,
                id
                  gi 51868608 } } } ,
          seqs {
            whole
              gi 6752937 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_033721" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 116266765 ,
                    to 116266921 ,
                    strand plus ,
                    id
                      gi 51868608 } ,
                  {
                    from 116267254 ,
                    to 116267408 ,
                    strand plus ,
                    id
                      gi 51868608 } ,
                  {
                    from 116267917 ,
                    to 116268222 ,
                    strand plus ,
                    id
                      gi 51868608 } } } ,
              seqs {
                whole
                  gi 6752938 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_039521" ,
      version 3 ,
      seqs {
        int {
          from 27994169 ,
          to 27998026 ,
          strand plus ,
          id
            gi 51766637 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_009591" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 27994169 ,
                to 27994256 ,
                strand plus ,
                id
                  gi 51766637 } ,
              int {
                from 27996058 ,
                to 27996275 ,
                strand plus ,
                id
                  gi 51766637 } ,
              int {
                from 27996608 ,
                to 27996762 ,
                strand plus ,
                id
                  gi 51766637 } ,
              int {
                from 27997271 ,
                to 27998026 ,
                strand plus ,
                id
                  gi 51766637 } } } ,
          seqs {
            whole
              gi 6752937 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_033721" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 27996119 ,
                    to 27996275 ,
                    strand plus ,
                    id
                      gi 51766637 } ,
                  {
                    from 27996608 ,
                    to 27996762 ,
                    strand plus ,
                    id
                      gi 51766637 } ,
                  {
                    from 27997271 ,
                    to 27997576 ,
                    strand plus ,
                    id
                      gi 51766637 } } } ,
              seqs {
                whole
                  gi 6752938 } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "Mouse Genome Informatics" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "Aanat" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "arylalkylamine N-acetyltransferase" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "MGI" ,
          url "http://www.informatics.jax.org/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 8080 } ,
                  anchor "N-acetyltransferase activity" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 8415 } ,
                  anchor "acyltransferase activity" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 4060 } ,
                  anchor "arylamine N-acetyltransferase activity" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16740 } ,
                  anchor "transferase activity" ,
                  post-text "evidence: IEA" } } } } } } } } ,
  homology {
    {
      type comment ,
      heading "Human, Rat" ,
      version 0 ,
      source {
        {
          src {
            db "HomoloGene" ,
            tag
              id 31013 } ,
          anchor "Map Viewer" ,
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&chr=11
&MAPS=genes-r-org/human-chr/mouse%3A11,genes-r-org/rat-chr/mouse%3A11,genes-r-
org/mouse-chr11&query=e%3A11298[id]+AND+gene[obj_type]&QSTR=aanat&cmd=focus&fi
ll=10" } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "MGI" ,
            tag
              id 1328365 } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "PROVISIONAL" ,
      version 0 } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 12138020 ,
        pmid 9838107 ,
        pmid 9708862 } } ,
    {
      type comment ,
      heading "Markers (Sequence Tagged Sites/STS)" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 126289 } ,
              anchor "D11Mit102" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "MGI:707739" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "MPC786" ,
              version 0 } } } } } ,
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_009591" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 6752937 } ,
              anchor "NM_009591" } } ,
          seqs {
            whole
              gi 6752937 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_033721" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 6752938 } ,
                  anchor "NP_033721" ,
                  post-text "arylalkylamine N-acetyltransferase" } } ,
              seqs {
                whole
                  gi 6752938 } ,
              comment {
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 6752938 } ,
                      pre-text "(1)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 25558 } ,
                          anchor "pfam00583: Acetyltransf_1; Acetyltransferase
 (GNAT) family" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 80 - 172  Blast Score: 118" ,
                          version 0 } } } } } } } } ,
          comment {
            {
              type other ,
              heading "Source Sequence" ,
              version 0 ,
              source {
                {
                  src {
                    db "Nucleotide" ,
                    tag
                      str "AF004108" } ,
                  anchor "AF004108" } } ,
              comment {
                {
                  type other ,
                  version 0 } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type genomic ,
          heading "Genomic" ,
          accession "U83462" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 4159794 } ,
              anchor "U83462" } } ,
          seqs {
            whole
              gi 4159794 } ,
          products {
            {
              type peptide ,
              accession "AAD08637" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 4099097 } ,
                  anchor "AAD08637" } } ,
              seqs {
                whole
                  gi 4099097 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "129/Sv" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AB013358" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 3298499 } ,
              anchor "AB013358" } } ,
          seqs {
            whole
              gi 3298499 } ,
          products {
            {
              type peptide ,
              accession "BAA31526" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 3298500 } ,
                  anchor "BAA31526" } } ,
              seqs {
                whole
                  gi 3298500 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "BALB/c" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AF004108" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 4159890 } ,
              anchor "AF004108" } } ,
          seqs {
            whole
              gi 4159890 } ,
          products {
            {
              type peptide ,
              accession "AAD09408" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 4159891 } ,
                  anchor "AAD09408" } } ,
              seqs {
                whole
                  gi 4159891 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C3H/He" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AF004109" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 4159892 } ,
              anchor "AF004109" } } ,
          seqs {
            whole
              gi 4159892 } ,
          products {
            {
              type peptide ,
              accession "AAD09409" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 4159893 } ,
                  anchor "AAD09409" } } ,
              seqs {
                whole
                  gi 4159893 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C3H/He" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AF004110" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 4159894 } ,
              anchor "AF004110" } } ,
          seqs {
            whole
              gi 4159894 } ,
          products {
            {
              type peptide ,
              accession "AAD09410" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 4159895 } ,
                  anchor "AAD09410" } } ,
              seqs {
                whole
                  gi 4159895 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AF004111" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 4159896 } ,
              anchor "AF004111" } } ,
          seqs {
            whole
              gi 4159896 } ,
          products {
            {
              type peptide ,
              accession "AAD09411" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 4159897 } ,
                  anchor "AAD09411" } } ,
              seqs {
                whole
                  gi 4159897 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6" ,
              version 0 } } } ,
        {
          type other ,
          text "None" ,
          version 0 ,
          products {
            {
              type peptide ,
              accession "O88816" ,
              version 0 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 11387071 } ,
                  anchor "O88816" } } ,
              seqs {
                whole
                  gi 11387071 } } } } } } ,
    {
      type comment ,
      heading "Additional Links" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Evidence Viewer" ,
                tag
                  str "11298" } ,
              anchor "Evidence Viewer" ,
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=10090&cont
ig=NT_039521.3&gene=Aanat&lid=11298&from=27994170&to=27998027" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "ModelMaker" ,
                tag
                  str "11298" } ,
              anchor "ModelMaker" ,
              url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=10
090&contig=NT_039521.3&gene=Aanat&lid=11298" } } } ,
        {
          type comment ,
          text "UniGene" ,
          version 0 ,
          xtra-properties {
            {
              tag "UNIGENE" ,
              value "Mm.42233" } } ,
          source {
            {
              src {
                db "UniGene" ,
                tag
                  str "Mm.42233" } ,
              anchor "Mm.42233" ,
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&CID=42
233" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "HomoloGene" ,
                tag
                  str "11298" } ,
              anchor "HomoloGene" ,
              url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=
11298[loc]&TAXID=10090" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGI" ,
                tag
                  id 1328365 } ,
              anchor "MGI" ,
              url "http://www.informatics.jax.org/searches/accession_report.cg
i?id=MGI:1328365" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Ensembl" ,
                tag
                  str "" } ,
              url "http://www.ensembl.org/Mus_musculus/contigview?geneid=AF004
110" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UCSC" ,
                tag
                  str "" } ,
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position=
AF004110" } } } } } ,
    {
      type generif ,
      text "AANAT expression and synthesis of N-acetylserotonin/melatonin
 could play a role in addictive properties of cocaine" ,
      version 0 ,
      refs {
        pmid 12138020 } ,
      create-date
        str "Aug 19 2002 12:00AM" ,
      update-date
        str "Aug 28 2002  6:19PM" } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11298 } ,
    {
      db "MGI" ,
      tag
        id 1328365 } } ,
  xtra-index-terms {
    "LOC11298" } }
Entrezgene ::= {
  track-info {
    geneid 11299 ,
    status secondary ,
    current-id {
      {
        db "LocusID" ,
        tag
          id 20249 } ,
      {
        db "GeneID" ,
        tag
          id 20249 } } ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 2 ,
        day 17 ,
        hour 12 ,
        minute 54 ,
        second 0 } } ,
  type unknown ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } } ,
  gene {
     } ,
  gene-source {
    src "LocusLink" ,
    src-int 11299 ,
    src-str2 "11299" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      version 0 } } ,
  properties {
    {
      type property ,
      label "Property" ,
      text "phenotype only" ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11299 } } ,
  xtra-index-terms {
    "LOC20249" } ,
  xtra-properties {
    {
      tag "PROP" ,
      value "phenotype only" } } }
Entrezgene ::= {
  track-info {
    geneid 11300 ,
    status secondary ,
    current-id {
      {
        db "LocusID" ,
        tag
          id 112133 } ,
      {
        db "GeneID" ,
        tag
          id 112133 } } ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 2 ,
        day 17 ,
        hour 12 ,
        minute 54 ,
        second 0 } } ,
  type unknown ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } } ,
  gene {
     } ,
  gene-source {
    src "LocusLink" ,
    src-int 11300 ,
    src-str2 "11300" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      version 0 } } ,
  properties {
    {
      type property ,
      label "Property" ,
      text "phenotype only" ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11300 } } ,
  xtra-index-terms {
    "LOC112133" } ,
  xtra-properties {
    {
      tag "PROP" ,
      value "phenotype only" } } }
Entrezgene ::= {
  track-info {
    geneid 11301 ,
    status secondary ,
    current-id {
      {
        db "LocusID" ,
        tag
          id 20700 } ,
      {
        db "GeneID" ,
        tag
          id 20700 } } ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 3 ,
        day 9 ,
        hour 17 ,
        minute 35 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } } ,
  gene {
     } ,
  gene-source {
    src "LocusLink" ,
    src-int 11301 ,
    src-str2 "11301" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11301 } } ,
  xtra-index-terms {
    "LOC20700" } }
Entrezgene ::= {
  track-info {
    geneid 11302 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 3 ,
        day 26 ,
        hour 10 ,
        minute 32 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } ,
    subtype {
      {
        subtype chromosome ,
        name "11" } } } ,
  gene {
    locus "Aatk" ,
    desc "apoptosis-associated tyrosine kinase" ,
    maploc "11 E2" ,
    syn {
      "AATYK" ,
      "mKIAA0641" } ,
    locus-tag "MGI:1197518" } ,
  prot {
    name {
      "apoptosis-associated tyrosine kinase" } } ,
  location {
    {
      display-str "11 E2" ,
      method
        map-type cyto } } ,
  gene-source {
    src "LocusLink" ,
    src-int 11302 ,
    src-str2 "11302" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000077" ,
      version 1 ,
      seqs {
        int {
          from 119678449 ,
          to 119692677 ,
          strand minus ,
          id
            gi 51868608 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_007377" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 119678449 ,
                to 119679572 ,
                strand minus ,
                id
                  gi 51868608 } ,
              int {
                from 119680403 ,
                to 119680603 ,
                strand minus ,
                id
                  gi 51868608 } ,
              int {
                from 119680735 ,
                to 119680882 ,
                strand minus ,
                id
                  gi 51868608 } ,
              int {
                from 119680962 ,
                to 119683554 ,
                strand minus ,
                id
                  gi 51868608 } ,
              int {
                from 119683851 ,
                to 119684000 ,
                strand minus ,
                id
                  gi 51868608 } ,
              int {
                from 119684576 ,
                to 119684697 ,
                strand minus ,
                id
                  gi 51868608 } ,
              int {
                from 119684778 ,
                to 119684862 ,
                strand minus ,
                id
                  gi 51868608 } ,
              int {
                from 119686587 ,
                to 119686720 ,
                strand minus ,
                id
                  gi 51868608 } ,
              int {
                from 119687234 ,
                to 119687321 ,
                strand minus ,
                id
                  gi 51868608 } ,
              int {
                from 119687441 ,
                to 119687559 ,
                strand minus ,
                id
                  gi 51868608 } ,
              int {
                from 119687856 ,
                to 119687935 ,
                strand minus ,
                id
                  gi 51868608 } ,
              int {
                from 119689873 ,
                to 119690020 ,
                strand minus ,
                id
                  gi 51868608 } ,
              int {
                from 119692530 ,
                to 119692677 ,
                strand minus ,
                id
                  gi 51868608 } } } ,
          seqs {
            whole
              gi 6680609 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_031403" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 119679532 ,
                    to 119679572 ,
                    strand minus ,
                    id
                      gi 51868608 } ,
                  {
                    from 119680403 ,
                    to 119680603 ,
                    strand minus ,
                    id
                      gi 51868608 } ,
                  {
                    from 119680735 ,
                    to 119680882 ,
                    strand minus ,
                    id
                      gi 51868608 } ,
                  {
                    from 119680962 ,
                    to 119683554 ,
                    strand minus ,
                    id
                      gi 51868608 } ,
                  {
                    from 119683851 ,
                    to 119684000 ,
                    strand minus ,
                    id
                      gi 51868608 } ,
                  {
                    from 119684576 ,
                    to 119684697 ,
                    strand minus ,
                    id
                      gi 51868608 } ,
                  {
                    from 119684778 ,
                    to 119684862 ,
                    strand minus ,
                    id
                      gi 51868608 } ,
                  {
                    from 119686587 ,
                    to 119686720 ,
                    strand minus ,
                    id
                      gi 51868608 } ,
                  {
                    from 119687234 ,
                    to 119687321 ,
                    strand minus ,
                    id
                      gi 51868608 } ,
                  {
                    from 119687441 ,
                    to 119687559 ,
                    strand minus ,
                    id
                      gi 51868608 } ,
                  {
                    from 119687856 ,
                    to 119687935 ,
                    strand minus ,
                    id
                      gi 51868608 } ,
                  {
                    from 119689873 ,
                    to 119690020 ,
                    strand minus ,
                    id
                      gi 51868608 } ,
                  {
                    from 119692530 ,
                    to 119692574 ,
                    strand minus ,
                    id
                      gi 51868608 } } } ,
              seqs {
                whole
                  gi 6680610 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_039521" ,
      version 3 ,
      seqs {
        int {
          from 31407803 ,
          to 31422031 ,
          strand minus ,
          id
            gi 51766637 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_007377" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 31407803 ,
                to 31408926 ,
                strand minus ,
                id
                  gi 51766637 } ,
              int {
                from 31409757 ,
                to 31409957 ,
                strand minus ,
                id
                  gi 51766637 } ,
              int {
                from 31410089 ,
                to 31410236 ,
                strand minus ,
                id
                  gi 51766637 } ,
              int {
                from 31410316 ,
                to 31412908 ,
                strand minus ,
                id
                  gi 51766637 } ,
              int {
                from 31413205 ,
                to 31413354 ,
                strand minus ,
                id
                  gi 51766637 } ,
              int {
                from 31413930 ,
                to 31414051 ,
                strand minus ,
                id
                  gi 51766637 } ,
              int {
                from 31414132 ,
                to 31414216 ,
                strand minus ,
                id
                  gi 51766637 } ,
              int {
                from 31415941 ,
                to 31416074 ,
                strand minus ,
                id
                  gi 51766637 } ,
              int {
                from 31416588 ,
                to 31416675 ,
                strand minus ,
                id
                  gi 51766637 } ,
              int {
                from 31416795 ,
                to 31416913 ,
                strand minus ,
                id
                  gi 51766637 } ,
              int {
                from 31417210 ,
                to 31417289 ,
                strand minus ,
                id
                  gi 51766637 } ,
              int {
                from 31419227 ,
                to 31419374 ,
                strand minus ,
                id
                  gi 51766637 } ,
              int {
                from 31421884 ,
                to 31422031 ,
                strand minus ,
                id
                  gi 51766637 } } } ,
          seqs {
            whole
              gi 6680609 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_031403" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 31408886 ,
                    to 31408926 ,
                    strand minus ,
                    id
                      gi 51766637 } ,
                  {
                    from 31409757 ,
                    to 31409957 ,
                    strand minus ,
                    id
                      gi 51766637 } ,
                  {
                    from 31410089 ,
                    to 31410236 ,
                    strand minus ,
                    id
                      gi 51766637 } ,
                  {
                    from 31410316 ,
                    to 31412908 ,
                    strand minus ,
                    id
                      gi 51766637 } ,
                  {
                    from 31413205 ,
                    to 31413354 ,
                    strand minus ,
                    id
                      gi 51766637 } ,
                  {
                    from 31413930 ,
                    to 31414051 ,
                    strand minus ,
                    id
                      gi 51766637 } ,
                  {
                    from 31414132 ,
                    to 31414216 ,
                    strand minus ,
                    id
                      gi 51766637 } ,
                  {
                    from 31415941 ,
                    to 31416074 ,
                    strand minus ,
                    id
                      gi 51766637 } ,
                  {
                    from 31416588 ,
                    to 31416675 ,
                    strand minus ,
                    id
                      gi 51766637 } ,
                  {
                    from 31416795 ,
                    to 31416913 ,
                    strand minus ,
                    id
                      gi 51766637 } ,
                  {
                    from 31417210 ,
                    to 31417289 ,
                    strand minus ,
                    id
                      gi 51766637 } ,
                  {
                    from 31419227 ,
                    to 31419374 ,
                    strand minus ,
                    id
                      gi 51766637 } ,
                  {
                    from 31421884 ,
                    to 31421928 ,
                    strand minus ,
                    id
                      gi 51766637 } } } ,
              seqs {
                whole
                  gi 6680610 } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "Mouse Genome Informatics" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "Aatk" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "apoptosis-associated tyrosine kinase" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "MGI" ,
          url "http://www.informatics.jax.org/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5524 } ,
                  anchor "ATP binding" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16301 } ,
                  anchor "kinase activity" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 12466851 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 4672 } ,
                  anchor "protein kinase activity" ,
                  post-text "evidence: ISS" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 12466851 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 4674 } ,
                  anchor "protein serine/threonine kinase activity" ,
                  post-text "evidence: ISS" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 9444961 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 4713 } ,
                  anchor "protein-tyrosine kinase activity" ,
                  post-text "evidence: ISS" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16740 } ,
                  anchor "transferase activity" ,
                  post-text "evidence: IEA" } } } } } ,
        {
          type comment ,
          label "Process" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 9444961 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 6915 } ,
                  anchor "apoptosis" ,
                  post-text "evidence: IDA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 12466851 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 6468 } ,
                  anchor "protein amino acid phosphorylation" ,
                  post-text "evidence: ISS" } } } } } } } } ,
  homology {
    {
      type comment ,
      heading "Rat" ,
      version 0 ,
      source {
        {
          src {
            db "HomoloGene" ,
            tag
              id 7223 } ,
          anchor "Map Viewer" ,
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&chr=11
&MAPS=genes-r-org/rat-chr/mouse%3A11,genes-r-org/mouse-chr11&query=e%3A11302[i
d]+AND+gene[obj_type]&QSTR=aatk&cmd=focus&fill=10" } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "MGI" ,
            tag
              id 1197518 } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "PROVISIONAL" ,
      version 0 } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 12670708 ,
        pmid 12477932 ,
        pmid 12466851 ,
        pmid 11314039 ,
        pmid 11217851 ,
        pmid 11076861 ,
        pmid 11042159 ,
        pmid 10349636 ,
        pmid 9444961 } } ,
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_007377" ,
          version 2 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 52345410 } ,
              anchor "NM_007377" } } ,
          seqs {
            whole
              gi 52345410 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_031403" ,
              version 2 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 52345411 } ,
                  anchor "NP_031403" ,
                  post-text "apoptosis-associated tyrosine kinase" } } ,
              seqs {
                whole
                  gi 52345411 } ,
              comment {
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 52345411 } ,
                      pre-text "(1)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 5392 } ,
                          anchor "cd00192: TyrKc; Tyrosine kinase, catalytic
 domain" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 75 - 348  Blast Score: 588" ,
                          version 0 } } } } } } } } ,
          comment {
            {
              type other ,
              heading "Source Sequence" ,
              version 0 ,
              source {
                {
                  src {
                    db "Nucleotide" ,
                    tag
                      str "BC080846" } ,
                  anchor "BC080846" } } ,
              comment {
                {
                  type other ,
                  version 0 } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AB093253" ,
          version 2 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 39104554 } ,
              anchor "AB093253" } } ,
          seqs {
            whole
              gi 39104554 } ,
          products {
            {
              type peptide ,
              accession "BAC41437" ,
              version 2 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 39104555 } ,
                  anchor "BAC41437" } } ,
              seqs {
                whole
                  gi 39104555 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AF011908" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 2459992 } ,
              anchor "AF011908" } } ,
          seqs {
            whole
              gi 2459992 } ,
          products {
            {
              type peptide ,
              accession "AAB71837" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 2459993 } ,
                  anchor "AAB71837" } } ,
              seqs {
                whole
                  gi 2459993 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AK036705" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 26331621 } ,
              anchor "AK036705" } } ,
          seqs {
            whole
              gi 26331621 } ,
          products {
            {
              type peptide ,
              accession "BAC29541" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 26331622 } ,
                  anchor "BAC29541" } } ,
              seqs {
                whole
                  gi 26331622 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6J" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AK076214" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 26096668 } ,
              anchor "AK076214" } } ,
          seqs {
            whole
              gi 26096668 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6J" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AY236858" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 29824955 } ,
              anchor "AY236858" } } ,
          seqs {
            whole
              gi 29824955 } ,
          products {
            {
              type peptide ,
              accession "AAO92350" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 29824956 } ,
                  anchor "AAO92350" } } ,
              seqs {
                whole
                  gi 29824956 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AY236859" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 29824957 } ,
              anchor "AY236859" } } ,
          seqs {
            whole
              gi 29824957 } ,
          products {
            {
              type peptide ,
              accession "AAO92351" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 29824958 } ,
                  anchor "AAO92351" } } ,
              seqs {
                whole
                  gi 29824958 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "129/SvJ" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC042837" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 27769340 } ,
              anchor "BC042837" } } ,
          seqs {
            whole
              gi 27769340 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC052323" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 30410866 } ,
              anchor "BC052323" } } ,
          seqs {
            whole
              gi 30410866 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC080846" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 51593713 } ,
              anchor "BC080846" } } ,
          seqs {
            whole
              gi 51593713 } ,
          products {
            {
              type peptide ,
              accession "AAH80846" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 51593714 } ,
                  anchor "AAH80846" } } ,
              seqs {
                whole
                  gi 51593714 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6" ,
              version 0 } } } } } ,
    {
      type comment ,
      heading "Additional Links" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Evidence Viewer" ,
                tag
                  str "11302" } ,
              anchor "Evidence Viewer" ,
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=10090&cont
ig=NT_039521.3&gene=Aatk&lid=11302&from=31407804&to=31422032" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "ModelMaker" ,
                tag
                  str "11302" } ,
              anchor "ModelMaker" ,
              url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=10
090&contig=NT_039521.3&gene=Aatk&lid=11302" } } } ,
        {
          type comment ,
          text "UniGene" ,
          version 0 ,
          xtra-properties {
            {
              tag "UNIGENE" ,
              value "Mm.6826" } } ,
          source {
            {
              src {
                db "UniGene" ,
                tag
                  str "Mm.6826" } ,
              anchor "Mm.6826" ,
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&CID=68
26" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "HomoloGene" ,
                tag
                  str "11302" } ,
              anchor "HomoloGene" ,
              url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=
11302[loc]&TAXID=10090" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGI" ,
                tag
                  id 1197518 } ,
              anchor "MGI" ,
              url "http://www.informatics.jax.org/searches/accession_report.cg
i?id=MGI:1197518" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Ensembl" ,
                tag
                  str "" } ,
              url "http://www.ensembl.org/Mus_musculus/contigview?geneid=BC052
323" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UCSC" ,
                tag
                  str "" } ,
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position=
BC052323" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGC" ,
                tag
                  str "BC080846" } ,
              anchor "MGC" ,
              url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Mm&LIST=BC080846" } } } } } ,
    {
      type generif ,
      text "Expression of AATYK mRNA and protein increased during postnatal
 brain development. In immature granule cells, overexpression of AATYK
 promoted neurite outgrowth; a tyrosine kinase-defective mutant significantly
 inhibited it." ,
      version 0 ,
      refs {
        pmid 12670708 } ,
      create-date
        str "Jun 17 2003 12:00AM" ,
      update-date
        str "Aug  3 2003  7:06AM" } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11302 } ,
    {
      db "MGI" ,
      tag
        id 1197518 } } ,
  xtra-index-terms {
    "LOC11302" } }
Entrezgene ::= {
  track-info {
    geneid 11303 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 4 ,
        day 19 ,
        hour 12 ,
        minute 12 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } ,
    subtype {
      {
        subtype chromosome ,
        name "4" } } } ,
  gene {
    locus "Abca1" ,
    desc "ATP-binding cassette, sub-family A (ABC1), member 1" ,
    maploc "4 23.1 cM" ,
    syn {
      "Abc1" } ,
    locus-tag "MGI:99607" } ,
  prot {
    name {
      "ATP-binding cassette 1, sub-family A, member 1" ,
      "ATP-binding cassette 1" } } ,
  summary "The membrane-associated protein encoded by this gene is a member of
 the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins
 transport various molecules across extra- and intracellular membranes. ABC
 genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD,
 OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members
 of the ABC1 subfamily comprise the only major ABC subfamily found exclusively
 in multicellular eukaryotes. In humans, this protein functions as a
 cholesterol efflux pump in the cellular lipid removal pathway. Mutations in
 the human gene have been associated with Tangier's disease and familial
 high-density lipoprotein deficiency." ,
  location {
    {
      display-str "4 A5-B3" ,
      method
        map-type cyto } ,
    {
      display-str "4 23.1 cM" ,
      method
        map-type cM } } ,
  gene-source {
    src "LocusLink" ,
    src-int 11303 ,
    src-str2 "11303" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000070" ,
      version 1 ,
      seqs {
        int {
          from 52275832 ,
          to 52404936 ,
          strand minus ,
          id
            gi 51860768 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_013454" ,
          version 2 ,
          genomic-coords {
            mix {
              int {
                from 52275832 ,
                to 52279127 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52280381 ,
                to 52280624 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52281306 ,
                to 52281398 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52281917 ,
                to 52282020 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52283201 ,
                to 52283335 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52283663 ,
                to 52283804 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52285763 ,
                to 52285869 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52286583 ,
                to 52286645 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52287358 ,
                to 52287478 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52287708 ,
                to 52287837 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52289159 ,
                to 52289282 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52290819 ,
                to 52290963 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52291074 ,
                to 52291189 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52294000 ,
                to 52294177 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52295333 ,
                to 52295502 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52295979 ,
                to 52296053 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52304301 ,
                to 52304406 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52305377 ,
                to 52305409 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52306531 ,
                to 52306625 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52307434 ,
                to 52307623 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52310945 ,
                to 52311043 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52312075 ,
                to 52312199 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52313731 ,
                to 52313879 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52314836 ,
                to 52314949 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52315120 ,
                to 52315168 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52316867 ,
                to 52317069 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52317942 ,
                to 52318014 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52319264 ,
                to 52319484 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52320175 ,
                to 52320312 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52320491 ,
                to 52320633 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52321935 ,
                to 52322066 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52322987 ,
                to 52323158 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52324615 ,
                to 52324728 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52325810 ,
                to 52326014 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52326966 ,
                to 52327187 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52328761 ,
                to 52328983 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52329428 ,
                to 52329604 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52330140 ,
                to 52330345 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52331037 ,
                to 52331234 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52334843 ,
                to 52334959 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52335298 ,
                to 52335437 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52337773 ,
                to 52338013 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52340629 ,
                to 52340721 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52352050 ,
                to 52352226 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52354208 ,
                to 52354329 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52372641 ,
                to 52372759 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52373765 ,
                to 52373906 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52377966 ,
                to 52378059 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52388974 ,
                to 52389139 ,
                strand minus ,
                id
                  gi 51860768 } ,
              int {
                from 52404720 ,
                to 52404936 ,
                strand minus ,
                id
                  gi 51860768 } } } ,
          seqs {
            whole
              gi 34577068 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_038482" ,
              version 2 ,
              genomic-coords {
                packed-int {
                  {
                    from 52278987 ,
                    to 52279127 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52280381 ,
                    to 52280624 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52281306 ,
                    to 52281398 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52281917 ,
                    to 52282020 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52283201 ,
                    to 52283335 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52283663 ,
                    to 52283804 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52285763 ,
                    to 52285869 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52286583 ,
                    to 52286645 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52287358 ,
                    to 52287478 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52287708 ,
                    to 52287837 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52289159 ,
                    to 52289282 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52290819 ,
                    to 52290963 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52291074 ,
                    to 52291189 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52294000 ,
                    to 52294177 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52295333 ,
                    to 52295502 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52295979 ,
                    to 52296053 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52304301 ,
                    to 52304406 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52305377 ,
                    to 52305409 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52306531 ,
                    to 52306625 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52307434 ,
                    to 52307623 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52310945 ,
                    to 52311043 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52312075 ,
                    to 52312199 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52313731 ,
                    to 52313879 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52314836 ,
                    to 52314949 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52315120 ,
                    to 52315168 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52316867 ,
                    to 52317069 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52317942 ,
                    to 52318014 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52319264 ,
                    to 52319484 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52320175 ,
                    to 52320312 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52320491 ,
                    to 52320633 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52321935 ,
                    to 52322066 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52322987 ,
                    to 52323158 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52324615 ,
                    to 52324728 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52325810 ,
                    to 52326014 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52326966 ,
                    to 52327187 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52328761 ,
                    to 52328983 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52329428 ,
                    to 52329604 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52330140 ,
                    to 52330345 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52331037 ,
                    to 52331234 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52334843 ,
                    to 52334959 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52335298 ,
                    to 52335437 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52337773 ,
                    to 52338013 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52340629 ,
                    to 52340721 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52352050 ,
                    to 52352226 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52354208 ,
                    to 52354329 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52372641 ,
                    to 52372759 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52373765 ,
                    to 52373906 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52377966 ,
                    to 52378059 ,
                    strand minus ,
                    id
                      gi 51860768 } ,
                  {
                    from 52388974 ,
                    to 52389039 ,
                    strand minus ,
                    id
                      gi 51860768 } } } ,
              seqs {
                whole
                  gi 34577069 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_039260" ,
      version 3 ,
      seqs {
        int {
          from 26554540 ,
          to 26683644 ,
          strand minus ,
          id
            gi 51709342 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_013454" ,
          version 2 ,
          genomic-coords {
            mix {
              int {
                from 26554540 ,
                to 26557835 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26559089 ,
                to 26559332 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26560014 ,
                to 26560106 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26560625 ,
                to 26560728 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26561909 ,
                to 26562043 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26562371 ,
                to 26562512 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26564471 ,
                to 26564577 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26565291 ,
                to 26565353 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26566066 ,
                to 26566186 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26566416 ,
                to 26566545 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26567867 ,
                to 26567990 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26569527 ,
                to 26569671 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26569782 ,
                to 26569897 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26572708 ,
                to 26572885 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26574041 ,
                to 26574210 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26574687 ,
                to 26574761 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26583009 ,
                to 26583114 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26584085 ,
                to 26584117 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26585239 ,
                to 26585333 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26586142 ,
                to 26586331 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26589653 ,
                to 26589751 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26590783 ,
                to 26590907 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26592439 ,
                to 26592587 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26593544 ,
                to 26593657 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26593828 ,
                to 26593876 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26595575 ,
                to 26595777 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26596650 ,
                to 26596722 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26597972 ,
                to 26598192 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26598883 ,
                to 26599020 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26599199 ,
                to 26599341 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26600643 ,
                to 26600774 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26601695 ,
                to 26601866 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26603323 ,
                to 26603436 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26604518 ,
                to 26604722 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26605674 ,
                to 26605895 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26607469 ,
                to 26607691 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26608136 ,
                to 26608312 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26608848 ,
                to 26609053 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26609745 ,
                to 26609942 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26613551 ,
                to 26613667 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26614006 ,
                to 26614145 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26616481 ,
                to 26616721 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26619337 ,
                to 26619429 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26630758 ,
                to 26630934 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26632916 ,
                to 26633037 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26651349 ,
                to 26651467 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26652473 ,
                to 26652614 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26656674 ,
                to 26656767 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26667682 ,
                to 26667847 ,
                strand minus ,
                id
                  gi 51709342 } ,
              int {
                from 26683428 ,
                to 26683644 ,
                strand minus ,
                id
                  gi 51709342 } } } ,
          seqs {
            whole
              gi 34577068 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_038482" ,
              version 2 ,
              genomic-coords {
                packed-int {
                  {
                    from 26557695 ,
                    to 26557835 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26559089 ,
                    to 26559332 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26560014 ,
                    to 26560106 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26560625 ,
                    to 26560728 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26561909 ,
                    to 26562043 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26562371 ,
                    to 26562512 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26564471 ,
                    to 26564577 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26565291 ,
                    to 26565353 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26566066 ,
                    to 26566186 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26566416 ,
                    to 26566545 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26567867 ,
                    to 26567990 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26569527 ,
                    to 26569671 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26569782 ,
                    to 26569897 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26572708 ,
                    to 26572885 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26574041 ,
                    to 26574210 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26574687 ,
                    to 26574761 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26583009 ,
                    to 26583114 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26584085 ,
                    to 26584117 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26585239 ,
                    to 26585333 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26586142 ,
                    to 26586331 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26589653 ,
                    to 26589751 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26590783 ,
                    to 26590907 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26592439 ,
                    to 26592587 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26593544 ,
                    to 26593657 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26593828 ,
                    to 26593876 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26595575 ,
                    to 26595777 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26596650 ,
                    to 26596722 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26597972 ,
                    to 26598192 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26598883 ,
                    to 26599020 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26599199 ,
                    to 26599341 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26600643 ,
                    to 26600774 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26601695 ,
                    to 26601866 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26603323 ,
                    to 26603436 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26604518 ,
                    to 26604722 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26605674 ,
                    to 26605895 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26607469 ,
                    to 26607691 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26608136 ,
                    to 26608312 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26608848 ,
                    to 26609053 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26609745 ,
                    to 26609942 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26613551 ,
                    to 26613667 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26614006 ,
                    to 26614145 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26616481 ,
                    to 26616721 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26619337 ,
                    to 26619429 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26630758 ,
                    to 26630934 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26632916 ,
                    to 26633037 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26651349 ,
                    to 26651467 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26652473 ,
                    to 26652614 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26656674 ,
                    to 26656767 ,
                    strand minus ,
                    id
                      gi 51709342 } ,
                  {
                    from 26667682 ,
                    to 26667747 ,
                    strand minus ,
                    id
                      gi 51709342 } } } ,
              seqs {
                whole
                  gi 34577069 } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "Mouse Genome Informatics" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "Abca1" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "ATP-binding cassette, sub-family A (ABC1), member 1" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "MGI" ,
          url "http://www.informatics.jax.org/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5524 } ,
                  anchor "ATP binding" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16887 } ,
                  anchor "ATPase activity" ,
                  post-text "evidence: IEA" } } } } } ,
        {
          type comment ,
          label "Process" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 11559713 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 8203 } ,
                  anchor "cholesterol metabolism" ,
                  post-text "evidence: IDA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 11559713 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 30301 } ,
                  anchor "cholesterol transport" ,
                  post-text "evidence: IDA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 12859204 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 42158 } ,
                  anchor "lipoprotein biosynthesis" ,
                  post-text "evidence: IMP" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 10878804 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 6911 } ,
                  anchor "phagocytosis, engulfment" ,
                  post-text "evidence: IMP" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 10878804 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 45332 } ,
                  anchor "phospholipid translocation" ,
                  post-text "evidence: IMP" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 6810 } ,
                  anchor "transport" ,
                  post-text "evidence: IEA" } } } } } ,
        {
          type comment ,
          label "Component" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 10878804 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5794 } ,
                  anchor "Golgi apparatus" ,
                  post-text "evidence: IDA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 12466851 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16021 } ,
                  anchor "integral to membrane" ,
                  post-text "evidence: TAS" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 10878804 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5887 } ,
                  anchor "integral to plasma membrane" ,
                  post-text "evidence: IDA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 10878804 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 43231 } ,
                  anchor "intracellular membrane-bound organelle" ,
                  post-text "evidence: IDA" } } } } } } } } ,
  homology {
    {
      type comment ,
      heading "Human, Rat" ,
      version 0 ,
      source {
        {
          src {
            db "HomoloGene" ,
            tag
              id 21130 } ,
          anchor "Map Viewer" ,
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&chr=4&
MAPS=genes-r-org/human-chr/mouse%3A4,genes-r-org/rat-chr/mouse%3A4,genes-r-org
/mouse-chr4&query=e%3A11303[id]+AND+gene[obj_type]&QSTR=abca1&cmd=focus&fill=1
0" } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "MGI" ,
            tag
              id 99607 } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "REVIEWED" ,
      version 0 } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 15632021 ,
        pmid 15269218 ,
        pmid 15269217 ,
        pmid 15163665 ,
        pmid 15051721 ,
        pmid 15033469 ,
        pmid 15026428 ,
        pmid 14993246 ,
        pmid 14729855 ,
        pmid 14726413 ,
        pmid 14722086 ,
        pmid 14703508 ,
        pmid 14560020 ,
        pmid 14559902 ,
        pmid 12928428 ,
        pmid 12897186 ,
        pmid 12897148 ,
        pmid 12859204 ,
        pmid 12777468 ,
        pmid 12754274 ,
        pmid 12615679 ,
        pmid 12586783 ,
        pmid 12576511 ,
        pmid 12551894 ,
        pmid 12547832 ,
        pmid 12511593 ,
        pmid 12488454 ,
        pmid 12487373 ,
        pmid 12466851 ,
        pmid 12384498 ,
        pmid 12215451 ,
        pmid 12196520 ,
        pmid 12151852 ,
        pmid 12105210 ,
        pmid 12050168 ,
        pmid 11972062 ,
        pmid 11909955 ,
        pmid 11896206 ,
        pmid 11893753 ,
        pmid 11752403 ,
        pmid 11741998 ,
        pmid 11559713 ,
        pmid 11352567 ,
        pmid 11217851 ,
        pmid 11076861 ,
        pmid 11042159 ,
        pmid 10878804 ,
        pmid 10760292 ,
        pmid 10655069 ,
        pmid 10581369 ,
        pmid 10349636 ,
        pmid 8889548 ,
        pmid 8088782 ,
        pmid 7774911 } } ,
    {
      type comment ,
      heading "Markers (Sequence Tagged Sites/STS)" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 179001 } ,
              anchor "X75926" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "3512" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "ND" ,
              version 0 } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 271599 } ,
              anchor "PMC16657P1" ,
              post-text "(e-PCR)" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 271951 } ,
              anchor "PMC207565P1" ,
              post-text "(e-PCR)" } } } } } ,
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_013454" ,
          version 2 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 34577068 } ,
              anchor "NM_013454" } } ,
          seqs {
            whole
              gi 34577068 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_038482" ,
              version 2 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 34577069 } ,
                  anchor "NP_038482" ,
                  post-text "ATP-binding cassette 1, sub-family A, member 1" } } ,
              seqs {
                whole
                  gi 34577069 } ,
              comment {
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 34577069 } ,
                      pre-text "(3)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 5341 } ,
                          anchor "cd00267: ABC_ATPase; ABC (ATP-binding
 cassette) transporter nucleotide-binding domain" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 899 - 1114  Blast Score: 462" ,
                          version 0 } ,
                        {
                          type other ,
                          text "Location: 1912 - 2121  Blast Score: 356" ,
                          version 0 } } } ,
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 13428 } ,
                          anchor "COG4152: COG4152; ABC-type uncharacterized
 transport system, ATPase component [General function prediction only]" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 1912 - 2218  Blast Score: 360" ,
                          version 0 } } } } } } } } ,
          comment {
            {
              type other ,
              heading "Source Sequence" ,
              version 0 ,
              source {
                {
                  src {
                    db "Nucleotide" ,
                    tag
                      str "AK045442,BB657864,CA885568,X75926" } ,
                  anchor "AK045442,BB657864,CA885568,X75926" } } ,
              comment {
                {
                  type other ,
                  version 0 } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type genomic ,
          heading "Genomic" ,
          accession "AF287263" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 11611824 } ,
              anchor "AF287263" } } ,
          seqs {
            whole
              gi 11611824 } ,
          products {
            {
              type peptide ,
              accession "AAG39073" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 11611825 } ,
                  anchor "AAG39073" } } ,
              seqs {
                whole
                  gi 11611825 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6J" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AK019548" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 12859824 } ,
              anchor "AK019548" } } ,
          seqs {
            whole
              gi 12859824 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6J" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AK045442" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 26090897 } ,
              anchor "AK045442" } } ,
          seqs {
            whole
              gi 26090897 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6J" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AK051920" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 26342297 } ,
              anchor "AK051920" } } ,
          seqs {
            whole
              gi 26342297 } ,
          products {
            {
              type peptide ,
              accession "BAC34811" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 26342298 } ,
                  anchor "BAC34811" } } ,
              seqs {
                whole
                  gi 26342298 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6J" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BB657864" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 16491690 } ,
              anchor "BB657864" } } ,
          seqs {
            whole
              gi 16491690 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "CA885568" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 27337117 } ,
              anchor "CA885568" } } ,
          seqs {
            whole
              gi 27337117 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "CD-1" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "X75926" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 495256 } ,
              anchor "X75926" } } ,
          seqs {
            whole
              gi 495256 } ,
          products {
            {
              type peptide ,
              accession "CAA53530" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 495257 } ,
                  anchor "CAA53530" } } ,
              seqs {
                whole
                  gi 495257 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "DBA/2" ,
              version 0 } } } ,
        {
          type other ,
          text "None" ,
          version 0 ,
          products {
            {
              type peptide ,
              accession "P41233" ,
              version 0 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 51338775 } ,
                  anchor "P41233" } } ,
              seqs {
                whole
                  gi 51338775 } } } } } } ,
    {
      type comment ,
      heading "Additional Links" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Evidence Viewer" ,
                tag
                  str "11303" } ,
              anchor "Evidence Viewer" ,
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=10090&cont
ig=NT_039260.3&gene=Abca1&lid=11303&from=26554541&to=26683645" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "ModelMaker" ,
                tag
                  str "11303" } ,
              anchor "ModelMaker" ,
              url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=10
090&contig=NT_039260.3&gene=Abca1&lid=11303" } } } ,
        {
          type comment ,
          text "UniGene" ,
          version 0 ,
          xtra-properties {
            {
              tag "UNIGENE" ,
              value "Mm.277376" } } ,
          source {
            {
              src {
                db "UniGene" ,
                tag
                  str "Mm.277376" } ,
              anchor "Mm.277376" ,
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&CID=27
7376" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "HomoloGene" ,
                tag
                  str "11303" } ,
              anchor "HomoloGene" ,
              url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=
11303[loc]&TAXID=10090" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGI" ,
                tag
                  id 99607 } ,
              anchor "MGI" ,
              url "http://www.informatics.jax.org/searches/accession_report.cg
i?id=MGI:99607" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Ensembl" ,
                tag
                  str "" } ,
              url "http://www.ensembl.org/Mus_musculus/contigview?geneid=X7592
6" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UCSC" ,
                tag
                  str "" } ,
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position=
X75926" } } } ,
        {
          type comment ,
          text "Gene Expression Database (GXD) at MGI" ,
          version 0 ,
          source {
            {
              src {
                db "Gene Expression Database (GXD) at MGI" ,
                tag
                  str "MGI:99607" } ,
              anchor "MGI:99607" ,
              url "http://www.informatics.jax.org/searches/expression_report.c
gi?id=MGI:99607" } } } ,
        {
          type comment ,
          text "Human ABC-Transporter Proteins" ,
          version 0 ,
          source {
            {
              src {
                db "Human ABC-Transporter Proteins" ,
                tag
                  str "Human ABC-Transporter Proteins" } ,
              anchor "Human ABC-Transporter Proteins" ,
              url "http://nutrigene.4t.com/humanabc.htm" } } } } } ,
    {
      type generif ,
      text "Gene deletion protects aginst cerebral malaria from Plasmodium
 berghei." ,
      version 0 ,
      refs {
        pmid 15632021 } ,
      create-date
        str "Mar  7 2005  7:07PM" ,
      update-date
        str "Mar  8 2005  3:26AM" } ,
    {
      type generif ,
      text "ABCA1-dependent cholesterol mobilization to apoA-I increased new
 cholesterol synthesis, indicating depletion of the regulatory pool of
 hepatocyte cholesterol during HDL formation" ,
      version 0 ,
      refs {
        pmid 14993246 } ,
      create-date
        str "Mar  7 2005  7:07PM" ,
      update-date
        str "Mar  8 2005 12:40AM" } ,
    {
      type generif ,
      text "a 21% decrease (P = 0.01) in fertility was observed between
 ABCA1(-/-) males compared with WT controls across their reproductive
 lifespans" ,
      version 0 ,
      refs {
        pmid 15026428 } ,
      create-date
        str "Mar  7 2005  7:07PM" ,
      update-date
        str "Mar  7 2005  9:28PM" } ,
    {
      type generif ,
      text "Verapamil increases ABCA1 expression through LXR-independent
 mechanism and thereby increases apoA-I-mediated cellular lipid release and
 production of HDL." ,
      version 0 ,
      refs {
        pmid 14726413 } ,
      create-date
        str "Jan  8 2005 10:01AM" ,
      update-date
        str "Jan  8 2005  2:49PM" } ,
    {
      type generif ,
      text "In murine macrophage cell line RAW264 cells, cAMP induced
 expression of ABCA1, release of cellular phospholipid and cholesterol by
 apoA-I, and reversible binding of apoA-I to the cell." ,
      version 0 ,
      refs {
        pmid 14729855 } ,
      create-date
        str "Dec  4 2004 10:01AM" ,
      update-date
        str "Dec  4 2004  2:26PM" } ,
    {
      type generif ,
      text "The time course and temperature dependence of ABCA1-mediated lipid
 efflux to apoA-I support a role for endocytosis in this process" ,
      version 0 ,
      refs {
        pmid 14703508 } ,
      create-date
        str "Dec  4 2004 10:01AM" ,
      update-date
        str "Dec  4 2004 11:09AM" } ,
    {
      type generif ,
      text "conclude that intact ATP binding cassette transporter A1 (ABCA1)
 function is necessary for proper maturation of dense bodies in platelets" ,
      version 0 ,
      refs {
        pmid 15163665 } ,
      create-date
        str "Oct 30 2004 10:01AM" ,
      update-date
        str "Oct 30 2004 10:58AM" } ,
    {
      type generif ,
      text "glial ABCA1 has a key role in apoE metabolism in the brain" ,
      version 0 ,
      refs {
        pmid 15269218 } ,
      create-date
        str "Oct 30 2004 10:01AM" ,
      update-date
        str "Oct 30 2004 10:43AM" } ,
    {
      type generif ,
      text "ABCA1 plays a critical role in central nervous system apoE
 metabolism" ,
      version 0 ,
      refs {
        pmid 15269217 } ,
      create-date
        str "Oct 30 2004 10:01AM" ,
      update-date
        str "Oct 30 2004 10:43AM" } ,
    {
      type generif ,
      text "PPAR alpha influences cholesterol absorption through modulating
 the ATP binding cassette transporter A1 activity in the intestine by a
 mechanism involving liver X receptor alpha" ,
      version 0 ,
      refs {
        pmid 12897186 } ,
      create-date
        str "Aug  9 2004  1:01PM" ,
      update-date
        str "Aug  9 2004  1:41PM" } ,
    {
      type generif ,
      text "When endotoxin or cytokines (tumor necrosis factor and
 interleukin-1) were incubated with J774 murine macrophages, the mRNA levels
 of ABCA1 were decreased." ,
      version 0 ,
      refs {
        pmid 12777468 } ,
      create-date
        str "Jul 12 2004 11:39AM" ,
      update-date
        str "Jul 12 2004 12:16PM" } ,
    {
      type generif ,
      text "ABCA1 is stabilized by a specific structural element possessing a
 linear array of acidic residues spanning two apoA-I amphipathic alpha-helices" ,
      version 0 ,
      refs {
        pmid 15051721 } ,
      create-date
        str "Jul 12 2004 11:39AM" ,
      update-date
        str "Jul 12 2004 11:52AM" } ,
    {
      type generif ,
      text "despite large induction of ABCA1 mRNA during differentiation,
 cholesterol efflux through the ABCA1 pathway remains limited in adipocytes
 and requires prolonged lipolysis" ,
      version 0 ,
      refs {
        pmid 12754274 } ,
      create-date
        str "Jun 23 2004  4:43PM" ,
      update-date
        str "Jun 23 2004  5:25PM" } ,
    {
      type generif ,
      text "ABCA1 turnover is modulated by alpha1-syntrophin" ,
      version 0 ,
      refs {
        pmid 14722086 } ,
      create-date
        str "Jun 14 2004  4:41PM" ,
      update-date
        str "Jun 14 2004  5:46PM" } ,
    {
      type generif ,
      text "Review. ABCA1-deficient mice are used to demonstrate the relation
 between ABCA1 expression, cellular lipid efflux, & HDL metabolism. The
 ABCA1-deficient mouse phenotype parallels that of human Tangier disease." ,
      version 0 ,
      refs {
        pmid 12615679 } ,
      create-date
        str "Jan 25 2004 12:00AM" ,
      update-date
        str "Feb 29 2004  7:03AM" } ,
    {
      type generif ,
      text "cellular ATP-binding cassette transporter A1 has a role in
 transporting cholesterol and phospholipids from cells to lipoprotein
 particles by a process involving PLTP interactions" ,
      version 0 ,
      refs {
        pmid 14559902 } ,
      create-date
        str "Jan 20 2004 12:00AM" ,
      update-date
        str "Feb 15 2004  6:35PM" } ,
    {
      type generif ,
      text "Results demonstrate that ABCA1 plays a key role in hepatic
 cholesterol efflux, inducing pathways that modulate cholesterol homeostasis
 in the liver, and establish the liver as a major source of plasma HDL-C." ,
      version 0 ,
      refs {
        pmid 12576511 } ,
      create-date
        str "Jan  5 2004 12:00AM" ,
      update-date
        str "Feb 29 2004  7:03AM" } ,
    {
      type generif ,
      text "ABCA1-mediated vesicle release involves lipid raft plasma membrane
 domains" ,
      version 0 ,
      refs {
        pmid 12928428 } ,
      create-date
        str "Nov 30 2003 12:00AM" ,
      update-date
        str "Jan  4 2004  7:03AM" } ,
    {
      type generif ,
      text "These studies indicate a direct role of retinoic acid receptor
 gamma/retinoid x receptor in induction of macrophage ABCA1." ,
      version 0 ,
      refs {
        pmid 14560020 } ,
      create-date
        str "Nov 17 2003 12:00AM" ,
      update-date
        str "Dec  7 2003  7:05AM" } ,
    {
      type generif ,
      text "As observed in knockout mice, ABCA1 is necessary for the adequate
 lipidation of apoAI, which enables the interaction with LCAT and subsequent
 maturation." ,
      version 0 ,
      refs {
        pmid 12859204 } ,
      create-date
        str "Sep 30 2003 12:00AM" ,
      update-date
        str "Oct 12 2003  7:03AM" } ,
    {
      type generif ,
      text "ABCA1 and SREBP1 are regulated by liver X receptor/corepressor
 complexes" ,
      version 0 ,
      refs {
        pmid 12897148 } ,
      create-date
        str "Aug 25 2003 12:00AM" ,
      update-date
        str "Aug 31 2003  7:04AM" } ,
    {
      type generif ,
      text "Estrogen's antiatherogenic effects may occur via ABCA1-mediated
 pathway, and circulating HDL levels may influence expression of ABCA1" ,
      version 0 ,
      refs {
        pmid 12487373 } ,
      create-date
        str "Jun  3 2003 12:00AM" ,
      update-date
        str "Jun  8 2003  7:28AM" } ,
    {
      type generif ,
      text "Hepatocyte expression of ABCA1 is central to the lipidation of
 newly synthesized apoA-I but also contributes to the lipidation of exogenous
 apoA-I." ,
      version 0 ,
      refs {
        pmid 12547832 } ,
      create-date
        str "Apr  2 2003 12:00AM" ,
      update-date
        str "May 11 2003  7:05AM" } ,
    {
      type generif ,
      text "Golgi is involved in ABCA1-mediated cholesterol efflux." ,
      version 0 ,
      refs {
        pmid 12551894 } ,
      create-date
        str "Apr  1 2003 12:00AM" ,
      update-date
        str "May 11 2003  7:05AM" } ,
    {
      type generif ,
      text "ATP-binding cassette transporter A1 (ABCA1)-mediated lipid efflux
 is promoted by central helices of ApoA-I; amino acid residues 220-231 of the
 wild-type ApoA-I are required for lipid efflux and high density lipoprotein
 formation" ,
      version 0 ,
      refs {
        pmid 12488454 } ,
      create-date
        str "Mar 20 2003 12:00AM" ,
      update-date
        str "Apr 13 2003  7:04AM" } ,
    {
      type generif ,
      text "annexin I is externalized from pituitary folliculo-stellate cells
 by an ABC transporter and the ATP binding cassette transporter A1 is a likely
 candidate" ,
      version 0 ,
      refs {
        pmid 12586783 } ,
      create-date
        str "Mar 19 2003 12:00AM" ,
      update-date
        str "Mar 31 2003  6:34AM" } ,
    {
      type generif ,
      text "ATP-binding-cassette transporter A1 gene expression in macrophages
 is downregulated by statins" ,
      version 0 ,
      refs {
        pmid 15033469 } ,
      create-date
        str "Apr 26 2004 12:00AM" ,
      update-date
        str "May 23 2004  7:05AM" } ,
    {
      type generif ,
      text "ABCA1 is regulated by PEST sequence-mediated calpain proteolysis
 that appears to be reversed by apolipoprotein-mediated phospholipid efflux" ,
      version 0 ,
      refs {
        pmid 12511593 } ,
      create-date
        str "Feb  7 2003 12:00AM" ,
      update-date
        str "Mar  9 2003  7:04AM" } ,
    {
      type generif ,
      text "REVIEW: ATP-binding cassette transporter A1 and cholesterol
 trafficking" ,
      version 0 ,
      refs {
        pmid 12151852 } ,
      create-date
        str "Jan 24 2003 12:00AM" ,
      update-date
        str "Feb  2 2003  7:50AM" } ,
    {
      type generif ,
      text "mediates cholesterol efflux and is defective in free
 cholesterol-loaded macrophages; mechanism involves enhanced degradation and
 full npc1 activity." ,
      version 0 ,
      refs {
        pmid 12215451 } ,
      create-date
        str "Jan 16 2003 12:00AM" ,
      update-date
        str "Feb  9 2003  7:14AM" } ,
    {
      type generif ,
      text "induction as a result of liver X receptor agonism increases
 secreted Abeta levels" ,
      version 0 ,
      refs {
        pmid 12384498 } ,
      create-date
        str "Jan  9 2003 12:00AM" ,
      update-date
        str "Feb  2 2003  7:50AM" } ,
    {
      type generif ,
      text "Increased hepatobiliary and fecal cholesterol excretion upon
 activation of the liver X receptor is independent of ABCA1." ,
      version 0 ,
      refs {
        pmid 12105210 } ,
      create-date
        str "Nov 20 2002 12:00AM" ,
      update-date
        str "Feb  2 2003  7:50AM" } ,
    {
      type generif ,
      text "A novel serine (Ser-2054) on the ABCA1 protein crucial for PKA
 phosphorylation and for regulation of ABCA1 transporter activity." ,
      version 0 ,
      refs {
        pmid 12196520 } ,
      create-date
        str "Nov 16 2002 12:00AM" ,
      update-date
        str "Feb  2 2003  7:50AM" } ,
    {
      type generif ,
      text "studies establish a novel binding site for apoA-I on the
 macrophage extracellular matrix that may function together with ABCA1 in
 promoting cholesterol efflux" ,
      version 0 ,
      refs {
        pmid 12050168 } ,
      create-date
        str "Sep 27 2002 12:00AM" ,
      update-date
        str "Feb  2 2003  7:49AM" } ,
    {
      type generif ,
      text "Role as a phosphatidylserine translocase" ,
      version 0 ,
      refs {
        pmid 11893753 } ,
      create-date
        str "Jul  8 2002 12:00AM" ,
      update-date
        str "Jul 22 2002  5:59AM" } ,
    {
      type generif ,
      text "Leukocyte ABCA1 controls susceptibility to atherosclerosis and
 macrophage recruitment into tissues" ,
      version 0 ,
      refs {
        pmid 11972062 } ,
      create-date
        str "May 31 2002 12:00AM" ,
      update-date
        str "Jun 15 2002  8:10AM" } ,
    {
      type generif ,
      text "Conditional disruption of the peroxisome proliferator-activated
 receptor gamma gene in mice results in lowered expression of ABCA1, ABCG1,
 and apoE in macrophages and reduced cholesterol efflux." ,
      version 0 ,
      refs {
        pmid 11909955 } ,
      create-date
        str "Apr 16 2002 12:00AM" ,
      update-date
        str "Apr 28 2002  6:21PM" } ,
    {
      type generif ,
      text "in the presence of apoE, overexpression of ABCA1 modulates HDL as
 well as apoB-containing lipoprotein metabolism and reduces atherosclerosis in
 vivo" ,
      version 0 ,
      refs {
        pmid 11752403 } ,
      create-date
        str "Apr  2 2002 12:00AM" ,
      update-date
        str "Apr 28 2002  6:21PM" } ,
    {
      type generif ,
      text "ABCA1 is expressed in a pattern consistent with its role in HDL-C
 metabolism" ,
      version 0 ,
      refs {
        pmid 11896206 } ,
      create-date
        str "Mar 27 2002 12:00AM" ,
      update-date
        str "Apr  8 2002  3:24PM" } ,
    {
      type generif ,
      text "unsaturated fatty acids reduce the macrophage ABCA1 content by
 enhancing its degradation rate" ,
      version 0 ,
      refs {
        pmid 11741998 } ,
      create-date
        str "Mar  5 2002 12:00AM" ,
      update-date
        str "Apr  1 2002  5:34AM" } ,
    {
      type comment ,
      heading "Alleles" ,
      version 0 ,
      comment {
        {
          type comment ,
          text "The following allele types are documented at Mouse Genome
 Informatics" ,
          version 0 ,
          source {
            {
              anchor "(MGI)" ,
              url "http://www.informatics.jax.org/searches/allele_report.cgi?m
arkerID=MGI:99607" } } } ,
        {
          type comment ,
          heading "Targeted (knock-out) (2)" ,
          version 0 ,
          refs {
            pmid 10760292 ,
            pmid 10980140 } } } } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11303 } ,
    {
      db "MGI" ,
      tag
        id 99607 } } ,
  xtra-index-terms {
    "LOC11303" } }
Entrezgene ::= {
  track-info {
    geneid 11304 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 4 ,
        day 15 ,
        hour 9 ,
        minute 44 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } ,
    subtype {
      {
        subtype chromosome ,
        name "3" } } } ,
  gene {
    locus "Abca4" ,
    desc "ATP-binding cassette, sub-family A (ABC1), member 4" ,
    maploc "3 61.8 cM" ,
    syn {
      "RmP" ,
      "Abcr" ,
      "Abc10" ,
      "D430003I15Rik" } ,
    locus-tag "MGI:109424" } ,
  prot {
    name {
      "ATP-binding cassette, sub-family A, member 4" ,
      "Rim protein" ,
      "ATP-binding cassette 10" } } ,
  summary "The membrane-associated protein encoded by this gene is a member of
 the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins
 transport various molecules across extra- and intracellular membranes. ABC
 genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD,
 OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members
 of the ABC1 subfamily comprise the only major ABC subfamily found exclusively
 in multicellular eukaryotes. This protein was the first of the ABC
 transporters to be observed in photoreceptors and may play a role in the
 photoresponse. Mutations in the human gene are found in patients diagnosed
 with Stargardt disease and are associated with retinitis pigmentosa-19 and
 macular degeneration age-related 2." ,
  location {
    {
      display-str "3 G1" ,
      method
        map-type cyto } ,
    {
      display-str "3 61.8 cM" ,
      method
        map-type cM } } ,
  gene-source {
    src "LocusLink" ,
    src-int 11304 ,
    src-str2 "11304" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000069" ,
      version 1 ,
      seqs {
        int {
          from 122426366 ,
          to 122561663 ,
          strand plus ,
          id
            gi 51860767 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_007378" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 122426366 ,
                to 122426518 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122434867 ,
                to 122434960 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122436157 ,
                to 122436298 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122437283 ,
                to 122437422 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122444741 ,
                to 122444868 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122451134 ,
                to 122451331 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122462504 ,
                to 122462593 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122465447 ,
                to 122465687 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122467129 ,
                to 122467268 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122468154 ,
                to 122468270 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122468889 ,
                to 122469086 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122484278 ,
                to 122484483 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122485037 ,
                to 122485213 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122486910 ,
                to 122487132 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122492064 ,
                to 122492285 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122493968 ,
                to 122494172 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122498257 ,
                to 122498322 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122501632 ,
                to 122501721 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122503233 ,
                to 122503407 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122505161 ,
                to 122505292 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122507723 ,
                to 122507862 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122508424 ,
                to 122508561 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122509727 ,
                to 122509920 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122510918 ,
                to 122511002 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122514126 ,
                to 122514331 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122514655 ,
                to 122514703 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122516604 ,
                to 122516866 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122518583 ,
                to 122518707 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122519172 ,
                to 122519270 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122520026 ,
                to 122520212 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122523293 ,
                to 122523387 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122525002 ,
                to 122525034 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122528800 ,
                to 122528905 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122529033 ,
                to 122529107 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122529332 ,
                to 122529501 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122530477 ,
                to 122530654 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122536879 ,
                to 122536994 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122537940 ,
                to 122538087 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122539437 ,
                to 122539560 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122539916 ,
                to 122540045 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122543903 ,
                to 122544023 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122544463 ,
                to 122544525 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122545390 ,
                to 122545496 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122548250 ,
                to 122548391 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122551495 ,
                to 122551629 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122552344 ,
                to 122552447 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122552531 ,
                to 122552623 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122555381 ,
                to 122555630 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122557676 ,
                to 122557762 ,
                strand plus ,
                id
                  gi 51860767 } ,
              int {
                from 122561316 ,
                to 122561663 ,
                strand plus ,
                id
                  gi 51860767 } } } ,
          seqs {
            whole
              gi 6671494 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_031404" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 122426453 ,
                    to 122426518 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122434867 ,
                    to 122434960 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122436157 ,
                    to 122436298 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122437283 ,
                    to 122437422 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122444741 ,
                    to 122444868 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122451134 ,
                    to 122451331 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122462504 ,
                    to 122462593 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122465447 ,
                    to 122465687 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122467129 ,
                    to 122467268 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122468154 ,
                    to 122468270 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122468889 ,
                    to 122469086 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122484278 ,
                    to 122484483 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122485037 ,
                    to 122485213 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122486910 ,
                    to 122487132 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122492064 ,
                    to 122492285 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122493968 ,
                    to 122494172 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122498257 ,
                    to 122498322 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122501632 ,
                    to 122501721 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122503233 ,
                    to 122503407 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122505161 ,
                    to 122505292 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122507723 ,
                    to 122507862 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122508424 ,
                    to 122508561 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122509727 ,
                    to 122509920 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122510918 ,
                    to 122511002 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122514126 ,
                    to 122514331 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122514655 ,
                    to 122514703 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122516604 ,
                    to 122516866 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122518583 ,
                    to 122518707 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122519172 ,
                    to 122519270 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122520026 ,
                    to 122520212 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122523293 ,
                    to 122523387 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122525002 ,
                    to 122525034 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122528800 ,
                    to 122528905 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122529033 ,
                    to 122529107 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122529332 ,
                    to 122529501 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122530477 ,
                    to 122530654 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122536879 ,
                    to 122536994 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122537940 ,
                    to 122538087 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122539437 ,
                    to 122539560 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122539916 ,
                    to 122540045 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122543903 ,
                    to 122544023 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122544463 ,
                    to 122544525 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122545390 ,
                    to 122545496 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122548250 ,
                    to 122548391 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122551495 ,
                    to 122551629 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122552344 ,
                    to 122552447 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122552531 ,
                    to 122552623 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122555381 ,
                    to 122555630 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122557676 ,
                    to 122557762 ,
                    strand plus ,
                    id
                      gi 51860767 } ,
                  {
                    from 122561316 ,
                    to 122561435 ,
                    strand plus ,
                    id
                      gi 51860767 } } } ,
              seqs {
                whole
                  gi 6671495 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_039240" ,
      version 3 ,
      seqs {
        int {
          from 8569036 ,
          to 8704333 ,
          strand plus ,
          id
            gi 51708444 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_007378" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 8569036 ,
                to 8569188 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8577537 ,
                to 8577630 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8578827 ,
                to 8578968 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8579953 ,
                to 8580092 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8587411 ,
                to 8587538 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8593804 ,
                to 8594001 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8605174 ,
                to 8605263 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8608117 ,
                to 8608357 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8609799 ,
                to 8609938 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8610824 ,
                to 8610940 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8611559 ,
                to 8611756 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8626948 ,
                to 8627153 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8627707 ,
                to 8627883 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8629580 ,
                to 8629802 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8634734 ,
                to 8634955 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8636638 ,
                to 8636842 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8640927 ,
                to 8640992 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8644302 ,
                to 8644391 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8645903 ,
                to 8646077 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8647831 ,
                to 8647962 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8650393 ,
                to 8650532 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8651094 ,
                to 8651231 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8652397 ,
                to 8652590 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8653588 ,
                to 8653672 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8656796 ,
                to 8657001 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8657325 ,
                to 8657373 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8659274 ,
                to 8659536 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8661253 ,
                to 8661377 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8661842 ,
                to 8661940 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8662696 ,
                to 8662882 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8665963 ,
                to 8666057 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8667672 ,
                to 8667704 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8671470 ,
                to 8671575 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8671703 ,
                to 8671777 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8672002 ,
                to 8672171 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8673147 ,
                to 8673324 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8679549 ,
                to 8679664 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8680610 ,
                to 8680757 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8682107 ,
                to 8682230 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8682586 ,
                to 8682715 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8686573 ,
                to 8686693 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8687133 ,
                to 8687195 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8688060 ,
                to 8688166 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8690920 ,
                to 8691061 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8694165 ,
                to 8694299 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8695014 ,
                to 8695117 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8695201 ,
                to 8695293 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8698051 ,
                to 8698300 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8700346 ,
                to 8700432 ,
                strand plus ,
                id
                  gi 51708444 } ,
              int {
                from 8703986 ,
                to 8704333 ,
                strand plus ,
                id
                  gi 51708444 } } } ,
          seqs {
            whole
              gi 6671494 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_031404" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 8569123 ,
                    to 8569188 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8577537 ,
                    to 8577630 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8578827 ,
                    to 8578968 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8579953 ,
                    to 8580092 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8587411 ,
                    to 8587538 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8593804 ,
                    to 8594001 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8605174 ,
                    to 8605263 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8608117 ,
                    to 8608357 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8609799 ,
                    to 8609938 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8610824 ,
                    to 8610940 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8611559 ,
                    to 8611756 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8626948 ,
                    to 8627153 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8627707 ,
                    to 8627883 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8629580 ,
                    to 8629802 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8634734 ,
                    to 8634955 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8636638 ,
                    to 8636842 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8640927 ,
                    to 8640992 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8644302 ,
                    to 8644391 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8645903 ,
                    to 8646077 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8647831 ,
                    to 8647962 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8650393 ,
                    to 8650532 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8651094 ,
                    to 8651231 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8652397 ,
                    to 8652590 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8653588 ,
                    to 8653672 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8656796 ,
                    to 8657001 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8657325 ,
                    to 8657373 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8659274 ,
                    to 8659536 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8661253 ,
                    to 8661377 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8661842 ,
                    to 8661940 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8662696 ,
                    to 8662882 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8665963 ,
                    to 8666057 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8667672 ,
                    to 8667704 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8671470 ,
                    to 8671575 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8671703 ,
                    to 8671777 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8672002 ,
                    to 8672171 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8673147 ,
                    to 8673324 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8679549 ,
                    to 8679664 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8680610 ,
                    to 8680757 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8682107 ,
                    to 8682230 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8682586 ,
                    to 8682715 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8686573 ,
                    to 8686693 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8687133 ,
                    to 8687195 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8688060 ,
                    to 8688166 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8690920 ,
                    to 8691061 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8694165 ,
                    to 8694299 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8695014 ,
                    to 8695117 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8695201 ,
                    to 8695293 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8698051 ,
                    to 8698300 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8700346 ,
                    to 8700432 ,
                    strand plus ,
                    id
                      gi 51708444 } ,
                  {
                    from 8703986 ,
                    to 8704105 ,
                    strand plus ,
                    id
                      gi 51708444 } } } ,
              seqs {
                whole
                  gi 6671495 } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "Mouse Genome Informatics" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "Abca4" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "ATP-binding cassette, sub-family A (ABC1), member 4" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "MGI" ,
          url "http://www.informatics.jax.org/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5524 } ,
                  anchor "ATP binding" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16887 } ,
                  anchor "ATPase activity" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 9202155 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 42626 } ,
                  anchor "ATPase activity, coupled to transmembrane movement
 of substances" ,
                  post-text "evidence: TAS" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 10412977 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5548 } ,
                  anchor "phospholipid transporter activity" ,
                  post-text "evidence: IMP" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 10412977 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 4012 } ,
                  anchor "phospholipid-translocating ATPase activity" ,
                  post-text "evidence: IMP" } } } } } ,
        {
          type comment ,
          label "Process" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 10412977 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 6649 } ,
                  anchor "phospholipid transfer to membrane" ,
                  post-text "evidence: IMP" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 11431429 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 45494 } ,
                  anchor "photoreceptor maintenance" ,
                  post-text "evidence: IMP" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 7600 } ,
                  anchor "sensory perception" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 6810 } ,
                  anchor "transport" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 10412977 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 7601 } ,
                  anchor "visual perception" ,
                  post-text "evidence: IMP" } } } } } ,
        {
          type comment ,
          label "Component" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16021 } ,
                  anchor "integral to membrane" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 9202155 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5887 } ,
                  anchor "integral to plasma membrane" ,
                  post-text "evidence: TAS" } } } } } } } } ,
  homology {
    {
      type comment ,
      heading "Human, Rat" ,
      version 0 ,
      source {
        {
          src {
            db "HomoloGene" ,
            tag
              id 298 } ,
          anchor "Map Viewer" ,
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&chr=3&
MAPS=genes-r-org/human-chr/mouse%3A3,genes-r-org/rat-chr/mouse%3A3,genes-r-org
/mouse-chr3&query=e%3A11304[id]+AND+gene[obj_type]&QSTR=abca4&cmd=focus&fill=1
0" } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "MGI" ,
            tag
              id 109424 } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "REVIEWED" ,
      version 0 } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 12477932 ,
        pmid 12466851 ,
        pmid 11431429 ,
        pmid 11217851 ,
        pmid 11076861 ,
        pmid 11042159 ,
        pmid 10852960 ,
        pmid 10412977 ,
        pmid 10349636 ,
        pmid 9202155 ,
        pmid 8889548 } } ,
    {
      type comment ,
      heading "Markers (Sequence Tagged Sites/STS)" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 140994 } ,
              anchor "Abca4" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "MGI:8523" ,
              version 0 } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 159184 } ,
              anchor "AF000149" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "192133" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "693384" ,
              version 0 } ,
            {
              type other ,
              label "Alternate name" ,
              text "ND" ,
              version 0 } } } } } ,
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_007378" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 6671494 } ,
              anchor "NM_007378" } } ,
          seqs {
            whole
              gi 6671494 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_031404" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 6671495 } ,
                  anchor "NP_031404" ,
                  post-text "ATP-binding cassette, sub-family A, member 4" } } ,
              seqs {
                whole
                  gi 6671495 } ,
              comment {
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 6671495 } ,
                      pre-text "(3)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 5341 } ,
                          anchor "cd00267: ABC_ATPase; ABC (ATP-binding
 cassette) transporter nucleotide-binding domain" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 931 - 1144  Blast Score: 454" ,
                          version 0 } ,
                        {
                          type other ,
                          text "Location: 1937 - 2152  Blast Score: 353" ,
                          version 0 } } } ,
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 13428 } ,
                          anchor "COG4152: COG4152; ABC-type uncharacterized
 transport system, ATPase component [General function prediction only]" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 1937 - 2253  Blast Score: 387" ,
                          version 0 } } } } } } } } ,
          comment {
            {
              type other ,
              heading "Source Sequence" ,
              version 0 ,
              source {
                {
                  src {
                    db "Nucleotide" ,
                    tag
                      str "AF000149" } ,
                  anchor "AF000149" } } ,
              comment {
                {
                  type other ,
                  version 0 } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AF000149" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 3243083 } ,
              anchor "AF000149" } } ,
          seqs {
            whole
              gi 3243083 } ,
          products {
            {
              type peptide ,
              accession "AAC23916" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 2547314 } ,
                  anchor "AAC23916" } } ,
              seqs {
                whole
                  gi 2547314 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AK053043" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 26095532 } ,
              anchor "AK053043" } } ,
          seqs {
            whole
              gi 26095532 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6J" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AK084860" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 26102289 } ,
              anchor "AK084860" } } ,
          seqs {
            whole
              gi 26102289 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6J" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC043937" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 27882179 } ,
              anchor "BC043937" } } ,
          seqs {
            whole
              gi 27882179 } ,
          products {
            {
              type peptide ,
              accession "AAH43937" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 27882180 } ,
                  anchor "AAH43937" } } ,
              seqs {
                whole
                  gi 27882180 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC057853" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 34783941 } ,
              anchor "BC057853" } } ,
          seqs {
            whole
              gi 34783941 } ,
          products {
            {
              type peptide ,
              accession "AAH57853" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 34783942 } ,
                  anchor "AAH57853" } } ,
              seqs {
                whole
                  gi 34783942 } } } } } } ,
    {
      type comment ,
      heading "Additional Links" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Evidence Viewer" ,
                tag
                  str "11304" } ,
              anchor "Evidence Viewer" ,
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=10090&cont
ig=NT_039240.3&gene=Abca4&lid=11304&from=8569037&to=8704334" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "ModelMaker" ,
                tag
                  str "11304" } ,
              anchor "ModelMaker" ,
              url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=10
090&contig=NT_039240.3&gene=Abca4&lid=11304" } } } ,
        {
          type comment ,
          text "UniGene" ,
          version 0 ,
          xtra-properties {
            {
              tag "UNIGENE" ,
              value "Mm.3918" } } ,
          source {
            {
              src {
                db "UniGene" ,
                tag
                  str "Mm.3918" } ,
              anchor "Mm.3918" ,
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&CID=39
18" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "HomoloGene" ,
                tag
                  str "11304" } ,
              anchor "HomoloGene" ,
              url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=
11304[loc]&TAXID=10090" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGI" ,
                tag
                  id 109424 } ,
              anchor "MGI" ,
              url "http://www.informatics.jax.org/searches/accession_report.cg
i?id=MGI:109424" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Ensembl" ,
                tag
                  str "" } ,
              url "http://www.ensembl.org/Mus_musculus/contigview?geneid=BC057
853" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UCSC" ,
                tag
                  str "" } ,
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position=
BC057853" } } } ,
        {
          type comment ,
          text "Human ABC-Transporter Proteins" ,
          version 0 ,
          source {
            {
              src {
                db "Human ABC-Transporter Proteins" ,
                tag
                  str "Human ABC-Transporter Proteins" } ,
              anchor "Human ABC-Transporter Proteins" ,
              url "http://nutrigene.4t.com/humanabc.htm" } } } } } ,
    {
      type comment ,
      heading "Alleles" ,
      version 0 ,
      comment {
        {
          type comment ,
          text "The following allele types are documented at Mouse Genome
 Informatics" ,
          version 0 ,
          source {
            {
              anchor "(MGI)" ,
              url "http://www.informatics.jax.org/searches/allele_report.cgi?m
arkerID=MGI:109424" } } } ,
        {
          type comment ,
          heading "Targeted (knock-out) (1)" ,
          version 0 ,
          refs {
            pmid 10412977 } } } } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11304 } ,
    {
      db "MGI" ,
      tag
        id 109424 } } ,
  xtra-index-terms {
    "LOC11304" } }
Entrezgene ::= {
  track-info {
    geneid 11305 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 2 ,
        day 17 ,
        hour 12 ,
        minute 54 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } ,
    subtype {
      {
        subtype chromosome ,
        name "2" } } } ,
  gene {
    locus "Abca2" ,
    desc "ATP-binding cassette, sub-family A (ABC1), member 2" ,
    maploc "2 12.6 cM" ,
    syn {
      "Abc2" ,
      "mKIAA1062" ,
      "D2H0S1474E" } ,
    locus-tag "MGI:99606" } ,
  prot {
    name {
      "ATP-binding cassette, sub-family A (ABC1), member 2" ,
      "ATP-binding cassette 2" } } ,
  location {
    {
      display-str "2 A2-B" ,
      method
        map-type cyto } ,
    {
      display-str "2 12.6 cM" ,
      method
        map-type cM } } ,
  gene-source {
    src "LocusLink" ,
    src-int 11305 ,
    src-str2 "11305" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000068" ,
      version 1 ,
      seqs {
        int {
          from 25388791 ,
          to 25408220 ,
          strand plus ,
          id
            gi 51860766 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_007379" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 25388791 ,
                to 25388856 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25392017 ,
                to 25392110 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25393119 ,
                to 25393230 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25393315 ,
                to 25393478 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25393703 ,
                to 25393830 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25393985 ,
                to 25394095 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25394330 ,
                to 25394548 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25394911 ,
                to 25395278 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25395520 ,
                to 25395679 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25396389 ,
                to 25396517 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25396610 ,
                to 25396774 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25396851 ,
                to 25396947 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25397266 ,
                to 25397439 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25397509 ,
                to 25397611 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25397686 ,
                to 25397800 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25397914 ,
                to 25398104 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25398252 ,
                to 25398402 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25398479 ,
                to 25398683 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25398822 ,
                to 25398986 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25399088 ,
                to 25399268 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25399348 ,
                to 25399560 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25400546 ,
                to 25400742 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25400831 ,
                to 25401013 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25401209 ,
                to 25401393 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25401500 ,
                to 25401620 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25401896 ,
                to 25402132 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25402212 ,
                to 25402418 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25402671 ,
                to 25402773 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25402856 ,
                to 25403175 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25403250 ,
                to 25403463 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25403550 ,
                to 25403655 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25403747 ,
                to 25403858 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25403948 ,
                to 25404008 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25404091 ,
                to 25404265 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25404346 ,
                to 25404461 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25404543 ,
                to 25404690 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25404835 ,
                to 25404958 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25405093 ,
                to 25405225 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25405329 ,
                to 25405446 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25405571 ,
                to 25405749 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25405991 ,
                to 25406132 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25406232 ,
                to 25406366 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25406459 ,
                to 25406562 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25406636 ,
                to 25406728 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25406812 ,
                to 25406914 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25406999 ,
                to 25407136 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25407221 ,
                to 25407421 ,
                strand plus ,
                id
                  gi 51860766 } ,
              int {
                from 25407862 ,
                to 25408220 ,
                strand plus ,
                id
                  gi 51860766 } } } ,
          seqs {
            whole
              gi 11993938 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_031405" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 25388791 ,
                    to 25388856 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25392017 ,
                    to 25392110 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25393119 ,
                    to 25393230 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25393315 ,
                    to 25393478 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25393703 ,
                    to 25393830 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25393985 ,
                    to 25394095 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25394330 ,
                    to 25394548 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25394911 ,
                    to 25395278 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25395520 ,
                    to 25395679 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25396389 ,
                    to 25396517 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25396610 ,
                    to 25396774 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25396851 ,
                    to 25396947 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25397266 ,
                    to 25397439 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25397509 ,
                    to 25397611 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25397686 ,
                    to 25397800 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25397914 ,
                    to 25398104 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25398252 ,
                    to 25398402 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25398479 ,
                    to 25398683 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25398822 ,
                    to 25398986 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25399088 ,
                    to 25399268 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25399348 ,
                    to 25399560 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25400546 ,
                    to 25400742 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25400831 ,
                    to 25401013 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25401209 ,
                    to 25401393 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25401500 ,
                    to 25401620 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25401896 ,
                    to 25402132 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25402212 ,
                    to 25402418 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25402671 ,
                    to 25402773 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25402856 ,
                    to 25403175 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25403250 ,
                    to 25403463 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25403550 ,
                    to 25403655 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25403747 ,
                    to 25403858 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25403948 ,
                    to 25404008 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25404091 ,
                    to 25404265 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25404346 ,
                    to 25404461 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25404543 ,
                    to 25404690 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25404835 ,
                    to 25404958 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25405093 ,
                    to 25405225 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25405329 ,
                    to 25405446 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25405571 ,
                    to 25405749 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25405991 ,
                    to 25406132 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25406232 ,
                    to 25406366 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25406459 ,
                    to 25406562 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25406636 ,
                    to 25406728 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25406812 ,
                    to 25406914 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25406999 ,
                    to 25407136 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25407221 ,
                    to 25407421 ,
                    strand plus ,
                    id
                      gi 51860766 } ,
                  {
                    from 25407862 ,
                    to 25407897 ,
                    strand plus ,
                    id
                      gi 51860766 } } } ,
              seqs {
                whole
                  gi 11993939 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_039206" ,
      version 3 ,
      seqs {
        int {
          from 2857415 ,
          to 2876844 ,
          strand plus ,
          id
            gi 51706164 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "NM_007379" ,
          version 1 ,
          genomic-coords {
            mix {
              int {
                from 2857415 ,
                to 2857480 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2860641 ,
                to 2860734 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2861743 ,
                to 2861854 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2861939 ,
                to 2862102 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2862327 ,
                to 2862454 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2862609 ,
                to 2862719 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2862954 ,
                to 2863172 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2863535 ,
                to 2863902 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2864144 ,
                to 2864303 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2865013 ,
                to 2865141 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2865234 ,
                to 2865398 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2865475 ,
                to 2865571 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2865890 ,
                to 2866063 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2866133 ,
                to 2866235 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2866310 ,
                to 2866424 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2866538 ,
                to 2866728 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2866876 ,
                to 2867026 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2867103 ,
                to 2867307 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2867446 ,
                to 2867610 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2867712 ,
                to 2867892 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2867972 ,
                to 2868184 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2869170 ,
                to 2869366 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2869455 ,
                to 2869637 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2869833 ,
                to 2870017 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2870124 ,
                to 2870244 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2870520 ,
                to 2870756 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2870836 ,
                to 2871042 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2871295 ,
                to 2871397 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2871480 ,
                to 2871799 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2871874 ,
                to 2872087 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2872174 ,
                to 2872279 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2872371 ,
                to 2872482 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2872572 ,
                to 2872632 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2872715 ,
                to 2872889 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2872970 ,
                to 2873085 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2873167 ,
                to 2873314 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2873459 ,
                to 2873582 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2873717 ,
                to 2873849 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2873953 ,
                to 2874070 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2874195 ,
                to 2874373 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2874615 ,
                to 2874756 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2874856 ,
                to 2874990 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2875083 ,
                to 2875186 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2875260 ,
                to 2875352 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2875436 ,
                to 2875538 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2875623 ,
                to 2875760 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2875845 ,
                to 2876045 ,
                strand plus ,
                id
                  gi 51706164 } ,
              int {
                from 2876486 ,
                to 2876844 ,
                strand plus ,
                id
                  gi 51706164 } } } ,
          seqs {
            whole
              gi 11993938 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "NP_031405" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 2857415 ,
                    to 2857480 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2860641 ,
                    to 2860734 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2861743 ,
                    to 2861854 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2861939 ,
                    to 2862102 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2862327 ,
                    to 2862454 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2862609 ,
                    to 2862719 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2862954 ,
                    to 2863172 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2863535 ,
                    to 2863902 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2864144 ,
                    to 2864303 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2865013 ,
                    to 2865141 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2865234 ,
                    to 2865398 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2865475 ,
                    to 2865571 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2865890 ,
                    to 2866063 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2866133 ,
                    to 2866235 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2866310 ,
                    to 2866424 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2866538 ,
                    to 2866728 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2866876 ,
                    to 2867026 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2867103 ,
                    to 2867307 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2867446 ,
                    to 2867610 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2867712 ,
                    to 2867892 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2867972 ,
                    to 2868184 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2869170 ,
                    to 2869366 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2869455 ,
                    to 2869637 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2869833 ,
                    to 2870017 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2870124 ,
                    to 2870244 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2870520 ,
                    to 2870756 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2870836 ,
                    to 2871042 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2871295 ,
                    to 2871397 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2871480 ,
                    to 2871799 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2871874 ,
                    to 2872087 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2872174 ,
                    to 2872279 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2872371 ,
                    to 2872482 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2872572 ,
                    to 2872632 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2872715 ,
                    to 2872889 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2872970 ,
                    to 2873085 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2873167 ,
                    to 2873314 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2873459 ,
                    to 2873582 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2873717 ,
                    to 2873849 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2873953 ,
                    to 2874070 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2874195 ,
                    to 2874373 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2874615 ,
                    to 2874756 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2874856 ,
                    to 2874990 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2875083 ,
                    to 2875186 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2875260 ,
                    to 2875352 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2875436 ,
                    to 2875538 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2875623 ,
                    to 2875760 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2875845 ,
                    to 2876045 ,
                    strand plus ,
                    id
                      gi 51706164 } ,
                  {
                    from 2876486 ,
                    to 2876521 ,
                    strand plus ,
                    id
                      gi 51706164 } } } ,
              seqs {
                whole
                  gi 11993939 } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "Mouse Genome Informatics" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "Abca2" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "ATP-binding cassette, sub-family A (ABC1), member 2" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "MGI" ,
          url "http://www.informatics.jax.org/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5524 } ,
                  anchor "ATP binding" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16887 } ,
                  anchor "ATPase activity" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              refs {
                pmid 12466851 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5215 } ,
                  anchor "transporter activity" ,
                  post-text "evidence: ISS" } } } } } ,
        {
          type comment ,
          label "Process" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 8203 } ,
                  anchor "cholesterol metabolism" ,
                  post-text "evidence: ISS" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 6810 } ,
                  anchor "transport" ,
                  post-text "evidence: IEA" } } } } } ,
        {
          type comment ,
          label "Component" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              refs {
                pmid 12466851 } ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16021 } ,
                  anchor "integral to membrane" ,
                  post-text "evidence: TAS" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5765 } ,
                  anchor "lysosomal membrane" ,
                  post-text "evidence: ISS" } } } } } } } } ,
  homology {
    {
      type comment ,
      heading "Human, Rat" ,
      version 0 ,
      source {
        {
          src {
            db "HomoloGene" ,
            tag
              id 55590 } ,
          anchor "Map Viewer" ,
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&chr=2&
MAPS=genes-r-org/human-chr/mouse%3A2,genes-r-org/rat-chr/mouse%3A2,genes-r-org
/mouse-chr2&query=e%3A11305[id]+AND+gene[obj_type]&QSTR=abca2&cmd=focus&fill=1
0" } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "MGI" ,
            tag
              id 99606 } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "PROVISIONAL" ,
      version 0 } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 14621295 ,
        pmid 12466851 ,
        pmid 8088782 } } ,
    {
      type comment ,
      heading "Markers (Sequence Tagged Sites/STS)" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 158928 } ,
              anchor "AI413825" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "421529" ,
              version 0 } } } } } ,
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_007379" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 11993938 } ,
              anchor "NM_007379" } } ,
          seqs {
            whole
              gi 11993938 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_031405" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 11993939 } ,
                  anchor "NP_031405" ,
                  post-text "ATP-binding cassette, sub-family A (ABC1), member
 2" } } ,
              seqs {
                whole
                  gi 11993939 } ,
              comment {
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 11993939 } ,
                      pre-text "(2)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 5341 } ,
                          anchor "cd00267: ABC_ATPase; ABC (ATP-binding
 cassette) transporter nucleotide-binding domain" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 1018 - 1205  Blast Score: 389" ,
                          version 0 } ,
                        {
                          type other ,
                          text "Location: 2051 - 2269  Blast Score: 372" ,
                          version 0 } } } } } } } } ,
          comment {
            {
              type other ,
              heading "Source Sequence" ,
              version 0 ,
              source {
                {
                  src {
                    db "Nucleotide" ,
                    tag
                      str "X75927" } ,
                  anchor "X75927" } } ,
              comment {
                {
                  type other ,
                  version 0 } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AK129274" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 37360211 } ,
              anchor "AK129274" } } ,
          seqs {
            whole
              gi 37360211 } ,
          products {
            {
              type peptide ,
              accession "BAC98084" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 37360212 } ,
                  anchor "BAC98084" } } ,
              seqs {
                whole
                  gi 37360212 } } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "X75927" ,
          version 2 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 11990230 } ,
              anchor "X75927" } } ,
          seqs {
            whole
              gi 11990230 } ,
          products {
            {
              type peptide ,
              accession "CAA53531" ,
              version 2 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 11990231 } ,
                  anchor "CAA53531" } } ,
              seqs {
                whole
                  gi 11990231 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "DBA/2" ,
              version 0 } } } ,
        {
          type other ,
          text "None" ,
          version 0 ,
          products {
            {
              type peptide ,
              accession "P41234" ,
              version 0 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 14916951 } ,
                  anchor "P41234" } } ,
              seqs {
                whole
                  gi 14916951 } } } } } } ,
    {
      type comment ,
      heading "Additional Links" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Evidence Viewer" ,
                tag
                  str "11305" } ,
              anchor "Evidence Viewer" ,
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=10090&cont
ig=NT_039206.3&gene=Abca2&lid=11305&from=2857416&to=2876845" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "ModelMaker" ,
                tag
                  str "11305" } ,
              anchor "ModelMaker" ,
              url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=10
090&contig=NT_039206.3&gene=Abca2&lid=11305" } } } ,
        {
          type comment ,
          text "UniGene" ,
          version 0 ,
          xtra-properties {
            {
              tag "UNIGENE" ,
              value "Mm.2210" } } ,
          source {
            {
              src {
                db "UniGene" ,
                tag
                  str "Mm.2210" } ,
              anchor "Mm.2210" ,
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&CID=22
10" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "HomoloGene" ,
                tag
                  str "11305" } ,
              anchor "HomoloGene" ,
              url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=
11305[loc]&TAXID=10090" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGI" ,
                tag
                  id 99606 } ,
              anchor "MGI" ,
              url "http://www.informatics.jax.org/searches/accession_report.cg
i?id=MGI:99606" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Ensembl" ,
                tag
                  str "" } ,
              url "http://www.ensembl.org/Mus_musculus/contigview?geneid=X7592
7" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UCSC" ,
                tag
                  str "" } ,
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position=
X75927" } } } ,
        {
          type comment ,
          text "Human ABC-Transporter Proteins" ,
          version 0 ,
          source {
            {
              src {
                db "Human ABC-Transporter Proteins" ,
                tag
                  str "Human ABC-Transporter Proteins" } ,
              anchor "Human ABC-Transporter Proteins" ,
              url "http://nutrigene.4t.com/humanabc.htm" } } } } } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 11305 } ,
    {
      db "MGI" ,
      tag
        id 99606 } } ,
  xtra-index-terms {
    "LOC11305" } }
Entrezgene ::= {
  track-info {
    geneid 11306 ,
    status live ,
    create-date
      std {
        year 2003 ,
        month 8 ,
        day 28 ,
        hour 21 ,
        minute 39 ,
        second 0 } ,
    update-date
      std {
        year 2005 ,
        month 4 ,
        day 19 ,
        hour 12 ,
        minute 12 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Mus musculus" ,
      common "house mouse" ,
      db {
        {
          db "taxon" ,
          tag
            id 10090 } } ,
      syn {
        "mouse" } ,
      orgname {
        name
          binomial {
            genus "Mus" ,
            species "musculus" } ,
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
 Sciurognathi; Muridae; Murinae; Mus" ,
        gcode 1 ,
        mgcode 2 ,
        div "ROD" } } ,
    subtype {
      {
        subtype chromosome ,
        name "X" } } } ,
  gene {
    locus "Abcb7" ,
    desc "ATP-binding cassette, sub-family B (MDR/TAP), member 7" ,
    maploc "X 39.0 cM" ,
    syn {
      "Abc7" } ,
    locus-tag "MGI:109533" } ,
  prot {
    name {
      "ATP-binding cassette, sub-family B (MDR/TAP), member 7" ,
      "ATP-binding cassette 7" } } ,
  location {
    {
      display-str "X C-D" ,
      method
        map-type cyto } ,
    {
      display-str "X 39.0 cM" ,
      method
        map-type cM } } ,
  gene-source {
    src "LocusLink" ,
    src-int 11306 ,
    src-str2 "11306" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      heading "Reference" ,
      accession "NC_000086" ,
      version 1 ,
      seqs {
        int {
          from 95684235 ,
          to 95817474 ,
          strand minus ,
          id
            gi 51869957 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "XM_356348" ,
          version 2 ,
          genomic-coords {
            mix {
              int {
                from 95684235 ,
                to 95687836 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95694701 ,
                to 95694808 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95698046 ,
                to 95698149 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95699409 ,
                to 95699580 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95703347 ,
                to 95703476 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95703628 ,
                to 95703791 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95704349 ,
                to 95704506 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95705372 ,
                to 95705546 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95706530 ,
                to 95706617 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95706707 ,
                to 95706795 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95707710 ,
                to 95707978 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95708848 ,
                to 95708980 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95726912 ,
                to 95727031 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95746072 ,
                to 95746158 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95748503 ,
                to 95748580 ,
                strand minus ,
                id
                  gi 51869957 } ,
              int {
                from 95817235 ,
                to 95817474 ,
                strand minus ,
                id
                  gi 51869957 } } } ,
          seqs {
            whole
              gi 51772276 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "XP_356348" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 95687621 ,
                    to 95687836 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95694701 ,
                    to 95694808 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95698046 ,
                    to 95698149 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95699409 ,
                    to 95699580 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95703347 ,
                    to 95703476 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95703628 ,
                    to 95703791 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95704349 ,
                    to 95704506 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95705372 ,
                    to 95705546 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95706530 ,
                    to 95706617 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95706707 ,
                    to 95706795 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95707710 ,
                    to 95707978 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95708848 ,
                    to 95708980 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95726912 ,
                    to 95727031 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95746072 ,
                    to 95746158 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95748503 ,
                    to 95748580 ,
                    strand minus ,
                    id
                      gi 51869957 } ,
                  {
                    from 95817235 ,
                    to 95817474 ,
                    strand minus ,
                    id
                      gi 51869957 } } } ,
              seqs {
                whole
                  gi 38086485 } } } } } } ,
    {
      type genomic ,
      heading "Reference" ,
      accession "NT_039711" ,
      version 3 ,
      seqs {
        int {
          from 9312469 ,
          to 9445708 ,
          strand minus ,
          id
            gi 51772331 } } ,
      products {
        {
          type mRNA ,
          heading "Reference" ,
          accession "XM_356348" ,
          version 2 ,
          genomic-coords {
            mix {
              int {
                from 9312469 ,
                to 9316070 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9322935 ,
                to 9323042 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9326280 ,
                to 9326383 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9327643 ,
                to 9327814 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9331581 ,
                to 9331710 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9331862 ,
                to 9332025 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9332583 ,
                to 9332740 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9333606 ,
                to 9333780 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9334764 ,
                to 9334851 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9334941 ,
                to 9335029 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9335944 ,
                to 9336212 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9337082 ,
                to 9337214 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9355146 ,
                to 9355265 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9374306 ,
                to 9374392 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9376737 ,
                to 9376814 ,
                strand minus ,
                id
                  gi 51772331 } ,
              int {
                from 9445469 ,
                to 9445708 ,
                strand minus ,
                id
                  gi 51772331 } } } ,
          seqs {
            whole
              gi 51772276 } ,
          products {
            {
              type peptide ,
              heading "Reference" ,
              accession "XP_356348" ,
              version 1 ,
              genomic-coords {
                packed-int {
                  {
                    from 9315855 ,
                    to 9316070 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9322935 ,
                    to 9323042 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9326280 ,
                    to 9326383 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9327643 ,
                    to 9327814 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9331581 ,
                    to 9331710 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9331862 ,
                    to 9332025 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9332583 ,
                    to 9332740 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9333606 ,
                    to 9333780 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9334764 ,
                    to 9334851 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9334941 ,
                    to 9335029 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9335944 ,
                    to 9336212 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9337082 ,
                    to 9337214 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9355146 ,
                    to 9355265 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9374306 ,
                    to 9374392 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9376737 ,
                    to 9376814 ,
                    strand minus ,
                    id
                      gi 51772331 } ,
                  {
                    from 9445469 ,
                    to 9445708 ,
                    strand minus ,
                    id
                      gi 51772331 } } } ,
              seqs {
                whole
                  gi 38086485 } } } } } } } ,
  properties {
    {
      type comment ,
      label "Nomenclature" ,
      version 0 ,
      source {
        {
          anchor "Mouse Genome Informatics" } } ,
      properties {
        {
          type property ,
          label "Official Symbol" ,
          text "Abcb7" ,
          version 0 } ,
        {
          type property ,
          label "Official Full Name" ,
          text "ATP-binding cassette, sub-family B (MDR/TAP), member 7" ,
          version 0 } } } ,
    {
      type comment ,
      heading "GeneOntology" ,
      version 0 ,
      source {
        {
          pre-text "Provided by" ,
          anchor "MGI" ,
          url "http://www.informatics.jax.org/" } } ,
      comment {
        {
          type comment ,
          label "Function" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5524 } ,
                  anchor "ATP binding" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16887 } ,
                  anchor "ATPase activity" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 42626 } ,
                  anchor "ATPase activity, coupled to transmembrane movement
 of substances" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 17111 } ,
                  anchor "nucleoside-triphosphatase activity" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 166 } ,
                  anchor "nucleotide binding" ,
                  post-text "evidence: IEA" } } } } } ,
        {
          type comment ,
          label "Process" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 6810 } ,
                  anchor "transport" ,
                  post-text "evidence: IEA" } } } } } ,
        {
          type comment ,
          label "Component" ,
          version 0 ,
          comment {
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 19866 } ,
                  anchor "inner membrane" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16021 } ,
                  anchor "integral to membrane" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 16020 } ,
                  anchor "membrane" ,
                  post-text "evidence: IEA" } } } ,
            {
              type comment ,
              version 0 ,
              source {
                {
                  src {
                    db "GO" ,
                    tag
                      id 5739 } ,
                  anchor "mitochondrion" ,
                  post-text "evidence: IEA" } } } } } } } } ,
  homology {
    {
      type comment ,
      heading "Human, Rat" ,
      version 0 ,
      source {
        {
          src {
            db "HomoloGene" ,
            tag
              id 3175 } ,
          anchor "Map Viewer" ,
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&chr=X&
MAPS=genes-r-org/human-chr/mouse%3AX,genes-r-org/rat-chr/mouse%3AX,genes-r-org
/mouse-chrX&query=e%3A11306[id]+AND+gene[obj_type]&QSTR=abcb7&cmd=focus&fill=1
0" } } } } ,
  comments {
    {
      type comment ,
      heading "LocusTagLink" ,
      version 0 ,
      source {
        {
          src {
            db "MGI" ,
            tag
              id 109533 } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "MODEL" ,
      version 0 } ,
    {
      type comment ,
      version 0 ,
      refs {
        pmid 14651853 ,
        pmid 12480705 ,
        pmid 12477932 ,
        pmid 11217851 ,
        pmid 11076861 ,
        pmid 11042159 ,
        pmid 10922068 ,
        pmid 10349636 ,
        pmid 9143506 } } ,
    {
      type comment ,
      heading "Markers (Sequence Tagged Sites/STS)" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 161105 } ,
              anchor "RH124283" ,
              post-text "(e-PCR)" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 178992 } ,
              anchor "AW537380" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "953972" ,
              version 0 } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UniSTS" ,
                tag
                  id 181314 } ,
              anchor "AU019072" ,
              post-text "(e-PCR)" } } ,
          comment {
            {
              type other ,
              label "Alternate name" ,
              text "359130" ,
              version 0 } } } } } ,
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "XM_356348" ,
          version 2 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 51772276 } ,
              anchor "XM_356348" } } ,
          seqs {
            whole
              gi 51772276 } ,
          products {
            {
              type peptide ,
              accession "XP_356348" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 38086485 } ,
                  anchor "XP_356348" } } ,
              seqs {
                whole
                  gi 38086485 } ,
              comment {
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 38086485 } ,
                      pre-text "(3)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 5341 } ,
                          anchor "cd00267: ABC_ATPase; ABC (ATP-binding
 cassette) transporter nucleotide-binding domain" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 496 - 714  Blast Score: 577" ,
                          version 0 } } } ,
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 14387 } ,
                          anchor "COG5265: ATM1; ABC-type transport system
 involved in Fe-S cluster assembly, permease and ATPase components
 [Posttranslational modification, protein turnover, chaperones]" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 234 - 729  Blast Score: 1506" ,
                          version 0 } } } ,
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 25581 } ,
                          anchor "pfam00664: ABC_membrane; ABC transporter
 transmembrane region" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 164 - 435  Blast Score: 247" ,
                          version 0 } } } } } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AA517758" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 2257282 } ,
              anchor "AA517758" } } ,
          seqs {
            whole
              gi 2257282 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6J x DBA/2J F1" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AK040069" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 26087598 } ,
              anchor "AK040069" } } ,
          seqs {
            whole
              gi 26087598 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6J" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AK084853" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 26102284 } ,
              anchor "AK084853" } } ,
          seqs {
            whole
              gi 26102284 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6J" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AU019072" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 3374656 } ,
              anchor "AU019072" } } ,
          seqs {
            whole
              gi 3374656 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6J" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "AW537380" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 7179797 } ,
              anchor "AW537380" } } ,
          seqs {
            whole
              gi 7179797 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "C57BL/6J" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
          accession "BC035534" ,
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          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 23243450 } ,
              anchor "BC035534" } } ,
          seqs {
            whole
              gi 23243450 } ,
          products {
            {
              type peptide ,
              text "None" ,
              version 0 } } } ,
        {
          type mRNA ,
          heading "mRNA" ,
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          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 1167981 } ,
              anchor "U43892" } } ,
          seqs {
            whole
              gi 1167981 } ,
          products {
            {
              type peptide ,
              accession "AAC53152" ,
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              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 1167982 } ,
                  anchor "AAC53152" } } ,
              seqs {
                whole
                  gi 1167982 } } } ,
          comment {
            {
              type other ,
              label "Strain" ,
              text "DBA/2" ,
              version 0 } } } ,
        {
          type other ,
          text "None" ,
          version 0 ,
          products {
            {
              type peptide ,
              accession "Q61102" ,
              version 0 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 5902709 } ,
                  anchor "Q61102" } } ,
              seqs {
                whole
                  gi 5902709 } } } } } } ,
    {
      type comment ,
      heading "Additional Links" ,
      version 0 ,
      comment {
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "Evidence Viewer" ,
                tag
                  str "11306" } ,
              anchor "Evidence Viewer" ,
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=10090&cont
ig=NT_039711.3&gene=Abcb7&lid=11306&from=9312470&to=9445709" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "ModelMaker" ,
                tag
                  str "11306" } ,
              anchor "ModelMaker" ,
              url "http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=10
090&contig=NT_039711.3&gene=Abcb7&lid=11306" } } } ,
        {
          type comment ,
          text "UniGene" ,
          version 0 ,
          xtra-properties {
            {
              tag "UNIGENE" ,
              value "Mm.262053" } } ,
          source {
            {
              src {
                db "UniGene" ,
                tag
                  str "Mm.262053" } ,
              anchor "Mm.262053" ,
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Mm&CID=26
2053" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "HomoloGene" ,
                tag
                  str "11306" } ,
              anchor "HomoloGene" ,
              url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=
11306[loc]&TAXID=10090" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "MGI" ,
                tag
                  id 109533 } ,
              anchor "MGI" ,
              url "http://www.informatics.jax.org/searches/accession_report.cg
i?id=MGI:109533" } } } ,
        {
          type comment ,
          version 0 ,
          source {
            {
              src {
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                tag
                  str "" } ,
              url "http://www.ensembl.org/Mus_musculus/contigview?geneid=BC035
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        {
          type comment ,
          version 0 ,
          source {
            {
              src {
                db "UCSC" ,
                tag
                  str "" } ,
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&position=
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        {
          type comment ,
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          version 0 ,
          source {
            {
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                tag
                  str "MGI:109533" } ,
              anchor "MGI:109533" ,
              url "http://www.informatics.jax.org/searches/expression_report.c
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        {
          type comment ,
          text "Human ABC-Transporter Proteins" ,
          version 0 ,
          source {
            {
              src {
                db "Human ABC-Transporter Proteins" ,
                tag
                  str "Human ABC-Transporter Proteins" } ,
              anchor "Human ABC-Transporter Proteins" ,
              url "http://nutrigene.4t.com/humanabc.htm" } } } } } ,
    {
      type generif ,
      text "ABC7 positively regulates the expression of extramitochondrial
 thioredoxin & that of an intramitochondrial iron-sulfur-containing protein,
 ferrochelatase. ABC7 contributes to the production of heme during the
 differentiation of erythroid cells." ,
      version 0 ,
      refs {
        pmid 12480705 } ,
      create-date
        str "May 23 2003 12:00AM" ,
      update-date
        str "Jun 22 2003  7:07AM" } } ,
  unique-keys {
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      db "LocusID" ,
      tag
        id 11306 } ,
    {
      db "MGI" ,
      tag
        id 109533 } } ,
  xtra-index-terms {
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Entrezgene ::= {
  track-info {
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    status live ,
    create-date
      std {
        year 2005 ,
        month 4 ,
        day 7 ,
        hour 13 ,
        minute 32 ,
        second 25 } ,
    update-date
      std {
        year 2005 ,
        month 1 ,
        day 18 ,
        hour 23 ,
        minute 7 ,
        second 0 } } ,
  type protein-coding ,
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          db "taxon" ,
          tag
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      orgname {
        name
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 Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis" ,
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        mgcode 5 ,
        div "INV" } } ,
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      {
        subtype chromosome ,
        name "I" } } } ,
  gene {
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        db "AceView/WormGenes" ,
        tag
          str "1A478" } ,
      {
        db "LocusID" ,
        tag
          id 171590 } ,
      {
        db "WormBase" ,
        tag
          str "Y74C9A.3" } } ,
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  prot {
    name {
      "AD-003 protein (26.6 kD) (1A478)" } } ,
  rna {
    type mRNA } ,
  location {
    {
      display-str "I;-17.75 cM (interpolated genetic position)" ,
      method
        map-type cM } } ,
  gene-source {
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    src-str1 "NC_003279" ,
    src-str2 "CE:1A478" ,
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    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      label "1A478" ,
      accession "NC_003279" ,
      version 2 ,
      seqs {
        int {
          from 4220 ,
          to 10147 ,
          strand minus ,
          id
            gi 25167480 } } ,
      products {
        {
          type mRNA ,
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          version 1 ,
          refs {
            pmid 9851916 } ,
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              int {
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                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 5194 ,
                to 5295 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 4220 ,
                to 4357 ,
                strand minus ,
                id
                  gi 25167480 } } } ,
          seqs {
            whole
              gi 17510630 } ,
          products {
            {
              type peptide ,
              label "AD-003 protein (26.6 kD) (1A478)" ,
              accession "NP_490660" ,
              version 1 ,
              refs {
                pmid 9851916 } ,
              genomic-coords {
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                      gi 25167480 } ,
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                      gi 25167480 } ,
                  int {
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                    strand minus ,
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                      gi 25167480 } ,
                  int {
                    from 4220 ,
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                    strand minus ,
                    id
                      gi 25167480 } } } ,
              seqs {
                whole
                  gi 17510631 } } } ,
          comment {
            {
              type comment ,
              text "" ,
              version 0 } } } } ,
      comment {
        {
          type comment ,
          text "Title: Caenorhabditis elegans gene 1A478, AD-003 protein." ,
          version 0 } } } } ,
  comments {
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_058260" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 17510630 } ,
              anchor "NM_058260" } } ,
          seqs {
            whole
              gi 17510630 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_490660" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 17510631 } ,
                  anchor "NP_490660" } } ,
              seqs {
                whole
                  gi 17510631 } ,
              comment {
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 17510631 } ,
                      pre-text "(1)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 24115 } ,
                          anchor "pfam05891: DUF858; Eukaryotic protein of
 unknown function (DUF858)" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 11 - 225  Blast Score: 824" ,
                          version 0 } } } } } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type genomic ,
          heading "Genomic" ,
          accession "AC024206" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 7105656 } ,
              anchor "AC024206" } } ,
          seqs {
            whole
              gi 7105656 } ,
          products {
            {
              type peptide ,
              accession "AAF36050" ,
              version 2 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 14550391 } ,
                  anchor "AAF36050" } } ,
              seqs {
                whole
                  gi 14550391 } } } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "Reviewed" ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 171590 } } ,
  xtra-iq {
    {
      tag "NUCLEOTIDE" ,
      value "7105656" } ,
    {
      tag "PROTEIN" ,
      value "14550391" } } ,
  non-unique-keys {
    {
      db "ID" ,
      tag
        id 25167480 } } }
Entrezgene ::= {
  track-info {
    geneid 171591 ,
    status live ,
    create-date
      std {
        year 2005 ,
        month 4 ,
        day 6 ,
        hour 18 ,
        minute 33 ,
        second 30 } ,
    update-date
      std {
        year 2005 ,
        month 1 ,
        day 18 ,
        hour 23 ,
        minute 7 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Caenorhabditis elegans" ,
      db {
        {
          db "taxon" ,
          tag
            id 6239 } } ,
      orgname {
        name
          binomial {
            genus "Caenorhabditis" ,
            species "elegans" } ,
        lineage "Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida;
 Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis" ,
        gcode 1 ,
        mgcode 5 ,
        div "INV" } } ,
    subtype {
      {
        subtype chromosome ,
        name "I" } } } ,
  gene {
    locus "1A489" ,
    maploc "I;-17.80 cM (interpolated genetic position)" ,
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      {
        db "AceView/WormGenes" ,
        tag
          str "1A489" } ,
      {
        db "LocusID" ,
        tag
          id 171591 } ,
      {
        db "WormBase" ,
        tag
          str "Y74C9A.2" } } ,
    syn {
      "Y74C9A.2" ,
      "CELK01753" } ,
    locus-tag "1A489" } ,
  prot {
    name {
      "putative protein, with a coiled coil-4 domain (13.7 kD) (1A489)" } } ,
  rna {
    type mRNA } ,
  location {
    {
      display-str "I;-17.80 cM (interpolated genetic position)" ,
      method
        map-type cM } } ,
  gene-source {
    src "Entrez Genomes" ,
    src-int 25167480 ,
    src-str1 "NC_003279" ,
    src-str2 "CE:1A489" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      label "1A489" ,
      accession "NC_003279" ,
      version 2 ,
      seqs {
        int {
          from 11640 ,
          to 16584 ,
          strand plus ,
          id
            gi 25167480 } } ,
      products {
        {
          type mRNA ,
          accession "NM_058259" ,
          version 1 ,
          refs {
            pmid 9851916 } ,
          genomic-coords {
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              int {
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                strand plus ,
                id
                  gi 25167480 } ,
              int {
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                strand plus ,
                id
                  gi 25167480 } ,
              int {
                from 16472 ,
                to 16584 ,
                strand plus ,
                id
                  gi 25167480 } } } ,
          seqs {
            whole
              gi 17510628 } ,
          products {
            {
              type peptide ,
              label "putative protein, with a coiled coil-4 domain (13.7 kD)
 (1A489)" ,
              accession "NP_490661" ,
              version 1 ,
              refs {
                pmid 9851916 ,
                pmid 11231151 } ,
              genomic-coords {
                mix {
                  int {
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                    strand plus ,
                    id
                      gi 25167480 } ,
                  int {
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                    strand plus ,
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                      gi 25167480 } ,
                  int {
                    from 16472 ,
                    to 16584 ,
                    strand plus ,
                    id
                      gi 25167480 } } } ,
              seqs {
                whole
                  gi 17510629 } } } ,
          comment {
            {
              type comment ,
              text "" ,
              version 0 } } } } ,
      comment {
        {
          type comment ,
          text "Title: Caenorhabditis elegans essential expressed gene 1A489." ,
          version 0 } } } } ,
  comments {
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
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      products {
        {
          type mRNA ,
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            {
              src {
                db "Nucleotide" ,
                tag
                  id 17510628 } ,
              anchor "NM_058259" } } ,
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            whole
              gi 17510628 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
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              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 17510629 } ,
                  anchor "NP_490661" } } ,
              seqs {
                whole
                  gi 17510629 } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type genomic ,
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          accession "AC024206" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 7105656 } ,
              anchor "AC024206" } } ,
          seqs {
            whole
              gi 7105656 } ,
          products {
            {
              type peptide ,
              accession "AAF36049" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 7105658 } ,
                  anchor "AAF36049" } } ,
              seqs {
                whole
                  gi 7105658 } } } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "Reviewed" ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 171591 } } ,
  xtra-iq {
    {
      tag "NUCLEOTIDE" ,
      value "7105656" } ,
    {
      tag "PROTEIN" ,
      value "7105658" } } ,
  non-unique-keys {
    {
      db "ID" ,
      tag
        id 25167480 } } }
Entrezgene ::= {
  track-info {
    geneid 171592 ,
    status live ,
    create-date
      std {
        year 2005 ,
        month 4 ,
        day 6 ,
        hour 18 ,
        minute 31 ,
        second 55 } ,
    update-date
      std {
        year 2005 ,
        month 1 ,
        day 18 ,
        hour 23 ,
        minute 7 ,
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  type protein-coding ,
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    genome genomic ,
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      db {
        {
          db "taxon" ,
          tag
            id 6239 } } ,
      orgname {
        name
          binomial {
            genus "Caenorhabditis" ,
            species "elegans" } ,
        lineage "Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida;
 Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis" ,
        gcode 1 ,
        mgcode 5 ,
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    subtype {
      {
        subtype chromosome ,
        name "I" } } } ,
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      {
        db "AceView/WormGenes" ,
        tag
          str "1A492" } ,
      {
        db "LocusID" ,
        tag
          id 171592 } ,
      {
        db "WormBase" ,
        tag
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      "CELK08126" } ,
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  prot {
    name {
      "suppressor of PResenilin defect SPR-1 related; similar to co-repressor
 of REST RE1-silencing transcription factor (65.9 kD) (1A492)" ,
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 of REST RE1-silencing transcription factor (65.6 kD) (1A492)" } } ,
  location {
    {
      display-str "I;-17.86 cM (interpolated genetic position)" ,
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        map-type cM } } ,
  gene-source {
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    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      label "1A492" ,
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          strand minus ,
          id
            gi 25167480 } } ,
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              int {
                from 26589 ,
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                strand minus ,
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                  gi 25167480 } ,
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              int {
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                strand minus ,
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                strand minus ,
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                  gi 25167480 } ,
              int {
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                strand minus ,
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                  gi 25167480 } ,
              int {
                from 20847 ,
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                strand minus ,
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                  gi 25167480 } ,
              int {
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                strand minus ,
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                  gi 25167480 } ,
              int {
                from 19014 ,
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                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 18005 ,
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                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 17910 ,
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                strand minus ,
                id
                  gi 25167480 } } } ,
          seqs {
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              gi 17510632 } ,
          products {
            {
              type peptide ,
              label "suppressor of PResenilin defect SPR-1 related; similar to
 co-repressor of REST RE1-silencing transcription factor (65.9 kD) (1A492)" ,
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              version 1 ,
              refs {
                pmid 9851916 } ,
              genomic-coords {
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                      gi 25167480 } ,
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                      gi 25167480 } ,
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                    strand minus ,
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                      gi 25167480 } ,
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                    strand minus ,
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                      gi 25167480 } ,
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                    strand minus ,
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                      gi 25167480 } ,
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                    strand minus ,
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                      gi 25167480 } ,
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                    from 21012 ,
                    to 21138 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 20847 ,
                    to 20963 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 20270 ,
                    to 20477 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 19014 ,
                    to 19240 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 18005 ,
                    to 18114 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 17910 ,
                    to 17957 ,
                    strand minus ,
                    id
                      gi 25167480 } } } ,
              seqs {
                whole
                  gi 17510633 } } } ,
          comment {
            {
              type comment ,
              text "" ,
              version 0 } } } ,
        {
          type mRNA ,
          accession "NM_058262" ,
          version 1 ,
          refs {
            pmid 9851916 } ,
          genomic-coords {
            mix {
              int {
                from 26732 ,
                to 26777 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 26589 ,
                to 26680 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 26370 ,
                to 26523 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 25272 ,
                to 25471 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 24928 ,
                to 25089 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 24650 ,
                to 24844 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 21012 ,
                to 21138 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 20847 ,
                to 20963 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
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                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 19014 ,
                to 19240 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 18005 ,
                to 18114 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 17910 ,
                to 17957 ,
                strand minus ,
                id
                  gi 25167480 } } } ,
          seqs {
            whole
              gi 17510634 } ,
          products {
            {
              type peptide ,
              label "suppressor of PResenilin defect SPR-1 related; similar to
 co-repressor of REST RE1-silencing transcription factor (65.6 kD) (1A492)" ,
              accession "NP_490663" ,
              version 1 ,
              refs {
                pmid 9851916 } ,
              genomic-coords {
                mix {
                  int {
                    from 26732 ,
                    to 26777 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 26589 ,
                    to 26680 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 26370 ,
                    to 26523 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 25272 ,
                    to 25471 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 24928 ,
                    to 25089 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 24650 ,
                    to 24844 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 21012 ,
                    to 21138 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 20847 ,
                    to 20963 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 20270 ,
                    to 20477 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 19014 ,
                    to 19240 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 18005 ,
                    to 18114 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 17910 ,
                    to 17957 ,
                    strand minus ,
                    id
                      gi 25167480 } } } ,
              seqs {
                whole
                  gi 17510635 } } } ,
          comment {
            {
              type comment ,
              text "" ,
              version 0 } } } } ,
      comment {
        {
          type comment ,
          text "Title: Caenorhabditis elegans gene 1A492, suppressor of
 PResenilin defect SPR-1 related; similar to co-repressor of REST
 RE1-silencing transcription factor." ,
          version 0 } } } } ,
  comments {
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_058261" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 17510632 } ,
              anchor "NM_058261" } } ,
          seqs {
            whole
              gi 17510632 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_490662" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 17510633 } ,
                  anchor "NP_490662" } } ,
              seqs {
                whole
                  gi 17510633 } } } } ,
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_058262" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 17510634 } ,
              anchor "NM_058262" } } ,
          seqs {
            whole
              gi 17510634 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_490663" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 17510635 } ,
                  anchor "NP_490663" } } ,
              seqs {
                whole
                  gi 17510635 } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type genomic ,
          heading "Genomic" ,
          accession "AC024206" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 7105656 } ,
              anchor "AC024206" } } ,
          seqs {
            whole
              gi 7105656 } ,
          products {
            {
              type peptide ,
              accession "AAK67240" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 14550392 } ,
                  anchor "AAK67240" } } ,
              seqs {
                whole
                  gi 14550392 } } } } ,
        {
          type genomic ,
          heading "Genomic" ,
          accession "AC024206" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 7105656 } ,
              anchor "AC024206" } } ,
          seqs {
            whole
              gi 7105656 } ,
          products {
            {
              type peptide ,
              accession "AAF36052" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 7105661 } ,
                  anchor "AAF36052" } } ,
              seqs {
                whole
                  gi 7105661 } } } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "Reviewed" ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 171592 } } ,
  xtra-iq {
    {
      tag "NUCLEOTIDE" ,
      value "7105656" } ,
    {
      tag "PROTEIN" ,
      value "14550392" } ,
    {
      tag "PROTEIN" ,
      value "7105661" } } ,
  non-unique-keys {
    {
      db "ID" ,
      tag
        id 25167480 } } }
Entrezgene ::= {
  track-info {
    geneid 171593 ,
    status live ,
    create-date
      std {
        year 2005 ,
        month 4 ,
        day 7 ,
        hour 13 ,
        minute 31 ,
        second 41 } ,
    update-date
      std {
        year 2005 ,
        month 1 ,
        day 18 ,
        hour 23 ,
        minute 7 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Caenorhabditis elegans" ,
      db {
        {
          db "taxon" ,
          tag
            id 6239 } } ,
      orgname {
        name
          binomial {
            genus "Caenorhabditis" ,
            species "elegans" } ,
        lineage "Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida;
 Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis" ,
        gcode 1 ,
        mgcode 5 ,
        div "INV" } } ,
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      {
        subtype chromosome ,
        name "I" } } } ,
  gene {
    locus "1A502" ,
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    db {
      {
        db "AceView/WormGenes" ,
        tag
          str "1A502" } ,
      {
        db "LocusID" ,
        tag
          id 171593 } ,
      {
        db "WormBase" ,
        tag
          str "Y74C9A.5" } } ,
    syn {
      "Y74C9A.5" ,
      "CELK09643" } ,
    locus-tag "1A502" } ,
  prot {
    name {
      "sestrin (1A502)" } } ,
  rna {
    type mRNA } ,
  location {
    {
      display-str "I;-17.91 cM (interpolated genetic position)" ,
      method
        map-type cM } } ,
  gene-source {
    src "Entrez Genomes" ,
    src-int 25167480 ,
    src-str1 "NC_003279" ,
    src-str2 "CE:1A502" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      label "1A502" ,
      accession "NC_003279" ,
      version 2 ,
      seqs {
        int {
          from 28279 ,
          to 34904 ,
          strand minus ,
          id
            gi 25167480 } } ,
      products {
        {
          type mRNA ,
          accession "NM_058263" ,
          version 1 ,
          refs {
            pmid 9851916 } ,
          genomic-coords {
            mix {
              int {
                from 34694 ,
                to 34904 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 32598 ,
                to 32764 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 32411 ,
                to 32541 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 31768 ,
                to 32071 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 29768 ,
                to 30423 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 29099 ,
                to 29366 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 28915 ,
                to 29025 ,
                strand minus ,
                id
                  gi 25167480 } ,
              int {
                from 28279 ,
                to 28404 ,
                strand minus ,
                id
                  gi 25167480 } } } ,
          seqs {
            whole
              gi 17510636 } ,
          products {
            {
              type peptide ,
              label "sestrin (1A502)" ,
              accession "NP_490664" ,
              version 1 ,
              refs {
                pmid 9851916 } ,
              genomic-coords {
                mix {
                  int {
                    from 34694 ,
                    to 34904 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 32598 ,
                    to 32764 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 32411 ,
                    to 32541 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 31768 ,
                    to 32071 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 29768 ,
                    to 30423 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 29099 ,
                    to 29366 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 28915 ,
                    to 29025 ,
                    strand minus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 28279 ,
                    to 28404 ,
                    strand minus ,
                    id
                      gi 25167480 } } } ,
              seqs {
                whole
                  gi 17510637 } } } ,
          comment {
            {
              type comment ,
              text "" ,
              version 0 } } } } ,
      comment {
        {
          type comment ,
          text "Title: Caenorhabditis elegans gene 1A502, sestrin." ,
          version 0 } } } } ,
  comments {
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_058263" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 17510636 } ,
              anchor "NM_058263" } } ,
          seqs {
            whole
              gi 17510636 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_490664" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 17510637 } ,
                  anchor "NP_490664" } } ,
              seqs {
                whole
                  gi 17510637 } ,
              comment {
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 17510637 } ,
                      pre-text "(1)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 15933 } ,
                          anchor "pfam04636: PA26; PA26 p53-induced protein
 (sestrin)" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 88 - 644  Blast Score: 1457" ,
                          version 0 } } } } } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type genomic ,
          heading "Genomic" ,
          accession "AC024206" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 7105656 } ,
              anchor "AC024206" } } ,
          seqs {
            whole
              gi 7105656 } ,
          products {
            {
              type peptide ,
              accession "AAF36051" ,
              version 1 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 7105660 } ,
                  anchor "AAF36051" } } ,
              seqs {
                whole
                  gi 7105660 } } } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "Reviewed" ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 171593 } } ,
  xtra-iq {
    {
      tag "NUCLEOTIDE" ,
      value "7105656" } ,
    {
      tag "PROTEIN" ,
      value "7105660" } } ,
  non-unique-keys {
    {
      db "ID" ,
      tag
        id 25167480 } } }
Entrezgene ::= {
  track-info {
    geneid 171594 ,
    status live ,
    create-date
      std {
        year 2005 ,
        month 4 ,
        day 7 ,
        hour 13 ,
        minute 31 ,
        second 47 } ,
    update-date
      std {
        year 2005 ,
        month 1 ,
        day 18 ,
        hour 23 ,
        minute 7 ,
        second 0 } } ,
  type protein-coding ,
  source {
    genome genomic ,
    origin natural ,
    org {
      taxname "Caenorhabditis elegans" ,
      db {
        {
          db "taxon" ,
          tag
            id 6239 } } ,
      orgname {
        name
          binomial {
            genus "Caenorhabditis" ,
            species "elegans" } ,
        lineage "Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida;
 Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis" ,
        gcode 1 ,
        mgcode 5 ,
        div "INV" } } ,
    subtype {
      {
        subtype chromosome ,
        name "I" } } } ,
  gene {
    locus "1A527" ,
    maploc "I;-18.07 cM (interpolated genetic position)" ,
    db {
      {
        db "AceView/WormGenes" ,
        tag
          str "1A527" } ,
      {
        db "LocusID" ,
        tag
          id 171594 } ,
      {
        db "WormBase" ,
        tag
          str "Y48G1C.4" } } ,
    syn {
      "Y48G1C.4" ,
      "CELK05819" } ,
    locus-tag "1A527" } ,
  prot {
    name {
      "putative phosphatidylglycerophosphate synthase, similar to
 silencer-associated factor (51.7 kD) (1A527)" } } ,
  rna {
    type mRNA } ,
  location {
    {
      display-str "I;-18.07 cM (interpolated genetic position)" ,
      method
        map-type cM } } ,
  gene-source {
    src "Entrez Genomes" ,
    src-int 25167480 ,
    src-str1 "NC_003279" ,
    src-str2 "CE:1A527" ,
    gene-display FALSE ,
    locus-display FALSE ,
    extra-terms FALSE } ,
  locus {
    {
      type genomic ,
      label "1A527" ,
      accession "NC_003279" ,
      version 2 ,
      seqs {
        int {
          from 49920 ,
          to 54359 ,
          strand plus ,
          id
            gi 25167480 } } ,
      products {
        {
          type mRNA ,
          accession "NM_058265" ,
          version 2 ,
          refs {
            pmid 9851916 } ,
          genomic-coords {
            mix {
              int {
                from 49920 ,
                to 50015 ,
                strand plus ,
                id
                  gi 25167480 } ,
              int {
                from 50814 ,
                to 51029 ,
                strand plus ,
                id
                  gi 25167480 } ,
              int {
                from 52282 ,
                to 52409 ,
                strand plus ,
                id
                  gi 25167480 } ,
              int {
                from 52465 ,
                to 52571 ,
                strand plus ,
                id
                  gi 25167480 } ,
              int {
                from 53265 ,
                to 53336 ,
                strand plus ,
                id
                  gi 25167480 } ,
              int {
                from 53390 ,
                to 53694 ,
                strand plus ,
                id
                  gi 25167480 } ,
              int {
                from 53943 ,
                to 54359 ,
                strand plus ,
                id
                  gi 25167480 } } } ,
          seqs {
            whole
              gi 25143330 } ,
          products {
            {
              type peptide ,
              label "putative phosphatidylglycerophosphate synthase, similar
 to silencer-associated factor (51.7 kD) (1A527)" ,
              accession "NP_490666" ,
              version 2 ,
              refs {
                pmid 9851916 ,
                pmid 11231151 } ,
              genomic-coords {
                mix {
                  int {
                    from 49920 ,
                    to 50015 ,
                    strand plus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 50814 ,
                    to 51029 ,
                    strand plus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 52282 ,
                    to 52409 ,
                    strand plus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 52465 ,
                    to 52571 ,
                    strand plus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 53265 ,
                    to 53336 ,
                    strand plus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 53390 ,
                    to 53694 ,
                    strand plus ,
                    id
                      gi 25167480 } ,
                  int {
                    from 53943 ,
                    to 54359 ,
                    strand plus ,
                    id
                      gi 25167480 } } } ,
              seqs {
                whole
                  gi 25143331 } } } ,
          comment {
            {
              type comment ,
              text "" ,
              version 0 } } } } ,
      comment {
        {
          type comment ,
          text "Title: Caenorhabditis elegans essential gene 1A527, putative
 phosphatidylglycerophosphate synthase, similar to silencer-associated factor." ,
          version 0 } } } } ,
  comments {
    {
      type comment ,
      heading "NCBI Reference Sequences (RefSeq)" ,
      version 0 ,
      products {
        {
          type mRNA ,
          heading "mRNA Sequence" ,
          accession "NM_058265" ,
          version 2 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 25143330 } ,
              anchor "NM_058265" } } ,
          seqs {
            whole
              gi 25143330 } ,
          products {
            {
              type peptide ,
              heading "Product" ,
              accession "NP_490666" ,
              version 2 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 25143331 } ,
                  anchor "NP_490666" } } ,
              seqs {
                whole
                  gi 25143331 } ,
              comment {
                {
                  type other ,
                  heading "Conserved Domains" ,
                  version 0 ,
                  source {
                    {
                      src {
                        db "PROT_CDD" ,
                        tag
                          id 25143331 } ,
                      pre-text "(1)" ,
                      anchor "summary" } } ,
                  comment {
                    {
                      type other ,
                      version 0 ,
                      source {
                        {
                          src {
                            db "CDD" ,
                            tag
                              id 5372 } ,
                          anchor "cd00138: PLDc; Phospholipase D" } } ,
                      comment {
                        {
                          type other ,
                          text "Location: 20 - 172  Blast Score: 135" ,
                          version 0 } } } } } } } } } } } ,
    {
      type comment ,
      heading "Related Sequences" ,
      version 0 ,
      products {
        {
          type genomic ,
          heading "Genomic" ,
          accession "AC024796" ,
          version 1 ,
          source {
            {
              src {
                db "Nucleotide" ,
                tag
                  id 7140352 } ,
              anchor "AC024796" } } ,
          seqs {
            whole
              gi 7140352 } ,
          products {
            {
              type peptide ,
              accession "AAK29892" ,
              version 2 ,
              source {
                {
                  src {
                    db "Protein" ,
                    tag
                      id 16950493 } ,
                  anchor "AAK29892" } } ,
              seqs {
                whole
                  gi 16950493 } } } } } } ,
    {
      type comment ,
      heading "RefSeq Status" ,
      label "Reviewed" ,
      version 0 } } ,
  unique-keys {
    {
      db "LocusID" ,
      tag
        id 171594 } } ,
  xtra-iq {
    {
      tag "NUCLEOTIDE" ,
      value "7140352" } ,
    {
      tag "PROTEIN" ,
      value "16950493" } } ,
  non-unique-keys {
    {
      db "ID" ,
      tag
        id 25167480 } } }
BioPerl-1.007002/t/data/entrezgene_bug3453.dat000444000766000024     51220313155576321 20747 0ustar00cjfieldsstaff000000000000Entrezgene ::= {
  track-info {
    geneid 3581,
    status live,
    create-date std {
      year 1997,
      month 11,
      day 18
    },
    update-date std {
      year 2013,
      month 12,
      day 8,
      hour 11,
      minute 11,
      second 0
    }
  },
  type protein-coding,
  source {
    genome genomic,
    origin natural,
    org {
      taxname "Homo sapiens",
      common "human",
      db {
        {
          db "taxon",
          tag id 9606
        }
      },
      syn {
        "man"
      },
      orgname {
        name binomial {
          genus "Homo",
          species "sapiens"
        },
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
 Catarrhini; Hominidae; Homo",
        gcode 1,
        mgcode 2,
        div "PRI",
        pgcode 0
      }
    },
    subtype {
      {
        subtype chromosome,
        name "X"
      },
      {
        subtype chromosome,
        name "Y"
      }
    }
  },
  gene {
    locus "IL9R",
    desc "interleukin 9 receptor",
    maploc "Xq28 and Yq12",
    db {
      {
        db "HGNC",
        tag id 6030
      },
      {
        db "Ensembl",
        tag str "ENSG00000124334"
      },
      {
        db "HPRD",
        tag str "02052"
      },
      {
        db "MIM",
        tag id 300007
      },
      {
        db "Vega",
        tag str "OTTHUMG00000022720"
      }
    },
    syn {
      "CD129",
      "IL-9R"
    }
  },
  prot {
    name {
      "interleukin-9 receptor",
      "IL-9 receptor"
    },
    desc "interleukin-9 receptor"
  },
  summary "The protein encoded by this gene is a cytokine receptor that
 specifically mediates the biological effects of interleukin 9 (IL9). The
 functional IL9 receptor complex requires this protein as well as the
 interleukin 2 receptor, gamma (IL2RG), a common gamma subunit shared by the
 receptors of many different cytokines. The ligand binding of this receptor
 leads to the activation of various JAK kinases and STAT proteins, which
 connect to different biologic responses. This gene is located at the
 pseudoautosomal regions of X and Y chromosomes. Genetic studies suggested an
 association of this gene with the development of asthma. Multiple pseudogenes
 on chromosome 9, 10, 16, and 18 have been described. Alternatively spliced
 transcript variants have been found for this gene. [provided by RefSeq, Jul
 2008]",
  location {
    {
      display-str "Xq28 and Yq12",
      method map-type cyto
    }
  },
  gene-source {
    src "LocusLink",
    src-int 3581,
    src-str2 "3581"
  },
  locus {
    {
      type genomic,
      heading "Reference GRCh37.p13 Primary Assembly",
      label "chromosome Y reference GRCh37.p13 Primary Assembly",
      accession "NC_000024",
      version 9,
      seqs {
        int {
          from 59330251,
          to 59343487,
          strand plus,
          id gi 224589823
        }
      },
      products {
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 2",
          accession "NM_176786",
          version 1,
          genomic-coords {
            mix {
              int {
                from 59330251,
                to 59330457,
                strand plus,
                id gi 224589823
              },
              int {
                from 59334078,
                to 59334178,
                strand plus,
                id gi 224589823
              },
              int {
                from 59335552,
                to 59335689,
                strand plus,
                id gi 224589823
              },
              int {
                from 59336119,
                to 59336230,
                strand plus,
                id gi 224589823
              },
              int {
                from 59336354,
                to 59336525,
                strand plus,
                id gi 224589823
              },
              int {
                from 59337119,
                to 59337235,
                strand plus,
                id gi 224589823
              },
              int {
                from 59337948,
                to 59338149,
                strand plus,
                id gi 224589823
              },
              int {
                from 59338753,
                to 59338858,
                strand plus,
                id gi 224589823
              },
              int {
                from 59342486,
                to 59343487,
                strand plus,
                id gi 224589823
              }
            }
          },
          seqs {
            whole gi 29171683
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 2",
              accession "NP_789743",
              version 2,
              source {
                {
                  src {
                    db "CCDS",
                    tag str "CCDS59180.1"
                  },
                  anchor "CCDS59180.1"
                }
              },
              genomic-coords {
                mix {
                  int {
                    from 59330414,
                    to 59330457,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59334078,
                    to 59334178,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59335552,
                    to 59335689,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59336119,
                    to 59336230,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59336354,
                    to 59336525,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59337119,
                    to 59337235,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59337948,
                    to 59338149,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59338753,
                    to 59338858,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59342486,
                    to 59342522,
                    strand plus,
                    id gi 224589823
                  }
                }
              },
              seqs {
                whole gi 388490122
              }
            }
          }
        },
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 1",
          accession "NM_002186",
          version 2,
          genomic-coords {
            mix {
              int {
                from 59330251,
                to 59330457,
                strand plus,
                id gi 224589823
              },
              int {
                from 59335576,
                to 59335689,
                strand plus,
                id gi 224589823
              },
              int {
                from 59336119,
                to 59336230,
                strand plus,
                id gi 224589823
              },
              int {
                from 59336347,
                to 59336525,
                strand plus,
                id gi 224589823
              },
              int {
                from 59337090,
                to 59337235,
                strand plus,
                id gi 224589823
              },
              int {
                from 59337948,
                to 59338149,
                strand plus,
                id gi 224589823
              },
              int {
                from 59338753,
                to 59338858,
                strand plus,
                id gi 224589823
              },
              int {
                from 59340193,
                to 59340277,
                strand plus,
                id gi 224589823
              },
              int {
                from 59342486,
                to 59343487,
                strand plus,
                id gi 224589823
              }
            }
          },
          seqs {
            whole gi 29171681
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 1 precursor",
              accession "NP_002177",
              version 2,
              source {
                {
                  src {
                    db "CCDS",
                    tag str "CCDS14771.4"
                  },
                  anchor "CCDS14771.4"
                }
              },
              genomic-coords {
                mix {
                  int {
                    from 59330430,
                    to 59330457,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59335576,
                    to 59335689,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59336119,
                    to 59336230,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59336347,
                    to 59336525,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59337090,
                    to 59337235,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59337948,
                    to 59338149,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59338753,
                    to 59338858,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59340193,
                    to 59340277,
                    strand plus,
                    id gi 224589823
                  },
                  int {
                    from 59342486,
                    to 59343079,
                    strand plus,
                    id gi 224589823
                  }
                }
              },
              seqs {
                whole gi 29171682
              }
            }
          }
        }
      }
    },
    {
      type genomic,
      heading "Reference GRCh37.p13 Primary Assembly",
      label "chromosome X reference GRCh37.p13 Primary Assembly",
      accession "NC_000023",
      version 10,
      seqs {
        int {
          from 155227245,
          to 155240481,
          strand plus,
          id gi 224589822
        }
      },
      products {
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 2",
          accession "NM_176786",
          version 1,
          genomic-coords {
            mix {
              int {
                from 155227245,
                to 155227451,
                strand plus,
                id gi 224589822
              },
              int {
                from 155231072,
                to 155231172,
                strand plus,
                id gi 224589822
              },
              int {
                from 155232546,
                to 155232683,
                strand plus,
                id gi 224589822
              },
              int {
                from 155233113,
                to 155233224,
                strand plus,
                id gi 224589822
              },
              int {
                from 155233348,
                to 155233519,
                strand plus,
                id gi 224589822
              },
              int {
                from 155234113,
                to 155234229,
                strand plus,
                id gi 224589822
              },
              int {
                from 155234942,
                to 155235143,
                strand plus,
                id gi 224589822
              },
              int {
                from 155235747,
                to 155235852,
                strand plus,
                id gi 224589822
              },
              int {
                from 155239480,
                to 155240481,
                strand plus,
                id gi 224589822
              }
            }
          },
          seqs {
            whole gi 29171683
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 2",
              accession "NP_789743",
              version 2,
              source {
                {
                  src {
                    db "CCDS",
                    tag str "CCDS59180.1"
                  },
                  anchor "CCDS59180.1"
                }
              },
              genomic-coords {
                mix {
                  int {
                    from 155227408,
                    to 155227451,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155231072,
                    to 155231172,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155232546,
                    to 155232683,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155233113,
                    to 155233224,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155233348,
                    to 155233519,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155234113,
                    to 155234229,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155234942,
                    to 155235143,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155235747,
                    to 155235852,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155239480,
                    to 155239516,
                    strand plus,
                    id gi 224589822
                  }
                }
              },
              seqs {
                whole gi 388490122
              }
            }
          }
        },
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 1",
          accession "NM_002186",
          version 2,
          genomic-coords {
            mix {
              int {
                from 155227245,
                to 155227451,
                strand plus,
                id gi 224589822
              },
              int {
                from 155232570,
                to 155232683,
                strand plus,
                id gi 224589822
              },
              int {
                from 155233113,
                to 155233224,
                strand plus,
                id gi 224589822
              },
              int {
                from 155233341,
                to 155233519,
                strand plus,
                id gi 224589822
              },
              int {
                from 155234084,
                to 155234229,
                strand plus,
                id gi 224589822
              },
              int {
                from 155234942,
                to 155235143,
                strand plus,
                id gi 224589822
              },
              int {
                from 155235747,
                to 155235852,
                strand plus,
                id gi 224589822
              },
              int {
                from 155237187,
                to 155237271,
                strand plus,
                id gi 224589822
              },
              int {
                from 155239480,
                to 155240481,
                strand plus,
                id gi 224589822
              }
            }
          },
          seqs {
            whole gi 29171681
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 1 precursor",
              accession "NP_002177",
              version 2,
              source {
                {
                  src {
                    db "CCDS",
                    tag str "CCDS14771.4"
                  },
                  anchor "CCDS14771.4"
                }
              },
              genomic-coords {
                mix {
                  int {
                    from 155227424,
                    to 155227451,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155232570,
                    to 155232683,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155233113,
                    to 155233224,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155233341,
                    to 155233519,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155234084,
                    to 155234229,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155234942,
                    to 155235143,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155235747,
                    to 155235852,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155237187,
                    to 155237271,
                    strand plus,
                    id gi 224589822
                  },
                  int {
                    from 155239480,
                    to 155240073,
                    strand plus,
                    id gi 224589822
                  }
                }
              },
              seqs {
                whole gi 29171682
              }
            }
          }
        }
      }
    },
    {
      type genomic,
      heading "Reference assembly",
      label "RefSeqGene",
      accession "NG_013238",
      version 1,
      seqs {
        int {
          from 5000,
          to 18236,
          strand plus,
          id gi 261823945
        }
      },
      products {
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 1",
          accession "NM_002186",
          version 2,
          genomic-coords {
            mix {
              int {
                from 5000,
                to 5206,
                strand plus,
                id gi 261823945
              },
              int {
                from 10325,
                to 10438,
                strand plus,
                id gi 261823945
              },
              int {
                from 10868,
                to 10979,
                strand plus,
                id gi 261823945
              },
              int {
                from 11096,
                to 11274,
                strand plus,
                id gi 261823945
              },
              int {
                from 11839,
                to 11984,
                strand plus,
                id gi 261823945
              },
              int {
                from 12697,
                to 12898,
                strand plus,
                id gi 261823945
              },
              int {
                from 13502,
                to 13607,
                strand plus,
                id gi 261823945
              },
              int {
                from 14942,
                to 15026,
                strand plus,
                id gi 261823945
              },
              int {
                from 17235,
                to 18236,
                strand plus,
                id gi 261823945
              }
            }
          },
          seqs {
            whole gi 29171681
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 1 precursor",
              accession "NP_002177",
              version 2,
              source {
                {
                  src {
                    db "CCDS",
                    tag str "CCDS14771.4"
                  },
                  anchor "CCDS14771.4"
                }
              },
              genomic-coords {
                mix {
                  int {
                    from 5179,
                    to 5206,
                    strand plus,
                    id gi 261823945
                  },
                  int {
                    from 10325,
                    to 10438,
                    strand plus,
                    id gi 261823945
                  },
                  int {
                    from 10868,
                    to 10979,
                    strand plus,
                    id gi 261823945
                  },
                  int {
                    from 11096,
                    to 11274,
                    strand plus,
                    id gi 261823945
                  },
                  int {
                    from 11839,
                    to 11984,
                    strand plus,
                    id gi 261823945
                  },
                  int {
                    from 12697,
                    to 12898,
                    strand plus,
                    id gi 261823945
                  },
                  int {
                    from 13502,
                    to 13607,
                    strand plus,
                    id gi 261823945
                  },
                  int {
                    from 14942,
                    to 15026,
                    strand plus,
                    id gi 261823945
                  },
                  int {
                    from 17235,
                    to 17828,
                    strand plus,
                    id gi 261823945
                  }
                }
              },
              seqs {
                whole gi 29171682
              }
            }
          }
        }
      }
    },
    {
      type genomic,
      heading "Alternate CHM1_1.1",
      label "chromosome X alternate CHM1_1.1",
      accession "NC_018934",
      version 2,
      seqs {
        int {
          from 155138862,
          to 155152088,
          strand plus,
          id gi 528476524
        }
      },
      products {
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 2",
          accession "NM_176786",
          version 1,
          genomic-coords {
            mix {
              int {
                from 155138862,
                to 155139068,
                strand plus,
                id gi 528476524
              },
              int {
                from 155142688,
                to 155142788,
                strand plus,
                id gi 528476524
              },
              int {
                from 155144166,
                to 155144303,
                strand plus,
                id gi 528476524
              },
              int {
                from 155144733,
                to 155144844,
                strand plus,
                id gi 528476524
              },
              int {
                from 155144968,
                to 155145139,
                strand plus,
                id gi 528476524
              },
              int {
                from 155145733,
                to 155145849,
                strand plus,
                id gi 528476524
              },
              int {
                from 155146562,
                to 155146763,
                strand plus,
                id gi 528476524
              },
              int {
                from 155147367,
                to 155147472,
                strand plus,
                id gi 528476524
              },
              int {
                from 155151087,
                to 155152088,
                strand plus,
                id gi 528476524
              }
            }
          },
          seqs {
            whole gi 29171683
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 2",
              accession "NP_789743",
              version 2,
              genomic-coords {
                mix {
                  int {
                    from 155139025,
                    to 155139068,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155142688,
                    to 155142788,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155144166,
                    to 155144303,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155144733,
                    to 155144844,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155144968,
                    to 155145139,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155145733,
                    to 155145849,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155146562,
                    to 155146763,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155147367,
                    to 155147472,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155151087,
                    to 155151123,
                    strand plus,
                    id gi 528476524
                  }
                }
              },
              seqs {
                whole gi 388490122
              }
            }
          }
        },
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 1",
          accession "NM_002186",
          version 2,
          genomic-coords {
            mix {
              int {
                from 155138862,
                to 155139068,
                strand plus,
                id gi 528476524
              },
              int {
                from 155144190,
                to 155144303,
                strand plus,
                id gi 528476524
              },
              int {
                from 155144733,
                to 155144844,
                strand plus,
                id gi 528476524
              },
              int {
                from 155144961,
                to 155145139,
                strand plus,
                id gi 528476524
              },
              int {
                from 155145704,
                to 155145849,
                strand plus,
                id gi 528476524
              },
              int {
                from 155146562,
                to 155146763,
                strand plus,
                id gi 528476524
              },
              int {
                from 155147367,
                to 155147472,
                strand plus,
                id gi 528476524
              },
              int {
                from 155148808,
                to 155148892,
                strand plus,
                id gi 528476524
              },
              int {
                from 155151087,
                to 155152088,
                strand plus,
                id gi 528476524
              }
            }
          },
          seqs {
            whole gi 29171681
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 1 precursor",
              accession "NP_002177",
              version 2,
              genomic-coords {
                mix {
                  int {
                    from 155139041,
                    to 155139068,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155144190,
                    to 155144303,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155144733,
                    to 155144844,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155144961,
                    to 155145139,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155145704,
                    to 155145849,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155146562,
                    to 155146763,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155147367,
                    to 155147472,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155148808,
                    to 155148892,
                    strand plus,
                    id gi 528476524
                  },
                  int {
                    from 155151087,
                    to 155151680,
                    strand plus,
                    id gi 528476524
                  }
                }
              },
              seqs {
                whole gi 29171682
              }
            }
          }
        }
      }
    },
    {
      type genomic,
      heading "Alternate HuRef",
      label "chromosome X alternate HuRef",
      accession "AC_000155",
      version 1,
      seqs {
        int {
          from 143710175,
          to 143723406,
          strand plus,
          id gi 157734237
        }
      },
      products {
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 2",
          accession "NM_176786",
          version 1,
          genomic-coords {
            mix {
              int {
                from 143710175,
                to 143710381,
                strand plus,
                id gi 157734237
              },
              int {
                from 143714002,
                to 143714102,
                strand plus,
                id gi 157734237
              },
              int {
                from 143715480,
                to 143715617,
                strand plus,
                id gi 157734237
              },
              int {
                from 143716047,
                to 143716158,
                strand plus,
                id gi 157734237
              },
              int {
                from 143716282,
                to 143716453,
                strand plus,
                id gi 157734237
              },
              int {
                from 143717047,
                to 143717163,
                strand plus,
                id gi 157734237
              },
              int {
                from 143717876,
                to 143718077,
                strand plus,
                id gi 157734237
              },
              int {
                from 143718681,
                to 143718786,
                strand plus,
                id gi 157734237
              },
              int {
                from 143722405,
                to 143723406,
                strand plus,
                id gi 157734237
              }
            }
          },
          seqs {
            whole gi 29171683
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 2",
              accession "NP_789743",
              version 2,
              genomic-coords {
                mix {
                  int {
                    from 143710338,
                    to 143710381,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143714002,
                    to 143714102,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143715480,
                    to 143715617,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143716047,
                    to 143716158,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143716282,
                    to 143716453,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143717047,
                    to 143717163,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143717876,
                    to 143718077,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143718681,
                    to 143718786,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143722405,
                    to 143722441,
                    strand plus,
                    id gi 157734237
                  }
                }
              },
              seqs {
                whole gi 388490122
              }
            }
          }
        },
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 1",
          accession "NM_002186",
          version 2,
          genomic-coords {
            mix {
              int {
                from 143710175,
                to 143710381,
                strand plus,
                id gi 157734237
              },
              int {
                from 143715504,
                to 143715617,
                strand plus,
                id gi 157734237
              },
              int {
                from 143716047,
                to 143716158,
                strand plus,
                id gi 157734237
              },
              int {
                from 143716275,
                to 143716453,
                strand plus,
                id gi 157734237
              },
              int {
                from 143717018,
                to 143717163,
                strand plus,
                id gi 157734237
              },
              int {
                from 143717876,
                to 143718077,
                strand plus,
                id gi 157734237
              },
              int {
                from 143718681,
                to 143718786,
                strand plus,
                id gi 157734237
              },
              int {
                from 143720118,
                to 143720202,
                strand plus,
                id gi 157734237
              },
              int {
                from 143722405,
                to 143723406,
                strand plus,
                id gi 157734237
              }
            }
          },
          seqs {
            whole gi 29171681
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 1 precursor",
              accession "NP_002177",
              version 2,
              genomic-coords {
                mix {
                  int {
                    from 143710354,
                    to 143710381,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143715504,
                    to 143715617,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143716047,
                    to 143716158,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143716275,
                    to 143716453,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143717018,
                    to 143717163,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143717876,
                    to 143718077,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143718681,
                    to 143718786,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143720118,
                    to 143720202,
                    strand plus,
                    id gi 157734237
                  },
                  int {
                    from 143722405,
                    to 143722998,
                    strand plus,
                    id gi 157734237
                  }
                }
              },
              seqs {
                whole gi 29171682
              }
            }
          }
        }
      }
    }
  },
  properties {
    {
      type comment,
      label "Nomenclature",
      source {
        {
          anchor "HUGO Gene Nomenclature Committee"
        }
      },
      properties {
        {
          type property,
          label "Official Symbol",
          text "IL9R"
        },
        {
          type property,
          label "Official Full Name",
          text "interleukin 9 receptor"
        }
      }
    },
    {
      type comment,
      heading "GeneOntology",
      source {
        {
          pre-text "Provided by",
          anchor "GOA",
          url "http://www.ebi.ac.uk/GOA/"
        }
      },
      comment {
        {
          type comment,
          label "Function",
          comment {
            {
              type comment,
              refs {
                pmid 1376929
              },
              source {
                {
                  src {
                    db "GO",
                    tag id 4919
                  },
                  anchor "interleukin-9 receptor activity",
                  post-text "evidence: TAS"
                }
              }
            }
          }
        },
        {
          type comment,
          label "Process",
          comment {
            {
              type comment,
              refs {
                pmid 1376929
              },
              source {
                {
                  src {
                    db "GO",
                    tag id 8283
                  },
                  anchor "cell proliferation",
                  post-text "evidence: TAS"
                }
              }
            },
            {
              type comment,
              refs {
                pmid 1376929
              },
              source {
                {
                  src {
                    db "GO",
                    tag id 38113
                  },
                  anchor "interleukin-9-mediated signaling pathway",
                  post-text "evidence: TAS"
                }
              }
            },
            {
              type comment,
              refs {
                pmid 1376929
              },
              source {
                {
                  src {
                    db "GO",
                    tag id 7165
                  },
                  anchor "signal transduction",
                  post-text "evidence: TAS"
                }
              }
            }
          }
        },
        {
          type comment,
          label "Component",
          comment {
            {
              type comment,
              refs {
                pmid 1376929
              },
              source {
                {
                  src {
                    db "GO",
                    tag id 5615
                  },
                  anchor "extracellular space",
                  post-text "evidence: TAS"
                }
              }
            },
            {
              type comment,
              refs {
                pmid 1376929
              },
              source {
                {
                  src {
                    db "GO",
                    tag id 5887
                  },
                  anchor "integral to plasma membrane",
                  post-text "evidence: TAS"
                }
              }
            }
          }
        }
      }
    }
  },
  homology {
    {
      type comment,
      heading "Mouse, Rat",
      source {
        {
          src {
            db "HomoloGene",
            tag id 37591
          },
          anchor "Map Viewer",
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=X&M
APS=genes-r-org/rat-chr/human%3AX,genes-r-org/mouse-chr/human%3AX,genes-r-org/
human-chrX&query=e%3A3581[egene_id]+AND+gene[obj_type]&QSTR=il9r&cmd=focus&fil
l=10",
          post-text "(chromosome X)"
        }
      }
    },
    {
      type comment,
      heading "Mouse, Rat",
      source {
        {
          src {
            db "HomoloGene",
            tag id 37591
          },
          anchor "Map Viewer",
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=Y&M
APS=genes-r-org/rat-chr/human%3AY,genes-r-org/mouse-chr/human%3AY,genes-r-org/
human-chrY&query=e%3A3581[egene_id]+AND+gene[obj_type]&QSTR=il9r&cmd=focus&fil
l=10",
          post-text "(chromosome Y)"
        }
      }
    }
  },
  comments {
    {
      type comment,
      heading "RefSeq Status",
      label "REVIEWED"
    },
    {
      type comment,
      heading "Annotation Information",
      properties {
        {
          type property,
          label "Annotation category",
          text "partial on reference assembly"
        }
      }
    },
    {
      type gene-group,
      heading "Related pseudogene(s)",
      source {
        {
          pre-text "5 found",
          anchor "Review record(s) in Gene"
        }
      }
    },
    {
      type comment,
      refs {
        pmid 23638223,
        pmid 22638550,
        pmid 21371865,
        pmid 20673868,
        pmid 20595916,
        pmid 20503287,
        pmid 20452482,
        pmid 20424473,
        pmid 19723899,
        pmid 19692168,
        pmid 19401191,
        pmid 19258923,
        pmid 19139102,
        pmid 18829468,
        pmid 18633131,
        pmid 18339896,
        pmid 17919707,
        pmid 17703412,
        pmid 17207965,
        pmid 17192395,
        pmid 17083349,
        pmid 15621723,
        pmid 15591265,
        pmid 12477932,
        pmid 11868823,
        pmid 11588013,
        pmid 11418623,
        pmid 11160343,
        pmid 11039580,
        pmid 10657622,
        pmid 10655549,
        pmid 10642536,
        pmid 10486269,
        pmid 10329852,
        pmid 9535918,
        pmid 9002663,
        pmid 8756628,
        pmid 8666384,
        pmid 8193355,
        pmid 7718508,
        pmid 1376929
      }
    },
    {
      type comment,
      heading "NCBI Reference Sequences (RefSeq)",
      comment {
        {
          type comment,
          heading "RefSeqs maintained independently of Annotated Genomes",
          products {
            {
              type mRNA,
              heading "mRNA Sequence",
              accession "NM_002186",
              version 2,
              source {
                {
                  src {
                    db "Nucleotide",
                    tag id 29171681
                  },
                  anchor "NM_002186"
                }
              },
              seqs {
                whole gi 29171681
              },
              products {
                {
                  type peptide,
                  heading "Product",
                  accession "NP_002177",
                  version 2,
                  source {
                    {
                      src {
                        db "Protein",
                        tag id 29171682
                      },
                      anchor "NP_002177",
                      post-text "interleukin-9 receptor isoform 1 precursor"
                    }
                  },
                  seqs {
                    whole gi 29171682
                  },
                  comment {
                    {
                      type other,
                      heading "Related",
                      source {
                        {
                          src {
                            db "Ensembl",
                            tag str "ENSP00000244174"
                          }
                        }
                      }
                    },
                    {
                      type other,
                      heading "UniProtKB",
                      source {
                      },
                      comment {
                        {
                          type other,
                          source {
                            {
                              src {
                                db "UniProtKB/Swiss-Prot",
                                tag str "Q01113"
                              },
                              anchor "Q01113"
                            }
                          }
                        }
                      }
                    },
                    {
                      type other,
                      heading "Consensus CDS (CCDS)",
                      source {
                        {
                          src {
                            db "CCDS",
                            tag str "CCDS14771.4"
                          },
                          anchor "CCDS14771.4"
                        }
                      }
                    },
                    {
                      type other,
                      heading "Related",
                      source {
                        {
                          src {
                            db "Vega",
                            tag str "OTTHUMP00000024332"
                          }
                        }
                      }
                    }
                  }
                }
              },
              comment {
                {
                  type comment,
                  label "RefSeq Status",
                  text "REVIEWED"
                },
                {
                  type comment,
                  heading "Transcriptional Variant",
                  comment {
                    {
                      type comment,
                      text "Transcript Variant: This variant (1) represent the
 longer transcript and encodes the longer isoform (1)."
                    }
                  }
                },
                {
                  type other,
                  heading "Source Sequence",
                  source {
                    {
                      src {
                        db "Nucleotide",
                        tag str "BC025298,M84747"
                      },
                      anchor "BC025298,M84747"
                    }
                  }
                },
                {
                  type other,
                  heading "Related",
                  source {
                    {
                      src {
                        db "Ensembl",
                        tag str "ENST00000244174"
                      }
                    }
                  }
                },
                {
                  type other,
                  heading "Related",
                  source {
                    {
                      src {
                        db "Vega",
                        tag str "OTTHUMT00000058981"
                      }
                    }
                  }
                }
              }
            },
            {
              type mRNA,
              heading "mRNA Sequence",
              accession "NM_176786",
              version 1,
              source {
                {
                  src {
                    db "Nucleotide",
                    tag id 29171683
                  },
                  anchor "NM_176786"
                }
              },
              seqs {
                whole gi 29171683
              },
              products {
                {
                  type peptide,
                  heading "Product",
                  accession "NP_789743",
                  version 2,
                  source {
                    {
                      src {
                        db "Protein",
                        tag id 388490122
                      },
                      anchor "NP_789743",
                      post-text "interleukin-9 receptor isoform 2"
                    }
                  },
                  seqs {
                    whole gi 388490122
                  },
                  comment {
                    {
                      type other,
                      heading "Related",
                      source {
                        {
                          src {
                            db "Ensembl",
                            tag str "ENSP00000358431"
                          }
                        }
                      }
                    },
                    {
                      type other,
                      heading "UniProtKB",
                      source {
                      },
                      comment {
                        {
                          type other,
                          source {
                            {
                              src {
                                db "UniProtKB/Swiss-Prot",
                                tag str "Q01113"
                              },
                              anchor "Q01113"
                            }
                          }
                        }
                      }
                    },
                    {
                      type other,
                      heading "Consensus CDS (CCDS)",
                      source {
                        {
                          src {
                            db "CCDS",
                            tag str "CCDS59180.1"
                          },
                          anchor "CCDS59180.1"
                        }
                      }
                    },
                    {
                      type other,
                      heading "Related",
                      source {
                        {
                          src {
                            db "Vega",
                            tag str "OTTHUMP00000024331"
                          }
                        }
                      }
                    }
                  }
                }
              },
              comment {
                {
                  type comment,
                  label "RefSeq Status",
                  text "REVIEWED"
                },
                {
                  type comment,
                  heading "Transcriptional Variant",
                  comment {
                    {
                      type comment,
                      text "Transcript Variant: This variant (2) differs in
 the 5' and 3' UTR and has multiple coding region differences, compared to
 variant 1. Some of these differences result in translational frameshifts. The
 resulting isoform (2) has distinct N- and C-termini and is shorter than
 isoform 1."
                    }
                  }
                },
                {
                  type other,
                  heading "Source Sequence",
                  source {
                    {
                      src {
                        db "Nucleotide",
                        tag str "AJ271736,BC025298"
                      },
                      anchor "AJ271736,BC025298"
                    }
                  }
                },
                {
                  type other,
                  heading "Related",
                  source {
                    {
                      src {
                        db "Ensembl",
                        tag str "ENST00000369423"
                      }
                    }
                  }
                },
                {
                  type other,
                  heading "Related",
                  source {
                    {
                      src {
                        db "Vega",
                        tag str "OTTHUMT00000058980"
                      }
                    }
                  }
                }
              }
            }
          },
          comment {
            {
              type genomic,
              heading "RefSeqGene",
              accession "NG_013238",
              version 1,
              source {
                {
                  src {
                    db "Nucleotide",
                    tag id 261823945
                  },
                  anchor "NG_013238"
                }
              },
              seqs {
                int {
                  from 5000,
                  to 18236,
                  strand plus,
                  id gi 261823945
                }
              }
            }
          }
        },
        {
          type comment,
          heading "RefSeqs of Annotated Genomes: Homo sapiens Annotation
 Release 105",
          products {
            {
              type genomic,
              heading "Reference GRCh37.p13 Primary Assembly",
              accession "NC_000023",
              version 10,
              source {
                {
                  src {
                    db "Nucleotide",
                    tag id 224589822
                  }
                }
              },
              seqs {
                int {
                  from 155227245,
                  to 155240481,
                  strand plus,
                  id gi 224589822
                }
              }
            },
            {
              type genomic,
              heading "Alternate HuRef",
              accession "AC_000155",
              version 1,
              source {
                {
                  src {
                    db "Nucleotide",
                    tag id 157734237
                  }
                }
              },
              seqs {
                int {
                  from 143710175,
                  to 143723406,
                  strand plus,
                  id gi 157734237
                }
              }
            },
            {
              type genomic,
              heading "Alternate CHM1_1.1",
              accession "NC_018934",
              version 2,
              source {
                {
                  src {
                    db "Nucleotide",
                    tag id 528476524
                  }
                }
              },
              seqs {
                int {
                  from 155138862,
                  to 155152088,
                  strand plus,
                  id gi 528476524
                }
              }
            }
          }
        }
      }
    },
    {
      type comment,
      heading "Related Sequences",
      products {
        {
          type genomic,
          heading "Genomic",
          accession "ABBA01028635",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 148163528
              },
              anchor "ABBA01028635"
            }
          },
          seqs {
            int {
              from 28050,
              to 41281,
              strand plus,
              id gi 148163528
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "AJ271736",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 8979791
              },
              anchor "AJ271736"
            }
          },
          seqs {
            whole gi 8979791
          },
          products {
            {
              type peptide,
              accession "CAB96817",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 8979793
                  },
                  anchor "CAB96817"
                }
              },
              seqs {
                whole gi 8979793
              }
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "AMYH02040904",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 511784226
              },
              anchor "AMYH02040904"
            }
          },
          seqs {
            int {
              from 17496,
              to 30722,
              strand plus,
              id gi 511784226
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "AY071830",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 18071671
              },
              anchor "AY071830"
            }
          },
          seqs {
            whole gi 18071671
          },
          products {
            {
              type peptide,
              accession "AAL55435",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 18071672
                  },
                  anchor "AAL55435"
                }
              },
              seqs {
                whole gi 18071672
              }
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "CH471247",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 71514074
              },
              anchor "CH471247"
            }
          },
          seqs {
            whole gi 71514074
          },
          products {
            {
              type peptide,
              accession "EAW55884",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 119576288
                  },
                  anchor "EAW55884"
                }
              },
              seqs {
                whole gi 119576288
              }
            },
            {
              type peptide,
              accession "EAW55885",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 119576289
                  },
                  anchor "EAW55885"
                }
              },
              seqs {
                whole gi 119576289
              }
            },
            {
              type peptide,
              accession "EAW55886",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 119576290
                  },
                  anchor "EAW55886"
                }
              },
              seqs {
                whole gi 119576290
              }
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "L39064",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 632992
              },
              anchor "L39064"
            }
          },
          seqs {
            whole gi 632992
          },
          products {
            {
              type peptide,
              accession "AAC29513",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 632993
                  },
                  anchor "AAC29513"
                }
              },
              seqs {
                whole gi 632993
              }
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "S71420",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 551360
              },
              anchor "S71420"
            }
          },
          seqs {
            whole gi 551360
          },
          products {
            {
              type peptide,
              accession "AAD14081",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 4261781
                  },
                  anchor "AAD14081"
                }
              },
              seqs {
                whole gi 4261781
              }
            }
          }
        },
        {
          type mRNA,
          heading "mRNA",
          accession "AK303178",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 194381807
              },
              anchor "AK303178"
            }
          },
          seqs {
            whole gi 194381807
          },
          products {
            {
              type peptide,
              accession "BAG64273",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 194381808
                  },
                  anchor "BAG64273"
                }
              },
              seqs {
                whole gi 194381808
              }
            }
          }
        },
        {
          type mRNA,
          heading "mRNA",
          accession "BC025298",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 22137637
              },
              anchor "BC025298"
            }
          },
          seqs {
            whole gi 22137637
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type mRNA,
          heading "mRNA",
          accession "BC051337",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 30410903
              },
              anchor "BC051337"
            }
          },
          seqs {
            whole gi 30410903
          },
          products {
            {
              type peptide,
              accession "AAH51337",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 30410904
                  },
                  anchor "AAH51337"
                }
              },
              seqs {
                whole gi 30410904
              }
            }
          }
        },
        {
          type mRNA,
          heading "mRNA",
          accession "M84747",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 184508
              },
              anchor "M84747"
            }
          },
          seqs {
            whole gi 184508
          },
          products {
            {
              type peptide,
              accession "AAA58679",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 184509
                  },
                  anchor "AAA58679"
                }
              },
              seqs {
                whole gi 184509
              }
            }
          }
        },
        {
          type mRNA,
          heading "mRNA",
          accession "S71404",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 551356
              },
              anchor "S71404"
            }
          },
          seqs {
            whole gi 551356
          },
          products {
            {
              type peptide,
              accession "AAB30844",
              version 2,
              source {
                {
                  src {
                    db "Protein",
                    tag id 13236921
                  },
                  anchor "AAB30844"
                }
              },
              seqs {
                whole gi 13236921
              }
            }
          }
        },
        {
          type other,
          text "None",
          products {
            {
              type peptide,
              accession "Q01113",
              version 3,
              source {
                {
                  src {
                    db "Protein",
                    tag id 116242526
                  }
                },
                {
                  src {
                    db "UniProtKB/Swiss-Prot",
                    tag str "Q01113"
                  }
                }
              },
              seqs {
                whole gi 116242526
              }
            }
          }
        },
        {
          type other-genetic,
          heading "Synthetic",
          accession "HQ447710",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 312151365
              },
              anchor "HQ447710"
            }
          },
          seqs {
            whole gi 312151365
          },
          products {
            {
              type peptide,
              accession "ADQ32195",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 312151366
                  },
                  anchor "ADQ32195"
                }
              },
              seqs {
                whole gi 312151366
              }
            }
          }
        }
      }
    },
    {
      type comment,
      heading "Additional Links",
      comment {
        {
          type comment,
          source {
            {
              src {
                db "Evidence Viewer",
                tag str "3581"
              },
              anchor "Evidence Viewer",
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti
g=NT_167198.1&gene=IL9R&lid=3581&from=6145183&to=6158419"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "Evidence Viewer",
                tag str "3581"
              },
              anchor "Evidence Viewer",
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti
g=NT_167206.1&gene=IL9R&lid=3581&from=296202&to=309438"
            }
          }
        },
        {
          type comment,
          text "MIM",
          source {
            {
              src {
                db "MIM",
                tag id 300007
              },
              anchor "300007"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "AceView",
                tag id 3581
              },
              anchor "AceView",
              url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=g
eneid&org=9606&l=3581"
            }
          }
        },
        {
          type comment,
          text "IL9R @ LOVD",
          source {
            {
              src {
                db "IL9R",
                tag str "IL9R"
              },
              anchor "IL9R",
              url "http://www.LOVD.nl/IL9R"
            }
          }
        },
        {
          type comment,
          text "UCSC",
          source {
            {
              src {
                db "UCSC",
                tag str "UCSC"
              },
              anchor "UCSC",
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=
NM_176786"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "MGC",
                tag str "BC051337"
              },
              anchor "MGC",
              url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC051337"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "HuGE Navigator",
                tag str "3581"
              },
              anchor "HuGE Navigator",
              url "http://hugenavigator.net/HuGENavigator/huGEPedia.do?firstQu
ery=IL9R&geneID=3581&typeOption=gene&which=2&pubOrderType=pubD&typeSubmit=GO&c
heck=y"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "KEGG",
                tag str "hsa:3581"
              },
              url "http://www.genome.jp/dbget-bin/www_bget?hsa:3581"
            }
          }
        },
        {
          type comment,
          text "UniGene",
          xtra-properties {
            {
              tag "UNIGENE",
              value "Hs.406228"
            }
          },
          source {
            {
              src {
                db "UniGene",
                tag str "Hs.406228"
              },
              anchor "Hs.406228",
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=40
6228"
            }
          }
        }
      }
    },
    {
      type generif,
      text "Our findings suggest that overexpression of IL-9R may contribute
 to the pathogenesis of diffuse large B-cell lymphoma",
      refs {
        pmid 23638223
      },
      create-date std {
        year 2013,
        month 11,
        day 30,
        hour 10,
        minute 1,
        second 0
      },
      update-date std {
        year 2013,
        month 11,
        day 30,
        hour 12,
        minute 36,
        second 0
      }
    },
    {
      type generif,
      text "One of the identified peptide sequences corresponded to a fragment
 of the human interleukin-9 receptor alpha (IL-9Ralpha).",
      refs {
        pmid 22638550
      },
      create-date std {
        year 2013,
        month 5,
        day 11,
        hour 10,
        minute 1,
        second 0
      },
      update-date std {
        year 2013,
        month 5,
        day 11,
        hour 10,
        minute 42,
        second 0
      }
    },
    {
      type generif,
      text "analysis of IL-9 and IL-9 receptor gene polymorphisms and atopic
 dermatitis in a Korean population",
      refs {
        pmid 21371865
      },
      create-date std {
        year 2011,
        month 7,
        day 23,
        hour 10,
        minute 1,
        second 0
      },
      update-date std {
        year 2011,
        month 7,
        day 23,
        hour 10,
        minute 31,
        second 0
      }
    },
    {
      type generif,
      text "There is an association of at least 2 X-chromosomal genes with
 rheumatoid arthritis: TIMP1 and IL9R.",
      refs {
        pmid 19723899
      },
      create-date std {
        year 2010,
        month 2,
        day 15,
        hour 11,
        minute 2,
        second 0
      },
      update-date std {
        year 2010,
        month 2,
        day 15,
        hour 11,
        minute 13,
        second 0
      }
    },
    {
      type generif,
      text "These results reveal a regulatory function for IFN-gamma and IL-10
 on modulating the inducible IL-9Ralpha expression levels on peripheral blood
 neutrophils by T(H)2 cytokines.",
      refs {
        pmid 19401191
      },
      create-date std {
        year 2009,
        month 6,
        day 15,
        hour 11,
        minute 2,
        second 0
      },
      update-date std {
        year 2010,
        month 1,
        day 21,
        hour 0,
        minute 0,
        second 0
      }
    },
    {
      type generif,
      text "IL-9Ralpha and IL-2Rbeta homodimers efficiently mediate
 constitutive activation of ALL-associated JAK1 mutants.",
      refs {
        pmid 19139102
      },
      create-date std {
        year 2009,
        month 5,
        day 9,
        hour 10,
        minute 1,
        second 0
      },
      update-date std {
        year 2010,
        month 1,
        day 21,
        hour 0,
        minute 0,
        second 0
      }
    },
    {
      type generif,
      text "Observational study of gene-disease association and
 gene-environment interaction. (HuGE Navigator)",
      refs {
        pmid 20595916,
        pmid 19258923
      },
      source {
        {
          src {
            db "HuGENet",
            tag str "3581.19258923"
          },
          anchor "HuGENet"
        }
      },
      create-date std {
        year 2009,
        month 3,
        day 25,
        hour 21,
        minute 36,
        second 0
      },
      update-date std {
        year 2009,
        month 3,
        day 25,
        hour 21,
        minute 36,
        second 0
      }
    },
    {
      type generif,
      text "Observational study of gene-disease association. (HuGE Navigator)",
      refs {
        pmid 20673868,
        pmid 20503287,
        pmid 20452482,
        pmid 20424473,
        pmid 19723899,
        pmid 19692168,
        pmid 17703412
      },
      source {
        {
          src {
            db "HuGENet",
            tag str "3581.17703412"
          },
          anchor "HuGENet"
        }
      },
      create-date std {
        year 2009,
        month 3,
        day 25,
        hour 21,
        minute 36,
        second 0
      },
      update-date std {
        year 2009,
        month 3,
        day 25,
        hour 21,
        minute 36,
        second 0
      }
    },
    {
      type generif,
      text "the preformed complexes between gamma c and IL-2Rbeta or
 IL-9Ralpha promote signaling by the JAK3 A572V mutant without ligand,
 identified in several human cancers.",
      refs {
        pmid 18829468
      },
      create-date std {
        year 2009,
        month 1,
        day 31,
        hour 10,
        minute 1,
        second 0
      },
      update-date std {
        year 2010,
        month 1,
        day 21,
        hour 0,
        minute 0,
        second 0
      }
    },
    {
      type generif,
      text "Observational study of gene-disease association and gene-gene
 interaction. (HuGE Navigator)",
      refs {
        pmid 18633131
      },
      source {
        {
          src {
            db "HuGENet",
            tag str "3581.18633131"
          },
          anchor "HuGENet"
        }
      },
      create-date std {
        year 2008,
        month 9,
        day 24,
        hour 21,
        minute 30,
        second 0
      },
      update-date std {
        year 2008,
        month 9,
        day 24,
        hour 21,
        minute 30,
        second 0
      }
    },
    {
      type generif,
      text "primary ATL cells, via IL-9, support the action of
 IL-9Ralpha/CD14-expressing monocytes, which subsequently support the ex vivo
 spontaneous proliferation of malignant T cells",
      refs {
        pmid 18339896
      },
      create-date std {
        year 2008,
        month 7,
        day 12,
        hour 10,
        minute 1,
        second 0
      },
      update-date std {
        year 2010,
        month 1,
        day 21,
        hour 0,
        minute 0,
        second 0
      }
    },
    {
      type generif,
      text "IL-9R alpha was expressed on human tonsillar B cells, with an
 ability to transduce signals through activation of signal transducer and
 activator of transcription 3 and 5.",
      refs {
        pmid 17919707
      },
      create-date std {
        year 2008,
        month 2,
        day 9,
        hour 10,
        minute 1,
        second 0
      },
      update-date std {
        year 2010,
        month 1,
        day 21,
        hour 0,
        minute 0,
        second 0
      }
    },
    {
      type generif,
      text "Human bronchial epithelium expresses interleukin-9 receptors.",
      refs {
        pmid 11868823
      },
      create-date std {
        year 2007,
        month 8,
        day 25,
        hour 10,
        minute 2,
        second 0
      },
      update-date std {
        year 2010,
        month 1,
        day 21,
        hour 0,
        minute 0,
        second 0
      }
    },
    {
      type generif,
      text "Variants in the IL4RA gene alone may not exert any major influence
 on susceptibility to asthma-related diseases in childhood, but in combination
 with other genes, such as IL9R, IL4RA may be an important gene for disease
 susceptibility",
      refs {
        pmid 17083349
      },
      create-date std {
        year 2007,
        month 8,
        day 25,
        hour 10,
        minute 2,
        second 0
      },
      update-date std {
        year 2010,
        month 1,
        day 21,
        hour 0,
        minute 0,
        second 0
      }
    },
    {
      type generif,
      text "IL-9 and its receptor have roles in cell growth and malignant
 transformation of lymphoid cells associated with constitutive activation of
 the Jak/STAT pathway [review]",
      refs {
        pmid 15621723
      },
      create-date std {
        year 2007,
        month 8,
        day 25,
        hour 10,
        minute 2,
        second 0
      },
      update-date std {
        year 2010,
        month 1,
        day 21,
        hour 0,
        minute 0,
        second 0
      }
    },
    {
      type generif,
      text "variations in the IL9R gene may influence susceptibility to
 childhood wheezing and atopy, and data support the notion that different
 haplotypes may have sex specific influences",
      refs {
        pmid 15591265
      },
      create-date std {
        year 2007,
        month 8,
        day 25,
        hour 10,
        minute 2,
        second 0
      },
      update-date std {
        year 2010,
        month 1,
        day 21,
        hour 0,
        minute 0,
        second 0
      }
    },
    {
      type generif,
      heading "Interactions",
      comment {
        {
          type generif,
          text "Two-hybrid",
          refs {
            pmid 21988832
          },
          source {
            {
              src {
                db "BioGRID",
                tag id 109795
              },
              anchor "BioGRID"
            }
          },
          comment {
            {
              type other,
              source {
                {
                  src {
                    db "BioGRID",
                    tag id 109795
                  }
                }
              }
            },
            {
              type other,
              source {
                {
                  src {
                    db "GeneID",
                    tag id 8738
                  },
                  anchor "CRADD"
                },
                {
                  src {
                    db "BioGRID",
                    tag id 114275
                  }
                }
              }
            }
          },
          create-date std {
            year 2013,
            month 4,
            day 7,
            hour 10,
            minute 36,
            second 0
          },
          update-date std {
            year 2013,
            month 12,
            day 8,
            hour 11,
            minute 11,
            second 0
          }
        },
        {
          type generif,
          text "Affinity Capture-Western; Two-hybrid",
          refs {
            pmid 10486269
          },
          source {
            {
              src {
                db "BioGRID",
                tag id 109795
              },
              anchor "BioGRID"
            }
          },
          comment {
            {
              type other,
              source {
                {
                  src {
                    db "BioGRID",
                    tag id 109795
                  }
                }
              }
            },
            {
              type other,
              source {
                {
                  src {
                    db "GeneID",
                    tag id 10524
                  },
                  anchor "KAT5"
                },
                {
                  src {
                    db "BioGRID",
                    tag id 115779
                  }
                }
              }
            }
          },
          create-date std {
            year 2012,
            month 7,
            day 8,
            hour 10,
            minute 24,
            second 0
          },
          update-date std {
            year 2013,
            month 12,
            day 8,
            hour 11,
            minute 11,
            second 0
          }
        },
        {
          type generif,
          refs {
            pmid 10486269
          },
          source {
            {
              src {
                db "HPRD",
                tag str "02052"
              },
              anchor "HPRD"
            }
          },
          comment {
            {
              type peptide,
              source {
                {
                  src {
                    db "Protein",
                    tag id 116242526
                  },
                  anchor "Q01113"
                }
              }
            },
            {
              type peptide,
              source {
                {
                  src {
                    db "GeneID",
                    tag id 10524
                  },
                  anchor "KAT5"
                },
                {
                  src {
                    db "Protein",
                    tag id 30923328
                  },
                  anchor "Q92993"
                }
              }
            }
          },
          create-date std {
            year 2009,
            month 12,
            day 17,
            hour 15,
            minute 28,
            second 0
          },
          update-date std {
            year 2009,
            month 12,
            day 17,
            hour 15,
            minute 31,
            second 0
          }
        },
        {
          type generif,
          refs {
            pmid 10642536
          },
          source {
            {
              src {
                db "HPRD",
                tag str "02052"
              },
              anchor "HPRD"
            }
          },
          comment {
            {
              type peptide,
              source {
                {
                  src {
                    db "Protein",
                    tag id 116242526
                  },
                  anchor "Q01113"
                }
              }
            },
            {
              type peptide,
              source {
                {
                  src {
                    db "GeneID",
                    tag id 7534
                  },
                  anchor "YWHAZ"
                },
                {
                  src {
                    db "Protein",
                    tag id 52000887
                  },
                  anchor "P63104"
                }
              }
            }
          },
          create-date std {
            year 2009,
            month 12,
            day 17,
            hour 15,
            minute 28,
            second 0
          },
          update-date std {
            year 2009,
            month 12,
            day 17,
            hour 15,
            minute 31,
            second 0
          }
        },
        {
          type generif,
          refs {
            pmid 11418623
          },
          source {
            {
              src {
                db "HPRD",
                tag str "02052"
              },
              anchor "HPRD"
            }
          },
          comment {
            {
              type peptide,
              source {
                {
                  src {
                    db "Protein",
                    tag id 116242526
                  },
                  anchor "Q01113"
                }
              }
            },
            {
              type peptide,
              source {
                {
                  src {
                    db "GeneID",
                    tag id 3561
                  },
                  anchor "IL2RG"
                },
                {
                  src {
                    db "Protein",
                    tag id 400048
                  },
                  anchor "P31785"
                }
              }
            }
          },
          create-date std {
            year 2009,
            month 12,
            day 17,
            hour 15,
            minute 28,
            second 0
          },
          update-date std {
            year 2009,
            month 12,
            day 17,
            hour 15,
            minute 31,
            second 0
          }
        },
        {
          type generif,
          refs {
            pmid 8756628
          },
          source {
            {
              src {
                db "HPRD",
                tag str "02052"
              },
              anchor "HPRD"
            }
          },
          comment {
            {
              type peptide,
              source {
                {
                  src {
                    db "Protein",
                    tag id 116242526
                  },
                  anchor "Q01113"
                }
              }
            },
            {
              type peptide,
              source {
                {
                  src {
                    db "GeneID",
                    tag id 3716
                  },
                  anchor "JAK1"
                },
                {
                  src {
                    db "Protein",
                    tag id 215274013
                  },
                  anchor "P23458"
                }
              }
            }
          },
          create-date std {
            year 2009,
            month 12,
            day 17,
            hour 15,
            minute 28,
            second 0
          },
          update-date std {
            year 2009,
            month 12,
            day 17,
            hour 15,
            minute 31,
            second 0
          }
        },
        {
          type generif,
          refs {
            pmid 11588013
          },
          source {
            {
              src {
                db "HPRD",
                tag str "02052"
              },
              anchor "HPRD"
            }
          },
          comment {
            {
              type peptide,
              source {
                {
                  src {
                    db "Protein",
                    tag id 116242526
                  },
                  anchor "Q01113"
                }
              }
            },
            {
              type peptide,
              source {
                {
                  src {
                    db "GeneID",
                    tag id 3578
                  },
                  anchor "IL9"
                },
                {
                  src {
                    db "Protein",
                    tag id 124362
                  },
                  anchor "P15248"
                }
              }
            }
          },
          create-date std {
            year 2009,
            month 12,
            day 17,
            hour 15,
            minute 28,
            second 0
          },
          update-date std {
            year 2009,
            month 12,
            day 17,
            hour 15,
            minute 31,
            second 0
          }
        },
        {
          type generif,
          text "Affinity Capture-Western; Two-hybrid",
          refs {
            pmid 10642536
          },
          source {
            {
              src {
                db "BioGRID",
                tag id 109795
              },
              anchor "BioGRID"
            }
          },
          comment {
            {
              type other,
              source {
                {
                  src {
                    db "BioGRID",
                    tag id 109795
                  }
                }
              }
            },
            {
              type other,
              source {
                {
                  src {
                    db "GeneID",
                    tag id 7534
                  },
                  anchor "YWHAZ"
                },
                {
                  src {
                    db "BioGRID",
                    tag id 113366
                  }
                }
              }
            }
          },
          create-date std {
            year 2008,
            month 12,
            day 23,
            hour 9,
            minute 6,
            second 0
          },
          update-date std {
            year 2013,
            month 12,
            day 8,
            hour 11,
            minute 11,
            second 0
          }
        },
        {
          type generif,
          text "Affinity Capture-Western",
          refs {
            pmid 8756628
          },
          source {
            {
              src {
                db "BioGRID",
                tag id 109795
              },
              anchor "BioGRID"
            }
          },
          comment {
            {
              type other,
              source {
                {
                  src {
                    db "BioGRID",
                    tag id 109795
                  }
                }
              }
            },
            {
              type other,
              source {
                {
                  src {
                    db "GeneID",
                    tag id 3716
                  },
                  anchor "JAK1"
                },
                {
                  src {
                    db "BioGRID",
                    tag id 109919
                  }
                }
              }
            }
          },
          create-date std {
            year 2008,
            month 12,
            day 23,
            hour 9,
            minute 6,
            second 0
          },
          update-date std {
            year 2013,
            month 12,
            day 8,
            hour 11,
            minute 11,
            second 0
          }
        }
      }
    },
    {
      type comment,
      heading "Pathways",
      comment {
        {
          type comment,
          text "KEGG pathway: Cytokine-cytokine receptor interaction",
          source {
            {
              src {
                db "KEGG pathway",
                tag str "04060"
              },
              anchor "04060",
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa04060+3581"
            }
          }
        },
        {
          type comment,
          text "KEGG pathway: Hematopoietic cell lineage",
          source {
            {
              src {
                db "KEGG pathway",
                tag str "04640"
              },
              anchor "04640",
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa04640+3581"
            }
          }
        },
        {
          type comment,
          text "KEGG pathway: Jak-STAT signaling pathway",
          source {
            {
              src {
                db "KEGG pathway",
                tag str "04630"
              },
              anchor "04630",
              url "http://www.genome.jp/dbget-bin/show_pathway?hsa04630+3581"
            }
          }
        }
      }
    },
    {
      type comment,
      heading "Markers (Sequence Tagged Sites/STS)",
      comment {
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 85806
              },
              anchor "RH69191",
              post-text "(e-PCR)"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 296037
              },
              anchor "ECD15020",
              post-text "(e-PCR)"
            }
          }
        }
      }
    },
    {
      type comment,
      heading "Gene Location History",
      comment {
        {
          type comment,
          heading "Homo sapiens Annotation Release 105",
          comment {
            {
              type assembly,
              heading "GRCh37.p13",
              label "Reference",
              accession "GCF_000001405",
              version 25,
              comment {
                {
                  type assembly-unit,
                  heading "Primary Assembly",
                  accession "GCF_000001305",
                  version 13,
                  comment {
                    {
                      type genomic,
                      label "chromosome Chromosome X",
                      accession "NC_000023",
                      version 10,
                      seqs {
                        int {
                          from 155227245,
                          to 155240481,
                          strand plus,
                          id gi 224589822
                        }
                      }
                    },
                    {
                      type genomic,
                      label "chromosome Chromosome Y",
                      accession "NC_000024",
                      version 9,
                      seqs {
                        int {
                          from 59330251,
                          to 59343487,
                          strand plus,
                          id gi 224589823
                        }
                      }
                    }
                  }
                }
              }
            },
            {
              type assembly,
              heading "HuRef",
              label "Alternate",
              accession "GCF_000002125",
              version 1,
              comment {
                {
                  type genomic,
                  label "chromosome Chromosome X",
                  accession "AC_000155",
                  version 1,
                  seqs {
                    int {
                      from 143710175,
                      to 143723406,
                      strand plus,
                      id gi 157734237
                    }
                  }
                }
              }
            },
            {
              type assembly,
              heading "CHM1_1.1",
              label "Alternate",
              accession "GCF_000306695",
              version 2,
              comment {
                {
                  type genomic,
                  label "chromosome Chromosome X",
                  accession "NC_018934",
                  version 2,
                  seqs {
                    int {
                      from 155138862,
                      to 155152088,
                      strand plus,
                      id gi 528476524
                    }
                  }
                }
              }
            }
          }
        },
        {
          type comment,
          heading "Homo sapiens Annotation Release 104",
          comment {
            {
              type assembly,
              heading "GRCh37.p10",
              label "Reference",
              accession "GCF_000001405",
              version 22,
              comment {
                {
                  type assembly-unit,
                  heading "Primary Assembly",
                  accession "GCF_000001305",
                  version 13,
                  comment {
                    {
                      type genomic,
                      label "chromosome Chromosome X",
                      accession "NC_000023",
                      version 10,
                      seqs {
                        int {
                          from 155227245,
                          to 155240481,
                          strand plus,
                          id gi 224589822
                        }
                      }
                    },
                    {
                      type genomic,
                      label "chromosome Chromosome Y",
                      accession "NC_000024",
                      version 9,
                      seqs {
                        int {
                          from 59330251,
                          to 59343487,
                          strand plus,
                          id gi 224589823
                        }
                      }
                    }
                  }
                }
              }
            },
            {
              type assembly,
              heading "HuRef",
              label "Alternate",
              accession "GCF_000002125",
              version 1,
              comment {
                {
                  type genomic,
                  label "chromosome Chromosome X",
                  accession "AC_000155",
                  version 1,
                  seqs {
                    int {
                      from 143710175,
                      to 143723406,
                      strand plus,
                      id gi 157734237
                    }
                  }
                }
              }
            },
            {
              type assembly,
              heading "CHM1_1.0",
              label "Alternate",
              accession "GCF_000306695",
              version 1,
              comment {
                {
                  type genomic,
                  label "chromosome Chromosome X",
                  accession "NC_018934",
                  version 1,
                  seqs {
                    int {
                      from 155094217,
                      to 155107460,
                      strand plus,
                      id gi 409253441
                    }
                  }
                }
              }
            }
          }
        },
        {
          type comment,
          heading "Build 37.3",
          comment {
            {
              type assembly,
              heading "GRCh37.p5",
              label "Reference",
              accession "GCF_000001405",
              version 17,
              comment {
                {
                  type assembly-unit,
                  heading "Primary Assembly",
                  accession "GCF_000001305",
                  version 13,
                  comment {
                    {
                      type genomic,
                      label "chromosome Chromosome X",
                      accession "NC_000023",
                      version 10,
                      seqs {
                        int {
                          from 155227245,
                          to 155240481,
                          strand plus,
                          id gi 224589822
                        }
                      }
                    },
                    {
                      type genomic,
                      label "chromosome Chromosome Y",
                      accession "NC_000024",
                      version 9,
                      seqs {
                        int {
                          from 59330251,
                          to 59343487,
                          strand plus,
                          id gi 224589823
                        }
                      }
                    }
                  }
                }
              }
            },
            {
              type assembly,
              heading "HuRef",
              label "Alternate",
              accession "GCF_000002125",
              version 1,
              comment {
                {
                  type assembly-unit,
                  heading "Primary Assembly",
                  accession "GCF_000000025",
                  version 1,
                  comment {
                    {
                      type genomic,
                      label "chromosome Chromosome X",
                      accession "AC_000155",
                      version 1,
                      seqs {
                        int {
                          from 143710175,
                          to 143723406,
                          strand plus,
                          id gi 157734237
                        }
                      }
                    }
                  }
                }
              }
            }
          }
        }
      }
    }
  },
  unique-keys {
    {
      db "HGNC",
      tag id 6030
    },
    {
      db "LocusID",
      tag id 3581
    },
    {
      db "MIM",
      tag id 300007
    }
  },
  xtra-index-terms {
    "LOC3581"
  }
}
Entrezgene ::= {
  track-info {
    geneid 56111,
    status live,
    create-date std {
      year 2000,
      month 7,
      day 13
    },
    update-date std {
      year 2013,
      month 12,
      day 3,
      hour 17,
      minute 40,
      second 0
    }
  },
  type protein-coding,
  source {
    genome genomic,
    origin natural,
    org {
      taxname "Homo sapiens",
      common "human",
      db {
        {
          db "taxon",
          tag id 9606
        }
      },
      syn {
        "man"
      },
      orgname {
        name binomial {
          genus "Homo",
          species "sapiens"
        },
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
 Catarrhini; Hominidae; Homo",
        gcode 1,
        mgcode 2,
        div "PRI",
        pgcode 0
      }
    },
    subtype {
      {
        subtype chromosome,
        name "5"
      }
    }
  },
  gene {
    locus "PCDHGA4",
    desc "protocadherin gamma subfamily A, 4",
    maploc "5q31",
    db {
      {
        db "HGNC",
        tag id 8702
      },
      {
        db "Ensembl",
        tag str "ENSG00000262576"
      },
      {
        db "HPRD",
        tag str "09381"
      },
      {
        db "MIM",
        tag id 606291
      },
      {
        db "Vega",
        tag str "OTTHUMG00000177593"
      }
    },
    syn {
      "PCDH-GAMMA-A4"
    }
  },
  prot {
    name {
      "protocadherin gamma-A4"
    },
    desc "protocadherin gamma-A4"
  },
  summary "This gene is a member of the protocadherin gamma gene cluster, one
 of three related clusters tandemly linked on chromosome five. These gene
 clusters have an immunoglobulin-like organization, suggesting that a novel
 mechanism may be involved in their regulation and expression. The gamma gene
 cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12
 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly
 related subfamily C contains 3 genes. The tandem array of 22 large, variable
 region exons are followed by a constant region, containing 3 exons shared by
 all genes in the cluster. Each variable region exon encodes the extracellular
 region, which includes 6 cadherin ectodomains and a transmembrane region. The
 constant region exons encode the common cytoplasmic region. These neural
 cadherin-like cell adhesion proteins most likely play a critical role in the
 establishment and function of specific cell-cell connections in the brain.
 Alternative splicing has been described for the gamma cluster genes.
 [provided by RefSeq, Jul 2008]",
  location {
    {
      display-str "5q31",
      method map-type cyto
    }
  },
  gene-source {
    src "LocusLink",
    src-int 56111,
    src-str2 "56111"
  },
  locus {
    {
      type genomic,
      heading "Reference GRCh37.p13 Primary Assembly",
      label "chromosome 5 reference GRCh37.p13 Primary Assembly",
      accession "NC_000005",
      version 9,
      seqs {
        int {
          from 140734767,
          to 140892545,
          strand plus,
          id gi 224589817
        }
      },
      products {
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 1",
          accession "NM_018917",
          version 2,
          genomic-coords {
            mix {
              int {
                from 140734767,
                to 140737187,
                strand plus,
                id gi 224589817
              },
              int {
                from 140874373,
                to 140874431,
                strand plus,
                id gi 224589817
              },
              int {
                from 140884959,
                to 140885047,
                strand plus,
                id gi 224589817
              },
              int {
                from 140890513,
                to 140892545,
                strand plus,
                id gi 224589817
              }
            }
          },
          seqs {
            whole gi 14196466
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 1 precursor",
              accession "NP_061740",
              version 1,
              source {
                {
                  src {
                    db "CCDS",
                    tag str "CCDS58979.1"
                  },
                  anchor "CCDS58979.1"
                }
              },
              genomic-coords {
                mix {
                  int {
                    from 140734767,
                    to 140737187,
                    strand plus,
                    id gi 224589817
                  },
                  int {
                    from 140874373,
                    to 140874431,
                    strand plus,
                    id gi 224589817
                  },
                  int {
                    from 140884959,
                    to 140885047,
                    strand plus,
                    id gi 224589817
                  },
                  int {
                    from 140890513,
                    to 140890739,
                    strand plus,
                    id gi 224589817
                  }
                }
              },
              seqs {
                whole gi 11056026
              }
            }
          }
        },
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 2",
          accession "NM_032053",
          version 1,
          genomic-coords {
            int {
              from 140734767,
              to 140737295,
              strand plus,
              id gi 224589817
            }
          },
          seqs {
            whole gi 14196467
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 2",
              accession "NP_114442",
              version 1,
              genomic-coords {
                int {
                  from 140734767,
                  to 140737229,
                  strand plus,
                  id gi 224589817
                }
              },
              seqs {
                whole gi 14196468
              }
            }
          }
        }
      }
    },
    {
      type genomic,
      heading "Reference assembly",
      label "genomic region",
      accession "NG_000012",
      version 2,
      seqs {
        int {
          from 65221,
          to 223175,
          strand plus,
          id gi 50284693
        }
      },
      products {
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 1",
          accession "NM_018917",
          version 3,
          genomic-coords {
            mix {
              int {
                from 65221,
                to 67817,
                strand plus,
                id gi 50284693
              },
              int {
                from 205003,
                to 205061,
                strand plus,
                id gi 50284693
              },
              int {
                from 215589,
                to 215677,
                strand plus,
                id gi 50284693
              },
              int {
                from 221143,
                to 223175,
                strand plus,
                id gi 50284693
              }
            }
          },
          seqs {
            whole gi 523567547
          }
        },
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 2",
          accession "NM_032053",
          version 2,
          genomic-coords {
            int {
              from 65221,
              to 67926,
              strand plus,
              id gi 50284693
            }
          },
          seqs {
            whole gi 523567549
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 1 precursor",
              accession "NP_061740",
              version 2,
              source {
                {
                  src {
                    db "CCDS",
                    tag str "CCDS58979.1"
                  },
                  anchor "CCDS58979.1"
                }
              },
              genomic-coords {
                mix {
                  int {
                    from 65304,
                    to 67817,
                    strand plus,
                    id gi 50284693
                  },
                  int {
                    from 205003,
                    to 205061,
                    strand plus,
                    id gi 50284693
                  },
                  int {
                    from 215589,
                    to 215677,
                    strand plus,
                    id gi 50284693
                  },
                  int {
                    from 221143,
                    to 221369,
                    strand plus,
                    id gi 50284693
                  }
                }
              },
              seqs {
                whole gi 523567548
              }
            },
            {
              type peptide,
              heading "Reference",
              label "isoform 2 precursor",
              accession "NP_114442",
              version 2,
              genomic-coords {
                int {
                  from 65304,
                  to 67859,
                  strand plus,
                  id gi 50284693
                }
              },
              seqs {
                whole gi 523567550
              }
            }
          }
        }
      }
    },
    {
      type genomic,
      heading "Alternate CHM1_1.1",
      label "chromosome 5 alternate CHM1_1.1",
      accession "NC_018916",
      version 2,
      seqs {
        int {
          from 140167974,
          to 140325822,
          strand plus,
          id gi 528476642
        }
      },
      products {
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 1",
          accession "NM_018917",
          version 2,
          genomic-coords {
            mix {
              int {
                from 140167974,
                to 140170394,
                strand plus,
                id gi 528476642
              },
              int {
                from 140307638,
                to 140307696,
                strand plus,
                id gi 528476642
              },
              int {
                from 140318237,
                to 140318325,
                strand plus,
                id gi 528476642
              },
              int {
                from 140323790,
                to 140325822,
                strand plus,
                id gi 528476642
              }
            }
          },
          seqs {
            whole gi 14196466
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 1 precursor",
              accession "NP_061740",
              version 1,
              genomic-coords {
                mix {
                  int {
                    from 140167974,
                    to 140170394,
                    strand plus,
                    id gi 528476642
                  },
                  int {
                    from 140307638,
                    to 140307696,
                    strand plus,
                    id gi 528476642
                  },
                  int {
                    from 140318237,
                    to 140318325,
                    strand plus,
                    id gi 528476642
                  },
                  int {
                    from 140323790,
                    to 140324016,
                    strand plus,
                    id gi 528476642
                  }
                }
              },
              seqs {
                whole gi 11056026
              }
            }
          }
        },
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 2",
          accession "NM_032053",
          version 1,
          genomic-coords {
            int {
              from 140167974,
              to 140170502,
              strand plus,
              id gi 528476642
            }
          },
          seqs {
            whole gi 14196467
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 2",
              accession "NP_114442",
              version 1,
              genomic-coords {
                int {
                  from 140167974,
                  to 140170436,
                  strand plus,
                  id gi 528476642
                }
              },
              seqs {
                whole gi 14196468
              }
            }
          }
        }
      }
    },
    {
      type genomic,
      heading "Alternate HuRef",
      label "chromosome 5 alternate HuRef",
      accession "AC_000137",
      version 1,
      seqs {
        int {
          from 135879842,
          to 136037385,
          strand plus,
          id gi 157734151
        }
      },
      products {
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 1",
          accession "NM_018917",
          version 2,
          genomic-coords {
            mix {
              int {
                from 135879842,
                to 135882262,
                strand plus,
                id gi 157734151
              },
              int {
                from 136019211,
                to 136019269,
                strand plus,
                id gi 157734151
              },
              int {
                from 136029799,
                to 136029887,
                strand plus,
                id gi 157734151
              },
              int {
                from 136035353,
                to 136037385,
                strand plus,
                id gi 157734151
              }
            }
          },
          seqs {
            whole gi 14196466
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 1 precursor",
              accession "NP_061740",
              version 1,
              genomic-coords {
                mix {
                  int {
                    from 135879842,
                    to 135882262,
                    strand plus,
                    id gi 157734151
                  },
                  int {
                    from 136019211,
                    to 136019269,
                    strand plus,
                    id gi 157734151
                  },
                  int {
                    from 136029799,
                    to 136029887,
                    strand plus,
                    id gi 157734151
                  },
                  int {
                    from 136035353,
                    to 136035579,
                    strand plus,
                    id gi 157734151
                  }
                }
              },
              seqs {
                whole gi 11056026
              }
            }
          }
        },
        {
          type mRNA,
          heading "Reference",
          label "transcript variant 2",
          accession "NM_032053",
          version 1,
          genomic-coords {
            int {
              from 135879842,
              to 135882370,
              strand plus,
              id gi 157734151
            }
          },
          seqs {
            whole gi 14196467
          },
          products {
            {
              type peptide,
              heading "Reference",
              label "isoform 2",
              accession "NP_114442",
              version 1,
              genomic-coords {
                int {
                  from 135879842,
                  to 135882304,
                  strand plus,
                  id gi 157734151
                }
              },
              seqs {
                whole gi 14196468
              }
            }
          }
        }
      }
    }
  },
  properties {
    {
      type comment,
      label "Nomenclature",
      source {
        {
          anchor "HUGO Gene Nomenclature Committee"
        }
      },
      properties {
        {
          type property,
          label "Official Symbol",
          text "PCDHGA4"
        },
        {
          type property,
          label "Official Full Name",
          text "protocadherin gamma subfamily A, 4"
        }
      }
    },
    {
      type comment,
      heading "GeneOntology",
      source {
        {
          pre-text "Provided by",
          anchor "GOA",
          url "http://www.ebi.ac.uk/GOA/"
        }
      },
      comment {
        {
          type comment,
          label "Function",
          comment {
            {
              type comment,
              source {
                {
                  src {
                    db "GO",
                    tag id 5509
                  },
                  anchor "calcium ion binding",
                  post-text "evidence: IEA"
                }
              }
            }
          }
        },
        {
          type comment,
          label "Process",
          comment {
            {
              type comment,
              source {
                {
                  src {
                    db "GO",
                    tag id 7156
                  },
                  anchor "homophilic cell adhesion",
                  post-text "evidence: IEA"
                }
              }
            }
          }
        },
        {
          type comment,
          label "Component",
          comment {
            {
              type comment,
              source {
                {
                  src {
                    db "GO",
                    tag id 16021
                  },
                  anchor "integral to membrane",
                  post-text "evidence: IEA"
                }
              }
            },
            {
              type comment,
              source {
                {
                  src {
                    db "GO",
                    tag id 5886
                  },
                  anchor "plasma membrane",
                  post-text "evidence: IEA"
                }
              }
            }
          }
        }
      }
    }
  },
  homology {
    {
      type comment,
      heading "Mouse, Rat",
      source {
        {
          src {
            db "HomoloGene",
            tag id 81866
          },
          anchor "Map Viewer",
          url "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=5&M
APS=genes-r-org/rat-chr/human%3A5,genes-r-org/mouse-chr/human%3A5,genes-r-org/
human-chr5&query=e%3A56111[egene_id]+AND+gene[obj_type]&QSTR=pcdhga4&cmd=focus
&fill=10"
        }
      }
    }
  },
  comments {
    {
      type comment,
      heading "RefSeq Status",
      label "REVIEWED"
    },
    {
      type comment,
      refs {
        pmid 16344560,
        pmid 11230163,
        pmid 10835267,
        pmid 10817752,
        pmid 10716726,
        pmid 10380929
      }
    },
    {
      type comment,
      heading "NCBI Reference Sequences (RefSeq)",
      comment {
        {
          type comment,
          heading "RefSeqs maintained independently of Annotated Genomes",
          products {
            {
              type mRNA,
              heading "mRNA Sequence",
              accession "NM_018917",
              version 3,
              source {
                {
                  src {
                    db "Nucleotide",
                    tag id 523567547
                  },
                  anchor "NM_018917"
                }
              },
              seqs {
                whole gi 523567547
              },
              products {
                {
                  type peptide,
                  heading "Product",
                  accession "NP_061740",
                  version 2,
                  source {
                    {
                      src {
                        db "Protein",
                        tag id 523567548
                      },
                      anchor "NP_061740",
                      post-text "protocadherin gamma-A4 isoform 1 precursor"
                    }
                  },
                  seqs {
                    whole gi 523567548
                  },
                  comment {
                    {
                      type other,
                      heading "Conserved Domains",
                      source {
                        {
                          pre-text "(6)",
                          anchor "summary"
                        }
                      },
                      comment {
                        {
                          type other,
                          source {
                            {
                              src {
                                db "CDD",
                                tag id 206637
                              },
                              anchor "cd11304: Cadherin_repeat; Cadherin
 tandem repeat domain"
                            }
                          },
                          comment {
                            {
                              type other,
                              text "Location: 277 - 374  Blast Score: 278"
                            },
                            {
                              type other,
                              text "Location: 393 - 479  Blast Score: 236"
                            },
                            {
                              type other,
                              text "Location: 170 - 269  Blast Score: 227"
                            },
                            {
                              type other,
                              text "Location: 610 - 697  Blast Score: 223"
                            },
                            {
                              type other,
                              text "Location: 487 - 589  Blast Score: 221"
                            },
                            {
                              type other,
                              text "Location: 64 - 160  Blast Score: 123"
                            }
                          }
                        }
                      }
                    },
                    {
                      type other,
                      heading "Related",
                      source {
                        {
                          src {
                            db "Ensembl",
                            tag str "ENSP00000458570"
                          }
                        }
                      }
                    },
                    {
                      type other,
                      heading "UniProtKB",
                      source {
                      },
                      comment {
                        {
                          type other,
                          source {
                            {
                              src {
                                db "UniProtKB/Swiss-Prot",
                                tag str "Q9Y5G9"
                              },
                              anchor "Q9Y5G9"
                            }
                          }
                        }
                      }
                    },
                    {
                      type other,
                      heading "Consensus CDS (CCDS)",
                      source {
                        {
                          src {
                            db "CCDS",
                            tag str "CCDS58979.1"
                          },
                          anchor "CCDS58979.1"
                        }
                      },
                      comment {
                        {
                          type other,
                          heading "CCDS Note",
                          text "The coding region has been updated to extend
 the N-terminus to one that is more supported by the available transcript and
 primate conservation data. "
                        }
                      }
                    },
                    {
                      type other,
                      heading "Related",
                      source {
                        {
                          src {
                            db "Vega",
                            tag str "OTTHUMP00000257173"
                          }
                        }
                      }
                    }
                  }
                }
              },
              comment {
                {
                  type comment,
                  label "RefSeq Status",
                  text "REVIEWED"
                },
                {
                  type comment,
                  heading "Transcriptional Variant",
                  comment {
                    {
                      type comment,
                      text "Transcript Variant: This variant (1) includes the
 constant region exons and encodes the longest isoform (1)."
                    }
                  }
                },
                {
                  type other,
                  heading "Source Sequence",
                  source {
                    {
                      src {
                        db "Nucleotide",
                        tag str "AF152324,DA392480"
                      },
                      anchor "AF152324,DA392480"
                    }
                  }
                },
                {
                  type other,
                  heading "Related",
                  source {
                    {
                      src {
                        db "Ensembl",
                        tag str "ENST00000571252"
                      }
                    }
                  }
                },
                {
                  type other,
                  heading "Related",
                  source {
                    {
                      src {
                        db "Vega",
                        tag str "OTTHUMT00000437959"
                      }
                    }
                  }
                }
              }
            },
            {
              type mRNA,
              heading "mRNA Sequence",
              accession "NM_032053",
              version 2,
              source {
                {
                  src {
                    db "Nucleotide",
                    tag id 523567549
                  },
                  anchor "NM_032053"
                }
              },
              seqs {
                whole gi 523567549
              },
              products {
                {
                  type peptide,
                  heading "Product",
                  accession "NP_114442",
                  version 2,
                  source {
                    {
                      src {
                        db "Protein",
                        tag id 523567550
                      },
                      anchor "NP_114442",
                      post-text "protocadherin gamma-A4 isoform 2 precursor"
                    }
                  },
                  seqs {
                    whole gi 523567550
                  },
                  comment {
                    {
                      type other,
                      heading "Conserved Domains",
                      source {
                        {
                          pre-text "(6)",
                          anchor "summary"
                        }
                      },
                      comment {
                        {
                          type other,
                          source {
                            {
                              src {
                                db "CDD",
                                tag id 206637
                              },
                              anchor "cd11304: Cadherin_repeat; Cadherin
 tandem repeat domain"
                            }
                          },
                          comment {
                            {
                              type other,
                              text "Location: 277 - 374  Blast Score: 275"
                            },
                            {
                              type other,
                              text "Location: 393 - 479  Blast Score: 233"
                            },
                            {
                              type other,
                              text "Location: 170 - 269  Blast Score: 224"
                            },
                            {
                              type other,
                              text "Location: 610 - 697  Blast Score: 220"
                            },
                            {
                              type other,
                              text "Location: 487 - 589  Blast Score: 218"
                            },
                            {
                              type other,
                              text "Location: 64 - 160  Blast Score: 121"
                            }
                          }
                        }
                      }
                    },
                    {
                      type other,
                      heading "UniProtKB",
                      source {
                      },
                      comment {
                        {
                          type other,
                          source {
                            {
                              src {
                                db "UniProtKB/Swiss-Prot",
                                tag str "Q9Y5G9"
                              },
                              anchor "Q9Y5G9"
                            }
                          }
                        }
                      }
                    }
                  }
                }
              },
              comment {
                {
                  type comment,
                  label "RefSeq Status",
                  text "REVIEWED"
                },
                {
                  type comment,
                  heading "Transcriptional Variant",
                  comment {
                    {
                      type comment,
                      text "Transcript Variant: This variant (2) utilizes the
 large, first exon then continues into the downstream intron 1 sequence before
 terminating. This one-exon transcript encodes the shorter isoform (2)."
                    }
                  }
                },
                {
                  type other,
                  heading "Source Sequence",
                  source {
                    {
                      src {
                        db "Nucleotide",
                        tag str "AF152511,BX100615,DA392480"
                      },
                      anchor "AF152511,BX100615,DA392480"
                    }
                  }
                }
              }
            }
          },
          comment {
            {
              type genomic,
              heading "Reference",
              accession "NG_000012",
              version 2,
              source {
                {
                  src {
                    db "Nucleotide",
                    tag id 50284693
                  },
                  anchor "NG_000012"
                }
              },
              seqs {
                int {
                  from 65221,
                  to 223175,
                  strand plus,
                  id gi 50284693
                }
              }
            }
          }
        },
        {
          type comment,
          heading "RefSeqs of Annotated Genomes: Homo sapiens Annotation
 Release 105",
          products {
            {
              type genomic,
              heading "Reference GRCh37.p13 Primary Assembly",
              accession "NC_000005",
              version 9,
              source {
                {
                  src {
                    db "Nucleotide",
                    tag id 224589817
                  }
                }
              },
              seqs {
                int {
                  from 140734767,
                  to 140892545,
                  strand plus,
                  id gi 224589817
                }
              }
            },
            {
              type genomic,
              heading "Alternate HuRef",
              accession "AC_000137",
              version 1,
              source {
                {
                  src {
                    db "Nucleotide",
                    tag id 157734151
                  }
                }
              },
              seqs {
                int {
                  from 135879842,
                  to 136037385,
                  strand plus,
                  id gi 157734151
                }
              }
            },
            {
              type genomic,
              heading "Alternate CHM1_1.1",
              accession "NC_018916",
              version 2,
              source {
                {
                  src {
                    db "Nucleotide",
                    tag id 528476642
                  }
                }
              },
              seqs {
                int {
                  from 140167974,
                  to 140325822,
                  strand plus,
                  id gi 528476642
                }
              }
            }
          }
        }
      }
    },
    {
      type comment,
      heading "Related Sequences",
      products {
        {
          type genomic,
          heading "Genomic",
          accession "ABBA01026410",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 148165753
              },
              anchor "ABBA01026410"
            }
          },
          seqs {
            int {
              from 18242,
              to 75873,
              strand minus,
              id gi 148165753
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "ABBA01026411",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 148165752
              },
              anchor "ABBA01026411"
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "ABBA01026412",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 148165751
              },
              anchor "ABBA01026412"
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "ABBA01026413",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 148165750
              },
              anchor "ABBA01026413"
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "ABBA01026414",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 148165749
              },
              anchor "ABBA01026414"
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "ABBA01026415",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 148165748
              },
              anchor "ABBA01026415"
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "ABBA01026416",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 148165747
              },
              anchor "ABBA01026416"
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "ABBA01026417",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 148165746
              },
              anchor "ABBA01026417"
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "AC005366",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 3367508
              },
              anchor "AC005366"
            }
          },
          seqs {
            int {
              from 17974,
              to 36136,
              strand minus,
              id gi 3367508
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "AC005618",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 3548785
              },
              anchor "AC005618"
            }
          },
          seqs {
            int {
              from 66536,
              to 176713,
              strand plus,
              id gi 3548785
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "AC008781",
          version 7,
          source {
            {
              src {
                db "Nucleotide",
                tag id 16303400
              },
              anchor "AC008781"
            }
          },
          seqs {
            int {
              from 138117,
              to 185893,
              strand minus,
              id gi 16303400
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "AL832028",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 21732568
              },
              anchor "AL832028"
            }
          },
          seqs {
            whole gi 21732568
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "AMYH02012344",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 511816418
              },
              anchor "AMYH02012344"
            }
          },
          seqs {
            int {
              from 151138,
              to 175836,
              strand plus,
              id gi 511816418
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "AMYH02012345",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 511816417
              },
              anchor "AMYH02012345"
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "AMYH02012346",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 511816416
              },
              anchor "AMYH02012346"
            }
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type genomic,
          heading "Genomic",
          accession "CH471062",
          version 2,
          source {
            {
              src {
                db "Nucleotide",
                tag id 74230048
              },
              anchor "CH471062"
            }
          },
          seqs {
            whole gi 74230048
          },
          products {
            {
              type peptide,
              accession "EAW61957",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 119582361
                  },
                  anchor "EAW61957"
                }
              },
              seqs {
                whole gi 119582361
              }
            },
            {
              type peptide,
              accession "EAW61964",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 119582368
                  },
                  anchor "EAW61964"
                }
              },
              seqs {
                whole gi 119582368
              }
            }
          }
        },
        {
          type mRNA,
          heading "mRNA",
          accession "AF152324",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 5456939
              },
              anchor "AF152324"
            }
          },
          seqs {
            whole gi 5456939
          },
          products {
            {
              type peptide,
              accession "AAD43718",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 5456940
                  },
                  anchor "AAD43718"
                }
              },
              seqs {
                whole gi 5456940
              }
            }
          }
        },
        {
          type mRNA,
          heading "mRNA",
          accession "AF152511",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 5457069
              },
              anchor "AF152511"
            }
          },
          seqs {
            whole gi 5457069
          },
          products {
            {
              type peptide,
              accession "AAD43771",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 5457070
                  },
                  anchor "AAD43771"
                }
              },
              seqs {
                whole gi 5457070
              }
            }
          }
        },
        {
          type mRNA,
          heading "mRNA",
          accession "AI805761",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 5392327
              },
              anchor "AI805761"
            }
          },
          seqs {
            whole gi 5392327
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type mRNA,
          heading "mRNA",
          accession "BX100615",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 27830686
              },
              anchor "BX100615"
            }
          },
          seqs {
            whole gi 27830686
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type mRNA,
          heading "mRNA",
          accession "DA392480",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 80578107
              },
              anchor "DA392480"
            }
          },
          seqs {
            whole gi 80578107
          },
          products {
            {
              type peptide,
              text "None"
            }
          }
        },
        {
          type other,
          text "None",
          products {
            {
              type peptide,
              accession "Q9Y5G9",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 37999839
                  }
                },
                {
                  src {
                    db "UniProtKB/Swiss-Prot",
                    tag str "Q9Y5G9"
                  }
                }
              },
              seqs {
                whole gi 37999839
              }
            }
          }
        },
        {
          type other-genetic,
          heading "Synthetic",
          accession "BC152812",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 157170235
              },
              anchor "BC152812"
            }
          },
          seqs {
            whole gi 157170235
          },
          products {
            {
              type peptide,
              accession "AAI52813",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 157170236
                  },
                  anchor "AAI52813"
                }
              },
              seqs {
                whole gi 157170236
              }
            }
          }
        },
        {
          type other-genetic,
          heading "Synthetic",
          accession "BC156730",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 162318805
              },
              anchor "BC156730"
            }
          },
          seqs {
            whole gi 162318805
          },
          products {
            {
              type peptide,
              accession "AAI56731",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 162318806
                  },
                  anchor "AAI56731"
                }
              },
              seqs {
                whole gi 162318806
              }
            }
          }
        }
      }
    },
    {
      type comment,
      heading "Additional Links",
      comment {
        {
          type comment,
          source {
            {
              src {
                db "Evidence Viewer",
                tag str "56111"
              },
              anchor "Evidence Viewer",
              url "http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&conti
g=NT_029289.11&gene=PCDHGA4&lid=56111&from=1897694&to=2055472"
            }
          }
        },
        {
          type comment,
          text "MIM",
          source {
            {
              src {
                db "MIM",
                tag id 606291
              },
              anchor "606291"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "AceView",
                tag id 56111
              },
              anchor "AceView",
              url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=g
eneid&org=9606&l=56111"
            }
          }
        },
        {
          type comment,
          text "UCSC",
          source {
            {
              src {
                db "UCSC",
                tag str "UCSC"
              },
              anchor "UCSC",
              url "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=
NM_018917"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "MGC",
                tag str "BC152812,BC156730"
              },
              anchor "MGC",
              url "http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC152812
,BC156730"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "KEGG",
                tag str "hsa:56111"
              },
              url "http://www.genome.jp/dbget-bin/www_bget?hsa:56111"
            }
          }
        },
        {
          type comment,
          text "UniGene",
          xtra-properties {
            {
              tag "UNIGENE",
              value "Hs.368160"
            }
          },
          source {
            {
              src {
                db "UniGene",
                tag str "Hs.368160"
              },
              anchor "Hs.368160",
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=36
8160"
            }
          }
        }
      }
    },
    {
      type comment,
      heading "Markers (Sequence Tagged Sites/STS)",
      comment {
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 68872
              },
              anchor "SHGC-76190",
              post-text "(e-PCR)"
            }
          },
          comment {
            {
              type other,
              label "Alternate name",
              text "HSA.981"
            },
            {
              type other,
              label "Alternate name",
              text "RH101644"
            },
            {
              type other,
              label "Alternate name",
              text "RH50318"
            },
            {
              type other,
              label "Alternate name",
              text "STS-L11373"
            },
            {
              type other,
              label "Alternate name",
              text "WI-18887"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 58378
              },
              anchor "T03558",
              post-text "(e-PCR)"
            }
          },
          comment {
            {
              type other,
              label "Alternate name",
              text "IB475"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 277566
              },
              anchor "PCDHGA9_1502",
              post-text "(e-PCR)"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 277567
              },
              anchor "PCDHGC3__1203",
              post-text "(e-PCR)"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 280897
              },
              anchor "PCDHGA4_2560",
              post-text "(e-PCR)"
            }
          },
          comment {
            {
              type other,
              label "Alternate name",
              text "PCDHGA4_2560.2"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 280898
              },
              anchor "PCDHGA6_2010",
              post-text "(e-PCR)"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 280900
              },
              anchor "PCDHGB4_2544",
              post-text "(e-PCR)"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 280901
              },
              anchor "PCDHGC4_2483",
              post-text "(e-PCR)"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 47440
              },
              anchor "AF022190",
              post-text "(e-PCR)"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 87645
              },
              anchor "RH91455",
              post-text "(e-PCR)"
            }
          },
          comment {
            {
              type other,
              label "Alternate name",
              text "stSG44640"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 256698
              },
              anchor "5q31-33_24",
              post-text "(e-PCR)"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 25793
              },
              anchor "AF053066",
              post-text "(e-PCR)"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 25794
              },
              anchor "AF022189",
              post-text "(e-PCR)"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 466384
              },
              anchor "PCDHGA10_7046",
              post-text "(e-PCR)"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 73201
              },
              anchor "D5S2538",
              post-text "(e-PCR)"
            }
          },
          comment {
            {
              type other,
              label "Alternate name",
              text "GDB:734416"
            },
            {
              type other,
              label "Alternate name",
              text "RH34348"
            },
            {
              type other,
              label "Alternate name",
              text "SHGC-5561"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 256498
              },
              anchor "5q31-33_16",
              post-text "(e-PCR)"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 256499
              },
              anchor "5q31-33_17",
              post-text "(e-PCR)"
            }
          }
        },
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 50676
              },
              anchor "STS-R97031",
              post-text "(e-PCR)"
            }
          },
          comment {
            {
              type other,
              label "Alternate name",
              text "RH41214"
            },
            {
              type other,
              label "Alternate name",
              text "sts-R97031"
            }
          }
        }
      }
    },
    {
      type comment,
      heading "Gene Location History",
      comment {
        {
          type comment,
          heading "Homo sapiens Annotation Release 105",
          comment {
            {
              type assembly,
              heading "GRCh37.p13",
              label "Reference",
              accession "GCF_000001405",
              version 25,
              comment {
                {
                  type assembly-unit,
                  heading "Primary Assembly",
                  accession "GCF_000001305",
                  version 13,
                  comment {
                    {
                      type genomic,
                      label "chromosome Chromosome 5",
                      accession "NC_000005",
                      version 9,
                      seqs {
                        int {
                          from 140734767,
                          to 140892545,
                          strand plus,
                          id gi 224589817
                        }
                      }
                    }
                  }
                }
              }
            },
            {
              type assembly,
              heading "HuRef",
              label "Alternate",
              accession "GCF_000002125",
              version 1,
              comment {
                {
                  type genomic,
                  label "chromosome Chromosome 5",
                  accession "AC_000137",
                  version 1,
                  seqs {
                    int {
                      from 135879842,
                      to 136037385,
                      strand plus,
                      id gi 157734151
                    }
                  }
                }
              }
            },
            {
              type assembly,
              heading "CHM1_1.1",
              label "Alternate",
              accession "GCF_000306695",
              version 2,
              comment {
                {
                  type genomic,
                  label "chromosome Chromosome 5",
                  accession "NC_018916",
                  version 2,
                  seqs {
                    int {
                      from 140167974,
                      to 140325822,
                      strand plus,
                      id gi 528476642
                    }
                  }
                }
              }
            }
          }
        },
        {
          type comment,
          heading "Homo sapiens Annotation Release 104",
          comment {
            {
              type assembly,
              heading "GRCh37.p10",
              label "Reference",
              accession "GCF_000001405",
              version 22,
              comment {
                {
                  type assembly-unit,
                  heading "Primary Assembly",
                  accession "GCF_000001305",
                  version 13,
                  comment {
                    {
                      type genomic,
                      label "chromosome Chromosome 5",
                      accession "NC_000005",
                      version 9,
                      seqs {
                        int {
                          from 140734767,
                          to 140892545,
                          strand plus,
                          id gi 224589817
                        }
                      }
                    }
                  }
                }
              }
            },
            {
              type assembly,
              heading "HuRef",
              label "Alternate",
              accession "GCF_000002125",
              version 1,
              comment {
                {
                  type genomic,
                  label "chromosome Chromosome 5",
                  accession "AC_000137",
                  version 1,
                  seqs {
                    int {
                      from 135879842,
                      to 136037385,
                      strand plus,
                      id gi 157734151
                    }
                  }
                }
              }
            },
            {
              type assembly,
              heading "CHM1_1.0",
              label "Alternate",
              accession "GCF_000306695",
              version 1,
              comment {
                {
                  type genomic,
                  label "chromosome Chromosome 5",
                  accession "NC_018916",
                  version 1,
                  seqs {
                    int {
                      from 141011444,
                      to 141169209,
                      strand plus,
                      id gi 409253459
                    }
                  }
                }
              }
            }
          }
        },
        {
          type comment,
          heading "Build 37.3",
          comment {
            {
              type assembly,
              heading "GRCh37.p5",
              label "Reference",
              accession "GCF_000001405",
              version 17,
              comment {
                {
                  type assembly-unit,
                  heading "Primary Assembly",
                  accession "GCF_000001305",
                  version 13,
                  comment {
                    {
                      type genomic,
                      label "chromosome Chromosome 5",
                      accession "NC_000005",
                      version 9,
                      seqs {
                        int {
                          from 140734767,
                          to 140892545,
                          strand plus,
                          id gi 224589817
                        }
                      }
                    }
                  }
                }
              }
            },
            {
              type assembly,
              heading "HuRef",
              label "Alternate",
              accession "GCF_000002125",
              version 1,
              comment {
                {
                  type assembly-unit,
                  heading "Primary Assembly",
                  accession "GCF_000000025",
                  version 1,
                  comment {
                    {
                      type genomic,
                      label "chromosome Chromosome 5",
                      accession "AC_000137",
                      version 1,
                      seqs {
                        int {
                          from 135879842,
                          to 136037385,
                          strand plus,
                          id gi 157734151
                        }
                      }
                    }
                  }
                }
              }
            }
          }
        }
      }
    }
  },
  unique-keys {
    {
      db "HGNC",
      tag id 8702
    },
    {
      db "LocusID",
      tag id 56111
    },
    {
      db "MIM",
      tag id 606291
    }
  },
  xtra-index-terms {
    "LOC56111"
  }
}
BioPerl-1.007002/t/data/ex1.nucl.nhx000444000766000024       245413155576321 17051 0ustar00cjfieldsstaff000000000000(((05_YEAST:0.493471[&&NHX:S=YEAST],
04_SCHPO:0.318204[&&NHX:S=SCHPO]
):0.157022[&&NHX:D=N:S=Ascomycota],
03_ARATH:0.308649[&&NHX:S=ARATH]
):0.04141[&&NHX:D=N:S=Eukaryota],
((((((((08_RAT:0.102249[&&NHX:S=RAT],
(13_RAT:0.095242[&&NHX:S=RAT],
10_RAT:0.031982[&&NHX:S=RAT]
):0.018615[&&NHX:D=Y:S=RAT]
):0.014489[&&NHX:D=Y:S=RAT],
11_MOUSE:0.042825[&&NHX:S=MOUSE]
):0.037198[&&NHX:D=N:S=Murinae],
12_HUMAN:0.060992[&&NHX:E=$-PANTR:S=HUMAN]
):0.109605[&&NHX:D=N:E=$-CANFA:S=Eutheria],
09_CHICK:0.105274[&&NHX:S=CHICK]
):0.086729[&&NHX:D=N:E=$-XENTR:S=Amniota],
06_BRARE:0.356832[&&NHX:E=$-Tetraodontidae:S=BRARE]
):0.073642[&&NHX:D=N:S=Euteleostomi],
(((18_HUMAN:0.077476[&&NHX:E=$-PANTR:S=HUMAN],
17_MOUSE:0.066898[&&NHX:E=$-RAT:S=MOUSE]
):0.142228[&&NHX:D=N:E=$-CANFA:S=Eutheria],
16_CHICK:0.196657[&&NHX:S=CHICK]
):0.083315[&&NHX:D=N:E=$-XENTR:S=Amniota],
(15_FUGRU:0.125305[&&NHX:E=$-TETNG:S=FUGRU],
14_BRARE:0.192069[&&NHX:S=BRARE]
):0.133036[&&NHX:D=N:S=Clupeocephala]
):0.096936[&&NHX:D=N:S=Euteleostomi]
):0.06101[&&NHX:D=Y:E=$-CIOIN:S=Euteleostomi],
07_DROME:0.262868[&&NHX:E=$-ANOGA-APIME:S=DROME]
):0.1118[&&NHX:D=N:S=Bilateria],
(02_CAEBR:0.168649[&&NHX:S=CAEBR],
01_CAEEL:0.166054[&&NHX:S=CAEEL]
):0.371596[&&NHX:D=N:Loglk=-18289.490411:S=Caenorhabditis]
):0.083573[&&NHX:D=N:S=Bilateria]
)[&&NHX:D=N:S=Eukaryota];
BioPerl-1.007002/t/data/example.hap000444000766000024      4054113155576321 17041 0ustar00cjfieldsstaff000000000000#Thu Mar 18 08:50:48 2004: HapMap genotype data dump, chr9 from 660000 to 759999
#For details on file format, see http://www.hapmap.org/genotypes/
#Settings:
#   minimum MAF: 0.00
rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID NA06985 NA06991 NA06993 NA06994 NA07000 NA07019 NA07022 NA07029 NA07034 NA07048 NA07055 NA07056 NA07345 NA07348 NA07357 NA10830 NA10831 NA10835 NA10838 NA10839 NA10846 NA10847 NA10851 NA10854 NA10855 NA10856 NA10857 NA10859 NA10860 NA10861 NA10863 NA11829 NA11830 NA11831 NA11832 NA11839 NA11840 NA11881 NA11882 NA11992 NA11993 NA11994 NA11995 NA12003 NA12004 NA12005 NA12006 NA12043 NA12044 NA12056 NA12057 NA12144 NA12145 NA12146 NA12154 NA12155 NA12156 NA12234 NA12236 NA12239 NA12248 NA12249 NA12264 NA12707 NA12716 NA12717 NA12740 NA12750 NA12751 NA12752 NA12753 NA12760 NA12761 NA12762 NA12763 NA12801 NA12802 NA12812 NA12813 NA12814 NA12815 NA12864 NA12865 NA12872 NA12873 NA12874 NA12875 NA12878 NA12891 NA12892
rs4584192 A/G chr9 661053 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177478:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AG AG AG AG AG AG AA AA GG AG AG GG GG AG AG AG AG GG AA AA AA AG AA GG GG AG AG AG AA GG AG AG AG GG GG AG GG GG AG AA AG AG GG AG AG AA AA AA GG AA AG AG AA GG AA AG AG AG GG AG GG AG AG AG AG AG AA AG AG AG AG AG AG AA GG AG AG AG GG AA AG AA AG AA AG AG GG AA AA AA
rs4740849 C/G chr9 662880 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177479:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 CG CG CG CG CG CG CC CC GG CG CG GG CC CC CG CG CC GG CC CC CC CG CC CC GG CG CC CC CC CG CG CG CG CG GG CC CG CG CC CC CG CG CG CC CG CC CC CC CC CC CG CG CC CG CC CC CG CG CG CC GG CG CG CC CC CG CC CG CG CC CC CG CC CC CG CG CC CG GG CC CC CC CG CC CG CG CG CC CC CC
rs4742215 G/T chr9 664017 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177480:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 GT GT GT TT GT GT GG GT TT TT TT TT TT GT GT TT GT TT GG GT GG GT GG TT TT GT GT GT TT TT GT GT GT TT TT TT TT TT GT GT TT GT TT GT GT GT TT GG TT GG GT GT GT TT GT TT GT TT TT GT TT TT GT TT GT TT GT TT GT TT TT TT TT TT TT GT TT GT TT GT GT GT TT GG TT TT TT GT TT GT
rs4742219 C/T chr9 665377 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177481:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 CT CT CT TT CT CT CC CT TT TT TT TT TT CT CT TT CT TT CC CT CC CT CC TT TT CT CT CT TT TT CT CT CT TT TT TT TT TT CT CT TT CT TT CT CT CT TT CC TT CC CT CT CT TT CT TT CT TT TT CT TT TT CT TT CT TT CT TT CT TT CT TT TT TT CT CT TT CT TT CT CT CT TT CC TT TT TT CT TT CT
rs4742220 A/G chr9 665419 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:245719:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AG AG AG GG AG AG AA AG GG GG GG GG GG AG AG GG AG GG AA AG AA AG AA GG GG AG AG AG GG GG AG AG NN GG GG GG GG GG AG AG GG AG GG AG NN AG GG NN GG AA AG AG AG GG AG GG AG GG GG AG GG GG AG GG AG GG AG GG AG GG GG GG GG GG GG AG GG AG NN AG AG NN GG AA GG GG GG AG GG AG
rs4742222 A/G chr9 665463 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:238601:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AG AG AG AA AG AG GG AG AA AA AA AA AA AG AG AA AG AA GG AG GG AG GG AA AA AG AG AG AA AA AG AG AG AA AA AA AA AA AG AG AA AG AA AG AG AG AA GG AA GG AG AG AG AA AG AA AG AA AA AG AA AA AG AA AG AA AG AA AG AA AA AA AA AA AA AG AA AG AA AG AG AG AA GG AA AA AA AG AA AG
rs4742223 C/T chr9 665600 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177482:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 CT CT CC CT CT CT TT CT CC CC CC CC CC CT CT CC CT CC TT CT TT CT TT CC CC CT CT CT CC CC CT CT CT CC CC CC CC CC CT CT CC CT CC CT CT CT CC TT CC TT CT CT CT CC CT CC CT CC CC CT CC CC CT CC CT CC CT CC CT CC CC CC CC CC CC CT CC CT CC CT CT CT CC TT CC CC CC CT CC CT
rs2296054 C/T chr9 667141 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177485:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT
rs4740850 A/G chr9 667772 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177486:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
rs4742225 G/T chr9 667938 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177487:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 GT GT GG GT GG GG GG GT GG GT GT GG TT GT GG GT GT GG GG GT GG GG GG NN GG GG GT GT TT GT GT GG GT GT GG TT GT GT GT TT GT GG GT GT GG GT TT GG TT GG GG GG GT GT GT TT GG GT GT GT GG GT GT TT GT GT GT GT GG TT TT GT TT TT GT GG TT GG GG GT GT GT GT GG GT GT GT GT TT GT
rs4740851 A/T chr9 667986 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:245218:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AT AT AA AA AA AA AA AA AA AA AA AA TT AT AA AA AT AA AA AA AA AA AA TT AA AA AT AT AA AT AT AA AT AT AA AT AT AT AT AT AA AA AT AT AA AA AA AA TT AA AA AA AA AT AA AT AA AA AT AT AA AA AT AT AT AA AA AA AA AT AT AA AT AA AT AA AT AA AA AA AT AA AA AA AA AA AT AA AA AA
rs4742227 C/G chr9 669184 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177488:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 GG GG CG GG CG CG CC CG GG GG GG GG GG CG CG GG CG GG CC CG CC CG CC GG GG CG CG CG GG GG CG CG GG GG GG GG GG GG CG GG GG CG GG CG CG CG GG CC GG CC CG CG CG GG CG GG CG GG GG CG GG GG GG GG CG GG CG GG CG GG GG GG GG GG GG CG GG CG GG CG CG CG GG CC GG GG GG CG GG CG
rs2025308 A/C chr9 673633 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177489:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
rs1323262 C/G chr9 674096 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177490:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 CG CG CG CC CG CG GG CG CC CC CC CC CC CG CG CC GG CC GG CG GG CG GG GG CC CG GG GG CC CC CG CG CG CC CC CG CG CG CG CG CC CG CC CG CG CG CC GG GG GG CG CG CG CC CG CG CG CC CG CG CC CC CG CG GG CC CG CC CG CG CG CC CG CC CG CG CG CG CC CG GG CG CC GG CC CC CG CG CC CG
rs4742236 A/G chr9 676753 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177491:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AG AA AG GG AG GG AG GG GG GG AG GG GG AG AG GG GG GG AG AG GG AG AG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG AG GG GG GG GG AG AG GG AG GG AG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AG GG AG
rs1359058 A/T chr9 679233 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:32734:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AT AT AT AA AA TT TT AA AA AA AA TT AA AT AT AA TT AA AT AT AT AT TT TT AA AT TT TT AA AA AT AT AT AA AA AT AT AT AT AT AA AT AA AA TT AT AA TT TT TT AT AT AA AA AA AT AT AA AT AT AA AA AT AT AT AA AT AA AT AT AT AA AT AA AT AT AT AT AA AT TT AT AA TT AA AA AT TT AT AT
rs1475202 C/G chr9 684826 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:32735:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 GG GG CG GG GG CG CC GG GG GG GG CG GG GG GG GG CC GG GG GG CG GG CG CC GG CG CC CC GG GG GG CG GG GG GG CG CG CG CG GG GG CG GG GG CG GG GG CG CC CG CG CG GG GG GG CG CG GG CG GG GG GG GG CG CG GG CG GG CG CG CG GG CG GG CG CG CG CG GG CG CC CG GG CC GG GG CG CG CG GG
rs745876 A/T chr9 685143 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177494:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AA AA AT AA AA AT TT AA AA AA AA AT AA AA AA AA TT AA AA AA AT AA AT TT AA AT TT TT AA AA AA AT AA AA AA AT AT AT AT AA AA AT AA AA AT AA AA AT TT AT AT AT AA AA AA AT AT AA AT AA AA AA AA AT AT AA AT AA AT AT AT AA AT AA AT AT AT AT AA AT TT AT AA TT AA AA AT AT AT AA
rs745877 C/T chr9 685310 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:246340:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 TT TT CT TT TT CT CC TT TT TT TT CT TT TT TT TT CC TT TT TT CT TT CT CC TT CT CT CC TT TT TT CT TT TT TT CC CT CT CT TT TT CT TT TT CT TT TT CT CT CT CT CT TT TT TT CT CT TT CT TT TT TT TT CT CT TT CT TT CT CT CT TT CT TT CT CT CT CT TT CT CC CT TT CC TT TT CT CT CT TT
rs732119 C/T chr9 685607 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:32738:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 TT TT CT TT TT CT CC TT TT TT TT CT TT TT TT TT CC TT TT TT CT TT CT CC TT CT CC CC TT TT TT CT TT TT TT CT CT CT CT TT TT CT TT TT CT TT TT CT CC CT CT CT TT TT TT CT CT TT CT TT TT TT TT CT CT TT CT TT CT CT CT TT CT TT CT CT CT CT TT CT CC CT TT CC TT TT CT CT CT TT
rs732118 A/C chr9 685614 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:32739:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AA AA AC AA AA AC CC AA AA AA AA AC AA AA AA AA CC AA AA AA AC AA AC CC AA AC CC CC AA AA AA AC AA AA AA AC AC AC AC AA AA AC AA AA AC AA AA AC CC AC AC AC AA AA AA AC AC AA AC AA AA AA AA AC AC AA AC AA AC AC AC AA AC AA AC AC AC AC AA AC CC AC AA CC AA AA AC AC AC AA
rs1570473 C/G chr9 685894 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:32740:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 GG GG CG GG GG CG CC GG GG GG GG CG GG GG GG GG CC GG GG GG CG GG CG CC GG CG CC CC GG GG GG CG GG GG GG CG CG CG CG GG GG CG GG GG CG GG GG CG CC CG CG CG GG GG GG CG CG GG CG GG GG GG GG CG CG GG CG GG CG CG CG GG CG GG CG CG CG CG GG CG CC CG GG CC GG GG CG CG CG GG
rs912175 C/G chr9 702137 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177496:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 CG CG CC CG CC CC CC CG CC CG CG CG CG CG CC GG CC CG CG CG CC CC CC CC CG CC CC CC CG GG CC CC CC CC CG CC CG CC CG CC CG CG CG CG CG CG GG CC CC CC CG CC CG CG CG CG CC CC CG CG CC GG CC CG CC CG CC CG CC CG CG CG CC GG CG CC CG CC CC CG CC CC CG CC CC CG CC CC CG CC
rs912174 A/C chr9 702156 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:32741:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AC AC AA AC AA AA AA AC AA AC AC AC AC AC AA CC AA AC AC AC AA AA AA AA AC AA AA AA AC CC AA AA AA AA AC AA AC AA AC AA AC AC AC AC AC AC CC AA AA AA AC AA AC AC AC AC AA AA AC AC AA CC AA AC AA AC AA AC AA AC AC AC AA CC AC AA AC AA AC AC AA AA AC AA AA AC AA AA AC AA
rs4740866 G/T chr9 706570 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177499:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 TT TT TT TT TT TT GT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT GT TT GT GT TT GT TT TT TT TT TT TT TT TT TT TT TT TT TT TT GT TT TT TT TT TT TT GT TT TT TT TT GT TT TT TT TT TT TT TT TT TT GT TT TT TT TT TT GT TT TT GT TT TT GT TT TT GT GT TT
rs1022827 A/G chr9 709608 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177500:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 GG GG AG GG AG AA AG AG GG GG GG AG GG GG GG GG AG GG GG GG AG GG GG AA GG AG AA AG GG GG GG AG GG GG GG AG AG GG AG GG GG AG GG GG GG GG GG AG AA AG GG GG AG GG AG GG AG GG AG GG GG GG GG AG AA GG AG GG AG GG GG GG GG GG GG AG AG AG GG AG AA AG GG AA GG GG AG GG GG AG
rs4742292 A/G chr9 710832 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177501:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AA AA AG AA AG GG AG AG AA AA AA AG AA AA AA AA AG AA AA AA AG AA AA GG AA AG GG AG AA AA AG AG AA AG AA GG AG AA AG AA AA AG AA AA AA AA AA AG GG AG AG AA AG AA AG AA AG AG AG AA AA AA AG AG GG AA AG AA AG AA AA AA AG AA AA AG AG AG AG AG GG GG AA GG AG AA AG AA AA AG
rs2296050 C/G chr9 730592 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177505:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 CG CG CG CG CG CC CG CC GG CG CG CC CG CC CG CC CG CG CC CC CC GG CC CC CG CG CC CG CG CC CG CG GG CG CG CC CC GG CC GG CG CC CG CG CC CG CC CC CG CC CC CC CC CG CC CG CC CG CC CG GG CC CG CC CC CG CG GG CG GG CG GG CG CG CG CG CC CG CG CC CC CC CG CC CG CG CG CC CC CG
rs2296049 A/G chr9 730901 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177506:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AG AG GG AG GG GG GG AG GG AG AG AG AG AA AG AA GG AG AA AA GG GG AA GG AG GG GG GG AG AA GG GG GG GG AG GG GG GG AG GG AG AG AG AG AA AG AA AG GG AG AA AG AG AG AG AG AG GG AG AG GG AA GG AG GG AG GG GG GG GG AG GG GG AG AG GG AG GG GG AG GG GG AG GG GG AG GG AG AG AG
rs3739586 C/T chr9 735413 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177507:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC NN CC CC CC CC CC CC CC CC CC
rs962817 C/T chr9 740892 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177508:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 CT CT CC CT CC CC CC CT CC CT CT CT TT TT CT TT CC CC TT TT CC CT TT CT CC CC CC CC CT CC TT CC CC CC CC CC CT CC CC CC CT CC CC CT TT CT TT CT CC CT CT CC CT CT CT CT CT CT CT CC CC CT CT CT CC CT CC CC CC CT CT TT CT CT CT CC CC CC CC CC CC CT CT CC CT CT CC TT TT CT
rs4400444 G/T chr9 744655 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177509:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 TT GT GT GT GT TT TT TT TT TT TT TT TT GT GT TT TT TT GT GT TT GT GT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT GT GT TT GT TT GT TT TT TT GT TT TT TT TT TT TT TT TT GT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT GT TT GT TT GT
rs881684 A/G chr9 750405 + ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177510:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AA AA AG AA AG AA AA AG AA AA AA AA AA AG AG AA AG AG AG AG AG AG AG AG AA AG GG AA AA AA AA AG AA AG AG GG AG AA AA AA AA AG AA AA GG AG AA GG AG GG AA AG AA AG AG AA AG AG AA AA AA AG AA AG GG AA AG AA AG AA AA AA AA AG AA AG GG AG AG GG GG AA AG AA AA AA AG AG AA AG
rs2025307 A/G chr9 752654 - ncbi_b34 illumina urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_1.0.0:1 urn:LSID:illumina.hapmap.org:Assay:177511:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 AA AA AG AG AA AA AA AG AA AA AA AG AG GG AG AG AG AG GG AG AG AG GG GG AA AG AG AA AG AA AG AG AA AG AG GG GG AA AA AG AA AA AA AG GG AG AA GG AA GG GG AG AA AG AA AA AG AG AG AA AA AG AG GG AG AG AG AA AG AA AA AG AA AA AG AG GG AG AG GG GG AA AA AA AA AA AA AG AA AG
BioPerl-1.007002/t/data/example.phase000444000766000024        15713155576321 17330 0ustar00cjfieldsstaff0000000000003
5
P 300 1313 1500 2023 5635
MSSSM
#1
12 1 0 1 3
11 0 1 0 3
#2
12 1 1 1 2
12 0 0 0 3
#3
-1 ? 0 0 2
-1 ? 1 1 13BioPerl-1.007002/t/data/example.vcf000444000766000024       273613155576321 17033 0ustar00cjfieldsstaff000000000000##fileformat=VCFv4.0
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=1000GenomesPilot-NCBI36
##phasing=partial
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##FILTER=
##FILTER=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
20	1234567	microsat1	GTCT	G,GTACT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3

BioPerl-1.007002/t/data/exonerate.output.dontwork000444000766000024       632313155576321 22016 0ustar00cjfieldsstaff000000000000Command line: [exonerate -q test_aa.fa -t test_cds.fa --model protein2dna]
Hostname: [fgu204.anat.ox.ac.uk]
C4 Alignment display:
  Model: protein2dna
  Raw score: 1059
  Aligned positions 0->204 of query
  Aligned positions 2->614 of target

Query: SJCHGC00851 AA
Target: SJCHGC00851 CDS

   1 : ArgAlaProArgProSerLeuLeuTyrPheAsnValPheLeuLeuLeuValHisSerPheSerG :  22
       ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
       ArgAlaProArgProSerLeuLeuTyrPheAsnValPheLeuLeuLeuValHisSerPheSerG
   3 : CGTGCCCCTCGTCCTTCTTTGCTCTACTTCAACGTGTTTCTTTTGTTGGTTCATTCATTTTCAC :  66

  23 : lnAspLysLysAspValLeuLysLysLeuAsnSerThrLeuLeuSerMetGluAsnSerLeuLe :  43
       ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
       lnAspLysLysAspValLeuLysLysLeuAsnSerThrLeuLeuSerMetGluAsnSerLeuLe
  67 : AAGATAAAAAGGATGTGTTGAAGAAGTTAAACTCTACTTTACTTTCAATGGAAAACAGCTTATT : 129

  44 : uLysValGlnGlnAsnIleGlnAsnThrAspHisGluValLysAsnSerThrLysArgIleAsn :  64
       ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
       uLysValGlnGlnAsnIleGlnAsnThrAspHisGluValLysAsnSerThrLysArgIleAsn
 130 : AAAAGTTCAACAAAACATTCAAAACACTGACCACGAAGTAAAGAATTCGACAAAGAGAATAAAT : 192

  65 : LysValLeuAlaProHisGlyArgThrIleAspGluTyrValLysCysLysThrAsnGluPheL :  86
       ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
       LysValLeuAlaProHisGlyArgThrIleAspGluTyrValLysCysLysThrAsnGluPheL
 193 : AAAGTACTTGCACCTCACGGAAGAACAATTGACGAATATGTCAAATGCAAAACTAATGAATTTA : 258

  87 : ysAlaGluGluGlyLeuSerThrAsnThrLysPheLeuLysGluPheIleProGlyThrPheAr : 107
       ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
       ysAlaGluGluGlyLeuSerThrAsnThrLysPheLeuLysGluPheIleProGlyThrPheAr
 259 : AAGCTGAAGAAGGTTTATCTACAAATACTAAATTCTTAAAAGAGTTTATTCCTGGAACTTTTCG : 321

 108 : gValTyrArgLysTyrLeuThrAspGluAspIleHisTrpLysAsnAlaAlaGluGluArgLys : 128
       ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
       gValTyrArgLysTyrLeuThrAspGluAspIleHisTrpLysAsnAlaAlaGluGluArgLys
 322 : TGTTTATAGAAAATACCTGACTGATGAAGATATACATTGGAAAAACGCCGCTGAAGAACGGAAG : 384

 129 : AlaLysTyrLysThrMetAlaLeuGluHisThrSerGluLysCysAspGluLeuAlaAspGlnP : 150
       ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
       AlaLysTyrLysThrMetAlaLeuGluHisThrSerGluLysCysAspGluLeuAlaAspGlnP
 385 : GCAAAATATAAAACAATGGCCTTAGAGCACACTTCGGAAAAGTGTGATGAACTTGCTGATCAAT : 450

 151 : heProGluAlaPheValGluIleGlnGluLeuLysAspGlnIleTyrGluArgGlnArgTyrGl : 171
       ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
       heProGluAlaPheValGluIleGlnGluLeuLysAspGlnIleTyrGluArgGlnArgTyrGl
 451 : TTCCTGAAGCGTTTGTAGAAATTCAAGAACTTAAGGATCAAATATATGAACGACAAAGATACGA : 513

 172 : uLeuGlnTyrAspTyrMetPheTyrLysPhePheValLeuLeuAspIleTyrArgLysValGln : 192
       ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
       uLeuGlnTyrAspTyrMetPheTyrLysPhePheValLeuLeuAspIleTyrArgLysValGln
 514 : ATTACAATATGATTATATGTTTTATAAGTTTTTCGTGCTATTAGATATTTATAGAAAAGTGCAA : 576

 193 : AlaPheAspGluThrArgGluGluHisGluGln*** : 204
       ||||||||||||||||||||||||||||||||||||
       AlaPheAspGluThrArgGluGluHisGluGln***
 577 : GCATTTGATGAAACACGTGAAGAACATGAGCAGTGA : 614

vulgar: SJCHGC00851 0 204 . SJCHGC00851 2 614 + 1059 M 204 612
-- completed exonerate analysis
BioPerl-1.007002/t/data/exonerate.output.negativescore.works000444000766000024        65213155576321 24130 0ustar00cjfieldsstaff000000000000C4 Alignment:
------------
         Query: aly-miR169a MIMAT0017485 Arabidopsis lyrata miR169a
        Target: contig15750__54-177
         Model: ungapped:dna2dna
     Raw score: -3
   Query range: 0 -> 21
  Target range: 19 -> 40

  1 : CAGCCAAGGATGACTTGCCGA : 21
       |||||||||||| ||||| |
 20 : TagccaaggaTgaaTTgccTa : 40

vulgar: aly-miR169a 0 21 + contig15750__54-177 19 40 + -3 M 21 21
-- completed exonerate analysis
BioPerl-1.007002/t/data/exonerate.output.works000444000766000024      1365013155576321 21335 0ustar00cjfieldsstaff000000000000Command line: [exonerate -q exonerate_cdna.fa -t exonerate_genomic.fa --model est2genome --bestn 1]
Hostname: [fgu204.anat.ox.ac.uk]
C4 Alignment display:
  Model: est2genome
  Raw score: 6137
  Aligned positions 3->1279 of query
  Aligned positions 28->3074 of target

Query: MUSSPSYN Mouse spermidine synthase mRNA, complete cds.
Target: 4.143962167-143965267 Slice, no description

    4 : GTTGTGCT-GGGGGGGTCCGCGCGCCCTGCAGTCCCGAACCCGCTACGCGCTCCGTCGGCCC :   64
        |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
   29 : GTTGTGCTGGGGGGGGTCCGCGCGCCCTGCAGTCCCGAACCCGCTACGCGCTCCGTCGGCCC :   90

   65 : GCCCGCCCGCCATGGAGCCTGGCCCCGACGGCCCAGCCGCGCCCGGCCCCGCCGCCATCCGT :  126
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
   91 : GCCCGCCCGCCATGGAGCCTGGCCCCGACGGCCCAGCCGCGCCCGGCCCCGCCGCCATCCGT :  152

  127 : GAGGGCTGGTTCCGAGAGACCTGCAGCCTGTGGCCCGGCCAGGCCCTGTCGCTGCAAGTGGA :  188
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  153 : GAGGGCTGGTTCCGAGAGACCTGCAGCCTGTGGCCCGGCCAGGCCCTGTCGCTGCAAGTGGA :  214

  189 : GCAGCTGCTTCACCACCGGCGATCGCGGTACCAAGACATCCTCGTCTTCCGCAG  >>>> T :  243
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||++      
  215 : GCAGCTGCTTCACCACCGGCGATCGCGGTACCAAGACATCCTCGTCTTCCGCAGgt...... :  271

  244 : arget Intron 1 >>>>  TAAAACCTACGGCAACGTGCTGGTTCTGGATGGCGTCATCC :  283
            257 bp         ++|||||||||||||||||||||||||||||||||||||||||
  272 : ...................agTAAAACCTACGGCAACGTGCTGGTTCTGGATGGCGTCATCC :  566

  284 : AGTGTACTGAGAGGGATGAGTTCTCCTACCAGGAGATGATCGCCAACCTGCCGCTCTGCAGC :  345
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  567 : AGTGTACTGAGAGGGATGAGTTCTCCTACCAGGAGATGATCGCCAACCTGCCGCTCTGCAGC :  628

  346 : CACCCCAACCCGCGGAAG  >>>> Target Intron 2 >>>>  GTGCTGATCATCGGG :  378
        ||||||||||||||||||++          317 bp         ++|||||||||||||||
  629 : CACCCCAACCCGCGGAAGgt.........................agGTGCTGATCATCGGG :  978

  379 : GGTGGAGATGGGGGCGTCCTACGGGAAGTGGTGAAGCACCCCTCTGTGGAGTCGGTGGTCCA :  440
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  979 : GGTGGAGATGGGGGCGTCCTACGGGAAGTGGTGAAGCACCCCTCTGTGGAGTCGGTGGTCCA : 1040

  441 : GTGCGAGATTGATGAG  >>>> Target Intron 3 >>>>  GATGTCATTGAAGTCTC :  473
        ||||||||||||||||++          713 bp         ++|||||||||||||||||
 1041 : GTGCGAGATTGATGAGgt.........................agGATGTCATTGAAGTCTC : 1786

  474 : TAAGAAGTTCCTGCCTGGCATGGCCGTTGGCTTCTCCAGCTCAAAGCTGACTCTCCACGTGG :  535
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1787 : TAAGAAGTTCCTGCCTGGCATGGCCGTTGGCTTCTCCAGCTCAAAGCTGACTCTCCACGTGG : 1848

  536 : GCGATGGCTTTGAGTTCATGAAACAGAACCAAGATGCCTTTGACGTCATCATCACCGACTCC :  597
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1849 : GCGATGGCTTTGAGTTCATGAAACAGAACCAAGATGCCTTTGACGTCATCATCACCGACTCC : 1910

  598 : TCAGACCCCATGG  >>>> Target Intron 4 >>>>  GCCCTGCTGAGAGCCTCTTC :  630
        |||||||||||||++          326 bp         ++||||||||||||||||||||
 1911 : TCAGACCCCATGGgt.........................agGCCCTGCTGAGAGCCTCTTC : 2269

  631 : AAGGAGTCCTATTACCAGCTCATGAAGACAGCACTCAAAGAAGATGGCATCCTGTGCTGCCA :  692
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 2270 : AAGGAGTCCTATTACCAGCTCATGAAGACAGCACTCAAAGAAGATGGCATCCTGTGCTGCCA : 2331

  693 : GGGTGAGTGCCAGTGGCTGCACCTGGACCTCATCAAGGAGATGAGGCACTTCTGCAAATCTC :  754
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 2332 : GGGTGAGTGCCAGTGGCTGCACCTGGACCTCATCAAGGAGATGAGGCACTTCTGCAAATCTC : 2393

  755 : TCTTCCCCGTGGTGGACTACGCCTACTGTAGCATTCCTACCTATCCCAGCGGCCAGATCGGC :  816
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 2394 : TCTTCCCCGTGGTGGACTACGCCTACTGTAGCATTCCTACCTATCCCAGCGGCCAGATCGGC : 2455

  817 : TTCATGCTGTGTAGCAAAAACCCG  >>>> Target Intron 5 >>>>  AGCACCAAC :  849
        ||||||||||||||||||||||||++          85 bp          ++|||||||||
 2456 : TTCATGCTGTGTAGCAAAAACCCGgt.........................agAGCACCAAC : 2573

  850 : TTCCGGGAGCCAGTGCAGCAGTTGACACAGGCCCAGGTGGAGCAGATGCAGCTGAAATACTA :  911
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 2574 : TTCCGGGAGCCAGTGCAGCAGTTGACACAGGCCCAGGTGGAGCAGATGCAGCTGAAATACTA : 2635

  912 : TAACTCGGACATGCACCGTGCCGCCTTCGTACTGCCTGAGTTCACCCGGAAG  >>>> Tar :  964
        |||||||||||||||||||||||||||||||||||| |||||||||||||||++        
 2636 : TAACTCGGACATGCACCGTGCCGCCTTCGTACTGCCCGAGTTCACCCGGAAGgt........ : 2690

  965 : get Intron 6 >>>>  GCCCTCAATGACATAAGCTGAATCCAGGTGCCACTGTGACACC : 1006
          81 bp          ++|||||||||||||||||||||||||||||||||||||||||||
 2691 : .................agGCCCTCAATGACATAAGCTGAATCCAGGTGCCACTGTGACACC : 2811

 1007 : ACCCGAGACCTCAATCGGATTGGACCAAGGATCTTCCAAGTTGTCTGGGGACCACCAGTCCT : 1068
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 2812 : ACCCGAGACCTCAATCGGATTGGACCAAGGATCTTCCAAGTTGTCTGGGGACCACCAGTCCT : 2873

 1069 : GGACCAGACTCCCAGATGACTCTTGCCCACCAACCAAGTGTTACAGGCCCCATGATGCTGCC : 1130
        |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
 2874 : GGACCAGACTCCCAGATGACTCTTGCCCACCAACCAAGTGTTACAGGCCCCACGATGCTGCC : 2935

 1131 : TGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGCCCTGCTGGGTGGACTCAGTCTCTGTCTGT : 1192
        |||||||||          |||||||||||||||||||||||||||||||||||||||||||
 2936 : TGGCCTGGC----------CTGGCCTGGCCTGCCCTGCTGGGTGGACTCAGTCTCTGTCTGT : 2987

 1193 : CTATCTCTGTGGCGTTCAGCCCCACGCCTATACCAGCTCTGTACAGCACCGCCTATGCCCTG : 1254
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 2988 : CTATCTCTGTGGCGTTCAGCCCCACGCCTATACCAGCTCTGTACAGCACCGCCTATGCCCTG : 3049

 1255 : TGACCCAACAAAATACATGTGTATT : 1279
        |||||||||||||||||||||||||
 3050 : TGACCCAACAAAATACATGTGTATT : 3074

vulgar: MUSSPSYN 3 1279 + 4.143962167-143965267 28 3074 + 6137 M 8 8 G 0 1 M 231 231 5 0 2 I 0 253 3 0 2 M 121 121 5 0 2 I 0 313 3 0 2 M 93 93 5 0 2 I 0 709 3 0 2 M 154 154 5 0 2 I 0 322 3 0 2 M 230 230 5 0 2 I 0 81 3 0 2 M 123 123 5 0 2 I 0 77 3 0 2 M 176 176 G 10 0 M 130 130
-- completed exonerate analysis
BioPerl-1.007002/t/data/exonerate.whitespace_before_query.works000444000766000024      1365113155576321 24701 0ustar00cjfieldsstaff000000000000Command line: [exonerate -q exonerate_cdna.fa -t exonerate_genomic.fa --model est2genome --bestn 1]
Hostname: [fgu204.anat.ox.ac.uk]
C4 Alignment display:
  Model: est2genome
  Raw score: 6137
  Aligned positions 3->1279 of query
  Aligned positions 28->3074 of target

 Query: MUSSPSYN Mouse spermidine synthase mRNA, complete cds.
Target: 4.143962167-143965267 Slice, no description

    4 : GTTGTGCT-GGGGGGGTCCGCGCGCCCTGCAGTCCCGAACCCGCTACGCGCTCCGTCGGCCC :   64
        |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
   29 : GTTGTGCTGGGGGGGGTCCGCGCGCCCTGCAGTCCCGAACCCGCTACGCGCTCCGTCGGCCC :   90

   65 : GCCCGCCCGCCATGGAGCCTGGCCCCGACGGCCCAGCCGCGCCCGGCCCCGCCGCCATCCGT :  126
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
   91 : GCCCGCCCGCCATGGAGCCTGGCCCCGACGGCCCAGCCGCGCCCGGCCCCGCCGCCATCCGT :  152

  127 : GAGGGCTGGTTCCGAGAGACCTGCAGCCTGTGGCCCGGCCAGGCCCTGTCGCTGCAAGTGGA :  188
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  153 : GAGGGCTGGTTCCGAGAGACCTGCAGCCTGTGGCCCGGCCAGGCCCTGTCGCTGCAAGTGGA :  214

  189 : GCAGCTGCTTCACCACCGGCGATCGCGGTACCAAGACATCCTCGTCTTCCGCAG  >>>> T :  243
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||++      
  215 : GCAGCTGCTTCACCACCGGCGATCGCGGTACCAAGACATCCTCGTCTTCCGCAGgt...... :  271

  244 : arget Intron 1 >>>>  TAAAACCTACGGCAACGTGCTGGTTCTGGATGGCGTCATCC :  283
            257 bp         ++|||||||||||||||||||||||||||||||||||||||||
  272 : ...................agTAAAACCTACGGCAACGTGCTGGTTCTGGATGGCGTCATCC :  566

  284 : AGTGTACTGAGAGGGATGAGTTCTCCTACCAGGAGATGATCGCCAACCTGCCGCTCTGCAGC :  345
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  567 : AGTGTACTGAGAGGGATGAGTTCTCCTACCAGGAGATGATCGCCAACCTGCCGCTCTGCAGC :  628

  346 : CACCCCAACCCGCGGAAG  >>>> Target Intron 2 >>>>  GTGCTGATCATCGGG :  378
        ||||||||||||||||||++          317 bp         ++|||||||||||||||
  629 : CACCCCAACCCGCGGAAGgt.........................agGTGCTGATCATCGGG :  978

  379 : GGTGGAGATGGGGGCGTCCTACGGGAAGTGGTGAAGCACCCCTCTGTGGAGTCGGTGGTCCA :  440
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  979 : GGTGGAGATGGGGGCGTCCTACGGGAAGTGGTGAAGCACCCCTCTGTGGAGTCGGTGGTCCA : 1040

  441 : GTGCGAGATTGATGAG  >>>> Target Intron 3 >>>>  GATGTCATTGAAGTCTC :  473
        ||||||||||||||||++          713 bp         ++|||||||||||||||||
 1041 : GTGCGAGATTGATGAGgt.........................agGATGTCATTGAAGTCTC : 1786

  474 : TAAGAAGTTCCTGCCTGGCATGGCCGTTGGCTTCTCCAGCTCAAAGCTGACTCTCCACGTGG :  535
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1787 : TAAGAAGTTCCTGCCTGGCATGGCCGTTGGCTTCTCCAGCTCAAAGCTGACTCTCCACGTGG : 1848

  536 : GCGATGGCTTTGAGTTCATGAAACAGAACCAAGATGCCTTTGACGTCATCATCACCGACTCC :  597
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1849 : GCGATGGCTTTGAGTTCATGAAACAGAACCAAGATGCCTTTGACGTCATCATCACCGACTCC : 1910

  598 : TCAGACCCCATGG  >>>> Target Intron 4 >>>>  GCCCTGCTGAGAGCCTCTTC :  630
        |||||||||||||++          326 bp         ++||||||||||||||||||||
 1911 : TCAGACCCCATGGgt.........................agGCCCTGCTGAGAGCCTCTTC : 2269

  631 : AAGGAGTCCTATTACCAGCTCATGAAGACAGCACTCAAAGAAGATGGCATCCTGTGCTGCCA :  692
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 2270 : AAGGAGTCCTATTACCAGCTCATGAAGACAGCACTCAAAGAAGATGGCATCCTGTGCTGCCA : 2331

  693 : GGGTGAGTGCCAGTGGCTGCACCTGGACCTCATCAAGGAGATGAGGCACTTCTGCAAATCTC :  754
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 2332 : GGGTGAGTGCCAGTGGCTGCACCTGGACCTCATCAAGGAGATGAGGCACTTCTGCAAATCTC : 2393

  755 : TCTTCCCCGTGGTGGACTACGCCTACTGTAGCATTCCTACCTATCCCAGCGGCCAGATCGGC :  816
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 2394 : TCTTCCCCGTGGTGGACTACGCCTACTGTAGCATTCCTACCTATCCCAGCGGCCAGATCGGC : 2455

  817 : TTCATGCTGTGTAGCAAAAACCCG  >>>> Target Intron 5 >>>>  AGCACCAAC :  849
        ||||||||||||||||||||||||++          85 bp          ++|||||||||
 2456 : TTCATGCTGTGTAGCAAAAACCCGgt.........................agAGCACCAAC : 2573

  850 : TTCCGGGAGCCAGTGCAGCAGTTGACACAGGCCCAGGTGGAGCAGATGCAGCTGAAATACTA :  911
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 2574 : TTCCGGGAGCCAGTGCAGCAGTTGACACAGGCCCAGGTGGAGCAGATGCAGCTGAAATACTA : 2635

  912 : TAACTCGGACATGCACCGTGCCGCCTTCGTACTGCCTGAGTTCACCCGGAAG  >>>> Tar :  964
        |||||||||||||||||||||||||||||||||||| |||||||||||||||++        
 2636 : TAACTCGGACATGCACCGTGCCGCCTTCGTACTGCCCGAGTTCACCCGGAAGgt........ : 2690

  965 : get Intron 6 >>>>  GCCCTCAATGACATAAGCTGAATCCAGGTGCCACTGTGACACC : 1006
          81 bp          ++|||||||||||||||||||||||||||||||||||||||||||
 2691 : .................agGCCCTCAATGACATAAGCTGAATCCAGGTGCCACTGTGACACC : 2811

 1007 : ACCCGAGACCTCAATCGGATTGGACCAAGGATCTTCCAAGTTGTCTGGGGACCACCAGTCCT : 1068
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 2812 : ACCCGAGACCTCAATCGGATTGGACCAAGGATCTTCCAAGTTGTCTGGGGACCACCAGTCCT : 2873

 1069 : GGACCAGACTCCCAGATGACTCTTGCCCACCAACCAAGTGTTACAGGCCCCATGATGCTGCC : 1130
        |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
 2874 : GGACCAGACTCCCAGATGACTCTTGCCCACCAACCAAGTGTTACAGGCCCCACGATGCTGCC : 2935

 1131 : TGGCCTGGCCTGGCCTGGCCTGGCCTGGCCTGCCCTGCTGGGTGGACTCAGTCTCTGTCTGT : 1192
        |||||||||          |||||||||||||||||||||||||||||||||||||||||||
 2936 : TGGCCTGGC----------CTGGCCTGGCCTGCCCTGCTGGGTGGACTCAGTCTCTGTCTGT : 2987

 1193 : CTATCTCTGTGGCGTTCAGCCCCACGCCTATACCAGCTCTGTACAGCACCGCCTATGCCCTG : 1254
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 2988 : CTATCTCTGTGGCGTTCAGCCCCACGCCTATACCAGCTCTGTACAGCACCGCCTATGCCCTG : 3049

 1255 : TGACCCAACAAAATACATGTGTATT : 1279
        |||||||||||||||||||||||||
 3050 : TGACCCAACAAAATACATGTGTATT : 3074

vulgar: MUSSPSYN 3 1279 + 4.143962167-143965267 28 3074 + 6137 M 8 8 G 0 1 M 231 231 5 0 2 I 0 253 3 0 2 M 121 121 5 0 2 I 0 313 3 0 2 M 93 93 5 0 2 I 0 709 3 0 2 M 154 154 5 0 2 I 0 322 3 0 2 M 230 230 5 0 2 I 0 81 3 0 2 M 123 123 5 0 2 I 0 77 3 0 2 M 176 176 G 10 0 M 130 130
-- completed exonerate analysis
BioPerl-1.007002/t/data/expected.blast.out000444000766000024       341213155576321 20326 0ustar00cjfieldsstaff000000000000QUERY	Q_LEN	SBJCT	S_LEN	EXPCT	SCORE	BITS	HSPS	IDEN	CONSV	Q_ALN	S_ALN	Q_GAP	S_GAP	Q_BEG	Q_END	S_BEG	S_END	Q_STR	S_STR	FRAM	DESC
-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----
gi|1401126	504	gb|U49928|HSU49928	3096	0.0e+00	2580	1009	1	1.00	1.00	504	504	0	0	1	504	21	1532		1		Homo sapiens TAK1 binding protein (TAB1) mRNA, complete cds
gi|1401126	504	emb|Z36985|PTPP2CMR	969	4.0e-07	137	57	1	0.25	0.43	261	221	2	42	64	324	182	844		1		P.tetraurelia mRNA for protein phosphatase type 2C
gi|1401126	504	emb|X77116|ATMRABI1	1981	1.0e-05	124	52	1	0.24	0.43	242	191	6	57	55	296	918	1490		1		A.thaliana mRNA for ABI1 protein
gi|1401126	504	gb|U12856|ATU12856	2000	1.0e-05	124	52	1	0.24	0.43	242	191	6	57	55	296	918	1490		1		Arabidopsis thaliana Col-0 abscisic acid insensitive protein (ABI1) mRNA, complete cds


QUERY	Q_LEN	SBJCT	S_LEN	EXPCT	SCORE	BITS	HSPS	FR_ID	FR_CN	FR_ALQ	FR_ALS	Q_ALN	S_ALN	Q_GAP	S_GAP	Q_BEG	Q_END	S_BEG	S_END	AMBIG
-----	-----	------	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----	-----
gi|1401126	504	gb|U49928|HSU49928	3096	0.0e+00	2580	1009	1	1.00	1.00	1.00	0.49	504	504	0	0	1	504	21	1532	-	Homo sapiens TAK1 binding protein (TAB1) mRNA, complete cds
gi|1401126	504	emb|Z36985|PTPP2CMR	969	4.0e-07	137	57	1	0.25	0.43	0.52	0.68	261	221	2	42	64	324	182	844	-	P.tetraurelia mRNA for protein phosphatase type 2C
gi|1401126	504	emb|X77116|ATMRABI1	1981	1.0e-05	124	52	1	0.24	0.43	0.48	0.29	242	191	6	57	55	296	918	1490	-	A.thaliana mRNA for ABI1 protein
gi|1401126	504	gb|U12856|ATU12856	2000	1.0e-05	124	52	1	0.24	0.43	0.48	0.29	242	191	6	57	55	296	918	1490	-	Arabidopsis thaliana Col-0 abscisic acid insensitive protein (ABI1) mRNA, complete cds


BioPerl-1.007002/t/data/exsignalp.out000444000766000024      1450213155576321 17435 0ustar00cjfieldsstaff000000000000*********************** SignalP 3.0 predictions ***********************
Using neural networks (NN) and hidden Markov models (HMM) trained on eukaryotes

----------------------------------------------------------------------
>BC1G_00001.1 predicted protein translation)

SignalP-NN result:
>BC1G_00001.1          length = 100
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    23       0.074   0.32   NO
  max. Y    33       0.014   0.33   NO
  max. S     2       0.075   0.87   NO
  mean S     1-32    0.024   0.48   NO
       D     1-32    0.019   0.43   NO

SignalP-HMM result:
>BC1G_00001.1
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Signal anchor probability: 0.000
Max cleavage site probability: 0.000 between pos. -1 and  0

----------------------------------------------------------------------
>BC1G_00002.1 predicted protein translation)

SignalP-NN result:
>BC1G_00002.1          length = 100
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    26       0.079   0.32   NO
  max. Y    22       0.057   0.33   NO
  max. S     1       0.382   0.87   NO
  mean S     1-21    0.094   0.48   NO
       D     1-21    0.075   0.43   NO

SignalP-HMM result:
>BC1G_00002.1
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Signal anchor probability: 0.000
Max cleavage site probability: 0.000 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00003.1 hypothetical protein translation)

SignalP-NN result:
>BC1G_00003.1          length = 100
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    22       0.934   0.32   YES
  max. Y    22       0.867   0.33   YES
  max. S    13       0.991   0.87   YES
  mean S     1-21    0.939   0.48   YES
       D     1-21    0.903   0.43   YES
# Most likely cleavage site between pos. 21 and 22: VQG-AP

SignalP-HMM result:
>BC1G_00003.1
Prediction: Signal peptide
Signal peptide probability: 1.000
Signal anchor probability: 0.000
Max cleavage site probability: 0.974 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00004.1 hypothetical protein translation)

SignalP-NN result:
>BC1G_00004.1          length = 100
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    30       0.078   0.32   NO
  max. Y    17       0.087   0.33   NO
  max. S     1       0.340   0.87   NO
  mean S     1-16    0.170   0.48   NO
       D     1-16    0.129   0.43   NO

SignalP-HMM result:
>BC1G_00004.1
Prediction: Non-secretory protein
Signal peptide probability: 0.026
Signal anchor probability: 0.000
Max cleavage site probability: 0.009 between pos. 18 and 19

----------------------------------------------------------------------
>BC1G_00005.1 predicted protein translation)

SignalP-NN result:
>BC1G_00005.1          length = 100
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    18       0.085   0.32   NO
  max. Y    18       0.073   0.33   NO
  max. S     3       0.659   0.87   NO
  mean S     1-17    0.176   0.48   NO
       D     1-17    0.125   0.43   NO

SignalP-HMM result:
>BC1G_00005.1
Prediction: Non-secretory protein
Signal peptide probability: 0.027
Signal anchor probability: 0.000
Max cleavage site probability: 0.026 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00006.1 hypothetical protein translation)

SignalP-NN result:
>BC1G_00006.1          length = 35
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    27       0.244   0.32   NO
  max. Y    27       0.035   0.33   NO
  max. S     2       0.161   0.87   NO
  mean S     1-26    0.053   0.48   NO
       D     1-26    0.044   0.43   NO

SignalP-HMM result:
>BC1G_00006.1
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Signal anchor probability: 0.000
Max cleavage site probability: 0.000 between pos. 22 and 23

----------------------------------------------------------------------
>BC1G_00007.1 predicted protein translation)

SignalP-NN result:
>BC1G_00007.1          length = 73
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    22       0.257   0.32   NO
  max. Y    22       0.176   0.33   NO
  max. S     2       0.620   0.87   NO
  mean S     1-21    0.258   0.48   NO
       D     1-21    0.217   0.43   NO

SignalP-HMM result:
>BC1G_00007.1
Prediction: Non-secretory protein
Signal peptide probability: 0.240
Signal anchor probability: 0.000
Max cleavage site probability: 0.228 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00008.1 Homologue of M.grisea pathogenicity protein translation)

SignalP-NN result:
>BC1G_00008.1          length = 100
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    83       0.576   0.32   YES
  max. Y    83       0.431   0.33   YES
  max. S    45       0.976   0.87   YES
  mean S     1-82    0.544   0.48   YES
       D     1-82    0.487   0.43   YES
# Most likely cleavage site between pos. 82 and 83: TQG-AR

SignalP-HMM result:
>BC1G_00008.1
Prediction: Signal anchor
Signal peptide probability: 0.194
Signal anchor probability: 0.737
Max cleavage site probability: 0.056 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00009.1 hypothetical protein translation)

SignalP-NN result:
>BC1G_00009.1          length = 100
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    28       0.425   0.32   YES
  max. Y    28       0.145   0.33   NO
  max. S     4       0.386   0.87   NO
  mean S     1-27    0.121   0.48   NO
       D     1-27    0.133   0.43   NO

SignalP-HMM result:
>BC1G_00009.1
Prediction: Non-secretory protein
Signal peptide probability: 0.005
Signal anchor probability: 0.000
Max cleavage site probability: 0.004 between pos. 19 and 20

----------------------------------------------------------------------
>BC1G_00010.1 hypothetical protein translation)

SignalP-NN result:
>BC1G_00010.1          length = 100
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    23       0.054   0.32   NO
  max. Y    15       0.051   0.33   NO
  max. S     4       0.301   0.87   NO
  mean S     1-14    0.118   0.48   NO
       D     1-14    0.084   0.43   NO

SignalP-HMM result:
>BC1G_00010.1
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Signal anchor probability: 0.113
Max cleavage site probability: 0.000 between pos. -1 and  0

BioPerl-1.007002/t/data/factor7.embl000444000766000024      5170613155576321 17127 0ustar00cjfieldsstaff000000000000ID   HSCFVII    standard; DNA; HUM; 12850 BP.
XX
AC   J02933;
XX
SV   J02933.1
XX
DT   02-APR-1988 (Rel. 15, Created)
DT   02-JUL-1999 (Rel. 60, Last updated, Version 6)
XX
DE   Human blood coagulation factor VII gene, complete cds.
XX
KW   coagulation factor; coagulation factor VII.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; Eutheria;
OC   Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-12850
RX   MEDLINE; 87260948.
RA   O'Hara P.J., Grant F.J., Haldeman B.A., Gray C.L., Insley M.Y., Hagen F.S.,
RA   Murray M.J.;
RT   "Nucleotide sequence of the gene coding for human factor VII, a vitamin
RT   K-dependent protein participating in blood coagulation";
RL   Proc. Natl. Acad. Sci. U.S.A. 84(15):5158-5162(1987).
XX
RN   [2]
RP   856-12446
RX   MEDLINE; 88329723.
RA   O'Hara P.J., Grant F.J.;
RT   "The human factor VII gene is polymorphic due to variation in repeat copy
RT   number in a minisatellite";
RL   Gene 66(1):147-158(1988).
XX
DR   GDB; 119897; F7.
DR   SWISS-PROT; P08709; FA7_HUMAN.
XX
CC   [2]  minisatellite imperfect repeats only.
CC   Draft entry and computer-readable copy of sequence in [1] kindly
CC   provided by P.J.O'Hara, 26-JUN-1987.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..12850
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
FT                   /map="13q34"
FT   prim_transcript 487..12686
FT                   /note="factor VII pre-mRNA (alt.)"
FT   prim_transcript 487..12660
FT                   /note="factor VII pre-mRNA (alt.)"
FT   prim_transcript 487..12664
FT                   /note="factor VII pre-mRNA (alt.)"
FT   exon            <522..585
FT                   /note="factor VII; G00-119-897"
FT                   /gene="F7"
FT   gene            522..585
FT                   /gene="F7"
FT   CDS             join(522..585,1654..1719,4294..4454,6383..6407,6478..6591,
FT                   8307..8447,9419..9528,10124..10247,11064..11659)
FT                   /codon_start=1
FT                   /db_xref="SWISS-PROT:P08709"
FT                   /note="factor VII"
FT                   /protein_id="AAA51983.1"
FT                   /translation="MVSQALRLLCLLLGLQGCLAAGGVAKASGGETRDMPWKPGPHRVF
FT                   VTQEEAHGVLHRRRRANAFLEELRPGSLERECKEEQCSFEEAREIFKDAERTKLFWISY
FT                   SDGDQCASSPCQNGGSCKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCS
FT                   DHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEKRNASKPQGRIVGGKVCPKG
FT                   ECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQ
FT                   SRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSL
FT                   VSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGYSDGSKDS
FT                   CKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPG
FT                   VLLRAPFP"
FT   intron          586..1653
FT                   /note="intron A1"
FT   exon            1654..1719
FT                   /note="optional"
FT   intron          1720..4293
FT                   /note="intron A"
FT   exon            4294..4454
FT                   /number=2
FT   intron          4455..6382
FT                   /note="intron B"
FT   exon            6383..6407
FT                   /number=3
FT   intron          6408..6477
FT                   /note="intron C"
FT   exon            6478..6591
FT                   /number=4
FT   intron          6592..8306
FT                   /note="Intron D"
FT   exon            8307..8447
FT                   /number=5
FT   intron          8448..9418
FT                   /note="Intron E"
FT   exon            9419..9528
FT                   /number=6
FT   intron          9529..10123
FT                   /note="Intron F"
FT   exon            10124..10247
FT                   /number=7
FT   intron          10248..11063
FT                   /note="Intron G"
FT   exon            11064..>11659
FT                   /note="factor VII"
XX
SQ   Sequence 12850 BP; 2532 A; 3888 C; 3902 G; 2528 T; 0 other;
     cccggcactt ctcagtgagg ctctgtggct cacctaagaa accagcctcc cttgcaggca        60
     acgcctagct ggcctggtct ggaggctctc ttcaaatatt tacatccaca cccaagatac       120
     ggtcttgaga tttgactcgc atgattgcta tgggacaagt tttcatctgc agtttaaatc       180
     tgtttcccaa cttacattag gggtttggaa ttctagatcg tatttgaagt gttggtgcca       240
     cacacacctt aacacctgca cgctggcaac aaaaccgtcc gctctgcagc acagctgggg       300
     tcacctgacc tttctcctgt cccccccact tgagctcagt ggctgggcag caggggatgc       360
     atggccactg gcggccaggt gcagctctca gctggggtgt tcagaggacg cctgtgtcct       420
     cccctccccc atccctctgt cacccttgga ggcagagaac tttgcccgtc agtcccatgg       480
     ggaatgtcaa caggcagggg cagcactgca gagatttcat catggtctcc caggccctca       540
     ggctcctctg ccttctgctt gggcttcagg gctgcctggc tgcaggtgcg tccggggagg       600
     ttttctccat aaacttggtg gaagggcagt gggcaaatcc aggagccagc ccgggcttcc       660
     caaaccccgc ccttgctccg gacaccccca tccaccagga gggttttctg gcggctcctg       720
     ttcaatttct ttccttctag aaaccagcat ccaggcacag gaggggaggc ccttcttggt       780
     agcccaggct ttggcgggat tatttttcaa agaactttag gagtgggtgg tgctttcctg       840
     gcccccatgg ccctgcctgt gaggtcggac aagcgcaggg agtctggggc ctctcagagt       900
     gcaggaagtg cgcacagggt gctcccaggc tggggagcac aggtagggga cggtgcgtgg       960
     gggatggcgc ctggggcatg ggggatgggg tgtgggaaac ggcatgtggg gcgtagggga      1020
     tggggtgtgg aggatcgggg gtggggatgg cgtgtggggt gtgggggatg ggccgtgggg      1080
     gggtggggcc tgggaaacag catgtggggc atggggtgtg ggggtgaggt gtgggaaagt      1140
     gtgtggggtg tgggggatgg ggcatggaaa gggcgtgtgg ggtgcagggg atggggcatg      1200
     gaggtgtggg ggatggggtg tgtggggtgt cggggatggg gcatgtgggg tgtgggggat      1260
     ggggcatgga aaggcgtgtg gggtgcagag gatggggcat ggaggtctgg ggcatggggt      1320
     gtgtggggtg tcggggatgg ggcatggaaa gggtgtgtgg ggtgtgggga tagggtcagg      1380
     ggatggcgtg gggggtgtgg catggggatg gcacgtgtgg catggggatg gggatggggg      1440
     gtggggcatg gccgagtggg gctggggctg ggaatggtga gtggggcatg gggatggcga      1500
     gtagggggtg tggcgtgagg atggctagtg gggcgtgggg atggcgtgtg gggatggcga      1560
     gtggggggtg ggctgtgagg gacagtgcct gggatgtggc tgcagcccta gctcacagca      1620
     tggccttatg accccggcca ccttcctgcc caggcggggt cgctaaggcc tcaggaggag      1680
     aaacacggga catgccgtgg aagccggggc ctcacagagg tgagcaggga ctgccactgg      1740
     ttttgtcctg gggcccagtg ggggcaacat cacctccttc ccctcccatg gcaaagagcc      1800
     agcccgcggg gtggctactg cagtgccccc caaggagggt gttccctgct cgagaggaag      1860
     tgaccgctcc agcttggcct tccctgggac tggggtgcag gcgattttat cttctttgct      1920
     ccattctgtt ccttccagat aatcgtgtgt tcttcatcag gttttcctca gttcttgaga      1980
     gcttttctga tgcaaatctg ctttcacccc agggcggtca ccggctctgc tcacaccagc      2040
     ctccaagggt gtgggtgtcc cgggagtgtg ggtgtcccgg gggcgtgggt gtcccgggag      2100
     tgtgggtgtc ccgggggcgt gggtgtcccg ggagtgtggg tgtcccgggg gcgtgggtgt      2160
     cccgggagtg tgggtgtccc gggggagtgg gtgtcccggg agtgtgggtg tcccaggggc      2220
     gtgggtgtcc cgggagtgtg ggtgtcccgg gggcgtgggt gtcccgggag tgtgggtgtc      2280
     ccggaggcga gggtgtcccg ggagtgtggg tgtcccgggg gcgtgggtgt cccgggagtg      2340
     tgggtgtccc gggggagtgg gtgtcccggg agtgtgggtg tcccaggggc gtgggtgtcc      2400
     cgggagtgtg ggtgtcccgg gggcgtgggt gtcccgggag tgtgggtgtc ccggagcgag      2460
     ggtgtcccgg gagtgtgggt gtcccggggg cgtgggtgtc ccggaggcga gggtgtccca      2520
     ggagtgtggg tgtcccgggg gcgtgggtgt cccgggagtg tgggtgtccc ggaggcgagg      2580
     gtgtcccggg agtgtgggtg tcccgggggc gtgggtgtcc cggaggcgag ggtgtcccag      2640
     gagtgtgggt gtcccggggg cgtgggtgtc ccgggagtgt gggtgttcca gaggcgaggg      2700
     tatcccagaa gtgtgagtgt cccgggggtg tgggtgtccc gggggcgtgg gtgtcccggg      2760
     agtgtgggtg tcccgggggc gtgggtatcc cagaagtgtg agtgtcccag gggcgtgggt      2820
     gtccgggggc gtgggtgtcc cgggggtgtg ggtgtcccgg gggtcgtggg tgtcccggga      2880
     gcgtgggtgt cggggactgc agggacatgg gcctcccctc ccactcctgc cgcccagggc      2940
     acctcctgtg aggactcgga gtccgtgagt tcccacctcc ttgagcccga ttctttggtg      3000
     tccccgcctg catcctcagc ctccttccaa accagaccag ttctctaggg gcgtcgacgt      3060
     gtgaaactga ttttaaagaa aacaggcggt ggcctttctc tcggccccac gtggcccagt      3120
     agcgctcacc ttccgtccct tcttccgcgc tcagtaacca atttaggccg ctcctgcaga      3180
     actcgggctc ctgcccaccg gcccacagcg tccacctgag gcctcttcct cccagcaaag      3240
     gtcgtccctc cggaacgcgc ctcctgcggc ctctccagag cccctcccgc gcgtcctctc      3300
     agccccgctc gcctcctccc ggggcctccc tctcccgcct gcccccaggc ccgtctccct      3360
     cgcgggctga ggcaggttcg gcagcacggc gcccggggcg ggggtcactc tccaccaccg      3420
     cgtggtgccc acagctcacg gcgctcccgg gtgacggtcc cctcggctgt agggcgtcct      3480
     gaagagcggc ctgctcggag ctgagcgcac ggggttgcct gcccctgggc gtctctggcc      3540
     ctcaccagcc ccgtcttccc atgggcaaaa cggcggtcct gtttgtccac aagtaaccgt      3600
     cggggttacg gaggggccag gagctgcggc ggggggctgt gctctcagga ccggccccag      3660
     gaggatccgc gcgaggtctg gagctctcag gggtcgcggg ggacagaggg gccccaagcg      3720
     gaggcgggaa ggcggcagaa gcccaggacc gccaagagct ggcgaggaag cccggggctc      3780
     gctgtcgggg gagccgggca ggggccgcgc ctcggcacca ggacgcgagg cctgggaagg      3840
     cggatctggc cgcgagcacg cggtgcgggt ggagacgcag ggatttggat ttccgcgggc      3900
     gctgcacgga tttccacgcg cggttcacgt gggccccagg gggtgcccgg cacccggggc      3960
     cgcgccgcct tctcctgccc ggcatcgacc cgcagcctca cgtttaccgc ggcgcccgca      4020
     gcccccttcg cccgcttccg cgcgtgcccc cgagcgcgcc ctcgggatca gcccccggaa      4080
     gcagagaggc caggccggga aggatgggcg aacggggtgg ctgacccggg agcacggcag      4140
     ggaggacacc cagccaggcc cgcgagcagc gccgctcccc tcctccagga cgggcgggaa      4200
     cctgcgatgc ccccgccgcg tgggccgtgg ggcggtctcc gaggcactgg gcggggcacg      4260
     cggtgggcgc ttcacggaac tcgcatttcc cagtcttcgt aacccaggag gaagcccacg      4320
     gcgtcctgca ccggcgccgg cgcgccaacg cgttcctgga ggagctgcgg ccgggctccc      4380
     tggagaggga gtgcaaggag gagcagtgct ccttcgagga ggcccgggag atcttcaagg      4440
     acgcggagag gacggtgagc ccagcctcgg ggcgccccgc gcggacactg cacggcggcg      4500
     gtgaaccagg ccgcgtgggg ccgcctgcgt ctctttggct gcggcctgtg ggcggcgaac      4560
     acgcagcggc gcccgcgcgc gcgctctctc tgcgggggtc gctttccgcc cggggtgact      4620
     ccgctttcct gggcgatgcc cccaccccca ggcacgcgct ctccccgtgc ggccgcaccg      4680
     cgcatgccgg ttttcacatc agaaaatacg atttgcacaa gcacacttag ggtgtccccc      4740
     ttaacttccc aagggagtcc ccccagtccc cgaagtccag ggcagcctgc gcatcgcaga      4800
     cgcgcgcggc tcgcagaagg gacgtggtga gaagctggcc cacagcatgc caccagcggc      4860
     acctcctcag ggcacgtgtc ggggagaaac aacacttagg gaccctggga ctttctccag      4920
     ctcacgctca cgggtccacc tcacactacc aagatcacct caatagacgg acactcacac      4980
     agggcacact tcacactcac aggtcacctc acactcacag gacacctcac actcacaggg      5040
     cacacttcac actcacgggt cacctcacac tccaagatca cctaaagagg acacctcaca      5100
     cagggcacac ttcacactca caggtcacac ctcacacaga tcatctcatt ctcacaggac      5160
     acctccctct cacaggtcac ctcacactca caggacacct cacagaggtc acctcacacc      5220
     cacaggacac ctcacagagg tcacctcaca cggggcacac ttcacactca ggtcacctca      5280
     cacccacagg acacctcaca gaggtcacct cacacccaca ggacaactca cagaggtcac      5340
     ctcacacagg acacctcaca aaggtcacct cacacccaca ggacacctca cactcatagg      5400
     cacctcagtc ttacaggaca actcacactc acaggtcacc tatctcacag gacacctcac      5460
     actcacaggt caccttactc tcacaggaca cctcacacag ggcacacttc actccacagg      5520
     tcaccatacc tcacacagat cacctcatac tcacagatca cttcattcat tctcacagga      5580
     tacctcacac tcagggcaca cttcacactc acaggtcaca cctcacacag atcatctcat      5640
     tctcacagga cacctccctc tcacaggtca ccttacactc atctcacact cacaggtcgc      5700
     cacacctcac actcacagga tgcctcacac tcacagaacc acatctcata tgcacaagac      5760
     acctcacact caggacacct catgctcaaa gaagcctcac actcacagga ggtccagctg      5820
     tctgaggcaa aggctaacat gaccctttcc agacaaattg aggatggtca tgcctagcat      5880
     ttttatacac ctagttttga aagcatttct catctgttgt attctcacag caccccgtga      5940
     gtttaagttc aggtggccaa cagtttcttc agcaatcact tttttctgtg gagtgctttt      6000
     gctgtttgtg gaatattttg catctgctac tgcaccctct ccccgtatgt gtggccaccc      6060
     tgtcagaggt ggagctgtgg ctcagagcct gtgtacctcg tcccaggtcc acagctcagc      6120
     gacagaagag tcagggttga acctcgggtg ttctgacttg ggagcaggaa atgtgtggtc      6180
     acccatagtt ccagatgtcc tggggagggg ccaagattag aagaaaccta cctcagctcc      6240
     agaggaaagt ctggcttcct gagcccaccc cgccagaccc aggtccaagt cccccaaccc      6300
     cagttcatgg tgtgtccagt gcttaccgtt gggtgctctg gtgaaggtgc atctcacgag      6360
     gcttgctctc ttgttccttc agaagctgtt ctggatttct tacagtggtg agtggatgat      6420
     caccaccagt cctgcctgca acccttctca gcttactgac accagcccac tccacagatg      6480
     gggaccagtg tgcctcaagt ccatgccaga atgggggctc ctgcaaggac cagctccagt      6540
     cctatatctg cttctgcctc cctgccttcg agggccggaa ctgtgagacg cgtaaggccc      6600
     cactttgggt cccatatttg cagagggccc tggggagctg gtggaggtgg cctggccaac      6660
     cgggctgcag ggtgcaacaa cctggtgggg tgtgtaggcc gggcattcag ggctcagccc      6720
     agttggaaat tggtctaggt gacctttaaa tcccttccag tctgaggtct ttgacaggga      6780
     cccaaggttc tgattatcag actcagtggc ccccttcgcg gtcccggccc tgggcaactt      6840
     ctcagccctg gagactggcc cagttgagag tccctgtgtc ccgtgtgccc attccagatc      6900
     ccacctagct aggtacccgt ttggtaaact tccccttctc ctactttcca ttacaaaggt      6960
     ttgaggggtt tgtttttttt tttaaccatc tgaatattaa attaatcaca aagtttaggg      7020
     cccccaacct cccttgggtt cagtaattca ctagaaggac acatagaaat ccaaatatcc      7080
     actgagtgga tacactcaca ggtaccgttt attacagcaa aggatgcagg cttaagtctg      7140
     cagagggacc agggacaagc ttccccttgt cctctcctgt ggggtcatgt ggacatcctt      7200
     aattctccca gaatgacgtg tgacgagaac gtgggaagta ctgccaaact tggggaacgc      7260
     tacgagcccc gtgtccagag gtttgatcag ggctcaatga catagaccca gctgaccagg      7320
     cacgcatggc tgacctcagt ctcagcccct ccagagctac gccgataatg cggccaaggc      7380
     cccaccatac atcacattgt cagctagacc atccagcatg gctcaaggcc caggtaaaca      7440
     ccaacattcc ctcaggcaag accttccaag ggcttagcgg tcatttccca ggagccaagg      7500
     caaaggctac cctttctctg gcacagcagt tcatccttga ccacccaaga ccacattctt      7560
     acactgaatg agctctcctg tgcagcagcc attttcttct ctaagcagaa gagagcccag      7620
     caagctggag gaggctgaag agagaggctt cctgctggtc atctgggtcc agaatgcctg      7680
     gagatctctg ctcagccctg gtgcccagca gccctggtgt gcatcctgca gggcagcctt      7740
     cccgccggag tcctggactt gctcagggcc actccccttg cccatgtcaa ccaaagtcag      7800
     gctgccggtt ctgcttcttc tgtctgagcc catgaccagt gctgggacta actgtccccc      7860
     aggcgggctc acggtggtac gaggccagct tggagaactg tctcagctct ctggtcctct      7920
     cgtcagttgg gtctctgatt ggaaagtccc ttggacactt taccatcccc attggacttt      7980
     cactttcccc caggctccca tcagctgctc ggaagagtgg tcaccctgga ggccactgcc      8040
     caccagccag gcacccccca aatgcaaccg cagccagcac tgccagccac tggcaaggct      8100
     gttcagacat gtggctcctc tgatccacgc cttgtccttt ggatcagtcc acggagcagt      8160
     gtgccaagct caggctctgt cacccacagc tcatgccacc ttccaggcag aacaccactg      8220
     ctgacccagg ggcatggcca ccccgggggc tggcgtctcg ctgaccccca gaagcccctc      8280
     tcagggtgtc cccttcctgt ccccagacaa ggatgaccag ctgatctgtg tgaacgagaa      8340
     cggcggctgt gagcagtact gcagtgacca cacgggcacc aagcgctcct gtcggtgcca      8400
     cgaggggtac tctctgctgg cagacggggt gtcctgcaca cccacaggtg accaggcttc      8460
     atgtcccagt cccagatgac accagtccct gtcccactag gattatctta ctggacaaaa      8520
     gacgggtggg actggccttc acatctactg agcactaact atgcactgac caattgtgag      8580
     gtgggatctg ggcaccaagg gtggcacagg ccagcagcga ccagtgacta ggatgggcac      8640
     cctgggggca atccctgaat ggcctcaggc cccctgccaa cttctaggca gaccagggga      8700
     gccaagcaag gcactatctc acgtccaact gcccactcgc aggaatcctc cgccagggtt      8760
     catgaatcta cttcggcaca gccaatgtct gtactgactg ctgcccactc tgcattccaa      8820
     aactcgtaaa ggctcctggg aaaatgggat gtttctccaa accagcctgg aacgaatggg      8880
     ctgcacttcc aaaagcaggg acaccccaca cccactgtct ctaaagaggc ggaacgtgcc      8940
     caccctggcc acacagcctg ggactcagcc tgccacctcc tcgggcttcc tttctggccc      9000
     aagaccttga ttgaagcaga tcaaaactaa gcatgggatc aaaacaacac agtttgattc      9060
     atctttaggt agaatttcat tcaccttcta ctaaagtcaa acaacacatc ttctccctga      9120
     aaagtgagca gagggcggtt ttaagacgta agccctctgt ttcctccaaa accagccctg      9180
     accattgtct cctcagccag ccacttcttc aagggcctct catggccggg ccccaccagt      9240
     caggcccagc cgaggccctg ccttccacca cccctgggcc ctgggagctc ctgctcctgg      9300
     gggcctccca tagcctcggc ctcaaggcct ctcagaggat gggtgtttct gaatctttcc      9360
     tagtggcacg ttcatccctc acaaatctct gcatctttct gacttttgtt ttacacagtt      9420
     gaatatccat gtggaaaaat acctattcta gaaaaaagaa atgccagcaa accccaaggc      9480
     cgaattgtgg ggggcaaggt gtgccccaaa ggggagtgtc catggcaggt aaggcttccc      9540
     ctggcttcag gattccaagc cctgagggtc ttgaagcctt ttgaatgtga acaacagctc      9600
     tggaagggaa aatgggcagg tcagcccaag cccacaggct ccaagtcagc acacctagca      9660
     cctccagctc gcggcacccc catgctttta gtggggcaag gaaggagaaa agaaaacgac      9720
     actcactgag ggtctaccct gtgcagagaa ccctgcgaga tgccccatcc gagttgtcac      9780
     gtcgtcctca cggttactct ttgaggtggg atctttgcct gatctttgca aaatcaggag      9840
     cattggatca aagctatgtg aagatcctgt gaggtgaaca gtgaaatctc acagcgacat      9900
     ttgtattctt gggccgtgcc caagagcacg tctcggctag agaggggcac agcctcccag      9960
     agccaggtct gagcagcttt gcctgggagg gatctgcaaa gaccccagga tttcagaaag     10020
     aaattgtgca atgccagagg ttccttggca tgcccgggag ggcgagtcat cagagaaaca     10080
     atgacagcaa tgtgacttcc acacctcctg tccccccgcc caggtcctgt tgttggtgaa     10140
     tggagctcag ttgtgtgggg ggaccctgat caacaccatc tgggtggtct ccgcggccca     10200
     ctgtttcgac aaaatcaaga actggaggaa cctgatcgcg gtgctgggtg ggtaccactc     10260
     tcccctgtcc gaccgcggtg ctgggtgggt gccactcttc cctgtccgac cgcggtgctg     10320
     ggtgggtgcc actctcccct gtccgaccgc ggtgctgggt gggtgccact ctcccctgtc     10380
     cgaccgcggt gctgggtggg tgccactctc cgctgtccga ccgcggtgct gggtgggtac     10440
     cactctcccc tgtctgaccg cagctctcaa gtgtctcagg ggctgtggct ctgggcttcg     10500
     tgctgtcact tccacagaca gacagacatc cccaaaaggg gagcaaccat gctgggcacg     10560
     actgcctgtg gcaccgtgct ctcagccact ttcccatgcc caaataaaac gataaaagac     10620
     tgggggcttc tgcccatcct gcctcacttg accaagagcc cagaagagga tgcgacaccc     10680
     agggcctcat gggaccaccg gctggcaggg gttctgctca ctgggtttat gggtgagacg     10740
     agcactccca ggagggccac tgggccggga agaactgtgg agaatcgggg cacgccctgt     10800
     cctcccagct gccagggcac agcatccctt ccccacctgc aacacccaga ccccagattc     10860
     accccagttc acttgtcccc acacgagcca caggctgcca cctggggcag gctggcccac     10920
     cttggggtta gatgcaggtc cccttgcccc agaaggagac tgcagcccct gcagacctag     10980
     aaatggccac agcccatccc catgcaccag ggggtgaggt ggcaggtggt ggaaagggcc     11040
     tgaggggggc ttcttccttc caggcgagca cgacctcagc gagcacgacg gggatgagca     11100
     gagccggcgg gtggcgcagg tcatcatccc cagcacgtac gtcccgggca ccaccaacca     11160
     cgacatcgcg ctgctccgcc tgcaccagcc cgtggtcctc actgaccatg tggtgcccct     11220
     ctgcctgccc gaacggacgt tctctgagag gacgctggcc ttcgtgcgct tctcattggt     11280
     cagcggctgg ggccagctgc tggaccgtgg cgccacggcc ctggagctca tggtcctcaa     11340
     cgtgccccgg ctgatgaccc aggactgcct gcagcagtca cggaaggtgg gagactcccc     11400
     aaatatcacg gagtacatgt tctgtgccgg ctactcggat ggcagcaagg actcctgcaa     11460
     gggggacagt ggaggcccac atgccaccca ctaccggggc acgtggtacc tgacgggcat     11520
     cgtcagctgg ggccagggct gcgcaaccgt gggccacttt ggggtgtaca ccagggtctc     11580
     ccagtacatc gagtggctgc aaaagctcat gcgctcagag ccacgcccag gagtcctcct     11640
     gcgagcccca tttccctagc ccagcagccc tggcctgtgg agagaaagcc aaggctgcgt     11700
     cgaactgtcc tggcaccaaa tcccatatat tcttctgcag ttaatggggt agaggagggc     11760
     atgggaggga gggagaggtg gggagggaga cagagacaga aacagagaga gacagagaca     11820
     gagagagact gagggagaga ctctgaggac atggagagag actcaaagag actccaagat     11880
     tcaaagagac taatagagac acagagatgg aatagaaaag atgagaggca gaggcagaca     11940
     ggcgctggac agaggggcag gggagtgcca aggttgtcct ggaggcagac agcccagctg     12000
     agcctcctta cctcccttca gccaagcccc acctgcacgt gatctgctgg ccctcaggct     12060
     gctgctctgc cttcattgct ggagacagta gaggcatgaa cacacatgga tgcacacaca     12120
     cacacgccaa tgcacacaca cagagatatg cacacacacg gatgcacaca cagatggtca     12180
     cacagagata cgcaaacaca ccgatgcaca cgcacataga gatatgcaca cacagatgca     12240
     cacacagata tacacatgga tgcacgcaca tgccaatgca cgcacacatc agtgcacacg     12300
     gatgcacaga gatatgcaca caccgatgtg cgcacacaca gatatgcaca cacatggatg     12360
     agcacacaca caccaagtgc gcacacacac cgatgtacac acacagatgc acacacagat     12420
     gcacacacac cgatgctgac tccatgtgtg ctgtcctctg aaggcggttg tttagctctc     12480
     acttttctgg ttcttatcca ttatcatctt cacttcagac aattcagaag catcaccatg     12540
     catggtggcg aatgccccca aactctcccc caaatgtatt tctcccttcg ctgggtgccg     12600
     ggctgcacag actattcccc acctgcttcc cagcttcaca ataaacggct gcgtctcctc     12660
     cgcacacctg tggtgcctgc cacccactgg gttgcccatg attcattttt ggagcccccg     12720
     gtgctcatcc tctgagatgc tcttttcttt cacaattttc aacatcactg aaatgaaccc     12780
     tcacatggaa gctatttttt aaaaacaaaa gctgtttgat agatgtttga ggctgtagct     12840
     cccaggatcc                                                            12850
//
BioPerl-1.007002/t/data/fgenesh.out000444000766000024       707013155576321 17044 0ustar00cjfieldsstaff000000000000 FGENESH 2.3 Prediction of potential genes in C_elegans genomic DNA
 Time    :   Wed Feb 27 13:43:15 2008
 Seq name: gi|1914348|emb|Z81551.1| Caenorhabditis elegans Cosmid F56A12, complete sequence 
 Length of sequence: 26028 
 Number of predicted genes 4 in +chain 1 in -chain 3
 Number of predicted exons 19 in +chain 4 in -chain 15
 Positions of predicted genes and exons:
   G Str   Feature   Start        End    Score           ORF           Len

   1 -      PolA        29               -0.94
   1 -    1 CDSl       828 -       903    2.72       828 -       902     75
   1 -    2 CDSf       996 -      1201    9.86       998 -      1201    204
   1 -      TSS       1869               -4.49

   2 -      PolA      9879                1.25
   2 -    1 CDSl     10132 -     10275    7.05     10132 -     10275    144
   2 -    2 CDSi     11180 -     11291    3.76     11180 -     11290    111
   2 -    3 CDSi     11786 -     12035    1.01     11788 -     12033    246
   2 -    4 CDSi     12238 -     12404    9.79     12239 -     12403    165
   2 -    5 CDSf     12884 -     12900    0.72     12886 -     12900     15
   2 -      TSS      13142               -4.89

   3 +      TSS      14096               -7.69
   3 +    1 CDSf     14778 -     15104   27.84     14778 -     15104    327
   3 +    2 CDSi     15673 -     15802   20.10     15673 -     15801    129
   3 +    3 CDSi     16175 -     16524   28.83     16177 -     16524    348
   3 +    4 CDSl     16988 -     17212   15.92     16988 -     17212    225
   3 +      PolA     17223                1.25

   4 -      PolA     17420                1.25
   4 -    1 CDSl     17552 -     17630    0.75     17552 -     17629     78
   4 -    2 CDSi     17690 -     17848   22.67     17692 -     17847    156
   4 -    3 CDSi     18221 -     18453   26.88     18223 -     18453    231
   4 -    4 CDSi     18501 -     18637   19.50     18501 -     18635    135
   4 -    5 CDSi     18850 -     19024    8.97     18851 -     19024    174
   4 -    6 CDSi     19073 -     19156    8.63     19073 -     19156     84
   4 -    7 CDSi     19206 -     19472   23.22     19206 -     19472    267
   4 -    8 CDSf     20381 -     20479   21.19     20381 -     20479     99
   4 -      TSS      21231               -5.29

Predicted protein(s):
>FGENESH:   1   2 exon (s)    828  -   1201    93 aa, chain -
MSCRHRSTSTTGCKHQNILYAREKMYVWECQHGNGKKGEKLIVGMGVLELLGVSMRILYA
REKVSAWEICFGFYKFSFQKAENHETCRKIIEN
>FGENESH:   2   5 exon (s)  10132  -  12900   229 aa, chain -
MNLLQSTSIDYHVAHNVWLQMENNLYFLRIHLLSSPIWGVGAAVNTFLIETVDQITIAGV
KRGLSLLNYFLFTYGKPLPIEHIVKGPLSTKIPSMCYWQLCSKIFRKMKTPKSGKTEFLC
VSIFVAQAFFSFKDPEARDKAETLDNDHVAGVVKIVAPITYIYTSPSILLAQTSCLERRT
PVKYIDLFLCFFFLFFFPDPLVLIGTGWHAWAPLTIICSMFSDEKSTNS
>FGENESH:   3   4 exon (s)  14778  -  17212   343 aa, chain +
MSSIPPYFMTDHPPIDTSSYFDCYQQHQLPLQYTFTSSSNSNTSNSSTSPSHISDQFSSS
GGPPYELSSHILTPSSVIPTPSPSVASASISSPTIPAFGCTMSEYSMEQMEAISTSLFQA
RDGDRLVAFFKQLESLYGPNAVDHLRSEAIIVAYTYALYHSNEFETLFHLLSNRHFQQRH
YNDLQDIWHHARYKESQLKRGKELNPVEKYRLRRKFPAPKTIWDGEEIVYSFKDSSRKFL
KQFFRNVSEYPTQEQKREISRATGLKIVQISNWFKNRRQRDKSNNSAKCSPPSSSSSTNG
GSDFLPIITPQSFNLAAAPFNMNMIYGTLRDSQSDNDQFTFNP
>FGENESH:   4   8 exon (s)  17552  -  20479   410 aa, chain -
MNETDDNWTVFTKLYSCQYRASDDSPQFTLWLDGPVTISAAIFSAIGTVYAIGFLRNGHL
NRRMSAALYTLCLMDFMLTMTTVLFLSIEPLSILLFRTNIFYQHQDMILILYGIRNSFAM
SSPMLVCYITYIRYRVVNNPLKFASHYGRSRKSISASKMSTAAQPSSTESAKFTISFPAE
MFYEFHTRSNAGKRGANFRRFFRPFLVPILLVILCFVIHSTSYFEFNLITCFDEVHQTES
KMLQMTQLRGDSYWYFQFKVALTMTTETLGPMLFISTLSLFTEYKMHQNVKERRRLFESQ
KRSRNTLVTEELKDKASKALAVFIVVKFLILRSLPTLIDLYEVLIENSINFGPFMTKVTR
ISDFLVILNSATNTLAYFGKVRFEKWLERRIRCRIVKKEAKEILSTSLTG
BioPerl-1.007002/t/data/footprinter.out000444000766000024      3411213155576321 20015 0ustar00cjfieldsstaff000000000000>TETRAODON
tcgtcaatgccctaatataattcttagtaaaaatacaggtataaaaatgcaacgtattttaatacaggcattttaataca
                                                                                
                                                                                

ggtatacaaatggcacgtattgtttgaaacctttaaacatgtgataagtgttaacacgtacactagccgtgtgtttttac
                                                                                
                                                                                

tggaactgctcaaacaatacgtggtgtttaagtttacttttgatgtacttttgtagtgttggatgtacttttgctgaccg
                                                                                
                                                                                

ttatcccagttctttagttttcacaacagctgttgtgtttgttgtcttacgtaacgtggtgcagatgtcgccaatgccgg
                                                                                
                                                                                

agagcctgtttcccagcaggcccgccccttttacaggatgcaccatatttggaaaatgacgtactggggatcccgtttct
                               2222222222222222222222                           
                               2222222222211111111111                           

ggaatattccatttattggaggtaccattaaacgacaacttttacgttagaatttccgctttaaacggtaaaaattctca
                                                                                
                                                                                

aatatgttaagtttttgcgtgttagatagaagaacgtgagtggttttgtgttactgccgcgttgttaggtcggtgttttg
                                                                                
                                                                                

gtgtttgcttcgcggcgtttgaaagggaacgctccccttttgctgacgtcatcagctcaggctatataagcgcgcgtgcg
                                                                                
                                                                                

gcgactccgccgaaagtttcagacgagagcaagagaagccagagcacgtccgcgggctcacacaccgacctgaccgaaga
                                                                                
                                                                                

ttccctcctttccagggttgaaatcccgaccgcagcctttgtttggatttaccagcttgctttttttcgcccggacagcg
                                                                                
                                                                                





>CHICKEN
ggctctccggagggccacgcggccccggggccgccccgcactgcttcccggccctccgtgcgcgtgaccccgccgggcgg
                                                                                
                                                                                

acgcgtccccgccgcgagccgcgacggccccgcacacgcggcacccgcccgccgcagggcacggggacgaagggcgccgc
                                                                                
                                                                                

gccccgccgcgccccacgcgtggccgcgcccggccccgttagtacggaacccccgccgggccgctcggggcggggggtgc
                                                                                
                                                                                

cggcggccggggggcgctacgcgggggggggggggggctggggcggccccgtcccaccgcgtcccgtcccgcgccgcact
                                                                                
                                                                                

tggccgcagcctggagcgcttcccgtcagtcacgccccctcgcacaggatgtatcccatataaggatatctgcgtcagtg
                                          22222222222  22222222222              
                                          22222222222  11111111111              

ggttcccgagcccggccgtaccactccgcgaggggggggggaaacccggaaccgctccccccgccccgccgcgctcctcc
                                                                                
                                                                                

cgccccgcggccccgttgttcccggcgcccggcggctcggcagggcgggcggcggggccgggcggggcgggacgagacgg
                                                                                
                                                                                

acgcgggcagagaggccccctccgcgggcgggcgtggtgcgtcccacgtgacgtaggcgattcacgcggcggcagggtat
                                                                                
                                                                                

aaagggggcggcgccgagcgatactccagcggcagaggcagctccgacagcggagagagagacgcgcggcgcggaccgga
                                                                                
                                                                                

cacagggacgcagccggcccctcttcgccttctcccgcagggcgctccgctagcaccgcacggccccgcaaacagccgac
                                                                                
                                                                                





>MOUSE
ataccagagactcaaaaaaaaaaaaaaagttccagattgctggacaatgacccgggtctcatcccttgaccctgggaacc
                                                                                
                                                                                

gggtccacattgaatcaggtgcgaatgttcgctcgccttctctgcctttcccgcctcccctcccccggccgcggccccgg
                                                                                
                                                                                

ttccccccctgcgctgcaccctcagagttggctgcagccggcgagctgttcccgtcaatccctccctcctttacacagga
                                                                         2222222
                                                                         2222222

tgtccatattaggacatctgcgtcagcaggtttccacggccggtccctgttgttctgggggggggaccatctccgaaatc
22222222222222                                                                  
22211111111111                                                                  

ctacacgcggaaggtctaggagaccccctaagatcccaaatgtgaacactcataggtgaaagatgtatgccaagacgggg
                                                                                
                                                                                

gttgaaagcctggggcgtagagttgacgacagagcgcccgcagagggccttggggcgcgcttccccccccttccagttcc
                                                                                
                                                                                

gcccagtgacgtaggaagtccatccattcacagcgcttctataaaggcgccagctgaggcgcctactactccaaccgcga
                                                                                
                                                                                

ctgcagcgagcaactgagaagactggatagagccggcggttccgcgaacgagcagtgaccgcgctcccacccagctctgc
                                                                                
                                                                                

tctgcagctcccaccagtgtctacccctggaccccttgccgggctttccccaaacttcgacc
                                                              
                                                              

>HAMSTER
ggctgagaaaattataacatttttttttgcactgatttgcggtgggcaagcttttcaagcctttagggctgcgtaccagt
                                                                                
                                                                                

ttctcctaatatcagattcagaaatgtcccaaattcctggacaatggaaaggaggcgacccccgccccccccaccccagt
                                                                                
                                                                                

ttcatggccctgacctgggaacagggtccacattgaatcaggtgcgaatgttcgctcgccttctctacctttcccgcctc
                                                                                
                                                                                

ccctcccccggccgcggccccagctcccccctcccccgcgctgcaccctcagagttggctgcagccggcaagcagttccc
                                                                                
                                                                                

gtcaatccctttcccacaggatgtccatattaggacatctgcgtcagcaggtttccacggccggtccttgtagacctggg
              222222222222222222222                                             
              222222222211111111111                                             

ggtgacgatccccaaaatcctacatgcggagagtccaggagaccccctaagacccctattgtgaacacaaatgggtgaaa
                                                                                
                                                                                

attacatgtcaagacggaggcgggggacccggggcgcggagttgacgccagggcggccgcagaaggcctgggggcgcgcg
                                                                                
                                                                                

gctcccctccgtcgccacagttccgcccagtgacgtgtaatgttcattcacaagcgcttctataaaggcaccggctgagg
                                                                                
                                                                                

cgcctactactccaaccgcgactgcagctagcgactgagaagactggatagagccggcggcgggaacgagcagtgaccgc
                                                                                
                                                                                

gctcccacccagctctgctccgcagctcgcaccagtgtctacccctggacccctcgccggactttccctagatctcgacc
                                                                                
                                                                                





>HUMAN
agaattggggatgggggtaggggcgcattccttcgggagccgaggcttaagtcctcggggtcctgtactcgatgccgttt
                                                                                
                                                                                

ctcctatctctgagcctcagaactgtcttcagtttccgtacaagggtaaaaaggcgctctctgccccatcccccccgacc
                                                                                
                                                                                

tcgggaacaagggtccgcattgaaccaggtgcgaatgttctctctcattctgcgccgttcccgcctcccctcccccagcc
                                                                                
                                                                                

gcggcccccgcctccccccgcactgcaccctcggtgttggctgcagcccgcgagcagttcccgtcaatccctcccccctt
                                                                                
                                                                                

acacaggatgtccatattaggacatctgcgtcagcaggtttccacggcctttccctgtagccctggggggagccatcccc
 222222222222222222222                                                          
 222222222211111111111                                                          

gaaacccctcatcttggggggcccacgagacctctgagacaggaactgcgaaatgctcacgagattaggacacgcgccaa
                                                                                
                                                                                

ggcgggggcagggagctgcgagcgctggggacgcagccgggcggccgcagaagcgcccaggcccgcgcgccacccctctg
                                                                                
                                                                                

gcgccaccgtggttgagcccgtgacgtttacactcattcataaaacgcttgttataaaagcagtggctgcggcgcctcgt
                                                                                
                                                                                

actccaaccgcatctgcagcgagcaactgagaagccaagactgagccggcggccgcggcgcagcgaacgagcagtgaccg
                                                                                
                                                                                

tgctcctacccagctctgcttcacagcgcccacctgtctccgcccctcggcccctcgcccggctttgcctaaccgccacg
                                                                                
                                                                                





>PIG
gcaccgaattagtgatagaatgaggaatgggggtggaggcgcattccttcgggggccaaggcttaagcccaaggggctgt
                                                                                
                                                                                

gtacctatctcgcctatacctgaacctcagaactcttcccgggtttctgtacacaagtaaaaaggcgcctacgccccatc
                                                                                
                                                                                

ccccaaccccgggaacaagggtccgcattgaaccaggtgcgaatgttcgctcgccttctctgcctttcccgcctcccctc
                                                                                
                                                                                

cccccggccacggcccccgcctcccccccgcgctgcacccttggtgttggctgcagcccgcgagcagttcccgtcaatcc
                                                                                
                                                                                

ctccctcccgtttacacaggatgtccatattaggacatctgcgtcagcaggtttccacggccgttccctgaagttgtggg
              222222222222222222222                                             
              222222222211111111111                                             

gggagccatccccgaagtccctcattttagggggtctacgcgaccccaagaccgagactgagaaaagctcagaagataaa
                                                                                
                                                                                

gaaacacaataagacgaaaggcagggggctgagacggcggaagaggcagcaaagaggctgcagaggtggcaagatccgag
                                                                                
                                                                                

cgccacccctcgagagctgcaatggtagcgctccgtgacgtattgggctcattcataaaatgctgttataaaagcagtgg
                                                                                
                                                                                

cctagtactccaaccgcatctgcagcgagcagctaagctgagacagaaccggcagcggcgcagcgagcgagcagcgaccg
                                                                                
                                                                                

cgctcttacccagctcagccccgcagctcctacctgtctccgcccctcagcccctcgcccggctttgactacctgcgatc
                                                                                
                                                                                





BioPerl-1.007002/t/data/forward_primer.fa000444000766000024         3413155576321 20157 0ustar00cjfieldsstaff000000000000>926F
AAACTTAAAGGAATTGACGG

BioPerl-1.007002/t/data/forward_reverse_primers.fa000444000766000024         6213155576321 22076 0ustar00cjfieldsstaff000000000000>926F
AAACTYAAAKGAATTGRCGG
>1392R
ACGGGCGGTGTGTRC
BioPerl-1.007002/t/data/frac_problems.blast000444000766000024      5117213155576321 20563 0ustar00cjfieldsstaff000000000000BLASTN 2.2.14 [May-07-2006]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.
Database: LTR_STRUC_8x_na 
           791 sequences; 6,808,925 total letters

Searching

Query= jgi|Phypa1|75037|fgenesh1_pg.scaffold_51000008
         (2511 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

scaffold_5_1_Scaffolds_seq10928_PT_B1_L1_270_rprt_txt                1356   0.0  

>scaffold_5_1_Scaffolds_seq10928_PT_B1_L1_270_rprt_txt
          Length = 16463

 Score = 1356 bits (684), Expect = 0.0
 Identities = 684/684 (100%)
 Strand = Plus / Plus

                                                                        
Query: 1088 ctacaatacgaggtacaataggttgggaggatcctgttgaatctctttcagttcatgcat 1147
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8914 ctacaatacgaggtacaataggttgggaggatcctgttgaatctctttcagttcatgcat 8973

                                                                        
Query: 1148 atattgctaagagccaacatgaagctttgatggaagaaaagaaacgaggaaattttgatg 1207
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8974 atattgctaagagccaacatgaagctttgatggaagaaaagaaacgaggaaattttgatg 9033

                                                                        
Query: 1208 atacgagagaaggaaattcttctaagaggcaaactcgaggagacaaggctcgggaggcag 1267
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 9034 atacgagagaaggaaattcttctaagaggcaaactcgaggagacaaggctcgggaggcag 9093

                                                                        
Query: 1268 cttcacaagaattgcctctaaaggatacctcaacatcattggaagaaaaaacaagggaga 1327
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 9094 cttcacaagaattgcctctaaaggatacctcaacatcattggaagaaaaaacaagggaga 9153

                                                                        
Query: 1328 caaatgataagggcaaatcaattgcttataaactactttctgacattgaagtggcaacaa 1387
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 9154 caaatgataagggcaaatcaattgcttataaactactttctgacattgaagtggcaacaa 9213

                                                                        
Query: 1388 atttgaaaggggtgttggaagaacgtatattaaatgctaaggtggaattcacattgaaag 1447
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 9214 atttgaaaggggtgttggaagaacgtatattaaatgctaaggtggaattcacattgaaag 9273

                                                                        
Query: 1448 aagttttggaaattgcaaagaaggagtttcatgatgttatcattgacagcattaagcaaa 1507
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 9274 aagttttggaaattgcaaagaaggagtttcatgatgttatcattgacagcattaagcaaa 9333

                                                                        
Query: 1508 agagaaaattaatggacaaaactggaatgagtcatactattgatgcaagaatatataaag 1567
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 9334 agagaaaattaatggacaaaactggaatgagtcatactattgatgcaagaatatataaag 9393

                                                                        
Query: 1568 atgaagaagaggttgatattggttacaagcaactaaaaaatgaaaagaataggtataatc 1627
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 9394 atgaagaagaggttgatattggttacaagcaactaaaaaatgaaaagaataggtataatc 9453

                                                                        
Query: 1628 aacgaatacgttttgaagattatattgataaggaaatggaaaccttgagccattatactc 1687
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 9454 aacgaatacgttttgaagattatattgataaggaaatggaaaccttgagccattatactc 9513

                                                                        
Query: 1688 gaaagcattggacaagagcaactaatgaggtattggtgaaagtaggagatatagaagaac 1747
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 9514 gaaagcattggacaagagcaactaatgaggtattggtgaaagtaggagatatagaagaac 9573

                                    
Query: 1748 caattgttgttttagttgaccatg 1771
            ||||||||||||||||||||||||
Sbjct: 9574 caattgttgttttagttgaccatg 9597



 Score = 1154 bits (582), Expect = 0.0
 Identities = 582/582 (100%)
 Strand = Plus / Plus

                                                                         
Query: 1930  ccagattatggaggtacaaaagaggaggtactctctcgagatgaaggtgccattgatgta 1989
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 10015 ccagattatggaggtacaaaagaggaggtactctctcgagatgaaggtgccattgatgta 10074

                                                                         
Query: 1990  agttttattggtattttggagaatgaaaatattatgtataagaaagttgatgattttaaa 2049
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 10075 agttttattggtattttggagaatgaaaatattatgtataagaaagttgatgattttaaa 10134

                                                                         
Query: 2050  agaaaagaaagaaaaaaaatatatcatattgaaggagaattatgcaagttaggtacattg 2109
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 10135 agaaaagaaagaaaaaaaatatatcatattgaaggagaattatgcaagttaggtacattg 10194

                                                                         
Query: 2110  caagatgatgagaggattttaggtgtttatgaagaaaatgggctggaagattcattggaa 2169
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 10195 caagatgatgagaggattttaggtgtttatgaagaaaatgggctggaagattcattggaa 10254

                                                                         
Query: 2170  ttgattacatctattcggttagaagataatgataagattgttgagattcattcgaaagaa 2229
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 10255 ttgattacatctattcggttagaagataatgataagattgttgagattcattcgaaagaa 10314

                                                                         
Query: 2230  gtttataccatacttgaatcttttcaagcaccagaagtcactatagagacaagatataaa 2289
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 10315 gtttataccatacttgaatcttttcaagcaccagaagtcactatagagacaagatataaa 10374

                                                                         
Query: 2290  atggcagataagaagataaagcctgttgccggaccattaccaaaagattctaaggaacaa 2349
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 10375 atggcagataagaagataaagcctgttgccggaccattaccaaaagattctaaggaacaa 10434

                                                                         
Query: 2350  atgggagaagaatcaaaagaagcaagtttaagggatccaatgagtattggacatcagttt 2409
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 10435 atgggagaagaatcaaaagaagcaagtttaagggatccaatgagtattggacatcagttt 10494

                                                                         
Query: 2410  actaaagagacttttgaagaattgaagattgattctgatggttctttattgccggaagaa 2469
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 10495 actaaagagacttttgaagaattgaagattgattctgatggttctttattgccggaagaa 10554

                                                       
Query: 2470  attacttacttcaaaaagatgttggctaaacaaggtagatag 2511
             ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 10555 attacttacttcaaaaagatgttggctaaacaaggtagatag 10596



 Score =  918 bits (463), Expect = 0.0
 Identities = 463/463 (100%)
 Strand = Plus / Plus

                                                                        
Query: 336  ggaatatttcaaggtatttacgataccaaagataagagaccatattacattgattacgga 395
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 7931 ggaatatttcaaggtatttacgataccaaagataagagaccatattacattgattacgga 7990

                                                                        
Query: 396  tcgttatggaaattcatgggaggttttttcacatgcattgaaagatgaatatttcttgga 455
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 7991 tcgttatggaaattcatgggaggttttttcacatgcattgaaagatgaatatttcttgga 8050

                                                                        
Query: 456  agatgctgatcacattactaagaagttgtttctggaatggattgaacggcctaataagaa 515
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8051 agatgctgatcacattactaagaagttgtttctggaatggattgaacggcctaataagaa 8110

                                                                        
Query: 516  tttacaagcaacagagctactaagggaatttgagaggcagtactctcaattattgaaggt 575
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8111 tttacaagcaacagagctactaagggaatttgagaggcagtactctcaattattgaaggt 8170

                                                                        
Query: 576  agaaaaattgacattggagccgaacaaatttgatctatttcttcaagctgctgatggaga 635
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8171 agaaaaattgacattggagccgaacaaatttgatctatttcttcaagctgctgatggaga 8230

                                                                        
Query: 636  attgcaagggaaattagaattccttcttgaagacaaagaagaaggtgaaggattgacaac 695
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8231 attgcaagggaaattagaattccttcttgaagacaaagaagaaggtgaaggattgacaac 8290

                                                                        
Query: 696  aaagtggaagaacattgaagatgcggtggagttgcttacaaaaagagaaaggaggaaaga 755
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8291 aaagtggaagaacattgaagatgcggtggagttgcttacaaaaagagaaaggaggaaaga 8350

                                                       
Query: 756  taggagtaatattccgaaaatagtacaagcacccaaagctcca 798
            |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8351 taggagtaatattccgaaaatagtacaagcacccaaagctcca 8393



 Score =  573 bits (289), Expect = e-163
 Identities = 289/289 (100%)
 Strand = Plus / Plus

                                                                        
Query: 799  aatgtttcaaaacaaggatatgtacaaagatgcatttggtgtgatgatgctttatacact 858
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8550 aatgtttcaaaacaaggatatgtacaaagatgcatttggtgtgatgatgctttatacact 8609

                                                                        
Query: 859  aggaaagattgcaatgaatttaataatatgatacggcaaggaattatttgctggaaagat 918
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8610 aggaaagattgcaatgaatttaataatatgatacggcaaggaattatttgctggaaagat 8669

                                                                        
Query: 919  ggaaagatagcattaaaagatagggaggatcttcttctaaccaactttgacaagagagga 978
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8670 ggaaagatagcattaaaagatagggaggatcttcttctaaccaactttgacaagagagga 8729

                                                                        
Query: 979  atgagagcattggttcaagattacttaaaagagcatgaaacagcagcacgagaaagtaca 1038
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8730 atgagagcattggttcaagattacttaaaagagcatgaaacagcagcacgagaaagtaca 8789

                                                             
Query: 1039 agttatggtgctagagtagatgatgaccttagtggaagtacggaaacta 1087
            |||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8790 agttatggtgctagagtagatgatgaccttagtggaagtacggaaacta 8838



 Score =  315 bits (159), Expect = 2e-85
 Identities = 159/159 (100%)
 Strand = Plus / Plus

                                                                        
Query: 1771 gctaataacacatggggcgaattatatggagctcgtccagatgtcaaaatttggattggg 1830
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 9684 gctaataacacatggggcgaattatatggagctcgtccagatgtcaaaatttggattggg 9743

                                                                        
Query: 1831 gatgttgcgacggagcaacatttctttgttcaagatacaacgtcttatccgttgatttta 1890
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 9744 gatgttgcgacggagcaacatttctttgttcaagatacaacgtcttatccgttgatttta 9803

                                                   
Query: 1891 gaacaaccttatattatggcaatacggatggaaacaaaa 1929
            |||||||||||||||||||||||||||||||||||||||
Sbjct: 9804 gaacaaccttatattatggcaatacggatggaaacaaaa 9842



 Score =  230 bits (116), Expect = 7e-60
 Identities = 116/116 (100%)
 Strand = Plus / Plus

                                                                        
Query: 95   acagtcagtggatacaagatcgtgagtataaagcggtatcgaagattagcagattgggtt 154
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 7360 acagtcagtggatacaagatcgtgagtataaagcggtatcgaagattagcagattgggtt 7419

                                                                    
Query: 155  gttcgggattctttgtaacgtctagagacctaccggctgaggcaaaaaggattttg 210
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 7420 gttcgggattctttgtaacgtctagagacctaccggctgaggcaaaaaggattttg 7475



 Score =  186 bits (94), Expect = 1e-46
 Identities = 94/94 (100%)
 Strand = Plus / Plus

                                                                        
Query: 1    atggtgtttaattgggcagcttatgtagcaactcgtattcatgcggaaatgggagccaag 60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6461 atggtgtttaattgggcagcttatgtagcaactcgtattcatgcggaaatgggagccaag 6520

                                              
Query: 61   tgcaaaatagagaagtttacagtgttgtcgtatt 94
            ||||||||||||||||||||||||||||||||||
Sbjct: 6521 tgcaaaatagagaagtttacagtgttgtcgtatt 6554



 Score =  182 bits (92), Expect = 2e-45
 Identities = 110/116 (94%)
 Strand = Plus / Plus

                                                                         
Query: 95    acagtcagtggatacaagatcgtgagtataaagcggtatcgaagattagcagattgggtt 154
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 14136 acagtcagtggatacaagatcgtgagtataaagcggtatcgaagattagcagattgggtt 14195

                                                                     
Query: 155   gttcgggattctttgtaacgtctagagacctaccggctgaggcaaaaaggattttg 210
             ||||||| |||| ||||| ||||||||||||||| |||| | ||||||||||||||
Sbjct: 14196 gttcggggttctctgtaatgtctagagacctaccagctgggacaaaaaggattttg 14251



 Score =  139 bits (70), Expect = 2e-32
 Identities = 70/70 (100%)
 Strand = Plus / Plus

                                                                        
Query: 210  gagaacgaaaataaaaattttgaaggatctttgggaggagtttctggtggaggttcttct 269
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 7717 gagaacgaaaataaaaattttgaaggatctttgggaggagtttctggtggaggttcttct 7776

                      
Query: 270  caaggacaag 279
            ||||||||||
Sbjct: 7777 caaggacaag 7786



 Score =  119 bits (60), Expect = 2e-26
 Identities = 60/60 (100%)
 Strand = Plus / Plus

                                                                        
Query: 278  agcaacagcaaagcaatgatcaagaggaagctttggcaaccaaagcattgcaagcagtgg 337
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 7844 agcaacagcaaagcaatgatcaagaggaagctttggcaaccaaagcattgcaagcagtgg 7903


  Database: LTR_STRUC_8x_na
    Posted date:  Sep 4, 2006  3:29 PM
  Number of letters in database: 6,808,925
  Number of sequences in database:  791
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 791
Number of Hits to DB: 350,368
Number of extensions: 23312
Number of successful extensions: 1851
Number of sequences better than 1.0e-04: 233
Number of HSP's gapped: 1699
Number of HSP's successfully gapped: 1236
Length of query: 2511
Length of database: 6,808,925
Length adjustment: 17
Effective length of query: 2494
Effective length of database: 6,795,478
Effective search space: 16947922132
Effective search space used: 16947922132
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 25 (49.6 bits)
S1: 15 (30.2 bits)
S2: 24 (48.1 bits)


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.
Database: LTR_STRUC_8x_na 
           791 sequences; 6,808,925 total letters

Searching

Query= jgi|Phypa1|96131|fgenesh1_pg.scaffold_296000015
         (456 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

scaffold_5_6_Scaffolds_seq_8392_PT_B8_L9_282_rprt_txt                 276   2e-74

>scaffold_5_6_Scaffolds_seq_8392_PT_B8_L9_282_rprt_txt
          Length = 8149

 Score =  276 bits (139), Expect = 2e-74
 Identities = 157/163 (96%)
 Strand = Plus / Minus

                                                                        
Query: 1    atgaatatgaaagaccttaatgaaggtacagagattccacagcaaaaagatgaaagtgat 60
            ||||||||| |||||||||||||||||||||||||||| |||||| ||||||||||||||
Sbjct: 1524 atgaatatggaagaccttaatgaaggtacagagattccgcagcaagaagatgaaagtgat 1465

                                                                        
Query: 61   atggataatgaaggtgacgaagacgaactggacaaagacgtaggggatatattcagaatc 120
            |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
Sbjct: 1464 atggataatgaaggtgacgaagacgaactggacaaagacgtaggggatatattctgaatc 1405

                                                       
Query: 121  aaacagcaattgggtaaattggtgcataccggaggatgcacag 163
            ||| ||||||||| |||||||||||||||||||||||||||||
Sbjct: 1404 aaatagcaattggataaattggtgcataccggaggatgcacag 1362



 Score =  151 bits (76), Expect = 9e-37
 Identities = 100/108 (92%)
 Strand = Plus / Minus

                                                                        
Query: 164  tcgtttatattccagcagtcaaaactgatagactgcttgactatcgacgaatctccatac 223
            ||||||||||||||||||| |||||||||||||||||||||||||| || ||||||||||
Sbjct: 6919 tcgtttatattccagcagtaaaaactgatagactgcttgactatcggcggatctccatac 6860

                                                            
Query: 224  taccttctacagctagacgcccgacgcgttctcgagcaggaaagcacg 271
            ||||||||| ||| ||| ||||| ||||||||||||||||| ||||||
Sbjct: 6859 taccttctagagccagaggcccggcgcgttctcgagcaggagagcacg 6812



 Score =  143 bits (72), Expect = 2e-34
 Identities = 96/104 (92%)
 Strand = Plus / Minus

                                                                       
Query: 161 cagtcgtttatattccagcagtcaaaactgatagactgcttgactatcgacgaatctcca 220
           |||||||||||||| ||||||| |||||||||||||||||||||||||| || |||||||
Sbjct: 120 cagtcgtttatatttcagcagtaaaaactgatagactgcttgactatcggcggatctcca 61

                                                       
Query: 221 tactaccttctacagctagacgcccgacgcgttctcgagcagga 264
           |||||||||||| ||| ||||||||| | |||||||||||||||
Sbjct: 60  tactaccttctagagccagacgcccggctcgttctcgagcagga 17



 Score = 60.0 bits (30), Expect = 3e-09
 Identities = 42/46 (91%)
 Strand = Plus / Minus

                                                         
Query: 312 ggagccaattctagatccaagacggaagattgaagaaattcagagg 357
           |||||||||||  |||| |||| |||||||||||||||||||||||
Sbjct: 739 ggagccaattccggatctaagatggaagattgaagaaattcagagg 694



 Score = 52.0 bits (26), Expect = 6e-07
 Identities = 41/46 (89%)
 Strand = Plus / Minus

                                                          
Query: 312  ggagccaattctagatccaagacggaagattgaagaaattcagagg 357
            ||||||||||   |||| |||| |||||||||||||||||||||||
Sbjct: 7543 ggagccaatttcggatctaagatggaagattgaagaaattcagagg 7498


  Database: LTR_STRUC_8x_na
    Posted date:  Sep 4, 2006  3:29 PM
  Number of letters in database: 6,808,925
  Number of sequences in database:  791
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 791
Number of Hits to DB: 50,062
Number of extensions: 3603
Number of successful extensions: 1243
Number of sequences better than 1.0e-04: 157
Number of HSP's gapped: 985
Number of HSP's successfully gapped: 621
Length of query: 456
Length of database: 6,808,925
Length adjustment: 16
Effective length of query: 440
Effective length of database: 6,796,269
Effective search space: 2990358360
Effective search space used: 2990358360
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 25 (49.6 bits)
S1: 14 (28.2 bits)
S2: 23 (46.1 bits)
BioPerl-1.007002/t/data/frac_problems2.blast000444000766000024      2525313155576321 20646 0ustar00cjfieldsstaff000000000000BLASTN 2.2.6 [Apr-09-2003]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= AEDES_02704.C
         (1069 letters)

Database: aaegypti.SCAFFOLDS-MASKED.AEDES1.fa
           4758 sequences; 1,383,971,543 total letters

Searching..........done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

supercontig:1:supercont1.157:1:2064756:1 supercontig supercont1.157   858   0.0

>supercontig:1:supercont1.157:1:2064756:1 supercontig supercont1.157
          Length = 2064756

 Score =  858 bits (433), Expect = 0.0
 Identities = 448/453 (98%)
 Strand = Plus / Plus


Query: 12     cattttaaatgcatatattgggtgccatcatgactgcctgactcctaaacttgacctcga 71
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 759400 cattttaaatgcatatattgggtgccatcatgactgcctgactcctaaacttgacctcga 759459


Query: 72     ggcctatattctatcccttcttacatgtagtggcttaatcctagattgctggtactcacg 131
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 759460 ggcctatattctatcccttcttacatgtagtggcttaatcctagattgctggtactcacg 759519


Query: 132    gcaccggctattatgctcccgccgcctctagctccaccagcctctgcatcctttctgacg 191
              |||||||| |||||||||||||||||| |||||||||||||||| |||||||||||||||
Sbjct: 759520 gcaccggccattatgctcccgccgcctttagctccaccagcctccgcatcctttctgacg 759579


Query: 192    gtctgcgctcgccgtcgtcgcacgctctgtgctcctgcaccacctcagctgaagcggcta 251
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 
Sbjct: 759580 gtctgcgctcgccgtcgtcgcacgctctgtgctcctgcaccacctcagctgaagcggctg 759639


Query: 252    gctctcgacggtcattcaccgccgacgaccttgcactactgtgttgggaacccctggtcg 311
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 759640 gctctcgacggtcattcaccgccgacgaccttgcactactgtgttgggaacccctggtcg 759699


Query: 312    tgagtcacagtccgctcttcctccgatgtgccaaatgtcaaacgctgatatggctacgga 371
              |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct: 759700 tgagtcacagtccgctcttcctccgatgtgtcaaatgtcaaacgctgatatggctacgga 759759


Query: 372    cgatcctccaccgcggtgttgggaacccctgagtgtagactcgctgggccttccttcgat 431
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 759760 cgatcctccaccgcggtgttgggaacccctgagtgtagactcgctgggccttccttcgat 759819


Query: 432    gagccaaagaacgaaactgcaacgaaaaaaccc 464
              |||||||||||||||||||||||||||||||||
Sbjct: 759820 gagccaaagaacgaaactgcaacgaaaaaaccc 759852



 Score =  803 bits (405), Expect = 0.0
 Identities = 441/453 (97%)
 Strand = Plus / Plus


Query: 12     cattttaaatgcatatattgggtgccatcatgactgcctgactcctaaacttgacctcga 71
              ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Sbjct: 768455 cattttaaatgcatatattgggtgccatcatgactacctgactcctaaacttgacctcga 768514


Query: 72     ggcctatattctatcccttcttacatgtagtggcttaatcctagattgctggtactcacg 131
              ||||||||||||||| ||||||||||||||||||||||||||||||| ||||||||||||
Sbjct: 768515 ggcctatattctatctcttcttacatgtagtggcttaatcctagatttctggtactcacg 768574


Query: 132    gcaccggctattatgctcccgccgcctctagctccaccagcctctgcatcctttctgacg 191
              |||||||| |||||||||||||||||| |||||||||||||||| |||| ||||||||||
Sbjct: 768575 gcaccggccattatgctcccgccgcctttagctccaccagcctccgcattctttctgacg 768634


Query: 192    gtctgcgctcgccgtcgtcgcacgctctgtgctcctgcaccacctcagctgaagcggcta 251
              ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| 
Sbjct: 768635 gtctgcgctcgccgtcgtcgcacgctctgtgctcctgcaccccctcagctgaagcggctg 768694


Query: 252    gctctcgacggtcattcaccgccgacgaccttgcactactgtgttgggaacccctggtcg 311
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 768695 gctctcgacggtcattcaccgccgacgaccttgcactactgtgttgggaacccctggtcg 768754


Query: 312    tgagtcacagtccgctcttcctccgatgtgccaaatgtcaaacgctgatatggctacgga 371
              |||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||
Sbjct: 768755 tgagtcacagtccgctcttcctccgatgtgccaaatgtcaactgctgatatggctacgga 768814


Query: 372    cgatcctccaccgcggtgttgggaacccctgagtgtagactcgctgggccttccttcgat 431
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 768815 cgatcctccaccgcggtgttgggaacccctgagtgtagactcgctgggccttccttcgat 768874


Query: 432    gagccaaagaacgaaactgcaacgaaaaaaccc 464
              |||||||||||| ||||||||||||||||||||
Sbjct: 768875 gagccaaagaacaaaactgcaacgaaaaaaccc 768907



 Score =  317 bits (160), Expect = 3e-84
 Identities = 170/172 (98%), Gaps = 1/172 (0%)
 Strand = Plus / Plus


Query: 899    ttcctttcaccgtatggccacgtgacgatgatgagctctggcgcctttcgcgtccggatg 958
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 769407 ttcctttcaccgtatggccacgtgacgatgatgagctctggcgcctttcgcgtccggatg 769466


Query: 959    ttttccgccacggccggtaacaactatgtaacctttcactatggaaaactgcaaaagttt 1018
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 
Sbjct: 769467 ttttccgccacggccggtaacaactatgtaacctttcactatggaaaactgcaaaagttc 769526


Query: 1019   tctttcgccggcttt-aacggcactaactttttgtggcaaaatccgcttatt 1069
              ||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct: 769527 tctttcgccggctttaaacggcactaactttttgtggcaaaatccgcttatt 769578



 Score =  311 bits (157), Expect = 2e-82
 Identities = 167/169 (98%), Gaps = 1/169 (0%)
 Strand = Plus / Plus


Query: 902    ctttcaccgtatggccacgtgacgatgatgagctctggcgcctttcgcgtccggatgttt 961
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 760355 ctttcaccgtatggccacgtgacgatgatgagctctggcgcctttcgcgtccggatgttt 760414


Query: 962    tccgccacggccggtaacaactatgtaacctttcactatggaaaactgcaaaagttttct 1021
              |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
Sbjct: 760415 tccgccacggccggtaacaactatgtaacctttcactatggaaaactgcaaaagttctct 760474


Query: 1022   ttcgccggcttt-aacggcactaactttttgtggcaaaatccgcttatt 1069
              |||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct: 760475 ttcgccggctttaaacggcactaactttttgtggcaaaatccgcttatt 760523



 Score =  293 bits (148), Expect = 5e-77
 Identities = 151/152 (99%)
 Strand = Plus / Plus


Query: 587    ccccctttctttccgtcggaatcacgatccgagcagtagcgtcagcagacaatggatttg 646
              ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct: 769138 ccccctttctttccgtcggaatcgcgatccgagcagtagcgtcagcagacaatggatttg 769197


Query: 647    cggcgttcttattgttgaacaatgcgtgcccgtcctgatgccagcgatgatctcgtgatc 706
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 769198 cggcgttcttattgttgaacaatgcgtgcccgtcctgatgccagcgatgatctcgtgatc 769257


Query: 707    ggacaatcacgtcggtttcgaagcggttggcc 738
              ||||||||||||||||||||||||||||||||
Sbjct: 769258 ggacaatcacgtcggtttcgaagcggttggcc 769289



 Score =  293 bits (148), Expect = 5e-77
 Identities = 151/152 (99%)
 Strand = Plus / Plus


Query: 587    ccccctttctttccgtcggaatcacgatccgagcagtagcgtcagcagacaatggatttg 646
              ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct: 760083 ccccctttctttccgtcggaatcgcgatccgagcagtagcgtcagcagacaatggatttg 760142


Query: 647    cggcgttcttattgttgaacaatgcgtgcccgtcctgatgccagcgatgatctcgtgatc 706
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 760143 cggcgttcttattgttgaacaatgcgtgcccgtcctgatgccagcgatgatctcgtgatc 760202


Query: 707    ggacaatcacgtcggtttcgaagcggttggcc 738
              ||||||||||||||||||||||||||||||||
Sbjct: 760203 ggacaatcacgtcggtttcgaagcggttggcc 760234



 Score =  242 bits (122), Expect = 2e-61
 Identities = 125/126 (99%)
 Strand = Plus / Plus


Query: 463    cccaataaggggtttctcgtcgtgtgtgggtgcttcgagggaagcgacagtcaacctggc 522
              |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Sbjct: 768959 cccaataaggggtttctcgtcgtgtgtgggtgcttcgagggaagcgacagccaacctggc 769018


Query: 523    tcgcttcgaggtcctcctacggctcttgcagtggctatgcgctattggtggatgcaaaat 582
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 769019 tcgcttcgaggtcctcctacggctcttgcagtggctatgcgctattggtggatgcaaaat 769078


Query: 583    cgtccc 588
              ||||||
Sbjct: 769079 cgtccc 769084



 Score =  242 bits (122), Expect = 2e-61
 Identities = 125/126 (99%)
 Strand = Plus / Plus


Query: 463    cccaataaggggtttctcgtcgtgtgtgggtgcttcgagggaagcgacagtcaacctggc 522
              |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Sbjct: 759904 cccaataaggggtttctcgtcgtgtgtgggtgcttcgagggaagcgacagccaacctggc 759963


Query: 523    tcgcttcgaggtcctcctacggctcttgcagtggctatgcgctattggtggatgcaaaat 582
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 759964 tcgcttcgaggtcctcctacggctcttgcagtggctatgcgctattggtggatgcaaaat 760023


Query: 583    cgtccc 588
              ||||||
Sbjct: 760024 cgtccc 760029



 Score =  123 bits (62), Expect = 1e-25
 Identities = 65/66 (98%)
 Strand = Plus / Plus


Query: 737    ccactctaaaatgcttcttcgtgccttctaggtcgtcgatatttgccgcgaaaaccgtga 796
              |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Sbjct: 769344 ccactctaaaatgcttcttcgtgccttctaggtcgttgatatttgccgcgaaaaccgtga 769403


Query: 797    tccttc 802
              ||||||
Sbjct: 769404 tccttc 769409



 Score =  121 bits (61), Expect = 4e-25
 Identities = 64/65 (98%)
 Strand = Plus / Plus


Query: 737    ccactctaaaatgcttcttcgtgccttctaggtcgtcgatatttgccgcgaaaaccgtga 796
              |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Sbjct: 760289 ccactctaaaatgcttcttcgtgccttctaggtcgttgatatttgccgcgaaaaccgtga 760348


Query: 797    tcctt 801
              |||||
Sbjct: 760349 tcctt 760353



 Score =  105 bits (53), Expect = 2e-20
 Identities = 68/73 (93%)
 Strand = Plus / Minus


Query: 806     gttaaaaataatgaagattacacgtcatctaaactccatttatgcgatgtaaacatgacg 865
               ||||||||||||||||||||||| |||| |||||| ||||||||| ||| ||||||||||
Sbjct: 1251522 gttaaaaataatgaagattacacatcatgtaaacttcatttatgcaatgcaaacatgacg 1251463


Query: 866     tcatgtaaattta 878
               |||||||||||||
Sbjct: 1251462 tcatgtaaattta 1251450



 Score = 97.6 bits (49), Expect = 6e-18
 Identities = 70/77 (90%)
 Strand = Plus / Plus


Query: 802     cacagttaaaaataatgaagattacacgtcatctaaactccatttatgcgatgtaaacat 861
               ||||||||||| |||||||||||| |||| |||||||||  || ||||||||||||||||
Sbjct: 1251086 cacagttaaaactaatgaagattaaacgttatctaaactttatatatgcgatgtaaacat 1251145


Query: 862     gacgtcatgtaaattta 878
               || ||||||||||||||
Sbjct: 1251146 gaagtcatgtaaattta 1251162



 Score = 61.9 bits (31), Expect = 3e-07
 Identities = 37/39 (94%)
 Strand = Plus / Minus


Query: 802     cacagttaaaaataatgaagattacacgtcatctaaact 840
               |||||| ||||||||||||||||||||||||| ||||||
Sbjct: 1601368 cacagtaaaaaataatgaagattacacgtcatgtaaact 1601330

BioPerl-1.007002/t/data/frac_problems3.blast000444000766000024      1466713155576321 20656 0ustar00cjfieldsstaff000000000000BLASTP 2.2.15 [Oct-15-2006]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= PAO1/1/1119519/1118158
         (453 letters)

Database: AES1.pep 
           7167 sequences; 1,831,049 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AES1/1/1154592/1158227 putative exonuclease {AES_1265} {PAN04385}      47   2e-06

>AES1/1/1154592/1158227 putative exonuclease {AES_1265} {PAN04385}
          Length = 1211

 Score = 47.4 bits (111), Expect = 2e-06
 Identities = 52/195 (26%), Positives = 88/195 (45%), Gaps = 24/195 (12%)

Query: 15  GLNAQLETSREAYQQLGERHARFAGEVAALRREAE---LMGEERQRASQAEARWASER-- 69
           GL     + RE   Q  +      G++AAL R+ +   L  E R     A+  W ++R  
Sbjct: 647 GLREGYSSQRERLNQSRQEQQELTGQLAALDRQLDQWTLPEELRLLQPSAQLEWLAQRLD 706

Query: 70  --QGREEELRR-----LASERAA--LAAELREQQESHQQRLTDLQSARDELRAQFAELAG 120
              G+ ++ +R     +A +R    L  ELR  +   QQR    Q A  E R ++  L  
Sbjct: 707 DLAGQRQQCQRDFDRLIARQRQTQQLQQELRAAETILQQR----QQALTEQRQRYEHLQQ 762

Query: 121 KIFDEREQRFAETSQQRLGQ-MLDPLKERIQAFEKRVEESYQQEARERFSLSKELERLQQ 179
           ++ ++ +Q     S +   +   DPL+   QA  + +E+  QQ+AR    L +  +RLQ+
Sbjct: 763 QVEEDSQQLRPLLSNEHWQRWQADPLRT-FQALGESIEQRRQQQAR----LQQIEQRLQE 817

Query: 180 LNLRLGEEATNLTRA 194
           L  R  E +  L ++
Sbjct: 818 LKQRCDESSWQLKQS 832



 Score = 44.7 bits (104), Expect = 2e-05
 Identities = 55/217 (25%), Positives = 97/217 (44%), Gaps = 21/217 (9%)

Query: 4    ERLATAQLAQDGLNAQLETSREAYQ-----QLGERHARFAGEVAALRREAEL--MGEERQ 56
            E  A A+LA+  LN +L      +      QL   HA  A + A    +A L  + EE+ 
Sbjct: 843  EERAQAELAE--LNGRLGAHLGQHACAQDWQLSLEHAAQAAQSAVETLQAPLDSLREEQL 900

Query: 57   RASQAEARWASERQGREEELRRLASERAALAAELREQQES-HQQRLTDLQSARDELRAQF 115
            R ++A      +RQ +++E +RL ++  A     RE+Q++    RL  L    +E   Q+
Sbjct: 901  RLAEALEHLQQQRQRQQDEFQRLQADWQA----WRERQDNLDDSRLDALLGLSEEQATQW 956

Query: 116  AELAGKIFDEREQRFAETSQQRLGQMLDPLKERIQAFEKRVEESYQQEARERFSLSKE-- 173
             E   ++  E   R      +R  Q+L   ++R +   + +E++ +Q+ RER + S++  
Sbjct: 957  REQLQRL-QEEITRQQTLEAERQAQLLQHRRQRPETDREALEDNLRQQ-RERLAASEQAY 1014

Query: 174  ---LERLQQLNLRLGEEATNLTRALKGQKTQGNWGEL 207
                 +LQ  N R  +    L    + +     WG L
Sbjct: 1015 LDTYSQLQADNQRREQSQALLAELERARAEFRRWGRL 1051



 Score = 39.7 bits (91), Expect = 5e-04
 Identities = 63/231 (27%), Positives = 99/231 (42%), Gaps = 25/231 (10%)

Query: 14  DGLNAQLETSREAYQQLGERHARFAGEVAALRREAELMGEERQRASQAEAR--WASERQ- 70
           D    QLE   E    L E+ AR AG  AAL   A+   +E+Q   + E +  W +E Q 
Sbjct: 213 DEQRKQLEQRLEGSLPLAEQ-AR-AGLEAALESHAQARLQEQQALQRLEGQQQWFTEEQR 270

Query: 71  ---GREEELRRLASERAALAAELREQQESHQ--QRLTDLQSARDELRAQFAELAGKIFDE 125
                E    +LA  R A  A L  ++E+ Q  +RL  ++   + L+    EL      E
Sbjct: 271 LLQSCEHAQGQLAEARQAWDA-LATERETLQWLERLAPVRGLIERLKQLEQELR---HSE 326

Query: 126 REQRFAETSQQRLGQMLDPLKERIQAFEKRVEESYQQEARERFSLSKELERLQQLNLRLG 185
           ++QR   T QQ  G       ER+Q  + R++E+ +++A+    L +    L++   +L 
Sbjct: 327 QQQR-QRTEQQAAGA------ERLQGLQARLQEARERQAQADNHLRQAQAPLREA-FQLE 378

Query: 186 EEATNLTRALKGQK---TQGNWGELVLERVLEHAGLEKGREYETQVSLKGA 233
            EA  L R L  ++    Q N              +E+ R    Q  L+ A
Sbjct: 379 SEARRLERTLAERQELHRQSNQRHAQQSDAARQLDMEQQRHVAEQAQLQAA 429



 Score = 39.7 bits (91), Expect = 5e-04
 Identities = 58/232 (25%), Positives = 96/232 (41%), Gaps = 50/232 (21%)

Query: 5   RLATAQLAQDGLNAQLETSR------------EAYQQLGERHARFAGEVAALRREAELMG 52
           +LA A+ A D L  + ET +            E  +QL E+  R + +    R E +  G
Sbjct: 281 QLAEARQAWDALATERETLQWLERLAPVRGLIERLKQL-EQELRHSEQQQRQRTEQQAAG 339

Query: 53  EERQRASQAEARWASERQGREE-----------ELRRLASERAALAAELREQQESHQQRL 101
            ER +  QA  + A ERQ + +           E  +L SE   L   L E+QE H+Q  
Sbjct: 340 AERLQGLQARLQEARERQAQADNHLRQAQAPLREAFQLESEARRLERTLAERQELHRQ-- 397

Query: 102 TDLQSARDELRAQFAELAGKIFDEREQRFAETSQQR-----------LGQMLDPLKERIQ 150
                  ++  AQ ++ A ++  E+++  AE +Q +           LG      + ++ 
Sbjct: 398 ------SNQRHAQQSDAARQLDMEQQRHVAEQAQLQAALRDSQTLAALGDAWVTHQGQLA 451

Query: 151 AFEKRVEESYQQEA------RERFSLSKELERLQ-QLNLRLGEEATNLTRAL 195
           AF +R + + + +A      +      + LERLQ Q     G E  +L   L
Sbjct: 452 AFVQRRQRALESQAQLPELEKSLAHAGEPLERLQAQWTALHGSEPDDLAARL 503



 Score = 38.9 bits (89), Expect = 9e-04
 Identities = 44/150 (29%), Positives = 61/150 (40%), Gaps = 23/150 (15%)

Query: 56  QRASQAEARWASERQGREEELRRLASERAALAAELREQQESHQQRLTDLQSARDELRAQ- 114
           QRASQA+ +     Q  E  L      RA L A L    ESH Q     Q A   L  Q 
Sbjct: 207 QRASQADEQRKQLEQRLEGSLPLAEQARAGLEAAL----ESHAQARLQEQQALQRLEGQQ 262

Query: 115 --FAE----------LAGKIFDEREQRFAETSQQRLGQMLDPLK------ERIQAFEKRV 156
             F E            G++ + R+   A  +++   Q L+ L       ER++  E+ +
Sbjct: 263 QWFTEEQRLLQSCEHAQGQLAEARQAWDALATERETLQWLERLAPVRGLIERLKQLEQEL 322

Query: 157 EESYQQEARERFSLSKELERLQQLNLRLGE 186
             S QQ+ +     +   ERLQ L  RL E
Sbjct: 323 RHSEQQQRQRTEQQAAGAERLQGLQARLQE 352



 Score = 37.4 bits (85), Expect = 0.003
 Identities = 74/300 (24%), Positives = 121/300 (40%), Gaps = 38/300 (12%)

Query: 2   LGERLATAQLAQDGLNAQLETSREAYQQLGERH--ARFAGEV--AALRREAELMGEERQR 57
           L  RL   +   D L  Q    +E  Q L +R   AR  GE+    + +E  L+  +RQ 
Sbjct: 499 LAARLVELRRQTDSLERQQALHKEWQQVLDQRAGLARRLGELDQRMVEQEQALLDLKRQG 558

Query: 58  ASQAEARWASER--QGREEELRRLASERAALAAELREQQ-ESHQQRLTDLQSARDELRAQ 114
           +  AE   A+E+  Q   E L+R    R+A   +LR    +     +   Q        Q
Sbjct: 559 SQCAEEVKAAEQALQVTRELLQRQRLARSASVEQLRAGLVDGEACPVCGSQEHPYHHSEQ 618

Query: 115 FAELAGKIFDEREQRFAETSQQRLGQMLDPLKERIQAFEKRVEESYQQEAR--------- 165
                G+  D++EQ  AE S +RL Q L  L+E   +  +R+ +S Q++           
Sbjct: 619 LLAALGE-HDDQEQVRAEQSLERLRQTLVGLREGYSSQRERLNQSRQEQQELTGQLAALD 677

Query: 166 ---ERFSLSKELERLQQLNLRLGEEATNLTRALKGQKTQGNWGELVLERVLEHAGLEKGR 222
              ++++L +EL RL Q + +L   A  L   L GQ+ Q        +R  +     + +
Sbjct: 678 RQLDQWTLPEEL-RLLQPSAQLEWLAQRLD-DLAGQRQQ-------CQRDFDRLIARQRQ 728

Query: 223 EYETQVSLKGAEGERFQPDVLIRLPGDKQVVVDAKVSLTAYQQYIAADDDLLRQQALKQH 282
             + Q  L+ AE           L   +Q + + +      QQ +  D   LR     +H
Sbjct: 729 TQQLQQELRAAE---------TILQQRQQALTEQRQRYEHLQQQVEEDSQQLRPLLSNEH 779

BioPerl-1.007002/t/data/geneid_1.0.out000444000766000024       345113155576321 17235 0ustar00cjfieldsstaff000000000000## source-version: GeneId v 3.0 EvoI -- geneid@imim.es
## date Tue Jun 13 10:17:01 2000
# Optimal Gene Structure. 3 genes. Score = 140.109665 
# Gene 1(Forward). 2 exons. 155 aa. Score = 36.870944 
   First     6090     6155	 1.40	+ 0 0	 2.15	 3.63	12.34	 0.00	AA   0: 22 gene_1
Terminal     6881     7276	35.47	+ 0 0	 3.33	 2.30	97.73	 0.00	AA  23:155 gene_1

>10|GeneId_predicted_protein_1|156_AA
MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGLAKGLHGFHVHEFGDNTNGCMSSG
PHFNPYGKEHGAPVDENRHLGDLGNIEATGDCPTKVNITDSKITLFGADSIIGRTVVVHA
DADDLGQGGHELSKSTGNAGARIGCGVIGIAKV*

# Gene 2(Reverse). 5 exons. 401 aa. Score = 70.179051 
Terminal     9100     9217	 5.49	- 1 0	 0.09	 6.09	21.94	 0.00	AA 362:401 gene_2
Internal     9294     9387	 0.61	- 2 2	 0.89	 4.23	11.34	 0.00	AA 331:362 gene_2
Internal     9479    10085	46.13	- 0 1	 3.97	 5.00	119.37	 0.00	AA 128:331 gene_2
Internal    10140    10273	 6.48	- 2 0	 3.37	 2.05	25.56	 0.00	AA  83:127 gene_2
   First    10334    10580	11.47	- 0 1	 5.04	-1.96	41.57	 0.00	AA   0: 83 gene_2

>10|GeneId_predicted_protein_2|402_AA
MQETGEHQHVLSRNANRSSVLRFNSNPYRNDHDDSAVPLTTEVGKIYGEYLMLDKLLDAQ
CMLSEEDKRPVHDEHLFIITHQAYELWFKQIIFEFDSIRDMLDAEVIDETKTLEIVKRLN
RVVLILKLLVDQVPILETMTPLDFMDFRKYLAPASGFQSLQFRLIENKLGVLTEQRVRYN
QKYSDVFSDEEARNSIRNSEKDPSLLELVQRWLERTPGLEESGFNFWAKFQESVDRFLEA
QVQSAMEEPVEKAKNYRLMDIEKRREVYRSIFDPAVHDALVRRGDRRFSHRALQGAIMIT
FYRDEPRFSQPHQLLTLLMDIDSLITKWRYNHVIMVQRMIGSQQLGTGGSSGYQYLRSTL
SDRYKVFLDLFNLSTFLIPREAIPPLDETIRKKLINKSV*

# Gene 3(Reverse). 1 exons. 187 aa. Score = 33.059670 
  Single    20955    21515	33.06	- 0 0	 0.48	-2.76	103.58	 0.00	AA   0:187 gene_3

>10|GeneId_predicted_protein_3|188_AA
MVPSTVEKIVEVDKHIGCATSGLMADARTLIERARVECQNHWFVYNERMSIESCAQAVST
LAIQFGDSGDSDGAAAMSRPFGVAILFAGIEAGQPQLWHMDPSGTFVGHGAKAIGSGSEG
AQQNLQDLFRPDLTLDEAIDISLNTLKQVMEEKLNSTNVEVMTMTKEREFYMFTKEEVEQ
HIKNIA*

BioPerl-1.007002/t/data/genemark-fragment.out000444000766000024       100613155576321 21010 0ustar00cjfieldsstaff000000000000GeneMark.hmm PROKARYOTIC (Version 2.6c)
Sequence file name: AAVN02000021.1.fasta,	RBS: N
Model file name: /gsc/pkg/bio/genemark.hmm/genemark_hmm_prok.linux/modeldir/heu_1_41.mod
Model organism: Heuristic_model_for_genetic_code_1_and_GC_41
Tue Mar 20 17:32:00 2007

Predicted genes
   Gene    Strand    LeftEnd    RightEnd       Gene     Class
    #                                         Length
    1        +          <2         214          213        1
    2        +         459        >596          138        1
BioPerl-1.007002/t/data/genemark.out000444000766000024      1516613155576321 17243 0ustar00cjfieldsstaff000000000000GeneMark.hmm (Version 2.2a)
Sequence name: Hvrn.contig8
Sequence length: 50124 bp
G+C content: 44.82%
Matrices file: /home/software/analysis/gene-prediction/genemark/matdir/osativa.mtx (Oryza sativa)
Thu Mar 22 10:25:00 2001

Predicted genes/exons

Gene Exon Strand Exon           Exon Range     Exon      Start/End
  #    #         Type                         Length       Frame
  1     1   -  Initial       1805      2176     372          3 1

  2     5   -  Terminal      3108      3229     122          3 2
  2     4   -  Internal      3869      4501     633          1 2
  2     3   -  Internal      4820      4888      69          1 2
  2     2   -  Internal      4981      5061      81          1 2
  2     1   -  Initial       5296      5656     361          1 1

  3     2   -  Terminal      7171      7288     118          3 3
  3     1   -  Initial       7540      7787     248          2 1

  4     1   +  Single       15431     15757     327          1 3

  5     1   +  Initial      17526     17696     171          1 3
  5     2   +  Internal     17772     17887     116          1 2
  5     3   +  Internal     18005     18074      70          3 3
  5     4   +  Internal     18456     18539      84          1 3
  5     5   +  Internal     18628     18714      87          1 3
  5     6   +  Internal     18807     18870      64          1 1
  5     7   +  Internal     19944     20038      95          2 3
  5     8   +  Internal     20139     20293     155          1 2
  5     9   +  Terminal     20779     20788      10          3 3

  6     5   -  Terminal     23000     23061      62          3 2
  6     4   -  Internal     23397     24101     705          1 2
  6     3   -  Internal     24708     24821     114          1 2
  6     2   -  Internal     25079     25356     278          1 3
  6     1   -  Initial      26970     26977       8          2 1

  7     3   -  Terminal     34218     34310      93          3 1
  7     2   -  Internal     35900     36301     402          3 1
  7     1   -  Initial      36392     36448      57          3 1

  8     1   +  Initial      36531     37064     534          1 3
  8     2   +  Terminal     37153     37161       9          1 3

  9     3   -  Terminal     37880     37917      38          3 2
  9     2   -  Internal     38938     39006      69          1 2
  9     1   -  Initial      39080     40214    1135          1 1

 10     2   -  Terminal     41091     41554     464          3 2
 10     1   -  Initial      41635     41713      79          1 1
 11     1   -  Single       41744     42061     318          3 1

 12     1   +  Initial      42171     42212      42          1 3
 12     2   +  Terminal     42432     42824     393          1 3

 13     7   -  Terminal     43798     43932     135          3 1
 13     6   -  Internal     44220     44297      78          3 1
 13     5   -  Internal     47595     47685      91          3 3
 13     4   -  Internal     48393     48526     134          2 1
 13     3   -  Internal     48643     49024     382          3 3
 13     2   -  Internal     49118     49149      32          2 1
 13     1   -  Initial      49457     49507      51          3 1

Predicted gene sequence(s):

>Hvrn.contig8|GeneMark.hmm|gene 1|124_aa
MEVAVKGYADASFDTDPDDSKSQTGYVFILNGGAVSWCSSKQSVVADSRCEAEYMAALEA
AKEGVWMKQFMTDLGVVSSALDPLTLLCDNTRAIALAKEPRFHNKTRHIKRRFNLIRDYV
EGED

>Hvrn.contig8|GeneMark.hmm|gene 2|421_aa
MAHAKVTLNFNTFLEKAKLKDDGSNFVDWARNLKLLLQAGKKDYVLNVALGDEPPAAADQ
DAKNAWLACKEDYSVVQCAVLYGLEPGLQRCFERHGAYEMFQELKFIFQKNARIERYETS
ESELRKEHQVLMVNKATSFKRSGKGKKGYGSLEAQLSKYLAGKKAAKEKSENNGCSISMS
NIFYGHAPNVRGLFILNLDSDNTHIHNIETKRVRVNNDSAMFLWHCRLGHIGVKRMKKLH
TDGLLESLDFDSLDTCEPCLMGKMTKTPFSGTMERASDLLEIIHTDVCGPMSAEARGGYR
YFLTFIDDLSRYGYVYLMKHKSETFEKFKQFQSEVENHRNKKIKFLRSDHGGEYLSFEFG
AHLRQCGIVSQLTPLGTPQRNEAMVGPDSNKWLEAMKSEIGSMYGNKVWTLEVLPEGRKA
I

>Hvrn.contig8|GeneMark.hmm|gene 3|121_aa
MVRRQRLIYRMTSFDYRKVFGHYRECTESDEWVPNVHREGPTHPGKPIGPRGGAPALGGL
VGQPKRALCAKDRKSKRKKKRKRSRYFTTTGAPSRCRRTHLLIRLACWIKKAEIIIELYV
C

>Hvrn.contig8|GeneMark.hmm|gene 4|108_aa
MFTTPKAGGGMYLCLSVGWGIVGRRRVMSGCGQGSEMGLVGLRTRRHWAKTGRGGAAGGA
ASIGDGPRRAADKATLGEDGPGRGVGRGGVGRRRVASGGGDREEDEWS

>Hvrn.contig8|GeneMark.hmm|gene 5|283_aa
MDAAVQEAKLLRQVNALIVAHLRDQNLTQAAAAVAAATMTPKADASLPNHLLRLVAKGLA
AEREEAARGGGAPPAFDSAGGGGLARPLGTSAVDFSVQNVRGPSKTFPKHETRHISDHKN
VARCAKFSPDGKHFATGSGDTSIKFFEVSKIKQTMLGDSKEGPGRPVVRTFYDHVQLLTQ
LLVHSTDKVSSFVTNIPGTDHPVAHLYDVNTFTCFLSANPQDSSAAINQVRYSGTGSMYV
TASKDGSLRIWDGVSAECVRPIIGAHGSVEATSAIFTKDESGF

>Hvrn.contig8|GeneMark.hmm|gene 6|388_aa
MGSVVFLEGSEGNLQALKDTLQAYQVASAQKVNLQKSSILDGKGCRDEDKGTLKQTIGID
SEALSERYSGLPTVVGRLKDGSFEYVRERSKGKVSGSVGKASVALQFPSSLCARVLKARY
FKECTIMNTTCPNAMFWKVLSSEKWVPVAIPPVSEGPHGELASWLLRWFAEVGDPERELM
VHAVYGLWLARNEARDGKRIVDPRVVEENVYQHIIEWNAIHMKKPRSTTPTLAVRWSPPE
QGWLKANSDGALAKLRDRGGGGVVLRDHDGAYRGGACYVFRDVSDPEVVEILACRKAVHL
AVQTGATRVHVEVDSKGMAAMLNDQAKNLSAAGPIVEEIKLLGRTLQGFIVSRVRRSGNH
GAHLLAREVRSVYTHVILKQPLFDTCRL

>Hvrn.contig8|GeneMark.hmm|gene 7|183_aa
MVLTEKEAKGFVFSGPVEEAWGLHHDAQFRDLGNNLFLVHFGGEGDWKHSRNNGPWQFDF
MILKGYDGKTRPSEMVFDSVEAWVRVEDLPLDRRTREFGEALGNWLGEVVKVDVERDGFA
KGKYLRVRAKIFVYEPVVRYFNLKESVDDEVETAEGQAGPLEAEAEARRGASVSAHSFGR
WGK

>Hvrn.contig8|GeneMark.hmm|gene 8|180_aa
MASTVSPWSETPQDILGLVIDRLHSSPDHEEPRLSAAWSRFLLAVPVAAANRRGFQRARR
TRHSAAADRARFRAVCRSWHLAMRQHVSTPRVLPWIILSDGYFFTPSDNGCRAPRRLPSL
PKNARCIGSTDGWLALDCTDARNVHTYLLHNPFSDTTVPLPELDPIIANVSEFFAVRKAA


>Hvrn.contig8|GeneMark.hmm|gene 9|413_aa
MPLKFWDETFSTAVYLINRVPSRVIHNQTPLERLFGLTPNYTFLRIFGCAVWPNLRPFNK
HKLEYRSKQCVFIGYNYLHKGYKCLDVSTGRVYVSQDVIFDEHIFPFASLHPNAGAQLRA
ELVLLPPTLLNLSSPLTPSAAPNDPMAISTIYAPTSANSVQDSAGISHDFMQPNVSTDLV
ATENPGLHASESATAAPGAGDPPLQASGSAAAAPGSSPGFVHQPAASVGRSPASTSDPAR
QPDASAARPPVSDPVRPTTVATALFPASDLVRSPQEIRLQRRAPPTAPWIGRGLPRVVGP
PCLLPWTREISLDVVTRYRLLRLRPMQRRRCPMQRPPRLLFLLVCHLIRYLLTLRCPVVS
STICNPCNQHLHPLGLILGEPENLKEAIADPKWKAAMDEEFDWAGCPDDRRST

>Hvrn.contig8|GeneMark.hmm|gene 10|180_aa
MAAAGKPLDDDELVSYILQGLDSDYNPEARIDAQNGSNTNSFSINLASKGGSRNNNDTRP
SGPGGGNPAAYRGAGGGFFPNTLVAPPPSGGRDETCQICKRQGHATWHCFKRYDKNFNPP
PKRQGGGGGNNSGGGGNSSGGNTKSANTVPAAYDVDTNWYLDTGAMDHVTGELEKLAMHD


>Hvrn.contig8|GeneMark.hmm|gene 11|105_aa
MGYLDGTMAEPPAVLTTETDVAGKKEISSTPNPAHVLWYTQDQQVLTFLLASLSRDVLLQ
VHSLASATGVWTAIQQMFASHSRARHIQLRGQLGNTKKGDSPVAI

>Hvrn.contig8|GeneMark.hmm|gene 12|144_aa
MVELEEEDDMSMEEVALMTNNSNYLIILIRPGKGVWLPKPDTAPFNLFIDIVFLQGKLYG
ITQAEDLASVSIDFDDCGMPTVTTVERLIKHPPLESCEFDVWSDAGEKLEADGDMGDEDQ
VENGGEDHDEALNEVDARIQKENR

>Hvrn.contig8|GeneMark.hmm|gene 13|300_aa
MSTATSLWDKAALMMREELAVAAVVAGCLDMTKLYVVGAGMFSCVTVALYPVSVIKTRMQ
VASGEAMRRNALATFKNILKVDGVPGLYRGFGTVITGAIPARIIFLTALEKTKATSLKLV
EPLQLSESMEAALANGLGGLTASLCSQAVFVPIDVVSQKLMVQGYSGHVRYKGGIDVVQK
IMKADGPRGLYRGFGLSVMTALGRLDDKEDTPSQLKIVGVQATGGMVAGATSLEDNPLSD
NVPQFAETSSAGSPLEKERVRQRASATISVTRDCQCSRRPTIGGVRQLGRSLPMRRDGAT

BioPerl-1.007002/t/data/genewise.out000444000766000024      3712113155576321 17253 0ustar00cjfieldsstaff000000000000genewise $Name: not supported by cvs2svn $ (unreleased release)
This program is freely distributed under a GPL. See source directory
Copyright (c) GRL limited: portions of the code are from separate copyright

Query protein:       SINFRUP00000067802
Comp Matrix:         blosum62.bla
Gap open:            12
Gap extension:       2
Start/End            default
Target Sequence      Scaffold_2042.1
Strand:              forward
Start/End (protein)  default
Gene Paras:          human.gf
Codon Table:         codon.table
Subs error:          1e-05
Indel error:         1e-05
Model splice?        model
Model codon bias?    flat
Model intron bias?   tied
Null model           syn
Algorithm            623

genewise output
Score 2054.68 bits over entire alignment
Scores as bits over a synchronous coding model

Warning: The bits scores is not probablistically correct for single seqs
See WWW help for more info

SINFRUP00000067    1 LDEDQLSHSSSRLSRSPLKGVKKAKIMQCKVTLLDNSDYTIDVE      
                     LDEDQLSHSSSRLSRSPLKGVKKAKIMQCKVTLLDNSDYTIDVE      
                     LDEDQLSHSSSRLSRSPLKGVKKAKIMQCKVTLLDNSDYTIDVE      
Scaffold_2042.122265 cgggcttcaaacctatccaggaagaaactagatcgatgtaaggg      
                     taaaatcaggggtcgcctagtaacattagatcttaacaactata      
                     gcgcgactccttccgtcgaacgaggaggtacaggcccccattag      


SINFRUP00000067   45                            KGARGQMLFDKVCEHLNLLERD 
                                                KGARGQMLFDKVCEHLNLLERD 
                                                KGARGQMLFDKVCEHLNLLERD 
Scaffold_2042.122397 GTGAGCA  Intron 1       CAGaggagcactgagtgccatcgag 
                     <0-----[22397  :  24223]-0>agcggatttaatgaatattaga 
                                                aacgcagcttaatgtatacgac 


SINFRUP00000067   67 YFGITYRDVENQK                           NWLDPSKEL 
                     YFGITYRDVENQK                           NWLDPSKEL 
                     YFGITYRDVENQK                           NWLDPSKEL 
Scaffold_2042.124290 ttgaatagggacaGTAAATA  Intron 2       CAGatcgctagc 
                     atgtcagataaaa<0-----[24329  :  24470]-0>agtaccaat 
                     ctccatactgtgg                           tggtttagg 


SINFRUP00000067   89 KKQIR                              GPWNFAFNVKFYPP 
                     KKQIR                              GPWNFAFNVKFYPP 
                     KKQIR          T:T[act]            GPWNFAFNVKFYPP 
Scaffold_2042.124498 aacacAGTAAGCA  Intron 3       CAGCTgctatgtagattcc 
                     aaatg <1-----[24514  :  24586]-1>  gcgatctatatacc 
                     aggcg                              tcgctcctcgtcta 


SINFRUP00000067  109 DPVQLAEDIT                              YYLCLQLRD 
                     DPVQLAEDIT                              YYLCLQLRD 
                     DPVQLAEDIT           R:R[agg]           YYLCLQLRD 
Scaffold_2042.124631 gcgccgggaaAGGTAAGAG  Intron 4       CAGGttttcccag 
                     actatcaatc  <2-----[24663  :  24816]-2> aatgtatga 
                     ttcggtgcca                              ctgtgggat 


SINFRUP00000067  129 DVVSGRLPCSFATHTVLGSYTVQSELGDYDHEELGSDYLSELRLAPNQT 
                     DVVSGRLPCSFATHTVLGSYTVQSELGDYDHEELGSDYLSELRLAPNQT 
                     DVVSGRLPCSFATHTVLGSYTVQSELGDYDHEELGSDYLSELRLAPNQT 
Scaffold_2042.124845 gggtgccctttgacagcgttagctgcggtgcggcgagtcagcccgcaca 
                     attcggtcgctccacttgcactacatgaaaaaatggaatgatgtccaac 
                     tgtgctgccttcccatactcgggtagactctgggccccctggctaccgc 


SINFRUP00000067  178 KELEEKVMELHKSY                              GMTPG 
                     KELEEKVMELHKSY                              GMTPG 
                     KELEEKVMELHKSY           K:K[aag]           GMTPG 
Scaffold_2042.124992 agcggagagccaatAAGTTGGTT  Intron 5       CAGGgaacg 
                     aataaattataaga  <2-----[25036  :  25161]-2> gtccg 
                     agtgagcgaccgcc                              ggatg 


SINFRUP00000067  198 EAEMHFLENAKKLSMYGVDLHHAK                          
                     EAEMHFLENAKKLSMYGVDLHHAK                          
                     EAEMHFLENAKKLSMYGVDLHHAK                          
Scaffold_2042.125178 gggactcgagaactatgggcccgaGTAATAA  Intron 6         
                     acatattaacaatctagtataaca<0-----[25250  :  26185]  
                     aaggccgatcgggcgccttccctg                          


SINFRUP00000067  222    DSEGVEIMLGVCSSGLLIYRDRLRINRFAWPKILKISYKRNNFYIK 
                        DSEGVEIMLGVCSSGLLIYRDRLRINRFAWPKILKISYKRNNFYIK 
                        DSEGVEIMLGVCSSGLLIYRDRLRINRFAWPKILKISYKRNNFYIK 
Scaffold_2042.126183 TAGgtggggaacggttagccatagatcaaatgtcaacaattaaaattaa 
                     -0>acagtatttgtgcggtttagagtgtagtcgcattatcaagaatata 
                        ctgatgcggatcgccgtccacgggccgttgtaacgttcggtcccca 


SINFRUP00000067  268 IRPGE                           FEQFESTIGFKLPNHRA 
                     IRPGE                           FEQFESTIGFKLPNHRA 
                     IRPGE                           FEQFESTIGFKLPNHRA 
Scaffold_2042.126324 accggGTAATTA  Intron 7       CAGtgctgaaagtaccaccg 
                     tgcga<0-----[26339  :  26457]-0>taatagctgtatcaagc 
                     ctgcg                           tggtgcgctcgtctttt 


SINFRUP00000067  290 AKRLWKVCVEHHTFFRQVMKEVL                           
                     AKRLWKVCVEHHTFFRQVMKEVL                           
                     AKRLWKVCVEHHTFFRQVMKEVL           G:G[ggg]        
Scaffold_2042.126509 gaactagtggccattacgaaggcGGGTTGCCA  Intron 8        
                     cagtgatgtaaacttgattaatt  <2-----[26580  :  26864] 
                     cagcggctggtccccgacggggg                           


SINFRUP00000067  313     LVSPEAPPKKFLSLGSKFRYSGRTQAQTRRASSQIIRPAPFFERS 
                         LVSPEAPPKKFLSLGSKFRYSGRTQAQTRRASSQIIRPAPFFERS 
                         LVSPEAPPKKFLSLGSKFRYSGRTQAQTRRASSQIIRPAPFFERS 
Scaffold_2042.126862 CAGGcgtcggccaatcacgtatctagaacgcaccgatcaaacgcttgct 
                     -2> ttccacccaattgtgcatgagggcacacggcgcattgcccttagc 
                         agttggtaggcgttctgtcctcaggtgcagcctgctattgctgtc 


SINFRUP00000067  359 SSKRYNMSRSLDG                              SSADGV 
                     SSKRYNMSRSLDG                              SSADGV 
                     SSKRYNMSRSLDG          D:D[gac]            SSADGV 
Scaffold_2042.127001 taactaatcatggGGTAGGAT  Intron 9       AAGACatgggg 
                     cgagaatcggtag <1-----[27041  :  27314]-1>  gccagt 
                     ccacccgcttata                              ctttag 


SINFRUP00000067  379 ARVKGNIITTVTPERKAEEENGEQEDAKNDAADKPDPAASSPLHQETKV 
                     ARVKGNIITTVTPERKAEEENGEQEDAKNDAADKPDPAASSPLHQETKV 
                     ARVKGNIITTVTPERKAEEENGEQEDAKNDAADKPDPAASSPLHQETKV 
Scaffold_2042.127335 gcgagaaaaagacgaaggggaggcgggaaggggacgcggtaccccgaag 
                     cgtagattcctccagacaaaagaaaacaaaccaacaccccgctaaacat 
                     tatgatccctatagaaaaagcagggtcgctgacgactttcctccaaaga 


SINFRUP00000067  428 TL                              DPLRSELSLPSSPISFT 
                     TL                              DPLRSELSLPSSPISFT 
                     TL          D:D[gac]            DPLRSELSLPSSPISFT 
Scaffold_2042.127482 acGGTCAACC  Intron 10      CAGACgccctgctccttcatta 
                     ct <1-----[27489  :  28576]-1>  actgcatctcccctctc 
                     aa                              tccctgctccattcact 


SINFRUP00000067  448 KIRRRRRENAHKRASSVSPGKSSTGRCRRQALADRKAALLDEQALLLVA 
                     KIRRRRRENAHKRASSVSPGKSSTGRCRRQALADRKAALLDEQALLLVA 
                     KIRRRRRENAHKRASSVSPGKSSTGRCRRQALADRKAALLDEQALLLVA 
Scaffold_2042.128630 aaccacagagcacgttgacgaaaagctcccgcggcaggccggcgtccgg 
                     atgggggaacaagccctgcgaggcgggggactcagaccttaaacttttc 
                     aagggcggcatgaccactacgccagtcctgctttcatggatgacggcga 


SINFRUP00000067  497 RKQRLEQGRNHGGTLFSFSLHLPDLSSVLDEDGYITFPDLSKMRFLPEC 
                     RKQRLEQGRNHGGTLFSFSLHLPDLSSVLDEDGYITFPDLSKMRFLPEC 
                     RKQRLEQGRNHGGTLFSFSLHLPDLSSVLDEDGYITFPDLSKMRFLPEC 
Scaffold_2042.128777 cacacgcgaacggacttttccccgcttgtggggtaatcgctaactccgt 
                     gaagtaaggaaggcttctctatcatccttaaagatctcatcatgttcag 
                     aggagggcgttccacccccgcgccgctcgcactccccctgcagccctgt 


SINFRUP00000067  546 AQNFLPIKS                              YLCSLLLFTL 
                     AQNFLPIKS                              YLCSLLLFTL 
                     AQNFLPIKS           P:P[cct]           YLCSLLLFTL 
Scaffold_2042.128924 gcatccaatCCGTCACTC  Intron 11      CAGTtcttccctac 
                     caattctac  <2-----[28953  :  30816]-2> atgcttttct 
                     ggccgccga                              ttcggatctc 


SINFRUP00000067  566 FTFFFLCLLNSLHLSSFAVSRKQTRNLKYRLRYTGLTFIDRPCSMHQIL 
                     FTFFFLCLLNSLHLSSFAVSRKQTRNLKYRLRYTGLTFIDRPCSMHQIL 
                     FTFFFLCLLNSLHLSSFAVSRKQTRNLKYRLRYTGLTFIDRPCSMHQIL 
Scaffold_2042.130848 tatttctccatccctttggacacaaacatacatagcatagccttaccac 
                     tcttttgttactatcctctggaacgataagtgacgtcttagcgctaatt 
                     cccttttaatttccctctctgggggtgacacgctgcttctgccggtact 


SINFRUP00000067  615 DILTRCPEPSASTISHFAVSILAYCF                        
                     DILTRCPEPSASTISHFAVSILAYCF                        
                     DILTRCPEPSASTISHFAVSILAYCF                        
Scaffold_2042.130995 gacaatcgctgtaaactggtatgttt                        
                     attcggcaccccctgatctcttcagt                        
                     cccaaccgagaccctcttcccgtccc                        


SINFRUP00000067  641                               EVVKHQTNISELKRSFLET 
                                                   EVVKHQTNISELKRSFLET 
                               S:S[tct]            EVVKHQTNISELKRSFLET 
Scaffold_2042.131073 TGTTGTCA  Intron 12      CAGCTgggaccaaaagcacttcga 
                      <1-----[31074  :  31980]-1>  attaaacatgatagcttac 
                                                   ggcacgccccaggcccggg 


SINFRUP00000067  661 GDGTQGPTEWEKRLSSSPMCSPRFDEAPMIEPLDVSV             
                     GDGTQGPTEWEKRLSSSPMCSPRFDEAPMIEPLDVSV             
                     GDGTQGPTEWEKRLSSSPMCSPRFDEAPMIEPLDVSV             
Scaffold_2042.132040 gggacgcagtgaactttcattcatgggcaagccggag             
                     gagcagccagaagtcccctgccgtaaccttactatgt             
                     ttcgacgcagggggcgtcgcaaattgaggtgggtacc             


SINFRUP00000067  698                               ERTSDSQEDVSERSMLKVS 
                                                   ERTSDSQEDVSERSMLKVS 
                               D:D[gat]            ERTSDSQEDVSERSMLKVS 
Scaffold_2042.132151 GGTCTGCA  Intron 13      CAGATgcatgtcgggtgatataga 
                      <1-----[32152  :  33223]-1>  agccacaaatcagcttatg 
                                                   gactccggcggggagggcc 


SINFRUP00000067  718 PRAVTQEVSQAISDKKGRLIILKDAEHKEEDEEPGEAEGVEKELPPSKE 
                     PRAVTQEVSQAISDKKGRLIILKDAEHKEEDEEPGEAEGVEKELPPSKE 
                     PRAVTQEVSQAISDKKGRLIILKDAEHKEEDEEPGEAEGVEKELPPSKE 
Scaffold_2042.133283 caggacggtcgaagaagacaatagggcagggggcgggggggagtcctag 
                     cgctcaatcactgaaaggttttaacaaaaaaaacgacagtaaatcccaa 
                     cattagagggcctcggagttcgattataggcaacagtacgggagtaaag 


SINFRUP00000067  767 KEMVKEDAADVLASITREIKKQHPKVEIKTNGTQQINGSDSPKKAMVSW 
                     KEMVKEDAADVLASITREIKKQHPKVEIKTNGTQQINGSDSPKKAMVSW 
                     KEMVKEDAADVLASITREIKKQHPKVEIKTNGTQQINGSDSPKKAMVSW 
Scaffold_2042.133430 agagaggggggcgtaaagaaacccaggaaaagaccaagagtcaagagtt 
                     aattaaaccattcctcgataaaacatatacagcaataggaccaacttcg 
                     aagtaacctttgctaagacgggtgggaaatccgagtcttcgtagcgggg 


SINFRUP00000067  816 ISEEVKTVATKEVSEGESVEAPQQTAEIFTFEEEQSKSSPTQITVSESS 
                     ISEEVKTVATKEVSEGESVEAPQQTAEIFTFEEEQSKSSPTQITVSESS 
                     ISEEVKTVATKEVSEGESVEAPQQTAEIFTFEEEQSKSSPTQITVSESS 
Scaffold_2042.133577 atgggaaggaaggagggagggcccaggatatgggctatacacaagtgtt 
                     tcaatactccaatgagagtaccaaccattctaaaacacgccatctcacc 
                     ctggggtcgagaatgagctagggagggccctagggagccgcgcattata 


SINFRUP00000067  865 ASFAVV                              LDTTDAGTKEMPV 
                     ASFAVV                              LDTTDAGTKEMPV 
                     ASFAVV           H:H[cat]           LDTTDAGTKEMPV 
Scaffold_2042.133724 gttgggCAGTATAAA  Intron 14      GAGTcgaagggaagacg 
                     cctctt  <2-----[33744  :  35243]-2> taccacgcaatct 
                     tttgga                              tcctttacaggcg 


SINFRUP00000067  885 IHTETKTITYESAE                           VDTNGDLD 
                     IHTETKTITYESAE                           VDTNGDLD 
                     IHTETKTITYESAE                           VDTNGDLD 
Scaffold_2042.135284 acagaaaaatgtggGTACACA  Intron 15      CAGggaaggtg 
                     tacacactcaacca<0-----[35326  :  36271]-0>tacagata 
                     ccagaatcccgtag                           tctttcgc 


SINFRUP00000067  907 PGVLLSAQTITSEITSTTTTTHITK                         
                     PGVLLSAQTITSEITSTTTTTHITK                         
                     PGVLLSAQTITSEITSTTTTTHITK                         
Scaffold_2042.136296 cggccagcaaatgaaaaaaaacaaaGTCAGTT  Intron 16       
                     cgtttgcactccatcgcccccatca<0-----[36371  :  36567] 
                     cttcgttgcctaatccccacaccag                         


SINFRUP00000067  932    MVKGGISETRIEKRIVISGDADIDHDQ                    
                        MVKGGISETRIEKRIVISGDADIDHDQ                    
                        MVKGGISETRIEKRIVISGDADIDHDQ                    
Scaffold_2042.136565 CAGagaggatgaaagaaagatggggagcgc                    
                     -0>ttaggtcacgtaagtttcgacataaaa                    
                        ggaagtaaaacgagcccaatacctctg                    


SINFRUP00000067  959                            ALAQAIKEAKEQHPDMSVTKVV 
                                                ALAQAIKEAKEQHPDMSVTKVV 
                                                ALAQAIKEAKEQHPDMSVTKVV 
Scaffold_2042.136649 GTCTCTT  Intron 17      CAGgcgcgaaggagcccgatgaagg 
                     <0-----[36649  :  36954]-0>ctcactaacaaaacatctcatt 
                                                tgtgcaagtaagttcgagcaag 


SINFRUP00000067  981 VHKETEITPEEGED                                    
                     VHKETEITPEEGED                                    
                     VHKETEITPEEGED                                    
Scaffold_2042.137021 gcagagaacggggg                                    
                     taaacatccaagaa                                    
                     atagagcgaagggc                                    


//
Gene 1
Gene 22265 37062 
  Exon 22265 22396 phase 0
     Supporting 22265 22396 1 44
  Exon 24224 24328 phase 0
     Supporting 24224 24328 45 79
  Exon 24471 24513 phase 0
     Supporting 24471 24512 80 93
  Exon 24587 24662 phase 1
     Supporting 24589 24660 95 118
  Exon 24817 25035 phase 2
     Supporting 24818 25033 120 191
  Exon 25162 25249 phase 2
     Supporting 25163 25249 193 221
  Exon 26186 26338 phase 0
     Supporting 26186 26338 222 272
  Exon 26458 26579 phase 0
     Supporting 26458 26577 273 312
  Exon 26865 27040 phase 2
     Supporting 26866 27039 314 371
  Exon 27315 27488 phase 1
     Supporting 27317 27487 373 429
  Exon 28577 28952 phase 1
     Supporting 28579 28950 431 554
  Exon 30817 31073 phase 2
     Supporting 30818 31072 556 640
  Exon 31981 32151 phase 1
     Supporting 31983 32150 642 697
  Exon 33224 33743 phase 1
     Supporting 33226 33741 699 870
  Exon 35244 35325 phase 2
     Supporting 35245 35325 872 898
  Exon 36272 36370 phase 0
     Supporting 36272 36370 899 931
  Exon 36568 36648 phase 0
     Supporting 36568 36648 932 958
  Exon 36955 37062 phase 0
     Supporting 36955 37062 959 994
//
BioPerl-1.007002/t/data/genewise_output.paracel_btk000444000766000024      1211113155576321 22323 0ustar00cjfieldsstaff000000000000GeneWise BTK 5.1.3-88/88 2002-08-09 (Fdf Client 1.500)

Copyright 2001 Paracel, Inc


Query=   protein sequence #1
        (10 letters)

Database:  /fdf/gm2build24/gm0/0//bwb/tmp/XrhARf0Sal.codon
           2 sequences; 64 total letters.
Searching.......................................................done.

WARNING:  No calibration or zscore calculation was done.
          Statistical information may not be valid.
                                                                        E
Sequences producing significant alignments:                    Score  Value

DNA sequence #1                                                   26  0.0
reverse-complement of DNA sequence #1                             26  0.0

>DNA sequence #1
          Length = 30
          
 Score = 26.4 bits (26), Expect = 0.0
 Identities = 10/10 (100%), Positives = 10/10 (100%)

Query: 1  SWPLSEALMR 10
          SWPLSEALMR
Sbjct: 1  SWPLSEALMR 28



>reverse-complement of DNA sequence #1
          Length = 30
          
 Score = 26.4 bits (26), Expect = 0.0
 Identities = 10/10 (100%), Positives = 10/10 (100%)

Query: 1  SWPLSEALMR 10
          SWPLSEALMR
Sbjct: 30 SWPLSEALMR 3





Histogram of all scores:
  score    obs    exp  (one '=' represents 1 hits)
  -----    ---    ---
<     6      2      - |==
      6      0      - |
      7      0      - |
      8      0      - |
      9      0      - |
     10      0      - |
     11      0      - |
     12      0      - |
     13      0      - |
     14      0      - |
     15      0      - |
     16      0      - |
     17      0      - |
     18      0      - |
     19      0      - |
     20      0      - |
     21      0      - |
     22      0      - |
     23      0      - |
     24      0      - |
     25      0      - |
>=   26      2      - |==
unknown(8) BTK 5.1.3-88/88 2002-08-09 (Fdf Client 1.500)

Copyright 2001 Paracel, Inc


Query=   protein sequence #2
        (9 letters)

Database:  /fdf/gm2build24/gm0/0//bwb/tmp/XrhARf0Sal.codon
           2 sequences; 64 total letters.
Searching.......................................................done.

WARNING:  No calibration or zscore calculation was done.
          Statistical information may not be valid.
                                                                        E
Sequences producing significant alignments:                    Score  Value

DNA sequence #1                                                   24  0.0
reverse-complement of DNA sequence #1                             24  0.0

>DNA sequence #1
          Length = 30
          
 Score = 23.8 bits (24), Expect = 0.0
 Identities = 9/9 (100%), Positives = 9/9 (100%)

Query: 1  SWPLSEALM 9
          SWPLSEALM
Sbjct: 1  SWPLSEALM 25



>reverse-complement of DNA sequence #1
          Length = 30
          
 Score = 23.8 bits (24), Expect = 0.0
 Identities = 9/9 (100%), Positives = 9/9 (100%)

Query: 1  SWPLSEALM 9
          SWPLSEALM
Sbjct: 30 SWPLSEALM 6





Histogram of all scores:
  score    obs    exp  (one '=' represents 1 hits)
  -----    ---    ---
<     5      2      - |==
      5      0      - |
      6      0      - |
      7      0      - |
      8      0      - |
      9      0      - |
     10      0      - |
     11      0      - |
     12      0      - |
     13      0      - |
     14      0      - |
     15      0      - |
     16      0      - |
     17      0      - |
     18      0      - |
     19      0      - |
     20      0      - |
     21      0      - |
     22      0      - |
>=   23      2      - |==
unknown(8) BTK 5.1.3-88/88 2002-08-09 (Fdf Client 1.500)

Copyright 2001 Paracel, Inc


Query=   protein sequence #3
        (8 letters)

Database:  /fdf/gm2build24/gm0/0//bwb/tmp/XrhARf0Sal.codon
           2 sequences; 64 total letters.
Searching.......................................................done.

WARNING:  No calibration or zscore calculation was done.
          Statistical information may not be valid.
                                                                        E
Sequences producing significant alignments:                    Score  Value

DNA sequence #1                                                   21  0.0
reverse-complement of DNA sequence #1                             21  0.0

>DNA sequence #1
          Length = 30
          
 Score = 21.1 bits (21), Expect = 0.0
 Identities = 8/8 (100%), Positives = 8/8 (100%)

Query: 1  SWPLSEAL 8
          SWPLSEAL
Sbjct: 1  SWPLSEAL 22



>reverse-complement of DNA sequence #1
          Length = 30
          
 Score = 21.1 bits (21), Expect = 0.0
 Identities = 8/8 (100%), Positives = 8/8 (100%)

Query: 1  SWPLSEAL 8
          SWPLSEAL
Sbjct: 30 SWPLSEAL 9





Histogram of all scores:
  score    obs    exp  (one '=' represents 1 hits)
  -----    ---    ---
<     5      2      - |==
      5      0      - |
      6      0      - |
      7      0      - |
      8      0      - |
      9      0      - |
     10      0      - |
     11      0      - |
     12      0      - |
     13      0      - |
     14      0      - |
     15      0      - |
     16      0      - |
     17      0      - |
     18      0      - |
     19      0      - |
>=   20      2      - |==
BioPerl-1.007002/t/data/genomewise.out000444000766000024        51513155576321 17544 0ustar00cjfieldsstaff000000000000Gene 1
Gene 4761 6713 
  Exon 4761 4874 phase 0
  Exon 4921 5003 phase 0
  Exon 5061 5236 phase 2
  Exon 5289 6623 phase 1
  Exon 6679 6713 phase 1
Gene 2
Gene 9862 10316 
  Exon 9862 9972 phase 0
  Exon 10024 10211 phase 0
  Exon 10262 10316 phase 2
Gene 3
Gene 10475 11726 
  Exon 10475 10921 phase 0
  Exon 10983 11726 phase 0
//
BioPerl-1.007002/t/data/genomic-seq.epcr000444000766000024       107313155576321 17753 0ustar00cjfieldsstaff000000000000HSBA536C5  6934..7060       SGC31907        (+) Chr.1, between D1S484 and D1S426
HSBA536C5  9167..9289       SHGC-474        (-) Chr.1, between D1S2707 and D1S2705
HSBA536C5  89424..89607     stSG1902        (+) Chr.1, between D1S2635 and D1S484
HSBA536C5  89436..89729     IB289           (-) Chr.1, between D1S2635 and D1S484
HSBA536C5  89440..89572     TIGR-A002L26    (+) Chr.1, between D1S2635 and D1S484
HSBA536C5  90058..90332     WI-9524         (-) Chr. 1, between D1S2635 and D1S484
HSBA536C5  161589..161812   SGC31641        Chr.1, between D1S2635 and D1S484
BioPerl-1.007002/t/data/genomic-seq.fasta000444000766000024     51700413155576321 20166 0ustar00cjfieldsstaff000000000000>HSBA536C5 LOCUS       HSBA536C5  168628 bp    DNA             HTG       16-MAY-2000
GCTGACGCTGCTGCTGCTGCTAATGCTAGGTAAGCCAGGCCCCCGTTCCGGTTCCCGGCC
CTGCCGGGCAGGTGCCTGCCATCCAGCACCCCCCTAGCATTTCGGGGCTCCTCACATCCT
CCTCCGTCAGGGGTACCTCCAGCCTCCCCGGGGTCGGCGTCCAGCTGCGCTTTGTGGCTG
TCCGCCGAGCCAGTCTTGGGAAGAGTGCAGGCTCCCCAGCTCTAAGCCAGGGACTGGGGC
GTAGAGAGGACCCACTAAGGTGCTGCCCCAGGCACTGCTCGGCCTCCCGGGGCAGGCCAC
ACATCTCAGCTAGCATACCCACGTACTGGGGTCGCTGCACCAAATGCTGCGACTCCTTTC
TGCCCCACACTCAGCTCCAGGCCTGGCCTTGGGTGCCCGCCCTACGAGGGCAGTGCCTGC
CCAGCTTCATAATTGCCCCAGAGTTGGCTGGAGGCCCAGAGGCCAGTTCTGCCCACGATC
TTTGAAGTAAGTCTCTCCCAGTTGCGCTCCACGCACTTCATCAACTGGGGGCAGTTCCCT
CTCTCACCCCCATCTCCACCCTGGGTTGGGTCCCTCTTTGCCCTTCTTCCTGTCTCCCAA
ATGGCACTTGGCTCTGCAGCCACCCATCAGTTTTCACACCGCTTAGTTCCAGCTTCCTTG
CCTCAGGAGAAACCAGGTTCCATGGAGACTGATCCTGGGATCTCCAAGCACCTTGTGCCT
GCTGTGGTGGGTGTTCATGGTGGGGTGTTCTGGGCCAATCTTGCATGGATGCATGGGGAT
AATGACAGTGGAATTGTTTTTGGCCTGAACTGGAGGGCTCCCTGTAGGAGGTGGTCTGGG
GAAGAGTATGGCATGGAGACAGTGAAACTGCCAGTACAGATGTTGATGAGGCTGAAGCCC
TTGAAATGAGAGTGAAGCGTGGGGGTGGGGATGGTGACTTCAGAGCTGCTGTCGTCAAGG
CAGAGGCTGAAGGTAGCCCCAGCTGCCTGTTTCTAGACCAGAGCTCCACAGTGGCACCAA
GCAAAGCCTTCCCCTGCTGCAGGTCCCTGGGCCCTGCAGGGTTAGGATGAGTCCTCTCCC
TGGTCCCTGGGCAGGTGGCAGGAGGATGTACAGAGAGGAAGGCGCTGTGGGGCCTGGGTT
GCCTAGCACTTGGTGTGTTTTCCCCAGTGGGCAGCATGGAGCAGGGAGGAGCCCAGGGAG
GTGGGGAAGTGCTGGCCTGTGTTTGAAAAAGGAGCACGCAGAGGTCTGAGCACCCACTGC
CTGTGGGCACTTACATTCATTTCACAAATGAGGAAAATGAAGTAACTTGCCCCAGAGAGC
ACATTTAGTGAGTGTTGGGGCTAGGATTTGAACACAGATCTGATTCCAAAGCAGGCCTCT
TTGCTGTCCCTTTCCTTGCTGCGACTGATACAGAGGAGGGGAGAGAGAGCTGTGTGGCAA
CTGATTTCCTAAGGCTGTGGAGGTGACTTTCCCATGGGCATCTCCAAGCATCAGCAGTTG
TGGAGCCAGGAAAATGGGAGGGGGCCTTCTGAGCAGTCTGCCCTGAGGCAGTCAGGGAAG
GTGTCAGCTTGGCTGTCTCCACCGTCACTCTGATTATGAAACTTGCCTGGCCTGGGGCAG
GGCTCTCCTGAGTCACATACGCACTCACACATGGTCAGAGCTGGAGCTCTTAGTTCTCCT
CCAGTGTGGAAACTGAGGCCTAGGACAGAAAGAGACTGGATCCCAGGCCACACAGCTGGG
CATGGGGATGGTGCTGGAATCCCACTTCCTGACTGGCAGCTGTGCCCTTAACAACAGACC
ATGAGTTCTCCCTGTGACCCAGCCAGAGGATGAAGGAAGGGGCTAGGAGCCCAGAAGCAG
GGGTGGGGAAGTTCAGAGGAGCCGTTCTAGAGAAGCTGGAGGGTAGAGTTTGACCACAGA
CTCCTGGGCATTTTCCTCTAGCTCCTGCAGAAAGTCCATGGTATCCCCCTGGGAGGCCTA
AAAGTGACACTCTGGTTGGTGAGGTCAGTCCCTTCAGGCCTGGCCTTGGAGTTTCCCCAT
CTTCCTCTCTGGTTTTGCCCCTCTGGAGGAGTGTGTGGAAGCCATCTAGGGACAGCATGA
TCTTGGCTAACATATTATACTTTTCCTGCCTTACCTTTCTCATCTGTAAAATTGGGAGAG
GTGGGGAGGGGTGGCCTAGCCCTCTTTACATTGAGGTTCTGTGATCTTATCTAGTGGGAG
CTATGGAAGGAAAGAAGGGAGGAGCTAAGCCCTCTAAGTCTGCCAGGAGTATCTGCTGGG
GTAGGGTTGGGCATAGGGGTGGAGTAGGGTGAAGAAGAGAGGTTTGGCCTTTCTGAAGGG
AGAGAGATGAGAAGGGGCAGCTGGGGATTTAGTGCCTCCCTACAGAAAGAGAGCCATATA
TGTAAATGAATGCATACCATGTGCAAATGAAGGCTTTTGTTAAGGAACTGGGGCAGGCAC
CTTCTGTATCTGCTGGGCTAGCCCGGAAGGTTGGCAGGCACTGGAGGAGGGGATCTTCTG
CCCCCAATGGCCAGGGCAGAGCCTGGATCTTGCCCCAGAAGCCCCAGCTGCCTGGGCAGC
CCTGTGGGGTGAGAGAAGCAGTGAGCTCATGGCGCAGCTGGAGAGGGGAGGGCATTGTGT
GGTGAGAACTGACTGGGCCTGTGCCCTTTCCAGCTAGGGTCACTGGCTCCATTGTCTCGC
CCAGGTGACACAGCTGAGCCAACTAGCACTTCTGAGCAAGACTGCCAGCTCCCCTCAAGC
AAAGGAGAGGGACATGTAGTCTCAGAGTCCCCTAGCCAGAAGGCTCCCCTTGCCAGGTGC
TGAGGAAGGAATGGCAGACATGGAGGTGGGTGAGTGGCAGGGACAGATCAAGGTTCAGTT
GGAACCAAGGCCTGGTTAGGTCAGGAATCAGATGTACTCCTTTCTGCCTTCAGGTGCTCT
GCTTCTAGTCCGCCAGAAATGGGATGCATCTGGATGCCAAGGCAATCCTGGGCCCATGCC
ACCTCCTTGAGATCCAGGTGTCTTATATCACAGCATCCCTTTCCTATTCTCAGAACAGGG
TCCAAGCTGTGGACAAGCTTTCCCAGGTCTCCTTTCCTTTTGTAGGCAGAGATCAAGAAT
GGTGCTTGTGGCGGCAGAGGGCATGGAATGAGGAACCAGGCATCTCCAACTCCTTCTGCC
TTTCCCTACAGGAATGGGATGCTGGGCCCGGGAGGTGCTGGTCCCCGAGGGGCCCTTGTA
CCGCGTGGCTGGCACAGCTGTCTCCATCTCCTGCAATGTGACCGGCTATGAGGGCCCTGC
CCAGCAGAACTTCGAGTGGTTCCTGTATAGGCCCGAGGCCCCAGATACTGCACTGGGCAT
TGTCAGTACCAAGGATACCCAGTTCTCCTATGCTGTCTTCAAGTCCCGAGTGGTGGCGGG
TGAGGTGCAGGTGCAGCGCCTACAAGGTGATGCCGTGGTGCTCAAGATTGCCCGCCTGCA
GGCCCAGGATGCCGGCATTTATGAGTGCCACACCCCCTCCACTGATACCCGCTACCTGGG
CAGCTACAGCGGCAAGGTGGAGCTGAGAGGTACTGGGCCCTGGGACGGGGTGGAGCCACA
CACCCTCTCAAGGCAGAAAGTCAAGGCCACAAGTGACCTATCTAGTTGCCCCTTAGGTTT
TGTAGCCAAGGAACTTGAGGCCCAAAGAGGTTAAGTGATTTGCACAAAGTCACCCAATAA
CTCAGTGGCTGATGTGGGACTCAAACCCAGAGTTCCTCACCCAGGCCAGTGCTCATCTTA
TCATATTAAGACCCCTCCTGGGAGAAGAAATGTCCTTAAGTTGTCCAGTCCACTTTCCAT
TCCCAAGAACGAAGAAGACTGTTGGGTTGAATAGCCTCTACTCCTGGACAGTACAGGACC
CAGATCTGGGAAAGAGAGTAGAGTTAGGGAAGGAGTTAGACCATGTGACATTCTCACTCT
CTTAAGTTTCTTTGTCTTCTGAGAAGAAAGAGCCGCTTTTCTCAGTATTTCAAACAGAGG
TCAGTCTCAAACATAAGGGTGAGTAGGCGATGGGCTGGTTCTATGAAATTCTACAAGTAT
TTATTGAGCGCCTGTGCTGTGCCCAGTACTGCCCTTGGCACCACTGAGTTACAGAAGAAA
TAATACAACATGCGATCTTTGCCCTCTGGGAGCTCACAGTTAATTTAGGGAGATAGGCTA
TACACAGGAAACAGTAACAAGGGCTGCCAGCTCCCAGCCCTCCCTCACTCCAGCTGTTCT
CTCCAGTTCTTCCAGATGTCCTCCAGGTGTCTGCTGCCCCCCCAGGGCCCCGAGGCCGCC
AGGCCCCAACCTCACCCCCACGCATGACGGTGCATGAGGGGCAGGAGCTGGCACTGGGCT
GCCTGGCGAGGACAAGCACACAGAAGCACACACACCTGGCAGTGTCCTTTGGGCGATCTG
TGCCCGAGGCACCAGTTGGGCGGTCAACTCTGCAGGAAGTGGTGGGAATCCGGTCAGACT
TGGCCGTGGAGGCTGGAGCTCCCTATGCTGAGCGATTGGCTGCAGGGGAGCTTCGTCTGG
GCAAGGAAGGGACCGATCGGTACCGCATGGTAGTAGGGGGTGCCCAGGCAGGGGACGCAG
GCACCTACCACTGCACTGCCGCTGAGTGGATTCAGGATCCTGATGGCAGCTGGGCCCAGA
TTGCAGAGAAAAGGGCCGTCCTGGCCCACGTGGATGTGCAGACGCTGTGTAAGTGCCACT
TATACATCCCACTGTGGGAGCTGGGAGGGACAGTATCCTGGTGGGCACTGTGGCCACAGG
GGGTACCAGATAGCCATCATCTGACTCCAAGGAACTCATCTTCCACAGAGTGAGCAGCCT
TGCTAGCATTTCTCTCCCCCGGCCCTTGATGGGTTTTCTCTGCTCAGAAATTGGGTATAG
AGATAGGAGGCCCATGCTGAGGGGTGAGATTCAAGCCCCTAAATAGAAAGATGGTCATAC
CTAGTGAGGGGGAGACAGGAGGTTTTGAAGTTGCTGCTGTCAAGTAGGAAACAGGAAGTT
GGGGAATCGGGTGCCTCTGTGTCCCCTCCTGCCTCCATGACACCTCTTCCCCTACCTGTG
TTTCAGCCAGCCAGCTGGCAGTGACAGTGGGGCCTGGTGAACGTCGGATCGGCCCAGGGG
AGCCCTTGGAACTGCTGTGCAATGTGTCAGGGGCACTTCCCCCAGCAGGCCGTCATGCTG
CATACTCTGTAGGTTGGGAGATGGCACCTGCGGGGGCACCTGGGGCCCGGCCGCCTGGTA
GCCCAGCTGGACACAGAGGGTGTGGGCAGCCTGGGCCCTGGCTATGAGGGCCGACACATT
GCCATGGAGAAGGTGGCATCCAGAACATACCGGCTACGGCTAGAGGCTGCCAGGCCTGGT
GATGCGGGCACCTACCGCTGCCTCGCCAAAGCCTATGTTCGAGGGTCTGGGACCCGGCTT
CGTGAAGCAGCCAGTGCCCGTTCCCGGCCTCTCCCTGTACATGTGCGGGAGGAAGGTGAG
AGGGGGCTGGGCCCTGGACGGGGTTCGAGGATTGTCAACCCCTTTTCCTTCTGTTTCCAT
GACCCCTCCCTCTCCGTCAGCTGTTTGCAGGCCACAGCCTCACGCTCCTCTTCTACCAAG
ATTGTGGGAATACCCTGAGTTTCCTGGGGCGGTGCTTGGCGGCAGCCCTAACCCCATGCT
CCCTGGCCCTGCACCCTCTGACCCCATGTCCTTTGTTCTGCAGGTGTGGTGCTGGAGGCT
GTGGCATGGCTAGCAGGAGGCACAGTGTACCGCGGGGAGACTGCCTCCCTGCTGTGCAAC
ATCTCTGTGCGGGGTGGCCCCCCAGGACTGCGGCTGGCCGCCAGCTGGTGGGTGGAGCGA
CCAGAGGACGGAGAGCTCAGCTCTGTCCCTGCCCAGCTGGTGGGTGGCGTAGGCCAGGAT
GGTGTGGCAGAGCTGGGAGTCCGGCCTGGAGGAGGCCCTGTCAGCGTAGAGCTGGTGGGG
CCCCGAAGCCATCGGCTGAGACTACACAGCTTGGGGCCCGAGGATGAAGGCGTGTACCAC
TGTGCCCCCAGCGCCTGGGTGCAGCATGCCGACTACAGCTGGTACCAGGCGGGCAGTGCC
CGCTCAGGGCCTGTTACAGTCTACCCCTACATGCATGGTGAGTGACACCCCCTCCACCCT
CCTCACTCTGCCTTCCTCCTGGCCTCTGCCACTGGCCTTCCCTTCCCATCTTCTGACCCT
CCTGCTACTATCTCTCTCCTCCACATTATGTCACATGAAGTCTCAAAAAATCCAACTTCC
AGCCCTGCAGTGCCCACCTGCACGGGGTCCTCTGTGGTTGATGCTGACTTGCATGCTGAG
GGGGCAGGCTGTGGGCAGGGATGGGGGTGTCTGTGAATGGAGAAGGTGGGTTCAGAGAAC
TTGATGGGGAAAGCGCAGAGGCAAGTGTATGGGTGGAGGATGATGGCATCCTCTCTGAAC
AGTCATCCTCTCTCCCCCAGCCCTGGACACCCTATTTGTGCCTCTGCTGGTGGGTACAGG
GGTGGCCCTAGTCACTGGTGCCACTGTCCTTGGTACCATCACTTGCTGCTTCATGAAGAG
GCTTCGAAAACGGTGATCCCTTACTCCCCAGGTGAGGGAAAAGAACCCCCCAACCTTGTT
TTCATTGGGCTTCCCACCCCCAAGTCCTGAACCAAGCTGCTCCCTCCCAGGCCCCACCTG
GAGGAGGAGTAGGCAGCTCAGATCCACAGGGCCCTGTTAAGGGGTGGAGGCCGCGAGGGA
GCCCCACTCAGGGCTCTCTGTCCTTAGCCCACACCGGGCACCCTTTTCAGGTCTTGCAGG
TGTCGACTGTCTTCCGGCCCAGCTCCAAGCCCTCCTCTGGTTGCCTGGACACCCTCTCCC
TCTGTCCACTCTTCCTTTAATTTATTTGACCTCCCACTACCCAGAATGGGAGACGTGCCT
CCCCTTCCCCACTCCTTCCCTCCCAAGCCCCTCCCTCTGGCCTTCTGTTCTTGATCTCTT
AGGGATCCTATAGGGAGGCCATTTCCTGTCCTGGAATTAGTTTTTCTAAAATGTGAATAA
ACTTGTTTTATAAAAAGCAGGCTTGGCTGTGTCTTCCCTACCATGAGACTGTAAAACGCT
CAGGGTGCATAGTAGGGAGGTGGTTGGGGATTGACAACCTATTCTGGATGACCCAGGCCT
CTCTTCCCACCACAAACACCATCTGGCCTCCATGGGCCATGCCACCCACCCCAGGAGGGG
ACACCTGGGTTCCATCTGCAGCCTGAACTGTCGGGGCTGAGACAACTCCTGATTGGACTC
CTACTTGGGGAGGGAAGCATAGAAAAGGAGGGTAGGTCCCAGCTGCCTGTGGTCACCCCC
GCACCAGCTTCTCCCATGTTAAAGGGCATGGGCCTCCAGGGGCAGTGCCTTTTCTGAGCT
TCCCAGACTTTCCCCAACTCTTCCCACGTTTCATTCTCCTGGTCAGGCTAGTCTTGGACC
TGACTCCTCCCACTAGGCCCTGGGCTGAAATTGTTGTTCCTTTTGACCCATAGCAGCAAG
AATAGAAAGCCTCAGAACACAACTGATACTCAGGCTGGGACAACAGGCAGTCAGGGGAGG
GCCTGTGTGTCCACAGAGCCATTGCACCCACATGTACTCGCTGTACCTGCATATACCCTC
TACCCGCATATACCCACTACACCTGCATATACCCGCTTCACCTGCCTGTACCTACCCTGG
GGTCTCCTCCCTCCCACCCTTCAGCTTCACCCCTCCTCCAGTGCCCCAGGAGTTTCATGA
ATTTTCTTGCCTAAGGATTCTCTGATCCTAAAATTCTTACCTGCACGGCACCTTAAGAGG
CATCTGGCAGGCCTCCTTCAGTTGTTATTTAAACATTTATTGAGCATTACGAGTTTGCTG
TCATTTTTACAGATGAGGAAACTGAGGCCCAGATATGCGATTTGCCCAGAGTCATAGAGC
TAATTAGCAAGTGTCAGGAGTAGGACCTAGGTCTCCTGACTTGTTGCACTGTACAGTGGT
GCCCTGAGTGGTGACAGTGGCGAGGAGAGGTGTGGCAGGGTCTCAGTGACTTCAGCAGGC
AGGAGGGGCCTTTCCAGACTGAGTTTCTCTGCTTGTTCAGCTGCAATGGGTTGGCTCCTG
TGTGAGTGCGTGTGTGTGGATACCAAGTAGCCCACCCGCTCTTGTCCAGACCCCCCTGTT
TTACTGAAACCCAAATGAATCCCCATTCTCCATCCCAACATCTGTTCTTAGGGGACCAGT
CAATGCCAGGCTTCAGGAATCTCATCTTTGATGACAGGGCCCCAGTGGCCCTGTGACCTG
AGGCAAAGATATCCGTGTTTTGACTGAAAGGAAGGGACTGGGACTTGGGTCCTCTCTGAG
TGAACCCCAGCTGTCTGGGCTGCTTCCATGGCCCCCTTTCTTGCTTCCAGAGGACCCATA
GGGCCCTGGCTATGCCCATAGGACCCTGGCTGTGCCCCATAGGACCCTATCTGCCCAGCC
TGGAACAGAGAAGACTGGAGTGCTTTCCCCAGGGGGCTTATGAAAGGGCAGGAGTGGGAT
GTGGCCAGGGCCAAGGGAGGAGGTCCTTGCTGGGCCAGTGCTGCTGTGTGGGAGACAGGC
GCTGTCCCAGGGCAGGCTCTCCTGGGCCTATGCTTTTCTCCAGGCCAGCTTCAGGTCCCT
TCCACCCCTCTGCCTCTCTCAACTTGCAGTTGTTCTCCCTCACTATCCAGGAAGCTGCCG
CTGGTGACTGGGATGTGATCAGGAAGCAGGTGGAGGTGGGGTGAGAATATGCGTCTTTGG
GACCCCCTGGCCCAATTGGGCTGACAGCAGGCTGCAGACACATCCAGATGTTCTAACTCC
TATCGCTTCTCTCCGATTTTCTCCCACATTCAATCTTGCCTCCAGTCCTACAAGGGGTTC
TGTCCTTTGCCCCTAAAACTCTTCCTGCTCCACCTCCCCCCGACCTCCCCAGGAGCCCCC
TCAAGTCCTTCTGATGGCTTCATCTCTCTGTCGGGCCTGCTCAGCTTCCAGACACCCCCT
CCACTTGTCACTGCCCTGTTTCCATTGATGGTTGAGTTTCTGGGCCCAAAGTTAAACTCT
TCAGCCTGGGCTTCGGGTCCCTTTCCCACACATAAAACCCCACCCTTCACATTTCTCTGT
CTGCTCCTGTGAGGATCCTCAGCTTCTTCTCAGCTTCTCTTCATCTTCCTCTCAGCTACT
CCTCAGTTTCTATGCCCCATGTCCTGAAACGACTTCCAAGTATTCACTTAGAGCACAGGT
TCTCAAAGTGTGGTCCTCAGTCCAGCAACAGCAGCATGACCTGGGGACTTCTTAGGAATG
CATGGTTTTGGTCCCCACCTCTTGGGTCAGAAACCCTTGGAGTGGAGCCCAAAAATCTGT
GTTTTACCAAGCCCTCCAGGTGATTCCAACGCACACTGGAGATTTCTAACTCCTGACTTA
CATATTCCCTATGCCTTACACTGGCCCCAGCCTTCTGATCACCCACACTCCCCTACCCTC
CACGGGACTGCACAGGTTGTCAGTTTGAATTATCCCTCGTTCAGTCACCACAGGTAGATT
CCTCTGTTTTCCCAGGTGCCCCTTATTTTGAGGACAGGAACCAGGTTTTTGAATGTCCAC
TCCACATGGCACCCAATCAGTGATGTGAATGACTGTGCCCCAAGGACACACTGCTTTCCT
AGGGGCTCCCTGTTTCCCAGCTCTAGTGAACCCACTTTCTAGATCTCTCTCCTGGCCCTT
CCTCCCCAGAACCTCTCTCTCTCTCTTCCTGCCTGTGCCTGATACCTGTAAGATCTCACT
CCACTGTAAGAAAATAGCTATCCCTGGTTTTCCTTTCCCAGGCCCCTCTCCAGGCCCCAG
CTCAGGCACCTCCCCGCTCTGCCTGCTTCCCTGAACTTGCGGACTAAGGTCATTCACACC
TTGCTGAGCCCCTTGCACGCCTTCATCCTGGTGAGGGTGGAGCTAGGAGGGCACCCTCCT
CATGTGCCCATCTTGGTCCGGCTCCTTTCTCCTTCACTTCAGCTTGGCCTACCGTGTCAT
TAGACAGTTGTGCCATATGTGGGGAGGCTGGCAGAAGAGGTGACTGGGGACTGCAATCCA
TCCTATACTCTGCTCCCCAAGCCATGCACCCTGGTTTGGGGCTGTATCTGTCTGGAGGAA
AAGGGTTCCTTTTTAAAATTTGCACAGGGGTGTTCTACAGGTTAGTGGCAGCCCTGAGTG
GACCAGTTGTCTACTGGTCCATCTATGTATCTGTCAGCTGTCTTTATCTGCTACCATCTT
CCCATCCAACCCCCAAAAGTCCATCATTCTGTCCATCCATCCACTCATGAACAAATGTGA
AGGTCAAACACAGACTGGCATTTTCACCCGGCCCCACCCTCCATTTCCCTGAAATCAGGA
CCCCTCCCTTCCATACTGGTTTCTAGACTTGAGGTTCTGGGGGACGGGGACTTTCCAACT
TTAGCACATTTCCAGGGGCTTTGCCTTCCTCCTCCTCCTCCTCCTCCACCACCTCCGATA
TGCAGTTCCCCATGTATCTGTGTCTGGCCCCCGGTCTGCCACAGGGGTCTGGAGGAAGCT
GGTCACACCTTGGACTCACTCTCTGGGGGTGGCAGGCAGCCATTCTGCTCCTTGTCAGCC
CCAGCTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCCCTCCCCCGCC
CCCTCCTCCTCCACCTTCTCATCCAGCCGGCTGGGGATGGACCAGTAGAGATGGGCATCA
AGGCGGGCGGCAGCCTCTGCCAGCTCTCGAGCACTGCACGAAGGTGTGGGCACCTCAAAA
GTCTCGTGAAAGCTGGCATAGTCCACTTCGTAGAAGCCGTCCTCCAGAGTCAGCACTGAC
GTGAAGCGGTGGCCCCACAGCCCCTCGTCTACCAGGTAGGAGCTCCGAGCTTGGCATGTC
ATTCCTGGGAGGAGGGGCACCGGTCAGGGGGAATCTCAGCTCCAGGCTTCCCTCTCCTCT
TCTCATTCCACAACCCTACTCCCAGCACCCTCCCTTCTATTCCTTCCTAAGGGCTCCCAC
CTCCCTTTGGTCCAGTCCATTTCCCCCCCTCCCTAGCTCCTGTTCTTACCCAGCTCCCTC
GTGTCTTCTCCATTTGCCCCAACTCCTCTTAATGTCCAGCTCTTTTTTCCCCTCCTGTCA
TTTGGTGATGCCAACCAAAAAAAGCTTAACCTTGAAACTAACCTTAGGGATCCTCTAGTC
CAACTTCTCACTCCATACAGGGCTCCCCAAAGGAGCATTTCTAACAATGGGCATCTAGCT
TATACTTGATTACCTCCCAGGATTGATAGCTCACCACTTCATAAAGGGCCCACTCCTTTG
TATGATAGCTCTAATAGTTGGGTTGTTCTTTATACAGAGCTAAAACCTGTACCCTGGGAT
TTCCAACTCTTGGCTTCATTCCCCTCCCACTTCACAGTCCTCTGAGTATCTGAAAACAGG
AGTCTCAGATTCCCTCATGTTTTCTCTCTTGACTTAACATCCCTGGCTTCCTCCACGATT
CCTCATTTGACCTGGTTTTCCAGAACTCTACTTTTTTGATTACAAGCCAGAATGGCCAAG
GAGGGCCCTTTAAGCATTTTGAGTATAGTAAATTTTCCAACTGTGGCCTGCTCCGTGCAT
AAGAGAGCGCGCACCATCTCTCTCTTCTGGCCATGATGCTTTCACTAATAGGGCCCAGGA
TAACATTACATAATCATTTTGGAGGCTGCATCACATTGCTACGACATCAAGACTGTAGCC
AACTAAAACTCCCAGTTCTTTTTTCACCAGTGCTCTTCCATGCTGTGCTTACATAAGTGA
TTTTTTTAAAGCCTAAATGTAGAATTTTATATTTATTCATTTTAAATGTCATCTTGCTGG
GTTTTGGCTCATTATTCTTGCTTTTCAAAAGCGTTTTGAATCCTGACTGTCTCACCCAAA
ATATTACCATCCTTTCCAGCTTTATCTCTCTAGAAAAACAGACAGATTCCTATCCTCATC
TCCTCTGTCCTGGTCCTCCCTGCCCGGGGCTTGTGTCCTATCTTCCTGTTGGGCTGGTGC
ACCCCTCAGGGCAGGTCATTCTCCTTTCTGCCACAGGGTCTTGCCCCCAACCCATATCCA
TCTCGGAACAAGGGGAAACAGAAGAGTGAACATTAGCTAACCGGAGAGTGGCTGTCAACT
CGGAAAGCCTGGCGCTGAGACATTGGTATTCCTCGGTGAAGTTGGAATAGAAAGTATCCA
GTGGGAGAGAAGAGAAAGAGGCATAAGGGACACTGGGGAGAGAAGGGCTTCGAGGAGGAG
AGGGCAGGGCTGGGGGTACAAAGAGAAAAGAGGGCCGGGCAGCAACTTCCCTGGAGGGTG
AGGGGCCTGCCTGAGATACTGGCAGAAAAGGAGTGACAGCTGGAGAGAGAGGAAAGGGAA
CGGGGTGAGTGGGGGAAGAGGAAAGAGTCGGGGTGAAGCAGGAATGGGAACAGTGATGCG
GAGCTGGGGTTGGGGTGTGAAGCGGAGTCTCAGCCTAAAGGGGCCAGGGAAAGGATCTGA
AGGCACCAGCTTGTCAGCGAAGCCGGCAGGGAGCATCAGCAGCTCTGGCGTCAGAGGAGG
GACTGCGGCGCCCCCTAGTGGGCCTTTGGTCCTCCACCCGCAGTTTCCTCATCCTCATCT
ATCCTCTAGATCTCAAGTCCTAAGTGACCTCCTTTGCGACTCCTGTAACACTGGTCTTTT
TTCACCTGCTCCCAAAGCCTTCACTGTGTAGGTCTGGGTTGGACTTATTGACATCACAGA
TGAGTTGCCAGTTCCTTTTGGAAAAGAGCTAGAAAAGGTAACATCATCTATATCCCTTGT
CAGTGGAAATGGATGAATTGGGAAACCGAGGTACAAGTGAGACTAGGTATTAAACTCCCC
TCAAGATCCGGCCTAGAAATAACTCAGGCAATGGAAAACCTTCACCGTCAAATTCCAGGG
GCCTGAACCTGACTGCAGTGAGAAAACCCCTGAACCTAACCCCTCCTTCCAACTCGGGAC
CACTAAACATTGAAGCCACATTGCCTGTGTCCAATCCAGGCATGGCCACTTATTGGCTTA
GGAAAGTGGACAACTTCCTTAATTTCTCATTGGAGCAATCTCATCTCTAAAAAGTGAGCA
CAATAACAAGAAGTTACCTTCAGAGGGTTCTTGTTAGGATTAAATCGACTCAGAGGTAGA
AAGTGCTTTGGAACTGCGCATGACACAGGGTGAATACTGGGCGAGCACTAGCTATTATTA
CTGTCCCTATTCCAAGTGACACATTCCTCTGGGCCCAGGGCCCCACGCCAGTGCCATTTC
GGAGAATTCCTCCAAGCTTTCTCTTGGCCTTCTGCGGCGTTGCTCGGTTCCACTCCCGCC
TCCGACCCCTGTCTCACCTCACTGTCTCATCCTCCACCAGCCCCTCCATCCATCCTCCCC
AGCTCCCCTGGCCCCTAGTCTCGCCCCTGCCTTCCTCGGTCCCGCCCACCCTCTGCCAAC
CCCGCTCCCCTCCCCAGGCCTGCTCGCACCCGTGGCTTCCACCATGCCCTCGAGGATAAC
GACGATCTCGAAGTCGTCCCTCTCGAGGGCACGGCGCGACGCCTCCCAGAAGGGGCTGGC
GGCGTCGATCTCGTGGCTGATAACCAGCGGCGAGACGAGGAAGAGGCGGTCGTCTCCCGT
GTCGAAGCCCACGCTGAGGTCGGTCTGGTGCAGCGGGATGAACTCGCCCTCCAGCGTCTG
GCGCGAGCGGATGAGCTTGGCGCGGATGGAGGCCTCCACTATGTGTGAGGAGCGCAAGTC
GCCCACGCGGAACATGAGGCAGAGGCGCCCGTCGCGCAGCGACACCACGGCGTGCGAGGA
GAAGACGAGCGTGGCTGCGCGCTTGTTGGGCTGCGAGATCTTGACGAACATGCAGCCCAC
CATGAAGGCGTTCACCATGGAGCCCAGGATGGCCTGCAGCAGCAGCAGCACGATGCCCTC
GGGGCACTGGTCGGTGATGACGCGGTGCCCGTAGCCGATGGTGGTCTCGGTCTCGATGGA
GAAGAGGAAGGCGGCCACGAAGCCGTTGAGGTTGTTGACGCACGGCGTCCACGCGGTGTC
CTCCAGGTGCTCCAGGTCGCCGCGGCCGTAGGCGATCAGCCACCAGATGGCGCCGAAGAA
GAGCCAGGTGAGCGCGTAGGCCAGGACGAAGAACAACAGGCTGAGGCGCCACTGCAGGTC
CACCAGCGTGGTGAACAGGTCCGTCAGGTAGCGGTATGTCTCGCGCACGTTGCCCTGCTG
CACGTTGCACCGGCCATCCTTCTCCACGTAGCGCTGGCGGCCGCGGCGCCGCGGCGGCTC
CTCCTGCCCGGGCGAGAAGGCCGCGTTCTCCTGCGCCATGGCGGCCGCGTCAGGGCGAGC
GCTGCGGGCGCCTGGAGTGCGGCGGGGGCCCGAGCTGCTGCCACCTGCCGCGCGTCGCTG
GGCGCCTAGGCGGCGTCGGGGGTCCTGGAGGGGCTTAATAAAGGTTTGCCGAATGAGTGG
CCCCTCGGGAGATGGGGAGGCACGGGGCATCAGGGCCAGCACCGAGCCCTGGGGGGCCCT
GGGCGAGTCCCTTCGTGTTGCCTGGCCTCTATTTCTGGGAATAACACATTCAGCCCTAAC
TGCCCCCCAGGCTCAGAAAGTTGTGAGGGTCAAATGGAATGATGTACCTGAACTGGATAG
AACTGTGCAAGTTCCACGATGATTTTCAGGGGAAGGAGGTACCAGATATTTTGGTGCCAT
CACCTCCAGCTGGGGTGTGCAGCACCTCAGGGGCAGCCCCGGGGCCAAAGACCCAGGCCC
AGATCCCCCTAGTGATTTCCTGAAATCAATAGACTGGGGGCTTTTTGGGGAGGGGGGCAG
GCGGGTAATGGAGCCCTCCCTGCCCTAAGGACTTCCACCATCCCTTCCCCAGCTGTAGCC
AGTGCAGCCACCAATGGCTCTCCTCGCAGGCTGTTTTGAAGTTCACCCCAAGACTGATAC
ACAGTCTTTCTCATTCTTCCCTCCTTGGACCTCACTCACTCCGCTCCATTCCCTCCCCTC
AACATGCTTACAAACGAGAAAGAAATGAAAGCTGTGGAAAGTCAGTGGAAACCCTCCAGT
GCACAAGGGTGGAACATTAGGAAATTCCCACTAGAAATCCTCCCTGAGACCTACCCACGA
TCACTGCTGCTCTTGGGCCAGCCTCATTTCCCTTGGGTTTTTTCTCCTAGTGGAGACAGC
CTGCAAATGGGGAGGGGAACTGGAAGATCCCAACACAGAAGCCTGGGAAAGGAAGCCCAG
AGTTATAAAGAGTTAGGCTCGTATCCCTCTGGGATCCTATTCTTCATGAGAGACATGGAA
TCAGATCAGGTGAAGCACTAAGCACCCACATTTATTTCCCCACTCCCTCTAGTTATATTT
TCCCCCAGCCTCTTACTTCCCATGGACTATCCTAACACCAGCCCCGCCCCCACCTGCCAT
ATGCCCCAAAGCCCACATTCCAAGCGAAGCCCACCTGATTTTTCTTCACATGCTTGCCTC
TGAGGAGCTCTCTGAGCTGCAATCTGCTCTGAGAGAGGTCCAGAGCCCTTCCCCAAAGCA
CCCAGGGTCCTCTAGGAGATATGGACCATACAGGGAAAGGTTTAGAATAGGATTTGGGAC
TCTTCCACCTTCCCTTCTCTTTCCTGGGAATGATCCTCTCCTCCCACTCCACGGAAACGT
GGGCTGGCTAGTGGGTGGGGGATGGAGGAGTGTGCCATAGGAACCACAGATGGCCTGGAT
GGTTGACCAGGTCCTGGGGAGAAACTGCCTGGGTATGTGACTCTAAACCTAGCACTCCAG
CATCTTATGTTCTGGGGTGAGGTCCTCTGCAGTCAGCACTCTGGAGAGGGTGTGTGTGTG
TGTGTTTGTGTGTCTTGGGGTAGAGAAGGTAGGAAGAGAAATCAAAATGAAATGGCTTTG
AGCTTAGGGGCACCCCCTGCATTTATTGTCCATGGAGTCAGGGGACACAGGGTCCAAGAG
CCCCATGGCAATGGAAGATTAGGGTTTCCCCTGCCCCCAACAATGGGCTTCCTTTTCCTT
CCCTGAAGCTCAGATGTCCTCAGGAAGAGTAAGCATTGACTGGCTCAGAGACCCCAGGTC
ATGCAGAAAACGACCCTGCTCCCATTATCCTAGCTTTAGTCCCAGGTGGGCTTCCAGATG
TTCTCTCAGGGTCTTAGGTAATCTGACCCCCAGTCGGCTTGCCTAGACAGATCTCTCTGC
CCAGGGATGGGGAAGGAACCCCGATGTCGGATCACCCCCAGAACTCTCTCACTCTCCATT
GCCCCAGGGATCTAGGTAAACCTTATTTTGAATGTGTCCCACATCCTGTCTTCCTGAGTG
GGGGACTGCACTTTTCTCAGGGGAAGGAAAAGTGTGAAATTGTTACCTCTATCTCAAGAT
CAAGGACTTGATTTCTCCATCTTCCCTCCAAGAATTTCAGTTCCTCCAACCTACTCCTCA
TTTCTTGTGCATGCTATGACCCCTTTGCAGAAGATTGCAATACCACTTTTCCTGGGCCCC
TCTTCCTCCCTCTAGAGAGCTGGGGAGTAAGGGGGCTCATTTTTTGGAAGGAGAGACCTG
GTGAAAACTCCCCCAAGAACCAGCTCCTCCCAAACCCCCACTTGCCTTGGAAATAGGGGC
CCAAACCCCAAGTCCCCCGCAACTCAACTCACAGCACGTGGAGAGGAGAGTAGCCGGCAG
CAGAGACCCCTGGGGGGTGGCGTCCATGCCCCTGACACCGCCCCCCCCACGGGCCCCCCG
AAGGGTGGGAGCCGCAGACACCGCTGTTTCTCCTAAATGTAGCGGCAGCTCTGACTAGGA
CTTGCTATCTGTGTCATCCCTACTTCCCAGGCTCCCCTGCTCCTCTCTTGTTTCCACGGC
AACCAGTCTGGCGACAGCTCCAGAGCATCCCCCTCCCCTCCCCAGTCCTGGGTACCACTA
GGGGTTGATCCAAACCACACGCCATAGCTATTTTTAGCCAAAGTCCCTCCTCCTGGACAA
CTCAGAGCTTGGCTCCTCACCCCCTCATAGGAAAAAAAAAAAAAGAAGAAGAAAGAAAAA
CAAAGCTGGCACGCTGGCTCTTTCCTAAGAAGCTCCTTCCTGGGGGAAAATACAAGCCCT
CATGTATTTGAGAATAAGGTGCTAGGTTCCCTGGGGTTTCAGAGGGCCATCTGGTAGCTG
GCAGCTCACCACCTTCAACATGGGTCTCTGCGTGCAGGTGCTGCTCTCAGGTCAGGCTGA
CCATCATGGTCTAGTTTTGGAGAGGCCATGGATCCAGAAGGCGGTAGCTAGAAGGAAAAT
AGATCTACTAAAGGAAGGGAGGCAGGGTCAGGGGTTCTAATTATTGCCACTGATTTGCAC
TGTGTCCCATAGGAGTCACTTCACTTCCCTGAGCCACAGTTATTCCATCTGTACCAGGGT
GTGGACAAGAGCAAATATCCCCTTTCTGCCTGCTTCACAGAGTCAGCAGATCAAACGAAG
AAAAAACAAACAAACAAAAACCAAAAAAACCACAAAGGGCTTTGAAATGTGTTTTATTCA
TAGCAAAAACCCTAGAAACAACCCAAATGTCCACCAGAGAGAAAAGCCTAGGTTAGGGCT
TACTAAGTATTCACTCGGCAAACTTCTGCGGAGCCCAAGTGCCAGGCAGTGTGTTAGATG
GGGTGGTTACAGAATGGGTGAGTCCCTGCCCACAAGGAGCTCATTAACCCAGGAGGGATA
AAGACACACAAACACACAGTGGCTGCTGCTACTAATTCACTGAGCATGGGATATGAACGA
GACACATGCCTCATGTCATCCCCATGGCAACTCTATAAGACAGGTGTTATTTTTCCCAGT
TATAGATGAGGAAACTGAAACAGAGACATGTTAAGTAATTTATCGAATGTCACAGAGTTG
GGCAGAGACAGGAGCCAAACTCCCACATCTGTATCACCTCATGCTTTGTAAATTGTTTTA
AAAGAAGACTTCTTAAAGGGTAGTTTTAGATTCAGAGCAAAACTGAGAGGAAAGTTATAG
AGATTTTCCGTATGCCCCCTGTCCCCACACATCCACCAGAATGGCACATTTGTTACAAGT
GATGAAGCTACATTGACATCATAATCGCCCAAAGTCCATAGCTGACATTAGGGTTCACTT
TTGGTGTTGTACACTCTGTGGGTTTGGACAAATATATAATGATGTGTATCCACCATTATA
GTCTCATTGCTGTAAAAGTCCTCTATGCTCTGCCTAGTCAATCCCCCTTCCCTAACCCCT
GGCAACAACTGCTCTTTTTCCTGTTTCCATAATTTTCCTTTTCCAGAATGTCATGTCGTT
GGAATTGTACAATATGTAGCCATTTCAAATTGGCTTCTTTCACTTAGTAATGTAAATTTA
AGGTTCCTCCATGTCTTTTCATGGCTTTGTAGTTCATTTCTTTTTGGCACTGAATAATAT
TCCATTTCAGGATGGCCATGGTTTATTTATCTATTTACCTACTGAAGGACATCTCGGTTG
CTTTCAAGATTTGGCCATGATGAATACAGCTGCTATAAACATCCATCGGCAGATTTTCAT
GTGGACGTAAGTTTTCATCTCCTTTGGGTAGATACCAAGGAGCATGATTCCTGGATCGTA
TGGTAAGAGTATGTTTAGTTTTTTAGGAAACTGCCACACTTTCTTCCAAAGTAGCTGTAC
CATTTTGCATTCCCATCAGCCACGAATTCCTGTTCCTGTTGCTCCACATTCCTGCCAGCA
TTTGGTGTTGTCAGCCTTAGCCTAGTGTGCCTCAGTAATGTAATATCTGTGGAATATTAA
TATCATGGGTTACTGTAAAGCCATAATAATTGCTGTGTTTAAATATGTGAATGTGTATAT
AACACACTGTTACATAAAAAAGCAGAACCTAAAAATATTCTTAGAAATTGATCATGACTA
TATTGAAATAGCTTCAGGAACACTGATAAAAATCAGAACAAAATTTGGAGAAACAGAAAT
ATCTTATTGTTTATTTTTCCCCAGGGAAATAATGAAGAGAAGAAAGTGGTTTACAAACGC
AAAGTGTTGTTGCTGTTGTTATCAGTATTATTATATCCCAGATATGGATCTATTCTTATC
CAGATCCTTTAAATTTGGATCAAGAAAATATGAGCTAGAGGAGCAGGAAGACATAGAGAT
GGACACGGAGGGCTAGAAGCTCCTGGAATGACCTGGCAAGGTGGGAAATTCGGTACTGGA
TAATATAAGCTCAGGAGGCAATGACTTGGGTTCAAATCCCACCTCTGTCCACTACTAGCT
GGGTGAACCTGAGCAATTATTTAACCCGTTAAACCTCAGATTCTTCATCTAAAAAAAAGA
AAACCATATTATTCATCTCTTAGAGGGTTGTCATGAAGACTACATAAGGCAATGCCTGAC
ACATTGTTAGTACTCAGTAAATGCTAGCTACTGTCTTCCTCTTCCTCCTCCTCATTGTCT
TCTTCATGGTCATCATCATTGTCACTGTCATCACCATCATCTCAGGGATGTCCTGAAAGC
CCCACCCTGCCTGTGCCACCTTCCTCTGTTCTGGCACCACCCTGTGAGGCCTGCAGGGGG
CGCCCCCGGTATACTGCCCTCTCCTCAGCTCTCTTGCTGGTGATTCTTGTTGTTCCAAGT
GAAAATATCGAGTTTTCAGCCCGAGATTGGCATCAAGAGTGCTGTTAAAGCCCCAGTCAA
CATCCCCGTCTCCTGGGCCTTGGTCCTGTCACCCGAGCTTTGGGACTGCTAGCCCTGCCC
TTCTCTGTCCTGCCAAGCAGCTGCTCACATTGGTTCCACTGTGCCAGGAGCTCAGAGAGA
AGAAACCAAACTCCTGGGCAAGAACACATTTGCATAGAGCTGGCCCTATTTGCTGGAGGG
GGCATCACTGGCAGGGCCCTCCACAAGGCAATTTCAGCCAGCCCCTCGCCTCAGTCCAGG
TGCCCCTGAACCTAGCCTGGCTGACAAGGAAGAAGACTACCACTCCCTCACCTGATTCAC
TCATCCTGCAGGTCCTAGACTTTACCTGTTATCTAACCTCAGTTCCTTATTTATCACTGA
GCTGAACTGAGGCAGGAGAAAAAAAGTTTTCCCAGGCACCAGGACACAAAAGCATAGACA
AGATTCTAGCTTTTGGCTTGGCACGGTGGCTCGAACCTATAATCCCAGCACTTTGGGAGG
CTGAGGTACACGGATCGCTTGAACCCAGGAGATGGAGACCAGCCTGGGCAACATGGCGAA
ACCCTGTCTCTACAAAAAATACAAAATTAGATGGGTGTAGTGGTATGTGCATGTGGTCCC
AGCCACCTTGGAGGTTGAGGTGGGAGGATCACCTGAGCCTGGGAGCTCAAGGCTGCAGTG
AGCCGTGATTGCGCCACTGCACTCCAGCCTGGACAACAGAGTGAGACCTTGTCTCAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAGGAACCGTGGTGCAAAATAGGAAAAGAGCTTAAAA
AGAGCCTACTGTGGCCTGTCACTTGGAGAACAGGGAACAGGTGATACTTTTGGGAGAAAA
TAAAAGGTTCCCTTCCTCCAGCAGACACAGCTCTGAGCTGGGTGCAGGAATTGGCAAGCT
GAATGCAGTTCAGTCCTCAACTTGCCCCATCAGCAGGTGCCTTTGTGGCAGCCCTGAGAT
CAGCCAAACTGGGGAGGCTTCCCTGGACAAGATCATGAGACATCTTGTGCAAAATCTGGC
AAGTGGAAGAGGAAGCATGATGGGGAAGACAGCAGACAGTTGAGGATATGAGTTTAGTGG
AGCAGGGAGGCCAATCTGGTTGATTGCAAAAATTTGTATAAATTCAAGGGGGATGGGGCT
CTAGAAAACTCAGAGCAGAGGAAAGATATGGTTGAAGGAGTAGATGTGGCAAATGACTGA
AGCTGAAGATTAGAGTGAAATGGGGAGAAGCAGAGCACAGCTCCAGGCCAGACGGAGGCA
ATTTCAGCCAGCCCCTTGCCTCAGGCTGGGTTCCTGAGGCTGAGGAGCTTGCTGCCTTTC
TGGCTACTTTCAGCAGAGCAGGAGGATCAGAAGCCTTCACACAGAGTTCTATCTTGCTTT
ATAGGACTGGGTAGAGATAGGCTAAGATTTAAAAGTTATATGACGGTTAGAGGTGGTACA
GGATTAGCCCTTACTTTACAGGTAGGAATAGGTCCCAAGAACATAGTCAGGACTAAGACT
CAGGCCACCCGACTCGAGATTCCTCGTGTTTCTTTATTCCCAGTTGCCTCCCTCCTATCA
CAGTGCATTGGATGTTAATGGAATTTCTATCAATTGGACCCAACTGGAAAGGTACTAGAA
GTCCCTAGTTAGAGAAATTTGTTTTTTTCTTTTTTCCTTTTTTTTTATTCCTTTTTGAGA
CAGAGTTCCGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCGCGATCTCCGCTCACTGCAAC
CCCCACCGCCCGGATTCAAGTGATTCTCTTGCCTCGCCCTCCTGAGTAGCTGAGATTACA
GGCACACACCACTATGCCTGGCTAATTTTTTTTTTTTTTTTGTATTTTCAGTAGAGATGG
GGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTTAGGTGATCCACCCACCT
TGGCTTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGTGCCTGGCCATGTTTTTCTT
TTTTAAAGGAAAGAATTCTTTAGTAGGTAACTAACTATTCCCTAAATTATGTCTTATAAA
TGTGGGTTTGTGTATATTGCATTTATTTAAAGGGGGTGATCTACTTACATAATGATTCGT
TAGTGACTAGGGGAATGTAGCTCAGTCCTTCTCTTGGATTTCTCCTCTGCGGCCTGAGTC
ATTCAGCTATGAGATGCTCCACTACTAATGGAATTTGTTCAGCACTGTGGGATGTGAGCA
CCAAAACGCCACTTGGAATCCTGAATCCTGTGGTGAGCCATGCCAGTGTCTCTGTTCTTT
CTAGCCACTTCCCCTGACTTGTTAAATACTAACTATTCTGAGTCTCTATCATGCCTCCCA
ACCCAAAGCTTTCCTGATTCCCTCTGTCCACATCTGCTTTGCCCAGCGCAAGCCCCTCAG
ACTGCTGCCCACTTGTGGATTCTTTCTAAAACAGGTGACACACCCCAACTCTCCTCCTCC
TCTGCTCTGAGGTAGCCTCTGCCCCATTATAAATGAAGTAAAAGTAGAGATGAGGCCAAA
GCTGGAAGCAGTGAGTCTGAAAGGAGAAATGGAGGAGAATAAGGAAGACGCAAGTTGGGA
AACTGAAAGAAGAGAGAGGGGTCCTCAAAAAGAGAAGTTTCCTCTGTCATGTTTCATGGT
GGACATTGGATGTTGTAATTCTGGGGAATTTTTCATACCAACATGTACTCAGGGGTCATA
GCCTCTGGTTGGCAAGATTGTGTTTAAAACGTGCAAATTCCCTCTGGCATTATTCTGAGA
CAAGCTTTGGGGTCAAATATATGTGGATTCAAATCTCAAAACACTTTCCAGCTATGTTAC
CATAGGCAAACCACTTAACTCCTCAGAACTTCAGTTTCCCCATCTTCTGATCTATCTGAT
GTAGTAAACACTCACAAATATTAGTGTCCTATGCCCCTTATTACTGATTCCCTACTGGGC
TCCTAGAGACTGTCCTAGGACTTCTCTTTTGCAAACAAATTTAAAAATGAAAACCTGACA
TTTGATATGTACAAAAGAATATAGATGGTGGACATATGTCTATATGTTATAAAGCATAAT
TTAAGAACAAAAACTCAATTTAAATCACTCTTTTAAATTCAGAACATTACAGTGCTGTTG
AAGCTACCTGTGTACTTTTCCACAAGCTCCCACCCCTGCTGTTCAAGGACTTATAAAGTC
TTTCTAACTGCCCAGTCCCACCCGACTCTATCCTCACTCTGATTGTTAGTAGAGGACACT
TCTGTAGATCACTTGTAGTTTTTTAGTCTGATTGACCAGAAGTAACATAGAATTAAGGAA
GTCATGAGCACTTCCAGCCTCAGAGAGAAAGATGCCGAGTTCAGTCTGAGGGCCTGTCAC
GTTTTTTATCTTCTTTTTTTTTTTTCTAGGTCTTCTGTGGTGAAGACCTCCTTCACTGTG
ACCTGTAAGCACGAGGCAACTGTTTGGGGTTTTAAAACAAGGGCACAGGGACCGACATGA
TGAAAACAGGTTGCCTCTTCCTTTGAGACTGGAGAGAAAGGTGAAGGATGGGTCAGGTCC
TGATCTTTCTGATTCTGATAGTGGTCATAGGAATGAAAAAGCACATTGCAAACAGATGAA
AGAAAGGGAGACTTGACAGCATTTGTTGGCTTATTTGACATGTCCAGGAATGGGCCCAAG
GCAACGGTGAAGAGTAAAGGTCACTTGTAGTTTTTTATTCTAATTGACCAGGAGTAACAC
AGAACTAAGGAAGTCACGAGCACTTCCACCTTTGGGGAGGAAGGTACTGAGTTCAGTTTG
GGGCCTGTCAAGTCAAGATGGAAATCCCCTGCAAGCAACTAGAAATATGGAGCTCCAAAA
AGAGTGTAGGATTGAAGATAGAGATTTGGGCATCACTCAGGGACAATCGTTGGAGCTATG
TAAATGACAAAGGCTCAAGGGGCAAGACACAGAAAGAGAACATAAGGCTGAACCTTGAGT
GTTAAAAGAAGTAGCTGTAGCTTTGGGTGTATAGGGGCAGTGGAAGAAGATAAGGCTGGA
ATGGCACCAGGTCCAGGTTATAATAGGCCTTCTCTTCCAGGGAAAGGAACTCGGACTTTA
CTTATAGATAGTTGGCAGTTACTGAAGGTTTTAAAACTTGGAAGTGGTACGGTCAGATGT
GTGTTTCAGAGAGATGTACTTTACTGGTGCTTAATTACTTTCAAATAAAGAAATTCATAA
TCCAAAGAATTATTAGAGTGGAGGAAGACTGGAGGCAGGGAGAGTAGTTAGAAGGCTGCT
GCAGTAGCCCTGGTGTATTAGGCCATTCTTGCATTGCTATAATGAAATACCTGAGATAGG
CCATGGTGGCTCAAGCCTGTAATCCAGCATTTTGGGAGGCTGAGGTGGGAGGACTGCTTG
AGCTCACAAGTTCAAGACCATCCTGATCTACATAGCGATTCTTCGTCTCTACTGAAAGTT
AAAAAAAAAAAAAAATAGCTGGGTGTAATGGTGAACACCTGTAGTTCCAGCTACGTTTGA
GGTTGAGGCAGGAAGACTACTTCAGCACAGGAGTTCAGGGGTACAAGTGATCTGTGATCA
CACCACTGCACTCCAGCTTAGGGGACAGAGTGAAACCCTGTCTCAAAAAAAAAAAAAAGA
TTAAAAATTAAAAAAAAAAAACCCCAGAGAGTGGGTAATTTATAAAGAAAAAAGGTTTAA
TTGGCACACAGTTCTGCAGGATTTACAGGAAGCATGGTGCTGACATCTGCTCAGCTTCTC
AGGAGACCTCAGGAAGCTTTTACTTGTGGTGGAAGGCAAAGCAGGAGCAGGCACATCACA
TGGCAAAAGCAGGAGCAAGAGAGAGTTGATGATGGGGGATGTTGCCATATACTTTTAAAC
ACCCAGATCTCACGAGAACTCACTATCATGAAGATAGCACCAAGCCGCTGAGGGACCTGC
CCCCATGATCAAAACACCTCCCACCAGGCCCATGTCCAGCATTGGCATTAAAATCCAGCA
TGAAATTTGAGCAGGATCAAAGATCCAAACTATTATTACCTGGTGAGAGGTAATGGTGTC
CTAGACTACAGCAATGATAGTGGAATAGAGAGGAAGGGGACAATATTGAGGCTATTTAGA
ATACAGATGCATTGATTCAATAAGGGAGATGAGGTGAGGAAGATTGAAGAATCTAGGATG
GCTGCCATGTTTCTGGTTGGGTGATGATAGTGTATCTACCATGGTAGAGAATAAATGGAG
AGGAGCACTCTTGTGAGCAAGGTGACATGTTCGACTTTAAATATGTTGAGTTTGAAATGG
ATATCCGGGTGGGCTGGACATATTGACACATGGGTGGTAGTTGAAGCTAAATGGATGGAT
AACATTTTTGGAAAAATAATAAGTGCACAATAAATGTCTGTTAATGATCCATAAATCATT
ACAGTCCCTTTGCTTTCTCTTCTGTGGTGTTCTTCATGTTTATTTTGGAGTTCCACCAGA
GCCTCCAAGCTAAGCTTGTCCAACCCACCGCCTGTGGGCTGCATGCAGCCCAGGACAGCT
TTGAATGAGGCCCAACACAAATTTGTAAACTTTCTTAAAACATCATGAGGGTTTTTTTTG
TGATTTTTTTTTTTTAAAGCTCATCAGCTACTGTTAGTGTTAGTGTATTTTATGTGTGGC
CCAAGACAATTCTTCTTCTTCCAATGTGGCCCAGGGAAACCAAAAAATTGGACACCCCTG
CCTAAGTCCTCTCTGTCTGTGAATGTCAAGACTGTGGCCCCCTTAAGGATCTTTTGGATG
TCCTATTTTTTGAAACTTAAAGGTCTTATACCAGTCTTGCAGGCTGGCCCTCAGACCACC
TCACCACAGCCCCTCATCCATATTGACTTAGGAAGAGAGGGCATTCGGAGTGTGAAGAAG
AAAAACTGGAAGACTGTTTCTTTTTCTTTTTATTTTGTGTTTTGTTTTGTTTTGTTTTTG
GAGACAGAGTCTAGCTCTGTCCCCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCACTG
CAACCTCTGCCTCCCAGGTTCAAGCGATTCACATGCCTCAGTCTCCCAAGTAGCTGGGAT
TACAGGCGCGTGCCACCAGGCCCGGCTAATTTTTGTATTTTTAGTAGAGATGGGTTTTTG
CCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCACCTTGGCCTC
CCAAAGTGCTGGGATTACAGGCATGAGCCACCTGGCCTGGCCTGTTTCTAGTACATTGTC
TGGTTTCTATTTCTCTCCTCTCTATGAGTAGAGTTCTCAAAAGTGTAACCTATACTTGCT
GACAGTTTCTCACTTTCTAGTGGTAACTTGTAATCTGGTTCCCACCTTGCTCACTCTTCT
GAAATTGCTCTCAAATGTCACTAGAGACTTTGTCACTGCCAAACCCAATGCCTCTTCTCT
CTGTACTTGTTGGCACTGTTAGAACCTCCTCCTTAACAGTCTCTCCTTCCTTAGCTCCAT
GACATCTCACTTTCTTTGTCTCCTTCCTGCCTGTCTGGTGGATTCTCTTTCACTCTTTGG
GGGTCCTTCTTCTTCCCATCCCCTAAACATAGGTGTTCCTCACTCTCTGTGCCAGGCTCT
CATTTCTCTGTGCAGTCTTTGTTGGGATCTACCCTGTTCTCATAGCTTCAACTCACACTG
CCCTGGCAGCAATGACCTCCTTTCTCTCTCTGGTTCTGACCCCTCTCCACAGCTTCCAGC
TCTGAACTCATCACTTCCTCTTCCCCCACCTCAGTCTCCTCACCAGGTGTGATCCCCCCC
AGGCTCCCCTATGCCCGTGAATGACCTCGCAGTTCTGATCACCTGACTTGAGACTCTAGT
ATGATCTCTGAAGCTTCCCTCTTTTGCTCAACATGTCAAGTTGGCTTCAAACTTTTTTCA
TTTTCTTTTGATTTTTCTGTACTCCAATTCATTTTCTGTGTTCCACTTTTCACCATTGCC
ACGCTGATTTGGGCTGTCATCTCTTCATGCTTATATTATTGCAATTATTTTCTATCGTCT
ACTTGCCTACTATATCCACTTGGTTCAAACTATTTTGTCACCTCCCGATTAATTTTCCTA
AAATGCCATAGCTTTCTCCTACTCCATCCTTCCCAAGAACCTTCAATTGCTCTCCGTAGC
CTACAGAAACTCTGGCCTGACCACAAATCAGCACAACTCTGTGTTTCTTCCGGATGTTCC
CCTTAACACAAACACTGCCTATGGTGCCTAACCTTTAGTCCCGTCCTTCCAGCTTCTCCA
ATGAGGCTATTTGAATGGACATTTACTTATCTTATGGCTTTTAGTGGTTAAACTAAGCTA
CATTCCTAGTTTCTTTCCTTTTTTTACCTGAATTTATAGCAATTCAATATGGTAACACTG
GTTATTGATTAGCAGTTAAATGTTTATGATGATCAGAAATGAGGAAATAATTATATTCTT
TTTAAATAAATGCTGGGGGTGGGGGTGAATTAAAACCTCTCAACACATAGATTCAGAAAA
TTAAAGAAATCTTTGGTGATGAAAGGGTTGAGAACCATCACCCTGCACTCTAATCTAGTA
AATGGGACAGTTTGATGCTGTTTCCCAAGTGAACTTGTATTTTCACGTCTCCCCAGGACT
CTGCTACGTTGTTCCCTCTGCCTTAAATGCAACAGAGTCCTGGGGACCATCTCTCAGCAC
CTGAATCTTCTGCTTCCTTTGGGACCCTAATCAGATGTTACCTCTTTCCTCCCACATCTG
CTAGGAGCCCTCTGAGTAGAATGACCTCTCCCTTTTACAGCCTTCAGTACCTCCCGCACT
TCGCTGAGGGTTCCGGCCTTATCTTTCCTTACAGAGAAAGCCGCTGCAGGTGGGCACCGT
GTGCTGCGCGTCTCTCACCCAGCACCGCACCGGGGACTTAGGAGACGGTGAACAACACGG
GAATTGTGCCCAAAGATACAGTCCTGTGGCTCAGGGAGCCCAGGCCTACTCCGCCCCAAT
CTCACTTCCAGGCGCCGCCTTCGGCGCTGCCTGCAGGGCCACTGGGCCGGTCCTGAATTC
ATTTCCACTTCGTTAACTCGGTCCCAGTCCCGCCCCCCGGCTCCAGCTCTCGTAACCCAT
CGCTGACAGGACCGCCTCCCTTTTCTTCCTTCTCCCTTCCCCTGTCACCCTGCCAGCTCA
GCTCCTATCGTTTCGCATATCGTCTCTTCATCTCTCTTTCTCCCCGGGTCTGTCTGGGTC
TCTGTCTTTGGATATTTCTCTCTGCGCCTGCAGCTGTCTGGGTCTCCGCTTCCTTGCCCC
GCACGCCCCGCCCCCTGCCCAAGACCCTCCAATCTCGGCGGCTCGAGCCTGGCGCTCCAC
TCTCCCATTGGTCTGTTCGGAGCCCCCAGCCCCCGGCTGACCGGCCCCCCTCCGGGCCCC
TTCATTCACACAAAGTATGGCTCCGNCGCTGCGGATGGAGGGGGCGGCCCGGCCCGGCCC
AGCTCTGCCCTCGGCCGGCCCGACTCCGGCCCCGGCCCCCGGACAAGCCCTTATCTGATC
ACAGCTCCGGGTTTAAGAGTCCTGGCCCGGCCCGTCGCACAGCTCTGCTCCTAACTCCTG
CCCGCCCCGTCCGTCCATCTGTCCCGCTGCCCCGCGGCCCATCCAAGGGGCCACTCCACC
TCGGACCCAAGGTAAGACCCTGGCCCTGATGAAGGAGTTCTGCCGCCCCGGCCGGGTCCT
GTCCCCCTAACTCTCCAGAGACATCGGGGTCCCAGATCCTCAGTCCCTACCCTGCCTGGC
CTCAGCGGTACCACCGTCTTGTTCCCCTGCCTCCCGCCTTGGGCAGTCCCAAATGGAGCC
TCCTGGGAAGGGCTCCCCACGAGGAAACTAGCCAGGCTGGTCACCTCAGCCCTTTCATCT
AAGGAAGGGGGATCCTCTAGAGTCGACGTGCAGGCAGCAAGCTGTCTGGGGGAAATGAGA
AGAGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTCCGGGTAAGGGA
TATCACTGGGGTCTCTGCATTAGAGCCACAGGGGGGCTGTGAACCATAACCCTGCATACC
CGTAACTATCCAAGTTGCTACACCATNACTCCATTTGATGTAAGGAAGGGGACTTTGCTC
TTCCCTGCTACAACTGGGCTGACCAGGCTCTGAGTGCGGGGTGTGTAGATAATACAGTGA
CAACCACACATAACCAGGCACCCCATACACAGGCACAACAGACAGTGCGCCCTCCTCCCC
ATATGGACAGGGTACTCCCATCCCCAGCCCCTCCCCCACTCCCCATACAGTGACAATCAC
ATAGTGACACCCATGATCGCTAGTTCCCACATGGGGAGAAAAACAGATACTGGCAGCTTA
AACCGGGGAGCCACCAAAGCCTGGTGTGCTCCAGACCCCTGCCCACCCAATCTCTTCCTT
CTATTCTGAGTGGCTCCCATTTTAAGACATCCCTCCTCATGGCCCCTCACCCTCACCCCA
GCTGTTTCGCACTGGGATTTCCAGAAGGAAAGGAGCAGGGCCACTTCTGCTAGAGTGAGA
AGGGCAGATTGGGTTCTATAAACTCACCCTCCAGATGGAGACGCCCCTTCCCATTCCATT
CCTCCTCTCATCAGAACTAACCCAGGGCACCTGTGTTAGGGAACAGATGAAGGATGGAAC
TTCCTGATTTGGGGGAGGAGAGCTGAACCCAGGAATGGGTAGAAGGACAACACTGGGAAA
AAGTGAGGGTGGGTTCTGGTGTCTTGAAGTTTAATTCCAGTGAGTGCCCCAGGCAGGGTG
AGGCAGATGGGGAAGAAGCTGGTGCAGATTTGGACCCCAAAGAGGCCAGTGCTTAAAGCC
TGCTTCTGTTGCTTACCAATACAAATTCTGACTAAAGATGTCTGGCCAGTCTGCTCTTGC
TGTGGTGTTTGAATTTTTTTTCTCCCCACTGGGACTGCTTTAGGCTGCCTGGGTGGGAGG
GAGATAATGACAGGAGATTTAGGGCCCCCATGTGAGAGATGGCCTTGTTTAAGGGTGCTG
AGGAGGGCCTGGAGTGGTTGTCATGAAATTAGCCCCAGGAGGGGTGGGCAGCCACCAGTG
AGTTCAATTTAGTTTCATCCTGAAACTCTCTCCCTAATCTCCAAGGATTTTTGAACATAT
TCCTGGCATGATGGTGGGTACCATCCTGTGCCAAGTGGTAGGGCTTGTAAATTTCTCTGG
GGGTAGACTGGGTATAGGGGACCAAGTTTGGAAGGAACCAGGCATCCTGACTCATAGCTG
GTTCTTCAGGGAGGAAGAAACGAGGGAGGAGGGGGATGGAAGGCATCATGCCAGGGAGAG
GGTCCAGGGCTGGATTGTGGAGGCAATAGGCACGGCCCAGGCAGTGCCAACTCCTTTCCC
CGCTGCCTTCCCCCAGTCCTTTGGTGGTGGTGGCAAGGGAGGAAGGGAGGGAGAGGGTGT
TGGGGGGTGATCTGGGCTGGTCCAGCCTCCCAAAGCCCTTGCCAACCTGGGTCCTGAAAG
GAGCTGCTGTTTTCTGAGCCATCCCCCCACCCCCCACTCAGAGCCTGAGCAGCCAAGTTG
TCTCAGCGGATATCAAATGGCAATGACTCCACCGATGGAGGGTGGGTGGGGAGTGGGAGT
GGCAGGGGTAGCAGGGTTATGGTTCCAGCCCCTCTGTGGCTCTAATGCAGAACCCCTCTG
CTATCCCTTACCCTGAGGAAAAAATAAATCCATCTTCCCCAACATCTGACCCACATCCAG
TCTATGGGTGCATATGTTTGTGTGAGGGGATTAATGATCTGCCCGCTGGTATCCCCTACC
TCCTCCGTGTGCCCCATTGAACCACATTCTAGCTCCCTCCCACCTGCATCACTGTGCATA
AGCTCATTTACAGCTCCAGCTTGGTTGGCTTGAGCTACAAGGAAGTGACTGGCAGAGGAC
CCGGGGACCTTCCTTCCCTTGACCTTCCTTGGGACCAGAGAGGCTGGGACACTTGGATCA
CGGTGGGCTCAGATGAAGTCCTCTGGAGTCATTCTGTGATTGGCAGGATAGGGGGTTTAA
AGCTCTAGGGGGTGGGTCATGCAGAAAGATCTGTTTCCTCAAAGGATACTCCTGAGCCTC
CTGGTAAAACTCTTGGTTTCTGCACACAAGATGGAAAGATAGGCCGAGCCTCCTGGCATT
GGTGGGGAGGAAAAGAGACATTGGGCAATGGAGTCCCTAAGCTTTCCAGCCACAGGTTAT
TTAGGACGGAAGAAAAAAACCTCCACTCTCCCTCCCCTCCTCGGCCTAGATTCTTCTCTT
GCCTGACTGGTCAGTGCTACTGTCCAGGCTGAGGCCAAGCTGTCCAGGATAGCAGTGGGG
CCCTGGAAGGGGGCAGAGAAGGAATCAGCCAAGGCACATCGTTGAGATGAAACTACAGAA
AGATTGGAGAGGAAAGGGAGATTTAAAATCTAAGTGTTTTAGCACCCAATGGTGGGTGGT
TGGCTGGGCAGCTCCTGGGAATGGGAGTTTGCCATGTCACTTCGGTCTCTCCAGCAGGCT
GAGTTCAATGCTTTTCTTCCCTCATTTGAGTTTAGCCTACATGTTTGCCACCATTCTTTA
GGGAGAGAGTGCATCTGGTGGCCCCTCTTCCTCCCCTCCCCCATCAGAACCTTGAAAGGG
CAAAGAGAAAGGGATTGTGGGAAATGCCCTCCCGTGGGTGTTTGCCAGCTTGGAGCCTGG
ATTTGAGGTGGTGGGGGAAGGGAGGGGCTGGCTCTGGAATGTGAGAGAGAAGTAAGAACA
GAACTTTGTGGCATGGAGAAGGAGGTTGGAGAAGCAGGAGCTAGAAGAGGACTGAATCAG
ACCTCAAGCCTCCAACAAGGTGCAGCACAGAAAGGGTATACATGGCCATTGTGCAACTTT
TCCGATGGCACAACACCTGGGGAAAGGATTGTGGCTGCAGCTAGAAGGACTTAGGTTAGA
TCTCAGGAAGCACATCCTAGAAAAGGAAAGACATTTGAAATGGAGACTGGGAAGGAAAGA
GAGACCACTTTCTGGACCAAAAAAACCAACCAAAACAAAACAAAAACCACCAACAAAATC
CCCAAACACAGAAGCCCATCCTTAAAGCTTCCGAGAGGAGTGATGGAGCTCAGAGTGCAG
GGATTATTGTGACAACTGTCAGGGGCCTCCCCTGGGTGGCTGCTGCACCTCTCTCTTGCT
GTTCCAGGGCTACTTTCCGCTCTGAGAGACAGCAGGCACTATGGTTAAGAGCATGGCCTT
GGAGTCTGACTTTGTGGGATTCGGTCCTGGTTTACCACTTAGTAGCTAAGGAAGTCCCAT
CCTCACAATAGGGCTCATAACTGCTGTGAGGATGCACAGTGACTACCGTAAGGGGCTTGG
AATGGTCCTTAGTCTGTAAAAAGTGGAGTTGTGGGCCATTGCTTTTCTCCCACCACTCTA
ATGTTTTCTACTGTGTCATCTTTCCTTGTTCCTGGGCTTTGTCCCAGCCCTTCTTTGTGG
GTTTTGCTTTGTTTTGTTTTGAGATTCTGTCCTAGGTTTTTTCTTCCCACCCTTCTGGAG
TTTGGGAAGGTAGAAGAATTATCAAGCAGTTTAAGATGCATTTCCTTCCTTGATTCCAAT
AGGCTGGGCATCACTTGAGGTGGGGTCTCCACACCCACAGCCCCTGCTTTCCACAAGTTT
TTGCCAAGCAGATGTCCTGTCTTCAGATTCAATAAATGAGAACTGAGTGGTTGAGCTTTC
ACCAAATAGTCTCTTTCCCCATTCTCAGCAACTTCTCTTTCAGCCAAAGACTTCTGTCAG
AGACTTCTTCTGTCGGTCAAGACAACCCCCACATCTCATTCCTGCTCCCATGGTCCTGCC
TATCGCTCTTGTATTCTTCATCCTGCCTCTCCCTCTCCCGGCCCAGGTTTGCCCCCACAA
CTTCTCTCAGGTTTATATGCCCTTCTCTTCTTGTGTCTCCTGATTGGCTTGTTCATCCCA
TCAGCCTGGATGCCCACAGCAGCCTCCTTAATGACCTCCCTGACTCCAGCCCCCTCTCTC
CTCGACTCCTTCCCTGTTACCCTATAATGAAATTATCACTGGAATTGTCATCATGAAGCA
TCAGTTTTATCTTGCCCTTTCTCTACCCAGACACATCTGTTGGCATTGGATAAAAATTTC
CCAATCACAGGCTTCAAGAGACTTTATGCCTTTCTCCCATCCCCTCCAGCCCCATATCTT
GTGGAACTGCACTCTTCAGACCCTGATCCTGGGGAGCATATCCCAGGCAGTCTCTGAGCC
ATGCTCCTCCCCACACTCTGGACCCTCACAAAGGCCATTCCAAGTCTCACCCCTCCCGCA
GATCTCTATTCTCCTGTTTCCCTCTCTGCTCTGCCATCTTGCTTGTTACTTGCATCTGCA
ACTTGGCCCAGGGTTCTCCATGCATGGCGATGTTGGAGGAGACTTGTCTCCCTCATTAGC
CGGGGGTTTCCTCTAGGGTGAGGCCTGTACCTCCGTCAGATTGGCAAAGGCATCTCTTCT
CTCTCTGGACCCTCTGGCACCCAGCAAAGGGCCTGCCTCCTAAGACACAGAGTAGCTACT
GTCCAGTTTGACTCTAGGTAGGAAACATTTCTGATCGCTTATTCTTGGGGAAGGAGCCTG
ACTTTGGAGGTTTATGTGAGCATCCTGCAGCAGGGTGTGTATAGGATCCTATTATCTAAT
TCTATAGGAGATCTCAAGAGAAACCCCTCTCCTACTAACGACCCCATCCTGTAGACATGG
CTTCACCCTAAGATTACAAGCCCTAGAACCCCCAATTTATAGTCTTCTAAGCATTGTTGC
TCCACCCACCCCCCCAACACAAATGCAGGTATGTAGGCCCCAGAGAGCCTTTCTCCCCTC
ACCAGGGCAGTCTGACTCCAGCCTGAGGCCGGGCTTGTCAGCAGCATCGTCTGGAATGAA
AAAGGGGGATAAAGGTCAGAGTCTAGTCTGAGGCAGCCCCATTGTCCTGAGCATACCTCT
GAGCAGGGGCTTGCAAGGTGGCAGACATGTGAGGTCACCTCCCAAGTGGGGTATAGGTCT
GACCTCTTAGCACTGCATTCTCCCTGGACCAGCCTCCTCAGCTCCACTTCTGATCCCAGT
TCCAACTGGTAGAGCCAGGCACACTCCTTCTCCACGTGTCTAAACCTCCCGGTTGACCCT
GTGATAAAAAAGATATAGGCAACTGGTAAGAGGAGAGGGTGAGTGTATTAGAGTCTAGAG
CACTGGTTTTTAAACTTTTTGACCTCAGGACCACTTTACATTCTAAAAAGTTACTGAAGA
CTCCAAAGAGCTTTGGTTTGTGTGGGTTCTATCTATGAACATTTACTGTGTTAGAAATGA
ACACTGGGACACATGAAATAATTATTAATTTTTGCATGTTAACAAAATGACGTATTTTTA
ATGAAAAACAGCTGTATTAAAGTAAACAAAAAGTTAATAAGAAGAGTGACATTGTCTTAT
ATTTTCACAAGTCTTTTTAAACATCTGGCTTAATCAAAGACAGTTGCTTTCTCATCTGCT
TCTGCATTTAGTGTGTTGCAATATCATAGGTCATGTACCTTCTGGAAAACTCTACTGAAC
ACTGTGAAATAATGAAAGTGAAAAGGGCAAATAATGTATTGTTAGCATTATTATGAAGAT
AGGTTTGACTTTGTAGAGCCTCCGAAAGGGTCTCAGGAACCCTCCGAAAGGGTCCAGGGA
CCATACTTTGAGAACTGCTAGTCTAGAGGAACCTTAGAAGACAGTTTCAAAAACCTGGGC
CAATTTGAATATCCTCGTTGATTTCCTTCAGCTGCCATGGTCTTTTGAATGTTCTCACCA
GGGAGGTAGTATGGGGTAGTGGTTCATCATGTTAAGTTCTGCCTCTGTTCTACTACTCAC
TAGCTATGTGGCCATGGGCAAATTATTAATATCTCTGTGCTTCAGTTTTCTCATCTATAA
AATGGGACTTTAAAAAGCACCCACCTTTAGAGTTGTTGAGAATTAAATGACATAATAGGA
AAGGGCTCAGCGTAGAGCTCAATGATGTGAGCTCTCATTAAATTCCGGAGCCTTGCCCCT
GAATCCACTGCGCATTGTCCCGAAGGCAGGGAGCTGCAGAGGAGATCCATCCAATGCTAC
ACATAGGAGCTCGGCCCAGAGAGGGAAAGTGACCTGTGCAAGTTCCCAGAGAGAGTTGAC
AGGGTTGTTGGGCCCCGAACCCAGGAGTTCTAAGGCCTAGCTCCATCTCTGCTCTCCCCG
CCAGAATTTTTTTGTGGAGAGTGGAGGAGCAAGGTCCTAAGACGGGGAAAGAAGCAGACT
TTACCTTTCTTTTCCCCAGCAATCTCAGGTGAGCCCAGGGCCAGGGCAGTACAGTGGGAA
GCCTTGAGGGCAGACAGCAGGGAGAACTTCCGATACTGACAGCAACTGAAAAGAGGAGAA
AGAAAGCTAGGAAGACATTTTCAAGCCCAGAGATTGTTCTGTCTTGCCGTGTGGGGAGCA
GTTCTGCAAAGTGTCCCCGGCCTTCTCTTCCTGGGGCTCGTAGGAAGTCTGTGATTGGGC
AACCCTGCTTCTCATGAGGTGCTCAGTCCCGCTCACTGCCCTCCTCTCAGCTCTCCCACC
ACCCAAGGCCCAGGAGCCCCTCCCCAGATCATGCCTTCTGGCCCTGCCCTTTGTGCTGAG
GCACCACAAGGCACAACATGGTGCCTTGGAAAAGCCAGTTGGTGGTGCTGAGGGCATTAA
TGAGGATAGGGGTGCCTGCTGGGGTTCCCTGGGCAGGAGAAGGGAAGCTTCTCCTCACAG
ATTGTAGAACAGGAGGAGGCAGATGGGGAGTTAGACATATACTGGGAAGAGCTAGTCCTG
GCTCATTGGCCCTTCAGTCAAATTCCCCTGAGCTGGGCTTCCAGCTCCACCTTCACTAGT
TCAGGTTGAATTCCCTGGAAGAGCACAGGTGGCAGGCGACTCTTGTCCCTAACCCCTGCT
TCCCCTGTAGTAGCTTCTTCAGCCTCCAGAACCAGAGCAGGTGGAGATCTCAAAGAAGGT
GGCACCCCAAGGAAGTAGAACCCCAAAGACCCCAAACCCTGAGCACATGCCCTTCCTGCT
GGGGTTGGGGAACTTGCTATGTATTACTCTGTTTTTCTTCTCCTGCCCACAAAATTCCTT
TGCATAGATGGTAAAACTGAGGCAAAACGTGGGAGGACTTAGACTGCCCACCCACTTCTT
TCTAGAGCCCAGCCTGGGACCAAGGGGCTTGGCATCCCGCAGCCCCTCCCGCTCCACTCC
TACCAGTCCCCGTGGCTTTTTCCATTTGGAAAGTCCTTTCTGGCGAGTGGCAGGTTTGGA
GGCCCTAGTCTAGTCTCCTCCCCTGTCTCCTGGGCAGTGCCCCCAGGGGAGCCCCTGTGG
GCCAAGATCTCCTTAGTCTCAGTCCTGGGCCCCCCTCACCCTCTACCAGCAGTCCCCCAG
CTCCCGCCCCTCGGCTGTGGGACAGGGAGAGGGCTGAGGGGCTGGCTCTGCATACTAATG
TCCTGCCCATTGTCAAAGCCCCTTTGTGCCAGGGAGCTCCATTGAGGCGGCTCCGGGGCA
GGCACAATGGGGGCTCTGTCCCCTAGTTCCCCCAAACAGTCACCTGCTTTCAGAGCCTTC
CCCACCACCCCCCCTTCGCCCCAGTGTCCGGAGGGCCCAGAGAGCACGGGGGAGTGGGCC
CTGGGCCAGGGGGGATGGGCAGGAGGTGACTCCCCCACTCTCTGGGCAGGCTGGGGAGAT
GGGCATTTGACAGGGCAGGCTGCAGAGGGCACACAGAGGGGAGAGGCCCTAGGCTCACAG
GGGCAGGGGCAGTCTGTGGAGGAGTTGGAATGCAGGTTCTCTGAGGCCTGAGAAGGGGAA
GGGGCACTCAGAGCCTGCCCACTTCTCGGTTCCGTATGCCCAGCCTGGACCTGTGGCTGC
CACCTCTCCTCCTCCCACTACAGGACTCCCCGGGGCTCATATATGCAGAGACACACAGGC
ATACACTCATCTATGCGGCCCCACACACGGCTTCCAACACACACCCAAACGGATGTGCCC
AGACACAACACACTGACCCCAGCACACAGATCGCACGTCCACAACACCACCTTCTGGCAT
ATGCACCTGCACACCCACCCTCCCTCCACCCCACCCCCCTTTCCCTTTTGCACCCCCTCC
ACGGCCGCAGGCATTTCAGCACCATGTCCCTCCCCCCCATGCCCTTGCTGCCCTCTGCTG
CTCTGACACTGGTTATAACAAGTTTGCACTTGTTGTGACCTTAAGAATGTGGCCCTGGGG
CTAAGAATGTCCCGCTGCCCCAGACTGCACCTGCTTATACGTTAACCATGGACACAGCCT
CTTGCTGCACTCTAAGCAATGCTCCCATTCCTGCCTCAACCATGGAAGCAGTTAGGTGGG
CCAGGCCCCCCACCCCAGAGCTGAGTCAAGTACCCTGGACTGAGCTCTATGTGAATAACT
AAAGCCCCACCTGGCCTCGCTGGCACAGGTCCAGTGTGTCCGTCTTTGCATTTGCCCAGG
GCACATAGATATTTCCTAGCCCTTCCTGGCCCTGGGAGGTAGATGGAACAGTTATCATTT
TCCCAGCAAGGCTCTGAGAGGTAAGATGATGGTGTCCAGGCAGCTGGTGGCAAGTCTGGG
ACTAGAATGGAGGTCTCTCACCGCTAGTTTTTTTGTGTTTTTCCCCCAACTATTTGTCTC
TTGGTTTCACTCAGATGACCCCACCCCCAACCCTATCTACAATTCCAACAGAGCTGTCTT
TTAGCCACCTTTTTTTGGGAAGGAGTGGGGGCATGGTGAGGGGAAGGGGTGGGGAGAAGA
ACGGGTCTAGGAGCCTTAAGTGGGCTTCTGGGTCTAGAAAGAACCTCCGAAGGTCACTTT
GACCCTTGCACTACCCCTAGGCAGAGTGAGCCTACCTCCTTTCACTTCCCACCCTCCTAC
CGGCCCCACTCCTGCTACGAACTCTGGATCACTGGAAAGTAACCCCACAGCCTTCTTAGC
TAGGGTTTGGAGTTGGGGATCTCTATCAATTATAAGTCCTTCATGCTGCCTAGTACTGGC
CTTTCCAGTTATTATCCTACGTCTGCACGAGGATCTGTAGGCTGTATCTACGGCTCACCT
GCTATTCTGGTCCAGAGCATCTTCTAGCAGTTGGGAGCAGATGCCCTAAAAAGGGAAGAG
AGGAAGGCCCATTGGGATCCCAGAGACTTGAGGGCTGACTGCACAGTGGTGTGCTGGGGC
CTGGGAGGGTGGATGGGGTCACAGTTGCAGAAACTCTGTTAGATAGAGAACTAAGCTGAT
ATTGGTTTGCTCATCAGCAAATATTATTGAGTGCTAATCTCCATGATGTTTCCTCCCATC
AAAATTGCATGGGAGAACCTCAGGGCCCTTCTACTCCTTCTCCTTTCCCCTCATCTAAAA
TGCTTCCCCTCTGGCTACTGGATTCTCCTTAAGCCGCCTCATCCATCTGTCTTCCTTCAT
GCAGGAACACACCTCCCCCAGCCCTTATACTCTGGTGTGATTCTTTTGCTCCAAATGTTC
CCTACTGGAGAAAGAGAACTGCTCAATGTATGTAACTTCAGCTTTCCCTGCTGTGCTCGG
GCAGTTAGTTACTATAGGAGACAGAGGACAGTGAGACACTCACCTCTGAATCTAGTTCTG
TATCTAGTAAGTGTCCTCATGCCATCCCTACCCCATCCTCCTTCTTAAGGGAGGAATGTG
GATAAGGAATAAGTAAAAAGTTGAGAGGGGGCAGAGAGATTGCCTCCCAGAGTCATGGTG
AGCTCCCTAGACTCCTCTGAGTGAGGGTCAGAGGCTGCTCTTCATGCAGGGAACAGGAGC
CCCAAGAAGGAAAGGGAGCTGAGAGGACACCTGTCAGGGAAACAGGCTCAATTTTCTGAA
TATGAATGACAGGTACAGAGTACCTCTGTGTCTCCAGCTCCATTAAGGGTACAAATAGGA
AGAAATTGCTCAGATAGCAACAGGTAAATTTTGACTTAACTGGAAGAATTCCCTGGGCAT
AAGGGGAGGGACAGAAAGAGGTGGAGAACTCATTGCCTTGATGAGAAGGAAAAGTCCCCC
TTTAGTCACCTACTGAACAAAGCTTGAGTGGCCTGGAAGATAGTTCCAATGACTCTCAGA
GCCCCTGTGGGGTTTCCAGCGGCCTCAAAGGAATCCCTTGATCATTTCCACAGACCCCAG
TAAGAGCATTGCTGAATGTCTCCTCCTCGTGGACCTCACTATTTGCTGCTTATTCTAACT
CTTCTTGTTGGGCCAGCTTCTGCAGGGGTGAGGGAGACCCTGAGACCTACTAGGTGGGAG
GCCCAGATTGAAGATAATGGGCTGTGGCTGTGGCTGTGGTTGGCTGGGGAAGAGTTTCTG
TGGATAATGCTCCAAGGTTGGCTCCACAGAAACTGGCACTTTTGGACCCCAGGGTGAGGA
AAAGGATCTTGTAGGAAGAGATAAGTTGAGATGAAGAAGAAGACCAGGGTTGTTGCTCTG
ATTCTGATGTAAAATAACATGAGCTACCAGCTAGCAGTGTGATCTTGGGAAAGTTACCCC
CCTCTTCTAGGCCTTGGCTTCCTCTTTAGTAAAATGTGGGTATTAAACGTGATGACCATA
GAGGACTTCCCAGCATGAATACTCTGTGACACAGTCCAGTAGCAAGTTGAGAAGCCCAGA
CTTTAAGCAGATTTAAGCAGGCCTGGGTTCAACTTGCAGTGCACCCCTTACGAGCAGTCC
TCCTGGGCAAGTTAGTTAACCCATGTAAGTCTAGTTTCCACCCGTTCATCTGAGGGCAAT
GCTATTGCCCCCCTAGGGAGGCTAGGATGAAGCACGGCATGGAGCGTCCAGCACAATGCC
TGGCGCACCGTAAAGCCTGAGGTAGGAAGTTCATGGTACTGTGGGAACACAGGGGGATAG
CAGCCCATGTTGTGGGTGGGGGCATCCAGAAAGGCTTTCCAGAGAAAGTGACATCTAAGC
TGAAGCCTGAAGGAGGAGTAGAAATTAAGCAAAGTGGGAAAGGAAGAGTGTTCCATGGAA
GAGACCCCATTATTTGCTAAGAAAAGCTTGGTCTGTTCAAGAACCGAGAGGTTTTGTGTG
GCTGGGGACATGATGCATGCGTGAAGTGGGTGGGTACAGATAGAGAACACTGATGCTAGG
GAGGTCAGCAGAGACCAGGTCATAAAGGACTCTGTTCCACCAGTAATTCTAGGGACTTCA
GAGATAGGGTCCCTCCACTTCCTCTCCTCTTCTTCCTACTTTTCATTCATCCTTTCTCCC
AAGACTAATTTCTCTTGTCCTTGGTCACACGAGCACAAGGAAGCATTGGGCTCCCCTAGG
ACGACCTGGCCAGTGCAGGAAGAAGCTTTAAGTTCAGAGTTGTCTGCCTCTGGACAAGTT
TTGGCTTAGGCCTGAAGTTTTCTGCCTCTGTCCTTTCTCACCACTAGAGAGAGATGTGCC
TTCCACAGAAGACCCTGGATTTTATCACTGAGGCACTCCTACTAAGCACTCCCACAGTGG
GCCTCAGTTTCCCCATCTGCCCCTCTCATTGTAGAGAGTAGGGAGAGTGTTGACAGGGTG
GGGCTGAGCACAGCCTGCAGAGAAGAGCTAGGGAAACTGACTCAGTGCCCCCAAGTGTCC
AAACGTTGAAACTTCAATGGGAAGCTCAGAGGAAGGACTTCCGAAGGATGAAGTGGGTGG
CACATGGAAAAGGGGGCCTGAAGGAGGAAAAGTGATGTAGAACATCAATCCTACAGGCTC
TTTAAAGTCAAGAAATGCCAGGCACTGAGAAGGACACAAAGATGAACAAAATACAGATTA
AGAAGCAGTCCAGAAAAGGTTCTCTGTTTGGGAAGATGGGGATGGTCCTTCCTGGAAGGC
ACAGAGCTGATGAAACAGCCTCTACAGGAGTTGGCCCTGGGGGTGCTCTCACAATGGGGA
GTAGCTCTTCTGCCTCCCCTACCCGCCACTACCTCTTGGGCCCTCCACCCCCTAGGTCCA
AGCCTCCCCTCATTTCCAGCCAACACCACTTCAAGTTCAAAGACAGGAAAGTGTACAGAG
AAGGGCCCTTCAGCTGGGATCTGGTCAGCCTCCCCCGCCCTTCTCTCAGGTGGAGAACCC
TGTCTTGGCCCTGGGACTCCAAGGAATAGGTCTCATCATACCCTCCCTAGTTTCTCAAAC
TCTTCTGGTAGATCAGGTGACAACTCATTAGCCTTCAGCCCAAGAACATTATCTCCAGGG
CCCTGGCCATCCTAGGCCTTGAGAAGGCTGCCAGCTGCCTGATACTCCTGAGGCTGGGGG
CAGACAAGAGGGCGAGAGGCTGAGGGATAGTAATTAAGGAACTTGGCTCTACTCAGCAGT
CTTCAGCACACACTTGCCCACCTCTTGGCAGGCTGAGAGGGTTTTGGAGGAATTATAGAG
AGGTGGGATAAAGAATAGTGGGTTGGAAGTCCCCTTCAATTCTGGGGCTAGAGTAAATCT
TACCCCACAACTCACCTGGAGAAAGGAGATCGAAGGGATGGTGTAACTTGAGCATCATCA
AGGCCACTGGGGTGTGGAGAGGCAACGTGAGGGAAAAGCCCACAGGATTTGGAGACATGG
GGTCTGGCTTTGCCATTAAATAAACGTCAGCAAGTGACTTTATGTCTCTGAACCTTAGTT
TCTCTGATTCAGTAATATTTTTCATTCATCTGCAAAGTAGGATAATAACATCTTTATTTG
CATAAGGGCCTTACAGATTTCATATACTTTAAATCTTGTAATCCTGACCACATAGTGGAA
GGTTTTATTGCCTCCTTAGATGAGGAAGCTGAGCTCTAGAGAGATTAAGAGATTGACTGA
AGTTCCCCTAGCTAGTAAGTGACACAGACAGGATGGCAAATAGCGGGAAAGGAGAATACA
TAGGGACCTTTGTGACTCAGACATGCCAGGATAAGAAATAGGTTTCATTTGTTGGGCTAA
CTCCATTTGATTGAAAATGACTCTCTGTATCACCATATTGAGGATGATTCTGAGGCTCAG
TCAGATAAAAAGCACTGTGATGAATTAGTGTTATCTGCTAAGGGGTGGTGGGGTGATGAG
TGATGGCTCACATGCTGTATAGTTGACATTCCTAGCCCAGAATCACCCAGAGATTCTAAT
TCCTCCCTCTTTACTAACCAATTAGGTTAAATTTAAAGGTAACAGCTTACAAAGGTGACT
AAAATACAGTCTGTGCCTTCAAAGAGCTCACAATCTCTAGAGGAGAACAAAGGATGATGT
GGCAAATGTCCCGGGAACATAGAGGGAGAGTAACTATTTCTACCTGGGAGGTGGGGAAGG
CTCCACAGTGGAGAGAGCACTGGGGAAGGGCCTTGAAGGAGGAAGGGGATTTGAAAGGGA
AGACAGCAGTCTGGAGGGGAGTCTTGGAGCAGGCAGAGGATGTTCTAGGTAGAGCGAGCT
GCCCGAGCAAAGACAGGGAGACAGACAAGTGGAGCACAGGCTATGTTTCACGTGGCTAGA
ATATGGGCTGCACAGGGAAAATATTCCAGGGGAGGCTGTGAACAGTAAGGTGGAGTCAGA
CATTGAAGGATTTTGCCAAGAAGTTTGAATTTTATCACGAAAGCTGTGGGAACTTTTTGA
AGATTTTAAAGCCAAGTGATGGGGTCAGAATGTGTGCACTGAGGCAGCCGAGGACCGAGA
TGAGCACAGTGAGCCTGGGTGCAAGAGAACCAGGAGACCATTGCAACACTTCAAGTGAAT
GAACTAGGGCAGCCTCCATGGACATGAAGAGGAGTCATGAAGGCAGAAATGATGGACCTA
GTTACCAATCAGATGAGGGGGAAGAGAGAAAGCAGGGGTAATTCTAAGGCTTGGGCACCT
AGTGGAGGGTAATTCTGTGAACAAGAAGGAAAACACAAAAGAGACTCTTCTGAGGAGACA
GGACGCTGAGTCTGAACATGTTAAAATTGGAATGCTCCAGGTAGCGGGAGCCTGTAAGTA
CTTGGACACCCAGGGCAGAGGTGACGTGGAATCCACGGAACGGGGGAAACAGTTGAGGAA
GATGGAGTACAGTGATCAAGGATGAGAGTCAAGAGTGGATGGATTCCTGAGAAACACCAA
CAGTTAAGGTGCAGAGGAGAGATTACAGCAAGAGAGATGATCCAAAGTAAACACAGAGGT
AGAGAAAGAACCCCGAGAACATGGTGTCCGAGAGTAACAGTGAGACTGTGCACACATGTA
GTGTTCACAACCCATGCAGTGTTCTCACACATATGATCACATGGAACTCTCCCGTCACCT
CTGTATTATTATGCCCCTTTTGCAGATAAGGGAAATAGAAACTCATGCATTTAAGTGATT
TGCCCCAAATCACAAAACCTAGAAATGGCAGAGCTACTTAATGGCTAATCAAGGTAGATA
AAATCAGTGGATTCCCACCACACCTCAATAAAAGCCAAAAGAGAGTGTTAAGAACAGACC
GGTCAGTCATCAGTCTCAAGTGTAGCAGAGACTGCTGGGGTCAAGGGCTGAGAAGACACC
CTTGGATTTAATGATGGAAGGTCAGCTGTGACACTGGAGAGAGCTTCCTGCTTCCTGTTG
CTTTAACTGCCCCCTGCCCCCCCTAGACTGGCTGTGTGGGGCAAATGGAGTAATTCTGAA
TTTATACAAGTGTTTTGTAGACTTCAAAACCCCATATTACAGAGGTGATTGTTACTGTTA
TTTTTACTGTTATTAGGTATTGTTAGATTGAACCCTTTGATATTGCCAATAGGGAACCCA
TGTATTAAATGGATGATTTCATAGAATTCAACCTAATAGTAAAAGGAGTGAGCTGGAGTC
GGGGAAGGGGCTGTGAGGTTATGAGACAGGCAACTGCGCAGGCAAGGGTGGCCCCAGGGG
ACTGGGGAGCCCCACCCCCTGATGGTTGGGGAGGTCAGTCTTCCGCATGGGGTGGAGAGT
GGTAAATCGCTGGTGAAGCTTGAAATTTGCAGGAGTTCCCTTTCACCTTCACCACTTCCA
CACTCCCCATCTGCAACCTGGTCAGCCCCCTCTGCAGAGACTAGGGGTGGGGGTACACTC
TCGTGAGGGGCTCTGACTGAAAAAATACTTCTGGTACCTAAACTAGGTTGATCCCCTCAA
CCAGCAGTCTTTGGAGATAAGTTGGGGATGGATTCTTCCTATGGGGAATCTCGGGGCCTA
GGCCAGGTGATGACTGATTGGAGATCCAGGCAGAGCTGACACAGGAAGGAGGGTCCTGAA
CAGACTTCTCGTTTATCACCTTGACTCTCCCTAACCTAGCTCGGATCCTCTTGAGATTTT
CCCTAGTGTCCTTCGGAACCTTTTCAGCATCGCATGTCTTAGCGGTAACAACAGGAATAA
CAATAGCAACAAGAGTTATTTCTATAGATGCCATTGCTTCCAGCTGACTCTTAGCACTGA
TACTAATTCTTCTGGCTGTTCAGTTAAGATGAGGAGGGATGGGTTAACATCTCCCAGTAG
ATGTTCTTCTGAGGTGAGGACCCAGATGGGGCCAGGCTGGGAGGCTACTGGGATTGCTGG
AGCTGGGGCTGAGGAGACAGTGGTATAGCCTCTGTCCTCAGTTGAACCCTGCCTAGTGCC
AAGCTCCTCACAAAGGACCAGCTCCTGTTGAGCCTTGCTGGCCCAGACAATGATTAGCAG
CAGATACCGGGATGGGGTGATGACTCAGGAGGGCGTGCAATAGGGGTAGTGTGAAAGGTT
GAGAGGGCAGGTGCATCAAAGAGGCAGCACCCACTTGTCACAGGAACCAGGAAGTCCTCC
TCCCTCTCCAGCCGGCGAAACAGGGGGTCCCCAAGATGCCATCCTGTGGGCAGGTCTCTA
CAGAACATTGTTTCTTTCTTGCAGGGGACAGAAGGCACCGCTTGGGGATTGAGGTGGAGG
AAGGGGCAGTGGTCCTAGTCAGCTCACATTGACAGGCAGGGGTGGTGTCTGGCCAGAGAA
TATCTGATGTGGCCCCATCTTTTGTCCCTCCCTCTCTTGACTGGAAAACACACAGGCAGG
TCAGAAGGGCCATGCAGAGGTTACAGACTCCCAGGAAATGCTTTGAAGGCTTTTATCCTT
TCTTTTGATCAGACTATGAGAACTTTCCAAACGTTGACACAAGAGAAGAAAAGCCTATTC
TTCCATGGGCCAGGGCCTCGATGTCAGGCTGGGGCTAGAGGATGGGAGGGAAAGGGGGAA
GGAGACCAGGGAGTGGGAGACAGAGGCAACAGTGATTCAGCTGGAGAGTCAGGCCCCAGG
ACACACACACACACACACACACACACTGCCCTCTTTTTCCCCACCTCAGGATTTGTGTGC
ATCTGGCTCCATTTCTATTTGTTTATTTTCCTTGGGGCAAGACAGGAGGCGGATTAATGA
ATAAAGACATCAAGTTTGAAAAGAACCCCAAATCCAGCTCCATTCTTCTTCCAACCTTGA
GGGCTTACATAACCATGCAGTGCTTTTCTTCCTGCCCTTCCTCTCTTACCCCTCTCCTTC
ATTTTCTCTTCCCCAACCCTCATTAAGAACACTTGGAAGCCCAGAAGTGCTTCTTTTTCA
TCCCAATGCAACTGATCTCCTTCTGGAGGACTCTAAGGTCGCTATTCAAGTTGGAACTGG
TATCCAAAAACAGATAATATGGTTGGTGAGATGAGGCTGAGTAGCTGTTTGCTCTCTCCA
CCGAGGCCGGGGGGAGGAGTGGGACCAGACTGCTGTGGAGGCAACTTGGGCTAGACATAG
AGATTTACAGCAGGAAGTGACCCTAATCATCCTCTAACGTAGCACCTCCCAGACTGACCT
CGCAATGTGTCCTGAAAGGCAGAGGAGAGGGAATTTGTGCCCTAGAATCTACAGGGATGA
GCTGTAAGCGGCCACACACTGGACATCCTTGAAATCTCTTTTTGTCTCAAGCCATTCAAA
ATGTTTATTCTACTTCATTGTACATTGTTGGCATAATATTAAAACAACATTTTCCCTCAA
AATCTGAGCAAAATTGATAACTTCAGGAAATATACTAAATTTAGTCCTGTGGCTTTGAGT
GCCTCCTGACATACTAGTGTATGCCCTAGTTTGAGAAGTGTGAAACTAATACCAACCCCT
ATTCCACAATGAAGGAAATACAGATCCGAGAGGCTGAGAGGCTTGACTGAGGTCACAGCT
AGTCAGTGGCAGAGTTGAGATCGGCACCCAAGTCTCTTACTTCCCAGTCCAGTGCATGTT
CCACCAAGCAGTGCTGTCTCTTAGTTCTGAGTGGCTTTTACACATCCTTGAGCCTAATTC
TCTCACTCTATCTTCAGAATACTGGGCATGGACAGATACCTAGCTCAACTGTCTAAGATA
AGTGTGGGTGTGGAGACCAGCCTAATCTCAGGTGCTGAGACATAGTGCTCAAAACCCCTC
TACTGCATACAGGGCTCTCCCAACATGGAAGAGGAAGGAGAAGGATAGGACAGGAAGGGA
AGGAAGAAAAGTACTGCAAGGATTATGTAAGCCCTCAAGGTTGGAAGAAGAACAGAGCTG
GATCTGGGGTTCTTGAGCATGATGGACAGATAGTAGGACAGAGAGCAAGCTGAGTCCCTA
TTTCTATCCACCTATTCATTTGTCTTTACCAAACAGTGATTGGTTCAGAAAGACCTTCAA
ACCTAAGATAATTGGATTAGTTAATAGCTATAGTAGGCACTGTTCTTATTTTCCAGGAAT
CTGCCTCCCTTTCTGATCTCATTTCCAGATCCCTCAATCAAAAGGCTCTTTTCTACAGGG
AAGAAGTAGGGAGAAGAATAGGAGGCTTTTGGGCTTAGAATATCTCTATTAATATGGACA
CATAGGCTGTGTGATACAGAAGAAGAATAGAAGGATAAAGTGTGGTAAAGAATTTGAAGG
CGAGAGTTATGATTAGATGGATAGCATACTATTACCAGGATGAGATACAGGAAGCTGGAG
AAACCATAAGGAAAAGAAGGGACAGCCAGAGAGATGTGTAGGCAATACAAAGGCAAAGAG
GGAGGTGAGAAGGAGGAACGGGTCGGGGAGACATTTTAGTGACAGCCAGGATGAAAAGAG
AGGACAAGCAGAGAAGCACCATTGATAGAGATGAGAAGACCGTTGGGAGGAGAGTCCACA
TGAAGGAAGTGGGGAGAATAAAGACAAATCATGCAAAACTAGGAGAAACAATGGGATCAA
GCAGCCATGAAGGAAGGGCGTCGCCTCCAACCCTTGGATACATCCTGGGCATCACTGCTG
GTGAATTTTGCATACCTGTCTGGCTCCTGCTAACCTCCACTATGCTTAAGGTGTCATCTC
TGCTTGTTGAGTGTTGAGTTTGCTCAGTGAAGACAAATAAACTATAGTATTAATTTGAAG
TAATGGTGGAAAGGACTTTGGAATCCAGCCAGGAAGAGGCATAAATTTCAGCTCTGCTAC
CAATAAATTGTGTCACCTGGGCTCTCTGAACCTCAATTTCCTCAGCAGTAATTATGAAGA
TAATAAGATTTGTTTTACAGAGTTAAAAAGATGAAATATGAAGTGCTGGTCTACAGTAGG
CATTCAATACATGATAGTTCCCCTCCATCTCTCCTTCCATGTCCCTGAACCAAACATTTG
CAAGAGGAAATACTCCACAGTCAAAAAACAGAAATCATCTAGTGGCTCTAAGAAAGAATG
ACCAGCAGGCTAGGCCAGACACCGTAGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCT
GAGGCAGGTGGATCATGATGTAAAGAAATCGAGACCATCCTGGCCAACATGGTGGCCAGC
TGGCCAGCTGGTTATGGTGGCTCATGCCTGTAATTCCAGCTACTCGGGAGGCTGAGGCAG
AAGAATCGCTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCTGAGATTGCATCACTGCACT
CCAGCCTGGAGACAGAGTGAGACTCCACAAAAAAAGAAAAGAAGAGAAAAGAAAAGACCA
GACCAGCAGGCTGGAGCACCATGGAGGAAGCCAAGGCTCTGTACCTGACCCTTGCAGGAG
CTGCAGGGCCTGACCCTGGCCCTGCAGCTGGCCATGAAGGAATCCACAGGGGCTGGCCAC
AAAGCAGGAGGGTGTTGAGGGGTCACAGCACATCACTGTTTTCCCAGTGTGTCCTATTAA
GATCTTTCATGTGCTCCCAACGCTTCAACCAAAATGAATGGATCCTTATTTCCTTATTTC
CTGGGTGGCCCTGGATTTCCTCATCTTTCCCAACCCTGTTCCCTTGCACTAGATGTCAGT
TTTCCCTTCACAAGCTCTTCTTGTACTTCACTGATGCCTTTTCCATGGCACTTATCACTT
CCTGCCTGTTTTACAGTTTTCTCCTTTATTAGATTGCAAGGTCTTCACGGAAAGAATCTA
CATCTGATCCATCTCCATAATTCCATTGTCTTGTTTAGAATTTGGCACCCAGTAGTTGCT
GGAAAAAAAAATGTTTACTGAGGCTGGGCATGATGACTCATGCTTGTAATCTCTGCATTT
AGGGAGGCTGAGGTGGGAGGATGGCTTGAGCCCAGGAGTTTGAGACAAGCCTGGGCAACA
TAGTGGGATCCCATCTCTACAAAAAAAAAAAAATTAGCTGGGTGTGGTGGTGTGCACCTG
TAGTCCCAGGTACTCAGGAGGATGAGGTAGTAGAATCACTTGAGCCCAGGAGGTCGAGGC
TGCAGTGAGCCATGATCACACCACTGCACTCCAGCCTGGGTGACAGAGTGAGACCCAGTT
TCAATAACAATAACAAAGTGTTTATTGTATAAATGAACAAAAACACAGCTCATACTGAAT
GTGGTGGGCAACATTAATACAGATGAAAACATTTGGTTTGTTTGCATACCTATTAGTGTT
GATAATTAGTTATCTCGGGTTTCCATGTGTACAAGGAAAAAAGAAAACATCATTAAAAAA
TCAAGAGAAGATACAGACAAGAAGGGGGAATGAGAAGGCCCCAGAGTGAGAAGTGCTGGA
CCAGAGTGAAGTTCCATCCATTCTACCTAGGACAAGAACTTCCACATCTCCCTGGCCCTA
TGATGATGGAGTCAGTTAGATTGGCCCCTATGGCTGGAGTGGGTTAGGAGTCCCCTCCTA
CTTTTAATTCAATCATAAAATACTTCTTGAGCACTTACTATGTGTCATACATTGTGCTAA
TCTTTAGGATAACATATATATATATATATATATATATATATATATATATATATATATAAA
TAAATAAAATGCTGGATCCTTCTTTCAATGACCTTATTTGTAGTAGAATACAAATGATAC
ACCATGTACTAAGAGCGGTGCCATTACGGGTATAGTTGGATATAGATATACATATATGGA
AACTCAGAAAAGAGAGGCATTACTTAAGGTTGTAGGAATCAGAGAAGGCTTCATGGAAGA
GGGGTTATTTGAACTGGACTCTGAAAGATAAGACTTGGATAGGTAAAGACAAGGAGGAAG
GGGAGCCCAGGAAGAGAGAAGTGCAGGATCATGGAAGGCAGAAAAGCATGGGAGTGCACA
GCAGGGAGCAGGGAGTGGTTGGTTTGCTTGCAATATGCAGTGTGCCATAGCAGAAAAGTG
GTCGGAGATAAGGCTAGAAAGCAGGTTCAGAAGCAGACTGCGGAAGGCCTTATATGCCAG
CCTGGGTTTGGCCTGTCTTTGATAGATAATGGGGAGACATTAAAATGTTTTGAGCTAGAG
AAAGAACTAAGACAATTATAGTAAAATGAAAAGTGGATGGATTTGGGAGACGGGACCTGG
GCATGAATCTAATTCCACAGTTTACTGAGTCACACCATCTCTCTGAGCCTCAGTTTCCTC
ATTCGTAAAACAAGGATTATAATCTTAATATTTCATAGGAATGCCATGAGAATAAAATGT
GAAAGTGCTTTCTAAAGTACTGGATAAATGTTCATTGATTCCTGATCAGAGGTGTATTTG
AGGAAGAGAAACCCAGGAGCAATGTAGGATGGATTTGAGGAGAGAAAGAACAGAGACATG
AGATGAGTAGGAGGCTGATGCAGTGATTCAGCCACAAGGCATTAGGACCTGAAAAAAGAC
AATGGAATGAAGGAGAGGAGGCACAAATAATAAATCCACAGCACATGGCTTTAGATAAAT
GTTGAGTTGAGGCAAGAAGAGAGTTTGAGATGATCCTGGCTTTGAGTGTGGGTAATGGGT
AGGATGATGGTCCCTTTAACTATTTTAGGAACCAAAATAGAGCAGCAAGTAGGAGAAGAA
AGGATTTTACAATTGGAAGTGAATGCATTTAGTATTCATATCCCAAAGCTCCTTTCAGTC
AACTTGCTCTTGCAACAGAGAAAACAGACAAAGCACTTTCCCTGTGGGTGCAGCTTTTCC
CCTCCCCCTGCACCTGCTGCCCCTGGGAGGGGGTTGAAGCATCTTCTCTAGTCACCTAAT
TTAGCATAATCAACTCCAATGCTCTGTAGCAATTTACAAAGGTCATTCTCTCCCCAGCCC
CCTGCAAATGGACAGTTGGCCCAGAAGAGAGCAGGGACTGATATCTTGGGCTTTTATTTT
CTTACCTTCTGAAAACAGGGTGTAGGCATCTGCAGCACTAGCAAAGCCTGTGTAAACCTG
GGTCCCCTCGCACTCTGAAGTGGCTCCTCCTGAAGGTCTGTGTGAACTAGGTGTCTCCTG
TGAGGCAGATAAAAACTGCAGCCCTCAGGGGGGCCTTGGCCCGTCCAGATCAGGCTTTCA
GTCATTCCCTTACTCTTTCTTAACAAACTATACTAGGCACTGGGGAAACAGATGAAAGGC
AGAGTCAGTGGTCTTAAATTAGGAGCACAAAGATGGTAAACAATGATAAACAAACCATCT
CAAAGCACTATAATGCTTCAAAATAGGAATATGTACAAGAGGGCCAGGTGCAGTGGCTCA
CACCTGTAATCCCAGCACTTTGGGAGGCCCAGGTGGGCAGATCACTTAAGTCCGGGAGTT
TGAGACCAGCCTGGGCAACAGGGTGAAACCCCGTCTCTACTAAAAGTACAAAAATTAGCT
GGGCATGGTGGCACATGCCTATAGTGCCAGCTACTTAGGAGGATGAGGTGGGAGGACTGC
TTGAGTCCAGGAGGCAGAGGTTGTAGCGAGCTGAGATTGCACCACTGCACTCCTGCACTT
CAGCCTGGGTAACAGAGTGAGATCCCATCTGGCGGGGGGTGAGGTGGGGGAAAGAGAATA
TGTACAAGAGCAAGCATAGTAAAGTAAACCCATTCTGGGCAGGGATGGGAGGGACAGAGA
AGATGAATTGTTTTTTTGAGAGTCAGGGAAGGCGTCAAAGGGAGTAACTAACAGTTGAGT
CGAGTTCTGAAAGATAAGGAGATCATCAGGTAGGCACGGAGCAGGGCAGTGCAGAAGCAG
GTCCAAAGGTAGAAAGGATTGGGTAGTGAGGCTCTGCGTTGGAGTTCAGGGGGCCTGTGA
AAGATTGTCAAGGGTAAAGTCAGAAGTAGGCAGAGACCAAATCATGAATGGTGTGCTGAG
AGGCTACAGAGAAAACAGATAAAGCACTTTCCCTGCTGGTGCAGCTTTTCTCTTTCCCCT
GTACCTGCTGTCCCTGGGAGGAGGTTGAAGCACTCTTTCTAGTCAGAAGTGTATTTGAGG
AAGAGAAACCCAGGAGCGAAGTAGCAAAAAGCAAAGGGGAGCCACAGATCAAGTTATTGA
GAGTCACAAGAACAACAGTGTCCTTACTCAAGAAAGGCCCTGATAAATCCATGTATTATC
CTGGAGAATAAATGACTCTCAAGTAGAACAAATGACTCTCAAGTAAAATAAATGAGTGCA
CAGGCAAAAAAAGACAGCTTCAGGAAGAACTTCCGGGGGTAGCAGTAAGTGGGAGTGGTA
CTTGCTGAGGGAACGTGCTGATCATCACTGTAGCTATGACTGGCTTTGTTTTAGGGAAAG
GATCACTAGTTCAGTCTTAGAGGAGAAAGAAGGTGAATATCTCTGTTTCTGTCTCTTTCG
CCACTCAGGCTGGTCTTCAGAATTCTGTCTCTGGTATTTGGCCGGCTGGGACTGTTTTGG
GGAAATAGCACCCTCTAGAGGAAAGAGTATGTTTTATTTTGCGGGGGTGCCCCGGGGTGG
TGGGGTGCGCAACAGATGATTTCCAGAGCTTTGGCTCGATTCCTTCCCCAGGGGCCTGGC
CAGCTTTGGGGTGGAGTGTAGCTGATTGTTTATCCGCTTCTGACTCTGGCCACCGCAGAG
AACAAAGCTGCCTGGCTGTGGGAGGTGGCACAACAGCTGGGAGCAGCAGATAACAGCTGG
AGGTGGCAGATACAAAGGCTGGCAACCACAGGCACTACAGCTGGAGGTGGCAATCACAAC
AGCCAGAGGCAACAAAGAGGCTAGCAGTGGCCGAAATCTCCAGTACCCTTGAGTCTAGAG
CCTTAACCCTGGGATGTGTGGTCTTACATACAGCGTACCATAGTGGCACCTGCTGAGAGC
ATGAGGTCCAAGAGAATGAACCTGGGGCACACAAAAGCAGTTGCTACAATTAAAAAGTTC
TGGACCAGGAGCTGGGAGACCTGGATTCTGGTTCCAACTTTACCACTAATCTACTTGGGG
CAAAGCTCTCTGAGCCTTAGCTTCTATGGTGTCTTTCTTACCTACCTCATGGTGTGAGGA
TCAAACTATATATTTTATAAATTTTAAAGTGAGAAGGAATTATAGACTAATATTTTGGGA
ATGATAAGCAAGGCTTTTCTTGGGCCCTAAGAGCTTCCATTCTCCAAGATATGTAGAATC
TCCCCTCAACATAAACAAAGCTAGGACTTCAGTAAAGGATCCCTGAATGTCACCATAGAA
AGTGCAGGGGTAGAAGTGGGGTGGAGAAGGCAGACATCCTCACCCACCATGGGTATAGAC
AGAATCTTCAAGACAGTCTTTCAATCTCCCATCCAAAGCTTTTATCTCCGCCATAGGATC
TCTGCAAAGTGCTTGTCCAAAGTGCCTTCCTGATTGTTACAATGCTCTTTATAATATCAA
CTTGCAATCTTTATCCCTGCAGTATGAACTCCCTGATTGTTCCTCTTGGAGCTCAAAGGA
CAAGTCCAAGCCTTTGATCACGTGATAGTCCTTCAAACCAAATATTTGCACACATTCATT
ATATCTTTCTGATTGTCTCTTCTCCTGAATCAACTTCCCTATTTCCTTCAATCATTTCTC
ATGTGGTCTGGTTCTGAATCCTCTCATATCCTGAGTGTTCCTTGATGCTGGATACTGCAG
GTGTGGGATGAACAGAGCAGAGTAGAATCAACTACTTTTTTGTTCTAGGGACTTCAGTTC
AACTGAAGGAGCTTAAGATTAGTTTGCTTTTTTGGCAATCAAAACACATGAATAACTCAT
ATTGGATTATTTTCTGCTAATATGTTTAATTTTTTTATATTGTACTGCTTTGCTAAATCA
CATCTTCTCAATCCAGAACTTGCTCAGGTAATTTTTGGACCCAAGTACATAATCCAGCAC
TTAACATTTTTGTTAGACTTGGCCTACTTATTTGACTCCTTTTGGATCCTAATTCTGCCC
CAGCTCTTGCATTTGCTATCTGTCCCAGCTTTCTGTCAGGCACACAATTGATGGCCATAG
CATTCTATAGTTTTGAATGAAGTTCATGTTAAGAAAATTGAATAGGGCAAGGCCAAAGAT
GAAGCTCTCTGGTGTATCAATAGAAAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNGGTTTTTATTTATTTTATTTTATTATTATTTTATAAATAACACACCCCCCCG
CCCCCCCATGACCACCTCCTGCATGCACGTCGACTCTAGAGGATCCCCCACCAGGACTAC
AGTCGGACTCCAATCCTGGCTCCTCCCCGGGCCCCGGCCCCGCCCCAGTCCCAAGCCGCA
CCCCTTCCCNGTCCCCGCAGGGCTAACGTCAGCCTCCAATCCTGGCTCCGCCCTGGACCC
CGGCCTCGCCCCGCCCCTGGCCCTGGCTCCGCCCGAGGCCCCCGCAGGAGTGAGCTAACT
GCACCTCTGCGCATCGAAATTCCCACCCACCCTCGCACAGAGCGCATTCCACCCCGCACC
TGCCAGCCTTTCCTGGAGAGTTGGGTGCAGGGTCCCTGGGATTGGCGAGGTGACTGTGAC
CACGCATTTAGAATTCAGTTATTTGCTCTGAGCCATAGTCCTCGCTGCAAACCCTGCTGA
AGTAGGGGTTGGCGGAAGCCAGGAGTTCCTGAATGCGAAGGGTTTGAGCTGAAGGGCGCT
TCCAGGATCCAGAAGGTCACTGGAGACCTGTTTTTCACCCCCTCAGAGGGCAAAACCAAA
AGAAAAATGGATTAGGAGAGGGGGCCGTCCATGTGACGTCATTTCTGGGTTGGGTGATCC
TAGCCCAGTTGTTTAACCTCCTTCAACTTCAGTTTTCTCCTCTGCAAATTGAATTGAGGT
TGATCACATCACCCAAAGGGTTATTGTGATGATAGGTAATGTACATAAAGTGTTTGGCAC
AGGAAACTAACACAAAATGGGAGATAAGGATTATTTTGTTTTAGGTTTTGAATTATTATT
TGAACTGCTTCCTAAGAGGCTTAGTTTAGACCTGGCATTTAGGTGAAGGAGTCTCTATGT
TCAGTGACAGTGGGAAGAGATGAACATTGCTCTGTTCTAGGAAGAGTGGGGCTTGCCCTG
GAGGTGGGAGAATGGAGGAGGCACCCTTCCCAGGTGCTCTGTCTCTTCCTGAACTGTAAA
GATGGGAAGTGGGCAGGGGCAGGAAGGATGAGACCAGAATGGGGAGAAGAGATGGCCAGG
TTTGCAAAGCCAAGGCTGTCAGAGTGGCTGTCAGTGGGAGGTGACCCCAGAGCCCATTTA
CCACCCTCTACCCTCCAACATCCTCCCTCTCCCCTCTCATCCCCCTTCCCTCCCACTCAC
TCACCCCCCTTTACAGAAGAGGAAACTGAGGCCCAGAGAGGGTAAGTGGCACAGGCCAGA
CCAGACCTTCCTTGACATGGTATTCCTCAAGCGTGGCACAGTGCCTGACTCTGAGAAGAT
GCTCACGGGGTTGCCAGTAGAAGCCACATTGAGGAACCCTGGAGAAACCAGAGAAACTGA
GGCCTTGAAGGGAGATCAGAGGTCCAGCCCTCACTTCCCAGGACTGCCAGCACTGGCCCA
TGAACAGGGCAATAAGGTGCCTGTTTATTCCCACTTTGAAATATCCAGAAGGTTGCTCCA
GAACCTCATCATCTAAATCCATCCACAGGCATATCGAGCTATGTGAAAACTGAAACTCAT
AGGGGAAGCTTTTGGAAGAATACGTCTCTCCCTTTATAATGGATTTAATTATCGAGTGGA
TTTAATGCCTTCATGATGCTTGAGGGATGAAAGATGTTACCAATTGTAATAATGATAGAT
GTCATTTATGAAATGCTTACACAAGAAGGCCCTTTTGGATATTAGTCCTAGTCCTTATAG
CATATTTTGCAAGGTGGTGTCATTTAACAGAAGAGAAACTTGAGGTTAGGCAGGTTAAGT
ACCTTGCCCAAGGCCACACAGTTTTTAAGTGGCTTAGGGGTGACTTCAGCCCAGGCTTGT
CTGTCTGTCCCCAAAGCCCCAAATCTTCCTACACCTCACTGTCCCTCCTCCCAAGCCTCT
CCACCCTGTAAACTCAGTCATTCAACAAATATTGATTGGGCCAGGCCTTGTACTGGGCAC
TGGAGATGCCATGGTAAACAAGGTGGGCCTGCTCCCCTGCCCTCAGGGAACATAGTTCTA
TATGTTAGGGATACATTTCATAAACAAGTCATAACCAACCCCCAGTATGAGTATGATGAG
AGGGGTCTTCAGGGAGGTGAGGTATCCTCTCTTACCCTGTGGCCTGGGGCTGGGAAGGAG
CTGGGGGCAGGTTGGCGTTGAGAACTGGGTTGGTGTCTCCCTCCAGAGGGGATAAGGCCC
AAGGAGAGAACAGTGTCTTCAGCAGGCCCCTCTGGAACCCAGGCCCCTCTGGAACCCAGA
CTGCGGGTTCCAGAGGCGGCCAGCAGAGGGAGCCCACAGCCCAGGCCTGACGGACCCCTC
AGCTGCTTATGTAACTGGGAAAGCTGGGGGAGGAGAACAAACCCCAGGCACGAGGCACGT
CACACACACAGACACATGTCCCCACTGTAATGGAGCGGGGATCAGACAGAAAGACGGCTC
CCAGAAACACACCCCCACAGAGCCATGGGCAAACACACACAAGCTGCAAAACAGCGATGC
ATGGTGTAGATTGGAGGGCACTCATCTCATCCATTAAAAACACACACCTAGGCTGGTGCC
CGAGGGTGGGGTGAGCAGAGAAAGGAGGAAGGAAGCCCTTCAGTGAGTTTCCAGGCCAGA
CTGAGACACGAAGGAGGAGGGAGCCTGGGTTTGCAGAGAGACCTGGCAGGTATGCAGTAG
TGACCATGAGGGACCCTGATGCCCGGCTGGGCTGTGTTGTCACTGCCATCACCAGCTTCC
CACCTGCCCTCCATGTACTACCCCAGGCATGGGCCTGCATCCGACACCCGTCCTGTTTCA
CATGAAACAGGTCTCATTTCACCTCAAGATGACATATACACAAGACACCAAGGTGACACT
GAGGTGTCATGAGTATTGTTAAAGATAATTGAGACCCACGCTCTGCCCAAAAGCAGTTTA
TAATCCAGCTGAGATGTGACACACCACAGTCACAACCAAGCAGACAGCTCTCAGAGAGGA
GCACGTTCAAAGACAGGACCATTCACATATGCTGACCTGTGTCAGGCACTAAATGTGATC
TCATTTATCCTCATGTGCTATTATTATCCCTGTGAGAAAACTGAGGCATAGAAAAGTTAA
GAAACTTGTCCAAGGTTAATGCATTAGTTACTGTCCACACAGGGATTCGAAATGGATCGC
CTCACTGTGGAGCCTGTGCTTCTAACTCCTGTTATGTTGCTGCTTAAAGACAAACGTCAC
TAGGGACACAGTTAAATATGGGCTTAGCACACATGAGTATACACCAAGCTGTAGACACAG
ATACTGCCGTGGGGACAAAGTGACAAATACATCAAATACATAAGCACACATGCTCGTCAG
ACTGTCAGACATATAGAAATGGCACAAGCATACACATAGGACTCAGCTCTCTCTCTTTTA
AATGTGTATCAACCGTAGCTTTGTGGGGAGCTAAGGATCACACACAAGAATGTCCTGTGA
TTTGTGTGTGTTTATAAAGCATTGGCCCATACTGCCCTGATGAGCTATATTTTCCCACCC
TCCCAGAAGGGAAGATTCTCTCTGCTGAGTTGCTGAGAGGCTCAAGCAGAGTCAGAGACA
GAAGTAGTGCAGAAACCTACCCTCGCCCTGATAACAAACTCATTCAGAGACACACTGAAA
CAGAAGTGCACACACAAAGATAAACACAGAGACATTATGCACACCCAAACACCAAACACA
CTCACAGAACCACAAAGCCATCTCCCCCCCGACACACACACACACATTCGCTTTCCACCC
TCTCCCTCCCCTCTTTTCTCCCTGAGCCAGGCATCTGCACCTTCATGGTGAACTGTGTGT
GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTACTCTCTGAACCCTCCTCTT
TCCCTGGCTAGGCCCACACTCCTGCCCCCATTCTTGAACCCTATGCCAAGGGGAGCAGCA
CAGCTGTTCAGGAATAGCAGAGCCGCGATGCCACTGGGGCTTTGGCACGACCTGGCCCTG
ACTCCTGAGGGGGCCCTGCCAGTTCTGAACCAAGGATTCGTGCCAGCTGCCACCCACGCT
CAAATGCCACACATGGATTCCTCAGAGCTGGAATCCCCTCGGTCTCCCTTCTGACCTCCT
GACAAGTTCTTTGTTCCCCAGTCCCATCGGGTGGGTGCTGGGAGCCTGGGCTCCGCCCCA
GATGCTCACCCATCCCACTTCTCCATTCCCAGTCTGCTAAGAGGGAACTGACAGCTCAGA
TATATGTCTGGAGGGTAGCGTGGGACTGAAGCAACCCCCACTGTGTGATATTACTTCTTC
TCTACCCTGAGCAGCCTAGGGTGGGGTGGGGGTCAGCCAAGGGCAGGAGATGGCAGTGGT
TTGGTTAGACAGAGGTTTGTGGGCTGAGTGTTGTAGATGAGCCTCAGGGGGCAGGAGGTG
GGTAGCACCAGGTGACTGCCAGTCATTTACGAGTTTGTCTCCACCCAGCTCTGAGTGGGG
TGAGAAGGGAACAATTACTAATACCTACAGAGCACCTACTTCATGCTGGGCACCGTTGCA
CACACTCTGTGCACATTCATTCATTCAGCTTTCACAACAACCCCATGAGGTGAATACTAC
GAGTATCTCTATTTTACAGCTGGGAGACAGAAGCACAGAAAGCTCATATAATTTACCCGA
GGTCACACAGCTAGCAAATGGTAGCACCCAGATGCAAATGCAAGCTACCTGATGCCCAAA
CTTCAGTTTCCCAAACATTCTTCTTCCCTTCTTCCTCCTGTTTCCCTAGCCTGCCCACAT
TGATTCATACATACATGTGCATATATTCAGGCACACACATGCATATCTGGTGCCTATGCA
ACCTTCTGAAATAACTTTTTCCACTACACAGCTCCAGCTTCCAGCACATAGTGAGTGTTC
AATAAATATGTGTTGAATGGATGAATGCAGAATTGAAGGCCCAGGGAACAATGAGCGTTG
TGTGTGTGGTGGTATGGGGAAAGAGGGAGGGGAAAGGAGGGATTTCACACACACACACAC
ACACACACACAGACACACACATACACAGCCCTCTGCTGTGAATAATGTCAAAGACTCACT
TCTAACTCTGGGGTCCCAGCCCTTCACAGCTACCTGGGTGGGAAAAGAGCAATGTAACCA
GGCTTTACAGGATTCTCTGAAGTGGAAGAAGTCTCAACTCTCTCTTCCAATCAGAACAGA
GGACAGGAGATGCAGAGAGAGCTCTGGAAGAGGACTCGAGGCACACAGCCACCTGGGCCT
TCCAGCCAGGCACAGCTCATCCTGTGTTTTCACCTCTCCCTGCCCCATGCCTGCCGCGCT
GCAGGCTCTCCCCTGGCTCCCTCGGGACAGTCCCTGCTTCCTCTGCTTGTCCACCTGGAC
TCTCCAGGAACCCGGCACCCCTTGGTTATTTTGGCTGAAGAGTAGACAATTCTCCTTTTC
CCTGTTCCAACTGAAACAAGGGTGGAATTTTTCCAAAGGCTCTCTATTAGGAAAGTGAAG
GGAAAACAAAGCCAGAAATAAAGACTCTGAAAAAACAAAGAAACAGATGGAACAGTGGGG
GTGACCGAGCTGGCCATGGGAGAGAGCGGGGGCCCAGAGTTTTGATGCTAACGCGACCCA
CCCCCTTGCTCCCACTGCACCCTGTTCTCAGCTCCTTGGTAGAGTTTCCCACTCTGCATT
GTAATTACAGTGCTTGTTTATATCTGCCTCTCCATCCTGGCTGTGAGCTTCTCAAAGCCA
CTGTTAACTCTTTTTTGCCTTTCCCCAAAGCCTACAGAGTTTCCTGGCAAGGAGTAGAAG
CTCAACAGACATTTGCTGTGTGACTGAGGAAGTGAGGACATGCCGAGTGACAAGAGAAGG
AATCTGGGCCCTTCCTCTCTTGTGGTCATGTCACCTCCACAGTGGACACTGTTAGTTCCT
CTGGAGTCCATCATACACTAGTCACTTCCATCTACAGCTGATAGAAAGTTCCTCCTCTTA
TTTCAGAACCTGAACCTTCCACCCCTCAGGAAACAACCAGGCTGGCTTCCTAAGCAGCCT
AGGAAGGGCTGAGTTCTGTCCTGTAGGGCGGGAAGGACGCTGGAGATCAGATCAAGCTGA
AAAAGAAATCACAGTCTGAAGGCCAGGACATTGGAAATCAAGGGCATAAAATAATTGCTA
ACCTTCACTGGGCACTGTAATTCTCAAAATGACTCTATAAGTTAGAGCTGTTAAAAAAAA
TTGAAGTTCAGAAAAGCTAAAAAATTTGCCCAAGCCAGGCACAGTGGCTCACACCTGTAA
TCCCAGCACTTTGGGAGGCCAAGGCCGGAGGATTGCTTGAGCCTAGGTGTTCCAGACCAG
CCTGGGCAACATAGCAAGACCCTGTCACTACTAAAAATTTTTCAAAAAAACAAACAACGA
GCCAGACATGGTGGGCACCAACTATAGTCCCAGCTACTCAAGAGGCTGAGGCAGGAGGTT
TGCTTGAGCCTAGGAAGGTGAGGCTGCAGTAAGCCACAGTTGCACCACTACACTCCAGCC
TGGACAACACAGCAAGACCCTGTCTCAAAAAAAAATGTGTCCAATTAGTGGTAGACCTAG
GATTTCTTCTCCGGGCATTCTGACTCCACAGCACAAGCCTTCAGCCATGTTGCGGGCCGC
ATCTATACCATACAAATTATTGTCCTCAGAAGGAGCTGGGAGACAACAAAGATGTAGAGG
TCCAACCAGCCAGCAGGGCAGGGTGACAGGGAATCCAGCTGGTACTGAGGCCCTGAGCAC
TGGCATGAAGGATCCCAGCTCCTGAACTGGATAGCCCTGGGGAAAGGGGACTGGCCAGAA
CGAACCTGGAAATCAGGGGATGAGCCAGGTTACCAATCAGGAGCTCAGGCGTAAGAAATA
AAGCTTCTGTGTTTTCAATTAAGTAAAAAGCTTGGGGGCTGGGATTTCAGAAGCAGACAG
CACAGACCTGAATTTGCCAGCTGTGTAGCCTGAATCCCGTTACTCACTTTCTCTAGCCTC
AGTGTCATCATCTGTAAAGTGAGAATTACTAGAGTACCGATCTCATTATTTTTTAAGGAT
TGTTGTGAAGATGAAATGAAAACATGTGTGTCATGGTGCCCCATTATGATCAAAGCTAGG
GCCCACAGGCGCAGTGGGACCAGTGGCAAAGGAGAGGAGACTTCTAAATGGGTCTCTACT
GTTCACTGCTTCCTCCATCTGCTGTCTCAGTTTACCCAGTCTTCTTTCCCCTTCCATCTC
CCACAATCCCCTTGGGAGAGGATAACCTACGCCCTGCCTCAGCTTCCTCACCACACTCCT
CAACGCTTCACAGGTTTATTTCCAAACTCAACCTGACATGGAAATGGTTTTCCCAAAGGA
CACACCAGTGACCTCTGAGTTGACAAAAAAAAAAGTGACCAGCTTTCCTTTCCCCCTGGC
ATCTGAAATCTGAAACTGTTAGTTTTTTGCCCCTTAAAACTTGTTCCTCTCTCAGCTTCC
TGGCCCCTCTACTCGGCCTAATTCTCCATCTCTCTGGCTTCCCTACCTTGCCATCTTCCA
GATCCTCTTCCTCTACCATAGGTGTTACTACCCAGGATCCTCAGACCTCTGTCCTCTAGC
TCCCCTGCCTGGGCCATCTCCTCTGCTCTCCTGGCTCAGTGTTCCCCTCCATGCAGGGGA
TTCCCATGGCCCATGCCCTCTCCCAAGCTCCAGTCCCCATTTCTATCACCCCCCACGTGC
CTTCATCTGAAGCCCTGCCTGGAGCACCTCAACCTTCATATGCCCCCATGCAAACTTGCG
GCTTATTTCCCAATCTCCTTTCTCCCCTACCCTTATTTTAGTTAACTTTGCACCAACGTC
CTCACCACCCCCACCATCTCCAACGGCTTCCTTCCTTACTCTGATGTCCAATCAGCTGCC
AAATACTGAAATTCTACCTCCCAAACATCTTTTTCATCCATCCCTGTCTCCTCTCTGTCT
TGCTCCAGACCTTCACCACCTATAGCCCCCATCAGTCTCTCCCTTCCAGCCCAACATCCC
GTCCACGTACAGGCACACACCCTGCCATCAAATGAGCCTTCCTAGAACGCAATTTCAATG
AGATTACTCCCCTGCTGAAAAACTTTAAGTGGCTCCATATTGTTTATAGCGATATTTCTC
AAACTTGCTTGGTGGTAGGAATACAGGTTCCCACTCTCCACGCCCACCCTCATGAATCAG
AATCTTGAAGAAATGTACCTGTTCTTTTATAGTTTTAACAAGCACCCAGGTGATTCTTAT
CATCAGAGCCTTTTTAGGAAACACTAGCAATTAGAGTGGCAATTACTCTGGCATTCAAGG
CCCTCCATGAAATGGCTCCAACATCTATTTCCAGTAGTACCGCCCATATTCCTTCCTTGT
GCAGAGTGCTTCTGCTGTCTGTGCCTGTGCTCACATTGTTCCTTCTCCTTTATCTCTCTG
AGTCAGATCCTACCTATCTGTCCAGGCCCAACTAGAATGCCACCTCTTCCATGAAGACCT
TTTTGATTCTTCCAACTGAGAACCATCTCCCCCTTCTCTGGGCTCCCACCACCCTCTAAA
TGCTATGGTGAGCAACCAGCAGCCAGCAATACCTGGCTCAACACAGATGCACAAGAGTTG
GCACTTTTTCTTCCCCTTTATCTTCTGGAGCACTCCTCACTGTCACCACTGCATCCAGAC
AGTTCTGGTCATTTACTCCTGGGGACAAGAACCCAAAGGAGAAGCTTCAGTGGGTCCTTA
CAGCATGGAAGTTAAATGTGCAGGCTCTGGAAACAAACTAACCAGGTTTGAACCGCAGCC
CCCCTACTTGGGTAAGCTGAGGATCTATGTGCCTCAGTTTTCCCATCTGTAAAATAGAGT
TGTGAGGACTAAGTTAAGTACTACATGCTGTCTTCATTAGTTCTGGAGACTGGGAAGTCC
AAGATCCAGGTGCTGGCAGATCCAGTATCTGGTGAGGGGTCCCTTCCTGGTTTGCAGATA
GCCACCTTCTTGCTGTGTACCCCACATGATGGCCAGCAGAGAGAAGAAGAAAGCTCTCTC
ATGCCTCCTCTTAAAAGAGCACTAATCCCACCCTCATGACCTAATTATCTCCCAAGTGCC
CCACCTCCTAATACCATCACATCAGAGGTTCAATCTGTAAATTCTGGGGAGACACAAACA
TGCAATCTACAATAAGTGCTCACTAACCGTTAGCTATGATGAGCTACAGATCTTAGGGAC
AATATAGTTCAGTGGTTCTCAAATCTGCCTGTTGATTCATCTGGGGAGTTAAAAAAAATA
CCGATGCGGCTGGGCGCAGTGGCTCACACCTGTAAGCCCGGCACTTTGGGAGGCCAAAGT
GCGTGGATCACGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACGTGGTGAAACCCCGTCT
TTACTAAAAATACAAAAATTAGCCAGGTGTGGTGGTGCATGCCTGTTATCCCAGCTACTC
AGGAGGCTGAGGCAGGAGAATCGCCTGAACCTGGGAGGTGGAAGTTGCAGTGAGCCGAGA
TTGTGCCATTGCACTGCAGCCTGGGCGACAGAGTGAGACTCAGTCTCGAAAAACAAAACA
AAACACTGATGCCTAAGCCCCACCTTAGATCAATTAAAAACATGGTACCTGAAGATGAGG
CCTGGGCATGGGATGTTAACATGAAGCTAAGGGTGAGAATCCTTAGCTAGTCCAACCCTC
CACCCACTACTTTATTGACGAGAGGTAAAGGACTTATTCAAGTGCGCACAGCTGGTTAAC
TGTAGAGCAAGTCCCACACTGAAAGCCTCTGCCCTCCCTCTAGCCTAATCCAGAGTGATT
TCCAATACGATTTCCAATACGCCATTGCGCAGCCTTTGCTCCCGCGTCATTGGGTTGGGA
GAATCATCTAGGCAGGAGGCAGAGCCAGGCCCACTCAACCTCACTCAGCAAAAGTAGAGG
TAAAGAAGTGGGGAAAGTTTGAGGAAATGGAAGTGGGGAGTCCCTAAGGACTATGAGCTT
GGGAGGACAAGGTCAAGAATGGATGGGGGGATTTTGTGACTAAATGGCATGAGATTCTGA
GAGAAAAGACAATGAGGGTGGGGATCTTGTTTGCCTTGATTGTAACTGTCTTTCTAGTAC
CTTGCACAGAATATAGCATAAAGTACGTGCTCAACAAATGTTTGTTGAATGTCTAAATGA
TGCAATAACATCAAAAAGCACATGTTCTGTTTATTAAGTCACCCAGAGGGCACTCACATT
CCTCAAGGGGGCAGTGGTGAGAACATCCAGAGGGGAGCACAAAAGTAAAAGAATCTTGGA
CTTTCAGAGACACTGAGGCACAGAGGAGGCCAAGCTCCCTGAAATTCCGAGGAGAGGCTG
CTATGTGGGAGGGAGGCAGTGGCCCTGTGTGCCAGATGTTTGCAGGGCATCCTGAACTCT
CTGAGCATACAGAATGCCACAGGGGACAGGCAGATAAACAGAGCTGTATCCTGGGCCAAG
TGGAGGGGGCCTGGTAAGGGAAGAGGGAGGTGGGAAGAAGGAGGCTGGGGGCCAAGCCAG
CTGCCTCTTGATAGGGGGAGCGGGGAGGCGGGGTGCTCTGGGCCAGTGGTTGGTTCAGAT
CTCTGGCCAAAGCAAACCTGCCTCAGGGGGCTGGGGGACCTCTCCCTCCCTGCCCGGATG
GAATCAAAGGCTAACAGGAACCCTGGAGGGTCCAGCTGTGACCCTTGCTCCTCACACTCA
GCAGGGCCCATTAACCCCGTCCTCCCCATATCCTCAACACACTTTTCCCAGCCCAAAGAA
TCTTTGCAAACAGACTCCCCTGGTATTTGCTGATCAGATACCAGCCAAGAGATGTCAGGT
TTTCCCAGTCTCACCACCAGCCCTGCCTTCCTCCCCCAAAGATACCCAGACCCTGTCCCA
CCTCTCACAGCGGTGCTCTGTAAGAACCCAGGGTAGCCTTTGCTCAAACCGGAGCCCTTC
CTTTTTTCCATGCCAAGAGTTAAAGGGATTCGATTCATTTCTATGAGTCATAATAATAAA
CAAAATAGGAGCACCTGCCTCCATGCTCACAAACAAGACAGGACAACCTACCCTCTTGGA
TCTCCTTCTGAACCCAGGTCTCCAACTGATGGTTCTCACACAGGTACAACCTGCAGGTAA
CTCCTGCTGTTTACCTGAGCTGAGCTGTGCGCTGAGGCAGAAATAGCCTGGAATTTGGGG
ATCATCAGAACTGGAGAGGGACCTCAGAGATTTTCTTTTTTTTTTCTTTTTTTGAGACAG
AGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCGCAACCTCAGCTCACTGCAACCTG
CACCTCCCAGGATCAAGCCATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGT
GTCTGCCACCACGCCCAGCTAATTTTGTGTGCATGTGTATTTTTAGTAGAGATGGAGTTT
CACGCATTAGCCAGGATGGTCTCAATCTCCTGACCTCGTGCCTCCCAAAGTGCTGGAATT
ACTCACAGATTTTCTCATCCCGTTCCTTGTCATTCAGATGAAGATGCCAAGGTCAGAGTA
GAGAAGCCTCTTGTCCAACATCACACAGGTGGTTAGTGGCTTCAGCAGGACTAGCCTCAG
CTGACTTGACTTTCAGGCAAGAGTCCATTGCATTGGACCACGGTGGGGACTGTGAGAGGA
CAGGAGGGAAAGCAGAGGCACAGAATAGCCCAGGCCTTCATGCTCCTGGGAAGGGTTGAC
ATGGGTTCCCTGGGCTACACCATGGGTCCTTTCCTTTTTCTCCCTTGGGACTTCCACGTG
AAGAAGGCACAGGCAGAACACAACATGGAGCTATCTGAATCCAGAGAGAAGTAAGAACGA
AAGGAGGTGGGAATGCAGCACAGGCAGAGGCTGGGGAAAATGCTTCTGGGTGCTTTTACA
TCCTATTTTCTAAATTCTATACAGTGTGGTTTTAACAATAAAGAGGATAATAAAAATACT
CTGGGGAGAGATTAAAATGACAGAACCAGCTGGGTGTGGTGGCGCATGCCAATGGATGCA
CAACTCTGGAGGCTGAGGCAGGATGACGGCTTGAGCCCAGGAGGTCGAGGCTGCAGTTGA
TCATGCCGCTGTACTCCAGCCTGGGTGACAGAGTGAGAATCTGTCCTTTTTTTTTAAGGG
AGAGAGAAGAAGAATTGTTTTTTTTTGTCTGTTTATTGTTTTTTGTTTGTTGTTGTTGTT
GTTGTTGTTGTTTTTGAGACAGGGTCTCACTTCGATTGCCCAGGCTGGAGTACAGTGGTG
CAATCTTGGCTCACTGCAGCCTCTCAACCTCCCTGGGCTCAGGTGATTCTCCCACTTCAG
CCTTATGAGTAGCTAAGACTACAGGTGCATGCCACCACGCTCAGCTAATTTTTTCGTATT
TTTATTAGAGACAGGTTTCACCATGTTGCCCAGGCTGGTCTTGAACTCATGGACTCAGGT
GATCTACCCACCTCAGCCTCCCAAAGTGCTGGGAAAACAGGCATGAGCCACCGCGCCCAG
CCAGCAGAGATTTTTAGAATCTACTTTGAGTAGACTGAAAAGAAAGACCATGTTGAAGGA
ATGGTTTAACAGATAAAGAAAAAAAATAAGATAAAAATAAAAGAAAGACCAAAAAGAAAA
CGGAGGAGCAGATGTTAAAGGAGAGATGGGGAGAAAATTCAACACCATCCTTGTAGTCCA
GTGAGGAAACTGACACAGCAGCAGGACTTGGACAGCCACTCTGGGGCTCTGAGCCCAACC
TTTTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTTTGAGACGGAG
TCTCGCTCTGTCGCCAGGCTGGAGTGCACTGGCACGATCTCGGCTCACTACAACCTCCGA
CTCCCTGGTTCAAGCGATTCTTCTGCCTCAGCCCCCCGAGTAGCTGGGATTACAGGCATG
TGCCACCACTCCCAGCTAATTTTTATATTTTTAGTAGAGACGGGGTTTCACCATGTTGGC
CAGGATGGTCTCAAACTCCTGACTTCATGATCCGCCCACCTCGGCCTCCTAAAGTGCTGG
GATTACAGGCATAAGCCACCCCACCTGGCTGATCCCAACCTTTTAACAGGTCACTATAAC
CTGAGGGAGTGGGAGGACAGAGGGCTGGAGAGGCAGGGAGAGTGAGAAGTCATCTTTCTT
GGACACTTGTCATGGCCAGTCCAGGCCTTCCCGGCTCCCCTCATCTCATCCCCCAAGGTG
GGCTCCCTTTGGAAGCAGAAAAACTCCACCCACACTCCCAGAAGACCTCAGAAGCCTGAT
AGCAGTGACAAGACCACAGGCCCTAAAGAAAAAAAGAAAGGAGAGTTAGAGGGAATGGAA
GAAGGAGAAGAAGGAGAGATGCCCAGAGGGGGGTTGGCAGCCGAGAGGAGGACCAGAGGA
GCAGGGCTGGAGAGCTGGGCCCAAATCAGGACTGGGGGAGAGAAGTGGGGTGCCGGGGCG
GGAGGAGGGACGATGGGGGTAGCTCTTCCTTCCCTCCCACTCTCCCTCCTCCTCTCTCTC
TTTCATGATCTTGAAACAACCTTCAAGTCTGGGCTGGAGGCCCCAGGAGGCCAGTCACTT
AGGAAACACCTCTGTTTCTTGGAGACCTTGAAAGACCATCTGCAGCTGAGCAGCGTCCCC
ACCCCCTCCCTGTGCGCACACGCAGCTCTCCTGGCTCTCGTGTCCTCTCTTACTTACGTC
ATCATTAGTCCGTCTCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCC
ATCTGCAGCTGAGCAGCGTCCCCACCCCCTCCCTGTGCACACACACATTCTCCCATGGAC
TCTCACGTACACCCACACCCGGCTTCACATGAGCTCCCCAATGGCCCACATGCACGCACA
CACGGACTCCACACTTGATCTTAGCCAAAAGGCCGAGAAGCGATGCGCACTCACGGACTC
ACACGCACCTCTGTACTCATGCTTGCATACAGACAACCGATTCATAGCAGATTGGCCACA
CATCCGAATGAGTGTTGTCCTCTCCCCTGAGGAGCTCCTCCTTTGGAATGTGGTTTGGTA
CCACCACTCCGTCTCATACCTCACACAGGACCCAACGCTCAGGTCCTCCCAGTCATTAAC
TAGCACACATCTGTACACAGGCACATGCACACTCCTGTCTCTCTCCAACTGTCTTGGTCT
CTCTCTCTCTCTCTCTCTCTCTCTGTCACACACACACACACACACACACACACACACACA
CACACACACTTCTTACCAACCAAATATTTGATTCAGGACCACTCCATCCCCACTTTGCCC
TTGGTGGATCCCCCTCCTGATCTGTGACTTTCTCAGCCCACTCCCCAGCCCAGGCATCTT
GGCCTTCCATCCTCCTGCTTTCAAGTCTTTCTTTCTCTCTCCTTTGCTCCTCTTACTCCA
AGGGCCTTGATCCAAACTGGTACTGCTGACTGTGTCTGAAGAAACAGTAGCCCAACCCAG
GCACTCCAGATCAAACGATCAGGTGTCTACACCTGTTAATATCCTGGAGGCTGAGGTTCA
TGGTGGACAAGAAGGAGGTAGACCACTCCAGAGCCTCAGCTCTCACTGGGCAAGGAGGGT
GGTCAGTGATGCACGGTGGAAGTATAGGCCCTGGGTGTCCTGCCCACTCTTTGATTTCTC
TGAGCCCTAAATATGTGAGCAGCAGCGCCCCTCGGGCTGTGCTCTCGCCCAAATGCAGGG
CATGGCAGGGAGCCCCAGCAGGCTGTAGGGGCAGAGGAAGGGCACATCCTTTCCGGTATT
GAGTTTGGCCACAGGGACCAGAGCCAGGGCCTTTGGAAGGACTGGGCAGTACTGGGAGGT
GCCAGCAGGGGTGAGGGGTGGGATGAAAACTGTTAGAGTGCTTGAGGTTTGCACACCTTC
AGATTCGGGGACTGACGTTTTCTCTCCTATCTCAGGTTGTGTTCTGGAGAGGGCTGGGCA
GAAGATTACCCAGGAATTCCAACCCAGGAACCTACGGAACAGGCGCTTCCTAAACCCCAA
TTTATCATGTTGTTCCCACAGCCCCCAGGCAAGCCTGCCCCAATGTTGATCTCCCTAGCT
GCCTCGGGGCCACTCTGGAGTGACTTTGCTTTAGACAGTCTCTCCTGGTGTCTAACCACA
GGCTTTCCCGCTACTCCCCTCTCACTCTCTCCTTAACACACAGGGGCTGAACTGGTATCT
GTTCCCTTCATTGTTTCCTCCCTCTGCCCATTCTCTCCCAAGACCAAATCTGAGCTCGGA
GAGGGGGGCCATGAGAAGGCCCTGTTGGCCCCATCCTACCCACCCTTTCTGACTGTAACC
CAGAGAGGGAAGGAGCGTGGAAGTGAGATGTGACCTACCAGGTCCCTGTAATGGAAAATC
TCAACTGCAGGCCCGGAGGGGGCCAGTTATTTAGGGAATTCAGATGTTAGCCTTGTGCCC
TGAGAGTGGATTTGCTAGAGGAGAGGCTGATAATCCCTCTGCAGGGAGTTCCCTCTGGGG
CCAGAGATGGACCCAGCCCAGCCAGCAGGCACCTTAGGCCTCTGGCCAAAGCCCCCCTTC
CCTCCCTCCCTTCCTCTCTGCTTTCTTTGCACTCAGGACACTTAGACCTGCCCCACTCCG
CTGGCTTCCCCTCACTCCATCTCTGTGCCCAGAGAAACAGGGGTACTCCAGGGGAATCCT
GTCCTCTGACTGTTCCCAGTAGAAGGCGGGAGCAGAATTTTTTCTTTTCTCTCTGCCCCT
TCTGGGTTCCCCTTCCTCTCTGTGCCCCTCATCCTTTGGATTACTCATCAAATGAGCAGC
AACAACACCCCTAGACCAGCTGGTCCTGTCCTGGGTCATCTCGTTGTCCCCAGTTTCTAG
CTGGTATAAGGTTAAAGATACCCTTTCCAGCCCCAGGCAAAGCCTTAGGCATTTCTGGGA
TTGCTCCTGACTCTGATGGGCATCCTCACTCCTCAGACATTTCCAATCTCCCCCACTTCA
CTGCAGAGAGGCCTGTTCTCCAGCCTCAGTCCTGCATGCTGCAGCTTTGCTTCCCCTTCC
CCACTGGAAGAAGGAAACAGTCGCTCTCCTTTCCCGTTCACATGTCTGATATTTGCTATG
ATATTGACCTTCACACACATCTTAGAGGTTCTGTATTTTCCTCTCTTTTGACTTCTCCCT
ATCACTACTCTACTCAGGCATAGATTCAGTCTAGAGCTCTTCAACAGCAATGAAACGGTA
AACGAGGGGTAAACAAAACCCAGAGATGTCATCAGGTGCCTGCTAGGAGTCCCACCCGTT
CCCCTCTAGCCCTGGCCTGCCCCTCCCTACCAGAGTCTTGATTCTCCTTCAAAACTTTGG
AGAGGTTACATCTGGCAGGGTTTGGGGACACCCTCTTGCCTCCATCTCCAAACTTCCCGC
TGCCTCCCGAGCCACCTTTGACTCCTCCTGGGCCCCCCTTCCAGGTGCCTCAAGTGCAGA
GGTCAGCCTTCGGTTCAAATTCTATTTCTGGGCTTCAGTGTCCCTGCAACCTCTATAATA
GAAGGAACAGAGTGGTCTATGTTTCTTTCTTTCTCTGGGAGATTGGATGTAGACTCGGGA
GACCTGAGTTCTGGCTCTGTCTTATCAATTCAAATTGTTTAATCTCTCTGAGCCTCAGTT
TACCCACTTGGAAAAGAAGAGTTAGGCCACATGGTCTCTGTCATCCTGGGATTCTGAGTC
AACTGCTCCCCTTCAGCCAGATCCAAGGGGGCATATCCCCCCAACCTGGGACCCAGGCCC
CCTTCCCTTGCAGCCTCTCTCAGTTGTGAGTGCCACAGGCCAGAGGGGGTTGAGAGGAGC
CAAGGGGGGGCATGCCGTGGGACAAACGGGCTGTCTAGGGCCAGTGGCTAAAGGGGCGGG
AGGGGAGGAGTCCTCAGGGATCCTGTTTCAACAAACGTTTCTTTCGGAGGAGGGGAAGGC
GGGGGAGAGGGGGAGAAGGACCTATTTAAAGCTACCCTGTTGCTTTGGCTTTCTCTGTCT
GCCAGGGTCTCCGACTGTCCCAGACGGGCTGGTGTGGGCTTGGGATCCTCCTGGTGACCT
CTCCCGCTAAGGTCCCTCAGCCACTCTGCCCCAAGATGGGCCGTGGGGTGAGTATCCCTA
AAGAGCAGGGGTCGCAGTCTAGAGGGTGAGGGAGGCTGCTGAGGAAGGATGAAGTGGGAA
TGGGATGTGGAAGGAGCCGGAAGAGAGGAGCTGAATTGGGATACTTGGAACCTTGAAACT
AACAGTCTCCAAACTACCAATGTGTGTACAGATCCCACGGCGGTCACATACCCTAGTGCT
CTCCTCTCCTCTGCACGCCCCAGCCCCCTGCCCACAGTTAGACCCACAGCCCACCACACA
TGCCCCCTCCATCTCTCCCTCCACCCCACTCCCACATCTCTAGTCCTTCCCTGCAGCAGT
CCCTCCTCTCACTGCATCTCCCGGCCTCCCAGCTGAAAGGATGTTTGGCACTGTGAGTCC
TCCTGTCTTTGCCACCTCCTGAAAATATCCATTCCTCTGGGAGTCCTAGCCTGAGAGGCT
GGGGGTCCATTTTGAGGTTAGAGAGGGGCAGTAGAGCATCCGGCTCCCAGAGTCACCAAG
TAGTTCCGGACACCAGCTCCAGGGGCCCTGAGTGCCAAGGACAGCTGGGCGGGGTGTGGG
GAGGAAGAATGATGACCCAGCCCCCACCCCAGCACCCCTCCGGATGTCCCGAGCAGCATT
GTCCGTGGGTTCCAAGCCATGGGCTTTGAGGACTTTCCCAGAGGCTGGTGACAGGTGACC
CCCCCCCCAGTCCACCCGTCCATGGCATTCTGCAGCAATGGCTACACCAAGAGGAAGATT
AACAACAATGGGGCGGGCAGGGAGAGGGCTTTGAATTCTTGGAAATGAAATTCCCATATG
GAGAAGAGTGGCCCAATCCTTTTACATGCTGTGCCTGGCTGCTTTCCTTTTGTGGAATAC
TGGCAAAAGAGGACACAGAGGGAAAGGGCATGCTGCGGAACAGGAGGGTATGAGGAAGAC
TGTGCCTAGGGGGAGCCGTGGGTGTTTCTGGGCCCAGGAGGAGTCAGGCAAGGACATGTT
ATTGCACCTAGTTGAGCAGCTGGGAAATCCTGAGCCTGGACACCAGGGTTCCTGAGCTAG
GGTTGGAGCCATAAATAGAATTGGAGTGCATGCATGTATCTGTGTGTCTGTGTCTGTGTG
TGTGTGAGTGTGTGCCCTTAACCACGTGTTCTCCATAGGCGGGAAGTCTGCCAGTTACTC
ATGGATGAGTACCTGTGTTTGTGTCTCAGCAGGCAAATTTGTAAATGTACAAGCCTTCAA
GCCTGCACAAGCATAAATGTCACTGTGTGGGGGTGCTTGAGAGTCTGTGAGCCTGCCCTT
AGGAGCTGTGAGGTATGGGCTTCACGGAGGAAGAGGTCATAGCTGCAGGAAGATATACTG
TCTTGGGACCTTCAGCTGCATCTTGACATCTCTGGCTCCCCATGGAAAGGGCATCCCTAG
CTGAGATGCAGGACCTCTGAGAAGAGGCAGGGGTTAAAGGATCAGATAAGCCCTCCATTT
CCCCCATCCAAGTGAAGAGAGAAGGAGGGGAGGTAGCCCCCTACCCTGCTCCATCTTAGA
GCAAGGTAGACCCAGCTCAGGAGGTCTTGCTTGGGAAGTGATGAGACCTTGACTTTTCCA
GTCTGTCTTTTTCCCCTAGCACCCCCAAACTCCCCTTAATCACCATCCTAAGTTGCTGTG
GGTGATGCAATAGCAAGATGAGGAGCAGATCTGGGCTGTTTAAACTAAGAGGCTGGGTGA
GGTGGGGGTATTTAGGGCCTGGAGCTTAGAGTTCAACCTACCAACGACCCCTGAAGAGGG
AAGGCATCTGACACCCACAACCTGTTCTAGGGATGATTTTTCCTCCAATCCCTTCTCCCC
TGCATCTCCACTGCAGAGGCAGGCTTCACTGTCCCCCCATTACCCAGTGGCTGTGAAGGG
CAGCGTGGGAGTTGGGGGAAGGGACGACACTGGTGGGAGGGAGCCCAGCCTGCTCCAGCT
ACCACGGAGAGGCTGAGATGGGGGGAGCGTTGGCGGATTCCCAGCTGCCCCCACTCTGTC
CCAGCCTCTGGCTTTCTCAAAAAGGACTCTCTGTTCTCCTTCAGCATTCAAGACCCAGAG
AGGGGGACTTGTGGTTGGGGGAGGGAGGAGTGGAGGGAGGTTGGGGGGGTCCTTGCTTCC
TCTCTTTCTTTCTTGCCTGGGCAGCCGCTGGCCCCAAATCTCTGCAGGCTCCTGGCTGCA
GAGCCTGAGATCTTTGCCAGGACAGGAGGAGGGGGAAGGGGCAGTGTGTCTCAAGCTCTA
AGCCTGCTGGAGAGCAGGGCGGGAGCTTGGGAAAAGGAGGCACTGCGTGGAGCTGCTTAG
CTCAGCCACAATCCAGCATGCCAAAGTGCATGGACCAGCAAGTTTTTAAAAAGCATGCAT
TTTATTCCAATTTTTATGAAATTTATTTCACATCTGAATATACAGAAATTCCTCTGCACC
CTGCTCTTCTGCCCACAGACCCAGCCCTGCTCCTCTGTGTATGCCTGGGCCCCCTTCTGT
CCCTGAAGTTCCTGAGGGTCACACTGAAGCTCAGCCAGCCTGATCTCTTGCCTCTGTTCC
CTTGATTGCATTTCTTCCTTTTCTCAGCTCTGTCCCACCACAGACAGTTAGTGAATGTAA
AGCATTTCAATCCACTCAATTAAATGAATCCTCTTAGGTCACCTGAGAAAGGCAGAGGCA
GAACCACTCACAAGCCTTTCCCCACCCCTTCCATTGGGCTGCTCGGTCTCCCCAAGAAGA
TCTGCCTTTAGGAGGCCAAAATTATACCAGATTCATAGATGCTTCAGGTGGAGACAAACC
CACGATTTTACTGGTCACCTTTTCTGAGAAGAGCACTTCTGAGCAACACAGCCTCCAAAA
GCTCATATCTTTTTAAATCATTGGTATCTTGGGAACAACAGTGTTGACTTCTCCTTGCAT
CCCCCACCCCTACCCTTGCTTCTGATTGTACTGGTCAGACTTCTACCTCTCAAGATGCTG
AATTGGCGACCTCTTATGAACAAGGCAGCTGCCATACTTCTGGGATTGCTCCTGACTCTG
ATAAGTAAAAAAGGCATTACCCTGGAGCACAAAAGTCTTAGGGCAGTGAAGCTATTCCAT
ATGATACCACAATGGCGGATACACGTCAGTATACATTTGCCCAAACCCATAGAATGTACA
CCAAGAGTGAACTCAAACTTAAACTATGGGCTTTGGACGATAAAGATGTATCAATGCAGG
TTCATGATTGCAGCAAATGTAACACTCTGATGCAGGGTGTTGATAGTGGGTGAGGCTGTG
CATGTGTGGGGGCAGGAGATATATGAGAACTTTCTCTACTTCCCACTCAATTTTGCTGTG
AACCAGAAAATTGCTCCAAAAAAAGTATATTTTTTAAAATGCAAACAAAACCCCCAAAAC
TGCATTATCCTGCAAAAAAAAAAAAAAAAAAAAAAAAAAAGCAAACACCTTGGCTGTGGA
CCCTACCCAGGTATCCACTCTTTATGGGAAACAAAAGTTAACATCATAGTGTGGGAAAAC
TAATTCCTGAAAGCCTAGTGCAGACTTTGCAGAATCCAGTGGAGAAATAGGCACCAGGTG
GAAACTGAGCAGCCCCTCTATGACAAGGACTCTATTTCCTGAGGGAAGTGGGAGGAGAGA
AGACTGGGGCAGAAGAGGAAGTAAGAAGGTACCTTTTTGGGAACTTTTCATGGCTACCCA
GGCCTTCCTCAGCCTCTATCCTATTCTATCACCCCAAGAGGGCCTCCTCTTAGAAGGAAA
GATTTCCCACCCTGTCCCCAAGAAGTTCCCTGTGAGACCCTGGAAGGCTGGTAGTGGTGA
GCCCACAGGCCCTGGAGTGGAAGGGAAATCAGGAGCCTCATAAGACTACAATTAAAATGT
CCATCTGCTCAGGCGCAGTGGCTCACACCTATAATCCCAGCATTCTGGGAGGCCAAGGTG
GGAGGATCACTTGAGCCCAGGCAATATAGTGAGACCTTATATCTAAAAAAAAAAAAAAAA
AAGAAAGAAAGAAAGAAAATTGTTTTAAATTAGCTGAGCGTGGTGGTGCATGCTTGTGGC
CCCAGCTACTTGAGAGGCTGAGGTGGGAGTATTGCTTGAGCCCTAGAAGCGGAGGGTGCA
GTGAGCTGAAATTGCACACTGCATTCCATCCTGGGTGACAGAGTGAGACCCTGTCTCAAG
AAAAAAAAAAAGGCCATCTGATTCACCAGATGACCCAGGAATGTCTAGACTTAAAAACTA
TATAAAATGTAGTTTTAGATTTACTCTCAGATACAATTTCTTATGTTTTGGGACAAATGG
GGCTCAGTTCCCATGTTACCCAATTGTGCTTTGGGGGTCCAGTCCTGTGAGTTGCCTCCC
GTCTAGTAACGGGCAGGCCTGCCCAGCAGGATGGAGAGGGCTCCCAGCACACCCCATGTC
TCCACTTCCTGGACATGCCCTGACTCTCCAGCTACTGCCTCCTCTCAGTCCATCAGGCCT
GCTCTTTCCATCCCTACCATTCCACCACCAGACCTGGCTCTCCTCTGGACACGTTCCTGC
CTAATCCCCTGGCTCCCCAAAGACTCTTGCTCCCCCAAGTTCCTGAGTATTTCTACCCCT
CTCTAAGTAAAATTGCCATGGTGTTGGGCTAAGACATTCCTACAGAGTGATTCTACTCCC
TCAACAACCCCCCACAAAACCCTGTCCACTCCCTTCCAGAATTTTCCCAAATAGTGTAGG
ATACAGGTTTTCAAAATTTTTGTTTTGTTTTGTATTTAGCAGCAGGGTCCTTTCAACAAA
CAAAATCTTAGCAGAAGCCCAAGCATTAAACCACTCAAGTGGTGCTTTTCAGTCCTGAGC
CCCTCACCCTTCTCTGAAACTCACATGGGAGCCCCTGGTTCTGCCAATAGTCTACAAACT
GAGGGCCTAGGGTCCCTCACCCTCCATCCCCCCTATCTCCCCCAAGGCAGCCGCTGCTTT
TGAACACACACCCCCACTGCCTGGGCTCCCTGGCTGAGTGGTGGGAATGGAGGCCCCAGC
CCCTCTCTTCCCTGACTCTCTGGCTCTCCCTTCCTCCCTCAGGCTGGCCGTGAGTACTCA
CCTGCCGCCACCACGGCAGAGAATGGGGGCGGCAAGAAGAAACAGAAGGAGAAGGAACTG
GATGAGCTGAAGAAGGAGGTGGCAATGGTGAGGGAACTGCTGGGCCATGGAGGAGGGGCC
CCATGCTGGGAGAGCTGTCCCTGCAGCCCATTGCACTCAGAGAAACTCCGTGTCCCCCAT
GCTGCTCAACTCACCCCTGTGCCCTGCAGTACCCTCATATGCATCTTAGATACCTCCTCC
CCAAAGTAACTCACCCTCCCTTCCCCAGGATGACCACAAGCTGTCCTTGGATGAGCTGGG
CCGCAAATACCAAGTGGACCTGTCCAAGGTGAGTGGAGGGGCTTCTAGGGAAGGAACAAA
AGAGGCAAGAAAACCATGCAGCATCAAGGTGGCAGGAGCCTTAAAACTGTAATCCAGCCT
TCTTTACAGATGAGGAAACTGAGGCCCAGAAACAAGGACTGGCCCAAGGACATGCAGCTA
GTTGGTGGCACAGCCAGAACTAGAATTTGGATCCCCTGCATCCTAGCCCAAAGCTCTCTC
CCTGTATACCCTAGAAGCCAGGACTCCCTATGACCCAGGCCCCAGAGGGCCTCCAGGCAG
GGCCCTTCCCTATACCCCAAGCAACTTCAGTTGCACACAGCCTTCCACAGAGCTGACAGC
TGATGCACATGGGCTGACAGCCCATTCCTGTGGTTACAGTGATTTGCTGGGCCCCTGCTA
CATATGTGACATTGTGATAGATGCGTTACATACATTTCTCTAATCTTTACAACAACCCTT
TGAGATAGGTATTGCAGACCTGTTTATTAAACAAAGGAGACTCAGAGAGGGAGAGTAACT
TCCCAAGGTCACATGAACAGTAACTGGTACAGTCAATTGCTAAGCCCTTCAATTAAAAAT
TTGTTTAAAAATCATTAATCAAAAAATGCTGGGTGTGGTGGCTCATGCCTATAATTTTAC
CACTTTGGGAGGCCAAGGCAGGCAGATCACTTAAGGTCAGCGGTTTGAGAGCAGCCTGGG
CAACATGGCAAAACCCCATCTCCACTAAAAATACAAAAATTAGCTTGGCACAGTGATGGG
CACCTGTAATCCCACCTACTCGAGAGGCTGAAGCAGGAGAATGGCTTGAACCCAGGAGGC
GGAGGTTTCAGTGAGCCGAGATCATACCACTGTACTCCAGACTGGGCGATAGAGTGAGAC
TCCATCTTGAAACAAGCAAACAAACAGACAAATATTTAGTGGGTGTATATCTCCTTTATG
GGCCTTCCCTGACTGCTCTTTCTAAAATTCTATGCCCCTATTCCTTTACCTTACTTTATT
TTCCTTAGTAACACTTTTCTATCTGGCACTAATATGTATTTGTTTATTGTGTGTCACCTC
TCCAGATCATAAGCTCCTCAAGGGCAGGGACTTTGTTGGTCTTGTCCATCTCTGCATCCG
CAGAGTGACAATTGTGCCTGGCACTGGATATACATTTATTAAATGAATGAATGAATGAAA
AAAAAAAAAAAAGAAACGGTCCCTGCTTTAAAGGAGCTCAAAGTCTAGTAGCAGAAAAAA
TGCAATCCTAGGATTCCAATGCAATATGGTGAGTGCAGCTCTAGAATCAAGTATAGAACA
CCATGGGGAACCAGAAAGAAGCATCTGAACCAGCCTGGGGCTGAGGGAATAGGGCCAGGC
AAGGCTTTCTGTGGAAAGTGACAGGTGATTGCCAAAGTTGTGTGACACTGACGGTCAATA
ATGTAGGACTTGAGCAGGGTGTGGAGGTGCCCACCTGTAGTCTCAGCTACTTGGGAGGCT
GAGGTGGAAGGATTGCTTTAGCCCAGGGTTCAAGGATGCAGTGAGCTATAATTGCACCAC
TGCGCTCCAGCCTGGGCAACATAGCAAGAATCCATCTCTTAAAAAAAAATCTAGGACTCT
CCTAGAATCCTTGATAAAATAATCTGAAGGAAGAGAGATGGGGAAAAAACAGTTGAGGTG
TCTTTCCAGGGAGCTTATCCAGACTGCCTCCAGGGGAGATGTTATGGCCCTAACCATAGG
TGTTGTCTCAATCCAATATAATTAGGGGTCAAGCCCAGTCAAACCCTTCTCAGCCCTCAA
GCCCTCCAAGTTGCATCACAAATGCCACCTCCTCCATGTGGTCTCTCCTGATGGTCCCCC
ACCCCTTCCAACCAGGTGGGACTTTCCTTCTGGGCATTCTTCCCATGCCCGGGAGCTGAA
GGGATGGGCATGGTGACTGGCTGGGTTGGCTCCGGATGCGTGCCCCTACGCCTCTCCTTG
CTCCCTCAGGGCCTCACCAACCAGCGGGCTCAGGACGTTCTGGCTCGAGATGGGCCCAAC
GCCCTCACACCACCTCCCACAACCCCTGAGTGGGTCAAGTTCTGCCGTCAGCTTTTCGGG
GGGTTCTCCATCCTGCTGTGGATTGGGGCTATCCTCTGCTTCCTGGCCTACGGCATCCAG
GCTGCCATGGAGGATGAACCATCCAACGACAATGTGAGCCCACACGCCCGACCCGGGAAC
AGCCCGTGACTGTCCTCCAACCCTGAACCCCCAACACAGTGGGGGGTGGGCAGGGAACAA
GGCCCTCACATAACAGTCCTACAGATGCCCCTGCATCTTAGGCTGGAAAGGGGAGAGGCT
TCTATATATATCTGTAAAGTACTCCTCCGCCAACAGTGCATACACATTCACATACTCATT
AATTAATGAAACAATCTCTCCCTGTTCCTCCCCGCTTAAGTGAGCCTGTCTGTGTGCCTG
GGTCTTCATCCCCTAGCAAAGTCCTAACCCTGGGAACTTCCTAAGACTTTCCCTCCCATT
TCTAGTCTTAACAGGCTTGAGGTTGGCAGATCAAGGGGGAGGTTAGTGAGAAGGGCTTTC
CCCTACCATCATCACTCTCAGTCACAGACAAAGGTCTGGGCTGTCATCTTGGATGGCACT
GCCTGCTCATCCCAAGTGGCAGCTGCCCCTTTAGGGTTGGGGGGAAGGTCAGGTCCCTGA
AACTCTTTCTCCTTACCAGCTATATCTGGGTGTGGTGCTGGCAGCTGTGGTCATTGTCAC
TGGCTGCTTCTCCTACTACCAGGAGGCCAAGAGCTCCAAGATCATGGATTCCTTCAAGAA
CATGGTACCTCAGGTAAGATGGCAGGGCTGGGCTCTGGGCTAGGCTGTAAGGTTTTGGCA
AGAGTCCAGCTCATCTTTTGTCAGCTCCCAGGCTCTAAGATAGAGATGGACAGAAAAGAT
CCTCCAGCTTTCCATGCCAGCACCTAATTGTTTATGGGGCTTCTCCTTCTGCTTGACGGT
GTGGGAGACCAGCAGGAGAAGAAGGCAGGGGCAGAGACAAGCATTTCATGAGCTGCCTGT
GGCTCCCCACAGCAAGCCCTTGTGATCCGGGAGGGAGAGAAGATGCAGATCAACGCAGAG
GAAGTGGTGGTGGGAGACCTGGTGGAGGTGAAGGGTGGAGACCGCGTCCCTGCTGACCTC
CGGATCATCTCTTCTCATGGCTGTAAGGTGAGGAGGTCATACCAGAGCAAGCAGTTGAGT
CTAAGGAGAAGGCTGTGTGCAGAGCTGAGAGGGGCCCAGTGAGGTTTAAAGGTGGAGAGA
CCCAGGTCCAAATGTCAACACCATGCCTATGCCCCTGCTAAACCTTCTCTCAGTGTGGGG
TGCTTGTGCAGTGCCTCCTTGCATCTGTGTGTTATGAATGCTCTATGCCCCAGGTATTTC
TTTGTTGTCCACTTTTTAGCAATCATGTATTGAATACCAATTATGTGTCAGCTGCTTTAT
ATATGTTCGATGTGCTATCTGATGTAATTCTGAAAGAGTGGTGTAATCATGCAGGGCTGC
TGAATGTGGCCACACACGTTGCATCCTGAATGACCCCAGGAGGTGCATTTTCATAACTAC
AGTGTTAGTGTCTCCCCCTGTGGTTGTGCAAGGCAGAGATTCTGTTTACATTCACCATTT
TACAGTTGAGTACATGGAGGCTCTCTTGGTTAAGCAAGTAACCCGAGGTCACATAAGAAG
TCAGGAGGAGTCAGAATTCCAAACCAGGGCAGGGGCAATAGATGAGTAATGCCATAAATA
TGTGATGAGGGCAAGTGTGACTTTGTTCCTCGTGTCATGAAGATTGAGTGTGGTTGGAGG
TGGTTCAGGAGACAGCTGTGTGCATACAAGTGGCTCTGCCAGTCTGATGACTATGCACTC
CTTCCTCCTCAGGTGGATAACTCATCCTTAACAGGAGAGTCGGAGCCCCAGACCCGCTCC
CCCGAGTTCACCCATGAGAACCCCCTGGAGACCCGCAATATCTGTTTCTTCTCCACCAAC
TGTGTTGAAGGTGAGAAGCCAGGCTGCCCCCTGTAGGAAAGAGTCTGAATCCTGAATCCA
TAGTCAGGATGAAGGGCTCTGGTAGTACTTACCTGGCAAAAGCTCTGCCATTGGTGGGGC
AATTGAGGGGTCAGGGGGCCCTGAATATTATGGAAACACCCTCCACAGAGCAGGGTATTG
ACTGAGGGCAGCCTGACTCCATGGGAAATGTATCTCCCTTCCCCAGGGAGATCTCTGTTC
TGTCCACCCCAAGACTGAGTGGATTTCAAAGCTTTCAGGTATTGGGTTAAGAACCCCTTA
CGCATGCGCACACACAGATGCACATACGCTCAGAACCAACCTGGATTCTTAGGAGTCTTT
GGATTTGATTGATGCTTCTATTCCTTGTGGTTCTGGGCCTCGCTGCCCCCTTCGATAACC
TTTGCTTTGGCCAGGGCCCCAGGGTCTGGGAGGGCCAAGAAGGCATTCTGGCCAGGTGAA
CACTTGGGGCCTACTTCAGGCTGCTTCTAACCTTTGTTACATCAAAAGACATGTTTCACC
ATGCACAGACTACCCAGTTTGCCCCATCCCTGTTCTGGGTTCTAGAGATAAACAAAGGTC
AATAAGAACTCCCAGAGCTGCCATCACTTAATGGCAGGGGTCCAAGCACAACTGAAACCT
GTGCCCTCTGTGGTAAAGCCAGTGAGCAGAGTCAGGGCTGCATCAGAGAAGGAGTAGGAG
GGAAGAGACAGAAAGAGGCCTCACTAGACCAGTGGCCTCTGAAAATAGGGCAAAGGAGGC
CTCATATCCCAATCCACACTTCCCCTGTCCATTACTCATTTCTCCTCAGTGTATTATGTT
TCTCTGTGGTTTTTTTCCCTTCTTCGACAAGTTGGAATTCCACTGCTTGGAATCCATGAG
GGATTGGTTCCAGGACCCCCTTCGTTACCAAAATCTAAGGATCCTCAAAGGCCCTGATAT
GAAATCGCATAATATTTGCATATAATCTGCGCACATCCTCCCATATACTTTGAATCAACT
CTAGATTACTTATAATACCGAGTGCAATGTAATTTTTATACTGTTTTGTTTTTAAATTTG
TATTATTTTTATTGTTGTATTGTTATTTTTATTTAGCTCCAAATATTTTCGATCTGAGGT
TGGTTGAATCTATGGACATGGAATCTGTGAATATGGAGGGCCAACTGTACAAATAAAAAT
CACCACACATTACATTTCCTAAGTTTGTTTTTTGTTTTGCTTTTGAGACAAGATCTTGCT
TTGTCACCCAGACTGGAGTGCAGTGGTGCAATCACAGCTCACTGCAGCCTTGACCTCCCA
GGCTCAAGCGATCTCCCACCTCAGCCTCCAGAGTATTTGGGACTACAGGCGCGTGATACC
ACACCCAGCTAATATATATATATGTATATTAGAGATGGGGTCTCACTATGTTACCCAGGC
TGGCCTCAAACTCCTGGGCTCAAGTGATCCTCCTGCCTCAGCCTCCCAAAGTGCTGGGAT
TACAGGCATGAGCCACCGAGCCTGGCCAAATTTCCTAAATTTTTAATGTACTGAGATTTT
GAAATTTACATTTCCCACAATTGATTTATTCAGAAATGCCTAGTAATACATTCCTATTGC
TTACTCTGCAATTGGCTTTGAAAAGAGGAAAGGAAATAAATGAGATATTTGTTGAGCACC
CGCTATGTTCCAGGCACTGGCCTAAGTATATTAAAGCACAATCTCATCTAAATATTAAAA
CAGCACCGAGATAGGAATTCAAATAAGGATTCAAACCCAAATTTGGCTGGCTCCAATGTG
CATGCTTTTTTCAATACACCACCCTTCCTTCCCAGAAGACCCCTGTAATGTCACACAAGG
GTTAGCAATTGCCTGGCTTCCTCTATAGAGATTCATGCCTAATGTTGAGAAAGAAAATCT
TAAGACTGGATGGAAAATCCATAATGAGTGCTTTACTTTGTGTTCATAATATACTTTTGG
ATGGTATCAAGTATGGGAATGATTTTACCAAAATGCCACAGGCAATTTTTATTTATTGAA
TCTTGTCTATTTGAACTTTGAGATTATTTGCAAGCTTCTCCCCAGGCTCGAGTACAAGAG
AAAATAATTTGCTGTTGTATTGATTCAAGGATTGGCGATCTATCCAGGGAAAGGAAGGCC
AAGTGGGGACAACCTACTGAATGTGGCCTCCAGATCTGCGGCTTTGGCTCACCTATCCTG
TGATGATTTTCCTTGCTCAGGAAATAGGATGGGACTGCAGTCCCTGGGAGCCACAAGGCA
CCCAACCTGATGCCCCACCATGTTGCAGGCACTGCCAGGGGCATTGTGATTGCCACAGGA
GACCGGACGGTGATGGGCCGCATAGCTACTCTCGCCTCAGGCCTGGAGGTTGGGCGGACA
CCCATAGCAATGGAGATTGAACACTTCATCCAGCTGATCACAGGGGTCGCTGTATTCCTG
GGGGTCTCCTTCTTCGTGCTCTCCCTCATCCTGGGCTACAGCTGGCTGGAGGCAGTCATC
TTCCTCATCGGCATCATAGTGGCCAACGTGCCTGAGGGGCTTCTGGCCACTGTCACTGTG
AGTGGGTCAGGCTGAGGTGCCACCAGGGGAGGGTCTCACTACTCTTTCCTCAGAGTGATA
GAGGCACAGTTGCTTGTAGCTTCTCACTACTTTTTCCCCCTAGAGTCACTTATTGGATGC
GATACTCAGAGATCACTTAATACATGGCTTAGGGTATGAGTTGAGAAATCTCAGGTGGGG
CTATTCTTAGGCACTCAGTTTCTCTTTTGGAGCTTGTCACGGCTGCCTTTTCTCACGATC
TGCCAGCAGTCTGGGTCTCATTCCGTCCAAGTCTCCTGTAGAGGCTGTCTCAAAGGTCAC
CAGTCACTAACTAGCAAATCCAGGGACCTTTTCTCAGCTCTCCTCCCTAACTCTGCTGCT
GAAACAGATACTGCTGTCCACCCTCCTACCATTCTCTCTTTTGTCGATTGCTGTGATGTG
TCACTATCCTGGTTCGCCTCTCCTCTGTCCCTTCCTGCTCCCCCTACACTGATTCTCAGG
CCTCAGCTGTCTGTTCTTCCTACACCCTGAGCAAGAGCCAATCTCCTCCCAGTTTGCAGT
GTCCCTTCTGTGTTGATGACTCAGACATCCCTATGCTCAGCTCTGCTCTGGCCCTCTCTG
GAGCTCTAGTCAAACGTCTTAAACCCCCTAATGGGCATTTCATCTTAACAGATACTCATG
ATCTCAACACATCTAAAATTGAACATTCATTATTTACAGCTAAGTCCCACCCATTCAAGT
TAGTGGAGTAGAATCAGGGGAGGAGGAATGGAGCCACGGTCTAGGGTAAGGTTATGGCCA
TCTCCGGCTTCAGCCTTAACCTTTTTTATTCTCCTCTTTCTCTACCAGGTGTGCCTGACC
CTGACAGCCAAGCGCATGGCACGGAAGAACTGCCTGGTGAAGAACCTGGAGGCGGTGGAG
ACGCTGGGCTCCACGTCCACCATCTGCTCGGACAAGACGGGCACCCTCACCCAGAACCGC
ATGACCGTCGCCCACATGTGGTTCGACAACCAAATCCATGAGGCTGACACCACCGAAGAT
CAGTCTGGTGATTGGGTGCTCCAGAGGGGGTGGATAGGATTAGAGGAGGCTGAGGGCAGT
GGCGTGGTGGGGTGAGTGGTTGAGATAAAGGCTCTAAAGGGAGCCACGCTCCTGGTTCCC
CCTCATTTCCTCCCAGGGGCCACTTTTGACAAACGATCCCCTACGTGGACGGCCCTGTCT
CGAATTGCTGGTCTCTGCAACCGCGCCGTCTTCAAGGCAGGACAGGAGAACATCTCCGTG
TCTAAGGTAGGGGGTCAGGACACACACCAGGTATGTTTTGGGGGTGTCTCCAAAGCCTCT
TGCTGGCCCCAGCTTTCCTTCTCACATGATGTGGCTGCCTTGGGGGTTTCAGTGCCGCCT
TCACCTGATCCTCCACTCCCTTCCCTCCCATGCTGACACTGAATTCTTGTCTCTTCTGGC
AGCGGGACACAGCTGGTGATGCCTCTGAGTCAGCTCTGCTCAAGTGCATTGAGCTCTCCT
GTGGCTCAGTGAGGAAAATGAGAGACAGAAACCCCAAGGTGGCAGAGATTCCTTTCAACT
CTACCAACAAGTACCAGGTCTGCTTGGGTTGCCAGGACAGAGGAAGAGAGAGGGATATAA
ATGGGTAAGGGTGGACAAAGCCAAGGGGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNTAACTCACATGTTGGTCTCCGAGGCCCTCCACCTTCCACCTGAAACCACC
AAAACTGAGGATGAGAGAGGGATATAAATGGGTTAGGGTGGACAAAGCCAAGGGGAATCA
TCACTAGCANAAGTGGGGGTGTCTGAGGGTCATGTTCCCTCCCCCTGCTAAGTCCCCCAG
GCCAGCTCATATGACTGCATGTCTGATTGCAACTAGCCCCAGCTCCCAAACCTTACTCCA
TCCCTTACTACAATCTGTCACTCTCTCAACTCTTCTTCCCATAGCTCCGCATCCTCTGGC
CTAGCCTTCCAACTCTTCTACCCCAGTCAGTGAAACCATAATTCTGTAATTCCTTTATGG
TGCCCCTTAGCCTTTAGGCACCTGTTAAATGCCAAGAATGCAATCTCAGCATTCCTTATT
ATCCATAGAGGTAAAGCCCCCTGAGGCCAGGTGGTGGTGGGGATGCTGAGGAGGGAGCCG
TTCAGCCCCTAGCACAGTGCCTGTCTTAACCTGACCTCAATAAATATTTGTTGAATGAAA
GACTGTCCTACGGAGGTGGCTCTCAGGTTACAAGTGTTGGAACTGTGAGGTCTAAACACC
CCCCTGCACAAGGAGATTCTCTTTGTTGACAATCTTTGATGGGTTGGGGCTACTTTTCTA
AGGTGGTTTCCTTACCAGCTGCTGCTCTATGCCGCGCTACCAAGACAAGTATGGCCCTCT
CTGTAACTACCTGTTGTCTCTCCAGCTGTCTATCCACGAGCGAGAAGACAGCCCCCAGAG
CCACGTGCTGGTGATGAAGGGGGCCCCAGAGCGCATTCTGGACCGGTGCTCCACCATCCT
GGTGCAGGGCAAGGAGATCCCGCTCGACAAGGAGATGCAAGATGCCTTTCAAAATGCCTA
CATGGAGCTGGGGGGACTTGGGGAGCGTGTGCTGGGTGAGAGGCCAGAAACAGGAGGCTC
AGAAGGGGATTCCCAAGCCTCTGCGGCATCCCTGGGGTGGGGGACTGTGGGGGCGTCCAG
GAAGCCACTCTGCGGATCTCACTGATCCCTTCTGCCCCCCTTTAGGATTCTGTCAACTGA
ATCTGCCATCTGGAAAGTTTCCTCGGGGCTTCAAATTCGACACGGATGAGCTGAACTTTC
CCACGGAGAAGCTTTGCTTTGTGGGGCTCATGTCTATGATTGACCCTCCCCGGGCTGCTG
TGCCAGATGCTGTGGGCAAGTGCCGAAGCGCAGGCATCAAGGTACTGGCCTCCCATCCTC
CCCTCCATTCTAGCCTCCCCCATGCCAGAGTTCAAGGAGCTGCAGTGGCTGCTGCCCTGG
AAAGGCCCAGGCCACGGTGGCCTCCTTCCCACTGACTCAGAGAAGAAGCTGTCCATCTGC
AAGGAAAGGCCCACCCCTGCCTTGGGGCACTCACCCTTATCCCTTTTGCTCAGAGAGGCC
AGTGTCCCATGCCCCTCCTCTCCCTCCCTGGCACAGCTCTTTGTCCCATCTGCATGTGTA
CCCTTCCATTCTGATTTGAAGCATAATCTGGCACTCCTATCTTGAAGACCTAGTTGTCCT
ACCCTTCCCAACTACTGCCCACCCTCTCTGTCAACTTAGGATGGGATTAGCAGGCTCTTG
TATGCTCCCAGTGGCTCAGCCCATAACCCCACAGAATGCCTCCCACTCAAGGTTCTCTTG
TTCAACTACAATTGCTTCTCACTGACCACTCCCTCCTCTGTGCTATGTTTGTTCTTCATT
CAACAAATATTTACTGTTTACTATGTTTCAGACACTGTGCAAGGTGCAAACTCTAGCACC
TTGCACAGTGCCTGATACATAGTAAACAATTTGTGTCACATGACACATCTAGATGGGACA
ATGAGCTGTGCCAGGGAGGACACATATAAATCAGGCACTATTCTAAGCACTAAACCTCTA
TGATTTCATTTAATCTACGCAACAACCCTGTGAATAAGCACCAGTATTTTTCCTTTTTTA
CAAAGAGGGAAACTGAGGCACAAAGTAACATGCCAAGGCCACACAGCTAGTGTAAGTCAT
AGAGCAGGTACTTGAACCAAGGCAGTCTGCTATTTCTTAACTATCATACCAGGAGACTTG
TTTCTGTGGGTGTATGTGGTTTCTGAACCCCATAACCACTCTGTCTCCGAGGCAGGCATC
ATTATCCCTGTTAAAAGTAAAACAAGGCTGGGCACAGTGGCTCATGCCTGTAATCCCAGC
ACTTTGGGGGGGTCCAAGGCTGGTGGATCACCTGAGATAAGGAGTCCAAGACCAGCCTGG
CCAACATGGTGAAACCCCGTCTCTACTGAAAAAAAAATACAAAAATTAGCCACGTGTAGT
GGCAGGTGCCTGTAATCCCAGCTCCTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCCG
GGAGGCAGAGGTTGCAGTGAGCCGAGATTAGGCCACTGCACTCCAGCCTAGGCGACAAGA
GCAAGACTCCATCTCAAAAAAAAAAAAAAAGTAAAACAAATGGAAACTGCAAGTGGGTAA
GTCTTTTCCCCAAAATAAAACCACCAGTAAGTGATGGACTGGGACTATGAAGCATGATCT
GCTTGACCGGAAAGCCTGAGCTCCTGCTGCTTGGCCAGGTGCCTCTCTCTGTGATCAGAA
CCATCACGGAGGCCTGGGCAGAGGACCTCTATGGGAAGTCAGCTCAGGGAAGCATTAATT
CTGCCTCAGAGAACTGGACGATGTTTGACAAAAGGAATGATATTTGAGCTGGGCTTTGGA
GGTCAAAGAGTATTCTGCAAAGCAGTGAGGGAGAGGAAGGCATGTCAAGATCAGGGAACA
GTGTGTACCCTGGCGTGGCTAGACTGTACGGAGCGTGTGTAGGGGTTGGCAGGGGAGAGG
TGGCAAGGAGTACTGGGGGTTGAGACTGGAACACTGGGTCAGAGCCAGTTGGAAGGACTT
GGCTTAAATGCCAGACTTGGGCTTTATCCTGCAGGCCACAGAGAGCCATCAGTGTCACGG
GGGAGGTTGAGCTTTTAGGAGACTACCTGGTTTGAGGAGGGACTGGATTTGGGGAAGAAC
TGGAGTCAGGGAGAGACAGGTTAAGAGGCCATTGCCATAGTTCAGGCAAAGAATGATGAC
CTGAACTAGGGCAGAAACAAAGGGAATGGAGAGGAATAGCCATGTCTGAGAAATGTTTTG
AGAACTTGGTGACCAAACTGGATATGGAAGGTGAGGAAGATACAGGAGAGAAGGGGACAG
GATGAATAGAGAGGACAACATCTAAGGTAGGGAGCAGTAGCAGGCTTGGTGGGGTGGCAG
GAGTAGAGAAAAGGAGTTCAATGTTGACCTTAAGCTTAAAGAGTCTATAAGATACCCCAG
GAAAGACAGATGTTCCAGTGAACATTGGAGTATGGTTTAGAGCTCATGAAAGATGGTCAG
GACTGGAGATTTGAATCTCATTAGCACAAGGGTGCAAACTAAAGGCTTATAGTATGTTGT
ATTATATTGCCCAGAAAGAGCAGACAGGTCAAGTGAAGGGAGGAGAATGAAATCCTGTGC
CAAACCAACATTTAGGCACAAGAGGAACCAGTGAGGAGGGGAGAGGGTGGTAGGAACCAA
TGCCATTTAATCTTCATGACCACCTAGAAAGGCAGGAATCATCTCTGCATTGTGCTGAGA
CCTCAGTGCTTCACTTGCCTAAGGTGCTGTAGCTGGAGAAGGTCGGTGTTTAAACTTGAG
CCCCTCATTCAACTCCAAAGCCACTGCTTCTTCCATCCTACTAGGCTGCCACCCTGAGAG
GCTGGGAAAGAGCATGCAGAGGAGTGGAGGGAAAACAGGAATGGAGGAGTATGTGGAAGC
CAGGGGAGGGCAGGGTTTCAAGGAGAAGAGGTCTACGGTGCCAAATGCCTCAGAGGGGTC
AAGTAGGATGAGGACGGCAAAGACACTTTTCATTTTTCAATTGAGAGNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNTTGCCCTTAAGTGCTTTTGCTGCTATTTTTTTG
CCCCCAGTTCCACAAGATCCAACCAAGAATTCTGTATCCTGGGACAGTCAGATTCTTCTA
AATCAGGCCAGGAAGGAGGGGAAAAGAGTGAGAGAATGGTATTCCCAGATACTTCTTCCT
CCTGCCCCTTTTCCCAGCAGCTCTGAGACCAGATGTTGGCTGCTGTACTTACTCCCTGAG
GTAGGGAATGTGTGGTGATCGAGTGGTCTGTGTTCCTATTGCTGGTGGGGTGATAGGGTG
GGCTAAAAACCATGCACTCTGGAATTTGTTGTATTTTCTCCCAGTAAAGCTTTTCTTCTC
CCGACTGCTGCTCTGTGTGGTATGTGGTCCATTTATTCACAATGGATGGTTTTTGTTCCT
ACTAATGTAGGTACCTAGCCTTCCCCTCTCATTCTGCACATGATACAGTGTTAGAAAGTC
CATTTTGGGAGACCCGTATTTCCAGTGCTTGGGCTCCAATTGGAGACTGTTGGAAGTAGG
ATACACTCCATTTAGCTCAGTGATACTTAGGAGATTGGGTGGGGTGAGGGTATACACTTG
GGGTATTTTCCCAGCCCTTATTCTGGGCCATAAATATTGTTCCCCCTCCCTTCCCAGTGA
TTCAAAGCCTGCAAAATCCTGGTCACTCACAGAAATTTTAAAATCAGTTAGTTGCAATAC
AATCAATCACCTTTATTCCGGGTTAGAACAAGGCCGTGCACACTGCAGACAGAAGAGCAC
AAGATGGGGCAATCTCACAGCAATATAAGGAGTGGGTGGGCAGGTTAGTCTTTTTAGATT
ATTTTGCCTTACAGAGAAACTACTAGACTCTGCTGAAAAGAACCCTGTCTCTCTTCTCCC
ATTTCTTCCATAAGAAAGGCTCCTTATTCTCTCTCTCACTCTAATGTAACATATCCCAAA
TGGAAGGACAGTTCATGCTCATTCCCCCCACCCAATTCTACAAGTATCTCTCTCTTCTTA
AGGGAGAAGCCAGACAGGGAAAGGGAGACTTGGGAAGGTCCTTTAAGGCAAAACTGTGGA
GTCCTAGAGGTGTGTGTGTTAAGGCAGGTGTCTGCAGCAGTGGCCAGAGGGGCAGGGCAC
GCTAGGCTGGGCTAGGAGTTAAGAGTACTGTCTAACCAGTCTGGCTTCTTCCTTCTTCCA
GCAGCCAGCCCTCCCCTCCCATTAAAGTTTTACTCCCACATCCTAAAAGCTCCTAACTTG
AACTTTGTCTAAATAGTCTCTGAGACTGCATGTGAATTTAATGTTTTTTGAAAAAGCCTT
CTTTTTTGTTTGGACTATGTAGCAATTTGATTCTGCCACTCCCTTCACTGTGGCATTCCC
CTCCCACCCCCGCTCTGGCCTAGACAATAAGTTAATGCTAGACACCACAAAAAAGGGCAG
ACATGGCAGTGCAGTTTTAATATACATATATGTAGAATATATATGTACACACAGTTAGCA
CGGTCAGGGTGGGGAGGGGCATCTTGGGGTAGGCAGGAGGCTGGGGTCACTCACTGTACT
GTAGTGATGTGGCTAGGAGGTGTTCACAAGCCCAGGGGGCCAGGATATCTAGTAAAGAAG
GGTTTCCTAAGTAAGTCCCTTCCGGGATTGAATTGGGGTGGGGATCGGTGCAAAGGAAAA
CACTGTAGTTAACTTCTTTCTGGCTTGGGATGTTCTTCACCAAGGAGAGAGGGAAGGTTG
CCTACAATAACCAAGTTGGGACCCTATAGATGGTGGTGTCAGGATTCGTGTTAAAACCTA
AGGGTCTCATTCTTCAACCTCCCTAGGTTTAGAGTGCAACAGTCTGAGTAGGAACAACTG
AGTGGAAGAGGGGGCTCCCCTCTCTCTGCCCTCATCCCCATCTCAGGCTCAGTGGTACAT
GTTCCCAGCACAGTCTCTCCAGAGTACAGGTGGGTGGGGGCATCTAACGCTGGCTGCTCC
ATGGGGTTTGATCTTAGGGACCAGGAAAGGATCCCTGGCTCATACCTATGCTAGGCCCAT
GAGAGACAAAAAGGGACCTGCTGGTACTCAGGAAACAGTCCAGCACAGGAGTACAAACAT
GGAACTCTGGCTTTTCTTTGCCCCTTCCAGGTGGGGGTTGAGTGGTCTCTTTGCCTTCCG
TCCCCACTGCTTTTCCCTGGATCCACCTACCTCTCCCATACCTTACCCCTATGTCAGCTC
CTCAATGTAGGAAAATGCAGGTCCTTTCTGCTTCCACACTTTAAAGATATGGGGGGAGTG
GAGGAAAGGGAAGTAGGAGGAATGTGCTGATTTCTATTTGCATAGAAATAGCCCCCACCT
CCTCCTAAAGTGGGGAAACTCAGCCCCCTCCCCTAGCCCCTGACCCCCATCCCCTTAAGA
AGAGGAACTAGATGAGCTAGACATATAGACAAACAGCCAGAGCGTGCGCACACGCACACA
CACGCGCACAGTAAGGGGGTTAGGACCAGGTTAGTAAGTGGGTAGATGGTGGGTTGCCCT
TGCCCCCTCTCCTGGAGGATGGGGGAAGGGAGTGGTCTGATGAAGGTCCAACCTTCCTCC
TCTTCCTCCCCCTTGCTCAGGCCTTCTTCGGTGGGGGAGCCAATTTGATGATCTCTTCCT
CAGAGGGCTGCCGGATAATGTCTGGGGGCAAAAAGGTATGTGTCCAGGGACAGCAGTGTG
GGAGATGCCAGGCAGGCCCATTGGGCATCTGCCTCCACTCTCCCAAAACTCAAGTACTCC
AAGGATAGTCAACGGGACGAGGCAGAGGTGCAGCTAGTTAAAGGAGTGGCCGCTTACCTT
TGTACTTCTTGGCACTGGGGATACGGGTTAGCTTGGTGTCCAGCTCATCCTCCTCAGAGA
TCTTCAGCACACGGGTTCTGTAGTCAACCACCATAGTGAGTAGGTCAGGACGGCGGGAGA
TCTCAAAGATGTGCTCAATGTAGGAGAGGTTGTCTGGAGGAAGGCAGGAGATAGGGTCAG
AGCTAGGCTGTAGAGGTCAGCTTCCCCTACTCCACCAGACTAGTGACCTGGAACCAAAGC
TGAGTTGCTGACATTGGTTATGGGAGGGTACAACACTGGAGGAAGAGGGGCTACTAATCC
AGGAGAAGAAAGCTAAGGTACCCAAACAACAATACAGAGGACTGTTCGCAGGAAGGGCAG
ATAGTTGGTCAGTGAAGTTTCTAGATTGTGGTTAGAATGAGGGGTTTAGCTTAGATACTA
GCTCCCATATGTTGTGGGGAGGGGACAAAAGAAAAATCAACTTGACTTCCAGATACCCCA
CCCCCACCCCCATCCTTTTCCACTTTCCATCCAAGTAAGTATCAGAATTTGCTGACAGCA
CATGTAGGACCAGCAGGGTGGAATCTCTAGGCAACCCAGGAGAGATTCTGGGCCTGGTGA
GAAAGGTTATTCTAAATGAGAGAAGGTATGGACACCACCAGAAGGACGATGTCCATGGCT
TGGCCAATTCCAGGAGATTATAGATGCCCTTAGACCTTCTTCCCTGGCTCCTCCCCTCTG
ACTGTTGCCATACAGTCTAACTGTAACACGTCCTCCTTTATACGTTCTCCCTGCCAGCCA
CACAGCAGTCAGAATAGTATATCTGAAGGGCCCTGAGTTCACTCACCTCACCTATCCAAT
ACCCAGGCTCTCTACAACACAGTCTTACCTTACCTTCCCAGCCATTTCTAAACACCCTAC
ATCCTAGTCAAGCCAAGCAGGACTGATTGCATTTCCAAACACACTAGATACTCTGTGACA
GTGTTCCTCTGCCTGGCATGCCCTCCTTTGGATCTTGCCTTAGAAATCCCACTCACCTTT
CAGGGCCATCTTAAACACCAATTCTTCCCTAAAGCCTCCAGCTGTGAGGGATTACTCTAA
TCCATAGATCCCACTCCCCAAGCAGTAGTCTCTCAAAGTGGATAAGAAAATGATAGAACT
TGTAGTTTTAAATTTTACCAGTTTTTAAAAAATGCTTAACAAAGATTAGTATTACTATTT
ACCAGTTAGATTACACTTCGAGTTCTCCCCTCATTCAGGTATTCTTCCATTTTTATTGTC
TAGAATTCTTCCCAATTTTTGCCACTTAAAATTTTACTATTTTTAGATTGTTTTTATGTT
CTGTTGTATATGTGATAATAGCACAGGAGTATCTGAATAACATTTTTTACCGATGAGGGG
CACAGTGAAAAATGTCTAAGGCCCCCATACTCTTAGAGCACCTCTCTTCTGCCTTGCTAT
AGAGGGGTACACATTGTGGATGTAAAAGCTTTGAGCTCATCTCTATTTGCTGAATGAACT
GAGCCTGAATGACTGATGACAGGACCCCTGTGCTCCCCTCCCCCACCTTTGTCCAGCTTG
TTGTGGCTCTCCAGGAAGCTAAACCAGGCACTGCCAGTAGTGATCTCCTCACTCTTTTCG
CTGGGGATGTCTTCCTTGCAGGCCGACTTGAGCTGTTCTAGATCTTCAAGGGTGATGTTG
TTGGTCAGGTCTTGCAGGAGGGTCCCGTACTCAGCCATGACTGGGGTTGGGAGGCGACAA
AGGGATAGGAGTTGAGCTTAAGGTATGGAGTCTGGTTTACTCACTGGCACTACCCTCCTA
CTCCCCACTCTGCCCTACCAGGCATGTGCCTGGAACATGGAGGCTGGAGGTGGCTAGGGC
TGGAGGGAGAAAAGGAAGACCTAGGGGAGGCAGTCAGGGTAGACGGGAAGCTAGGAGCCA
GGCTGGAGCCTAGAGTGACAAGTCATACCTCCTTCCCCCCACCATCTTTTTCTTCTGTTT
TCCCCCTCTAACAGTAACCCTGGCAACAGTTCCCCTGACTGAGGAGGCGGTTACCATAGC
AACCTGCTCCCGACTTTCTCACCCGCTCTCTCCAAGTCCCCCCTCAGAATCGCCCCACCC
ACTTCCAACCCCTCCCCATGTCAGGGAAAAAAAACTCCAAAACAACCAGGGCGAGGCTTG
CTGTGGCAGTGAGAAGCTGAGAAAGAGCTGGAGGGTCTGGTAGGAACTCATGTGTTCTAG
CTTCCCCATTCTGCCTCAAAGGCAAAGGGGTCCCTCACTTCAACTCCCCACCACCCCACT
AATGACTCATTTTGGATAGATGCCTAGTTGCTTGGTCTGATGGTTCCTTGGCCCCACCAT
GCTAGCCTTGTATTCAGTCATTAGGGTTCGAGGTGGGGGAAGCAATGGACCACCCCCACC
TTTGTGGAGCCCATTTTCTCCTTTGATGGTTACCAGGCCCCCACTCAGCTCTCTCTCCTA
CCCTTTGTGCTGTGCCTGCAGCCCCCGTGCCCAAGAATACCAAGCAACTGGCTCTGGCCC
CCTGCCCAGTTCCCAGGCTGGCTGGGTGGTGGGGGGAGGGGACTTTAGATGCGGCTTTGG
GAGAATGGCAAAAGGGGACTGCCCCCCCTTCTCGTATCGTATCAACATCCTACTGGCACT
ACCTTCAGCATGGTCTGATGAGATCAGCAAGGCCAGATCTCACCTAGGCTTTCACCCTAT
CCCTCTTTCATGATCCTTAGGTGAGAAGTAGAGAACATTCAAGGCCTTCCTTCCACTAAG
ATAGGAACTGTGGCTAAGACAGAAGAAAGAAGGTCAGATGTTTGAATGGACTTTCTGGAT
TTGATAAAATGTGACACTAGTGGTAAGCTCAAAAATGGAACTTATTTCCACAATGAGTAT
CTATTTCCTTTTAGTCAGAAAAGTAAAGCATGTTTTAAAAAGTAAATTGTATCATAAACA
CTCTGTATGCGACTAGACCAAGGGGTGGGCAAGCAGCAAGATGACCTTGTCCCTGACGGA
GGCTGCCTGCAAATCACCCCAGCATTAGGCTGGGAATGTGGCAGATCAAAGGGGCTTGGT
TGACACATTCACATTTTCCTTCTTGCTCTACTGCAGGGGAACTGAGATTGGCATGGTGGT
CACAAAATAAGAGATACAGACCCAGAAGTCCCCATTCCCAGCCCCCTACCTGGACCAGAA
TAAACAAGCCTCCCTTGGTGGCAGGCACCATGACACAGGCAGACAATGAGCCAGACAGGA
GGGCTACCATGACCCCCGCAAGAAACAGGCAGTCATAGGCATGCTCAGTTGCACACCCAG
GTGCAACCAGACAGAAGGGCCCAGCAGTGGCCCTGCCAGGCCGGGCCAGGAACAATGCTC
TCTGACTGTCAGCACCAGGAACTGTCTCTGCCTTGAAATCTAGGTCACAGCAGCAAGCTC
TGGAGCCCAACCCCCCTCACTTCACTGATAATCCAAGGACAGAAGGAGGGGGGTACGGGT
GAGGGGGATGATGGGGAGGGGACTAGAGATGGAGATAAGAATGAGTAGGGGGGCATGAGT
ACAACTGGAAGGGAAAGCGCAGCAGGAGACAAGAAGACCCTGCCCCAGTGGAGGAAACTC
TGGGGCCAAGCCCTCAGCTGGAAAAGGGGGCAGGATTGGGGGTTATACTTCCCTGCTTTC
ATATGGAAGGAGAGTTTGTAAATATTACAGATCCTGCGGGAGGAAAGAGTGCATCTGTGT
GTGTGTCTGTGTGTGTGTGTGTGTGTGTGTGTCGGGAGGAGTTCAGATTTAGGGCTTTGA
ATCTAAAACAGATCTACAGAGGAGGTAGGCGGGAAGAGATTAATGTGTGTAACACACTCA
CCCACAAAGACTTGGGGCCAGTGGGTAGGAGCTTTCTAAGAGAGTGAAAGATACAAGGAG
GCCCCTAAGAGAGATGGGGGTAGGAATGTTAAAGTGGCAGAGGAGAAATGTGTGTGTGCT
CGGATCTTATGGATGCTAATCCCCGGGTTGTGGGCACAGCTCTGGAGGAGGCAGTGGCTG
GGTATCTGTGGGTGTGTTTGGATGTTCTGGTAATGGAGGTGTATGTGCCAGCACTGGATA
TATGGCTGTGGGTGCACTGGCTGTGAGTATCTGTCATGTGTGTGTTTGTATGTGTCTAAA
CCAGCCAAGAGCATGTGTAAGAAGGCATATAACCACAGGCTCACATCCAGAGGGGTGAGG
GGAGCCTACAGAATGGAGAAAGAGAGCTGGAGTTGGGAGACAGAAAGAGACTAAGGCTGC
AAATGAGGCATGGGGGGCGAGGGGGAGGAGAGCATACAGTCCACAACTATAGAAGGCTGT
AGCCTCATCTCATCTGTTACTATAGCAACCTCAGTTCTGGGTGCCCCCCACCCCCAGTCG
TTAGGATGACACCACTAGATGGGAGGAGTGTAGGGAATGGTGAGTAAGAAGGGACAGAAA
GGATAGGAATAAGGCCCCCTGACGGTACAAGGAAAGGCAGCCCAGTTGCCTCCCTTCTTG
GAGAGATCCATTTGCCTAGGCCTTAGTATGGCAGAAGAAGCAAAGGGAGTGTTGTTTAGG
GGAACTGCTCTCAATTCTCACTGATCAACAGTTGTACCTGGGCTGGTCTGGCCTGGCCAT
GGTGGGGCTTGGCAGAGCTTGTTTCCTTCATCCTCCATGTCACTTTCCTCACCAGAGATT
CAGATTTCCTTAGGGCTCGTGGAGAAATCTGCTCTCTGGGCTCTGAAAAATCCTCCTGAT
TTCTGGAGCAGTGCAAAGAGCTGCTCAGGGATCACCAGGCAGTCTGGGCGGAGGCCATTC
TTGGGACAGGATACCAGGGCAGGAATCAGGAACCGGAGCCCCGGCTGCCAGGAAGTCAGT
CCTCTTCCCTCCCAGCTTTCTGTGCTAGGCTCACCGCTTCCTCACACCTTCCTTCCTTCC
TGCCTCCCTCTCCTTCCAAGCTGGCCCCAGGCACAGCCCTGACAAAGGTCAAACCAACTG
AGGATGCTGGGGAAGAGGGGCAGGAGGTAAGGACCATTATATACTGACCTTTTAGGGTGG
GACAGGTGGGAGCTCCATGGGCACTGGGGTAAGAAGAGCCAGGCCCTGGGAGTGCTTTGA
GAAGCCTGGCAATTGGGATAACCACCTGTGGAGGAGGTGGCAGCACCAAAAGAATTTCTG
TGCATTTTGACATTAAGTCGTGGTAGATTATCCCTTCTAACGTTTGGTTCCAAATCCTCT
GTAAATTCGAGAAGGAAGCCTGAAGATTAAGAGTTGCTGCCCGTCCCTCTTCCACATCTG
TTGCAGCTGCCTAAGCCTGAGGGGAGGGGCCATCCCAGACAGCTGCAAGGACCTAGAGGT
CCCTGTATTGGGCAGGAGGGGACTCCCAGGCACTCAAGTCTGTCAGTCTTCTGCCTGAAG
TTGGAAGTAATCACGGAGAGGCAGAGGGGTTGGAAGGGAGAGAGTAGGGGTCCAGCTTTC
CTATTTTAAATTATAACTGGGCCCCAAATTCAAGCAGTCCTGTAGTTTATTTCCTTTAAT
ATCATTCTCAATTAATTTCTTCTTTAAGCTTTTTATCCAGCTTTGTGGGGGAGGAGGGGG
TTGTCTTTACTCCTGTAACAAGGAAATTGAGGGTTCTGAGGCTCCAGGGTCAGCCTGGAA
GTGACGAGAGGCAGGACATCTGGGCCCTAAAATGTTCACTTCAGTCCAAGAAGCAAAATG
GATTACCTTTGGGCATGGGGACAAGGATTAGCCTTCAGCCCTTGGTCTAGAAAGAGCCAG
ACCCAAGATGGGGCATCAGGAGATAGCTGGCACTGGATCAGGCAGAGCAGAGGAGGGCCG
GCTGATGGCGAGGAGGGGAATGGGGCCTAGGACTCTCCCCAGCCCATCTCTGTTTCCACT
CTTCTGGTGTGGCACTCCCTGCTTCTATTTCTGTCTCTCTCCATCTCTCTCACTCTTTGT
CATGCATTTCCTTTCTACTTCATCTTTCAGTCTCTCTTTTCCTCCTTTCTATAGGCTTTC
ACCCCTTCTAGCATTTCCTACTCACCTATCCAACTTAGTGGTAGCCATGAATACTTAGGA
CTCCTGAGATCTGTGCTTCACTGTCCCCATCTGAATATTCGGAGCTGCAATTAGGAAGGG
GTGAGCATCCCTGCTACAAAAGACAGAGTAAGTTTGGTCGGAGTGGCTTGGAGATTCAGT
GGTTGGCTGCCTACCAGCTGGTGAAGATATCCATCATGACATTGTGCGTGAGGATCTGTG
TGAGAGAGTGAGGCGCTCTGTGATTCTGTGACCCTCTTCATGCATGATAATACATCCACA
CATGATGGGCACGGAATTGAGGAAGTAGGCAACCAGGGAAGCCTGCAGCCTAGGGCATCA
CTGGCAATTTCCCCAATGGAGTATTTAACCACAAAGGGAAGAGCAATTAAAGCTAATCGC
TCTGACAGCCTGGGGCCCAGACACACGTACCACTTTCCCTAACTCCCAGTGGTCTCCCCC
AACCTTCATCCTCCCTAATTTGTTTAGTGCACTCTCAAACACTGTTTGCACTTCTCTGAC
CATCTCTTTCTCTCACTTCCTCCCTCTCCCTGGTTCCCTGACTATCTCTAGACCTCTCTG
GAGATGTCTGTCTGCTTCTCACACACATTCCTCTCATTCTCTCTCTGACTTGGGTTCCAT
TCTTGGCTGACTCATACCCATTCTTTTTCCTTTCCGTTTCTTCCACCCCCTCCTCCTCCA
TCCCTTGGCCACTCTTACCCAGAAACTAGCCACTCCCAGCACGCTAAGCCCTAACTGGAC
CCAGGAAGAGAAGCCACCAGAAGCCCCTACCCTCATTAGTCCGCAAAATCCTGTCTCCTT
GTGTTAGAGGAATGAGACCAAGATTTTCTCCCATCTTTCCCCACAGTTTTAAAGAGGAAC
AATCTGAAACCATGGGGCTGGGAAAAGCTGCCAGAAAATCAGGATGGATTTGGGGACAGT
GGCCCTTTCTGTCCACTCAGCTGTCCTGTCGGACTGATGACTTGGAGCCCGCAGTTCAGA
AGACTCCTCATGGGATGCCCCACCCCACAGAGTGGGGGTGTGGTGGGCGGCCGGATGCGT
AGTCCAGGGACGTTTGTGATTTGGAGTGTGCTAGACTATGTGTATAAGTCACATGGGTGT
GTGTCACTGTGTGTGCTGGCGTGCCTTATAGGTGTGCGTGTTTCCCTGTCAGTTTTGACA
CGGATTATATGAAATTAATAAGGGTTTTTACGTTAGATATACATCACTTCTCTACACCCC
CAGCTCCTCCTTCCCTCTGGACAAGCTTTCCGCCAAGCCCACCTCTTCCCCAGGTGCAGT
GAGCTGGGGGTGAGGGCACATGGTACCAGCCGCCCGCGGAACCGAGACAGGGCTGGGCCG
GGAGACCGCCAGCGGAGGCGAGTCCGAAGCCTGAGCGGGGAGGGAGGGGCGGGCGCTGGC
CTGGCCGAGCCGGCTGGGCGGGAAGCAGGCTGCATCCTAATCCACAGGCCCCGGTCCGAC
TCCCAAACTGCCGTTCAGCGTGGAACGGGCTGGCCGGAGCCACGCCGCCTCCAGCACACG
CTCGGCGCTCGGGACGCACCGACCGAGGGACGGACCCCGTGAGGCCTGACACAAAGTGGA
CTCGTCCGGGGTCCCCACACTCCCCGTCTGGCCCCCGGTGTCCCAGATCGTTGCCCCTCC
AAGCCTAGACCCCGAAATCTGCCCCTTCCCCGCGACATGTCTCCTCTCCGCCCCTCTCAC
CGCCTCTGGAGCTGAGCGCTCAGGGCGCGGGCACTCCTGAGTCCCCGGTTCCTAAGCAGC
GTCCGGAACCTCCTCCTCGGCTCCCGCCGCCGCCGCCGCCGCTTCTGCCGGCGCCGGCGC
CTCTTCCGCCCGCGGAGCCGGAGCCCGAGCCCAGCGCCGCTCACTTCACCCGGCTGGCCG
GTGATGTCAGAGCCGGGGAGGGGCTGGGGGCGGAGAATGGCGGGAGGAGGGGGAGGACTT
CTATTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGAGGGGGAGGGAT
GGAGAGGCAGGAGGGGGCGGGGGACCGAGGGGCTGGGGTTCTGGAAGACTCCTAGGATGG
GGGACAGAATTGGGCGGAGGGCTGGAGCGGAGACGGTCTCTTCCCCCTGAACTGCGAAAC
AATTCTCATATTTAATTCTTACCCAGTAGGGCACCCTCCTCCCCTTTTGACCTTTGGATG
ACCACGGTGCCTAGGACCCCTGGGAGGCACAGAGTAGGTTTGGTTTAGGGGGTTGGAAAG
CCTTTGGGGGCTGGATTCTCTTAGCTGCTGGCTTTAATATTTGTAAAAACTTCTTGCCTT
GCCTTAAGGGTCAGGGGCGCAGTGGAAAATGACTGATCAGACTTATCCACATTGGGAGTG
AGGGGTTGGGGCCACATGGGGACTTGAGGAGCCCTGGATCTTCTCTTTCCAGGATGATGC
CTTCAGGCCCTCTTGCGTGCCTCTCACCTTTCCCAAACATGCCCCACTCCTGCCTTCCCC
CTACCATGATGTAATTTTATTTTCTGGGGAGAAAAAGAGCAGCAGTGAGCTCAGCATGCA
AATATAGACAACTTGCAAAGCCACACTTAGCTCCATCTCCTAGCTCTGCCCCTCTGCCCA
GGCCCAATGTGGCAGCTCTCACTTCCCCTCTACCCCAGGGACTTTCCTCCCCCAGATTCT
CAGCCAGACTGAAAAGAGGAAAGGAAGAATTGGAGAAGCATCTGTTTTCACCCCCATCTC
TATAGCCTAAGGGGTCTTGCCTCAGCTCTGGGGCAGGGTTTGGCCCTGGAAAGAAGTCTG
ACCCTGGGTAGGTCCTTCCTGCCAGGAACTCCAGCAGGCCCAGGTTGGGGGATTCCCCTC
AGTGTTTGTGCCACTTCCAGGATCACCCATCTCATCTCAGTTCCTACCTGGCAGAGACTC
CTCCAGAAACCTCAAACGAGCCCCTCCTTTCTTGGGTCTACACCATTCCTAGAAGAGGCC
CAAGTTCCTGCTGCTCTGGGTTTCATAGCATTTCTCTGCTGTTTCCTCTCCCCAGCATTC
CCTGTCACACACTAATCATTTGCCTTTGTATATATCATGTTTGCTCTGTGTTGTAGGGAC
AAAAACTATTTCGTTGACCCATCTTTGAGACTCATGTAGTTTCTAAGTGAAAGGCTCAGG
TCTGGAGGCAACAAGACACAGGGGCCTTGGGCTGCGTGCTAGTTCCACCCATTCCTTGGG
CAAGTTATGCCTGAAAGCCTTAGTGTCCTCACCGGTCAGATCAGGGTGCCAATGTCTATT
TCTGAGGGTTCTTCTGAGATTCAGAAATAGTAAGTCTCTAGGGACTGGCACAGATGGGTG
CTTAAAAAATAGGAGCTATTATTTAGACCGGGGCCTTCCACTGACCTATGCTAGACAGTA
AGCTCCACAATATTATTGTAAGACTAGCTTAGTGCCCATACTACTTATTAAACATTTATT
AAATAGCTACAAGTTGGAATGAATACATAGTTTCTGCTTTCTACACCCCTGCCACATTCT
CTAGGAACACTTCCTGGACTTGTCTGTGGAGAGTGAAAATATATCTAATCTCAGGTCTCA
TCTTTCCGTACTTAGAAATCCTCTAAGTCTCTCAGCAACAACTTTACACCTGATCCATGA
AAAATATAATGTTGGCTTGGCGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGC
TGAGGCAGGTGGATCACCTGAGGTCAGGAGTTCAAGACTAGCCTGACCAACATGGTGAAA
CCCCATCTCTACTAAAACTACAAAAAAGTTAGCTGAGTGTGGTGGTGGGCACCTGTAGTC
CCAGTTACCTGGGAGGCTGAGATAGGAGAATCTCTTGAACCCGGGAGTCGGAGGTTGCAG
TGAACCGAGATCTCACCACTGCACTCCAACCTGGCAACAGAGTGAGACTCCATCTCAAAA
AAAAAAAAAAAAAAGAAAAAAATATATATATATACACACACATATATATGTATATGTATA
TATATATAATGTTTATTATTTATGGGCATCATCTCAAAAATATATATATAATGTTTATTA
TTTATGGGCTTGTTTAGCTATTTGTATATATTATATATATAAAATGTTTATTGTTCATGG
GCATCATCTCAAAACTATATATGTATATGTTTATTATTTATGGGCTTATTTAGCTATTTG
GCCCTCCCATCCCCAACTCCCTAAACTCCTTTTTGCTTACCCCAGCCTGGGCCTATTCTG
GAAAGACTGTGGGTCCTTTCTTTGCCAAGACCTCCAGCAGGGCCCAGGTCTGGGAGATCC
CCATTGTATACAATATCTCCTCTCCATTCCCATGGCCACCACTTGGGTCCATGTTCTCCC
AACATCACTCCAATTATTATAACAGCCACTGATTATGGGTTGGGCCCCTTACCTCTGGCA
TCTCCATCATCTCCCCTCCCCATCCTGCTTATCGCTACCAGATTAAATTTTGCCCTGCCT
CCTCGGCTGGCAGGATTCAATTCAAACAGCTCTACAACCCAGCCCCATTATGCTTACCCA
ACTTCATGGCCACAACTTGATTTTTCTTCTTGTCTCTCTGGGCTCTGTGCCCCCAATATG
ACAAACATATCCTGCCAGTACTTGATGTTTTCCACTGACTGAAATGTCTCCTCCTCAGCT
CCTTTGTCTCCAACCAAATCCCATTCTTCAATTTAAGGCCTAGTAAAGGCTTACTTCCTT
TGTGAAGTCATCAAGCCCACTCTGATCTCTCTTCTGAGTTCATTCTGTTCTTTCCTTTGT
TCTTCCTTTAGGAAACATTTACTAGGGACAACTTTTGAGTGTCAGACCCTGTGGACACAA
AGAAAAAGCTTGGGTTCCTGCCTTCAAGGGGCTCACAGTTGAGTGGGGAAGACAGACACG
TAAATGAAGAACAATAACAGACTGTGCTGAGTACTGGAATGGAAGTGCAGCAGGAACTCA
GAAGAGGTCATCACTGGAGGGGCCACCTCTGGGAAGGCTTCACCAAGGAAGTATAATTGG
AGCTCTGTCTTGATGTTCAAATAAGAGCTGCAGAGAGGGTGCTATCGAGCAGCACATAAT
CACTTAATTACATATTGCTTTGTATTCTTCTTCGATTGTTTAGTATGCTTGTCTTGACTT
CTCCGTGAGGCTAATCAGCTCAAGATCAGGGACAGGCCTAGCACTCTCTGTTCTCCCAGA
GCCTAACAGTGGCCCTGGACAAACACCATGTGTTCAGAAAAGGCTTGTTGACTTGAAGCA
GATTAACAATCCAGGCTTCTCTGGGAAAGCTGCCTGGAGGAACCCCAGTCCCCACTATAA
GAGTCCCCCAGCTCATCCCTAGCAAGGCACCCACATCTGAATTCCCCATCAGTGGCCACC
TCCTCCTGCCATAGGGGTGAGACTTCACCAAAATACACTTGTTCATGCTGCCCCAGATGT
CTTTATTGAGGCCTCTCATTTGACCCAAATACATTAACAAGTGATTGCTGAGATACAGTC
CCAAACACAGTATTCTCCCTTCCTTCTGGCCAAGGACAGGACAGTCAGAAAGATACAGGA
TTAGAGAGAGTGGGGGAAAGCTGTGCATAGATGGAGGGAACAGAACAGAGATGGGGCCCA
TATATATGGCTAGAGGAGAATCACAAGAAAGAGTATGGAGAGTGATGGAAGAGACACATA
ATAGATACAAGTAAGTTATGGGATAAGAAACAGAAGTCAGATAAGAGAGAGCTGGCCTGG
TGTCTAGGGAAAAGTAGCTCATTTGCTCATCAAATGAGGGGGATCAGTGTCTCAGCACCC
AGCATATAGACCCCAGTTAGCTCTATGGCAGAGAATAACCTAGTCTCCCTGGAGGAACTC
AGGGAAGGACAAGGGAAGGCAGGAGAGAGCATGAAAAGACCAGTGGGGCTGAAAGATGGT
TGCCATAGCAACTAGTCATCATCATCATCGTCATCGTCCTCTGTGTTGATCTCGCCCTCC
AGGACATCCTCCAGCCAGTCCTCCAGCTCCTCAGCAGAAGGCAGGTCCTCCTCATCGTCC
ATTTCCATCCATACGCTATCCGCCTAGGAGATGGCACAGGCAGGGACGGAAGCTAAGTCC
AACCCGGGTCTTAGGATCTGTCTTCCCACTCACTGGACTCTGTACATCCTTCCCTACATT
CTCAGTCCCTTCCTTTCATCTGCCAAAGGCCAGGGAAACTGTCCAGGTGAAGGTATGGGT
TATGGGTTAGAATAGTGACAGGTGAGAGTGGGAAGAAAAGTTGGATTGGCAAATAGACCT
TCTCCCTTCAATCTGTCTCCCGTGCTCTTGCCACACTGAACTTCCCTATTATGCCTTTGG
TGCAAAACCACTGGTAGCTCTTCATGGCTTATAAGAATAAAGTTAGCAACTCTTCGGCAT
TCAGGACATTTCTTTCTTTCTTTCTTTTCTAAAAGAGACATGGTCTCACTCTATTGCCCG
GGCTGAAGCGCAGAGGGGCAGTCATGGCTCACTGCAGCCTTGAACACCTGGCCTCAAGTG
ATTCTCCCACCTTGGCCTCCCAAAATGCTGGGATTACAGGCCTGAGCCACTACCCTGGCC
CCAGGGCTTTTCATAACCTGCTTTTCTAGTACCATTCTCAGTGATCTCTAGACTCTCAAC
CATAAAAATCCACCTGCCTTTTCCGGGAACCTGATATTCATTTTCCTGTTTTTAACTTTT
GATCTTGCTTTTTCCTCAGTTTGGAAATGACTTCCCTGAATCATCACTTGTTGAAATCGT
ATACATTGTAGAATCTCCATTTTGAATATCACTTTTTCTTAAACTTTTCTCTGATTCTGT
CAAGCAGAAATCAATGTGATCCTGTGTCTTATTTGTATCGTTATTATAAAGTTTATCAGA
TCTGGCCTTGTAGTTAATGGAACACTTGCCTCTCTAATTAGTCTGAGAATTCTATGAAAG
CAGAGACTGTGGCTCATTCAGTTCAACTTAGCAGTTTTGAAGCACCTACTGTGTGTGCAT
AAGAAGACTTCTGCCCTGAACAAGCTCAAAAATCTACTGGAAGAGACACACATAATACAT
AAATAGCCATTTAAATGTCATGTTCTCAATGGCTATTGAGCCCTGGGAGTGCCAGGGAGG
GAATGATTTTAAATGGGAGATCTGGAAAGACTTCACAGAGGAGAAAGAATTTGAACTGGG
CCTTGAAGGATGAGCCACTGATTCCAACATGTGGGACAGGGCCACATTCAGATCCTAAGT
CTCCCCCTCCATCCAGCCACTAGACTGGGCATGTCTGCGTCCTGTGAGAAGGGCCCAACT
CCTAGTTAGCAGAGAGGAGGAGAGCTAGCTATGCTAGGAAGTAGAGTCGGGGGTCAACCC
GGGATGAGGACAGGAAACTCACATCAGTAACATTGACGACTCCTATTTGTGGGGCTGACA
AGTCGATGTCAAACGTCTTCTCCCAGTATGGGACCAGCTGTAGAGAGATCAAAATACAGC
AACTTAATAGATACTAGGGAGCACATGAATCCAGGAGGATGAGTGTGAGGGTCAGCCCAG
GGATGGAGAGGGGACAGTGCGAACTGGCAGTGGATGGGGACAGGTCCACCTGTGAGGGCA
TCAAGGCAAGGGTAGAACTAAACAACAAAAGAGGAGAAATCCTAAAGGGAGAGAATCGGG
AGGGTCAGCTGGGTGCACTGGCCCCTCTTTTCTGAGGAAAACTGGATAGGAAACCCTGTT
CTGATCCTGGATCAGATCCTTGTGTTCAAGGTCAAGTCACTTCTCTCTGGCCCTCAGATC
TTACATTTCTAAAATAAGGCAAGTATACCTGGTAAGTGCCAATGTTTCTCACGTTTCTCT
TTGTTCTTTCAGTTACTCATTCAACAGCGAGTGCTAGGTGTTGGGAATGTAGCTGAGAAC
AAAATCATCTCCTGAAACAGGGAATCTCTGTGCTATGATTCTATGATTGAGTGTGTATAC
CCATGTGCAGGACTATTGTGCCTCACAACATTGGTTTTCTTTAGGAGTCAGCCCTAGCAC
CTGAGCTACCCATCCAGCCTCTGCTCTGGGAATGTGTGTGATGTCCGTCCTGTTTCCCCT
TGCTCAGGATGCCCTCCATGCCAACAGTGCCCTTAAGCATGCAACACGCATACCCTCCCA
GGGCCCCCCAGCTAGGAGGTGGGGATGGGACCTCTGAAACAAAGCCCTCACTAAGAAGAT
GTCACAGTCCAAGGCCCCACCTTAAGATAGCAGTGCCTGAGCTGTGCCTCTTACCAGGGG
GAAGTCATCAGGGTCAATCCAGATGATGCTAAGATCTGGGTTTTCAGTGTTATCTTGGGC
CACAGCCTTGAGAGTCTCTAAGAACTCGAAACCATCTTGGAGGGAACACAAGTACAAGGT
ATGAGGTGTGTAGAGAGGAAAGGGACCCAGGTGAAACAGGAGTGCAGAGCTACCTCCCTG
CTCCCCAAGCTTCACATGTCTAGCCCTAGGCTGTTTGCAAACTCCCAGGAAAGCCTCCTA
GTGAGGCCCATGCTCCAATAAACACACCCACCTCCCCCTGCCTTCCCTCCAGTCCAACCC
GGTATTCCTCCCTCACCAGGATCAGCTTCCTCTGCGAAGGCCACAATGTGGATTCCATCC
ATATCATCCTCCTGTCAGGGGGTAAGAAGGAGAACAGGGTTTTGGAGAAGACCTTACTAT
ACTCCCTGAAGTTGAGGAGCCCAGAACAGATCCTAGATGTTCATTGAACCTCAATTTTGT
GGAAATCCAGCTTCAGGACCAGATATATTCTTTCGTTTTTTGGGGTTTGTTTTTTTTTGT
TTTTGAGACAGAGTTTCACTCTGTCCCCCAGGGTAGAGTGCAATGGCGCGATCTCGGCTC
ACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTG
GGATTACAGCCATGCGCCACCACACCTGGCTAATTTTGTATTTTTAGTACAACATTGTTT
CACCTTGTTGATCGGGCTGGTCTCAAACTCCTGACCTCAGATGATCTGCCTGCCTCAGCC
TCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCGCCTGGCCATATATATTCTTGTGA
TGGTGACCTTTTTCCAAGTGACACTCCTTTCAGCTCCAAGGCCCCACACTTCCTCTGATA
ATCCCTTTATCCCCAGGCTTGAGGCTCTTCCCTTGTCATCTTCAATTATGTCTGTCTCCC
ATTTCCTCACACATTCTTCAGTGTAGAAATCTTTCAGTTGCTGCTAGTGCACTGTTTTTT
CTTTTTTCTTTTTTTTTGAGACGGAGTCTCACTCTGTCCCCCAGGCTGGTGTGCAGTGGC
GGATCACTGCAAGCTCCGCCTCCTGGGTTCAAGCCATTCTCCTGCCTCAGCCTCCCAAGT
AGCTGGGACTACAGGCGCCCGCCACCACACCCTGCTATTTTTTTTGTATTTTCAGTAGAG
ATGGGGTTTCACTGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCACCCAC
CTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCACACCCAGCTGGTCAGTGC
ACTGTTTTTTCTAAAAATGGGCCTGAGGAGCAGTAGGGTGGGGTTTTTCTAGGACTTGAG
TCTTCTGGCACCCATGCTTCCCTGAGGGCTTGACCCTGGCCAGGGGCACTCACCCAGGTC
TCATACATACTCTCCGGCTTCAGTTTCCTCAGGGTTGATCTAGAAGAGACAGACAGAGTG
TCATTACTCAGTGGGTTAGAAGGATGCCCCCTCCAGAGGGTCCTGTAGCAAAGGCTGCCT
CTAGGTCAGGCCCAGGGCACAGACAGCTTGTAGCCTACAACAAAGCCATCTGGCAAGGCC
TCAACTCTGGGCACCAGGCCCGGCTCATTGCATGGTTAAAGCGGTGGGAGAGGGGAGGGT
GGGCAAAGGGACTGGAAGAGAGACTGGGGGAGAAAGGCAAGAACTGGACATCAGGATATT
CATTAATTTATTCATTCATTCACTCACTCACTATGATTGAGTGCCCGATATGTTCTAAGC
ACTATGCTAGGTGCTGGGTACATACAGTTGAACCAGGCAAGCATGTTCCTGCCTTGATGA
AGGGAGCCAGTAGTATGGGAGAGTAAGTACTGTATATACTGCAAGGGAGCTTGCAGTGAT
CCACCACTGCACGCTAGCCTGGGGGACAGAGTGATTGGATATTTCCAGCTGTGGACTACT
ATGAAGGAAGGGAATTATGTGTGAGTGCCCGGCAGGATTATTCAACCTCAGCACTATTGC
CATTTGGAGCCAGATAATTCTTTGTAGTAGGGGGCTGTCCTGCGCACTGTAGAATGTTTA
GCAGTATCCCTGGGCTCTAGCCACTAAATACTAGTAGCACTCTGCACAACCAAAAATGTG
TCTAGACATTGCCAAACATCCTTTGGAGGGCAAAAACCTATGCCCACCTCGCCACGCCTT
CCCACCTTGTAGAGAACCATTGGTGTACGATATTGTATTAGAAAGAACATGGGGCCAGGC
GCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGACCGAGGCAGGCGCATCACTTGA
GGTCAGGAGTTTGAGACCAGCCAGGCCAACGTGGTGAAACCCCATCTCTACTAAAAATAC
AAAAATTAGCCAGGTGTGGTGGCGTGCCTGTAATTCCAGCTACCTGGGAGGCTGAGGAAG
GAGAATCGCTTGAACCTGGGAGGCGGAGGCTGCAGTGAGCCAAGATGGCGCCACTGTGCT
CCAGCCTAGGGGATAGAGTAAGACTCGGTCTCGGAAGAAAAAAAAAAAAAGAAGAAGAAG
AAAAAAAGAACAAACATGGGACACATCAGGGTTAAAATCAGGGTTAAAAGCTCTGACACT
TATTACCTGTAGAAACTTTCACTGAGGTTAAAAGGACTTAATATAATCATAGAGATGGAA
AGTACCTTGCAGTTCCTGCCCCACCACAGGCAGTCAACACTCATTTGTTGACAGAGATTA
TTTAAGTCTCAATCAACCTCACACTGAATTATACACACTTATGAAGGACCCTCTCGGTGT
AGGGCTCAGGGCTAAGTAGTGGGGTATAAAATATTGTGCAAAATTGTCAGTGTATCAGAG
AGCACTGGTGCCCAAAGTGTATTCATCTCCAGGCAAGATTGGCTTCCCGGTTGGCTAAGC
TTTCCCCAGCCCATCTCACACAGTGTGTTCTAGCCCAAGGAGGAGCCGACCCCGCTGAGA
GGGTTGCCCTTGGTCCCCACCTCCTGTGCTCCTCCACGAAGTTGACAATCTCCTCTTCGC
TATTGGGCTTGTCTGGGATGGTCACAGGCTCTTCCATGAAGGCCTCGTAGAAATCAATCT
CATTCAGCTTCAGGGTCAGCTTCTTTGCCACCTTTGGGAGAGGGGGTAGGAGGGGAGTGG
AGCAGGAGACACAGGGTCATGTCGAGAAGCAGTATAATGGGGGAACAAATATTAGGAAGG
GAGTCAGAAAGCCGGGATCCTTGTCACTGCCACTGTGACACCTGACAAGTGTCTTAACTT
GCCTGGGGTTGGGTTTAACATGAGAGGGGTGTTAGATCATCTAAAGCCCCTCTTCAGCTC
TAAATCTATGGAGTGGGAGGAGCCGGGGGGGGGGGCAGGTAGGGAGTGCCAGCACGTAGG
AAGGGACCAGGTCAGCCATCGATTCTGGGAGAGGAAACTGGAGGACAGCTTCAGGACATG
AGGCAGAACCAATACAGCTGCGGGGAGGAGAACCTTGCTGTCGAAGGTGGCGAAGAAGGG
GATGTAGGGATGAAACTCCTCAGCTGCATCCTCGAAGGCTTTGTAATCTGGGGGGTGGAA
TGCAGAGTCAGTCTCTGGGGAAACCAGGGTCTGCCCGGGAATCATCCCCCACTATCGTCC
CCAATTCTTTGCAGGCAGGGTTCATTTTGAGACCCACCCCTTCTAGTTCTTCGAGAGTGA
GGGGAAGGTGGAATACTGGAGGTGCTTGTCTGGGAACCCCCAGAGTACAGGGAGGTCAGA
GCTGTTGATGGTGCTGACCACGGCTGGAGGAAGAGGTGGGAAGTGCAGAGGTAGAGGCTG
AGACACTGGGTGATGTGGGGAGGTGGGAGGACAGGTGAGATGGGGATCCAGAGAGGGGCA
CAGTGGAGTCTGAGGGTTACCCACGCTCTGAGTCTTTGCTCTTGAAGTAGCCAATGAGTT
TGATCTCATCCTCAATATTCTCAAACGCCTGCAGCTCTCGTTCACCTTCAATCAATTCCA
CAGGGTCCTCTAGGACCTGAAAGAGGAGGACATTGCAGGAAGAGAGTTTCTATCCTCAAG
TAGAACCAGAAAGGGACCTAGGGAAAAGAAGGCTGGGGAACTGGAGGAGGGGGCTAGATG
TTGACAGTGTGTGGGTGTGTGTGTGGGGGATTGCATGTGCGTGTGTGTGTATAGTGTGTG
ATGTGTGCAGTGTGTGGTGTGCATGTGTGGTGTGTGTGTGCATGTGATATATATGTATGG
TGGGTGTGTGGTATGTATATGATGTGTGTGTGATGTGTGTGGATGGTATGAGTGTGGTGT
GCATGTGGTGCATATGTGTAGTGTTCGGTATGTAGGTGATGTGTGGCCTACTGTGTACAT
GTGTGGCATGTGTGTGATGTGTGTGAATGTGTGGTGTGTGTACGTGTGGAGTGTGCATGT
GGTGTGTGCATGTGTGTAGTGTGTGCATGTGTGGTGTGCAGGTATGTATGTGCATGTGGT
GTGTGTGTGCGCATGTACGGTGTGTGTGCATGTGATATATCTGGTGGGTGTGTGGCATGT
ATATGTTGTGTGTGGTGTGTATGGATGGGTGTGTGTGGTGTGTGTTGTGTGTGTGGTGTG
CATGTGGTGCATATGCATAGTGTGTGGTATCTAGGTGATGTGTGGCCTATTGTGTGCATG
TGTGGCATATGTGTGATGTGTGTGCATGTGTGTAGTGTGTGTGTACATGTAAAGAGTGTG
TGGTGTGTGCATTTGCGTGGCATGGATGTGGTGTGTGTGCATGTGTGGTGTGTGTTTGTT
GTGTATCGTCATGTGGTGTGTGATGTGTGTGGAGTGTGTGGNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNCCTGGATTAAGCCTAGGGGGCTAGCGTGGCCCCAGAGCT
TTCTAGGGAGTAGCTGGGGGATCAGGTAGGGTGAGGGGAGGGAATAGAGAGGTGTAGATT
CTAGCAGTATTTCTCCCCTTCTCTGACCGCAACGACTAGAGATGAGTATTCATGCCACCC
CCTCTGAGCACTCTAGTAGCTGGTTCCCAGTCAAGCTCTTTAATTGCTATTACTGACCAG
ATGACTTCATTATTACTGACCACCCCTCCCCCATGCATGTCCAGAATCCCGTCTCAAGCC
TGTGCTGCCCCCTAGTGGCTGACTGCTCTAACAACCATGGCTCTGGATGGGAGGGGTTGG
AAGCGGAGTTTGCAGAGGTCTGGCCAGCCCCGCCTGTATTCCCCGACTCCCCTTCCCTCC
AGCACCTAGCCATGTTTTAAGGTAAGTATAAAGAAGGCCTCCCCCACCTCTTTCTGGGAT
TTGAGCATGGAACTTCATAAGGAATAGAGAGGCAGAGTCTCCGAGCCATAACCCTCCCAA
CCTCATATTTTCTCACCCCCTCTTTTAGAATAGACATAAATCTGAGAGATTCCCAAGCCC
CTCGGATCCCAAGGACTGCCTGACAGGTCCTCCGCCCTAAGCCTCCCCTTGTCTCAATGC
CACCTTCCCCTCCCCTGCCCTCCCCTCTCTTACCTAGTTTCTTGGCCACAGCTGCATCCT
TCTCAGAGTCTACCAGCCCGAAGCCAACACCCTTGTCTTCTAGGACTTGGGCTGCTAACT
GGAGGGAAGGATTATGATTAAAATTAGCCCCTGGAATTTTTATTATCCCCTATTCTCCCT
CTCATGCTTTCAAGTTGGGTCAGTTGAGGTGCGGGAGATATAAGAGTTGACCTTGACCCT
TTGCTAAGATCCAGAATATCCCCCAAATTCCCTACAGCCACACAGTTCTGTTTTTGGCTC
AACTTAGTTCATGAATATTGATTGCTCATTTGCAATGTGCTTATTATGTTGGACTTGAAG
ACACTGCACTCAATACTTCCCAGTGCCTAAGAGGTACTGAGGAGTCTGGCTTCAGAGTGA
CTGAGGGCCCCTTCCCTCCTTCAGGGTTGAGTCCTGCATTCCATCCTGCTCAAGTCACAC
CTGGAGGTCCCTGTCCCTGGTCAAGGGCCAAGCTCAGTGTGGGGTTGATCTTGGAAGTCC
CTGAGATTCTTCAGAGTGACTCCCAATGGGAAGAATTTTGGAGGGTGGGAGGGTAGTGGT
GGGTCTGGTCATGTTGTTGAGGAGTTGGGGAAGGCCAGAGAGCTGAGATAAGAGGTCACC
ATTTGTTACCCCCCAGAGGGAGAGAGACTGACAGCGACCGGACAGTTCTCCCCATCAGGG
CCCAACTTTCCCCTTTCGCACTCTACTTCAGCCTGTCCTTAGGCTGTGGACAGTCACACC
TGGAGGTCCCTGCCCCCATAAGCCTTCCAGCTTAGCGTTCAACCCTGATTTTCTCTGCTG
TGGGCACAGCTTGCAGCTCTACCCCCACTCAGCACAGACTCAGGTACTGTGATTCTCAGA
GGGGTGGGGAAGGGAGGCGGTTGGCAGGTGGATGGCCAGGGATACTGAGCACTCAGGATA
AAAATACTCGGCTCATTAATCAGATGGCAGGTTCTAGCACCCAGCAGGGGTGCACAAAAT
GAGAGCCTGTGGTTCTGGTGTCTCACCCTGAAATGCTCCAAGCTCTGGACAAGCTGAGGC
CAGAGAAGGGGCCACAGGAGCTTGGACAAGAAAACTCACATCCCATTTCCTAAAGGTGTG
TGTGTATGAACACATTCCCAAACATAGGTTTTTTTTCTTTTCTTATGATAACTTCTTTCT
CCTTTGGGCCTGAAGTCATTTTGGAGGTGAGGAGACTTTTCCCACAAAAAGAAGATTGGG
GAAGACATTCTGACACCTCCTGCAACCATAAGAATTTTCCAGTGAGGGCATCCAGCTTAT
CCAATGGAGACAAATGGGGAATTAGGGAGGGGGAAGGAAGAGAGAGGGGACTGGGAGTCC
AATGGGAGGCATGATCTCTAGGAGATATTTAAACATGGCATGCAAGTATCATAACATTTA
CATTTACACTCAGTTTGGATCTCTTTGGGGTGCAGCCCCTGAAGTATGTGGAGAGGACGT
GTTCTGGCTAAGCAGATGGGTGGGGTAGGGGAGTGCAATATACACTGCTGTTCTCCCCTG
GCCCTCCAAGTACCTCCCTTTTTCACCCTCAGTGTCCTAGCCAAACCTAAGTCAAATACT
ACCAGCCTCCTATAGCAGGGAGGGGAGCTCTTCCTGCAGCACCCCTGCTAAAGGTTTCCT
GACGCTGATAGTACTTTTGGGTTCCTGAGACTCTGTTTCTCATTTGACTAAAGCCACATG
CCACTTGCATCCTGTTGGTCAGGACAGGGTTCCTACCACACTGCCCCTCACCCCCAGATC
CCATCCTCAAAGAGCTACATGGGTGTAGGATAGGGGATTCCGGAGAGGGGCTAGACATGC
TCTGCAGGCCTGCAGTGCCCCCAACTCACCTCCAGGATCAGCTCCTCCATCTCAAATTGT
CTTTGTGAGGCCTTGTCATCCTCGGGGGGTTCATGGTAGAGGAGTGCCAGCACCTCATAC
TTCTTGAACACATTCTTGTAGTTCTTTGCATTGACATTGATCACACGGTCCACACCATCG
TACTCAGGGAAGTCCAGCCCTTCCTGCCCCTGTACCCCTGACTTGGGTGTCCCTAGCACC
AGCAGCAACAGCAGTGCCAGCCGCAGACCCGGCACAGCTCTGGGCCCCATCCTGTCTGTA
GCACTCATGGAGGTAGTGGGATCTGGGTTGGCTCTCCTGGTCCAGAAGAGGTTAGCTGGG
GTAGGGAGGGGCCCCTGGGTCCCAGATTCTGAGTTAGGGGCTCAAGTGGGAGGGGGGATT
GGGGAATGGCCCAGAGCAGTGGACAGAGGGCACTGCTGGGTCCTGGAGAAACTGTCGACA
GAGCCAAGGGAAAAAGGGTCAGGTGGAGGAATAGGAGCAGGGGGCGGGGAGGGAACCGGA
GCTGCCCCCTGAAATTGGCACCCCTCAGTCCCCACCTGGTCCTGTCTAAATATGTCTCCA
TGGTTGGCAGGAGAGACGGATAACCTTCTGAGGCCAGGACAGCTCCATGCGGGCCGGAAT
CCTCCCACCTCCTACACTTCTACCCCAGGCTCCCAGGGGCTCCTTCCCTCCCCCTCCTCC
AGTGTCCAGGGCACCTCAGCCCCGGTCCCCACACTGGCCTAAGAGCTCATCGCCATATTA
AGAAAGGAAAAGGAGAGATGCCGGAGCTAAAAATAAGACCAGATGAGTCGGAGGTAAATG
AAGCTGGGGCTGGGGGAGGGGAGGTATAAGGGTAATTAGGGTGGGCCGAGGGTGGGGCAA
GGGTAATTAGAAGTTAAATGCAGTGGAGAGGAGGAGCTAACTGGGTCAGAGGCTAAATTG
ATAATATAGGACAAAAGGGGGACAAATGTGGTATTGGCTCTATGTCCTAAAGCCTGGGAA
TCTTCTGTAGGTGAAGTCTGATTCTGATTCTTTGATACTATGTAGGAGAGTGGGGCGATA
AAAGTGCAAGCCAGGCTGCAGGAAAGAGACCCCCTCCACTTTCTTTTAAAGAACCAGGAC
CAAGGATGAGGTCATTCTCTGAATAAAAGATGGAGCCGCGTCCAAGACTGGCAACCTGGC
TCAGCTCCAGCCAGTTTCCTTTGCTTCACTCAGCACTCCTAACTTGGGAATGCAGGGAAG
GACAGGGCTGGCCCAGATCCTGTCCTGTAGAGATGTGGGTTTGGGGTTTCTCTGCCTATA
AAGCCCACAATGAGAAGGGGTCTGTCCTTTGGTTGCCACCTGTGTGTGCACTCCCTACCC
TGATCCTATGGGACTCGGTTTTCTGGGGCACAGTGGGAAGGGAGGTTTTCCCAGGCTGCA
TGCTTCCAAGGAGAGTGAATAGCTACTATTTATTCCCATGTCTTTGACAAGACAAAGAGG
ATCAGGTATTGACACCAGGGCAAAAAAAAATTAACATTAGGCAAGCATGAAGAGGTGAAC
CCTGTGCCCTGAACCAAGACTGATGATTAATTCTGTGCACCCGAGATCCAAAGCAGAGAT
GGGCGGGTAGGGGCTTAAACTTCTGGATCCAGCTTGGGGGGTGAGGACAGAGTAGTGAGT
TTAACTCTGGATACGTAGGAAGGAAGGATCCTCTTCATGGCCCTCCAGGGTTCTTACTAT
GCACAGGTAAACTGAGGCATGAGGGAGACCATAGAGGGTCAGATCAAAGTCACATGCTGC
CACTGCACCCTGAGGTATCTCTGATTCTAGAGGGACAGTGGTGTTTTTTTTGTTTTGTTT
TGCATCCAGGGAGGGTCATGTAATTATGTTAGCAGAATAACTTTTCCACATGTCTGTGTG
GTGGACCTTACACAGCTGAACACGGAAGGCCACAGAAAATCTCAAAAGCATGGCAGGAGT
GAGGCCAAGAGGGACAGCTGTCACTGTAGCAGGAGAGGTTGGAGCTAGCCTAAGCACAGC
ACGTTGGAGCTGAAGAGACCTCAGAAGCCCATATCCTGGTCTCCCTGAAGAGTGGCTAAC
GTGGGAAAGCCCCAAGGCCAGAGCAAAGGCAGCCAGGTGAGATGGGGAGGCCTGCCCAGA
AGCAGATGATCTAGGTGATGTCCAGCCCTGATTTCTCACTTCTGCATTCCAGGGGAGGCG
GGAGACACTGGGACAGAGACGCTGGAGCATAAAACTTGTTCCATCTTGAATCTGACCTTT
TGTACCCCCAAGAGTATGAGATGGGACTCTGGTGGCGAGTCTGTTCCATCTCCTGGTCCT
TTCCTACAGCTACCGGACATTGCCATCCATCCCGTTCCCTCTCGTTGCCCTCTCTGGCTC
CAGTCCCACCCTTCCCCTTTCCAGCGCCCGCCCCCACTGCTCTCTCTTGATGCTTCACTC
TGTCTACTTTCTACTCAGTCTCCTTCCCTTCAGGCCCTTGGACTTGAGAAGCCTCAGCCA
CTGGTATCAAATGACCGTGAGTTGGGGCCTCTGTATTTTTAACCCACCAGACACCTGAAG
CTCCTGCTACTGAAACCTGAGGAGCTGGCCCCTCTGTGCTCCTGCTTCCCACCTCACTCA
CATATACCCTGGCCCACTGATCTTCCAGGGTCTGGTTCAGCGATGTCAGCAATTGGGGAA
GGACCCCAGGCTGATATAGCACTGTTCCTAGGAGACCTTGTGATGGAAGAGGGAGGAGAA
GAGGGAGAGAGACCTCTGAGGAGGGGCCTGATGTAGGGAAAATGGCGGGCGATACTCACG
ATGGCCTTCTCTTTGCTAGCTCATGGCCTCTCATCCTCCAGACCCACCCCGGGTCCTTCC
CCATCACTAGCCTATTTTTTTTGTTTGCTTTGTTTTGTTTTTGTGTATTTTTGGCCCAGC
CCTCACTGAAAGACTAGTCTGAAAGTGATTAAGGGCCCACGTTCTGAAAATGGACAGACC
TTGGTTTCTTCTTGGGTAACATGGAGTGGGTGGTAGGGAAACATTTATGTGACTTTCTTG
ATGGTGTGTATATAAAACCCTCGTCCCAGTGTTAGGTGTAGTGTGCAGACACCTAGTACA
TATGTGTTTTGTTGTGGAAATAGCTGATGGTGTTCCCCTAGCTTTCGTTAGCATTTCTCT
TCCACCCTGTACACATTTGGGAACAGCCAATGCTCTACTCTGAAAGAGGCCTGAGAATGA
ACTGACCCACATGGCACAGTGGAGGGGCTCACAGAGCAAAAGTGAATGAGCGGGTGAAGG
GGAAGGAAGAAATGCTGAGACGAAGGTGGGCAGGAGAGAAAGGCCCTCCACGAGTTTTCA
CTCATCTGAGAATGCACCTGGGCCCAGGCACAGAGGCCAGGCTCTTGGGAAAGTCCATCA
CCCCGTGCAGAGCAGGGGCGGCTGCTTCACAGTAAAGGCCACAGGGATTCAGAAAGTCTT
GTTACAGCCTCTATCTCAAGGCTACACCAGAGAAAACAGGCCGAGGGCCAGAATGGGGTT
GAGGAGCCCTGATGACCGAGGGTAGAGGGCAGGGACCACCAGTATGCCTGGAGACTGTCC
TTCCTACCTGTCCCTTTCTCAGATGAGGGACAACACTCAGCACATGGCCATTCCCAAGTC
ATTTAACCTCTCTGGACTTCAGGCTTTTCACTGATGCAATCTGATCTCTTCTAGCACCAC
AGCGCTGTGGTCTGCAAGCTGGTCTCAGGAACTGCAAGGTGGGGTCAGATGACTCCACCC
CACCTACCCCCTGTGCGGATGCTGTGGACCCTCTTCCCACGTGTGACTTAGCTGCTCCTC
TCTCCCCCACCTTCCATTTCTCTGATCTCAGCTGGAATTTTGAGGCAGTCATTTGCCCTG
TCCTTGCTGTCCAGTGGCTCGGAGAGTGACTTTAAAGGGCAAGGATGCTTGATACTGATC
CTATCCCAGCCTTGACTCTGGTCCTTAAAACACTTCCCCAGCCTGGTCATCATGAAGACC
TGTGGAGGGAGCTTCACAGTAATCCCCACTCCCCCAAGATCAGATTTGACACATCCAGCT
GGTGAGGGCTTTTCCAGACATTTACTGTCTAGACTGGCTACGGGATTCAGCAGGACCATG
CCCCTCCCTGCGGGGCTCCAGCTAGATGCAGGCTGGGCTTCCCTTCAGCCCACCTCATCC
TCTGCCCATGATTCCCTCAAGCCAGCCCAGGATTGCCCATCTTTCTCATCCAAGATAATT
CATCCTAGTGTCTCAGATGTTGTGTCAAACTTATAATCTCTGGCCCCATCCCAGCTCTCA
CAACACCCCTGTGTCACATGAAGCTCTTCATCTGCTGAGTTTAGTAGTACGTCTCCCTTT
CCACCCAGCCTGTGGAAGAGAAGAGGCCAGCGTGAACTGGGAGAAGGAATTAGAGGCATC
CAGGGGAGACAGGCAGAAGGGAAAGCAGGGACAAGGTTGGAGGTGGGAGGTCTGGAACAC
AGGGCACTGAGGGTCAGATGGAGCAGAGGGGTGCAGCCAAGGGGTAGAGAGGTCTCGGCT
CCAGGCGCAGTCAAGGCTGGCAGCGAGGAGGGGAGAAAGTCAGTGGTGGGTCTGGAGGGA
CTAGGTGGGATGGGAGAGCTAGTGAGGGGGCTGGTGACCACTCAGTCAGAGCGGGGCCCA
GGGGAGCCTCACCATCCGGGTGCTGACGGATGAGGAGTTTTCTGATTTCATCATAGACGA
AGATGAGAATACTGTAGGGAATGGCACAGAGCCACCAGGTTATCCTGTAGAGAGCAAGAG
CCAGTCAGCATGGCAGGAGAGAGAGATGCCAGAGGACAGGTGCAGAGGGCAATGCACAGG
AATTGCACGTTTCATTGCTTGTGTCTACTGTGTGCGTGGGACTGTGCTGGGTGCTGGAGA
CAGTGCAGTTGAATAAGATCTGGTTGATCCCTTTTTTTTTTTTTTTTTTTTTTGCGACAG
AGTCTTGTTCTGTTGCCCAGGCTGGAGTGCAATCTCGGCTCACTGCAACCTCTGCCTCCC
GGATTTAAGCGATTCTCATGCCTTAGCCTCCTGAGTAGCTGAGATTACAGGTGTGCACCA
CCACGCCCAGCTAATTTTTTGCAATTTTTTTTTTTTTTTTTGAGACGGAGTCTCACTCTG
TCACCCAGGCTGGAGTGCAGTGGCTTGATCTCGGCTCACTGCAAACTCTGCCTCCCAGGT
TCAAGTGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGCGCCTTCCACCAT
GCCCGGCTAATTTTTGTATTTTTAGTAGAGGCGGGGTTTCACTGTGTTGGTCAGGATGGT
CTCGAACTCCAGACCTTGTGATCCGCCTGCCTCCACCTCCCAGAGTGCTGGGATTATAAG
TGTGAGCCACCATGCCTGGCCAAATTTTGTATTTTTAGGAGAGATGGGGTTTCGCCATGT
TGCCCAGACCGGTCTTGAACTCTTGAGCTCAGGCAGTCCACCCGCCTCAGCCTCCCAAAG
TGCTAGGATTATAGGCATGAGCCATCGTGCCCGGCCTGAGCCCTACCTTTGAGGAGGTCA
AATCCTGTGGGATTAGTGATACGGGAGTGGAGAGGAGAGGCACGAGACAGAAACATAAAG
AGCCAGTGATAGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAGCCTG
ACCAACATGAAGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCTGGGTGTGGTGACG
CGTGCCTGTAATCCCAGCTACTCAGGAGACTGAGGCAGGAGAATTGCTTGAACCAGCGGG
GCGGAGTTTGCAGTGAGCCGAGATTGCGCTACTGCACTCCAGCCTGGGCAACAGAGTGAC
ACTCCATCTCAAAAAAAAAAAAAAAAAGCATTATCAATAAGATATTTTACATTCTTCTTC
TCAACCTAAGTCTTGGAAATTCAGTGAATATTTTTCACTGACAGAATGTTTGAACTCAGA
TACAAAATTATTTTCAACAGTTGAAGGGGAACGTAGTCCAACCAAAATAATGAAGTTATA
ATATAGAAAAACATTACTTTAGTTTTTGACTTTGATTAAAATTAAATAAAATTACCAATT
TACTTCCCCAGCCTCCCTAGTCTCATATGTCAAAAGCACAATAGTTGTATATGGATAGTG
GCCACTGTATTGGACAGTACAAGCCTAGGCCATGGCTCATTCCACACACACACAAATATA
AACATTTCTACACAAACAGCCACCCCACCCCTTCATTCAACAAACAATTGTTTTATGTAC
TCTGTGTCTGTGTTAGGTATTGGGGAAATAAAAATGATAACATGTTGGTCTCAAGTAGCT
CTCAAGGAGCTCAGGGGAATCAGAGAAAAGAGGGTGAACACACACACACACAGAATACAG
AATCGCAAGATTAGGTGCTAAGTTTTATGGTTAATGTGTACACAGAGTGTTTGAAAGCAC
AGATAATACCAACCACATTTGTTATTATGTCTATAATGGCATTAATAACAGCAAGAATAA
AGCTACTAGTAACAAGGCATCTACCATGACCTAAGCATGCTTGGTGCTTTATGCCCATTT
CTACGTGTAAATCTCACAACACTCTGCAAGGTCTATCCCTGGAGTGTATTATTGAGACTT
TGCAGGTGTAGCTGAGGCTCAGAATGGTTCCATACTTGTCCAAGGCCACAGAATAATACA
TAGTAGAGTTGAGATTTCCACCTTGGATTGTGAGTGTCTAAGGCCAGTGCCAATGTCTCC
TATTAAACATTAATTGAGTGCCTACATTGTATAAAACATCGTGTAAAACATTACAAGGGA
TGGAAAGGTGAGCAGAGTAGAGACATGCATAGAAATGTGTTGGAAGAAGGCCGGATGTGG
TGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCACAGGCAGGTGGATCACCTGAGGTC
AGGAGTTCGAGACCATCCTGGCCAACATGGTGAAACCACGTCTCTACTAAAAATACAAAA
AATTAGCCCGGCATGGTGGCGGGTGCCTGTAATCCCAGCTGCTTGGAAGGCTGAAGCAGG
AGAATCACTTGAACCTGGGAGGCAGAGGTTGCAGTAAGCCGAGAATGCGCCATTTCACTC
CAGCCTGGGCAGTAAGAGCAAAACTCCATCTCAAAATAAAAAATAAAATAAAATAAAGAA
ATGTGTTGGAAGAATACATACTAAATCCTTAACTGAGGCTACCTATGCAAGTTGGGTTGG
GTAATGGGGATGGGAGTGGAATGGAACATTTGCTTTTTTCTCTGTACATTTTTAAATATA
AATTTTTCCACATCAAGCATATACTAATGTTAATGCAAAGCAAAACAAAGCAAAAACCTG
GAGTTGAACAAGACAAGGCACCAGACAATAAGAATTTCAGTAGGCACGATCACATACATA
TACATTAAAACATATTTGCATAAGTACAACAGAATTAGCTAAGCATAGATTAGGCTATTT
TTATGGTTACTTCAGCTCCAAGCAATATGTATCCTTGGACAACTACAGCACACATCATCA
CGAAAAAGATTTCACTCTGTTAAACACTGGTAAGTCTGCTAAATTTGTGTGTCTAGTGGG
TTGTGATCATTTGGCACAGTCTCTAATATCTCCCTAAATAAGATCCACTTATCAGAGCAC
AGATGACTCTCCTTGTATCACTGAGTGTACATGTAGCTCCATGTATCCAGGCAGCTCCTG
GCTCATGACAATCCTAGTGAAACACACCCTTCCTCTGTATGCTCCCCCGTGCCTGCACAT
CCCCTGCTTGCATCCCTTCCCTTACTCACTTGAGTGGGTACATTCGCAGGGCCACGTCCA
TGCCTGGAGTGTAGGACAGAAATGCAGCCAAGAGTGTCTCCTCCAGGATCCCAAATATTA
AGACTTTGTTTCTGGGAAGAAACATTCATGGGTGTGGCGGGGAGGGAGAAGAAAAGGCAG
GGGGAAATGGCATGTCCTGGTGTGTGGGGCTTGGGAGAGTGCTGGGCTGTTTTGTGAGAT
GTTCACCTCATGCCCTGCTGGAAAAGTGAGTTGCGGCGAGTCTTGGAGATGATGAGATCC
GCCCACTGCACAACCACGATGGTGACAAAAAAGGCCGTTTGGCATGTGAACTCCACAACT
TTTCGTTGCTCATAGGTCTAGAGACAGCAGGGAGAGAGGAAACAGTGTCAGAAGGGGATT
CTGTACACCCTAAAGGCTTCTTTCCTCTCCCACCTTCCAGGACCCCTGGGCTGAGTCAGG
TCCTCATTCTTTTTTTTTTTTTTTTTGAGACTAAGTCTCGCTCTTGTTGCCTAGGCTGGA
GTGCAATGGTGTGGTCTCTGCTTACTGCAACCTCCGCCTCTGGGGTTCAAGCAATTCTCC
TGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCTGCCACCACACCCAGCTAATTTT
TGTGTATTTTTAGTAGAGACGGGGTTTCACCATATTGGCCAGACTGGTCTCGAACTCCTG
ACCTCAGGCGATCTGACCGCCTCTGCTTCCCAAAGTGCTGGGAATACAGGCGTGACTCAC
TGTGCCCGGCCAGGTCCTCACTCTTTAGACCCCACAGCACTTCACAGATGTCTCTGTTTT
AGCGCTTTTCATGTTGTATCATGATTTGTTTATGTTTTCCTTGCCTGACTGAGAGCTTCT
CAAGAACAAGCACTTGCCTTATTTAGCTTTATGTCCTCTCCCTGTGCTTAGTTCGGTGGA
TGGCATGTAGCATGGCTCAATAAATATGGATTGAATTAATAAGAAGGATAGGGTAAGAGA
AGAAGGTGGAGTTAGAAAGGAAGGCAGGCTGGGCGTGTGGTGGCTCATGCCTGTAATCCC
AGCACTTTGGGAGGCCGAGGTGGGCAGATCACGAGGTCAGGAGATCAAGACCATCCTGGC
TAACACAATGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGG
GTGCCTGTAGTCCCAGCTGCTCGGGAGGCTGAGGCGAGAGAATGGTGTGAACCCGGGAGG
CGGAGCTTGTAGTGAGCCGAGATCATGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGA
CTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGAAGAAGGCAG
AGTCAGGGGATATAGGTCAGAAAGAAAGGATGGTGGGGCCAGAGGACAATGTGAGTACAG
GGGGGAAAGAAATACCCCAAAGAGTGGTATCAGATAGGAGACATTCATTCATTCATTTGT
TCTTTCATTCACACTTTACACTTAAGGAACTTAGAGTCTAGTGGGGAAAATAATTATGCT
AACCATGTCAGCGCAATAGACAGGTTATGAGAGAGAGACTGCAGAGGGCTATGGGAACAC
AGAAGGGGTGCATCTAAATTAGACTGGAGAGAAAAAGCTTCTGTTTTAAAAACTAAAGCA
GCATGTTTATCAACAACTCGTAGATCCAATAAATTTGAAAACAGGTAGGACCGCACAATA
ATGAAATACTACATATCAAACCCCACGGGATGTGGCAAAGTGGTACTTGGAGAGGAATGT
AGAGCCTTAAACGGTAGAACACAAAGGCTGGAAATTGATGAGCCGAGCATGGAACTTAGA
ATAAGACCAATCAGTCAGTTGCCGTTACCCGCGTCACTCCCTATCATTTCTTGAAGATTT
TAGCTTCTGACACTGTTACTCCACGATTACTTCTGTCCTTGTTTTTGGAGATTGAATTGT
CCATGTTGATGATCCTTCCAATGCCGTGGTCTCACAGTTCCTTGATCTCCTCCAATGATG
TTGTCCTGTACTCCCCACCTGGGCTGCTTGCTCCCATCCTTAAACTCTAGATATTATCCT
TTCCAATACCTATTATTTCTCTGTAATTTCAAGCATCTTTCTCTCTCTGACTAGCATTTT
TATAATTCCATCTCACTCTAGTATTCTAGTTCCAACACTTCTTGGACCCCCTTGGACTTA
CAATATCTTGATTAAATATATTATATATTTGGTTATTATCTGTCTTCCCATCCCTAACTA
GAAATAAGCTCCATGAGAGCAATAACTTGATGATTTTTGTTCACTATCATATCCCCAGGC
CCTAGAACAGTACCTGGTACATAGAAGATGCTCAGTAAATATTGTCTGAATGAACAAATG
AGTGAGGGAATCACTGGAATTAATGAAAGATATTTAGAAAGTAAGGAGCGATCCTTGCTT
CTAGCAGTGCATCATGCACTTCCCGGGTGGGTGGCTCTATACCAGATTATCTGAAAATTA
CAGTCATAGAAGAGACACGGACACGCCTTTGTAGAGTTTGTTGCTCAGGGCAACTGTTCT
CAACACATTTTTGTGACACTTCAAGATGTCTTCAATGTGCAGGGGGGAATTCTTAACTTT
TTACCTCAAATTACTTTTAATTACCTTTAATTTATTGTCAGTAAATTTATGTTATGCTGC
ATCTTGGCAGCAGGGAGGAAGTATCAAGATGGAAAACAAGGGCTTGAGCTGGGAGTTGAG
ATGTTGGCAGGGTACACAGCAATGAGAACTTTGGGTGTCACTGGATCCTGCAGCAGTGTT
AATAGCTGGGAATATTGACATCTGATGGCCTTACAGCCTCAGCTAATGGAAGCCAACTGT
ATGTGAGGGGCACCTTCCCAACAATTCAGATTTGAACACAATTTGAGAAACCTGCAATTG
GCTTGGTTTGGAGACATCGTGGTGAAGTGGGAAAGTGCTGGGCAGGGATCTAGAGTCCAG
AATTCAAGTCCAGCTCTTTTAGGGATTCACTGTGGGACTTTAAGCAAGTTACAGAATCTT
CCTAGATCAGGTTCCTCATCTACAGAATGATGAAAATTTACTGTGTCCTCTATGACGCTA
CAATTCTAGCAATAATTGCTGTCACATGTCACATGACCCATTGTCTTAGAAATTGGGACA
GGAGTATCACAGATACCAAAAAAGCATACCTACTAAAATTCTTAAACACATATTGTTGGG
GAGAGGGCTTCAGTTTGAGCCTCATTCATCTTGGTTGTTAGAAAAGACAACTATAGAGAG
GTATCCTCTAGGTTAAAAAGGTTTAGAATGATTAGGAAGGGATATACAAAGAAAATAGGT
TTTCAGGGTTTTGTTTTTTTTTTTCTTTGAGACGGAGTCTCGCTCTGTTGCCAGGCTGGA
GTACAGTGGTGCAATCTTGGCTCACTGCAATCTCCGCCTCCTGGGATCAAGTGATTCTCC
TGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACCCACGACCATACCCAGCTTATTTT
TGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGATGGTCTTGATCTCTTGAC
CTTGTAATCTGCCTGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGTCACTGTG
CCCAGCTGGTTTTCAAATTTTATATTTATTTATTTATTTATTTTTTGAGACAGAGTTTTA
CTCTTGTTGCCCAGGCTGCAGTGCAATGGCGTGATCTTGGCTCACTGCAAACTTTGCCCC
CCGGGTTCAAGTGATTCTCCTGACTCAGCCTCCCGAGTGGTTGGGATTACAGGCATGCGC
CACCACGCCCGGCTAATTTTGTATTTTTAGTAGAGACGGGGTATCTCCATGTTGGCCAGG
ATGGTCTCAACTCCCAACCTCAAGTGATCCGCCCACTTCGGCCTCCCAAAGTGCTGGGAT
TACAGGCGTGAGCCACTGCACCCTGCCTCAAATTTTAAATCATATCATTTGAACTCTCAT
GGAGGGAGAGTATAAGAGGAGAGGACCCAGCATTTATTTCTGGGGCAATCATGGTTGAAA
CCTGGGAAAAGAGAAACCGGCTCAGAAAAGTTGATATGACAAAGACTCCAAGGAGCCAAA
GGACTCAGACAGGCAGGGCCAGACAACAGACAGGAGGAGCCAACCAGAATGAGCCTATGC
TAAACAGAAGAGGATTTGCTGTTGTGGCTGAAGACTGAGGGCAAGTGTGAGAAGGCTCAT
ACAGGACTGAAGAAAAGGCATCAGCTCTGTTTGTGTGGTGCTTCCCTTCTTCTCTCTTAA
AAAATTTGCTGCACTCACTCTCCCCTGTCACTCTCACTCTTACTGGTCTCAGCTCCTACC
TTATCCCTTCTACTCACCCACTGCTGTCCGTAGCTGTCCTCCAGGTCATTCAAGTATTTA
TCTTCCCAGTGGAGGCGGATGCCCAGCAGATCAACAGGCCTAAAACCATTCTCAGCCAGG
ATTACAAAGTAGGTAAAGAATCCAGCCAGAGCCTGGATCATCCCTGTGAATGACAGAGTT
GCAGGACAGGGGAGCCTGGTTCAGAGAAGGGCCCCAAAAGGTAGGCCAGGGGAGGGCTGG
GGGCTGGGACTTGCTTCTGGCTGGGCTGGTGTGTGTCTGAAGAGTAATGCGGAAGAATCT
TGCCATCAGCTGCCTAAGCCTGTTATCTCTCATCTCTGTGGGACTTTCCTTCAAGCCCTG
ACATTTGTTTCTAAACTCTGACCCAGAGTCAGCTTTGAATCACATGGTCTTAAAACTAAA
AAGGACTTTAGAGGCCACTGATTCCCTCTCCCAATTTTTTCTTTTGAGACAGGATCTTAC
TCTGTTCATCACTCACCCTATTTTCTGAAATACCATTGCACCTGGAAAATCAAGAACAAA
GACTTCTAATGACTCTCAAATGTCTGTCAAGGCTGACCCCAACACAAATGATATCTCTGT
CTACAGTCTTATTTTTCACTACTTTATAAAGACTAAGGGCTCTACCAACCTGGTTTATTC
AGTCTTCTTTAACTGTGCCATCTGAAATTCCCCACTCCTTTGGTCTCCCACACCTGACCA
TACACTTACTAGTCTAAGCCCCACTCTCCCACACCAAGTTTAAGTCCTATTTCCTGCATA
AGGCCTCTCTGGCTATCCTCATAATGGTGAGCCTGCTTGCTTTGTAATCCTGTAGTATGT
TCTGTCTATACTCATTACTTGGCACTTGGAGATGCTATCATTTTATGTATGTTTGTTCCT
TTTGTACTGGACTCTAAGTCAAGGACAGATCAGAGATGAGTGGTTCTTTGTGTTTTCAGG
GCCTAGCACAGTTTGTTGCTGAGAAAATATCTCCCTGACTTCCAAACTGAGATGGCTCAC
GTTGCCAGGCAGGGGAAACCACTCCCTGCTCCCTCCACCCCTCATTCCTCTGGGCGCACC
AATCTGTCCATAGGCCATGCCAATGAGACGGTGGTTCACCAGATTATCCGTCTTTGGGTT
CCTTGGAAGCCTCTTCATGATGTCGCTTTCAGCTGACTCATAAGCCAAGGAGATGGCAGG
GACCTGGAGGATGGAGGGTGGGGATGACAGGGGTCACAAAGTTCAGAAGGAAACCCAGCA
GTAATTCAAGCTCTACCATTCTGTCTTGACGCAGCCTCAATCCATCTTGCAGGAGGTGCG
AGAGCTGGATCATAAGTGGGTTGTCATGAGTTTTAGTAAGATAGCTCCAGGCAGAAAGCA
GGGAGCTTAGGAGGCAGAATTCTGGGAATCTCTTGCTCACCAGCTTGGCCCTTACCATGT
CAGTGCCGAGATCAATGCAGAGGATGGTTATGGTTCCCAGAGGCAGGGGTATACCGAGGA
TGATGAACATCAGGAAGGGCGTGATCTCGGGGATGTTGCTGGTCAGGGTGTACATGATGG
ATTTCTTCAGGTTGTCAAAGATCAGGCGGCCTGGGGAGGAAGGTCAACCTCCTGTGAGAA
GCCCTGGGAGAACACGCCTCCCTCAAACCAGCTCCGGGACAGACAGGCCACCTCAAAGAA
GTGTCACAGTCCAGGAAAGGGTCTGGAGGTCCTAGACCTCCAGGGTCCCAGTATTGTTTC
TAAATTGTGTGCCTTTTAATCAGAGCCATGCCGTCTGTGTACTGTTTGTTCTTAGATTCA
CCCTAGCTAACGTTATCTGATCTCTGAAAATTAGCAGGGTTGGGCCTGGTTAATCCTGCG
ATGTTTGAGAATGTCAGTATAAAAGCCTTTACAAGATTAAGGCTGGAATGGAAACAGCCA
GGGCTTGGGACAGGCTTGTGTTCAAATCCCATCTTCTGCCATAGCTAGCTGTGACCTTGG
GCACCCTCACCTCCGTGAGCTTCATTCCTCCTGCCTTGCAAGATTGCTGCATCCGTCTCT
GACTGCCTTTTCAAAGATCGAATCCCTCTCTGCACTCTCTGCTTGGTCTGTCCCATGGCA
CTTATCTTCTTTTAACATACTATATAATTTAATTATTTTATTGTTTGTCATCCCCACTAG
AAATTAAGTTACACGAGGGCAGGGATTTGTGTCTTTGTTCTCCCTACTGTTGTATCCCCA
GCATCAAGCATAGTGCCTCCCACATAGTCAGTGTTCAAACGAACTTATTGAATTGAGTGG
ATATAAAATACCAAGCAAAGTGTCAGGATTATACAAGGTTTCAATGAAATGGTAATCATG
ATTATGATGTGGATTGCCATATGTTTTAGTAAGATAGCTCCAGGCAGAAAGCAGGGAACC
TGGAATGCAGAATTCTGGATCTCTCCTGTTCGCAGGAGGGCATTCTCTTCACAGTTCTCT
GGGGAAGAGGGTGTGTAATTGGGCTCATGCAGTCAATTCACGGGTCAAGCTCCAGCTGAT
CCTGATGTGTCACCATTATTTAGGCAACAGGTTCCTAGGGGACCCTCCTAAAGATTGCAG
CGCATGGAATAGTCCCAGGGGTGTGGCTACATCTTGGAACTGGCTGTGGGCCTACTTGAA
GTCCAGTGAGAGGACAATGACGATATTATGTATACCAGAGTCTCAGTCTCCCTGATAGGA
AAACAAAATGAATAAAAGGGACTTTTCTCCGATCTCATCAAAAGGGGTTGCAGATAGTGA
TGGTCTATGTACCAGCTGATCTAATTTGCAAAATTTTGTCTTACAGTGATTTTCTTCTGA
GCCCGTACAGGCTCATGGAGGTTGGATGATGGGAAAACGGAAAGAGGGGATGTACACCAA
CCCCCACCTGAGTCCAGGGTTGAAGTCTCCACCATGGGCACCCTGCCTCCTCACCCTCCT
CCACCCCCGTGACGATGGAGGCAAAGTTGTCATCCAGCAGGATCATGTCGGCTGCCTGCT
TAGAGACGTCAGAGCCAGAGATGCCCATGGCAATGCCAATGTCAGCCTTCTTCAGCGCAG
GGGAGTCGTTCACCCCGTCACCTGTCACGGCCACAACGGCTCCCTGAGGAAGTCCAGACA
GAGAGAGTGAACAATTTATTGCATCAGATCCAGAACTAGTCCCAAAGATCAGTACGCTTT
CTGCATCCCTTGTTTCCTGATGTAATCATGCTTGATTTAGGGCTCCCGTCCTTCTCCCAC
TCCTCCTGAGATATTTAAACTTTCAGGGAGCCCCAAACTGAAGGCCACCATGGAGGTTCC
AGATGGGGTACTCTCTGGAGTCTCCTCTAGCCCAGCCCACATGTTCCTCTGCTTGGTTTG
GGACGGGGCTAAGCCACAGGAGTTCTGCCAGTTTCCTTGGGGCTCCTTTTCGTTCCTTAC
CAGCCTCTGACATCCCTCGACAATGATGAGCTTCTGCTGAGGGGAGGTCCGAGCAAACAC
GATCTCAGGGTGGTTCTGGAGGATCTGATCAAGCTGCTTGGACTGTATGTCCTTCAGTTC
TGCACCATGCACCACAATGGCTTTGGCAGCACTGAGGGAAAATAATTTCAAAAGGCTAGT
TTTGAGTGTTGAGAATTCACCAGGGGTCTTGGTGCCCATCTTGACTATAGCTTCATTGCT
TCTTCTTTCAACCTAGTCTCCTCACTTGTCCCTAGCCCTATATTGTCCCCAAATTGACAC
ATCCTATTCCCTCCCCACACTTTTGCCAACCACTCCTCTCTTTACCTCTTTCTTCATCTT
GCTTCCTTTGAAAACCCACTGACATATTCACTTTATTTTCCTATTATGTTTTACTTTGTA
GTGTAAACCCCACACATCCTACCTATTGAAGGAGACTCCAAGAACTTTAGTAAAGTGGCA
TCTGGGTGGGGCAGGCTGGGGATGGAGGGAACATGGCAGATCTTGAGTTCTTTAGTGATC
TCACCTGGCATCGACCTTGCTGATAGGGATCTTAAGCCGGGCAGCGACTTCCTCTGCCGT
CTCAGTGCCTTCTGAGATGATGCCCACACCCTTGGCAATGGCCTTAGCTGTAATGGGATG
ATCTCCTGTTACCATGATCACCTGGGTTGGGAAGGAGAGGGAAGAGGAGCAGAATCATCT
TCAGAGCCCGGATCCTTCATTTTTCTCCTCTGAGAACTGACAGACCACTGCTTTTTTCAA
CAAGGGTTTTAGTCGCTCATTCCCAAGAACTTGTGGTGTAGACCAAAAACCATGCTACTG
TGATTTCAACCCTTGGGAGTGGGTCAAGACCATGAGACCATAAAACAGGACAATTTGGGT
CCTAGATTTACCAGGAATAAGCCAGAGATTTGACTATATTCAGAATTTCATTTAATTGCT
CCAGAAGCTATTCTGCTTCCTTAAGTGCAAAGACAGAAACACCTACACATAGAACAAGTG
GTAATAAAGGAATGTCTGGAATAATCCATCTGCCTAGCAAAATTTCATCTAAGGCCCAGT
GCATTGAAATTCTCACTCTACCTTTCTTCTTTCTGTGGCCTCACCCTGTGCCTTGGTTTC
AGCTTGGTTTTGGATACCTGGTACCTAGTCCTGTCCCATTTCTACCCAAAGATGAATACC
CAGGCCACGTGCTTTCACAGCATTCCGTTCCTGCCATATTTCAGCACTTGCCACACTTCT
CTGTATGGTGATTGCCTGTTTATCTCTCTTCCCCACTGAACTGAGAGCTCTGCAAGGGTG
GCTTCCTTGTAAAGTTTCCTGCCCTAGCACAATGCCTAGCACATAGTAAGCCATCAACAA
ATAATTACTGAATGAAGGAATGGAGGAATGATCACTACCTGGAAACCACTGCCCAGGGTT
CCCAAGTCCCTCCCAGCACACATGGCCCAGACTGACCCTGGACAAACTGCCAACAGTCAC
AGGTCTAACATAAAGCCAGTTCCAACAGAGAACACCTAGTTCTCCTTAAATACCTCCAAT
CCCCCAAGTCTAGGAGCCAGAATACACAGGTAATCCAGAATGTAAGGTATGAGCACGGAA
GGTGTCTATATCTAAGCTGTAAAGATGTATATGATGAGTCTTAGAATTTGACCTGGGAAA
CATGGGACACAGAACACCTCAGAATTTGAAGAATTCTACTGCTGCCATCCCATGAAGTTC
AAGGCCCACCCTGACCAAAGAGGATTTTCTACCTCTGGGTTTGTTCTGAAGCTGAACTTT
CACTCTTGCTCTGACCGATTTTTGGTTTCCAGTTTTTAGACCTGGGCATATACCTCTTAG
GGCAGCTGCTCACACCCATTGAAGATCCTTCAGCTCTCAATATCTCATTCTCACTATTGC
CTGGTCCAGAGCCCCAGGCCTCCTAGCCTCACCCTTTTACCGCCCATCTCGGCAGCACAT
TTACACGACATCTTCTAGCACTTTGCTATTCCTAGTGTGGTCTGCAGACCAGCAGCAACA
GCATCGCCTGGGAGCTCGTTAAAAATGCAGTCTCTCAGGTTTCCATGGACCTTCTGAAGC
CAGATCTGCATTTCAAAACAATCCCTGAGGGATCTGCACGCACGTTGGTCTGAGAAGCAC
TGGGCTGGACGCTGGTTCTCAAACTTCTCTGCTCATTGGAATCTCCAGGAAAGTTTTTAA
AAATACTGTTGCCAGGATCCTATCCTGAGAGTTTCTAATTAAATCGGTCTGGGGTGTGTC
CTAGACATCCGATTTTTAAAGCCTCCCTGGTGATTCTAATGTTCAATGCAAGTAGAATTC
TAACTGGAGAGGAAACTTACTATTAATTAAAAATCATAAGCCCAAGGAAACAGAAATCCG
CTCAATTAAACTAAGGGTATTAAGCATCTACTCTGCGCAAGGCCTTCTAGTAGATGCTTC
AACTTGTGACAGGTGAGGGGCTCCTGGTCTGGGCAAGTATTTACCTTAATTCCTGCACTG
CGACACTTGCTCACAGCATCAGGCACTGCAGCTCGGGGAGGGTCAATCATGGATATGAGG
CCCACAAAACAAAGGTTGTCCATGGGGAAATTTATTTCATCTGTATTAAATGGGAATCCC
TTGGAGAAGCTGCTAGGCAGATTCAAGAAGCAGAAGCCTGGAGAGAGACAGAGGGAGGGA
CCAGTAGTCATCCAGCACTCTACATTCCTATCTGCTTACCCCAACATCCTTGATTTCTCA
CCCCAGGGATAATAACCATTTTGATGCCATTCTTTTAAAAACTTCTCCCAAAGCTCCTCA
CCTAGCACACGTTCCCCCAGACCTCCCAGTTCTAAGTAGGCATTTTGGAAGGCTTCCTTC
ATTTCATCGTTCATTGAGTACTCCTGCCCATTCAGAAGAAAGGTAGAACAAAACTCCAAG
ATCCTCTCCGGAGCACCCTTCATCATCAGTACGTGGGTCTGGGAGCTGTCCTCCCGAAGG
TGGATGGACATCTAGGGAGAGCAAAGGGAGCACTGATGGGACAGGAGGAGAGACCAAGGA
TCAGGGGCAAAAAGAAGGGGAAGGTTTCAAAGGTAAAAAAATGTGTTTCATACCCCCATT
TCTTTTGTTCCCTCCCCTCCCCAGTCACATCTCGCCCCAGGTTGAACCCAGCCCCTCCTC
CTTTTTCCAGAAAACTGCAGCCTGGTATTATTTGCACAGGAATCTCCATTATCTTCTCAG
CCTGAAGCTCCCTGGGGGCAGAACCAGGCACTCTCACTTTTCCCCTGCATCCTTGCCAAC
TGGATGGCGAGAGAGCAGAAATAGTGGGGCTGGCAAAGAAAGAAAAGAGAGTAGACAGGA
AAGAAAAAGAGTCGGAAGGCCAGGCGTAGCGGCTCATGCCTGTAATCCCAGCACTTTGGG
AGGCCGAGGCGGGTGGATTGCTTGAGGTCAGGAGTTCAAGACTAGCCTGGCCAGCATGGC
AAAACCCCGTCTCCTACTAAAAATACAAAAATTAGCTGGGCATGGTGGCATGTGCCCATA
ATCCCAGCCACTTGGGAGGCTAAGGCAGGAGAATCGCTGGAACCCTGGAAGCAGAGGTTG
CAGTGAGCCAAGATTGCGCTATTGCACTCTAGCCTGGGTGACAGAGCCAGACGCCGTCTC
AAAAAAAAAAAAAACAAAAAAAGTCCAAAGACCTGTGTTCTGGGGCTAGCAAGAATGCAT
TATGACCATTGGTCAGTCCATGTAACTTCGCAAAATCTTANNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNTCTGTCGCCCAGGCTGGAGTGCAGTGGTGTGATCTCAGCT
CACTGCAACCTCTGCCTCTGGGTTCAAGTGATTCTCCTGCTTCAGCCTCCCGAGTAGCTG
GGATTACAGGCACCGCCACTATGCCGGGCTGATTTTTTGAATTTTTAGCAGAGACGGGGG
TTTTACCATGCTGGTCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCTACCAACCTTG
GCCTCGGAAACTGCTGGGATTACAGGCACCGCCACTATGCCTGGCTGATTTTTTGCATTT
TTAGCAGAGATGGGGGTTTCACCATGTTGGTCAGCCTGGTCTTGAATTCCTGACCTCAGG
TGATCTGCCCACCTTGGCCTCCCAAACTGCTGGGATTACAGGCATGAGCCACACACCTGG
CCCTTCATTGGGTTTTTATAAGAGATAGTGTAGAAAATACTTTGAAAACTGTGAAGTACA
ATCCAAAAATAAGTTAGTCATTCTAGTCCCTGGGCCTCTGTCTCCTAAAAGCGTGAGAAG
TCTCCTGAGAGGGGCTAGCTAGTGTGGTTGGGCATGGGAGTCCTTGTGGCTGTGGTGGGG
GAGGGAAAGGGCACATTCATGAAATGAACCCGAGGGGACAACCCGCAGCAAGGAGAGAGA
AATGTGGGTTTTGCATTTCCTCTTGATCTCTGATGTATGAAAAGGAGCTCTCCATGGGGT
TCCTCTTGTGATGGACAGGAAATGCCCGCTAGGTCGCCTGTTGAGAACAAAATCGATGCA
TTGAAAGGAACAGCGGGAGTGCAGAGGAGGCCGGACTGTACTGCCCACAGGGTAAGCAGG
GTGGGAAACCAGTGCACAAAACGTGGTTACAACTGTTCTGTTCGTTTGTTCAGTTACATT
CAAAATATGCTTAAGCAATTAAGAGGAAGAACCGTAACTCACTTAAGCAGAAAGCTGGAA
AAAGTTTAAAGAGCTCAGTTTTCTAAGTGCTCAGTAAAATGTGTTGAATAAGTGAAGGGC
CCAGGAGGTGATGGCAAGACCTACTAGTAATCTCAGAGGTCACGGAAGAAAATCACATCT
TGATAGAAAATTACATATAAAAGAGACGGAGGGAGAAGTCTGGAAATGCTGGAACAGAGC
ATCTTCTTCGTTTCATTTTTATCTCAGAGGGAGACAGACCAGGCTCTGCAAACCGCCAGC
AGTCTGAGATGTCTCTTGCAAAGACTGGAGTCTCCACCTTTAGGGCAAGCTAAGGAAGGC
AGCAAACTGAGGGCCTCCCAGAACAAGTGCCTGCCAGAGCTTGGCGGCCAGTGGGACAGC
CTGTCACACTCGGTGAACCACTGAGGACAAGTCTGCCATTTGAGCCGCATGTTTGGTAGC
TCGGAAGAGGCAGCAACATAGTCATCTGAGAGAAAGTCACTATTTGTTGGATGCCCCAAC
AAATGTTGTGAATATGTTTTGCTTTTATTTTGAATCACATGGACGGAGAGGTACCTAATT
CTTTCCAGTTAAAGGCTATGCTGCCGTCAAAGGCCCTGCCAAGCCACAGAATTCCTGTCA
GACTAGTGAGGCCACTAAACATCAGAAAAAAATGGGAATAAGTTTGCCATTTGGGCCTAA
GAGACCTATTTTATTACATTGACTAACAACCAGTTGAGACAGAAAAGGATAGATCTATTT
AACCCTTACTTGCTCAGTTTTCAGTGTAAAACGATGAGTAATTCAGTTAAAAAAAATTTA
TATAGAGGCCAGGCATGGTGGCTCACGCCTGTAATCCTAGCACTTTGGGAGGCTGAGGCG
GGTGGATCACCTGAGGTCAGGAGTTCAAGACCAGCATAGCCAACATGGTAAAATCCCGTC
TCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCACATGCCTGTAATCCCAGCTAT
TCTGGAGGCTGAGACAGGAGAATCCCTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCCAA
GATTGCGCCATTGCACTCCAGCCTGGGCAACAAGAGCAAAACTCCTTCTCAAAAAAAAAA
AAAAAAAAAAAAGATACCAGCAGACTTGGGAGTCTCATTGTCATTTTCTCTGAGACATTT
TACCCACACCTGAATGTCTGGCCTTTTCAGTAATGCAAGGAGTTGAAGAATCTACTTCCC
TGAGCAAATCATGATTGCCCCGTGGAACTCAGCTTGAGCCTGGCAAAGCTCCAATTCTGA
TAATGTCACTGTTCCTGCATCCTACCATAACCTTCTCTTCAGTCTGCCCAGATTCTACTT
TGGAGAGAAAGACTCTTTCCTGTCCCTTCATGGTCCCTCACTCAGCATTTCCCCTGCTCT
TGTCCACTCCTCCCCGGAGAGTGGACCAAAATGTTCCTGGGAAATGAAAAACTTCACGAA
CACGAACACACGTAATTAGTTAAGGTTACATAGAAGTAGGGGAGGCCCTAATCTAATATG
ATTTGCATCCTTATAAGAAAAGAAGTTACAAGACACACAGGGGAGAGGGTCAGGCGCCAA
TGGAGGCAGAGACTCCTGATCGCCTACCCGCTGGCAGTCACTAGAACTGCAAGCCAAGTG
TGGGGTGAAAGGAAATATTGATGGCTAATGAAATAAAGTGTCTGCAAATGCAACCTAATA
CTGCAGCGGCAAATCTCCTAGTAGACACAGAGGGGCCTCCTAACAGCTGCATGTGACTCT
AACATGACTTTCACCAACCAGCTTCTGCTGTCTACAGACATTTCAGAGAGGATTTTATGA
CTCGCTTTTTCCCCAAGTGGCAGAGCTCAGATCTCTGCATAGGACTGACTGATGCCTCTC
CCTTTATCACCTGTTTCGCCTCTCTTTACCTGTTTGTCACGTTCTCTTGATGTGAGTCTT
CCGTTAATTGGGATGCAGGTTCTGCTGAGCTCCTCTGCTTCTCCGAGGTGAAGTTGAAGG
CAGAGGCAAAGCTCCCCTTGTTCCAGTGATAAGCCCATCCCCCCACCACCATTCTCCTAC
CTTTGTGGGTTCTGTACCTGGTACTTGTTGGTAGAATTAAAGGGAATCTCTGCCACCTTG
GGGTTTTTCTCTCTCATCTCCGCCACAGAGCTGTAAGACTGCTCGATGAACTTGAGGAGG
GCTGACTCGGAAGCATCACCTGTTGTGGCCCTCTGCCAGGATGGGGTTTGTATAGTAAGC
CCCAGGGGCATGCTACCTGGGCATGAGGCATACCTGTGGCAACATGAAGAGGGGACAAAT
GGGGAGGGCGGGTACCTGGGGGGAAATTACTGAGCTCCAGGAGAGGATTTTTTGGGAGAG
GTCAGGTTACACCCTGGACACTGAGGTACCCTCTTCCCCTTGGGCCTGACACCTTAGCAA
TGGGCAGGATCTCCTGATTAGCCTTAAAGTCAGCCCGGTTGCAGAGGCCAGCGATTCGGG
CCAGCATAAACCAGGTATCAGAGCTCTTGGTAAATGTTTTTCCTAGGGAGAAAGAAAAGC
AGAATTGTGAGCAGGGAATGAGAATTTTAAGCAAGCGGTTATTCACATCCTCTTTGGCAC
CCAGATACTTCACAGGAGCAGCATTTCTTTTCCTTCACACCTCCCTCTTCTCCACTCCAC
TTTCAGGCTCCCTCCTGTCTGTCTGGACTCACCATTCTCTCTCAGCTCACTCATCACATC
CCCCAAATCCCTCCACTCTTGTTCCACCAATACCACTAGTCACCAGTCTGTTCTTCAGTG
GTGTCGGCCTCATACACGGTCATATCAAACCACATGTGGGCGACGGTCATGCGGTTCTGG
GTGAGGGTGCCCGTCTTGTCTGAGCAGATGGTGGACGTGGAGCCCAGCGTCTCCACCGCC
TCCAGGTTCTTCACCAGGCAGTTCTTCCGCGCCATGCGCTTGGCTGTGAGGGTCAGGCAC
ACCTAAAGCCAAGAAGAGAGGAGAGAATACACATGGGAGATGGAATACTCACACCATTTT
GCATTGTGGATATTTGATCATTTTTAATGCTATTTTGATTTTTTGTACTTACTTCCCTTT
TGTTCCCACCTACTCTTTACACATTTCATTTCTGGCTGTGGTAAAGGAAATTAGGAAAGT
GATTGTGGTTTGTGCTTTATGGTAAGAGTTTCAAAAAAGAGTGTATTTAAAAAAAATGTC
TTTTTCTGTTTTTGTTTTTGAGACAGAGTCTCACTCTGTGTTACCCAGGCTGGAGTGCAG
AGTATGATCTTGGCTAACTGCAACCTCCATCCCCCAGGTTAAAGCAATTCTTCTGCCTCA
GGCTCCCGAGTAGCTCAGACTACAGGCATGCACCACCATGTTCAGCTAATTTTTGTATTT
TTAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGGGCTCAAGT
GATCTGCATGCCTTGGCCTCCCAAAGTGCTGGGATTATAGATGTGAGCCACCGTGCCTGG
CCAAAAAAGAGTGTATTTCTTTACCAGGGTATCATAGACAGGGATCCTCTTTATTCCCCC
CTGGAATATTCTGCTCCCTCAGGATCTTTGCATCTTTTCTATTCAGCAATCTCTTTTTCA
TTCAAGTTTAGGCCACACCTCTTTAAGTCCAATCTTTCCAGGGACCACATAGATAGCTAA
TCTTTTATGGTGGTATAAGATGCTAGGTGTGGAGGGGGTGTTGGACCAATAGTTCTTTTT
TTTTCTCGAGACGGAGTCTCATTCTGTGGCGTGATCTCTGCTGACTGCAAACTCCACGTC
CCAGGTTCAAGCCATTCTCCTGCCTCATCTTCCCAAGTAGCTGGGACTACAGGCGCCAGC
CACCATGCCTGTCTAATTTTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTA
GCCAGAACGGTCTCGATCTCCTGACCTCGTGATCCGCCCACCTTGGCCTCCCAAAGTGCT
GGGATTACAGGTGTGAGCCACCGCGCCCGGCAGACCAATAGTTTAAACAAAGAACGTGGA
GGAGATAACAATAATATCACAGCATTGAAAAGGACTTGAAAAATCATTTAAACCAAAAGA
CTTTTGTTGATTGTGAAGGCAATGTAAGTCAAGTGTGAAGCAAGATTGTTTTAAAAGCTA
ATGAATTCTTAGGCTGTGGTTATCTAAGTATGGGCTTCTAATAACAGGATTAGGGGTTAT
AATGTATTTACATAATATCACTAGTCCCTACATTTTTGTGCTAGTCCAAACACACCCCAA
GTATTATTGTCATTTCTCTTTTAAGAATATTGACAAACTAGAGCATACCCTCAACAGGTG
ATCATCAAGACAGGTGGCCTACAGACCATGTCATAGGAAGAATGGCTAAGGGAAGAGGGA
TTATTTCACCTGCTACCACCAGAGTTTGAGGGGACATAATGGCTACCATCAAAAATCTAA
AGGGCTAGTCTGTAGAAGAGAAAGAATTGACTTATTTTGTGTTTCTTCAGCTGGGAAACT
TAGGACAAACAGGGATTTATAGTTCTGCTTAACACAGTGAAATGTAAATAGAGCAAGACA
ACAATGAAACGAATTGAGACAGAAAGGGGTGGGCTTCCCAATTAATAGAAATAATAATCA
TCTCCCATGGGTTTTATAGAGGATATTCAGCACTGGTTGAAAGGTTGAATTTATATGATC
TTTGAAGTCCTTTCCTGTAGGATTCTATAATTCCAAATTAATCTTCCTCCATAAACTGAT
GAATAAATTGAGGTCTGGAGATGTTAAGTGATTTAGCCAATACTAGAACTCACTCTCAGT
GACTGATAATCCAATGCACTTTCCATTGAAACTTGCTTCCTCTCTCATTGAGGAAAGAGA
AGACACCGAAATATATGGGCAGAAGGAGTCAGTGTAATATTGAGAGCTAAATTATTCCTG
ATACCTATTTACATATCAGGAAGACCCTGCACTTGAAAGGTTCAACAACAAAAGAGACGC
TAGTGATCCCTTTTCCCTGGGGTGGTTTGTCTGCCCTGAGGCCATTTTCCACCCTGTCTA
CTCACAGTGACTGTGGCCAACAGCCCCTCAGGCACATTGGCCACAATGATGCCAATGAGA
AAAATGATAGCCTCCAGCCAACCATAGCCCAAGAGAAGTGAGAGCGCAAAAAAAGTGACA
CCAAGGAAGACGGCCACCACAGTGATCAGATGGATGAAGTGTTCGATCTCAGCAGCGATA
GGTGTCTGGCCAACCGCCAGGCCTGACGTCAGGGAGGCAATTCTGCCCATCACTGTGGAG
TCTCCCGTAGCAATCACAATACCCCGGGCGGTTCCTGTGGATGAAGCAGGAGAGGGCAAT
GTGATGTTGTGATATGATAAGAAGTATAGATATTGGTCTCTGCCCCCACTTCCTGACATA
GAGCTTCTAAAAACCCTTAAAGATAGGGGTGCTAGGAGAATCTTTTGTTCTAATATTTGG
TCTTTGACCCAGTTCTGGACACAGAGCTCCTGAGACCCTTGTAATTTCTTGAGTGATAGG
AGTGTCTGACACAGAACTCTTAAATGCCTTGGAGTTTCCTGGGTGATAGGAGTATCTTTG
TTCTAATGAGGTGACTCTTGGTGGGTTCCTGGATAGCCACAGGATGGGGCTGGTGGCCAG
GGCAGATAACCATGTGATTAGAGAGTTGGAACTTGCAGTTCATGGACTGACCTCTTTGGA
AGGGAGGAGGGATGAAGGTTGAGTTGATCACCAATGGCTAATAATGTAACCGATTATACC
TATGTAATGAAATCTCCATTAAAAACCTCAAAGGACTGGGTTTGGAAAGTGTCTATGTGT
ATGACCATGTGGAGGGTTACTGGAGGGCACCCTGGACAGGAGAGGGCACAGACGCTCCTC
CATGCTCCTTCCCACGTGCCTTGTCCTGTGCGTCTCTTCCATATGACTGCTCATCTGTAT
CCTTGTAATATCCTTTATAATAATGGGTAAACCTAAGTAAGGTGTTTCCCTGAGTTCTGT
GAGCCATCCTAGCAAATTAATCAAACCTGAGGAGGGAGTCGTGGGAACCCCAATTTATAG
CCAGGCCATAACCTAGGACTTGTGACTGGGGTCTAGAGTTAGGGACTGTCTTGTGGGGCT
GAGCCCTAACCTGTGGGATCTGATGCTATCTCCAGGTGGATTGTGTCAGAGTTGAATTGA
ATTATAGGACACCCAATCATTGTCCTTTGGAGAACTGGTTGTTGGTGGGGAGAACTGTCT
ACACATGTTGGACACAGAAGTGTTCTGTGTTCAGCGTGAGTGTAGAGAAAAAAAAAAGCT
GTTTCTTGTTTTTTCCATCAGAGATGGTCACCCAAGACATGCCGAGTCTGAATTGAGGAA
GCTGTTTGGTTTGGTTCCCACAAAGAGCAAGCTGTCAATGGTCAAAAACAAACTGGAGAC
TCAAGGCCCTCTGAGAGGTCATTATGTTCTGCTCTCCTCATATTTAGTTTATACAAATAA
AGGTCTTCTAGTCTGAAAAATCTCTGAAGAGGTCTCACAGTTCTCCTGAAATACCCAATT
TTATTGCCTAATTTCCTTCACTGTCAAGAAGGCCTTTATTATACTTAATCTGAGTATCTT
CTATTGCCTATATAGTTCTTATCTTGCCCTCAGCAGCTGAGGAGTTTCTAGATCCCAGGA
ATAGTGGTTACCCTTCTGGTAGAGCACCTATGTTCCAACATCCCCTTATCCCACTAACAC
AGTGGTTCTCAACTGGAGGCAATCCCTACCCACCAACCCCCTTCCCTGGGGACATTTGGC
AATGCTTGGAGACATTTTTGGTGGTCACTACTGGGGTGGGAGAAGGCTCCTACTGGCATG
CAGTGGGTAGAGGCCAGGATGCTGTTAAACATCCTGCCACGCACAAGACAGCTCTCCTGT
CCCGCACAACAAAGAATTATCCAGCCCCAAATGTGAGTGGTTGAGAAATCCTGCTGTAAC
TTGCGCCCCCTCCCTGCTTTGCTGGCTGGAGCCAATCTGACCTCTGCTGGGTAGCACGGG
CCATAACAGCTGGGCTTCTGTGCTTATGAGGTCCCTCTTTCCTCTCCACCAGCACTGCCC
CAGTCAGAAGGGCAGCTTGGACATCATGTTTGGCTTTACACACACATGATGCAGGCCACT
CACCTTGAAATGAGGGGCATGACAAAATTCTTTTCTTAAAGTAATTCTTCCTGCTTTACC
ATAATGACTGAAATTTCTACCATTGAAATCAGAGTCAGAATCACTTAGGCAACATATCAC
TGAAACTGCATTTATTTTAAAAGCAGAAAGACTCAGGGCCGGAAGTTCAGCTTTCTAAAT
TACTAGCTCTTTTCCTTGGGGCAAGTTACTTAAATGCTGAGAGTCAGGCTTCCTCATCTT
CGAAATGGAATGAAAGCACTTACTAAACTGTGAGGACTGAATATTTTTAAGAGTCTAGAA
GGTTAGGTACATCATAGGCACTTGAAAATTAGTTTCTTTCTCTTTCTTCTCATCATTTAG
ATGAACTTAGGGTTTCCAGTAGGACCAATATAGACTCATACTTGTGACTTAGTAGGAGCA
TCTCTAATCTGGGAGCTCCCATGAACATTGCTGCACGTGGTGGTCTCCGTTTTCTAAGGT
TGCCTTTAGCTGTATGAGTCTGAGAGCAGGGTCCTACTCGAGGAGCAGACAGGTCAGGTC
AGTGTTTATGTGGAGGAGGAATCCTGAAAAGATTCCCAGGCCGAGGCATTCTATAGATGG
GCTTCAAACTGGTTGCCAAAGGCATATATTGGGTCCTATGGAATGAAGATGCTGAAATAC
TTGAGAGATGCTGAGGAGTTTCCTATTTTGGGCCGGGTGGAGGAGGGTGGGTAGTGTATG
GTGTCACCTACATATATCTTGTGTCATGGTTTAGTCTAGTTCTTCTATTTTATTCCTTCT
GCTATGGTTTCCTCACACTTGGAGAAACGGGATTTAATAATTAATCTCAGTGTGTCTAGA
GATGGGGTTGGGTTGATGTCAACCTCAGGGAAGGCTGAGAAGGCCAAGCATCCAGCACCC
CAGGCCAGACTGGCTTCTTCATACACCTTCCATGTATTGCCAGAGAAATAGCTTGGGCTC
CCTTGAAGATGCATGAGAACCCAAAGAGAAGTCTGTGCCACAGCCATGTCAAGGTCTACG
GTGATGAGACATGGGAGGCAAGGGTAAAGGTTAAAGTTATGCTACTAATTTGCAAATTGG
TCTAAGGCAAAGGTTAAAAGTCTAGGGTAAAGGTTAAAGGGCAAATTGATCTAGGGTAAA
TGCTATCGGTCTGTGAATTGCTGAGAAATTCCTCAACTGAAAGTCCTTCCGCCCAGCTCC
TTCTACCTAGCTCCACCTTCTTGGCCACATGTTGGGTTTTTTTAGCCTCCTACAAAACCA
TTTTCTATCTAAACAGACCCTTGCTTCCCAGTCGAAATGCCACCATCCACTTTCCTCCAT
ACCCTTTATCTGAACATATACTTAGCTGATGAAAACCCTACTTTGTAAGGGTAAATTTGG
GCAAATTTTTTCCTAAAATCTAATAGTAGACATCTAGTGTTTTTGGGGAAAGCTTGCTAA
CTTGCTTCTGTCCAATCAATTTTAAAACATTTTTAATATATGTATTTTATTTTCTAGTTG
GATTCTTTCTCATAGTCTATTCTGTCTTAACATTACGCTTCTTCTTTAAGGTATTTTCAA
ATTAAATAGCAATCTTTCAGCACAGAGCAGGGTCTGTGGAAGGAGCACGAGATATGGAGA
CAGACCTACATTAGAATCCCTGACCCGCCTCCTTTCTATTGAGTTGTACTCTTGGATATG
GTGCTTAATTTCTTTGAACCTTAGTCTGCTACATGTAAAATAGGGATAATATCTGGTATT
GTGCGCATGTGGGAATTAGAGATAATATTTATAATATTTAACAAATACTATGCATTCAAA
TAAAAAATATTTCTAGGCTGGGTATGGTGGCTCACGTCTGTAATCCCAGCACTTTGGGAG
GCCGAGGAGGGCAGATCACTTGAGGTCAGTAGTTCGAGACCAGCCTGGCCAACATGGTGA
AAACCCATCTCTACTAAAAATACACAAAATAACTGGGCGTGGTGGTGGGCACCTGTAATC
CCAGCTACTCGGGAGGCTGAGGCAGGATAATTGCTTGAACTTGGGAGGCAGAGGTTGCAG
TGAGCTGAGATCACACCACTGCATTCCAGCCTGAGCAACAGAGAGAGACTCTGTTTCAAA
AAAACACAAAACAAACAAAAGAACTATTTTTAGATAACCAAACATTTGTTCTTAAGCATG
AATAATAGTTTTCAAGTGTGCTCCATGGAGTCTTCAGGCCTTCTTAAGGGGAAAGGGCAA
AGGAGAGATTGACAGAATGATGTTCAGTCCCCTTTTATTACCACTTTGCCAGAACTGTCT
CCCAGTTCAAGGATTCCTAGATTCTAGGAGCAAAGCCAAAGTTTAAGTGGTAAAGTCTAA
GTGGCACCTCTGGTAATTCAAGTTTCCAATGCCAATATCTTCTCTTGGATAGGGGACTAG
TTAGAAGTTAGGGCTTACCTTAAGAGAAGAATGACTTAGCAGGGCTGAACAATTTTCCTC
CCCTCTGTGCCATTTTCAGCTTAAACAGCATAGTCCATTCACAAGCTAAAATAATAGCTA
ATAATTGTAGGTCACTTACAATGTATTAGGTCTTGTGCTGGGCATTTTACATATATTATC
TCAATTCACACGAAAATCTACAGAGTAACGACTTTTACTGTCATCACTGTGCGAATGTGG
AAATGATGACCTTGACCTTTCACCAGAGGTCATACAGCTCGTGATGGAGAAGCTCGACTT
TTTACTGGCTCTTACCTACCTCGCTACCTTTAGAAGACAGTTATTAAAATCTTTATGTTT
TGGTGCCTGCTTTTGAATCTATGCTACTTATGGTTCGATATTCACCTTCCACACAGTTGG
TGGAAAAGAAGCAGATGTTTCGGGTCTCCAGAGGGTTCTCATGGGTGAAGTCAGGGGAGC
GGCTCTGGGGTTCTGACTCCCCAGTCAAGGATGAGTTGTCCACCTGGGATGGGAGAGGGG
ACGCGTTGTAAGGTGAGCATAGGAAAAAAGGCAGATTTATTTACAAAAATAGTATGTCTT
CATCTGGTCACCAACATCATCACTGACAGACTGAGAGAAACAAATTTACACATCTGTTGT
CTCTAACATCAAATCTGCACTTGTAACTTCTCAAGATTCTGAGTAATAAGCTTATACTTT
CTCTAACGGCCCAGGTGTCTACCCTGCCATGAGATCACGCTTGGGTCCCTCACATAGCTT
TCGGCATCCCCTCACCTTACATCCTTGTGCAGAGATAAGCCGGAGGTCAGCAGGGACTCG
GTCTCCACCCTTGATTTCCACCAGGTCTCCCAACACCACCTCTTGTACATTAATTTGCAT
CTTCTCTCCTCCTCGAATTACCAGAGCTTGCTATGAGAGGATAGTGCAGGATCATTTCCA
AAACTTTTGGCTTTCCTCATCCCACTCTTAGCCTAAAACCTTCTGTTATTGGTCTCCCTC
CTCCTTACTCCCCTTTCTTACTGTCACCCACCACATCATTCTTGAAGGTGTCTTTGGCAG
ATTGCAAATTCCCATGATGCTGTTTGCAGGGCCCTTTGCAATGTGACTTTGACGCTCTTC
CCATTAAGAGGTGGAGTCTATCTCTCTACCCCTAAACCTGGGCTTGACCACGTGACTTGC
TTTGGCCCATAGAATGAATGTGATGGAAAGAGGAGTTTAAAAAGTGCTTTCAGGCCGTGA
CTGGTGGCTCACACCTGTAATCCCAGCACACTGGGAGGCCGAGGTGGGAGGATTGCTTGA
ACCCAGGAGTTTAAGACCAGACTGGGCAACATAGGGAGACCCTGTCTCTACAAAAATTGA
AAAAAAAATTAGCCAGGTGTGGTGGCATGCACCTGTAGTCCCAGCTGTTTGGGAGGCTAA
AGTTGGAGGATCGCTTGAGCCCAGAAGGTTAAGGCTGCAGTGAGCCGTGATCACATCACT
ACGCTTCAGTCTGAGTGACAGAGTGAGACCCTGTCTCAAAAAATTAAAAAAAAAGTGCTT
TCATGCTGGGGCTTGCATTCCTGTTTCTGAGAATCCTCTGCCACCCTATGAACAAGCCCA
AGCTAACCTCTCTGTAAAAAGAGAGATCACGAAGAAAAAGGCCCCAGCTGTCCCAGTCAT
CTCAGCTAAGGGCCCAGACATGTGGATGAGGTCATCTAAGACCATCCAGCCCCAGCTGAG
GAACAACAGCACAGCCACAGAATTATGAGAAACAGGAGCTTGCTATTTTAAGCCACTAAG
TTTTAGGGTAGTTTGTTAGGTAGCAAAAGCTAACCGACCATGCCTAAACTCCTAGTCTCC
AAAACTGCCCAAACACTTTGTCCCAAAACTCTTACCCAAGGAAGGAATTAAGTGATACCA
AAAAGAGAAGGAAATCCTGGGCTATACTACTGGAACATGATCATATTATAGGGAAAATGT
GGAGCCTATTCCTTTGCAAGTTTCCAGTCCCGTGCCTAGGAACCTCTGTTTACCGTCGTA
TTCTTTCCAGGTACCTTTAAAAAACATTTAACTTGAAAATAATTTTAAACTTTCAGAGAA
GTTGCAAGAATAAAAATAGCACCAAGAACACCTATATAACCTTTATCCAGATTCACCTAT
TAACATTTCACCCCAGTTACTTTGTCATTTGTTTTCATCCTCTCTCTCTCTGTGTATACT
CTTTTCCTGAACTACTTGAGGGTAAGTTACCTACATCATGATCTTTTATCTTAAAAACTT
CATTGTGCATTTCCCAAGAATTAAGATATTGTCTTAAACAACCACAATGTAGTTATCAAT
TTCAGTAAGTTTCACATTGATACTTTAATCTACTGTATTAATCTGTCAGTATTCCAGTTT
TGCCAATTGACCCAATACATCCTTTAACGCATTATCTTTGGTGGAGCTGGAGGACATTGT
CCTAAGCAAACTAACAGGAACAGAAAGTCAAATACCTTATGTTCTCACTTATAACTGGAA
GCTAAACACTGAGTACATATGGACACAAAGAAGGGGAAAAACAGACACCAAGGCCTACTT
GAGGGTGGAGGGTGGGAGGAGCGTGAGGACAGAAAACCTACCTATCAGGTACTATGCTTA
TTACCTGGGTGATGAAATAATTCGTACACCAAATCCCTGTGACACACAGTTTACTTATAT
AACAAACCTGCACATGTATCCCCGAATCTAAAATAAAAGCTCAAAATAAAAAAGTAAAAA
TAAAGCATTACTTTCTCCTCTGGCACAGAATCAGATCTAGGGTTAGATATTGCATTTAGT
TGCCACGTCCCTGTCTTTTTTTTGAGACAGCGTCTCTGTCTGTCACCAGGCTGGAGTGCA
ATGGCATGCAATCTCTGCCTTCCGTGCTCAAGCAATCCTCCTACCTCAGCCTCCTGAGTA
GCTGGCACTACAGGCACGCTCAGCTAATTTTTAAATTTTTTTGTAGAGATAAGGTCTCAC
TATACTACTCAGGCTCGTCTTGAACTCCTGGACTCAAGTAGTGCTCTTGCCTCGGTCCCC
CAAACGGTTGGGATTACAGGTGGGAGCCACCACCCTCGGAATAGTTGTCATGCCTCTTTA
GCCTCTTTTTATTATTATTATTATTTTTTGAGACAGGGTCTTGCCCAGGTTGGTCACAGT
TCACTGCAGACTTAAATTCCTGGGTTCAAGTAATCCTCCCGTCTCAGCTGCCTGTGTAGC
TTGGACTACAGATGTAGACCAGCTATTTTATTTTATTTTATTTTTGTAGAGATAGCATCT
CAAACTCCTGGGTGATCCTGTTGCCTCAGCCTCCCAGAGTGCTGGGATTACAGGCGTGAG
CCACTATGCCTGGTCTGTTTAATCTGGAACATCCCCACAGCTGTTCTTTGTCTTTGAGGT
CATCGATATTTGAAGAATCCAGCCACCCCCCACCGCACCCCGCTCCCACCCCCACCAACA
CTTGTCTCTTTAAAAAAATAGAATGTTCTTATTTGGGGTTTGTATGGTGTTTCCTCTTTA
GATTCAGATTCTGCCTTCTAGATCAGAGCACTTCATAGGTGACGTTATGTCTTTCTCAGG
GTTTCACAGCTTTTCCAGGTACTTTTAAGGACTGATACAGTACCTTGACCCCCTCATCAC
CAACCTCACTCAGCTCACTTATCATAGGATATAATTTTCCACGGGACTTCATCATTGTGT
ATTTGGCCACATCCTGCTCCTGCTCCCACTAGATCCTCCCACTCCAATCCTACCTGAGGC
ACCATGTTCTTAAAAGACTCCATGATCTTGGAGCTCTTGGCCTCCTGATAATAGGAGAAG
CAGCCAGTGACGATGACCACGACGGACAGTACGATGCTCAGGTAGAGCTGAGGGTGGGGA
AAGAAAGCGTTTATCAGTGGGACCTTGTCGTCTTCTTCATCCTCAGAAAATCAGTCTGCA
AGGGGCACAGCAGTTTCACCAGGTGTAAGAGACCGTAAGACTGAGTTGAGAGCAGAGGGG
TAGAGAAGAATCTGAGGTGGGACCAGTACACTTGGCTTCCTGGGGAAGGAACCCTGAGCC
ATGGTGAGCCGTCAGCAAAATTCCTGGTCAGAGAAGGCCTGTATCTTTCTCTCCAGGAAG
GCTAATCTCTGGATGGAGGGGGTGGATTGTGAGGGAGGCTGGGAGGAAGGAGATGAGGTT
AAAATTGTGGAGAAGAGAAAGGGACTGCAAAGTGCTTTGGGGATCAATTGGGAAGGTCAT
CAAAGAACAGCAAGTTTTTCGGGGACATTGTGCACCTCAGGGAACTGGACCAGAAGCTTT
TTAGATTAAAAGGTGAGAGGAACCAAGATGGAACTTAGAAAGTGGAGTATTAGGGATTTT
GGTTTATTACATTAATGTACATTTATTACATTATTATGTAATGTACATTTATTACATTAA
TGTACATTTAATTACATTTTATAATTAATTACATTCATTACAATGTAATTAATCAATTAC
ATTGTAATTAATTACAATCAATTACATTTATAATTAATGTACATTTATTACATTATTACA
TTAATGTAATAATGTAATTAGGGATTTGGGCCAGAGGACTTCAGGAGTGCTAGGCTGCTG
AGCAAAAGAGTGTCTGGGGCTAAGCAGAGATAGGGCTGGCTAGTAGTAGCTGAAGAGACT
CACGTTGTCTTTGGTAGGCTCCTCATTGAAATATATCTGGATGCTGTAGGCCACAAAGCA
GAGAATGGCCCCAGTCCATAGTAGGAGGGAGAAGCCTCCGAACAGTTGCTTACAGAATTT
GACCCATTCTGGAGTGGTGGGGGGTGGGGTAACAGTATTGGGTCCACCTCGAGTCAGGAT
TTCCTTTGCCCTTTGGTGGCTATGGCCCTGTGCAGAGAAGAAATAGGGTTGGATAGAGAG
CTGTGAAAAGAGGAACAGCCATAGCAAAAGGGAACCTGACATTTGGAGCCCCAGAATGGG
TCTAGAGACTAAAGACGCTTTCAGAAGGTCAGTCTGGAAGTTCTTCCTGGATAAGGTGAG
GTTTCAAAATTTGCATTAGAGGAGGGATGTCATTTAGCATGCTTACATAGGAAGGTTTTT
GTTTATGGATTGATTCACAAACCTTTTTGAACTTGAGAACCTATCTCGGGTCCTAGGTGC
TGAGGATACCAACATGAATAAGAATGGTCCCTACCCTTAAGGTGCTCCAGTGGGGAGATA
AATACATACAGATAATTATAATGTGCAGGGCCAATGTCATGATGAAATATAATACTTAAT
GTTGATAACATATTAACACCACGCTTTGACTCTCCAACTTAGAGGGAATAAGATCTAGTG
TTTGGTAGCACAATAGGGCAACTATAGTTAATAATTTATTATGGATATCAAAATAATTAG
AGGAGTGGATTTGGAATGTTCCCATGCAAAGAAATGATAAATGTTTGAGGTTATGGGTAT
CCTAAATACCCTGATTTGATCATTACACATTGTATGCTTATATCAGAATAATACATGTAT
ACCATAAATATGTACATCTACATATCCATTTTTTTTTTTGAGACAGAGTCTTGCTCTGTC
ACCTAGGCTGGAGTGCAGTGGCATGATCTCGGCTTACTGCAACCTCCATCTCCCAGGTTC
AAGTGATTCTCCTGCATTCAAGTGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGAGATTG
CAGATGTGTGCCACTATGCCAGGATAATTTTTGTATTTTTAATACAGATGGGGTTTCACC
ATGTTGGCCAGGCTGGTCTCCAACTACTGACCTCAAGTGATCTGCCTGCCTTGGATTACA
GGTGTGAGCCACGGCACCTGGCCCATAAATTTTTAAAAAACATAAATAGAAAAGAATACT
AACAAAAAACATGAATGCATAGATTCTCATTCCACTCTTGTGCACAAGCTTATGTGCTTT
TTCCTGTTAATGAAAATGATAGTAGAACCTGCCAATCACCACCAGCCACTCCCCAACCTC
TGCCTGAAACACCCGAGGGGCCCCAAAACCCTTTCAGGGGGTCCACAAGGTCAATTTTCA
TAGTAATACTAAATCATTGTTTGCCTTTTTTTACTCTCATTTTCTTAAGAGTATATAGTG
GAATTTTCTGAAGGCCAACTGGCATAACATCACAACAGATTTTATCCAGAAAATATTTGA
GAATCCAGCTATCTTCTATTAAAAAGCAAGACATTGAAGAGGTTTGCAAAAATGTAAGAT
GCTGCTAATTTTTTTGTTTTGAAAAATACAGTTATTTGTCAAAACATATATGAATATATG
ATAACTTTATTTTTGTTATTTTTAAATGAATTGAGAAATACATTTTAAAACTCTCAATTT
TAATTTCTAATATGGTAAATATAGACAGACTTAAGCCACATAAGCACAAGTTCTTTGCGG
TCCTAGATAAATTCTAAGAGTGTAAAGGAGACCTAAGGACAAGACGTTTGACCAGCACTG
CCCTAAAGCATTCTTATTCTCTTATCTAGTCCCACACTCTCTTTGAGGGTAGTTACCATT
TGCAGCTTTTTCCAGGTAGTGTCCATGGAACGTGGCCAGGCAGAGGGTGAGGGGTGGGAA
CGTTGGACTTGAAGTTAGGGGGCTGGATTCCTAGTTCAGCTTTTGTCCTGGCAGCCTCAC
AGTCAGAGTTGGAGACTCTCTGCCTCCTCAGGGAGCTTCTTACTCACCTTTGTCAGGTCC
ACGGAGTACTTGGTGCTCAGCTCTTCCAAGGTTAATTTGTGATCATCCTGAGGGGACAGT
AGAGGCATTGAGGGACAGGGGGTGGCCCAGGTCATTTCCAGGGAGAGGGGGAGAAACAGA
CTGGAGAATGTTAGTCCAAACTGAGACTGCTCCATTTTGTAAGCTCCCTGCAATTCTTTT
TTTGAGATGGAGTCACTCTGTTGCCCAGGCTGGTGTACAGTGGTGCGATTTCGACTCACT
GCAACCTCTGCCTCCCAACAGGTGTTTCTCCTGCCTCAGCCTCCCAAGCAGCTGGGATTA
CAGGGGCCCATCACCAGGACCAGCTAATTTTTGTATTTTTAGAGGCGGGGTTTCACCATG
TTGGCCAGGCTTGTCTCAAACTCCTGACCTCAGGTGATCTGCCTGCCTCAGCCTCCCAAA
GTGCTGGGATTACAGGTGTGAGCCACCACGCCCGGCCTAGCTCCCCACTATTTTACAGGC
CTTGGTCAAAGTGAAACATTTCACGGGGGTTCGGGCCAGAGAAACAGCCTGCCTAACCAC
CTGACCACAGGGCAGACGAAGGCCCAATTAAAGACAAAGACCCCACTAAAGAAACATCCC
TATCACATCCTGCTGGGCAAAGGTCCAGGGAATACCATGATTATATTCTGTGGAAACAAG
GGCCAAAAATCACCTCATCATGAGAACATCTTATCGATATCCTGCCAGGCAGCAGGCCAT
ACAGCCCAGACTCCTCCCATCCATCCCTATAAGTACCCAGCCTGTAAGTGGCAGTGGACT
GTGGAATTAAGCTGATCCCCCACTTCCACAGGTGTCTGCAATATACCTGTGCTTGCTGTT
GAGCTGCCCTGTCTCTCTGTGTGTATCTTTTTTTTTTTTTTTAACCCTCTCCTTCCCTCC
AAAGCCTAACAGAGAAGAGATGTGGCTCTGGCCTGTGTGTTTCATTCTCAAGGTAAGATG
TTAAAGATAGGTGGAGGAGTGTTTTCAGAGGGCAGCTGTCAGCGCCCACTTTGGGTGGCC
TCACCATGACCACTTCCTTCTTCAGTTCCTCCATATTGCGCTTCTGTTTTTCCCTCTTCA
CCATTTTTTTCTTGATAAGCCCTTTTTTAGGTCTTCGTCTTGGACTCTGGTCATGGGGAG
CCACTGTCCCTTTCTTCCCCCAAAGCCCCATAGCTATCCCCAGAAAGAGCTGCCCGAGCT
CAACTGTGGGAAGAAAGCTGAGAGAGTGAGGCAAGGGGAAGGGAAGAGGGCGCGCGGGCA
AGGGGGCCACGAGAAGAGAGTGGTGGGGAGAGAATGAGGGAGCAGAAAGAAAGAGGCAGG
GAGGGAGGTGTTGGGTGGTGAAGGTGAGAGAGAGGAAGGGAAGTGAGAGAGGAGAGACTG
AGCGGTCCTCCAGCCGTCCGCTGGGAAGAGGAAGAGTCAGGAGTGAGGGAAGAGGGAGGA
GAGAAGCCTAGGGTGGAAGGATAAAAAGGTAGAGGTGAGGGAATGCAGTGAGGGCAGGAA
ACAAGAGGTGAAGCGTAACCAGGTGCCTCAGTGATGAAGATGCCGCAAGGCCCACAGGAA
GGTGGGAAATGCAGTGAGAGTGAGGAGGCGGAGTGAGCTTCAAGGATCTGGGAACCCCCC
AGTCCCAGGCCCTGTGGTTGCTGGGGCAATGACCCAGGTCTGGCATCACAAAGGCCTCCT
GAAAGTTCTAACCAAGAATCCAGAAGTCTTGCCTTGGCGATGGTCCAGGTCTGCTGTCGC
AAAGGCCTCATGAAGGTTTTAACCAAGAACCTAGAAGTCTCAGTCTTTGGGTTTGAGGAC
GATTGGAGCAGGCCCTGCTACAGAAAGAGTTTCAGTCTGAGGGCAGAACTAGAACAAAGT
TCTTGTGTGGTCCTGCAGACTTTGGAGGCTTAGAGGTATGCCAAATAGATGACTCAAAAA
TAAAGCGGGTATTCGGCCGGGCGCGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGG
CTGAGATCGAGACCTTCGTGGCCAGTATGGTGAAACCCCATCTCTACTAAAAATACAAAA
TTTAGCCAGGTGTGGTGGTGGGCACCTGTAATCCCAGCTGCTCGGGAGGCTGAGGCAGGA
GAAACATCTGAATCCAGAAGGCAGAGGTTGCAGTGAATTGAGATTGCATCACTGCACTCC
AGCCTCGGTGACAGAGTGACTCCATCTCAGACAAACAAACAAACAAACAAACAAACAAAC
AAACAAACAAAAAACCATAGCAGGGAGCTTACAAAATGGTGCAGTTGCAGTTTGGACTAA
TATTCTCCCGTCTGTTTTTGAGACTCCATCTCAAAAAAAAAAAAAAAGCAGGTACTCTGT
GTGTGTTTTTTAGCAAGGCACACTTTTCCACTAACATTGGGTTTGATCTTTTAATTTTAG
GAGATCAGCTAGCAGAATAGATCAGATCTTGGGCTCTGGAACCAGTCCTGGATTTCAATC
CCAACTCCTCCACTTGTCAGCTGTGTGGCTTTGAGCAAGTTACCTAACCTCTGTACCTCT
CTTTTCTTATTTTTAAAAGAGGATACCTTCTACCTTAAGTGAGGTGCTCTACAAAAAGCA
CTATGTGACATATATAGTATGTGCTCAATAGGTAGCTTGAATTCAGTAGTAGTTTTATTT
GTGGATTAATATGCAGCTCTTCTCAGTGAGGGTAAAAATATGCTTTTCCATGTGATAGCG
TTGCATTTTCTCATTTTAAAATGATGTACTTACCTCTTCCATTGACCTTCTCTGGTGTCT
CAGTAAGTGCTTTGACTATATTAACTGTATATATGTTTTGCATGTCCATAGGATTCTACC
TCCTTCCAAGAATAATCTGAAGCATCTATACTTTTCTGTCAACCATTATATATATTTTTC
AATTATGCACGTCACATAGATTTTCCCATTCTGTTGTTTGATATTTGTTTATTTACTTTT
TGAGACAGGATCTCACTTTGTTGCCCAGGCTGGAGTGTAATGGTGCGATTATGGCTTACT
CCAGCCTCAACCTCCCAGGTCCAAGTGATCCTCCCACCTCAGCCTCCCAAGTAGCTGGGA
CCACAGGCATGTGCCACCATGCCCGGCTAATTTTTTTTATTTTATTTTAGTAAAGACGGG
GTGCCCCTGTGTTGCCCAGGCTGGTCTCAAACTCCTGGGCTCAAGCAATCCTTGGCCTTG
GCCTCCTAAAATGTTGGGATTACATAAGTGAGACACCAAGCCTGGCCTGATATTTATTTA
ATTGCATTTTGGTTGGGCATGCTTTTTAAAAATATGACTGTATCTGGAAACATTCATCTT
GGTGCTGATGCAATCCTCCTTGAATATTCAGAAATAGAAATGCTCCCTTCCCAGCTGGGA
TAAATGATCGTCTATTTCTTTAACAGATTGGATTTTTCTTCTCTATTAAAAATGTTTAAG
ATAAAAATTGAAAGCCCCACCTTCCCTCCCTCCAAACTCAGATTCTCCCCACTGCTGAAG
TTACTGCTGGTAACAATGTGCTGCATGTCCTTCCAGTCTTTTTTCTATGTTTATACAAAT
AGATATCTAAAAGGAGGTATTTTTCAACTTTTAAACAATCATTCAACTCTCTACCAACCT
GTCATGTACATAAAGCTTCTTTTTTTCAGTGCTGTGAGGCTTCCATATTCTGTATTGACC
ATGCTCTATTCAATCATTCCCATTACTGATGGATTTATGAGATATTTTCCATTTTTTTAA
CCATTAATAAAATTGCTAGAGTGTCATTCTTGCACATAGATATCATCAGGCCCTTGAGCT
TCTATTTCTGTAGAATCAGTTCCTGTTGCTGAATCATAGAGTACACTCATTAACAATCTT
AAAAGATTCTGCCAATTGGTCTTTAAAAGTGTTTATCTATCTGCATCCCAACAACAGGAT
GCAAGAATGTCTGCCTTCCACACCTTTGATTATGCTAGATGACCTTGATTTTTACTATTA
TAATCAGTGAACTTTGATATCTTGTAGTTTTAATTTGCATTTTTAAATTGTCAATGTGAG
CATTTTCTCTTATGTTTACTGGCTTTCTGGTTTTCTTTCTTTCTTTCATTTCTTCTTTTC
TTTCTTTCTCTCTTTCCTTTCTTCCTTCCTTTCTTTCTCTCTTTCTTTCTTTTGACAGGC
TGGAGTGCAGCGGTGCAATCTCAGCTCACTGCAACCTCCACCACCTGTGTTCAAGCGATT
CTCGTGCCTCAGCCTTCTAAGTAGCTGAGACTACAGGCACACGCCACCATACCCAGCTGA
TTTTTTTGTATTTTTTAGTAGAGATGGGGTTTTGCCATGTTGGCCAGGCTGATCTTGAAC
TCCTGACCTTGGGTGATCCGCCTGCCTGGGCATCCCAAAGTGCTGGGATTACAGGCATGA
GCCACCATGCCTGGTCTTGGACTTTATTTATTTATTTTGTAAATTGTCATTCTTACAATT
TGCCCAATTTTCCATTGTTTTCTTTTTTATATTGATTTGTAGGAAACCCTTGTCATATAT
AACACAAATGTTTTCTCCCAGTCTTTGTGTTTAATGTAGATGAACATAAAATTCTTAAGA
AGAAGGTTAGAATTAAAGTTAAAATTCATATGTTTTTCTATGCATCATCTATGTGACAAT
AACACTTAGCTCAGTCTTGCAGATGGGCATTGCCCAAAAGCAACTTTATGGAGATACAAT
CAATTGAAATTATTTTTAGAAACCTCATTTTGTTCTAGAGATCTTAGCTCAAAAGTCCAC
CTCTTCGGAGAGGCCTTCTCTCATAGTTAAATCCAAAACAGCCCCTCCGGCGCCAGCCCT
CTCTCTATCACTTTTGATCTTCACAACACTTCTCTCCCTCTGAAATTATCCTGCCTGTTA
ACTGTTGACTTGTCTGATTGACTTGTCTTGTTGACTTGTCTGGTTCTCCATGACCCTAGG
GACCTTCCCTGTTTTTTTCCACAGCTATATACCTGGCTCCTAGGATAGTGCTTGGCACAG
GGCAGCTGGTCCACAAATAGTCCCTGAATAGATGTTGAATGACTAATGAGTTTTCAGGTT
TTATCTTAATGCTACAAGGTTTTGATAATTGCCACTTTGGTCTGATTTTTTTTTTTTTTT
TGAGACGAAGTCTCACTCTGTTGCCCAAACTGGAGTGCAGTGGTGCAATCTCAGCTCACT
GCAACCTCCACCTACCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGA
CTACAGACATGCGCCACCATGTCTGGCTAATTTTTGTATTTTTAGTAAAGACAGGGTTTC
ACTATGTTGGCCAGGCTGGTCTTGAACTCCCGACCTCTTGATCTGCCGACCTTGGCCTCC
CAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCAGTGGTCTGATGTGTTTTA
AAATCTGTTGGGGTAAATATGTTAGCATCAGTGATCTATTCATTTGCTTCATAATTACTT
AGAAAAAACCTCTGAGATTCTTGCCTGATTACTCTTGCAGCTGAATGTCACAACCAATAT
GTCATGTTTTATAAAAATGCAGCGAGGATTTTAATTGATATTGAATTGACTCTTTCATAG
TAACTTATTTTTATCTTTACTACGTTCTGCCTTCCCAAATGGCAGTCAAGTTTAGCTTTC
CATGAATTCATGTTTTTTTATTTTTCTCATTGTACTTTTAAATTTTCTTTAATAGTTACT
ATGTGCTGCACACAGTAAACCTTGAGCGTAATTTGTTTTCATTCTATTGTAAATAGAAGC
TCTTTATGCTGTATTTTCTGTCTCCCTAATATTTAGGGATACATTTGCTTCTTTGAAAAC
TGATACCCATATACCCTGTAACTTTGAATTTATTGCTTCTAGGATTTTTTTTGTTATTGA
TGCTGTTGCTTTGTTTTGGCTGAATTTCTTGGATTTTTAGGGAGTTATGCTCGCTAAAAA
CAAAGTTTTATTTATTTAGAATTTTTATTTATTTATTTTTATTTTTTGAAACAGAGTCTT
GCTCTGTTACCCAGGCTGGAGTGCAGTGGTCCAACCATGGCTCATTGCAGCTTCAACCTC
TCAGACTCAAGCGATCCTCCTCCCTCAGCCTCCCAAGTGACTGGGACCATAGGTGTGGGC
CACCACCCCAGGCTAATTTTTTTTTTTTTTTTTTTAATAGAGATGAGGTCTCACTGTGTT
GCCCAGGCTGGTCTCAAATTCCTGGGCTCAAGCAATCCTCCTGCGTCAGCTTCCCAAAGT
GCTGGGGTTGTAGACGTGAACCATAGCACCTGGCTTATTTAGAACTTTTTTTTTTGGAGA
TGGAGTCTCTGTTGCCCAGGCTGGGGTGCTGTGGCACCATCTCGGTTCATTGCAACCTCT
GCCTCCTGGATTCAAGTGATTCTCAAACCTCAGCATCTCAAGTAGCTGGGATTACAGGCA
CCCGCCACCATGCCTGGCTAATTTTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCA
TGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAAGAGATCCGCCCACCTCAGCTTCCCA
AAGTGCTGGGATTACAGACGTGAGCCACCGCGCTCGGCCTTTGTAGAACTTTTAAACACA
AACTGCTTATCGAGGATTTCAAATGTTTTATTGCAATTATTTGTTATAGTTGCTGTTATT
GGTTTTCTAGACTTACTACATCCTTTCCTCTCTTCTCTGAACATGATTACATTTTCTTTT
TTTTTGAGACCGAGTTTCACTCTTGTACCCCAGACTGGAGGTGCAATGGCGGGATCTCAG
CTCATTGCAACCTATGCCTTCCGGGTTCAAGTGATTCTCCTTCCTCAGCCACCCGAGTAG
TTGGGATTACAGGCGCGCGTGCCACCACGCGCAAATTTTTGCATTTTTAGTAGAGACAAG
GTTTCACTACGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGACCCACCTACCTC
GGCCTCCCAAAGTGCTAGGATTACAGGCGTGAGCCACCGCGACTGGCCCATGATTATATT
TTCTGATACACTTTTTCCTCCAACATTTTTATCAGTAATAGATACTGAATTTTACTGATA
GCCTCCTCAACCTTTTTTGAAATGATTATTTCATCCTTTGTCTAGTTAATGTTAGTTGTT
TGTAACATTTTCCTTGTAATATGCTATCCTTGCATTCCACCATTTGGGGTAGTCAATTTA
TTATCTATATTAAATATAAAATTTTAACAAAATAGTACTTATCTCATAAAATAGGCTGGG
CAACACAAAACACAAAATAATTTTTTATATTCCAGCACATTTTAAATAATATAAGGAAAT
TCTTTGAGGAATTTGCAAAAAATCCTTCATTGAATTCACTGGAGCCAAGGATATTTTTGA
AAGACTCACTTTGTATTAAATGTCTTCCTTTGATATTGATCTAACCACTTTCTTCCTATT
TTTTGCTGCGTTCTTAGCATTATGAATATTTAGTGACTATCTCTGATTATCTCTGATGCA
TGATCACATTTCCTATTCTGTAGATAAAAAGAAAATGCCATGGAAAGACTTTCTGCCTGG
GTCAAAAGTTGGCCTTAGCTTCTCAGATTACATTCAATAGTAAGATTCTTCTTTTTGCTA
AAATCCTCTAGCAGACCATCAAATCTCTTTGGATCTTTTTCTTTCTTTCTTTTCTTTTCT
TTCTTTCTTTTTTTTTTTTTTTTCTGAGATGAAGTCTTGCTCTGTCACCCAGGCTGGAGT
ATAGTGGCACAATCTCGGCTCACTGCAGCCTCTGCCTCCTGGGTTCAAGCCATTCTTCTA
CTTCAGCCTCCTGAGTAGCTGGGATTACAGGTGTATACCCGGCTAATTTTTGTATTTTTA
GTGGAAGACAGGGTTTCACCATGTTGGCCAGGATGGTCTCGAACTCCTGACCTCAAGTGA
TCTGCCCACCTTGGCTTCTCAAAGTGCTGGGATTACAGGCGTTAGCCACTGTGCCTGGCC
TGGATCTTTTTCTTAACCCCCTACCGCATCTTTGAGATCATATCTTCTCCCTTTCTCACG
GATCTGCCTTGCCCCTGCTGCTCAAATGTTAATTGTCCACAAATTCCTGGCTCCCTTGGC
AGCCTCCCCAGTTCACTGAGCCATTGGGCTAGTCAGGCTCTGTCCATGCACATAGGCTTT
CTGTTCTTGCAGTTGCAGAGCATGGCATGGTTAAGAGGGCAGGCCCTGGAGTCAGACTGG
CCTAGGTTTGAATCCTGCTTCAGATGCTTACTACCTTTGAAACTTTGAATAATAATTTAA
CTTTCTGAGCACCAGTTTTCTCATCTGTAAATTGGAGATAATAATAGTCTCCATCTTACT
GAATTACTGTGAGGATCCTTTCAGTCATCCAACACATATTTATTAATTGTCTAACGTGTG
TCAGATGTTTTAGGTGCTAAGGATAAAGGTGTTGAACAAAAGAAATAGAGTCTCTGTCTT
CATGGAACTTATACTGGAGGAGTCAGACAAACAAAAGCATAAACAGCAACAAAATACATG
TATATCTTTCTAAATATTACATCTAGCTGTCTTTCTATCTAAATTTAAGGTAATAAGTAT
TTATGAACAAAAACGAAGAGAACAGAGAAAGAGGTTCCAGGAAGTCATTTTATTTGAGGT
CCTCTGTGAGGATCTTACTGATGTTTAAGGAGTGATCTGAATGAAGTGACAAAGCCAGGC
ATGTGAATAACTAGGGAAAAGTGTTCCTGGCAGAGGGACCATCAAGAATAAAGGCCCTGT
GGTGGGATGAACGGAGACTATACAAATAAAATTTTGGCATAGTTATGGCACAAAATGAGC
TGTGATTAAGGCTCTTATAATCACTACTAACTATAACTGTCATTAATGACACTGTTAAGA
GTCATAATAAAGGGGCTGCAATATGGCTTGGGCAAGAATTGACTTCTGACCGTTATTCTG
AAATCCTGGCATAGGTTGTAAGAGTTGGTGTCTTTCTCTCTCCCATTCCCAGGGCCCCCC
TGGAGCAATGCACACCCACCCACCCACCCCTCCATGTCCAGCACACAAGCGTCCCCCCTA
CTGCTCATTACATTCTGTCCATGATGGTTTCTGATGTCTACTACTCAGGTGAATTTCAAG
GATTGCATCCACTTTACCCCCACCCCTTAAAGAGAGCACCCAGGACAAAGCTCTGCATGA
AGTACAGATTGTGAATTGGTGTTGACTCTTGGGCTCCTCAACCCACTATCTCCTTCCCCC
ATCCCATCAGATAGAGAATGGCCTGATTTTGGTCTGGAACAGAAAAAGCAGAAGTGCCCC
TGAGGATCTTGTTCTTAATAGACTCACAGGCCCCTCCCTGTCCTGGACAAACTCTTGTGG
CTCTTAGGGTGGGATCAGCATGAGGAAGGAGGCTCCTGCTATAGTTTCTTGTAGGTTATT
TTGCAACCTAACTTCTTCCCCTCTTGCTTTCTCCACGGACATCATCTGCTCCCAGACCAT
TTCCCTCCCATCCCTGACACTTGCTATCTCTTTGTTGCTTTCCCTACAAGCCGAGTTCTG
CCACAGCACATATTTCAATATCACGATTTAGGAGGGAGGCAAGTATAAAGTGTAGAAATC
TGAATTATGGAAGAGATTTCTTTTTTTTTCATAAAGAAATGCCACTTTATTATTTTCAAG
TACATAGGTAGTACCTCAAACTAATGTCTTACAAAAGGTCACCAATAAAGATCCTGTAGA
TGTTTCTTTAACAAATACATAAAGATTGATGATAATTAGCCCATGCACTCGCTGCTTCTA
AAAGGATATTTCTAAAGTGCCTGAAAAGTATTGTTTTTGGTAGACTAAACATGCCACCTC
TAGCAATATTGTTTATGCTCTTAATTTACTAAAAAAATGCCATTTTTATTGATTGTGCAA
AGATAAACTTTTGTCCACAGTTAGTAATCTCCAATTAATCGGATCCAAATTAATATTGTC
TCCCACTTAGATTCCCAGGCCCAAGGCAATGACTCCCTTACTTCCTTGCTTCTGATAAAG
CAAAATTCCAGTGCAATGAAATGACAGCCTTTGGGAGGTGGTTTATGGGTCTGACCCAAT
GCTTGTCTTTTGTGCTTCCTTCCTGTCTGCCTTAGGTCTTCCATTTTCCTCAGATGTCTT
TCTCACTTGCATGACCTATCTAGGTCTCTCTCTACAGGACATTCCCAGTGCCTTCTAAGC
CAGGCTTAGAGAATGGGCAAGGCTGCCTGCAGAGCAAAAGTGTTAGATAGGGAGTAAGGG
AAAGAAAGCTATCTCCTGTAGGAACCTGAAACCAACTCTCCAGCCCAGGGTAAGTGGGCA
CAATGATCGTCGGTTTGAAGGGCATTTGCCTGGAGGGAACAGCCCTGCCACCTAAGACGT
CAAAAGCAAATCATTTTTTTTTTTTTTGAGATGGAGTCTCACCCTTTCGCCCAGGCTGGA
GTGTAATGGCACGATCTCAGCTCACTGCAACCTCTTCCTCACAGGTTCAAGCAATTCTCC
TGCCTCAGCCTCCTGAGTAGCTGAGATTACAGGCGTGTGCCACCATGACTGGCTAATTTT
TTGTACTTTTAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTCGCCTCGAACTCCTGA
CCTCATGATCCACCTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGC
ACCCAGAAAAAGCAAATCTCTTAGTATTTTTCCTCTTGTCCAAAGGTTCTGACCATGTTC
ATGACCTAAGCTTGTCCCTGGAAGCATACATGTCCCTGGGAGACAGGAAGGTTCAGGGAA
CTTCTCCACCCTGATTCTAGCCAATGGCCAGCGAACTCCTTTTCCAGGGTTGGCTTGGCA
GTGTCGGGGAATGATGCAGGTTCATCGGGATGGGCATGAAAAGAAAGGGAATGGAAGAGG
CTGGGAAAGAACTTGTGGCCATCCCTTTCAGAACAGCATGGAGCTCTGAGGACTTAGTAT
TACAGAAGGTGAAGTGTTATTAAGTACATGAGTGACATCCGGACCTTGTGGACTAAGAGG
ACCCCTAACCAAGGGTCAGCGGGGAACTCTGTGGCACACAAGTGTGGCATTTCTGGAAGC
TCTTGATTGCCTTCTGGTCCTGCCTCTGCTGCTACCCTGATGAGATCTGAGTTTGTTCTG
CTGGTGGGGTATTCTAAAATGTGGGACGTAGAGCTGGAGTCCACGACATCTATCTGGAGA
CTCATGTCAAATGTCCTGTCATTGGCACTACCTCACTTCCTTTGTTGTTTCCTTCCTCCA
GCCAGCCCTACCTCCATCTCCCACCTGTCTGCCCAGCTCTCCCTGAAGGTCCCTTACCAG
CCTCGACTGGGAGACAAGTCCACCTTTTCCAGTCTCAGGCTCTTGCACTCACCAGAAGAA
CCTTTTGTGATTGCAAGGTCTGAAGGGGAAGCCAGGGATAGAGTCCTGCAGGAAGCTAAC
GGGGGTGGAAGTGGGAAATGGAGTGAGGCTGGGGTGATCTGAGAGGGCTTCCTTCTGGTT
TAGATGGGTTCCTGCTTTTGGATGCTGATCTATTACAGTAGGAAGTGGGGTTGAAGGGAT
GGGAGTGGGCAGGGTGGGGTAACCCTTAATTCCTCAGAAAAAATAGACAACATAGTGGAG
TGGGATGGAAAAGGATCTGGTCGGGGGGACTCTAACACATAGTGTCTAATCTGATTGTTC
ACAGTTAGGTCTATGGGGTCATCACCCCAATTTATATACCCCGCAACTTAGCCTGCTGAG
TTGCCTCATTATCTCTCCCCAAATGTTGCCACCCAATGCCACCCGTTATTTCCATCCCTC
TCCATCACCATCCCCACAACACCTCCAGAGCTCCCCATCTTTCCATGCCTGGTTCTTCTT
CCAATGGGGTCAGTAGTATGTCTCCTTCTCCACCCAGCCTGTTAGAGAGATTGGGAGTGG
AGATTGCAGCATGAGCTTAAAAGGAGGCAAGAGATCAATTTCCTAGGGGCTTGGGTCGCT
GAAGCCAGGTGGAAGGAGAAGCCTGGTGAAGGGCACTGGGGGAAGTGGCTTAGGAAGGTG
GAAGGAGGCTGGGTGCAGTGGCTCATGCCTGTAATCCCAGCATACTGGGAGGCTGAGGCA
GGCGGAGATCAAGACTCCTGGCTAACCCAGTGAAACCCTGTCTGTACTAAAAATACAAAA
AATTAGTCGGGCATAGTGGCATGCGCCTGCAATCCCAGCTACTCTGGAGGCTGAGGCAAG
AGAATTGCTTGAACCCAGGAGGCGGAGCTTGCAGTGAGCCGAGATCGTGCCACTGCACTG
CACTCCTGGTTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAGAAGGTGAAAGGGAGGAGAAGGAGGTCCAGTGAGCTGGGGCCATAGGTTAAAGGA
AGGGAGGGTGAACCTGCCTTTAGGGGAGACTTGTATTTAGCACATTGGAGGCTGGGGCAG
AATAGGTCGAGGGTGAAAATGCAAACGCCCACAGGGCCTCTTCAGGTGACGAACGAGAGT
CTAAGGGAGCAGCTGTCCATTCTTGCTGTGCAGAGATGTGGACATGGGATTAACAGCTCT
TCTGATCTTCAGGAGAAGTCGAATTCAGATTTTATGTGAAAGACCCTAAATTTTCTATAT
CGGACCAATTAATCCACCCTCCTCCCCCCACACACACAAAATATGGCACAGGTCAAACCA
AACAGTATTCCTGGACAGTATTTGGTTTGTAAGCCATCATATTTTAACCTCTACTAAGTG
ATTAAAAAACGCTTGTAGGAAAAACAATAACTTGTCGGTTGATGAGTGGGGATCAGGAGG
CCTGGGTTCTAGTACCAGTCCTGCTATTCTTTGCTTTACGACCCTGAACAGATTCACCTC
TGAGCCTCCTCTATCTGTAAAATATGGACGTGGGACTAGGTGACCTGGAAAGGCCCTTCT
AATTCTGATGTTCTGTGGTTTCAGGTGGAAGGTGGAGGGCCTCGGAGACCAACTGTGAGT
TAGGCGGGGTTTAGAATCTGATGGGAAGAGGGCAGAGACAACAGGTTCGAAAGAGTCAGG
GCTCCTGGGACCTGGGACCCCAGGATCTGAGGGTGTTGAGGAACAGAAGCAGGAACCAGT
AGTGGGAGTGGAGTCTGCGTGTGGTCCTGGAGGGAGGAGCTGGTGGTGGGGCTTGCACTT
TGCTGGGGGGAATGTGGAGGGGCTTACCACCAGGATACCGCCGCAGGATGAGCTTTCGGA
CCTCATCATAGATGAAGATGAGGAGGCTGTAGGGGAAGGCGCAGAACCACCAGGTGACTC
TGAAAGCAATGGAGGAGAGTGTCAGCAGCATCAGAGGTTGGCTTGGTGGCTGTCACATAA
AGGAGCATTCAAAGCGATCAGAACTTGGATCCTGGAGGGGGCTGAAGGCCCCCCGTATGA
CTACTCAGGCCGCCCGAAAGAGACACTCACTTGAGCGGGTACATGCGGAGGGCTACACCC
ATGCCTGGGCAGTAAGAGAGAAAGGCAGCCAACGCCGTCTCCTCCAGGAGCCCAAAAATC
AGGATCTTGTTCCTGAAAGGCAAAGAAAGGAGGTGGCAGGTGAAGGGGGATCATGGAGGC
AGAGATCCTGGGATACCCCTGGGGTGCAAGGGAAAGAGGAGAGAGAATTCTAAACGACAT
AGTCGCATGTCTTCTTCCAACAGCCTCTTCTCATGCTTTATGTAACCAAAGGAAGATGTT
ATTTGTTTTTCTGCTTACTGAGTTTACGTCCGAATGTTGTCTATTGCACGTATATTCATT
CATTAAATAATTGTTTCTAGGTGTTGGGTGACGTGTTCTGTACTGGAGACACGGTGGTCA
ACATGGGGCCTGTCTCATGATCTTGTTATTGCTCCAGGCACAGGGCCCATGAAAGTGTGT
CTCCCCAGCAAGATGCTTGAAAGCTCCTTCAGTGCAGGGCCCATGTATGTCTTCTACCGT
CTCAGCATCTCCCACAGTTCCTGGTGGTGGTTTCATTATAGATATTTAATTCAGAGAATG
TAAAGGGGATCACTGCATAATAAGTGGTTAATATATGTTCACTTTATCAGAATTGAAAAG
CAGGATAGAATAAGGAGGTTCTCAGGGCAGTTTCTGCAGTCAGACAGGTGGTGTCTATTC
CCAGTTCTGCCATTGACTAGCTTTGGGTTGCAGGCAATGTTGAATTTCTCTGAGCCTCAC
GTTCCTTCTCTATCAAATGGAGATTTTACCTTTTTATCATAGGGTTGCTGGGAAAATTAA
GGGAGATAACACGTGAAAAGCTCTGCAATGTTCTGTCACTGAAATGTTCAGTGACAGACC
TGGAAAATGTTCAGTCACATTATTACTCCACTTTTTTTTTCTGAGACAGAGTCTCACTCT
GTTGCCCAGGCTGGACGATCACAGCTCACTGTAACCTCCACCTCTTGGGCTCAAGTGACC
CTCTTGCCTCAGCCTCTCCAGTAGCTGGAATTACAGGTGTGTGCCACCACGCCCTGCTAA
TTTTTATATTTTTTGTAGAGATAGAGTTTCACCATGTGCCCAGGCTAGTACCAAACTCTT
GGGCTCAATTGATTCTCCTGTCTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAACCA
CTGTCCCCGGCTACTCCATCTTTTGTATTCTTACACAAGGTACCTCTTTTTGGTTCAAGC
CAGTGATTTCCAAATTTTCACTCACTAAGGACCTCCTTATTTTCTTCTGTAAAGGCCACA
TTTAATTGTTTGTCTCTCAAGCTACATTTGTGAATAAGTATTGAATACATTTCCCCATTT
AAAATTAATTAGAACTATCCATGGCTTCCAGACAGAACTGTGAATCAGCATCCGATCACC
ACGTCATGATATGCGCTCTTGGCTTTTGCCTAAGAATGACACATTAGTAAGCCTGGTTGC
CTTCGCATAGGTGAGTGCTTTATTTTCATAAAGCTTTTCAAAATAAGGCAAATAGCATCT
CTGAGGATCCCCAGTGGCCCAGGGACCTAAGGTGAGGCCTGTGGTGGTATTAGTACTCTT
CCTCTGTACCCAGCCTGATTTTCATTTGCCATTTTTCCCATTTGCCTCTAAGATGGGCTG
GATGCAGCCACTATGGCCATGTTCCCACCTTCGTGTGTCATCCCTGCAGTGCATAGCAAG
TCCCAGGCCCCAGAATTATACCCAATTTCTTAGACTCTCTGCTCCTTGTTCTCTTCAAAT
TGCATTTTTTTTCCATTAGTATTTTTAGCTTACTGGAATCTCCTTCCTTCATGTTACCTT
TATTTATCTAACAGGCTTTTCACTTTATTCTCCCTTGGATCTTAAGTGTTATTAACTTCA
CTTTGGCATCTTCTCCCCACCCTCCCCAGCCCCAAACTAAGAAACTGTAACAACCTCATG
TGAGGAATTGTGGCCATTGTTTATGGTAGGAGAAAATAAAAGGAACCAGCATGAAACCTT
CAGCGCTCAACCACCACCCATAATAGAATCACAGTCATTACTGAGTTCCAAACAGTGCCA
GATGGTGTGAGCACAGAAATGTTGGGTAGTAGCCAGGGCTGGGTTTTAGAGACAGATCTG
GTGAACCCTTACCATCTTGGTGACCTTGGGCACATCATTTAACCTGTTTGGGGCCTCTTA
TCCATGAAATGTAAACAGTAATACCCACCTCATAGAGCTATCGTGGGGCTAAACAATGTG
TTAGGCACTTAGCACAGTGCCTGGCACGCTGGAACTCACACTGCAAGAAGCGCTGAACCC
GACCCTCGGCAGCACGTGGCCTCCAGAACCACAGTGCAAGTGCTATAAACTAGACTGCCT
GCGGAAGGCCAGGGGAGGGGTGGGCACAGAAGACACTGGATTTAGGGCTGGGCAAAGGAT
AGGAGCAGGTGGCACTCAAGTAGGAGATGGGGGAAAGAAGGGAGGGAGAGAAGGAGAGAA
GAAAGGTGGAGAGAGACAATAACAAAATGCAAAATTAGGAGCCTGAAGCATGGCTTCTCT
CTTCTATATGAAACCTATCTATGGATATACAGATGGAAGATTAAAATCTGATGCCCTCCT
TACAGCTCTGGTCCAGGGCTGAGTTGGAAGCTTGGCCTGTGTGGGTTGGTGAGTGTGCCC
AGAGCCTGGGTGGGTAGGTGCCATGGGGGTGGGCACTCACTTCATGCCCTGCTGGAAGAC
TGAGTTGCGGCGGGTCTTGCAGATGATGAGGTCAGCCCACTGCACCACCACGATGCTGGC
AAAGAATGCCGTGTGGCACGTGAACTCCACCACCTTCCGCTGCTCATAGGTCTGGAGGGA
GGGTGGGCAGAGACAGATGAGAGTGTCGGAGGAAAGGGTAGGACCAGAAGGTAGCATGGT
TTCTCCTGATCCACCCCTAGCCCCAGTCCCAGTTGGCCACCACTGGCCACTCCTGCCAGG
CATTCAGCTTCCCGTACCTTCACACATGTGCGCTGTGTTTACACAGCACCACTCACCCAC
TCCTGTCCATAGCTGTCCTCCAGATCATTCATGGTCCGGTCATCCCAGTCGAGGCGGATT
CCCAGTAGCCGTGATGGCAGGAAACCGTTCTCTGCCAGGATCACAAAGTAGGTGAAGAAG
CCACCCAGTGCCTGGATCATCCCTGTGGGTAGAGGGCCAAAGGCAGGGGCAGGGTCAGAG
CAGGAAGCAGAAGGGGCACAGCCCCTCAGGGCCAGAGATGGAGGTCCCTGACCCTTGGGT
AGCTGGCCTCTGTCCTGGAATTTTGCTTGGGGCTCATTCCTCTGAAAGCTGGGAAAAGAA
CCCTGTTGGGGTTCCCTCCCGAGGCCCGGGGCTTGGCGCACCGATCTGTCCGTAGGCCAT
GCTGATGAGCCTCTCATTCACCAGCTTGTCCGTCTGGGAGTTTCGTGGCTGCCGCTTCAT
GATATCACTCTCAGCTGCCTCATAGGCCAAGGAGATGGCAGGGACCTGTGTGGGGTAGGA
AATGGGGCAGGGAGGGCATTTGAAGGGACGTAGGAGATGACAGAAGCAATTGATCTTCGA
CAGTGACGATCGTTGACACAGTTAAAAAAGCGTGTATTCAGACCCCATTGTCTTCCAGGC
CTGTGCCTGTCTCCTGTAACCCCCACAGCTGGGGCCACTGCCCCAGTGCACCTCTCCTCC
CTGCCACTGTGCCATCACGATTGCCTTGCCTGTCCCCTCCTCCACCTCCTGCGCTCACCA
TATCTGTGCCCAGGTCAATGCAAAGGATGGTCACAGTGCCCAGAGGTAGGGGGATGTTGG
CAATGATGAACAGCAGGAAGGGGGTGATCTCGGGGATGTTGCTGGTCAGGGTGTAGGCGA
TGGATTTCTTCAAGTTGTCAAAGATCAGGCGGCCTGTGGGGAGATTCTGAGGGCATCAGG
GAGGTCAGAGGGACTCTTCCCCACCCCCAGCCCCTGAAGCATGGCTGCCTGTCTTCCCAA
GAGAGGAAGATTTTGTGTTCAAGGGAAGCTAAAGTGGGCTGGGCTGCCTAGAGTTGTGGA
ATGATTCTTCAACTGGGGTAAAGGGACAGGGAACAGAGGTGCCGGCTTCAGTATCCTGCA
AACCATCCCAACCCATGCAGCCTCCTCACCCTCCTCCACCCCCGTGACGATGGAGGCAAA
GTTGTCATCCAGCAGGATCATGTCGGCTGCCTGCTTAGAGACGTCAGAGCCAGAGATGCC
CATGGCAATGCCAATGTCAGCCTTCTTCAATGCAGGGGAGTCGTTCACCCCGTCACCCGT
CACGGCCACAATGGCTCCCTGGAGGGAAGACGGCCACACTTGAGGACGAAACCCCTTCCC
AAGCCTGGCTCCTCGCCTCTCACTCCATGCTTGTCTTGGCCCTGTCCCTGCCTCCCCGGT
CCCTGCCTGTCATCTGCCTCCCGTGGCTGTGCTCACCTGCCTCTGACATCCCTCCACAAT
GATGAGCTTCTGCTGGGGAGACGTTCGAGCAAAGACGATCTCTGTGTGGTTCTTGAGGAT
CTCATCGAGCTGCTCCGATGTCATGTCCTTCAGGTCAGAGCCGTGCACCACGCATGCCTT
GGCTTCTCTGGAGGGTGGGTGGGGACAGAGACAGCTGACCCCTGGCACCTGTACCAGCCC
CTCCTGCCCCCTGCCTCTCTTCACCACCGCAGCCTGCAGGCTCCCTGCTGAGCCTGCTTC
CCCTGTTGCTTCAGTTCTCCTCTCCTCAGTACTCACTTCCCCCATTTCTCTTTGAGAATG
TGAGTCTAAATCCTCACCATGGGATCATCGCAGTTGTAAGTGCAGTTTGCTAGGCCCTGG
GCTAGTTTCTTTACTCACATCCCACTCCTACAGCAGTGGAGATGGCATCCTAATTTTGTG
GTGAGAAAATGGAGGCTCAGGAAGGGAATGTGACATCTCCAAGGTTACATGGGTATTCAG
TGGCACAGCCTGGATACAAGCTCAGGGCTGAGGAACCAGTCACAATAGTGTCAGAGGTAA
GGCCTATAAAGGTCCCAGAAATGCTATCCAAATACTCCCAGGGGACACCCAAGCCTTCTG
TGCAAGAGGACGTGTTGATTAGGGCACAGGGGCTTCCTGCAGAGGCCTCACCTGGGGTTG
ACTTGACTCATGGGAATGTTGAGCCGGGCTGCAATGTCCTCCACAGTCTCGTTACCCTCT
GATATGATGCCCACGCCTTTGGCAATGG
BioPerl-1.007002/t/data/genomic-seq.genscan000444000766000024      3077313155576321 20471 0ustar00cjfieldsstaff000000000000GENSCAN 1.0	Date run:  1-Aug-100	Time: 16:43:38

Sequence HSBA536C5 : 168628 bp : 49.21% C+G : Isochore 2 (43 - 51 C+G%)

Parameter matrix: HumanIso.smat

Predicted genes/exons:

Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------

 2.04 PlyA -   7901   7896    6                               1.05
 2.03 Term -  10642  10463  180  1  0   28   43   120 0.957  -0.89
 2.02 Intr -  11044  10815  230  2  2   84   44   310 0.981  23.79
 2.01 Init -  14499  13650  850  0  1  126   53  2079 0.818 202.23
 2.00 Prom -  16112  16073   40                              -5.56

 3.00 Prom +  18327  18366   40                              -5.06
 3.01 Init +  18680  18726   47  1  2   84  105    30 0.585   4.46
 3.02 Intr +  23250  23284   35  0  2  151   69    35 0.533   5.77
 3.03 Term +  26615  26664   50  0  2  108   43    36 0.267  -1.43
 3.04 PlyA +  27305  27310    6                               1.05

 8.32 PlyA - 114694 114689    6                               1.05
 8.31 Term - 117609 117581   29  1  2  139   37    35 0.986   1.74
 8.30 Intr - 118004 117913   92  1  2  126   77   101 0.988  12.44
 8.29 Intr - 121211 121110  102  1  0   85   89    95 0.997   8.59
 8.28 Intr - 121457 121327  131  2  2  130   51   125 0.999  12.49
 8.27 Intr - 125623 125478  146  2  2  108   92   121 0.958  14.50
 8.26 Intr - 126663 126540  124  0  1  113   58   151 0.981  14.76
 8.25 Intr - 127050 126896  155  1  2   72   91   196 0.685  18.09
 8.24 Intr - 128563 128395  169  1  1   91   72   343 0.999  32.52
 8.23 Intr - 129031 128881  151  0  1   68   95   202 0.996  19.06
 8.22 Intr - 129561 129425  137  0  2  113   94   171 0.999  19.57
 8.21 Intr - 131557 131385  173  2  2  121   94    69 0.957  10.46
 8.20 Intr - 131891 131702  190  2  1  126   66   153 0.780  16.06
 8.19 Intr - 135872 135738  135  2  0   37   92   171 0.802  13.16
 8.18 Intr - 136182 136073  110  1  2  139   33   122 0.867  11.80
 8.17 Intr - 136622 136424  199  2  1   96   22   400 0.999  33.12
 8.16 Intr - 138994 138726  269  2  2   89   74   152 0.257  11.15
 8.15 Intr - 143743 143626  118  1  1  100   63   113 0.289  10.04
 8.14 Intr - 144150 144016  135  0  0   43  100   129 0.999  10.36
 8.13 Intr - 147107 146994  114  2  0  102   91   154 0.995  17.74
 8.12 Intr - 148107 147904  204  0  0  104   92    97 0.839  11.10
 8.11 Intr - 149987 149928   60  2  0  114  113    90 0.999  13.03
 8.10 Intr - 151157 150965  193  1  1   75   77   125 0.355   9.59
 8.09 Intr - 161359 161278   82  2  1  105   95    51 0.520   6.20
 8.08 Intr - 163259 163168   92  1  2  117   91   174 0.980  20.24
 8.07 Intr - 163512 163411  102  2  0  141   89    85 0.999  13.19
 8.06 Intr - 166251 166121  131  0  2  113   81   212 0.999  22.49
 8.05 Intr - 166582 166437  146  2  2  111   92   215 0.999  24.20
 8.04 Intr - 166905 166782  124  0  1  107   70   221 0.999  22.36
 8.03 Intr - 167313 167159  155  1  2  116   89   268 0.999  29.49
 8.02 Intr - 167718 167550  169  0  1   96   72   360 0.999  34.72
 8.01 Intr - 168007 167857  151  0  1   75   99   227 0.984  22.66

Predicted peptide sequence(s):

Predicted coding sequence(s):


>HSBA536C5|GENSCAN_predicted_peptide_2|419_aa
MAQENAAFSPGQEEPPRRRGRQRYVEKDGRCNVQQGNVRETYRYLTDLFTTLVDLQWRLS
LLFFVLAYALTWLFFGAIWWLIAYGRGDLEHLEDTAWTPCVNNLNGFVAAFLFSIETETT
IGYGHRVITDQCPEGIVLLLLQAILGSMVNAFMVGCMFVKISQPNKRAATLVFSSHAVVS
LRDGRLCLMFRVGDLRSSHIVEASIRAKLIRSRQTLEGEFIPLHQTDLSVGFDTGDDRLF
LVSPLVISHEIDAASPFWEASRRALERDDFEIVVILEGMVEATGMTCQARSSYLVDEGLW
GHRFTSVLTLEDGFYEVDYASFHETFEVPTPSCSARELAEAAARLDAHLYWSIPSRLDEK
RVSPRCDQLPPDPCGRPGARHRYMGNCISEVVEEEEEEEGKAPGNVLKLESPRPPEPQV

>HSBA536C5|GENSCAN_predicted_CDS_2|1260_bp
atggcgcaggagaacgcggccttctcgcccgggcaggaggagccgccgcggcgccgcggc
cgccagcgctacgtggagaaggatggccggtgcaacgtgcagcagggcaacgtgcgcgag
acataccgctacctgacggacctgttcaccacgctggtggacctgcagtggcgcctcagc
ctgttgttcttcgtcctggcctacgcgctcacctggctcttcttcggcgccatctggtgg
ctgatcgcctacggccgcggcgacctggagcacctggaggacaccgcgtggacgccgtgc
gtcaacaacctcaacggcttcgtggccgccttcctcttctccatcgagaccgagaccacc
atcggctacgggcaccgcgtcatcaccgaccagtgccccgagggcatcgtgctgctgctg
ctgcaggccatcctgggctccatggtgaacgccttcatggtgggctgcatgttcgtcaag
atctcgcagcccaacaagcgcgcagccacgctcgtcttctcctcgcacgccgtggtgtcg
ctgcgcgacgggcgcctctgcctcatgttccgcgtgggcgacttgcgctcctcacacata
gtggaggcctccatccgcgccaagctcatccgctcgcgccagacgctggagggcgagttc
atcccgctgcaccagaccgacctcagcgtgggcttcgacacgggagacgaccgcctcttc
ctcgtctcgccgctggttatcagccacgagatcgacgccgccagccccttctgggaggcg
tcgcgccgtgccctcgagagggacgacttcgagatcgtcgttatcctcgagggcatggtg
gaagccacgggaatgacatgccaagctcggagctcctacctggtagacgaggggctgtgg
ggccaccgcttcacgtcagtgctgactctggaggacggcttctacgaagtggactatgcc
agctttcacgagacttttgaggtgcccacaccttcgtgcagtgctcgagagctggcagag
gctgccgcccgccttgatgcccatctctactggtccatccccagccggctggatgagaag
agagtgagtccaaggtgtgaccagcttcctccagacccctgtggcagaccgggggccaga
cacagatacatggggaactgcatatcggaggtggtggaggaggaggaggaggaggaaggc
aaagcccctggaaatgtgctaaagttggaaagtccccgtcccccagaacctcaagtctag

>HSBA536C5|GENSCAN_predicted_peptide_3|43_aa
MNTAAINIHRQIFMWTSSVVKTSFTVTFSSPGVIPPRLPYARE

>HSBA536C5|GENSCAN_predicted_CDS_3|132_bp
atgaatacagctgctataaacatccatcggcagattttcatgtggacgtcttctgtggtg
aagacctccttcactgtgaccttctcctcaccaggtgtgatcccccccaggctcccctat
gcccgtgaatga

>HSBA536C5|GENSCAN_predicted_peptide_8|1429_aa
XEAKACVVHGSDLKDMTSEQLDEILKNHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGD
GVNDSPALKKADIGIAMGISGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIA
YTLTSNIPEITPFLLFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEAAESDIMKRQPR
NSQTDKLVNERLISMAYGQIGMIQALGGFFTYFVILAENGFLPSRLLGIRLDWDDRTMND
LEDSYGQEWTYEQRKVVEFTCHTAFFASIVVVQWADLIICKTRRNSVFQQGMKNKILIFG
LLEETALAAFLSYCPGMGVALRMYPLKVTWWFCAFPYSLLIFIYDEVRKLILRRYPGDLA
ITKGSSGECKSLRLEKVDLSPSRGCFLPTVELGQLFLGIAMGLWGKKGTVAPHDQSPRRR
PKKGLIKKKMVKREKQKRNMEELKKEVVMDDHKLTLEELSTKYSVDLTKGHSHQRAKEIL
TRGGPNTVTPPPTTPEWVKFCKQLFGGFSLLLWTGAILCFVAYSIQIYFNEEPTKDNLYL
SIVLSVVVIVTGCFSYYQEAKSSKIMESFKNMVPQQALVIRGGEKMQINVQEVVLGDLVE
IKGGDRVPADLRLISAQGCKVDNSSLTGESEPQSRSPDFTHENPLETRNICFFSTNCVEG
TARGIVIATGDSTVMGRIASLTSGLAVGQTPIAAEIEHFIHLITVVAVFLGVTFFALSLL
LGYGWLEAIIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTST
ICSDKTGTLTQNRMTVAHMWFDMTVYEADTTEEQTGKTFTKSSDTWFMLARIAGLCNRAD
FKANQEILPIAKRATTGDASESALLKFIEQSYSSVAEMREKNPKVAEIPFNSTNKYQMSI
HLREDSSQTHVLMMKGAPERILEFCSTFLLNGQEYSMNDEMKEAFQNAYLELGGLGERVL
GFCFLNLPSSFSKGFPFNTDEINFPMDNLCFVGLISMIDPPRAAVPDAVSKCRSAGIKVI
MVTGDHPITAKAIAKGVGIISEGTETAEEVAARLKIPISKVDASAAKAIVVHGAELKDIQ
SKQLDQILQNHPEIVFARTSPQQKLIIVEGCQRLGAVVAVTGDGVNDSPALKKADIGIAM
GISGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIMYTLTSNIPEITPFLMFI
ILGIPLPLGTITILCIDLGTDMVPAISLAYESAESDIMKRLPRNPKTDNLVNHRLIGMAY
GQIGMIQALAGFFTYFVILAENGFRPVDLLGIRLHWEDKYLNDLEDSYGQQWTYEQRKVV
EFTCQTAFFVTIVVVQWADLIISKTRRNSLFQQGMRNKVLIFGILEETLLAAFLSYTPGM
DVALRMYPLKITWWLCAIPYSILIFVYDEIRKLLIRQHPDGWVERETYY

>HSBA536C5|GENSCAN_predicted_CDS_8|4290_bp
nnagaagccaaggcatgcgtggtgcacggctctgacctgaaggacatgacatcggagcag
ctcgatgagatcctcaagaaccacacagagatcgtctttgctcgaacgtctccccagcag
aagctcatcattgtggagggatgtcagaggcagggagccattgtggccgtgacgggtgac
ggggtgaacgactcccctgcattgaagaaggctgacattggcattgccatgggcatctct
ggctctgacgtctctaagcaggcagccgacatgatcctgctggatgacaactttgcctcc
atcgtcacgggggtggaggagggccgcctgatctttgacaacttgaagaaatccatcgcc
tacaccctgaccagcaacatccccgagatcacccccttcctgctgttcatcattgccaac
atccccctacctctgggcactgtgaccatcctttgcattgacctgggcacagatatggtc
cctgccatctccttggcctatgaggcagctgagagtgatatcatgaagcggcagccacga
aactcccagacggacaagctggtgaatgagaggctcatcagcatggcctacggacagatc
gggatgatccaggcactgggtggcttcttcacctactttgtgatcctggcagagaacggt
ttcctgccatcacggctactgggaatccgcctcgactgggatgaccggaccatgaatgat
ctggaggacagctatggacaggagtggacctatgagcagcggaaggtggtggagttcacg
tgccacacggcattctttgccagcatcgtggtggtgcagtgggctgacctcatcatctgc
aagacccgccgcaactcagtcttccagcagggcatgaagaacaagatcctgatttttggg
ctcctggaggagacggcgttggctgcctttctctcttactgcccaggcatgggtgtagcc
ctccgcatgtacccgctcaaagtcacctggtggttctgcgccttcccctacagcctcctc
atcttcatctatgatgaggtccgaaagctcatcctgcggcggtatcctggtgaccttgca
atcacaaaaggttcttctggtgagtgcaagagcctgagactggaaaaggtggacttgtct
cccagtcgaggctgctttcttcccacagttgagctcgggcagctctttctggggatagct
atggggctttgggggaagaaagggacagtggctccccatgaccagagtccaagacgaaga
cctaaaaaagggcttatcaagaaaaaaatggtgaagagggaaaaacagaagcgcaatatg
gaggaactgaagaaggaagtggtcatggatgatcacaaattaaccttggaagagctgagc
accaagtactccgtggacctgacaaagggccatagccaccaaagggcaaaggaaatcctg
actcgaggtggacccaatactgttaccccaccccccaccactccagaatgggtcaaattc
tgtaagcaactgttcggaggcttctccctcctactatggactggggccattctctgcttt
gtggcctacagcatccagatatatttcaatgaggagcctaccaaagacaacctctacctg
agcatcgtactgtccgtcgtggtcatcgtcactggctgcttctcctattatcaggaggcc
aagagctccaagatcatggagtcttttaagaacatggtgcctcagcaagctctggtaatt
cgaggaggagagaagatgcaaattaatgtacaagaggtggtgttgggagacctggtggaa
atcaagggtggagaccgagtccctgctgacctccggcttatctctgcacaaggatgtaag
gtggacaactcatccttgactggggagtcagaaccccagagccgctcccctgacttcacc
catgagaaccctctggagacccgaaacatctgcttcttttccaccaactgtgtggaagga
accgcccggggtattgtgattgctacgggagactccacagtgatgggcagaattgcctcc
ctgacgtcaggcctggcggttggccagacacctatcgctgctgagatcgaacacttcatc
catctgatcactgtggtggccgtcttccttggtgtcactttttttgcgctctcacttctc
ttgggctatggttggctggaggctatcatttttctcattggcatcattgtggccaatgtg
cctgaggggctgttggccacagtcactgtgtgcctgaccctcacagccaagcgcatggcg
cggaagaactgcctggtgaagaacctggaggcggtggagacgctgggctccacgtccacc
atctgctcagacaagacgggcaccctcacccagaaccgcatgaccgtcgcccacatgtgg
tttgatatgaccgtgtatgaggccgacaccactgaagaacagactggaaaaacatttacc
aagagctctgatacctggtttatgctggcccgaatcgctggcctctgcaaccgggctgac
tttaaggctaatcaggagatcctgcccattgctaagagggccacaacaggtgatgcttcc
gagtcagccctcctcaagttcatcgagcagtcttacagctctgtggcggagatgagagag
aaaaaccccaaggtggcagagattccctttaattctaccaacaagtaccagatgtccatc
caccttcgggaggacagctcccagacccacgtactgatgatgaagggtgctccggagagg
atcttggagttttgttctacctttcttctgaatgggcaggagtactcaatgaacgatgaa
atgaaggaagccttccaaaatgcctacttagaactgggaggtctgggggaacgtgtgcta
ggcttctgcttcttgaatctgcctagcagcttctccaagggattcccatttaatacagat
gaaataaatttccccatggacaacctttgttttgtgggcctcatatccatgattgaccct
ccccgagctgcagtgcctgatgctgtgagcaagtgtcgcagtgcaggaattaaggtgatc
atggtaacaggagatcatcccattacagctaaggccattgccaagggtgtgggcatcatc
tcagaaggcactgagacggcagaggaagtcgctgcccggcttaagatccctatcagcaag
gtcgatgccagtgctgccaaagccattgtggtgcatggtgcagaactgaaggacatacag
tccaagcagcttgatcagatcctccagaaccaccctgagatcgtgtttgctcggacctcc
cctcagcagaagctcatcattgtcgagggatgtcagaggctgggagccgttgtggccgtg
acaggtgacggggtgaacgactcccctgcgctgaagaaggctgacattggcattgccatg
ggcatctctggctctgacgtctctaagcaggcagccgacatgatcctgctggatgacaac
tttgcctccatcgtcacgggggtggaggagggccgcctgatctttgacaacctgaagaaa
tccatcatgtacaccctgaccagcaacatccccgagatcacgcccttcctgatgttcatc
atcctcggtatacccctgcctctgggaaccataaccatcctctgcattgatctcggcact
gacatggtccctgccatctccttggcttatgagtcagctgaaagcgacatcatgaagagg
cttccaaggaacccaaagacggataatctggtgaaccaccgtctcattggcatggcctat
ggacagattgggatgatccaggctctggctggattctttacctactttgtaatcctggct
gagaatggttttaggcctgttgatctgctgggcatccgcctccactgggaagataaatac
ttgaatgacctggaggacagctacggacagcagtggacctatgagcaacgaaaagttgtg
gagttcacatgccaaacggccttttttgtcaccatcgtggttgtgcagtgggcggatctc
atcatctccaagactcgccgcaactcacttttccagcagggcatgagaaacaaagtctta
atatttgggatcctggaggagacactcttggctgcatttctgtcctacactccaggcatg
gacgtggccctgcgaatgtacccactcaagataacctggtggctctgtgccattccctac
agtattctcatcttcgtctatgatgaaatcagaaaactcctcatccgtcagcacccggat
ggctgggtggaaagggagacgtactactaa


Explanation

Gn.Ex : gene number, exon number (for reference)
Type  : Init = Initial exon
        Intr = Internal exon
        Term = Terminal exon
        Sngl = Single-exon gene
        Prom = Promoter
        PlyA = poly-A signal
S     : DNA strand (+ = input strand; - = opposite strand)
Begin : beginning of exon or signal (numbered on input strand)
End   : end point of exon or signal (numbered on input strand)
Len   : length of exon or signal (bp)
Fr    : reading frame (a codon ending at x is in frame f = x mod 3)
Ph    : net phase of exon (length mod 3)
I/Ac  : initiation signal or acceptor splice site score (x 10)
Do/T  : donor splice site or termination signal score (x 10)
CodRg : coding region score (x 10)
P     : probability of exon (sum over all parses containing exon)
Tscr  : exon score (depends on length, I/Ac, Do/T and CodRg scores)

Comments

The SCORE of a predicted feature (e.g., exon or splice site) is a
log-odds measure of the quality of the feature based on local sequence
properties. Thus, for example, a predicted donor splice site with
score > 100 is excellent; 50-100 is acceptable; 0-50 is weak; and
below 0 is poor (probably not a real donor site).

The PROBABILITY of a predicted exon is the estimated probability under
GENSCAN's model of genomic sequence structure that the exon is correct.
This probability depends in general on global as well as local sequence
properties.  This information can be used to assess the reliability of the
predicted exon, e.g., it would be better to design PCR primers based on
a predicted exon with probability > 0.95 than one with lower probability.

BioPerl-1.007002/t/data/genomic-seq.mzef000444000766000024       335413155576321 17767 0ustar00cjfieldsstaff000000000000 ENTER NAME OF THE SEQUENCE FILE (in single quotes)
genomic-seq.fasta
 ENTER 1 FOR FORWARD, 2 FOR REVERSE
1
 ENTER PRIOR PROBABILITY (suggesting .04)
.04
 ENTER OVER LAPPING NUMBER (suggesting 0)
0
 Internal coding exons predicted by MZEF
 File_Name: genomic-se  Sequence_length: 168628  G+C_content:  0.492
  Coordinates    P    Fr1   Fr2   Fr3  Orf   3ss   Cds   5ss
  3192 -  3569 0.965 0.393 0.636 0.377 212 0.575 0.545 0.501
  4476 -  4728 0.885 0.436 0.396 0.593 221 0.521 0.540 0.586
  5744 -  6157 0.997 0.571 0.443 0.394 122 0.573 0.535 0.649
  8751 -  8800 0.553 0.368 0.428 0.627 221 0.515 0.559 0.547
 13638 - 13818 0.689 0.624 0.563 0.402 112 0.561 0.592 0.499
 35165 - 35248 0.774 0.400 0.344 0.488 121 0.545 0.461 0.642
 75943 - 76047 1.000 0.711 0.398 0.463 122 0.545 0.619 0.555
 76229 - 76288 1.000 0.359 0.712 0.511 211 0.548 0.601 0.691
 78250 - 78453 0.992 0.596 0.404 0.427 112 0.567 0.537 0.566
 78980 - 79093 1.000 0.395 0.660 0.354 111 0.521 0.569 0.658
 79333 - 79467 0.997 0.648 0.407 0.372 122 0.511 0.559 0.640
 80173 - 80290 0.995 0.587 0.341 0.395 122 0.565 0.506 0.651
 82589 - 82857 0.996 0.603 0.334 0.402 122 0.532 0.531 0.555
 83689 - 83887 1.000 0.703 0.376 0.480 122 0.541 0.605 0.412
 84017 - 84126 0.996 0.627 0.395 0.445 112 0.514 0.564 0.562
 84303 - 84484 0.936 0.356 0.411 0.543 221 0.529 0.508 0.571
 85346 - 85535 0.904 0.422 0.656 0.421 112 0.535 0.577 0.562
 85666 - 85841 0.970 0.426 0.420 0.592 221 0.581 0.552 0.532
 96381 - 96446 0.960 0.389 0.351 0.560 221 0.490 0.503 0.657
115714 -115756 0.508 0.509 0.504 0.381 112 0.529 0.537 0.611
125505 -125588 0.980 0.400 0.383 0.641 121 0.536 0.538 0.515
135080 -135131 0.540 0.630 0.571 0.413 112 0.482 0.586 0.517
147055 -147214 0.914 0.436 0.393 0.577 221 0.498 0.540 0.619
BioPerl-1.007002/t/data/gf-s71.needle000444000766000024       541213155576321 17054 0ustar00cjfieldsstaff000000000000########################################
# Program:  needle
# Rundate:  Thu Jun 20 10:53:54 2002
# Report_file: /tmp/jason/water/1/gf.s71.44_Y50C1A.2.water
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: gf.s71.44
# 2: Y50C1A.2
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 468
# Identity:     285/468 (60.9%)
# Similarity:   339/468 (72.4%)
# Gaps:          82/468 (17.5%)
# Score: 1394.0
# 
#
#=======================================

gf.s71.44          1 MEDVTLHHFRWRKPVENKNGEIVYKTSETQTAEISRKDVECVANFQKSQE     50
                     ||||||..|.||||: ...||||||||||||.|.::||||||||||:::|
Y50C1A.2           1 MEDVTLFQFTWRKPI-RLQGEIVYKTSETQTIETNKKDVECVANFQENKE     49

gf.s71.44         51 SQTDDFMQNGVGDGIKKEIRISKEVLGHIYDFLRDDSKVNYDRLLEFHKF    100
                     .|||. :.||||:.:||:|.||||||..:|||:|||||||||||||||||
Y50C1A.2          50 VQTDS-VDNGVGENVKKDITISKEVLNLLYDFVRDDSKVNYDRLLEFHKF     98

gf.s71.44        101 DKVSLETVQKYHVETRNENIILMISNSSRKTLILFGGLSHETFCSHQARA    150
                     |||:|||||||||||||||||||||:|||||||||||:||||||||||||
Y50C1A.2          99 DKVALETVQKYHVETRNENIILMISSSSRKTLILFGGISHETFCSHQARA    148

gf.s71.44        151 VLCSSSTTSSLPLPVCAISAVFYSSTQFLLGDISGNISMWTKEKMIFENK    200
                     :||||||:.|:|||||||||||||||||:|||:||||||.:|:|:|||.|
Y50C1A.2         149 LLCSSSTSFSIPLPVCAISAVFYSSTQFILGDVSGNISMCSKDKIIFEKK    198

gf.s71.44        201 VTDGSVTSLELCRYGLLSGSDDGNVILWKVEESKIEKIEGIKLTVSDLSR    250
                     :|||:||.||:||:||||||||||:|||::..|.:||:.|.|||||||||
Y50C1A.2         199 ITDGAVTCLEMCRHGLLSGSDDGNIILWQIGTSGLEKLGGTKLTVSDLSR    248

gf.s71.44        251 KIRRSSTSNKPVAIVSMQV----SGDEVCVATETGGLYLLTLPTLESKPL    296
                     |||||||||||||||||||    ||:|.|||||||||||||||||:.|||
Y50C1A.2         249 KIRRSSTSNKPVAIVSMQVYVWPSGEEACVATETGGLYLLTLPTLDYKPL    298

gf.s71.44        297 T-QSATSIFKILYEHPYIAVVYHTSNSAIFNSEGLVDEIPFVATLAVRCG    345
                     : |:||||.|||:|:.::||:|||||:|:|||||||||||||||||||  
Y50C1A.2         299 SHQTATSINKILFENQFVAVIYHTSNAAVFNSEGLVDEIPFVATLAVR--    346

gf.s71.44        346 AYFIFSNQSRLIIWSMNTRSTVIDENLNCHS-ICSLSND-----------    383
                             .:|:::  .|...|.|..|||.| ....:|:           
Y50C1A.2         347 --------PKLVLF--YTSVCVQDITLNCTSPFREFNNEYNPVIKFSKIR    386

gf.s71.44        384 ---TLQVLDGDFNLNSQSENSATSESENLRISDLQNLRMLKLQNLRTSEF    430
                        .|.|::| |..:|.:.|:                             
Y50C1A.2         387 FSADLSVING-FRTSSPNSNN                                 406

gf.s71.44        431 QNFRTSESQYFKKDNGEL    448
                                       
Y50C1A.2         407                       406


#---------------------------------------
#---------------------------------------
BioPerl-1.007002/t/data/glimmer3-fragment.detail000444000766000024      1042313155576321 21414 0ustar00cjfieldsstaff000000000000Command:  glimmer3 -l -X AAVN02000021.1.fasta aavn.icm glimmer3-fragment

Sequence file = AAVN02000021.1.fasta
Number of sequences = 1
ICM model file = aavn.icm
Excluded regions file = none
List of orfs file = none
Input is NOT separate orfs
Independent (non-coding) scores are used
Circular genome = false
Truncated orfs = true
Minimum gene length = 100 bp
Maximum overlap bases = 30
Threshold score = 30
Use first start codon = false
Start codons = atg,gtg,ttg
Start probs = 0.600,0.300,0.100
Stop codons = taa,tag,tga
GC percentage = 53.3%
Ignore score on orfs longer than 812


>gi|123977258|gb|AAVN02000021.1| Collinsella aerofaciens ATCC 25986 C_aerofaciens-2.0_Cont1.6, whole genome shotgun sequence
Sequence length = 2932

           ----- Start -----           --- Length ----  ------------- Scores -------------
 ID  Frame   of Orf  of Gene     Stop   of Orf of Gene      Raw InFrm F1 F2 F3 R1 R2 R3 NC
        +1       -2       79      192      189     111    -5.50     0  0  - 99  -  -  0  0
        -1      333      270      154      177     114   -13.99     0  -  0 99  0  -  0  0
        -2      340      328      221      117     105    -9.96     0  -  0 93  0  0  1  5
        +2      134      263      424      288     159   -10.03     0  0  0 99  -  -  0  0
        -3      458      233        3      453     228     1.15     0  -  - 99  -  -  0  0
        +1      229      277      540      309     261    -9.76     0  0  - 99  -  -  -  0
0001    +3        0        0      674      669     669     7.01    99  -  - 99  -  -  -  0
        -2      727      580      368      357     210    -3.05     0  -  - 99  -  0  -  0
        -1      786      771      658      126     111   -14.03     0  -  -  -  0  -  - 99
        -2      904      859      728      174     129   -12.38     0  1  -  -  -  0  - 98
        -3      914      905      750      162     153    -0.96    17  0  -  9  -  0 17 72
        +1      718      778      930      210     150    -3.84     0  0  -  1  -  -  - 98
        -1      978      918      787      189     129   -12.66     0  0  -  1  0  - 80 17
        +3      750      804      986      234     180    -4.06     0  -  -  0  -  -  - 99
        -1     1110     1089      979      129     108   -11.01     0  -  0  -  0  -  - 99
        +2      983     1016     1234      249     216    -6.83     0  -  0 96  -  0  -  3
0002    +3     1005     1071     1253      246     180     5.32    99  -  - 99  -  0  -  0
        -2     1339     1225     1013      324     210    -6.58     0  -  0 49  -  0  - 50
        +2     1322     1388     1492      168     102    -8.80     0 99  0  -  0  -  0  0
        -3     1514     1514     1302      210     210    -4.98     0 99  -  -  0  -  0  0
        -1     1605     1221     1111      492     108   -14.08     0  -  0 99  0  0  0  0
        -2     1771     1744     1619      150     123   -16.35     0 99  -  -  0  0  0  0
        +2     1814     1820     1930      114     108    -7.50     0 99  0  -  -  -  0  0
        -3     1973     1622     1515      456     105    -1.02     0 99  0  -  -  -  0  0
        -3     2258     2090     1974      282     114    -5.13     0 99  -  -  0  -  0  0
        +2     2000     2081     2287      285     204   -14.54     0 99  0  -  0  0  -  0
        -2     2335     2332     2018      315     312   -12.59     0 99  -  -  0  0  -  0
        -1     2340     2247     1891      447     354    -3.45     0 99  -  -  0  -  -  0
0003    +1     1177     1231     2511     1332    1278    12.08    99 99  -  -  -  -  -  0
        +2     2288     2453     2560      270     105    -9.51     0  -  0  0  0  -  - 99
        -1     2562     2502     2341      219     159    -1.23     0 99  0  -  0  -  -  0
        +3     2457     2478     2594      135     114   -12.83     0  -  -  0  -  -  - 99
        -3     2831     2816     2652      177     162    -9.05     0 84  -  -  -  -  0 15
        -2     2935     2935     2813      117     117    -9.81     0 99  0  0  0  0  -  0
0004    -1     2934     2880     2755      174     123     2.72    40 25 32  - 40  -  -  1
        +3     2802     2805     2933      129     126    -8.60     0 99  0  0  0  -  -  0
0005    +1     2656     2677     2934      276     255     5.90    99 99  -  -  -  -  -  0
        +2     2699     2798     2935      234     135    -3.20     0 99  0  0  0  -  -  0
BioPerl-1.007002/t/data/glimmer3-fragment.predict000444000766000024        43513155576321 21546 0ustar00cjfieldsstaff000000000000>gi|123977258|gb|AAVN02000021.1| Collinsella aerofaciens ATCC 25986 C_aerofaciens-2.0_Cont1.6, whole genome shotgun sequence
orf00001        0      674  +3     6.98
orf00002     1071     1253  +3     4.94
orf00003     1231     2511  +1    11.93
orf00005     2677     2934  +1     5.63
BioPerl-1.007002/t/data/gmap_f9-multiple_results.txt000444000766000024   1267305013155576321 22503 0ustar00cjfieldsstaff000000000000>ENSP00000362111 
1 M	1 A	-X:99778347 2966876690 A	M
1	2 T	-X:99778346 2966876689 T	
1	3 G	-X:99778345 2966876688 G	
2 A	4 G	-X:99778344 2966876687 G	A
2	5 C	-X:99778343 2966876686 C	
2	6 G	-X:99778342 2966876685 G	
3 S	7 T	-X:99778341 2966876684 T	S
3	8 C	-X:99778340 2966876683 C	
3	9 C	-X:99778339 2966876682 C	
4 P	10 C	-X:99778338 2966876681 C	P
4	11 C	-X:99778337 2966876680 C	
4	12 G	-X:99778336 2966876679 G	
5 S	13 T	-X:99778335 2966876678 T	S
5	14 C	-X:99778334 2966876677 C	
5	15 T	-X:99778333 2966876676 T	
6 R	16 C	-X:99778332 2966876675 C	R
6	17 G	-X:99778331 2966876674 G	
6	18 G	-X:99778330 2966876673 G	
7 R	19 A	-X:99778329 2966876672 A	R
7	20 G	-X:99778328 2966876671 G	
7	21 A	-X:99778327 2966876670 A	
8 L	22 C	-X:99778326 2966876669 C	L
8	23 T	-X:99778325 2966876668 T	
8	24 G	-X:99778324 2966876667 G	
9 Q	25 C	-X:99778323 2966876666 C	Q
9	26 A	-X:99778322 2966876665 A	
9	27 G	-X:99778321 2966876664 G	
10 T	28 A	-X:99778320 2966876663 A	T
10	29 C	-X:99778319 2966876662 C	
10	30 T	-X:99778318 2966876661 T	
11 K	31 A	-X:99778317 2966876660 A	K
11	32 A	-X:99778316 2966876659 A	
11	33 A	-X:99778315 2966876658 A	
12 P	34 C	-X:99778314 2966876657 C	P
12	35 C	-X:99778313 2966876656 C	
12	36 A	-X:99778312 2966876655 A	
13 V	37 G	-X:99778311 2966876654 G	V
13	38 T	-X:99778310 2966876653 T	
13	39 C	-X:99778309 2966876652 C	
14 I	40 A	-X:99778308 2966876651 A	I
14	41 T	-X:99778307 2966876650 T	
14	42 T	-X:99778306 2966876649 T	
15 T	43 A	-X:99778305 2966876648 A	T
15	44 C	-X:99778304 2966876647 C	
15	45 T	-X:99778303 2966876646 T	
16 C	46 T	-X:99778302 2966876645 T	C
16	47 G	-X:99778301 2966876644 G	
16	48 T	-X:99778300 2966876643 T	
17 F	49 T	-X:99778299 2966876642 T	F
17	50 T	-X:99778298 2966876641 T	
17	51 C	-X:99778297 2966876640 C	
18 K	52 A	-X:99778296 2966876639 A	K
18	53 A	-X:99778295 2966876638 A	
18	54 G	-X:99778294 2966876637 G	
19 S	55 A	-X:99778293 2966876636 A	S
19	56 G	-X:99778292 2966876635 G	
19	57 C	-X:99778291 2966876634 C	
20 V	58 G	-X:99778290 2966876633 G	V
20	59 T	-X:99778289 2966876632 T	
20	60 T	-X:99778288 2966876631 T	
21 L	61 C	-X:99778287 2966876630 C	L
21	62 T	-X:99778286 2966876629 T	
21	63 G	-X:99778285 2966876628 G	
22 L	64 C	-X:99778284 2966876627 C	L
22	65 T	-X:99778283 2966876626 T	
22	66 A	-X:99778282 2966876625 A	
23 I	67 A	-X:99778281 2966876624 A	I
23	68 T	-X:99778280 2966876623 T	
23	69 C	-X:99778279 2966876622 C	
24 Y	70 T	-X:99778278 2966876621 T	Y
24	71 A	-X:99778277 2966876620 A	
24	72 C	-X:99778276 2966876619 C	
25 T	73 A	-X:99778275 2966876618 A	T
25	74 C	-X:99778274 2966876617 C	
25	75 T	-X:99778273 2966876616 T	
26 F	76 T	-X:99778272 2966876615 T	F
26	77 T	-X:99778271 2966876614 T	
26	78 T	-X:99778270 2966876613 T	
27 I	79 A	-X:99778269 2966876612 A	I
27	80 T	-X:99778268 2966876611 T	
27	81 T	-X:99778267 2966876610 T	
28 F	82 T	-X:99778266 2966876609 T	F
28	83 T	-X:99778265 2966876608 T	
28	84 C	-X:99778264 2966876607 C	
29 W	85 T	-X:99778263 2966876606 T	W
29	86 G	-X:99778262 2966876605 G	
29	87 G	-X:99778261 2966876604 G	
30 I	88 A	-X:99777399 2966875742 A	I
30	89 T	-X:99777398 2966875741 T	
30	90 C	-X:99777397 2966875740 C	
31 T	91 A	-X:99777396 2966875739 A	T
31	92 C	-X:99777395 2966875738 C	
31	93 T	-X:99777394 2966875737 T	
32 G	94 G	-X:99777393 2966875736 G	G
32	95 G	-X:99777392 2966875735 G	
32	96 C	-X:99777391 2966875734 C	
33 V	97 G	-X:99777390 2966875733 G	V
33	98 T	-X:99777389 2966875732 T	
33	99 T	-X:99777388 2966875731 T	
34 I	100 A	-X:99777387 2966875730 A	I
34	101 T	-X:99777386 2966875729 T	
34	102 C	-X:99777385 2966875728 C	
35 L	103 C	-X:99777384 2966875727 C	L
35	104 T	-X:99777383 2966875726 T	
35	105 T	-X:99777382 2966875725 T	
36 L	106 C	-X:99777381 2966875724 C	L
36	107 T	-X:99777380 2966875723 T	
36	108 T	-X:99777379 2966875722 T	
37 A	109 G	-X:99777378 2966875721 G	A
37	110 C	-X:99777377 2966875720 C	
37	111 A	-X:99777376 2966875719 A	
38 V	112 G	-X:99777375 2966875718 G	V
38	113 T	-X:99777374 2966875717 T	
38	114 T	-X:99777373 2966875716 T	
39 G	115 G	-X:99777372 2966875715 G	G
39	116 G	-X:99777371 2966875714 G	
39	117 C	-X:99777370 2966875713 C	
40 I	118 A	-X:99777369 2966875712 A	I
40	119 T	-X:99777368 2966875711 T	
40	120 T	-X:99777367 2966875710 T	
41 W	121 T	-X:99777366 2966875709 T	W
41	122 G	-X:99777365 2966875708 G	
41	123 G	-X:99777364 2966875707 G	
42 G	124 G	-X:99777363 2966875706 G	G
42	125 G	-X:99777362 2966875705 G	
42	126 C	-X:99777361 2966875704 C	
43 K	127 A	-X:99777360 2966875703 A	K
43	128 A	-X:99777359 2966875702 A	
43	129 G	-X:99777358 2966875701 G	
44 V	130 G	-X:99777357 2966875700 G	V
44	131 T	-X:99777356 2966875699 T	
44	132 G	-X:99777355 2966875698 G	
45 S	133 A	-X:99777354 2966875697 A	S
45	134 G	-X:99777353 2966875696 G	
45	135 C	-X:99777352 2966875695 C	
46 L	136 C	-X:99777351 2966875694 C	L
46	137 T	-X:99777350 2966875693 T	
46	138 G	-X:99777349 2966875692 G	
47 E	139 G	-X:99777348 2966875691 G	E
47	140 A	-X:99777347 2966875690 A	
47	141 G	-X:99777346 2966875689 G	
48 N	142 A	-X:99777345 2966875688 A	N
48	143 A	-X:99777344 2966875687 A	
48	144 T	-X:99777343 2966875686 T	
49 Y	145 T	-X:99777342 2966875685 T	Y
49	146 A	-X:99777341 2966875684 A	
49	147 C	-X:99777340 2966875683 C	
50 F	148 T	-X:99777339 2966875682 T	F
50	149 T	-X:99777338 2966875681 T	
50	150 T	-X:99777337 2966875680 T	
51 S	151 T	-X:99777336 2966875679 T	S
51	152 C	-X:99777335 2966875678 C	
51	153 T	-X:99777334 2966875677 T	
52 L	154 C	-X:99777333 2966875676 C	L
52	155 T	-X:99777332 2966875675 T	
52	156 T	-X:99777331 2966875674 T	
53 L	157 T	-X:99777330 2966875673 T	L
53	158 T	-X:99777329 2966875672 T	
53	159 A	-X:99777328 2966875671 A	
54 N	160 A	-X:99777327 2966875670 A	N
54	161 A	-X:99777326 2966875669 A	
54	162 T	-X:99777325 2966875668 T	
55 E	163 G	-X:99777324 2966875667 G	E
55	164 A	-X:99777323 2966875666 A	
55	165 G	-X:99777322 2966875665 G	
56 K	166 A	-X:99777321 2966875664 A	K
56	167 A	-X:99777320 2966875663 A	
56	168 G	-X:99777319 2966875662 G	
57 A	169 G	-X:99777318 2966875661 G	A
57	170 C	-X:99777317 2966875660 C	
57	171 C	-X:99777316 2966875659 C	
58 T	172 A	-X:99777315 2966875658 A	T
58	173 C	-X:99777314 2966875657 C	
58	174 C	-X:99777313 2966875656 C	
59 N	175 A	-X:99777312 2966875655 A	N
59	176 A	-X:99777311 2966875654 A	
59	177 T	-X:99777310 2966875653 T	
60 V	178 G	-X:99777309 2966875652 G	V
60	179 T	-X:99777308 2966875651 T	
60	180 C	-X:99777307 2966875650 C	
61 P	181 C	-X:99777306 2966875649 C	P
61	182 C	-X:99777305 2966875648 C	
61	183 C	-X:99777304 2966875647 C	
62 F	184 T	-X:99777303 2966875646 T	F
62	185 T	-X:99777302 2966875645 T	
62	186 C	-X:99777301 2966875644 C	
63 V	187 G	-X:99777300 2966875643 G	V
63	188 T	-X:99777299 2966875642 T	
63	189 G	-X:99777298 2966875641 G	
64 L	190 C	-X:99777297 2966875640 C	L
64	191 T	-X:99777296 2966875639 T	
64	192 C	-X:99777295 2966875638 C	
65 I	193 A	-X:99777294 2966875637 A	I
65	194 T	-X:99777293 2966875636 T	
65	195 T	-X:99777292 2966875635 T	
66 A	196 G	-X:99777291 2966875634 G	A
66	197 C	-X:99777290 2966875633 C	
66	198 T	-X:99777289 2966875632 T	
67 T	199 A	-X:99777288 2966875631 A	T
67	200 C	-X:99777287 2966875630 C	
67	201 T	-X:99777286 2966875629 T	
68 G	202 G	-X:99777285 2966875628 G	G
68	203 G	-X:99777284 2966875627 G	
68	204 T	-X:99777283 2966875626 T	
69 T	205 A	-X:99777282 2966875625 A	T
69	206 C	-X:99777281 2966875624 C	
69	207 C	-X:99777280 2966875623 C	
70 V	208 G	-X:99777279 2966875622 G	V
70	209 T	-X:99777278 2966875621 T	
70	210 C	-X:99777277 2966875620 C	
71 I	211 A	-X:99777276 2966875619 A	I
71	212 T	-X:99777275 2966875618 T	
71	213 T	-X:99777274 2966875617 T	
72 I	214 A	-X:99777273 2966875616 A	I
72	215 T	-X:99777272 2966875615 T	
72	216 T	-X:99777271 2966875614 T	
73 L	217 C	-X:99777270 2966875613 C	L
73	218 T	-X:99777269 2966875612 T	
73	219 T	-X:99777268 2966875611 T	
74 L	220 T	-X:99777267 2966875610 T	L
74	221 T	-X:99777266 2966875609 T	
74	222 G	-X:99777265 2966875608 G	
75 G	223 G	-X:99777264 2966875607 G	G
75	224 G	-X:99777263 2966875606 G	
75	225 C	-X:99777262 2966875605 C	
76 T	226 A	-X:99777261 2966875604 A	T
76	227 C	-X:99777260 2966875603 C	
76	228 C	-X:99777259 2966875602 C	
77 F	229 T	-X:99777258 2966875601 T	F
77	230 T	-X:99777257 2966875600 T	
77	231 T	-X:99777256 2966875599 T	
78 G	232 G	-X:99777255 2966875598 G	G
78	233 G	-X:99777254 2966875597 G	
78	234 T	-X:99777253 2966875596 T	
79 C	235 T	-X:99777252 2966875595 T	C
79	236 G	-X:99777251 2966875594 G	
79	237 T	-X:99777250 2966875593 T	
80 F	238 T	-X:99777249 2966875592 T	F
80	239 T	-X:99777248 2966875591 T	
80	240 T	-X:99777247 2966875590 T	
81 A	241 G	-X:99777246 2966875589 G	A
81	242 C	-X:99777245 2966875588 C	
81	243 T	-X:99777244 2966875587 T	
82 T	244 A	-X:99777243 2966875586 A	T
82	245 C	-X:99777242 2966875585 C	
82	246 C	-X:99777241 2966875584 C	
83 C	247 T	-X:99777240 2966875583 T	C
83	248 G	-X:99777239 2966875582 G	
83	249 C	-X:99777238 2966875581 C	
84 R	250 C	-X:99777237 2966875580 C	R
84	251 G	-X:99777236 2966875579 G	
84	252 A	-X:99777235 2966875578 A	
85 A	253 G	-X:99777234 2966875577 G	A
85	254 C	-X:99777233 2966875576 C	
85	255 T	-X:99777232 2966875575 T	
86 S	256 T	-X:99777231 2966875574 T	S
86	257 C	-X:99777230 2966875573 C	
86	258 T	-X:99777229 2966875572 T	
87 A	259 G	-X:99777228 2966875571 G	A
87	260 C	-X:99777227 2966875570 C	
87	261 A	-X:99777226 2966875569 A	
88 W	262 T	-X:99777225 2966875568 T	W
88	263 G	-X:99777224 2966875567 G	
88	264 G	-X:99777223 2966875566 G	
89 M	265 A	-X:99777222 2966875565 A	M
89	266 T	-X:99777221 2966875564 T	
89	267 G	-X:99777220 2966875563 G	
90 L	268 C	-X:99777219 2966875562 C	L
90	269 T	-X:99777218 2966875561 T	
90	270 A	-X:99777217 2966875560 A	
91 K	271 A	-X:99777216 2966875559 A	K
91	272 A	-X:99777215 2966875558 A	
91	273 A	-X:99777214 2966875557 A	
92 L	274 C	-X:99777213 2966875556 C	L
92	275 T	-X:99777212 2966875555 T	
92	276 G	-X:99777211 2966875554 G	
93 Y	277 T	-X:99776905 2966875248 T	Y
93	278 A	-X:99776904 2966875247 A	
93	279 T	-X:99776903 2966875246 T	
94 A	280 G	-X:99776902 2966875245 G	A
94	281 C	-X:99776901 2966875244 C	
94	282 A	-X:99776900 2966875243 A	
95 M	283 A	-X:99776899 2966875242 A	M
95	284 T	-X:99776898 2966875241 T	
95	285 G	-X:99776897 2966875240 G	
96 F	286 T	-X:99776896 2966875239 T	F
96	287 T	-X:99776895 2966875238 T	
96	288 T	-X:99776894 2966875237 T	
97 L	289 C	-X:99776893 2966875236 C	L
97	290 T	-X:99776892 2966875235 T	
97	291 G	-X:99776891 2966875234 G	
98 T	292 A	-X:99776890 2966875233 A	T
98	293 C	-X:99776889 2966875232 C	
98	294 T	-X:99776888 2966875231 T	
99 L	295 C	-X:99776887 2966875230 C	L
99	296 T	-X:99776886 2966875229 T	
99	297 C	-X:99776885 2966875228 C	
100 V	298 G	-X:99776884 2966875227 G	V
100	299 T	-X:99776883 2966875226 T	
100	300 T	-X:99776882 2966875225 T	
101 F	301 T	-X:99776881 2966875224 T	F
101	302 T	-X:99776880 2966875223 T	
101	303 T	-X:99776879 2966875222 T	
102 L	304 T	-X:99776878 2966875221 T	L
102	305 T	-X:99776877 2966875220 T	
102	306 G	-X:99776876 2966875219 G	
103 V	307 G	-X:99776875 2966875218 G	V
103	308 T	-X:99776874 2966875217 T	
103	309 C	-X:99776873 2966875216 C	
104 E	310 G	-X:99776872 2966875215 G	E
104	311 A	-X:99776871 2966875214 A	
104	312 A	-X:99776870 2966875213 A	
105 L	313 C	-X:99776869 2966875212 C	L
105	314 T	-X:99776868 2966875211 T	
105	315 G	-X:99776867 2966875210 G	
106 V	316 G	-X:99776866 2966875209 G	V
106	317 T	-X:99776865 2966875208 T	
106	318 C	-X:99776864 2966875207 C	
107 A	319 G	-X:99776863 2966875206 G	A
107	320 C	-X:99776862 2966875205 C	
107	321 T	-X:99776861 2966875204 T	
108 A	322 G	-X:99776860 2966875203 G	A
108	323 C	-X:99776859 2966875202 C	
108	324 C	-X:99776858 2966875201 C	
109 I	325 A	-X:99776857 2966875200 A	I
109	326 T	-X:99776856 2966875199 T	
109	327 C	-X:99776855 2966875198 C	
110 V	328 G	-X:99776854 2966875197 G	V
110	329 T	-X:99776853 2966875196 T	
110	330 A	-X:99776852 2966875195 A	
111 G	331 G	-X:99776851 2966875194 G	G
111	332 G	-X:99776850 2966875193 G	
111	333 A	-X:99776849 2966875192 A	
112 F	334 T	-X:99776848 2966875191 T	F
112	335 T	-X:99776847 2966875190 T	
112	336 T	-X:99776846 2966875189 T	
113 V	337 G	-X:99776845 2966875188 G	V
113	338 T	-X:99776844 2966875187 T	
113	339 T	-X:99776843 2966875186 T	
114 F	340 T	-X:99776842 2966875185 T	F
114	341 T	-X:99776841 2966875184 T	
114	342 C	-X:99776840 2966875183 C	
115 R	343 A	-X:99776839 2966875182 A	R
115	344 G	-X:99776838 2966875181 G	
115	345 A	-X:99776837 2966875180 A	
116 H	346 C	-X:99776836 2966875179 C	H
116	347 A	-X:99776835 2966875178 A	
116	348 T	-X:99776834 2966875177 T	
117 E	349 G	-X:99776833 2966875176 G	E
117	350 A	-X:99776832 2966875175 A	
117	351 G	-X:99776831 2966875174 G	
118 I	352 A	-X:99775682 2966874025 A	I
118	353 T	-X:99775681 2966874024 T	
118	354 T	-X:99775680 2966874023 T	
119 K	355 A	-X:99775679 2966874022 A	K
119	356 A	-X:99775678 2966874021 A	
119	357 G	-X:99775677 2966874020 G	
120 N	358 A	-X:99775676 2966874019 A	N
120	359 A	-X:99775675 2966874018 A	
120	360 C	-X:99775674 2966874017 C	
121 S	361 A	-X:99775673 2966874016 A	S
121	362 G	-X:99775672 2966874015 G	
121	363 C	-X:99775671 2966874014 C	
122 F	364 T	-X:99775670 2966874013 T	F
122	365 T	-X:99775669 2966874012 T	
122	366 T	-X:99775668 2966874011 T	
123 K	367 A	-X:99775667 2966874010 A	K
123	368 A	-X:99775666 2966874009 A	
123	369 G	-X:99775665 2966874008 G	
124 N	370 A	-X:99775664 2966874007 A	N
124	371 A	-X:99775663 2966874006 A	
124	372 T	-X:99775662 2966874005 T	
125 N	373 A	-X:99775661 2966874004 A	N
125	374 A	-X:99775660 2966874003 A	
125	375 T	-X:99775659 2966874002 T	
126 Y	376 T	-X:99775658 2966874001 T	Y
126	377 A	-X:99775657 2966874000 A	
126	378 T	-X:99775656 2966873999 T	
127 E	379 G	-X:99775655 2966873998 G	E
127	380 A	-X:99775654 2966873997 A	
127	381 G	-X:99775653 2966873996 G	
128 K	382 A	-X:99775652 2966873995 A	K
128	383 A	-X:99775651 2966873994 A	
128	384 G	-X:99775650 2966873993 G	
129 A	385 G	-X:99775649 2966873992 G	A
129	386 C	-X:99775648 2966873991 C	
129	387 T	-X:99775647 2966873990 T	
130 L	388 T	-X:99775646 2966873989 T	L
130	389 T	-X:99775645 2966873988 T	
130	390 G	-X:99775644 2966873987 G	
131 K	391 A	-X:99775643 2966873986 A	K
131	392 A	-X:99775642 2966873985 A	
131	393 G	-X:99775641 2966873984 G	
132 Q	394 C	-X:99775640 2966873983 C	Q
132	395 A	-X:99775639 2966873982 A	
132	396 G	-X:99775638 2966873981 G	
133 Y	397 T	-X:99775637 2966873980 T	Y
133	398 A	-X:99775636 2966873979 A	
133	399 T	-X:99775635 2966873978 T	
134 N	400 A	-X:99775634 2966873977 A	N
134	401 A	-X:99775633 2966873976 A	
134	402 C	-X:99775632 2966873975 C	
135 S	403 T	-X:99775631 2966873974 T	S
135	404 C	-X:99775630 2966873973 C	
135	405 T	-X:99775629 2966873972 T	
136 T	406 A	-X:99775628 2966873971 A	T
136	407 C	-X:99775627 2966873970 C	
136	408 A	-X:99775626 2966873969 A	
137 G	409 G	-X:99775625 2966873968 G	G
137	410 G	-X:99775624 2966873967 G	
137	411 A	-X:99775623 2966873966 A	
138 D	412 G	-X:99775622 2966873965 G	D
138	413 A	-X:99775621 2966873964 A	
138	414 T	-X:99775620 2966873963 T	
139 Y	415 T	-X:99775619 2966873962 T	Y
139	416 A	-X:99775618 2966873961 A	
139	417 T	-X:99775617 2966873960 T	
140 R	418 A	-X:99775616 2966873959 A	R
140	419 G	-X:99775615 2966873958 G	
140	420 A	-X:99775614 2966873957 A	
141 S	421 A	-X:99775613 2966873956 A	S
141	422 G	-X:99775612 2966873955 G	
141	423 C	-X:99775611 2966873954 C	
142 H	424 C	-X:99775610 2966873953 C	H
142	425 A	-X:99775609 2966873952 A	
142	426 T	-X:99775608 2966873951 T	
143 A	427 G	-X:99775607 2966873950 G	A
143	428 C	-X:99775606 2966873949 C	
143	429 A	-X:99775605 2966873948 A	
144 V	430 G	-X:99775604 2966873947 G	V
144	431 T	-X:99775603 2966873946 T	
144	432 A	-X:99775602 2966873945 A	
145 D	433 G	-X:99775601 2966873944 G	D
145	434 A	-X:99775600 2966873943 A	
145	435 C	-X:99775599 2966873942 C	
146 K	436 A	-X:99775598 2966873941 A	K
146	437 A	-X:99775597 2966873940 A	
146	438 G	-X:99775596 2966873939 G	
147 I	439 A	-X:99775595 2966873938 A	I
147	440 T	-X:99775594 2966873937 T	
147	441 C	-X:99775593 2966873936 C	
148 Q	442 C	-X:99775592 2966873935 C	Q
148	443 A	-X:99775591 2966873934 A	
148	444 A	-X:99775590 2966873933 A	
149 N	445 A	-X:99775589 2966873932 A	N
149	446 A	-X:99775588 2966873931 A	
149	447 T	-X:99775587 2966873930 T	
150 T	448 A	-X:99775586 2966873929 A	T
150	449 C	-X:99775585 2966873928 C	
150	450 G	-X:99775584 2966873927 G	
151 L	451 T	-X:99775192 2966873535 T	L
151	452 T	-X:99775191 2966873534 T	
151	453 G	-X:99775190 2966873533 G	
152 H	454 C	-X:99775189 2966873532 C	H
152	455 A	-X:99775188 2966873531 A	
152	456 T	-X:99775187 2966873530 T	
153 C	457 T	-X:99775186 2966873529 T	C
153	458 G	-X:99775185 2966873528 G	
153	459 T	-X:99775184 2966873527 T	
154 C	460 T	-X:99775183 2966873526 T	C
154	461 G	-X:99775182 2966873525 G	
154	462 T	-X:99775181 2966873524 T	
155 G	463 G	-X:99775180 2966873523 G	G
155	464 G	-X:99775179 2966873522 G	
155	465 T	-X:99775178 2966873521 T	
156 V	466 G	-X:99775177 2966873520 G	V
156	467 T	-X:99775176 2966873519 T	
156	468 C	-X:99775175 2966873518 C	
157 T	469 A	-X:99775174 2966873517 A	T
157	470 C	-X:99775173 2966873516 C	
157	471 C	-X:99775172 2966873515 C	
158 D	472 G	-X:99775171 2966873514 G	D
158	473 A	-X:99775170 2966873513 A	
158	474 T	-X:99775169 2966873512 T	
159 Y	475 T	-X:99775168 2966873511 T	Y
159	476 A	-X:99775167 2966873510 A	
159	477 T	-X:99775166 2966873509 T	
160 R	478 A	-X:99775165 2966873508 A	R
160	479 G	-X:99775164 2966873507 G	
160	480 A	-X:99775163 2966873506 A	
161 D	481 G	-X:99775162 2966873505 G	D
161	482 A	-X:99775161 2966873504 A	
161	483 T	-X:99775160 2966873503 T	
162 W	484 T	-X:99775159 2966873502 T	W
162	485 G	-X:99775158 2966873501 G	
162	486 G	-X:99775157 2966873500 G	
163 T	487 A	-X:99775156 2966873499 A	T
163	488 C	-X:99775155 2966873498 C	
163	489 A	-X:99775154 2966873497 A	
164 D	490 G	-X:99775153 2966873496 G	D
164	491 A	-X:99775152 2966873495 A	
164	492 T	-X:99775151 2966873494 T	
165 T	493 A	-X:99775150 2966873493 A	T
165	494 C	-X:99775149 2966873492 C	
165	495 T	-X:99775148 2966873491 T	
166 N	496 A	-X:99775147 2966873490 A	N
166	497 A	-X:99775146 2966873489 A	
166	498 T	-X:99775145 2966873488 T	
167 Y	499 T	-X:99775144 2966873487 T	Y
167	500 A	-X:99775143 2966873486 A	
167	501 T	-X:99775142 2966873485 T	
168 Y	502 T	-X:99775141 2966873484 T	Y
168	503 A	-X:99775140 2966873483 A	
168	504 C	-X:99775139 2966873482 C	
169 S	505 T	-X:99775138 2966873481 T	S
169	506 C	-X:99775137 2966873480 C	
169	507 A	-X:99775136 2966873479 A	
170 E	508 G	-X:99775135 2966873478 G	E
170	509 A	-X:99775134 2966873477 A	
170	510 A	-X:99775133 2966873476 A	
171 K	511 A	-X:99775132 2966873475 A	K
171	512 A	-X:99775131 2966873474 A	
171	513 A	-X:99775130 2966873473 A	
172 G	514 G	-X:99775129 2966873472 G	G
172	515 G	-X:99775128 2966873471 G	
172	516 A	-X:99775127 2966873470 A	
173 F	517 T	-X:99775126 2966873469 T	F
173	518 T	-X:99775125 2966873468 T	
173	519 T	-X:99775124 2966873467 T	
174 P	520 C	-X:99775123 2966873466 C	P
174	521 C	-X:99775122 2966873465 C	
174	522 T	-X:99775121 2966873464 T	
175 K	523 A	-X:99775120 2966873463 A	K
175	524 A	-X:99775119 2966873462 A	
175	525 G	-X:99775118 2966873461 G	
176 S	526 A	-X:99775117 2966873460 A	S
176	527 G	-X:99775116 2966873459 G	
176	528 T	-X:99775115 2966873458 T	
177 C	529 T	-X:99775114 2966873457 T	C
177	530 G	-X:99775113 2966873456 G	
177	531 C	-X:99775112 2966873455 C	
178 C	532 T	-X:99775111 2966873454 T	C
178	533 G	-X:99775110 2966873453 G	
178	534 T	-X:99775109 2966873452 T	
179 K	535 A	-X:99775108 2966873451 A	K
179	536 A	-X:99775107 2966873450 A	
179	537 A	-X:99775106 2966873449 A	
180 L	538 C	-X:99775105 2966873448 C	L
180	539 T	-X:99775104 2966873447 T	
180	540 T	-X:99775103 2966873446 T	
181 E	541 G	-X:99775102 2966873445 G	E
181	542 A	-X:99775101 2966873444 A	
181	543 A	-X:99775100 2966873443 A	
182 D	544 G	-X:99775099 2966873442 G	D
182	545 A	-X:99775098 2966873441 A	
182	546 T	-X:99775097 2966873440 T	
183 C	547 T	-X:99775096 2966873439 T	C
183	548 G	-X:99775095 2966873438 G	
183	549 T	-X:99775094 2966873437 T	
184 T	550 A	-X:99775093 2966873436 A	T
184	551 C	-X:99775092 2966873435 C	
184	552 T	-X:99775091 2966873434 T	
185 P	553 C	-X:99775090 2966873433 C	P
185	554 C	-X:99775089 2966873432 C	
185	555 A	-X:99775088 2966873431 A	
186 Q	556 C	-X:99775087 2966873430 C	Q
186	557 A	-X:99775086 2966873429 A	
186	558 G	-X:99775085 2966873428 G	
187 R	559 A	-X:99775084 2966873427 A	R
187	560 G	-X:99775083 2966873426 G	
187	561 A	-X:99775082 2966873425 A	
188 D	562 G	-X:99775081 2966873424 G	D
188	563 A	-X:99775080 2966873423 A	
188	564 T	-X:99775079 2966873422 T	
189 A	565 G	-X:99775078 2966873421 G	A
189	566 C	-X:99775077 2966873420 C	
189	567 A	-X:99775076 2966873419 A	
190 D	568 G	-X:99775075 2966873418 G	D
190	569 A	-X:99775074 2966873417 A	
190	570 C	-X:99775073 2966873416 C	
191 K	571 A	-X:99775072 2966873415 A	K
191	572 A	-X:99775071 2966873414 A	
191	573 A	-X:99775070 2966873413 A	
192 V	574 G	-X:99775069 2966873412 G	V
192	575 T	-X:99775068 2966873411 T	
192	576 A	-X:99775067 2966873410 A	
193 N	577 A	-X:99775066 2966873409 A	N
193	578 A	-X:99775065 2966873408 A	
193	579 C	-X:99775064 2966873407 C	
194 N	580 A	-X:99775063 2966873406 A	N
194	581 A	-X:99775062 2966873405 A	
194	582 T	-X:99775061 2966873404 T	
195 E	583 G	-X:99775060 2966873403 G	E
195	584 A	-X:99775059 2966873402 A	
195	585 A	-X:99775058 2966873401 A	
196 G	586 G	-X:99774221 2966872564 G	G
196	587 G	-X:99774220 2966872563 G	
196	588 T	-X:99774219 2966872562 T	
197 C	589 T	-X:99774218 2966872561 T	C
197	590 G	-X:99774217 2966872560 G	
197	591 T	-X:99774216 2966872559 T	
198 F	592 T	-X:99774215 2966872558 T	F
198	593 T	-X:99774214 2966872557 T	
198	594 T	-X:99774213 2966872556 T	
199 I	595 A	-X:99774212 2966872555 A	I
199	596 T	-X:99774211 2966872554 T	
199	597 A	-X:99774210 2966872553 A	
200 K	598 A	-X:99774209 2966872552 A	K
200	599 A	-X:99774208 2966872551 A	
200	600 G	-X:99774207 2966872550 G	
201 V	601 G	-X:99774206 2966872549 G	V
201	602 T	-X:99774205 2966872548 T	
201	603 G	-X:99774204 2966872547 G	
202 M	604 A	-X:99774203 2966872546 A	M
202	605 T	-X:99774202 2966872545 T	
202	606 G	-X:99774201 2966872544 G	
203 T	607 A	-X:99774200 2966872543 A	T
203	608 C	-X:99774199 2966872542 C	
203	609 C	-X:99774198 2966872541 C	
204 I	610 A	-X:99774197 2966872540 A	I
204	611 T	-X:99774196 2966872539 T	
204	612 T	-X:99774195 2966872538 T	
205 I	613 A	-X:99774194 2966872537 A	I
205	614 T	-X:99774193 2966872536 T	
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>ENSP00000362122 
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313 M	937 A	+X:99741353 2966839696 A	M
313	938 T	+X:99741354 2966839697 T	
313	939 G	+X:99741355 2966839698 G	
314 L	940 C	+X:99741356 2966839699 C	L
314	941 T	+X:99741357 2966839700 T	
314	942 G	+X:99741358 2966839701 G	
315 G	943 G	+X:99741359 2966839702 G	G
315	944 G	+X:99741360 2966839703 G	
315	945 G	+X:99741361 2966839704 G	
316 R	946 A	+X:99741362 2966839705 A	R
316	947 G	+X:99741363 2966839706 G	
316	948 G	+X:99741364 2966839707 G	
317 V	949 G	+X:99741365 2966839708 G	V
317	950 T	+X:99741366 2966839709 T	
317	951 C	+X:99741367 2966839710 C	
>ENSP00000360640 
1 M	1 A	-20:49008467 2757118520 A	M
1	2 T	-20:49008466 2757118519 T	
1	3 G	-20:49008465 2757118518 G	
2 A	4 G	-20:49008464 2757118517 G	A
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2	6 C	-20:49008462 2757118515 C	
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3	8 C	-20:49008460 2757118513 C	
3	9 C	-20:49008459 2757118512 C	
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4	11 T	-20:49008457 2757118510 T	
4	12 G	-20:49008456 2757118509 G	
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5	14 A	-20:49008454 2757118507 A	
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9	26 G	-20:49008442 2757118495 G	
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13	38 C	-20:49008430 2757118483 C	
13	39 T	-20:49008429 2757118482 T	
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14	41 G	-20:49008427 2757118480 G	
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17	51 G	-20:49008417 2757118470 G	
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18	54 A	-20:49008414 2757118467 A	
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19	56 T	-20:49008412 2757118465 T	
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20	59 G	-20:49008409 2757118462 G	
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23	68 G	-20:49008400 2757118453 G	
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24	71 A	-20:49008397 2757118450 A	
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25	74 A	-20:49008394 2757118447 A	
25	75 C	-20:49008393 2757118446 C	
26 K	76 A	-20:49008392 2757118445 A	K
26	77 A	-20:49008391 2757118444 A	
26	78 A	-20:49008390 2757118443 A	
27 Y	79 T	-20:49008389 2757118442 T	Y
27	80 A	-20:49008388 2757118441 A	
27	81 T	-20:49008387 2757118440 T	
28 S	82 T	-20:49008386 2757118439 T	S
28	83 C	-20:49008385 2757118438 C	
28	84 G	-20:49008384 2757118437 G	
29 V	85 G	-20:49008383 2757118436 G	V
29	86 T	-20:49008382 2757118435 T	
29	87 G	-20:49008381 2757118434 G	
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30	89 T	-20:49008379 2757118432 T	
30	90 T	-20:49008378 2757118431 T	
31 L	91 T	-20:49008377 2757118430 T	L
31	92 T	-20:49008376 2757118429 T	
31	93 A	-20:49008375 2757118428 A	
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32	95 C	-20:49008373 2757118426 C	
32	96 T	-20:49008372 2757118425 T	
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33	98 C	-20:49008370 2757118423 C	
33	99 C	-20:49008369 2757118422 C	
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34	101 A	-20:49008367 2757118420 A	
34	102 C	-20:49008366 2757118419 C	
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35	104 A	-20:49008364 2757118417 A	
35	105 C	-20:49008363 2757118416 C	
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36	107 A	-20:49008361 2757118414 A	
36	108 G	-20:49008360 2757118413 G	
37 R	109 C	-20:49008359 2757118412 C	R
37	110 G	-20:49008358 2757118411 G	
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39 N	115 A	-20:49008353 2757118406 A	N
39	116 A	-20:49008352 2757118405 A	
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40	119 T	-20:49008349 2757118402 T	
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41	122 C	-20:49008346 2757118399 C	
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42	125 T	-20:49008343 2757118396 T	
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43	128 T	-20:49008340 2757118393 T	
43	129 C	-20:49008339 2757118392 C	
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44	131 T	-20:49008337 2757118390 T	
44	132 G	-20:49008336 2757118389 G	
45 W	133 T	-20:49008335 2757118388 T	W
45	134 G	-20:49008334 2757118387 G	
45	135 G	-20:49008333 2757118386 G	
46 L	136 C	-20:49008332 2757118385 C	L
46	137 T	-20:49008331 2757118384 T	
46	138 G	-20:49008330 2757118383 G	
47 L	139 C	-20:49008329 2757118382 C	L
47	140 T	-20:49008328 2757118381 T	
47	141 G	-20:49008327 2757118380 G	
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48	143 T	-20:49008325 2757118378 T	
48	144 G	-20:49008324 2757118377 G	
49 K	145 A	-20:49008323 2757118376 A	K
49	146 A	-20:49008322 2757118375 A	
49	147 A	-20:49008321 2757118374 A	
50 S	148 A	-20:49008320 2757118373 A	S
50	149 G	-20:49008319 2757118372 G	
50	150 C	-20:49008318 2757118371 C	
51 F	151 T	-20:49008317 2757118370 T	F
51	152 T	-20:49008316 2757118369 T	
51	153 C	-20:49008315 2757118368 C	
52 S	154 T	-20:49008314 2757118367 T	S
52	155 C	-20:49008313 2757118366 C	
52	156 C	-20:49008312 2757118365 C	
53 E	157 G	-20:49008311 2757118364 G	E
53	158 A	-20:49008310 2757118363 A	
53	159 G	-20:49008309 2757118362 G	
54 S	160 A	-20:49008308 2757118361 A	S
54	161 G	-20:49008307 2757118360 G	
54	162 T	-20:49005229 2757115282 T	
55 G	163 G	-20:49005228 2757115281 G	G
55	164 G	-20:49005227 2757115280 G	
55	165 A	-20:49005226 2757115279 A	
56 I	166 A	-20:49005225 2757115278 A	I
56	167 T	-20:49005224 2757115277 T	
56	168 C	-20:49005223 2757115276 C	
57 N	169 A	-20:49005222 2757115275 A	N
57	170 A	-20:49005221 2757115274 A	
57	171 C	-20:49005220 2757115273 C	
58 Y	172 T	-20:49005219 2757115272 T	Y
58	173 A	-20:49005218 2757115271 A	
58	174 T	-20:49005217 2757115270 T	
59 E	175 G	-20:49005216 2757115269 G	E
59	176 A	-20:49005215 2757115268 A	
59	177 A	-20:49005214 2757115267 A	
60 I	178 A	-20:49005213 2757115266 A	I
60	179 T	-20:49005212 2757115265 T	
60	180 T	-20:49005211 2757115264 T	
61 I	181 A	-20:49005210 2757115263 A	I
61	182 T	-20:49005209 2757115262 T	
61	183 A	-20:49005208 2757115261 A	
62 I	184 A	-20:49005207 2757115260 A	I
62	185 T	-20:49005206 2757115259 T	
62	186 C	-20:49005205 2757115258 C	
63 I	187 A	-20:49005204 2757115257 A	I
63	188 T	-20:49005203 2757115256 T	
63	189 A	-20:49005202 2757115255 A	
64 D	190 G	-20:49005201 2757115254 G	D
64	191 A	-20:49005200 2757115253 A	
64	192 T	-20:49005199 2757115252 T	
65 D	193 G	-20:49005198 2757115251 G	D
65	194 A	-20:49005197 2757115250 A	
65	195 T	-20:49005196 2757115249 T	
66 G	196 G	-20:49005195 2757115248 G	G
66	197 G	-20:49005194 2757115247 G	
66	198 A	-20:49005193 2757115246 A	
67 S	199 A	-20:49005192 2757115245 A	S
67	200 G	-20:49005191 2757115244 G	
67	201 C	-20:49005190 2757115243 C	
68 P	202 C	-20:49005189 2757115242 C	P
68	203 C	-20:49005188 2757115241 C	
68	204 A	-20:49005187 2757115240 A	
69 D	205 G	-20:49005186 2757115239 G	D
69	206 A	-20:49005185 2757115238 A	
69	207 T	-20:49005184 2757115237 T	
70 G	208 G	-20:49005183 2757115236 G	G
70	209 G	-20:49005182 2757115235 G	
70	210 A	-20:49005181 2757115234 A	
71 T	211 A	-20:49005180 2757115233 A	T
71	212 C	-20:49005179 2757115232 C	
71	213 A	-20:49005178 2757115231 A	
72 R	214 A	-20:49005177 2757115230 A	R
72	215 G	-20:49005176 2757115229 G	
72	216 G	-20:49005175 2757115228 G	
73 D	217 G	-20:49005174 2757115227 G	D
73	218 A	-20:49005173 2757115226 A	
73	219 T	-20:49005172 2757115225 T	
74 V	220 G	-20:49005171 2757115224 G	V
74	221 T	-20:49005170 2757115223 T	
74	222 T	-20:49005169 2757115222 T	
75 A	223 G	-20:49005168 2757115221 G	A
75	224 C	-20:49005167 2757115220 C	
75	225 T	-20:49005166 2757115219 T	
76 E	226 G	-20:49005165 2757115218 G	E
76	227 A	-20:49005164 2757115217 A	
76	228 A	-20:49005163 2757115216 A	
77 Q	229 C	-20:49005162 2757115215 C	Q
77	230 A	-20:49005161 2757115214 A	
77	231 G	-20:49005160 2757115213 G	
78 L	232 T	-20:49005159 2757115212 T	L
78	233 T	-20:49005158 2757115211 T	
78	234 G	-20:49005157 2757115210 G	
79 E	235 G	-20:49005156 2757115209 G	E
79	236 A	-20:49005155 2757115208 A	
79	237 G	-20:49005154 2757115207 G	
80 K	238 A	-20:49005153 2757115206 A	K
80	239 A	-20:49005152 2757115205 A	
80	240 G	-20:49005151 2757115204 G	
81 I	241 A	-20:49005150 2757115203 A	I
81	242 T	-20:49005149 2757115202 T	
81	243 C	-20:49005148 2757115201 C	
82 Y	244 T	-20:49005147 2757115200 T	Y
82	245 A	-20:49005146 2757115199 A	
82	246 T	-20:49005145 2757115198 T	
83 G	247 G	-20:49005144 2757115197 G	G
83	248 G	-20:49005143 2757115196 G	
83	249 G	-20:49005142 2757115195 G	
84 S	250 T	-20:49005141 2757115194 T	S
84	251 C	-20:49005140 2757115193 C	
84	252 A	-20:49005139 2757115192 A	
85 D	253 G	-20:49005138 2757115191 G	D
85	254 A	-20:49005137 2757115190 A	
85	255 C	-20:49005136 2757115189 C	
86 R	256 A	-20:49005135 2757115188 A	R
86	257 G	-20:49005134 2757115187 G	
86	258 A	-20:49005133 2757115186 A	
87 I	259 A	-20:49005132 2757115185 A	I
87	260 T	-20:49005131 2757115184 T	
87	261 T	-20:49005130 2757115183 T	
88 L	262 C	-20:48998606 2757108659 C	L
88	263 T	-20:48998605 2757108658 T	
88	264 T	-20:48998604 2757108657 T	
89 L	265 C	-20:48998603 2757108656 C	L
89	266 T	-20:48998602 2757108655 T	
89	267 A	-20:48998601 2757108654 A	
90 R	268 A	-20:48998600 2757108653 A	R
90	269 G	-20:48998599 2757108652 G	
90	270 A	-20:48998598 2757108651 A	
91 P	271 C	-20:48998597 2757108650 C	P
91	272 C	-20:48998596 2757108649 C	
91	273 A	-20:48998595 2757108648 A	
92 R	274 C	-20:48998594 2757108647 C	R
92	275 G	-20:48998593 2757108646 G	
92	276 A	-20:48998592 2757108645 A	
93 E	277 G	-20:48998591 2757108644 G	E
93	278 A	-20:48998590 2757108643 A	
93	279 G	-20:48998589 2757108642 G	
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94	281 A	-20:48998587 2757108640 A	
94	282 A	-20:48998586 2757108639 A	
95 K	283 A	-20:48998585 2757108638 A	K
95	284 A	-20:48998584 2757108637 A	
95	285 G	-20:48998583 2757108636 G	
96 L	286 T	-20:48998582 2757108635 T	L
96	287 T	-20:48998581 2757108634 T	
96	288 G	-20:48998580 2757108633 G	
97 G	289 G	-20:48998579 2757108632 G	G
97	290 G	-20:48998578 2757108631 G	
97	291 A	-20:48998577 2757108630 A	
98 L	292 C	-20:48998576 2757108629 C	L
98	293 T	-20:48998575 2757108628 T	
98	294 A	-20:48998574 2757108627 A	
99 G	295 G	-20:48998573 2757108626 G	G
99	296 G	-20:48995867 2757105920 G	
99	297 A	-20:48995866 2757105919 A	
100 T	298 A	-20:48995865 2757105918 A	T
100	299 C	-20:48995864 2757105917 C	
100	300 T	-20:48995863 2757105916 T	
101 A	301 G	-20:48995862 2757105915 G	A
101	302 C	-20:48995861 2757105914 C	
101	303 A	-20:48995860 2757105913 A	
102 Y	304 T	-20:48995859 2757105912 T	Y
102	305 A	-20:48995858 2757105911 A	
102	306 T	-20:48995857 2757105910 T	
103 I	307 A	-20:48995856 2757105909 A	I
103	308 T	-20:48995855 2757105908 T	
103	309 T	-20:48995854 2757105907 T	
104 H	310 C	-20:48995853 2757105906 C	H
104	311 A	-20:48995852 2757105905 A	
104	312 T	-20:48995851 2757105904 T	
105 G	313 G	-20:48995850 2757105903 G	G
105	314 G	-20:48995849 2757105902 G	
105	315 A	-20:48995848 2757105901 A	
106 M	316 A	-20:48995847 2757105900 A	M
106	317 T	-20:48995846 2757105899 T	
106	318 G	-20:48995845 2757105898 G	
107 K	319 A	-20:48995844 2757105897 A	K
107	320 A	-20:48995843 2757105896 A	
107	321 A	-20:48995842 2757105895 A	
108 H	322 C	-20:48995841 2757105894 C	H
108	323 A	-20:48995840 2757105893 A	
108	324 T	-20:48995839 2757105892 T	
109 A	325 G	-20:48995838 2757105891 G	A
109	326 C	-20:48995837 2757105890 C	
109	327 C	-20:48995836 2757105889 C	
110 T	328 A	-20:48995835 2757105888 A	T
110	329 C	-20:48995834 2757105887 C	
110	330 A	-20:48995833 2757105886 A	
111 G	331 G	-20:48995832 2757105885 G	G
111	332 G	-20:48995831 2757105884 G	
111	333 A	-20:48995830 2757105883 A	
112 N	334 A	-20:48995829 2757105882 A	N
112	335 A	-20:48995828 2757105881 A	
112	336 C	-20:48995827 2757105880 C	
113 Y	337 T	-20:48995826 2757105879 T	Y
113	338 A	-20:48995825 2757105878 A	
113	339 C	-20:48995824 2757105877 C	
114 I	340 A	-20:48995823 2757105876 A	I
114	341 T	-20:48995822 2757105875 T	
114	342 C	-20:48995821 2757105874 C	
115 I	343 A	-20:48995820 2757105873 A	I
115	344 T	-20:48995819 2757105872 T	
115	345 T	-20:48995818 2757105871 T	
116 I	346 A	-20:48995817 2757105870 A	I
116	347 T	-20:48995816 2757105869 T	
116	348 T	-20:48995815 2757105868 T	
117 M	349 A	-20:48995814 2757105867 A	M
117	350 T	-20:48995813 2757105866 T	
117	351 G	-20:48995812 2757105865 G	
118 D	352 G	-20:48995811 2757105864 G	D
118	353 A	-20:48995810 2757105863 A	
118	354 T	-20:48995809 2757105862 T	
119 A	355 G	-20:48995808 2757105861 G	A
119	356 C	-20:48995807 2757105860 C	
119	357 T	-20:48995806 2757105859 T	
120 D	358 G	-20:48995805 2757105858 G	D
120	359 A	-20:48995804 2757105857 A	
120	360 T	-20:48995803 2757105856 T	
121 L	361 C	-20:48995802 2757105855 C	L
121	362 T	-20:48995801 2757105854 T	
121	363 C	-20:48995800 2757105853 C	
122 S	364 T	-20:48995799 2757105852 T	S
122	365 C	-20:48995798 2757105851 C	
122	366 A	-20:48995797 2757105850 A	
123 H	367 C	-20:48995796 2757105849 C	H
123	368 A	-20:48995795 2757105848 A	
123	369 C	-20:48995794 2757105847 C	
124 H	370 C	-20:48995793 2757105846 C	H
124	371 A	-20:48995792 2757105845 A	
124	372 T	-20:48995791 2757105844 T	
125 P	373 C	-20:48995706 2757105759 C	P
125	374 C	-20:48995705 2757105758 C	
125	375 A	-20:48995704 2757105757 A	
126 K	376 A	-20:48995703 2757105756 A	K
126	377 A	-20:48995702 2757105755 A	
126	378 A	-20:48995701 2757105754 A	
127 F	379 T	-20:48995700 2757105753 T	F
127	380 T	-20:48995699 2757105752 T	
127	381 T	-20:48995698 2757105751 T	
128 I	382 A	-20:48995697 2757105750 A	I
128	383 T	-20:48995696 2757105749 T	
128	384 T	-20:48995695 2757105748 T	
129 P	385 C	-20:48995694 2757105747 C	P
129	386 C	-20:48995693 2757105746 C	
129	387 T	-20:48995692 2757105745 T	
130 E	388 G	-20:48995691 2757105744 G	E
130	389 A	-20:48995690 2757105743 A	
130	390 A	-20:48995689 2757105742 A	
131 F	391 T	-20:48995688 2757105741 T	F
131	392 T	-20:48995687 2757105740 T	
131	393 T	-20:48995686 2757105739 T	
132 I	394 A	-20:48995685 2757105738 A	I
132	395 T	-20:48995684 2757105737 T	
132	396 T	-20:48995683 2757105736 T	
133 R	397 A	-20:48995682 2757105735 A	R
133	398 G	-20:48995681 2757105734 G	
133	399 G	-20:48992070 2757102123 G	
134 K	400 A	-20:48992069 2757102122 A	K
134	401 A	-20:48992068 2757102121 A	
134	402 G	-20:48992067 2757102120 G	
135 Q	403 C	-20:48992066 2757102119 C	Q
135	404 A	-20:48992065 2757102118 A	
135	405 A	-20:48992064 2757102117 A	
136 K	406 A	-20:48992063 2757102116 A	K
136	407 A	-20:48992062 2757102115 A	
136	408 G	-20:48992061 2757102114 G	
137 E	409 G	-20:48992060 2757102113 G	E
137	410 A	-20:48992059 2757102112 A	
137	411 G	-20:48992058 2757102111 G	
138 G	412 G	-20:48992057 2757102110 G	G
138	413 G	-20:48992056 2757102109 G	
138	414 T	-20:48992055 2757102108 T	
139 N	415 A	-20:48992054 2757102107 A	N
139	416 A	-20:48992053 2757102106 A	
139	417 T	-20:48992052 2757102105 T	
140 F	418 T	-20:48992051 2757102104 T	F
140	419 T	-20:48992050 2757102103 T	
140	420 T	-20:48992049 2757102102 T	
141 D	421 G	-20:48992048 2757102101 G	D
141	422 A	-20:48992047 2757102100 A	
141	423 T	-20:48992046 2757102099 T	
142 I	424 A	-20:48992045 2757102098 A	I
142	425 T	-20:48992044 2757102097 T	
142	426 T	-20:48992043 2757102096 T	
143 V	427 G	-20:48992042 2757102095 G	V
143	428 T	-20:48992041 2757102094 T	
143	429 C	-20:48992040 2757102093 C	
144 S	430 T	-20:48992039 2757102092 T	S
144	431 C	-20:48992038 2757102091 C	
144	432 T	-20:48992037 2757102090 T	
145 G	433 G	-20:48992036 2757102089 G	G
145	434 G	-20:48992035 2757102088 G	
145	435 A	-20:48992034 2757102087 A	
146 T	436 A	-20:48992033 2757102086 A	T
146	437 C	-20:48992032 2757102085 C	
146	438 T	-20:48992031 2757102084 T	
147 R	439 C	-20:48992030 2757102083 C	R
147	440 G	-20:48992029 2757102082 G	
147	441 C	-20:48992028 2757102081 C	
148 Y	442 T	-20:48992027 2757102080 T	Y
148	443 A	-20:48992026 2757102079 A	
148	444 C	-20:48992025 2757102078 C	
149 K	445 A	-20:48992024 2757102077 A	K
149	446 A	-20:48992023 2757102076 A	
149	447 A	-20:48992022 2757102075 A	
150 G	448 G	-20:48992021 2757102074 G	G
150	449 G	-20:48992020 2757102073 G	
150	450 A	-20:48992019 2757102072 A	
151 N	451 A	-20:48992018 2757102071 A	N
151	452 A	-20:48992017 2757102070 A	
151	453 T	-20:48992016 2757102069 T	
152 G	454 G	-20:48992015 2757102068 G	G
152	455 G	-20:48992014 2757102067 G	
152	456 A	-20:48992013 2757102066 A	
153 G	457 G	-20:48992012 2757102065 G	G
153	458 G	-20:48992011 2757102064 G	
153	459 T	-20:48992010 2757102063 T	
154 V	460 G	-20:48992009 2757102062 G	V
154	461 T	-20:48992008 2757102061 T	
154	462 A	-20:48992007 2757102060 A	
155 Y	463 T	-20:48992006 2757102059 T	Y
155	464 A	-20:48992005 2757102058 A	
155	465 T	-20:48992004 2757102057 T	
156 G	466 G	-20:48992003 2757102056 G	G
156	467 G	-20:48992002 2757102055 G	
156	468 C	-20:48992001 2757102054 C	
157 W	469 T	-20:48992000 2757102053 T	W
157	470 G	-20:48991999 2757102052 G	
157	471 G	-20:48991998 2757102051 G	
158 D	472 G	-20:48991997 2757102050 G	D
158	473 A	-20:48991996 2757102049 A	
158	474 T	-20:48991995 2757102048 T	
159 L	475 T	-20:48991994 2757102047 T	L
159	476 T	-20:48991993 2757102046 T	
159	477 G	-20:48991992 2757102045 G	
160 K	478 A	-20:48991991 2757102044 A	K
160	479 A	-20:48991990 2757102043 A	
160	480 A	-20:48991989 2757102042 A	
161 R	481 A	-20:48991988 2757102041 A	R
161	482 G	-20:48991987 2757102040 G	
161	483 A	-20:48991986 2757102039 A	
162 K	484 A	-20:48991985 2757102038 A	K
162	485 A	-20:48991984 2757102037 A	
162	486 A	-20:48991983 2757102036 A	
163 I	487 A	-20:48991982 2757102035 A	I
163	488 T	-20:48991981 2757102034 T	
163	489 A	-20:48991980 2757102033 A	
164 I	490 A	-20:48991979 2757102032 A	I
164	491 T	-20:48991978 2757102031 T	
164	492 C	-20:48991977 2757102030 C	
165 S	493 A	-20:48991976 2757102029 A	S
165	494 G	-20:48991975 2757102028 G	
165	495 T	-20:48991153 2757101206 T	
166 D	496 G	-20:48991152 2757101205 G	D
166	497 A	-20:48991151 2757101204 A	
166	498 T	-20:48991150 2757101203 T	
167 G	499 G	-20:48991149 2757101202 G	G
167	500 G	-20:48991148 2757101201 G	
167	501 A	-20:48991147 2757101200 A	
168 V	502 G	-20:48991146 2757101199 G	V
168	503 T	-20:48991145 2757101198 T	
168	504 T	-20:48991144 2757101197 T	
169 L	505 T	-20:48991143 2757101196 T	L
169	506 T	-20:48991142 2757101195 T	
169	507 G	-20:48991141 2757101194 G	
170 P	508 C	-20:48991140 2757101193 C	P
170	509 C	-20:48991139 2757101192 C	
170	510 A	-20:48991138 2757101191 A	
171 C	511 T	-20:48991137 2757101190 T	C
171	512 G	-20:48991136 2757101189 G	
171	513 T	-20:48991135 2757101188 T	
172 C	514 T	-20:48991134 2757101187 T	C
172	515 G	-20:48991133 2757101186 G	
172	516 C	-20:48991132 2757101185 C	
173 P	517 C	-20:48991131 2757101184 C	P
173	518 C	-20:48991130 2757101183 C	
173	519 A	-20:48991129 2757101182 A	
174 G	520 G	-20:48991128 2757101181 G	G
174	521 G	-20:48991127 2757101180 G	
174	522 C	-20:48991126 2757101179 C	
175 W	523 T	-20:48991125 2757101178 T	W
175	524 G	-20:48991124 2757101177 G	
175	525 G	-20:48991123 2757101176 G	
176 S	526 T	-20:48991122 2757101175 T	S
176	527 C	-20:48991121 2757101174 C	
176	528 A	-20:48991120 2757101173 A	
177 L	529 C	-20:48991119 2757101172 C	L
177	530 T	-20:48991118 2757101171 T	
177	531 C	-20:48991117 2757101170 C	
178 L	532 C	-20:48991116 2757101169 C	L
178	533 T	-20:48991115 2757101168 T	
178	534 G	-20:48991114 2757101167 G	
179 G	535 G	-20:48991113 2757101166 G	G
179	536 G	-20:48991112 2757101165 G	
179	537 C	-20:48991111 2757101164 C	
180 S	538 T	-20:48991110 2757101163 T	S
180	539 C	-20:48991109 2757101162 C	
180	540 A	-20:48991108 2757101161 A	
181 S	541 A	-20:48991107 2757101160 A	S
181	542 G	-20:48991106 2757101159 G	
181	543 T	-20:48991105 2757101158 T	
182 D	544 G	-20:48991104 2757101157 G	D
182	545 A	-20:48991103 2757101156 A	
182	546 T	-20:48991102 2757101155 T	
183 P	547 C	-20:48991101 2757101154 C	P
183	548 C	-20:48991100 2757101153 C	
183	549 A	-20:48991099 2757101152 A	
184 A	550 G	-20:48991098 2757101151 G	A
184	551 C	-20:48991097 2757101150 C	
184	552 C	-20:48991096 2757101149 C	
185 I	553 A	-20:48991095 2757101148 A	I
185	554 T	-20:48991094 2757101147 T	
185	555 C	-20:48991093 2757101146 C	
186 L	556 T	-20:48991092 2757101145 T	L
186	557 T	-20:48991091 2757101144 T	
186	558 G	-20:48991090 2757101143 G	
187 A	559 G	-20:48991089 2757101142 G	A
187	560 C	-20:48991088 2757101141 C	
187	561 C	-20:48991087 2757101140 C	
188 S	562 T	-20:48991086 2757101139 T	S
188	563 C	-20:48991085 2757101138 C	
188	564 C	-20:48991084 2757101137 C	
189 W	565 T	-20:48991083 2757101136 T	W
189	566 G	-20:48991082 2757101135 G	
189	567 G	-20:48991081 2757101134 G	
190 D	568 G	-20:48991080 2757101133 G	D
190	569 A	-20:48991079 2757101132 A	
190	570 T	-20:48991078 2757101131 T	
191 Y	571 T	-20:48991077 2757101130 T	Y
191	572 A	-20:48991076 2757101129 A	
191	573 C	-20:48991075 2757101128 C	
192 R	574 A	-20:48991074 2757101127 A	R
192	575 G	-20:48991073 2757101126 G	
192	576 G	-20:48991072 2757101125 G	
193 C	577 T	-20:48991071 2757101124 T	C
193	578 G	-20:48991070 2757101123 G	
193	579 T	-20:48991069 2757101122 T	
194 E	580 G	-20:48991068 2757101121 G	E
194	581 A	-20:48991067 2757101120 A	
194	582 G	-20:48991066 2757101119 G	
195 P	583 C	-20:48991065 2757101118 C	P
195	584 C	-20:48991064 2757101117 C	
195	585 A	-20:48991063 2757101116 A	
196 P	586 C	-20:48991062 2757101115 C	P
196	587 C	-20:48991061 2757101114 C	
196	588 G	-20:48991060 2757101113 G	
197 R	589 C	-20:48991059 2757101112 C	R
197	590 G	-20:48991058 2757101111 G	
197	591 C	-20:48991057 2757101110 C	
198 L	592 C	-20:48991056 2757101109 C	L
198	593 T	-20:48991055 2757101108 T	
198	594 A	-20:48991054 2757101107 A	
199 A	595 G	-20:48991053 2757101106 G	A
199	596 C	-20:48991052 2757101105 C	
199	597 C	-20:48991051 2757101104 C	
200 S	598 A	-20:48991050 2757101103 A	S
200	599 G	-20:48991049 2757101102 G	
200	600 C	-20:48990877 2757100930 C	
201 R	601 C	-20:48990876 2757100929 C	R
201	602 G	-20:48990875 2757100928 G	
201	603 T	-20:48990874 2757100927 T	
202 G	604 G	-20:48990873 2757100926 G	G
202	605 G	-20:48990872 2757100925 G	
202	606 G	-20:48990871 2757100924 G	
203 A	607 G	-20:48990870 2757100923 G	A
203	608 C	-20:48990869 2757100922 C	
203	609 C	-20:48990868 2757100921 C	
204 N	610 A	-20:48990867 2757100920 A	N
204	611 A	-20:48990866 2757100919 A	
204	612 T	-20:48990865 2757100918 T	
205 F	613 T	-20:48990864 2757100917 T	F
205	614 T	-20:48990863 2757100916 T	
205	615 T	-20:48990862 2757100915 T	
206 L	616 T	-20:48990861 2757100914 T	L
206	617 T	-20:48990860 2757100913 T	
206	618 A	-20:48990859 2757100912 A	
207 T	619 A	-20:48990858 2757100911 A	T
207	620 C	-20:48990857 2757100910 C	
207	621 T	-20:48990856 2757100909 T	
208 Q	622 C	-20:48990855 2757100908 C	Q
208	623 A	-20:48990854 2757100907 A	
208	624 G	-20:48990853 2757100906 G	
209 I	625 A	-20:48990852 2757100905 A	I
209	626 T	-20:48990851 2757100904 T	
209	627 C	-20:48990850 2757100903 C	
210 L	628 T	-20:48990849 2757100902 T	L
210	629 T	-20:48990848 2757100901 T	
210	630 G	-20:48990847 2757100900 G	
211 L	631 C	-20:48990846 2757100899 C	L
211	632 T	-20:48990845 2757100898 T	
211	633 G	-20:48990844 2757100897 G	
212 R	634 A	-20:48990843 2757100896 A	R
212	635 G	-20:48990842 2757100895 G	
212	636 A	-20:48990841 2757100894 A	
213 P	637 C	-20:48990840 2757100893 C	P
213	638 C	-20:48990839 2757100892 C	
213	639 A	-20:48990838 2757100891 A	
214 G	640 G	-20:48990837 2757100890 G	G
214	641 G	-20:48990836 2757100889 G	
214	642 A	-20:48990835 2757100888 A	
215 A	643 G	-20:48990834 2757100887 G	A
215	644 C	-20:48990833 2757100886 C	
215	645 A	-20:48990832 2757100885 A	
216 S	646 T	-20:48990831 2757100884 T	S
216	647 C	-20:48990830 2757100883 C	
216	648 T	-20:48990829 2757100882 T	
217 D	649 G	-20:48990828 2757100881 G	D
217	650 A	-20:48990827 2757100880 A	
217	651 T	-20:48990826 2757100879 T	
218 L	652 T	-20:48990825 2757100878 T	L
218	653 T	-20:48990824 2757100877 T	
218	654 A	-20:48990823 2757100876 A	
219 T	655 A	-20:48990822 2757100875 A	T
219	656 C	-20:48990821 2757100874 C	
219	657 A	-20:48990820 2757100873 A	
220 G	658 G	-20:48990819 2757100872 G	G
220	659 G	-20:48990818 2757100871 G	
220	660 A	-20:48990817 2757100870 A	
221 S	661 A	-20:48990816 2757100869 A	S
221	662 G	-20:48990815 2757100868 G	
221	663 T	-20:48990814 2757100867 T	
222 F	664 T	-20:48990813 2757100866 T	F
222	665 T	-20:48990812 2757100865 T	
222	666 C	-20:48990811 2757100864 C	
223 R	667 A	-20:48990810 2757100863 A	R
223	668 G	-20:48990809 2757100862 G	
223	669 A	-20:48986206 2757096259 A	
224 L	670 T	-20:48986205 2757096258 T	L
224	671 T	-20:48986204 2757096257 T	
224	672 A	-20:48986203 2757096256 A	
225 Y	673 T	-20:48986202 2757096255 T	Y
225	674 A	-20:48986201 2757096254 A	
225	675 C	-20:48986200 2757096253 C	
226 R	676 C	-20:48986199 2757096252 C	R
226	677 G	-20:48986198 2757096251 G	
226	678 A	-20:48986197 2757096250 A	
227 K	679 A	-20:48986196 2757096249 A	K
227	680 A	-20:48986195 2757096248 A	
227	681 A	-20:48986194 2757096247 A	
228 E	682 G	-20:48986193 2757096246 G	E
228	683 A	-20:48986192 2757096245 A	
228	684 A	-20:48986191 2757096244 A	
229 V	685 G	-20:48986190 2757096243 G	V
229	686 T	-20:48986189 2757096242 T	
229	687 T	-20:48986188 2757096241 T	
230 L	688 C	-20:48986187 2757096240 C	L
230	689 T	-20:48986186 2757096239 T	
230	690 A	-20:48986185 2757096238 A	
231 E	691 G	-20:48986184 2757096237 G	E
231	692 A	-20:48986183 2757096236 A	
231	693 G	-20:48986182 2757096235 G	
232 K	694 A	-20:48986181 2757096234 A	K
232	695 A	-20:48986180 2757096233 A	
232	696 A	-20:48986179 2757096232 A	
233 L	697 T	-20:48986178 2757096231 T	L
233	698 T	-20:48986177 2757096230 T	
233	699 A	-20:48986176 2757096229 A	
234 I	700 A	-20:48986175 2757096228 A	I
234	701 T	-20:48986174 2757096227 T	
234	702 A	-20:48986173 2757096226 A	
235 E	703 G	-20:48986172 2757096225 G	E
235	704 A	-20:48986171 2757096224 A	
235	705 A	-20:48986170 2757096223 A	
236 K	706 A	-20:48986169 2757096222 A	K
236	707 A	-20:48986168 2757096221 A	
236	708 A	-20:48986167 2757096220 A	
237 C	709 T	-20:48986166 2757096219 T	C
237	710 G	-20:48986165 2757096218 G	
237	711 T	-20:48986164 2757096217 T	
238 V	712 G	-20:48986163 2757096216 G	V
238	713 T	-20:48986162 2757096215 T	
238	714 T	-20:48986161 2757096214 T	
239 S	715 T	-20:48986160 2757096213 T	S
239	716 C	-20:48986159 2757096212 C	
239	717 T	-20:48986158 2757096211 T	
240 K	718 A	-20:48986157 2757096210 A	K
240	719 A	-20:48986156 2757096209 A	
240	720 A	-20:48986155 2757096208 A	
241 G	721 G	-20:48986154 2757096207 G	G
241	722 G	-20:48986153 2757096206 G	
241	723 C	-20:48986152 2757096205 C	
242 Y	724 T	-20:48986151 2757096204 T	Y
242	725 A	-20:48986150 2757096203 A	
242	726 C	-20:48986149 2757096202 C	
243 V	727 G	-20:48986148 2757096201 G	V
243	728 T	-20:48986147 2757096200 T	
243	729 C	-20:48986146 2757096199 C	
244 F	730 T	-20:48986145 2757096198 T	F
244	731 T	-20:48986144 2757096197 T	
244	732 C	-20:48986143 2757096196 C	
245 Q	733 C	-20:48986142 2757096195 C	Q
245	734 A	-20:48986141 2757096194 A	
245	735 G	-20:48986140 2757096193 G	
246 M	736 A	-20:48986139 2757096192 A	M
246	737 T	-20:48986138 2757096191 T	
246	738 G	-20:48986137 2757096190 G	
247 E	739 G	-20:48986136 2757096189 G	E
247	740 A	-20:48986135 2757096188 A	
247	741 G	-20:48986134 2757096187 G	
248 M	742 A	-20:48986133 2757096186 A	M
248	743 T	-20:48986132 2757096185 T	
248	744 G	-20:48986131 2757096184 G	
249 I	745 A	-20:48986130 2757096183 A	I
249	746 T	-20:48986129 2757096182 T	
249	747 T	-20:48986128 2757096181 T	
250 V	748 G	-20:48986127 2757096180 G	V
250	749 T	-20:48986126 2757096179 T	
250	750 T	-20:48986125 2757096178 T	
251 R	751 C	-20:48986124 2757096177 C	R
251	752 G	-20:48986123 2757096176 G	
251	753 G	-20:48986122 2757096175 G	
252 A	754 G	-20:48986121 2757096174 G	A
252	755 C	-20:48986120 2757096173 C	
252	756 A	-20:48986119 2757096172 A	
253 R	757 A	-20:48986118 2757096171 A	R
253	758 G	-20:48986117 2757096170 G	
253	759 A	-20:48986116 2757096169 A	
254 Q	760 C	-20:48986115 2757096168 C	Q
254	761 A	-20:48986114 2757096167 A	
254	762 G	-20:48986113 2757096166 G	
255 L	763 T	-20:48986112 2757096165 T	L
255	764 T	-20:48986111 2757096164 T	
255	765 G	-20:48986110 2757096163 G	
256 N	766 A	-20:48986109 2757096162 A	N
256	767 A	-20:48986108 2757096161 A	
256	768 T	-20:48986107 2757096160 T	
257 Y	769 T	-20:48986106 2757096159 T	Y
257	770 A	-20:48986105 2757096158 A	
257	771 T	-20:48986104 2757096157 T	
258 T	772 A	-20:48986103 2757096156 A	T
258	773 C	-20:48986102 2757096155 C	
258	774 T	-20:48986101 2757096154 T	
259 I	775 A	-20:48986100 2757096153 A	I
259	776 T	-20:48986099 2757096152 T	
259	777 T	-20:48986098 2757096151 T	
260 G	778 G	-20:48986097 2757096150 G	G
260	779 G	-20:48986096 2757096149 G	
260	780 C	-20:48986095 2757096148 C	
261 E	781 G	-20:48986094 2757096147 G	E
261	782 A	-20:48986093 2757096146 A	
261	783 G	-20:48986092 2757096145 G	
>ENSP00000360638 
1 M	1 A	-20:49008467 2757118520 A	M
1	2 T	-20:49008466 2757118519 T	
1	3 G	-20:49008465 2757118518 G	
2 A	4 G	-20:49008464 2757118517 G	A
2	5 C	-20:49008463 2757118516 C	
2	6 C	-20:49008462 2757118515 C	
3 S	7 T	-20:49008461 2757118514 T	S
3	8 C	-20:49008460 2757118513 C	
3	9 C	-20:49008459 2757118512 C	
4 L	10 T	-20:49008458 2757118511 T	L
4	11 T	-20:49008457 2757118510 T	
4	12 G	-20:49008456 2757118509 G	
5 E	13 G	-20:49008455 2757118508 G	E
5	14 A	-20:49008454 2757118507 A	
5	15 A	-20:49008453 2757118506 A	
6 V	16 G	-20:49008452 2757118505 G	V
6	17 T	-20:49008451 2757118504 T	
6	18 C	-20:49008450 2757118503 C	
7 S	19 A	-20:49008449 2757118502 A	S
7	20 G	-20:49008448 2757118501 G	
7	21 T	-20:49008447 2757118500 T	
8 R	22 C	-20:49008446 2757118499 C	R
8	23 G	-20:49008445 2757118498 G	
8	24 T	-20:49008444 2757118497 T	
9 S	25 A	-20:49008443 2757118496 A	S
9	26 G	-20:49008442 2757118495 G	
9	27 T	-20:49008441 2757118494 T	
10 P	28 C	-20:49008440 2757118493 C	P
10	29 C	-20:49008439 2757118492 C	
10	30 T	-20:49008438 2757118491 T	
11 R	31 C	-20:49008437 2757118490 C	R
11	32 G	-20:49008436 2757118489 G	
11	33 C	-20:49008435 2757118488 C	
12 R	34 A	-20:49008434 2757118487 A	R
12	35 G	-20:49008433 2757118486 G	
12	36 G	-20:49008432 2757118485 G	
13 S	37 T	-20:49008431 2757118484 T	S
13	38 C	-20:49008430 2757118483 C	
13	39 T	-20:49008429 2757118482 T	
14 R	40 C	-20:49008428 2757118481 C	R
14	41 G	-20:49008427 2757118480 G	
14	42 G	-20:49008426 2757118479 G	
15 R	43 C	-20:49008425 2757118478 C	R
15	44 G	-20:49008424 2757118477 G	
15	45 G	-20:49008423 2757118476 G	
16 E	46 G	-20:49008422 2757118475 G	E
16	47 A	-20:49008421 2757118474 A	
16	48 G	-20:49008420 2757118473 G	
17 L	49 C	-20:49008419 2757118472 C	L
17	50 T	-20:49008418 2757118471 T	
17	51 G	-20:49008417 2757118470 G	
18 E	52 G	-20:49008416 2757118469 G	E
18	53 A	-20:49008415 2757118468 A	
18	54 A	-20:49008414 2757118467 A	
19 V	55 G	-20:49008413 2757118466 G	V
19	56 T	-20:49008412 2757118465 T	
19	57 G	-20:49008411 2757118464 G	
20 R	58 C	-20:49008410 2757118463 C	R
20	59 G	-20:49008409 2757118462 G	
20	60 C	-20:49008408 2757118461 C	
21 S	61 A	-20:49008407 2757118460 A	S
21	62 G	-20:49008406 2757118459 G	
21	63 T	-20:49008405 2757118458 T	
22 P	64 C	-20:49008404 2757118457 C	P
22	65 C	-20:49008403 2757118456 C	
22	66 A	-20:49008402 2757118455 A	
23 R	67 C	-20:49008401 2757118454 C	R
23	68 G	-20:49008400 2757118453 G	
23	69 A	-20:49008399 2757118452 A	
24 Q	70 C	-20:49008398 2757118451 C	Q
24	71 A	-20:49008397 2757118450 A	
24	72 G	-20:49008396 2757118449 G	
25 N	73 A	-20:49008395 2757118448 A	N
25	74 A	-20:49008394 2757118447 A	
25	75 C	-20:49008393 2757118446 C	
26 K	76 A	-20:49008392 2757118445 A	K
26	77 A	-20:49008391 2757118444 A	
26	78 A	-20:49008390 2757118443 A	
27 Y	79 T	-20:49008389 2757118442 T	Y
27	80 A	-20:49008388 2757118441 A	
27	81 T	-20:49008387 2757118440 T	
28 S	82 T	-20:49008386 2757118439 T	S
28	83 C	-20:49008385 2757118438 C	
28	84 G	-20:49008384 2757118437 G	
29 V	85 G	-20:49008383 2757118436 G	V
29	86 T	-20:49008382 2757118435 T	
29	87 G	-20:49008381 2757118434 G	
30 L	88 C	-20:49008380 2757118433 C	L
30	89 T	-20:49008379 2757118432 T	
30	90 T	-20:49008378 2757118431 T	
31 L	91 T	-20:49008377 2757118430 T	L
31	92 T	-20:49008376 2757118429 T	
31	93 A	-20:49008375 2757118428 A	
32 P	94 C	-20:49008374 2757118427 C	P
32	95 C	-20:49008373 2757118426 C	
32	96 T	-20:49008372 2757118425 T	
33 T	97 A	-20:49008371 2757118424 A	T
33	98 C	-20:49008370 2757118423 C	
33	99 C	-20:49008369 2757118422 C	
34 Y	100 T	-20:49008368 2757118421 T	Y
34	101 A	-20:49008367 2757118420 A	
34	102 C	-20:49008366 2757118419 C	
35 N	103 A	-20:49008365 2757118418 A	N
35	104 A	-20:49008364 2757118417 A	
35	105 C	-20:49008363 2757118416 C	
36 E	106 G	-20:49008362 2757118415 G	E
36	107 A	-20:49008361 2757118414 A	
36	108 G	-20:49008360 2757118413 G	
37 R	109 C	-20:49008359 2757118412 C	R
37	110 G	-20:49008358 2757118411 G	
37	111 C	-20:49008357 2757118410 C	
38 E	112 G	-20:49008356 2757118409 G	E
38	113 A	-20:49008355 2757118408 A	
38	114 G	-20:49008354 2757118407 G	
39 N	115 A	-20:49008353 2757118406 A	N
39	116 A	-20:49008352 2757118405 A	
39	117 C	-20:49008351 2757118404 C	
40 L	118 C	-20:49008350 2757118403 C	L
40	119 T	-20:49008349 2757118402 T	
40	120 G	-20:49008348 2757118401 G	
41 P	121 C	-20:49008347 2757118400 C	P
41	122 C	-20:49008346 2757118399 C	
41	123 G	-20:49008345 2757118398 G	
42 L	124 C	-20:49008344 2757118397 C	L
42	125 T	-20:49008343 2757118396 T	
42	126 C	-20:49008342 2757118395 C	
43 I	127 A	-20:49008341 2757118394 A	I
43	128 T	-20:49008340 2757118393 T	
43	129 C	-20:49008339 2757118392 C	
44 V	130 G	-20:49008338 2757118391 G	V
44	131 T	-20:49008337 2757118390 T	
44	132 G	-20:49008336 2757118389 G	
45 W	133 T	-20:49008335 2757118388 T	W
45	134 G	-20:49008334 2757118387 G	
45	135 G	-20:49008333 2757118386 G	
46 L	136 C	-20:49008332 2757118385 C	L
46	137 T	-20:49008331 2757118384 T	
46	138 G	-20:49008330 2757118383 G	
47 L	139 C	-20:49008329 2757118382 C	L
47	140 T	-20:49008328 2757118381 T	
47	141 G	-20:49008327 2757118380 G	
48 V	142 G	-20:49008326 2757118379 G	V
48	143 T	-20:49008325 2757118378 T	
48	144 G	-20:49008324 2757118377 G	
49 K	145 A	-20:49008323 2757118376 A	K
49	146 A	-20:49008322 2757118375 A	
49	147 A	-20:49008321 2757118374 A	
50 S	148 A	-20:49008320 2757118373 A	S
50	149 G	-20:49008319 2757118372 G	
50	150 C	-20:49008318 2757118371 C	
51 F	151 T	-20:49008317 2757118370 T	F
51	152 T	-20:49008316 2757118369 T	
51	153 C	-20:49008315 2757118368 C	
52 S	154 T	-20:49008314 2757118367 T	S
52	155 C	-20:49008313 2757118366 C	
52	156 C	-20:49008312 2757118365 C	
53 E	157 G	-20:49008311 2757118364 G	E
53	158 A	-20:49008310 2757118363 A	
53	159 G	-20:49008309 2757118362 G	
54 S	160 A	-20:49008308 2757118361 A	S
54	161 G	-20:49008307 2757118360 G	
54	162 T	-20:49005229 2757115282 T	
55 G	163 G	-20:49005228 2757115281 G	G
55	164 G	-20:49005227 2757115280 G	
55	165 A	-20:49005226 2757115279 A	
56 I	166 A	-20:49005225 2757115278 A	I
56	167 T	-20:49005224 2757115277 T	
56	168 C	-20:49005223 2757115276 C	
57 N	169 A	-20:49005222 2757115275 A	N
57	170 A	-20:49005221 2757115274 A	
57	171 C	-20:49005220 2757115273 C	
58 Y	172 T	-20:49005219 2757115272 T	Y
58	173 A	-20:49005218 2757115271 A	
58	174 T	-20:49005217 2757115270 T	
59 E	175 G	-20:49005216 2757115269 G	E
59	176 A	-20:49005215 2757115268 A	
59	177 A	-20:49005214 2757115267 A	
60 I	178 A	-20:49005213 2757115266 A	I
60	179 T	-20:49005212 2757115265 T	
60	180 T	-20:49005211 2757115264 T	
61 I	181 A	-20:49005210 2757115263 A	I
61	182 T	-20:49005209 2757115262 T	
61	183 A	-20:49005208 2757115261 A	
62 I	184 A	-20:49005207 2757115260 A	I
62	185 T	-20:49005206 2757115259 T	
62	186 C	-20:49005205 2757115258 C	
63 I	187 A	-20:49005204 2757115257 A	I
63	188 T	-20:49005203 2757115256 T	
63	189 A	-20:49005202 2757115255 A	
64 D	190 G	-20:49005201 2757115254 G	D
64	191 A	-20:49005200 2757115253 A	
64	192 T	-20:49005199 2757115252 T	
65 D	193 G	-20:49005198 2757115251 G	D
65	194 A	-20:49005197 2757115250 A	
65	195 T	-20:49005196 2757115249 T	
66 G	196 G	-20:49005195 2757115248 G	G
66	197 G	-20:49005194 2757115247 G	
66	198 A	-20:49005193 2757115246 A	
67 S	199 A	-20:49005192 2757115245 A	S
67	200 G	-20:49005191 2757115244 G	
67	201 C	-20:49005190 2757115243 C	
68 P	202 C	-20:49005189 2757115242 C	P
68	203 C	-20:49005188 2757115241 C	
68	204 A	-20:49005187 2757115240 A	
69 D	205 G	-20:49005186 2757115239 G	D
69	206 A	-20:49005185 2757115238 A	
69	207 T	-20:49005184 2757115237 T	
70 G	208 G	-20:49005183 2757115236 G	G
70	209 G	-20:49005182 2757115235 G	
70	210 A	-20:49005181 2757115234 A	
71 T	211 A	-20:49005180 2757115233 A	T
71	212 C	-20:49005179 2757115232 C	
71	213 A	-20:49005178 2757115231 A	
72 R	214 A	-20:49005177 2757115230 A	R
72	215 G	-20:49005176 2757115229 G	
72	216 G	-20:49005175 2757115228 G	
73 D	217 G	-20:49005174 2757115227 G	D
73	218 A	-20:49005173 2757115226 A	
73	219 T	-20:49005172 2757115225 T	
74 V	220 G	-20:49005171 2757115224 G	V
74	221 T	-20:49005170 2757115223 T	
74	222 T	-20:49005169 2757115222 T	
75 A	223 G	-20:49005168 2757115221 G	A
75	224 C	-20:49005167 2757115220 C	
75	225 T	-20:49005166 2757115219 T	
76 E	226 G	-20:49005165 2757115218 G	E
76	227 A	-20:49005164 2757115217 A	
76	228 A	-20:49005163 2757115216 A	
77 Q	229 C	-20:49005162 2757115215 C	Q
77	230 A	-20:49005161 2757115214 A	
77	231 G	-20:49005160 2757115213 G	
78 L	232 T	-20:49005159 2757115212 T	L
78	233 T	-20:49005158 2757115211 T	
78	234 G	-20:49005157 2757115210 G	
79 E	235 G	-20:49005156 2757115209 G	E
79	236 A	-20:49005155 2757115208 A	
79	237 G	-20:49005154 2757115207 G	
80 K	238 A	-20:49005153 2757115206 A	K
80	239 A	-20:49005152 2757115205 A	
80	240 G	-20:49005151 2757115204 G	
81 I	241 A	-20:49005150 2757115203 A	I
81	242 T	-20:49005149 2757115202 T	
81	243 C	-20:49005148 2757115201 C	
82 Y	244 T	-20:49005147 2757115200 T	Y
82	245 A	-20:49005146 2757115199 A	
82	246 T	-20:49005145 2757115198 T	
83 G	247 G	-20:49005144 2757115197 G	G
83	248 G	-20:49005143 2757115196 G	
83	249 G	-20:49005142 2757115195 G	
84 S	250 T	-20:49005141 2757115194 T	S
84	251 C	-20:49005140 2757115193 C	
84	252 A	-20:49005139 2757115192 A	
85 D	253 G	-20:49005138 2757115191 G	D
85	254 A	-20:49005137 2757115190 A	
85	255 C	-20:49005136 2757115189 C	
86 R	256 A	-20:49005135 2757115188 A	R
86	257 G	-20:49005134 2757115187 G	
86	258 A	-20:49005133 2757115186 A	
87 I	259 A	-20:49005132 2757115185 A	I
87	260 T	-20:49005131 2757115184 T	
87	261 T	-20:49005130 2757115183 T	
88 L	262 C	-20:48998606 2757108659 C	L
88	263 T	-20:48998605 2757108658 T	
88	264 T	-20:48998604 2757108657 T	
89 L	265 C	-20:48998603 2757108656 C	L
89	266 T	-20:48998602 2757108655 T	
89	267 A	-20:48998601 2757108654 A	
90 R	268 A	-20:48998600 2757108653 A	R
90	269 G	-20:48998599 2757108652 G	
90	270 A	-20:48998598 2757108651 A	
91 P	271 C	-20:48998597 2757108650 C	P
91	272 C	-20:48998596 2757108649 C	
91	273 A	-20:48998595 2757108648 A	
92 R	274 C	-20:48998594 2757108647 C	R
92	275 G	-20:48998593 2757108646 G	
92	276 A	-20:48998592 2757108645 A	
93 E	277 G	-20:48998591 2757108644 G	E
93	278 A	-20:48998590 2757108643 A	
93	279 G	-20:48998589 2757108642 G	
94 K	280 A	-20:48998588 2757108641 A	K
94	281 A	-20:48998587 2757108640 A	
94	282 A	-20:48998586 2757108639 A	
95 K	283 A	-20:48998585 2757108638 A	K
95	284 A	-20:48998584 2757108637 A	
95	285 G	-20:48998583 2757108636 G	
96 L	286 T	-20:48998582 2757108635 T	L
96	287 T	-20:48998581 2757108634 T	
96	288 G	-20:48998580 2757108633 G	
97 G	289 G	-20:48998579 2757108632 G	G
97	290 G	-20:48998578 2757108631 G	
97	291 A	-20:48998577 2757108630 A	
98 L	292 C	-20:48998576 2757108629 C	L
98	293 T	-20:48998575 2757108628 T	
98	294 A	-20:48998574 2757108627 A	
99 G	295 G	-20:48998573 2757108626 G	G
99	296 G	-20:48995867 2757105920 G	
99	297 A	-20:48995866 2757105919 A	
100 T	298 A	-20:48995865 2757105918 A	T
100	299 C	-20:48995864 2757105917 C	
100	300 T	-20:48995863 2757105916 T	
101 A	301 G	-20:48995862 2757105915 G	A
101	302 C	-20:48995861 2757105914 C	
101	303 A	-20:48995860 2757105913 A	
102 Y	304 T	-20:48995859 2757105912 T	Y
102	305 A	-20:48995858 2757105911 A	
102	306 T	-20:48995857 2757105910 T	
103 I	307 A	-20:48995856 2757105909 A	I
103	308 T	-20:48995855 2757105908 T	
103	309 T	-20:48995854 2757105907 T	
104 H	310 C	-20:48995853 2757105906 C	H
104	311 A	-20:48995852 2757105905 A	
104	312 T	-20:48995851 2757105904 T	
105 G	313 G	-20:48995850 2757105903 G	G
105	314 G	-20:48995849 2757105902 G	
105	315 A	-20:48995848 2757105901 A	
106 M	316 A	-20:48995847 2757105900 A	M
106	317 T	-20:48995846 2757105899 T	
106	318 G	-20:48995845 2757105898 G	
107 K	319 A	-20:48995844 2757105897 A	K
107	320 A	-20:48995843 2757105896 A	
107	321 A	-20:48995842 2757105895 A	
108 H	322 C	-20:48995841 2757105894 C	H
108	323 A	-20:48995840 2757105893 A	
108	324 T	-20:48995839 2757105892 T	
109 A	325 G	-20:48995838 2757105891 G	A
109	326 C	-20:48995837 2757105890 C	
109	327 C	-20:48995836 2757105889 C	
110 T	328 A	-20:48995835 2757105888 A	T
110	329 C	-20:48995834 2757105887 C	
110	330 A	-20:48995833 2757105886 A	
111 G	331 G	-20:48995832 2757105885 G	G
111	332 G	-20:48995831 2757105884 G	
111	333 A	-20:48995830 2757105883 A	
112 N	334 A	-20:48995829 2757105882 A	N
112	335 A	-20:48995828 2757105881 A	
112	336 C	-20:48995827 2757105880 C	
113 Y	337 T	-20:48995826 2757105879 T	Y
113	338 A	-20:48995825 2757105878 A	
113	339 C	-20:48995824 2757105877 C	
114 I	340 A	-20:48995823 2757105876 A	I
114	341 T	-20:48995822 2757105875 T	
114	342 C	-20:48995821 2757105874 C	
115 I	343 A	-20:48995820 2757105873 A	I
115	344 T	-20:48995819 2757105872 T	
115	345 T	-20:48995818 2757105871 T	
116 I	346 A	-20:48995817 2757105870 A	I
116	347 T	-20:48995816 2757105869 T	
116	348 T	-20:48995815 2757105868 T	
117 M	349 A	-20:48995814 2757105867 A	M
117	350 T	-20:48995813 2757105866 T	
117	351 G	-20:48995812 2757105865 G	
118 D	352 G	-20:48995811 2757105864 G	D
118	353 A	-20:48995810 2757105863 A	
118	354 T	-20:48995809 2757105862 T	
119 A	355 G	-20:48995808 2757105861 G	A
119	356 C	-20:48995807 2757105860 C	
119	357 T	-20:48995806 2757105859 T	
120 D	358 G	-20:48995805 2757105858 G	D
120	359 A	-20:48995804 2757105857 A	
120	360 T	-20:48995803 2757105856 T	
121 L	361 C	-20:48995802 2757105855 C	L
121	362 T	-20:48995801 2757105854 T	
121	363 C	-20:48995800 2757105853 C	
122 S	364 T	-20:48995799 2757105852 T	S
122	365 C	-20:48995798 2757105851 C	
122	366 A	-20:48995797 2757105850 A	
123 H	367 C	-20:48995796 2757105849 C	H
123	368 A	-20:48995795 2757105848 A	
123	369 C	-20:48995794 2757105847 C	
124 H	370 C	-20:48995793 2757105846 C	H
124	371 A	-20:48995792 2757105845 A	
124	372 T	-20:48995791 2757105844 T	
125 P	373 C	-20:48995706 2757105759 C	P
125	374 C	-20:48995705 2757105758 C	
125	375 A	-20:48995704 2757105757 A	
126 K	376 A	-20:48995703 2757105756 A	K
126	377 A	-20:48995702 2757105755 A	
126	378 A	-20:48995701 2757105754 A	
127 F	379 T	-20:48995700 2757105753 T	F
127	380 T	-20:48995699 2757105752 T	
127	381 T	-20:48995698 2757105751 T	
128 I	382 A	-20:48995697 2757105750 A	I
128	383 T	-20:48995696 2757105749 T	
128	384 T	-20:48995695 2757105748 T	
129 P	385 C	-20:48995694 2757105747 C	P
129	386 C	-20:48995693 2757105746 C	
129	387 T	-20:48995692 2757105745 T	
130 E	388 G	-20:48995691 2757105744 G	E
130	389 A	-20:48995690 2757105743 A	
130	390 A	-20:48995689 2757105742 A	
131 F	391 T	-20:48995688 2757105741 T	F
131	392 T	-20:48995687 2757105740 T	
131	393 T	-20:48995686 2757105739 T	
132 I	394 A	-20:48995685 2757105738 A	I
132	395 T	-20:48995684 2757105737 T	
132	396 T	-20:48995683 2757105736 T	
133 R	397 A	-20:48995682 2757105735 A	R
133	398 G	-20:48995681 2757105734 G	
133	399 G	-20:48992070 2757102123 G	
134 K	400 A	-20:48992069 2757102122 A	K
134	401 A	-20:48992068 2757102121 A	
134	402 G	-20:48992067 2757102120 G	
135 Q	403 C	-20:48992066 2757102119 C	Q
135	404 A	-20:48992065 2757102118 A	
135	405 A	-20:48992064 2757102117 A	
136 K	406 A	-20:48992063 2757102116 A	K
136	407 A	-20:48992062 2757102115 A	
136	408 G	-20:48992061 2757102114 G	
137 E	409 G	-20:48992060 2757102113 G	E
137	410 A	-20:48992059 2757102112 A	
137	411 G	-20:48992058 2757102111 G	
138 G	412 G	-20:48992057 2757102110 G	G
138	413 G	-20:48992056 2757102109 G	
138	414 T	-20:48992055 2757102108 T	
139 N	415 A	-20:48992054 2757102107 A	N
139	416 A	-20:48992053 2757102106 A	
139	417 T	-20:48992052 2757102105 T	
140 F	418 T	-20:48992051 2757102104 T	F
140	419 T	-20:48992050 2757102103 T	
140	420 T	-20:48992049 2757102102 T	
141 D	421 G	-20:48992048 2757102101 G	D
141	422 A	-20:48992047 2757102100 A	
141	423 T	-20:48992046 2757102099 T	
142 I	424 A	-20:48992045 2757102098 A	I
142	425 T	-20:48992044 2757102097 T	
142	426 T	-20:48992043 2757102096 T	
143 V	427 G	-20:48992042 2757102095 G	V
143	428 T	-20:48992041 2757102094 T	
143	429 C	-20:48992040 2757102093 C	
144 S	430 T	-20:48992039 2757102092 T	S
144	431 C	-20:48992038 2757102091 C	
144	432 T	-20:48992037 2757102090 T	
145 G	433 G	-20:48992036 2757102089 G	G
145	434 G	-20:48992035 2757102088 G	
145	435 A	-20:48992034 2757102087 A	
146 T	436 A	-20:48992033 2757102086 A	T
146	437 C	-20:48992032 2757102085 C	
146	438 T	-20:48992031 2757102084 T	
147 R	439 C	-20:48992030 2757102083 C	R
147	440 G	-20:48992029 2757102082 G	
147	441 C	-20:48992028 2757102081 C	
148 Y	442 T	-20:48992027 2757102080 T	Y
148	443 A	-20:48992026 2757102079 A	
148	444 C	-20:48992025 2757102078 C	
149 K	445 A	-20:48992024 2757102077 A	K
149	446 A	-20:48992023 2757102076 A	
149	447 A	-20:48992022 2757102075 A	
150 G	448 G	-20:48992021 2757102074 G	G
150	449 G	-20:48992020 2757102073 G	
150	450 A	-20:48992019 2757102072 A	
151 N	451 A	-20:48992018 2757102071 A	N
151	452 A	-20:48992017 2757102070 A	
151	453 T	-20:48992016 2757102069 T	
152 G	454 G	-20:48992015 2757102068 G	G
152	455 G	-20:48992014 2757102067 G	
152	456 A	-20:48992013 2757102066 A	
153 G	457 G	-20:48992012 2757102065 G	G
153	458 G	-20:48992011 2757102064 G	
153	459 T	-20:48992010 2757102063 T	
154 V	460 G	-20:48992009 2757102062 G	V
154	461 T	-20:48992008 2757102061 T	
154	462 A	-20:48992007 2757102060 A	
155 Y	463 T	-20:48992006 2757102059 T	Y
155	464 A	-20:48992005 2757102058 A	
155	465 T	-20:48992004 2757102057 T	
156 G	466 G	-20:48992003 2757102056 G	G
156	467 G	-20:48992002 2757102055 G	
156	468 C	-20:48992001 2757102054 C	
157 W	469 T	-20:48992000 2757102053 T	W
157	470 G	-20:48991999 2757102052 G	
157	471 G	-20:48991998 2757102051 G	
158 D	472 G	-20:48991997 2757102050 G	D
158	473 A	-20:48991996 2757102049 A	
158	474 T	-20:48991995 2757102048 T	
159 L	475 T	-20:48991994 2757102047 T	L
159	476 T	-20:48991993 2757102046 T	
159	477 G	-20:48991992 2757102045 G	
160 K	478 A	-20:48991991 2757102044 A	K
160	479 A	-20:48991990 2757102043 A	
160	480 A	-20:48991989 2757102042 A	
161 R	481 A	-20:48991988 2757102041 A	R
161	482 G	-20:48991987 2757102040 G	
161	483 A	-20:48991986 2757102039 A	
162 K	484 A	-20:48991985 2757102038 A	K
162	485 A	-20:48991984 2757102037 A	
162	486 A	-20:48991983 2757102036 A	
163 I	487 A	-20:48991982 2757102035 A	I
163	488 T	-20:48991981 2757102034 T	
163	489 A	-20:48991980 2757102033 A	
164 I	490 A	-20:48991979 2757102032 A	I
164	491 T	-20:48991978 2757102031 T	
164	492 C	-20:48991977 2757102030 C	
165 S	493 A	-20:48991976 2757102029 A	S
165	494 G	-20:48991975 2757102028 G	
165	495 T	-20:48991153 2757101206 T	
166 D	496 G	-20:48991152 2757101205 G	D
166	497 A	-20:48991151 2757101204 A	
166	498 T	-20:48991150 2757101203 T	
167 G	499 G	-20:48991149 2757101202 G	G
167	500 G	-20:48991148 2757101201 G	
167	501 A	-20:48991147 2757101200 A	
168 V	502 G	-20:48991146 2757101199 G	V
168	503 T	-20:48991145 2757101198 T	
168	504 T	-20:48991144 2757101197 T	
169 L	505 T	-20:48991143 2757101196 T	L
169	506 T	-20:48991142 2757101195 T	
169	507 G	-20:48991141 2757101194 G	
170 P	508 C	-20:48991140 2757101193 C	P
170	509 C	-20:48991139 2757101192 C	
170	510 A	-20:48991138 2757101191 A	
171 C	511 T	-20:48991137 2757101190 T	C
171	512 G	-20:48991136 2757101189 G	
171	513 T	-20:48991135 2757101188 T	
172 C	514 T	-20:48991134 2757101187 T	C
172	515 G	-20:48991133 2757101186 G	
172	516 C	-20:48991132 2757101185 C	
173 P	517 C	-20:48991131 2757101184 C	P
173	518 C	-20:48991130 2757101183 C	
173	519 A	-20:48991129 2757101182 A	
174 G	520 G	-20:48991128 2757101181 G	G
174	521 G	-20:48991127 2757101180 G	
174	522 C	-20:48991126 2757101179 C	
175 W	523 T	-20:48991125 2757101178 T	W
175	524 G	-20:48991124 2757101177 G	
175	525 G	-20:48991123 2757101176 G	
176 S	526 T	-20:48991122 2757101175 T	S
176	527 C	-20:48991121 2757101174 C	
176	528 A	-20:48991120 2757101173 A	
177 L	529 C	-20:48991119 2757101172 C	L
177	530 T	-20:48991118 2757101171 T	
177	531 C	-20:48991117 2757101170 C	
178 L	532 C	-20:48991116 2757101169 C	L
178	533 T	-20:48991115 2757101168 T	
178	534 G	-20:48991114 2757101167 G	
179 G	535 G	-20:48991113 2757101166 G	G
179	536 G	-20:48991112 2757101165 G	
179	537 C	-20:48991111 2757101164 C	
180 S	538 T	-20:48991110 2757101163 T	S
180	539 C	-20:48991109 2757101162 C	
180	540 A	-20:48991108 2757101161 A	
181 S	541 A	-20:48991107 2757101160 A	S
181	542 G	-20:48991106 2757101159 G	
181	543 T	-20:48991105 2757101158 T	
182 D	544 G	-20:48991104 2757101157 G	D
182	545 A	-20:48991103 2757101156 A	
182	546 T	-20:48991102 2757101155 T	
183 P	547 C	-20:48991101 2757101154 C	P
183	548 C	-20:48991100 2757101153 C	
183	549 A	-20:48991099 2757101152 A	
184 A	550 G	-20:48991098 2757101151 G	A
184	551 C	-20:48991097 2757101150 C	
184	552 C	-20:48991096 2757101149 C	
185 I	553 A	-20:48991095 2757101148 A	I
185	554 T	-20:48991094 2757101147 T	
185	555 C	-20:48991093 2757101146 C	
186 L	556 T	-20:48991092 2757101145 T	L
186	557 T	-20:48991091 2757101144 T	
186	558 G	-20:48991090 2757101143 G	
187 A	559 G	-20:48991089 2757101142 G	A
187	560 C	-20:48991088 2757101141 C	
187	561 C	-20:48991087 2757101140 C	
188 S	562 T	-20:48991086 2757101139 T	S
188	563 C	-20:48991085 2757101138 C	
188	564 C	-20:48991084 2757101137 C	
189 W	565 T	-20:48991083 2757101136 T	W
189	566 G	-20:48991082 2757101135 G	
189	567 G	-20:48991081 2757101134 G	
190 D	568 G	-20:48991080 2757101133 G	D
190	569 A	-20:48991079 2757101132 A	
190	570 T	-20:48991078 2757101131 T	
191 Y	571 T	-20:48991077 2757101130 T	Y
191	572 A	-20:48991076 2757101129 A	
191	573 C	-20:48991075 2757101128 C	
192 S	574 A	-20:48991074 2757101127 A	S
192	575 G	-20:48991073 2757101126 G	
192	576 C	-20:48990877 2757100930 C	
193 R	577 C	-20:48990876 2757100929 C	R
193	578 G	-20:48990875 2757100928 G	
193	579 T	-20:48990874 2757100927 T	
194 G	580 G	-20:48990873 2757100926 G	G
194	581 G	-20:48990872 2757100925 G	
194	582 G	-20:48990871 2757100924 G	
195 A	583 G	-20:48990870 2757100923 G	A
195	584 C	-20:48990869 2757100922 C	
195	585 C	-20:48990868 2757100921 C	
196 N	586 A	-20:48990867 2757100920 A	N
196	587 A	-20:48990866 2757100919 A	
196	588 T	-20:48990865 2757100918 T	
197 F	589 T	-20:48990864 2757100917 T	F
197	590 T	-20:48990863 2757100916 T	
197	591 T	-20:48990862 2757100915 T	
198 L	592 T	-20:48990861 2757100914 T	L
198	593 T	-20:48990860 2757100913 T	
198	594 A	-20:48990859 2757100912 A	
199 T	595 A	-20:48990858 2757100911 A	T
199	596 C	-20:48990857 2757100910 C	
199	597 T	-20:48990856 2757100909 T	
200 Q	598 C	-20:48990855 2757100908 C	Q
200	599 A	-20:48990854 2757100907 A	
200	600 G	-20:48990853 2757100906 G	
201 I	601 A	-20:48990852 2757100905 A	I
201	602 T	-20:48990851 2757100904 T	
201	603 C	-20:48990850 2757100903 C	
202 L	604 T	-20:48990849 2757100902 T	L
202	605 T	-20:48990848 2757100901 T	
202	606 G	-20:48990847 2757100900 G	
203 L	607 C	-20:48990846 2757100899 C	L
203	608 T	-20:48990845 2757100898 T	
203	609 G	-20:48990844 2757100897 G	
204 R	610 A	-20:48990843 2757100896 A	R
204	611 G	-20:48990842 2757100895 G	
204	612 A	-20:48990841 2757100894 A	
205 P	613 C	-20:48990840 2757100893 C	P
205	614 C	-20:48990839 2757100892 C	
205	615 A	-20:48990838 2757100891 A	
206 G	616 G	-20:48990837 2757100890 G	G
206	617 G	-20:48990836 2757100889 G	
206	618 A	-20:48990835 2757100888 A	
207 A	619 G	-20:48990834 2757100887 G	A
207	620 C	-20:48990833 2757100886 C	
207	621 A	-20:48990832 2757100885 A	
208 S	622 T	-20:48990831 2757100884 T	S
208	623 C	-20:48990830 2757100883 C	
208	624 T	-20:48990829 2757100882 T	
209 D	625 G	-20:48990828 2757100881 G	D
209	626 A	-20:48990827 2757100880 A	
209	627 T	-20:48990826 2757100879 T	
210 L	628 T	-20:48990825 2757100878 T	L
210	629 T	-20:48990824 2757100877 T	
210	630 A	-20:48990823 2757100876 A	
211 T	631 A	-20:48990822 2757100875 A	T
211	632 C	-20:48990821 2757100874 C	
211	633 A	-20:48990820 2757100873 A	
212 G	634 G	-20:48990819 2757100872 G	G
212	635 G	-20:48990818 2757100871 G	
212	636 A	-20:48990817 2757100870 A	
213 S	637 A	-20:48990816 2757100869 A	S
213	638 G	-20:48990815 2757100868 G	
213	639 T	-20:48990814 2757100867 T	
214 F	640 T	-20:48990813 2757100866 T	F
214	641 T	-20:48990812 2757100865 T	
214	642 C	-20:48990811 2757100864 C	
215 R	643 A	-20:48990810 2757100863 A	R
215	644 G	-20:48990809 2757100862 G	
215	645 A	-20:48986206 2757096259 A	
216 L	646 T	-20:48986205 2757096258 T	L
216	647 T	-20:48986204 2757096257 T	
216	648 A	-20:48986203 2757096256 A	
217 Y	649 T	-20:48986202 2757096255 T	Y
217	650 A	-20:48986201 2757096254 A	
217	651 C	-20:48986200 2757096253 C	
218 R	652 C	-20:48986199 2757096252 C	R
218	653 G	-20:48986198 2757096251 G	
218	654 A	-20:48986197 2757096250 A	
219 K	655 A	-20:48986196 2757096249 A	K
219	656 A	-20:48986195 2757096248 A	
219	657 A	-20:48986194 2757096247 A	
220 E	658 G	-20:48986193 2757096246 G	E
220	659 A	-20:48986192 2757096245 A	
220	660 A	-20:48986191 2757096244 A	
221 V	661 G	-20:48986190 2757096243 G	V
221	662 T	-20:48986189 2757096242 T	
221	663 T	-20:48986188 2757096241 T	
222 L	664 C	-20:48986187 2757096240 C	L
222	665 T	-20:48986186 2757096239 T	
222	666 A	-20:48986185 2757096238 A	
223 E	667 G	-20:48986184 2757096237 G	E
223	668 A	-20:48986183 2757096236 A	
223	669 G	-20:48986182 2757096235 G	
224 K	670 A	-20:48986181 2757096234 A	K
224	671 A	-20:48986180 2757096233 A	
224	672 A	-20:48986179 2757096232 A	
225 L	673 T	-20:48986178 2757096231 T	L
225	674 T	-20:48986177 2757096230 T	
225	675 A	-20:48986176 2757096229 A	
226 I	676 A	-20:48986175 2757096228 A	I
226	677 T	-20:48986174 2757096227 T	
226	678 A	-20:48986173 2757096226 A	
227 E	679 G	-20:48986172 2757096225 G	E
227	680 A	-20:48986171 2757096224 A	
227	681 A	-20:48986170 2757096223 A	
228 K	682 A	-20:48986169 2757096222 A	K
228	683 A	-20:48986168 2757096221 A	
228	684 A	-20:48986167 2757096220 A	
229 C	685 T	-20:48986166 2757096219 T	C
229	686 G	-20:48986165 2757096218 G	
229	687 T	-20:48986164 2757096217 T	
230 V	688 G	-20:48986163 2757096216 G	V
230	689 T	-20:48986162 2757096215 T	
230	690 T	-20:48986161 2757096214 T	
231 S	691 T	-20:48986160 2757096213 T	S
231	692 C	-20:48986159 2757096212 C	
231	693 T	-20:48986158 2757096211 T	
232 K	694 A	-20:48986157 2757096210 A	K
232	695 A	-20:48986156 2757096209 A	
232	696 A	-20:48986155 2757096208 A	
233 G	697 G	-20:48986154 2757096207 G	G
233	698 G	-20:48986153 2757096206 G	
233	699 C	-20:48986152 2757096205 C	
234 Y	700 T	-20:48986151 2757096204 T	Y
234	701 A	-20:48986150 2757096203 A	
234	702 C	-20:48986149 2757096202 C	
235 V	703 G	-20:48986148 2757096201 G	V
235	704 T	-20:48986147 2757096200 T	
235	705 C	-20:48986146 2757096199 C	
236 F	706 T	-20:48986145 2757096198 T	F
236	707 T	-20:48986144 2757096197 T	
236	708 C	-20:48986143 2757096196 C	
237 Q	709 C	-20:48986142 2757096195 C	Q
237	710 A	-20:48986141 2757096194 A	
237	711 G	-20:48986140 2757096193 G	
238 M	712 A	-20:48986139 2757096192 A	M
238	713 T	-20:48986138 2757096191 T	
238	714 G	-20:48986137 2757096190 G	
239 E	715 G	-20:48986136 2757096189 G	E
239	716 A	-20:48986135 2757096188 A	
239	717 G	-20:48986134 2757096187 G	
240 M	718 A	-20:48986133 2757096186 A	M
240	719 T	-20:48986132 2757096185 T	
240	720 G	-20:48986131 2757096184 G	
241 I	721 A	-20:48986130 2757096183 A	I
241	722 T	-20:48986129 2757096182 T	
241	723 T	-20:48986128 2757096181 T	
242 V	724 G	-20:48986127 2757096180 G	V
242	725 T	-20:48986126 2757096179 T	
242	726 T	-20:48986125 2757096178 T	
243 R	727 C	-20:48986124 2757096177 C	R
243	728 G	-20:48986123 2757096176 G	
243	729 G	-20:48986122 2757096175 G	
244 A	730 G	-20:48986121 2757096174 G	A
244	731 C	-20:48986120 2757096173 C	
244	732 A	-20:48986119 2757096172 A	
245 R	733 A	-20:48986118 2757096171 A	R
245	734 G	-20:48986117 2757096170 G	
245	735 A	-20:48986116 2757096169 A	
246 Q	736 C	-20:48986115 2757096168 C	Q
246	737 A	-20:48986114 2757096167 A	
246	738 G	-20:48986113 2757096166 G	
247 L	739 T	-20:48986112 2757096165 T	L
247	740 T	-20:48986111 2757096164 T	
247	741 G	-20:48986110 2757096163 G	
248 N	742 A	-20:48986109 2757096162 A	N
248	743 A	-20:48986108 2757096161 A	
248	744 T	-20:48986107 2757096160 T	
249 Y	745 T	-20:48986106 2757096159 T	Y
249	746 A	-20:48986105 2757096158 A	
249	747 T	-20:48986104 2757096157 T	
250 T	748 A	-20:48986103 2757096156 A	T
250	749 C	-20:48986102 2757096155 C	
250	750 T	-20:48986101 2757096154 T	
251 I	751 A	-20:48986100 2757096153 A	I
251	752 T	-20:48986099 2757096152 T	
251	753 T	-20:48986098 2757096151 T	
252 G	754 G	-20:48986097 2757096150 G	G
252	755 G	-20:48986096 2757096149 G	
252	756 C	-20:48986095 2757096148 C	
253 E	757 G	-20:48986094 2757096147 G	E
253	758 A	-20:48986093 2757096146 A	
253	759 G	-20:48986092 2757096145 G	
>ENSP00000360639 
1 M	1 A	-20:49008467 2757118520 A	M
1	2 T	-20:49008466 2757118519 T	
1	3 G	-20:49008465 2757118518 G	
2 A	4 G	-20:49008464 2757118517 G	A
2	5 C	-20:49008463 2757118516 C	
2	6 C	-20:49008462 2757118515 C	
3 S	7 T	-20:49008461 2757118514 T	S
3	8 C	-20:49008460 2757118513 C	
3	9 C	-20:49008459 2757118512 C	
4 L	10 T	-20:49008458 2757118511 T	L
4	11 T	-20:49008457 2757118510 T	
4	12 G	-20:49008456 2757118509 G	
5 E	13 G	-20:49008455 2757118508 G	E
5	14 A	-20:49008454 2757118507 A	
5	15 A	-20:49008453 2757118506 A	
6 V	16 G	-20:49008452 2757118505 G	V
6	17 T	-20:49008451 2757118504 T	
6	18 C	-20:49008450 2757118503 C	
7 S	19 A	-20:49008449 2757118502 A	S
7	20 G	-20:49008448 2757118501 G	
7	21 T	-20:49008447 2757118500 T	
8 R	22 C	-20:49008446 2757118499 C	R
8	23 G	-20:49008445 2757118498 G	
8	24 T	-20:49008444 2757118497 T	
9 S	25 A	-20:49008443 2757118496 A	S
9	26 G	-20:49008442 2757118495 G	
9	27 T	-20:49008441 2757118494 T	
10 P	28 C	-20:49008440 2757118493 C	P
10	29 C	-20:49008439 2757118492 C	
10	30 T	-20:49008438 2757118491 T	
11 R	31 C	-20:49008437 2757118490 C	R
11	32 G	-20:49008436 2757118489 G	
11	33 C	-20:49008435 2757118488 C	
12 R	34 A	-20:49008434 2757118487 A	R
12	35 G	-20:49008433 2757118486 G	
12	36 G	-20:49008432 2757118485 G	
13 S	37 T	-20:49008431 2757118484 T	S
13	38 C	-20:49008430 2757118483 C	
13	39 T	-20:49008429 2757118482 T	
14 R	40 C	-20:49008428 2757118481 C	R
14	41 G	-20:49008427 2757118480 G	
14	42 G	-20:49008426 2757118479 G	
15 R	43 C	-20:49008425 2757118478 C	R
15	44 G	-20:49008424 2757118477 G	
15	45 G	-20:49008423 2757118476 G	
16 E	46 G	-20:49008422 2757118475 G	E
16	47 A	-20:49008421 2757118474 A	
16	48 G	-20:49008420 2757118473 G	
17 L	49 C	-20:49008419 2757118472 C	L
17	50 T	-20:49008418 2757118471 T	
17	51 G	-20:49008417 2757118470 G	
18 E	52 G	-20:49008416 2757118469 G	E
18	53 A	-20:49008415 2757118468 A	
18	54 A	-20:49008414 2757118467 A	
19 V	55 G	-20:49008413 2757118466 G	V
19	56 T	-20:49008412 2757118465 T	
19	57 G	-20:49008411 2757118464 G	
20 R	58 C	-20:49008410 2757118463 C	R
20	59 G	-20:49008409 2757118462 G	
20	60 C	-20:49008408 2757118461 C	
21 S	61 A	-20:49008407 2757118460 A	S
21	62 G	-20:49008406 2757118459 G	
21	63 T	-20:49008405 2757118458 T	
22 P	64 C	-20:49008404 2757118457 C	P
22	65 C	-20:49008403 2757118456 C	
22	66 A	-20:49008402 2757118455 A	
23 R	67 C	-20:49008401 2757118454 C	R
23	68 G	-20:49008400 2757118453 G	
23	69 A	-20:49008399 2757118452 A	
24 Q	70 C	-20:49008398 2757118451 C	Q
24	71 A	-20:49008397 2757118450 A	
24	72 G	-20:49008396 2757118449 G	
25 N	73 A	-20:49008395 2757118448 A	N
25	74 A	-20:49008394 2757118447 A	
25	75 C	-20:49008393 2757118446 C	
26 K	76 A	-20:49008392 2757118445 A	K
26	77 A	-20:49008391 2757118444 A	
26	78 A	-20:49008390 2757118443 A	
27 Y	79 T	-20:49008389 2757118442 T	Y
27	80 A	-20:49008388 2757118441 A	
27	81 T	-20:49008387 2757118440 T	
28 S	82 T	-20:49008386 2757118439 T	S
28	83 C	-20:49008385 2757118438 C	
28	84 G	-20:49008384 2757118437 G	
29 V	85 G	-20:49008383 2757118436 G	V
29	86 T	-20:49008382 2757118435 T	
29	87 G	-20:49008381 2757118434 G	
30 L	88 C	-20:49008380 2757118433 C	L
30	89 T	-20:49008379 2757118432 T	
30	90 T	-20:49008378 2757118431 T	
31 L	91 T	-20:49008377 2757118430 T	L
31	92 T	-20:49008376 2757118429 T	
31	93 A	-20:49008375 2757118428 A	
32 P	94 C	-20:49008374 2757118427 C	P
32	95 C	-20:49008373 2757118426 C	
32	96 T	-20:49008372 2757118425 T	
33 T	97 A	-20:49008371 2757118424 A	T
33	98 C	-20:49008370 2757118423 C	
33	99 C	-20:49008369 2757118422 C	
34 Y	100 T	-20:49008368 2757118421 T	Y
34	101 A	-20:49008367 2757118420 A	
34	102 C	-20:49008366 2757118419 C	
35 N	103 A	-20:49008365 2757118418 A	N
35	104 A	-20:49008364 2757118417 A	
35	105 C	-20:49008363 2757118416 C	
36 E	106 G	-20:49008362 2757118415 G	E
36	107 A	-20:49008361 2757118414 A	
36	108 G	-20:49008360 2757118413 G	
37 R	109 C	-20:49008359 2757118412 C	R
37	110 G	-20:49008358 2757118411 G	
37	111 C	-20:49008357 2757118410 C	
38 E	112 G	-20:49008356 2757118409 G	E
38	113 A	-20:49008355 2757118408 A	
38	114 G	-20:49008354 2757118407 G	
39 N	115 A	-20:49008353 2757118406 A	N
39	116 A	-20:49008352 2757118405 A	
39	117 C	-20:49008351 2757118404 C	
40 L	118 C	-20:49008350 2757118403 C	L
40	119 T	-20:49008349 2757118402 T	
40	120 G	-20:49008348 2757118401 G	
41 P	121 C	-20:49008347 2757118400 C	P
41	122 C	-20:49008346 2757118399 C	
41	123 G	-20:49008345 2757118398 G	
42 L	124 C	-20:49008344 2757118397 C	L
42	125 T	-20:49008343 2757118396 T	
42	126 C	-20:49008342 2757118395 C	
43 I	127 A	-20:49008341 2757118394 A	I
43	128 T	-20:49008340 2757118393 T	
43	129 C	-20:49008339 2757118392 C	
44 V	130 G	-20:49008338 2757118391 G	V
44	131 T	-20:49008337 2757118390 T	
44	132 G	-20:49008336 2757118389 G	
45 W	133 T	-20:49008335 2757118388 T	W
45	134 G	-20:49008334 2757118387 G	
45	135 G	-20:49008333 2757118386 G	
46 L	136 C	-20:49008332 2757118385 C	L
46	137 T	-20:49008331 2757118384 T	
46	138 G	-20:49008330 2757118383 G	
47 L	139 C	-20:49008329 2757118382 C	L
47	140 T	-20:49008328 2757118381 T	
47	141 G	-20:49008327 2757118380 G	
48 V	142 G	-20:49008326 2757118379 G	V
48	143 T	-20:49008325 2757118378 T	
48	144 G	-20:49008324 2757118377 G	
49 K	145 A	-20:49008323 2757118376 A	K
49	146 A	-20:49008322 2757118375 A	
49	147 A	-20:49008321 2757118374 A	
50 S	148 A	-20:49008320 2757118373 A	S
50	149 G	-20:49008319 2757118372 G	
50	150 C	-20:49008318 2757118371 C	
51 F	151 T	-20:49008317 2757118370 T	F
51	152 T	-20:49008316 2757118369 T	
51	153 C	-20:49008315 2757118368 C	
52 S	154 T	-20:49008314 2757118367 T	S
52	155 C	-20:49008313 2757118366 C	
52	156 C	-20:49008312 2757118365 C	
53 E	157 G	-20:49008311 2757118364 G	E
53	158 A	-20:49008310 2757118363 A	
53	159 G	-20:49008309 2757118362 G	
54 S	160 A	-20:49008308 2757118361 A	S
54	161 G	-20:49008307 2757118360 G	
54	162 T	-20:49005229 2757115282 T	
55 G	163 G	-20:49005228 2757115281 G	G
55	164 G	-20:49005227 2757115280 G	
55	165 A	-20:49005226 2757115279 A	
56 I	166 A	-20:49005225 2757115278 A	I
56	167 T	-20:49005224 2757115277 T	
56	168 C	-20:49005223 2757115276 C	
57 N	169 A	-20:49005222 2757115275 A	N
57	170 A	-20:49005221 2757115274 A	
57	171 C	-20:49005220 2757115273 C	
58 Y	172 T	-20:49005219 2757115272 T	Y
58	173 A	-20:49005218 2757115271 A	
58	174 T	-20:49005217 2757115270 T	
59 E	175 G	-20:49005216 2757115269 G	E
59	176 A	-20:49005215 2757115268 A	
59	177 A	-20:49005214 2757115267 A	
60 I	178 A	-20:49005213 2757115266 A	I
60	179 T	-20:49005212 2757115265 T	
60	180 T	-20:49005211 2757115264 T	
61 I	181 A	-20:49005210 2757115263 A	I
61	182 T	-20:49005209 2757115262 T	
61	183 A	-20:49005208 2757115261 A	
62 I	184 A	-20:49005207 2757115260 A	I
62	185 T	-20:49005206 2757115259 T	
62	186 C	-20:49005205 2757115258 C	
63 I	187 A	-20:49005204 2757115257 A	I
63	188 T	-20:49005203 2757115256 T	
63	189 A	-20:49005202 2757115255 A	
64 D	190 G	-20:49005201 2757115254 G	D
64	191 A	-20:49005200 2757115253 A	
64	192 T	-20:49005199 2757115252 T	
65 D	193 G	-20:49005198 2757115251 G	D
65	194 A	-20:49005197 2757115250 A	
65	195 T	-20:49005196 2757115249 T	
66 G	196 G	-20:49005195 2757115248 G	G
66	197 G	-20:49005194 2757115247 G	
66	198 A	-20:49005193 2757115246 A	
67 S	199 A	-20:49005192 2757115245 A	S
67	200 G	-20:49005191 2757115244 G	
67	201 C	-20:49005190 2757115243 C	
68 P	202 C	-20:49005189 2757115242 C	P
68	203 C	-20:49005188 2757115241 C	
68	204 A	-20:49005187 2757115240 A	
69 D	205 G	-20:49005186 2757115239 G	D
69	206 A	-20:49005185 2757115238 A	
69	207 T	-20:49005184 2757115237 T	
70 G	208 G	-20:49005183 2757115236 G	G
70	209 G	-20:49005182 2757115235 G	
70	210 A	-20:49005181 2757115234 A	
71 T	211 A	-20:49005180 2757115233 A	T
71	212 C	-20:49005179 2757115232 C	
71	213 A	-20:49005178 2757115231 A	
72 R	214 A	-20:49005177 2757115230 A	R
72	215 G	-20:49005176 2757115229 G	
72	216 G	-20:49005175 2757115228 G	
73 D	217 G	-20:49005174 2757115227 G	D
73	218 A	-20:49005173 2757115226 A	
73	219 T	-20:49005172 2757115225 T	
74 V	220 G	-20:49005171 2757115224 G	V
74	221 T	-20:49005170 2757115223 T	
74	222 T	-20:49005169 2757115222 T	
75 A	223 G	-20:49005168 2757115221 G	A
75	224 C	-20:49005167 2757115220 C	
75	225 T	-20:49005166 2757115219 T	
76 E	226 G	-20:49005165 2757115218 G	E
76	227 A	-20:49005164 2757115217 A	
76	228 A	-20:49005163 2757115216 A	
77 Q	229 C	-20:49005162 2757115215 C	Q
77	230 A	-20:49005161 2757115214 A	
77	231 G	-20:49005160 2757115213 G	
78 L	232 T	-20:49005159 2757115212 T	L
78	233 T	-20:49005158 2757115211 T	
78	234 G	-20:49005157 2757115210 G	
79 E	235 G	-20:49005156 2757115209 G	E
79	236 A	-20:49005155 2757115208 A	
79	237 G	-20:49005154 2757115207 G	
80 K	238 A	-20:49005153 2757115206 A	K
80	239 A	-20:49005152 2757115205 A	
80	240 G	-20:49005151 2757115204 G	
81 I	241 A	-20:49005150 2757115203 A	I
81	242 T	-20:49005149 2757115202 T	
81	243 C	-20:49005148 2757115201 C	
82 Y	244 T	-20:49005147 2757115200 T	Y
82	245 A	-20:49005146 2757115199 A	
82	246 T	-20:49005145 2757115198 T	
83 G	247 G	-20:49005144 2757115197 G	G
83	248 G	-20:49005143 2757115196 G	
83	249 G	-20:49005142 2757115195 G	
84 S	250 T	-20:49005141 2757115194 T	S
84	251 C	-20:49005140 2757115193 C	
84	252 A	-20:49005139 2757115192 A	
85 D	253 G	-20:49005138 2757115191 G	D
85	254 A	-20:49005137 2757115190 A	
85	255 C	-20:49005136 2757115189 C	
86 R	256 A	-20:49005135 2757115188 A	R
86	257 G	-20:49005134 2757115187 G	
86	258 A	-20:49005133 2757115186 A	
87 I	259 A	-20:49005132 2757115185 A	I
87	260 T	-20:49005131 2757115184 T	
87	261 T	-20:49005130 2757115183 T	
88 L	262 C	-20:48998606 2757108659 C	L
88	263 T	-20:48998605 2757108658 T	
88	264 T	-20:48998604 2757108657 T	
89 L	265 C	-20:48998603 2757108656 C	L
89	266 T	-20:48998602 2757108655 T	
89	267 A	-20:48998601 2757108654 A	
90 R	268 A	-20:48998600 2757108653 A	R
90	269 G	-20:48998599 2757108652 G	
90	270 A	-20:48998598 2757108651 A	
91 P	271 C	-20:48998597 2757108650 C	P
91	272 C	-20:48998596 2757108649 C	
91	273 A	-20:48998595 2757108648 A	
92 R	274 C	-20:48998594 2757108647 C	R
92	275 G	-20:48998593 2757108646 G	
92	276 A	-20:48998592 2757108645 A	
93 E	277 G	-20:48998591 2757108644 G	E
93	278 A	-20:48998590 2757108643 A	
93	279 G	-20:48998589 2757108642 G	
94 K	280 A	-20:48998588 2757108641 A	K
94	281 A	-20:48998587 2757108640 A	
94	282 A	-20:48998586 2757108639 A	
95 K	283 A	-20:48998585 2757108638 A	K
95	284 A	-20:48998584 2757108637 A	
95	285 G	-20:48998583 2757108636 G	
96 L	286 T	-20:48998582 2757108635 T	L
96	287 T	-20:48998581 2757108634 T	
96	288 G	-20:48998580 2757108633 G	
97 G	289 G	-20:48998579 2757108632 G	G
97	290 G	-20:48998578 2757108631 G	
97	291 A	-20:48998577 2757108630 A	
98 L	292 C	-20:48998576 2757108629 C	L
98	293 T	-20:48998575 2757108628 T	
98	294 A	-20:48998574 2757108627 A	
99 G	295 G	-20:48998573 2757108626 G	G
99	296 G	-20:48995867 2757105920 G	
99	297 A	-20:48995866 2757105919 A	
100 T	298 A	-20:48995865 2757105918 A	T
100	299 C	-20:48995864 2757105917 C	
100	300 T	-20:48995863 2757105916 T	
101 A	301 G	-20:48995862 2757105915 G	A
101	302 C	-20:48995861 2757105914 C	
101	303 A	-20:48995860 2757105913 A	
102 Y	304 T	-20:48995859 2757105912 T	Y
102	305 A	-20:48995858 2757105911 A	
102	306 T	-20:48995857 2757105910 T	
103 I	307 A	-20:48995856 2757105909 A	I
103	308 T	-20:48995855 2757105908 T	
103	309 T	-20:48995854 2757105907 T	
104 H	310 C	-20:48995853 2757105906 C	H
104	311 A	-20:48995852 2757105905 A	
104	312 T	-20:48995851 2757105904 T	
105 G	313 G	-20:48995850 2757105903 G	G
105	314 G	-20:48995849 2757105902 G	
105	315 A	-20:48995848 2757105901 A	
106 M	316 A	-20:48995847 2757105900 A	M
106	317 T	-20:48995846 2757105899 T	
106	318 G	-20:48995845 2757105898 G	
107 K	319 A	-20:48995844 2757105897 A	K
107	320 A	-20:48995843 2757105896 A	
107	321 A	-20:48995842 2757105895 A	
108 H	322 C	-20:48995841 2757105894 C	H
108	323 A	-20:48995840 2757105893 A	
108	324 T	-20:48995839 2757105892 T	
109 A	325 G	-20:48995838 2757105891 G	A
109	326 C	-20:48995837 2757105890 C	
109	327 C	-20:48995836 2757105889 C	
110 T	328 A	-20:48995835 2757105888 A	T
110	329 C	-20:48995834 2757105887 C	
110	330 A	-20:48995833 2757105886 A	
111 G	331 G	-20:48995832 2757105885 G	G
111	332 G	-20:48995831 2757105884 G	
111	333 A	-20:48995830 2757105883 A	
112 N	334 A	-20:48995829 2757105882 A	N
112	335 A	-20:48995828 2757105881 A	
112	336 C	-20:48995827 2757105880 C	
113 Y	337 T	-20:48995826 2757105879 T	Y
113	338 A	-20:48995825 2757105878 A	
113	339 C	-20:48995824 2757105877 C	
114 I	340 A	-20:48995823 2757105876 A	I
114	341 T	-20:48995822 2757105875 T	
114	342 C	-20:48995821 2757105874 C	
115 I	343 A	-20:48995820 2757105873 A	I
115	344 T	-20:48995819 2757105872 T	
115	345 T	-20:48995818 2757105871 T	
116 I	346 A	-20:48995817 2757105870 A	I
116	347 T	-20:48995816 2757105869 T	
116	348 T	-20:48995815 2757105868 T	
117 M	349 A	-20:48995814 2757105867 A	M
117	350 T	-20:48995813 2757105866 T	
117	351 G	-20:48995812 2757105865 G	
118 D	352 G	-20:48995811 2757105864 G	D
118	353 A	-20:48995810 2757105863 A	
118	354 T	-20:48995809 2757105862 T	
119 A	355 G	-20:48995808 2757105861 G	A
119	356 C	-20:48995807 2757105860 C	
119	357 T	-20:48995806 2757105859 T	
120 D	358 G	-20:48995805 2757105858 G	D
120	359 A	-20:48995804 2757105857 A	
120	360 T	-20:48995803 2757105856 T	
121 L	361 C	-20:48995802 2757105855 C	L
121	362 T	-20:48995801 2757105854 T	
121	363 C	-20:48995800 2757105853 C	
122 S	364 T	-20:48995799 2757105852 T	S
122	365 C	-20:48995798 2757105851 C	
122	366 A	-20:48995797 2757105850 A	
123 H	367 C	-20:48995796 2757105849 C	H
123	368 A	-20:48995795 2757105848 A	
123	369 C	-20:48995794 2757105847 C	
124 H	370 C	-20:48995793 2757105846 C	H
124	371 A	-20:48995792 2757105845 A	
124	372 T	-20:48995791 2757105844 T	
125 P	373 C	-20:48995706 2757105759 C	P
125	374 C	-20:48995705 2757105758 C	
125	375 A	-20:48995704 2757105757 A	
126 K	376 A	-20:48995703 2757105756 A	K
126	377 A	-20:48995702 2757105755 A	
126	378 A	-20:48995701 2757105754 A	
127 F	379 T	-20:48995700 2757105753 T	F
127	380 T	-20:48995699 2757105752 T	
127	381 T	-20:48995698 2757105751 T	
128 I	382 A	-20:48995697 2757105750 A	I
128	383 T	-20:48995696 2757105749 T	
128	384 T	-20:48995695 2757105748 T	
129 P	385 C	-20:48995694 2757105747 C	P
129	386 C	-20:48995693 2757105746 C	
129	387 T	-20:48995692 2757105745 T	
130 E	388 G	-20:48995691 2757105744 G	E
130	389 A	-20:48995690 2757105743 A	
130	390 A	-20:48995689 2757105742 A	
131 F	391 T	-20:48995688 2757105741 T	F
131	392 T	-20:48995687 2757105740 T	
131	393 T	-20:48995686 2757105739 T	
132 I	394 A	-20:48995685 2757105738 A	I
132	395 T	-20:48995684 2757105737 T	
132	396 T	-20:48995683 2757105736 T	
133 S	397 A	-20:48995682 2757105735 A	S
133	398 G	-20:48995681 2757105734 G	
133	399 T	-20:48991153 2757101206 T	
134 D	400 G	-20:48991152 2757101205 G	D
134	401 A	-20:48991151 2757101204 A	
134	402 T	-20:48991150 2757101203 T	
135 G	403 G	-20:48991149 2757101202 G	G
135	404 G	-20:48991148 2757101201 G	
135	405 A	-20:48991147 2757101200 A	
136 V	406 G	-20:48991146 2757101199 G	V
136	407 T	-20:48991145 2757101198 T	
136	408 T	-20:48991144 2757101197 T	
137 L	409 T	-20:48991143 2757101196 T	L
137	410 T	-20:48991142 2757101195 T	
137	411 G	-20:48991141 2757101194 G	
138 P	412 C	-20:48991140 2757101193 C	P
138	413 C	-20:48991139 2757101192 C	
138	414 A	-20:48991138 2757101191 A	
139 C	415 T	-20:48991137 2757101190 T	C
139	416 G	-20:48991136 2757101189 G	
139	417 T	-20:48991135 2757101188 T	
140 C	418 T	-20:48991134 2757101187 T	C
140	419 G	-20:48991133 2757101186 G	
140	420 C	-20:48991132 2757101185 C	
141 P	421 C	-20:48991131 2757101184 C	P
141	422 C	-20:48991130 2757101183 C	
141	423 A	-20:48991129 2757101182 A	
142 G	424 G	-20:48991128 2757101181 G	G
142	425 G	-20:48991127 2757101180 G	
142	426 C	-20:48991126 2757101179 C	
143 W	427 T	-20:48991125 2757101178 T	W
143	428 G	-20:48991124 2757101177 G	
143	429 G	-20:48991123 2757101176 G	
144 S	430 T	-20:48991122 2757101175 T	S
144	431 C	-20:48991121 2757101174 C	
144	432 A	-20:48991120 2757101173 A	
145 L	433 C	-20:48991119 2757101172 C	L
145	434 T	-20:48991118 2757101171 T	
145	435 C	-20:48991117 2757101170 C	
146 L	436 C	-20:48991116 2757101169 C	L
146	437 T	-20:48991115 2757101168 T	
146	438 G	-20:48991114 2757101167 G	
147 G	439 G	-20:48991113 2757101166 G	G
147	440 G	-20:48991112 2757101165 G	
147	441 C	-20:48991111 2757101164 C	
148 S	442 T	-20:48991110 2757101163 T	S
148	443 C	-20:48991109 2757101162 C	
148	444 A	-20:48991108 2757101161 A	
149 S	445 A	-20:48991107 2757101160 A	S
149	446 G	-20:48991106 2757101159 G	
149	447 T	-20:48991105 2757101158 T	
150 D	448 G	-20:48991104 2757101157 G	D
150	449 A	-20:48991103 2757101156 A	
150	450 T	-20:48991102 2757101155 T	
151 P	451 C	-20:48991101 2757101154 C	P
151	452 C	-20:48991100 2757101153 C	
151	453 A	-20:48991099 2757101152 A	
152 A	454 G	-20:48991098 2757101151 G	A
152	455 C	-20:48991097 2757101150 C	
152	456 C	-20:48991096 2757101149 C	
153 I	457 A	-20:48991095 2757101148 A	I
153	458 T	-20:48991094 2757101147 T	
153	459 C	-20:48991093 2757101146 C	
154 L	460 T	-20:48991092 2757101145 T	L
154	461 T	-20:48991091 2757101144 T	
154	462 G	-20:48991090 2757101143 G	
155 A	463 G	-20:48991089 2757101142 G	A
155	464 C	-20:48991088 2757101141 C	
155	465 C	-20:48991087 2757101140 C	
156 S	466 T	-20:48991086 2757101139 T	S
156	467 C	-20:48991085 2757101138 C	
156	468 C	-20:48991084 2757101137 C	
157 W	469 T	-20:48991083 2757101136 T	W
157	470 G	-20:48991082 2757101135 G	
157	471 G	-20:48991081 2757101134 G	
158 D	472 G	-20:48991080 2757101133 G	D
158	473 A	-20:48991079 2757101132 A	
158	474 T	-20:48991078 2757101131 T	
159 Y	475 T	-20:48991077 2757101130 T	Y
159	476 A	-20:48991076 2757101129 A	
159	477 C	-20:48991075 2757101128 C	
160 S	478 A	-20:48991074 2757101127 A	S
160	479 G	-20:48991073 2757101126 G	
160	480 C	-20:48990877 2757100930 C	
161 R	481 C	-20:48990876 2757100929 C	R
161	482 G	-20:48990875 2757100928 G	
161	483 T	-20:48990874 2757100927 T	
162 G	484 G	-20:48990873 2757100926 G	G
162	485 G	-20:48990872 2757100925 G	
162	486 G	-20:48990871 2757100924 G	
163 A	487 G	-20:48990870 2757100923 G	A
163	488 C	-20:48990869 2757100922 C	
163	489 C	-20:48990868 2757100921 C	
164 N	490 A	-20:48990867 2757100920 A	N
164	491 A	-20:48990866 2757100919 A	
164	492 T	-20:48990865 2757100918 T	
165 F	493 T	-20:48990864 2757100917 T	F
165	494 T	-20:48990863 2757100916 T	
165	495 T	-20:48990862 2757100915 T	
166 L	496 T	-20:48990861 2757100914 T	L
166	497 T	-20:48990860 2757100913 T	
166	498 A	-20:48990859 2757100912 A	
167 T	499 A	-20:48990858 2757100911 A	T
167	500 C	-20:48990857 2757100910 C	
167	501 T	-20:48990856 2757100909 T	
168 Q	502 C	-20:48990855 2757100908 C	Q
168	503 A	-20:48990854 2757100907 A	
168	504 G	-20:48990853 2757100906 G	
169 I	505 A	-20:48990852 2757100905 A	I
169	506 T	-20:48990851 2757100904 T	
169	507 C	-20:48990850 2757100903 C	
170 L	508 T	-20:48990849 2757100902 T	L
170	509 T	-20:48990848 2757100901 T	
170	510 G	-20:48990847 2757100900 G	
171 L	511 C	-20:48990846 2757100899 C	L
171	512 T	-20:48990845 2757100898 T	
171	513 G	-20:48990844 2757100897 G	
172 R	514 A	-20:48990843 2757100896 A	R
172	515 G	-20:48990842 2757100895 G	
172	516 A	-20:48990841 2757100894 A	
173 P	517 C	-20:48990840 2757100893 C	P
173	518 C	-20:48990839 2757100892 C	
173	519 A	-20:48990838 2757100891 A	
174 G	520 G	-20:48990837 2757100890 G	G
174	521 G	-20:48990836 2757100889 G	
174	522 A	-20:48990835 2757100888 A	
175 A	523 G	-20:48990834 2757100887 G	A
175	524 C	-20:48990833 2757100886 C	
175	525 A	-20:48990832 2757100885 A	
176 S	526 T	-20:48990831 2757100884 T	S
176	527 C	-20:48990830 2757100883 C	
176	528 T	-20:48990829 2757100882 T	
177 D	529 G	-20:48990828 2757100881 G	D
177	530 A	-20:48990827 2757100880 A	
177	531 T	-20:48990826 2757100879 T	
178 L	532 T	-20:48990825 2757100878 T	L
178	533 T	-20:48990824 2757100877 T	
178	534 A	-20:48990823 2757100876 A	
179 T	535 A	-20:48990822 2757100875 A	T
179	536 C	-20:48990821 2757100874 C	
179	537 A	-20:48990820 2757100873 A	
180 G	538 G	-20:48990819 2757100872 G	G
180	539 G	-20:48990818 2757100871 G	
180	540 A	-20:48990817 2757100870 A	
181 S	541 A	-20:48990816 2757100869 A	S
181	542 G	-20:48990815 2757100868 G	
181	543 T	-20:48990814 2757100867 T	
182 F	544 T	-20:48990813 2757100866 T	F
182	545 T	-20:48990812 2757100865 T	
182	546 C	-20:48990811 2757100864 C	
183 R	547 A	-20:48990810 2757100863 A	R
183	548 G	-20:48990809 2757100862 G	
183	549 A	-20:48986206 2757096259 A	
184 L	550 T	-20:48986205 2757096258 T	L
184	551 T	-20:48986204 2757096257 T	
184	552 A	-20:48986203 2757096256 A	
185 Y	553 T	-20:48986202 2757096255 T	Y
185	554 A	-20:48986201 2757096254 A	
185	555 C	-20:48986200 2757096253 C	
186 R	556 C	-20:48986199 2757096252 C	R
186	557 G	-20:48986198 2757096251 G	
186	558 A	-20:48986197 2757096250 A	
187 K	559 A	-20:48986196 2757096249 A	K
187	560 A	-20:48986195 2757096248 A	
187	561 A	-20:48986194 2757096247 A	
188 E	562 G	-20:48986193 2757096246 G	E
188	563 A	-20:48986192 2757096245 A	
188	564 A	-20:48986191 2757096244 A	
189 V	565 G	-20:48986190 2757096243 G	V
189	566 T	-20:48986189 2757096242 T	
189	567 T	-20:48986188 2757096241 T	
190 L	568 C	-20:48986187 2757096240 C	L
190	569 T	-20:48986186 2757096239 T	
190	570 A	-20:48986185 2757096238 A	
191 E	571 G	-20:48986184 2757096237 G	E
191	572 A	-20:48986183 2757096236 A	
191	573 G	-20:48986182 2757096235 G	
192 K	574 A	-20:48986181 2757096234 A	K
192	575 A	-20:48986180 2757096233 A	
192	576 A	-20:48986179 2757096232 A	
193 L	577 T	-20:48986178 2757096231 T	L
193	578 T	-20:48986177 2757096230 T	
193	579 A	-20:48986176 2757096229 A	
194 I	580 A	-20:48986175 2757096228 A	I
194	581 T	-20:48986174 2757096227 T	
194	582 A	-20:48986173 2757096226 A	
195 E	583 G	-20:48986172 2757096225 G	E
195	584 A	-20:48986171 2757096224 A	
195	585 A	-20:48986170 2757096223 A	
196 K	586 A	-20:48986169 2757096222 A	K
196	587 A	-20:48986168 2757096221 A	
196	588 A	-20:48986167 2757096220 A	
197 C	589 T	-20:48986166 2757096219 T	C
197	590 G	-20:48986165 2757096218 G	
197	591 T	-20:48986164 2757096217 T	
198 V	592 G	-20:48986163 2757096216 G	V
198	593 T	-20:48986162 2757096215 T	
198	594 T	-20:48986161 2757096214 T	
199 S	595 T	-20:48986160 2757096213 T	S
199	596 C	-20:48986159 2757096212 C	
199	597 T	-20:48986158 2757096211 T	
200 K	598 A	-20:48986157 2757096210 A	K
200	599 A	-20:48986156 2757096209 A	
200	600 A	-20:48986155 2757096208 A	
201 G	601 G	-20:48986154 2757096207 G	G
201	602 G	-20:48986153 2757096206 G	
201	603 C	-20:48986152 2757096205 C	
202 Y	604 T	-20:48986151 2757096204 T	Y
202	605 A	-20:48986150 2757096203 A	
202	606 C	-20:48986149 2757096202 C	
203 V	607 G	-20:48986148 2757096201 G	V
203	608 T	-20:48986147 2757096200 T	
203	609 C	-20:48986146 2757096199 C	
204 F	610 T	-20:48986145 2757096198 T	F
204	611 T	-20:48986144 2757096197 T	
204	612 C	-20:48986143 2757096196 C	
205 Q	613 C	-20:48986142 2757096195 C	Q
205	614 A	-20:48986141 2757096194 A	
205	615 G	-20:48986140 2757096193 G	
206 M	616 A	-20:48986139 2757096192 A	M
206	617 T	-20:48986138 2757096191 T	
206	618 G	-20:48986137 2757096190 G	
207 E	619 G	-20:48986136 2757096189 G	E
207	620 A	-20:48986135 2757096188 A	
207	621 G	-20:48986134 2757096187 G	
208 M	622 A	-20:48986133 2757096186 A	M
208	623 T	-20:48986132 2757096185 T	
208	624 G	-20:48986131 2757096184 G	
209 I	625 A	-20:48986130 2757096183 A	I
209	626 T	-20:48986129 2757096182 T	
209	627 T	-20:48986128 2757096181 T	
210 V	628 G	-20:48986127 2757096180 G	V
210	629 T	-20:48986126 2757096179 T	
210	630 T	-20:48986125 2757096178 T	
211 R	631 C	-20:48986124 2757096177 C	R
211	632 G	-20:48986123 2757096176 G	
211	633 G	-20:48986122 2757096175 G	
212 A	634 G	-20:48986121 2757096174 G	A
212	635 C	-20:48986120 2757096173 C	
212	636 A	-20:48986119 2757096172 A	
213 R	637 A	-20:48986118 2757096171 A	R
213	638 G	-20:48986117 2757096170 G	
213	639 A	-20:48986116 2757096169 A	
214 Q	640 C	-20:48986115 2757096168 C	Q
214	641 A	-20:48986114 2757096167 A	
214	642 G	-20:48986113 2757096166 G	
215 L	643 T	-20:48986112 2757096165 T	L
215	644 T	-20:48986111 2757096164 T	
215	645 G	-20:48986110 2757096163 G	
216 N	646 A	-20:48986109 2757096162 A	N
216	647 A	-20:48986108 2757096161 A	
216	648 T	-20:48986107 2757096160 T	
217 Y	649 T	-20:48986106 2757096159 T	Y
217	650 A	-20:48986105 2757096158 A	
217	651 T	-20:48986104 2757096157 T	
218 T	652 A	-20:48986103 2757096156 A	T
218	653 C	-20:48986102 2757096155 C	
218	654 T	-20:48986101 2757096154 T	
219 I	655 A	-20:48986100 2757096153 A	I
219	656 T	-20:48986099 2757096152 T	
219	657 T	-20:48986098 2757096151 T	
220 G	658 G	-20:48986097 2757096150 G	G
220	659 G	-20:48986096 2757096149 G	
220	660 C	-20:48986095 2757096148 C	
221 E	661 G	-20:48986094 2757096147 G	E
221	662 A	-20:48986093 2757096146 A	
221	663 G	-20:48986092 2757096145 G	
>ENSP00000360644 
1 M	1 A	-20:49008467 2757118520 A	M
1	2 T	-20:49008466 2757118519 T	
1	3 G	-20:49008465 2757118518 G	
2 A	4 G	-20:49008464 2757118517 G	A
2	5 C	-20:49008463 2757118516 C	
2	6 C	-20:49008462 2757118515 C	
3 S	7 T	-20:49008461 2757118514 T	S
3	8 C	-20:49008460 2757118513 C	
3	9 C	-20:49008459 2757118512 C	
4 L	10 T	-20:49008458 2757118511 T	L
4	11 T	-20:49008457 2757118510 T	
4	12 G	-20:49008456 2757118509 G	
5 E	13 G	-20:49008455 2757118508 G	E
5	14 A	-20:49008454 2757118507 A	
5	15 A	-20:49008453 2757118506 A	
6 V	16 G	-20:49008452 2757118505 G	V
6	17 T	-20:49008451 2757118504 T	
6	18 C	-20:49008450 2757118503 C	
7 S	19 A	-20:49008449 2757118502 A	S
7	20 G	-20:49008448 2757118501 G	
7	21 T	-20:49008447 2757118500 T	
8 R	22 C	-20:49008446 2757118499 C	R
8	23 G	-20:49008445 2757118498 G	
8	24 T	-20:49008444 2757118497 T	
9 S	25 A	-20:49008443 2757118496 A	S
9	26 G	-20:49008442 2757118495 G	
9	27 T	-20:49008441 2757118494 T	
10 P	28 C	-20:49008440 2757118493 C	P
10	29 C	-20:49008439 2757118492 C	
10	30 T	-20:49008438 2757118491 T	
11 R	31 C	-20:49008437 2757118490 C	R
11	32 G	-20:49008436 2757118489 G	
11	33 C	-20:49008435 2757118488 C	
12 R	34 A	-20:49008434 2757118487 A	R
12	35 G	-20:49008433 2757118486 G	
12	36 G	-20:49008432 2757118485 G	
13 S	37 T	-20:49008431 2757118484 T	S
13	38 C	-20:49008430 2757118483 C	
13	39 T	-20:49008429 2757118482 T	
14 R	40 C	-20:49008428 2757118481 C	R
14	41 G	-20:49008427 2757118480 G	
14	42 G	-20:49008426 2757118479 G	
15 R	43 C	-20:49008425 2757118478 C	R
15	44 G	-20:49008424 2757118477 G	
15	45 G	-20:49008423 2757118476 G	
16 E	46 G	-20:49008422 2757118475 G	E
16	47 A	-20:49008421 2757118474 A	
16	48 G	-20:49008420 2757118473 G	
17 L	49 C	-20:49008419 2757118472 C	L
17	50 T	-20:49008418 2757118471 T	
17	51 G	-20:49008417 2757118470 G	
18 E	52 G	-20:49008416 2757118469 G	E
18	53 A	-20:49008415 2757118468 A	
18	54 A	-20:49008414 2757118467 A	
19 V	55 G	-20:49008413 2757118466 G	V
19	56 T	-20:49008412 2757118465 T	
19	57 G	-20:49008411 2757118464 G	
20 R	58 C	-20:49008410 2757118463 C	R
20	59 G	-20:49008409 2757118462 G	
20	60 C	-20:49008408 2757118461 C	
21 S	61 A	-20:49008407 2757118460 A	S
21	62 G	-20:49008406 2757118459 G	
21	63 T	-20:49008405 2757118458 T	
22 P	64 C	-20:49008404 2757118457 C	P
22	65 C	-20:49008403 2757118456 C	
22	66 A	-20:49008402 2757118455 A	
23 R	67 C	-20:49008401 2757118454 C	R
23	68 G	-20:49008400 2757118453 G	
23	69 A	-20:49008399 2757118452 A	
24 Q	70 C	-20:49008398 2757118451 C	Q
24	71 A	-20:49008397 2757118450 A	
24	72 G	-20:49008396 2757118449 G	
25 N	73 A	-20:49008395 2757118448 A	N
25	74 A	-20:49008394 2757118447 A	
25	75 C	-20:49008393 2757118446 C	
26 K	76 A	-20:49008392 2757118445 A	K
26	77 A	-20:49008391 2757118444 A	
26	78 A	-20:49008390 2757118443 A	
27 Y	79 T	-20:49008389 2757118442 T	Y
27	80 A	-20:49008388 2757118441 A	
27	81 T	-20:49008387 2757118440 T	
28 S	82 T	-20:49008386 2757118439 T	S
28	83 C	-20:49008385 2757118438 C	
28	84 G	-20:49008384 2757118437 G	
29 V	85 G	-20:49008383 2757118436 G	V
29	86 T	-20:49008382 2757118435 T	
29	87 G	-20:49008381 2757118434 G	
30 L	88 C	-20:49008380 2757118433 C	L
30	89 T	-20:49008379 2757118432 T	
30	90 T	-20:49008378 2757118431 T	
31 L	91 T	-20:49008377 2757118430 T	L
31	92 T	-20:49008376 2757118429 T	
31	93 A	-20:49008375 2757118428 A	
32 P	94 C	-20:49008374 2757118427 C	P
32	95 C	-20:49008373 2757118426 C	
32	96 T	-20:49008372 2757118425 T	
33 T	97 A	-20:49008371 2757118424 A	T
33	98 C	-20:49008370 2757118423 C	
33	99 C	-20:49008369 2757118422 C	
34 Y	100 T	-20:49008368 2757118421 T	Y
34	101 A	-20:49008367 2757118420 A	
34	102 C	-20:49008366 2757118419 C	
35 N	103 A	-20:49008365 2757118418 A	N
35	104 A	-20:49008364 2757118417 A	
35	105 C	-20:49008363 2757118416 C	
36 E	106 G	-20:49008362 2757118415 G	E
36	107 A	-20:49008361 2757118414 A	
36	108 G	-20:49008360 2757118413 G	
37 R	109 C	-20:49008359 2757118412 C	R
37	110 G	-20:49008358 2757118411 G	
37	111 C	-20:49008357 2757118410 C	
38 E	112 G	-20:49008356 2757118409 G	E
38	113 A	-20:49008355 2757118408 A	
38	114 G	-20:49008354 2757118407 G	
39 N	115 A	-20:49008353 2757118406 A	N
39	116 A	-20:49008352 2757118405 A	
39	117 C	-20:49008351 2757118404 C	
40 L	118 C	-20:49008350 2757118403 C	L
40	119 T	-20:49008349 2757118402 T	
40	120 G	-20:49008348 2757118401 G	
41 P	121 C	-20:49008347 2757118400 C	P
41	122 C	-20:49008346 2757118399 C	
41	123 G	-20:49008345 2757118398 G	
42 L	124 C	-20:49008344 2757118397 C	L
42	125 T	-20:49008343 2757118396 T	
42	126 C	-20:49008342 2757118395 C	
43 I	127 A	-20:49008341 2757118394 A	I
43	128 T	-20:49008340 2757118393 T	
43	129 C	-20:49008339 2757118392 C	
44 V	130 G	-20:49008338 2757118391 G	V
44	131 T	-20:49008337 2757118390 T	
44	132 G	-20:49008336 2757118389 G	
45 W	133 T	-20:49008335 2757118388 T	W
45	134 G	-20:49008334 2757118387 G	
45	135 G	-20:49008333 2757118386 G	
46 L	136 C	-20:49008332 2757118385 C	L
46	137 T	-20:49008331 2757118384 T	
46	138 G	-20:49008330 2757118383 G	
47 L	139 C	-20:49008329 2757118382 C	L
47	140 T	-20:49008328 2757118381 T	
47	141 G	-20:49008327 2757118380 G	
48 V	142 G	-20:49008326 2757118379 G	V
48	143 T	-20:49008325 2757118378 T	
48	144 G	-20:49008324 2757118377 G	
49 K	145 A	-20:49008323 2757118376 A	K
49	146 A	-20:49008322 2757118375 A	
49	147 A	-20:49008321 2757118374 A	
50 S	148 A	-20:49008320 2757118373 A	S
50	149 G	-20:49008319 2757118372 G	
50	150 C	-20:49008318 2757118371 C	
51 F	151 T	-20:49008317 2757118370 T	F
51	152 T	-20:49008316 2757118369 T	
51	153 C	-20:49008315 2757118368 C	
52 S	154 T	-20:49008314 2757118367 T	S
52	155 C	-20:49008313 2757118366 C	
52	156 C	-20:49008312 2757118365 C	
53 E	157 G	-20:49008311 2757118364 G	E
53	158 A	-20:49008310 2757118363 A	
53	159 G	-20:49008309 2757118362 G	
54 S	160 A	-20:49008308 2757118361 A	S
54	161 G	-20:49008307 2757118360 G	
54	162 T	-20:49005229 2757115282 T	
55 G	163 G	-20:49005228 2757115281 G	G
55	164 G	-20:49005227 2757115280 G	
55	165 A	-20:49005226 2757115279 A	
56 I	166 A	-20:49005225 2757115278 A	I
56	167 T	-20:49005224 2757115277 T	
56	168 C	-20:49005223 2757115276 C	
57 N	169 A	-20:49005222 2757115275 A	N
57	170 A	-20:49005221 2757115274 A	
57	171 C	-20:49005220 2757115273 C	
58 Y	172 T	-20:49005219 2757115272 T	Y
58	173 A	-20:49005218 2757115271 A	
58	174 T	-20:49005217 2757115270 T	
59 E	175 G	-20:49005216 2757115269 G	E
59	176 A	-20:49005215 2757115268 A	
59	177 A	-20:49005214 2757115267 A	
60 I	178 A	-20:49005213 2757115266 A	I
60	179 T	-20:49005212 2757115265 T	
60	180 T	-20:49005211 2757115264 T	
61 I	181 A	-20:49005210 2757115263 A	I
61	182 T	-20:49005209 2757115262 T	
61	183 A	-20:49005208 2757115261 A	
62 I	184 A	-20:49005207 2757115260 A	I
62	185 T	-20:49005206 2757115259 T	
62	186 C	-20:49005205 2757115258 C	
63 I	187 A	-20:49005204 2757115257 A	I
63	188 T	-20:49005203 2757115256 T	
63	189 A	-20:49005202 2757115255 A	
64 D	190 G	-20:49005201 2757115254 G	D
64	191 A	-20:49005200 2757115253 A	
64	192 T	-20:49005199 2757115252 T	
65 D	193 G	-20:49005198 2757115251 G	D
65	194 A	-20:49005197 2757115250 A	
65	195 T	-20:49005196 2757115249 T	
66 G	196 G	-20:49005195 2757115248 G	G
66	197 G	-20:49005194 2757115247 G	
66	198 A	-20:49005193 2757115246 A	
67 S	199 A	-20:49005192 2757115245 A	S
67	200 G	-20:49005191 2757115244 G	
67	201 C	-20:49005190 2757115243 C	
68 P	202 C	-20:49005189 2757115242 C	P
68	203 C	-20:49005188 2757115241 C	
68	204 A	-20:49005187 2757115240 A	
69 D	205 G	-20:49005186 2757115239 G	D
69	206 A	-20:49005185 2757115238 A	
69	207 T	-20:49005184 2757115237 T	
70 G	208 G	-20:49005183 2757115236 G	G
70	209 G	-20:49005182 2757115235 G	
70	210 A	-20:49005181 2757115234 A	
71 T	211 A	-20:49005180 2757115233 A	T
71	212 C	-20:49005179 2757115232 C	
71	213 A	-20:49005178 2757115231 A	
72 R	214 A	-20:49005177 2757115230 A	R
72	215 G	-20:49005176 2757115229 G	
72	216 G	-20:49005175 2757115228 G	
73 D	217 G	-20:49005174 2757115227 G	D
73	218 A	-20:49005173 2757115226 A	
73	219 T	-20:49005172 2757115225 T	
74 V	220 G	-20:49005171 2757115224 G	V
74	221 T	-20:49005170 2757115223 T	
74	222 T	-20:49005169 2757115222 T	
75 A	223 G	-20:49005168 2757115221 G	A
75	224 C	-20:49005167 2757115220 C	
75	225 T	-20:49005166 2757115219 T	
76 E	226 G	-20:49005165 2757115218 G	E
76	227 A	-20:49005164 2757115217 A	
76	228 A	-20:49005163 2757115216 A	
77 Q	229 C	-20:49005162 2757115215 C	Q
77	230 A	-20:49005161 2757115214 A	
77	231 G	-20:49005160 2757115213 G	
78 L	232 T	-20:49005159 2757115212 T	L
78	233 T	-20:49005158 2757115211 T	
78	234 G	-20:49005157 2757115210 G	
79 E	235 G	-20:49005156 2757115209 G	E
79	236 A	-20:49005155 2757115208 A	
79	237 G	-20:49005154 2757115207 G	
80 K	238 A	-20:49005153 2757115206 A	K
80	239 A	-20:49005152 2757115205 A	
80	240 G	-20:49005151 2757115204 G	
81 I	241 A	-20:49005150 2757115203 A	I
81	242 T	-20:49005149 2757115202 T	
81	243 C	-20:49005148 2757115201 C	
82 Y	244 T	-20:49005147 2757115200 T	Y
82	245 A	-20:49005146 2757115199 A	
82	246 T	-20:49005145 2757115198 T	
83 G	247 G	-20:49005144 2757115197 G	G
83	248 G	-20:49005143 2757115196 G	
83	249 G	-20:49005142 2757115195 G	
84 S	250 T	-20:49005141 2757115194 T	S
84	251 C	-20:49005140 2757115193 C	
84	252 A	-20:49005139 2757115192 A	
85 D	253 G	-20:49005138 2757115191 G	D
85	254 A	-20:49005137 2757115190 A	
85	255 C	-20:49005136 2757115189 C	
86 R	256 A	-20:49005135 2757115188 A	R
86	257 G	-20:49005134 2757115187 G	
86	258 A	-20:49005133 2757115186 A	
87 I	259 A	-20:49005132 2757115185 A	I
87	260 T	-20:49005131 2757115184 T	
87	261 T	-20:49005130 2757115183 T	
88 L	262 C	-20:48998606 2757108659 C	L
88	263 T	-20:48998605 2757108658 T	
88	264 T	-20:48998604 2757108657 T	
89 L	265 C	-20:48998603 2757108656 C	L
89	266 T	-20:48998602 2757108655 T	
89	267 A	-20:48998601 2757108654 A	
90 R	268 A	-20:48998600 2757108653 A	R
90	269 G	-20:48998599 2757108652 G	
90	270 A	-20:48998598 2757108651 A	
91 P	271 C	-20:48998597 2757108650 C	P
91	272 C	-20:48998596 2757108649 C	
91	273 A	-20:48998595 2757108648 A	
92 R	274 C	-20:48998594 2757108647 C	R
92	275 G	-20:48998593 2757108646 G	
92	276 A	-20:48998592 2757108645 A	
93 E	277 G	-20:48998591 2757108644 G	E
93	278 A	-20:48998590 2757108643 A	
93	279 G	-20:48998589 2757108642 G	
94 K	280 A	-20:48998588 2757108641 A	K
94	281 A	-20:48998587 2757108640 A	
94	282 A	-20:48998586 2757108639 A	
95 K	283 A	-20:48998585 2757108638 A	K
95	284 A	-20:48998584 2757108637 A	
95	285 G	-20:48998583 2757108636 G	
96 L	286 T	-20:48998582 2757108635 T	L
96	287 T	-20:48998581 2757108634 T	
96	288 G	-20:48998580 2757108633 G	
97 G	289 G	-20:48998579 2757108632 G	G
97	290 G	-20:48998578 2757108631 G	
97	291 A	-20:48998577 2757108630 A	
98 L	292 C	-20:48998576 2757108629 C	L
98	293 T	-20:48998575 2757108628 T	
98	294 A	-20:48998574 2757108627 A	
99 G	295 G	-20:48998573 2757108626 G	G
99	296 G	-20:48995867 2757105920 G	
99	297 A	-20:48995866 2757105919 A	
100 T	298 A	-20:48995865 2757105918 A	T
100	299 C	-20:48995864 2757105917 C	
100	300 T	-20:48995863 2757105916 T	
101 A	301 G	-20:48995862 2757105915 G	A
101	302 C	-20:48995861 2757105914 C	
101	303 A	-20:48995860 2757105913 A	
102 Y	304 T	-20:48995859 2757105912 T	Y
102	305 A	-20:48995858 2757105911 A	
102	306 T	-20:48995857 2757105910 T	
103 I	307 A	-20:48995856 2757105909 A	I
103	308 T	-20:48995855 2757105908 T	
103	309 T	-20:48995854 2757105907 T	
104 H	310 C	-20:48995853 2757105906 C	H
104	311 A	-20:48995852 2757105905 A	
104	312 T	-20:48995851 2757105904 T	
105 G	313 G	-20:48995850 2757105903 G	G
105	314 G	-20:48995849 2757105902 G	
105	315 A	-20:48995848 2757105901 A	
106 M	316 A	-20:48995847 2757105900 A	M
106	317 T	-20:48995846 2757105899 T	
106	318 G	-20:48995845 2757105898 G	
107 K	319 A	-20:48995844 2757105897 A	K
107	320 A	-20:48995843 2757105896 A	
107	321 A	-20:48995842 2757105895 A	
108 H	322 C	-20:48995841 2757105894 C	H
108	323 A	-20:48995840 2757105893 A	
108	324 T	-20:48995839 2757105892 T	
109 A	325 G	-20:48995838 2757105891 G	A
109	326 C	-20:48995837 2757105890 C	
109	327 C	-20:48995836 2757105889 C	
110 T	328 A	-20:48995835 2757105888 A	T
110	329 C	-20:48995834 2757105887 C	
110	330 A	-20:48995833 2757105886 A	
111 G	331 G	-20:48995832 2757105885 G	G
111	332 G	-20:48995831 2757105884 G	
111	333 A	-20:48995830 2757105883 A	
112 N	334 A	-20:48995829 2757105882 A	N
112	335 A	-20:48995828 2757105881 A	
112	336 C	-20:48995827 2757105880 C	
113 Y	337 T	-20:48995826 2757105879 T	Y
113	338 A	-20:48995825 2757105878 A	
113	339 C	-20:48995824 2757105877 C	
114 I	340 A	-20:48995823 2757105876 A	I
114	341 T	-20:48995822 2757105875 T	
114	342 C	-20:48995821 2757105874 C	
115 I	343 A	-20:48995820 2757105873 A	I
115	344 T	-20:48995819 2757105872 T	
115	345 T	-20:48995818 2757105871 T	
116 I	346 A	-20:48995817 2757105870 A	I
116	347 T	-20:48995816 2757105869 T	
116	348 T	-20:48995815 2757105868 T	
117 M	349 A	-20:48995814 2757105867 A	M
117	350 T	-20:48995813 2757105866 T	
117	351 G	-20:48995812 2757105865 G	
118 D	352 G	-20:48995811 2757105864 G	D
118	353 A	-20:48995810 2757105863 A	
118	354 T	-20:48995809 2757105862 T	
119 A	355 G	-20:48995808 2757105861 G	A
119	356 C	-20:48995807 2757105860 C	
119	357 T	-20:48995806 2757105859 T	
120 D	358 G	-20:48995805 2757105858 G	D
120	359 A	-20:48995804 2757105857 A	
120	360 T	-20:48995803 2757105856 T	
121 L	361 C	-20:48995802 2757105855 C	L
121	362 T	-20:48995801 2757105854 T	
121	363 C	-20:48995800 2757105853 C	
122 S	364 T	-20:48995799 2757105852 T	S
122	365 C	-20:48995798 2757105851 C	
122	366 A	-20:48995797 2757105850 A	
123 H	367 C	-20:48995796 2757105849 C	H
123	368 A	-20:48995795 2757105848 A	
123	369 C	-20:48995794 2757105847 C	
124 H	370 C	-20:48995793 2757105846 C	H
124	371 A	-20:48995792 2757105845 A	
124	372 T	-20:48995791 2757105844 T	
125 P	373 C	-20:48995706 2757105759 C	P
125	374 C	-20:48995705 2757105758 C	
125	375 A	-20:48995704 2757105757 A	
126 K	376 A	-20:48995703 2757105756 A	K
126	377 A	-20:48995702 2757105755 A	
126	378 A	-20:48995701 2757105754 A	
127 F	379 T	-20:48995700 2757105753 T	F
127	380 T	-20:48995699 2757105752 T	
127	381 T	-20:48995698 2757105751 T	
128 I	382 A	-20:48995697 2757105750 A	I
128	383 T	-20:48995696 2757105749 T	
128	384 T	-20:48995695 2757105748 T	
129 P	385 C	-20:48995694 2757105747 C	P
129	386 C	-20:48995693 2757105746 C	
129	387 T	-20:48995692 2757105745 T	
130 E	388 G	-20:48995691 2757105744 G	E
130	389 A	-20:48995690 2757105743 A	
130	390 A	-20:48995689 2757105742 A	
131 F	391 T	-20:48995688 2757105741 T	F
131	392 T	-20:48995687 2757105740 T	
131	393 T	-20:48995686 2757105739 T	
132 I	394 A	-20:48995685 2757105738 A	I
132	395 T	-20:48995684 2757105737 T	
132	396 T	-20:48995683 2757105736 T	
133 R	397 A	-20:48995682 2757105735 A	R
133	398 G	-20:48995681 2757105734 G	
133	399 G	-20:48992070 2757102123 G	
134 K	400 A	-20:48992069 2757102122 A	K
134	401 A	-20:48992068 2757102121 A	
134	402 G	-20:48992067 2757102120 G	
135 Q	403 C	-20:48992066 2757102119 C	Q
135	404 A	-20:48992065 2757102118 A	
135	405 A	-20:48992064 2757102117 A	
136 K	406 A	-20:48992063 2757102116 A	K
136	407 A	-20:48992062 2757102115 A	
136	408 G	-20:48992061 2757102114 G	
137 E	409 G	-20:48992060 2757102113 G	E
137	410 A	-20:48992059 2757102112 A	
137	411 G	-20:48992058 2757102111 G	
138 G	412 G	-20:48992057 2757102110 G	G
138	413 G	-20:48992056 2757102109 G	
138	414 T	-20:48992055 2757102108 T	
139 N	415 A	-20:48992054 2757102107 A	N
139	416 A	-20:48992053 2757102106 A	
139	417 T	-20:48992052 2757102105 T	
140 F	418 T	-20:48992051 2757102104 T	F
140	419 T	-20:48992050 2757102103 T	
140	420 T	-20:48992049 2757102102 T	
141 D	421 G	-20:48992048 2757102101 G	D
141	422 A	-20:48992047 2757102100 A	
141	423 T	-20:48992046 2757102099 T	
142 I	424 A	-20:48992045 2757102098 A	I
142	425 T	-20:48992044 2757102097 T	
142	426 T	-20:48992043 2757102096 T	
143 V	427 G	-20:48992042 2757102095 G	V
143	428 T	-20:48992041 2757102094 T	
143	429 C	-20:48992040 2757102093 C	
144 S	430 T	-20:48992039 2757102092 T	S
144	431 C	-20:48992038 2757102091 C	
144	432 T	-20:48992037 2757102090 T	
145 G	433 G	-20:48992036 2757102089 G	G
145	434 G	-20:48992035 2757102088 G	
145	435 A	-20:48992034 2757102087 A	
146 T	436 A	-20:48992033 2757102086 A	T
146	437 C	-20:48992032 2757102085 C	
146	438 T	-20:48992031 2757102084 T	
147 R	439 C	-20:48992030 2757102083 C	R
147	440 G	-20:48992029 2757102082 G	
147	441 C	-20:48992028 2757102081 C	
148 Y	442 T	-20:48992027 2757102080 T	Y
148	443 A	-20:48992026 2757102079 A	
148	444 C	-20:48992025 2757102078 C	
149 K	445 A	-20:48992024 2757102077 A	K
149	446 A	-20:48992023 2757102076 A	
149	447 A	-20:48992022 2757102075 A	
150 G	448 G	-20:48992021 2757102074 G	G
150	449 G	-20:48992020 2757102073 G	
150	450 A	-20:48992019 2757102072 A	
151 N	451 A	-20:48992018 2757102071 A	N
151	452 A	-20:48992017 2757102070 A	
151	453 T	-20:48992016 2757102069 T	
152 G	454 G	-20:48992015 2757102068 G	G
152	455 G	-20:48992014 2757102067 G	
152	456 A	-20:48992013 2757102066 A	
153 G	457 G	-20:48992012 2757102065 G	G
153	458 G	-20:48992011 2757102064 G	
153	459 T	-20:48992010 2757102063 T	
154 V	460 G	-20:48992009 2757102062 G	V
154	461 T	-20:48992008 2757102061 T	
154	462 A	-20:48992007 2757102060 A	
155 Y	463 T	-20:48992006 2757102059 T	Y
155	464 A	-20:48992005 2757102058 A	
155	465 T	-20:48992004 2757102057 T	
156 G	466 G	-20:48992003 2757102056 G	G
156	467 G	-20:48992002 2757102055 G	
156	468 C	-20:48992001 2757102054 C	
157 W	469 T	-20:48992000 2757102053 T	W
157	470 G	-20:48991999 2757102052 G	
157	471 G	-20:48991998 2757102051 G	
158 D	472 G	-20:48991997 2757102050 G	D
158	473 A	-20:48991996 2757102049 A	
158	474 T	-20:48991995 2757102048 T	
159 L	475 T	-20:48991994 2757102047 T	L
159	476 T	-20:48991993 2757102046 T	
159	477 G	-20:48991992 2757102045 G	
160 K	478 A	-20:48991991 2757102044 A	K
160	479 A	-20:48991990 2757102043 A	
160	480 A	-20:48991989 2757102042 A	
161 R	481 A	-20:48991988 2757102041 A	R
161	482 G	-20:48991987 2757102040 G	
161	483 A	-20:48991986 2757102039 A	
162 K	484 A	-20:48991985 2757102038 A	K
162	485 A	-20:48991984 2757102037 A	
162	486 A	-20:48991983 2757102036 A	
163 I	487 A	-20:48991982 2757102035 A	I
163	488 T	-20:48991981 2757102034 T	
163	489 A	-20:48991980 2757102033 A	
164 I	490 A	-20:48991979 2757102032 A	I
164	491 T	-20:48991978 2757102031 T	
164	492 C	-20:48991977 2757102030 C	
165 S	493 A	-20:48991976 2757102029 A	S
165	494 G	-20:48991975 2757102028 G	
165	495 C	-20:48990877 2757100930 C	
166 R	496 C	-20:48990876 2757100929 C	R
166	497 G	-20:48990875 2757100928 G	
166	498 T	-20:48990874 2757100927 T	
167 G	499 G	-20:48990873 2757100926 G	G
167	500 G	-20:48990872 2757100925 G	
167	501 G	-20:48990871 2757100924 G	
168 A	502 G	-20:48990870 2757100923 G	A
168	503 C	-20:48990869 2757100922 C	
168	504 C	-20:48990868 2757100921 C	
169 N	505 A	-20:48990867 2757100920 A	N
169	506 A	-20:48990866 2757100919 A	
169	507 T	-20:48990865 2757100918 T	
170 F	508 T	-20:48990864 2757100917 T	F
170	509 T	-20:48990863 2757100916 T	
170	510 T	-20:48990862 2757100915 T	
171 L	511 T	-20:48990861 2757100914 T	L
171	512 T	-20:48990860 2757100913 T	
171	513 A	-20:48990859 2757100912 A	
172 T	514 A	-20:48990858 2757100911 A	T
172	515 C	-20:48990857 2757100910 C	
172	516 T	-20:48990856 2757100909 T	
173 Q	517 C	-20:48990855 2757100908 C	Q
173	518 A	-20:48990854 2757100907 A	
173	519 G	-20:48990853 2757100906 G	
174 I	520 A	-20:48990852 2757100905 A	I
174	521 T	-20:48990851 2757100904 T	
174	522 C	-20:48990850 2757100903 C	
175 L	523 T	-20:48990849 2757100902 T	L
175	524 T	-20:48990848 2757100901 T	
175	525 G	-20:48990847 2757100900 G	
176 L	526 C	-20:48990846 2757100899 C	L
176	527 T	-20:48990845 2757100898 T	
176	528 G	-20:48990844 2757100897 G	
177 R	529 A	-20:48990843 2757100896 A	R
177	530 G	-20:48990842 2757100895 G	
177	531 A	-20:48990841 2757100894 A	
178 P	532 C	-20:48990840 2757100893 C	P
178	533 C	-20:48990839 2757100892 C	
178	534 A	-20:48990838 2757100891 A	
179 G	535 G	-20:48990837 2757100890 G	G
179	536 G	-20:48990836 2757100889 G	
179	537 A	-20:48990835 2757100888 A	
180 A	538 G	-20:48990834 2757100887 G	A
180	539 C	-20:48990833 2757100886 C	
180	540 A	-20:48990832 2757100885 A	
181 S	541 T	-20:48990831 2757100884 T	S
181	542 C	-20:48990830 2757100883 C	
181	543 T	-20:48990829 2757100882 T	
182 D	544 G	-20:48990828 2757100881 G	D
182	545 A	-20:48990827 2757100880 A	
182	546 T	-20:48990826 2757100879 T	
183 L	547 T	-20:48990825 2757100878 T	L
183	548 T	-20:48990824 2757100877 T	
183	549 A	-20:48990823 2757100876 A	
184 T	550 A	-20:48990822 2757100875 A	T
184	551 C	-20:48990821 2757100874 C	
184	552 A	-20:48990820 2757100873 A	
185 G	553 G	-20:48990819 2757100872 G	G
185	554 G	-20:48990818 2757100871 G	
185	555 A	-20:48990817 2757100870 A	
186 S	556 A	-20:48990816 2757100869 A	S
186	557 G	-20:48990815 2757100868 G	
186	558 T	-20:48990814 2757100867 T	
187 F	559 T	-20:48990813 2757100866 T	F
187	560 T	-20:48990812 2757100865 T	
187	561 C	-20:48990811 2757100864 C	
188 R	562 A	-20:48990810 2757100863 A	R
188	563 G	-20:48990809 2757100862 G	
188	564 A	-20:48986206 2757096259 A	
189 L	565 T	-20:48986205 2757096258 T	L
189	566 T	-20:48986204 2757096257 T	
189	567 A	-20:48986203 2757096256 A	
190 Y	568 T	-20:48986202 2757096255 T	Y
190	569 A	-20:48986201 2757096254 A	
190	570 C	-20:48986200 2757096253 C	
191 R	571 C	-20:48986199 2757096252 C	R
191	572 G	-20:48986198 2757096251 G	
191	573 A	-20:48986197 2757096250 A	
192 K	574 A	-20:48986196 2757096249 A	K
192	575 A	-20:48986195 2757096248 A	
192	576 A	-20:48986194 2757096247 A	
193 E	577 G	-20:48986193 2757096246 G	E
193	578 A	-20:48986192 2757096245 A	
193	579 A	-20:48986191 2757096244 A	
194 V	580 G	-20:48986190 2757096243 G	V
194	581 T	-20:48986189 2757096242 T	
194	582 T	-20:48986188 2757096241 T	
195 L	583 C	-20:48986187 2757096240 C	L
195	584 T	-20:48986186 2757096239 T	
195	585 A	-20:48986185 2757096238 A	
196 E	586 G	-20:48986184 2757096237 G	E
196	587 A	-20:48986183 2757096236 A	
196	588 G	-20:48986182 2757096235 G	
197 K	589 A	-20:48986181 2757096234 A	K
197	590 A	-20:48986180 2757096233 A	
197	591 A	-20:48986179 2757096232 A	
198 L	592 T	-20:48986178 2757096231 T	L
198	593 T	-20:48986177 2757096230 T	
198	594 A	-20:48986176 2757096229 A	
199 I	595 A	-20:48986175 2757096228 A	I
199	596 T	-20:48986174 2757096227 T	
199	597 A	-20:48986173 2757096226 A	
200 E	598 G	-20:48986172 2757096225 G	E
200	599 A	-20:48986171 2757096224 A	
200	600 A	-20:48986170 2757096223 A	
201 K	601 A	-20:48986169 2757096222 A	K
201	602 A	-20:48986168 2757096221 A	
201	603 A	-20:48986167 2757096220 A	
202 C	604 T	-20:48986166 2757096219 T	C
202	605 G	-20:48986165 2757096218 G	
202	606 T	-20:48986164 2757096217 T	
203 V	607 G	-20:48986163 2757096216 G	V
203	608 T	-20:48986162 2757096215 T	
203	609 T	-20:48986161 2757096214 T	
204 S	610 T	-20:48986160 2757096213 T	S
204	611 C	-20:48986159 2757096212 C	
204	612 T	-20:48986158 2757096211 T	
205 K	613 A	-20:48986157 2757096210 A	K
205	614 A	-20:48986156 2757096209 A	
205	615 A	-20:48986155 2757096208 A	
206 G	616 G	-20:48986154 2757096207 G	G
206	617 G	-20:48986153 2757096206 G	
206	618 C	-20:48986152 2757096205 C	
207 Y	619 T	-20:48986151 2757096204 T	Y
207	620 A	-20:48986150 2757096203 A	
207	621 C	-20:48986149 2757096202 C	
208 V	622 G	-20:48986148 2757096201 G	V
208	623 T	-20:48986147 2757096200 T	
208	624 C	-20:48986146 2757096199 C	
209 F	625 T	-20:48986145 2757096198 T	F
209	626 T	-20:48986144 2757096197 T	
209	627 C	-20:48986143 2757096196 C	
210 Q	628 C	-20:48986142 2757096195 C	Q
210	629 A	-20:48986141 2757096194 A	
210	630 G	-20:48986140 2757096193 G	
211 M	631 A	-20:48986139 2757096192 A	M
211	632 T	-20:48986138 2757096191 T	
211	633 G	-20:48986137 2757096190 G	
212 E	634 G	-20:48986136 2757096189 G	E
212	635 A	-20:48986135 2757096188 A	
212	636 G	-20:48986134 2757096187 G	
213 M	637 A	-20:48986133 2757096186 A	M
213	638 T	-20:48986132 2757096185 T	
213	639 G	-20:48986131 2757096184 G	
214 I	640 A	-20:48986130 2757096183 A	I
214	641 T	-20:48986129 2757096182 T	
214	642 T	-20:48986128 2757096181 T	
215 V	643 G	-20:48986127 2757096180 G	V
215	644 T	-20:48986126 2757096179 T	
215	645 T	-20:48986125 2757096178 T	
216 R	646 C	-20:48986124 2757096177 C	R
216	647 G	-20:48986123 2757096176 G	
216	648 G	-20:48986122 2757096175 G	
217 A	649 G	-20:48986121 2757096174 G	A
217	650 C	-20:48986120 2757096173 C	
217	651 A	-20:48986119 2757096172 A	
218 R	652 A	-20:48986118 2757096171 A	R
218	653 G	-20:48986117 2757096170 G	
218	654 A	-20:48986116 2757096169 A	
219 Q	655 C	-20:48986115 2757096168 C	Q
219	656 A	-20:48986114 2757096167 A	
219	657 G	-20:48986113 2757096166 G	
220 L	658 T	-20:48986112 2757096165 T	L
220	659 T	-20:48986111 2757096164 T	
220	660 G	-20:48986110 2757096163 G	
221 N	661 A	-20:48986109 2757096162 A	N
221	662 A	-20:48986108 2757096161 A	
221	663 T	-20:48986107 2757096160 T	
222 Y	664 T	-20:48986106 2757096159 T	Y
222	665 A	-20:48986105 2757096158 A	
222	666 T	-20:48986104 2757096157 T	
223 T	667 A	-20:48986103 2757096156 A	T
223	668 C	-20:48986102 2757096155 C	
223	669 T	-20:48986101 2757096154 T	
224 I	670 A	-20:48986100 2757096153 A	I
224	671 T	-20:48986099 2757096152 T	
224	672 T	-20:48986098 2757096151 T	
225 G	673 G	-20:48986097 2757096150 G	G
225	674 G	-20:48986096 2757096149 G	
225	675 C	-20:48986095 2757096148 C	
226 E	676 G	-20:48986094 2757096147 G	E
226	677 A	-20:48986093 2757096146 A	
226	678 G	-20:48986092 2757096145 G	
>ENSP00000356744 
1 M	1 A	-1:168124605 168124605 A	M
1	2 T	-1:168124604 168124604 T	
1	3 G	-1:168124603 168124603 G	
2 G	4 G	-1:168124602 168124602 G	G
2	5 G	-1:168124601 168124601 G	
2	6 A	-1:168124600 168124600 A	
3 S	7 T	-1:168124599 168124599 T	S
3	8 C	-1:168124598 168124598 C	
3	9 A	-1:168124597 168124597 A	
4 E	10 G	-1:168124596 168124596 G	E
4	11 A	-1:168124595 168124595 A	
4	12 G	-1:168124594 168124594 G	
5 N	13 A	-1:168124593 168124593 A	N
5	14 A	-1:168124592 168124592 A	
5	15 C	-1:168124591 168124591 C	
6 S	16 A	-1:168124590 168124590 A	S
6	17 G	-1:168124589 168124589 G	
6	18 T	-1:168124588 168124588 T	
7 A	19 G	-1:168124587 168124587 G	A
7	20 C	-1:168124586 168124586 C	
7	21 T	-1:168124585 168124585 T	
8 L	22 T	-1:168124584 168124584 T	L
8	23 T	-1:168124583 168124583 T	
8	24 A	-1:168124582 168124582 A	
9 K	25 A	-1:168124581 168124581 A	K
9	26 A	-1:168124580 168124580 A	
9	27 G	-1:168124579 168124579 G	
10 S	28 A	-1:168124578 168124578 A	S
10	29 G	-1:168124577 168124577 G	
10	30 C	-1:168124576 168124576 C	
11 Y	31 T	-1:168124575 168124575 T	Y
11	32 A	-1:168124574 168124574 A	
11	33 T	-1:168124573 168124573 T	
12 T	34 A	-1:168124572 168124572 A	T
12	35 C	-1:168124571 168124571 C	
12	36 A	-1:168124570 168124570 A	
13 L	37 C	-1:168124569 168124569 C	L
13	38 T	-1:168124568 168124568 T	
13	39 G	-1:168124567 168124567 G	
14 R	40 A	-1:168124566 168124566 A	R
14	41 G	-1:168124565 168124565 G	
14	42 A	-1:168124564 168124564 A	
15 E	43 G	-1:168124563 168124563 G	E
15	44 A	-1:168124562 168124562 A	
15	45 A	-1:168124561 168124561 A	
16 P	46 C	-1:168124560 168124560 C	P
16	47 C	-1:168124559 168124559 C	
16	48 A	-1:168124558 168124558 A	
17 P	49 C	-1:168124557 168124557 C	P
17	50 C	-1:168124556 168124556 C	
17	51 A	-1:168124555 168124555 A	
18 F	52 T	-1:168124554 168124554 T	F
18	53 T	-1:168124553 168124553 T	
18	54 T	-1:168124552 168124552 T	
19 T	55 A	-1:168124551 168124551 A	T
19	56 C	-1:168124550 168124550 C	
19	57 C	-1:168124549 168124549 C	
20 L	58 T	-1:168124548 168124548 T	L
20	59 T	-1:168124547 168124547 T	
20	60 A	-1:168124546 168124546 A	
21 P	61 C	-1:168124545 168124545 C	P
21	62 C	-1:168124544 168124544 C	
21	63 C	-1:168124543 168124543 C	
22 S	64 T	-1:168124542 168124542 T	S
22	65 C	-1:168124541 168124541 C	
22	66 T	-1:168124540 168124540 T	
23 G	67 G	-1:168124539 168124539 G	G
23	68 G	-1:168124538 168124538 G	
23	69 A	-1:168124537 168124537 A	
24 L	70 C	-1:168124536 168124536 C	L
24	71 T	-1:168124535 168124535 T	
24	72 T	-1:168124534 168124534 T	
25 A	73 G	-1:168124533 168124533 G	A
25	74 C	-1:168124532 168124532 C	
25	75 T	-1:168124531 168124531 T	
26 V	76 G	-1:168124530 168124530 G	V
26	77 T	-1:168124529 168124529 T	
26	78 T	-1:168124528 168124528 T	
27 Y	79 T	-1:168124527 168124527 T	Y
27	80 A	-1:168124526 168124526 A	
27	81 T	-1:168124525 168124525 T	
28 P	82 C	-1:168124524 168124524 C	P
28	83 C	-1:168124523 168124523 C	
28	84 C	-1:168124522 168124522 C	
29 A	85 G	-1:168124521 168124521 G	A
29	86 C	-1:168124520 168124520 C	
29	87 T	-1:168124519 168124519 T	
30 V	88 G	-1:168124518 168124518 G	V
30	89 T	-1:168124517 168124517 T	
30	90 A	-1:168124516 168124516 A	
31 L	91 C	-1:168124515 168124515 C	L
31	92 T	-1:168124514 168124514 T	
31	93 G	-1:168124513 168124513 G	
32 Q	94 C	-1:168124512 168124512 C	Q
32	95 A	-1:168124511 168124511 A	
32	96 A	-1:168124510 168124510 A	
33 D	97 G	-1:168124509 168124509 G	D
33	98 A	-1:168124508 168124508 A	
33	99 T	-1:168124507 168124507 T	
34 G	100 G	-1:168124506 168124506 G	G
34	101 G	-1:168124505 168124505 G	
34	102 C	-1:168124504 168124504 C	
35 K	103 A	-1:168124503 168124503 A	K
35	104 A	-1:168124502 168124502 A	
35	105 A	-1:168124501 168124501 A	
36 F	106 T	-1:168124500 168124500 T	F
36	107 T	-1:168124499 168124499 T	
36	108 T	-1:168124498 168124498 T	
37 A	109 G	-1:168124497 168124497 G	A
37	110 C	-1:168124496 168124496 C	
37	111 T	-1:168124495 168124495 T	
38 S	112 T	-1:168124494 168124494 T	S
38	113 C	-1:168124493 168124493 C	
38	114 A	-1:168124492 168124492 A	
39 V	115 G	-1:168124491 168124491 G	V
39	116 T	-1:168124490 168124490 T	
39	117 T	-1:168124489 168124489 T	
40 F	118 T	-1:168124488 168124488 T	F
40	119 T	-1:168124487 168124487 T	
40	120 T	-1:168124486 168124486 T	
41 V	121 G	-1:168124485 168124485 G	V
41	122 T	-1:168124484 168124484 T	
41	123 G	-1:168124483 168124483 G	
42 Y	124 T	-1:168124482 168124482 T	Y
42	125 A	-1:168124481 168124481 A	
42	126 T	-1:168124480 168124480 T	
43 K	127 A	-1:168124479 168124479 A	K
43	128 A	-1:168124478 168124478 A	
43	129 G	-1:168124477 168124477 G	
44 R	130 A	-1:168124476 168124476 A	R
44	131 G	-1:168124475 168124475 G	
44	132 A	-1:168124474 168124474 A	
45 E	133 G	-1:168124473 168124473 G	E
45	134 A	-1:168124472 168124472 A	
45	135 A	-1:168124471 168124471 A	
46 N	136 A	-1:168124470 168124470 A	N
46	137 A	-1:168124469 168124469 A	
46	138 T	-1:168124468 168124468 T	
47 E	139 G	-1:168124467 168124467 G	E
47	140 A	-1:168124466 168124466 A	
47	141 A	-1:168124465 168124465 A	
48 D	142 G	-1:168124464 168124464 G	D
48	143 A	-1:168124463 168124463 A	
48	144 C	-1:168124462 168124462 C	
49 K	145 A	-1:168124461 168124461 A	K
49	146 A	-1:168124460 168124460 A	
49	147 G	-1:168124459 168124459 G	
50 V	148 G	-1:168124458 168124458 G	V
50	149 T	-1:168124457 168124457 T	
50	150 T	-1:168124456 168124456 T	
51 N	151 A	-1:168124455 168124455 A	N
51	152 A	-1:168124454 168124454 A	
51	153 T	-1:168124453 168124453 T	
52 K	154 A	-1:168124452 168124452 A	K
52	155 A	-1:168124451 168124451 A	
52	156 A	-1:168124450 168124450 A	
53 A	157 G	-1:168124449 168124449 G	A
53	158 C	-1:168124448 168124448 C	
53	159 T	-1:168124447 168124447 T	
54 A	160 G	-1:168124446 168124446 G	A
54	161 C	-1:168124445 168124445 C	
54	162 C	-1:168124444 168124444 C	
55 K	163 A	-1:168124443 168124443 A	K
55	164 A	-1:168124442 168124442 A	
55	165 G	-1:168124441 168124441 G	
56 H	166 C	-1:168114584 168114584 C	H
56	167 A	-1:168114583 168114583 A	
56	168 T	-1:168114582 168114582 T	
57 L	169 T	-1:168114581 168114581 T	L
57	170 T	-1:168114580 168114580 T	
57	171 G	-1:168114579 168114579 G	
58 K	172 A	-1:168114578 168114578 A	K
58	173 A	-1:168114577 168114577 A	
58	174 G	-1:168114576 168114576 G	
59 T	175 A	-1:168114575 168114575 A	T
59	176 C	-1:168114574 168114574 C	
59	177 A	-1:168114573 168114573 A	
60 L	178 C	-1:168114572 168114572 C	L
60	179 T	-1:168114571 168114571 T	
60	180 T	-1:168114570 168114570 T	
61 R	181 C	-1:168114569 168114569 C	R
61	182 G	-1:168114568 168114568 G	
61	183 T	-1:168114567 168114567 T	
62 H	184 C	-1:168114566 168114566 C	H
62	185 A	-1:168114565 168114565 A	
62	186 C	-1:168114564 168114564 C	
63 P	187 C	-1:168114563 168114563 C	P
63	188 C	-1:168114562 168114562 C	
63	189 T	-1:168114561 168114561 T	
64 C	190 T	-1:168114560 168114560 T	C
64	191 G	-1:168114559 168114559 G	
64	192 C	-1:168114558 168114558 C	
65 L	193 T	-1:168114557 168114557 T	L
65	194 T	-1:168114556 168114556 T	
65	195 G	-1:168114555 168114555 G	
66 L	196 C	-1:168114554 168114554 C	L
66	197 T	-1:168114553 168114553 T	
66	198 A	-1:168114552 168114552 A	
67 R	199 A	-1:168114551 168114551 A	R
67	200 G	-1:168114550 168114550 G	
67	201 A	-1:168114549 168114549 A	
68 F	202 T	-1:168114548 168114548 T	F
68	203 T	-1:168114547 168114547 T	
68	204 T	-1:168114546 168114546 T	
69 L	205 T	-1:168114545 168114545 T	L
69	206 T	-1:168114544 168114544 T	
69	207 A	-1:168114543 168114543 A	
70 S	208 T	-1:168114542 168114542 T	S
70	209 C	-1:168114541 168114541 C	
70	210 T	-1:168114540 168114540 T	
71 C	211 T	-1:168114539 168114539 T	C
71	212 G	-1:168114538 168114538 G	
71	213 T	-1:168114537 168114537 T	
72 T	214 A	-1:168114536 168114536 A	T
72	215 C	-1:168114535 168114535 C	
72	216 T	-1:168114534 168114534 T	
73 V	217 G	-1:168114533 168114533 G	V
73	218 T	-1:168114532 168114532 T	
73	219 G	-1:168114531 168114531 G	
74 E	220 G	-1:168114530 168114530 G	E
74	221 A	-1:168114529 168114529 A	
74	222 A	-1:168114528 168114528 A	
75 A	223 G	-1:168114527 168114527 G	A
75	224 C	-1:168114526 168114526 C	
75	225 G	-1:168114525 168114525 G	
76 D	226 G	-1:168114524 168114524 G	D
76	227 A	-1:168114523 168114523 A	
76	228 T	-1:168114522 168114522 T	
77 G	229 G	-1:168114521 168114521 G	G
77	230 G	-1:168114520 168114520 G	
77	231 C	-1:168114519 168114519 C	
78 I	232 A	-1:168114518 168114518 A	I
78	233 T	-1:168114517 168114517 T	
78	234 T	-1:168114516 168114516 T	
79 H	235 C	-1:168114515 168114515 C	H
79	236 A	-1:168114514 168114514 A	
79	237 T	-1:168114513 168114513 T	
80 L	238 C	-1:168114512 168114512 C	L
80	239 T	-1:168114511 168114511 T	
80	240 T	-1:168114510 168114510 T	
81 V	241 G	-1:168114509 168114509 G	V
81	242 T	-1:168114508 168114508 T	
81	243 C	-1:168114507 168114507 C	
82 T	244 A	-1:168114506 168114506 A	T
82	245 C	-1:168114505 168114505 C	
82	246 T	-1:168114504 168114504 T	
83 E	247 G	-1:168114503 168114503 G	E
83	248 A	-1:168114502 168114502 A	
83	249 G	-1:168114501 168114501 G	
84 R	250 C	-1:168114500 168114500 C	R
84	251 G	-1:168114499 168114499 G	
84	252 A	-1:168114498 168114498 A	
85 V	253 G	-1:168114497 168114497 G	V
85	254 T	-1:168114496 168114496 T	
85	255 A	-1:168114495 168114495 A	
86 Q	256 C	-1:168114494 168114494 C	Q
86	257 A	-1:168114493 168114493 A	
86	258 G	-1:168114492 168114492 G	
87 P	259 C	-1:168114491 168114491 C	P
87	260 C	-1:168114490 168114490 C	
87	261 C	-1:168114489 168114489 C	
88 L	262 C	-1:168114488 168114488 C	L
88	263 T	-1:168114487 168114487 T	
88	264 G	-1:168114486 168114486 G	
89 E	265 G	-1:168114485 168114485 G	E
89	266 A	-1:168114484 168114484 A	
89	267 A	-1:168114483 168114483 A	
90 V	268 G	-1:168114482 168114482 G	V
90	269 T	-1:168114481 168114481 T	
90	270 G	-1:168114480 168114480 G	
91 A	271 G	-1:168114479 168114479 G	A
91	272 C	-1:168114478 168114478 C	
91	273 T	-1:168114477 168114477 T	
92 L	274 T	-1:168114476 168114476 T	L
92	275 T	-1:168114475 168114475 T	
92	276 G	-1:168114474 168114474 G	
93 E	277 G	-1:168114473 168114473 G	E
93	278 A	-1:168114472 168114472 A	
93	279 A	-1:168114471 168114471 A	
94 T	280 A	-1:168114470 168114470 A	T
94	281 C	-1:168114469 168114469 C	
94	282 A	-1:168114468 168114468 A	
95 L	283 T	-1:168114467 168114467 T	L
95	284 T	-1:168114466 168114466 T	
95	285 G	-1:168114465 168114465 G	
96 S	286 T	-1:168114464 168114464 T	S
96	287 C	-1:168114463 168114463 C	
96	288 T	-1:168114462 168114462 T	
97 S	289 T	-1:168114461 168114461 T	S
97	290 C	-1:168114460 168114460 C	
97	291 T	-1:168114459 168114459 T	
98 A	292 G	-1:168114458 168114458 G	A
98	293 C	-1:168114457 168114457 C	
98	294 A	-1:168114456 168114456 A	
99 E	295 G	-1:168114455 168114455 G	E
99	296 A	-1:168114454 168114454 A	
99	297 G	-1:168114453 168114453 G	
100 V	298 G	-1:168114452 168114452 G	V
100	299 T	-1:168114451 168114451 T	
100	300 C	-1:168114450 168114450 C	
101 C	301 T	-1:168114449 168114449 T	C
101	302 G	-1:168114448 168114448 G	
101	303 T	-1:168114447 168114447 T	
102 A	304 G	-1:168114446 168114446 G	A
102	305 C	-1:168114445 168114445 C	
102	306 T	-1:168114444 168114444 T	
103 G	307 G	-1:168114443 168114443 G	G
103	308 G	-1:168114442 168114442 G	
103	309 G	-1:168114441 168114441 G	
104 I	310 A	-1:168114440 168114440 A	I
104	311 T	-1:168114439 168114439 T	
104	312 C	-1:168114438 168114438 C	
105 Y	313 T	-1:168114437 168114437 T	Y
105	314 A	-1:168114436 168114436 A	
105	315 T	-1:168114435 168114435 T	
106 D	316 G	-1:168114434 168114434 G	D
106	317 A	-1:168114433 168114433 A	
106	318 C	-1:168114432 168114432 C	
107 I	319 A	-1:168114431 168114431 A	I
107	320 T	-1:168114430 168114430 T	
107	321 A	-1:168114429 168114429 A	
108 L	322 T	-1:168114428 168114428 T	L
108	323 T	-1:168114427 168114427 T	
108	324 G	-1:168114426 168114426 G	
109 L	325 C	-1:168114425 168114425 C	L
109	326 T	-1:168114424 168114424 T	
109	327 G	-1:168114423 168114423 G	
110 A	328 G	-1:168114422 168114422 G	A
110	329 C	-1:168114421 168114421 C	
110	330 T	-1:168114420 168114420 T	
111 L	331 C	-1:168114419 168114419 C	L
111	332 T	-1:168114418 168114418 T	
111	333 T	-1:168114417 168114417 T	
112 I	334 A	-1:168114416 168114416 A	I
112	335 T	-1:168114415 168114415 T	
112	336 C	-1:168114414 168114414 C	
113 F	337 T	-1:168114413 168114413 T	F
113	338 T	-1:168114412 168114412 T	
113	339 C	-1:168114411 168114411 C	
114 L	340 C	-1:168114410 168114410 C	L
114	341 T	-1:168114409 168114409 T	
114	342 T	-1:168114408 168114408 T	
115 H	343 C	-1:168114407 168114407 C	H
115	344 A	-1:168114406 168114406 A	
115	345 T	-1:168114405 168114405 T	
116 D	346 G	-1:168114404 168114404 G	D
116	347 A	-1:168114403 168114403 A	
116	348 C	-1:168114402 168114402 C	
117 R	349 A	-1:168114401 168114401 A	R
117	350 G	-1:168114400 168114400 G	
117	351 A	-1:168114399 168114399 A	
118 G	352 G	-1:168111856 168111856 G	G
118	353 G	-1:168111855 168111855 G	
118	354 A	-1:168111854 168111854 A	
119 H	355 C	-1:168111853 168111853 C	H
119	356 A	-1:168111852 168111852 A	
119	357 C	-1:168111851 168111851 C	
120 L	358 C	-1:168111850 168111850 C	L
120	359 T	-1:168111849 168111849 T	
120	360 A	-1:168111848 168111848 A	
121 T	361 A	-1:168111847 168111847 A	T
121	362 C	-1:168111846 168111846 C	
121	363 A	-1:168111845 168111845 A	
122 H	364 C	-1:168111844 168111844 C	H
122	365 A	-1:168111843 168111843 A	
122	366 C	-1:168111842 168111842 C	
123 N	367 A	-1:168111841 168111841 A	N
123	368 A	-1:168111840 168111840 A	
123	369 T	-1:168111839 168111839 T	
124 N	370 A	-1:168111838 168111838 A	N
124	371 A	-1:168111837 168111837 A	
124	372 T	-1:168111836 168111836 T	
125 V	373 G	-1:168111835 168111835 G	V
125	374 T	-1:168111834 168111834 T	
125	375 C	-1:168111833 168111833 C	
126 C	376 T	-1:168111832 168111832 T	C
126	377 G	-1:168111831 168111831 G	
126	378 T	-1:168111830 168111830 T	
127 L	379 T	-1:168111829 168111829 T	L
127	380 T	-1:168111828 168111828 T	
127	381 A	-1:168111827 168111827 A	
128 S	382 T	-1:168111826 168111826 T	S
128	383 C	-1:168111825 168111825 C	
128	384 A	-1:168111824 168111824 A	
129 S	385 T	-1:168111823 168111823 T	S
129	386 C	-1:168111822 168111822 C	
129	387 T	-1:168111821 168111821 T	
130 V	388 G	-1:168111820 168111820 G	V
130	389 T	-1:168111819 168111819 T	
130	390 G	-1:168111818 168111818 G	
131 F	391 T	-1:168111817 168111817 T	F
131	392 T	-1:168111816 168111816 T	
131	393 T	-1:168111815 168111815 T	
132 V	394 G	-1:168111814 168111814 G	V
132	395 T	-1:168111813 168111813 T	
132	396 G	-1:168111812 168111812 G	
133 S	397 A	-1:168111811 168111811 A	S
133	398 G	-1:168111810 168111810 G	
133	399 T	-1:168111809 168111809 T	
134 E	400 G	-1:168111808 168111808 G	E
134	401 A	-1:168111807 168111807 A	
134	402 A	-1:168111806 168111806 A	
135 D	403 G	-1:168111805 168111805 G	D
135	404 A	-1:168111804 168111804 A	
135	405 T	-1:168111803 168111803 T	
136 G	406 G	-1:168111802 168111802 G	G
136	407 G	-1:168111801 168111801 G	
136	408 A	-1:168111800 168111800 A	
137 H	409 C	-1:168111799 168111799 C	H
137	410 A	-1:168111798 168111798 A	
137	411 C	-1:168111797 168111797 C	
138 W	412 T	-1:168111796 168111796 T	W
138	413 G	-1:168111795 168111795 G	
138	414 G	-1:168111794 168111794 G	
139 K	415 A	-1:168111793 168111793 A	K
139	416 A	-1:168111792 168111792 A	
139	417 G	-1:168111791 168111791 G	
140 L	418 C	-1:168111790 168111790 C	L
140	419 T	-1:168111789 168111789 T	
140	420 A	-1:168111788 168111788 A	
141 G	421 G	-1:168111787 168111787 G	G
141	422 G	-1:168111786 168111786 G	
141	423 A	-1:168111785 168111785 A	
142 G	424 G	-1:168111784 168111784 G	G
142	425 G	-1:168111783 168111783 G	
142	426 A	-1:168111782 168111782 A	
143 M	427 A	-1:168111781 168111781 A	M
143	428 T	-1:168111780 168111780 T	
143	429 G	-1:168111779 168111779 G	
144 E	430 G	-1:168111778 168111778 G	E
144	431 A	-1:168111777 168111777 A	
144	432 A	-1:168111776 168111776 A	
145 T	433 A	-1:168111775 168111775 A	T
145	434 C	-1:168111774 168111774 C	
145	435 T	-1:168111773 168111773 T	
146 V	436 G	-1:168111772 168111772 G	V
146	437 T	-1:168111771 168111771 T	
146	438 T	-1:168111770 168111770 T	
147 C	439 T	-1:168111769 168111769 T	C
147	440 G	-1:168111768 168111768 G	
147	441 T	-1:168111767 168111767 T	
148 K	442 A	-1:168111766 168111766 A	K
148	443 A	-1:168111765 168111765 A	
148	444 A	-1:168111764 168111764 A	
149 V	445 G	-1:168111763 168111763 G	V
149	446 T	-1:168111762 168111762 T	
149	447 T	-1:168111761 168111761 T	
150 S	448 T	-1:168111760 168111760 T	S
150	449 C	-1:168111759 168111759 C	
150	450 T	-1:168111758 168111758 T	
151 Q	451 C	-1:168111757 168111757 C	Q
151	452 A	-1:168111756 168111756 A	
151	453 G	-1:168111755 168111755 G	
152 A	454 G	-1:168111754 168111754 G	A
152	455 C	-1:168111753 168111753 C	
152	456 C	-1:168111752 168111752 C	
153 T	457 A	-1:168111751 168111751 A	T
153	458 C	-1:168111750 168111750 C	
153	459 A	-1:168111749 168111749 A	
154 P	460 C	-1:168111748 168111748 C	P
154	461 C	-1:168111747 168111747 C	
154	462 A	-1:168111746 168111746 A	
155 E	463 G	-1:168111745 168111745 G	E
155	464 A	-1:168111744 168111744 A	
155	465 G	-1:168111743 168111743 G	
156 F	466 T	-1:168109517 168109517 T	F
156	467 T	-1:168109516 168109516 T	
156	468 T	-1:168109515 168109515 T	
157 L	469 C	-1:168109514 168109514 C	L
157	470 T	-1:168109513 168109513 T	
157	471 G	-1:168109512 168109512 G	
158 R	472 A	-1:168109511 168109511 A	R
158	473 G	-1:168109510 168109510 G	
158	474 G	-1:168109509 168109509 G	
159 S	475 A	-1:168109508 168109508 A	S
159	476 G	-1:168109507 168109507 G	
159	477 T	-1:168109506 168109506 T	
160 I	478 A	-1:168109505 168109505 A	I
160	479 T	-1:168109504 168109504 T	
160	480 T	-1:168109503 168109503 T	
161 Q	481 C	-1:168109502 168109502 C	Q
161	482 A	-1:168109501 168109501 A	
161	483 G	-1:168109500 168109500 G	
162 S	484 T	-1:168109499 168109499 T	S
162	485 C	-1:168109498 168109498 C	
162	486 A	-1:168109497 168109497 A	
163 I	487 A	-1:168109496 168109496 A	I
163	488 T	-1:168109495 168109495 T	
163	489 A	-1:168109494 168109494 A	
164 R	490 A	-1:168109493 168109493 A	R
164	491 G	-1:168109492 168109492 G	
164	492 A	-1:168109491 168109491 A	
165 D	493 G	-1:168109490 168109490 G	D
165	494 A	-1:168109489 168109489 A	
165	495 C	-1:168109488 168109488 C	
166 P	496 C	-1:168109487 168109487 C	P
166	497 C	-1:168109486 168109486 C	
166	498 A	-1:168109485 168109485 A	
167 A	499 G	-1:168109484 168109484 G	A
167	500 C	-1:168109483 168109483 C	
167	501 A	-1:168109482 168109482 A	
168 S	502 T	-1:168109481 168109481 T	S
168	503 C	-1:168109480 168109480 C	
168	504 T	-1:168109479 168109479 T	
169 I	505 A	-1:168109478 168109478 A	I
169	506 T	-1:168109477 168109477 T	
169	507 C	-1:168109476 168109476 C	
170 P	508 C	-1:168109475 168109475 C	P
170	509 C	-1:168109474 168109474 C	
170	510 T	-1:168109473 168109473 T	
171 P	511 C	-1:168109472 168109472 C	P
171	512 C	-1:168109471 168109471 C	
171	513 T	-1:168109470 168109470 T	
172 E	514 G	-1:168109469 168109469 G	E
172	515 A	-1:168109468 168109468 A	
172	516 A	-1:168109467 168109467 A	
173 E	517 G	-1:168109466 168109466 G	E
173	518 A	-1:168109465 168109465 A	
173	519 G	-1:168109464 168109464 G	
174 M	520 A	-1:168109463 168109463 A	M
174	521 T	-1:168109462 168109462 T	
174	522 G	-1:168109461 168109461 G	
175 S	523 T	-1:168106122 168106122 T	S
175	524 C	-1:168106121 168106121 C	
175	525 T	-1:168106120 168106120 T	
176 P	526 C	-1:168106119 168106119 C	P
176	527 C	-1:168106118 168106118 C	
176	528 A	-1:168106117 168106117 A	
177 E	529 G	-1:168106116 168106116 G	E
177	530 A	-1:168106115 168106115 A	
177	531 A	-1:168106114 168106114 A	
178 F	532 T	-1:168106113 168106113 T	F
178	533 T	-1:168106112 168106112 T	
178	534 C	-1:168106111 168106111 C	
179 T	535 A	-1:168106110 168106110 A	T
179	536 C	-1:168106109 168106109 C	
179	537 A	-1:168106108 168106108 A	
180 T	538 A	-1:168106107 168106107 A	T
180	539 C	-1:168106106 168106106 C	
180	540 T	-1:168106105 168106105 T	
181 L	541 C	-1:168106104 168106104 C	L
181	542 T	-1:168106103 168106103 T	
181	543 C	-1:168106102 168106102 C	
182 P	544 C	-1:168106101 168106101 C	P
182	545 C	-1:168106100 168106100 C	
182	546 A	-1:168106099 168106099 A	
183 E	547 G	-1:168106098 168106098 G	E
183	548 A	-1:168106097 168106097 A	
183	549 G	-1:168106096 168106096 G	
184 C	550 T	-1:168106095 168106095 T	C
184	551 G	-1:168106094 168106094 G	
184	552 T	-1:168106093 168106093 T	
185 H	553 C	-1:168106092 168106092 C	H
185	554 A	-1:168106091 168106091 A	
185	555 T	-1:168106090 168106090 T	
186 G	556 G	-1:168106089 168106089 G	G
186	557 G	-1:168106088 168106088 G	
186	558 A	-1:168106087 168106087 A	
187 H	559 C	-1:168106086 168106086 C	H
187	560 A	-1:168106085 168106085 A	
187	561 T	-1:168106084 168106084 T	
188 A	562 G	-1:168106083 168106083 G	A
188	563 C	-1:168106082 168106082 C	
188	564 C	-1:168106081 168106081 C	
189 R	565 C	-1:168106080 168106080 C	R
189	566 G	-1:168106079 168106079 G	
189	567 G	-1:168106078 168106078 G	
190 D	568 G	-1:168106077 168106077 G	D
190	569 A	-1:168106076 168106076 A	
190	570 T	-1:168106075 168106075 T	
191 A	571 G	-1:168106074 168106074 G	A
191	572 C	-1:168106073 168106073 C	
191	573 C	-1:168106072 168106072 C	
192 F	574 T	-1:168106071 168106071 T	F
192	575 T	-1:168106070 168106070 T	
192	576 T	-1:168106069 168106069 T	
193 S	577 T	-1:168106068 168106068 T	S
193	578 C	-1:168106067 168106067 C	
193	579 A	-1:168106066 168106066 A	
194 F	580 T	-1:168106065 168106065 T	F
194	581 T	-1:168106064 168106064 T	
194	582 T	-1:168106063 168106063 T	
195 G	583 G	-1:168106062 168106062 G	G
195	584 G	-1:168106061 168106061 G	
195	585 A	-1:168106060 168106060 A	
196 T	586 A	-1:168106059 168106059 A	T
196	587 C	-1:168106058 168106058 C	
196	588 A	-1:168106057 168106057 A	
197 L	589 T	-1:168106056 168106056 T	L
197	590 T	-1:168106055 168106055 T	
197	591 G	-1:168106054 168106054 G	
198 V	592 G	-1:168106053 168106053 G	V
198	593 T	-1:168106052 168106052 T	
198	594 G	-1:168106051 168106051 G	
199 E	595 G	-1:168106050 168106050 G	E
199	596 A	-1:168106049 168106049 A	
199	597 A	-1:168106048 168106048 A	
200 S	598 A	-1:168106047 168106047 A	S
200	599 G	-1:168106046 168106046 G	
200	600 T	-1:168106045 168106045 T	
201 L	601 T	-1:168106044 168106044 T	L
201	602 T	-1:168106043 168106043 T	
201	603 G	-1:168106042 168106042 G	
202 L	604 C	-1:168106041 168106041 C	L
202	605 T	-1:168106040 168106040 T	
202	606 C	-1:168106039 168106039 C	
203 T	607 A	-1:168106038 168106038 A	T
203	608 C	-1:168106037 168106037 C	
203	609 A	-1:168106036 168106036 A	
204 I	610 A	-1:168106035 168106035 A	I
204	611 T	-1:168106034 168106034 T	
204	612 C	-1:168106033 168106033 C	
205 L	613 T	-1:168106032 168106032 T	L
205	614 T	-1:168106031 168106031 T	
205	615 A	-1:168106030 168106030 A	
206 N	616 A	-1:168106029 168106029 A	N
206	617 A	-1:168106028 168106028 A	
206	618 T	-1:168106027 168106027 T	
207 E	619 G	-1:168106026 168106026 G	E
207	620 A	-1:168106025 168106025 A	
207	621 A	-1:168106024 168106024 A	
208 Q	622 C	-1:168106023 168106023 C	Q
208	623 A	-1:168106022 168106022 A	
208	624 G	-1:168106021 168106021 G	
209 V	625 G	-1:168106020 168106020 G	V
209	626 T	-1:168104804 168104804 T	
209	627 T	-1:168104803 168104803 T	
210 S	628 T	-1:168104802 168104802 T	S
210	629 C	-1:168104801 168104801 C	
210	630 A	-1:168104800 168104800 A	
211 A	631 G	-1:168104799 168104799 G	A
211	632 C	-1:168104798 168104798 C	
211	633 G	-1:168104797 168104797 G	
212 D	634 G	-1:168104796 168104796 G	D
212	635 A	-1:168104795 168104795 A	
212	636 T	-1:168104794 168104794 T	
213 V	637 G	-1:168104793 168104793 G	V
213	638 T	-1:168104792 168104792 T	
213	639 T	-1:168104791 168104791 T	
214 L	640 C	-1:168104790 168104790 C	L
214	641 T	-1:168104789 168104789 T	
214	642 C	-1:168104788 168104788 C	
215 S	643 T	-1:168104787 168104787 T	S
215	644 C	-1:168104786 168104786 C	
215	645 C	-1:168104785 168104785 C	
216 S	646 A	-1:168104784 168104784 A	S
216	647 G	-1:168104783 168104783 G	
216	648 C	-1:168104782 168104782 C	
217 F	649 T	-1:168104781 168104781 T	F
217	650 T	-1:168104780 168104780 T	
217	651 T	-1:168104779 168104779 T	
218 Q	652 C	-1:168104778 168104778 C	Q
218	653 A	-1:168104777 168104777 A	
218	654 A	-1:168104776 168104776 A	
219 Q	655 C	-1:168104775 168104775 C	Q
219	656 A	-1:168104774 168104774 A	
219	657 G	-1:168104773 168104773 G	
220 T	658 A	-1:168104772 168104772 A	T
220	659 C	-1:168104771 168104771 C	
220	660 C	-1:168104770 168104770 C	
221 L	661 T	-1:168104769 168104769 T	L
221	662 T	-1:168104768 168104768 T	
221	663 G	-1:168104767 168104767 G	
222 H	664 C	-1:168104766 168104766 C	H
222	665 A	-1:168104765 168104765 A	
222	666 C	-1:168104764 168104764 C	
223 S	667 T	-1:168104763 168104763 T	S
223	668 C	-1:168104762 168104762 C	
223	669 A	-1:168104761 168104761 A	
224 T	670 A	-1:168104760 168104760 A	T
224	671 C	-1:168104759 168104759 C	
224	672 T	-1:168104758 168104758 T	
225 L	673 T	-1:168104757 168104757 T	L
225	674 T	-1:168104756 168104756 T	
225	675 G	-1:168104755 168104755 G	
226 L	676 C	-1:168104754 168104754 C	L
226	677 T	-1:168104753 168104753 T	
226	678 G	-1:168104752 168104752 G	
227 N	679 A	-1:168104751 168104751 A	N
227	680 A	-1:168104750 168104750 A	
227	681 T	-1:168104749 168104749 T	
228 P	682 C	-1:168104748 168104748 C	P
228	683 C	-1:168104747 168104747 C	
228	684 C	-1:168104746 168104746 C	
229 I	685 A	-1:168104745 168104745 A	I
229	686 T	-1:168104744 168104744 T	
229	687 T	-1:168104743 168104743 T	
230 P	688 C	-1:168104742 168104742 C	P
230	689 C	-1:168104741 168104741 C	
230	690 A	-1:168104740 168104740 A	
231 K	691 A	-1:168104739 168104739 A	K
231	692 A	-1:168104738 168104738 A	
231	693 A	-1:168104737 168104737 A	
232 C	694 T	-1:168104736 168104736 T	C
232	695 G	-1:168104735 168104735 G	
232	696 T	-1:168104734 168104734 T	
233 R	697 C	-1:168104733 168104733 C	R
233	698 G	-1:168104732 168104732 G	
233	699 G	-1:168104731 168104731 G	
234 P	700 C	-1:168104730 168104730 C	P
234	701 C	-1:168104729 168104729 C	
234	702 A	-1:168104728 168104728 A	
235 A	703 G	-1:168104727 168104727 G	A
235	704 C	-1:168104726 168104726 C	
235	705 G	-1:168104725 168104725 G	
236 L	706 C	-1:168104724 168104724 C	L
236	707 T	-1:168104723 168104723 T	
236	708 C	-1:168104722 168104722 C	
237 C	709 T	-1:168104721 168104721 T	C
237	710 G	-1:168104720 168104720 G	
237	711 C	-1:168104719 168104719 C	
238 T	712 A	-1:168104718 168104718 A	T
238	713 C	-1:168104717 168104717 C	
238	714 C	-1:168104716 168104716 C	
239 L	715 T	-1:168104715 168104715 T	L
239	716 T	-1:168104714 168104714 T	
239	717 A	-1:168104713 168104713 A	
240 L	718 C	-1:168104712 168104712 C	L
240	719 T	-1:168104711 168104711 T	
240	720 A	-1:168104710 168104710 A	
241 S	721 T	-1:168104709 168104709 T	S
241	722 C	-1:168104708 168104708 C	
241	723 T	-1:168104707 168104707 T	
242 H	724 C	-1:168104706 168104706 C	H
242	725 A	-1:168104705 168104705 A	
242	726 T	-1:168104704 168104704 T	
243 D	727 G	-1:168104703 168104703 G	D
243	728 A	-1:168104702 168104702 A	
243	729 C	-1:168104701 168104701 C	
244 F	730 T	-1:168104700 168104700 T	F
244	731 T	-1:168104699 168104699 T	
244	732 C	-1:168104698 168104698 C	
245 F	733 T	-1:168104697 168104697 T	F
245	734 T	-1:168104696 168104696 T	
245	735 C	-1:168104695 168104695 C	
246 R	736 A	-1:168104694 168104694 A	R
246	737 G	-1:168104693 168104693 G	
246	738 A	-1:168102738 168102738 A	
247 N	739 A	-1:168102737 168102737 A	N
247	740 A	-1:168102736 168102736 A	
247	741 T	-1:168102735 168102735 T	
248 D	742 G	-1:168102734 168102734 G	D
248	743 A	-1:168102733 168102733 A	
248	744 T	-1:168102732 168102732 T	
249 F	745 T	-1:168102731 168102731 T	F
249	746 T	-1:168102730 168102730 T	
249	747 T	-1:168102729 168102729 T	
250 L	748 C	-1:168102728 168102728 C	L
250	749 T	-1:168102727 168102727 T	
250	750 G	-1:168102726 168102726 G	
251 E	751 G	-1:168102725 168102725 G	E
251	752 A	-1:168102724 168102724 A	
251	753 A	-1:168102723 168102723 A	
252 V	754 G	-1:168102722 168102722 G	V
252	755 T	-1:168102721 168102721 T	
252	756 T	-1:168102720 168102720 T	
253 V	757 G	-1:168102719 168102719 G	V
253	758 T	-1:168102718 168102718 T	
253	759 G	-1:168102717 168102717 G	
254 N	760 A	-1:168102716 168102716 A	N
254	761 A	-1:168102715 168102715 A	
254	762 T	-1:168102714 168102714 T	
255 F	763 T	-1:168102713 168102713 T	F
255	764 T	-1:168102712 168102712 T	
255	765 C	-1:168102711 168102711 C	
256 L	766 T	-1:168102710 168102710 T	L
256	767 T	-1:168102709 168102709 T	
256	768 G	-1:168102708 168102708 G	
257 K	769 A	-1:168102707 168102707 A	K
257	770 A	-1:168102706 168102706 A	
257	771 A	-1:168102705 168102705 A	
258 S	772 A	-1:168102704 168102704 A	S
258	773 G	-1:168102703 168102703 G	
258	774 T	-1:168102702 168102702 T	
259 L	775 T	-1:168102701 168102701 T	L
259	776 T	-1:168102700 168102700 T	
259	777 A	-1:168102699 168102699 A	
260 T	778 A	-1:168102698 168102698 A	T
260	779 C	-1:168102697 168102697 C	
260	780 A	-1:168102696 168102696 A	
261 L	781 T	-1:168102695 168102695 T	L
261	782 T	-1:168102694 168102694 T	
261	783 G	-1:168102693 168102693 G	
262 K	784 A	-1:168102692 168102692 A	K
262	785 A	-1:168102691 168102691 A	
262	786 G	-1:168102690 168102690 G	
263 S	787 A	-1:168102689 168102689 A	S
263	788 G	-1:168102688 168102688 G	
263	789 T	-1:168102687 168102687 T	
264 E	790 G	-1:168102686 168102686 G	E
264	791 A	-1:168102685 168102685 A	
264	792 A	-1:168102684 168102684 A	
265 E	793 G	-1:168102683 168102683 G	E
265	794 A	-1:168102682 168102682 A	
265	795 G	-1:168102681 168102681 G	
266 E	796 G	-1:168102680 168102680 G	E
266	797 A	-1:168102679 168102679 A	
266	798 G	-1:168102678 168102678 G	
267 K	799 A	-1:168102677 168102677 A	K
267	800 A	-1:168102676 168102676 A	
267	801 A	-1:168102675 168102675 A	
268 T	802 A	-1:168102674 168102674 A	T
268	803 C	-1:168102673 168102673 C	
268	804 G	-1:168102672 168102672 G	
269 E	805 G	-1:168102671 168102671 G	E
269	806 A	-1:168102670 168102670 A	
269	807 A	-1:168102669 168102669 A	
270 F	808 T	-1:168102668 168102668 T	F
270	809 T	-1:168102667 168102667 T	
270	810 C	-1:168102666 168102666 C	
271 F	811 T	-1:168102665 168102665 T	F
271	812 T	-1:168102664 168102664 T	
271	813 T	-1:168102663 168102663 T	
272 K	814 A	-1:168102662 168102662 A	K
272	815 A	-1:168102661 168102661 A	
272	816 A	-1:168100273 168100273 A	
273 F	817 T	-1:168100272 168100272 T	F
273	818 T	-1:168100271 168100271 T	
273	819 T	-1:168100270 168100270 T	
274 L	820 C	-1:168100269 168100269 C	L
274	821 T	-1:168100268 168100268 T	
274	822 G	-1:168100267 168100267 G	
275 L	823 C	-1:168100266 168100266 C	L
275	824 T	-1:168100265 168100265 T	
275	825 G	-1:168100264 168100264 G	
276 D	826 G	-1:168100263 168100263 G	D
276	827 A	-1:168100262 168100262 A	
276	828 C	-1:168100261 168100261 C	
277 R	829 A	-1:168100260 168100260 A	R
277	830 G	-1:168100259 168100259 G	
277	831 A	-1:168100258 168100258 A	
278 V	832 G	-1:168100257 168100257 G	V
278	833 T	-1:168100256 168100256 T	
278	834 C	-1:168100255 168100255 C	
279 S	835 A	-1:168100254 168100254 A	S
279	836 G	-1:168100253 168100253 G	
279	837 C	-1:168100252 168100252 C	
280 C	838 T	-1:168100251 168100251 T	C
280	839 G	-1:168100250 168100250 G	
280	840 C	-1:168100249 168100249 C	
281 L	841 T	-1:168100248 168100248 T	L
281	842 T	-1:168100247 168100247 T	
281	843 G	-1:168100246 168100246 G	
282 S	844 T	-1:168100245 168100245 T	S
282	845 C	-1:168100244 168100244 C	
282	846 A	-1:168100243 168100243 A	
283 E	847 G	-1:168100242 168100242 G	E
283	848 A	-1:168100241 168100241 A	
283	849 G	-1:168100240 168100240 G	
284 E	850 G	-1:168100239 168100239 G	E
284	851 A	-1:168100238 168100238 A	
284	852 A	-1:168100237 168100237 A	
285 L	853 T	-1:168100236 168100236 T	L
285	854 T	-1:168100235 168100235 T	
285	855 G	-1:168100234 168100234 G	
286 I	856 A	-1:168100233 168100233 A	I
286	857 T	-1:168100232 168100232 T	
286	858 A	-1:168100231 168100231 A	
287 A	859 G	-1:168100230 168100230 G	A
287	860 C	-1:168100229 168100229 C	
287	861 T	-1:168100228 168100228 T	
288 S	862 T	-1:168100227 168100227 T	S
288	863 C	-1:168100226 168100226 C	
288	864 A	-1:168100225 168100225 A	
289 R	865 A	-1:168100224 168100224 A	R
289	866 G	-1:168100223 168100223 G	
289	867 G	-1:168100222 168100222 G	
290 L	868 T	-1:168100221 168100221 T	L
290	869 T	-1:168100220 168100220 T	
290	870 G	-1:168100219 168100219 G	
291 V	871 G	-1:168100218 168100218 G	V
291	872 T	-1:168100217 168100217 T	
291	873 G	-1:168100216 168100216 G	
292 P	874 C	-1:168100215 168100215 C	P
292	875 C	-1:168100214 168100214 C	
292	876 T	-1:168100213 168100213 T	
293 L	877 C	-1:168100212 168100212 C	L
293	878 T	-1:168100211 168100211 T	
293	879 T	-1:168100210 168100210 T	
294 L	880 C	-1:168100209 168100209 C	L
294	881 T	-1:168100208 168100208 T	
294	882 G	-1:168100207 168100207 G	
295 L	883 C	-1:168100206 168100206 C	L
295	884 T	-1:168100205 168100205 T	
295	885 T	-1:168100204 168100204 T	
296 N	886 A	-1:168100203 168100203 A	N
296	887 A	-1:168100202 168100202 A	
296	888 T	-1:168100201 168100201 T	
297 Q	889 C	-1:168100200 168100200 C	Q
297	890 A	-1:168100199 168100199 A	
297	891 G	-1:168100198 168100198 G	
298 L	892 T	-1:168100197 168100197 T	L
298	893 T	-1:168100196 168100196 T	
298	894 G	-1:168100195 168100195 G	
299 V	895 G	-1:168100194 168100194 G	V
299	896 T	-1:168100193 168100193 T	
299	897 G	-1:168100192 168100192 G	
300 F	898 T	-1:168100191 168100191 T	F
300	899 T	-1:168100190 168100190 T	
300	900 T	-1:168100189 168100189 T	
301 A	901 G	-1:168100188 168100188 G	A
301	902 C	-1:168100187 168100187 C	
301	903 A	-1:168100186 168100186 A	
302 E	904 G	-1:168100185 168100185 G	E
302	905 A	-1:168100184 168100184 A	
302	906 G	-1:168100183 168100183 G	
303 P	907 C	-1:168100182 168100182 C	P
303	908 C	-1:168100181 168100181 C	
303	909 A	-1:168100180 168100180 A	
304 V	910 G	-1:168100179 168100179 G	V
304	911 T	-1:168100178 168100178 T	
304	912 G	-1:168100177 168100177 G	
305 A	913 G	-1:168100176 168100176 G	A
305	914 C	-1:168100175 168100175 C	
305	915 T	-1:168100174 168100174 T	
306 V	916 G	-1:168100173 168100173 G	V
306	917 T	-1:168100172 168100172 T	
306	918 T	-1:168100171 168100171 T	
307 K	919 A	-1:168100170 168100170 A	K
307	920 A	-1:168100169 168100169 A	
307	921 G	-1:168100168 168100168 G	
308 S	922 A	-1:168100167 168100167 A	S
308	923 G	-1:168100166 168100166 G	
308	924 T	-1:168100165 168100165 T	
309 F	925 T	-1:168100164 168100164 T	F
309	926 T	-1:168100163 168100163 T	
309	927 T	-1:168100162 168100162 T	
310 L	928 C	-1:168100161 168100161 C	L
310	929 T	-1:168100160 168100160 T	
310	930 T	-1:168100159 168100159 T	
311 P	931 C	-1:168100158 168100158 C	P
311	932 C	-1:168100157 168100157 C	
311	933 T	-1:168100156 168100156 T	
312 Y	934 T	-1:168100155 168100155 T	Y
312	935 A	-1:168100154 168100154 A	
312	936 T	-1:168100153 168100153 T	
313 L	937 C	-1:168100152 168100152 C	L
313	938 T	-1:168100151 168100151 T	
313	939 G	-1:168100150 168100150 G	
314 L	940 C	-1:168100149 168100149 C	L
314	941 T	-1:168100148 168100148 T	
314	942 T	-1:168100147 168100147 T	
315 G	943 G	-1:168100146 168100146 G	G
315	944 G	-1:168100145 168100145 G	
315	945 C	-1:168100144 168100144 C	
316 P	946 C	-1:168100143 168100143 C	P
316	947 C	-1:168100142 168100142 C	
316	948 C	-1:168100141 168100141 C	
317 K	949 A	-1:168100140 168100140 A	K
317	950 A	-1:168100139 168100139 A	
317	951 A	-1:168100138 168100138 A	
318 K	952 A	-1:168100137 168100137 A	K
318	953 A	-1:168100136 168100136 A	
318	954 A	-1:168100135 168100135 A	
319 D	955 G	-1:168100134 168100134 G	D
319	956 A	-1:168098562 168098562 A	
319	957 T	-1:168098561 168098561 T	
320 H	958 C	-1:168098560 168098560 C	H
320	959 A	-1:168098559 168098559 A	
320	960 T	-1:168098558 168098558 T	
321 A	961 G	-1:168098557 168098557 G	A
321	962 C	-1:168098556 168098556 C	
321	963 G	-1:168098555 168098555 G	
322 Q	964 C	-1:168098554 168098554 C	Q
322	965 A	-1:168098553 168098553 A	
322	966 G	-1:168098552 168098552 G	
323 G	967 G	-1:168098551 168098551 G	G
323	968 G	-1:168098550 168098550 G	
323	969 A	-1:168098549 168098549 A	
324 E	970 G	-1:168098548 168098548 G	E
324	971 A	-1:168098547 168098547 A	
324	972 A	-1:168098546 168098546 A	
325 T	973 A	-1:168098545 168098545 A	T
325	974 C	-1:168098544 168098544 C	
325	975 T	-1:168098543 168098543 T	
326 P	976 C	-1:168098542 168098542 C	P
326	977 C	-1:168098541 168098541 C	
326	978 T	-1:168098540 168098540 T	
327 C	979 T	-1:168098539 168098539 T	C
327	980 G	-1:168098538 168098538 G	
327	981 C	-1:168098537 168098537 C	
328 L	982 T	-1:168098536 168098536 T	L
328	983 T	-1:168098535 168098535 T	
328	984 G	-1:168098534 168098534 G	
329 L	985 C	-1:168098533 168098533 C	L
329	986 T	-1:168098532 168098532 T	
329	987 C	-1:168098531 168098531 C	
330 S	988 T	-1:168098530 168098530 T	S
330	989 C	-1:168098529 168098529 C	
330	990 A	-1:168098528 168098528 A	
331 P	991 C	-1:168098527 168098527 C	P
331	992 C	-1:168098526 168098526 C	
331	993 A	-1:168098525 168098525 A	
332 A	994 G	-1:168098524 168098524 G	A
332	995 C	-1:168098523 168098523 C	
332	996 C	-1:168098522 168098522 C	
333 L	997 C	-1:168098521 168098521 C	L
333	998 T	-1:168098520 168098520 T	
333	999 G	-1:168098519 168098519 G	
334 F	1000 T	-1:168098518 168098518 T	F
334	1001 T	-1:168098517 168098517 T	
334	1002 C	-1:168098516 168098516 C	
335 Q	1003 C	-1:168098515 168098515 C	Q
335	1004 A	-1:168098514 168098514 A	
335	1005 G	-1:168098513 168098513 G	
336 S	1006 T	-1:168098512 168098512 T	S
336	1007 C	-1:168098511 168098511 C	
336	1008 A	-1:168098510 168098510 A	
337 R	1009 C	-1:168098509 168098509 C	R
337	1010 G	-1:168098508 168098508 G	
337	1011 G	-1:168098507 168098507 G	
338 V	1012 G	-1:168098506 168098506 G	V
338	1013 T	-1:168098505 168098505 T	
338	1014 G	-1:168098504 168098504 G	
339 I	1015 A	-1:168098503 168098503 A	I
339	1016 T	-1:168098502 168098502 T	
339	1017 C	-1:168098501 168098501 C	
340 P	1018 C	-1:168098500 168098500 C	P
340	1019 C	-1:168098499 168098499 C	
340	1020 C	-1:168098498 168098498 C	
341 V	1021 G	-1:168098497 168098497 G	V
341	1022 T	-1:168098496 168098496 T	
341	1023 G	-1:168098495 168098495 G	
342 L	1024 C	-1:168098494 168098494 C	L
342	1025 T	-1:168098493 168098493 T	
342	1026 T	-1:168098492 168098492 T	
343 L	1027 C	-1:168098491 168098491 C	L
343	1028 T	-1:168098490 168098490 T	
343	1029 C	-1:168098489 168098489 C	
344 Q	1030 C	-1:168098488 168098488 C	Q
344	1031 A	-1:168098487 168098487 A	
344	1032 G	-1:168098486 168098486 G	
345 L	1033 T	-1:168098485 168098485 T	L
345	1034 T	-1:168098484 168098484 T	
345	1035 G	-1:168098483 168098483 G	
346 F	1036 T	-1:168098482 168098482 T	F
346	1037 T	-1:168098481 168098481 T	
346	1038 T	-1:168098480 168098480 T	
347 E	1039 G	-1:168098479 168098479 G	E
347	1040 A	-1:168098478 168098478 A	
347	1041 A	-1:168098477 168098477 A	
348 V	1042 G	-1:168098476 168098476 G	V
348	1043 T	-1:168098475 168098475 T	
348	1044 T	-1:168098474 168098474 T	
349 H	1045 C	-1:168098473 168098473 C	H
349	1046 A	-1:168098472 168098472 A	
349	1047 T	-1:168098471 168098471 T	
350 E	1048 G	-1:168098470 168098470 G	E
350	1049 A	-1:168098469 168098469 A	
350	1050 A	-1:168098468 168098468 A	
351 E	1051 G	-1:168098467 168098467 G	E
351	1052 A	-1:168098466 168098466 A	
351	1053 G	-1:168098465 168098465 G	
352 H	1054 C	-1:168098464 168098464 C	H
352	1055 A	-1:168098463 168098463 A	
352	1056 T	-1:168098462 168098462 T	
353 V	1057 G	-1:168098461 168098461 G	V
353	1058 T	-1:168098460 168098460 T	
353	1059 G	-1:168098459 168098459 G	
354 R	1060 C	-1:168098458 168098458 C	R
354	1061 G	-1:168098457 168098457 G	
354	1062 G	-1:168098456 168098456 G	
355 M	1063 A	-1:168098455 168098455 A	M
355	1064 T	-1:168098454 168098454 T	
355	1065 G	-1:168098453 168098453 G	
356 V	1066 G	-1:168098452 168098452 G	V
356	1067 T	-1:168098451 168098451 T	
356	1068 G	-1:168098450 168098450 G	
357 L	1069 C	-1:168098449 168098449 C	L
357	1070 T	-1:168098448 168098448 T	
357	1071 G	-1:168098447 168098447 G	
358 L	1072 C	-1:168098446 168098446 C	L
358	1073 T	-1:168098445 168098445 T	
358	1074 G	-1:168098444 168098444 G	
359 S	1075 T	-1:168098443 168098443 T	S
359	1076 C	-1:168098442 168098442 C	
359	1077 T	-1:168098441 168098441 T	
360 H	1078 C	-1:168098440 168098440 C	H
360	1079 A	-1:168098439 168098439 A	
360	1080 C	-1:168098438 168098438 C	
361 I	1081 A	-1:168098437 168098437 A	I
361	1082 T	-1:168098436 168098436 T	
361	1083 C	-1:168098435 168098435 C	
362 E	1084 G	-1:168098434 168098434 G	E
362	1085 A	-1:168098433 168098433 A	
362	1086 G	-1:168098432 168098432 G	
363 A	1087 G	-1:168098431 168098431 G	A
363	1088 C	-1:168098430 168098430 C	
363	1089 C	-1:168098429 168098429 C	
364 Y	1090 T	-1:168098428 168098428 T	Y
364	1091 A	-1:168098427 168098427 A	
364	1092 C	-1:168098426 168098426 C	
365 V	1093 G	-1:168098425 168098425 G	V
365	1094 T	-1:168098424 168098424 T	
365	1095 G	-1:168098423 168098423 G	
366 E	1096 G	-1:168098422 168098422 G	E
366	1097 A	-1:168098421 168098421 A	
366	1098 G	-1:168098420 168098420 G	
367 H	1099 C	-1:168098419 168098419 C	H
367	1100 A	-1:168098418 168098418 A	
367	1101 C	-1:168098417 168098417 C	
368 F	1102 T	-1:168098416 168098416 T	F
368	1103 T	-1:168098415 168098415 T	
368	1104 C	-1:168098414 168098414 C	
369 T	1105 A	-1:168098413 168098413 A	T
369	1106 C	-1:168098412 168098412 C	
369	1107 T	-1:168098411 168098411 T	
370 Q	1108 C	-1:168098410 168098410 C	Q
370	1109 A	-1:168098409 168098409 A	
370	1110 G	-1:168098408 168098408 G	
371 E	1111 G	-1:168098407 168098407 G	E
371	1112 A	-1:168098406 168098406 A	
371	1113 G	-1:168098405 168098405 G	
372 Q	1114 C	-1:168098404 168098404 C	Q
372	1115 A	-1:168098403 168098403 A	
372	1116 G	-1:168098402 168098402 G	
373 L	1117 C	-1:168098401 168098401 C	L
373	1118 T	-1:168098400 168098400 T	
373	1119 G	-1:168098399 168098399 G	
374 K	1120 A	-1:168098398 168098398 A	K
374	1121 A	-1:168098397 168098397 A	
374	1122 G	-1:168098396 168098396 G	
375 K	1123 A	-1:168098395 168098395 A	K
375	1124 A	-1:168098394 168098394 A	
375	1125 A	-1:168098393 168098393 A	
376 V	1126 G	-1:168098392 168098392 G	V
376	1127 T	-1:168098391 168098391 T	
376	1128 C	-1:168098390 168098390 C	
377 I	1129 A	-1:168098389 168098389 A	I
377	1130 T	-1:168098388 168098388 T	
377	1131 C	-1:168098387 168098387 C	
378 L	1132 T	-1:168098386 168098386 T	L
378	1133 T	-1:168098385 168098385 T	
378	1134 G	-1:168098384 168098384 G	
379 P	1135 C	-1:168098383 168098383 C	P
379	1136 C	-1:168098382 168098382 C	
379	1137 A	-1:168098381 168098381 A	
380 Q	1138 C	-1:168098380 168098380 C	Q
380	1139 A	-1:168098379 168098379 A	
380	1140 G	-1:168098378 168098378 G	
381 V	1141 G	-1:168094977 168094977 G	V
381	1142 T	-1:168094976 168094976 T	
381	1143 T	-1:168094975 168094975 T	
382 L	1144 T	-1:168094974 168094974 T	L
382	1145 T	-1:168094973 168094973 T	
382	1146 G	-1:168094972 168094972 G	
383 L	1147 C	-1:168094971 168094971 C	L
383	1148 T	-1:168094970 168094970 T	
383	1149 G	-1:168094969 168094969 G	
384 G	1150 G	-1:168094968 168094968 G	G
384	1151 G	-1:168094967 168094967 G	
384	1152 C	-1:168094966 168094966 C	
385 L	1153 C	-1:168094965 168094965 C	L
385	1154 T	-1:168094964 168094964 T	
385	1155 G	-1:168094963 168094963 G	
386 R	1156 C	-1:168094962 168094962 C	R
386	1157 G	-1:168094961 168094961 G	
386	1158 T	-1:168094960 168094960 T	
387 D	1159 G	-1:168094959 168094959 G	D
387	1160 A	-1:168094958 168094958 A	
387	1161 T	-1:168094957 168094957 T	
388 T	1162 A	-1:168094956 168094956 A	T
388	1163 C	-1:168094955 168094955 C	
388	1164 T	-1:168094954 168094954 T	
389 S	1165 A	-1:168094953 168094953 A	S
389	1166 G	-1:168094952 168094952 G	
389	1167 C	-1:168094951 168094951 C	
390 D	1168 G	-1:168094950 168094950 G	D
390	1169 A	-1:168094949 168094949 A	
390	1170 T	-1:168094948 168094948 T	
391 S	1171 T	-1:168094947 168094947 T	S
391	1172 C	-1:168094946 168094946 C	
391	1173 C	-1:168094945 168094945 C	
392 I	1174 A	-1:168094944 168094944 A	I
392	1175 T	-1:168094943 168094943 T	
392	1176 T	-1:168094942 168094942 T	
393 V	1177 G	-1:168094941 168094941 G	V
393	1178 T	-1:168094940 168094940 T	
393	1179 G	-1:168094939 168094939 G	
394 A	1180 G	-1:168094938 168094938 G	A
394	1181 C	-1:168094937 168094937 C	
394	1182 A	-1:168094936 168094936 A	
395 I	1183 A	-1:168094935 168094935 A	I
395	1184 T	-1:168094934 168094934 T	
395	1185 T	-1:168094933 168094933 T	
396 T	1186 A	-1:168094932 168094932 A	T
396	1187 C	-1:168094931 168094931 C	
396	1188 T	-1:168094930 168094930 T	
397 L	1189 C	-1:168094929 168094929 C	L
397	1190 T	-1:168094928 168094928 T	
397	1191 G	-1:168094927 168094927 G	
398 H	1192 C	-1:168094926 168094926 C	H
398	1193 A	-1:168094925 168094925 A	
398	1194 T	-1:168094924 168094924 T	
399 S	1195 A	-1:168094923 168094923 A	S
399	1196 G	-1:168094922 168094922 G	
399	1197 C	-1:168094921 168094921 C	
400 L	1198 C	-1:168094920 168094920 C	L
400	1199 T	-1:168094919 168094919 T	
400	1200 A	-1:168094918 168094918 A	
401 A	1201 G	-1:168094917 168094917 G	A
401	1202 C	-1:168094916 168094916 C	
401	1203 A	-1:168094915 168094915 A	
402 V	1204 G	-1:168094914 168094914 G	V
402	1205 T	-1:168094913 168094913 T	
402	1206 G	-1:168094912 168094912 G	
403 L	1207 C	-1:168094911 168094911 C	L
403	1208 T	-1:168094910 168094910 T	
403	1209 G	-1:168094909 168094909 G	
404 V	1210 G	-1:168094908 168094908 G	V
404	1211 T	-1:168094907 168094907 T	
404	1212 C	-1:168094906 168094906 C	
405 S	1213 T	-1:168094905 168094905 T	S
405	1214 C	-1:168094904 168094904 C	
405	1215 T	-1:168094903 168094903 T	
406 L	1216 C	-1:168094902 168094902 C	L
406	1217 T	-1:168094901 168094901 T	
406	1218 G	-1:168094900 168094900 G	
407 L	1219 C	-1:168094899 168094899 C	L
407	1220 T	-1:168094898 168094898 T	
407	1221 T	-1:168094897 168094897 T	
408 G	1222 G	-1:168094896 168094896 G	G
408	1223 G	-1:168094895 168094895 G	
408	1224 A	-1:168094894 168094894 A	
409 P	1225 C	-1:168094893 168094893 C	P
409	1226 C	-1:168094892 168094892 C	
409	1227 A	-1:168094891 168094891 A	
410 E	1228 G	-1:168094890 168094890 G	E
410	1229 A	-1:168094889 168094889 A	
410	1230 G	-1:168094888 168094888 G	
411 V	1231 G	-1:168094887 168094887 G	V
411	1232 T	-1:168094886 168094886 T	
411	1233 G	-1:168094885 168094885 G	
412 V	1234 G	-1:168094884 168094884 G	V
412	1235 T	-1:168094883 168094883 T	
412	1236 T	-1:168094882 168094882 T	
413 V	1237 G	-1:168094881 168094881 G	V
413	1238 T	-1:168094880 168094880 T	
413	1239 G	-1:168094879 168094879 G	
414 G	1240 G	-1:168094878 168094878 G	G
414	1241 G	-1:168094877 168094877 G	
414	1242 A	-1:168094876 168094876 A	
415 G	1243 G	-1:168094875 168094875 G	G
415	1244 G	-1:168094874 168094874 G	
415	1245 A	-1:168094873 168094873 A	
416 E	1246 G	-1:168094872 168094872 G	E
416	1247 A	-1:168094871 168094871 A	
416	1248 A	-1:168094870 168094870 A	
417 R	1249 C	-1:168094869 168094869 C	R
417	1250 G	-1:168094868 168094868 G	
417	1251 A	-1:168094867 168094867 A	
418 T	1252 A	-1:168094866 168094866 A	T
418	1253 C	-1:168094865 168094865 C	
418	1254 C	-1:168094864 168094864 C	
419 K	1255 A	-1:168094863 168094863 A	K
419	1256 A	-1:168094862 168094862 A	
419	1257 G	-1:168094861 168094861 G	
420 I	1258 A	-1:168094860 168094860 A	I
420	1259 T	-1:168094859 168094859 T	
420	1260 C	-1:168094858 168094858 C	
421 F	1261 T	-1:168094857 168094857 T	F
421	1262 T	-1:168094856 168094856 T	
421	1263 C	-1:168094855 168094855 C	
422 K	1264 A	-1:168094854 168094854 A	K
422	1265 A	-1:168094853 168094853 A	
422	1266 A	-1:168094852 168094852 A	
423 R	1267 C	-1:168094851 168094851 C	R
423	1268 G	-1:168094850 168094850 G	
423	1269 C	-1:168094849 168094849 C	
424 T	1270 A	-1:168094848 168094848 A	T
424	1271 C	-1:168094847 168094847 C	
424	1272 T	-1:168094846 168094846 T	
425 A	1273 G	-1:168094845 168094845 G	A
425	1274 C	-1:168094844 168094844 C	
425	1275 C	-1:168094843 168094843 C	
426 P	1276 C	-1:168094842 168094842 C	P
426	1277 C	-1:168094841 168094841 C	
426	1278 A	-1:168094840 168094840 A	
427 S	1279 A	-1:168094839 168094839 A	S
427	1280 G	-1:168094838 168094838 G	
427	1281 T	-1:168094837 168094837 T	
428 F	1282 T	-1:168094836 168094836 T	F
428	1283 T	-1:168094835 168094835 T	
428	1284 T	-1:168094834 168094834 T	
429 T	1285 A	-1:168094833 168094833 A	T
429	1286 C	-1:168094832 168094832 C	
429	1287 T	-1:168094831 168094831 T	
430 K	1288 A	-1:168094830 168094830 A	K
430	1289 A	-1:168094829 168094829 A	
430	1290 A	-1:168094828 168094828 A	
431 N	1291 A	-1:168094827 168094827 A	N
431	1292 A	-1:168094826 168094826 A	
431	1293 T	-1:168094825 168094825 T	
432 T	1294 A	-1:168094824 168094824 A	T
432	1295 C	-1:168094823 168094823 C	
432	1296 T	-1:168094822 168094822 T	
433 D	1297 G	-1:168094821 168094821 G	D
433	1298 A	-1:168094820 168094820 A	
433	1299 C	-1:168094819 168094819 C	
434 L	1300 C	-1:168094818 168094818 C	L
434	1301 T	-1:168094817 168094817 T	
434	1302 T	-1:168094816 168094816 T	
435 S	1303 T	-1:168094815 168094815 T	S
435	1304 C	-1:168094814 168094814 C	
435	1305 T	-1:168094813 168094813 T	
436 L	1306 C	-1:168094812 168094812 C	L
436	1307 T	-1:168094811 168094811 T	
436	1308 A	-1:168094810 168094810 A	
437 E	1309 G	-1:168094809 168094809 G	E
437	1310 A	-1:168094808 168094808 A	
437	1311 A	-1:168094807 168094807 A	
438 D	1312 G	-1:168094806 168094806 G	D
438	1313 A	-1:168091722 168091722 A	
438	1314 T	-1:168091721 168091721 T	
439 S	1315 T	-1:168091720 168091720 T	S
439	1316 C	-1:168091719 168091719 C	
439	1317 T	-1:168091718 168091718 T	
440 P	1318 C	-1:168091717 168091717 C	P
440	1319 C	-1:168091716 168091716 C	
440	1320 T	-1:168091715 168091715 T	
441 M	1321 A	-1:168091714 168091714 A	M
441	1322 T	-1:168091713 168091713 T	
441	1323 G	-1:168091712 168091712 G	
442 C	1324 T	-1:168091711 168091711 T	C
442	1325 G	-1:168091710 168091710 G	
442	1326 T	-1:168091709 168091709 T	
443 V	1327 G	-1:168091708 168091708 G	V
443	1328 T	-1:168091707 168091707 T	
443	1329 C	-1:168091706 168091706 C	
444 V	1330 G	-1:168091705 168091705 G	V
444	1331 T	-1:168091704 168091704 T	
444	1332 C	-1:168091703 168091703 C	
445 C	1333 T	-1:168091702 168091702 T	C
445	1334 G	-1:168091701 168091701 G	
445	1335 C	-1:168091700 168091700 C	
446 S	1336 A	-1:168091699 168091699 A	S
446	1337 G	-1:168091698 168091698 G	
446	1338 C	-1:168091697 168091697 C	
447 H	1339 C	-1:168091696 168091696 C	H
447	1340 A	-1:168091695 168091695 A	
447	1341 T	-1:168091694 168091694 T	
448 H	1342 C	-1:168091693 168091693 C	H
448	1343 A	-1:168091692 168091692 A	
448	1344 C	-1:168091691 168091691 C	
449 S	1345 A	-1:168091690 168091690 A	S
449	1346 G	-1:168091689 168091689 G	
449	1347 T	-1:168091688 168091688 T	
450 Q	1348 C	-1:168091687 168091687 C	Q
450	1349 A	-1:168091686 168091686 A	
450	1350 G	-1:168091685 168091685 G	
451 I	1351 A	-1:168091684 168091684 A	I
451	1352 T	-1:168091683 168091683 T	
451	1353 C	-1:168091682 168091682 C	
452 S	1354 T	-1:168091681 168091681 T	S
452	1355 C	-1:168091680 168091680 C	
452	1356 G	-1:168091679 168091679 G	
453 P	1357 C	-1:168091678 168091678 C	P
453	1358 C	-1:168091677 168091677 C	
453	1359 A	-1:168091676 168091676 A	
454 I	1360 A	-1:168091675 168091675 A	I
454	1361 T	-1:168091674 168091674 T	
454	1362 C	-1:168091673 168091673 C	
455 L	1363 T	-1:168091672 168091672 T	L
455	1364 T	-1:168091671 168091671 T	
455	1365 G	-1:168091670 168091670 G	
456 E	1366 G	-1:168091669 168091669 G	E
456	1367 A	-1:168091668 168091668 A	
456	1368 G	-1:168091667 168091667 G	
457 N	1369 A	-1:168091666 168091666 A	N
457	1370 A	-1:168091665 168091665 A	
457	1371 C	-1:168091664 168091664 C	
458 P	1372 C	-1:168091663 168091663 C	P
458	1373 C	-1:168091662 168091662 C	
458	1374 C	-1:168091661 168091661 C	
459 F	1375 T	-1:168091660 168091660 T	F
459	1376 T	-1:168091659 168091659 T	
459	1377 C	-1:168091658 168091658 C	
460 S	1378 T	-1:168091657 168091657 T	S
460	1379 C	-1:168091656 168091656 C	
460	1380 T	-1:168091655 168091655 T	
461 S	1381 A	-1:168091654 168091654 A	S
461	1382 G	-1:168091653 168091653 G	
461	1383 C	-1:168091652 168091652 C	
462 I	1384 A	-1:168091651 168091651 A	I
462	1385 T	-1:168091650 168091650 T	
462	1386 A	-1:168091649 168091649 A	
463 F	1387 T	-1:168091648 168091648 T	F
463	1388 T	-1:168091647 168091647 T	
463	1389 C	-1:168091646 168091646 C	
464 P	1390 C	-1:168091645 168091645 C	P
464	1391 C	-1:168091644 168091644 C	
464	1392 T	-1:168091643 168091643 T	
465 K	1393 A	-1:168091642 168091642 A	K
465	1394 A	-1:168091641 168091641 A	
465	1395 A	-1:168091640 168091640 A	
466 C	1396 T	-1:168091639 168091639 T	C
466	1397 G	-1:168091638 168091638 G	
466	1398 T	-1:168091637 168091637 T	
467 F	1399 T	-1:168091636 168091636 T	F
467	1400 T	-1:168091635 168091635 T	
467	1401 C	-1:168091634 168091634 C	
468 F	1402 T	-1:168091633 168091633 T	F
468	1403 T	-1:168091632 168091632 T	
468	1404 T	-1:168091631 168091631 T	
469 S	1405 T	-1:168091630 168091630 T	S
469	1406 C	-1:168091629 168091629 C	
469	1407 T	-1:168091628 168091628 T	
470 G	1408 G	-1:168091627 168091627 G	G
470	1409 G	-1:168091626 168091626 G	
470	1410 C	-1:168091625 168091625 C	
471 S	1411 A	-1:168091624 168091624 A	S
471	1412 G	-1:168091623 168091623 G	
471	1413 C	-1:168091622 168091622 C	
472 T	1414 A	-1:168091621 168091621 A	T
472	1415 C	-1:168091620 168091620 C	
472	1416 G	-1:168091619 168091619 G	
473 P	1417 C	-1:168091618 168091618 C	P
473	1418 C	-1:168091617 168091617 C	
473	1419 C	-1:168091616 168091616 C	
474 I	1420 A	-1:168091615 168091615 A	I
474	1421 T	-1:168091614 168091614 T	
474	1422 C	-1:168091613 168091613 C	
475 N	1423 A	-1:168091612 168091612 A	N
475	1424 A	-1:168091611 168091611 A	
475	1425 C	-1:168091610 168091610 C	
476 S	1426 A	-1:168091609 168091609 A	S
476	1427 G	-1:168091608 168091608 G	
476	1428 C	-1:168091607 168091607 C	
477 K	1429 A	-1:168091606 168091606 A	K
477	1430 A	-1:168091605 168091605 A	
477	1431 G	-1:168091604 168091604 G	
478 K	1432 A	-1:168091603 168091603 A	K
478	1433 A	-1:168091602 168091602 A	
478	1434 G	-1:168091601 168091601 G	
479 H	1435 C	-1:168091600 168091600 C	H
479	1436 A	-1:168091599 168091599 A	
479	1437 C	-1:168091598 168091598 C	
480 I	1438 A	-1:168091597 168091597 A	I
480	1439 T	-1:168091596 168091596 T	
480	1440 A	-1:168091595 168091595 A	
481 Q	1441 C	-1:168091594 168091594 C	Q
481	1442 A	-1:168091593 168091593 A	
481	1443 G	-1:168091592 168091592 G	
482 R	1444 C	-1:168091591 168091591 C	R
482	1445 G	-1:168091590 168091590 G	
482	1446 A	-1:168091589 168091589 A	
483 D	1447 G	-1:168091588 168091588 G	D
483	1448 A	-1:168091587 168091587 A	
483	1449 T	-1:168091586 168091586 T	
484 Y	1450 T	-1:168091585 168091585 T	Y
484	1451 A	-1:168091584 168091584 A	
484	1452 C	-1:168091583 168091583 C	
485 Y	1453 T	-1:168091582 168091582 T	Y
485	1454 A	-1:168091581 168091581 A	
485	1455 C	-1:168091580 168091580 C	
486 N	1456 A	-1:168091579 168091579 A	N
486	1457 A	-1:168091578 168091578 A	
486	1458 T	-1:168091577 168091577 T	
487 T	1459 A	-1:168091576 168091576 A	T
487	1460 C	-1:168091575 168091575 C	
487	1461 T	-1:168091574 168091574 T	
488 L	1462 C	-1:168091573 168091573 C	L
488	1463 T	-1:168091572 168091572 T	
488	1464 T	-1:168091571 168091571 T	
489 L	1465 T	-1:168091570 168091570 T	L
489	1466 T	-1:168091569 168091569 T	
489	1467 A	-1:168091568 168091568 A	
490 Q	1468 C	-1:168091567 168091567 C	Q
490	1469 A	-1:168091566 168091566 A	
490	1470 G	-1:168091565 168091565 G	
491 T	1471 A	-1:168091564 168091564 A	T
491	1472 C	-1:168091563 168091563 C	
491	1473 A	-1:168091562 168091562 A	
492 G	1474 G	-1:168091561 168091561 G	G
492	1475 G	-1:168090729 168090729 G	
492	1476 C	-1:168090728 168090728 C	
493 D	1477 G	-1:168090727 168090727 G	D
493	1478 A	-1:168090726 168090726 A	
493	1479 T	-1:168090725 168090725 T	
494 P	1480 C	-1:168090724 168090724 C	P
494	1481 C	-1:168090723 168090723 C	
494	1482 A	-1:168090722 168090722 A	
495 F	1483 T	-1:168090721 168090721 T	F
495	1484 T	-1:168090720 168090720 T	
495	1485 T	-1:168090719 168090719 T	
496 S	1486 T	-1:168090718 168090718 T	S
496	1487 C	-1:168090717 168090717 C	
496	1488 T	-1:168090716 168090716 T	
497 Q	1489 C	-1:168090715 168090715 C	Q
497	1490 A	-1:168090714 168090714 A	
497	1491 G	-1:168090713 168090713 G	
498 P	1492 C	-1:168090712 168090712 C	P
498	1493 C	-1:168090711 168090711 C	
498	1494 T	-1:168090710 168090710 T	
499 I	1495 A	-1:168090709 168090709 A	I
499	1496 T	-1:168090708 168090708 T	
499	1497 T	-1:168090707 168090707 T	
500 K	1498 A	-1:168090706 168090706 A	K
500	1499 A	-1:168090705 168090705 A	
500	1500 A	-1:168090704 168090704 A	
501 F	1501 T	-1:168090703 168090703 T	F
501	1502 T	-1:168090702 168090702 T	
501	1503 T	-1:168090701 168090701 T	
502 P	1504 C	-1:168090700 168090700 C	P
502	1505 C	-1:168090699 168090699 C	
502	1506 C	-1:168090698 168090698 C	
503 I	1507 A	-1:168090697 168090697 A	I
503	1508 T	-1:168090696 168090696 T	
503	1509 A	-1:168090695 168090695 A	
504 N	1510 A	-1:168090694 168090694 A	N
504	1511 A	-1:168090693 168090693 A	
504	1512 T	-1:168090692 168090692 T	
505 G	1513 G	-1:168090691 168090691 G	G
505	1514 G	-1:168090690 168090690 G	
505	1515 A	-1:168090689 168090689 A	
506 L	1516 C	-1:168090688 168090688 C	L
506	1517 T	-1:168090687 168090687 T	
506	1518 C	-1:168090686 168090686 C	
507 S	1519 T	-1:168090685 168090685 T	S
507	1520 C	-1:168090684 168090684 C	
507	1521 A	-1:168090683 168090683 A	
508 D	1522 G	-1:168090682 168090682 G	D
508	1523 A	-1:168090681 168090681 A	
508	1524 T	-1:168090680 168090680 T	
509 V	1525 G	-1:168090679 168090679 G	V
509	1526 T	-1:168090678 168090678 T	
509	1527 A	-1:168090677 168090677 A	
510 K	1528 A	-1:168090676 168090676 A	K
510	1529 A	-1:168090675 168090675 A	
510	1530 A	-1:168090674 168090674 A	
511 N	1531 A	-1:168090673 168090673 A	N
511	1532 A	-1:168090672 168090672 A	
511	1533 T	-1:168090671 168090671 T	
512 T	1534 A	-1:168090670 168090670 A	T
512	1535 C	-1:168090669 168090669 C	
512	1536 T	-1:168090668 168090668 T	
513 S	1537 T	-1:168090667 168090667 T	S
513	1538 C	-1:168090666 168090666 C	
513	1539 G	-1:168090665 168090665 G	
514 E	1540 G	-1:168090664 168090664 G	E
514	1541 A	-1:168090663 168090663 A	
514	1542 G	-1:168090662 168090662 G	
515 D	1543 G	-1:168090661 168090661 G	D
515	1544 A	-1:168090660 168090660 A	
515	1545 C	-1:168090659 168090659 C	
516 S	1546 A	-1:168090658 168090658 A	S
516	1547 G	-1:168090657 168090657 G	
516	1548 T	-1:168090656 168090656 T	
517 E	1549 G	-1:168090655 168090655 G	E
517	1550 A	-1:168090654 168090654 A	
517	1551 A	-1:168090653 168090653 A	
518 N	1552 A	-1:168090652 168090652 A	N
518	1553 A	-1:168090651 168090651 A	
518	1554 C	-1:168090650 168090650 C	
519 F	1555 T	-1:168090649 168090649 T	F
519	1556 T	-1:168090648 168090648 T	
519	1557 C	-1:168090647 168090647 C	
520 P	1558 C	-1:168090646 168090646 C	P
520	1559 C	-1:168090645 168090645 C	
520	1560 A	-1:168090644 168090644 A	
521 S	1561 T	-1:168090643 168090643 T	S
521	1562 C	-1:168090642 168090642 C	
521	1563 A	-1:168090641 168090641 A	
522 S	1564 A	-1:168090640 168090640 A	S
522	1565 G	-1:168090639 168090639 G	
522	1566 T	-1:168090638 168090638 T	
523 S	1567 T	-1:168090637 168090637 T	S
523	1568 C	-1:168090636 168090636 C	
523	1569 T	-1:168090635 168090635 T	
524 K	1570 A	-1:168090634 168090634 A	K
524	1571 A	-1:168090633 168090633 A	
524	1572 A	-1:168090632 168090632 A	
525 K	1573 A	-1:168090631 168090631 A	K
525	1574 A	-1:168090630 168090630 A	
525	1575 G	-1:168090629 168090629 G	
526 S	1576 T	-1:168090628 168090628 T	S
526	1577 C	-1:168090627 168090627 C	
526	1578 T	-1:168090626 168090626 T	
527 E	1579 G	-1:168090625 168090625 G	E
527	1580 A	-1:168090624 168090624 A	
527	1581 G	-1:168090623 168090623 G	
528 E	1582 G	-1:168090622 168090622 G	E
528	1583 A	-1:168090621 168090621 A	
528	1584 G	-1:168090620 168090620 G	
529 W	1585 T	-1:168090619 168090619 T	W
529	1586 G	-1:168090618 168090618 G	
529	1587 G	-1:168090617 168090617 G	
530 P	1588 C	-1:168090616 168090616 C	P
530	1589 C	-1:168090615 168090615 C	
530	1590 T	-1:168090614 168090614 T	
531 D	1591 G	-1:168090613 168090613 G	D
531	1592 A	-1:168090612 168090612 A	
531	1593 C	-1:168090611 168090611 C	
532 W	1594 T	-1:168090610 168090610 T	W
532	1595 G	-1:168090609 168090609 G	
532	1596 G	-1:168090608 168090608 G	
533 S	1597 A	-1:168090607 168090607 A	S
533	1598 G	-1:168090606 168090606 G	
533	1599 T	-1:168090605 168090605 T	
534 E	1600 G	-1:168090604 168090604 G	E
534	1601 A	-1:168090603 168090603 A	
534	1602 A	-1:168090602 168090602 A	
535 P	1603 C	-1:168090601 168090601 C	P
535	1604 C	-1:168090600 168090600 C	
535	1605 T	-1:168090599 168090599 T	
536 E	1606 G	-1:168090598 168090598 G	E
536	1607 A	-1:168090597 168090597 A	
536	1608 G	-1:168090596 168090596 G	
537 E	1609 G	-1:168090595 168090595 G	E
537	1610 A	-1:168090594 168090594 A	
537	1611 G	-1:168090593 168090593 G	
538 P	1612 C	-1:168090592 168090592 C	P
538	1613 C	-1:168090591 168090591 C	
538	1614 T	-1:168090590 168090590 T	
539 E	1615 G	-1:168090589 168090589 G	E
539	1616 A	-1:168090588 168090588 A	
539	1617 A	-1:168090587 168090587 A	
540 N	1618 A	-1:168090586 168090586 A	N
540	1619 A	-1:168090585 168090585 A	
540	1620 T	-1:168090584 168090584 T	
541 Q	1621 C	-1:168090583 168090583 C	Q
541	1622 A	-1:168090582 168090582 A	
541	1623 A	-1:168090581 168090581 A	
542 T	1624 A	-1:168090580 168090580 A	T
542	1625 C	-1:168090579 168090579 C	
542	1626 T	-1:168090578 168090578 T	
543 V	1627 G	-1:168090577 168090577 G	V
543	1628 T	-1:168090576 168090576 T	
543	1629 C	-1:168090575 168090575 C	
544 N	1630 A	-1:168090574 168090574 A	N
544	1631 A	-1:168090573 168090573 A	
544	1632 C	-1:168090572 168090572 C	
545 I	1633 A	-1:168090571 168090571 A	I
545	1634 T	-1:168090570 168090570 T	
545	1635 A	-1:168090569 168090569 A	
546 Q	1636 C	-1:168090568 168090568 C	Q
546	1637 A	-1:168090567 168090567 A	
546	1638 G	-1:168090566 168090566 G	
547 I	1639 A	-1:168090565 168090565 A	I
547	1640 T	-1:168090564 168090564 T	
547	1641 T	-1:168090563 168090563 T	
548 W	1642 T	-1:168090562 168090562 T	W
548	1643 G	-1:168090561 168090561 G	
548	1644 G	-1:168090560 168090560 G	
549 P	1645 C	-1:168090559 168090559 C	P
549	1646 C	-1:168090558 168090558 C	
549	1647 T	-1:168090557 168090557 T	
550 R	1648 A	-1:168090556 168090556 A	R
550	1649 G	-1:168090555 168090555 G	
550	1650 A	-1:168090554 168090554 A	
551 E	1651 G	-1:168090553 168090553 G	E
551	1652 A	-1:168090552 168090552 A	
551	1653 A	-1:168090551 168090551 A	
552 P	1654 C	-1:168090550 168090550 C	P
552	1655 C	-1:168090549 168090549 C	
552	1656 T	-1:168090548 168090548 T	
553 C	1657 T	-1:168090547 168090547 T	C
553	1658 G	-1:168090546 168090546 G	
553	1659 T	-1:168090545 168090545 T	
554 D	1660 G	-1:168090544 168090544 G	D
554	1661 A	-1:168090543 168090543 A	
554	1662 T	-1:168090542 168090542 T	
555 D	1663 G	-1:168090541 168090541 G	D
555	1664 A	-1:168090540 168090540 A	
555	1665 T	-1:168090539 168090539 T	
556 V	1666 G	-1:168090538 168090538 G	V
556	1667 T	-1:168090537 168090537 T	
556	1668 C	-1:168090536 168090536 C	
557 K	1669 A	-1:168090535 168090535 A	K
557	1670 A	-1:168090534 168090534 A	
557	1671 G	-1:168090533 168090533 G	
558 S	1672 T	-1:168090532 168090532 T	S
558	1673 C	-1:168090531 168090531 C	
558	1674 C	-1:168090530 168090530 C	
559 Q	1675 C	-1:168090529 168090529 C	Q
559	1676 A	-1:168090528 168090528 A	
559	1677 G	-1:168090527 168090527 G	
560 C	1678 T	-1:168090526 168090526 T	C
560	1679 G	-1:168090525 168090525 G	
560	1680 C	-1:168090524 168090524 C	
561 T	1681 A	-1:168090523 168090523 A	T
561	1682 C	-1:168090522 168090522 C	
561	1683 T	-1:168090521 168090521 T	
562 T	1684 A	-1:168090520 168090520 A	T
562	1685 C	-1:168090519 168090519 C	
562	1686 C	-1:168090518 168090518 C	
563 L	1687 T	-1:168090517 168090517 T	L
563	1688 T	-1:168090516 168090516 T	
563	1689 G	-1:168090515 168090515 G	
564 D	1690 G	-1:168090514 168090514 G	D
564	1691 A	-1:168090513 168090513 A	
564	1692 T	-1:168090512 168090512 T	
565 V	1693 G	-1:168090511 168090511 G	V
565	1694 T	-1:168090510 168090510 T	
565	1695 G	-1:168090509 168090509 G	
566 E	1696 G	-1:168090508 168090508 G	E
566	1697 A	-1:168090507 168090507 A	
566	1698 A	-1:168090506 168090506 A	
567 E	1699 G	-1:168090505 168090505 G	E
567	1700 A	-1:168090504 168090504 A	
567	1701 G	-1:168090503 168090503 G	
568 S	1702 T	-1:168090502 168090502 T	S
568	1703 C	-1:168090501 168090501 C	
568	1704 A	-1:168090500 168090500 A	
569 S	1705 T	-1:168090499 168090499 T	S
569	1706 C	-1:168090498 168090498 C	
569	1707 T	-1:168090497 168090497 T	
570 W	1708 T	-1:168090496 168090496 T	W
570	1709 G	-1:168090495 168090495 G	
570	1710 G	-1:168090494 168090494 G	
571 D	1711 G	-1:168090493 168090493 G	D
571	1712 A	-1:168090492 168090492 A	
571	1713 T	-1:168090491 168090491 T	
572 D	1714 G	-1:168090490 168090490 G	D
572	1715 A	-1:168090489 168090489 A	
572	1716 C	-1:168090488 168090488 C	
573 C	1717 T	-1:168090487 168090487 T	C
573	1718 G	-1:168090486 168090486 G	
573	1719 C	-1:168090485 168090485 C	
574 E	1720 G	-1:168090484 168090484 G	E
574	1721 A	-1:168090483 168090483 A	
574	1722 G	-1:168090482 168090482 G	
575 P	1723 C	-1:168090481 168090481 C	P
575	1724 C	-1:168090480 168090480 C	
575	1725 C	-1:168090479 168090479 C	
576 S	1726 A	-1:168090478 168090478 A	S
576	1727 G	-1:168090477 168090477 G	
576	1728 C	-1:168090476 168090476 C	
577 S	1729 A	-1:168090475 168090475 A	S
577	1730 G	-1:168090474 168090474 G	
577	1731 C	-1:168090473 168090473 C	
578 L	1732 T	-1:168090472 168090472 T	L
578	1733 T	-1:168090471 168090471 T	
578	1734 A	-1:168090470 168090470 A	
579 D	1735 G	-1:168090469 168090469 G	D
579	1736 A	-1:168090468 168090468 A	
579	1737 T	-1:168090467 168090467 T	
580 T	1738 A	-1:168090466 168090466 A	T
580	1739 C	-1:168090465 168090465 C	
580	1740 T	-1:168090464 168090464 T	
581 K	1741 A	-1:168090463 168090463 A	K
581	1742 A	-1:168090462 168090462 A	
581	1743 A	-1:168090461 168090461 A	
582 V	1744 G	-1:168090460 168090460 G	V
582	1745 T	-1:168090459 168090459 T	
582	1746 A	-1:168090458 168090458 A	
583 N	1747 A	-1:168090457 168090457 A	N
583	1748 A	-1:168090456 168090456 A	
583	1749 C	-1:168090455 168090455 C	
584 P	1750 C	-1:168090454 168090454 C	P
584	1751 C	-1:168090453 168090453 C	
584	1752 A	-1:168090452 168090452 A	
585 G	1753 G	-1:168090451 168090451 G	G
585	1754 G	-1:168090450 168090450 G	
585	1755 A	-1:168090449 168090449 A	
586 G	1756 G	-1:168090448 168090448 G	G
586	1757 G	-1:168090447 168090447 G	
586	1758 T	-1:168090446 168090446 T	
587 G	1759 G	-1:168090445 168090445 G	G
587	1760 G	-1:168090444 168090444 G	
587	1761 A	-1:168090443 168090443 A	
588 I	1762 A	-1:168090442 168090442 A	I
588	1763 T	-1:168090441 168090441 T	
588	1764 C	-1:168090440 168090440 C	
589 T	1765 A	-1:168090439 168090439 A	T
589	1766 C	-1:168090438 168090438 C	
589	1767 T	-1:168090437 168090437 T	
590 A	1768 G	-1:168090436 168090436 G	A
590	1769 C	-1:168090435 168090435 C	
590	1770 T	-1:168090434 168090434 T	
591 T	1771 A	-1:168090433 168090433 A	T
591	1772 C	-1:168090432 168090432 C	
591	1773 A	-1:168090431 168090431 A	
592 K	1774 A	-1:168090430 168090430 A	K
592	1775 A	-1:168090429 168090429 A	
592	1776 A	-1:168090428 168090428 A	
593 P	1777 C	-1:168090427 168090427 C	P
593	1778 C	-1:168090426 168090426 C	
593	1779 T	-1:168090425 168090425 T	
594 V	1780 G	-1:168090424 168090424 G	V
594	1781 T	-1:168090423 168090423 T	
594	1782 T	-1:168090422 168090422 T	
595 T	1783 A	-1:168090421 168090421 A	T
595	1784 C	-1:168090420 168090420 C	
595	1785 C	-1:168090419 168090419 C	
596 S	1786 T	-1:168090418 168090418 T	S
596	1787 C	-1:168090417 168090417 C	
596	1788 A	-1:168090416 168090416 A	
597 G	1789 G	-1:168090415 168090415 G	G
597	1790 G	-1:168090414 168090414 G	
597	1791 G	-1:168090413 168090413 G	
598 E	1792 G	-1:168090412 168090412 G	E
598	1793 A	-1:168090411 168090411 A	
598	1794 G	-1:168090410 168090410 G	
599 Q	1795 C	-1:168090409 168090409 C	Q
599	1796 A	-1:168090408 168090408 A	
599	1797 G	-1:168090407 168090407 G	
600 K	1798 A	-1:168090406 168090406 A	K
600	1799 A	-1:168090405 168090405 A	
600	1800 G	-1:168090404 168090404 G	
601 P	1801 C	-1:168090403 168090403 C	P
601	1802 C	-1:168090402 168090402 C	
601	1803 T	-1:168090401 168090401 T	
602 I	1804 A	-1:168090400 168090400 A	I
602	1805 T	-1:168090399 168090399 T	
602	1806 T	-1:168090398 168090398 T	
603 P	1807 C	-1:168090397 168090397 C	P
603	1808 C	-1:168090396 168090396 C	
603	1809 T	-1:168090395 168090395 T	
604 A	1810 G	-1:168090394 168090394 G	A
604	1811 C	-1:168090393 168090393 C	
604	1812 T	-1:168090392 168090392 T	
605 L	1813 T	-1:168090391 168090391 T	L
605	1814 T	-1:168090390 168090390 T	
605	1815 G	-1:168090389 168090389 G	
606 L	1816 C	-1:168090388 168090388 C	L
606	1817 T	-1:168090387 168090387 T	
606	1818 T	-1:168090386 168090386 T	
607 S	1819 T	-1:168090385 168090385 T	S
607	1820 C	-1:168090384 168090384 C	
607	1821 A	-1:168090383 168090383 A	
608 L	1822 C	-1:168090382 168090382 C	L
608	1823 T	-1:168090381 168090381 T	
608	1824 C	-1:168090380 168090380 C	
609 T	1825 A	-1:168090379 168090379 A	T
609	1826 C	-1:168090378 168090378 C	
609	1827 T	-1:168090377 168090377 T	
610 E	1828 G	-1:168090376 168090376 G	E
610	1829 A	-1:168090375 168090375 A	
610	1830 A	-1:168090374 168090374 A	
611 E	1831 G	-1:168090373 168090373 G	E
611	1832 A	-1:168090372 168090372 A	
611	1833 G	-1:168090371 168090371 G	
612 S	1834 T	-1:168090370 168090370 T	S
612	1835 C	-1:168090369 168090369 C	
612	1836 T	-1:168090368 168090368 T	
613 M	1837 A	-1:168090367 168090367 A	M
613	1838 T	-1:168090366 168090366 T	
613	1839 G	-1:168090365 168090365 G	
614 P	1840 C	-1:168090364 168090364 C	P
614	1841 C	-1:168090363 168090363 C	
614	1842 T	-1:168090362 168090362 T	
615 W	1843 T	-1:168090361 168090361 T	W
615	1844 G	-1:168090360 168090360 G	
615	1845 G	-1:168090359 168090359 G	
616 K	1846 A	-1:168090358 168090358 A	K
616	1847 A	-1:168090357 168090357 A	
616	1848 A	-1:168090356 168090356 A	
617 S	1849 T	-1:168090355 168090355 T	S
617	1850 C	-1:168090354 168090354 C	
617	1851 A	-1:168090353 168090353 A	
618 S	1852 A	-1:168090352 168090352 A	S
618	1853 G	-1:168090351 168090351 G	
618	1854 C	-1:168090350 168090350 C	
619 L	1855 T	-1:168090349 168090349 T	L
619	1856 T	-1:168090348 168090348 T	
619	1857 A	-1:168090347 168090347 A	
620 P	1858 C	-1:168090346 168090346 C	P
620	1859 C	-1:168090345 168090345 C	
620	1860 C	-1:168090344 168090344 C	
621 Q	1861 C	-1:168090343 168090343 C	Q
621	1862 A	-1:168090342 168090342 A	
621	1863 A	-1:168090341 168090341 A	
622 K	1864 A	-1:168090340 168090340 A	K
622	1865 A	-1:168090339 168090339 A	
622	1866 G	-1:168090338 168090338 G	
623 I	1867 A	-1:168090337 168090337 A	I
623	1868 T	-1:168090336 168090336 T	
623	1869 T	-1:168090335 168090335 T	
624 S	1870 A	-1:168090334 168090334 A	S
624	1871 G	-1:168090333 168090333 G	
624	1872 C	-1:168090332 168090332 C	
625 L	1873 C	-1:168090331 168090331 C	L
625	1874 T	-1:168090330 168090330 T	
625	1875 T	-1:168090329 168090329 T	
626 V	1876 G	-1:168090328 168090328 G	V
626	1877 T	-1:168090327 168090327 T	
626	1878 A	-1:168090326 168090326 A	
627 Q	1879 C	-1:168090325 168090325 C	Q
627	1880 A	-1:168090324 168090324 A	
627	1881 A	-1:168090323 168090323 A	
628 R	1882 A	-1:168090322 168090322 A	R
628	1883 G	-1:168090321 168090321 G	
628	1884 G	-1:168090320 168090320 G	
629 G	1885 G	-1:168090319 168090319 G	G
629	1886 G	-1:168090318 168090318 G	
629	1887 G	-1:168090317 168090317 G	
630 D	1888 G	-1:168090316 168090316 G	D
630	1889 A	-1:168090315 168090315 A	
630	1890 T	-1:168090314 168090314 T	
631 D	1891 G	-1:168090313 168090313 G	D
631	1892 A	-1:168090312 168090312 A	
631	1893 C	-1:168090311 168090311 C	
632 A	1894 G	-1:168090310 168090310 G	A
632	1895 C	-1:168090309 168090309 C	
632	1896 A	-1:168090308 168090308 A	
633 D	1897 G	-1:168090307 168090307 G	D
633	1898 A	-1:168090306 168090306 A	
633	1899 C	-1:168090305 168090305 C	
634 Q	1900 C	-1:168090304 168090304 C	Q
634	1901 A	-1:168090303 168090303 A	
634	1902 A	-1:168090302 168090302 A	
635 I	1903 A	-1:168090301 168090301 A	I
635	1904 T	-1:168090300 168090300 T	
635	1905 C	-1:168090299 168090299 C	
636 E	1906 G	-1:168090298 168090298 G	E
636	1907 A	-1:168090297 168090297 A	
636	1908 G	-1:168090296 168090296 G	
637 P	1909 C	-1:168090295 168090295 C	P
637	1910 C	-1:168090294 168090294 C	
637	1911 G	-1:168090293 168090293 G	
638 P	1912 C	-1:168090292 168090292 C	P
638	1913 C	-1:168090291 168090291 C	
638	1914 A	-1:168090290 168090290 A	
639 K	1915 A	-1:168090289 168090289 A	K
639	1916 A	-1:168090288 168090288 A	
639	1917 A	-1:168090287 168090287 A	
640 V	1918 G	-1:168090286 168090286 G	V
640	1919 T	-1:168090285 168090285 T	
640	1920 G	-1:168090284 168090284 G	
641 S	1921 T	-1:168090283 168090283 T	S
641	1922 C	-1:168090282 168090282 C	
641	1923 A	-1:168090281 168090281 A	
642 S	1924 T	-1:168090280 168090280 T	S
642	1925 C	-1:168090279 168090279 C	
642	1926 A	-1:168090278 168090278 A	
643 Q	1927 C	-1:168090277 168090277 C	Q
643	1928 A	-1:168090276 168090276 A	
643	1929 A	-1:168090275 168090275 A	
644 E	1930 G	-1:168090274 168090274 G	E
644	1931 A	-1:168090273 168090273 A	
644	1932 A	-1:168090272 168090272 A	
645 R	1933 A	-1:168090271 168090271 A	R
645	1934 G	-1:168090270 168090270 G	
645	1935 G	-1:168090269 168090269 G	
646 P	1936 C	-1:168090268 168090268 C	P
646	1937 C	-1:168090267 168090267 C	
646	1938 C	-1:168090266 168090266 C	
>ENSP00000356745 
1 M	1 A	-1:168124605 168124605 A	M
1	2 T	-1:168124604 168124604 T	
1	3 G	-1:168124603 168124603 G	
2 G	4 G	-1:168124602 168124602 G	G
2	5 G	-1:168124601 168124601 G	
2	6 A	-1:168124600 168124600 A	
3 S	7 T	-1:168124599 168124599 T	S
3	8 C	-1:168124598 168124598 C	
3	9 A	-1:168124597 168124597 A	
4 E	10 G	-1:168124596 168124596 G	E
4	11 A	-1:168124595 168124595 A	
4	12 G	-1:168124594 168124594 G	
5 N	13 A	-1:168124593 168124593 A	N
5	14 A	-1:168124592 168124592 A	
5	15 C	-1:168124591 168124591 C	
6 S	16 A	-1:168124590 168124590 A	S
6	17 G	-1:168124589 168124589 G	
6	18 T	-1:168124588 168124588 T	
7 A	19 G	-1:168124587 168124587 G	A
7	20 C	-1:168124586 168124586 C	
7	21 T	-1:168124585 168124585 T	
8 L	22 T	-1:168124584 168124584 T	L
8	23 T	-1:168124583 168124583 T	
8	24 A	-1:168124582 168124582 A	
9 K	25 A	-1:168124581 168124581 A	K
9	26 A	-1:168124580 168124580 A	
9	27 G	-1:168124579 168124579 G	
10 S	28 A	-1:168124578 168124578 A	S
10	29 G	-1:168124577 168124577 G	
10	30 C	-1:168124576 168124576 C	
11 Y	31 T	-1:168124575 168124575 T	Y
11	32 A	-1:168124574 168124574 A	
11	33 T	-1:168124573 168124573 T	
12 T	34 A	-1:168124572 168124572 A	T
12	35 C	-1:168124571 168124571 C	
12	36 A	-1:168124570 168124570 A	
13 L	37 C	-1:168124569 168124569 C	L
13	38 T	-1:168124568 168124568 T	
13	39 G	-1:168124567 168124567 G	
14 R	40 A	-1:168124566 168124566 A	R
14	41 G	-1:168124565 168124565 G	
14	42 A	-1:168124564 168124564 A	
15 E	43 G	-1:168124563 168124563 G	E
15	44 A	-1:168124562 168124562 A	
15	45 A	-1:168124561 168124561 A	
16 P	46 C	-1:168124560 168124560 C	P
16	47 C	-1:168124559 168124559 C	
16	48 A	-1:168124558 168124558 A	
17 P	49 C	-1:168124557 168124557 C	P
17	50 C	-1:168124556 168124556 C	
17	51 A	-1:168124555 168124555 A	
18 F	52 T	-1:168124554 168124554 T	F
18	53 T	-1:168124553 168124553 T	
18	54 T	-1:168124552 168124552 T	
19 T	55 A	-1:168124551 168124551 A	T
19	56 C	-1:168124550 168124550 C	
19	57 C	-1:168124549 168124549 C	
20 L	58 T	-1:168124548 168124548 T	L
20	59 T	-1:168124547 168124547 T	
20	60 A	-1:168124546 168124546 A	
21 P	61 C	-1:168124545 168124545 C	P
21	62 C	-1:168124544 168124544 C	
21	63 C	-1:168124543 168124543 C	
22 S	64 T	-1:168124542 168124542 T	S
22	65 C	-1:168124541 168124541 C	
22	66 T	-1:168124540 168124540 T	
23 G	67 G	-1:168124539 168124539 G	G
23	68 G	-1:168124538 168124538 G	
23	69 A	-1:168124537 168124537 A	
24 L	70 C	-1:168124536 168124536 C	L
24	71 T	-1:168124535 168124535 T	
24	72 T	-1:168124534 168124534 T	
25 A	73 G	-1:168124533 168124533 G	A
25	74 C	-1:168124532 168124532 C	
25	75 T	-1:168124531 168124531 T	
26 V	76 G	-1:168124530 168124530 G	V
26	77 T	-1:168124529 168124529 T	
26	78 T	-1:168124528 168124528 T	
27 Y	79 T	-1:168124527 168124527 T	Y
27	80 A	-1:168124526 168124526 A	
27	81 T	-1:168124525 168124525 T	
28 P	82 C	-1:168124524 168124524 C	P
28	83 C	-1:168124523 168124523 C	
28	84 C	-1:168124522 168124522 C	
29 A	85 G	-1:168124521 168124521 G	A
29	86 C	-1:168124520 168124520 C	
29	87 T	-1:168124519 168124519 T	
30 V	88 G	-1:168124518 168124518 G	V
30	89 T	-1:168124517 168124517 T	
30	90 A	-1:168124516 168124516 A	
31 L	91 C	-1:168124515 168124515 C	L
31	92 T	-1:168124514 168124514 T	
31	93 G	-1:168124513 168124513 G	
32 Q	94 C	-1:168124512 168124512 C	Q
32	95 A	-1:168124511 168124511 A	
32	96 A	-1:168124510 168124510 A	
33 D	97 G	-1:168124509 168124509 G	D
33	98 A	-1:168124508 168124508 A	
33	99 T	-1:168124507 168124507 T	
34 G	100 G	-1:168124506 168124506 G	G
34	101 G	-1:168124505 168124505 G	
34	102 C	-1:168124504 168124504 C	
35 K	103 A	-1:168124503 168124503 A	K
35	104 A	-1:168124502 168124502 A	
35	105 A	-1:168124501 168124501 A	
36 F	106 T	-1:168124500 168124500 T	F
36	107 T	-1:168124499 168124499 T	
36	108 T	-1:168124498 168124498 T	
37 A	109 G	-1:168124497 168124497 G	A
37	110 C	-1:168124496 168124496 C	
37	111 T	-1:168124495 168124495 T	
38 S	112 T	-1:168124494 168124494 T	S
38	113 C	-1:168124493 168124493 C	
38	114 A	-1:168124492 168124492 A	
39 V	115 G	-1:168124491 168124491 G	V
39	116 T	-1:168124490 168124490 T	
39	117 T	-1:168124489 168124489 T	
40 F	118 T	-1:168124488 168124488 T	F
40	119 T	-1:168124487 168124487 T	
40	120 T	-1:168124486 168124486 T	
41 V	121 G	-1:168124485 168124485 G	V
41	122 T	-1:168124484 168124484 T	
41	123 G	-1:168124483 168124483 G	
42 Y	124 T	-1:168124482 168124482 T	Y
42	125 A	-1:168124481 168124481 A	
42	126 T	-1:168124480 168124480 T	
43 K	127 A	-1:168124479 168124479 A	K
43	128 A	-1:168124478 168124478 A	
43	129 G	-1:168124477 168124477 G	
44 R	130 A	-1:168124476 168124476 A	R
44	131 G	-1:168124475 168124475 G	
44	132 A	-1:168124474 168124474 A	
45 E	133 G	-1:168124473 168124473 G	E
45	134 A	-1:168124472 168124472 A	
45	135 A	-1:168124471 168124471 A	
46 N	136 A	-1:168124470 168124470 A	N
46	137 A	-1:168124469 168124469 A	
46	138 T	-1:168124468 168124468 T	
47 E	139 G	-1:168124467 168124467 G	E
47	140 A	-1:168124466 168124466 A	
47	141 A	-1:168124465 168124465 A	
48 D	142 G	-1:168124464 168124464 G	D
48	143 A	-1:168124463 168124463 A	
48	144 C	-1:168124462 168124462 C	
49 K	145 A	-1:168124461 168124461 A	K
49	146 A	-1:168124460 168124460 A	
49	147 G	-1:168124459 168124459 G	
50 V	148 G	-1:168124458 168124458 G	V
50	149 T	-1:168124457 168124457 T	
50	150 T	-1:168124456 168124456 T	
51 N	151 A	-1:168124455 168124455 A	N
51	152 A	-1:168124454 168124454 A	
51	153 T	-1:168124453 168124453 T	
52 K	154 A	-1:168124452 168124452 A	K
52	155 A	-1:168124451 168124451 A	
52	156 A	-1:168124450 168124450 A	
53 A	157 G	-1:168124449 168124449 G	A
53	158 C	-1:168124448 168124448 C	
53	159 T	-1:168124447 168124447 T	
54 A	160 G	-1:168124446 168124446 G	A
54	161 C	-1:168124445 168124445 C	
54	162 C	-1:168124444 168124444 C	
55 K	163 A	-1:168124443 168124443 A	K
55	164 A	-1:168124442 168124442 A	
55	165 G	-1:168124441 168124441 G	
56 H	166 C	-1:168114584 168114584 C	H
56	167 A	-1:168114583 168114583 A	
56	168 T	-1:168114582 168114582 T	
57 L	169 T	-1:168114581 168114581 T	L
57	170 T	-1:168114580 168114580 T	
57	171 G	-1:168114579 168114579 G	
58 K	172 A	-1:168114578 168114578 A	K
58	173 A	-1:168114577 168114577 A	
58	174 G	-1:168114576 168114576 G	
59 T	175 A	-1:168114575 168114575 A	T
59	176 C	-1:168114574 168114574 C	
59	177 A	-1:168114573 168114573 A	
60 L	178 C	-1:168114572 168114572 C	L
60	179 T	-1:168114571 168114571 T	
60	180 T	-1:168114570 168114570 T	
61 R	181 C	-1:168114569 168114569 C	R
61	182 G	-1:168114568 168114568 G	
61	183 T	-1:168114567 168114567 T	
62 H	184 C	-1:168114566 168114566 C	H
62	185 A	-1:168114565 168114565 A	
62	186 C	-1:168114564 168114564 C	
63 P	187 C	-1:168114563 168114563 C	P
63	188 C	-1:168114562 168114562 C	
63	189 T	-1:168114561 168114561 T	
64 C	190 T	-1:168114560 168114560 T	C
64	191 G	-1:168114559 168114559 G	
64	192 C	-1:168114558 168114558 C	
65 L	193 T	-1:168114557 168114557 T	L
65	194 T	-1:168114556 168114556 T	
65	195 G	-1:168114555 168114555 G	
66 L	196 C	-1:168114554 168114554 C	L
66	197 T	-1:168114553 168114553 T	
66	198 A	-1:168114552 168114552 A	
67 R	199 A	-1:168114551 168114551 A	R
67	200 G	-1:168114550 168114550 G	
67	201 A	-1:168114549 168114549 A	
68 F	202 T	-1:168114548 168114548 T	F
68	203 T	-1:168114547 168114547 T	
68	204 T	-1:168114546 168114546 T	
69 L	205 T	-1:168114545 168114545 T	L
69	206 T	-1:168114544 168114544 T	
69	207 A	-1:168114543 168114543 A	
70 S	208 T	-1:168114542 168114542 T	S
70	209 C	-1:168114541 168114541 C	
70	210 T	-1:168114540 168114540 T	
71 C	211 T	-1:168114539 168114539 T	C
71	212 G	-1:168114538 168114538 G	
71	213 T	-1:168114537 168114537 T	
72 T	214 A	-1:168114536 168114536 A	T
72	215 C	-1:168114535 168114535 C	
72	216 T	-1:168114534 168114534 T	
73 V	217 G	-1:168114533 168114533 G	V
73	218 T	-1:168114532 168114532 T	
73	219 G	-1:168114531 168114531 G	
74 E	220 G	-1:168114530 168114530 G	E
74	221 A	-1:168114529 168114529 A	
74	222 A	-1:168114528 168114528 A	
75 A	223 G	-1:168114527 168114527 G	A
75	224 C	-1:168114526 168114526 C	
75	225 G	-1:168114525 168114525 G	
76 D	226 G	-1:168114524 168114524 G	D
76	227 A	-1:168114523 168114523 A	
76	228 T	-1:168114522 168114522 T	
77 G	229 G	-1:168114521 168114521 G	G
77	230 G	-1:168114520 168114520 G	
77	231 C	-1:168114519 168114519 C	
78 I	232 A	-1:168114518 168114518 A	I
78	233 T	-1:168114517 168114517 T	
78	234 T	-1:168114516 168114516 T	
79 H	235 C	-1:168114515 168114515 C	H
79	236 A	-1:168114514 168114514 A	
79	237 T	-1:168114513 168114513 T	
80 L	238 C	-1:168114512 168114512 C	L
80	239 T	-1:168114511 168114511 T	
80	240 T	-1:168114510 168114510 T	
81 V	241 G	-1:168114509 168114509 G	V
81	242 T	-1:168114508 168114508 T	
81	243 C	-1:168114507 168114507 C	
82 T	244 A	-1:168114506 168114506 A	T
82	245 C	-1:168114505 168114505 C	
82	246 T	-1:168114504 168114504 T	
83 E	247 G	-1:168114503 168114503 G	E
83	248 A	-1:168114502 168114502 A	
83	249 G	-1:168114501 168114501 G	
84 R	250 C	-1:168114500 168114500 C	R
84	251 G	-1:168114499 168114499 G	
84	252 A	-1:168114498 168114498 A	
85 V	253 G	-1:168114497 168114497 G	V
85	254 T	-1:168114496 168114496 T	
85	255 A	-1:168114495 168114495 A	
86 Q	256 C	-1:168114494 168114494 C	Q
86	257 A	-1:168114493 168114493 A	
86	258 G	-1:168114492 168114492 G	
87 P	259 C	-1:168114491 168114491 C	P
87	260 C	-1:168114490 168114490 C	
87	261 C	-1:168114489 168114489 C	
88 L	262 C	-1:168114488 168114488 C	L
88	263 T	-1:168114487 168114487 T	
88	264 G	-1:168114486 168114486 G	
89 E	265 G	-1:168114485 168114485 G	E
89	266 A	-1:168114484 168114484 A	
89	267 A	-1:168114483 168114483 A	
90 V	268 G	-1:168114482 168114482 G	V
90	269 T	-1:168114481 168114481 T	
90	270 G	-1:168114480 168114480 G	
91 A	271 G	-1:168114479 168114479 G	A
91	272 C	-1:168114478 168114478 C	
91	273 T	-1:168114477 168114477 T	
92 L	274 T	-1:168114476 168114476 T	L
92	275 T	-1:168114475 168114475 T	
92	276 G	-1:168114474 168114474 G	
93 E	277 G	-1:168114473 168114473 G	E
93	278 A	-1:168114472 168114472 A	
93	279 A	-1:168114471 168114471 A	
94 T	280 A	-1:168114470 168114470 A	T
94	281 C	-1:168114469 168114469 C	
94	282 A	-1:168114468 168114468 A	
95 L	283 T	-1:168114467 168114467 T	L
95	284 T	-1:168114466 168114466 T	
95	285 G	-1:168114465 168114465 G	
96 S	286 T	-1:168114464 168114464 T	S
96	287 C	-1:168114463 168114463 C	
96	288 T	-1:168114462 168114462 T	
97 S	289 T	-1:168114461 168114461 T	S
97	290 C	-1:168114460 168114460 C	
97	291 T	-1:168114459 168114459 T	
98 A	292 G	-1:168114458 168114458 G	A
98	293 C	-1:168114457 168114457 C	
98	294 A	-1:168114456 168114456 A	
99 E	295 G	-1:168114455 168114455 G	E
99	296 A	-1:168114454 168114454 A	
99	297 G	-1:168114453 168114453 G	
100 V	298 G	-1:168114452 168114452 G	V
100	299 T	-1:168114451 168114451 T	
100	300 C	-1:168114450 168114450 C	
101 C	301 T	-1:168114449 168114449 T	C
101	302 G	-1:168114448 168114448 G	
101	303 T	-1:168114447 168114447 T	
102 A	304 G	-1:168114446 168114446 G	A
102	305 C	-1:168114445 168114445 C	
102	306 T	-1:168114444 168114444 T	
103 G	307 G	-1:168114443 168114443 G	G
103	308 G	-1:168114442 168114442 G	
103	309 G	-1:168114441 168114441 G	
104 I	310 A	-1:168114440 168114440 A	I
104	311 T	-1:168114439 168114439 T	
104	312 C	-1:168114438 168114438 C	
105 Y	313 T	-1:168114437 168114437 T	Y
105	314 A	-1:168114436 168114436 A	
105	315 T	-1:168114435 168114435 T	
106 D	316 G	-1:168114434 168114434 G	D
106	317 A	-1:168114433 168114433 A	
106	318 C	-1:168114432 168114432 C	
107 I	319 A	-1:168114431 168114431 A	I
107	320 T	-1:168114430 168114430 T	
107	321 A	-1:168114429 168114429 A	
108 L	322 T	-1:168114428 168114428 T	L
108	323 T	-1:168114427 168114427 T	
108	324 G	-1:168114426 168114426 G	
109 L	325 C	-1:168114425 168114425 C	L
109	326 T	-1:168114424 168114424 T	
109	327 G	-1:168114423 168114423 G	
110 A	328 G	-1:168114422 168114422 G	A
110	329 C	-1:168114421 168114421 C	
110	330 T	-1:168114420 168114420 T	
111 L	331 C	-1:168114419 168114419 C	L
111	332 T	-1:168114418 168114418 T	
111	333 T	-1:168114417 168114417 T	
112 I	334 A	-1:168114416 168114416 A	I
112	335 T	-1:168114415 168114415 T	
112	336 C	-1:168114414 168114414 C	
113 F	337 T	-1:168114413 168114413 T	F
113	338 T	-1:168114412 168114412 T	
113	339 C	-1:168114411 168114411 C	
114 L	340 C	-1:168114410 168114410 C	L
114	341 T	-1:168114409 168114409 T	
114	342 T	-1:168114408 168114408 T	
115 H	343 C	-1:168114407 168114407 C	H
115	344 A	-1:168114406 168114406 A	
115	345 T	-1:168114405 168114405 T	
116 D	346 G	-1:168114404 168114404 G	D
116	347 A	-1:168114403 168114403 A	
116	348 C	-1:168114402 168114402 C	
117 R	349 A	-1:168114401 168114401 A	R
117	350 G	-1:168114400 168114400 G	
117	351 A	-1:168114399 168114399 A	
118 G	352 G	-1:168111856 168111856 G	G
118	353 G	-1:168111855 168111855 G	
118	354 A	-1:168111854 168111854 A	
119 H	355 C	-1:168111853 168111853 C	H
119	356 A	-1:168111852 168111852 A	
119	357 C	-1:168111851 168111851 C	
120 L	358 C	-1:168111850 168111850 C	L
120	359 T	-1:168111849 168111849 T	
120	360 A	-1:168111848 168111848 A	
121 T	361 A	-1:168111847 168111847 A	T
121	362 C	-1:168111846 168111846 C	
121	363 A	-1:168111845 168111845 A	
122 H	364 C	-1:168111844 168111844 C	H
122	365 A	-1:168111843 168111843 A	
122	366 C	-1:168111842 168111842 C	
123 N	367 A	-1:168111841 168111841 A	N
123	368 A	-1:168111840 168111840 A	
123	369 T	-1:168111839 168111839 T	
124 N	370 A	-1:168111838 168111838 A	N
124	371 A	-1:168111837 168111837 A	
124	372 T	-1:168111836 168111836 T	
125 V	373 G	-1:168111835 168111835 G	V
125	374 T	-1:168111834 168111834 T	
125	375 C	-1:168111833 168111833 C	
126 C	376 T	-1:168111832 168111832 T	C
126	377 G	-1:168111831 168111831 G	
126	378 T	-1:168111830 168111830 T	
127 L	379 T	-1:168111829 168111829 T	L
127	380 T	-1:168111828 168111828 T	
127	381 A	-1:168111827 168111827 A	
128 S	382 T	-1:168111826 168111826 T	S
128	383 C	-1:168111825 168111825 C	
128	384 A	-1:168111824 168111824 A	
129 S	385 T	-1:168111823 168111823 T	S
129	386 C	-1:168111822 168111822 C	
129	387 T	-1:168111821 168111821 T	
130 V	388 G	-1:168111820 168111820 G	V
130	389 T	-1:168111819 168111819 T	
130	390 G	-1:168111818 168111818 G	
131 F	391 T	-1:168111817 168111817 T	F
131	392 T	-1:168111816 168111816 T	
131	393 T	-1:168111815 168111815 T	
132 V	394 G	-1:168111814 168111814 G	V
132	395 T	-1:168111813 168111813 T	
132	396 G	-1:168111812 168111812 G	
133 S	397 A	-1:168111811 168111811 A	S
133	398 G	-1:168111810 168111810 G	
133	399 T	-1:168111809 168111809 T	
134 E	400 G	-1:168111808 168111808 G	E
134	401 A	-1:168111807 168111807 A	
134	402 A	-1:168111806 168111806 A	
135 D	403 G	-1:168111805 168111805 G	D
135	404 A	-1:168111804 168111804 A	
135	405 T	-1:168111803 168111803 T	
136 G	406 G	-1:168111802 168111802 G	G
136	407 G	-1:168111801 168111801 G	
136	408 A	-1:168111800 168111800 A	
137 H	409 C	-1:168111799 168111799 C	H
137	410 A	-1:168111798 168111798 A	
137	411 C	-1:168111797 168111797 C	
138 W	412 T	-1:168111796 168111796 T	W
138	413 G	-1:168111795 168111795 G	
138	414 G	-1:168111794 168111794 G	
139 K	415 A	-1:168111793 168111793 A	K
139	416 A	-1:168111792 168111792 A	
139	417 G	-1:168111791 168111791 G	
140 L	418 C	-1:168111790 168111790 C	L
140	419 T	-1:168111789 168111789 T	
140	420 A	-1:168111788 168111788 A	
141 G	421 G	-1:168111787 168111787 G	G
141	422 G	-1:168111786 168111786 G	
141	423 A	-1:168111785 168111785 A	
142 G	424 G	-1:168111784 168111784 G	G
142	425 G	-1:168111783 168111783 G	
142	426 A	-1:168111782 168111782 A	
143 M	427 A	-1:168111781 168111781 A	M
143	428 T	-1:168111780 168111780 T	
143	429 G	-1:168111779 168111779 G	
144 E	430 G	-1:168111778 168111778 G	E
144	431 A	-1:168111777 168111777 A	
144	432 A	-1:168111776 168111776 A	
145 T	433 A	-1:168111775 168111775 A	T
145	434 C	-1:168111774 168111774 C	
145	435 T	-1:168111773 168111773 T	
146 V	436 G	-1:168111772 168111772 G	V
146	437 T	-1:168111771 168111771 T	
146	438 T	-1:168111770 168111770 T	
147 C	439 T	-1:168111769 168111769 T	C
147	440 G	-1:168111768 168111768 G	
147	441 T	-1:168111767 168111767 T	
148 K	442 A	-1:168111766 168111766 A	K
148	443 A	-1:168111765 168111765 A	
148	444 A	-1:168111764 168111764 A	
149 V	445 G	-1:168111763 168111763 G	V
149	446 T	-1:168111762 168111762 T	
149	447 T	-1:168111761 168111761 T	
150 S	448 T	-1:168111760 168111760 T	S
150	449 C	-1:168111759 168111759 C	
150	450 T	-1:168111758 168111758 T	
151 Q	451 C	-1:168111757 168111757 C	Q
151	452 A	-1:168111756 168111756 A	
151	453 G	-1:168111755 168111755 G	
152 A	454 G	-1:168111754 168111754 G	A
152	455 C	-1:168111753 168111753 C	
152	456 C	-1:168111752 168111752 C	
153 T	457 A	-1:168111751 168111751 A	T
153	458 C	-1:168111750 168111750 C	
153	459 A	-1:168111749 168111749 A	
154 P	460 C	-1:168111748 168111748 C	P
154	461 C	-1:168111747 168111747 C	
154	462 A	-1:168111746 168111746 A	
155 E	463 G	-1:168111745 168111745 G	E
155	464 A	-1:168111744 168111744 A	
155	465 G	-1:168111743 168111743 G	
156 F	466 T	-1:168109517 168109517 T	F
156	467 T	-1:168109516 168109516 T	
156	468 T	-1:168109515 168109515 T	
157 L	469 C	-1:168109514 168109514 C	L
157	470 T	-1:168109513 168109513 T	
157	471 G	-1:168109512 168109512 G	
158 R	472 A	-1:168109511 168109511 A	R
158	473 G	-1:168109510 168109510 G	
158	474 G	-1:168109509 168109509 G	
159 S	475 A	-1:168109508 168109508 A	S
159	476 G	-1:168109507 168109507 G	
159	477 T	-1:168109506 168109506 T	
160 I	478 A	-1:168109505 168109505 A	I
160	479 T	-1:168109504 168109504 T	
160	480 T	-1:168109503 168109503 T	
161 Q	481 C	-1:168109502 168109502 C	Q
161	482 A	-1:168109501 168109501 A	
161	483 G	-1:168109500 168109500 G	
162 S	484 T	-1:168109499 168109499 T	S
162	485 C	-1:168109498 168109498 C	
162	486 A	-1:168109497 168109497 A	
163 I	487 A	-1:168109496 168109496 A	I
163	488 T	-1:168109495 168109495 T	
163	489 A	-1:168109494 168109494 A	
164 R	490 A	-1:168109493 168109493 A	R
164	491 G	-1:168109492 168109492 G	
164	492 A	-1:168109491 168109491 A	
165 D	493 G	-1:168109490 168109490 G	D
165	494 A	-1:168109489 168109489 A	
165	495 C	-1:168109488 168109488 C	
166 P	496 C	-1:168109487 168109487 C	P
166	497 C	-1:168109486 168109486 C	
166	498 A	-1:168109485 168109485 A	
167 A	499 G	-1:168109484 168109484 G	A
167	500 C	-1:168109483 168109483 C	
167	501 A	-1:168109482 168109482 A	
168 S	502 T	-1:168109481 168109481 T	S
168	503 C	-1:168109480 168109480 C	
168	504 T	-1:168109479 168109479 T	
169 I	505 A	-1:168109478 168109478 A	I
169	506 T	-1:168109477 168109477 T	
169	507 C	-1:168109476 168109476 C	
170 P	508 C	-1:168109475 168109475 C	P
170	509 C	-1:168109474 168109474 C	
170	510 T	-1:168109473 168109473 T	
171 P	511 C	-1:168109472 168109472 C	P
171	512 C	-1:168109471 168109471 C	
171	513 T	-1:168109470 168109470 T	
172 E	514 G	-1:168109469 168109469 G	E
172	515 A	-1:168109468 168109468 A	
172	516 A	-1:168109467 168109467 A	
173 E	517 G	-1:168109466 168109466 G	E
173	518 A	-1:168109465 168109465 A	
173	519 G	-1:168109464 168109464 G	
174 M	520 A	-1:168109463 168109463 A	M
174	521 T	-1:168109462 168109462 T	
174	522 G	-1:168109461 168109461 G	
175 S	523 T	-1:168106122 168106122 T	S
175	524 C	-1:168106121 168106121 C	
175	525 T	-1:168106120 168106120 T	
176 P	526 C	-1:168106119 168106119 C	P
176	527 C	-1:168106118 168106118 C	
176	528 A	-1:168106117 168106117 A	
177 E	529 G	-1:168106116 168106116 G	E
177	530 A	-1:168106115 168106115 A	
177	531 A	-1:168106114 168106114 A	
178 F	532 T	-1:168106113 168106113 T	F
178	533 T	-1:168106112 168106112 T	
178	534 C	-1:168106111 168106111 C	
179 T	535 A	-1:168106110 168106110 A	T
179	536 C	-1:168106109 168106109 C	
179	537 A	-1:168106108 168106108 A	
180 T	538 A	-1:168106107 168106107 A	T
180	539 C	-1:168106106 168106106 C	
180	540 T	-1:168106105 168106105 T	
181 L	541 C	-1:168106104 168106104 C	L
181	542 T	-1:168106103 168106103 T	
181	543 C	-1:168106102 168106102 C	
182 P	544 C	-1:168106101 168106101 C	P
182	545 C	-1:168106100 168106100 C	
182	546 A	-1:168106099 168106099 A	
183 E	547 G	-1:168106098 168106098 G	E
183	548 A	-1:168106097 168106097 A	
183	549 G	-1:168106096 168106096 G	
184 C	550 T	-1:168106095 168106095 T	C
184	551 G	-1:168106094 168106094 G	
184	552 T	-1:168106093 168106093 T	
185 H	553 C	-1:168106092 168106092 C	H
185	554 A	-1:168106091 168106091 A	
185	555 T	-1:168106090 168106090 T	
186 G	556 G	-1:168106089 168106089 G	G
186	557 G	-1:168106088 168106088 G	
186	558 A	-1:168106087 168106087 A	
187 H	559 C	-1:168106086 168106086 C	H
187	560 A	-1:168106085 168106085 A	
187	561 T	-1:168106084 168106084 T	
188 A	562 G	-1:168106083 168106083 G	A
188	563 C	-1:168106082 168106082 C	
188	564 C	-1:168106081 168106081 C	
189 R	565 C	-1:168106080 168106080 C	R
189	566 G	-1:168106079 168106079 G	
189	567 G	-1:168106078 168106078 G	
190 D	568 G	-1:168106077 168106077 G	D
190	569 A	-1:168106076 168106076 A	
190	570 T	-1:168106075 168106075 T	
191 A	571 G	-1:168106074 168106074 G	A
191	572 C	-1:168106073 168106073 C	
191	573 C	-1:168106072 168106072 C	
192 F	574 T	-1:168106071 168106071 T	F
192	575 T	-1:168106070 168106070 T	
192	576 T	-1:168106069 168106069 T	
193 S	577 T	-1:168106068 168106068 T	S
193	578 C	-1:168106067 168106067 C	
193	579 A	-1:168106066 168106066 A	
194 F	580 T	-1:168106065 168106065 T	F
194	581 T	-1:168106064 168106064 T	
194	582 T	-1:168106063 168106063 T	
195 G	583 G	-1:168106062 168106062 G	G
195	584 G	-1:168106061 168106061 G	
195	585 A	-1:168106060 168106060 A	
196 T	586 A	-1:168106059 168106059 A	T
196	587 C	-1:168106058 168106058 C	
196	588 A	-1:168106057 168106057 A	
197 L	589 T	-1:168106056 168106056 T	L
197	590 T	-1:168106055 168106055 T	
197	591 G	-1:168106054 168106054 G	
198 V	592 G	-1:168106053 168106053 G	V
198	593 T	-1:168106052 168106052 T	
198	594 G	-1:168106051 168106051 G	
199 E	595 G	-1:168106050 168106050 G	E
199	596 A	-1:168106049 168106049 A	
199	597 A	-1:168106048 168106048 A	
200 S	598 A	-1:168106047 168106047 A	S
200	599 G	-1:168106046 168106046 G	
200	600 T	-1:168106045 168106045 T	
201 L	601 T	-1:168106044 168106044 T	L
201	602 T	-1:168106043 168106043 T	
201	603 G	-1:168106042 168106042 G	
202 L	604 C	-1:168106041 168106041 C	L
202	605 T	-1:168106040 168106040 T	
202	606 C	-1:168106039 168106039 C	
203 T	607 A	-1:168106038 168106038 A	T
203	608 C	-1:168106037 168106037 C	
203	609 A	-1:168106036 168106036 A	
204 I	610 A	-1:168106035 168106035 A	I
204	611 T	-1:168106034 168106034 T	
204	612 C	-1:168106033 168106033 C	
205 L	613 T	-1:168106032 168106032 T	L
205	614 T	-1:168106031 168106031 T	
205	615 A	-1:168106030 168106030 A	
206 N	616 A	-1:168106029 168106029 A	N
206	617 A	-1:168106028 168106028 A	
206	618 T	-1:168106027 168106027 T	
207 E	619 G	-1:168106026 168106026 G	E
207	620 A	-1:168106025 168106025 A	
207	621 A	-1:168106024 168106024 A	
208 Q	622 C	-1:168106023 168106023 C	Q
208	623 A	-1:168106022 168106022 A	
208	624 G	-1:168106021 168106021 G	
209 V	625 G	-1:168106020 168106020 G	V
209	626 T	-1:168104804 168104804 T	
209	627 T	-1:168104803 168104803 T	
210 S	628 T	-1:168104802 168104802 T	S
210	629 C	-1:168104801 168104801 C	
210	630 A	-1:168104800 168104800 A	
211 A	631 G	-1:168104799 168104799 G	A
211	632 C	-1:168104798 168104798 C	
211	633 G	-1:168104797 168104797 G	
212 D	634 G	-1:168104796 168104796 G	D
212	635 A	-1:168104795 168104795 A	
212	636 T	-1:168104794 168104794 T	
213 V	637 G	-1:168104793 168104793 G	V
213	638 T	-1:168104792 168104792 T	
213	639 T	-1:168104791 168104791 T	
214 L	640 C	-1:168104790 168104790 C	L
214	641 T	-1:168104789 168104789 T	
214	642 C	-1:168104788 168104788 C	
215 S	643 T	-1:168104787 168104787 T	S
215	644 C	-1:168104786 168104786 C	
215	645 C	-1:168104785 168104785 C	
216 S	646 A	-1:168104784 168104784 A	S
216	647 G	-1:168104783 168104783 G	
216	648 C	-1:168104782 168104782 C	
217 F	649 T	-1:168104781 168104781 T	F
217	650 T	-1:168104780 168104780 T	
217	651 T	-1:168104779 168104779 T	
218 Q	652 C	-1:168104778 168104778 C	Q
218	653 A	-1:168104777 168104777 A	
218	654 A	-1:168104776 168104776 A	
219 Q	655 C	-1:168104775 168104775 C	Q
219	656 A	-1:168104774 168104774 A	
219	657 G	-1:168104773 168104773 G	
220 T	658 A	-1:168104772 168104772 A	T
220	659 C	-1:168104771 168104771 C	
220	660 C	-1:168104770 168104770 C	
221 L	661 T	-1:168104769 168104769 T	L
221	662 T	-1:168104768 168104768 T	
221	663 G	-1:168104767 168104767 G	
222 H	664 C	-1:168104766 168104766 C	H
222	665 A	-1:168104765 168104765 A	
222	666 C	-1:168104764 168104764 C	
223 S	667 T	-1:168104763 168104763 T	S
223	668 C	-1:168104762 168104762 C	
223	669 A	-1:168104761 168104761 A	
224 T	670 A	-1:168104760 168104760 A	T
224	671 C	-1:168104759 168104759 C	
224	672 T	-1:168104758 168104758 T	
225 L	673 T	-1:168104757 168104757 T	L
225	674 T	-1:168104756 168104756 T	
225	675 G	-1:168104755 168104755 G	
226 L	676 C	-1:168104754 168104754 C	L
226	677 T	-1:168104753 168104753 T	
226	678 G	-1:168104752 168104752 G	
227 N	679 A	-1:168104751 168104751 A	N
227	680 A	-1:168104750 168104750 A	
227	681 T	-1:168104749 168104749 T	
228 P	682 C	-1:168104748 168104748 C	P
228	683 C	-1:168104747 168104747 C	
228	684 C	-1:168104746 168104746 C	
229 I	685 A	-1:168104745 168104745 A	I
229	686 T	-1:168104744 168104744 T	
229	687 T	-1:168104743 168104743 T	
230 P	688 C	-1:168104742 168104742 C	P
230	689 C	-1:168104741 168104741 C	
230	690 A	-1:168104740 168104740 A	
231 K	691 A	-1:168104739 168104739 A	K
231	692 A	-1:168104738 168104738 A	
231	693 A	-1:168104737 168104737 A	
232 C	694 T	-1:168104736 168104736 T	C
232	695 G	-1:168104735 168104735 G	
232	696 T	-1:168104734 168104734 T	
233 R	697 C	-1:168104733 168104733 C	R
233	698 G	-1:168104732 168104732 G	
233	699 G	-1:168104731 168104731 G	
234 P	700 C	-1:168104730 168104730 C	P
234	701 C	-1:168104729 168104729 C	
234	702 A	-1:168104728 168104728 A	
235 A	703 G	-1:168104727 168104727 G	A
235	704 C	-1:168104726 168104726 C	
235	705 G	-1:168104725 168104725 G	
236 L	706 C	-1:168104724 168104724 C	L
236	707 T	-1:168104723 168104723 T	
236	708 C	-1:168104722 168104722 C	
237 C	709 T	-1:168104721 168104721 T	C
237	710 G	-1:168104720 168104720 G	
237	711 C	-1:168104719 168104719 C	
238 T	712 A	-1:168104718 168104718 A	T
238	713 C	-1:168104717 168104717 C	
238	714 C	-1:168104716 168104716 C	
239 L	715 T	-1:168104715 168104715 T	L
239	716 T	-1:168104714 168104714 T	
239	717 A	-1:168104713 168104713 A	
240 L	718 C	-1:168104712 168104712 C	L
240	719 T	-1:168104711 168104711 T	
240	720 A	-1:168104710 168104710 A	
241 S	721 T	-1:168104709 168104709 T	S
241	722 C	-1:168104708 168104708 C	
241	723 T	-1:168104707 168104707 T	
242 H	724 C	-1:168104706 168104706 C	H
242	725 A	-1:168104705 168104705 A	
242	726 T	-1:168104704 168104704 T	
243 D	727 G	-1:168104703 168104703 G	D
243	728 A	-1:168104702 168104702 A	
243	729 C	-1:168104701 168104701 C	
244 F	730 T	-1:168104700 168104700 T	F
244	731 T	-1:168104699 168104699 T	
244	732 C	-1:168104698 168104698 C	
245 F	733 T	-1:168104697 168104697 T	F
245	734 T	-1:168104696 168104696 T	
245	735 C	-1:168104695 168104695 C	
246 R	736 A	-1:168104694 168104694 A	R
246	737 G	-1:168104693 168104693 G	
246	738 A	-1:168102738 168102738 A	
247 N	739 A	-1:168102737 168102737 A	N
247	740 A	-1:168102736 168102736 A	
247	741 T	-1:168102735 168102735 T	
248 D	742 G	-1:168102734 168102734 G	D
248	743 A	-1:168102733 168102733 A	
248	744 T	-1:168102732 168102732 T	
249 F	745 T	-1:168102731 168102731 T	F
249	746 T	-1:168102730 168102730 T	
249	747 T	-1:168102729 168102729 T	
250 L	748 C	-1:168102728 168102728 C	L
250	749 T	-1:168102727 168102727 T	
250	750 G	-1:168102726 168102726 G	
251 E	751 G	-1:168102725 168102725 G	E
251	752 A	-1:168102724 168102724 A	
251	753 A	-1:168102723 168102723 A	
252 V	754 G	-1:168102722 168102722 G	V
252	755 T	-1:168102721 168102721 T	
252	756 T	-1:168102720 168102720 T	
253 V	757 G	-1:168102719 168102719 G	V
253	758 T	-1:168102718 168102718 T	
253	759 G	-1:168102717 168102717 G	
254 N	760 A	-1:168102716 168102716 A	N
254	761 A	-1:168102715 168102715 A	
254	762 T	-1:168102714 168102714 T	
255 F	763 T	-1:168102713 168102713 T	F
255	764 T	-1:168102712 168102712 T	
255	765 C	-1:168102711 168102711 C	
256 L	766 T	-1:168102710 168102710 T	L
256	767 T	-1:168102709 168102709 T	
256	768 G	-1:168102708 168102708 G	
257 K	769 A	-1:168102707 168102707 A	K
257	770 A	-1:168102706 168102706 A	
257	771 A	-1:168102705 168102705 A	
258 S	772 A	-1:168102704 168102704 A	S
258	773 G	-1:168102703 168102703 G	
258	774 T	-1:168102702 168102702 T	
259 L	775 T	-1:168102701 168102701 T	L
259	776 T	-1:168102700 168102700 T	
259	777 A	-1:168102699 168102699 A	
260 T	778 A	-1:168102698 168102698 A	T
260	779 C	-1:168102697 168102697 C	
260	780 A	-1:168102696 168102696 A	
261 L	781 T	-1:168102695 168102695 T	L
261	782 T	-1:168102694 168102694 T	
261	783 G	-1:168102693 168102693 G	
262 K	784 A	-1:168102692 168102692 A	K
262	785 A	-1:168102691 168102691 A	
262	786 G	-1:168102690 168102690 G	
263 S	787 A	-1:168102689 168102689 A	S
263	788 G	-1:168102688 168102688 G	
263	789 T	-1:168102687 168102687 T	
264 E	790 G	-1:168102686 168102686 G	E
264	791 A	-1:168102685 168102685 A	
264	792 A	-1:168102684 168102684 A	
265 E	793 G	-1:168102683 168102683 G	E
265	794 A	-1:168102682 168102682 A	
265	795 G	-1:168102681 168102681 G	
266 E	796 G	-1:168102680 168102680 G	E
266	797 A	-1:168102679 168102679 A	
266	798 G	-1:168102678 168102678 G	
267 K	799 A	-1:168102677 168102677 A	K
267	800 A	-1:168102676 168102676 A	
267	801 A	-1:168102675 168102675 A	
268 T	802 A	-1:168102674 168102674 A	T
268	803 C	-1:168102673 168102673 C	
268	804 G	-1:168102672 168102672 G	
269 E	805 G	-1:168102671 168102671 G	E
269	806 A	-1:168102670 168102670 A	
269	807 A	-1:168102669 168102669 A	
270 F	808 T	-1:168102668 168102668 T	F
270	809 T	-1:168102667 168102667 T	
270	810 C	-1:168102666 168102666 C	
271 F	811 T	-1:168102665 168102665 T	F
271	812 T	-1:168102664 168102664 T	
271	813 T	-1:168102663 168102663 T	
272 K	814 A	-1:168102662 168102662 A	K
272	815 A	-1:168102661 168102661 A	
272	816 A	-1:168100273 168100273 A	
273 F	817 T	-1:168100272 168100272 T	F
273	818 T	-1:168100271 168100271 T	
273	819 T	-1:168100270 168100270 T	
274 L	820 C	-1:168100269 168100269 C	L
274	821 T	-1:168100268 168100268 T	
274	822 G	-1:168100267 168100267 G	
275 L	823 C	-1:168100266 168100266 C	L
275	824 T	-1:168100265 168100265 T	
275	825 G	-1:168100264 168100264 G	
276 D	826 G	-1:168100263 168100263 G	D
276	827 A	-1:168100262 168100262 A	
276	828 C	-1:168100261 168100261 C	
277 R	829 A	-1:168100260 168100260 A	R
277	830 G	-1:168100259 168100259 G	
277	831 A	-1:168100258 168100258 A	
278 V	832 G	-1:168100257 168100257 G	V
278	833 T	-1:168100256 168100256 T	
278	834 C	-1:168100255 168100255 C	
279 S	835 A	-1:168100254 168100254 A	S
279	836 G	-1:168100253 168100253 G	
279	837 C	-1:168100252 168100252 C	
280 C	838 T	-1:168100251 168100251 T	C
280	839 G	-1:168100250 168100250 G	
280	840 C	-1:168100249 168100249 C	
281 L	841 T	-1:168100248 168100248 T	L
281	842 T	-1:168100247 168100247 T	
281	843 G	-1:168100246 168100246 G	
282 S	844 T	-1:168100245 168100245 T	S
282	845 C	-1:168100244 168100244 C	
282	846 A	-1:168100243 168100243 A	
283 E	847 G	-1:168100242 168100242 G	E
283	848 A	-1:168100241 168100241 A	
283	849 G	-1:168100240 168100240 G	
284 E	850 G	-1:168100239 168100239 G	E
284	851 A	-1:168100238 168100238 A	
284	852 A	-1:168100237 168100237 A	
285 L	853 T	-1:168100236 168100236 T	L
285	854 T	-1:168100235 168100235 T	
285	855 G	-1:168100234 168100234 G	
286 I	856 A	-1:168100233 168100233 A	I
286	857 T	-1:168100232 168100232 T	
286	858 A	-1:168100231 168100231 A	
287 A	859 G	-1:168100230 168100230 G	A
287	860 C	-1:168100229 168100229 C	
287	861 T	-1:168100228 168100228 T	
288 S	862 T	-1:168100227 168100227 T	S
288	863 C	-1:168100226 168100226 C	
288	864 A	-1:168100225 168100225 A	
289 R	865 A	-1:168100224 168100224 A	R
289	866 G	-1:168100223 168100223 G	
289	867 G	-1:168100222 168100222 G	
290 L	868 T	-1:168100221 168100221 T	L
290	869 T	-1:168100220 168100220 T	
290	870 G	-1:168100219 168100219 G	
291 V	871 G	-1:168100218 168100218 G	V
291	872 T	-1:168100217 168100217 T	
291	873 G	-1:168100216 168100216 G	
292 P	874 C	-1:168100215 168100215 C	P
292	875 C	-1:168100214 168100214 C	
292	876 T	-1:168100213 168100213 T	
293 L	877 C	-1:168100212 168100212 C	L
293	878 T	-1:168100211 168100211 T	
293	879 T	-1:168100210 168100210 T	
294 L	880 C	-1:168100209 168100209 C	L
294	881 T	-1:168100208 168100208 T	
294	882 G	-1:168100207 168100207 G	
295 L	883 C	-1:168100206 168100206 C	L
295	884 T	-1:168100205 168100205 T	
295	885 T	-1:168100204 168100204 T	
296 N	886 A	-1:168100203 168100203 A	N
296	887 A	-1:168100202 168100202 A	
296	888 T	-1:168100201 168100201 T	
297 Q	889 C	-1:168100200 168100200 C	Q
297	890 A	-1:168100199 168100199 A	
297	891 G	-1:168100198 168100198 G	
298 L	892 T	-1:168100197 168100197 T	L
298	893 T	-1:168100196 168100196 T	
298	894 G	-1:168100195 168100195 G	
299 V	895 G	-1:168100194 168100194 G	V
299	896 T	-1:168100193 168100193 T	
299	897 G	-1:168100192 168100192 G	
300 F	898 T	-1:168100191 168100191 T	F
300	899 T	-1:168100190 168100190 T	
300	900 T	-1:168100189 168100189 T	
301 A	901 G	-1:168100188 168100188 G	A
301	902 C	-1:168100187 168100187 C	
301	903 A	-1:168100186 168100186 A	
302 E	904 G	-1:168100185 168100185 G	E
302	905 A	-1:168100184 168100184 A	
302	906 G	-1:168100183 168100183 G	
303 P	907 C	-1:168100182 168100182 C	P
303	908 C	-1:168100181 168100181 C	
303	909 A	-1:168100180 168100180 A	
304 V	910 G	-1:168100179 168100179 G	V
304	911 T	-1:168100178 168100178 T	
304	912 G	-1:168100177 168100177 G	
305 A	913 G	-1:168100176 168100176 G	A
305	914 C	-1:168100175 168100175 C	
305	915 T	-1:168100174 168100174 T	
306 V	916 G	-1:168100173 168100173 G	V
306	917 T	-1:168100172 168100172 T	
306	918 T	-1:168100171 168100171 T	
307 K	919 A	-1:168100170 168100170 A	K
307	920 A	-1:168100169 168100169 A	
307	921 G	-1:168100168 168100168 G	
308 S	922 A	-1:168100167 168100167 A	S
308	923 G	-1:168100166 168100166 G	
308	924 T	-1:168100165 168100165 T	
309 F	925 T	-1:168100164 168100164 T	F
309	926 T	-1:168100163 168100163 T	
309	927 T	-1:168100162 168100162 T	
310 L	928 C	-1:168100161 168100161 C	L
310	929 T	-1:168100160 168100160 T	
310	930 T	-1:168100159 168100159 T	
311 P	931 C	-1:168100158 168100158 C	P
311	932 C	-1:168100157 168100157 C	
311	933 T	-1:168100156 168100156 T	
312 Y	934 T	-1:168100155 168100155 T	Y
312	935 A	-1:168100154 168100154 A	
312	936 T	-1:168100153 168100153 T	
313 L	937 C	-1:168100152 168100152 C	L
313	938 T	-1:168100151 168100151 T	
313	939 G	-1:168100150 168100150 G	
314 L	940 C	-1:168100149 168100149 C	L
314	941 T	-1:168100148 168100148 T	
314	942 T	-1:168100147 168100147 T	
315 G	943 G	-1:168100146 168100146 G	G
315	944 G	-1:168100145 168100145 G	
315	945 C	-1:168100144 168100144 C	
316 P	946 C	-1:168100143 168100143 C	P
316	947 C	-1:168100142 168100142 C	
316	948 C	-1:168100141 168100141 C	
317 K	949 A	-1:168100140 168100140 A	K
317	950 A	-1:168100139 168100139 A	
317	951 A	-1:168100138 168100138 A	
318 K	952 A	-1:168100137 168100137 A	K
318	953 A	-1:168100136 168100136 A	
318	954 A	-1:168100135 168100135 A	
319 D	955 G	-1:168100134 168100134 G	D
319	956 A	-1:168098562 168098562 A	
319	957 T	-1:168098561 168098561 T	
320 H	958 C	-1:168098560 168098560 C	H
320	959 A	-1:168098559 168098559 A	
320	960 T	-1:168098558 168098558 T	
321 A	961 G	-1:168098557 168098557 G	A
321	962 C	-1:168098556 168098556 C	
321	963 G	-1:168098555 168098555 G	
322 Q	964 C	-1:168098554 168098554 C	Q
322	965 A	-1:168098553 168098553 A	
322	966 G	-1:168098552 168098552 G	
323 G	967 G	-1:168098551 168098551 G	G
323	968 G	-1:168098550 168098550 G	
323	969 A	-1:168098549 168098549 A	
324 E	970 G	-1:168098548 168098548 G	E
324	971 A	-1:168098547 168098547 A	
324	972 A	-1:168098546 168098546 A	
325 T	973 A	-1:168098545 168098545 A	T
325	974 C	-1:168098544 168098544 C	
325	975 T	-1:168098543 168098543 T	
326 P	976 C	-1:168098542 168098542 C	P
326	977 C	-1:168098541 168098541 C	
326	978 T	-1:168098540 168098540 T	
327 C	979 T	-1:168098539 168098539 T	C
327	980 G	-1:168098538 168098538 G	
327	981 C	-1:168098537 168098537 C	
328 L	982 T	-1:168098536 168098536 T	L
328	983 T	-1:168098535 168098535 T	
328	984 G	-1:168098534 168098534 G	
329 L	985 C	-1:168098533 168098533 C	L
329	986 T	-1:168098532 168098532 T	
329	987 C	-1:168098531 168098531 C	
330 S	988 T	-1:168098530 168098530 T	S
330	989 C	-1:168098529 168098529 C	
330	990 A	-1:168098528 168098528 A	
331 P	991 C	-1:168098527 168098527 C	P
331	992 C	-1:168098526 168098526 C	
331	993 A	-1:168098525 168098525 A	
332 A	994 G	-1:168098524 168098524 G	A
332	995 C	-1:168098523 168098523 C	
332	996 C	-1:168098522 168098522 C	
333 L	997 C	-1:168098521 168098521 C	L
333	998 T	-1:168098520 168098520 T	
333	999 G	-1:168098519 168098519 G	
334 F	1000 T	-1:168098518 168098518 T	F
334	1001 T	-1:168098517 168098517 T	
334	1002 C	-1:168098516 168098516 C	
335 Q	1003 C	-1:168098515 168098515 C	Q
335	1004 A	-1:168098514 168098514 A	
335	1005 G	-1:168098513 168098513 G	
336 S	1006 T	-1:168098512 168098512 T	S
336	1007 C	-1:168098511 168098511 C	
336	1008 A	-1:168098510 168098510 A	
337 R	1009 C	-1:168098509 168098509 C	R
337	1010 G	-1:168098508 168098508 G	
337	1011 G	-1:168098507 168098507 G	
338 V	1012 G	-1:168098506 168098506 G	V
338	1013 T	-1:168098505 168098505 T	
338	1014 G	-1:168098504 168098504 G	
339 I	1015 A	-1:168098503 168098503 A	I
339	1016 T	-1:168098502 168098502 T	
339	1017 C	-1:168098501 168098501 C	
340 P	1018 C	-1:168098500 168098500 C	P
340	1019 C	-1:168098499 168098499 C	
340	1020 C	-1:168098498 168098498 C	
341 V	1021 G	-1:168098497 168098497 G	V
341	1022 T	-1:168098496 168098496 T	
341	1023 G	-1:168098495 168098495 G	
342 L	1024 C	-1:168098494 168098494 C	L
342	1025 T	-1:168098493 168098493 T	
342	1026 T	-1:168098492 168098492 T	
343 L	1027 C	-1:168098491 168098491 C	L
343	1028 T	-1:168098490 168098490 T	
343	1029 C	-1:168098489 168098489 C	
344 Q	1030 C	-1:168098488 168098488 C	Q
344	1031 A	-1:168098487 168098487 A	
344	1032 G	-1:168098486 168098486 G	
345 L	1033 T	-1:168098485 168098485 T	L
345	1034 T	-1:168098484 168098484 T	
345	1035 G	-1:168098483 168098483 G	
346 F	1036 T	-1:168098482 168098482 T	F
346	1037 T	-1:168098481 168098481 T	
346	1038 T	-1:168098480 168098480 T	
347 E	1039 G	-1:168098479 168098479 G	E
347	1040 A	-1:168098478 168098478 A	
347	1041 A	-1:168098477 168098477 A	
348 V	1042 G	-1:168098476 168098476 G	V
348	1043 T	-1:168098475 168098475 T	
348	1044 T	-1:168098474 168098474 T	
349 H	1045 C	-1:168098473 168098473 C	H
349	1046 A	-1:168098472 168098472 A	
349	1047 T	-1:168098471 168098471 T	
350 E	1048 G	-1:168098470 168098470 G	E
350	1049 A	-1:168098469 168098469 A	
350	1050 A	-1:168098468 168098468 A	
351 E	1051 G	-1:168098467 168098467 G	E
351	1052 A	-1:168098466 168098466 A	
351	1053 G	-1:168098465 168098465 G	
352 H	1054 C	-1:168098464 168098464 C	H
352	1055 A	-1:168098463 168098463 A	
352	1056 T	-1:168098462 168098462 T	
353 V	1057 G	-1:168098461 168098461 G	V
353	1058 T	-1:168098460 168098460 T	
353	1059 G	-1:168098459 168098459 G	
354 R	1060 C	-1:168098458 168098458 C	R
354	1061 G	-1:168098457 168098457 G	
354	1062 G	-1:168098456 168098456 G	
355 M	1063 A	-1:168098455 168098455 A	M
355	1064 T	-1:168098454 168098454 T	
355	1065 G	-1:168098453 168098453 G	
356 V	1066 G	-1:168098452 168098452 G	V
356	1067 T	-1:168098451 168098451 T	
356	1068 G	-1:168098450 168098450 G	
357 L	1069 C	-1:168098449 168098449 C	L
357	1070 T	-1:168098448 168098448 T	
357	1071 G	-1:168098447 168098447 G	
358 L	1072 C	-1:168098446 168098446 C	L
358	1073 T	-1:168098445 168098445 T	
358	1074 G	-1:168098444 168098444 G	
359 S	1075 T	-1:168098443 168098443 T	S
359	1076 C	-1:168098442 168098442 C	
359	1077 T	-1:168098441 168098441 T	
360 H	1078 C	-1:168098440 168098440 C	H
360	1079 A	-1:168098439 168098439 A	
360	1080 C	-1:168098438 168098438 C	
361 I	1081 A	-1:168098437 168098437 A	I
361	1082 T	-1:168098436 168098436 T	
361	1083 C	-1:168098435 168098435 C	
362 E	1084 G	-1:168098434 168098434 G	E
362	1085 A	-1:168098433 168098433 A	
362	1086 G	-1:168098432 168098432 G	
363 A	1087 G	-1:168098431 168098431 G	A
363	1088 C	-1:168098430 168098430 C	
363	1089 C	-1:168098429 168098429 C	
364 Y	1090 T	-1:168098428 168098428 T	Y
364	1091 A	-1:168098427 168098427 A	
364	1092 C	-1:168098426 168098426 C	
365 V	1093 G	-1:168098425 168098425 G	V
365	1094 T	-1:168098424 168098424 T	
365	1095 G	-1:168098423 168098423 G	
366 E	1096 G	-1:168098422 168098422 G	E
366	1097 A	-1:168098421 168098421 A	
366	1098 G	-1:168098420 168098420 G	
367 H	1099 C	-1:168098419 168098419 C	H
367	1100 A	-1:168098418 168098418 A	
367	1101 C	-1:168098417 168098417 C	
368 F	1102 T	-1:168098416 168098416 T	F
368	1103 T	-1:168098415 168098415 T	
368	1104 C	-1:168098414 168098414 C	
369 T	1105 A	-1:168098413 168098413 A	T
369	1106 C	-1:168098412 168098412 C	
369	1107 T	-1:168098411 168098411 T	
370 Q	1108 C	-1:168098410 168098410 C	Q
370	1109 A	-1:168098409 168098409 A	
370	1110 G	-1:168098408 168098408 G	
371 E	1111 G	-1:168098407 168098407 G	E
371	1112 A	-1:168098406 168098406 A	
371	1113 G	-1:168098405 168098405 G	
372 Q	1114 C	-1:168098404 168098404 C	Q
372	1115 A	-1:168098403 168098403 A	
372	1116 G	-1:168098402 168098402 G	
373 L	1117 C	-1:168098401 168098401 C	L
373	1118 T	-1:168098400 168098400 T	
373	1119 G	-1:168098399 168098399 G	
374 K	1120 A	-1:168098398 168098398 A	K
374	1121 A	-1:168098397 168098397 A	
374	1122 G	-1:168098396 168098396 G	
375 K	1123 A	-1:168098395 168098395 A	K
375	1124 A	-1:168098394 168098394 A	
375	1125 A	-1:168098393 168098393 A	
376 V	1126 G	-1:168098392 168098392 G	V
376	1127 T	-1:168098391 168098391 T	
376	1128 C	-1:168098390 168098390 C	
377 I	1129 A	-1:168098389 168098389 A	I
377	1130 T	-1:168098388 168098388 T	
377	1131 C	-1:168098387 168098387 C	
378 L	1132 T	-1:168098386 168098386 T	L
378	1133 T	-1:168098385 168098385 T	
378	1134 G	-1:168098384 168098384 G	
379 P	1135 C	-1:168098383 168098383 C	P
379	1136 C	-1:168098382 168098382 C	
379	1137 A	-1:168098381 168098381 A	
380 Q	1138 C	-1:168098380 168098380 C	Q
380	1139 A	-1:168098379 168098379 A	
380	1140 G	-1:168098378 168098378 G	
381 V	1141 G	-1:168094977 168094977 G	V
381	1142 T	-1:168094976 168094976 T	
381	1143 T	-1:168094975 168094975 T	
382 L	1144 T	-1:168094974 168094974 T	L
382	1145 T	-1:168094973 168094973 T	
382	1146 G	-1:168094972 168094972 G	
383 L	1147 C	-1:168094971 168094971 C	L
383	1148 T	-1:168094970 168094970 T	
383	1149 G	-1:168094969 168094969 G	
384 G	1150 G	-1:168094968 168094968 G	G
384	1151 G	-1:168094967 168094967 G	
384	1152 C	-1:168094966 168094966 C	
385 L	1153 C	-1:168094965 168094965 C	L
385	1154 T	-1:168094964 168094964 T	
385	1155 G	-1:168094963 168094963 G	
386 R	1156 C	-1:168094962 168094962 C	R
386	1157 G	-1:168094961 168094961 G	
386	1158 T	-1:168094960 168094960 T	
387 D	1159 G	-1:168094959 168094959 G	D
387	1160 A	-1:168094958 168094958 A	
387	1161 T	-1:168094957 168094957 T	
388 T	1162 A	-1:168094956 168094956 A	T
388	1163 C	-1:168094955 168094955 C	
388	1164 T	-1:168094954 168094954 T	
389 S	1165 A	-1:168094953 168094953 A	S
389	1166 G	-1:168094952 168094952 G	
389	1167 C	-1:168094951 168094951 C	
390 D	1168 G	-1:168094950 168094950 G	D
390	1169 A	-1:168094949 168094949 A	
390	1170 T	-1:168094948 168094948 T	
391 S	1171 T	-1:168094947 168094947 T	S
391	1172 C	-1:168094946 168094946 C	
391	1173 C	-1:168094945 168094945 C	
392 I	1174 A	-1:168094944 168094944 A	I
392	1175 T	-1:168094943 168094943 T	
392	1176 T	-1:168094942 168094942 T	
393 V	1177 G	-1:168094941 168094941 G	V
393	1178 T	-1:168094940 168094940 T	
393	1179 G	-1:168094939 168094939 G	
394 A	1180 G	-1:168094938 168094938 G	A
394	1181 C	-1:168094937 168094937 C	
394	1182 A	-1:168094936 168094936 A	
395 I	1183 A	-1:168094935 168094935 A	I
395	1184 T	-1:168094934 168094934 T	
395	1185 T	-1:168094933 168094933 T	
396 T	1186 A	-1:168094932 168094932 A	T
396	1187 C	-1:168094931 168094931 C	
396	1188 T	-1:168094930 168094930 T	
397 L	1189 C	-1:168094929 168094929 C	L
397	1190 T	-1:168094928 168094928 T	
397	1191 G	-1:168094927 168094927 G	
398 H	1192 C	-1:168094926 168094926 C	H
398	1193 A	-1:168094925 168094925 A	
398	1194 T	-1:168094924 168094924 T	
399 S	1195 A	-1:168094923 168094923 A	S
399	1196 G	-1:168094922 168094922 G	
399	1197 C	-1:168094921 168094921 C	
400 L	1198 C	-1:168094920 168094920 C	L
400	1199 T	-1:168094919 168094919 T	
400	1200 A	-1:168094918 168094918 A	
401 A	1201 G	-1:168094917 168094917 G	A
401	1202 C	-1:168094916 168094916 C	
401	1203 A	-1:168094915 168094915 A	
402 V	1204 G	-1:168094914 168094914 G	V
402	1205 T	-1:168094913 168094913 T	
402	1206 G	-1:168094912 168094912 G	
403 L	1207 C	-1:168094911 168094911 C	L
403	1208 T	-1:168094910 168094910 T	
403	1209 G	-1:168094909 168094909 G	
404 V	1210 G	-1:168094908 168094908 G	V
404	1211 T	-1:168094907 168094907 T	
404	1212 C	-1:168094906 168094906 C	
405 S	1213 T	-1:168094905 168094905 T	S
405	1214 C	-1:168094904 168094904 C	
405	1215 T	-1:168094903 168094903 T	
406 L	1216 C	-1:168094902 168094902 C	L
406	1217 T	-1:168094901 168094901 T	
406	1218 G	-1:168094900 168094900 G	
407 L	1219 C	-1:168094899 168094899 C	L
407	1220 T	-1:168094898 168094898 T	
407	1221 T	-1:168094897 168094897 T	
408 G	1222 G	-1:168094896 168094896 G	G
408	1223 G	-1:168094895 168094895 G	
408	1224 A	-1:168094894 168094894 A	
409 P	1225 C	-1:168094893 168094893 C	P
409	1226 C	-1:168094892 168094892 C	
409	1227 A	-1:168094891 168094891 A	
410 E	1228 G	-1:168094890 168094890 G	E
410	1229 A	-1:168094889 168094889 A	
410	1230 G	-1:168094888 168094888 G	
411 V	1231 G	-1:168094887 168094887 G	V
411	1232 T	-1:168094886 168094886 T	
411	1233 G	-1:168094885 168094885 G	
412 V	1234 G	-1:168094884 168094884 G	V
412	1235 T	-1:168094883 168094883 T	
412	1236 T	-1:168094882 168094882 T	
413 V	1237 G	-1:168094881 168094881 G	V
413	1238 T	-1:168094880 168094880 T	
413	1239 G	-1:168094879 168094879 G	
414 G	1240 G	-1:168094878 168094878 G	G
414	1241 G	-1:168094877 168094877 G	
414	1242 A	-1:168094876 168094876 A	
415 G	1243 G	-1:168094875 168094875 G	G
415	1244 G	-1:168094874 168094874 G	
415	1245 A	-1:168094873 168094873 A	
416 E	1246 G	-1:168094872 168094872 G	E
416	1247 A	-1:168094871 168094871 A	
416	1248 A	-1:168094870 168094870 A	
417 R	1249 C	-1:168094869 168094869 C	R
417	1250 G	-1:168094868 168094868 G	
417	1251 A	-1:168094867 168094867 A	
418 T	1252 A	-1:168094866 168094866 A	T
418	1253 C	-1:168094865 168094865 C	
418	1254 C	-1:168094864 168094864 C	
419 K	1255 A	-1:168094863 168094863 A	K
419	1256 A	-1:168094862 168094862 A	
419	1257 G	-1:168094861 168094861 G	
420 I	1258 A	-1:168094860 168094860 A	I
420	1259 T	-1:168094859 168094859 T	
420	1260 C	-1:168094858 168094858 C	
421 F	1261 T	-1:168094857 168094857 T	F
421	1262 T	-1:168094856 168094856 T	
421	1263 C	-1:168094855 168094855 C	
422 K	1264 A	-1:168094854 168094854 A	K
422	1265 A	-1:168094853 168094853 A	
422	1266 A	-1:168094852 168094852 A	
423 R	1267 C	-1:168094851 168094851 C	R
423	1268 G	-1:168094850 168094850 G	
423	1269 C	-1:168094849 168094849 C	
424 T	1270 A	-1:168094848 168094848 A	T
424	1271 C	-1:168094847 168094847 C	
424	1272 T	-1:168094846 168094846 T	
425 A	1273 G	-1:168094845 168094845 G	A
425	1274 C	-1:168094844 168094844 C	
425	1275 C	-1:168094843 168094843 C	
426 P	1276 C	-1:168094842 168094842 C	P
426	1277 C	-1:168094841 168094841 C	
426	1278 A	-1:168094840 168094840 A	
427 S	1279 A	-1:168094839 168094839 A	S
427	1280 G	-1:168094838 168094838 G	
427	1281 T	-1:168094837 168094837 T	
428 F	1282 T	-1:168094836 168094836 T	F
428	1283 T	-1:168094835 168094835 T	
428	1284 T	-1:168094834 168094834 T	
429 T	1285 A	-1:168094833 168094833 A	T
429	1286 C	-1:168094832 168094832 C	
429	1287 T	-1:168094831 168094831 T	
430 K	1288 A	-1:168094830 168094830 A	K
430	1289 A	-1:168094829 168094829 A	
430	1290 A	-1:168094828 168094828 A	
431 N	1291 A	-1:168094827 168094827 A	N
431	1292 A	-1:168094826 168094826 A	
431	1293 T	-1:168094825 168094825 T	
432 T	1294 A	-1:168094824 168094824 A	T
432	1295 C	-1:168094823 168094823 C	
432	1296 T	-1:168094822 168094822 T	
433 D	1297 G	-1:168094821 168094821 G	D
433	1298 A	-1:168094820 168094820 A	
433	1299 C	-1:168094819 168094819 C	
434 L	1300 C	-1:168094818 168094818 C	L
434	1301 T	-1:168094817 168094817 T	
434	1302 T	-1:168094816 168094816 T	
435 S	1303 T	-1:168094815 168094815 T	S
435	1304 C	-1:168094814 168094814 C	
435	1305 T	-1:168094813 168094813 T	
436 L	1306 C	-1:168094812 168094812 C	L
436	1307 T	-1:168094811 168094811 T	
436	1308 A	-1:168094810 168094810 A	
437 E	1309 G	-1:168094809 168094809 G	E
437	1310 A	-1:168094808 168094808 A	
437	1311 A	-1:168094807 168094807 A	
438 G	1312 G	-1:168094806 168094806 G	G
438	1313 G	-1:168090729 168090729 G	
438	1314 C	-1:168090728 168090728 C	
439 D	1315 G	-1:168090727 168090727 G	D
439	1316 A	-1:168090726 168090726 A	
439	1317 T	-1:168090725 168090725 T	
440 P	1318 C	-1:168090724 168090724 C	P
440	1319 C	-1:168090723 168090723 C	
440	1320 A	-1:168090722 168090722 A	
441 F	1321 T	-1:168090721 168090721 T	F
441	1322 T	-1:168090720 168090720 T	
441	1323 T	-1:168090719 168090719 T	
442 S	1324 T	-1:168090718 168090718 T	S
442	1325 C	-1:168090717 168090717 C	
442	1326 T	-1:168090716 168090716 T	
443 Q	1327 C	-1:168090715 168090715 C	Q
443	1328 A	-1:168090714 168090714 A	
443	1329 G	-1:168090713 168090713 G	
444 P	1330 C	-1:168090712 168090712 C	P
444	1331 C	-1:168090711 168090711 C	
444	1332 T	-1:168090710 168090710 T	
445 I	1333 A	-1:168090709 168090709 A	I
445	1334 T	-1:168090708 168090708 T	
445	1335 T	-1:168090707 168090707 T	
446 K	1336 A	-1:168090706 168090706 A	K
446	1337 A	-1:168090705 168090705 A	
446	1338 A	-1:168090704 168090704 A	
447 F	1339 T	-1:168090703 168090703 T	F
447	1340 T	-1:168090702 168090702 T	
447	1341 T	-1:168090701 168090701 T	
448 P	1342 C	-1:168090700 168090700 C	P
448	1343 C	-1:168090699 168090699 C	
448	1344 C	-1:168090698 168090698 C	
449 I	1345 A	-1:168090697 168090697 A	I
449	1346 T	-1:168090696 168090696 T	
449	1347 A	-1:168090695 168090695 A	
450 N	1348 A	-1:168090694 168090694 A	N
450	1349 A	-1:168090693 168090693 A	
450	1350 T	-1:168090692 168090692 T	
451 G	1351 G	-1:168090691 168090691 G	G
451	1352 G	-1:168090690 168090690 G	
451	1353 A	-1:168090689 168090689 A	
452 L	1354 C	-1:168090688 168090688 C	L
452	1355 T	-1:168090687 168090687 T	
452	1356 C	-1:168090686 168090686 C	
453 S	1357 T	-1:168090685 168090685 T	S
453	1358 C	-1:168090684 168090684 C	
453	1359 A	-1:168090683 168090683 A	
454 D	1360 G	-1:168090682 168090682 G	D
454	1361 A	-1:168090681 168090681 A	
454	1362 T	-1:168090680 168090680 T	
455 V	1363 G	-1:168090679 168090679 G	V
455	1364 T	-1:168090678 168090678 T	
455	1365 A	-1:168090677 168090677 A	
456 K	1366 A	-1:168090676 168090676 A	K
456	1367 A	-1:168090675 168090675 A	
456	1368 A	-1:168090674 168090674 A	
457 N	1369 A	-1:168090673 168090673 A	N
457	1370 A	-1:168090672 168090672 A	
457	1371 T	-1:168090671 168090671 T	
458 T	1372 A	-1:168090670 168090670 A	T
458	1373 C	-1:168090669 168090669 C	
458	1374 T	-1:168090668 168090668 T	
459 S	1375 T	-1:168090667 168090667 T	S
459	1376 C	-1:168090666 168090666 C	
459	1377 G	-1:168090665 168090665 G	
460 E	1378 G	-1:168090664 168090664 G	E
460	1379 A	-1:168090663 168090663 A	
460	1380 G	-1:168090662 168090662 G	
461 D	1381 G	-1:168090661 168090661 G	D
461	1382 A	-1:168090660 168090660 A	
461	1383 C	-1:168090659 168090659 C	
462 S	1384 A	-1:168090658 168090658 A	S
462	1385 G	-1:168090657 168090657 G	
462	1386 T	-1:168090656 168090656 T	
463 E	1387 G	-1:168090655 168090655 G	E
463	1388 A	-1:168090654 168090654 A	
463	1389 A	-1:168090653 168090653 A	
464 N	1390 A	-1:168090652 168090652 A	N
464	1391 A	-1:168090651 168090651 A	
464	1392 C	-1:168090650 168090650 C	
465 F	1393 T	-1:168090649 168090649 T	F
465	1394 T	-1:168090648 168090648 T	
465	1395 C	-1:168090647 168090647 C	
466 P	1396 C	-1:168090646 168090646 C	P
466	1397 C	-1:168090645 168090645 C	
466	1398 A	-1:168090644 168090644 A	
467 S	1399 T	-1:168090643 168090643 T	S
467	1400 C	-1:168090642 168090642 C	
467	1401 A	-1:168090641 168090641 A	
468 S	1402 A	-1:168090640 168090640 A	S
468	1403 G	-1:168090639 168090639 G	
468	1404 T	-1:168090638 168090638 T	
469 S	1405 T	-1:168090637 168090637 T	S
469	1406 C	-1:168090636 168090636 C	
469	1407 T	-1:168090635 168090635 T	
470 K	1408 A	-1:168090634 168090634 A	K
470	1409 A	-1:168090633 168090633 A	
470	1410 A	-1:168090632 168090632 A	
471 K	1411 A	-1:168090631 168090631 A	K
471	1412 A	-1:168090630 168090630 A	
471	1413 G	-1:168090629 168090629 G	
472 S	1414 T	-1:168090628 168090628 T	S
472	1415 C	-1:168090627 168090627 C	
472	1416 T	-1:168090626 168090626 T	
473 E	1417 G	-1:168090625 168090625 G	E
473	1418 A	-1:168090624 168090624 A	
473	1419 G	-1:168090623 168090623 G	
474 E	1420 G	-1:168090622 168090622 G	E
474	1421 A	-1:168090621 168090621 A	
474	1422 G	-1:168090620 168090620 G	
475 W	1423 T	-1:168090619 168090619 T	W
475	1424 G	-1:168090618 168090618 G	
475	1425 G	-1:168090617 168090617 G	
476 P	1426 C	-1:168090616 168090616 C	P
476	1427 C	-1:168090615 168090615 C	
476	1428 T	-1:168090614 168090614 T	
477 D	1429 G	-1:168090613 168090613 G	D
477	1430 A	-1:168090612 168090612 A	
477	1431 C	-1:168090611 168090611 C	
478 W	1432 T	-1:168090610 168090610 T	W
478	1433 G	-1:168090609 168090609 G	
478	1434 G	-1:168090608 168090608 G	
479 S	1435 A	-1:168090607 168090607 A	S
479	1436 G	-1:168090606 168090606 G	
479	1437 T	-1:168090605 168090605 T	
480 E	1438 G	-1:168090604 168090604 G	E
480	1439 A	-1:168090603 168090603 A	
480	1440 A	-1:168090602 168090602 A	
481 P	1441 C	-1:168090601 168090601 C	P
481	1442 C	-1:168090600 168090600 C	
481	1443 T	-1:168090599 168090599 T	
482 E	1444 G	-1:168090598 168090598 G	E
482	1445 A	-1:168090597 168090597 A	
482	1446 G	-1:168090596 168090596 G	
483 E	1447 G	-1:168090595 168090595 G	E
483	1448 A	-1:168090594 168090594 A	
483	1449 G	-1:168090593 168090593 G	
484 P	1450 C	-1:168090592 168090592 C	P
484	1451 C	-1:168090591 168090591 C	
484	1452 T	-1:168090590 168090590 T	
485 E	1453 G	-1:168090589 168090589 G	E
485	1454 A	-1:168090588 168090588 A	
485	1455 A	-1:168090587 168090587 A	
486 N	1456 A	-1:168090586 168090586 A	N
486	1457 A	-1:168090585 168090585 A	
486	1458 T	-1:168090584 168090584 T	
487 Q	1459 C	-1:168090583 168090583 C	Q
487	1460 A	-1:168090582 168090582 A	
487	1461 A	-1:168090581 168090581 A	
488 T	1462 A	-1:168090580 168090580 A	T
488	1463 C	-1:168090579 168090579 C	
488	1464 T	-1:168090578 168090578 T	
489 V	1465 G	-1:168090577 168090577 G	V
489	1466 T	-1:168090576 168090576 T	
489	1467 C	-1:168090575 168090575 C	
490 N	1468 A	-1:168090574 168090574 A	N
490	1469 A	-1:168090573 168090573 A	
490	1470 C	-1:168090572 168090572 C	
491 I	1471 A	-1:168090571 168090571 A	I
491	1472 T	-1:168090570 168090570 T	
491	1473 A	-1:168090569 168090569 A	
492 Q	1474 C	-1:168090568 168090568 C	Q
492	1475 A	-1:168090567 168090567 A	
492	1476 G	-1:168090566 168090566 G	
493 I	1477 A	-1:168090565 168090565 A	I
493	1478 T	-1:168090564 168090564 T	
493	1479 T	-1:168090563 168090563 T	
494 W	1480 T	-1:168090562 168090562 T	W
494	1481 G	-1:168090561 168090561 G	
494	1482 G	-1:168090560 168090560 G	
495 P	1483 C	-1:168090559 168090559 C	P
495	1484 C	-1:168090558 168090558 C	
495	1485 T	-1:168090557 168090557 T	
496 R	1486 A	-1:168090556 168090556 A	R
496	1487 G	-1:168090555 168090555 G	
496	1488 A	-1:168090554 168090554 A	
497 E	1489 G	-1:168090553 168090553 G	E
497	1490 A	-1:168090552 168090552 A	
497	1491 A	-1:168090551 168090551 A	
498 P	1492 C	-1:168090550 168090550 C	P
498	1493 C	-1:168090549 168090549 C	
498	1494 T	-1:168090548 168090548 T	
499 C	1495 T	-1:168090547 168090547 T	C
499	1496 G	-1:168090546 168090546 G	
499	1497 T	-1:168090545 168090545 T	
500 D	1498 G	-1:168090544 168090544 G	D
500	1499 A	-1:168090543 168090543 A	
500	1500 T	-1:168090542 168090542 T	
501 D	1501 G	-1:168090541 168090541 G	D
501	1502 A	-1:168090540 168090540 A	
501	1503 T	-1:168090539 168090539 T	
502 V	1504 G	-1:168090538 168090538 G	V
502	1505 T	-1:168090537 168090537 T	
502	1506 C	-1:168090536 168090536 C	
503 K	1507 A	-1:168090535 168090535 A	K
503	1508 A	-1:168090534 168090534 A	
503	1509 G	-1:168090533 168090533 G	
504 S	1510 T	-1:168090532 168090532 T	S
504	1511 C	-1:168090531 168090531 C	
504	1512 C	-1:168090530 168090530 C	
505 Q	1513 C	-1:168090529 168090529 C	Q
505	1514 A	-1:168090528 168090528 A	
505	1515 G	-1:168090527 168090527 G	
506 C	1516 T	-1:168090526 168090526 T	C
506	1517 G	-1:168090525 168090525 G	
506	1518 C	-1:168090524 168090524 C	
507 T	1519 A	-1:168090523 168090523 A	T
507	1520 C	-1:168090522 168090522 C	
507	1521 T	-1:168090521 168090521 T	
508 T	1522 A	-1:168090520 168090520 A	T
508	1523 C	-1:168090519 168090519 C	
508	1524 C	-1:168090518 168090518 C	
509 L	1525 T	-1:168090517 168090517 T	L
509	1526 T	-1:168090516 168090516 T	
509	1527 G	-1:168090515 168090515 G	
510 D	1528 G	-1:168090514 168090514 G	D
510	1529 A	-1:168090513 168090513 A	
510	1530 T	-1:168090512 168090512 T	
511 V	1531 G	-1:168090511 168090511 G	V
511	1532 T	-1:168090510 168090510 T	
511	1533 G	-1:168090509 168090509 G	
512 E	1534 G	-1:168090508 168090508 G	E
512	1535 A	-1:168090507 168090507 A	
512	1536 A	-1:168090506 168090506 A	
513 E	1537 G	-1:168090505 168090505 G	E
513	1538 A	-1:168090504 168090504 A	
513	1539 G	-1:168090503 168090503 G	
514 S	1540 T	-1:168090502 168090502 T	S
514	1541 C	-1:168090501 168090501 C	
514	1542 A	-1:168090500 168090500 A	
515 S	1543 T	-1:168090499 168090499 T	S
515	1544 C	-1:168090498 168090498 C	
515	1545 T	-1:168090497 168090497 T	
516 W	1546 T	-1:168090496 168090496 T	W
516	1547 G	-1:168090495 168090495 G	
516	1548 G	-1:168090494 168090494 G	
517 D	1549 G	-1:168090493 168090493 G	D
517	1550 A	-1:168090492 168090492 A	
517	1551 T	-1:168090491 168090491 T	
518 D	1552 G	-1:168090490 168090490 G	D
518	1553 A	-1:168090489 168090489 A	
518	1554 C	-1:168090488 168090488 C	
519 C	1555 T	-1:168090487 168090487 T	C
519	1556 G	-1:168090486 168090486 G	
519	1557 C	-1:168090485 168090485 C	
520 E	1558 G	-1:168090484 168090484 G	E
520	1559 A	-1:168090483 168090483 A	
520	1560 G	-1:168090482 168090482 G	
521 P	1561 C	-1:168090481 168090481 C	P
521	1562 C	-1:168090480 168090480 C	
521	1563 C	-1:168090479 168090479 C	
522 S	1564 A	-1:168090478 168090478 A	S
522	1565 G	-1:168090477 168090477 G	
522	1566 C	-1:168090476 168090476 C	
523 S	1567 A	-1:168090475 168090475 A	S
523	1568 G	-1:168090474 168090474 G	
523	1569 C	-1:168090473 168090473 C	
524 L	1570 T	-1:168090472 168090472 T	L
524	1571 T	-1:168090471 168090471 T	
524	1572 A	-1:168090470 168090470 A	
525 D	1573 G	-1:168090469 168090469 G	D
525	1574 A	-1:168090468 168090468 A	
525	1575 T	-1:168090467 168090467 T	
526 T	1576 A	-1:168090466 168090466 A	T
526	1577 C	-1:168090465 168090465 C	
526	1578 T	-1:168090464 168090464 T	
527 K	1579 A	-1:168090463 168090463 A	K
527	1580 A	-1:168090462 168090462 A	
527	1581 A	-1:168090461 168090461 A	
528 V	1582 G	-1:168090460 168090460 G	V
528	1583 T	-1:168090459 168090459 T	
528	1584 A	-1:168090458 168090458 A	
529 N	1585 A	-1:168090457 168090457 A	N
529	1586 A	-1:168090456 168090456 A	
529	1587 C	-1:168090455 168090455 C	
530 P	1588 C	-1:168090454 168090454 C	P
530	1589 C	-1:168090453 168090453 C	
530	1590 A	-1:168090452 168090452 A	
531 G	1591 G	-1:168090451 168090451 G	G
531	1592 G	-1:168090450 168090450 G	
531	1593 A	-1:168090449 168090449 A	
532 G	1594 G	-1:168090448 168090448 G	G
532	1595 G	-1:168090447 168090447 G	
532	1596 T	-1:168090446 168090446 T	
533 G	1597 G	-1:168090445 168090445 G	G
533	1598 G	-1:168090444 168090444 G	
533	1599 A	-1:168090443 168090443 A	
534 I	1600 A	-1:168090442 168090442 A	I
534	1601 T	-1:168090441 168090441 T	
534	1602 C	-1:168090440 168090440 C	
535 T	1603 A	-1:168090439 168090439 A	T
535	1604 C	-1:168090438 168090438 C	
535	1605 T	-1:168090437 168090437 T	
536 A	1606 G	-1:168090436 168090436 G	A
536	1607 C	-1:168090435 168090435 C	
536	1608 T	-1:168090434 168090434 T	
537 T	1609 A	-1:168090433 168090433 A	T
537	1610 C	-1:168090432 168090432 C	
537	1611 A	-1:168090431 168090431 A	
538 K	1612 A	-1:168090430 168090430 A	K
538	1613 A	-1:168090429 168090429 A	
538	1614 A	-1:168090428 168090428 A	
539 P	1615 C	-1:168090427 168090427 C	P
539	1616 C	-1:168090426 168090426 C	
539	1617 T	-1:168090425 168090425 T	
540 V	1618 G	-1:168090424 168090424 G	V
540	1619 T	-1:168090423 168090423 T	
540	1620 T	-1:168090422 168090422 T	
541 T	1621 A	-1:168090421 168090421 A	T
541	1622 C	-1:168090420 168090420 C	
541	1623 C	-1:168090419 168090419 C	
542 S	1624 T	-1:168090418 168090418 T	S
542	1625 C	-1:168090417 168090417 C	
542	1626 A	-1:168090416 168090416 A	
543 G	1627 G	-1:168090415 168090415 G	G
543	1628 G	-1:168090414 168090414 G	
543	1629 G	-1:168090413 168090413 G	
544 E	1630 G	-1:168090412 168090412 G	E
544	1631 A	-1:168090411 168090411 A	
544	1632 G	-1:168090410 168090410 G	
545 Q	1633 C	-1:168090409 168090409 C	Q
545	1634 A	-1:168090408 168090408 A	
545	1635 G	-1:168090407 168090407 G	
546 K	1636 A	-1:168090406 168090406 A	K
546	1637 A	-1:168090405 168090405 A	
546	1638 G	-1:168090404 168090404 G	
547 P	1639 C	-1:168090403 168090403 C	P
547	1640 C	-1:168090402 168090402 C	
547	1641 T	-1:168090401 168090401 T	
548 I	1642 A	-1:168090400 168090400 A	I
548	1643 T	-1:168090399 168090399 T	
548	1644 T	-1:168090398 168090398 T	
549 P	1645 C	-1:168090397 168090397 C	P
549	1646 C	-1:168090396 168090396 C	
549	1647 T	-1:168090395 168090395 T	
550 A	1648 G	-1:168090394 168090394 G	A
550	1649 C	-1:168090393 168090393 C	
550	1650 T	-1:168090392 168090392 T	
551 L	1651 T	-1:168090391 168090391 T	L
551	1652 T	-1:168090390 168090390 T	
551	1653 G	-1:168090389 168090389 G	
552 L	1654 C	-1:168090388 168090388 C	L
552	1655 T	-1:168090387 168090387 T	
552	1656 T	-1:168090386 168090386 T	
553 S	1657 T	-1:168090385 168090385 T	S
553	1658 C	-1:168090384 168090384 C	
553	1659 A	-1:168090383 168090383 A	
554 L	1660 C	-1:168090382 168090382 C	L
554	1661 T	-1:168090381 168090381 T	
554	1662 C	-1:168090380 168090380 C	
555 T	1663 A	-1:168090379 168090379 A	T
555	1664 C	-1:168090378 168090378 C	
555	1665 T	-1:168090377 168090377 T	
556 E	1666 G	-1:168090376 168090376 G	E
556	1667 A	-1:168090375 168090375 A	
556	1668 A	-1:168090374 168090374 A	
557 E	1669 G	-1:168090373 168090373 G	E
557	1670 A	-1:168090372 168090372 A	
557	1671 G	-1:168090371 168090371 G	
558 S	1672 T	-1:168090370 168090370 T	S
558	1673 C	-1:168090369 168090369 C	
558	1674 T	-1:168090368 168090368 T	
559 M	1675 A	-1:168090367 168090367 A	M
559	1676 T	-1:168090366 168090366 T	
559	1677 G	-1:168090365 168090365 G	
560 P	1678 C	-1:168090364 168090364 C	P
560	1679 C	-1:168090363 168090363 C	
560	1680 T	-1:168090362 168090362 T	
561 W	1681 T	-1:168090361 168090361 T	W
561	1682 G	-1:168090360 168090360 G	
561	1683 G	-1:168090359 168090359 G	
562 K	1684 A	-1:168090358 168090358 A	K
562	1685 A	-1:168090357 168090357 A	
562	1686 A	-1:168090356 168090356 A	
563 S	1687 T	-1:168090355 168090355 T	S
563	1688 C	-1:168090354 168090354 C	
563	1689 A	-1:168090353 168090353 A	
564 S	1690 A	-1:168090352 168090352 A	S
564	1691 G	-1:168090351 168090351 G	
564	1692 C	-1:168090350 168090350 C	
565 L	1693 T	-1:168090349 168090349 T	L
565	1694 T	-1:168090348 168090348 T	
565	1695 A	-1:168090347 168090347 A	
566 P	1696 C	-1:168090346 168090346 C	P
566	1697 C	-1:168090345 168090345 C	
566	1698 C	-1:168090344 168090344 C	
567 Q	1699 C	-1:168090343 168090343 C	Q
567	1700 A	-1:168090342 168090342 A	
567	1701 A	-1:168090341 168090341 A	
568 K	1702 A	-1:168090340 168090340 A	K
568	1703 A	-1:168090339 168090339 A	
568	1704 G	-1:168090338 168090338 G	
569 I	1705 A	-1:168090337 168090337 A	I
569	1706 T	-1:168090336 168090336 T	
569	1707 T	-1:168090335 168090335 T	
570 S	1708 A	-1:168090334 168090334 A	S
570	1709 G	-1:168090333 168090333 G	
570	1710 C	-1:168090332 168090332 C	
571 L	1711 C	-1:168090331 168090331 C	L
571	1712 T	-1:168090330 168090330 T	
571	1713 T	-1:168090329 168090329 T	
572 V	1714 G	-1:168090328 168090328 G	V
572	1715 T	-1:168090327 168090327 T	
572	1716 A	-1:168090326 168090326 A	
573 Q	1717 C	-1:168090325 168090325 C	Q
573	1718 A	-1:168090324 168090324 A	
573	1719 A	-1:168090323 168090323 A	
574 R	1720 A	-1:168090322 168090322 A	R
574	1721 G	-1:168090321 168090321 G	
574	1722 G	-1:168090320 168090320 G	
575 G	1723 G	-1:168090319 168090319 G	G
575	1724 G	-1:168090318 168090318 G	
575	1725 G	-1:168090317 168090317 G	
576 D	1726 G	-1:168090316 168090316 G	D
576	1727 A	-1:168090315 168090315 A	
576	1728 T	-1:168090314 168090314 T	
577 D	1729 G	-1:168090313 168090313 G	D
577	1730 A	-1:168090312 168090312 A	
577	1731 C	-1:168090311 168090311 C	
578 A	1732 G	-1:168090310 168090310 G	A
578	1733 C	-1:168090309 168090309 C	
578	1734 A	-1:168090308 168090308 A	
579 D	1735 G	-1:168090307 168090307 G	D
579	1736 A	-1:168090306 168090306 A	
579	1737 C	-1:168090305 168090305 C	
580 Q	1738 C	-1:168090304 168090304 C	Q
580	1739 A	-1:168090303 168090303 A	
580	1740 A	-1:168090302 168090302 A	
581 I	1741 A	-1:168090301 168090301 A	I
581	1742 T	-1:168090300 168090300 T	
581	1743 C	-1:168090299 168090299 C	
582 E	1744 G	-1:168090298 168090298 G	E
582	1745 A	-1:168090297 168090297 A	
582	1746 G	-1:168090296 168090296 G	
583 P	1747 C	-1:168090295 168090295 C	P
583	1748 C	-1:168090294 168090294 C	
583	1749 G	-1:168090293 168090293 G	
584 P	1750 C	-1:168090292 168090292 C	P
584	1751 C	-1:168090291 168090291 C	
584	1752 A	-1:168090290 168090290 A	
585 K	1753 A	-1:168090289 168090289 A	K
585	1754 A	-1:168090288 168090288 A	
585	1755 A	-1:168090287 168090287 A	
586 V	1756 G	-1:168090286 168090286 G	V
586	1757 T	-1:168090285 168090285 T	
586	1758 G	-1:168090284 168090284 G	
587 S	1759 T	-1:168090283 168090283 T	S
587	1760 C	-1:168090282 168090282 C	
587	1761 A	-1:168090281 168090281 A	
588 S	1762 T	-1:168090280 168090280 T	S
588	1763 C	-1:168090279 168090279 C	
588	1764 A	-1:168090278 168090278 A	
589 Q	1765 C	-1:168090277 168090277 C	Q
589	1766 A	-1:168090276 168090276 A	
589	1767 A	-1:168090275 168090275 A	
590 E	1768 G	-1:168090274 168090274 G	E
590	1769 A	-1:168090273 168090273 A	
590	1770 A	-1:168090272 168090272 A	
591 R	1771 A	-1:168090271 168090271 A	R
591	1772 G	-1:168090270 168090270 G	
591	1773 G	-1:168090269 168090269 G	
592 P	1774 C	-1:168090268 168090268 C	P
592	1775 C	-1:168090267 168090267 C	
592	1776 C	-1:168090266 168090266 C	
593 L	1777 C	-1:168090265 168090265 C	L
593	1778 T	-1:168090264 168090264 T	
593	1779 T	-1:168090263 168090263 T	
594 K	1780 A	-1:168090262 168090262 A	K
594	1781 A	-1:168090261 168090261 A	
594	1782 G	-1:168090260 168090260 G	
595 V	1783 G	-1:168090259 168090259 G	V
595	1784 T	-1:168090258 168090258 T	
595	1785 T	-1:168090257 168090257 T	
596 P	1786 C	-1:168090256 168090256 C	P
596	1787 C	-1:168090255 168090255 C	
596	1788 A	-1:168090254 168090254 A	
597 S	1789 T	-1:168090253 168090253 T	S
597	1790 C	-1:168090252 168090252 C	
597	1791 A	-1:168090251 168090251 A	
598 E	1792 G	-1:168090250 168090250 G	E
598	1793 A	-1:168090249 168090249 A	
598	1794 A	-1:168090248 168090248 A	
599 L	1795 C	-1:168090247 168090247 C	L
599	1796 T	-1:168090246 168090246 T	
599	1797 T	-1:168090245 168090245 T	
600 G	1798 G	-1:168090244 168090244 G	G
600	1799 G	-1:168090243 168090243 G	
600	1800 T	-1:168090242 168090242 T	
601 L	1801 T	-1:168090241 168090241 T	L
601	1802 T	-1:168090240 168090240 T	
601	1803 A	-1:168090239 168090239 A	
602 G	1804 G	-1:168090238 168090238 G	G
602	1805 G	-1:168090237 168090237 G	
602	1806 A	-1:168090236 168090236 A	
603 E	1807 G	-1:168090235 168090235 G	E
603	1808 A	-1:168090234 168090234 A	
603	1809 G	-1:168090233 168090233 G	
604 E	1810 G	-1:168090232 168090232 G	E
604	1811 A	-1:168090231 168090231 A	
604	1812 A	-1:168090230 168090230 A	
605 F	1813 T	-1:168090229 168090229 T	F
605	1814 T	-1:168090228 168090228 T	
605	1815 C	-1:168090227 168090227 C	
606 T	1816 A	-1:168090226 168090226 A	T
606	1817 C	-1:168090225 168090225 C	
606	1818 C	-1:168090224 168090224 C	
607 I	1819 A	-1:168090223 168090223 A	I
607	1820 T	-1:168090222 168090222 T	
607	1821 T	-1:168090221 168090221 T	
608 Q	1822 C	-1:168090220 168090220 C	Q
608	1823 A	-1:168090219 168090219 A	
608	1824 A	-1:168090218 168090218 A	
609 V	1825 G	-1:168090217 168090217 G	V
609	1826 T	-1:168090216 168090216 T	
609	1827 A	-1:168090215 168090215 A	
610 K	1828 A	-1:168090214 168090214 A	K
610	1829 A	-1:168090213 168090213 A	
610	1830 A	-1:168090212 168090212 A	
>ENSP00000356746 
1 M	1 A	-1:168124605 168124605 A	M
1	2 T	-1:168124604 168124604 T	
1	3 G	-1:168124603 168124603 G	
2 G	4 G	-1:168124602 168124602 G	G
2	5 G	-1:168124601 168124601 G	
2	6 A	-1:168124600 168124600 A	
3 S	7 T	-1:168124599 168124599 T	S
3	8 C	-1:168124598 168124598 C	
3	9 A	-1:168124597 168124597 A	
4 E	10 G	-1:168124596 168124596 G	E
4	11 A	-1:168124595 168124595 A	
4	12 G	-1:168124594 168124594 G	
5 N	13 A	-1:168124593 168124593 A	N
5	14 A	-1:168124592 168124592 A	
5	15 C	-1:168124591 168124591 C	
6 S	16 A	-1:168124590 168124590 A	S
6	17 G	-1:168124589 168124589 G	
6	18 T	-1:168124588 168124588 T	
7 A	19 G	-1:168124587 168124587 G	A
7	20 C	-1:168124586 168124586 C	
7	21 T	-1:168124585 168124585 T	
8 L	22 T	-1:168124584 168124584 T	L
8	23 T	-1:168124583 168124583 T	
8	24 A	-1:168124582 168124582 A	
9 K	25 A	-1:168124581 168124581 A	K
9	26 A	-1:168124580 168124580 A	
9	27 G	-1:168124579 168124579 G	
10 S	28 A	-1:168124578 168124578 A	S
10	29 G	-1:168124577 168124577 G	
10	30 C	-1:168124576 168124576 C	
11 Y	31 T	-1:168124575 168124575 T	Y
11	32 A	-1:168124574 168124574 A	
11	33 T	-1:168124573 168124573 T	
12 T	34 A	-1:168124572 168124572 A	T
12	35 C	-1:168124571 168124571 C	
12	36 A	-1:168124570 168124570 A	
13 L	37 C	-1:168124569 168124569 C	L
13	38 T	-1:168124568 168124568 T	
13	39 G	-1:168124567 168124567 G	
14 R	40 A	-1:168124566 168124566 A	R
14	41 G	-1:168124565 168124565 G	
14	42 A	-1:168124564 168124564 A	
15 E	43 G	-1:168124563 168124563 G	E
15	44 A	-1:168124562 168124562 A	
15	45 A	-1:168124561 168124561 A	
16 P	46 C	-1:168124560 168124560 C	P
16	47 C	-1:168124559 168124559 C	
16	48 A	-1:168124558 168124558 A	
17 P	49 C	-1:168124557 168124557 C	P
17	50 C	-1:168124556 168124556 C	
17	51 A	-1:168124555 168124555 A	
18 F	52 T	-1:168124554 168124554 T	F
18	53 T	-1:168124553 168124553 T	
18	54 T	-1:168124552 168124552 T	
19 T	55 A	-1:168124551 168124551 A	T
19	56 C	-1:168124550 168124550 C	
19	57 C	-1:168124549 168124549 C	
20 L	58 T	-1:168124548 168124548 T	L
20	59 T	-1:168124547 168124547 T	
20	60 A	-1:168124546 168124546 A	
21 P	61 C	-1:168124545 168124545 C	P
21	62 C	-1:168124544 168124544 C	
21	63 C	-1:168124543 168124543 C	
22 S	64 T	-1:168124542 168124542 T	S
22	65 C	-1:168124541 168124541 C	
22	66 T	-1:168124540 168124540 T	
23 G	67 G	-1:168124539 168124539 G	G
23	68 G	-1:168124538 168124538 G	
23	69 A	-1:168124537 168124537 A	
24 L	70 C	-1:168124536 168124536 C	L
24	71 T	-1:168124535 168124535 T	
24	72 T	-1:168124534 168124534 T	
25 A	73 G	-1:168124533 168124533 G	A
25	74 C	-1:168124532 168124532 C	
25	75 T	-1:168124531 168124531 T	
26 V	76 G	-1:168124530 168124530 G	V
26	77 T	-1:168124529 168124529 T	
26	78 T	-1:168124528 168124528 T	
27 Y	79 T	-1:168124527 168124527 T	Y
27	80 A	-1:168124526 168124526 A	
27	81 T	-1:168124525 168124525 T	
28 P	82 C	-1:168124524 168124524 C	P
28	83 C	-1:168124523 168124523 C	
28	84 C	-1:168124522 168124522 C	
29 A	85 G	-1:168124521 168124521 G	A
29	86 C	-1:168124520 168124520 C	
29	87 T	-1:168124519 168124519 T	
30 V	88 G	-1:168124518 168124518 G	V
30	89 T	-1:168124517 168124517 T	
30	90 A	-1:168124516 168124516 A	
31 L	91 C	-1:168124515 168124515 C	L
31	92 T	-1:168124514 168124514 T	
31	93 G	-1:168124513 168124513 G	
32 Q	94 C	-1:168124512 168124512 C	Q
32	95 A	-1:168124511 168124511 A	
32	96 A	-1:168124510 168124510 A	
33 D	97 G	-1:168124509 168124509 G	D
33	98 A	-1:168124508 168124508 A	
33	99 T	-1:168124507 168124507 T	
34 G	100 G	-1:168124506 168124506 G	G
34	101 G	-1:168124505 168124505 G	
34	102 C	-1:168124504 168124504 C	
35 K	103 A	-1:168124503 168124503 A	K
35	104 A	-1:168124502 168124502 A	
35	105 A	-1:168124501 168124501 A	
36 F	106 T	-1:168124500 168124500 T	F
36	107 T	-1:168124499 168124499 T	
36	108 T	-1:168124498 168124498 T	
37 A	109 G	-1:168124497 168124497 G	A
37	110 C	-1:168124496 168124496 C	
37	111 T	-1:168124495 168124495 T	
38 S	112 T	-1:168124494 168124494 T	S
38	113 C	-1:168124493 168124493 C	
38	114 A	-1:168124492 168124492 A	
39 V	115 G	-1:168124491 168124491 G	V
39	116 T	-1:168124490 168124490 T	
39	117 T	-1:168124489 168124489 T	
40 F	118 T	-1:168124488 168124488 T	F
40	119 T	-1:168124487 168124487 T	
40	120 T	-1:168124486 168124486 T	
41 V	121 G	-1:168124485 168124485 G	V
41	122 T	-1:168124484 168124484 T	
41	123 G	-1:168124483 168124483 G	
42 Y	124 T	-1:168124482 168124482 T	Y
42	125 A	-1:168124481 168124481 A	
42	126 T	-1:168124480 168124480 T	
43 K	127 A	-1:168124479 168124479 A	K
43	128 A	-1:168124478 168124478 A	
43	129 G	-1:168124477 168124477 G	
44 R	130 A	-1:168124476 168124476 A	R
44	131 G	-1:168124475 168124475 G	
44	132 A	-1:168124474 168124474 A	
45 E	133 G	-1:168124473 168124473 G	E
45	134 A	-1:168124472 168124472 A	
45	135 A	-1:168124471 168124471 A	
46 N	136 A	-1:168124470 168124470 A	N
46	137 A	-1:168124469 168124469 A	
46	138 T	-1:168124468 168124468 T	
47 E	139 G	-1:168124467 168124467 G	E
47	140 A	-1:168124466 168124466 A	
47	141 A	-1:168124465 168124465 A	
48 D	142 G	-1:168124464 168124464 G	D
48	143 A	-1:168124463 168124463 A	
48	144 C	-1:168124462 168124462 C	
49 K	145 A	-1:168124461 168124461 A	K
49	146 A	-1:168124460 168124460 A	
49	147 G	-1:168124459 168124459 G	
50 V	148 G	-1:168124458 168124458 G	V
50	149 T	-1:168124457 168124457 T	
50	150 T	-1:168124456 168124456 T	
51 N	151 A	-1:168124455 168124455 A	N
51	152 A	-1:168124454 168124454 A	
51	153 T	-1:168124453 168124453 T	
52 K	154 A	-1:168124452 168124452 A	K
52	155 A	-1:168124451 168124451 A	
52	156 A	-1:168124450 168124450 A	
53 A	157 G	-1:168124449 168124449 G	A
53	158 C	-1:168124448 168124448 C	
53	159 T	-1:168124447 168124447 T	
54 A	160 G	-1:168124446 168124446 G	A
54	161 C	-1:168124445 168124445 C	
54	162 C	-1:168124444 168124444 C	
55 K	163 A	-1:168124443 168124443 A	K
55	164 A	-1:168124442 168124442 A	
55	165 G	-1:168124441 168124441 G	
56 H	166 C	-1:168114584 168114584 C	H
56	167 A	-1:168114583 168114583 A	
56	168 T	-1:168114582 168114582 T	
57 L	169 T	-1:168114581 168114581 T	L
57	170 T	-1:168114580 168114580 T	
57	171 G	-1:168114579 168114579 G	
58 K	172 A	-1:168114578 168114578 A	K
58	173 A	-1:168114577 168114577 A	
58	174 G	-1:168114576 168114576 G	
59 T	175 A	-1:168114575 168114575 A	T
59	176 C	-1:168114574 168114574 C	
59	177 A	-1:168114573 168114573 A	
60 L	178 C	-1:168114572 168114572 C	L
60	179 T	-1:168114571 168114571 T	
60	180 T	-1:168114570 168114570 T	
61 R	181 C	-1:168114569 168114569 C	R
61	182 G	-1:168114568 168114568 G	
61	183 T	-1:168114567 168114567 T	
62 H	184 C	-1:168114566 168114566 C	H
62	185 A	-1:168114565 168114565 A	
62	186 C	-1:168114564 168114564 C	
63 P	187 C	-1:168114563 168114563 C	P
63	188 C	-1:168114562 168114562 C	
63	189 T	-1:168114561 168114561 T	
64 C	190 T	-1:168114560 168114560 T	C
64	191 G	-1:168114559 168114559 G	
64	192 C	-1:168114558 168114558 C	
65 L	193 T	-1:168114557 168114557 T	L
65	194 T	-1:168114556 168114556 T	
65	195 G	-1:168114555 168114555 G	
66 L	196 C	-1:168114554 168114554 C	L
66	197 T	-1:168114553 168114553 T	
66	198 A	-1:168114552 168114552 A	
67 R	199 A	-1:168114551 168114551 A	R
67	200 G	-1:168114550 168114550 G	
67	201 A	-1:168114549 168114549 A	
68 F	202 T	-1:168114548 168114548 T	F
68	203 T	-1:168114547 168114547 T	
68	204 T	-1:168114546 168114546 T	
69 L	205 T	-1:168114545 168114545 T	L
69	206 T	-1:168114544 168114544 T	
69	207 A	-1:168114543 168114543 A	
70 S	208 T	-1:168114542 168114542 T	S
70	209 C	-1:168114541 168114541 C	
70	210 T	-1:168114540 168114540 T	
71 C	211 T	-1:168114539 168114539 T	C
71	212 G	-1:168114538 168114538 G	
71	213 T	-1:168114537 168114537 T	
72 T	214 A	-1:168114536 168114536 A	T
72	215 C	-1:168114535 168114535 C	
72	216 T	-1:168114534 168114534 T	
73 V	217 G	-1:168114533 168114533 G	V
73	218 T	-1:168114532 168114532 T	
73	219 G	-1:168114531 168114531 G	
74 E	220 G	-1:168114530 168114530 G	E
74	221 A	-1:168114529 168114529 A	
74	222 A	-1:168114528 168114528 A	
75 A	223 G	-1:168114527 168114527 G	A
75	224 C	-1:168114526 168114526 C	
75	225 G	-1:168114525 168114525 G	
76 D	226 G	-1:168114524 168114524 G	D
76	227 A	-1:168114523 168114523 A	
76	228 T	-1:168114522 168114522 T	
77 G	229 G	-1:168114521 168114521 G	G
77	230 G	-1:168114520 168114520 G	
77	231 C	-1:168114519 168114519 C	
78 I	232 A	-1:168114518 168114518 A	I
78	233 T	-1:168114517 168114517 T	
78	234 T	-1:168114516 168114516 T	
79 H	235 C	-1:168114515 168114515 C	H
79	236 A	-1:168114514 168114514 A	
79	237 T	-1:168114513 168114513 T	
80 L	238 C	-1:168114512 168114512 C	L
80	239 T	-1:168114511 168114511 T	
80	240 T	-1:168114510 168114510 T	
81 V	241 G	-1:168114509 168114509 G	V
81	242 T	-1:168114508 168114508 T	
81	243 C	-1:168114507 168114507 C	
82 T	244 A	-1:168114506 168114506 A	T
82	245 C	-1:168114505 168114505 C	
82	246 T	-1:168114504 168114504 T	
83 E	247 G	-1:168114503 168114503 G	E
83	248 A	-1:168114502 168114502 A	
83	249 G	-1:168114501 168114501 G	
84 R	250 C	-1:168114500 168114500 C	R
84	251 G	-1:168114499 168114499 G	
84	252 A	-1:168114498 168114498 A	
85 V	253 G	-1:168114497 168114497 G	V
85	254 T	-1:168114496 168114496 T	
85	255 A	-1:168114495 168114495 A	
86 Q	256 C	-1:168114494 168114494 C	Q
86	257 A	-1:168114493 168114493 A	
86	258 G	-1:168114492 168114492 G	
87 P	259 C	-1:168114491 168114491 C	P
87	260 C	-1:168114490 168114490 C	
87	261 C	-1:168114489 168114489 C	
88 L	262 C	-1:168114488 168114488 C	L
88	263 T	-1:168114487 168114487 T	
88	264 G	-1:168114486 168114486 G	
89 E	265 G	-1:168114485 168114485 G	E
89	266 A	-1:168114484 168114484 A	
89	267 A	-1:168114483 168114483 A	
90 V	268 G	-1:168114482 168114482 G	V
90	269 T	-1:168114481 168114481 T	
90	270 G	-1:168114480 168114480 G	
91 A	271 G	-1:168114479 168114479 G	A
91	272 C	-1:168114478 168114478 C	
91	273 T	-1:168114477 168114477 T	
92 L	274 T	-1:168114476 168114476 T	L
92	275 T	-1:168114475 168114475 T	
92	276 G	-1:168114474 168114474 G	
93 E	277 G	-1:168114473 168114473 G	E
93	278 A	-1:168114472 168114472 A	
93	279 A	-1:168114471 168114471 A	
94 T	280 A	-1:168114470 168114470 A	T
94	281 C	-1:168114469 168114469 C	
94	282 A	-1:168114468 168114468 A	
95 L	283 T	-1:168114467 168114467 T	L
95	284 T	-1:168114466 168114466 T	
95	285 G	-1:168114465 168114465 G	
96 S	286 T	-1:168114464 168114464 T	S
96	287 C	-1:168114463 168114463 C	
96	288 T	-1:168114462 168114462 T	
97 S	289 T	-1:168114461 168114461 T	S
97	290 C	-1:168114460 168114460 C	
97	291 T	-1:168114459 168114459 T	
98 A	292 G	-1:168114458 168114458 G	A
98	293 C	-1:168114457 168114457 C	
98	294 A	-1:168114456 168114456 A	
99 E	295 G	-1:168114455 168114455 G	E
99	296 A	-1:168114454 168114454 A	
99	297 G	-1:168114453 168114453 G	
100 V	298 G	-1:168114452 168114452 G	V
100	299 T	-1:168114451 168114451 T	
100	300 C	-1:168114450 168114450 C	
101 C	301 T	-1:168114449 168114449 T	C
101	302 G	-1:168114448 168114448 G	
101	303 T	-1:168114447 168114447 T	
102 A	304 G	-1:168114446 168114446 G	A
102	305 C	-1:168114445 168114445 C	
102	306 T	-1:168114444 168114444 T	
103 G	307 G	-1:168114443 168114443 G	G
103	308 G	-1:168114442 168114442 G	
103	309 G	-1:168114441 168114441 G	
104 I	310 A	-1:168114440 168114440 A	I
104	311 T	-1:168114439 168114439 T	
104	312 C	-1:168114438 168114438 C	
105 Y	313 T	-1:168114437 168114437 T	Y
105	314 A	-1:168114436 168114436 A	
105	315 T	-1:168114435 168114435 T	
106 D	316 G	-1:168114434 168114434 G	D
106	317 A	-1:168114433 168114433 A	
106	318 C	-1:168114432 168114432 C	
107 I	319 A	-1:168114431 168114431 A	I
107	320 T	-1:168114430 168114430 T	
107	321 A	-1:168114429 168114429 A	
108 L	322 T	-1:168114428 168114428 T	L
108	323 T	-1:168114427 168114427 T	
108	324 G	-1:168114426 168114426 G	
109 L	325 C	-1:168114425 168114425 C	L
109	326 T	-1:168114424 168114424 T	
109	327 G	-1:168114423 168114423 G	
110 A	328 G	-1:168114422 168114422 G	A
110	329 C	-1:168114421 168114421 C	
110	330 T	-1:168114420 168114420 T	
111 L	331 C	-1:168114419 168114419 C	L
111	332 T	-1:168114418 168114418 T	
111	333 T	-1:168114417 168114417 T	
112 I	334 A	-1:168114416 168114416 A	I
112	335 T	-1:168114415 168114415 T	
112	336 C	-1:168114414 168114414 C	
113 F	337 T	-1:168114413 168114413 T	F
113	338 T	-1:168114412 168114412 T	
113	339 C	-1:168114411 168114411 C	
114 L	340 C	-1:168114410 168114410 C	L
114	341 T	-1:168114409 168114409 T	
114	342 T	-1:168114408 168114408 T	
115 H	343 C	-1:168114407 168114407 C	H
115	344 A	-1:168114406 168114406 A	
115	345 T	-1:168114405 168114405 T	
116 D	346 G	-1:168114404 168114404 G	D
116	347 A	-1:168114403 168114403 A	
116	348 C	-1:168114402 168114402 C	
117 R	349 A	-1:168114401 168114401 A	R
117	350 G	-1:168114400 168114400 G	
117	351 A	-1:168114399 168114399 A	
118 G	352 G	-1:168111856 168111856 G	G
118	353 G	-1:168111855 168111855 G	
118	354 A	-1:168111854 168111854 A	
119 H	355 C	-1:168111853 168111853 C	H
119	356 A	-1:168111852 168111852 A	
119	357 C	-1:168111851 168111851 C	
120 L	358 C	-1:168111850 168111850 C	L
120	359 T	-1:168111849 168111849 T	
120	360 A	-1:168111848 168111848 A	
121 T	361 A	-1:168111847 168111847 A	T
121	362 C	-1:168111846 168111846 C	
121	363 A	-1:168111845 168111845 A	
122 H	364 C	-1:168111844 168111844 C	H
122	365 A	-1:168111843 168111843 A	
122	366 C	-1:168111842 168111842 C	
123 N	367 A	-1:168111841 168111841 A	N
123	368 A	-1:168111840 168111840 A	
123	369 T	-1:168111839 168111839 T	
124 N	370 A	-1:168111838 168111838 A	N
124	371 A	-1:168111837 168111837 A	
124	372 T	-1:168111836 168111836 T	
125 V	373 G	-1:168111835 168111835 G	V
125	374 T	-1:168111834 168111834 T	
125	375 C	-1:168111833 168111833 C	
126 C	376 T	-1:168111832 168111832 T	C
126	377 G	-1:168111831 168111831 G	
126	378 T	-1:168111830 168111830 T	
127 L	379 T	-1:168111829 168111829 T	L
127	380 T	-1:168111828 168111828 T	
127	381 A	-1:168111827 168111827 A	
128 S	382 T	-1:168111826 168111826 T	S
128	383 C	-1:168111825 168111825 C	
128	384 A	-1:168111824 168111824 A	
129 S	385 T	-1:168111823 168111823 T	S
129	386 C	-1:168111822 168111822 C	
129	387 T	-1:168111821 168111821 T	
130 V	388 G	-1:168111820 168111820 G	V
130	389 T	-1:168111819 168111819 T	
130	390 G	-1:168111818 168111818 G	
131 F	391 T	-1:168111817 168111817 T	F
131	392 T	-1:168111816 168111816 T	
131	393 T	-1:168111815 168111815 T	
132 V	394 G	-1:168111814 168111814 G	V
132	395 T	-1:168111813 168111813 T	
132	396 G	-1:168111812 168111812 G	
133 S	397 A	-1:168111811 168111811 A	S
133	398 G	-1:168111810 168111810 G	
133	399 T	-1:168111809 168111809 T	
134 E	400 G	-1:168111808 168111808 G	E
134	401 A	-1:168111807 168111807 A	
134	402 A	-1:168111806 168111806 A	
135 D	403 G	-1:168111805 168111805 G	D
135	404 A	-1:168111804 168111804 A	
135	405 T	-1:168111803 168111803 T	
136 G	406 G	-1:168111802 168111802 G	G
136	407 G	-1:168111801 168111801 G	
136	408 A	-1:168111800 168111800 A	
137 H	409 C	-1:168111799 168111799 C	H
137	410 A	-1:168111798 168111798 A	
137	411 C	-1:168111797 168111797 C	
138 W	412 T	-1:168111796 168111796 T	W
138	413 G	-1:168111795 168111795 G	
138	414 G	-1:168111794 168111794 G	
139 K	415 A	-1:168111793 168111793 A	K
139	416 A	-1:168111792 168111792 A	
139	417 G	-1:168111791 168111791 G	
140 L	418 C	-1:168111790 168111790 C	L
140	419 T	-1:168111789 168111789 T	
140	420 A	-1:168111788 168111788 A	
141 G	421 G	-1:168111787 168111787 G	G
141	422 G	-1:168111786 168111786 G	
141	423 A	-1:168111785 168111785 A	
142 G	424 G	-1:168111784 168111784 G	G
142	425 G	-1:168111783 168111783 G	
142	426 A	-1:168111782 168111782 A	
143 M	427 A	-1:168111781 168111781 A	M
143	428 T	-1:168111780 168111780 T	
143	429 G	-1:168111779 168111779 G	
144 E	430 G	-1:168111778 168111778 G	E
144	431 A	-1:168111777 168111777 A	
144	432 A	-1:168111776 168111776 A	
145 T	433 A	-1:168111775 168111775 A	T
145	434 C	-1:168111774 168111774 C	
145	435 T	-1:168111773 168111773 T	
146 V	436 G	-1:168111772 168111772 G	V
146	437 T	-1:168111771 168111771 T	
146	438 T	-1:168111770 168111770 T	
147 C	439 T	-1:168111769 168111769 T	C
147	440 G	-1:168111768 168111768 G	
147	441 T	-1:168111767 168111767 T	
148 K	442 A	-1:168111766 168111766 A	K
148	443 A	-1:168111765 168111765 A	
148	444 A	-1:168111764 168111764 A	
149 V	445 G	-1:168111763 168111763 G	V
149	446 T	-1:168111762 168111762 T	
149	447 T	-1:168111761 168111761 T	
150 S	448 T	-1:168111760 168111760 T	S
150	449 C	-1:168111759 168111759 C	
150	450 T	-1:168111758 168111758 T	
151 Q	451 C	-1:168111757 168111757 C	Q
151	452 A	-1:168111756 168111756 A	
151	453 G	-1:168111755 168111755 G	
152 A	454 G	-1:168111754 168111754 G	A
152	455 C	-1:168111753 168111753 C	
152	456 C	-1:168111752 168111752 C	
153 T	457 A	-1:168111751 168111751 A	T
153	458 C	-1:168111750 168111750 C	
153	459 A	-1:168111749 168111749 A	
154 P	460 C	-1:168111748 168111748 C	P
154	461 C	-1:168111747 168111747 C	
154	462 A	-1:168111746 168111746 A	
155 E	463 G	-1:168111745 168111745 G	E
155	464 A	-1:168111744 168111744 A	
155	465 G	-1:168111743 168111743 G	
156 F	466 T	-1:168109517 168109517 T	F
156	467 T	-1:168109516 168109516 T	
156	468 T	-1:168109515 168109515 T	
157 L	469 C	-1:168109514 168109514 C	L
157	470 T	-1:168109513 168109513 T	
157	471 G	-1:168109512 168109512 G	
158 R	472 A	-1:168109511 168109511 A	R
158	473 G	-1:168109510 168109510 G	
158	474 G	-1:168109509 168109509 G	
159 S	475 A	-1:168109508 168109508 A	S
159	476 G	-1:168109507 168109507 G	
159	477 T	-1:168109506 168109506 T	
160 I	478 A	-1:168109505 168109505 A	I
160	479 T	-1:168109504 168109504 T	
160	480 T	-1:168109503 168109503 T	
161 Q	481 C	-1:168109502 168109502 C	Q
161	482 A	-1:168109501 168109501 A	
161	483 G	-1:168109500 168109500 G	
162 S	484 T	-1:168109499 168109499 T	S
162	485 C	-1:168109498 168109498 C	
162	486 A	-1:168109497 168109497 A	
163 I	487 A	-1:168109496 168109496 A	I
163	488 T	-1:168109495 168109495 T	
163	489 A	-1:168109494 168109494 A	
164 R	490 A	-1:168109493 168109493 A	R
164	491 G	-1:168109492 168109492 G	
164	492 A	-1:168109491 168109491 A	
165 D	493 G	-1:168109490 168109490 G	D
165	494 A	-1:168109489 168109489 A	
165	495 C	-1:168109488 168109488 C	
166 P	496 C	-1:168109487 168109487 C	P
166	497 C	-1:168109486 168109486 C	
166	498 A	-1:168109485 168109485 A	
167 A	499 G	-1:168109484 168109484 G	A
167	500 C	-1:168109483 168109483 C	
167	501 A	-1:168109482 168109482 A	
168 S	502 T	-1:168109481 168109481 T	S
168	503 C	-1:168109480 168109480 C	
168	504 T	-1:168109479 168109479 T	
169 I	505 A	-1:168109478 168109478 A	I
169	506 T	-1:168109477 168109477 T	
169	507 C	-1:168109476 168109476 C	
170 P	508 C	-1:168109475 168109475 C	P
170	509 C	-1:168109474 168109474 C	
170	510 T	-1:168109473 168109473 T	
171 P	511 C	-1:168109472 168109472 C	P
171	512 C	-1:168109471 168109471 C	
171	513 T	-1:168109470 168109470 T	
172 E	514 G	-1:168109469 168109469 G	E
172	515 A	-1:168109468 168109468 A	
172	516 A	-1:168109467 168109467 A	
173 E	517 G	-1:168109466 168109466 G	E
173	518 A	-1:168109465 168109465 A	
173	519 G	-1:168109464 168109464 G	
174 M	520 A	-1:168109463 168109463 A	M
174	521 T	-1:168109462 168109462 T	
174	522 G	-1:168109461 168109461 G	
175 S	523 T	-1:168106122 168106122 T	S
175	524 C	-1:168106121 168106121 C	
175	525 T	-1:168106120 168106120 T	
176 P	526 C	-1:168106119 168106119 C	P
176	527 C	-1:168106118 168106118 C	
176	528 A	-1:168106117 168106117 A	
177 E	529 G	-1:168106116 168106116 G	E
177	530 A	-1:168106115 168106115 A	
177	531 A	-1:168106114 168106114 A	
178 F	532 T	-1:168106113 168106113 T	F
178	533 T	-1:168106112 168106112 T	
178	534 C	-1:168106111 168106111 C	
179 T	535 A	-1:168106110 168106110 A	T
179	536 C	-1:168106109 168106109 C	
179	537 A	-1:168106108 168106108 A	
180 T	538 A	-1:168106107 168106107 A	T
180	539 C	-1:168106106 168106106 C	
180	540 T	-1:168106105 168106105 T	
181 L	541 C	-1:168106104 168106104 C	L
181	542 T	-1:168106103 168106103 T	
181	543 C	-1:168106102 168106102 C	
182 P	544 C	-1:168106101 168106101 C	P
182	545 C	-1:168106100 168106100 C	
182	546 A	-1:168106099 168106099 A	
183 E	547 G	-1:168106098 168106098 G	E
183	548 A	-1:168106097 168106097 A	
183	549 G	-1:168106096 168106096 G	
184 C	550 T	-1:168106095 168106095 T	C
184	551 G	-1:168106094 168106094 G	
184	552 T	-1:168106093 168106093 T	
185 H	553 C	-1:168106092 168106092 C	H
185	554 A	-1:168106091 168106091 A	
185	555 T	-1:168106090 168106090 T	
186 G	556 G	-1:168106089 168106089 G	G
186	557 G	-1:168106088 168106088 G	
186	558 A	-1:168106087 168106087 A	
187 H	559 C	-1:168106086 168106086 C	H
187	560 A	-1:168106085 168106085 A	
187	561 T	-1:168106084 168106084 T	
188 A	562 G	-1:168106083 168106083 G	A
188	563 C	-1:168106082 168106082 C	
188	564 C	-1:168106081 168106081 C	
189 R	565 C	-1:168106080 168106080 C	R
189	566 G	-1:168106079 168106079 G	
189	567 G	-1:168106078 168106078 G	
190 D	568 G	-1:168106077 168106077 G	D
190	569 A	-1:168106076 168106076 A	
190	570 T	-1:168106075 168106075 T	
191 A	571 G	-1:168106074 168106074 G	A
191	572 C	-1:168106073 168106073 C	
191	573 C	-1:168106072 168106072 C	
192 F	574 T	-1:168106071 168106071 T	F
192	575 T	-1:168106070 168106070 T	
192	576 T	-1:168106069 168106069 T	
193 S	577 T	-1:168106068 168106068 T	S
193	578 C	-1:168106067 168106067 C	
193	579 A	-1:168106066 168106066 A	
194 F	580 T	-1:168106065 168106065 T	F
194	581 T	-1:168106064 168106064 T	
194	582 T	-1:168106063 168106063 T	
195 G	583 G	-1:168106062 168106062 G	G
195	584 G	-1:168106061 168106061 G	
195	585 A	-1:168106060 168106060 A	
196 T	586 A	-1:168106059 168106059 A	T
196	587 C	-1:168106058 168106058 C	
196	588 A	-1:168106057 168106057 A	
197 L	589 T	-1:168106056 168106056 T	L
197	590 T	-1:168106055 168106055 T	
197	591 G	-1:168106054 168106054 G	
198 V	592 G	-1:168106053 168106053 G	V
198	593 T	-1:168106052 168106052 T	
198	594 G	-1:168106051 168106051 G	
199 E	595 G	-1:168106050 168106050 G	E
199	596 A	-1:168106049 168106049 A	
199	597 A	-1:168106048 168106048 A	
200 S	598 A	-1:168106047 168106047 A	S
200	599 G	-1:168106046 168106046 G	
200	600 T	-1:168106045 168106045 T	
201 L	601 T	-1:168106044 168106044 T	L
201	602 T	-1:168106043 168106043 T	
201	603 G	-1:168106042 168106042 G	
202 L	604 C	-1:168106041 168106041 C	L
202	605 T	-1:168106040 168106040 T	
202	606 C	-1:168106039 168106039 C	
203 T	607 A	-1:168106038 168106038 A	T
203	608 C	-1:168106037 168106037 C	
203	609 A	-1:168106036 168106036 A	
204 I	610 A	-1:168106035 168106035 A	I
204	611 T	-1:168106034 168106034 T	
204	612 C	-1:168106033 168106033 C	
205 L	613 T	-1:168106032 168106032 T	L
205	614 T	-1:168106031 168106031 T	
205	615 A	-1:168106030 168106030 A	
206 N	616 A	-1:168106029 168106029 A	N
206	617 A	-1:168106028 168106028 A	
206	618 T	-1:168106027 168106027 T	
207 E	619 G	-1:168106026 168106026 G	E
207	620 A	-1:168106025 168106025 A	
207	621 A	-1:168106024 168106024 A	
208 Q	622 C	-1:168106023 168106023 C	Q
208	623 A	-1:168106022 168106022 A	
208	624 G	-1:168106021 168106021 G	
209 V	625 G	-1:168106020 168106020 G	V
209	626 T	-1:168104804 168104804 T	
209	627 T	-1:168104803 168104803 T	
210 S	628 T	-1:168104802 168104802 T	S
210	629 C	-1:168104801 168104801 C	
210	630 A	-1:168104800 168104800 A	
211 A	631 G	-1:168104799 168104799 G	A
211	632 C	-1:168104798 168104798 C	
211	633 G	-1:168104797 168104797 G	
212 D	634 G	-1:168104796 168104796 G	D
212	635 A	-1:168104795 168104795 A	
212	636 T	-1:168104794 168104794 T	
213 V	637 G	-1:168104793 168104793 G	V
213	638 T	-1:168104792 168104792 T	
213	639 T	-1:168104791 168104791 T	
214 L	640 C	-1:168104790 168104790 C	L
214	641 T	-1:168104789 168104789 T	
214	642 C	-1:168104788 168104788 C	
215 S	643 T	-1:168104787 168104787 T	S
215	644 C	-1:168104786 168104786 C	
215	645 C	-1:168104785 168104785 C	
216 S	646 A	-1:168104784 168104784 A	S
216	647 G	-1:168104783 168104783 G	
216	648 C	-1:168104782 168104782 C	
217 F	649 T	-1:168104781 168104781 T	F
217	650 T	-1:168104780 168104780 T	
217	651 T	-1:168104779 168104779 T	
218 Q	652 C	-1:168104778 168104778 C	Q
218	653 A	-1:168104777 168104777 A	
218	654 A	-1:168104776 168104776 A	
219 Q	655 C	-1:168104775 168104775 C	Q
219	656 A	-1:168104774 168104774 A	
219	657 G	-1:168104773 168104773 G	
220 T	658 A	-1:168104772 168104772 A	T
220	659 C	-1:168104771 168104771 C	
220	660 C	-1:168104770 168104770 C	
221 L	661 T	-1:168104769 168104769 T	L
221	662 T	-1:168104768 168104768 T	
221	663 G	-1:168104767 168104767 G	
222 H	664 C	-1:168104766 168104766 C	H
222	665 A	-1:168104765 168104765 A	
222	666 C	-1:168104764 168104764 C	
223 S	667 T	-1:168104763 168104763 T	S
223	668 C	-1:168104762 168104762 C	
223	669 A	-1:168104761 168104761 A	
224 T	670 A	-1:168104760 168104760 A	T
224	671 C	-1:168104759 168104759 C	
224	672 T	-1:168104758 168104758 T	
225 L	673 T	-1:168104757 168104757 T	L
225	674 T	-1:168104756 168104756 T	
225	675 G	-1:168104755 168104755 G	
226 L	676 C	-1:168104754 168104754 C	L
226	677 T	-1:168104753 168104753 T	
226	678 G	-1:168104752 168104752 G	
227 N	679 A	-1:168104751 168104751 A	N
227	680 A	-1:168104750 168104750 A	
227	681 T	-1:168104749 168104749 T	
228 P	682 C	-1:168104748 168104748 C	P
228	683 C	-1:168104747 168104747 C	
228	684 C	-1:168104746 168104746 C	
229 I	685 A	-1:168104745 168104745 A	I
229	686 T	-1:168104744 168104744 T	
229	687 T	-1:168104743 168104743 T	
230 P	688 C	-1:168104742 168104742 C	P
230	689 C	-1:168104741 168104741 C	
230	690 A	-1:168104740 168104740 A	
231 K	691 A	-1:168104739 168104739 A	K
231	692 A	-1:168104738 168104738 A	
231	693 A	-1:168104737 168104737 A	
232 C	694 T	-1:168104736 168104736 T	C
232	695 G	-1:168104735 168104735 G	
232	696 T	-1:168104734 168104734 T	
233 R	697 C	-1:168104733 168104733 C	R
233	698 G	-1:168104732 168104732 G	
233	699 G	-1:168104731 168104731 G	
234 P	700 C	-1:168104730 168104730 C	P
234	701 C	-1:168104729 168104729 C	
234	702 A	-1:168104728 168104728 A	
235 A	703 G	-1:168104727 168104727 G	A
235	704 C	-1:168104726 168104726 C	
235	705 G	-1:168104725 168104725 G	
236 L	706 C	-1:168104724 168104724 C	L
236	707 T	-1:168104723 168104723 T	
236	708 C	-1:168104722 168104722 C	
237 C	709 T	-1:168104721 168104721 T	C
237	710 G	-1:168104720 168104720 G	
237	711 C	-1:168104719 168104719 C	
238 T	712 A	-1:168104718 168104718 A	T
238	713 C	-1:168104717 168104717 C	
238	714 C	-1:168104716 168104716 C	
239 L	715 T	-1:168104715 168104715 T	L
239	716 T	-1:168104714 168104714 T	
239	717 A	-1:168104713 168104713 A	
240 L	718 C	-1:168104712 168104712 C	L
240	719 T	-1:168104711 168104711 T	
240	720 A	-1:168104710 168104710 A	
241 S	721 T	-1:168104709 168104709 T	S
241	722 C	-1:168104708 168104708 C	
241	723 T	-1:168104707 168104707 T	
242 H	724 C	-1:168104706 168104706 C	H
242	725 A	-1:168104705 168104705 A	
242	726 T	-1:168104704 168104704 T	
243 D	727 G	-1:168104703 168104703 G	D
243	728 A	-1:168104702 168104702 A	
243	729 C	-1:168104701 168104701 C	
244 F	730 T	-1:168104700 168104700 T	F
244	731 T	-1:168104699 168104699 T	
244	732 C	-1:168104698 168104698 C	
245 F	733 T	-1:168104697 168104697 T	F
245	734 T	-1:168104696 168104696 T	
245	735 C	-1:168104695 168104695 C	
246 R	736 A	-1:168104694 168104694 A	R
246	737 G	-1:168104693 168104693 G	
246	738 A	-1:168102738 168102738 A	
247 N	739 A	-1:168102737 168102737 A	N
247	740 A	-1:168102736 168102736 A	
247	741 T	-1:168102735 168102735 T	
248 D	742 G	-1:168102734 168102734 G	D
248	743 A	-1:168102733 168102733 A	
248	744 T	-1:168102732 168102732 T	
249 F	745 T	-1:168102731 168102731 T	F
249	746 T	-1:168102730 168102730 T	
249	747 T	-1:168102729 168102729 T	
250 L	748 C	-1:168102728 168102728 C	L
250	749 T	-1:168102727 168102727 T	
250	750 G	-1:168102726 168102726 G	
251 E	751 G	-1:168102725 168102725 G	E
251	752 A	-1:168102724 168102724 A	
251	753 A	-1:168102723 168102723 A	
252 V	754 G	-1:168102722 168102722 G	V
252	755 T	-1:168102721 168102721 T	
252	756 T	-1:168102720 168102720 T	
253 V	757 G	-1:168102719 168102719 G	V
253	758 T	-1:168102718 168102718 T	
253	759 G	-1:168102717 168102717 G	
254 N	760 A	-1:168102716 168102716 A	N
254	761 A	-1:168102715 168102715 A	
254	762 T	-1:168102714 168102714 T	
255 F	763 T	-1:168102713 168102713 T	F
255	764 T	-1:168102712 168102712 T	
255	765 C	-1:168102711 168102711 C	
256 L	766 T	-1:168102710 168102710 T	L
256	767 T	-1:168102709 168102709 T	
256	768 G	-1:168102708 168102708 G	
257 K	769 A	-1:168102707 168102707 A	K
257	770 A	-1:168102706 168102706 A	
257	771 A	-1:168102705 168102705 A	
258 S	772 A	-1:168102704 168102704 A	S
258	773 G	-1:168102703 168102703 G	
258	774 T	-1:168102702 168102702 T	
259 L	775 T	-1:168102701 168102701 T	L
259	776 T	-1:168102700 168102700 T	
259	777 A	-1:168102699 168102699 A	
260 T	778 A	-1:168102698 168102698 A	T
260	779 C	-1:168102697 168102697 C	
260	780 A	-1:168102696 168102696 A	
261 L	781 T	-1:168102695 168102695 T	L
261	782 T	-1:168102694 168102694 T	
261	783 G	-1:168102693 168102693 G	
262 K	784 A	-1:168102692 168102692 A	K
262	785 A	-1:168102691 168102691 A	
262	786 G	-1:168102690 168102690 G	
263 S	787 A	-1:168102689 168102689 A	S
263	788 G	-1:168102688 168102688 G	
263	789 T	-1:168102687 168102687 T	
264 E	790 G	-1:168102686 168102686 G	E
264	791 A	-1:168102685 168102685 A	
264	792 A	-1:168102684 168102684 A	
265 E	793 G	-1:168102683 168102683 G	E
265	794 A	-1:168102682 168102682 A	
265	795 G	-1:168102681 168102681 G	
266 E	796 G	-1:168102680 168102680 G	E
266	797 A	-1:168102679 168102679 A	
266	798 G	-1:168102678 168102678 G	
267 K	799 A	-1:168102677 168102677 A	K
267	800 A	-1:168102676 168102676 A	
267	801 A	-1:168102675 168102675 A	
268 T	802 A	-1:168102674 168102674 A	T
268	803 C	-1:168102673 168102673 C	
268	804 G	-1:168102672 168102672 G	
269 E	805 G	-1:168102671 168102671 G	E
269	806 A	-1:168102670 168102670 A	
269	807 A	-1:168102669 168102669 A	
270 F	808 T	-1:168102668 168102668 T	F
270	809 T	-1:168102667 168102667 T	
270	810 C	-1:168102666 168102666 C	
271 F	811 T	-1:168102665 168102665 T	F
271	812 T	-1:168102664 168102664 T	
271	813 T	-1:168102663 168102663 T	
272 K	814 A	-1:168102662 168102662 A	K
272	815 A	-1:168102661 168102661 A	
272	816 A	-1:168100273 168100273 A	
273 F	817 T	-1:168100272 168100272 T	F
273	818 T	-1:168100271 168100271 T	
273	819 T	-1:168100270 168100270 T	
274 L	820 C	-1:168100269 168100269 C	L
274	821 T	-1:168100268 168100268 T	
274	822 G	-1:168100267 168100267 G	
275 L	823 C	-1:168100266 168100266 C	L
275	824 T	-1:168100265 168100265 T	
275	825 G	-1:168100264 168100264 G	
276 D	826 G	-1:168100263 168100263 G	D
276	827 A	-1:168100262 168100262 A	
276	828 C	-1:168100261 168100261 C	
277 R	829 A	-1:168100260 168100260 A	R
277	830 G	-1:168100259 168100259 G	
277	831 A	-1:168100258 168100258 A	
278 V	832 G	-1:168100257 168100257 G	V
278	833 T	-1:168100256 168100256 T	
278	834 C	-1:168100255 168100255 C	
279 S	835 A	-1:168100254 168100254 A	S
279	836 G	-1:168100253 168100253 G	
279	837 C	-1:168100252 168100252 C	
280 C	838 T	-1:168100251 168100251 T	C
280	839 G	-1:168100250 168100250 G	
280	840 C	-1:168100249 168100249 C	
281 L	841 T	-1:168100248 168100248 T	L
281	842 T	-1:168100247 168100247 T	
281	843 G	-1:168100246 168100246 G	
282 S	844 T	-1:168100245 168100245 T	S
282	845 C	-1:168100244 168100244 C	
282	846 A	-1:168100243 168100243 A	
283 E	847 G	-1:168100242 168100242 G	E
283	848 A	-1:168100241 168100241 A	
283	849 G	-1:168100240 168100240 G	
284 E	850 G	-1:168100239 168100239 G	E
284	851 A	-1:168100238 168100238 A	
284	852 A	-1:168100237 168100237 A	
285 L	853 T	-1:168100236 168100236 T	L
285	854 T	-1:168100235 168100235 T	
285	855 G	-1:168100234 168100234 G	
286 I	856 A	-1:168100233 168100233 A	I
286	857 T	-1:168100232 168100232 T	
286	858 A	-1:168100231 168100231 A	
287 A	859 G	-1:168100230 168100230 G	A
287	860 C	-1:168100229 168100229 C	
287	861 T	-1:168100228 168100228 T	
288 S	862 T	-1:168100227 168100227 T	S
288	863 C	-1:168100226 168100226 C	
288	864 A	-1:168100225 168100225 A	
289 R	865 A	-1:168100224 168100224 A	R
289	866 G	-1:168100223 168100223 G	
289	867 G	-1:168100222 168100222 G	
290 L	868 T	-1:168100221 168100221 T	L
290	869 T	-1:168100220 168100220 T	
290	870 G	-1:168100219 168100219 G	
291 V	871 G	-1:168100218 168100218 G	V
291	872 T	-1:168100217 168100217 T	
291	873 G	-1:168100216 168100216 G	
292 P	874 C	-1:168100215 168100215 C	P
292	875 C	-1:168100214 168100214 C	
292	876 T	-1:168100213 168100213 T	
293 L	877 C	-1:168100212 168100212 C	L
293	878 T	-1:168100211 168100211 T	
293	879 T	-1:168100210 168100210 T	
294 L	880 C	-1:168100209 168100209 C	L
294	881 T	-1:168100208 168100208 T	
294	882 G	-1:168100207 168100207 G	
295 L	883 C	-1:168100206 168100206 C	L
295	884 T	-1:168100205 168100205 T	
295	885 T	-1:168100204 168100204 T	
296 N	886 A	-1:168100203 168100203 A	N
296	887 A	-1:168100202 168100202 A	
296	888 T	-1:168100201 168100201 T	
297 Q	889 C	-1:168100200 168100200 C	Q
297	890 A	-1:168100199 168100199 A	
297	891 G	-1:168100198 168100198 G	
298 L	892 T	-1:168100197 168100197 T	L
298	893 T	-1:168100196 168100196 T	
298	894 G	-1:168100195 168100195 G	
299 V	895 G	-1:168100194 168100194 G	V
299	896 T	-1:168100193 168100193 T	
299	897 G	-1:168100192 168100192 G	
300 F	898 T	-1:168100191 168100191 T	F
300	899 T	-1:168100190 168100190 T	
300	900 T	-1:168100189 168100189 T	
301 A	901 G	-1:168100188 168100188 G	A
301	902 C	-1:168100187 168100187 C	
301	903 A	-1:168100186 168100186 A	
302 E	904 G	-1:168100185 168100185 G	E
302	905 A	-1:168100184 168100184 A	
302	906 G	-1:168100183 168100183 G	
303 P	907 C	-1:168100182 168100182 C	P
303	908 C	-1:168100181 168100181 C	
303	909 A	-1:168100180 168100180 A	
304 V	910 G	-1:168100179 168100179 G	V
304	911 T	-1:168100178 168100178 T	
304	912 G	-1:168100177 168100177 G	
305 A	913 G	-1:168100176 168100176 G	A
305	914 C	-1:168100175 168100175 C	
305	915 T	-1:168100174 168100174 T	
306 V	916 G	-1:168100173 168100173 G	V
306	917 T	-1:168100172 168100172 T	
306	918 T	-1:168100171 168100171 T	
307 K	919 A	-1:168100170 168100170 A	K
307	920 A	-1:168100169 168100169 A	
307	921 G	-1:168100168 168100168 G	
308 S	922 A	-1:168100167 168100167 A	S
308	923 G	-1:168100166 168100166 G	
308	924 T	-1:168100165 168100165 T	
309 F	925 T	-1:168100164 168100164 T	F
309	926 T	-1:168100163 168100163 T	
309	927 T	-1:168100162 168100162 T	
310 L	928 C	-1:168100161 168100161 C	L
310	929 T	-1:168100160 168100160 T	
310	930 T	-1:168100159 168100159 T	
311 P	931 C	-1:168100158 168100158 C	P
311	932 C	-1:168100157 168100157 C	
311	933 T	-1:168100156 168100156 T	
312 Y	934 T	-1:168100155 168100155 T	Y
312	935 A	-1:168100154 168100154 A	
312	936 T	-1:168100153 168100153 T	
313 L	937 C	-1:168100152 168100152 C	L
313	938 T	-1:168100151 168100151 T	
313	939 G	-1:168100150 168100150 G	
314 L	940 C	-1:168100149 168100149 C	L
314	941 T	-1:168100148 168100148 T	
314	942 T	-1:168100147 168100147 T	
315 G	943 G	-1:168100146 168100146 G	G
315	944 G	-1:168100145 168100145 G	
315	945 C	-1:168100144 168100144 C	
316 P	946 C	-1:168100143 168100143 C	P
316	947 C	-1:168100142 168100142 C	
316	948 C	-1:168100141 168100141 C	
317 K	949 A	-1:168100140 168100140 A	K
317	950 A	-1:168100139 168100139 A	
317	951 A	-1:168100138 168100138 A	
318 K	952 A	-1:168100137 168100137 A	K
318	953 A	-1:168100136 168100136 A	
318	954 A	-1:168100135 168100135 A	
319 D	955 G	-1:168100134 168100134 G	D
319	956 A	-1:168098562 168098562 A	
319	957 T	-1:168098561 168098561 T	
320 H	958 C	-1:168098560 168098560 C	H
320	959 A	-1:168098559 168098559 A	
320	960 T	-1:168098558 168098558 T	
321 A	961 G	-1:168098557 168098557 G	A
321	962 C	-1:168098556 168098556 C	
321	963 G	-1:168098555 168098555 G	
322 Q	964 C	-1:168098554 168098554 C	Q
322	965 A	-1:168098553 168098553 A	
322	966 G	-1:168098552 168098552 G	
323 G	967 G	-1:168098551 168098551 G	G
323	968 G	-1:168098550 168098550 G	
323	969 A	-1:168098549 168098549 A	
324 E	970 G	-1:168098548 168098548 G	E
324	971 A	-1:168098547 168098547 A	
324	972 A	-1:168098546 168098546 A	
325 T	973 A	-1:168098545 168098545 A	T
325	974 C	-1:168098544 168098544 C	
325	975 T	-1:168098543 168098543 T	
326 P	976 C	-1:168098542 168098542 C	P
326	977 C	-1:168098541 168098541 C	
326	978 T	-1:168098540 168098540 T	
327 C	979 T	-1:168098539 168098539 T	C
327	980 G	-1:168098538 168098538 G	
327	981 C	-1:168098537 168098537 C	
328 L	982 T	-1:168098536 168098536 T	L
328	983 T	-1:168098535 168098535 T	
328	984 G	-1:168098534 168098534 G	
329 L	985 C	-1:168098533 168098533 C	L
329	986 T	-1:168098532 168098532 T	
329	987 C	-1:168098531 168098531 C	
330 S	988 T	-1:168098530 168098530 T	S
330	989 C	-1:168098529 168098529 C	
330	990 A	-1:168098528 168098528 A	
331 P	991 C	-1:168098527 168098527 C	P
331	992 C	-1:168098526 168098526 C	
331	993 A	-1:168098525 168098525 A	
332 A	994 G	-1:168098524 168098524 G	A
332	995 C	-1:168098523 168098523 C	
332	996 C	-1:168098522 168098522 C	
333 L	997 C	-1:168098521 168098521 C	L
333	998 T	-1:168098520 168098520 T	
333	999 G	-1:168098519 168098519 G	
334 F	1000 T	-1:168098518 168098518 T	F
334	1001 T	-1:168098517 168098517 T	
334	1002 C	-1:168098516 168098516 C	
335 Q	1003 C	-1:168098515 168098515 C	Q
335	1004 A	-1:168098514 168098514 A	
335	1005 G	-1:168098513 168098513 G	
336 S	1006 T	-1:168098512 168098512 T	S
336	1007 C	-1:168098511 168098511 C	
336	1008 A	-1:168098510 168098510 A	
337 R	1009 C	-1:168098509 168098509 C	R
337	1010 G	-1:168098508 168098508 G	
337	1011 G	-1:168098507 168098507 G	
338 V	1012 G	-1:168098506 168098506 G	V
338	1013 T	-1:168098505 168098505 T	
338	1014 G	-1:168098504 168098504 G	
339 I	1015 A	-1:168098503 168098503 A	I
339	1016 T	-1:168098502 168098502 T	
339	1017 C	-1:168098501 168098501 C	
340 P	1018 C	-1:168098500 168098500 C	P
340	1019 C	-1:168098499 168098499 C	
340	1020 C	-1:168098498 168098498 C	
341 V	1021 G	-1:168098497 168098497 G	V
341	1022 T	-1:168098496 168098496 T	
341	1023 G	-1:168098495 168098495 G	
342 L	1024 C	-1:168098494 168098494 C	L
342	1025 T	-1:168098493 168098493 T	
342	1026 T	-1:168098492 168098492 T	
343 L	1027 C	-1:168098491 168098491 C	L
343	1028 T	-1:168098490 168098490 T	
343	1029 C	-1:168098489 168098489 C	
344 Q	1030 C	-1:168098488 168098488 C	Q
344	1031 A	-1:168098487 168098487 A	
344	1032 G	-1:168098486 168098486 G	
345 L	1033 T	-1:168098485 168098485 T	L
345	1034 T	-1:168098484 168098484 T	
345	1035 G	-1:168098483 168098483 G	
346 F	1036 T	-1:168098482 168098482 T	F
346	1037 T	-1:168098481 168098481 T	
346	1038 T	-1:168098480 168098480 T	
347 E	1039 G	-1:168098479 168098479 G	E
347	1040 A	-1:168098478 168098478 A	
347	1041 A	-1:168098477 168098477 A	
348 V	1042 G	-1:168098476 168098476 G	V
348	1043 T	-1:168098475 168098475 T	
348	1044 T	-1:168098474 168098474 T	
349 H	1045 C	-1:168098473 168098473 C	H
349	1046 A	-1:168098472 168098472 A	
349	1047 T	-1:168098471 168098471 T	
350 E	1048 G	-1:168098470 168098470 G	E
350	1049 A	-1:168098469 168098469 A	
350	1050 A	-1:168098468 168098468 A	
351 E	1051 G	-1:168098467 168098467 G	E
351	1052 A	-1:168098466 168098466 A	
351	1053 G	-1:168098465 168098465 G	
352 H	1054 C	-1:168098464 168098464 C	H
352	1055 A	-1:168098463 168098463 A	
352	1056 T	-1:168098462 168098462 T	
353 V	1057 G	-1:168098461 168098461 G	V
353	1058 T	-1:168098460 168098460 T	
353	1059 G	-1:168098459 168098459 G	
354 R	1060 C	-1:168098458 168098458 C	R
354	1061 G	-1:168098457 168098457 G	
354	1062 G	-1:168098456 168098456 G	
355 M	1063 A	-1:168098455 168098455 A	M
355	1064 T	-1:168098454 168098454 T	
355	1065 G	-1:168098453 168098453 G	
356 V	1066 G	-1:168098452 168098452 G	V
356	1067 T	-1:168098451 168098451 T	
356	1068 G	-1:168098450 168098450 G	
357 L	1069 C	-1:168098449 168098449 C	L
357	1070 T	-1:168098448 168098448 T	
357	1071 G	-1:168098447 168098447 G	
358 L	1072 C	-1:168098446 168098446 C	L
358	1073 T	-1:168098445 168098445 T	
358	1074 G	-1:168098444 168098444 G	
359 S	1075 T	-1:168098443 168098443 T	S
359	1076 C	-1:168098442 168098442 C	
359	1077 T	-1:168098441 168098441 T	
360 H	1078 C	-1:168098440 168098440 C	H
360	1079 A	-1:168098439 168098439 A	
360	1080 C	-1:168098438 168098438 C	
361 I	1081 A	-1:168098437 168098437 A	I
361	1082 T	-1:168098436 168098436 T	
361	1083 C	-1:168098435 168098435 C	
362 E	1084 G	-1:168098434 168098434 G	E
362	1085 A	-1:168098433 168098433 A	
362	1086 G	-1:168098432 168098432 G	
363 A	1087 G	-1:168098431 168098431 G	A
363	1088 C	-1:168098430 168098430 C	
363	1089 C	-1:168098429 168098429 C	
364 Y	1090 T	-1:168098428 168098428 T	Y
364	1091 A	-1:168098427 168098427 A	
364	1092 C	-1:168098426 168098426 C	
365 V	1093 G	-1:168098425 168098425 G	V
365	1094 T	-1:168098424 168098424 T	
365	1095 G	-1:168098423 168098423 G	
366 E	1096 G	-1:168098422 168098422 G	E
366	1097 A	-1:168098421 168098421 A	
366	1098 G	-1:168098420 168098420 G	
367 H	1099 C	-1:168098419 168098419 C	H
367	1100 A	-1:168098418 168098418 A	
367	1101 C	-1:168098417 168098417 C	
368 F	1102 T	-1:168098416 168098416 T	F
368	1103 T	-1:168098415 168098415 T	
368	1104 C	-1:168098414 168098414 C	
369 T	1105 A	-1:168098413 168098413 A	T
369	1106 C	-1:168098412 168098412 C	
369	1107 T	-1:168098411 168098411 T	
370 Q	1108 C	-1:168098410 168098410 C	Q
370	1109 A	-1:168098409 168098409 A	
370	1110 G	-1:168098408 168098408 G	
371 E	1111 G	-1:168098407 168098407 G	E
371	1112 A	-1:168098406 168098406 A	
371	1113 G	-1:168098405 168098405 G	
372 Q	1114 C	-1:168098404 168098404 C	Q
372	1115 A	-1:168098403 168098403 A	
372	1116 G	-1:168098402 168098402 G	
373 L	1117 C	-1:168098401 168098401 C	L
373	1118 T	-1:168098400 168098400 T	
373	1119 G	-1:168098399 168098399 G	
374 K	1120 A	-1:168098398 168098398 A	K
374	1121 A	-1:168098397 168098397 A	
374	1122 G	-1:168098396 168098396 G	
375 K	1123 A	-1:168098395 168098395 A	K
375	1124 A	-1:168098394 168098394 A	
375	1125 A	-1:168098393 168098393 A	
376 V	1126 G	-1:168098392 168098392 G	V
376	1127 T	-1:168098391 168098391 T	
376	1128 C	-1:168098390 168098390 C	
377 I	1129 A	-1:168098389 168098389 A	I
377	1130 T	-1:168098388 168098388 T	
377	1131 C	-1:168098387 168098387 C	
378 L	1132 T	-1:168098386 168098386 T	L
378	1133 T	-1:168098385 168098385 T	
378	1134 G	-1:168098384 168098384 G	
379 P	1135 C	-1:168098383 168098383 C	P
379	1136 C	-1:168098382 168098382 C	
379	1137 A	-1:168098381 168098381 A	
380 Q	1138 C	-1:168098380 168098380 C	Q
380	1139 A	-1:168098379 168098379 A	
380	1140 G	-1:168098378 168098378 G	
381 V	1141 G	-1:168094977 168094977 G	V
381	1142 T	-1:168094976 168094976 T	
381	1143 T	-1:168094975 168094975 T	
382 L	1144 T	-1:168094974 168094974 T	L
382	1145 T	-1:168094973 168094973 T	
382	1146 G	-1:168094972 168094972 G	
383 L	1147 C	-1:168094971 168094971 C	L
383	1148 T	-1:168094970 168094970 T	
383	1149 G	-1:168094969 168094969 G	
384 G	1150 G	-1:168094968 168094968 G	G
384	1151 G	-1:168094967 168094967 G	
384	1152 C	-1:168094966 168094966 C	
385 L	1153 C	-1:168094965 168094965 C	L
385	1154 T	-1:168094964 168094964 T	
385	1155 G	-1:168094963 168094963 G	
386 R	1156 C	-1:168094962 168094962 C	R
386	1157 G	-1:168094961 168094961 G	
386	1158 T	-1:168094960 168094960 T	
387 D	1159 G	-1:168094959 168094959 G	D
387	1160 A	-1:168094958 168094958 A	
387	1161 T	-1:168094957 168094957 T	
388 T	1162 A	-1:168094956 168094956 A	T
388	1163 C	-1:168094955 168094955 C	
388	1164 T	-1:168094954 168094954 T	
389 S	1165 A	-1:168094953 168094953 A	S
389	1166 G	-1:168094952 168094952 G	
389	1167 C	-1:168094951 168094951 C	
390 D	1168 G	-1:168094950 168094950 G	D
390	1169 A	-1:168094949 168094949 A	
390	1170 T	-1:168094948 168094948 T	
391 S	1171 T	-1:168094947 168094947 T	S
391	1172 C	-1:168094946 168094946 C	
391	1173 C	-1:168094945 168094945 C	
392 I	1174 A	-1:168094944 168094944 A	I
392	1175 T	-1:168094943 168094943 T	
392	1176 T	-1:168094942 168094942 T	
393 V	1177 G	-1:168094941 168094941 G	V
393	1178 T	-1:168094940 168094940 T	
393	1179 G	-1:168094939 168094939 G	
394 A	1180 G	-1:168094938 168094938 G	A
394	1181 C	-1:168094937 168094937 C	
394	1182 A	-1:168094936 168094936 A	
395 I	1183 A	-1:168094935 168094935 A	I
395	1184 T	-1:168094934 168094934 T	
395	1185 T	-1:168094933 168094933 T	
396 T	1186 A	-1:168094932 168094932 A	T
396	1187 C	-1:168094931 168094931 C	
396	1188 T	-1:168094930 168094930 T	
397 L	1189 C	-1:168094929 168094929 C	L
397	1190 T	-1:168094928 168094928 T	
397	1191 G	-1:168094927 168094927 G	
398 H	1192 C	-1:168094926 168094926 C	H
398	1193 A	-1:168094925 168094925 A	
398	1194 T	-1:168094924 168094924 T	
399 S	1195 A	-1:168094923 168094923 A	S
399	1196 G	-1:168094922 168094922 G	
399	1197 C	-1:168094921 168094921 C	
400 L	1198 C	-1:168094920 168094920 C	L
400	1199 T	-1:168094919 168094919 T	
400	1200 A	-1:168094918 168094918 A	
401 A	1201 G	-1:168094917 168094917 G	A
401	1202 C	-1:168094916 168094916 C	
401	1203 A	-1:168094915 168094915 A	
402 V	1204 G	-1:168094914 168094914 G	V
402	1205 T	-1:168094913 168094913 T	
402	1206 G	-1:168094912 168094912 G	
403 L	1207 C	-1:168094911 168094911 C	L
403	1208 T	-1:168094910 168094910 T	
403	1209 G	-1:168094909 168094909 G	
404 V	1210 G	-1:168094908 168094908 G	V
404	1211 T	-1:168094907 168094907 T	
404	1212 C	-1:168094906 168094906 C	
405 S	1213 T	-1:168094905 168094905 T	S
405	1214 C	-1:168094904 168094904 C	
405	1215 T	-1:168094903 168094903 T	
406 L	1216 C	-1:168094902 168094902 C	L
406	1217 T	-1:168094901 168094901 T	
406	1218 G	-1:168094900 168094900 G	
407 L	1219 C	-1:168094899 168094899 C	L
407	1220 T	-1:168094898 168094898 T	
407	1221 T	-1:168094897 168094897 T	
408 G	1222 G	-1:168094896 168094896 G	G
408	1223 G	-1:168094895 168094895 G	
408	1224 A	-1:168094894 168094894 A	
409 P	1225 C	-1:168094893 168094893 C	P
409	1226 C	-1:168094892 168094892 C	
409	1227 A	-1:168094891 168094891 A	
410 E	1228 G	-1:168094890 168094890 G	E
410	1229 A	-1:168094889 168094889 A	
410	1230 G	-1:168094888 168094888 G	
411 V	1231 G	-1:168094887 168094887 G	V
411	1232 T	-1:168094886 168094886 T	
411	1233 G	-1:168094885 168094885 G	
412 V	1234 G	-1:168094884 168094884 G	V
412	1235 T	-1:168094883 168094883 T	
412	1236 T	-1:168094882 168094882 T	
413 V	1237 G	-1:168094881 168094881 G	V
413	1238 T	-1:168094880 168094880 T	
413	1239 G	-1:168094879 168094879 G	
414 G	1240 G	-1:168094878 168094878 G	G
414	1241 G	-1:168094877 168094877 G	
414	1242 A	-1:168094876 168094876 A	
415 G	1243 G	-1:168094875 168094875 G	G
415	1244 G	-1:168094874 168094874 G	
415	1245 A	-1:168094873 168094873 A	
416 E	1246 G	-1:168094872 168094872 G	E
416	1247 A	-1:168094871 168094871 A	
416	1248 A	-1:168094870 168094870 A	
417 R	1249 C	-1:168094869 168094869 C	R
417	1250 G	-1:168094868 168094868 G	
417	1251 A	-1:168094867 168094867 A	
418 T	1252 A	-1:168094866 168094866 A	T
418	1253 C	-1:168094865 168094865 C	
418	1254 C	-1:168094864 168094864 C	
419 K	1255 A	-1:168094863 168094863 A	K
419	1256 A	-1:168094862 168094862 A	
419	1257 G	-1:168094861 168094861 G	
420 I	1258 A	-1:168094860 168094860 A	I
420	1259 T	-1:168094859 168094859 T	
420	1260 C	-1:168094858 168094858 C	
421 F	1261 T	-1:168094857 168094857 T	F
421	1262 T	-1:168094856 168094856 T	
421	1263 C	-1:168094855 168094855 C	
422 K	1264 A	-1:168094854 168094854 A	K
422	1265 A	-1:168094853 168094853 A	
422	1266 A	-1:168094852 168094852 A	
423 R	1267 C	-1:168094851 168094851 C	R
423	1268 G	-1:168094850 168094850 G	
423	1269 C	-1:168094849 168094849 C	
424 T	1270 A	-1:168094848 168094848 A	T
424	1271 C	-1:168094847 168094847 C	
424	1272 T	-1:168094846 168094846 T	
425 A	1273 G	-1:168094845 168094845 G	A
425	1274 C	-1:168094844 168094844 C	
425	1275 C	-1:168094843 168094843 C	
426 P	1276 C	-1:168094842 168094842 C	P
426	1277 C	-1:168094841 168094841 C	
426	1278 A	-1:168094840 168094840 A	
427 S	1279 A	-1:168094839 168094839 A	S
427	1280 G	-1:168094838 168094838 G	
427	1281 T	-1:168094837 168094837 T	
428 F	1282 T	-1:168094836 168094836 T	F
428	1283 T	-1:168094835 168094835 T	
428	1284 T	-1:168094834 168094834 T	
429 T	1285 A	-1:168094833 168094833 A	T
429	1286 C	-1:168094832 168094832 C	
429	1287 T	-1:168094831 168094831 T	
430 K	1288 A	-1:168094830 168094830 A	K
430	1289 A	-1:168094829 168094829 A	
430	1290 A	-1:168094828 168094828 A	
431 N	1291 A	-1:168094827 168094827 A	N
431	1292 A	-1:168094826 168094826 A	
431	1293 T	-1:168094825 168094825 T	
432 T	1294 A	-1:168094824 168094824 A	T
432	1295 C	-1:168094823 168094823 C	
432	1296 T	-1:168094822 168094822 T	
433 D	1297 G	-1:168094821 168094821 G	D
433	1298 A	-1:168094820 168094820 A	
433	1299 C	-1:168094819 168094819 C	
434 L	1300 C	-1:168094818 168094818 C	L
434	1301 T	-1:168094817 168094817 T	
434	1302 T	-1:168094816 168094816 T	
435 S	1303 T	-1:168094815 168094815 T	S
435	1304 C	-1:168094814 168094814 C	
435	1305 T	-1:168094813 168094813 T	
436 L	1306 C	-1:168094812 168094812 C	L
436	1307 T	-1:168094811 168094811 T	
436	1308 A	-1:168094810 168094810 A	
437 E	1309 G	-1:168094809 168094809 G	E
437	1310 A	-1:168094808 168094808 A	
437	1311 A	-1:168094807 168094807 A	
438 D	1312 G	-1:168094806 168094806 G	D
438	1313 A	-1:168091722 168091722 A	
438	1314 T	-1:168091721 168091721 T	
439 S	1315 T	-1:168091720 168091720 T	S
439	1316 C	-1:168091719 168091719 C	
439	1317 T	-1:168091718 168091718 T	
440 P	1318 C	-1:168091717 168091717 C	P
440	1319 C	-1:168091716 168091716 C	
440	1320 T	-1:168091715 168091715 T	
441 M	1321 A	-1:168091714 168091714 A	M
441	1322 T	-1:168091713 168091713 T	
441	1323 G	-1:168091712 168091712 G	
442 C	1324 T	-1:168091711 168091711 T	C
442	1325 G	-1:168091710 168091710 G	
442	1326 T	-1:168091709 168091709 T	
443 V	1327 G	-1:168091708 168091708 G	V
443	1328 T	-1:168091707 168091707 T	
443	1329 C	-1:168091706 168091706 C	
444 V	1330 G	-1:168091705 168091705 G	V
444	1331 T	-1:168091704 168091704 T	
444	1332 C	-1:168091703 168091703 C	
445 C	1333 T	-1:168091702 168091702 T	C
445	1334 G	-1:168091701 168091701 G	
445	1335 C	-1:168091700 168091700 C	
446 S	1336 A	-1:168091699 168091699 A	S
446	1337 G	-1:168091698 168091698 G	
446	1338 C	-1:168091697 168091697 C	
447 H	1339 C	-1:168091696 168091696 C	H
447	1340 A	-1:168091695 168091695 A	
447	1341 T	-1:168091694 168091694 T	
448 H	1342 C	-1:168091693 168091693 C	H
448	1343 A	-1:168091692 168091692 A	
448	1344 C	-1:168091691 168091691 C	
449 S	1345 A	-1:168091690 168091690 A	S
449	1346 G	-1:168091689 168091689 G	
449	1347 T	-1:168091688 168091688 T	
450 Q	1348 C	-1:168091687 168091687 C	Q
450	1349 A	-1:168091686 168091686 A	
450	1350 G	-1:168091685 168091685 G	
451 I	1351 A	-1:168091684 168091684 A	I
451	1352 T	-1:168091683 168091683 T	
451	1353 C	-1:168091682 168091682 C	
452 S	1354 T	-1:168091681 168091681 T	S
452	1355 C	-1:168091680 168091680 C	
452	1356 G	-1:168091679 168091679 G	
453 P	1357 C	-1:168091678 168091678 C	P
453	1358 C	-1:168091677 168091677 C	
453	1359 A	-1:168091676 168091676 A	
454 I	1360 A	-1:168091675 168091675 A	I
454	1361 T	-1:168091674 168091674 T	
454	1362 C	-1:168091673 168091673 C	
455 L	1363 T	-1:168091672 168091672 T	L
455	1364 T	-1:168091671 168091671 T	
455	1365 G	-1:168091670 168091670 G	
456 E	1366 G	-1:168091669 168091669 G	E
456	1367 A	-1:168091668 168091668 A	
456	1368 G	-1:168091667 168091667 G	
457 N	1369 A	-1:168091666 168091666 A	N
457	1370 A	-1:168091665 168091665 A	
457	1371 C	-1:168091664 168091664 C	
458 P	1372 C	-1:168091663 168091663 C	P
458	1373 C	-1:168091662 168091662 C	
458	1374 C	-1:168091661 168091661 C	
459 F	1375 T	-1:168091660 168091660 T	F
459	1376 T	-1:168091659 168091659 T	
459	1377 C	-1:168091658 168091658 C	
460 S	1378 T	-1:168091657 168091657 T	S
460	1379 C	-1:168091656 168091656 C	
460	1380 T	-1:168091655 168091655 T	
461 S	1381 A	-1:168091654 168091654 A	S
461	1382 G	-1:168091653 168091653 G	
461	1383 C	-1:168091652 168091652 C	
462 I	1384 A	-1:168091651 168091651 A	I
462	1385 T	-1:168091650 168091650 T	
462	1386 A	-1:168091649 168091649 A	
463 F	1387 T	-1:168091648 168091648 T	F
463	1388 T	-1:168091647 168091647 T	
463	1389 C	-1:168091646 168091646 C	
464 P	1390 C	-1:168091645 168091645 C	P
464	1391 C	-1:168091644 168091644 C	
464	1392 T	-1:168091643 168091643 T	
465 K	1393 A	-1:168091642 168091642 A	K
465	1394 A	-1:168091641 168091641 A	
465	1395 A	-1:168091640 168091640 A	
466 C	1396 T	-1:168091639 168091639 T	C
466	1397 G	-1:168091638 168091638 G	
466	1398 T	-1:168091637 168091637 T	
467 F	1399 T	-1:168091636 168091636 T	F
467	1400 T	-1:168091635 168091635 T	
467	1401 C	-1:168091634 168091634 C	
468 F	1402 T	-1:168091633 168091633 T	F
468	1403 T	-1:168091632 168091632 T	
468	1404 T	-1:168091631 168091631 T	
469 S	1405 T	-1:168091630 168091630 T	S
469	1406 C	-1:168091629 168091629 C	
469	1407 T	-1:168091628 168091628 T	
470 G	1408 G	-1:168091627 168091627 G	G
470	1409 G	-1:168091626 168091626 G	
470	1410 C	-1:168091625 168091625 C	
471 S	1411 A	-1:168091624 168091624 A	S
471	1412 G	-1:168091623 168091623 G	
471	1413 C	-1:168091622 168091622 C	
472 T	1414 A	-1:168091621 168091621 A	T
472	1415 C	-1:168091620 168091620 C	
472	1416 G	-1:168091619 168091619 G	
473 P	1417 C	-1:168091618 168091618 C	P
473	1418 C	-1:168091617 168091617 C	
473	1419 C	-1:168091616 168091616 C	
474 I	1420 A	-1:168091615 168091615 A	I
474	1421 T	-1:168091614 168091614 T	
474	1422 C	-1:168091613 168091613 C	
475 N	1423 A	-1:168091612 168091612 A	N
475	1424 A	-1:168091611 168091611 A	
475	1425 C	-1:168091610 168091610 C	
476 S	1426 A	-1:168091609 168091609 A	S
476	1427 G	-1:168091608 168091608 G	
476	1428 C	-1:168091607 168091607 C	
477 K	1429 A	-1:168091606 168091606 A	K
477	1430 A	-1:168091605 168091605 A	
477	1431 G	-1:168091604 168091604 G	
478 K	1432 A	-1:168091603 168091603 A	K
478	1433 A	-1:168091602 168091602 A	
478	1434 G	-1:168091601 168091601 G	
479 H	1435 C	-1:168091600 168091600 C	H
479	1436 A	-1:168091599 168091599 A	
479	1437 C	-1:168091598 168091598 C	
480 I	1438 A	-1:168091597 168091597 A	I
480	1439 T	-1:168091596 168091596 T	
480	1440 A	-1:168091595 168091595 A	
481 Q	1441 C	-1:168091594 168091594 C	Q
481	1442 A	-1:168091593 168091593 A	
481	1443 G	-1:168091592 168091592 G	
482 R	1444 C	-1:168091591 168091591 C	R
482	1445 G	-1:168091590 168091590 G	
482	1446 A	-1:168091589 168091589 A	
483 D	1447 G	-1:168091588 168091588 G	D
483	1448 A	-1:168091587 168091587 A	
483	1449 T	-1:168091586 168091586 T	
484 Y	1450 T	-1:168091585 168091585 T	Y
484	1451 A	-1:168091584 168091584 A	
484	1452 C	-1:168091583 168091583 C	
485 Y	1453 T	-1:168091582 168091582 T	Y
485	1454 A	-1:168091581 168091581 A	
485	1455 C	-1:168091580 168091580 C	
486 N	1456 A	-1:168091579 168091579 A	N
486	1457 A	-1:168091578 168091578 A	
486	1458 T	-1:168091577 168091577 T	
487 T	1459 A	-1:168091576 168091576 A	T
487	1460 C	-1:168091575 168091575 C	
487	1461 T	-1:168091574 168091574 T	
488 L	1462 C	-1:168091573 168091573 C	L
488	1463 T	-1:168091572 168091572 T	
488	1464 T	-1:168091571 168091571 T	
489 L	1465 T	-1:168091570 168091570 T	L
489	1466 T	-1:168091569 168091569 T	
489	1467 A	-1:168091568 168091568 A	
490 Q	1468 C	-1:168091567 168091567 C	Q
490	1469 A	-1:168091566 168091566 A	
490	1470 G	-1:168091565 168091565 G	
491 T	1471 A	-1:168091564 168091564 A	T
491	1472 C	-1:168091563 168091563 C	
491	1473 A	-1:168091562 168091562 A	
492 G	1474 G	-1:168091561 168091561 G	G
492	1475 G	-1:168090729 168090729 G	
492	1476 C	-1:168090728 168090728 C	
493 D	1477 G	-1:168090727 168090727 G	D
493	1478 A	-1:168090726 168090726 A	
493	1479 T	-1:168090725 168090725 T	
494 P	1480 C	-1:168090724 168090724 C	P
494	1481 C	-1:168090723 168090723 C	
494	1482 A	-1:168090722 168090722 A	
495 F	1483 T	-1:168090721 168090721 T	F
495	1484 T	-1:168090720 168090720 T	
495	1485 T	-1:168090719 168090719 T	
496 S	1486 T	-1:168090718 168090718 T	S
496	1487 C	-1:168090717 168090717 C	
496	1488 T	-1:168090716 168090716 T	
497 Q	1489 C	-1:168090715 168090715 C	Q
497	1490 A	-1:168090714 168090714 A	
497	1491 G	-1:168090713 168090713 G	
498 P	1492 C	-1:168090712 168090712 C	P
498	1493 C	-1:168090711 168090711 C	
498	1494 T	-1:168090710 168090710 T	
499 I	1495 A	-1:168090709 168090709 A	I
499	1496 T	-1:168090708 168090708 T	
499	1497 T	-1:168090707 168090707 T	
500 K	1498 A	-1:168090706 168090706 A	K
500	1499 A	-1:168090705 168090705 A	
500	1500 A	-1:168090704 168090704 A	
501 F	1501 T	-1:168090703 168090703 T	F
501	1502 T	-1:168090702 168090702 T	
501	1503 T	-1:168090701 168090701 T	
502 P	1504 C	-1:168090700 168090700 C	P
502	1505 C	-1:168090699 168090699 C	
502	1506 C	-1:168090698 168090698 C	
503 I	1507 A	-1:168090697 168090697 A	I
503	1508 T	-1:168090696 168090696 T	
503	1509 A	-1:168090695 168090695 A	
504 N	1510 A	-1:168090694 168090694 A	N
504	1511 A	-1:168090693 168090693 A	
504	1512 T	-1:168090692 168090692 T	
505 G	1513 G	-1:168090691 168090691 G	G
505	1514 G	-1:168090690 168090690 G	
505	1515 A	-1:168090689 168090689 A	
506 L	1516 C	-1:168090688 168090688 C	L
506	1517 T	-1:168090687 168090687 T	
506	1518 C	-1:168090686 168090686 C	
507 S	1519 T	-1:168090685 168090685 T	S
507	1520 C	-1:168090684 168090684 C	
507	1521 A	-1:168090683 168090683 A	
508 D	1522 G	-1:168090682 168090682 G	D
508	1523 A	-1:168090681 168090681 A	
508	1524 T	-1:168090680 168090680 T	
509 V	1525 G	-1:168090679 168090679 G	V
509	1526 T	-1:168090678 168090678 T	
509	1527 A	-1:168090677 168090677 A	
510 K	1528 A	-1:168090676 168090676 A	K
510	1529 A	-1:168090675 168090675 A	
510	1530 A	-1:168090674 168090674 A	
511 N	1531 A	-1:168090673 168090673 A	N
511	1532 A	-1:168090672 168090672 A	
511	1533 T	-1:168090671 168090671 T	
512 T	1534 A	-1:168090670 168090670 A	T
512	1535 C	-1:168090669 168090669 C	
512	1536 T	-1:168090668 168090668 T	
513 S	1537 T	-1:168090667 168090667 T	S
513	1538 C	-1:168090666 168090666 C	
513	1539 G	-1:168090665 168090665 G	
514 E	1540 G	-1:168090664 168090664 G	E
514	1541 A	-1:168090663 168090663 A	
514	1542 G	-1:168090662 168090662 G	
515 D	1543 G	-1:168090661 168090661 G	D
515	1544 A	-1:168090660 168090660 A	
515	1545 C	-1:168090659 168090659 C	
516 S	1546 A	-1:168090658 168090658 A	S
516	1547 G	-1:168090657 168090657 G	
516	1548 T	-1:168090656 168090656 T	
517 E	1549 G	-1:168090655 168090655 G	E
517	1550 A	-1:168090654 168090654 A	
517	1551 A	-1:168090653 168090653 A	
518 N	1552 A	-1:168090652 168090652 A	N
518	1553 A	-1:168090651 168090651 A	
518	1554 C	-1:168090650 168090650 C	
519 F	1555 T	-1:168090649 168090649 T	F
519	1556 T	-1:168090648 168090648 T	
519	1557 C	-1:168090647 168090647 C	
520 P	1558 C	-1:168090646 168090646 C	P
520	1559 C	-1:168090645 168090645 C	
520	1560 A	-1:168090644 168090644 A	
521 S	1561 T	-1:168090643 168090643 T	S
521	1562 C	-1:168090642 168090642 C	
521	1563 A	-1:168090641 168090641 A	
522 S	1564 A	-1:168090640 168090640 A	S
522	1565 G	-1:168090639 168090639 G	
522	1566 T	-1:168090638 168090638 T	
523 S	1567 T	-1:168090637 168090637 T	S
523	1568 C	-1:168090636 168090636 C	
523	1569 T	-1:168090635 168090635 T	
524 K	1570 A	-1:168090634 168090634 A	K
524	1571 A	-1:168090633 168090633 A	
524	1572 A	-1:168090632 168090632 A	
525 K	1573 A	-1:168090631 168090631 A	K
525	1574 A	-1:168090630 168090630 A	
525	1575 G	-1:168090629 168090629 G	
526 S	1576 T	-1:168090628 168090628 T	S
526	1577 C	-1:168090627 168090627 C	
526	1578 T	-1:168090626 168090626 T	
527 E	1579 G	-1:168090625 168090625 G	E
527	1580 A	-1:168090624 168090624 A	
527	1581 G	-1:168090623 168090623 G	
528 E	1582 G	-1:168090622 168090622 G	E
528	1583 A	-1:168090621 168090621 A	
528	1584 G	-1:168090620 168090620 G	
529 W	1585 T	-1:168090619 168090619 T	W
529	1586 G	-1:168090618 168090618 G	
529	1587 G	-1:168090617 168090617 G	
530 P	1588 C	-1:168090616 168090616 C	P
530	1589 C	-1:168090615 168090615 C	
530	1590 T	-1:168090614 168090614 T	
531 D	1591 G	-1:168090613 168090613 G	D
531	1592 A	-1:168090612 168090612 A	
531	1593 C	-1:168090611 168090611 C	
532 W	1594 T	-1:168090610 168090610 T	W
532	1595 G	-1:168090609 168090609 G	
532	1596 G	-1:168090608 168090608 G	
533 S	1597 A	-1:168090607 168090607 A	S
533	1598 G	-1:168090606 168090606 G	
533	1599 T	-1:168090605 168090605 T	
534 E	1600 G	-1:168090604 168090604 G	E
534	1601 A	-1:168090603 168090603 A	
534	1602 A	-1:168090602 168090602 A	
535 P	1603 C	-1:168090601 168090601 C	P
535	1604 C	-1:168090600 168090600 C	
535	1605 T	-1:168090599 168090599 T	
536 E	1606 G	-1:168090598 168090598 G	E
536	1607 A	-1:168090597 168090597 A	
536	1608 G	-1:168090596 168090596 G	
537 E	1609 G	-1:168090595 168090595 G	E
537	1610 A	-1:168090594 168090594 A	
537	1611 G	-1:168090593 168090593 G	
538 P	1612 C	-1:168090592 168090592 C	P
538	1613 C	-1:168090591 168090591 C	
538	1614 T	-1:168090590 168090590 T	
539 E	1615 G	-1:168090589 168090589 G	E
539	1616 A	-1:168090588 168090588 A	
539	1617 A	-1:168090587 168090587 A	
540 N	1618 A	-1:168090586 168090586 A	N
540	1619 A	-1:168090585 168090585 A	
540	1620 T	-1:168090584 168090584 T	
541 Q	1621 C	-1:168090583 168090583 C	Q
541	1622 A	-1:168090582 168090582 A	
541	1623 A	-1:168090581 168090581 A	
542 T	1624 A	-1:168090580 168090580 A	T
542	1625 C	-1:168090579 168090579 C	
542	1626 T	-1:168090578 168090578 T	
543 V	1627 G	-1:168090577 168090577 G	V
543	1628 T	-1:168090576 168090576 T	
543	1629 C	-1:168090575 168090575 C	
544 N	1630 A	-1:168090574 168090574 A	N
544	1631 A	-1:168090573 168090573 A	
544	1632 C	-1:168090572 168090572 C	
545 I	1633 A	-1:168090571 168090571 A	I
545	1634 T	-1:168090570 168090570 T	
545	1635 A	-1:168090569 168090569 A	
546 Q	1636 C	-1:168090568 168090568 C	Q
546	1637 A	-1:168090567 168090567 A	
546	1638 G	-1:168090566 168090566 G	
547 I	1639 A	-1:168090565 168090565 A	I
547	1640 T	-1:168090564 168090564 T	
547	1641 T	-1:168090563 168090563 T	
548 W	1642 T	-1:168090562 168090562 T	W
548	1643 G	-1:168090561 168090561 G	
548	1644 G	-1:168090560 168090560 G	
549 P	1645 C	-1:168090559 168090559 C	P
549	1646 C	-1:168090558 168090558 C	
549	1647 T	-1:168090557 168090557 T	
550 R	1648 A	-1:168090556 168090556 A	R
550	1649 G	-1:168090555 168090555 G	
550	1650 A	-1:168090554 168090554 A	
551 E	1651 G	-1:168090553 168090553 G	E
551	1652 A	-1:168090552 168090552 A	
551	1653 A	-1:168090551 168090551 A	
552 P	1654 C	-1:168090550 168090550 C	P
552	1655 C	-1:168090549 168090549 C	
552	1656 T	-1:168090548 168090548 T	
553 C	1657 T	-1:168090547 168090547 T	C
553	1658 G	-1:168090546 168090546 G	
553	1659 T	-1:168090545 168090545 T	
554 D	1660 G	-1:168090544 168090544 G	D
554	1661 A	-1:168090543 168090543 A	
554	1662 T	-1:168090542 168090542 T	
555 D	1663 G	-1:168090541 168090541 G	D
555	1664 A	-1:168090540 168090540 A	
555	1665 T	-1:168090539 168090539 T	
556 V	1666 G	-1:168090538 168090538 G	V
556	1667 T	-1:168090537 168090537 T	
556	1668 C	-1:168090536 168090536 C	
557 K	1669 A	-1:168090535 168090535 A	K
557	1670 A	-1:168090534 168090534 A	
557	1671 G	-1:168090533 168090533 G	
558 S	1672 T	-1:168090532 168090532 T	S
558	1673 C	-1:168090531 168090531 C	
558	1674 C	-1:168090530 168090530 C	
559 Q	1675 C	-1:168090529 168090529 C	Q
559	1676 A	-1:168090528 168090528 A	
559	1677 G	-1:168090527 168090527 G	
560 C	1678 T	-1:168090526 168090526 T	C
560	1679 G	-1:168090525 168090525 G	
560	1680 C	-1:168090524 168090524 C	
561 T	1681 A	-1:168090523 168090523 A	T
561	1682 C	-1:168090522 168090522 C	
561	1683 T	-1:168090521 168090521 T	
562 T	1684 A	-1:168090520 168090520 A	T
562	1685 C	-1:168090519 168090519 C	
562	1686 C	-1:168090518 168090518 C	
563 L	1687 T	-1:168090517 168090517 T	L
563	1688 T	-1:168090516 168090516 T	
563	1689 G	-1:168090515 168090515 G	
564 D	1690 G	-1:168090514 168090514 G	D
564	1691 A	-1:168090513 168090513 A	
564	1692 T	-1:168090512 168090512 T	
565 V	1693 G	-1:168090511 168090511 G	V
565	1694 T	-1:168090510 168090510 T	
565	1695 G	-1:168090509 168090509 G	
566 E	1696 G	-1:168090508 168090508 G	E
566	1697 A	-1:168090507 168090507 A	
566	1698 A	-1:168090506 168090506 A	
567 E	1699 G	-1:168090505 168090505 G	E
567	1700 A	-1:168090504 168090504 A	
567	1701 G	-1:168090503 168090503 G	
568 S	1702 T	-1:168090502 168090502 T	S
568	1703 C	-1:168090501 168090501 C	
568	1704 A	-1:168090500 168090500 A	
569 S	1705 T	-1:168090499 168090499 T	S
569	1706 C	-1:168090498 168090498 C	
569	1707 T	-1:168090497 168090497 T	
570 W	1708 T	-1:168090496 168090496 T	W
570	1709 G	-1:168090495 168090495 G	
570	1710 G	-1:168090494 168090494 G	
571 D	1711 G	-1:168090493 168090493 G	D
571	1712 A	-1:168090492 168090492 A	
571	1713 T	-1:168090491 168090491 T	
572 D	1714 G	-1:168090490 168090490 G	D
572	1715 A	-1:168090489 168090489 A	
572	1716 C	-1:168090488 168090488 C	
573 C	1717 T	-1:168090487 168090487 T	C
573	1718 G	-1:168090486 168090486 G	
573	1719 C	-1:168090485 168090485 C	
574 E	1720 G	-1:168090484 168090484 G	E
574	1721 A	-1:168090483 168090483 A	
574	1722 G	-1:168090482 168090482 G	
575 P	1723 C	-1:168090481 168090481 C	P
575	1724 C	-1:168090480 168090480 C	
575	1725 C	-1:168090479 168090479 C	
576 S	1726 A	-1:168090478 168090478 A	S
576	1727 G	-1:168090477 168090477 G	
576	1728 C	-1:168090476 168090476 C	
577 S	1729 A	-1:168090475 168090475 A	S
577	1730 G	-1:168090474 168090474 G	
577	1731 C	-1:168090473 168090473 C	
578 L	1732 T	-1:168090472 168090472 T	L
578	1733 T	-1:168090471 168090471 T	
578	1734 A	-1:168090470 168090470 A	
579 D	1735 G	-1:168090469 168090469 G	D
579	1736 A	-1:168090468 168090468 A	
579	1737 T	-1:168090467 168090467 T	
580 T	1738 A	-1:168090466 168090466 A	T
580	1739 C	-1:168090465 168090465 C	
580	1740 T	-1:168090464 168090464 T	
581 K	1741 A	-1:168090463 168090463 A	K
581	1742 A	-1:168090462 168090462 A	
581	1743 A	-1:168090461 168090461 A	
582 V	1744 G	-1:168090460 168090460 G	V
582	1745 T	-1:168090459 168090459 T	
582	1746 A	-1:168090458 168090458 A	
583 N	1747 A	-1:168090457 168090457 A	N
583	1748 A	-1:168090456 168090456 A	
583	1749 C	-1:168090455 168090455 C	
584 P	1750 C	-1:168090454 168090454 C	P
584	1751 C	-1:168090453 168090453 C	
584	1752 A	-1:168090452 168090452 A	
585 G	1753 G	-1:168090451 168090451 G	G
585	1754 G	-1:168090450 168090450 G	
585	1755 A	-1:168090449 168090449 A	
586 G	1756 G	-1:168090448 168090448 G	G
586	1757 G	-1:168090447 168090447 G	
586	1758 T	-1:168090446 168090446 T	
587 G	1759 G	-1:168090445 168090445 G	G
587	1760 G	-1:168090444 168090444 G	
587	1761 A	-1:168090443 168090443 A	
588 I	1762 A	-1:168090442 168090442 A	I
588	1763 T	-1:168090441 168090441 T	
588	1764 C	-1:168090440 168090440 C	
589 T	1765 A	-1:168090439 168090439 A	T
589	1766 C	-1:168090438 168090438 C	
589	1767 T	-1:168090437 168090437 T	
590 A	1768 G	-1:168090436 168090436 G	A
590	1769 C	-1:168090435 168090435 C	
590	1770 T	-1:168090434 168090434 T	
591 T	1771 A	-1:168090433 168090433 A	T
591	1772 C	-1:168090432 168090432 C	
591	1773 A	-1:168090431 168090431 A	
592 K	1774 A	-1:168090430 168090430 A	K
592	1775 A	-1:168090429 168090429 A	
592	1776 A	-1:168090428 168090428 A	
593 P	1777 C	-1:168090427 168090427 C	P
593	1778 C	-1:168090426 168090426 C	
593	1779 T	-1:168090425 168090425 T	
594 V	1780 G	-1:168090424 168090424 G	V
594	1781 T	-1:168090423 168090423 T	
594	1782 T	-1:168090422 168090422 T	
595 T	1783 A	-1:168090421 168090421 A	T
595	1784 C	-1:168090420 168090420 C	
595	1785 C	-1:168090419 168090419 C	
596 S	1786 T	-1:168090418 168090418 T	S
596	1787 C	-1:168090417 168090417 C	
596	1788 A	-1:168090416 168090416 A	
597 G	1789 G	-1:168090415 168090415 G	G
597	1790 G	-1:168090414 168090414 G	
597	1791 G	-1:168090413 168090413 G	
598 E	1792 G	-1:168090412 168090412 G	E
598	1793 A	-1:168090411 168090411 A	
598	1794 G	-1:168090410 168090410 G	
599 Q	1795 C	-1:168090409 168090409 C	Q
599	1796 A	-1:168090408 168090408 A	
599	1797 G	-1:168090407 168090407 G	
600 K	1798 A	-1:168090406 168090406 A	K
600	1799 A	-1:168090405 168090405 A	
600	1800 G	-1:168090404 168090404 G	
601 P	1801 C	-1:168090403 168090403 C	P
601	1802 C	-1:168090402 168090402 C	
601	1803 T	-1:168090401 168090401 T	
602 I	1804 A	-1:168090400 168090400 A	I
602	1805 T	-1:168090399 168090399 T	
602	1806 T	-1:168090398 168090398 T	
603 P	1807 C	-1:168090397 168090397 C	P
603	1808 C	-1:168090396 168090396 C	
603	1809 T	-1:168090395 168090395 T	
604 A	1810 G	-1:168090394 168090394 G	A
604	1811 C	-1:168090393 168090393 C	
604	1812 T	-1:168090392 168090392 T	
605 L	1813 T	-1:168090391 168090391 T	L
605	1814 T	-1:168090390 168090390 T	
605	1815 G	-1:168090389 168090389 G	
606 L	1816 C	-1:168090388 168090388 C	L
606	1817 T	-1:168090387 168090387 T	
606	1818 T	-1:168090386 168090386 T	
607 S	1819 T	-1:168090385 168090385 T	S
607	1820 C	-1:168090384 168090384 C	
607	1821 A	-1:168090383 168090383 A	
608 L	1822 C	-1:168090382 168090382 C	L
608	1823 T	-1:168090381 168090381 T	
608	1824 C	-1:168090380 168090380 C	
609 T	1825 A	-1:168090379 168090379 A	T
609	1826 C	-1:168090378 168090378 C	
609	1827 T	-1:168090377 168090377 T	
610 E	1828 G	-1:168090376 168090376 G	E
610	1829 A	-1:168090375 168090375 A	
610	1830 A	-1:168090374 168090374 A	
611 E	1831 G	-1:168090373 168090373 G	E
611	1832 A	-1:168090372 168090372 A	
611	1833 G	-1:168090371 168090371 G	
612 S	1834 T	-1:168090370 168090370 T	S
612	1835 C	-1:168090369 168090369 C	
612	1836 T	-1:168090368 168090368 T	
613 M	1837 A	-1:168090367 168090367 A	M
613	1838 T	-1:168090366 168090366 T	
613	1839 G	-1:168090365 168090365 G	
614 P	1840 C	-1:168090364 168090364 C	P
614	1841 C	-1:168090363 168090363 C	
614	1842 T	-1:168090362 168090362 T	
615 W	1843 T	-1:168090361 168090361 T	W
615	1844 G	-1:168090360 168090360 G	
615	1845 G	-1:168090359 168090359 G	
616 K	1846 A	-1:168090358 168090358 A	K
616	1847 A	-1:168090357 168090357 A	
616	1848 A	-1:168090356 168090356 A	
617 S	1849 T	-1:168090355 168090355 T	S
617	1850 C	-1:168090354 168090354 C	
617	1851 A	-1:168090353 168090353 A	
618 S	1852 A	-1:168090352 168090352 A	S
618	1853 G	-1:168090351 168090351 G	
618	1854 C	-1:168090350 168090350 C	
619 L	1855 T	-1:168090349 168090349 T	L
619	1856 T	-1:168090348 168090348 T	
619	1857 A	-1:168090347 168090347 A	
620 P	1858 C	-1:168090346 168090346 C	P
620	1859 C	-1:168090345 168090345 C	
620	1860 C	-1:168090344 168090344 C	
621 Q	1861 C	-1:168090343 168090343 C	Q
621	1862 A	-1:168090342 168090342 A	
621	1863 A	-1:168090341 168090341 A	
622 K	1864 A	-1:168090340 168090340 A	K
622	1865 A	-1:168090339 168090339 A	
622	1866 G	-1:168090338 168090338 G	
623 I	1867 A	-1:168090337 168090337 A	I
623	1868 T	-1:168090336 168090336 T	
623	1869 T	-1:168090335 168090335 T	
624 S	1870 A	-1:168090334 168090334 A	S
624	1871 G	-1:168090333 168090333 G	
624	1872 C	-1:168090332 168090332 C	
625 L	1873 C	-1:168090331 168090331 C	L
625	1874 T	-1:168090330 168090330 T	
625	1875 T	-1:168090329 168090329 T	
626 V	1876 G	-1:168090328 168090328 G	V
626	1877 T	-1:168090327 168090327 T	
626	1878 A	-1:168090326 168090326 A	
627 Q	1879 C	-1:168090325 168090325 C	Q
627	1880 A	-1:168090324 168090324 A	
627	1881 A	-1:168090323 168090323 A	
628 R	1882 A	-1:168090322 168090322 A	R
628	1883 G	-1:168090321 168090321 G	
628	1884 G	-1:168090320 168090320 G	
629 G	1885 G	-1:168090319 168090319 G	G
629	1886 G	-1:168090318 168090318 G	
629	1887 G	-1:168090317 168090317 G	
630 D	1888 G	-1:168090316 168090316 G	D
630	1889 A	-1:168090315 168090315 A	
630	1890 T	-1:168090314 168090314 T	
631 D	1891 G	-1:168090313 168090313 G	D
631	1892 A	-1:168090312 168090312 A	
631	1893 C	-1:168090311 168090311 C	
632 A	1894 G	-1:168090310 168090310 G	A
632	1895 C	-1:168090309 168090309 C	
632	1896 A	-1:168090308 168090308 A	
633 D	1897 G	-1:168090307 168090307 G	D
633	1898 A	-1:168090306 168090306 A	
633	1899 C	-1:168090305 168090305 C	
634 Q	1900 C	-1:168090304 168090304 C	Q
634	1901 A	-1:168090303 168090303 A	
634	1902 A	-1:168090302 168090302 A	
635 I	1903 A	-1:168090301 168090301 A	I
635	1904 T	-1:168090300 168090300 T	
635	1905 C	-1:168090299 168090299 C	
636 E	1906 G	-1:168090298 168090298 G	E
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636	1908 G	-1:168090296 168090296 G	
637 P	1909 C	-1:168090295 168090295 C	P
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637	1911 G	-1:168090293 168090293 G	
638 P	1912 C	-1:168090292 168090292 C	P
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638	1914 A	-1:168090290 168090290 A	
639 K	1915 A	-1:168090289 168090289 A	K
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639	1917 A	-1:168090287 168090287 A	
640 V	1918 G	-1:168090286 168090286 G	V
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640	1920 G	-1:168090284 168090284 G	
641 S	1921 T	-1:168090283 168090283 T	S
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641	1923 A	-1:168090281 168090281 A	
642 S	1924 T	-1:168090280 168090280 T	S
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642	1926 A	-1:168090278 168090278 A	
643 Q	1927 C	-1:168090277 168090277 C	Q
643	1928 A	-1:168090276 168090276 A	
643	1929 A	-1:168090275 168090275 A	
644 E	1930 G	-1:168090274 168090274 G	E
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646 P	1936 C	-1:168090268 168090268 C	P
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646	1938 C	-1:168090266 168090266 C	
>ENSP00000286031 
23 T	67 A	+1:168038386 168038386 A	T
23	68 C	+1:168038387 168038387 C	
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26 L	76 T	+1:168038395 168038395 T	L
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27 F	79 T	+1:168038398 168038398 T	F
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32 Y	94 T	+1:168038413 168038413 T	Y
32	95 A	+1:168038414 168038414 A	
32	96 T	+1:168038415 168038415 T	
33 E	97 G	+1:168038416 168038416 G	E
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33	99 A	+1:168038418 168038418 A	
34 L	100 T	+1:168038419 168038419 T	L
34	101 T	+1:168038420 168038420 T	
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35 T	103 A	+1:168038422 168038422 A	T
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36 S	106 A	+1:168038425 168038425 A	S
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37 Q	109 C	+1:168038428 168038428 C	Q
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37	111 A	+1:168038430 168038430 A	
38 A	112 G	+1:168038431 168038431 G	A
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41 L	121 C	+1:168038440 168038440 C	L
41	122 T	+1:168038441 168038441 T	
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385 Y	1153 T	+1:168065053 168065053 T	Y
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410 E	1228 G	+1:168065128 168065128 G	E
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429	1286 C	+1:168065186 168065186 C	
429	1287 C	+1:168065187 168065187 C	
430 F	1288 T	+1:168065188 168065188 T	F
430	1289 T	+1:168065189 168065189 T	
430	1290 T	+1:168065190 168065190 T	
431 H	1291 C	+1:168065191 168065191 C	H
431	1292 A	+1:168065192 168065192 A	
431	1293 T	+1:168065193 168065193 T	
432 P	1294 C	+1:168065194 168065194 C	P
432	1295 C	+1:168065195 168065195 C	
432	1296 C	+1:168065196 168065196 C	
433 S	1297 T	+1:168065197 168065197 T	S
433	1298 C	+1:168065198 168065198 C	
433	1299 A	+1:168065199 168065199 A	
434 L	1300 C	+1:168065200 168065200 C	L
434	1301 T	+1:168065201 168065201 T	
434	1302 G	+1:168065202 168065202 G	
435 F	1303 T	+1:168065203 168065203 T	F
435	1304 T	+1:168065204 168065204 T	
435	1305 T	+1:168065205 168065205 T	
436 A	1306 G	+1:168065206 168065206 G	A
436	1307 C	+1:168065207 168065207 C	
436	1308 T	+1:168065208 168065208 T	
437 E	1309 G	+1:168065209 168065209 G	E
437	1310 A	+1:168065210 168065210 A	
437	1311 A	+1:168065211 168065211 A	
438 L	1312 C	+1:168065212 168065212 C	L
438	1313 T	+1:168065213 168065213 T	
438	1314 G	+1:168065214 168065214 G	
439 D	1315 G	+1:168066024 168066024 G	D
439	1316 A	+1:168066025 168066025 A	
439	1317 T	+1:168066026 168066026 T	
440 A	1318 G	+1:168066027 168066027 G	A
440	1319 C	+1:168066028 168066028 C	
440	1320 T	+1:168066029 168066029 T	
441 A	1321 G	+1:168066030 168066030 G	A
441	1322 C	+1:168066031 168066031 C	
441	1323 T	+1:168066032 168066032 T	
442 L	1324 C	+1:168066033 168066033 C	L
442	1325 T	+1:168066034 168066034 T	
442	1326 G	+1:168066035 168066035 G	
443 L	1327 C	+1:168066036 168066036 C	L
443	1328 T	+1:168066037 168066037 T	
443	1329 G	+1:168066038 168066038 G	
444 N	1330 A	+1:168066039 168066039 A	N
444	1331 A	+1:168066040 168066040 A	
444	1332 T	+1:168066041 168066041 T	
445 A	1333 G	+1:168066042 168066042 G	A
445	1334 C	+1:168066043 168066043 C	
445	1335 T	+1:168066044 168066044 T	
446 V	1336 G	+1:168066045 168066045 G	V
446	1337 T	+1:168066046 168066046 T	
446	1338 A	+1:168066047 168066047 A	
447 L	1339 C	+1:168066048 168066048 C	L
447	1340 T	+1:168066049 168066049 T	
447	1341 T	+1:168066050 168066050 T	
448 S	1342 A	+1:168066051 168066051 A	S
448	1343 G	+1:168066052 168066052 G	
448	1344 T	+1:168066053 168066053 T	
449 A	1345 G	+1:168066054 168066054 G	A
449	1346 C	+1:168066055 168066055 C	
449	1347 T	+1:168066056 168066056 T	
450 N	1348 A	+1:168066057 168066057 A	N
450	1349 A	+1:168066058 168066058 A	
450	1350 T	+1:168066059 168066059 T	
451 M	1351 A	+1:168066060 168066060 A	M
451	1352 T	+1:168066061 168066061 T	
451	1353 G	+1:168066062 168066062 G	
452 I	1354 A	+1:168066063 168066063 A	I
452	1355 T	+1:168066064 168066064 T	
452	1356 C	+1:168066065 168066065 C	
453 T	1357 A	+1:168066066 168066066 A	T
453	1358 C	+1:168066067 168066067 C	
453	1359 C	+1:168066068 168066068 C	
454 S	1360 T	+1:168066069 168066069 T	S
454	1361 C	+1:168066070 168066070 C	
454	1362 T	+1:168066071 168066071 T	
455 L	1363 T	+1:168066072 168066072 T	L
455	1364 T	+1:168066073 168066073 T	
455	1365 G	+1:168066074 168066074 G	
456 L	1366 T	+1:168066075 168066075 T	L
456	1367 T	+1:168066076 168066076 T	
456	1368 A	+1:168066077 168066077 A	
457 A	1369 G	+1:168066078 168066078 G	A
457	1370 C	+1:168066079 168066079 C	
457	1371 T	+1:168066080 168066080 T	
458 M	1372 A	+1:168066081 168066081 A	M
458	1373 T	+1:168066082 168066082 T	
458	1374 G	+1:168066083 168066083 G	
459 D	1375 G	+1:168066084 168066084 G	D
459	1376 A	+1:168066085 168066085 A	
459	1377 T	+1:168066086 168066086 T	
460 A	1378 G	+1:168066087 168066087 G	A
460	1379 C	+1:168066088 168066088 C	
460	1380 A	+1:168066089 168066089 A	
461 W	1381 T	+1:168066090 168066090 T	W
461	1382 G	+1:168066091 168066091 G	
461	1383 G	+1:168066092 168066092 G	
462 C	1384 T	+1:168066093 168066093 T	C
462	1385 G	+1:168066094 168066094 G	
462	1386 C	+1:168066095 168066095 C	
463 F	1387 T	+1:168066096 168066096 T	F
463	1388 T	+1:168066097 168066097 T	
463	1389 C	+1:168066098 168066098 C	
464 L	1390 C	+1:168066099 168066099 C	L
464	1391 T	+1:168066100 168066100 T	
464	1392 T	+1:168066101 168066101 T	
465 A	1393 G	+1:168066102 168066102 G	A
465	1394 C	+1:168066103 168066103 C	
465	1395 T	+1:168066104 168066104 T	
466 R	1396 C	+1:168066105 168066105 C	R
466	1397 G	+1:168066106 168066106 G	
466	1398 A	+1:168066461 168066461 A	
467 Y	1399 T	+1:168066462 168066462 T	Y
467	1400 A	+1:168066463 168066463 A	
467	1401 T	+1:168066464 168066464 T	
468 G	1402 G	+1:168066465 168066465 G	G
468	1403 G	+1:168066466 168066466 G	
468	1404 G	+1:168066467 168066467 G	
469 T	1405 A	+1:168066468 168066468 A	T
469	1406 C	+1:168066469 168066469 C	
469	1407 T	+1:168066470 168066470 T	
470 A	1408 G	+1:168066471 168066471 G	A
470	1409 C	+1:168066472 168066472 C	
470	1410 T	+1:168066473 168066473 T	
471 E	1411 G	+1:168066474 168066474 G	E
471	1412 A	+1:168066475 168066475 A	
471	1413 A	+1:168066476 168066476 A	
472 L	1414 C	+1:168066477 168066477 C	L
472	1415 T	+1:168066478 168066478 T	
472	1416 G	+1:168066479 168066479 G	
473 C	1417 T	+1:168066480 168066480 T	C
473	1418 G	+1:168066481 168066481 G	
473	1419 T	+1:168066482 168066482 T	
474 A	1420 G	+1:168066483 168066483 G	A
474	1421 C	+1:168066484 168066484 C	
474	1422 A	+1:168066485 168066485 A	
475 H	1423 C	+1:168066486 168066486 C	H
475	1424 A	+1:168066487 168066487 A	
475	1425 C	+1:168066488 168066488 C	
476 H	1426 C	+1:168066489 168066489 C	H
476	1427 A	+1:168066490 168066490 A	
476	1428 T	+1:168066491 168066491 T	
477 V	1429 G	+1:168066492 168066492 G	V
477	1430 T	+1:168066493 168066493 T	
477	1431 C	+1:168066494 168066494 C	
478 T	1432 A	+1:168066495 168066495 A	T
478	1433 C	+1:168066496 168066496 C	
478	1434 C	+1:168066497 168066497 C	
479 I	1435 A	+1:168066498 168066498 A	I
479	1436 T	+1:168066499 168066499 T	
479	1437 A	+1:168066500 168066500 A	
480 V	1438 G	+1:168066501 168066501 G	V
480	1439 T	+1:168066502 168066502 T	
480	1440 G	+1:168066503 168066503 G	
481 A	1441 G	+1:168066504 168066504 G	A
481	1442 C	+1:168066505 168066505 C	
481	1443 T	+1:168066506 168066506 T	
482 H	1444 C	+1:168066507 168066507 C	H
482	1445 A	+1:168066508 168066508 A	
482	1446 T	+1:168066509 168066509 T	
483 L	1447 C	+1:168066510 168066510 C	L
483	1448 T	+1:168066511 168066511 T	
483	1449 G	+1:168066512 168066512 G	
484 I	1450 A	+1:168068182 168068182 A	I
484	1451 T	+1:168068183 168068183 T	
484	1452 A	+1:168068184 168068184 A	
485 K	1453 A	+1:168068185 168068185 A	K
485	1454 A	+1:168068186 168068186 A	
485	1455 G	+1:168068187 168068187 G	
486 S	1456 T	+1:168068188 168068188 T	S
486	1457 C	+1:168068189 168068189 C	
486	1458 A	+1:168068190 168068190 A	
487 C	1459 T	+1:168068191 168068191 T	C
487	1460 G	+1:168068192 168068192 G	
487	1461 C	+1:168068193 168068193 C	
488 P	1462 C	+1:168068194 168068194 C	P
488	1463 C	+1:168068195 168068195 C	
488	1464 T	+1:168068196 168068196 T	
489 G	1465 G	+1:168068197 168068197 G	G
489	1466 G	+1:168068198 168068198 G	
489	1467 A	+1:168068199 168068199 A	
490 E	1468 G	+1:168068200 168068200 G	E
490	1469 A	+1:168068201 168068201 A	
490	1470 A	+1:168068202 168068202 A	
491 C	1471 T	+1:168068203 168068203 T	C
491	1472 G	+1:168068204 168068204 G	
491	1473 T	+1:168068205 168068205 T	
492 Y	1474 T	+1:168068206 168068206 T	Y
492	1475 A	+1:168068207 168068207 A	
492	1476 T	+1:168068208 168068208 T	
493 Q	1477 C	+1:168068209 168068209 C	Q
493	1478 A	+1:168068210 168068210 A	
493	1479 A	+1:168068211 168068211 A	
494 L	1480 C	+1:168068212 168068212 C	L
494	1481 T	+1:168068213 168068213 T	
494	1482 C	+1:168068214 168068214 C	
495 I	1483 A	+1:168068215 168068215 A	I
495	1484 T	+1:168068216 168068216 T	
495	1485 C	+1:168068217 168068217 C	
496 N	1486 A	+1:168068218 168068218 A	N
496	1487 A	+1:168068219 168068219 A	
496	1488 C	+1:168068220 168068220 C	
497 L	1489 C	+1:168068221 168068221 C	L
497	1490 T	+1:168068222 168068222 T	
497	1491 A	+1:168068223 168068223 A	
498 S	1492 T	+1:168068224 168068224 T	S
498	1493 C	+1:168068225 168068225 C	
498	1494 A	+1:168068226 168068226 A	
499 I	1495 A	+1:168068227 168068227 A	I
499	1496 T	+1:168068228 168068228 T	
499	1497 A	+1:168068229 168068229 A	
500 L	1498 C	+1:168068230 168068230 C	L
500	1499 T	+1:168068231 168068231 T	
500	1500 G	+1:168068232 168068232 G	
501 L	1501 T	+1:168068233 168068233 T	L
501	1502 T	+1:168068234 168068234 T	
501	1503 G	+1:168068235 168068235 G	
502 K	1504 A	+1:168068236 168068236 A	K
502	1505 A	+1:168068237 168068237 A	
502	1506 G	+1:168068238 168068238 G	
503 R	1507 C	+1:168068239 168068239 C	R
503	1508 G	+1:168068240 168068240 G	
503	1509 T	+1:168068241 168068241 T	
504 L	1510 C	+1:168068242 168068242 C	L
504	1511 T	+1:168068243 168068243 T	
504	1512 C	+1:168068244 168068244 C	
505 F	1513 T	+1:168068245 168068245 T	F
505	1514 T	+1:168068246 168068246 T	
505	1515 T	+1:168068247 168068247 T	
506 F	1516 T	+1:168068248 168068248 T	F
506	1517 T	+1:168068249 168068249 T	
506	1518 C	+1:168068250 168068250 C	
507 F	1519 T	+1:168068251 168068251 T	F
507	1520 T	+1:168068252 168068252 T	
507	1521 C	+1:168068253 168068253 C	
508 M	1522 A	+1:168068254 168068254 A	M
508	1523 T	+1:168068255 168068255 T	
508	1524 G	+1:168068256 168068256 G	
509 A	1525 G	+1:168068257 168068257 G	A
509	1526 C	+1:168068258 168068258 C	
509	1527 A	+1:168068259 168068259 A	
510 P	1528 C	+1:168068260 168068260 C	P
510	1529 C	+1:168068261 168068261 C	
510	1530 A	+1:168068262 168068262 A	
511 P	1531 C	+1:168068263 168068263 C	P
511	1532 C	+1:168068264 168068264 C	
511	1533 C	+1:168068265 168068265 C	
512 H	1534 C	+1:168068266 168068266 C	H
512	1535 A	+1:168068267 168068267 A	
512	1536 T	+1:168068268 168068268 T	
513 Q	1537 C	+1:168068269 168068269 C	Q
513	1538 A	+1:168068270 168068270 A	
513	1539 G	+1:168068271 168068271 G	
514 L	1540 C	+1:168072692 168072692 C	L
514	1541 T	+1:168072693 168072693 T	
514	1542 G	+1:168072694 168072694 G	
515 E	1543 G	+1:168072695 168072695 G	E
515	1544 A	+1:168072696 168072696 A	
515	1545 G	+1:168072697 168072697 G	
516 F	1546 T	+1:168072698 168072698 T	F
516	1547 T	+1:168072699 168072699 T	
516	1548 T	+1:168072700 168072700 T	
517 I	1549 A	+1:168072701 168072701 A	I
517	1550 T	+1:168072702 168072702 T	
517	1551 C	+1:168072703 168072703 C	
518 Q	1552 C	+1:168072704 168072704 C	Q
518	1553 A	+1:168072705 168072705 A	
518	1554 G	+1:168072706 168072706 G	
519 K	1555 A	+1:168072707 168072707 A	K
519	1556 A	+1:168072708 168072708 A	
519	1557 A	+1:168072709 168072709 A	
520 F	1558 T	+1:168072710 168072710 T	F
520	1559 T	+1:168072711 168072711 T	
520	1560 T	+1:168072712 168072712 T	
521 S	1561 T	+1:168072713 168072713 T	S
521	1562 C	+1:168072714 168072714 C	
521	1563 C	+1:168072715 168072715 C	
522 P	1564 C	+1:168072716 168072716 C	P
522	1565 C	+1:168072717 168072717 C	
522	1566 A	+1:168072718 168072718 A	
523 K	1567 A	+1:168072719 168072719 A	K
523	1568 A	+1:168072720 168072720 A	
523	1569 A	+1:168072721 168072721 A	
524 E	1570 G	+1:168072722 168072722 G	E
524	1571 A	+1:168072723 168072723 A	
524	1572 A	+1:168072724 168072724 A	
525 A	1573 G	+1:168072725 168072725 G	A
525	1574 C	+1:168072726 168072726 C	
525	1575 A	+1:168072727 168072727 A	
526 E	1576 G	+1:168072728 168072728 G	E
526	1577 A	+1:168072729 168072729 A	
526	1578 A	+1:168072730 168072730 A	
527 N	1579 A	+1:168072731 168072731 A	N
527	1580 A	+1:168072732 168072732 A	
527	1581 T	+1:168072733 168072733 T	
528 L	1582 C	+1:168072734 168072734 C	L
528	1583 T	+1:168072735 168072735 T	
528	1584 G	+1:168072736 168072736 G	
529 P	1585 C	+1:168072737 168072737 C	P
529	1586 C	+1:168072738 168072738 C	
529	1587 T	+1:168072739 168072739 T	
530 L	1588 C	+1:168072740 168072740 C	L
530	1589 T	+1:168072741 168072741 T	
530	1590 G	+1:168072742 168072742 G	
531 W	1591 T	+1:168072743 168072743 T	W
531	1592 G	+1:168072744 168072744 G	
531	1593 G	+1:168072745 168072745 G	
532 Q	1594 C	+1:168072746 168072746 C	Q
532	1595 A	+1:168072747 168072747 A	
532	1596 A	+1:168072748 168072748 A	
533 H	1597 C	+1:168072749 168072749 C	H
533	1598 A	+1:168072750 168072750 A	
533	1599 T	+1:168072751 168072751 T	
534 I	1600 A	+1:168072752 168072752 A	I
534	1601 T	+1:168072753 168072753 T	
534	1602 T	+1:168072754 168072754 T	
535 S	1603 T	+1:168072755 168072755 T	S
535	1604 C	+1:168072756 168072756 C	
535	1605 C	+1:168072757 168072757 C	
536 F	1606 T	+1:168072758 168072758 T	F
536	1607 T	+1:168072759 168072759 T	
536	1608 C	+1:168072760 168072760 C	
537 Q	1609 C	+1:168072761 168072761 C	Q
537	1610 A	+1:168072762 168072762 A	
537	1611 G	+1:168072763 168072763 G	
538 A	1612 G	+1:168072764 168072764 G	A
538	1613 C	+1:168072765 168072765 C	
538	1614 G	+1:168072766 168072766 G	
539 L	1615 T	+1:168072767 168072767 T	L
539	1616 T	+1:168072768 168072768 T	
539	1617 A	+1:168072769 168072769 A	
540 P	1618 C	+1:168072770 168072770 C	P
540	1619 C	+1:168072771 168072771 C	
540	1620 T	+1:168072772 168072772 T	
541 P	1621 C	+1:168072773 168072773 C	P
541	1622 C	+1:168072774 168072774 C	
541	1623 T	+1:168072775 168072775 T	
542 E	1624 G	+1:168072776 168072776 G	E
542	1625 A	+1:168072777 168072777 A	
542	1626 G	+1:168072778 168072778 G	
543 L	1627 C	+1:168072779 168072779 C	L
543	1628 T	+1:168072780 168072780 T	
543	1629 T	+1:168072781 168072781 T	
544 R	1630 A	+1:168072782 168072782 A	R
544	1631 G	+1:168072783 168072783 G	
544	1632 G	+1:168072784 168072784 G	
545 E	1633 G	+1:168072785 168072785 G	E
545	1634 A	+1:168072786 168072786 A	
545	1635 A	+1:168072787 168072787 A	
546 Q	1636 C	+1:168072788 168072788 C	Q
546	1637 A	+1:168072789 168072789 A	
546	1638 A	+1:168072790 168072790 A	
547 T	1639 A	+1:168072791 168072791 A	T
547	1640 C	+1:168072792 168072792 C	
547	1641 T	+1:168072793 168072793 T	
548 V	1642 G	+1:168072794 168072794 G	V
548	1643 T	+1:168072795 168072795 T	
548	1644 C	+1:168072796 168072796 C	
549 H	1645 C	+1:168072797 168072797 C	H
549	1646 A	+1:168072798 168072798 A	
549	1647 T	+1:168072799 168072799 T	
550 E	1648 G	+1:168072800 168072800 G	E
550	1649 A	+1:168072801 168072801 A	
550	1650 G	+1:168072802 168072802 G	
551 V	1651 G	+1:168072803 168072803 G	V
551	1652 T	+1:168072804 168072804 T	
551	1653 C	+1:168072805 168072805 C	
552 T	1654 A	+1:168072806 168072806 A	T
552	1655 C	+1:168072807 168072807 C	
552	1656 C	+1:168072808 168072808 C	
553 T	1657 A	+1:168072809 168072809 A	T
553	1658 C	+1:168072810 168072810 C	
553	1659 A	+1:168072811 168072811 A	
554 V	1660 G	+1:168072812 168072812 G	V
554	1661 T	+1:168072813 168072813 T	
554	1662 A	+1:168072814 168072814 A	
555 G	1663 G	+1:168072815 168072815 G	G
555	1664 G	+1:168072816 168072816 G	
555	1665 C	+1:168072817 168072817 C	
556 T	1666 A	+1:168072818 168072818 A	T
556	1667 C	+1:168072819 168072819 C	
556	1668 T	+1:168072820 168072820 T	
557 A	1669 G	+1:168072821 168072821 G	A
557	1670 C	+1:168072822 168072822 C	
557	1671 A	+1:168072823 168072823 A	
558 E	1672 G	+1:168072824 168072824 G	E
558	1673 A	+1:168072825 168072825 A	
558	1674 A	+1:168072826 168072826 A	
559 C	1675 T	+1:168072827 168072827 T	C
559	1676 G	+1:168072828 168072828 G	
559	1677 C	+1:168072829 168072829 C	
560 R	1678 A	+1:168072830 168072830 A	R
560	1679 G	+1:168072831 168072831 G	
560	1680 G	+1:168072832 168072832 G	
561 K	1681 A	+1:168072833 168072833 A	K
561	1682 A	+1:168072834 168072834 A	
561	1683 A	+1:168072835 168072835 A	
562 W	1684 T	+1:168072836 168072836 T	W
562	1685 G	+1:168072837 168072837 G	
562	1686 G	+1:168072838 168072838 G	
563 L	1687 C	+1:168072839 168072839 C	L
563	1688 T	+1:168072840 168072840 T	
563	1689 G	+1:168072841 168072841 G	
564 S	1690 A	+1:168072842 168072842 A	S
564	1691 G	+1:168072843 168072843 G	
564	1692 C	+1:168072844 168072844 C	
565 R	1693 A	+1:168072845 168072845 A	R
565	1694 G	+1:168072846 168072846 G	
565	1695 G	+1:168072847 168072847 G	
566 S	1696 A	+1:168072848 168072848 A	S
566	1697 G	+1:168072849 168072849 G	
566	1698 T	+1:168072850 168072850 T	
567 R	1699 C	+1:168072851 168072851 C	R
567	1700 G	+1:168072852 168072852 G	
567	1701 T	+1:168072853 168072853 T	
568 T	1702 A	+1:168072854 168072854 A	T
568	1703 C	+1:168072855 168072855 C	
568	1704 T	+1:168072856 168072856 T	
569 L	1705 T	+1:168072857 168072857 T	L
569	1706 T	+1:168072858 168072858 T	
569	1707 G	+1:168072859 168072859 G	
570 G	1708 G	+1:168072860 168072860 G	G
570	1709 G	+1:168072861 168072861 G	
570	1710 A	+1:168072862 168072862 A	
571 E	1711 G	+1:168072863 168072863 G	E
571	1712 A	+1:168072864 168072864 A	
571	1713 A	+1:168072865 168072865 A	
572 L	1714 C	+1:168072866 168072866 C	L
572	1715 T	+1:168072867 168072867 T	
572	1716 A	+1:168072868 168072868 A	
573 E	1717 G	+1:168072869 168072869 G	E
573	1718 A	+1:168072870 168072870 A	
573	1719 A	+1:168072871 168072871 A	
574 S	1720 T	+1:168072872 168072872 T	S
574	1721 C	+1:168072873 168072873 C	
574	1722 T	+1:168072874 168072874 T	
575 L	1723 C	+1:168072875 168072875 C	L
575	1724 T	+1:168072876 168072876 T	
575	1725 G	+1:168072877 168072877 G	
576 N	1726 A	+1:168078182 168078182 A	N
576	1727 A	+1:168078183 168078183 A	
576	1728 C	+1:168078184 168078184 C	
577 T	1729 A	+1:168078185 168078185 A	T
577	1730 C	+1:168078186 168078186 C	
577	1731 A	+1:168078187 168078187 A	
578 V	1732 G	+1:168078188 168078188 G	V
578	1733 T	+1:168078189 168078189 T	
578	1734 A	+1:168078190 168078190 A	
579 L	1735 C	+1:168078191 168078191 C	L
579	1736 T	+1:168078192 168078192 T	
579	1737 G	+1:168078193 168078193 G	
580 S	1738 T	+1:168078194 168078194 T	S
580	1739 C	+1:168078195 168078195 C	
580	1740 T	+1:168078196 168078196 T	
581 A	1741 G	+1:168078197 168078197 G	A
581	1742 C	+1:168078198 168078198 C	
581	1743 T	+1:168078199 168078199 T	
582 L	1744 T	+1:168078200 168078200 T	L
582	1745 T	+1:168078201 168078201 T	
582	1746 G	+1:168078202 168078202 G	
583 L	1747 C	+1:168078203 168078203 C	L
583	1748 T	+1:168078204 168078204 T	
583	1749 T	+1:168078205 168078205 T	
584 A	1750 G	+1:168078206 168078206 G	A
584	1751 C	+1:168078207 168078207 C	
584	1752 A	+1:168078208 168078208 A	
585 V	1753 G	+1:168078209 168078209 G	V
585	1754 T	+1:168078210 168078210 T	
585	1755 A	+1:168078211 168078211 A	
586 C	1756 T	+1:168078212 168078212 T	C
586	1757 G	+1:168078213 168078213 G	
586	1758 T	+1:168078214 168078214 T	
587 N	1759 A	+1:168078215 168078215 A	N
587	1760 A	+1:168078216 168078216 A	
587	1761 T	+1:168078217 168078217 T	
588 S	1762 T	+1:168078218 168078218 T	S
588	1763 C	+1:168078219 168078219 C	
588	1764 T	+1:168078220 168078220 T	
589 A	1765 G	+1:168078221 168078221 G	A
589	1766 C	+1:168078222 168078222 C	
589	1767 T	+1:168078223 168078223 T	
590 G	1768 G	+1:168078224 168078224 G	G
590	1769 G	+1:168078225 168078225 G	
590	1770 T	+1:168078226 168078226 T	
591 E	1771 G	+1:168078227 168078227 G	E
591	1772 A	+1:168078228 168078228 A	
591	1773 A	+1:168078229 168078229 A	
592 A	1774 G	+1:168078230 168078230 G	A
592	1775 C	+1:168078231 168078231 C	
592	1776 T	+1:168078232 168078232 T	
593 L	1777 T	+1:168078233 168078233 T	L
593	1778 T	+1:168078234 168078234 T	
593	1779 G	+1:168078235 168078235 G	
594 D	1780 G	+1:168078236 168078236 G	D
594	1781 A	+1:168078237 168078237 A	
594	1782 T	+1:168078238 168078238 T	
595 T	1783 A	+1:168078239 168078239 A	T
595	1784 C	+1:168078240 168078240 C	
595	1785 A	+1:168078241 168078241 A	
596 G	1786 G	+1:168078242 168078242 G	G
596	1787 G	+1:168078243 168078243 G	
596	1788 A	+1:168078244 168078244 A	
597 K	1789 A	+1:168078245 168078245 A	K
597	1790 A	+1:168078246 168078246 A	
597	1791 A	+1:168078247 168078247 A	
598 Q	1792 C	+1:168078248 168078248 C	Q
598	1793 A	+1:168078249 168078249 A	
598	1794 A	+1:168078250 168078250 A	
599 T	1795 A	+1:168078251 168078251 A	T
599	1796 C	+1:168078252 168078252 C	
599	1797 T	+1:168078253 168078253 T	
600 A	1798 G	+1:168078254 168078254 G	A
600	1799 C	+1:168078255 168078255 C	
600	1800 A	+1:168078256 168078256 A	
601 I	1801 A	+1:168078257 168078257 A	I
601	1802 T	+1:168078258 168078258 T	
601	1803 T	+1:168078259 168078259 T	
602 I	1804 A	+1:168078260 168078260 A	I
602	1805 T	+1:168078261 168078261 T	
602	1806 C	+1:168078262 168078262 C	
603 E	1807 G	+1:168078263 168078263 G	E
603	1808 A	+1:168078264 168078264 A	
603	1809 A	+1:168078265 168078265 A	
604 V	1810 G	+1:168078266 168078266 G	V
604	1811 T	+1:168078267 168078267 T	
604	1812 T	+1:168078268 168078268 T	
605 V	1813 G	+1:168078269 168078269 G	V
605	1814 T	+1:168078270 168078270 T	
605	1815 G	+1:168078271 168078271 G	
606 S	1816 A	+1:168078272 168078272 A	S
606	1817 G	+1:168078273 168078273 G	
606	1818 T	+1:168078274 168078274 T	
607 Q	1819 C	+1:168078275 168078275 C	Q
607	1820 A	+1:168078276 168078276 A	
607	1821 G	+1:168078277 168078277 G	
608 L	1822 C	+1:168078278 168078278 C	L
608	1823 T	+1:168078279 168078279 T	
608	1824 T	+1:168078280 168078280 T	
609 W	1825 T	+1:168078281 168078281 T	W
609	1826 G	+1:168078282 168078282 G	
609	1827 G	+1:168078283 168078283 G	
610 A	1828 G	+1:168078284 168078284 G	A
610	1829 C	+1:168078285 168078285 C	
610	1830 T	+1:168078286 168078286 T	
611 F	1831 T	+1:168078287 168078287 T	F
611	1832 T	+1:168078288 168078288 T	
611	1833 T	+1:168078289 168078289 T	
612 L	1834 T	+1:168078290 168078290 T	L
612	1835 T	+1:168078291 168078291 T	
612	1836 A	+1:168078292 168078292 A	
613 N	1837 A	+1:168078293 168078293 A	N
613	1838 A	+1:168078294 168078294 A	
613	1839 C	+1:168078295 168078295 C	
614 I	1840 A	+1:168078296 168078296 A	I
614	1841 T	+1:168078297 168078297 T	
614	1842 T	+1:168078298 168078298 T	
615 K	1843 A	+1:168078299 168078299 A	K
615	1844 A	+1:168078300 168078300 A	
615	1845 A	+1:168078301 168078301 A	
616 Q	1846 C	+1:168078302 168078302 C	Q
616	1847 A	+1:168078303 168078303 A	
616	1848 G	+1:168078304 168078304 G	
617 V	1849 G	+1:168079439 168079439 G	V
617	1850 T	+1:168079440 168079440 T	
617	1851 A	+1:168079441 168079441 A	
618 A	1852 G	+1:168079442 168079442 G	A
618	1853 C	+1:168079443 168079443 C	
618	1854 A	+1:168079444 168079444 A	
619 D	1855 G	+1:168079445 168079445 G	D
619	1856 A	+1:168079446 168079446 A	
619	1857 T	+1:168079447 168079447 T	
620 Q	1858 C	+1:168079448 168079448 C	Q
620	1859 A	+1:168079449 168079449 A	
620	1860 A	+1:168079450 168079450 A	
621 P	1861 C	+1:168079451 168079451 C	P
621	1862 C	+1:168079452 168079452 C	
621	1863 T	+1:168079453 168079453 T	
622 Y	1864 T	+1:168079454 168079454 T	Y
622	1865 A	+1:168079455 168079455 A	
622	1866 T	+1:168079456 168079456 T	
623 V	1867 G	+1:168079457 168079457 G	V
623	1868 T	+1:168079458 168079458 T	
623	1869 T	+1:168079459 168079459 T	
624 Q	1870 C	+1:168079460 168079460 C	Q
624	1871 A	+1:168079461 168079461 A	
624	1872 A	+1:168079462 168079462 A	
625 Q	1873 C	+1:168079463 168079463 C	Q
625	1874 A	+1:168079464 168079464 A	
625	1875 G	+1:168079465 168079465 G	
626 T	1876 A	+1:168079466 168079466 A	T
626	1877 C	+1:168079467 168079467 C	
626	1878 A	+1:168079468 168079468 A	
627 F	1879 T	+1:168079469 168079469 T	F
627	1880 T	+1:168079470 168079470 T	
627	1881 C	+1:168079471 168079471 C	
628 S	1882 A	+1:168079472 168079472 A	S
628	1883 G	+1:168079473 168079473 G	
628	1884 C	+1:168079474 168079474 C	
629 L	1885 C	+1:168079475 168079475 C	L
629	1886 T	+1:168079476 168079476 T	
629	1887 T	+1:168079477 168079477 T	
630 L	1888 T	+1:168079478 168079478 T	L
630	1889 T	+1:168079479 168079479 T	
630	1890 A	+1:168079480 168079480 A	
631 L	1891 C	+1:168079481 168079481 C	L
631	1892 T	+1:168079482 168079482 T	
631	1893 T	+1:168079483 168079483 T	
632 P	1894 C	+1:168079484 168079484 C	P
632	1895 C	+1:168079485 168079485 C	
632	1896 A	+1:168079486 168079486 A	
633 L	1897 C	+1:168079487 168079487 C	L
633	1898 T	+1:168079488 168079488 T	
633	1899 G	+1:168079489 168079489 G	
634 L	1900 T	+1:168079490 168079490 T	L
634	1901 T	+1:168079491 168079491 T	
634	1902 G	+1:168079492 168079492 G	
635 G	1903 G	+1:168079493 168079493 G	G
635	1904 G	+1:168079494 168079494 G	
635	1905 A	+1:168079495 168079495 A	
636 F	1906 T	+1:168079496 168079496 T	F
636	1907 T	+1:168079497 168079497 T	
636	1908 T	+1:168079498 168079498 T	
637 F	1909 T	+1:168079499 168079499 T	F
637	1910 T	+1:168079500 168079500 T	
637	1911 C	+1:168079501 168079501 C	
638 I	1912 A	+1:168079502 168079502 A	I
638	1913 T	+1:168079503 168079503 T	
638	1914 T	+1:168079504 168079504 T	
639 Q	1915 C	+1:168079505 168079505 C	Q
639	1916 A	+1:168079506 168079506 A	
639	1917 A	+1:168079507 168079507 A	
640 T	1918 A	+1:168079508 168079508 A	T
640	1919 C	+1:168079509 168079509 C	
640	1920 T	+1:168079510 168079510 T	
641 L	1921 C	+1:168079511 168079511 C	L
641	1922 T	+1:168079512 168079512 T	
641	1923 A	+1:168079513 168079513 A	
642 D	1924 G	+1:168079514 168079514 G	D
642	1925 A	+1:168079515 168079515 A	
642	1926 T	+1:168079516 168079516 T	
643 P	1927 C	+1:168079517 168079517 C	P
643	1928 C	+1:168079518 168079518 C	
643	1929 T	+1:168079519 168079519 T	
644 K	1930 A	+1:168079520 168079520 A	K
644	1931 A	+1:168079521 168079521 A	
644	1932 A	+1:168079522 168079522 A	
645 L	1933 C	+1:168079523 168079523 C	L
645	1934 T	+1:168079524 168079524 T	
645	1935 G	+1:168079525 168079525 G	
646 I	1936 A	+1:168079526 168079526 A	I
646	1937 T	+1:168079527 168079527 T	
646	1938 A	+1:168079528 168079528 A	
647 L	1939 C	+1:168079529 168079529 C	L
647	1940 T	+1:168079530 168079530 T	
647	1941 T	+1:168079531 168079531 T	
648 Q	1942 C	+1:168079532 168079532 C	Q
648	1943 A	+1:168079533 168079533 A	
648	1944 G	+1:168079534 168079534 G	
649 A	1945 G	+1:168083455 168083455 G	A
649	1946 C	+1:168083456 168083456 C	
649	1947 A	+1:168083457 168083457 A	
650 V	1948 G	+1:168083458 168083458 G	V
650	1949 T	+1:168083459 168083459 T	
650	1950 A	+1:168083460 168083460 A	
651 T	1951 A	+1:168083461 168083461 A	T
651	1952 C	+1:168083462 168083462 C	
651	1953 T	+1:168083463 168083463 T	
652 L	1954 T	+1:168083464 168083464 T	L
652	1955 T	+1:168083465 168083465 T	
652	1956 G	+1:168083466 168083466 G	
653 Q	1957 C	+1:168083467 168083467 C	Q
653	1958 A	+1:168083468 168083468 A	
653	1959 G	+1:168083469 168083469 G	
654 T	1960 A	+1:168083470 168083470 A	T
654	1961 C	+1:168083471 168083471 C	
654	1962 C	+1:168083472 168083472 C	
655 S	1963 T	+1:168083473 168083473 T	S
655	1964 C	+1:168083474 168083474 C	
655	1965 G	+1:168083475 168083475 G	
656 L	1966 C	+1:168083476 168083476 C	L
656	1967 T	+1:168083477 168083477 T	
656	1968 A	+1:168083478 168083478 A	
657 L	1969 C	+1:168083479 168083479 C	L
657	1970 T	+1:168083480 168083480 T	
657	1971 T	+1:168083481 168083481 T	
658 K	1972 A	+1:168083482 168083482 A	K
658	1973 A	+1:168083483 168083483 A	
658	1974 A	+1:168083484 168083484 A	
659 L	1975 T	+1:168083485 168083485 T	L
659	1976 T	+1:168083486 168083486 T	
659	1977 A	+1:168083487 168083487 A	
660 E	1978 G	+1:168083488 168083488 G	E
660	1979 A	+1:168083489 168083489 A	
660	1980 G	+1:168083490 168083490 G	
661 L	1981 C	+1:168083491 168083491 C	L
661	1982 T	+1:168083492 168083492 T	
661	1983 T	+1:168083493 168083493 T	
662 P	1984 C	+1:168083494 168083494 C	P
662	1985 C	+1:168083495 168083495 C	
662	1986 T	+1:168083496 168083496 T	
663 D	1987 G	+1:168083497 168083497 G	D
663	1988 A	+1:168083498 168083498 A	
663	1989 C	+1:168083499 168083499 C	
664 Y	1990 T	+1:168083500 168083500 T	Y
664	1991 A	+1:168083501 168083501 A	
664	1992 T	+1:168083502 168083502 T	
665 V	1993 G	+1:168083503 168083503 G	V
665	1994 T	+1:168083504 168083504 T	
665	1995 T	+1:168083505 168083505 T	
666 R	1996 C	+1:168083506 168083506 C	R
666	1997 G	+1:168083507 168083507 G	
666	1998 T	+1:168083508 168083508 T	
667 L	1999 T	+1:168083509 168083509 T	L
667	2000 T	+1:168083510 168083510 T	
667	2001 G	+1:168083511 168083511 G	
668 A	2002 G	+1:168083512 168083512 G	A
668	2003 C	+1:168083513 168083513 C	
668	2004 A	+1:168083514 168083514 A	
669 M	2005 A	+1:168083515 168083515 A	M
669	2006 T	+1:168083516 168083516 T	
669	2007 G	+1:168083517 168083517 G	
670 L	2008 T	+1:168083518 168083518 T	L
670	2009 T	+1:168083519 168083519 T	
670	2010 G	+1:168083520 168083520 G	
671 D	2011 G	+1:168083521 168083521 G	D
671	2012 A	+1:168083522 168083522 A	
671	2013 T	+1:168083523 168083523 T	
672 F	2014 T	+1:168083524 168083524 T	F
672	2015 T	+1:168083525 168083525 T	
672	2016 T	+1:168083526 168083526 T	
673 V	2017 G	+1:168083527 168083527 G	V
673	2018 T	+1:168083528 168083528 T	
673	2019 A	+1:168083529 168083529 A	
674 S	2020 T	+1:168083530 168083530 T	S
674	2021 C	+1:168083531 168083531 C	
674	2022 T	+1:168083532 168083532 T	
675 S	2023 T	+1:168083533 168083533 T	S
675	2024 C	+1:168083534 168083534 C	
675	2025 T	+1:168083535 168083535 T	
676 L	2026 T	+1:168083536 168083536 T	L
676	2027 T	+1:168083537 168083537 T	
676	2028 A	+1:168083538 168083538 A	
677 G	2029 G	+1:168083539 168083539 G	G
677	2030 G	+1:168083540 168083540 G	
677	2031 A	+1:168083541 168083541 A	
678 K	2032 A	+1:168083542 168083542 A	K
678	2033 A	+1:168083543 168083543 A	
678	2034 A	+1:168083544 168083544 A	
679 L	2035 C	+1:168083545 168083545 C	L
679	2036 T	+1:168083546 168083546 T	
679	2037 T	+1:168083547 168083547 T	
680 F	2038 T	+1:168083548 168083548 T	F
680	2039 T	+1:168083549 168083549 T	
680	2040 T	+1:168083550 168083550 T	
681 I	2041 A	+1:168083551 168083551 A	I
681	2042 T	+1:168083552 168083552 T	
681	2043 A	+1:168083553 168083553 A	
682 P	2044 C	+1:168083554 168083554 C	P
682	2045 C	+1:168083555 168083555 C	
682	2046 T	+1:168083556 168083556 T	
683 E	2047 G	+1:168083557 168083557 G	E
683	2048 A	+1:168083558 168083558 A	
683	2049 A	+1:168083559 168083559 A	
684 A	2050 G	+1:168083560 168083560 G	A
684	2051 C	+1:168083561 168083561 C	
684	2052 T	+1:168083562 168083562 T	
685 I	2053 A	+1:168083563 168083563 A	I
685	2054 T	+1:168083564 168083564 T	
685	2055 C	+1:168083565 168083565 C	
686 Q	2056 C	+1:168083566 168083566 C	Q
686	2057 A	+1:168083567 168083567 A	
686	2058 G	+1:168083568 168083568 G	
687 D	2059 G	+1:168085265 168085265 G	D
687	2060 A	+1:168085266 168085266 A	
687	2061 C	+1:168085267 168085267 C	
688 R	2062 A	+1:168085268 168085268 A	R
688	2063 G	+1:168085269 168085269 G	
688	2064 A	+1:168085270 168085270 A	
689 I	2065 A	+1:168085271 168085271 A	I
689	2066 T	+1:168085272 168085272 T	
689	2067 T	+1:168085273 168085273 T	
690 L	2068 C	+1:168085274 168085274 C	L
690	2069 T	+1:168085275 168085275 T	
690	2070 G	+1:168085276 168085276 G	
691 P	2071 C	+1:168085277 168085277 C	P
691	2072 C	+1:168085278 168085278 C	
691	2073 C	+1:168085279 168085279 C	
692 N	2074 A	+1:168085280 168085280 A	N
692	2075 A	+1:168085281 168085281 A	
692	2076 C	+1:168085282 168085282 C	
693 L	2077 C	+1:168085283 168085283 C	L
693	2078 T	+1:168085284 168085284 T	
693	2079 G	+1:168085285 168085285 G	
694 S	2080 T	+1:168085286 168085286 T	S
694	2081 C	+1:168085287 168085287 C	
694	2082 C	+1:168085288 168085288 C	
695 C	2083 T	+1:168085289 168085289 T	C
695	2084 G	+1:168085290 168085290 G	
695	2085 T	+1:168085291 168085291 T	
696 M	2086 A	+1:168085292 168085292 A	M
696	2087 T	+1:168085293 168085293 T	
696	2088 G	+1:168085294 168085294 G	
697 F	2089 T	+1:168085295 168085295 T	F
697	2090 T	+1:168085296 168085296 T	
697	2091 T	+1:168085297 168085297 T	
698 A	2092 G	+1:168085298 168085298 G	A
698	2093 C	+1:168085299 168085299 C	
698	2094 C	+1:168085300 168085300 C	
699 L	2095 T	+1:168085301 168085301 T	L
699	2096 T	+1:168085302 168085302 T	
699	2097 A	+1:168085303 168085303 A	
700 L	2098 C	+1:168085304 168085304 C	L
700	2099 T	+1:168085305 168085305 T	
700	2100 G	+1:168085306 168085306 G	
701 L	2101 C	+1:168085307 168085307 C	L
701	2102 T	+1:168085308 168085308 T	
701	2103 A	+1:168085309 168085309 A	
702 A	2104 G	+1:168085310 168085310 G	A
702	2105 C	+1:168085311 168085311 C	
702	2106 T	+1:168085312 168085312 T	
703 D	2107 G	+1:168085313 168085313 G	D
703	2108 A	+1:168085314 168085314 A	
703	2109 C	+1:168085315 168085315 C	
704 R	2110 A	+1:168085316 168085316 A	R
704	2111 G	+1:168085317 168085317 G	
704	2112 G	+1:168085318 168085318 G	
705 S	2113 A	+1:168085319 168085319 A	S
705	2114 G	+1:168085320 168085320 G	
705	2115 T	+1:168085321 168085321 T	
706 W	2116 T	+1:168085322 168085322 T	W
706	2117 G	+1:168085323 168085323 G	
706	2118 G	+1:168085324 168085324 G	
707 L	2119 C	+1:168085325 168085325 C	L
707	2120 T	+1:168085326 168085326 T	
707	2121 G	+1:168085327 168085327 G	
708 L	2122 C	+1:168085328 168085328 C	L
708	2123 T	+1:168085329 168085329 T	
708	2124 A	+1:168085330 168085330 A	
709 E	2125 G	+1:168085331 168085331 G	E
709	2126 A	+1:168085332 168085332 A	
709	2127 A	+1:168085333 168085333 A	
710 Q	2128 C	+1:168085334 168085334 C	Q
710	2129 A	+1:168085335 168085335 A	
710	2130 A	+1:168085336 168085336 A	
711 H	2131 C	+1:168085337 168085337 C	H
711	2132 A	+1:168085338 168085338 A	
711	2133 T	+1:168085339 168085339 T	
712 T	2134 A	+1:168085340 168085340 A	T
712	2135 C	+1:168085341 168085341 C	
712	2136 C	+1:168085342 168085342 C	
713 L	2137 T	+1:168085343 168085343 T	L
713	2138 T	+1:168085344 168085344 T	
713	2139 G	+1:168085345 168085345 G	
714 E	2140 G	+1:168085346 168085346 G	E
714	2141 A	+1:168085347 168085347 A	
714	2142 G	+1:168085348 168085348 G	
715 A	2143 G	+1:168085349 168085349 G	A
715	2144 C	+1:168085350 168085350 C	
715	2145 G	+1:168085351 168085351 G	
716 F	2146 T	+1:168085352 168085352 T	F
716	2147 T	+1:168085353 168085353 T	
716	2148 T	+1:168085354 168085354 T	
717 T	2149 A	+1:168085355 168085355 A	T
717	2150 C	+1:168085356 168085356 C	
717	2151 T	+1:168085357 168085357 T	
718 Q	2152 C	+1:168085358 168085358 C	Q
718	2153 A	+1:168085359 168085359 A	
718	2154 G	+1:168085360 168085360 G	
719 F	2155 T	+1:168085361 168085361 T	F
719	2156 T	+1:168085362 168085362 T	
719	2157 C	+1:168085363 168085363 C	
720 A	2158 G	+1:168085364 168085364 G	A
720	2159 C	+1:168085365 168085365 C	
720	2160 T	+1:168085366 168085366 T	
721 E	2161 G	+1:168085367 168085367 G	E
721	2162 A	+1:168085368 168085368 A	
721	2163 G	+1:168085369 168085369 G	
722 G	2164 G	+1:168086030 168086030 G	G
722	2165 G	+1:168086031 168086031 G	
722	2166 A	+1:168086032 168086032 A	
723 T	2167 A	+1:168086033 168086033 A	T
723	2168 C	+1:168086034 168086034 C	
723	2169 A	+1:168086035 168086035 A	
724 N	2170 A	+1:168086036 168086036 A	N
724	2171 A	+1:168086037 168086037 A	
724	2172 T	+1:168086038 168086038 T	
725 H	2173 C	+1:168086039 168086039 C	H
725	2174 A	+1:168086040 168086040 A	
725	2175 T	+1:168086041 168086041 T	
726 E	2176 G	+1:168086042 168086042 G	E
726	2177 A	+1:168086043 168086043 A	
726	2178 A	+1:168086044 168086044 A	
727 E	2179 G	+1:168086045 168086045 G	E
727	2180 A	+1:168086046 168086046 A	
727	2181 G	+1:168086047 168086047 G	
728 I	2182 A	+1:168086048 168086048 A	I
728	2183 T	+1:168086049 168086049 T	
728	2184 A	+1:168086050 168086050 A	
729 V	2185 G	+1:168086051 168086051 G	V
729	2186 T	+1:168086052 168086052 T	
729	2187 T	+1:168086053 168086053 T	
730 P	2188 C	+1:168086054 168086054 C	P
730	2189 C	+1:168086055 168086055 C	
730	2190 A	+1:168086056 168086056 A	
731 Q	2191 C	+1:168086057 168086057 C	Q
731	2192 A	+1:168086058 168086058 A	
731	2193 G	+1:168086059 168086059 G	
732 C	2194 T	+1:168086060 168086060 T	C
732	2195 G	+1:168086061 168086061 G	
732	2196 T	+1:168086062 168086062 T	
733 L	2197 C	+1:168086063 168086063 C	L
733	2198 T	+1:168086064 168086064 T	
733	2199 C	+1:168086065 168086065 C	
734 S	2200 A	+1:168086066 168086066 A	S
734	2201 G	+1:168086067 168086067 G	
734	2202 T	+1:168086068 168086068 T	
735 S	2203 T	+1:168086069 168086069 T	S
735	2204 C	+1:168086070 168086070 C	
735	2205 T	+1:168086071 168086071 T	
736 E	2206 G	+1:168086072 168086072 G	E
736	2207 A	+1:168086073 168086073 A	
736	2208 A	+1:168086074 168086074 A	
737 E	2209 G	+1:168086075 168086075 G	E
737	2210 A	+1:168086076 168086076 A	
737	2211 A	+1:168086077 168086077 A	
738 T	2212 A	+1:168086078 168086078 A	T
738	2213 C	+1:168086079 168086079 C	
738	2214 T	+1:168086080 168086080 T	
739 K	2215 A	+1:168086081 168086081 A	K
739	2216 A	+1:168086082 168086082 A	
739	2217 G	+1:168086083 168086083 G	
740 N	2218 A	+1:168086084 168086084 A	N
740	2219 A	+1:168086085 168086085 A	
740	2220 C	+1:168086086 168086086 C	
741 K	2221 A	+1:168086087 168086087 A	K
741	2222 A	+1:168086088 168086088 A	
741	2223 A	+1:168086089 168086089 A	
742 V	2224 G	+1:168086090 168086090 G	V
742	2225 T	+1:168086091 168086091 T	
742	2226 T	+1:168086092 168086092 T	
743 V	2227 G	+1:168086093 168086093 G	V
743	2228 T	+1:168086094 168086094 T	
743	2229 A	+1:168086095 168086095 A	
744 S	2230 T	+1:168086096 168086096 T	S
744	2231 C	+1:168086097 168086097 C	
744	2232 C	+1:168086098 168086098 C	
745 F	2233 T	+1:168086099 168086099 T	F
745	2234 T	+1:168086100 168086100 T	
745	2235 T	+1:168086101 168086101 T	
746 L	2236 C	+1:168086102 168086102 C	L
746	2237 T	+1:168086103 168086103 T	
746	2238 G	+1:168086104 168086104 G	
747 E	2239 G	+1:168086105 168086105 G	E
747	2240 A	+1:168086106 168086106 A	
747	2241 G	+1:168086107 168086107 G	
748 K	2242 A	+1:168086108 168086108 A	K
748	2243 A	+1:168086109 168086109 A	
748	2244 G	+1:168086110 168086110 G	
749 T	2245 A	+1:168087582 168087582 A	T
749	2246 C	+1:168087583 168087583 C	
749	2247 T	+1:168087584 168087584 T	
750 G	2248 G	+1:168087585 168087585 G	G
750	2249 G	+1:168087586 168087586 G	
750	2250 G	+1:168087587 168087587 G	
751 F	2251 T	+1:168087588 168087588 T	F
751	2252 T	+1:168087589 168087589 T	
751	2253 T	+1:168087590 168087590 T	
752 V	2254 G	+1:168087591 168087591 G	V
752	2255 T	+1:168087592 168087592 T	
752	2256 A	+1:168087593 168087593 A	
753 D	2257 G	+1:168087594 168087594 G	D
753	2258 A	+1:168087595 168087595 A	
753	2259 T	+1:168087596 168087596 T	
754 E	2260 G	+1:168087597 168087597 G	E
754	2261 A	+1:168087598 168087598 A	
754	2262 A	+1:168087599 168087599 A	
755 T	2263 A	+1:168087600 168087600 A	T
755	2264 C	+1:168087601 168087601 C	
755	2265 T	+1:168087602 168087602 T	
756 E	2266 G	+1:168087603 168087603 G	E
756	2267 A	+1:168087604 168087604 A	
756	2268 A	+1:168087605 168087605 A	
757 A	2269 G	+1:168087606 168087606 G	A
757	2270 C	+1:168087607 168087607 C	
757	2271 T	+1:168087608 168087608 T	
758 A	2272 G	+1:168087609 168087609 G	A
758	2273 C	+1:168087610 168087610 C	
758	2274 C	+1:168087611 168087611 C	
759 K	2275 A	+1:168087612 168087612 A	K
759	2276 A	+1:168087613 168087613 A	
759	2277 A	+1:168087614 168087614 A	
760 V	2278 G	+1:168087615 168087615 G	V
760	2279 T	+1:168087616 168087616 T	
760	2280 G	+1:168087617 168087617 G	
761 E	2281 G	+1:168087618 168087618 G	E
761	2282 A	+1:168087619 168087619 A	
761	2283 A	+1:168087620 168087620 A	
762 R	2284 C	+1:168087621 168087621 C	R
762	2285 G	+1:168087622 168087622 G	
762	2286 T	+1:168087623 168087623 T	
763 V	2287 G	+1:168087624 168087624 G	V
763	2288 T	+1:168087625 168087625 T	
763	2289 G	+1:168087626 168087626 G	
764 K	2290 A	+1:168087627 168087627 A	K
764	2291 A	+1:168087628 168087628 A	
764	2292 A	+1:168087629 168087629 A	
765 Q	2293 C	+1:168087630 168087630 C	Q
765	2294 A	+1:168087631 168087631 A	
765	2295 G	+1:168087632 168087632 G	
766 E	2296 G	+1:168087633 168087633 G	E
766	2297 A	+1:168087634 168087634 A	
766	2298 A	+1:168087635 168087635 A	
767 K	2299 A	+1:168087636 168087636 A	K
767	2300 A	+1:168087637 168087637 A	
767	2301 A	+1:168087638 168087638 A	
768 G	2302 G	+1:168087639 168087639 G	G
768	2303 G	+1:168087640 168087640 G	
768	2304 T	+1:168087641 168087641 T	
769 I	2305 A	+1:168087642 168087642 A	I
769	2306 T	+1:168087643 168087643 T	
769	2307 T	+1:168087644 168087644 T	
770 F	2308 T	+1:168087645 168087645 T	F
770	2309 T	+1:168087646 168087646 T	
770	2310 C	+1:168087647 168087647 C	
771 W	2311 T	+1:168087648 168087648 T	W
771	2312 G	+1:168087649 168087649 G	
771	2313 G	+1:168087650 168087650 G	
772 E	2314 G	+1:168087651 168087651 G	E
772	2315 A	+1:168087652 168087652 A	
772	2316 A	+1:168087653 168087653 A	
773 P	2317 C	+1:168087654 168087654 C	P
773	2318 C	+1:168087655 168087655 C	
773	2319 C	+1:168087656 168087656 C	
774 F	2320 T	+1:168087657 168087657 T	F
774	2321 T	+1:168087658 168087658 T	
774	2322 T	+1:168087659 168087659 T	
775 A	2323 G	+1:168087660 168087660 G	A
775	2324 C	+1:168087661 168087661 C	
775	2325 T	+1:168087662 168087662 T	
776 N	2326 A	+1:168087663 168087663 A	N
776	2327 A	+1:168087664 168087664 A	
776	2328 T	+1:168087665 168087665 T	
777 V	2329 G	+1:168087666 168087666 G	V
777	2330 T	+1:168087667 168087667 T	
777	2331 G	+1:168087668 168087668 G	
778 T	2332 A	+1:168087669 168087669 A	T
778	2333 C	+1:168087670 168087670 C	
778	2334 T	+1:168087671 168087671 T	
779 V	2335 G	+1:168087672 168087672 G	V
779	2336 T	+1:168087673 168087673 T	
779	2337 A	+1:168087674 168087674 A	
780 E	2338 G	+1:168087675 168087675 G	E
780	2339 A	+1:168087676 168087676 A	
780	2340 A	+1:168087677 168087677 A	
781 E	2341 G	+1:168087678 168087678 G	E
781	2342 A	+1:168087679 168087679 A	
781	2343 A	+1:168087680 168087680 A	
782 A	2344 G	+1:168087681 168087681 G	A
782	2345 C	+1:168087682 168087682 C	
782	2346 A	+1:168087683 168087683 A	
783 K	2347 A	+1:168087684 168087684 A	K
783	2348 A	+1:168087685 168087685 A	
783	2349 G	+1:168087686 168087686 G	
784 R	2350 A	+1:168087687 168087687 A	R
784	2351 G	+1:168087688 168087688 G	
784	2352 G	+1:168087689 168087689 G	
785 S	2353 T	+1:168087690 168087690 T	S
785	2354 C	+1:168087691 168087691 C	
785	2355 A	+1:168087692 168087692 A	
786 S	2356 T	+1:168087693 168087693 T	S
786	2357 C	+1:168087694 168087694 C	
786	2358 T	+1:168087695 168087695 T	
787 L	2359 T	+1:168087696 168087696 T	L
787	2360 T	+1:168087697 168087697 T	
787	2361 A	+1:168087698 168087698 A	
788 Q	2362 C	+1:168087699 168087699 C	Q
788	2363 A	+1:168087700 168087700 A	
788	2364 G	+1:168087701 168087701 G	
789 P	2365 C	+1:168088555 168088555 C	P
789	2366 C	+1:168088556 168088556 C	
789	2367 T	+1:168088557 168088557 T	
790 Y	2368 T	+1:168088558 168088558 T	Y
790	2369 A	+1:168088559 168088559 A	
790	2370 T	+1:168088560 168088560 T	
791 A	2371 G	+1:168088561 168088561 G	A
791	2372 C	+1:168088562 168088562 C	
791	2373 A	+1:168088563 168088563 A	
792 K	2374 A	+1:168088564 168088564 A	K
792	2375 A	+1:168088565 168088565 A	
792	2376 A	+1:168088566 168088566 A	
793 R	2377 A	+1:168088567 168088567 A	R
793	2378 G	+1:168088568 168088568 G	
793	2379 A	+1:168088569 168088569 A	
794 A	2380 G	+1:168088570 168088570 G	A
794	2381 C	+1:168088571 168088571 C	
794	2382 T	+1:168088572 168088572 T	
795 R	2383 C	+1:168088573 168088573 C	R
795	2384 G	+1:168088574 168088574 G	
795	2385 T	+1:168088575 168088575 T	
796 Q	2386 C	+1:168088576 168088576 C	Q
796	2387 A	+1:168088577 168088577 A	
796	2388 G	+1:168088578 168088578 G	
797 E	2389 G	+1:168088579 168088579 G	E
797	2390 A	+1:168088580 168088580 A	
797	2391 G	+1:168088581 168088581 G	
798 F	2392 T	+1:168088582 168088582 T	F
798	2393 T	+1:168088583 168088583 T	
798	2394 C	+1:168088584 168088584 C	
799 P	2395 C	+1:168088585 168088585 C	P
799	2396 C	+1:168088586 168088586 C	
799	2397 C	+1:168088587 168088587 C	
800 W	2398 T	+1:168088588 168088588 T	W
800	2399 G	+1:168088589 168088589 G	
800	2400 G	+1:168088590 168088590 G	
801 E	2401 G	+1:168088591 168088591 G	E
801	2402 A	+1:168088592 168088592 A	
801	2403 A	+1:168088593 168088593 A	
802 E	2404 G	+1:168088594 168088594 G	E
802	2405 A	+1:168088595 168088595 A	
802	2406 A	+1:168088596 168088596 A	
803 E	2407 G	+1:168088597 168088597 G	E
803	2408 A	+1:168088598 168088598 A	
803	2409 G	+1:168088599 168088599 G	
804 Y	2410 T	+1:168088600 168088600 T	Y
804	2411 A	+1:168088601 168088601 A	
804	2412 C	+1:168088602 168088602 C	
805 R	2413 A	+1:168088603 168088603 A	R
805	2414 G	+1:168088604 168088604 G	
805	2415 G	+1:168088605 168088605 G	
806 S	2416 T	+1:168088606 168088606 T	S
806	2417 C	+1:168088607 168088607 C	
806	2418 A	+1:168088608 168088608 A	
807 A	2419 G	+1:168088609 168088609 G	A
807	2420 C	+1:168088610 168088610 C	
807	2421 G	+1:168088611 168088611 G	
808 L	2422 C	+1:168088612 168088612 C	L
808	2423 T	+1:168088613 168088613 T	
808	2424 G	+1:168088614 168088614 G	
809 H	2425 C	+1:168088615 168088615 C	H
809	2426 A	+1:168088616 168088616 A	
809	2427 T	+1:168088617 168088617 T	
810 T	2428 A	+1:168088618 168088618 A	T
810	2429 C	+1:168088619 168088619 C	
810	2430 A	+1:168088620 168088620 A	
811 I	2431 A	+1:168088621 168088621 A	I
811	2432 T	+1:168088622 168088622 T	
811	2433 A	+1:168088623 168088623 A	
812 A	2434 G	+1:168088624 168088624 G	A
812	2435 C	+1:168088625 168088625 C	
812	2436 A	+1:168088626 168088626 A	
813 G	2437 G	+1:168088627 168088627 G	G
813	2438 G	+1:168088628 168088628 G	
813	2439 G	+1:168088629 168088629 G	
814 A	2440 G	+1:168088630 168088630 G	A
814	2441 C	+1:168088631 168088631 C	
814	2442 T	+1:168088632 168088632 T	
815 L	2443 T	+1:168088633 168088633 T	L
815	2444 T	+1:168088634 168088634 T	
815	2445 G	+1:168088635 168088635 G	
816 E	2446 G	+1:168088636 168088636 G	E
816	2447 A	+1:168088637 168088637 A	
816	2448 A	+1:168088638 168088638 A	
817 A	2449 G	+1:168088639 168088639 G	A
817	2450 C	+1:168088640 168088640 C	
817	2451 A	+1:168088641 168088641 A	
818 T	2452 A	+1:168088642 168088642 A	T
818	2453 C	+1:168088643 168088643 C	
818	2454 T	+1:168088644 168088644 T	
819 E	2455 G	+1:168088645 168088645 G	E
819	2456 A	+1:168088646 168088646 A	
819	2457 G	+1:168088647 168088647 G	
820 S	2458 T	+1:168088648 168088648 T	S
820	2459 C	+1:168088649 168088649 C	
820	2460 A	+1:168088650 168088650 A	
821 L	2461 C	+1:168088651 168088651 C	L
821	2462 T	+1:168088652 168088652 T	
821	2463 A	+1:168088653 168088653 A	
822 L	2464 C	+1:168088654 168088654 C	L
822	2465 T	+1:168088655 168088655 T	
822	2466 C	+1:168088656 168088656 C	
823 Q	2467 C	+1:168088657 168088657 C	Q
823	2468 A	+1:168088658 168088658 A	
823	2469 A	+1:168088659 168088659 A	
824 K	2470 A	+1:168088660 168088660 A	K
824	2471 A	+1:168088661 168088661 A	
824	2472 G	+1:168088662 168088662 G	
825 G	2473 G	+1:168088663 168088663 G	G
825	2474 G	+1:168088664 168088664 G	
825	2475 T	+1:168088665 168088665 T	
826 P	2476 C	+1:168088666 168088666 C	P
826	2477 C	+1:168088667 168088667 C	
826	2478 T	+1:168088668 168088668 T	
827 A	2479 G	+1:168088669 168088669 G	A
827	2480 C	+1:168088670 168088670 C	
827	2481 T	+1:168088671 168088671 T	
828 P	2482 C	+1:168088672 168088672 C	P
828	2483 C	+1:168088673 168088673 C	
828	2484 A	+1:168088674 168088674 A	
829 A	2485 G	+1:168088675 168088675 G	A
829	2486 C	+1:168088676 168088676 C	
829	2487 C	+1:168088677 168088677 C	
830 W	2488 T	+1:168088678 168088678 T	W
830	2489 G	+1:168088679 168088679 G	
830	2490 G	+1:168088680 168088680 G	
831 L	2491 C	+1:168088681 168088681 C	L
831	2492 T	+1:168088682 168088682 T	
831	2493 T	+1:168088683 168088683 T	
832 S	2494 T	+1:168088684 168088684 T	S
832	2495 C	+1:168088685 168088685 C	
832	2496 A	+1:168088686 168088686 A	
833 M	2497 A	+1:168088687 168088687 A	M
833	2498 T	+1:168088688 168088688 T	
833	2499 G	+1:168088689 168088689 G	
834 E	2500 G	+1:168088690 168088690 G	E
834	2501 A	+1:168088691 168088691 A	
834	2502 A	+1:168088692 168088692 A	
835 M	2503 A	+1:168088693 168088693 A	M
835	2504 T	+1:168088694 168088694 T	
835	2505 G	+1:168088695 168088695 G	
836 E	2506 G	+1:168088696 168088696 G	E
836	2507 A	+1:168088697 168088697 A	
836	2508 G	+1:168088698 168088698 G	
837 A	2509 G	+1:168088699 168088699 G	A
837	2510 C	+1:168088700 168088700 C	
837	2511 G	+1:168088701 168088701 G	
838 L	2512 C	+1:168088702 168088702 C	L
838	2513 T	+1:168088703 168088703 T	
838	2514 C	+1:168088704 168088704 C	
839 Q	2515 C	+1:168088705 168088705 C	Q
839	2516 A	+1:168088706 168088706 A	
839	2517 A	+1:168088707 168088707 A	
840 E	2518 G	+1:168088708 168088708 G	E
840	2519 A	+1:168088709 168088709 A	
840	2520 A	+1:168088710 168088710 A	
841 R	2521 A	+1:168088711 168088711 A	R
841	2522 G	+1:168088712 168088712 G	
841	2523 G	+1:168088713 168088713 G	
842 M	2524 A	+1:168088714 168088714 A	M
842	2525 T	+1:168088715 168088715 T	
842	2526 G	+1:168088716 168088716 G	
843 D	2527 G	+1:168088717 168088717 G	D
843	2528 A	+1:168088718 168088718 A	
843	2529 T	+1:168088719 168088719 T	
844 K	2530 A	+1:168088720 168088720 A	K
844	2531 A	+1:168088721 168088721 A	
844	2532 G	+1:168088722 168088722 G	
845 L	2533 C	+1:168088723 168088723 C	L
845	2534 T	+1:168088724 168088724 T	
845	2535 A	+1:168088725 168088725 A	
846 K	2536 A	+1:168088726 168088726 A	K
846	2537 A	+1:168088727 168088727 A	
846	2538 A	+1:168088728 168088728 A	
847 R	2539 C	+1:168088729 168088729 C	R
847	2540 G	+1:168088730 168088730 G	
847	2541 T	+1:168088731 168088731 T	
848 Y	2542 T	+1:168088732 168088732 T	Y
848	2543 A	+1:168088733 168088733 A	
848	2544 C	+1:168088734 168088734 C	
849 I	2545 A	+1:168088735 168088735 A	I
849	2546 T	+1:168088736 168088736 T	
849	2547 A	+1:168088737 168088737 A	
850 H	2548 C	+1:168088738 168088738 C	H
850	2549 A	+1:168088739 168088739 A	
850	2550 T	+1:168088740 168088740 T	
851 T	2551 A	+1:168088741 168088741 A	T
851	2552 C	+1:168088742 168088742 C	
851	2553 T	+1:168088743 168088743 T	
852 L	2554 C	+1:168088744 168088744 C	L
852	2555 T	+1:168088745 168088745 T	
852	2556 A	+1:168088746 168088746 A	
853 G	2557 G	+1:168088747 168088747 G	G
853	2558 G	+1:168088748 168088748 G	
853	2559 G	+1:168088749 168088749 G	
>ENSP00000352276 
23 T	67 A	+1:168038386 168038386 A	T
23	68 C	+1:168038387 168038387 C	
23	69 T	+1:168038388 168038388 T	
24 V	70 G	+1:168038389 168038389 G	V
24	71 T	+1:168038390 168038390 T	
24	72 G	+1:168038391 168038391 G	
25 K	73 A	+1:168038392 168038392 A	K
25	74 A	+1:168038393 168038393 A	
25	75 A	+1:168038394 168038394 A	
26 L	76 T	+1:168038395 168038395 T	L
26	77 T	+1:168038396 168038396 T	
26	78 A	+1:168038397 168038397 A	
27 F	79 T	+1:168038398 168038398 T	F
27	80 T	+1:168038399 168038399 T	
27	81 C	+1:168038400 168038400 C	
28 D	82 G	+1:168038401 168038401 G	D
28	83 A	+1:168038402 168038402 A	
28	84 T	+1:168038403 168038403 T	
29 D	85 G	+1:168038404 168038404 G	D
29	86 A	+1:168038405 168038405 A	
29	87 C	+1:168038406 168038406 C	
30 M	88 A	+1:168038407 168038407 A	M
30	89 T	+1:168038408 168038408 T	
30	90 G	+1:168038409 168038409 G	
31 M	91 A	+1:168038410 168038410 A	M
31	92 T	+1:168038411 168038411 T	
31	93 G	+1:168038412 168038412 G	
32 Y	94 T	+1:168038413 168038413 T	Y
32	95 A	+1:168038414 168038414 A	
32	96 T	+1:168038415 168038415 T	
33 E	97 G	+1:168038416 168038416 G	E
33	98 A	+1:168038417 168038417 A	
33	99 A	+1:168038418 168038418 A	
34 L	100 T	+1:168038419 168038419 T	L
34	101 T	+1:168038420 168038420 T	
34	102 A	+1:168038421 168038421 A	
35 T	103 A	+1:168038422 168038422 A	T
35	104 C	+1:168038423 168038423 C	
35	105 C	+1:168038424 168038424 C	
36 S	106 A	+1:168038425 168038425 A	S
36	107 G	+1:168038426 168038426 G	
36	108 T	+1:168038427 168038427 T	
37 Q	109 C	+1:168038428 168038428 C	Q
37	110 A	+1:168038429 168038429 A	
37	111 A	+1:168038430 168038430 A	
38 A	112 G	+1:168038431 168038431 G	A
38	113 C	+1:168038432 168038432 C	
38	114 C	+1:168038433 168038433 C	
39 R	115 A	+1:168038434 168038434 A	R
39	116 G	+1:168038435 168038435 G	
39	117 A	+1:168038436 168038436 A	
40 G	118 G	+1:168038437 168038437 G	G
40	119 G	+1:168038438 168038438 G	
40	120 A	+1:168038439 168038439 A	
41 L	121 C	+1:168038440 168038440 C	L
41	122 T	+1:168038441 168038441 T	
41	123 G	+1:168038442 168038442 G	
42 S	124 T	+1:168038443 168038443 T	S
42	125 C	+1:168038444 168038444 C	
42	126 A	+1:168038445 168038445 A	
43 S	127 A	+1:168038446 168038446 A	S
43	128 G	+1:168038447 168038447 G	
43	129 C	+1:168038448 168038448 C	
44 Q	130 C	+1:168038449 168038449 C	Q
44	131 A	+1:168038450 168038450 A	
44	132 A	+1:168038451 168038451 A	
45 N	133 A	+1:168038452 168038452 A	N
45	134 A	+1:168038453 168038453 A	
45	135 T	+1:168038454 168038454 T	
46 L	136 T	+1:168038455 168038455 T	L
46	137 T	+1:168038456 168038456 T	
46	138 G	+1:168038457 168038457 G	
47 E	139 G	+1:168038458 168038458 G	E
47	140 A	+1:168038459 168038459 A	
47	141 A	+1:168038460 168038460 A	
48 I	142 A	+1:168038461 168038461 A	I
48	143 T	+1:168038462 168038462 T	
48	144 C	+1:168038463 168038463 C	
49 Q	145 C	+1:168038464 168038464 C	Q
49	146 A	+1:168038465 168038465 A	
49	147 G	+1:168038466 168038466 G	
50 T	148 A	+1:168038467 168038467 A	T
50	149 C	+1:168038468 168038468 C	
50	150 C	+1:168038469 168038469 C	
51 T	151 A	+1:168038470 168038470 A	T
51	152 C	+1:168038471 168038471 C	
51	153 T	+1:168038472 168038472 T	
52 L	154 C	+1:168038473 168038473 C	L
52	155 T	+1:168038474 168038474 T	
52	156 A	+1:168038475 168038475 A	
53 R	157 A	+1:168038476 168038476 A	R
53	158 G	+1:168038477 168038477 G	
53	159 G	+1:168038478 168038478 G	
54 N	160 A	+1:168038479 168038479 A	N
54	161 A	+1:168038480 168038480 A	
54	162 T	+1:168038481 168038481 T	
55 I	163 A	+1:168038482 168038482 A	I
55	164 T	+1:168038483 168038483 T	
55	165 T	+1:168038484 168038484 T	
56 L	166 T	+1:168038485 168038485 T	L
56	167 T	+1:168038486 168038486 T	
56	168 A	+1:168038487 168038487 A	
57 Q	169 C	+1:168038488 168038488 C	Q
57	170 A	+1:168038489 168038489 A	
57	171 A	+1:168038490 168038490 A	
58 T	172 A	+1:168038934 168038934 A	T
58	173 C	+1:168038935 168038935 C	
58	174 A	+1:168038936 168038936 A	
59 M	175 A	+1:168038937 168038937 A	M
59	176 T	+1:168038938 168038938 T	
59	177 G	+1:168038939 168038939 G	
60 V	178 G	+1:168038940 168038940 G	V
60	179 T	+1:168038941 168038941 T	
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61	182 A	+1:168038944 168038944 A	
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62 L	184 C	+1:168038946 168038946 C	L
62	185 T	+1:168038947 168038947 T	
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63 L	187 T	+1:168038949 168038949 T	L
63	188 T	+1:168038950 168038950 T	
63	189 A	+1:168038951 168038951 A	
64 G	190 G	+1:168038952 168038952 G	G
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64	192 A	+1:168038954 168038954 A	
65 A	193 G	+1:168038955 168038955 G	A
65	194 C	+1:168038956 168038956 C	
65	195 T	+1:168038957 168038957 T	
66 L	196 C	+1:168038958 168038958 C	L
66	197 T	+1:168038959 168038959 T	
66	198 C	+1:168038960 168038960 C	
67 T	199 A	+1:168038961 168038961 A	T
67	200 C	+1:168038962 168038962 C	
67	201 A	+1:168038963 168038963 A	
68 G	202 G	+1:168038964 168038964 G	G
68	203 G	+1:168038965 168038965 G	
68	204 A	+1:168038966 168038966 A	
69 C	205 T	+1:168038967 168038967 T	C
69	206 G	+1:168038968 168038968 G	
69	207 T	+1:168038969 168038969 T	
70 V	208 G	+1:168038970 168038970 G	V
70	209 T	+1:168038971 168038971 T	
70	210 T	+1:168038972 168038972 T	
71 Q	211 C	+1:168038973 168038973 C	Q
71	212 A	+1:168038974 168038974 A	
71	213 G	+1:168038975 168038975 G	
72 H	214 C	+1:168038976 168038976 C	H
72	215 A	+1:168038977 168038977 A	
72	216 T	+1:168038978 168038978 T	
73 I	217 A	+1:168038979 168038979 A	I
73	218 T	+1:168038980 168038980 T	
73	219 C	+1:168038981 168038981 C	
74 C	220 T	+1:168038982 168038982 T	C
74	221 G	+1:168038983 168038983 G	
74	222 T	+1:168038984 168038984 T	
75 A	223 G	+1:168038985 168038985 G	A
75	224 C	+1:168038986 168038986 C	
75	225 C	+1:168038987 168038987 C	
76 T	226 A	+1:168038988 168038988 A	T
76	227 C	+1:168038989 168038989 C	
76	228 A	+1:168038990 168038990 A	
77 Q	229 C	+1:168038991 168038991 C	Q
77	230 A	+1:168038992 168038992 A	
77	231 G	+1:168038993 168038993 G	
78 E	232 G	+1:168038994 168038994 G	E
78	233 A	+1:168038995 168038995 A	
78	234 A	+1:168038996 168038996 A	
79 S	235 T	+1:168038997 168038997 T	S
79	236 C	+1:168038998 168038998 C	
79	237 C	+1:168038999 168038999 C	
80 I	238 A	+1:168039000 168039000 A	I
80	239 T	+1:168039001 168039001 T	
80	240 C	+1:168039002 168039002 C	
81 I	241 A	+1:168039003 168039003 A	I
81	242 T	+1:168039004 168039004 T	
81	243 T	+1:168039005 168039005 T	
82 L	244 T	+1:168039006 168039006 T	L
82	245 T	+1:168039007 168039007 T	
82	246 G	+1:168039008 168039008 G	
83 E	247 G	+1:168039009 168039009 G	E
83	248 A	+1:168039010 168039010 A	
83	249 A	+1:168039011 168039011 A	
84 N	250 A	+1:168039012 168039012 A	N
84	251 A	+1:168039013 168039013 A	
84	252 T	+1:168039014 168039014 T	
85 I	253 A	+1:168039015 168039015 A	I
85	254 T	+1:168039016 168039016 T	
85	255 T	+1:168039017 168039017 T	
86 Q	256 C	+1:168039018 168039018 C	Q
86	257 A	+1:168039019 168039019 A	
86	258 G	+1:168039020 168039020 G	
87 S	259 A	+1:168039021 168039021 A	S
87	260 G	+1:168039022 168039022 G	
87	261 T	+1:168039023 168039023 T	
88 L	262 C	+1:168039024 168039024 C	L
88	263 T	+1:168039025 168039025 T	
88	264 C	+1:168039026 168039026 C	
89 P	265 C	+1:168039027 168039027 C	P
89	266 C	+1:168039028 168039028 C	
89	267 C	+1:168039029 168039029 C	
90 S	268 T	+1:168039030 168039030 T	S
90	269 C	+1:168039031 168039031 C	
90	270 C	+1:168039032 168039032 C	
91 S	271 T	+1:168039033 168039033 T	S
91	272 C	+1:168039034 168039034 C	
91	273 A	+1:168039035 168039035 A	
92 V	274 G	+1:168039036 168039036 G	V
92	275 T	+1:168039037 168039037 T	
92	276 C	+1:168039038 168039038 C	
93 L	277 C	+1:168039039 168039039 C	L
93	278 T	+1:168039040 168039040 T	
93	279 T	+1:168039041 168039041 T	
94 H	280 C	+1:168039042 168039042 C	H
94	281 A	+1:168039043 168039043 A	
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95 I	283 A	+1:168039045 168039045 A	I
95	284 T	+1:168039046 168039046 T	
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96 I	286 A	+1:168039048 168039048 A	I
96	287 T	+1:168039049 168039049 T	
96	288 T	+1:168039050 168039050 T	
97 K	289 A	+1:168039051 168039051 A	K
97	290 A	+1:168039052 168039052 A	
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98 S	292 A	+1:168039054 168039054 A	S
98	293 G	+1:168039055 168039055 G	
98	294 C	+1:168039056 168039056 C	
99 T	295 A	+1:168039057 168039057 A	T
99	296 C	+1:168039058 168039058 C	
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100 F	298 T	+1:168039060 168039060 T	F
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101 V	301 G	+1:168039063 168039063 G	V
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361	1083 A	+1:168063561 168063561 A	
362 T	1084 A	+1:168063562 168063562 A	T
362	1085 C	+1:168063563 168063563 C	
362	1086 C	+1:168063564 168063564 C	
363 L	1087 C	+1:168063565 168063565 C	L
363	1088 T	+1:168063566 168063566 T	
363	1089 G	+1:168063567 168063567 G	
364 W	1090 T	+1:168063568 168063568 T	W
364	1091 G	+1:168063569 168063569 G	
364	1092 G	+1:168063570 168063570 G	
365 C	1093 T	+1:168063571 168063571 T	C
365	1094 G	+1:168063572 168063572 G	
365	1095 C	+1:168063573 168063573 C	
366 T	1096 A	+1:168063574 168063574 A	T
366	1097 C	+1:168063575 168063575 C	
366	1098 A	+1:168063576 168063576 A	
367 D	1099 G	+1:168063577 168063577 G	D
367	1100 A	+1:168063578 168063578 A	
367	1101 C	+1:168063579 168063579 C	
368 S	1102 A	+1:168063580 168063580 A	S
368	1103 G	+1:168063581 168063581 G	
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369 Q	1105 C	+1:168063583 168063583 C	Q
369	1106 A	+1:168063584 168063584 A	
369	1107 G	+1:168063585 168063585 G	
370 V	1108 G	+1:168063586 168063586 G	V
370	1109 T	+1:168063587 168063587 T	
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371 S	1111 T	+1:168063589 168063589 T	S
371	1112 C	+1:168063590 168063590 C	
371	1113 A	+1:168063591 168063591 A	
372 E	1114 G	+1:168063592 168063592 G	E
372	1115 A	+1:168063593 168063593 A	
372	1116 A	+1:168063594 168063594 A	
373 T	1117 A	+1:168063595 168063595 A	T
373	1118 C	+1:168063596 168063596 C	
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374 T	1120 A	+1:168063598 168063598 A	T
374	1121 C	+1:168063599 168063599 C	
374	1122 A	+1:168063600 168063600 A	
375 T	1123 A	+1:168063601 168063601 A	T
375	1124 C	+1:168063602 168063602 C	
375	1125 C	+1:168063603 168063603 C	
376 R	1126 A	+1:168063604 168063604 A	R
376	1127 G	+1:168063605 168063605 G	
376	1128 G	+1:168065028 168065028 G	
377 I	1129 A	+1:168065029 168065029 A	I
377	1130 T	+1:168065030 168065030 T	
377	1131 A	+1:168065031 168065031 A	
378 S	1132 T	+1:168065032 168065032 T	S
378	1133 C	+1:168065033 168065033 C	
378	1134 T	+1:168065034 168065034 T	
379 L	1135 C	+1:168065035 168065035 C	L
379	1136 T	+1:168065036 168065036 T	
379	1137 A	+1:168065037 168065037 A	
380 L	1138 C	+1:168065038 168065038 C	L
380	1139 T	+1:168065039 168065039 T	
380	1140 C	+1:168065040 168065040 C	
381 K	1141 A	+1:168065041 168065041 A	K
381	1142 A	+1:168065042 168065042 A	
381	1143 A	+1:168065043 168065043 A	
382 A	1144 G	+1:168065044 168065044 G	A
382	1145 C	+1:168065045 168065045 C	
382	1146 C	+1:168065046 168065046 C	
383 V	1147 G	+1:168065047 168065047 G	V
383	1148 T	+1:168065048 168065048 T	
383	1149 T	+1:168065049 168065049 T	
384 F	1150 T	+1:168065050 168065050 T	F
384	1151 T	+1:168065051 168065051 T	
384	1152 C	+1:168065052 168065052 C	
385 Y	1153 T	+1:168065053 168065053 T	Y
385	1154 A	+1:168065054 168065054 A	
385	1155 C	+1:168065055 168065055 C	
386 S	1156 A	+1:168065056 168065056 A	S
386	1157 G	+1:168065057 168065057 G	
386	1158 T	+1:168065058 168065058 T	
387 F	1159 T	+1:168065059 168065059 T	F
387	1160 T	+1:168065060 168065060 T	
387	1161 T	+1:168065061 168065061 T	
388 E	1162 G	+1:168065062 168065062 G	E
388	1163 A	+1:168065063 168065063 A	
388	1164 G	+1:168065064 168065064 G	
389 Q	1165 C	+1:168065065 168065065 C	Q
389	1166 A	+1:168065066 168065066 A	
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390 C	1168 T	+1:168065068 168065068 T	C
390	1169 G	+1:168065069 168065069 G	
390	1170 T	+1:168065070 168065070 T	
391 S	1171 T	+1:168065071 168065071 T	S
391	1172 C	+1:168065072 168065072 C	
391	1173 T	+1:168065073 168065073 T	
392 G	1174 G	+1:168065074 168065074 G	G
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392	1176 T	+1:168065076 168065076 T	
393 E	1177 G	+1:168065077 168065077 G	E
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393	1179 A	+1:168065079 168065079 A	
394 L	1180 C	+1:168065080 168065080 C	L
394	1181 T	+1:168065081 168065081 T	
394	1182 C	+1:168065082 168065082 C	
395 S	1183 T	+1:168065083 168065083 T	S
395	1184 C	+1:168065084 168065084 C	
395	1185 T	+1:168065085 168065085 T	
396 L	1186 C	+1:168065086 168065086 C	L
396	1187 T	+1:168065087 168065087 T	
396	1188 A	+1:168065088 168065088 A	
397 P	1189 C	+1:168065089 168065089 C	P
397	1190 C	+1:168065090 168065090 C	
397	1191 T	+1:168065091 168065091 T	
398 V	1192 G	+1:168065092 168065092 G	V
398	1193 T	+1:168065093 168065093 T	
398	1194 T	+1:168065094 168065094 T	
399 H	1195 C	+1:168065095 168065095 C	H
399	1196 A	+1:168065096 168065096 A	
399	1197 T	+1:168065097 168065097 T	
400 L	1198 T	+1:168065098 168065098 T	L
400	1199 T	+1:168065099 168065099 T	
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401 Q	1201 C	+1:168065101 168065101 C	Q
401	1202 A	+1:168065102 168065102 A	
401	1203 G	+1:168065103 168065103 G	
402 G	1204 G	+1:168065104 168065104 G	G
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403 L	1207 T	+1:168065107 168065107 T	L
403	1208 T	+1:168065108 168065108 T	
403	1209 A	+1:168065109 168065109 A	
404 K	1210 A	+1:168065110 168065110 A	K
404	1211 A	+1:168065111 168065111 A	
404	1212 G	+1:168065112 168065112 G	
405 S	1213 A	+1:168065113 168065113 A	S
405	1214 G	+1:168065114 168065114 G	
405	1215 T	+1:168065115 168065115 T	
406 K	1216 A	+1:168065116 168065116 A	K
406	1217 A	+1:168065117 168065117 A	
406	1218 G	+1:168065118 168065118 G	
407 G	1219 G	+1:168065119 168065119 G	G
407	1220 G	+1:168065120 168065120 G	
407	1221 G	+1:168065121 168065121 G	
408 K	1222 A	+1:168065122 168065122 A	K
408	1223 A	+1:168065123 168065123 A	
408	1224 A	+1:168065124 168065124 A	
409 A	1225 G	+1:168065125 168065125 G	A
409	1226 C	+1:168065126 168065126 C	
409	1227 T	+1:168065127 168065127 T	
410 E	1228 G	+1:168065128 168065128 G	E
410	1229 A	+1:168065129 168065129 A	
410	1230 G	+1:168065130 168065130 G	
411 V	1231 G	+1:168065131 168065131 G	V
411	1232 T	+1:168065132 168065132 T	
411	1233 G	+1:168065133 168065133 G	
412 A	1234 G	+1:168065134 168065134 G	A
412	1235 C	+1:168065135 168065135 C	
412	1236 T	+1:168065136 168065136 T	
413 V	1237 G	+1:168065137 168065137 G	V
413	1238 T	+1:168065138 168065138 T	
413	1239 C	+1:168065139 168065139 C	
414 T	1240 A	+1:168065140 168065140 A	T
414	1241 C	+1:168065141 168065141 C	
414	1242 C	+1:168065142 168065142 C	
415 L	1243 T	+1:168065143 168065143 T	L
415	1244 T	+1:168065144 168065144 T	
415	1245 G	+1:168065145 168065145 G	
416 Y	1246 T	+1:168065146 168065146 T	Y
416	1247 A	+1:168065147 168065147 A	
416	1248 T	+1:168065148 168065148 T	
417 Q	1249 C	+1:168065149 168065149 C	Q
417	1250 A	+1:168065150 168065150 A	
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418 H	1252 C	+1:168065152 168065152 C	H
418	1253 A	+1:168065153 168065153 A	
418	1254 T	+1:168065154 168065154 T	
419 V	1255 G	+1:168065155 168065155 G	V
419	1256 T	+1:168065156 168065156 T	
419	1257 T	+1:168065157 168065157 T	
420 C	1258 T	+1:168065158 168065158 T	C
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420	1260 T	+1:168065160 168065160 T	
421 V	1261 G	+1:168065161 168065161 G	V
421	1262 T	+1:168065162 168065162 T	
421	1263 T	+1:168065163 168065163 T	
422 H	1264 C	+1:168065164 168065164 C	H
422	1265 A	+1:168065165 168065165 A	
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423 L	1267 C	+1:168065167 168065167 C	L
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424 C	1270 T	+1:168065170 168065170 T	C
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425 T	1273 A	+1:168065173 168065173 A	T
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426 F	1276 T	+1:168065176 168065176 T	F
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427 I	1279 A	+1:168065179 168065179 A	I
427	1280 T	+1:168065180 168065180 T	
427	1281 T	+1:168065181 168065181 T	
428 T	1282 A	+1:168065182 168065182 A	T
428	1283 C	+1:168065183 168065183 C	
428	1284 T	+1:168065184 168065184 T	
429 S	1285 T	+1:168065185 168065185 T	S
429	1286 C	+1:168065186 168065186 C	
429	1287 C	+1:168065187 168065187 C	
430 F	1288 T	+1:168065188 168065188 T	F
430	1289 T	+1:168065189 168065189 T	
430	1290 T	+1:168065190 168065190 T	
431 H	1291 C	+1:168065191 168065191 C	H
431	1292 A	+1:168065192 168065192 A	
431	1293 T	+1:168065193 168065193 T	
432 P	1294 C	+1:168065194 168065194 C	P
432	1295 C	+1:168065195 168065195 C	
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433 S	1297 T	+1:168065197 168065197 T	S
433	1298 C	+1:168065198 168065198 C	
433	1299 A	+1:168065199 168065199 A	
434 L	1300 C	+1:168065200 168065200 C	L
434	1301 T	+1:168065201 168065201 T	
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435 F	1303 T	+1:168065203 168065203 T	F
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435	1305 T	+1:168065205 168065205 T	
436 A	1306 G	+1:168065206 168065206 G	A
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436	1308 T	+1:168065208 168065208 T	
437 E	1309 G	+1:168065209 168065209 G	E
437	1310 A	+1:168065210 168065210 A	
437	1311 A	+1:168065211 168065211 A	
438 L	1312 C	+1:168065212 168065212 C	L
438	1313 T	+1:168065213 168065213 T	
438	1314 G	+1:168065214 168065214 G	
439 D	1315 G	+1:168066024 168066024 G	D
439	1316 A	+1:168066025 168066025 A	
439	1317 T	+1:168066026 168066026 T	
440 A	1318 G	+1:168066027 168066027 G	A
440	1319 C	+1:168066028 168066028 C	
440	1320 T	+1:168066029 168066029 T	
441 A	1321 G	+1:168066030 168066030 G	A
441	1322 C	+1:168066031 168066031 C	
441	1323 T	+1:168066032 168066032 T	
442 L	1324 C	+1:168066033 168066033 C	L
442	1325 T	+1:168066034 168066034 T	
442	1326 G	+1:168066035 168066035 G	
443 L	1327 C	+1:168066036 168066036 C	L
443	1328 T	+1:168066037 168066037 T	
443	1329 G	+1:168066038 168066038 G	
444 N	1330 A	+1:168066039 168066039 A	N
444	1331 A	+1:168066040 168066040 A	
444	1332 T	+1:168066041 168066041 T	
445 A	1333 G	+1:168066042 168066042 G	A
445	1334 C	+1:168066043 168066043 C	
445	1335 T	+1:168066044 168066044 T	
446 V	1336 G	+1:168066045 168066045 G	V
446	1337 T	+1:168066046 168066046 T	
446	1338 A	+1:168066047 168066047 A	
447 L	1339 C	+1:168066048 168066048 C	L
447	1340 T	+1:168066049 168066049 T	
447	1341 T	+1:168066050 168066050 T	
448 S	1342 A	+1:168066051 168066051 A	S
448	1343 G	+1:168066052 168066052 G	
448	1344 T	+1:168066053 168066053 T	
449 A	1345 G	+1:168066054 168066054 G	A
449	1346 C	+1:168066055 168066055 C	
449	1347 T	+1:168066056 168066056 T	
450 N	1348 A	+1:168066057 168066057 A	N
450	1349 A	+1:168066058 168066058 A	
450	1350 T	+1:168066059 168066059 T	
451 M	1351 A	+1:168066060 168066060 A	M
451	1352 T	+1:168066061 168066061 T	
451	1353 G	+1:168066062 168066062 G	
452 I	1354 A	+1:168066063 168066063 A	I
452	1355 T	+1:168066064 168066064 T	
452	1356 C	+1:168066065 168066065 C	
453 T	1357 A	+1:168066066 168066066 A	T
453	1358 C	+1:168066067 168066067 C	
453	1359 C	+1:168066068 168066068 C	
454 S	1360 T	+1:168066069 168066069 T	S
454	1361 C	+1:168066070 168066070 C	
454	1362 T	+1:168066071 168066071 T	
455 L	1363 T	+1:168066072 168066072 T	L
455	1364 T	+1:168066073 168066073 T	
455	1365 G	+1:168066074 168066074 G	
456 L	1366 T	+1:168066075 168066075 T	L
456	1367 T	+1:168066076 168066076 T	
456	1368 A	+1:168066077 168066077 A	
457 A	1369 G	+1:168066078 168066078 G	A
457	1370 C	+1:168066079 168066079 C	
457	1371 T	+1:168066080 168066080 T	
458 M	1372 A	+1:168066081 168066081 A	M
458	1373 T	+1:168066082 168066082 T	
458	1374 G	+1:168066083 168066083 G	
459 D	1375 G	+1:168066084 168066084 G	D
459	1376 A	+1:168066085 168066085 A	
459	1377 T	+1:168066086 168066086 T	
460 A	1378 G	+1:168066087 168066087 G	A
460	1379 C	+1:168066088 168066088 C	
460	1380 A	+1:168066089 168066089 A	
461 W	1381 T	+1:168066090 168066090 T	W
461	1382 G	+1:168066091 168066091 G	
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462 C	1384 T	+1:168066093 168066093 T	C
462	1385 G	+1:168066094 168066094 G	
462	1386 C	+1:168066095 168066095 C	
463 F	1387 T	+1:168066096 168066096 T	F
463	1388 T	+1:168066097 168066097 T	
463	1389 C	+1:168066098 168066098 C	
464 L	1390 C	+1:168066099 168066099 C	L
464	1391 T	+1:168066100 168066100 T	
464	1392 T	+1:168066101 168066101 T	
465 A	1393 G	+1:168066102 168066102 G	A
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465	1395 T	+1:168066104 168066104 T	
466 R	1396 C	+1:168066105 168066105 C	R
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466	1398 A	+1:168066461 168066461 A	
467 Y	1399 T	+1:168066462 168066462 T	Y
467	1400 A	+1:168066463 168066463 A	
467	1401 T	+1:168066464 168066464 T	
468 G	1402 G	+1:168066465 168066465 G	G
468	1403 G	+1:168066466 168066466 G	
468	1404 G	+1:168066467 168066467 G	
469 T	1405 A	+1:168066468 168066468 A	T
469	1406 C	+1:168066469 168066469 C	
469	1407 T	+1:168066470 168066470 T	
470 A	1408 G	+1:168066471 168066471 G	A
470	1409 C	+1:168066472 168066472 C	
470	1410 T	+1:168066473 168066473 T	
471 E	1411 G	+1:168066474 168066474 G	E
471	1412 A	+1:168066475 168066475 A	
471	1413 A	+1:168066476 168066476 A	
472 L	1414 C	+1:168066477 168066477 C	L
472	1415 T	+1:168066478 168066478 T	
472	1416 G	+1:168066479 168066479 G	
473 C	1417 T	+1:168066480 168066480 T	C
473	1418 G	+1:168066481 168066481 G	
473	1419 T	+1:168066482 168066482 T	
474 A	1420 G	+1:168066483 168066483 G	A
474	1421 C	+1:168066484 168066484 C	
474	1422 A	+1:168066485 168066485 A	
475 H	1423 C	+1:168066486 168066486 C	H
475	1424 A	+1:168066487 168066487 A	
475	1425 C	+1:168066488 168066488 C	
476 H	1426 C	+1:168066489 168066489 C	H
476	1427 A	+1:168066490 168066490 A	
476	1428 T	+1:168066491 168066491 T	
477 V	1429 G	+1:168066492 168066492 G	V
477	1430 T	+1:168066493 168066493 T	
477	1431 C	+1:168066494 168066494 C	
478 T	1432 A	+1:168066495 168066495 A	T
478	1433 C	+1:168066496 168066496 C	
478	1434 C	+1:168066497 168066497 C	
479 I	1435 A	+1:168066498 168066498 A	I
479	1436 T	+1:168066499 168066499 T	
479	1437 A	+1:168066500 168066500 A	
480 V	1438 G	+1:168066501 168066501 G	V
480	1439 T	+1:168066502 168066502 T	
480	1440 G	+1:168066503 168066503 G	
481 A	1441 G	+1:168066504 168066504 G	A
481	1442 C	+1:168066505 168066505 C	
481	1443 T	+1:168066506 168066506 T	
482 H	1444 C	+1:168066507 168066507 C	H
482	1445 A	+1:168066508 168066508 A	
482	1446 T	+1:168066509 168066509 T	
483 L	1447 C	+1:168066510 168066510 C	L
483	1448 T	+1:168066511 168066511 T	
483	1449 G	+1:168066512 168066512 G	
484 I	1450 A	+1:168068182 168068182 A	I
484	1451 T	+1:168068183 168068183 T	
484	1452 A	+1:168068184 168068184 A	
485 K	1453 A	+1:168068185 168068185 A	K
485	1454 A	+1:168068186 168068186 A	
485	1455 G	+1:168068187 168068187 G	
486 S	1456 T	+1:168068188 168068188 T	S
486	1457 C	+1:168068189 168068189 C	
486	1458 A	+1:168068190 168068190 A	
487 C	1459 T	+1:168068191 168068191 T	C
487	1460 G	+1:168068192 168068192 G	
487	1461 C	+1:168068193 168068193 C	
488 P	1462 C	+1:168068194 168068194 C	P
488	1463 C	+1:168068195 168068195 C	
488	1464 T	+1:168068196 168068196 T	
489 G	1465 G	+1:168068197 168068197 G	G
489	1466 G	+1:168068198 168068198 G	
489	1467 A	+1:168068199 168068199 A	
490 E	1468 G	+1:168068200 168068200 G	E
490	1469 A	+1:168068201 168068201 A	
490	1470 A	+1:168068202 168068202 A	
491 C	1471 T	+1:168068203 168068203 T	C
491	1472 G	+1:168068204 168068204 G	
491	1473 T	+1:168068205 168068205 T	
492 Y	1474 T	+1:168068206 168068206 T	Y
492	1475 A	+1:168068207 168068207 A	
492	1476 T	+1:168068208 168068208 T	
493 Q	1477 C	+1:168068209 168068209 C	Q
493	1478 A	+1:168068210 168068210 A	
493	1479 A	+1:168068211 168068211 A	
494 L	1480 C	+1:168068212 168068212 C	L
494	1481 T	+1:168068213 168068213 T	
494	1482 C	+1:168068214 168068214 C	
495 I	1483 A	+1:168068215 168068215 A	I
495	1484 T	+1:168068216 168068216 T	
495	1485 C	+1:168068217 168068217 C	
496 N	1486 A	+1:168068218 168068218 A	N
496	1487 A	+1:168068219 168068219 A	
496	1488 C	+1:168068220 168068220 C	
497 L	1489 C	+1:168068221 168068221 C	L
497	1490 T	+1:168068222 168068222 T	
497	1491 A	+1:168068223 168068223 A	
498 S	1492 T	+1:168068224 168068224 T	S
498	1493 C	+1:168068225 168068225 C	
498	1494 A	+1:168068226 168068226 A	
499 I	1495 A	+1:168068227 168068227 A	I
499	1496 T	+1:168068228 168068228 T	
499	1497 A	+1:168068229 168068229 A	
500 L	1498 C	+1:168068230 168068230 C	L
500	1499 T	+1:168068231 168068231 T	
500	1500 G	+1:168068232 168068232 G	
501 L	1501 T	+1:168068233 168068233 T	L
501	1502 T	+1:168068234 168068234 T	
501	1503 G	+1:168068235 168068235 G	
502 K	1504 A	+1:168068236 168068236 A	K
502	1505 A	+1:168068237 168068237 A	
502	1506 G	+1:168068238 168068238 G	
503 R	1507 C	+1:168068239 168068239 C	R
503	1508 G	+1:168068240 168068240 G	
503	1509 T	+1:168068241 168068241 T	
504 L	1510 C	+1:168068242 168068242 C	L
504	1511 T	+1:168068243 168068243 T	
504	1512 C	+1:168068244 168068244 C	
505 F	1513 T	+1:168068245 168068245 T	F
505	1514 T	+1:168068246 168068246 T	
505	1515 T	+1:168068247 168068247 T	
506 F	1516 T	+1:168068248 168068248 T	F
506	1517 T	+1:168068249 168068249 T	
506	1518 C	+1:168068250 168068250 C	
507 F	1519 T	+1:168068251 168068251 T	F
507	1520 T	+1:168068252 168068252 T	
507	1521 C	+1:168068253 168068253 C	
508 M	1522 A	+1:168068254 168068254 A	M
508	1523 T	+1:168068255 168068255 T	
508	1524 G	+1:168068256 168068256 G	
509 A	1525 G	+1:168068257 168068257 G	A
509	1526 C	+1:168068258 168068258 C	
509	1527 A	+1:168068259 168068259 A	
510 P	1528 C	+1:168068260 168068260 C	P
510	1529 C	+1:168068261 168068261 C	
510	1530 A	+1:168068262 168068262 A	
511 P	1531 C	+1:168068263 168068263 C	P
511	1532 C	+1:168068264 168068264 C	
511	1533 C	+1:168068265 168068265 C	
512 H	1534 C	+1:168068266 168068266 C	H
512	1535 A	+1:168068267 168068267 A	
512	1536 T	+1:168068268 168068268 T	
513 Q	1537 C	+1:168068269 168068269 C	Q
513	1538 A	+1:168068270 168068270 A	
513	1539 G	+1:168068271 168068271 G	
514 L	1540 C	+1:168072692 168072692 C	L
514	1541 T	+1:168072693 168072693 T	
514	1542 G	+1:168072694 168072694 G	
515 E	1543 G	+1:168072695 168072695 G	E
515	1544 A	+1:168072696 168072696 A	
515	1545 G	+1:168072697 168072697 G	
516 F	1546 T	+1:168072698 168072698 T	F
516	1547 T	+1:168072699 168072699 T	
516	1548 T	+1:168072700 168072700 T	
517 I	1549 A	+1:168072701 168072701 A	I
517	1550 T	+1:168072702 168072702 T	
517	1551 C	+1:168072703 168072703 C	
518 Q	1552 C	+1:168072704 168072704 C	Q
518	1553 A	+1:168072705 168072705 A	
518	1554 G	+1:168072706 168072706 G	
519 K	1555 A	+1:168072707 168072707 A	K
519	1556 A	+1:168072708 168072708 A	
519	1557 A	+1:168072709 168072709 A	
520 F	1558 T	+1:168072710 168072710 T	F
520	1559 T	+1:168072711 168072711 T	
520	1560 T	+1:168072712 168072712 T	
521 S	1561 T	+1:168072713 168072713 T	S
521	1562 C	+1:168072714 168072714 C	
521	1563 C	+1:168072715 168072715 C	
522 P	1564 C	+1:168072716 168072716 C	P
522	1565 C	+1:168072717 168072717 C	
522	1566 A	+1:168072718 168072718 A	
523 K	1567 A	+1:168072719 168072719 A	K
523	1568 A	+1:168072720 168072720 A	
523	1569 A	+1:168072721 168072721 A	
524 E	1570 G	+1:168072722 168072722 G	E
524	1571 A	+1:168072723 168072723 A	
524	1572 A	+1:168072724 168072724 A	
525 A	1573 G	+1:168072725 168072725 G	A
525	1574 C	+1:168072726 168072726 C	
525	1575 A	+1:168072727 168072727 A	
526 E	1576 G	+1:168072728 168072728 G	E
526	1577 A	+1:168072729 168072729 A	
526	1578 A	+1:168072730 168072730 A	
527 N	1579 A	+1:168072731 168072731 A	N
527	1580 A	+1:168072732 168072732 A	
527	1581 T	+1:168072733 168072733 T	
528 L	1582 C	+1:168072734 168072734 C	L
528	1583 T	+1:168072735 168072735 T	
528	1584 G	+1:168072736 168072736 G	
529 P	1585 C	+1:168072737 168072737 C	P
529	1586 C	+1:168072738 168072738 C	
529	1587 T	+1:168072739 168072739 T	
530 L	1588 C	+1:168072740 168072740 C	L
530	1589 T	+1:168072741 168072741 T	
530	1590 G	+1:168072742 168072742 G	
531 W	1591 T	+1:168072743 168072743 T	W
531	1592 G	+1:168072744 168072744 G	
531	1593 G	+1:168072745 168072745 G	
532 Q	1594 C	+1:168072746 168072746 C	Q
532	1595 A	+1:168072747 168072747 A	
532	1596 A	+1:168072748 168072748 A	
533 H	1597 C	+1:168072749 168072749 C	H
533	1598 A	+1:168072750 168072750 A	
533	1599 T	+1:168072751 168072751 T	
534 I	1600 A	+1:168072752 168072752 A	I
534	1601 T	+1:168072753 168072753 T	
534	1602 T	+1:168072754 168072754 T	
535 S	1603 T	+1:168072755 168072755 T	S
535	1604 C	+1:168072756 168072756 C	
535	1605 C	+1:168072757 168072757 C	
536 F	1606 T	+1:168072758 168072758 T	F
536	1607 T	+1:168072759 168072759 T	
536	1608 C	+1:168072760 168072760 C	
537 Q	1609 C	+1:168072761 168072761 C	Q
537	1610 A	+1:168072762 168072762 A	
537	1611 G	+1:168072763 168072763 G	
538 A	1612 G	+1:168072764 168072764 G	A
538	1613 C	+1:168072765 168072765 C	
538	1614 G	+1:168072766 168072766 G	
539 L	1615 T	+1:168072767 168072767 T	L
539	1616 T	+1:168072768 168072768 T	
539	1617 A	+1:168072769 168072769 A	
540 P	1618 C	+1:168072770 168072770 C	P
540	1619 C	+1:168072771 168072771 C	
540	1620 T	+1:168072772 168072772 T	
541 P	1621 C	+1:168072773 168072773 C	P
541	1622 C	+1:168072774 168072774 C	
541	1623 T	+1:168072775 168072775 T	
542 E	1624 G	+1:168072776 168072776 G	E
542	1625 A	+1:168072777 168072777 A	
542	1626 G	+1:168072778 168072778 G	
543 L	1627 C	+1:168072779 168072779 C	L
543	1628 T	+1:168072780 168072780 T	
543	1629 T	+1:168072781 168072781 T	
544 R	1630 A	+1:168072782 168072782 A	R
544	1631 G	+1:168072783 168072783 G	
544	1632 G	+1:168072784 168072784 G	
545 E	1633 G	+1:168072785 168072785 G	E
545	1634 A	+1:168072786 168072786 A	
545	1635 A	+1:168072787 168072787 A	
546 Q	1636 C	+1:168072788 168072788 C	Q
546	1637 A	+1:168072789 168072789 A	
546	1638 A	+1:168072790 168072790 A	
547 T	1639 A	+1:168072791 168072791 A	T
547	1640 C	+1:168072792 168072792 C	
547	1641 T	+1:168072793 168072793 T	
548 V	1642 G	+1:168072794 168072794 G	V
548	1643 T	+1:168072795 168072795 T	
548	1644 C	+1:168072796 168072796 C	
549 H	1645 C	+1:168072797 168072797 C	H
549	1646 A	+1:168072798 168072798 A	
549	1647 T	+1:168072799 168072799 T	
550 E	1648 G	+1:168072800 168072800 G	E
550	1649 A	+1:168072801 168072801 A	
550	1650 G	+1:168072802 168072802 G	
551 V	1651 G	+1:168072803 168072803 G	V
551	1652 T	+1:168072804 168072804 T	
551	1653 C	+1:168072805 168072805 C	
552 T	1654 A	+1:168072806 168072806 A	T
552	1655 C	+1:168072807 168072807 C	
552	1656 C	+1:168072808 168072808 C	
553 T	1657 A	+1:168072809 168072809 A	T
553	1658 C	+1:168072810 168072810 C	
553	1659 A	+1:168072811 168072811 A	
554 V	1660 G	+1:168072812 168072812 G	V
554	1661 T	+1:168072813 168072813 T	
554	1662 A	+1:168072814 168072814 A	
555 G	1663 G	+1:168072815 168072815 G	G
555	1664 G	+1:168072816 168072816 G	
555	1665 C	+1:168072817 168072817 C	
556 T	1666 A	+1:168072818 168072818 A	T
556	1667 C	+1:168072819 168072819 C	
556	1668 T	+1:168072820 168072820 T	
557 A	1669 G	+1:168072821 168072821 G	A
557	1670 C	+1:168072822 168072822 C	
557	1671 A	+1:168072823 168072823 A	
558 E	1672 G	+1:168072824 168072824 G	E
558	1673 A	+1:168072825 168072825 A	
558	1674 A	+1:168072826 168072826 A	
559 C	1675 T	+1:168072827 168072827 T	C
559	1676 G	+1:168072828 168072828 G	
559	1677 C	+1:168072829 168072829 C	
560 R	1678 A	+1:168072830 168072830 A	R
560	1679 G	+1:168072831 168072831 G	
560	1680 G	+1:168072832 168072832 G	
561 K	1681 A	+1:168072833 168072833 A	K
561	1682 A	+1:168072834 168072834 A	
561	1683 A	+1:168072835 168072835 A	
562 W	1684 T	+1:168072836 168072836 T	W
562	1685 G	+1:168072837 168072837 G	
562	1686 G	+1:168072838 168072838 G	
563 L	1687 C	+1:168072839 168072839 C	L
563	1688 T	+1:168072840 168072840 T	
563	1689 G	+1:168072841 168072841 G	
564 S	1690 A	+1:168072842 168072842 A	S
564	1691 G	+1:168072843 168072843 G	
564	1692 C	+1:168072844 168072844 C	
565 R	1693 A	+1:168072845 168072845 A	R
565	1694 G	+1:168072846 168072846 G	
565	1695 G	+1:168072847 168072847 G	
566 S	1696 A	+1:168072848 168072848 A	S
566	1697 G	+1:168072849 168072849 G	
566	1698 T	+1:168072850 168072850 T	
567 R	1699 C	+1:168072851 168072851 C	R
567	1700 G	+1:168072852 168072852 G	
567	1701 T	+1:168072853 168072853 T	
568 T	1702 A	+1:168072854 168072854 A	T
568	1703 C	+1:168072855 168072855 C	
568	1704 T	+1:168072856 168072856 T	
569 L	1705 T	+1:168072857 168072857 T	L
569	1706 T	+1:168072858 168072858 T	
569	1707 G	+1:168072859 168072859 G	
570 G	1708 G	+1:168072860 168072860 G	G
570	1709 G	+1:168072861 168072861 G	
570	1710 A	+1:168072862 168072862 A	
571 E	1711 G	+1:168072863 168072863 G	E
571	1712 A	+1:168072864 168072864 A	
571	1713 A	+1:168072865 168072865 A	
572 L	1714 C	+1:168072866 168072866 C	L
572	1715 T	+1:168072867 168072867 T	
572	1716 A	+1:168072868 168072868 A	
573 E	1717 G	+1:168072869 168072869 G	E
573	1718 A	+1:168072870 168072870 A	
573	1719 A	+1:168072871 168072871 A	
574 S	1720 T	+1:168072872 168072872 T	S
574	1721 C	+1:168072873 168072873 C	
574	1722 T	+1:168072874 168072874 T	
575 L	1723 C	+1:168072875 168072875 C	L
575	1724 T	+1:168072876 168072876 T	
575	1725 G	+1:168072877 168072877 G	
576 N	1726 A	+1:168078182 168078182 A	N
576	1727 A	+1:168078183 168078183 A	
576	1728 C	+1:168078184 168078184 C	
577 T	1729 A	+1:168078185 168078185 A	T
577	1730 C	+1:168078186 168078186 C	
577	1731 A	+1:168078187 168078187 A	
578 V	1732 G	+1:168078188 168078188 G	V
578	1733 T	+1:168078189 168078189 T	
578	1734 A	+1:168078190 168078190 A	
579 L	1735 C	+1:168078191 168078191 C	L
579	1736 T	+1:168078192 168078192 T	
579	1737 G	+1:168078193 168078193 G	
580 S	1738 T	+1:168078194 168078194 T	S
580	1739 C	+1:168078195 168078195 C	
580	1740 T	+1:168078196 168078196 T	
581 A	1741 G	+1:168078197 168078197 G	A
581	1742 C	+1:168078198 168078198 C	
581	1743 T	+1:168078199 168078199 T	
582 L	1744 T	+1:168078200 168078200 T	L
582	1745 T	+1:168078201 168078201 T	
582	1746 G	+1:168078202 168078202 G	
583 L	1747 C	+1:168078203 168078203 C	L
583	1748 T	+1:168078204 168078204 T	
583	1749 T	+1:168078205 168078205 T	
584 A	1750 G	+1:168078206 168078206 G	A
584	1751 C	+1:168078207 168078207 C	
584	1752 A	+1:168078208 168078208 A	
585 V	1753 G	+1:168078209 168078209 G	V
585	1754 T	+1:168078210 168078210 T	
585	1755 A	+1:168078211 168078211 A	
586 C	1756 T	+1:168078212 168078212 T	C
586	1757 G	+1:168078213 168078213 G	
586	1758 T	+1:168078214 168078214 T	
587 N	1759 A	+1:168078215 168078215 A	N
587	1760 A	+1:168078216 168078216 A	
587	1761 T	+1:168078217 168078217 T	
588 S	1762 T	+1:168078218 168078218 T	S
588	1763 C	+1:168078219 168078219 C	
588	1764 T	+1:168078220 168078220 T	
589 A	1765 G	+1:168078221 168078221 G	A
589	1766 C	+1:168078222 168078222 C	
589	1767 T	+1:168078223 168078223 T	
590 G	1768 G	+1:168078224 168078224 G	G
590	1769 G	+1:168078225 168078225 G	
590	1770 T	+1:168078226 168078226 T	
591 E	1771 G	+1:168078227 168078227 G	E
591	1772 A	+1:168078228 168078228 A	
591	1773 A	+1:168078229 168078229 A	
592 A	1774 G	+1:168078230 168078230 G	A
592	1775 C	+1:168078231 168078231 C	
592	1776 T	+1:168078232 168078232 T	
593 L	1777 T	+1:168078233 168078233 T	L
593	1778 T	+1:168078234 168078234 T	
593	1779 G	+1:168078235 168078235 G	
594 D	1780 G	+1:168078236 168078236 G	D
594	1781 A	+1:168078237 168078237 A	
594	1782 T	+1:168078238 168078238 T	
595 T	1783 A	+1:168078239 168078239 A	T
595	1784 C	+1:168078240 168078240 C	
595	1785 A	+1:168078241 168078241 A	
596 G	1786 G	+1:168078242 168078242 G	G
596	1787 G	+1:168078243 168078243 G	
596	1788 A	+1:168078244 168078244 A	
597 K	1789 A	+1:168078245 168078245 A	K
597	1790 A	+1:168078246 168078246 A	
597	1791 A	+1:168078247 168078247 A	
598 Q	1792 C	+1:168078248 168078248 C	Q
598	1793 A	+1:168078249 168078249 A	
598	1794 A	+1:168078250 168078250 A	
599 T	1795 A	+1:168078251 168078251 A	T
599	1796 C	+1:168078252 168078252 C	
599	1797 T	+1:168078253 168078253 T	
600 A	1798 G	+1:168078254 168078254 G	A
600	1799 C	+1:168078255 168078255 C	
600	1800 A	+1:168078256 168078256 A	
601 I	1801 A	+1:168078257 168078257 A	I
601	1802 T	+1:168078258 168078258 T	
601	1803 T	+1:168078259 168078259 T	
602 I	1804 A	+1:168078260 168078260 A	I
602	1805 T	+1:168078261 168078261 T	
602	1806 C	+1:168078262 168078262 C	
603 E	1807 G	+1:168078263 168078263 G	E
603	1808 A	+1:168078264 168078264 A	
603	1809 A	+1:168078265 168078265 A	
604 V	1810 G	+1:168078266 168078266 G	V
604	1811 T	+1:168078267 168078267 T	
604	1812 T	+1:168078268 168078268 T	
605 V	1813 G	+1:168078269 168078269 G	V
605	1814 T	+1:168078270 168078270 T	
605	1815 G	+1:168078271 168078271 G	
606 S	1816 A	+1:168078272 168078272 A	S
606	1817 G	+1:168078273 168078273 G	
606	1818 T	+1:168078274 168078274 T	
607 Q	1819 C	+1:168078275 168078275 C	Q
607	1820 A	+1:168078276 168078276 A	
607	1821 G	+1:168078277 168078277 G	
608 L	1822 C	+1:168078278 168078278 C	L
608	1823 T	+1:168078279 168078279 T	
608	1824 T	+1:168078280 168078280 T	
609 W	1825 T	+1:168078281 168078281 T	W
609	1826 G	+1:168078282 168078282 G	
609	1827 G	+1:168078283 168078283 G	
610 A	1828 G	+1:168078284 168078284 G	A
610	1829 C	+1:168078285 168078285 C	
610	1830 T	+1:168078286 168078286 T	
611 F	1831 T	+1:168078287 168078287 T	F
611	1832 T	+1:168078288 168078288 T	
611	1833 T	+1:168078289 168078289 T	
612 L	1834 T	+1:168078290 168078290 T	L
612	1835 T	+1:168078291 168078291 T	
612	1836 A	+1:168078292 168078292 A	
613 N	1837 A	+1:168078293 168078293 A	N
613	1838 A	+1:168078294 168078294 A	
613	1839 C	+1:168078295 168078295 C	
614 I	1840 A	+1:168078296 168078296 A	I
614	1841 T	+1:168078297 168078297 T	
614	1842 T	+1:168078298 168078298 T	
615 K	1843 A	+1:168078299 168078299 A	K
615	1844 A	+1:168078300 168078300 A	
615	1845 A	+1:168078301 168078301 A	
616 Q	1846 C	+1:168078302 168078302 C	Q
616	1847 A	+1:168078303 168078303 A	
616	1848 G	+1:168078304 168078304 G	
617 V	1849 G	+1:168079439 168079439 G	V
617	1850 T	+1:168079440 168079440 T	
617	1851 A	+1:168079441 168079441 A	
618 A	1852 G	+1:168079442 168079442 G	A
618	1853 C	+1:168079443 168079443 C	
618	1854 A	+1:168079444 168079444 A	
619 D	1855 G	+1:168079445 168079445 G	D
619	1856 A	+1:168079446 168079446 A	
619	1857 T	+1:168079447 168079447 T	
620 Q	1858 C	+1:168079448 168079448 C	Q
620	1859 A	+1:168079449 168079449 A	
620	1860 A	+1:168079450 168079450 A	
621 P	1861 C	+1:168079451 168079451 C	P
621	1862 C	+1:168079452 168079452 C	
621	1863 T	+1:168079453 168079453 T	
622 Y	1864 T	+1:168079454 168079454 T	Y
622	1865 A	+1:168079455 168079455 A	
622	1866 T	+1:168079456 168079456 T	
623 V	1867 G	+1:168079457 168079457 G	V
623	1868 T	+1:168079458 168079458 T	
623	1869 T	+1:168079459 168079459 T	
624 Q	1870 C	+1:168079460 168079460 C	Q
624	1871 A	+1:168079461 168079461 A	
624	1872 A	+1:168079462 168079462 A	
625 Q	1873 C	+1:168079463 168079463 C	Q
625	1874 A	+1:168079464 168079464 A	
625	1875 G	+1:168079465 168079465 G	
626 T	1876 A	+1:168079466 168079466 A	T
626	1877 C	+1:168079467 168079467 C	
626	1878 A	+1:168079468 168079468 A	
627 F	1879 T	+1:168079469 168079469 T	F
627	1880 T	+1:168079470 168079470 T	
627	1881 C	+1:168079471 168079471 C	
628 S	1882 A	+1:168079472 168079472 A	S
628	1883 G	+1:168079473 168079473 G	
628	1884 C	+1:168079474 168079474 C	
629 L	1885 C	+1:168079475 168079475 C	L
629	1886 T	+1:168079476 168079476 T	
629	1887 T	+1:168079477 168079477 T	
630 L	1888 T	+1:168079478 168079478 T	L
630	1889 T	+1:168079479 168079479 T	
630	1890 A	+1:168079480 168079480 A	
631 L	1891 C	+1:168079481 168079481 C	L
631	1892 T	+1:168079482 168079482 T	
631	1893 T	+1:168079483 168079483 T	
632 P	1894 C	+1:168079484 168079484 C	P
632	1895 C	+1:168079485 168079485 C	
632	1896 A	+1:168079486 168079486 A	
633 L	1897 C	+1:168079487 168079487 C	L
633	1898 T	+1:168079488 168079488 T	
633	1899 G	+1:168079489 168079489 G	
634 L	1900 T	+1:168079490 168079490 T	L
634	1901 T	+1:168079491 168079491 T	
634	1902 G	+1:168079492 168079492 G	
635 G	1903 G	+1:168079493 168079493 G	G
635	1904 G	+1:168079494 168079494 G	
635	1905 A	+1:168079495 168079495 A	
636 F	1906 T	+1:168079496 168079496 T	F
636	1907 T	+1:168079497 168079497 T	
636	1908 T	+1:168079498 168079498 T	
637 F	1909 T	+1:168079499 168079499 T	F
637	1910 T	+1:168079500 168079500 T	
637	1911 C	+1:168079501 168079501 C	
638 I	1912 A	+1:168079502 168079502 A	I
638	1913 T	+1:168079503 168079503 T	
638	1914 T	+1:168079504 168079504 T	
639 Q	1915 C	+1:168079505 168079505 C	Q
639	1916 A	+1:168079506 168079506 A	
639	1917 A	+1:168079507 168079507 A	
640 T	1918 A	+1:168079508 168079508 A	T
640	1919 C	+1:168079509 168079509 C	
640	1920 T	+1:168079510 168079510 T	
641 L	1921 C	+1:168079511 168079511 C	L
641	1922 T	+1:168079512 168079512 T	
641	1923 A	+1:168079513 168079513 A	
642 D	1924 G	+1:168079514 168079514 G	D
642	1925 A	+1:168079515 168079515 A	
642	1926 T	+1:168079516 168079516 T	
643 P	1927 C	+1:168079517 168079517 C	P
643	1928 C	+1:168079518 168079518 C	
643	1929 T	+1:168079519 168079519 T	
644 K	1930 A	+1:168079520 168079520 A	K
644	1931 A	+1:168079521 168079521 A	
644	1932 A	+1:168079522 168079522 A	
645 L	1933 C	+1:168079523 168079523 C	L
645	1934 T	+1:168079524 168079524 T	
645	1935 G	+1:168079525 168079525 G	
646 I	1936 A	+1:168079526 168079526 A	I
646	1937 T	+1:168079527 168079527 T	
646	1938 A	+1:168079528 168079528 A	
647 L	1939 C	+1:168079529 168079529 C	L
647	1940 T	+1:168079530 168079530 T	
647	1941 T	+1:168079531 168079531 T	
648 Q	1942 C	+1:168079532 168079532 C	Q
648	1943 A	+1:168079533 168079533 A	
648	1944 G	+1:168079534 168079534 G	
649 A	1945 G	+1:168083455 168083455 G	A
649	1946 C	+1:168083456 168083456 C	
649	1947 A	+1:168083457 168083457 A	
650 V	1948 G	+1:168083458 168083458 G	V
650	1949 T	+1:168083459 168083459 T	
650	1950 A	+1:168083460 168083460 A	
651 T	1951 A	+1:168083461 168083461 A	T
651	1952 C	+1:168083462 168083462 C	
651	1953 T	+1:168083463 168083463 T	
652 L	1954 T	+1:168083464 168083464 T	L
652	1955 T	+1:168083465 168083465 T	
652	1956 G	+1:168083466 168083466 G	
653 Q	1957 C	+1:168083467 168083467 C	Q
653	1958 A	+1:168083468 168083468 A	
653	1959 G	+1:168083469 168083469 G	
654 T	1960 A	+1:168083470 168083470 A	T
654	1961 C	+1:168083471 168083471 C	
654	1962 C	+1:168083472 168083472 C	
655 S	1963 T	+1:168083473 168083473 T	S
655	1964 C	+1:168083474 168083474 C	
655	1965 G	+1:168083475 168083475 G	
656 L	1966 C	+1:168083476 168083476 C	L
656	1967 T	+1:168083477 168083477 T	
656	1968 A	+1:168083478 168083478 A	
657 L	1969 C	+1:168083479 168083479 C	L
657	1970 T	+1:168083480 168083480 T	
657	1971 T	+1:168083481 168083481 T	
658 K	1972 A	+1:168083482 168083482 A	K
658	1973 A	+1:168083483 168083483 A	
658	1974 A	+1:168083484 168083484 A	
659 L	1975 T	+1:168083485 168083485 T	L
659	1976 T	+1:168083486 168083486 T	
659	1977 A	+1:168083487 168083487 A	
660 E	1978 G	+1:168083488 168083488 G	E
660	1979 A	+1:168083489 168083489 A	
660	1980 G	+1:168083490 168083490 G	
661 L	1981 C	+1:168083491 168083491 C	L
661	1982 T	+1:168083492 168083492 T	
661	1983 T	+1:168083493 168083493 T	
662 P	1984 C	+1:168083494 168083494 C	P
662	1985 C	+1:168083495 168083495 C	
662	1986 T	+1:168083496 168083496 T	
663 D	1987 G	+1:168083497 168083497 G	D
663	1988 A	+1:168083498 168083498 A	
663	1989 C	+1:168083499 168083499 C	
664 Y	1990 T	+1:168083500 168083500 T	Y
664	1991 A	+1:168083501 168083501 A	
664	1992 T	+1:168083502 168083502 T	
665 V	1993 G	+1:168083503 168083503 G	V
665	1994 T	+1:168083504 168083504 T	
665	1995 T	+1:168083505 168083505 T	
666 R	1996 C	+1:168083506 168083506 C	R
666	1997 G	+1:168083507 168083507 G	
666	1998 T	+1:168083508 168083508 T	
667 L	1999 T	+1:168083509 168083509 T	L
667	2000 T	+1:168083510 168083510 T	
667	2001 G	+1:168083511 168083511 G	
668 A	2002 G	+1:168083512 168083512 G	A
668	2003 C	+1:168083513 168083513 C	
668	2004 A	+1:168083514 168083514 A	
669 M	2005 A	+1:168083515 168083515 A	M
669	2006 T	+1:168083516 168083516 T	
669	2007 G	+1:168083517 168083517 G	
670 L	2008 T	+1:168083518 168083518 T	L
670	2009 T	+1:168083519 168083519 T	
670	2010 G	+1:168083520 168083520 G	
671 D	2011 G	+1:168083521 168083521 G	D
671	2012 A	+1:168083522 168083522 A	
671	2013 T	+1:168083523 168083523 T	
672 F	2014 T	+1:168083524 168083524 T	F
672	2015 T	+1:168083525 168083525 T	
672	2016 T	+1:168083526 168083526 T	
673 V	2017 G	+1:168083527 168083527 G	V
673	2018 T	+1:168083528 168083528 T	
673	2019 A	+1:168083529 168083529 A	
674 S	2020 T	+1:168083530 168083530 T	S
674	2021 C	+1:168083531 168083531 C	
674	2022 T	+1:168083532 168083532 T	
675 S	2023 T	+1:168083533 168083533 T	S
675	2024 C	+1:168083534 168083534 C	
675	2025 T	+1:168083535 168083535 T	
676 L	2026 T	+1:168083536 168083536 T	L
676	2027 T	+1:168083537 168083537 T	
676	2028 A	+1:168083538 168083538 A	
677 G	2029 G	+1:168083539 168083539 G	G
677	2030 G	+1:168083540 168083540 G	
677	2031 A	+1:168083541 168083541 A	
678 K	2032 A	+1:168083542 168083542 A	K
678	2033 A	+1:168083543 168083543 A	
678	2034 A	+1:168083544 168083544 A	
679 L	2035 C	+1:168083545 168083545 C	L
679	2036 T	+1:168083546 168083546 T	
679	2037 T	+1:168083547 168083547 T	
680 F	2038 T	+1:168083548 168083548 T	F
680	2039 T	+1:168083549 168083549 T	
680	2040 T	+1:168083550 168083550 T	
681 I	2041 A	+1:168083551 168083551 A	I
681	2042 T	+1:168083552 168083552 T	
681	2043 A	+1:168083553 168083553 A	
682 P	2044 C	+1:168083554 168083554 C	P
682	2045 C	+1:168083555 168083555 C	
682	2046 T	+1:168083556 168083556 T	
683 E	2047 G	+1:168083557 168083557 G	E
683	2048 A	+1:168083558 168083558 A	
683	2049 A	+1:168083559 168083559 A	
684 A	2050 G	+1:168083560 168083560 G	A
684	2051 C	+1:168083561 168083561 C	
684	2052 T	+1:168083562 168083562 T	
685 I	2053 A	+1:168083563 168083563 A	I
685	2054 T	+1:168083564 168083564 T	
685	2055 C	+1:168083565 168083565 C	
686 Q	2056 C	+1:168083566 168083566 C	Q
686	2057 A	+1:168083567 168083567 A	
686	2058 G	+1:168083568 168083568 G	
687 D	2059 G	+1:168085265 168085265 G	D
687	2060 A	+1:168085266 168085266 A	
687	2061 C	+1:168085267 168085267 C	
688 R	2062 A	+1:168085268 168085268 A	R
688	2063 G	+1:168085269 168085269 G	
688	2064 A	+1:168085270 168085270 A	
689 I	2065 A	+1:168085271 168085271 A	I
689	2066 T	+1:168085272 168085272 T	
689	2067 T	+1:168085273 168085273 T	
690 L	2068 C	+1:168085274 168085274 C	L
690	2069 T	+1:168085275 168085275 T	
690	2070 G	+1:168085276 168085276 G	
691 P	2071 C	+1:168085277 168085277 C	P
691	2072 C	+1:168085278 168085278 C	
691	2073 C	+1:168085279 168085279 C	
692 N	2074 A	+1:168085280 168085280 A	N
692	2075 A	+1:168085281 168085281 A	
692	2076 C	+1:168085282 168085282 C	
693 L	2077 C	+1:168085283 168085283 C	L
693	2078 T	+1:168085284 168085284 T	
693	2079 G	+1:168085285 168085285 G	
694 S	2080 T	+1:168085286 168085286 T	S
694	2081 C	+1:168085287 168085287 C	
694	2082 C	+1:168085288 168085288 C	
695 C	2083 T	+1:168085289 168085289 T	C
695	2084 G	+1:168085290 168085290 G	
695	2085 T	+1:168085291 168085291 T	
696 M	2086 A	+1:168085292 168085292 A	M
696	2087 T	+1:168085293 168085293 T	
696	2088 G	+1:168085294 168085294 G	
697 F	2089 T	+1:168085295 168085295 T	F
697	2090 T	+1:168085296 168085296 T	
697	2091 T	+1:168085297 168085297 T	
698 A	2092 G	+1:168085298 168085298 G	A
698	2093 C	+1:168085299 168085299 C	
698	2094 C	+1:168085300 168085300 C	
699 L	2095 T	+1:168085301 168085301 T	L
699	2096 T	+1:168085302 168085302 T	
699	2097 A	+1:168085303 168085303 A	
700 L	2098 C	+1:168085304 168085304 C	L
700	2099 T	+1:168085305 168085305 T	
700	2100 G	+1:168085306 168085306 G	
701 L	2101 C	+1:168085307 168085307 C	L
701	2102 T	+1:168085308 168085308 T	
701	2103 A	+1:168085309 168085309 A	
702 A	2104 G	+1:168085310 168085310 G	A
702	2105 C	+1:168085311 168085311 C	
702	2106 T	+1:168085312 168085312 T	
703 D	2107 G	+1:168085313 168085313 G	D
703	2108 A	+1:168085314 168085314 A	
703	2109 C	+1:168085315 168085315 C	
704 R	2110 A	+1:168085316 168085316 A	R
704	2111 G	+1:168085317 168085317 G	
704	2112 G	+1:168085318 168085318 G	
705 S	2113 A	+1:168085319 168085319 A	S
705	2114 G	+1:168085320 168085320 G	
705	2115 T	+1:168085321 168085321 T	
706 W	2116 T	+1:168085322 168085322 T	W
706	2117 G	+1:168085323 168085323 G	
706	2118 G	+1:168085324 168085324 G	
707 L	2119 C	+1:168085325 168085325 C	L
707	2120 T	+1:168085326 168085326 T	
707	2121 G	+1:168085327 168085327 G	
708 L	2122 C	+1:168085328 168085328 C	L
708	2123 T	+1:168085329 168085329 T	
708	2124 A	+1:168085330 168085330 A	
709 E	2125 G	+1:168085331 168085331 G	E
709	2126 A	+1:168085332 168085332 A	
709	2127 A	+1:168085333 168085333 A	
710 Q	2128 C	+1:168085334 168085334 C	Q
710	2129 A	+1:168085335 168085335 A	
710	2130 A	+1:168085336 168085336 A	
711 H	2131 C	+1:168085337 168085337 C	H
711	2132 A	+1:168085338 168085338 A	
711	2133 T	+1:168085339 168085339 T	
712 T	2134 A	+1:168085340 168085340 A	T
712	2135 C	+1:168085341 168085341 C	
712	2136 C	+1:168085342 168085342 C	
713 L	2137 T	+1:168085343 168085343 T	L
713	2138 T	+1:168085344 168085344 T	
713	2139 G	+1:168085345 168085345 G	
714 E	2140 G	+1:168085346 168085346 G	E
714	2141 A	+1:168085347 168085347 A	
714	2142 G	+1:168085348 168085348 G	
715 A	2143 G	+1:168085349 168085349 G	A
715	2144 C	+1:168085350 168085350 C	
715	2145 G	+1:168085351 168085351 G	
716 F	2146 T	+1:168085352 168085352 T	F
716	2147 T	+1:168085353 168085353 T	
716	2148 T	+1:168085354 168085354 T	
717 T	2149 A	+1:168085355 168085355 A	T
717	2150 C	+1:168085356 168085356 C	
717	2151 T	+1:168085357 168085357 T	
718 Q	2152 C	+1:168085358 168085358 C	Q
718	2153 A	+1:168085359 168085359 A	
718	2154 G	+1:168085360 168085360 G	
719 F	2155 T	+1:168085361 168085361 T	F
719	2156 T	+1:168085362 168085362 T	
719	2157 C	+1:168085363 168085363 C	
720 A	2158 G	+1:168085364 168085364 G	A
720	2159 C	+1:168085365 168085365 C	
720	2160 T	+1:168085366 168085366 T	
721 E	2161 G	+1:168085367 168085367 G	E
721	2162 A	+1:168085368 168085368 A	
721	2163 G	+1:168085369 168085369 G	
722 G	2164 G	+1:168086030 168086030 G	G
722	2165 G	+1:168086031 168086031 G	
722	2166 A	+1:168086032 168086032 A	
723 T	2167 A	+1:168086033 168086033 A	T
723	2168 C	+1:168086034 168086034 C	
723	2169 A	+1:168086035 168086035 A	
724 N	2170 A	+1:168086036 168086036 A	N
724	2171 A	+1:168086037 168086037 A	
724	2172 T	+1:168086038 168086038 T	
725 H	2173 C	+1:168086039 168086039 C	H
725	2174 A	+1:168086040 168086040 A	
725	2175 T	+1:168086041 168086041 T	
726 E	2176 G	+1:168086042 168086042 G	E
726	2177 A	+1:168086043 168086043 A	
726	2178 A	+1:168086044 168086044 A	
727 E	2179 G	+1:168086045 168086045 G	E
727	2180 A	+1:168086046 168086046 A	
727	2181 G	+1:168086047 168086047 G	
728 I	2182 A	+1:168086048 168086048 A	I
728	2183 T	+1:168086049 168086049 T	
728	2184 A	+1:168086050 168086050 A	
729 V	2185 G	+1:168086051 168086051 G	V
729	2186 T	+1:168086052 168086052 T	
729	2187 T	+1:168086053 168086053 T	
730 P	2188 C	+1:168086054 168086054 C	P
730	2189 C	+1:168086055 168086055 C	
730	2190 A	+1:168086056 168086056 A	
731 Q	2191 C	+1:168086057 168086057 C	Q
731	2192 A	+1:168086058 168086058 A	
731	2193 G	+1:168086059 168086059 G	
732 C	2194 T	+1:168086060 168086060 T	C
732	2195 G	+1:168086061 168086061 G	
732	2196 T	+1:168086062 168086062 T	
733 L	2197 C	+1:168086063 168086063 C	L
733	2198 T	+1:168086064 168086064 T	
733	2199 C	+1:168086065 168086065 C	
734 S	2200 A	+1:168086066 168086066 A	S
734	2201 G	+1:168086067 168086067 G	
734	2202 T	+1:168086068 168086068 T	
735 S	2203 T	+1:168086069 168086069 T	S
735	2204 C	+1:168086070 168086070 C	
735	2205 T	+1:168086071 168086071 T	
736 E	2206 G	+1:168086072 168086072 G	E
736	2207 A	+1:168086073 168086073 A	
736	2208 A	+1:168086074 168086074 A	
737 E	2209 G	+1:168086075 168086075 G	E
737	2210 A	+1:168086076 168086076 A	
737	2211 A	+1:168086077 168086077 A	
738 T	2212 A	+1:168086078 168086078 A	T
738	2213 C	+1:168086079 168086079 C	
738	2214 T	+1:168086080 168086080 T	
739 K	2215 A	+1:168086081 168086081 A	K
739	2216 A	+1:168086082 168086082 A	
739	2217 G	+1:168086083 168086083 G	
740 N	2218 A	+1:168086084 168086084 A	N
740	2219 A	+1:168086085 168086085 A	
740	2220 C	+1:168086086 168086086 C	
741 K	2221 A	+1:168086087 168086087 A	K
741	2222 A	+1:168086088 168086088 A	
741	2223 A	+1:168086089 168086089 A	
742 V	2224 G	+1:168086090 168086090 G	V
742	2225 T	+1:168086091 168086091 T	
742	2226 T	+1:168086092 168086092 T	
743 V	2227 G	+1:168086093 168086093 G	V
743	2228 T	+1:168086094 168086094 T	
743	2229 A	+1:168086095 168086095 A	
744 S	2230 T	+1:168086096 168086096 T	S
744	2231 C	+1:168086097 168086097 C	
744	2232 C	+1:168086098 168086098 C	
745 F	2233 T	+1:168086099 168086099 T	F
745	2234 T	+1:168086100 168086100 T	
745	2235 T	+1:168086101 168086101 T	
746 L	2236 C	+1:168086102 168086102 C	L
746	2237 T	+1:168086103 168086103 T	
746	2238 G	+1:168086104 168086104 G	
747 E	2239 G	+1:168086105 168086105 G	E
747	2240 A	+1:168086106 168086106 A	
747	2241 G	+1:168086107 168086107 G	
748 K	2242 A	+1:168086108 168086108 A	K
748	2243 A	+1:168086109 168086109 A	
748	2244 G	+1:168086110 168086110 G	
749 T	2245 A	+1:168087582 168087582 A	T
749	2246 C	+1:168087583 168087583 C	
749	2247 T	+1:168087584 168087584 T	
750 G	2248 G	+1:168087585 168087585 G	G
750	2249 G	+1:168087586 168087586 G	
750	2250 G	+1:168087587 168087587 G	
751 F	2251 T	+1:168087588 168087588 T	F
751	2252 T	+1:168087589 168087589 T	
751	2253 T	+1:168087590 168087590 T	
752 V	2254 G	+1:168087591 168087591 G	V
752	2255 T	+1:168087592 168087592 T	
752	2256 A	+1:168087593 168087593 A	
753 D	2257 G	+1:168087594 168087594 G	D
753	2258 A	+1:168087595 168087595 A	
753	2259 T	+1:168087596 168087596 T	
754 E	2260 G	+1:168087597 168087597 G	E
754	2261 A	+1:168087598 168087598 A	
754	2262 A	+1:168087599 168087599 A	
755 T	2263 A	+1:168087600 168087600 A	T
755	2264 C	+1:168087601 168087601 C	
755	2265 T	+1:168087602 168087602 T	
756 E	2266 G	+1:168087603 168087603 G	E
756	2267 A	+1:168087604 168087604 A	
756	2268 A	+1:168087605 168087605 A	
757 A	2269 G	+1:168087606 168087606 G	A
757	2270 C	+1:168087607 168087607 C	
757	2271 T	+1:168087608 168087608 T	
758 A	2272 G	+1:168087609 168087609 G	A
758	2273 C	+1:168087610 168087610 C	
758	2274 C	+1:168087611 168087611 C	
759 K	2275 A	+1:168087612 168087612 A	K
759	2276 A	+1:168087613 168087613 A	
759	2277 A	+1:168087614 168087614 A	
760 V	2278 G	+1:168087615 168087615 G	V
760	2279 T	+1:168087616 168087616 T	
760	2280 G	+1:168087617 168087617 G	
761 E	2281 G	+1:168087618 168087618 G	E
761	2282 A	+1:168087619 168087619 A	
761	2283 A	+1:168087620 168087620 A	
762 R	2284 C	+1:168087621 168087621 C	R
762	2285 G	+1:168087622 168087622 G	
762	2286 T	+1:168087623 168087623 T	
763 V	2287 G	+1:168087624 168087624 G	V
763	2288 T	+1:168087625 168087625 T	
763	2289 G	+1:168087626 168087626 G	
764 K	2290 A	+1:168087627 168087627 A	K
764	2291 A	+1:168087628 168087628 A	
764	2292 A	+1:168087629 168087629 A	
765 Q	2293 C	+1:168087630 168087630 C	Q
765	2294 A	+1:168087631 168087631 A	
765	2295 G	+1:168087632 168087632 G	
766 E	2296 G	+1:168087633 168087633 G	E
766	2297 A	+1:168087634 168087634 A	
766	2298 A	+1:168087635 168087635 A	
767 K	2299 A	+1:168087636 168087636 A	K
767	2300 A	+1:168087637 168087637 A	
767	2301 A	+1:168087638 168087638 A	
768 G	2302 G	+1:168087639 168087639 G	G
768	2303 G	+1:168087640 168087640 G	
768	2304 T	+1:168087641 168087641 T	
769 I	2305 A	+1:168087642 168087642 A	I
769	2306 T	+1:168087643 168087643 T	
769	2307 T	+1:168087644 168087644 T	
770 F	2308 T	+1:168087645 168087645 T	F
770	2309 T	+1:168087646 168087646 T	
770	2310 C	+1:168087647 168087647 C	
771 W	2311 T	+1:168087648 168087648 T	W
771	2312 G	+1:168087649 168087649 G	
771	2313 G	+1:168087650 168087650 G	
772 E	2314 G	+1:168087651 168087651 G	E
772	2315 A	+1:168087652 168087652 A	
772	2316 A	+1:168087653 168087653 A	
773 P	2317 C	+1:168087654 168087654 C	P
773	2318 C	+1:168087655 168087655 C	
773	2319 C	+1:168087656 168087656 C	
774 F	2320 T	+1:168087657 168087657 T	F
774	2321 T	+1:168087658 168087658 T	
774	2322 T	+1:168087659 168087659 T	
775 A	2323 G	+1:168087660 168087660 G	A
775	2324 C	+1:168087661 168087661 C	
775	2325 T	+1:168087662 168087662 T	
776 N	2326 A	+1:168087663 168087663 A	N
776	2327 A	+1:168087664 168087664 A	
776	2328 T	+1:168087665 168087665 T	
777 V	2329 G	+1:168087666 168087666 G	V
777	2330 T	+1:168087667 168087667 T	
777	2331 G	+1:168087668 168087668 G	
778 T	2332 A	+1:168087669 168087669 A	T
778	2333 C	+1:168087670 168087670 C	
778	2334 T	+1:168087671 168087671 T	
779 V	2335 G	+1:168087672 168087672 G	V
779	2336 T	+1:168087673 168087673 T	
779	2337 A	+1:168087674 168087674 A	
780 E	2338 G	+1:168087675 168087675 G	E
780	2339 A	+1:168087676 168087676 A	
780	2340 A	+1:168087677 168087677 A	
781 E	2341 G	+1:168087678 168087678 G	E
781	2342 A	+1:168087679 168087679 A	
781	2343 A	+1:168087680 168087680 A	
782 A	2344 G	+1:168087681 168087681 G	A
782	2345 C	+1:168087682 168087682 C	
782	2346 A	+1:168087683 168087683 A	
783 K	2347 A	+1:168087684 168087684 A	K
783	2348 A	+1:168087685 168087685 A	
783	2349 G	+1:168087686 168087686 G	
784 R	2350 A	+1:168087687 168087687 A	R
784	2351 G	+1:168087688 168087688 G	
784	2352 G	+1:168087689 168087689 G	
785 S	2353 T	+1:168087690 168087690 T	S
785	2354 C	+1:168087691 168087691 C	
785	2355 A	+1:168087692 168087692 A	
786 S	2356 T	+1:168087693 168087693 T	S
786	2357 C	+1:168087694 168087694 C	
786	2358 T	+1:168087695 168087695 T	
787 L	2359 T	+1:168087696 168087696 T	L
787	2360 T	+1:168087697 168087697 T	
787	2361 A	+1:168087698 168087698 A	
788 Q	2362 C	+1:168087699 168087699 C	Q
788	2363 A	+1:168087700 168087700 A	
788	2364 G	+1:168087701 168087701 G	
789 P	2365 C	+1:168088555 168088555 C	P
789	2366 C	+1:168088556 168088556 C	
789	2367 T	+1:168088557 168088557 T	
790 Y	2368 T	+1:168088558 168088558 T	Y
790	2369 A	+1:168088559 168088559 A	
790	2370 T	+1:168088560 168088560 T	
791 A	2371 G	+1:168088561 168088561 G	A
791	2372 C	+1:168088562 168088562 C	
791	2373 A	+1:168088563 168088563 A	
792 K	2374 A	+1:168088564 168088564 A	K
792	2375 A	+1:168088565 168088565 A	
792	2376 A	+1:168088566 168088566 A	
793 R	2377 A	+1:168088567 168088567 A	R
793	2378 G	+1:168088568 168088568 G	
793	2379 A	+1:168088569 168088569 A	
794 A	2380 G	+1:168088570 168088570 G	A
794	2381 C	+1:168088571 168088571 C	
794	2382 T	+1:168088572 168088572 T	
795 R	2383 C	+1:168088573 168088573 C	R
795	2384 G	+1:168088574 168088574 G	
795	2385 T	+1:168088575 168088575 T	
796 Q	2386 C	+1:168088576 168088576 C	Q
796	2387 A	+1:168088577 168088577 A	
796	2388 G	+1:168088578 168088578 G	
797 E	2389 G	+1:168088579 168088579 G	E
797	2390 A	+1:168088580 168088580 A	
797	2391 G	+1:168088581 168088581 G	
798 F	2392 T	+1:168088582 168088582 T	F
798	2393 T	+1:168088583 168088583 T	
798	2394 C	+1:168088584 168088584 C	
799 P	2395 C	+1:168088585 168088585 C	P
799	2396 C	+1:168088586 168088586 C	
799	2397 C	+1:168088587 168088587 C	
800 W	2398 T	+1:168088588 168088588 T	W
800	2399 G	+1:168088589 168088589 G	
800	2400 G	+1:168088590 168088590 G	
801 E	2401 G	+1:168088591 168088591 G	E
801	2402 A	+1:168088592 168088592 A	
801	2403 A	+1:168088593 168088593 A	
802 E	2404 G	+1:168088594 168088594 G	E
802	2405 A	+1:168088595 168088595 A	
802	2406 A	+1:168088596 168088596 A	
803 E	2407 G	+1:168088597 168088597 G	E
803	2408 A	+1:168088598 168088598 A	
803	2409 G	+1:168088599 168088599 G	
804 Y	2410 T	+1:168088600 168088600 T	Y
804	2411 A	+1:168088601 168088601 A	
804	2412 C	+1:168088602 168088602 C	
805 R	2413 A	+1:168088603 168088603 A	R
805	2414 G	+1:168088604 168088604 G	
805	2415 G	+1:168088605 168088605 G	
806 S	2416 T	+1:168088606 168088606 T	S
806	2417 C	+1:168088607 168088607 C	
806	2418 A	+1:168088608 168088608 A	
807 A	2419 G	+1:168088609 168088609 G	A
807	2420 C	+1:168088610 168088610 C	
807	2421 G	+1:168088611 168088611 G	
808 L	2422 C	+1:168088612 168088612 C	L
808	2423 T	+1:168088613 168088613 T	
808	2424 G	+1:168088614 168088614 G	
809 H	2425 C	+1:168088615 168088615 C	H
809	2426 A	+1:168088616 168088616 A	
809	2427 T	+1:168088617 168088617 T	
810 T	2428 A	+1:168088618 168088618 A	T
810	2429 C	+1:168088619 168088619 C	
810	2430 A	+1:168088620 168088620 A	
811 I	2431 A	+1:168088621 168088621 A	I
811	2432 T	+1:168088622 168088622 T	
811	2433 A	+1:168088623 168088623 A	
812 A	2434 G	+1:168088624 168088624 G	A
812	2435 C	+1:168088625 168088625 C	
812	2436 A	+1:168088626 168088626 A	
813 G	2437 G	+1:168088627 168088627 G	G
813	2438 G	+1:168088628 168088628 G	
813	2439 G	+1:168088629 168088629 G	
814 A	2440 G	+1:168088630 168088630 G	A
814	2441 C	+1:168088631 168088631 C	
814	2442 T	+1:168088632 168088632 T	
815 L	2443 T	+1:168088633 168088633 T	L
815	2444 T	+1:168088634 168088634 T	
815	2445 G	+1:168088635 168088635 G	
816 E	2446 G	+1:168088636 168088636 G	E
816	2447 A	+1:168088637 168088637 A	
816	2448 A	+1:168088638 168088638 A	
817 A	2449 G	+1:168088639 168088639 G	A
817	2450 C	+1:168088640 168088640 C	
817	2451 A	+1:168088641 168088641 A	
818 T	2452 A	+1:168088642 168088642 A	T
818	2453 C	+1:168088643 168088643 C	
818	2454 T	+1:168088644 168088644 T	
819 E	2455 G	+1:168088645 168088645 G	E
819	2456 A	+1:168088646 168088646 A	
819	2457 G	+1:168088647 168088647 G	
820 S	2458 T	+1:168088648 168088648 T	S
820	2459 C	+1:168088649 168088649 C	
820	2460 A	+1:168088650 168088650 A	
821 L	2461 C	+1:168088651 168088651 C	L
821	2462 T	+1:168088652 168088652 T	
821	2463 A	+1:168088653 168088653 A	
822 L	2464 C	+1:168088654 168088654 C	L
822	2465 T	+1:168088655 168088655 T	
822	2466 C	+1:168088656 168088656 C	
823 Q	2467 C	+1:168088657 168088657 C	Q
823	2468 A	+1:168088658 168088658 A	
823	2469 A	+1:168088659 168088659 A	
824 K	2470 A	+1:168088660 168088660 A	K
824	2471 A	+1:168088661 168088661 A	
824	2472 G	+1:168088662 168088662 G	
825 G	2473 G	+1:168088663 168088663 G	G
825	2474 G	+1:168088664 168088664 G	
825	2475 T	+1:168088665 168088665 T	
826 P	2476 C	+1:168088666 168088666 C	P
826	2477 C	+1:168088667 168088667 C	
826	2478 T	+1:168088668 168088668 T	
827 A	2479 G	+1:168088669 168088669 G	A
827	2480 C	+1:168088670 168088670 C	
827	2481 T	+1:168088671 168088671 T	
828 P	2482 C	+1:168088672 168088672 C	P
828	2483 C	+1:168088673 168088673 C	
828	2484 A	+1:168088674 168088674 A	
829 A	2485 G	+1:168088675 168088675 G	A
829	2486 C	+1:168088676 168088676 C	
829	2487 C	+1:168088677 168088677 C	
830 W	2488 T	+1:168088678 168088678 T	W
830	2489 G	+1:168088679 168088679 G	
830	2490 G	+1:168088680 168088680 G	
831 L	2491 C	+1:168088681 168088681 C	L
831	2492 T	+1:168088682 168088682 T	
831	2493 T	+1:168088683 168088683 T	
832 S	2494 T	+1:168088684 168088684 T	S
832	2495 C	+1:168088685 168088685 C	
832	2496 A	+1:168088686 168088686 A	
833 M	2497 A	+1:168088687 168088687 A	M
833	2498 T	+1:168088688 168088688 T	
833	2499 G	+1:168088689 168088689 G	
834 E	2500 G	+1:168088690 168088690 G	E
834	2501 A	+1:168088691 168088691 A	
834	2502 A	+1:168088692 168088692 A	
835 M	2503 A	+1:168088693 168088693 A	M
835	2504 T	+1:168088694 168088694 T	
835	2505 G	+1:168088695 168088695 G	
836 E	2506 G	+1:168088696 168088696 G	E
836	2507 A	+1:168088697 168088697 A	
836	2508 G	+1:168088698 168088698 G	
837 A	2509 G	+1:168088699 168088699 G	A
837	2510 C	+1:168088700 168088700 C	
837	2511 G	+1:168088701 168088701 G	
838 L	2512 C	+1:168088702 168088702 C	L
838	2513 T	+1:168088703 168088703 T	
838	2514 C	+1:168088704 168088704 C	
839 Q	2515 C	+1:168088705 168088705 C	Q
839	2516 A	+1:168088706 168088706 A	
839	2517 A	+1:168088707 168088707 A	
840 E	2518 G	+1:168088708 168088708 G	E
840	2519 A	+1:168088709 168088709 A	
840	2520 A	+1:168088710 168088710 A	
841 R	2521 A	+1:168088711 168088711 A	R
841	2522 G	+1:168088712 168088712 G	
841	2523 G	+1:168088713 168088713 G	
842 M	2524 A	+1:168088714 168088714 A	M
842	2525 T	+1:168088715 168088715 T	
842	2526 G	+1:168088716 168088716 G	
843 D	2527 G	+1:168088717 168088717 G	D
843	2528 A	+1:168088718 168088718 A	
843	2529 T	+1:168088719 168088719 T	
844 K	2530 A	+1:168088720 168088720 A	K
844	2531 A	+1:168088721 168088721 A	
844	2532 G	+1:168088722 168088722 G	
845 L	2533 C	+1:168088723 168088723 C	L
845	2534 T	+1:168088724 168088724 T	
845	2535 A	+1:168088725 168088725 A	
846 K	2536 A	+1:168088726 168088726 A	K
846	2537 A	+1:168088727 168088727 A	
846	2538 A	+1:168088728 168088728 A	
847 R	2539 C	+1:168088729 168088729 C	R
847	2540 G	+1:168088730 168088730 G	
847	2541 T	+1:168088731 168088731 T	
848 Y	2542 T	+1:168088732 168088732 T	Y
848	2543 A	+1:168088733 168088733 A	
848	2544 C	+1:168088734 168088734 C	
849 I	2545 A	+1:168088735 168088735 A	I
849	2546 T	+1:168088736 168088736 T	
849	2547 A	+1:168088737 168088737 A	
850 H	2548 C	+1:168088738 168088738 C	H
850	2549 A	+1:168088739 168088739 A	
850	2550 T	+1:168088740 168088740 T	
851 T	2551 A	+1:168088741 168088741 A	T
851	2552 C	+1:168088742 168088742 C	
851	2553 T	+1:168088743 168088743 T	
852 L	2554 C	+1:168088744 168088744 C	L
852	2555 T	+1:168088745 168088745 T	
852	2556 A	+1:168088746 168088746 A	
853 G	2557 G	+1:168088747 168088747 G	G
853	2558 G	+1:168088748 168088748 G	
853	2559 G	+1:168088749 168088749 G	
>ENSP00000382126 
1 M	1 A	-1:27823014 27823014 A	M
1	2 T	-1:27823013 27823013 T	
1	3 G	-1:27823012 27823012 G	
2 G	4 G	-1:27823011 27823011 G	G
2	5 G	-1:27823010 27823010 G	
2	6 C	-1:27823009 27823009 C	
3 C	7 T	-1:27823008 27823008 T	C
3	8 G	-1:27823007 27823007 G	
3	9 T	-1:27823006 27823006 T	
4 V	10 G	-1:27823005 27823005 G	V
4	11 T	-1:27823004 27823004 T	
4	12 G	-1:27823003 27823003 G	
5 F	13 T	-1:27823002 27823002 T	F
5	14 T	-1:27823001 27823001 T	
5	15 C	-1:27823000 27823000 C	
6 C	16 T	-1:27822999 27822999 T	C
6	17 G	-1:27822998 27822998 G	
6	18 C	-1:27822997 27822997 C	
7 K	19 A	-1:27822996 27822996 A	K
7	20 A	-1:27822995 27822995 A	
7	21 G	-1:27822994 27822994 G	
8 K	22 A	-1:27822993 27822993 A	K
8	23 A	-1:27822992 27822992 A	
8	24 A	-1:27822991 27822991 A	
9 L	25 T	-1:27822990 27822990 T	L
9	26 T	-1:27822989 27822989 T	
9	27 G	-1:27822988 27822988 G	
10 E	28 G	-1:27822987 27822987 G	E
10	29 A	-1:27822986 27822986 A	
10	30 G	-1:27822985 27822985 G	
11 P	31 C	-1:27822984 27822984 C	P
11	32 C	-1:27822983 27822983 C	
11	33 G	-1:27822982 27822982 G	
12 V	34 G	-1:27822981 27822981 G	V
12	35 T	-1:27822980 27822980 T	
12	36 G	-1:27822979 27822979 G	
13 A	37 G	-1:27822978 27822978 G	A
13	38 C	-1:27822977 27822977 C	
13	39 C	-1:27822976 27822976 C	
14 T	40 A	-1:27822975 27822975 A	T
14	41 C	-1:27822974 27822974 C	
14	42 G	-1:27822973 27822973 G	
15 A	43 G	-1:27822972 27822972 G	A
15	44 C	-1:27822971 27822971 C	
15	45 C	-1:27822970 27822970 C	
16 K	46 A	-1:27822969 27822969 A	K
16	47 A	-1:27822968 27822968 A	
16	48 G	-1:27822967 27822967 G	
17 E	49 G	-1:27822966 27822966 G	E
17	50 A	-1:27822965 27822965 A	
17	51 G	-1:27822964 27822964 G	
18 D	52 G	-1:27822963 27822963 G	D
18	53 A	-1:27822962 27822962 A	
18	54 T	-1:27822961 27822961 T	
19 A	55 G	-1:27822960 27822960 G	A
19	56 C	-1:27822959 27822959 C	
19	57 T	-1:27822958 27822958 T	
20 G	58 G	-1:27822957 27822957 G	G
20	59 G	-1:27822956 27822956 G	
20	60 C	-1:27822955 27822955 C	
21 L	61 C	-1:27822954 27822954 C	L
21	62 T	-1:27822953 27822953 T	
21	63 G	-1:27822952 27822952 G	
22 E	64 G	-1:27822951 27822951 G	E
22	65 A	-1:27822950 27822950 A	
22	66 A	-1:27822949 27822949 A	
23 G	67 G	-1:27822948 27822948 G	G
23	68 G	-1:27822947 27822947 G	
23	69 G	-1:27822946 27822946 G	
24 D	70 G	-1:27822945 27822945 G	D
24	71 A	-1:27822944 27822944 A	
24	72 C	-1:27822943 27822943 C	
25 F	73 T	-1:27822942 27822942 T	F
25	74 T	-1:27822941 27822941 T	
25	75 C	-1:27822940 27822940 C	
26 R	76 A	-1:27822939 27822939 A	R
26	77 G	-1:27822938 27822938 G	
26	78 A	-1:27822937 27822937 A	
27 S	79 A	-1:27822936 27822936 A	S
27	80 G	-1:27822935 27822935 G	
27	81 C	-1:27822934 27822934 C	
28 Y	82 T	-1:27822933 27822933 T	Y
28	83 A	-1:27822932 27822932 A	
28	84 C	-1:27822931 27822931 C	
29 G	85 G	-1:27822930 27822930 G	G
29	86 G	-1:27822929 27822929 G	
29	87 G	-1:27822928 27822928 G	
30 A	88 G	-1:27822927 27822927 G	A
30	89 C	-1:27822926 27822926 C	
30	90 A	-1:27822925 27822925 A	
31 A	91 G	-1:27822924 27822924 G	A
31	92 C	-1:27822923 27822923 C	
31	93 A	-1:27822922 27822922 A	
32 D	94 G	-1:27822921 27822921 G	D
32	95 A	-1:27822920 27822920 A	
32	96 C	-1:27822919 27822919 C	
33 H	97 C	-1:27822918 27822918 C	H
33	98 A	-1:27822917 27822917 A	
33	99 C	-1:27822916 27822916 C	
34 Y	100 T	-1:27822915 27822915 T	Y
34	101 A	-1:27822914 27822914 A	
34	102 T	-1:27822913 27822913 T	
35 G	103 G	-1:27822912 27822912 G	G
35	104 G	-1:27822911 27822911 G	
35	105 G	-1:27822910 27822910 G	
36 P	106 C	-1:27822909 27822909 C	P
36	107 C	-1:27822908 27822908 C	
36	108 T	-1:27822907 27822907 T	
37 D	109 G	-1:27822906 27822906 G	D
37	110 A	-1:27822905 27822905 A	
37	111 C	-1:27822904 27822904 C	
38 P	112 C	-1:27822903 27822903 C	P
38	113 C	-1:27822902 27822902 C	
38	114 C	-1:27822901 27822901 C	
39 T	115 A	-1:27822900 27822900 A	T
39	116 C	-1:27822899 27822899 C	
39	117 T	-1:27822898 27822898 T	
40 K	118 A	-1:27822897 27822897 A	K
40	119 A	-1:27822896 27822896 A	
40	120 G	-1:27822895 27822895 G	
41 A	121 G	-1:27822894 27822894 G	A
41	122 C	-1:27822893 27822893 C	
41	123 C	-1:27822892 27822892 C	
42 R	124 C	-1:27822891 27822891 C	R
42	125 G	-1:27822890 27822890 G	
42	126 G	-1:27822889 27822889 G	
43 P	127 C	-1:27822888 27822888 C	P
43	128 C	-1:27822887 27822887 C	
43	129 T	-1:27822886 27822886 T	
44 A	130 G	-1:27822885 27822885 G	A
44	131 C	-1:27822884 27822884 C	
44	132 A	-1:27822883 27822883 A	
45 S	133 T	-1:27822882 27822882 T	S
45	134 C	-1:27822881 27822881 C	
45	135 C	-1:27822880 27822880 C	
46 S	136 T	-1:27822879 27822879 T	S
46	137 C	-1:27822878 27822878 C	
46	138 A	-1:27822877 27822877 A	
47 F	139 T	-1:27822876 27822876 T	F
47	140 T	-1:27822875 27822875 T	
47	141 T	-1:27822874 27822874 T	
48 A	142 G	-1:27822873 27822873 G	A
48	143 C	-1:27822872 27822872 C	
48	144 C	-1:27822871 27822871 C	
49 H	145 C	-1:27822870 27822870 C	H
49	146 A	-1:27822869 27822869 A	
49	147 C	-1:27822868 27822868 C	
50 I	148 A	-1:27822867 27822867 A	I
50	149 T	-1:27822866 27822866 T	
50	150 C	-1:27822865 27822865 C	
51 P	151 C	-1:27822864 27822864 C	P
51	152 C	-1:27822863 27822863 C	
51	153 C	-1:27822862 27822862 C	
52 N	154 A	-1:27822861 27822861 A	N
52	155 A	-1:27822860 27822860 A	
52	156 C	-1:27822859 27822859 C	
53 Y	157 T	-1:27822858 27822858 T	Y
53	158 A	-1:27822857 27822857 A	
53	159 C	-1:27822856 27822856 C	
54 S	160 A	-1:27822855 27822855 A	S
54	161 G	-1:27822854 27822854 G	
54	162 C	-1:27822853 27822853 C	
55 N	163 A	-1:27822852 27822852 A	N
55	164 A	-1:27822851 27822851 A	
55	165 C	-1:27822850 27822850 C	
56 F	166 T	-1:27822849 27822849 T	F
56	167 T	-1:27822848 27822848 T	
56	168 C	-1:27822847 27822847 C	
57 S	169 T	-1:27822846 27822846 T	S
57	170 C	-1:27822845 27822845 C	
57	171 C	-1:27822844 27822844 C	
58 S	172 T	-1:27822843 27822843 T	S
58	173 C	-1:27822842 27822842 C	
58	174 T	-1:27822841 27822841 T	
59 Q	175 C	-1:27822840 27822840 C	Q
59	176 A	-1:27822839 27822839 A	
59	177 G	-1:27822838 27822838 G	
60 A	178 G	-1:27822837 27822837 G	A
60	179 C	-1:27822836 27822836 C	
60	180 C	-1:27822835 27822835 C	
61 I	181 A	-1:27822834 27822834 A	I
61	182 T	-1:27822833 27822833 T	
61	183 C	-1:27822832 27822832 C	
62 N	184 A	-1:27822831 27822831 A	N
62	185 A	-1:27822830 27822830 A	
62	186 C	-1:27822829 27822829 C	
63 P	187 C	-1:27822828 27822828 C	P
63	188 C	-1:27822827 27822827 C	
63	189 T	-1:27822826 27822826 T	
64 G	190 G	-1:27822825 27822825 G	G
64	191 G	-1:27822824 27822824 G	
64	192 C	-1:27822823 27822823 C	
65 F	193 T	-1:27822822 27822822 T	F
65	194 T	-1:27822821 27822821 T	
65	195 C	-1:27822820 27822820 C	
66 L	196 C	-1:27822819 27822819 C	L
66	197 T	-1:27822818 27822818 T	
66	198 T	-1:27822817 27822817 T	
67 D	199 G	-1:27822816 27822816 G	D
67	200 A	-1:27822815 27822815 A	
67	201 T	-1:27822814 27822814 T	
68 S	202 A	-1:27822813 27822813 A	S
68	203 G	-1:27822812 27822812 G	
68	204 T	-1:27822811 27822811 T	
69 G	205 G	-1:27822810 27822810 G	G
69	206 G	-1:27822809 27822809 G	
69	207 C	-1:27822808 27822808 C	
70 T	208 A	-1:27822807 27822807 A	T
70	209 C	-1:27822806 27822806 C	
70	210 C	-1:27822805 27822805 C	
71 I	211 A	-1:27822804 27822804 A	I
71	212 T	-1:27822803 27822803 T	
71	213 C	-1:27822802 27822802 C	
72 R	214 A	-1:27822801 27822801 A	R
72	215 G	-1:27822800 27822800 G	
72	216 G	-1:27822799 27822799 G	
73 G	217 G	-1:27822798 27822798 G	G
73	218 G	-1:27822797 27822797 G	
73	219 T	-1:27822796 27822796 T	
74 V	220 G	-1:27822795 27822795 G	V
74	221 T	-1:27822794 27822794 T	
74	222 G	-1:27822793 27822793 G	
75 S	223 T	-1:27822792 27822792 T	S
75	224 C	-1:27822791 27822791 C	
75	225 A	-1:27822790 27822790 A	
76 G	226 G	-1:27822789 27822789 G	G
76	227 G	-1:27822242 27822242 G	
76	228 G	-1:27822241 27822241 G	
77 I	229 A	-1:27822240 27822240 A	I
77	230 T	-1:27822239 27822239 T	
77	231 T	-1:27822238 27822238 T	
78 G	232 G	-1:27822237 27822237 G	G
78	233 G	-1:27822236 27822236 G	
78	234 G	-1:27822235 27822235 G	
79 V	235 G	-1:27822234 27822234 G	V
79	236 T	-1:27822233 27822233 T	
79	237 G	-1:27822232 27822232 G	
80 T	238 A	-1:27822231 27822231 A	T
80	239 C	-1:27822230 27822230 C	
80	240 C	-1:27822229 27822229 C	
81 L	241 C	-1:27822228 27822228 C	L
81	242 T	-1:27822227 27822227 T	
81	243 G	-1:27822226 27822226 G	
82 F	244 T	-1:27822225 27822225 T	F
82	245 T	-1:27822224 27822224 T	
82	246 C	-1:27822223 27822223 C	
83 I	247 A	-1:27822222 27822222 A	I
83	248 T	-1:27822221 27822221 T	
83	249 T	-1:27822220 27822220 T	
84 A	250 G	-1:27822219 27822219 G	A
84	251 C	-1:27822218 27822218 C	
84	252 C	-1:27822217 27822217 C	
85 L	253 C	-1:27822216 27822216 C	L
85	254 T	-1:27822215 27822215 T	
85	255 G	-1:27822214 27822214 G	
86 Y	256 T	-1:27822213 27822213 T	Y
86	257 A	-1:27822212 27822212 A	
86	258 T	-1:27822211 27822211 T	
87 D	259 G	-1:27822210 27822210 G	D
87	260 A	-1:27822209 27822209 A	
87	261 C	-1:27822208 27822208 C	
88 Y	262 T	-1:27822207 27822207 T	Y
88	263 A	-1:27822206 27822206 A	
88	264 T	-1:27822205 27822205 T	
89 E	265 G	-1:27822204 27822204 G	E
89	266 A	-1:27822203 27822203 A	
89	267 G	-1:27822202 27822202 G	
90 A	268 G	-1:27822201 27822201 G	A
90	269 C	-1:27822200 27822200 C	
90	270 T	-1:27822199 27822199 T	
91 R	271 C	-1:27822198 27822198 C	R
91	272 G	-1:27822197 27822197 G	
91	273 A	-1:27822196 27822196 A	
92 T	274 A	-1:27822195 27822195 A	T
92	275 C	-1:27822194 27822194 C	
92	276 T	-1:27822193 27822193 T	
93 E	277 G	-1:27822192 27822192 G	E
93	278 A	-1:27822191 27822191 A	
93	279 G	-1:27822190 27822190 G	
94 D	280 G	-1:27822189 27822189 G	D
94	281 A	-1:27822188 27822188 A	
94	282 T	-1:27822187 27822187 T	
95 D	283 G	-1:27822186 27822186 G	D
95	284 A	-1:27822185 27822185 A	
95	285 C	-1:27822184 27822184 C	
96 L	286 C	-1:27822183 27822183 C	L
96	287 T	-1:27822182 27822182 T	
96	288 C	-1:27822181 27822181 C	
97 T	289 A	-1:27822180 27822180 A	T
97	290 C	-1:27822179 27822179 C	
97	291 C	-1:27822178 27822178 C	
98 F	292 T	-1:27822177 27822177 T	F
98	293 T	-1:27822176 27822176 T	
98	294 C	-1:27822175 27822175 C	
99 T	295 A	-1:27822174 27822174 A	T
99	296 C	-1:27822173 27822173 C	
99	297 C	-1:27822172 27822172 C	
100 K	298 A	-1:27822171 27822171 A	K
100	299 A	-1:27822170 27822170 A	
100	300 G	-1:27822169 27822169 G	
101 G	301 G	-1:27822168 27822168 G	G
101	302 G	-1:27822167 27822167 G	
101	303 C	-1:27822166 27822166 C	
102 E	304 G	-1:27822165 27822165 G	E
102	305 A	-1:27822164 27822164 A	
102	306 G	-1:27822163 27822163 G	
103 K	307 A	-1:27822162 27822162 A	K
103	308 A	-1:27822161 27822161 A	
103	309 G	-1:27822160 27822160 G	
104 F	310 T	-1:27822159 27822159 T	F
104	311 T	-1:27822158 27822158 T	
104	312 C	-1:27822157 27822157 C	
105 H	313 C	-1:27822156 27822156 C	H
105	314 A	-1:27822155 27822155 A	
105	315 C	-1:27822154 27822154 C	
106 I	316 A	-1:27822153 27822153 A	I
106	317 T	-1:27822152 27822152 T	
106	318 C	-1:27822151 27822151 C	
107 L	319 C	-1:27822150 27822150 C	L
107	320 T	-1:27822149 27822149 T	
107	321 G	-1:27822148 27822148 G	
108 N	322 A	-1:27822147 27822147 A	N
108	323 A	-1:27822146 27822146 A	
108	324 C	-1:27822145 27822145 C	
109 N	325 A	-1:27822144 27822144 A	N
109	326 A	-1:27822143 27822143 A	
109	327 T	-1:27822142 27822142 T	
110 T	328 A	-1:27822141 27822141 A	T
110	329 C	-1:27822140 27822140 C	
110	330 T	-1:27820755 27820755 T	
111 E	331 G	-1:27820754 27820754 G	E
111	332 A	-1:27820753 27820753 A	
111	333 A	-1:27820752 27820752 A	
112 G	334 G	-1:27820751 27820751 G	G
112	335 G	-1:27820750 27820750 G	
112	336 T	-1:27820749 27820749 T	
113 D	337 G	-1:27820748 27820748 G	D
113	338 A	-1:27820747 27820747 A	
113	339 C	-1:27820746 27820746 C	
114 W	340 T	-1:27820745 27820745 T	W
114	341 G	-1:27820744 27820744 G	
114	342 G	-1:27820743 27820743 G	
115 W	343 T	-1:27820742 27820742 T	W
115	344 G	-1:27820741 27820741 G	
115	345 G	-1:27820740 27820740 G	
116 E	346 G	-1:27820739 27820739 G	E
116	347 A	-1:27820738 27820738 A	
116	348 G	-1:27820737 27820737 G	
117 A	349 G	-1:27820736 27820736 G	A
117	350 C	-1:27820735 27820735 C	
117	351 T	-1:27820734 27820734 T	
118 R	352 C	-1:27820733 27820733 C	R
118	353 G	-1:27820732 27820732 G	
118	354 G	-1:27820731 27820731 G	
119 S	355 T	-1:27820730 27820730 T	S
119	356 C	-1:27820729 27820729 C	
119	357 T	-1:27820728 27820728 T	
120 L	358 C	-1:27820727 27820727 C	L
120	359 T	-1:27820726 27820726 T	
120	360 C	-1:27820725 27820725 C	
121 S	361 A	-1:27820724 27820724 A	S
121	362 G	-1:27820723 27820723 G	
121	363 C	-1:27820722 27820722 C	
122 S	364 T	-1:27820721 27820721 T	S
122	365 C	-1:27820720 27820720 C	
122	366 C	-1:27820719 27820719 C	
123 G	367 G	-1:27820718 27820718 G	G
123	368 G	-1:27820717 27820717 G	
123	369 A	-1:27820716 27820716 A	
124 K	370 A	-1:27820715 27820715 A	K
124	371 A	-1:27820714 27820714 A	
124	372 A	-1:27820713 27820713 A	
125 T	373 A	-1:27820712 27820712 A	T
125	374 C	-1:27820711 27820711 C	
125	375 T	-1:27820710 27820710 T	
126 G	376 G	-1:27820709 27820709 G	G
126	377 G	-1:27820708 27820708 G	
126	378 C	-1:27820707 27820707 C	
127 C	379 T	-1:27820706 27820706 T	C
127	380 G	-1:27820705 27820705 G	
127	381 C	-1:27820704 27820704 C	
128 I	382 A	-1:27820703 27820703 A	I
128	383 T	-1:27820702 27820702 T	
128	384 T	-1:27820701 27820701 T	
129 P	385 C	-1:27820700 27820700 C	P
129	386 C	-1:27820699 27820699 C	
129	387 C	-1:27820698 27820698 C	
130 S	388 A	-1:27820697 27820697 A	S
130	389 G	-1:27820696 27820696 G	
130	390 C	-1:27820695 27820695 C	
131 N	391 A	-1:27820694 27820694 A	N
131	392 A	-1:27820693 27820693 A	
131	393 C	-1:27820692 27820692 C	
132 Y	394 T	-1:27820691 27820691 T	Y
132	395 A	-1:27820690 27820690 A	
132	396 C	-1:27820689 27820689 C	
133 V	397 G	-1:27820688 27820688 G	V
133	398 T	-1:27820687 27820687 T	
133	399 G	-1:27820686 27820686 G	
134 A	400 G	-1:27820685 27820685 G	A
134	401 C	-1:27820684 27820684 C	
134	402 C	-1:27820683 27820683 C	
135 P	403 C	-1:27820682 27820682 C	P
135	404 C	-1:27820681 27820681 C	
135	405 T	-1:27820680 27820680 T	
136 V	406 G	-1:27820679 27820679 G	V
136	407 T	-1:27820678 27820678 T	
136	408 T	-1:27820677 27820677 T	
137 D	409 G	-1:27820676 27820676 G	D
137	410 A	-1:27820675 27820675 A	
137	411 C	-1:27820674 27820674 C	
138 S	412 T	-1:27820673 27820673 T	S
138	413 C	-1:27820672 27820672 C	
138	414 A	-1:27820671 27820671 A	
139 I	415 A	-1:27820670 27820670 A	I
139	416 T	-1:27820669 27820669 T	
139	417 C	-1:27820668 27820668 C	
140 Q	418 C	-1:27820667 27820667 C	Q
140	419 A	-1:27820666 27820666 A	
140	420 A	-1:27820665 27820665 A	
141 A	421 G	-1:27820664 27820664 G	A
141	422 C	-1:27820663 27820663 C	
141	423 T	-1:27820662 27820662 T	
142 E	424 G	-1:27820661 27820661 G	E
142	425 A	-1:27820660 27820660 A	
142	426 A	-1:27820659 27820659 A	
143 E	427 G	-1:27820658 27820658 G	E
143	428 A	-1:27820657 27820657 A	
143	429 G	-1:27816394 27816394 G	
144 W	430 T	-1:27816393 27816393 T	W
144	431 G	-1:27816392 27816392 G	
144	432 G	-1:27816391 27816391 G	
145 Y	433 T	-1:27816390 27816390 T	Y
145	434 A	-1:27816389 27816389 A	
145	435 C	-1:27816388 27816388 C	
146 F	436 T	-1:27816387 27816387 T	F
146	437 T	-1:27816386 27816386 T	
146	438 T	-1:27816385 27816385 T	
147 G	439 G	-1:27816384 27816384 G	G
147	440 G	-1:27816383 27816383 G	
147	441 A	-1:27816382 27816382 A	
148 K	442 A	-1:27816381 27816381 A	K
148	443 A	-1:27816380 27816380 A	
148	444 G	-1:27816379 27816379 G	
149 I	445 A	-1:27816378 27816378 A	I
149	446 T	-1:27816377 27816377 T	
149	447 T	-1:27816376 27816376 T	
150 G	448 G	-1:27816375 27816375 G	G
150	449 G	-1:27816374 27816374 G	
150	450 G	-1:27816373 27816373 G	
151 R	451 A	-1:27816372 27816372 A	R
151	452 G	-1:27816371 27816371 G	
151	453 A	-1:27816370 27816370 A	
152 K	454 A	-1:27816369 27816369 A	K
152	455 A	-1:27816368 27816368 A	
152	456 G	-1:27816367 27816367 G	
153 D	457 G	-1:27816366 27816366 G	D
153	458 A	-1:27816365 27816365 A	
153	459 T	-1:27816364 27816364 T	
154 A	460 G	-1:27816363 27816363 G	A
154	461 C	-1:27816362 27816362 C	
154	462 A	-1:27816361 27816361 A	
155 E	463 G	-1:27816360 27816360 G	E
155	464 A	-1:27816359 27816359 A	
155	465 G	-1:27816358 27816358 G	
156 R	466 A	-1:27816357 27816357 A	R
156	467 G	-1:27816356 27816356 G	
156	468 G	-1:27816355 27816355 G	
157 Q	469 C	-1:27816354 27816354 C	Q
157	470 A	-1:27816353 27816353 A	
157	471 G	-1:27816352 27816352 G	
158 L	472 C	-1:27816351 27816351 C	L
158	473 T	-1:27816350 27816350 T	
158	474 G	-1:27816349 27816349 G	
159 L	475 C	-1:27816348 27816348 C	L
159	476 T	-1:27816347 27816347 T	
159	477 T	-1:27816346 27816346 T	
160 S	478 T	-1:27816345 27816345 T	S
160	479 C	-1:27816344 27816344 C	
160	480 A	-1:27816343 27816343 A	
161 P	481 C	-1:27816342 27816342 C	P
161	482 C	-1:27816341 27816341 C	
161	483 A	-1:27816340 27816340 A	
162 G	484 G	-1:27816339 27816339 G	G
162	485 G	-1:27816338 27816338 G	
162	486 C	-1:27816337 27816337 C	
163 N	487 A	-1:27816336 27816336 A	N
163	488 A	-1:27816335 27816335 A	
163	489 C	-1:27816334 27816334 C	
164 P	490 C	-1:27816333 27816333 C	P
164	491 C	-1:27816332 27816332 C	
164	492 C	-1:27816331 27816331 C	
165 Q	493 C	-1:27816330 27816330 C	Q
165	494 A	-1:27816329 27816329 A	
165	495 G	-1:27816328 27816328 G	
166 G	496 G	-1:27816327 27816327 G	G
166	497 G	-1:27816326 27816326 G	
166	498 G	-1:27816325 27816325 G	
167 A	499 G	-1:27816324 27816324 G	A
167	500 C	-1:27816323 27816323 C	
167	501 C	-1:27816322 27816322 C	
168 F	502 T	-1:27816321 27816321 T	F
168	503 T	-1:27816320 27816320 T	
168	504 T	-1:27816319 27816319 T	
169 L	505 C	-1:27816318 27816318 C	L
169	506 T	-1:27816317 27816317 T	
169	507 C	-1:27816316 27816316 C	
170 I	508 A	-1:27816315 27816315 A	I
170	509 T	-1:27816314 27816314 T	
170	510 T	-1:27816313 27816313 T	
171 R	511 C	-1:27816312 27816312 C	R
171	512 G	-1:27816311 27816311 G	
171	513 G	-1:27816310 27816310 G	
172 E	514 G	-1:27816309 27816309 G	E
172	515 A	-1:27816308 27816308 A	
172	516 A	-1:27816307 27816307 A	
173 S	517 A	-1:27816306 27816306 A	S
173	518 G	-1:27816305 27816305 G	
173	519 C	-1:27816304 27816304 C	
174 E	520 G	-1:27816303 27816303 G	E
174	521 A	-1:27816302 27816302 A	
174	522 G	-1:27816301 27816301 G	
175 T	523 A	-1:27816300 27816300 A	T
175	524 C	-1:27816299 27816299 C	
175	525 C	-1:27816298 27816298 C	
176 T	526 A	-1:27816297 27816297 A	T
176	527 C	-1:27816296 27816296 C	
176	528 C	-1:27816295 27816295 C	
177 K	529 A	-1:27816294 27816294 A	K
177	530 A	-1:27816293 27816293 A	
177	531 A	-1:27816292 27816292 A	
178 G	532 G	-1:27816291 27816291 G	G
178	533 G	-1:27816104 27816104 G	
178	534 T	-1:27816103 27816103 T	
179 A	535 G	-1:27816102 27816102 G	A
179	536 C	-1:27816101 27816101 C	
179	537 C	-1:27816100 27816100 C	
180 Y	538 T	-1:27816099 27816099 T	Y
180	539 A	-1:27816098 27816098 A	
180	540 C	-1:27816097 27816097 C	
181 S	541 T	-1:27816096 27816096 T	S
181	542 C	-1:27816095 27816095 C	
181	543 C	-1:27816094 27816094 C	
182 L	544 C	-1:27816093 27816093 C	L
182	545 T	-1:27816092 27816092 T	
182	546 G	-1:27816091 27816091 G	
183 S	547 T	-1:27816090 27816090 T	S
183	548 C	-1:27816089 27816089 C	
183	549 C	-1:27816088 27816088 C	
184 I	550 A	-1:27816087 27816087 A	I
184	551 T	-1:27816086 27816086 T	
184	552 C	-1:27816085 27816085 C	
185 R	553 C	-1:27816084 27816084 C	R
185	554 G	-1:27816083 27816083 G	
185	555 G	-1:27816082 27816082 G	
186 D	556 G	-1:27816081 27816081 G	D
186	557 A	-1:27816080 27816080 A	
186	558 C	-1:27816079 27816079 C	
187 W	559 T	-1:27816078 27816078 T	W
187	560 G	-1:27816077 27816077 G	
187	561 G	-1:27816076 27816076 G	
188 D	562 G	-1:27816075 27816075 G	D
188	563 A	-1:27816074 27816074 A	
188	564 T	-1:27816073 27816073 T	
189 Q	565 C	-1:27816072 27816072 C	Q
189	566 A	-1:27816071 27816071 A	
189	567 G	-1:27816070 27816070 G	
190 T	568 A	-1:27816069 27816069 A	T
190	569 C	-1:27816068 27816068 C	
190	570 C	-1:27816067 27816067 C	
191 R	571 A	-1:27816066 27816066 A	R
191	572 G	-1:27816065 27816065 G	
191	573 A	-1:27816064 27816064 A	
192 G	574 G	-1:27816063 27816063 G	G
192	575 G	-1:27816062 27816062 G	
192	576 C	-1:27816061 27816061 C	
193 D	577 G	-1:27816060 27816060 G	D
193	578 A	-1:27816059 27816059 A	
193	579 T	-1:27816058 27816058 T	
194 H	580 C	-1:27816057 27816057 C	H
194	581 A	-1:27816056 27816056 A	
194	582 T	-1:27816055 27816055 T	
195 V	583 G	-1:27816054 27816054 G	V
195	584 T	-1:27816053 27816053 T	
195	585 G	-1:27816052 27816052 G	
196 K	586 A	-1:27816051 27816051 A	K
196	587 A	-1:27816050 27816050 A	
196	588 G	-1:27816049 27816049 G	
197 H	589 C	-1:27816048 27816048 C	H
197	590 A	-1:27816047 27816047 A	
197	591 T	-1:27816046 27816046 T	
198 Y	592 T	-1:27816045 27816045 T	Y
198	593 A	-1:27816044 27816044 A	
198	594 C	-1:27816043 27816043 C	
199 K	595 A	-1:27816042 27816042 A	K
199	596 A	-1:27816041 27816041 A	
199	597 G	-1:27816040 27816040 G	
200 I	598 A	-1:27816039 27816039 A	I
200	599 T	-1:27816038 27816038 T	
200	600 C	-1:27816037 27816037 C	
201 R	601 C	-1:27816036 27816036 C	R
201	602 G	-1:27816035 27816035 G	
201	603 C	-1:27816034 27816034 C	
202 K	604 A	-1:27816033 27816033 A	K
202	605 A	-1:27816032 27816032 A	
202	606 A	-1:27816031 27816031 A	
203 L	607 C	-1:27816030 27816030 C	L
203	608 T	-1:27816029 27816029 T	
203	609 G	-1:27816028 27816028 G	
204 D	610 G	-1:27816027 27816027 G	D
204	611 A	-1:27816026 27816026 A	
204	612 C	-1:27816025 27816025 C	
205 M	613 A	-1:27816024 27816024 A	M
205	614 T	-1:27816023 27816023 T	
205	615 G	-1:27816022 27816022 G	
206 G	616 G	-1:27816021 27816021 G	G
206	617 G	-1:27816020 27816020 G	
206	618 C	-1:27816019 27816019 C	
207 G	619 G	-1:27816018 27816018 G	G
207	620 G	-1:27816017 27816017 G	
207	621 C	-1:27816016 27816016 C	
208 Y	622 T	-1:27816015 27816015 T	Y
208	623 A	-1:27816014 27816014 A	
208	624 C	-1:27816013 27816013 C	
209 Y	625 T	-1:27816012 27816012 T	Y
209	626 A	-1:27816011 27816011 A	
209	627 C	-1:27816010 27816010 C	
210 I	628 A	-1:27816009 27816009 A	I
210	629 T	-1:27816008 27816008 T	
210	630 C	-1:27816007 27816007 C	
211 T	631 A	-1:27816006 27816006 A	T
211	632 C	-1:27816005 27816005 C	
211	633 C	-1:27816004 27816004 C	
212 T	634 A	-1:27816003 27816003 A	T
212	635 C	-1:27816002 27816002 C	
212	636 A	-1:27816001 27816001 A	
213 R	637 C	-1:27816000 27816000 C	R
213	638 G	-1:27815999 27815999 G	
213	639 G	-1:27815998 27815998 G	
214 V	640 G	-1:27815997 27815997 G	V
214	641 T	-1:27815996 27815996 T	
214	642 T	-1:27815995 27815995 T	
215 Q	643 C	-1:27815994 27815994 C	Q
215	644 A	-1:27815993 27815993 A	
215	645 G	-1:27815992 27815992 G	
216 F	646 T	-1:27815991 27815991 T	F
216	647 T	-1:27815990 27815990 T	
216	648 C	-1:27815989 27815989 C	
217 N	649 A	-1:27815988 27815988 A	N
217	650 A	-1:27815987 27815987 A	
217	651 C	-1:27815986 27815986 C	
218 S	652 T	-1:27815985 27815985 T	S
218	653 C	-1:27815984 27815984 C	
218	654 G	-1:27815983 27815983 G	
219 V	655 G	-1:27815982 27815982 G	V
219	656 T	-1:27815981 27815981 T	
219	657 G	-1:27815980 27815980 G	
220 Q	658 C	-1:27815979 27815979 C	Q
220	659 A	-1:27815978 27815978 A	
220	660 G	-1:27815977 27815977 G	
221 E	661 G	-1:27815976 27815976 G	E
221	662 A	-1:27815975 27815975 A	
221	663 G	-1:27815974 27815974 G	
222 L	664 C	-1:27815973 27815973 C	L
222	665 T	-1:27815972 27815972 T	
222	666 G	-1:27815971 27815971 G	
223 V	667 G	-1:27815970 27815970 G	V
223	668 T	-1:27815969 27815969 T	
223	669 G	-1:27815968 27815968 G	
224 Q	670 C	-1:27815967 27815967 C	Q
224	671 A	-1:27815966 27815966 A	
224	672 G	-1:27815965 27815965 G	
225 H	673 C	-1:27815964 27815964 C	H
225	674 A	-1:27815963 27815963 A	
225	675 C	-1:27815962 27815962 C	
226 Y	676 T	-1:27815961 27815961 T	Y
226	677 A	-1:27815960 27815960 A	
226	678 C	-1:27815959 27815959 C	
227 M	679 A	-1:27815958 27815958 A	M
227	680 T	-1:27815957 27815957 T	
227	681 G	-1:27815956 27815956 G	
228 E	682 G	-1:27815955 27815955 G	E
228	683 A	-1:27814942 27814942 A	
228	684 G	-1:27814941 27814941 G	
229 V	685 G	-1:27814940 27814940 G	V
229	686 T	-1:27814939 27814939 T	
229	687 G	-1:27814938 27814938 G	
230 N	688 A	-1:27814937 27814937 A	N
230	689 A	-1:27814936 27814936 A	
230	690 T	-1:27814935 27814935 T	
231 D	691 G	-1:27814934 27814934 G	D
231	692 A	-1:27814933 27814933 A	
231	693 C	-1:27814932 27814932 C	
232 G	694 G	-1:27814931 27814931 G	G
232	695 G	-1:27814930 27814930 G	
232	696 G	-1:27814929 27814929 G	
233 L	697 C	-1:27814928 27814928 C	L
233	698 T	-1:27814927 27814927 T	
233	699 G	-1:27814926 27814926 G	
234 C	700 T	-1:27814925 27814925 T	C
234	701 G	-1:27814924 27814924 G	
234	702 C	-1:27814923 27814923 C	
235 N	703 A	-1:27814922 27814922 A	N
235	704 A	-1:27814921 27814921 A	
235	705 C	-1:27814920 27814920 C	
236 L	706 C	-1:27814919 27814919 C	L
236	707 T	-1:27814918 27814918 T	
236	708 G	-1:27814917 27814917 G	
237 L	709 C	-1:27814916 27814916 C	L
237	710 T	-1:27814915 27814915 T	
237	711 C	-1:27814914 27814914 C	
238 I	712 A	-1:27814913 27814913 A	I
238	713 T	-1:27814912 27814912 T	
238	714 C	-1:27814911 27814911 C	
239 A	715 G	-1:27814910 27814910 G	A
239	716 C	-1:27814909 27814909 C	
239	717 G	-1:27814908 27814908 G	
240 P	718 C	-1:27814907 27814907 C	P
240	719 C	-1:27814906 27814906 C	
240	720 C	-1:27814905 27814905 C	
241 C	721 T	-1:27814904 27814904 T	C
241	722 G	-1:27814903 27814903 G	
241	723 C	-1:27814902 27814902 C	
242 T	724 A	-1:27814901 27814901 A	T
242	725 C	-1:27814900 27814900 C	
242	726 C	-1:27814899 27814899 C	
243 I	727 A	-1:27814898 27814898 A	I
243	728 T	-1:27814897 27814897 T	
243	729 C	-1:27814896 27814896 C	
244 M	730 A	-1:27814895 27814895 A	M
244	731 T	-1:27814894 27814894 T	
244	732 G	-1:27814893 27814893 G	
245 K	733 A	-1:27814892 27814892 A	K
245	734 A	-1:27814891 27814891 A	
245	735 G	-1:27814890 27814890 G	
246 P	736 C	-1:27814889 27814889 C	P
246	737 C	-1:27814888 27814888 C	
246	738 G	-1:27814887 27814887 G	
247 Q	739 C	-1:27814886 27814886 C	Q
247	740 A	-1:27814885 27814885 A	
247	741 G	-1:27814884 27814884 G	
248 T	742 A	-1:27814883 27814883 A	T
248	743 C	-1:27814882 27814882 C	
248	744 G	-1:27814881 27814881 G	
249 L	745 C	-1:27814880 27814880 C	L
249	746 T	-1:27814879 27814879 T	
249	747 G	-1:27814878 27814878 G	
250 G	748 G	-1:27814877 27814877 G	G
250	749 G	-1:27814876 27814876 G	
250	750 C	-1:27814875 27814875 C	
251 L	751 C	-1:27814874 27814874 C	L
251	752 T	-1:27814873 27814873 T	
251	753 G	-1:27814872 27814872 G	
252 A	754 G	-1:27814871 27814871 G	A
252	755 C	-1:27814870 27814870 C	
252	756 C	-1:27814869 27814869 C	
253 K	757 A	-1:27814868 27814868 A	K
253	758 A	-1:27814867 27814867 A	
253	759 G	-1:27814866 27814866 G	
254 D	760 G	-1:27814865 27814865 G	D
254	761 A	-1:27814864 27814864 A	
254	762 C	-1:27814863 27814863 C	
255 A	763 G	-1:27814862 27814862 G	A
255	764 C	-1:27814861 27814861 C	
255	765 C	-1:27814860 27814860 C	
256 W	766 T	-1:27814859 27814859 T	W
256	767 G	-1:27814858 27814858 G	
256	768 G	-1:27814857 27814857 G	
257 E	769 G	-1:27814856 27814856 G	E
257	770 A	-1:27814855 27814855 A	
257	771 G	-1:27814854 27814854 G	
258 I	772 A	-1:27814853 27814853 A	I
258	773 T	-1:27814852 27814852 T	
258	774 C	-1:27814851 27814851 C	
259 S	775 A	-1:27814850 27814850 A	S
259	776 G	-1:27814849 27814849 G	
259	777 C	-1:27814848 27814848 C	
260 R	778 C	-1:27814847 27814847 C	R
260	779 G	-1:27814846 27814846 G	
260	780 C	-1:27814845 27814845 C	
261 S	781 A	-1:27814844 27814844 A	S
261	782 G	-1:27814843 27814843 G	
261	783 C	-1:27814842 27814842 C	
262 S	784 T	-1:27814841 27814841 T	S
262	785 C	-1:27814840 27814840 C	
262	786 C	-1:27814839 27814839 C	
263 I	787 A	-1:27814838 27814838 A	I
263	788 T	-1:27814837 27814837 T	
263	789 C	-1:27814836 27814836 C	
264 T	790 A	-1:27814835 27814835 A	T
264	791 C	-1:27814834 27814834 C	
264	792 G	-1:27814833 27814833 G	
265 L	793 C	-1:27814832 27814832 C	L
265	794 T	-1:27814831 27814831 T	
265	795 G	-1:27814830 27814830 G	
266 E	796 G	-1:27814829 27814829 G	E
266	797 A	-1:27814828 27814828 A	
266	798 G	-1:27814827 27814827 G	
267 R	799 C	-1:27814826 27814826 C	R
267	800 G	-1:27814825 27814825 G	
267	801 C	-1:27814824 27814824 C	
268 R	802 C	-1:27814823 27814823 C	R
268	803 G	-1:27814822 27814822 G	
268	804 G	-1:27814821 27814821 G	
269 L	805 C	-1:27814820 27814820 C	L
269	806 T	-1:27814819 27814819 T	
269	807 G	-1:27814818 27814818 G	
270 G	808 G	-1:27814817 27814817 G	G
270	809 G	-1:27814816 27814816 G	
270	810 C	-1:27814815 27814815 C	
271 T	811 A	-1:27814814 27814814 A	T
271	812 C	-1:27814813 27814813 C	
271	813 C	-1:27814812 27814812 C	
272 G	814 G	-1:27814811 27814811 G	G
272	815 G	-1:27814810 27814810 G	
272	816 C	-1:27814809 27814809 C	
273 C	817 T	-1:27814808 27814808 T	C
273	818 G	-1:27814807 27814807 G	
273	819 C	-1:27814806 27814806 C	
274 F	820 T	-1:27814805 27814805 T	F
274	821 T	-1:27814804 27814804 T	
274	822 C	-1:27814803 27814803 C	
275 G	823 G	-1:27814802 27814802 G	G
275	824 G	-1:27814801 27814801 G	
275	825 G	-1:27814800 27814800 G	
276 D	826 G	-1:27814799 27814799 G	D
276	827 A	-1:27814798 27814798 A	
276	828 T	-1:27814797 27814797 T	
277 V	829 G	-1:27814796 27814796 G	V
277	830 T	-1:27814795 27814795 T	
277	831 G	-1:27814794 27814794 G	
278 W	832 T	-1:27814793 27814793 T	W
278	833 G	-1:27814792 27814792 G	
278	834 G	-1:27814791 27814791 G	
279 L	835 C	-1:27814790 27814790 C	L
279	836 T	-1:27814789 27814789 T	
279	837 G	-1:27814788 27814788 G	
280 G	838 G	-1:27814787 27814787 G	G
280	839 G	-1:27814711 27814711 G	
280	840 C	-1:27814710 27814710 C	
281 T	841 A	-1:27814709 27814709 A	T
281	842 C	-1:27814708 27814708 C	
281	843 G	-1:27814707 27814707 G	
282 W	844 T	-1:27814706 27814706 T	W
282	845 G	-1:27814705 27814705 G	
282	846 G	-1:27814704 27814704 G	
283 N	847 A	-1:27814703 27814703 A	N
283	848 A	-1:27814702 27814702 A	
283	849 C	-1:27814701 27814701 C	
284 G	850 G	-1:27814700 27814700 G	G
284	851 G	-1:27814699 27814699 G	
284	852 C	-1:27814698 27814698 C	
285 S	853 A	-1:27814697 27814697 A	S
285	854 G	-1:27814696 27814696 G	
285	855 C	-1:27814695 27814695 C	
286 T	856 A	-1:27814694 27814694 A	T
286	857 C	-1:27814693 27814693 C	
286	858 T	-1:27814692 27814692 T	
287 K	859 A	-1:27814691 27814691 A	K
287	860 A	-1:27814690 27814690 A	
287	861 G	-1:27814689 27814689 G	
288 V	862 G	-1:27814688 27814688 G	V
288	863 T	-1:27814687 27814687 T	
288	864 G	-1:27814686 27814686 G	
289 A	865 G	-1:27814685 27814685 G	A
289	866 C	-1:27814684 27814684 C	
289	867 G	-1:27814683 27814683 G	
290 V	868 G	-1:27814682 27814682 G	V
290	869 T	-1:27814681 27814681 T	
290	870 G	-1:27814680 27814680 G	
291 K	871 A	-1:27814679 27814679 A	K
291	872 A	-1:27814678 27814678 A	
291	873 G	-1:27814677 27814677 G	
292 T	874 A	-1:27814676 27814676 A	T
292	875 C	-1:27814675 27814675 C	
292	876 G	-1:27814674 27814674 G	
293 L	877 C	-1:27814673 27814673 C	L
293	878 T	-1:27814672 27814672 T	
293	879 G	-1:27814671 27814671 G	
294 K	880 A	-1:27814670 27814670 A	K
294	881 A	-1:27814669 27814669 A	
294	882 G	-1:27814668 27814668 G	
295 P	883 C	-1:27814667 27814667 C	P
295	884 C	-1:27814666 27814666 C	
295	885 G	-1:27814665 27814665 G	
296 G	886 G	-1:27814664 27814664 G	G
296	887 G	-1:27814663 27814663 G	
296	888 C	-1:27814662 27814662 C	
297 T	889 A	-1:27814661 27814661 A	T
297	890 C	-1:27814660 27814660 C	
297	891 C	-1:27814659 27814659 C	
298 M	892 A	-1:27814658 27814658 A	M
298	893 T	-1:27814657 27814657 T	
298	894 G	-1:27814656 27814656 G	
299 S	895 T	-1:27814655 27814655 T	S
299	896 C	-1:27814654 27814654 C	
299	897 C	-1:27814653 27814653 C	
300 P	898 C	-1:27814652 27814652 C	P
300	899 C	-1:27814651 27814651 C	
300	900 G	-1:27814650 27814650 G	
301 K	901 A	-1:27814649 27814649 A	K
301	902 A	-1:27814648 27814648 A	
301	903 G	-1:27814647 27814647 G	
302 A	904 G	-1:27814646 27814646 G	A
302	905 C	-1:27814645 27814645 C	
302	906 C	-1:27814644 27814644 C	
303 F	907 T	-1:27814643 27814643 T	F
303	908 T	-1:27814642 27814642 T	
303	909 C	-1:27814641 27814641 C	
304 L	910 C	-1:27814640 27814640 C	L
304	911 T	-1:27814639 27814639 T	
304	912 G	-1:27814638 27814638 G	
305 E	913 G	-1:27814637 27814637 G	E
305	914 A	-1:27814636 27814636 A	
305	915 G	-1:27814635 27814635 G	
306 E	916 G	-1:27814634 27814634 G	E
306	917 A	-1:27814633 27814633 A	
306	918 G	-1:27814632 27814632 G	
307 A	919 G	-1:27814631 27814631 G	A
307	920 C	-1:27814630 27814630 C	
307	921 G	-1:27814629 27814629 G	
308 Q	922 C	-1:27814628 27814628 C	Q
308	923 A	-1:27814627 27814627 A	
308	924 G	-1:27814626 27814626 G	
309 V	925 G	-1:27814625 27814625 G	V
309	926 T	-1:27814624 27814624 T	
309	927 C	-1:27814623 27814623 C	
310 M	928 A	-1:27814622 27814622 A	M
310	929 T	-1:27814621 27814621 T	
310	930 G	-1:27814620 27814620 G	
311 K	931 A	-1:27814619 27814619 A	K
311	932 A	-1:27814618 27814618 A	
311	933 G	-1:27814617 27814617 G	
312 L	934 C	-1:27814616 27814616 C	L
312	935 T	-1:27814615 27814615 T	
312	936 G	-1:27814614 27814614 G	
313 L	937 C	-1:27814613 27814613 C	L
313	938 T	-1:27814612 27814612 T	
313	939 G	-1:27814611 27814611 G	
314 R	940 C	-1:27814610 27814610 C	R
314	941 G	-1:27814609 27814609 G	
314	942 G	-1:27814608 27814608 G	
315 H	943 C	-1:27814607 27814607 C	H
315	944 A	-1:27814606 27814606 A	
315	945 C	-1:27814605 27814605 C	
316 D	946 G	-1:27814604 27814604 G	D
316	947 A	-1:27814603 27814603 A	
316	948 C	-1:27814602 27814602 C	
317 K	949 A	-1:27814601 27814601 A	K
317	950 A	-1:27814600 27814600 A	
317	951 G	-1:27814599 27814599 G	
318 L	952 C	-1:27814598 27814598 C	L
318	953 T	-1:27814597 27814597 T	
318	954 G	-1:27814596 27814596 G	
319 V	955 G	-1:27814595 27814595 G	V
319	956 T	-1:27814594 27814594 T	
319	957 G	-1:27814593 27814593 G	
320 Q	958 C	-1:27814592 27814592 C	Q
320	959 A	-1:27814591 27814591 A	
320	960 G	-1:27814590 27814590 G	
321 L	961 C	-1:27814589 27814589 C	L
321	962 T	-1:27814588 27814588 T	
321	963 G	-1:27814587 27814587 G	
322 Y	964 T	-1:27814586 27814586 T	Y
322	965 A	-1:27814585 27814585 A	
322	966 C	-1:27814584 27814584 C	
323 A	967 G	-1:27814583 27814583 G	A
323	968 C	-1:27814582 27814582 C	
323	969 C	-1:27814581 27814581 C	
324 V	970 G	-1:27814580 27814580 G	V
324	971 T	-1:27814579 27814579 T	
324	972 G	-1:27814578 27814578 G	
325 V	973 G	-1:27814577 27814577 G	V
325	974 T	-1:27814576 27814576 T	
325	975 G	-1:27814575 27814575 G	
326 S	976 T	-1:27814574 27814574 T	S
326	977 C	-1:27814573 27814573 C	
326	978 G	-1:27814572 27814572 G	
327 E	979 G	-1:27814571 27814571 G	E
327	980 A	-1:27814570 27814570 A	
327	981 G	-1:27814569 27814569 G	
328 E	982 G	-1:27814568 27814568 G	E
328	983 A	-1:27814567 27814567 A	
328	984 G	-1:27814566 27814566 G	
329 P	985 C	-1:27814565 27814565 C	P
329	986 C	-1:27814564 27814564 C	
329	987 C	-1:27814563 27814563 C	
330 I	988 A	-1:27814562 27814562 A	I
330	989 T	-1:27814561 27814561 T	
330	990 C	-1:27814560 27814560 C	
331 Y	991 T	-1:27814559 27814559 T	Y
331	992 A	-1:27814558 27814558 A	
331	993 C	-1:27814557 27814557 C	
332 I	994 A	-1:27814556 27814556 A	I
332	995 T	-1:27814555 27814555 T	
332	996 C	-1:27814554 27814554 C	
333 V	997 G	-1:27814553 27814553 G	V
333	998 T	-1:27814552 27814552 T	
333	999 G	-1:27814551 27814551 G	
334 T	1000 A	-1:27814550 27814550 A	T
334	1001 C	-1:27814549 27814549 C	
334	1002 C	-1:27814548 27814548 C	
335 E	1003 G	-1:27814547 27814547 G	E
335	1004 A	-1:27814546 27814546 A	
335	1005 G	-1:27814545 27814545 G	
336 F	1006 T	-1:27814544 27814544 T	F
336	1007 T	-1:27814543 27814543 T	
336	1008 C	-1:27814542 27814542 C	
337 M	1009 A	-1:27814541 27814541 A	M
337	1010 T	-1:27814540 27814540 T	
337	1011 G	-1:27814539 27814539 G	
338 C	1012 T	-1:27814538 27814538 T	C
338	1013 G	-1:27814537 27814537 G	
338	1014 T	-1:27814536 27814536 T	
339 H	1015 C	-1:27814535 27814535 C	H
339	1016 A	-1:27814534 27814534 A	
339	1017 C	-1:27814533 27814533 C	
340 G	1018 G	-1:27814532 27814532 G	G
340	1019 G	-1:27814024 27814024 G	
340	1020 C	-1:27814023 27814023 C	
341 S	1021 A	-1:27814022 27814022 A	S
341	1022 G	-1:27814021 27814021 G	
341	1023 C	-1:27814020 27814020 C	
342 L	1024 T	-1:27814019 27814019 T	L
342	1025 T	-1:27814018 27814018 T	
342	1026 G	-1:27814017 27814017 G	
343 L	1027 C	-1:27814016 27814016 C	L
343	1028 T	-1:27814015 27814015 T	
343	1029 G	-1:27814014 27814014 G	
344 D	1030 G	-1:27814013 27814013 G	D
344	1031 A	-1:27814012 27814012 A	
344	1032 T	-1:27814011 27814011 T	
345 F	1033 T	-1:27814010 27814010 T	F
345	1034 T	-1:27814009 27814009 T	
345	1035 T	-1:27814008 27814008 T	
346 L	1036 C	-1:27814007 27814007 C	L
346	1037 T	-1:27814006 27814006 T	
346	1038 C	-1:27814005 27814005 C	
347 K	1039 A	-1:27814004 27814004 A	K
347	1040 A	-1:27814003 27814003 A	
347	1041 G	-1:27814002 27814002 G	
348 N	1042 A	-1:27814001 27814001 A	N
348	1043 A	-1:27814000 27814000 A	
348	1044 C	-1:27813999 27813999 C	
349 P	1045 C	-1:27813998 27813998 C	P
349	1046 C	-1:27813997 27813997 C	
349	1047 A	-1:27813996 27813996 A	
350 E	1048 G	-1:27813995 27813995 G	E
350	1049 A	-1:27813994 27813994 A	
350	1050 G	-1:27813993 27813993 G	
351 G	1051 G	-1:27813992 27813992 G	G
351	1052 G	-1:27813991 27813991 G	
351	1053 C	-1:27813990 27813990 C	
352 Q	1054 C	-1:27813989 27813989 C	Q
352	1055 A	-1:27813988 27813988 A	
352	1056 G	-1:27813987 27813987 G	
353 D	1057 G	-1:27813986 27813986 G	D
353	1058 A	-1:27813985 27813985 A	
353	1059 T	-1:27813984 27813984 T	
354 L	1060 T	-1:27813983 27813983 T	L
354	1061 T	-1:27813982 27813982 T	
354	1062 G	-1:27813981 27813981 G	
355 R	1063 A	-1:27813980 27813980 A	R
355	1064 G	-1:27813979 27813979 G	
355	1065 G	-1:27813978 27813978 G	
356 L	1066 C	-1:27813977 27813977 C	L
356	1067 T	-1:27813976 27813976 T	
356	1068 G	-1:27813975 27813975 G	
357 P	1069 C	-1:27813974 27813974 C	P
357	1070 C	-1:27813973 27813973 C	
357	1071 C	-1:27813972 27813972 C	
358 Q	1072 C	-1:27813971 27813971 C	Q
358	1073 A	-1:27813970 27813970 A	
358	1074 A	-1:27813969 27813969 A	
359 L	1075 T	-1:27813968 27813968 T	L
359	1076 T	-1:27813967 27813967 T	
359	1077 G	-1:27813966 27813966 G	
360 V	1078 G	-1:27813965 27813965 G	V
360	1079 T	-1:27813964 27813964 T	
360	1080 G	-1:27813963 27813963 G	
361 D	1081 G	-1:27813962 27813962 G	D
361	1082 A	-1:27813961 27813961 A	
361	1083 C	-1:27813960 27813960 C	
362 M	1084 A	-1:27813959 27813959 A	M
362	1085 T	-1:27813958 27813958 T	
362	1086 G	-1:27813957 27813957 G	
363 A	1087 G	-1:27813956 27813956 G	A
363	1088 C	-1:27813955 27813955 C	
363	1089 A	-1:27813954 27813954 A	
364 A	1090 G	-1:27813953 27813953 G	A
364	1091 C	-1:27813952 27813952 C	
364	1092 C	-1:27813951 27813951 C	
365 Q	1093 C	-1:27813950 27813950 C	Q
365	1094 A	-1:27813949 27813949 A	
365	1095 G	-1:27813948 27813948 G	
366 V	1096 G	-1:27813681 27813681 G	V
366	1097 T	-1:27813680 27813680 T	
366	1098 A	-1:27813679 27813679 A	
367 A	1099 G	-1:27813678 27813678 G	A
367	1100 C	-1:27813677 27813677 C	
367	1101 T	-1:27813676 27813676 T	
368 E	1102 G	-1:27813675 27813675 G	E
368	1103 A	-1:27813674 27813674 A	
368	1104 G	-1:27813673 27813673 G	
369 G	1105 G	-1:27813672 27813672 G	G
369	1106 G	-1:27813671 27813671 G	
369	1107 C	-1:27813670 27813670 C	
370 M	1108 A	-1:27813669 27813669 A	M
370	1109 T	-1:27813668 27813668 T	
370	1110 G	-1:27813667 27813667 G	
371 A	1111 G	-1:27813666 27813666 G	A
371	1112 C	-1:27813665 27813665 C	
371	1113 C	-1:27813664 27813664 C	
372 Y	1114 T	-1:27813663 27813663 T	Y
372	1115 A	-1:27813662 27813662 A	
372	1116 C	-1:27813661 27813661 C	
373 M	1117 A	-1:27813660 27813660 A	M
373	1118 T	-1:27813659 27813659 T	
373	1119 G	-1:27813658 27813658 G	
374 E	1120 G	-1:27813657 27813657 G	E
374	1121 A	-1:27813656 27813656 A	
374	1122 A	-1:27813655 27813655 A	
375 R	1123 C	-1:27813654 27813654 C	R
375	1124 G	-1:27813653 27813653 G	
375	1125 C	-1:27813652 27813652 C	
376 M	1126 A	-1:27813651 27813651 A	M
376	1127 T	-1:27813650 27813650 T	
376	1128 G	-1:27813649 27813649 G	
377 N	1129 A	-1:27813648 27813648 A	N
377	1130 A	-1:27813647 27813647 A	
377	1131 C	-1:27813646 27813646 C	
378 Y	1132 T	-1:27813645 27813645 T	Y
378	1133 A	-1:27813644 27813644 A	
378	1134 C	-1:27813643 27813643 C	
379 I	1135 A	-1:27813642 27813642 A	I
379	1136 T	-1:27813641 27813641 T	
379	1137 T	-1:27813640 27813640 T	
380 H	1138 C	-1:27813639 27813639 C	H
380	1139 A	-1:27813638 27813638 A	
380	1140 C	-1:27813637 27813637 C	
381 R	1141 C	-1:27813636 27813636 C	R
381	1142 G	-1:27813635 27813635 G	
381	1143 C	-1:27813634 27813634 C	
382 D	1144 G	-1:27813633 27813633 G	D
382	1145 A	-1:27813632 27813632 A	
382	1146 C	-1:27813631 27813631 C	
383 L	1147 C	-1:27813630 27813630 C	L
383	1148 T	-1:27813629 27813629 T	
383	1149 G	-1:27813628 27813628 G	
384 R	1150 A	-1:27813627 27813627 A	R
384	1151 G	-1:27813626 27813626 G	
384	1152 G	-1:27813625 27813625 G	
385 A	1153 G	-1:27813624 27813624 G	A
385	1154 C	-1:27813623 27813623 C	
385	1155 A	-1:27813622 27813622 A	
386 A	1156 G	-1:27813621 27813621 G	A
386	1157 C	-1:27813620 27813620 C	
386	1158 C	-1:27813619 27813619 C	
387 N	1159 A	-1:27813618 27813618 A	N
387	1160 A	-1:27813617 27813617 A	
387	1161 C	-1:27813616 27813616 C	
388 I	1162 A	-1:27813615 27813615 A	I
388	1163 T	-1:27813614 27813614 T	
388	1164 C	-1:27813613 27813613 C	
389 L	1165 C	-1:27813612 27813612 C	L
389	1166 T	-1:27813611 27813611 T	
389	1167 G	-1:27813610 27813610 G	
390 V	1168 G	-1:27813609 27813609 G	V
390	1169 T	-1:27813608 27813608 T	
390	1170 T	-1:27813607 27813607 T	
391 G	1171 G	-1:27813606 27813606 G	G
391	1172 G	-1:27813605 27813605 G	
391	1173 G	-1:27813604 27813604 G	
392 E	1174 G	-1:27813603 27813603 G	E
392	1175 A	-1:27813602 27813602 A	
392	1176 G	-1:27813601 27813601 G	
393 R	1177 C	-1:27813600 27813600 C	R
393	1178 G	-1:27813599 27813599 G	
393	1179 G	-1:27813598 27813598 G	
394 L	1180 C	-1:27813597 27813597 C	L
394	1181 T	-1:27813596 27813596 T	
394	1182 G	-1:27813595 27813595 G	
395 A	1183 G	-1:27813594 27813594 G	A
395	1184 C	-1:27813593 27813593 C	
395	1185 G	-1:27813592 27813592 G	
396 C	1186 T	-1:27813591 27813591 T	C
396	1187 G	-1:27813590 27813590 G	
396	1188 C	-1:27813589 27813589 C	
397 K	1189 A	-1:27813588 27813588 A	K
397	1190 A	-1:27813587 27813587 A	
397	1191 G	-1:27813586 27813586 G	
398 I	1192 A	-1:27813585 27813585 A	I
398	1193 T	-1:27813584 27813584 T	
398	1194 C	-1:27813583 27813583 C	
399 A	1195 G	-1:27813582 27813582 G	A
399	1196 C	-1:27813581 27813581 C	
399	1197 A	-1:27813580 27813580 A	
400 D	1198 G	-1:27813579 27813579 G	D
400	1199 A	-1:27813578 27813578 A	
400	1200 C	-1:27813577 27813577 C	
401 F	1201 T	-1:27813576 27813576 T	F
401	1202 T	-1:27813575 27813575 T	
401	1203 T	-1:27813574 27813574 T	
402 G	1204 G	-1:27813573 27813573 G	G
402	1205 G	-1:27813572 27813572 G	
402	1206 C	-1:27813571 27813571 C	
403 L	1207 T	-1:27813570 27813570 T	L
403	1208 T	-1:27813569 27813569 T	
403	1209 G	-1:27813568 27813568 G	
404 A	1210 G	-1:27813567 27813567 G	A
404	1211 C	-1:27813566 27813566 C	
404	1212 G	-1:27813565 27813565 G	
405 R	1213 C	-1:27813564 27813564 C	R
405	1214 G	-1:27813563 27813563 G	
405	1215 T	-1:27813562 27813562 T	
406 L	1216 C	-1:27813561 27813561 C	L
406	1217 T	-1:27813560 27813560 T	
406	1218 C	-1:27813559 27813559 C	
407 I	1219 A	-1:27813558 27813558 A	I
407	1220 T	-1:27813557 27813557 T	
407	1221 C	-1:27813556 27813556 C	
408 K	1222 A	-1:27813555 27813555 A	K
408	1223 A	-1:27813554 27813554 A	
408	1224 G	-1:27813553 27813553 G	
409 D	1225 G	-1:27813552 27813552 G	D
409	1226 A	-1:27813551 27813551 A	
409	1227 C	-1:27813550 27813550 C	
410 D	1228 G	-1:27813549 27813549 G	D
410	1229 A	-1:27813548 27813548 A	
410	1230 T	-1:27813547 27813547 T	
411 E	1231 G	-1:27813546 27813546 G	E
411	1232 A	-1:27813545 27813545 A	
411	1233 G	-1:27813544 27813544 G	
412 Y	1234 T	-1:27813543 27813543 T	Y
412	1235 A	-1:27813542 27813542 A	
412	1236 C	-1:27813541 27813541 C	
413 N	1237 A	-1:27813540 27813540 A	N
413	1238 A	-1:27813539 27813539 A	
413	1239 C	-1:27813538 27813538 C	
414 P	1240 C	-1:27813537 27813537 C	P
414	1241 C	-1:27813536 27813536 C	
414	1242 C	-1:27813535 27813535 C	
415 C	1243 T	-1:27813534 27813534 T	C
415	1244 G	-1:27813533 27813533 G	
415	1245 C	-1:27813532 27813532 C	
416 Q	1246 C	-1:27813531 27813531 C	Q
416	1247 A	-1:27813530 27813530 A	
416	1248 A	-1:27813529 27813529 A	
>ENSP00000363117 
1 M	1 A	-1:27823014 27823014 A	M
1	2 T	-1:27823013 27823013 T	
1	3 G	-1:27823012 27823012 G	
2 G	4 G	-1:27823011 27823011 G	G
2	5 G	-1:27823010 27823010 G	
2	6 C	-1:27823009 27823009 C	
3 C	7 T	-1:27823008 27823008 T	C
3	8 G	-1:27823007 27823007 G	
3	9 T	-1:27823006 27823006 T	
4 V	10 G	-1:27823005 27823005 G	V
4	11 T	-1:27823004 27823004 T	
4	12 G	-1:27823003 27823003 G	
5 F	13 T	-1:27823002 27823002 T	F
5	14 T	-1:27823001 27823001 T	
5	15 C	-1:27823000 27823000 C	
6 C	16 T	-1:27822999 27822999 T	C
6	17 G	-1:27822998 27822998 G	
6	18 C	-1:27822997 27822997 C	
7 K	19 A	-1:27822996 27822996 A	K
7	20 A	-1:27822995 27822995 A	
7	21 G	-1:27822994 27822994 G	
8 K	22 A	-1:27822993 27822993 A	K
8	23 A	-1:27822992 27822992 A	
8	24 A	-1:27822991 27822991 A	
9 L	25 T	-1:27822990 27822990 T	L
9	26 T	-1:27822989 27822989 T	
9	27 G	-1:27822988 27822988 G	
10 E	28 G	-1:27822987 27822987 G	E
10	29 A	-1:27822986 27822986 A	
10	30 G	-1:27822985 27822985 G	
11 P	31 C	-1:27822984 27822984 C	P
11	32 C	-1:27822983 27822983 C	
11	33 G	-1:27822982 27822982 G	
12 V	34 G	-1:27822981 27822981 G	V
12	35 T	-1:27822980 27822980 T	
12	36 G	-1:27822979 27822979 G	
13 A	37 G	-1:27822978 27822978 G	A
13	38 C	-1:27822977 27822977 C	
13	39 C	-1:27822976 27822976 C	
14 T	40 A	-1:27822975 27822975 A	T
14	41 C	-1:27822974 27822974 C	
14	42 G	-1:27822973 27822973 G	
15 A	43 G	-1:27822972 27822972 G	A
15	44 C	-1:27822971 27822971 C	
15	45 C	-1:27822970 27822970 C	
16 K	46 A	-1:27822969 27822969 A	K
16	47 A	-1:27822968 27822968 A	
16	48 G	-1:27822967 27822967 G	
17 E	49 G	-1:27822966 27822966 G	E
17	50 A	-1:27822965 27822965 A	
17	51 G	-1:27822964 27822964 G	
18 D	52 G	-1:27822963 27822963 G	D
18	53 A	-1:27822962 27822962 A	
18	54 T	-1:27822961 27822961 T	
19 A	55 G	-1:27822960 27822960 G	A
19	56 C	-1:27822959 27822959 C	
19	57 T	-1:27822958 27822958 T	
20 G	58 G	-1:27822957 27822957 G	G
20	59 G	-1:27822956 27822956 G	
20	60 C	-1:27822955 27822955 C	
21 L	61 C	-1:27822954 27822954 C	L
21	62 T	-1:27822953 27822953 T	
21	63 G	-1:27822952 27822952 G	
22 E	64 G	-1:27822951 27822951 G	E
22	65 A	-1:27822950 27822950 A	
22	66 A	-1:27822949 27822949 A	
23 G	67 G	-1:27822948 27822948 G	G
23	68 G	-1:27822947 27822947 G	
23	69 G	-1:27822946 27822946 G	
24 D	70 G	-1:27822945 27822945 G	D
24	71 A	-1:27822944 27822944 A	
24	72 C	-1:27822943 27822943 C	
25 F	73 T	-1:27822942 27822942 T	F
25	74 T	-1:27822941 27822941 T	
25	75 C	-1:27822940 27822940 C	
26 R	76 A	-1:27822939 27822939 A	R
26	77 G	-1:27822938 27822938 G	
26	78 A	-1:27822937 27822937 A	
27 S	79 A	-1:27822936 27822936 A	S
27	80 G	-1:27822935 27822935 G	
27	81 C	-1:27822934 27822934 C	
28 Y	82 T	-1:27822933 27822933 T	Y
28	83 A	-1:27822932 27822932 A	
28	84 C	-1:27822931 27822931 C	
29 G	85 G	-1:27822930 27822930 G	G
29	86 G	-1:27822929 27822929 G	
29	87 G	-1:27822928 27822928 G	
30 A	88 G	-1:27822927 27822927 G	A
30	89 C	-1:27822926 27822926 C	
30	90 A	-1:27822925 27822925 A	
31 A	91 G	-1:27822924 27822924 G	A
31	92 C	-1:27822923 27822923 C	
31	93 A	-1:27822922 27822922 A	
32 D	94 G	-1:27822921 27822921 G	D
32	95 A	-1:27822920 27822920 A	
32	96 C	-1:27822919 27822919 C	
33 H	97 C	-1:27822918 27822918 C	H
33	98 A	-1:27822917 27822917 A	
33	99 C	-1:27822916 27822916 C	
34 Y	100 T	-1:27822915 27822915 T	Y
34	101 A	-1:27822914 27822914 A	
34	102 T	-1:27822913 27822913 T	
35 G	103 G	-1:27822912 27822912 G	G
35	104 G	-1:27822911 27822911 G	
35	105 G	-1:27822910 27822910 G	
36 P	106 C	-1:27822909 27822909 C	P
36	107 C	-1:27822908 27822908 C	
36	108 T	-1:27822907 27822907 T	
37 D	109 G	-1:27822906 27822906 G	D
37	110 A	-1:27822905 27822905 A	
37	111 C	-1:27822904 27822904 C	
38 P	112 C	-1:27822903 27822903 C	P
38	113 C	-1:27822902 27822902 C	
38	114 C	-1:27822901 27822901 C	
39 T	115 A	-1:27822900 27822900 A	T
39	116 C	-1:27822899 27822899 C	
39	117 T	-1:27822898 27822898 T	
40 K	118 A	-1:27822897 27822897 A	K
40	119 A	-1:27822896 27822896 A	
40	120 G	-1:27822895 27822895 G	
41 A	121 G	-1:27822894 27822894 G	A
41	122 C	-1:27822893 27822893 C	
41	123 C	-1:27822892 27822892 C	
42 R	124 C	-1:27822891 27822891 C	R
42	125 G	-1:27822890 27822890 G	
42	126 G	-1:27822889 27822889 G	
43 P	127 C	-1:27822888 27822888 C	P
43	128 C	-1:27822887 27822887 C	
43	129 T	-1:27822886 27822886 T	
44 A	130 G	-1:27822885 27822885 G	A
44	131 C	-1:27822884 27822884 C	
44	132 A	-1:27822883 27822883 A	
45 S	133 T	-1:27822882 27822882 T	S
45	134 C	-1:27822881 27822881 C	
45	135 C	-1:27822880 27822880 C	
46 S	136 T	-1:27822879 27822879 T	S
46	137 C	-1:27822878 27822878 C	
46	138 A	-1:27822877 27822877 A	
47 F	139 T	-1:27822876 27822876 T	F
47	140 T	-1:27822875 27822875 T	
47	141 T	-1:27822874 27822874 T	
48 A	142 G	-1:27822873 27822873 G	A
48	143 C	-1:27822872 27822872 C	
48	144 C	-1:27822871 27822871 C	
49 H	145 C	-1:27822870 27822870 C	H
49	146 A	-1:27822869 27822869 A	
49	147 C	-1:27822868 27822868 C	
50 I	148 A	-1:27822867 27822867 A	I
50	149 T	-1:27822866 27822866 T	
50	150 C	-1:27822865 27822865 C	
51 P	151 C	-1:27822864 27822864 C	P
51	152 C	-1:27822863 27822863 C	
51	153 C	-1:27822862 27822862 C	
52 N	154 A	-1:27822861 27822861 A	N
52	155 A	-1:27822860 27822860 A	
52	156 C	-1:27822859 27822859 C	
53 Y	157 T	-1:27822858 27822858 T	Y
53	158 A	-1:27822857 27822857 A	
53	159 C	-1:27822856 27822856 C	
54 S	160 A	-1:27822855 27822855 A	S
54	161 G	-1:27822854 27822854 G	
54	162 C	-1:27822853 27822853 C	
55 N	163 A	-1:27822852 27822852 A	N
55	164 A	-1:27822851 27822851 A	
55	165 C	-1:27822850 27822850 C	
56 F	166 T	-1:27822849 27822849 T	F
56	167 T	-1:27822848 27822848 T	
56	168 C	-1:27822847 27822847 C	
57 S	169 T	-1:27822846 27822846 T	S
57	170 C	-1:27822845 27822845 C	
57	171 C	-1:27822844 27822844 C	
58 S	172 T	-1:27822843 27822843 T	S
58	173 C	-1:27822842 27822842 C	
58	174 T	-1:27822841 27822841 T	
59 Q	175 C	-1:27822840 27822840 C	Q
59	176 A	-1:27822839 27822839 A	
59	177 G	-1:27822838 27822838 G	
60 A	178 G	-1:27822837 27822837 G	A
60	179 C	-1:27822836 27822836 C	
60	180 C	-1:27822835 27822835 C	
61 I	181 A	-1:27822834 27822834 A	I
61	182 T	-1:27822833 27822833 T	
61	183 C	-1:27822832 27822832 C	
62 N	184 A	-1:27822831 27822831 A	N
62	185 A	-1:27822830 27822830 A	
62	186 C	-1:27822829 27822829 C	
63 P	187 C	-1:27822828 27822828 C	P
63	188 C	-1:27822827 27822827 C	
63	189 T	-1:27822826 27822826 T	
64 G	190 G	-1:27822825 27822825 G	G
64	191 G	-1:27822824 27822824 G	
64	192 C	-1:27822823 27822823 C	
65 F	193 T	-1:27822822 27822822 T	F
65	194 T	-1:27822821 27822821 T	
65	195 C	-1:27822820 27822820 C	
66 L	196 C	-1:27822819 27822819 C	L
66	197 T	-1:27822818 27822818 T	
66	198 T	-1:27822817 27822817 T	
67 D	199 G	-1:27822816 27822816 G	D
67	200 A	-1:27822815 27822815 A	
67	201 T	-1:27822814 27822814 T	
68 S	202 A	-1:27822813 27822813 A	S
68	203 G	-1:27822812 27822812 G	
68	204 T	-1:27822811 27822811 T	
69 G	205 G	-1:27822810 27822810 G	G
69	206 G	-1:27822809 27822809 G	
69	207 C	-1:27822808 27822808 C	
70 T	208 A	-1:27822807 27822807 A	T
70	209 C	-1:27822806 27822806 C	
70	210 C	-1:27822805 27822805 C	
71 I	211 A	-1:27822804 27822804 A	I
71	212 T	-1:27822803 27822803 T	
71	213 C	-1:27822802 27822802 C	
72 R	214 A	-1:27822801 27822801 A	R
72	215 G	-1:27822800 27822800 G	
72	216 G	-1:27822799 27822799 G	
73 G	217 G	-1:27822798 27822798 G	G
73	218 G	-1:27822797 27822797 G	
73	219 T	-1:27822796 27822796 T	
74 V	220 G	-1:27822795 27822795 G	V
74	221 T	-1:27822794 27822794 T	
74	222 G	-1:27822793 27822793 G	
75 S	223 T	-1:27822792 27822792 T	S
75	224 C	-1:27822791 27822791 C	
75	225 A	-1:27822790 27822790 A	
76 G	226 G	-1:27822789 27822789 G	G
76	227 G	-1:27822242 27822242 G	
76	228 G	-1:27822241 27822241 G	
77 I	229 A	-1:27822240 27822240 A	I
77	230 T	-1:27822239 27822239 T	
77	231 T	-1:27822238 27822238 T	
78 G	232 G	-1:27822237 27822237 G	G
78	233 G	-1:27822236 27822236 G	
78	234 G	-1:27822235 27822235 G	
79 V	235 G	-1:27822234 27822234 G	V
79	236 T	-1:27822233 27822233 T	
79	237 G	-1:27822232 27822232 G	
80 T	238 A	-1:27822231 27822231 A	T
80	239 C	-1:27822230 27822230 C	
80	240 C	-1:27822229 27822229 C	
81 L	241 C	-1:27822228 27822228 C	L
81	242 T	-1:27822227 27822227 T	
81	243 G	-1:27822226 27822226 G	
82 F	244 T	-1:27822225 27822225 T	F
82	245 T	-1:27822224 27822224 T	
82	246 C	-1:27822223 27822223 C	
83 I	247 A	-1:27822222 27822222 A	I
83	248 T	-1:27822221 27822221 T	
83	249 T	-1:27822220 27822220 T	
84 A	250 G	-1:27822219 27822219 G	A
84	251 C	-1:27822218 27822218 C	
84	252 C	-1:27822217 27822217 C	
85 L	253 C	-1:27822216 27822216 C	L
85	254 T	-1:27822215 27822215 T	
85	255 G	-1:27822214 27822214 G	
86 Y	256 T	-1:27822213 27822213 T	Y
86	257 A	-1:27822212 27822212 A	
86	258 T	-1:27822211 27822211 T	
87 D	259 G	-1:27822210 27822210 G	D
87	260 A	-1:27822209 27822209 A	
87	261 C	-1:27822208 27822208 C	
88 Y	262 T	-1:27822207 27822207 T	Y
88	263 A	-1:27822206 27822206 A	
88	264 T	-1:27822205 27822205 T	
89 E	265 G	-1:27822204 27822204 G	E
89	266 A	-1:27822203 27822203 A	
89	267 G	-1:27822202 27822202 G	
90 A	268 G	-1:27822201 27822201 G	A
90	269 C	-1:27822200 27822200 C	
90	270 T	-1:27822199 27822199 T	
91 R	271 C	-1:27822198 27822198 C	R
91	272 G	-1:27822197 27822197 G	
91	273 A	-1:27822196 27822196 A	
92 T	274 A	-1:27822195 27822195 A	T
92	275 C	-1:27822194 27822194 C	
92	276 T	-1:27822193 27822193 T	
93 E	277 G	-1:27822192 27822192 G	E
93	278 A	-1:27822191 27822191 A	
93	279 G	-1:27822190 27822190 G	
94 D	280 G	-1:27822189 27822189 G	D
94	281 A	-1:27822188 27822188 A	
94	282 T	-1:27822187 27822187 T	
95 D	283 G	-1:27822186 27822186 G	D
95	284 A	-1:27822185 27822185 A	
95	285 C	-1:27822184 27822184 C	
96 L	286 C	-1:27822183 27822183 C	L
96	287 T	-1:27822182 27822182 T	
96	288 C	-1:27822181 27822181 C	
97 T	289 A	-1:27822180 27822180 A	T
97	290 C	-1:27822179 27822179 C	
97	291 C	-1:27822178 27822178 C	
98 F	292 T	-1:27822177 27822177 T	F
98	293 T	-1:27822176 27822176 T	
98	294 C	-1:27822175 27822175 C	
99 T	295 A	-1:27822174 27822174 A	T
99	296 C	-1:27822173 27822173 C	
99	297 C	-1:27822172 27822172 C	
100 K	298 A	-1:27822171 27822171 A	K
100	299 A	-1:27822170 27822170 A	
100	300 G	-1:27822169 27822169 G	
101 G	301 G	-1:27822168 27822168 G	G
101	302 G	-1:27822167 27822167 G	
101	303 C	-1:27822166 27822166 C	
102 E	304 G	-1:27822165 27822165 G	E
102	305 A	-1:27822164 27822164 A	
102	306 G	-1:27822163 27822163 G	
103 K	307 A	-1:27822162 27822162 A	K
103	308 A	-1:27822161 27822161 A	
103	309 G	-1:27822160 27822160 G	
104 F	310 T	-1:27822159 27822159 T	F
104	311 T	-1:27822158 27822158 T	
104	312 C	-1:27822157 27822157 C	
105 H	313 C	-1:27822156 27822156 C	H
105	314 A	-1:27822155 27822155 A	
105	315 C	-1:27822154 27822154 C	
106 I	316 A	-1:27822153 27822153 A	I
106	317 T	-1:27822152 27822152 T	
106	318 C	-1:27822151 27822151 C	
107 L	319 C	-1:27822150 27822150 C	L
107	320 T	-1:27822149 27822149 T	
107	321 G	-1:27822148 27822148 G	
108 N	322 A	-1:27822147 27822147 A	N
108	323 A	-1:27822146 27822146 A	
108	324 C	-1:27822145 27822145 C	
109 N	325 A	-1:27822144 27822144 A	N
109	326 A	-1:27822143 27822143 A	
109	327 T	-1:27822142 27822142 T	
110 T	328 A	-1:27822141 27822141 A	T
110	329 C	-1:27822140 27822140 C	
110	330 T	-1:27820755 27820755 T	
111 E	331 G	-1:27820754 27820754 G	E
111	332 A	-1:27820753 27820753 A	
111	333 A	-1:27820752 27820752 A	
112 G	334 G	-1:27820751 27820751 G	G
112	335 G	-1:27820750 27820750 G	
112	336 T	-1:27820749 27820749 T	
113 D	337 G	-1:27820748 27820748 G	D
113	338 A	-1:27820747 27820747 A	
113	339 C	-1:27820746 27820746 C	
114 W	340 T	-1:27820745 27820745 T	W
114	341 G	-1:27820744 27820744 G	
114	342 G	-1:27820743 27820743 G	
115 W	343 T	-1:27820742 27820742 T	W
115	344 G	-1:27820741 27820741 G	
115	345 G	-1:27820740 27820740 G	
116 E	346 G	-1:27820739 27820739 G	E
116	347 A	-1:27820738 27820738 A	
116	348 G	-1:27820737 27820737 G	
117 A	349 G	-1:27820736 27820736 G	A
117	350 C	-1:27820735 27820735 C	
117	351 T	-1:27820734 27820734 T	
118 R	352 C	-1:27820733 27820733 C	R
118	353 G	-1:27820732 27820732 G	
118	354 G	-1:27820731 27820731 G	
119 S	355 T	-1:27820730 27820730 T	S
119	356 C	-1:27820729 27820729 C	
119	357 T	-1:27820728 27820728 T	
120 L	358 C	-1:27820727 27820727 C	L
120	359 T	-1:27820726 27820726 T	
120	360 C	-1:27820725 27820725 C	
121 S	361 A	-1:27820724 27820724 A	S
121	362 G	-1:27820723 27820723 G	
121	363 C	-1:27820722 27820722 C	
122 S	364 T	-1:27820721 27820721 T	S
122	365 C	-1:27820720 27820720 C	
122	366 C	-1:27820719 27820719 C	
123 G	367 G	-1:27820718 27820718 G	G
123	368 G	-1:27820717 27820717 G	
123	369 A	-1:27820716 27820716 A	
124 K	370 A	-1:27820715 27820715 A	K
124	371 A	-1:27820714 27820714 A	
124	372 A	-1:27820713 27820713 A	
125 T	373 A	-1:27820712 27820712 A	T
125	374 C	-1:27820711 27820711 C	
125	375 T	-1:27820710 27820710 T	
126 G	376 G	-1:27820709 27820709 G	G
126	377 G	-1:27820708 27820708 G	
126	378 C	-1:27820707 27820707 C	
127 C	379 T	-1:27820706 27820706 T	C
127	380 G	-1:27820705 27820705 G	
127	381 C	-1:27820704 27820704 C	
128 I	382 A	-1:27820703 27820703 A	I
128	383 T	-1:27820702 27820702 T	
128	384 T	-1:27820701 27820701 T	
129 P	385 C	-1:27820700 27820700 C	P
129	386 C	-1:27820699 27820699 C	
129	387 C	-1:27820698 27820698 C	
130 S	388 A	-1:27820697 27820697 A	S
130	389 G	-1:27820696 27820696 G	
130	390 C	-1:27820695 27820695 C	
131 N	391 A	-1:27820694 27820694 A	N
131	392 A	-1:27820693 27820693 A	
131	393 C	-1:27820692 27820692 C	
132 Y	394 T	-1:27820691 27820691 T	Y
132	395 A	-1:27820690 27820690 A	
132	396 C	-1:27820689 27820689 C	
133 V	397 G	-1:27820688 27820688 G	V
133	398 T	-1:27820687 27820687 T	
133	399 G	-1:27820686 27820686 G	
134 A	400 G	-1:27820685 27820685 G	A
134	401 C	-1:27820684 27820684 C	
134	402 C	-1:27820683 27820683 C	
135 P	403 C	-1:27820682 27820682 C	P
135	404 C	-1:27820681 27820681 C	
135	405 T	-1:27820680 27820680 T	
136 V	406 G	-1:27820679 27820679 G	V
136	407 T	-1:27820678 27820678 T	
136	408 T	-1:27820677 27820677 T	
137 D	409 G	-1:27820676 27820676 G	D
137	410 A	-1:27820675 27820675 A	
137	411 C	-1:27820674 27820674 C	
138 S	412 T	-1:27820673 27820673 T	S
138	413 C	-1:27820672 27820672 C	
138	414 A	-1:27820671 27820671 A	
139 I	415 A	-1:27820670 27820670 A	I
139	416 T	-1:27820669 27820669 T	
139	417 C	-1:27820668 27820668 C	
140 Q	418 C	-1:27820667 27820667 C	Q
140	419 A	-1:27820666 27820666 A	
140	420 A	-1:27820665 27820665 A	
141 A	421 G	-1:27820664 27820664 G	A
141	422 C	-1:27820663 27820663 C	
141	423 T	-1:27820662 27820662 T	
142 E	424 G	-1:27820661 27820661 G	E
142	425 A	-1:27820660 27820660 A	
142	426 A	-1:27820659 27820659 A	
143 E	427 G	-1:27820658 27820658 G	E
143	428 A	-1:27820657 27820657 A	
143	429 G	-1:27816394 27816394 G	
144 W	430 T	-1:27816393 27816393 T	W
144	431 G	-1:27816392 27816392 G	
144	432 G	-1:27816391 27816391 G	
145 Y	433 T	-1:27816390 27816390 T	Y
145	434 A	-1:27816389 27816389 A	
145	435 C	-1:27816388 27816388 C	
146 F	436 T	-1:27816387 27816387 T	F
146	437 T	-1:27816386 27816386 T	
146	438 T	-1:27816385 27816385 T	
147 G	439 G	-1:27816384 27816384 G	G
147	440 G	-1:27816383 27816383 G	
147	441 A	-1:27816382 27816382 A	
148 K	442 A	-1:27816381 27816381 A	K
148	443 A	-1:27816380 27816380 A	
148	444 G	-1:27816379 27816379 G	
149 I	445 A	-1:27816378 27816378 A	I
149	446 T	-1:27816377 27816377 T	
149	447 T	-1:27816376 27816376 T	
150 G	448 G	-1:27816375 27816375 G	G
150	449 G	-1:27816374 27816374 G	
150	450 G	-1:27816373 27816373 G	
151 R	451 A	-1:27816372 27816372 A	R
151	452 G	-1:27816371 27816371 G	
151	453 A	-1:27816370 27816370 A	
152 K	454 A	-1:27816369 27816369 A	K
152	455 A	-1:27816368 27816368 A	
152	456 G	-1:27816367 27816367 G	
153 D	457 G	-1:27816366 27816366 G	D
153	458 A	-1:27816365 27816365 A	
153	459 T	-1:27816364 27816364 T	
154 A	460 G	-1:27816363 27816363 G	A
154	461 C	-1:27816362 27816362 C	
154	462 A	-1:27816361 27816361 A	
155 E	463 G	-1:27816360 27816360 G	E
155	464 A	-1:27816359 27816359 A	
155	465 G	-1:27816358 27816358 G	
156 R	466 A	-1:27816357 27816357 A	R
156	467 G	-1:27816356 27816356 G	
156	468 G	-1:27816355 27816355 G	
157 Q	469 C	-1:27816354 27816354 C	Q
157	470 A	-1:27816353 27816353 A	
157	471 G	-1:27816352 27816352 G	
158 L	472 C	-1:27816351 27816351 C	L
158	473 T	-1:27816350 27816350 T	
158	474 G	-1:27816349 27816349 G	
159 L	475 C	-1:27816348 27816348 C	L
159	476 T	-1:27816347 27816347 T	
159	477 T	-1:27816346 27816346 T	
160 S	478 T	-1:27816345 27816345 T	S
160	479 C	-1:27816344 27816344 C	
160	480 A	-1:27816343 27816343 A	
161 P	481 C	-1:27816342 27816342 C	P
161	482 C	-1:27816341 27816341 C	
161	483 A	-1:27816340 27816340 A	
162 G	484 G	-1:27816339 27816339 G	G
162	485 G	-1:27816338 27816338 G	
162	486 C	-1:27816337 27816337 C	
163 N	487 A	-1:27816336 27816336 A	N
163	488 A	-1:27816335 27816335 A	
163	489 C	-1:27816334 27816334 C	
164 P	490 C	-1:27816333 27816333 C	P
164	491 C	-1:27816332 27816332 C	
164	492 C	-1:27816331 27816331 C	
165 Q	493 C	-1:27816330 27816330 C	Q
165	494 A	-1:27816329 27816329 A	
165	495 G	-1:27816328 27816328 G	
166 G	496 G	-1:27816327 27816327 G	G
166	497 G	-1:27816326 27816326 G	
166	498 G	-1:27816325 27816325 G	
167 A	499 G	-1:27816324 27816324 G	A
167	500 C	-1:27816323 27816323 C	
167	501 C	-1:27816322 27816322 C	
168 F	502 T	-1:27816321 27816321 T	F
168	503 T	-1:27816320 27816320 T	
168	504 T	-1:27816319 27816319 T	
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169	506 T	-1:27816317 27816317 T	
169	507 C	-1:27816316 27816316 C	
170 I	508 A	-1:27816315 27816315 A	I
170	509 T	-1:27816314 27816314 T	
170	510 T	-1:27816313 27816313 T	
171 R	511 C	-1:27816312 27816312 C	R
171	512 G	-1:27816311 27816311 G	
171	513 G	-1:27816310 27816310 G	
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172	516 A	-1:27816307 27816307 A	
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174	522 G	-1:27816301 27816301 G	
175 T	523 A	-1:27816300 27816300 A	T
175	524 C	-1:27816299 27816299 C	
175	525 C	-1:27816298 27816298 C	
176 T	526 A	-1:27816297 27816297 A	T
176	527 C	-1:27816296 27816296 C	
176	528 C	-1:27816295 27816295 C	
177 K	529 A	-1:27816294 27816294 A	K
177	530 A	-1:27816293 27816293 A	
177	531 A	-1:27816292 27816292 A	
178 G	532 G	-1:27816291 27816291 G	G
178	533 G	-1:27816104 27816104 G	
178	534 T	-1:27816103 27816103 T	
179 A	535 G	-1:27816102 27816102 G	A
179	536 C	-1:27816101 27816101 C	
179	537 C	-1:27816100 27816100 C	
180 Y	538 T	-1:27816099 27816099 T	Y
180	539 A	-1:27816098 27816098 A	
180	540 C	-1:27816097 27816097 C	
181 S	541 T	-1:27816096 27816096 T	S
181	542 C	-1:27816095 27816095 C	
181	543 C	-1:27816094 27816094 C	
182 L	544 C	-1:27816093 27816093 C	L
182	545 T	-1:27816092 27816092 T	
182	546 G	-1:27816091 27816091 G	
183 S	547 T	-1:27816090 27816090 T	S
183	548 C	-1:27816089 27816089 C	
183	549 C	-1:27816088 27816088 C	
184 I	550 A	-1:27816087 27816087 A	I
184	551 T	-1:27816086 27816086 T	
184	552 C	-1:27816085 27816085 C	
185 R	553 C	-1:27816084 27816084 C	R
185	554 G	-1:27816083 27816083 G	
185	555 G	-1:27816082 27816082 G	
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186	557 A	-1:27816080 27816080 A	
186	558 C	-1:27816079 27816079 C	
187 W	559 T	-1:27816078 27816078 T	W
187	560 G	-1:27816077 27816077 G	
187	561 G	-1:27816076 27816076 G	
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188	563 A	-1:27816074 27816074 A	
188	564 T	-1:27816073 27816073 T	
189 Q	565 C	-1:27816072 27816072 C	Q
189	566 A	-1:27816071 27816071 A	
189	567 G	-1:27816070 27816070 G	
190 T	568 A	-1:27816069 27816069 A	T
190	569 C	-1:27816068 27816068 C	
190	570 C	-1:27816067 27816067 C	
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191	572 G	-1:27816065 27816065 G	
191	573 A	-1:27816064 27816064 A	
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192	575 G	-1:27816062 27816062 G	
192	576 C	-1:27816061 27816061 C	
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193	578 A	-1:27816059 27816059 A	
193	579 T	-1:27816058 27816058 T	
194 H	580 C	-1:27816057 27816057 C	H
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194	582 T	-1:27816055 27816055 T	
195 V	583 G	-1:27816054 27816054 G	V
195	584 T	-1:27816053 27816053 T	
195	585 G	-1:27816052 27816052 G	
196 K	586 A	-1:27816051 27816051 A	K
196	587 A	-1:27816050 27816050 A	
196	588 G	-1:27816049 27816049 G	
197 H	589 C	-1:27816048 27816048 C	H
197	590 A	-1:27816047 27816047 A	
197	591 T	-1:27816046 27816046 T	
198 Y	592 T	-1:27816045 27816045 T	Y
198	593 A	-1:27816044 27816044 A	
198	594 C	-1:27816043 27816043 C	
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199	596 A	-1:27816041 27816041 A	
199	597 G	-1:27816040 27816040 G	
200 I	598 A	-1:27816039 27816039 A	I
200	599 T	-1:27816038 27816038 T	
200	600 C	-1:27816037 27816037 C	
201 R	601 C	-1:27816036 27816036 C	R
201	602 G	-1:27816035 27816035 G	
201	603 C	-1:27816034 27816034 C	
202 K	604 A	-1:27816033 27816033 A	K
202	605 A	-1:27816032 27816032 A	
202	606 A	-1:27816031 27816031 A	
203 L	607 C	-1:27816030 27816030 C	L
203	608 T	-1:27816029 27816029 T	
203	609 G	-1:27816028 27816028 G	
204 D	610 G	-1:27816027 27816027 G	D
204	611 A	-1:27816026 27816026 A	
204	612 C	-1:27816025 27816025 C	
205 M	613 A	-1:27816024 27816024 A	M
205	614 T	-1:27816023 27816023 T	
205	615 G	-1:27816022 27816022 G	
206 G	616 G	-1:27816021 27816021 G	G
206	617 G	-1:27816020 27816020 G	
206	618 C	-1:27816019 27816019 C	
207 G	619 G	-1:27816018 27816018 G	G
207	620 G	-1:27816017 27816017 G	
207	621 C	-1:27816016 27816016 C	
208 Y	622 T	-1:27816015 27816015 T	Y
208	623 A	-1:27816014 27816014 A	
208	624 C	-1:27816013 27816013 C	
209 Y	625 T	-1:27816012 27816012 T	Y
209	626 A	-1:27816011 27816011 A	
209	627 C	-1:27816010 27816010 C	
210 I	628 A	-1:27816009 27816009 A	I
210	629 T	-1:27816008 27816008 T	
210	630 C	-1:27816007 27816007 C	
211 T	631 A	-1:27816006 27816006 A	T
211	632 C	-1:27816005 27816005 C	
211	633 C	-1:27816004 27816004 C	
212 T	634 A	-1:27816003 27816003 A	T
212	635 C	-1:27816002 27816002 C	
212	636 A	-1:27816001 27816001 A	
213 R	637 C	-1:27816000 27816000 C	R
213	638 G	-1:27815999 27815999 G	
213	639 G	-1:27815998 27815998 G	
214 V	640 G	-1:27815997 27815997 G	V
214	641 T	-1:27815996 27815996 T	
214	642 T	-1:27815995 27815995 T	
215 Q	643 C	-1:27815994 27815994 C	Q
215	644 A	-1:27815993 27815993 A	
215	645 G	-1:27815992 27815992 G	
216 F	646 T	-1:27815991 27815991 T	F
216	647 T	-1:27815990 27815990 T	
216	648 C	-1:27815989 27815989 C	
217 N	649 A	-1:27815988 27815988 A	N
217	650 A	-1:27815987 27815987 A	
217	651 C	-1:27815986 27815986 C	
218 S	652 T	-1:27815985 27815985 T	S
218	653 C	-1:27815984 27815984 C	
218	654 G	-1:27815983 27815983 G	
219 V	655 G	-1:27815982 27815982 G	V
219	656 T	-1:27815981 27815981 T	
219	657 G	-1:27815980 27815980 G	
220 Q	658 C	-1:27815979 27815979 C	Q
220	659 A	-1:27815978 27815978 A	
220	660 G	-1:27815977 27815977 G	
221 E	661 G	-1:27815976 27815976 G	E
221	662 A	-1:27815975 27815975 A	
221	663 G	-1:27815974 27815974 G	
222 L	664 C	-1:27815973 27815973 C	L
222	665 T	-1:27815972 27815972 T	
222	666 G	-1:27815971 27815971 G	
223 V	667 G	-1:27815970 27815970 G	V
223	668 T	-1:27815969 27815969 T	
223	669 G	-1:27815968 27815968 G	
224 Q	670 C	-1:27815967 27815967 C	Q
224	671 A	-1:27815966 27815966 A	
224	672 G	-1:27815965 27815965 G	
225 H	673 C	-1:27815964 27815964 C	H
225	674 A	-1:27815963 27815963 A	
225	675 C	-1:27815962 27815962 C	
226 Y	676 T	-1:27815961 27815961 T	Y
226	677 A	-1:27815960 27815960 A	
226	678 C	-1:27815959 27815959 C	
227 M	679 A	-1:27815958 27815958 A	M
227	680 T	-1:27815957 27815957 T	
227	681 G	-1:27815956 27815956 G	
228 E	682 G	-1:27815955 27815955 G	E
228	683 A	-1:27814942 27814942 A	
228	684 G	-1:27814941 27814941 G	
229 V	685 G	-1:27814940 27814940 G	V
229	686 T	-1:27814939 27814939 T	
229	687 G	-1:27814938 27814938 G	
230 N	688 A	-1:27814937 27814937 A	N
230	689 A	-1:27814936 27814936 A	
230	690 T	-1:27814935 27814935 T	
231 D	691 G	-1:27814934 27814934 G	D
231	692 A	-1:27814933 27814933 A	
231	693 C	-1:27814932 27814932 C	
232 G	694 G	-1:27814931 27814931 G	G
232	695 G	-1:27814930 27814930 G	
232	696 G	-1:27814929 27814929 G	
233 L	697 C	-1:27814928 27814928 C	L
233	698 T	-1:27814927 27814927 T	
233	699 G	-1:27814926 27814926 G	
234 C	700 T	-1:27814925 27814925 T	C
234	701 G	-1:27814924 27814924 G	
234	702 C	-1:27814923 27814923 C	
235 N	703 A	-1:27814922 27814922 A	N
235	704 A	-1:27814921 27814921 A	
235	705 C	-1:27814920 27814920 C	
236 L	706 C	-1:27814919 27814919 C	L
236	707 T	-1:27814918 27814918 T	
236	708 G	-1:27814917 27814917 G	
237 L	709 C	-1:27814916 27814916 C	L
237	710 T	-1:27814915 27814915 T	
237	711 C	-1:27814914 27814914 C	
238 I	712 A	-1:27814913 27814913 A	I
238	713 T	-1:27814912 27814912 T	
238	714 C	-1:27814911 27814911 C	
239 A	715 G	-1:27814910 27814910 G	A
239	716 C	-1:27814909 27814909 C	
239	717 G	-1:27814908 27814908 G	
240 P	718 C	-1:27814907 27814907 C	P
240	719 C	-1:27814906 27814906 C	
240	720 C	-1:27814905 27814905 C	
241 C	721 T	-1:27814904 27814904 T	C
241	722 G	-1:27814903 27814903 G	
241	723 C	-1:27814902 27814902 C	
242 T	724 A	-1:27814901 27814901 A	T
242	725 C	-1:27814900 27814900 C	
242	726 C	-1:27814899 27814899 C	
243 I	727 A	-1:27814898 27814898 A	I
243	728 T	-1:27814897 27814897 T	
243	729 C	-1:27814896 27814896 C	
244 M	730 A	-1:27814895 27814895 A	M
244	731 T	-1:27814894 27814894 T	
244	732 G	-1:27814893 27814893 G	
245 K	733 A	-1:27814892 27814892 A	K
245	734 A	-1:27814891 27814891 A	
245	735 G	-1:27814890 27814890 G	
246 P	736 C	-1:27814889 27814889 C	P
246	737 C	-1:27814888 27814888 C	
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247 Q	739 C	-1:27814886 27814886 C	Q
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248 T	742 A	-1:27814883 27814883 A	T
248	743 C	-1:27814882 27814882 C	
248	744 G	-1:27814881 27814881 G	
249 L	745 C	-1:27814880 27814880 C	L
249	746 T	-1:27814879 27814879 T	
249	747 G	-1:27814878 27814878 G	
250 G	748 G	-1:27814877 27814877 G	G
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250	750 C	-1:27814875 27814875 C	
251 L	751 C	-1:27814874 27814874 C	L
251	752 T	-1:27814873 27814873 T	
251	753 G	-1:27814872 27814872 G	
252 A	754 G	-1:27814871 27814871 G	A
252	755 C	-1:27814870 27814870 C	
252	756 C	-1:27814869 27814869 C	
253 K	757 A	-1:27814868 27814868 A	K
253	758 A	-1:27814867 27814867 A	
253	759 G	-1:27814866 27814866 G	
254 D	760 G	-1:27814865 27814865 G	D
254	761 A	-1:27814864 27814864 A	
254	762 C	-1:27814863 27814863 C	
255 A	763 G	-1:27814862 27814862 G	A
255	764 C	-1:27814861 27814861 C	
255	765 C	-1:27814860 27814860 C	
256 W	766 T	-1:27814859 27814859 T	W
256	767 G	-1:27814858 27814858 G	
256	768 G	-1:27814857 27814857 G	
257 E	769 G	-1:27814856 27814856 G	E
257	770 A	-1:27814855 27814855 A	
257	771 G	-1:27814854 27814854 G	
258 I	772 A	-1:27814853 27814853 A	I
258	773 T	-1:27814852 27814852 T	
258	774 C	-1:27814851 27814851 C	
259 S	775 A	-1:27814850 27814850 A	S
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259	777 C	-1:27814848 27814848 C	
260 R	778 C	-1:27814847 27814847 C	R
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260	780 C	-1:27814845 27814845 C	
261 S	781 A	-1:27814844 27814844 A	S
261	782 G	-1:27814843 27814843 G	
261	783 C	-1:27814842 27814842 C	
262 S	784 T	-1:27814841 27814841 T	S
262	785 C	-1:27814840 27814840 C	
262	786 C	-1:27814839 27814839 C	
263 I	787 A	-1:27814838 27814838 A	I
263	788 T	-1:27814837 27814837 T	
263	789 C	-1:27814836 27814836 C	
264 T	790 A	-1:27814835 27814835 A	T
264	791 C	-1:27814834 27814834 C	
264	792 G	-1:27814833 27814833 G	
265 L	793 C	-1:27814832 27814832 C	L
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265	795 G	-1:27814830 27814830 G	
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267	801 C	-1:27814824 27814824 C	
268 R	802 C	-1:27814823 27814823 C	R
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268	804 G	-1:27814821 27814821 G	
269 L	805 C	-1:27814820 27814820 C	L
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269	807 G	-1:27814818 27814818 G	
270 G	808 G	-1:27814817 27814817 G	G
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270	810 C	-1:27814815 27814815 C	
271 T	811 A	-1:27814814 27814814 A	T
271	812 C	-1:27814813 27814813 C	
271	813 C	-1:27814812 27814812 C	
272 G	814 G	-1:27814811 27814811 G	G
272	815 G	-1:27814810 27814810 G	
272	816 C	-1:27814809 27814809 C	
273 C	817 T	-1:27814808 27814808 T	C
273	818 G	-1:27814807 27814807 G	
273	819 C	-1:27814806 27814806 C	
274 F	820 T	-1:27814805 27814805 T	F
274	821 T	-1:27814804 27814804 T	
274	822 C	-1:27814803 27814803 C	
275 G	823 G	-1:27814802 27814802 G	G
275	824 G	-1:27814801 27814801 G	
275	825 G	-1:27814800 27814800 G	
276 D	826 G	-1:27814799 27814799 G	D
276	827 A	-1:27814798 27814798 A	
276	828 T	-1:27814797 27814797 T	
277 V	829 G	-1:27814796 27814796 G	V
277	830 T	-1:27814795 27814795 T	
277	831 G	-1:27814794 27814794 G	
278 W	832 T	-1:27814793 27814793 T	W
278	833 G	-1:27814792 27814792 G	
278	834 G	-1:27814791 27814791 G	
279 L	835 C	-1:27814790 27814790 C	L
279	836 T	-1:27814789 27814789 T	
279	837 G	-1:27814788 27814788 G	
280 G	838 G	-1:27814787 27814787 G	G
280	839 G	-1:27814711 27814711 G	
280	840 C	-1:27814710 27814710 C	
281 T	841 A	-1:27814709 27814709 A	T
281	842 C	-1:27814708 27814708 C	
281	843 G	-1:27814707 27814707 G	
282 W	844 T	-1:27814706 27814706 T	W
282	845 G	-1:27814705 27814705 G	
282	846 G	-1:27814704 27814704 G	
283 N	847 A	-1:27814703 27814703 A	N
283	848 A	-1:27814702 27814702 A	
283	849 C	-1:27814701 27814701 C	
284 G	850 G	-1:27814700 27814700 G	G
284	851 G	-1:27814699 27814699 G	
284	852 C	-1:27814698 27814698 C	
285 S	853 A	-1:27814697 27814697 A	S
285	854 G	-1:27814696 27814696 G	
285	855 C	-1:27814695 27814695 C	
286 T	856 A	-1:27814694 27814694 A	T
286	857 C	-1:27814693 27814693 C	
286	858 T	-1:27814692 27814692 T	
287 K	859 A	-1:27814691 27814691 A	K
287	860 A	-1:27814690 27814690 A	
287	861 G	-1:27814689 27814689 G	
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288	863 T	-1:27814687 27814687 T	
288	864 G	-1:27814686 27814686 G	
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289	866 C	-1:27814684 27814684 C	
289	867 G	-1:27814683 27814683 G	
290 V	868 G	-1:27814682 27814682 G	V
290	869 T	-1:27814681 27814681 T	
290	870 G	-1:27814680 27814680 G	
291 K	871 A	-1:27814679 27814679 A	K
291	872 A	-1:27814678 27814678 A	
291	873 G	-1:27814677 27814677 G	
292 T	874 A	-1:27814676 27814676 A	T
292	875 C	-1:27814675 27814675 C	
292	876 G	-1:27814674 27814674 G	
293 L	877 C	-1:27814673 27814673 C	L
293	878 T	-1:27814672 27814672 T	
293	879 G	-1:27814671 27814671 G	
294 K	880 A	-1:27814670 27814670 A	K
294	881 A	-1:27814669 27814669 A	
294	882 G	-1:27814668 27814668 G	
295 P	883 C	-1:27814667 27814667 C	P
295	884 C	-1:27814666 27814666 C	
295	885 G	-1:27814665 27814665 G	
296 G	886 G	-1:27814664 27814664 G	G
296	887 G	-1:27814663 27814663 G	
296	888 C	-1:27814662 27814662 C	
297 T	889 A	-1:27814661 27814661 A	T
297	890 C	-1:27814660 27814660 C	
297	891 C	-1:27814659 27814659 C	
298 M	892 A	-1:27814658 27814658 A	M
298	893 T	-1:27814657 27814657 T	
298	894 G	-1:27814656 27814656 G	
299 S	895 T	-1:27814655 27814655 T	S
299	896 C	-1:27814654 27814654 C	
299	897 C	-1:27814653 27814653 C	
300 P	898 C	-1:27814652 27814652 C	P
300	899 C	-1:27814651 27814651 C	
300	900 G	-1:27814650 27814650 G	
301 K	901 A	-1:27814649 27814649 A	K
301	902 A	-1:27814648 27814648 A	
301	903 G	-1:27814647 27814647 G	
302 A	904 G	-1:27814646 27814646 G	A
302	905 C	-1:27814645 27814645 C	
302	906 C	-1:27814644 27814644 C	
303 F	907 T	-1:27814643 27814643 T	F
303	908 T	-1:27814642 27814642 T	
303	909 C	-1:27814641 27814641 C	
304 L	910 C	-1:27814640 27814640 C	L
304	911 T	-1:27814639 27814639 T	
304	912 G	-1:27814638 27814638 G	
305 E	913 G	-1:27814637 27814637 G	E
305	914 A	-1:27814636 27814636 A	
305	915 G	-1:27814635 27814635 G	
306 E	916 G	-1:27814634 27814634 G	E
306	917 A	-1:27814633 27814633 A	
306	918 G	-1:27814632 27814632 G	
307 A	919 G	-1:27814631 27814631 G	A
307	920 C	-1:27814630 27814630 C	
307	921 G	-1:27814629 27814629 G	
308 Q	922 C	-1:27814628 27814628 C	Q
308	923 A	-1:27814627 27814627 A	
308	924 G	-1:27814626 27814626 G	
309 V	925 G	-1:27814625 27814625 G	V
309	926 T	-1:27814624 27814624 T	
309	927 C	-1:27814623 27814623 C	
310 M	928 A	-1:27814622 27814622 A	M
310	929 T	-1:27814621 27814621 T	
310	930 G	-1:27814620 27814620 G	
311 K	931 A	-1:27814619 27814619 A	K
311	932 A	-1:27814618 27814618 A	
311	933 G	-1:27814617 27814617 G	
312 L	934 C	-1:27814616 27814616 C	L
312	935 T	-1:27814615 27814615 T	
312	936 G	-1:27814614 27814614 G	
313 L	937 C	-1:27814613 27814613 C	L
313	938 T	-1:27814612 27814612 T	
313	939 G	-1:27814611 27814611 G	
314 R	940 C	-1:27814610 27814610 C	R
314	941 G	-1:27814609 27814609 G	
314	942 G	-1:27814608 27814608 G	
315 H	943 C	-1:27814607 27814607 C	H
315	944 A	-1:27814606 27814606 A	
315	945 C	-1:27814605 27814605 C	
316 D	946 G	-1:27814604 27814604 G	D
316	947 A	-1:27814603 27814603 A	
316	948 C	-1:27814602 27814602 C	
317 K	949 A	-1:27814601 27814601 A	K
317	950 A	-1:27814600 27814600 A	
317	951 G	-1:27814599 27814599 G	
318 L	952 C	-1:27814598 27814598 C	L
318	953 T	-1:27814597 27814597 T	
318	954 G	-1:27814596 27814596 G	
319 V	955 G	-1:27814595 27814595 G	V
319	956 T	-1:27814594 27814594 T	
319	957 G	-1:27814593 27814593 G	
320 Q	958 C	-1:27814592 27814592 C	Q
320	959 A	-1:27814591 27814591 A	
320	960 G	-1:27814590 27814590 G	
321 L	961 C	-1:27814589 27814589 C	L
321	962 T	-1:27814588 27814588 T	
321	963 G	-1:27814587 27814587 G	
322 Y	964 T	-1:27814586 27814586 T	Y
322	965 A	-1:27814585 27814585 A	
322	966 C	-1:27814584 27814584 C	
323 A	967 G	-1:27814583 27814583 G	A
323	968 C	-1:27814582 27814582 C	
323	969 C	-1:27814581 27814581 C	
324 V	970 G	-1:27814580 27814580 G	V
324	971 T	-1:27814579 27814579 T	
324	972 G	-1:27814578 27814578 G	
325 V	973 G	-1:27814577 27814577 G	V
325	974 T	-1:27814576 27814576 T	
325	975 G	-1:27814575 27814575 G	
326 S	976 T	-1:27814574 27814574 T	S
326	977 C	-1:27814573 27814573 C	
326	978 G	-1:27814572 27814572 G	
327 E	979 G	-1:27814571 27814571 G	E
327	980 A	-1:27814570 27814570 A	
327	981 G	-1:27814569 27814569 G	
328 E	982 G	-1:27814568 27814568 G	E
328	983 A	-1:27814567 27814567 A	
328	984 G	-1:27814566 27814566 G	
329 P	985 C	-1:27814565 27814565 C	P
329	986 C	-1:27814564 27814564 C	
329	987 C	-1:27814563 27814563 C	
330 I	988 A	-1:27814562 27814562 A	I
330	989 T	-1:27814561 27814561 T	
330	990 C	-1:27814560 27814560 C	
331 Y	991 T	-1:27814559 27814559 T	Y
331	992 A	-1:27814558 27814558 A	
331	993 C	-1:27814557 27814557 C	
332 I	994 A	-1:27814556 27814556 A	I
332	995 T	-1:27814555 27814555 T	
332	996 C	-1:27814554 27814554 C	
333 V	997 G	-1:27814553 27814553 G	V
333	998 T	-1:27814552 27814552 T	
333	999 G	-1:27814551 27814551 G	
334 T	1000 A	-1:27814550 27814550 A	T
334	1001 C	-1:27814549 27814549 C	
334	1002 C	-1:27814548 27814548 C	
335 E	1003 G	-1:27814547 27814547 G	E
335	1004 A	-1:27814546 27814546 A	
335	1005 G	-1:27814545 27814545 G	
336 F	1006 T	-1:27814544 27814544 T	F
336	1007 T	-1:27814543 27814543 T	
336	1008 C	-1:27814542 27814542 C	
337 M	1009 A	-1:27814541 27814541 A	M
337	1010 T	-1:27814540 27814540 T	
337	1011 G	-1:27814539 27814539 G	
338 C	1012 T	-1:27814538 27814538 T	C
338	1013 G	-1:27814537 27814537 G	
338	1014 T	-1:27814536 27814536 T	
339 H	1015 C	-1:27814535 27814535 C	H
339	1016 A	-1:27814534 27814534 A	
339	1017 C	-1:27814533 27814533 C	
340 G	1018 G	-1:27814532 27814532 G	G
340	1019 G	-1:27814024 27814024 G	
340	1020 C	-1:27814023 27814023 C	
341 S	1021 A	-1:27814022 27814022 A	S
341	1022 G	-1:27814021 27814021 G	
341	1023 C	-1:27814020 27814020 C	
342 L	1024 T	-1:27814019 27814019 T	L
342	1025 T	-1:27814018 27814018 T	
342	1026 G	-1:27814017 27814017 G	
343 L	1027 C	-1:27814016 27814016 C	L
343	1028 T	-1:27814015 27814015 T	
343	1029 G	-1:27814014 27814014 G	
344 D	1030 G	-1:27814013 27814013 G	D
344	1031 A	-1:27814012 27814012 A	
344	1032 T	-1:27814011 27814011 T	
345 F	1033 T	-1:27814010 27814010 T	F
345	1034 T	-1:27814009 27814009 T	
345	1035 T	-1:27814008 27814008 T	
346 L	1036 C	-1:27814007 27814007 C	L
346	1037 T	-1:27814006 27814006 T	
346	1038 C	-1:27814005 27814005 C	
347 K	1039 A	-1:27814004 27814004 A	K
347	1040 A	-1:27814003 27814003 A	
347	1041 G	-1:27814002 27814002 G	
348 N	1042 A	-1:27814001 27814001 A	N
348	1043 A	-1:27814000 27814000 A	
348	1044 C	-1:27813999 27813999 C	
349 P	1045 C	-1:27813998 27813998 C	P
349	1046 C	-1:27813997 27813997 C	
349	1047 A	-1:27813996 27813996 A	
350 E	1048 G	-1:27813995 27813995 G	E
350	1049 A	-1:27813994 27813994 A	
350	1050 G	-1:27813993 27813993 G	
351 G	1051 G	-1:27813992 27813992 G	G
351	1052 G	-1:27813991 27813991 G	
351	1053 C	-1:27813990 27813990 C	
352 Q	1054 C	-1:27813989 27813989 C	Q
352	1055 A	-1:27813988 27813988 A	
352	1056 G	-1:27813987 27813987 G	
353 D	1057 G	-1:27813986 27813986 G	D
353	1058 A	-1:27813985 27813985 A	
353	1059 T	-1:27813984 27813984 T	
354 L	1060 T	-1:27813983 27813983 T	L
354	1061 T	-1:27813982 27813982 T	
354	1062 G	-1:27813981 27813981 G	
355 R	1063 A	-1:27813980 27813980 A	R
355	1064 G	-1:27813979 27813979 G	
355	1065 G	-1:27813978 27813978 G	
356 L	1066 C	-1:27813977 27813977 C	L
356	1067 T	-1:27813976 27813976 T	
356	1068 G	-1:27813975 27813975 G	
357 P	1069 C	-1:27813974 27813974 C	P
357	1070 C	-1:27813973 27813973 C	
357	1071 C	-1:27813972 27813972 C	
358 Q	1072 C	-1:27813971 27813971 C	Q
358	1073 A	-1:27813970 27813970 A	
358	1074 A	-1:27813969 27813969 A	
359 L	1075 T	-1:27813968 27813968 T	L
359	1076 T	-1:27813967 27813967 T	
359	1077 G	-1:27813966 27813966 G	
360 V	1078 G	-1:27813965 27813965 G	V
360	1079 T	-1:27813964 27813964 T	
360	1080 G	-1:27813963 27813963 G	
361 D	1081 G	-1:27813962 27813962 G	D
361	1082 A	-1:27813961 27813961 A	
361	1083 C	-1:27813960 27813960 C	
362 M	1084 A	-1:27813959 27813959 A	M
362	1085 T	-1:27813958 27813958 T	
362	1086 G	-1:27813957 27813957 G	
363 A	1087 G	-1:27813956 27813956 G	A
363	1088 C	-1:27813955 27813955 C	
363	1089 A	-1:27813954 27813954 A	
364 A	1090 G	-1:27813953 27813953 G	A
364	1091 C	-1:27813952 27813952 C	
364	1092 C	-1:27813951 27813951 C	
365 Q	1093 C	-1:27813950 27813950 C	Q
365	1094 A	-1:27813949 27813949 A	
365	1095 G	-1:27813948 27813948 G	
366 V	1096 G	-1:27813681 27813681 G	V
366	1097 T	-1:27813680 27813680 T	
366	1098 A	-1:27813679 27813679 A	
367 A	1099 G	-1:27813678 27813678 G	A
367	1100 C	-1:27813677 27813677 C	
367	1101 T	-1:27813676 27813676 T	
368 E	1102 G	-1:27813675 27813675 G	E
368	1103 A	-1:27813674 27813674 A	
368	1104 G	-1:27813673 27813673 G	
369 G	1105 G	-1:27813672 27813672 G	G
369	1106 G	-1:27813671 27813671 G	
369	1107 C	-1:27813670 27813670 C	
370 M	1108 A	-1:27813669 27813669 A	M
370	1109 T	-1:27813668 27813668 T	
370	1110 G	-1:27813667 27813667 G	
371 A	1111 G	-1:27813666 27813666 G	A
371	1112 C	-1:27813665 27813665 C	
371	1113 C	-1:27813664 27813664 C	
372 Y	1114 T	-1:27813663 27813663 T	Y
372	1115 A	-1:27813662 27813662 A	
372	1116 C	-1:27813661 27813661 C	
373 M	1117 A	-1:27813660 27813660 A	M
373	1118 T	-1:27813659 27813659 T	
373	1119 G	-1:27813658 27813658 G	
374 E	1120 G	-1:27813657 27813657 G	E
374	1121 A	-1:27813656 27813656 A	
374	1122 A	-1:27813655 27813655 A	
375 R	1123 C	-1:27813654 27813654 C	R
375	1124 G	-1:27813653 27813653 G	
375	1125 C	-1:27813652 27813652 C	
376 M	1126 A	-1:27813651 27813651 A	M
376	1127 T	-1:27813650 27813650 T	
376	1128 G	-1:27813649 27813649 G	
377 N	1129 A	-1:27813648 27813648 A	N
377	1130 A	-1:27813647 27813647 A	
377	1131 C	-1:27813646 27813646 C	
378 Y	1132 T	-1:27813645 27813645 T	Y
378	1133 A	-1:27813644 27813644 A	
378	1134 C	-1:27813643 27813643 C	
379 I	1135 A	-1:27813642 27813642 A	I
379	1136 T	-1:27813641 27813641 T	
379	1137 T	-1:27813640 27813640 T	
380 H	1138 C	-1:27813639 27813639 C	H
380	1139 A	-1:27813638 27813638 A	
380	1140 C	-1:27813637 27813637 C	
381 R	1141 C	-1:27813636 27813636 C	R
381	1142 G	-1:27813635 27813635 G	
381	1143 C	-1:27813634 27813634 C	
382 D	1144 G	-1:27813633 27813633 G	D
382	1145 A	-1:27813632 27813632 A	
382	1146 C	-1:27813631 27813631 C	
383 L	1147 C	-1:27813630 27813630 C	L
383	1148 T	-1:27813629 27813629 T	
383	1149 G	-1:27813628 27813628 G	
384 R	1150 A	-1:27813627 27813627 A	R
384	1151 G	-1:27813626 27813626 G	
384	1152 G	-1:27813625 27813625 G	
385 A	1153 G	-1:27813624 27813624 G	A
385	1154 C	-1:27813623 27813623 C	
385	1155 A	-1:27813622 27813622 A	
386 A	1156 G	-1:27813621 27813621 G	A
386	1157 C	-1:27813620 27813620 C	
386	1158 C	-1:27813619 27813619 C	
387 N	1159 A	-1:27813618 27813618 A	N
387	1160 A	-1:27813617 27813617 A	
387	1161 C	-1:27813616 27813616 C	
388 I	1162 A	-1:27813615 27813615 A	I
388	1163 T	-1:27813614 27813614 T	
388	1164 C	-1:27813613 27813613 C	
389 L	1165 C	-1:27813612 27813612 C	L
389	1166 T	-1:27813611 27813611 T	
389	1167 G	-1:27813610 27813610 G	
390 V	1168 G	-1:27813609 27813609 G	V
390	1169 T	-1:27813608 27813608 T	
390	1170 T	-1:27813607 27813607 T	
391 G	1171 G	-1:27813606 27813606 G	G
391	1172 G	-1:27813605 27813605 G	
391	1173 G	-1:27813604 27813604 G	
392 E	1174 G	-1:27813603 27813603 G	E
392	1175 A	-1:27813602 27813602 A	
392	1176 G	-1:27813601 27813601 G	
393 R	1177 C	-1:27813600 27813600 C	R
393	1178 G	-1:27813599 27813599 G	
393	1179 G	-1:27813598 27813598 G	
394 L	1180 C	-1:27813597 27813597 C	L
394	1181 T	-1:27813596 27813596 T	
394	1182 G	-1:27813595 27813595 G	
395 A	1183 G	-1:27813594 27813594 G	A
395	1184 C	-1:27813593 27813593 C	
395	1185 G	-1:27813592 27813592 G	
396 C	1186 T	-1:27813591 27813591 T	C
396	1187 G	-1:27813590 27813590 G	
396	1188 C	-1:27813589 27813589 C	
397 K	1189 A	-1:27813588 27813588 A	K
397	1190 A	-1:27813587 27813587 A	
397	1191 G	-1:27813586 27813586 G	
398 I	1192 A	-1:27813585 27813585 A	I
398	1193 T	-1:27813584 27813584 T	
398	1194 C	-1:27813583 27813583 C	
399 A	1195 G	-1:27813582 27813582 G	A
399	1196 C	-1:27813581 27813581 C	
399	1197 A	-1:27813580 27813580 A	
400 D	1198 G	-1:27813579 27813579 G	D
400	1199 A	-1:27813578 27813578 A	
400	1200 C	-1:27813577 27813577 C	
401 F	1201 T	-1:27813576 27813576 T	F
401	1202 T	-1:27813575 27813575 T	
401	1203 T	-1:27813574 27813574 T	
402 G	1204 G	-1:27813573 27813573 G	G
402	1205 G	-1:27813572 27813572 G	
402	1206 C	-1:27813571 27813571 C	
403 L	1207 T	-1:27813570 27813570 T	L
403	1208 T	-1:27813569 27813569 T	
403	1209 G	-1:27813568 27813568 G	
404 A	1210 G	-1:27813567 27813567 G	A
404	1211 C	-1:27813566 27813566 C	
404	1212 G	-1:27813565 27813565 G	
405 R	1213 C	-1:27813564 27813564 C	R
405	1214 G	-1:27813563 27813563 G	
405	1215 T	-1:27813562 27813562 T	
406 L	1216 C	-1:27813561 27813561 C	L
406	1217 T	-1:27813560 27813560 T	
406	1218 C	-1:27813559 27813559 C	
407 I	1219 A	-1:27813558 27813558 A	I
407	1220 T	-1:27813557 27813557 T	
407	1221 C	-1:27813556 27813556 C	
408 K	1222 A	-1:27813555 27813555 A	K
408	1223 A	-1:27813554 27813554 A	
408	1224 G	-1:27813553 27813553 G	
409 D	1225 G	-1:27813552 27813552 G	D
409	1226 A	-1:27813551 27813551 A	
409	1227 C	-1:27813550 27813550 C	
410 D	1228 G	-1:27813549 27813549 G	D
410	1229 A	-1:27813548 27813548 A	
410	1230 T	-1:27813547 27813547 T	
411 E	1231 G	-1:27813546 27813546 G	E
411	1232 A	-1:27813545 27813545 A	
411	1233 G	-1:27813544 27813544 G	
412 Y	1234 T	-1:27813543 27813543 T	Y
412	1235 A	-1:27813542 27813542 A	
412	1236 C	-1:27813541 27813541 C	
413 N	1237 A	-1:27813540 27813540 A	N
413	1238 A	-1:27813539 27813539 A	
413	1239 C	-1:27813538 27813538 C	
414 P	1240 C	-1:27813537 27813537 C	P
414	1241 C	-1:27813536 27813536 C	
414	1242 C	-1:27813535 27813535 C	
415 C	1243 T	-1:27813534 27813534 T	C
415	1244 G	-1:27813533 27813533 G	
415	1245 C	-1:27813532 27813532 C	
416 Q	1246 C	-1:27813531 27813531 C	Q
416	1247 A	-1:27813530 27813530 A	
416	1248 A	-1:27813529 27813529 A	
>ENSP00000363115 
1 M	1 A	-1:27823014 27823014 A	M
1	2 T	-1:27823013 27823013 T	
1	3 G	-1:27823012 27823012 G	
2 G	4 G	-1:27823011 27823011 G	G
2	5 G	-1:27823010 27823010 G	
2	6 C	-1:27823009 27823009 C	
3 C	7 T	-1:27823008 27823008 T	C
3	8 G	-1:27823007 27823007 G	
3	9 T	-1:27823006 27823006 T	
4 V	10 G	-1:27823005 27823005 G	V
4	11 T	-1:27823004 27823004 T	
4	12 G	-1:27823003 27823003 G	
5 F	13 T	-1:27823002 27823002 T	F
5	14 T	-1:27823001 27823001 T	
5	15 C	-1:27823000 27823000 C	
6 C	16 T	-1:27822999 27822999 T	C
6	17 G	-1:27822998 27822998 G	
6	18 C	-1:27822997 27822997 C	
7 K	19 A	-1:27822996 27822996 A	K
7	20 A	-1:27822995 27822995 A	
7	21 G	-1:27822994 27822994 G	
8 K	22 A	-1:27822993 27822993 A	K
8	23 A	-1:27822992 27822992 A	
8	24 A	-1:27822991 27822991 A	
9 L	25 T	-1:27822990 27822990 T	L
9	26 T	-1:27822989 27822989 T	
9	27 G	-1:27822988 27822988 G	
10 E	28 G	-1:27822987 27822987 G	E
10	29 A	-1:27822986 27822986 A	
10	30 G	-1:27822985 27822985 G	
11 P	31 C	-1:27822984 27822984 C	P
11	32 C	-1:27822983 27822983 C	
11	33 G	-1:27822982 27822982 G	
12 V	34 G	-1:27822981 27822981 G	V
12	35 T	-1:27822980 27822980 T	
12	36 G	-1:27822979 27822979 G	
13 A	37 G	-1:27822978 27822978 G	A
13	38 C	-1:27822977 27822977 C	
13	39 C	-1:27822976 27822976 C	
14 T	40 A	-1:27822975 27822975 A	T
14	41 C	-1:27822974 27822974 C	
14	42 G	-1:27822973 27822973 G	
15 A	43 G	-1:27822972 27822972 G	A
15	44 C	-1:27822971 27822971 C	
15	45 C	-1:27822970 27822970 C	
16 K	46 A	-1:27822969 27822969 A	K
16	47 A	-1:27822968 27822968 A	
16	48 G	-1:27822967 27822967 G	
17 E	49 G	-1:27822966 27822966 G	E
17	50 A	-1:27822965 27822965 A	
17	51 G	-1:27822964 27822964 G	
18 D	52 G	-1:27822963 27822963 G	D
18	53 A	-1:27822962 27822962 A	
18	54 T	-1:27822961 27822961 T	
19 A	55 G	-1:27822960 27822960 G	A
19	56 C	-1:27822959 27822959 C	
19	57 T	-1:27822958 27822958 T	
20 G	58 G	-1:27822957 27822957 G	G
20	59 G	-1:27822956 27822956 G	
20	60 C	-1:27822955 27822955 C	
21 L	61 C	-1:27822954 27822954 C	L
21	62 T	-1:27822953 27822953 T	
21	63 G	-1:27822952 27822952 G	
22 E	64 G	-1:27822951 27822951 G	E
22	65 A	-1:27822950 27822950 A	
22	66 A	-1:27822949 27822949 A	
23 G	67 G	-1:27822948 27822948 G	G
23	68 G	-1:27822947 27822947 G	
23	69 G	-1:27822946 27822946 G	
24 D	70 G	-1:27822945 27822945 G	D
24	71 A	-1:27822944 27822944 A	
24	72 C	-1:27822943 27822943 C	
25 F	73 T	-1:27822942 27822942 T	F
25	74 T	-1:27822941 27822941 T	
25	75 C	-1:27822940 27822940 C	
26 R	76 A	-1:27822939 27822939 A	R
26	77 G	-1:27822938 27822938 G	
26	78 A	-1:27822937 27822937 A	
27 S	79 A	-1:27822936 27822936 A	S
27	80 G	-1:27822935 27822935 G	
27	81 C	-1:27822934 27822934 C	
28 Y	82 T	-1:27822933 27822933 T	Y
28	83 A	-1:27822932 27822932 A	
28	84 C	-1:27822931 27822931 C	
29 G	85 G	-1:27822930 27822930 G	G
29	86 G	-1:27822929 27822929 G	
29	87 G	-1:27822928 27822928 G	
30 A	88 G	-1:27822927 27822927 G	A
30	89 C	-1:27822926 27822926 C	
30	90 A	-1:27822925 27822925 A	
31 A	91 G	-1:27822924 27822924 G	A
31	92 C	-1:27822923 27822923 C	
31	93 A	-1:27822922 27822922 A	
32 D	94 G	-1:27822921 27822921 G	D
32	95 A	-1:27822920 27822920 A	
32	96 C	-1:27822919 27822919 C	
33 H	97 C	-1:27822918 27822918 C	H
33	98 A	-1:27822917 27822917 A	
33	99 C	-1:27822916 27822916 C	
34 Y	100 T	-1:27822915 27822915 T	Y
34	101 A	-1:27822914 27822914 A	
34	102 T	-1:27822913 27822913 T	
35 G	103 G	-1:27822912 27822912 G	G
35	104 G	-1:27822911 27822911 G	
35	105 G	-1:27822910 27822910 G	
36 P	106 C	-1:27822909 27822909 C	P
36	107 C	-1:27822908 27822908 C	
36	108 T	-1:27822907 27822907 T	
37 D	109 G	-1:27822906 27822906 G	D
37	110 A	-1:27822905 27822905 A	
37	111 C	-1:27822904 27822904 C	
38 P	112 C	-1:27822903 27822903 C	P
38	113 C	-1:27822902 27822902 C	
38	114 C	-1:27822901 27822901 C	
39 T	115 A	-1:27822900 27822900 A	T
39	116 C	-1:27822899 27822899 C	
39	117 T	-1:27822898 27822898 T	
40 K	118 A	-1:27822897 27822897 A	K
40	119 A	-1:27822896 27822896 A	
40	120 G	-1:27822895 27822895 G	
41 A	121 G	-1:27822894 27822894 G	A
41	122 C	-1:27822893 27822893 C	
41	123 C	-1:27822892 27822892 C	
42 R	124 C	-1:27822891 27822891 C	R
42	125 G	-1:27822890 27822890 G	
42	126 G	-1:27822889 27822889 G	
43 P	127 C	-1:27822888 27822888 C	P
43	128 C	-1:27822887 27822887 C	
43	129 T	-1:27822886 27822886 T	
44 A	130 G	-1:27822885 27822885 G	A
44	131 C	-1:27822884 27822884 C	
44	132 A	-1:27822883 27822883 A	
45 S	133 T	-1:27822882 27822882 T	S
45	134 C	-1:27822881 27822881 C	
45	135 C	-1:27822880 27822880 C	
46 S	136 T	-1:27822879 27822879 T	S
46	137 C	-1:27822878 27822878 C	
46	138 A	-1:27822877 27822877 A	
47 F	139 T	-1:27822876 27822876 T	F
47	140 T	-1:27822875 27822875 T	
47	141 T	-1:27822874 27822874 T	
48 A	142 G	-1:27822873 27822873 G	A
48	143 C	-1:27822872 27822872 C	
48	144 C	-1:27822871 27822871 C	
49 H	145 C	-1:27822870 27822870 C	H
49	146 A	-1:27822869 27822869 A	
49	147 C	-1:27822868 27822868 C	
50 I	148 A	-1:27822867 27822867 A	I
50	149 T	-1:27822866 27822866 T	
50	150 C	-1:27822865 27822865 C	
51 P	151 C	-1:27822864 27822864 C	P
51	152 C	-1:27822863 27822863 C	
51	153 C	-1:27822862 27822862 C	
52 N	154 A	-1:27822861 27822861 A	N
52	155 A	-1:27822860 27822860 A	
52	156 C	-1:27822859 27822859 C	
53 Y	157 T	-1:27822858 27822858 T	Y
53	158 A	-1:27822857 27822857 A	
53	159 C	-1:27822856 27822856 C	
54 S	160 A	-1:27822855 27822855 A	S
54	161 G	-1:27822854 27822854 G	
54	162 C	-1:27822853 27822853 C	
55 N	163 A	-1:27822852 27822852 A	N
55	164 A	-1:27822851 27822851 A	
55	165 C	-1:27822850 27822850 C	
56 F	166 T	-1:27822849 27822849 T	F
56	167 T	-1:27822848 27822848 T	
56	168 C	-1:27822847 27822847 C	
57 S	169 T	-1:27822846 27822846 T	S
57	170 C	-1:27822845 27822845 C	
57	171 C	-1:27822844 27822844 C	
58 S	172 T	-1:27822843 27822843 T	S
58	173 C	-1:27822842 27822842 C	
58	174 T	-1:27822841 27822841 T	
59 Q	175 C	-1:27822840 27822840 C	Q
59	176 A	-1:27822839 27822839 A	
59	177 G	-1:27822838 27822838 G	
60 A	178 G	-1:27822837 27822837 G	A
60	179 C	-1:27822836 27822836 C	
60	180 C	-1:27822835 27822835 C	
61 I	181 A	-1:27822834 27822834 A	I
61	182 T	-1:27822833 27822833 T	
61	183 C	-1:27822832 27822832 C	
62 N	184 A	-1:27822831 27822831 A	N
62	185 A	-1:27822830 27822830 A	
62	186 C	-1:27822829 27822829 C	
63 P	187 C	-1:27822828 27822828 C	P
63	188 C	-1:27822827 27822827 C	
63	189 T	-1:27822826 27822826 T	
64 G	190 G	-1:27822825 27822825 G	G
64	191 G	-1:27822824 27822824 G	
64	192 C	-1:27822823 27822823 C	
65 F	193 T	-1:27822822 27822822 T	F
65	194 T	-1:27822821 27822821 T	
65	195 C	-1:27822820 27822820 C	
66 L	196 C	-1:27822819 27822819 C	L
66	197 T	-1:27822818 27822818 T	
66	198 T	-1:27822817 27822817 T	
67 D	199 G	-1:27822816 27822816 G	D
67	200 A	-1:27822815 27822815 A	
67	201 T	-1:27822814 27822814 T	
68 S	202 A	-1:27822813 27822813 A	S
68	203 G	-1:27822812 27822812 G	
68	204 T	-1:27822811 27822811 T	
69 G	205 G	-1:27822810 27822810 G	G
69	206 G	-1:27822809 27822809 G	
69	207 C	-1:27822808 27822808 C	
70 T	208 A	-1:27822807 27822807 A	T
70	209 C	-1:27822806 27822806 C	
70	210 C	-1:27822805 27822805 C	
71 I	211 A	-1:27822804 27822804 A	I
71	212 T	-1:27822803 27822803 T	
71	213 C	-1:27822802 27822802 C	
72 R	214 A	-1:27822801 27822801 A	R
72	215 G	-1:27822800 27822800 G	
72	216 G	-1:27822799 27822799 G	
73 G	217 G	-1:27822798 27822798 G	G
73	218 G	-1:27822797 27822797 G	
73	219 T	-1:27822796 27822796 T	
74 V	220 G	-1:27822795 27822795 G	V
74	221 T	-1:27822794 27822794 T	
74	222 G	-1:27822793 27822793 G	
75 S	223 T	-1:27822792 27822792 T	S
75	224 C	-1:27822791 27822791 C	
75	225 A	-1:27822790 27822790 A	
76 G	226 G	-1:27822789 27822789 G	G
76	227 G	-1:27822242 27822242 G	
76	228 G	-1:27822241 27822241 G	
77 I	229 A	-1:27822240 27822240 A	I
77	230 T	-1:27822239 27822239 T	
77	231 T	-1:27822238 27822238 T	
78 G	232 G	-1:27822237 27822237 G	G
78	233 G	-1:27822236 27822236 G	
78	234 G	-1:27822235 27822235 G	
79 V	235 G	-1:27822234 27822234 G	V
79	236 T	-1:27822233 27822233 T	
79	237 G	-1:27822232 27822232 G	
80 T	238 A	-1:27822231 27822231 A	T
80	239 C	-1:27822230 27822230 C	
80	240 C	-1:27822229 27822229 C	
81 L	241 C	-1:27822228 27822228 C	L
81	242 T	-1:27822227 27822227 T	
81	243 G	-1:27822226 27822226 G	
82 F	244 T	-1:27822225 27822225 T	F
82	245 T	-1:27822224 27822224 T	
82	246 C	-1:27822223 27822223 C	
83 I	247 A	-1:27822222 27822222 A	I
83	248 T	-1:27822221 27822221 T	
83	249 T	-1:27822220 27822220 T	
84 A	250 G	-1:27822219 27822219 G	A
84	251 C	-1:27822218 27822218 C	
84	252 C	-1:27822217 27822217 C	
85 L	253 C	-1:27822216 27822216 C	L
85	254 T	-1:27822215 27822215 T	
85	255 G	-1:27822214 27822214 G	
86 Y	256 T	-1:27822213 27822213 T	Y
86	257 A	-1:27822212 27822212 A	
86	258 T	-1:27822211 27822211 T	
87 D	259 G	-1:27822210 27822210 G	D
87	260 A	-1:27822209 27822209 A	
87	261 C	-1:27822208 27822208 C	
88 Y	262 T	-1:27822207 27822207 T	Y
88	263 A	-1:27822206 27822206 A	
88	264 T	-1:27822205 27822205 T	
89 E	265 G	-1:27822204 27822204 G	E
89	266 A	-1:27822203 27822203 A	
89	267 G	-1:27822202 27822202 G	
90 A	268 G	-1:27822201 27822201 G	A
90	269 C	-1:27822200 27822200 C	
90	270 T	-1:27822199 27822199 T	
91 R	271 C	-1:27822198 27822198 C	R
91	272 G	-1:27822197 27822197 G	
91	273 A	-1:27822196 27822196 A	
92 T	274 A	-1:27822195 27822195 A	T
92	275 C	-1:27822194 27822194 C	
92	276 T	-1:27822193 27822193 T	
93 E	277 G	-1:27822192 27822192 G	E
93	278 A	-1:27822191 27822191 A	
93	279 G	-1:27822190 27822190 G	
94 D	280 G	-1:27822189 27822189 G	D
94	281 A	-1:27822188 27822188 A	
94	282 T	-1:27822187 27822187 T	
95 D	283 G	-1:27822186 27822186 G	D
95	284 A	-1:27822185 27822185 A	
95	285 C	-1:27822184 27822184 C	
96 L	286 C	-1:27822183 27822183 C	L
96	287 T	-1:27822182 27822182 T	
96	288 C	-1:27822181 27822181 C	
97 T	289 A	-1:27822180 27822180 A	T
97	290 C	-1:27822179 27822179 C	
97	291 C	-1:27822178 27822178 C	
98 F	292 T	-1:27822177 27822177 T	F
98	293 T	-1:27822176 27822176 T	
98	294 C	-1:27822175 27822175 C	
99 T	295 A	-1:27822174 27822174 A	T
99	296 C	-1:27822173 27822173 C	
99	297 C	-1:27822172 27822172 C	
100 K	298 A	-1:27822171 27822171 A	K
100	299 A	-1:27822170 27822170 A	
100	300 G	-1:27822169 27822169 G	
101 G	301 G	-1:27822168 27822168 G	G
101	302 G	-1:27822167 27822167 G	
101	303 C	-1:27822166 27822166 C	
102 E	304 G	-1:27822165 27822165 G	E
102	305 A	-1:27822164 27822164 A	
102	306 G	-1:27822163 27822163 G	
103 K	307 A	-1:27822162 27822162 A	K
103	308 A	-1:27822161 27822161 A	
103	309 G	-1:27822160 27822160 G	
104 F	310 T	-1:27822159 27822159 T	F
104	311 T	-1:27822158 27822158 T	
104	312 C	-1:27822157 27822157 C	
105 H	313 C	-1:27822156 27822156 C	H
105	314 A	-1:27822155 27822155 A	
105	315 C	-1:27822154 27822154 C	
106 I	316 A	-1:27822153 27822153 A	I
106	317 T	-1:27822152 27822152 T	
106	318 C	-1:27822151 27822151 C	
107 L	319 C	-1:27822150 27822150 C	L
107	320 T	-1:27822149 27822149 T	
107	321 G	-1:27822148 27822148 G	
108 N	322 A	-1:27822147 27822147 A	N
108	323 A	-1:27822146 27822146 A	
108	324 C	-1:27822145 27822145 C	
109 N	325 A	-1:27822144 27822144 A	N
109	326 A	-1:27822143 27822143 A	
109	327 T	-1:27822142 27822142 T	
110 T	328 A	-1:27822141 27822141 A	T
110	329 C	-1:27822140 27822140 C	
110	330 T	-1:27820755 27820755 T	
111 E	331 G	-1:27820754 27820754 G	E
111	332 A	-1:27820753 27820753 A	
111	333 A	-1:27820752 27820752 A	
112 G	334 G	-1:27820751 27820751 G	G
112	335 G	-1:27820750 27820750 G	
112	336 T	-1:27820749 27820749 T	
113 D	337 G	-1:27820748 27820748 G	D
113	338 A	-1:27820747 27820747 A	
113	339 C	-1:27820746 27820746 C	
114 W	340 T	-1:27820745 27820745 T	W
114	341 G	-1:27820744 27820744 G	
114	342 G	-1:27820743 27820743 G	
115 W	343 T	-1:27820742 27820742 T	W
115	344 G	-1:27820741 27820741 G	
115	345 G	-1:27820740 27820740 G	
116 E	346 G	-1:27820739 27820739 G	E
116	347 A	-1:27820738 27820738 A	
116	348 G	-1:27820737 27820737 G	
117 A	349 G	-1:27820736 27820736 G	A
117	350 C	-1:27820735 27820735 C	
117	351 T	-1:27820734 27820734 T	
118 R	352 C	-1:27820733 27820733 C	R
118	353 G	-1:27820732 27820732 G	
118	354 G	-1:27820731 27820731 G	
119 S	355 T	-1:27820730 27820730 T	S
119	356 C	-1:27820729 27820729 C	
119	357 T	-1:27820728 27820728 T	
120 L	358 C	-1:27820727 27820727 C	L
120	359 T	-1:27820726 27820726 T	
120	360 C	-1:27820725 27820725 C	
121 S	361 A	-1:27820724 27820724 A	S
121	362 G	-1:27820723 27820723 G	
121	363 C	-1:27820722 27820722 C	
122 S	364 T	-1:27820721 27820721 T	S
122	365 C	-1:27820720 27820720 C	
122	366 C	-1:27820719 27820719 C	
123 G	367 G	-1:27820718 27820718 G	G
123	368 G	-1:27820717 27820717 G	
123	369 A	-1:27820716 27820716 A	
124 K	370 A	-1:27820715 27820715 A	K
124	371 A	-1:27820714 27820714 A	
124	372 A	-1:27820713 27820713 A	
125 T	373 A	-1:27820712 27820712 A	T
125	374 C	-1:27820711 27820711 C	
125	375 T	-1:27820710 27820710 T	
126 G	376 G	-1:27820709 27820709 G	G
126	377 G	-1:27820708 27820708 G	
126	378 C	-1:27820707 27820707 C	
127 C	379 T	-1:27820706 27820706 T	C
127	380 G	-1:27820705 27820705 G	
127	381 C	-1:27820704 27820704 C	
128 I	382 A	-1:27820703 27820703 A	I
128	383 T	-1:27820702 27820702 T	
128	384 T	-1:27820701 27820701 T	
129 P	385 C	-1:27820700 27820700 C	P
129	386 C	-1:27820699 27820699 C	
129	387 C	-1:27820698 27820698 C	
130 S	388 A	-1:27820697 27820697 A	S
130	389 G	-1:27820696 27820696 G	
130	390 C	-1:27820695 27820695 C	
131 N	391 A	-1:27820694 27820694 A	N
131	392 A	-1:27820693 27820693 A	
131	393 C	-1:27820692 27820692 C	
132 Y	394 T	-1:27820691 27820691 T	Y
132	395 A	-1:27820690 27820690 A	
132	396 C	-1:27820689 27820689 C	
133 V	397 G	-1:27820688 27820688 G	V
133	398 T	-1:27820687 27820687 T	
133	399 G	-1:27820686 27820686 G	
134 A	400 G	-1:27820685 27820685 G	A
134	401 C	-1:27820684 27820684 C	
134	402 C	-1:27820683 27820683 C	
135 P	403 C	-1:27820682 27820682 C	P
135	404 C	-1:27820681 27820681 C	
135	405 T	-1:27820680 27820680 T	
136 V	406 G	-1:27820679 27820679 G	V
136	407 T	-1:27820678 27820678 T	
136	408 T	-1:27820677 27820677 T	
137 D	409 G	-1:27820676 27820676 G	D
137	410 A	-1:27820675 27820675 A	
137	411 C	-1:27820674 27820674 C	
138 S	412 T	-1:27820673 27820673 T	S
138	413 C	-1:27820672 27820672 C	
138	414 A	-1:27820671 27820671 A	
139 I	415 A	-1:27820670 27820670 A	I
139	416 T	-1:27820669 27820669 T	
139	417 C	-1:27820668 27820668 C	
140 Q	418 C	-1:27820667 27820667 C	Q
140	419 A	-1:27820666 27820666 A	
140	420 A	-1:27820665 27820665 A	
141 A	421 G	-1:27820664 27820664 G	A
141	422 C	-1:27820663 27820663 C	
141	423 T	-1:27820662 27820662 T	
142 E	424 G	-1:27820661 27820661 G	E
142	425 A	-1:27820660 27820660 A	
142	426 A	-1:27820659 27820659 A	
143 E	427 G	-1:27820658 27820658 G	E
143	428 A	-1:27820657 27820657 A	
143	429 G	-1:27816394 27816394 G	
144 W	430 T	-1:27816393 27816393 T	W
144	431 G	-1:27816392 27816392 G	
144	432 G	-1:27816391 27816391 G	
145 Y	433 T	-1:27816390 27816390 T	Y
145	434 A	-1:27816389 27816389 A	
145	435 C	-1:27816388 27816388 C	
146 F	436 T	-1:27816387 27816387 T	F
146	437 T	-1:27816386 27816386 T	
146	438 T	-1:27816385 27816385 T	
147 G	439 G	-1:27816384 27816384 G	G
147	440 G	-1:27816383 27816383 G	
147	441 A	-1:27816382 27816382 A	
148 K	442 A	-1:27816381 27816381 A	K
148	443 A	-1:27816380 27816380 A	
148	444 G	-1:27816379 27816379 G	
149 I	445 A	-1:27816378 27816378 A	I
149	446 T	-1:27816377 27816377 T	
149	447 T	-1:27816376 27816376 T	
150 G	448 G	-1:27816375 27816375 G	G
150	449 G	-1:27816374 27816374 G	
150	450 G	-1:27816373 27816373 G	
151 R	451 A	-1:27816372 27816372 A	R
151	452 G	-1:27816371 27816371 G	
151	453 A	-1:27816370 27816370 A	
152 K	454 A	-1:27816369 27816369 A	K
152	455 A	-1:27816368 27816368 A	
152	456 G	-1:27816367 27816367 G	
153 D	457 G	-1:27816366 27816366 G	D
153	458 A	-1:27816365 27816365 A	
153	459 T	-1:27816364 27816364 T	
154 A	460 G	-1:27816363 27816363 G	A
154	461 C	-1:27816362 27816362 C	
154	462 A	-1:27816361 27816361 A	
155 E	463 G	-1:27816360 27816360 G	E
155	464 A	-1:27816359 27816359 A	
155	465 G	-1:27816358 27816358 G	
156 R	466 A	-1:27816357 27816357 A	R
156	467 G	-1:27816356 27816356 G	
156	468 G	-1:27816355 27816355 G	
157 Q	469 C	-1:27816354 27816354 C	Q
157	470 A	-1:27816353 27816353 A	
157	471 G	-1:27816352 27816352 G	
158 L	472 C	-1:27816351 27816351 C	L
158	473 T	-1:27816350 27816350 T	
158	474 G	-1:27816349 27816349 G	
159 L	475 C	-1:27816348 27816348 C	L
159	476 T	-1:27816347 27816347 T	
159	477 T	-1:27816346 27816346 T	
160 S	478 T	-1:27816345 27816345 T	S
160	479 C	-1:27816344 27816344 C	
160	480 A	-1:27816343 27816343 A	
161 P	481 C	-1:27816342 27816342 C	P
161	482 C	-1:27816341 27816341 C	
161	483 A	-1:27816340 27816340 A	
162 G	484 G	-1:27816339 27816339 G	G
162	485 G	-1:27816338 27816338 G	
162	486 C	-1:27816337 27816337 C	
163 N	487 A	-1:27816336 27816336 A	N
163	488 A	-1:27816335 27816335 A	
163	489 C	-1:27816334 27816334 C	
164 P	490 C	-1:27816333 27816333 C	P
164	491 C	-1:27816332 27816332 C	
164	492 C	-1:27816331 27816331 C	
165 Q	493 C	-1:27816330 27816330 C	Q
165	494 A	-1:27816329 27816329 A	
165	495 G	-1:27816328 27816328 G	
166 G	496 G	-1:27816327 27816327 G	G
166	497 G	-1:27816326 27816326 G	
166	498 G	-1:27816325 27816325 G	
167 A	499 G	-1:27816324 27816324 G	A
167	500 C	-1:27816323 27816323 C	
167	501 C	-1:27816322 27816322 C	
168 F	502 T	-1:27816321 27816321 T	F
168	503 T	-1:27816320 27816320 T	
168	504 T	-1:27816319 27816319 T	
169 L	505 C	-1:27816318 27816318 C	L
169	506 T	-1:27816317 27816317 T	
169	507 C	-1:27816316 27816316 C	
170 I	508 A	-1:27816315 27816315 A	I
170	509 T	-1:27816314 27816314 T	
170	510 T	-1:27816313 27816313 T	
171 R	511 C	-1:27816312 27816312 C	R
171	512 G	-1:27816311 27816311 G	
171	513 G	-1:27816310 27816310 G	
172 E	514 G	-1:27816309 27816309 G	E
172	515 A	-1:27816308 27816308 A	
172	516 A	-1:27816307 27816307 A	
173 S	517 A	-1:27816306 27816306 A	S
173	518 G	-1:27816305 27816305 G	
173	519 C	-1:27816304 27816304 C	
174 E	520 G	-1:27816303 27816303 G	E
174	521 A	-1:27816302 27816302 A	
174	522 G	-1:27816301 27816301 G	
175 T	523 A	-1:27816300 27816300 A	T
175	524 C	-1:27816299 27816299 C	
175	525 C	-1:27816298 27816298 C	
176 T	526 A	-1:27816297 27816297 A	T
176	527 C	-1:27816296 27816296 C	
176	528 C	-1:27816295 27816295 C	
177 K	529 A	-1:27816294 27816294 A	K
177	530 A	-1:27816293 27816293 A	
177	531 A	-1:27816292 27816292 A	
178 G	532 G	-1:27816291 27816291 G	G
178	533 G	-1:27816104 27816104 G	
178	534 T	-1:27816103 27816103 T	
179 A	535 G	-1:27816102 27816102 G	A
179	536 C	-1:27816101 27816101 C	
179	537 C	-1:27816100 27816100 C	
180 Y	538 T	-1:27816099 27816099 T	Y
180	539 A	-1:27816098 27816098 A	
180	540 C	-1:27816097 27816097 C	
181 S	541 T	-1:27816096 27816096 T	S
181	542 C	-1:27816095 27816095 C	
181	543 C	-1:27816094 27816094 C	
182 L	544 C	-1:27816093 27816093 C	L
182	545 T	-1:27816092 27816092 T	
182	546 G	-1:27816091 27816091 G	
183 S	547 T	-1:27816090 27816090 T	S
183	548 C	-1:27816089 27816089 C	
183	549 C	-1:27816088 27816088 C	
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184	551 T	-1:27816086 27816086 T	
184	552 C	-1:27816085 27816085 C	
185 R	553 C	-1:27816084 27816084 C	R
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185	555 G	-1:27816082 27816082 G	
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186	557 A	-1:27816080 27816080 A	
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187 W	559 T	-1:27816078 27816078 T	W
187	560 G	-1:27816077 27816077 G	
187	561 G	-1:27816076 27816076 G	
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189 Q	565 C	-1:27816072 27816072 C	Q
189	566 A	-1:27816071 27816071 A	
189	567 G	-1:27816070 27816070 G	
190 T	568 A	-1:27816069 27816069 A	T
190	569 C	-1:27816068 27816068 C	
190	570 C	-1:27816067 27816067 C	
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191	572 G	-1:27816065 27816065 G	
191	573 A	-1:27816064 27816064 A	
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193	578 A	-1:27816059 27816059 A	
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194 H	580 C	-1:27816057 27816057 C	H
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194	582 T	-1:27816055 27816055 T	
195 V	583 G	-1:27816054 27816054 G	V
195	584 T	-1:27816053 27816053 T	
195	585 G	-1:27816052 27816052 G	
196 K	586 A	-1:27816051 27816051 A	K
196	587 A	-1:27816050 27816050 A	
196	588 G	-1:27816049 27816049 G	
197 H	589 C	-1:27816048 27816048 C	H
197	590 A	-1:27816047 27816047 A	
197	591 T	-1:27816046 27816046 T	
198 Y	592 T	-1:27816045 27816045 T	Y
198	593 A	-1:27816044 27816044 A	
198	594 C	-1:27816043 27816043 C	
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199	596 A	-1:27816041 27816041 A	
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200 I	598 A	-1:27816039 27816039 A	I
200	599 T	-1:27816038 27816038 T	
200	600 C	-1:27816037 27816037 C	
201 R	601 C	-1:27816036 27816036 C	R
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201	603 C	-1:27816034 27816034 C	
202 K	604 A	-1:27816033 27816033 A	K
202	605 A	-1:27816032 27816032 A	
202	606 A	-1:27816031 27816031 A	
203 L	607 C	-1:27816030 27816030 C	L
203	608 T	-1:27816029 27816029 T	
203	609 G	-1:27816028 27816028 G	
204 D	610 G	-1:27816027 27816027 G	D
204	611 A	-1:27816026 27816026 A	
204	612 C	-1:27816025 27816025 C	
205 M	613 A	-1:27816024 27816024 A	M
205	614 T	-1:27816023 27816023 T	
205	615 G	-1:27816022 27816022 G	
206 G	616 G	-1:27816021 27816021 G	G
206	617 G	-1:27816020 27816020 G	
206	618 C	-1:27816019 27816019 C	
207 G	619 G	-1:27816018 27816018 G	G
207	620 G	-1:27816017 27816017 G	
207	621 C	-1:27816016 27816016 C	
208 Y	622 T	-1:27816015 27816015 T	Y
208	623 A	-1:27816014 27816014 A	
208	624 C	-1:27816013 27816013 C	
209 Y	625 T	-1:27816012 27816012 T	Y
209	626 A	-1:27816011 27816011 A	
209	627 C	-1:27816010 27816010 C	
210 I	628 A	-1:27816009 27816009 A	I
210	629 T	-1:27816008 27816008 T	
210	630 C	-1:27816007 27816007 C	
211 T	631 A	-1:27816006 27816006 A	T
211	632 C	-1:27816005 27816005 C	
211	633 C	-1:27816004 27816004 C	
212 T	634 A	-1:27816003 27816003 A	T
212	635 C	-1:27816002 27816002 C	
212	636 A	-1:27816001 27816001 A	
213 R	637 C	-1:27816000 27816000 C	R
213	638 G	-1:27815999 27815999 G	
213	639 G	-1:27815998 27815998 G	
214 V	640 G	-1:27815997 27815997 G	V
214	641 T	-1:27815996 27815996 T	
214	642 T	-1:27815995 27815995 T	
215 Q	643 C	-1:27815994 27815994 C	Q
215	644 A	-1:27815993 27815993 A	
215	645 G	-1:27815992 27815992 G	
216 F	646 T	-1:27815991 27815991 T	F
216	647 T	-1:27815990 27815990 T	
216	648 C	-1:27815989 27815989 C	
217 N	649 A	-1:27815988 27815988 A	N
217	650 A	-1:27815987 27815987 A	
217	651 C	-1:27815986 27815986 C	
218 S	652 T	-1:27815985 27815985 T	S
218	653 C	-1:27815984 27815984 C	
218	654 G	-1:27815983 27815983 G	
219 V	655 G	-1:27815982 27815982 G	V
219	656 T	-1:27815981 27815981 T	
219	657 G	-1:27815980 27815980 G	
220 Q	658 C	-1:27815979 27815979 C	Q
220	659 A	-1:27815978 27815978 A	
220	660 G	-1:27815977 27815977 G	
221 E	661 G	-1:27815976 27815976 G	E
221	662 A	-1:27815975 27815975 A	
221	663 G	-1:27815974 27815974 G	
222 L	664 C	-1:27815973 27815973 C	L
222	665 T	-1:27815972 27815972 T	
222	666 G	-1:27815971 27815971 G	
223 V	667 G	-1:27815970 27815970 G	V
223	668 T	-1:27815969 27815969 T	
223	669 G	-1:27815968 27815968 G	
224 Q	670 C	-1:27815967 27815967 C	Q
224	671 A	-1:27815966 27815966 A	
224	672 G	-1:27815965 27815965 G	
225 H	673 C	-1:27815964 27815964 C	H
225	674 A	-1:27815963 27815963 A	
225	675 C	-1:27815962 27815962 C	
226 Y	676 T	-1:27815961 27815961 T	Y
226	677 A	-1:27815960 27815960 A	
226	678 C	-1:27815959 27815959 C	
227 M	679 A	-1:27815958 27815958 A	M
227	680 T	-1:27815957 27815957 T	
227	681 G	-1:27815956 27815956 G	
228 E	682 G	-1:27815955 27815955 G	E
228	683 A	-1:27814942 27814942 A	
228	684 G	-1:27814941 27814941 G	
229 V	685 G	-1:27814940 27814940 G	V
229	686 T	-1:27814939 27814939 T	
229	687 G	-1:27814938 27814938 G	
230 N	688 A	-1:27814937 27814937 A	N
230	689 A	-1:27814936 27814936 A	
230	690 T	-1:27814935 27814935 T	
231 D	691 G	-1:27814934 27814934 G	D
231	692 A	-1:27814933 27814933 A	
231	693 C	-1:27814932 27814932 C	
232 G	694 G	-1:27814931 27814931 G	G
232	695 G	-1:27814930 27814930 G	
232	696 G	-1:27814929 27814929 G	
233 L	697 C	-1:27814928 27814928 C	L
233	698 T	-1:27814927 27814927 T	
233	699 G	-1:27814926 27814926 G	
234 C	700 T	-1:27814925 27814925 T	C
234	701 G	-1:27814924 27814924 G	
234	702 C	-1:27814923 27814923 C	
235 N	703 A	-1:27814922 27814922 A	N
235	704 A	-1:27814921 27814921 A	
235	705 C	-1:27814920 27814920 C	
236 L	706 C	-1:27814919 27814919 C	L
236	707 T	-1:27814918 27814918 T	
236	708 G	-1:27814917 27814917 G	
237 L	709 C	-1:27814916 27814916 C	L
237	710 T	-1:27814915 27814915 T	
237	711 C	-1:27814914 27814914 C	
238 I	712 A	-1:27814913 27814913 A	I
238	713 T	-1:27814912 27814912 T	
238	714 C	-1:27814911 27814911 C	
239 A	715 G	-1:27814910 27814910 G	A
239	716 C	-1:27814909 27814909 C	
239	717 G	-1:27814908 27814908 G	
240 P	718 C	-1:27814907 27814907 C	P
240	719 C	-1:27814906 27814906 C	
240	720 C	-1:27814905 27814905 C	
241 C	721 T	-1:27814904 27814904 T	C
241	722 G	-1:27814903 27814903 G	
241	723 C	-1:27814902 27814902 C	
242 T	724 A	-1:27814901 27814901 A	T
242	725 C	-1:27814900 27814900 C	
242	726 C	-1:27814899 27814899 C	
243 I	727 A	-1:27814898 27814898 A	I
243	728 T	-1:27814897 27814897 T	
243	729 C	-1:27814896 27814896 C	
244 M	730 A	-1:27814895 27814895 A	M
244	731 T	-1:27814894 27814894 T	
244	732 G	-1:27814893 27814893 G	
245 K	733 A	-1:27814892 27814892 A	K
245	734 A	-1:27814891 27814891 A	
245	735 G	-1:27814890 27814890 G	
246 P	736 C	-1:27814889 27814889 C	P
246	737 C	-1:27814888 27814888 C	
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247 Q	739 C	-1:27814886 27814886 C	Q
247	740 A	-1:27814885 27814885 A	
247	741 G	-1:27814884 27814884 G	
248 T	742 A	-1:27814883 27814883 A	T
248	743 C	-1:27814882 27814882 C	
248	744 G	-1:27814881 27814881 G	
249 L	745 C	-1:27814880 27814880 C	L
249	746 T	-1:27814879 27814879 T	
249	747 G	-1:27814878 27814878 G	
250 G	748 G	-1:27814877 27814877 G	G
250	749 G	-1:27814876 27814876 G	
250	750 C	-1:27814875 27814875 C	
251 L	751 C	-1:27814874 27814874 C	L
251	752 T	-1:27814873 27814873 T	
251	753 G	-1:27814872 27814872 G	
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252	755 C	-1:27814870 27814870 C	
252	756 C	-1:27814869 27814869 C	
253 K	757 A	-1:27814868 27814868 A	K
253	758 A	-1:27814867 27814867 A	
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254	761 A	-1:27814864 27814864 A	
254	762 C	-1:27814863 27814863 C	
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255	764 C	-1:27814861 27814861 C	
255	765 C	-1:27814860 27814860 C	
256 W	766 T	-1:27814859 27814859 T	W
256	767 G	-1:27814858 27814858 G	
256	768 G	-1:27814857 27814857 G	
257 E	769 G	-1:27814856 27814856 G	E
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257	771 G	-1:27814854 27814854 G	
258 I	772 A	-1:27814853 27814853 A	I
258	773 T	-1:27814852 27814852 T	
258	774 C	-1:27814851 27814851 C	
259 S	775 A	-1:27814850 27814850 A	S
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259	777 C	-1:27814848 27814848 C	
260 R	778 C	-1:27814847 27814847 C	R
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260	780 C	-1:27814845 27814845 C	
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261	782 G	-1:27814843 27814843 G	
261	783 C	-1:27814842 27814842 C	
262 S	784 T	-1:27814841 27814841 T	S
262	785 C	-1:27814840 27814840 C	
262	786 C	-1:27814839 27814839 C	
263 I	787 A	-1:27814838 27814838 A	I
263	788 T	-1:27814837 27814837 T	
263	789 C	-1:27814836 27814836 C	
264 T	790 A	-1:27814835 27814835 A	T
264	791 C	-1:27814834 27814834 C	
264	792 G	-1:27814833 27814833 G	
265 L	793 C	-1:27814832 27814832 C	L
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265	795 G	-1:27814830 27814830 G	
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269 L	805 C	-1:27814820 27814820 C	L
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269	807 G	-1:27814818 27814818 G	
270 G	808 G	-1:27814817 27814817 G	G
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270	810 C	-1:27814815 27814815 C	
271 T	811 A	-1:27814814 27814814 A	T
271	812 C	-1:27814813 27814813 C	
271	813 C	-1:27814812 27814812 C	
272 G	814 G	-1:27814811 27814811 G	G
272	815 G	-1:27814810 27814810 G	
272	816 C	-1:27814809 27814809 C	
273 C	817 T	-1:27814808 27814808 T	C
273	818 G	-1:27814807 27814807 G	
273	819 C	-1:27814806 27814806 C	
274 F	820 T	-1:27814805 27814805 T	F
274	821 T	-1:27814804 27814804 T	
274	822 C	-1:27814803 27814803 C	
275 G	823 G	-1:27814802 27814802 G	G
275	824 G	-1:27814801 27814801 G	
275	825 G	-1:27814800 27814800 G	
276 D	826 G	-1:27814799 27814799 G	D
276	827 A	-1:27814798 27814798 A	
276	828 T	-1:27814797 27814797 T	
277 V	829 G	-1:27814796 27814796 G	V
277	830 T	-1:27814795 27814795 T	
277	831 G	-1:27814794 27814794 G	
278 W	832 T	-1:27814793 27814793 T	W
278	833 G	-1:27814792 27814792 G	
278	834 G	-1:27814791 27814791 G	
279 L	835 C	-1:27814790 27814790 C	L
279	836 T	-1:27814789 27814789 T	
279	837 G	-1:27814788 27814788 G	
280 G	838 G	-1:27814787 27814787 G	G
280	839 G	-1:27814711 27814711 G	
280	840 C	-1:27814710 27814710 C	
281 T	841 A	-1:27814709 27814709 A	T
281	842 C	-1:27814708 27814708 C	
281	843 G	-1:27814707 27814707 G	
282 W	844 T	-1:27814706 27814706 T	W
282	845 G	-1:27814705 27814705 G	
282	846 G	-1:27814704 27814704 G	
283 N	847 A	-1:27814703 27814703 A	N
283	848 A	-1:27814702 27814702 A	
283	849 C	-1:27814701 27814701 C	
284 G	850 G	-1:27814700 27814700 G	G
284	851 G	-1:27814699 27814699 G	
284	852 C	-1:27814698 27814698 C	
285 S	853 A	-1:27814697 27814697 A	S
285	854 G	-1:27814696 27814696 G	
285	855 C	-1:27814695 27814695 C	
286 T	856 A	-1:27814694 27814694 A	T
286	857 C	-1:27814693 27814693 C	
286	858 T	-1:27814692 27814692 T	
287 K	859 A	-1:27814691 27814691 A	K
287	860 A	-1:27814690 27814690 A	
287	861 G	-1:27814689 27814689 G	
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288	863 T	-1:27814687 27814687 T	
288	864 G	-1:27814686 27814686 G	
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289	866 C	-1:27814684 27814684 C	
289	867 G	-1:27814683 27814683 G	
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290	869 T	-1:27814681 27814681 T	
290	870 G	-1:27814680 27814680 G	
291 K	871 A	-1:27814679 27814679 A	K
291	872 A	-1:27814678 27814678 A	
291	873 G	-1:27814677 27814677 G	
292 T	874 A	-1:27814676 27814676 A	T
292	875 C	-1:27814675 27814675 C	
292	876 G	-1:27814674 27814674 G	
293 L	877 C	-1:27814673 27814673 C	L
293	878 T	-1:27814672 27814672 T	
293	879 G	-1:27814671 27814671 G	
294 K	880 A	-1:27814670 27814670 A	K
294	881 A	-1:27814669 27814669 A	
294	882 G	-1:27814668 27814668 G	
295 P	883 C	-1:27814667 27814667 C	P
295	884 C	-1:27814666 27814666 C	
295	885 G	-1:27814665 27814665 G	
296 G	886 G	-1:27814664 27814664 G	G
296	887 G	-1:27814663 27814663 G	
296	888 C	-1:27814662 27814662 C	
297 T	889 A	-1:27814661 27814661 A	T
297	890 C	-1:27814660 27814660 C	
297	891 C	-1:27814659 27814659 C	
298 M	892 A	-1:27814658 27814658 A	M
298	893 T	-1:27814657 27814657 T	
298	894 G	-1:27814656 27814656 G	
299 S	895 T	-1:27814655 27814655 T	S
299	896 C	-1:27814654 27814654 C	
299	897 C	-1:27814653 27814653 C	
300 P	898 C	-1:27814652 27814652 C	P
300	899 C	-1:27814651 27814651 C	
300	900 G	-1:27814650 27814650 G	
301 K	901 A	-1:27814649 27814649 A	K
301	902 A	-1:27814648 27814648 A	
301	903 G	-1:27814647 27814647 G	
302 A	904 G	-1:27814646 27814646 G	A
302	905 C	-1:27814645 27814645 C	
302	906 C	-1:27814644 27814644 C	
303 F	907 T	-1:27814643 27814643 T	F
303	908 T	-1:27814642 27814642 T	
303	909 C	-1:27814641 27814641 C	
304 L	910 C	-1:27814640 27814640 C	L
304	911 T	-1:27814639 27814639 T	
304	912 G	-1:27814638 27814638 G	
305 E	913 G	-1:27814637 27814637 G	E
305	914 A	-1:27814636 27814636 A	
305	915 G	-1:27814635 27814635 G	
306 E	916 G	-1:27814634 27814634 G	E
306	917 A	-1:27814633 27814633 A	
306	918 G	-1:27814632 27814632 G	
307 A	919 G	-1:27814631 27814631 G	A
307	920 C	-1:27814630 27814630 C	
307	921 G	-1:27814629 27814629 G	
308 Q	922 C	-1:27814628 27814628 C	Q
308	923 A	-1:27814627 27814627 A	
308	924 G	-1:27814626 27814626 G	
309 V	925 G	-1:27814625 27814625 G	V
309	926 T	-1:27814624 27814624 T	
309	927 C	-1:27814623 27814623 C	
310 M	928 A	-1:27814622 27814622 A	M
310	929 T	-1:27814621 27814621 T	
310	930 G	-1:27814620 27814620 G	
311 K	931 A	-1:27814619 27814619 A	K
311	932 A	-1:27814618 27814618 A	
311	933 G	-1:27814617 27814617 G	
312 L	934 C	-1:27814616 27814616 C	L
312	935 T	-1:27814615 27814615 T	
312	936 G	-1:27814614 27814614 G	
313 L	937 C	-1:27814613 27814613 C	L
313	938 T	-1:27814612 27814612 T	
313	939 G	-1:27814611 27814611 G	
314 R	940 C	-1:27814610 27814610 C	R
314	941 G	-1:27814609 27814609 G	
314	942 G	-1:27814608 27814608 G	
315 H	943 C	-1:27814607 27814607 C	H
315	944 A	-1:27814606 27814606 A	
315	945 C	-1:27814605 27814605 C	
316 D	946 G	-1:27814604 27814604 G	D
316	947 A	-1:27814603 27814603 A	
316	948 C	-1:27814602 27814602 C	
317 K	949 A	-1:27814601 27814601 A	K
317	950 A	-1:27814600 27814600 A	
317	951 G	-1:27814599 27814599 G	
318 L	952 C	-1:27814598 27814598 C	L
318	953 T	-1:27814597 27814597 T	
318	954 G	-1:27814596 27814596 G	
319 V	955 G	-1:27814595 27814595 G	V
319	956 T	-1:27814594 27814594 T	
319	957 G	-1:27814593 27814593 G	
320 Q	958 C	-1:27814592 27814592 C	Q
320	959 A	-1:27814591 27814591 A	
320	960 G	-1:27814590 27814590 G	
321 L	961 C	-1:27814589 27814589 C	L
321	962 T	-1:27814588 27814588 T	
321	963 G	-1:27814587 27814587 G	
322 Y	964 T	-1:27814586 27814586 T	Y
322	965 A	-1:27814585 27814585 A	
322	966 C	-1:27814584 27814584 C	
323 A	967 G	-1:27814583 27814583 G	A
323	968 C	-1:27814582 27814582 C	
323	969 C	-1:27814581 27814581 C	
324 V	970 G	-1:27814580 27814580 G	V
324	971 T	-1:27814579 27814579 T	
324	972 G	-1:27814578 27814578 G	
325 V	973 G	-1:27814577 27814577 G	V
325	974 T	-1:27814576 27814576 T	
325	975 G	-1:27814575 27814575 G	
326 S	976 T	-1:27814574 27814574 T	S
326	977 C	-1:27814573 27814573 C	
326	978 G	-1:27814572 27814572 G	
327 E	979 G	-1:27814571 27814571 G	E
327	980 A	-1:27814570 27814570 A	
327	981 G	-1:27814569 27814569 G	
328 E	982 G	-1:27814568 27814568 G	E
328	983 A	-1:27814567 27814567 A	
328	984 G	-1:27814566 27814566 G	
329 P	985 C	-1:27814565 27814565 C	P
329	986 C	-1:27814564 27814564 C	
329	987 C	-1:27814563 27814563 C	
330 I	988 A	-1:27814562 27814562 A	I
330	989 T	-1:27814561 27814561 T	
330	990 C	-1:27814560 27814560 C	
331 Y	991 T	-1:27814559 27814559 T	Y
331	992 A	-1:27814558 27814558 A	
331	993 C	-1:27814557 27814557 C	
332 I	994 A	-1:27814556 27814556 A	I
332	995 T	-1:27814555 27814555 T	
332	996 C	-1:27814554 27814554 C	
333 V	997 G	-1:27814553 27814553 G	V
333	998 T	-1:27814552 27814552 T	
333	999 G	-1:27814551 27814551 G	
334 T	1000 A	-1:27814550 27814550 A	T
334	1001 C	-1:27814549 27814549 C	
334	1002 C	-1:27814548 27814548 C	
335 E	1003 G	-1:27814547 27814547 G	E
335	1004 A	-1:27814546 27814546 A	
335	1005 G	-1:27814545 27814545 G	
336 F	1006 T	-1:27814544 27814544 T	F
336	1007 T	-1:27814543 27814543 T	
336	1008 C	-1:27814542 27814542 C	
337 M	1009 A	-1:27814541 27814541 A	M
337	1010 T	-1:27814540 27814540 T	
337	1011 G	-1:27814539 27814539 G	
338 C	1012 T	-1:27814538 27814538 T	C
338	1013 G	-1:27814537 27814537 G	
338	1014 T	-1:27814536 27814536 T	
339 H	1015 C	-1:27814535 27814535 C	H
339	1016 A	-1:27814534 27814534 A	
339	1017 C	-1:27814533 27814533 C	
340 G	1018 G	-1:27814532 27814532 G	G
340	1019 G	-1:27814024 27814024 G	
340	1020 C	-1:27814023 27814023 C	
341 S	1021 A	-1:27814022 27814022 A	S
341	1022 G	-1:27814021 27814021 G	
341	1023 C	-1:27814020 27814020 C	
342 L	1024 T	-1:27814019 27814019 T	L
342	1025 T	-1:27814018 27814018 T	
342	1026 G	-1:27814017 27814017 G	
343 L	1027 C	-1:27814016 27814016 C	L
343	1028 T	-1:27814015 27814015 T	
343	1029 G	-1:27814014 27814014 G	
344 D	1030 G	-1:27814013 27814013 G	D
344	1031 A	-1:27814012 27814012 A	
344	1032 T	-1:27814011 27814011 T	
345 F	1033 T	-1:27814010 27814010 T	F
345	1034 T	-1:27814009 27814009 T	
345	1035 T	-1:27814008 27814008 T	
346 L	1036 C	-1:27814007 27814007 C	L
346	1037 T	-1:27814006 27814006 T	
346	1038 C	-1:27814005 27814005 C	
347 K	1039 A	-1:27814004 27814004 A	K
347	1040 A	-1:27814003 27814003 A	
347	1041 G	-1:27814002 27814002 G	
348 N	1042 A	-1:27814001 27814001 A	N
348	1043 A	-1:27814000 27814000 A	
348	1044 C	-1:27813999 27813999 C	
349 P	1045 C	-1:27813998 27813998 C	P
349	1046 C	-1:27813997 27813997 C	
349	1047 A	-1:27813996 27813996 A	
350 E	1048 G	-1:27813995 27813995 G	E
350	1049 A	-1:27813994 27813994 A	
350	1050 G	-1:27813993 27813993 G	
351 G	1051 G	-1:27813992 27813992 G	G
351	1052 G	-1:27813991 27813991 G	
351	1053 C	-1:27813990 27813990 C	
352 Q	1054 C	-1:27813989 27813989 C	Q
352	1055 A	-1:27813988 27813988 A	
352	1056 G	-1:27813987 27813987 G	
353 D	1057 G	-1:27813986 27813986 G	D
353	1058 A	-1:27813985 27813985 A	
353	1059 T	-1:27813984 27813984 T	
354 L	1060 T	-1:27813983 27813983 T	L
354	1061 T	-1:27813982 27813982 T	
354	1062 G	-1:27813981 27813981 G	
355 R	1063 A	-1:27813980 27813980 A	R
355	1064 G	-1:27813979 27813979 G	
355	1065 G	-1:27813978 27813978 G	
356 L	1066 C	-1:27813977 27813977 C	L
356	1067 T	-1:27813976 27813976 T	
356	1068 G	-1:27813975 27813975 G	
357 P	1069 C	-1:27813974 27813974 C	P
357	1070 C	-1:27813973 27813973 C	
357	1071 C	-1:27813972 27813972 C	
358 Q	1072 C	-1:27813971 27813971 C	Q
358	1073 A	-1:27813970 27813970 A	
358	1074 A	-1:27813969 27813969 A	
359 L	1075 T	-1:27813968 27813968 T	L
359	1076 T	-1:27813967 27813967 T	
359	1077 G	-1:27813966 27813966 G	
360 V	1078 G	-1:27813965 27813965 G	V
360	1079 T	-1:27813964 27813964 T	
360	1080 G	-1:27813963 27813963 G	
361 D	1081 G	-1:27813962 27813962 G	D
361	1082 A	-1:27813961 27813961 A	
361	1083 C	-1:27813960 27813960 C	
362 M	1084 A	-1:27813959 27813959 A	M
362	1085 T	-1:27813958 27813958 T	
362	1086 G	-1:27813957 27813957 G	
363 A	1087 G	-1:27813956 27813956 G	A
363	1088 C	-1:27813955 27813955 C	
363	1089 A	-1:27813954 27813954 A	
364 A	1090 G	-1:27813953 27813953 G	A
364	1091 C	-1:27813952 27813952 C	
364	1092 C	-1:27813951 27813951 C	
365 Q	1093 C	-1:27813950 27813950 C	Q
365	1094 A	-1:27813949 27813949 A	
365	1095 G	-1:27813948 27813948 G	
366 V	1096 G	-1:27813681 27813681 G	V
366	1097 T	-1:27813680 27813680 T	
366	1098 A	-1:27813679 27813679 A	
367 A	1099 G	-1:27813678 27813678 G	A
367	1100 C	-1:27813677 27813677 C	
367	1101 T	-1:27813676 27813676 T	
368 E	1102 G	-1:27813675 27813675 G	E
368	1103 A	-1:27813674 27813674 A	
368	1104 G	-1:27813673 27813673 G	
369 G	1105 G	-1:27813672 27813672 G	G
369	1106 G	-1:27813671 27813671 G	
369	1107 C	-1:27813670 27813670 C	
370 M	1108 A	-1:27813669 27813669 A	M
370	1109 T	-1:27813668 27813668 T	
370	1110 G	-1:27813667 27813667 G	
371 A	1111 G	-1:27813666 27813666 G	A
371	1112 C	-1:27813665 27813665 C	
371	1113 C	-1:27813664 27813664 C	
372 Y	1114 T	-1:27813663 27813663 T	Y
372	1115 A	-1:27813662 27813662 A	
372	1116 C	-1:27813661 27813661 C	
373 M	1117 A	-1:27813660 27813660 A	M
373	1118 T	-1:27813659 27813659 T	
373	1119 G	-1:27813658 27813658 G	
374 E	1120 G	-1:27813657 27813657 G	E
374	1121 A	-1:27813656 27813656 A	
374	1122 A	-1:27813655 27813655 A	
375 R	1123 C	-1:27813654 27813654 C	R
375	1124 G	-1:27813653 27813653 G	
375	1125 C	-1:27813652 27813652 C	
376 M	1126 A	-1:27813651 27813651 A	M
376	1127 T	-1:27813650 27813650 T	
376	1128 G	-1:27813649 27813649 G	
377 N	1129 A	-1:27813648 27813648 A	N
377	1130 A	-1:27813647 27813647 A	
377	1131 C	-1:27813646 27813646 C	
378 Y	1132 T	-1:27813645 27813645 T	Y
378	1133 A	-1:27813644 27813644 A	
378	1134 C	-1:27813643 27813643 C	
379 I	1135 A	-1:27813642 27813642 A	I
379	1136 T	-1:27813641 27813641 T	
379	1137 T	-1:27813640 27813640 T	
380 H	1138 C	-1:27813639 27813639 C	H
380	1139 A	-1:27813638 27813638 A	
380	1140 C	-1:27813637 27813637 C	
381 R	1141 C	-1:27813636 27813636 C	R
381	1142 G	-1:27813635 27813635 G	
381	1143 C	-1:27813634 27813634 C	
382 D	1144 G	-1:27813633 27813633 G	D
382	1145 A	-1:27813632 27813632 A	
382	1146 C	-1:27813631 27813631 C	
383 L	1147 C	-1:27813630 27813630 C	L
383	1148 T	-1:27813629 27813629 T	
383	1149 G	-1:27813628 27813628 G	
384 R	1150 A	-1:27813627 27813627 A	R
384	1151 G	-1:27813626 27813626 G	
384	1152 G	-1:27813625 27813625 G	
385 A	1153 G	-1:27813624 27813624 G	A
385	1154 C	-1:27813623 27813623 C	
385	1155 A	-1:27813622 27813622 A	
386 A	1156 G	-1:27813621 27813621 G	A
386	1157 C	-1:27813620 27813620 C	
386	1158 C	-1:27813619 27813619 C	
387 N	1159 A	-1:27813618 27813618 A	N
387	1160 A	-1:27813617 27813617 A	
387	1161 C	-1:27813616 27813616 C	
388 I	1162 A	-1:27813615 27813615 A	I
388	1163 T	-1:27813614 27813614 T	
388	1164 C	-1:27813613 27813613 C	
389 L	1165 C	-1:27813612 27813612 C	L
389	1166 T	-1:27813611 27813611 T	
389	1167 G	-1:27813610 27813610 G	
390 V	1168 G	-1:27813609 27813609 G	V
390	1169 T	-1:27813608 27813608 T	
390	1170 T	-1:27813607 27813607 T	
391 G	1171 G	-1:27813606 27813606 G	G
391	1172 G	-1:27813605 27813605 G	
391	1173 G	-1:27813604 27813604 G	
392 E	1174 G	-1:27813603 27813603 G	E
392	1175 A	-1:27813602 27813602 A	
392	1176 G	-1:27813601 27813601 G	
393 R	1177 C	-1:27813600 27813600 C	R
393	1178 G	-1:27813599 27813599 G	
393	1179 G	-1:27813598 27813598 G	
394 L	1180 C	-1:27813597 27813597 C	L
394	1181 T	-1:27813596 27813596 T	
394	1182 G	-1:27813595 27813595 G	
395 A	1183 G	-1:27813594 27813594 G	A
395	1184 C	-1:27813593 27813593 C	
395	1185 G	-1:27813592 27813592 G	
396 C	1186 T	-1:27813591 27813591 T	C
396	1187 G	-1:27813590 27813590 G	
396	1188 C	-1:27813589 27813589 C	
397 K	1189 A	-1:27813588 27813588 A	K
397	1190 A	-1:27813587 27813587 A	
397	1191 G	-1:27813586 27813586 G	
398 I	1192 A	-1:27813585 27813585 A	I
398	1193 T	-1:27813584 27813584 T	
398	1194 C	-1:27813583 27813583 C	
399 A	1195 G	-1:27813582 27813582 G	A
399	1196 C	-1:27813581 27813581 C	
399	1197 A	-1:27813580 27813580 A	
400 D	1198 G	-1:27813579 27813579 G	D
400	1199 A	-1:27813578 27813578 A	
400	1200 C	-1:27813577 27813577 C	
401 F	1201 T	-1:27813576 27813576 T	F
401	1202 T	-1:27813575 27813575 T	
401	1203 T	-1:27813574 27813574 T	
402 G	1204 G	-1:27813573 27813573 G	G
402	1205 G	-1:27813572 27813572 G	
402	1206 C	-1:27813571 27813571 C	
403 L	1207 T	-1:27813570 27813570 T	L
403	1208 T	-1:27813569 27813569 T	
403	1209 G	-1:27813568 27813568 G	
404 A	1210 G	-1:27813567 27813567 G	A
404	1211 C	-1:27813566 27813566 C	
404	1212 G	-1:27813565 27813565 G	
405 R	1213 C	-1:27813564 27813564 C	R
405	1214 G	-1:27813563 27813563 G	
405	1215 T	-1:27813562 27813562 T	
406 L	1216 C	-1:27813561 27813561 C	L
406	1217 T	-1:27813560 27813560 T	
406	1218 C	-1:27813559 27813559 C	
407 I	1219 A	-1:27813558 27813558 A	I
407	1220 T	-1:27813557 27813557 T	
407	1221 C	-1:27813556 27813556 C	
408 K	1222 A	-1:27813555 27813555 A	K
408	1223 A	-1:27813554 27813554 A	
408	1224 G	-1:27813553 27813553 G	
409 D	1225 G	-1:27813552 27813552 G	D
409	1226 A	-1:27813551 27813551 A	
409	1227 C	-1:27813550 27813550 C	
410 D	1228 G	-1:27813549 27813549 G	D
410	1229 A	-1:27813548 27813548 A	
410	1230 T	-1:27813547 27813547 T	
411 E	1231 G	-1:27813546 27813546 G	E
411	1232 A	-1:27813545 27813545 A	
411	1233 G	-1:27813544 27813544 G	
412 Y	1234 T	-1:27813543 27813543 T	Y
412	1235 A	-1:27813542 27813542 A	
412	1236 C	-1:27813541 27813541 C	
413 N	1237 A	-1:27813540 27813540 A	N
413	1238 A	-1:27813539 27813539 A	
413	1239 C	-1:27813538 27813538 C	
414 P	1240 C	-1:27813537 27813537 C	P
414	1241 C	-1:27813536 27813536 C	
414	1242 C	-1:27813535 27813535 C	
415 C	1243 T	-1:27813534 27813534 T	C
415	1244 G	-1:27813533 27813533 G	
415	1245 C	-1:27813532 27813532 C	
416 Q	1246 C	-1:27813531 27813531 C	Q
416	1247 A	-1:27813530 27813530 A	
416	1248 A	-1:27813529 27813529 A	
>ENSP00000363116 
1 M	1 A	-1:27823014 27823014 A	M
1	2 T	-1:27823013 27823013 T	
1	3 G	-1:27823012 27823012 G	
2 G	4 G	-1:27823011 27823011 G	G
2	5 G	-1:27823010 27823010 G	
2	6 C	-1:27823009 27823009 C	
3 C	7 T	-1:27823008 27823008 T	C
3	8 G	-1:27823007 27823007 G	
3	9 T	-1:27823006 27823006 T	
4 V	10 G	-1:27823005 27823005 G	V
4	11 T	-1:27823004 27823004 T	
4	12 G	-1:27823003 27823003 G	
5 F	13 T	-1:27823002 27823002 T	F
5	14 T	-1:27823001 27823001 T	
5	15 C	-1:27823000 27823000 C	
6 C	16 T	-1:27822999 27822999 T	C
6	17 G	-1:27822998 27822998 G	
6	18 C	-1:27822997 27822997 C	
7 K	19 A	-1:27822996 27822996 A	K
7	20 A	-1:27822995 27822995 A	
7	21 G	-1:27822994 27822994 G	
8 K	22 A	-1:27822993 27822993 A	K
8	23 A	-1:27822992 27822992 A	
8	24 A	-1:27822991 27822991 A	
9 L	25 T	-1:27822990 27822990 T	L
9	26 T	-1:27822989 27822989 T	
9	27 G	-1:27822988 27822988 G	
10 E	28 G	-1:27822987 27822987 G	E
10	29 A	-1:27822986 27822986 A	
10	30 G	-1:27822985 27822985 G	
11 P	31 C	-1:27822984 27822984 C	P
11	32 C	-1:27822983 27822983 C	
11	33 G	-1:27822982 27822982 G	
12 V	34 G	-1:27822981 27822981 G	V
12	35 T	-1:27822980 27822980 T	
12	36 G	-1:27822979 27822979 G	
13 A	37 G	-1:27822978 27822978 G	A
13	38 C	-1:27822977 27822977 C	
13	39 C	-1:27822976 27822976 C	
14 T	40 A	-1:27822975 27822975 A	T
14	41 C	-1:27822974 27822974 C	
14	42 G	-1:27822973 27822973 G	
15 A	43 G	-1:27822972 27822972 G	A
15	44 C	-1:27822971 27822971 C	
15	45 C	-1:27822970 27822970 C	
16 K	46 A	-1:27822969 27822969 A	K
16	47 A	-1:27822968 27822968 A	
16	48 G	-1:27822967 27822967 G	
17 E	49 G	-1:27822966 27822966 G	E
17	50 A	-1:27822965 27822965 A	
17	51 G	-1:27822964 27822964 G	
18 D	52 G	-1:27822963 27822963 G	D
18	53 A	-1:27822962 27822962 A	
18	54 T	-1:27822961 27822961 T	
19 A	55 G	-1:27822960 27822960 G	A
19	56 C	-1:27822959 27822959 C	
19	57 T	-1:27822958 27822958 T	
20 G	58 G	-1:27822957 27822957 G	G
20	59 G	-1:27822956 27822956 G	
20	60 C	-1:27822955 27822955 C	
21 L	61 C	-1:27822954 27822954 C	L
21	62 T	-1:27822953 27822953 T	
21	63 G	-1:27822952 27822952 G	
22 E	64 G	-1:27822951 27822951 G	E
22	65 A	-1:27822950 27822950 A	
22	66 A	-1:27822949 27822949 A	
23 G	67 G	-1:27822948 27822948 G	G
23	68 G	-1:27822947 27822947 G	
23	69 G	-1:27822946 27822946 G	
24 D	70 G	-1:27822945 27822945 G	D
24	71 A	-1:27822944 27822944 A	
24	72 C	-1:27822943 27822943 C	
25 F	73 T	-1:27822942 27822942 T	F
25	74 T	-1:27822941 27822941 T	
25	75 C	-1:27822940 27822940 C	
26 R	76 A	-1:27822939 27822939 A	R
26	77 G	-1:27822938 27822938 G	
26	78 A	-1:27822937 27822937 A	
27 S	79 A	-1:27822936 27822936 A	S
27	80 G	-1:27822935 27822935 G	
27	81 C	-1:27822934 27822934 C	
28 Y	82 T	-1:27822933 27822933 T	Y
28	83 A	-1:27822932 27822932 A	
28	84 C	-1:27822931 27822931 C	
29 G	85 G	-1:27822930 27822930 G	G
29	86 G	-1:27822929 27822929 G	
29	87 G	-1:27822928 27822928 G	
30 A	88 G	-1:27822927 27822927 G	A
30	89 C	-1:27822926 27822926 C	
30	90 A	-1:27822925 27822925 A	
31 A	91 G	-1:27822924 27822924 G	A
31	92 C	-1:27822923 27822923 C	
31	93 A	-1:27822922 27822922 A	
32 D	94 G	-1:27822921 27822921 G	D
32	95 A	-1:27822920 27822920 A	
32	96 C	-1:27822919 27822919 C	
33 H	97 C	-1:27822918 27822918 C	H
33	98 A	-1:27822917 27822917 A	
33	99 C	-1:27822916 27822916 C	
34 Y	100 T	-1:27822915 27822915 T	Y
34	101 A	-1:27822914 27822914 A	
34	102 T	-1:27822913 27822913 T	
35 G	103 G	-1:27822912 27822912 G	G
35	104 G	-1:27822911 27822911 G	
35	105 G	-1:27822910 27822910 G	
36 P	106 C	-1:27822909 27822909 C	P
36	107 C	-1:27822908 27822908 C	
36	108 T	-1:27822907 27822907 T	
37 D	109 G	-1:27822906 27822906 G	D
37	110 A	-1:27822905 27822905 A	
37	111 C	-1:27822904 27822904 C	
38 P	112 C	-1:27822903 27822903 C	P
38	113 C	-1:27822902 27822902 C	
38	114 C	-1:27822901 27822901 C	
39 T	115 A	-1:27822900 27822900 A	T
39	116 C	-1:27822899 27822899 C	
39	117 T	-1:27822898 27822898 T	
40 K	118 A	-1:27822897 27822897 A	K
40	119 A	-1:27822896 27822896 A	
40	120 G	-1:27822895 27822895 G	
41 A	121 G	-1:27822894 27822894 G	A
41	122 C	-1:27822893 27822893 C	
41	123 C	-1:27822892 27822892 C	
42 R	124 C	-1:27822891 27822891 C	R
42	125 G	-1:27822890 27822890 G	
42	126 G	-1:27822889 27822889 G	
43 P	127 C	-1:27822888 27822888 C	P
43	128 C	-1:27822887 27822887 C	
43	129 T	-1:27822886 27822886 T	
44 A	130 G	-1:27822885 27822885 G	A
44	131 C	-1:27822884 27822884 C	
44	132 A	-1:27822883 27822883 A	
45 S	133 T	-1:27822882 27822882 T	S
45	134 C	-1:27822881 27822881 C	
45	135 C	-1:27822880 27822880 C	
46 S	136 T	-1:27822879 27822879 T	S
46	137 C	-1:27822878 27822878 C	
46	138 A	-1:27822877 27822877 A	
47 F	139 T	-1:27822876 27822876 T	F
47	140 T	-1:27822875 27822875 T	
47	141 T	-1:27822874 27822874 T	
48 A	142 G	-1:27822873 27822873 G	A
48	143 C	-1:27822872 27822872 C	
48	144 C	-1:27822871 27822871 C	
49 H	145 C	-1:27822870 27822870 C	H
49	146 A	-1:27822869 27822869 A	
49	147 C	-1:27822868 27822868 C	
50 I	148 A	-1:27822867 27822867 A	I
50	149 T	-1:27822866 27822866 T	
50	150 C	-1:27822865 27822865 C	
51 P	151 C	-1:27822864 27822864 C	P
51	152 C	-1:27822863 27822863 C	
51	153 C	-1:27822862 27822862 C	
52 N	154 A	-1:27822861 27822861 A	N
52	155 A	-1:27822860 27822860 A	
52	156 C	-1:27822859 27822859 C	
53 Y	157 T	-1:27822858 27822858 T	Y
53	158 A	-1:27822857 27822857 A	
53	159 C	-1:27822856 27822856 C	
54 S	160 A	-1:27822855 27822855 A	S
54	161 G	-1:27822854 27822854 G	
54	162 C	-1:27822853 27822853 C	
55 N	163 A	-1:27822852 27822852 A	N
55	164 A	-1:27822851 27822851 A	
55	165 C	-1:27822850 27822850 C	
56 F	166 T	-1:27822849 27822849 T	F
56	167 T	-1:27822848 27822848 T	
56	168 C	-1:27822847 27822847 C	
57 S	169 T	-1:27822846 27822846 T	S
57	170 C	-1:27822845 27822845 C	
57	171 C	-1:27822844 27822844 C	
58 S	172 T	-1:27822843 27822843 T	S
58	173 C	-1:27822842 27822842 C	
58	174 T	-1:27822841 27822841 T	
59 Q	175 C	-1:27822840 27822840 C	Q
59	176 A	-1:27822839 27822839 A	
59	177 G	-1:27822838 27822838 G	
60 A	178 G	-1:27822837 27822837 G	A
60	179 C	-1:27822836 27822836 C	
60	180 C	-1:27822835 27822835 C	
61 I	181 A	-1:27822834 27822834 A	I
61	182 T	-1:27822833 27822833 T	
61	183 C	-1:27822832 27822832 C	
62 N	184 A	-1:27822831 27822831 A	N
62	185 A	-1:27822830 27822830 A	
62	186 C	-1:27822829 27822829 C	
63 P	187 C	-1:27822828 27822828 C	P
63	188 C	-1:27822827 27822827 C	
63	189 T	-1:27822826 27822826 T	
64 G	190 G	-1:27822825 27822825 G	G
64	191 G	-1:27822824 27822824 G	
64	192 C	-1:27822823 27822823 C	
65 F	193 T	-1:27822822 27822822 T	F
65	194 T	-1:27822821 27822821 T	
65	195 C	-1:27822820 27822820 C	
66 L	196 C	-1:27822819 27822819 C	L
66	197 T	-1:27822818 27822818 T	
66	198 T	-1:27822817 27822817 T	
67 D	199 G	-1:27822816 27822816 G	D
67	200 A	-1:27822815 27822815 A	
67	201 T	-1:27822814 27822814 T	
68 S	202 A	-1:27822813 27822813 A	S
68	203 G	-1:27822812 27822812 G	
68	204 T	-1:27822811 27822811 T	
69 G	205 G	-1:27822810 27822810 G	G
69	206 G	-1:27822809 27822809 G	
69	207 C	-1:27822808 27822808 C	
70 T	208 A	-1:27822807 27822807 A	T
70	209 C	-1:27822806 27822806 C	
70	210 C	-1:27822805 27822805 C	
71 I	211 A	-1:27822804 27822804 A	I
71	212 T	-1:27822803 27822803 T	
71	213 C	-1:27822802 27822802 C	
72 R	214 A	-1:27822801 27822801 A	R
72	215 G	-1:27822800 27822800 G	
72	216 G	-1:27822799 27822799 G	
73 G	217 G	-1:27822798 27822798 G	G
73	218 G	-1:27822797 27822797 G	
73	219 T	-1:27822796 27822796 T	
74 V	220 G	-1:27822795 27822795 G	V
74	221 T	-1:27822794 27822794 T	
74	222 G	-1:27822793 27822793 G	
75 S	223 T	-1:27822792 27822792 T	S
75	224 C	-1:27822791 27822791 C	
75	225 A	-1:27822790 27822790 A	
76 G	226 G	-1:27822789 27822789 G	G
76	227 G	-1:27822242 27822242 G	
76	228 G	-1:27822241 27822241 G	
77 I	229 A	-1:27822240 27822240 A	I
77	230 T	-1:27822239 27822239 T	
77	231 T	-1:27822238 27822238 T	
78 G	232 G	-1:27822237 27822237 G	G
78	233 G	-1:27822236 27822236 G	
78	234 G	-1:27822235 27822235 G	
79 V	235 G	-1:27822234 27822234 G	V
79	236 T	-1:27822233 27822233 T	
79	237 G	-1:27822232 27822232 G	
80 T	238 A	-1:27822231 27822231 A	T
80	239 C	-1:27822230 27822230 C	
80	240 C	-1:27822229 27822229 C	
81 L	241 C	-1:27822228 27822228 C	L
81	242 T	-1:27822227 27822227 T	
81	243 G	-1:27822226 27822226 G	
82 F	244 T	-1:27822225 27822225 T	F
82	245 T	-1:27822224 27822224 T	
82	246 C	-1:27822223 27822223 C	
83 I	247 A	-1:27822222 27822222 A	I
83	248 T	-1:27822221 27822221 T	
83	249 T	-1:27822220 27822220 T	
84 A	250 G	-1:27822219 27822219 G	A
84	251 C	-1:27822218 27822218 C	
84	252 C	-1:27822217 27822217 C	
85 L	253 C	-1:27822216 27822216 C	L
85	254 T	-1:27822215 27822215 T	
85	255 G	-1:27822214 27822214 G	
86 Y	256 T	-1:27822213 27822213 T	Y
86	257 A	-1:27822212 27822212 A	
86	258 T	-1:27822211 27822211 T	
87 D	259 G	-1:27822210 27822210 G	D
87	260 A	-1:27822209 27822209 A	
87	261 C	-1:27822208 27822208 C	
88 Y	262 T	-1:27822207 27822207 T	Y
88	263 A	-1:27822206 27822206 A	
88	264 T	-1:27822205 27822205 T	
89 E	265 G	-1:27822204 27822204 G	E
89	266 A	-1:27822203 27822203 A	
89	267 G	-1:27822202 27822202 G	
90 A	268 G	-1:27822201 27822201 G	A
90	269 C	-1:27822200 27822200 C	
90	270 T	-1:27822199 27822199 T	
91 R	271 C	-1:27822198 27822198 C	R
91	272 G	-1:27822197 27822197 G	
91	273 A	-1:27822196 27822196 A	
92 T	274 A	-1:27822195 27822195 A	T
92	275 C	-1:27822194 27822194 C	
92	276 T	-1:27822193 27822193 T	
93 E	277 G	-1:27822192 27822192 G	E
93	278 A	-1:27822191 27822191 A	
93	279 G	-1:27822190 27822190 G	
94 D	280 G	-1:27822189 27822189 G	D
94	281 A	-1:27822188 27822188 A	
94	282 T	-1:27822187 27822187 T	
95 D	283 G	-1:27822186 27822186 G	D
95	284 A	-1:27822185 27822185 A	
95	285 C	-1:27822184 27822184 C	
96 L	286 C	-1:27822183 27822183 C	L
96	287 T	-1:27822182 27822182 T	
96	288 C	-1:27822181 27822181 C	
97 T	289 A	-1:27822180 27822180 A	T
97	290 C	-1:27822179 27822179 C	
97	291 C	-1:27822178 27822178 C	
98 F	292 T	-1:27822177 27822177 T	F
98	293 T	-1:27822176 27822176 T	
98	294 C	-1:27822175 27822175 C	
99 T	295 A	-1:27822174 27822174 A	T
99	296 C	-1:27822173 27822173 C	
99	297 C	-1:27822172 27822172 C	
100 K	298 A	-1:27822171 27822171 A	K
100	299 A	-1:27822170 27822170 A	
100	300 G	-1:27822169 27822169 G	
101 G	301 G	-1:27822168 27822168 G	G
101	302 G	-1:27822167 27822167 G	
101	303 C	-1:27822166 27822166 C	
102 E	304 G	-1:27822165 27822165 G	E
102	305 A	-1:27822164 27822164 A	
102	306 G	-1:27822163 27822163 G	
103 K	307 A	-1:27822162 27822162 A	K
103	308 A	-1:27822161 27822161 A	
103	309 G	-1:27822160 27822160 G	
104 F	310 T	-1:27822159 27822159 T	F
104	311 T	-1:27822158 27822158 T	
104	312 C	-1:27822157 27822157 C	
105 H	313 C	-1:27822156 27822156 C	H
105	314 A	-1:27822155 27822155 A	
105	315 C	-1:27822154 27822154 C	
106 I	316 A	-1:27822153 27822153 A	I
106	317 T	-1:27822152 27822152 T	
106	318 C	-1:27822151 27822151 C	
107 L	319 C	-1:27822150 27822150 C	L
107	320 T	-1:27822149 27822149 T	
107	321 G	-1:27822148 27822148 G	
108 N	322 A	-1:27822147 27822147 A	N
108	323 A	-1:27822146 27822146 A	
108	324 C	-1:27822145 27822145 C	
109 N	325 A	-1:27822144 27822144 A	N
109	326 A	-1:27822143 27822143 A	
109	327 T	-1:27822142 27822142 T	
110 T	328 A	-1:27822141 27822141 A	T
110	329 C	-1:27822140 27822140 C	
110	330 T	-1:27820755 27820755 T	
111 E	331 G	-1:27820754 27820754 G	E
111	332 A	-1:27820753 27820753 A	
111	333 A	-1:27820752 27820752 A	
112 G	334 G	-1:27820751 27820751 G	G
112	335 G	-1:27820750 27820750 G	
112	336 T	-1:27820749 27820749 T	
113 D	337 G	-1:27820748 27820748 G	D
113	338 A	-1:27820747 27820747 A	
113	339 C	-1:27820746 27820746 C	
114 W	340 T	-1:27820745 27820745 T	W
114	341 G	-1:27820744 27820744 G	
114	342 G	-1:27820743 27820743 G	
115 W	343 T	-1:27820742 27820742 T	W
115	344 G	-1:27820741 27820741 G	
115	345 G	-1:27820740 27820740 G	
116 E	346 G	-1:27820739 27820739 G	E
116	347 A	-1:27820738 27820738 A	
116	348 G	-1:27820737 27820737 G	
117 A	349 G	-1:27820736 27820736 G	A
117	350 C	-1:27820735 27820735 C	
117	351 T	-1:27820734 27820734 T	
118 R	352 C	-1:27820733 27820733 C	R
118	353 G	-1:27820732 27820732 G	
118	354 G	-1:27820731 27820731 G	
119 S	355 T	-1:27820730 27820730 T	S
119	356 C	-1:27820729 27820729 C	
119	357 T	-1:27820728 27820728 T	
120 L	358 C	-1:27820727 27820727 C	L
120	359 T	-1:27820726 27820726 T	
120	360 C	-1:27820725 27820725 C	
121 S	361 A	-1:27820724 27820724 A	S
121	362 G	-1:27820723 27820723 G	
121	363 C	-1:27820722 27820722 C	
122 S	364 T	-1:27820721 27820721 T	S
122	365 C	-1:27820720 27820720 C	
122	366 C	-1:27820719 27820719 C	
123 G	367 G	-1:27820718 27820718 G	G
123	368 G	-1:27820717 27820717 G	
123	369 A	-1:27820716 27820716 A	
124 K	370 A	-1:27820715 27820715 A	K
124	371 A	-1:27820714 27820714 A	
124	372 A	-1:27820713 27820713 A	
125 T	373 A	-1:27820712 27820712 A	T
125	374 C	-1:27820711 27820711 C	
125	375 T	-1:27820710 27820710 T	
126 G	376 G	-1:27820709 27820709 G	G
126	377 G	-1:27820708 27820708 G	
126	378 C	-1:27820707 27820707 C	
127 C	379 T	-1:27820706 27820706 T	C
127	380 G	-1:27820705 27820705 G	
127	381 C	-1:27820704 27820704 C	
128 I	382 A	-1:27820703 27820703 A	I
128	383 T	-1:27820702 27820702 T	
128	384 T	-1:27820701 27820701 T	
129 P	385 C	-1:27820700 27820700 C	P
129	386 C	-1:27820699 27820699 C	
129	387 C	-1:27820698 27820698 C	
130 S	388 A	-1:27820697 27820697 A	S
130	389 G	-1:27820696 27820696 G	
130	390 C	-1:27820695 27820695 C	
131 N	391 A	-1:27820694 27820694 A	N
131	392 A	-1:27820693 27820693 A	
131	393 C	-1:27820692 27820692 C	
132 Y	394 T	-1:27820691 27820691 T	Y
132	395 A	-1:27820690 27820690 A	
132	396 C	-1:27820689 27820689 C	
133 V	397 G	-1:27820688 27820688 G	V
133	398 T	-1:27820687 27820687 T	
133	399 G	-1:27820686 27820686 G	
134 A	400 G	-1:27820685 27820685 G	A
134	401 C	-1:27820684 27820684 C	
134	402 C	-1:27820683 27820683 C	
135 P	403 C	-1:27820682 27820682 C	P
135	404 C	-1:27820681 27820681 C	
135	405 T	-1:27820680 27820680 T	
136 V	406 G	-1:27820679 27820679 G	V
136	407 T	-1:27820678 27820678 T	
136	408 T	-1:27820677 27820677 T	
137 D	409 G	-1:27820676 27820676 G	D
137	410 A	-1:27820675 27820675 A	
137	411 C	-1:27820674 27820674 C	
138 S	412 T	-1:27820673 27820673 T	S
138	413 C	-1:27820672 27820672 C	
138	414 A	-1:27820671 27820671 A	
139 I	415 A	-1:27820670 27820670 A	I
139	416 T	-1:27820669 27820669 T	
139	417 C	-1:27820668 27820668 C	
140 Q	418 C	-1:27820667 27820667 C	Q
140	419 A	-1:27820666 27820666 A	
140	420 A	-1:27820665 27820665 A	
141 A	421 G	-1:27820664 27820664 G	A
141	422 C	-1:27820663 27820663 C	
141	423 T	-1:27820662 27820662 T	
142 E	424 G	-1:27820661 27820661 G	E
142	425 A	-1:27820660 27820660 A	
142	426 A	-1:27820659 27820659 A	
143 E	427 G	-1:27820658 27820658 G	E
143	428 A	-1:27820657 27820657 A	
143	429 G	-1:27816394 27816394 G	
144 W	430 T	-1:27816393 27816393 T	W
144	431 G	-1:27816392 27816392 G	
144	432 G	-1:27816391 27816391 G	
145 Y	433 T	-1:27816390 27816390 T	Y
145	434 A	-1:27816389 27816389 A	
145	435 C	-1:27816388 27816388 C	
146 F	436 T	-1:27816387 27816387 T	F
146	437 T	-1:27816386 27816386 T	
146	438 T	-1:27816385 27816385 T	
147 G	439 G	-1:27816384 27816384 G	G
147	440 G	-1:27816383 27816383 G	
147	441 A	-1:27816382 27816382 A	
148 K	442 A	-1:27816381 27816381 A	K
148	443 A	-1:27816380 27816380 A	
148	444 G	-1:27816379 27816379 G	
149 I	445 A	-1:27816378 27816378 A	I
149	446 T	-1:27816377 27816377 T	
149	447 T	-1:27816376 27816376 T	
150 G	448 G	-1:27816375 27816375 G	G
150	449 G	-1:27816374 27816374 G	
150	450 G	-1:27816373 27816373 G	
151 R	451 A	-1:27816372 27816372 A	R
151	452 G	-1:27816371 27816371 G	
151	453 A	-1:27816370 27816370 A	
152 K	454 A	-1:27816369 27816369 A	K
152	455 A	-1:27816368 27816368 A	
152	456 G	-1:27816367 27816367 G	
153 D	457 G	-1:27816366 27816366 G	D
153	458 A	-1:27816365 27816365 A	
153	459 T	-1:27816364 27816364 T	
154 A	460 G	-1:27816363 27816363 G	A
154	461 C	-1:27816362 27816362 C	
154	462 A	-1:27816361 27816361 A	
155 E	463 G	-1:27816360 27816360 G	E
155	464 A	-1:27816359 27816359 A	
155	465 G	-1:27816358 27816358 G	
156 R	466 A	-1:27816357 27816357 A	R
156	467 G	-1:27816356 27816356 G	
156	468 G	-1:27816355 27816355 G	
157 Q	469 C	-1:27816354 27816354 C	Q
157	470 A	-1:27816353 27816353 A	
157	471 G	-1:27816352 27816352 G	
158 L	472 C	-1:27816351 27816351 C	L
158	473 T	-1:27816350 27816350 T	
158	474 G	-1:27816349 27816349 G	
159 L	475 C	-1:27816348 27816348 C	L
159	476 T	-1:27816347 27816347 T	
159	477 T	-1:27816346 27816346 T	
160 S	478 T	-1:27816345 27816345 T	S
160	479 C	-1:27816344 27816344 C	
160	480 A	-1:27816343 27816343 A	
161 P	481 C	-1:27816342 27816342 C	P
161	482 C	-1:27816341 27816341 C	
161	483 A	-1:27816340 27816340 A	
162 G	484 G	-1:27816339 27816339 G	G
162	485 G	-1:27816338 27816338 G	
162	486 C	-1:27816337 27816337 C	
163 N	487 A	-1:27816336 27816336 A	N
163	488 A	-1:27816335 27816335 A	
163	489 C	-1:27816334 27816334 C	
164 P	490 C	-1:27816333 27816333 C	P
164	491 C	-1:27816332 27816332 C	
164	492 C	-1:27816331 27816331 C	
165 Q	493 C	-1:27816330 27816330 C	Q
165	494 A	-1:27816329 27816329 A	
165	495 G	-1:27816328 27816328 G	
166 G	496 G	-1:27816327 27816327 G	G
166	497 G	-1:27816326 27816326 G	
166	498 G	-1:27816325 27816325 G	
167 A	499 G	-1:27816324 27816324 G	A
167	500 C	-1:27816323 27816323 C	
167	501 C	-1:27816322 27816322 C	
168 F	502 T	-1:27816321 27816321 T	F
168	503 T	-1:27816320 27816320 T	
168	504 T	-1:27816319 27816319 T	
169 L	505 C	-1:27816318 27816318 C	L
169	506 T	-1:27816317 27816317 T	
169	507 C	-1:27816316 27816316 C	
170 I	508 A	-1:27816315 27816315 A	I
170	509 T	-1:27816314 27816314 T	
170	510 T	-1:27816313 27816313 T	
171 R	511 C	-1:27816312 27816312 C	R
171	512 G	-1:27816311 27816311 G	
171	513 G	-1:27816310 27816310 G	
172 E	514 G	-1:27816309 27816309 G	E
172	515 A	-1:27816308 27816308 A	
172	516 A	-1:27816307 27816307 A	
173 S	517 A	-1:27816306 27816306 A	S
173	518 G	-1:27816305 27816305 G	
173	519 C	-1:27816304 27816304 C	
174 E	520 G	-1:27816303 27816303 G	E
174	521 A	-1:27816302 27816302 A	
174	522 G	-1:27816301 27816301 G	
175 T	523 A	-1:27816300 27816300 A	T
175	524 C	-1:27816299 27816299 C	
175	525 C	-1:27816298 27816298 C	
176 T	526 A	-1:27816297 27816297 A	T
176	527 C	-1:27816296 27816296 C	
176	528 C	-1:27816295 27816295 C	
177 K	529 A	-1:27816294 27816294 A	K
177	530 A	-1:27816293 27816293 A	
177	531 A	-1:27816292 27816292 A	
178 G	532 G	-1:27816291 27816291 G	G
178	533 G	-1:27816104 27816104 G	
178	534 T	-1:27816103 27816103 T	
179 A	535 G	-1:27816102 27816102 G	A
179	536 C	-1:27816101 27816101 C	
179	537 C	-1:27816100 27816100 C	
180 Y	538 T	-1:27816099 27816099 T	Y
180	539 A	-1:27816098 27816098 A	
180	540 C	-1:27816097 27816097 C	
181 S	541 T	-1:27816096 27816096 T	S
181	542 C	-1:27816095 27816095 C	
181	543 C	-1:27816094 27816094 C	
182 L	544 C	-1:27816093 27816093 C	L
182	545 T	-1:27816092 27816092 T	
182	546 G	-1:27816091 27816091 G	
183 S	547 T	-1:27816090 27816090 T	S
183	548 C	-1:27816089 27816089 C	
183	549 C	-1:27816088 27816088 C	
184 I	550 A	-1:27816087 27816087 A	I
184	551 T	-1:27816086 27816086 T	
184	552 C	-1:27816085 27816085 C	
185 R	553 C	-1:27816084 27816084 C	R
185	554 G	-1:27816083 27816083 G	
185	555 G	-1:27816082 27816082 G	
186 D	556 G	-1:27816081 27816081 G	D
186	557 A	-1:27816080 27816080 A	
186	558 C	-1:27816079 27816079 C	
187 W	559 T	-1:27816078 27816078 T	W
187	560 G	-1:27816077 27816077 G	
187	561 G	-1:27816076 27816076 G	
188 D	562 G	-1:27816075 27816075 G	D
188	563 A	-1:27816074 27816074 A	
188	564 T	-1:27816073 27816073 T	
189 Q	565 C	-1:27816072 27816072 C	Q
189	566 A	-1:27816071 27816071 A	
189	567 G	-1:27816070 27816070 G	
190 T	568 A	-1:27816069 27816069 A	T
190	569 C	-1:27816068 27816068 C	
190	570 C	-1:27816067 27816067 C	
191 R	571 A	-1:27816066 27816066 A	R
191	572 G	-1:27816065 27816065 G	
191	573 A	-1:27816064 27816064 A	
192 G	574 G	-1:27816063 27816063 G	G
192	575 G	-1:27816062 27816062 G	
192	576 C	-1:27816061 27816061 C	
193 D	577 G	-1:27816060 27816060 G	D
193	578 A	-1:27816059 27816059 A	
193	579 T	-1:27816058 27816058 T	
194 H	580 C	-1:27816057 27816057 C	H
194	581 A	-1:27816056 27816056 A	
194	582 T	-1:27816055 27816055 T	
195 V	583 G	-1:27816054 27816054 G	V
195	584 T	-1:27816053 27816053 T	
195	585 G	-1:27816052 27816052 G	
196 K	586 A	-1:27816051 27816051 A	K
196	587 A	-1:27816050 27816050 A	
196	588 G	-1:27816049 27816049 G	
197 H	589 C	-1:27816048 27816048 C	H
197	590 A	-1:27816047 27816047 A	
197	591 T	-1:27816046 27816046 T	
198 Y	592 T	-1:27816045 27816045 T	Y
198	593 A	-1:27816044 27816044 A	
198	594 C	-1:27816043 27816043 C	
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199	596 A	-1:27816041 27816041 A	
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200 I	598 A	-1:27816039 27816039 A	I
200	599 T	-1:27816038 27816038 T	
200	600 C	-1:27816037 27816037 C	
201 R	601 C	-1:27816036 27816036 C	R
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201	603 C	-1:27816034 27816034 C	
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202	605 A	-1:27816032 27816032 A	
202	606 A	-1:27816031 27816031 A	
203 L	607 C	-1:27816030 27816030 C	L
203	608 T	-1:27816029 27816029 T	
203	609 G	-1:27816028 27816028 G	
204 D	610 G	-1:27816027 27816027 G	D
204	611 A	-1:27816026 27816026 A	
204	612 C	-1:27816025 27816025 C	
205 M	613 A	-1:27816024 27816024 A	M
205	614 T	-1:27816023 27816023 T	
205	615 G	-1:27816022 27816022 G	
206 G	616 G	-1:27816021 27816021 G	G
206	617 G	-1:27816020 27816020 G	
206	618 C	-1:27816019 27816019 C	
207 G	619 G	-1:27816018 27816018 G	G
207	620 G	-1:27816017 27816017 G	
207	621 C	-1:27816016 27816016 C	
208 Y	622 T	-1:27816015 27816015 T	Y
208	623 A	-1:27816014 27816014 A	
208	624 C	-1:27816013 27816013 C	
209 Y	625 T	-1:27816012 27816012 T	Y
209	626 A	-1:27816011 27816011 A	
209	627 C	-1:27816010 27816010 C	
210 I	628 A	-1:27816009 27816009 A	I
210	629 T	-1:27816008 27816008 T	
210	630 C	-1:27816007 27816007 C	
211 T	631 A	-1:27816006 27816006 A	T
211	632 C	-1:27816005 27816005 C	
211	633 C	-1:27816004 27816004 C	
212 T	634 A	-1:27816003 27816003 A	T
212	635 C	-1:27816002 27816002 C	
212	636 A	-1:27816001 27816001 A	
213 R	637 C	-1:27816000 27816000 C	R
213	638 G	-1:27815999 27815999 G	
213	639 G	-1:27815998 27815998 G	
214 V	640 G	-1:27815997 27815997 G	V
214	641 T	-1:27815996 27815996 T	
214	642 T	-1:27815995 27815995 T	
215 Q	643 C	-1:27815994 27815994 C	Q
215	644 A	-1:27815993 27815993 A	
215	645 G	-1:27815992 27815992 G	
216 F	646 T	-1:27815991 27815991 T	F
216	647 T	-1:27815990 27815990 T	
216	648 C	-1:27815989 27815989 C	
217 N	649 A	-1:27815988 27815988 A	N
217	650 A	-1:27815987 27815987 A	
217	651 C	-1:27815986 27815986 C	
218 S	652 T	-1:27815985 27815985 T	S
218	653 C	-1:27815984 27815984 C	
218	654 G	-1:27815983 27815983 G	
219 V	655 G	-1:27815982 27815982 G	V
219	656 T	-1:27815981 27815981 T	
219	657 G	-1:27815980 27815980 G	
220 Q	658 C	-1:27815979 27815979 C	Q
220	659 A	-1:27815978 27815978 A	
220	660 G	-1:27815977 27815977 G	
221 E	661 G	-1:27815976 27815976 G	E
221	662 A	-1:27815975 27815975 A	
221	663 G	-1:27815974 27815974 G	
222 L	664 C	-1:27815973 27815973 C	L
222	665 T	-1:27815972 27815972 T	
222	666 G	-1:27815971 27815971 G	
223 V	667 G	-1:27815970 27815970 G	V
223	668 T	-1:27815969 27815969 T	
223	669 G	-1:27815968 27815968 G	
224 Q	670 C	-1:27815967 27815967 C	Q
224	671 A	-1:27815966 27815966 A	
224	672 G	-1:27815965 27815965 G	
225 H	673 C	-1:27815964 27815964 C	H
225	674 A	-1:27815963 27815963 A	
225	675 C	-1:27815962 27815962 C	
226 Y	676 T	-1:27815961 27815961 T	Y
226	677 A	-1:27815960 27815960 A	
226	678 C	-1:27815959 27815959 C	
227 M	679 A	-1:27815958 27815958 A	M
227	680 T	-1:27815957 27815957 T	
227	681 G	-1:27815956 27815956 G	
228 E	682 G	-1:27815955 27815955 G	E
228	683 A	-1:27814942 27814942 A	
228	684 G	-1:27814941 27814941 G	
229 V	685 G	-1:27814940 27814940 G	V
229	686 T	-1:27814939 27814939 T	
229	687 G	-1:27814938 27814938 G	
230 N	688 A	-1:27814937 27814937 A	N
230	689 A	-1:27814936 27814936 A	
230	690 T	-1:27814935 27814935 T	
231 D	691 G	-1:27814934 27814934 G	D
231	692 A	-1:27814933 27814933 A	
231	693 C	-1:27814932 27814932 C	
232 G	694 G	-1:27814931 27814931 G	G
232	695 G	-1:27814930 27814930 G	
232	696 G	-1:27814929 27814929 G	
233 L	697 C	-1:27814928 27814928 C	L
233	698 T	-1:27814927 27814927 T	
233	699 G	-1:27814926 27814926 G	
234 C	700 T	-1:27814925 27814925 T	C
234	701 G	-1:27814924 27814924 G	
234	702 C	-1:27814923 27814923 C	
235 N	703 A	-1:27814922 27814922 A	N
235	704 A	-1:27814921 27814921 A	
235	705 C	-1:27814920 27814920 C	
236 L	706 C	-1:27814919 27814919 C	L
236	707 T	-1:27814918 27814918 T	
236	708 G	-1:27814917 27814917 G	
237 L	709 C	-1:27814916 27814916 C	L
237	710 T	-1:27814915 27814915 T	
237	711 C	-1:27814914 27814914 C	
238 I	712 A	-1:27814913 27814913 A	I
238	713 T	-1:27814912 27814912 T	
238	714 C	-1:27814911 27814911 C	
239 A	715 G	-1:27814910 27814910 G	A
239	716 C	-1:27814909 27814909 C	
239	717 G	-1:27814908 27814908 G	
240 P	718 C	-1:27814907 27814907 C	P
240	719 C	-1:27814906 27814906 C	
240	720 C	-1:27814905 27814905 C	
241 C	721 T	-1:27814904 27814904 T	C
241	722 G	-1:27814903 27814903 G	
241	723 C	-1:27814902 27814902 C	
242 T	724 A	-1:27814901 27814901 A	T
242	725 C	-1:27814900 27814900 C	
242	726 C	-1:27814899 27814899 C	
243 I	727 A	-1:27814898 27814898 A	I
243	728 T	-1:27814897 27814897 T	
243	729 C	-1:27814896 27814896 C	
244 M	730 A	-1:27814895 27814895 A	M
244	731 T	-1:27814894 27814894 T	
244	732 G	-1:27814893 27814893 G	
245 K	733 A	-1:27814892 27814892 A	K
245	734 A	-1:27814891 27814891 A	
245	735 G	-1:27814890 27814890 G	
246 P	736 C	-1:27814889 27814889 C	P
246	737 C	-1:27814888 27814888 C	
246	738 G	-1:27814887 27814887 G	
247 Q	739 C	-1:27814886 27814886 C	Q
247	740 A	-1:27814885 27814885 A	
247	741 G	-1:27814884 27814884 G	
248 T	742 A	-1:27814883 27814883 A	T
248	743 C	-1:27814882 27814882 C	
248	744 G	-1:27814881 27814881 G	
249 L	745 C	-1:27814880 27814880 C	L
249	746 T	-1:27814879 27814879 T	
249	747 G	-1:27814878 27814878 G	
250 G	748 G	-1:27814877 27814877 G	G
250	749 G	-1:27814876 27814876 G	
250	750 C	-1:27814875 27814875 C	
251 L	751 C	-1:27814874 27814874 C	L
251	752 T	-1:27814873 27814873 T	
251	753 G	-1:27814872 27814872 G	
252 A	754 G	-1:27814871 27814871 G	A
252	755 C	-1:27814870 27814870 C	
252	756 C	-1:27814869 27814869 C	
253 K	757 A	-1:27814868 27814868 A	K
253	758 A	-1:27814867 27814867 A	
253	759 G	-1:27814866 27814866 G	
254 D	760 G	-1:27814865 27814865 G	D
254	761 A	-1:27814864 27814864 A	
254	762 C	-1:27814863 27814863 C	
255 A	763 G	-1:27814862 27814862 G	A
255	764 C	-1:27814861 27814861 C	
255	765 C	-1:27814860 27814860 C	
256 W	766 T	-1:27814859 27814859 T	W
256	767 G	-1:27814858 27814858 G	
256	768 G	-1:27814857 27814857 G	
257 E	769 G	-1:27814856 27814856 G	E
257	770 A	-1:27814855 27814855 A	
257	771 G	-1:27814854 27814854 G	
258 I	772 A	-1:27814853 27814853 A	I
258	773 T	-1:27814852 27814852 T	
258	774 C	-1:27814851 27814851 C	
259 S	775 A	-1:27814850 27814850 A	S
259	776 G	-1:27814849 27814849 G	
259	777 C	-1:27814848 27814848 C	
260 R	778 C	-1:27814847 27814847 C	R
260	779 G	-1:27814846 27814846 G	
260	780 C	-1:27814845 27814845 C	
261 S	781 A	-1:27814844 27814844 A	S
261	782 G	-1:27814843 27814843 G	
261	783 C	-1:27814842 27814842 C	
262 S	784 T	-1:27814841 27814841 T	S
262	785 C	-1:27814840 27814840 C	
262	786 C	-1:27814839 27814839 C	
263 I	787 A	-1:27814838 27814838 A	I
263	788 T	-1:27814837 27814837 T	
263	789 C	-1:27814836 27814836 C	
264 T	790 A	-1:27814835 27814835 A	T
264	791 C	-1:27814834 27814834 C	
264	792 G	-1:27814833 27814833 G	
265 L	793 C	-1:27814832 27814832 C	L
265	794 T	-1:27814831 27814831 T	
265	795 G	-1:27814830 27814830 G	
266 E	796 G	-1:27814829 27814829 G	E
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266	798 G	-1:27814827 27814827 G	
267 R	799 C	-1:27814826 27814826 C	R
267	800 G	-1:27814825 27814825 G	
267	801 C	-1:27814824 27814824 C	
268 R	802 C	-1:27814823 27814823 C	R
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268	804 G	-1:27814821 27814821 G	
269 L	805 C	-1:27814820 27814820 C	L
269	806 T	-1:27814819 27814819 T	
269	807 G	-1:27814818 27814818 G	
270 G	808 G	-1:27814817 27814817 G	G
270	809 G	-1:27814816 27814816 G	
270	810 C	-1:27814815 27814815 C	
271 T	811 A	-1:27814814 27814814 A	T
271	812 C	-1:27814813 27814813 C	
271	813 C	-1:27814812 27814812 C	
272 G	814 G	-1:27814811 27814811 G	G
272	815 G	-1:27814810 27814810 G	
272	816 C	-1:27814809 27814809 C	
273 C	817 T	-1:27814808 27814808 T	C
273	818 G	-1:27814807 27814807 G	
273	819 C	-1:27814806 27814806 C	
274 F	820 T	-1:27814805 27814805 T	F
274	821 T	-1:27814804 27814804 T	
274	822 C	-1:27814803 27814803 C	
275 G	823 G	-1:27814802 27814802 G	G
275	824 G	-1:27814801 27814801 G	
275	825 G	-1:27814800 27814800 G	
276 D	826 G	-1:27814799 27814799 G	D
276	827 A	-1:27814798 27814798 A	
276	828 T	-1:27814797 27814797 T	
277 V	829 G	-1:27814796 27814796 G	V
277	830 T	-1:27814795 27814795 T	
277	831 G	-1:27814794 27814794 G	
278 W	832 T	-1:27814793 27814793 T	W
278	833 G	-1:27814792 27814792 G	
278	834 G	-1:27814791 27814791 G	
279 L	835 C	-1:27814790 27814790 C	L
279	836 T	-1:27814789 27814789 T	
279	837 G	-1:27814788 27814788 G	
280 G	838 G	-1:27814787 27814787 G	G
280	839 G	-1:27814711 27814711 G	
280	840 C	-1:27814710 27814710 C	
281 T	841 A	-1:27814709 27814709 A	T
281	842 C	-1:27814708 27814708 C	
281	843 G	-1:27814707 27814707 G	
282 W	844 T	-1:27814706 27814706 T	W
282	845 G	-1:27814705 27814705 G	
282	846 G	-1:27814704 27814704 G	
283 N	847 A	-1:27814703 27814703 A	N
283	848 A	-1:27814702 27814702 A	
283	849 C	-1:27814701 27814701 C	
284 G	850 G	-1:27814700 27814700 G	G
284	851 G	-1:27814699 27814699 G	
284	852 C	-1:27814698 27814698 C	
285 S	853 A	-1:27814697 27814697 A	S
285	854 G	-1:27814696 27814696 G	
285	855 C	-1:27814695 27814695 C	
286 T	856 A	-1:27814694 27814694 A	T
286	857 C	-1:27814693 27814693 C	
286	858 T	-1:27814692 27814692 T	
287 K	859 A	-1:27814691 27814691 A	K
287	860 A	-1:27814690 27814690 A	
287	861 G	-1:27814689 27814689 G	
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288	863 T	-1:27814687 27814687 T	
288	864 G	-1:27814686 27814686 G	
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289	866 C	-1:27814684 27814684 C	
289	867 G	-1:27814683 27814683 G	
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290	869 T	-1:27814681 27814681 T	
290	870 G	-1:27814680 27814680 G	
291 K	871 A	-1:27814679 27814679 A	K
291	872 A	-1:27814678 27814678 A	
291	873 G	-1:27814677 27814677 G	
292 T	874 A	-1:27814676 27814676 A	T
292	875 C	-1:27814675 27814675 C	
292	876 G	-1:27814674 27814674 G	
293 L	877 C	-1:27814673 27814673 C	L
293	878 T	-1:27814672 27814672 T	
293	879 G	-1:27814671 27814671 G	
294 K	880 A	-1:27814670 27814670 A	K
294	881 A	-1:27814669 27814669 A	
294	882 G	-1:27814668 27814668 G	
295 P	883 C	-1:27814667 27814667 C	P
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295	885 G	-1:27814665 27814665 G	
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296	888 C	-1:27814662 27814662 C	
297 T	889 A	-1:27814661 27814661 A	T
297	890 C	-1:27814660 27814660 C	
297	891 C	-1:27814659 27814659 C	
298 M	892 A	-1:27814658 27814658 A	M
298	893 T	-1:27814657 27814657 T	
298	894 G	-1:27814656 27814656 G	
299 S	895 T	-1:27814655 27814655 T	S
299	896 C	-1:27814654 27814654 C	
299	897 C	-1:27814653 27814653 C	
300 P	898 C	-1:27814652 27814652 C	P
300	899 C	-1:27814651 27814651 C	
300	900 G	-1:27814650 27814650 G	
301 K	901 A	-1:27814649 27814649 A	K
301	902 A	-1:27814648 27814648 A	
301	903 G	-1:27814647 27814647 G	
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302	905 C	-1:27814645 27814645 C	
302	906 C	-1:27814644 27814644 C	
303 F	907 T	-1:27814643 27814643 T	F
303	908 T	-1:27814642 27814642 T	
303	909 C	-1:27814641 27814641 C	
304 L	910 C	-1:27814640 27814640 C	L
304	911 T	-1:27814639 27814639 T	
304	912 G	-1:27814638 27814638 G	
305 E	913 G	-1:27814637 27814637 G	E
305	914 A	-1:27814636 27814636 A	
305	915 G	-1:27814635 27814635 G	
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306	917 A	-1:27814633 27814633 A	
306	918 G	-1:27814632 27814632 G	
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307	920 C	-1:27814630 27814630 C	
307	921 G	-1:27814629 27814629 G	
308 Q	922 C	-1:27814628 27814628 C	Q
308	923 A	-1:27814627 27814627 A	
308	924 G	-1:27814626 27814626 G	
309 V	925 G	-1:27814625 27814625 G	V
309	926 T	-1:27814624 27814624 T	
309	927 C	-1:27814623 27814623 C	
310 M	928 A	-1:27814622 27814622 A	M
310	929 T	-1:27814621 27814621 T	
310	930 G	-1:27814620 27814620 G	
311 K	931 A	-1:27814619 27814619 A	K
311	932 A	-1:27814618 27814618 A	
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312 L	934 C	-1:27814616 27814616 C	L
312	935 T	-1:27814615 27814615 T	
312	936 G	-1:27814614 27814614 G	
313 L	937 C	-1:27814613 27814613 C	L
313	938 T	-1:27814612 27814612 T	
313	939 G	-1:27814611 27814611 G	
314 R	940 C	-1:27814610 27814610 C	R
314	941 G	-1:27814609 27814609 G	
314	942 G	-1:27814608 27814608 G	
315 H	943 C	-1:27814607 27814607 C	H
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315	945 C	-1:27814605 27814605 C	
316 D	946 G	-1:27814604 27814604 G	D
316	947 A	-1:27814603 27814603 A	
316	948 C	-1:27814602 27814602 C	
317 K	949 A	-1:27814601 27814601 A	K
317	950 A	-1:27814600 27814600 A	
317	951 G	-1:27814599 27814599 G	
318 L	952 C	-1:27814598 27814598 C	L
318	953 T	-1:27814597 27814597 T	
318	954 G	-1:27814596 27814596 G	
319 V	955 G	-1:27814595 27814595 G	V
319	956 T	-1:27814594 27814594 T	
319	957 G	-1:27814593 27814593 G	
320 Q	958 C	-1:27814592 27814592 C	Q
320	959 A	-1:27814591 27814591 A	
320	960 G	-1:27814590 27814590 G	
321 L	961 C	-1:27814589 27814589 C	L
321	962 T	-1:27814588 27814588 T	
321	963 G	-1:27814587 27814587 G	
322 Y	964 T	-1:27814586 27814586 T	Y
322	965 A	-1:27814585 27814585 A	
322	966 C	-1:27814584 27814584 C	
323 A	967 G	-1:27814583 27814583 G	A
323	968 C	-1:27814582 27814582 C	
323	969 C	-1:27814581 27814581 C	
324 V	970 G	-1:27814580 27814580 G	V
324	971 T	-1:27814579 27814579 T	
324	972 G	-1:27814578 27814578 G	
325 V	973 G	-1:27814577 27814577 G	V
325	974 T	-1:27814576 27814576 T	
325	975 G	-1:27814575 27814575 G	
326 S	976 T	-1:27814574 27814574 T	S
326	977 C	-1:27814573 27814573 C	
326	978 G	-1:27814572 27814572 G	
327 E	979 G	-1:27814571 27814571 G	E
327	980 A	-1:27814570 27814570 A	
327	981 G	-1:27814569 27814569 G	
328 E	982 G	-1:27814568 27814568 G	E
328	983 A	-1:27814567 27814567 A	
328	984 G	-1:27814566 27814566 G	
329 P	985 C	-1:27814565 27814565 C	P
329	986 C	-1:27814564 27814564 C	
329	987 C	-1:27814563 27814563 C	
330 I	988 A	-1:27814562 27814562 A	I
330	989 T	-1:27814561 27814561 T	
330	990 C	-1:27814560 27814560 C	
331 Y	991 T	-1:27814559 27814559 T	Y
331	992 A	-1:27814558 27814558 A	
331	993 C	-1:27814557 27814557 C	
332 I	994 A	-1:27814556 27814556 A	I
332	995 T	-1:27814555 27814555 T	
332	996 C	-1:27814554 27814554 C	
333 V	997 G	-1:27814553 27814553 G	V
333	998 T	-1:27814552 27814552 T	
333	999 G	-1:27814551 27814551 G	
334 T	1000 A	-1:27814550 27814550 A	T
334	1001 C	-1:27814549 27814549 C	
334	1002 C	-1:27814548 27814548 C	
335 E	1003 G	-1:27814547 27814547 G	E
335	1004 A	-1:27814546 27814546 A	
335	1005 G	-1:27814545 27814545 G	
336 F	1006 T	-1:27814544 27814544 T	F
336	1007 T	-1:27814543 27814543 T	
336	1008 C	-1:27814542 27814542 C	
337 M	1009 A	-1:27814541 27814541 A	M
337	1010 T	-1:27814540 27814540 T	
337	1011 G	-1:27814539 27814539 G	
338 C	1012 T	-1:27814538 27814538 T	C
338	1013 G	-1:27814537 27814537 G	
338	1014 T	-1:27814536 27814536 T	
339 H	1015 C	-1:27814535 27814535 C	H
339	1016 A	-1:27814534 27814534 A	
339	1017 C	-1:27814533 27814533 C	
340 G	1018 G	-1:27814532 27814532 G	G
340	1019 G	-1:27814024 27814024 G	
340	1020 C	-1:27814023 27814023 C	
341 S	1021 A	-1:27814022 27814022 A	S
341	1022 G	-1:27814021 27814021 G	
341	1023 C	-1:27814020 27814020 C	
342 L	1024 T	-1:27814019 27814019 T	L
342	1025 T	-1:27814018 27814018 T	
342	1026 G	-1:27814017 27814017 G	
343 L	1027 C	-1:27814016 27814016 C	L
343	1028 T	-1:27814015 27814015 T	
343	1029 G	-1:27814014 27814014 G	
344 D	1030 G	-1:27814013 27814013 G	D
344	1031 A	-1:27814012 27814012 A	
344	1032 T	-1:27814011 27814011 T	
345 F	1033 T	-1:27814010 27814010 T	F
345	1034 T	-1:27814009 27814009 T	
345	1035 T	-1:27814008 27814008 T	
346 L	1036 C	-1:27814007 27814007 C	L
346	1037 T	-1:27814006 27814006 T	
346	1038 C	-1:27814005 27814005 C	
347 K	1039 A	-1:27814004 27814004 A	K
347	1040 A	-1:27814003 27814003 A	
347	1041 G	-1:27814002 27814002 G	
348 N	1042 A	-1:27814001 27814001 A	N
348	1043 A	-1:27814000 27814000 A	
348	1044 C	-1:27813999 27813999 C	
349 P	1045 C	-1:27813998 27813998 C	P
349	1046 C	-1:27813997 27813997 C	
349	1047 A	-1:27813996 27813996 A	
350 E	1048 G	-1:27813995 27813995 G	E
350	1049 A	-1:27813994 27813994 A	
350	1050 G	-1:27813993 27813993 G	
351 G	1051 G	-1:27813992 27813992 G	G
351	1052 G	-1:27813991 27813991 G	
351	1053 C	-1:27813990 27813990 C	
352 Q	1054 C	-1:27813989 27813989 C	Q
352	1055 A	-1:27813988 27813988 A	
352	1056 G	-1:27813987 27813987 G	
353 D	1057 G	-1:27813986 27813986 G	D
353	1058 A	-1:27813985 27813985 A	
353	1059 T	-1:27813984 27813984 T	
354 L	1060 T	-1:27813983 27813983 T	L
354	1061 T	-1:27813982 27813982 T	
354	1062 G	-1:27813981 27813981 G	
355 R	1063 A	-1:27813980 27813980 A	R
355	1064 G	-1:27813979 27813979 G	
355	1065 G	-1:27813978 27813978 G	
356 L	1066 C	-1:27813977 27813977 C	L
356	1067 T	-1:27813976 27813976 T	
356	1068 G	-1:27813975 27813975 G	
357 P	1069 C	-1:27813974 27813974 C	P
357	1070 C	-1:27813973 27813973 C	
357	1071 C	-1:27813972 27813972 C	
358 Q	1072 C	-1:27813971 27813971 C	Q
358	1073 A	-1:27813970 27813970 A	
358	1074 A	-1:27813969 27813969 A	
359 L	1075 T	-1:27813968 27813968 T	L
359	1076 T	-1:27813967 27813967 T	
359	1077 G	-1:27813966 27813966 G	
360 V	1078 G	-1:27813965 27813965 G	V
360	1079 T	-1:27813964 27813964 T	
360	1080 G	-1:27813963 27813963 G	
361 D	1081 G	-1:27813962 27813962 G	D
361	1082 A	-1:27813961 27813961 A	
361	1083 C	-1:27813960 27813960 C	
362 M	1084 A	-1:27813959 27813959 A	M
362	1085 T	-1:27813958 27813958 T	
362	1086 G	-1:27813957 27813957 G	
363 A	1087 G	-1:27813956 27813956 G	A
363	1088 C	-1:27813955 27813955 C	
363	1089 A	-1:27813954 27813954 A	
364 A	1090 G	-1:27813953 27813953 G	A
364	1091 C	-1:27813952 27813952 C	
364	1092 C	-1:27813951 27813951 C	
365 Q	1093 C	-1:27813950 27813950 C	Q
365	1094 A	-1:27813949 27813949 A	
365	1095 G	-1:27813948 27813948 G	
366 V	1096 G	-1:27813681 27813681 G	V
366	1097 T	-1:27813680 27813680 T	
366	1098 A	-1:27813679 27813679 A	
367 A	1099 G	-1:27813678 27813678 G	A
367	1100 C	-1:27813677 27813677 C	
367	1101 T	-1:27813676 27813676 T	
368 E	1102 G	-1:27813675 27813675 G	E
368	1103 A	-1:27813674 27813674 A	
368	1104 G	-1:27813673 27813673 G	
369 G	1105 G	-1:27813672 27813672 G	G
369	1106 G	-1:27813671 27813671 G	
369	1107 C	-1:27813670 27813670 C	
370 M	1108 A	-1:27813669 27813669 A	M
370	1109 T	-1:27813668 27813668 T	
370	1110 G	-1:27813667 27813667 G	
371 A	1111 G	-1:27813666 27813666 G	A
371	1112 C	-1:27813665 27813665 C	
371	1113 C	-1:27813664 27813664 C	
372 Y	1114 T	-1:27813663 27813663 T	Y
372	1115 A	-1:27813662 27813662 A	
372	1116 C	-1:27813661 27813661 C	
373 M	1117 A	-1:27813660 27813660 A	M
373	1118 T	-1:27813659 27813659 T	
373	1119 G	-1:27813658 27813658 G	
374 E	1120 G	-1:27813657 27813657 G	E
374	1121 A	-1:27813656 27813656 A	
374	1122 A	-1:27813655 27813655 A	
375 R	1123 C	-1:27813654 27813654 C	R
375	1124 G	-1:27813653 27813653 G	
375	1125 C	-1:27813652 27813652 C	
376 M	1126 A	-1:27813651 27813651 A	M
376	1127 T	-1:27813650 27813650 T	
376	1128 G	-1:27813649 27813649 G	
377 N	1129 A	-1:27813648 27813648 A	N
377	1130 A	-1:27813647 27813647 A	
377	1131 C	-1:27813646 27813646 C	
378 Y	1132 T	-1:27813645 27813645 T	Y
378	1133 A	-1:27813644 27813644 A	
378	1134 C	-1:27813643 27813643 C	
379 I	1135 A	-1:27813642 27813642 A	I
379	1136 T	-1:27813641 27813641 T	
379	1137 T	-1:27813640 27813640 T	
380 H	1138 C	-1:27813639 27813639 C	H
380	1139 A	-1:27813638 27813638 A	
380	1140 C	-1:27813637 27813637 C	
381 R	1141 C	-1:27813636 27813636 C	R
381	1142 G	-1:27813635 27813635 G	
381	1143 C	-1:27813634 27813634 C	
382 D	1144 G	-1:27813633 27813633 G	D
382	1145 A	-1:27813632 27813632 A	
382	1146 C	-1:27813631 27813631 C	
383 L	1147 C	-1:27813630 27813630 C	L
383	1148 T	-1:27813629 27813629 T	
383	1149 G	-1:27813628 27813628 G	
384 R	1150 A	-1:27813627 27813627 A	R
384	1151 G	-1:27813626 27813626 G	
384	1152 G	-1:27813625 27813625 G	
385 A	1153 G	-1:27813624 27813624 G	A
385	1154 C	-1:27813623 27813623 C	
385	1155 A	-1:27813622 27813622 A	
386 A	1156 G	-1:27813621 27813621 G	A
386	1157 C	-1:27813620 27813620 C	
386	1158 C	-1:27813619 27813619 C	
387 N	1159 A	-1:27813618 27813618 A	N
387	1160 A	-1:27813617 27813617 A	
387	1161 C	-1:27813616 27813616 C	
388 I	1162 A	-1:27813615 27813615 A	I
388	1163 T	-1:27813614 27813614 T	
388	1164 C	-1:27813613 27813613 C	
389 L	1165 C	-1:27813612 27813612 C	L
389	1166 T	-1:27813611 27813611 T	
389	1167 G	-1:27813610 27813610 G	
390 V	1168 G	-1:27813609 27813609 G	V
390	1169 T	-1:27813608 27813608 T	
390	1170 T	-1:27813607 27813607 T	
391 G	1171 G	-1:27813606 27813606 G	G
391	1172 G	-1:27813605 27813605 G	
391	1173 G	-1:27813604 27813604 G	
392 E	1174 G	-1:27813603 27813603 G	E
392	1175 A	-1:27813602 27813602 A	
392	1176 G	-1:27813601 27813601 G	
393 R	1177 C	-1:27813600 27813600 C	R
393	1178 G	-1:27813599 27813599 G	
393	1179 G	-1:27813598 27813598 G	
394 L	1180 C	-1:27813597 27813597 C	L
394	1181 T	-1:27813596 27813596 T	
394	1182 G	-1:27813595 27813595 G	
395 A	1183 G	-1:27813594 27813594 G	A
395	1184 C	-1:27813593 27813593 C	
395	1185 G	-1:27813592 27813592 G	
396 C	1186 T	-1:27813591 27813591 T	C
396	1187 G	-1:27813590 27813590 G	
396	1188 C	-1:27813589 27813589 C	
397 K	1189 A	-1:27813588 27813588 A	K
397	1190 A	-1:27813587 27813587 A	
397	1191 G	-1:27813586 27813586 G	
398 I	1192 A	-1:27813585 27813585 A	I
398	1193 T	-1:27813584 27813584 T	
398	1194 C	-1:27813583 27813583 C	
399 A	1195 G	-1:27813582 27813582 G	A
399	1196 C	-1:27813581 27813581 C	
399	1197 A	-1:27813580 27813580 A	
400 D	1198 G	-1:27813579 27813579 G	D
400	1199 A	-1:27813578 27813578 A	
400	1200 C	-1:27813577 27813577 C	
401 F	1201 T	-1:27813576 27813576 T	F
401	1202 T	-1:27813575 27813575 T	
401	1203 T	-1:27813574 27813574 T	
402 G	1204 G	-1:27813573 27813573 G	G
402	1205 G	-1:27813572 27813572 G	
402	1206 C	-1:27813571 27813571 C	
403 L	1207 T	-1:27813570 27813570 T	L
403	1208 T	-1:27813569 27813569 T	
403	1209 G	-1:27813568 27813568 G	
404 A	1210 G	-1:27813567 27813567 G	A
404	1211 C	-1:27813566 27813566 C	
404	1212 G	-1:27813565 27813565 G	
405 R	1213 C	-1:27813564 27813564 C	R
405	1214 G	-1:27813563 27813563 G	
405	1215 T	-1:27813562 27813562 T	
406 L	1216 C	-1:27813561 27813561 C	L
406	1217 T	-1:27813560 27813560 T	
406	1218 C	-1:27813559 27813559 C	
407 I	1219 A	-1:27813558 27813558 A	I
407	1220 T	-1:27813557 27813557 T	
407	1221 C	-1:27813556 27813556 C	
408 K	1222 A	-1:27813555 27813555 A	K
408	1223 A	-1:27813554 27813554 A	
408	1224 G	-1:27813553 27813553 G	
409 D	1225 G	-1:27813552 27813552 G	D
409	1226 A	-1:27813551 27813551 A	
409	1227 C	-1:27813550 27813550 C	
410 D	1228 G	-1:27813549 27813549 G	D
410	1229 A	-1:27813548 27813548 A	
410	1230 T	-1:27813547 27813547 T	
411 E	1231 G	-1:27813546 27813546 G	E
411	1232 A	-1:27813545 27813545 A	
411	1233 G	-1:27813544 27813544 G	
412 Y	1234 T	-1:27813543 27813543 T	Y
412	1235 A	-1:27813542 27813542 A	
412	1236 C	-1:27813541 27813541 C	
413 N	1237 A	-1:27813540 27813540 A	N
413	1238 A	-1:27813539 27813539 A	
413	1239 C	-1:27813538 27813538 C	
414 P	1240 C	-1:27813537 27813537 C	P
414	1241 C	-1:27813536 27813536 C	
414	1242 C	-1:27813535 27813535 C	
415 C	1243 T	-1:27813534 27813534 T	C
415	1244 G	-1:27813533 27813533 G	
415	1245 C	-1:27813532 27813532 C	
416 Q	1246 C	-1:27813531 27813531 C	Q
416	1247 A	-1:27813530 27813530 A	
416	1248 A	-1:27813529 27813529 A	
>ENSP00000356398 
1 M	1 A	+1:194887871 194887871 A	M
1	2 T	+1:194887872 194887872 T	
1	3 G	+1:194887873 194887873 G	
2 R	4 A	+1:194887874 194887874 A	R
2	5 G	+1:194887875 194887875 G	
2	6 A	+1:194887876 194887876 A	
3 L	7 C	+1:194887877 194887877 C	L
3	8 T	+1:194887878 194887878 T	
3	9 T	+1:194887879 194887879 T	
4 L	10 C	+1:194887880 194887880 C	L
4	11 T	+1:194887881 194887881 T	
4	12 A	+1:194887882 194887882 A	
5 A	13 G	+1:194887883 194887883 G	A
5	14 C	+1:194887884 194887884 C	
5	15 A	+1:194887885 194887885 A	
6 K	16 A	+1:194887886 194887886 A	K
6	17 A	+1:194887887 194887887 A	
6	18 G	+1:194887888 194887888 G	
7 I	19 A	+1:194887889 194887889 A	I
7	20 T	+1:194887890 194887890 T	
7	21 T	+1:194887891 194887891 T	
8 I	22 A	+1:194887892 194887892 A	I
8	23 T	+1:194887893 194887893 T	
8	24 T	+1:194887894 194887894 T	
9 C	25 T	+1:194887895 194887895 T	C
9	26 G	+1:194887896 194887896 G	
9	27 C	+1:194887897 194887897 C	
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10	29 T	+1:194887899 194887899 T	
10	30 T	+1:194887900 194887900 T	
11 M	31 A	+1:194887901 194887901 A	M
11	32 T	+1:194887902 194887902 T	
11	33 G	+1:194887903 194887903 G	
12 L	34 T	+1:194887904 194887904 T	L
12	35 T	+1:194887905 194887905 T	
12	36 A	+1:194887906 194887906 A	
13 W	37 T	+1:194887907 194887907 T	W
13	38 G	+1:194887908 194887908 G	
13	39 G	+1:194887909 194887909 G	
14 A	40 G	+1:194887910 194887910 G	A
14	41 C	+1:194887911 194887911 C	
14	42 T	+1:194887912 194887912 T	
15 I	43 A	+1:194887913 194887913 A	I
15	44 T	+1:194887914 194887914 T	
15	45 T	+1:194887915 194887915 T	
16 C	46 T	+1:194887916 194887916 T	C
16	47 G	+1:194887917 194887917 G	
16	48 T	+1:194887918 194887918 T	
17 V	49 G	+1:194887919 194887919 G	V
17	50 T	+1:194887920 194887920 T	
17	51 A	+1:194887921 194887921 A	
18 A	52 G	+1:194887922 194887922 G	A
18	53 C	+1:194887923 194887923 C	
18	54 A	+1:194887924 194887924 A	
19 E	55 G	+1:194887925 194887925 G	E
19	56 A	+1:194887926 194887926 A	
19	57 A	+1:194887927 194887927 A	
20 D	58 G	+1:194887928 194887928 G	D
20	59 A	+1:194908731 194908731 A	
20	60 T	+1:194908732 194908732 T	
21 C	61 T	+1:194908733 194908733 T	C
21	62 G	+1:194908734 194908734 G	
21	63 C	+1:194908735 194908735 C	
22 N	64 A	+1:194908736 194908736 A	N
22	65 A	+1:194908737 194908737 A	
22	66 T	+1:194908738 194908738 T	
23 E	67 G	+1:194908739 194908739 G	E
23	68 A	+1:194908740 194908740 A	
23	69 A	+1:194908741 194908741 A	
24 L	70 C	+1:194908742 194908742 C	L
24	71 T	+1:194908743 194908743 T	
24	72 T	+1:194908744 194908744 T	
25 P	73 C	+1:194908745 194908745 C	P
25	74 C	+1:194908746 194908746 C	
25	75 T	+1:194908747 194908747 T	
26 P	76 C	+1:194908748 194908748 C	P
26	77 C	+1:194908749 194908749 C	
26	78 A	+1:194908750 194908750 A	
27 R	79 A	+1:194908751 194908751 A	R
27	80 G	+1:194908752 194908752 G	
27	81 A	+1:194908753 194908753 A	
28 R	82 A	+1:194908754 194908754 A	R
28	83 G	+1:194908755 194908755 G	
28	84 A	+1:194908756 194908756 A	
29 N	85 A	+1:194908757 194908757 A	N
29	86 A	+1:194908758 194908758 A	
29	87 T	+1:194908759 194908759 T	
30 T	88 A	+1:194908760 194908760 A	T
30	89 C	+1:194908761 194908761 C	
30	90 A	+1:194908762 194908762 A	
31 E	91 G	+1:194908763 194908763 G	E
31	92 A	+1:194908764 194908764 A	
31	93 A	+1:194908765 194908765 A	
32 I	94 A	+1:194908766 194908766 A	I
32	95 T	+1:194908767 194908767 T	
32	96 T	+1:194908768 194908768 T	
33 L	97 C	+1:194908769 194908769 C	L
33	98 T	+1:194908770 194908770 T	
33	99 G	+1:194908771 194908771 G	
34 T	100 A	+1:194908772 194908772 A	T
34	101 C	+1:194908773 194908773 C	
34	102 A	+1:194908774 194908774 A	
35 G	103 G	+1:194908775 194908775 G	G
35	104 G	+1:194908776 194908776 G	
35	105 T	+1:194908777 194908777 T	
36 S	106 T	+1:194908778 194908778 T	S
36	107 C	+1:194908779 194908779 C	
36	108 C	+1:194908780 194908780 C	
37 W	109 T	+1:194908781 194908781 T	W
37	110 G	+1:194908782 194908782 G	
37	111 G	+1:194908783 194908783 G	
38 S	112 T	+1:194908784 194908784 T	S
38	113 C	+1:194908785 194908785 C	
38	114 T	+1:194908786 194908786 T	
39 D	115 G	+1:194908787 194908787 G	D
39	116 A	+1:194908788 194908788 A	
39	117 C	+1:194908789 194908789 C	
40 Q	118 C	+1:194908790 194908790 C	Q
40	119 A	+1:194908791 194908791 A	
40	120 A	+1:194908792 194908792 A	
41 T	121 A	+1:194908793 194908793 A	T
41	122 C	+1:194908794 194908794 C	
41	123 A	+1:194908795 194908795 A	
42 Y	124 T	+1:194908796 194908796 T	Y
42	125 A	+1:194908797 194908797 A	
42	126 T	+1:194908798 194908798 T	
43 P	127 C	+1:194908799 194908799 C	P
43	128 C	+1:194908800 194908800 C	
43	129 A	+1:194908801 194908801 A	
44 E	130 G	+1:194908802 194908802 G	E
44	131 A	+1:194908803 194908803 A	
44	132 A	+1:194908804 194908804 A	
45 G	133 G	+1:194908805 194908805 G	G
45	134 G	+1:194908806 194908806 G	
45	135 C	+1:194908807 194908807 C	
46 T	136 A	+1:194908808 194908808 A	T
46	137 C	+1:194908809 194908809 C	
46	138 C	+1:194908810 194908810 C	
47 Q	139 C	+1:194908811 194908811 C	Q
47	140 A	+1:194908812 194908812 A	
47	141 G	+1:194908813 194908813 G	
48 A	142 G	+1:194908814 194908814 G	A
48	143 C	+1:194908815 194908815 C	
48	144 T	+1:194908816 194908816 T	
49 I	145 A	+1:194908817 194908817 A	I
49	146 T	+1:194908818 194908818 T	
49	147 C	+1:194908819 194908819 C	
50 Y	148 T	+1:194908820 194908820 T	Y
50	149 A	+1:194908821 194908821 A	
50	150 T	+1:194908822 194908822 T	
51 K	151 A	+1:194908823 194908823 A	K
51	152 A	+1:194908824 194908824 A	
51	153 A	+1:194908825 194908825 A	
52 C	154 T	+1:194908826 194908826 T	C
52	155 G	+1:194908827 194908827 G	
52	156 C	+1:194908828 194908828 C	
53 R	157 C	+1:194908829 194908829 C	R
53	158 G	+1:194908830 194908830 G	
53	159 C	+1:194908831 194908831 C	
54 P	160 C	+1:194908832 194908832 C	P
54	161 C	+1:194908833 194908833 C	
54	162 T	+1:194908834 194908834 T	
55 G	163 G	+1:194908835 194908835 G	G
55	164 G	+1:194908836 194908836 G	
55	165 A	+1:194908837 194908837 A	
56 Y	166 T	+1:194908838 194908838 T	Y
56	167 A	+1:194908839 194908839 A	
56	168 T	+1:194908840 194908840 T	
57 R	169 A	+1:194908841 194908841 A	R
57	170 G	+1:194908842 194908842 G	
57	171 A	+1:194908843 194908843 A	
58 S	172 T	+1:194908844 194908844 T	S
58	173 C	+1:194908845 194908845 C	
58	174 T	+1:194908846 194908846 T	
59 L	175 C	+1:194908847 194908847 C	L
59	176 T	+1:194908848 194908848 T	
59	177 T	+1:194908849 194908849 T	
60 G	178 G	+1:194908850 194908850 G	G
60	179 G	+1:194908851 194908851 G	
60	180 A	+1:194908852 194908852 A	
61 N	181 A	+1:194908853 194908853 A	N
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62 V	184 G	+1:194908856 194908856 G	V
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63 I	187 A	+1:194908859 194908859 A	I
63	188 T	+1:194908860 194908860 T	
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67 R	199 A	+1:194908871 194908871 A	R
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69 G	205 G	+1:194908877 194908877 G	G
69	206 G	+1:194908878 194908878 G	
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72	216 T	+1:194908888 194908888 T	
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75	224 A	+1:194908896 194908896 A	
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77	230 T	+1:194908902 194908902 T	
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79	236 A	+1:194908908 194908908 A	
79	237 A	+1:194908909 194908909 A	
80 C	238 T	+1:194908910 194908910 T	C
80	239 G	+1:194908911 194908911 G	
80	240 T	+1:194908912 194908912 T	
81 Q	241 C	+1:194908913 194908913 C	Q
81	242 A	+1:194908914 194908914 A	
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82 K	244 A	+1:194908916 194908916 A	K
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83	248 G	+1:194909613 194909613 G	
83	249 G	+1:194909614 194909614 G	
84 P	250 C	+1:194909615 194909615 C	P
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84	252 C	+1:194909617 194909617 C	
85 C	253 T	+1:194909618 194909618 T	C
85	254 G	+1:194909619 194909619 G	
85	255 T	+1:194909620 194909620 T	
86 G	256 G	+1:194909621 194909621 G	G
86	257 G	+1:194909622 194909622 G	
86	258 A	+1:194909623 194909623 A	
87 H	259 C	+1:194909624 194909624 C	H
87	260 A	+1:194909625 194909625 A	
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89 G	265 G	+1:194909630 194909630 G	G
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91	272 C	+1:194909637 194909637 C	
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92	276 T	+1:194909641 194909641 T	
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93	279 T	+1:194909644 194909644 T	
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95	284 C	+1:194909649 194909649 C	
95	285 T	+1:194909650 194909650 T	
96 F	286 T	+1:194909651 194909651 T	F
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96	288 T	+1:194909653 194909653 T	
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98	294 T	+1:194909659 194909659 T	
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99	296 C	+1:194909661 194909661 C	
99	297 A	+1:194909662 194909662 A	
100 G	298 G	+1:194909663 194909663 G	G
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100	300 A	+1:194909665 194909665 A	
101 G	301 G	+1:194909666 194909666 G	G
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102 N	304 A	+1:194909669 194909669 A	N
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102	306 T	+1:194909671 194909671 T	
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104	312 T	+1:194909677 194909677 T	
105 E	313 G	+1:194909678 194909678 G	E
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105	315 A	+1:194909680 194909680 A	
106 Y	316 T	+1:194909681 194909681 T	Y
106	317 A	+1:194909682 194909682 A	
106	318 T	+1:194909683 194909683 T	
107 G	319 G	+1:194909684 194909684 G	G
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107	321 T	+1:194909686 194909686 T	
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108	324 A	+1:194909689 194909689 A	
109 K	325 A	+1:194909690 194909690 A	K
109	326 A	+1:194909691 194909691 A	
109	327 A	+1:194909692 194909692 A	
110 A	328 G	+1:194909693 194909693 G	A
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110	330 T	+1:194909695 194909695 T	
111 V	331 G	+1:194909696 194909696 G	V
111	332 T	+1:194909697 194909697 T	
111	333 G	+1:194909698 194909698 G	
112 Y	334 T	+1:194909699 194909699 T	Y
112	335 A	+1:194909700 194909700 A	
112	336 T	+1:194909701 194909701 T	
113 T	337 A	+1:194909702 194909702 A	T
113	338 C	+1:194909703 194909703 C	
113	339 A	+1:194909704 194909704 A	
114 C	340 T	+1:194909705 194909705 T	C
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114	342 T	+1:194909707 194909707 T	
115 N	343 A	+1:194909708 194909708 A	N
115	344 A	+1:194909709 194909709 A	
115	345 T	+1:194909710 194909710 T	
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117	351 G	+1:194911742 194911742 G	
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118	353 A	+1:194911744 194911744 A	
118	354 T	+1:194911745 194911745 T	
119 Q	355 C	+1:194911746 194911746 C	Q
119	356 A	+1:194911747 194911747 A	
119	357 A	+1:194911748 194911748 A	
120 L	358 T	+1:194911749 194911749 T	L
120	359 T	+1:194911750 194911750 T	
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121	363 A	+1:194911754 194911754 A	
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123	369 G	+1:194911760 194911760 G	
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124	371 T	+1:194911762 194911762 T	
124	372 T	+1:194911763 194911763 T	
125 N	373 A	+1:194911764 194911764 A	N
125	374 A	+1:194911765 194911765 A	
125	375 T	+1:194911766 194911766 T	
126 Y	376 T	+1:194911767 194911767 T	Y
126	377 A	+1:194911768 194911768 A	
126	378 C	+1:194911769 194911769 C	
127 R	379 C	+1:194911770 194911770 C	R
127	380 G	+1:194911771 194911771 G	
127	381 T	+1:194911772 194911772 T	
128 E	382 G	+1:194911773 194911773 G	E
128	383 A	+1:194911774 194911774 A	
128	384 A	+1:194911775 194911775 A	
129 C	385 T	+1:194911776 194911776 T	C
129	386 G	+1:194911777 194911777 G	
129	387 T	+1:194911778 194911778 T	
130 D	388 G	+1:194911779 194911779 G	D
130	389 A	+1:194911780 194911780 A	
130	390 C	+1:194911781 194911781 C	
131 T	391 A	+1:194911782 194911782 A	T
131	392 C	+1:194911783 194911783 C	
131	393 A	+1:194911784 194911784 A	
132 D	394 G	+1:194911785 194911785 G	D
132	395 A	+1:194911786 194911786 A	
132	396 T	+1:194911787 194911787 T	
133 G	397 G	+1:194911788 194911788 G	G
133	398 G	+1:194911789 194911789 G	
133	399 A	+1:194911790 194911790 A	
134 W	400 T	+1:194911791 194911791 T	W
134	401 G	+1:194911792 194911792 G	
134	402 G	+1:194911793 194911793 G	
135 T	403 A	+1:194911794 194911794 A	T
135	404 C	+1:194911795 194911795 C	
135	405 C	+1:194911796 194911796 C	
136 N	406 A	+1:194911797 194911797 A	N
136	407 A	+1:194911798 194911798 A	
136	408 T	+1:194911799 194911799 T	
137 D	409 G	+1:194911800 194911800 G	D
137	410 A	+1:194911801 194911801 A	
137	411 T	+1:194911802 194911802 T	
138 I	412 A	+1:194911803 194911803 A	I
138	413 T	+1:194911804 194911804 T	
138	414 T	+1:194911805 194911805 T	
139 P	415 C	+1:194911806 194911806 C	P
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139	417 T	+1:194911808 194911808 T	
140 I	418 A	+1:194911809 194911809 A	I
140	419 T	+1:194911810 194911810 T	
140	420 A	+1:194911811 194911811 A	
141 C	421 T	+1:194911812 194911812 T	C
141	422 G	+1:194911813 194911813 G	
141	423 T	+1:194911814 194911814 T	
142 E	424 G	+1:194911815 194911815 G	E
142	425 A	+1:194911816 194911816 A	
142	426 A	+1:194911817 194911817 A	
143 E	427 G	+1:194911818 194911818 G	E
143	428 A	+1:194915376 194915376 A	
143	429 A	+1:194915377 194915377 A	
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144	431 T	+1:194915379 194915379 T	
144	432 T	+1:194915380 194915380 T	
145 S	433 T	+1:194915381 194915381 T	S
145	434 C	+1:194915382 194915382 C	
145	435 A	+1:194915383 194915383 A	
146 C	436 T	+1:194915384 194915384 T	C
146	437 G	+1:194915385 194915385 G	
146	438 C	+1:194915386 194915386 C	
147 K	439 A	+1:194915387 194915387 A	K
147	440 A	+1:194915388 194915388 A	
147	441 A	+1:194915389 194915389 A	
148 S	442 T	+1:194915390 194915390 T	S
148	443 C	+1:194915391 194915391 C	
148	444 C	+1:194915392 194915392 C	
149 P	445 C	+1:194915393 194915393 C	P
149	446 C	+1:194915394 194915394 C	
149	447 A	+1:194915395 194915395 A	
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150	449 A	+1:194915397 194915397 A	
150	450 T	+1:194915398 194915398 T	
151 V	451 G	+1:194915399 194915399 G	V
151	452 T	+1:194915400 194915400 T	
151	453 T	+1:194915401 194915401 T	
152 I	454 A	+1:194915402 194915402 A	I
152	455 T	+1:194915403 194915403 T	
152	456 A	+1:194915404 194915404 A	
153 N	457 A	+1:194915405 194915405 A	N
153	458 A	+1:194915406 194915406 A	
153	459 T	+1:194915407 194915407 T	
154 G	460 G	+1:194915408 194915408 G	G
154	461 G	+1:194915409 194915409 G	
154	462 A	+1:194915410 194915410 A	
155 S	463 T	+1:194915411 194915411 T	S
155	464 C	+1:194915412 194915412 C	
155	465 T	+1:194915413 194915413 T	
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156	467 C	+1:194915415 194915415 C	
156	468 T	+1:194915416 194915416 T	
157 I	469 A	+1:194915417 194915417 A	I
157	470 T	+1:194915418 194915418 T	
157	471 A	+1:194915419 194915419 A	
158 S	472 T	+1:194915420 194915420 T	S
158	473 C	+1:194915421 194915421 C	
158	474 T	+1:194915422 194915422 T	
159 Q	475 C	+1:194915423 194915423 C	Q
159	476 A	+1:194915424 194915424 A	
159	477 G	+1:194915425 194915425 G	
160 K	478 A	+1:194915426 194915426 A	K
160	479 A	+1:194915427 194915427 A	
160	480 G	+1:194915428 194915428 G	
161 I	481 A	+1:194915429 194915429 A	I
161	482 T	+1:194915430 194915430 T	
161	483 T	+1:194915431 194915431 T	
162 I	484 A	+1:194915432 194915432 A	I
162	485 T	+1:194915433 194915433 T	
162	486 T	+1:194915434 194915434 T	
163 Y	487 T	+1:194915435 194915435 T	Y
163	488 A	+1:194915436 194915436 A	
163	489 T	+1:194915437 194915437 T	
164 K	490 A	+1:194915438 194915438 A	K
164	491 A	+1:194915439 194915439 A	
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166	497 A	+1:194915445 194915445 A	
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167	500 A	+1:194915448 194915448 A	
167	501 A	+1:194915449 194915449 A	
168 R	502 C	+1:194915450 194915450 C	R
168	503 G	+1:194915451 194915451 G	
168	504 A	+1:194915452 194915452 A	
169 F	505 T	+1:194915453 194915453 T	F
169	506 T	+1:194915454 194915454 T	
169	507 T	+1:194915455 194915455 T	
170 Q	508 C	+1:194915456 194915456 C	Q
170	509 A	+1:194915457 194915457 A	
170	510 A	+1:194915458 194915458 A	
171 Y	511 T	+1:194915459 194915459 T	Y
171	512 A	+1:194915460 194915460 A	
171	513 T	+1:194915461 194915461 T	
172 K	514 A	+1:194915462 194915462 A	K
172	515 A	+1:194915463 194915463 A	
172	516 A	+1:194915464 194915464 A	
173 C	517 T	+1:194915465 194915465 T	C
173	518 G	+1:194915466 194915466 G	
173	519 T	+1:194915467 194915467 T	
174 N	520 A	+1:194915468 194915468 A	N
174	521 A	+1:194915469 194915469 A	
174	522 C	+1:194915470 194915470 C	
175 M	523 A	+1:194915471 194915471 A	M
175	524 T	+1:194915472 194915472 T	
175	525 G	+1:194915473 194915473 G	
176 G	526 G	+1:194915474 194915474 G	G
176	527 G	+1:194915475 194915475 G	
176	528 T	+1:194915476 194915476 T	
177 Y	529 T	+1:194915477 194915477 T	Y
177	530 A	+1:194915478 194915478 A	
177	531 T	+1:194915479 194915479 T	
178 E	532 G	+1:194915480 194915480 G	E
178	533 A	+1:194915481 194915481 A	
178	534 A	+1:194915482 194915482 A	
179 Y	535 T	+1:194915483 194915483 T	Y
179	536 A	+1:194915484 194915484 A	
179	537 C	+1:194915485 194915485 C	
180 S	538 A	+1:194915486 194915486 A	S
180	539 G	+1:194915487 194915487 G	
180	540 T	+1:194915488 194915488 T	
181 E	541 G	+1:194915489 194915489 G	E
181	542 A	+1:194915490 194915490 A	
181	543 A	+1:194915491 194915491 A	
182 R	544 A	+1:194915492 194915492 A	R
182	545 G	+1:194915493 194915493 G	
182	546 A	+1:194915494 194915494 A	
183 G	547 G	+1:194915495 194915495 G	G
183	548 G	+1:194915496 194915496 G	
183	549 A	+1:194915497 194915497 A	
184 D	550 G	+1:194915498 194915498 G	D
184	551 A	+1:194915499 194915499 A	
184	552 T	+1:194915500 194915500 T	
185 A	553 G	+1:194915501 194915501 G	A
185	554 C	+1:194915502 194915502 C	
185	555 T	+1:194915503 194915503 T	
186 V	556 G	+1:194915504 194915504 G	V
186	557 T	+1:194915505 194915505 T	
186	558 A	+1:194915506 194915506 A	
187 C	559 T	+1:194915507 194915507 T	C
187	560 G	+1:194915508 194915508 G	
187	561 C	+1:194915509 194915509 C	
188 T	562 A	+1:194915510 194915510 A	T
188	563 C	+1:194915511 194915511 C	
188	564 T	+1:194915512 194915512 T	
189 E	565 G	+1:194915513 194915513 G	E
189	566 A	+1:194915514 194915514 A	
189	567 A	+1:194915515 194915515 A	
190 S	568 T	+1:194915516 194915516 T	S
190	569 C	+1:194915517 194915517 C	
190	570 T	+1:194915518 194915518 T	
191 G	571 G	+1:194915519 194915519 G	G
191	572 G	+1:194915520 194915520 G	
191	573 A	+1:194915521 194915521 A	
192 W	574 T	+1:194915522 194915522 T	W
192	575 G	+1:194915523 194915523 G	
192	576 G	+1:194915524 194915524 G	
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193	578 G	+1:194915526 194915526 G	
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195 L	583 T	+1:194915531 194915531 T	L
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196	587 C	+1:194915535 194915535 C	
196	588 T	+1:194915536 194915536 T	
197 S	589 T	+1:194915537 194915537 T	S
197	590 C	+1:194915538 194915538 C	
197	591 A	+1:194915539 194915539 A	
198 C	592 T	+1:194915540 194915540 T	C
198	593 G	+1:194915541 194915541 G	
198	594 T	+1:194915542 194915542 T	
199 E	595 G	+1:194915543 194915543 G	E
199	596 A	+1:194915544 194915544 A	
199	597 A	+1:194915545 194915545 A	
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200	599 A	+1:194920817 194920817 A	
200	600 A	+1:194920818 194920818 A	
201 K	601 A	+1:194920819 194920819 A	K
201	602 A	+1:194920820 194920820 A	
201	603 A	+1:194920821 194920821 A	
202 S	604 T	+1:194920822 194920822 T	S
202	605 C	+1:194920823 194920823 C	
202	606 A	+1:194920824 194920824 A	
203 C	607 T	+1:194920825 194920825 T	C
203	608 G	+1:194920826 194920826 G	
203	609 T	+1:194920827 194920827 T	
204 D	610 G	+1:194920828 194920828 G	D
204	611 A	+1:194920829 194920829 A	
204	612 T	+1:194920830 194920830 T	
205 N	613 A	+1:194920831 194920831 A	N
205	614 A	+1:194920832 194920832 A	
205	615 T	+1:194920833 194920833 T	
206 P	616 C	+1:194920834 194920834 C	P
206	617 C	+1:194920835 194920835 C	
206	618 T	+1:194920836 194920836 T	
207 Y	619 T	+1:194920837 194920837 T	Y
207	620 A	+1:194920838 194920838 A	
207	621 T	+1:194920839 194920839 T	
208 I	622 A	+1:194920840 194920840 A	I
208	623 T	+1:194920841 194920841 T	
208	624 T	+1:194920842 194920842 T	
209 P	625 C	+1:194920843 194920843 C	P
209	626 C	+1:194920844 194920844 C	
209	627 A	+1:194920845 194920845 A	
210 N	628 A	+1:194920846 194920846 A	N
210	629 A	+1:194920847 194920847 A	
210	630 T	+1:194920848 194920848 T	
211 G	631 G	+1:194920849 194920849 G	G
211	632 G	+1:194920850 194920850 G	
211	633 T	+1:194920851 194920851 T	
212 D	634 G	+1:194920852 194920852 G	D
212	635 A	+1:194920853 194920853 A	
212	636 C	+1:194920854 194920854 C	
213 Y	637 T	+1:194920855 194920855 T	Y
213	638 A	+1:194920856 194920856 A	
213	639 C	+1:194920857 194920857 C	
214 S	640 T	+1:194920858 194920858 T	S
214	641 C	+1:194920859 194920859 C	
214	642 A	+1:194920860 194920860 A	
215 P	643 C	+1:194920861 194920861 C	P
215	644 C	+1:194920862 194920862 C	
215	645 T	+1:194920863 194920863 T	
216 L	646 T	+1:194920864 194920864 T	L
216	647 T	+1:194920865 194920865 T	
216	648 A	+1:194920866 194920866 A	
217 R	649 A	+1:194920867 194920867 A	R
217	650 G	+1:194920868 194920868 G	
217	651 G	+1:194920869 194920869 G	
218 I	652 A	+1:194920870 194920870 A	I
218	653 T	+1:194920871 194920871 T	
218	654 T	+1:194920872 194920872 T	
219 K	655 A	+1:194920873 194920873 A	K
219	656 A	+1:194920874 194920874 A	
219	657 A	+1:194920875 194920875 A	
220 H	658 C	+1:194920876 194920876 C	H
220	659 A	+1:194920877 194920877 A	
220	660 C	+1:194920878 194920878 C	
221 R	661 A	+1:194920879 194920879 A	R
221	662 G	+1:194920880 194920880 G	
221	663 A	+1:194920881 194920881 A	
222 T	664 A	+1:194920882 194920882 A	T
222	665 C	+1:194920883 194920883 C	
222	666 T	+1:194920884 194920884 T	
223 G	667 G	+1:194920885 194920885 G	G
223	668 G	+1:194920886 194920886 G	
223	669 A	+1:194920887 194920887 A	
224 D	670 G	+1:194920888 194920888 G	D
224	671 A	+1:194920889 194920889 A	
224	672 T	+1:194920890 194920890 T	
225 E	673 G	+1:194920891 194920891 G	E
225	674 A	+1:194920892 194920892 A	
225	675 A	+1:194920893 194920893 A	
226 I	676 A	+1:194920894 194920894 A	I
226	677 T	+1:194920895 194920895 T	
226	678 C	+1:194920896 194920896 C	
227 T	679 A	+1:194920897 194920897 A	T
227	680 C	+1:194920898 194920898 C	
227	681 G	+1:194920899 194920899 G	
228 Y	682 T	+1:194920900 194920900 T	Y
228	683 A	+1:194920901 194920901 A	
228	684 C	+1:194920902 194920902 C	
229 Q	685 C	+1:194920903 194920903 C	Q
229	686 A	+1:194920904 194920904 A	
229	687 G	+1:194920905 194920905 G	
230 C	688 T	+1:194920906 194920906 T	C
230	689 G	+1:194920907 194920907 G	
230	690 T	+1:194920908 194920908 T	
231 R	691 A	+1:194920909 194920909 A	R
231	692 G	+1:194920910 194920910 G	
231	693 A	+1:194920911 194920911 A	
232 N	694 A	+1:194920912 194920912 A	N
232	695 A	+1:194920913 194920913 A	
232	696 T	+1:194920914 194920914 T	
233 G	697 G	+1:194920915 194920915 G	G
233	698 G	+1:194920916 194920916 G	
233	699 T	+1:194920917 194920917 T	
234 F	700 T	+1:194920918 194920918 T	F
234	701 T	+1:194920919 194920919 T	
234	702 T	+1:194920920 194920920 T	
235 Y	703 T	+1:194920921 194920921 T	Y
235	704 A	+1:194920922 194920922 A	
235	705 T	+1:194920923 194920923 T	
236 P	706 C	+1:194920924 194920924 C	P
236	707 C	+1:194920925 194920925 C	
236	708 T	+1:194920926 194920926 T	
237 A	709 G	+1:194920927 194920927 G	A
237	710 C	+1:194920928 194920928 C	
237	711 A	+1:194920929 194920929 A	
238 T	712 A	+1:194920930 194920930 A	T
238	713 C	+1:194920931 194920931 C	
238	714 C	+1:194920932 194920932 C	
239 R	715 C	+1:194920933 194920933 C	R
239	716 G	+1:194920934 194920934 G	
239	717 G	+1:194920935 194920935 G	
240 G	718 G	+1:194920936 194920936 G	G
240	719 G	+1:194920937 194920937 G	
240	720 A	+1:194920938 194920938 A	
241 N	721 A	+1:194920939 194920939 A	N
241	722 A	+1:194920940 194920940 A	
241	723 T	+1:194920941 194920941 T	
242 T	724 A	+1:194920942 194920942 A	T
242	725 C	+1:194920943 194920943 C	
242	726 A	+1:194920944 194920944 A	
243 A	727 G	+1:194920945 194920945 G	A
243	728 C	+1:194920946 194920946 C	
243	729 A	+1:194920947 194920947 A	
244 K	730 A	+1:194920948 194920948 A	K
244	731 A	+1:194920949 194920949 A	
244	732 A	+1:194920950 194920950 A	
245 C	733 T	+1:194920951 194920951 T	C
245	734 G	+1:194920952 194920952 G	
245	735 C	+1:194920953 194920953 C	
246 T	736 A	+1:194920954 194920954 A	T
246	737 C	+1:194920955 194920955 C	
246	738 A	+1:194920956 194920956 A	
247 S	739 A	+1:194920957 194920957 A	S
247	740 G	+1:194920958 194920958 G	
247	741 T	+1:194920959 194920959 T	
248 T	742 A	+1:194920960 194920960 A	T
248	743 C	+1:194920961 194920961 C	
248	744 T	+1:194920962 194920962 T	
249 G	745 G	+1:194920963 194920963 G	G
249	746 G	+1:194920964 194920964 G	
249	747 C	+1:194920965 194920965 C	
250 W	748 T	+1:194920966 194920966 T	W
250	749 G	+1:194920967 194920967 G	
250	750 G	+1:194920968 194920968 G	
251 I	751 A	+1:194920969 194920969 A	I
251	752 T	+1:194920970 194920970 T	
251	753 A	+1:194920971 194920971 A	
252 P	754 C	+1:194920972 194920972 C	P
252	755 C	+1:194920973 194920973 C	
252	756 T	+1:194920974 194920974 T	
253 A	757 G	+1:194920975 194920975 G	A
253	758 C	+1:194920976 194920976 C	
253	759 T	+1:194920977 194920977 T	
254 P	760 C	+1:194920978 194920978 C	P
254	761 C	+1:194920979 194920979 C	
254	762 G	+1:194920980 194920980 G	
255 R	763 A	+1:194920981 194920981 A	R
255	764 G	+1:194920982 194920982 G	
255	765 A	+1:194920983 194920983 A	
256 C	766 T	+1:194920984 194920984 T	C
256	767 G	+1:194920985 194920985 G	
256	768 T	+1:194920986 194920986 T	
257 T	769 A	+1:194920987 194920987 A	T
257	770 C	+1:194920988 194920988 C	
257	771 C	+1:194920989 194920989 C	
258 L	772 T	+1:194920990 194920990 T	L
258	773 T	+1:194925173 194925173 T	
258	774 G	+1:194925174 194925174 G	
259 K	775 A	+1:194925175 194925175 A	K
259	776 A	+1:194925176 194925176 A	
259	777 A	+1:194925177 194925177 A	
260 P	778 C	+1:194925178 194925178 C	P
260	779 C	+1:194925179 194925179 C	
260	780 T	+1:194925180 194925180 T	
261 C	781 T	+1:194925181 194925181 T	C
261	782 G	+1:194925182 194925182 G	
261	783 T	+1:194925183 194925183 T	
262 D	784 G	+1:194925184 194925184 G	D
262	785 A	+1:194925185 194925185 A	
262	786 T	+1:194925186 194925186 T	
263 Y	787 T	+1:194925187 194925187 T	Y
263	788 A	+1:194925188 194925188 A	
263	789 T	+1:194925189 194925189 T	
264 P	790 C	+1:194925190 194925190 C	P
264	791 C	+1:194925191 194925191 C	
264	792 A	+1:194925192 194925192 A	
265 D	793 G	+1:194925193 194925193 G	D
265	794 A	+1:194925194 194925194 A	
265	795 C	+1:194925195 194925195 C	
266 I	796 A	+1:194925196 194925196 A	I
266	797 T	+1:194925197 194925197 T	
266	798 T	+1:194925198 194925198 T	
267 K	799 A	+1:194925199 194925199 A	K
267	800 A	+1:194925200 194925200 A	
267	801 A	+1:194925201 194925201 A	
268 H	802 C	+1:194925202 194925202 C	H
268	803 A	+1:194925203 194925203 A	
268	804 T	+1:194925204 194925204 T	
269 G	805 G	+1:194925205 194925205 G	G
269	806 G	+1:194925206 194925206 G	
269	807 A	+1:194925207 194925207 A	
270 G	808 G	+1:194925208 194925208 G	G
270	809 G	+1:194925209 194925209 G	
270	810 T	+1:194925210 194925210 T	
271 L	811 C	+1:194925211 194925211 C	L
271	812 T	+1:194925212 194925212 T	
271	813 A	+1:194925213 194925213 A	
272 Y	814 T	+1:194925214 194925214 T	Y
272	815 A	+1:194925215 194925215 A	
272	816 T	+1:194925216 194925216 T	
273 H	817 C	+1:194925217 194925217 C	H
273	818 A	+1:194925218 194925218 A	
273	819 T	+1:194925219 194925219 T	
274 E	820 G	+1:194925220 194925220 G	E
274	821 A	+1:194925221 194925221 A	
274	822 G	+1:194925222 194925222 G	
275 N	823 A	+1:194925223 194925223 A	N
275	824 A	+1:194925224 194925224 A	
275	825 T	+1:194925225 194925225 T	
276 M	826 A	+1:194925226 194925226 A	M
276	827 T	+1:194925227 194925227 T	
276	828 G	+1:194925228 194925228 G	
277 R	829 C	+1:194925229 194925229 C	R
277	830 G	+1:194925230 194925230 G	
277	831 T	+1:194925231 194925231 T	
278 R	832 A	+1:194925232 194925232 A	R
278	833 G	+1:194925233 194925233 G	
278	834 A	+1:194925234 194925234 A	
279 P	835 C	+1:194925235 194925235 C	P
279	836 C	+1:194925236 194925236 C	
279	837 A	+1:194925237 194925237 A	
280 Y	838 T	+1:194925238 194925238 T	Y
280	839 A	+1:194925239 194925239 A	
280	840 C	+1:194925240 194925240 C	
281 F	841 T	+1:194925241 194925241 T	F
281	842 T	+1:194925242 194925242 T	
281	843 T	+1:194925243 194925243 T	
282 P	844 C	+1:194925244 194925244 C	P
282	845 C	+1:194925245 194925245 C	
282	846 A	+1:194925246 194925246 A	
283 V	847 G	+1:194925247 194925247 G	V
283	848 T	+1:194925248 194925248 T	
283	849 A	+1:194925249 194925249 A	
284 A	850 G	+1:194925250 194925250 G	A
284	851 C	+1:194925251 194925251 C	
284	852 T	+1:194925252 194925252 T	
285 V	853 G	+1:194925253 194925253 G	V
285	854 T	+1:194925254 194925254 T	
285	855 A	+1:194925255 194925255 A	
286 G	856 G	+1:194925256 194925256 G	G
286	857 G	+1:194925257 194925257 G	
286	858 A	+1:194925258 194925258 A	
287 K	859 A	+1:194925259 194925259 A	K
287	860 A	+1:194925260 194925260 A	
287	861 A	+1:194925261 194925261 A	
288 Y	862 T	+1:194925262 194925262 T	Y
288	863 A	+1:194925263 194925263 A	
288	864 T	+1:194925264 194925264 T	
289 Y	865 T	+1:194925265 194925265 T	Y
289	866 A	+1:194925266 194925266 A	
289	867 C	+1:194925267 194925267 C	
290 S	868 T	+1:194925268 194925268 T	S
290	869 C	+1:194925269 194925269 C	
290	870 C	+1:194925270 194925270 C	
291 Y	871 T	+1:194925271 194925271 T	Y
291	872 A	+1:194925272 194925272 A	
291	873 T	+1:194925273 194925273 T	
292 Y	874 T	+1:194925274 194925274 T	Y
292	875 A	+1:194925275 194925275 A	
292	876 C	+1:194925276 194925276 C	
293 C	877 T	+1:194925277 194925277 T	C
293	878 G	+1:194925278 194925278 G	
293	879 T	+1:194925279 194925279 T	
294 D	880 G	+1:194925280 194925280 G	D
294	881 A	+1:194925281 194925281 A	
294	882 T	+1:194925282 194925282 T	
295 E	883 G	+1:194925283 194925283 G	E
295	884 A	+1:194925284 194925284 A	
295	885 A	+1:194925285 194925285 A	
296 H	886 C	+1:194925286 194925286 C	H
296	887 A	+1:194925287 194925287 A	
296	888 T	+1:194925288 194925288 T	
297 F	889 T	+1:194925289 194925289 T	F
297	890 T	+1:194925290 194925290 T	
297	891 T	+1:194925291 194925291 T	
298 E	892 G	+1:194925292 194925292 G	E
298	893 A	+1:194925293 194925293 A	
298	894 G	+1:194925294 194925294 G	
299 T	895 A	+1:194925295 194925295 A	T
299	896 C	+1:194925296 194925296 C	
299	897 T	+1:194925297 194925297 T	
300 P	898 C	+1:194925298 194925298 C	P
300	899 C	+1:194925299 194925299 C	
300	900 G	+1:194925300 194925300 G	
301 S	901 T	+1:194925301 194925301 T	S
301	902 C	+1:194925302 194925302 C	
301	903 A	+1:194925303 194925303 A	
302 G	904 G	+1:194925304 194925304 G	G
302	905 G	+1:194925305 194925305 G	
302	906 A	+1:194925306 194925306 A	
303 S	907 A	+1:194925307 194925307 A	S
303	908 G	+1:194925308 194925308 G	
303	909 T	+1:194925309 194925309 T	
304 Y	910 T	+1:194925310 194925310 T	Y
304	911 A	+1:194925311 194925311 A	
304	912 C	+1:194925312 194925312 C	
305 W	913 T	+1:194925313 194925313 T	W
305	914 G	+1:194925314 194925314 G	
305	915 G	+1:194925315 194925315 G	
306 D	916 G	+1:194925316 194925316 G	D
306	917 A	+1:194925317 194925317 A	
306	918 T	+1:194925318 194925318 T	
307 H	919 C	+1:194925319 194925319 C	H
307	920 A	+1:194925320 194925320 A	
307	921 C	+1:194925321 194925321 C	
308 I	922 A	+1:194925322 194925322 A	I
308	923 T	+1:194925323 194925323 T	
308	924 T	+1:194925324 194925324 T	
309 H	925 C	+1:194925325 194925325 C	H
309	926 A	+1:194925326 194925326 A	
309	927 T	+1:194925327 194925327 T	
310 C	928 T	+1:194925328 194925328 T	C
310	929 G	+1:194925329 194925329 G	
310	930 C	+1:194925330 194925330 C	
311 T	931 A	+1:194925331 194925331 A	T
311	932 C	+1:194925332 194925332 C	
311	933 A	+1:194925333 194925333 A	
312 Q	934 C	+1:194925334 194925334 C	Q
312	935 A	+1:194925335 194925335 A	
312	936 A	+1:194925336 194925336 A	
313 D	937 G	+1:194925337 194925337 G	D
313	938 A	+1:194925338 194925338 A	
313	939 T	+1:194925339 194925339 T	
314 G	940 G	+1:194925340 194925340 G	G
314	941 G	+1:194925341 194925341 G	
314	942 A	+1:194925342 194925342 A	
315 W	943 T	+1:194925343 194925343 T	W
315	944 G	+1:194925344 194925344 G	
315	945 G	+1:194925345 194925345 G	
316 S	946 T	+1:194925346 194925346 T	S
316	947 C	+1:194925347 194925347 C	
316	948 G	+1:194925348 194925348 G	
317 P	949 C	+1:194925349 194925349 C	P
317	950 C	+1:194925350 194925350 C	
317	951 A	+1:194925351 194925351 A	
318 A	952 G	+1:194925352 194925352 G	A
318	953 C	+1:194925353 194925353 C	
318	954 A	+1:194925354 194925354 A	
319 V	955 G	+1:194925355 194925355 G	V
319	956 T	+1:194925356 194925356 T	
319	957 A	+1:194925357 194925357 A	
320 P	958 C	+1:194925358 194925358 C	P
320	959 C	+1:194925359 194925359 C	
320	960 A	+1:194925360 194925360 A	
321 C	961 T	+1:194925361 194925361 T	C
321	962 G	+1:194925362 194925362 G	
321	963 C	+1:194925363 194925363 C	
322 L	964 C	+1:194925364 194925364 C	L
322	965 T	+1:194925365 194925365 T	
322	966 C	+1:194925366 194925366 C	
323 R	967 A	+1:194925367 194925367 A	R
323	968 G	+1:194925816 194925816 G	
323	969 A	+1:194925817 194925817 A	
324 K	970 A	+1:194925818 194925818 A	K
324	971 A	+1:194925819 194925819 A	
324	972 A	+1:194925820 194925820 A	
325 C	973 T	+1:194925821 194925821 T	C
325	974 G	+1:194925822 194925822 G	
325	975 T	+1:194925823 194925823 T	
326 Y	976 T	+1:194925824 194925824 T	Y
326	977 A	+1:194925825 194925825 A	
326	978 T	+1:194925826 194925826 T	
327 F	979 T	+1:194925827 194925827 T	F
327	980 T	+1:194925828 194925828 T	
327	981 T	+1:194925829 194925829 T	
328 P	982 C	+1:194925830 194925830 C	P
328	983 C	+1:194925831 194925831 C	
328	984 T	+1:194925832 194925832 T	
329 Y	985 T	+1:194925833 194925833 T	Y
329	986 A	+1:194925834 194925834 A	
329	987 T	+1:194925835 194925835 T	
330 L	988 T	+1:194925836 194925836 T	L
330	989 T	+1:194925837 194925837 T	
330	990 G	+1:194925838 194925838 G	
331 E	991 G	+1:194925839 194925839 G	E
331	992 A	+1:194925840 194925840 A	
331	993 A	+1:194925841 194925841 A	
332 N	994 A	+1:194925842 194925842 A	N
332	995 A	+1:194925843 194925843 A	
332	996 T	+1:194925844 194925844 T	
333 G	997 G	+1:194925845 194925845 G	G
333	998 G	+1:194925846 194925846 G	
333	999 A	+1:194925847 194925847 A	
334 Y	1000 T	+1:194925848 194925848 T	Y
334	1001 A	+1:194925849 194925849 A	
334	1002 T	+1:194925850 194925850 T	
335 N	1003 A	+1:194925851 194925851 A	N
335	1004 A	+1:194925852 194925852 A	
335	1005 T	+1:194925853 194925853 T	
336 Q	1006 C	+1:194925854 194925854 C	Q
336	1007 A	+1:194925855 194925855 A	
336	1008 A	+1:194925856 194925856 A	
337 N	1009 A	+1:194925857 194925857 A	N
337	1010 A	+1:194925858 194925858 A	
337	1011 T	+1:194925859 194925859 T	
338 H	1012 C	+1:194925860 194925860 C	H
338	1013 A	+1:194925861 194925861 A	
338	1014 T	+1:194925862 194925862 T	
339 G	1015 G	+1:194925863 194925863 G	G
339	1016 G	+1:194925864 194925864 G	
339	1017 A	+1:194925865 194925865 A	
340 R	1018 A	+1:194925866 194925866 A	R
340	1019 G	+1:194925867 194925867 G	
340	1020 A	+1:194925868 194925868 A	
341 K	1021 A	+1:194925869 194925869 A	K
341	1022 A	+1:194925870 194925870 A	
341	1023 G	+1:194925871 194925871 G	
342 F	1024 T	+1:194925872 194925872 T	F
342	1025 T	+1:194925873 194925873 T	
342	1026 T	+1:194925874 194925874 T	
343 V	1027 G	+1:194925875 194925875 G	V
343	1028 T	+1:194925876 194925876 T	
343	1029 A	+1:194925877 194925877 A	
344 Q	1030 C	+1:194925878 194925878 C	Q
344	1031 A	+1:194925879 194925879 A	
344	1032 G	+1:194925880 194925880 G	
345 G	1033 G	+1:194925881 194925881 G	G
345	1034 G	+1:194925882 194925882 G	
345	1035 T	+1:194925883 194925883 T	
346 K	1036 A	+1:194925884 194925884 A	K
346	1037 A	+1:194925885 194925885 A	
346	1038 A	+1:194925886 194925886 A	
347 S	1039 T	+1:194925887 194925887 T	S
347	1040 C	+1:194925888 194925888 C	
347	1041 T	+1:194925889 194925889 T	
348 I	1042 A	+1:194925890 194925890 A	I
348	1043 T	+1:194925891 194925891 T	
348	1044 A	+1:194925892 194925892 A	
349 D	1045 G	+1:194925893 194925893 G	D
349	1046 A	+1:194925894 194925894 A	
349	1047 C	+1:194925895 194925895 C	
350 V	1048 G	+1:194925896 194925896 G	V
350	1049 T	+1:194925897 194925897 T	
350	1050 T	+1:194925898 194925898 T	
351 A	1051 G	+1:194925899 194925899 G	A
351	1052 C	+1:194925900 194925900 C	
351	1053 C	+1:194925901 194925901 C	
352 C	1054 T	+1:194925902 194925902 T	C
352	1055 G	+1:194925903 194925903 G	
352	1056 C	+1:194925904 194925904 C	
353 H	1057 C	+1:194925905 194925905 C	H
353	1058 A	+1:194925906 194925906 A	
353	1059 T	+1:194925907 194925907 T	
354 P	1060 C	+1:194925908 194925908 C	P
354	1061 C	+1:194925909 194925909 C	
354	1062 T	+1:194925910 194925910 T	
355 G	1063 G	+1:194925911 194925911 G	G
355	1064 G	+1:194925912 194925912 G	
355	1065 C	+1:194925913 194925913 C	
356 Y	1066 T	+1:194925914 194925914 T	Y
356	1067 A	+1:194925915 194925915 A	
356	1068 C	+1:194925916 194925916 C	
357 A	1069 G	+1:194925917 194925917 G	A
357	1070 C	+1:194925918 194925918 C	
357	1071 T	+1:194925919 194925919 T	
358 L	1072 C	+1:194925920 194925920 C	L
358	1073 T	+1:194925921 194925921 T	
358	1074 T	+1:194925922 194925922 T	
359 P	1075 C	+1:194925923 194925923 C	P
359	1076 C	+1:194925924 194925924 C	
359	1077 A	+1:194925925 194925925 A	
360 K	1078 A	+1:194925926 194925926 A	K
360	1079 A	+1:194925927 194925927 A	
360	1080 A	+1:194925928 194925928 A	
361 A	1081 G	+1:194925929 194925929 G	A
361	1082 C	+1:194925930 194925930 C	
361	1083 G	+1:194925931 194925931 G	
362 Q	1084 C	+1:194925932 194925932 C	Q
362	1085 A	+1:194925933 194925933 A	
362	1086 G	+1:194925934 194925934 G	
363 T	1087 A	+1:194925935 194925935 A	T
363	1088 C	+1:194925936 194925936 C	
363	1089 C	+1:194925937 194925937 C	
364 T	1090 A	+1:194925938 194925938 A	T
364	1091 C	+1:194925939 194925939 C	
364	1092 A	+1:194925940 194925940 A	
365 V	1093 G	+1:194925941 194925941 G	V
365	1094 T	+1:194925942 194925942 T	
365	1095 T	+1:194925943 194925943 T	
366 T	1096 A	+1:194925944 194925944 A	T
366	1097 C	+1:194925945 194925945 C	
366	1098 A	+1:194925946 194925946 A	
367 C	1099 T	+1:194925947 194925947 T	C
367	1100 G	+1:194925948 194925948 G	
367	1101 T	+1:194925949 194925949 T	
368 M	1102 A	+1:194925950 194925950 A	M
368	1103 T	+1:194925951 194925951 T	
368	1104 G	+1:194925952 194925952 G	
369 E	1105 G	+1:194925953 194925953 G	E
369	1106 A	+1:194925954 194925954 A	
369	1107 G	+1:194925955 194925955 G	
370 N	1108 A	+1:194925956 194925956 A	N
370	1109 A	+1:194925957 194925957 A	
370	1110 T	+1:194925958 194925958 T	
371 G	1111 G	+1:194925959 194925959 G	G
371	1112 G	+1:194925960 194925960 G	
371	1113 C	+1:194925961 194925961 C	
372 W	1114 T	+1:194925962 194925962 T	W
372	1115 G	+1:194925963 194925963 G	
372	1116 G	+1:194925964 194925964 G	
373 S	1117 T	+1:194925965 194925965 T	S
373	1118 C	+1:194925966 194925966 C	
373	1119 T	+1:194925967 194925967 T	
374 P	1120 C	+1:194925968 194925968 C	P
374	1121 C	+1:194925969 194925969 C	
374	1122 T	+1:194925970 194925970 T	
375 T	1123 A	+1:194925971 194925971 A	T
375	1124 C	+1:194925972 194925972 C	
375	1125 T	+1:194925973 194925973 T	
376 P	1126 C	+1:194925974 194925974 C	P
376	1127 C	+1:194925975 194925975 C	
376	1128 C	+1:194925976 194925976 C	
377 R	1129 A	+1:194925977 194925977 A	R
377	1130 G	+1:194925978 194925978 G	
377	1131 A	+1:194925979 194925979 A	
378 C	1132 T	+1:194925980 194925980 T	C
378	1133 G	+1:194925981 194925981 G	
378	1134 C	+1:194925982 194925982 C	
379 I	1135 A	+1:194925983 194925983 A	I
379	1136 T	+1:194925984 194925984 T	
379	1137 C	+1:194925985 194925985 C	
380 R	1138 C	+1:194925986 194925986 C	R
380	1139 G	+1:194925987 194925987 G	
380	1140 T	+1:194925988 194925988 T	
381 V	1141 G	+1:194925989 194925989 G	V
381	1142 T	+1:194925990 194925990 T	
381	1143 C	+1:194925991 194925991 C	
>ENSP00000375846 
1 M	1 A	+1:194887871 194887871 A	M
1	2 T	+1:194887872 194887872 T	
1	3 G	+1:194887873 194887873 G	
2 R	4 A	+1:194887874 194887874 A	R
2	5 G	+1:194887875 194887875 G	
2	6 A	+1:194887876 194887876 A	
3 L	7 C	+1:194887877 194887877 C	L
3	8 T	+1:194887878 194887878 T	
3	9 T	+1:194887879 194887879 T	
4 L	10 C	+1:194887880 194887880 C	L
4	11 T	+1:194887881 194887881 T	
4	12 A	+1:194887882 194887882 A	
5 A	13 G	+1:194887883 194887883 G	A
5	14 C	+1:194887884 194887884 C	
5	15 A	+1:194887885 194887885 A	
6 K	16 A	+1:194887886 194887886 A	K
6	17 A	+1:194887887 194887887 A	
6	18 G	+1:194887888 194887888 G	
7 I	19 A	+1:194887889 194887889 A	I
7	20 T	+1:194887890 194887890 T	
7	21 T	+1:194887891 194887891 T	
8 I	22 A	+1:194887892 194887892 A	I
8	23 T	+1:194887893 194887893 T	
8	24 T	+1:194887894 194887894 T	
9 C	25 T	+1:194887895 194887895 T	C
9	26 G	+1:194887896 194887896 G	
9	27 C	+1:194887897 194887897 C	
10 L	28 C	+1:194887898 194887898 C	L
10	29 T	+1:194887899 194887899 T	
10	30 T	+1:194887900 194887900 T	
11 M	31 A	+1:194887901 194887901 A	M
11	32 T	+1:194887902 194887902 T	
11	33 G	+1:194887903 194887903 G	
12 L	34 T	+1:194887904 194887904 T	L
12	35 T	+1:194887905 194887905 T	
12	36 A	+1:194887906 194887906 A	
13 W	37 T	+1:194887907 194887907 T	W
13	38 G	+1:194887908 194887908 G	
13	39 G	+1:194887909 194887909 G	
14 A	40 G	+1:194887910 194887910 G	A
14	41 C	+1:194887911 194887911 C	
14	42 T	+1:194887912 194887912 T	
15 I	43 A	+1:194887913 194887913 A	I
15	44 T	+1:194887914 194887914 T	
15	45 T	+1:194887915 194887915 T	
16 C	46 T	+1:194887916 194887916 T	C
16	47 G	+1:194887917 194887917 G	
16	48 T	+1:194887918 194887918 T	
17 V	49 G	+1:194887919 194887919 G	V
17	50 T	+1:194887920 194887920 T	
17	51 A	+1:194887921 194887921 A	
18 A	52 G	+1:194887922 194887922 G	A
18	53 C	+1:194887923 194887923 C	
18	54 A	+1:194887924 194887924 A	
19 E	55 G	+1:194887925 194887925 G	E
19	56 A	+1:194887926 194887926 A	
19	57 A	+1:194887927 194887927 A	
20 D	58 G	+1:194887928 194887928 G	D
20	59 A	+1:194908731 194908731 A	
20	60 T	+1:194908732 194908732 T	
21 C	61 T	+1:194908733 194908733 T	C
21	62 G	+1:194908734 194908734 G	
21	63 C	+1:194908735 194908735 C	
22 N	64 A	+1:194908736 194908736 A	N
22	65 A	+1:194908737 194908737 A	
22	66 T	+1:194908738 194908738 T	
23 E	67 G	+1:194908739 194908739 G	E
23	68 A	+1:194908740 194908740 A	
23	69 A	+1:194908741 194908741 A	
24 L	70 C	+1:194908742 194908742 C	L
24	71 T	+1:194908743 194908743 T	
24	72 T	+1:194908744 194908744 T	
25 P	73 C	+1:194908745 194908745 C	P
25	74 C	+1:194908746 194908746 C	
25	75 T	+1:194908747 194908747 T	
26 P	76 C	+1:194908748 194908748 C	P
26	77 C	+1:194908749 194908749 C	
26	78 A	+1:194908750 194908750 A	
27 R	79 A	+1:194908751 194908751 A	R
27	80 G	+1:194908752 194908752 G	
27	81 A	+1:194908753 194908753 A	
28 R	82 A	+1:194908754 194908754 A	R
28	83 G	+1:194908755 194908755 G	
28	84 A	+1:194908756 194908756 A	
29 N	85 A	+1:194908757 194908757 A	N
29	86 A	+1:194908758 194908758 A	
29	87 T	+1:194908759 194908759 T	
30 T	88 A	+1:194908760 194908760 A	T
30	89 C	+1:194908761 194908761 C	
30	90 A	+1:194908762 194908762 A	
31 E	91 G	+1:194908763 194908763 G	E
31	92 A	+1:194908764 194908764 A	
31	93 A	+1:194908765 194908765 A	
32 I	94 A	+1:194908766 194908766 A	I
32	95 T	+1:194908767 194908767 T	
32	96 T	+1:194908768 194908768 T	
33 L	97 C	+1:194908769 194908769 C	L
33	98 T	+1:194908770 194908770 T	
33	99 G	+1:194908771 194908771 G	
34 T	100 A	+1:194908772 194908772 A	T
34	101 C	+1:194908773 194908773 C	
34	102 A	+1:194908774 194908774 A	
35 G	103 G	+1:194908775 194908775 G	G
35	104 G	+1:194908776 194908776 G	
35	105 T	+1:194908777 194908777 T	
36 S	106 T	+1:194908778 194908778 T	S
36	107 C	+1:194908779 194908779 C	
36	108 C	+1:194908780 194908780 C	
37 W	109 T	+1:194908781 194908781 T	W
37	110 G	+1:194908782 194908782 G	
37	111 G	+1:194908783 194908783 G	
38 S	112 T	+1:194908784 194908784 T	S
38	113 C	+1:194908785 194908785 C	
38	114 T	+1:194908786 194908786 T	
39 D	115 G	+1:194908787 194908787 G	D
39	116 A	+1:194908788 194908788 A	
39	117 C	+1:194908789 194908789 C	
40 Q	118 C	+1:194908790 194908790 C	Q
40	119 A	+1:194908791 194908791 A	
40	120 A	+1:194908792 194908792 A	
41 T	121 A	+1:194908793 194908793 A	T
41	122 C	+1:194908794 194908794 C	
41	123 A	+1:194908795 194908795 A	
42 Y	124 T	+1:194908796 194908796 T	Y
42	125 A	+1:194908797 194908797 A	
42	126 T	+1:194908798 194908798 T	
43 P	127 C	+1:194908799 194908799 C	P
43	128 C	+1:194908800 194908800 C	
43	129 A	+1:194908801 194908801 A	
44 E	130 G	+1:194908802 194908802 G	E
44	131 A	+1:194908803 194908803 A	
44	132 A	+1:194908804 194908804 A	
45 G	133 G	+1:194908805 194908805 G	G
45	134 G	+1:194908806 194908806 G	
45	135 C	+1:194908807 194908807 C	
46 T	136 A	+1:194908808 194908808 A	T
46	137 C	+1:194908809 194908809 C	
46	138 C	+1:194908810 194908810 C	
47 Q	139 C	+1:194908811 194908811 C	Q
47	140 A	+1:194908812 194908812 A	
47	141 G	+1:194908813 194908813 G	
48 A	142 G	+1:194908814 194908814 G	A
48	143 C	+1:194908815 194908815 C	
48	144 T	+1:194908816 194908816 T	
49 I	145 A	+1:194908817 194908817 A	I
49	146 T	+1:194908818 194908818 T	
49	147 C	+1:194908819 194908819 C	
50 Y	148 T	+1:194908820 194908820 T	Y
50	149 A	+1:194908821 194908821 A	
50	150 T	+1:194908822 194908822 T	
51 K	151 A	+1:194908823 194908823 A	K
51	152 A	+1:194908824 194908824 A	
51	153 A	+1:194908825 194908825 A	
52 C	154 T	+1:194908826 194908826 T	C
52	155 G	+1:194908827 194908827 G	
52	156 C	+1:194908828 194908828 C	
53 R	157 C	+1:194908829 194908829 C	R
53	158 G	+1:194908830 194908830 G	
53	159 C	+1:194908831 194908831 C	
54 P	160 C	+1:194908832 194908832 C	P
54	161 C	+1:194908833 194908833 C	
54	162 T	+1:194908834 194908834 T	
55 G	163 G	+1:194908835 194908835 G	G
55	164 G	+1:194908836 194908836 G	
55	165 A	+1:194908837 194908837 A	
56 Y	166 T	+1:194908838 194908838 T	Y
56	167 A	+1:194908839 194908839 A	
56	168 T	+1:194908840 194908840 T	
57 R	169 A	+1:194908841 194908841 A	R
57	170 G	+1:194908842 194908842 G	
57	171 A	+1:194908843 194908843 A	
58 S	172 T	+1:194908844 194908844 T	S
58	173 C	+1:194908845 194908845 C	
58	174 T	+1:194908846 194908846 T	
59 L	175 C	+1:194908847 194908847 C	L
59	176 T	+1:194908848 194908848 T	
59	177 T	+1:194908849 194908849 T	
60 G	178 G	+1:194908850 194908850 G	G
60	179 G	+1:194908851 194908851 G	
60	180 A	+1:194908852 194908852 A	
61 N	181 A	+1:194908853 194908853 A	N
61	182 A	+1:194908854 194908854 A	
61	183 T	+1:194908855 194908855 T	
62 V	184 G	+1:194908856 194908856 G	V
62	185 T	+1:194908857 194908857 T	
62	186 A	+1:194908858 194908858 A	
63 I	187 A	+1:194908859 194908859 A	I
63	188 T	+1:194908860 194908860 T	
63	189 A	+1:194908861 194908861 A	
64 M	190 A	+1:194908862 194908862 A	M
64	191 T	+1:194908863 194908863 T	
64	192 G	+1:194908864 194908864 G	
65 V	193 G	+1:194908865 194908865 G	V
65	194 T	+1:194908866 194908866 T	
65	195 A	+1:194908867 194908867 A	
66 C	196 T	+1:194908868 194908868 T	C
66	197 G	+1:194908869 194908869 G	
66	198 C	+1:194908870 194908870 C	
67 R	199 A	+1:194908871 194908871 A	R
67	200 G	+1:194908872 194908872 G	
67	201 G	+1:194908873 194908873 G	
68 K	202 A	+1:194908874 194908874 A	K
68	203 A	+1:194908875 194908875 A	
68	204 G	+1:194908876 194908876 G	
69 G	205 G	+1:194908877 194908877 G	G
69	206 G	+1:194908878 194908878 G	
69	207 A	+1:194908879 194908879 A	
70 E	208 G	+1:194908880 194908880 G	E
70	209 A	+1:194908881 194908881 A	
70	210 A	+1:194908882 194908882 A	
71 W	211 T	+1:194908883 194908883 T	W
71	212 G	+1:194908884 194908884 G	
71	213 G	+1:194908885 194908885 G	
72 V	214 G	+1:194908886 194908886 G	V
72	215 T	+1:194908887 194908887 T	
72	216 T	+1:194908888 194908888 T	
73 A	217 G	+1:194908889 194908889 G	A
73	218 C	+1:194908890 194908890 C	
73	219 T	+1:194908891 194908891 T	
74 L	220 C	+1:194908892 194908892 C	L
74	221 T	+1:194908893 194908893 T	
74	222 T	+1:194908894 194908894 T	
75 N	223 A	+1:194908895 194908895 A	N
75	224 A	+1:194908896 194908896 A	
75	225 T	+1:194908897 194908897 T	
76 P	226 C	+1:194908898 194908898 C	P
76	227 C	+1:194908899 194908899 C	
76	228 A	+1:194908900 194908900 A	
77 L	229 T	+1:194908901 194908901 T	L
77	230 T	+1:194908902 194908902 T	
77	231 A	+1:194908903 194908903 A	
78 R	232 A	+1:194908904 194908904 A	R
78	233 G	+1:194908905 194908905 G	
78	234 G	+1:194908906 194908906 G	
79 K	235 A	+1:194908907 194908907 A	K
79	236 A	+1:194908908 194908908 A	
79	237 A	+1:194908909 194908909 A	
80 C	238 T	+1:194908910 194908910 T	C
80	239 G	+1:194908911 194908911 G	
80	240 T	+1:194908912 194908912 T	
81 Q	241 C	+1:194908913 194908913 C	Q
81	242 A	+1:194908914 194908914 A	
81	243 G	+1:194908915 194908915 G	
82 K	244 A	+1:194908916 194908916 A	K
82	245 A	+1:194909610 194909610 A	
82	246 A	+1:194909611 194909611 A	
83 R	247 A	+1:194909612 194909612 A	R
83	248 G	+1:194909613 194909613 G	
83	249 G	+1:194909614 194909614 G	
84 P	250 C	+1:194909615 194909615 C	P
84	251 C	+1:194909616 194909616 C	
84	252 C	+1:194909617 194909617 C	
85 C	253 T	+1:194909618 194909618 T	C
85	254 G	+1:194909619 194909619 G	
85	255 T	+1:194909620 194909620 T	
86 G	256 G	+1:194909621 194909621 G	G
86	257 G	+1:194909622 194909622 G	
86	258 A	+1:194909623 194909623 A	
87 H	259 C	+1:194909624 194909624 C	H
87	260 A	+1:194909625 194909625 A	
87	261 T	+1:194909626 194909626 T	
88 P	262 C	+1:194909627 194909627 C	P
88	263 C	+1:194909628 194909628 C	
88	264 T	+1:194909629 194909629 T	
89 G	265 G	+1:194909630 194909630 G	G
89	266 G	+1:194909631 194909631 G	
89	267 A	+1:194909632 194909632 A	
90 D	268 G	+1:194909633 194909633 G	D
90	269 A	+1:194909634 194909634 A	
90	270 T	+1:194909635 194909635 T	
91 T	271 A	+1:194909636 194909636 A	T
91	272 C	+1:194909637 194909637 C	
91	273 T	+1:194909638 194909638 T	
92 P	274 C	+1:194909639 194909639 C	P
92	275 C	+1:194909640 194909640 C	
92	276 T	+1:194909641 194909641 T	
93 F	277 T	+1:194909642 194909642 T	F
93	278 T	+1:194909643 194909643 T	
93	279 T	+1:194909644 194909644 T	
94 G	280 G	+1:194909645 194909645 G	G
94	281 G	+1:194909646 194909646 G	
94	282 T	+1:194909647 194909647 T	
95 T	283 A	+1:194909648 194909648 A	T
95	284 C	+1:194909649 194909649 C	
95	285 T	+1:194909650 194909650 T	
96 F	286 T	+1:194909651 194909651 T	F
96	287 T	+1:194909652 194909652 T	
96	288 T	+1:194909653 194909653 T	
97 T	289 A	+1:194909654 194909654 A	T
97	290 C	+1:194909655 194909655 C	
97	291 C	+1:194909656 194909656 C	
98 L	292 C	+1:194909657 194909657 C	L
98	293 T	+1:194909658 194909658 T	
98	294 T	+1:194909659 194909659 T	
99 T	295 A	+1:194909660 194909660 A	T
99	296 C	+1:194909661 194909661 C	
99	297 A	+1:194909662 194909662 A	
100 G	298 G	+1:194909663 194909663 G	G
100	299 G	+1:194909664 194909664 G	
100	300 A	+1:194909665 194909665 A	
101 G	301 G	+1:194909666 194909666 G	G
101	302 G	+1:194909667 194909667 G	
101	303 A	+1:194909668 194909668 A	
102 N	304 A	+1:194909669 194909669 A	N
102	305 A	+1:194909670 194909670 A	
102	306 T	+1:194909671 194909671 T	
103 V	307 G	+1:194909672 194909672 G	V
103	308 T	+1:194909673 194909673 T	
103	309 G	+1:194909674 194909674 G	
104 F	310 T	+1:194909675 194909675 T	F
104	311 T	+1:194909676 194909676 T	
104	312 T	+1:194909677 194909677 T	
105 E	313 G	+1:194909678 194909678 G	E
105	314 A	+1:194909679 194909679 A	
105	315 A	+1:194909680 194909680 A	
106 Y	316 T	+1:194909681 194909681 T	Y
106	317 A	+1:194909682 194909682 A	
106	318 T	+1:194909683 194909683 T	
107 G	319 G	+1:194909684 194909684 G	G
107	320 G	+1:194909685 194909685 G	
107	321 T	+1:194909686 194909686 T	
108 V	322 G	+1:194909687 194909687 G	V
108	323 T	+1:194909688 194909688 T	
108	324 A	+1:194909689 194909689 A	
109 K	325 A	+1:194909690 194909690 A	K
109	326 A	+1:194909691 194909691 A	
109	327 A	+1:194909692 194909692 A	
110 A	328 G	+1:194909693 194909693 G	A
110	329 C	+1:194909694 194909694 C	
110	330 T	+1:194909695 194909695 T	
111 V	331 G	+1:194909696 194909696 G	V
111	332 T	+1:194909697 194909697 T	
111	333 G	+1:194909698 194909698 G	
112 Y	334 T	+1:194909699 194909699 T	Y
112	335 A	+1:194909700 194909700 A	
112	336 T	+1:194909701 194909701 T	
113 T	337 A	+1:194909702 194909702 A	T
113	338 C	+1:194909703 194909703 C	
113	339 A	+1:194909704 194909704 A	
114 C	340 T	+1:194909705 194909705 T	C
114	341 G	+1:194909706 194909706 G	
114	342 T	+1:194909707 194909707 T	
115 N	343 A	+1:194909708 194909708 A	N
115	344 A	+1:194909709 194909709 A	
115	345 T	+1:194909710 194909710 T	
116 E	346 G	+1:194909711 194909711 G	E
116	347 A	+1:194909712 194909712 A	
116	348 G	+1:194909713 194909713 G	
117 G	349 G	+1:194909714 194909714 G	G
117	350 G	+1:194909715 194909715 G	
117	351 G	+1:194911742 194911742 G	
118 Y	352 T	+1:194911743 194911743 T	Y
118	353 A	+1:194911744 194911744 A	
118	354 T	+1:194911745 194911745 T	
119 Q	355 C	+1:194911746 194911746 C	Q
119	356 A	+1:194911747 194911747 A	
119	357 A	+1:194911748 194911748 A	
120 L	358 T	+1:194911749 194911749 T	L
120	359 T	+1:194911750 194911750 T	
120	360 G	+1:194911751 194911751 G	
121 L	361 C	+1:194911752 194911752 C	L
121	362 T	+1:194911753 194911753 T	
121	363 A	+1:194911754 194911754 A	
122 G	364 G	+1:194911755 194911755 G	G
122	365 G	+1:194911756 194911756 G	
122	366 T	+1:194911757 194911757 T	
123 E	367 G	+1:194911758 194911758 G	E
123	368 A	+1:194911759 194911759 A	
123	369 G	+1:194911760 194911760 G	
124 I	370 A	+1:194911761 194911761 A	I
124	371 T	+1:194911762 194911762 T	
124	372 T	+1:194911763 194911763 T	
125 N	373 A	+1:194911764 194911764 A	N
125	374 A	+1:194911765 194911765 A	
125	375 T	+1:194911766 194911766 T	
126 Y	376 T	+1:194911767 194911767 T	Y
126	377 A	+1:194911768 194911768 A	
126	378 C	+1:194911769 194911769 C	
127 R	379 C	+1:194911770 194911770 C	R
127	380 G	+1:194911771 194911771 G	
127	381 T	+1:194911772 194911772 T	
128 E	382 G	+1:194911773 194911773 G	E
128	383 A	+1:194911774 194911774 A	
128	384 A	+1:194911775 194911775 A	
129 C	385 T	+1:194911776 194911776 T	C
129	386 G	+1:194911777 194911777 G	
129	387 T	+1:194911778 194911778 T	
130 D	388 G	+1:194911779 194911779 G	D
130	389 A	+1:194911780 194911780 A	
130	390 C	+1:194911781 194911781 C	
131 T	391 A	+1:194911782 194911782 A	T
131	392 C	+1:194911783 194911783 C	
131	393 A	+1:194911784 194911784 A	
132 D	394 G	+1:194911785 194911785 G	D
132	395 A	+1:194911786 194911786 A	
132	396 T	+1:194911787 194911787 T	
133 G	397 G	+1:194911788 194911788 G	G
133	398 G	+1:194911789 194911789 G	
133	399 A	+1:194911790 194911790 A	
134 W	400 T	+1:194911791 194911791 T	W
134	401 G	+1:194911792 194911792 G	
134	402 G	+1:194911793 194911793 G	
135 T	403 A	+1:194911794 194911794 A	T
135	404 C	+1:194911795 194911795 C	
135	405 C	+1:194911796 194911796 C	
136 N	406 A	+1:194911797 194911797 A	N
136	407 A	+1:194911798 194911798 A	
136	408 T	+1:194911799 194911799 T	
137 D	409 G	+1:194911800 194911800 G	D
137	410 A	+1:194911801 194911801 A	
137	411 T	+1:194911802 194911802 T	
138 I	412 A	+1:194911803 194911803 A	I
138	413 T	+1:194911804 194911804 T	
138	414 T	+1:194911805 194911805 T	
139 P	415 C	+1:194911806 194911806 C	P
139	416 C	+1:194911807 194911807 C	
139	417 T	+1:194911808 194911808 T	
140 I	418 A	+1:194911809 194911809 A	I
140	419 T	+1:194911810 194911810 T	
140	420 A	+1:194911811 194911811 A	
141 C	421 T	+1:194911812 194911812 T	C
141	422 G	+1:194911813 194911813 G	
141	423 T	+1:194911814 194911814 T	
142 E	424 G	+1:194911815 194911815 G	E
142	425 A	+1:194911816 194911816 A	
142	426 A	+1:194911817 194911817 A	
143 V	427 G	+1:194911818 194911818 G	V
143	428 T	+1:194913229 194913229 T	
143	429 T	+1:194913230 194913230 T	
144 V	430 G	+1:194913231 194913231 G	V
144	431 T	+1:194913232 194913232 T	
144	432 G	+1:194913233 194913233 G	
145 K	433 A	+1:194913234 194913234 A	K
145	434 A	+1:194913235 194913235 A	
145	435 G	+1:194913236 194913236 G	
146 C	436 T	+1:194913237 194913237 T	C
146	437 G	+1:194913238 194913238 G	
146	438 T	+1:194913239 194913239 T	
147 L	439 T	+1:194913240 194913240 T	L
147	440 T	+1:194913241 194913241 T	
147	441 A	+1:194913242 194913242 A	
148 P	442 C	+1:194913243 194913243 C	P
148	443 C	+1:194913244 194913244 C	
148	444 A	+1:194913245 194913245 A	
149 V	445 G	+1:194913246 194913246 G	V
149	446 T	+1:194913247 194913247 T	
149	447 G	+1:194913248 194913248 G	
150 T	448 A	+1:194913249 194913249 A	T
150	449 C	+1:194913250 194913250 C	
150	450 A	+1:194913251 194913251 A	
151 A	451 G	+1:194913252 194913252 G	A
151	452 C	+1:194913253 194913253 C	
151	453 A	+1:194913254 194913254 A	
152 P	454 C	+1:194913255 194913255 C	P
152	455 C	+1:194913256 194913256 C	
152	456 A	+1:194913257 194913257 A	
153 E	457 G	+1:194913258 194913258 G	E
153	458 A	+1:194913259 194913259 A	
153	459 G	+1:194913260 194913260 G	
154 N	460 A	+1:194913261 194913261 A	N
154	461 A	+1:194913262 194913262 A	
154	462 T	+1:194913263 194913263 T	
155 G	463 G	+1:194913264 194913264 G	G
155	464 G	+1:194913265 194913265 G	
155	465 A	+1:194913266 194913266 A	
156 K	466 A	+1:194913267 194913267 A	K
156	467 A	+1:194913268 194913268 A	
156	468 A	+1:194913269 194913269 A	
157 I	469 A	+1:194913270 194913270 A	I
157	470 T	+1:194913271 194913271 T	
157	471 T	+1:194913272 194913272 T	
158 V	472 G	+1:194913273 194913273 G	V
158	473 T	+1:194913274 194913274 T	
158	474 C	+1:194913275 194913275 C	
159 S	475 A	+1:194913276 194913276 A	S
159	476 G	+1:194913277 194913277 G	
159	477 T	+1:194913278 194913278 T	
160 S	478 A	+1:194913279 194913279 A	S
160	479 G	+1:194913280 194913280 G	
160	480 T	+1:194913281 194913281 T	
161 A	481 G	+1:194913282 194913282 G	A
161	482 C	+1:194913283 194913283 C	
161	483 A	+1:194913284 194913284 A	
162 M	484 A	+1:194913285 194913285 A	M
162	485 T	+1:194913286 194913286 T	
162	486 G	+1:194913287 194913287 G	
163 E	487 G	+1:194913288 194913288 G	E
163	488 A	+1:194913289 194913289 A	
163	489 A	+1:194913290 194913290 A	
164 P	490 C	+1:194913291 194913291 C	P
164	491 C	+1:194913292 194913292 C	
164	492 A	+1:194913293 194913293 A	
165 D	493 G	+1:194913294 194913294 G	D
165	494 A	+1:194913295 194913295 A	
165	495 T	+1:194913296 194913296 T	
166 R	496 C	+1:194913297 194913297 C	R
166	497 G	+1:194913298 194913298 G	
166	498 G	+1:194913299 194913299 G	
167 E	499 G	+1:194913300 194913300 G	E
167	500 A	+1:194913301 194913301 A	
167	501 A	+1:194913302 194913302 A	
168 Y	502 T	+1:194913303 194913303 T	Y
168	503 A	+1:194913304 194913304 A	
168	504 C	+1:194913305 194913305 C	
169 H	505 C	+1:194913306 194913306 C	H
169	506 A	+1:194913307 194913307 A	
169	507 T	+1:194913308 194913308 T	
170 F	508 T	+1:194913309 194913309 T	F
170	509 T	+1:194913310 194913310 T	
170	510 T	+1:194913311 194913311 T	
171 G	511 G	+1:194913312 194913312 G	G
171	512 G	+1:194913313 194913313 G	
171	513 A	+1:194913314 194913314 A	
172 Q	514 C	+1:194913315 194913315 C	Q
172	515 A	+1:194913316 194913316 A	
172	516 A	+1:194913317 194913317 A	
173 A	517 G	+1:194913318 194913318 G	A
173	518 C	+1:194913319 194913319 C	
173	519 A	+1:194913320 194913320 A	
174 V	520 G	+1:194913321 194913321 G	V
174	521 T	+1:194913322 194913322 T	
174	522 A	+1:194913323 194913323 A	
175 R	523 C	+1:194913324 194913324 C	R
175	524 G	+1:194913325 194913325 G	
175	525 G	+1:194913326 194913326 G	
176 F	526 T	+1:194913327 194913327 T	F
176	527 T	+1:194913328 194913328 T	
176	528 T	+1:194913329 194913329 T	
177 V	529 G	+1:194913330 194913330 G	V
177	530 T	+1:194913331 194913331 T	
177	531 A	+1:194913332 194913332 A	
178 C	532 T	+1:194913333 194913333 T	C
178	533 G	+1:194913334 194913334 G	
178	534 T	+1:194913335 194913335 T	
179 N	535 A	+1:194913336 194913336 A	N
179	536 A	+1:194913337 194913337 A	
179	537 C	+1:194913338 194913338 C	
180 S	538 T	+1:194913339 194913339 T	S
180	539 C	+1:194913340 194913340 C	
180	540 A	+1:194913341 194913341 A	
181 G	541 G	+1:194913342 194913342 G	G
181	542 G	+1:194913343 194913343 G	
181	543 C	+1:194913344 194913344 C	
182 Y	544 T	+1:194913345 194913345 T	Y
182	545 A	+1:194913346 194913346 A	
182	546 C	+1:194913347 194913347 C	
183 K	547 A	+1:194913348 194913348 A	K
183	548 A	+1:194913349 194913349 A	
183	549 G	+1:194913350 194913350 G	
184 I	550 A	+1:194913351 194913351 A	I
184	551 T	+1:194913352 194913352 T	
184	552 T	+1:194913353 194913353 T	
185 E	553 G	+1:194913354 194913354 G	E
185	554 A	+1:194913355 194913355 A	
185	555 A	+1:194913356 194913356 A	
186 G	556 G	+1:194913357 194913357 G	G
186	557 G	+1:194913358 194913358 G	
186	558 A	+1:194913359 194913359 A	
187 D	559 G	+1:194913360 194913360 G	D
187	560 A	+1:194913361 194913361 A	
187	561 T	+1:194913362 194913362 T	
188 E	562 G	+1:194913363 194913363 G	E
188	563 A	+1:194913364 194913364 A	
188	564 A	+1:194913365 194913365 A	
189 E	565 G	+1:194913366 194913366 G	E
189	566 A	+1:194913367 194913367 A	
189	567 A	+1:194913368 194913368 A	
190 M	568 A	+1:194913369 194913369 A	M
190	569 T	+1:194913370 194913370 T	
190	570 G	+1:194913371 194913371 G	
191 H	571 C	+1:194913372 194913372 C	H
191	572 A	+1:194913373 194913373 A	
191	573 T	+1:194913374 194913374 T	
192 C	574 T	+1:194913375 194913375 T	C
192	575 G	+1:194913376 194913376 G	
192	576 T	+1:194913377 194913377 T	
193 S	577 T	+1:194913378 194913378 T	S
193	578 C	+1:194913379 194913379 C	
193	579 A	+1:194913380 194913380 A	
194 D	580 G	+1:194913381 194913381 G	D
194	581 A	+1:194913382 194913382 A	
194	582 C	+1:194913383 194913383 C	
195 D	583 G	+1:194913384 194913384 G	D
195	584 A	+1:194913385 194913385 A	
195	585 T	+1:194913386 194913386 T	
196 G	586 G	+1:194913387 194913387 G	G
196	587 G	+1:194913388 194913388 G	
196	588 T	+1:194913389 194913389 T	
197 F	589 T	+1:194913390 194913390 T	F
197	590 T	+1:194913391 194913391 T	
197	591 T	+1:194913392 194913392 T	
198 W	592 T	+1:194913393 194913393 T	W
198	593 G	+1:194913394 194913394 G	
198	594 G	+1:194913395 194913395 G	
199 S	595 A	+1:194913396 194913396 A	S
199	596 G	+1:194913397 194913397 G	
199	597 T	+1:194913398 194913398 T	
200 K	598 A	+1:194913399 194913399 A	K
200	599 A	+1:194913400 194913400 A	
200	600 A	+1:194913401 194913401 A	
201 E	601 G	+1:194913402 194913402 G	E
201	602 A	+1:194913403 194913403 A	
201	603 G	+1:194913404 194913404 G	
202 K	604 A	+1:194913405 194913405 A	K
202	605 A	+1:194913406 194913406 A	
202	606 A	+1:194913407 194913407 A	
203 P	607 C	+1:194913408 194913408 C	P
203	608 C	+1:194913409 194913409 C	
203	609 A	+1:194913410 194913410 A	
204 K	610 A	+1:194913411 194913411 A	K
204	611 A	+1:194913412 194913412 A	
204	612 G	+1:194913413 194913413 G	
205 C	613 T	+1:194913414 194913414 T	C
205	614 G	+1:194913415 194913415 G	
205	615 T	+1:194913416 194913416 T	
206 V	616 G	+1:194913417 194913417 G	V
206	617 T	+1:194913418 194913418 T	
206	618 G	+1:194913419 194913419 G	
207 E	619 G	+1:194913420 194913420 G	E
207	620 A	+1:194915376 194915376 A	
207	621 A	+1:194915377 194915377 A	
208 I	622 A	+1:194915378 194915378 A	I
208	623 T	+1:194915379 194915379 T	
208	624 T	+1:194915380 194915380 T	
209 S	625 T	+1:194915381 194915381 T	S
209	626 C	+1:194915382 194915382 C	
209	627 A	+1:194915383 194915383 A	
210 C	628 T	+1:194915384 194915384 T	C
210	629 G	+1:194915385 194915385 G	
210	630 C	+1:194915386 194915386 C	
211 K	631 A	+1:194915387 194915387 A	K
211	632 A	+1:194915388 194915388 A	
211	633 A	+1:194915389 194915389 A	
212 S	634 T	+1:194915390 194915390 T	S
212	635 C	+1:194915391 194915391 C	
212	636 C	+1:194915392 194915392 C	
213 P	637 C	+1:194915393 194915393 C	P
213	638 C	+1:194915394 194915394 C	
213	639 A	+1:194915395 194915395 A	
214 D	640 G	+1:194915396 194915396 G	D
214	641 A	+1:194915397 194915397 A	
214	642 T	+1:194915398 194915398 T	
215 V	643 G	+1:194915399 194915399 G	V
215	644 T	+1:194915400 194915400 T	
215	645 T	+1:194915401 194915401 T	
216 I	646 A	+1:194915402 194915402 A	I
216	647 T	+1:194915403 194915403 T	
216	648 A	+1:194915404 194915404 A	
217 N	649 A	+1:194915405 194915405 A	N
217	650 A	+1:194915406 194915406 A	
217	651 T	+1:194915407 194915407 T	
218 G	652 G	+1:194915408 194915408 G	G
218	653 G	+1:194915409 194915409 G	
218	654 A	+1:194915410 194915410 A	
219 S	655 T	+1:194915411 194915411 T	S
219	656 C	+1:194915412 194915412 C	
219	657 T	+1:194915413 194915413 T	
220 P	658 C	+1:194915414 194915414 C	P
220	659 C	+1:194915415 194915415 C	
220	660 T	+1:194915416 194915416 T	
221 I	661 A	+1:194915417 194915417 A	I
221	662 T	+1:194915418 194915418 T	
221	663 A	+1:194915419 194915419 A	
222 S	664 T	+1:194915420 194915420 T	S
222	665 C	+1:194915421 194915421 C	
222	666 T	+1:194915422 194915422 T	
223 Q	667 C	+1:194915423 194915423 C	Q
223	668 A	+1:194915424 194915424 A	
223	669 G	+1:194915425 194915425 G	
224 K	670 A	+1:194915426 194915426 A	K
224	671 A	+1:194915427 194915427 A	
224	672 G	+1:194915428 194915428 G	
225 I	673 A	+1:194915429 194915429 A	I
225	674 T	+1:194915430 194915430 T	
225	675 T	+1:194915431 194915431 T	
226 I	676 A	+1:194915432 194915432 A	I
226	677 T	+1:194915433 194915433 T	
226	678 T	+1:194915434 194915434 T	
227 Y	679 T	+1:194915435 194915435 T	Y
227	680 A	+1:194915436 194915436 A	
227	681 T	+1:194915437 194915437 T	
228 K	682 A	+1:194915438 194915438 A	K
228	683 A	+1:194915439 194915439 A	
228	684 G	+1:194915440 194915440 G	
229 E	685 G	+1:194915441 194915441 G	E
229	686 A	+1:194915442 194915442 A	
229	687 G	+1:194915443 194915443 G	
230 N	688 A	+1:194915444 194915444 A	N
230	689 A	+1:194915445 194915445 A	
230	690 T	+1:194915446 194915446 T	
231 E	691 G	+1:194915447 194915447 G	E
231	692 A	+1:194915448 194915448 A	
231	693 A	+1:194915449 194915449 A	
232 R	694 C	+1:194915450 194915450 C	R
232	695 G	+1:194915451 194915451 G	
232	696 A	+1:194915452 194915452 A	
233 F	697 T	+1:194915453 194915453 T	F
233	698 T	+1:194915454 194915454 T	
233	699 T	+1:194915455 194915455 T	
234 Q	700 C	+1:194915456 194915456 C	Q
234	701 A	+1:194915457 194915457 A	
234	702 A	+1:194915458 194915458 A	
235 Y	703 T	+1:194915459 194915459 T	Y
235	704 A	+1:194915460 194915460 A	
235	705 T	+1:194915461 194915461 T	
236 K	706 A	+1:194915462 194915462 A	K
236	707 A	+1:194915463 194915463 A	
236	708 A	+1:194915464 194915464 A	
237 C	709 T	+1:194915465 194915465 T	C
237	710 G	+1:194915466 194915466 G	
237	711 T	+1:194915467 194915467 T	
238 N	712 A	+1:194915468 194915468 A	N
238	713 A	+1:194915469 194915469 A	
238	714 C	+1:194915470 194915470 C	
239 M	715 A	+1:194915471 194915471 A	M
239	716 T	+1:194915472 194915472 T	
239	717 G	+1:194915473 194915473 G	
240 G	718 G	+1:194915474 194915474 G	G
240	719 G	+1:194915475 194915475 G	
240	720 T	+1:194915476 194915476 T	
241 Y	721 T	+1:194915477 194915477 T	Y
241	722 A	+1:194915478 194915478 A	
241	723 T	+1:194915479 194915479 T	
242 E	724 G	+1:194915480 194915480 G	E
242	725 A	+1:194915481 194915481 A	
242	726 A	+1:194915482 194915482 A	
243 Y	727 T	+1:194915483 194915483 T	Y
243	728 A	+1:194915484 194915484 A	
243	729 C	+1:194915485 194915485 C	
244 S	730 A	+1:194915486 194915486 A	S
244	731 G	+1:194915487 194915487 G	
244	732 T	+1:194915488 194915488 T	
245 E	733 G	+1:194915489 194915489 G	E
245	734 A	+1:194915490 194915490 A	
245	735 A	+1:194915491 194915491 A	
246 R	736 A	+1:194915492 194915492 A	R
246	737 G	+1:194915493 194915493 G	
246	738 A	+1:194915494 194915494 A	
247 G	739 G	+1:194915495 194915495 G	G
247	740 G	+1:194915496 194915496 G	
247	741 A	+1:194915497 194915497 A	
248 D	742 G	+1:194915498 194915498 G	D
248	743 A	+1:194915499 194915499 A	
248	744 T	+1:194915500 194915500 T	
249 A	745 G	+1:194915501 194915501 G	A
249	746 C	+1:194915502 194915502 C	
249	747 T	+1:194915503 194915503 T	
250 V	748 G	+1:194915504 194915504 G	V
250	749 T	+1:194915505 194915505 T	
250	750 A	+1:194915506 194915506 A	
251 C	751 T	+1:194915507 194915507 T	C
251	752 G	+1:194915508 194915508 G	
251	753 C	+1:194915509 194915509 C	
252 T	754 A	+1:194915510 194915510 A	T
252	755 C	+1:194915511 194915511 C	
252	756 T	+1:194915512 194915512 T	
253 E	757 G	+1:194915513 194915513 G	E
253	758 A	+1:194915514 194915514 A	
253	759 A	+1:194915515 194915515 A	
254 S	760 T	+1:194915516 194915516 T	S
254	761 C	+1:194915517 194915517 C	
254	762 T	+1:194915518 194915518 T	
255 G	763 G	+1:194915519 194915519 G	G
255	764 G	+1:194915520 194915520 G	
255	765 A	+1:194915521 194915521 A	
256 W	766 T	+1:194915522 194915522 T	W
256	767 G	+1:194915523 194915523 G	
256	768 G	+1:194915524 194915524 G	
257 R	769 C	+1:194915525 194915525 C	R
257	770 G	+1:194915526 194915526 G	
257	771 T	+1:194915527 194915527 T	
258 P	772 C	+1:194915528 194915528 C	P
258	773 C	+1:194915529 194915529 C	
258	774 G	+1:194915530 194915530 G	
259 L	775 T	+1:194915531 194915531 T	L
259	776 T	+1:194915532 194915532 T	
259	777 G	+1:194915533 194915533 G	
260 P	778 C	+1:194915534 194915534 C	P
260	779 C	+1:194915535 194915535 C	
260	780 T	+1:194915536 194915536 T	
261 S	781 T	+1:194915537 194915537 T	S
261	782 C	+1:194915538 194915538 C	
261	783 A	+1:194915539 194915539 A	
262 C	784 T	+1:194915540 194915540 T	C
262	785 G	+1:194915541 194915541 G	
262	786 T	+1:194915542 194915542 T	
263 E	787 G	+1:194915543 194915543 G	E
263	788 A	+1:194915544 194915544 A	
263	789 A	+1:194915545 194915545 A	
264 E	790 G	+1:194915546 194915546 G	E
264	791 A	+1:194920817 194920817 A	
264	792 A	+1:194920818 194920818 A	
265 K	793 A	+1:194920819 194920819 A	K
265	794 A	+1:194920820 194920820 A	
265	795 A	+1:194920821 194920821 A	
266 S	796 T	+1:194920822 194920822 T	S
266	797 C	+1:194920823 194920823 C	
266	798 A	+1:194920824 194920824 A	
267 C	799 T	+1:194920825 194920825 T	C
267	800 G	+1:194920826 194920826 G	
267	801 T	+1:194920827 194920827 T	
268 D	802 G	+1:194920828 194920828 G	D
268	803 A	+1:194920829 194920829 A	
268	804 T	+1:194920830 194920830 T	
269 N	805 A	+1:194920831 194920831 A	N
269	806 A	+1:194920832 194920832 A	
269	807 T	+1:194920833 194920833 T	
270 P	808 C	+1:194920834 194920834 C	P
270	809 C	+1:194920835 194920835 C	
270	810 T	+1:194920836 194920836 T	
271 Y	811 T	+1:194920837 194920837 T	Y
271	812 A	+1:194920838 194920838 A	
271	813 T	+1:194920839 194920839 T	
272 I	814 A	+1:194920840 194920840 A	I
272	815 T	+1:194920841 194920841 T	
272	816 T	+1:194920842 194920842 T	
273 P	817 C	+1:194920843 194920843 C	P
273	818 C	+1:194920844 194920844 C	
273	819 A	+1:194920845 194920845 A	
274 N	820 A	+1:194920846 194920846 A	N
274	821 A	+1:194920847 194920847 A	
274	822 T	+1:194920848 194920848 T	
275 G	823 G	+1:194920849 194920849 G	G
275	824 G	+1:194920850 194920850 G	
275	825 T	+1:194920851 194920851 T	
276 D	826 G	+1:194920852 194920852 G	D
276	827 A	+1:194920853 194920853 A	
276	828 C	+1:194920854 194920854 C	
277 Y	829 T	+1:194920855 194920855 T	Y
277	830 A	+1:194920856 194920856 A	
277	831 C	+1:194920857 194920857 C	
278 S	832 T	+1:194920858 194920858 T	S
278	833 C	+1:194920859 194920859 C	
278	834 A	+1:194920860 194920860 A	
279 P	835 C	+1:194920861 194920861 C	P
279	836 C	+1:194920862 194920862 C	
279	837 T	+1:194920863 194920863 T	
280 L	838 T	+1:194920864 194920864 T	L
280	839 T	+1:194920865 194920865 T	
280	840 A	+1:194920866 194920866 A	
281 R	841 A	+1:194920867 194920867 A	R
281	842 G	+1:194920868 194920868 G	
281	843 G	+1:194920869 194920869 G	
282 I	844 A	+1:194920870 194920870 A	I
282	845 T	+1:194920871 194920871 T	
282	846 T	+1:194920872 194920872 T	
283 K	847 A	+1:194920873 194920873 A	K
283	848 A	+1:194920874 194920874 A	
283	849 A	+1:194920875 194920875 A	
284 H	850 C	+1:194920876 194920876 C	H
284	851 A	+1:194920877 194920877 A	
284	852 C	+1:194920878 194920878 C	
285 R	853 A	+1:194920879 194920879 A	R
285	854 G	+1:194920880 194920880 G	
285	855 A	+1:194920881 194920881 A	
286 T	856 A	+1:194920882 194920882 A	T
286	857 C	+1:194920883 194920883 C	
286	858 T	+1:194920884 194920884 T	
287 G	859 G	+1:194920885 194920885 G	G
287	860 G	+1:194920886 194920886 G	
287	861 A	+1:194920887 194920887 A	
288 D	862 G	+1:194920888 194920888 G	D
288	863 A	+1:194920889 194920889 A	
288	864 T	+1:194920890 194920890 T	
289 E	865 G	+1:194920891 194920891 G	E
289	866 A	+1:194920892 194920892 A	
289	867 A	+1:194920893 194920893 A	
290 I	868 A	+1:194920894 194920894 A	I
290	869 T	+1:194920895 194920895 T	
290	870 C	+1:194920896 194920896 C	
291 T	871 A	+1:194920897 194920897 A	T
291	872 C	+1:194920898 194920898 C	
291	873 G	+1:194920899 194920899 G	
292 Y	874 T	+1:194920900 194920900 T	Y
292	875 A	+1:194920901 194920901 A	
292	876 C	+1:194920902 194920902 C	
293 Q	877 C	+1:194920903 194920903 C	Q
293	878 A	+1:194920904 194920904 A	
293	879 G	+1:194920905 194920905 G	
294 C	880 T	+1:194920906 194920906 T	C
294	881 G	+1:194920907 194920907 G	
294	882 T	+1:194920908 194920908 T	
295 R	883 A	+1:194920909 194920909 A	R
295	884 G	+1:194920910 194920910 G	
295	885 A	+1:194920911 194920911 A	
296 N	886 A	+1:194920912 194920912 A	N
296	887 A	+1:194920913 194920913 A	
296	888 T	+1:194920914 194920914 T	
297 G	889 G	+1:194920915 194920915 G	G
297	890 G	+1:194920916 194920916 G	
297	891 T	+1:194920917 194920917 T	
298 F	892 T	+1:194920918 194920918 T	F
298	893 T	+1:194920919 194920919 T	
298	894 T	+1:194920920 194920920 T	
299 Y	895 T	+1:194920921 194920921 T	Y
299	896 A	+1:194920922 194920922 A	
299	897 T	+1:194920923 194920923 T	
300 P	898 C	+1:194920924 194920924 C	P
300	899 C	+1:194920925 194920925 C	
300	900 T	+1:194920926 194920926 T	
301 A	901 G	+1:194920927 194920927 G	A
301	902 C	+1:194920928 194920928 C	
301	903 A	+1:194920929 194920929 A	
302 T	904 A	+1:194920930 194920930 A	T
302	905 C	+1:194920931 194920931 C	
302	906 C	+1:194920932 194920932 C	
303 R	907 C	+1:194920933 194920933 C	R
303	908 G	+1:194920934 194920934 G	
303	909 G	+1:194920935 194920935 G	
304 G	910 G	+1:194920936 194920936 G	G
304	911 G	+1:194920937 194920937 G	
304	912 A	+1:194920938 194920938 A	
305 N	913 A	+1:194920939 194920939 A	N
305	914 A	+1:194920940 194920940 A	
305	915 T	+1:194920941 194920941 T	
306 T	916 A	+1:194920942 194920942 A	T
306	917 C	+1:194920943 194920943 C	
306	918 A	+1:194920944 194920944 A	
307 A	919 G	+1:194920945 194920945 G	A
307	920 C	+1:194920946 194920946 C	
307	921 A	+1:194920947 194920947 A	
308 K	922 A	+1:194920948 194920948 A	K
308	923 A	+1:194920949 194920949 A	
308	924 A	+1:194920950 194920950 A	
309 C	925 T	+1:194920951 194920951 T	C
309	926 G	+1:194920952 194920952 G	
309	927 C	+1:194920953 194920953 C	
310 T	928 A	+1:194920954 194920954 A	T
310	929 C	+1:194920955 194920955 C	
310	930 A	+1:194920956 194920956 A	
311 S	931 A	+1:194920957 194920957 A	S
311	932 G	+1:194920958 194920958 G	
311	933 T	+1:194920959 194920959 T	
312 T	934 A	+1:194920960 194920960 A	T
312	935 C	+1:194920961 194920961 C	
312	936 T	+1:194920962 194920962 T	
313 G	937 G	+1:194920963 194920963 G	G
313	938 G	+1:194920964 194920964 G	
313	939 C	+1:194920965 194920965 C	
314 W	940 T	+1:194920966 194920966 T	W
314	941 G	+1:194920967 194920967 G	
314	942 G	+1:194920968 194920968 G	
315 I	943 A	+1:194920969 194920969 A	I
315	944 T	+1:194920970 194920970 T	
315	945 A	+1:194920971 194920971 A	
316 P	946 C	+1:194920972 194920972 C	P
316	947 C	+1:194920973 194920973 C	
316	948 T	+1:194920974 194920974 T	
317 A	949 G	+1:194920975 194920975 G	A
317	950 C	+1:194920976 194920976 C	
317	951 T	+1:194920977 194920977 T	
318 P	952 C	+1:194920978 194920978 C	P
318	953 C	+1:194920979 194920979 C	
318	954 G	+1:194920980 194920980 G	
319 R	955 A	+1:194920981 194920981 A	R
319	956 G	+1:194920982 194920982 G	
319	957 A	+1:194920983 194920983 A	
320 C	958 T	+1:194920984 194920984 T	C
320	959 G	+1:194920985 194920985 G	
320	960 T	+1:194920986 194920986 T	
321 T	961 A	+1:194920987 194920987 A	T
321	962 C	+1:194920988 194920988 C	
321	963 C	+1:194920989 194920989 C	
322 L	964 T	+1:194920990 194920990 T	L
322	965 T	+1:194925173 194925173 T	
322	966 G	+1:194925174 194925174 G	
323 K	967 A	+1:194925175 194925175 A	K
323	968 A	+1:194925176 194925176 A	
323	969 A	+1:194925177 194925177 A	
324 P	970 C	+1:194925178 194925178 C	P
324	971 C	+1:194925179 194925179 C	
324	972 T	+1:194925180 194925180 T	
325 C	973 T	+1:194925181 194925181 T	C
325	974 G	+1:194925182 194925182 G	
325	975 T	+1:194925183 194925183 T	
326 D	976 G	+1:194925184 194925184 G	D
326	977 A	+1:194925185 194925185 A	
326	978 T	+1:194925186 194925186 T	
327 Y	979 T	+1:194925187 194925187 T	Y
327	980 A	+1:194925188 194925188 A	
327	981 T	+1:194925189 194925189 T	
328 P	982 C	+1:194925190 194925190 C	P
328	983 C	+1:194925191 194925191 C	
328	984 A	+1:194925192 194925192 A	
329 D	985 G	+1:194925193 194925193 G	D
329	986 A	+1:194925194 194925194 A	
329	987 C	+1:194925195 194925195 C	
330 I	988 A	+1:194925196 194925196 A	I
330	989 T	+1:194925197 194925197 T	
330	990 T	+1:194925198 194925198 T	
331 K	991 A	+1:194925199 194925199 A	K
331	992 A	+1:194925200 194925200 A	
331	993 A	+1:194925201 194925201 A	
332 H	994 C	+1:194925202 194925202 C	H
332	995 A	+1:194925203 194925203 A	
332	996 T	+1:194925204 194925204 T	
333 G	997 G	+1:194925205 194925205 G	G
333	998 G	+1:194925206 194925206 G	
333	999 A	+1:194925207 194925207 A	
334 G	1000 G	+1:194925208 194925208 G	G
334	1001 G	+1:194925209 194925209 G	
334	1002 T	+1:194925210 194925210 T	
335 L	1003 C	+1:194925211 194925211 C	L
335	1004 T	+1:194925212 194925212 T	
335	1005 A	+1:194925213 194925213 A	
336 Y	1006 T	+1:194925214 194925214 T	Y
336	1007 A	+1:194925215 194925215 A	
336	1008 T	+1:194925216 194925216 T	
337 H	1009 C	+1:194925217 194925217 C	H
337	1010 A	+1:194925218 194925218 A	
337	1011 T	+1:194925219 194925219 T	
338 E	1012 G	+1:194925220 194925220 G	E
338	1013 A	+1:194925221 194925221 A	
338	1014 G	+1:194925222 194925222 G	
339 N	1015 A	+1:194925223 194925223 A	N
339	1016 A	+1:194925224 194925224 A	
339	1017 T	+1:194925225 194925225 T	
340 M	1018 A	+1:194925226 194925226 A	M
340	1019 T	+1:194925227 194925227 T	
340	1020 G	+1:194925228 194925228 G	
341 R	1021 C	+1:194925229 194925229 C	R
341	1022 G	+1:194925230 194925230 G	
341	1023 T	+1:194925231 194925231 T	
342 R	1024 A	+1:194925232 194925232 A	R
342	1025 G	+1:194925233 194925233 G	
342	1026 A	+1:194925234 194925234 A	
343 P	1027 C	+1:194925235 194925235 C	P
343	1028 C	+1:194925236 194925236 C	
343	1029 A	+1:194925237 194925237 A	
344 Y	1030 T	+1:194925238 194925238 T	Y
344	1031 A	+1:194925239 194925239 A	
344	1032 C	+1:194925240 194925240 C	
345 F	1033 T	+1:194925241 194925241 T	F
345	1034 T	+1:194925242 194925242 T	
345	1035 T	+1:194925243 194925243 T	
346 P	1036 C	+1:194925244 194925244 C	P
346	1037 C	+1:194925245 194925245 C	
346	1038 A	+1:194925246 194925246 A	
347 V	1039 G	+1:194925247 194925247 G	V
347	1040 T	+1:194925248 194925248 T	
347	1041 A	+1:194925249 194925249 A	
348 A	1042 G	+1:194925250 194925250 G	A
348	1043 C	+1:194925251 194925251 C	
348	1044 T	+1:194925252 194925252 T	
349 V	1045 G	+1:194925253 194925253 G	V
349	1046 T	+1:194925254 194925254 T	
349	1047 A	+1:194925255 194925255 A	
350 G	1048 G	+1:194925256 194925256 G	G
350	1049 G	+1:194925257 194925257 G	
350	1050 A	+1:194925258 194925258 A	
351 K	1051 A	+1:194925259 194925259 A	K
351	1052 A	+1:194925260 194925260 A	
351	1053 A	+1:194925261 194925261 A	
352 Y	1054 T	+1:194925262 194925262 T	Y
352	1055 A	+1:194925263 194925263 A	
352	1056 T	+1:194925264 194925264 T	
353 Y	1057 T	+1:194925265 194925265 T	Y
353	1058 A	+1:194925266 194925266 A	
353	1059 C	+1:194925267 194925267 C	
354 S	1060 T	+1:194925268 194925268 T	S
354	1061 C	+1:194925269 194925269 C	
354	1062 C	+1:194925270 194925270 C	
355 Y	1063 T	+1:194925271 194925271 T	Y
355	1064 A	+1:194925272 194925272 A	
355	1065 T	+1:194925273 194925273 T	
356 Y	1066 T	+1:194925274 194925274 T	Y
356	1067 A	+1:194925275 194925275 A	
356	1068 C	+1:194925276 194925276 C	
357 C	1069 T	+1:194925277 194925277 T	C
357	1070 G	+1:194925278 194925278 G	
357	1071 T	+1:194925279 194925279 T	
358 D	1072 G	+1:194925280 194925280 G	D
358	1073 A	+1:194925281 194925281 A	
358	1074 T	+1:194925282 194925282 T	
359 E	1075 G	+1:194925283 194925283 G	E
359	1076 A	+1:194925284 194925284 A	
359	1077 A	+1:194925285 194925285 A	
360 H	1078 C	+1:194925286 194925286 C	H
360	1079 A	+1:194925287 194925287 A	
360	1080 T	+1:194925288 194925288 T	
361 F	1081 T	+1:194925289 194925289 T	F
361	1082 T	+1:194925290 194925290 T	
361	1083 T	+1:194925291 194925291 T	
362 E	1084 G	+1:194925292 194925292 G	E
362	1085 A	+1:194925293 194925293 A	
362	1086 G	+1:194925294 194925294 G	
363 T	1087 A	+1:194925295 194925295 A	T
363	1088 C	+1:194925296 194925296 C	
363	1089 T	+1:194925297 194925297 T	
364 P	1090 C	+1:194925298 194925298 C	P
364	1091 C	+1:194925299 194925299 C	
364	1092 G	+1:194925300 194925300 G	
365 S	1093 T	+1:194925301 194925301 T	S
365	1094 C	+1:194925302 194925302 C	
365	1095 A	+1:194925303 194925303 A	
366 G	1096 G	+1:194925304 194925304 G	G
366	1097 G	+1:194925305 194925305 G	
366	1098 A	+1:194925306 194925306 A	
367 S	1099 A	+1:194925307 194925307 A	S
367	1100 G	+1:194925308 194925308 G	
367	1101 T	+1:194925309 194925309 T	
368 Y	1102 T	+1:194925310 194925310 T	Y
368	1103 A	+1:194925311 194925311 A	
368	1104 C	+1:194925312 194925312 C	
369 W	1105 T	+1:194925313 194925313 T	W
369	1106 G	+1:194925314 194925314 G	
369	1107 G	+1:194925315 194925315 G	
370 D	1108 G	+1:194925316 194925316 G	D
370	1109 A	+1:194925317 194925317 A	
370	1110 T	+1:194925318 194925318 T	
371 H	1111 C	+1:194925319 194925319 C	H
371	1112 A	+1:194925320 194925320 A	
371	1113 C	+1:194925321 194925321 C	
372 I	1114 A	+1:194925322 194925322 A	I
372	1115 T	+1:194925323 194925323 T	
372	1116 T	+1:194925324 194925324 T	
373 H	1117 C	+1:194925325 194925325 C	H
373	1118 A	+1:194925326 194925326 A	
373	1119 T	+1:194925327 194925327 T	
374 C	1120 T	+1:194925328 194925328 T	C
374	1121 G	+1:194925329 194925329 G	
374	1122 C	+1:194925330 194925330 C	
375 T	1123 A	+1:194925331 194925331 A	T
375	1124 C	+1:194925332 194925332 C	
375	1125 A	+1:194925333 194925333 A	
376 Q	1126 C	+1:194925334 194925334 C	Q
376	1127 A	+1:194925335 194925335 A	
376	1128 A	+1:194925336 194925336 A	
377 D	1129 G	+1:194925337 194925337 G	D
377	1130 A	+1:194925338 194925338 A	
377	1131 T	+1:194925339 194925339 T	
378 G	1132 G	+1:194925340 194925340 G	G
378	1133 G	+1:194925341 194925341 G	
378	1134 A	+1:194925342 194925342 A	
379 W	1135 T	+1:194925343 194925343 T	W
379	1136 G	+1:194925344 194925344 G	
379	1137 G	+1:194925345 194925345 G	
380 S	1138 T	+1:194925346 194925346 T	S
380	1139 C	+1:194925347 194925347 C	
380	1140 G	+1:194925348 194925348 G	
381 P	1141 C	+1:194925349 194925349 C	P
381	1142 C	+1:194925350 194925350 C	
381	1143 A	+1:194925351 194925351 A	
382 A	1144 G	+1:194925352 194925352 G	A
382	1145 C	+1:194925353 194925353 C	
382	1146 A	+1:194925354 194925354 A	
383 V	1147 G	+1:194925355 194925355 G	V
383	1148 T	+1:194925356 194925356 T	
383	1149 A	+1:194925357 194925357 A	
384 P	1150 C	+1:194925358 194925358 C	P
384	1151 C	+1:194925359 194925359 C	
384	1152 A	+1:194925360 194925360 A	
385 C	1153 T	+1:194925361 194925361 T	C
385	1154 G	+1:194925362 194925362 G	
385	1155 C	+1:194925363 194925363 C	
386 L	1156 C	+1:194925364 194925364 C	L
386	1157 T	+1:194925365 194925365 T	
386	1158 C	+1:194925366 194925366 C	
387 R	1159 A	+1:194925367 194925367 A	R
387	1160 G	+1:194925816 194925816 G	
387	1161 A	+1:194925817 194925817 A	
388 K	1162 A	+1:194925818 194925818 A	K
388	1163 A	+1:194925819 194925819 A	
388	1164 A	+1:194925820 194925820 A	
389 C	1165 T	+1:194925821 194925821 T	C
389	1166 G	+1:194925822 194925822 G	
389	1167 T	+1:194925823 194925823 T	
390 Y	1168 T	+1:194925824 194925824 T	Y
390	1169 A	+1:194925825 194925825 A	
390	1170 T	+1:194925826 194925826 T	
391 F	1171 T	+1:194925827 194925827 T	F
391	1172 T	+1:194925828 194925828 T	
391	1173 T	+1:194925829 194925829 T	
392 P	1174 C	+1:194925830 194925830 C	P
392	1175 C	+1:194925831 194925831 C	
392	1176 T	+1:194925832 194925832 T	
393 Y	1177 T	+1:194925833 194925833 T	Y
393	1178 A	+1:194925834 194925834 A	
393	1179 T	+1:194925835 194925835 T	
394 L	1180 T	+1:194925836 194925836 T	L
394	1181 T	+1:194925837 194925837 T	
394	1182 G	+1:194925838 194925838 G	
395 E	1183 G	+1:194925839 194925839 G	E
395	1184 A	+1:194925840 194925840 A	
395	1185 A	+1:194925841 194925841 A	
396 N	1186 A	+1:194925842 194925842 A	N
396	1187 A	+1:194925843 194925843 A	
396	1188 T	+1:194925844 194925844 T	
397 G	1189 G	+1:194925845 194925845 G	G
397	1190 G	+1:194925846 194925846 G	
397	1191 A	+1:194925847 194925847 A	
398 Y	1192 T	+1:194925848 194925848 T	Y
398	1193 A	+1:194925849 194925849 A	
398	1194 T	+1:194925850 194925850 T	
399 N	1195 A	+1:194925851 194925851 A	N
399	1196 A	+1:194925852 194925852 A	
399	1197 T	+1:194925853 194925853 T	
400 Q	1198 C	+1:194925854 194925854 C	Q
400	1199 A	+1:194925855 194925855 A	
400	1200 A	+1:194925856 194925856 A	
401 N	1201 A	+1:194925857 194925857 A	N
401	1202 A	+1:194925858 194925858 A	
401	1203 T	+1:194925859 194925859 T	
402 H	1204 C	+1:194925860 194925860 C	H
402	1205 A	+1:194925861 194925861 A	
402	1206 T	+1:194925862 194925862 T	
403 G	1207 G	+1:194925863 194925863 G	G
403	1208 G	+1:194925864 194925864 G	
403	1209 A	+1:194925865 194925865 A	
404 R	1210 A	+1:194925866 194925866 A	R
404	1211 G	+1:194925867 194925867 G	
404	1212 A	+1:194925868 194925868 A	
405 K	1213 A	+1:194925869 194925869 A	K
405	1214 A	+1:194925870 194925870 A	
405	1215 G	+1:194925871 194925871 G	
406 F	1216 T	+1:194925872 194925872 T	F
406	1217 T	+1:194925873 194925873 T	
406	1218 T	+1:194925874 194925874 T	
407 V	1219 G	+1:194925875 194925875 G	V
407	1220 T	+1:194925876 194925876 T	
407	1221 A	+1:194925877 194925877 A	
408 Q	1222 C	+1:194925878 194925878 C	Q
408	1223 A	+1:194925879 194925879 A	
408	1224 G	+1:194925880 194925880 G	
409 G	1225 G	+1:194925881 194925881 G	G
409	1226 G	+1:194925882 194925882 G	
409	1227 T	+1:194925883 194925883 T	
410 K	1228 A	+1:194925884 194925884 A	K
410	1229 A	+1:194925885 194925885 A	
410	1230 A	+1:194925886 194925886 A	
411 S	1231 T	+1:194925887 194925887 T	S
411	1232 C	+1:194925888 194925888 C	
411	1233 T	+1:194925889 194925889 T	
412 I	1234 A	+1:194925890 194925890 A	I
412	1235 T	+1:194925891 194925891 T	
412	1236 A	+1:194925892 194925892 A	
413 D	1237 G	+1:194925893 194925893 G	D
413	1238 A	+1:194925894 194925894 A	
413	1239 C	+1:194925895 194925895 C	
414 V	1240 G	+1:194925896 194925896 G	V
414	1241 T	+1:194925897 194925897 T	
414	1242 T	+1:194925898 194925898 T	
415 A	1243 G	+1:194925899 194925899 G	A
415	1244 C	+1:194925900 194925900 C	
415	1245 C	+1:194925901 194925901 C	
416 C	1246 T	+1:194925902 194925902 T	C
416	1247 G	+1:194925903 194925903 G	
416	1248 C	+1:194925904 194925904 C	
417 H	1249 C	+1:194925905 194925905 C	H
417	1250 A	+1:194925906 194925906 A	
417	1251 T	+1:194925907 194925907 T	
418 P	1252 C	+1:194925908 194925908 C	P
418	1253 C	+1:194925909 194925909 C	
418	1254 T	+1:194925910 194925910 T	
419 G	1255 G	+1:194925911 194925911 G	G
419	1256 G	+1:194925912 194925912 G	
419	1257 C	+1:194925913 194925913 C	
420 Y	1258 T	+1:194925914 194925914 T	Y
420	1259 A	+1:194925915 194925915 A	
420	1260 C	+1:194925916 194925916 C	
421 A	1261 G	+1:194925917 194925917 G	A
421	1262 C	+1:194925918 194925918 C	
421	1263 T	+1:194925919 194925919 T	
422 L	1264 C	+1:194925920 194925920 C	L
422	1265 T	+1:194925921 194925921 T	
422	1266 T	+1:194925922 194925922 T	
423 P	1267 C	+1:194925923 194925923 C	P
423	1268 C	+1:194925924 194925924 C	
423	1269 A	+1:194925925 194925925 A	
424 K	1270 A	+1:194925926 194925926 A	K
424	1271 A	+1:194925927 194925927 A	
424	1272 A	+1:194925928 194925928 A	
425 A	1273 G	+1:194925929 194925929 G	A
425	1274 C	+1:194925930 194925930 C	
425	1275 G	+1:194925931 194925931 G	
426 Q	1276 C	+1:194925932 194925932 C	Q
426	1277 A	+1:194925933 194925933 A	
426	1278 G	+1:194925934 194925934 G	
427 T	1279 A	+1:194925935 194925935 A	T
427	1280 C	+1:194925936 194925936 C	
427	1281 C	+1:194925937 194925937 C	
428 T	1282 A	+1:194925938 194925938 A	T
428	1283 C	+1:194925939 194925939 C	
428	1284 A	+1:194925940 194925940 A	
429 V	1285 G	+1:194925941 194925941 G	V
429	1286 T	+1:194925942 194925942 T	
429	1287 T	+1:194925943 194925943 T	
430 T	1288 A	+1:194925944 194925944 A	T
430	1289 C	+1:194925945 194925945 C	
430	1290 A	+1:194925946 194925946 A	
431 C	1291 T	+1:194925947 194925947 T	C
431	1292 G	+1:194925948 194925948 G	
431	1293 T	+1:194925949 194925949 T	
432 M	1294 A	+1:194925950 194925950 A	M
432	1295 T	+1:194925951 194925951 T	
432	1296 G	+1:194925952 194925952 G	
433 E	1297 G	+1:194925953 194925953 G	E
433	1298 A	+1:194925954 194925954 A	
433	1299 G	+1:194925955 194925955 G	
434 N	1300 A	+1:194925956 194925956 A	N
434	1301 A	+1:194925957 194925957 A	
434	1302 T	+1:194925958 194925958 T	
435 G	1303 G	+1:194925959 194925959 G	G
435	1304 G	+1:194925960 194925960 G	
435	1305 C	+1:194925961 194925961 C	
436 W	1306 T	+1:194925962 194925962 T	W
436	1307 G	+1:194925963 194925963 G	
436	1308 G	+1:194925964 194925964 G	
437 S	1309 T	+1:194925965 194925965 T	S
437	1310 C	+1:194925966 194925966 C	
437	1311 T	+1:194925967 194925967 T	
438 P	1312 C	+1:194925968 194925968 C	P
438	1313 C	+1:194925969 194925969 C	
438	1314 T	+1:194925970 194925970 T	
439 T	1315 A	+1:194925971 194925971 A	T
439	1316 C	+1:194925972 194925972 C	
439	1317 T	+1:194925973 194925973 T	
440 P	1318 C	+1:194925974 194925974 C	P
440	1319 C	+1:194925975 194925975 C	
440	1320 C	+1:194925976 194925976 C	
441 R	1321 A	+1:194925977 194925977 A	R
441	1322 G	+1:194925978 194925978 G	
441	1323 A	+1:194925979 194925979 A	
442 C	1324 T	+1:194925980 194925980 T	C
442	1325 G	+1:194925981 194925981 G	
442	1326 C	+1:194925982 194925982 C	
443 I	1327 A	+1:194925983 194925983 A	I
443	1328 T	+1:194925984 194925984 T	
443	1329 C	+1:194925985 194925985 C	
444 R	1330 C	+1:194925986 194925986 C	R
444	1331 G	+1:194925987 194925987 G	
444	1332 T	+1:194925988 194925988 T	
445 V	1333 G	+1:194925989 194925989 G	V
445	1334 T	+1:194925990 194925990 T	
445	1335 C	+1:194925991 194925991 C	
>ENSP00000352658 
1 M	1 A	+1:194887871 194887871 A	M
1	2 T	+1:194887872 194887872 T	
1	3 G	+1:194887873 194887873 G	
2 R	4 A	+1:194887874 194887874 A	R
2	5 G	+1:194887875 194887875 G	
2	6 A	+1:194887876 194887876 A	
3 L	7 C	+1:194887877 194887877 C	L
3	8 T	+1:194887878 194887878 T	
3	9 T	+1:194887879 194887879 T	
4 L	10 C	+1:194887880 194887880 C	L
4	11 T	+1:194887881 194887881 T	
4	12 A	+1:194887882 194887882 A	
5 A	13 G	+1:194887883 194887883 G	A
5	14 C	+1:194887884 194887884 C	
5	15 A	+1:194887885 194887885 A	
6 K	16 A	+1:194887886 194887886 A	K
6	17 A	+1:194887887 194887887 A	
6	18 G	+1:194887888 194887888 G	
7 I	19 A	+1:194887889 194887889 A	I
7	20 T	+1:194887890 194887890 T	
7	21 T	+1:194887891 194887891 T	
8 I	22 A	+1:194887892 194887892 A	I
8	23 T	+1:194887893 194887893 T	
8	24 T	+1:194887894 194887894 T	
9 C	25 T	+1:194887895 194887895 T	C
9	26 G	+1:194887896 194887896 G	
9	27 C	+1:194887897 194887897 C	
10 L	28 C	+1:194887898 194887898 C	L
10	29 T	+1:194887899 194887899 T	
10	30 T	+1:194887900 194887900 T	
11 M	31 A	+1:194887901 194887901 A	M
11	32 T	+1:194887902 194887902 T	
11	33 G	+1:194887903 194887903 G	
12 L	34 T	+1:194887904 194887904 T	L
12	35 T	+1:194887905 194887905 T	
12	36 A	+1:194887906 194887906 A	
13 W	37 T	+1:194887907 194887907 T	W
13	38 G	+1:194887908 194887908 G	
13	39 G	+1:194887909 194887909 G	
14 A	40 G	+1:194887910 194887910 G	A
14	41 C	+1:194887911 194887911 C	
14	42 T	+1:194887912 194887912 T	
15 I	43 A	+1:194887913 194887913 A	I
15	44 T	+1:194887914 194887914 T	
15	45 T	+1:194887915 194887915 T	
16 C	46 T	+1:194887916 194887916 T	C
16	47 G	+1:194887917 194887917 G	
16	48 T	+1:194887918 194887918 T	
17 V	49 G	+1:194887919 194887919 G	V
17	50 T	+1:194887920 194887920 T	
17	51 A	+1:194887921 194887921 A	
18 A	52 G	+1:194887922 194887922 G	A
18	53 C	+1:194887923 194887923 C	
18	54 A	+1:194887924 194887924 A	
19 E	55 G	+1:194887925 194887925 G	E
19	56 A	+1:194887926 194887926 A	
19	57 A	+1:194887927 194887927 A	
20 D	58 G	+1:194887928 194887928 G	D
20	59 A	+1:194908731 194908731 A	
20	60 T	+1:194908732 194908732 T	
21 C	61 T	+1:194908733 194908733 T	C
21	62 G	+1:194908734 194908734 G	
21	63 C	+1:194908735 194908735 C	
22 N	64 A	+1:194908736 194908736 A	N
22	65 A	+1:194908737 194908737 A	
22	66 T	+1:194908738 194908738 T	
23 E	67 G	+1:194908739 194908739 G	E
23	68 A	+1:194908740 194908740 A	
23	69 A	+1:194908741 194908741 A	
24 L	70 C	+1:194908742 194908742 C	L
24	71 T	+1:194908743 194908743 T	
24	72 T	+1:194908744 194908744 T	
25 P	73 C	+1:194908745 194908745 C	P
25	74 C	+1:194908746 194908746 C	
25	75 T	+1:194908747 194908747 T	
26 P	76 C	+1:194908748 194908748 C	P
26	77 C	+1:194908749 194908749 C	
26	78 A	+1:194908750 194908750 A	
27 R	79 A	+1:194908751 194908751 A	R
27	80 G	+1:194908752 194908752 G	
27	81 A	+1:194908753 194908753 A	
28 R	82 A	+1:194908754 194908754 A	R
28	83 G	+1:194908755 194908755 G	
28	84 A	+1:194908756 194908756 A	
29 N	85 A	+1:194908757 194908757 A	N
29	86 A	+1:194908758 194908758 A	
29	87 T	+1:194908759 194908759 T	
30 T	88 A	+1:194908760 194908760 A	T
30	89 C	+1:194908761 194908761 C	
30	90 A	+1:194908762 194908762 A	
31 E	91 G	+1:194908763 194908763 G	E
31	92 A	+1:194908764 194908764 A	
31	93 A	+1:194908765 194908765 A	
32 I	94 A	+1:194908766 194908766 A	I
32	95 T	+1:194908767 194908767 T	
32	96 T	+1:194908768 194908768 T	
33 L	97 C	+1:194908769 194908769 C	L
33	98 T	+1:194908770 194908770 T	
33	99 G	+1:194908771 194908771 G	
34 T	100 A	+1:194908772 194908772 A	T
34	101 C	+1:194908773 194908773 C	
34	102 A	+1:194908774 194908774 A	
35 G	103 G	+1:194908775 194908775 G	G
35	104 G	+1:194908776 194908776 G	
35	105 T	+1:194908777 194908777 T	
36 S	106 T	+1:194908778 194908778 T	S
36	107 C	+1:194908779 194908779 C	
36	108 C	+1:194908780 194908780 C	
37 W	109 T	+1:194908781 194908781 T	W
37	110 G	+1:194908782 194908782 G	
37	111 G	+1:194908783 194908783 G	
38 S	112 T	+1:194908784 194908784 T	S
38	113 C	+1:194908785 194908785 C	
38	114 T	+1:194908786 194908786 T	
39 D	115 G	+1:194908787 194908787 G	D
39	116 A	+1:194908788 194908788 A	
39	117 C	+1:194908789 194908789 C	
40 Q	118 C	+1:194908790 194908790 C	Q
40	119 A	+1:194908791 194908791 A	
40	120 A	+1:194908792 194908792 A	
41 T	121 A	+1:194908793 194908793 A	T
41	122 C	+1:194908794 194908794 C	
41	123 A	+1:194908795 194908795 A	
42 Y	124 T	+1:194908796 194908796 T	Y
42	125 A	+1:194908797 194908797 A	
42	126 T	+1:194908798 194908798 T	
43 P	127 C	+1:194908799 194908799 C	P
43	128 C	+1:194908800 194908800 C	
43	129 A	+1:194908801 194908801 A	
44 E	130 G	+1:194908802 194908802 G	E
44	131 A	+1:194908803 194908803 A	
44	132 A	+1:194908804 194908804 A	
45 G	133 G	+1:194908805 194908805 G	G
45	134 G	+1:194908806 194908806 G	
45	135 C	+1:194908807 194908807 C	
46 T	136 A	+1:194908808 194908808 A	T
46	137 C	+1:194908809 194908809 C	
46	138 C	+1:194908810 194908810 C	
47 Q	139 C	+1:194908811 194908811 C	Q
47	140 A	+1:194908812 194908812 A	
47	141 G	+1:194908813 194908813 G	
48 A	142 G	+1:194908814 194908814 G	A
48	143 C	+1:194908815 194908815 C	
48	144 T	+1:194908816 194908816 T	
49 I	145 A	+1:194908817 194908817 A	I
49	146 T	+1:194908818 194908818 T	
49	147 C	+1:194908819 194908819 C	
50 Y	148 T	+1:194908820 194908820 T	Y
50	149 A	+1:194908821 194908821 A	
50	150 T	+1:194908822 194908822 T	
51 K	151 A	+1:194908823 194908823 A	K
51	152 A	+1:194908824 194908824 A	
51	153 A	+1:194908825 194908825 A	
52 C	154 T	+1:194908826 194908826 T	C
52	155 G	+1:194908827 194908827 G	
52	156 C	+1:194908828 194908828 C	
53 R	157 C	+1:194908829 194908829 C	R
53	158 G	+1:194908830 194908830 G	
53	159 C	+1:194908831 194908831 C	
54 P	160 C	+1:194908832 194908832 C	P
54	161 C	+1:194908833 194908833 C	
54	162 T	+1:194908834 194908834 T	
55 G	163 G	+1:194908835 194908835 G	G
55	164 G	+1:194908836 194908836 G	
55	165 A	+1:194908837 194908837 A	
56 Y	166 T	+1:194908838 194908838 T	Y
56	167 A	+1:194908839 194908839 A	
56	168 T	+1:194908840 194908840 T	
57 R	169 A	+1:194908841 194908841 A	R
57	170 G	+1:194908842 194908842 G	
57	171 A	+1:194908843 194908843 A	
58 S	172 T	+1:194908844 194908844 T	S
58	173 C	+1:194908845 194908845 C	
58	174 T	+1:194908846 194908846 T	
59 L	175 C	+1:194908847 194908847 C	L
59	176 T	+1:194908848 194908848 T	
59	177 T	+1:194908849 194908849 T	
60 G	178 G	+1:194908850 194908850 G	G
60	179 G	+1:194908851 194908851 G	
60	180 A	+1:194908852 194908852 A	
61 N	181 A	+1:194908853 194908853 A	N
61	182 A	+1:194908854 194908854 A	
61	183 T	+1:194908855 194908855 T	
62 V	184 G	+1:194908856 194908856 G	V
62	185 T	+1:194908857 194908857 T	
62	186 A	+1:194908858 194908858 A	
63 I	187 A	+1:194908859 194908859 A	I
63	188 T	+1:194908860 194908860 T	
63	189 A	+1:194908861 194908861 A	
64 M	190 A	+1:194908862 194908862 A	M
64	191 T	+1:194908863 194908863 T	
64	192 G	+1:194908864 194908864 G	
65 V	193 G	+1:194908865 194908865 G	V
65	194 T	+1:194908866 194908866 T	
65	195 A	+1:194908867 194908867 A	
66 C	196 T	+1:194908868 194908868 T	C
66	197 G	+1:194908869 194908869 G	
66	198 C	+1:194908870 194908870 C	
67 R	199 A	+1:194908871 194908871 A	R
67	200 G	+1:194908872 194908872 G	
67	201 G	+1:194908873 194908873 G	
68 K	202 A	+1:194908874 194908874 A	K
68	203 A	+1:194908875 194908875 A	
68	204 G	+1:194908876 194908876 G	
69 G	205 G	+1:194908877 194908877 G	G
69	206 G	+1:194908878 194908878 G	
69	207 A	+1:194908879 194908879 A	
70 E	208 G	+1:194908880 194908880 G	E
70	209 A	+1:194908881 194908881 A	
70	210 A	+1:194908882 194908882 A	
71 W	211 T	+1:194908883 194908883 T	W
71	212 G	+1:194908884 194908884 G	
71	213 G	+1:194908885 194908885 G	
72 V	214 G	+1:194908886 194908886 G	V
72	215 T	+1:194908887 194908887 T	
72	216 T	+1:194908888 194908888 T	
73 A	217 G	+1:194908889 194908889 G	A
73	218 C	+1:194908890 194908890 C	
73	219 T	+1:194908891 194908891 T	
74 L	220 C	+1:194908892 194908892 C	L
74	221 T	+1:194908893 194908893 T	
74	222 T	+1:194908894 194908894 T	
75 N	223 A	+1:194908895 194908895 A	N
75	224 A	+1:194908896 194908896 A	
75	225 T	+1:194908897 194908897 T	
76 P	226 C	+1:194908898 194908898 C	P
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77 L	229 T	+1:194908901 194908901 T	L
77	230 T	+1:194908902 194908902 T	
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78 R	232 A	+1:194908904 194908904 A	R
78	233 G	+1:194908905 194908905 G	
78	234 G	+1:194908906 194908906 G	
79 K	235 A	+1:194908907 194908907 A	K
79	236 A	+1:194908908 194908908 A	
79	237 A	+1:194908909 194908909 A	
80 C	238 T	+1:194908910 194908910 T	C
80	239 G	+1:194908911 194908911 G	
80	240 T	+1:194908912 194908912 T	
81 Q	241 C	+1:194908913 194908913 C	Q
81	242 A	+1:194908914 194908914 A	
81	243 G	+1:194908915 194908915 G	
82 K	244 A	+1:194908916 194908916 A	K
82	245 A	+1:194909610 194909610 A	
82	246 A	+1:194909611 194909611 A	
83 R	247 A	+1:194909612 194909612 A	R
83	248 G	+1:194909613 194909613 G	
83	249 G	+1:194909614 194909614 G	
84 P	250 C	+1:194909615 194909615 C	P
84	251 C	+1:194909616 194909616 C	
84	252 C	+1:194909617 194909617 C	
85 C	253 T	+1:194909618 194909618 T	C
85	254 G	+1:194909619 194909619 G	
85	255 T	+1:194909620 194909620 T	
86 G	256 G	+1:194909621 194909621 G	G
86	257 G	+1:194909622 194909622 G	
86	258 A	+1:194909623 194909623 A	
87 H	259 C	+1:194909624 194909624 C	H
87	260 A	+1:194909625 194909625 A	
87	261 T	+1:194909626 194909626 T	
88 P	262 C	+1:194909627 194909627 C	P
88	263 C	+1:194909628 194909628 C	
88	264 T	+1:194909629 194909629 T	
89 G	265 G	+1:194909630 194909630 G	G
89	266 G	+1:194909631 194909631 G	
89	267 A	+1:194909632 194909632 A	
90 D	268 G	+1:194909633 194909633 G	D
90	269 A	+1:194909634 194909634 A	
90	270 T	+1:194909635 194909635 T	
91 T	271 A	+1:194909636 194909636 A	T
91	272 C	+1:194909637 194909637 C	
91	273 T	+1:194909638 194909638 T	
92 P	274 C	+1:194909639 194909639 C	P
92	275 C	+1:194909640 194909640 C	
92	276 T	+1:194909641 194909641 T	
93 F	277 T	+1:194909642 194909642 T	F
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93	279 T	+1:194909644 194909644 T	
94 G	280 G	+1:194909645 194909645 G	G
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95	284 C	+1:194909649 194909649 C	
95	285 T	+1:194909650 194909650 T	
96 F	286 T	+1:194909651 194909651 T	F
96	287 T	+1:194909652 194909652 T	
96	288 T	+1:194909653 194909653 T	
97 T	289 A	+1:194909654 194909654 A	T
97	290 C	+1:194909655 194909655 C	
97	291 C	+1:194909656 194909656 C	
98 L	292 C	+1:194909657 194909657 C	L
98	293 T	+1:194909658 194909658 T	
98	294 T	+1:194909659 194909659 T	
99 T	295 A	+1:194909660 194909660 A	T
99	296 C	+1:194909661 194909661 C	
99	297 A	+1:194909662 194909662 A	
100 G	298 G	+1:194909663 194909663 G	G
100	299 G	+1:194909664 194909664 G	
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101 G	301 G	+1:194909666 194909666 G	G
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102 N	304 A	+1:194909669 194909669 A	N
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102	306 T	+1:194909671 194909671 T	
103 V	307 G	+1:194909672 194909672 G	V
103	308 T	+1:194909673 194909673 T	
103	309 G	+1:194909674 194909674 G	
104 F	310 T	+1:194909675 194909675 T	F
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104	312 T	+1:194909677 194909677 T	
105 E	313 G	+1:194909678 194909678 G	E
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105	315 A	+1:194909680 194909680 A	
106 Y	316 T	+1:194909681 194909681 T	Y
106	317 A	+1:194909682 194909682 A	
106	318 T	+1:194909683 194909683 T	
107 G	319 G	+1:194909684 194909684 G	G
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107	321 T	+1:194909686 194909686 T	
108 V	322 G	+1:194909687 194909687 G	V
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108	324 A	+1:194909689 194909689 A	
109 K	325 A	+1:194909690 194909690 A	K
109	326 A	+1:194909691 194909691 A	
109	327 A	+1:194909692 194909692 A	
110 A	328 G	+1:194909693 194909693 G	A
110	329 C	+1:194909694 194909694 C	
110	330 T	+1:194909695 194909695 T	
111 V	331 G	+1:194909696 194909696 G	V
111	332 T	+1:194909697 194909697 T	
111	333 G	+1:194909698 194909698 G	
112 Y	334 T	+1:194909699 194909699 T	Y
112	335 A	+1:194909700 194909700 A	
112	336 T	+1:194909701 194909701 T	
113 T	337 A	+1:194909702 194909702 A	T
113	338 C	+1:194909703 194909703 C	
113	339 A	+1:194909704 194909704 A	
114 C	340 T	+1:194909705 194909705 T	C
114	341 G	+1:194909706 194909706 G	
114	342 T	+1:194909707 194909707 T	
115 N	343 A	+1:194909708 194909708 A	N
115	344 A	+1:194909709 194909709 A	
115	345 T	+1:194909710 194909710 T	
116 E	346 G	+1:194909711 194909711 G	E
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117	351 G	+1:194911742 194911742 G	
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118	353 A	+1:194911744 194911744 A	
118	354 T	+1:194911745 194911745 T	
119 Q	355 C	+1:194911746 194911746 C	Q
119	356 A	+1:194911747 194911747 A	
119	357 A	+1:194911748 194911748 A	
120 L	358 T	+1:194911749 194911749 T	L
120	359 T	+1:194911750 194911750 T	
120	360 G	+1:194911751 194911751 G	
121 L	361 C	+1:194911752 194911752 C	L
121	362 T	+1:194911753 194911753 T	
121	363 A	+1:194911754 194911754 A	
122 G	364 G	+1:194911755 194911755 G	G
122	365 G	+1:194911756 194911756 G	
122	366 T	+1:194911757 194911757 T	
123 E	367 G	+1:194911758 194911758 G	E
123	368 A	+1:194911759 194911759 A	
123	369 G	+1:194911760 194911760 G	
124 I	370 A	+1:194911761 194911761 A	I
124	371 T	+1:194911762 194911762 T	
124	372 T	+1:194911763 194911763 T	
125 N	373 A	+1:194911764 194911764 A	N
125	374 A	+1:194911765 194911765 A	
125	375 T	+1:194911766 194911766 T	
126 Y	376 T	+1:194911767 194911767 T	Y
126	377 A	+1:194911768 194911768 A	
126	378 C	+1:194911769 194911769 C	
127 R	379 C	+1:194911770 194911770 C	R
127	380 G	+1:194911771 194911771 G	
127	381 T	+1:194911772 194911772 T	
128 E	382 G	+1:194911773 194911773 G	E
128	383 A	+1:194911774 194911774 A	
128	384 A	+1:194911775 194911775 A	
129 C	385 T	+1:194911776 194911776 T	C
129	386 G	+1:194911777 194911777 G	
129	387 T	+1:194911778 194911778 T	
130 D	388 G	+1:194911779 194911779 G	D
130	389 A	+1:194911780 194911780 A	
130	390 C	+1:194911781 194911781 C	
131 T	391 A	+1:194911782 194911782 A	T
131	392 C	+1:194911783 194911783 C	
131	393 A	+1:194911784 194911784 A	
132 D	394 G	+1:194911785 194911785 G	D
132	395 A	+1:194911786 194911786 A	
132	396 T	+1:194911787 194911787 T	
133 G	397 G	+1:194911788 194911788 G	G
133	398 G	+1:194911789 194911789 G	
133	399 A	+1:194911790 194911790 A	
134 W	400 T	+1:194911791 194911791 T	W
134	401 G	+1:194911792 194911792 G	
134	402 G	+1:194911793 194911793 G	
135 T	403 A	+1:194911794 194911794 A	T
135	404 C	+1:194911795 194911795 C	
135	405 C	+1:194911796 194911796 C	
136 N	406 A	+1:194911797 194911797 A	N
136	407 A	+1:194911798 194911798 A	
136	408 T	+1:194911799 194911799 T	
137 D	409 G	+1:194911800 194911800 G	D
137	410 A	+1:194911801 194911801 A	
137	411 T	+1:194911802 194911802 T	
138 I	412 A	+1:194911803 194911803 A	I
138	413 T	+1:194911804 194911804 T	
138	414 T	+1:194911805 194911805 T	
139 P	415 C	+1:194911806 194911806 C	P
139	416 C	+1:194911807 194911807 C	
139	417 T	+1:194911808 194911808 T	
140 I	418 A	+1:194911809 194911809 A	I
140	419 T	+1:194911810 194911810 T	
140	420 A	+1:194911811 194911811 A	
141 C	421 T	+1:194911812 194911812 T	C
141	422 G	+1:194911813 194911813 G	
141	423 T	+1:194911814 194911814 T	
142 E	424 G	+1:194911815 194911815 G	E
142	425 A	+1:194911816 194911816 A	
142	426 A	+1:194911817 194911817 A	
143 E	427 G	+1:194911818 194911818 G	E
143	428 A	+1:194915376 194915376 A	
143	429 A	+1:194915377 194915377 A	
144 I	430 A	+1:194915378 194915378 A	I
144	431 T	+1:194915379 194915379 T	
144	432 T	+1:194915380 194915380 T	
145 S	433 T	+1:194915381 194915381 T	S
145	434 C	+1:194915382 194915382 C	
145	435 A	+1:194915383 194915383 A	
146 C	436 T	+1:194915384 194915384 T	C
146	437 G	+1:194915385 194915385 G	
146	438 C	+1:194915386 194915386 C	
147 K	439 A	+1:194915387 194915387 A	K
147	440 A	+1:194915388 194915388 A	
147	441 A	+1:194915389 194915389 A	
148 S	442 T	+1:194915390 194915390 T	S
148	443 C	+1:194915391 194915391 C	
148	444 C	+1:194915392 194915392 C	
149 P	445 C	+1:194915393 194915393 C	P
149	446 C	+1:194915394 194915394 C	
149	447 A	+1:194915395 194915395 A	
150 D	448 G	+1:194915396 194915396 G	D
150	449 A	+1:194915397 194915397 A	
150	450 T	+1:194915398 194915398 T	
151 V	451 G	+1:194915399 194915399 G	V
151	452 T	+1:194915400 194915400 T	
151	453 T	+1:194915401 194915401 T	
152 I	454 A	+1:194915402 194915402 A	I
152	455 T	+1:194915403 194915403 T	
152	456 A	+1:194915404 194915404 A	
153 N	457 A	+1:194915405 194915405 A	N
153	458 A	+1:194915406 194915406 A	
153	459 T	+1:194915407 194915407 T	
154 G	460 G	+1:194915408 194915408 G	G
154	461 G	+1:194915409 194915409 G	
154	462 A	+1:194915410 194915410 A	
155 S	463 T	+1:194915411 194915411 T	S
155	464 C	+1:194915412 194915412 C	
155	465 T	+1:194915413 194915413 T	
156 P	466 C	+1:194915414 194915414 C	P
156	467 C	+1:194915415 194915415 C	
156	468 T	+1:194915416 194915416 T	
157 I	469 A	+1:194915417 194915417 A	I
157	470 T	+1:194915418 194915418 T	
157	471 A	+1:194915419 194915419 A	
158 S	472 T	+1:194915420 194915420 T	S
158	473 C	+1:194915421 194915421 C	
158	474 T	+1:194915422 194915422 T	
159 Q	475 C	+1:194915423 194915423 C	Q
159	476 A	+1:194915424 194915424 A	
159	477 G	+1:194915425 194915425 G	
160 K	478 A	+1:194915426 194915426 A	K
160	479 A	+1:194915427 194915427 A	
160	480 G	+1:194915428 194915428 G	
161 I	481 A	+1:194915429 194915429 A	I
161	482 T	+1:194915430 194915430 T	
161	483 T	+1:194915431 194915431 T	
162 I	484 A	+1:194915432 194915432 A	I
162	485 T	+1:194915433 194915433 T	
162	486 T	+1:194915434 194915434 T	
163 Y	487 T	+1:194915435 194915435 T	Y
163	488 A	+1:194915436 194915436 A	
163	489 T	+1:194915437 194915437 T	
164 K	490 A	+1:194915438 194915438 A	K
164	491 A	+1:194915439 194915439 A	
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168 R	502 C	+1:194915450 194915450 C	R
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168	504 A	+1:194915452 194915452 A	
169 F	505 T	+1:194915453 194915453 T	F
169	506 T	+1:194915454 194915454 T	
169	507 T	+1:194915455 194915455 T	
170 Q	508 C	+1:194915456 194915456 C	Q
170	509 A	+1:194915457 194915457 A	
170	510 A	+1:194915458 194915458 A	
171 Y	511 T	+1:194915459 194915459 T	Y
171	512 A	+1:194915460 194915460 A	
171	513 T	+1:194915461 194915461 T	
172 K	514 A	+1:194915462 194915462 A	K
172	515 A	+1:194915463 194915463 A	
172	516 A	+1:194915464 194915464 A	
173 C	517 T	+1:194915465 194915465 T	C
173	518 G	+1:194915466 194915466 G	
173	519 T	+1:194915467 194915467 T	
174 N	520 A	+1:194915468 194915468 A	N
174	521 A	+1:194915469 194915469 A	
174	522 C	+1:194915470 194915470 C	
175 M	523 A	+1:194915471 194915471 A	M
175	524 T	+1:194915472 194915472 T	
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176 G	526 G	+1:194915474 194915474 G	G
176	527 G	+1:194915475 194915475 G	
176	528 T	+1:194915476 194915476 T	
177 Y	529 T	+1:194915477 194915477 T	Y
177	530 A	+1:194915478 194915478 A	
177	531 T	+1:194915479 194915479 T	
178 E	532 G	+1:194915480 194915480 G	E
178	533 A	+1:194915481 194915481 A	
178	534 A	+1:194915482 194915482 A	
179 Y	535 T	+1:194915483 194915483 T	Y
179	536 A	+1:194915484 194915484 A	
179	537 C	+1:194915485 194915485 C	
180 S	538 A	+1:194915486 194915486 A	S
180	539 G	+1:194915487 194915487 G	
180	540 T	+1:194915488 194915488 T	
181 E	541 G	+1:194915489 194915489 G	E
181	542 A	+1:194915490 194915490 A	
181	543 A	+1:194915491 194915491 A	
182 R	544 A	+1:194915492 194915492 A	R
182	545 G	+1:194915493 194915493 G	
182	546 A	+1:194915494 194915494 A	
183 G	547 G	+1:194915495 194915495 G	G
183	548 G	+1:194915496 194915496 G	
183	549 A	+1:194915497 194915497 A	
184 D	550 G	+1:194915498 194915498 G	D
184	551 A	+1:194915499 194915499 A	
184	552 T	+1:194915500 194915500 T	
185 A	553 G	+1:194915501 194915501 G	A
185	554 C	+1:194915502 194915502 C	
185	555 T	+1:194915503 194915503 T	
186 V	556 G	+1:194915504 194915504 G	V
186	557 T	+1:194915505 194915505 T	
186	558 A	+1:194915506 194915506 A	
187 C	559 T	+1:194915507 194915507 T	C
187	560 G	+1:194915508 194915508 G	
187	561 C	+1:194915509 194915509 C	
188 T	562 A	+1:194915510 194915510 A	T
188	563 C	+1:194915511 194915511 C	
188	564 T	+1:194915512 194915512 T	
189 E	565 G	+1:194915513 194915513 G	E
189	566 A	+1:194915514 194915514 A	
189	567 A	+1:194915515 194915515 A	
190 S	568 T	+1:194915516 194915516 T	S
190	569 C	+1:194915517 194915517 C	
190	570 T	+1:194915518 194915518 T	
191 G	571 G	+1:194915519 194915519 G	G
191	572 G	+1:194915520 194915520 G	
191	573 A	+1:194915521 194915521 A	
192 W	574 T	+1:194915522 194915522 T	W
192	575 G	+1:194915523 194915523 G	
192	576 G	+1:194915524 194915524 G	
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193	578 G	+1:194915526 194915526 G	
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194 P	580 C	+1:194915528 194915528 C	P
194	581 C	+1:194915529 194915529 C	
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195 L	583 T	+1:194915531 194915531 T	L
195	584 T	+1:194915532 194915532 T	
195	585 G	+1:194915533 194915533 G	
196 P	586 C	+1:194915534 194915534 C	P
196	587 C	+1:194915535 194915535 C	
196	588 T	+1:194915536 194915536 T	
197 S	589 T	+1:194915537 194915537 T	S
197	590 C	+1:194915538 194915538 C	
197	591 A	+1:194915539 194915539 A	
198 C	592 T	+1:194915540 194915540 T	C
198	593 G	+1:194915541 194915541 G	
198	594 T	+1:194915542 194915542 T	
199 E	595 G	+1:194915543 194915543 G	E
199	596 A	+1:194915544 194915544 A	
199	597 A	+1:194915545 194915545 A	
200 E	598 G	+1:194915546 194915546 G	E
200	599 A	+1:194920817 194920817 A	
200	600 A	+1:194920818 194920818 A	
201 K	601 A	+1:194920819 194920819 A	K
201	602 A	+1:194920820 194920820 A	
201	603 A	+1:194920821 194920821 A	
202 S	604 T	+1:194920822 194920822 T	S
202	605 C	+1:194920823 194920823 C	
202	606 A	+1:194920824 194920824 A	
203 C	607 T	+1:194920825 194920825 T	C
203	608 G	+1:194920826 194920826 G	
203	609 T	+1:194920827 194920827 T	
204 D	610 G	+1:194920828 194920828 G	D
204	611 A	+1:194920829 194920829 A	
204	612 T	+1:194920830 194920830 T	
205 N	613 A	+1:194920831 194920831 A	N
205	614 A	+1:194920832 194920832 A	
205	615 T	+1:194920833 194920833 T	
206 P	616 C	+1:194920834 194920834 C	P
206	617 C	+1:194920835 194920835 C	
206	618 T	+1:194920836 194920836 T	
207 Y	619 T	+1:194920837 194920837 T	Y
207	620 A	+1:194920838 194920838 A	
207	621 T	+1:194920839 194920839 T	
208 I	622 A	+1:194920840 194920840 A	I
208	623 T	+1:194920841 194920841 T	
208	624 T	+1:194920842 194920842 T	
209 P	625 C	+1:194920843 194920843 C	P
209	626 C	+1:194920844 194920844 C	
209	627 A	+1:194920845 194920845 A	
210 N	628 A	+1:194920846 194920846 A	N
210	629 A	+1:194920847 194920847 A	
210	630 T	+1:194920848 194920848 T	
211 G	631 G	+1:194920849 194920849 G	G
211	632 G	+1:194920850 194920850 G	
211	633 T	+1:194920851 194920851 T	
212 D	634 G	+1:194920852 194920852 G	D
212	635 A	+1:194920853 194920853 A	
212	636 C	+1:194920854 194920854 C	
213 Y	637 T	+1:194920855 194920855 T	Y
213	638 A	+1:194920856 194920856 A	
213	639 C	+1:194920857 194920857 C	
214 S	640 T	+1:194920858 194920858 T	S
214	641 C	+1:194920859 194920859 C	
214	642 A	+1:194920860 194920860 A	
215 P	643 C	+1:194920861 194920861 C	P
215	644 C	+1:194920862 194920862 C	
215	645 T	+1:194920863 194920863 T	
216 L	646 T	+1:194920864 194920864 T	L
216	647 T	+1:194920865 194920865 T	
216	648 A	+1:194920866 194920866 A	
217 R	649 A	+1:194920867 194920867 A	R
217	650 G	+1:194920868 194920868 G	
217	651 G	+1:194920869 194920869 G	
218 I	652 A	+1:194920870 194920870 A	I
218	653 T	+1:194920871 194920871 T	
218	654 T	+1:194920872 194920872 T	
219 K	655 A	+1:194920873 194920873 A	K
219	656 A	+1:194920874 194920874 A	
219	657 A	+1:194920875 194920875 A	
220 H	658 C	+1:194920876 194920876 C	H
220	659 A	+1:194920877 194920877 A	
220	660 C	+1:194920878 194920878 C	
221 R	661 A	+1:194920879 194920879 A	R
221	662 G	+1:194920880 194920880 G	
221	663 A	+1:194920881 194920881 A	
222 T	664 A	+1:194920882 194920882 A	T
222	665 C	+1:194920883 194920883 C	
222	666 T	+1:194920884 194920884 T	
223 G	667 G	+1:194920885 194920885 G	G
223	668 G	+1:194920886 194920886 G	
223	669 A	+1:194920887 194920887 A	
224 D	670 G	+1:194920888 194920888 G	D
224	671 A	+1:194920889 194920889 A	
224	672 T	+1:194920890 194920890 T	
225 E	673 G	+1:194920891 194920891 G	E
225	674 A	+1:194920892 194920892 A	
225	675 A	+1:194920893 194920893 A	
226 I	676 A	+1:194920894 194920894 A	I
226	677 T	+1:194920895 194920895 T	
226	678 C	+1:194920896 194920896 C	
227 T	679 A	+1:194920897 194920897 A	T
227	680 C	+1:194920898 194920898 C	
227	681 G	+1:194920899 194920899 G	
228 Y	682 T	+1:194920900 194920900 T	Y
228	683 A	+1:194920901 194920901 A	
228	684 C	+1:194920902 194920902 C	
229 Q	685 C	+1:194920903 194920903 C	Q
229	686 A	+1:194920904 194920904 A	
229	687 G	+1:194920905 194920905 G	
230 C	688 T	+1:194920906 194920906 T	C
230	689 G	+1:194920907 194920907 G	
230	690 T	+1:194920908 194920908 T	
231 R	691 A	+1:194920909 194920909 A	R
231	692 G	+1:194920910 194920910 G	
231	693 A	+1:194920911 194920911 A	
232 N	694 A	+1:194920912 194920912 A	N
232	695 A	+1:194920913 194920913 A	
232	696 T	+1:194920914 194920914 T	
233 G	697 G	+1:194920915 194920915 G	G
233	698 G	+1:194920916 194920916 G	
233	699 T	+1:194920917 194920917 T	
234 F	700 T	+1:194920918 194920918 T	F
234	701 T	+1:194920919 194920919 T	
234	702 T	+1:194920920 194920920 T	
235 Y	703 T	+1:194920921 194920921 T	Y
235	704 A	+1:194920922 194920922 A	
235	705 T	+1:194920923 194920923 T	
236 P	706 C	+1:194920924 194920924 C	P
236	707 C	+1:194920925 194920925 C	
236	708 T	+1:194920926 194920926 T	
237 A	709 G	+1:194920927 194920927 G	A
237	710 C	+1:194920928 194920928 C	
237	711 A	+1:194920929 194920929 A	
238 T	712 A	+1:194920930 194920930 A	T
238	713 C	+1:194920931 194920931 C	
238	714 C	+1:194920932 194920932 C	
239 R	715 C	+1:194920933 194920933 C	R
239	716 G	+1:194920934 194920934 G	
239	717 G	+1:194920935 194920935 G	
240 G	718 G	+1:194920936 194920936 G	G
240	719 G	+1:194920937 194920937 G	
240	720 A	+1:194920938 194920938 A	
241 N	721 A	+1:194920939 194920939 A	N
241	722 A	+1:194920940 194920940 A	
241	723 T	+1:194920941 194920941 T	
242 T	724 A	+1:194920942 194920942 A	T
242	725 C	+1:194920943 194920943 C	
242	726 A	+1:194920944 194920944 A	
243 A	727 G	+1:194920945 194920945 G	A
243	728 C	+1:194920946 194920946 C	
243	729 A	+1:194920947 194920947 A	
244 K	730 A	+1:194920948 194920948 A	K
244	731 A	+1:194920949 194920949 A	
244	732 A	+1:194920950 194920950 A	
245 C	733 T	+1:194920951 194920951 T	C
245	734 G	+1:194920952 194920952 G	
245	735 C	+1:194920953 194920953 C	
246 T	736 A	+1:194920954 194920954 A	T
246	737 C	+1:194920955 194920955 C	
246	738 A	+1:194920956 194920956 A	
247 S	739 A	+1:194920957 194920957 A	S
247	740 G	+1:194920958 194920958 G	
247	741 T	+1:194920959 194920959 T	
248 T	742 A	+1:194920960 194920960 A	T
248	743 C	+1:194920961 194920961 C	
248	744 T	+1:194920962 194920962 T	
249 G	745 G	+1:194920963 194920963 G	G
249	746 G	+1:194920964 194920964 G	
249	747 C	+1:194920965 194920965 C	
250 W	748 T	+1:194920966 194920966 T	W
250	749 G	+1:194920967 194920967 G	
250	750 G	+1:194920968 194920968 G	
251 I	751 A	+1:194920969 194920969 A	I
251	752 T	+1:194920970 194920970 T	
251	753 A	+1:194920971 194920971 A	
252 P	754 C	+1:194920972 194920972 C	P
252	755 C	+1:194920973 194920973 C	
252	756 T	+1:194920974 194920974 T	
253 A	757 G	+1:194920975 194920975 G	A
253	758 C	+1:194920976 194920976 C	
253	759 T	+1:194920977 194920977 T	
254 P	760 C	+1:194920978 194920978 C	P
254	761 C	+1:194920979 194920979 C	
254	762 G	+1:194920980 194920980 G	
255 R	763 A	+1:194920981 194920981 A	R
255	764 G	+1:194920982 194920982 G	
255	765 A	+1:194920983 194920983 A	
256 C	766 T	+1:194920984 194920984 T	C
256	767 G	+1:194920985 194920985 G	
256	768 T	+1:194920986 194920986 T	
257 T	769 A	+1:194920987 194920987 A	T
257	770 C	+1:194920988 194920988 C	
257	771 C	+1:194920989 194920989 C	
258 L	772 T	+1:194920990 194920990 T	L
258	773 T	+1:194925173 194925173 T	
258	774 G	+1:194925174 194925174 G	
259 K	775 A	+1:194925175 194925175 A	K
259	776 A	+1:194925176 194925176 A	
259	777 A	+1:194925177 194925177 A	
260 P	778 C	+1:194925178 194925178 C	P
260	779 C	+1:194925179 194925179 C	
260	780 T	+1:194925180 194925180 T	
261 C	781 T	+1:194925181 194925181 T	C
261	782 G	+1:194925182 194925182 G	
261	783 T	+1:194925183 194925183 T	
262 D	784 G	+1:194925184 194925184 G	D
262	785 A	+1:194925185 194925185 A	
262	786 T	+1:194925186 194925186 T	
263 Y	787 T	+1:194925187 194925187 T	Y
263	788 A	+1:194925188 194925188 A	
263	789 T	+1:194925189 194925189 T	
264 P	790 C	+1:194925190 194925190 C	P
264	791 C	+1:194925191 194925191 C	
264	792 A	+1:194925192 194925192 A	
265 D	793 G	+1:194925193 194925193 G	D
265	794 A	+1:194925194 194925194 A	
265	795 C	+1:194925195 194925195 C	
266 I	796 A	+1:194925196 194925196 A	I
266	797 T	+1:194925197 194925197 T	
266	798 T	+1:194925198 194925198 T	
267 K	799 A	+1:194925199 194925199 A	K
267	800 A	+1:194925200 194925200 A	
267	801 A	+1:194925201 194925201 A	
268 H	802 C	+1:194925202 194925202 C	H
268	803 A	+1:194925203 194925203 A	
268	804 T	+1:194925204 194925204 T	
269 G	805 G	+1:194925205 194925205 G	G
269	806 G	+1:194925206 194925206 G	
269	807 A	+1:194925207 194925207 A	
270 G	808 G	+1:194925208 194925208 G	G
270	809 G	+1:194925209 194925209 G	
270	810 T	+1:194925210 194925210 T	
271 L	811 C	+1:194925211 194925211 C	L
271	812 T	+1:194925212 194925212 T	
271	813 A	+1:194925213 194925213 A	
272 Y	814 T	+1:194925214 194925214 T	Y
272	815 A	+1:194925215 194925215 A	
272	816 T	+1:194925216 194925216 T	
273 H	817 C	+1:194925217 194925217 C	H
273	818 A	+1:194925218 194925218 A	
273	819 T	+1:194925219 194925219 T	
274 E	820 G	+1:194925220 194925220 G	E
274	821 A	+1:194925221 194925221 A	
274	822 G	+1:194925222 194925222 G	
275 N	823 A	+1:194925223 194925223 A	N
275	824 A	+1:194925224 194925224 A	
275	825 T	+1:194925225 194925225 T	
276 M	826 A	+1:194925226 194925226 A	M
276	827 T	+1:194925227 194925227 T	
276	828 G	+1:194925228 194925228 G	
277 R	829 C	+1:194925229 194925229 C	R
277	830 G	+1:194925230 194925230 G	
277	831 T	+1:194925231 194925231 T	
278 R	832 A	+1:194925232 194925232 A	R
278	833 G	+1:194925233 194925233 G	
278	834 A	+1:194925234 194925234 A	
279 P	835 C	+1:194925235 194925235 C	P
279	836 C	+1:194925236 194925236 C	
279	837 A	+1:194925237 194925237 A	
280 Y	838 T	+1:194925238 194925238 T	Y
280	839 A	+1:194925239 194925239 A	
280	840 C	+1:194925240 194925240 C	
281 F	841 T	+1:194925241 194925241 T	F
281	842 T	+1:194925242 194925242 T	
281	843 T	+1:194925243 194925243 T	
282 P	844 C	+1:194925244 194925244 C	P
282	845 C	+1:194925245 194925245 C	
282	846 A	+1:194925246 194925246 A	
283 V	847 G	+1:194925247 194925247 G	V
283	848 T	+1:194925248 194925248 T	
283	849 A	+1:194925249 194925249 A	
284 A	850 G	+1:194925250 194925250 G	A
284	851 C	+1:194925251 194925251 C	
284	852 T	+1:194925252 194925252 T	
285 V	853 G	+1:194925253 194925253 G	V
285	854 T	+1:194925254 194925254 T	
285	855 A	+1:194925255 194925255 A	
286 G	856 G	+1:194925256 194925256 G	G
286	857 G	+1:194925257 194925257 G	
286	858 A	+1:194925258 194925258 A	
287 K	859 A	+1:194925259 194925259 A	K
287	860 A	+1:194925260 194925260 A	
287	861 A	+1:194925261 194925261 A	
288 Y	862 T	+1:194925262 194925262 T	Y
288	863 A	+1:194925263 194925263 A	
288	864 T	+1:194925264 194925264 T	
289 Y	865 T	+1:194925265 194925265 T	Y
289	866 A	+1:194925266 194925266 A	
289	867 C	+1:194925267 194925267 C	
290 S	868 T	+1:194925268 194925268 T	S
290	869 C	+1:194925269 194925269 C	
290	870 C	+1:194925270 194925270 C	
291 Y	871 T	+1:194925271 194925271 T	Y
291	872 A	+1:194925272 194925272 A	
291	873 T	+1:194925273 194925273 T	
292 Y	874 T	+1:194925274 194925274 T	Y
292	875 A	+1:194925275 194925275 A	
292	876 C	+1:194925276 194925276 C	
293 C	877 T	+1:194925277 194925277 T	C
293	878 G	+1:194925278 194925278 G	
293	879 T	+1:194925279 194925279 T	
294 D	880 G	+1:194925280 194925280 G	D
294	881 A	+1:194925281 194925281 A	
294	882 T	+1:194925282 194925282 T	
295 E	883 G	+1:194925283 194925283 G	E
295	884 A	+1:194925284 194925284 A	
295	885 A	+1:194925285 194925285 A	
296 H	886 C	+1:194925286 194925286 C	H
296	887 A	+1:194925287 194925287 A	
296	888 T	+1:194925288 194925288 T	
297 F	889 T	+1:194925289 194925289 T	F
297	890 T	+1:194925290 194925290 T	
297	891 T	+1:194925291 194925291 T	
298 E	892 G	+1:194925292 194925292 G	E
298	893 A	+1:194925293 194925293 A	
298	894 G	+1:194925294 194925294 G	
299 T	895 A	+1:194925295 194925295 A	T
299	896 C	+1:194925296 194925296 C	
299	897 T	+1:194925297 194925297 T	
300 P	898 C	+1:194925298 194925298 C	P
300	899 C	+1:194925299 194925299 C	
300	900 G	+1:194925300 194925300 G	
301 S	901 T	+1:194925301 194925301 T	S
301	902 C	+1:194925302 194925302 C	
301	903 A	+1:194925303 194925303 A	
302 G	904 G	+1:194925304 194925304 G	G
302	905 G	+1:194925305 194925305 G	
302	906 A	+1:194925306 194925306 A	
303 S	907 A	+1:194925307 194925307 A	S
303	908 G	+1:194925308 194925308 G	
303	909 T	+1:194925309 194925309 T	
304 Y	910 T	+1:194925310 194925310 T	Y
304	911 A	+1:194925311 194925311 A	
304	912 C	+1:194925312 194925312 C	
305 W	913 T	+1:194925313 194925313 T	W
305	914 G	+1:194925314 194925314 G	
305	915 G	+1:194925315 194925315 G	
306 D	916 G	+1:194925316 194925316 G	D
306	917 A	+1:194925317 194925317 A	
306	918 T	+1:194925318 194925318 T	
307 H	919 C	+1:194925319 194925319 C	H
307	920 A	+1:194925320 194925320 A	
307	921 C	+1:194925321 194925321 C	
308 I	922 A	+1:194925322 194925322 A	I
308	923 T	+1:194925323 194925323 T	
308	924 T	+1:194925324 194925324 T	
309 H	925 C	+1:194925325 194925325 C	H
309	926 A	+1:194925326 194925326 A	
309	927 T	+1:194925327 194925327 T	
310 C	928 T	+1:194925328 194925328 T	C
310	929 G	+1:194925329 194925329 G	
310	930 C	+1:194925330 194925330 C	
311 T	931 A	+1:194925331 194925331 A	T
311	932 C	+1:194925332 194925332 C	
311	933 A	+1:194925333 194925333 A	
312 Q	934 C	+1:194925334 194925334 C	Q
312	935 A	+1:194925335 194925335 A	
312	936 A	+1:194925336 194925336 A	
313 D	937 G	+1:194925337 194925337 G	D
313	938 A	+1:194925338 194925338 A	
313	939 T	+1:194925339 194925339 T	
314 G	940 G	+1:194925340 194925340 G	G
314	941 G	+1:194925341 194925341 G	
314	942 A	+1:194925342 194925342 A	
315 W	943 T	+1:194925343 194925343 T	W
315	944 G	+1:194925344 194925344 G	
315	945 G	+1:194925345 194925345 G	
316 S	946 T	+1:194925346 194925346 T	S
316	947 C	+1:194925347 194925347 C	
316	948 G	+1:194925348 194925348 G	
317 P	949 C	+1:194925349 194925349 C	P
317	950 C	+1:194925350 194925350 C	
317	951 A	+1:194925351 194925351 A	
318 A	952 G	+1:194925352 194925352 G	A
318	953 C	+1:194925353 194925353 C	
318	954 A	+1:194925354 194925354 A	
319 V	955 G	+1:194925355 194925355 G	V
319	956 T	+1:194925356 194925356 T	
319	957 A	+1:194925357 194925357 A	
320 P	958 C	+1:194925358 194925358 C	P
320	959 C	+1:194925359 194925359 C	
320	960 A	+1:194925360 194925360 A	
321 C	961 T	+1:194925361 194925361 T	C
321	962 G	+1:194925362 194925362 G	
321	963 C	+1:194925363 194925363 C	
322 L	964 C	+1:194925364 194925364 C	L
322	965 T	+1:194925365 194925365 T	
322	966 C	+1:194925366 194925366 C	
323 R	967 A	+1:194925367 194925367 A	R
323	968 G	+1:194925816 194925816 G	
323	969 A	+1:194925817 194925817 A	
324 K	970 A	+1:194925818 194925818 A	K
324	971 A	+1:194925819 194925819 A	
324	972 A	+1:194925820 194925820 A	
325 C	973 T	+1:194925821 194925821 T	C
325	974 G	+1:194925822 194925822 G	
325	975 T	+1:194925823 194925823 T	
326 Y	976 T	+1:194925824 194925824 T	Y
326	977 A	+1:194925825 194925825 A	
326	978 T	+1:194925826 194925826 T	
327 F	979 T	+1:194925827 194925827 T	F
327	980 T	+1:194925828 194925828 T	
327	981 T	+1:194925829 194925829 T	
328 P	982 C	+1:194925830 194925830 C	P
328	983 C	+1:194925831 194925831 C	
328	984 T	+1:194925832 194925832 T	
329 Y	985 T	+1:194925833 194925833 T	Y
329	986 A	+1:194925834 194925834 A	
329	987 T	+1:194925835 194925835 T	
330 L	988 T	+1:194925836 194925836 T	L
330	989 T	+1:194925837 194925837 T	
330	990 G	+1:194925838 194925838 G	
331 E	991 G	+1:194925839 194925839 G	E
331	992 A	+1:194925840 194925840 A	
331	993 A	+1:194925841 194925841 A	
332 N	994 A	+1:194925842 194925842 A	N
332	995 A	+1:194925843 194925843 A	
332	996 T	+1:194925844 194925844 T	
333 G	997 G	+1:194925845 194925845 G	G
333	998 G	+1:194925846 194925846 G	
333	999 A	+1:194925847 194925847 A	
334 Y	1000 T	+1:194925848 194925848 T	Y
334	1001 A	+1:194925849 194925849 A	
334	1002 T	+1:194925850 194925850 T	
335 N	1003 A	+1:194925851 194925851 A	N
335	1004 A	+1:194925852 194925852 A	
335	1005 T	+1:194925853 194925853 T	
336 Q	1006 C	+1:194925854 194925854 C	Q
336	1007 A	+1:194925855 194925855 A	
336	1008 A	+1:194925856 194925856 A	
337 N	1009 A	+1:194925857 194925857 A	N
337	1010 A	+1:194925858 194925858 A	
337	1011 T	+1:194925859 194925859 T	
338 H	1012 C	+1:194925860 194925860 C	H
338	1013 A	+1:194925861 194925861 A	
338	1014 T	+1:194925862 194925862 T	
339 G	1015 G	+1:194925863 194925863 G	G
339	1016 G	+1:194925864 194925864 G	
339	1017 A	+1:194925865 194925865 A	
340 R	1018 A	+1:194925866 194925866 A	R
340	1019 G	+1:194925867 194925867 G	
340	1020 A	+1:194925868 194925868 A	
341 K	1021 A	+1:194925869 194925869 A	K
341	1022 A	+1:194925870 194925870 A	
341	1023 G	+1:194925871 194925871 G	
342 F	1024 T	+1:194925872 194925872 T	F
342	1025 T	+1:194925873 194925873 T	
342	1026 T	+1:194925874 194925874 T	
343 V	1027 G	+1:194925875 194925875 G	V
343	1028 T	+1:194925876 194925876 T	
343	1029 A	+1:194925877 194925877 A	
344 Q	1030 C	+1:194925878 194925878 C	Q
344	1031 A	+1:194925879 194925879 A	
344	1032 G	+1:194925880 194925880 G	
345 G	1033 G	+1:194925881 194925881 G	G
345	1034 G	+1:194925882 194925882 G	
345	1035 T	+1:194925883 194925883 T	
346 K	1036 A	+1:194925884 194925884 A	K
346	1037 A	+1:194925885 194925885 A	
346	1038 A	+1:194925886 194925886 A	
347 S	1039 T	+1:194925887 194925887 T	S
347	1040 C	+1:194925888 194925888 C	
347	1041 T	+1:194925889 194925889 T	
348 I	1042 A	+1:194925890 194925890 A	I
348	1043 T	+1:194925891 194925891 T	
348	1044 A	+1:194925892 194925892 A	
349 D	1045 G	+1:194925893 194925893 G	D
349	1046 A	+1:194925894 194925894 A	
349	1047 C	+1:194925895 194925895 C	
350 V	1048 G	+1:194925896 194925896 G	V
350	1049 T	+1:194925897 194925897 T	
350	1050 T	+1:194925898 194925898 T	
351 A	1051 G	+1:194925899 194925899 G	A
351	1052 C	+1:194925900 194925900 C	
351	1053 C	+1:194925901 194925901 C	
352 C	1054 T	+1:194925902 194925902 T	C
352	1055 G	+1:194925903 194925903 G	
352	1056 C	+1:194925904 194925904 C	
353 H	1057 C	+1:194925905 194925905 C	H
353	1058 A	+1:194925906 194925906 A	
353	1059 T	+1:194925907 194925907 T	
354 P	1060 C	+1:194925908 194925908 C	P
354	1061 C	+1:194925909 194925909 C	
354	1062 T	+1:194925910 194925910 T	
355 G	1063 G	+1:194925911 194925911 G	G
355	1064 G	+1:194925912 194925912 G	
355	1065 C	+1:194925913 194925913 C	
356 Y	1066 T	+1:194925914 194925914 T	Y
356	1067 A	+1:194925915 194925915 A	
356	1068 C	+1:194925916 194925916 C	
357 A	1069 G	+1:194925917 194925917 G	A
357	1070 C	+1:194925918 194925918 C	
357	1071 T	+1:194925919 194925919 T	
358 L	1072 C	+1:194925920 194925920 C	L
358	1073 T	+1:194925921 194925921 T	
358	1074 T	+1:194925922 194925922 T	
359 P	1075 C	+1:194925923 194925923 C	P
359	1076 C	+1:194925924 194925924 C	
359	1077 A	+1:194925925 194925925 A	
360 K	1078 A	+1:194925926 194925926 A	K
360	1079 A	+1:194925927 194925927 A	
360	1080 A	+1:194925928 194925928 A	
361 A	1081 G	+1:194925929 194925929 G	A
361	1082 C	+1:194925930 194925930 C	
361	1083 G	+1:194925931 194925931 G	
362 Q	1084 C	+1:194925932 194925932 C	Q
362	1085 A	+1:194925933 194925933 A	
362	1086 G	+1:194925934 194925934 G	
363 T	1087 A	+1:194925935 194925935 A	T
363	1088 C	+1:194925936 194925936 C	
363	1089 C	+1:194925937 194925937 C	
364 T	1090 A	+1:194925938 194925938 A	T
364	1091 C	+1:194925939 194925939 C	
364	1092 A	+1:194925940 194925940 A	
365 V	1093 G	+1:194925941 194925941 G	V
365	1094 T	+1:194925942 194925942 T	
365	1095 T	+1:194925943 194925943 T	
366 T	1096 A	+1:194925944 194925944 A	T
366	1097 C	+1:194925945 194925945 C	
366	1098 A	+1:194925946 194925946 A	
367 C	1099 T	+1:194925947 194925947 T	C
367	1100 G	+1:194925948 194925948 G	
367	1101 T	+1:194925949 194925949 T	
368 M	1102 A	+1:194925950 194925950 A	M
368	1103 T	+1:194925951 194925951 T	
368	1104 G	+1:194925952 194925952 G	
369 E	1105 G	+1:194925953 194925953 G	E
369	1106 A	+1:194925954 194925954 A	
369	1107 G	+1:194925955 194925955 G	
370 N	1108 A	+1:194925956 194925956 A	N
370	1109 A	+1:194925957 194925957 A	
370	1110 T	+1:194925958 194925958 T	
371 G	1111 G	+1:194925959 194925959 G	G
371	1112 G	+1:194925960 194925960 G	
371	1113 C	+1:194925961 194925961 C	
372 W	1114 T	+1:194925962 194925962 T	W
372	1115 G	+1:194925963 194925963 G	
372	1116 G	+1:194925964 194925964 G	
373 S	1117 T	+1:194925965 194925965 T	S
373	1118 C	+1:194925966 194925966 C	
373	1119 T	+1:194925967 194925967 T	
374 P	1120 C	+1:194925968 194925968 C	P
374	1121 C	+1:194925969 194925969 C	
374	1122 T	+1:194925970 194925970 T	
375 T	1123 A	+1:194925971 194925971 A	T
375	1124 C	+1:194925972 194925972 C	
375	1125 T	+1:194925973 194925973 T	
376 P	1126 C	+1:194925974 194925974 C	P
376	1127 C	+1:194925975 194925975 C	
376	1128 C	+1:194925976 194925976 C	
377 R	1129 A	+1:194925977 194925977 A	R
377	1130 G	+1:194925978 194925978 G	
377	1131 A	+1:194925979 194925979 A	
378 C	1132 T	+1:194925980 194925980 T	C
378	1133 G	+1:194925981 194925981 G	
378	1134 C	+1:194925982 194925982 C	
379 I	1135 A	+1:194925983 194925983 A	I
379	1136 T	+1:194925984 194925984 T	
379	1137 C	+1:194925985 194925985 C	
380 R	1138 C	+1:194925986 194925986 C	R
380	1139 G	+1:194925987 194925987 G	
380	1140 T	+1:194925988 194925988 T	
>ENSP00000356399 
1 M	1 A	+1:194887871 194887871 A	M
1	2 T	+1:194887872 194887872 T	
1	3 G	+1:194887873 194887873 G	
2 R	4 A	+1:194887874 194887874 A	R
2	5 G	+1:194887875 194887875 G	
2	6 A	+1:194887876 194887876 A	
3 L	7 C	+1:194887877 194887877 C	L
3	8 T	+1:194887878 194887878 T	
3	9 T	+1:194887879 194887879 T	
4 L	10 C	+1:194887880 194887880 C	L
4	11 T	+1:194887881 194887881 T	
4	12 A	+1:194887882 194887882 A	
5 A	13 G	+1:194887883 194887883 G	A
5	14 C	+1:194887884 194887884 C	
5	15 A	+1:194887885 194887885 A	
6 K	16 A	+1:194887886 194887886 A	K
6	17 A	+1:194887887 194887887 A	
6	18 G	+1:194887888 194887888 G	
7 I	19 A	+1:194887889 194887889 A	I
7	20 T	+1:194887890 194887890 T	
7	21 T	+1:194887891 194887891 T	
8 I	22 A	+1:194887892 194887892 A	I
8	23 T	+1:194887893 194887893 T	
8	24 T	+1:194887894 194887894 T	
9 C	25 T	+1:194887895 194887895 T	C
9	26 G	+1:194887896 194887896 G	
9	27 C	+1:194887897 194887897 C	
10 L	28 C	+1:194887898 194887898 C	L
10	29 T	+1:194887899 194887899 T	
10	30 T	+1:194887900 194887900 T	
11 M	31 A	+1:194887901 194887901 A	M
11	32 T	+1:194887902 194887902 T	
11	33 G	+1:194887903 194887903 G	
12 L	34 T	+1:194887904 194887904 T	L
12	35 T	+1:194887905 194887905 T	
12	36 A	+1:194887906 194887906 A	
13 W	37 T	+1:194887907 194887907 T	W
13	38 G	+1:194887908 194887908 G	
13	39 G	+1:194887909 194887909 G	
14 A	40 G	+1:194887910 194887910 G	A
14	41 C	+1:194887911 194887911 C	
14	42 T	+1:194887912 194887912 T	
15 I	43 A	+1:194887913 194887913 A	I
15	44 T	+1:194887914 194887914 T	
15	45 T	+1:194887915 194887915 T	
16 C	46 T	+1:194887916 194887916 T	C
16	47 G	+1:194887917 194887917 G	
16	48 T	+1:194887918 194887918 T	
17 V	49 G	+1:194887919 194887919 G	V
17	50 T	+1:194887920 194887920 T	
17	51 A	+1:194887921 194887921 A	
18 A	52 G	+1:194887922 194887922 G	A
18	53 C	+1:194887923 194887923 C	
18	54 A	+1:194887924 194887924 A	
19 E	55 G	+1:194887925 194887925 G	E
19	56 A	+1:194887926 194887926 A	
19	57 A	+1:194887927 194887927 A	
20 D	58 G	+1:194887928 194887928 G	D
20	59 A	+1:194908731 194908731 A	
20	60 T	+1:194908732 194908732 T	
21 C	61 T	+1:194908733 194908733 T	C
21	62 G	+1:194908734 194908734 G	
21	63 C	+1:194908735 194908735 C	
22 N	64 A	+1:194908736 194908736 A	N
22	65 A	+1:194908737 194908737 A	
22	66 T	+1:194908738 194908738 T	
23 E	67 G	+1:194908739 194908739 G	E
23	68 A	+1:194908740 194908740 A	
23	69 A	+1:194908741 194908741 A	
24 L	70 C	+1:194908742 194908742 C	L
24	71 T	+1:194908743 194908743 T	
24	72 T	+1:194908744 194908744 T	
25 P	73 C	+1:194908745 194908745 C	P
25	74 C	+1:194908746 194908746 C	
25	75 T	+1:194908747 194908747 T	
26 P	76 C	+1:194908748 194908748 C	P
26	77 C	+1:194908749 194908749 C	
26	78 A	+1:194908750 194908750 A	
27 R	79 A	+1:194908751 194908751 A	R
27	80 G	+1:194908752 194908752 G	
27	81 A	+1:194908753 194908753 A	
28 R	82 A	+1:194908754 194908754 A	R
28	83 G	+1:194908755 194908755 G	
28	84 A	+1:194908756 194908756 A	
29 N	85 A	+1:194908757 194908757 A	N
29	86 A	+1:194908758 194908758 A	
29	87 T	+1:194908759 194908759 T	
30 T	88 A	+1:194908760 194908760 A	T
30	89 C	+1:194908761 194908761 C	
30	90 A	+1:194908762 194908762 A	
31 E	91 G	+1:194908763 194908763 G	E
31	92 A	+1:194908764 194908764 A	
31	93 A	+1:194908765 194908765 A	
32 I	94 A	+1:194908766 194908766 A	I
32	95 T	+1:194908767 194908767 T	
32	96 T	+1:194908768 194908768 T	
33 L	97 C	+1:194908769 194908769 C	L
33	98 T	+1:194908770 194908770 T	
33	99 G	+1:194908771 194908771 G	
34 T	100 A	+1:194908772 194908772 A	T
34	101 C	+1:194908773 194908773 C	
34	102 A	+1:194908774 194908774 A	
35 G	103 G	+1:194908775 194908775 G	G
35	104 G	+1:194908776 194908776 G	
35	105 T	+1:194908777 194908777 T	
36 S	106 T	+1:194908778 194908778 T	S
36	107 C	+1:194908779 194908779 C	
36	108 C	+1:194908780 194908780 C	
37 W	109 T	+1:194908781 194908781 T	W
37	110 G	+1:194908782 194908782 G	
37	111 G	+1:194908783 194908783 G	
38 S	112 T	+1:194908784 194908784 T	S
38	113 C	+1:194908785 194908785 C	
38	114 T	+1:194908786 194908786 T	
39 D	115 G	+1:194908787 194908787 G	D
39	116 A	+1:194908788 194908788 A	
39	117 C	+1:194908789 194908789 C	
40 Q	118 C	+1:194908790 194908790 C	Q
40	119 A	+1:194908791 194908791 A	
40	120 A	+1:194908792 194908792 A	
41 T	121 A	+1:194908793 194908793 A	T
41	122 C	+1:194908794 194908794 C	
41	123 A	+1:194908795 194908795 A	
42 Y	124 T	+1:194908796 194908796 T	Y
42	125 A	+1:194908797 194908797 A	
42	126 T	+1:194908798 194908798 T	
43 P	127 C	+1:194908799 194908799 C	P
43	128 C	+1:194908800 194908800 C	
43	129 A	+1:194908801 194908801 A	
44 E	130 G	+1:194908802 194908802 G	E
44	131 A	+1:194908803 194908803 A	
44	132 A	+1:194908804 194908804 A	
45 G	133 G	+1:194908805 194908805 G	G
45	134 G	+1:194908806 194908806 G	
45	135 C	+1:194908807 194908807 C	
46 T	136 A	+1:194908808 194908808 A	T
46	137 C	+1:194908809 194908809 C	
46	138 C	+1:194908810 194908810 C	
47 Q	139 C	+1:194908811 194908811 C	Q
47	140 A	+1:194908812 194908812 A	
47	141 G	+1:194908813 194908813 G	
48 A	142 G	+1:194908814 194908814 G	A
48	143 C	+1:194908815 194908815 C	
48	144 T	+1:194908816 194908816 T	
49 I	145 A	+1:194908817 194908817 A	I
49	146 T	+1:194908818 194908818 T	
49	147 C	+1:194908819 194908819 C	
50 Y	148 T	+1:194908820 194908820 T	Y
50	149 A	+1:194908821 194908821 A	
50	150 T	+1:194908822 194908822 T	
51 K	151 A	+1:194908823 194908823 A	K
51	152 A	+1:194908824 194908824 A	
51	153 A	+1:194908825 194908825 A	
52 C	154 T	+1:194908826 194908826 T	C
52	155 G	+1:194908827 194908827 G	
52	156 C	+1:194908828 194908828 C	
53 R	157 C	+1:194908829 194908829 C	R
53	158 G	+1:194908830 194908830 G	
53	159 C	+1:194908831 194908831 C	
54 P	160 C	+1:194908832 194908832 C	P
54	161 C	+1:194908833 194908833 C	
54	162 T	+1:194908834 194908834 T	
55 G	163 G	+1:194908835 194908835 G	G
55	164 G	+1:194908836 194908836 G	
55	165 A	+1:194908837 194908837 A	
56 Y	166 T	+1:194908838 194908838 T	Y
56	167 A	+1:194908839 194908839 A	
56	168 T	+1:194908840 194908840 T	
57 R	169 A	+1:194908841 194908841 A	R
57	170 G	+1:194908842 194908842 G	
57	171 A	+1:194908843 194908843 A	
58 S	172 T	+1:194908844 194908844 T	S
58	173 C	+1:194908845 194908845 C	
58	174 T	+1:194908846 194908846 T	
59 L	175 C	+1:194908847 194908847 C	L
59	176 T	+1:194908848 194908848 T	
59	177 T	+1:194908849 194908849 T	
60 G	178 G	+1:194908850 194908850 G	G
60	179 G	+1:194908851 194908851 G	
60	180 A	+1:194908852 194908852 A	
61 N	181 A	+1:194908853 194908853 A	N
61	182 A	+1:194908854 194908854 A	
61	183 T	+1:194908855 194908855 T	
62 V	184 G	+1:194908856 194908856 G	V
62	185 T	+1:194908857 194908857 T	
62	186 A	+1:194908858 194908858 A	
63 I	187 A	+1:194908859 194908859 A	I
63	188 T	+1:194908860 194908860 T	
63	189 A	+1:194908861 194908861 A	
64 M	190 A	+1:194908862 194908862 A	M
64	191 T	+1:194908863 194908863 T	
64	192 G	+1:194908864 194908864 G	
65 V	193 G	+1:194908865 194908865 G	V
65	194 T	+1:194908866 194908866 T	
65	195 A	+1:194908867 194908867 A	
66 C	196 T	+1:194908868 194908868 T	C
66	197 G	+1:194908869 194908869 G	
66	198 C	+1:194908870 194908870 C	
67 R	199 A	+1:194908871 194908871 A	R
67	200 G	+1:194908872 194908872 G	
67	201 G	+1:194908873 194908873 G	
68 K	202 A	+1:194908874 194908874 A	K
68	203 A	+1:194908875 194908875 A	
68	204 G	+1:194908876 194908876 G	
69 G	205 G	+1:194908877 194908877 G	G
69	206 G	+1:194908878 194908878 G	
69	207 A	+1:194908879 194908879 A	
70 E	208 G	+1:194908880 194908880 G	E
70	209 A	+1:194908881 194908881 A	
70	210 A	+1:194908882 194908882 A	
71 W	211 T	+1:194908883 194908883 T	W
71	212 G	+1:194908884 194908884 G	
71	213 G	+1:194908885 194908885 G	
72 V	214 G	+1:194908886 194908886 G	V
72	215 T	+1:194908887 194908887 T	
72	216 T	+1:194908888 194908888 T	
73 A	217 G	+1:194908889 194908889 G	A
73	218 C	+1:194908890 194908890 C	
73	219 T	+1:194908891 194908891 T	
74 L	220 C	+1:194908892 194908892 C	L
74	221 T	+1:194908893 194908893 T	
74	222 T	+1:194908894 194908894 T	
75 N	223 A	+1:194908895 194908895 A	N
75	224 A	+1:194908896 194908896 A	
75	225 T	+1:194908897 194908897 T	
76 P	226 C	+1:194908898 194908898 C	P
76	227 C	+1:194908899 194908899 C	
76	228 A	+1:194908900 194908900 A	
77 L	229 T	+1:194908901 194908901 T	L
77	230 T	+1:194908902 194908902 T	
77	231 A	+1:194908903 194908903 A	
78 R	232 A	+1:194908904 194908904 A	R
78	233 G	+1:194908905 194908905 G	
78	234 G	+1:194908906 194908906 G	
79 K	235 A	+1:194908907 194908907 A	K
79	236 A	+1:194908908 194908908 A	
79	237 A	+1:194908909 194908909 A	
80 C	238 T	+1:194908910 194908910 T	C
80	239 G	+1:194908911 194908911 G	
80	240 T	+1:194908912 194908912 T	
81 Q	241 C	+1:194908913 194908913 C	Q
81	242 A	+1:194908914 194908914 A	
81	243 G	+1:194908915 194908915 G	
82 K	244 A	+1:194908916 194908916 A	K
82	245 A	+1:194909610 194909610 A	
82	246 A	+1:194909611 194909611 A	
83 R	247 A	+1:194909612 194909612 A	R
83	248 G	+1:194909613 194909613 G	
83	249 G	+1:194909614 194909614 G	
84 P	250 C	+1:194909615 194909615 C	P
84	251 C	+1:194909616 194909616 C	
84	252 C	+1:194909617 194909617 C	
85 C	253 T	+1:194909618 194909618 T	C
85	254 G	+1:194909619 194909619 G	
85	255 T	+1:194909620 194909620 T	
86 G	256 G	+1:194909621 194909621 G	G
86	257 G	+1:194909622 194909622 G	
86	258 A	+1:194909623 194909623 A	
87 H	259 C	+1:194909624 194909624 C	H
87	260 A	+1:194909625 194909625 A	
87	261 T	+1:194909626 194909626 T	
88 P	262 C	+1:194909627 194909627 C	P
88	263 C	+1:194909628 194909628 C	
88	264 T	+1:194909629 194909629 T	
89 G	265 G	+1:194909630 194909630 G	G
89	266 G	+1:194909631 194909631 G	
89	267 A	+1:194909632 194909632 A	
90 D	268 G	+1:194909633 194909633 G	D
90	269 A	+1:194909634 194909634 A	
90	270 T	+1:194909635 194909635 T	
91 T	271 A	+1:194909636 194909636 A	T
91	272 C	+1:194909637 194909637 C	
91	273 T	+1:194909638 194909638 T	
92 P	274 C	+1:194909639 194909639 C	P
92	275 C	+1:194909640 194909640 C	
92	276 T	+1:194909641 194909641 T	
93 F	277 T	+1:194909642 194909642 T	F
93	278 T	+1:194909643 194909643 T	
93	279 T	+1:194909644 194909644 T	
94 G	280 G	+1:194909645 194909645 G	G
94	281 G	+1:194909646 194909646 G	
94	282 T	+1:194909647 194909647 T	
95 T	283 A	+1:194909648 194909648 A	T
95	284 C	+1:194909649 194909649 C	
95	285 T	+1:194909650 194909650 T	
96 F	286 T	+1:194909651 194909651 T	F
96	287 T	+1:194909652 194909652 T	
96	288 T	+1:194909653 194909653 T	
97 T	289 A	+1:194909654 194909654 A	T
97	290 C	+1:194909655 194909655 C	
97	291 C	+1:194909656 194909656 C	
98 L	292 C	+1:194909657 194909657 C	L
98	293 T	+1:194909658 194909658 T	
98	294 T	+1:194909659 194909659 T	
99 T	295 A	+1:194909660 194909660 A	T
99	296 C	+1:194909661 194909661 C	
99	297 A	+1:194909662 194909662 A	
100 G	298 G	+1:194909663 194909663 G	G
100	299 G	+1:194909664 194909664 G	
100	300 A	+1:194909665 194909665 A	
101 G	301 G	+1:194909666 194909666 G	G
101	302 G	+1:194909667 194909667 G	
101	303 A	+1:194909668 194909668 A	
102 N	304 A	+1:194909669 194909669 A	N
102	305 A	+1:194909670 194909670 A	
102	306 T	+1:194909671 194909671 T	
103 V	307 G	+1:194909672 194909672 G	V
103	308 T	+1:194909673 194909673 T	
103	309 G	+1:194909674 194909674 G	
104 F	310 T	+1:194909675 194909675 T	F
104	311 T	+1:194909676 194909676 T	
104	312 T	+1:194909677 194909677 T	
105 E	313 G	+1:194909678 194909678 G	E
105	314 A	+1:194909679 194909679 A	
105	315 A	+1:194909680 194909680 A	
106 Y	316 T	+1:194909681 194909681 T	Y
106	317 A	+1:194909682 194909682 A	
106	318 T	+1:194909683 194909683 T	
107 G	319 G	+1:194909684 194909684 G	G
107	320 G	+1:194909685 194909685 G	
107	321 T	+1:194909686 194909686 T	
108 V	322 G	+1:194909687 194909687 G	V
108	323 T	+1:194909688 194909688 T	
108	324 A	+1:194909689 194909689 A	
109 K	325 A	+1:194909690 194909690 A	K
109	326 A	+1:194909691 194909691 A	
109	327 A	+1:194909692 194909692 A	
110 A	328 G	+1:194909693 194909693 G	A
110	329 C	+1:194909694 194909694 C	
110	330 T	+1:194909695 194909695 T	
111 V	331 G	+1:194909696 194909696 G	V
111	332 T	+1:194909697 194909697 T	
111	333 G	+1:194909698 194909698 G	
112 Y	334 T	+1:194909699 194909699 T	Y
112	335 A	+1:194909700 194909700 A	
112	336 T	+1:194909701 194909701 T	
113 T	337 A	+1:194909702 194909702 A	T
113	338 C	+1:194909703 194909703 C	
113	339 A	+1:194909704 194909704 A	
114 C	340 T	+1:194909705 194909705 T	C
114	341 G	+1:194909706 194909706 G	
114	342 T	+1:194909707 194909707 T	
115 N	343 A	+1:194909708 194909708 A	N
115	344 A	+1:194909709 194909709 A	
115	345 T	+1:194909710 194909710 T	
116 E	346 G	+1:194909711 194909711 G	E
116	347 A	+1:194909712 194909712 A	
116	348 G	+1:194909713 194909713 G	
117 G	349 G	+1:194909714 194909714 G	G
117	350 G	+1:194909715 194909715 G	
117	351 G	+1:194911742 194911742 G	
118 Y	352 T	+1:194911743 194911743 T	Y
118	353 A	+1:194911744 194911744 A	
118	354 T	+1:194911745 194911745 T	
119 Q	355 C	+1:194911746 194911746 C	Q
119	356 A	+1:194911747 194911747 A	
119	357 A	+1:194911748 194911748 A	
120 L	358 T	+1:194911749 194911749 T	L
120	359 T	+1:194911750 194911750 T	
120	360 G	+1:194911751 194911751 G	
121 L	361 C	+1:194911752 194911752 C	L
121	362 T	+1:194911753 194911753 T	
121	363 A	+1:194911754 194911754 A	
122 G	364 G	+1:194911755 194911755 G	G
122	365 G	+1:194911756 194911756 G	
122	366 T	+1:194911757 194911757 T	
123 E	367 G	+1:194911758 194911758 G	E
123	368 A	+1:194911759 194911759 A	
123	369 G	+1:194911760 194911760 G	
124 I	370 A	+1:194911761 194911761 A	I
124	371 T	+1:194911762 194911762 T	
124	372 T	+1:194911763 194911763 T	
125 N	373 A	+1:194911764 194911764 A	N
125	374 A	+1:194911765 194911765 A	
125	375 T	+1:194911766 194911766 T	
126 Y	376 T	+1:194911767 194911767 T	Y
126	377 A	+1:194911768 194911768 A	
126	378 C	+1:194911769 194911769 C	
127 R	379 C	+1:194911770 194911770 C	R
127	380 G	+1:194911771 194911771 G	
127	381 T	+1:194911772 194911772 T	
128 E	382 G	+1:194911773 194911773 G	E
128	383 A	+1:194911774 194911774 A	
128	384 A	+1:194911775 194911775 A	
129 C	385 T	+1:194911776 194911776 T	C
129	386 G	+1:194911777 194911777 G	
129	387 T	+1:194911778 194911778 T	
130 D	388 G	+1:194911779 194911779 G	D
130	389 A	+1:194911780 194911780 A	
130	390 C	+1:194911781 194911781 C	
131 T	391 A	+1:194911782 194911782 A	T
131	392 C	+1:194911783 194911783 C	
131	393 A	+1:194911784 194911784 A	
132 D	394 G	+1:194911785 194911785 G	D
132	395 A	+1:194911786 194911786 A	
132	396 T	+1:194911787 194911787 T	
133 G	397 G	+1:194911788 194911788 G	G
133	398 G	+1:194911789 194911789 G	
133	399 A	+1:194911790 194911790 A	
134 W	400 T	+1:194911791 194911791 T	W
134	401 G	+1:194911792 194911792 G	
134	402 G	+1:194911793 194911793 G	
135 T	403 A	+1:194911794 194911794 A	T
135	404 C	+1:194911795 194911795 C	
135	405 C	+1:194911796 194911796 C	
136 N	406 A	+1:194911797 194911797 A	N
136	407 A	+1:194911798 194911798 A	
136	408 T	+1:194911799 194911799 T	
137 D	409 G	+1:194911800 194911800 G	D
137	410 A	+1:194911801 194911801 A	
137	411 T	+1:194911802 194911802 T	
138 I	412 A	+1:194911803 194911803 A	I
138	413 T	+1:194911804 194911804 T	
138	414 T	+1:194911805 194911805 T	
139 P	415 C	+1:194911806 194911806 C	P
139	416 C	+1:194911807 194911807 C	
139	417 T	+1:194911808 194911808 T	
140 I	418 A	+1:194911809 194911809 A	I
140	419 T	+1:194911810 194911810 T	
140	420 A	+1:194911811 194911811 A	
141 C	421 T	+1:194911812 194911812 T	C
141	422 G	+1:194911813 194911813 G	
141	423 T	+1:194911814 194911814 T	
142 E	424 G	+1:194911815 194911815 G	E
142	425 A	+1:194911816 194911816 A	
142	426 A	+1:194911817 194911817 A	
143 V	427 G	+1:194911818 194911818 G	V
143	428 T	+1:194913229 194913229 T	
143	429 T	+1:194913230 194913230 T	
144 V	430 G	+1:194913231 194913231 G	V
144	431 T	+1:194913232 194913232 T	
144	432 G	+1:194913233 194913233 G	
145 K	433 A	+1:194913234 194913234 A	K
145	434 A	+1:194913235 194913235 A	
145	435 G	+1:194913236 194913236 G	
146 C	436 T	+1:194913237 194913237 T	C
146	437 G	+1:194913238 194913238 G	
146	438 T	+1:194913239 194913239 T	
147 L	439 T	+1:194913240 194913240 T	L
147	440 T	+1:194913241 194913241 T	
147	441 A	+1:194913242 194913242 A	
148 P	442 C	+1:194913243 194913243 C	P
148	443 C	+1:194913244 194913244 C	
148	444 A	+1:194913245 194913245 A	
149 V	445 G	+1:194913246 194913246 G	V
149	446 T	+1:194913247 194913247 T	
149	447 G	+1:194913248 194913248 G	
150 T	448 A	+1:194913249 194913249 A	T
150	449 C	+1:194913250 194913250 C	
150	450 A	+1:194913251 194913251 A	
151 A	451 G	+1:194913252 194913252 G	A
151	452 C	+1:194913253 194913253 C	
151	453 A	+1:194913254 194913254 A	
152 P	454 C	+1:194913255 194913255 C	P
152	455 C	+1:194913256 194913256 C	
152	456 A	+1:194913257 194913257 A	
153 E	457 G	+1:194913258 194913258 G	E
153	458 A	+1:194913259 194913259 A	
153	459 G	+1:194913260 194913260 G	
154 N	460 A	+1:194913261 194913261 A	N
154	461 A	+1:194913262 194913262 A	
154	462 T	+1:194913263 194913263 T	
155 G	463 G	+1:194913264 194913264 G	G
155	464 G	+1:194913265 194913265 G	
155	465 A	+1:194913266 194913266 A	
156 K	466 A	+1:194913267 194913267 A	K
156	467 A	+1:194913268 194913268 A	
156	468 A	+1:194913269 194913269 A	
157 I	469 A	+1:194913270 194913270 A	I
157	470 T	+1:194913271 194913271 T	
157	471 T	+1:194913272 194913272 T	
158 V	472 G	+1:194913273 194913273 G	V
158	473 T	+1:194913274 194913274 T	
158	474 C	+1:194913275 194913275 C	
159 S	475 A	+1:194913276 194913276 A	S
159	476 G	+1:194913277 194913277 G	
159	477 T	+1:194913278 194913278 T	
160 S	478 A	+1:194913279 194913279 A	S
160	479 G	+1:194913280 194913280 G	
160	480 T	+1:194913281 194913281 T	
161 A	481 G	+1:194913282 194913282 G	A
161	482 C	+1:194913283 194913283 C	
161	483 A	+1:194913284 194913284 A	
162 M	484 A	+1:194913285 194913285 A	M
162	485 T	+1:194913286 194913286 T	
162	486 G	+1:194913287 194913287 G	
163 E	487 G	+1:194913288 194913288 G	E
163	488 A	+1:194913289 194913289 A	
163	489 A	+1:194913290 194913290 A	
164 P	490 C	+1:194913291 194913291 C	P
164	491 C	+1:194913292 194913292 C	
164	492 A	+1:194913293 194913293 A	
165 D	493 G	+1:194913294 194913294 G	D
165	494 A	+1:194913295 194913295 A	
165	495 T	+1:194913296 194913296 T	
166 R	496 C	+1:194913297 194913297 C	R
166	497 G	+1:194913298 194913298 G	
166	498 G	+1:194913299 194913299 G	
167 E	499 G	+1:194913300 194913300 G	E
167	500 A	+1:194913301 194913301 A	
167	501 A	+1:194913302 194913302 A	
168 Y	502 T	+1:194913303 194913303 T	Y
168	503 A	+1:194913304 194913304 A	
168	504 C	+1:194913305 194913305 C	
169 H	505 C	+1:194913306 194913306 C	H
169	506 A	+1:194913307 194913307 A	
169	507 T	+1:194913308 194913308 T	
170 F	508 T	+1:194913309 194913309 T	F
170	509 T	+1:194913310 194913310 T	
170	510 T	+1:194913311 194913311 T	
171 G	511 G	+1:194913312 194913312 G	G
171	512 G	+1:194913313 194913313 G	
171	513 A	+1:194913314 194913314 A	
172 Q	514 C	+1:194913315 194913315 C	Q
172	515 A	+1:194913316 194913316 A	
172	516 A	+1:194913317 194913317 A	
173 A	517 G	+1:194913318 194913318 G	A
173	518 C	+1:194913319 194913319 C	
173	519 A	+1:194913320 194913320 A	
174 V	520 G	+1:194913321 194913321 G	V
174	521 T	+1:194913322 194913322 T	
174	522 A	+1:194913323 194913323 A	
175 R	523 C	+1:194913324 194913324 C	R
175	524 G	+1:194913325 194913325 G	
175	525 G	+1:194913326 194913326 G	
176 F	526 T	+1:194913327 194913327 T	F
176	527 T	+1:194913328 194913328 T	
176	528 T	+1:194913329 194913329 T	
177 V	529 G	+1:194913330 194913330 G	V
177	530 T	+1:194913331 194913331 T	
177	531 A	+1:194913332 194913332 A	
178 C	532 T	+1:194913333 194913333 T	C
178	533 G	+1:194913334 194913334 G	
178	534 T	+1:194913335 194913335 T	
179 N	535 A	+1:194913336 194913336 A	N
179	536 A	+1:194913337 194913337 A	
179	537 C	+1:194913338 194913338 C	
180 S	538 T	+1:194913339 194913339 T	S
180	539 C	+1:194913340 194913340 C	
180	540 A	+1:194913341 194913341 A	
181 G	541 G	+1:194913342 194913342 G	G
181	542 G	+1:194913343 194913343 G	
181	543 C	+1:194913344 194913344 C	
182 Y	544 T	+1:194913345 194913345 T	Y
182	545 A	+1:194913346 194913346 A	
182	546 C	+1:194913347 194913347 C	
183 K	547 A	+1:194913348 194913348 A	K
183	548 A	+1:194913349 194913349 A	
183	549 G	+1:194913350 194913350 G	
184 I	550 A	+1:194913351 194913351 A	I
184	551 T	+1:194913352 194913352 T	
184	552 T	+1:194913353 194913353 T	
185 E	553 G	+1:194913354 194913354 G	E
185	554 A	+1:194913355 194913355 A	
185	555 A	+1:194913356 194913356 A	
186 G	556 G	+1:194913357 194913357 G	G
186	557 G	+1:194913358 194913358 G	
186	558 A	+1:194913359 194913359 A	
187 D	559 G	+1:194913360 194913360 G	D
187	560 A	+1:194913361 194913361 A	
187	561 T	+1:194913362 194913362 T	
188 E	562 G	+1:194913363 194913363 G	E
188	563 A	+1:194913364 194913364 A	
188	564 A	+1:194913365 194913365 A	
189 E	565 G	+1:194913366 194913366 G	E
189	566 A	+1:194913367 194913367 A	
189	567 A	+1:194913368 194913368 A	
190 M	568 A	+1:194913369 194913369 A	M
190	569 T	+1:194913370 194913370 T	
190	570 G	+1:194913371 194913371 G	
191 H	571 C	+1:194913372 194913372 C	H
191	572 A	+1:194913373 194913373 A	
191	573 T	+1:194913374 194913374 T	
192 C	574 T	+1:194913375 194913375 T	C
192	575 G	+1:194913376 194913376 G	
192	576 T	+1:194913377 194913377 T	
193 S	577 T	+1:194913378 194913378 T	S
193	578 C	+1:194913379 194913379 C	
193	579 A	+1:194913380 194913380 A	
194 D	580 G	+1:194913381 194913381 G	D
194	581 A	+1:194913382 194913382 A	
194	582 C	+1:194913383 194913383 C	
195 D	583 G	+1:194913384 194913384 G	D
195	584 A	+1:194913385 194913385 A	
195	585 T	+1:194913386 194913386 T	
196 G	586 G	+1:194913387 194913387 G	G
196	587 G	+1:194913388 194913388 G	
196	588 T	+1:194913389 194913389 T	
197 F	589 T	+1:194913390 194913390 T	F
197	590 T	+1:194913391 194913391 T	
197	591 T	+1:194913392 194913392 T	
198 W	592 T	+1:194913393 194913393 T	W
198	593 G	+1:194913394 194913394 G	
198	594 G	+1:194913395 194913395 G	
199 S	595 A	+1:194913396 194913396 A	S
199	596 G	+1:194913397 194913397 G	
199	597 T	+1:194913398 194913398 T	
200 K	598 A	+1:194913399 194913399 A	K
200	599 A	+1:194913400 194913400 A	
200	600 A	+1:194913401 194913401 A	
201 E	601 G	+1:194913402 194913402 G	E
201	602 A	+1:194913403 194913403 A	
201	603 G	+1:194913404 194913404 G	
202 K	604 A	+1:194913405 194913405 A	K
202	605 A	+1:194913406 194913406 A	
202	606 A	+1:194913407 194913407 A	
203 P	607 C	+1:194913408 194913408 C	P
203	608 C	+1:194913409 194913409 C	
203	609 A	+1:194913410 194913410 A	
204 K	610 A	+1:194913411 194913411 A	K
204	611 A	+1:194913412 194913412 A	
204	612 G	+1:194913413 194913413 G	
205 C	613 T	+1:194913414 194913414 T	C
205	614 G	+1:194913415 194913415 G	
205	615 T	+1:194913416 194913416 T	
206 V	616 G	+1:194913417 194913417 G	V
206	617 T	+1:194913418 194913418 T	
206	618 G	+1:194913419 194913419 G	
207 E	619 G	+1:194913420 194913420 G	E
207	620 A	+1:194915376 194915376 A	
207	621 A	+1:194915377 194915377 A	
208 I	622 A	+1:194915378 194915378 A	I
208	623 T	+1:194915379 194915379 T	
208	624 T	+1:194915380 194915380 T	
209 S	625 T	+1:194915381 194915381 T	S
209	626 C	+1:194915382 194915382 C	
209	627 A	+1:194915383 194915383 A	
210 C	628 T	+1:194915384 194915384 T	C
210	629 G	+1:194915385 194915385 G	
210	630 C	+1:194915386 194915386 C	
211 K	631 A	+1:194915387 194915387 A	K
211	632 A	+1:194915388 194915388 A	
211	633 A	+1:194915389 194915389 A	
212 S	634 T	+1:194915390 194915390 T	S
212	635 C	+1:194915391 194915391 C	
212	636 C	+1:194915392 194915392 C	
213 P	637 C	+1:194915393 194915393 C	P
213	638 C	+1:194915394 194915394 C	
213	639 A	+1:194915395 194915395 A	
214 D	640 G	+1:194915396 194915396 G	D
214	641 A	+1:194915397 194915397 A	
214	642 T	+1:194915398 194915398 T	
215 V	643 G	+1:194915399 194915399 G	V
215	644 T	+1:194915400 194915400 T	
215	645 T	+1:194915401 194915401 T	
216 I	646 A	+1:194915402 194915402 A	I
216	647 T	+1:194915403 194915403 T	
216	648 A	+1:194915404 194915404 A	
217 N	649 A	+1:194915405 194915405 A	N
217	650 A	+1:194915406 194915406 A	
217	651 T	+1:194915407 194915407 T	
218 G	652 G	+1:194915408 194915408 G	G
218	653 G	+1:194915409 194915409 G	
218	654 A	+1:194915410 194915410 A	
219 S	655 T	+1:194915411 194915411 T	S
219	656 C	+1:194915412 194915412 C	
219	657 T	+1:194915413 194915413 T	
220 P	658 C	+1:194915414 194915414 C	P
220	659 C	+1:194915415 194915415 C	
220	660 T	+1:194915416 194915416 T	
221 I	661 A	+1:194915417 194915417 A	I
221	662 T	+1:194915418 194915418 T	
221	663 A	+1:194915419 194915419 A	
222 S	664 T	+1:194915420 194915420 T	S
222	665 C	+1:194915421 194915421 C	
222	666 T	+1:194915422 194915422 T	
223 Q	667 C	+1:194915423 194915423 C	Q
223	668 A	+1:194915424 194915424 A	
223	669 G	+1:194915425 194915425 G	
224 K	670 A	+1:194915426 194915426 A	K
224	671 A	+1:194915427 194915427 A	
224	672 G	+1:194915428 194915428 G	
225 I	673 A	+1:194915429 194915429 A	I
225	674 T	+1:194915430 194915430 T	
225	675 T	+1:194915431 194915431 T	
226 I	676 A	+1:194915432 194915432 A	I
226	677 T	+1:194915433 194915433 T	
226	678 T	+1:194915434 194915434 T	
227 Y	679 T	+1:194915435 194915435 T	Y
227	680 A	+1:194915436 194915436 A	
227	681 T	+1:194915437 194915437 T	
228 K	682 A	+1:194915438 194915438 A	K
228	683 A	+1:194915439 194915439 A	
228	684 G	+1:194915440 194915440 G	
229 E	685 G	+1:194915441 194915441 G	E
229	686 A	+1:194915442 194915442 A	
229	687 G	+1:194915443 194915443 G	
230 N	688 A	+1:194915444 194915444 A	N
230	689 A	+1:194915445 194915445 A	
230	690 T	+1:194915446 194915446 T	
231 E	691 G	+1:194915447 194915447 G	E
231	692 A	+1:194915448 194915448 A	
231	693 A	+1:194915449 194915449 A	
232 R	694 C	+1:194915450 194915450 C	R
232	695 G	+1:194915451 194915451 G	
232	696 A	+1:194915452 194915452 A	
233 F	697 T	+1:194915453 194915453 T	F
233	698 T	+1:194915454 194915454 T	
233	699 T	+1:194915455 194915455 T	
234 Q	700 C	+1:194915456 194915456 C	Q
234	701 A	+1:194915457 194915457 A	
234	702 A	+1:194915458 194915458 A	
235 Y	703 T	+1:194915459 194915459 T	Y
235	704 A	+1:194915460 194915460 A	
235	705 T	+1:194915461 194915461 T	
236 K	706 A	+1:194915462 194915462 A	K
236	707 A	+1:194915463 194915463 A	
236	708 A	+1:194915464 194915464 A	
237 C	709 T	+1:194915465 194915465 T	C
237	710 G	+1:194915466 194915466 G	
237	711 T	+1:194915467 194915467 T	
238 N	712 A	+1:194915468 194915468 A	N
238	713 A	+1:194915469 194915469 A	
238	714 C	+1:194915470 194915470 C	
239 M	715 A	+1:194915471 194915471 A	M
239	716 T	+1:194915472 194915472 T	
239	717 G	+1:194915473 194915473 G	
240 G	718 G	+1:194915474 194915474 G	G
240	719 G	+1:194915475 194915475 G	
240	720 T	+1:194915476 194915476 T	
241 Y	721 T	+1:194915477 194915477 T	Y
241	722 A	+1:194915478 194915478 A	
241	723 T	+1:194915479 194915479 T	
242 E	724 G	+1:194915480 194915480 G	E
242	725 A	+1:194915481 194915481 A	
242	726 A	+1:194915482 194915482 A	
243 Y	727 T	+1:194915483 194915483 T	Y
243	728 A	+1:194915484 194915484 A	
243	729 C	+1:194915485 194915485 C	
244 S	730 A	+1:194915486 194915486 A	S
244	731 G	+1:194915487 194915487 G	
244	732 T	+1:194915488 194915488 T	
245 E	733 G	+1:194915489 194915489 G	E
245	734 A	+1:194915490 194915490 A	
245	735 A	+1:194915491 194915491 A	
246 R	736 A	+1:194915492 194915492 A	R
246	737 G	+1:194915493 194915493 G	
246	738 A	+1:194915494 194915494 A	
247 G	739 G	+1:194915495 194915495 G	G
247	740 G	+1:194915496 194915496 G	
247	741 A	+1:194915497 194915497 A	
248 D	742 G	+1:194915498 194915498 G	D
248	743 A	+1:194915499 194915499 A	
248	744 T	+1:194915500 194915500 T	
249 A	745 G	+1:194915501 194915501 G	A
249	746 C	+1:194915502 194915502 C	
249	747 T	+1:194915503 194915503 T	
250 V	748 G	+1:194915504 194915504 G	V
250	749 T	+1:194915505 194915505 T	
250	750 A	+1:194915506 194915506 A	
251 C	751 T	+1:194915507 194915507 T	C
251	752 G	+1:194915508 194915508 G	
251	753 C	+1:194915509 194915509 C	
252 T	754 A	+1:194915510 194915510 A	T
252	755 C	+1:194915511 194915511 C	
252	756 T	+1:194915512 194915512 T	
253 E	757 G	+1:194915513 194915513 G	E
253	758 A	+1:194915514 194915514 A	
253	759 A	+1:194915515 194915515 A	
254 S	760 T	+1:194915516 194915516 T	S
254	761 C	+1:194915517 194915517 C	
254	762 T	+1:194915518 194915518 T	
255 G	763 G	+1:194915519 194915519 G	G
255	764 G	+1:194915520 194915520 G	
255	765 A	+1:194915521 194915521 A	
256 W	766 T	+1:194915522 194915522 T	W
256	767 G	+1:194915523 194915523 G	
256	768 G	+1:194915524 194915524 G	
257 R	769 C	+1:194915525 194915525 C	R
257	770 G	+1:194915526 194915526 G	
257	771 T	+1:194915527 194915527 T	
258 P	772 C	+1:194915528 194915528 C	P
258	773 C	+1:194915529 194915529 C	
258	774 G	+1:194915530 194915530 G	
259 L	775 T	+1:194915531 194915531 T	L
259	776 T	+1:194915532 194915532 T	
259	777 G	+1:194915533 194915533 G	
260 P	778 C	+1:194915534 194915534 C	P
260	779 C	+1:194915535 194915535 C	
260	780 T	+1:194915536 194915536 T	
261 S	781 T	+1:194915537 194915537 T	S
261	782 C	+1:194915538 194915538 C	
261	783 A	+1:194915539 194915539 A	
262 C	784 T	+1:194915540 194915540 T	C
262	785 G	+1:194915541 194915541 G	
262	786 T	+1:194915542 194915542 T	
263 E	787 G	+1:194915543 194915543 G	E
263	788 A	+1:194915544 194915544 A	
263	789 A	+1:194915545 194915545 A	
264 E	790 G	+1:194915546 194915546 G	E
264	791 A	+1:194920817 194920817 A	
264	792 A	+1:194920818 194920818 A	
265 K	793 A	+1:194920819 194920819 A	K
265	794 A	+1:194920820 194920820 A	
265	795 A	+1:194920821 194920821 A	
266 S	796 T	+1:194920822 194920822 T	S
266	797 C	+1:194920823 194920823 C	
266	798 A	+1:194920824 194920824 A	
267 C	799 T	+1:194920825 194920825 T	C
267	800 G	+1:194920826 194920826 G	
267	801 T	+1:194920827 194920827 T	
268 D	802 G	+1:194920828 194920828 G	D
268	803 A	+1:194920829 194920829 A	
268	804 T	+1:194920830 194920830 T	
269 N	805 A	+1:194920831 194920831 A	N
269	806 A	+1:194920832 194920832 A	
269	807 T	+1:194920833 194920833 T	
270 P	808 C	+1:194920834 194920834 C	P
270	809 C	+1:194920835 194920835 C	
270	810 T	+1:194920836 194920836 T	
271 Y	811 T	+1:194920837 194920837 T	Y
271	812 A	+1:194920838 194920838 A	
271	813 T	+1:194920839 194920839 T	
272 I	814 A	+1:194920840 194920840 A	I
272	815 T	+1:194920841 194920841 T	
272	816 T	+1:194920842 194920842 T	
273 P	817 C	+1:194920843 194920843 C	P
273	818 C	+1:194920844 194920844 C	
273	819 A	+1:194920845 194920845 A	
274 N	820 A	+1:194920846 194920846 A	N
274	821 A	+1:194920847 194920847 A	
274	822 T	+1:194920848 194920848 T	
275 G	823 G	+1:194920849 194920849 G	G
275	824 G	+1:194920850 194920850 G	
275	825 T	+1:194920851 194920851 T	
276 D	826 G	+1:194920852 194920852 G	D
276	827 A	+1:194920853 194920853 A	
276	828 C	+1:194920854 194920854 C	
277 Y	829 T	+1:194920855 194920855 T	Y
277	830 A	+1:194920856 194920856 A	
277	831 C	+1:194920857 194920857 C	
278 S	832 T	+1:194920858 194920858 T	S
278	833 C	+1:194920859 194920859 C	
278	834 A	+1:194920860 194920860 A	
279 P	835 C	+1:194920861 194920861 C	P
279	836 C	+1:194920862 194920862 C	
279	837 T	+1:194920863 194920863 T	
280 L	838 T	+1:194920864 194920864 T	L
280	839 T	+1:194920865 194920865 T	
280	840 A	+1:194920866 194920866 A	
281 R	841 A	+1:194920867 194920867 A	R
281	842 G	+1:194920868 194920868 G	
281	843 G	+1:194920869 194920869 G	
282 I	844 A	+1:194920870 194920870 A	I
282	845 T	+1:194920871 194920871 T	
282	846 T	+1:194920872 194920872 T	
283 K	847 A	+1:194920873 194920873 A	K
283	848 A	+1:194920874 194920874 A	
283	849 A	+1:194920875 194920875 A	
284 H	850 C	+1:194920876 194920876 C	H
284	851 A	+1:194920877 194920877 A	
284	852 C	+1:194920878 194920878 C	
285 R	853 A	+1:194920879 194920879 A	R
285	854 G	+1:194920880 194920880 G	
285	855 A	+1:194920881 194920881 A	
286 T	856 A	+1:194920882 194920882 A	T
286	857 C	+1:194920883 194920883 C	
286	858 T	+1:194920884 194920884 T	
287 G	859 G	+1:194920885 194920885 G	G
287	860 G	+1:194920886 194920886 G	
287	861 A	+1:194920887 194920887 A	
288 D	862 G	+1:194920888 194920888 G	D
288	863 A	+1:194920889 194920889 A	
288	864 T	+1:194920890 194920890 T	
289 E	865 G	+1:194920891 194920891 G	E
289	866 A	+1:194920892 194920892 A	
289	867 A	+1:194920893 194920893 A	
290 I	868 A	+1:194920894 194920894 A	I
290	869 T	+1:194920895 194920895 T	
290	870 C	+1:194920896 194920896 C	
291 T	871 A	+1:194920897 194920897 A	T
291	872 C	+1:194920898 194920898 C	
291	873 G	+1:194920899 194920899 G	
292 Y	874 T	+1:194920900 194920900 T	Y
292	875 A	+1:194920901 194920901 A	
292	876 C	+1:194920902 194920902 C	
293 Q	877 C	+1:194920903 194920903 C	Q
293	878 A	+1:194920904 194920904 A	
293	879 G	+1:194920905 194920905 G	
294 C	880 T	+1:194920906 194920906 T	C
294	881 G	+1:194920907 194920907 G	
294	882 T	+1:194920908 194920908 T	
295 R	883 A	+1:194920909 194920909 A	R
295	884 G	+1:194920910 194920910 G	
295	885 A	+1:194920911 194920911 A	
296 N	886 A	+1:194920912 194920912 A	N
296	887 A	+1:194920913 194920913 A	
296	888 T	+1:194920914 194920914 T	
297 G	889 G	+1:194920915 194920915 G	G
297	890 G	+1:194920916 194920916 G	
297	891 T	+1:194920917 194920917 T	
298 F	892 T	+1:194920918 194920918 T	F
298	893 T	+1:194920919 194920919 T	
298	894 T	+1:194920920 194920920 T	
299 Y	895 T	+1:194920921 194920921 T	Y
299	896 A	+1:194920922 194920922 A	
299	897 T	+1:194920923 194920923 T	
300 P	898 C	+1:194920924 194920924 C	P
300	899 C	+1:194920925 194920925 C	
300	900 T	+1:194920926 194920926 T	
301 A	901 G	+1:194920927 194920927 G	A
301	902 C	+1:194920928 194920928 C	
301	903 A	+1:194920929 194920929 A	
302 T	904 A	+1:194920930 194920930 A	T
302	905 C	+1:194920931 194920931 C	
302	906 C	+1:194920932 194920932 C	
303 R	907 C	+1:194920933 194920933 C	R
303	908 G	+1:194920934 194920934 G	
303	909 G	+1:194920935 194920935 G	
304 G	910 G	+1:194920936 194920936 G	G
304	911 G	+1:194920937 194920937 G	
304	912 A	+1:194920938 194920938 A	
305 N	913 A	+1:194920939 194920939 A	N
305	914 A	+1:194920940 194920940 A	
305	915 T	+1:194920941 194920941 T	
306 T	916 A	+1:194920942 194920942 A	T
306	917 C	+1:194920943 194920943 C	
306	918 A	+1:194920944 194920944 A	
307 A	919 G	+1:194920945 194920945 G	A
307	920 C	+1:194920946 194920946 C	
307	921 A	+1:194920947 194920947 A	
308 K	922 A	+1:194920948 194920948 A	K
308	923 A	+1:194920949 194920949 A	
308	924 A	+1:194920950 194920950 A	
309 C	925 T	+1:194920951 194920951 T	C
309	926 G	+1:194920952 194920952 G	
309	927 C	+1:194920953 194920953 C	
310 T	928 A	+1:194920954 194920954 A	T
310	929 C	+1:194920955 194920955 C	
310	930 A	+1:194920956 194920956 A	
311 S	931 A	+1:194920957 194920957 A	S
311	932 G	+1:194920958 194920958 G	
311	933 T	+1:194920959 194920959 T	
312 T	934 A	+1:194920960 194920960 A	T
312	935 C	+1:194920961 194920961 C	
312	936 T	+1:194920962 194920962 T	
313 G	937 G	+1:194920963 194920963 G	G
313	938 G	+1:194920964 194920964 G	
313	939 C	+1:194920965 194920965 C	
314 W	940 T	+1:194920966 194920966 T	W
314	941 G	+1:194920967 194920967 G	
314	942 G	+1:194920968 194920968 G	
315 I	943 A	+1:194920969 194920969 A	I
315	944 T	+1:194920970 194920970 T	
315	945 A	+1:194920971 194920971 A	
316 P	946 C	+1:194920972 194920972 C	P
316	947 C	+1:194920973 194920973 C	
316	948 T	+1:194920974 194920974 T	
317 A	949 G	+1:194920975 194920975 G	A
317	950 C	+1:194920976 194920976 C	
317	951 T	+1:194920977 194920977 T	
318 P	952 C	+1:194920978 194920978 C	P
318	953 C	+1:194920979 194920979 C	
318	954 G	+1:194920980 194920980 G	
319 R	955 A	+1:194920981 194920981 A	R
319	956 G	+1:194920982 194920982 G	
319	957 A	+1:194920983 194920983 A	
320 C	958 T	+1:194920984 194920984 T	C
320	959 G	+1:194920985 194920985 G	
320	960 T	+1:194920986 194920986 T	
321 T	961 A	+1:194920987 194920987 A	T
321	962 C	+1:194920988 194920988 C	
321	963 C	+1:194920989 194920989 C	
322 L	964 T	+1:194920990 194920990 T	L
322	965 T	+1:194925173 194925173 T	
322	966 G	+1:194925174 194925174 G	
323 K	967 A	+1:194925175 194925175 A	K
323	968 A	+1:194925176 194925176 A	
323	969 A	+1:194925177 194925177 A	
324 P	970 C	+1:194925178 194925178 C	P
324	971 C	+1:194925179 194925179 C	
324	972 T	+1:194925180 194925180 T	
325 C	973 T	+1:194925181 194925181 T	C
325	974 G	+1:194925182 194925182 G	
325	975 T	+1:194925183 194925183 T	
326 D	976 G	+1:194925184 194925184 G	D
326	977 A	+1:194925185 194925185 A	
326	978 T	+1:194925186 194925186 T	
327 Y	979 T	+1:194925187 194925187 T	Y
327	980 A	+1:194925188 194925188 A	
327	981 T	+1:194925189 194925189 T	
328 P	982 C	+1:194925190 194925190 C	P
328	983 C	+1:194925191 194925191 C	
328	984 A	+1:194925192 194925192 A	
329 D	985 G	+1:194925193 194925193 G	D
329	986 A	+1:194925194 194925194 A	
329	987 C	+1:194925195 194925195 C	
330 I	988 A	+1:194925196 194925196 A	I
330	989 T	+1:194925197 194925197 T	
330	990 T	+1:194925198 194925198 T	
331 K	991 A	+1:194925199 194925199 A	K
331	992 A	+1:194925200 194925200 A	
331	993 A	+1:194925201 194925201 A	
332 H	994 C	+1:194925202 194925202 C	H
332	995 A	+1:194925203 194925203 A	
332	996 T	+1:194925204 194925204 T	
333 G	997 G	+1:194925205 194925205 G	G
333	998 G	+1:194925206 194925206 G	
333	999 A	+1:194925207 194925207 A	
334 G	1000 G	+1:194925208 194925208 G	G
334	1001 G	+1:194925209 194925209 G	
334	1002 T	+1:194925210 194925210 T	
335 L	1003 C	+1:194925211 194925211 C	L
335	1004 T	+1:194925212 194925212 T	
335	1005 A	+1:194925213 194925213 A	
336 Y	1006 T	+1:194925214 194925214 T	Y
336	1007 A	+1:194925215 194925215 A	
336	1008 T	+1:194925216 194925216 T	
337 H	1009 C	+1:194925217 194925217 C	H
337	1010 A	+1:194925218 194925218 A	
337	1011 T	+1:194925219 194925219 T	
338 E	1012 G	+1:194925220 194925220 G	E
338	1013 A	+1:194925221 194925221 A	
338	1014 G	+1:194925222 194925222 G	
339 N	1015 A	+1:194925223 194925223 A	N
339	1016 A	+1:194925224 194925224 A	
339	1017 T	+1:194925225 194925225 T	
340 M	1018 A	+1:194925226 194925226 A	M
340	1019 T	+1:194925227 194925227 T	
340	1020 G	+1:194925228 194925228 G	
341 R	1021 C	+1:194925229 194925229 C	R
341	1022 G	+1:194925230 194925230 G	
341	1023 T	+1:194925231 194925231 T	
342 R	1024 A	+1:194925232 194925232 A	R
342	1025 G	+1:194925233 194925233 G	
342	1026 A	+1:194925234 194925234 A	
343 P	1027 C	+1:194925235 194925235 C	P
343	1028 C	+1:194925236 194925236 C	
343	1029 A	+1:194925237 194925237 A	
344 Y	1030 T	+1:194925238 194925238 T	Y
344	1031 A	+1:194925239 194925239 A	
344	1032 C	+1:194925240 194925240 C	
345 F	1033 T	+1:194925241 194925241 T	F
345	1034 T	+1:194925242 194925242 T	
345	1035 T	+1:194925243 194925243 T	
346 P	1036 C	+1:194925244 194925244 C	P
346	1037 C	+1:194925245 194925245 C	
346	1038 A	+1:194925246 194925246 A	
347 V	1039 G	+1:194925247 194925247 G	V
347	1040 T	+1:194925248 194925248 T	
347	1041 A	+1:194925249 194925249 A	
348 A	1042 G	+1:194925250 194925250 G	A
348	1043 C	+1:194925251 194925251 C	
348	1044 T	+1:194925252 194925252 T	
349 V	1045 G	+1:194925253 194925253 G	V
349	1046 T	+1:194925254 194925254 T	
349	1047 A	+1:194925255 194925255 A	
350 G	1048 G	+1:194925256 194925256 G	G
350	1049 G	+1:194925257 194925257 G	
350	1050 A	+1:194925258 194925258 A	
351 K	1051 A	+1:194925259 194925259 A	K
351	1052 A	+1:194925260 194925260 A	
351	1053 A	+1:194925261 194925261 A	
352 Y	1054 T	+1:194925262 194925262 T	Y
352	1055 A	+1:194925263 194925263 A	
352	1056 T	+1:194925264 194925264 T	
353 Y	1057 T	+1:194925265 194925265 T	Y
353	1058 A	+1:194925266 194925266 A	
353	1059 C	+1:194925267 194925267 C	
354 S	1060 T	+1:194925268 194925268 T	S
354	1061 C	+1:194925269 194925269 C	
354	1062 C	+1:194925270 194925270 C	
355 Y	1063 T	+1:194925271 194925271 T	Y
355	1064 A	+1:194925272 194925272 A	
355	1065 T	+1:194925273 194925273 T	
356 Y	1066 T	+1:194925274 194925274 T	Y
356	1067 A	+1:194925275 194925275 A	
356	1068 C	+1:194925276 194925276 C	
357 C	1069 T	+1:194925277 194925277 T	C
357	1070 G	+1:194925278 194925278 G	
357	1071 T	+1:194925279 194925279 T	
358 D	1072 G	+1:194925280 194925280 G	D
358	1073 A	+1:194925281 194925281 A	
358	1074 T	+1:194925282 194925282 T	
359 E	1075 G	+1:194925283 194925283 G	E
359	1076 A	+1:194925284 194925284 A	
359	1077 A	+1:194925285 194925285 A	
360 H	1078 C	+1:194925286 194925286 C	H
360	1079 A	+1:194925287 194925287 A	
360	1080 T	+1:194925288 194925288 T	
361 F	1081 T	+1:194925289 194925289 T	F
361	1082 T	+1:194925290 194925290 T	
361	1083 T	+1:194925291 194925291 T	
362 E	1084 G	+1:194925292 194925292 G	E
362	1085 A	+1:194925293 194925293 A	
362	1086 G	+1:194925294 194925294 G	
363 T	1087 A	+1:194925295 194925295 A	T
363	1088 C	+1:194925296 194925296 C	
363	1089 T	+1:194925297 194925297 T	
364 P	1090 C	+1:194925298 194925298 C	P
364	1091 C	+1:194925299 194925299 C	
364	1092 G	+1:194925300 194925300 G	
365 S	1093 T	+1:194925301 194925301 T	S
365	1094 C	+1:194925302 194925302 C	
365	1095 A	+1:194925303 194925303 A	
366 G	1096 G	+1:194925304 194925304 G	G
366	1097 G	+1:194925305 194925305 G	
366	1098 A	+1:194925306 194925306 A	
367 S	1099 A	+1:194925307 194925307 A	S
367	1100 G	+1:194925308 194925308 G	
367	1101 T	+1:194925309 194925309 T	
368 Y	1102 T	+1:194925310 194925310 T	Y
368	1103 A	+1:194925311 194925311 A	
368	1104 C	+1:194925312 194925312 C	
369 W	1105 T	+1:194925313 194925313 T	W
369	1106 G	+1:194925314 194925314 G	
369	1107 G	+1:194925315 194925315 G	
370 D	1108 G	+1:194925316 194925316 G	D
370	1109 A	+1:194925317 194925317 A	
370	1110 T	+1:194925318 194925318 T	
371 H	1111 C	+1:194925319 194925319 C	H
371	1112 A	+1:194925320 194925320 A	
371	1113 C	+1:194925321 194925321 C	
372 I	1114 A	+1:194925322 194925322 A	I
372	1115 T	+1:194925323 194925323 T	
372	1116 T	+1:194925324 194925324 T	
373 H	1117 C	+1:194925325 194925325 C	H
373	1118 A	+1:194925326 194925326 A	
373	1119 T	+1:194925327 194925327 T	
374 C	1120 T	+1:194925328 194925328 T	C
374	1121 G	+1:194925329 194925329 G	
374	1122 C	+1:194925330 194925330 C	
375 T	1123 A	+1:194925331 194925331 A	T
375	1124 C	+1:194925332 194925332 C	
375	1125 A	+1:194925333 194925333 A	
376 Q	1126 C	+1:194925334 194925334 C	Q
376	1127 A	+1:194925335 194925335 A	
376	1128 A	+1:194925336 194925336 A	
377 D	1129 G	+1:194925337 194925337 G	D
377	1130 A	+1:194925338 194925338 A	
377	1131 T	+1:194925339 194925339 T	
378 G	1132 G	+1:194925340 194925340 G	G
378	1133 G	+1:194925341 194925341 G	
378	1134 A	+1:194925342 194925342 A	
379 W	1135 T	+1:194925343 194925343 T	W
379	1136 G	+1:194925344 194925344 G	
379	1137 G	+1:194925345 194925345 G	
380 S	1138 T	+1:194925346 194925346 T	S
380	1139 C	+1:194925347 194925347 C	
380	1140 G	+1:194925348 194925348 G	
381 P	1141 C	+1:194925349 194925349 C	P
381	1142 C	+1:194925350 194925350 C	
381	1143 A	+1:194925351 194925351 A	
382 A	1144 G	+1:194925352 194925352 G	A
382	1145 C	+1:194925353 194925353 C	
382	1146 A	+1:194925354 194925354 A	
383 V	1147 G	+1:194925355 194925355 G	V
383	1148 T	+1:194925356 194925356 T	
383	1149 A	+1:194925357 194925357 A	
384 P	1150 C	+1:194925358 194925358 C	P
384	1151 C	+1:194925359 194925359 C	
384	1152 A	+1:194925360 194925360 A	
385 C	1153 T	+1:194925361 194925361 T	C
385	1154 G	+1:194925362 194925362 G	
385	1155 C	+1:194925363 194925363 C	
386 L	1156 C	+1:194925364 194925364 C	L
386	1157 T	+1:194925365 194925365 T	
386	1158 C	+1:194925366 194925366 C	
387 R	1159 A	+1:194925367 194925367 A	R
387	1160 G	+1:194925816 194925816 G	
387	1161 A	+1:194925817 194925817 A	
388 K	1162 A	+1:194925818 194925818 A	K
388	1163 A	+1:194925819 194925819 A	
388	1164 A	+1:194925820 194925820 A	
389 C	1165 T	+1:194925821 194925821 T	C
389	1166 G	+1:194925822 194925822 G	
389	1167 T	+1:194925823 194925823 T	
390 Y	1168 T	+1:194925824 194925824 T	Y
390	1169 A	+1:194925825 194925825 A	
390	1170 T	+1:194925826 194925826 T	
391 F	1171 T	+1:194925827 194925827 T	F
391	1172 T	+1:194925828 194925828 T	
391	1173 T	+1:194925829 194925829 T	
392 P	1174 C	+1:194925830 194925830 C	P
392	1175 C	+1:194925831 194925831 C	
392	1176 T	+1:194925832 194925832 T	
393 Y	1177 T	+1:194925833 194925833 T	Y
393	1178 A	+1:194925834 194925834 A	
393	1179 T	+1:194925835 194925835 T	
394 L	1180 T	+1:194925836 194925836 T	L
394	1181 T	+1:194925837 194925837 T	
394	1182 G	+1:194925838 194925838 G	
395 E	1183 G	+1:194925839 194925839 G	E
395	1184 A	+1:194925840 194925840 A	
395	1185 A	+1:194925841 194925841 A	
396 N	1186 A	+1:194925842 194925842 A	N
396	1187 A	+1:194925843 194925843 A	
396	1188 T	+1:194925844 194925844 T	
397 G	1189 G	+1:194925845 194925845 G	G
397	1190 G	+1:194925846 194925846 G	
397	1191 A	+1:194925847 194925847 A	
398 Y	1192 T	+1:194925848 194925848 T	Y
398	1193 A	+1:194925849 194925849 A	
398	1194 T	+1:194925850 194925850 T	
399 N	1195 A	+1:194925851 194925851 A	N
399	1196 A	+1:194925852 194925852 A	
399	1197 T	+1:194925853 194925853 T	
400 Q	1198 C	+1:194925854 194925854 C	Q
400	1199 A	+1:194925855 194925855 A	
400	1200 A	+1:194925856 194925856 A	
401 N	1201 A	+1:194925857 194925857 A	N
401	1202 A	+1:194925858 194925858 A	
401	1203 T	+1:194925859 194925859 T	
402 H	1204 C	+1:194925860 194925860 C	H
402	1205 A	+1:194925861 194925861 A	
402	1206 T	+1:194925862 194925862 T	
403 G	1207 G	+1:194925863 194925863 G	G
403	1208 G	+1:194925864 194925864 G	
403	1209 A	+1:194925865 194925865 A	
404 R	1210 A	+1:194925866 194925866 A	R
404	1211 G	+1:194925867 194925867 G	
404	1212 A	+1:194925868 194925868 A	
405 K	1213 A	+1:194925869 194925869 A	K
405	1214 A	+1:194925870 194925870 A	
405	1215 G	+1:194925871 194925871 G	
406 F	1216 T	+1:194925872 194925872 T	F
406	1217 T	+1:194925873 194925873 T	
406	1218 T	+1:194925874 194925874 T	
407 V	1219 G	+1:194925875 194925875 G	V
407	1220 T	+1:194925876 194925876 T	
407	1221 A	+1:194925877 194925877 A	
408 Q	1222 C	+1:194925878 194925878 C	Q
408	1223 A	+1:194925879 194925879 A	
408	1224 G	+1:194925880 194925880 G	
409 G	1225 G	+1:194925881 194925881 G	G
409	1226 G	+1:194925882 194925882 G	
409	1227 T	+1:194925883 194925883 T	
410 K	1228 A	+1:194925884 194925884 A	K
410	1229 A	+1:194925885 194925885 A	
410	1230 A	+1:194925886 194925886 A	
411 S	1231 T	+1:194925887 194925887 T	S
411	1232 C	+1:194925888 194925888 C	
411	1233 T	+1:194925889 194925889 T	
412 I	1234 A	+1:194925890 194925890 A	I
412	1235 T	+1:194925891 194925891 T	
412	1236 A	+1:194925892 194925892 A	
413 D	1237 G	+1:194925893 194925893 G	D
413	1238 A	+1:194925894 194925894 A	
413	1239 C	+1:194925895 194925895 C	
414 V	1240 G	+1:194925896 194925896 G	V
414	1241 T	+1:194925897 194925897 T	
414	1242 T	+1:194925898 194925898 T	
415 A	1243 G	+1:194925899 194925899 G	A
415	1244 C	+1:194925900 194925900 C	
415	1245 C	+1:194925901 194925901 C	
416 C	1246 T	+1:194925902 194925902 T	C
416	1247 G	+1:194925903 194925903 G	
416	1248 C	+1:194925904 194925904 C	
417 H	1249 C	+1:194925905 194925905 C	H
417	1250 A	+1:194925906 194925906 A	
417	1251 T	+1:194925907 194925907 T	
418 P	1252 C	+1:194925908 194925908 C	P
418	1253 C	+1:194925909 194925909 C	
418	1254 T	+1:194925910 194925910 T	
419 G	1255 G	+1:194925911 194925911 G	G
419	1256 G	+1:194925912 194925912 G	
419	1257 C	+1:194925913 194925913 C	
420 Y	1258 T	+1:194925914 194925914 T	Y
420	1259 A	+1:194925915 194925915 A	
420	1260 C	+1:194925916 194925916 C	
421 A	1261 G	+1:194925917 194925917 G	A
421	1262 C	+1:194925918 194925918 C	
421	1263 T	+1:194925919 194925919 T	
422 L	1264 C	+1:194925920 194925920 C	L
422	1265 T	+1:194925921 194925921 T	
422	1266 T	+1:194925922 194925922 T	
423 P	1267 C	+1:194925923 194925923 C	P
423	1268 C	+1:194925924 194925924 C	
423	1269 A	+1:194925925 194925925 A	
424 K	1270 A	+1:194925926 194925926 A	K
424	1271 A	+1:194925927 194925927 A	
424	1272 A	+1:194925928 194925928 A	
425 A	1273 G	+1:194925929 194925929 G	A
425	1274 C	+1:194925930 194925930 C	
425	1275 G	+1:194925931 194925931 G	
426 Q	1276 C	+1:194925932 194925932 C	Q
426	1277 A	+1:194925933 194925933 A	
426	1278 G	+1:194925934 194925934 G	
427 T	1279 A	+1:194925935 194925935 A	T
427	1280 C	+1:194925936 194925936 C	
427	1281 C	+1:194925937 194925937 C	
428 T	1282 A	+1:194925938 194925938 A	T
428	1283 C	+1:194925939 194925939 C	
428	1284 A	+1:194925940 194925940 A	
429 V	1285 G	+1:194925941 194925941 G	V
429	1286 T	+1:194925942 194925942 T	
429	1287 T	+1:194925943 194925943 T	
430 T	1288 A	+1:194925944 194925944 A	T
430	1289 C	+1:194925945 194925945 C	
430	1290 A	+1:194925946 194925946 A	
431 C	1291 T	+1:194925947 194925947 T	C
431	1292 G	+1:194925948 194925948 G	
431	1293 T	+1:194925949 194925949 T	
432 M	1294 A	+1:194925950 194925950 A	M
432	1295 T	+1:194925951 194925951 T	
432	1296 G	+1:194925952 194925952 G	
433 E	1297 G	+1:194925953 194925953 G	E
433	1298 A	+1:194925954 194925954 A	
433	1299 G	+1:194925955 194925955 G	
434 N	1300 A	+1:194925956 194925956 A	N
434	1301 A	+1:194925957 194925957 A	
434	1302 T	+1:194925958 194925958 T	
435 G	1303 G	+1:194925959 194925959 G	G
435	1304 G	+1:194925960 194925960 G	
435	1305 C	+1:194925961 194925961 C	
436 W	1306 T	+1:194925962 194925962 T	W
436	1307 G	+1:194925963 194925963 G	
436	1308 G	+1:194925964 194925964 G	
437 S	1309 T	+1:194925965 194925965 T	S
437	1310 C	+1:194925966 194925966 C	
437	1311 T	+1:194925967 194925967 T	
438 P	1312 C	+1:194925968 194925968 C	P
438	1313 C	+1:194925969 194925969 C	
438	1314 T	+1:194925970 194925970 T	
439 T	1315 A	+1:194925971 194925971 A	T
439	1316 C	+1:194925972 194925972 C	
439	1317 T	+1:194925973 194925973 T	
440 P	1318 C	+1:194925974 194925974 C	P
440	1319 C	+1:194925975 194925975 C	
440	1320 C	+1:194925976 194925976 C	
441 R	1321 A	+1:194925977 194925977 A	R
441	1322 G	+1:194925978 194925978 G	
441	1323 A	+1:194925979 194925979 A	
442 C	1324 T	+1:194925980 194925980 T	C
442	1325 G	+1:194925981 194925981 G	
442	1326 C	+1:194925982 194925982 C	
443 I	1327 A	+1:194925983 194925983 A	I
443	1328 T	+1:194925984 194925984 T	
443	1329 C	+1:194925985 194925985 C	
444 R	1330 C	+1:194925986 194925986 C	R
444	1331 G	+1:194925987 194925987 G	
444	1332 T	+1:194925988 194925988 T	
445 V	1333 G	+1:194925989 194925989 G	V
445	1334 T	+1:194925990 194925990 T	
445	1335 C	+1:194925991 194925991 C	
446 K	1336 A	+1:194925992 194925992 A	K
446	1337 A	+1:194949488 194949488 A	
446	1338 A	+1:194949489 194949489 A	
447 T	1339 A	+1:194949490 194949490 A	T
447	1340 C	+1:194949491 194949491 C	
447	1341 A	+1:194949492 194949492 A	
448 C	1342 T	+1:194949493 194949493 T	C
448	1343 G	+1:194949494 194949494 G	
448	1344 T	+1:194949495 194949495 T	
449 S	1345 T	+1:194949496 194949496 T	S
449	1346 C	+1:194949497 194949497 C	
449	1347 C	+1:194949498 194949498 C	
450 K	1348 A	+1:194949499 194949499 A	K
450	1349 A	+1:194949500 194949500 A	
450	1350 A	+1:194949501 194949501 A	
451 S	1351 T	+1:194949502 194949502 T	S
451	1352 C	+1:194949503 194949503 C	
451	1353 A	+1:194949504 194949504 A	
452 S	1354 A	+1:194949505 194949505 A	S
452	1355 G	+1:194949506 194949506 G	
452	1356 T	+1:194949507 194949507 T	
453 I	1357 A	+1:194949508 194949508 A	I
453	1358 T	+1:194949509 194949509 T	
453	1359 A	+1:194949510 194949510 A	
454 D	1360 G	+1:194949511 194949511 G	D
454	1361 A	+1:194949512 194949512 A	
454	1362 T	+1:194949513 194949513 T	
455 I	1363 A	+1:194949514 194949514 A	I
455	1364 T	+1:194949515 194949515 T	
455	1365 T	+1:194949516 194949516 T	
456 E	1366 G	+1:194949517 194949517 G	E
456	1367 A	+1:194949518 194949518 A	
456	1368 G	+1:194949519 194949519 G	
457 N	1369 A	+1:194949520 194949520 A	N
457	1370 A	+1:194949521 194949521 A	
457	1371 T	+1:194949522 194949522 T	
458 G	1372 G	+1:194949523 194949523 G	G
458	1373 G	+1:194949524 194949524 G	
458	1374 G	+1:194949525 194949525 G	
459 F	1375 T	+1:194949526 194949526 T	F
459	1376 T	+1:194949527 194949527 T	
459	1377 T	+1:194949528 194949528 T	
460 I	1378 A	+1:194949529 194949529 A	I
460	1379 T	+1:194949530 194949530 T	
460	1380 T	+1:194949531 194949531 T	
461 S	1381 T	+1:194949532 194949532 T	S
461	1382 C	+1:194949533 194949533 C	
461	1383 T	+1:194949534 194949534 T	
462 E	1384 G	+1:194949535 194949535 G	E
462	1385 A	+1:194949536 194949536 A	
462	1386 A	+1:194949537 194949537 A	
463 S	1387 T	+1:194949538 194949538 T	S
463	1388 C	+1:194949539 194949539 C	
463	1389 T	+1:194949540 194949540 T	
464 Q	1390 C	+1:194949541 194949541 C	Q
464	1391 A	+1:194949542 194949542 A	
464	1392 G	+1:194949543 194949543 G	
465 Y	1393 T	+1:194949544 194949544 T	Y
465	1394 A	+1:194949545 194949545 A	
465	1395 T	+1:194949546 194949546 T	
466 T	1396 A	+1:194949547 194949547 A	T
466	1397 C	+1:194949548 194949548 C	
466	1398 A	+1:194949549 194949549 A	
467 Y	1399 T	+1:194949550 194949550 T	Y
467	1400 A	+1:194949551 194949551 A	
467	1401 T	+1:194949552 194949552 T	
468 A	1402 G	+1:194949553 194949553 G	A
468	1403 C	+1:194949554 194949554 C	
468	1404 C	+1:194949555 194949555 C	
469 L	1405 T	+1:194949556 194949556 T	L
469	1406 T	+1:194949557 194949557 T	
469	1407 A	+1:194949558 194949558 A	
470 K	1408 A	+1:194949559 194949559 A	K
470	1409 A	+1:194949560 194949560 A	
470	1410 A	+1:194949561 194949561 A	
471 E	1411 G	+1:194949562 194949562 G	E
471	1412 A	+1:194949563 194949563 A	
471	1413 A	+1:194949564 194949564 A	
472 K	1414 A	+1:194949565 194949565 A	K
472	1415 A	+1:194949566 194949566 A	
472	1416 A	+1:194949567 194949567 A	
473 A	1417 G	+1:194949568 194949568 G	A
473	1418 C	+1:194949569 194949569 C	
473	1419 G	+1:194949570 194949570 G	
474 K	1420 A	+1:194949571 194949571 A	K
474	1421 A	+1:194949572 194949572 A	
474	1422 A	+1:194949573 194949573 A	
475 Y	1423 T	+1:194949574 194949574 T	Y
475	1424 A	+1:194949575 194949575 A	
475	1425 T	+1:194949576 194949576 T	
476 Q	1426 C	+1:194949577 194949577 C	Q
476	1427 A	+1:194949578 194949578 A	
476	1428 A	+1:194949579 194949579 A	
477 C	1429 T	+1:194949580 194949580 T	C
477	1430 G	+1:194949581 194949581 G	
477	1431 C	+1:194949582 194949582 C	
478 K	1432 A	+1:194949583 194949583 A	K
478	1433 A	+1:194949584 194949584 A	
478	1434 A	+1:194949585 194949585 A	
479 L	1435 C	+1:194949586 194949586 C	L
479	1436 T	+1:194949587 194949587 T	
479	1437 A	+1:194949588 194949588 A	
480 G	1438 G	+1:194949589 194949589 G	G
480	1439 G	+1:194949590 194949590 G	
480	1440 A	+1:194949591 194949591 A	
481 Y	1441 T	+1:194949592 194949592 T	Y
481	1442 A	+1:194949593 194949593 A	
481	1443 T	+1:194949594 194949594 T	
482 V	1444 G	+1:194949595 194949595 G	V
482	1445 T	+1:194949596 194949596 T	
482	1446 A	+1:194949597 194949597 A	
483 T	1447 A	+1:194949598 194949598 A	T
483	1448 C	+1:194949599 194949599 C	
483	1449 A	+1:194949600 194949600 A	
484 A	1450 G	+1:194949601 194949601 G	A
484	1451 C	+1:194949602 194949602 C	
484	1452 A	+1:194949603 194949603 A	
485 D	1453 G	+1:194949604 194949604 G	D
485	1454 A	+1:194949605 194949605 A	
485	1455 T	+1:194949606 194949606 T	
486 G	1456 G	+1:194949607 194949607 G	G
486	1457 G	+1:194949608 194949608 G	
486	1458 T	+1:194949609 194949609 T	
487 E	1459 G	+1:194949610 194949610 G	E
487	1460 A	+1:194949611 194949611 A	
487	1461 A	+1:194949612 194949612 A	
488 T	1462 A	+1:194949613 194949613 A	T
488	1463 C	+1:194949614 194949614 C	
488	1464 A	+1:194949615 194949615 A	
489 S	1465 T	+1:194949616 194949616 T	S
489	1466 C	+1:194949617 194949617 C	
489	1467 A	+1:194949618 194949618 A	
490 G	1468 G	+1:194949619 194949619 G	G
490	1469 G	+1:194949620 194949620 G	
490	1470 A	+1:194949621 194949621 A	
491 S	1471 T	+1:194949622 194949622 T	S
491	1472 C	+1:194949623 194949623 C	
491	1473 A	+1:194949624 194949624 A	
492 I	1474 A	+1:194949625 194949625 A	I
492	1475 T	+1:194949626 194949626 T	
492	1476 T	+1:194949627 194949627 T	
493 T	1477 A	+1:194949628 194949628 A	T
493	1478 C	+1:194949629 194949629 C	
493	1479 A	+1:194949630 194949630 A	
494 C	1480 T	+1:194949631 194949631 T	C
494	1481 G	+1:194949632 194949632 G	
494	1482 T	+1:194949633 194949633 T	
495 G	1483 G	+1:194949634 194949634 G	G
495	1484 G	+1:194949635 194949635 G	
495	1485 G	+1:194949636 194949636 G	
496 K	1486 A	+1:194949637 194949637 A	K
496	1487 A	+1:194949638 194949638 A	
496	1488 A	+1:194949639 194949639 A	
497 D	1489 G	+1:194949640 194949640 G	D
497	1490 A	+1:194949641 194949641 A	
497	1491 T	+1:194949642 194949642 T	
498 G	1492 G	+1:194949643 194949643 G	G
498	1493 G	+1:194949644 194949644 G	
498	1494 A	+1:194949645 194949645 A	
499 W	1495 T	+1:194949646 194949646 T	W
499	1496 G	+1:194949647 194949647 G	
499	1497 G	+1:194949648 194949648 G	
500 S	1498 T	+1:194949649 194949649 T	S
500	1499 C	+1:194949650 194949650 C	
500	1500 A	+1:194949651 194949651 A	
501 A	1501 G	+1:194949652 194949652 G	A
501	1502 C	+1:194949653 194949653 C	
501	1503 T	+1:194949654 194949654 T	
502 Q	1504 C	+1:194949655 194949655 C	Q
502	1505 A	+1:194949656 194949656 A	
502	1506 A	+1:194949657 194949657 A	
503 P	1507 C	+1:194949658 194949658 C	P
503	1508 C	+1:194949659 194949659 C	
503	1509 C	+1:194949660 194949660 C	
504 T	1510 A	+1:194949661 194949661 A	T
504	1511 C	+1:194949662 194949662 C	
504	1512 G	+1:194949663 194949663 G	
505 C	1513 T	+1:194949664 194949664 T	C
505	1514 G	+1:194949665 194949665 G	
505	1515 C	+1:194949666 194949666 C	
506 I	1516 A	+1:194949667 194949667 A	I
506	1517 T	+1:194949668 194949668 T	
506	1518 T	+1:194949669 194949669 T	
507 K	1519 A	+1:194949670 194949670 A	K
507	1520 A	+1:194951346 194951346 A	
507	1521 A	+1:194951347 194951347 A	
508 S	1522 T	+1:194951348 194951348 T	S
508	1523 C	+1:194951349 194951349 C	
508	1524 T	+1:194951350 194951350 T	
509 C	1525 T	+1:194951351 194951351 T	C
509	1526 G	+1:194951352 194951352 G	
509	1527 T	+1:194951353 194951353 T	
510 D	1528 G	+1:194951354 194951354 G	D
510	1529 A	+1:194951355 194951355 A	
510	1530 T	+1:194951356 194951356 T	
511 I	1531 A	+1:194951357 194951357 A	I
511	1532 T	+1:194951358 194951358 T	
511	1533 C	+1:194951359 194951359 C	
512 P	1534 C	+1:194951360 194951360 C	P
512	1535 C	+1:194951361 194951361 C	
512	1536 A	+1:194951362 194951362 A	
513 V	1537 G	+1:194951363 194951363 G	V
513	1538 T	+1:194951364 194951364 T	
513	1539 A	+1:194951365 194951365 A	
514 F	1540 T	+1:194951366 194951366 T	F
514	1541 T	+1:194951367 194951367 T	
514	1542 T	+1:194951368 194951368 T	
515 M	1543 A	+1:194951369 194951369 A	M
515	1544 T	+1:194951370 194951370 T	
515	1545 G	+1:194951371 194951371 G	
516 N	1546 A	+1:194951372 194951372 A	N
516	1547 A	+1:194951373 194951373 A	
516	1548 T	+1:194951374 194951374 T	
517 A	1549 G	+1:194951375 194951375 G	A
517	1550 C	+1:194951376 194951376 C	
517	1551 C	+1:194951377 194951377 C	
518 R	1552 A	+1:194951378 194951378 A	R
518	1553 G	+1:194951379 194951379 G	
518	1554 A	+1:194951380 194951380 A	
519 T	1555 A	+1:194951381 194951381 A	T
519	1556 C	+1:194951382 194951382 C	
519	1557 T	+1:194951383 194951383 T	
520 K	1558 A	+1:194951384 194951384 A	K
520	1559 A	+1:194951385 194951385 A	
520	1560 A	+1:194951386 194951386 A	
521 N	1561 A	+1:194951387 194951387 A	N
521	1562 A	+1:194951388 194951388 A	
521	1563 T	+1:194951389 194951389 T	
522 D	1564 G	+1:194951390 194951390 G	D
522	1565 A	+1:194951391 194951391 A	
522	1566 C	+1:194951392 194951392 C	
523 F	1567 T	+1:194951393 194951393 T	F
523	1568 T	+1:194951394 194951394 T	
523	1569 C	+1:194951395 194951395 C	
524 T	1570 A	+1:194951396 194951396 A	T
524	1571 C	+1:194951397 194951397 C	
524	1572 A	+1:194951398 194951398 A	
525 W	1573 T	+1:194951399 194951399 T	W
525	1574 G	+1:194951400 194951400 G	
525	1575 G	+1:194951401 194951401 G	
526 F	1576 T	+1:194951402 194951402 T	F
526	1577 T	+1:194951403 194951403 T	
526	1578 T	+1:194951404 194951404 T	
527 K	1579 A	+1:194951405 194951405 A	K
527	1580 A	+1:194951406 194951406 A	
527	1581 G	+1:194951407 194951407 G	
528 L	1582 C	+1:194951408 194951408 C	L
528	1583 T	+1:194951409 194951409 T	
528	1584 G	+1:194951410 194951410 G	
529 N	1585 A	+1:194951411 194951411 A	N
529	1586 A	+1:194951412 194951412 A	
529	1587 T	+1:194951413 194951413 T	
530 D	1588 G	+1:194951414 194951414 G	D
530	1589 A	+1:194951415 194951415 A	
530	1590 C	+1:194951416 194951416 C	
531 T	1591 A	+1:194951417 194951417 A	T
531	1592 C	+1:194951418 194951418 C	
531	1593 A	+1:194951419 194951419 A	
532 L	1594 T	+1:194951420 194951420 T	L
532	1595 T	+1:194951421 194951421 T	
532	1596 G	+1:194951422 194951422 G	
533 D	1597 G	+1:194951423 194951423 G	D
533	1598 A	+1:194951424 194951424 A	
533	1599 C	+1:194951425 194951425 C	
534 Y	1600 T	+1:194951426 194951426 T	Y
534	1601 A	+1:194951427 194951427 A	
534	1602 T	+1:194951428 194951428 T	
535 E	1603 G	+1:194951429 194951429 G	E
535	1604 A	+1:194951430 194951430 A	
535	1605 A	+1:194951431 194951431 A	
536 C	1606 T	+1:194951432 194951432 T	C
536	1607 G	+1:194951433 194951433 G	
536	1608 C	+1:194951434 194951434 C	
537 H	1609 C	+1:194951435 194951435 C	H
537	1610 A	+1:194951436 194951436 A	
537	1611 T	+1:194951437 194951437 T	
538 D	1612 G	+1:194951438 194951438 G	D
538	1613 A	+1:194951439 194951439 A	
538	1614 T	+1:194951440 194951440 T	
539 G	1615 G	+1:194951441 194951441 G	G
539	1616 G	+1:194951442 194951442 G	
539	1617 T	+1:194951443 194951443 T	
540 Y	1618 T	+1:194951444 194951444 T	Y
540	1619 A	+1:194951445 194951445 A	
540	1620 T	+1:194951446 194951446 T	
541 E	1621 G	+1:194951447 194951447 G	E
541	1622 A	+1:194951448 194951448 A	
541	1623 A	+1:194951449 194951449 A	
542 S	1624 A	+1:194951450 194951450 A	S
542	1625 G	+1:194951451 194951451 G	
542	1626 C	+1:194951452 194951452 C	
543 N	1627 A	+1:194951453 194951453 A	N
543	1628 A	+1:194951454 194951454 A	
543	1629 T	+1:194951455 194951455 T	
544 T	1630 A	+1:194951456 194951456 A	T
544	1631 C	+1:194951457 194951457 C	
544	1632 T	+1:194951458 194951458 T	
545 G	1633 G	+1:194951459 194951459 G	G
545	1634 G	+1:194951460 194951460 G	
545	1635 A	+1:194951461 194951461 A	
546 S	1636 A	+1:194951462 194951462 A	S
546	1637 G	+1:194951463 194951463 G	
546	1638 C	+1:194951464 194951464 C	
547 T	1639 A	+1:194951465 194951465 A	T
547	1640 C	+1:194951466 194951466 C	
547	1641 C	+1:194951467 194951467 C	
548 T	1642 A	+1:194951468 194951468 A	T
548	1643 C	+1:194951469 194951469 C	
548	1644 T	+1:194951470 194951470 T	
549 G	1645 G	+1:194951471 194951471 G	G
549	1646 G	+1:194951472 194951472 G	
549	1647 T	+1:194951473 194951473 T	
550 S	1648 T	+1:194951474 194951474 T	S
550	1649 C	+1:194951475 194951475 C	
550	1650 C	+1:194951476 194951476 C	
551 I	1651 A	+1:194951477 194951477 A	I
551	1652 T	+1:194951478 194951478 T	
551	1653 A	+1:194951479 194951479 A	
552 V	1654 G	+1:194951480 194951480 G	V
552	1655 T	+1:194951481 194951481 T	
552	1656 G	+1:194951482 194951482 G	
553 C	1657 T	+1:194951483 194951483 T	C
553	1658 G	+1:194951484 194951484 G	
553	1659 T	+1:194951485 194951485 T	
554 G	1660 G	+1:194951486 194951486 G	G
554	1661 G	+1:194951487 194951487 G	
554	1662 T	+1:194951488 194951488 T	
555 Y	1663 T	+1:194951489 194951489 T	Y
555	1664 A	+1:194951490 194951490 A	
555	1665 C	+1:194951491 194951491 C	
556 N	1666 A	+1:194951492 194951492 A	N
556	1667 A	+1:194951493 194951493 A	
556	1668 T	+1:194951494 194951494 T	
557 G	1669 G	+1:194951495 194951495 G	G
557	1670 G	+1:194951496 194951496 G	
557	1671 T	+1:194951497 194951497 T	
558 W	1672 T	+1:194951498 194951498 T	W
558	1673 G	+1:194951499 194951499 G	
558	1674 G	+1:194951500 194951500 G	
559 S	1675 T	+1:194951501 194951501 T	S
559	1676 C	+1:194951502 194951502 C	
559	1677 T	+1:194951503 194951503 T	
560 D	1678 G	+1:194951504 194951504 G	D
560	1679 A	+1:194951505 194951505 A	
560	1680 T	+1:194951506 194951506 T	
561 L	1681 T	+1:194951507 194951507 T	L
561	1682 T	+1:194951508 194951508 T	
561	1683 A	+1:194951509 194951509 A	
562 P	1684 C	+1:194951510 194951510 C	P
562	1685 C	+1:194951511 194951511 C	
562	1686 C	+1:194951512 194951512 C	
563 I	1687 A	+1:194951513 194951513 A	I
563	1688 T	+1:194951514 194951514 T	
563	1689 A	+1:194951515 194951515 A	
564 C	1690 T	+1:194951516 194951516 T	C
564	1691 G	+1:194951517 194951517 G	
564	1692 T	+1:194951518 194951518 T	
565 Y	1693 T	+1:194951519 194951519 T	Y
565	1694 A	+1:194951520 194951520 A	
565	1695 T	+1:194951521 194951521 T	
566 E	1696 G	+1:194951522 194951522 G	E
566	1697 A	+1:194960874 194960874 A	
566	1698 A	+1:194960875 194960875 A	
567 R	1699 A	+1:194960876 194960876 A	R
567	1700 G	+1:194960877 194960877 G	
567	1701 A	+1:194960878 194960878 A	
568 E	1702 G	+1:194960879 194960879 G	E
568	1703 A	+1:194960880 194960880 A	
568	1704 A	+1:194960881 194960881 A	
569 C	1705 T	+1:194960882 194960882 T	C
569	1706 G	+1:194960883 194960883 G	
569	1707 C	+1:194960884 194960884 C	
570 E	1708 G	+1:194960885 194960885 G	E
570	1709 A	+1:194960886 194960886 A	
570	1710 A	+1:194960887 194960887 A	
571 L	1711 C	+1:194960888 194960888 C	L
571	1712 T	+1:194960889 194960889 T	
571	1713 T	+1:194960890 194960890 T	
572 P	1714 C	+1:194960891 194960891 C	P
572	1715 C	+1:194960892 194960892 C	
572	1716 T	+1:194960893 194960893 T	
573 K	1717 A	+1:194960894 194960894 A	K
573	1718 A	+1:194960895 194960895 A	
573	1719 A	+1:194960896 194960896 A	
574 I	1720 A	+1:194960897 194960897 A	I
574	1721 T	+1:194960898 194960898 T	
574	1722 A	+1:194960899 194960899 A	
575 D	1723 G	+1:194960900 194960900 G	D
575	1724 A	+1:194960901 194960901 A	
575	1725 T	+1:194960902 194960902 T	
576 V	1726 G	+1:194960903 194960903 G	V
576	1727 T	+1:194960904 194960904 T	
576	1728 A	+1:194960905 194960905 A	
577 H	1729 C	+1:194960906 194960906 C	H
577	1730 A	+1:194960907 194960907 A	
577	1731 C	+1:194960908 194960908 C	
578 L	1732 T	+1:194960909 194960909 T	L
578	1733 T	+1:194960910 194960910 T	
578	1734 A	+1:194960911 194960911 A	
579 V	1735 G	+1:194960912 194960912 G	V
579	1736 T	+1:194960913 194960913 T	
579	1737 T	+1:194960914 194960914 T	
580 P	1738 C	+1:194960915 194960915 C	P
580	1739 C	+1:194960916 194960916 C	
580	1740 T	+1:194960917 194960917 T	
581 D	1741 G	+1:194960918 194960918 G	D
581	1742 A	+1:194960919 194960919 A	
581	1743 T	+1:194960920 194960920 T	
582 R	1744 C	+1:194960921 194960921 C	R
582	1745 G	+1:194960922 194960922 G	
582	1746 C	+1:194960923 194960923 C	
583 K	1747 A	+1:194960924 194960924 A	K
583	1748 A	+1:194960925 194960925 A	
583	1749 G	+1:194960926 194960926 G	
584 K	1750 A	+1:194960927 194960927 A	K
584	1751 A	+1:194960928 194960928 A	
584	1752 A	+1:194960929 194960929 A	
585 D	1753 G	+1:194960930 194960930 G	D
585	1754 A	+1:194960931 194960931 A	
585	1755 C	+1:194960932 194960932 C	
586 Q	1756 C	+1:194960933 194960933 C	Q
586	1757 A	+1:194960934 194960934 A	
586	1758 G	+1:194960935 194960935 G	
587 Y	1759 T	+1:194960936 194960936 T	Y
587	1760 A	+1:194960937 194960937 A	
587	1761 T	+1:194960938 194960938 T	
588 K	1762 A	+1:194960939 194960939 A	K
588	1763 A	+1:194960940 194960940 A	
588	1764 A	+1:194960941 194960941 A	
589 V	1765 G	+1:194960942 194960942 G	V
589	1766 T	+1:194960943 194960943 T	
589	1767 T	+1:194960944 194960944 T	
590 G	1768 G	+1:194960945 194960945 G	G
590	1769 G	+1:194960946 194960946 G	
590	1770 A	+1:194960947 194960947 A	
591 E	1771 G	+1:194960948 194960948 G	E
591	1772 A	+1:194960949 194960949 A	
591	1773 G	+1:194960950 194960950 G	
592 V	1774 G	+1:194960951 194960951 G	V
592	1775 T	+1:194960952 194960952 T	
592	1776 G	+1:194960953 194960953 G	
593 L	1777 T	+1:194960954 194960954 T	L
593	1778 T	+1:194960955 194960955 T	
593	1779 G	+1:194960956 194960956 G	
594 K	1780 A	+1:194960957 194960957 A	K
594	1781 A	+1:194960958 194960958 A	
594	1782 A	+1:194960959 194960959 A	
595 F	1783 T	+1:194960960 194960960 T	F
595	1784 T	+1:194960961 194960961 T	
595	1785 C	+1:194960962 194960962 C	
596 S	1786 T	+1:194960963 194960963 T	S
596	1787 C	+1:194960964 194960964 C	
596	1788 C	+1:194960965 194960965 C	
597 C	1789 T	+1:194960966 194960966 T	C
597	1790 G	+1:194960967 194960967 G	
597	1791 C	+1:194960968 194960968 C	
598 K	1792 A	+1:194960969 194960969 A	K
598	1793 A	+1:194960970 194960970 A	
598	1794 A	+1:194960971 194960971 A	
599 P	1795 C	+1:194960972 194960972 C	P
599	1796 C	+1:194960973 194960973 C	
599	1797 A	+1:194960974 194960974 A	
600 G	1798 G	+1:194960975 194960975 G	G
600	1799 G	+1:194960976 194960976 G	
600	1800 A	+1:194960977 194960977 A	
601 F	1801 T	+1:194960978 194960978 T	F
601	1802 T	+1:194960979 194960979 T	
601	1803 T	+1:194960980 194960980 T	
602 T	1804 A	+1:194960981 194960981 A	T
602	1805 C	+1:194960982 194960982 C	
602	1806 A	+1:194960983 194960983 A	
603 I	1807 A	+1:194960984 194960984 A	I
603	1808 T	+1:194960985 194960985 T	
603	1809 A	+1:194960986 194960986 A	
604 V	1810 G	+1:194960987 194960987 G	V
604	1811 T	+1:194960988 194960988 T	
604	1812 T	+1:194960989 194960989 T	
605 G	1813 G	+1:194960990 194960990 G	G
605	1814 G	+1:194960991 194960991 G	
605	1815 A	+1:194960992 194960992 A	
606 P	1816 C	+1:194960993 194960993 C	P
606	1817 C	+1:194960994 194960994 C	
606	1818 T	+1:194960995 194960995 T	
607 N	1819 A	+1:194960996 194960996 A	N
607	1820 A	+1:194960997 194960997 A	
607	1821 T	+1:194960998 194960998 T	
608 S	1822 T	+1:194960999 194960999 T	S
608	1823 C	+1:194961000 194961000 C	
608	1824 C	+1:194961001 194961001 C	
609 V	1825 G	+1:194961002 194961002 G	V
609	1826 T	+1:194961003 194961003 T	
609	1827 T	+1:194961004 194961004 T	
610 Q	1828 C	+1:194961005 194961005 C	Q
610	1829 A	+1:194961006 194961006 A	
610	1830 G	+1:194961007 194961007 G	
611 C	1831 T	+1:194961008 194961008 T	C
611	1832 G	+1:194961009 194961009 G	
611	1833 C	+1:194961010 194961010 C	
612 Y	1834 T	+1:194961011 194961011 T	Y
612	1835 A	+1:194961012 194961012 A	
612	1836 C	+1:194961013 194961013 C	
613 H	1837 C	+1:194961014 194961014 C	H
613	1838 A	+1:194961015 194961015 A	
613	1839 C	+1:194961016 194961016 C	
614 F	1840 T	+1:194961017 194961017 T	F
614	1841 T	+1:194961018 194961018 T	
614	1842 T	+1:194961019 194961019 T	
615 G	1843 G	+1:194961020 194961020 G	G
615	1844 G	+1:194961021 194961021 G	
615	1845 A	+1:194961022 194961022 A	
616 L	1846 T	+1:194961023 194961023 T	L
616	1847 T	+1:194961024 194961024 T	
616	1848 G	+1:194961025 194961025 G	
617 S	1849 T	+1:194961026 194961026 T	S
617	1850 C	+1:194961027 194961027 C	
617	1851 T	+1:194961028 194961028 T	
618 P	1852 C	+1:194961029 194961029 C	P
618	1853 C	+1:194961030 194961030 C	
618	1854 T	+1:194961031 194961031 T	
619 D	1855 G	+1:194961032 194961032 G	D
619	1856 A	+1:194961033 194961033 A	
619	1857 C	+1:194961034 194961034 C	
620 L	1858 C	+1:194961035 194961035 C	L
620	1859 T	+1:194961036 194961036 T	
620	1860 C	+1:194961037 194961037 C	
621 P	1861 C	+1:194961038 194961038 C	P
621	1862 C	+1:194961039 194961039 C	
621	1863 A	+1:194961040 194961040 A	
622 I	1864 A	+1:194961041 194961041 A	I
622	1865 T	+1:194961042 194961042 T	
622	1866 A	+1:194961043 194961043 A	
623 C	1867 T	+1:194961044 194961044 T	C
623	1868 G	+1:194961045 194961045 G	
623	1869 T	+1:194961046 194961046 T	
624 K	1870 A	+1:194961047 194961047 A	K
624	1871 A	+1:194961048 194961048 A	
624	1872 A	+1:194961049 194961049 A	
625 E	1873 G	+1:194961050 194961050 G	E
625	1874 A	+1:194962223 194962223 A	
625	1875 G	+1:194962224 194962224 G	
626 Q	1876 C	+1:194962225 194962225 C	Q
626	1877 A	+1:194962226 194962226 A	
626	1878 A	+1:194962227 194962227 A	
627 V	1879 G	+1:194962228 194962228 G	V
627	1880 T	+1:194962229 194962229 T	
627	1881 A	+1:194962230 194962230 A	
628 Q	1882 C	+1:194962231 194962231 C	Q
628	1883 A	+1:194962232 194962232 A	
628	1884 A	+1:194962233 194962233 A	
629 S	1885 T	+1:194962234 194962234 T	S
629	1886 C	+1:194962235 194962235 C	
629	1887 A	+1:194962236 194962236 A	
630 C	1888 T	+1:194962237 194962237 T	C
630	1889 G	+1:194962238 194962238 G	
630	1890 T	+1:194962239 194962239 T	
631 G	1891 G	+1:194962240 194962240 G	G
631	1892 G	+1:194962241 194962241 G	
631	1893 T	+1:194962242 194962242 T	
632 P	1894 C	+1:194962243 194962243 C	P
632	1895 C	+1:194962244 194962244 C	
632	1896 A	+1:194962245 194962245 A	
633 P	1897 C	+1:194962246 194962246 C	P
633	1898 C	+1:194962247 194962247 C	
633	1899 T	+1:194962248 194962248 T	
634 P	1900 C	+1:194962249 194962249 C	P
634	1901 C	+1:194962250 194962250 C	
634	1902 T	+1:194962251 194962251 T	
635 E	1903 G	+1:194962252 194962252 G	E
635	1904 A	+1:194962253 194962253 A	
635	1905 A	+1:194962254 194962254 A	
636 L	1906 C	+1:194962255 194962255 C	L
636	1907 T	+1:194962256 194962256 T	
636	1908 C	+1:194962257 194962257 C	
637 L	1909 C	+1:194962258 194962258 C	L
637	1910 T	+1:194962259 194962259 T	
637	1911 C	+1:194962260 194962260 C	
638 N	1912 A	+1:194962261 194962261 A	N
638	1913 A	+1:194962262 194962262 A	
638	1914 T	+1:194962263 194962263 T	
639 G	1915 G	+1:194962264 194962264 G	G
639	1916 G	+1:194962265 194962265 G	
639	1917 G	+1:194962266 194962266 G	
640 N	1918 A	+1:194962267 194962267 A	N
640	1919 A	+1:194962268 194962268 A	
640	1920 T	+1:194962269 194962269 T	
641 V	1921 G	+1:194962270 194962270 G	V
641	1922 T	+1:194962271 194962271 T	
641	1923 T	+1:194962272 194962272 T	
642 K	1924 A	+1:194962273 194962273 A	K
642	1925 A	+1:194962274 194962274 A	
642	1926 G	+1:194962275 194962275 G	
643 E	1927 G	+1:194962276 194962276 G	E
643	1928 A	+1:194962277 194962277 A	
643	1929 A	+1:194962278 194962278 A	
644 K	1930 A	+1:194962279 194962279 A	K
644	1931 A	+1:194962280 194962280 A	
644	1932 A	+1:194962281 194962281 A	
645 T	1933 A	+1:194962282 194962282 A	T
645	1934 C	+1:194962283 194962283 C	
645	1935 G	+1:194962284 194962284 G	
646 K	1936 A	+1:194962285 194962285 A	K
646	1937 A	+1:194962286 194962286 A	
646	1938 A	+1:194962287 194962287 A	
647 E	1939 G	+1:194962288 194962288 G	E
647	1940 A	+1:194962289 194962289 A	
647	1941 A	+1:194962290 194962290 A	
648 E	1942 G	+1:194962291 194962291 G	E
648	1943 A	+1:194962292 194962292 A	
648	1944 A	+1:194962293 194962293 A	
649 Y	1945 T	+1:194962294 194962294 T	Y
649	1946 A	+1:194962295 194962295 A	
649	1947 T	+1:194962296 194962296 T	
650 G	1948 G	+1:194962297 194962297 G	G
650	1949 G	+1:194962298 194962298 G	
650	1950 A	+1:194962299 194962299 A	
651 H	1951 C	+1:194962300 194962300 C	H
651	1952 A	+1:194962301 194962301 A	
651	1953 C	+1:194962302 194962302 C	
652 S	1954 A	+1:194962303 194962303 A	S
652	1955 G	+1:194962304 194962304 G	
652	1956 T	+1:194962305 194962305 T	
653 E	1957 G	+1:194962306 194962306 G	E
653	1958 A	+1:194962307 194962307 A	
653	1959 A	+1:194962308 194962308 A	
654 V	1960 G	+1:194962309 194962309 G	V
654	1961 T	+1:194962310 194962310 T	
654	1962 G	+1:194962311 194962311 G	
655 V	1963 G	+1:194962312 194962312 G	V
655	1964 T	+1:194962313 194962313 T	
655	1965 G	+1:194962314 194962314 G	
656 E	1966 G	+1:194962315 194962315 G	E
656	1967 A	+1:194962316 194962316 A	
656	1968 A	+1:194962317 194962317 A	
657 Y	1969 T	+1:194962318 194962318 T	Y
657	1970 A	+1:194962319 194962319 A	
657	1971 T	+1:194962320 194962320 T	
658 Y	1972 T	+1:194962321 194962321 T	Y
658	1973 A	+1:194962322 194962322 A	
658	1974 T	+1:194962323 194962323 T	
659 C	1975 T	+1:194962324 194962324 T	C
659	1976 G	+1:194962325 194962325 G	
659	1977 C	+1:194962326 194962326 C	
660 N	1978 A	+1:194962327 194962327 A	N
660	1979 A	+1:194962328 194962328 A	
660	1980 T	+1:194962329 194962329 T	
661 P	1981 C	+1:194962330 194962330 C	P
661	1982 C	+1:194962331 194962331 C	
661	1983 T	+1:194962332 194962332 T	
662 R	1984 A	+1:194962333 194962333 A	R
662	1985 G	+1:194962334 194962334 G	
662	1986 A	+1:194962335 194962335 A	
663 F	1987 T	+1:194962336 194962336 T	F
663	1988 T	+1:194962337 194962337 T	
663	1989 T	+1:194962338 194962338 T	
664 L	1990 C	+1:194962339 194962339 C	L
664	1991 T	+1:194962340 194962340 T	
664	1992 A	+1:194962341 194962341 A	
665 M	1993 A	+1:194962342 194962342 A	M
665	1994 T	+1:194962343 194962343 T	
665	1995 G	+1:194962344 194962344 G	
666 K	1996 A	+1:194962345 194962345 A	K
666	1997 A	+1:194962346 194962346 A	
666	1998 G	+1:194962347 194962347 G	
667 G	1999 G	+1:194962348 194962348 G	G
667	2000 G	+1:194962349 194962349 G	
667	2001 A	+1:194962350 194962350 A	
668 P	2002 C	+1:194962351 194962351 C	P
668	2003 C	+1:194962352 194962352 C	
668	2004 T	+1:194962353 194962353 T	
669 N	2005 A	+1:194962354 194962354 A	N
669	2006 A	+1:194962355 194962355 A	
669	2007 T	+1:194962356 194962356 T	
670 K	2008 A	+1:194962357 194962357 A	K
670	2009 A	+1:194962358 194962358 A	
670	2010 A	+1:194962359 194962359 A	
671 I	2011 A	+1:194962360 194962360 A	I
671	2012 T	+1:194962361 194962361 T	
671	2013 T	+1:194962362 194962362 T	
672 Q	2014 C	+1:194962363 194962363 C	Q
672	2015 A	+1:194962364 194962364 A	
672	2016 A	+1:194962365 194962365 A	
673 C	2017 T	+1:194962366 194962366 T	C
673	2018 G	+1:194962367 194962367 G	
673	2019 T	+1:194962368 194962368 T	
674 V	2020 G	+1:194962369 194962369 G	V
674	2021 T	+1:194962370 194962370 T	
674	2022 T	+1:194962371 194962371 T	
675 D	2023 G	+1:194962372 194962372 G	D
675	2024 A	+1:194962373 194962373 A	
675	2025 T	+1:194962374 194962374 T	
676 G	2026 G	+1:194962375 194962375 G	G
676	2027 G	+1:194962376 194962376 G	
676	2028 A	+1:194962377 194962377 A	
677 E	2029 G	+1:194962378 194962378 G	E
677	2030 A	+1:194962379 194962379 A	
677	2031 G	+1:194962380 194962380 G	
678 W	2032 T	+1:194962381 194962381 T	W
678	2033 G	+1:194962382 194962382 G	
678	2034 G	+1:194962383 194962383 G	
679 T	2035 A	+1:194962384 194962384 A	T
679	2036 C	+1:194962385 194962385 C	
679	2037 A	+1:194962386 194962386 A	
680 T	2038 A	+1:194962387 194962387 A	T
680	2039 C	+1:194962388 194962388 C	
680	2040 T	+1:194962389 194962389 T	
681 L	2041 T	+1:194962390 194962390 T	L
681	2042 T	+1:194962391 194962391 T	
681	2043 A	+1:194962392 194962392 A	
682 P	2044 C	+1:194962393 194962393 C	P
682	2045 C	+1:194962394 194962394 C	
682	2046 A	+1:194962395 194962395 A	
683 V	2047 G	+1:194962396 194962396 G	V
683	2048 T	+1:194962397 194962397 T	
683	2049 G	+1:194962398 194962398 G	
684 C	2050 T	+1:194962399 194962399 T	C
684	2051 G	+1:194962400 194962400 G	
684	2052 T	+1:194962401 194962401 T	
685 I	2053 A	+1:194962402 194962402 A	I
685	2054 T	+1:194962403 194962403 T	
685	2055 T	+1:194962404 194962404 T	
686 V	2056 G	+1:194962405 194962405 G	V
686	2057 T	+1:194962514 194962514 T	
686	2058 G	+1:194962515 194962515 G	
687 E	2059 G	+1:194962516 194962516 G	E
687	2060 A	+1:194962517 194962517 A	
687	2061 G	+1:194962518 194962518 G	
688 E	2062 G	+1:194962519 194962519 G	E
688	2063 A	+1:194962520 194962520 A	
688	2064 G	+1:194962521 194962521 G	
689 S	2065 A	+1:194962522 194962522 A	S
689	2066 G	+1:194962523 194962523 G	
689	2067 T	+1:194962524 194962524 T	
690 T	2068 A	+1:194962525 194962525 A	T
690	2069 C	+1:194962526 194962526 C	
690	2070 C	+1:194962527 194962527 C	
691 C	2071 T	+1:194962528 194962528 T	C
691	2072 G	+1:194962529 194962529 G	
691	2073 T	+1:194962530 194962530 T	
692 G	2074 G	+1:194962531 194962531 G	G
692	2075 G	+1:194962532 194962532 G	
692	2076 A	+1:194962533 194962533 A	
693 D	2077 G	+1:194962534 194962534 G	D
693	2078 A	+1:194962535 194962535 A	
693	2079 T	+1:194962536 194962536 T	
694 I	2080 A	+1:194962537 194962537 A	I
694	2081 T	+1:194962538 194962538 T	
694	2082 A	+1:194962539 194962539 A	
695 P	2083 C	+1:194962540 194962540 C	P
695	2084 C	+1:194962541 194962541 C	
695	2085 T	+1:194962542 194962542 T	
696 E	2086 G	+1:194962543 194962543 G	E
696	2087 A	+1:194962544 194962544 A	
696	2088 A	+1:194962545 194962545 A	
697 L	2089 C	+1:194962546 194962546 C	L
697	2090 T	+1:194962547 194962547 T	
697	2091 T	+1:194962548 194962548 T	
698 E	2092 G	+1:194962549 194962549 G	E
698	2093 A	+1:194962550 194962550 A	
698	2094 A	+1:194962551 194962551 A	
699 H	2095 C	+1:194962552 194962552 C	H
699	2096 A	+1:194962553 194962553 A	
699	2097 T	+1:194962554 194962554 T	
700 G	2098 G	+1:194962555 194962555 G	G
700	2099 G	+1:194962556 194962556 G	
700	2100 C	+1:194962557 194962557 C	
701 W	2101 T	+1:194962558 194962558 T	W
701	2102 G	+1:194962559 194962559 G	
701	2103 G	+1:194962560 194962560 G	
702 A	2104 G	+1:194962561 194962561 G	A
702	2105 C	+1:194962562 194962562 C	
702	2106 C	+1:194962563 194962563 C	
703 Q	2107 C	+1:194962564 194962564 C	Q
703	2108 A	+1:194962565 194962565 A	
703	2109 G	+1:194962566 194962566 G	
704 L	2110 C	+1:194962567 194962567 C	L
704	2111 T	+1:194962568 194962568 T	
704	2112 T	+1:194962569 194962569 T	
705 S	2113 T	+1:194962570 194962570 T	S
705	2114 C	+1:194962571 194962571 C	
705	2115 T	+1:194962572 194962572 T	
706 S	2116 T	+1:194962573 194962573 T	S
706	2117 C	+1:194962574 194962574 C	
706	2118 C	+1:194962575 194962575 C	
707 P	2119 C	+1:194962576 194962576 C	P
707	2120 C	+1:194962577 194962577 C	
707	2121 T	+1:194962578 194962578 T	
708 P	2122 C	+1:194962579 194962579 C	P
708	2123 C	+1:194962580 194962580 C	
708	2124 T	+1:194962581 194962581 T	
709 Y	2125 T	+1:194962582 194962582 T	Y
709	2126 A	+1:194962583 194962583 A	
709	2127 T	+1:194962584 194962584 T	
710 Y	2128 T	+1:194962585 194962585 T	Y
710	2129 A	+1:194962586 194962586 A	
710	2130 C	+1:194962587 194962587 C	
711 Y	2131 T	+1:194962588 194962588 T	Y
711	2132 A	+1:194962589 194962589 A	
711	2133 T	+1:194962590 194962590 T	
712 G	2134 G	+1:194962591 194962591 G	G
712	2135 G	+1:194962592 194962592 G	
712	2136 A	+1:194962593 194962593 A	
713 D	2137 G	+1:194962594 194962594 G	D
713	2138 A	+1:194962595 194962595 A	
713	2139 T	+1:194962596 194962596 T	
714 S	2140 T	+1:194962597 194962597 T	S
714	2141 C	+1:194962598 194962598 C	
714	2142 A	+1:194962599 194962599 A	
715 V	2143 G	+1:194962600 194962600 G	V
715	2144 T	+1:194962601 194962601 T	
715	2145 G	+1:194962602 194962602 G	
716 E	2146 G	+1:194962603 194962603 G	E
716	2147 A	+1:194962604 194962604 A	
716	2148 A	+1:194962605 194962605 A	
717 F	2149 T	+1:194962606 194962606 T	F
717	2150 T	+1:194962607 194962607 T	
717	2151 C	+1:194962608 194962608 C	
718 N	2152 A	+1:194962609 194962609 A	N
718	2153 A	+1:194962610 194962610 A	
718	2154 T	+1:194962611 194962611 T	
719 C	2155 T	+1:194962612 194962612 T	C
719	2156 G	+1:194962613 194962613 G	
719	2157 C	+1:194962614 194962614 C	
720 S	2158 T	+1:194962615 194962615 T	S
720	2159 C	+1:194962616 194962616 C	
720	2160 A	+1:194962617 194962617 A	
721 E	2161 G	+1:194962618 194962618 G	E
721	2162 A	+1:194962619 194962619 A	
721	2163 A	+1:194962620 194962620 A	
722 S	2164 T	+1:194962621 194962621 T	S
722	2165 C	+1:194962622 194962622 C	
722	2166 A	+1:194962623 194962623 A	
723 F	2167 T	+1:194962624 194962624 T	F
723	2168 T	+1:194962625 194962625 T	
723	2169 T	+1:194962626 194962626 T	
724 T	2170 A	+1:194962627 194962627 A	T
724	2171 C	+1:194962628 194962628 C	
724	2172 A	+1:194962629 194962629 A	
725 M	2173 A	+1:194962630 194962630 A	M
725	2174 T	+1:194962631 194962631 T	
725	2175 G	+1:194962632 194962632 G	
726 I	2176 A	+1:194962633 194962633 A	I
726	2177 T	+1:194962634 194962634 T	
726	2178 T	+1:194962635 194962635 T	
727 G	2179 G	+1:194962636 194962636 G	G
727	2180 G	+1:194962637 194962637 G	
727	2181 A	+1:194962638 194962638 A	
728 H	2182 C	+1:194962639 194962639 C	H
728	2183 A	+1:194962640 194962640 A	
728	2184 C	+1:194962641 194962641 C	
729 R	2185 A	+1:194962642 194962642 A	R
729	2186 G	+1:194962643 194962643 G	
729	2187 A	+1:194962644 194962644 A	
730 S	2188 T	+1:194962645 194962645 T	S
730	2189 C	+1:194962646 194962646 C	
730	2190 A	+1:194962647 194962647 A	
731 I	2191 A	+1:194962648 194962648 A	I
731	2192 T	+1:194962649 194962649 T	
731	2193 T	+1:194962650 194962650 T	
732 T	2194 A	+1:194962651 194962651 A	T
732	2195 C	+1:194962652 194962652 C	
732	2196 G	+1:194962653 194962653 G	
733 C	2197 T	+1:194962654 194962654 T	C
733	2198 G	+1:194962655 194962655 G	
733	2199 T	+1:194962656 194962656 T	
734 I	2200 A	+1:194962657 194962657 A	I
734	2201 T	+1:194962658 194962658 T	
734	2202 T	+1:194962659 194962659 T	
735 H	2203 C	+1:194962660 194962660 C	H
735	2204 A	+1:194962661 194962661 A	
735	2205 T	+1:194962662 194962662 T	
736 G	2206 G	+1:194962663 194962663 G	G
736	2207 G	+1:194962664 194962664 G	
736	2208 A	+1:194962665 194962665 A	
737 V	2209 G	+1:194962666 194962666 G	V
737	2210 T	+1:194962667 194962667 T	
737	2211 A	+1:194962668 194962668 A	
738 W	2212 T	+1:194962669 194962669 T	W
738	2213 G	+1:194962670 194962670 G	
738	2214 G	+1:194962671 194962671 G	
739 T	2215 A	+1:194962672 194962672 A	T
739	2216 C	+1:194962673 194962673 C	
739	2217 C	+1:194962674 194962674 C	
740 Q	2218 C	+1:194962675 194962675 C	Q
740	2219 A	+1:194962676 194962676 A	
740	2220 A	+1:194962677 194962677 A	
741 L	2221 C	+1:194962678 194962678 C	L
741	2222 T	+1:194962679 194962679 T	
741	2223 T	+1:194962680 194962680 T	
742 P	2224 C	+1:194962681 194962681 C	P
742	2225 C	+1:194962682 194962682 C	
742	2226 C	+1:194962683 194962683 C	
743 Q	2227 C	+1:194962684 194962684 C	Q
743	2228 A	+1:194962685 194962685 A	
743	2229 G	+1:194962686 194962686 G	
744 C	2230 T	+1:194962687 194962687 T	C
744	2231 G	+1:194962688 194962688 G	
744	2232 T	+1:194962689 194962689 T	
745 V	2233 G	+1:194962690 194962690 G	V
745	2234 T	+1:194962691 194962691 T	
745	2235 G	+1:194962692 194962692 G	
746 A	2236 G	+1:194962693 194962693 G	A
746	2237 C	+1:194964099 194964099 C	
746	2238 A	+1:194964100 194964100 A	
747 I	2239 A	+1:194964101 194964101 A	I
747	2240 T	+1:194964102 194964102 T	
747	2241 A	+1:194964103 194964103 A	
748 D	2242 G	+1:194964104 194964104 G	D
748	2243 A	+1:194964105 194964105 A	
748	2244 T	+1:194964106 194964106 T	
749 K	2245 A	+1:194964107 194964107 A	K
749	2246 A	+1:194964108 194964108 A	
749	2247 A	+1:194964109 194964109 A	
750 L	2248 C	+1:194964110 194964110 C	L
750	2249 T	+1:194964111 194964111 T	
750	2250 T	+1:194964112 194964112 T	
751 K	2251 A	+1:194964113 194964113 A	K
751	2252 A	+1:194964114 194964114 A	
751	2253 G	+1:194964115 194964115 G	
752 K	2254 A	+1:194964116 194964116 A	K
752	2255 A	+1:194964117 194964117 A	
752	2256 G	+1:194964118 194964118 G	
753 C	2257 T	+1:194964119 194964119 T	C
753	2258 G	+1:194964120 194964120 G	
753	2259 C	+1:194964121 194964121 C	
754 K	2260 A	+1:194964122 194964122 A	K
754	2261 A	+1:194964123 194964123 A	
754	2262 A	+1:194964124 194964124 A	
755 S	2263 T	+1:194964125 194964125 T	S
755	2264 C	+1:194964126 194964126 C	
755	2265 A	+1:194964127 194964127 A	
756 S	2266 T	+1:194964128 194964128 T	S
756	2267 C	+1:194964129 194964129 C	
756	2268 A	+1:194964130 194964130 A	
757 N	2269 A	+1:194964131 194964131 A	N
757	2270 A	+1:194964132 194964132 A	
757	2271 T	+1:194964133 194964133 T	
758 L	2272 T	+1:194964134 194964134 T	L
758	2273 T	+1:194964135 194964135 T	
758	2274 A	+1:194964136 194964136 A	
759 I	2275 A	+1:194964137 194964137 A	I
759	2276 T	+1:194964138 194964138 T	
759	2277 T	+1:194964139 194964139 T	
760 I	2278 A	+1:194964140 194964140 A	I
760	2279 T	+1:194964141 194964141 T	
760	2280 A	+1:194964142 194964142 A	
761 L	2281 C	+1:194964143 194964143 C	L
761	2282 T	+1:194964144 194964144 T	
761	2283 T	+1:194964145 194964145 T	
762 E	2284 G	+1:194964146 194964146 G	E
762	2285 A	+1:194964147 194964147 A	
762	2286 G	+1:194964148 194964148 G	
763 E	2287 G	+1:194964149 194964149 G	E
763	2288 A	+1:194964150 194964150 A	
763	2289 A	+1:194964151 194964151 A	
764 H	2290 C	+1:194964152 194964152 C	H
764	2291 A	+1:194964153 194964153 A	
764	2292 T	+1:194964154 194964154 T	
765 L	2293 T	+1:194964155 194964155 T	L
765	2294 T	+1:194964156 194964156 T	
765	2295 A	+1:194964157 194964157 A	
766 K	2296 A	+1:194964158 194964158 A	K
766	2297 A	+1:194964159 194964159 A	
766	2298 A	+1:194964160 194964160 A	
767 N	2299 A	+1:194964161 194964161 A	N
767	2300 A	+1:194964162 194964162 A	
767	2301 C	+1:194964163 194964163 C	
768 K	2302 A	+1:194964164 194964164 A	K
768	2303 A	+1:194964165 194964165 A	
768	2304 G	+1:194964166 194964166 G	
769 K	2305 A	+1:194964167 194964167 A	K
769	2306 A	+1:194964168 194964168 A	
769	2307 G	+1:194964169 194964169 G	
770 E	2308 G	+1:194964170 194964170 G	E
770	2309 A	+1:194964171 194964171 A	
770	2310 A	+1:194964172 194964172 A	
771 F	2311 T	+1:194964173 194964173 T	F
771	2312 T	+1:194964174 194964174 T	
771	2313 C	+1:194964175 194964175 C	
772 D	2314 G	+1:194964176 194964176 G	D
772	2315 A	+1:194964177 194964177 A	
772	2316 T	+1:194964178 194964178 T	
773 H	2317 C	+1:194964179 194964179 C	H
773	2318 A	+1:194964180 194964180 A	
773	2319 T	+1:194964181 194964181 T	
774 N	2320 A	+1:194964182 194964182 A	N
774	2321 A	+1:194964183 194964183 A	
774	2322 T	+1:194964184 194964184 T	
775 S	2323 T	+1:194964185 194964185 T	S
775	2324 C	+1:194964186 194964186 C	
775	2325 T	+1:194964187 194964187 T	
776 N	2326 A	+1:194964188 194964188 A	N
776	2327 A	+1:194964189 194964189 A	
776	2328 C	+1:194964190 194964190 C	
777 I	2329 A	+1:194964191 194964191 A	I
777	2330 T	+1:194964192 194964192 T	
777	2331 A	+1:194964193 194964193 A	
778 R	2332 A	+1:194964194 194964194 A	R
778	2333 G	+1:194964195 194964195 G	
778	2334 G	+1:194964196 194964196 G	
779 Y	2335 T	+1:194964197 194964197 T	Y
779	2336 A	+1:194964198 194964198 A	
779	2337 C	+1:194964199 194964199 C	
780 R	2338 A	+1:194964200 194964200 A	R
780	2339 G	+1:194964201 194964201 G	
780	2340 A	+1:194964202 194964202 A	
781 C	2341 T	+1:194964203 194964203 T	C
781	2342 G	+1:194964204 194964204 G	
781	2343 T	+1:194964205 194964205 T	
782 R	2344 A	+1:194964206 194964206 A	R
782	2345 G	+1:194964207 194964207 G	
782	2346 A	+1:194964208 194964208 A	
783 G	2347 G	+1:194964209 194964209 G	G
783	2348 G	+1:194964210 194964210 G	
783	2349 A	+1:194964211 194964211 A	
784 K	2350 A	+1:194964212 194964212 A	K
784	2351 A	+1:194964213 194964213 A	
784	2352 A	+1:194964214 194964214 A	
785 E	2353 G	+1:194964215 194964215 G	E
785	2354 A	+1:194964216 194964216 A	
785	2355 A	+1:194964217 194964217 A	
786 G	2356 G	+1:194964218 194964218 G	G
786	2357 G	+1:194964219 194964219 G	
786	2358 A	+1:194964220 194964220 A	
787 W	2359 T	+1:194964221 194964221 T	W
787	2360 G	+1:194964222 194964222 G	
787	2361 G	+1:194964223 194964223 G	
788 I	2362 A	+1:194964224 194964224 A	I
788	2363 T	+1:194964225 194964225 T	
788	2364 A	+1:194964226 194964226 A	
789 H	2365 C	+1:194964227 194964227 C	H
789	2366 A	+1:194964228 194964228 A	
789	2367 C	+1:194964229 194964229 C	
790 T	2368 A	+1:194964230 194964230 A	T
790	2369 C	+1:194964231 194964231 C	
790	2370 A	+1:194964232 194964232 A	
791 V	2371 G	+1:194964233 194964233 G	V
791	2372 T	+1:194964234 194964234 T	
791	2373 C	+1:194964235 194964235 C	
792 C	2374 T	+1:194964236 194964236 T	C
792	2375 G	+1:194964237 194964237 G	
792	2376 C	+1:194964238 194964238 C	
793 I	2377 A	+1:194964239 194964239 A	I
793	2378 T	+1:194964240 194964240 T	
793	2379 A	+1:194964241 194964241 A	
794 N	2380 A	+1:194964242 194964242 A	N
794	2381 A	+1:194964243 194964243 A	
794	2382 T	+1:194964244 194964244 T	
795 G	2383 G	+1:194964245 194964245 G	G
795	2384 G	+1:194964246 194964246 G	
795	2385 A	+1:194964247 194964247 A	
796 R	2386 A	+1:194964248 194964248 A	R
796	2387 G	+1:194964249 194964249 G	
796	2388 A	+1:194964250 194964250 A	
797 W	2389 T	+1:194964251 194964251 T	W
797	2390 G	+1:194964252 194964252 G	
797	2391 G	+1:194964253 194964253 G	
798 D	2392 G	+1:194964254 194964254 G	D
798	2393 A	+1:194964255 194964255 A	
798	2394 T	+1:194964256 194964256 T	
799 P	2395 C	+1:194964257 194964257 C	P
799	2396 C	+1:194964258 194964258 C	
799	2397 A	+1:194964259 194964259 A	
800 E	2398 G	+1:194964260 194964260 G	E
800	2399 A	+1:194964261 194964261 A	
800	2400 A	+1:194964262 194964262 A	
801 V	2401 G	+1:194964263 194964263 G	V
801	2402 T	+1:194964264 194964264 T	
801	2403 G	+1:194964265 194964265 G	
802 N	2404 A	+1:194964266 194964266 A	N
802	2405 A	+1:194964267 194964267 A	
802	2406 C	+1:194964268 194964268 C	
803 C	2407 T	+1:194964269 194964269 T	C
803	2408 G	+1:194964270 194964270 G	
803	2409 C	+1:194964271 194964271 C	
804 S	2410 T	+1:194964272 194964272 T	S
804	2411 C	+1:194964273 194964273 C	
804	2412 A	+1:194964274 194964274 A	
805 M	2413 A	+1:194964275 194964275 A	M
805	2414 T	+1:194972577 194972577 T	
805	2415 G	+1:194972578 194972578 G	
806 A	2416 G	+1:194972579 194972579 G	A
806	2417 C	+1:194972580 194972580 C	
806	2418 A	+1:194972581 194972581 A	
807 Q	2419 C	+1:194972582 194972582 C	Q
807	2420 A	+1:194972583 194972583 A	
807	2421 A	+1:194972584 194972584 A	
808 I	2422 A	+1:194972585 194972585 A	I
808	2423 T	+1:194972586 194972586 T	
808	2424 A	+1:194972587 194972587 A	
809 Q	2425 C	+1:194972588 194972588 C	Q
809	2426 A	+1:194972589 194972589 A	
809	2427 A	+1:194972590 194972590 A	
810 L	2428 T	+1:194972591 194972591 T	L
810	2429 T	+1:194972592 194972592 T	
810	2430 A	+1:194972593 194972593 A	
811 C	2431 T	+1:194972594 194972594 T	C
811	2432 G	+1:194972595 194972595 G	
811	2433 C	+1:194972596 194972596 C	
812 P	2434 C	+1:194972597 194972597 C	P
812	2435 C	+1:194972598 194972598 C	
812	2436 A	+1:194972599 194972599 A	
813 P	2437 C	+1:194972600 194972600 C	P
813	2438 C	+1:194972601 194972601 C	
813	2439 T	+1:194972602 194972602 T	
814 P	2440 C	+1:194972603 194972603 C	P
814	2441 C	+1:194972604 194972604 C	
814	2442 A	+1:194972605 194972605 A	
815 P	2443 C	+1:194972606 194972606 C	P
815	2444 C	+1:194972607 194972607 C	
815	2445 T	+1:194972608 194972608 T	
816 Q	2446 C	+1:194972609 194972609 C	Q
816	2447 A	+1:194972610 194972610 A	
816	2448 G	+1:194972611 194972611 G	
817 I	2449 A	+1:194972612 194972612 A	I
817	2450 T	+1:194972613 194972613 T	
817	2451 T	+1:194972614 194972614 T	
818 P	2452 C	+1:194972615 194972615 C	P
818	2453 C	+1:194972616 194972616 C	
818	2454 C	+1:194972617 194972617 C	
819 N	2455 A	+1:194972618 194972618 A	N
819	2456 A	+1:194972619 194972619 A	
819	2457 T	+1:194972620 194972620 T	
820 S	2458 T	+1:194972621 194972621 T	S
820	2459 C	+1:194972622 194972622 C	
820	2460 T	+1:194972623 194972623 T	
821 H	2461 C	+1:194972624 194972624 C	H
821	2462 A	+1:194972625 194972625 A	
821	2463 C	+1:194972626 194972626 C	
822 N	2464 A	+1:194972627 194972627 A	N
822	2465 A	+1:194972628 194972628 A	
822	2466 T	+1:194972629 194972629 T	
823 M	2467 A	+1:194972630 194972630 A	M
823	2468 T	+1:194972631 194972631 T	
823	2469 G	+1:194972632 194972632 G	
824 T	2470 A	+1:194972633 194972633 A	T
824	2471 C	+1:194972634 194972634 C	
824	2472 A	+1:194972635 194972635 A	
825 T	2473 A	+1:194972636 194972636 A	T
825	2474 C	+1:194972637 194972637 C	
825	2475 C	+1:194972638 194972638 C	
826 T	2476 A	+1:194972639 194972639 A	T
826	2477 C	+1:194972640 194972640 C	
826	2478 A	+1:194972641 194972641 A	
827 L	2479 C	+1:194972642 194972642 C	L
827	2480 T	+1:194972643 194972643 T	
827	2481 G	+1:194972644 194972644 G	
828 N	2482 A	+1:194972645 194972645 A	N
828	2483 A	+1:194972646 194972646 A	
828	2484 T	+1:194972647 194972647 T	
829 Y	2485 T	+1:194972648 194972648 T	Y
829	2486 A	+1:194972649 194972649 A	
829	2487 T	+1:194972650 194972650 T	
830 R	2488 C	+1:194972651 194972651 C	R
830	2489 G	+1:194972652 194972652 G	
830	2490 G	+1:194972653 194972653 G	
831 D	2491 G	+1:194972654 194972654 G	D
831	2492 A	+1:194972655 194972655 A	
831	2493 T	+1:194972656 194972656 T	
832 G	2494 G	+1:194972657 194972657 G	G
832	2495 G	+1:194972658 194972658 G	
832	2496 A	+1:194972659 194972659 A	
833 E	2497 G	+1:194972660 194972660 G	E
833	2498 A	+1:194972661 194972661 A	
833	2499 A	+1:194972662 194972662 A	
834 K	2500 A	+1:194972663 194972663 A	K
834	2501 A	+1:194972664 194972664 A	
834	2502 A	+1:194972665 194972665 A	
835 V	2503 G	+1:194972666 194972666 G	V
835	2504 T	+1:194972667 194972667 T	
835	2505 A	+1:194972668 194972668 A	
836 S	2506 T	+1:194972669 194972669 T	S
836	2507 C	+1:194972670 194972670 C	
836	2508 T	+1:194972671 194972671 T	
837 V	2509 G	+1:194972672 194972672 G	V
837	2510 T	+1:194972673 194972673 T	
837	2511 T	+1:194972674 194972674 T	
838 L	2512 C	+1:194972675 194972675 C	L
838	2513 T	+1:194972676 194972676 T	
838	2514 T	+1:194972677 194972677 T	
839 C	2515 T	+1:194972678 194972678 T	C
839	2516 G	+1:194972679 194972679 G	
839	2517 C	+1:194972680 194972680 C	
840 Q	2518 C	+1:194972681 194972681 C	Q
840	2519 A	+1:194972682 194972682 A	
840	2520 A	+1:194972683 194972683 A	
841 E	2521 G	+1:194972684 194972684 G	E
841	2522 A	+1:194972685 194972685 A	
841	2523 A	+1:194972686 194972686 A	
842 N	2524 A	+1:194972687 194972687 A	N
842	2525 A	+1:194972688 194972688 A	
842	2526 T	+1:194972689 194972689 T	
843 Y	2527 T	+1:194972690 194972690 T	Y
843	2528 A	+1:194972691 194972691 A	
843	2529 T	+1:194972692 194972692 T	
844 L	2530 C	+1:194972693 194972693 C	L
844	2531 T	+1:194972694 194972694 T	
844	2532 A	+1:194972695 194972695 A	
845 I	2533 A	+1:194972696 194972696 A	I
845	2534 T	+1:194972697 194972697 T	
845	2535 T	+1:194972698 194972698 T	
846 Q	2536 C	+1:194972699 194972699 C	Q
846	2537 A	+1:194972700 194972700 A	
846	2538 G	+1:194972701 194972701 G	
847 E	2539 G	+1:194972702 194972702 G	E
847	2540 A	+1:194972703 194972703 A	
847	2541 A	+1:194972704 194972704 A	
848 G	2542 G	+1:194972705 194972705 G	G
848	2543 G	+1:194972706 194972706 G	
848	2544 A	+1:194972707 194972707 A	
849 E	2545 G	+1:194972708 194972708 G	E
849	2546 A	+1:194972709 194972709 A	
849	2547 A	+1:194972710 194972710 A	
850 E	2548 G	+1:194972711 194972711 G	E
850	2549 A	+1:194972712 194972712 A	
850	2550 A	+1:194972713 194972713 A	
851 I	2551 A	+1:194972714 194972714 A	I
851	2552 T	+1:194972715 194972715 T	
851	2553 T	+1:194972716 194972716 T	
852 T	2554 A	+1:194972717 194972717 A	T
852	2555 C	+1:194972718 194972718 C	
852	2556 A	+1:194972719 194972719 A	
853 C	2557 T	+1:194972720 194972720 T	C
853	2558 G	+1:194972721 194972721 G	
853	2559 C	+1:194972722 194972722 C	
854 K	2560 A	+1:194972723 194972723 A	K
854	2561 A	+1:194972724 194972724 A	
854	2562 A	+1:194972725 194972725 A	
855 D	2563 G	+1:194972726 194972726 G	D
855	2564 A	+1:194972727 194972727 A	
855	2565 T	+1:194972728 194972728 T	
856 G	2566 G	+1:194972729 194972729 G	G
856	2567 G	+1:194972730 194972730 G	
856	2568 A	+1:194972731 194972731 A	
857 R	2569 A	+1:194972732 194972732 A	R
857	2570 G	+1:194972733 194972733 G	
857	2571 A	+1:194972734 194972734 A	
858 W	2572 T	+1:194972735 194972735 T	W
858	2573 G	+1:194972736 194972736 G	
858	2574 G	+1:194972737 194972737 G	
859 Q	2575 C	+1:194972738 194972738 C	Q
859	2576 A	+1:194972739 194972739 A	
859	2577 G	+1:194972740 194972740 G	
860 S	2578 T	+1:194972741 194972741 T	S
860	2579 C	+1:194972742 194972742 C	
860	2580 A	+1:194972743 194972743 A	
861 I	2581 A	+1:194972744 194972744 A	I
861	2582 T	+1:194972745 194972745 T	
861	2583 A	+1:194972746 194972746 A	
862 P	2584 C	+1:194972747 194972747 C	P
862	2585 C	+1:194972748 194972748 C	
862	2586 A	+1:194972749 194972749 A	
863 L	2587 C	+1:194972750 194972750 C	L
863	2588 T	+1:194972751 194972751 T	
863	2589 C	+1:194972752 194972752 C	
864 C	2590 T	+1:194972753 194972753 T	C
864	2591 G	+1:194972754 194972754 G	
864	2592 T	+1:194972755 194972755 T	
865 V	2593 G	+1:194972756 194972756 G	V
865	2594 T	+1:194972757 194972757 T	
865	2595 T	+1:194972758 194972758 T	
866 E	2596 G	+1:194972759 194972759 G	E
866	2597 A	+1:194973228 194973228 A	
866	2598 A	+1:194973229 194973229 A	
867 K	2599 A	+1:194973230 194973230 A	K
867	2600 A	+1:194973231 194973231 A	
867	2601 A	+1:194973232 194973232 A	
868 I	2602 A	+1:194973233 194973233 A	I
868	2603 T	+1:194973234 194973234 T	
868	2604 T	+1:194973235 194973235 T	
869 P	2605 C	+1:194973236 194973236 C	P
869	2606 C	+1:194973237 194973237 C	
869	2607 A	+1:194973238 194973238 A	
870 C	2608 T	+1:194973239 194973239 T	C
870	2609 G	+1:194973240 194973240 G	
870	2610 T	+1:194973241 194973241 T	
871 S	2611 T	+1:194973242 194973242 T	S
871	2612 C	+1:194973243 194973243 C	
871	2613 A	+1:194973244 194973244 A	
872 Q	2614 C	+1:194973245 194973245 C	Q
872	2615 A	+1:194973246 194973246 A	
872	2616 A	+1:194973247 194973247 A	
873 P	2617 C	+1:194973248 194973248 C	P
873	2618 C	+1:194973249 194973249 C	
873	2619 A	+1:194973250 194973250 A	
874 P	2620 C	+1:194973251 194973251 C	P
874	2621 C	+1:194973252 194973252 C	
874	2622 T	+1:194973253 194973253 T	
875 Q	2623 C	+1:194973254 194973254 C	Q
875	2624 A	+1:194973255 194973255 A	
875	2625 G	+1:194973256 194973256 G	
876 I	2626 A	+1:194973257 194973257 A	I
876	2627 T	+1:194973258 194973258 T	
876	2628 A	+1:194973259 194973259 A	
877 E	2629 G	+1:194973260 194973260 G	E
877	2630 A	+1:194973261 194973261 A	
877	2631 A	+1:194973262 194973262 A	
878 H	2632 C	+1:194973263 194973263 C	H
878	2633 A	+1:194973264 194973264 A	
878	2634 C	+1:194973265 194973265 C	
879 G	2635 G	+1:194973266 194973266 G	G
879	2636 G	+1:194973267 194973267 G	
879	2637 A	+1:194973268 194973268 A	
880 T	2638 A	+1:194973269 194973269 A	T
880	2639 C	+1:194973270 194973270 C	
880	2640 C	+1:194973271 194973271 C	
881 I	2641 A	+1:194973272 194973272 A	I
881	2642 T	+1:194973273 194973273 T	
881	2643 T	+1:194973274 194973274 T	
882 N	2644 A	+1:194973275 194973275 A	N
882	2645 A	+1:194973276 194973276 A	
882	2646 T	+1:194973277 194973277 T	
883 S	2647 T	+1:194973278 194973278 T	S
883	2648 C	+1:194973279 194973279 C	
883	2649 A	+1:194973280 194973280 A	
884 S	2650 T	+1:194973281 194973281 T	S
884	2651 C	+1:194973282 194973282 C	
884	2652 C	+1:194973283 194973283 C	
885 R	2653 A	+1:194973284 194973284 A	R
885	2654 G	+1:194973285 194973285 G	
885	2655 G	+1:194973286 194973286 G	
886 S	2656 T	+1:194973287 194973287 T	S
886	2657 C	+1:194973288 194973288 C	
886	2658 T	+1:194973289 194973289 T	
887 S	2659 T	+1:194973290 194973290 T	S
887	2660 C	+1:194973291 194973291 C	
887	2661 A	+1:194973292 194973292 A	
888 Q	2662 C	+1:194973293 194973293 C	Q
888	2663 A	+1:194973294 194973294 A	
888	2664 A	+1:194973295 194973295 A	
889 E	2665 G	+1:194973296 194973296 G	E
889	2666 A	+1:194973297 194973297 A	
889	2667 A	+1:194973298 194973298 A	
890 S	2668 A	+1:194973299 194973299 A	S
890	2669 G	+1:194973300 194973300 G	
890	2670 T	+1:194973301 194973301 T	
891 Y	2671 T	+1:194973302 194973302 T	Y
891	2672 A	+1:194973303 194973303 A	
891	2673 T	+1:194973304 194973304 T	
892 A	2674 G	+1:194973305 194973305 G	A
892	2675 C	+1:194973306 194973306 C	
892	2676 A	+1:194973307 194973307 A	
893 H	2677 C	+1:194973308 194973308 C	H
893	2678 A	+1:194973309 194973309 A	
893	2679 T	+1:194973310 194973310 T	
894 G	2680 G	+1:194973311 194973311 G	G
894	2681 G	+1:194973312 194973312 G	
894	2682 G	+1:194973313 194973313 G	
895 T	2683 A	+1:194973314 194973314 A	T
895	2684 C	+1:194973315 194973315 C	
895	2685 T	+1:194973316 194973316 T	
896 K	2686 A	+1:194973317 194973317 A	K
896	2687 A	+1:194973318 194973318 A	
896	2688 A	+1:194973319 194973319 A	
897 L	2689 T	+1:194973320 194973320 T	L
897	2690 T	+1:194973321 194973321 T	
897	2691 G	+1:194973322 194973322 G	
898 S	2692 A	+1:194973323 194973323 A	S
898	2693 G	+1:194973324 194973324 G	
898	2694 T	+1:194973325 194973325 T	
899 Y	2695 T	+1:194973326 194973326 T	Y
899	2696 A	+1:194973327 194973327 A	
899	2697 T	+1:194973328 194973328 T	
900 T	2698 A	+1:194973329 194973329 A	T
900	2699 C	+1:194973330 194973330 C	
900	2700 T	+1:194973331 194973331 T	
901 C	2701 T	+1:194973332 194973332 T	C
901	2702 G	+1:194973333 194973333 G	
901	2703 T	+1:194973334 194973334 T	
902 E	2704 G	+1:194973335 194973335 G	E
902	2705 A	+1:194973336 194973336 A	
902	2706 G	+1:194973337 194973337 G	
903 G	2707 G	+1:194973338 194973338 G	G
903	2708 G	+1:194973339 194973339 G	
903	2709 T	+1:194973340 194973340 T	
904 G	2710 G	+1:194973341 194973341 G	G
904	2711 G	+1:194973342 194973342 G	
904	2712 T	+1:194973343 194973343 T	
905 F	2713 T	+1:194973344 194973344 T	F
905	2714 T	+1:194973345 194973345 T	
905	2715 C	+1:194973346 194973346 C	
906 R	2716 A	+1:194973347 194973347 A	R
906	2717 G	+1:194973348 194973348 G	
906	2718 G	+1:194973349 194973349 G	
907 I	2719 A	+1:194973350 194973350 A	I
907	2720 T	+1:194973351 194973351 T	
907	2721 A	+1:194973352 194973352 A	
908 S	2722 T	+1:194973353 194973353 T	S
908	2723 C	+1:194973354 194973354 C	
908	2724 T	+1:194973355 194973355 T	
909 E	2725 G	+1:194973356 194973356 G	E
909	2726 A	+1:194973357 194973357 A	
909	2727 A	+1:194973358 194973358 A	
910 E	2728 G	+1:194973359 194973359 G	E
910	2729 A	+1:194973360 194973360 A	
910	2730 A	+1:194973361 194973361 A	
911 N	2731 A	+1:194973362 194973362 A	N
911	2732 A	+1:194973363 194973363 A	
911	2733 T	+1:194973364 194973364 T	
912 E	2734 G	+1:194973365 194973365 G	E
912	2735 A	+1:194973366 194973366 A	
912	2736 A	+1:194973367 194973367 A	
913 T	2737 A	+1:194973368 194973368 A	T
913	2738 C	+1:194973369 194973369 C	
913	2739 A	+1:194973370 194973370 A	
914 T	2740 A	+1:194973371 194973371 A	T
914	2741 C	+1:194973372 194973372 C	
914	2742 A	+1:194973373 194973373 A	
915 C	2743 T	+1:194973374 194973374 T	C
915	2744 G	+1:194973375 194973375 G	
915	2745 C	+1:194973376 194973376 C	
916 Y	2746 T	+1:194973377 194973377 T	Y
916	2747 A	+1:194973378 194973378 A	
916	2748 C	+1:194973379 194973379 C	
917 M	2749 A	+1:194973380 194973380 A	M
917	2750 T	+1:194973381 194973381 T	
917	2751 G	+1:194973382 194973382 G	
918 G	2752 G	+1:194973383 194973383 G	G
918	2753 G	+1:194973384 194973384 G	
918	2754 A	+1:194973385 194973385 A	
919 K	2755 A	+1:194973386 194973386 A	K
919	2756 A	+1:194973387 194973387 A	
919	2757 A	+1:194973388 194973388 A	
920 W	2758 T	+1:194973389 194973389 T	W
920	2759 G	+1:194973390 194973390 G	
920	2760 G	+1:194973391 194973391 G	
921 S	2761 A	+1:194973392 194973392 A	S
921	2762 G	+1:194973393 194973393 G	
921	2763 T	+1:194973394 194973394 T	
922 S	2764 T	+1:194973395 194973395 T	S
922	2765 C	+1:194973396 194973396 C	
922	2766 T	+1:194973397 194973397 T	
923 P	2767 C	+1:194973398 194973398 C	P
923	2768 C	+1:194973399 194973399 C	
923	2769 A	+1:194973400 194973400 A	
924 P	2770 C	+1:194973401 194973401 C	P
924	2771 C	+1:194973402 194973402 C	
924	2772 T	+1:194973403 194973403 T	
925 Q	2773 C	+1:194973404 194973404 C	Q
925	2774 A	+1:194973405 194973405 A	
925	2775 G	+1:194973406 194973406 G	
926 C	2776 T	+1:194973407 194973407 T	C
926	2777 G	+1:194973408 194973408 G	
926	2778 T	+1:194973409 194973409 T	
927 E	2779 G	+1:194973410 194973410 G	E
927	2780 A	+1:194973411 194973411 A	
927	2781 A	+1:194973412 194973412 A	
928 G	2782 G	+1:194973413 194973413 G	G
928	2783 G	+1:194976372 194976372 G	
928	2784 C	+1:194976373 194976373 C	
929 L	2785 C	+1:194976374 194976374 C	L
929	2786 T	+1:194976375 194976375 T	
929	2787 T	+1:194976376 194976376 T	
930 P	2788 C	+1:194976377 194976377 C	P
930	2789 C	+1:194976378 194976378 C	
930	2790 T	+1:194976379 194976379 T	
931 C	2791 T	+1:194976380 194976380 T	C
931	2792 G	+1:194976381 194976381 G	
931	2793 T	+1:194976382 194976382 T	
932 K	2794 A	+1:194976383 194976383 A	K
932	2795 A	+1:194976384 194976384 A	
932	2796 A	+1:194976385 194976385 A	
933 S	2797 T	+1:194976386 194976386 T	S
933	2798 C	+1:194976387 194976387 C	
933	2799 T	+1:194976388 194976388 T	
934 P	2800 C	+1:194976389 194976389 C	P
934	2801 C	+1:194976390 194976390 C	
934	2802 A	+1:194976391 194976391 A	
935 P	2803 C	+1:194976392 194976392 C	P
935	2804 C	+1:194976393 194976393 C	
935	2805 T	+1:194976394 194976394 T	
936 E	2806 G	+1:194976395 194976395 G	E
936	2807 A	+1:194976396 194976396 A	
936	2808 G	+1:194976397 194976397 G	
937 I	2809 A	+1:194976398 194976398 A	I
937	2810 T	+1:194976399 194976399 T	
937	2811 T	+1:194976400 194976400 T	
938 S	2812 T	+1:194976401 194976401 T	S
938	2813 C	+1:194976402 194976402 C	
938	2814 T	+1:194976403 194976403 T	
939 H	2815 C	+1:194976404 194976404 C	H
939	2816 A	+1:194976405 194976405 A	
939	2817 T	+1:194976406 194976406 T	
940 G	2818 G	+1:194976407 194976407 G	G
940	2819 G	+1:194976408 194976408 G	
940	2820 T	+1:194976409 194976409 T	
941 V	2821 G	+1:194976410 194976410 G	V
941	2822 T	+1:194976411 194976411 T	
941	2823 T	+1:194976412 194976412 T	
942 V	2824 G	+1:194976413 194976413 G	V
942	2825 T	+1:194976414 194976414 T	
942	2826 A	+1:194976415 194976415 A	
943 A	2827 G	+1:194976416 194976416 G	A
943	2828 C	+1:194976417 194976417 C	
943	2829 T	+1:194976418 194976418 T	
944 H	2830 C	+1:194976419 194976419 C	H
944	2831 A	+1:194976420 194976420 A	
944	2832 C	+1:194976421 194976421 C	
945 M	2833 A	+1:194976422 194976422 A	M
945	2834 T	+1:194976423 194976423 T	
945	2835 G	+1:194976424 194976424 G	
946 S	2836 T	+1:194976425 194976425 T	S
946	2837 C	+1:194976426 194976426 C	
946	2838 A	+1:194976427 194976427 A	
947 D	2839 G	+1:194976428 194976428 G	D
947	2840 A	+1:194976429 194976429 A	
947	2841 C	+1:194976430 194976430 C	
948 S	2842 A	+1:194976431 194976431 A	S
948	2843 G	+1:194976432 194976432 G	
948	2844 T	+1:194976433 194976433 T	
949 Y	2845 T	+1:194976434 194976434 T	Y
949	2846 A	+1:194976435 194976435 A	
949	2847 T	+1:194976436 194976436 T	
950 Q	2848 C	+1:194976437 194976437 C	Q
950	2849 A	+1:194976438 194976438 A	
950	2850 G	+1:194976439 194976439 G	
951 Y	2851 T	+1:194976440 194976440 T	Y
951	2852 A	+1:194976441 194976441 A	
951	2853 T	+1:194976442 194976442 T	
952 G	2854 G	+1:194976443 194976443 G	G
952	2855 G	+1:194976444 194976444 G	
952	2856 A	+1:194976445 194976445 A	
953 E	2857 G	+1:194976446 194976446 G	E
953	2858 A	+1:194976447 194976447 A	
953	2859 A	+1:194976448 194976448 A	
954 E	2860 G	+1:194976449 194976449 G	E
954	2861 A	+1:194976450 194976450 A	
954	2862 A	+1:194976451 194976451 A	
955 V	2863 G	+1:194976452 194976452 G	V
955	2864 T	+1:194976453 194976453 T	
955	2865 T	+1:194976454 194976454 T	
956 T	2866 A	+1:194976455 194976455 A	T
956	2867 C	+1:194976456 194976456 C	
956	2868 G	+1:194976457 194976457 G	
957 Y	2869 T	+1:194976458 194976458 T	Y
957	2870 A	+1:194976459 194976459 A	
957	2871 C	+1:194976460 194976460 C	
958 K	2872 A	+1:194976461 194976461 A	K
958	2873 A	+1:194976462 194976462 A	
958	2874 A	+1:194976463 194976463 A	
959 C	2875 T	+1:194976464 194976464 T	C
959	2876 G	+1:194976465 194976465 G	
959	2877 T	+1:194976466 194976466 T	
960 F	2878 T	+1:194976467 194976467 T	F
960	2879 T	+1:194976468 194976468 T	
960	2880 T	+1:194976469 194976469 T	
961 E	2881 G	+1:194976470 194976470 G	E
961	2882 A	+1:194976471 194976471 A	
961	2883 A	+1:194976472 194976472 A	
962 G	2884 G	+1:194976473 194976473 G	G
962	2885 G	+1:194976474 194976474 G	
962	2886 T	+1:194976475 194976475 T	
963 F	2887 T	+1:194976476 194976476 T	F
963	2888 T	+1:194976477 194976477 T	
963	2889 T	+1:194976478 194976478 T	
964 G	2890 G	+1:194976479 194976479 G	G
964	2891 G	+1:194976480 194976480 G	
964	2892 A	+1:194976481 194976481 A	
965 I	2893 A	+1:194976482 194976482 A	I
965	2894 T	+1:194976483 194976483 T	
965	2895 T	+1:194976484 194976484 T	
966 D	2896 G	+1:194976485 194976485 G	D
966	2897 A	+1:194976486 194976486 A	
966	2898 T	+1:194976487 194976487 T	
967 G	2899 G	+1:194976488 194976488 G	G
967	2900 G	+1:194976489 194976489 G	
967	2901 G	+1:194976490 194976490 G	
968 P	2902 C	+1:194976491 194976491 C	P
968	2903 C	+1:194976492 194976492 C	
968	2904 T	+1:194976493 194976493 T	
969 A	2905 G	+1:194976494 194976494 G	A
969	2906 C	+1:194976495 194976495 C	
969	2907 A	+1:194976496 194976496 A	
970 I	2908 A	+1:194976497 194976497 A	I
970	2909 T	+1:194976498 194976498 T	
970	2910 T	+1:194976499 194976499 T	
971 A	2911 G	+1:194976500 194976500 G	A
971	2912 C	+1:194976501 194976501 C	
971	2913 A	+1:194976502 194976502 A	
972 K	2914 A	+1:194976503 194976503 A	K
972	2915 A	+1:194976504 194976504 A	
972	2916 A	+1:194976505 194976505 A	
973 C	2917 T	+1:194976506 194976506 T	C
973	2918 G	+1:194976507 194976507 G	
973	2919 C	+1:194976508 194976508 C	
974 L	2920 T	+1:194976509 194976509 T	L
974	2921 T	+1:194976510 194976510 T	
974	2922 A	+1:194976511 194976511 A	
975 G	2923 G	+1:194976512 194976512 G	G
975	2924 G	+1:194976513 194976513 G	
975	2925 A	+1:194976514 194976514 A	
976 E	2926 G	+1:194976515 194976515 G	E
976	2927 A	+1:194976516 194976516 A	
976	2928 A	+1:194976517 194976517 A	
977 K	2929 A	+1:194976518 194976518 A	K
977	2930 A	+1:194976519 194976519 A	
977	2931 A	+1:194976520 194976520 A	
978 W	2932 T	+1:194976521 194976521 T	W
978	2933 G	+1:194976522 194976522 G	
978	2934 G	+1:194976523 194976523 G	
979 S	2935 T	+1:194976524 194976524 T	S
979	2936 C	+1:194976525 194976525 C	
979	2937 T	+1:194976526 194976526 T	
980 H	2938 C	+1:194976527 194976527 C	H
980	2939 A	+1:194976528 194976528 A	
980	2940 C	+1:194976529 194976529 C	
981 P	2941 C	+1:194976530 194976530 C	P
981	2942 C	+1:194976531 194976531 C	
981	2943 T	+1:194976532 194976532 T	
982 P	2944 C	+1:194976533 194976533 C	P
982	2945 C	+1:194976534 194976534 C	
982	2946 A	+1:194976535 194976535 A	
983 S	2947 T	+1:194976536 194976536 T	S
983	2948 C	+1:194976537 194976537 C	
983	2949 A	+1:194976538 194976538 A	
984 C	2950 T	+1:194976539 194976539 T	C
984	2951 G	+1:194976540 194976540 G	
984	2952 C	+1:194976541 194976541 C	
985 I	2953 A	+1:194976542 194976542 A	I
985	2954 T	+1:194976543 194976543 T	
985	2955 A	+1:194976544 194976544 A	
986 K	2956 A	+1:194976545 194976545 A	K
986	2957 A	+1:194977628 194977628 A	
986	2958 A	+1:194977629 194977629 A	
987 T	2959 A	+1:194977630 194977630 A	T
987	2960 C	+1:194977631 194977631 C	
987	2961 A	+1:194977632 194977632 A	
988 D	2962 G	+1:194977633 194977633 G	D
988	2963 A	+1:194977634 194977634 A	
988	2964 T	+1:194977635 194977635 T	
989 C	2965 T	+1:194977636 194977636 T	C
989	2966 G	+1:194977637 194977637 G	
989	2967 T	+1:194977638 194977638 T	
990 L	2968 C	+1:194977639 194977639 C	L
990	2969 T	+1:194977640 194977640 T	
990	2970 C	+1:194977641 194977641 C	
991 S	2971 A	+1:194977642 194977642 A	S
991	2972 G	+1:194977643 194977643 G	
991	2973 T	+1:194977644 194977644 T	
992 L	2974 T	+1:194977645 194977645 T	L
992	2975 T	+1:194977646 194977646 T	
992	2976 A	+1:194977647 194977647 A	
993 P	2977 C	+1:194977648 194977648 C	P
993	2978 C	+1:194977649 194977649 C	
993	2979 T	+1:194977650 194977650 T	
994 S	2980 A	+1:194977651 194977651 A	S
994	2981 G	+1:194977652 194977652 G	
994	2982 C	+1:194977653 194977653 C	
995 F	2983 T	+1:194977654 194977654 T	F
995	2984 T	+1:194977655 194977655 T	
995	2985 T	+1:194977656 194977656 T	
996 E	2986 G	+1:194977657 194977657 G	E
996	2987 A	+1:194977658 194977658 A	
996	2988 A	+1:194977659 194977659 A	
997 N	2989 A	+1:194977660 194977660 A	N
997	2990 A	+1:194977661 194977661 A	
997	2991 T	+1:194977662 194977662 T	
998 A	2992 G	+1:194977663 194977663 G	A
998	2993 C	+1:194977664 194977664 C	
998	2994 C	+1:194977665 194977665 C	
999 I	2995 A	+1:194977666 194977666 A	I
999	2996 T	+1:194977667 194977667 T	
999	2997 A	+1:194977668 194977668 A	
1000 P	2998 C	+1:194977669 194977669 C	P
1000	2999 C	+1:194977670 194977670 C	
1000	3000 C	+1:194977671 194977671 C	
1001 M	3001 A	+1:194977672 194977672 A	M
1001	3002 T	+1:194977673 194977673 T	
1001	3003 G	+1:194977674 194977674 G	
1002 G	3004 G	+1:194977675 194977675 G	G
1002	3005 G	+1:194977676 194977676 G	
1002	3006 A	+1:194977677 194977677 A	
1003 E	3007 G	+1:194977678 194977678 G	E
1003	3008 A	+1:194977679 194977679 A	
1003	3009 G	+1:194977680 194977680 G	
1004 K	3010 A	+1:194977681 194977681 A	K
1004	3011 A	+1:194977682 194977682 A	
1004	3012 G	+1:194977683 194977683 G	
1005 K	3013 A	+1:194977684 194977684 A	K
1005	3014 A	+1:194977685 194977685 A	
1005	3015 G	+1:194977686 194977686 G	
1006 D	3016 G	+1:194977687 194977687 G	D
1006	3017 A	+1:194977688 194977688 A	
1006	3018 T	+1:194977689 194977689 T	
1007 V	3019 G	+1:194977690 194977690 G	V
1007	3020 T	+1:194977691 194977691 T	
1007	3021 G	+1:194977692 194977692 G	
1008 Y	3022 T	+1:194977693 194977693 T	Y
1008	3023 A	+1:194977694 194977694 A	
1008	3024 T	+1:194977695 194977695 T	
1009 K	3025 A	+1:194977696 194977696 A	K
1009	3026 A	+1:194977697 194977697 A	
1009	3027 G	+1:194977698 194977698 G	
1010 A	3028 G	+1:194977699 194977699 G	A
1010	3029 C	+1:194977700 194977700 C	
1010	3030 G	+1:194977701 194977701 G	
1011 G	3031 G	+1:194977702 194977702 G	G
1011	3032 G	+1:194977703 194977703 G	
1011	3033 T	+1:194977704 194977704 T	
1012 E	3034 G	+1:194977705 194977705 G	E
1012	3035 A	+1:194977706 194977706 A	
1012	3036 G	+1:194977707 194977707 G	
1013 Q	3037 C	+1:194977708 194977708 C	Q
1013	3038 A	+1:194977709 194977709 A	
1013	3039 A	+1:194977710 194977710 A	
1014 V	3040 G	+1:194977711 194977711 G	V
1014	3041 T	+1:194977712 194977712 T	
1014	3042 G	+1:194977713 194977713 G	
1015 T	3043 A	+1:194977714 194977714 A	T
1015	3044 C	+1:194977715 194977715 C	
1015	3045 T	+1:194977716 194977716 T	
1016 Y	3046 T	+1:194977717 194977717 T	Y
1016	3047 A	+1:194977718 194977718 A	
1016	3048 C	+1:194977719 194977719 C	
1017 T	3049 A	+1:194977720 194977720 A	T
1017	3050 C	+1:194977721 194977721 C	
1017	3051 T	+1:194977722 194977722 T	
1018 C	3052 T	+1:194977723 194977723 T	C
1018	3053 G	+1:194977724 194977724 G	
1018	3054 T	+1:194977725 194977725 T	
1019 A	3055 G	+1:194977726 194977726 G	A
1019	3056 C	+1:194977727 194977727 C	
1019	3057 A	+1:194977728 194977728 A	
1020 T	3058 A	+1:194977729 194977729 A	T
1020	3059 C	+1:194977730 194977730 C	
1020	3060 A	+1:194977731 194977731 A	
1021 Y	3061 T	+1:194977732 194977732 T	Y
1021	3062 A	+1:194977733 194977733 A	
1021	3063 T	+1:194977734 194977734 T	
1022 Y	3064 T	+1:194977735 194977735 T	Y
1022	3065 A	+1:194977736 194977736 A	
1022	3066 C	+1:194977737 194977737 C	
1023 K	3067 A	+1:194977738 194977738 A	K
1023	3068 A	+1:194977739 194977739 A	
1023	3069 A	+1:194977740 194977740 A	
1024 M	3070 A	+1:194977741 194977741 A	M
1024	3071 T	+1:194977742 194977742 T	
1024	3072 G	+1:194977743 194977743 G	
1025 D	3073 G	+1:194977744 194977744 G	D
1025	3074 A	+1:194977745 194977745 A	
1025	3075 T	+1:194977746 194977746 T	
1026 G	3076 G	+1:194977747 194977747 G	G
1026	3077 G	+1:194977748 194977748 G	
1026	3078 A	+1:194977749 194977749 A	
1027 A	3079 G	+1:194977750 194977750 G	A
1027	3080 C	+1:194977751 194977751 C	
1027	3081 C	+1:194977752 194977752 C	
1028 S	3082 A	+1:194977753 194977753 A	S
1028	3083 G	+1:194977754 194977754 G	
1028	3084 T	+1:194977755 194977755 T	
1029 N	3085 A	+1:194977756 194977756 A	N
1029	3086 A	+1:194977757 194977757 A	
1029	3087 T	+1:194977758 194977758 T	
1030 V	3088 G	+1:194977759 194977759 G	V
1030	3089 T	+1:194977760 194977760 T	
1030	3090 A	+1:194977761 194977761 A	
1031 T	3091 A	+1:194977762 194977762 A	T
1031	3092 C	+1:194977763 194977763 C	
1031	3093 A	+1:194977764 194977764 A	
1032 C	3094 T	+1:194977765 194977765 T	C
1032	3095 G	+1:194977766 194977766 G	
1032	3096 C	+1:194977767 194977767 C	
1033 I	3097 A	+1:194977768 194977768 A	I
1033	3098 T	+1:194977769 194977769 T	
1033	3099 T	+1:194977770 194977770 T	
1034 N	3100 A	+1:194977771 194977771 A	N
1034	3101 A	+1:194977772 194977772 A	
1034	3102 T	+1:194977773 194977773 T	
1035 S	3103 A	+1:194977774 194977774 A	S
1035	3104 G	+1:194977775 194977775 G	
1035	3105 C	+1:194977776 194977776 C	
1036 R	3106 A	+1:194977777 194977777 A	R
1036	3107 G	+1:194977778 194977778 G	
1036	3108 A	+1:194977779 194977779 A	
1037 W	3109 T	+1:194977780 194977780 T	W
1037	3110 G	+1:194977781 194977781 G	
1037	3111 G	+1:194977782 194977782 G	
1038 T	3112 A	+1:194977783 194977783 A	T
1038	3113 C	+1:194977784 194977784 C	
1038	3114 A	+1:194977785 194977785 A	
1039 G	3115 G	+1:194977786 194977786 G	G
1039	3116 G	+1:194977787 194977787 G	
1039	3117 A	+1:194977788 194977788 A	
1040 R	3118 A	+1:194977789 194977789 A	R
1040	3119 G	+1:194977790 194977790 G	
1040	3120 G	+1:194977791 194977791 G	
1041 P	3121 C	+1:194977792 194977792 C	P
1041	3122 C	+1:194977793 194977793 C	
1041	3123 A	+1:194977794 194977794 A	
1042 T	3124 A	+1:194977795 194977795 A	T
1042	3125 C	+1:194977796 194977796 C	
1042	3126 A	+1:194977797 194977797 A	
1043 C	3127 T	+1:194977798 194977798 T	C
1043	3128 G	+1:194977799 194977799 G	
1043	3129 C	+1:194977800 194977800 C	
1044 R	3130 A	+1:194977801 194977801 A	R
1044	3131 G	+1:194977802 194977802 G	
1044	3132 A	+1:194977803 194977803 A	
1045 D	3133 G	+1:194977804 194977804 G	D
1045	3134 A	+1:194979205 194979205 A	
1045	3135 C	+1:194979206 194979206 C	
1046 T	3136 A	+1:194979207 194979207 A	T
1046	3137 C	+1:194979208 194979208 C	
1046	3138 C	+1:194979209 194979209 C	
1047 S	3139 T	+1:194979210 194979210 T	S
1047	3140 C	+1:194979211 194979211 C	
1047	3141 C	+1:194979212 194979212 C	
1048 C	3142 T	+1:194979213 194979213 T	C
1048	3143 G	+1:194979214 194979214 G	
1048	3144 T	+1:194979215 194979215 T	
1049 V	3145 G	+1:194979216 194979216 G	V
1049	3146 T	+1:194979217 194979217 T	
1049	3147 G	+1:194979218 194979218 G	
1050 N	3148 A	+1:194979219 194979219 A	N
1050	3149 A	+1:194979220 194979220 A	
1050	3150 T	+1:194979221 194979221 T	
1051 P	3151 C	+1:194979222 194979222 C	P
1051	3152 C	+1:194979223 194979223 C	
1051	3153 G	+1:194979224 194979224 G	
1052 P	3154 C	+1:194979225 194979225 C	P
1052	3155 C	+1:194979226 194979226 C	
1052	3156 C	+1:194979227 194979227 C	
1053 T	3157 A	+1:194979228 194979228 A	T
1053	3158 C	+1:194979229 194979229 C	
1053	3159 A	+1:194979230 194979230 A	
1054 V	3160 G	+1:194979231 194979231 G	V
1054	3161 T	+1:194979232 194979232 T	
1054	3162 A	+1:194979233 194979233 A	
1055 Q	3163 C	+1:194979234 194979234 C	Q
1055	3164 A	+1:194979235 194979235 A	
1055	3165 A	+1:194979236 194979236 A	
1056 N	3166 A	+1:194979237 194979237 A	N
1056	3167 A	+1:194979238 194979238 A	
1056	3168 T	+1:194979239 194979239 T	
1057 A	3169 G	+1:194979240 194979240 G	A
1057	3170 C	+1:194979241 194979241 C	
1057	3171 T	+1:194979242 194979242 T	
1058 Y	3172 T	+1:194979243 194979243 T	Y
1058	3173 A	+1:194979244 194979244 A	
1058	3174 T	+1:194979245 194979245 T	
1059 I	3175 A	+1:194979246 194979246 A	I
1059	3176 T	+1:194979247 194979247 T	
1059	3177 A	+1:194979248 194979248 A	
1060 V	3178 G	+1:194979249 194979249 G	V
1060	3179 T	+1:194979250 194979250 T	
1060	3180 G	+1:194979251 194979251 G	
1061 S	3181 T	+1:194979252 194979252 T	S
1061	3182 C	+1:194979253 194979253 C	
1061	3183 G	+1:194979254 194979254 G	
1062 R	3184 A	+1:194979255 194979255 A	R
1062	3185 G	+1:194979256 194979256 G	
1062	3186 A	+1:194979257 194979257 A	
1063 Q	3187 C	+1:194979258 194979258 C	Q
1063	3188 A	+1:194979259 194979259 A	
1063	3189 G	+1:194979260 194979260 G	
1064 M	3190 A	+1:194979261 194979261 A	M
1064	3191 T	+1:194979262 194979262 T	
1064	3192 G	+1:194979263 194979263 G	
1065 S	3193 A	+1:194979264 194979264 A	S
1065	3194 G	+1:194979265 194979265 G	
1065	3195 T	+1:194979266 194979266 T	
1066 K	3196 A	+1:194979267 194979267 A	K
1066	3197 A	+1:194979268 194979268 A	
1066	3198 A	+1:194979269 194979269 A	
1067 Y	3199 T	+1:194979270 194979270 T	Y
1067	3200 A	+1:194979271 194979271 A	
1067	3201 T	+1:194979272 194979272 T	
1068 P	3202 C	+1:194979273 194979273 C	P
1068	3203 C	+1:194979274 194979274 C	
1068	3204 A	+1:194979275 194979275 A	
1069 S	3205 T	+1:194979276 194979276 T	S
1069	3206 C	+1:194979277 194979277 C	
1069	3207 T	+1:194979278 194979278 T	
1070 G	3208 G	+1:194979279 194979279 G	G
1070	3209 G	+1:194979280 194979280 G	
1070	3210 T	+1:194979281 194979281 T	
1071 E	3211 G	+1:194979282 194979282 G	E
1071	3212 A	+1:194979283 194979283 A	
1071	3213 G	+1:194979284 194979284 G	
1072 R	3214 A	+1:194979285 194979285 A	R
1072	3215 G	+1:194979286 194979286 G	
1072	3216 A	+1:194979287 194979287 A	
1073 V	3217 G	+1:194979288 194979288 G	V
1073	3218 T	+1:194979289 194979289 T	
1073	3219 A	+1:194979290 194979290 A	
1074 R	3220 C	+1:194979291 194979291 C	R
1074	3221 G	+1:194979292 194979292 G	
1074	3222 T	+1:194979293 194979293 T	
1075 Y	3223 T	+1:194979294 194979294 T	Y
1075	3224 A	+1:194979295 194979295 A	
1075	3225 T	+1:194979296 194979296 T	
1076 Q	3226 C	+1:194979297 194979297 C	Q
1076	3227 A	+1:194979298 194979298 A	
1076	3228 A	+1:194979299 194979299 A	
1077 C	3229 T	+1:194979300 194979300 T	C
1077	3230 G	+1:194979301 194979301 G	
1077	3231 T	+1:194979302 194979302 T	
1078 R	3232 A	+1:194979303 194979303 A	R
1078	3233 G	+1:194979304 194979304 G	
1078	3234 G	+1:194979305 194979305 G	
1079 S	3235 A	+1:194979306 194979306 A	S
1079	3236 G	+1:194979307 194979307 G	
1079	3237 C	+1:194979308 194979308 C	
1080 P	3238 C	+1:194979309 194979309 C	P
1080	3239 C	+1:194979310 194979310 C	
1080	3240 T	+1:194979311 194979311 T	
1081 Y	3241 T	+1:194979312 194979312 T	Y
1081	3242 A	+1:194979313 194979313 A	
1081	3243 T	+1:194979314 194979314 T	
1082 E	3244 G	+1:194979315 194979315 G	E
1082	3245 A	+1:194979316 194979316 A	
1082	3246 A	+1:194979317 194979317 A	
1083 M	3247 A	+1:194979318 194979318 A	M
1083	3248 T	+1:194979319 194979319 T	
1083	3249 G	+1:194979320 194979320 G	
1084 F	3250 T	+1:194979321 194979321 T	F
1084	3251 T	+1:194979322 194979322 T	
1084	3252 T	+1:194979323 194979323 T	
1085 G	3253 G	+1:194979324 194979324 G	G
1085	3254 G	+1:194979325 194979325 G	
1085	3255 G	+1:194979326 194979326 G	
1086 D	3256 G	+1:194979327 194979327 G	D
1086	3257 A	+1:194979328 194979328 A	
1086	3258 T	+1:194979329 194979329 T	
1087 E	3259 G	+1:194979330 194979330 G	E
1087	3260 A	+1:194979331 194979331 A	
1087	3261 A	+1:194979332 194979332 A	
1088 E	3262 G	+1:194979333 194979333 G	E
1088	3263 A	+1:194979334 194979334 A	
1088	3264 A	+1:194979335 194979335 A	
1089 V	3265 G	+1:194979336 194979336 G	V
1089	3266 T	+1:194979337 194979337 T	
1089	3267 G	+1:194979338 194979338 G	
1090 M	3268 A	+1:194979339 194979339 A	M
1090	3269 T	+1:194979340 194979340 T	
1090	3270 G	+1:194979341 194979341 G	
1091 C	3271 T	+1:194979342 194979342 T	C
1091	3272 G	+1:194979343 194979343 G	
1091	3273 T	+1:194979344 194979344 T	
1092 L	3274 T	+1:194979345 194979345 T	L
1092	3275 T	+1:194979346 194979346 T	
1092	3276 A	+1:194979347 194979347 A	
1093 N	3277 A	+1:194979348 194979348 A	N
1093	3278 A	+1:194979349 194979349 A	
1093	3279 T	+1:194979350 194979350 T	
1094 G	3280 G	+1:194979351 194979351 G	G
1094	3281 G	+1:194979352 194979352 G	
1094	3282 A	+1:194979353 194979353 A	
1095 N	3283 A	+1:194979354 194979354 A	N
1095	3284 A	+1:194979355 194979355 A	
1095	3285 C	+1:194979356 194979356 C	
1096 W	3286 T	+1:194979357 194979357 T	W
1096	3287 G	+1:194979358 194979358 G	
1096	3288 G	+1:194979359 194979359 G	
1097 T	3289 A	+1:194979360 194979360 A	T
1097	3290 C	+1:194979361 194979361 C	
1097	3291 G	+1:194979362 194979362 G	
1098 E	3292 G	+1:194979363 194979363 G	E
1098	3293 A	+1:194979364 194979364 A	
1098	3294 A	+1:194979365 194979365 A	
1099 P	3295 C	+1:194979366 194979366 C	P
1099	3296 C	+1:194979367 194979367 C	
1099	3297 A	+1:194979368 194979368 A	
1100 P	3298 C	+1:194979369 194979369 C	P
1100	3299 C	+1:194979370 194979370 C	
1100	3300 T	+1:194979371 194979371 T	
1101 Q	3301 C	+1:194979372 194979372 C	Q
1101	3302 A	+1:194979373 194979373 A	
1101	3303 A	+1:194979374 194979374 A	
1102 C	3304 T	+1:194979375 194979375 T	C
1102	3305 G	+1:194979376 194979376 G	
1102	3306 C	+1:194979377 194979377 C	
1103 K	3307 A	+1:194979378 194979378 A	K
1103	3308 A	+1:194979379 194979379 A	
1103	3309 A	+1:194979380 194979380 A	
1104 D	3310 G	+1:194979381 194979381 G	D
1104	3311 A	+1:194981570 194981570 A	
1104	3312 T	+1:194981571 194981571 T	
1105 S	3313 T	+1:194981572 194981572 T	S
1105	3314 C	+1:194981573 194981573 C	
1105	3315 T	+1:194981574 194981574 T	
1106 T	3316 A	+1:194981575 194981575 A	T
1106	3317 C	+1:194981576 194981576 C	
1106	3318 A	+1:194981577 194981577 A	
1107 G	3319 G	+1:194981578 194981578 G	G
1107	3320 G	+1:194981579 194981579 G	
1107	3321 A	+1:194981580 194981580 A	
1108 K	3322 A	+1:194981581 194981581 A	K
1108	3323 A	+1:194981582 194981582 A	
1108	3324 A	+1:194981583 194981583 A	
1109 C	3325 T	+1:194981584 194981584 T	C
1109	3326 G	+1:194981585 194981585 G	
1109	3327 T	+1:194981586 194981586 T	
1110 G	3328 G	+1:194981587 194981587 G	G
1110	3329 G	+1:194981588 194981588 G	
1110	3330 G	+1:194981589 194981589 G	
1111 P	3331 C	+1:194981590 194981590 C	P
1111	3332 C	+1:194981591 194981591 C	
1111	3333 C	+1:194981592 194981592 C	
1112 P	3334 C	+1:194981593 194981593 C	P
1112	3335 C	+1:194981594 194981594 C	
1112	3336 T	+1:194981595 194981595 T	
1113 P	3337 C	+1:194981596 194981596 C	P
1113	3338 C	+1:194981597 194981597 C	
1113	3339 A	+1:194981598 194981598 A	
1114 P	3340 C	+1:194981599 194981599 C	P
1114	3341 C	+1:194981600 194981600 C	
1114	3342 T	+1:194981601 194981601 T	
1115 I	3343 A	+1:194981602 194981602 A	I
1115	3344 T	+1:194981603 194981603 T	
1115	3345 T	+1:194981604 194981604 T	
1116 D	3346 G	+1:194981605 194981605 G	D
1116	3347 A	+1:194981606 194981606 A	
1116	3348 C	+1:194981607 194981607 C	
1117 N	3349 A	+1:194981608 194981608 A	N
1117	3350 A	+1:194981609 194981609 A	
1117	3351 T	+1:194981610 194981610 T	
1118 G	3352 G	+1:194981611 194981611 G	G
1118	3353 G	+1:194981612 194981612 G	
1118	3354 G	+1:194981613 194981613 G	
1119 D	3355 G	+1:194981614 194981614 G	D
1119	3356 A	+1:194981615 194981615 A	
1119	3357 C	+1:194981616 194981616 C	
1120 I	3358 A	+1:194981617 194981617 A	I
1120	3359 T	+1:194981618 194981618 T	
1120	3360 T	+1:194981619 194981619 T	
1121 T	3361 A	+1:194981620 194981620 A	T
1121	3362 C	+1:194981621 194981621 C	
1121	3363 T	+1:194981622 194981622 T	
1122 S	3364 T	+1:194981623 194981623 T	S
1122	3365 C	+1:194981624 194981624 C	
1122	3366 A	+1:194981625 194981625 A	
1123 F	3367 T	+1:194981626 194981626 T	F
1123	3368 T	+1:194981627 194981627 T	
1123	3369 C	+1:194981628 194981628 C	
1124 P	3370 C	+1:194981629 194981629 C	P
1124	3371 C	+1:194981630 194981630 C	
1124	3372 G	+1:194981631 194981631 G	
1125 L	3373 T	+1:194981632 194981632 T	L
1125	3374 T	+1:194981633 194981633 T	
1125	3375 G	+1:194981634 194981634 G	
1126 S	3376 T	+1:194981635 194981635 T	S
1126	3377 C	+1:194981636 194981636 C	
1126	3378 A	+1:194981637 194981637 A	
1127 V	3379 G	+1:194981638 194981638 G	V
1127	3380 T	+1:194981639 194981639 T	
1127	3381 A	+1:194981640 194981640 A	
1128 Y	3382 T	+1:194981641 194981641 T	Y
1128	3383 A	+1:194981642 194981642 A	
1128	3384 T	+1:194981643 194981643 T	
1129 A	3385 G	+1:194981644 194981644 G	A
1129	3386 C	+1:194981645 194981645 C	
1129	3387 T	+1:194981646 194981646 T	
1130 P	3388 C	+1:194981647 194981647 C	P
1130	3389 C	+1:194981648 194981648 C	
1130	3390 A	+1:194981649 194981649 A	
1131 A	3391 G	+1:194981650 194981650 G	A
1131	3392 C	+1:194981651 194981651 C	
1131	3393 T	+1:194981652 194981652 T	
1132 S	3394 T	+1:194981653 194981653 T	S
1132	3395 C	+1:194981654 194981654 C	
1132	3396 A	+1:194981655 194981655 A	
1133 S	3397 T	+1:194981656 194981656 T	S
1133	3398 C	+1:194981657 194981657 C	
1133	3399 A	+1:194981658 194981658 A	
1134 V	3400 G	+1:194981659 194981659 G	V
1134	3401 T	+1:194981660 194981660 T	
1134	3402 T	+1:194981661 194981661 T	
1135 E	3403 G	+1:194981662 194981662 G	E
1135	3404 A	+1:194981663 194981663 A	
1135	3405 G	+1:194981664 194981664 G	
1136 Y	3406 T	+1:194981665 194981665 T	Y
1136	3407 A	+1:194981666 194981666 A	
1136	3408 C	+1:194981667 194981667 C	
1137 Q	3409 C	+1:194981668 194981668 C	Q
1137	3410 A	+1:194981669 194981669 A	
1137	3411 A	+1:194981670 194981670 A	
1138 C	3412 T	+1:194981671 194981671 T	C
1138	3413 G	+1:194981672 194981672 G	
1138	3414 C	+1:194981673 194981673 C	
1139 Q	3415 C	+1:194981674 194981674 C	Q
1139	3416 A	+1:194981675 194981675 A	
1139	3417 G	+1:194981676 194981676 G	
1140 N	3418 A	+1:194981677 194981677 A	N
1140	3419 A	+1:194981678 194981678 A	
1140	3420 C	+1:194981679 194981679 C	
1141 L	3421 T	+1:194981680 194981680 T	L
1141	3422 T	+1:194981681 194981681 T	
1141	3423 G	+1:194981682 194981682 G	
1142 Y	3424 T	+1:194981683 194981683 T	Y
1142	3425 A	+1:194981684 194981684 A	
1142	3426 T	+1:194981685 194981685 T	
1143 Q	3427 C	+1:194981686 194981686 C	Q
1143	3428 A	+1:194981687 194981687 A	
1143	3429 A	+1:194981688 194981688 A	
1144 L	3430 C	+1:194981689 194981689 C	L
1144	3431 T	+1:194981690 194981690 T	
1144	3432 T	+1:194981691 194981691 T	
1145 E	3433 G	+1:194981692 194981692 G	E
1145	3434 A	+1:194981693 194981693 A	
1145	3435 G	+1:194981694 194981694 G	
1146 G	3436 G	+1:194981695 194981695 G	G
1146	3437 G	+1:194981696 194981696 G	
1146	3438 T	+1:194981697 194981697 T	
1147 N	3439 A	+1:194981698 194981698 A	N
1147	3440 A	+1:194981699 194981699 A	
1147	3441 C	+1:194981700 194981700 C	
1148 K	3442 A	+1:194981701 194981701 A	K
1148	3443 A	+1:194981702 194981702 A	
1148	3444 G	+1:194981703 194981703 G	
1149 R	3445 C	+1:194981704 194981704 C	R
1149	3446 G	+1:194981705 194981705 G	
1149	3447 A	+1:194981706 194981706 A	
1150 I	3448 A	+1:194981707 194981707 A	I
1150	3449 T	+1:194981708 194981708 T	
1150	3450 A	+1:194981709 194981709 A	
1151 T	3451 A	+1:194981710 194981710 A	T
1151	3452 C	+1:194981711 194981711 C	
1151	3453 A	+1:194981712 194981712 A	
1152 C	3454 T	+1:194981713 194981713 T	C
1152	3455 G	+1:194981714 194981714 G	
1152	3456 T	+1:194981715 194981715 T	
1153 R	3457 A	+1:194981716 194981716 A	R
1153	3458 G	+1:194981717 194981717 G	
1153	3459 A	+1:194981718 194981718 A	
1154 N	3460 A	+1:194981719 194981719 A	N
1154	3461 A	+1:194981720 194981720 A	
1154	3462 T	+1:194981721 194981721 T	
1155 G	3463 G	+1:194981722 194981722 G	G
1155	3464 G	+1:194981723 194981723 G	
1155	3465 A	+1:194981724 194981724 A	
1156 Q	3466 C	+1:194981725 194981725 C	Q
1156	3467 A	+1:194981726 194981726 A	
1156	3468 A	+1:194981727 194981727 A	
1157 W	3469 T	+1:194981728 194981728 T	W
1157	3470 G	+1:194981729 194981729 G	
1157	3471 G	+1:194981730 194981730 G	
1158 S	3472 T	+1:194981731 194981731 T	S
1158	3473 C	+1:194981732 194981732 C	
1158	3474 A	+1:194981733 194981733 A	
1159 E	3475 G	+1:194981734 194981734 G	E
1159	3476 A	+1:194981735 194981735 A	
1159	3477 A	+1:194981736 194981736 A	
1160 P	3478 C	+1:194981737 194981737 C	P
1160	3479 C	+1:194981738 194981738 C	
1160	3480 A	+1:194981739 194981739 A	
1161 P	3481 C	+1:194981740 194981740 C	P
1161	3482 C	+1:194981741 194981741 C	
1161	3483 A	+1:194981742 194981742 A	
1162 K	3484 A	+1:194981743 194981743 A	K
1162	3485 A	+1:194981744 194981744 A	
1162	3486 A	+1:194981745 194981745 A	
1163 C	3487 T	+1:194981746 194981746 T	C
1163	3488 G	+1:194981747 194981747 G	
1163	3489 C	+1:194981748 194981748 C	
1164 L	3490 T	+1:194981749 194981749 T	L
1164	3491 T	+1:194981750 194981750 T	
1164	3492 A	+1:194981751 194981751 A	
1165 H	3493 C	+1:194981752 194981752 C	H
1165	3494 A	+1:194982864 194982864 A	
1165	3495 T	+1:194982865 194982865 T	
1166 P	3496 C	+1:194982866 194982866 C	P
1166	3497 C	+1:194982867 194982867 C	
1166	3498 G	+1:194982868 194982868 G	
1167 C	3499 T	+1:194982869 194982869 T	C
1167	3500 G	+1:194982870 194982870 G	
1167	3501 T	+1:194982871 194982871 T	
1168 V	3502 G	+1:194982872 194982872 G	V
1168	3503 T	+1:194982873 194982873 T	
1168	3504 A	+1:194982874 194982874 A	
1169 I	3505 A	+1:194982875 194982875 A	I
1169	3506 T	+1:194982876 194982876 T	
1169	3507 A	+1:194982877 194982877 A	
1170 S	3508 T	+1:194982878 194982878 T	S
1170	3509 C	+1:194982879 194982879 C	
1170	3510 C	+1:194982880 194982880 C	
1171 R	3511 C	+1:194982881 194982881 C	R
1171	3512 G	+1:194982882 194982882 G	
1171	3513 A	+1:194982883 194982883 A	
1172 E	3514 G	+1:194982884 194982884 G	E
1172	3515 A	+1:194982885 194982885 A	
1172	3516 A	+1:194982886 194982886 A	
1173 I	3517 A	+1:194982887 194982887 A	I
1173	3518 T	+1:194982888 194982888 T	
1173	3519 T	+1:194982889 194982889 T	
1174 M	3520 A	+1:194982890 194982890 A	M
1174	3521 T	+1:194982891 194982891 T	
1174	3522 G	+1:194982892 194982892 G	
1175 E	3523 G	+1:194982893 194982893 G	E
1175	3524 A	+1:194982894 194982894 A	
1175	3525 A	+1:194982895 194982895 A	
1176 N	3526 A	+1:194982896 194982896 A	N
1176	3527 A	+1:194982897 194982897 A	
1176	3528 T	+1:194982898 194982898 T	
1177 Y	3529 T	+1:194982899 194982899 T	Y
1177	3530 A	+1:194982900 194982900 A	
1177	3531 T	+1:194982901 194982901 T	
1178 N	3532 A	+1:194982902 194982902 A	N
1178	3533 A	+1:194982903 194982903 A	
1178	3534 C	+1:194982904 194982904 C	
1179 I	3535 A	+1:194982905 194982905 A	I
1179	3536 T	+1:194982906 194982906 T	
1179	3537 A	+1:194982907 194982907 A	
1180 A	3538 G	+1:194982908 194982908 G	A
1180	3539 C	+1:194982909 194982909 C	
1180	3540 A	+1:194982910 194982910 A	
1181 L	3541 T	+1:194982911 194982911 T	L
1181	3542 T	+1:194982912 194982912 T	
1181	3543 A	+1:194982913 194982913 A	
1182 R	3544 A	+1:194982914 194982914 A	R
1182	3545 G	+1:194982915 194982915 G	
1182	3546 G	+1:194982916 194982916 G	
1183 W	3547 T	+1:194982917 194982917 T	W
1183	3548 G	+1:194982918 194982918 G	
1183	3549 G	+1:194982919 194982919 G	
1184 T	3550 A	+1:194982920 194982920 A	T
1184	3551 C	+1:194982921 194982921 C	
1184	3552 A	+1:194982922 194982922 A	
1185 A	3553 G	+1:194982923 194982923 G	A
1185	3554 C	+1:194982924 194982924 C	
1185	3555 C	+1:194982925 194982925 C	
1186 K	3556 A	+1:194982926 194982926 A	K
1186	3557 A	+1:194982927 194982927 A	
1186	3558 A	+1:194982928 194982928 A	
1187 Q	3559 C	+1:194982929 194982929 C	Q
1187	3560 A	+1:194982930 194982930 A	
1187	3561 G	+1:194982931 194982931 G	
1188 K	3562 A	+1:194982932 194982932 A	K
1188	3563 A	+1:194982933 194982933 A	
1188	3564 G	+1:194982934 194982934 G	
1189 L	3565 C	+1:194982935 194982935 C	L
1189	3566 T	+1:194982936 194982936 T	
1189	3567 T	+1:194982937 194982937 T	
1190 Y	3568 T	+1:194982938 194982938 T	Y
1190	3569 A	+1:194982939 194982939 A	
1190	3570 T	+1:194982940 194982940 T	
1191 S	3571 T	+1:194982941 194982941 T	S
1191	3572 C	+1:194982942 194982942 C	
1191	3573 G	+1:194982943 194982943 G	
1192 R	3574 A	+1:194982944 194982944 A	R
1192	3575 G	+1:194982945 194982945 G	
1192	3576 A	+1:194982946 194982946 A	
1193 T	3577 A	+1:194982947 194982947 A	T
1193	3578 C	+1:194982948 194982948 C	
1193	3579 A	+1:194982949 194982949 A	
1194 G	3580 G	+1:194982950 194982950 G	G
1194	3581 G	+1:194982951 194982951 G	
1194	3582 T	+1:194982952 194982952 T	
1195 E	3583 G	+1:194982953 194982953 G	E
1195	3584 A	+1:194982954 194982954 A	
1195	3585 A	+1:194982955 194982955 A	
1196 S	3586 T	+1:194982956 194982956 T	S
1196	3587 C	+1:194982957 194982957 C	
1196	3588 A	+1:194982958 194982958 A	
1197 V	3589 G	+1:194982959 194982959 G	V
1197	3590 T	+1:194982960 194982960 T	
1197	3591 T	+1:194982961 194982961 T	
1198 E	3592 G	+1:194982962 194982962 G	E
1198	3593 A	+1:194982963 194982963 A	
1198	3594 A	+1:194982964 194982964 A	
1199 F	3595 T	+1:194982965 194982965 T	F
1199	3596 T	+1:194982966 194982966 T	
1199	3597 T	+1:194982967 194982967 T	
1200 V	3598 G	+1:194982968 194982968 G	V
1200	3599 T	+1:194982969 194982969 T	
1200	3600 G	+1:194982970 194982970 G	
1201 C	3601 T	+1:194982971 194982971 T	C
1201	3602 G	+1:194982972 194982972 G	
1201	3603 T	+1:194982973 194982973 T	
1202 K	3604 A	+1:194982974 194982974 A	K
1202	3605 A	+1:194982975 194982975 A	
1202	3606 A	+1:194982976 194982976 A	
1203 R	3607 C	+1:194982977 194982977 C	R
1203	3608 G	+1:194982978 194982978 G	
1203	3609 G	+1:194982979 194982979 G	
1204 G	3610 G	+1:194982980 194982980 G	G
1204	3611 G	+1:194982981 194982981 G	
1204	3612 A	+1:194982982 194982982 A	
1205 Y	3613 T	+1:194982983 194982983 T	Y
1205	3614 A	+1:194982984 194982984 A	
1205	3615 T	+1:194982985 194982985 T	
1206 R	3616 C	+1:194982986 194982986 C	R
1206	3617 G	+1:194982987 194982987 G	
1206	3618 T	+1:194982988 194982988 T	
1207 L	3619 C	+1:194982989 194982989 C	L
1207	3620 T	+1:194982990 194982990 T	
1207	3621 T	+1:194982991 194982991 T	
1208 S	3622 T	+1:194982992 194982992 T	S
1208	3623 C	+1:194982993 194982993 C	
1208	3624 A	+1:194982994 194982994 A	
1209 S	3625 T	+1:194982995 194982995 T	S
1209	3626 C	+1:194982996 194982996 C	
1209	3627 A	+1:194982997 194982997 A	
1210 R	3628 C	+1:194982998 194982998 C	R
1210	3629 G	+1:194982999 194982999 G	
1210	3630 T	+1:194983000 194983000 T	
1211 S	3631 T	+1:194983001 194983001 T	S
1211	3632 C	+1:194983002 194983002 C	
1211	3633 T	+1:194983003 194983003 T	
1212 H	3634 C	+1:194983004 194983004 C	H
1212	3635 A	+1:194983005 194983005 A	
1212	3636 C	+1:194983006 194983006 C	
1213 T	3637 A	+1:194983007 194983007 A	T
1213	3638 C	+1:194983008 194983008 C	
1213	3639 A	+1:194983009 194983009 A	
1214 L	3640 T	+1:194983010 194983010 T	L
1214	3641 T	+1:194983011 194983011 T	
1214	3642 G	+1:194983012 194983012 G	
1215 R	3643 C	+1:194983013 194983013 C	R
1215	3644 G	+1:194983014 194983014 G	
1215	3645 A	+1:194983015 194983015 A	
1216 T	3646 A	+1:194983016 194983016 A	T
1216	3647 C	+1:194983017 194983017 C	
1216	3648 A	+1:194983018 194983018 A	
1217 T	3649 A	+1:194983019 194983019 A	T
1217	3650 C	+1:194983020 194983020 C	
1217	3651 A	+1:194983021 194983021 A	
1218 C	3652 T	+1:194983022 194983022 T	C
1218	3653 G	+1:194983023 194983023 G	
1218	3654 T	+1:194983024 194983024 T	
1219 W	3655 T	+1:194983025 194983025 T	W
1219	3656 G	+1:194983026 194983026 G	
1219	3657 G	+1:194983027 194983027 G	
1220 D	3658 G	+1:194983028 194983028 G	D
1220	3659 A	+1:194983029 194983029 A	
1220	3660 T	+1:194983030 194983030 T	
1221 G	3661 G	+1:194983031 194983031 G	G
1221	3662 G	+1:194983032 194983032 G	
1221	3663 G	+1:194983033 194983033 G	
1222 K	3664 A	+1:194983034 194983034 A	K
1222	3665 A	+1:194983035 194983035 A	
1222	3666 A	+1:194983036 194983036 A	
1223 L	3667 C	+1:194983037 194983037 C	L
1223	3668 T	+1:194983038 194983038 T	
1223	3669 G	+1:194983039 194983039 G	
1224 E	3670 G	+1:194983040 194983040 G	E
1224	3671 A	+1:194983041 194983041 A	
1224	3672 G	+1:194983042 194983042 G	
1225 Y	3673 T	+1:194983043 194983043 T	Y
1225	3674 A	+1:194983044 194983044 A	
1225	3675 T	+1:194983045 194983045 T	
1226 P	3676 C	+1:194983046 194983046 C	P
1226	3677 C	+1:194983047 194983047 C	
1226	3678 A	+1:194983048 194983048 A	
1227 T	3679 A	+1:194983049 194983049 A	T
1227	3680 C	+1:194983050 194983050 C	
1227	3681 T	+1:194983051 194983051 T	
1228 C	3682 T	+1:194983052 194983052 T	C
1228	3683 G	+1:194983053 194983053 G	
1228	3684 T	+1:194983054 194983054 T	
1229 A	3685 G	+1:194983055 194983055 G	A
1229	3686 C	+1:194983056 194983056 C	
1229	3687 A	+1:194983057 194983057 A	
1230 K	3688 A	+1:194983058 194983058 A	K
1230	3689 A	+1:194983059 194983059 A	
1230	3690 A	+1:194983060 194983060 A	
1231 R	3691 A	+1:194983061 194983061 A	R
1231	3692 G	+1:194983062 194983062 G	
1231	3693 A	+1:194983063 194983063 A	
>ENSP00000356557 
1 M	1 A	-6:143874464 1205373088 A	M
1	2 T	-6:143874463 1205373087 T	
1	3 G	-6:143874462 1205373086 G	
2 R	4 C	-6:143874461 1205373085 C	R
2	5 G	-6:143874460 1205373084 G	
2	6 G	-6:143874459 1205373083 G	
3 P	7 C	-6:143874458 1205373082 C	P
3	8 C	-6:143874457 1205373081 C	
3	9 C	-6:143874456 1205373080 C	
4 Q	10 C	-6:143874455 1205373079 C	Q
4	11 A	-6:143874454 1205373078 A	
4	12 G	-6:143874453 1205373077 G	
5 E	13 G	-6:143874452 1205373076 G	E
5	14 A	-6:143874451 1205373075 A	
5	15 G	-6:143874450 1205373074 G	
6 L	16 C	-6:143874449 1205373073 C	L
6	17 T	-6:143874448 1205373072 T	
6	18 C	-6:143874447 1205373071 C	
7 P	19 C	-6:143874446 1205373070 C	P
7	20 C	-6:143874445 1205373069 C	
7	21 C	-6:143874444 1205373068 C	
8 R	22 A	-6:143874443 1205373067 A	R
8	23 G	-6:143874442 1205373066 G	
8	24 G	-6:143874441 1205373065 G	
9 L	25 C	-6:143874440 1205373064 C	L
9	26 T	-6:143874439 1205373063 T	
9	27 C	-6:143874438 1205373062 C	
10 A	28 G	-6:143874437 1205373061 G	A
10	29 C	-6:143874436 1205373060 C	
10	30 G	-6:143874435 1205373059 G	
11 F	31 T	-6:143874434 1205373058 T	F
11	32 T	-6:143874433 1205373057 T	
11	33 C	-6:143874432 1205373056 C	
12 P	34 C	-6:143874431 1205373055 C	P
12	35 C	-6:143874430 1205373054 C	
12	36 G	-6:143874429 1205373053 G	
13 L	37 T	-6:143874428 1205373052 T	L
13	38 T	-6:143874427 1205373051 T	
13	39 G	-6:143874426 1205373050 G	
14 L	40 C	-6:143874425 1205373049 C	L
14	41 T	-6:143874424 1205373048 T	
14	42 G	-6:143874423 1205373047 G	
15 L	43 C	-6:143874422 1205373046 C	L
15	44 T	-6:143874421 1205373045 T	
15	45 G	-6:143874420 1205373044 G	
16 L	46 T	-6:143874419 1205373043 T	L
16	47 T	-6:143874418 1205373042 T	
16	48 G	-6:143874417 1205373041 G	
17 L	49 C	-6:143874416 1205373040 C	L
17	50 T	-6:143874415 1205373039 T	
17	51 G	-6:143874414 1205373038 G	
18 L	52 T	-6:143874413 1205373037 T	L
18	53 T	-6:143874412 1205373036 T	
18	54 G	-6:143874411 1205373035 G	
19 L	55 C	-6:143874410 1205373034 C	L
19	56 T	-6:143874409 1205373033 T	
19	57 G	-6:143874408 1205373032 G	
20 L	58 C	-6:143874407 1205373031 C	L
20	59 T	-6:143874406 1205373030 T	
20	60 G	-6:143874405 1205373029 G	
21 L	61 C	-6:143874404 1205373028 C	L
21	62 T	-6:143874403 1205373027 T	
21	63 G	-6:143874402 1205373026 G	
22 P	64 C	-6:143874401 1205373025 C	P
22	65 C	-6:143874400 1205373024 C	
22	66 G	-6:143874399 1205373023 G	
23 P	67 C	-6:143874398 1205373022 C	P
23	68 C	-6:143874397 1205373021 C	
23	69 G	-6:143874396 1205373020 G	
24 P	70 C	-6:143874395 1205373019 C	P
24	71 C	-6:143874394 1205373018 C	
24	72 G	-6:143874393 1205373017 G	
25 P	73 C	-6:143874392 1205373016 C	P
25	74 C	-6:143874391 1205373015 C	
25	75 G	-6:143874390 1205373014 G	
26 C	76 T	-6:143874389 1205373013 T	C
26	77 G	-6:143874388 1205373012 G	
26	78 C	-6:143874387 1205373011 C	
27 P	79 C	-6:143874386 1205373010 C	P
27	80 C	-6:143874385 1205373009 C	
27	81 T	-6:143874384 1205373008 T	
28 A	82 G	-6:143874383 1205373007 G	A
28	83 C	-6:143874382 1205373006 C	
28	84 C	-6:143874381 1205373005 C	
29 H	85 C	-6:143874380 1205373004 C	H
29	86 A	-6:143874379 1205373003 A	
29	87 C	-6:143874378 1205373002 C	
30 S	88 A	-6:143874377 1205373001 A	S
30	89 G	-6:143874376 1205373000 G	
30	90 C	-6:143874375 1205372999 C	
31 A	91 G	-6:143874374 1205372998 G	A
31	92 C	-6:143874373 1205372997 C	
31	93 C	-6:143874372 1205372996 C	
32 T	94 A	-6:143874371 1205372995 A	T
32	95 C	-6:143874370 1205372994 C	
32	96 G	-6:143874369 1205372993 G	
33 R	97 C	-6:143874368 1205372992 C	R
33	98 G	-6:143874367 1205372991 G	
33	99 C	-6:143874366 1205372990 C	
34 F	100 T	-6:143874365 1205372989 T	F
34	101 T	-6:143874364 1205372988 T	
34	102 C	-6:143874363 1205372987 C	
35 D	103 G	-6:143874362 1205372986 G	D
35	104 A	-6:143874361 1205372985 A	
35	105 C	-6:143874360 1205372984 C	
36 P	106 C	-6:143874359 1205372983 C	P
36	107 C	-6:143874358 1205372982 C	
36	108 C	-6:143874357 1205372981 C	
37 T	109 A	-6:143874356 1205372980 A	T
37	110 C	-6:143874355 1205372979 C	
37	111 C	-6:143874354 1205372978 C	
38 W	112 T	-6:143874353 1205372977 T	W
38	113 G	-6:143874352 1205372976 G	
38	114 G	-6:143874351 1205372975 G	
39 E	115 G	-6:143874350 1205372974 G	E
39	116 A	-6:143874349 1205372973 A	
39	117 G	-6:143874348 1205372972 G	
40 S	118 T	-6:143874347 1205372971 T	S
40	119 C	-6:143874346 1205372970 C	
40	120 C	-6:143874345 1205372969 C	
41 L	121 C	-6:143874344 1205372968 C	L
41	122 T	-6:143874343 1205372967 T	
41	123 G	-6:143874342 1205372966 G	
42 D	124 G	-6:143874341 1205372965 G	D
42	125 A	-6:143874340 1205372964 A	
42	126 C	-6:143874339 1205372963 C	
43 A	127 G	-6:143874338 1205372962 G	A
43	128 C	-6:143874337 1205372961 C	
43	129 C	-6:143874336 1205372960 C	
44 R	130 C	-6:143874335 1205372959 C	R
44	131 G	-6:143874334 1205372958 G	
44	132 C	-6:143874333 1205372957 C	
45 Q	133 C	-6:143874332 1205372956 C	Q
45	134 A	-6:143874331 1205372955 A	
45	135 G	-6:143874330 1205372954 G	
46 L	136 C	-6:143874329 1205372953 C	L
46	137 T	-6:143874328 1205372952 T	
46	138 G	-6:143874327 1205372951 G	
47 P	139 C	-6:143874326 1205372950 C	P
47	140 C	-6:143874325 1205372949 C	
47	141 C	-6:143874324 1205372948 C	
48 A	142 G	-6:143874323 1205372947 G	A
48	143 C	-6:143874322 1205372946 C	
48	144 G	-6:143874321 1205372945 G	
49 W	145 T	-6:143874320 1205372944 T	W
49	146 G	-6:143874319 1205372943 G	
49	147 G	-6:143874318 1205372942 G	
50 F	148 T	-6:143874317 1205372941 T	F
50	149 T	-6:143874316 1205372940 T	
50	150 T	-6:143874315 1205372939 T	
51 D	151 G	-6:143874314 1205372938 G	D
51	152 A	-6:143874313 1205372937 A	
51	153 C	-6:143874312 1205372936 C	
52 Q	154 C	-6:143874311 1205372935 C	Q
52	155 A	-6:143874310 1205372934 A	
52	156 G	-6:143874309 1205372933 G	
53 A	157 G	-6:143874308 1205372932 G	A
53	158 C	-6:143874307 1205372931 C	
53	159 C	-6:143874306 1205372930 C	
54 K	160 A	-6:143874305 1205372929 A	K
54	161 A	-6:143874304 1205372928 A	
54	162 G	-6:143874303 1205372927 G	
55 F	163 T	-6:143874302 1205372926 T	F
55	164 T	-6:143874301 1205372925 T	
55	165 C	-6:143874300 1205372924 C	
56 G	166 G	-6:143874299 1205372923 G	G
56	167 G	-6:143874298 1205372922 G	
56	168 C	-6:143874297 1205372921 C	
57 I	169 A	-6:143874296 1205372920 A	I
57	170 T	-6:143874295 1205372919 T	
57	171 C	-6:143874294 1205372918 C	
58 F	172 T	-6:143874293 1205372917 T	F
58	173 T	-6:143874292 1205372916 T	
58	174 C	-6:143874291 1205372915 C	
59 I	175 A	-6:143874290 1205372914 A	I
59	176 T	-6:143874289 1205372913 T	
59	177 C	-6:143874288 1205372912 C	
60 H	178 C	-6:143874287 1205372911 C	H
60	179 A	-6:143874286 1205372910 A	
60	180 C	-6:143874285 1205372909 C	
61 W	181 T	-6:143874284 1205372908 T	W
61	182 G	-6:143874283 1205372907 G	
61	183 G	-6:143874282 1205372906 G	
62 G	184 G	-6:143874281 1205372905 G	G
62	185 G	-6:143874280 1205372904 G	
62	186 A	-6:143874279 1205372903 A	
63 V	187 G	-6:143874278 1205372902 G	V
63	188 T	-6:143874277 1205372901 T	
63	189 G	-6:143874276 1205372900 G	
64 F	190 T	-6:143874275 1205372899 T	F
64	191 T	-6:143874274 1205372898 T	
64	192 T	-6:143874273 1205372897 T	
65 S	193 T	-6:143874272 1205372896 T	S
65	194 C	-6:143874271 1205372895 C	
65	195 C	-6:143874270 1205372894 C	
66 V	196 G	-6:143874269 1205372893 G	V
66	197 T	-6:143874268 1205372892 T	
66	198 G	-6:143874267 1205372891 G	
67 P	199 C	-6:143874266 1205372890 C	P
67	200 C	-6:143874265 1205372889 C	
67	201 C	-6:143874264 1205372888 C	
68 S	202 A	-6:143874263 1205372887 A	S
68	203 G	-6:143874262 1205372886 G	
68	204 C	-6:143874261 1205372885 C	
69 F	205 T	-6:143874260 1205372884 T	F
69	206 T	-6:143874259 1205372883 T	
69	207 C	-6:143874258 1205372882 C	
70 G	208 G	-6:143874257 1205372881 G	G
70	209 G	-6:143874256 1205372880 G	
70	210 T	-6:143874255 1205372879 T	
71 S	211 A	-6:143874254 1205372878 A	S
71	212 G	-6:143874253 1205372877 G	
71	213 C	-6:143874252 1205372876 C	
72 E	214 G	-6:143874251 1205372875 G	E
72	215 A	-6:143874250 1205372874 A	
72	216 G	-6:143874249 1205372873 G	
73 W	217 T	-6:143874248 1205372872 T	W
73	218 G	-6:143874247 1205372871 G	
73	219 G	-6:143874246 1205372870 G	
74 F	220 T	-6:143874245 1205372869 T	F
74	221 T	-6:143874244 1205372868 T	
74	222 C	-6:143874243 1205372867 C	
75 W	223 T	-6:143874242 1205372866 T	W
75	224 G	-6:143874241 1205372865 G	
75	225 G	-6:143870254 1205368878 G	
76 W	226 T	-6:143870253 1205368877 T	W
76	227 G	-6:143870252 1205368876 G	
76	228 G	-6:143870251 1205368875 G	
77 Y	229 T	-6:143870250 1205368874 T	Y
77	230 A	-6:143870249 1205368873 A	
77	231 T	-6:143870248 1205368872 T	
78 W	232 T	-6:143870247 1205368871 T	W
78	233 G	-6:143870246 1205368870 G	
78	234 G	-6:143870245 1205368869 G	
79 Q	235 C	-6:143870244 1205368868 C	Q
79	236 A	-6:143870243 1205368867 A	
79	237 A	-6:143870242 1205368866 A	
80 K	238 A	-6:143870241 1205368865 A	K
80	239 A	-6:143870240 1205368864 A	
80	240 G	-6:143870239 1205368863 G	
81 E	241 G	-6:143870238 1205368862 G	E
81	242 A	-6:143870237 1205368861 A	
81	243 A	-6:143870236 1205368860 A	
82 K	244 A	-6:143870235 1205368859 A	K
82	245 A	-6:143870234 1205368858 A	
82	246 G	-6:143870233 1205368857 G	
83 I	247 A	-6:143870232 1205368856 A	I
83	248 T	-6:143870231 1205368855 T	
83	249 A	-6:143870230 1205368854 A	
84 P	250 C	-6:143870229 1205368853 C	P
84	251 C	-6:143870228 1205368852 C	
84	252 G	-6:143870227 1205368851 G	
85 K	253 A	-6:143870226 1205368850 A	K
85	254 A	-6:143870225 1205368849 A	
85	255 G	-6:143870224 1205368848 G	
86 Y	256 T	-6:143870223 1205368847 T	Y
86	257 A	-6:143870222 1205368846 A	
86	258 T	-6:143870221 1205368845 T	
87 V	259 G	-6:143870220 1205368844 G	V
87	260 T	-6:143870219 1205368843 T	
87	261 G	-6:143870218 1205368842 G	
88 E	262 G	-6:143870217 1205368841 G	E
88	263 A	-6:143870216 1205368840 A	
88	264 A	-6:143870215 1205368839 A	
89 F	265 T	-6:143870214 1205368838 T	F
89	266 T	-6:143870213 1205368837 T	
89	267 T	-6:143870212 1205368836 T	
90 M	268 A	-6:143870211 1205368835 A	M
90	269 T	-6:143870210 1205368834 T	
90	270 G	-6:143870209 1205368833 G	
91 K	271 A	-6:143870208 1205368832 A	K
91	272 A	-6:143870207 1205368831 A	
91	273 A	-6:143870206 1205368830 A	
92 D	274 G	-6:143870205 1205368829 G	D
92	275 A	-6:143870204 1205368828 A	
92	276 T	-6:143870203 1205368827 T	
93 N	277 A	-6:143870202 1205368826 A	N
93	278 A	-6:143870201 1205368825 A	
93	279 T	-6:143870200 1205368824 T	
94 Y	280 T	-6:143870199 1205368823 T	Y
94	281 A	-6:143870198 1205368822 A	
94	282 C	-6:143870197 1205368821 C	
95 P	283 C	-6:143870196 1205368820 C	P
95	284 C	-6:143870195 1205368819 C	
95	285 T	-6:143870194 1205368818 T	
96 P	286 C	-6:143870193 1205368817 C	P
96	287 C	-6:143870192 1205368816 C	
96	288 T	-6:143870191 1205368815 T	
97 S	289 A	-6:143870190 1205368814 A	S
97	290 G	-6:143870189 1205368813 G	
97	291 T	-6:143870188 1205368812 T	
98 F	292 T	-6:143870187 1205368811 T	F
98	293 T	-6:143870186 1205368810 T	
98	294 C	-6:143870185 1205368809 C	
99 K	295 A	-6:143870184 1205368808 A	K
99	296 A	-6:143870183 1205368807 A	
99	297 A	-6:143870182 1205368806 A	
100 Y	298 T	-6:143870181 1205368805 T	Y
100	299 A	-6:143870180 1205368804 A	
100	300 T	-6:143870179 1205368803 T	
101 E	301 G	-6:143870178 1205368802 G	E
101	302 A	-6:143870177 1205368801 A	
101	303 A	-6:143870176 1205368800 A	
102 D	304 G	-6:143870175 1205368799 G	D
102	305 A	-6:143870174 1205368798 A	
102	306 T	-6:143870173 1205368797 T	
103 F	307 T	-6:143870172 1205368796 T	F
103	308 T	-6:143870171 1205368795 T	
103	309 T	-6:143870170 1205368794 T	
104 G	310 G	-6:143870169 1205368793 G	G
104	311 G	-6:143870168 1205368792 G	
104	312 A	-6:143870167 1205368791 A	
105 P	313 C	-6:143870166 1205368790 C	P
105	314 C	-6:143870165 1205368789 C	
105	315 A	-6:143870164 1205368788 A	
106 L	316 C	-6:143870163 1205368787 C	L
106	317 T	-6:143870162 1205368786 T	
106	318 A	-6:143870161 1205368785 A	
107 F	319 T	-6:143870160 1205368784 T	F
107	320 T	-6:143870159 1205368783 T	
107	321 T	-6:143870158 1205368782 T	
108 T	322 A	-6:143870157 1205368781 A	T
108	323 C	-6:143870156 1205368780 C	
108	324 A	-6:143870155 1205368779 A	
109 A	325 G	-6:143870154 1205368778 G	A
109	326 C	-6:143870153 1205368777 C	
109	327 A	-6:143870152 1205368776 A	
110 K	328 A	-6:143870151 1205368775 A	K
110	329 A	-6:143870150 1205368774 A	
110	330 A	-6:143870149 1205368773 A	
111 F	331 T	-6:143870148 1205368772 T	F
111	332 T	-6:143870147 1205368771 T	
111	333 T	-6:143870146 1205368770 T	
112 F	334 T	-6:143870145 1205368769 T	F
112	335 T	-6:143870144 1205368768 T	
112	336 T	-6:143870143 1205368767 T	
113 N	337 A	-6:143870142 1205368766 A	N
113	338 A	-6:143870141 1205368765 A	
113	339 T	-6:143870140 1205368764 T	
114 A	340 G	-6:143870139 1205368763 G	A
114	341 C	-6:143870138 1205368762 C	
114	342 C	-6:143870137 1205368761 C	
115 N	343 A	-6:143870136 1205368760 A	N
115	344 A	-6:143870135 1205368759 A	
115	345 C	-6:143870134 1205368758 C	
116 Q	346 C	-6:143870133 1205368757 C	Q
116	347 A	-6:143870132 1205368756 A	
116	348 G	-6:143870131 1205368755 G	
117 W	349 T	-6:143870130 1205368754 T	W
117	350 G	-6:143870129 1205368753 G	
117	351 G	-6:143870128 1205368752 G	
118 A	352 G	-6:143870127 1205368751 G	A
118	353 C	-6:143870126 1205368750 C	
118	354 A	-6:143870125 1205368749 A	
119 D	355 G	-6:143870124 1205368748 G	D
119	356 A	-6:143870123 1205368747 A	
119	357 T	-6:143870122 1205368746 T	
120 I	358 A	-6:143870121 1205368745 A	I
120	359 T	-6:143870120 1205368744 T	
120	360 T	-6:143870119 1205368743 T	
121 F	361 T	-6:143870118 1205368742 T	F
121	362 T	-6:143870117 1205368741 T	
121	363 T	-6:143870116 1205368740 T	
122 Q	364 C	-6:143870115 1205368739 C	Q
122	365 A	-6:143870114 1205368738 A	
122	366 G	-6:143870113 1205368737 G	
123 A	367 G	-6:143870112 1205368736 G	A
123	368 C	-6:143870111 1205368735 C	
123	369 C	-6:143870110 1205368734 C	
124 S	370 T	-6:143870109 1205368733 T	S
124	371 C	-6:143870108 1205368732 C	
124	372 T	-6:143870107 1205368731 T	
125 G	373 G	-6:143870106 1205368730 G	G
125	374 G	-6:143870105 1205368729 G	
125	375 T	-6:143870104 1205368728 T	
126 A	376 G	-6:143870103 1205368727 G	A
126	377 C	-6:143870102 1205368726 C	
126	378 C	-6:143870101 1205368725 C	
127 K	379 A	-6:143870100 1205368724 A	K
127	380 A	-6:143870099 1205368723 A	
127	381 A	-6:143870098 1205368722 A	
128 Y	382 T	-6:143870097 1205368721 T	Y
128	383 A	-6:143870096 1205368720 A	
128	384 C	-6:143870095 1205368719 C	
129 I	385 A	-6:143870094 1205368718 A	I
129	386 T	-6:143870093 1205368717 T	
129	387 T	-6:143870092 1205368716 T	
130 V	388 G	-6:143870091 1205368715 G	V
130	389 T	-6:143870090 1205368714 T	
130	390 C	-6:143870089 1205368713 C	
131 L	391 T	-6:143870088 1205368712 T	L
131	392 T	-6:143870087 1205368711 T	
131	393 A	-6:143870086 1205368710 A	
132 T	394 A	-6:143870085 1205368709 A	T
132	395 C	-6:143870084 1205368708 C	
132	396 T	-6:143870083 1205368707 T	
133 S	397 T	-6:143870082 1205368706 T	S
133	398 C	-6:143870081 1205368705 C	
133	399 C	-6:143870080 1205368704 C	
134 K	400 A	-6:143870079 1205368703 A	K
134	401 A	-6:143870078 1205368702 A	
134	402 A	-6:143870077 1205368701 A	
135 H	403 C	-6:143870076 1205368700 C	H
135	404 A	-6:143870075 1205368699 A	
135	405 T	-6:143870074 1205368698 T	
136 H	406 C	-6:143870073 1205368697 C	H
136	407 A	-6:143870072 1205368696 A	
136	408 T	-6:143870071 1205368695 T	
137 E	409 G	-6:143870070 1205368694 G	E
137	410 A	-6:143870069 1205368693 A	
137	411 A	-6:143870068 1205368692 A	
138 A	412 G	-6:143870067 1205368691 G	A
138	413 C	-6:143864952 1205363576 C	
138	414 A	-6:143864951 1205363575 A	
139 T	415 A	-6:143864950 1205363574 A	T
139	416 C	-6:143864949 1205363573 C	
139	417 T	-6:143864948 1205363572 T	
140 C	418 T	-6:143864947 1205363571 T	C
140	419 G	-6:143864946 1205363570 G	
140	420 T	-6:143864945 1205363569 T	
141 R	421 A	-6:143864944 1205363568 A	R
141	422 G	-6:143864943 1205363567 G	
141	423 A	-6:143864942 1205363566 A	
142 D	424 G	-6:143864941 1205363565 G	D
142	425 A	-6:143864940 1205363564 A	
142	426 C	-6:143864939 1205363563 C	
143 S	427 A	-6:143864938 1205363562 A	S
143	428 G	-6:143864937 1205363561 G	
143	429 T	-6:143864936 1205363560 T	
144 F	430 T	-6:143864935 1205363559 T	F
144	431 T	-6:143864934 1205363558 T	
144	432 C	-6:143864933 1205363557 C	
145 M	433 A	-6:143864932 1205363556 A	M
145	434 T	-6:143864931 1205363555 T	
145	435 G	-6:143864930 1205363554 G	
146 W	436 T	-6:143864929 1205363553 T	W
146	437 G	-6:143864928 1205363552 G	
146	438 G	-6:143864927 1205363551 G	
147 R	439 A	-6:143864926 1205363550 A	R
147	440 G	-6:143864925 1205363549 G	
147	441 G	-6:143864924 1205363548 G	
148 K	442 A	-6:143864923 1205363547 A	K
148	443 A	-6:143864922 1205363546 A	
148	444 A	-6:143864921 1205363545 A	
149 S	445 T	-6:143864920 1205363544 T	S
149	446 C	-6:143864919 1205363543 C	
149	447 T	-6:143864918 1205363542 T	
150 F	448 T	-6:143864917 1205363541 T	F
150	449 T	-6:143864916 1205363540 T	
150	450 T	-6:143864915 1205363539 T	
151 D	451 G	-6:143864914 1205363538 G	D
151	452 A	-6:143864913 1205363537 A	
151	453 T	-6:143864912 1205363536 T	
152 E	454 G	-6:143864911 1205363535 G	E
152	455 A	-6:143864910 1205363534 A	
152	456 A	-6:143864909 1205363533 A	
153 Y	457 T	-6:143864908 1205363532 T	Y
153	458 A	-6:143864907 1205363531 A	
153	459 T	-6:143864906 1205363530 T	
154 W	460 T	-6:143864905 1205363529 T	W
154	461 G	-6:143864904 1205363528 G	
154	462 G	-6:143864903 1205363527 G	
155 A	463 G	-6:143864902 1205363526 G	A
155	464 C	-6:143864901 1205363525 C	
155	465 C	-6:143864900 1205363524 C	
156 H	466 C	-6:143864899 1205363523 C	H
156	467 A	-6:143864898 1205363522 A	
156	468 C	-6:143864897 1205363521 C	
157 T	469 A	-6:143864896 1205363520 A	T
157	470 C	-6:143864895 1205363519 C	
157	471 T	-6:143864894 1205363518 T	
158 R	472 A	-6:143864893 1205363517 A	R
158	473 G	-6:143864892 1205363516 G	
158	474 A	-6:143864891 1205363515 A	
159 W	475 T	-6:143864890 1205363514 T	W
159	476 G	-6:143864889 1205363513 G	
159	477 G	-6:143864888 1205363512 G	
160 H	478 C	-6:143864887 1205363511 C	H
160	479 A	-6:143864886 1205363510 A	
160	480 C	-6:143864885 1205363509 C	
161 H	481 C	-6:143864884 1205363508 C	H
161	482 A	-6:143864883 1205363507 A	
161	483 T	-6:143864882 1205363506 T	
162 F	484 T	-6:143864881 1205363505 T	F
162	485 T	-6:143864880 1205363504 T	
162	486 C	-6:143864879 1205363503 C	
163 C	487 T	-6:143864878 1205363502 T	C
163	488 G	-6:143864877 1205363501 G	
163	489 T	-6:143864876 1205363500 T	
164 S	490 A	-6:143864875 1205363499 A	S
164	491 G	-6:143864874 1205363498 G	
164	492 T	-6:143864873 1205363497 T	
165 F	493 T	-6:143864872 1205363496 T	F
165	494 T	-6:143864871 1205363495 T	
165	495 T	-6:143864870 1205363494 T	
>ENSP00000343380 
1 M	1 A	-6:143874464 1205373088 A	M
1	2 T	-6:143874463 1205373087 T	
1	3 G	-6:143874462 1205373086 G	
2 R	4 C	-6:143874461 1205373085 C	R
2	5 G	-6:143874460 1205373084 G	
2	6 G	-6:143874459 1205373083 G	
3 P	7 C	-6:143874458 1205373082 C	P
3	8 C	-6:143874457 1205373081 C	
3	9 C	-6:143874456 1205373080 C	
4 Q	10 C	-6:143874455 1205373079 C	Q
4	11 A	-6:143874454 1205373078 A	
4	12 G	-6:143874453 1205373077 G	
5 E	13 G	-6:143874452 1205373076 G	E
5	14 A	-6:143874451 1205373075 A	
5	15 G	-6:143874450 1205373074 G	
6 L	16 C	-6:143874449 1205373073 C	L
6	17 T	-6:143874448 1205373072 T	
6	18 C	-6:143874447 1205373071 C	
7 P	19 C	-6:143874446 1205373070 C	P
7	20 C	-6:143874445 1205373069 C	
7	21 C	-6:143874444 1205373068 C	
8 R	22 A	-6:143874443 1205373067 A	R
8	23 G	-6:143874442 1205373066 G	
8	24 G	-6:143874441 1205373065 G	
9 L	25 C	-6:143874440 1205373064 C	L
9	26 T	-6:143874439 1205373063 T	
9	27 C	-6:143874438 1205373062 C	
10 A	28 G	-6:143874437 1205373061 G	A
10	29 C	-6:143874436 1205373060 C	
10	30 G	-6:143874435 1205373059 G	
11 F	31 T	-6:143874434 1205373058 T	F
11	32 T	-6:143874433 1205373057 T	
11	33 C	-6:143874432 1205373056 C	
12 P	34 C	-6:143874431 1205373055 C	P
12	35 C	-6:143874430 1205373054 C	
12	36 G	-6:143874429 1205373053 G	
13 L	37 T	-6:143874428 1205373052 T	L
13	38 T	-6:143874427 1205373051 T	
13	39 G	-6:143874426 1205373050 G	
14 L	40 C	-6:143874425 1205373049 C	L
14	41 T	-6:143874424 1205373048 T	
14	42 G	-6:143874423 1205373047 G	
15 L	43 C	-6:143874422 1205373046 C	L
15	44 T	-6:143874421 1205373045 T	
15	45 G	-6:143874420 1205373044 G	
16 L	46 T	-6:143874419 1205373043 T	L
16	47 T	-6:143874418 1205373042 T	
16	48 G	-6:143874417 1205373041 G	
17 L	49 C	-6:143874416 1205373040 C	L
17	50 T	-6:143874415 1205373039 T	
17	51 G	-6:143874414 1205373038 G	
18 L	52 T	-6:143874413 1205373037 T	L
18	53 T	-6:143874412 1205373036 T	
18	54 G	-6:143874411 1205373035 G	
19 L	55 C	-6:143874410 1205373034 C	L
19	56 T	-6:143874409 1205373033 T	
19	57 G	-6:143874408 1205373032 G	
20 L	58 C	-6:143874407 1205373031 C	L
20	59 T	-6:143874406 1205373030 T	
20	60 G	-6:143874405 1205373029 G	
21 L	61 C	-6:143874404 1205373028 C	L
21	62 T	-6:143874403 1205373027 T	
21	63 G	-6:143874402 1205373026 G	
22 P	64 C	-6:143874401 1205373025 C	P
22	65 C	-6:143874400 1205373024 C	
22	66 G	-6:143874399 1205373023 G	
23 P	67 C	-6:143874398 1205373022 C	P
23	68 C	-6:143874397 1205373021 C	
23	69 G	-6:143874396 1205373020 G	
24 P	70 C	-6:143874395 1205373019 C	P
24	71 C	-6:143874394 1205373018 C	
24	72 G	-6:143874393 1205373017 G	
25 P	73 C	-6:143874392 1205373016 C	P
25	74 C	-6:143874391 1205373015 C	
25	75 G	-6:143874390 1205373014 G	
26 C	76 T	-6:143874389 1205373013 T	C
26	77 G	-6:143874388 1205373012 G	
26	78 C	-6:143874387 1205373011 C	
27 P	79 C	-6:143874386 1205373010 C	P
27	80 C	-6:143874385 1205373009 C	
27	81 T	-6:143874384 1205373008 T	
28 A	82 G	-6:143874383 1205373007 G	A
28	83 C	-6:143874382 1205373006 C	
28	84 C	-6:143874381 1205373005 C	
29 H	85 C	-6:143874380 1205373004 C	H
29	86 A	-6:143874379 1205373003 A	
29	87 C	-6:143874378 1205373002 C	
30 S	88 A	-6:143874377 1205373001 A	S
30	89 G	-6:143874376 1205373000 G	
30	90 C	-6:143874375 1205372999 C	
31 A	91 G	-6:143874374 1205372998 G	A
31	92 C	-6:143874373 1205372997 C	
31	93 C	-6:143874372 1205372996 C	
32 T	94 A	-6:143874371 1205372995 A	T
32	95 C	-6:143874370 1205372994 C	
32	96 G	-6:143874369 1205372993 G	
33 R	97 C	-6:143874368 1205372992 C	R
33	98 G	-6:143874367 1205372991 G	
33	99 C	-6:143874366 1205372990 C	
34 F	100 T	-6:143874365 1205372989 T	F
34	101 T	-6:143874364 1205372988 T	
34	102 C	-6:143874363 1205372987 C	
35 D	103 G	-6:143874362 1205372986 G	D
35	104 A	-6:143874361 1205372985 A	
35	105 C	-6:143874360 1205372984 C	
36 P	106 C	-6:143874359 1205372983 C	P
36	107 C	-6:143874358 1205372982 C	
36	108 C	-6:143874357 1205372981 C	
37 T	109 A	-6:143874356 1205372980 A	T
37	110 C	-6:143874355 1205372979 C	
37	111 C	-6:143874354 1205372978 C	
38 W	112 T	-6:143874353 1205372977 T	W
38	113 G	-6:143874352 1205372976 G	
38	114 G	-6:143874351 1205372975 G	
39 E	115 G	-6:143874350 1205372974 G	E
39	116 A	-6:143874349 1205372973 A	
39	117 G	-6:143874348 1205372972 G	
40 S	118 T	-6:143874347 1205372971 T	S
40	119 C	-6:143874346 1205372970 C	
40	120 C	-6:143874345 1205372969 C	
41 L	121 C	-6:143874344 1205372968 C	L
41	122 T	-6:143874343 1205372967 T	
41	123 G	-6:143874342 1205372966 G	
42 D	124 G	-6:143874341 1205372965 G	D
42	125 A	-6:143874340 1205372964 A	
42	126 C	-6:143874339 1205372963 C	
43 A	127 G	-6:143874338 1205372962 G	A
43	128 C	-6:143874337 1205372961 C	
43	129 C	-6:143874336 1205372960 C	
44 R	130 C	-6:143874335 1205372959 C	R
44	131 G	-6:143874334 1205372958 G	
44	132 C	-6:143874333 1205372957 C	
45 Q	133 C	-6:143874332 1205372956 C	Q
45	134 A	-6:143874331 1205372955 A	
45	135 G	-6:143874330 1205372954 G	
46 L	136 C	-6:143874329 1205372953 C	L
46	137 T	-6:143874328 1205372952 T	
46	138 G	-6:143874327 1205372951 G	
47 P	139 C	-6:143874326 1205372950 C	P
47	140 C	-6:143874325 1205372949 C	
47	141 C	-6:143874324 1205372948 C	
48 A	142 G	-6:143874323 1205372947 G	A
48	143 C	-6:143874322 1205372946 C	
48	144 G	-6:143874321 1205372945 G	
49 W	145 T	-6:143874320 1205372944 T	W
49	146 G	-6:143874319 1205372943 G	
49	147 G	-6:143874318 1205372942 G	
50 F	148 T	-6:143874317 1205372941 T	F
50	149 T	-6:143874316 1205372940 T	
50	150 T	-6:143874315 1205372939 T	
51 D	151 G	-6:143874314 1205372938 G	D
51	152 A	-6:143874313 1205372937 A	
51	153 C	-6:143874312 1205372936 C	
52 Q	154 C	-6:143874311 1205372935 C	Q
52	155 A	-6:143874310 1205372934 A	
52	156 G	-6:143874309 1205372933 G	
53 A	157 G	-6:143874308 1205372932 G	A
53	158 C	-6:143874307 1205372931 C	
53	159 C	-6:143874306 1205372930 C	
54 K	160 A	-6:143874305 1205372929 A	K
54	161 A	-6:143874304 1205372928 A	
54	162 G	-6:143874303 1205372927 G	
55 F	163 T	-6:143874302 1205372926 T	F
55	164 T	-6:143874301 1205372925 T	
55	165 C	-6:143874300 1205372924 C	
56 G	166 G	-6:143874299 1205372923 G	G
56	167 G	-6:143874298 1205372922 G	
56	168 C	-6:143874297 1205372921 C	
57 I	169 A	-6:143874296 1205372920 A	I
57	170 T	-6:143874295 1205372919 T	
57	171 C	-6:143874294 1205372918 C	
58 F	172 T	-6:143874293 1205372917 T	F
58	173 T	-6:143874292 1205372916 T	
58	174 C	-6:143874291 1205372915 C	
59 I	175 A	-6:143874290 1205372914 A	I
59	176 T	-6:143874289 1205372913 T	
59	177 C	-6:143874288 1205372912 C	
60 H	178 C	-6:143874287 1205372911 C	H
60	179 A	-6:143874286 1205372910 A	
60	180 C	-6:143874285 1205372909 C	
61 W	181 T	-6:143874284 1205372908 T	W
61	182 G	-6:143874283 1205372907 G	
61	183 G	-6:143874282 1205372906 G	
62 G	184 G	-6:143874281 1205372905 G	G
62	185 G	-6:143874280 1205372904 G	
62	186 A	-6:143874279 1205372903 A	
63 V	187 G	-6:143874278 1205372902 G	V
63	188 T	-6:143874277 1205372901 T	
63	189 G	-6:143874276 1205372900 G	
64 F	190 T	-6:143874275 1205372899 T	F
64	191 T	-6:143874274 1205372898 T	
64	192 T	-6:143874273 1205372897 T	
65 S	193 T	-6:143874272 1205372896 T	S
65	194 C	-6:143874271 1205372895 C	
65	195 C	-6:143874270 1205372894 C	
66 V	196 G	-6:143874269 1205372893 G	V
66	197 T	-6:143874268 1205372892 T	
66	198 G	-6:143874267 1205372891 G	
67 P	199 C	-6:143874266 1205372890 C	P
67	200 C	-6:143874265 1205372889 C	
67	201 C	-6:143874264 1205372888 C	
68 S	202 A	-6:143874263 1205372887 A	S
68	203 G	-6:143874262 1205372886 G	
68	204 C	-6:143874261 1205372885 C	
69 F	205 T	-6:143874260 1205372884 T	F
69	206 T	-6:143874259 1205372883 T	
69	207 C	-6:143874258 1205372882 C	
70 G	208 G	-6:143874257 1205372881 G	G
70	209 G	-6:143874256 1205372880 G	
70	210 T	-6:143874255 1205372879 T	
71 S	211 A	-6:143874254 1205372878 A	S
71	212 G	-6:143874253 1205372877 G	
71	213 C	-6:143874252 1205372876 C	
72 E	214 G	-6:143874251 1205372875 G	E
72	215 A	-6:143874250 1205372874 A	
72	216 G	-6:143874249 1205372873 G	
73 W	217 T	-6:143874248 1205372872 T	W
73	218 G	-6:143874247 1205372871 G	
73	219 G	-6:143874246 1205372870 G	
74 F	220 T	-6:143874245 1205372869 T	F
74	221 T	-6:143874244 1205372868 T	
74	222 C	-6:143874243 1205372867 C	
75 W	223 T	-6:143874242 1205372866 T	W
75	224 G	-6:143874241 1205372865 G	
75	225 G	-6:143870254 1205368878 G	
76 W	226 T	-6:143870253 1205368877 T	W
76	227 G	-6:143870252 1205368876 G	
76	228 G	-6:143870251 1205368875 G	
77 Y	229 T	-6:143870250 1205368874 T	Y
77	230 A	-6:143870249 1205368873 A	
77	231 T	-6:143870248 1205368872 T	
78 W	232 T	-6:143870247 1205368871 T	W
78	233 G	-6:143870246 1205368870 G	
78	234 G	-6:143870245 1205368869 G	
79 Q	235 C	-6:143870244 1205368868 C	Q
79	236 A	-6:143870243 1205368867 A	
79	237 A	-6:143870242 1205368866 A	
80 K	238 A	-6:143870241 1205368865 A	K
80	239 A	-6:143870240 1205368864 A	
80	240 G	-6:143870239 1205368863 G	
81 E	241 G	-6:143870238 1205368862 G	E
81	242 A	-6:143870237 1205368861 A	
81	243 A	-6:143870236 1205368860 A	
82 K	244 A	-6:143870235 1205368859 A	K
82	245 A	-6:143870234 1205368858 A	
82	246 G	-6:143870233 1205368857 G	
83 I	247 A	-6:143870232 1205368856 A	I
83	248 T	-6:143870231 1205368855 T	
83	249 A	-6:143870230 1205368854 A	
84 P	250 C	-6:143870229 1205368853 C	P
84	251 C	-6:143870228 1205368852 C	
84	252 G	-6:143870227 1205368851 G	
85 K	253 A	-6:143870226 1205368850 A	K
85	254 A	-6:143870225 1205368849 A	
85	255 G	-6:143870224 1205368848 G	
86 Y	256 T	-6:143870223 1205368847 T	Y
86	257 A	-6:143870222 1205368846 A	
86	258 T	-6:143870221 1205368845 T	
87 V	259 G	-6:143870220 1205368844 G	V
87	260 T	-6:143870219 1205368843 T	
87	261 G	-6:143870218 1205368842 G	
88 E	262 G	-6:143870217 1205368841 G	E
88	263 A	-6:143870216 1205368840 A	
88	264 A	-6:143870215 1205368839 A	
89 F	265 T	-6:143870214 1205368838 T	F
89	266 T	-6:143870213 1205368837 T	
89	267 T	-6:143870212 1205368836 T	
90 M	268 A	-6:143870211 1205368835 A	M
90	269 T	-6:143870210 1205368834 T	
90	270 G	-6:143870209 1205368833 G	
91 K	271 A	-6:143870208 1205368832 A	K
91	272 A	-6:143870207 1205368831 A	
91	273 A	-6:143870206 1205368830 A	
92 D	274 G	-6:143870205 1205368829 G	D
92	275 A	-6:143870204 1205368828 A	
92	276 T	-6:143870203 1205368827 T	
93 N	277 A	-6:143870202 1205368826 A	N
93	278 A	-6:143870201 1205368825 A	
93	279 T	-6:143870200 1205368824 T	
94 Y	280 T	-6:143870199 1205368823 T	Y
94	281 A	-6:143870198 1205368822 A	
94	282 C	-6:143870197 1205368821 C	
95 P	283 C	-6:143870196 1205368820 C	P
95	284 C	-6:143870195 1205368819 C	
95	285 T	-6:143870194 1205368818 T	
96 P	286 C	-6:143870193 1205368817 C	P
96	287 C	-6:143870192 1205368816 C	
96	288 T	-6:143870191 1205368815 T	
97 S	289 A	-6:143870190 1205368814 A	S
97	290 G	-6:143870189 1205368813 G	
97	291 T	-6:143870188 1205368812 T	
98 F	292 T	-6:143870187 1205368811 T	F
98	293 T	-6:143870186 1205368810 T	
98	294 C	-6:143870185 1205368809 C	
99 K	295 A	-6:143870184 1205368808 A	K
99	296 A	-6:143870183 1205368807 A	
99	297 A	-6:143870182 1205368806 A	
100 Y	298 T	-6:143870181 1205368805 T	Y
100	299 A	-6:143870180 1205368804 A	
100	300 T	-6:143870179 1205368803 T	
101 E	301 G	-6:143870178 1205368802 G	E
101	302 A	-6:143870177 1205368801 A	
101	303 A	-6:143870176 1205368800 A	
102 D	304 G	-6:143870175 1205368799 G	D
102	305 A	-6:143870174 1205368798 A	
102	306 T	-6:143870173 1205368797 T	
103 F	307 T	-6:143870172 1205368796 T	F
103	308 T	-6:143870171 1205368795 T	
103	309 T	-6:143870170 1205368794 T	
104 G	310 G	-6:143870169 1205368793 G	G
104	311 G	-6:143870168 1205368792 G	
104	312 A	-6:143870167 1205368791 A	
105 P	313 C	-6:143870166 1205368790 C	P
105	314 C	-6:143870165 1205368789 C	
105	315 A	-6:143870164 1205368788 A	
106 L	316 C	-6:143870163 1205368787 C	L
106	317 T	-6:143870162 1205368786 T	
106	318 A	-6:143870161 1205368785 A	
107 F	319 T	-6:143870160 1205368784 T	F
107	320 T	-6:143870159 1205368783 T	
107	321 T	-6:143870158 1205368782 T	
108 T	322 A	-6:143870157 1205368781 A	T
108	323 C	-6:143870156 1205368780 C	
108	324 A	-6:143870155 1205368779 A	
109 A	325 G	-6:143870154 1205368778 G	A
109	326 C	-6:143870153 1205368777 C	
109	327 A	-6:143870152 1205368776 A	
110 K	328 A	-6:143870151 1205368775 A	K
110	329 A	-6:143870150 1205368774 A	
110	330 A	-6:143870149 1205368773 A	
111 F	331 T	-6:143870148 1205368772 T	F
111	332 T	-6:143870147 1205368771 T	
111	333 T	-6:143870146 1205368770 T	
112 F	334 T	-6:143870145 1205368769 T	F
112	335 T	-6:143870144 1205368768 T	
112	336 T	-6:143870143 1205368767 T	
113 N	337 A	-6:143870142 1205368766 A	N
113	338 A	-6:143870141 1205368765 A	
113	339 T	-6:143870140 1205368764 T	
114 A	340 G	-6:143870139 1205368763 G	A
114	341 C	-6:143870138 1205368762 C	
114	342 C	-6:143870137 1205368761 C	
115 N	343 A	-6:143870136 1205368760 A	N
115	344 A	-6:143870135 1205368759 A	
115	345 C	-6:143870134 1205368758 C	
116 Q	346 C	-6:143870133 1205368757 C	Q
116	347 A	-6:143870132 1205368756 A	
116	348 G	-6:143870131 1205368755 G	
117 W	349 T	-6:143870130 1205368754 T	W
117	350 G	-6:143870129 1205368753 G	
117	351 G	-6:143870128 1205368752 G	
118 A	352 G	-6:143870127 1205368751 G	A
118	353 C	-6:143870126 1205368750 C	
118	354 A	-6:143870125 1205368749 A	
119 D	355 G	-6:143870124 1205368748 G	D
119	356 A	-6:143870123 1205368747 A	
119	357 T	-6:143870122 1205368746 T	
120 I	358 A	-6:143870121 1205368745 A	I
120	359 T	-6:143870120 1205368744 T	
120	360 T	-6:143870119 1205368743 T	
121 F	361 T	-6:143870118 1205368742 T	F
121	362 T	-6:143870117 1205368741 T	
121	363 T	-6:143870116 1205368740 T	
122 Q	364 C	-6:143870115 1205368739 C	Q
122	365 A	-6:143870114 1205368738 A	
122	366 G	-6:143870113 1205368737 G	
123 A	367 G	-6:143870112 1205368736 G	A
123	368 C	-6:143870111 1205368735 C	
123	369 C	-6:143870110 1205368734 C	
124 S	370 T	-6:143870109 1205368733 T	S
124	371 C	-6:143870108 1205368732 C	
124	372 T	-6:143870107 1205368731 T	
125 G	373 G	-6:143870106 1205368730 G	G
125	374 G	-6:143870105 1205368729 G	
125	375 T	-6:143870104 1205368728 T	
126 A	376 G	-6:143870103 1205368727 G	A
126	377 C	-6:143870102 1205368726 C	
126	378 C	-6:143870101 1205368725 C	
127 K	379 A	-6:143870100 1205368724 A	K
127	380 A	-6:143870099 1205368723 A	
127	381 A	-6:143870098 1205368722 A	
128 Y	382 T	-6:143870097 1205368721 T	Y
128	383 A	-6:143870096 1205368720 A	
128	384 C	-6:143870095 1205368719 C	
129 I	385 A	-6:143870094 1205368718 A	I
129	386 T	-6:143870093 1205368717 T	
129	387 T	-6:143870092 1205368716 T	
130 V	388 G	-6:143870091 1205368715 G	V
130	389 T	-6:143870090 1205368714 T	
130	390 C	-6:143870089 1205368713 C	
131 L	391 T	-6:143870088 1205368712 T	L
131	392 T	-6:143870087 1205368711 T	
131	393 A	-6:143870086 1205368710 A	
132 T	394 A	-6:143870085 1205368709 A	T
132	395 C	-6:143870084 1205368708 C	
132	396 T	-6:143870083 1205368707 T	
133 S	397 T	-6:143870082 1205368706 T	S
133	398 C	-6:143870081 1205368705 C	
133	399 C	-6:143870080 1205368704 C	
134 K	400 A	-6:143870079 1205368703 A	K
134	401 A	-6:143870078 1205368702 A	
134	402 A	-6:143870077 1205368701 A	
135 H	403 C	-6:143870076 1205368700 C	H
135	404 A	-6:143870075 1205368699 A	
135	405 T	-6:143870074 1205368698 T	
136 H	406 C	-6:143870073 1205368697 C	H
136	407 A	-6:143870072 1205368696 A	
136	408 T	-6:143870071 1205368695 T	
137 E	409 G	-6:143870070 1205368694 G	E
137	410 A	-6:143870069 1205368693 A	
137	411 A	-6:143870068 1205368692 A	
138 A	412 G	-6:143870067 1205368691 G	A
138	413 C	-6:143864952 1205363576 C	
138	414 A	-6:143864951 1205363575 A	
139 T	415 A	-6:143864950 1205363574 A	T
139	416 C	-6:143864949 1205363573 C	
139	417 T	-6:143864948 1205363572 T	
140 C	418 T	-6:143864947 1205363571 T	C
140	419 G	-6:143864946 1205363570 G	
140	420 T	-6:143864945 1205363569 T	
141 R	421 A	-6:143864944 1205363568 A	R
141	422 G	-6:143864943 1205363567 G	
141	423 A	-6:143864942 1205363566 A	
142 D	424 G	-6:143864941 1205363565 G	D
142	425 A	-6:143864940 1205363564 A	
142	426 C	-6:143864939 1205363563 C	
143 S	427 A	-6:143864938 1205363562 A	S
143	428 G	-6:143864937 1205363561 G	
143	429 T	-6:143864936 1205363560 T	
144 F	430 T	-6:143864935 1205363559 T	F
144	431 T	-6:143864934 1205363558 T	
144	432 C	-6:143864933 1205363557 C	
145 M	433 A	-6:143864932 1205363556 A	M
145	434 T	-6:143864931 1205363555 T	
145	435 G	-6:143864930 1205363554 G	
146 W	436 T	-6:143864929 1205363553 T	W
146	437 G	-6:143864928 1205363552 G	
146	438 G	-6:143864927 1205363551 G	
147 R	439 A	-6:143864926 1205363550 A	R
147	440 G	-6:143864925 1205363549 G	
147	441 G	-6:143864924 1205363548 G	
148 K	442 A	-6:143864923 1205363547 A	K
148	443 A	-6:143864922 1205363546 A	
148	444 A	-6:143864921 1205363545 A	
149 S	445 T	-6:143864920 1205363544 T	S
149	446 C	-6:143864919 1205363543 C	
149	447 T	-6:143864918 1205363542 T	
150 F	448 T	-6:143864917 1205363541 T	F
150	449 T	-6:143864916 1205363540 T	
150	450 T	-6:143864915 1205363539 T	
151 D	451 G	-6:143864914 1205363538 G	D
151	452 A	-6:143864913 1205363537 A	
151	453 T	-6:143864912 1205363536 T	
152 E	454 G	-6:143864911 1205363535 G	E
152	455 A	-6:143864910 1205363534 A	
152	456 A	-6:143864909 1205363533 A	
153 Y	457 T	-6:143864908 1205363532 T	Y
153	458 A	-6:143864907 1205363531 A	
153	459 T	-6:143864906 1205363530 T	
154 W	460 T	-6:143864905 1205363529 T	W
154	461 G	-6:143864904 1205363528 G	
154	462 G	-6:143864903 1205363527 G	
155 A	463 G	-6:143864902 1205363526 G	A
155	464 C	-6:143864901 1205363525 C	
155	465 C	-6:143864900 1205363524 C	
156 H	466 C	-6:143864899 1205363523 C	H
156	467 A	-6:143864898 1205363522 A	
156	468 C	-6:143864897 1205363521 C	
157 T	469 A	-6:143864896 1205363520 A	T
157	470 C	-6:143864895 1205363519 C	
157	471 T	-6:143864894 1205363518 T	
158 R	472 A	-6:143864893 1205363517 A	R
158	473 G	-6:143864892 1205363516 G	
158	474 A	-6:143864891 1205363515 A	
159 W	475 T	-6:143864890 1205363514 T	W
159	476 G	-6:143864889 1205363513 G	
159	477 G	-6:143864888 1205363512 G	
160 H	478 C	-6:143864887 1205363511 C	H
160	479 A	-6:143864886 1205363510 A	
160	480 C	-6:143864885 1205363509 C	
161 H	481 C	-6:143864884 1205363508 C	H
161	482 A	-6:143864883 1205363507 A	
161	483 T	-6:143864882 1205363506 T	
162 F	484 T	-6:143864881 1205363505 T	F
162	485 T	-6:143864880 1205363504 T	
162	486 C	-6:143864879 1205363503 C	
163 C	487 T	-6:143864878 1205363502 T	C
163	488 G	-6:143864877 1205363501 G	
163	489 T	-6:143864876 1205363500 T	
164 S	490 A	-6:143864875 1205363499 A	S
164	491 G	-6:143864874 1205363498 G	
164	492 T	-6:143864873 1205363497 T	
165 F	493 T	-6:143864872 1205363496 T	F
165	494 T	-6:143864871 1205363495 T	
165	495 T	-6:143864870 1205363494 T	
>ENSP00000002165 
1 M	1 A	-6:143874464 1205373088 A	M
1	2 T	-6:143874463 1205373087 T	
1	3 G	-6:143874462 1205373086 G	
2 R	4 C	-6:143874461 1205373085 C	R
2	5 G	-6:143874460 1205373084 G	
2	6 G	-6:143874459 1205373083 G	
3 P	7 C	-6:143874458 1205373082 C	P
3	8 C	-6:143874457 1205373081 C	
3	9 C	-6:143874456 1205373080 C	
4 Q	10 C	-6:143874455 1205373079 C	Q
4	11 A	-6:143874454 1205373078 A	
4	12 G	-6:143874453 1205373077 G	
5 E	13 G	-6:143874452 1205373076 G	E
5	14 A	-6:143874451 1205373075 A	
5	15 G	-6:143874450 1205373074 G	
6 L	16 C	-6:143874449 1205373073 C	L
6	17 T	-6:143874448 1205373072 T	
6	18 C	-6:143874447 1205373071 C	
7 P	19 C	-6:143874446 1205373070 C	P
7	20 C	-6:143874445 1205373069 C	
7	21 C	-6:143874444 1205373068 C	
8 R	22 A	-6:143874443 1205373067 A	R
8	23 G	-6:143874442 1205373066 G	
8	24 G	-6:143874441 1205373065 G	
9 L	25 C	-6:143874440 1205373064 C	L
9	26 T	-6:143874439 1205373063 T	
9	27 C	-6:143874438 1205373062 C	
10 A	28 G	-6:143874437 1205373061 G	A
10	29 C	-6:143874436 1205373060 C	
10	30 G	-6:143874435 1205373059 G	
11 F	31 T	-6:143874434 1205373058 T	F
11	32 T	-6:143874433 1205373057 T	
11	33 C	-6:143874432 1205373056 C	
12 P	34 C	-6:143874431 1205373055 C	P
12	35 C	-6:143874430 1205373054 C	
12	36 G	-6:143874429 1205373053 G	
13 L	37 T	-6:143874428 1205373052 T	L
13	38 T	-6:143874427 1205373051 T	
13	39 G	-6:143874426 1205373050 G	
14 L	40 C	-6:143874425 1205373049 C	L
14	41 T	-6:143874424 1205373048 T	
14	42 G	-6:143874423 1205373047 G	
15 L	43 C	-6:143874422 1205373046 C	L
15	44 T	-6:143874421 1205373045 T	
15	45 G	-6:143874420 1205373044 G	
16 L	46 T	-6:143874419 1205373043 T	L
16	47 T	-6:143874418 1205373042 T	
16	48 G	-6:143874417 1205373041 G	
17 L	49 C	-6:143874416 1205373040 C	L
17	50 T	-6:143874415 1205373039 T	
17	51 G	-6:143874414 1205373038 G	
18 L	52 T	-6:143874413 1205373037 T	L
18	53 T	-6:143874412 1205373036 T	
18	54 G	-6:143874411 1205373035 G	
19 L	55 C	-6:143874410 1205373034 C	L
19	56 T	-6:143874409 1205373033 T	
19	57 G	-6:143874408 1205373032 G	
20 L	58 C	-6:143874407 1205373031 C	L
20	59 T	-6:143874406 1205373030 T	
20	60 G	-6:143874405 1205373029 G	
21 L	61 C	-6:143874404 1205373028 C	L
21	62 T	-6:143874403 1205373027 T	
21	63 G	-6:143874402 1205373026 G	
22 P	64 C	-6:143874401 1205373025 C	P
22	65 C	-6:143874400 1205373024 C	
22	66 G	-6:143874399 1205373023 G	
23 P	67 C	-6:143874398 1205373022 C	P
23	68 C	-6:143874397 1205373021 C	
23	69 G	-6:143874396 1205373020 G	
24 P	70 C	-6:143874395 1205373019 C	P
24	71 C	-6:143874394 1205373018 C	
24	72 G	-6:143874393 1205373017 G	
25 P	73 C	-6:143874392 1205373016 C	P
25	74 C	-6:143874391 1205373015 C	
25	75 G	-6:143874390 1205373014 G	
26 C	76 T	-6:143874389 1205373013 T	C
26	77 G	-6:143874388 1205373012 G	
26	78 C	-6:143874387 1205373011 C	
27 P	79 C	-6:143874386 1205373010 C	P
27	80 C	-6:143874385 1205373009 C	
27	81 T	-6:143874384 1205373008 T	
28 A	82 G	-6:143874383 1205373007 G	A
28	83 C	-6:143874382 1205373006 C	
28	84 C	-6:143874381 1205373005 C	
29 H	85 C	-6:143874380 1205373004 C	H
29	86 A	-6:143874379 1205373003 A	
29	87 C	-6:143874378 1205373002 C	
30 S	88 A	-6:143874377 1205373001 A	S
30	89 G	-6:143874376 1205373000 G	
30	90 C	-6:143874375 1205372999 C	
31 A	91 G	-6:143874374 1205372998 G	A
31	92 C	-6:143874373 1205372997 C	
31	93 C	-6:143874372 1205372996 C	
32 T	94 A	-6:143874371 1205372995 A	T
32	95 C	-6:143874370 1205372994 C	
32	96 G	-6:143874369 1205372993 G	
33 R	97 C	-6:143874368 1205372992 C	R
33	98 G	-6:143874367 1205372991 G	
33	99 C	-6:143874366 1205372990 C	
34 F	100 T	-6:143874365 1205372989 T	F
34	101 T	-6:143874364 1205372988 T	
34	102 C	-6:143874363 1205372987 C	
35 D	103 G	-6:143874362 1205372986 G	D
35	104 A	-6:143874361 1205372985 A	
35	105 C	-6:143874360 1205372984 C	
36 P	106 C	-6:143874359 1205372983 C	P
36	107 C	-6:143874358 1205372982 C	
36	108 C	-6:143874357 1205372981 C	
37 T	109 A	-6:143874356 1205372980 A	T
37	110 C	-6:143874355 1205372979 C	
37	111 C	-6:143874354 1205372978 C	
38 W	112 T	-6:143874353 1205372977 T	W
38	113 G	-6:143874352 1205372976 G	
38	114 G	-6:143874351 1205372975 G	
39 E	115 G	-6:143874350 1205372974 G	E
39	116 A	-6:143874349 1205372973 A	
39	117 G	-6:143874348 1205372972 G	
40 S	118 T	-6:143874347 1205372971 T	S
40	119 C	-6:143874346 1205372970 C	
40	120 C	-6:143874345 1205372969 C	
41 L	121 C	-6:143874344 1205372968 C	L
41	122 T	-6:143874343 1205372967 T	
41	123 G	-6:143874342 1205372966 G	
42 D	124 G	-6:143874341 1205372965 G	D
42	125 A	-6:143874340 1205372964 A	
42	126 C	-6:143874339 1205372963 C	
43 A	127 G	-6:143874338 1205372962 G	A
43	128 C	-6:143874337 1205372961 C	
43	129 C	-6:143874336 1205372960 C	
44 R	130 C	-6:143874335 1205372959 C	R
44	131 G	-6:143874334 1205372958 G	
44	132 C	-6:143874333 1205372957 C	
45 Q	133 C	-6:143874332 1205372956 C	Q
45	134 A	-6:143874331 1205372955 A	
45	135 G	-6:143874330 1205372954 G	
46 L	136 C	-6:143874329 1205372953 C	L
46	137 T	-6:143874328 1205372952 T	
46	138 G	-6:143874327 1205372951 G	
47 P	139 C	-6:143874326 1205372950 C	P
47	140 C	-6:143874325 1205372949 C	
47	141 C	-6:143874324 1205372948 C	
48 A	142 G	-6:143874323 1205372947 G	A
48	143 C	-6:143874322 1205372946 C	
48	144 G	-6:143874321 1205372945 G	
49 W	145 T	-6:143874320 1205372944 T	W
49	146 G	-6:143874319 1205372943 G	
49	147 G	-6:143874318 1205372942 G	
50 F	148 T	-6:143874317 1205372941 T	F
50	149 T	-6:143874316 1205372940 T	
50	150 T	-6:143874315 1205372939 T	
51 D	151 G	-6:143874314 1205372938 G	D
51	152 A	-6:143874313 1205372937 A	
51	153 C	-6:143874312 1205372936 C	
52 Q	154 C	-6:143874311 1205372935 C	Q
52	155 A	-6:143874310 1205372934 A	
52	156 G	-6:143874309 1205372933 G	
53 A	157 G	-6:143874308 1205372932 G	A
53	158 C	-6:143874307 1205372931 C	
53	159 C	-6:143874306 1205372930 C	
54 K	160 A	-6:143874305 1205372929 A	K
54	161 A	-6:143874304 1205372928 A	
54	162 G	-6:143874303 1205372927 G	
55 F	163 T	-6:143874302 1205372926 T	F
55	164 T	-6:143874301 1205372925 T	
55	165 C	-6:143874300 1205372924 C	
56 G	166 G	-6:143874299 1205372923 G	G
56	167 G	-6:143874298 1205372922 G	
56	168 C	-6:143874297 1205372921 C	
57 I	169 A	-6:143874296 1205372920 A	I
57	170 T	-6:143874295 1205372919 T	
57	171 C	-6:143874294 1205372918 C	
58 F	172 T	-6:143874293 1205372917 T	F
58	173 T	-6:143874292 1205372916 T	
58	174 C	-6:143874291 1205372915 C	
59 I	175 A	-6:143874290 1205372914 A	I
59	176 T	-6:143874289 1205372913 T	
59	177 C	-6:143874288 1205372912 C	
60 H	178 C	-6:143874287 1205372911 C	H
60	179 A	-6:143874286 1205372910 A	
60	180 C	-6:143874285 1205372909 C	
61 W	181 T	-6:143874284 1205372908 T	W
61	182 G	-6:143874283 1205372907 G	
61	183 G	-6:143874282 1205372906 G	
62 G	184 G	-6:143874281 1205372905 G	G
62	185 G	-6:143874280 1205372904 G	
62	186 A	-6:143874279 1205372903 A	
63 V	187 G	-6:143874278 1205372902 G	V
63	188 T	-6:143874277 1205372901 T	
63	189 G	-6:143874276 1205372900 G	
64 F	190 T	-6:143874275 1205372899 T	F
64	191 T	-6:143874274 1205372898 T	
64	192 T	-6:143874273 1205372897 T	
65 S	193 T	-6:143874272 1205372896 T	S
65	194 C	-6:143874271 1205372895 C	
65	195 C	-6:143874270 1205372894 C	
66 V	196 G	-6:143874269 1205372893 G	V
66	197 T	-6:143874268 1205372892 T	
66	198 G	-6:143874267 1205372891 G	
67 P	199 C	-6:143874266 1205372890 C	P
67	200 C	-6:143874265 1205372889 C	
67	201 C	-6:143874264 1205372888 C	
68 S	202 A	-6:143874263 1205372887 A	S
68	203 G	-6:143874262 1205372886 G	
68	204 C	-6:143874261 1205372885 C	
69 F	205 T	-6:143874260 1205372884 T	F
69	206 T	-6:143874259 1205372883 T	
69	207 C	-6:143874258 1205372882 C	
70 G	208 G	-6:143874257 1205372881 G	G
70	209 G	-6:143874256 1205372880 G	
70	210 T	-6:143874255 1205372879 T	
71 S	211 A	-6:143874254 1205372878 A	S
71	212 G	-6:143874253 1205372877 G	
71	213 C	-6:143874252 1205372876 C	
72 E	214 G	-6:143874251 1205372875 G	E
72	215 A	-6:143874250 1205372874 A	
72	216 G	-6:143874249 1205372873 G	
73 W	217 T	-6:143874248 1205372872 T	W
73	218 G	-6:143874247 1205372871 G	
73	219 G	-6:143874246 1205372870 G	
74 F	220 T	-6:143874245 1205372869 T	F
74	221 T	-6:143874244 1205372868 T	
74	222 C	-6:143874243 1205372867 C	
75 W	223 T	-6:143874242 1205372866 T	W
75	224 G	-6:143874241 1205372865 G	
75	225 G	-6:143870254 1205368878 G	
76 W	226 T	-6:143870253 1205368877 T	W
76	227 G	-6:143870252 1205368876 G	
76	228 G	-6:143870251 1205368875 G	
77 Y	229 T	-6:143870250 1205368874 T	Y
77	230 A	-6:143870249 1205368873 A	
77	231 T	-6:143870248 1205368872 T	
78 W	232 T	-6:143870247 1205368871 T	W
78	233 G	-6:143870246 1205368870 G	
78	234 G	-6:143870245 1205368869 G	
79 Q	235 C	-6:143870244 1205368868 C	Q
79	236 A	-6:143870243 1205368867 A	
79	237 A	-6:143870242 1205368866 A	
80 K	238 A	-6:143870241 1205368865 A	K
80	239 A	-6:143870240 1205368864 A	
80	240 G	-6:143870239 1205368863 G	
81 E	241 G	-6:143870238 1205368862 G	E
81	242 A	-6:143870237 1205368861 A	
81	243 A	-6:143870236 1205368860 A	
82 K	244 A	-6:143870235 1205368859 A	K
82	245 A	-6:143870234 1205368858 A	
82	246 G	-6:143870233 1205368857 G	
83 I	247 A	-6:143870232 1205368856 A	I
83	248 T	-6:143870231 1205368855 T	
83	249 A	-6:143870230 1205368854 A	
84 P	250 C	-6:143870229 1205368853 C	P
84	251 C	-6:143870228 1205368852 C	
84	252 G	-6:143870227 1205368851 G	
85 K	253 A	-6:143870226 1205368850 A	K
85	254 A	-6:143870225 1205368849 A	
85	255 G	-6:143870224 1205368848 G	
86 Y	256 T	-6:143870223 1205368847 T	Y
86	257 A	-6:143870222 1205368846 A	
86	258 T	-6:143870221 1205368845 T	
87 V	259 G	-6:143870220 1205368844 G	V
87	260 T	-6:143870219 1205368843 T	
87	261 G	-6:143870218 1205368842 G	
88 E	262 G	-6:143870217 1205368841 G	E
88	263 A	-6:143870216 1205368840 A	
88	264 A	-6:143870215 1205368839 A	
89 F	265 T	-6:143870214 1205368838 T	F
89	266 T	-6:143870213 1205368837 T	
89	267 T	-6:143870212 1205368836 T	
90 M	268 A	-6:143870211 1205368835 A	M
90	269 T	-6:143870210 1205368834 T	
90	270 G	-6:143870209 1205368833 G	
91 K	271 A	-6:143870208 1205368832 A	K
91	272 A	-6:143870207 1205368831 A	
91	273 A	-6:143870206 1205368830 A	
92 D	274 G	-6:143870205 1205368829 G	D
92	275 A	-6:143870204 1205368828 A	
92	276 T	-6:143870203 1205368827 T	
93 N	277 A	-6:143870202 1205368826 A	N
93	278 A	-6:143870201 1205368825 A	
93	279 T	-6:143870200 1205368824 T	
94 Y	280 T	-6:143870199 1205368823 T	Y
94	281 A	-6:143870198 1205368822 A	
94	282 C	-6:143870197 1205368821 C	
95 P	283 C	-6:143870196 1205368820 C	P
95	284 C	-6:143870195 1205368819 C	
95	285 T	-6:143870194 1205368818 T	
96 P	286 C	-6:143870193 1205368817 C	P
96	287 C	-6:143870192 1205368816 C	
96	288 T	-6:143870191 1205368815 T	
97 S	289 A	-6:143870190 1205368814 A	S
97	290 G	-6:143870189 1205368813 G	
97	291 T	-6:143870188 1205368812 T	
98 F	292 T	-6:143870187 1205368811 T	F
98	293 T	-6:143870186 1205368810 T	
98	294 C	-6:143870185 1205368809 C	
99 K	295 A	-6:143870184 1205368808 A	K
99	296 A	-6:143870183 1205368807 A	
99	297 A	-6:143870182 1205368806 A	
100 Y	298 T	-6:143870181 1205368805 T	Y
100	299 A	-6:143870180 1205368804 A	
100	300 T	-6:143870179 1205368803 T	
101 E	301 G	-6:143870178 1205368802 G	E
101	302 A	-6:143870177 1205368801 A	
101	303 A	-6:143870176 1205368800 A	
102 D	304 G	-6:143870175 1205368799 G	D
102	305 A	-6:143870174 1205368798 A	
102	306 T	-6:143870173 1205368797 T	
103 F	307 T	-6:143870172 1205368796 T	F
103	308 T	-6:143870171 1205368795 T	
103	309 T	-6:143870170 1205368794 T	
104 G	310 G	-6:143870169 1205368793 G	G
104	311 G	-6:143870168 1205368792 G	
104	312 A	-6:143870167 1205368791 A	
105 P	313 C	-6:143870166 1205368790 C	P
105	314 C	-6:143870165 1205368789 C	
105	315 A	-6:143870164 1205368788 A	
106 L	316 C	-6:143870163 1205368787 C	L
106	317 T	-6:143870162 1205368786 T	
106	318 A	-6:143870161 1205368785 A	
107 F	319 T	-6:143870160 1205368784 T	F
107	320 T	-6:143870159 1205368783 T	
107	321 T	-6:143870158 1205368782 T	
108 T	322 A	-6:143870157 1205368781 A	T
108	323 C	-6:143870156 1205368780 C	
108	324 A	-6:143870155 1205368779 A	
109 A	325 G	-6:143870154 1205368778 G	A
109	326 C	-6:143870153 1205368777 C	
109	327 A	-6:143870152 1205368776 A	
110 K	328 A	-6:143870151 1205368775 A	K
110	329 A	-6:143870150 1205368774 A	
110	330 A	-6:143870149 1205368773 A	
111 F	331 T	-6:143870148 1205368772 T	F
111	332 T	-6:143870147 1205368771 T	
111	333 T	-6:143870146 1205368770 T	
112 F	334 T	-6:143870145 1205368769 T	F
112	335 T	-6:143870144 1205368768 T	
112	336 T	-6:143870143 1205368767 T	
113 N	337 A	-6:143870142 1205368766 A	N
113	338 A	-6:143870141 1205368765 A	
113	339 T	-6:143870140 1205368764 T	
114 A	340 G	-6:143870139 1205368763 G	A
114	341 C	-6:143870138 1205368762 C	
114	342 C	-6:143870137 1205368761 C	
115 N	343 A	-6:143870136 1205368760 A	N
115	344 A	-6:143870135 1205368759 A	
115	345 C	-6:143870134 1205368758 C	
116 Q	346 C	-6:143870133 1205368757 C	Q
116	347 A	-6:143870132 1205368756 A	
116	348 G	-6:143870131 1205368755 G	
117 W	349 T	-6:143870130 1205368754 T	W
117	350 G	-6:143870129 1205368753 G	
117	351 G	-6:143870128 1205368752 G	
118 A	352 G	-6:143870127 1205368751 G	A
118	353 C	-6:143870126 1205368750 C	
118	354 A	-6:143870125 1205368749 A	
119 D	355 G	-6:143870124 1205368748 G	D
119	356 A	-6:143870123 1205368747 A	
119	357 T	-6:143870122 1205368746 T	
120 I	358 A	-6:143870121 1205368745 A	I
120	359 T	-6:143870120 1205368744 T	
120	360 T	-6:143870119 1205368743 T	
121 F	361 T	-6:143870118 1205368742 T	F
121	362 T	-6:143870117 1205368741 T	
121	363 T	-6:143870116 1205368740 T	
122 Q	364 C	-6:143870115 1205368739 C	Q
122	365 A	-6:143870114 1205368738 A	
122	366 G	-6:143870113 1205368737 G	
123 A	367 G	-6:143870112 1205368736 G	A
123	368 C	-6:143870111 1205368735 C	
123	369 C	-6:143870110 1205368734 C	
124 S	370 T	-6:143870109 1205368733 T	S
124	371 C	-6:143870108 1205368732 C	
124	372 T	-6:143870107 1205368731 T	
125 G	373 G	-6:143870106 1205368730 G	G
125	374 G	-6:143870105 1205368729 G	
125	375 T	-6:143870104 1205368728 T	
126 A	376 G	-6:143870103 1205368727 G	A
126	377 C	-6:143870102 1205368726 C	
126	378 C	-6:143870101 1205368725 C	
127 K	379 A	-6:143870100 1205368724 A	K
127	380 A	-6:143870099 1205368723 A	
127	381 A	-6:143870098 1205368722 A	
128 Y	382 T	-6:143870097 1205368721 T	Y
128	383 A	-6:143870096 1205368720 A	
128	384 C	-6:143870095 1205368719 C	
129 I	385 A	-6:143870094 1205368718 A	I
129	386 T	-6:143870093 1205368717 T	
129	387 T	-6:143870092 1205368716 T	
130 V	388 G	-6:143870091 1205368715 G	V
130	389 T	-6:143870090 1205368714 T	
130	390 C	-6:143870089 1205368713 C	
131 L	391 T	-6:143870088 1205368712 T	L
131	392 T	-6:143870087 1205368711 T	
131	393 A	-6:143870086 1205368710 A	
132 T	394 A	-6:143870085 1205368709 A	T
132	395 C	-6:143870084 1205368708 C	
132	396 T	-6:143870083 1205368707 T	
133 S	397 T	-6:143870082 1205368706 T	S
133	398 C	-6:143870081 1205368705 C	
133	399 C	-6:143870080 1205368704 C	
134 K	400 A	-6:143870079 1205368703 A	K
134	401 A	-6:143870078 1205368702 A	
134	402 A	-6:143870077 1205368701 A	
135 H	403 C	-6:143870076 1205368700 C	H
135	404 A	-6:143870075 1205368699 A	
135	405 T	-6:143870074 1205368698 T	
136 H	406 C	-6:143870073 1205368697 C	H
136	407 A	-6:143870072 1205368696 A	
136	408 T	-6:143870071 1205368695 T	
137 E	409 G	-6:143870070 1205368694 G	E
137	410 A	-6:143870069 1205368693 A	
137	411 A	-6:143870068 1205368692 A	
138 G	412 G	-6:143870067 1205368691 G	G
138	413 G	-6:143867082 1205365706 G	
138	414 C	-6:143867081 1205365705 C	
139 F	415 T	-6:143867080 1205365704 T	F
139	416 T	-6:143867079 1205365703 T	
139	417 T	-6:143867078 1205365702 T	
140 T	418 A	-6:143867077 1205365701 A	T
140	419 C	-6:143867076 1205365700 C	
140	420 C	-6:143867075 1205365699 C	
141 L	421 T	-6:143867074 1205365698 T	L
141	422 T	-6:143867073 1205365697 T	
141	423 G	-6:143867072 1205365696 G	
142 W	424 T	-6:143867071 1205365695 T	W
142	425 G	-6:143867070 1205365694 G	
142	426 G	-6:143867069 1205365693 G	
143 G	427 G	-6:143867068 1205365692 G	G
143	428 G	-6:143867067 1205365691 G	
143	429 G	-6:143867066 1205365690 G	
144 S	430 T	-6:143867065 1205365689 T	S
144	431 C	-6:143867064 1205365688 C	
144	432 A	-6:143867063 1205365687 A	
145 E	433 G	-6:143867062 1205365686 G	E
145	434 A	-6:143867061 1205365685 A	
145	435 A	-6:143867060 1205365684 A	
146 Y	436 T	-6:143867059 1205365683 T	Y
146	437 A	-6:143867058 1205365682 A	
146	438 T	-6:143867057 1205365681 T	
147 S	439 T	-6:143867056 1205365680 T	S
147	440 C	-6:143867055 1205365679 C	
147	441 G	-6:143867054 1205365678 G	
148 W	442 T	-6:143867053 1205365677 T	W
148	443 G	-6:143867052 1205365676 G	
148	444 G	-6:143867051 1205365675 G	
149 N	445 A	-6:143867050 1205365674 A	N
149	446 A	-6:143867049 1205365673 A	
149	447 C	-6:143867048 1205365672 C	
150 W	448 T	-6:143867047 1205365671 T	W
150	449 G	-6:143867046 1205365670 G	
150	450 G	-6:143867045 1205365669 G	
151 N	451 A	-6:143867044 1205365668 A	N
151	452 A	-6:143867043 1205365667 A	
151	453 T	-6:143867042 1205365666 T	
152 A	454 G	-6:143867041 1205365665 G	A
152	455 C	-6:143867040 1205365664 C	
152	456 C	-6:143867039 1205365663 C	
153 I	457 A	-6:143867038 1205365662 A	I
153	458 T	-6:143867037 1205365661 T	
153	459 A	-6:143867036 1205365660 A	
154 D	460 G	-6:143867035 1205365659 G	D
154	461 A	-6:143867034 1205365658 A	
154	462 T	-6:143867033 1205365657 T	
155 E	463 G	-6:143867032 1205365656 G	E
155	464 A	-6:143867031 1205365655 A	
155	465 G	-6:143867030 1205365654 G	
156 G	466 G	-6:143867029 1205365653 G	G
156	467 G	-6:143867028 1205365652 G	
156	468 G	-6:143867027 1205365651 G	
157 P	469 C	-6:143867026 1205365650 C	P
157	470 C	-6:143867025 1205365649 C	
157	471 C	-6:143867024 1205365648 C	
158 K	472 A	-6:143867023 1205365647 A	K
158	473 A	-6:143867022 1205365646 A	
158	474 G	-6:143867021 1205365645 G	
159 R	475 A	-6:143867020 1205365644 A	R
159	476 G	-6:143867019 1205365643 G	
159	477 G	-6:143867018 1205365642 G	
160 D	478 G	-6:143867017 1205365641 G	D
160	479 A	-6:143867016 1205365640 A	
160	480 C	-6:143867015 1205365639 C	
161 I	481 A	-6:143867014 1205365638 A	I
161	482 T	-6:143867013 1205365637 T	
161	483 T	-6:143867012 1205365636 T	
162 V	484 G	-6:143867011 1205365635 G	V
162	485 T	-6:143867010 1205365634 T	
162	486 C	-6:143867009 1205365633 C	
163 K	487 A	-6:143867008 1205365632 A	K
163	488 A	-6:143867007 1205365631 A	
163	489 G	-6:143867006 1205365630 G	
164 E	490 G	-6:143867005 1205365629 G	E
164	491 A	-6:143867004 1205365628 A	
164	492 A	-6:143867003 1205365627 A	
165 L	493 C	-6:143867002 1205365626 C	L
165	494 T	-6:143867001 1205365625 T	
165	495 T	-6:143867000 1205365624 T	
166 E	496 G	-6:143866999 1205365623 G	E
166	497 A	-6:143866998 1205365622 A	
166	498 G	-6:143866997 1205365621 G	
167 V	499 G	-6:143866996 1205365620 G	V
167	500 T	-6:143866995 1205365619 T	
167	501 A	-6:143866994 1205365618 A	
168 A	502 G	-6:143866993 1205365617 G	A
168	503 C	-6:143866992 1205365616 C	
168	504 C	-6:143866991 1205365615 C	
169 I	505 A	-6:143866990 1205365614 A	I
169	506 T	-6:143866989 1205365613 T	
169	507 T	-6:143866988 1205365612 T	
170 R	508 A	-6:143866987 1205365611 A	R
170	509 G	-6:143866986 1205365610 G	
170	510 G	-6:143866985 1205365609 G	
171 N	511 A	-6:143866984 1205365608 A	N
171	512 A	-6:143866983 1205365607 A	
171	513 C	-6:143866982 1205365606 C	
172 R	514 A	-6:143866981 1205365605 A	R
172	515 G	-6:143866980 1205365604 G	
172	516 A	-6:143866979 1205365603 A	
173 T	517 A	-6:143866978 1205365602 A	T
173	518 C	-6:143866977 1205365601 C	
173	519 T	-6:143866976 1205365600 T	
174 D	520 G	-6:143866975 1205365599 G	D
174	521 A	-6:143866974 1205365598 A	
174	522 C	-6:143866973 1205365597 C	
175 L	523 C	-6:143866972 1205365596 C	L
175	524 T	-6:143866971 1205365595 T	
175	525 G	-6:143866970 1205365594 G	
176 R	526 C	-6:143866969 1205365593 C	R
176	527 G	-6:143866968 1205365592 G	
176	528 T	-6:143866967 1205365591 T	
177 F	529 T	-6:143866966 1205365590 T	F
177	530 T	-6:143866965 1205365589 T	
177	531 T	-6:143866964 1205365588 T	
178 G	532 G	-6:143866963 1205365587 G	G
178	533 G	-6:143866962 1205365586 G	
178	534 A	-6:143866961 1205365585 A	
179 L	535 C	-6:143866960 1205365584 C	L
179	536 T	-6:143866959 1205365583 T	
179	537 G	-6:143866958 1205365582 G	
180 Y	538 T	-6:143866957 1205365581 T	Y
180	539 A	-6:143866956 1205365580 A	
180	540 C	-6:143866955 1205365579 C	
181 Y	541 T	-6:143866954 1205365578 T	Y
181	542 A	-6:143866953 1205365577 A	
181	543 T	-6:143866952 1205365576 T	
182 S	544 T	-6:143866951 1205365575 T	S
182	545 C	-6:143866950 1205365574 C	
182	546 C	-6:143866949 1205365573 C	
183 L	547 C	-6:143866948 1205365572 C	L
183	548 T	-6:143866947 1205365571 T	
183	549 T	-6:143866946 1205365570 T	
184 F	550 T	-6:143866945 1205365569 T	F
184	551 T	-6:143866944 1205365568 T	
184	552 T	-6:143866943 1205365567 T	
185 E	553 G	-6:143866942 1205365566 G	E
185	554 A	-6:143866941 1205365565 A	
185	555 A	-6:143866940 1205365564 A	
186 W	556 T	-6:143866939 1205365563 T	W
186	557 G	-6:143866938 1205365562 G	
186	558 G	-6:143866937 1205365561 G	
187 F	559 T	-6:143866936 1205365560 T	F
187	560 T	-6:143866935 1205365559 T	
187	561 T	-6:143866934 1205365558 T	
188 H	562 C	-6:143866933 1205365557 C	H
188	563 A	-6:143866932 1205365556 A	
188	564 T	-6:143866931 1205365555 T	
189 P	565 C	-6:143866930 1205365554 C	P
189	566 C	-6:143866929 1205365553 C	
189	567 G	-6:143866928 1205365552 G	
190 L	568 C	-6:143866927 1205365551 C	L
190	569 T	-6:143866926 1205365550 T	
190	570 C	-6:143866925 1205365549 C	
191 F	571 T	-6:143866924 1205365548 T	F
191	572 T	-6:143866923 1205365547 T	
191	573 C	-6:143866922 1205365546 C	
192 L	574 C	-6:143866921 1205365545 C	L
192	575 T	-6:143866920 1205365544 T	
192	576 T	-6:143866919 1205365543 T	
193 E	577 G	-6:143866918 1205365542 G	E
193	578 A	-6:143866917 1205365541 A	
193	579 G	-6:143866916 1205365540 G	
194 D	580 G	-6:143866915 1205365539 G	D
194	581 A	-6:143866914 1205365538 A	
194	582 T	-6:143866913 1205365537 T	
195 E	583 G	-6:143866912 1205365536 G	E
195	584 A	-6:143866911 1205365535 A	
195	585 A	-6:143866910 1205365534 A	
196 S	586 T	-6:143866909 1205365533 T	S
196	587 C	-6:143866908 1205365532 C	
196	588 C	-6:143866907 1205365531 C	
197 S	589 A	-6:143866906 1205365530 A	S
197	590 G	-6:143866905 1205365529 G	
197	591 T	-6:143866904 1205365528 T	
198 S	592 T	-6:143866903 1205365527 T	S
198	593 C	-6:143866902 1205365526 C	
198	594 A	-6:143866901 1205365525 A	
199 F	595 T	-6:143866900 1205365524 T	F
199	596 T	-6:143866899 1205365523 T	
199	597 C	-6:143866898 1205365522 C	
200 H	598 C	-6:143866897 1205365521 C	H
200	599 A	-6:143866896 1205365520 A	
200	600 T	-6:143866895 1205365519 T	
201 K	601 A	-6:143866894 1205365518 A	K
201	602 A	-6:143866893 1205365517 A	
201	603 G	-6:143866892 1205365516 G	
202 R	604 C	-6:143866891 1205365515 C	R
202	605 G	-6:143866890 1205365514 G	
202	606 G	-6:143866889 1205365513 G	
203 Q	607 C	-6:143866888 1205365512 C	Q
203	608 A	-6:143866887 1205365511 A	
203	609 A	-6:143866886 1205365510 A	
204 F	610 T	-6:143866885 1205365509 T	F
204	611 T	-6:143866884 1205365508 T	
204	612 T	-6:143866883 1205365507 T	
205 P	613 C	-6:143866882 1205365506 C	P
205	614 C	-6:143866881 1205365505 C	
205	615 A	-6:143866880 1205365504 A	
206 V	616 G	-6:143866879 1205365503 G	V
206	617 T	-6:143866878 1205365502 T	
206	618 T	-6:143866877 1205365501 T	
207 S	619 T	-6:143866876 1205365500 T	S
207	620 C	-6:143866875 1205365499 C	
207	621 T	-6:143866874 1205365498 T	
208 K	622 A	-6:143866873 1205365497 A	K
208	623 A	-6:143866872 1205365496 A	
208	624 G	-6:143866871 1205365495 G	
209 T	625 A	-6:143866870 1205365494 A	T
209	626 C	-6:143866869 1205365493 C	
209	627 A	-6:143866868 1205365492 A	
210 L	628 T	-6:143866867 1205365491 T	L
210	629 T	-6:143866866 1205365490 T	
210	630 G	-6:143866865 1205365489 G	
211 P	631 C	-6:143866864 1205365488 C	P
211	632 C	-6:143866863 1205365487 C	
211	633 A	-6:143866862 1205365486 A	
212 E	634 G	-6:143866861 1205365485 G	E
212	635 A	-6:143866860 1205365484 A	
212	636 G	-6:143866859 1205365483 G	
213 L	637 C	-6:143866858 1205365482 C	L
213	638 T	-6:143866857 1205365481 T	
213	639 C	-6:143866856 1205365480 C	
214 Y	640 T	-6:143866855 1205365479 T	Y
214	641 A	-6:143866854 1205365478 A	
214	642 T	-6:143866853 1205365477 T	
215 E	643 G	-6:143866852 1205365476 G	E
215	644 A	-6:143866851 1205365475 A	
215	645 G	-6:143866850 1205365474 G	
216 L	646 T	-6:143866849 1205365473 T	L
216	647 T	-6:143866848 1205365472 T	
216	648 A	-6:143866847 1205365471 A	
217 V	649 G	-6:143866846 1205365470 G	V
217	650 T	-6:143866845 1205365469 T	
217	651 G	-6:143866844 1205365468 G	
218 N	652 A	-6:143866843 1205365467 A	N
218	653 A	-6:143866842 1205365466 A	
218	654 C	-6:143866841 1205365465 C	
219 N	655 A	-6:143866840 1205365464 A	N
219	656 A	-6:143866839 1205365463 A	
219	657 C	-6:143866838 1205365462 C	
220 Y	658 T	-6:143866837 1205365461 T	Y
220	659 A	-6:143866836 1205365460 A	
220	660 T	-6:143866835 1205365459 T	
221 Q	661 C	-6:143866834 1205365458 C	Q
221	662 A	-6:143866833 1205365457 A	
221	663 G	-6:143866832 1205365456 G	
222 P	664 C	-6:143866831 1205365455 C	P
222	665 C	-6:143866830 1205365454 C	
222	666 T	-6:143866829 1205365453 T	
223 E	667 G	-6:143866828 1205365452 G	E
223	668 A	-6:143866827 1205365451 A	
223	669 G	-6:143866826 1205365450 G	
224 V	670 G	-6:143866825 1205365449 G	V
224	671 T	-6:143866824 1205365448 T	
224	672 T	-6:143866823 1205365447 T	
225 L	673 C	-6:143866822 1205365446 C	L
225	674 T	-6:143866821 1205365445 T	
225	675 G	-6:143866820 1205365444 G	
226 W	676 T	-6:143866819 1205365443 T	W
226	677 G	-6:143866818 1205365442 G	
226	678 G	-6:143866817 1205365441 G	
227 S	679 T	-6:143866816 1205365440 T	S
227	680 C	-6:143866815 1205365439 C	
227	681 G	-6:143866814 1205365438 G	
228 D	682 G	-6:143866813 1205365437 G	D
228	683 A	-6:143866812 1205365436 A	
228	684 T	-6:143866811 1205365435 T	
229 G	685 G	-6:143866810 1205365434 G	G
229	686 G	-6:143866809 1205365433 G	
229	687 T	-6:143866808 1205365432 T	
230 D	688 G	-6:143866807 1205365431 G	D
230	689 A	-6:143866806 1205365430 A	
230	690 C	-6:143866805 1205365429 C	
231 G	691 G	-6:143866804 1205365428 G	G
231	692 G	-6:143866803 1205365427 G	
231	693 A	-6:143866802 1205365426 A	
232 G	694 G	-6:143866801 1205365425 G	G
232	695 G	-6:143866800 1205365424 G	
232	696 A	-6:143866799 1205365423 A	
233 A	697 G	-6:143866798 1205365422 G	A
233	698 C	-6:143866797 1205365421 C	
233	699 A	-6:143866796 1205365420 A	
234 P	700 C	-6:143866795 1205365419 C	P
234	701 C	-6:143866794 1205365418 C	
234	702 G	-6:143866793 1205365417 G	
235 D	703 G	-6:143866792 1205365416 G	D
235	704 A	-6:143866791 1205365415 A	
235	705 T	-6:143866790 1205365414 T	
236 Q	706 C	-6:143866789 1205365413 C	Q
236	707 A	-6:143866788 1205365412 A	
236	708 A	-6:143866787 1205365411 A	
237 Y	709 T	-6:143866786 1205365410 T	Y
237	710 A	-6:143866785 1205365409 A	
237	711 C	-6:143866784 1205365408 C	
238 W	712 T	-6:143866783 1205365407 T	W
238	713 G	-6:143866782 1205365406 G	
238	714 G	-6:143866781 1205365405 G	
239 N	715 A	-6:143866780 1205365404 A	N
239	716 A	-6:143866779 1205365403 A	
239	717 C	-6:143866778 1205365402 C	
240 S	718 A	-6:143866777 1205365401 A	S
240	719 G	-6:143866776 1205365400 G	
240	720 C	-6:143866775 1205365399 C	
241 T	721 A	-6:143866774 1205365398 A	T
241	722 C	-6:143866773 1205365397 C	
241	723 A	-6:143866772 1205365396 A	
242 G	724 G	-6:143866771 1205365395 G	G
242	725 G	-6:143866770 1205365394 G	
242	726 C	-6:143866769 1205365393 C	
243 F	727 T	-6:143866768 1205365392 T	F
243	728 T	-6:143866767 1205365391 T	
243	729 C	-6:143866766 1205365390 C	
244 L	730 T	-6:143866765 1205365389 T	L
244	731 T	-6:143866764 1205365388 T	
244	732 G	-6:143866763 1205365387 G	
245 A	733 G	-6:143866762 1205365386 G	A
245	734 C	-6:143866761 1205365385 C	
245	735 C	-6:143866760 1205365384 C	
246 W	736 T	-6:143866759 1205365383 T	W
246	737 G	-6:143866758 1205365382 G	
246	738 G	-6:143866757 1205365381 G	
247 L	739 T	-6:143866756 1205365380 T	L
247	740 T	-6:143866755 1205365379 T	
247	741 A	-6:143866754 1205365378 A	
248 Y	742 T	-6:143866753 1205365377 T	Y
248	743 A	-6:143866752 1205365376 A	
248	744 T	-6:143866751 1205365375 T	
249 N	745 A	-6:143866750 1205365374 A	N
249	746 A	-6:143866749 1205365373 A	
249	747 T	-6:143866748 1205365372 T	
250 E	748 G	-6:143866747 1205365371 G	E
250	749 A	-6:143866746 1205365370 A	
250	750 A	-6:143866745 1205365369 A	
251 S	751 A	-6:143866744 1205365368 A	S
251	752 G	-6:143866743 1205365367 G	
251	753 C	-6:143865395 1205364019 C	
252 P	754 C	-6:143865394 1205364018 C	P
252	755 C	-6:143865393 1205364017 C	
252	756 A	-6:143865392 1205364016 A	
253 V	757 G	-6:143865391 1205364015 G	V
253	758 T	-6:143865390 1205364014 T	
253	759 T	-6:143865389 1205364013 T	
254 R	760 C	-6:143865388 1205364012 C	R
254	761 G	-6:143865387 1205364011 G	
254	762 G	-6:143865386 1205364010 G	
255 G	763 G	-6:143865385 1205364009 G	G
255	764 G	-6:143865384 1205364008 G	
255	765 C	-6:143865383 1205364007 C	
256 T	766 A	-6:143865382 1205364006 A	T
256	767 C	-6:143865381 1205364005 C	
256	768 A	-6:143865380 1205364004 A	
257 V	769 G	-6:143865379 1205364003 G	V
257	770 T	-6:143865378 1205364002 T	
257	771 A	-6:143865377 1205364001 A	
258 V	772 G	-6:143865376 1205364000 G	V
258	773 T	-6:143865375 1205363999 T	
258	774 C	-6:143865374 1205363998 C	
259 T	775 A	-6:143865373 1205363997 A	T
259	776 C	-6:143865372 1205363996 C	
259	777 C	-6:143865371 1205363995 C	
260 N	778 A	-6:143865370 1205363994 A	N
260	779 A	-6:143865369 1205363993 A	
260	780 T	-6:143865368 1205363992 T	
261 D	781 G	-6:143865367 1205363991 G	D
261	782 A	-6:143865366 1205363990 A	
261	783 T	-6:143865365 1205363989 T	
262 R	784 C	-6:143865364 1205363988 C	R
262	785 G	-6:143865363 1205363987 G	
262	786 T	-6:143865362 1205363986 T	
263 W	787 T	-6:143865361 1205363985 T	W
263	788 G	-6:143865360 1205363984 G	
263	789 G	-6:143865359 1205363983 G	
264 G	790 G	-6:143865358 1205363982 G	G
264	791 G	-6:143865357 1205363981 G	
264	792 A	-6:143865356 1205363980 A	
265 A	793 G	-6:143865355 1205363979 G	A
265	794 C	-6:143865354 1205363978 C	
265	795 T	-6:143865353 1205363977 T	
266 G	796 G	-6:143865352 1205363976 G	G
266	797 G	-6:143865351 1205363975 G	
266	798 T	-6:143865350 1205363974 T	
267 S	799 A	-6:143865349 1205363973 A	S
267	800 G	-6:143865348 1205363972 G	
267	801 C	-6:143865347 1205363971 C	
268 I	802 A	-6:143865346 1205363970 A	I
268	803 T	-6:143865345 1205363969 T	
268	804 C	-6:143865344 1205363968 C	
269 C	805 T	-6:143865343 1205363967 T	C
269	806 G	-6:143865342 1205363966 G	
269	807 T	-6:143865341 1205363965 T	
270 K	808 A	-6:143865340 1205363964 A	K
270	809 A	-6:143865339 1205363963 A	
270	810 G	-6:143865338 1205363962 G	
271 H	811 C	-6:143865337 1205363961 C	H
271	812 A	-6:143865336 1205363960 A	
271	813 T	-6:143865335 1205363959 T	
272 G	814 G	-6:143865334 1205363958 G	G
272	815 G	-6:143865333 1205363957 G	
272	816 T	-6:143865332 1205363956 T	
273 G	817 G	-6:143865331 1205363955 G	G
273	818 G	-6:143865330 1205363954 G	
273	819 C	-6:143865329 1205363953 C	
274 F	820 T	-6:143865328 1205363952 T	F
274	821 T	-6:143865327 1205363951 T	
274	822 C	-6:143865326 1205363950 C	
275 Y	823 T	-6:143865325 1205363949 T	Y
275	824 A	-6:143865324 1205363948 A	
275	825 T	-6:143865323 1205363947 T	
276 T	826 A	-6:143865322 1205363946 A	T
276	827 C	-6:143865321 1205363945 C	
276	828 C	-6:143865320 1205363944 C	
277 C	829 T	-6:143865319 1205363943 T	C
277	830 G	-6:143865318 1205363942 G	
277	831 C	-6:143865317 1205363941 C	
278 S	832 A	-6:143865316 1205363940 A	S
278	833 G	-6:143865315 1205363939 G	
278	834 T	-6:143865314 1205363938 T	
279 D	835 G	-6:143865313 1205363937 G	D
279	836 A	-6:143865312 1205363936 A	
279	837 T	-6:143865311 1205363935 T	
280 R	838 C	-6:143865310 1205363934 C	R
280	839 G	-6:143865309 1205363933 G	
280	840 T	-6:143865308 1205363932 T	
281 Y	841 T	-6:143865307 1205363931 T	Y
281	842 A	-6:143865306 1205363930 A	
281	843 T	-6:143865305 1205363929 T	
282 N	844 A	-6:143865304 1205363928 A	N
282	845 A	-6:143865303 1205363927 A	
282	846 C	-6:143865302 1205363926 C	
283 P	847 C	-6:143865301 1205363925 C	P
283	848 C	-6:143865300 1205363924 C	
283	849 A	-6:143865299 1205363923 A	
284 G	850 G	-6:143865298 1205363922 G	G
284	851 G	-6:143865297 1205363921 G	
284	852 A	-6:143865296 1205363920 A	
285 H	853 C	-6:143865295 1205363919 C	H
285	854 A	-6:143865294 1205363918 A	
285	855 T	-6:143865293 1205363917 T	
286 L	856 C	-6:143865292 1205363916 C	L
286	857 T	-6:143865291 1205363915 T	
286	858 T	-6:143865290 1205363914 T	
287 L	859 T	-6:143865289 1205363913 T	L
287	860 T	-6:143865288 1205363912 T	
287	861 G	-6:143865287 1205363911 G	
288 P	862 C	-6:143865286 1205363910 C	P
288	863 C	-6:143865285 1205363909 C	
288	864 A	-6:143865284 1205363908 A	
289 H	865 C	-6:143865283 1205363907 C	H
289	866 A	-6:143865282 1205363906 A	
289	867 T	-6:143865281 1205363905 T	
290 K	868 A	-6:143865280 1205363904 A	K
290	869 A	-6:143865279 1205363903 A	
290	870 A	-6:143865278 1205363902 A	
291 W	871 T	-6:143865277 1205363901 T	W
291	872 G	-6:143865276 1205363900 G	
291	873 G	-6:143865275 1205363899 G	
292 E	874 G	-6:143865274 1205363898 G	E
292	875 A	-6:143865273 1205363897 A	
292	876 A	-6:143865272 1205363896 A	
293 N	877 A	-6:143865271 1205363895 A	N
293	878 A	-6:143865270 1205363894 A	
293	879 C	-6:143865269 1205363893 C	
294 C	880 T	-6:143865268 1205363892 T	C
294	881 G	-6:143865267 1205363891 G	
294	882 C	-6:143865266 1205363890 C	
295 M	883 A	-6:143865265 1205363889 A	M
295	884 T	-6:143865264 1205363888 T	
295	885 G	-6:143865263 1205363887 G	
296 T	886 A	-6:143865262 1205363886 A	T
296	887 C	-6:143865261 1205363885 C	
296	888 A	-6:143865260 1205363884 A	
297 I	889 A	-6:143865259 1205363883 A	I
297	890 T	-6:143865258 1205363882 T	
297	891 A	-6:143865257 1205363881 A	
298 D	892 G	-6:143865256 1205363880 G	D
298	893 A	-6:143865255 1205363879 A	
298	894 C	-6:143865254 1205363878 C	
299 K	895 A	-6:143865253 1205363877 A	K
299	896 A	-6:143865252 1205363876 A	
299	897 A	-6:143865251 1205363875 A	
300 L	898 C	-6:143865250 1205363874 C	L
300	899 T	-6:143865249 1205363873 T	
300	900 G	-6:143865248 1205363872 G	
301 S	901 T	-6:143865247 1205363871 T	S
301	902 C	-6:143865246 1205363870 C	
301	903 C	-6:143865245 1205363869 C	
302 W	904 T	-6:143865244 1205363868 T	W
302	905 G	-6:143865243 1205363867 G	
302	906 G	-6:143865242 1205363866 G	
303 G	907 G	-6:143865241 1205363865 G	G
303	908 G	-6:143865240 1205363864 G	
303	909 C	-6:143865239 1205363863 C	
304 Y	910 T	-6:143865238 1205363862 T	Y
304	911 A	-6:143865237 1205363861 A	
304	912 T	-6:143865236 1205363860 T	
305 R	913 A	-6:143865235 1205363859 A	R
305	914 G	-6:143865234 1205363858 G	
305	915 G	-6:143865233 1205363857 G	
306 R	916 A	-6:143865232 1205363856 A	R
306	917 G	-6:143865231 1205363855 G	
306	918 G	-6:143865230 1205363854 G	
307 E	919 G	-6:143865229 1205363853 G	E
307	920 A	-6:143865228 1205363852 A	
307	921 A	-6:143865227 1205363851 A	
308 A	922 G	-6:143865226 1205363850 G	A
308	923 C	-6:143865225 1205363849 C	
308	924 T	-6:143865224 1205363848 T	
309 G	925 G	-6:143865223 1205363847 G	G
309	926 G	-6:143865222 1205363846 G	
309	927 A	-6:143865221 1205363845 A	
310 I	928 A	-6:143865220 1205363844 A	I
310	929 T	-6:143865219 1205363843 T	
310	930 C	-6:143865218 1205363842 C	
311 S	931 T	-6:143865217 1205363841 T	S
311	932 C	-6:143865216 1205363840 C	
311	933 T	-6:143865215 1205363839 T	
312 D	934 G	-6:143865214 1205363838 G	D
312	935 A	-6:143865213 1205363837 A	
312	936 C	-6:143865212 1205363836 C	
313 Y	937 T	-6:143865211 1205363835 T	Y
313	938 A	-6:143865210 1205363834 A	
313	939 T	-6:143865209 1205363833 T	
314 L	940 C	-6:143865208 1205363832 C	L
314	941 T	-6:143865207 1205363831 T	
314	942 T	-6:143865206 1205363830 T	
315 T	943 A	-6:143865205 1205363829 A	T
315	944 C	-6:143865204 1205363828 C	
315	945 A	-6:143865203 1205363827 A	
316 I	946 A	-6:143865202 1205363826 A	I
316	947 T	-6:143865201 1205363825 T	
316	948 T	-6:143865200 1205363824 T	
317 E	949 G	-6:143865199 1205363823 G	E
317	950 A	-6:143865198 1205363822 A	
317	951 A	-6:143865197 1205363821 A	
318 E	952 G	-6:143865196 1205363820 G	E
318	953 A	-6:143865195 1205363819 A	
318	954 A	-6:143865194 1205363818 A	
319 L	955 T	-6:143865193 1205363817 T	L
319	956 T	-6:143865192 1205363816 T	
319	957 G	-6:143865191 1205363815 G	
320 V	958 G	-6:143865190 1205363814 G	V
320	959 T	-6:143865189 1205363813 T	
320	960 G	-6:143865188 1205363812 G	
321 K	961 A	-6:143865187 1205363811 A	K
321	962 A	-6:143865186 1205363810 A	
321	963 G	-6:143865185 1205363809 G	
322 Q	964 C	-6:143864952 1205363576 C	Q
322	965 A	-6:143864951 1205363575 A	
322	966 A	-6:143864950 1205363574 A	
323 L	967 C	-6:143864949 1205363573 C	L
323	968 T	-6:143864948 1205363572 T	
323	969 T	-6:143864947 1205363571 T	
324 V	970 G	-6:143864946 1205363570 G	V
324	971 T	-6:143864945 1205363569 T	
324	972 A	-6:143864944 1205363568 A	
325 E	973 G	-6:143864943 1205363567 G	E
325	974 A	-6:143864942 1205363566 A	
325	975 G	-6:143864941 1205363565 G	
326 T	976 A	-6:143864940 1205363564 A	T
326	977 C	-6:143864939 1205363563 C	
326	978 A	-6:143864938 1205363562 A	
327 V	979 G	-6:143864937 1205363561 G	V
327	980 T	-6:143864936 1205363560 T	
327	981 T	-6:143864935 1205363559 T	
328 S	982 T	-6:143864934 1205363558 T	S
328	983 C	-6:143864933 1205363557 C	
328	984 A	-6:143864932 1205363556 A	
329 C	985 T	-6:143864931 1205363555 T	C
329	986 G	-6:143864930 1205363554 G	
329	987 T	-6:143864929 1205363553 T	
330 G	988 G	-6:143864928 1205363552 G	G
330	989 G	-6:143864927 1205363551 G	
330	990 A	-6:143864926 1205363550 A	
331 G	991 G	-6:143864925 1205363549 G	G
331	992 G	-6:143864924 1205363548 G	
331	993 A	-6:143864923 1205363547 A	
332 N	994 A	-6:143864922 1205363546 A	N
332	995 A	-6:143864921 1205363545 A	
332	996 T	-6:143864920 1205363544 T	
333 L	997 C	-6:143864919 1205363543 C	L
333	998 T	-6:143864918 1205363542 T	
333	999 T	-6:143864917 1205363541 T	
334 L	1000 T	-6:143864916 1205363540 T	L
334	1001 T	-6:143864915 1205363539 T	
334	1002 G	-6:143864914 1205363538 G	
335 M	1003 A	-6:143864913 1205363537 A	M
335	1004 T	-6:143864912 1205363536 T	
335	1005 G	-6:143864911 1205363535 G	
336 N	1006 A	-6:143864910 1205363534 A	N
336	1007 A	-6:143864909 1205363533 A	
336	1008 T	-6:143864908 1205363532 T	
337 I	1009 A	-6:143864907 1205363531 A	I
337	1010 T	-6:143864906 1205363530 T	
337	1011 T	-6:143864905 1205363529 T	
338 G	1012 G	-6:143864904 1205363528 G	G
338	1013 G	-6:143864903 1205363527 G	
338	1014 G	-6:143864902 1205363526 G	
339 P	1015 C	-6:143864901 1205363525 C	P
339	1016 C	-6:143864900 1205363524 C	
339	1017 C	-6:143864899 1205363523 C	
340 T	1018 A	-6:143864898 1205363522 A	T
340	1019 C	-6:143864897 1205363521 C	
340	1020 A	-6:143864896 1205363520 A	
341 L	1021 C	-6:143864895 1205363519 C	L
341	1022 T	-6:143864894 1205363518 T	
341	1023 A	-6:143864893 1205363517 A	
342 D	1024 G	-6:143864892 1205363516 G	D
342	1025 A	-6:143864891 1205363515 A	
342	1026 T	-6:143864890 1205363514 T	
343 G	1027 G	-6:143864889 1205363513 G	G
343	1028 G	-6:143864888 1205363512 G	
343	1029 C	-6:143864887 1205363511 C	
344 T	1030 A	-6:143864886 1205363510 A	T
344	1031 C	-6:143864885 1205363509 C	
344	1032 C	-6:143864884 1205363508 C	
345 I	1033 A	-6:143864883 1205363507 A	I
345	1034 T	-6:143864882 1205363506 T	
345	1035 T	-6:143864881 1205363505 T	
346 S	1036 T	-6:143864880 1205363504 T	S
346	1037 C	-6:143864879 1205363503 C	
346	1038 T	-6:143864878 1205363502 T	
347 V	1039 G	-6:143864877 1205363501 G	V
347	1040 T	-6:143864876 1205363500 T	
347	1041 A	-6:143864875 1205363499 A	
348 V	1042 G	-6:143864874 1205363498 G	V
348	1043 T	-6:143864873 1205363497 T	
348	1044 T	-6:143864872 1205363496 T	
349 F	1045 T	-6:143864871 1205363495 T	F
349	1046 T	-6:143864870 1205363494 T	
349	1047 T	-6:143864869 1205363493 T	
350 E	1048 G	-6:143864868 1205363492 G	E
350	1049 A	-6:143864867 1205363491 A	
350	1050 G	-6:143864866 1205363490 G	
351 E	1051 G	-6:143864865 1205363489 G	E
351	1052 A	-6:143864864 1205363488 A	
351	1053 G	-6:143864863 1205363487 G	
352 R	1054 C	-6:143864862 1205363486 C	R
352	1055 G	-6:143864861 1205363485 G	
352	1056 A	-6:143864860 1205363484 A	
353 L	1057 C	-6:143864859 1205363483 C	L
353	1058 T	-6:143864858 1205363482 T	
353	1059 G	-6:143864857 1205363481 G	
354 R	1060 A	-6:143864856 1205363480 A	R
354	1061 G	-6:143864855 1205363479 G	
354	1062 G	-6:143864854 1205363478 G	
355 Q	1063 C	-6:143864853 1205363477 C	Q
355	1064 A	-6:143864852 1205363476 A	
355	1065 A	-6:143864851 1205363475 A	
356 M	1066 A	-6:143864850 1205363474 A	M
356	1067 T	-6:143864849 1205363473 T	
356	1068 G	-6:143864848 1205363472 G	
357 G	1069 G	-6:143864847 1205363471 G	G
357	1070 G	-6:143864846 1205363470 G	
357	1071 G	-6:143864845 1205363469 G	
358 S	1072 T	-6:143864844 1205363468 T	S
358	1073 C	-6:143864843 1205363467 C	
358	1074 C	-6:143864842 1205363466 C	
359 W	1075 T	-6:143864841 1205363465 T	W
359	1076 G	-6:143864840 1205363464 G	
359	1077 G	-6:143864839 1205363463 G	
360 L	1078 C	-6:143864838 1205363462 C	L
360	1079 T	-6:143864837 1205363461 T	
360	1080 A	-6:143864836 1205363460 A	
361 K	1081 A	-6:143864835 1205363459 A	K
361	1082 A	-6:143864834 1205363458 A	
361	1083 A	-6:143864833 1205363457 A	
362 V	1084 G	-6:143864832 1205363456 G	V
362	1085 T	-6:143864831 1205363455 T	
362	1086 C	-6:143864830 1205363454 C	
363 N	1087 A	-6:143864829 1205363453 A	N
363	1088 A	-6:143864828 1205363452 A	
363	1089 T	-6:143864827 1205363451 T	
364 G	1090 G	-6:143864826 1205363450 G	G
364	1091 G	-6:143864825 1205363449 G	
364	1092 A	-6:143864824 1205363448 A	
365 E	1093 G	-6:143864823 1205363447 G	E
365	1094 A	-6:143864822 1205363446 A	
365	1095 A	-6:143864821 1205363445 A	
366 A	1096 G	-6:143864820 1205363444 G	A
366	1097 C	-6:143864819 1205363443 C	
366	1098 T	-6:143864818 1205363442 T	
367 I	1099 A	-6:143864817 1205363441 A	I
367	1100 T	-6:143864816 1205363440 T	
367	1101 T	-6:143864815 1205363439 T	
368 Y	1102 T	-6:143864814 1205363438 T	Y
368	1103 A	-6:143864813 1205363437 A	
368	1104 T	-6:143864812 1205363436 T	
369 E	1105 G	-6:143864811 1205363435 G	E
369	1106 A	-6:143864810 1205363434 A	
369	1107 A	-6:143864809 1205363433 A	
370 T	1108 A	-6:143864808 1205363432 A	T
370	1109 C	-6:143864807 1205363431 C	
370	1110 C	-6:143864806 1205363430 C	
371 H	1111 C	-6:143864805 1205363429 C	H
371	1112 A	-6:143864804 1205363428 A	
371	1113 T	-6:143864803 1205363427 T	
372 T	1114 A	-6:143864802 1205363426 A	T
372	1115 C	-6:143864801 1205363425 C	
372	1116 C	-6:143864800 1205363424 C	
373 W	1117 T	-6:143864799 1205363423 T	W
373	1118 G	-6:143864798 1205363422 G	
373	1119 G	-6:143864797 1205363421 G	
374 R	1120 C	-6:143864796 1205363420 C	R
374	1121 G	-6:143864795 1205363419 G	
374	1122 A	-6:143864794 1205363418 A	
375 S	1123 T	-6:143864793 1205363417 T	S
375	1124 C	-6:143864792 1205363416 C	
375	1125 C	-6:143864791 1205363415 C	
376 Q	1126 C	-6:143864790 1205363414 C	Q
376	1127 A	-6:143864789 1205363413 A	
376	1128 G	-6:143864788 1205363412 G	
377 N	1129 A	-6:143864787 1205363411 A	N
377	1130 A	-6:143864786 1205363410 A	
377	1131 T	-6:143864785 1205363409 T	
378 D	1132 G	-6:143864784 1205363408 G	D
378	1133 A	-6:143864783 1205363407 A	
378	1134 C	-6:143864782 1205363406 C	
379 T	1135 A	-6:143864781 1205363405 A	T
379	1136 C	-6:143864780 1205363404 C	
379	1137 T	-6:143864779 1205363403 T	
380 V	1138 G	-6:143864778 1205363402 G	V
380	1139 T	-6:143864777 1205363401 T	
380	1140 C	-6:143864776 1205363400 C	
381 T	1141 A	-6:143864775 1205363399 A	T
381	1142 C	-6:143864774 1205363398 C	
381	1143 C	-6:143864773 1205363397 C	
382 P	1144 C	-6:143864772 1205363396 C	P
382	1145 C	-6:143864771 1205363395 C	
382	1146 A	-6:143864770 1205363394 A	
383 D	1147 G	-6:143864769 1205363393 G	D
383	1148 A	-6:143864768 1205363392 A	
383	1149 T	-6:143864767 1205363391 T	
384 V	1150 G	-6:143864766 1205363390 G	V
384	1151 T	-6:143864765 1205363389 T	
384	1152 G	-6:143864764 1205363388 G	
385 W	1153 T	-6:143864763 1205363387 T	W
385	1154 G	-6:143864762 1205363386 G	
385	1155 G	-6:143860327 1205358951 G	
386 Y	1156 T	-6:143860326 1205358950 T	Y
386	1157 A	-6:143860325 1205358949 A	
386	1158 C	-6:143860324 1205358948 C	
387 T	1159 A	-6:143860323 1205358947 A	T
387	1160 C	-6:143860322 1205358946 C	
387	1161 A	-6:143860321 1205358945 A	
388 S	1162 T	-6:143860320 1205358944 T	S
388	1163 C	-6:143860319 1205358943 C	
388	1164 C	-6:143860318 1205358942 C	
389 K	1165 A	-6:143860317 1205358941 A	K
389	1166 A	-6:143860316 1205358940 A	
389	1167 G	-6:143860315 1205358939 G	
390 P	1168 C	-6:143860314 1205358938 C	P
390	1169 C	-6:143860313 1205358937 C	
390	1170 T	-6:143860312 1205358936 T	
391 K	1171 A	-6:143860311 1205358935 A	K
391	1172 A	-6:143860310 1205358934 A	
391	1173 A	-6:143860309 1205358933 A	
392 E	1174 G	-6:143860308 1205358932 G	E
392	1175 A	-6:143860307 1205358931 A	
392	1176 A	-6:143860306 1205358930 A	
393 K	1177 A	-6:143860305 1205358929 A	K
393	1178 A	-6:143860304 1205358928 A	
393	1179 A	-6:143860303 1205358927 A	
394 L	1180 T	-6:143860302 1205358926 T	L
394	1181 T	-6:143860301 1205358925 T	
394	1182 A	-6:143860300 1205358924 A	
395 V	1183 G	-6:143860299 1205358923 G	V
395	1184 T	-6:143860298 1205358922 T	
395	1185 C	-6:143860297 1205358921 C	
396 Y	1186 T	-6:143860296 1205358920 T	Y
396	1187 A	-6:143860295 1205358919 A	
396	1188 T	-6:143860294 1205358918 T	
397 A	1189 G	-6:143860293 1205358917 G	A
397	1190 C	-6:143860292 1205358916 C	
397	1191 C	-6:143860291 1205358915 C	
398 I	1192 A	-6:143860290 1205358914 A	I
398	1193 T	-6:143860289 1205358913 T	
398	1194 T	-6:143860288 1205358912 T	
399 F	1195 T	-6:143860287 1205358911 T	F
399	1196 T	-6:143860286 1205358910 T	
399	1197 T	-6:143860285 1205358909 T	
400 L	1198 C	-6:143860284 1205358908 C	L
400	1199 T	-6:143860283 1205358907 T	
400	1200 T	-6:143860282 1205358906 T	
401 K	1201 A	-6:143860281 1205358905 A	K
401	1202 A	-6:143860280 1205358904 A	
401	1203 A	-6:143860279 1205358903 A	
402 W	1204 T	-6:143860278 1205358902 T	W
402	1205 G	-6:143860277 1205358901 G	
402	1206 G	-6:143860276 1205358900 G	
403 P	1207 C	-6:143860275 1205358899 C	P
403	1208 C	-6:143860274 1205358898 C	
403	1209 C	-6:143860273 1205358897 C	
404 T	1210 A	-6:143860272 1205358896 A	T
404	1211 C	-6:143860271 1205358895 C	
404	1212 A	-6:143860270 1205358894 A	
405 S	1213 T	-6:143860269 1205358893 T	S
405	1214 C	-6:143860268 1205358892 C	
405	1215 A	-6:143860267 1205358891 A	
406 G	1216 G	-6:143860266 1205358890 G	G
406	1217 G	-6:143860265 1205358889 G	
406	1218 A	-6:143860264 1205358888 A	
407 Q	1219 C	-6:143860263 1205358887 C	Q
407	1220 A	-6:143860262 1205358886 A	
407	1221 G	-6:143860261 1205358885 G	
408 L	1222 C	-6:143860260 1205358884 C	L
408	1223 T	-6:143860259 1205358883 T	
408	1224 G	-6:143860258 1205358882 G	
409 F	1225 T	-6:143860257 1205358881 T	F
409	1226 T	-6:143860256 1205358880 T	
409	1227 C	-6:143860255 1205358879 C	
410 L	1228 C	-6:143860254 1205358878 C	L
410	1229 T	-6:143860253 1205358877 T	
410	1230 T	-6:143860252 1205358876 T	
411 G	1231 G	-6:143860251 1205358875 G	G
411	1232 G	-6:143860250 1205358874 G	
411	1233 C	-6:143860249 1205358873 C	
412 H	1234 C	-6:143860248 1205358872 C	H
412	1235 A	-6:143860247 1205358871 A	
412	1236 T	-6:143860246 1205358870 T	
413 P	1237 C	-6:143860245 1205358869 C	P
413	1238 C	-6:143860244 1205358868 C	
413	1239 C	-6:143860243 1205358867 C	
414 K	1240 A	-6:143860242 1205358866 A	K
414	1241 A	-6:143860241 1205358865 A	
414	1242 A	-6:143860240 1205358864 A	
415 A	1243 G	-6:143860239 1205358863 G	A
415	1244 C	-6:143860238 1205358862 C	
415	1245 T	-6:143860237 1205358861 T	
416 I	1246 A	-6:143860236 1205358860 A	I
416	1247 T	-6:143860235 1205358859 T	
416	1248 T	-6:143860234 1205358858 T	
417 L	1249 C	-6:143860233 1205358857 C	L
417	1250 T	-6:143860232 1205358856 T	
417	1251 G	-6:143860231 1205358855 G	
418 G	1252 G	-6:143860230 1205358854 G	G
418	1253 G	-6:143860229 1205358853 G	
418	1254 G	-6:143860228 1205358852 G	
419 A	1255 G	-6:143860227 1205358851 G	A
419	1256 C	-6:143860226 1205358850 C	
419	1257 A	-6:143860225 1205358849 A	
420 T	1258 A	-6:143860224 1205358848 A	T
420	1259 C	-6:143860223 1205358847 C	
420	1260 A	-6:143860222 1205358846 A	
421 E	1261 G	-6:143860221 1205358845 G	E
421	1262 A	-6:143860220 1205358844 A	
421	1263 G	-6:143860219 1205358843 G	
422 V	1264 G	-6:143858677 1205357301 G	V
422	1265 T	-6:143858676 1205357300 T	
422	1266 G	-6:143858675 1205357299 G	
423 K	1267 A	-6:143858674 1205357298 A	K
423	1268 A	-6:143858673 1205357297 A	
423	1269 A	-6:143858672 1205357296 A	
424 L	1270 C	-6:143858671 1205357295 C	L
424	1271 T	-6:143858670 1205357294 T	
424	1272 A	-6:143858669 1205357293 A	
425 L	1273 C	-6:143858668 1205357292 C	L
425	1274 T	-6:143858667 1205357291 T	
425	1275 G	-6:143858666 1205357290 G	
426 G	1276 G	-6:143858665 1205357289 G	G
426	1277 G	-6:143858664 1205357288 G	
426	1278 C	-6:143858663 1205357287 C	
427 H	1279 C	-6:143858662 1205357286 C	H
427	1280 A	-6:143858661 1205357285 A	
427	1281 T	-6:143858660 1205357284 T	
428 G	1282 G	-6:143858659 1205357283 G	G
428	1283 G	-6:143858658 1205357282 G	
428	1284 A	-6:143858657 1205357281 A	
429 Q	1285 C	-6:143858656 1205357280 C	Q
429	1286 A	-6:143858655 1205357279 A	
429	1287 G	-6:143858654 1205357278 G	
430 P	1288 C	-6:143858653 1205357277 C	P
430	1289 C	-6:143858652 1205357276 C	
430	1290 A	-6:143858651 1205357275 A	
431 L	1291 C	-6:143858650 1205357274 C	L
431	1292 T	-6:143858649 1205357273 T	
431	1293 T	-6:143858648 1205357272 T	
432 N	1294 A	-6:143858647 1205357271 A	N
432	1295 A	-6:143858646 1205357270 A	
432	1296 C	-6:143858645 1205357269 C	
433 W	1297 T	-6:143858644 1205357268 T	W
433	1298 G	-6:143858643 1205357267 G	
433	1299 G	-6:143858642 1205357266 G	
434 I	1300 A	-6:143858641 1205357265 A	I
434	1301 T	-6:143858640 1205357264 T	
434	1302 T	-6:143858639 1205357263 T	
435 S	1303 T	-6:143858638 1205357262 T	S
435	1304 C	-6:143858637 1205357261 C	
435	1305 T	-6:143858636 1205357260 T	
436 L	1306 T	-6:143858635 1205357259 T	L
436	1307 T	-6:143858634 1205357258 T	
436	1308 G	-6:143858633 1205357257 G	
437 E	1309 G	-6:143858632 1205357256 G	E
437	1310 A	-6:143858631 1205357255 A	
437	1311 G	-6:143858630 1205357254 G	
438 Q	1312 C	-6:143858629 1205357253 C	Q
438	1313 A	-6:143858628 1205357252 A	
438	1314 A	-6:143858627 1205357251 A	
439 N	1315 A	-6:143858626 1205357250 A	N
439	1316 A	-6:143858625 1205357249 A	
439	1317 T	-6:143858624 1205357248 T	
440 G	1318 G	-6:143858623 1205357247 G	G
440	1319 G	-6:143858622 1205357246 G	
440	1320 C	-6:143858621 1205357245 C	
441 I	1321 A	-6:143858620 1205357244 A	I
441	1322 T	-6:143858619 1205357243 T	
441	1323 T	-6:143858618 1205357242 T	
442 M	1324 A	-6:143858617 1205357241 A	M
442	1325 T	-6:143858616 1205357240 T	
442	1326 G	-6:143858615 1205357239 G	
443 V	1327 G	-6:143858614 1205357238 G	V
443	1328 T	-6:143858613 1205357237 T	
443	1329 A	-6:143858612 1205357236 A	
444 E	1330 G	-6:143858611 1205357235 G	E
444	1331 A	-6:143858610 1205357234 A	
444	1332 A	-6:143858609 1205357233 A	
445 L	1333 C	-6:143858608 1205357232 C	L
445	1334 T	-6:143858607 1205357231 T	
445	1335 G	-6:143858606 1205357230 G	
446 P	1336 C	-6:143858605 1205357229 C	P
446	1337 C	-6:143858604 1205357228 C	
446	1338 A	-6:143858603 1205357227 A	
447 Q	1339 C	-6:143858602 1205357226 C	Q
447	1340 A	-6:143858601 1205357225 A	
447	1341 G	-6:143858600 1205357224 G	
448 L	1342 C	-6:143858599 1205357223 C	L
448	1343 T	-6:143858598 1205357222 T	
448	1344 A	-6:143858597 1205357221 A	
449 T	1345 A	-6:143858596 1205357220 A	T
449	1346 C	-6:143858595 1205357219 C	
449	1347 C	-6:143858594 1205357218 C	
450 I	1348 A	-6:143858593 1205357217 A	I
450	1349 T	-6:143858592 1205357216 T	
450	1350 T	-6:143858591 1205357215 T	
451 H	1351 C	-6:143858590 1205357214 C	H
451	1352 A	-6:143858589 1205357213 A	
451	1353 T	-6:143858588 1205357212 T	
452 Q	1354 C	-6:143858587 1205357211 C	Q
452	1355 A	-6:143858586 1205357210 A	
452	1356 G	-6:143858585 1205357209 G	
453 M	1357 A	-6:143858584 1205357208 A	M
453	1358 T	-6:143858583 1205357207 T	
453	1359 G	-6:143858582 1205357206 G	
454 P	1360 C	-6:143858581 1205357205 C	P
454	1361 C	-6:143858580 1205357204 C	
454	1362 G	-6:143858579 1205357203 G	
455 C	1363 T	-6:143858578 1205357202 T	C
455	1364 G	-6:143858577 1205357201 G	
455	1365 T	-6:143858576 1205357200 T	
456 K	1366 A	-6:143858575 1205357199 A	K
456	1367 A	-6:143858574 1205357198 A	
456	1368 A	-6:143858573 1205357197 A	
457 W	1369 T	-6:143858572 1205357196 T	W
457	1370 G	-6:143858571 1205357195 G	
457	1371 G	-6:143858570 1205357194 G	
458 G	1372 G	-6:143858569 1205357193 G	G
458	1373 G	-6:143858568 1205357192 G	
458	1374 C	-6:143858567 1205357191 C	
459 W	1375 T	-6:143858566 1205357190 T	W
459	1376 G	-6:143858565 1205357189 G	
459	1377 G	-6:143858564 1205357188 G	
460 A	1378 G	-6:143858563 1205357187 G	A
460	1379 C	-6:143858562 1205357186 C	
460	1380 T	-6:143858561 1205357185 T	
461 L	1381 C	-6:143858560 1205357184 C	L
461	1382 T	-6:143858559 1205357183 T	
461	1383 A	-6:143858558 1205357182 A	
462 A	1384 G	-6:143858557 1205357181 G	A
462	1385 C	-6:143858556 1205357180 C	
462	1386 C	-6:143858555 1205357179 C	
463 L	1387 C	-6:143858554 1205357178 C	L
463	1388 T	-6:143858553 1205357177 T	
463	1389 G	-6:143858552 1205357176 G	
464 T	1390 A	-6:143858551 1205357175 A	T
464	1391 C	-6:143858550 1205357174 C	
464	1392 T	-6:143858549 1205357173 T	
465 N	1393 A	-6:143858548 1205357172 A	N
465	1394 A	-6:143858547 1205357171 A	
465	1395 T	-6:143858546 1205357170 T	
466 V	1396 G	-6:143858545 1205357169 G	V
466	1397 T	-6:143858544 1205357168 T	
466	1398 G	-6:143858543 1205357167 G	
467 I	1399 A	-6:143858542 1205357166 A	I
467	1400 T	-6:143858541 1205357165 T	
467	1401 C	-6:143858540 1205357164 C	
>ENSP00000229416 
1 M	1 A	-6:53517402 1115016026 A	M
1	2 T	-6:53517401 1115016025 T	
1	3 G	-6:53517400 1115016024 G	
2 G	4 G	-6:53517399 1115016023 G	G
2	5 G	-6:53517398 1115016022 G	
2	6 G	-6:53517397 1115016021 G	
3 L	7 C	-6:53517396 1115016020 C	L
3	8 T	-6:53517395 1115016019 T	
3	9 G	-6:53517394 1115016018 G	
4 L	10 C	-6:53517393 1115016017 C	L
4	11 T	-6:53517392 1115016016 T	
4	12 G	-6:53517391 1115016015 G	
5 S	13 T	-6:53517390 1115016014 T	S
5	14 C	-6:53517389 1115016013 C	
5	15 C	-6:53517388 1115016012 C	
6 Q	16 C	-6:53517387 1115016011 C	Q
6	17 A	-6:53517386 1115016010 A	
6	18 G	-6:53517385 1115016009 G	
7 G	19 G	-6:53517384 1115016008 G	G
7	20 G	-6:53517383 1115016007 G	
7	21 C	-6:53517382 1115016006 C	
8 S	22 T	-6:53517381 1115016005 T	S
8	23 C	-6:53517380 1115016004 C	
8	24 G	-6:53517379 1115016003 G	
9 P	25 C	-6:53517378 1115016002 C	P
9	26 C	-6:53517377 1115016001 C	
9	27 G	-6:53517376 1115016000 G	
10 L	28 C	-6:53517375 1115015999 C	L
10	29 T	-6:53517374 1115015998 T	
10	30 G	-6:53517373 1115015997 G	
11 S	31 A	-6:53517372 1115015996 A	S
11	32 G	-6:53517371 1115015995 G	
11	33 C	-6:53517370 1115015994 C	
12 W	34 T	-6:53517369 1115015993 T	W
12	35 G	-6:53517368 1115015992 G	
12	36 G	-6:53517367 1115015991 G	
13 E	37 G	-6:53517366 1115015990 G	E
13	38 A	-6:53517365 1115015989 A	
13	39 G	-6:53517364 1115015988 G	
14 E	40 G	-6:53517363 1115015987 G	E
14	41 A	-6:53517362 1115015986 A	
14	42 A	-6:53517361 1115015985 A	
15 T	43 A	-6:53517360 1115015984 A	T
15	44 C	-6:53517359 1115015983 C	
15	45 C	-6:53517358 1115015982 C	
16 K	46 A	-6:53517357 1115015981 A	K
16	47 A	-6:53517356 1115015980 A	
16	48 G	-6:53517355 1115015979 G	
17 R	49 C	-6:53517354 1115015978 C	R
17	50 G	-6:53517353 1115015977 G	
17	51 C	-6:53517352 1115015976 C	
18 H	52 C	-6:53517351 1115015975 C	H
18	53 A	-6:53517350 1115015974 A	
18	54 T	-6:53517349 1115015973 T	
19 A	55 G	-6:53517348 1115015972 G	A
19	56 C	-6:53517347 1115015971 C	
19	57 C	-6:53517346 1115015970 C	
20 D	58 G	-6:53517345 1115015969 G	D
20	59 A	-6:53517344 1115015968 A	
20	60 C	-6:53517343 1115015967 C	
21 H	61 C	-6:53517342 1115015966 C	H
21	62 A	-6:53517341 1115015965 A	
21	63 C	-6:53517340 1115015964 C	
22 V	64 G	-6:53517339 1115015963 G	V
22	65 T	-6:53517338 1115015962 T	
22	66 G	-6:53517337 1115015961 G	
23 R	67 C	-6:53517336 1115015960 C	R
23	68 G	-6:53517335 1115015959 G	
23	69 G	-6:53517334 1115015958 G	
24 R	70 C	-6:53517333 1115015957 C	R
24	71 G	-6:53517332 1115015956 G	
24	72 G	-6:53517331 1115015955 G	
25 H	73 C	-6:53517330 1115015954 C	H
25	74 A	-6:53517329 1115015953 A	
25	75 C	-6:53517328 1115015952 C	
26 G	76 G	-6:53517327 1115015951 G	G
26	77 G	-6:53517326 1115015950 G	
26	78 G	-6:53517325 1115015949 G	
27 I	79 A	-6:53517324 1115015948 A	I
27	80 T	-6:53517323 1115015947 T	
27	81 C	-6:53517322 1115015946 C	
28 L	82 C	-6:53517321 1115015945 C	L
28	83 T	-6:53517320 1115015944 T	
28	84 C	-6:53517319 1115015943 C	
29 Q	85 C	-6:53517318 1115015942 C	Q
29	86 A	-6:53517317 1115015941 A	
29	87 G	-6:53517316 1115015940 G	
30 F	88 T	-6:53517315 1115015939 T	F
30	89 T	-6:53517314 1115015938 T	
30	90 C	-6:53517313 1115015937 C	
31 L	91 C	-6:53517312 1115015936 C	L
31	92 T	-6:53517311 1115015935 T	
31	93 G	-6:53517310 1115015934 G	
32 H	94 C	-6:53517309 1115015933 C	H
32	95 A	-6:53517308 1115015932 A	
32	96 C	-6:53517307 1115015931 C	
33 I	97 A	-6:53517306 1115015930 A	I
33	98 T	-6:53517305 1115015929 T	
33	99 C	-6:53517304 1115015928 C	
34 Y	100 T	-6:53517303 1115015927 T	Y
34	101 A	-6:53517302 1115015926 A	
34	102 C	-6:53517301 1115015925 C	
35 H	103 C	-6:53517300 1115015924 C	H
35	104 A	-6:53517299 1115015923 A	
35	105 C	-6:53517298 1115015922 C	
36 A	106 G	-6:53517297 1115015921 G	A
36	107 C	-6:53517296 1115015920 C	
36	108 C	-6:53517295 1115015919 C	
37 V	109 G	-6:53517294 1115015918 G	V
37	110 T	-6:53517293 1115015917 T	
37	111 C	-6:53517292 1115015916 C	
38 K	112 A	-6:53517291 1115015915 A	K
38	113 A	-6:53517290 1115015914 A	
38	114 G	-6:53517289 1115015913 G	
39 D	115 G	-6:53517288 1115015912 G	D
39	116 A	-6:53517287 1115015911 A	
39	117 C	-6:53517286 1115015910 C	
40 R	118 C	-6:53517285 1115015909 C	R
40	119 G	-6:53517284 1115015908 G	
40	120 G	-6:53517283 1115015907 G	
41 H	121 C	-6:53517282 1115015906 C	H
41	122 A	-6:53517281 1115015905 A	
41	123 C	-6:53517280 1115015904 C	
42 K	124 A	-6:53517279 1115015903 A	K
42	125 A	-6:53517278 1115015902 A	
42	126 G	-6:53517277 1115015901 G	
43 D	127 G	-6:53517276 1115015900 G	D
43	128 A	-6:53517275 1115015899 A	
43	129 C	-6:53517274 1115015898 C	
44 V	130 G	-6:53517273 1115015897 G	V
44	131 T	-6:53517272 1115015896 T	
44	132 T	-6:53517271 1115015895 T	
45 L	133 C	-6:53517270 1115015894 C	L
45	134 T	-6:53517269 1115015893 T	
45	135 C	-6:53517268 1115015892 C	
46 K	136 A	-6:53517267 1115015891 A	K
46	137 A	-6:53517266 1115015890 A	
46	138 G	-6:53517265 1115015889 G	
47 W	139 T	-6:53517264 1115015888 T	W
47	140 G	-6:53517263 1115015887 G	
47	141 G	-6:53517262 1115015886 G	
48 G	142 G	-6:53517261 1115015885 G	G
48	143 G	-6:53517260 1115015884 G	
48	144 C	-6:53517259 1115015883 C	
49 D	145 G	-6:53517258 1115015882 G	D
49	146 A	-6:53517257 1115015881 A	
49	147 T	-6:53517256 1115015880 T	
50 E	148 G	-6:53517255 1115015879 G	E
50	149 A	-6:53517254 1115015878 A	
50	150 G	-6:53517253 1115015877 G	
51 V	151 G	-6:53495284 1114993908 G	V
51	152 T	-6:53495283 1114993907 T	
51	153 G	-6:53495282 1114993906 G	
52 E	154 G	-6:53495281 1114993905 G	E
52	155 A	-6:53495280 1114993904 A	
52	156 A	-6:53495279 1114993903 A	
53 Y	157 T	-6:53495278 1114993902 T	Y
53	158 A	-6:53495277 1114993901 A	
53	159 C	-6:53495276 1114993900 C	
54 M	160 A	-6:53495275 1114993899 A	M
54	161 T	-6:53495274 1114993898 T	
54	162 G	-6:53495273 1114993897 G	
55 L	163 T	-6:53495272 1114993896 T	L
55	164 T	-6:53495271 1114993895 T	
55	165 G	-6:53495270 1114993894 G	
56 V	166 G	-6:53495269 1114993893 G	V
56	167 T	-6:53495268 1114993892 T	
56	168 A	-6:53495267 1114993891 A	
57 S	169 T	-6:53495266 1114993890 T	S
57	170 C	-6:53495265 1114993889 C	
57	171 T	-6:53495264 1114993888 T	
58 F	172 T	-6:53495263 1114993887 T	F
58	173 T	-6:53495262 1114993886 T	
58	174 T	-6:53495261 1114993885 T	
59 D	175 G	-6:53495260 1114993884 G	D
59	176 A	-6:53495259 1114993883 A	
59	177 T	-6:53495258 1114993882 T	
60 H	178 C	-6:53495257 1114993881 C	H
60	179 A	-6:53495256 1114993880 A	
60	180 T	-6:53495255 1114993879 T	
61 E	181 G	-6:53495254 1114993878 G	E
61	182 A	-6:53495253 1114993877 A	
61	183 A	-6:53495252 1114993876 A	
62 N	184 A	-6:53495251 1114993875 A	N
62	185 A	-6:53495250 1114993874 A	
62	186 T	-6:53495249 1114993873 T	
63 K	187 A	-6:53495248 1114993872 A	K
63	188 A	-6:53495247 1114993871 A	
63	189 A	-6:53495246 1114993870 A	
64 K	190 A	-6:53495245 1114993869 A	K
64	191 A	-6:53495244 1114993868 A	
64	192 A	-6:53495243 1114993867 A	
65 V	193 G	-6:53495242 1114993866 G	V
65	194 T	-6:53495241 1114993865 T	
65	195 C	-6:53495240 1114993864 C	
66 R	196 C	-6:53495239 1114993863 C	R
66	197 G	-6:53495238 1114993862 G	
66	198 G	-6:53495237 1114993861 G	
67 L	199 T	-6:53495236 1114993860 T	L
67	200 T	-6:53495235 1114993859 T	
67	201 G	-6:53495234 1114993858 G	
68 V	202 G	-6:53495233 1114993857 G	V
68	203 T	-6:53495232 1114993856 T	
68	204 C	-6:53495231 1114993855 C	
69 L	205 C	-6:53495230 1114993854 C	L
69	206 T	-6:53495229 1114993853 T	
69	207 G	-6:53495228 1114993852 G	
70 S	208 T	-6:53495227 1114993851 T	S
70	209 C	-6:53495226 1114993850 C	
70	210 T	-6:53495225 1114993849 T	
71 G	211 G	-6:53495224 1114993848 G	G
71	212 G	-6:53495223 1114993847 G	
71	213 G	-6:53495222 1114993846 G	
72 E	214 G	-6:53495221 1114993845 G	E
72	215 A	-6:53495220 1114993844 A	
72	216 G	-6:53495219 1114993843 G	
73 K	217 A	-6:53495218 1114993842 A	K
73	218 A	-6:53495217 1114993841 A	
73	219 A	-6:53495216 1114993840 A	
74 V	220 G	-6:53495215 1114993839 G	V
74	221 T	-6:53495214 1114993838 T	
74	222 T	-6:53495213 1114993837 T	
75 L	223 C	-6:53495212 1114993836 C	L
75	224 T	-6:53495211 1114993835 T	
75	225 T	-6:53495210 1114993834 T	
76 E	226 G	-6:53495209 1114993833 G	E
76	227 A	-6:53495208 1114993832 A	
76	228 A	-6:53495207 1114993831 A	
77 T	229 A	-6:53495206 1114993830 A	T
77	230 C	-6:53495205 1114993829 C	
77	231 T	-6:53495204 1114993828 T	
78 L	232 C	-6:53495203 1114993827 C	L
78	233 T	-6:53495202 1114993826 T	
78	234 G	-6:53495201 1114993825 G	
79 Q	235 C	-6:53495200 1114993824 C	Q
79	236 A	-6:53495199 1114993823 A	
79	237 A	-6:53495198 1114993822 A	
80 E	238 G	-6:53495197 1114993821 G	E
80	239 A	-6:53495196 1114993820 A	
80	240 G	-6:53495195 1114993819 G	
81 K	241 A	-6:53495194 1114993818 A	K
81	242 A	-6:53495193 1114993817 A	
81	243 G	-6:53495192 1114993816 G	
82 G	244 G	-6:53495191 1114993815 G	G
82	245 G	-6:53495190 1114993814 G	
82	246 G	-6:53495189 1114993813 G	
83 E	247 G	-6:53495188 1114993812 G	E
83	248 A	-6:53495187 1114993811 A	
83	249 A	-6:53495186 1114993810 A	
84 R	250 A	-6:53495185 1114993809 A	R
84	251 G	-6:53495184 1114993808 G	
84	252 G	-6:53495183 1114993807 G	
85 T	253 A	-6:53495182 1114993806 A	T
85	254 C	-6:53495181 1114993805 C	
85	255 A	-6:53495180 1114993804 A	
86 N	256 A	-6:53495179 1114993803 A	N
86	257 A	-6:53495178 1114993802 A	
86	258 C	-6:53495177 1114993801 C	
87 P	259 C	-6:53495176 1114993800 C	P
87	260 C	-6:53495175 1114993799 C	
87	261 A	-6:53495174 1114993798 A	
88 N	262 A	-6:53495173 1114993797 A	N
88	263 A	-6:53495172 1114993796 A	
88	264 C	-6:53493717 1114992341 C	
89 H	265 C	-6:53493716 1114992340 C	H
89	266 A	-6:53493715 1114992339 A	
89	267 T	-6:53493714 1114992338 T	
90 P	268 C	-6:53493713 1114992337 C	P
90	269 C	-6:53493712 1114992336 C	
90	270 T	-6:53493711 1114992335 T	
91 T	271 A	-6:53493710 1114992334 A	T
91	272 C	-6:53493709 1114992333 C	
91	273 C	-6:53493708 1114992332 C	
92 L	274 C	-6:53493707 1114992331 C	L
92	275 T	-6:53493706 1114992330 T	
92	276 T	-6:53493705 1114992329 T	
93 W	277 T	-6:53493704 1114992328 T	W
93	278 G	-6:53493703 1114992327 G	
93	279 G	-6:53493702 1114992326 G	
94 R	280 A	-6:53493701 1114992325 A	R
94	281 G	-6:53493700 1114992324 G	
94	282 A	-6:53493699 1114992323 A	
95 P	283 C	-6:53493698 1114992322 C	P
95	284 C	-6:53493697 1114992321 C	
95	285 A	-6:53493696 1114992320 A	
96 E	286 G	-6:53493695 1114992319 G	E
96	287 A	-6:53493694 1114992318 A	
96	288 G	-6:53493693 1114992317 G	
97 Y	289 T	-6:53493692 1114992316 T	Y
97	290 A	-6:53493691 1114992315 A	
97	291 T	-6:53493690 1114992314 T	
98 G	292 G	-6:53493689 1114992313 G	G
98	293 G	-6:53493688 1114992312 G	
98	294 G	-6:53493687 1114992311 G	
99 S	295 A	-6:53493686 1114992310 A	S
99	296 G	-6:53493685 1114992309 G	
99	297 T	-6:53493684 1114992308 T	
100 Y	298 T	-6:53493683 1114992307 T	Y
100	299 A	-6:53493682 1114992306 A	
100	300 C	-6:53493681 1114992305 C	
101 M	301 A	-6:53493680 1114992304 A	M
101	302 T	-6:53493679 1114992303 T	
101	303 G	-6:53493678 1114992302 G	
102 I	304 A	-6:53493677 1114992301 A	I
102	305 T	-6:53493676 1114992300 T	
102	306 T	-6:53493675 1114992299 T	
103 E	307 G	-6:53493674 1114992298 G	E
103	308 A	-6:53493673 1114992297 A	
103	309 A	-6:53493672 1114992296 A	
104 G	310 G	-6:53493671 1114992295 G	G
104	311 G	-6:53493670 1114992294 G	
104	312 G	-6:53493669 1114992293 G	
105 T	313 A	-6:53493668 1114992292 A	T
105	314 C	-6:53493667 1114992291 C	
105	315 A	-6:53493666 1114992290 A	
106 P	316 C	-6:53493665 1114992289 C	P
106	317 C	-6:53493664 1114992288 C	
106	318 A	-6:53493663 1114992287 A	
107 G	319 G	-6:53493662 1114992286 G	G
107	320 G	-6:53493661 1114992285 G	
107	321 A	-6:53493660 1114992284 A	
108 Q	322 C	-6:53493659 1114992283 C	Q
108	323 A	-6:53493658 1114992282 A	
108	324 G	-6:53493657 1114992281 G	
109 P	325 C	-6:53493656 1114992280 C	P
109	326 C	-6:53493655 1114992279 C	
109	327 C	-6:53493654 1114992278 C	
110 Y	328 T	-6:53493653 1114992277 T	Y
110	329 A	-6:53493652 1114992276 A	
110	330 C	-6:53493651 1114992275 C	
111 G	331 G	-6:53493650 1114992274 G	G
111	332 G	-6:53493649 1114992273 G	
111	333 A	-6:53493648 1114992272 A	
112 G	334 G	-6:53493647 1114992271 G	G
112	335 G	-6:53493646 1114992270 G	
112	336 A	-6:53493645 1114992269 A	
113 T	337 A	-6:53493644 1114992268 A	T
113	338 C	-6:53493643 1114992267 C	
113	339 A	-6:53493642 1114992266 A	
114 M	340 A	-6:53493641 1114992265 A	M
114	341 T	-6:53493640 1114992264 T	
114	342 G	-6:53493639 1114992263 G	
115 S	343 T	-6:53493638 1114992262 T	S
115	344 C	-6:53493637 1114992261 C	
115	345 C	-6:53493636 1114992260 C	
116 E	346 G	-6:53493635 1114992259 G	E
116	347 A	-6:53493634 1114992258 A	
116	348 G	-6:53493633 1114992257 G	
117 F	349 T	-6:53493632 1114992256 T	F
117	350 T	-6:53493631 1114992255 T	
117	351 C	-6:53493630 1114992254 C	
118 N	352 A	-6:53493629 1114992253 A	N
118	353 A	-6:53493628 1114992252 A	
118	354 T	-6:53493627 1114992251 T	
119 T	355 A	-6:53493626 1114992250 A	T
119	356 C	-6:53493625 1114992249 C	
119	357 A	-6:53493624 1114992248 A	
120 V	358 G	-6:53493623 1114992247 G	V
120	359 T	-6:53493622 1114992246 T	
120	360 T	-6:53493621 1114992245 T	
121 E	361 G	-6:53493620 1114992244 G	E
121	362 A	-6:53493619 1114992243 A	
121	363 G	-6:53493618 1114992242 G	
122 A	364 G	-6:53493617 1114992241 G	A
122	365 C	-6:53493616 1114992240 C	
122	366 C	-6:53493615 1114992239 C	
123 N	367 A	-6:53493614 1114992238 A	N
123	368 A	-6:53493613 1114992237 A	
123	369 C	-6:53493612 1114992236 C	
124 M	370 A	-6:53493611 1114992235 A	M
124	371 T	-6:53493610 1114992234 T	
124	372 G	-6:53493609 1114992233 G	
125 R	373 C	-6:53493608 1114992232 C	R
125	374 G	-6:53493607 1114992231 G	
125	375 A	-6:53493606 1114992230 A	
126 K	376 A	-6:53493605 1114992229 A	K
126	377 A	-6:53493604 1114992228 A	
126	378 A	-6:53493603 1114992227 A	
127 R	379 C	-6:53493602 1114992226 C	R
127	380 G	-6:53493601 1114992225 G	
127	381 C	-6:53493600 1114992224 C	
128 R	382 C	-6:53493599 1114992223 C	R
128	383 G	-6:53493598 1114992222 G	
128	384 G	-6:53493597 1114992221 G	
129 K	385 A	-6:53493596 1114992220 A	K
129	386 A	-6:53493595 1114992219 A	
129	387 G	-6:53493594 1114992218 G	
130 E	388 G	-6:53493593 1114992217 G	E
130	389 A	-6:53493592 1114992216 A	
130	390 G	-6:53493591 1114992215 G	
131 A	391 G	-6:53493590 1114992214 G	A
131	392 C	-6:53493589 1114992213 C	
131	393 T	-6:53493588 1114992212 T	
132 T	394 A	-6:53493587 1114992211 A	T
132	395 C	-6:53493586 1114992210 C	
132	396 T	-6:53493585 1114992209 T	
133 S	397 T	-6:53493584 1114992208 T	S
133	398 C	-6:53493583 1114992207 C	
133	399 T	-6:53493582 1114992206 T	
134 I	400 A	-6:53493581 1114992205 A	I
134	401 T	-6:53493580 1114992204 T	
134	402 A	-6:53493579 1114992203 A	
135 L	403 T	-6:53493578 1114992202 T	L
135	404 T	-6:53493577 1114992201 T	
135	405 A	-6:53493576 1114992200 A	
136 E	406 G	-6:53493575 1114992199 G	E
136	407 A	-6:53493574 1114992198 A	
136	408 A	-6:53493573 1114992197 A	
137 E	409 G	-6:53493572 1114992196 G	E
137	410 A	-6:53493571 1114992195 A	
137	411 A	-6:53493570 1114992194 A	
138 N	412 A	-6:53493569 1114992193 A	N
138	413 A	-6:53493568 1114992192 A	
138	414 T	-6:53493567 1114992191 T	
139 Q	415 C	-6:53493566 1114992190 C	Q
139	416 A	-6:53493565 1114992189 A	
139	417 G	-6:53493564 1114992188 G	
140 A	418 G	-6:53493563 1114992187 G	A
140	419 C	-6:53493562 1114992186 C	
140	420 T	-6:53493561 1114992185 T	
141 L	421 C	-6:53493560 1114992184 C	L
141	422 T	-6:53493559 1114992183 T	
141	423 T	-6:53493558 1114992182 T	
142 C	424 T	-6:53493557 1114992181 T	C
142	425 G	-6:53493556 1114992180 G	
142	426 C	-6:53493555 1114992179 C	
143 T	427 A	-6:53493554 1114992178 A	T
143	428 C	-6:53493553 1114992177 C	
143	429 A	-6:53493552 1114992176 A	
144 I	430 A	-6:53493551 1114992175 A	I
144	431 T	-6:53493550 1114992174 T	
144	432 A	-6:53493549 1114992173 A	
145 T	433 A	-6:53493548 1114992172 A	T
145	434 C	-6:53493547 1114992171 C	
145	435 T	-6:53493546 1114992170 T	
146 S	436 T	-6:53493545 1114992169 T	S
146	437 C	-6:53493544 1114992168 C	
146	438 A	-6:53493543 1114992167 A	
147 F	439 T	-6:53493542 1114992166 T	F
147	440 T	-6:53493541 1114992165 T	
147	441 T	-6:53493540 1114992164 T	
148 P	442 C	-6:53493539 1114992163 C	P
148	443 C	-6:53493538 1114992162 C	
148	444 C	-6:53493537 1114992161 C	
149 R	445 A	-6:53493536 1114992160 A	R
149	446 G	-6:53493535 1114992159 G	
149	447 A	-6:53488979 1114987603 A	
150 L	448 T	-6:53488978 1114987602 T	L
150	449 T	-6:53488977 1114987601 T	
150	450 A	-6:53488976 1114987600 A	
151 G	451 G	-6:53488975 1114987599 G	G
151	452 G	-6:53488974 1114987598 G	
151	453 C	-6:53488973 1114987597 C	
152 C	454 T	-6:53488972 1114987596 T	C
152	455 G	-6:53488971 1114987595 G	
152	456 T	-6:53488970 1114987594 T	
153 P	457 C	-6:53488969 1114987593 C	P
153	458 C	-6:53488968 1114987592 C	
153	459 T	-6:53488967 1114987591 T	
154 G	460 G	-6:53488966 1114987590 G	G
154	461 G	-6:53488965 1114987589 G	
154	462 G	-6:53488964 1114987588 G	
155 F	463 T	-6:53488963 1114987587 T	F
155	464 T	-6:53488962 1114987586 T	
155	465 C	-6:53488961 1114987585 C	
156 T	466 A	-6:53488960 1114987584 A	T
156	467 C	-6:53488959 1114987583 C	
156	468 A	-6:53488958 1114987582 A	
157 L	469 C	-6:53488957 1114987581 C	L
157	470 T	-6:53488956 1114987580 T	
157	471 G	-6:53488955 1114987579 G	
158 P	472 C	-6:53488954 1114987578 C	P
158	473 C	-6:53488953 1114987577 C	
158	474 C	-6:53488952 1114987576 C	
159 E	475 G	-6:53488951 1114987575 G	E
159	476 A	-6:53488950 1114987574 A	
159	477 G	-6:53488949 1114987573 G	
160 V	478 G	-6:53488948 1114987572 G	V
160	479 T	-6:53488947 1114987571 T	
160	480 C	-6:53488946 1114987570 C	
161 K	481 A	-6:53488945 1114987569 A	K
161	482 A	-6:53488944 1114987568 A	
161	483 A	-6:53488943 1114987567 A	
162 P	484 C	-6:53488942 1114987566 C	P
162	485 C	-6:53488941 1114987565 C	
162	486 C	-6:53488940 1114987564 C	
163 N	487 A	-6:53488939 1114987563 A	N
163	488 A	-6:53488938 1114987562 A	
163	489 C	-6:53488937 1114987561 C	
164 P	490 C	-6:53488936 1114987560 C	P
164	491 C	-6:53488935 1114987559 C	
164	492 A	-6:53488934 1114987558 A	
165 V	493 G	-6:53488933 1114987557 G	V
165	494 T	-6:53488932 1114987556 T	
165	495 G	-6:53488931 1114987555 G	
166 E	496 G	-6:53488930 1114987554 G	E
166	497 A	-6:53488929 1114987553 A	
166	498 A	-6:53488928 1114987552 A	
167 G	499 G	-6:53488927 1114987551 G	G
167	500 G	-6:53488926 1114987550 G	
167	501 A	-6:53488925 1114987549 A	
168 G	502 G	-6:53488924 1114987548 G	G
168	503 G	-6:53488923 1114987547 G	
168	504 A	-6:53488922 1114987546 A	
169 A	505 G	-6:53488921 1114987545 G	A
169	506 C	-6:53488920 1114987544 C	
169	507 T	-6:53488919 1114987543 T	
170 S	508 T	-6:53488918 1114987542 T	S
170	509 C	-6:53488917 1114987541 C	
170	510 C	-6:53488916 1114987540 C	
171 K	511 A	-6:53488915 1114987539 A	K
171	512 A	-6:53488914 1114987538 A	
171	513 G	-6:53488913 1114987537 G	
172 S	514 T	-6:53488912 1114987536 T	S
172	515 C	-6:53488911 1114987535 C	
172	516 C	-6:53488910 1114987534 C	
173 L	517 C	-6:53488909 1114987533 C	L
173	518 T	-6:53488908 1114987532 T	
173	519 C	-6:53488907 1114987531 C	
174 F	520 T	-6:53488906 1114987530 T	F
174	521 T	-6:53488905 1114987529 T	
174	522 C	-6:53488904 1114987528 C	
175 F	523 T	-6:53488903 1114987527 T	F
175	524 T	-6:53488902 1114987526 T	
175	525 T	-6:53488901 1114987525 T	
176 P	526 C	-6:53488900 1114987524 C	P
176	527 C	-6:53488899 1114987523 C	
176	528 A	-6:53488898 1114987522 A	
177 D	529 G	-6:53488897 1114987521 G	D
177	530 A	-6:53488896 1114987520 A	
177	531 T	-6:53488895 1114987519 T	
178 E	532 G	-6:53488894 1114987518 G	E
178	533 A	-6:53488893 1114987517 A	
178	534 A	-6:53488892 1114987516 A	
179 A	535 G	-6:53488891 1114987515 G	A
179	536 C	-6:53488890 1114987514 C	
179	537 A	-6:53488889 1114987513 A	
180 I	538 A	-6:53488888 1114987512 A	I
180	539 T	-6:53488887 1114987511 T	
180	540 A	-6:53488886 1114987510 A	
181 N	541 A	-6:53488885 1114987509 A	N
181	542 A	-6:53488884 1114987508 A	
181	543 C	-6:53488883 1114987507 C	
182 K	544 A	-6:53488882 1114987506 A	K
182	545 A	-6:53488881 1114987505 A	
182	546 G	-6:53488880 1114987504 G	
183 H	547 C	-6:53488879 1114987503 C	H
183	548 A	-6:53488878 1114987502 A	
183	549 C	-6:53488877 1114987501 C	
184 P	550 C	-6:53488876 1114987500 C	P
184	551 C	-6:53488875 1114987499 C	
184	552 T	-6:53488874 1114987498 T	
185 R	553 C	-6:53488873 1114987497 C	R
185	554 G	-6:53488872 1114987496 G	
185	555 C	-6:53488871 1114987495 C	
186 F	556 T	-6:53488870 1114987494 T	F
186	557 T	-6:53488869 1114987493 T	
186	558 C	-6:53488868 1114987492 C	
187 S	559 A	-6:53488867 1114987491 A	S
187	560 G	-6:53488866 1114987490 G	
187	561 T	-6:53487254 1114985878 T	
188 T	562 A	-6:53487253 1114985877 A	T
188	563 C	-6:53487252 1114985876 C	
188	564 C	-6:53487251 1114985875 C	
189 L	565 T	-6:53487250 1114985874 T	L
189	566 T	-6:53487249 1114985873 T	
189	567 A	-6:53487248 1114985872 A	
190 T	568 A	-6:53487247 1114985871 A	T
190	569 C	-6:53487246 1114985870 C	
190	570 A	-6:53487245 1114985869 A	
191 R	571 A	-6:53487244 1114985868 A	R
191	572 G	-6:53487243 1114985867 G	
191	573 A	-6:53487242 1114985866 A	
192 N	574 A	-6:53487241 1114985865 A	N
192	575 A	-6:53487240 1114985864 A	
192	576 T	-6:53487239 1114985863 T	
193 I	577 A	-6:53487238 1114985862 A	I
193	578 T	-6:53487237 1114985861 T	
193	579 C	-6:53487236 1114985860 C	
194 R	580 C	-6:53487235 1114985859 C	R
194	581 G	-6:53487234 1114985858 G	
194	582 A	-6:53487233 1114985857 A	
195 H	583 C	-6:53487232 1114985856 C	H
195	584 A	-6:53487231 1114985855 A	
195	585 T	-6:53487230 1114985854 T	
196 R	586 A	-6:53487229 1114985853 A	R
196	587 G	-6:53487228 1114985852 G	
196	588 G	-6:53487227 1114985851 G	
197 R	589 A	-6:53487226 1114985850 A	R
197	590 G	-6:53487225 1114985849 G	
197	591 A	-6:53487224 1114985848 A	
198 G	592 G	-6:53487223 1114985847 G	G
198	593 G	-6:53487222 1114985846 G	
198	594 A	-6:53487221 1114985845 A	
199 E	595 G	-6:53487220 1114985844 G	E
199	596 A	-6:53487219 1114985843 A	
199	597 A	-6:53487218 1114985842 A	
200 K	598 A	-6:53487217 1114985841 A	K
200	599 A	-6:53487216 1114985840 A	
200	600 G	-6:53487215 1114985839 G	
201 V	601 G	-6:53487214 1114985838 G	V
201	602 T	-6:53487213 1114985837 T	
201	603 T	-6:53487212 1114985836 T	
202 V	604 G	-6:53487211 1114985835 G	V
202	605 T	-6:53487210 1114985834 T	
202	606 C	-6:53487209 1114985833 C	
203 I	607 A	-6:53487208 1114985832 A	I
203	608 T	-6:53487207 1114985831 T	
203	609 C	-6:53487206 1114985830 C	
204 N	610 A	-6:53487205 1114985829 A	N
204	611 A	-6:53487204 1114985828 A	
204	612 T	-6:53487203 1114985827 T	
205 V	613 G	-6:53487202 1114985826 G	V
205	614 T	-6:53487201 1114985825 T	
205	615 A	-6:53487200 1114985824 A	
206 P	616 C	-6:53487199 1114985823 C	P
206	617 C	-6:53487198 1114985822 C	
206	618 A	-6:53487197 1114985821 A	
207 I	619 A	-6:53487196 1114985820 A	I
207	620 T	-6:53487094 1114985718 T	
207	621 A	-6:53487093 1114985717 A	
208 F	622 T	-6:53487092 1114985716 T	F
208	623 T	-6:53487091 1114985715 T	
208	624 T	-6:53487090 1114985714 T	
209 K	625 A	-6:53487089 1114985713 A	K
209	626 A	-6:53487088 1114985712 A	
209	627 G	-6:53487087 1114985711 G	
210 D	628 G	-6:53487086 1114985710 G	D
210	629 A	-6:53487085 1114985709 A	
210	630 C	-6:53487084 1114985708 C	
211 K	631 A	-6:53487083 1114985707 A	K
211	632 A	-6:53487082 1114985706 A	
211	633 G	-6:53487081 1114985705 G	
212 N	634 A	-6:53487080 1114985704 A	N
212	635 A	-6:53487079 1114985703 A	
212	636 T	-6:53487078 1114985702 T	
213 T	637 A	-6:53487077 1114985701 A	T
213	638 C	-6:53487076 1114985700 C	
213	639 A	-6:53487075 1114985699 A	
214 P	640 C	-6:53487074 1114985698 C	P
214	641 C	-6:53487073 1114985697 C	
214	642 A	-6:53487072 1114985696 A	
215 S	643 T	-6:53487071 1114985695 T	S
215	644 C	-6:53487070 1114985694 C	
215	645 T	-6:53487069 1114985693 T	
216 P	646 C	-6:53487068 1114985692 C	P
216	647 C	-6:53487067 1114985691 C	
216	648 A	-6:53487066 1114985690 A	
217 F	649 T	-6:53487065 1114985689 T	F
217	650 T	-6:53487064 1114985688 T	
217	651 T	-6:53487063 1114985687 T	
218 I	652 A	-6:53487062 1114985686 A	I
218	653 T	-6:53487061 1114985685 T	
218	654 A	-6:53487060 1114985684 A	
219 E	655 G	-6:53487059 1114985683 G	E
219	656 A	-6:53487058 1114985682 A	
219	657 A	-6:53487057 1114985681 A	
220 T	658 A	-6:53487056 1114985680 A	T
220	659 C	-6:53487055 1114985679 C	
220	660 A	-6:53487054 1114985678 A	
221 F	661 T	-6:53487053 1114985677 T	F
221	662 T	-6:53487052 1114985676 T	
221	663 T	-6:53487051 1114985675 T	
222 T	664 A	-6:53487050 1114985674 A	T
222	665 C	-6:53487049 1114985673 C	
222	666 T	-6:53487048 1114985672 T	
223 E	667 G	-6:53487047 1114985671 G	E
223	668 A	-6:53487046 1114985670 A	
223	669 G	-6:53487045 1114985669 G	
224 D	670 G	-6:53487044 1114985668 G	D
224	671 A	-6:53487043 1114985667 A	
224	672 T	-6:53487042 1114985666 T	
225 D	673 G	-6:53487041 1114985665 G	D
225	674 A	-6:53487040 1114985664 A	
225	675 T	-6:53487039 1114985663 T	
226 E	676 G	-6:53487038 1114985662 G	E
226	677 A	-6:53487037 1114985661 A	
226	678 A	-6:53487036 1114985660 A	
227 A	679 G	-6:53487035 1114985659 G	A
227	680 C	-6:53487034 1114985658 C	
227	681 T	-6:53487033 1114985657 T	
228 S	682 T	-6:53487032 1114985656 T	S
228	683 C	-6:53487031 1114985655 C	
228	684 A	-6:53487030 1114985654 A	
229 R	685 A	-6:53487029 1114985653 A	R
229	686 G	-6:53487028 1114985652 G	
229	687 G	-6:53487027 1114985651 G	
230 A	688 G	-6:53487026 1114985650 G	A
230	689 C	-6:53487025 1114985649 C	
230	690 T	-6:53487024 1114985648 T	
231 S	691 T	-6:53487023 1114985647 T	S
231	692 C	-6:53487022 1114985646 C	
231	693 T	-6:53487021 1114985645 T	
232 K	694 A	-6:53487020 1114985644 A	K
232	695 A	-6:53487019 1114985643 A	
232	696 G	-6:53487018 1114985642 G	
233 P	697 C	-6:53487017 1114985641 C	P
233	698 C	-6:53487016 1114985640 C	
233	699 G	-6:53487015 1114985639 G	
234 D	700 G	-6:53487014 1114985638 G	D
234	701 A	-6:53487013 1114985637 A	
234	702 T	-6:53487012 1114985636 T	
235 H	703 C	-6:53487011 1114985635 C	H
235	704 A	-6:53487010 1114985634 A	
235	705 T	-6:53487009 1114985633 T	
236 I	706 A	-6:53487008 1114985632 A	I
236	707 T	-6:53487007 1114985631 T	
236	708 T	-6:53487006 1114985630 T	
237 Y	709 T	-6:53487005 1114985629 T	Y
237	710 A	-6:53487004 1114985628 A	
237	711 C	-6:53487003 1114985627 C	
238 M	712 A	-6:53487002 1114985626 A	M
238	713 T	-6:53487001 1114985625 T	
238	714 G	-6:53487000 1114985624 G	
239 D	715 G	-6:53486999 1114985623 G	D
239	716 A	-6:53486998 1114985622 A	
239	717 T	-6:53486997 1114985621 T	
240 A	718 G	-6:53486996 1114985620 G	A
240	719 C	-6:53486995 1114985619 C	
240	720 C	-6:53486994 1114985618 C	
241 M	721 A	-6:53486993 1114985617 A	M
241	722 T	-6:53486992 1114985616 T	
241	723 G	-6:53486991 1114985615 G	
242 G	724 G	-6:53486990 1114985614 G	G
242	725 G	-6:53486989 1114985613 G	
242	726 A	-6:53486988 1114985612 A	
243 F	727 T	-6:53486987 1114985611 T	F
243	728 T	-6:53486986 1114985610 T	
243	729 T	-6:53486985 1114985609 T	
244 G	730 G	-6:53486984 1114985608 G	G
244	731 G	-6:53486983 1114985607 G	
244	732 A	-6:53486982 1114985606 A	
245 M	733 A	-6:53486981 1114985605 A	M
245	734 T	-6:53486980 1114985604 T	
245	735 G	-6:53486979 1114985603 G	
246 G	736 G	-6:53486978 1114985602 G	G
246	737 G	-6:53486977 1114985601 G	
246	738 C	-6:53486976 1114985600 C	
247 N	739 A	-6:53486975 1114985599 A	N
247	740 A	-6:53486974 1114985598 A	
247	741 T	-6:53486973 1114985597 T	
248 C	742 T	-6:53486972 1114985596 T	C
248	743 G	-6:53486971 1114985595 G	
248	744 C	-6:53486970 1114985594 C	
249 C	745 T	-6:53486969 1114985593 T	C
249	746 G	-6:53486968 1114985592 G	
249	747 T	-6:53486967 1114985591 T	
250 L	748 C	-6:53486966 1114985590 C	L
250	749 T	-6:53486965 1114985589 T	
250	750 C	-6:53486964 1114985588 C	
251 Q	751 C	-6:53486963 1114985587 C	Q
251	752 A	-6:53486962 1114985586 A	
251	753 G	-6:53486961 1114985585 G	
252 V	754 G	-6:53482007 1114980631 G	V
252	755 T	-6:53482006 1114980630 T	
252	756 G	-6:53482005 1114980629 G	
253 T	757 A	-6:53482004 1114980628 A	T
253	758 C	-6:53482003 1114980627 C	
253	759 A	-6:53482002 1114980626 A	
254 F	760 T	-6:53482001 1114980625 T	F
254	761 T	-6:53482000 1114980624 T	
254	762 C	-6:53481999 1114980623 C	
255 Q	763 C	-6:53481998 1114980622 C	Q
255	764 A	-6:53481997 1114980621 A	
255	765 A	-6:53481996 1114980620 A	
256 A	766 G	-6:53481995 1114980619 G	A
256	767 C	-6:53481994 1114980618 C	
256	768 C	-6:53481993 1114980617 C	
257 C	769 T	-6:53481992 1114980616 T	C
257	770 G	-6:53481991 1114980615 G	
257	771 C	-6:53481990 1114980614 C	
258 S	772 A	-6:53481989 1114980613 A	S
258	773 G	-6:53481988 1114980612 G	
258	774 T	-6:53481987 1114980611 T	
259 I	775 A	-6:53481986 1114980610 A	I
259	776 T	-6:53481985 1114980609 T	
259	777 A	-6:53481984 1114980608 A	
260 S	778 T	-6:53481983 1114980607 T	S
260	779 C	-6:53481982 1114980606 C	
260	780 T	-6:53481981 1114980605 T	
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261	782 A	-6:53481979 1114980603 A	
261	783 G	-6:53481978 1114980602 G	
262 A	784 G	-6:53481977 1114980601 G	A
262	785 C	-6:53481976 1114980600 C	
262	786 C	-6:53481975 1114980599 C	
263 R	787 A	-6:53481974 1114980598 A	R
263	788 G	-6:53481973 1114980597 G	
263	789 A	-6:53481972 1114980596 A	
264 Y	790 T	-6:53481971 1114980595 T	Y
264	791 A	-6:53481970 1114980594 A	
264	792 C	-6:53481969 1114980593 C	
265 L	793 C	-6:53481968 1114980592 C	L
265	794 T	-6:53481967 1114980591 T	
265	795 T	-6:53481966 1114980590 T	
266 Y	796 T	-6:53481965 1114980589 T	Y
266	797 A	-6:53481964 1114980588 A	
266	798 T	-6:53481963 1114980587 T	
267 D	799 G	-6:53481962 1114980586 G	D
267	800 A	-6:53481961 1114980585 A	
267	801 T	-6:53481960 1114980584 T	
268 Q	802 C	-6:53481959 1114980583 C	Q
268	803 A	-6:53481958 1114980582 A	
268	804 G	-6:53481957 1114980581 G	
269 L	805 T	-6:53481956 1114980580 T	L
269	806 T	-6:53481955 1114980579 T	
269	807 G	-6:53481954 1114980578 G	
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270	810 T	-6:53481951 1114980575 T	
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271	812 C	-6:53481949 1114980573 C	
271	813 T	-6:53481948 1114980572 T	
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272	815 T	-6:53481946 1114980570 T	
272	816 C	-6:53481945 1114980569 C	
273 C	817 T	-6:53481944 1114980568 T	C
273	818 G	-6:53481943 1114980567 G	
273	819 T	-6:53481942 1114980566 T	
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274	821 C	-6:53481940 1114980564 C	
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276	827 T	-6:53481934 1114980558 T	
276	828 T	-6:53481933 1114980557 T	
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278	834 T	-6:53481463 1114980087 T	
279 L	835 T	-6:53481462 1114980086 T	L
279	836 T	-6:53481461 1114980085 T	
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280 S	838 A	-6:53481459 1114980083 A	S
280	839 G	-6:53481458 1114980082 G	
280	840 T	-6:53481457 1114980081 T	
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281	842 C	-6:53481455 1114980079 C	
281	843 T	-6:53481454 1114980078 T	
282 A	844 G	-6:53481453 1114980077 G	A
282	845 C	-6:53481452 1114980076 C	
282	846 A	-6:53481451 1114980075 A	
283 S	847 T	-6:53481450 1114980074 T	S
283	848 C	-6:53481449 1114980073 C	
283	849 T	-6:53481448 1114980072 T	
284 P	850 C	-6:53481447 1114980071 C	P
284	851 C	-6:53481446 1114980070 C	
284	852 C	-6:53481445 1114980069 C	
285 F	853 T	-6:53481444 1114980068 T	F
285	854 T	-6:53481443 1114980067 T	
285	855 T	-6:53481442 1114980066 T	
286 Y	856 T	-6:53481441 1114980065 T	Y
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289	866 A	-6:53481431 1114980055 A	
289	867 T	-6:53481430 1114980054 T	
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290	869 T	-6:53481428 1114980052 T	
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292	875 A	-6:53481422 1114980046 A	
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293	878 T	-6:53481419 1114980043 T	
293	879 T	-6:53481418 1114980042 T	
294 D	880 G	-6:53481417 1114980041 G	D
294	881 A	-6:53481416 1114980040 A	
294	882 T	-6:53481415 1114980039 T	
295 C	883 T	-6:53481414 1114980038 T	C
295	884 G	-6:53481413 1114980037 G	
295	885 T	-6:53481412 1114980036 T	
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299	897 G	-6:53481400 1114980024 G	
300 I	898 A	-6:53481399 1114980023 A	I
300	899 T	-6:53481398 1114980022 T	
300	900 T	-6:53481397 1114980021 T	
301 S	901 T	-6:53481396 1114980020 T	S
301	902 C	-6:53481395 1114980019 C	
301	903 T	-6:53481394 1114980018 T	
302 A	904 G	-6:53481393 1114980017 G	A
302	905 C	-6:53481392 1114980016 C	
302	906 A	-6:53481391 1114980015 A	
303 S	907 T	-6:53481390 1114980014 T	S
303	908 C	-6:53481389 1114980013 C	
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306 D	916 G	-6:53481381 1114980005 G	D
306	917 A	-6:53481380 1114980004 A	
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308	923 C	-6:53481374 1114979998 C	
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317	950 T	-6:53480371 1114978995 T	
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318	953 A	-6:53480368 1114978992 A	
318	954 G	-6:53480367 1114978991 G	
319 N	955 A	-6:53480366 1114978990 A	N
319	956 A	-6:53480365 1114978989 A	
319	957 C	-6:53480364 1114978988 C	
320 N	958 A	-6:53480363 1114978987 A	N
320	959 A	-6:53480362 1114978986 A	
320	960 T	-6:53480361 1114978985 T	
321 N	961 A	-6:53480360 1114978984 A	N
321	962 A	-6:53480359 1114978983 A	
321	963 C	-6:53480358 1114978982 C	
322 Y	964 T	-6:53480357 1114978981 T	Y
322	965 A	-6:53480356 1114978980 A	
322	966 T	-6:53480355 1114978979 T	
323 R	967 A	-6:53480354 1114978978 A	R
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324	971 T	-6:53480350 1114978974 T	
324	972 C	-6:53480349 1114978973 C	
325 S	973 A	-6:53480348 1114978972 A	S
325	974 G	-6:53480347 1114978971 G	
325	975 T	-6:53480346 1114978970 T	
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326	977 A	-6:53480344 1114978968 A	
326	978 A	-6:53480343 1114978967 A	
327 S	979 T	-6:53480342 1114978966 T	S
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329	986 A	-6:53480335 1114978959 A	
329	987 T	-6:53480334 1114978958 T	
330 D	988 G	-6:53480333 1114978957 G	D
330	989 A	-6:53480332 1114978956 A	
330	990 C	-6:53480331 1114978955 C	
331 S	991 T	-6:53480330 1114978954 T	S
331	992 C	-6:53480329 1114978953 C	
331	993 A	-6:53480328 1114978952 A	
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332	995 T	-6:53480326 1114978950 T	
332	996 A	-6:53480325 1114978949 A	
333 D	997 G	-6:53480324 1114978948 G	D
333	998 A	-6:53480323 1114978947 A	
333	999 C	-6:53480322 1114978946 C	
334 S	1000 A	-6:53480321 1114978945 A	S
334	1001 G	-6:53480320 1114978944 G	
334	1002 C	-6:53480319 1114978943 C	
335 Y	1003 T	-6:53480318 1114978942 T	Y
335	1004 A	-6:53480317 1114978941 A	
335	1005 T	-6:53480316 1114978940 T	
336 L	1006 T	-6:53480315 1114978939 T	L
336	1007 T	-6:53480314 1114978938 T	
336	1008 A	-6:53480313 1114978937 A	
337 S	1009 T	-6:53480312 1114978936 T	S
337	1010 C	-6:53480311 1114978935 C	
337	1011 T	-6:53480310 1114978934 T	
338 K	1012 A	-6:53480309 1114978933 A	K
338	1013 A	-6:53480308 1114978932 A	
338	1014 G	-6:53480307 1114978931 G	
339 C	1015 T	-6:53480306 1114978930 T	C
339	1016 G	-6:53480305 1114978929 G	
339	1017 T	-6:53480304 1114978928 T	
340 G	1018 G	-6:53480303 1114978927 G	G
340	1019 G	-6:53480302 1114978926 G	
340	1020 T	-6:53480301 1114978925 T	
341 E	1021 G	-6:53480300 1114978924 G	E
341	1022 A	-6:53480299 1114978923 A	
341	1023 G	-6:53480298 1114978922 G	
342 K	1024 A	-6:53480297 1114978921 A	K
342	1025 A	-6:53480296 1114978920 A	
342	1026 A	-6:53480295 1114978919 A	
343 Y	1027 T	-6:53480294 1114978918 T	Y
343	1028 A	-6:53480293 1114978917 A	
343	1029 T	-6:53480292 1114978916 T	
344 N	1030 A	-6:53480291 1114978915 A	N
344	1031 A	-6:53480290 1114978914 A	
344	1032 T	-6:53480289 1114978913 T	
345 D	1033 G	-6:53480288 1114978912 G	D
345	1034 A	-6:53480287 1114978911 A	
345	1035 C	-6:53480286 1114978910 C	
346 I	1036 A	-6:53480285 1114978909 A	I
346	1037 T	-6:53480284 1114978908 T	
346	1038 C	-6:53480283 1114978907 C	
347 D	1039 G	-6:53480282 1114978906 G	D
347	1040 A	-6:53480281 1114978905 A	
347	1041 C	-6:53480280 1114978904 C	
348 L	1042 T	-6:53480279 1114978903 T	L
348	1043 T	-6:53480278 1114978902 T	
348	1044 G	-6:53480277 1114978901 G	
349 T	1045 A	-6:53480276 1114978900 A	T
349	1046 C	-6:53480275 1114978899 C	
349	1047 G	-6:53480274 1114978898 G	
350 I	1048 A	-6:53480273 1114978897 A	I
350	1049 T	-6:53480272 1114978896 T	
350	1050 A	-6:53480271 1114978895 A	
351 D	1051 G	-6:53480270 1114978894 G	D
351	1052 A	-6:53480269 1114978893 A	
351	1053 T	-6:53480268 1114978892 T	
352 K	1054 A	-6:53480267 1114978891 A	K
352	1055 A	-6:53480266 1114978890 A	
352	1056 A	-6:53480265 1114978889 A	
353 E	1057 G	-6:53480264 1114978888 G	E
353	1058 A	-6:53480263 1114978887 A	
353	1059 G	-6:53480262 1114978886 G	
354 I	1060 A	-6:53480261 1114978885 A	I
354	1061 T	-6:53480260 1114978884 T	
354	1062 C	-6:53480259 1114978883 C	
355 Y	1063 T	-6:53480258 1114978882 T	Y
355	1064 A	-6:53480257 1114978881 A	
355	1065 C	-6:53480256 1114978880 C	
356 E	1066 G	-6:53480255 1114978879 G	E
356	1067 A	-6:53480254 1114978878 A	
356	1068 A	-6:53480253 1114978877 A	
357 Q	1069 C	-6:53480252 1114978876 C	Q
357	1070 A	-6:53480251 1114978875 A	
357	1071 G	-6:53480250 1114978874 G	
358 L	1072 C	-6:53480249 1114978873 C	L
358	1073 T	-6:53480248 1114978872 T	
358	1074 G	-6:53480247 1114978871 G	
359 L	1075 T	-6:53480246 1114978870 T	L
359	1076 T	-6:53480245 1114978869 T	
359	1077 G	-6:53480244 1114978868 G	
360 Q	1078 C	-6:53480243 1114978867 C	Q
360	1079 A	-6:53480242 1114978866 A	
360	1080 G	-6:53480241 1114978865 G	
361 E	1081 G	-6:53480240 1114978864 G	E
361	1082 A	-6:53480239 1114978863 A	
361	1083 A	-6:53480238 1114978862 A	
362 G	1084 G	-6:53480237 1114978861 G	G
362	1085 G	-6:53479782 1114978406 G	
362	1086 C	-6:53479781 1114978405 C	
363 I	1087 A	-6:53479780 1114978404 A	I
363	1088 T	-6:53479779 1114978403 T	
363	1089 T	-6:53479778 1114978402 T	
364 D	1090 G	-6:53479777 1114978401 G	D
364	1091 A	-6:53479776 1114978400 A	
364	1092 T	-6:53479775 1114978399 T	
365 H	1093 C	-6:53479774 1114978398 C	H
365	1094 A	-6:53479773 1114978397 A	
365	1095 T	-6:53479772 1114978396 T	
366 L	1096 C	-6:53479771 1114978395 C	L
366	1097 T	-6:53479770 1114978394 T	
366	1098 C	-6:53479769 1114978393 C	
367 L	1099 C	-6:53479768 1114978392 C	L
367	1100 T	-6:53479767 1114978391 T	
367	1101 G	-6:53479766 1114978390 G	
368 A	1102 G	-6:53479765 1114978389 G	A
368	1103 C	-6:53479764 1114978388 C	
368	1104 C	-6:53479763 1114978387 C	
369 Q	1105 C	-6:53479762 1114978386 C	Q
369	1106 A	-6:53479761 1114978385 A	
369	1107 G	-6:53479760 1114978384 G	
370 H	1108 C	-6:53479759 1114978383 C	H
370	1109 A	-6:53479758 1114978382 A	
370	1110 T	-6:53479757 1114978381 T	
371 V	1111 G	-6:53479756 1114978380 G	V
371	1112 T	-6:53479755 1114978379 T	
371	1113 T	-6:53479754 1114978378 T	
372 A	1114 G	-6:53479753 1114978377 G	A
372	1115 C	-6:53479752 1114978376 C	
372	1116 T	-6:53479751 1114978375 T	
373 H	1117 C	-6:53479750 1114978374 C	H
373	1118 A	-6:53479749 1114978373 A	
373	1119 T	-6:53479748 1114978372 T	
374 L	1120 C	-6:53479747 1114978371 C	L
374	1121 T	-6:53479746 1114978370 T	
374	1122 C	-6:53479745 1114978369 C	
375 F	1123 T	-6:53479744 1114978368 T	F
375	1124 T	-6:53479743 1114978367 T	
375	1125 T	-6:53479742 1114978366 T	
376 I	1126 A	-6:53479741 1114978365 A	I
376	1127 T	-6:53479740 1114978364 T	
376	1128 T	-6:53479739 1114978363 T	
377 R	1129 A	-6:53479738 1114978362 A	R
377	1130 G	-6:53479737 1114978361 G	
377	1131 A	-6:53479736 1114978360 A	
378 D	1132 G	-6:53479735 1114978359 G	D
378	1133 A	-6:53479734 1114978358 A	
378	1134 C	-6:53479733 1114978357 C	
379 P	1135 C	-6:53479732 1114978356 C	P
379	1136 C	-6:53479731 1114978355 C	
379	1137 A	-6:53479730 1114978354 A	
380 L	1138 C	-6:53479729 1114978353 C	L
380	1139 T	-6:53479728 1114978352 T	
380	1140 G	-6:53479727 1114978351 G	
381 T	1141 A	-6:53479726 1114978350 A	T
381	1142 C	-6:53479725 1114978349 C	
381	1143 A	-6:53479724 1114978348 A	
382 L	1144 C	-6:53479723 1114978347 C	L
382	1145 T	-6:53479722 1114978346 T	
382	1146 G	-6:53479721 1114978345 G	
383 F	1147 T	-6:53479720 1114978344 T	F
383	1148 T	-6:53479719 1114978343 T	
383	1149 T	-6:53479718 1114978342 T	
384 E	1150 G	-6:53479717 1114978341 G	E
384	1151 A	-6:53479716 1114978340 A	
384	1152 A	-6:53479715 1114978339 A	
385 E	1153 G	-6:53479714 1114978338 G	E
385	1154 A	-6:53479713 1114978337 A	
385	1155 G	-6:53479712 1114978336 G	
386 K	1156 A	-6:53479711 1114978335 A	K
386	1157 A	-6:53479710 1114978334 A	
386	1158 A	-6:53479709 1114978333 A	
387 I	1159 A	-6:53479708 1114978332 A	I
387	1160 T	-6:53479707 1114978331 T	
387	1161 A	-6:53479706 1114978330 A	
388 H	1162 C	-6:53479705 1114978329 C	H
388	1163 A	-6:53479704 1114978328 A	
388	1164 C	-6:53479703 1114978327 C	
389 L	1165 C	-6:53479702 1114978326 C	L
389	1166 T	-6:53479701 1114978325 T	
389	1167 G	-6:53479700 1114978324 G	
390 D	1168 G	-6:53479699 1114978323 G	D
390	1169 A	-6:53479698 1114978322 A	
390	1170 T	-6:53479697 1114978321 T	
391 D	1171 G	-6:53479696 1114978320 G	D
391	1172 A	-6:53479695 1114978319 A	
391	1173 T	-6:53479694 1114978318 T	
392 A	1174 G	-6:53479693 1114978317 G	A
392	1175 C	-6:53479692 1114978316 C	
392	1176 T	-6:53479691 1114978315 T	
393 N	1177 A	-6:53479690 1114978314 A	N
393	1178 A	-6:53479689 1114978313 A	
393	1179 T	-6:53479688 1114978312 T	
394 E	1180 G	-6:53479687 1114978311 G	E
394	1181 A	-6:53479686 1114978310 A	
394	1182 G	-6:53479685 1114978309 G	
395 S	1183 T	-6:53479684 1114978308 T	S
395	1184 C	-6:53479683 1114978307 C	
395	1185 T	-6:53479682 1114978306 T	
396 D	1186 G	-6:53479681 1114978305 G	D
396	1187 A	-6:53479680 1114978304 A	
396	1188 C	-6:53479679 1114978303 C	
397 H	1189 C	-6:53479678 1114978302 C	H
397	1190 A	-6:53479677 1114978301 A	
397	1191 T	-6:53479676 1114978300 T	
398 F	1192 T	-6:53479675 1114978299 T	F
398	1193 T	-6:53479674 1114978298 T	
398	1194 T	-6:53479673 1114978297 T	
399 E	1195 G	-6:53479672 1114978296 G	E
399	1196 A	-6:53479671 1114978295 A	
399	1197 G	-6:53479670 1114978294 G	
400 N	1198 A	-6:53478652 1114977276 A	N
400	1199 A	-6:53478651 1114977275 A	
400	1200 T	-6:53478650 1114977274 T	
401 I	1201 A	-6:53478649 1114977273 A	I
401	1202 T	-6:53478648 1114977272 T	
401	1203 T	-6:53478647 1114977271 T	
402 Q	1204 C	-6:53478646 1114977270 C	Q
402	1205 A	-6:53478645 1114977269 A	
402	1206 G	-6:53478644 1114977268 G	
403 S	1207 T	-6:53478643 1114977267 T	S
403	1208 C	-6:53478642 1114977266 C	
403	1209 C	-6:53478641 1114977265 C	
404 T	1210 A	-6:53478640 1114977264 A	T
404	1211 C	-6:53478639 1114977263 C	
404	1212 A	-6:53478638 1114977262 A	
405 N	1213 A	-6:53478637 1114977261 A	N
405	1214 A	-6:53478636 1114977260 A	
405	1215 T	-6:53478635 1114977259 T	
406 W	1216 T	-6:53478634 1114977258 T	W
406	1217 G	-6:53478633 1114977257 G	
406	1218 G	-6:53478632 1114977256 G	
407 Q	1219 C	-6:53478631 1114977255 C	Q
407	1220 A	-6:53478630 1114977254 A	
407	1221 G	-6:53478629 1114977253 G	
408 T	1222 A	-6:53478628 1114977252 A	T
408	1223 C	-6:53478627 1114977251 C	
408	1224 A	-6:53478626 1114977250 A	
409 M	1225 A	-6:53478625 1114977249 A	M
409	1226 T	-6:53478624 1114977248 T	
409	1227 G	-6:53478623 1114977247 G	
410 R	1228 A	-6:53478622 1114977246 A	R
410	1229 G	-6:53478621 1114977245 G	
410	1230 A	-6:53478620 1114977244 A	
411 F	1231 T	-6:53478619 1114977243 T	F
411	1232 T	-6:53478618 1114977242 T	
411	1233 T	-6:53478617 1114977241 T	
412 K	1234 A	-6:53478616 1114977240 A	K
412	1235 A	-6:53478615 1114977239 A	
412	1236 G	-6:53478614 1114977238 G	
413 P	1237 C	-6:53478613 1114977237 C	P
413	1238 C	-6:53478612 1114977236 C	
413	1239 C	-6:53478611 1114977235 C	
414 P	1240 C	-6:53478610 1114977234 C	P
414	1241 C	-6:53478609 1114977233 C	
414	1242 T	-6:53478608 1114977232 T	
415 P	1243 C	-6:53478607 1114977231 C	P
415	1244 C	-6:53478606 1114977230 C	
415	1245 T	-6:53478605 1114977229 T	
416 P	1246 C	-6:53478604 1114977228 C	P
416	1247 C	-6:53478603 1114977227 C	
416	1248 A	-6:53478602 1114977226 A	
417 N	1249 A	-6:53478601 1114977225 A	N
417	1250 A	-6:53478600 1114977224 A	
417	1251 C	-6:53478599 1114977223 C	
418 S	1252 T	-6:53478598 1114977222 T	S
418	1253 C	-6:53478597 1114977221 C	
418	1254 A	-6:53478596 1114977220 A	
419 D	1255 G	-6:53478595 1114977219 G	D
419	1256 A	-6:53478594 1114977218 A	
419	1257 C	-6:53478593 1114977217 C	
420 I	1258 A	-6:53478592 1114977216 A	I
420	1259 T	-6:53478591 1114977215 T	
420	1260 T	-6:53478590 1114977214 T	
421 G	1261 G	-6:53478589 1114977213 G	G
421	1262 G	-6:53478588 1114977212 G	
421	1263 A	-6:53478587 1114977211 A	
422 W	1264 T	-6:53478586 1114977210 T	W
422	1265 G	-6:53478585 1114977209 G	
422	1266 G	-6:53478584 1114977208 G	
423 R	1267 A	-6:53478583 1114977207 A	R
423	1268 G	-6:53478582 1114977206 G	
423	1269 A	-6:53478581 1114977205 A	
424 V	1270 G	-6:53478580 1114977204 G	V
424	1271 T	-6:53478579 1114977203 T	
424	1272 A	-6:53478578 1114977202 A	
425 E	1273 G	-6:53478577 1114977201 G	E
425	1274 A	-6:53478576 1114977200 A	
425	1275 A	-6:53478575 1114977199 A	
426 F	1276 T	-6:53478574 1114977198 T	F
426	1277 T	-6:53478573 1114977197 T	
426	1278 T	-6:53478572 1114977196 T	
427 R	1279 C	-6:53478571 1114977195 C	R
427	1280 G	-6:53478570 1114977194 G	
427	1281 A	-6:53478569 1114977193 A	
428 P	1282 C	-6:53478568 1114977192 C	P
428	1283 C	-6:53478567 1114977191 C	
428	1284 C	-6:53478566 1114977190 C	
429 M	1285 A	-6:53478565 1114977189 A	M
429	1286 T	-6:53478564 1114977188 T	
429	1287 G	-6:53478563 1114977187 G	
430 E	1288 G	-6:53478562 1114977186 G	E
430	1289 A	-6:53478561 1114977185 A	
430	1290 G	-6:53478560 1114977184 G	
431 V	1291 G	-6:53478253 1114976877 G	V
431	1292 T	-6:53478252 1114976876 T	
431	1293 G	-6:53478251 1114976875 G	
432 Q	1294 C	-6:53478250 1114976874 C	Q
432	1295 A	-6:53478249 1114976873 A	
432	1296 A	-6:53478248 1114976872 A	
433 L	1297 T	-6:53478247 1114976871 T	L
433	1298 T	-6:53478246 1114976870 T	
433	1299 A	-6:53478245 1114976869 A	
434 T	1300 A	-6:53478244 1114976868 A	T
434	1301 C	-6:53478243 1114976867 C	
434	1302 A	-6:53478242 1114976866 A	
435 D	1303 G	-6:53478241 1114976865 G	D
435	1304 A	-6:53478240 1114976864 A	
435	1305 C	-6:53478239 1114976863 C	
436 F	1306 T	-6:53478238 1114976862 T	F
436	1307 T	-6:53478237 1114976861 T	
436	1308 T	-6:53478236 1114976860 T	
437 E	1309 G	-6:53478235 1114976859 G	E
437	1310 A	-6:53478234 1114976858 A	
437	1311 G	-6:53478233 1114976857 G	
438 N	1312 A	-6:53478232 1114976856 A	N
438	1313 A	-6:53478231 1114976855 A	
438	1314 C	-6:53478230 1114976854 C	
439 S	1315 T	-6:53478229 1114976853 T	S
439	1316 C	-6:53478228 1114976852 C	
439	1317 T	-6:53478227 1114976851 T	
440 A	1318 G	-6:53478226 1114976850 G	A
440	1319 C	-6:53478225 1114976849 C	
440	1320 C	-6:53478224 1114976848 C	
441 Y	1321 T	-6:53478223 1114976847 T	Y
441	1322 A	-6:53478222 1114976846 A	
441	1323 T	-6:53478221 1114976845 T	
442 V	1324 G	-6:53478220 1114976844 G	V
442	1325 T	-6:53478219 1114976843 T	
442	1326 G	-6:53478218 1114976842 G	
443 V	1327 G	-6:53478217 1114976841 G	V
443	1328 T	-6:53478216 1114976840 T	
443	1329 G	-6:53478215 1114976839 G	
444 F	1330 T	-6:53478214 1114976838 T	F
444	1331 T	-6:53478213 1114976837 T	
444	1332 T	-6:53478212 1114976836 T	
445 V	1333 G	-6:53478211 1114976835 G	V
445	1334 T	-6:53478210 1114976834 T	
445	1335 G	-6:53478209 1114976833 G	
446 V	1336 G	-6:53478208 1114976832 G	V
446	1337 T	-6:53478207 1114976831 T	
446	1338 A	-6:53478206 1114976830 A	
447 L	1339 C	-6:53478205 1114976829 C	L
447	1340 T	-6:53478204 1114976828 T	
447	1341 G	-6:53478203 1114976827 G	
448 L	1342 C	-6:53478202 1114976826 C	L
448	1343 T	-6:53478201 1114976825 T	
448	1344 C	-6:53478200 1114976824 C	
449 T	1345 A	-6:53478199 1114976823 A	T
449	1346 C	-6:53478198 1114976822 C	
449	1347 C	-6:53478197 1114976821 C	
450 R	1348 A	-6:53478196 1114976820 A	R
450	1349 G	-6:53478195 1114976819 G	
450	1350 A	-6:53478194 1114976818 A	
451 V	1351 G	-6:53478193 1114976817 G	V
451	1352 T	-6:53478192 1114976816 T	
451	1353 G	-6:53478191 1114976815 G	
452 I	1354 A	-6:53478190 1114976814 A	I
452	1355 T	-6:53478189 1114976813 T	
452	1356 C	-6:53478188 1114976812 C	
453 L	1357 C	-6:53478187 1114976811 C	L
453	1358 T	-6:53478186 1114976810 T	
453	1359 T	-6:53478185 1114976809 T	
454 S	1360 T	-6:53478184 1114976808 T	S
454	1361 C	-6:53478183 1114976807 C	
454	1362 C	-6:53478182 1114976806 C	
455 Y	1363 T	-6:53478181 1114976805 T	Y
455	1364 A	-6:53478180 1114976804 A	
455	1365 C	-6:53478179 1114976803 C	
456 K	1366 A	-6:53478178 1114976802 A	K
456	1367 A	-6:53478177 1114976801 A	
456	1368 A	-6:53478176 1114976800 A	
457 L	1369 T	-6:53478175 1114976799 T	L
457	1370 T	-6:53478174 1114976798 T	
457	1371 G	-6:53478173 1114976797 G	
458 D	1372 G	-6:53478172 1114976796 G	D
458	1373 A	-6:53478171 1114976795 A	
458	1374 T	-6:53478170 1114976794 T	
459 F	1375 T	-6:53478169 1114976793 T	F
459	1376 T	-6:53478168 1114976792 T	
459	1377 T	-6:53478167 1114976791 T	
460 L	1378 C	-6:53478166 1114976790 C	L
460	1379 T	-6:53478165 1114976789 T	
460	1380 C	-6:53478164 1114976788 C	
461 I	1381 A	-6:53478163 1114976787 A	I
461	1382 T	-6:53478162 1114976786 T	
461	1383 T	-6:53478161 1114976785 T	
462 P	1384 C	-6:53478160 1114976784 C	P
462	1385 C	-6:53478159 1114976783 C	
462	1386 A	-6:53478158 1114976782 A	
463 L	1387 C	-6:53478157 1114976781 C	L
463	1388 T	-6:53478156 1114976780 T	
463	1389 G	-6:53478155 1114976779 G	
464 S	1390 T	-6:53478154 1114976778 T	S
464	1391 C	-6:53478153 1114976777 C	
464	1392 A	-6:53478152 1114976776 A	
465 K	1393 A	-6:53478151 1114976775 A	K
465	1394 A	-6:53478150 1114976774 A	
465	1395 G	-6:53478149 1114976773 G	
466 V	1396 G	-6:53473270 1114971894 G	V
466	1397 T	-6:53473269 1114971893 T	
466	1398 T	-6:53473268 1114971892 T	
467 D	1399 G	-6:53473267 1114971891 G	D
467	1400 A	-6:53473266 1114971890 A	
467	1401 T	-6:53473265 1114971889 T	
468 E	1402 G	-6:53473264 1114971888 G	E
468	1403 A	-6:53473263 1114971887 A	
468	1404 G	-6:53473262 1114971886 G	
469 N	1405 A	-6:53473261 1114971885 A	N
469	1406 A	-6:53473260 1114971884 A	
469	1407 C	-6:53473259 1114971883 C	
470 M	1408 A	-6:53473258 1114971882 A	M
470	1409 T	-6:53473257 1114971881 T	
470	1410 G	-6:53473256 1114971880 G	
471 K	1411 A	-6:53473255 1114971879 A	K
471	1412 A	-6:53473254 1114971878 A	
471	1413 G	-6:53473253 1114971877 G	
472 V	1414 G	-6:53473252 1114971876 G	V
472	1415 T	-6:53473251 1114971875 T	
472	1416 A	-6:53473250 1114971874 A	
473 A	1417 G	-6:53473249 1114971873 G	A
473	1418 C	-6:53473248 1114971872 C	
473	1419 A	-6:53473247 1114971871 A	
474 Q	1420 C	-6:53473246 1114971870 C	Q
474	1421 A	-6:53473245 1114971869 A	
474	1422 G	-6:53473244 1114971868 G	
475 K	1423 A	-6:53473243 1114971867 A	K
475	1424 A	-6:53473242 1114971866 A	
475	1425 A	-6:53473241 1114971865 A	
476 R	1426 A	-6:53473240 1114971864 A	R
476	1427 G	-6:53473239 1114971863 G	
476	1428 A	-6:53473238 1114971862 A	
477 D	1429 G	-6:53473237 1114971861 G	D
477	1430 A	-6:53473236 1114971860 A	
477	1431 T	-6:53473235 1114971859 T	
478 A	1432 G	-6:53473234 1114971858 G	A
478	1433 C	-6:53473233 1114971857 C	
478	1434 T	-6:53473232 1114971856 T	
479 V	1435 G	-6:53473231 1114971855 G	V
479	1436 T	-6:53473230 1114971854 T	
479	1437 C	-6:53473229 1114971853 C	
480 L	1438 T	-6:53473228 1114971852 T	L
480	1439 T	-6:53473227 1114971851 T	
480	1440 G	-6:53473226 1114971850 G	
481 Q	1441 C	-6:53473225 1114971849 C	Q
481	1442 A	-6:53473224 1114971848 A	
481	1443 G	-6:53473223 1114971847 G	
482 G	1444 G	-6:53473222 1114971846 G	G
482	1445 G	-6:53473221 1114971845 G	
482	1446 A	-6:53473220 1114971844 A	
483 M	1447 A	-6:53473219 1114971843 A	M
483	1448 T	-6:53473218 1114971842 T	
483	1449 G	-6:53473217 1114971841 G	
484 F	1450 T	-6:53473216 1114971840 T	F
484	1451 T	-6:53473215 1114971839 T	
484	1452 T	-6:53473214 1114971838 T	
485 Y	1453 T	-6:53473213 1114971837 T	Y
485	1454 A	-6:53473212 1114971836 A	
485	1455 T	-6:53473211 1114971835 T	
486 F	1456 T	-6:53473210 1114971834 T	F
486	1457 T	-6:53473209 1114971833 T	
486	1458 C	-6:53473208 1114971832 C	
487 R	1459 A	-6:53473207 1114971831 A	R
487	1460 G	-6:53473206 1114971830 G	
487	1461 G	-6:53473205 1114971829 G	
488 K	1462 A	-6:53473204 1114971828 A	K
488	1463 A	-6:53473203 1114971827 A	
488	1464 A	-6:53473202 1114971826 A	
489 D	1465 G	-6:53473201 1114971825 G	D
489	1466 A	-6:53473200 1114971824 A	
489	1467 T	-6:53473199 1114971823 T	
490 I	1468 A	-6:53473198 1114971822 A	I
490	1469 T	-6:53473197 1114971821 T	
490	1470 T	-6:53473196 1114971820 T	
491 C	1471 T	-6:53473195 1114971819 T	C
491	1472 G	-6:53473194 1114971818 G	
491	1473 C	-6:53473193 1114971817 C	
492 K	1474 A	-6:53473192 1114971816 A	K
492	1475 A	-6:53473191 1114971815 A	
492	1476 A	-6:53473190 1114971814 A	
493 G	1477 G	-6:53473189 1114971813 G	G
493	1478 G	-6:53473107 1114971731 G	
493	1479 T	-6:53473106 1114971730 T	
494 G	1480 G	-6:53473105 1114971729 G	G
494	1481 G	-6:53473104 1114971728 G	
494	1482 C	-6:53473103 1114971727 C	
495 N	1483 A	-6:53473102 1114971726 A	N
495	1484 A	-6:53473101 1114971725 A	
495	1485 T	-6:53473100 1114971724 T	
496 A	1486 G	-6:53473099 1114971723 G	A
496	1487 C	-6:53473098 1114971722 C	
496	1488 A	-6:53473097 1114971721 A	
497 V	1489 G	-6:53473096 1114971720 G	V
497	1490 T	-6:53473095 1114971719 T	
497	1491 G	-6:53473094 1114971718 G	
498 V	1492 G	-6:53473093 1114971717 G	V
498	1493 T	-6:53473092 1114971716 T	
498	1494 G	-6:53473091 1114971715 G	
499 D	1495 G	-6:53473090 1114971714 G	D
499	1496 A	-6:53473089 1114971713 A	
499	1497 T	-6:53473088 1114971712 T	
500 G	1498 G	-6:53473087 1114971711 G	G
500	1499 G	-6:53473086 1114971710 G	
500	1500 T	-6:53473085 1114971709 T	
501 C	1501 T	-6:53473084 1114971708 T	C
501	1502 G	-6:53473083 1114971707 G	
501	1503 T	-6:53473082 1114971706 T	
502 G	1504 G	-6:53473081 1114971705 G	G
502	1505 G	-6:53473080 1114971704 G	
502	1506 C	-6:53473079 1114971703 C	
503 K	1507 A	-6:53473078 1114971702 A	K
503	1508 A	-6:53473077 1114971701 A	
503	1509 G	-6:53473076 1114971700 G	
504 A	1510 G	-6:53473075 1114971699 G	A
504	1511 C	-6:53473074 1114971698 C	
504	1512 C	-6:53473073 1114971697 C	
505 Q	1513 C	-6:53473072 1114971696 C	Q
505	1514 A	-6:53473071 1114971695 A	
505	1515 G	-6:53473070 1114971694 G	
506 N	1516 A	-6:53473069 1114971693 A	N
506	1517 A	-6:53473068 1114971692 A	
506	1518 C	-6:53473067 1114971691 C	
507 S	1519 A	-6:53473066 1114971690 A	S
507	1520 G	-6:53473065 1114971689 G	
507	1521 C	-6:53473064 1114971688 C	
508 T	1522 A	-6:53473063 1114971687 A	T
508	1523 C	-6:53473062 1114971686 C	
508	1524 G	-6:53473061 1114971685 G	
509 E	1525 G	-6:53473060 1114971684 G	E
509	1526 A	-6:53473059 1114971683 A	
509	1527 G	-6:53473058 1114971682 G	
510 L	1528 C	-6:53473057 1114971681 C	L
510	1529 T	-6:53473056 1114971680 T	
510	1530 C	-6:53473055 1114971679 C	
511 A	1531 G	-6:53473054 1114971678 G	A
511	1532 C	-6:53473053 1114971677 C	
511	1533 T	-6:53473052 1114971676 T	
512 A	1534 G	-6:53473051 1114971675 G	A
512	1535 C	-6:53473050 1114971674 C	
512	1536 A	-6:53473049 1114971673 A	
513 E	1537 G	-6:53473048 1114971672 G	E
513	1538 A	-6:53473047 1114971671 A	
513	1539 G	-6:53473046 1114971670 G	
514 E	1540 G	-6:53473045 1114971669 G	E
514	1541 A	-6:53473044 1114971668 A	
514	1542 G	-6:53473043 1114971667 G	
515 Y	1543 T	-6:53473042 1114971666 T	Y
515	1544 A	-6:53473041 1114971665 A	
515	1545 C	-6:53473040 1114971664 C	
516 T	1546 A	-6:53473039 1114971663 A	T
516	1547 C	-6:53473038 1114971662 C	
516	1548 C	-6:53473037 1114971661 C	
517 L	1549 C	-6:53473036 1114971660 C	L
517	1550 T	-6:53473035 1114971659 T	
517	1551 C	-6:53473034 1114971658 C	
518 M	1552 A	-6:53473033 1114971657 A	M
518	1553 T	-6:53473032 1114971656 T	
518	1554 G	-6:53473031 1114971655 G	
519 S	1555 A	-6:53473030 1114971654 A	S
519	1556 G	-6:53473029 1114971653 G	
519	1557 C	-6:53473028 1114971652 C	
520 I	1558 A	-6:53473027 1114971651 A	I
520	1559 T	-6:53473026 1114971650 T	
520	1560 A	-6:53473025 1114971649 A	
521 D	1561 G	-6:53473024 1114971648 G	D
521	1562 A	-6:53473023 1114971647 A	
521	1563 C	-6:53473022 1114971646 C	
522 T	1564 A	-6:53473021 1114971645 A	T
522	1565 C	-6:53473020 1114971644 C	
522	1566 C	-6:53473019 1114971643 C	
523 I	1567 A	-6:53473018 1114971642 A	I
523	1568 T	-6:53473017 1114971641 T	
523	1569 C	-6:53473016 1114971640 C	
524 I	1570 A	-6:53473015 1114971639 A	I
524	1571 T	-6:53473014 1114971638 T	
524	1572 C	-6:53473013 1114971637 C	
525 N	1573 A	-6:53473012 1114971636 A	N
525	1574 A	-6:53473011 1114971635 A	
525	1575 T	-6:53473010 1114971634 T	
526 G	1576 G	-6:53473009 1114971633 G	G
526	1577 G	-6:53473008 1114971632 G	
526	1578 G	-6:53473007 1114971631 G	
527 K	1579 A	-6:53473006 1114971630 A	K
527	1580 A	-6:53473005 1114971629 A	
527	1581 G	-6:53473004 1114971628 G	
528 E	1582 G	-6:53472922 1114971546 G	E
528	1583 A	-6:53472921 1114971545 A	
528	1584 A	-6:53472920 1114971544 A	
529 G	1585 G	-6:53472919 1114971543 G	G
529	1586 G	-6:53472918 1114971542 G	
529	1587 T	-6:53472917 1114971541 T	
530 V	1588 G	-6:53472916 1114971540 G	V
530	1589 T	-6:53472915 1114971539 T	
530	1590 G	-6:53472914 1114971538 G	
531 F	1591 T	-6:53472913 1114971537 T	F
531	1592 T	-6:53472912 1114971536 T	
531	1593 T	-6:53472911 1114971535 T	
532 P	1594 C	-6:53472910 1114971534 C	P
532	1595 C	-6:53472909 1114971533 C	
532	1596 T	-6:53472908 1114971532 T	
533 G	1597 G	-6:53472907 1114971531 G	G
533	1598 G	-6:53472906 1114971530 G	
533	1599 A	-6:53472905 1114971529 A	
534 L	1600 C	-6:53472904 1114971528 C	L
534	1601 T	-6:53472903 1114971527 T	
534	1602 G	-6:53472902 1114971526 G	
535 I	1603 A	-6:53472901 1114971525 A	I
535	1604 T	-6:53472900 1114971524 T	
535	1605 C	-6:53472899 1114971523 C	
536 P	1606 C	-6:53472898 1114971522 C	P
536	1607 C	-6:53472897 1114971521 C	
536	1608 A	-6:53472896 1114971520 A	
537 I	1609 A	-6:53472895 1114971519 A	I
537	1610 T	-6:53472894 1114971518 T	
537	1611 T	-6:53472893 1114971517 T	
538 L	1612 C	-6:53472892 1114971516 C	L
538	1613 T	-6:53472891 1114971515 T	
538	1614 G	-6:53472890 1114971514 G	
539 N	1615 A	-6:53472889 1114971513 A	N
539	1616 A	-6:53472888 1114971512 A	
539	1617 C	-6:53472887 1114971511 C	
540 S	1618 T	-6:53472886 1114971510 T	S
540	1619 C	-6:53472885 1114971509 C	
540	1620 T	-6:53472884 1114971508 T	
541 Y	1621 T	-6:53472883 1114971507 T	Y
541	1622 A	-6:53472882 1114971506 A	
541	1623 C	-6:53472881 1114971505 C	
542 L	1624 C	-6:53472880 1114971504 C	L
542	1625 T	-6:53472879 1114971503 T	
542	1626 T	-6:53472878 1114971502 T	
543 E	1627 G	-6:53472877 1114971501 G	E
543	1628 A	-6:53472876 1114971500 A	
543	1629 A	-6:53472875 1114971499 A	
544 N	1630 A	-6:53472874 1114971498 A	N
544	1631 A	-6:53472873 1114971497 A	
544	1632 C	-6:53472872 1114971496 C	
545 M	1633 A	-6:53472871 1114971495 A	M
545	1634 T	-6:53472870 1114971494 T	
545	1635 G	-6:53472869 1114971493 G	
546 E	1636 G	-6:53472868 1114971492 G	E
546	1637 A	-6:53472867 1114971491 A	
546	1638 A	-6:53472866 1114971490 A	
547 V	1639 G	-6:53472865 1114971489 G	V
547	1640 T	-6:53472864 1114971488 T	
547	1641 G	-6:53472863 1114971487 G	
548 D	1642 G	-6:53472862 1114971486 G	D
548	1643 A	-6:53472861 1114971485 A	
548	1644 T	-6:53472860 1114971484 T	
549 V	1645 G	-6:53472859 1114971483 G	V
549	1646 T	-6:53472858 1114971482 T	
549	1647 G	-6:53472857 1114971481 G	
550 D	1648 G	-6:53472856 1114971480 G	D
550	1649 A	-6:53472855 1114971479 A	
550	1650 C	-6:53472854 1114971478 C	
551 T	1651 A	-6:53472853 1114971477 A	T
551	1652 C	-6:53472852 1114971476 C	
551	1653 C	-6:53472851 1114971475 C	
552 R	1654 A	-6:53472850 1114971474 A	R
552	1655 G	-6:53472849 1114971473 G	
552	1656 A	-6:53472848 1114971472 A	
553 C	1657 T	-6:53472847 1114971471 T	C
553	1658 G	-6:53472846 1114971470 G	
553	1659 T	-6:53472845 1114971469 T	
554 S	1660 A	-6:53472844 1114971468 A	S
554	1661 G	-6:53472843 1114971467 G	
554	1662 T	-6:53472842 1114971466 T	
555 I	1663 A	-6:53472841 1114971465 A	I
555	1664 T	-6:53472840 1114971464 T	
555	1665 T	-6:53472839 1114971463 T	
556 L	1666 C	-6:53472838 1114971462 C	L
556	1667 T	-6:53472837 1114971461 T	
556	1668 G	-6:53472836 1114971460 G	
557 N	1669 A	-6:53472835 1114971459 A	N
557	1670 A	-6:53472834 1114971458 A	
557	1671 C	-6:53472833 1114971457 C	
558 Y	1672 T	-6:53472832 1114971456 T	Y
558	1673 A	-6:53472831 1114971455 A	
558	1674 C	-6:53472830 1114971454 C	
559 L	1675 C	-6:53472829 1114971453 C	L
559	1676 T	-6:53472828 1114971452 T	
559	1677 A	-6:53472827 1114971451 A	
560 K	1678 A	-6:53472826 1114971450 A	K
560	1679 A	-6:53472825 1114971449 A	
560	1680 G	-6:53472824 1114971448 G	
561 L	1681 C	-6:53472823 1114971447 C	L
561	1682 T	-6:53472822 1114971446 T	
561	1683 A	-6:53472821 1114971445 A	
562 I	1684 A	-6:53472820 1114971444 A	I
562	1685 T	-6:53472819 1114971443 T	
562	1686 T	-6:53472818 1114971442 T	
563 K	1687 A	-6:53472817 1114971441 A	K
563	1688 A	-6:53472816 1114971440 A	
563	1689 G	-6:53472815 1114971439 G	
564 K	1690 A	-6:53472814 1114971438 A	K
564	1691 A	-6:53472813 1114971437 A	
564	1692 G	-6:53472812 1114971436 G	
565 R	1693 A	-6:53472811 1114971435 A	R
565	1694 G	-6:53472810 1114971434 G	
565	1695 A	-6:53472809 1114971433 A	
566 A	1696 G	-6:53472808 1114971432 G	A
566	1697 C	-6:53472807 1114971431 C	
566	1698 A	-6:53472806 1114971430 A	
567 S	1699 T	-6:53472805 1114971429 T	S
567	1700 C	-6:53472804 1114971428 C	
567	1701 T	-6:53472803 1114971427 T	
>ENSP00000229418 
26 V	76 G	+6:41159763 1102658387 G	V
26	77 T	+6:41159764 1102658388 T	
26	78 C	+6:41159765 1102658389 C	
27 Q	79 C	+6:41159766 1102658390 C	Q
27	80 A	+6:41159767 1102658391 A	
27	81 A	+6:41159768 1102658392 A	
28 G	82 G	+6:41159769 1102658393 G	G
28	83 G	+6:41159770 1102658394 G	
28	84 G	+6:41159771 1102658395 G	
29 Q	85 C	+6:41159772 1102658396 C	Q
29	86 A	+6:41159773 1102658397 A	
29	87 G	+6:41159774 1102658398 G	
30 P	88 C	+6:41159775 1102658399 C	P
30	89 C	+6:41159776 1102658400 C	
30	90 A	+6:41159777 1102658401 A	
31 L	91 T	+6:41159778 1102658402 T	L
31	92 T	+6:41159779 1102658403 T	
31	93 A	+6:41159780 1102658404 A	
32 M	94 A	+6:41159781 1102658405 A	M
32	95 T	+6:41159782 1102658406 T	
32	96 G	+6:41159783 1102658407 G	
33 V	97 G	+6:41159784 1102658408 G	V
33	98 T	+6:41159785 1102658409 T	
33	99 G	+6:41159786 1102658410 G	
34 Q	100 C	+6:41159787 1102658411 C	Q
34	101 A	+6:41159788 1102658412 A	
34	102 G	+6:41159789 1102658413 G	
35 V	103 G	+6:41159790 1102658414 G	V
35	104 T	+6:41159791 1102658415 T	
35	105 C	+6:41159792 1102658416 C	
36 S	106 A	+6:41159793 1102658417 A	S
36	107 G	+6:41159794 1102658418 G	
36	108 T	+6:41159795 1102658419 T	
37 G	109 G	+6:41159796 1102658420 G	G
37	110 G	+6:41159797 1102658421 G	
37	111 A	+6:41159798 1102658422 A	
38 G	112 G	+6:41159799 1102658423 G	G
38	113 G	+6:41159800 1102658424 G	
38	114 C	+6:41159801 1102658425 C	
39 Q	115 C	+6:41159802 1102658426 C	Q
39	116 A	+6:41159803 1102658427 A	
39	117 G	+6:41159804 1102658428 G	
40 L	118 C	+6:41159805 1102658429 C	L
40	119 T	+6:41159806 1102658430 T	
40	120 A	+6:41159807 1102658431 A	
41 I	121 A	+6:41159808 1102658432 A	I
41	122 T	+6:41159809 1102658433 T	
41	123 C	+6:41159810 1102658434 C	
42 T	124 A	+6:41159811 1102658435 A	T
42	125 C	+6:41159812 1102658436 C	
42	126 A	+6:41159813 1102658437 A	
43 S	127 T	+6:41159814 1102658438 T	S
43	128 C	+6:41159815 1102658439 C	
43	129 A	+6:41159816 1102658440 A	
44 T	130 A	+6:41159817 1102658441 A	T
44	131 C	+6:41159818 1102658442 C	
44	132 T	+6:41159819 1102658443 T	
45 G	133 G	+6:41159820 1102658444 G	G
45	134 G	+6:41159821 1102658445 G	
45	135 C	+6:41159822 1102658446 C	
46 Q	136 C	+6:41159823 1102658447 C	Q
46	137 A	+6:41159824 1102658448 A	
46	138 A	+6:41159825 1102658449 A	
47 P	139 C	+6:41159826 1102658450 C	P
47	140 C	+6:41159827 1102658451 C	
47	141 C	+6:41159828 1102658452 C	
48 I	142 A	+6:41159829 1102658453 A	I
48	143 T	+6:41159830 1102658454 T	
48	144 C	+6:41159831 1102658455 C	
49 M	145 A	+6:41159832 1102658456 A	M
49	146 T	+6:41159833 1102658457 T	
49	147 G	+6:41159834 1102658458 G	
50 V	148 G	+6:41159835 1102658459 G	V
50	149 T	+6:41159836 1102658460 T	
50	150 C	+6:41159837 1102658461 C	
51 Q	151 C	+6:41159838 1102658462 C	Q
51	152 A	+6:41159839 1102658463 A	
51	153 G	+6:41159840 1102658464 G	
52 A	154 G	+6:41159841 1102658465 G	A
52	155 C	+6:41159842 1102658466 C	
52	156 T	+6:41159843 1102658467 T	
53 V	157 G	+6:41159844 1102658468 G	V
53	158 T	+6:41159845 1102658469 T	
53	159 C	+6:41159846 1102658470 C	
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>ENSP00000345702 
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305 R	913 C	+6:41170137 1102668761 C	R
305	914 G	+6:41170138 1102668762 G	
305	915 T	+6:41170139 1102668763 T	
306 H	916 C	+6:41170140 1102668764 C	H
306	917 A	+6:41170141 1102668765 A	
306	918 T	+6:41170142 1102668766 T	
307 A	919 G	+6:41170143 1102668767 G	A
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308 M	922 A	+6:41170146 1102668770 A	M
308	923 T	+6:41170147 1102668771 T	
308	924 G	+6:41170148 1102668772 G	
309 A	925 G	+6:41170149 1102668773 G	A
309	926 C	+6:41170150 1102668774 C	
309	927 A	+6:41170151 1102668775 A	
310 R	928 C	+6:41170152 1102668776 C	R
310	929 G	+6:41170153 1102668777 G	
310	930 G	+6:41170154 1102668778 G	
311 K	931 A	+6:41170155 1102668779 A	K
311	932 A	+6:41170156 1102668780 A	
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312 R	934 C	+6:41170158 1102668782 C	R
312	935 G	+6:41170159 1102668783 G	
312	936 T	+6:41170160 1102668784 T	
313 G	937 G	+6:41170161 1102668785 G	G
313	938 G	+6:41170162 1102668786 G	
313	939 T	+6:41170163 1102668787 T	
314 E	940 G	+6:41170164 1102668788 G	E
314	941 A	+6:41170165 1102668789 A	
314	942 A	+6:41170166 1102668790 A	
315 G	943 G	+6:41170167 1102668791 G	G
315	944 G	+6:41170168 1102668792 G	
315	945 T	+6:41170169 1102668793 T	
316 G	946 G	+6:41170170 1102668794 G	G
316	947 G	+6:41170171 1102668795 G	
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317 R	949 C	+6:41170173 1102668797 C	R
317	950 G	+6:41170174 1102668798 G	
317	951 A	+6:41170175 1102668799 A	
318 F	952 T	+6:41170176 1102668800 T	F
318	953 T	+6:41170177 1102668801 T	
318	954 T	+6:41170178 1102668802 T	
319 F	955 T	+6:41170179 1102668803 T	F
319	956 T	+6:41170180 1102668804 T	
319	957 C	+6:41170181 1102668805 C	
320 S	958 T	+6:41170182 1102668806 T	S
320	959 C	+6:41170183 1102668807 C	
320	960 T	+6:41170184 1102668808 T	
321 P	961 C	+6:41170185 1102668809 C	P
321	962 C	+6:41170186 1102668810 C	
321	963 A	+6:41170187 1102668811 A	
322 K	964 A	+6:41170188 1102668812 A	K
322	965 A	+6:41170189 1102668813 A	
322	966 G	+6:41170190 1102668814 G	
323 E	967 G	+6:41170191 1102668815 G	E
323	968 A	+6:41170192 1102668816 A	
323	969 A	+6:41170193 1102668817 A	
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325 D	973 G	+6:41170197 1102668821 G	D
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326 S	976 A	+6:41170200 1102668824 A	S
326	977 G	+6:41170201 1102668825 G	
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327	980 C	+6:41170204 1102668828 C	
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329 M	985 A	+6:41170209 1102668833 A	M
329	986 T	+6:41170210 1102668834 T	
329	987 G	+6:41170211 1102668835 G	
330 Q	988 C	+6:41170212 1102668836 C	Q
330	989 A	+6:41170213 1102668837 A	
330	990 G	+6:41170214 1102668838 G	
331 D	991 G	+6:41173074 1102671698 G	D
331	992 A	+6:41173075 1102671699 A	
331	993 T	+6:41173076 1102671700 T	
332 P	994 C	+6:41173077 1102671701 C	P
332	995 C	+6:41173078 1102671702 C	
332	996 A	+6:41173079 1102671703 A	
333 N	997 A	+6:41173080 1102671704 A	N
333	998 A	+6:41173081 1102671705 A	
333	999 C	+6:41173082 1102671706 C	
334 Q	1000 C	+6:41173083 1102671707 C	Q
334	1001 A	+6:41173084 1102671708 A	
334	1002 A	+6:41173085 1102671709 A	
335 A	1003 G	+6:41173086 1102671710 G	A
335	1004 C	+6:41173087 1102671711 C	
335	1005 C	+6:41173088 1102671712 C	
336 D	1006 G	+6:41173089 1102671713 G	D
336	1007 A	+6:41173090 1102671714 A	
336	1008 T	+6:41173091 1102671715 T	
337 E	1009 G	+6:41173092 1102671716 G	E
337	1010 A	+6:41173093 1102671717 A	
337	1011 A	+6:41173094 1102671718 A	
338 E	1012 G	+6:41173095 1102671719 G	E
338	1013 A	+6:41173096 1102671720 A	
338	1014 A	+6:41173097 1102671721 A	
339 A	1015 G	+6:41173098 1102671722 G	A
339	1016 C	+6:41173099 1102671723 C	
339	1017 A	+6:41173100 1102671724 A	
340 M	1018 A	+6:41173101 1102671725 A	M
340	1019 T	+6:41173102 1102671726 T	
340	1020 G	+6:41173103 1102671727 G	
341 T	1021 A	+6:41173104 1102671728 A	T
341	1022 C	+6:41173105 1102671729 C	
341	1023 A	+6:41173106 1102671730 A	
342 Q	1024 C	+6:41173107 1102671731 C	Q
342	1025 A	+6:41173108 1102671732 A	
342	1026 G	+6:41173109 1102671733 G	
343 I	1027 A	+6:41173110 1102671734 A	I
343	1028 T	+6:41173111 1102671735 T	
343	1029 C	+6:41173112 1102671736 C	
344 I	1030 A	+6:41173113 1102671737 A	I
344	1031 T	+6:41173114 1102671738 T	
344	1032 C	+6:41173115 1102671739 C	
345 R	1033 C	+6:41173116 1102671740 C	R
345	1034 G	+6:41173117 1102671741 G	
345	1035 A	+6:41173118 1102671742 A	
346 V	1036 G	+6:41173119 1102671743 G	V
346	1037 T	+6:41173120 1102671744 T	
346	1038 G	+6:41173121 1102671745 G	
347 S	1039 T	+6:41173122 1102671746 T	S
347	1040 C	+6:41173123 1102671747 C	
347	1041 C	+6:41173124 1102671748 C	
>ENSP00000382856 
1 M	1 A	-1:24578795 24578795 A	M
1	2 T	-1:24578794 24578794 T	
1	3 G	-1:24578793 24578793 G	
2 F	4 T	-1:24578792 24578792 T	F
2	5 T	-1:24578791 24578791 T	
2	6 C	-1:24578790 24578790 C	
3 Q	7 C	-1:24578789 24578789 C	Q
3	8 A	-1:24578788 24578788 A	
3	9 G	-1:24578787 24578787 G	
4 L	10 T	-1:24578786 24578786 T	L
4	11 T	-1:24578785 24578785 T	
4	12 G	-1:24578784 24578784 G	
5 P	13 C	-1:24578783 24578783 C	P
5	14 C	-1:24578782 24578782 C	
5	15 A	-1:24578781 24578781 A	
6 S	16 A	-1:24578780 24578780 A	S
6	17 G	-1:24578779 24578779 G	
6	18 C	-1:24578778 24578778 C	
7 F	19 T	-1:24578777 24578777 T	F
7	20 T	-1:24578776 24578776 T	
7	21 T	-1:24578775 24578775 T	
8 M	22 A	-1:24578774 24578774 A	M
8	23 T	-1:24578773 24578773 T	
8	24 G	-1:24578772 24578772 G	
9 K	25 A	-1:24578771 24578771 A	K
9	26 A	-1:24578770 24578770 A	
9	27 A	-1:24578769 24578769 A	
10 A	28 G	-1:24578768 24578768 G	A
10	29 C	-1:24578767 24578767 C	
10	30 T	-1:24578766 24578766 T	
11 L	31 C	-1:24578765 24578765 C	L
11	32 T	-1:24578764 24578764 T	
11	33 C	-1:24578763 24578763 C	
12 K	34 A	-1:24578762 24578762 A	K
12	35 A	-1:24578761 24578761 A	
12	36 G	-1:24578760 24578760 G	
13 F	37 T	-1:24578759 24578759 T	F
13	38 T	-1:24578758 24578758 T	
13	39 T	-1:24578757 24578757 T	
14 E	40 G	-1:24578756 24578756 G	E
14	41 A	-1:24578755 24578755 A	
14	42 A	-1:24578754 24578754 A	
15 T	43 A	-1:24578753 24578753 A	T
15	44 C	-1:24578752 24578752 C	
15	45 T	-1:24578751 24578751 T	
16 P	46 C	-1:24578750 24578750 C	P
16	47 C	-1:24578749 24578749 C	
16	48 T	-1:24578748 24578748 T	
17 A	49 G	-1:24578747 24578747 G	A
17	50 C	-1:24578746 24578746 C	
17	51 A	-1:24578745 24578745 A	
18 P	52 C	-1:24578744 24578744 C	P
18	53 C	-1:24578743 24578743 C	
18	54 A	-1:24578742 24578742 A	
19 N	55 A	-1:24578741 24578741 A	N
19	56 A	-1:24578740 24578740 A	
19	57 C	-1:24578739 24578739 C	
20 Y	58 T	-1:24578738 24578738 T	Y
20	59 A	-1:24578737 24578737 A	
20	60 T	-1:24578736 24578736 T	
21 Y	61 T	-1:24578735 24578735 T	Y
21	62 A	-1:24578734 24578734 A	
21	63 C	-1:24578733 24578733 C	
22 N	64 A	-1:24578732 24578732 A	N
22	65 A	-1:24578731 24578731 A	
22	66 T	-1:24578730 24578730 T	
23 A	67 G	-1:24572887 24572887 G	A
23	68 C	-1:24572886 24572886 C	
23	69 C	-1:24572885 24572885 C	
24 S	70 T	-1:24572884 24572884 T	S
24	71 C	-1:24572883 24572883 C	
24	72 T	-1:24572882 24572882 T	
25 V	73 G	-1:24572881 24572881 G	V
25	74 T	-1:24572880 24572880 T	
25	75 C	-1:24572879 24572879 C	
26 S	76 T	-1:24572878 24572878 T	S
26	77 C	-1:24572877 24572877 C	
26	78 T	-1:24572876 24572876 T	
27 C	79 T	-1:24572875 24572875 T	C
27	80 G	-1:24572874 24572874 G	
27	81 C	-1:24572873 24572873 C	
28 C	82 T	-1:24572872 24572872 T	C
28	83 G	-1:24572871 24572871 G	
28	84 C	-1:24572870 24572870 C	
29 K	85 A	-1:24572869 24572869 A	K
29	86 A	-1:24572868 24572868 A	
29	87 G	-1:24572867 24572867 G	
30 Q	88 C	-1:24572866 24572866 C	Q
30	89 A	-1:24572865 24572865 A	
30	90 G	-1:24572864 24572864 G	
31 R	91 A	-1:24572863 24572863 A	R
31	92 G	-1:24572862 24572862 G	
31	93 A	-1:24572861 24572861 A	
32 N	94 A	-1:24572860 24572860 A	N
32	95 A	-1:24572859 24572859 A	
32	96 C	-1:24572858 24572858 C	
33 N	97 A	-1:24572857 24572857 A	N
33	98 A	-1:24572856 24572856 A	
33	99 C	-1:24572855 24572855 C	
34 V	100 G	-1:24572854 24572854 G	V
34	101 T	-1:24572853 24572853 T	
34	102 C	-1:24572852 24572852 C	
35 C	103 T	-1:24572851 24572851 T	C
35	104 G	-1:24572850 24572850 G	
35	105 T	-1:24572849 24572849 T	
36 T	106 A	-1:24572848 24572848 A	T
36	107 C	-1:24572847 24572847 C	
36	108 T	-1:24572846 24572846 T	
37 R	109 C	-1:24572845 24572845 C	R
37	110 G	-1:24572844 24572844 G	
37	111 A	-1:24572843 24572843 A	
38 A	112 G	-1:24572842 24572842 G	A
38	113 C	-1:24572841 24572841 C	
38	114 C	-1:24572840 24572840 C	
39 G	115 G	-1:24572839 24572839 G	G
39	116 G	-1:24572838 24572838 G	
39	117 G	-1:24572837 24572837 G	
40 F	118 T	-1:24572836 24572836 T	F
40	119 T	-1:24572835 24572835 T	
40	120 T	-1:24572834 24572834 T	
41 M	121 A	-1:24572833 24572833 A	M
41	122 T	-1:24572832 24572832 T	
41	123 G	-1:24572831 24572831 G	
42 S	124 T	-1:24572830 24572830 T	S
42	125 C	-1:24572829 24572829 C	
42	126 A	-1:24572828 24572828 A	
43 K	127 A	-1:24572827 24572827 A	K
43	128 A	-1:24572826 24572826 A	
43	129 A	-1:24572825 24572825 A	
44 T	130 A	-1:24572824 24572824 A	T
44	131 C	-1:24572823 24572823 C	
44	132 C	-1:24572822 24572822 C	
45 Q	133 C	-1:24572821 24572821 C	Q
45	134 A	-1:24572820 24572820 A	
45	135 A	-1:24572819 24572819 A	
46 R	136 A	-1:24572818 24572818 A	R
46	137 G	-1:24572817 24572817 G	
46	138 A	-1:24572816 24572816 A	
47 G	139 G	-1:24572815 24572815 G	G
47	140 G	-1:24572814 24572814 G	
47	141 A	-1:24572813 24572813 A	
48 S	142 T	-1:24572812 24572812 T	S
48	143 C	-1:24572811 24572811 C	
48	144 T	-1:24572810 24572810 T	
49 F	145 T	-1:24572809 24572809 T	F
49	146 T	-1:24572808 24572808 T	
49	147 C	-1:24572807 24572807 C	
50 A	148 G	-1:24572806 24572806 G	A
50	149 C	-1:24572805 24572805 C	
50	150 T	-1:24572804 24572804 T	
51 F	151 T	-1:24572803 24572803 T	F
51	152 T	-1:24572802 24572802 T	
51	153 T	-1:24572801 24572801 T	
52 A	154 G	-1:24572800 24572800 G	A
52	155 C	-1:24572799 24572799 C	
52	156 T	-1:24572798 24572798 T	
53 D	157 G	-1:24572797 24572797 G	D
53	158 A	-1:24572796 24572796 A	
53	159 T	-1:24572795 24572795 T	
54 K	160 A	-1:24572794 24572794 A	K
54	161 A	-1:24572793 24572793 A	
54	162 A	-1:24572792 24572792 A	
55 G	163 G	-1:24572791 24572791 G	G
55	164 G	-1:24572790 24572790 G	
55	165 A	-1:24572789 24572789 A	
56 P	166 C	-1:24572788 24572788 C	P
56	167 C	-1:24572787 24572787 C	
56	168 T	-1:24572786 24572786 T	
57 P	169 C	-1:24572785 24572785 C	P
57	170 C	-1:24572784 24572784 C	
57	171 C	-1:24572783 24572783 C	
58 P	172 C	-1:24572782 24572782 C	P
58	173 C	-1:24572781 24572781 C	
58	174 A	-1:24572780 24572780 A	
59 G	175 G	-1:24572779 24572779 G	G
59	176 G	-1:24568916 24568916 G	
59	177 G	-1:24568915 24568915 G	
60 H	178 C	-1:24568914 24568914 C	H
60	179 A	-1:24568913 24568913 A	
60	180 T	-1:24568912 24568912 T	
61 Y	181 T	-1:24568911 24568911 T	Y
61	182 A	-1:24568910 24568910 A	
61	183 T	-1:24568909 24568909 T	
62 D	184 G	-1:24568908 24568908 G	D
62	185 A	-1:24568907 24568907 A	
62	186 T	-1:24568906 24568906 T	
63 I	187 A	-1:24568905 24568905 A	I
63	188 T	-1:24568904 24568904 T	
63	189 C	-1:24568903 24568903 C	
64 N	190 A	-1:24568902 24568902 A	N
64	191 A	-1:24568901 24568901 A	
64	192 C	-1:24568900 24568900 C	
65 E	193 G	-1:24568899 24568899 G	E
65	194 A	-1:24568898 24568898 A	
65	195 A	-1:24568897 24568897 A	
66 S	196 T	-1:24568896 24568896 T	S
66	197 C	-1:24568895 24568895 C	
66	198 C	-1:24568894 24568894 C	
67 L	199 C	-1:24568893 24568893 C	L
67	200 T	-1:24568892 24568892 T	
67	201 T	-1:24568891 24568891 T	
68 V	202 G	-1:24568890 24568890 G	V
68	203 T	-1:24568889 24568889 T	
68	204 G	-1:24568888 24568888 G	
69 K	205 A	-1:24568887 24568887 A	K
69	206 A	-1:24568886 24568886 A	
69	207 G	-1:24568885 24568885 G	
70 Q	208 C	-1:24568884 24568884 C	Q
70	209 A	-1:24568883 24568883 A	
70	210 G	-1:24568882 24568882 G	
71 S	211 T	-1:24568881 24568881 T	S
71	212 C	-1:24568880 24568880 C	
71	213 G	-1:24568879 24568879 G	
72 P	214 C	-1:24568878 24568878 C	P
72	215 C	-1:24568877 24568877 C	
72	216 A	-1:24568876 24568876 A	
73 N	217 A	-1:24568875 24568875 A	N
73	218 A	-1:24568874 24568874 A	
73	219 T	-1:24568873 24568873 T	
74 T	220 A	-1:24568872 24568872 A	T
74	221 C	-1:24568871 24568871 C	
74	222 A	-1:24568870 24568870 A	
75 L	223 T	-1:24568869 24568869 T	L
75	224 T	-1:24568868 24568868 T	
75	225 A	-1:24568867 24568867 A	
76 M	226 A	-1:24568866 24568866 A	M
76	227 T	-1:24568865 24568865 T	
76	228 G	-1:24568864 24568864 G	
77 S	229 T	-1:24568863 24568863 T	S
77	230 C	-1:24568862 24568862 C	
77	231 T	-1:24568861 24568861 T	
78 C	232 T	-1:24568860 24568860 T	C
78	233 G	-1:24568859 24568859 G	
78	234 T	-1:24568858 24568858 T	
79 F	235 T	-1:24568857 24568857 T	F
79	236 T	-1:24568856 24568856 T	
79	237 T	-1:24568855 24568855 T	
80 K	238 A	-1:24568854 24568854 A	K
80	239 A	-1:24568853 24568853 A	
80	240 A	-1:24568852 24568852 A	
81 S	241 T	-1:24568851 24568851 T	S
81	242 C	-1:24568850 24568850 C	
81	243 A	-1:24568849 24568849 A	
82 K	244 A	-1:24568848 24568848 A	K
82	245 A	-1:24568847 24568847 A	
82	246 A	-1:24568846 24568846 A	
83 T	247 A	-1:24568845 24568845 A	T
83	248 C	-1:24568844 24568844 C	
83	249 C	-1:24568843 24568843 C	
84 N	250 A	-1:24568842 24568842 A	N
84	251 A	-1:24568841 24568841 A	
84	252 C	-1:24568840 24568840 C	
85 R	253 C	-1:24568839 24568839 C	R
85	254 G	-1:24568838 24568838 G	
85	255 T	-1:24568837 24568837 T	
86 G	256 G	-1:24568836 24568836 G	G
86	257 G	-1:24568835 24568835 G	
86	258 A	-1:24568834 24568834 A	
87 L	259 T	-1:24568833 24568833 T	L
87	260 T	-1:24568832 24568832 T	
87	261 A	-1:24568831 24568831 A	
88 K	262 A	-1:24568830 24568830 A	K
88	263 A	-1:24568829 24568829 A	
88	264 A	-1:24568828 24568828 A	
89 L	265 C	-1:24568827 24568827 C	L
89	266 T	-1:24568826 24568826 T	
89	267 G	-1:24568825 24568825 G	
90 T	268 A	-1:24568824 24568824 A	T
90	269 C	-1:24568823 24568823 C	
90	270 G	-1:24568822 24568822 G	
91 S	271 T	-1:24568821 24568821 T	S
91	272 C	-1:24568820 24568820 C	
91	273 A	-1:24568819 24568819 A	
92 T	274 A	-1:24568818 24568818 A	T
92	275 C	-1:24568817 24568817 C	
92	276 A	-1:24568816 24568816 A	
93 G	277 G	-1:24568815 24568815 G	G
93	278 G	-1:24568814 24568814 G	
93	279 C	-1:24568813 24568813 C	
94 P	280 C	-1:24568812 24568812 C	P
94	281 C	-1:24568811 24568811 C	
94	282 G	-1:24568810 24568810 G	
95 G	283 G	-1:24568809 24568809 G	G
95	284 G	-1:24568808 24568808 G	
95	285 A	-1:24568807 24568807 A	
96 P	286 C	-1:24568806 24568806 C	P
96	287 C	-1:24568805 24568805 C	
96	288 T	-1:24568804 24568804 T	
97 G	289 G	-1:24568803 24568803 G	G
97	290 G	-1:24568802 24568802 G	
97	291 T	-1:24568801 24568801 T	
98 Y	292 T	-1:24568800 24568800 T	Y
98	293 A	-1:24568799 24568799 A	
98	294 T	-1:24568798 24568798 T	
99 Y	295 T	-1:24568797 24568797 T	Y
99	296 A	-1:24568796 24568796 A	
99	297 C	-1:24568795 24568795 C	
100 N	298 A	-1:24568794 24568794 A	N
100	299 A	-1:24568793 24568793 A	
100	300 C	-1:24568792 24568792 C	
101 P	301 C	-1:24568791 24568791 C	P
101	302 C	-1:24568790 24568790 C	
101	303 C	-1:24568789 24568789 C	
102 S	304 A	-1:24568788 24568788 A	S
102	305 G	-1:24568787 24568787 G	
102	306 T	-1:24568786 24568786 T	
103 D	307 G	-1:24568785 24568785 G	D
103	308 A	-1:24568784 24568784 A	
103	309 T	-1:24568783 24568783 T	
104 C	310 T	-1:24568782 24568782 T	C
104	311 G	-1:24568781 24568781 G	
104	312 C	-1:24568780 24568780 C	
105 T	313 A	-1:24568779 24568779 A	T
105	314 C	-1:24568778 24568778 C	
105	315 A	-1:24568777 24568777 A	
106 K	316 A	-1:24568776 24568776 A	K
106	317 A	-1:24568775 24568775 A	
106	318 A	-1:24568774 24568774 A	
107 V	319 G	-1:24568773 24568773 G	V
107	320 T	-1:24568772 24568772 T	
107	321 T	-1:24568771 24568771 T	
108 P	322 C	-1:24568770 24568770 C	P
108	323 C	-1:24568769 24568769 C	
108	324 A	-1:24568768 24568768 A	
109 K	325 A	-1:24568767 24568767 A	K
109	326 A	-1:24568766 24568766 A	
109	327 A	-1:24568765 24568765 A	
110 K	328 A	-1:24568764 24568764 A	K
110	329 A	-1:24568763 24568763 A	
110	330 G	-1:24568762 24568762 G	
111 T	331 A	-1:24568761 24568761 A	T
111	332 C	-1:24568760 24568760 C	
111	333 T	-1:24568759 24568759 T	
112 L	334 C	-1:24568758 24568758 C	L
112	335 T	-1:24568757 24568757 T	
112	336 T	-1:24568756 24568756 T	
113 F	337 T	-1:24568755 24568755 T	F
113	338 T	-1:24568754 24568754 T	
113	339 C	-1:24568753 24568753 C	
114 P	340 C	-1:24568752 24568752 C	P
114	341 C	-1:24568751 24568751 C	
114	342 G	-1:24560118 24560118 G	
115 K	343 A	-1:24560117 24560117 A	K
115	344 A	-1:24560116 24560116 A	
115	345 A	-1:24560115 24560115 A	
116 N	346 A	-1:24560114 24560114 A	N
116	347 A	-1:24560113 24560113 A	
116	348 C	-1:24560112 24560112 C	
117 P	349 C	-1:24560111 24560111 C	P
117	350 C	-1:24560110 24560110 C	
117	351 C	-1:24560109 24560109 C	
118 I	352 A	-1:24560108 24560108 A	I
118	353 T	-1:24560107 24560107 T	
118	354 C	-1:24560106 24560106 C	
119 L	355 C	-1:24560105 24560105 C	L
119	356 T	-1:24560104 24560104 T	
119	357 G	-1:24560103 24560103 G	
120 N	358 A	-1:24560102 24560102 A	N
120	359 A	-1:24560101 24560101 A	
120	360 C	-1:24560100 24560100 C	
121 F	361 T	-1:24560099 24560099 T	F
121	362 T	-1:24560098 24560098 T	
121	363 C	-1:24560097 24560097 C	
122 S	364 T	-1:24560096 24560096 T	S
122	365 C	-1:24560095 24560095 C	
122	366 T	-1:24560094 24560094 T	
123 A	367 G	-1:24560093 24560093 G	A
123	368 C	-1:24560092 24560092 C	
123	369 T	-1:24560091 24560091 T	
124 Q	370 C	-1:24560090 24560090 C	Q
124	371 A	-1:24560089 24560089 A	
124	372 G	-1:24560088 24560088 G	
125 P	373 C	-1:24560087 24560087 C	P
125	374 C	-1:24560086 24560086 C	
125	375 T	-1:24560085 24560085 T	
126 S	376 T	-1:24560084 24560084 T	S
126	377 C	-1:24560083 24560083 C	
126	378 G	-1:24560082 24560082 G	
127 P	379 C	-1:24560081 24560081 C	P
127	380 C	-1:24560080 24560080 C	
127	381 T	-1:24560079 24560079 T	
128 L	382 C	-1:24560078 24560078 C	L
128	383 T	-1:24560077 24560077 T	
128	384 G	-1:24560076 24560076 G	
129 P	385 C	-1:24560075 24560075 C	P
129	386 C	-1:24560074 24560074 C	
129	387 T	-1:24560073 24560073 T	
130 P	388 C	-1:24560072 24560072 C	P
130	389 C	-1:24560071 24560071 C	
130	390 G	-1:24560070 24560070 G	
131 K	391 A	-1:24560069 24560069 A	K
131	392 A	-1:24560068 24560068 A	
131	393 G	-1:24560067 24560067 G	
132 P	394 C	-1:24560066 24560066 C	P
132	395 C	-1:24560065 24560065 C	
132	396 A	-1:24560064 24560064 A	
133 P	397 C	-1:24560063 24560063 C	P
133	398 C	-1:24560062 24560062 C	
133	399 T	-1:24560061 24560061 T	
134 F	400 T	-1:24560060 24560060 T	F
134	401 T	-1:24560059 24560059 T	
134	402 C	-1:24560058 24560058 C	
135 P	403 C	-1:24560057 24560057 C	P
135	404 C	-1:24560056 24560056 C	
135	405 A	-1:24560055 24560055 A	
136 G	406 G	-1:24560054 24560054 G	G
136	407 G	-1:24560053 24560053 G	
136	408 T	-1:24560052 24560052 T	
137 P	409 C	-1:24560051 24560051 C	P
137	410 C	-1:24560050 24560050 C	
137	411 T	-1:24560049 24560049 T	
138 G	412 G	-1:24560048 24560048 G	G
138	413 G	-1:24560047 24560047 G	
138	414 T	-1:24560046 24560046 T	
139 Q	415 C	-1:24560045 24560045 C	Q
139	416 A	-1:24560044 24560044 A	
139	417 G	-1:24560043 24560043 G	
140 Y	418 T	-1:24560042 24560042 T	Y
140	419 A	-1:24560041 24560041 A	
140	420 T	-1:24560040 24560040 T	
141 E	421 G	-1:24560039 24560039 G	E
141	422 A	-1:24560038 24560038 A	
141	423 G	-1:24560037 24560037 G	
142 I	424 A	-1:24560036 24560036 A	I
142	425 T	-1:24560035 24560035 T	
142	426 C	-1:24560034 24560034 C	
143 V	427 G	-1:24560033 24560033 G	V
143	428 T	-1:24560032 24560032 T	
143	429 G	-1:24560031 24560031 G	
144 D	430 G	-1:24560030 24560030 G	D
144	431 A	-1:24560029 24560029 A	
144	432 C	-1:24560028 24560028 C	
145 Y	433 T	-1:24560027 24560027 T	Y
145	434 A	-1:24560026 24560026 A	
145	435 C	-1:24560025 24560025 C	
146 L	436 T	-1:24560024 24560024 T	L
146	437 T	-1:24560023 24560023 T	
146	438 A	-1:24560022 24560022 A	
147 G	439 G	-1:24560021 24560021 G	G
147	440 G	-1:24560020 24560020 G	
147	441 C	-1:24560019 24560019 C	
148 P	442 C	-1:24560018 24560018 C	P
148	443 C	-1:24560017 24560017 C	
148	444 C	-1:24560016 24560016 C	
149 R	445 C	-1:24560015 24560015 C	R
149	446 G	-1:24560014 24560014 G	
149	447 C	-1:24560013 24560013 C	
150 K	448 A	-1:24560012 24560012 A	K
150	449 A	-1:24560011 24560011 A	
150	450 G	-1:24560010 24560010 G	
151 H	451 C	-1:24560009 24560009 C	H
151	452 A	-1:24560008 24560008 A	
151	453 T	-1:24560007 24560007 T	
152 F	454 T	-1:24560006 24560006 T	F
152	455 T	-1:24560005 24560005 T	
152	456 C	-1:24560004 24560004 C	
153 I	457 A	-1:24560003 24560003 A	I
153	458 T	-1:24560002 24560002 T	
153	459 C	-1:24560001 24560001 C	
154 S	460 T	-1:24560000 24560000 T	S
154	461 C	-1:24559999 24559999 C	
154	462 T	-1:24559998 24559998 T	
155 S	463 A	-1:24559997 24559997 A	S
155	464 G	-1:24559996 24559996 G	
155	465 T	-1:24559995 24559995 T	
156 A	466 G	-1:24559994 24559994 G	A
156	467 C	-1:24559993 24559993 C	
156	468 A	-1:24559992 24559992 A	
157 S	469 T	-1:24559991 24559991 T	S
157	470 C	-1:24559990 24559990 C	
157	471 A	-1:24559989 24559989 A	
158 F	472 T	-1:24559988 24559988 T	F
158	473 T	-1:24559987 24559987 T	
158	474 C	-1:24559986 24559986 C	
159 V	475 G	-1:24559985 24559985 G	V
159	476 T	-1:24559984 24559984 T	
159	477 G	-1:24559983 24559983 G	
160 S	478 T	-1:24559982 24559982 T	S
160	479 C	-1:24559981 24559981 C	
160	480 C	-1:24559980 24559980 C	
161 N	481 A	-1:24559979 24559979 A	N
161	482 A	-1:24559978 24559978 A	
161	483 T	-1:24559977 24559977 T	
162 T	484 A	-1:24559976 24559976 A	T
162	485 C	-1:24559975 24559975 C	
162	486 C	-1:24559974 24559974 C	
163 S	487 A	-1:24559973 24559973 A	S
163	488 G	-1:24559972 24559972 G	
163	489 C	-1:24559971 24559971 C	
164 R	490 C	-1:24559970 24559970 C	R
164	491 G	-1:24559969 24559969 G	
164	492 G	-1:24559968 24559968 G	
165 W	493 T	-1:24559967 24559967 T	W
165	494 G	-1:24559966 24559966 G	
165	495 G	-1:24559965 24559965 G	
166 T	496 A	-1:24559964 24559964 A	T
166	497 C	-1:24559963 24559963 C	
166	498 A	-1:24559962 24559962 A	
167 A	499 G	-1:24559961 24559961 G	A
167	500 C	-1:24559960 24559960 C	
167	501 G	-1:24559959 24559959 G	
168 A	502 G	-1:24559958 24559958 G	A
168	503 C	-1:24559957 24559957 C	
168	504 G	-1:24559956 24559956 G	
169 P	505 C	-1:24559955 24559955 C	P
169	506 C	-1:24559954 24559954 C	
169	507 G	-1:24559953 24559953 G	
170 P	508 C	-1:24559952 24559952 C	P
170	509 C	-1:24559951 24559951 C	
170	510 T	-1:24559950 24559950 T	
171 Q	511 C	-1:24559949 24559949 C	Q
171	512 A	-1:24559948 24559948 A	
171	513 G	-1:24559947 24559947 G	
172 P	514 C	-1:24559946 24559946 C	P
172	515 C	-1:24559945 24559945 C	
172	516 A	-1:24559944 24559944 A	
173 G	517 G	-1:24559943 24559943 G	G
173	518 G	-1:24559942 24559942 G	
173	519 C	-1:24559941 24559941 C	
174 L	520 C	-1:24559940 24559940 C	L
174	521 T	-1:24559939 24559939 T	
174	522 G	-1:24559938 24559938 G	
175 P	523 C	-1:24559937 24559937 C	P
175	524 C	-1:24559936 24559936 C	
175	525 T	-1:24559935 24559935 T	
176 G	526 G	-1:24559934 24559934 G	G
176	527 G	-1:24559933 24559933 G	
176	528 C	-1:24559932 24559932 C	
177 P	529 C	-1:24559931 24559931 C	P
177	530 C	-1:24559930 24559930 C	
177	531 A	-1:24559929 24559929 A	
178 G	532 G	-1:24559928 24559928 G	G
178	533 G	-1:24559927 24559927 G	
178	534 T	-1:24559926 24559926 T	
179 Q	535 C	-1:24559925 24559925 C	Q
179	536 A	-1:24559924 24559924 A	
179	537 G	-1:24559923 24559923 G	
180 R	538 A	-1:24559922 24559922 A	R
180	539 G	-1:24559921 24559921 G	
180	540 G	-1:24559920 24559920 G	
181 D	541 G	-1:24559919 24559919 A	I
181	542 A	-1:24559918 24559918 T	
181	543 T	-1:24559917 24559917 T	
182 V	544 G	-1:24559448 24559448 G	V
182	545 T	-1:24559447 24559447 T	
182	546 T	-1:24559446 24559446 T	
183 Q	547 C	-1:24559445 24559445 C	Q
183	548 A	-1:24559444 24559444 A	
183	549 G	-1:24559443 24559443 G	
184 A	550 G	-1:24559442 24559442 G	A
184	551 C	-1:24559441 24559441 C	
184	552 A	-1:24559440 24559440 A	
185 I	553 A	-1:24559439 24559439 A	I
185	554 T	-1:24559438 24559438 T	
185	555 T	-1:24559437 24559437 T	
186 L	556 C	-1:24559436 24559436 C	L
186	557 T	-1:24559435 24559435 T	
186	558 C	-1:24559434 24559434 C	
187 M	559 A	-1:24559433 24559433 A	M
187	560 T	-1:24559432 24559432 T	
187	561 G	-1:24559431 24559431 G	
188 P	562 C	-1:24559430 24559430 C	P
188	563 C	-1:24559429 24559429 C	
188	564 T	-1:24559428 24559428 T	
189 Q	565 C	-1:24559427 24559427 C	Q
189	566 A	-1:24559426 24559426 A	
189	567 G	-1:24559425 24559425 G	
190 P	568 C	-1:24559424 24559424 C	P
190	569 C	-1:24559423 24559423 C	
190	570 T	-1:24559422 24559422 T	
191 P	571 C	-1:24559421 24559421 C	P
191	572 C	-1:24559420 24559420 C	
191	573 C	-1:24559419 24559419 C	
192 N	574 A	-1:24559418 24559418 A	K
192	575 A	-1:24559417 24559417 A	
192	576  	-1:24559416 24559416 G	
192	576  	-1:24559415 24559415 T	*
192	576  	-1:24559414 24559414 A	
192	576  	-1:24559413 24559413 G	
192	576  	-1:24559412 24559412 C	
192	576  	-1:24559411 24559411 T	
192	576  	-1:24559410 24559410 G	
192	576  	-1:24559409 24559409 G	
192	576  	-1:24559408 24559408 A	
192	576  	-1:24559407 24559407 A	
192	576  	-1:24559406 24559406 T	
192	576  	-1:24559405 24559405 T	
192	576  	-1:24559404 24559404 A	
192	576  	-1:24559403 24559403 C	
192	576  	-1:24559402 24559402 A	
192	576  	-1:24559401 24559401 G	
192	576  	-1:24559400 24559400 G	
192	576  	-1:24559399 24559399 T	
192	576  	-1:24559398 24559398 A	
192	576  	-1:24559397 24559397 C	
192	576  	-1:24559396 24559396 A	
192	576  	-1:24559395 24559395 T	
192	576  	-1:24559394 24559394 G	
192	576  	-1:24559393 24559393 C	
192	576  	-1:24559392 24559392 C	
192	576  	-1:24559391 24559391 A	
192	576  	-1:24559390 24559390 C	
192	576  	-1:24559389 24559389 C	
192	576  	-1:24559388 24559388 A	
192	576  	-1:24559387 24559387 C	
192	576  	-1:24559386 24559386 A	
192	576  	-1:24559385 24559385 C	
192	576 C	-1:24559384 24559384 C	
193 Q	577 C	-1:24559383 24559383 C	
193	578 A	-1:24559382 24559382 A	
193	579 G	-1:24559381 24559381 G	
194 L	580 C	-1:24559380 24559380 C	
194	581 T	-1:24559379 24559379 T	
194	582 A	-1:24559378 24559378 A	
195 L	583 C	-1:24559377 24559377 C	
195	584 T	-1:24559376 24559376 T	
195	585 T	-1:24559375 24559375 T	
196 F	586 T	-1:24559374 24559374 T	
196	587 T	-1:24559373 24559373 T	
196	588 T	-1:24559372 24559372 T	
197 V	589 G	-1:24559371 24559371 G	
197	590 T	-1:24559370 24559370 T	
197	591 A	-1:24559369 24559369 A	
198 F	592 T	-1:24559368 24559368 T	
198	593 T	-1:24559367 24559367 T	
198	594 T	-1:24559366 24559366 T	
199 L	595 T	-1:24559365 24559365 T	
199	596 T	-1:24559364 24559364 T	
199	597 A	-1:24559363 24559363 A	
200 A	598 G	-1:24559362 24559362 G	
200	599 C	-1:24559361 24559361 C	
200	600 A	-1:24559360 24559360 A	
201 E	601 G	-1:24559359 24559359 G	
201	602 A	-1:24559358 24559358 A	
201	603 G	-1:24559357 24559357 G	
202 T	604 A	-1:24559356 24559356 A	
202	605 C	-1:24559355 24559355 C	
202	606 A	-1:24559354 24559354 A	
203 D	607 G	-1:24559353 24559353 G	
203	608 A	-1:24559352 24559352 A	
203	609 C	-1:24559351 24559351 C	
204 R	610 A	-1:24559350 24559350 A	
204	611 G	-1:24559349 24559349 G	
204	612 G	-1:24559348 24559348 G	
205 G	613 G	-1:24559347 24559347 G	
205	614 G	-1:24559346 24559346 G	
205	615 T	-1:24559345 24559345 T	
206 S	616 T	-1:24559344 24559344 T	
206	617 C	-1:24559343 24559343 C	
206	618 G	-1:24559342 24559342 G	
>ENSP00000003583 
1 M	1 A	-1:24600443 24600443 A	M
1	2 T	-1:24600442 24600442 T	
1	3 G	-1:24600441 24600441 G	
2 N	4 A	-1:24600440 24600440 A	N
2	5 A	-1:24600439 24600439 A	
2	6 C	-1:24600438 24600438 C	
3 A	7 G	-1:24600437 24600437 G	A
3	8 C	-1:24600436 24600436 C	
3	9 A	-1:24600435 24600435 A	
4 L	10 C	-1:24600434 24600434 C	L
4	11 T	-1:24600433 24600433 T	
4	12 G	-1:24600432 24600432 G	
5 A	13 G	-1:24600431 24600431 G	A
5	14 C	-1:24600430 24600430 C	
5	15 A	-1:24600429 24600429 A	
6 N	16 A	-1:24600428 24600428 A	N
6	17 A	-1:24600427 24600427 A	
6	18 C	-1:24600426 24600426 C	
7 I	19 A	-1:24600425 24600425 A	I
7	20 T	-1:24600424 24600424 T	
7	21 C	-1:24600423 24600423 C	
8 P	22 C	-1:24600422 24600422 C	P
8	23 C	-1:24600421 24600421 C	
8	24 A	-1:24600420 24600420 A	
9 D	25 G	-1:24600419 24600419 G	D
9	26 A	-1:24600418 24600418 A	
9	27 C	-1:24600417 24600417 C	
10 V	28 G	-1:24600416 24600416 G	V
10	29 T	-1:24600415 24600415 T	
10	30 G	-1:24600414 24600414 G	
11 P	31 C	-1:24600413 24600413 C	P
11	32 C	-1:24600412 24600412 C	
11	33 A	-1:24600411 24600411 A	
12 V	34 G	-1:24600410 24600410 G	V
12	35 T	-1:24600409 24600409 T	
12	36 G	-1:24600408 24600408 G	
13 K	37 A	-1:24600407 24600407 A	K
13	38 A	-1:24600406 24600406 A	
13	39 G	-1:24600405 24600405 G	
14 Y	40 T	-1:24600404 24600404 T	Y
14	41 A	-1:24600403 24600403 A	
14	42 C	-1:24600402 24600402 C	
15 R	43 A	-1:24600401 24600401 A	R
15	44 G	-1:24600400 24600400 G	
15	45 A	-1:24600399 24600399 A	
16 K	46 A	-1:24600398 24600398 A	K
16	47 A	-1:24600397 24600397 A	
16	48 G	-1:24600396 24600396 G	
17 N	49 A	-1:24583080 24583080 A	N
17	50 A	-1:24583079 24583079 A	
17	51 T	-1:24583078 24583078 T	
18 D	52 G	-1:24583077 24583077 G	D
18	53 A	-1:24583076 24583076 A	
18	54 T	-1:24583075 24583075 T	
19 I	55 A	-1:24583074 24583074 A	I
19	56 T	-1:24583073 24583073 T	
19	57 C	-1:24583072 24583072 C	
20 P	58 C	-1:24583071 24583071 C	P
20	59 C	-1:24583070 24583070 C	
20	60 A	-1:24583069 24583069 A	
21 G	61 G	-1:24583068 24583068 G	G
21	62 G	-1:24583067 24583067 G	
21	63 A	-1:24583066 24583066 A	
22 P	64 C	-1:24583065 24583065 C	P
22	65 C	-1:24583064 24583064 C	
22	66 T	-1:24583063 24583063 T	
23 G	67 G	-1:24583062 24583062 G	G
23	68 G	-1:24583061 24583061 G	
23	69 G	-1:24583060 24583060 G	
24 F	70 T	-1:24583059 24583059 T	F
24	71 T	-1:24583058 24583058 T	
24	72 C	-1:24583057 24583057 C	
25 Y	73 T	-1:24583056 24583056 T	Y
25	74 A	-1:24583055 24583055 A	
25	75 C	-1:24583054 24583054 C	
26 N	76 A	-1:24583053 24583053 A	N
26	77 A	-1:24583052 24583052 A	
26	78 T	-1:24583051 24583051 T	
27 V	79 G	-1:24583050 24583050 G	V
27	80 T	-1:24583049 24583049 T	
27	81 T	-1:24583048 24583048 T	
28 I	82 A	-1:24583047 24583047 A	I
28	83 T	-1:24583046 24583046 T	
28	84 T	-1:24583045 24583045 T	
29 H	85 C	-1:24583044 24583044 C	H
29	86 A	-1:24583043 24583043 A	
29	87 C	-1:24583042 24583042 C	
30 Q	88 C	-1:24583041 24583041 C	Q
30	89 A	-1:24583040 24583040 A	
30	90 G	-1:24583039 24583039 G	
31 S	91 T	-1:24583038 24583038 T	S
31	92 C	-1:24583037 24583037 C	
31	93 A	-1:24583036 24583036 A	
32 P	94 C	-1:24583035 24583035 C	P
32	95 C	-1:24583034 24583034 C	
32	96 G	-1:24583033 24583033 G	
33 V	97 G	-1:24583032 24583032 G	V
33	98 T	-1:24583031 24583031 T	
33	99 G	-1:24583030 24583030 G	
34 S	100 T	-1:24583029 24583029 T	S
34	101 C	-1:24583028 24583028 C	
34	102 C	-1:24583027 24583027 C	
35 N	103 A	-1:24583026 24583026 A	N
35	104 A	-1:24583025 24583025 A	
35	105 C	-1:24583024 24583024 C	
36 S	106 A	-1:24583023 24583023 A	S
36	107 G	-1:24583022 24583022 G	
36	108 T	-1:24583021 24583021 T	
37 V	109 G	-1:24583020 24583020 G	V
37	110 T	-1:24583019 24583019 T	
37	111 C	-1:24583018 24583018 C	
38 S	112 T	-1:24583017 24583017 T	S
38	113 C	-1:24583016 24583016 C	
38	114 A	-1:24583015 24583015 A	
39 L	115 T	-1:24583014 24583014 T	L
39	116 T	-1:24583013 24583013 T	
39	117 G	-1:24583012 24583012 G	
40 S	118 T	-1:24583011 24583011 T	S
40	119 C	-1:24583010 24583010 C	
40	120 C	-1:24583009 24583009 C	
41 K	121 A	-1:24583008 24583008 A	K
41	122 A	-1:24583007 24583007 A	
41	123 G	-1:24583006 24583006 G	
42 K	124 A	-1:24583005 24583005 A	K
42	125 A	-1:24583004 24583004 A	
42	126 A	-1:24583003 24583003 A	
43 G	127 G	-1:24583002 24583002 G	G
43	128 G	-1:24583001 24583001 G	
43	129 A	-1:24583000 24583000 A	
44 T	130 A	-1:24582999 24582999 A	T
44	131 C	-1:24582998 24582998 C	
44	132 T	-1:24582997 24582997 T	
45 C	133 T	-1:24582996 24582996 T	C
45	134 G	-1:24582995 24582995 G	
45	135 C	-1:24582994 24582994 C	
46 M	136 A	-1:24582993 24582993 A	M
46	137 T	-1:24582992 24582992 T	
46	138 G	-1:24582991 24582991 G	
47 F	139 T	-1:24582990 24582990 T	F
47	140 T	-1:24582989 24582989 T	
47	141 T	-1:24582988 24582988 T	
48 P	142 C	-1:24582987 24582987 C	P
48	143 C	-1:24582986 24582986 C	
48	144 C	-1:24582985 24582985 C	
49 S	145 T	-1:24582984 24582984 T	S
49	146 C	-1:24582983 24582983 C	
49	147 A	-1:24582982 24582982 A	
50 M	148 A	-1:24582981 24582981 A	M
50	149 T	-1:24582980 24582980 T	
50	150 G	-1:24582979 24582979 G	
51 C	151 T	-1:24578900 24578900 T	C
51	152 G	-1:24578899 24578899 G	
51	153 C	-1:24578898 24578898 C	
52 A	154 G	-1:24578897 24578897 G	A
52	155 C	-1:24578896 24578896 C	
52	156 C	-1:24578895 24578895 C	
53 R	157 C	-1:24578894 24578894 C	R
53	158 G	-1:24578893 24578893 G	
53	159 A	-1:24578892 24578892 A	
54 L	160 T	-1:24578891 24578891 T	L
54	161 T	-1:24578890 24578890 T	
54	162 G	-1:24578889 24578889 G	
55 D	163 G	-1:24578888 24578888 G	D
55	164 A	-1:24578887 24578887 A	
55	165 C	-1:24578886 24578886 C	
56 T	166 A	-1:24578885 24578885 A	T
56	167 C	-1:24578884 24578884 C	
56	168 C	-1:24578883 24578883 C	
57 I	169 A	-1:24578882 24578882 A	I
57	170 T	-1:24578881 24578881 T	
57	171 C	-1:24578880 24578880 C	
58 I	172 A	-1:24578879 24578879 A	I
58	173 T	-1:24578878 24578878 T	
58	174 T	-1:24578877 24578877 T	
59 S	175 T	-1:24578876 24578876 T	S
59	176 C	-1:24578875 24578875 C	
59	177 T	-1:24578874 24578874 T	
60 K	178 A	-1:24578873 24578873 A	K
60	179 A	-1:24578872 24578872 A	
60	180 A	-1:24578871 24578871 A	
61 Y	181 T	-1:24578870 24578870 T	Y
61	182 A	-1:24578869 24578869 A	
61	183 C	-1:24578868 24578868 C	
62 P	184 C	-1:24578867 24578867 C	P
62	185 C	-1:24578866 24578866 C	
62	186 T	-1:24578865 24578865 T	
63 A	187 G	-1:24578864 24578864 G	A
63	188 C	-1:24578863 24578863 C	
63	189 A	-1:24578862 24578862 A	
64 A	190 G	-1:24578861 24578861 G	A
64	191 C	-1:24578860 24578860 C	
64	192 G	-1:24578859 24578859 G	
65 N	193 A	-1:24578858 24578858 A	N
65	194 A	-1:24578857 24578857 A	
65	195 T	-1:24578856 24578856 T	
66 A	196 G	-1:24578855 24578855 G	A
66	197 C	-1:24578854 24578854 C	
66	198 A	-1:24578853 24578853 A	
67 Y	199 T	-1:24578852 24578852 T	Y
67	200 A	-1:24578851 24578851 A	
67	201 C	-1:24578850 24578850 C	
68 T	202 A	-1:24578849 24578849 A	T
68	203 C	-1:24578848 24578848 C	
68	204 T	-1:24578847 24578847 T	
69 I	205 A	-1:24578846 24578846 A	I
69	206 T	-1:24578845 24578845 T	
69	207 C	-1:24578844 24578844 C	
70 P	208 C	-1:24578843 24578843 C	P
70	209 C	-1:24578842 24578842 C	
70	210 A	-1:24578841 24578841 A	
71 S	211 T	-1:24578840 24578840 T	S
71	212 C	-1:24578839 24578839 C	
71	213 G	-1:24578838 24578838 G	
72 D	214 G	-1:24578837 24578837 G	D
72	215 A	-1:24578836 24578836 A	
72	216 T	-1:24578835 24578835 T	
73 F	217 T	-1:24578834 24578834 T	F
73	218 T	-1:24578833 24578833 T	
73	219 T	-1:24578832 24578832 T	
74 I	220 A	-1:24578831 24578831 A	I
74	221 T	-1:24578830 24578830 T	
74	222 T	-1:24578829 24578829 T	
75 S	223 T	-1:24578828 24578828 T	S
75	224 C	-1:24578827 24578827 C	
75	225 C	-1:24578826 24578826 C	
76 K	226 A	-1:24578825 24578825 A	K
76	227 A	-1:24578824 24578824 A	
76	228 G	-1:24578823 24578823 G	
77 R	229 A	-1:24578822 24578822 A	R
77	230 G	-1:24578821 24578821 G	
77	231 A	-1:24578820 24578820 A	
78 D	232 G	-1:24578819 24578819 G	D
78	233 A	-1:24578818 24578818 A	
78	234 C	-1:24578817 24578817 C	
79 F	235 T	-1:24578816 24578816 T	F
79	236 T	-1:24578815 24578815 T	
79	237 T	-1:24578814 24578814 T	
80 S	238 A	-1:24578813 24578813 A	S
80	239 G	-1:24578812 24578812 G	
80	240 T	-1:24578811 24578811 T	
81 N	241 A	-1:24578810 24578810 A	N
81	242 A	-1:24578809 24578809 A	
81	243 T	-1:24578808 24578808 T	
82 S	244 T	-1:24578807 24578807 T	S
82	245 C	-1:24578806 24578806 C	
82	246 G	-1:24578805 24578805 G	
83 C	247 T	-1:24578804 24578804 T	C
83	248 G	-1:24578803 24578803 G	
83	249 T	-1:24578802 24578802 T	
84 S	250 T	-1:24578801 24578801 T	S
84	251 C	-1:24578800 24578800 C	
84	252 C	-1:24578799 24578799 C	
85 S	253 A	-1:24578798 24578798 A	S
85	254 G	-1:24578797 24578797 G	
85	255 C	-1:24578796 24578796 C	
86 M	256 A	-1:24578795 24578795 A	M
86	257 T	-1:24578794 24578794 T	
86	258 G	-1:24578793 24578793 G	
87 F	259 T	-1:24578792 24578792 T	F
87	260 T	-1:24578791 24578791 T	
87	261 C	-1:24578790 24578790 C	
88 Q	262 C	-1:24578789 24578789 C	Q
88	263 A	-1:24578788 24578788 A	
88	264 G	-1:24578787 24578787 G	
89 L	265 T	-1:24578786 24578786 T	L
89	266 T	-1:24578785 24578785 T	
89	267 G	-1:24578784 24578784 G	
90 P	268 C	-1:24578783 24578783 C	P
90	269 C	-1:24578782 24578782 C	
90	270 A	-1:24578781 24578781 A	
91 S	271 A	-1:24578780 24578780 A	S
91	272 G	-1:24578779 24578779 G	
91	273 C	-1:24578778 24578778 C	
92 F	274 T	-1:24578777 24578777 T	F
92	275 T	-1:24578776 24578776 T	
92	276 T	-1:24578775 24578775 T	
93 M	277 A	-1:24578774 24578774 A	M
93	278 T	-1:24578773 24578773 T	
93	279 G	-1:24578772 24578772 G	
94 K	280 A	-1:24578771 24578771 A	K
94	281 A	-1:24578770 24578770 A	
94	282 A	-1:24578769 24578769 A	
95 A	283 G	-1:24578768 24578768 G	A
95	284 C	-1:24578767 24578767 C	
95	285 T	-1:24578766 24578766 T	
96 L	286 C	-1:24578765 24578765 C	L
96	287 T	-1:24578764 24578764 T	
96	288 C	-1:24578763 24578763 C	
97 K	289 A	-1:24578762 24578762 A	K
97	290 A	-1:24578761 24578761 A	
97	291 G	-1:24578760 24578760 G	
98 F	292 T	-1:24578759 24578759 T	F
98	293 T	-1:24578758 24578758 T	
98	294 T	-1:24578757 24578757 T	
99 E	295 G	-1:24578756 24578756 G	E
99	296 A	-1:24578755 24578755 A	
99	297 A	-1:24578754 24578754 A	
100 T	298 A	-1:24578753 24578753 A	T
100	299 C	-1:24578752 24578752 C	
100	300 T	-1:24578751 24578751 T	
101 P	301 C	-1:24578750 24578750 C	P
101	302 C	-1:24578749 24578749 C	
101	303 T	-1:24578748 24578748 T	
102 A	304 G	-1:24578747 24578747 G	A
102	305 C	-1:24578746 24578746 C	
102	306 A	-1:24578745 24578745 A	
103 P	307 C	-1:24578744 24578744 C	P
103	308 C	-1:24578743 24578743 C	
103	309 A	-1:24578742 24578742 A	
104 N	310 A	-1:24578741 24578741 A	N
104	311 A	-1:24578740 24578740 A	
104	312 C	-1:24578739 24578739 C	
105 Y	313 T	-1:24578738 24578738 T	Y
105	314 A	-1:24578737 24578737 A	
105	315 T	-1:24578736 24578736 T	
106 Y	316 T	-1:24578735 24578735 T	Y
106	317 A	-1:24578734 24578734 A	
106	318 C	-1:24578733 24578733 C	
107 N	319 A	-1:24578732 24578732 A	N
107	320 A	-1:24578731 24578731 A	
107	321 T	-1:24578730 24578730 T	
108 A	322 G	-1:24572887 24572887 G	A
108	323 C	-1:24572886 24572886 C	
108	324 C	-1:24572885 24572885 C	
109 S	325 T	-1:24572884 24572884 T	S
109	326 C	-1:24572883 24572883 C	
109	327 T	-1:24572882 24572882 T	
110 V	328 G	-1:24572881 24572881 G	V
110	329 T	-1:24572880 24572880 T	
110	330 C	-1:24572879 24572879 C	
111 S	331 T	-1:24572878 24572878 T	S
111	332 C	-1:24572877 24572877 C	
111	333 T	-1:24572876 24572876 T	
112 C	334 T	-1:24572875 24572875 T	C
112	335 G	-1:24572874 24572874 G	
112	336 C	-1:24572873 24572873 C	
113 C	337 T	-1:24572872 24572872 T	C
113	338 G	-1:24572871 24572871 G	
113	339 C	-1:24572870 24572870 C	
114 K	340 A	-1:24572869 24572869 A	K
114	341 A	-1:24572868 24572868 A	
114	342 G	-1:24572867 24572867 G	
115 Q	343 C	-1:24572866 24572866 C	Q
115	344 A	-1:24572865 24572865 A	
115	345 G	-1:24572864 24572864 G	
116 R	346 A	-1:24572863 24572863 A	R
116	347 G	-1:24572862 24572862 G	
116	348 A	-1:24572861 24572861 A	
117 N	349 A	-1:24572860 24572860 A	N
117	350 A	-1:24572859 24572859 A	
117	351 C	-1:24572858 24572858 C	
118 N	352 A	-1:24572857 24572857 A	N
118	353 A	-1:24572856 24572856 A	
118	354 C	-1:24572855 24572855 C	
119 V	355 G	-1:24572854 24572854 G	V
119	356 T	-1:24572853 24572853 T	
119	357 C	-1:24572852 24572852 C	
120 C	358 T	-1:24572851 24572851 T	C
120	359 G	-1:24572850 24572850 G	
120	360 T	-1:24572849 24572849 T	
121 T	361 A	-1:24572848 24572848 A	T
121	362 C	-1:24572847 24572847 C	
121	363 T	-1:24572846 24572846 T	
122 R	364 C	-1:24572845 24572845 C	R
122	365 G	-1:24572844 24572844 G	
122	366 A	-1:24572843 24572843 A	
123 A	367 G	-1:24572842 24572842 G	A
123	368 C	-1:24572841 24572841 C	
123	369 C	-1:24572840 24572840 C	
124 G	370 G	-1:24572839 24572839 G	G
124	371 G	-1:24572838 24572838 G	
124	372 G	-1:24572837 24572837 G	
125 F	373 T	-1:24572836 24572836 T	F
125	374 T	-1:24572835 24572835 T	
125	375 T	-1:24572834 24572834 T	
126 M	376 A	-1:24572833 24572833 A	M
126	377 T	-1:24572832 24572832 T	
126	378 G	-1:24572831 24572831 G	
127 S	379 T	-1:24572830 24572830 T	S
127	380 C	-1:24572829 24572829 C	
127	381 A	-1:24572828 24572828 A	
128 K	382 A	-1:24572827 24572827 A	K
128	383 A	-1:24572826 24572826 A	
128	384 A	-1:24572825 24572825 A	
129 T	385 A	-1:24572824 24572824 A	T
129	386 C	-1:24572823 24572823 C	
129	387 C	-1:24572822 24572822 C	
130 Q	388 C	-1:24572821 24572821 C	Q
130	389 A	-1:24572820 24572820 A	
130	390 A	-1:24572819 24572819 A	
131 R	391 A	-1:24572818 24572818 A	R
131	392 G	-1:24572817 24572817 G	
131	393 A	-1:24572816 24572816 A	
132 G	394 G	-1:24572815 24572815 G	G
132	395 G	-1:24572814 24572814 G	
132	396 A	-1:24572813 24572813 A	
133 S	397 T	-1:24572812 24572812 T	S
133	398 C	-1:24572811 24572811 C	
133	399 T	-1:24572810 24572810 T	
134 F	400 T	-1:24572809 24572809 T	F
134	401 T	-1:24572808 24572808 T	
134	402 C	-1:24572807 24572807 C	
135 A	403 G	-1:24572806 24572806 G	A
135	404 C	-1:24572805 24572805 C	
135	405 T	-1:24572804 24572804 T	
136 F	406 T	-1:24572803 24572803 T	F
136	407 T	-1:24572802 24572802 T	
136	408 T	-1:24572801 24572801 T	
137 A	409 G	-1:24572800 24572800 G	A
137	410 C	-1:24572799 24572799 C	
137	411 T	-1:24572798 24572798 T	
138 D	412 G	-1:24572797 24572797 G	D
138	413 A	-1:24572796 24572796 A	
138	414 T	-1:24572795 24572795 T	
139 K	415 A	-1:24572794 24572794 A	K
139	416 A	-1:24572793 24572793 A	
139	417 A	-1:24572792 24572792 A	
140 G	418 G	-1:24572791 24572791 G	G
140	419 G	-1:24572790 24572790 G	
140	420 A	-1:24572789 24572789 A	
141 P	421 C	-1:24572788 24572788 C	P
141	422 C	-1:24572787 24572787 C	
141	423 T	-1:24572786 24572786 T	
142 P	424 C	-1:24572785 24572785 C	P
142	425 C	-1:24572784 24572784 C	
142	426 C	-1:24572783 24572783 C	
143 P	427 C	-1:24572782 24572782 C	P
143	428 C	-1:24572781 24572781 C	
143	429 A	-1:24572780 24572780 A	
144 G	430 G	-1:24572779 24572779 G	G
144	431 G	-1:24568916 24568916 G	
144	432 G	-1:24568915 24568915 G	
145 H	433 C	-1:24568914 24568914 C	H
145	434 A	-1:24568913 24568913 A	
145	435 T	-1:24568912 24568912 T	
146 Y	436 T	-1:24568911 24568911 T	Y
146	437 A	-1:24568910 24568910 A	
146	438 T	-1:24568909 24568909 T	
147 D	439 G	-1:24568908 24568908 G	D
147	440 A	-1:24568907 24568907 A	
147	441 T	-1:24568906 24568906 T	
148 I	442 A	-1:24568905 24568905 A	I
148	443 T	-1:24568904 24568904 T	
148	444 C	-1:24568903 24568903 C	
149 N	445 A	-1:24568902 24568902 A	N
149	446 A	-1:24568901 24568901 A	
149	447 C	-1:24568900 24568900 C	
150 E	448 G	-1:24568899 24568899 G	E
150	449 A	-1:24568898 24568898 A	
150	450 A	-1:24568897 24568897 A	
151 S	451 T	-1:24568896 24568896 T	S
151	452 C	-1:24568895 24568895 C	
151	453 C	-1:24568894 24568894 C	
152 L	454 C	-1:24568893 24568893 C	L
152	455 T	-1:24568892 24568892 T	
152	456 T	-1:24568891 24568891 T	
153 V	457 G	-1:24568890 24568890 G	V
153	458 T	-1:24568889 24568889 T	
153	459 G	-1:24568888 24568888 G	
154 K	460 A	-1:24568887 24568887 A	K
154	461 A	-1:24568886 24568886 A	
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206	618 C	-1:24560097 24560097 C	
207 S	619 T	-1:24560096 24560096 T	S
207	620 C	-1:24560095 24560095 C	
207	621 T	-1:24560094 24560094 T	
208 A	622 G	-1:24560093 24560093 G	A
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213 L	637 C	-1:24560078 24560078 C	L
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245	734 C	-1:24559981 24559981 C	
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>ENSP00000363525 
2 C	4 T	-1:24578900 24578900 T	C
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25	74 T	-1:24578830 24578830 T	
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30 F	88 T	-1:24578816 24578816 T	F
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30	90 T	-1:24578814 24578814 T	
31 S	91 A	-1:24578813 24578813 A	S
31	92 G	-1:24578812 24578812 G	
31	93 T	-1:24578811 24578811 T	
32 N	94 A	-1:24578810 24578810 A	N
32	95 A	-1:24578809 24578809 A	
32	96 T	-1:24578808 24578808 T	
33 S	97 T	-1:24578807 24578807 T	S
33	98 C	-1:24578806 24578806 C	
33	99 G	-1:24578805 24578805 G	
34 C	100 T	-1:24578804 24578804 T	C
34	101 G	-1:24578803 24578803 G	
34	102 T	-1:24578802 24578802 T	
35 S	103 T	-1:24578801 24578801 T	S
35	104 C	-1:24578800 24578800 C	
35	105 C	-1:24578799 24578799 C	
36 S	106 A	-1:24578798 24578798 A	S
36	107 G	-1:24578797 24578797 G	
36	108 C	-1:24578796 24578796 C	
37 M	109 A	-1:24578795 24578795 A	M
37	110 T	-1:24578794 24578794 T	
37	111 G	-1:24578793 24578793 G	
38 F	112 T	-1:24578792 24578792 T	F
38	113 T	-1:24578791 24578791 T	
38	114 C	-1:24578790 24578790 C	
39 Q	115 C	-1:24578789 24578789 C	Q
39	116 A	-1:24578788 24578788 A	
39	117 G	-1:24578787 24578787 G	
40 L	118 T	-1:24578786 24578786 T	L
40	119 T	-1:24578785 24578785 T	
40	120 G	-1:24578784 24578784 G	
41 P	121 C	-1:24578783 24578783 C	P
41	122 C	-1:24578782 24578782 C	
41	123 A	-1:24578781 24578781 A	
42 S	124 A	-1:24578780 24578780 A	S
42	125 G	-1:24578779 24578779 G	
42	126 C	-1:24578778 24578778 C	
43 F	127 T	-1:24578777 24578777 T	F
43	128 T	-1:24578776 24578776 T	
43	129 T	-1:24578775 24578775 T	
44 M	130 A	-1:24578774 24578774 A	M
44	131 T	-1:24578773 24578773 T	
44	132 G	-1:24578772 24578772 G	
45 K	133 A	-1:24578771 24578771 A	K
45	134 A	-1:24578770 24578770 A	
45	135 A	-1:24578769 24578769 A	
46 A	136 G	-1:24578768 24578768 G	A
46	137 C	-1:24578767 24578767 C	
46	138 T	-1:24578766 24578766 T	
47 L	139 C	-1:24578765 24578765 C	L
47	140 T	-1:24578764 24578764 T	
47	141 C	-1:24578763 24578763 C	
48 K	142 A	-1:24578762 24578762 A	K
48	143 A	-1:24578761 24578761 A	
48	144 G	-1:24578760 24578760 G	
49 F	145 T	-1:24578759 24578759 T	F
49	146 T	-1:24578758 24578758 T	
49	147 T	-1:24578757 24578757 T	
50 E	148 G	-1:24578756 24578756 G	E
50	149 A	-1:24578755 24578755 A	
50	150 A	-1:24578754 24578754 A	
51 T	151 A	-1:24578753 24578753 A	T
51	152 C	-1:24578752 24578752 C	
51	153 T	-1:24578751 24578751 T	
52 P	154 C	-1:24578750 24578750 C	P
52	155 C	-1:24578749 24578749 C	
52	156 T	-1:24578748 24578748 T	
53 A	157 G	-1:24578747 24578747 G	A
53	158 C	-1:24578746 24578746 C	
53	159 A	-1:24578745 24578745 A	
54 P	160 C	-1:24578744 24578744 C	P
54	161 C	-1:24578743 24578743 C	
54	162 A	-1:24578742 24578742 A	
55 N	163 A	-1:24578741 24578741 A	N
55	164 A	-1:24578740 24578740 A	
55	165 C	-1:24578739 24578739 C	
56 Y	166 T	-1:24578738 24578738 T	Y
56	167 A	-1:24578737 24578737 A	
56	168 T	-1:24578736 24578736 T	
57 Y	169 T	-1:24578735 24578735 T	Y
57	170 A	-1:24578734 24578734 A	
57	171 C	-1:24578733 24578733 C	
58 N	172 A	-1:24578732 24578732 A	N
58	173 A	-1:24578731 24578731 A	
58	174 T	-1:24578730 24578730 T	
59 A	175 G	-1:24572887 24572887 G	A
59	176 C	-1:24572886 24572886 C	
59	177 C	-1:24572885 24572885 C	
60 S	178 T	-1:24572884 24572884 T	S
60	179 C	-1:24572883 24572883 C	
60	180 T	-1:24572882 24572882 T	
61 V	181 G	-1:24572881 24572881 G	V
61	182 T	-1:24572880 24572880 T	
61	183 C	-1:24572879 24572879 C	
62 S	184 T	-1:24572878 24572878 T	S
62	185 C	-1:24572877 24572877 C	
62	186 T	-1:24572876 24572876 T	
63 C	187 T	-1:24572875 24572875 T	C
63	188 G	-1:24572874 24572874 G	
63	189 C	-1:24572873 24572873 C	
64 C	190 T	-1:24572872 24572872 T	C
64	191 G	-1:24572871 24572871 G	
64	192 C	-1:24572870 24572870 C	
65 K	193 A	-1:24572869 24572869 A	K
65	194 A	-1:24572868 24572868 A	
65	195 G	-1:24572867 24572867 G	
66 Q	196 C	-1:24572866 24572866 C	Q
66	197 A	-1:24572865 24572865 A	
66	198 G	-1:24572864 24572864 G	
67 R	199 A	-1:24572863 24572863 A	R
67	200 G	-1:24572862 24572862 G	
67	201 A	-1:24572861 24572861 A	
68 N	202 A	-1:24572860 24572860 A	N
68	203 A	-1:24572859 24572859 A	
68	204 C	-1:24572858 24572858 C	
69 N	205 A	-1:24572857 24572857 A	N
69	206 A	-1:24572856 24572856 A	
69	207 C	-1:24572855 24572855 C	
70 V	208 G	-1:24572854 24572854 G	V
70	209 T	-1:24572853 24572853 T	
70	210 C	-1:24572852 24572852 C	
71 C	211 T	-1:24572851 24572851 T	C
71	212 G	-1:24572850 24572850 G	
71	213 T	-1:24572849 24572849 T	
72 T	214 A	-1:24572848 24572848 A	T
72	215 C	-1:24572847 24572847 C	
72	216 T	-1:24572846 24572846 T	
73 R	217 C	-1:24572845 24572845 C	R
73	218 G	-1:24572844 24572844 G	
73	219 A	-1:24572843 24572843 A	
74 A	220 G	-1:24572842 24572842 G	A
74	221 C	-1:24572841 24572841 C	
74	222 C	-1:24572840 24572840 C	
75 G	223 G	-1:24572839 24572839 G	G
75	224 G	-1:24572838 24572838 G	
75	225 G	-1:24572837 24572837 G	
76 F	226 T	-1:24572836 24572836 T	F
76	227 T	-1:24572835 24572835 T	
76	228 T	-1:24572834 24572834 T	
77 M	229 A	-1:24572833 24572833 A	M
77	230 T	-1:24572832 24572832 T	
77	231 G	-1:24572831 24572831 G	
78 S	232 T	-1:24572830 24572830 T	S
78	233 C	-1:24572829 24572829 C	
78	234 A	-1:24572828 24572828 A	
79 K	235 A	-1:24572827 24572827 A	K
79	236 A	-1:24572826 24572826 A	
79	237 A	-1:24572825 24572825 A	
80 T	238 A	-1:24572824 24572824 A	T
80	239 C	-1:24572823 24572823 C	
80	240 C	-1:24572822 24572822 C	
81 Q	241 C	-1:24572821 24572821 C	Q
81	242 A	-1:24572820 24572820 A	
81	243 A	-1:24572819 24572819 A	
82 R	244 A	-1:24572818 24572818 A	R
82	245 G	-1:24572817 24572817 G	
82	246 A	-1:24572816 24572816 A	
83 G	247 G	-1:24572815 24572815 G	G
83	248 G	-1:24572814 24572814 G	
83	249 A	-1:24572813 24572813 A	
84 S	250 T	-1:24572812 24572812 T	S
84	251 C	-1:24572811 24572811 C	
84	252 T	-1:24572810 24572810 T	
85 F	253 T	-1:24572809 24572809 T	F
85	254 T	-1:24572808 24572808 T	
85	255 C	-1:24572807 24572807 C	
86 A	256 G	-1:24572806 24572806 G	A
86	257 C	-1:24572805 24572805 C	
86	258 T	-1:24572804 24572804 T	
87 F	259 T	-1:24572803 24572803 T	F
87	260 T	-1:24572802 24572802 T	
87	261 T	-1:24572801 24572801 T	
88 A	262 G	-1:24572800 24572800 G	A
88	263 C	-1:24572799 24572799 C	
88	264 T	-1:24572798 24572798 T	
89 D	265 G	-1:24572797 24572797 G	D
89	266 A	-1:24572796 24572796 A	
89	267 T	-1:24572795 24572795 T	
90 K	268 A	-1:24572794 24572794 A	K
90	269 A	-1:24572793 24572793 A	
90	270 A	-1:24572792 24572792 A	
91 G	271 G	-1:24572791 24572791 G	G
91	272 G	-1:24572790 24572790 G	
91	273 A	-1:24572789 24572789 A	
92 P	274 C	-1:24572788 24572788 C	P
92	275 C	-1:24572787 24572787 C	
92	276 T	-1:24572786 24572786 T	
93 P	277 C	-1:24572785 24572785 C	P
93	278 C	-1:24572784 24572784 C	
93	279 C	-1:24572783 24572783 C	
94 P	280 C	-1:24572782 24572782 C	P
94	281 C	-1:24572781 24572781 C	
94	282 A	-1:24572780 24572780 A	
95 G	283 G	-1:24572779 24572779 G	G
95	284 G	-1:24568916 24568916 G	
95	285 G	-1:24568915 24568915 G	
96 H	286 C	-1:24568914 24568914 C	H
96	287 A	-1:24568913 24568913 A	
96	288 T	-1:24568912 24568912 T	
97 Y	289 T	-1:24568911 24568911 T	Y
97	290 A	-1:24568910 24568910 A	
97	291 T	-1:24568909 24568909 T	
98 D	292 G	-1:24568908 24568908 G	D
98	293 A	-1:24568907 24568907 A	
98	294 T	-1:24568906 24568906 T	
99 I	295 A	-1:24568905 24568905 A	I
99	296 T	-1:24568904 24568904 T	
99	297 C	-1:24568903 24568903 C	
100 N	298 A	-1:24568902 24568902 A	N
100	299 A	-1:24568901 24568901 A	
100	300 C	-1:24568900 24568900 C	
101 E	301 G	-1:24568899 24568899 G	E
101	302 A	-1:24568898 24568898 A	
101	303 A	-1:24568897 24568897 A	
102 S	304 T	-1:24568896 24568896 T	S
102	305 C	-1:24568895 24568895 C	
102	306 C	-1:24568894 24568894 C	
103 L	307 C	-1:24568893 24568893 C	L
103	308 T	-1:24568892 24568892 T	
103	309 T	-1:24568891 24568891 T	
104 V	310 G	-1:24568890 24568890 G	V
104	311 T	-1:24568889 24568889 T	
104	312 G	-1:24568888 24568888 G	
105 K	313 A	-1:24568887 24568887 A	K
105	314 A	-1:24568886 24568886 A	
105	315 G	-1:24568885 24568885 G	
106 Q	316 C	-1:24568884 24568884 C	Q
106	317 A	-1:24568883 24568883 A	
106	318 G	-1:24568882 24568882 G	
107 S	319 T	-1:24568881 24568881 T	S
107	320 C	-1:24568880 24568880 C	
107	321 G	-1:24568879 24568879 G	
108 P	322 C	-1:24568878 24568878 C	P
108	323 C	-1:24568877 24568877 C	
108	324 A	-1:24568876 24568876 A	
109 N	325 A	-1:24568875 24568875 A	N
109	326 A	-1:24568874 24568874 A	
109	327 T	-1:24568873 24568873 T	
110 T	328 A	-1:24568872 24568872 A	T
110	329 C	-1:24568871 24568871 C	
110	330 A	-1:24568870 24568870 A	
111 L	331 T	-1:24568869 24568869 T	L
111	332 T	-1:24568868 24568868 T	
111	333 A	-1:24568867 24568867 A	
112 M	334 A	-1:24568866 24568866 A	M
112	335 T	-1:24568865 24568865 T	
112	336 G	-1:24568864 24568864 G	
113 S	337 T	-1:24568863 24568863 T	S
113	338 C	-1:24568862 24568862 C	
113	339 T	-1:24568861 24568861 T	
114 C	340 T	-1:24568860 24568860 T	C
114	341 G	-1:24568859 24568859 G	
114	342 T	-1:24568858 24568858 T	
115 F	343 T	-1:24568857 24568857 T	F
115	344 T	-1:24568856 24568856 T	
115	345 T	-1:24568855 24568855 T	
116 K	346 A	-1:24568854 24568854 A	K
116	347 A	-1:24568853 24568853 A	
116	348 A	-1:24568852 24568852 A	
117 S	349 T	-1:24568851 24568851 T	S
117	350 C	-1:24568850 24568850 C	
117	351 A	-1:24568849 24568849 A	
118 K	352 A	-1:24568848 24568848 A	K
118	353 A	-1:24568847 24568847 A	
118	354 A	-1:24568846 24568846 A	
119 T	355 A	-1:24568845 24568845 A	T
119	356 C	-1:24568844 24568844 C	
119	357 C	-1:24568843 24568843 C	
120 N	358 A	-1:24568842 24568842 A	N
120	359 A	-1:24568841 24568841 A	
120	360 C	-1:24568840 24568840 C	
121 R	361 C	-1:24568839 24568839 C	R
121	362 G	-1:24568838 24568838 G	
121	363 T	-1:24568837 24568837 T	
122 G	364 G	-1:24568836 24568836 G	G
122	365 G	-1:24568835 24568835 G	
122	366 A	-1:24568834 24568834 A	
123 L	367 T	-1:24568833 24568833 T	L
123	368 T	-1:24568832 24568832 T	
123	369 A	-1:24568831 24568831 A	
124 K	370 A	-1:24568830 24568830 A	K
124	371 A	-1:24568829 24568829 A	
124	372 A	-1:24568828 24568828 A	
125 L	373 C	-1:24568827 24568827 C	L
125	374 T	-1:24568826 24568826 T	
125	375 G	-1:24568825 24568825 G	
126 T	376 A	-1:24568824 24568824 A	T
126	377 C	-1:24568823 24568823 C	
126	378 G	-1:24568822 24568822 G	
127 S	379 T	-1:24568821 24568821 T	S
127	380 C	-1:24568820 24568820 C	
127	381 A	-1:24568819 24568819 A	
128 T	382 A	-1:24568818 24568818 A	T
128	383 C	-1:24568817 24568817 C	
128	384 A	-1:24568816 24568816 A	
129 G	385 G	-1:24568815 24568815 G	G
129	386 G	-1:24568814 24568814 G	
129	387 C	-1:24568813 24568813 C	
130 P	388 C	-1:24568812 24568812 C	P
130	389 C	-1:24568811 24568811 C	
130	390 G	-1:24568810 24568810 G	
131 G	391 G	-1:24568809 24568809 G	G
131	392 G	-1:24568808 24568808 G	
131	393 A	-1:24568807 24568807 A	
132 P	394 C	-1:24568806 24568806 C	P
132	395 C	-1:24568805 24568805 C	
132	396 T	-1:24568804 24568804 T	
133 G	397 G	-1:24568803 24568803 G	G
133	398 G	-1:24568802 24568802 G	
133	399 T	-1:24568801 24568801 T	
134 Y	400 T	-1:24568800 24568800 T	Y
134	401 A	-1:24568799 24568799 A	
134	402 T	-1:24568798 24568798 T	
135 Y	403 T	-1:24568797 24568797 T	Y
135	404 A	-1:24568796 24568796 A	
135	405 C	-1:24568795 24568795 C	
136 N	406 A	-1:24568794 24568794 A	N
136	407 A	-1:24568793 24568793 A	
136	408 C	-1:24568792 24568792 C	
137 P	409 C	-1:24568791 24568791 C	P
137	410 C	-1:24568790 24568790 C	
137	411 C	-1:24568789 24568789 C	
138 S	412 A	-1:24568788 24568788 A	S
138	413 G	-1:24568787 24568787 G	
138	414 T	-1:24568786 24568786 T	
139 D	415 G	-1:24568785 24568785 G	D
139	416 A	-1:24568784 24568784 A	
139	417 T	-1:24568783 24568783 T	
140 C	418 T	-1:24568782 24568782 T	C
140	419 G	-1:24568781 24568781 G	
140	420 C	-1:24568780 24568780 C	
141 T	421 A	-1:24568779 24568779 A	T
141	422 C	-1:24568778 24568778 C	
141	423 A	-1:24568777 24568777 A	
142 K	424 A	-1:24568776 24568776 A	K
142	425 A	-1:24568775 24568775 A	
142	426 A	-1:24568774 24568774 A	
143 V	427 G	-1:24568773 24568773 G	V
143	428 T	-1:24568772 24568772 T	
143	429 T	-1:24568771 24568771 T	
144 P	430 C	-1:24568770 24568770 C	P
144	431 C	-1:24568769 24568769 C	
144	432 A	-1:24568768 24568768 A	
145 K	433 A	-1:24568767 24568767 A	K
145	434 A	-1:24568766 24568766 A	
145	435 A	-1:24568765 24568765 A	
146 K	436 A	-1:24568764 24568764 A	K
146	437 A	-1:24568763 24568763 A	
146	438 G	-1:24568762 24568762 G	
147 T	439 A	-1:24568761 24568761 A	T
147	440 C	-1:24568760 24568760 C	
147	441 T	-1:24568759 24568759 T	
148 L	442 C	-1:24568758 24568758 C	L
148	443 T	-1:24568757 24568757 T	
148	444 T	-1:24568756 24568756 T	
149 F	445 T	-1:24568755 24568755 T	F
149	446 T	-1:24568754 24568754 T	
149	447 C	-1:24568753 24568753 C	
150 P	448 C	-1:24568752 24568752 C	P
150	449 C	-1:24568751 24568751 C	
150	450 G	-1:24568750 24568750 G	
151 G	451 G	-1:24568749 24568749 T	*
151	452 G	-1:24568748 24568748 G	
151	453 A	-1:24568747 24568747 A	
>ENSP00000337461 
1 M	1 A	-1:24600465 24600465 A	M
1	2 T	-1:24600464 24600464 T	
1	3 G	-1:24600463 24600463 G	
2 D	4 G	-1:24600462 24600462 G	D
2	5 A	-1:24600461 24600461 A	
2	6 C	-1:24600460 24600460 C	
3 N	7 A	-1:24600459 24600459 A	N
3	8 A	-1:24600458 24600458 A	
3	9 C	-1:24600457 24600457 C	
4 S	10 T	-1:24600456 24600456 T	S
4	11 C	-1:24600455 24600455 C	
4	12 T	-1:24600454 24600454 T	
5 A	13 G	-1:24600453 24600453 G	A
5	14 C	-1:24600452 24600452 C	
5	15 A	-1:24600451 24600451 A	
6 Q	16 C	-1:24600450 24600450 C	Q
6	17 A	-1:24600449 24600449 A	
6	18 G	-1:24600448 24600448 G	
7 K	19 A	-1:24600447 24600447 A	K
7	20 A	-1:24600446 24600446 A	
7	21 A	-1:24600445 24600445 A	
8 N	22 A	-1:24600444 24600444 A	N
8	23 A	-1:24600443 24600443 A	
8	24 T	-1:24600442 24600442 T	
9 E	25 G	-1:24600441 24600441 G	E
9	26 A	-1:24600440 24600440 A	
9	27 A	-1:24600439 24600439 A	
10 R	28 C	-1:24600438 24600438 C	R
10	29 G	-1:24600437 24600437 G	
10	30 C	-1:24600436 24600436 C	
11 T	31 A	-1:24600435 24600435 A	T
11	32 C	-1:24600434 24600434 C	
11	33 T	-1:24600433 24600433 T	
12 G	34 G	-1:24600432 24600432 G	G
12	35 G	-1:24600431 24600431 G	
12	36 C	-1:24600430 24600430 C	
13 K	37 A	-1:24600429 24600429 A	K
13	38 A	-1:24600428 24600428 A	
13	39 A	-1:24600427 24600427 A	
14 H	40 C	-1:24600426 24600426 C	H
14	41 A	-1:24600425 24600425 A	
14	42 T	-1:24600424 24600424 T	
15 P	43 C	-1:24600423 24600423 C	P
15	44 C	-1:24600422 24600422 C	
15	45 C	-1:24600421 24600421 C	
16 R	46 A	-1:24600420 24600420 A	R
16	47 G	-1:24600419 24600419 G	
16	48 A	-1:24600418 24600418 A	
17 R	49 C	-1:24600417 24600417 C	R
17	50 G	-1:24600416 24600416 G	
17	51 T	-1:24600415 24600415 T	
18 A	52 G	-1:24600414 24600414 G	A
18	53 C	-1:24600413 24600413 C	
18	54 C	-1:24600412 24600412 C	
19 S	55 A	-1:24600411 24600411 A	S
19	56 G	-1:24600410 24600410 G	
19	57 T	-1:24600409 24600409 T	
20 E	58 G	-1:24600408 24600408 G	E
20	59 A	-1:24600407 24600407 A	
20	60 A	-1:24600406 24600406 A	
21 V	61 G	-1:24600405 24600405 G	V
21	62 T	-1:24600404 24600404 T	
21	63 A	-1:24600403 24600403 A	
22 Q	64 C	-1:24600402 24600402 C	Q
22	65 A	-1:24600401 24600401 A	
22	66 G	-1:24600400 24600400 G	
23 K	67 A	-1:24600399 24600399 A	K
23	68 A	-1:24600398 24600398 A	
23	69 A	-1:24600397 24600397 A	
24 G	70 G	-1:24600396 24600396 G	G
24	71 G	-1:24590756 24590756 G	
24	72 T	-1:24590755 24590755 T	
25 F	73 T	-1:24590754 24590754 T	F
25	74 T	-1:24590753 24590753 T	
25	75 T	-1:24590752 24590752 T	
26 T	76 A	-1:24590751 24590751 A	T
26	77 C	-1:24590750 24590750 C	
26	78 T	-1:24590749 24590749 T	
27 A	79 G	-1:24590748 24590748 G	A
27	80 C	-1:24590747 24590747 C	
27	81 T	-1:24590746 24590746 T	
28 A	82 G	-1:24590745 24590745 G	A
28	83 C	-1:24590744 24590744 C	
28	84 A	-1:24590743 24590743 A	
29 Y	85 T	-1:24590742 24590742 T	Y
29	86 A	-1:24590741 24590741 A	
29	87 T	-1:24590740 24590740 T	
30 P	88 C	-1:24590739 24590739 C	P
30	89 C	-1:24590738 24590738 C	
30	90 A	-1:24590737 24590737 A	
31 T	91 A	-1:24590736 24590736 A	T
31	92 C	-1:24590735 24590735 C	
31	93 A	-1:24590734 24590734 A	
32 Q	94 C	-1:24590733 24590733 C	Q
32	95 A	-1:24590732 24590732 A	
32	96 A	-1:24590731 24590731 A	
33 S	97 T	-1:24590730 24590730 T	S
33	98 C	-1:24590729 24590729 C	
33	99 C	-1:24590728 24590728 C	
34 S	100 T	-1:24590727 24590727 T	S
34	101 C	-1:24590726 24590726 C	
34	102 C	-1:24590725 24590725 C	
35 I	103 A	-1:24590724 24590724 A	I
35	104 T	-1:24590723 24590723 T	
35	105 T	-1:24590722 24590722 T	
36 P	106 C	-1:24590721 24590721 C	P
36	107 C	-1:24590720 24590720 C	
36	108 T	-1:24590719 24590719 T	
37 F	109 T	-1:24590718 24590718 T	F
37	110 T	-1:24590717 24590717 T	
37	111 T	-1:24590716 24590716 T	
38 K	112 A	-1:24590715 24590715 A	K
38	113 A	-1:24590714 24590714 A	
38	114 A	-1:24590713 24590713 A	
39 S	115 T	-1:24590712 24590712 T	S
39	116 C	-1:24590711 24590711 C	
39	117 T	-1:24590710 24590710 T	
40 Q	118 C	-1:24590709 24590709 C	Q
40	119 A	-1:24590708 24590708 A	
40	120 A	-1:24590707 24590707 A	
41 A	121 G	-1:24590706 24590706 G	A
41	122 C	-1:24590705 24590705 C	
41	123 T	-1:24590704 24590704 T	
42 S	124 T	-1:24590703 24590703 T	S
42	125 C	-1:24590702 24590702 C	
42	126 A	-1:24590701 24590701 A	
43 V	127 G	-1:24590700 24590700 G	V
43	128 T	-1:24590699 24590699 T	
43	129 A	-1:24590698 24590698 A	
44 I	130 A	-1:24590697 24590697 A	I
44	131 T	-1:24590696 24590696 T	
44	132 C	-1:24590695 24590695 C	
45 P	133 C	-1:24590694 24590694 C	P
45	134 C	-1:24590693 24590693 C	
45	135 A	-1:24590692 24590692 A	
46 E	136 G	-1:24590691 24590691 G	E
46	137 A	-1:24590690 24590690 A	
46	138 A	-1:24590689 24590689 A	
47 S	139 T	-1:24590688 24590688 T	S
47	140 C	-1:24590687 24590687 C	
47	141 A	-1:24590686 24590686 A	
48 E	142 G	-1:24590685 24590685 G	E
48	143 A	-1:24590684 24590684 A	
48	144 A	-1:24590683 24590683 A	
49 K	145 A	-1:24590682 24590682 A	K
49	146 A	-1:24590681 24590681 A	
49	147 A	-1:24590680 24590680 A	
50 K	148 A	-1:24590679 24590679 A	K
50	149 A	-1:24590678 24590678 A	
50	150 A	-1:24590677 24590677 A	
51 G	151 G	-1:24590676 24590676 G	G
51	152 G	-1:24590675 24590675 G	
51	153 A	-1:24590674 24590674 A	
52 F	154 T	-1:24590673 24590673 T	F
52	155 T	-1:24590672 24590672 T	
52	156 C	-1:24590671 24590671 C	
53 N	157 A	-1:24590670 24590670 A	N
53	158 A	-1:24590669 24590669 A	
53	159 T	-1:24590668 24590668 T	
54 S	160 A	-1:24590667 24590667 A	S
54	161 G	-1:24590666 24590666 G	
54	162 T	-1:24590665 24590665 T	
55 Q	163 C	-1:24590664 24590664 C	Q
55	164 A	-1:24590663 24590663 A	
55	165 A	-1:24590662 24590662 A	
56 A	166 G	-1:24590661 24590661 G	A
56	167 C	-1:24590660 24590660 C	
56	168 C	-1:24590659 24590659 C	
57 K	169 A	-1:24590658 24590658 A	K
57	170 A	-1:24590657 24590657 A	
57	171 G	-1:24590656 24590656 G	
58 R	172 A	-1:24590655 24590655 A	R
58	173 G	-1:24590654 24590654 G	
58	174 A	-1:24590653 24590653 A	
59 F	175 T	-1:24590652 24590652 T	F
59	176 T	-1:24590651 24590651 T	
59	177 T	-1:24590650 24590650 T	
60 P	178 C	-1:24590649 24590649 C	P
60	179 C	-1:24590648 24590648 C	
60	180 T	-1:24590647 24590647 T	
61 H	181 C	-1:24590646 24590646 C	H
61	182 A	-1:24590645 24590645 A	
61	183 T	-1:24590644 24590644 T	
62 K	184 A	-1:24590643 24590643 A	K
62	185 A	-1:24590642 24590642 A	
62	186 G	-1:24590641 24590641 G	
63 K	187 A	-1:24590640 24590640 A	K
63	188 A	-1:24590639 24590639 A	
63	189 G	-1:24590638 24590638 G	
64 N	190 A	-1:24583080 24583080 A	N
64	191 A	-1:24583079 24583079 A	
64	192 T	-1:24583078 24583078 T	
65 D	193 G	-1:24583077 24583077 G	D
65	194 A	-1:24583076 24583076 A	
65	195 T	-1:24583075 24583075 T	
66 I	196 A	-1:24583074 24583074 A	I
66	197 T	-1:24583073 24583073 T	
66	198 C	-1:24583072 24583072 C	
67 P	199 C	-1:24583071 24583071 C	P
67	200 C	-1:24583070 24583070 C	
67	201 A	-1:24583069 24583069 A	
68 G	202 G	-1:24583068 24583068 G	G
68	203 G	-1:24583067 24583067 G	
68	204 A	-1:24583066 24583066 A	
69 P	205 C	-1:24583065 24583065 C	P
69	206 C	-1:24583064 24583064 C	
69	207 T	-1:24583063 24583063 T	
70 G	208 G	-1:24583062 24583062 G	G
70	209 G	-1:24583061 24583061 G	
70	210 G	-1:24583060 24583060 G	
71 F	211 T	-1:24583059 24583059 T	F
71	212 T	-1:24583058 24583058 T	
71	213 C	-1:24583057 24583057 C	
72 Y	214 T	-1:24583056 24583056 T	Y
72	215 A	-1:24583055 24583055 A	
72	216 C	-1:24583054 24583054 C	
73 N	217 A	-1:24583053 24583053 A	N
73	218 A	-1:24583052 24583052 A	
73	219 T	-1:24583051 24583051 T	
74 V	220 G	-1:24583050 24583050 G	V
74	221 T	-1:24583049 24583049 T	
74	222 T	-1:24583048 24583048 T	
75 I	223 A	-1:24583047 24583047 A	I
75	224 T	-1:24583046 24583046 T	
75	225 T	-1:24583045 24583045 T	
76 H	226 C	-1:24583044 24583044 C	H
76	227 A	-1:24583043 24583043 A	
76	228 C	-1:24583042 24583042 C	
77 Q	229 C	-1:24583041 24583041 C	Q
77	230 A	-1:24583040 24583040 A	
77	231 G	-1:24583039 24583039 G	
78 S	232 T	-1:24583038 24583038 T	S
78	233 C	-1:24583037 24583037 C	
78	234 A	-1:24583036 24583036 A	
79 P	235 C	-1:24583035 24583035 C	P
79	236 C	-1:24583034 24583034 C	
79	237 G	-1:24583033 24583033 G	
80 V	238 G	-1:24583032 24583032 G	V
80	239 T	-1:24583031 24583031 T	
80	240 G	-1:24583030 24583030 G	
81 S	241 T	-1:24583029 24583029 T	S
81	242 C	-1:24583028 24583028 C	
81	243 C	-1:24583027 24583027 C	
82 N	244 A	-1:24583026 24583026 A	N
82	245 A	-1:24583025 24583025 A	
82	246 C	-1:24583024 24583024 C	
83 S	247 A	-1:24583023 24583023 A	S
83	248 G	-1:24583022 24583022 G	
83	249 T	-1:24583021 24583021 T	
84 V	250 G	-1:24583020 24583020 G	V
84	251 T	-1:24583019 24583019 T	
84	252 C	-1:24583018 24583018 C	
85 S	253 T	-1:24583017 24583017 T	S
85	254 C	-1:24583016 24583016 C	
85	255 A	-1:24583015 24583015 A	
86 L	256 T	-1:24583014 24583014 T	L
86	257 T	-1:24583013 24583013 T	
86	258 G	-1:24583012 24583012 G	
87 S	259 T	-1:24583011 24583011 T	S
87	260 C	-1:24583010 24583010 C	
87	261 C	-1:24583009 24583009 C	
88 K	262 A	-1:24583008 24583008 A	K
88	263 A	-1:24583007 24583007 A	
88	264 G	-1:24583006 24583006 G	
89 K	265 A	-1:24583005 24583005 A	K
89	266 A	-1:24583004 24583004 A	
89	267 A	-1:24583003 24583003 A	
90 G	268 G	-1:24583002 24583002 G	G
90	269 G	-1:24583001 24583001 G	
90	270 A	-1:24583000 24583000 A	
91 T	271 A	-1:24582999 24582999 A	T
91	272 C	-1:24582998 24582998 C	
91	273 T	-1:24582997 24582997 T	
92 C	274 T	-1:24582996 24582996 T	C
92	275 G	-1:24582995 24582995 G	
92	276 C	-1:24582994 24582994 C	
93 M	277 A	-1:24582993 24582993 A	M
93	278 T	-1:24582992 24582992 T	
93	279 G	-1:24582991 24582991 G	
94 F	280 T	-1:24582990 24582990 T	F
94	281 T	-1:24582989 24582989 T	
94	282 T	-1:24582988 24582988 T	
95 P	283 C	-1:24582987 24582987 C	P
95	284 C	-1:24582986 24582986 C	
95	285 C	-1:24582985 24582985 C	
96 S	286 T	-1:24582984 24582984 T	S
96	287 C	-1:24582983 24582983 C	
96	288 A	-1:24582982 24582982 A	
97 M	289 A	-1:24582981 24582981 A	M
97	290 T	-1:24582980 24582980 T	
97	291 G	-1:24582979 24582979 G	
98 C	292 T	-1:24578900 24578900 T	C
98	293 G	-1:24578899 24578899 G	
98	294 C	-1:24578898 24578898 C	
99 A	295 G	-1:24578897 24578897 G	A
99	296 C	-1:24578896 24578896 C	
99	297 C	-1:24578895 24578895 C	
100 R	298 C	-1:24578894 24578894 C	R
100	299 G	-1:24578893 24578893 G	
100	300 A	-1:24578892 24578892 A	
101 L	301 T	-1:24578891 24578891 T	L
101	302 T	-1:24578890 24578890 T	
101	303 G	-1:24578889 24578889 G	
102 D	304 G	-1:24578888 24578888 G	D
102	305 A	-1:24578887 24578887 A	
102	306 C	-1:24578886 24578886 C	
103 T	307 A	-1:24578885 24578885 A	T
103	308 C	-1:24578884 24578884 C	
103	309 C	-1:24578883 24578883 C	
104 I	310 A	-1:24578882 24578882 A	I
104	311 T	-1:24578881 24578881 T	
104	312 C	-1:24578880 24578880 C	
105 I	313 A	-1:24578879 24578879 A	I
105	314 T	-1:24578878 24578878 T	
105	315 T	-1:24578877 24578877 T	
106 S	316 T	-1:24578876 24578876 T	S
106	317 C	-1:24578875 24578875 C	
106	318 T	-1:24578874 24578874 T	
107 K	319 A	-1:24578873 24578873 A	K
107	320 A	-1:24578872 24578872 A	
107	321 A	-1:24578871 24578871 A	
108 Y	322 T	-1:24578870 24578870 T	Y
108	323 A	-1:24578869 24578869 A	
108	324 C	-1:24578868 24578868 C	
109 P	325 C	-1:24578867 24578867 C	P
109	326 C	-1:24578866 24578866 C	
109	327 T	-1:24578865 24578865 T	
110 A	328 G	-1:24578864 24578864 G	A
110	329 C	-1:24578863 24578863 C	
110	330 A	-1:24578862 24578862 A	
111 A	331 G	-1:24578861 24578861 G	A
111	332 C	-1:24578860 24578860 C	
111	333 G	-1:24578859 24578859 G	
112 N	334 A	-1:24578858 24578858 A	N
112	335 A	-1:24578857 24578857 A	
112	336 T	-1:24578856 24578856 T	
113 A	337 G	-1:24578855 24578855 G	A
113	338 C	-1:24578854 24578854 C	
113	339 A	-1:24578853 24578853 A	
114 Y	340 T	-1:24578852 24578852 T	Y
114	341 A	-1:24578851 24578851 A	
114	342 C	-1:24578850 24578850 C	
115 T	343 A	-1:24578849 24578849 A	T
115	344 C	-1:24578848 24578848 C	
115	345 T	-1:24578847 24578847 T	
116 I	346 A	-1:24578846 24578846 A	I
116	347 T	-1:24578845 24578845 T	
116	348 C	-1:24578844 24578844 C	
117 P	349 C	-1:24578843 24578843 C	P
117	350 C	-1:24578842 24578842 C	
117	351 A	-1:24578841 24578841 A	
118 S	352 T	-1:24578840 24578840 T	S
118	353 C	-1:24578839 24578839 C	
118	354 G	-1:24578838 24578838 G	
119 D	355 G	-1:24578837 24578837 G	D
119	356 A	-1:24578836 24578836 A	
119	357 T	-1:24578835 24578835 T	
120 F	358 T	-1:24578834 24578834 T	F
120	359 T	-1:24578833 24578833 T	
120	360 T	-1:24578832 24578832 T	
121 I	361 A	-1:24578831 24578831 A	I
121	362 T	-1:24578830 24578830 T	
121	363 T	-1:24578829 24578829 T	
122 S	364 T	-1:24578828 24578828 T	S
122	365 C	-1:24578827 24578827 C	
122	366 C	-1:24578826 24578826 C	
123 K	367 A	-1:24578825 24578825 A	K
123	368 A	-1:24578824 24578824 A	
123	369 G	-1:24578823 24578823 G	
124 R	370 A	-1:24578822 24578822 A	R
124	371 G	-1:24578821 24578821 G	
124	372 A	-1:24578820 24578820 A	
125 D	373 G	-1:24578819 24578819 G	D
125	374 A	-1:24578818 24578818 A	
125	375 C	-1:24578817 24578817 C	
126 F	376 T	-1:24578816 24578816 T	F
126	377 T	-1:24578815 24578815 T	
126	378 T	-1:24578814 24578814 T	
127 S	379 A	-1:24578813 24578813 A	S
127	380 G	-1:24578812 24578812 G	
127	381 T	-1:24578811 24578811 T	
128 N	382 A	-1:24578810 24578810 A	N
128	383 A	-1:24578809 24578809 A	
128	384 T	-1:24578808 24578808 T	
129 S	385 T	-1:24578807 24578807 T	S
129	386 C	-1:24578806 24578806 C	
129	387 G	-1:24578805 24578805 G	
130 C	388 T	-1:24578804 24578804 T	C
130	389 G	-1:24578803 24578803 G	
130	390 T	-1:24578802 24578802 T	
131 S	391 T	-1:24578801 24578801 T	S
131	392 C	-1:24578800 24578800 C	
131	393 C	-1:24578799 24578799 C	
132 S	394 A	-1:24578798 24578798 A	S
132	395 G	-1:24578797 24578797 G	
132	396 C	-1:24578796 24578796 C	
133 M	397 A	-1:24578795 24578795 A	M
133	398 T	-1:24578794 24578794 T	
133	399 G	-1:24578793 24578793 G	
134 F	400 T	-1:24578792 24578792 T	F
134	401 T	-1:24578791 24578791 T	
134	402 C	-1:24578790 24578790 C	
135 Q	403 C	-1:24578789 24578789 C	Q
135	404 A	-1:24578788 24578788 A	
135	405 G	-1:24578787 24578787 G	
136 L	406 T	-1:24578786 24578786 T	L
136	407 T	-1:24578785 24578785 T	
136	408 G	-1:24578784 24578784 G	
137 P	409 C	-1:24578783 24578783 C	P
137	410 C	-1:24578782 24578782 C	
137	411 A	-1:24578781 24578781 A	
138 S	412 A	-1:24578780 24578780 A	S
138	413 G	-1:24578779 24578779 G	
138	414 C	-1:24578778 24578778 C	
139 F	415 T	-1:24578777 24578777 T	F
139	416 T	-1:24578776 24578776 T	
139	417 T	-1:24578775 24578775 T	
140 M	418 A	-1:24578774 24578774 A	M
140	419 T	-1:24578773 24578773 T	
140	420 G	-1:24578772 24578772 G	
141 K	421 A	-1:24578771 24578771 A	K
141	422 A	-1:24578770 24578770 A	
141	423 A	-1:24578769 24578769 A	
142 A	424 G	-1:24578768 24578768 G	A
142	425 C	-1:24578767 24578767 C	
142	426 T	-1:24578766 24578766 T	
143 L	427 C	-1:24578765 24578765 C	L
143	428 T	-1:24578764 24578764 T	
143	429 C	-1:24578763 24578763 C	
144 K	430 A	-1:24578762 24578762 A	K
144	431 A	-1:24578761 24578761 A	
144	432 G	-1:24578760 24578760 G	
145 F	433 T	-1:24578759 24578759 T	F
145	434 T	-1:24578758 24578758 T	
145	435 T	-1:24578757 24578757 T	
146 E	436 G	-1:24578756 24578756 G	E
146	437 A	-1:24578755 24578755 A	
146	438 A	-1:24578754 24578754 A	
147 T	439 A	-1:24578753 24578753 A	T
147	440 C	-1:24578752 24578752 C	
147	441 T	-1:24578751 24578751 T	
148 P	442 C	-1:24578750 24578750 C	P
148	443 C	-1:24578749 24578749 C	
148	444 T	-1:24578748 24578748 T	
149 A	445 G	-1:24578747 24578747 G	A
149	446 C	-1:24578746 24578746 C	
149	447 A	-1:24578745 24578745 A	
150 P	448 C	-1:24578744 24578744 C	P
150	449 C	-1:24578743 24578743 C	
150	450 A	-1:24578742 24578742 A	
151 N	451 A	-1:24578741 24578741 A	N
151	452 A	-1:24578740 24578740 A	
151	453 C	-1:24578739 24578739 C	
152 Y	454 T	-1:24578738 24578738 T	Y
152	455 A	-1:24578737 24578737 A	
152	456 T	-1:24578736 24578736 T	
153 Y	457 T	-1:24578735 24578735 T	Y
153	458 A	-1:24578734 24578734 A	
153	459 C	-1:24578733 24578733 C	
154 N	460 A	-1:24578732 24578732 A	N
154	461 A	-1:24578731 24578731 A	
154	462 T	-1:24578730 24578730 T	
155 A	463 G	-1:24572887 24572887 G	A
155	464 C	-1:24572886 24572886 C	
155	465 C	-1:24572885 24572885 C	
156 S	466 T	-1:24572884 24572884 T	S
156	467 C	-1:24572883 24572883 C	
156	468 T	-1:24572882 24572882 T	
157 V	469 G	-1:24572881 24572881 G	V
157	470 T	-1:24572880 24572880 T	
157	471 C	-1:24572879 24572879 C	
158 S	472 T	-1:24572878 24572878 T	S
158	473 C	-1:24572877 24572877 C	
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195	584 T	-1:24568904 24568904 T	
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206	617 C	-1:24568871 24568871 C	
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215	644 C	-1:24568844 24568844 C	
215	645 C	-1:24568843 24568843 C	
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223	668 C	-1:24568820 24568820 C	
223	669 A	-1:24568819 24568819 A	
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229	687 T	-1:24568801 24568801 T	
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297 W	889 T	-1:24559967 24559967 T	W
297	890 G	-1:24559966 24559966 G	
297	891 G	-1:24559965 24559965 G	
298 T	892 A	-1:24559964 24559964 A	T
298	893 C	-1:24559963 24559963 C	
298	894 A	-1:24559962 24559962 A	
299 A	895 G	-1:24559961 24559961 G	A
299	896 C	-1:24559960 24559960 C	
299	897 G	-1:24559959 24559959 G	
300 A	898 G	-1:24559958 24559958 G	A
300	899 C	-1:24559957 24559957 C	
300	900 G	-1:24559956 24559956 G	
301 P	901 C	-1:24559955 24559955 C	P
301	902 C	-1:24559954 24559954 C	
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302 P	904 C	-1:24559952 24559952 C	P
302	905 C	-1:24559951 24559951 C	
302	906 T	-1:24559950 24559950 T	
303 Q	907 C	-1:24559949 24559949 C	Q
303	908 A	-1:24559948 24559948 A	
303	909 G	-1:24559947 24559947 G	
304 P	910 C	-1:24559946 24559946 C	P
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305 G	913 G	-1:24559943 24559943 G	G
305	914 G	-1:24559942 24559942 G	
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306 L	916 C	-1:24559940 24559940 C	L
306	917 T	-1:24559939 24559939 T	
306	918 G	-1:24559938 24559938 G	
307 P	919 C	-1:24559937 24559937 C	P
307	920 C	-1:24559936 24559936 C	
307	921 T	-1:24559935 24559935 T	
308 G	922 G	-1:24559934 24559934 G	G
308	923 G	-1:24559933 24559933 G	
308	924 C	-1:24559932 24559932 C	
309 P	925 C	-1:24559931 24559931 C	P
309	926 C	-1:24559930 24559930 C	
309	927 A	-1:24559929 24559929 A	
>ENSP00000363530 
1 M	1 A	-1:24600465 24600465 A	M
1	2 T	-1:24600464 24600464 T	
1	3 G	-1:24600463 24600463 G	
2 D	4 G	-1:24600462 24600462 G	D
2	5 A	-1:24600461 24600461 A	
2	6 C	-1:24600460 24600460 C	
3 N	7 A	-1:24600459 24600459 A	N
3	8 A	-1:24600458 24600458 A	
3	9 C	-1:24600457 24600457 C	
4 S	10 T	-1:24600456 24600456 T	S
4	11 C	-1:24600455 24600455 C	
4	12 T	-1:24600454 24600454 T	
5 A	13 G	-1:24600453 24600453 G	A
5	14 C	-1:24600452 24600452 C	
5	15 A	-1:24600451 24600451 A	
6 Q	16 C	-1:24600450 24600450 C	Q
6	17 A	-1:24600449 24600449 A	
6	18 G	-1:24600448 24600448 G	
7 K	19 A	-1:24600447 24600447 A	K
7	20 A	-1:24600446 24600446 A	
7	21 A	-1:24600445 24600445 A	
8 N	22 A	-1:24600444 24600444 A	N
8	23 A	-1:24600443 24600443 A	
8	24 T	-1:24600442 24600442 T	
9 E	25 G	-1:24600441 24600441 G	E
9	26 A	-1:24600440 24600440 A	
9	27 A	-1:24600439 24600439 A	
10 R	28 C	-1:24600438 24600438 C	R
10	29 G	-1:24600437 24600437 G	
10	30 C	-1:24600436 24600436 C	
11 T	31 A	-1:24600435 24600435 A	T
11	32 C	-1:24600434 24600434 C	
11	33 T	-1:24600433 24600433 T	
12 G	34 G	-1:24600432 24600432 G	G
12	35 G	-1:24600431 24600431 G	
12	36 C	-1:24600430 24600430 C	
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13	38 A	-1:24600428 24600428 A	
13	39 A	-1:24600427 24600427 A	
14 H	40 C	-1:24600426 24600426 C	H
14	41 A	-1:24600425 24600425 A	
14	42 T	-1:24600424 24600424 T	
15 P	43 C	-1:24600423 24600423 C	P
15	44 C	-1:24600422 24600422 C	
15	45 C	-1:24600421 24600421 C	
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16	47 G	-1:24600419 24600419 G	
16	48 A	-1:24600418 24600418 A	
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17	50 G	-1:24600416 24600416 G	
17	51 T	-1:24600415 24600415 T	
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18	53 C	-1:24600413 24600413 C	
18	54 C	-1:24600412 24600412 C	
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19	56 G	-1:24600410 24600410 G	
19	57 T	-1:24600409 24600409 T	
20 E	58 G	-1:24600408 24600408 G	E
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20	60 A	-1:24600406 24600406 A	
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21	62 T	-1:24600404 24600404 T	
21	63 A	-1:24600403 24600403 A	
22 Q	64 C	-1:24600402 24600402 C	Q
22	65 A	-1:24600401 24600401 A	
22	66 G	-1:24600400 24600400 G	
23 K	67 A	-1:24600399 24600399 A	K
23	68 A	-1:24600398 24600398 A	
23	69 A	-1:24600397 24600397 A	
24 G	70 G	-1:24600396 24600396 G	G
24	71 G	-1:24590756 24590756 G	
24	72 T	-1:24590755 24590755 T	
25 F	73 T	-1:24590754 24590754 T	F
25	74 T	-1:24590753 24590753 T	
25	75 T	-1:24590752 24590752 T	
26 T	76 A	-1:24590751 24590751 A	T
26	77 C	-1:24590750 24590750 C	
26	78 T	-1:24590749 24590749 T	
27 A	79 G	-1:24590748 24590748 G	A
27	80 C	-1:24590747 24590747 C	
27	81 T	-1:24590746 24590746 T	
28 A	82 G	-1:24590745 24590745 G	A
28	83 C	-1:24590744 24590744 C	
28	84 A	-1:24590743 24590743 A	
29 Y	85 T	-1:24590742 24590742 T	Y
29	86 A	-1:24590741 24590741 A	
29	87 T	-1:24590740 24590740 T	
30 P	88 C	-1:24590739 24590739 C	P
30	89 C	-1:24590738 24590738 C	
30	90 A	-1:24590737 24590737 A	
31 T	91 A	-1:24590736 24590736 A	T
31	92 C	-1:24590735 24590735 C	
31	93 A	-1:24590734 24590734 A	
32 Q	94 C	-1:24590733 24590733 C	Q
32	95 A	-1:24590732 24590732 A	
32	96 A	-1:24590731 24590731 A	
33 S	97 T	-1:24590730 24590730 T	S
33	98 C	-1:24590729 24590729 C	
33	99 C	-1:24590728 24590728 C	
34 S	100 T	-1:24590727 24590727 T	S
34	101 C	-1:24590726 24590726 C	
34	102 C	-1:24590725 24590725 C	
35 I	103 A	-1:24590724 24590724 A	I
35	104 T	-1:24590723 24590723 T	
35	105 T	-1:24590722 24590722 T	
36 P	106 C	-1:24590721 24590721 C	P
36	107 C	-1:24590720 24590720 C	
36	108 T	-1:24590719 24590719 T	
37 F	109 T	-1:24590718 24590718 T	F
37	110 T	-1:24590717 24590717 T	
37	111 T	-1:24590716 24590716 T	
38 K	112 A	-1:24590715 24590715 A	K
38	113 A	-1:24590714 24590714 A	
38	114 A	-1:24590713 24590713 A	
39 S	115 T	-1:24590712 24590712 T	S
39	116 C	-1:24590711 24590711 C	
39	117 T	-1:24590710 24590710 T	
40 Q	118 C	-1:24590709 24590709 C	Q
40	119 A	-1:24590708 24590708 A	
40	120 A	-1:24590707 24590707 A	
41 A	121 G	-1:24590706 24590706 G	A
41	122 C	-1:24590705 24590705 C	
41	123 T	-1:24590704 24590704 T	
42 S	124 T	-1:24590703 24590703 T	S
42	125 C	-1:24590702 24590702 C	
42	126 A	-1:24590701 24590701 A	
43 V	127 G	-1:24590700 24590700 G	V
43	128 T	-1:24590699 24590699 T	
43	129 A	-1:24590698 24590698 A	
44 I	130 A	-1:24590697 24590697 A	I
44	131 T	-1:24590696 24590696 T	
44	132 C	-1:24590695 24590695 C	
45 P	133 C	-1:24590694 24590694 C	P
45	134 C	-1:24590693 24590693 C	
45	135 A	-1:24590692 24590692 A	
46 E	136 G	-1:24590691 24590691 G	E
46	137 A	-1:24590690 24590690 A	
46	138 A	-1:24590689 24590689 A	
47 S	139 T	-1:24590688 24590688 T	S
47	140 C	-1:24590687 24590687 C	
47	141 A	-1:24590686 24590686 A	
48 E	142 G	-1:24590685 24590685 G	E
48	143 A	-1:24590684 24590684 A	
48	144 A	-1:24590683 24590683 A	
49 K	145 A	-1:24590682 24590682 A	K
49	146 A	-1:24590681 24590681 A	
49	147 A	-1:24590680 24590680 A	
50 K	148 A	-1:24590679 24590679 A	K
50	149 A	-1:24590678 24590678 A	
50	150 A	-1:24590677 24590677 A	
51 G	151 G	-1:24590676 24590676 G	G
51	152 G	-1:24590675 24590675 G	
51	153 A	-1:24590674 24590674 A	
52 F	154 T	-1:24590673 24590673 T	F
52	155 T	-1:24590672 24590672 T	
52	156 C	-1:24590671 24590671 C	
53 N	157 A	-1:24590670 24590670 A	N
53	158 A	-1:24590669 24590669 A	
53	159 T	-1:24590668 24590668 T	
54 S	160 A	-1:24590667 24590667 A	S
54	161 G	-1:24590666 24590666 G	
54	162 T	-1:24590665 24590665 T	
55 Q	163 C	-1:24590664 24590664 C	Q
55	164 A	-1:24590663 24590663 A	
55	165 A	-1:24590662 24590662 A	
56 A	166 G	-1:24590661 24590661 G	A
56	167 C	-1:24590660 24590660 C	
56	168 C	-1:24590659 24590659 C	
57 K	169 A	-1:24590658 24590658 A	K
57	170 A	-1:24590657 24590657 A	
57	171 G	-1:24590656 24590656 G	
58 R	172 A	-1:24590655 24590655 A	R
58	173 G	-1:24590654 24590654 G	
58	174 A	-1:24590653 24590653 A	
59 F	175 T	-1:24590652 24590652 T	F
59	176 T	-1:24590651 24590651 T	
59	177 T	-1:24590650 24590650 T	
60 P	178 C	-1:24590649 24590649 C	P
60	179 C	-1:24590648 24590648 C	
60	180 T	-1:24590647 24590647 T	
61 H	181 C	-1:24590646 24590646 C	H
61	182 A	-1:24590645 24590645 A	
61	183 T	-1:24590644 24590644 T	
62 K	184 A	-1:24590643 24590643 A	K
62	185 A	-1:24590642 24590642 A	
62	186 G	-1:24590641 24590641 G	
63 K	187 A	-1:24590640 24590640 A	K
63	188 A	-1:24590639 24590639 A	
63	189 G	-1:24590638 24590638 G	
64 N	190 A	-1:24583080 24583080 A	N
64	191 A	-1:24583079 24583079 A	
64	192 T	-1:24583078 24583078 T	
65 D	193 G	-1:24583077 24583077 G	D
65	194 A	-1:24583076 24583076 A	
65	195 T	-1:24583075 24583075 T	
66 I	196 A	-1:24583074 24583074 A	I
66	197 T	-1:24583073 24583073 T	
66	198 C	-1:24583072 24583072 C	
67 P	199 C	-1:24583071 24583071 C	P
67	200 C	-1:24583070 24583070 C	
67	201 A	-1:24583069 24583069 A	
68 G	202 G	-1:24583068 24583068 G	G
68	203 G	-1:24583067 24583067 G	
68	204 A	-1:24583066 24583066 A	
69 P	205 C	-1:24583065 24583065 C	P
69	206 C	-1:24583064 24583064 C	
69	207 T	-1:24583063 24583063 T	
70 G	208 G	-1:24583062 24583062 G	G
70	209 G	-1:24583061 24583061 G	
70	210 G	-1:24583060 24583060 G	
71 F	211 T	-1:24583059 24583059 T	F
71	212 T	-1:24583058 24583058 T	
71	213 C	-1:24583057 24583057 C	
72 Y	214 T	-1:24583056 24583056 T	Y
72	215 A	-1:24583055 24583055 A	
72	216 C	-1:24583054 24583054 C	
73 N	217 A	-1:24583053 24583053 A	N
73	218 A	-1:24583052 24583052 A	
73	219 T	-1:24583051 24583051 T	
74 V	220 G	-1:24583050 24583050 G	V
74	221 T	-1:24583049 24583049 T	
74	222 T	-1:24583048 24583048 T	
75 I	223 A	-1:24583047 24583047 A	I
75	224 T	-1:24583046 24583046 T	
75	225 T	-1:24583045 24583045 T	
76 H	226 C	-1:24583044 24583044 C	H
76	227 A	-1:24583043 24583043 A	
76	228 C	-1:24583042 24583042 C	
77 Q	229 C	-1:24583041 24583041 C	Q
77	230 A	-1:24583040 24583040 A	
77	231 G	-1:24583039 24583039 G	
78 S	232 T	-1:24583038 24583038 T	S
78	233 C	-1:24583037 24583037 C	
78	234 A	-1:24583036 24583036 A	
79 P	235 C	-1:24583035 24583035 C	P
79	236 C	-1:24583034 24583034 C	
79	237 G	-1:24583033 24583033 G	
80 V	238 G	-1:24583032 24583032 G	V
80	239 T	-1:24583031 24583031 T	
80	240 G	-1:24583030 24583030 G	
81 S	241 T	-1:24583029 24583029 T	S
81	242 C	-1:24583028 24583028 C	
81	243 C	-1:24583027 24583027 C	
82 N	244 A	-1:24583026 24583026 A	N
82	245 A	-1:24583025 24583025 A	
82	246 C	-1:24583024 24583024 C	
83 S	247 A	-1:24583023 24583023 A	S
83	248 G	-1:24583022 24583022 G	
83	249 T	-1:24583021 24583021 T	
84 V	250 G	-1:24583020 24583020 G	V
84	251 T	-1:24583019 24583019 T	
84	252 C	-1:24583018 24583018 C	
85 S	253 T	-1:24583017 24583017 T	S
85	254 C	-1:24583016 24583016 C	
85	255 A	-1:24583015 24583015 A	
86 L	256 T	-1:24583014 24583014 T	L
86	257 T	-1:24583013 24583013 T	
86	258 G	-1:24583012 24583012 G	
87 S	259 T	-1:24583011 24583011 T	S
87	260 C	-1:24583010 24583010 C	
87	261 C	-1:24583009 24583009 C	
88 K	262 A	-1:24583008 24583008 A	K
88	263 A	-1:24583007 24583007 A	
88	264 G	-1:24583006 24583006 G	
89 K	265 A	-1:24583005 24583005 A	K
89	266 A	-1:24583004 24583004 A	
89	267 A	-1:24583003 24583003 A	
90 G	268 G	-1:24583002 24583002 G	G
90	269 G	-1:24583001 24583001 G	
90	270 A	-1:24583000 24583000 A	
91 T	271 A	-1:24582999 24582999 A	T
91	272 C	-1:24582998 24582998 C	
91	273 T	-1:24582997 24582997 T	
92 C	274 T	-1:24582996 24582996 T	C
92	275 G	-1:24582995 24582995 G	
92	276 C	-1:24582994 24582994 C	
93 M	277 A	-1:24582993 24582993 A	M
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93	279 G	-1:24582991 24582991 G	
94 F	280 T	-1:24582990 24582990 T	F
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94	282 T	-1:24582988 24582988 T	
95 P	283 C	-1:24582987 24582987 C	P
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95	285 C	-1:24582985 24582985 C	
96 S	286 T	-1:24582984 24582984 T	S
96	287 C	-1:24582983 24582983 C	
96	288 A	-1:24582982 24582982 A	
97 M	289 A	-1:24582981 24582981 A	M
97	290 T	-1:24582980 24582980 T	
97	291 G	-1:24582979 24582979 G	
98 C	292 T	-1:24578900 24578900 T	C
98	293 G	-1:24578899 24578899 G	
98	294 C	-1:24578898 24578898 C	
99 A	295 G	-1:24578897 24578897 G	A
99	296 C	-1:24578896 24578896 C	
99	297 C	-1:24578895 24578895 C	
100 R	298 C	-1:24578894 24578894 C	R
100	299 G	-1:24578893 24578893 G	
100	300 A	-1:24578892 24578892 A	
101 L	301 T	-1:24578891 24578891 T	L
101	302 T	-1:24578890 24578890 T	
101	303 G	-1:24578889 24578889 G	
102 D	304 G	-1:24578888 24578888 G	D
102	305 A	-1:24578887 24578887 A	
102	306 C	-1:24578886 24578886 C	
103 T	307 A	-1:24578885 24578885 A	T
103	308 C	-1:24578884 24578884 C	
103	309 C	-1:24578883 24578883 C	
104 I	310 A	-1:24578882 24578882 A	I
104	311 T	-1:24578881 24578881 T	
104	312 C	-1:24578880 24578880 C	
105 I	313 A	-1:24578879 24578879 A	I
105	314 T	-1:24578878 24578878 T	
105	315 T	-1:24578877 24578877 T	
106 S	316 T	-1:24578876 24578876 T	S
106	317 C	-1:24578875 24578875 C	
106	318 T	-1:24578874 24578874 T	
107 K	319 A	-1:24578873 24578873 A	K
107	320 A	-1:24578872 24578872 A	
107	321 A	-1:24578871 24578871 A	
108 Y	322 T	-1:24578870 24578870 T	Y
108	323 A	-1:24578869 24578869 A	
108	324 C	-1:24578868 24578868 C	
109 P	325 C	-1:24578867 24578867 C	P
109	326 C	-1:24578866 24578866 C	
109	327 T	-1:24578865 24578865 T	
110 A	328 G	-1:24578864 24578864 G	A
110	329 C	-1:24578863 24578863 C	
110	330 A	-1:24578862 24578862 A	
111 A	331 G	-1:24578861 24578861 G	A
111	332 C	-1:24578860 24578860 C	
111	333 G	-1:24578859 24578859 G	
112 N	334 A	-1:24578858 24578858 A	N
112	335 A	-1:24578857 24578857 A	
112	336 T	-1:24578856 24578856 T	
113 A	337 G	-1:24578855 24578855 G	A
113	338 C	-1:24578854 24578854 C	
113	339 A	-1:24578853 24578853 A	
114 Y	340 T	-1:24578852 24578852 T	Y
114	341 A	-1:24578851 24578851 A	
114	342 C	-1:24578850 24578850 C	
115 T	343 A	-1:24578849 24578849 A	T
115	344 C	-1:24578848 24578848 C	
115	345 T	-1:24578847 24578847 T	
116 I	346 A	-1:24578846 24578846 A	I
116	347 T	-1:24578845 24578845 T	
116	348 C	-1:24578844 24578844 C	
117 P	349 C	-1:24578843 24578843 C	P
117	350 C	-1:24578842 24578842 C	
117	351 A	-1:24578841 24578841 A	
118 S	352 T	-1:24578840 24578840 T	S
118	353 C	-1:24578839 24578839 C	
118	354 G	-1:24578838 24578838 G	
119 D	355 G	-1:24578837 24578837 G	D
119	356 A	-1:24578836 24578836 A	
119	357 T	-1:24578835 24578835 T	
120 F	358 T	-1:24578834 24578834 T	F
120	359 T	-1:24578833 24578833 T	
120	360 T	-1:24578832 24578832 T	
121 I	361 A	-1:24578831 24578831 A	I
121	362 T	-1:24578830 24578830 T	
121	363 T	-1:24578829 24578829 T	
122 S	364 T	-1:24578828 24578828 T	S
122	365 C	-1:24578827 24578827 C	
122	366 C	-1:24578826 24578826 C	
123 K	367 A	-1:24578825 24578825 A	K
123	368 A	-1:24578824 24578824 A	
123	369 G	-1:24578823 24578823 G	
124 R	370 A	-1:24578822 24578822 A	R
124	371 G	-1:24578821 24578821 G	
124	372 A	-1:24578820 24578820 A	
125 D	373 G	-1:24578819 24578819 G	D
125	374 A	-1:24578818 24578818 A	
125	375 C	-1:24578817 24578817 C	
126 F	376 T	-1:24578816 24578816 T	F
126	377 T	-1:24578815 24578815 T	
126	378 T	-1:24578814 24578814 T	
127 S	379 A	-1:24578813 24578813 A	S
127	380 G	-1:24578812 24578812 G	
127	381 T	-1:24578811 24578811 T	
128 N	382 A	-1:24578810 24578810 A	N
128	383 A	-1:24578809 24578809 A	
128	384 T	-1:24578808 24578808 T	
129 S	385 T	-1:24578807 24578807 T	S
129	386 C	-1:24578806 24578806 C	
129	387 G	-1:24578805 24578805 G	
130 C	388 T	-1:24578804 24578804 T	C
130	389 G	-1:24578803 24578803 G	
130	390 T	-1:24578802 24578802 T	
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131	393 C	-1:24578799 24578799 C	
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133 M	397 A	-1:24578795 24578795 A	M
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133	399 G	-1:24578793 24578793 G	
134 F	400 T	-1:24578792 24578792 T	F
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134	402 C	-1:24578790 24578790 C	
135 Q	403 C	-1:24578789 24578789 C	Q
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135	405 G	-1:24578787 24578787 G	
136 L	406 T	-1:24578786 24578786 T	L
136	407 T	-1:24578785 24578785 T	
136	408 G	-1:24578784 24578784 G	
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138	414 C	-1:24578778 24578778 C	
139 F	415 T	-1:24578777 24578777 T	F
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140 M	418 A	-1:24578774 24578774 A	M
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141	423 A	-1:24578769 24578769 A	
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143 L	427 C	-1:24578765 24578765 C	L
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143	429 C	-1:24578763 24578763 C	
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144	431 A	-1:24578761 24578761 A	
144	432 G	-1:24578760 24578760 G	
145 F	433 T	-1:24578759 24578759 T	F
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145	435 T	-1:24578757 24578757 T	
146 E	436 G	-1:24578756 24578756 G	E
146	437 A	-1:24578755 24578755 A	
146	438 A	-1:24578754 24578754 A	
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147	440 C	-1:24578752 24578752 C	
147	441 T	-1:24578751 24578751 T	
148 P	442 C	-1:24578750 24578750 C	P
148	443 C	-1:24578749 24578749 C	
148	444 T	-1:24578748 24578748 T	
149 A	445 G	-1:24578747 24578747 G	A
149	446 C	-1:24578746 24578746 C	
149	447 A	-1:24578745 24578745 A	
150 P	448 C	-1:24578744 24578744 C	P
150	449 C	-1:24578743 24578743 C	
150	450 A	-1:24578742 24578742 A	
151 N	451 A	-1:24578741 24578741 A	N
151	452 A	-1:24578740 24578740 A	
151	453 C	-1:24578739 24578739 C	
152 Y	454 T	-1:24578738 24578738 T	Y
152	455 A	-1:24578737 24578737 A	
152	456 T	-1:24578736 24578736 T	
153 Y	457 T	-1:24578735 24578735 T	Y
153	458 A	-1:24578734 24578734 A	
153	459 C	-1:24578733 24578733 C	
154 N	460 A	-1:24578732 24578732 A	N
154	461 A	-1:24578731 24578731 A	
154	462 T	-1:24578730 24578730 T	
155 A	463 G	-1:24572887 24572887 G	A
155	464 C	-1:24572886 24572886 C	
155	465 C	-1:24572885 24572885 C	
156 S	466 T	-1:24572884 24572884 T	S
156	467 C	-1:24572883 24572883 C	
156	468 T	-1:24572882 24572882 T	
157 V	469 G	-1:24572881 24572881 G	V
157	470 T	-1:24572880 24572880 T	
157	471 C	-1:24572879 24572879 C	
158 S	472 T	-1:24572878 24572878 T	S
158	473 C	-1:24572877 24572877 C	
158	474 T	-1:24572876 24572876 T	
159 C	475 T	-1:24572875 24572875 T	C
159	476 G	-1:24572874 24572874 G	
159	477 C	-1:24572873 24572873 C	
160 C	478 T	-1:24572872 24572872 T	C
160	479 G	-1:24572871 24572871 G	
160	480 C	-1:24572870 24572870 C	
161 K	481 A	-1:24572869 24572869 A	K
161	482 A	-1:24572868 24572868 A	
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162	485 A	-1:24572865 24572865 A	
162	486 G	-1:24572864 24572864 G	
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163	488 G	-1:24572862 24572862 G	
163	489 A	-1:24572861 24572861 A	
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164	491 A	-1:24572859 24572859 A	
164	492 C	-1:24572858 24572858 C	
165 N	493 A	-1:24572857 24572857 A	N
165	494 A	-1:24572856 24572856 A	
165	495 C	-1:24572855 24572855 C	
166 V	496 G	-1:24572854 24572854 G	V
166	497 T	-1:24572853 24572853 T	
166	498 C	-1:24572852 24572852 C	
167 C	499 T	-1:24572851 24572851 T	C
167	500 G	-1:24572850 24572850 G	
167	501 T	-1:24572849 24572849 T	
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168	503 C	-1:24572847 24572847 C	
168	504 T	-1:24572846 24572846 T	
169 R	505 C	-1:24572845 24572845 C	R
169	506 G	-1:24572844 24572844 G	
169	507 A	-1:24572843 24572843 A	
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170	509 C	-1:24572841 24572841 C	
170	510 C	-1:24572840 24572840 C	
171 G	511 G	-1:24572839 24572839 G	G
171	512 G	-1:24572838 24572838 G	
171	513 G	-1:24572837 24572837 G	
172 F	514 T	-1:24572836 24572836 T	F
172	515 T	-1:24572835 24572835 T	
172	516 T	-1:24572834 24572834 T	
173 M	517 A	-1:24572833 24572833 A	M
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174 S	520 T	-1:24572830 24572830 T	S
174	521 C	-1:24572829 24572829 C	
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175	524 A	-1:24572826 24572826 A	
175	525 A	-1:24572825 24572825 A	
176 T	526 A	-1:24572824 24572824 A	T
176	527 C	-1:24572823 24572823 C	
176	528 C	-1:24572822 24572822 C	
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177	531 A	-1:24572819 24572819 A	
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178	533 G	-1:24572817 24572817 G	
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179	537 A	-1:24572813 24572813 A	
180 S	538 T	-1:24572812 24572812 T	S
180	539 C	-1:24572811 24572811 C	
180	540 T	-1:24572810 24572810 T	
181 F	541 T	-1:24572809 24572809 T	F
181	542 T	-1:24572808 24572808 T	
181	543 C	-1:24572807 24572807 C	
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182	545 C	-1:24572805 24572805 C	
182	546 T	-1:24572804 24572804 T	
183 F	547 T	-1:24572803 24572803 T	F
183	548 T	-1:24572802 24572802 T	
183	549 T	-1:24572801 24572801 T	
184 A	550 G	-1:24572800 24572800 G	A
184	551 C	-1:24572799 24572799 C	
184	552 T	-1:24572798 24572798 T	
185 D	553 G	-1:24572797 24572797 G	D
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185	555 T	-1:24572795 24572795 T	
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186	557 A	-1:24572793 24572793 A	
186	558 A	-1:24572792 24572792 A	
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188	564 T	-1:24572786 24572786 T	
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190	570 A	-1:24572780 24572780 A	
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192	576 T	-1:24568912 24568912 T	
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193	578 A	-1:24568910 24568910 A	
193	579 T	-1:24568909 24568909 T	
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194	582 T	-1:24568906 24568906 T	
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195	584 T	-1:24568904 24568904 T	
195	585 C	-1:24568903 24568903 C	
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196	587 A	-1:24568901 24568901 A	
196	588 C	-1:24568900 24568900 C	
197 E	589 G	-1:24568899 24568899 G	E
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197	591 A	-1:24568897 24568897 A	
198 S	592 T	-1:24568896 24568896 T	S
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198	594 C	-1:24568894 24568894 C	
199 L	595 C	-1:24568893 24568893 C	L
199	596 T	-1:24568892 24568892 T	
199	597 T	-1:24568891 24568891 T	
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200	600 G	-1:24568888 24568888 G	
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202	606 G	-1:24568882 24568882 G	
203 S	607 T	-1:24568881 24568881 T	S
203	608 C	-1:24568880 24568880 C	
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204	611 C	-1:24568877 24568877 C	
204	612 A	-1:24568876 24568876 A	
205 N	613 A	-1:24568875 24568875 A	N
205	614 A	-1:24568874 24568874 A	
205	615 T	-1:24568873 24568873 T	
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206	617 C	-1:24568871 24568871 C	
206	618 A	-1:24568870 24568870 A	
207 L	619 T	-1:24568869 24568869 T	L
207	620 T	-1:24568868 24568868 T	
207	621 A	-1:24568867 24568867 A	
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208	623 T	-1:24568865 24568865 T	
208	624 G	-1:24568864 24568864 G	
209 S	625 T	-1:24568863 24568863 T	S
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209	627 T	-1:24568861 24568861 T	
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210	629 G	-1:24568859 24568859 G	
210	630 T	-1:24568858 24568858 T	
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211	633 T	-1:24568855 24568855 T	
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212	635 A	-1:24568853 24568853 A	
212	636 A	-1:24568852 24568852 A	
213 S	637 T	-1:24568851 24568851 T	S
213	638 C	-1:24568850 24568850 C	
213	639 A	-1:24568849 24568849 A	
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214	641 A	-1:24568847 24568847 A	
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215 T	643 A	-1:24568845 24568845 A	T
215	644 C	-1:24568844 24568844 C	
215	645 C	-1:24568843 24568843 C	
216 N	646 A	-1:24568842 24568842 A	N
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217 R	649 C	-1:24568839 24568839 C	R
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217	651 T	-1:24568837 24568837 T	
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219 L	655 T	-1:24568833 24568833 T	L
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219	657 A	-1:24568831 24568831 A	
220 K	658 A	-1:24568830 24568830 A	K
220	659 A	-1:24568829 24568829 A	
220	660 A	-1:24568828 24568828 A	
221 L	661 C	-1:24568827 24568827 C	L
221	662 T	-1:24568826 24568826 T	
221	663 G	-1:24568825 24568825 G	
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222	665 C	-1:24568823 24568823 C	
222	666 G	-1:24568822 24568822 G	
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223	668 C	-1:24568820 24568820 C	
223	669 A	-1:24568819 24568819 A	
224 T	670 A	-1:24568818 24568818 A	T
224	671 C	-1:24568817 24568817 C	
224	672 A	-1:24568816 24568816 A	
225 G	673 G	-1:24568815 24568815 G	G
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226	678 G	-1:24568810 24568810 G	
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227	681 A	-1:24568807 24568807 A	
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228	683 C	-1:24568805 24568805 C	
228	684 T	-1:24568804 24568804 T	
229 G	685 G	-1:24568803 24568803 G	G
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229	687 T	-1:24568801 24568801 T	
230 Y	688 T	-1:24568800 24568800 T	Y
230	689 A	-1:24568799 24568799 A	
230	690 T	-1:24568798 24568798 T	
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231	692 A	-1:24568796 24568796 A	
231	693 C	-1:24568795 24568795 C	
232 N	694 A	-1:24568794 24568794 A	N
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232	696 C	-1:24568792 24568792 C	
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233	698 C	-1:24568790 24568790 C	
233	699 C	-1:24568789 24568789 C	
234 S	700 A	-1:24568788 24568788 A	S
234	701 G	-1:24568787 24568787 G	
234	702 T	-1:24568786 24568786 T	
235 D	703 G	-1:24568785 24568785 G	D
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236 C	706 T	-1:24568782 24568782 T	C
236	707 G	-1:24568781 24568781 G	
236	708 C	-1:24568780 24568780 C	
237 T	709 A	-1:24568779 24568779 A	T
237	710 C	-1:24568778 24568778 C	
237	711 A	-1:24568777 24568777 A	
238 K	712 A	-1:24568776 24568776 A	K
238	713 A	-1:24568775 24568775 A	
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239	716 T	-1:24568772 24568772 T	
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241	722 A	-1:24568766 24568766 A	
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242	725 A	-1:24568763 24568763 A	
242	726 G	-1:24568762 24568762 G	
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243	728 C	-1:24568760 24568760 C	
243	729 T	-1:24568759 24568759 T	
244 L	730 C	-1:24568758 24568758 C	L
244	731 T	-1:24568757 24568757 T	
244	732 T	-1:24568756 24568756 T	
245 F	733 T	-1:24568755 24568755 T	F
245	734 T	-1:24568754 24568754 T	
245	735 C	-1:24568753 24568753 C	
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246	737 C	-1:24568751 24568751 C	
246	738 G	-1:24560118 24560118 G	
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247	741 A	-1:24560115 24560115 A	
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249	747 C	-1:24560109 24560109 C	
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250	749 T	-1:24560107 24560107 T	
250	750 C	-1:24560106 24560106 C	
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251	752 T	-1:24560104 24560104 T	
251	753 G	-1:24560103 24560103 G	
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252	756 C	-1:24560100 24560100 C	
253 F	757 T	-1:24560099 24560099 T	F
253	758 T	-1:24560098 24560098 T	
253	759 C	-1:24560097 24560097 C	
254 S	760 T	-1:24560096 24560096 T	S
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254	762 T	-1:24560094 24560094 T	
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255	765 T	-1:24560091 24560091 T	
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>ENSP00000343549 
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>ENSP00000350722 
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1	2 T	+1:24618626 24618626 T	
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11	32 T	+1:24618656 24618656 T	
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26 A	76 G	+1:24618700 24618700 G	A
26	77 C	+1:24618701 24618701 C	
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27 S	79 T	+1:24618703 24618703 T	S
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28 F	82 T	+1:24618706 24618706 T	F
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29 S	85 T	+1:24618709 24618709 T	S
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30 Y	88 T	+1:24618712 24618712 T	Y
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>ENSP00000003912 
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>ENSP00000374140 
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>ENSP00000363520 
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10	30 T	-X:64671291 2931769634 T	
11 L	31 C	-X:64671290 2931769633 C	L
11	32 T	-X:64671289 2931769632 T	
11	33 A	-X:64671288 2931769631 A	
12 G	34 G	-X:64671287 2931769630 G	G
12	35 G	-X:64671286 2931769629 G	
12	36 T	-X:64671285 2931769628 T	
13 S	37 T	-X:64671284 2931769627 T	S
13	38 C	-X:64671283 2931769626 C	
13	39 C	-X:64671282 2931769625 C	
14 Q	40 C	-X:64671281 2931769624 C	Q
14	41 A	-X:64671280 2931769623 A	
14	42 G	-X:64671279 2931769622 G	
15 G	43 G	-X:64671278 2931769621 G	G
15	44 G	-X:64671277 2931769620 G	
15	45 G	-X:64671276 2931769619 G	
16 M	46 A	-X:64671275 2931769618 A	M
16	47 T	-X:64671274 2931769617 T	
16	48 G	-X:64671273 2931769616 G	
17 D	49 G	-X:64671272 2931769615 G	D
17	50 A	-X:64671271 2931769614 A	
17	51 T	-X:64671270 2931769613 T	
18 L	52 C	-X:64671269 2931769612 C	L
18	53 T	-X:64671268 2931769611 T	
18	54 C	-X:64671267 2931769610 C	
19 V	55 G	-X:64671266 2931769609 G	V
19	56 T	-X:64671265 2931769608 T	
19	57 G	-X:64671264 2931769607 G	
20 W	58 T	-X:64671263 2931769606 T	W
20	59 G	-X:64671262 2931769605 G	
20	60 G	-X:64671261 2931769604 G	
21 S	61 A	-X:64671260 2931769603 A	S
21	62 G	-X:64671259 2931769602 G	
21	63 T	-X:64671258 2931769601 T	
22 A	64 G	-X:64671257 2931769600 G	A
22	65 C	-X:64671256 2931769599 C	
22	66 G	-X:64671255 2931769598 G	
23 W	67 T	-X:64671254 2931769597 T	W
23	68 G	-X:64671253 2931769596 G	
23	69 G	-X:64671252 2931769595 G	
24 Y	70 T	-X:64671251 2931769594 T	Y
24	71 A	-X:64671250 2931769593 A	
24	72 C	-X:64671249 2931769592 C	
25 G	73 G	-X:64671248 2931769591 G	G
25	74 G	-X:64671247 2931769590 G	
25	75 A	-X:64671246 2931769589 A	
26 K	76 A	-X:64671245 2931769588 A	K
26	77 A	-X:64671244 2931769587 A	
26	78 G	-X:64671243 2931769586 G	
27 C	79 T	-X:64671242 2931769585 T	C
27	80 G	-X:64671241 2931769584 G	
27	81 C	-X:64671240 2931769583 C	
28 V	82 G	-X:64671239 2931769582 G	V
28	83 T	-X:64671238 2931769581 T	
28	84 T	-X:64671237 2931769580 T	
29 K	85 A	-X:64671236 2931769579 A	K
29	86 A	-X:64671235 2931769578 A	
29	87 A	-X:64671234 2931769577 A	
30 G	88 G	-X:64671233 2931769576 G	G
30	89 G	-X:64671232 2931769575 G	
30	90 G	-X:64671231 2931769574 G	
31 K	91 A	-X:64671230 2931769573 A	K
31	92 A	-X:64671229 2931769572 A	
31	93 A	-X:64671228 2931769571 A	
32 G	94 G	-X:64671227 2931769570 G	G
32	95 G	-X:64671226 2931769569 G	
32	96 G	-X:64671225 2931769568 G	
33 S	97 T	-X:64671224 2931769567 T	S
33	98 C	-X:64671223 2931769566 C	
33	99 G	-X:64671222 2931769565 G	
34 L	100 T	-X:64671221 2931769564 T	L
34	101 T	-X:64671220 2931769563 T	
34	102 G	-X:64671219 2931769562 G	
35 P	103 C	-X:64671218 2931769561 C	P
35	104 C	-X:64671217 2931769560 C	
35	105 A	-X:64671216 2931769559 A	
36 L	106 C	-X:64671215 2931769558 C	L
36	107 T	-X:64671214 2931769557 T	
36	108 C	-X:64671213 2931769556 C	
37 S	109 T	-X:64671212 2931769555 T	S
37	110 C	-X:64671211 2931769554 C	
37	111 G	-X:64671210 2931769553 G	
38 A	112 G	-X:64671209 2931769552 G	A
38	113 C	-X:64671208 2931769551 C	
38	114 C	-X:64671207 2931769550 C	
39 H	115 C	-X:64671206 2931769549 C	H
39	116 A	-X:64671205 2931769548 A	
39	117 C	-X:64671204 2931769547 C	
40 G	118 G	-X:64671203 2931769546 G	G
40	119 G	-X:64671202 2931769545 G	
40	120 C	-X:64671201 2931769544 C	
41 I	121 A	-X:64671200 2931769543 A	I
41	122 T	-X:64671199 2931769542 T	
41	123 C	-X:64671198 2931769541 C	
42 V	124 G	-X:64671197 2931769540 G	V
42	125 T	-X:64671196 2931769539 T	
42	126 G	-X:64671195 2931769538 G	
43 V	127 G	-X:64671194 2931769537 G	V
43	128 T	-X:64671193 2931769536 T	
43	129 C	-X:64671192 2931769535 C	
44 A	130 G	-X:64671191 2931769534 G	A
44	131 C	-X:64671190 2931769533 C	
44	132 C	-X:64671189 2931769532 C	
45 W	133 T	-X:64671188 2931769531 T	W
45	134 G	-X:64671187 2931769530 G	
45	135 G	-X:64671186 2931769529 G	
46 L	136 C	-X:64671185 2931769528 C	L
46	137 T	-X:64671184 2931769527 T	
46	138 C	-X:64671183 2931769526 C	
47 S	139 A	-X:64671182 2931769525 A	S
47	140 G	-X:64671181 2931769524 G	
47	141 C	-X:64671180 2931769523 C	
48 R	142 A	-X:64671179 2931769522 A	R
48	143 G	-X:64671178 2931769521 G	
48	144 G	-X:64671177 2931769520 G	
49 A	145 G	-X:64671176 2931769519 G	A
49	146 C	-X:64671175 2931769518 C	
49	147 C	-X:64671174 2931769517 C	
50 E	148 G	-X:64671173 2931769516 G	E
50	149 A	-X:64671172 2931769515 A	
50	150 G	-X:64671171 2931769514 G	
51 W	151 T	-X:64671170 2931769513 T	W
51	152 G	-X:64671169 2931769512 G	
51	153 G	-X:64671168 2931769511 G	
52 D	154 G	-X:64671167 2931769510 G	D
52	155 A	-X:64671166 2931769509 A	
52	156 C	-X:64671165 2931769508 C	
53 Q	157 C	-X:64671164 2931769507 C	Q
53	158 A	-X:64671163 2931769506 A	
53	159 G	-X:64671162 2931769505 G	
54 V	160 G	-X:64671161 2931769504 G	V
54	161 T	-X:64671160 2931769503 T	
54	162 G	-X:64671159 2931769502 G	
55 T	163 A	-X:64671158 2931769501 A	T
55	164 C	-X:64671157 2931769500 C	
55	165 G	-X:64671156 2931769499 G	
56 V	166 G	-X:64671155 2931769498 G	V
56	167 T	-X:64671154 2931769497 T	
56	168 T	-X:64671153 2931769496 T	
57 Y	169 T	-X:64671152 2931769495 T	Y
57	170 A	-X:64671151 2931769494 A	
57	171 T	-X:64671150 2931769493 T	
58 L	172 C	-X:64671149 2931769492 C	L
58	173 T	-X:64671148 2931769491 T	
58	174 G	-X:64671147 2931769490 G	
59 F	175 T	-X:64671146 2931769489 T	F
59	176 T	-X:64671145 2931769488 T	
59	177 C	-X:64671144 2931769487 C	
60 C	178 T	-X:64671143 2931769486 T	C
60	179 G	-X:64671142 2931769485 G	
60	180 T	-X:64671141 2931769484 T	
61 D	181 G	-X:64671140 2931769483 G	D
61	182 A	-X:64671139 2931769482 A	
61	183 C	-X:64671138 2931769481 C	
62 D	184 G	-X:64671137 2931769480 G	D
62	185 A	-X:64671136 2931769479 A	
62	186 C	-X:64671135 2931769478 C	
63 H	187 C	-X:64671134 2931769477 C	H
63	188 A	-X:64671133 2931769476 A	
63	189 T	-X:64671132 2931769475 T	
64 K	190 A	-X:64671131 2931769474 A	K
64	191 A	-X:64671130 2931769473 A	
64	192 G	-X:64671129 2931769472 G	
65 L	193 T	-X:64671128 2931769471 T	L
65	194 T	-X:64671127 2931769470 T	
65	195 G	-X:64671126 2931769469 G	
66 Q	196 C	-X:64671125 2931769468 C	Q
66	197 A	-X:64671124 2931769467 A	
66	198 G	-X:64671123 2931769466 G	
67 R	199 C	-X:64671122 2931769465 C	R
67	200 G	-X:64671121 2931769464 G	
67	201 G	-X:64671120 2931769463 G	
68 Y	202 T	-X:64671119 2931769462 T	Y
68	203 A	-X:64671118 2931769461 A	
68	204 C	-X:64671117 2931769460 C	
69 A	205 G	-X:64671116 2931769459 G	A
69	206 C	-X:64671115 2931769458 C	
69	207 G	-X:64671114 2931769457 G	
70 L	208 C	-X:64671113 2931769456 C	L
70	209 T	-X:64671112 2931769455 T	
70	210 T	-X:64671111 2931769454 T	
71 N	211 A	-X:64671110 2931769453 A	N
71	212 A	-X:64671109 2931769452 A	
71	213 C	-X:64671108 2931769451 C	
72 R	214 C	-X:64671107 2931769450 C	R
72	215 G	-X:64671106 2931769449 G	
72	216 C	-X:64671105 2931769448 C	
73 I	217 A	-X:64671104 2931769447 A	I
73	218 T	-X:64671103 2931769446 T	
73	219 C	-X:64671102 2931769445 C	
74 T	220 A	-X:64671101 2931769444 A	T
74	221 C	-X:64671100 2931769443 C	
74	222 G	-X:64671099 2931769442 G	
75 V	223 G	-X:64671098 2931769441 G	V
75	224 T	-X:64671097 2931769440 T	
75	225 G	-X:64671096 2931769439 G	
76 W	226 T	-X:64671095 2931769438 T	W
76	227 G	-X:64671094 2931769437 G	
76	228 G	-X:64671093 2931769436 G	
77 R	229 A	-X:64671092 2931769435 A	R
77	230 G	-X:64671091 2931769434 G	
77	231 G	-X:64671090 2931769433 G	
78 S	232 A	-X:64671089 2931769432 A	S
78	233 G	-X:64671088 2931769431 G	
78	234 C	-X:64671087 2931769430 C	
79 R	235 A	-X:64671086 2931769429 A	R
79	236 G	-X:64671085 2931769428 G	
79	237 G	-X:64670340 2931768683 G	
80 S	238 T	-X:64670339 2931768682 T	S
80	239 C	-X:64670338 2931768681 C	
80	240 A	-X:64670337 2931768680 A	
81 G	241 G	-X:64670336 2931768679 G	G
81	242 G	-X:64670335 2931768678 G	
81	243 C	-X:64670334 2931768677 C	
82 N	244 A	-X:64670333 2931768676 A	N
82	245 A	-X:64670332 2931768675 A	
82	246 C	-X:64670331 2931768674 C	
83 E	247 G	-X:64670330 2931768673 G	E
83	248 A	-X:64670329 2931768672 A	
83	249 A	-X:64670328 2931768671 A	
84 L	250 C	-X:64670327 2931768670 C	L
84	251 T	-X:64670326 2931768669 T	
84	252 C	-X:64670325 2931768668 C	
85 P	253 C	-X:64670324 2931768667 C	P
85	254 C	-X:64670323 2931768666 C	
85	255 T	-X:64670322 2931768665 T	
86 L	256 C	-X:64670321 2931768664 C	L
86	257 T	-X:64670320 2931768663 T	
86	258 G	-X:64670319 2931768662 G	
87 A	259 G	-X:64670318 2931768661 G	A
87	260 C	-X:64670317 2931768660 C	
87	261 A	-X:64670316 2931768659 A	
88 V	262 G	-X:64670315 2931768658 G	V
88	263 T	-X:64670314 2931768657 T	
88	264 G	-X:64670313 2931768656 G	
89 A	265 G	-X:64670312 2931768655 G	A
89	266 C	-X:64670311 2931768654 C	
89	267 T	-X:64670310 2931768653 T	
90 S	268 T	-X:64670309 2931768652 T	S
90	269 C	-X:64670308 2931768651 C	
90	270 T	-X:64670307 2931768650 T	
91 T	271 A	-X:64670306 2931768649 A	T
91	272 C	-X:64670305 2931768648 C	
91	273 T	-X:64670304 2931768647 T	
92 A	274 G	-X:64670303 2931768646 G	A
92	275 C	-X:64670302 2931768645 C	
92	276 T	-X:64670301 2931768644 T	
93 D	277 G	-X:64670300 2931768643 G	D
93	278 A	-X:64670299 2931768642 A	
93	279 C	-X:64670298 2931768641 C	
94 L	280 C	-X:64670297 2931768640 C	L
94	281 T	-X:64670296 2931768639 T	
94	282 G	-X:64670295 2931768638 G	
95 I	283 A	-X:64670294 2931768637 A	I
95	284 T	-X:64670293 2931768636 T	
95	285 A	-X:64670292 2931768635 A	
96 R	286 C	-X:64670291 2931768634 C	R
96	287 G	-X:64670290 2931768633 G	
96	288 C	-X:64670289 2931768632 C	
97 C	289 T	-X:64670288 2931768631 T	C
97	290 G	-X:64670287 2931768630 G	
97	291 T	-X:64670286 2931768629 T	
98 K	292 A	-X:64670285 2931768628 A	K
98	293 A	-X:64670284 2931768627 A	
98	294 G	-X:64670283 2931768626 G	
99 L	295 C	-X:64670282 2931768625 C	L
99	296 T	-X:64670281 2931768624 T	
99	297 C	-X:64670280 2931768623 C	
100 L	298 T	-X:64670279 2931768622 T	L
100	299 T	-X:64670278 2931768621 T	
100	300 G	-X:64670277 2931768620 G	
101 D	301 G	-X:64670276 2931768619 G	D
101	302 A	-X:64670275 2931768618 A	
101	303 T	-X:64670274 2931768617 T	
102 V	304 G	-X:64670273 2931768616 G	V
102	305 T	-X:64670272 2931768615 T	
102	306 A	-X:64670271 2931768614 A	
103 T	307 A	-X:64670270 2931768613 A	T
103	308 C	-X:64670269 2931768612 C	
103	309 T	-X:64670268 2931768611 T	
104 G	310 G	-X:64670267 2931768610 G	G
104	311 G	-X:64670266 2931768609 G	
104	312 T	-X:64670265 2931768608 T	
105 G	313 G	-X:64670264 2931768607 G	G
105	314 G	-X:64670263 2931768606 G	
105	315 C	-X:64670262 2931768605 C	
106 L	316 T	-X:64670261 2931768604 T	L
106	317 T	-X:64670260 2931768603 T	
106	318 G	-X:64670259 2931768602 G	
107 G	319 G	-X:64670258 2931768601 G	G
107	320 G	-X:64670257 2931768600 G	
107	321 C	-X:64670256 2931768599 C	
108 T	322 A	-X:64670255 2931768598 A	T
108	323 C	-X:64670254 2931768597 C	
108	324 T	-X:64670253 2931768596 T	
109 D	325 G	-X:64670252 2931768595 G	D
109	326 A	-X:64670251 2931768594 A	
109	327 T	-X:64670250 2931768593 T	
110 E	328 G	-X:64670249 2931768592 G	E
110	329 A	-X:64670248 2931768591 A	
110	330 A	-X:64670247 2931768590 A	
111 L	331 C	-X:64670246 2931768589 C	L
111	332 T	-X:64670245 2931768588 T	
111	333 T	-X:64670244 2931768587 T	
112 R	334 A	-X:64670243 2931768586 A	R
112	335 G	-X:64670242 2931768585 G	
112	336 A	-X:64670241 2931768584 A	
113 L	337 C	-X:64670240 2931768583 C	L
113	338 T	-X:64670239 2931768582 T	
113	339 G	-X:64670238 2931768581 G	
114 L	340 C	-X:64670237 2931768580 C	L
114	341 T	-X:64670236 2931768579 T	
114	342 C	-X:64670235 2931768578 C	
115 Y	343 T	-X:64670234 2931768577 T	Y
115	344 A	-X:64670233 2931768576 A	
115	345 T	-X:64670232 2931768575 T	
116 G	346 G	-X:64670231 2931768574 G	G
116	347 G	-X:64670230 2931768573 G	
116	348 C	-X:64670229 2931768572 C	
117 M	349 A	-X:64670228 2931768571 A	M
117	350 T	-X:64670227 2931768570 T	
117	351 G	-X:64670226 2931768569 G	
118 A	352 G	-X:64670225 2931768568 G	A
118	353 C	-X:64670224 2931768567 C	
118	354 A	-X:64670223 2931768566 A	
119 L	355 T	-X:64670222 2931768565 T	L
119	356 T	-X:64670221 2931768564 T	
119	357 G	-X:64670220 2931768563 G	
120 V	358 G	-X:64670219 2931768562 G	V
120	359 T	-X:64670218 2931768561 T	
120	360 C	-X:64670217 2931768560 C	
121 R	361 A	-X:64670216 2931768559 A	R
121	362 G	-X:64670215 2931768558 G	
121	363 G	-X:64669235 2931767578 G	
122 F	364 T	-X:64669234 2931767577 T	F
122	365 T	-X:64669233 2931767576 T	
122	366 T	-X:64669232 2931767575 T	
123 V	367 G	-X:64669231 2931767574 G	V
123	368 T	-X:64669230 2931767573 T	
123	369 G	-X:64669229 2931767572 G	
124 N	370 A	-X:64669228 2931767571 A	N
124	371 A	-X:64669227 2931767570 A	
124	372 T	-X:64669226 2931767569 T	
125 L	373 C	-X:64669225 2931767568 C	L
125	374 T	-X:64669224 2931767567 T	
125	375 T	-X:64669223 2931767566 T	
126 I	376 A	-X:64669222 2931767565 A	I
126	377 T	-X:64669221 2931767564 T	
126	378 C	-X:64669220 2931767563 C	
127 S	379 T	-X:64669219 2931767562 T	S
127	380 C	-X:64669218 2931767561 C	
127	381 A	-X:64669217 2931767560 A	
128 E	382 G	-X:64669216 2931767559 G	E
128	383 A	-X:64669215 2931767558 A	
128	384 G	-X:64669214 2931767557 G	
129 R	385 A	-X:64669213 2931767556 A	R
129	386 G	-X:64669212 2931767555 G	
129	387 G	-X:64669211 2931767554 G	
130 K	388 A	-X:64669210 2931767553 A	K
130	389 A	-X:64669209 2931767552 A	
130	390 G	-X:64669208 2931767551 G	
131 T	391 A	-X:64669207 2931767550 A	T
131	392 C	-X:64669206 2931767549 C	
131	393 A	-X:64669205 2931767548 A	
132 K	394 A	-X:64669204 2931767547 A	K
132	395 A	-X:64669203 2931767546 A	
132	396 G	-X:64669202 2931767545 G	
133 F	397 T	-X:64669201 2931767544 T	F
133	398 T	-X:64669200 2931767543 T	
133	399 T	-X:64669199 2931767542 T	
134 A	400 G	-X:64669198 2931767541 G	A
134	401 C	-X:64669197 2931767540 C	
134	402 C	-X:64669196 2931767539 C	
135 K	403 A	-X:64669195 2931767538 A	K
135	404 A	-X:64669194 2931767537 A	
135	405 G	-X:64669193 2931767536 G	
136 V	406 G	-X:64669192 2931767535 G	V
136	407 T	-X:64669191 2931767534 T	
136	408 C	-X:64669190 2931767533 C	
137 P	409 C	-X:64669189 2931767532 C	P
137	410 C	-X:64669188 2931767531 C	
137	411 C	-X:64669187 2931767530 C	
138 L	412 C	-X:64669186 2931767529 C	L
138	413 T	-X:64669185 2931767528 T	
138	414 C	-X:64669184 2931767527 C	
139 K	415 A	-X:64669183 2931767526 A	K
139	416 A	-X:64669182 2931767525 A	
139	417 G	-X:64669181 2931767524 G	
140 C	418 T	-X:64669180 2931767523 T	C
140	419 G	-X:64669179 2931767522 G	
140	420 T	-X:64669178 2931767521 T	
141 L	421 C	-X:64669177 2931767520 C	L
141	422 T	-X:64669176 2931767519 T	
141	423 G	-X:64669175 2931767518 G	
142 A	424 G	-X:64669174 2931767517 G	A
142	425 C	-X:64669173 2931767516 C	
142	426 T	-X:64669172 2931767515 T	
143 Q	427 C	-X:64669171 2931767514 C	Q
143	428 A	-X:64669170 2931767513 A	
143	429 A	-X:64669169 2931767512 A	
144 E	430 G	-X:64669168 2931767511 G	E
144	431 A	-X:64669167 2931767510 A	
144	432 G	-X:64669166 2931767509 G	
145 V	433 G	-X:64668043 2931766386 G	V
145	434 T	-X:64668042 2931766385 T	
145	435 A	-X:64668041 2931766384 A	
146 N	436 A	-X:64668040 2931766383 A	N
146	437 A	-X:64668039 2931766382 A	
146	438 T	-X:64668038 2931766381 T	
147 I	439 A	-X:64668037 2931766380 A	I
147	440 T	-X:64668036 2931766379 T	
147	441 T	-X:64668035 2931766378 T	
148 P	442 C	-X:64668034 2931766377 C	P
148	443 C	-X:64668033 2931766376 C	
148	444 G	-X:64668032 2931766375 G	
149 D	445 G	-X:64668031 2931766374 G	D
149	446 A	-X:64668030 2931766373 A	
149	447 T	-X:64668029 2931766372 T	
150 W	448 T	-X:64668028 2931766371 T	W
150	449 G	-X:64668027 2931766370 G	
150	450 G	-X:64668026 2931766369 G	
151 I	451 A	-X:64668025 2931766368 A	I
151	452 T	-X:64668024 2931766367 T	
151	453 T	-X:64668023 2931766366 T	
152 V	454 G	-X:64668022 2931766365 G	V
152	455 T	-X:64668021 2931766364 T	
152	456 T	-X:64668020 2931766363 T	
153 D	457 G	-X:64668019 2931766362 G	D
153	458 A	-X:64668018 2931766361 A	
153	459 C	-X:64668017 2931766360 C	
154 L	460 C	-X:64668016 2931766359 C	L
154	461 T	-X:64668015 2931766358 T	
154	462 T	-X:64668014 2931766357 T	
155 R	463 C	-X:64668013 2931766356 C	R
155	464 G	-X:64668012 2931766355 G	
155	465 C	-X:64668011 2931766354 C	
156 H	466 C	-X:64668010 2931766353 C	H
156	467 A	-X:64668009 2931766352 A	
156	468 T	-X:64668008 2931766351 T	
157 E	469 G	-X:64668007 2931766350 G	E
157	470 A	-X:64668006 2931766349 A	
157	471 G	-X:64668005 2931766348 G	
158 L	472 T	-X:64668004 2931766347 T	L
158	473 T	-X:64668003 2931766346 T	
158	474 G	-X:64668002 2931766345 G	
159 T	475 A	-X:64668001 2931766344 A	T
159	476 C	-X:64668000 2931766343 C	
159	477 C	-X:64667999 2931766342 C	
160 H	478 C	-X:64667998 2931766341 C	H
160	479 A	-X:64667997 2931766340 A	
160	480 C	-X:64667996 2931766339 C	
161 K	481 A	-X:64667995 2931766338 A	K
161	482 A	-X:64667994 2931766337 A	
161	483 G	-X:64667993 2931766336 G	
162 K	484 A	-X:64667992 2931766335 A	K
162	485 A	-X:64667991 2931766334 A	
162	486 A	-X:64667990 2931766333 A	
163 M	487 A	-X:64667989 2931766332 A	M
163	488 T	-X:64667988 2931766331 T	
163	489 G	-X:64667987 2931766330 G	
164 P	490 C	-X:64667986 2931766329 C	P
164	491 C	-X:64667985 2931766328 C	
164	492 C	-X:64667984 2931766327 C	
165 H	493 C	-X:64667983 2931766326 C	H
165	494 A	-X:64667982 2931766325 A	
165	495 T	-X:64667981 2931766324 T	
166 I	496 A	-X:64667980 2931766323 A	I
166	497 T	-X:64667979 2931766322 T	
166	498 A	-X:64667978 2931766321 A	
167 N	499 A	-X:64667977 2931766320 A	N
167	500 A	-X:64667976 2931766319 A	
167	501 T	-X:64667975 2931766318 T	
168 D	502 G	-X:64667974 2931766317 G	D
168	503 A	-X:64667973 2931766316 A	
168	504 C	-X:64667972 2931766315 C	
169 C	505 T	-X:64667971 2931766314 T	C
169	506 G	-X:64667970 2931766313 G	
169	507 C	-X:64667969 2931766312 C	
170 R	508 C	-X:64667968 2931766311 C	R
170	509 G	-X:64667967 2931766310 G	
170	510 C	-X:64667966 2931766309 C	
171 R	511 A	-X:64667965 2931766308 A	R
171	512 G	-X:64667964 2931766307 G	
171	513 A	-X:64667963 2931766306 A	
172 G	514 G	-X:64667962 2931766305 G	G
172	515 G	-X:64666483 2931764826 G	
172	516 C	-X:64666482 2931764825 C	
173 C	517 T	-X:64666481 2931764824 T	C
173	518 G	-X:64666480 2931764823 G	
173	519 C	-X:64666479 2931764822 C	
174 Y	520 T	-X:64666478 2931764821 T	Y
174	521 A	-X:64666477 2931764820 A	
174	522 C	-X:64666476 2931764819 C	
175 F	523 T	-X:64666475 2931764818 T	F
175	524 T	-X:64666474 2931764817 T	
175	525 T	-X:64666473 2931764816 T	
176 V	526 G	-X:64666472 2931764815 G	V
176	527 T	-X:64666471 2931764814 T	
176	528 C	-X:64666470 2931764813 C	
177 L	529 C	-X:64666469 2931764812 C	L
177	530 T	-X:64666468 2931764811 T	
177	531 G	-X:64666467 2931764810 G	
178 D	532 G	-X:64666466 2931764809 G	D
178	533 A	-X:64666465 2931764808 A	
178	534 T	-X:64666464 2931764807 T	
179 W	535 T	-X:64666463 2931764806 T	W
179	536 G	-X:64666462 2931764805 G	
179	537 G	-X:64666461 2931764804 G	
180 L	538 C	-X:64666460 2931764803 C	L
180	539 T	-X:64666459 2931764802 T	
180	540 C	-X:64666458 2931764801 C	
181 Q	541 C	-X:64666457 2931764800 C	Q
181	542 A	-X:64666456 2931764799 A	
181	543 G	-X:64666455 2931764798 G	
182 K	544 A	-X:64666454 2931764797 A	K
182	545 A	-X:64666453 2931764796 A	
182	546 G	-X:64666452 2931764795 G	
183 T	547 A	-X:64666451 2931764794 A	T
183	548 C	-X:64666450 2931764793 C	
183	549 C	-X:64666449 2931764792 C	
184 Y	550 T	-X:64666448 2931764791 T	Y
184	551 A	-X:64666447 2931764790 A	
184	552 T	-X:64666446 2931764789 T	
185 W	553 T	-X:64666445 2931764788 T	W
185	554 G	-X:64666444 2931764787 G	
185	555 G	-X:64666443 2931764786 G	
186 C	556 T	-X:64666442 2931764785 T	C
186	557 G	-X:64666441 2931764784 G	
186	558 C	-X:64666440 2931764783 C	
187 R	559 C	-X:64666439 2931764782 C	R
187	560 G	-X:64666438 2931764781 G	
187	561 C	-X:64666437 2931764780 C	
188 Q	562 C	-X:64666436 2931764779 C	Q
188	563 A	-X:64666435 2931764778 A	
188	564 A	-X:64666434 2931764777 A	
189 L	565 C	-X:64666433 2931764776 C	L
189	566 T	-X:64666432 2931764775 T	
189	567 G	-X:64666431 2931764774 G	
190 E	568 G	-X:64666430 2931764773 G	E
190	569 A	-X:64666429 2931764772 A	
190	570 G	-X:64666428 2931764771 G	
191 N	571 A	-X:64666427 2931764770 A	N
191	572 A	-X:64666426 2931764769 A	
191	573 C	-X:64666425 2931764768 C	
192 S	574 A	-X:64666424 2931764767 A	S
192	575 G	-X:64666423 2931764766 G	
192	576 C	-X:64666422 2931764765 C	
193 L	577 C	-X:64666421 2931764764 C	L
193	578 T	-X:64666420 2931764763 T	
193	579 G	-X:64666419 2931764762 G	
194 R	580 A	-X:64666418 2931764761 A	R
194	581 G	-X:64666417 2931764760 G	
194	582 A	-X:64666416 2931764759 A	
195 E	583 G	-X:64666415 2931764758 G	E
195	584 A	-X:64666414 2931764757 A	
195	585 G	-X:64666413 2931764756 G	
196 T	586 A	-X:64666412 2931764755 A	T
196	587 C	-X:64666411 2931764754 C	
196	588 C	-X:64666410 2931764753 C	
197 W	589 T	-X:64666409 2931764752 T	W
197	590 G	-X:64666408 2931764751 G	
197	591 G	-X:64666407 2931764750 G	
198 E	592 G	-X:64666406 2931764749 G	E
198	593 A	-X:64666405 2931764748 A	
198	594 G	-X:64666404 2931764747 G	
199 L	595 T	-X:64666403 2931764746 T	L
199	596 T	-X:64666402 2931764745 T	
199	597 G	-X:64666401 2931764744 G	
200 E	598 G	-X:64666400 2931764743 G	E
200	599 A	-X:64666399 2931764742 A	
200	600 G	-X:64666398 2931764741 G	
201 E	601 G	-X:64666397 2931764740 G	E
201	602 A	-X:64666396 2931764739 A	
201	603 G	-X:64666395 2931764738 G	
202 F	604 T	-X:64666394 2931764737 T	F
202	605 T	-X:64666393 2931764736 T	
202	606 C	-X:64666392 2931764735 C	
203 R	607 A	-X:64666391 2931764734 A	R
203	608 G	-X:64666390 2931764733 G	
203	609 G	-X:64666389 2931764732 G	
204 E	610 G	-X:64666388 2931764731 G	E
204	611 A	-X:64666387 2931764730 A	
204	612 A	-X:64666386 2931764729 A	
205 G	613 G	-X:64666385 2931764728 G	G
205	614 G	-X:64666384 2931764727 G	
205	615 G	-X:64666383 2931764726 G	
206 I	616 A	-X:64666382 2931764725 A	I
206	617 T	-X:64666381 2931764724 T	
206	618 A	-X:64666380 2931764723 A	
207 E	619 G	-X:64666379 2931764722 G	E
207	620 A	-X:64666378 2931764721 A	
207	621 G	-X:64666377 2931764720 G	
208 E	622 G	-X:64666376 2931764719 G	E
208	623 A	-X:64666375 2931764718 A	
208	624 A	-X:64666374 2931764717 A	
209 E	625 G	-X:64666373 2931764716 G	E
209	626 A	-X:64666372 2931764715 A	
209	627 G	-X:64666371 2931764714 G	
210 D	628 G	-X:64666370 2931764713 G	D
210	629 A	-X:64666369 2931764712 A	
210	630 T	-X:64666368 2931764711 T	
211 Q	631 C	-X:64666367 2931764710 C	Q
211	632 A	-X:64666366 2931764709 A	
211	633 A	-X:64666365 2931764708 A	
212 E	634 G	-X:64666364 2931764707 G	E
212	635 A	-X:64666363 2931764706 A	
212	636 G	-X:64666362 2931764705 G	
213 E	637 G	-X:64666361 2931764704 G	E
213	638 A	-X:64666360 2931764703 A	
213	639 A	-X:64666359 2931764702 A	
214 D	640 G	-X:64666358 2931764701 G	D
214	641 A	-X:64666357 2931764700 A	
214	642 T	-X:64666356 2931764699 T	
215 K	643 A	-X:64666355 2931764698 A	K
215	644 A	-X:64666354 2931764697 A	
215	645 G	-X:64666353 2931764696 G	
216 N	646 A	-X:64666352 2931764695 A	N
216	647 A	-X:64666351 2931764694 A	
216	648 C	-X:64666350 2931764693 C	
217 I	649 A	-X:64666349 2931764692 A	I
217	650 T	-X:64666348 2931764691 T	
217	651 T	-X:64666347 2931764690 T	
218 V	652 G	-X:64666346 2931764689 G	V
218	653 T	-X:64666345 2931764688 T	
218	654 T	-X:64666344 2931764687 T	
219 V	655 G	-X:64666343 2931764686 G	V
219	656 T	-X:64666342 2931764685 T	
219	657 T	-X:64666341 2931764684 T	
220 D	658 G	-X:64666340 2931764683 G	D
220	659 A	-X:64666339 2931764682 A	
220	660 T	-X:64666338 2931764681 T	
221 D	661 G	-X:64666337 2931764680 G	D
221	662 A	-X:64666336 2931764679 A	
221	663 C	-X:64666335 2931764678 C	
222 I	664 A	-X:64666334 2931764677 A	I
222	665 T	-X:64666333 2931764676 T	
222	666 C	-X:64666332 2931764675 C	
223 T	667 A	-X:64666331 2931764674 A	T
223	668 C	-X:64666330 2931764673 C	
223	669 A	-X:64666329 2931764672 A	
224 E	670 G	-X:64666328 2931764671 G	E
224	671 A	-X:64666327 2931764670 A	
224	672 A	-X:64666326 2931764669 A	
225 Q	673 C	-X:64666325 2931764668 C	Q
225	674 A	-X:64666324 2931764667 A	
225	675 G	-X:64666323 2931764666 G	
226 K	676 A	-X:64666322 2931764665 A	K
226	677 A	-X:64666321 2931764664 A	
226	678 A	-X:64666320 2931764663 A	
227 P	679 C	-X:64666319 2931764662 C	P
227	680 C	-X:64666318 2931764661 C	
227	681 A	-X:64666317 2931764660 A	
228 E	682 G	-X:64666316 2931764659 G	E
228	683 A	-X:64666315 2931764658 A	
228	684 G	-X:64666314 2931764657 G	
229 P	685 C	-X:64666313 2931764656 C	P
229	686 C	-X:64666312 2931764655 C	
229	687 T	-X:64666311 2931764654 T	
230 Q	688 C	-X:64666310 2931764653 C	Q
230	689 A	-X:64666309 2931764652 A	
230	690 G	-X:64666308 2931764651 G	
231 D	691 G	-X:64666307 2931764650 G	D
231	692 A	-X:64666306 2931764649 A	
231	693 T	-X:64666305 2931764648 T	
232 D	694 G	-X:64666304 2931764647 G	D
232	695 A	-X:64666303 2931764646 A	
232	696 T	-X:64666302 2931764645 T	
233 G	697 G	-X:64666301 2931764644 G	G
233	698 G	-X:64666300 2931764643 G	
233	699 G	-X:64666299 2931764642 G	
234 K	700 A	-X:64666298 2931764641 A	K
234	701 A	-X:64666297 2931764640 A	
234	702 A	-X:64666296 2931764639 A	
235 S	703 A	-X:64666295 2931764638 A	S
235	704 G	-X:64666294 2931764637 G	
235	705 T	-X:64666293 2931764636 T	
236 T	706 A	-X:64666292 2931764635 A	T
236	707 C	-X:64666291 2931764634 C	
236	708 G	-X:64666290 2931764633 G	
237 E	709 G	-X:64666289 2931764632 G	E
237	710 A	-X:64666288 2931764631 A	
237	711 G	-X:64666287 2931764630 G	
238 S	712 T	-X:64666286 2931764629 T	S
238	713 C	-X:64666285 2931764628 C	
238	714 A	-X:64666284 2931764627 A	
239 D	715 G	-X:64666283 2931764626 G	D
239	716 A	-X:64666282 2931764625 A	
239	717 T	-X:64666281 2931764624 T	
240 V	718 G	-X:64666280 2931764623 G	V
240	719 T	-X:64666279 2931764622 T	
240	720 A	-X:64666278 2931764621 A	
241 K	721 A	-X:64666277 2931764620 A	K
241	722 A	-X:64666276 2931764619 A	
241	723 G	-X:64666275 2931764618 G	
242 A	724 G	-X:64666274 2931764617 G	A
242	725 C	-X:64666273 2931764616 C	
242	726 C	-X:64666272 2931764615 C	
243 D	727 G	-X:64666271 2931764614 G	D
243	728 A	-X:64666270 2931764613 A	
243	729 T	-X:64666269 2931764612 T	
244 G	730 G	-X:64666268 2931764611 G	G
244	731 G	-X:64666267 2931764610 G	
244	732 A	-X:64666266 2931764609 A	
245 D	733 G	-X:64666265 2931764608 G	D
245	734 A	-X:64666264 2931764607 A	
245	735 C	-X:64666263 2931764606 C	
246 S	736 A	-X:64666262 2931764605 A	S
246	737 G	-X:64666261 2931764604 G	
246	738 C	-X:64666260 2931764603 C	
247 K	739 A	-X:64666259 2931764602 A	K
247	740 A	-X:64666258 2931764601 A	
247	741 A	-X:64666257 2931764600 A	
248 G	742 G	-X:64666256 2931764599 G	G
248	743 G	-X:64666255 2931764598 G	
248	744 C	-X:64666254 2931764597 C	
249 S	745 A	-X:64666253 2931764596 A	S
249	746 G	-X:64666252 2931764595 G	
249	747 C	-X:64666251 2931764594 C	
250 E	748 G	-X:64666250 2931764593 G	E
250	749 A	-X:64666249 2931764592 A	
250	750 A	-X:64666248 2931764591 A	
251 E	751 G	-X:64666247 2931764590 G	E
251	752 A	-X:64666246 2931764589 A	
251	753 G	-X:64666245 2931764588 G	
252 V	754 G	-X:64666244 2931764587 G	V
252	755 T	-X:64666243 2931764586 T	
252	756 G	-X:64666242 2931764585 G	
253 D	757 G	-X:64666241 2931764584 G	D
253	758 A	-X:64666240 2931764583 A	
253	759 T	-X:64666239 2931764582 T	
254 S	760 T	-X:64666238 2931764581 T	S
254	761 C	-X:64666237 2931764580 C	
254	762 T	-X:64666236 2931764579 T	
255 H	763 C	-X:64666235 2931764578 C	H
255	764 A	-X:64666234 2931764577 A	
255	765 T	-X:64666233 2931764576 T	
256 C	766 T	-X:64666232 2931764575 T	C
256	767 G	-X:64666231 2931764574 G	
256	768 C	-X:64666230 2931764573 C	
257 K	769 A	-X:64666229 2931764572 A	K
257	770 A	-X:64666228 2931764571 A	
257	771 A	-X:64666227 2931764570 A	
258 K	772 A	-X:64666226 2931764569 A	K
258	773 A	-X:64666225 2931764568 A	
258	774 G	-X:64666224 2931764567 G	
259 A	775 G	-X:64666223 2931764566 G	A
259	776 C	-X:64666222 2931764565 C	
259	777 C	-X:64666221 2931764564 C	
260 L	778 C	-X:64666220 2931764563 C	L
260	779 T	-X:64666219 2931764562 T	
260	780 G	-X:64666218 2931764561 G	
261 S	781 A	-X:64666217 2931764560 A	S
261	782 G	-X:64666216 2931764559 G	
261	783 T	-X:64666215 2931764558 T	
262 H	784 C	-X:64666214 2931764557 C	H
262	785 A	-X:64666213 2931764556 A	
262	786 T	-X:64666212 2931764555 T	
263 K	787 A	-X:64666211 2931764554 A	K
263	788 A	-X:64666210 2931764553 A	
263	789 A	-X:64666209 2931764552 A	
264 E	790 G	-X:64666208 2931764551 G	E
264	791 A	-X:64666207 2931764550 A	
264	792 G	-X:64666206 2931764549 G	
265 L	793 C	-X:64666205 2931764548 C	L
265	794 T	-X:64666204 2931764547 T	
265	795 A	-X:64666203 2931764546 A	
266 Y	796 T	-X:64666202 2931764545 T	Y
266	797 A	-X:64666201 2931764544 A	
266	798 T	-X:64666200 2931764543 T	
267 E	799 G	-X:64666199 2931764542 G	E
267	800 A	-X:64665863 2931764206 A	
267	801 A	-X:64665862 2931764205 A	
268 R	802 A	-X:64665861 2931764204 A	R
268	803 G	-X:64665860 2931764203 G	
268	804 A	-X:64665859 2931764202 A	
269 A	805 G	-X:64665858 2931764201 G	A
269	806 C	-X:64665857 2931764200 C	
269	807 C	-X:64665856 2931764199 C	
270 R	808 C	-X:64665855 2931764198 C	R
270	809 G	-X:64665854 2931764197 G	
270	810 A	-X:64665853 2931764196 A	
271 E	811 G	-X:64665852 2931764195 G	E
271	812 A	-X:64665851 2931764194 A	
271	813 A	-X:64665850 2931764193 A	
272 L	814 C	-X:64665849 2931764192 C	L
272	815 T	-X:64665848 2931764191 T	
272	816 G	-X:64665847 2931764190 G	
273 L	817 C	-X:64665846 2931764189 C	L
273	818 T	-X:64665845 2931764188 T	
273	819 G	-X:64665844 2931764187 G	
274 V	820 G	-X:64665843 2931764186 G	V
274	821 T	-X:64665842 2931764185 T	
274	822 A	-X:64665841 2931764184 A	
275 S	823 T	-X:64665840 2931764183 T	S
275	824 C	-X:64665839 2931764182 C	
275	825 A	-X:64665838 2931764181 A	
276 Y	826 T	-X:64665837 2931764180 T	Y
276	827 A	-X:64665836 2931764179 A	
276	828 C	-X:64665835 2931764178 C	
277 E	829 G	-X:64665834 2931764177 G	E
277	830 A	-X:64665833 2931764176 A	
277	831 A	-X:64665832 2931764175 A	
278 E	832 G	-X:64665831 2931764174 G	E
278	833 A	-X:64665830 2931764173 A	
278	834 G	-X:64665829 2931764172 G	
279 E	835 G	-X:64665828 2931764171 G	E
279	836 A	-X:64665827 2931764170 A	
279	837 G	-X:64665826 2931764169 G	
280 Q	838 C	-X:64665825 2931764168 C	Q
280	839 A	-X:64665824 2931764167 A	
280	840 G	-X:64665823 2931764166 G	
281 F	841 T	-X:64665822 2931764165 T	F
281	842 T	-X:64665821 2931764164 T	
281	843 T	-X:64665820 2931764163 T	
282 T	844 A	-X:64665819 2931764162 A	T
282	845 C	-X:64665818 2931764161 C	
282	846 G	-X:64665817 2931764160 G	
283 G	847 G	-X:64661655 2931759998 G	G
283	848 G	-X:64661654 2931759997 G	
283	849 A	-X:64661653 2931759996 A	
284 G	850 G	-X:64661652 2931759995 G	G
284	851 G	-X:64661651 2931759994 G	
284	852 C	-X:64661650 2931759993 C	
285 C	853 T	-X:64661649 2931759992 T	C
285	854 G	-X:64661648 2931759991 G	
285	855 T	-X:64661647 2931759990 T	
286 A	856 G	-X:64661646 2931759989 G	A
286	857 C	-X:64661645 2931759988 C	
286	858 T	-X:64661644 2931759987 T	
287 G	859 G	-X:64661643 2931759986 G	G
287	860 G	-X:64661642 2931759985 G	
287	861 A	-X:64661641 2931759984 A	
288 C	862 T	-X:64661640 2931759983 T	C
288	863 G	-X:64661639 2931759982 G	
288	864 C	-X:64661638 2931759981 C	
289 F	865 T	-X:64661637 2931759980 T	F
289	866 T	-X:64661636 2931759979 T	
289	867 T	-X:64661635 2931759978 T	
290 S	868 T	-X:64661634 2931759977 T	S
290	869 C	-X:64661633 2931759976 C	
290	870 T	-X:64661632 2931759975 T	
291 G	871 G	-X:64661631 2931759974 G	G
291	872 G	-X:64661630 2931759973 G	
291	873 A	-X:64661629 2931759972 A	
>ENSP00000363944 
1 M	1 A	-X:64671320 2931769663 A	M
1	2 T	-X:64671319 2931769662 T	
1	3 G	-X:64671318 2931769661 G	
2 S	4 T	-X:64671317 2931769660 T	S
2	5 C	-X:64671316 2931769659 C	
2	6 G	-X:64671315 2931769658 G	
3 W	7 T	-X:64671314 2931769657 T	W
3	8 G	-X:64671313 2931769656 G	
3	9 G	-X:64671312 2931769655 G	
4 E	10 G	-X:64671311 2931769654 G	E
4	11 A	-X:64671310 2931769653 A	
4	12 A	-X:64671309 2931769652 A	
5 S	13 T	-X:64671308 2931769651 T	S
5	14 C	-X:64671307 2931769650 C	
5	15 C	-X:64671306 2931769649 C	
6 G	16 G	-X:64671305 2931769648 G	G
6	17 G	-X:64671304 2931769647 G	
6	18 G	-X:64671303 2931769646 G	
7 A	19 G	-X:64671302 2931769645 G	A
7	20 C	-X:64671301 2931769644 C	
7	21 C	-X:64671300 2931769643 C	
8 G	22 G	-X:64671299 2931769642 G	G
8	23 G	-X:64671298 2931769641 G	
8	24 G	-X:64671297 2931769640 G	
9 P	25 C	-X:64671296 2931769639 C	P
9	26 C	-X:64671295 2931769638 C	
9	27 A	-X:64671294 2931769637 A	
10 G	28 G	-X:64671293 2931769636 G	G
10	29 G	-X:64671292 2931769635 G	
10	30 T	-X:64671291 2931769634 T	
11 L	31 C	-X:64671290 2931769633 C	L
11	32 T	-X:64671289 2931769632 T	
11	33 A	-X:64671288 2931769631 A	
12 G	34 G	-X:64671287 2931769630 G	G
12	35 G	-X:64671286 2931769629 G	
12	36 T	-X:64671285 2931769628 T	
13 S	37 T	-X:64671284 2931769627 T	S
13	38 C	-X:64671283 2931769626 C	
13	39 C	-X:64671282 2931769625 C	
14 Q	40 C	-X:64671281 2931769624 C	Q
14	41 A	-X:64671280 2931769623 A	
14	42 G	-X:64671279 2931769622 G	
15 G	43 G	-X:64671278 2931769621 G	G
15	44 G	-X:64671277 2931769620 G	
15	45 G	-X:64671276 2931769619 G	
16 M	46 A	-X:64671275 2931769618 A	M
16	47 T	-X:64671274 2931769617 T	
16	48 G	-X:64671273 2931769616 G	
17 D	49 G	-X:64671272 2931769615 G	D
17	50 A	-X:64671271 2931769614 A	
17	51 T	-X:64671270 2931769613 T	
18 L	52 C	-X:64671269 2931769612 C	L
18	53 T	-X:64671268 2931769611 T	
18	54 C	-X:64671267 2931769610 C	
19 V	55 G	-X:64671266 2931769609 G	V
19	56 T	-X:64671265 2931769608 T	
19	57 G	-X:64671264 2931769607 G	
20 W	58 T	-X:64671263 2931769606 T	W
20	59 G	-X:64671262 2931769605 G	
20	60 G	-X:64671261 2931769604 G	
21 S	61 A	-X:64671260 2931769603 A	S
21	62 G	-X:64671259 2931769602 G	
21	63 T	-X:64671258 2931769601 T	
22 A	64 G	-X:64671257 2931769600 G	A
22	65 C	-X:64671256 2931769599 C	
22	66 G	-X:64671255 2931769598 G	
23 W	67 T	-X:64671254 2931769597 T	W
23	68 G	-X:64671253 2931769596 G	
23	69 G	-X:64671252 2931769595 G	
24 Y	70 T	-X:64671251 2931769594 T	Y
24	71 A	-X:64671250 2931769593 A	
24	72 C	-X:64671249 2931769592 C	
25 G	73 G	-X:64671248 2931769591 G	G
25	74 G	-X:64671247 2931769590 G	
25	75 A	-X:64671246 2931769589 A	
26 K	76 A	-X:64671245 2931769588 A	K
26	77 A	-X:64671244 2931769587 A	
26	78 G	-X:64671243 2931769586 G	
27 C	79 T	-X:64671242 2931769585 T	C
27	80 G	-X:64671241 2931769584 G	
27	81 C	-X:64671240 2931769583 C	
28 V	82 G	-X:64671239 2931769582 G	V
28	83 T	-X:64671238 2931769581 T	
28	84 T	-X:64671237 2931769580 T	
29 K	85 A	-X:64671236 2931769579 A	K
29	86 A	-X:64671235 2931769578 A	
29	87 A	-X:64671234 2931769577 A	
30 G	88 G	-X:64671233 2931769576 G	G
30	89 G	-X:64671232 2931769575 G	
30	90 G	-X:64671231 2931769574 G	
31 K	91 A	-X:64671230 2931769573 A	K
31	92 A	-X:64671229 2931769572 A	
31	93 A	-X:64671228 2931769571 A	
32 G	94 G	-X:64671227 2931769570 G	G
32	95 G	-X:64671226 2931769569 G	
32	96 G	-X:64671225 2931769568 G	
33 S	97 T	-X:64671224 2931769567 T	S
33	98 C	-X:64671223 2931769566 C	
33	99 G	-X:64671222 2931769565 G	
34 L	100 T	-X:64671221 2931769564 T	L
34	101 T	-X:64671220 2931769563 T	
34	102 G	-X:64671219 2931769562 G	
35 P	103 C	-X:64671218 2931769561 C	P
35	104 C	-X:64671217 2931769560 C	
35	105 A	-X:64671216 2931769559 A	
36 L	106 C	-X:64671215 2931769558 C	L
36	107 T	-X:64671214 2931769557 T	
36	108 C	-X:64671213 2931769556 C	
37 S	109 T	-X:64671212 2931769555 T	S
37	110 C	-X:64671211 2931769554 C	
37	111 G	-X:64671210 2931769553 G	
38 A	112 G	-X:64671209 2931769552 G	A
38	113 C	-X:64671208 2931769551 C	
38	114 C	-X:64671207 2931769550 C	
39 H	115 C	-X:64671206 2931769549 C	H
39	116 A	-X:64671205 2931769548 A	
39	117 C	-X:64671204 2931769547 C	
40 G	118 G	-X:64671203 2931769546 G	G
40	119 G	-X:64671202 2931769545 G	
40	120 C	-X:64671201 2931769544 C	
41 I	121 A	-X:64671200 2931769543 A	I
41	122 T	-X:64671199 2931769542 T	
41	123 C	-X:64671198 2931769541 C	
42 V	124 G	-X:64671197 2931769540 G	V
42	125 T	-X:64671196 2931769539 T	
42	126 G	-X:64671195 2931769538 G	
43 V	127 G	-X:64671194 2931769537 G	V
43	128 T	-X:64671193 2931769536 T	
43	129 C	-X:64671192 2931769535 C	
44 A	130 G	-X:64671191 2931769534 G	A
44	131 C	-X:64671190 2931769533 C	
44	132 C	-X:64671189 2931769532 C	
45 W	133 T	-X:64671188 2931769531 T	W
45	134 G	-X:64671187 2931769530 G	
45	135 G	-X:64671186 2931769529 G	
46 L	136 C	-X:64671185 2931769528 C	L
46	137 T	-X:64671184 2931769527 T	
46	138 C	-X:64671183 2931769526 C	
47 S	139 A	-X:64671182 2931769525 A	S
47	140 G	-X:64671181 2931769524 G	
47	141 C	-X:64671180 2931769523 C	
48 R	142 A	-X:64671179 2931769522 A	R
48	143 G	-X:64671178 2931769521 G	
48	144 G	-X:64671177 2931769520 G	
49 A	145 G	-X:64671176 2931769519 G	A
49	146 C	-X:64671175 2931769518 C	
49	147 C	-X:64671174 2931769517 C	
50 E	148 G	-X:64671173 2931769516 G	E
50	149 A	-X:64671172 2931769515 A	
50	150 G	-X:64671171 2931769514 G	
51 W	151 T	-X:64671170 2931769513 T	W
51	152 G	-X:64671169 2931769512 G	
51	153 G	-X:64671168 2931769511 G	
52 D	154 G	-X:64671167 2931769510 G	D
52	155 A	-X:64671166 2931769509 A	
52	156 C	-X:64671165 2931769508 C	
53 Q	157 C	-X:64671164 2931769507 C	Q
53	158 A	-X:64671163 2931769506 A	
53	159 G	-X:64671162 2931769505 G	
54 V	160 G	-X:64671161 2931769504 G	V
54	161 T	-X:64671160 2931769503 T	
54	162 G	-X:64671159 2931769502 G	
55 T	163 A	-X:64671158 2931769501 A	T
55	164 C	-X:64671157 2931769500 C	
55	165 G	-X:64671156 2931769499 G	
56 V	166 G	-X:64671155 2931769498 G	V
56	167 T	-X:64671154 2931769497 T	
56	168 T	-X:64671153 2931769496 T	
57 Y	169 T	-X:64671152 2931769495 T	Y
57	170 A	-X:64671151 2931769494 A	
57	171 T	-X:64671150 2931769493 T	
58 L	172 C	-X:64671149 2931769492 C	L
58	173 T	-X:64671148 2931769491 T	
58	174 G	-X:64671147 2931769490 G	
59 F	175 T	-X:64671146 2931769489 T	F
59	176 T	-X:64671145 2931769488 T	
59	177 C	-X:64671144 2931769487 C	
60 C	178 T	-X:64671143 2931769486 T	C
60	179 G	-X:64671142 2931769485 G	
60	180 T	-X:64671141 2931769484 T	
61 D	181 G	-X:64671140 2931769483 G	D
61	182 A	-X:64671139 2931769482 A	
61	183 C	-X:64671138 2931769481 C	
62 D	184 G	-X:64671137 2931769480 G	D
62	185 A	-X:64671136 2931769479 A	
62	186 C	-X:64671135 2931769478 C	
63 H	187 C	-X:64671134 2931769477 C	H
63	188 A	-X:64671133 2931769476 A	
63	189 T	-X:64671132 2931769475 T	
64 K	190 A	-X:64671131 2931769474 A	K
64	191 A	-X:64671130 2931769473 A	
64	192 G	-X:64671129 2931769472 G	
65 L	193 T	-X:64671128 2931769471 T	L
65	194 T	-X:64671127 2931769470 T	
65	195 G	-X:64671126 2931769469 G	
66 Q	196 C	-X:64671125 2931769468 C	Q
66	197 A	-X:64671124 2931769467 A	
66	198 G	-X:64671123 2931769466 G	
67 R	199 C	-X:64671122 2931769465 C	R
67	200 G	-X:64671121 2931769464 G	
67	201 G	-X:64671120 2931769463 G	
68 Y	202 T	-X:64671119 2931769462 T	Y
68	203 A	-X:64671118 2931769461 A	
68	204 C	-X:64671117 2931769460 C	
69 A	205 G	-X:64671116 2931769459 G	A
69	206 C	-X:64671115 2931769458 C	
69	207 G	-X:64671114 2931769457 G	
70 L	208 C	-X:64671113 2931769456 C	L
70	209 T	-X:64671112 2931769455 T	
70	210 T	-X:64671111 2931769454 T	
71 N	211 A	-X:64671110 2931769453 A	N
71	212 A	-X:64671109 2931769452 A	
71	213 C	-X:64671108 2931769451 C	
72 R	214 C	-X:64671107 2931769450 C	R
72	215 G	-X:64671106 2931769449 G	
72	216 C	-X:64671105 2931769448 C	
73 I	217 A	-X:64671104 2931769447 A	I
73	218 T	-X:64671103 2931769446 T	
73	219 C	-X:64671102 2931769445 C	
74 T	220 A	-X:64671101 2931769444 A	T
74	221 C	-X:64671100 2931769443 C	
74	222 G	-X:64671099 2931769442 G	
75 V	223 G	-X:64671098 2931769441 G	V
75	224 T	-X:64671097 2931769440 T	
75	225 G	-X:64671096 2931769439 G	
76 W	226 T	-X:64671095 2931769438 T	W
76	227 G	-X:64671094 2931769437 G	
76	228 G	-X:64671093 2931769436 G	
77 R	229 A	-X:64671092 2931769435 A	R
77	230 G	-X:64671091 2931769434 G	
77	231 G	-X:64671090 2931769433 G	
78 S	232 A	-X:64671089 2931769432 A	S
78	233 G	-X:64671088 2931769431 G	
78	234 C	-X:64671087 2931769430 C	
79 R	235 A	-X:64671086 2931769429 A	R
79	236 G	-X:64671085 2931769428 G	
79	237 G	-X:64670340 2931768683 G	
80 S	238 T	-X:64670339 2931768682 T	S
80	239 C	-X:64670338 2931768681 C	
80	240 A	-X:64670337 2931768680 A	
81 G	241 G	-X:64670336 2931768679 G	G
81	242 G	-X:64670335 2931768678 G	
81	243 C	-X:64670334 2931768677 C	
82 N	244 A	-X:64670333 2931768676 A	N
82	245 A	-X:64670332 2931768675 A	
82	246 C	-X:64670331 2931768674 C	
83 E	247 G	-X:64670330 2931768673 G	E
83	248 A	-X:64670329 2931768672 A	
83	249 A	-X:64670328 2931768671 A	
84 L	250 C	-X:64670327 2931768670 C	L
84	251 T	-X:64670326 2931768669 T	
84	252 C	-X:64670325 2931768668 C	
85 P	253 C	-X:64670324 2931768667 C	P
85	254 C	-X:64670323 2931768666 C	
85	255 T	-X:64670322 2931768665 T	
86 L	256 C	-X:64670321 2931768664 C	L
86	257 T	-X:64670320 2931768663 T	
86	258 G	-X:64670319 2931768662 G	
87 A	259 G	-X:64670318 2931768661 G	A
87	260 C	-X:64670317 2931768660 C	
87	261 A	-X:64670316 2931768659 A	
88 V	262 G	-X:64670315 2931768658 G	V
88	263 T	-X:64670314 2931768657 T	
88	264 G	-X:64670313 2931768656 G	
89 A	265 G	-X:64670312 2931768655 G	A
89	266 C	-X:64670311 2931768654 C	
89	267 T	-X:64670310 2931768653 T	
90 S	268 T	-X:64670309 2931768652 T	S
90	269 C	-X:64670308 2931768651 C	
90	270 T	-X:64670307 2931768650 T	
91 T	271 A	-X:64670306 2931768649 A	T
91	272 C	-X:64670305 2931768648 C	
91	273 T	-X:64670304 2931768647 T	
92 A	274 G	-X:64670303 2931768646 G	A
92	275 C	-X:64670302 2931768645 C	
92	276 T	-X:64670301 2931768644 T	
93 D	277 G	-X:64670300 2931768643 G	D
93	278 A	-X:64670299 2931768642 A	
93	279 C	-X:64670298 2931768641 C	
94 L	280 C	-X:64670297 2931768640 C	L
94	281 T	-X:64670296 2931768639 T	
94	282 G	-X:64670295 2931768638 G	
95 I	283 A	-X:64670294 2931768637 A	I
95	284 T	-X:64670293 2931768636 T	
95	285 A	-X:64670292 2931768635 A	
96 R	286 C	-X:64670291 2931768634 C	R
96	287 G	-X:64670290 2931768633 G	
96	288 C	-X:64670289 2931768632 C	
97 C	289 T	-X:64670288 2931768631 T	C
97	290 G	-X:64670287 2931768630 G	
97	291 T	-X:64670286 2931768629 T	
98 K	292 A	-X:64670285 2931768628 A	K
98	293 A	-X:64670284 2931768627 A	
98	294 G	-X:64670283 2931768626 G	
99 L	295 C	-X:64670282 2931768625 C	L
99	296 T	-X:64670281 2931768624 T	
99	297 C	-X:64670280 2931768623 C	
100 L	298 T	-X:64670279 2931768622 T	L
100	299 T	-X:64670278 2931768621 T	
100	300 G	-X:64670277 2931768620 G	
101 D	301 G	-X:64670276 2931768619 G	D
101	302 A	-X:64670275 2931768618 A	
101	303 T	-X:64670274 2931768617 T	
102 V	304 G	-X:64670273 2931768616 G	V
102	305 T	-X:64670272 2931768615 T	
102	306 A	-X:64670271 2931768614 A	
103 T	307 A	-X:64670270 2931768613 A	T
103	308 C	-X:64670269 2931768612 C	
103	309 T	-X:64670268 2931768611 T	
104 G	310 G	-X:64670267 2931768610 G	G
104	311 G	-X:64670266 2931768609 G	
104	312 T	-X:64670265 2931768608 T	
105 G	313 G	-X:64670264 2931768607 G	G
105	314 G	-X:64670263 2931768606 G	
105	315 C	-X:64670262 2931768605 C	
106 L	316 T	-X:64670261 2931768604 T	L
106	317 T	-X:64670260 2931768603 T	
106	318 G	-X:64670259 2931768602 G	
107 G	319 G	-X:64670258 2931768601 G	G
107	320 G	-X:64670257 2931768600 G	
107	321 C	-X:64670256 2931768599 C	
108 T	322 A	-X:64670255 2931768598 A	T
108	323 C	-X:64670254 2931768597 C	
108	324 T	-X:64670253 2931768596 T	
109 D	325 G	-X:64670252 2931768595 G	D
109	326 A	-X:64670251 2931768594 A	
109	327 T	-X:64670250 2931768593 T	
110 E	328 G	-X:64670249 2931768592 G	E
110	329 A	-X:64670248 2931768591 A	
110	330 A	-X:64670247 2931768590 A	
111 L	331 C	-X:64670246 2931768589 C	L
111	332 T	-X:64670245 2931768588 T	
111	333 T	-X:64670244 2931768587 T	
112 R	334 A	-X:64670243 2931768586 A	R
112	335 G	-X:64670242 2931768585 G	
112	336 A	-X:64670241 2931768584 A	
113 L	337 C	-X:64670240 2931768583 C	L
113	338 T	-X:64670239 2931768582 T	
113	339 G	-X:64670238 2931768581 G	
114 L	340 C	-X:64670237 2931768580 C	L
114	341 T	-X:64670236 2931768579 T	
114	342 C	-X:64670235 2931768578 C	
115 Y	343 T	-X:64670234 2931768577 T	Y
115	344 A	-X:64670233 2931768576 A	
115	345 T	-X:64670232 2931768575 T	
116 G	346 G	-X:64670231 2931768574 G	G
116	347 G	-X:64670230 2931768573 G	
116	348 C	-X:64670229 2931768572 C	
117 M	349 A	-X:64670228 2931768571 A	M
117	350 T	-X:64670227 2931768570 T	
117	351 G	-X:64670226 2931768569 G	
118 A	352 G	-X:64670225 2931768568 G	A
118	353 C	-X:64670224 2931768567 C	
118	354 A	-X:64670223 2931768566 A	
119 L	355 T	-X:64670222 2931768565 T	L
119	356 T	-X:64670221 2931768564 T	
119	357 G	-X:64670220 2931768563 G	
120 V	358 G	-X:64670219 2931768562 G	V
120	359 T	-X:64670218 2931768561 T	
120	360 C	-X:64670217 2931768560 C	
121 R	361 A	-X:64670216 2931768559 A	R
121	362 G	-X:64670215 2931768558 G	
121	363 G	-X:64669235 2931767578 G	
122 F	364 T	-X:64669234 2931767577 T	F
122	365 T	-X:64669233 2931767576 T	
122	366 T	-X:64669232 2931767575 T	
123 V	367 G	-X:64669231 2931767574 G	V
123	368 T	-X:64669230 2931767573 T	
123	369 G	-X:64669229 2931767572 G	
124 N	370 A	-X:64669228 2931767571 A	N
124	371 A	-X:64669227 2931767570 A	
124	372 T	-X:64669226 2931767569 T	
125 L	373 C	-X:64669225 2931767568 C	L
125	374 T	-X:64669224 2931767567 T	
125	375 T	-X:64669223 2931767566 T	
126 I	376 A	-X:64669222 2931767565 A	I
126	377 T	-X:64669221 2931767564 T	
126	378 C	-X:64669220 2931767563 C	
127 S	379 T	-X:64669219 2931767562 T	S
127	380 C	-X:64669218 2931767561 C	
127	381 A	-X:64669217 2931767560 A	
128 E	382 G	-X:64669216 2931767559 G	E
128	383 A	-X:64669215 2931767558 A	
128	384 G	-X:64669214 2931767557 G	
129 R	385 A	-X:64669213 2931767556 A	R
129	386 G	-X:64669212 2931767555 G	
129	387 G	-X:64669211 2931767554 G	
130 K	388 A	-X:64669210 2931767553 A	K
130	389 A	-X:64669209 2931767552 A	
130	390 G	-X:64669208 2931767551 G	
131 T	391 A	-X:64669207 2931767550 A	T
131	392 C	-X:64669206 2931767549 C	
131	393 A	-X:64669205 2931767548 A	
132 K	394 A	-X:64669204 2931767547 A	K
132	395 A	-X:64669203 2931767546 A	
132	396 G	-X:64669202 2931767545 G	
133 F	397 T	-X:64669201 2931767544 T	F
133	398 T	-X:64669200 2931767543 T	
133	399 T	-X:64669199 2931767542 T	
134 A	400 G	-X:64669198 2931767541 G	A
134	401 C	-X:64669197 2931767540 C	
134	402 C	-X:64669196 2931767539 C	
135 K	403 A	-X:64669195 2931767538 A	K
135	404 A	-X:64669194 2931767537 A	
135	405 G	-X:64669193 2931767536 G	
136 V	406 G	-X:64669192 2931767535 G	V
136	407 T	-X:64669191 2931767534 T	
136	408 C	-X:64669190 2931767533 C	
137 P	409 C	-X:64669189 2931767532 C	P
137	410 C	-X:64669188 2931767531 C	
137	411 C	-X:64669187 2931767530 C	
138 L	412 C	-X:64669186 2931767529 C	L
138	413 T	-X:64669185 2931767528 T	
138	414 C	-X:64669184 2931767527 C	
139 K	415 A	-X:64669183 2931767526 A	K
139	416 A	-X:64669182 2931767525 A	
139	417 G	-X:64669181 2931767524 G	
140 C	418 T	-X:64669180 2931767523 T	C
140	419 G	-X:64669179 2931767522 G	
140	420 T	-X:64669178 2931767521 T	
141 L	421 C	-X:64669177 2931767520 C	L
141	422 T	-X:64669176 2931767519 T	
141	423 G	-X:64669175 2931767518 G	
142 A	424 G	-X:64669174 2931767517 G	A
142	425 C	-X:64669173 2931767516 C	
142	426 T	-X:64669172 2931767515 T	
143 Q	427 C	-X:64669171 2931767514 C	Q
143	428 A	-X:64669170 2931767513 A	
143	429 A	-X:64669169 2931767512 A	
144 E	430 G	-X:64669168 2931767511 G	E
144	431 A	-X:64669167 2931767510 A	
144	432 G	-X:64669166 2931767509 G	
145 V	433 G	-X:64668043 2931766386 G	V
145	434 T	-X:64668042 2931766385 T	
145	435 A	-X:64668041 2931766384 A	
146 N	436 A	-X:64668040 2931766383 A	N
146	437 A	-X:64668039 2931766382 A	
146	438 T	-X:64668038 2931766381 T	
147 I	439 A	-X:64668037 2931766380 A	I
147	440 T	-X:64668036 2931766379 T	
147	441 T	-X:64668035 2931766378 T	
148 P	442 C	-X:64668034 2931766377 C	P
148	443 C	-X:64668033 2931766376 C	
148	444 G	-X:64668032 2931766375 G	
149 D	445 G	-X:64668031 2931766374 G	D
149	446 A	-X:64668030 2931766373 A	
149	447 T	-X:64668029 2931766372 T	
150 W	448 T	-X:64668028 2931766371 T	W
150	449 G	-X:64668027 2931766370 G	
150	450 G	-X:64668026 2931766369 G	
151 I	451 A	-X:64668025 2931766368 A	I
151	452 T	-X:64668024 2931766367 T	
151	453 T	-X:64668023 2931766366 T	
152 V	454 G	-X:64668022 2931766365 G	V
152	455 T	-X:64668021 2931766364 T	
152	456 T	-X:64668020 2931766363 T	
153 D	457 G	-X:64668019 2931766362 G	D
153	458 A	-X:64668018 2931766361 A	
153	459 C	-X:64668017 2931766360 C	
154 L	460 C	-X:64668016 2931766359 C	L
154	461 T	-X:64668015 2931766358 T	
154	462 T	-X:64668014 2931766357 T	
155 R	463 C	-X:64668013 2931766356 C	R
155	464 G	-X:64668012 2931766355 G	
155	465 C	-X:64668011 2931766354 C	
156 H	466 C	-X:64668010 2931766353 C	H
156	467 A	-X:64668009 2931766352 A	
156	468 T	-X:64668008 2931766351 T	
157 E	469 G	-X:64668007 2931766350 G	E
157	470 A	-X:64668006 2931766349 A	
157	471 G	-X:64668005 2931766348 G	
158 L	472 T	-X:64668004 2931766347 T	L
158	473 T	-X:64668003 2931766346 T	
158	474 G	-X:64668002 2931766345 G	
159 T	475 A	-X:64668001 2931766344 A	T
159	476 C	-X:64668000 2931766343 C	
159	477 C	-X:64667999 2931766342 C	
160 H	478 C	-X:64667998 2931766341 C	H
160	479 A	-X:64667997 2931766340 A	
160	480 C	-X:64667996 2931766339 C	
161 K	481 A	-X:64667995 2931766338 A	K
161	482 A	-X:64667994 2931766337 A	
161	483 G	-X:64667993 2931766336 G	
162 K	484 A	-X:64667992 2931766335 A	K
162	485 A	-X:64667991 2931766334 A	
162	486 A	-X:64667990 2931766333 A	
163 M	487 A	-X:64667989 2931766332 A	M
163	488 T	-X:64667988 2931766331 T	
163	489 G	-X:64667987 2931766330 G	
164 P	490 C	-X:64667986 2931766329 C	P
164	491 C	-X:64667985 2931766328 C	
164	492 C	-X:64667984 2931766327 C	
165 H	493 C	-X:64667983 2931766326 C	H
165	494 A	-X:64667982 2931766325 A	
165	495 T	-X:64667981 2931766324 T	
166 I	496 A	-X:64667980 2931766323 A	I
166	497 T	-X:64667979 2931766322 T	
166	498 A	-X:64667978 2931766321 A	
167 N	499 A	-X:64667977 2931766320 A	N
167	500 A	-X:64667976 2931766319 A	
167	501 T	-X:64667975 2931766318 T	
168 D	502 G	-X:64667974 2931766317 G	D
168	503 A	-X:64667973 2931766316 A	
168	504 C	-X:64667972 2931766315 C	
169 C	505 T	-X:64667971 2931766314 T	C
169	506 G	-X:64667970 2931766313 G	
169	507 C	-X:64667969 2931766312 C	
170 R	508 C	-X:64667968 2931766311 C	R
170	509 G	-X:64667967 2931766310 G	
170	510 C	-X:64667966 2931766309 C	
171 R	511 A	-X:64667965 2931766308 A	R
171	512 G	-X:64667964 2931766307 G	
171	513 A	-X:64667963 2931766306 A	
172 G	514 G	-X:64667962 2931766305 G	G
172	515 G	-X:64666483 2931764826 G	
172	516 C	-X:64666482 2931764825 C	
173 C	517 T	-X:64666481 2931764824 T	C
173	518 G	-X:64666480 2931764823 G	
173	519 C	-X:64666479 2931764822 C	
174 Y	520 T	-X:64666478 2931764821 T	Y
174	521 A	-X:64666477 2931764820 A	
174	522 C	-X:64666476 2931764819 C	
175 F	523 T	-X:64666475 2931764818 T	F
175	524 T	-X:64666474 2931764817 T	
175	525 T	-X:64666473 2931764816 T	
176 V	526 G	-X:64666472 2931764815 G	V
176	527 T	-X:64666471 2931764814 T	
176	528 C	-X:64666470 2931764813 C	
177 L	529 C	-X:64666469 2931764812 C	L
177	530 T	-X:64666468 2931764811 T	
177	531 G	-X:64666467 2931764810 G	
178 D	532 G	-X:64666466 2931764809 G	D
178	533 A	-X:64666465 2931764808 A	
178	534 T	-X:64666464 2931764807 T	
179 W	535 T	-X:64666463 2931764806 T	W
179	536 G	-X:64666462 2931764805 G	
179	537 G	-X:64666461 2931764804 G	
180 L	538 C	-X:64666460 2931764803 C	L
180	539 T	-X:64666459 2931764802 T	
180	540 C	-X:64666458 2931764801 C	
181 Q	541 C	-X:64666457 2931764800 C	Q
181	542 A	-X:64666456 2931764799 A	
181	543 G	-X:64666455 2931764798 G	
182 K	544 A	-X:64666454 2931764797 A	K
182	545 A	-X:64666453 2931764796 A	
182	546 G	-X:64666452 2931764795 G	
183 T	547 A	-X:64666451 2931764794 A	T
183	548 C	-X:64666450 2931764793 C	
183	549 C	-X:64666449 2931764792 C	
184 Y	550 T	-X:64666448 2931764791 T	Y
184	551 A	-X:64666447 2931764790 A	
184	552 T	-X:64666446 2931764789 T	
185 W	553 T	-X:64666445 2931764788 T	W
185	554 G	-X:64666444 2931764787 G	
185	555 G	-X:64666443 2931764786 G	
186 C	556 T	-X:64666442 2931764785 T	C
186	557 G	-X:64666441 2931764784 G	
186	558 C	-X:64666440 2931764783 C	
187 R	559 C	-X:64666439 2931764782 C	R
187	560 G	-X:64666438 2931764781 G	
187	561 C	-X:64666437 2931764780 C	
188 Q	562 C	-X:64666436 2931764779 C	Q
188	563 A	-X:64666435 2931764778 A	
188	564 A	-X:64666434 2931764777 A	
189 L	565 C	-X:64666433 2931764776 C	L
189	566 T	-X:64666432 2931764775 T	
189	567 G	-X:64666431 2931764774 G	
190 E	568 G	-X:64666430 2931764773 G	E
190	569 A	-X:64666429 2931764772 A	
190	570 G	-X:64666428 2931764771 G	
191 N	571 A	-X:64666427 2931764770 A	N
191	572 A	-X:64666426 2931764769 A	
191	573 C	-X:64666425 2931764768 C	
192 S	574 A	-X:64666424 2931764767 A	S
192	575 G	-X:64666423 2931764766 G	
192	576 C	-X:64666422 2931764765 C	
193 L	577 C	-X:64666421 2931764764 C	L
193	578 T	-X:64666420 2931764763 T	
193	579 G	-X:64666419 2931764762 G	
194 R	580 A	-X:64666418 2931764761 A	R
194	581 G	-X:64666417 2931764760 G	
194	582 A	-X:64666416 2931764759 A	
195 E	583 G	-X:64666415 2931764758 G	E
195	584 A	-X:64666414 2931764757 A	
195	585 G	-X:64666413 2931764756 G	
196 T	586 A	-X:64666412 2931764755 A	T
196	587 C	-X:64666411 2931764754 C	
196	588 C	-X:64666410 2931764753 C	
197 W	589 T	-X:64666409 2931764752 T	W
197	590 G	-X:64666408 2931764751 G	
197	591 G	-X:64666407 2931764750 G	
198 E	592 G	-X:64666406 2931764749 G	E
198	593 A	-X:64666405 2931764748 A	
198	594 G	-X:64666404 2931764747 G	
199 L	595 T	-X:64666403 2931764746 T	L
199	596 T	-X:64666402 2931764745 T	
199	597 G	-X:64666401 2931764744 G	
200 E	598 G	-X:64666400 2931764743 G	E
200	599 A	-X:64666399 2931764742 A	
200	600 G	-X:64666398 2931764741 G	
201 E	601 G	-X:64666397 2931764740 G	E
201	602 A	-X:64666396 2931764739 A	
201	603 G	-X:64666395 2931764738 G	
202 F	604 T	-X:64666394 2931764737 T	F
202	605 T	-X:64666393 2931764736 T	
202	606 C	-X:64666392 2931764735 C	
203 R	607 A	-X:64666391 2931764734 A	R
203	608 G	-X:64666390 2931764733 G	
203	609 G	-X:64666389 2931764732 G	
204 E	610 G	-X:64666388 2931764731 G	E
204	611 A	-X:64666387 2931764730 A	
204	612 A	-X:64666386 2931764729 A	
205 G	613 G	-X:64666385 2931764728 G	G
205	614 G	-X:64666384 2931764727 G	
205	615 G	-X:64666383 2931764726 G	
206 I	616 A	-X:64666382 2931764725 A	I
206	617 T	-X:64666381 2931764724 T	
206	618 A	-X:64666380 2931764723 A	
207 E	619 G	-X:64666379 2931764722 G	E
207	620 A	-X:64666378 2931764721 A	
207	621 G	-X:64666377 2931764720 G	
208 E	622 G	-X:64666376 2931764719 G	E
208	623 A	-X:64666375 2931764718 A	
208	624 A	-X:64666374 2931764717 A	
209 E	625 G	-X:64666373 2931764716 G	E
209	626 A	-X:64666372 2931764715 A	
209	627 G	-X:64666371 2931764714 G	
210 D	628 G	-X:64666370 2931764713 G	D
210	629 A	-X:64666369 2931764712 A	
210	630 T	-X:64666368 2931764711 T	
211 Q	631 C	-X:64666367 2931764710 C	Q
211	632 A	-X:64666366 2931764709 A	
211	633 A	-X:64666365 2931764708 A	
212 E	634 G	-X:64666364 2931764707 G	E
212	635 A	-X:64666363 2931764706 A	
212	636 G	-X:64666362 2931764705 G	
213 E	637 G	-X:64666361 2931764704 G	E
213	638 A	-X:64666360 2931764703 A	
213	639 A	-X:64666359 2931764702 A	
214 D	640 G	-X:64666358 2931764701 G	D
214	641 A	-X:64666357 2931764700 A	
214	642 T	-X:64666356 2931764699 T	
215 K	643 A	-X:64666355 2931764698 A	K
215	644 A	-X:64666354 2931764697 A	
215	645 G	-X:64666353 2931764696 G	
216 N	646 A	-X:64666352 2931764695 A	N
216	647 A	-X:64666351 2931764694 A	
216	648 C	-X:64666350 2931764693 C	
217 I	649 A	-X:64666349 2931764692 A	I
217	650 T	-X:64666348 2931764691 T	
217	651 T	-X:64666347 2931764690 T	
218 V	652 G	-X:64666346 2931764689 G	V
218	653 T	-X:64666345 2931764688 T	
218	654 T	-X:64666344 2931764687 T	
219 V	655 G	-X:64666343 2931764686 G	V
219	656 T	-X:64666342 2931764685 T	
219	657 T	-X:64666341 2931764684 T	
220 D	658 G	-X:64666340 2931764683 G	D
220	659 A	-X:64666339 2931764682 A	
220	660 T	-X:64666338 2931764681 T	
221 D	661 G	-X:64666337 2931764680 G	D
221	662 A	-X:64666336 2931764679 A	
221	663 C	-X:64666335 2931764678 C	
222 I	664 A	-X:64666334 2931764677 A	I
222	665 T	-X:64666333 2931764676 T	
222	666 C	-X:64666332 2931764675 C	
223 T	667 A	-X:64666331 2931764674 A	T
223	668 C	-X:64666330 2931764673 C	
223	669 A	-X:64666329 2931764672 A	
224 E	670 G	-X:64666328 2931764671 G	E
224	671 A	-X:64666327 2931764670 A	
224	672 A	-X:64666326 2931764669 A	
225 Q	673 C	-X:64666325 2931764668 C	Q
225	674 A	-X:64666324 2931764667 A	
225	675 G	-X:64666323 2931764666 G	
226 K	676 A	-X:64666322 2931764665 A	K
226	677 A	-X:64666321 2931764664 A	
226	678 A	-X:64666320 2931764663 A	
227 P	679 C	-X:64666319 2931764662 C	P
227	680 C	-X:64666318 2931764661 C	
227	681 A	-X:64666317 2931764660 A	
228 E	682 G	-X:64666316 2931764659 G	E
228	683 A	-X:64666315 2931764658 A	
228	684 G	-X:64666314 2931764657 G	
229 P	685 C	-X:64666313 2931764656 C	P
229	686 C	-X:64666312 2931764655 C	
229	687 T	-X:64666311 2931764654 T	
230 Q	688 C	-X:64666310 2931764653 C	Q
230	689 A	-X:64666309 2931764652 A	
230	690 G	-X:64666308 2931764651 G	
231 D	691 G	-X:64666307 2931764650 G	D
231	692 A	-X:64666306 2931764649 A	
231	693 T	-X:64666305 2931764648 T	
232 D	694 G	-X:64666304 2931764647 G	D
232	695 A	-X:64666303 2931764646 A	
232	696 T	-X:64666302 2931764645 T	
233 G	697 G	-X:64666301 2931764644 G	G
233	698 G	-X:64666300 2931764643 G	
233	699 G	-X:64666299 2931764642 G	
234 K	700 A	-X:64666298 2931764641 A	K
234	701 A	-X:64666297 2931764640 A	
234	702 A	-X:64666296 2931764639 A	
235 S	703 A	-X:64666295 2931764638 A	S
235	704 G	-X:64666294 2931764637 G	
235	705 T	-X:64666293 2931764636 T	
236 T	706 A	-X:64666292 2931764635 A	T
236	707 C	-X:64666291 2931764634 C	
236	708 G	-X:64666290 2931764633 G	
237 E	709 G	-X:64666289 2931764632 G	E
237	710 A	-X:64666288 2931764631 A	
237	711 G	-X:64666287 2931764630 G	
238 S	712 T	-X:64666286 2931764629 T	S
238	713 C	-X:64666285 2931764628 C	
238	714 A	-X:64666284 2931764627 A	
239 D	715 G	-X:64666283 2931764626 G	D
239	716 A	-X:64666282 2931764625 A	
239	717 T	-X:64666281 2931764624 T	
240 V	718 G	-X:64666280 2931764623 G	V
240	719 T	-X:64666279 2931764622 T	
240	720 A	-X:64666278 2931764621 A	
241 K	721 A	-X:64666277 2931764620 A	K
241	722 A	-X:64666276 2931764619 A	
241	723 G	-X:64666275 2931764618 G	
242 A	724 G	-X:64666274 2931764617 G	A
242	725 C	-X:64666273 2931764616 C	
242	726 C	-X:64666272 2931764615 C	
243 D	727 G	-X:64666271 2931764614 G	D
243	728 A	-X:64666270 2931764613 A	
243	729 T	-X:64666269 2931764612 T	
244 G	730 G	-X:64666268 2931764611 G	G
244	731 G	-X:64666267 2931764610 G	
244	732 A	-X:64666266 2931764609 A	
245 D	733 G	-X:64666265 2931764608 G	D
245	734 A	-X:64666264 2931764607 A	
245	735 C	-X:64666263 2931764606 C	
246 S	736 A	-X:64666262 2931764605 A	S
246	737 G	-X:64666261 2931764604 G	
246	738 C	-X:64666260 2931764603 C	
247 K	739 A	-X:64666259 2931764602 A	K
247	740 A	-X:64666258 2931764601 A	
247	741 A	-X:64666257 2931764600 A	
248 G	742 G	-X:64666256 2931764599 G	G
248	743 G	-X:64666255 2931764598 G	
248	744 C	-X:64666254 2931764597 C	
249 S	745 A	-X:64666253 2931764596 A	S
249	746 G	-X:64666252 2931764595 G	
249	747 C	-X:64666251 2931764594 C	
250 E	748 G	-X:64666250 2931764593 G	E
250	749 A	-X:64666249 2931764592 A	
250	750 A	-X:64666248 2931764591 A	
251 E	751 G	-X:64666247 2931764590 G	E
251	752 A	-X:64666246 2931764589 A	
251	753 G	-X:64666245 2931764588 G	
252 V	754 G	-X:64666244 2931764587 G	V
252	755 T	-X:64666243 2931764586 T	
252	756 G	-X:64666242 2931764585 G	
253 D	757 G	-X:64666241 2931764584 G	D
253	758 A	-X:64666240 2931764583 A	
253	759 T	-X:64666239 2931764582 T	
254 S	760 T	-X:64666238 2931764581 T	S
254	761 C	-X:64666237 2931764580 C	
254	762 T	-X:64666236 2931764579 T	
255 H	763 C	-X:64666235 2931764578 C	H
255	764 A	-X:64666234 2931764577 A	
255	765 T	-X:64666233 2931764576 T	
256 C	766 T	-X:64666232 2931764575 T	C
256	767 G	-X:64666231 2931764574 G	
256	768 C	-X:64666230 2931764573 C	
257 K	769 A	-X:64666229 2931764572 A	K
257	770 A	-X:64666228 2931764571 A	
257	771 A	-X:64666227 2931764570 A	
258 K	772 A	-X:64666226 2931764569 A	K
258	773 A	-X:64666225 2931764568 A	
258	774 G	-X:64666224 2931764567 G	
259 A	775 G	-X:64666223 2931764566 G	A
259	776 C	-X:64666222 2931764565 C	
259	777 C	-X:64666221 2931764564 C	
260 L	778 C	-X:64666220 2931764563 C	L
260	779 T	-X:64666219 2931764562 T	
260	780 G	-X:64666218 2931764561 G	
261 S	781 A	-X:64666217 2931764560 A	S
261	782 G	-X:64666216 2931764559 G	
261	783 T	-X:64666215 2931764558 T	
262 H	784 C	-X:64666214 2931764557 C	H
262	785 A	-X:64666213 2931764556 A	
262	786 T	-X:64666212 2931764555 T	
263 K	787 A	-X:64666211 2931764554 A	K
263	788 A	-X:64666210 2931764553 A	
263	789 A	-X:64666209 2931764552 A	
264 E	790 G	-X:64666208 2931764551 G	E
264	791 A	-X:64666207 2931764550 A	
264	792 G	-X:64666206 2931764549 G	
265 L	793 C	-X:64666205 2931764548 C	L
265	794 T	-X:64666204 2931764547 T	
265	795 A	-X:64666203 2931764546 A	
266 Y	796 T	-X:64666202 2931764545 T	Y
266	797 A	-X:64666201 2931764544 A	
266	798 T	-X:64666200 2931764543 T	
267 E	799 G	-X:64666199 2931764542 G	E
267	800 A	-X:64665863 2931764206 A	
267	801 A	-X:64665862 2931764205 A	
268 R	802 A	-X:64665861 2931764204 A	R
268	803 G	-X:64665860 2931764203 G	
268	804 A	-X:64665859 2931764202 A	
269 A	805 G	-X:64665858 2931764201 G	A
269	806 C	-X:64665857 2931764200 C	
269	807 C	-X:64665856 2931764199 C	
270 R	808 C	-X:64665855 2931764198 C	R
270	809 G	-X:64665854 2931764197 G	
270	810 A	-X:64665853 2931764196 A	
271 E	811 G	-X:64665852 2931764195 G	E
271	812 A	-X:64665851 2931764194 A	
271	813 A	-X:64665850 2931764193 A	
272 L	814 C	-X:64665849 2931764192 C	L
272	815 T	-X:64665848 2931764191 T	
272	816 G	-X:64665847 2931764190 G	
273 L	817 C	-X:64665846 2931764189 C	L
273	818 T	-X:64665845 2931764188 T	
273	819 G	-X:64665844 2931764187 G	
274 V	820 G	-X:64665843 2931764186 G	V
274	821 T	-X:64665842 2931764185 T	
274	822 A	-X:64665841 2931764184 A	
275 S	823 T	-X:64665840 2931764183 T	S
275	824 C	-X:64665839 2931764182 C	
275	825 A	-X:64665838 2931764181 A	
276 Y	826 T	-X:64665837 2931764180 T	Y
276	827 A	-X:64665836 2931764179 A	
276	828 C	-X:64665835 2931764178 C	
277 E	829 G	-X:64665834 2931764177 G	E
277	830 A	-X:64665833 2931764176 A	
277	831 A	-X:64665832 2931764175 A	
278 E	832 G	-X:64665831 2931764174 G	E
278	833 A	-X:64665830 2931764173 A	
278	834 G	-X:64665829 2931764172 G	
279 E	835 G	-X:64665828 2931764171 G	E
279	836 A	-X:64665827 2931764170 A	
279	837 G	-X:64665826 2931764169 G	
280 Q	838 C	-X:64665825 2931764168 C	Q
280	839 A	-X:64665824 2931764167 A	
280	840 G	-X:64665823 2931764166 G	
281 F	841 T	-X:64665822 2931764165 T	F
281	842 T	-X:64665821 2931764164 T	
281	843 T	-X:64665820 2931764163 T	
282 T	844 A	-X:64665819 2931764162 A	T
282	845 C	-X:64665818 2931764161 C	
282	846 G	-X:64665817 2931764160 G	
283 V	847 G	-X:64664974 2931763317 G	V
283	848 T	-X:64664973 2931763316 T	
283	849 G	-X:64664972 2931763315 G	
284 L	850 C	-X:64664971 2931763314 C	L
284	851 T	-X:64664970 2931763313 T	
284	852 G	-X:64664969 2931763312 G	
285 E	853 G	-X:64664968 2931763311 G	E
285	854 A	-X:64664967 2931763310 A	
285	855 G	-X:64664966 2931763309 G	
286 K	856 A	-X:64664965 2931763308 A	K
286	857 A	-X:64664964 2931763307 A	
286	858 A	-X:64664963 2931763306 A	
287 F	859 T	-X:64664962 2931763305 T	F
287	860 T	-X:64664961 2931763304 T	
287	861 T	-X:64664960 2931763303 T	
288 R	862 A	-X:64664959 2931763302 A	R
288	863 G	-X:64664958 2931763301 G	
288	864 G	-X:64664957 2931763300 G	
289 Y	865 T	-X:64664956 2931763299 T	Y
289	866 A	-X:64664955 2931763298 A	
289	867 T	-X:64664954 2931763297 T	
290 L	868 T	-X:64664953 2931763296 T	L
290	869 T	-X:64664952 2931763295 T	
290	870 A	-X:64664951 2931763294 A	
291 P	871 C	-X:64664950 2931763293 C	P
291	872 C	-X:64664949 2931763292 C	
291	873 T	-X:64664948 2931763291 T	
292 K	874 A	-X:64664947 2931763290 A	K
292	875 A	-X:64664946 2931763289 A	
292	876 G	-X:64664945 2931763288 G	
293 A	877 G	-X:64664944 2931763287 G	A
293	878 C	-X:64664943 2931763286 C	
293	879 C	-X:64664942 2931763285 C	
294 I	880 A	-X:64664941 2931763284 A	I
294	881 T	-X:64664940 2931763283 T	
294	882 T	-X:64664939 2931763282 T	
295 K	883 A	-X:64664938 2931763281 A	K
295	884 A	-X:64664937 2931763280 A	
295	885 G	-X:64664936 2931763279 G	
296 A	886 G	-X:64664935 2931763278 G	A
296	887 C	-X:64664934 2931763277 C	
296	888 G	-X:64664933 2931763276 G	
297 W	889 T	-X:64664932 2931763275 T	W
297	890 G	-X:64664931 2931763274 G	
297	891 G	-X:64664930 2931763273 G	
298 N	892 A	-X:64664929 2931763272 A	N
298	893 A	-X:64664928 2931763271 A	
298	894 T	-X:64664927 2931763270 T	
299 N	895 A	-X:64664926 2931763269 A	N
299	896 A	-X:64664925 2931763268 A	
299	897 C	-X:64664924 2931763267 C	
300 P	898 C	-X:64664923 2931763266 C	P
300	899 C	-X:64664922 2931763265 C	
300	900 G	-X:64664921 2931763264 G	
301 S	901 T	-X:64664920 2931763263 T	S
301	902 C	-X:64664919 2931763262 C	
301	903 C	-X:64664918 2931763261 C	
302 P	904 C	-X:64664917 2931763260 C	P
302	905 C	-X:64664916 2931763259 C	
302	906 A	-X:64664915 2931763258 A	
303 R	907 C	-X:64664914 2931763257 C	R
303	908 G	-X:64664913 2931763256 G	
303	909 T	-X:64664912 2931763255 T	
304 V	910 G	-X:64664911 2931763254 G	V
304	911 T	-X:64664910 2931763253 T	
304	912 A	-X:64664909 2931763252 A	
305 E	913 G	-X:64664908 2931763251 G	E
305	914 A	-X:64664907 2931763250 A	
305	915 A	-X:64664906 2931763249 A	
306 C	916 T	-X:64664905 2931763248 T	C
306	917 G	-X:64664904 2931763247 G	
306	918 T	-X:64664903 2931763246 T	
307 V	919 G	-X:64664902 2931763245 G	V
307	920 T	-X:64664901 2931763244 T	
307	921 C	-X:64664900 2931763243 C	
308 L	922 C	-X:64664899 2931763242 C	L
308	923 T	-X:64664898 2931763241 T	
308	924 G	-X:64664897 2931763240 G	
309 A	925 G	-X:64664896 2931763239 G	A
309	926 C	-X:64664895 2931763238 C	
309	927 A	-X:64664894 2931763237 A	
310 E	928 G	-X:64664893 2931763236 G	E
310	929 A	-X:64664892 2931763235 A	
310	930 G	-X:64664891 2931763234 G	
311 L	931 C	-X:64664890 2931763233 C	L
311	932 T	-X:64664889 2931763232 T	
311	933 C	-X:64664888 2931763231 C	
312 K	934 A	-X:64664887 2931763230 A	K
312	935 A	-X:64664886 2931763229 A	
312	936 G	-X:64664885 2931763228 G	
313 G	937 G	-X:64664884 2931763227 G	G
313	938 G	-X:64664883 2931763226 G	
313	939 C	-X:64664882 2931763225 C	
314 V	940 G	-X:64664881 2931763224 G	V
314	941 T	-X:64664880 2931763223 T	
314	942 T	-X:64664879 2931763222 T	
315 T	943 A	-X:64664878 2931763221 A	T
315	944 C	-X:64664877 2931763220 C	
315	945 A	-X:64664876 2931763219 A	
316 C	946 T	-X:64664875 2931763218 T	C
316	947 G	-X:64664874 2931763217 G	
316	948 C	-X:64664873 2931763216 C	
317 E	949 G	-X:64664872 2931763215 G	E
317	950 A	-X:64664871 2931763214 A	
317	951 G	-X:64664870 2931763213 G	
318 N	952 A	-X:64664869 2931763212 A	N
318	953 A	-X:64664868 2931763211 A	
318	954 C	-X:64664867 2931763210 C	
319 R	955 A	-X:64664866 2931763209 A	R
319	956 G	-X:64664865 2931763208 G	
319	957 G	-X:64661655 2931759998 G	
320 E	958 G	-X:64661654 2931759997 G	E
320	959 A	-X:64661653 2931759996 A	
320	960 G	-X:64661652 2931759995 G	
321 A	961 G	-X:64661651 2931759994 G	A
321	962 C	-X:64661650 2931759993 C	
321	963 T	-X:64661649 2931759992 T	
322 V	964 G	-X:64661648 2931759991 G	V
322	965 T	-X:64661647 2931759990 T	
322	966 G	-X:64661646 2931759989 G	
323 L	967 C	-X:64661645 2931759988 C	L
323	968 T	-X:64661644 2931759987 T	
323	969 G	-X:64661643 2931759986 G	
324 D	970 G	-X:64661642 2931759985 G	D
324	971 A	-X:64661641 2931759984 A	
324	972 T	-X:64661640 2931759983 T	
325 A	973 G	-X:64661639 2931759982 G	A
325	974 C	-X:64661638 2931759981 C	
325	975 T	-X:64661637 2931759980 T	
326 F	976 T	-X:64661636 2931759979 T	F
326	977 T	-X:64661635 2931759978 T	
326	978 T	-X:64661634 2931759977 T	
327 L	979 C	-X:64661633 2931759976 C	L
327	980 T	-X:64661632 2931759975 T	
327	981 G	-X:64661631 2931759974 G	
328 D	982 G	-X:64661630 2931759973 G	D
328	983 A	-X:64661629 2931759972 A	
328	984 T	-X:64661628 2931759971 T	
329 D	985 G	-X:64661627 2931759970 G	D
329	986 A	-X:64661626 2931759969 A	
329	987 T	-X:64661625 2931759968 T	
330 G	988 G	-X:64661624 2931759967 G	G
330	989 G	-X:64661623 2931759966 G	
330	990 C	-X:64661622 2931759965 C	
331 F	991 T	-X:64661621 2931759964 T	F
331	992 T	-X:64661620 2931759963 T	
331	993 C	-X:64661619 2931759962 C	
332 L	994 C	-X:64661618 2931759961 C	L
332	995 T	-X:64661617 2931759960 T	
332	996 T	-X:64661616 2931759959 T	
333 V	997 G	-X:64661615 2931759958 G	V
333	998 T	-X:64661614 2931759957 T	
333	999 C	-X:64661613 2931759956 C	
334 P	1000 C	-X:64661612 2931759955 C	P
334	1001 C	-X:64661611 2931759954 C	
334	1002 C	-X:64661610 2931759953 C	
335 T	1003 A	-X:64661609 2931759952 A	T
335	1004 C	-X:64661608 2931759951 C	
335	1005 A	-X:64661607 2931759950 A	
336 F	1006 T	-X:64661606 2931759949 T	F
336	1007 T	-X:64661605 2931759948 T	
336	1008 T	-X:64661604 2931759947 T	
337 E	1009 G	-X:64661603 2931759946 G	E
337	1010 A	-X:64661602 2931759945 A	
337	1011 A	-X:64661601 2931759944 A	
338 Q	1012 C	-X:64661600 2931759943 C	Q
338	1013 A	-X:64661599 2931759942 A	
338	1014 G	-X:64661598 2931759941 G	
339 L	1015 T	-X:64661597 2931759940 T	L
339	1016 T	-X:64661596 2931759939 T	
339	1017 G	-X:64661595 2931759938 G	
340 A	1018 G	-X:64661594 2931759937 G	A
340	1019 C	-X:64661593 2931759936 C	
340	1020 A	-X:64661592 2931759935 A	
341 A	1021 G	-X:64661591 2931759934 G	A
341	1022 C	-X:64661590 2931759933 C	
341	1023 T	-X:64661589 2931759932 T	
342 L	1024 T	-X:64661588 2931759931 T	L
342	1025 T	-X:64661587 2931759930 T	
342	1026 G	-X:64661586 2931759929 G	
343 Q	1027 C	-X:64661585 2931759928 C	Q
343	1028 A	-X:64661584 2931759927 A	
343	1029 G	-X:64661583 2931759926 G	
344 I	1030 A	-X:64661582 2931759925 A	I
344	1031 T	-X:64661581 2931759924 T	
344	1032 A	-X:64661580 2931759923 A	
345 E	1033 G	-X:64661579 2931759922 G	E
345	1034 A	-X:64661578 2931759921 A	
345	1035 A	-X:64661577 2931759920 A	
346 Y	1036 T	-X:64661576 2931759919 T	Y
346	1037 A	-X:64661575 2931759918 A	
346	1038 T	-X:64661574 2931759917 T	
347 E	1039 G	-X:64661573 2931759916 G	E
347	1040 A	-X:64661572 2931759915 A	
347	1041 A	-X:64661571 2931759914 A	
348 D	1042 G	-X:64661570 2931759913 G	D
348	1043 A	-X:64661219 2931759562 A	
348	1044 T	-X:64661218 2931759561 T	
349 G	1045 G	-X:64661217 2931759560 G	G
349	1046 G	-X:64661216 2931759559 G	
349	1047 T	-X:64661215 2931759558 T	
350 Q	1048 C	-X:64661214 2931759557 C	Q
350	1049 A	-X:64661213 2931759556 A	
350	1050 G	-X:64661212 2931759555 G	
351 T	1051 A	-X:64661211 2931759554 A	T
351	1052 C	-X:64661210 2931759553 C	
351	1053 T	-X:64661209 2931759552 T	
352 E	1054 G	-X:64661208 2931759551 G	E
352	1055 A	-X:64661207 2931759550 A	
352	1056 G	-X:64661206 2931759549 G	
353 V	1057 G	-X:64661205 2931759548 G	V
353	1058 T	-X:64661204 2931759547 T	
353	1059 C	-X:64661203 2931759546 C	
354 Q	1060 C	-X:64661202 2931759545 C	Q
354	1061 A	-X:64661201 2931759544 A	
354	1062 G	-X:64661200 2931759543 G	
355 R	1063 A	-X:64661199 2931759542 A	R
355	1064 G	-X:64661198 2931759541 G	
355	1065 A	-X:64661197 2931759540 A	
356 G	1066 G	-X:64661196 2931759539 G	G
356	1067 G	-X:64661195 2931759538 G	
356	1068 G	-X:64661194 2931759537 G	
357 E	1069 G	-X:64661193 2931759536 G	E
357	1070 A	-X:64661192 2931759535 A	
357	1071 A	-X:64661191 2931759534 A	
358 G	1072 G	-X:64661190 2931759533 G	G
358	1073 G	-X:64661189 2931759532 G	
358	1074 T	-X:64661188 2931759531 T	
359 T	1075 A	-X:64661187 2931759530 A	T
359	1076 C	-X:64661186 2931759529 C	
359	1077 T	-X:64661185 2931759528 T	
360 D	1078 G	-X:64661184 2931759527 G	D
360	1079 A	-X:64661183 2931759526 A	
360	1080 C	-X:64661182 2931759525 C	
361 P	1081 C	-X:64661181 2931759524 C	P
361	1082 C	-X:64661180 2931759523 C	
361	1083 A	-X:64661179 2931759522 A	
362 K	1084 A	-X:64661178 2931759521 A	K
362	1085 A	-X:64661177 2931759520 A	
362	1086 G	-X:64661176 2931759519 G	
363 S	1087 T	-X:64661175 2931759518 T	S
363	1088 C	-X:64661174 2931759517 C	
363	1089 A	-X:64661173 2931759516 A	
364 H	1090 C	-X:64661172 2931759515 C	H
364	1091 A	-X:64661171 2931759514 A	
364	1092 C	-X:64661170 2931759513 C	
365 K	1093 A	-X:64661169 2931759512 A	K
365	1094 A	-X:64660867 2931759210 A	
365	1095 A	-X:64660866 2931759209 A	
366 N	1096 A	-X:64660865 2931759208 A	N
366	1097 A	-X:64660864 2931759207 A	
366	1098 C	-X:64660863 2931759206 C	
367 V	1099 G	-X:64660862 2931759205 G	V
367	1100 T	-X:64660861 2931759204 T	
367	1101 G	-X:64660860 2931759203 G	
368 D	1102 G	-X:64660859 2931759202 G	D
368	1103 A	-X:64660858 2931759201 A	
368	1104 C	-X:64660857 2931759200 C	
369 L	1105 T	-X:64660856 2931759199 T	L
369	1106 T	-X:64660855 2931759198 T	
369	1107 G	-X:64660854 2931759197 G	
370 N	1108 A	-X:64660853 2931759196 A	N
370	1109 A	-X:64660852 2931759195 A	
370	1110 T	-X:64660851 2931759194 T	
371 D	1111 G	-X:64660850 2931759193 G	D
371	1112 A	-X:64660849 2931759192 A	
371	1113 C	-X:64660848 2931759191 C	
372 V	1114 G	-X:64660847 2931759190 G	V
372	1115 T	-X:64660846 2931759189 T	
372	1116 C	-X:64660845 2931759188 C	
373 L	1117 C	-X:64660844 2931759187 C	L
373	1118 T	-X:64660843 2931759186 T	
373	1119 G	-X:64660842 2931759185 G	
374 V	1120 G	-X:64660841 2931759184 G	V
374	1121 T	-X:64660840 2931759183 T	
374	1122 G	-X:64660839 2931759182 G	
375 P	1123 C	-X:64660838 2931759181 C	P
375	1124 C	-X:64660837 2931759180 C	
375	1125 A	-X:64660836 2931759179 A	
376 K	1126 A	-X:64660835 2931759178 A	K
376	1127 A	-X:64660834 2931759177 A	
376	1128 G	-X:64660833 2931759176 G	
377 P	1129 C	-X:64660832 2931759175 C	P
377	1130 C	-X:64660831 2931759174 C	
377	1131 G	-X:64660830 2931759173 G	
378 F	1132 T	-X:64660829 2931759172 T	F
378	1133 T	-X:64660828 2931759171 T	
378	1134 C	-X:64660827 2931759170 C	
379 S	1135 T	-X:64660826 2931759169 T	S
379	1136 C	-X:64660825 2931759168 C	
379	1137 T	-X:64660824 2931759167 T	
380 Q	1138 C	-X:64660823 2931759166 C	Q
380	1139 A	-X:64660822 2931759165 A	
380	1140 G	-X:64660821 2931759164 G	
381 F	1141 T	-X:64660820 2931759163 T	F
381	1142 T	-X:64660819 2931759162 T	
381	1143 C	-X:64660818 2931759161 C	
382 W	1144 T	-X:64660817 2931759160 T	W
382	1145 G	-X:64660816 2931759159 G	
382	1146 G	-X:64660815 2931759158 G	
383 Q	1147 C	-X:64660814 2931759157 C	Q
383	1148 A	-X:64660813 2931759156 A	
383	1149 G	-X:64660812 2931759155 G	
384 P	1150 C	-X:64660811 2931759154 C	P
384	1151 C	-X:64660810 2931759153 C	
384	1152 C	-X:64660809 2931759152 C	
385 L	1153 C	-X:64660808 2931759151 C	L
385	1154 T	-X:64660807 2931759150 T	
385	1155 G	-X:64660806 2931759149 G	
386 L	1156 C	-X:64660805 2931759148 C	L
386	1157 T	-X:64660804 2931759147 T	
386	1158 C	-X:64660803 2931759146 C	
387 R	1159 A	-X:64660802 2931759145 A	R
387	1160 G	-X:64660801 2931759144 G	
387	1161 G	-X:64660800 2931759143 G	
388 G	1162 G	-X:64660799 2931759142 G	G
388	1163 G	-X:64660798 2931759141 G	
388	1164 C	-X:64660797 2931759140 C	
389 L	1165 C	-X:64660796 2931759139 C	L
389	1166 T	-X:64660795 2931759138 T	
389	1167 G	-X:64660794 2931759137 G	
390 H	1168 C	-X:64660793 2931759136 C	H
390	1169 A	-X:64660792 2931759135 A	
390	1170 C	-X:64660791 2931759134 C	
391 S	1171 T	-X:64660790 2931759133 T	S
391	1172 C	-X:64660789 2931759132 C	
391	1173 C	-X:64660788 2931759131 C	
392 Q	1174 C	-X:64660787 2931759130 C	Q
392	1175 A	-X:64660786 2931759129 A	
392	1176 G	-X:64660785 2931759128 G	
393 N	1177 A	-X:64660784 2931759127 A	N
393	1178 A	-X:64660783 2931759126 A	
393	1179 C	-X:64660782 2931759125 C	
394 F	1180 T	-X:64660781 2931759124 T	F
394	1181 T	-X:64660780 2931759123 T	
394	1182 C	-X:64660779 2931759122 C	
395 T	1183 A	-X:64660778 2931759121 A	T
395	1184 C	-X:64660777 2931759120 C	
395	1185 G	-X:64660776 2931759119 G	
396 Q	1186 C	-X:64660775 2931759118 C	Q
396	1187 A	-X:64660774 2931759117 A	
396	1188 G	-X:64660773 2931759116 G	
397 A	1189 G	-X:64660772 2931759115 G	A
397	1190 C	-X:64660771 2931759114 C	
397	1191 C	-X:64660770 2931759113 C	
398 L	1192 C	-X:64660769 2931759112 C	L
398	1193 T	-X:64660768 2931759111 T	
398	1194 A	-X:64660767 2931759110 A	
399 L	1195 T	-X:64660766 2931759109 T	L
399	1196 T	-X:64660765 2931759108 T	
399	1197 G	-X:64660764 2931759107 G	
400 E	1198 G	-X:64660763 2931759106 G	E
400	1199 A	-X:64660762 2931759105 A	
400	1200 G	-X:64660761 2931759104 G	
401 R	1201 A	-X:64660760 2931759103 A	R
401	1202 G	-X:64660759 2931759102 G	
401	1203 G	-X:64660758 2931759101 G	
402 M	1204 A	-X:64660757 2931759100 A	M
402	1205 T	-X:64660756 2931759099 T	
402	1206 G	-X:64660755 2931759098 G	
403 L	1207 C	-X:64660754 2931759097 C	L
403	1208 T	-X:64660753 2931759096 T	
403	1209 C	-X:64660752 2931759095 C	
404 S	1210 T	-X:64660751 2931759094 T	S
404	1211 C	-X:64660750 2931759093 C	
404	1212 T	-X:64660749 2931759092 T	
405 E	1213 G	-X:64660748 2931759091 G	E
405	1214 A	-X:64660747 2931759090 A	
405	1215 A	-X:64660746 2931759089 A	
406 L	1216 C	-X:64660745 2931759088 C	L
406	1217 T	-X:64660744 2931759087 T	
406	1218 G	-X:64660743 2931759086 G	
407 P	1219 C	-X:64660742 2931759085 C	P
407	1220 C	-X:64660741 2931759084 C	
407	1221 A	-X:64660740 2931759083 A	
408 A	1222 G	-X:64660739 2931759082 G	A
408	1223 C	-X:64660738 2931759081 C	
408	1224 C	-X:64660737 2931759080 C	
409 L	1225 T	-X:64660736 2931759079 T	L
409	1226 T	-X:64660735 2931759078 T	
409	1227 G	-X:64660734 2931759077 G	
410 G	1228 G	-X:64660733 2931759076 G	G
410	1229 G	-X:64660732 2931759075 G	
410	1230 G	-X:64660731 2931759074 G	
411 I	1231 A	-X:64660730 2931759073 A	I
411	1232 T	-X:64660729 2931759072 T	
411	1233 C	-X:64660728 2931759071 C	
412 S	1234 A	-X:64660727 2931759070 A	S
412	1235 G	-X:64660726 2931759069 G	
412	1236 C	-X:64660725 2931759068 C	
413 G	1237 G	-X:64660724 2931759067 G	G
413	1238 G	-X:64660723 2931759066 G	
413	1239 G	-X:64660722 2931759065 G	
414 I	1240 A	-X:64660721 2931759064 A	I
414	1241 T	-X:64660720 2931759063 T	
414	1242 C	-X:64660719 2931759062 C	
415 R	1243 C	-X:64660718 2931759061 C	R
415	1244 G	-X:64660717 2931759060 G	
415	1245 G	-X:64660716 2931759059 G	
416 P	1246 C	-X:64660715 2931759058 C	P
416	1247 C	-X:64660714 2931759057 C	
416	1248 T	-X:64660713 2931759056 T	
417 T	1249 A	-X:64660712 2931759055 A	T
417	1250 C	-X:64660711 2931759054 C	
417	1251 C	-X:64660710 2931759053 C	
418 Y	1252 T	-X:64660709 2931759052 T	Y
418	1253 A	-X:64660708 2931759051 A	
418	1254 C	-X:64660707 2931759050 C	
419 I	1255 A	-X:64660706 2931759049 A	I
419	1256 T	-X:64660705 2931759048 T	
419	1257 C	-X:64660704 2931759047 C	
420 L	1258 C	-X:64660703 2931759046 C	L
420	1259 T	-X:64660702 2931759045 T	
420	1260 C	-X:64660701 2931759044 C	
421 R	1261 A	-X:64660700 2931759043 A	R
421	1262 G	-X:64660699 2931759042 G	
421	1263 A	-X:64660698 2931759041 A	
422 W	1264 T	-X:64660697 2931759040 T	W
422	1265 G	-X:64660696 2931759039 G	
422	1266 G	-X:64660695 2931759038 G	
423 T	1267 A	-X:64660694 2931759037 A	T
423	1268 C	-X:64660693 2931759036 C	
423	1269 C	-X:64660692 2931759035 C	
424 V	1270 G	-X:64660691 2931759034 G	V
424	1271 T	-X:64660690 2931759033 T	
424	1272 T	-X:64660689 2931759032 T	
425 E	1273 G	-X:64660688 2931759031 G	E
425	1274 A	-X:64660687 2931759030 A	
425	1275 A	-X:64660686 2931759029 A	
426 L	1276 C	-X:64660685 2931759028 C	L
426	1277 T	-X:64660684 2931759027 T	
426	1278 G	-X:64660683 2931759026 G	
427 I	1279 A	-X:64660682 2931759025 A	I
427	1280 T	-X:64660681 2931759024 T	
427	1281 C	-X:64660680 2931759023 C	
428 V	1282 G	-X:64660679 2931759022 G	V
428	1283 T	-X:64660678 2931759021 T	
428	1284 G	-X:64660677 2931759020 G	
429 A	1285 G	-X:64660676 2931759019 G	A
429	1286 C	-X:64660675 2931759018 C	
429	1287 C	-X:64660674 2931759017 C	
430 N	1288 A	-X:64660673 2931759016 A	N
430	1289 A	-X:64660672 2931759015 A	
430	1290 C	-X:64660671 2931759014 C	
431 T	1291 A	-X:64660670 2931759013 A	T
431	1292 C	-X:64660669 2931759012 C	
431	1293 C	-X:64660668 2931759011 C	
432 K	1294 A	-X:64660667 2931759010 A	K
432	1295 A	-X:64660666 2931759009 A	
432	1296 G	-X:64660665 2931759008 G	
433 T	1297 A	-X:64660664 2931759007 A	T
433	1298 C	-X:64660663 2931759006 C	
433	1299 T	-X:64660662 2931759005 T	
434 G	1300 G	-X:64660661 2931759004 G	G
434	1301 G	-X:64660312 2931758655 G	
434	1302 A	-X:64660311 2931758654 A	
435 R	1303 C	-X:64660310 2931758653 C	R
435	1304 G	-X:64660309 2931758652 G	
435	1305 G	-X:64660308 2931758651 G	
436 N	1306 A	-X:64660307 2931758650 A	N
436	1307 A	-X:64660306 2931758649 A	
436	1308 T	-X:64660305 2931758648 T	
437 A	1309 G	-X:64660304 2931758647 G	A
437	1310 C	-X:64660303 2931758646 C	
437	1311 T	-X:64660302 2931758645 T	
438 R	1312 C	-X:64660301 2931758644 C	R
438	1313 G	-X:64660300 2931758643 G	
438	1314 C	-X:64660299 2931758642 C	
439 R	1315 C	-X:64660298 2931758641 C	R
439	1316 G	-X:64660297 2931758640 G	
439	1317 A	-X:64660296 2931758639 A	
440 F	1318 T	-X:64660295 2931758638 T	F
440	1319 T	-X:64660294 2931758637 T	
440	1320 T	-X:64660293 2931758636 T	
441 S	1321 T	-X:64660292 2931758635 T	S
441	1322 C	-X:64660291 2931758634 C	
441	1323 T	-X:64660290 2931758633 T	
442 A	1324 G	-X:64660289 2931758632 G	A
442	1325 C	-X:64660288 2931758631 C	
442	1326 A	-X:64660287 2931758630 A	
443 G	1327 G	-X:64660286 2931758629 G	G
443	1328 G	-X:64660285 2931758628 G	
443	1329 C	-X:64660284 2931758627 C	
444 Q	1330 C	-X:64660283 2931758626 C	Q
444	1331 A	-X:64660282 2931758625 A	
444	1332 G	-X:64660281 2931758624 G	
445 W	1333 T	-X:64660280 2931758623 T	W
445	1334 G	-X:64660279 2931758622 G	
445	1335 G	-X:64660278 2931758621 G	
446 E	1336 G	-X:64660277 2931758620 G	E
446	1337 A	-X:64660276 2931758619 A	
446	1338 A	-X:64660275 2931758618 A	
447 A	1339 G	-X:64660274 2931758617 G	A
447	1340 C	-X:64660273 2931758616 C	
447	1341 A	-X:64660272 2931758615 A	
448 R	1342 A	-X:64660271 2931758614 A	R
448	1343 G	-X:64660270 2931758613 G	
448	1344 A	-X:64660269 2931758612 A	
449 R	1345 A	-X:64660268 2931758611 A	R
449	1346 G	-X:64660267 2931758610 G	
449	1347 G	-X:64660266 2931758609 G	
450 G	1348 G	-X:64660265 2931758608 G	G
450	1349 G	-X:64660264 2931758607 G	
450	1350 C	-X:64660263 2931758606 C	
451 W	1351 T	-X:64660262 2931758605 T	W
451	1352 G	-X:64660261 2931758604 G	
451	1353 G	-X:64660260 2931758603 G	
452 R	1354 A	-X:64660259 2931758602 A	R
452	1355 G	-X:64660258 2931758601 G	
452	1356 G	-X:64660257 2931758600 G	
453 L	1357 C	-X:64660256 2931758599 C	L
453	1358 T	-X:64660255 2931758598 T	
453	1359 G	-X:64660254 2931758597 G	
454 F	1360 T	-X:64660253 2931758596 T	F
454	1361 T	-X:64660252 2931758595 T	
454	1362 C	-X:64660251 2931758594 C	
455 N	1363 A	-X:64660250 2931758593 A	N
455	1364 A	-X:64660249 2931758592 A	
455	1365 C	-X:64660248 2931758591 C	
456 C	1366 T	-X:64660247 2931758590 T	C
456	1367 G	-X:64660246 2931758589 G	
456	1368 C	-X:64660245 2931758588 C	
457 S	1369 T	-X:64660244 2931758587 T	S
457	1370 C	-X:64660243 2931758586 C	
457	1371 C	-X:64660242 2931758585 C	
458 A	1372 G	-X:64660241 2931758584 G	A
458	1373 C	-X:64660240 2931758583 C	
458	1374 C	-X:64660239 2931758582 C	
459 S	1375 T	-X:64660238 2931758581 T	S
459	1376 C	-X:64660237 2931758580 C	
459	1377 C	-X:64660236 2931758579 C	
460 L	1378 C	-X:64660235 2931758578 C	L
460	1379 T	-X:64660234 2931758577 T	
460	1380 T	-X:64660233 2931758576 T	
461 D	1381 G	-X:64660232 2931758575 G	D
461	1382 A	-X:64660231 2931758574 A	
461	1383 C	-X:64660230 2931758573 C	
462 W	1384 T	-X:64660229 2931758572 T	W
462	1385 G	-X:64660228 2931758571 G	
462	1386 G	-X:64660227 2931758570 G	
463 P	1387 C	-X:64660226 2931758569 C	P
463	1388 C	-X:64660225 2931758568 C	
463	1389 C	-X:64660224 2931758567 C	
464 R	1390 C	-X:64660223 2931758566 C	R
464	1391 G	-X:64660222 2931758565 G	
464	1392 G	-X:64660221 2931758564 G	
465 M	1393 A	-X:64660220 2931758563 A	M
465	1394 T	-X:64660219 2931758562 T	
465	1395 G	-X:64660218 2931758561 G	
466 V	1396 G	-X:64660217 2931758560 G	V
466	1397 T	-X:64660216 2931758559 T	
466	1398 T	-X:64660215 2931758558 T	
467 E	1399 G	-X:64660214 2931758557 G	E
467	1400 A	-X:64660213 2931758556 A	
467	1401 G	-X:64660212 2931758555 G	
468 S	1402 T	-X:64660211 2931758554 T	S
468	1403 C	-X:64660210 2931758553 C	
468	1404 C	-X:64660209 2931758552 C	
469 C	1405 T	-X:64660208 2931758551 T	C
469	1406 G	-X:64660207 2931758550 G	
469	1407 C	-X:64660206 2931758549 C	
470 L	1408 T	-X:64660205 2931758548 T	L
470	1409 T	-X:64660204 2931758547 T	
470	1410 G	-X:64660203 2931758546 G	
471 G	1411 G	-X:64660202 2931758545 G	G
471	1412 G	-X:64660201 2931758544 G	
471	1413 C	-X:64660200 2931758543 C	
472 S	1414 T	-X:64660199 2931758542 T	S
472	1415 C	-X:64660198 2931758541 C	
472	1416 A	-X:64660197 2931758540 A	
473 P	1417 C	-X:64660196 2931758539 C	P
473	1418 C	-X:64660195 2931758538 C	
473	1419 T	-X:64660194 2931758537 T	
474 C	1420 T	-X:64660193 2931758536 T	C
474	1421 G	-X:64660192 2931758535 G	
474	1422 C	-X:64660191 2931758534 C	
475 W	1423 T	-X:64660190 2931758533 T	W
475	1424 G	-X:64660189 2931758532 G	
475	1425 G	-X:64660188 2931758531 G	
476 A	1426 G	-X:64660187 2931758530 G	A
476	1427 C	-X:64660186 2931758529 C	
476	1428 C	-X:64660185 2931758528 C	
477 S	1429 A	-X:64660184 2931758527 A	S
477	1430 G	-X:64660183 2931758526 G	
477	1431 C	-X:64660182 2931758525 C	
478 P	1432 C	-X:64660181 2931758524 C	P
478	1433 C	-X:64660180 2931758523 C	
478	1434 C	-X:64660179 2931758522 C	
479 Q	1435 C	-X:64660178 2931758521 C	Q
479	1436 A	-X:64660177 2931758520 A	
479	1437 A	-X:64660176 2931758519 A	
480 L	1438 C	-X:64660175 2931758518 C	L
480	1439 T	-X:64660174 2931758517 T	
480	1440 C	-X:64660173 2931758516 C	
481 L	1441 C	-X:64660172 2931758515 C	L
481	1442 T	-X:64660171 2931758514 T	
481	1443 T	-X:64660170 2931758513 T	
482 R	1444 C	-X:64660169 2931758512 C	R
482	1445 G	-X:64660168 2931758511 G	
482	1446 G	-X:64660167 2931758510 G	
483 I	1447 A	-X:64660166 2931758509 A	I
483	1448 T	-X:64660165 2931758508 T	
483	1449 C	-X:64655070 2931753413 C	
484 I	1450 A	-X:64655069 2931753412 A	I
484	1451 T	-X:64655068 2931753411 T	
484	1452 C	-X:64655067 2931753410 C	
485 F	1453 T	-X:64655066 2931753409 T	F
485	1454 T	-X:64655065 2931753408 T	
485	1455 C	-X:64655064 2931753407 C	
486 K	1456 A	-X:64655063 2931753406 A	K
486	1457 A	-X:64655062 2931753405 A	
486	1458 A	-X:64655061 2931753404 A	
487 A	1459 G	-X:64655060 2931753403 G	A
487	1460 C	-X:64655059 2931753402 C	
487	1461 C	-X:64655058 2931753401 C	
488 M	1462 A	-X:64655057 2931753400 A	M
488	1463 T	-X:64655056 2931753399 T	
488	1464 G	-X:64655055 2931753398 G	
489 G	1465 G	-X:64655054 2931753397 G	G
489	1466 G	-X:64655053 2931753396 G	
489	1467 G	-X:64655052 2931753395 G	
490 Q	1468 C	-X:64655051 2931753394 C	Q
490	1469 A	-X:64655050 2931753393 A	
490	1470 G	-X:64655049 2931753392 G	
491 G	1471 G	-X:64655048 2931753391 G	G
491	1472 G	-X:64655047 2931753390 G	
491	1473 C	-X:64655046 2931753389 C	
492 L	1474 C	-X:64655045 2931753388 C	L
492	1475 T	-X:64655044 2931753387 T	
492	1476 G	-X:64655043 2931753386 G	
493 P	1477 C	-X:64655042 2931753385 C	P
493	1478 C	-X:64655041 2931753384 C	
493	1479 A	-X:64655040 2931753383 A	
494 D	1480 G	-X:64655039 2931753382 G	D
494	1481 A	-X:64655038 2931753381 A	
494	1482 C	-X:64655037 2931753380 C	
495 E	1483 G	-X:64655036 2931753379 G	E
495	1484 A	-X:64655035 2931753378 A	
495	1485 G	-X:64655034 2931753377 G	
496 E	1486 G	-X:64655033 2931753376 G	E
496	1487 A	-X:64655032 2931753375 A	
496	1488 G	-X:64655031 2931753374 G	
497 Q	1489 C	-X:64655030 2931753373 C	Q
497	1490 A	-X:64655029 2931753372 A	
497	1491 G	-X:64655028 2931753371 G	
498 E	1492 G	-X:64655027 2931753370 G	E
498	1493 A	-X:64655026 2931753369 A	
498	1494 G	-X:64655025 2931753368 G	
499 K	1495 A	-X:64655024 2931753367 A	K
499	1496 A	-X:64655023 2931753366 A	
499	1497 G	-X:64655022 2931753365 G	
500 L	1498 C	-X:64655021 2931753364 C	L
500	1499 T	-X:64655020 2931753363 T	
500	1500 G	-X:64655019 2931753362 G	
501 L	1501 C	-X:64655018 2931753361 C	L
501	1502 T	-X:64655017 2931753360 T	
501	1503 G	-X:64655016 2931753359 G	
502 R	1504 C	-X:64655015 2931753358 C	R
502	1505 G	-X:64655014 2931753357 G	
502	1506 C	-X:64655013 2931753356 C	
503 I	1507 A	-X:64655012 2931753355 A	I
503	1508 T	-X:64655011 2931753354 T	
503	1509 C	-X:64655010 2931753353 C	
504 C	1510 T	-X:64655009 2931753352 T	C
504	1511 G	-X:64655008 2931753351 G	
504	1512 T	-X:64655007 2931753350 T	
505 S	1513 T	-X:64655006 2931753349 T	S
505	1514 C	-X:64655005 2931753348 C	
505	1515 C	-X:64655004 2931753347 C	
506 I	1516 A	-X:64655003 2931753346 A	I
506	1517 T	-X:64655002 2931753345 T	
506	1518 T	-X:64655001 2931753344 T	
507 Y	1519 T	-X:64655000 2931753343 T	Y
507	1520 A	-X:64654999 2931753342 A	
507	1521 T	-X:64654998 2931753341 T	
508 T	1522 A	-X:64654997 2931753340 A	T
508	1523 C	-X:64654996 2931753339 C	
508	1524 C	-X:64654995 2931753338 C	
509 Q	1525 C	-X:64654994 2931753337 C	Q
509	1526 A	-X:64654993 2931753336 A	
509	1527 G	-X:64654992 2931753335 G	
510 S	1528 A	-X:64654991 2931753334 A	S
510	1529 G	-X:64654990 2931753333 G	
510	1530 T	-X:64654989 2931753332 T	
511 G	1531 G	-X:64654988 2931753331 G	G
511	1532 G	-X:64654987 2931753330 G	
511	1533 A	-X:64654986 2931753329 A	
512 E	1534 G	-X:64654985 2931753328 G	E
512	1535 A	-X:64654984 2931753327 A	
512	1536 A	-X:64654983 2931753326 A	
513 N	1537 A	-X:64654982 2931753325 A	N
513	1538 A	-X:64654981 2931753324 A	
513	1539 C	-X:64654980 2931753323 C	
514 S	1540 A	-X:64654979 2931753322 A	S
514	1541 G	-X:64654978 2931753321 G	
514	1542 C	-X:64654977 2931753320 C	
515 L	1543 C	-X:64654976 2931753319 C	L
515	1544 T	-X:64654975 2931753318 T	
515	1545 G	-X:64654974 2931753317 G	
516 V	1546 G	-X:64654973 2931753316 G	V
516	1547 T	-X:64654972 2931753315 T	
516	1548 G	-X:64654971 2931753314 G	
517 Q	1549 C	-X:64654970 2931753313 C	Q
517	1550 A	-X:64654969 2931753312 A	
517	1551 G	-X:64654968 2931753311 G	
518 E	1552 G	-X:64654967 2931753310 G	E
518	1553 A	-X:64654966 2931753309 A	
518	1554 G	-X:64654965 2931753308 G	
519 G	1555 G	-X:64654964 2931753307 G	G
519	1556 G	-X:64654963 2931753306 G	
519	1557 C	-X:64654962 2931753305 C	
520 S	1558 T	-X:64654961 2931753304 T	S
520	1559 C	-X:64654960 2931753303 C	
520	1560 T	-X:64654959 2931753302 T	
521 E	1561 G	-X:64654958 2931753301 G	E
521	1562 A	-X:64654957 2931753300 A	
521	1563 G	-X:64654956 2931753299 G	
522 A	1564 G	-X:64654955 2931753298 G	A
522	1565 C	-X:64654954 2931753297 C	
522	1566 C	-X:64654953 2931753296 C	
523 S	1567 T	-X:64654952 2931753295 T	S
523	1568 C	-X:64654951 2931753294 C	
523	1569 C	-X:64654950 2931753293 C	
524 P	1570 C	-X:64654949 2931753292 C	P
524	1571 C	-X:64654948 2931753291 C	
524	1572 C	-X:64654947 2931753290 C	
525 I	1573 A	-X:64654946 2931753289 A	I
525	1574 T	-X:64654945 2931753288 T	
525	1575 T	-X:64654944 2931753287 T	
526 G	1576 G	-X:64654943 2931753286 G	G
526	1577 G	-X:64654942 2931753285 G	
526	1578 G	-X:64654941 2931753284 G	
527 K	1579 A	-X:64654940 2931753283 A	K
527	1580 A	-X:64654939 2931753282 A	
527	1581 G	-X:64654938 2931753281 G	
528 S	1582 T	-X:64654937 2931753280 T	S
528	1583 C	-X:64654936 2931753279 C	
528	1584 T	-X:64654935 2931753278 T	
529 P	1585 C	-X:64654934 2931753277 C	P
529	1586 C	-X:64654933 2931753276 C	
529	1587 A	-X:64654932 2931753275 A	
530 Y	1588 T	-X:64654931 2931753274 T	Y
530	1589 A	-X:64654930 2931753273 A	
530	1590 T	-X:64654929 2931753272 T	
531 T	1591 A	-X:64654928 2931753271 A	T
531	1592 C	-X:64654927 2931753270 C	
531	1593 A	-X:64654926 2931753269 A	
532 L	1594 C	-X:64654925 2931753268 C	L
532	1595 T	-X:64654924 2931753267 T	
532	1596 A	-X:64654923 2931753266 A	
533 D	1597 G	-X:64654922 2931753265 G	D
533	1598 A	-X:64654921 2931753264 A	
533	1599 C	-X:64654920 2931753263 C	
534 S	1600 A	-X:64654919 2931753262 A	S
534	1601 G	-X:64654918 2931753261 G	
534	1602 C	-X:64654917 2931753260 C	
535 L	1603 C	-X:64654916 2931753259 C	L
535	1604 T	-X:64654915 2931753258 T	
535	1605 G	-X:64654914 2931753257 G	
536 Y	1606 T	-X:64654913 2931753256 T	Y
536	1607 A	-X:64654912 2931753255 A	
536	1608 T	-X:64654911 2931753254 T	
537 W	1609 T	-X:64654910 2931753253 T	W
537	1610 G	-X:64654909 2931753252 G	
537	1611 G	-X:64654908 2931753251 G	
538 S	1612 A	-X:64654907 2931753250 A	S
538	1613 G	-X:64654906 2931753249 G	
538	1614 C	-X:64654905 2931753248 C	
539 V	1615 G	-X:64654904 2931753247 G	V
539	1616 T	-X:64654903 2931753246 T	
539	1617 C	-X:64654902 2931753245 C	
540 K	1618 A	-X:64654901 2931753244 A	K
540	1619 A	-X:64654900 2931753243 A	
540	1620 G	-X:64654899 2931753242 G	
541 P	1621 C	-X:64654898 2931753241 C	P
541	1622 C	-X:64654897 2931753240 C	
541	1623 A	-X:64654896 2931753239 A	
542 A	1624 G	-X:64654895 2931753238 G	A
542	1625 C	-X:64654894 2931753237 C	
542	1626 C	-X:64654893 2931753236 C	
543 S	1627 A	-X:64654892 2931753235 A	S
543	1628 G	-X:64654891 2931753234 G	
543	1629 C	-X:64654890 2931753233 C	
544 S	1630 T	-X:64654889 2931753232 T	S
544	1631 C	-X:64654888 2931753231 C	
544	1632 C	-X:64654887 2931753230 C	
545 S	1633 A	-X:64654886 2931753229 A	S
545	1634 G	-X:64654885 2931753228 G	
545	1635 C	-X:64654884 2931753227 C	
546 F	1636 T	-X:64654883 2931753226 T	F
546	1637 T	-X:64654882 2931753225 T	
546	1638 C	-X:64654881 2931753224 C	
547 G	1639 G	-X:64654880 2931753223 G	G
547	1640 G	-X:64654879 2931753222 G	
547	1641 G	-X:64654878 2931753221 G	
548 S	1642 T	-X:64654877 2931753220 T	S
548	1643 C	-X:64654876 2931753219 C	
548	1644 T	-X:64654875 2931753218 T	
549 E	1645 G	-X:64654874 2931753217 G	E
549	1646 A	-X:64654873 2931753216 A	
549	1647 A	-X:64654872 2931753215 A	
550 A	1648 G	-X:64654871 2931753214 G	A
550	1649 C	-X:64654870 2931753213 C	
550	1650 A	-X:64654869 2931753212 A	
551 K	1651 A	-X:64654868 2931753211 A	K
551	1652 A	-X:64654867 2931753210 A	
551	1653 G	-X:64654866 2931753209 G	
552 A	1654 G	-X:64654865 2931753208 G	A
552	1655 C	-X:64654864 2931753207 C	
552	1656 C	-X:64654863 2931753206 C	
553 Q	1657 C	-X:64654862 2931753205 C	Q
553	1658 A	-X:64654861 2931753204 A	
553	1659 G	-X:64654860 2931753203 G	
554 Q	1660 C	-X:64654859 2931753202 C	Q
554	1661 A	-X:64654858 2931753201 A	
554	1662 A	-X:64654857 2931753200 A	
555 Q	1663 C	-X:64654856 2931753199 C	Q
555	1664 A	-X:64654855 2931753198 A	
555	1665 G	-X:64654854 2931753197 G	
556 E	1666 G	-X:64654853 2931753196 G	E
556	1667 A	-X:64654852 2931753195 A	
556	1668 G	-X:64654851 2931753194 G	
557 E	1669 G	-X:64654850 2931753193 G	E
557	1670 A	-X:64654849 2931753192 A	
557	1671 G	-X:64654848 2931753191 G	
558 Q	1672 C	-X:64654847 2931753190 C	Q
558	1673 A	-X:64654846 2931753189 A	
558	1674 G	-X:64654845 2931753188 G	
559 G	1675 G	-X:64654844 2931753187 G	G
559	1676 G	-X:64654843 2931753186 G	
559	1677 C	-X:64654842 2931753185 C	
560 S	1678 A	-X:64654841 2931753184 A	S
560	1679 G	-X:64654840 2931753183 G	
560	1680 T	-X:64654839 2931753182 T	
561 V	1681 G	-X:64654838 2931753181 G	V
561	1682 T	-X:64654837 2931753180 T	
561	1683 T	-X:64654836 2931753179 T	
562 N	1684 A	-X:64654835 2931753178 A	N
562	1685 A	-X:64654834 2931753177 A	
562	1686 T	-X:64654833 2931753176 T	
563 D	1687 G	-X:64654832 2931753175 G	D
563	1688 A	-X:64654831 2931753174 A	
563	1689 T	-X:64654830 2931753173 T	
564 V	1690 G	-X:64654829 2931753172 G	V
564	1691 T	-X:64654828 2931753171 T	
564	1692 C	-X:64654827 2931753170 C	
565 K	1693 A	-X:64654826 2931753169 A	K
565	1694 A	-X:64654825 2931753168 A	
565	1695 G	-X:64654824 2931753167 G	
566 E	1696 G	-X:64654823 2931753166 G	E
566	1697 A	-X:64654822 2931753165 A	
566	1698 A	-X:64654821 2931753164 A	
567 E	1699 G	-X:64654820 2931753163 G	E
567	1700 A	-X:64654819 2931753162 A	
567	1701 G	-X:64654818 2931753161 G	
568 E	1702 G	-X:64654817 2931753160 G	E
568	1703 A	-X:64654816 2931753159 A	
568	1704 G	-X:64654815 2931753158 G	
569 K	1705 A	-X:64654814 2931753157 A	K
569	1706 A	-X:64654813 2931753156 A	
569	1707 G	-X:64654812 2931753155 G	
570 E	1708 G	-X:64654811 2931753154 G	E
570	1709 A	-X:64654810 2931753153 A	
570	1710 G	-X:64654809 2931753152 G	
571 E	1711 G	-X:64654808 2931753151 G	E
571	1712 A	-X:64654807 2931753150 A	
571	1713 G	-X:64654806 2931753149 G	
572 K	1714 A	-X:64654805 2931753148 A	K
572	1715 A	-X:64654804 2931753147 A	
572	1716 A	-X:64654803 2931753146 A	
573 E	1717 G	-X:64654802 2931753145 G	E
573	1718 A	-X:64654801 2931753144 A	
573	1719 G	-X:64654800 2931753143 G	
574 V	1720 G	-X:64654799 2931753142 G	V
574	1721 T	-X:64654798 2931753141 T	
574	1722 C	-X:64654797 2931753140 C	
575 L	1723 T	-X:64654796 2931753139 T	L
575	1724 T	-X:64654795 2931753138 T	
575	1725 G	-X:64654794 2931753137 G	
576 P	1726 C	-X:64654793 2931753136 C	P
576	1727 C	-X:64654792 2931753135 C	
576	1728 A	-X:64654791 2931753134 A	
577 D	1729 G	-X:64654790 2931753133 G	D
577	1730 A	-X:64654789 2931753132 A	
577	1731 C	-X:64654788 2931753131 C	
578 Q	1732 C	-X:64654787 2931753130 C	Q
578	1733 A	-X:64654786 2931753129 A	
578	1734 G	-X:64654785 2931753128 G	
579 V	1735 G	-X:64654784 2931753127 G	V
579	1736 T	-X:64654783 2931753126 T	
579	1737 A	-X:64654782 2931753125 A	
580 E	1738 G	-X:64654781 2931753124 G	E
580	1739 A	-X:64654780 2931753123 A	
580	1740 G	-X:64654779 2931753122 G	
581 E	1741 G	-X:64654778 2931753121 G	E
581	1742 A	-X:64654777 2931753120 A	
581	1743 G	-X:64654776 2931753119 G	
582 E	1744 G	-X:64654775 2931753118 G	E
582	1745 A	-X:64654774 2931753117 A	
582	1746 G	-X:64654773 2931753116 G	
583 E	1747 G	-X:64654772 2931753115 G	E
583	1748 A	-X:64654771 2931753114 A	
583	1749 A	-X:64654770 2931753113 A	
584 E	1750 G	-X:64654769 2931753112 G	E
584	1751 A	-X:64654768 2931753111 A	
584	1752 A	-X:64654767 2931753110 A	
585 N	1753 A	-X:64654766 2931753109 A	N
585	1754 A	-X:64654765 2931753108 A	
585	1755 T	-X:64654764 2931753107 T	
586 D	1756 G	-X:64654763 2931753106 G	D
586	1757 A	-X:64654762 2931753105 A	
586	1758 T	-X:64654761 2931753104 T	
587 D	1759 G	-X:64654760 2931753103 G	D
587	1760 A	-X:64654759 2931753102 A	
587	1761 C	-X:64654758 2931753101 C	
588 Q	1762 C	-X:64654757 2931753100 C	Q
588	1763 A	-X:64654756 2931753099 A	
588	1764 A	-X:64654755 2931753098 A	
589 E	1765 G	-X:64654754 2931753097 G	E
589	1766 A	-X:64654753 2931753096 A	
589	1767 G	-X:64654752 2931753095 G	
590 E	1768 G	-X:64654751 2931753094 G	E
590	1769 A	-X:64654750 2931753093 A	
590	1770 G	-X:64654749 2931753092 G	
591 E	1771 G	-X:64654748 2931753091 G	E
591	1772 A	-X:64654747 2931753090 A	
591	1773 A	-X:64654746 2931753089 A	
592 E	1774 G	-X:64654745 2931753088 G	E
592	1775 A	-X:64654744 2931753087 A	
592	1776 G	-X:64654743 2931753086 G	
593 E	1777 G	-X:64654742 2931753085 G	E
593	1778 A	-X:64654741 2931753084 A	
593	1779 G	-X:64654740 2931753083 G	
594 D	1780 G	-X:64654739 2931753082 G	D
594	1781 A	-X:64654738 2931753081 A	
594	1782 T	-X:64654737 2931753080 T	
595 E	1783 G	-X:64654736 2931753079 G	E
595	1784 A	-X:64654735 2931753078 A	
595	1785 A	-X:64654734 2931753077 A	
596 D	1786 G	-X:64654733 2931753076 G	D
596	1787 A	-X:64654732 2931753075 A	
596	1788 T	-X:64654731 2931753074 T	
597 D	1789 G	-X:64654730 2931753073 G	D
597	1790 A	-X:64654729 2931753072 A	
597	1791 T	-X:64654728 2931753071 T	
598 E	1792 G	-X:64654727 2931753070 G	E
598	1793 A	-X:64654726 2931753069 A	
598	1794 A	-X:64654725 2931753068 A	
599 D	1795 G	-X:64654724 2931753067 G	D
599	1796 A	-X:64654723 2931753066 A	
599	1797 T	-X:64654722 2931753065 T	
600 D	1798 G	-X:64654721 2931753064 G	D
600	1799 A	-X:64654720 2931753063 A	
600	1800 T	-X:64654719 2931753062 T	
601 E	1801 G	-X:64654718 2931753061 G	E
601	1802 A	-X:64654717 2931753060 A	
601	1803 A	-X:64654716 2931753059 A	
602 E	1804 G	-X:64654715 2931753058 G	E
602	1805 A	-X:64654714 2931753057 A	
602	1806 G	-X:64654713 2931753056 G	
603 E	1807 G	-X:64654712 2931753055 G	E
603	1808 A	-X:64654711 2931753054 A	
603	1809 A	-X:64654710 2931753053 A	
604 D	1810 G	-X:64654709 2931753052 G	D
604	1811 A	-X:64654708 2931753051 A	
604	1812 C	-X:64654707 2931753050 C	
605 R	1813 A	-X:64654706 2931753049 A	R
605	1814 G	-X:64654705 2931753048 G	
605	1815 A	-X:64654704 2931753047 A	
606 M	1816 A	-X:64654703 2931753046 A	M
606	1817 T	-X:64654702 2931753045 T	
606	1818 G	-X:64654701 2931753044 G	
607 E	1819 G	-X:64654700 2931753043 G	E
607	1820 A	-X:64654699 2931753042 A	
607	1821 G	-X:64654698 2931753041 G	
608 V	1822 G	-X:64654697 2931753040 G	V
608	1823 T	-X:64654696 2931753039 T	
608	1824 G	-X:64654695 2931753038 G	
609 G	1825 G	-X:64654694 2931753037 G	G
609	1826 G	-X:64654693 2931753036 G	
609	1827 G	-X:64654692 2931753035 G	
610 P	1828 C	-X:64654691 2931753034 C	P
610	1829 C	-X:64654690 2931753033 C	
610	1830 T	-X:64654689 2931753032 T	
611 F	1831 T	-X:64654688 2931753031 T	F
611	1832 T	-X:64654687 2931753030 T	
611	1833 C	-X:64654686 2931753029 C	
612 S	1834 T	-X:64654685 2931753028 T	S
612	1835 C	-X:64654684 2931753027 C	
612	1836 T	-X:64654683 2931753026 T	
613 T	1837 A	-X:64654682 2931753025 A	T
613	1838 C	-X:64654681 2931753024 C	
613	1839 A	-X:64654680 2931753023 A	
614 G	1840 G	-X:64654679 2931753022 G	G
614	1841 G	-X:64654678 2931753021 G	
614	1842 G	-X:64654677 2931753020 G	
615 Q	1843 C	-X:64654676 2931753019 C	Q
615	1844 A	-X:64654675 2931753018 A	
615	1845 A	-X:64654674 2931753017 A	
616 E	1846 G	-X:64654673 2931753016 G	E
616	1847 A	-X:64654672 2931753015 A	
616	1848 G	-X:64654671 2931753014 G	
617 S	1849 T	-X:64654670 2931753013 T	S
617	1850 C	-X:64654669 2931753012 C	
617	1851 C	-X:64654668 2931753011 C	
618 P	1852 C	-X:64654667 2931753010 C	P
618	1853 C	-X:64654666 2931753009 C	
618	1854 C	-X:64654665 2931753008 C	
619 T	1855 A	-X:64654664 2931753007 A	T
619	1856 C	-X:64654663 2931753006 C	
619	1857 T	-X:64654662 2931753005 T	
620 A	1858 G	-X:64654661 2931753004 G	A
620	1859 C	-X:64654660 2931753003 C	
620	1860 C	-X:64654659 2931753002 C	
621 E	1861 G	-X:64654658 2931753001 G	E
621	1862 A	-X:64654657 2931753000 A	
621	1863 G	-X:64654656 2931752999 G	
622 N	1864 A	-X:64654655 2931752998 A	N
622	1865 A	-X:64654654 2931752997 A	
622	1866 T	-X:64654653 2931752996 T	
623 A	1867 G	-X:64654652 2931752995 G	A
623	1868 C	-X:64654651 2931752994 C	
623	1869 T	-X:64654650 2931752993 T	
624 R	1870 A	-X:64654649 2931752992 A	R
624	1871 G	-X:64654648 2931752991 G	
624	1872 G	-X:64654647 2931752990 G	
625 L	1873 C	-X:64654646 2931752989 C	L
625	1874 T	-X:64654645 2931752988 T	
625	1875 T	-X:64654644 2931752987 T	
626 L	1876 C	-X:64654643 2931752986 C	L
626	1877 T	-X:64654642 2931752985 T	
626	1878 G	-X:64654641 2931752984 G	
627 A	1879 G	-X:64654640 2931752983 G	A
627	1880 C	-X:64654639 2931752982 C	
627	1881 C	-X:64654638 2931752981 C	
628 Q	1882 C	-X:64654637 2931752980 C	Q
628	1883 A	-X:64654636 2931752979 A	
628	1884 G	-X:64654635 2931752978 G	
629 K	1885 A	-X:64654634 2931752977 A	K
629	1886 A	-X:64654633 2931752976 A	
629	1887 A	-X:64654632 2931752975 A	
630 R	1888 A	-X:64654631 2931752974 A	R
630	1889 G	-X:64654630 2931752973 G	
630	1890 A	-X:64654629 2931752972 A	
631 G	1891 G	-X:64654628 2931752971 G	G
631	1892 G	-X:64654627 2931752970 G	
631	1893 A	-X:64654626 2931752969 A	
632 A	1894 G	-X:64654625 2931752968 G	A
632	1895 C	-X:64654624 2931752967 C	
632	1896 T	-X:64654623 2931752966 T	
633 L	1897 T	-X:64654622 2931752965 T	L
633	1898 T	-X:64654621 2931752964 T	
633	1899 G	-X:64654620 2931752963 G	
634 Q	1900 C	-X:64654619 2931752962 C	Q
634	1901 A	-X:64654618 2931752961 A	
634	1902 G	-X:64654617 2931752960 G	
635 G	1903 G	-X:64654616 2931752959 G	G
635	1904 G	-X:64654615 2931752958 G	
635	1905 C	-X:64654614 2931752957 C	
636 S	1906 T	-X:64654613 2931752956 T	S
636	1907 C	-X:64654612 2931752955 C	
636	1908 T	-X:64654611 2931752954 T	
637 A	1909 G	-X:64654610 2931752953 G	A
637	1910 C	-X:64654609 2931752952 C	
637	1911 A	-X:64654608 2931752951 A	
638 W	1912 T	-X:64654607 2931752950 T	W
638	1913 G	-X:64654606 2931752949 G	
638	1914 G	-X:64654605 2931752948 G	
639 Q	1915 C	-X:64654604 2931752947 C	Q
639	1916 A	-X:64654603 2931752946 A	
639	1917 G	-X:64654602 2931752945 G	
640 V	1918 G	-X:64654601 2931752944 G	V
640	1919 T	-X:64654600 2931752943 T	
640	1920 T	-X:64654599 2931752942 T	
641 S	1921 A	-X:64654598 2931752941 A	S
641	1922 G	-X:64654597 2931752940 G	
641	1923 C	-X:64654596 2931752939 C	
642 S	1924 T	-X:64654595 2931752938 T	S
642	1925 C	-X:64654594 2931752937 C	
642	1926 A	-X:64654593 2931752936 A	
643 E	1927 G	-X:64654592 2931752935 G	E
643	1928 A	-X:64651578 2931749921 A	
643	1929 A	-X:64651577 2931749920 A	
644 D	1930 G	-X:64651576 2931749919 G	D
644	1931 A	-X:64651575 2931749918 A	
644	1932 C	-X:64651574 2931749917 C	
645 V	1933 G	-X:64651573 2931749916 G	V
645	1934 T	-X:64651572 2931749915 T	
645	1935 G	-X:64651571 2931749914 G	
646 R	1936 C	-X:64651570 2931749913 C	R
646	1937 G	-X:64651569 2931749912 G	
646	1938 A	-X:64651568 2931749911 A	
647 W	1939 T	-X:64651567 2931749910 T	W
647	1940 G	-X:64651566 2931749909 G	
647	1941 G	-X:64651565 2931749908 G	
648 D	1942 G	-X:64651564 2931749907 G	D
648	1943 A	-X:64651563 2931749906 A	
648	1944 C	-X:64651562 2931749905 C	
649 T	1945 A	-X:64651561 2931749904 A	T
649	1946 C	-X:64651560 2931749903 C	
649	1947 A	-X:64651559 2931749902 A	
650 F	1948 T	-X:64651558 2931749901 T	F
650	1949 T	-X:64651557 2931749900 T	
650	1950 T	-X:64651556 2931749899 T	
651 P	1951 C	-X:64651555 2931749898 C	P
651	1952 C	-X:64651554 2931749897 C	
651	1953 C	-X:64651553 2931749896 C	
652 L	1954 C	-X:64651552 2931749895 C	L
652	1955 T	-X:64651551 2931749894 T	
652	1956 A	-X:64651550 2931749893 A	
653 G	1957 G	-X:64651549 2931749892 G	G
653	1958 G	-X:64651548 2931749891 G	
653	1959 C	-X:64651547 2931749890 C	
654 R	1960 C	-X:64651546 2931749889 C	R
654	1961 G	-X:64651545 2931749888 G	
654	1962 A	-X:64651544 2931749887 A	
655 M	1963 A	-X:64651543 2931749886 A	M
655	1964 T	-X:64651542 2931749885 T	
655	1965 G	-X:64651541 2931749884 G	
656 P	1966 C	-X:64651540 2931749883 C	P
656	1967 C	-X:64651539 2931749882 C	
656	1968 A	-X:64651538 2931749881 A	
657 G	1969 G	-X:64651537 2931749880 G	G
657	1970 G	-X:64651536 2931749879 G	
657	1971 T	-X:64651535 2931749878 T	
658 Q	1972 C	-X:64651534 2931749877 C	Q
658	1973 A	-X:64651533 2931749876 A	
658	1974 G	-X:64651532 2931749875 G	
659 T	1975 A	-X:64651531 2931749874 A	T
659	1976 C	-X:64651530 2931749873 C	
659	1977 C	-X:64651529 2931749872 C	
660 E	1978 G	-X:64651528 2931749871 G	E
660	1979 A	-X:64651527 2931749870 A	
660	1980 G	-X:64651526 2931749869 G	
661 D	1981 G	-X:64651525 2931749868 G	D
661	1982 A	-X:64651524 2931749867 A	
661	1983 C	-X:64651523 2931749866 C	
662 P	1984 C	-X:64651522 2931749865 C	P
662	1985 C	-X:64651521 2931749864 C	
662	1986 A	-X:64651520 2931749863 A	
663 A	1987 G	-X:64651519 2931749862 G	A
663	1988 C	-X:64651518 2931749861 C	
663	1989 A	-X:64651517 2931749860 A	
664 E	1990 G	-X:64651516 2931749859 G	E
664	1991 A	-X:64651515 2931749858 A	
664	1992 G	-X:64651514 2931749857 G	
665 L	1993 C	-X:64651513 2931749856 C	L
665	1994 T	-X:64651512 2931749855 T	
665	1995 C	-X:64651511 2931749854 C	
666 M	1996 A	-X:64651510 2931749853 A	M
666	1997 T	-X:64651509 2931749852 T	
666	1998 G	-X:64651508 2931749851 G	
667 L	1999 C	-X:64651507 2931749850 C	L
667	2000 T	-X:64651506 2931749849 T	
667	2001 G	-X:64651505 2931749848 G	
668 E	2002 G	-X:64651504 2931749847 G	E
668	2003 A	-X:64651503 2931749846 A	
668	2004 G	-X:64651502 2931749845 G	
669 N	2005 A	-X:64651501 2931749844 A	N
669	2006 A	-X:64651500 2931749843 A	
669	2007 T	-X:64651499 2931749842 T	
670 Y	2008 T	-X:64651498 2931749841 T	Y
670	2009 A	-X:64651497 2931749840 A	
670	2010 T	-X:64651496 2931749839 T	
671 D	2011 G	-X:64651495 2931749838 G	D
671	2012 A	-X:64651494 2931749837 A	
671	2013 C	-X:64651493 2931749836 C	
672 T	2014 A	-X:64651492 2931749835 A	T
672	2015 C	-X:64651491 2931749834 C	
672	2016 C	-X:64651490 2931749833 C	
673 M	2017 A	-X:64651489 2931749832 A	M
673	2018 T	-X:64651488 2931749831 T	
673	2019 G	-X:64651487 2931749830 G	
674 Y	2020 T	-X:64651486 2931749829 T	Y
674	2021 A	-X:64651485 2931749828 A	
674	2022 T	-X:64651484 2931749827 T	
675 L	2023 C	-X:64651483 2931749826 C	L
675	2024 T	-X:64651482 2931749825 T	
675	2025 T	-X:64651481 2931749824 T	
676 L	2026 T	-X:64651480 2931749823 T	L
676	2027 T	-X:64651479 2931749822 T	
676	2028 G	-X:64651478 2931749821 G	
677 D	2029 G	-X:64651477 2931749820 G	D
677	2030 A	-X:64651476 2931749819 A	
677	2031 C	-X:64651475 2931749818 C	
678 Q	2032 C	-X:64651474 2931749817 C	Q
678	2033 A	-X:64651473 2931749816 A	
678	2034 G	-X:64651472 2931749815 G	
679 P	2035 C	-X:64651471 2931749814 C	P
679	2036 C	-X:64651470 2931749813 C	
679	2037 T	-X:64651469 2931749812 T	
680 V	2038 G	-X:64651468 2931749811 G	V
680	2039 T	-X:64651467 2931749810 T	
680	2040 G	-X:64651466 2931749809 G	
681 L	2041 C	-X:64651465 2931749808 C	L
681	2042 T	-X:64651464 2931749807 T	
681	2043 A	-X:64651463 2931749806 A	
682 E	2044 G	-X:64651462 2931749805 G	E
682	2045 A	-X:64651461 2931749804 A	
682	2046 G	-X:64651460 2931749803 G	
683 Q	2047 C	-X:64651459 2931749802 C	Q
683	2048 A	-X:64651458 2931749801 A	
683	2049 G	-X:64651457 2931749800 G	
684 R	2050 C	-X:64651456 2931749799 C	R
684	2051 G	-X:64651455 2931749798 G	
684	2052 G	-X:64651454 2931749797 G	
685 L	2053 C	-X:64651453 2931749796 C	L
685	2054 T	-X:64651452 2931749795 T	
685	2055 G	-X:64651451 2931749794 G	
686 E	2056 G	-X:64651450 2931749793 G	E
686	2057 A	-X:64651449 2931749792 A	
686	2058 A	-X:64651448 2931749791 A	
687 P	2059 C	-X:64651447 2931749790 C	P
687	2060 C	-X:64651446 2931749789 C	
687	2061 C	-X:64651445 2931749788 C	
688 S	2062 T	-X:64651444 2931749787 T	S
688	2063 C	-X:64651443 2931749786 C	
688	2064 A	-X:64651442 2931749785 A	
689 T	2065 A	-X:64651441 2931749784 A	T
689	2066 C	-X:64651440 2931749783 C	
689	2067 A	-X:64651439 2931749782 A	
690 C	2068 T	-X:64651438 2931749781 T	C
690	2069 G	-X:64651437 2931749780 G	
690	2070 C	-X:64651436 2931749779 C	
691 K	2071 A	-X:64651435 2931749778 A	K
691	2072 A	-X:64651434 2931749777 A	
691	2073 G	-X:64651433 2931749776 G	
692 T	2074 A	-X:64651432 2931749775 A	T
692	2075 C	-X:64651431 2931749774 C	
692	2076 T	-X:64651430 2931749773 T	
>ENSP00000363937 
1 M	1 A	-X:64671320 2931769663 A	M
1	2 T	-X:64671319 2931769662 T	
1	3 G	-X:64671318 2931769661 G	
2 S	4 T	-X:64671317 2931769660 T	S
2	5 C	-X:64671316 2931769659 C	
2	6 G	-X:64671315 2931769658 G	
3 W	7 T	-X:64671314 2931769657 T	W
3	8 G	-X:64671313 2931769656 G	
3	9 G	-X:64671312 2931769655 G	
4 E	10 G	-X:64671311 2931769654 G	E
4	11 A	-X:64671310 2931769653 A	
4	12 A	-X:64671309 2931769652 A	
5 S	13 T	-X:64671308 2931769651 T	S
5	14 C	-X:64671307 2931769650 C	
5	15 C	-X:64671306 2931769649 C	
6 G	16 G	-X:64671305 2931769648 G	G
6	17 G	-X:64671304 2931769647 G	
6	18 G	-X:64671303 2931769646 G	
7 A	19 G	-X:64671302 2931769645 G	A
7	20 C	-X:64671301 2931769644 C	
7	21 C	-X:64671300 2931769643 C	
8 G	22 G	-X:64671299 2931769642 G	G
8	23 G	-X:64671298 2931769641 G	
8	24 G	-X:64671297 2931769640 G	
9 P	25 C	-X:64671296 2931769639 C	P
9	26 C	-X:64671295 2931769638 C	
9	27 A	-X:64671294 2931769637 A	
10 G	28 G	-X:64671293 2931769636 G	G
10	29 G	-X:64671292 2931769635 G	
10	30 T	-X:64671291 2931769634 T	
11 L	31 C	-X:64671290 2931769633 C	L
11	32 T	-X:64671289 2931769632 T	
11	33 A	-X:64671288 2931769631 A	
12 G	34 G	-X:64671287 2931769630 G	G
12	35 G	-X:64671286 2931769629 G	
12	36 T	-X:64671285 2931769628 T	
13 S	37 T	-X:64671284 2931769627 T	S
13	38 C	-X:64671283 2931769626 C	
13	39 C	-X:64671282 2931769625 C	
14 Q	40 C	-X:64671281 2931769624 C	Q
14	41 A	-X:64671280 2931769623 A	
14	42 G	-X:64671279 2931769622 G	
15 G	43 G	-X:64671278 2931769621 G	G
15	44 G	-X:64671277 2931769620 G	
15	45 G	-X:64671276 2931769619 G	
16 M	46 A	-X:64671275 2931769618 A	M
16	47 T	-X:64671274 2931769617 T	
16	48 G	-X:64671273 2931769616 G	
17 D	49 G	-X:64671272 2931769615 G	D
17	50 A	-X:64671271 2931769614 A	
17	51 T	-X:64671270 2931769613 T	
18 L	52 C	-X:64671269 2931769612 C	L
18	53 T	-X:64671268 2931769611 T	
18	54 C	-X:64671267 2931769610 C	
19 V	55 G	-X:64671266 2931769609 G	V
19	56 T	-X:64671265 2931769608 T	
19	57 G	-X:64671264 2931769607 G	
20 W	58 T	-X:64671263 2931769606 T	W
20	59 G	-X:64671262 2931769605 G	
20	60 G	-X:64671261 2931769604 G	
21 S	61 A	-X:64671260 2931769603 A	S
21	62 G	-X:64671259 2931769602 G	
21	63 T	-X:64671258 2931769601 T	
22 A	64 G	-X:64671257 2931769600 G	A
22	65 C	-X:64671256 2931769599 C	
22	66 G	-X:64671255 2931769598 G	
23 W	67 T	-X:64671254 2931769597 T	W
23	68 G	-X:64671253 2931769596 G	
23	69 G	-X:64671252 2931769595 G	
24 Y	70 T	-X:64671251 2931769594 T	Y
24	71 A	-X:64671250 2931769593 A	
24	72 C	-X:64671249 2931769592 C	
25 G	73 G	-X:64671248 2931769591 G	G
25	74 G	-X:64671247 2931769590 G	
25	75 A	-X:64671246 2931769589 A	
26 K	76 A	-X:64671245 2931769588 A	K
26	77 A	-X:64671244 2931769587 A	
26	78 G	-X:64671243 2931769586 G	
27 C	79 T	-X:64671242 2931769585 T	C
27	80 G	-X:64671241 2931769584 G	
27	81 C	-X:64671240 2931769583 C	
28 V	82 G	-X:64671239 2931769582 G	V
28	83 T	-X:64671238 2931769581 T	
28	84 T	-X:64671237 2931769580 T	
29 K	85 A	-X:64671236 2931769579 A	K
29	86 A	-X:64671235 2931769578 A	
29	87 A	-X:64671234 2931769577 A	
30 G	88 G	-X:64671233 2931769576 G	G
30	89 G	-X:64671232 2931769575 G	
30	90 G	-X:64671231 2931769574 G	
31 K	91 A	-X:64671230 2931769573 A	K
31	92 A	-X:64671229 2931769572 A	
31	93 A	-X:64671228 2931769571 A	
32 G	94 G	-X:64671227 2931769570 G	G
32	95 G	-X:64671226 2931769569 G	
32	96 G	-X:64671225 2931769568 G	
33 S	97 T	-X:64671224 2931769567 T	S
33	98 C	-X:64671223 2931769566 C	
33	99 G	-X:64671222 2931769565 G	
34 L	100 T	-X:64671221 2931769564 T	L
34	101 T	-X:64671220 2931769563 T	
34	102 G	-X:64671219 2931769562 G	
35 P	103 C	-X:64671218 2931769561 C	P
35	104 C	-X:64671217 2931769560 C	
35	105 A	-X:64671216 2931769559 A	
36 L	106 C	-X:64671215 2931769558 C	L
36	107 T	-X:64671214 2931769557 T	
36	108 C	-X:64671213 2931769556 C	
37 S	109 T	-X:64671212 2931769555 T	S
37	110 C	-X:64671211 2931769554 C	
37	111 G	-X:64671210 2931769553 G	
38 A	112 G	-X:64671209 2931769552 G	A
38	113 C	-X:64671208 2931769551 C	
38	114 C	-X:64671207 2931769550 C	
39 H	115 C	-X:64671206 2931769549 C	H
39	116 A	-X:64671205 2931769548 A	
39	117 C	-X:64671204 2931769547 C	
40 G	118 G	-X:64671203 2931769546 G	G
40	119 G	-X:64671202 2931769545 G	
40	120 C	-X:64671201 2931769544 C	
41 I	121 A	-X:64671200 2931769543 A	I
41	122 T	-X:64671199 2931769542 T	
41	123 C	-X:64671198 2931769541 C	
42 V	124 G	-X:64671197 2931769540 G	V
42	125 T	-X:64671196 2931769539 T	
42	126 G	-X:64671195 2931769538 G	
43 V	127 G	-X:64671194 2931769537 G	V
43	128 T	-X:64671193 2931769536 T	
43	129 C	-X:64671192 2931769535 C	
44 A	130 G	-X:64671191 2931769534 G	A
44	131 C	-X:64671190 2931769533 C	
44	132 C	-X:64671189 2931769532 C	
45 W	133 T	-X:64671188 2931769531 T	W
45	134 G	-X:64671187 2931769530 G	
45	135 G	-X:64671186 2931769529 G	
46 L	136 C	-X:64671185 2931769528 C	L
46	137 T	-X:64671184 2931769527 T	
46	138 C	-X:64671183 2931769526 C	
47 S	139 A	-X:64671182 2931769525 A	S
47	140 G	-X:64671181 2931769524 G	
47	141 C	-X:64671180 2931769523 C	
48 R	142 A	-X:64671179 2931769522 A	R
48	143 G	-X:64671178 2931769521 G	
48	144 G	-X:64671177 2931769520 G	
49 A	145 G	-X:64671176 2931769519 G	A
49	146 C	-X:64671175 2931769518 C	
49	147 C	-X:64671174 2931769517 C	
50 E	148 G	-X:64671173 2931769516 G	E
50	149 A	-X:64671172 2931769515 A	
50	150 G	-X:64671171 2931769514 G	
51 W	151 T	-X:64671170 2931769513 T	W
51	152 G	-X:64671169 2931769512 G	
51	153 G	-X:64671168 2931769511 G	
52 D	154 G	-X:64671167 2931769510 G	D
52	155 A	-X:64671166 2931769509 A	
52	156 C	-X:64671165 2931769508 C	
53 Q	157 C	-X:64671164 2931769507 C	Q
53	158 A	-X:64671163 2931769506 A	
53	159 G	-X:64671162 2931769505 G	
54 V	160 G	-X:64671161 2931769504 G	V
54	161 T	-X:64671160 2931769503 T	
54	162 G	-X:64671159 2931769502 G	
55 T	163 A	-X:64671158 2931769501 A	T
55	164 C	-X:64671157 2931769500 C	
55	165 G	-X:64671156 2931769499 G	
56 V	166 G	-X:64671155 2931769498 G	V
56	167 T	-X:64671154 2931769497 T	
56	168 T	-X:64671153 2931769496 T	
57 Y	169 T	-X:64671152 2931769495 T	Y
57	170 A	-X:64671151 2931769494 A	
57	171 T	-X:64671150 2931769493 T	
58 L	172 C	-X:64671149 2931769492 C	L
58	173 T	-X:64671148 2931769491 T	
58	174 G	-X:64671147 2931769490 G	
59 F	175 T	-X:64671146 2931769489 T	F
59	176 T	-X:64671145 2931769488 T	
59	177 C	-X:64671144 2931769487 C	
60 C	178 T	-X:64671143 2931769486 T	C
60	179 G	-X:64671142 2931769485 G	
60	180 T	-X:64671141 2931769484 T	
61 D	181 G	-X:64671140 2931769483 G	D
61	182 A	-X:64671139 2931769482 A	
61	183 C	-X:64671138 2931769481 C	
62 D	184 G	-X:64671137 2931769480 G	D
62	185 A	-X:64671136 2931769479 A	
62	186 C	-X:64671135 2931769478 C	
63 H	187 C	-X:64671134 2931769477 C	H
63	188 A	-X:64671133 2931769476 A	
63	189 T	-X:64671132 2931769475 T	
64 K	190 A	-X:64671131 2931769474 A	K
64	191 A	-X:64671130 2931769473 A	
64	192 G	-X:64671129 2931769472 G	
65 L	193 T	-X:64671128 2931769471 T	L
65	194 T	-X:64671127 2931769470 T	
65	195 G	-X:64671126 2931769469 G	
66 Q	196 C	-X:64671125 2931769468 C	Q
66	197 A	-X:64671124 2931769467 A	
66	198 G	-X:64671123 2931769466 G	
67 R	199 C	-X:64671122 2931769465 C	R
67	200 G	-X:64671121 2931769464 G	
67	201 G	-X:64671120 2931769463 G	
68 Y	202 T	-X:64671119 2931769462 T	Y
68	203 A	-X:64671118 2931769461 A	
68	204 C	-X:64671117 2931769460 C	
69 A	205 G	-X:64671116 2931769459 G	A
69	206 C	-X:64671115 2931769458 C	
69	207 G	-X:64671114 2931769457 G	
70 L	208 C	-X:64671113 2931769456 C	L
70	209 T	-X:64671112 2931769455 T	
70	210 T	-X:64671111 2931769454 T	
71 N	211 A	-X:64671110 2931769453 A	N
71	212 A	-X:64671109 2931769452 A	
71	213 C	-X:64671108 2931769451 C	
72 R	214 C	-X:64671107 2931769450 C	R
72	215 G	-X:64671106 2931769449 G	
72	216 C	-X:64671105 2931769448 C	
73 I	217 A	-X:64671104 2931769447 A	I
73	218 T	-X:64671103 2931769446 T	
73	219 C	-X:64671102 2931769445 C	
74 T	220 A	-X:64671101 2931769444 A	T
74	221 C	-X:64671100 2931769443 C	
74	222 G	-X:64671099 2931769442 G	
75 V	223 G	-X:64671098 2931769441 G	V
75	224 T	-X:64671097 2931769440 T	
75	225 G	-X:64671096 2931769439 G	
76 W	226 T	-X:64671095 2931769438 T	W
76	227 G	-X:64671094 2931769437 G	
76	228 G	-X:64671093 2931769436 G	
77 R	229 A	-X:64671092 2931769435 A	R
77	230 G	-X:64671091 2931769434 G	
77	231 G	-X:64671090 2931769433 G	
78 S	232 A	-X:64671089 2931769432 A	S
78	233 G	-X:64671088 2931769431 G	
78	234 C	-X:64671087 2931769430 C	
79 R	235 A	-X:64671086 2931769429 A	R
79	236 G	-X:64671085 2931769428 G	
79	237 G	-X:64669235 2931767578 G	
80 F	238 T	-X:64669234 2931767577 T	F
80	239 T	-X:64669233 2931767576 T	
80	240 T	-X:64669232 2931767575 T	
81 V	241 G	-X:64669231 2931767574 G	V
81	242 T	-X:64669230 2931767573 T	
81	243 G	-X:64669229 2931767572 G	
82 N	244 A	-X:64669228 2931767571 A	N
82	245 A	-X:64669227 2931767570 A	
82	246 T	-X:64669226 2931767569 T	
83 L	247 C	-X:64669225 2931767568 C	L
83	248 T	-X:64669224 2931767567 T	
83	249 T	-X:64669223 2931767566 T	
84 I	250 A	-X:64669222 2931767565 A	I
84	251 T	-X:64669221 2931767564 T	
84	252 C	-X:64669220 2931767563 C	
85 S	253 T	-X:64669219 2931767562 T	S
85	254 C	-X:64669218 2931767561 C	
85	255 A	-X:64669217 2931767560 A	
86 E	256 G	-X:64669216 2931767559 G	E
86	257 A	-X:64669215 2931767558 A	
86	258 G	-X:64669214 2931767557 G	
87 R	259 A	-X:64669213 2931767556 A	R
87	260 G	-X:64669212 2931767555 G	
87	261 G	-X:64669211 2931767554 G	
88 K	262 A	-X:64669210 2931767553 A	K
88	263 A	-X:64669209 2931767552 A	
88	264 G	-X:64669208 2931767551 G	
89 T	265 A	-X:64669207 2931767550 A	T
89	266 C	-X:64669206 2931767549 C	
89	267 A	-X:64669205 2931767548 A	
90 K	268 A	-X:64669204 2931767547 A	K
90	269 A	-X:64669203 2931767546 A	
90	270 G	-X:64669202 2931767545 G	
91 F	271 T	-X:64669201 2931767544 T	F
91	272 T	-X:64669200 2931767543 T	
91	273 T	-X:64669199 2931767542 T	
92 A	274 G	-X:64669198 2931767541 G	A
92	275 C	-X:64669197 2931767540 C	
92	276 C	-X:64669196 2931767539 C	
93 K	277 A	-X:64669195 2931767538 A	K
93	278 A	-X:64669194 2931767537 A	
93	279 G	-X:64669193 2931767536 G	
94 V	280 G	-X:64669192 2931767535 G	V
94	281 T	-X:64669191 2931767534 T	
94	282 C	-X:64669190 2931767533 C	
95 P	283 C	-X:64669189 2931767532 C	P
95	284 C	-X:64669188 2931767531 C	
95	285 C	-X:64669187 2931767530 C	
96 L	286 C	-X:64669186 2931767529 C	L
96	287 T	-X:64669185 2931767528 T	
96	288 C	-X:64669184 2931767527 C	
97 K	289 A	-X:64669183 2931767526 A	K
97	290 A	-X:64669182 2931767525 A	
97	291 G	-X:64669181 2931767524 G	
98 C	292 T	-X:64669180 2931767523 T	C
98	293 G	-X:64669179 2931767522 G	
98	294 T	-X:64669178 2931767521 T	
99 L	295 C	-X:64669177 2931767520 C	L
99	296 T	-X:64669176 2931767519 T	
99	297 G	-X:64669175 2931767518 G	
100 A	298 G	-X:64669174 2931767517 G	A
100	299 C	-X:64669173 2931767516 C	
100	300 T	-X:64669172 2931767515 T	
101 Q	301 C	-X:64669171 2931767514 C	Q
101	302 A	-X:64669170 2931767513 A	
101	303 A	-X:64669169 2931767512 A	
102 E	304 G	-X:64669168 2931767511 G	E
102	305 A	-X:64669167 2931767510 A	
102	306 G	-X:64669166 2931767509 G	
103 V	307 G	-X:64668043 2931766386 G	V
103	308 T	-X:64668042 2931766385 T	
103	309 A	-X:64668041 2931766384 A	
104 N	310 A	-X:64668040 2931766383 A	N
104	311 A	-X:64668039 2931766382 A	
104	312 T	-X:64668038 2931766381 T	
105 I	313 A	-X:64668037 2931766380 A	I
105	314 T	-X:64668036 2931766379 T	
105	315 T	-X:64668035 2931766378 T	
106 P	316 C	-X:64668034 2931766377 C	P
106	317 C	-X:64668033 2931766376 C	
106	318 G	-X:64668032 2931766375 G	
107 D	319 G	-X:64668031 2931766374 G	D
107	320 A	-X:64668030 2931766373 A	
107	321 T	-X:64668029 2931766372 T	
108 W	322 T	-X:64668028 2931766371 T	W
108	323 G	-X:64668027 2931766370 G	
108	324 G	-X:64668026 2931766369 G	
109 I	325 A	-X:64668025 2931766368 A	I
109	326 T	-X:64668024 2931766367 T	
109	327 T	-X:64668023 2931766366 T	
110 V	328 G	-X:64668022 2931766365 G	V
110	329 T	-X:64668021 2931766364 T	
110	330 T	-X:64668020 2931766363 T	
111 D	331 G	-X:64668019 2931766362 G	D
111	332 A	-X:64668018 2931766361 A	
111	333 C	-X:64668017 2931766360 C	
112 L	334 C	-X:64668016 2931766359 C	L
112	335 T	-X:64668015 2931766358 T	
112	336 T	-X:64668014 2931766357 T	
113 R	337 C	-X:64668013 2931766356 C	R
113	338 G	-X:64668012 2931766355 G	
113	339 C	-X:64668011 2931766354 C	
114 H	340 C	-X:64668010 2931766353 C	H
114	341 A	-X:64668009 2931766352 A	
114	342 T	-X:64668008 2931766351 T	
115 E	343 G	-X:64668007 2931766350 G	E
115	344 A	-X:64668006 2931766349 A	
115	345 G	-X:64668005 2931766348 G	
116 L	346 T	-X:64668004 2931766347 T	L
116	347 T	-X:64668003 2931766346 T	
116	348 G	-X:64668002 2931766345 G	
117 T	349 A	-X:64668001 2931766344 A	T
117	350 C	-X:64668000 2931766343 C	
117	351 C	-X:64667999 2931766342 C	
118 H	352 C	-X:64667998 2931766341 C	H
118	353 A	-X:64667997 2931766340 A	
118	354 C	-X:64667996 2931766339 C	
119 K	355 A	-X:64667995 2931766338 A	K
119	356 A	-X:64667994 2931766337 A	
119	357 G	-X:64667993 2931766336 G	
120 K	358 A	-X:64667992 2931766335 A	K
120	359 A	-X:64667991 2931766334 A	
120	360 A	-X:64667990 2931766333 A	
121 M	361 A	-X:64667989 2931766332 A	M
121	362 T	-X:64667988 2931766331 T	
121	363 G	-X:64667987 2931766330 G	
122 P	364 C	-X:64667986 2931766329 C	P
122	365 C	-X:64667985 2931766328 C	
122	366 C	-X:64667984 2931766327 C	
123 H	367 C	-X:64667983 2931766326 C	H
123	368 A	-X:64667982 2931766325 A	
123	369 T	-X:64667981 2931766324 T	
124 I	370 A	-X:64667980 2931766323 A	I
124	371 T	-X:64667979 2931766322 T	
124	372 A	-X:64667978 2931766321 A	
125 N	373 A	-X:64667977 2931766320 A	N
125	374 A	-X:64667976 2931766319 A	
125	375 T	-X:64667975 2931766318 T	
126 D	376 G	-X:64667974 2931766317 G	D
126	377 A	-X:64667973 2931766316 A	
126	378 C	-X:64667972 2931766315 C	
127 C	379 T	-X:64667971 2931766314 T	C
127	380 G	-X:64667970 2931766313 G	
127	381 C	-X:64667969 2931766312 C	
128 R	382 C	-X:64667968 2931766311 C	R
128	383 G	-X:64667967 2931766310 G	
128	384 C	-X:64667966 2931766309 C	
129 R	385 A	-X:64667965 2931766308 A	R
129	386 G	-X:64667964 2931766307 G	
129	387 A	-X:64667963 2931766306 A	
130 G	388 G	-X:64667962 2931766305 G	G
130	389 G	-X:64666483 2931764826 G	
130	390 C	-X:64666482 2931764825 C	
131 C	391 T	-X:64666481 2931764824 T	C
131	392 G	-X:64666480 2931764823 G	
131	393 C	-X:64666479 2931764822 C	
132 Y	394 T	-X:64666478 2931764821 T	Y
132	395 A	-X:64666477 2931764820 A	
132	396 C	-X:64666476 2931764819 C	
133 F	397 T	-X:64666475 2931764818 T	F
133	398 T	-X:64666474 2931764817 T	
133	399 T	-X:64666473 2931764816 T	
134 V	400 G	-X:64666472 2931764815 G	V
134	401 T	-X:64666471 2931764814 T	
134	402 C	-X:64666470 2931764813 C	
135 L	403 C	-X:64666469 2931764812 C	L
135	404 T	-X:64666468 2931764811 T	
135	405 G	-X:64666467 2931764810 G	
136 D	406 G	-X:64666466 2931764809 G	D
136	407 A	-X:64666465 2931764808 A	
136	408 T	-X:64666464 2931764807 T	
137 W	409 T	-X:64666463 2931764806 T	W
137	410 G	-X:64666462 2931764805 G	
137	411 G	-X:64666461 2931764804 G	
138 L	412 C	-X:64666460 2931764803 C	L
138	413 T	-X:64666459 2931764802 T	
138	414 C	-X:64666458 2931764801 C	
139 Q	415 C	-X:64666457 2931764800 C	Q
139	416 A	-X:64666456 2931764799 A	
139	417 G	-X:64666455 2931764798 G	
140 K	418 A	-X:64666454 2931764797 A	K
140	419 A	-X:64666453 2931764796 A	
140	420 G	-X:64666452 2931764795 G	
141 T	421 A	-X:64666451 2931764794 A	T
141	422 C	-X:64666450 2931764793 C	
141	423 C	-X:64666449 2931764792 C	
142 Y	424 T	-X:64666448 2931764791 T	Y
142	425 A	-X:64666447 2931764790 A	
142	426 T	-X:64666446 2931764789 T	
143 W	427 T	-X:64666445 2931764788 T	W
143	428 G	-X:64666444 2931764787 G	
143	429 G	-X:64666443 2931764786 G	
144 C	430 T	-X:64666442 2931764785 T	C
144	431 G	-X:64666441 2931764784 G	
144	432 C	-X:64666440 2931764783 C	
145 R	433 C	-X:64666439 2931764782 C	R
145	434 G	-X:64666438 2931764781 G	
145	435 C	-X:64666437 2931764780 C	
146 Q	436 C	-X:64666436 2931764779 C	Q
146	437 A	-X:64666435 2931764778 A	
146	438 A	-X:64666434 2931764777 A	
147 L	439 C	-X:64666433 2931764776 C	L
147	440 T	-X:64666432 2931764775 T	
147	441 G	-X:64666431 2931764774 G	
148 E	442 G	-X:64666430 2931764773 G	E
148	443 A	-X:64666429 2931764772 A	
148	444 G	-X:64666428 2931764771 G	
149 N	445 A	-X:64666427 2931764770 A	N
149	446 A	-X:64666426 2931764769 A	
149	447 C	-X:64666425 2931764768 C	
150 S	448 A	-X:64666424 2931764767 A	S
150	449 G	-X:64666423 2931764766 G	
150	450 C	-X:64666422 2931764765 C	
151 L	451 C	-X:64666421 2931764764 C	L
151	452 T	-X:64666420 2931764763 T	
151	453 G	-X:64666419 2931764762 G	
152 R	454 A	-X:64666418 2931764761 A	R
152	455 G	-X:64666417 2931764760 G	
152	456 A	-X:64666416 2931764759 A	
153 E	457 G	-X:64666415 2931764758 G	E
153	458 A	-X:64666414 2931764757 A	
153	459 G	-X:64666413 2931764756 G	
154 T	460 A	-X:64666412 2931764755 A	T
154	461 C	-X:64666411 2931764754 C	
154	462 C	-X:64666410 2931764753 C	
155 W	463 T	-X:64666409 2931764752 T	W
155	464 G	-X:64666408 2931764751 G	
155	465 G	-X:64666407 2931764750 G	
156 E	466 G	-X:64666406 2931764749 G	E
156	467 A	-X:64666405 2931764748 A	
156	468 G	-X:64666404 2931764747 G	
157 L	469 T	-X:64666403 2931764746 T	L
157	470 T	-X:64666402 2931764745 T	
157	471 G	-X:64666401 2931764744 G	
158 E	472 G	-X:64666400 2931764743 G	E
158	473 A	-X:64666399 2931764742 A	
158	474 G	-X:64666398 2931764741 G	
159 E	475 G	-X:64666397 2931764740 G	E
159	476 A	-X:64666396 2931764739 A	
159	477 G	-X:64666395 2931764738 G	
160 F	478 T	-X:64666394 2931764737 T	F
160	479 T	-X:64666393 2931764736 T	
160	480 C	-X:64666392 2931764735 C	
161 R	481 A	-X:64666391 2931764734 A	R
161	482 G	-X:64666390 2931764733 G	
161	483 G	-X:64666389 2931764732 G	
162 E	484 G	-X:64666388 2931764731 G	E
162	485 A	-X:64666387 2931764730 A	
162	486 A	-X:64666386 2931764729 A	
163 G	487 G	-X:64666385 2931764728 G	G
163	488 G	-X:64666384 2931764727 G	
163	489 G	-X:64666383 2931764726 G	
164 I	490 A	-X:64666382 2931764725 A	I
164	491 T	-X:64666381 2931764724 T	
164	492 A	-X:64666380 2931764723 A	
165 E	493 G	-X:64666379 2931764722 G	E
165	494 A	-X:64666378 2931764721 A	
165	495 G	-X:64666377 2931764720 G	
166 E	496 G	-X:64666376 2931764719 G	E
166	497 A	-X:64666375 2931764718 A	
166	498 A	-X:64666374 2931764717 A	
167 E	499 G	-X:64666373 2931764716 G	E
167	500 A	-X:64666372 2931764715 A	
167	501 G	-X:64666371 2931764714 G	
168 D	502 G	-X:64666370 2931764713 G	D
168	503 A	-X:64666369 2931764712 A	
168	504 T	-X:64666368 2931764711 T	
169 Q	505 C	-X:64666367 2931764710 C	Q
169	506 A	-X:64666366 2931764709 A	
169	507 A	-X:64666365 2931764708 A	
170 E	508 G	-X:64666364 2931764707 G	E
170	509 A	-X:64666363 2931764706 A	
170	510 G	-X:64666362 2931764705 G	
171 E	511 G	-X:64666361 2931764704 G	E
171	512 A	-X:64666360 2931764703 A	
171	513 A	-X:64666359 2931764702 A	
172 D	514 G	-X:64666358 2931764701 G	D
172	515 A	-X:64666357 2931764700 A	
172	516 T	-X:64666356 2931764699 T	
173 K	517 A	-X:64666355 2931764698 A	K
173	518 A	-X:64666354 2931764697 A	
173	519 G	-X:64666353 2931764696 G	
174 N	520 A	-X:64666352 2931764695 A	N
174	521 A	-X:64666351 2931764694 A	
174	522 C	-X:64666350 2931764693 C	
175 I	523 A	-X:64666349 2931764692 A	I
175	524 T	-X:64666348 2931764691 T	
175	525 T	-X:64666347 2931764690 T	
176 V	526 G	-X:64666346 2931764689 G	V
176	527 T	-X:64666345 2931764688 T	
176	528 T	-X:64666344 2931764687 T	
177 V	529 G	-X:64666343 2931764686 G	V
177	530 T	-X:64666342 2931764685 T	
177	531 T	-X:64666341 2931764684 T	
178 D	532 G	-X:64666340 2931764683 G	D
178	533 A	-X:64666339 2931764682 A	
178	534 T	-X:64666338 2931764681 T	
179 D	535 G	-X:64666337 2931764680 G	D
179	536 A	-X:64666336 2931764679 A	
179	537 C	-X:64666335 2931764678 C	
180 I	538 A	-X:64666334 2931764677 A	I
180	539 T	-X:64666333 2931764676 T	
180	540 C	-X:64666332 2931764675 C	
181 T	541 A	-X:64666331 2931764674 A	T
181	542 C	-X:64666330 2931764673 C	
181	543 A	-X:64666329 2931764672 A	
182 E	544 G	-X:64666328 2931764671 G	E
182	545 A	-X:64666327 2931764670 A	
182	546 A	-X:64666326 2931764669 A	
183 Q	547 C	-X:64666325 2931764668 C	Q
183	548 A	-X:64666324 2931764667 A	
183	549 G	-X:64666323 2931764666 G	
184 K	550 A	-X:64666322 2931764665 A	K
184	551 A	-X:64666321 2931764664 A	
184	552 A	-X:64666320 2931764663 A	
185 P	553 C	-X:64666319 2931764662 C	P
185	554 C	-X:64666318 2931764661 C	
185	555 A	-X:64666317 2931764660 A	
186 E	556 G	-X:64666316 2931764659 G	E
186	557 A	-X:64666315 2931764658 A	
186	558 G	-X:64666314 2931764657 G	
187 P	559 C	-X:64666313 2931764656 C	P
187	560 C	-X:64666312 2931764655 C	
187	561 T	-X:64666311 2931764654 T	
188 Q	562 C	-X:64666310 2931764653 C	Q
188	563 A	-X:64666309 2931764652 A	
188	564 G	-X:64666308 2931764651 G	
189 D	565 G	-X:64666307 2931764650 G	D
189	566 A	-X:64666306 2931764649 A	
189	567 T	-X:64666305 2931764648 T	
190 D	568 G	-X:64666304 2931764647 G	D
190	569 A	-X:64666303 2931764646 A	
190	570 T	-X:64666302 2931764645 T	
191 G	571 G	-X:64666301 2931764644 G	G
191	572 G	-X:64666300 2931764643 G	
191	573 G	-X:64666299 2931764642 G	
192 K	574 A	-X:64666298 2931764641 A	K
192	575 A	-X:64666297 2931764640 A	
192	576 A	-X:64666296 2931764639 A	
193 S	577 A	-X:64666295 2931764638 A	S
193	578 G	-X:64666294 2931764637 G	
193	579 T	-X:64666293 2931764636 T	
194 T	580 A	-X:64666292 2931764635 A	T
194	581 C	-X:64666291 2931764634 C	
194	582 G	-X:64666290 2931764633 G	
195 E	583 G	-X:64666289 2931764632 G	E
195	584 A	-X:64666288 2931764631 A	
195	585 G	-X:64666287 2931764630 G	
196 S	586 T	-X:64666286 2931764629 T	S
196	587 C	-X:64666285 2931764628 C	
196	588 A	-X:64666284 2931764627 A	
197 D	589 G	-X:64666283 2931764626 G	D
197	590 A	-X:64666282 2931764625 A	
197	591 T	-X:64666281 2931764624 T	
198 V	592 G	-X:64666280 2931764623 G	V
198	593 T	-X:64666279 2931764622 T	
198	594 A	-X:64666278 2931764621 A	
199 K	595 A	-X:64666277 2931764620 A	K
199	596 A	-X:64666276 2931764619 A	
199	597 G	-X:64666275 2931764618 G	
200 A	598 G	-X:64666274 2931764617 G	A
200	599 C	-X:64666273 2931764616 C	
200	600 C	-X:64666272 2931764615 C	
201 D	601 G	-X:64666271 2931764614 G	D
201	602 A	-X:64666270 2931764613 A	
201	603 T	-X:64666269 2931764612 T	
202 G	604 G	-X:64666268 2931764611 G	G
202	605 G	-X:64666267 2931764610 G	
202	606 A	-X:64666266 2931764609 A	
203 D	607 G	-X:64666265 2931764608 G	D
203	608 A	-X:64666264 2931764607 A	
203	609 C	-X:64666263 2931764606 C	
204 S	610 A	-X:64666262 2931764605 A	S
204	611 G	-X:64666261 2931764604 G	
204	612 C	-X:64666260 2931764603 C	
205 K	613 A	-X:64666259 2931764602 A	K
205	614 A	-X:64666258 2931764601 A	
205	615 A	-X:64666257 2931764600 A	
206 G	616 G	-X:64666256 2931764599 G	G
206	617 G	-X:64666255 2931764598 G	
206	618 C	-X:64666254 2931764597 C	
207 S	619 A	-X:64666253 2931764596 A	S
207	620 G	-X:64666252 2931764595 G	
207	621 C	-X:64666251 2931764594 C	
208 E	622 G	-X:64666250 2931764593 G	E
208	623 A	-X:64666249 2931764592 A	
208	624 A	-X:64666248 2931764591 A	
209 E	625 G	-X:64666247 2931764590 G	E
209	626 A	-X:64666246 2931764589 A	
209	627 G	-X:64666245 2931764588 G	
210 V	628 G	-X:64666244 2931764587 G	V
210	629 T	-X:64666243 2931764586 T	
210	630 G	-X:64666242 2931764585 G	
211 D	631 G	-X:64666241 2931764584 G	D
211	632 A	-X:64666240 2931764583 A	
211	633 T	-X:64666239 2931764582 T	
212 S	634 T	-X:64666238 2931764581 T	S
212	635 C	-X:64666237 2931764580 C	
212	636 T	-X:64666236 2931764579 T	
213 H	637 C	-X:64666235 2931764578 C	H
213	638 A	-X:64666234 2931764577 A	
213	639 T	-X:64666233 2931764576 T	
214 C	640 T	-X:64666232 2931764575 T	C
214	641 G	-X:64666231 2931764574 G	
214	642 C	-X:64666230 2931764573 C	
215 K	643 A	-X:64666229 2931764572 A	K
215	644 A	-X:64666228 2931764571 A	
215	645 A	-X:64666227 2931764570 A	
216 K	646 A	-X:64666226 2931764569 A	K
216	647 A	-X:64666225 2931764568 A	
216	648 G	-X:64666224 2931764567 G	
217 A	649 G	-X:64666223 2931764566 G	A
217	650 C	-X:64666222 2931764565 C	
217	651 C	-X:64666221 2931764564 C	
218 L	652 C	-X:64666220 2931764563 C	L
218	653 T	-X:64666219 2931764562 T	
218	654 G	-X:64666218 2931764561 G	
219 S	655 A	-X:64666217 2931764560 A	S
219	656 G	-X:64666216 2931764559 G	
219	657 T	-X:64666215 2931764558 T	
220 H	658 C	-X:64666214 2931764557 C	H
220	659 A	-X:64666213 2931764556 A	
220	660 T	-X:64666212 2931764555 T	
221 K	661 A	-X:64666211 2931764554 A	K
221	662 A	-X:64666210 2931764553 A	
221	663 A	-X:64666209 2931764552 A	
222 E	664 G	-X:64666208 2931764551 G	E
222	665 A	-X:64666207 2931764550 A	
222	666 G	-X:64666206 2931764549 G	
223 L	667 C	-X:64666205 2931764548 C	L
223	668 T	-X:64666204 2931764547 T	
223	669 A	-X:64666203 2931764546 A	
224 Y	670 T	-X:64666202 2931764545 T	Y
224	671 A	-X:64666201 2931764544 A	
224	672 T	-X:64666200 2931764543 T	
225 E	673 G	-X:64666199 2931764542 G	E
225	674 A	-X:64665863 2931764206 A	
225	675 A	-X:64665862 2931764205 A	
226 R	676 A	-X:64665861 2931764204 A	R
226	677 G	-X:64665860 2931764203 G	
226	678 A	-X:64665859 2931764202 A	
227 A	679 G	-X:64665858 2931764201 G	A
227	680 C	-X:64665857 2931764200 C	
227	681 C	-X:64665856 2931764199 C	
228 R	682 C	-X:64665855 2931764198 C	R
228	683 G	-X:64665854 2931764197 G	
228	684 A	-X:64665853 2931764196 A	
229 E	685 G	-X:64665852 2931764195 G	E
229	686 A	-X:64665851 2931764194 A	
229	687 A	-X:64665850 2931764193 A	
230 L	688 C	-X:64665849 2931764192 C	L
230	689 T	-X:64665848 2931764191 T	
230	690 G	-X:64665847 2931764190 G	
231 L	691 C	-X:64665846 2931764189 C	L
231	692 T	-X:64665845 2931764188 T	
231	693 G	-X:64665844 2931764187 G	
232 V	694 G	-X:64665843 2931764186 G	V
232	695 T	-X:64665842 2931764185 T	
232	696 A	-X:64665841 2931764184 A	
233 S	697 T	-X:64665840 2931764183 T	S
233	698 C	-X:64665839 2931764182 C	
233	699 A	-X:64665838 2931764181 A	
234 Y	700 T	-X:64665837 2931764180 T	Y
234	701 A	-X:64665836 2931764179 A	
234	702 C	-X:64665835 2931764178 C	
235 E	703 G	-X:64665834 2931764177 G	E
235	704 A	-X:64665833 2931764176 A	
235	705 A	-X:64665832 2931764175 A	
236 E	706 G	-X:64665831 2931764174 G	E
236	707 A	-X:64665830 2931764173 A	
236	708 G	-X:64665829 2931764172 G	
237 E	709 G	-X:64665828 2931764171 G	E
237	710 A	-X:64665827 2931764170 A	
237	711 G	-X:64665826 2931764169 G	
238 Q	712 C	-X:64665825 2931764168 C	Q
238	713 A	-X:64665824 2931764167 A	
238	714 G	-X:64665823 2931764166 G	
239 F	715 T	-X:64665822 2931764165 T	F
239	716 T	-X:64665821 2931764164 T	
239	717 T	-X:64665820 2931764163 T	
240 T	718 A	-X:64665819 2931764162 A	T
240	719 C	-X:64665818 2931764161 C	
240	720 G	-X:64665817 2931764160 G	
241 V	721 G	-X:64664974 2931763317 G	V
241	722 T	-X:64664973 2931763316 T	
241	723 G	-X:64664972 2931763315 G	
242 L	724 C	-X:64664971 2931763314 C	L
242	725 T	-X:64664970 2931763313 T	
242	726 G	-X:64664969 2931763312 G	
243 E	727 G	-X:64664968 2931763311 G	E
243	728 A	-X:64664967 2931763310 A	
243	729 G	-X:64664966 2931763309 G	
244 K	730 A	-X:64664965 2931763308 A	K
244	731 A	-X:64664964 2931763307 A	
244	732 A	-X:64664963 2931763306 A	
245 F	733 T	-X:64664962 2931763305 T	F
245	734 T	-X:64664961 2931763304 T	
245	735 T	-X:64664960 2931763303 T	
246 R	736 A	-X:64664959 2931763302 A	R
246	737 G	-X:64664958 2931763301 G	
246	738 G	-X:64664957 2931763300 G	
247 Y	739 T	-X:64664956 2931763299 T	Y
247	740 A	-X:64664955 2931763298 A	
247	741 T	-X:64664954 2931763297 T	
248 L	742 T	-X:64664953 2931763296 T	L
248	743 T	-X:64664952 2931763295 T	
248	744 A	-X:64664951 2931763294 A	
249 P	745 C	-X:64664950 2931763293 C	P
249	746 C	-X:64664949 2931763292 C	
249	747 T	-X:64664948 2931763291 T	
250 K	748 A	-X:64664947 2931763290 A	K
250	749 A	-X:64664946 2931763289 A	
250	750 G	-X:64664945 2931763288 G	
251 A	751 G	-X:64664944 2931763287 G	A
251	752 C	-X:64664943 2931763286 C	
251	753 C	-X:64664942 2931763285 C	
252 I	754 A	-X:64664941 2931763284 A	I
252	755 T	-X:64664940 2931763283 T	
252	756 T	-X:64664939 2931763282 T	
253 K	757 A	-X:64664938 2931763281 A	K
253	758 A	-X:64664937 2931763280 A	
253	759 G	-X:64664936 2931763279 G	
254 A	760 G	-X:64664935 2931763278 G	A
254	761 C	-X:64664934 2931763277 C	
254	762 G	-X:64664933 2931763276 G	
255 W	763 T	-X:64664932 2931763275 T	W
255	764 G	-X:64664931 2931763274 G	
255	765 G	-X:64664930 2931763273 G	
256 N	766 A	-X:64664929 2931763272 A	N
256	767 A	-X:64664928 2931763271 A	
256	768 T	-X:64664927 2931763270 T	
257 N	769 A	-X:64664926 2931763269 A	N
257	770 A	-X:64664925 2931763268 A	
257	771 C	-X:64664924 2931763267 C	
258 P	772 C	-X:64664923 2931763266 C	P
258	773 C	-X:64664922 2931763265 C	
258	774 G	-X:64664921 2931763264 G	
259 S	775 T	-X:64664920 2931763263 T	S
259	776 C	-X:64664919 2931763262 C	
259	777 C	-X:64664918 2931763261 C	
260 P	778 C	-X:64664917 2931763260 C	P
260	779 C	-X:64664916 2931763259 C	
260	780 A	-X:64664915 2931763258 A	
261 R	781 C	-X:64664914 2931763257 C	R
261	782 G	-X:64664913 2931763256 G	
261	783 T	-X:64664912 2931763255 T	
262 V	784 G	-X:64664911 2931763254 G	V
262	785 T	-X:64664910 2931763253 T	
262	786 A	-X:64664909 2931763252 A	
263 E	787 G	-X:64664908 2931763251 G	E
263	788 A	-X:64664907 2931763250 A	
263	789 A	-X:64664906 2931763249 A	
264 C	790 T	-X:64664905 2931763248 T	C
264	791 G	-X:64664904 2931763247 G	
264	792 T	-X:64664903 2931763246 T	
265 V	793 G	-X:64664902 2931763245 G	V
265	794 T	-X:64664901 2931763244 T	
265	795 C	-X:64664900 2931763243 C	
266 L	796 C	-X:64664899 2931763242 C	L
266	797 T	-X:64664898 2931763241 T	
266	798 G	-X:64664897 2931763240 G	
267 A	799 G	-X:64664896 2931763239 G	A
267	800 C	-X:64664895 2931763238 C	
267	801 A	-X:64664894 2931763237 A	
268 E	802 G	-X:64664893 2931763236 G	E
268	803 A	-X:64664892 2931763235 A	
268	804 G	-X:64664891 2931763234 G	
269 L	805 C	-X:64664890 2931763233 C	L
269	806 T	-X:64664889 2931763232 T	
269	807 C	-X:64664888 2931763231 C	
270 K	808 A	-X:64664887 2931763230 A	K
270	809 A	-X:64664886 2931763229 A	
270	810 G	-X:64664885 2931763228 G	
271 G	811 G	-X:64664884 2931763227 G	G
271	812 G	-X:64664883 2931763226 G	
271	813 C	-X:64664882 2931763225 C	
272 V	814 G	-X:64664881 2931763224 G	V
272	815 T	-X:64664880 2931763223 T	
272	816 T	-X:64664879 2931763222 T	
273 T	817 A	-X:64664878 2931763221 A	T
273	818 C	-X:64664877 2931763220 C	
273	819 A	-X:64664876 2931763219 A	
274 C	820 T	-X:64664875 2931763218 T	C
274	821 G	-X:64664874 2931763217 G	
274	822 C	-X:64664873 2931763216 C	
275 E	823 G	-X:64664872 2931763215 G	E
275	824 A	-X:64664871 2931763214 A	
275	825 G	-X:64664870 2931763213 G	
276 N	826 A	-X:64664869 2931763212 A	N
276	827 A	-X:64664868 2931763211 A	
276	828 C	-X:64664867 2931763210 C	
277 R	829 A	-X:64664866 2931763209 A	R
277	830 G	-X:64664865 2931763208 G	
277	831 G	-X:64661655 2931759998 G	
278 E	832 G	-X:64661654 2931759997 G	E
278	833 A	-X:64661653 2931759996 A	
278	834 G	-X:64661652 2931759995 G	
279 A	835 G	-X:64661651 2931759994 G	A
279	836 C	-X:64661650 2931759993 C	
279	837 T	-X:64661649 2931759992 T	
280 V	838 G	-X:64661648 2931759991 G	V
280	839 T	-X:64661647 2931759990 T	
280	840 G	-X:64661646 2931759989 G	
281 L	841 C	-X:64661645 2931759988 C	L
281	842 T	-X:64661644 2931759987 T	
281	843 G	-X:64661643 2931759986 G	
282 D	844 G	-X:64661642 2931759985 G	D
282	845 A	-X:64661641 2931759984 A	
282	846 T	-X:64661640 2931759983 T	
283 A	847 G	-X:64661639 2931759982 G	A
283	848 C	-X:64661638 2931759981 C	
283	849 T	-X:64661637 2931759980 T	
284 F	850 T	-X:64661636 2931759979 T	F
284	851 T	-X:64661635 2931759978 T	
284	852 T	-X:64661634 2931759977 T	
285 L	853 C	-X:64661633 2931759976 C	L
285	854 T	-X:64661632 2931759975 T	
285	855 G	-X:64661631 2931759974 G	
286 D	856 G	-X:64661630 2931759973 G	D
286	857 A	-X:64661629 2931759972 A	
286	858 T	-X:64661628 2931759971 T	
287 D	859 G	-X:64661627 2931759970 G	D
287	860 A	-X:64661626 2931759969 A	
287	861 T	-X:64661625 2931759968 T	
288 G	862 G	-X:64661624 2931759967 G	G
288	863 G	-X:64661623 2931759966 G	
288	864 C	-X:64661622 2931759965 C	
289 F	865 T	-X:64661621 2931759964 T	F
289	866 T	-X:64661620 2931759963 T	
289	867 C	-X:64661619 2931759962 C	
290 L	868 C	-X:64661618 2931759961 C	L
290	869 T	-X:64661617 2931759960 T	
290	870 T	-X:64661616 2931759959 T	
291 V	871 G	-X:64661615 2931759958 G	V
291	872 T	-X:64661614 2931759957 T	
291	873 C	-X:64661613 2931759956 C	
292 P	874 C	-X:64661612 2931759955 C	P
292	875 C	-X:64661611 2931759954 C	
292	876 C	-X:64661610 2931759953 C	
293 T	877 A	-X:64661609 2931759952 A	T
293	878 C	-X:64661608 2931759951 C	
293	879 A	-X:64661607 2931759950 A	
294 F	880 T	-X:64661606 2931759949 T	F
294	881 T	-X:64661605 2931759948 T	
294	882 T	-X:64661604 2931759947 T	
295 E	883 G	-X:64661603 2931759946 G	E
295	884 A	-X:64661602 2931759945 A	
295	885 A	-X:64661601 2931759944 A	
296 Q	886 C	-X:64661600 2931759943 C	Q
296	887 A	-X:64661599 2931759942 A	
296	888 G	-X:64661598 2931759941 G	
297 L	889 T	-X:64661597 2931759940 T	L
297	890 T	-X:64661596 2931759939 T	
297	891 G	-X:64661595 2931759938 G	
298 A	892 G	-X:64661594 2931759937 G	A
298	893 C	-X:64661593 2931759936 C	
298	894 A	-X:64661592 2931759935 A	
299 A	895 G	-X:64661591 2931759934 G	A
299	896 C	-X:64661590 2931759933 C	
299	897 T	-X:64661589 2931759932 T	
300 L	898 T	-X:64661588 2931759931 T	L
300	899 T	-X:64661587 2931759930 T	
300	900 G	-X:64661586 2931759929 G	
301 Q	901 C	-X:64661585 2931759928 C	Q
301	902 A	-X:64661584 2931759927 A	
301	903 G	-X:64661583 2931759926 G	
302 I	904 A	-X:64661582 2931759925 A	I
302	905 T	-X:64661581 2931759924 T	
302	906 A	-X:64661580 2931759923 A	
303 E	907 G	-X:64661579 2931759922 G	E
303	908 A	-X:64661578 2931759921 A	
303	909 A	-X:64661577 2931759920 A	
304 Y	910 T	-X:64661576 2931759919 T	Y
304	911 A	-X:64661575 2931759918 A	
304	912 T	-X:64661574 2931759917 T	
305 E	913 G	-X:64661573 2931759916 G	E
305	914 A	-X:64661572 2931759915 A	
305	915 A	-X:64661571 2931759914 A	
306 E	916 G	-X:64661570 2931759913 G	E
306	917 A	-X:64660867 2931759210 A	
306	918 A	-X:64660866 2931759209 A	
307 N	919 A	-X:64660865 2931759208 A	N
307	920 A	-X:64660864 2931759207 A	
307	921 C	-X:64660863 2931759206 C	
308 V	922 G	-X:64660862 2931759205 G	V
308	923 T	-X:64660861 2931759204 T	
308	924 G	-X:64660860 2931759203 G	
309 D	925 G	-X:64660859 2931759202 G	D
309	926 A	-X:64660858 2931759201 A	
309	927 C	-X:64660857 2931759200 C	
310 L	928 T	-X:64660856 2931759199 T	L
310	929 T	-X:64660855 2931759198 T	
310	930 G	-X:64660854 2931759197 G	
311 N	931 A	-X:64660853 2931759196 A	N
311	932 A	-X:64660852 2931759195 A	
311	933 T	-X:64660851 2931759194 T	
312 D	934 G	-X:64660850 2931759193 G	D
312	935 A	-X:64660849 2931759192 A	
312	936 C	-X:64660848 2931759191 C	
313 V	937 G	-X:64660847 2931759190 G	V
313	938 T	-X:64660846 2931759189 T	
313	939 C	-X:64660845 2931759188 C	
314 L	940 C	-X:64660844 2931759187 C	L
314	941 T	-X:64660843 2931759186 T	
314	942 G	-X:64660842 2931759185 G	
315 V	943 G	-X:64660841 2931759184 G	V
315	944 T	-X:64660840 2931759183 T	
315	945 G	-X:64660839 2931759182 G	
316 P	946 C	-X:64660838 2931759181 C	P
316	947 C	-X:64660837 2931759180 C	
316	948 A	-X:64660836 2931759179 A	
317 K	949 A	-X:64660835 2931759178 A	K
317	950 A	-X:64660834 2931759177 A	
317	951 G	-X:64660833 2931759176 G	
318 P	952 C	-X:64660832 2931759175 C	P
318	953 C	-X:64660831 2931759174 C	
318	954 G	-X:64660830 2931759173 G	
319 F	955 T	-X:64660829 2931759172 T	F
319	956 T	-X:64660828 2931759171 T	
319	957 C	-X:64660827 2931759170 C	
320 S	958 T	-X:64660826 2931759169 T	S
320	959 C	-X:64660825 2931759168 C	
320	960 T	-X:64660824 2931759167 T	
321 Q	961 C	-X:64660823 2931759166 C	Q
321	962 A	-X:64660822 2931759165 A	
321	963 G	-X:64660821 2931759164 G	
322 F	964 T	-X:64660820 2931759163 T	F
322	965 T	-X:64660819 2931759162 T	
322	966 C	-X:64660818 2931759161 C	
323 W	967 T	-X:64660817 2931759160 T	W
323	968 G	-X:64660816 2931759159 G	
323	969 G	-X:64660815 2931759158 G	
324 Q	970 C	-X:64660814 2931759157 C	Q
324	971 A	-X:64660813 2931759156 A	
324	972 G	-X:64660812 2931759155 G	
325 P	973 C	-X:64660811 2931759154 C	P
325	974 C	-X:64660810 2931759153 C	
325	975 C	-X:64660809 2931759152 C	
326 L	976 C	-X:64660808 2931759151 C	L
326	977 T	-X:64660807 2931759150 T	
326	978 G	-X:64660806 2931759149 G	
327 L	979 C	-X:64660805 2931759148 C	L
327	980 T	-X:64660804 2931759147 T	
327	981 C	-X:64660803 2931759146 C	
328 R	982 A	-X:64660802 2931759145 A	R
328	983 G	-X:64660801 2931759144 G	
328	984 G	-X:64660800 2931759143 G	
329 G	985 G	-X:64660799 2931759142 G	G
329	986 G	-X:64660798 2931759141 G	
329	987 C	-X:64660797 2931759140 C	
330 L	988 C	-X:64660796 2931759139 C	L
330	989 T	-X:64660795 2931759138 T	
330	990 G	-X:64660794 2931759137 G	
331 H	991 C	-X:64660793 2931759136 C	H
331	992 A	-X:64660792 2931759135 A	
331	993 C	-X:64660791 2931759134 C	
332 S	994 T	-X:64660790 2931759133 T	S
332	995 C	-X:64660789 2931759132 C	
332	996 C	-X:64660788 2931759131 C	
333 Q	997 C	-X:64660787 2931759130 C	Q
333	998 A	-X:64660786 2931759129 A	
333	999 G	-X:64660785 2931759128 G	
334 N	1000 A	-X:64660784 2931759127 A	N
334	1001 A	-X:64660783 2931759126 A	
334	1002 C	-X:64660782 2931759125 C	
335 F	1003 T	-X:64660781 2931759124 T	F
335	1004 T	-X:64660780 2931759123 T	
335	1005 C	-X:64660779 2931759122 C	
336 T	1006 A	-X:64660778 2931759121 A	T
336	1007 C	-X:64660777 2931759120 C	
336	1008 G	-X:64660776 2931759119 G	
337 Q	1009 C	-X:64660775 2931759118 C	Q
337	1010 A	-X:64660774 2931759117 A	
337	1011 G	-X:64660773 2931759116 G	
338 A	1012 G	-X:64660772 2931759115 G	A
338	1013 C	-X:64660771 2931759114 C	
338	1014 C	-X:64660770 2931759113 C	
339 L	1015 C	-X:64660769 2931759112 C	L
339	1016 T	-X:64660768 2931759111 T	
339	1017 A	-X:64660767 2931759110 A	
340 L	1018 T	-X:64660766 2931759109 T	L
340	1019 T	-X:64660765 2931759108 T	
340	1020 G	-X:64660764 2931759107 G	
341 E	1021 G	-X:64660763 2931759106 G	E
341	1022 A	-X:64660762 2931759105 A	
341	1023 G	-X:64660761 2931759104 G	
342 R	1024 A	-X:64660760 2931759103 A	R
342	1025 G	-X:64660759 2931759102 G	
342	1026 G	-X:64660758 2931759101 G	
343 M	1027 A	-X:64660757 2931759100 A	M
343	1028 T	-X:64660756 2931759099 T	
343	1029 G	-X:64660755 2931759098 G	
344 L	1030 C	-X:64660754 2931759097 C	L
344	1031 T	-X:64660753 2931759096 T	
344	1032 C	-X:64660752 2931759095 C	
345 S	1033 T	-X:64660751 2931759094 T	S
345	1034 C	-X:64660750 2931759093 C	
345	1035 T	-X:64660749 2931759092 T	
346 E	1036 G	-X:64660748 2931759091 G	E
346	1037 A	-X:64660747 2931759090 A	
346	1038 A	-X:64660746 2931759089 A	
347 L	1039 C	-X:64660745 2931759088 C	L
347	1040 T	-X:64660744 2931759087 T	
347	1041 G	-X:64660743 2931759086 G	
348 P	1042 C	-X:64660742 2931759085 C	P
348	1043 C	-X:64660741 2931759084 C	
348	1044 A	-X:64660740 2931759083 A	
349 A	1045 G	-X:64660739 2931759082 G	A
349	1046 C	-X:64660738 2931759081 C	
349	1047 C	-X:64660737 2931759080 C	
350 L	1048 T	-X:64660736 2931759079 T	L
350	1049 T	-X:64660735 2931759078 T	
350	1050 G	-X:64660734 2931759077 G	
351 G	1051 G	-X:64660733 2931759076 G	G
351	1052 G	-X:64660732 2931759075 G	
351	1053 G	-X:64660731 2931759074 G	
352 I	1054 A	-X:64660730 2931759073 A	I
352	1055 T	-X:64660729 2931759072 T	
352	1056 C	-X:64660728 2931759071 C	
353 S	1057 A	-X:64660727 2931759070 A	S
353	1058 G	-X:64660726 2931759069 G	
353	1059 C	-X:64660725 2931759068 C	
354 G	1060 G	-X:64660724 2931759067 G	G
354	1061 G	-X:64660723 2931759066 G	
354	1062 G	-X:64660722 2931759065 G	
355 I	1063 A	-X:64660721 2931759064 A	I
355	1064 T	-X:64660720 2931759063 T	
355	1065 C	-X:64660719 2931759062 C	
356 R	1066 C	-X:64660718 2931759061 C	R
356	1067 G	-X:64660717 2931759060 G	
356	1068 G	-X:64660716 2931759059 G	
357 P	1069 C	-X:64660715 2931759058 C	P
357	1070 C	-X:64660714 2931759057 C	
357	1071 T	-X:64660713 2931759056 T	
358 T	1072 A	-X:64660712 2931759055 A	T
358	1073 C	-X:64660711 2931759054 C	
358	1074 C	-X:64660710 2931759053 C	
359 Y	1075 T	-X:64660709 2931759052 T	Y
359	1076 A	-X:64660708 2931759051 A	
359	1077 C	-X:64660707 2931759050 C	
360 I	1078 A	-X:64660706 2931759049 A	I
360	1079 T	-X:64660705 2931759048 T	
360	1080 C	-X:64660704 2931759047 C	
361 L	1081 C	-X:64660703 2931759046 C	L
361	1082 T	-X:64660702 2931759045 T	
361	1083 C	-X:64660701 2931759044 C	
362 R	1084 A	-X:64660700 2931759043 A	R
362	1085 G	-X:64660699 2931759042 G	
362	1086 A	-X:64660698 2931759041 A	
363 W	1087 T	-X:64660697 2931759040 T	W
363	1088 G	-X:64660696 2931759039 G	
363	1089 G	-X:64660695 2931759038 G	
364 T	1090 A	-X:64660694 2931759037 A	T
364	1091 C	-X:64660693 2931759036 C	
364	1092 C	-X:64660692 2931759035 C	
365 V	1093 G	-X:64660691 2931759034 G	V
365	1094 T	-X:64660690 2931759033 T	
365	1095 T	-X:64660689 2931759032 T	
366 E	1096 G	-X:64660688 2931759031 G	E
366	1097 A	-X:64660687 2931759030 A	
366	1098 A	-X:64660686 2931759029 A	
367 L	1099 C	-X:64660685 2931759028 C	L
367	1100 T	-X:64660684 2931759027 T	
367	1101 G	-X:64660683 2931759026 G	
368 I	1102 A	-X:64660682 2931759025 A	I
368	1103 T	-X:64660681 2931759024 T	
368	1104 C	-X:64660680 2931759023 C	
369 V	1105 G	-X:64660679 2931759022 G	V
369	1106 T	-X:64660678 2931759021 T	
369	1107 G	-X:64660677 2931759020 G	
370 A	1108 G	-X:64660676 2931759019 G	A
370	1109 C	-X:64660675 2931759018 C	
370	1110 C	-X:64660674 2931759017 C	
371 N	1111 A	-X:64660673 2931759016 A	N
371	1112 A	-X:64660672 2931759015 A	
371	1113 C	-X:64660671 2931759014 C	
372 T	1114 A	-X:64660670 2931759013 A	T
372	1115 C	-X:64660669 2931759012 C	
372	1116 C	-X:64660668 2931759011 C	
373 K	1117 A	-X:64660667 2931759010 A	K
373	1118 A	-X:64660666 2931759009 A	
373	1119 G	-X:64660665 2931759008 G	
374 T	1120 A	-X:64660664 2931759007 A	T
374	1121 C	-X:64660663 2931759006 C	
374	1122 T	-X:64660662 2931759005 T	
375 G	1123 G	-X:64660661 2931759004 G	G
375	1124 G	-X:64660312 2931758655 G	
375	1125 A	-X:64660311 2931758654 A	
376 R	1126 C	-X:64660310 2931758653 C	R
376	1127 G	-X:64660309 2931758652 G	
376	1128 G	-X:64660308 2931758651 G	
377 N	1129 A	-X:64660307 2931758650 A	N
377	1130 A	-X:64660306 2931758649 A	
377	1131 T	-X:64660305 2931758648 T	
378 A	1132 G	-X:64660304 2931758647 G	A
378	1133 C	-X:64660303 2931758646 C	
378	1134 T	-X:64660302 2931758645 T	
379 R	1135 C	-X:64660301 2931758644 C	R
379	1136 G	-X:64660300 2931758643 G	
379	1137 C	-X:64660299 2931758642 C	
380 R	1138 C	-X:64660298 2931758641 C	R
380	1139 G	-X:64660297 2931758640 G	
380	1140 A	-X:64660296 2931758639 A	
381 F	1141 T	-X:64660295 2931758638 T	F
381	1142 T	-X:64660294 2931758637 T	
381	1143 T	-X:64660293 2931758636 T	
382 S	1144 T	-X:64660292 2931758635 T	S
382	1145 C	-X:64660291 2931758634 C	
382	1146 T	-X:64660290 2931758633 T	
383 A	1147 G	-X:64660289 2931758632 G	A
383	1148 C	-X:64660288 2931758631 C	
383	1149 A	-X:64660287 2931758630 A	
384 G	1150 G	-X:64660286 2931758629 G	G
384	1151 G	-X:64660285 2931758628 G	
384	1152 C	-X:64660284 2931758627 C	
385 Q	1153 C	-X:64660283 2931758626 C	Q
385	1154 A	-X:64660282 2931758625 A	
385	1155 G	-X:64660281 2931758624 G	
386 W	1156 T	-X:64660280 2931758623 T	W
386	1157 G	-X:64660279 2931758622 G	
386	1158 G	-X:64660278 2931758621 G	
387 E	1159 G	-X:64660277 2931758620 G	E
387	1160 A	-X:64660276 2931758619 A	
387	1161 A	-X:64660275 2931758618 A	
388 A	1162 G	-X:64660274 2931758617 G	A
388	1163 C	-X:64660273 2931758616 C	
388	1164 A	-X:64660272 2931758615 A	
389 R	1165 A	-X:64660271 2931758614 A	R
389	1166 G	-X:64660270 2931758613 G	
389	1167 A	-X:64660269 2931758612 A	
390 R	1168 A	-X:64660268 2931758611 A	R
390	1169 G	-X:64660267 2931758610 G	
390	1170 G	-X:64660266 2931758609 G	
391 G	1171 G	-X:64660265 2931758608 G	G
391	1172 G	-X:64660264 2931758607 G	
391	1173 C	-X:64660263 2931758606 C	
392 W	1174 T	-X:64660262 2931758605 T	W
392	1175 G	-X:64660261 2931758604 G	
392	1176 G	-X:64660260 2931758603 G	
393 R	1177 A	-X:64660259 2931758602 A	R
393	1178 G	-X:64660258 2931758601 G	
393	1179 G	-X:64660257 2931758600 G	
394 L	1180 C	-X:64660256 2931758599 C	L
394	1181 T	-X:64660255 2931758598 T	
394	1182 G	-X:64660254 2931758597 G	
395 F	1183 T	-X:64660253 2931758596 T	F
395	1184 T	-X:64660252 2931758595 T	
395	1185 C	-X:64660251 2931758594 C	
396 N	1186 A	-X:64660250 2931758593 A	N
396	1187 A	-X:64660249 2931758592 A	
396	1188 C	-X:64660248 2931758591 C	
397 C	1189 T	-X:64660247 2931758590 T	C
397	1190 G	-X:64660246 2931758589 G	
397	1191 C	-X:64660245 2931758588 C	
398 S	1192 T	-X:64660244 2931758587 T	S
398	1193 C	-X:64660243 2931758586 C	
398	1194 C	-X:64660242 2931758585 C	
399 A	1195 G	-X:64660241 2931758584 G	A
399	1196 C	-X:64660240 2931758583 C	
399	1197 C	-X:64660239 2931758582 C	
400 S	1198 T	-X:64660238 2931758581 T	S
400	1199 C	-X:64660237 2931758580 C	
400	1200 C	-X:64660236 2931758579 C	
401 L	1201 C	-X:64660235 2931758578 C	L
401	1202 T	-X:64660234 2931758577 T	
401	1203 T	-X:64660233 2931758576 T	
402 D	1204 G	-X:64660232 2931758575 G	D
402	1205 A	-X:64660231 2931758574 A	
402	1206 C	-X:64660230 2931758573 C	
403 W	1207 T	-X:64660229 2931758572 T	W
403	1208 G	-X:64660228 2931758571 G	
403	1209 G	-X:64660227 2931758570 G	
404 P	1210 C	-X:64660226 2931758569 C	P
404	1211 C	-X:64660225 2931758568 C	
404	1212 C	-X:64660224 2931758567 C	
405 R	1213 C	-X:64660223 2931758566 C	R
405	1214 G	-X:64660222 2931758565 G	
405	1215 G	-X:64660221 2931758564 G	
406 M	1216 A	-X:64660220 2931758563 A	M
406	1217 T	-X:64660219 2931758562 T	
406	1218 G	-X:64660218 2931758561 G	
407 V	1219 G	-X:64660217 2931758560 G	V
407	1220 T	-X:64660216 2931758559 T	
407	1221 T	-X:64660215 2931758558 T	
408 E	1222 G	-X:64660214 2931758557 G	E
408	1223 A	-X:64660213 2931758556 A	
408	1224 G	-X:64660212 2931758555 G	
409 S	1225 T	-X:64660211 2931758554 T	S
409	1226 C	-X:64660210 2931758553 C	
409	1227 C	-X:64660209 2931758552 C	
410 C	1228 T	-X:64660208 2931758551 T	C
410	1229 G	-X:64660207 2931758550 G	
410	1230 C	-X:64660206 2931758549 C	
411 L	1231 T	-X:64660205 2931758548 T	L
411	1232 T	-X:64660204 2931758547 T	
411	1233 G	-X:64660203 2931758546 G	
412 G	1234 G	-X:64660202 2931758545 G	G
412	1235 G	-X:64660201 2931758544 G	
412	1236 C	-X:64660200 2931758543 C	
413 S	1237 T	-X:64660199 2931758542 T	S
413	1238 C	-X:64660198 2931758541 C	
413	1239 A	-X:64660197 2931758540 A	
414 P	1240 C	-X:64660196 2931758539 C	P
414	1241 C	-X:64660195 2931758538 C	
414	1242 T	-X:64660194 2931758537 T	
415 C	1243 T	-X:64660193 2931758536 T	C
415	1244 G	-X:64660192 2931758535 G	
415	1245 C	-X:64660191 2931758534 C	
416 W	1246 T	-X:64660190 2931758533 T	W
416	1247 G	-X:64660189 2931758532 G	
416	1248 G	-X:64660188 2931758531 G	
417 A	1249 G	-X:64660187 2931758530 G	A
417	1250 C	-X:64660186 2931758529 C	
417	1251 C	-X:64660185 2931758528 C	
418 S	1252 A	-X:64660184 2931758527 A	S
418	1253 G	-X:64660183 2931758526 G	
418	1254 C	-X:64660182 2931758525 C	
419 P	1255 C	-X:64660181 2931758524 C	P
419	1256 C	-X:64660180 2931758523 C	
419	1257 C	-X:64660179 2931758522 C	
420 Q	1258 C	-X:64660178 2931758521 C	Q
420	1259 A	-X:64660177 2931758520 A	
420	1260 A	-X:64660176 2931758519 A	
421 L	1261 C	-X:64660175 2931758518 C	L
421	1262 T	-X:64660174 2931758517 T	
421	1263 C	-X:64660173 2931758516 C	
422 L	1264 C	-X:64660172 2931758515 C	L
422	1265 T	-X:64660171 2931758514 T	
422	1266 T	-X:64660170 2931758513 T	
423 R	1267 C	-X:64660169 2931758512 C	R
423	1268 G	-X:64660168 2931758511 G	
423	1269 G	-X:64660167 2931758510 G	
424 I	1270 A	-X:64660166 2931758509 A	I
424	1271 T	-X:64660165 2931758508 T	
424	1272 C	-X:64655070 2931753413 C	
425 I	1273 A	-X:64655069 2931753412 A	I
425	1274 T	-X:64655068 2931753411 T	
425	1275 C	-X:64655067 2931753410 C	
426 F	1276 T	-X:64655066 2931753409 T	F
426	1277 T	-X:64655065 2931753408 T	
426	1278 C	-X:64655064 2931753407 C	
427 K	1279 A	-X:64655063 2931753406 A	K
427	1280 A	-X:64655062 2931753405 A	
427	1281 A	-X:64655061 2931753404 A	
428 A	1282 G	-X:64655060 2931753403 G	A
428	1283 C	-X:64655059 2931753402 C	
428	1284 C	-X:64655058 2931753401 C	
429 M	1285 A	-X:64655057 2931753400 A	M
429	1286 T	-X:64655056 2931753399 T	
429	1287 G	-X:64655055 2931753398 G	
430 G	1288 G	-X:64655054 2931753397 G	G
430	1289 G	-X:64655053 2931753396 G	
430	1290 G	-X:64655052 2931753395 G	
431 Q	1291 C	-X:64655051 2931753394 C	Q
431	1292 A	-X:64655050 2931753393 A	
431	1293 G	-X:64655049 2931753392 G	
432 G	1294 G	-X:64655048 2931753391 G	G
432	1295 G	-X:64655047 2931753390 G	
432	1296 C	-X:64655046 2931753389 C	
433 L	1297 C	-X:64655045 2931753388 C	L
433	1298 T	-X:64655044 2931753387 T	
433	1299 G	-X:64655043 2931753386 G	
434 P	1300 C	-X:64655042 2931753385 C	P
434	1301 C	-X:64655041 2931753384 C	
434	1302 A	-X:64655040 2931753383 A	
435 D	1303 G	-X:64655039 2931753382 G	D
435	1304 A	-X:64655038 2931753381 A	
435	1305 C	-X:64655037 2931753380 C	
436 E	1306 G	-X:64655036 2931753379 G	E
436	1307 A	-X:64655035 2931753378 A	
436	1308 G	-X:64655034 2931753377 G	
437 E	1309 G	-X:64655033 2931753376 G	E
437	1310 A	-X:64655032 2931753375 A	
437	1311 G	-X:64655031 2931753374 G	
438 Q	1312 C	-X:64655030 2931753373 C	Q
438	1313 A	-X:64655029 2931753372 A	
438	1314 G	-X:64655028 2931753371 G	
439 E	1315 G	-X:64655027 2931753370 G	E
439	1316 A	-X:64655026 2931753369 A	
439	1317 G	-X:64655025 2931753368 G	
440 K	1318 A	-X:64655024 2931753367 A	K
440	1319 A	-X:64655023 2931753366 A	
440	1320 G	-X:64655022 2931753365 G	
441 L	1321 C	-X:64655021 2931753364 C	L
441	1322 T	-X:64655020 2931753363 T	
441	1323 G	-X:64655019 2931753362 G	
442 L	1324 C	-X:64655018 2931753361 C	L
442	1325 T	-X:64655017 2931753360 T	
442	1326 G	-X:64655016 2931753359 G	
443 R	1327 C	-X:64655015 2931753358 C	R
443	1328 G	-X:64655014 2931753357 G	
443	1329 C	-X:64655013 2931753356 C	
444 I	1330 A	-X:64655012 2931753355 A	I
444	1331 T	-X:64655011 2931753354 T	
444	1332 C	-X:64655010 2931753353 C	
445 C	1333 T	-X:64655009 2931753352 T	C
445	1334 G	-X:64655008 2931753351 G	
445	1335 T	-X:64655007 2931753350 T	
446 S	1336 T	-X:64655006 2931753349 T	S
446	1337 C	-X:64655005 2931753348 C	
446	1338 C	-X:64655004 2931753347 C	
447 I	1339 A	-X:64655003 2931753346 A	I
447	1340 T	-X:64655002 2931753345 T	
447	1341 T	-X:64655001 2931753344 T	
448 Y	1342 T	-X:64655000 2931753343 T	Y
448	1343 A	-X:64654999 2931753342 A	
448	1344 T	-X:64654998 2931753341 T	
449 T	1345 A	-X:64654997 2931753340 A	T
449	1346 C	-X:64654996 2931753339 C	
449	1347 C	-X:64654995 2931753338 C	
450 Q	1348 C	-X:64654994 2931753337 C	Q
450	1349 A	-X:64654993 2931753336 A	
450	1350 G	-X:64654992 2931753335 G	
451 S	1351 A	-X:64654991 2931753334 A	S
451	1352 G	-X:64654990 2931753333 G	
451	1353 T	-X:64654989 2931753332 T	
452 G	1354 G	-X:64654988 2931753331 G	G
452	1355 G	-X:64654987 2931753330 G	
452	1356 A	-X:64654986 2931753329 A	
453 E	1357 G	-X:64654985 2931753328 G	E
453	1358 A	-X:64654984 2931753327 A	
453	1359 A	-X:64654983 2931753326 A	
454 N	1360 A	-X:64654982 2931753325 A	N
454	1361 A	-X:64654981 2931753324 A	
454	1362 C	-X:64654980 2931753323 C	
455 S	1363 A	-X:64654979 2931753322 A	S
455	1364 G	-X:64654978 2931753321 G	
455	1365 C	-X:64654977 2931753320 C	
456 L	1366 C	-X:64654976 2931753319 C	L
456	1367 T	-X:64654975 2931753318 T	
456	1368 G	-X:64654974 2931753317 G	
457 V	1369 G	-X:64654973 2931753316 G	V
457	1370 T	-X:64654972 2931753315 T	
457	1371 G	-X:64654971 2931753314 G	
458 Q	1372 C	-X:64654970 2931753313 C	Q
458	1373 A	-X:64654969 2931753312 A	
458	1374 G	-X:64654968 2931753311 G	
459 E	1375 G	-X:64654967 2931753310 G	E
459	1376 A	-X:64654966 2931753309 A	
459	1377 G	-X:64654965 2931753308 G	
460 G	1378 G	-X:64654964 2931753307 G	G
460	1379 G	-X:64654963 2931753306 G	
460	1380 C	-X:64654962 2931753305 C	
461 S	1381 T	-X:64654961 2931753304 T	S
461	1382 C	-X:64654960 2931753303 C	
461	1383 T	-X:64654959 2931753302 T	
462 E	1384 G	-X:64654958 2931753301 G	E
462	1385 A	-X:64654957 2931753300 A	
462	1386 G	-X:64654956 2931753299 G	
463 A	1387 G	-X:64654955 2931753298 G	A
463	1388 C	-X:64654954 2931753297 C	
463	1389 C	-X:64654953 2931753296 C	
464 S	1390 T	-X:64654952 2931753295 T	S
464	1391 C	-X:64654951 2931753294 C	
464	1392 C	-X:64654950 2931753293 C	
465 P	1393 C	-X:64654949 2931753292 C	P
465	1394 C	-X:64654948 2931753291 C	
465	1395 C	-X:64654947 2931753290 C	
466 I	1396 A	-X:64654946 2931753289 A	I
466	1397 T	-X:64654945 2931753288 T	
466	1398 T	-X:64654944 2931753287 T	
467 G	1399 G	-X:64654943 2931753286 G	G
467	1400 G	-X:64654942 2931753285 G	
467	1401 G	-X:64654941 2931753284 G	
468 K	1402 A	-X:64654940 2931753283 A	K
468	1403 A	-X:64654939 2931753282 A	
468	1404 G	-X:64654938 2931753281 G	
469 S	1405 T	-X:64654937 2931753280 T	S
469	1406 C	-X:64654936 2931753279 C	
469	1407 T	-X:64654935 2931753278 T	
470 P	1408 C	-X:64654934 2931753277 C	P
470	1409 C	-X:64654933 2931753276 C	
470	1410 A	-X:64654932 2931753275 A	
471 Y	1411 T	-X:64654931 2931753274 T	Y
471	1412 A	-X:64654930 2931753273 A	
471	1413 T	-X:64654929 2931753272 T	
472 T	1414 A	-X:64654928 2931753271 A	T
472	1415 C	-X:64654927 2931753270 C	
472	1416 A	-X:64654926 2931753269 A	
473 L	1417 C	-X:64654925 2931753268 C	L
473	1418 T	-X:64654924 2931753267 T	
473	1419 A	-X:64654923 2931753266 A	
474 D	1420 G	-X:64654922 2931753265 G	D
474	1421 A	-X:64654921 2931753264 A	
474	1422 C	-X:64654920 2931753263 C	
475 S	1423 A	-X:64654919 2931753262 A	S
475	1424 G	-X:64654918 2931753261 G	
475	1425 C	-X:64654917 2931753260 C	
476 L	1426 C	-X:64654916 2931753259 C	L
476	1427 T	-X:64654915 2931753258 T	
476	1428 G	-X:64654914 2931753257 G	
477 Y	1429 T	-X:64654913 2931753256 T	Y
477	1430 A	-X:64654912 2931753255 A	
477	1431 T	-X:64654911 2931753254 T	
478 W	1432 T	-X:64654910 2931753253 T	W
478	1433 G	-X:64654909 2931753252 G	
478	1434 G	-X:64654908 2931753251 G	
479 S	1435 A	-X:64654907 2931753250 A	S
479	1436 G	-X:64654906 2931753249 G	
479	1437 C	-X:64654905 2931753248 C	
480 V	1438 G	-X:64654904 2931753247 G	V
480	1439 T	-X:64654903 2931753246 T	
480	1440 C	-X:64654902 2931753245 C	
481 K	1441 A	-X:64654901 2931753244 A	K
481	1442 A	-X:64654900 2931753243 A	
481	1443 G	-X:64654899 2931753242 G	
482 P	1444 C	-X:64654898 2931753241 C	P
482	1445 C	-X:64654897 2931753240 C	
482	1446 A	-X:64654896 2931753239 A	
483 A	1447 G	-X:64654895 2931753238 G	A
483	1448 C	-X:64654894 2931753237 C	
483	1449 C	-X:64654893 2931753236 C	
484 S	1450 A	-X:64654892 2931753235 A	S
484	1451 G	-X:64654891 2931753234 G	
484	1452 C	-X:64654890 2931753233 C	
485 S	1453 T	-X:64654889 2931753232 T	S
485	1454 C	-X:64654888 2931753231 C	
485	1455 C	-X:64654887 2931753230 C	
486 S	1456 A	-X:64654886 2931753229 A	S
486	1457 G	-X:64654885 2931753228 G	
486	1458 C	-X:64654884 2931753227 C	
487 F	1459 T	-X:64654883 2931753226 T	F
487	1460 T	-X:64654882 2931753225 T	
487	1461 C	-X:64654881 2931753224 C	
488 G	1462 G	-X:64654880 2931753223 G	G
488	1463 G	-X:64654879 2931753222 G	
488	1464 G	-X:64654878 2931753221 G	
489 S	1465 T	-X:64654877 2931753220 T	S
489	1466 C	-X:64654876 2931753219 C	
489	1467 T	-X:64654875 2931753218 T	
490 E	1468 G	-X:64654874 2931753217 G	E
490	1469 A	-X:64654873 2931753216 A	
490	1470 A	-X:64654872 2931753215 A	
491 A	1471 G	-X:64654871 2931753214 G	A
491	1472 C	-X:64654870 2931753213 C	
491	1473 A	-X:64654869 2931753212 A	
492 K	1474 A	-X:64654868 2931753211 A	K
492	1475 A	-X:64654867 2931753210 A	
492	1476 G	-X:64654866 2931753209 G	
493 A	1477 G	-X:64654865 2931753208 G	A
493	1478 C	-X:64654864 2931753207 C	
493	1479 C	-X:64654863 2931753206 C	
494 Q	1480 C	-X:64654862 2931753205 C	Q
494	1481 A	-X:64654861 2931753204 A	
494	1482 G	-X:64654860 2931753203 G	
495 Q	1483 C	-X:64654859 2931753202 C	Q
495	1484 A	-X:64654858 2931753201 A	
495	1485 A	-X:64654857 2931753200 A	
496 Q	1486 C	-X:64654856 2931753199 C	Q
496	1487 A	-X:64654855 2931753198 A	
496	1488 G	-X:64654854 2931753197 G	
497 E	1489 G	-X:64654853 2931753196 G	E
497	1490 A	-X:64654852 2931753195 A	
497	1491 G	-X:64654851 2931753194 G	
498 E	1492 G	-X:64654850 2931753193 G	E
498	1493 A	-X:64654849 2931753192 A	
498	1494 G	-X:64654848 2931753191 G	
499 Q	1495 C	-X:64654847 2931753190 C	Q
499	1496 A	-X:64654846 2931753189 A	
499	1497 G	-X:64654845 2931753188 G	
500 G	1498 G	-X:64654844 2931753187 G	G
500	1499 G	-X:64654843 2931753186 G	
500	1500 C	-X:64654842 2931753185 C	
501 S	1501 A	-X:64654841 2931753184 A	S
501	1502 G	-X:64654840 2931753183 G	
501	1503 T	-X:64654839 2931753182 T	
502 V	1504 G	-X:64654838 2931753181 G	V
502	1505 T	-X:64654837 2931753180 T	
502	1506 T	-X:64654836 2931753179 T	
503 N	1507 A	-X:64654835 2931753178 A	N
503	1508 A	-X:64654834 2931753177 A	
503	1509 T	-X:64654833 2931753176 T	
504 D	1510 G	-X:64654832 2931753175 G	D
504	1511 A	-X:64654831 2931753174 A	
504	1512 T	-X:64654830 2931753173 T	
505 V	1513 G	-X:64654829 2931753172 G	V
505	1514 T	-X:64654828 2931753171 T	
505	1515 C	-X:64654827 2931753170 C	
506 K	1516 A	-X:64654826 2931753169 A	K
506	1517 A	-X:64654825 2931753168 A	
506	1518 G	-X:64654824 2931753167 G	
507 E	1519 G	-X:64654823 2931753166 G	E
507	1520 A	-X:64654822 2931753165 A	
507	1521 A	-X:64654821 2931753164 A	
508 E	1522 G	-X:64654820 2931753163 G	E
508	1523 A	-X:64654819 2931753162 A	
508	1524 G	-X:64654818 2931753161 G	
509 E	1525 G	-X:64654817 2931753160 G	E
509	1526 A	-X:64654816 2931753159 A	
509	1527 G	-X:64654815 2931753158 G	
510 K	1528 A	-X:64654814 2931753157 A	K
510	1529 A	-X:64654813 2931753156 A	
510	1530 G	-X:64654812 2931753155 G	
511 E	1531 G	-X:64654811 2931753154 G	E
511	1532 A	-X:64654810 2931753153 A	
511	1533 G	-X:64654809 2931753152 G	
512 E	1534 G	-X:64654808 2931753151 G	E
512	1535 A	-X:64654807 2931753150 A	
512	1536 G	-X:64654806 2931753149 G	
513 K	1537 A	-X:64654805 2931753148 A	K
513	1538 A	-X:64654804 2931753147 A	
513	1539 A	-X:64654803 2931753146 A	
514 E	1540 G	-X:64654802 2931753145 G	E
514	1541 A	-X:64654801 2931753144 A	
514	1542 G	-X:64654800 2931753143 G	
515 V	1543 G	-X:64654799 2931753142 G	V
515	1544 T	-X:64654798 2931753141 T	
515	1545 C	-X:64654797 2931753140 C	
516 L	1546 T	-X:64654796 2931753139 T	L
516	1547 T	-X:64654795 2931753138 T	
516	1548 G	-X:64654794 2931753137 G	
517 P	1549 C	-X:64654793 2931753136 C	P
517	1550 C	-X:64654792 2931753135 C	
517	1551 A	-X:64654791 2931753134 A	
518 D	1552 G	-X:64654790 2931753133 G	D
518	1553 A	-X:64654789 2931753132 A	
518	1554 C	-X:64654788 2931753131 C	
519 Q	1555 C	-X:64654787 2931753130 C	Q
519	1556 A	-X:64654786 2931753129 A	
519	1557 G	-X:64654785 2931753128 G	
520 V	1558 G	-X:64654784 2931753127 G	V
520	1559 T	-X:64654783 2931753126 T	
520	1560 A	-X:64654782 2931753125 A	
521 E	1561 G	-X:64654781 2931753124 G	E
521	1562 A	-X:64654780 2931753123 A	
521	1563 G	-X:64654779 2931753122 G	
522 E	1564 G	-X:64654778 2931753121 G	E
522	1565 A	-X:64654777 2931753120 A	
522	1566 G	-X:64654776 2931753119 G	
523 E	1567 G	-X:64654775 2931753118 G	E
523	1568 A	-X:64654774 2931753117 A	
523	1569 G	-X:64654773 2931753116 G	
524 E	1570 G	-X:64654772 2931753115 G	E
524	1571 A	-X:64654771 2931753114 A	
524	1572 A	-X:64654770 2931753113 A	
525 E	1573 G	-X:64654769 2931753112 G	E
525	1574 A	-X:64654768 2931753111 A	
525	1575 A	-X:64654767 2931753110 A	
526 N	1576 A	-X:64654766 2931753109 A	N
526	1577 A	-X:64654765 2931753108 A	
526	1578 T	-X:64654764 2931753107 T	
527 D	1579 G	-X:64654763 2931753106 G	D
527	1580 A	-X:64654762 2931753105 A	
527	1581 T	-X:64654761 2931753104 T	
528 D	1582 G	-X:64654760 2931753103 G	D
528	1583 A	-X:64654759 2931753102 A	
528	1584 C	-X:64654758 2931753101 C	
529 Q	1585 C	-X:64654757 2931753100 C	Q
529	1586 A	-X:64654756 2931753099 A	
529	1587 A	-X:64654755 2931753098 A	
530 E	1588 G	-X:64654754 2931753097 G	E
530	1589 A	-X:64654753 2931753096 A	
530	1590 G	-X:64654752 2931753095 G	
531 E	1591 G	-X:64654751 2931753094 G	E
531	1592 A	-X:64654750 2931753093 A	
531	1593 G	-X:64654749 2931753092 G	
532 E	1594 G	-X:64654748 2931753091 G	E
532	1595 A	-X:64654747 2931753090 A	
532	1596 A	-X:64654746 2931753089 A	
533 E	1597 G	-X:64654745 2931753088 G	E
533	1598 A	-X:64654744 2931753087 A	
533	1599 G	-X:64654743 2931753086 G	
534 E	1600 G	-X:64654742 2931753085 G	E
534	1601 A	-X:64654741 2931753084 A	
534	1602 G	-X:64654740 2931753083 G	
535 D	1603 G	-X:64654739 2931753082 G	D
535	1604 A	-X:64654738 2931753081 A	
535	1605 T	-X:64654737 2931753080 T	
536 E	1606 G	-X:64654736 2931753079 G	E
536	1607 A	-X:64654735 2931753078 A	
536	1608 A	-X:64654734 2931753077 A	
537 D	1609 G	-X:64654733 2931753076 G	D
537	1610 A	-X:64654732 2931753075 A	
537	1611 T	-X:64654731 2931753074 T	
538 D	1612 G	-X:64654730 2931753073 G	D
538	1613 A	-X:64654729 2931753072 A	
538	1614 T	-X:64654728 2931753071 T	
539 E	1615 G	-X:64654727 2931753070 G	E
539	1616 A	-X:64654726 2931753069 A	
539	1617 A	-X:64654725 2931753068 A	
540 D	1618 G	-X:64654724 2931753067 G	D
540	1619 A	-X:64654723 2931753066 A	
540	1620 T	-X:64654722 2931753065 T	
541 D	1621 G	-X:64654721 2931753064 G	D
541	1622 A	-X:64654720 2931753063 A	
541	1623 T	-X:64654719 2931753062 T	
542 E	1624 G	-X:64654718 2931753061 G	E
542	1625 A	-X:64654717 2931753060 A	
542	1626 A	-X:64654716 2931753059 A	
543 E	1627 G	-X:64654715 2931753058 G	E
543	1628 A	-X:64654714 2931753057 A	
543	1629 G	-X:64654713 2931753056 G	
544 E	1630 G	-X:64654712 2931753055 G	E
544	1631 A	-X:64654711 2931753054 A	
544	1632 A	-X:64654710 2931753053 A	
545 D	1633 G	-X:64654709 2931753052 G	D
545	1634 A	-X:64654708 2931753051 A	
545	1635 C	-X:64654707 2931753050 C	
546 R	1636 A	-X:64654706 2931753049 A	R
546	1637 G	-X:64654705 2931753048 G	
546	1638 A	-X:64654704 2931753047 A	
547 M	1639 A	-X:64654703 2931753046 A	M
547	1640 T	-X:64654702 2931753045 T	
547	1641 G	-X:64654701 2931753044 G	
548 E	1642 G	-X:64654700 2931753043 G	E
548	1643 A	-X:64654699 2931753042 A	
548	1644 G	-X:64654698 2931753041 G	
549 V	1645 G	-X:64654697 2931753040 G	V
549	1646 T	-X:64654696 2931753039 T	
549	1647 G	-X:64654695 2931753038 G	
550 G	1648 G	-X:64654694 2931753037 G	G
550	1649 G	-X:64654693 2931753036 G	
550	1650 G	-X:64654692 2931753035 G	
551 P	1651 C	-X:64654691 2931753034 C	P
551	1652 C	-X:64654690 2931753033 C	
551	1653 T	-X:64654689 2931753032 T	
552 F	1654 T	-X:64654688 2931753031 T	F
552	1655 T	-X:64654687 2931753030 T	
552	1656 C	-X:64654686 2931753029 C	
553 S	1657 T	-X:64654685 2931753028 T	S
553	1658 C	-X:64654684 2931753027 C	
553	1659 T	-X:64654683 2931753026 T	
554 T	1660 A	-X:64654682 2931753025 A	T
554	1661 C	-X:64654681 2931753024 C	
554	1662 A	-X:64654680 2931753023 A	
555 G	1663 G	-X:64654679 2931753022 G	G
555	1664 G	-X:64654678 2931753021 G	
555	1665 G	-X:64654677 2931753020 G	
556 Q	1666 C	-X:64654676 2931753019 C	Q
556	1667 A	-X:64654675 2931753018 A	
556	1668 A	-X:64654674 2931753017 A	
557 E	1669 G	-X:64654673 2931753016 G	E
557	1670 A	-X:64654672 2931753015 A	
557	1671 G	-X:64654671 2931753014 G	
558 S	1672 T	-X:64654670 2931753013 T	S
558	1673 C	-X:64654669 2931753012 C	
558	1674 C	-X:64654668 2931753011 C	
559 P	1675 C	-X:64654667 2931753010 C	P
559	1676 C	-X:64654666 2931753009 C	
559	1677 C	-X:64654665 2931753008 C	
560 T	1678 A	-X:64654664 2931753007 A	T
560	1679 C	-X:64654663 2931753006 C	
560	1680 T	-X:64654662 2931753005 T	
561 A	1681 G	-X:64654661 2931753004 G	A
561	1682 C	-X:64654660 2931753003 C	
561	1683 C	-X:64654659 2931753002 C	
562 E	1684 G	-X:64654658 2931753001 G	E
562	1685 A	-X:64654657 2931753000 A	
562	1686 G	-X:64654656 2931752999 G	
563 N	1687 A	-X:64654655 2931752998 A	N
563	1688 A	-X:64654654 2931752997 A	
563	1689 T	-X:64654653 2931752996 T	
564 A	1690 G	-X:64654652 2931752995 G	A
564	1691 C	-X:64654651 2931752994 C	
564	1692 T	-X:64654650 2931752993 T	
565 R	1693 A	-X:64654649 2931752992 A	R
565	1694 G	-X:64654648 2931752991 G	
565	1695 G	-X:64654647 2931752990 G	
566 L	1696 C	-X:64654646 2931752989 C	L
566	1697 T	-X:64654645 2931752988 T	
566	1698 T	-X:64654644 2931752987 T	
567 L	1699 C	-X:64654643 2931752986 C	L
567	1700 T	-X:64654642 2931752985 T	
567	1701 G	-X:64654641 2931752984 G	
568 A	1702 G	-X:64654640 2931752983 G	A
568	1703 C	-X:64654639 2931752982 C	
568	1704 C	-X:64654638 2931752981 C	
569 Q	1705 C	-X:64654637 2931752980 C	Q
569	1706 A	-X:64654636 2931752979 A	
569	1707 G	-X:64654635 2931752978 G	
570 K	1708 A	-X:64654634 2931752977 A	K
570	1709 A	-X:64654633 2931752976 A	
570	1710 A	-X:64654632 2931752975 A	
571 R	1711 A	-X:64654631 2931752974 A	R
571	1712 G	-X:64654630 2931752973 G	
571	1713 A	-X:64654629 2931752972 A	
572 G	1714 G	-X:64654628 2931752971 G	G
572	1715 G	-X:64654627 2931752970 G	
572	1716 A	-X:64654626 2931752969 A	
573 A	1717 G	-X:64654625 2931752968 G	A
573	1718 C	-X:64654624 2931752967 C	
573	1719 T	-X:64654623 2931752966 T	
574 L	1720 T	-X:64654622 2931752965 T	L
574	1721 T	-X:64654621 2931752964 T	
574	1722 G	-X:64654620 2931752963 G	
575 Q	1723 C	-X:64654619 2931752962 C	Q
575	1724 A	-X:64654618 2931752961 A	
575	1725 G	-X:64654617 2931752960 G	
576 G	1726 G	-X:64654616 2931752959 G	G
576	1727 G	-X:64654615 2931752958 G	
576	1728 C	-X:64654614 2931752957 C	
577 S	1729 T	-X:64654613 2931752956 T	S
577	1730 C	-X:64654612 2931752955 C	
577	1731 T	-X:64654611 2931752954 T	
578 A	1732 G	-X:64654610 2931752953 G	A
578	1733 C	-X:64654609 2931752952 C	
578	1734 A	-X:64654608 2931752951 A	
579 W	1735 T	-X:64654607 2931752950 T	W
579	1736 G	-X:64654606 2931752949 G	
579	1737 G	-X:64654605 2931752948 G	
580 Q	1738 C	-X:64654604 2931752947 C	Q
580	1739 A	-X:64654603 2931752946 A	
580	1740 G	-X:64654602 2931752945 G	
581 V	1741 G	-X:64654601 2931752944 G	V
581	1742 T	-X:64654600 2931752943 T	
581	1743 T	-X:64654599 2931752942 T	
582 S	1744 A	-X:64654598 2931752941 A	S
582	1745 G	-X:64654597 2931752940 G	
582	1746 C	-X:64654596 2931752939 C	
583 S	1747 T	-X:64654595 2931752938 T	S
583	1748 C	-X:64654594 2931752937 C	
583	1749 A	-X:64654593 2931752936 A	
584 E	1750 G	-X:64654592 2931752935 G	E
584	1751 A	-X:64651578 2931749921 A	
584	1752 A	-X:64651577 2931749920 A	
585 D	1753 G	-X:64651576 2931749919 G	D
585	1754 A	-X:64651575 2931749918 A	
585	1755 C	-X:64651574 2931749917 C	
586 V	1756 G	-X:64651573 2931749916 G	V
586	1757 T	-X:64651572 2931749915 T	
586	1758 G	-X:64651571 2931749914 G	
587 R	1759 C	-X:64651570 2931749913 C	R
587	1760 G	-X:64651569 2931749912 G	
587	1761 A	-X:64651568 2931749911 A	
588 W	1762 T	-X:64651567 2931749910 T	W
588	1763 G	-X:64651566 2931749909 G	
588	1764 G	-X:64651565 2931749908 G	
589 D	1765 G	-X:64651564 2931749907 G	D
589	1766 A	-X:64651563 2931749906 A	
589	1767 C	-X:64651562 2931749905 C	
590 T	1768 A	-X:64651561 2931749904 A	T
590	1769 C	-X:64651560 2931749903 C	
590	1770 A	-X:64651559 2931749902 A	
591 F	1771 T	-X:64651558 2931749901 T	F
591	1772 T	-X:64651557 2931749900 T	
591	1773 T	-X:64651556 2931749899 T	
592 P	1774 C	-X:64651555 2931749898 C	P
592	1775 C	-X:64651554 2931749897 C	
592	1776 C	-X:64651553 2931749896 C	
593 L	1777 C	-X:64651552 2931749895 C	L
593	1778 T	-X:64651551 2931749894 T	
593	1779 A	-X:64651550 2931749893 A	
594 G	1780 G	-X:64651549 2931749892 G	G
594	1781 G	-X:64651548 2931749891 G	
594	1782 C	-X:64651547 2931749890 C	
595 R	1783 C	-X:64651546 2931749889 C	R
595	1784 G	-X:64651545 2931749888 G	
595	1785 A	-X:64651544 2931749887 A	
596 M	1786 A	-X:64651543 2931749886 A	M
596	1787 T	-X:64651542 2931749885 T	
596	1788 G	-X:64651541 2931749884 G	
597 P	1789 C	-X:64651540 2931749883 C	P
597	1790 C	-X:64651539 2931749882 C	
597	1791 A	-X:64651538 2931749881 A	
598 G	1792 G	-X:64651537 2931749880 G	G
598	1793 G	-X:64651536 2931749879 G	
598	1794 T	-X:64651535 2931749878 T	
599 Q	1795 C	-X:64651534 2931749877 C	Q
599	1796 A	-X:64651533 2931749876 A	
599	1797 G	-X:64651532 2931749875 G	
600 T	1798 A	-X:64651531 2931749874 A	T
600	1799 C	-X:64651530 2931749873 C	
600	1800 C	-X:64651529 2931749872 C	
601 E	1801 G	-X:64651528 2931749871 G	E
601	1802 A	-X:64651527 2931749870 A	
601	1803 G	-X:64651526 2931749869 G	
602 D	1804 G	-X:64651525 2931749868 G	D
602	1805 A	-X:64651524 2931749867 A	
602	1806 C	-X:64651523 2931749866 C	
603 P	1807 C	-X:64651522 2931749865 C	P
603	1808 C	-X:64651521 2931749864 C	
603	1809 A	-X:64651520 2931749863 A	
604 A	1810 G	-X:64651519 2931749862 G	A
604	1811 C	-X:64651518 2931749861 C	
604	1812 A	-X:64651517 2931749860 A	
605 E	1813 G	-X:64651516 2931749859 G	E
605	1814 A	-X:64651515 2931749858 A	
605	1815 G	-X:64651514 2931749857 G	
606 L	1816 C	-X:64651513 2931749856 C	L
606	1817 T	-X:64651512 2931749855 T	
606	1818 C	-X:64651511 2931749854 C	
607 M	1819 A	-X:64651510 2931749853 A	M
607	1820 T	-X:64651509 2931749852 T	
607	1821 G	-X:64651508 2931749851 G	
608 L	1822 C	-X:64651507 2931749850 C	L
608	1823 T	-X:64651506 2931749849 T	
608	1824 G	-X:64651505 2931749848 G	
609 E	1825 G	-X:64651504 2931749847 G	E
609	1826 A	-X:64651503 2931749846 A	
609	1827 G	-X:64651502 2931749845 G	
610 N	1828 A	-X:64651501 2931749844 A	N
610	1829 A	-X:64651500 2931749843 A	
610	1830 T	-X:64651499 2931749842 T	
611 Y	1831 T	-X:64651498 2931749841 T	Y
611	1832 A	-X:64651497 2931749840 A	
611	1833 T	-X:64651496 2931749839 T	
612 D	1834 G	-X:64651495 2931749838 G	D
612	1835 A	-X:64651494 2931749837 A	
612	1836 C	-X:64651493 2931749836 C	
613 T	1837 A	-X:64651492 2931749835 A	T
613	1838 C	-X:64651491 2931749834 C	
613	1839 C	-X:64651490 2931749833 C	
614 M	1840 A	-X:64651489 2931749832 A	M
614	1841 T	-X:64651488 2931749831 T	
614	1842 G	-X:64651487 2931749830 G	
615 Y	1843 T	-X:64651486 2931749829 T	Y
615	1844 A	-X:64651485 2931749828 A	
615	1845 T	-X:64651484 2931749827 T	
616 L	1846 C	-X:64651483 2931749826 C	L
616	1847 T	-X:64651482 2931749825 T	
616	1848 T	-X:64651481 2931749824 T	
617 L	1849 T	-X:64651480 2931749823 T	L
617	1850 T	-X:64651479 2931749822 T	
617	1851 G	-X:64651478 2931749821 G	
618 D	1852 G	-X:64651477 2931749820 G	D
618	1853 A	-X:64651476 2931749819 A	
618	1854 C	-X:64651475 2931749818 C	
619 Q	1855 C	-X:64651474 2931749817 C	Q
619	1856 A	-X:64651473 2931749816 A	
619	1857 G	-X:64651472 2931749815 G	
620 P	1858 C	-X:64651471 2931749814 C	P
620	1859 C	-X:64651470 2931749813 C	
620	1860 T	-X:64651469 2931749812 T	
621 V	1861 G	-X:64651468 2931749811 G	V
621	1862 T	-X:64651467 2931749810 T	
621	1863 G	-X:64651466 2931749809 G	
622 L	1864 C	-X:64651465 2931749808 C	L
622	1865 T	-X:64651464 2931749807 T	
622	1866 A	-X:64651463 2931749806 A	
623 E	1867 G	-X:64651462 2931749805 G	E
623	1868 A	-X:64651461 2931749804 A	
623	1869 G	-X:64651460 2931749803 G	
624 Q	1870 C	-X:64651459 2931749802 C	Q
624	1871 A	-X:64651458 2931749801 A	
624	1872 G	-X:64651457 2931749800 G	
625 R	1873 C	-X:64651456 2931749799 C	R
625	1874 G	-X:64651455 2931749798 G	
625	1875 G	-X:64651454 2931749797 G	
626 L	1876 C	-X:64651453 2931749796 C	L
626	1877 T	-X:64651452 2931749795 T	
626	1878 G	-X:64651451 2931749794 G	
627 E	1879 G	-X:64651450 2931749793 G	E
627	1880 A	-X:64651449 2931749792 A	
627	1881 A	-X:64651448 2931749791 A	
628 P	1882 C	-X:64651447 2931749790 C	P
628	1883 C	-X:64651446 2931749789 C	
628	1884 C	-X:64651445 2931749788 C	
629 S	1885 T	-X:64651444 2931749787 T	S
629	1886 C	-X:64651443 2931749786 C	
629	1887 A	-X:64651442 2931749785 A	
630 T	1888 A	-X:64651441 2931749784 A	T
630	1889 C	-X:64651440 2931749783 C	
630	1890 A	-X:64651439 2931749782 A	
631 C	1891 T	-X:64651438 2931749781 T	C
631	1892 G	-X:64651437 2931749780 G	
631	1893 C	-X:64651436 2931749779 C	
632 K	1894 A	-X:64651435 2931749778 A	K
632	1895 A	-X:64651434 2931749777 A	
632	1896 G	-X:64651433 2931749776 G	
633 T	1897 A	-X:64651432 2931749775 A	T
633	1898 C	-X:64651431 2931749774 C	
633	1899 T	-X:64651430 2931749773 T	
>ENSP00000363940 
1 M	1 A	-X:64671320 2931769663 A	M
1	2 T	-X:64671319 2931769662 T	
1	3 G	-X:64671318 2931769661 G	
2 S	4 T	-X:64671317 2931769660 T	S
2	5 C	-X:64671316 2931769659 C	
2	6 G	-X:64671315 2931769658 G	
3 W	7 T	-X:64671314 2931769657 T	W
3	8 G	-X:64671313 2931769656 G	
3	9 G	-X:64671312 2931769655 G	
4 E	10 G	-X:64671311 2931769654 G	E
4	11 A	-X:64671310 2931769653 A	
4	12 A	-X:64671309 2931769652 A	
5 S	13 T	-X:64671308 2931769651 T	S
5	14 C	-X:64671307 2931769650 C	
5	15 C	-X:64671306 2931769649 C	
6 G	16 G	-X:64671305 2931769648 G	G
6	17 G	-X:64671304 2931769647 G	
6	18 G	-X:64671303 2931769646 G	
7 A	19 G	-X:64671302 2931769645 G	A
7	20 C	-X:64671301 2931769644 C	
7	21 C	-X:64671300 2931769643 C	
8 G	22 G	-X:64671299 2931769642 G	G
8	23 G	-X:64671298 2931769641 G	
8	24 G	-X:64671297 2931769640 G	
9 P	25 C	-X:64671296 2931769639 C	P
9	26 C	-X:64671295 2931769638 C	
9	27 A	-X:64671294 2931769637 A	
10 G	28 G	-X:64671293 2931769636 G	G
10	29 G	-X:64671292 2931769635 G	
10	30 T	-X:64671291 2931769634 T	
11 L	31 C	-X:64671290 2931769633 C	L
11	32 T	-X:64671289 2931769632 T	
11	33 A	-X:64671288 2931769631 A	
12 G	34 G	-X:64671287 2931769630 G	G
12	35 G	-X:64671286 2931769629 G	
12	36 T	-X:64671285 2931769628 T	
13 S	37 T	-X:64671284 2931769627 T	S
13	38 C	-X:64671283 2931769626 C	
13	39 C	-X:64671282 2931769625 C	
14 Q	40 C	-X:64671281 2931769624 C	Q
14	41 A	-X:64671280 2931769623 A	
14	42 G	-X:64671279 2931769622 G	
15 G	43 G	-X:64671278 2931769621 G	G
15	44 G	-X:64671277 2931769620 G	
15	45 G	-X:64671276 2931769619 G	
16 M	46 A	-X:64671275 2931769618 A	M
16	47 T	-X:64671274 2931769617 T	
16	48 G	-X:64671273 2931769616 G	
17 D	49 G	-X:64671272 2931769615 G	D
17	50 A	-X:64671271 2931769614 A	
17	51 T	-X:64671270 2931769613 T	
18 L	52 C	-X:64671269 2931769612 C	L
18	53 T	-X:64671268 2931769611 T	
18	54 C	-X:64671267 2931769610 C	
19 V	55 G	-X:64671266 2931769609 G	V
19	56 T	-X:64671265 2931769608 T	
19	57 G	-X:64671264 2931769607 G	
20 W	58 T	-X:64671263 2931769606 T	W
20	59 G	-X:64671262 2931769605 G	
20	60 G	-X:64671261 2931769604 G	
21 S	61 A	-X:64671260 2931769603 A	S
21	62 G	-X:64671259 2931769602 G	
21	63 T	-X:64671258 2931769601 T	
22 A	64 G	-X:64671257 2931769600 G	A
22	65 C	-X:64671256 2931769599 C	
22	66 G	-X:64671255 2931769598 G	
23 W	67 T	-X:64671254 2931769597 T	W
23	68 G	-X:64671253 2931769596 G	
23	69 G	-X:64671252 2931769595 G	
24 Y	70 T	-X:64671251 2931769594 T	Y
24	71 A	-X:64671250 2931769593 A	
24	72 C	-X:64671249 2931769592 C	
25 G	73 G	-X:64671248 2931769591 G	G
25	74 G	-X:64671247 2931769590 G	
25	75 A	-X:64671246 2931769589 A	
26 K	76 A	-X:64671245 2931769588 A	K
26	77 A	-X:64671244 2931769587 A	
26	78 G	-X:64671243 2931769586 G	
27 C	79 T	-X:64671242 2931769585 T	C
27	80 G	-X:64671241 2931769584 G	
27	81 C	-X:64671240 2931769583 C	
28 V	82 G	-X:64671239 2931769582 G	V
28	83 T	-X:64671238 2931769581 T	
28	84 T	-X:64671237 2931769580 T	
29 K	85 A	-X:64671236 2931769579 A	K
29	86 A	-X:64671235 2931769578 A	
29	87 A	-X:64671234 2931769577 A	
30 G	88 G	-X:64671233 2931769576 G	G
30	89 G	-X:64671232 2931769575 G	
30	90 G	-X:64671231 2931769574 G	
31 K	91 A	-X:64671230 2931769573 A	K
31	92 A	-X:64671229 2931769572 A	
31	93 A	-X:64671228 2931769571 A	
32 G	94 G	-X:64671227 2931769570 G	G
32	95 G	-X:64671226 2931769569 G	
32	96 G	-X:64671225 2931769568 G	
33 S	97 T	-X:64671224 2931769567 T	S
33	98 C	-X:64671223 2931769566 C	
33	99 G	-X:64671222 2931769565 G	
34 L	100 T	-X:64671221 2931769564 T	L
34	101 T	-X:64671220 2931769563 T	
34	102 G	-X:64671219 2931769562 G	
35 P	103 C	-X:64671218 2931769561 C	P
35	104 C	-X:64671217 2931769560 C	
35	105 A	-X:64671216 2931769559 A	
36 L	106 C	-X:64671215 2931769558 C	L
36	107 T	-X:64671214 2931769557 T	
36	108 C	-X:64671213 2931769556 C	
37 S	109 T	-X:64671212 2931769555 T	S
37	110 C	-X:64671211 2931769554 C	
37	111 G	-X:64671210 2931769553 G	
38 A	112 G	-X:64671209 2931769552 G	A
38	113 C	-X:64671208 2931769551 C	
38	114 C	-X:64671207 2931769550 C	
39 H	115 C	-X:64671206 2931769549 C	H
39	116 A	-X:64671205 2931769548 A	
39	117 C	-X:64671204 2931769547 C	
40 G	118 G	-X:64671203 2931769546 G	G
40	119 G	-X:64671202 2931769545 G	
40	120 C	-X:64671201 2931769544 C	
41 I	121 A	-X:64671200 2931769543 A	I
41	122 T	-X:64671199 2931769542 T	
41	123 C	-X:64671198 2931769541 C	
42 V	124 G	-X:64671197 2931769540 G	V
42	125 T	-X:64671196 2931769539 T	
42	126 G	-X:64671195 2931769538 G	
43 V	127 G	-X:64671194 2931769537 G	V
43	128 T	-X:64671193 2931769536 T	
43	129 C	-X:64671192 2931769535 C	
44 A	130 G	-X:64671191 2931769534 G	A
44	131 C	-X:64671190 2931769533 C	
44	132 C	-X:64671189 2931769532 C	
45 W	133 T	-X:64671188 2931769531 T	W
45	134 G	-X:64671187 2931769530 G	
45	135 G	-X:64671186 2931769529 G	
46 L	136 C	-X:64671185 2931769528 C	L
46	137 T	-X:64671184 2931769527 T	
46	138 C	-X:64671183 2931769526 C	
47 S	139 A	-X:64671182 2931769525 A	S
47	140 G	-X:64671181 2931769524 G	
47	141 C	-X:64671180 2931769523 C	
48 R	142 A	-X:64671179 2931769522 A	R
48	143 G	-X:64671178 2931769521 G	
48	144 G	-X:64671177 2931769520 G	
49 A	145 G	-X:64671176 2931769519 G	A
49	146 C	-X:64671175 2931769518 C	
49	147 C	-X:64671174 2931769517 C	
50 E	148 G	-X:64671173 2931769516 G	E
50	149 A	-X:64671172 2931769515 A	
50	150 G	-X:64671171 2931769514 G	
51 W	151 T	-X:64671170 2931769513 T	W
51	152 G	-X:64671169 2931769512 G	
51	153 G	-X:64671168 2931769511 G	
52 D	154 G	-X:64671167 2931769510 G	D
52	155 A	-X:64671166 2931769509 A	
52	156 C	-X:64671165 2931769508 C	
53 Q	157 C	-X:64671164 2931769507 C	Q
53	158 A	-X:64671163 2931769506 A	
53	159 G	-X:64671162 2931769505 G	
54 V	160 G	-X:64671161 2931769504 G	V
54	161 T	-X:64671160 2931769503 T	
54	162 G	-X:64671159 2931769502 G	
55 T	163 A	-X:64671158 2931769501 A	T
55	164 C	-X:64671157 2931769500 C	
55	165 G	-X:64671156 2931769499 G	
56 V	166 G	-X:64671155 2931769498 G	V
56	167 T	-X:64671154 2931769497 T	
56	168 T	-X:64671153 2931769496 T	
57 Y	169 T	-X:64671152 2931769495 T	Y
57	170 A	-X:64671151 2931769494 A	
57	171 T	-X:64671150 2931769493 T	
58 L	172 C	-X:64671149 2931769492 C	L
58	173 T	-X:64671148 2931769491 T	
58	174 G	-X:64671147 2931769490 G	
59 F	175 T	-X:64671146 2931769489 T	F
59	176 T	-X:64671145 2931769488 T	
59	177 C	-X:64671144 2931769487 C	
60 C	178 T	-X:64671143 2931769486 T	C
60	179 G	-X:64671142 2931769485 G	
60	180 T	-X:64671141 2931769484 T	
61 D	181 G	-X:64671140 2931769483 G	D
61	182 A	-X:64671139 2931769482 A	
61	183 C	-X:64671138 2931769481 C	
62 D	184 G	-X:64671137 2931769480 G	D
62	185 A	-X:64671136 2931769479 A	
62	186 C	-X:64671135 2931769478 C	
63 H	187 C	-X:64671134 2931769477 C	H
63	188 A	-X:64671133 2931769476 A	
63	189 T	-X:64671132 2931769475 T	
64 K	190 A	-X:64671131 2931769474 A	K
64	191 A	-X:64671130 2931769473 A	
64	192 G	-X:64671129 2931769472 G	
65 L	193 T	-X:64671128 2931769471 T	L
65	194 T	-X:64671127 2931769470 T	
65	195 G	-X:64671126 2931769469 G	
66 Q	196 C	-X:64671125 2931769468 C	Q
66	197 A	-X:64671124 2931769467 A	
66	198 G	-X:64671123 2931769466 G	
67 R	199 C	-X:64671122 2931769465 C	R
67	200 G	-X:64671121 2931769464 G	
67	201 G	-X:64671120 2931769463 G	
68 Y	202 T	-X:64671119 2931769462 T	Y
68	203 A	-X:64671118 2931769461 A	
68	204 C	-X:64671117 2931769460 C	
69 A	205 G	-X:64671116 2931769459 G	A
69	206 C	-X:64671115 2931769458 C	
69	207 G	-X:64671114 2931769457 G	
70 L	208 C	-X:64671113 2931769456 C	L
70	209 T	-X:64671112 2931769455 T	
70	210 T	-X:64671111 2931769454 T	
71 N	211 A	-X:64671110 2931769453 A	N
71	212 A	-X:64671109 2931769452 A	
71	213 C	-X:64671108 2931769451 C	
72 R	214 C	-X:64671107 2931769450 C	R
72	215 G	-X:64671106 2931769449 G	
72	216 C	-X:64671105 2931769448 C	
73 I	217 A	-X:64671104 2931769447 A	I
73	218 T	-X:64671103 2931769446 T	
73	219 C	-X:64671102 2931769445 C	
74 T	220 A	-X:64671101 2931769444 A	T
74	221 C	-X:64671100 2931769443 C	
74	222 G	-X:64671099 2931769442 G	
75 V	223 G	-X:64671098 2931769441 G	V
75	224 T	-X:64671097 2931769440 T	
75	225 G	-X:64671096 2931769439 G	
76 W	226 T	-X:64671095 2931769438 T	W
76	227 G	-X:64671094 2931769437 G	
76	228 G	-X:64671093 2931769436 G	
77 R	229 A	-X:64671092 2931769435 A	R
77	230 G	-X:64671091 2931769434 G	
77	231 G	-X:64671090 2931769433 G	
78 S	232 A	-X:64671089 2931769432 A	S
78	233 G	-X:64671088 2931769431 G	
78	234 C	-X:64671087 2931769430 C	
79 R	235 A	-X:64671086 2931769429 A	R
79	236 G	-X:64671085 2931769428 G	
79	237 G	-X:64670340 2931768683 G	
80 S	238 T	-X:64670339 2931768682 T	S
80	239 C	-X:64670338 2931768681 C	
80	240 A	-X:64670337 2931768680 A	
81 G	241 G	-X:64670336 2931768679 G	G
81	242 G	-X:64670335 2931768678 G	
81	243 C	-X:64670334 2931768677 C	
82 N	244 A	-X:64670333 2931768676 A	N
82	245 A	-X:64670332 2931768675 A	
82	246 C	-X:64670331 2931768674 C	
83 E	247 G	-X:64670330 2931768673 G	E
83	248 A	-X:64670329 2931768672 A	
83	249 A	-X:64670328 2931768671 A	
84 L	250 C	-X:64670327 2931768670 C	L
84	251 T	-X:64670326 2931768669 T	
84	252 C	-X:64670325 2931768668 C	
85 P	253 C	-X:64670324 2931768667 C	P
85	254 C	-X:64670323 2931768666 C	
85	255 T	-X:64670322 2931768665 T	
86 L	256 C	-X:64670321 2931768664 C	L
86	257 T	-X:64670320 2931768663 T	
86	258 G	-X:64670319 2931768662 G	
87 A	259 G	-X:64670318 2931768661 G	A
87	260 C	-X:64670317 2931768660 C	
87	261 A	-X:64670316 2931768659 A	
88 V	262 G	-X:64670315 2931768658 G	V
88	263 T	-X:64670314 2931768657 T	
88	264 G	-X:64670313 2931768656 G	
89 A	265 G	-X:64670312 2931768655 G	A
89	266 C	-X:64670311 2931768654 C	
89	267 T	-X:64670310 2931768653 T	
90 S	268 T	-X:64670309 2931768652 T	S
90	269 C	-X:64670308 2931768651 C	
90	270 T	-X:64670307 2931768650 T	
91 T	271 A	-X:64670306 2931768649 A	T
91	272 C	-X:64670305 2931768648 C	
91	273 T	-X:64670304 2931768647 T	
92 A	274 G	-X:64670303 2931768646 G	A
92	275 C	-X:64670302 2931768645 C	
92	276 T	-X:64670301 2931768644 T	
93 D	277 G	-X:64670300 2931768643 G	D
93	278 A	-X:64670299 2931768642 A	
93	279 C	-X:64670298 2931768641 C	
94 L	280 C	-X:64670297 2931768640 C	L
94	281 T	-X:64670296 2931768639 T	
94	282 G	-X:64670295 2931768638 G	
95 I	283 A	-X:64670294 2931768637 A	I
95	284 T	-X:64670293 2931768636 T	
95	285 A	-X:64670292 2931768635 A	
96 R	286 C	-X:64670291 2931768634 C	R
96	287 G	-X:64670290 2931768633 G	
96	288 C	-X:64670289 2931768632 C	
97 C	289 T	-X:64670288 2931768631 T	C
97	290 G	-X:64670287 2931768630 G	
97	291 T	-X:64670286 2931768629 T	
98 K	292 A	-X:64670285 2931768628 A	K
98	293 A	-X:64670284 2931768627 A	
98	294 G	-X:64670283 2931768626 G	
99 L	295 C	-X:64670282 2931768625 C	L
99	296 T	-X:64670281 2931768624 T	
99	297 C	-X:64670280 2931768623 C	
100 L	298 T	-X:64670279 2931768622 T	L
100	299 T	-X:64670278 2931768621 T	
100	300 G	-X:64670277 2931768620 G	
101 D	301 G	-X:64670276 2931768619 G	D
101	302 A	-X:64670275 2931768618 A	
101	303 T	-X:64670274 2931768617 T	
102 V	304 G	-X:64670273 2931768616 G	V
102	305 T	-X:64670272 2931768615 T	
102	306 A	-X:64670271 2931768614 A	
103 T	307 A	-X:64670270 2931768613 A	T
103	308 C	-X:64670269 2931768612 C	
103	309 T	-X:64670268 2931768611 T	
104 G	310 G	-X:64670267 2931768610 G	G
104	311 G	-X:64670266 2931768609 G	
104	312 T	-X:64670265 2931768608 T	
105 G	313 G	-X:64670264 2931768607 G	G
105	314 G	-X:64670263 2931768606 G	
105	315 C	-X:64670262 2931768605 C	
106 L	316 T	-X:64670261 2931768604 T	L
106	317 T	-X:64670260 2931768603 T	
106	318 G	-X:64670259 2931768602 G	
107 G	319 G	-X:64670258 2931768601 G	G
107	320 G	-X:64670257 2931768600 G	
107	321 C	-X:64670256 2931768599 C	
108 T	322 A	-X:64670255 2931768598 A	T
108	323 C	-X:64670254 2931768597 C	
108	324 T	-X:64670253 2931768596 T	
109 D	325 G	-X:64670252 2931768595 G	D
109	326 A	-X:64670251 2931768594 A	
109	327 T	-X:64670250 2931768593 T	
110 E	328 G	-X:64670249 2931768592 G	E
110	329 A	-X:64670248 2931768591 A	
110	330 A	-X:64670247 2931768590 A	
111 L	331 C	-X:64670246 2931768589 C	L
111	332 T	-X:64670245 2931768588 T	
111	333 T	-X:64670244 2931768587 T	
112 R	334 A	-X:64670243 2931768586 A	R
112	335 G	-X:64670242 2931768585 G	
112	336 A	-X:64670241 2931768584 A	
113 L	337 C	-X:64670240 2931768583 C	L
113	338 T	-X:64670239 2931768582 T	
113	339 G	-X:64670238 2931768581 G	
114 L	340 C	-X:64670237 2931768580 C	L
114	341 T	-X:64670236 2931768579 T	
114	342 C	-X:64670235 2931768578 C	
115 Y	343 T	-X:64670234 2931768577 T	Y
115	344 A	-X:64670233 2931768576 A	
115	345 T	-X:64670232 2931768575 T	
116 G	346 G	-X:64670231 2931768574 G	G
116	347 G	-X:64670230 2931768573 G	
116	348 C	-X:64670229 2931768572 C	
117 M	349 A	-X:64670228 2931768571 A	M
117	350 T	-X:64670227 2931768570 T	
117	351 G	-X:64670226 2931768569 G	
118 A	352 G	-X:64670225 2931768568 G	A
118	353 C	-X:64670224 2931768567 C	
118	354 A	-X:64670223 2931768566 A	
119 L	355 T	-X:64670222 2931768565 T	L
119	356 T	-X:64670221 2931768564 T	
119	357 G	-X:64670220 2931768563 G	
120 V	358 G	-X:64670219 2931768562 G	V
120	359 T	-X:64670218 2931768561 T	
120	360 C	-X:64670217 2931768560 C	
121 R	361 A	-X:64670216 2931768559 A	R
121	362 G	-X:64670215 2931768558 G	
121	363 G	-X:64669235 2931767578 G	
122 F	364 T	-X:64669234 2931767577 T	F
122	365 T	-X:64669233 2931767576 T	
122	366 T	-X:64669232 2931767575 T	
123 V	367 G	-X:64669231 2931767574 G	V
123	368 T	-X:64669230 2931767573 T	
123	369 G	-X:64669229 2931767572 G	
124 N	370 A	-X:64669228 2931767571 A	N
124	371 A	-X:64669227 2931767570 A	
124	372 T	-X:64669226 2931767569 T	
125 L	373 C	-X:64669225 2931767568 C	L
125	374 T	-X:64669224 2931767567 T	
125	375 T	-X:64669223 2931767566 T	
126 I	376 A	-X:64669222 2931767565 A	I
126	377 T	-X:64669221 2931767564 T	
126	378 C	-X:64669220 2931767563 C	
127 S	379 T	-X:64669219 2931767562 T	S
127	380 C	-X:64669218 2931767561 C	
127	381 A	-X:64669217 2931767560 A	
128 E	382 G	-X:64669216 2931767559 G	E
128	383 A	-X:64669215 2931767558 A	
128	384 G	-X:64669214 2931767557 G	
129 R	385 A	-X:64669213 2931767556 A	R
129	386 G	-X:64669212 2931767555 G	
129	387 G	-X:64669211 2931767554 G	
130 K	388 A	-X:64669210 2931767553 A	K
130	389 A	-X:64669209 2931767552 A	
130	390 G	-X:64669208 2931767551 G	
131 T	391 A	-X:64669207 2931767550 A	T
131	392 C	-X:64669206 2931767549 C	
131	393 A	-X:64669205 2931767548 A	
132 K	394 A	-X:64669204 2931767547 A	K
132	395 A	-X:64669203 2931767546 A	
132	396 G	-X:64669202 2931767545 G	
133 F	397 T	-X:64669201 2931767544 T	F
133	398 T	-X:64669200 2931767543 T	
133	399 T	-X:64669199 2931767542 T	
134 A	400 G	-X:64669198 2931767541 G	A
134	401 C	-X:64669197 2931767540 C	
134	402 C	-X:64669196 2931767539 C	
135 K	403 A	-X:64669195 2931767538 A	K
135	404 A	-X:64669194 2931767537 A	
135	405 G	-X:64669193 2931767536 G	
136 V	406 G	-X:64669192 2931767535 G	V
136	407 T	-X:64669191 2931767534 T	
136	408 C	-X:64669190 2931767533 C	
137 P	409 C	-X:64669189 2931767532 C	P
137	410 C	-X:64669188 2931767531 C	
137	411 C	-X:64669187 2931767530 C	
138 L	412 C	-X:64669186 2931767529 C	L
138	413 T	-X:64669185 2931767528 T	
138	414 C	-X:64669184 2931767527 C	
139 K	415 A	-X:64669183 2931767526 A	K
139	416 A	-X:64669182 2931767525 A	
139	417 G	-X:64669181 2931767524 G	
140 C	418 T	-X:64669180 2931767523 T	C
140	419 G	-X:64669179 2931767522 G	
140	420 T	-X:64669178 2931767521 T	
141 L	421 C	-X:64669177 2931767520 C	L
141	422 T	-X:64669176 2931767519 T	
141	423 G	-X:64669175 2931767518 G	
142 A	424 G	-X:64669174 2931767517 G	A
142	425 C	-X:64669173 2931767516 C	
142	426 T	-X:64669172 2931767515 T	
143 Q	427 C	-X:64669171 2931767514 C	Q
143	428 A	-X:64669170 2931767513 A	
143	429 A	-X:64669169 2931767512 A	
144 E	430 G	-X:64669168 2931767511 G	E
144	431 A	-X:64669167 2931767510 A	
144	432 G	-X:64669166 2931767509 G	
145 V	433 G	-X:64668043 2931766386 G	V
145	434 T	-X:64668042 2931766385 T	
145	435 A	-X:64668041 2931766384 A	
146 N	436 A	-X:64668040 2931766383 A	N
146	437 A	-X:64668039 2931766382 A	
146	438 T	-X:64668038 2931766381 T	
147 I	439 A	-X:64668037 2931766380 A	I
147	440 T	-X:64668036 2931766379 T	
147	441 T	-X:64668035 2931766378 T	
148 P	442 C	-X:64668034 2931766377 C	P
148	443 C	-X:64668033 2931766376 C	
148	444 G	-X:64668032 2931766375 G	
149 D	445 G	-X:64668031 2931766374 G	D
149	446 A	-X:64668030 2931766373 A	
149	447 T	-X:64668029 2931766372 T	
150 W	448 T	-X:64668028 2931766371 T	W
150	449 G	-X:64668027 2931766370 G	
150	450 G	-X:64668026 2931766369 G	
151 I	451 A	-X:64668025 2931766368 A	I
151	452 T	-X:64668024 2931766367 T	
151	453 T	-X:64668023 2931766366 T	
152 V	454 G	-X:64668022 2931766365 G	V
152	455 T	-X:64668021 2931766364 T	
152	456 T	-X:64668020 2931766363 T	
153 D	457 G	-X:64668019 2931766362 G	D
153	458 A	-X:64668018 2931766361 A	
153	459 C	-X:64668017 2931766360 C	
154 L	460 C	-X:64668016 2931766359 C	L
154	461 T	-X:64668015 2931766358 T	
154	462 T	-X:64668014 2931766357 T	
155 R	463 C	-X:64668013 2931766356 C	R
155	464 G	-X:64668012 2931766355 G	
155	465 C	-X:64668011 2931766354 C	
156 H	466 C	-X:64668010 2931766353 C	H
156	467 A	-X:64668009 2931766352 A	
156	468 T	-X:64668008 2931766351 T	
157 E	469 G	-X:64668007 2931766350 G	E
157	470 A	-X:64668006 2931766349 A	
157	471 G	-X:64668005 2931766348 G	
158 L	472 T	-X:64668004 2931766347 T	L
158	473 T	-X:64668003 2931766346 T	
158	474 G	-X:64668002 2931766345 G	
159 T	475 A	-X:64668001 2931766344 A	T
159	476 C	-X:64668000 2931766343 C	
159	477 C	-X:64667999 2931766342 C	
160 H	478 C	-X:64667998 2931766341 C	H
160	479 A	-X:64667997 2931766340 A	
160	480 C	-X:64667996 2931766339 C	
161 K	481 A	-X:64667995 2931766338 A	K
161	482 A	-X:64667994 2931766337 A	
161	483 G	-X:64667993 2931766336 G	
162 K	484 A	-X:64667992 2931766335 A	K
162	485 A	-X:64667991 2931766334 A	
162	486 A	-X:64667990 2931766333 A	
163 M	487 A	-X:64667989 2931766332 A	M
163	488 T	-X:64667988 2931766331 T	
163	489 G	-X:64667987 2931766330 G	
164 P	490 C	-X:64667986 2931766329 C	P
164	491 C	-X:64667985 2931766328 C	
164	492 C	-X:64667984 2931766327 C	
165 H	493 C	-X:64667983 2931766326 C	H
165	494 A	-X:64667982 2931766325 A	
165	495 T	-X:64667981 2931766324 T	
166 I	496 A	-X:64667980 2931766323 A	I
166	497 T	-X:64667979 2931766322 T	
166	498 A	-X:64667978 2931766321 A	
167 N	499 A	-X:64667977 2931766320 A	N
167	500 A	-X:64667976 2931766319 A	
167	501 T	-X:64667975 2931766318 T	
168 D	502 G	-X:64667974 2931766317 G	D
168	503 A	-X:64667973 2931766316 A	
168	504 C	-X:64667972 2931766315 C	
169 C	505 T	-X:64667971 2931766314 T	C
169	506 G	-X:64667970 2931766313 G	
169	507 C	-X:64667969 2931766312 C	
170 R	508 C	-X:64667968 2931766311 C	R
170	509 G	-X:64667967 2931766310 G	
170	510 C	-X:64667966 2931766309 C	
171 R	511 A	-X:64667965 2931766308 A	R
171	512 G	-X:64667964 2931766307 G	
171	513 A	-X:64667963 2931766306 A	
172 G	514 G	-X:64667962 2931766305 G	G
172	515 G	-X:64666483 2931764826 G	
172	516 C	-X:64666482 2931764825 C	
173 C	517 T	-X:64666481 2931764824 T	C
173	518 G	-X:64666480 2931764823 G	
173	519 C	-X:64666479 2931764822 C	
174 Y	520 T	-X:64666478 2931764821 T	Y
174	521 A	-X:64666477 2931764820 A	
174	522 C	-X:64666476 2931764819 C	
175 F	523 T	-X:64666475 2931764818 T	F
175	524 T	-X:64666474 2931764817 T	
175	525 T	-X:64666473 2931764816 T	
176 V	526 G	-X:64666472 2931764815 G	V
176	527 T	-X:64666471 2931764814 T	
176	528 C	-X:64666470 2931764813 C	
177 L	529 C	-X:64666469 2931764812 C	L
177	530 T	-X:64666468 2931764811 T	
177	531 G	-X:64666467 2931764810 G	
178 D	532 G	-X:64666466 2931764809 G	D
178	533 A	-X:64666465 2931764808 A	
178	534 T	-X:64666464 2931764807 T	
179 W	535 T	-X:64666463 2931764806 T	W
179	536 G	-X:64666462 2931764805 G	
179	537 G	-X:64666461 2931764804 G	
180 L	538 C	-X:64666460 2931764803 C	L
180	539 T	-X:64666459 2931764802 T	
180	540 C	-X:64666458 2931764801 C	
181 Q	541 C	-X:64666457 2931764800 C	Q
181	542 A	-X:64666456 2931764799 A	
181	543 G	-X:64666455 2931764798 G	
182 K	544 A	-X:64666454 2931764797 A	K
182	545 A	-X:64666453 2931764796 A	
182	546 G	-X:64666452 2931764795 G	
183 T	547 A	-X:64666451 2931764794 A	T
183	548 C	-X:64666450 2931764793 C	
183	549 C	-X:64666449 2931764792 C	
184 Y	550 T	-X:64666448 2931764791 T	Y
184	551 A	-X:64666447 2931764790 A	
184	552 T	-X:64666446 2931764789 T	
185 W	553 T	-X:64666445 2931764788 T	W
185	554 G	-X:64666444 2931764787 G	
185	555 G	-X:64666443 2931764786 G	
186 C	556 T	-X:64666442 2931764785 T	C
186	557 G	-X:64666441 2931764784 G	
186	558 C	-X:64666440 2931764783 C	
187 R	559 C	-X:64666439 2931764782 C	R
187	560 G	-X:64666438 2931764781 G	
187	561 C	-X:64666437 2931764780 C	
188 Q	562 C	-X:64666436 2931764779 C	Q
188	563 A	-X:64666435 2931764778 A	
188	564 A	-X:64666434 2931764777 A	
189 L	565 C	-X:64666433 2931764776 C	L
189	566 T	-X:64666432 2931764775 T	
189	567 G	-X:64666431 2931764774 G	
190 E	568 G	-X:64666430 2931764773 G	E
190	569 A	-X:64666429 2931764772 A	
190	570 G	-X:64666428 2931764771 G	
191 N	571 A	-X:64666427 2931764770 A	N
191	572 A	-X:64666426 2931764769 A	
191	573 C	-X:64666425 2931764768 C	
192 S	574 A	-X:64666424 2931764767 A	S
192	575 G	-X:64666423 2931764766 G	
192	576 C	-X:64666422 2931764765 C	
193 L	577 C	-X:64666421 2931764764 C	L
193	578 T	-X:64666420 2931764763 T	
193	579 G	-X:64666419 2931764762 G	
194 R	580 A	-X:64666418 2931764761 A	R
194	581 G	-X:64666417 2931764760 G	
194	582 A	-X:64666416 2931764759 A	
195 E	583 G	-X:64666415 2931764758 G	E
195	584 A	-X:64666414 2931764757 A	
195	585 G	-X:64666413 2931764756 G	
196 T	586 A	-X:64666412 2931764755 A	T
196	587 C	-X:64666411 2931764754 C	
196	588 C	-X:64666410 2931764753 C	
197 W	589 T	-X:64666409 2931764752 T	W
197	590 G	-X:64666408 2931764751 G	
197	591 G	-X:64666407 2931764750 G	
198 E	592 G	-X:64666406 2931764749 G	E
198	593 A	-X:64666405 2931764748 A	
198	594 G	-X:64666404 2931764747 G	
199 L	595 T	-X:64666403 2931764746 T	L
199	596 T	-X:64666402 2931764745 T	
199	597 G	-X:64666401 2931764744 G	
200 E	598 G	-X:64666400 2931764743 G	E
200	599 A	-X:64666399 2931764742 A	
200	600 G	-X:64666398 2931764741 G	
201 E	601 G	-X:64666397 2931764740 G	E
201	602 A	-X:64666396 2931764739 A	
201	603 G	-X:64666395 2931764738 G	
202 F	604 T	-X:64666394 2931764737 T	F
202	605 T	-X:64666393 2931764736 T	
202	606 C	-X:64666392 2931764735 C	
203 R	607 A	-X:64666391 2931764734 A	R
203	608 G	-X:64666390 2931764733 G	
203	609 G	-X:64666389 2931764732 G	
204 E	610 G	-X:64666388 2931764731 G	E
204	611 A	-X:64666387 2931764730 A	
204	612 A	-X:64666386 2931764729 A	
205 G	613 G	-X:64666385 2931764728 G	G
205	614 G	-X:64666384 2931764727 G	
205	615 G	-X:64666383 2931764726 G	
206 I	616 A	-X:64666382 2931764725 A	I
206	617 T	-X:64666381 2931764724 T	
206	618 A	-X:64666380 2931764723 A	
207 E	619 G	-X:64666379 2931764722 G	E
207	620 A	-X:64666378 2931764721 A	
207	621 G	-X:64666377 2931764720 G	
208 E	622 G	-X:64666376 2931764719 G	E
208	623 A	-X:64666375 2931764718 A	
208	624 A	-X:64666374 2931764717 A	
209 E	625 G	-X:64666373 2931764716 G	E
209	626 A	-X:64666372 2931764715 A	
209	627 G	-X:64666371 2931764714 G	
210 D	628 G	-X:64666370 2931764713 G	D
210	629 A	-X:64666369 2931764712 A	
210	630 T	-X:64666368 2931764711 T	
211 Q	631 C	-X:64666367 2931764710 C	Q
211	632 A	-X:64666366 2931764709 A	
211	633 A	-X:64666365 2931764708 A	
212 E	634 G	-X:64666364 2931764707 G	E
212	635 A	-X:64666363 2931764706 A	
212	636 G	-X:64666362 2931764705 G	
213 E	637 G	-X:64666361 2931764704 G	E
213	638 A	-X:64666360 2931764703 A	
213	639 A	-X:64666359 2931764702 A	
214 D	640 G	-X:64666358 2931764701 G	D
214	641 A	-X:64666357 2931764700 A	
214	642 T	-X:64666356 2931764699 T	
215 K	643 A	-X:64666355 2931764698 A	K
215	644 A	-X:64666354 2931764697 A	
215	645 G	-X:64666353 2931764696 G	
216 N	646 A	-X:64666352 2931764695 A	N
216	647 A	-X:64666351 2931764694 A	
216	648 C	-X:64666350 2931764693 C	
217 I	649 A	-X:64666349 2931764692 A	I
217	650 T	-X:64666348 2931764691 T	
217	651 T	-X:64666347 2931764690 T	
218 V	652 G	-X:64666346 2931764689 G	V
218	653 T	-X:64666345 2931764688 T	
218	654 T	-X:64666344 2931764687 T	
219 V	655 G	-X:64666343 2931764686 G	V
219	656 T	-X:64666342 2931764685 T	
219	657 T	-X:64666341 2931764684 T	
220 D	658 G	-X:64666340 2931764683 G	D
220	659 A	-X:64666339 2931764682 A	
220	660 T	-X:64666338 2931764681 T	
221 D	661 G	-X:64666337 2931764680 G	D
221	662 A	-X:64666336 2931764679 A	
221	663 C	-X:64666335 2931764678 C	
222 I	664 A	-X:64666334 2931764677 A	I
222	665 T	-X:64666333 2931764676 T	
222	666 C	-X:64666332 2931764675 C	
223 T	667 A	-X:64666331 2931764674 A	T
223	668 C	-X:64666330 2931764673 C	
223	669 A	-X:64666329 2931764672 A	
224 E	670 G	-X:64666328 2931764671 G	E
224	671 A	-X:64666327 2931764670 A	
224	672 A	-X:64666326 2931764669 A	
225 Q	673 C	-X:64666325 2931764668 C	Q
225	674 A	-X:64666324 2931764667 A	
225	675 G	-X:64666323 2931764666 G	
226 K	676 A	-X:64666322 2931764665 A	K
226	677 A	-X:64666321 2931764664 A	
226	678 A	-X:64666320 2931764663 A	
227 P	679 C	-X:64666319 2931764662 C	P
227	680 C	-X:64666318 2931764661 C	
227	681 A	-X:64666317 2931764660 A	
228 E	682 G	-X:64666316 2931764659 G	E
228	683 A	-X:64666315 2931764658 A	
228	684 G	-X:64666314 2931764657 G	
229 P	685 C	-X:64666313 2931764656 C	P
229	686 C	-X:64666312 2931764655 C	
229	687 T	-X:64666311 2931764654 T	
230 Q	688 C	-X:64666310 2931764653 C	Q
230	689 A	-X:64666309 2931764652 A	
230	690 G	-X:64666308 2931764651 G	
231 D	691 G	-X:64666307 2931764650 G	D
231	692 A	-X:64666306 2931764649 A	
231	693 T	-X:64666305 2931764648 T	
232 D	694 G	-X:64666304 2931764647 G	D
232	695 A	-X:64666303 2931764646 A	
232	696 T	-X:64666302 2931764645 T	
233 G	697 G	-X:64666301 2931764644 G	G
233	698 G	-X:64666300 2931764643 G	
233	699 G	-X:64666299 2931764642 G	
234 K	700 A	-X:64666298 2931764641 A	K
234	701 A	-X:64666297 2931764640 A	
234	702 A	-X:64666296 2931764639 A	
235 S	703 A	-X:64666295 2931764638 A	S
235	704 G	-X:64666294 2931764637 G	
235	705 T	-X:64666293 2931764636 T	
236 T	706 A	-X:64666292 2931764635 A	T
236	707 C	-X:64666291 2931764634 C	
236	708 G	-X:64666290 2931764633 G	
237 E	709 G	-X:64666289 2931764632 G	E
237	710 A	-X:64666288 2931764631 A	
237	711 G	-X:64666287 2931764630 G	
238 S	712 T	-X:64666286 2931764629 T	S
238	713 C	-X:64666285 2931764628 C	
238	714 A	-X:64666284 2931764627 A	
239 D	715 G	-X:64666283 2931764626 G	D
239	716 A	-X:64666282 2931764625 A	
239	717 T	-X:64666281 2931764624 T	
240 V	718 G	-X:64666280 2931764623 G	V
240	719 T	-X:64666279 2931764622 T	
240	720 A	-X:64666278 2931764621 A	
241 K	721 A	-X:64666277 2931764620 A	K
241	722 A	-X:64666276 2931764619 A	
241	723 G	-X:64666275 2931764618 G	
242 A	724 G	-X:64666274 2931764617 G	A
242	725 C	-X:64666273 2931764616 C	
242	726 C	-X:64666272 2931764615 C	
243 D	727 G	-X:64666271 2931764614 G	D
243	728 A	-X:64666270 2931764613 A	
243	729 T	-X:64666269 2931764612 T	
244 G	730 G	-X:64666268 2931764611 G	G
244	731 G	-X:64666267 2931764610 G	
244	732 A	-X:64666266 2931764609 A	
245 D	733 G	-X:64666265 2931764608 G	D
245	734 A	-X:64666264 2931764607 A	
245	735 C	-X:64666263 2931764606 C	
246 S	736 A	-X:64666262 2931764605 A	S
246	737 G	-X:64666261 2931764604 G	
246	738 C	-X:64666260 2931764603 C	
247 K	739 A	-X:64666259 2931764602 A	K
247	740 A	-X:64666258 2931764601 A	
247	741 A	-X:64666257 2931764600 A	
248 G	742 G	-X:64666256 2931764599 G	G
248	743 G	-X:64666255 2931764598 G	
248	744 C	-X:64666254 2931764597 C	
249 S	745 A	-X:64666253 2931764596 A	S
249	746 G	-X:64666252 2931764595 G	
249	747 C	-X:64666251 2931764594 C	
250 E	748 G	-X:64666250 2931764593 G	E
250	749 A	-X:64666249 2931764592 A	
250	750 A	-X:64666248 2931764591 A	
251 E	751 G	-X:64666247 2931764590 G	E
251	752 A	-X:64666246 2931764589 A	
251	753 G	-X:64666245 2931764588 G	
252 V	754 G	-X:64666244 2931764587 G	V
252	755 T	-X:64666243 2931764586 T	
252	756 G	-X:64666242 2931764585 G	
253 D	757 G	-X:64666241 2931764584 G	D
253	758 A	-X:64666240 2931764583 A	
253	759 T	-X:64666239 2931764582 T	
254 S	760 T	-X:64666238 2931764581 T	S
254	761 C	-X:64666237 2931764580 C	
254	762 T	-X:64666236 2931764579 T	
255 H	763 C	-X:64666235 2931764578 C	H
255	764 A	-X:64666234 2931764577 A	
255	765 T	-X:64666233 2931764576 T	
256 C	766 T	-X:64666232 2931764575 T	C
256	767 G	-X:64666231 2931764574 G	
256	768 C	-X:64666230 2931764573 C	
257 K	769 A	-X:64666229 2931764572 A	K
257	770 A	-X:64666228 2931764571 A	
257	771 A	-X:64666227 2931764570 A	
258 K	772 A	-X:64666226 2931764569 A	K
258	773 A	-X:64666225 2931764568 A	
258	774 G	-X:64666224 2931764567 G	
259 A	775 G	-X:64666223 2931764566 G	A
259	776 C	-X:64666222 2931764565 C	
259	777 C	-X:64666221 2931764564 C	
260 L	778 C	-X:64666220 2931764563 C	L
260	779 T	-X:64666219 2931764562 T	
260	780 G	-X:64666218 2931764561 G	
261 S	781 A	-X:64666217 2931764560 A	S
261	782 G	-X:64666216 2931764559 G	
261	783 T	-X:64666215 2931764558 T	
262 H	784 C	-X:64666214 2931764557 C	H
262	785 A	-X:64666213 2931764556 A	
262	786 T	-X:64666212 2931764555 T	
263 K	787 A	-X:64666211 2931764554 A	K
263	788 A	-X:64666210 2931764553 A	
263	789 A	-X:64666209 2931764552 A	
264 E	790 G	-X:64666208 2931764551 G	E
264	791 A	-X:64666207 2931764550 A	
264	792 G	-X:64666206 2931764549 G	
265 L	793 C	-X:64666205 2931764548 C	L
265	794 T	-X:64666204 2931764547 T	
265	795 A	-X:64666203 2931764546 A	
266 Y	796 T	-X:64666202 2931764545 T	Y
266	797 A	-X:64666201 2931764544 A	
266	798 T	-X:64666200 2931764543 T	
267 E	799 G	-X:64666199 2931764542 G	E
267	800 A	-X:64665863 2931764206 A	
267	801 A	-X:64665862 2931764205 A	
268 R	802 A	-X:64665861 2931764204 A	R
268	803 G	-X:64665860 2931764203 G	
268	804 A	-X:64665859 2931764202 A	
269 A	805 G	-X:64665858 2931764201 G	A
269	806 C	-X:64665857 2931764200 C	
269	807 C	-X:64665856 2931764199 C	
270 R	808 C	-X:64665855 2931764198 C	R
270	809 G	-X:64665854 2931764197 G	
270	810 A	-X:64665853 2931764196 A	
271 E	811 G	-X:64665852 2931764195 G	E
271	812 A	-X:64665851 2931764194 A	
271	813 A	-X:64665850 2931764193 A	
272 L	814 C	-X:64665849 2931764192 C	L
272	815 T	-X:64665848 2931764191 T	
272	816 G	-X:64665847 2931764190 G	
273 L	817 C	-X:64665846 2931764189 C	L
273	818 T	-X:64665845 2931764188 T	
273	819 G	-X:64665844 2931764187 G	
274 V	820 G	-X:64665843 2931764186 G	V
274	821 T	-X:64665842 2931764185 T	
274	822 A	-X:64665841 2931764184 A	
275 S	823 T	-X:64665840 2931764183 T	S
275	824 C	-X:64665839 2931764182 C	
275	825 A	-X:64665838 2931764181 A	
276 Y	826 T	-X:64665837 2931764180 T	Y
276	827 A	-X:64665836 2931764179 A	
276	828 C	-X:64665835 2931764178 C	
277 E	829 G	-X:64665834 2931764177 G	E
277	830 A	-X:64665833 2931764176 A	
277	831 A	-X:64665832 2931764175 A	
278 E	832 G	-X:64665831 2931764174 G	E
278	833 A	-X:64665830 2931764173 A	
278	834 G	-X:64665829 2931764172 G	
279 E	835 G	-X:64665828 2931764171 G	E
279	836 A	-X:64665827 2931764170 A	
279	837 G	-X:64665826 2931764169 G	
280 Q	838 C	-X:64665825 2931764168 C	Q
280	839 A	-X:64665824 2931764167 A	
280	840 G	-X:64665823 2931764166 G	
281 F	841 T	-X:64665822 2931764165 T	F
281	842 T	-X:64665821 2931764164 T	
281	843 T	-X:64665820 2931764163 T	
282 T	844 A	-X:64665819 2931764162 A	T
282	845 C	-X:64665818 2931764161 C	
282	846 G	-X:64665817 2931764160 G	
283 V	847 G	-X:64664974 2931763317 G	V
283	848 T	-X:64664973 2931763316 T	
283	849 G	-X:64664972 2931763315 G	
284 L	850 C	-X:64664971 2931763314 C	L
284	851 T	-X:64664970 2931763313 T	
284	852 G	-X:64664969 2931763312 G	
285 E	853 G	-X:64664968 2931763311 G	E
285	854 A	-X:64664967 2931763310 A	
285	855 G	-X:64664966 2931763309 G	
286 K	856 A	-X:64664965 2931763308 A	K
286	857 A	-X:64664964 2931763307 A	
286	858 A	-X:64664963 2931763306 A	
287 F	859 T	-X:64664962 2931763305 T	F
287	860 T	-X:64664961 2931763304 T	
287	861 T	-X:64664960 2931763303 T	
288 R	862 A	-X:64664959 2931763302 A	R
288	863 G	-X:64664958 2931763301 G	
288	864 G	-X:64664957 2931763300 G	
289 Y	865 T	-X:64664956 2931763299 T	Y
289	866 A	-X:64664955 2931763298 A	
289	867 T	-X:64664954 2931763297 T	
290 L	868 T	-X:64664953 2931763296 T	L
290	869 T	-X:64664952 2931763295 T	
290	870 A	-X:64664951 2931763294 A	
291 P	871 C	-X:64664950 2931763293 C	P
291	872 C	-X:64664949 2931763292 C	
291	873 T	-X:64664948 2931763291 T	
292 K	874 A	-X:64664947 2931763290 A	K
292	875 A	-X:64664946 2931763289 A	
292	876 G	-X:64664945 2931763288 G	
293 A	877 G	-X:64664944 2931763287 G	A
293	878 C	-X:64664943 2931763286 C	
293	879 C	-X:64664942 2931763285 C	
294 I	880 A	-X:64664941 2931763284 A	I
294	881 T	-X:64664940 2931763283 T	
294	882 T	-X:64664939 2931763282 T	
295 K	883 A	-X:64664938 2931763281 A	K
295	884 A	-X:64664937 2931763280 A	
295	885 G	-X:64664936 2931763279 G	
296 A	886 G	-X:64664935 2931763278 G	A
296	887 C	-X:64664934 2931763277 C	
296	888 G	-X:64664933 2931763276 G	
297 W	889 T	-X:64664932 2931763275 T	W
297	890 G	-X:64664931 2931763274 G	
297	891 G	-X:64664930 2931763273 G	
298 N	892 A	-X:64664929 2931763272 A	N
298	893 A	-X:64664928 2931763271 A	
298	894 T	-X:64664927 2931763270 T	
299 N	895 A	-X:64664926 2931763269 A	N
299	896 A	-X:64664925 2931763268 A	
299	897 C	-X:64664924 2931763267 C	
300 P	898 C	-X:64664923 2931763266 C	P
300	899 C	-X:64664922 2931763265 C	
300	900 G	-X:64664921 2931763264 G	
301 S	901 T	-X:64664920 2931763263 T	S
301	902 C	-X:64664919 2931763262 C	
301	903 C	-X:64664918 2931763261 C	
302 P	904 C	-X:64664917 2931763260 C	P
302	905 C	-X:64664916 2931763259 C	
302	906 A	-X:64664915 2931763258 A	
303 R	907 C	-X:64664914 2931763257 C	R
303	908 G	-X:64664913 2931763256 G	
303	909 T	-X:64664912 2931763255 T	
304 V	910 G	-X:64664911 2931763254 G	V
304	911 T	-X:64664910 2931763253 T	
304	912 A	-X:64664909 2931763252 A	
305 E	913 G	-X:64664908 2931763251 G	E
305	914 A	-X:64664907 2931763250 A	
305	915 A	-X:64664906 2931763249 A	
306 C	916 T	-X:64664905 2931763248 T	C
306	917 G	-X:64664904 2931763247 G	
306	918 T	-X:64664903 2931763246 T	
307 V	919 G	-X:64664902 2931763245 G	V
307	920 T	-X:64664901 2931763244 T	
307	921 C	-X:64664900 2931763243 C	
308 L	922 C	-X:64664899 2931763242 C	L
308	923 T	-X:64664898 2931763241 T	
308	924 G	-X:64664897 2931763240 G	
309 A	925 G	-X:64664896 2931763239 G	A
309	926 C	-X:64664895 2931763238 C	
309	927 A	-X:64664894 2931763237 A	
310 E	928 G	-X:64664893 2931763236 G	E
310	929 A	-X:64664892 2931763235 A	
310	930 G	-X:64664891 2931763234 G	
311 L	931 C	-X:64664890 2931763233 C	L
311	932 T	-X:64664889 2931763232 T	
311	933 C	-X:64664888 2931763231 C	
312 K	934 A	-X:64664887 2931763230 A	K
312	935 A	-X:64664886 2931763229 A	
312	936 G	-X:64664885 2931763228 G	
313 G	937 G	-X:64664884 2931763227 G	G
313	938 G	-X:64664883 2931763226 G	
313	939 C	-X:64664882 2931763225 C	
314 V	940 G	-X:64664881 2931763224 G	V
314	941 T	-X:64664880 2931763223 T	
314	942 T	-X:64664879 2931763222 T	
315 T	943 A	-X:64664878 2931763221 A	T
315	944 C	-X:64664877 2931763220 C	
315	945 A	-X:64664876 2931763219 A	
316 C	946 T	-X:64664875 2931763218 T	C
316	947 G	-X:64664874 2931763217 G	
316	948 C	-X:64664873 2931763216 C	
317 E	949 G	-X:64664872 2931763215 G	E
317	950 A	-X:64664871 2931763214 A	
317	951 G	-X:64664870 2931763213 G	
318 N	952 A	-X:64664869 2931763212 A	N
318	953 A	-X:64664868 2931763211 A	
318	954 C	-X:64664867 2931763210 C	
319 R	955 A	-X:64664866 2931763209 A	R
319	956 G	-X:64664865 2931763208 G	
319	957 G	-X:64661655 2931759998 G	
320 E	958 G	-X:64661654 2931759997 G	E
320	959 A	-X:64661653 2931759996 A	
320	960 G	-X:64661652 2931759995 G	
321 A	961 G	-X:64661651 2931759994 G	A
321	962 C	-X:64661650 2931759993 C	
321	963 T	-X:64661649 2931759992 T	
322 V	964 G	-X:64661648 2931759991 G	V
322	965 T	-X:64661647 2931759990 T	
322	966 G	-X:64661646 2931759989 G	
323 L	967 C	-X:64661645 2931759988 C	L
323	968 T	-X:64661644 2931759987 T	
323	969 G	-X:64661643 2931759986 G	
324 D	970 G	-X:64661642 2931759985 G	D
324	971 A	-X:64661641 2931759984 A	
324	972 T	-X:64661640 2931759983 T	
325 A	973 G	-X:64661639 2931759982 G	A
325	974 C	-X:64661638 2931759981 C	
325	975 T	-X:64661637 2931759980 T	
326 F	976 T	-X:64661636 2931759979 T	F
326	977 T	-X:64661635 2931759978 T	
326	978 T	-X:64661634 2931759977 T	
327 L	979 C	-X:64661633 2931759976 C	L
327	980 T	-X:64661632 2931759975 T	
327	981 G	-X:64661631 2931759974 G	
328 D	982 G	-X:64661630 2931759973 G	D
328	983 A	-X:64661629 2931759972 A	
328	984 T	-X:64661628 2931759971 T	
329 D	985 G	-X:64661627 2931759970 G	D
329	986 A	-X:64661626 2931759969 A	
329	987 T	-X:64661625 2931759968 T	
330 G	988 G	-X:64661624 2931759967 G	G
330	989 G	-X:64661623 2931759966 G	
330	990 C	-X:64661622 2931759965 C	
331 F	991 T	-X:64661621 2931759964 T	F
331	992 T	-X:64661620 2931759963 T	
331	993 C	-X:64661619 2931759962 C	
332 L	994 C	-X:64661618 2931759961 C	L
332	995 T	-X:64661617 2931759960 T	
332	996 T	-X:64661616 2931759959 T	
333 V	997 G	-X:64661615 2931759958 G	V
333	998 T	-X:64661614 2931759957 T	
333	999 C	-X:64661613 2931759956 C	
334 P	1000 C	-X:64661612 2931759955 C	P
334	1001 C	-X:64661611 2931759954 C	
334	1002 C	-X:64661610 2931759953 C	
335 T	1003 A	-X:64661609 2931759952 A	T
335	1004 C	-X:64661608 2931759951 C	
335	1005 A	-X:64661607 2931759950 A	
336 F	1006 T	-X:64661606 2931759949 T	F
336	1007 T	-X:64661605 2931759948 T	
336	1008 T	-X:64661604 2931759947 T	
337 E	1009 G	-X:64661603 2931759946 G	E
337	1010 A	-X:64661602 2931759945 A	
337	1011 A	-X:64661601 2931759944 A	
338 Q	1012 C	-X:64661600 2931759943 C	Q
338	1013 A	-X:64661599 2931759942 A	
338	1014 G	-X:64661598 2931759941 G	
339 L	1015 T	-X:64661597 2931759940 T	L
339	1016 T	-X:64661596 2931759939 T	
339	1017 G	-X:64661595 2931759938 G	
340 A	1018 G	-X:64661594 2931759937 G	A
340	1019 C	-X:64661593 2931759936 C	
340	1020 A	-X:64661592 2931759935 A	
341 A	1021 G	-X:64661591 2931759934 G	A
341	1022 C	-X:64661590 2931759933 C	
341	1023 T	-X:64661589 2931759932 T	
342 L	1024 T	-X:64661588 2931759931 T	L
342	1025 T	-X:64661587 2931759930 T	
342	1026 G	-X:64661586 2931759929 G	
343 Q	1027 C	-X:64661585 2931759928 C	Q
343	1028 A	-X:64661584 2931759927 A	
343	1029 G	-X:64661583 2931759926 G	
344 I	1030 A	-X:64661582 2931759925 A	I
344	1031 T	-X:64661581 2931759924 T	
344	1032 A	-X:64661580 2931759923 A	
345 E	1033 G	-X:64661579 2931759922 G	E
345	1034 A	-X:64661578 2931759921 A	
345	1035 A	-X:64661577 2931759920 A	
346 Y	1036 T	-X:64661576 2931759919 T	Y
346	1037 A	-X:64661575 2931759918 A	
346	1038 T	-X:64661574 2931759917 T	
347 E	1039 G	-X:64661573 2931759916 G	E
347	1040 A	-X:64661572 2931759915 A	
347	1041 A	-X:64661571 2931759914 A	
348 E	1042 G	-X:64661570 2931759913 G	E
348	1043 A	-X:64660867 2931759210 A	
348	1044 A	-X:64660866 2931759209 A	
349 N	1045 A	-X:64660865 2931759208 A	N
349	1046 A	-X:64660864 2931759207 A	
349	1047 C	-X:64660863 2931759206 C	
350 V	1048 G	-X:64660862 2931759205 G	V
350	1049 T	-X:64660861 2931759204 T	
350	1050 G	-X:64660860 2931759203 G	
351 D	1051 G	-X:64660859 2931759202 G	D
351	1052 A	-X:64660858 2931759201 A	
351	1053 C	-X:64660857 2931759200 C	
352 L	1054 T	-X:64660856 2931759199 T	L
352	1055 T	-X:64660855 2931759198 T	
352	1056 G	-X:64660854 2931759197 G	
353 N	1057 A	-X:64660853 2931759196 A	N
353	1058 A	-X:64660852 2931759195 A	
353	1059 T	-X:64660851 2931759194 T	
354 D	1060 G	-X:64660850 2931759193 G	D
354	1061 A	-X:64660849 2931759192 A	
354	1062 C	-X:64660848 2931759191 C	
355 V	1063 G	-X:64660847 2931759190 G	V
355	1064 T	-X:64660846 2931759189 T	
355	1065 C	-X:64660845 2931759188 C	
356 L	1066 C	-X:64660844 2931759187 C	L
356	1067 T	-X:64660843 2931759186 T	
356	1068 G	-X:64660842 2931759185 G	
357 V	1069 G	-X:64660841 2931759184 G	V
357	1070 T	-X:64660840 2931759183 T	
357	1071 G	-X:64660839 2931759182 G	
358 P	1072 C	-X:64660838 2931759181 C	P
358	1073 C	-X:64660837 2931759180 C	
358	1074 A	-X:64660836 2931759179 A	
359 K	1075 A	-X:64660835 2931759178 A	K
359	1076 A	-X:64660834 2931759177 A	
359	1077 G	-X:64660833 2931759176 G	
360 P	1078 C	-X:64660832 2931759175 C	P
360	1079 C	-X:64660831 2931759174 C	
360	1080 G	-X:64660830 2931759173 G	
361 F	1081 T	-X:64660829 2931759172 T	F
361	1082 T	-X:64660828 2931759171 T	
361	1083 C	-X:64660827 2931759170 C	
362 S	1084 T	-X:64660826 2931759169 T	S
362	1085 C	-X:64660825 2931759168 C	
362	1086 T	-X:64660824 2931759167 T	
363 Q	1087 C	-X:64660823 2931759166 C	Q
363	1088 A	-X:64660822 2931759165 A	
363	1089 G	-X:64660821 2931759164 G	
364 F	1090 T	-X:64660820 2931759163 T	F
364	1091 T	-X:64660819 2931759162 T	
364	1092 C	-X:64660818 2931759161 C	
365 W	1093 T	-X:64660817 2931759160 T	W
365	1094 G	-X:64660816 2931759159 G	
365	1095 G	-X:64660815 2931759158 G	
366 Q	1096 C	-X:64660814 2931759157 C	Q
366	1097 A	-X:64660813 2931759156 A	
366	1098 G	-X:64660812 2931759155 G	
367 P	1099 C	-X:64660811 2931759154 C	P
367	1100 C	-X:64660810 2931759153 C	
367	1101 C	-X:64660809 2931759152 C	
368 L	1102 C	-X:64660808 2931759151 C	L
368	1103 T	-X:64660807 2931759150 T	
368	1104 G	-X:64660806 2931759149 G	
369 L	1105 C	-X:64660805 2931759148 C	L
369	1106 T	-X:64660804 2931759147 T	
369	1107 C	-X:64660803 2931759146 C	
370 R	1108 A	-X:64660802 2931759145 A	R
370	1109 G	-X:64660801 2931759144 G	
370	1110 G	-X:64660800 2931759143 G	
371 G	1111 G	-X:64660799 2931759142 G	G
371	1112 G	-X:64660798 2931759141 G	
371	1113 C	-X:64660797 2931759140 C	
372 L	1114 C	-X:64660796 2931759139 C	L
372	1115 T	-X:64660795 2931759138 T	
372	1116 G	-X:64660794 2931759137 G	
373 H	1117 C	-X:64660793 2931759136 C	H
373	1118 A	-X:64660792 2931759135 A	
373	1119 C	-X:64660791 2931759134 C	
374 S	1120 T	-X:64660790 2931759133 T	S
374	1121 C	-X:64660789 2931759132 C	
374	1122 C	-X:64660788 2931759131 C	
375 Q	1123 C	-X:64660787 2931759130 C	Q
375	1124 A	-X:64660786 2931759129 A	
375	1125 G	-X:64660785 2931759128 G	
376 N	1126 A	-X:64660784 2931759127 A	N
376	1127 A	-X:64660783 2931759126 A	
376	1128 C	-X:64660782 2931759125 C	
377 F	1129 T	-X:64660781 2931759124 T	F
377	1130 T	-X:64660780 2931759123 T	
377	1131 C	-X:64660779 2931759122 C	
378 T	1132 A	-X:64660778 2931759121 A	T
378	1133 C	-X:64660777 2931759120 C	
378	1134 G	-X:64660776 2931759119 G	
379 Q	1135 C	-X:64660775 2931759118 C	Q
379	1136 A	-X:64660774 2931759117 A	
379	1137 G	-X:64660773 2931759116 G	
380 A	1138 G	-X:64660772 2931759115 G	A
380	1139 C	-X:64660771 2931759114 C	
380	1140 C	-X:64660770 2931759113 C	
381 L	1141 C	-X:64660769 2931759112 C	L
381	1142 T	-X:64660768 2931759111 T	
381	1143 A	-X:64660767 2931759110 A	
382 L	1144 T	-X:64660766 2931759109 T	L
382	1145 T	-X:64660765 2931759108 T	
382	1146 G	-X:64660764 2931759107 G	
383 E	1147 G	-X:64660763 2931759106 G	E
383	1148 A	-X:64660762 2931759105 A	
383	1149 G	-X:64660761 2931759104 G	
384 R	1150 A	-X:64660760 2931759103 A	R
384	1151 G	-X:64660759 2931759102 G	
384	1152 G	-X:64660758 2931759101 G	
385 M	1153 A	-X:64660757 2931759100 A	M
385	1154 T	-X:64660756 2931759099 T	
385	1155 G	-X:64660755 2931759098 G	
386 L	1156 C	-X:64660754 2931759097 C	L
386	1157 T	-X:64660753 2931759096 T	
386	1158 C	-X:64660752 2931759095 C	
387 S	1159 T	-X:64660751 2931759094 T	S
387	1160 C	-X:64660750 2931759093 C	
387	1161 T	-X:64660749 2931759092 T	
388 E	1162 G	-X:64660748 2931759091 G	E
388	1163 A	-X:64660747 2931759090 A	
388	1164 A	-X:64660746 2931759089 A	
389 L	1165 C	-X:64660745 2931759088 C	L
389	1166 T	-X:64660744 2931759087 T	
389	1167 G	-X:64660743 2931759086 G	
390 P	1168 C	-X:64660742 2931759085 C	P
390	1169 C	-X:64660741 2931759084 C	
390	1170 A	-X:64660740 2931759083 A	
391 A	1171 G	-X:64660739 2931759082 G	A
391	1172 C	-X:64660738 2931759081 C	
391	1173 C	-X:64660737 2931759080 C	
392 L	1174 T	-X:64660736 2931759079 T	L
392	1175 T	-X:64660735 2931759078 T	
392	1176 G	-X:64660734 2931759077 G	
393 G	1177 G	-X:64660733 2931759076 G	G
393	1178 G	-X:64660732 2931759075 G	
393	1179 G	-X:64660731 2931759074 G	
394 I	1180 A	-X:64660730 2931759073 A	I
394	1181 T	-X:64660729 2931759072 T	
394	1182 C	-X:64660728 2931759071 C	
395 S	1183 A	-X:64660727 2931759070 A	S
395	1184 G	-X:64660726 2931759069 G	
395	1185 C	-X:64660725 2931759068 C	
396 G	1186 G	-X:64660724 2931759067 G	G
396	1187 G	-X:64660723 2931759066 G	
396	1188 G	-X:64660722 2931759065 G	
397 I	1189 A	-X:64660721 2931759064 A	I
397	1190 T	-X:64660720 2931759063 T	
397	1191 C	-X:64660719 2931759062 C	
398 R	1192 C	-X:64660718 2931759061 C	R
398	1193 G	-X:64660717 2931759060 G	
398	1194 G	-X:64660716 2931759059 G	
399 P	1195 C	-X:64660715 2931759058 C	P
399	1196 C	-X:64660714 2931759057 C	
399	1197 T	-X:64660713 2931759056 T	
400 T	1198 A	-X:64660712 2931759055 A	T
400	1199 C	-X:64660711 2931759054 C	
400	1200 C	-X:64660710 2931759053 C	
401 Y	1201 T	-X:64660709 2931759052 T	Y
401	1202 A	-X:64660708 2931759051 A	
401	1203 C	-X:64660707 2931759050 C	
402 I	1204 A	-X:64660706 2931759049 A	I
402	1205 T	-X:64660705 2931759048 T	
402	1206 C	-X:64660704 2931759047 C	
403 L	1207 C	-X:64660703 2931759046 C	L
403	1208 T	-X:64660702 2931759045 T	
403	1209 C	-X:64660701 2931759044 C	
404 R	1210 A	-X:64660700 2931759043 A	R
404	1211 G	-X:64660699 2931759042 G	
404	1212 A	-X:64660698 2931759041 A	
405 W	1213 T	-X:64660697 2931759040 T	W
405	1214 G	-X:64660696 2931759039 G	
405	1215 G	-X:64660695 2931759038 G	
406 T	1216 A	-X:64660694 2931759037 A	T
406	1217 C	-X:64660693 2931759036 C	
406	1218 C	-X:64660692 2931759035 C	
407 V	1219 G	-X:64660691 2931759034 G	V
407	1220 T	-X:64660690 2931759033 T	
407	1221 T	-X:64660689 2931759032 T	
408 E	1222 G	-X:64660688 2931759031 G	E
408	1223 A	-X:64660687 2931759030 A	
408	1224 A	-X:64660686 2931759029 A	
409 L	1225 C	-X:64660685 2931759028 C	L
409	1226 T	-X:64660684 2931759027 T	
409	1227 G	-X:64660683 2931759026 G	
410 I	1228 A	-X:64660682 2931759025 A	I
410	1229 T	-X:64660681 2931759024 T	
410	1230 C	-X:64660680 2931759023 C	
411 V	1231 G	-X:64660679 2931759022 G	V
411	1232 T	-X:64660678 2931759021 T	
411	1233 G	-X:64660677 2931759020 G	
412 A	1234 G	-X:64660676 2931759019 G	A
412	1235 C	-X:64660675 2931759018 C	
412	1236 C	-X:64660674 2931759017 C	
413 N	1237 A	-X:64660673 2931759016 A	N
413	1238 A	-X:64660672 2931759015 A	
413	1239 C	-X:64660671 2931759014 C	
414 T	1240 A	-X:64660670 2931759013 A	T
414	1241 C	-X:64660669 2931759012 C	
414	1242 C	-X:64660668 2931759011 C	
415 K	1243 A	-X:64660667 2931759010 A	K
415	1244 A	-X:64660666 2931759009 A	
415	1245 G	-X:64660665 2931759008 G	
416 T	1246 A	-X:64660664 2931759007 A	T
416	1247 C	-X:64660663 2931759006 C	
416	1248 T	-X:64660662 2931759005 T	
417 G	1249 G	-X:64660661 2931759004 G	G
417	1250 G	-X:64660312 2931758655 G	
417	1251 A	-X:64660311 2931758654 A	
418 R	1252 C	-X:64660310 2931758653 C	R
418	1253 G	-X:64660309 2931758652 G	
418	1254 G	-X:64660308 2931758651 G	
419 N	1255 A	-X:64660307 2931758650 A	N
419	1256 A	-X:64660306 2931758649 A	
419	1257 T	-X:64660305 2931758648 T	
420 A	1258 G	-X:64660304 2931758647 G	A
420	1259 C	-X:64660303 2931758646 C	
420	1260 T	-X:64660302 2931758645 T	
421 R	1261 C	-X:64660301 2931758644 C	R
421	1262 G	-X:64660300 2931758643 G	
421	1263 C	-X:64660299 2931758642 C	
422 R	1264 C	-X:64660298 2931758641 C	R
422	1265 G	-X:64660297 2931758640 G	
422	1266 A	-X:64660296 2931758639 A	
423 F	1267 T	-X:64660295 2931758638 T	F
423	1268 T	-X:64660294 2931758637 T	
423	1269 T	-X:64660293 2931758636 T	
424 S	1270 T	-X:64660292 2931758635 T	S
424	1271 C	-X:64660291 2931758634 C	
424	1272 T	-X:64660290 2931758633 T	
425 A	1273 G	-X:64660289 2931758632 G	A
425	1274 C	-X:64660288 2931758631 C	
425	1275 A	-X:64660287 2931758630 A	
426 G	1276 G	-X:64660286 2931758629 G	G
426	1277 G	-X:64660285 2931758628 G	
426	1278 C	-X:64660284 2931758627 C	
427 Q	1279 C	-X:64660283 2931758626 C	Q
427	1280 A	-X:64660282 2931758625 A	
427	1281 G	-X:64660281 2931758624 G	
428 W	1282 T	-X:64660280 2931758623 T	W
428	1283 G	-X:64660279 2931758622 G	
428	1284 G	-X:64660278 2931758621 G	
429 E	1285 G	-X:64660277 2931758620 G	E
429	1286 A	-X:64660276 2931758619 A	
429	1287 A	-X:64660275 2931758618 A	
430 A	1288 G	-X:64660274 2931758617 G	A
430	1289 C	-X:64660273 2931758616 C	
430	1290 A	-X:64660272 2931758615 A	
431 R	1291 A	-X:64660271 2931758614 A	R
431	1292 G	-X:64660270 2931758613 G	
431	1293 A	-X:64660269 2931758612 A	
432 R	1294 A	-X:64660268 2931758611 A	R
432	1295 G	-X:64660267 2931758610 G	
432	1296 G	-X:64660266 2931758609 G	
433 G	1297 G	-X:64660265 2931758608 G	G
433	1298 G	-X:64660264 2931758607 G	
433	1299 C	-X:64660263 2931758606 C	
434 W	1300 T	-X:64660262 2931758605 T	W
434	1301 G	-X:64660261 2931758604 G	
434	1302 G	-X:64660260 2931758603 G	
435 R	1303 A	-X:64660259 2931758602 A	R
435	1304 G	-X:64660258 2931758601 G	
435	1305 G	-X:64660257 2931758600 G	
436 L	1306 C	-X:64660256 2931758599 C	L
436	1307 T	-X:64660255 2931758598 T	
436	1308 G	-X:64660254 2931758597 G	
437 F	1309 T	-X:64660253 2931758596 T	F
437	1310 T	-X:64660252 2931758595 T	
437	1311 C	-X:64660251 2931758594 C	
438 N	1312 A	-X:64660250 2931758593 A	N
438	1313 A	-X:64660249 2931758592 A	
438	1314 C	-X:64660248 2931758591 C	
439 C	1315 T	-X:64660247 2931758590 T	C
439	1316 G	-X:64660246 2931758589 G	
439	1317 C	-X:64660245 2931758588 C	
440 S	1318 T	-X:64660244 2931758587 T	S
440	1319 C	-X:64660243 2931758586 C	
440	1320 C	-X:64660242 2931758585 C	
441 A	1321 G	-X:64660241 2931758584 G	A
441	1322 C	-X:64660240 2931758583 C	
441	1323 C	-X:64660239 2931758582 C	
442 S	1324 T	-X:64660238 2931758581 T	S
442	1325 C	-X:64660237 2931758580 C	
442	1326 C	-X:64660236 2931758579 C	
443 L	1327 C	-X:64660235 2931758578 C	L
443	1328 T	-X:64660234 2931758577 T	
443	1329 T	-X:64660233 2931758576 T	
444 D	1330 G	-X:64660232 2931758575 G	D
444	1331 A	-X:64660231 2931758574 A	
444	1332 C	-X:64660230 2931758573 C	
445 W	1333 T	-X:64660229 2931758572 T	W
445	1334 G	-X:64660228 2931758571 G	
445	1335 G	-X:64660227 2931758570 G	
446 P	1336 C	-X:64660226 2931758569 C	P
446	1337 C	-X:64660225 2931758568 C	
446	1338 C	-X:64660224 2931758567 C	
447 R	1339 C	-X:64660223 2931758566 C	R
447	1340 G	-X:64660222 2931758565 G	
447	1341 G	-X:64660221 2931758564 G	
448 M	1342 A	-X:64660220 2931758563 A	M
448	1343 T	-X:64660219 2931758562 T	
448	1344 G	-X:64660218 2931758561 G	
449 V	1345 G	-X:64660217 2931758560 G	V
449	1346 T	-X:64660216 2931758559 T	
449	1347 T	-X:64660215 2931758558 T	
450 E	1348 G	-X:64660214 2931758557 G	E
450	1349 A	-X:64660213 2931758556 A	
450	1350 G	-X:64660212 2931758555 G	
451 S	1351 T	-X:64660211 2931758554 T	S
451	1352 C	-X:64660210 2931758553 C	
451	1353 C	-X:64660209 2931758552 C	
452 C	1354 T	-X:64660208 2931758551 T	C
452	1355 G	-X:64660207 2931758550 G	
452	1356 C	-X:64660206 2931758549 C	
453 L	1357 T	-X:64660205 2931758548 T	L
453	1358 T	-X:64660204 2931758547 T	
453	1359 G	-X:64660203 2931758546 G	
454 G	1360 G	-X:64660202 2931758545 G	G
454	1361 G	-X:64660201 2931758544 G	
454	1362 C	-X:64660200 2931758543 C	
455 S	1363 T	-X:64660199 2931758542 T	S
455	1364 C	-X:64660198 2931758541 C	
455	1365 A	-X:64660197 2931758540 A	
456 P	1366 C	-X:64660196 2931758539 C	P
456	1367 C	-X:64660195 2931758538 C	
456	1368 T	-X:64660194 2931758537 T	
457 C	1369 T	-X:64660193 2931758536 T	C
457	1370 G	-X:64660192 2931758535 G	
457	1371 C	-X:64660191 2931758534 C	
458 W	1372 T	-X:64660190 2931758533 T	W
458	1373 G	-X:64660189 2931758532 G	
458	1374 G	-X:64660188 2931758531 G	
459 A	1375 G	-X:64660187 2931758530 G	A
459	1376 C	-X:64660186 2931758529 C	
459	1377 C	-X:64660185 2931758528 C	
460 S	1378 A	-X:64660184 2931758527 A	S
460	1379 G	-X:64660183 2931758526 G	
460	1380 C	-X:64660182 2931758525 C	
461 P	1381 C	-X:64660181 2931758524 C	P
461	1382 C	-X:64660180 2931758523 C	
461	1383 C	-X:64660179 2931758522 C	
462 Q	1384 C	-X:64660178 2931758521 C	Q
462	1385 A	-X:64660177 2931758520 A	
462	1386 A	-X:64660176 2931758519 A	
463 L	1387 C	-X:64660175 2931758518 C	L
463	1388 T	-X:64660174 2931758517 T	
463	1389 C	-X:64660173 2931758516 C	
464 L	1390 C	-X:64660172 2931758515 C	L
464	1391 T	-X:64660171 2931758514 T	
464	1392 T	-X:64660170 2931758513 T	
465 R	1393 C	-X:64660169 2931758512 C	R
465	1394 G	-X:64660168 2931758511 G	
465	1395 G	-X:64660167 2931758510 G	
466 I	1396 A	-X:64660166 2931758509 A	I
466	1397 T	-X:64660165 2931758508 T	
466	1398 C	-X:64655070 2931753413 C	
467 I	1399 A	-X:64655069 2931753412 A	I
467	1400 T	-X:64655068 2931753411 T	
467	1401 C	-X:64655067 2931753410 C	
468 F	1402 T	-X:64655066 2931753409 T	F
468	1403 T	-X:64655065 2931753408 T	
468	1404 C	-X:64655064 2931753407 C	
469 K	1405 A	-X:64655063 2931753406 A	K
469	1406 A	-X:64655062 2931753405 A	
469	1407 A	-X:64655061 2931753404 A	
470 A	1408 G	-X:64655060 2931753403 G	A
470	1409 C	-X:64655059 2931753402 C	
470	1410 C	-X:64655058 2931753401 C	
471 M	1411 A	-X:64655057 2931753400 A	M
471	1412 T	-X:64655056 2931753399 T	
471	1413 G	-X:64655055 2931753398 G	
472 G	1414 G	-X:64655054 2931753397 G	G
472	1415 G	-X:64655053 2931753396 G	
472	1416 G	-X:64655052 2931753395 G	
473 Q	1417 C	-X:64655051 2931753394 C	Q
473	1418 A	-X:64655050 2931753393 A	
473	1419 G	-X:64655049 2931753392 G	
474 G	1420 G	-X:64655048 2931753391 G	G
474	1421 G	-X:64655047 2931753390 G	
474	1422 C	-X:64655046 2931753389 C	
475 L	1423 C	-X:64655045 2931753388 C	L
475	1424 T	-X:64655044 2931753387 T	
475	1425 G	-X:64655043 2931753386 G	
476 P	1426 C	-X:64655042 2931753385 C	P
476	1427 C	-X:64655041 2931753384 C	
476	1428 A	-X:64655040 2931753383 A	
477 D	1429 G	-X:64655039 2931753382 G	D
477	1430 A	-X:64655038 2931753381 A	
477	1431 C	-X:64655037 2931753380 C	
478 E	1432 G	-X:64655036 2931753379 G	E
478	1433 A	-X:64655035 2931753378 A	
478	1434 G	-X:64655034 2931753377 G	
479 E	1435 G	-X:64655033 2931753376 G	E
479	1436 A	-X:64655032 2931753375 A	
479	1437 G	-X:64655031 2931753374 G	
480 Q	1438 C	-X:64655030 2931753373 C	Q
480	1439 A	-X:64655029 2931753372 A	
480	1440 G	-X:64655028 2931753371 G	
481 E	1441 G	-X:64655027 2931753370 G	E
481	1442 A	-X:64655026 2931753369 A	
481	1443 G	-X:64655025 2931753368 G	
482 K	1444 A	-X:64655024 2931753367 A	K
482	1445 A	-X:64655023 2931753366 A	
482	1446 G	-X:64655022 2931753365 G	
483 L	1447 C	-X:64655021 2931753364 C	L
483	1448 T	-X:64655020 2931753363 T	
483	1449 G	-X:64655019 2931753362 G	
484 L	1450 C	-X:64655018 2931753361 C	L
484	1451 T	-X:64655017 2931753360 T	
484	1452 G	-X:64655016 2931753359 G	
485 R	1453 C	-X:64655015 2931753358 C	R
485	1454 G	-X:64655014 2931753357 G	
485	1455 C	-X:64655013 2931753356 C	
486 I	1456 A	-X:64655012 2931753355 A	I
486	1457 T	-X:64655011 2931753354 T	
486	1458 C	-X:64655010 2931753353 C	
487 C	1459 T	-X:64655009 2931753352 T	C
487	1460 G	-X:64655008 2931753351 G	
487	1461 T	-X:64655007 2931753350 T	
488 S	1462 T	-X:64655006 2931753349 T	S
488	1463 C	-X:64655005 2931753348 C	
488	1464 C	-X:64655004 2931753347 C	
489 I	1465 A	-X:64655003 2931753346 A	I
489	1466 T	-X:64655002 2931753345 T	
489	1467 T	-X:64655001 2931753344 T	
490 Y	1468 T	-X:64655000 2931753343 T	Y
490	1469 A	-X:64654999 2931753342 A	
490	1470 T	-X:64654998 2931753341 T	
491 T	1471 A	-X:64654997 2931753340 A	T
491	1472 C	-X:64654996 2931753339 C	
491	1473 C	-X:64654995 2931753338 C	
492 Q	1474 C	-X:64654994 2931753337 C	Q
492	1475 A	-X:64654993 2931753336 A	
492	1476 G	-X:64654992 2931753335 G	
493 S	1477 A	-X:64654991 2931753334 A	S
493	1478 G	-X:64654990 2931753333 G	
493	1479 T	-X:64654989 2931753332 T	
494 G	1480 G	-X:64654988 2931753331 G	G
494	1481 G	-X:64654987 2931753330 G	
494	1482 A	-X:64654986 2931753329 A	
495 E	1483 G	-X:64654985 2931753328 G	E
495	1484 A	-X:64654984 2931753327 A	
495	1485 A	-X:64654983 2931753326 A	
496 N	1486 A	-X:64654982 2931753325 A	N
496	1487 A	-X:64654981 2931753324 A	
496	1488 C	-X:64654980 2931753323 C	
497 S	1489 A	-X:64654979 2931753322 A	S
497	1490 G	-X:64654978 2931753321 G	
497	1491 C	-X:64654977 2931753320 C	
498 L	1492 C	-X:64654976 2931753319 C	L
498	1493 T	-X:64654975 2931753318 T	
498	1494 G	-X:64654974 2931753317 G	
499 V	1495 G	-X:64654973 2931753316 G	V
499	1496 T	-X:64654972 2931753315 T	
499	1497 G	-X:64654971 2931753314 G	
500 Q	1498 C	-X:64654970 2931753313 C	Q
500	1499 A	-X:64654969 2931753312 A	
500	1500 G	-X:64654968 2931753311 G	
501 E	1501 G	-X:64654967 2931753310 G	E
501	1502 A	-X:64654966 2931753309 A	
501	1503 G	-X:64654965 2931753308 G	
502 G	1504 G	-X:64654964 2931753307 G	G
502	1505 G	-X:64654963 2931753306 G	
502	1506 C	-X:64654962 2931753305 C	
503 S	1507 T	-X:64654961 2931753304 T	S
503	1508 C	-X:64654960 2931753303 C	
503	1509 T	-X:64654959 2931753302 T	
504 E	1510 G	-X:64654958 2931753301 G	E
504	1511 A	-X:64654957 2931753300 A	
504	1512 G	-X:64654956 2931753299 G	
505 A	1513 G	-X:64654955 2931753298 G	A
505	1514 C	-X:64654954 2931753297 C	
505	1515 C	-X:64654953 2931753296 C	
506 S	1516 T	-X:64654952 2931753295 T	S
506	1517 C	-X:64654951 2931753294 C	
506	1518 C	-X:64654950 2931753293 C	
507 P	1519 C	-X:64654949 2931753292 C	P
507	1520 C	-X:64654948 2931753291 C	
507	1521 C	-X:64654947 2931753290 C	
508 I	1522 A	-X:64654946 2931753289 A	I
508	1523 T	-X:64654945 2931753288 T	
508	1524 T	-X:64654944 2931753287 T	
509 G	1525 G	-X:64654943 2931753286 G	G
509	1526 G	-X:64654942 2931753285 G	
509	1527 G	-X:64654941 2931753284 G	
510 K	1528 A	-X:64654940 2931753283 A	K
510	1529 A	-X:64654939 2931753282 A	
510	1530 G	-X:64654938 2931753281 G	
511 S	1531 T	-X:64654937 2931753280 T	S
511	1532 C	-X:64654936 2931753279 C	
511	1533 T	-X:64654935 2931753278 T	
512 P	1534 C	-X:64654934 2931753277 C	P
512	1535 C	-X:64654933 2931753276 C	
512	1536 A	-X:64654932 2931753275 A	
513 Y	1537 T	-X:64654931 2931753274 T	Y
513	1538 A	-X:64654930 2931753273 A	
513	1539 T	-X:64654929 2931753272 T	
514 T	1540 A	-X:64654928 2931753271 A	T
514	1541 C	-X:64654927 2931753270 C	
514	1542 A	-X:64654926 2931753269 A	
515 L	1543 C	-X:64654925 2931753268 C	L
515	1544 T	-X:64654924 2931753267 T	
515	1545 A	-X:64654923 2931753266 A	
516 D	1546 G	-X:64654922 2931753265 G	D
516	1547 A	-X:64654921 2931753264 A	
516	1548 C	-X:64654920 2931753263 C	
517 S	1549 A	-X:64654919 2931753262 A	S
517	1550 G	-X:64654918 2931753261 G	
517	1551 C	-X:64654917 2931753260 C	
518 L	1552 C	-X:64654916 2931753259 C	L
518	1553 T	-X:64654915 2931753258 T	
518	1554 G	-X:64654914 2931753257 G	
519 Y	1555 T	-X:64654913 2931753256 T	Y
519	1556 A	-X:64654912 2931753255 A	
519	1557 T	-X:64654911 2931753254 T	
520 W	1558 T	-X:64654910 2931753253 T	W
520	1559 G	-X:64654909 2931753252 G	
520	1560 G	-X:64654908 2931753251 G	
521 S	1561 A	-X:64654907 2931753250 A	S
521	1562 G	-X:64654906 2931753249 G	
521	1563 C	-X:64654905 2931753248 C	
522 V	1564 G	-X:64654904 2931753247 G	V
522	1565 T	-X:64654903 2931753246 T	
522	1566 C	-X:64654902 2931753245 C	
523 K	1567 A	-X:64654901 2931753244 A	K
523	1568 A	-X:64654900 2931753243 A	
523	1569 G	-X:64654899 2931753242 G	
524 P	1570 C	-X:64654898 2931753241 C	P
524	1571 C	-X:64654897 2931753240 C	
524	1572 A	-X:64654896 2931753239 A	
525 A	1573 G	-X:64654895 2931753238 G	A
525	1574 C	-X:64654894 2931753237 C	
525	1575 C	-X:64654893 2931753236 C	
526 S	1576 A	-X:64654892 2931753235 A	S
526	1577 G	-X:64654891 2931753234 G	
526	1578 C	-X:64654890 2931753233 C	
527 S	1579 T	-X:64654889 2931753232 T	S
527	1580 C	-X:64654888 2931753231 C	
527	1581 C	-X:64654887 2931753230 C	
528 S	1582 A	-X:64654886 2931753229 A	S
528	1583 G	-X:64654885 2931753228 G	
528	1584 C	-X:64654884 2931753227 C	
529 F	1585 T	-X:64654883 2931753226 T	F
529	1586 T	-X:64654882 2931753225 T	
529	1587 C	-X:64654881 2931753224 C	
530 G	1588 G	-X:64654880 2931753223 G	G
530	1589 G	-X:64654879 2931753222 G	
530	1590 G	-X:64654878 2931753221 G	
531 S	1591 T	-X:64654877 2931753220 T	S
531	1592 C	-X:64654876 2931753219 C	
531	1593 T	-X:64654875 2931753218 T	
532 E	1594 G	-X:64654874 2931753217 G	E
532	1595 A	-X:64654873 2931753216 A	
532	1596 A	-X:64654872 2931753215 A	
533 A	1597 G	-X:64654871 2931753214 G	A
533	1598 C	-X:64654870 2931753213 C	
533	1599 A	-X:64654869 2931753212 A	
534 K	1600 A	-X:64654868 2931753211 A	K
534	1601 A	-X:64654867 2931753210 A	
534	1602 G	-X:64654866 2931753209 G	
535 A	1603 G	-X:64654865 2931753208 G	A
535	1604 C	-X:64654864 2931753207 C	
535	1605 C	-X:64654863 2931753206 C	
536 Q	1606 C	-X:64654862 2931753205 C	Q
536	1607 A	-X:64654861 2931753204 A	
536	1608 G	-X:64654860 2931753203 G	
537 Q	1609 C	-X:64654859 2931753202 C	Q
537	1610 A	-X:64654858 2931753201 A	
537	1611 A	-X:64654857 2931753200 A	
538 Q	1612 C	-X:64654856 2931753199 C	Q
538	1613 A	-X:64654855 2931753198 A	
538	1614 G	-X:64654854 2931753197 G	
539 E	1615 G	-X:64654853 2931753196 G	E
539	1616 A	-X:64654852 2931753195 A	
539	1617 G	-X:64654851 2931753194 G	
540 E	1618 G	-X:64654850 2931753193 G	E
540	1619 A	-X:64654849 2931753192 A	
540	1620 G	-X:64654848 2931753191 G	
541 Q	1621 C	-X:64654847 2931753190 C	Q
541	1622 A	-X:64654846 2931753189 A	
541	1623 G	-X:64654845 2931753188 G	
542 G	1624 G	-X:64654844 2931753187 G	G
542	1625 G	-X:64654843 2931753186 G	
542	1626 C	-X:64654842 2931753185 C	
543 S	1627 A	-X:64654841 2931753184 A	S
543	1628 G	-X:64654840 2931753183 G	
543	1629 T	-X:64654839 2931753182 T	
544 V	1630 G	-X:64654838 2931753181 G	V
544	1631 T	-X:64654837 2931753180 T	
544	1632 T	-X:64654836 2931753179 T	
545 N	1633 A	-X:64654835 2931753178 A	N
545	1634 A	-X:64654834 2931753177 A	
545	1635 T	-X:64654833 2931753176 T	
546 D	1636 G	-X:64654832 2931753175 G	D
546	1637 A	-X:64654831 2931753174 A	
546	1638 T	-X:64654830 2931753173 T	
547 V	1639 G	-X:64654829 2931753172 G	V
547	1640 T	-X:64654828 2931753171 T	
547	1641 C	-X:64654827 2931753170 C	
548 K	1642 A	-X:64654826 2931753169 A	K
548	1643 A	-X:64654825 2931753168 A	
548	1644 G	-X:64654824 2931753167 G	
549 E	1645 G	-X:64654823 2931753166 G	E
549	1646 A	-X:64654822 2931753165 A	
549	1647 A	-X:64654821 2931753164 A	
550 E	1648 G	-X:64654820 2931753163 G	E
550	1649 A	-X:64654819 2931753162 A	
550	1650 G	-X:64654818 2931753161 G	
551 E	1651 G	-X:64654817 2931753160 G	E
551	1652 A	-X:64654816 2931753159 A	
551	1653 G	-X:64654815 2931753158 G	
552 K	1654 A	-X:64654814 2931753157 A	K
552	1655 A	-X:64654813 2931753156 A	
552	1656 G	-X:64654812 2931753155 G	
553 E	1657 G	-X:64654811 2931753154 G	E
553	1658 A	-X:64654810 2931753153 A	
553	1659 G	-X:64654809 2931753152 G	
554 E	1660 G	-X:64654808 2931753151 G	E
554	1661 A	-X:64654807 2931753150 A	
554	1662 G	-X:64654806 2931753149 G	
555 K	1663 A	-X:64654805 2931753148 A	K
555	1664 A	-X:64654804 2931753147 A	
555	1665 A	-X:64654803 2931753146 A	
556 E	1666 G	-X:64654802 2931753145 G	E
556	1667 A	-X:64654801 2931753144 A	
556	1668 G	-X:64654800 2931753143 G	
557 V	1669 G	-X:64654799 2931753142 G	V
557	1670 T	-X:64654798 2931753141 T	
557	1671 C	-X:64654797 2931753140 C	
558 L	1672 T	-X:64654796 2931753139 T	L
558	1673 T	-X:64654795 2931753138 T	
558	1674 G	-X:64654794 2931753137 G	
559 P	1675 C	-X:64654793 2931753136 C	P
559	1676 C	-X:64654792 2931753135 C	
559	1677 A	-X:64654791 2931753134 A	
560 D	1678 G	-X:64654790 2931753133 G	D
560	1679 A	-X:64654789 2931753132 A	
560	1680 C	-X:64654788 2931753131 C	
561 Q	1681 C	-X:64654787 2931753130 C	Q
561	1682 A	-X:64654786 2931753129 A	
561	1683 G	-X:64654785 2931753128 G	
562 V	1684 G	-X:64654784 2931753127 G	V
562	1685 T	-X:64654783 2931753126 T	
562	1686 A	-X:64654782 2931753125 A	
563 E	1687 G	-X:64654781 2931753124 G	E
563	1688 A	-X:64654780 2931753123 A	
563	1689 G	-X:64654779 2931753122 G	
564 E	1690 G	-X:64654778 2931753121 G	E
564	1691 A	-X:64654777 2931753120 A	
564	1692 G	-X:64654776 2931753119 G	
565 E	1693 G	-X:64654775 2931753118 G	E
565	1694 A	-X:64654774 2931753117 A	
565	1695 G	-X:64654773 2931753116 G	
566 E	1696 G	-X:64654772 2931753115 G	E
566	1697 A	-X:64654771 2931753114 A	
566	1698 A	-X:64654770 2931753113 A	
567 E	1699 G	-X:64654769 2931753112 G	E
567	1700 A	-X:64654768 2931753111 A	
567	1701 A	-X:64654767 2931753110 A	
568 N	1702 A	-X:64654766 2931753109 A	N
568	1703 A	-X:64654765 2931753108 A	
568	1704 T	-X:64654764 2931753107 T	
569 D	1705 G	-X:64654763 2931753106 G	D
569	1706 A	-X:64654762 2931753105 A	
569	1707 T	-X:64654761 2931753104 T	
570 D	1708 G	-X:64654760 2931753103 G	D
570	1709 A	-X:64654759 2931753102 A	
570	1710 C	-X:64654758 2931753101 C	
571 Q	1711 C	-X:64654757 2931753100 C	Q
571	1712 A	-X:64654756 2931753099 A	
571	1713 A	-X:64654755 2931753098 A	
572 E	1714 G	-X:64654754 2931753097 G	E
572	1715 A	-X:64654753 2931753096 A	
572	1716 G	-X:64654752 2931753095 G	
573 E	1717 G	-X:64654751 2931753094 G	E
573	1718 A	-X:64654750 2931753093 A	
573	1719 G	-X:64654749 2931753092 G	
574 E	1720 G	-X:64654748 2931753091 G	E
574	1721 A	-X:64654747 2931753090 A	
574	1722 A	-X:64654746 2931753089 A	
575 E	1723 G	-X:64654745 2931753088 G	E
575	1724 A	-X:64654744 2931753087 A	
575	1725 G	-X:64654743 2931753086 G	
576 E	1726 G	-X:64654742 2931753085 G	E
576	1727 A	-X:64654741 2931753084 A	
576	1728 G	-X:64654740 2931753083 G	
577 D	1729 G	-X:64654739 2931753082 G	D
577	1730 A	-X:64654738 2931753081 A	
577	1731 T	-X:64654737 2931753080 T	
578 E	1732 G	-X:64654736 2931753079 G	E
578	1733 A	-X:64654735 2931753078 A	
578	1734 A	-X:64654734 2931753077 A	
579 D	1735 G	-X:64654733 2931753076 G	D
579	1736 A	-X:64654732 2931753075 A	
579	1737 T	-X:64654731 2931753074 T	
580 D	1738 G	-X:64654730 2931753073 G	D
580	1739 A	-X:64654729 2931753072 A	
580	1740 T	-X:64654728 2931753071 T	
581 E	1741 G	-X:64654727 2931753070 G	E
581	1742 A	-X:64654726 2931753069 A	
581	1743 A	-X:64654725 2931753068 A	
582 D	1744 G	-X:64654724 2931753067 G	D
582	1745 A	-X:64654723 2931753066 A	
582	1746 T	-X:64654722 2931753065 T	
583 D	1747 G	-X:64654721 2931753064 G	D
583	1748 A	-X:64654720 2931753063 A	
583	1749 T	-X:64654719 2931753062 T	
584 E	1750 G	-X:64654718 2931753061 G	E
584	1751 A	-X:64654717 2931753060 A	
584	1752 A	-X:64654716 2931753059 A	
585 E	1753 G	-X:64654715 2931753058 G	E
585	1754 A	-X:64654714 2931753057 A	
585	1755 G	-X:64654713 2931753056 G	
586 E	1756 G	-X:64654712 2931753055 G	E
586	1757 A	-X:64654711 2931753054 A	
586	1758 A	-X:64654710 2931753053 A	
587 D	1759 G	-X:64654709 2931753052 G	D
587	1760 A	-X:64654708 2931753051 A	
587	1761 C	-X:64654707 2931753050 C	
588 R	1762 A	-X:64654706 2931753049 A	R
588	1763 G	-X:64654705 2931753048 G	
588	1764 A	-X:64654704 2931753047 A	
589 M	1765 A	-X:64654703 2931753046 A	M
589	1766 T	-X:64654702 2931753045 T	
589	1767 G	-X:64654701 2931753044 G	
590 E	1768 G	-X:64654700 2931753043 G	E
590	1769 A	-X:64654699 2931753042 A	
590	1770 G	-X:64654698 2931753041 G	
591 V	1771 G	-X:64654697 2931753040 G	V
591	1772 T	-X:64654696 2931753039 T	
591	1773 G	-X:64654695 2931753038 G	
592 G	1774 G	-X:64654694 2931753037 G	G
592	1775 G	-X:64654693 2931753036 G	
592	1776 G	-X:64654692 2931753035 G	
593 P	1777 C	-X:64654691 2931753034 C	P
593	1778 C	-X:64654690 2931753033 C	
593	1779 T	-X:64654689 2931753032 T	
594 F	1780 T	-X:64654688 2931753031 T	F
594	1781 T	-X:64654687 2931753030 T	
594	1782 C	-X:64654686 2931753029 C	
595 S	1783 T	-X:64654685 2931753028 T	S
595	1784 C	-X:64654684 2931753027 C	
595	1785 T	-X:64654683 2931753026 T	
596 T	1786 A	-X:64654682 2931753025 A	T
596	1787 C	-X:64654681 2931753024 C	
596	1788 A	-X:64654680 2931753023 A	
597 G	1789 G	-X:64654679 2931753022 G	G
597	1790 G	-X:64654678 2931753021 G	
597	1791 G	-X:64654677 2931753020 G	
598 Q	1792 C	-X:64654676 2931753019 C	Q
598	1793 A	-X:64654675 2931753018 A	
598	1794 A	-X:64654674 2931753017 A	
599 E	1795 G	-X:64654673 2931753016 G	E
599	1796 A	-X:64654672 2931753015 A	
599	1797 G	-X:64654671 2931753014 G	
600 S	1798 T	-X:64654670 2931753013 T	S
600	1799 C	-X:64654669 2931753012 C	
600	1800 C	-X:64654668 2931753011 C	
601 P	1801 C	-X:64654667 2931753010 C	P
601	1802 C	-X:64654666 2931753009 C	
601	1803 C	-X:64654665 2931753008 C	
602 T	1804 A	-X:64654664 2931753007 A	T
602	1805 C	-X:64654663 2931753006 C	
602	1806 T	-X:64654662 2931753005 T	
603 A	1807 G	-X:64654661 2931753004 G	A
603	1808 C	-X:64654660 2931753003 C	
603	1809 C	-X:64654659 2931753002 C	
604 E	1810 G	-X:64654658 2931753001 G	E
604	1811 A	-X:64654657 2931753000 A	
604	1812 G	-X:64654656 2931752999 G	
605 N	1813 A	-X:64654655 2931752998 A	N
605	1814 A	-X:64654654 2931752997 A	
605	1815 T	-X:64654653 2931752996 T	
606 A	1816 G	-X:64654652 2931752995 G	A
606	1817 C	-X:64654651 2931752994 C	
606	1818 T	-X:64654650 2931752993 T	
607 R	1819 A	-X:64654649 2931752992 A	R
607	1820 G	-X:64654648 2931752991 G	
607	1821 G	-X:64654647 2931752990 G	
608 L	1822 C	-X:64654646 2931752989 C	L
608	1823 T	-X:64654645 2931752988 T	
608	1824 T	-X:64654644 2931752987 T	
609 L	1825 C	-X:64654643 2931752986 C	L
609	1826 T	-X:64654642 2931752985 T	
609	1827 G	-X:64654641 2931752984 G	
610 A	1828 G	-X:64654640 2931752983 G	A
610	1829 C	-X:64654639 2931752982 C	
610	1830 C	-X:64654638 2931752981 C	
611 Q	1831 C	-X:64654637 2931752980 C	Q
611	1832 A	-X:64654636 2931752979 A	
611	1833 G	-X:64654635 2931752978 G	
612 K	1834 A	-X:64654634 2931752977 A	K
612	1835 A	-X:64654633 2931752976 A	
612	1836 A	-X:64654632 2931752975 A	
613 R	1837 A	-X:64654631 2931752974 A	R
613	1838 G	-X:64654630 2931752973 G	
613	1839 A	-X:64654629 2931752972 A	
614 G	1840 G	-X:64654628 2931752971 G	G
614	1841 G	-X:64654627 2931752970 G	
614	1842 A	-X:64654626 2931752969 A	
615 A	1843 G	-X:64654625 2931752968 G	A
615	1844 C	-X:64654624 2931752967 C	
615	1845 T	-X:64654623 2931752966 T	
616 L	1846 T	-X:64654622 2931752965 T	L
616	1847 T	-X:64654621 2931752964 T	
616	1848 G	-X:64654620 2931752963 G	
617 Q	1849 C	-X:64654619 2931752962 C	Q
617	1850 A	-X:64654618 2931752961 A	
617	1851 G	-X:64654617 2931752960 G	
618 G	1852 G	-X:64654616 2931752959 G	G
618	1853 G	-X:64654615 2931752958 G	
618	1854 C	-X:64654614 2931752957 C	
619 S	1855 T	-X:64654613 2931752956 T	S
619	1856 C	-X:64654612 2931752955 C	
619	1857 T	-X:64654611 2931752954 T	
620 A	1858 G	-X:64654610 2931752953 G	A
620	1859 C	-X:64654609 2931752952 C	
620	1860 A	-X:64654608 2931752951 A	
621 W	1861 T	-X:64654607 2931752950 T	W
621	1862 G	-X:64654606 2931752949 G	
621	1863 G	-X:64654605 2931752948 G	
622 Q	1864 C	-X:64654604 2931752947 C	Q
622	1865 A	-X:64654603 2931752946 A	
622	1866 G	-X:64654602 2931752945 G	
623 V	1867 G	-X:64654601 2931752944 G	V
623	1868 T	-X:64654600 2931752943 T	
623	1869 T	-X:64654599 2931752942 T	
624 S	1870 A	-X:64654598 2931752941 A	S
624	1871 G	-X:64654597 2931752940 G	
624	1872 C	-X:64654596 2931752939 C	
625 S	1873 T	-X:64654595 2931752938 T	S
625	1874 C	-X:64654594 2931752937 C	
625	1875 A	-X:64654593 2931752936 A	
626 E	1876 G	-X:64654592 2931752935 G	E
626	1877 A	-X:64651578 2931749921 A	
626	1878 A	-X:64651577 2931749920 A	
627 D	1879 G	-X:64651576 2931749919 G	D
627	1880 A	-X:64651575 2931749918 A	
627	1881 C	-X:64651574 2931749917 C	
628 V	1882 G	-X:64651573 2931749916 G	V
628	1883 T	-X:64651572 2931749915 T	
628	1884 G	-X:64651571 2931749914 G	
629 R	1885 C	-X:64651570 2931749913 C	R
629	1886 G	-X:64651569 2931749912 G	
629	1887 A	-X:64651568 2931749911 A	
630 W	1888 T	-X:64651567 2931749910 T	W
630	1889 G	-X:64651566 2931749909 G	
630	1890 G	-X:64651565 2931749908 G	
631 D	1891 G	-X:64651564 2931749907 G	D
631	1892 A	-X:64651563 2931749906 A	
631	1893 C	-X:64651562 2931749905 C	
632 T	1894 A	-X:64651561 2931749904 A	T
632	1895 C	-X:64651560 2931749903 C	
632	1896 A	-X:64651559 2931749902 A	
633 F	1897 T	-X:64651558 2931749901 T	F
633	1898 T	-X:64651557 2931749900 T	
633	1899 T	-X:64651556 2931749899 T	
634 P	1900 C	-X:64651555 2931749898 C	P
634	1901 C	-X:64651554 2931749897 C	
634	1902 C	-X:64651553 2931749896 C	
635 L	1903 C	-X:64651552 2931749895 C	L
635	1904 T	-X:64651551 2931749894 T	
635	1905 A	-X:64651550 2931749893 A	
636 G	1906 G	-X:64651549 2931749892 G	G
636	1907 G	-X:64651548 2931749891 G	
636	1908 C	-X:64651547 2931749890 C	
637 R	1909 C	-X:64651546 2931749889 C	R
637	1910 G	-X:64651545 2931749888 G	
637	1911 A	-X:64651544 2931749887 A	
638 M	1912 A	-X:64651543 2931749886 A	M
638	1913 T	-X:64651542 2931749885 T	
638	1914 G	-X:64651541 2931749884 G	
639 P	1915 C	-X:64651540 2931749883 C	P
639	1916 C	-X:64651539 2931749882 C	
639	1917 A	-X:64651538 2931749881 A	
640 G	1918 G	-X:64651537 2931749880 G	G
640	1919 G	-X:64651536 2931749879 G	
640	1920 T	-X:64651535 2931749878 T	
641 Q	1921 C	-X:64651534 2931749877 C	Q
641	1922 A	-X:64651533 2931749876 A	
641	1923 G	-X:64651532 2931749875 G	
642 T	1924 A	-X:64651531 2931749874 A	T
642	1925 C	-X:64651530 2931749873 C	
642	1926 C	-X:64651529 2931749872 C	
643 E	1927 G	-X:64651528 2931749871 G	E
643	1928 A	-X:64651527 2931749870 A	
643	1929 G	-X:64651526 2931749869 G	
644 D	1930 G	-X:64651525 2931749868 G	D
644	1931 A	-X:64651524 2931749867 A	
644	1932 C	-X:64651523 2931749866 C	
645 P	1933 C	-X:64651522 2931749865 C	P
645	1934 C	-X:64651521 2931749864 C	
645	1935 A	-X:64651520 2931749863 A	
646 A	1936 G	-X:64651519 2931749862 G	A
646	1937 C	-X:64651518 2931749861 C	
646	1938 A	-X:64651517 2931749860 A	
647 E	1939 G	-X:64651516 2931749859 G	E
647	1940 A	-X:64651515 2931749858 A	
647	1941 G	-X:64651514 2931749857 G	
648 L	1942 C	-X:64651513 2931749856 C	L
648	1943 T	-X:64651512 2931749855 T	
648	1944 C	-X:64651511 2931749854 C	
649 M	1945 A	-X:64651510 2931749853 A	M
649	1946 T	-X:64651509 2931749852 T	
649	1947 G	-X:64651508 2931749851 G	
650 L	1948 C	-X:64651507 2931749850 C	L
650	1949 T	-X:64651506 2931749849 T	
650	1950 G	-X:64651505 2931749848 G	
651 E	1951 G	-X:64651504 2931749847 G	E
651	1952 A	-X:64651503 2931749846 A	
651	1953 G	-X:64651502 2931749845 G	
652 N	1954 A	-X:64651501 2931749844 A	N
652	1955 A	-X:64651500 2931749843 A	
652	1956 T	-X:64651499 2931749842 T	
653 Y	1957 T	-X:64651498 2931749841 T	Y
653	1958 A	-X:64651497 2931749840 A	
653	1959 T	-X:64651496 2931749839 T	
654 D	1960 G	-X:64651495 2931749838 G	D
654	1961 A	-X:64651494 2931749837 A	
654	1962 C	-X:64651493 2931749836 C	
655 T	1963 A	-X:64651492 2931749835 A	T
655	1964 C	-X:64651491 2931749834 C	
655	1965 C	-X:64651490 2931749833 C	
656 M	1966 A	-X:64651489 2931749832 A	M
656	1967 T	-X:64651488 2931749831 T	
656	1968 G	-X:64651487 2931749830 G	
657 Y	1969 T	-X:64651486 2931749829 T	Y
657	1970 A	-X:64651485 2931749828 A	
657	1971 T	-X:64651484 2931749827 T	
658 L	1972 C	-X:64651483 2931749826 C	L
658	1973 T	-X:64651482 2931749825 T	
658	1974 T	-X:64651481 2931749824 T	
659 L	1975 T	-X:64651480 2931749823 T	L
659	1976 T	-X:64651479 2931749822 T	
659	1977 G	-X:64651478 2931749821 G	
660 D	1978 G	-X:64651477 2931749820 G	D
660	1979 A	-X:64651476 2931749819 A	
660	1980 C	-X:64651475 2931749818 C	
661 Q	1981 C	-X:64651474 2931749817 C	Q
661	1982 A	-X:64651473 2931749816 A	
661	1983 G	-X:64651472 2931749815 G	
662 P	1984 C	-X:64651471 2931749814 C	P
662	1985 C	-X:64651470 2931749813 C	
662	1986 T	-X:64651469 2931749812 T	
663 V	1987 G	-X:64651468 2931749811 G	V
663	1988 T	-X:64651467 2931749810 T	
663	1989 G	-X:64651466 2931749809 G	
664 L	1990 C	-X:64651465 2931749808 C	L
664	1991 T	-X:64651464 2931749807 T	
664	1992 A	-X:64651463 2931749806 A	
665 E	1993 G	-X:64651462 2931749805 G	E
665	1994 A	-X:64651461 2931749804 A	
665	1995 G	-X:64651460 2931749803 G	
666 Q	1996 C	-X:64651459 2931749802 C	Q
666	1997 A	-X:64651458 2931749801 A	
666	1998 G	-X:64651457 2931749800 G	
667 R	1999 C	-X:64651456 2931749799 C	R
667	2000 G	-X:64651455 2931749798 G	
667	2001 G	-X:64651454 2931749797 G	
668 L	2002 C	-X:64651453 2931749796 C	L
668	2003 T	-X:64651452 2931749795 T	
668	2004 G	-X:64651451 2931749794 G	
669 E	2005 G	-X:64651450 2931749793 G	E
669	2006 A	-X:64651449 2931749792 A	
669	2007 A	-X:64651448 2931749791 A	
670 P	2008 C	-X:64651447 2931749790 C	P
670	2009 C	-X:64651446 2931749789 C	
670	2010 C	-X:64651445 2931749788 C	
671 S	2011 T	-X:64651444 2931749787 T	S
671	2012 C	-X:64651443 2931749786 C	
671	2013 A	-X:64651442 2931749785 A	
672 T	2014 A	-X:64651441 2931749784 A	T
672	2015 C	-X:64651440 2931749783 C	
672	2016 A	-X:64651439 2931749782 A	
673 C	2017 T	-X:64651438 2931749781 T	C
673	2018 G	-X:64651437 2931749780 G	
673	2019 C	-X:64651436 2931749779 C	
674 K	2020 A	-X:64651435 2931749778 A	K
674	2021 A	-X:64651434 2931749777 A	
674	2022 G	-X:64651433 2931749776 G	
675 T	2023 A	-X:64651432 2931749775 A	T
675	2024 C	-X:64651431 2931749774 C	
675	2025 T	-X:64651430 2931749773 T	
>ENSP00000360454 
164 L	490 C	+6:46215769 1107714393 C	L
164	491 T	+6:46215770 1107714394 T	
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165	494 A	+6:46215773 1107714397 A	
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166	497 A	+6:46215776 1107714400 A	
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167	500 T	+6:46215779 1107714403 T	
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168	503 C	+6:46215782 1107714406 C	
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169	506 T	+6:46215785 1107714409 T	
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170	509 G	+6:46215788 1107714412 G	
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171	512 T	+6:46215791 1107714415 T	
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172	515 A	+6:46215794 1107714418 A	
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173	518 A	+6:46215797 1107714421 A	
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174	521 C	+6:46215800 1107714424 C	
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176	527 C	+6:46215806 1107714430 C	
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179	536 C	+6:46215815 1107714439 C	
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180	539 T	+6:46215818 1107714442 T	
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182	545 C	+6:46215824 1107714448 C	
182	546 A	+6:46215825 1107714449 A	
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183	548 T	+6:46215827 1107714451 T	
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184	551 A	+6:46215830 1107714454 A	
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191	572 G	+6:46215851 1107714475 G	
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195	584 A	+6:46215863 1107714487 A	
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200	599 A	+6:46215878 1107714502 A	
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201	603 A	+6:46215882 1107714506 A	
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210	629 T	+6:46215908 1107714532 T	
210	630 A	+6:46215909 1107714533 A	
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213	638 T	+6:46215917 1107714541 T	
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214	641 T	+6:46215920 1107714544 T	
214	642 C	+6:46215921 1107714545 C	
215 G	643 G	+6:46215922 1107714546 G	G
215	644 G	+6:46215923 1107714547 G	
215	645 T	+6:46215924 1107714548 T	
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221	662 T	+6:46215941 1107714565 T	
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222	665 A	+6:46215944 1107714568 A	
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227	680 G	+6:46215959 1107714583 G	
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230	689 T	+6:46215968 1107714592 T	
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235	704 C	+6:46215983 1107714607 C	
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236	707 G	+6:46215986 1107714610 G	
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385	1155 T	+6:46219129 1107717753 T	
386 N	1156 A	+6:46219130 1107717754 A	N
386	1157 A	+6:46219131 1107717755 A	
386	1158 T	+6:46219132 1107717756 T	
387 G	1159 G	+6:46219133 1107717757 G	G
387	1160 G	+6:46219134 1107717758 G	
387	1161 G	+6:46219135 1107717759 G	
388 T	1162 A	+6:46219136 1107717760 A	T
388	1163 C	+6:46219137 1107717761 C	
388	1164 C	+6:46219138 1107717762 C	
389 F	1165 T	+6:46219139 1107717763 T	F
389	1166 T	+6:46219140 1107717764 T	
389	1167 T	+6:46219141 1107717765 T	
390 G	1168 G	+6:46219142 1107717766 G	G
390	1169 G	+6:46219143 1107717767 G	
390	1170 T	+6:46219144 1107717768 T	
391 H	1171 C	+6:46219145 1107717769 C	H
391	1172 A	+6:46219146 1107717770 A	
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392 T	1174 A	+6:46219148 1107717772 A	T
392	1175 C	+6:46219149 1107717773 C	
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393 K	1177 A	+6:46219151 1107717775 A	K
393	1178 A	+6:46219152 1107717776 A	
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394 C	1180 T	+6:46219154 1107717778 T	C
394	1181 G	+6:46219155 1107717779 G	
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395 L	1183 T	+6:46219157 1107717781 T	L
395	1184 T	+6:46219158 1107717782 T	
395	1185 G	+6:46219159 1107717783 G	
396 L	1186 T	+6:46219160 1107717784 T	L
396	1187 T	+6:46219161 1107717785 T	
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397 V	1189 G	+6:46219163 1107717787 G	V
397	1190 T	+6:46219164 1107717788 T	
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398 D	1192 G	+6:46219166 1107717790 G	D
398	1193 A	+6:46219167 1107717791 A	
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399 Q	1195 C	+6:46219169 1107717793 C	Q
399	1196 A	+6:46219170 1107717794 A	
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400 W	1198 T	+6:46219172 1107717796 T	W
400	1199 G	+6:46219173 1107717797 G	
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401 C	1201 T	+6:46219175 1107717799 T	C
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402	1205 T	+6:46219179 1107717803 T	
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403 N	1207 A	+6:46219181 1107717805 A	N
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404 L	1210 C	+6:46219184 1107717808 C	L
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406 E	1216 G	+6:46219190 1107717814 G	E
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408 I	1222 A	+6:46219196 1107717820 A	I
408	1223 T	+6:46219197 1107717821 T	
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409 A	1225 G	+6:46219199 1107717823 G	A
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410 I	1228 A	+6:46219202 1107717826 A	I
410	1229 T	+6:46219203 1107717827 T	
410	1230 T	+6:46219204 1107717828 T	
411 V	1231 G	+6:46219205 1107717829 G	V
411	1232 T	+6:46219206 1107717830 T	
411	1233 T	+6:46219207 1107717831 T	
412 I	1234 A	+6:46219208 1107717832 A	I
412	1235 T	+6:46219209 1107717833 T	
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414 S	1240 T	+6:46219214 1107717838 T	S
414	1241 C	+6:46219215 1107717839 C	
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416 L	1246 T	+6:46219220 1107717844 T	L
416	1247 T	+6:46219221 1107717845 T	
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418 L	1252 T	+6:46219226 1107717850 T	L
418	1253 T	+6:46219227 1107717851 T	
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419	1256 C	+6:46219230 1107717854 C	
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420	1259 T	+6:46219233 1107717857 T	
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421	1262 T	+6:46219236 1107717860 T	
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422 T	1264 A	+6:46219238 1107717862 A	T
422	1265 C	+6:46219239 1107717863 C	
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423 C	1267 T	+6:46219241 1107717865 T	C
423	1268 G	+6:46219242 1107717866 G	
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424	1271 T	+6:46219245 1107717869 T	
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425 I	1273 A	+6:46219247 1107717871 A	I
425	1274 T	+6:46219248 1107717872 T	
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426 I	1276 A	+6:46219250 1107717874 A	I
426	1277 T	+6:46219251 1107717875 T	
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427 I	1279 A	+6:46219253 1107717877 A	I
427	1280 T	+6:46219254 1107717878 T	
427	1281 C	+6:46219255 1107717879 C	
428 M	1282 A	+6:46219256 1107717880 A	M
428	1283 T	+6:46219257 1107717881 T	
428	1284 G	+6:46219258 1107717882 G	
429 Q	1285 C	+6:46219259 1107717883 C	Q
429	1286 A	+6:46219260 1107717884 A	
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430 N	1288 A	+6:46219262 1107717886 A	N
430	1289 A	+6:46219263 1107717887 A	
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431 R	1291 A	+6:46219265 1107717889 A	R
431	1292 G	+6:46219266 1107717890 G	
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432 L	1294 C	+6:46219268 1107717892 C	L
432	1295 T	+6:46219269 1107717893 T	
432	1296 T	+6:46219270 1107717894 T	
433 S	1297 T	+6:46219271 1107717895 T	S
433	1298 C	+6:46219272 1107717896 C	
433	1299 T	+6:46219273 1107717897 T	
434 V	1300 G	+6:46219274 1107717898 G	V
434	1301 T	+6:46219275 1107717899 T	
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435 P	1303 C	+6:46219277 1107717901 C	P
435	1304 C	+6:46219278 1107717902 C	
435	1305 T	+6:46219279 1107717903 T	
436 R	1306 C	+6:46219280 1107717904 C	R
436	1307 G	+6:46219281 1107717905 G	
436	1308 T	+6:46219282 1107717906 T	
437 P	1309 C	+6:46219283 1107717907 C	P
437	1310 C	+6:46219284 1107717908 C	
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438 F	1312 T	+6:46219286 1107717910 T	F
438	1313 T	+6:46219287 1107717911 T	
438	1314 T	+6:46219288 1107717912 T	
439 S	1315 T	+6:46219289 1107717913 T	S
439	1316 C	+6:46219290 1107717914 C	
439	1317 T	+6:46219291 1107717915 T	
440 R	1318 C	+6:46219292 1107717916 C	R
440	1319 G	+6:46219293 1107717917 G	
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441 L	1321 C	+6:46219295 1107717919 C	L
441	1322 T	+6:46219296 1107717920 T	
441	1323 T	+6:46219297 1107717921 T	
442 Q	1324 C	+6:46219298 1107717922 C	Q
442	1325 A	+6:46219299 1107717923 A	
442	1326 G	+6:46219300 1107717924 G	
443 L	1327 C	+6:46219301 1107717925 C	L
443	1328 T	+6:46219302 1107717926 T	
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444 Q	1330 C	+6:46219304 1107717928 C	Q
444	1331 A	+6:46219305 1107717929 A	
444	1332 A	+6:46219306 1107717930 A	
445 E	1333 G	+6:46219307 1107717931 G	E
445	1334 A	+6:46219308 1107717932 A	
445	1335 A	+6:46219309 1107717933 A	
446 D	1336 G	+6:46219310 1107717934 G	D
446	1337 A	+6:46219311 1107717935 A	
446	1338 T	+6:46219312 1107717936 T	
447 D	1339 G	+6:46219313 1107717937 G	D
447	1340 A	+6:46219314 1107717938 A	
447	1341 T	+6:46219315 1107717939 T	
448 D	1342 G	+6:46219316 1107717940 G	D
448	1343 A	+6:46219317 1107717941 A	
448	1344 T	+6:46219318 1107717942 T	
449 D	1345 G	+6:46219319 1107717943 G	D
449	1346 A	+6:46219320 1107717944 A	
449	1347 T	+6:46219321 1107717945 T	
450 P	1348 C	+6:46219322 1107717946 C	P
450	1349 C	+6:46219323 1107717947 C	
450	1350 T	+6:46219324 1107717948 T	
451 L	1351 T	+6:46219325 1107717949 T	L
451	1352 T	+6:46219326 1107717950 T	
451	1353 A	+6:46219327 1107717951 A	
452 I	1354 A	+6:46219328 1107717952 A	I
452	1355 T	+6:46219329 1107717953 T	
452	1356 T	+6:46219330 1107717954 T	
453 G	1357 G	+6:46219331 1107717955 G	G
453	1358 G	+6:46219332 1107717956 G	
453	1359 G	+6:46219333 1107717957 G	
>ENSP00000318066 
164 L	490 C	+6:46215769 1107714393 C	L
164	491 T	+6:46215770 1107714394 T	
164	492 A	+6:46215771 1107714395 A	
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165	494 A	+6:46215773 1107714397 A	
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167	500 T	+6:46215779 1107714403 T	
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168	503 C	+6:46215782 1107714406 C	
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169	506 T	+6:46215785 1107714409 T	
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170	509 G	+6:46215788 1107714412 G	
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171	512 T	+6:46215791 1107714415 T	
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172	515 A	+6:46215794 1107714418 A	
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173	518 A	+6:46215797 1107714421 A	
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174	521 C	+6:46215800 1107714424 C	
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178	533 T	+6:46215812 1107714436 T	
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179	536 C	+6:46215815 1107714439 C	
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180 F	538 T	+6:46215817 1107714441 T	F
180	539 T	+6:46215818 1107714442 T	
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182	545 C	+6:46215824 1107714448 C	
182	546 A	+6:46215825 1107714449 A	
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183	548 T	+6:46215827 1107714451 T	
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184	551 A	+6:46215830 1107714454 A	
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185	554 G	+6:46215833 1107714457 G	
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191	572 G	+6:46215851 1107714475 G	
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193	578 A	+6:46215857 1107714481 A	
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195	584 A	+6:46215863 1107714487 A	
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200	599 A	+6:46215878 1107714502 A	
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210	629 T	+6:46215908 1107714532 T	
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213	638 T	+6:46215917 1107714541 T	
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214	641 T	+6:46215920 1107714544 T	
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215 G	643 G	+6:46215922 1107714546 G	G
215	644 G	+6:46215923 1107714547 G	
215	645 T	+6:46215924 1107714548 T	
216 D	646 G	+6:46215925 1107714549 G	D
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217	650 T	+6:46215929 1107714553 T	
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218	653 T	+6:46215932 1107714556 T	
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219	656 A	+6:46215935 1107714559 A	
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220	659 G	+6:46215938 1107714562 G	
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222	665 A	+6:46215944 1107714568 A	
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226	677 T	+6:46215956 1107714580 T	
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227	680 G	+6:46215959 1107714583 G	
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228	683 A	+6:46215962 1107714586 A	
228	684 A	+6:46215963 1107714587 A	
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364	1091 C	+6:46219065 1107717689 C	
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365 I	1093 A	+6:46219067 1107717691 A	I
365	1094 T	+6:46219068 1107717692 T	
365	1095 T	+6:46219069 1107717693 T	
366 N	1096 A	+6:46219070 1107717694 A	N
366	1097 A	+6:46219071 1107717695 A	
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367	1100 T	+6:46219074 1107717698 T	
367	1101 T	+6:46219075 1107717699 T	
368 V	1102 G	+6:46219076 1107717700 G	V
368	1103 T	+6:46219077 1107717701 T	
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370	1109 T	+6:46219083 1107717707 T	
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377	1130 T	+6:46219104 1107717728 T	
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378	1133 T	+6:46219107 1107717731 T	
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380 L	1138 T	+6:46219112 1107717736 T	L
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383	1148 A	+6:46219122 1107717746 A	
383	1149 T	+6:46219123 1107717747 T	
384 P	1150 C	+6:46219124 1107717748 C	P
384	1151 C	+6:46219125 1107717749 C	
384	1152 C	+6:46219126 1107717750 C	
385 N	1153 A	+6:46219127 1107717751 A	N
385	1154 A	+6:46219128 1107717752 A	
385	1155 T	+6:46219129 1107717753 T	
386 N	1156 A	+6:46219130 1107717754 A	N
386	1157 A	+6:46219131 1107717755 A	
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387 G	1159 G	+6:46219133 1107717757 G	G
387	1160 G	+6:46219134 1107717758 G	
387	1161 G	+6:46219135 1107717759 G	
388 T	1162 A	+6:46219136 1107717760 A	T
388	1163 C	+6:46219137 1107717761 C	
388	1164 C	+6:46219138 1107717762 C	
389 F	1165 T	+6:46219139 1107717763 T	F
389	1166 T	+6:46219140 1107717764 T	
389	1167 T	+6:46219141 1107717765 T	
390 G	1168 G	+6:46219142 1107717766 G	G
390	1169 G	+6:46219143 1107717767 G	
390	1170 T	+6:46219144 1107717768 T	
391 H	1171 C	+6:46219145 1107717769 C	H
391	1172 A	+6:46219146 1107717770 A	
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392 T	1174 A	+6:46219148 1107717772 A	T
392	1175 C	+6:46219149 1107717773 C	
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393 K	1177 A	+6:46219151 1107717775 A	K
393	1178 A	+6:46219152 1107717776 A	
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394 C	1180 T	+6:46219154 1107717778 T	C
394	1181 G	+6:46219155 1107717779 G	
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395 L	1183 T	+6:46219157 1107717781 T	L
395	1184 T	+6:46219158 1107717782 T	
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396	1187 T	+6:46219161 1107717785 T	
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397 V	1189 G	+6:46219163 1107717787 G	V
397	1190 T	+6:46219164 1107717788 T	
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398 D	1192 G	+6:46219166 1107717790 G	D
398	1193 A	+6:46219167 1107717791 A	
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399 Q	1195 C	+6:46219169 1107717793 C	Q
399	1196 A	+6:46219170 1107717794 A	
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400 W	1198 T	+6:46219172 1107717796 T	W
400	1199 G	+6:46219173 1107717797 G	
400	1200 G	+6:46219174 1107717798 G	
401 C	1201 T	+6:46219175 1107717799 T	C
401	1202 G	+6:46219176 1107717800 G	
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402	1205 T	+6:46219179 1107717803 T	
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403 N	1207 A	+6:46219181 1107717805 A	N
403	1208 A	+6:46219182 1107717806 A	
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404 L	1210 C	+6:46219184 1107717808 C	L
404	1211 T	+6:46219185 1107717809 T	
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405 P	1213 C	+6:46219187 1107717811 C	P
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406 E	1216 G	+6:46219190 1107717814 G	E
406	1217 A	+6:46219191 1107717815 A	
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407 A	1219 G	+6:46219193 1107717817 G	A
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408 I	1222 A	+6:46219196 1107717820 A	I
408	1223 T	+6:46219197 1107717821 T	
408	1224 C	+6:46219198 1107717822 C	
409 A	1225 G	+6:46219199 1107717823 G	A
409	1226 C	+6:46219200 1107717824 C	
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410 I	1228 A	+6:46219202 1107717826 A	I
410	1229 T	+6:46219203 1107717827 T	
410	1230 T	+6:46219204 1107717828 T	
411 V	1231 G	+6:46219205 1107717829 G	V
411	1232 T	+6:46219206 1107717830 T	
411	1233 T	+6:46219207 1107717831 T	
412 I	1234 A	+6:46219208 1107717832 A	I
412	1235 T	+6:46219209 1107717833 T	
412	1236 C	+6:46219210 1107717834 C	
413 G	1237 G	+6:46219211 1107717835 G	G
413	1238 G	+6:46219212 1107717836 G	
413	1239 T	+6:46219213 1107717837 T	
414 S	1240 T	+6:46219214 1107717838 T	S
414	1241 C	+6:46219215 1107717839 C	
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415	1244 T	+6:46219218 1107717842 T	
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416 L	1246 T	+6:46219220 1107717844 T	L
416	1247 T	+6:46219221 1107717845 T	
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418 L	1252 T	+6:46219226 1107717850 T	L
418	1253 T	+6:46219227 1107717851 T	
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419 T	1255 A	+6:46219229 1107717853 A	T
419	1256 C	+6:46219230 1107717854 C	
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420	1259 T	+6:46219233 1107717857 T	
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421	1262 T	+6:46219236 1107717860 T	
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422 T	1264 A	+6:46219238 1107717862 A	T
422	1265 C	+6:46219239 1107717863 C	
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423 C	1267 T	+6:46219241 1107717865 T	C
423	1268 G	+6:46219242 1107717866 G	
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424 L	1270 C	+6:46219244 1107717868 C	L
424	1271 T	+6:46219245 1107717869 T	
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425 I	1273 A	+6:46219247 1107717871 A	I
425	1274 T	+6:46219248 1107717872 T	
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426 I	1276 A	+6:46219250 1107717874 A	I
426	1277 T	+6:46219251 1107717875 T	
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427 I	1279 A	+6:46219253 1107717877 A	I
427	1280 T	+6:46219254 1107717878 T	
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428 M	1282 A	+6:46219256 1107717880 A	M
428	1283 T	+6:46219257 1107717881 T	
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430 N	1288 A	+6:46219262 1107717886 A	N
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431 R	1291 A	+6:46219265 1107717889 A	R
431	1292 G	+6:46219266 1107717890 G	
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432 L	1294 C	+6:46219268 1107717892 C	L
432	1295 T	+6:46219269 1107717893 T	
432	1296 T	+6:46219270 1107717894 T	
433 S	1297 T	+6:46219271 1107717895 T	S
433	1298 C	+6:46219272 1107717896 C	
433	1299 T	+6:46219273 1107717897 T	
434 V	1300 G	+6:46219274 1107717898 G	V
434	1301 T	+6:46219275 1107717899 T	
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435 P	1303 C	+6:46219277 1107717901 C	P
435	1304 C	+6:46219278 1107717902 C	
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436 R	1306 C	+6:46219280 1107717904 C	R
436	1307 G	+6:46219281 1107717905 G	
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437 P	1309 C	+6:46219283 1107717907 C	P
437	1310 C	+6:46219284 1107717908 C	
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438 F	1312 T	+6:46219286 1107717910 T	F
438	1313 T	+6:46219287 1107717911 T	
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439 S	1315 T	+6:46219289 1107717913 T	S
439	1316 C	+6:46219290 1107717914 C	
439	1317 T	+6:46219291 1107717915 T	
440 R	1318 C	+6:46219292 1107717916 C	R
440	1319 G	+6:46219293 1107717917 G	
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441	1322 T	+6:46219296 1107717920 T	
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442 Q	1324 C	+6:46219298 1107717922 C	Q
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443 L	1327 C	+6:46219301 1107717925 C	L
443	1328 T	+6:46219302 1107717926 T	
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444 Q	1330 C	+6:46219304 1107717928 C	Q
444	1331 A	+6:46219305 1107717929 A	
444	1332 A	+6:46219306 1107717930 A	
445 E	1333 G	+6:46219307 1107717931 G	E
445	1334 A	+6:46219308 1107717932 A	
445	1335 A	+6:46219309 1107717933 A	
446 D	1336 G	+6:46219310 1107717934 G	D
446	1337 A	+6:46219311 1107717935 A	
446	1338 T	+6:46219312 1107717936 T	
447 D	1339 G	+6:46219313 1107717937 G	D
447	1340 A	+6:46219314 1107717938 A	
447	1341 T	+6:46219315 1107717939 T	
448 D	1342 G	+6:46219316 1107717940 G	D
448	1343 A	+6:46219317 1107717941 A	
448	1344 T	+6:46219318 1107717942 T	
449 D	1345 G	+6:46219319 1107717943 G	D
449	1346 A	+6:46219320 1107717944 A	
449	1347 T	+6:46219321 1107717945 T	
450 P	1348 C	+6:46219322 1107717946 C	P
450	1349 C	+6:46219323 1107717947 C	
450	1350 T	+6:46219324 1107717948 T	
451 L	1351 T	+6:46219325 1107717949 T	L
451	1352 T	+6:46219326 1107717950 T	
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452 I	1354 A	+6:46219328 1107717952 A	I
452	1355 T	+6:46219329 1107717953 T	
452	1356 T	+6:46219330 1107717954 T	
453 G	1357 G	+6:46219331 1107717955 G	G
453	1358 G	+6:46219332 1107717956 G	
453	1359 G	+6:46219333 1107717957 G	
>ENSP00000373232 
20 D	58 G	+3:50172129 540122997 G	D
20	59 A	+3:50172130 540122998 A	
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21	62 A	+3:50172133 540123001 A	
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22	65 T	+3:50172136 540123004 T	
22	66 C	+3:50172137 540123005 C	
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23	68 C	+3:50172139 540123007 C	
23	69 G	+3:50172140 540123008 G	
24 A	70 G	+3:50172141 540123009 G	A
24	71 C	+3:50172142 540123010 C	
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25	74 C	+3:50172145 540123013 C	
25	75 G	+3:50172146 540123014 G	
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29	86 G	+3:50172157 540123025 G	
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30	89 T	+3:50172160 540123028 T	
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31 S	91 T	+3:50172162 540123030 T	S
31	92 C	+3:50172163 540123031 C	
31	93 A	+3:50172164 540123032 A	
32 F	94 T	+3:50172165 540123033 T	F
32	95 T	+3:50172166 540123034 T	
32	96 C	+3:50172167 540123035 C	
33 K	97 A	+3:50172168 540123036 A	K
33	98 A	+3:50172169 540123037 A	
33	99 A	+3:50172170 540123038 A	
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34	101 A	+3:50186230 540137098 A	
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35	104 T	+3:50186233 540137101 T	
35	105 G	+3:50186234 540137102 G	
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36	107 A	+3:50186236 540137104 A	
36	108 G	+3:50186237 540137105 G	
37 A	109 G	+3:50186238 540137106 G	A
37	110 C	+3:50186239 540137107 C	
37	111 C	+3:50186240 540137108 C	
38 T	112 A	+3:50186241 540137109 A	T
38	113 C	+3:50186242 540137110 C	
38	114 A	+3:50186243 540137111 A	
39 G	115 G	+3:50186244 540137112 G	G
39	116 G	+3:50186245 540137113 G	
39	117 C	+3:50186246 540137114 C	
40 T	118 A	+3:50186247 540137115 A	T
40	119 C	+3:50186248 540137116 C	
40	120 C	+3:50186249 540137117 C	
41 A	121 G	+3:50186250 540137118 G	A
41	122 C	+3:50186251 540137119 C	
41	123 C	+3:50186252 540137120 C	
42 H	124 C	+3:50186253 540137121 C	H
42	125 A	+3:50186254 540137122 A	
42	126 C	+3:50186255 540137123 C	
43 F	127 T	+3:50186256 540137124 T	F
43	128 T	+3:50186257 540137125 T	
43	129 C	+3:50186258 540137126 C	
44 F	130 T	+3:50186259 540137127 T	F
44	131 T	+3:50186260 540137128 T	
44	132 C	+3:50186261 540137129 C	
45 N	133 A	+3:50186262 540137130 A	N
45	134 A	+3:50186263 540137131 A	
45	135 C	+3:50186264 540137132 C	
46 F	136 T	+3:50186265 540137133 T	F
46	137 T	+3:50186266 540137134 T	
46	138 C	+3:50186267 540137135 C	
47 L	139 C	+3:50186268 540137136 C	L
47	140 T	+3:50186269 540137137 T	
47	141 G	+3:50186270 540137138 G	
48 L	142 C	+3:50186271 540137139 C	L
48	143 T	+3:50186272 540137140 T	
48	144 C	+3:50186273 540137141 C	
49 N	145 A	+3:50186274 540137142 A	N
49	146 A	+3:50186275 540137143 A	
49	147 C	+3:50186276 540137144 C	
50 T	148 A	+3:50186277 540137145 A	T
50	149 C	+3:50186278 540137146 C	
50	150 A	+3:50186279 540137147 A	
51 T	151 A	+3:50186280 540137148 A	T
51	152 C	+3:50186281 540137149 C	
51	153 C	+3:50186282 540137150 C	
52 D	154 G	+3:50186283 540137151 G	D
52	155 A	+3:50186284 540137152 A	
52	156 C	+3:50186285 540137153 C	
53 Y	157 T	+3:50186286 540137154 T	Y
53	158 A	+3:50186287 540137155 A	
53	159 C	+3:50186288 540137156 C	
54 R	160 C	+3:50186289 540137157 C	R
54	161 G	+3:50186290 540137158 G	
54	162 A	+3:50186291 540137159 A	
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55	164 T	+3:50186293 540137161 T	
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56	167 T	+3:50186296 540137164 T	
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58	173 A	+3:50186302 540137170 A	
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59	176 A	+3:50186305 540137173 A	
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60 E	178 G	+3:50186307 540137175 G	E
60	179 A	+3:50186308 540137176 A	
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61	182 A	+3:50186311 540137179 A	
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62 H	184 C	+3:50186313 540137181 C	H
62	185 A	+3:50186314 540137182 A	
62	186 C	+3:50186315 540137183 C	
63 D	187 G	+3:50186316 540137184 G	D
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465 D	1393 G	+3:50197921 540148789 G	D
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479 F	1435 T	+3:50197963 540148831 T	F
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501 S	1501 T	+3:50198344 540149212 T	S
501	1502 C	+3:50198345 540149213 C	
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503	1508 T	+3:50198351 540149219 T	
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504 G	1510 G	+3:50198353 540149221 G	G
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505 V	1513 G	+3:50198356 540149224 G	V
505	1514 T	+3:50198357 540149225 T	
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506 T	1516 A	+3:50198359 540149227 A	T
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510	1529 T	+3:50198372 540149240 T	
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511 H	1531 C	+3:50198374 540149242 C	H
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513 C	1537 T	+3:50198380 540149248 T	C
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514 Q	1540 C	+3:50198383 540149251 C	Q
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515 A	1543 G	+3:50198386 540149254 G	A
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517 G	1549 G	+3:50198392 540149260 G	G
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518 A	1552 G	+3:50198395 540149263 G	A
518	1553 C	+3:50198396 540149264 C	
518	1554 T	+3:50198397 540149265 T	
519 A	1555 G	+3:50198398 540149266 G	A
519	1556 C	+3:50198399 540149267 C	
519	1557 C	+3:50198400 540149268 C	
520 C	1558 T	+3:50198401 540149269 T	C
520	1559 G	+3:50198402 540149270 G	
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521 A	1561 G	+3:50198404 540149272 G	A
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522 D	1564 G	+3:50198407 540149275 G	D
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523 C	1567 T	+3:50198410 540149278 T	C
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524 C	1570 T	+3:50198413 540149281 T	C
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526 A	1576 G	+3:50198419 540149287 G	A
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528 D	1582 G	+3:50198425 540149293 G	D
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529 P	1585 C	+3:50198428 540149296 C	P
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530 Y	1588 T	+3:50198431 540149299 T	Y
530	1589 A	+3:50198432 540149300 A	
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531 C	1591 T	+3:50198434 540149302 T	C
531	1592 G	+3:50198435 540149303 G	
531	1593 T	+3:50198436 540149304 T	
532 A	1594 G	+3:50198437 540149305 G	A
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533 W	1597 T	+3:50198440 540149308 T	W
533	1598 G	+3:50198441 540149309 G	
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535 G	1603 G	+3:50198446 540149314 G	G
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538 C	1612 T	+3:50198455 540149323 T	C
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539 S	1615 T	+3:50198458 540149326 T	S
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541 Y	1621 T	+3:50198464 540149332 T	Y
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542 T	1624 A	+3:50198467 540149335 A	T
542	1625 C	+3:50198468 540149336 C	
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543 A	1627 G	+3:50198470 540149338 G	A
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549 S	1645 A	+3:50198722 540149590 A	S
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551 R	1651 C	+3:50198728 540149596 C	R
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552 Q	1654 C	+3:50198731 540149599 C	Q
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553 D	1657 G	+3:50198734 540149602 G	D
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554 V	1660 G	+3:50198737 540149605 G	V
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555 R	1663 C	+3:50198740 540149608 C	R
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556 H	1666 C	+3:50198743 540149611 C	H
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557 G	1669 G	+3:50198746 540149614 G	G
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558 N	1672 A	+3:50198749 540149617 A	N
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563 C	1687 T	+3:50198764 540149632 T	C
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564 R	1690 C	+3:50198767 540149635 C	R
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565 G	1693 G	+3:50198770 540149638 G	G
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566 F	1696 T	+3:50198773 540149641 T	F
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566	1698 C	+3:50198775 540149643 C	
567 N	1699 A	+3:50198776 540149644 A	N
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568 S	1702 T	+3:50198779 540149647 T	S
568	1703 C	+3:50198780 540149648 C	
568	1704 C	+3:50198781 540149649 C	
569 N	1705 A	+3:50198782 540149650 A	N
569	1706 A	+3:50198783 540149651 A	
569	1707 T	+3:50198784 540149652 T	
570 A	1708 G	+3:50198785 540149653 G	A
570	1709 C	+3:50199050 540149918 C	
570	1710 C	+3:50199051 540149919 C	
571 N	1711 A	+3:50199052 540149920 A	N
571	1712 A	+3:50199053 540149921 A	
571	1713 C	+3:50199054 540149922 C	
572 K	1714 A	+3:50199055 540149923 A	K
572	1715 A	+3:50199056 540149924 A	
572	1716 G	+3:50199057 540149925 G	
573 N	1717 A	+3:50199058 540149926 A	N
573	1718 A	+3:50199059 540149927 A	
573	1719 T	+3:50199060 540149928 T	
574 A	1720 G	+3:50199061 540149929 G	A
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574	1722 C	+3:50199063 540149931 C	
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575	1724 T	+3:50199065 540149933 T	
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577 S	1729 T	+3:50199070 540149938 T	S
577	1730 C	+3:50199071 540149939 C	
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578 V	1732 G	+3:50199073 540149941 G	V
578	1733 T	+3:50199074 540149942 T	
578	1734 G	+3:50199075 540149943 G	
579 Q	1735 C	+3:50199076 540149944 C	Q
579	1736 A	+3:50199077 540149945 A	
579	1737 G	+3:50199078 540149946 G	
580 Y	1738 T	+3:50199079 540149947 T	Y
580	1739 A	+3:50199080 540149948 A	
580	1740 T	+3:50199081 540149949 T	
581 G	1741 G	+3:50199082 540149950 G	G
581	1742 G	+3:50199083 540149951 G	
581	1743 C	+3:50199084 540149952 C	
582 V	1744 G	+3:50199085 540149953 G	V
582	1745 T	+3:50199086 540149954 T	
582	1746 G	+3:50199087 540149955 G	
583 A	1747 G	+3:50199088 540149956 G	A
583	1748 C	+3:50199089 540149957 C	
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584 G	1750 G	+3:50199091 540149959 G	G
584	1751 G	+3:50199092 540149960 G	
584	1752 C	+3:50199093 540149961 C	
585 S	1753 A	+3:50199094 540149962 A	S
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586 A	1756 G	+3:50199097 540149965 G	A
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591	1772 G	+3:50199113 540149981 G	
591	1773 C	+3:50199114 540149982 C	
592 Q	1774 C	+3:50199115 540149983 C	Q
592	1775 A	+3:50199116 540149984 A	
592	1776 G	+3:50199117 540149985 G	
593 P	1777 C	+3:50199118 540149986 C	P
593	1778 C	+3:50199119 540149987 C	
593	1779 C	+3:50199120 540149988 C	
594 R	1780 C	+3:50199121 540149989 C	R
594	1781 G	+3:50199122 540149990 G	
594	1782 C	+3:50199123 540149991 C	
595 S	1783 T	+3:50199124 540149992 T	S
595	1784 C	+3:50199125 540149993 C	
595	1785 G	+3:50199126 540149994 G	
596 P	1786 C	+3:50199127 540149995 C	P
596	1787 C	+3:50199128 540149996 C	
596	1788 C	+3:50199129 540149997 C	
597 Q	1789 C	+3:50199130 540149998 C	Q
597	1790 A	+3:50199131 540149999 A	
597	1791 A	+3:50199132 540150000 A	
598 A	1792 G	+3:50199133 540150001 G	A
598	1793 C	+3:50199134 540150002 C	
598	1794 C	+3:50199135 540150003 C	
599 T	1795 A	+3:50199136 540150004 A	T
599	1796 C	+3:50199137 540150005 C	
599	1797 T	+3:50199138 540150006 T	
600 V	1798 G	+3:50199139 540150007 G	V
600	1799 T	+3:50199140 540150008 T	
600	1800 T	+3:50199141 540150009 T	
601 K	1801 A	+3:50199142 540150010 A	K
601	1802 A	+3:50199143 540150011 A	
601	1803 G	+3:50199144 540150012 G	
602 W	1804 T	+3:50199145 540150013 T	W
602	1805 G	+3:50199146 540150014 G	
602	1806 G	+3:50199147 540150015 G	
603 L	1807 C	+3:50199148 540150016 C	L
603	1808 T	+3:50199149 540150017 T	
603	1809 G	+3:50199150 540150018 G	
604 F	1810 T	+3:50199151 540150019 T	F
604	1811 T	+3:50199152 540150020 T	
604	1812 C	+3:50199153 540150021 C	
605 Q	1813 C	+3:50199154 540150022 C	Q
605	1814 A	+3:50199155 540150023 A	
605	1815 G	+3:50199156 540150024 G	
606 R	1816 C	+3:50199157 540150025 C	R
606	1817 G	+3:50199158 540150026 G	
606	1818 A	+3:50199159 540150027 A	
607 D	1819 G	+3:50199160 540150028 G	D
607	1820 A	+3:50199161 540150029 A	
607	1821 T	+3:50199162 540150030 T	
608 P	1822 C	+3:50199163 540150031 C	P
608	1823 C	+3:50199164 540150032 C	
608	1824 T	+3:50199165 540150033 T	
609 G	1825 G	+3:50199166 540150034 G	G
609	1826 G	+3:50199167 540150035 G	
609	1827 T	+3:50199168 540150036 T	
610 D	1828 G	+3:50199169 540150037 G	D
610	1829 A	+3:50199170 540150038 A	
610	1830 C	+3:50199171 540150039 C	
611 R	1831 C	+3:50199172 540150040 C	R
611	1832 G	+3:50199173 540150041 G	
611	1833 G	+3:50199174 540150042 G	
612 R	1834 C	+3:50199175 540150043 C	R
612	1835 G	+3:50199176 540150044 G	
612	1836 C	+3:50199177 540150045 C	
613 R	1837 C	+3:50199178 540150046 C	R
613	1838 G	+3:50199179 540150047 G	
613	1839 A	+3:50199180 540150048 A	
614 E	1840 G	+3:50199181 540150049 G	E
614	1841 A	+3:50199182 540150050 A	
614	1842 G	+3:50199183 540150051 G	
615 I	1843 A	+3:50200142 540151010 A	I
615	1844 T	+3:50200143 540151011 T	
615	1845 T	+3:50200144 540151012 T	
616 R	1846 C	+3:50200145 540151013 C	R
616	1847 G	+3:50200146 540151014 G	
616	1848 T	+3:50200147 540151015 T	
617 A	1849 G	+3:50200148 540151016 G	A
617	1850 C	+3:50200149 540151017 C	
617	1851 A	+3:50200150 540151018 A	
618 E	1852 G	+3:50200151 540151019 G	E
618	1853 A	+3:50200152 540151020 A	
618	1854 G	+3:50200153 540151021 G	
619 D	1855 G	+3:50200154 540151022 G	D
619	1856 A	+3:50200155 540151023 A	
619	1857 C	+3:50200156 540151024 C	
620 R	1858 C	+3:50200157 540151025 C	R
620	1859 G	+3:50200158 540151026 G	
620	1860 C	+3:50200159 540151027 C	
621 F	1861 T	+3:50200160 540151028 T	F
621	1862 T	+3:50200161 540151029 T	
621	1863 C	+3:50200162 540151030 C	
622 L	1864 C	+3:50200163 540151031 C	L
622	1865 T	+3:50200164 540151032 T	
622	1866 G	+3:50200165 540151033 G	
623 R	1867 C	+3:50200166 540151034 C	R
623	1868 G	+3:50200167 540151035 G	
623	1869 C	+3:50200168 540151036 C	
624 T	1870 A	+3:50200169 540151037 A	T
624	1871 C	+3:50200170 540151038 C	
624	1872 A	+3:50200171 540151039 A	
625 E	1873 G	+3:50200172 540151040 G	E
625	1874 A	+3:50200173 540151041 A	
625	1875 G	+3:50200174 540151042 G	
626 Q	1876 C	+3:50200175 540151043 C	Q
626	1877 A	+3:50200176 540151044 A	
626	1878 G	+3:50200177 540151045 G	
627 G	1879 G	+3:50200178 540151046 G	G
627	1880 G	+3:50200179 540151047 G	
627	1881 C	+3:50200180 540151048 C	
628 L	1882 T	+3:50200181 540151049 T	L
628	1883 T	+3:50200182 540151050 T	
628	1884 G	+3:50200183 540151051 G	
629 L	1885 T	+3:50200184 540151052 T	L
629	1886 T	+3:50200185 540151053 T	
629	1887 G	+3:50200186 540151054 G	
630 L	1888 C	+3:50200187 540151055 C	L
630	1889 T	+3:50200188 540151056 T	
630	1890 C	+3:50200189 540151057 C	
631 R	1891 C	+3:50200190 540151058 C	R
631	1892 G	+3:50200191 540151059 G	
631	1893 T	+3:50200192 540151060 T	
632 A	1894 G	+3:50200193 540151061 G	A
632	1895 C	+3:50200194 540151062 C	
632	1896 A	+3:50200195 540151063 A	
633 L	1897 C	+3:50200196 540151064 C	L
633	1898 T	+3:50200197 540151065 T	
633	1899 G	+3:50200198 540151066 G	
634 Q	1900 C	+3:50200199 540151067 C	Q
634	1901 A	+3:50200200 540151068 A	
634	1902 G	+3:50200201 540151069 G	
635 L	1903 C	+3:50200202 540151070 C	L
635	1904 T	+3:50200203 540151071 T	
635	1905 C	+3:50200204 540151072 C	
636 S	1906 A	+3:50200205 540151073 A	S
636	1907 G	+3:50200206 540151074 G	
636	1908 C	+3:50200207 540151075 C	
637 D	1909 G	+3:50200208 540151076 G	D
637	1910 A	+3:50200209 540151077 A	
637	1911 T	+3:50200210 540151078 T	
638 R	1912 C	+3:50200211 540151079 C	R
638	1913 G	+3:50200212 540151080 G	
638	1914 T	+3:50200213 540151081 T	
639 G	1915 G	+3:50200214 540151082 G	G
639	1916 G	+3:50200215 540151083 G	
639	1917 C	+3:50200216 540151084 C	
640 L	1918 C	+3:50200217 540151085 C	L
640	1919 T	+3:50200218 540151086 T	
640	1920 C	+3:50200219 540151087 C	
641 Y	1921 T	+3:50200220 540151088 T	Y
641	1922 A	+3:50200221 540151089 A	
641	1923 C	+3:50200222 540151090 C	
642 S	1924 T	+3:50200223 540151091 T	S
642	1925 C	+3:50200224 540151092 C	
642	1926 C	+3:50200225 540151093 C	
643 C	1927 T	+3:50200226 540151094 T	C
643	1928 G	+3:50200227 540151095 G	
643	1929 C	+3:50200228 540151096 C	
644 T	1930 A	+3:50200229 540151097 A	T
644	1931 C	+3:50200230 540151098 C	
644	1932 A	+3:50200231 540151099 A	
645 A	1933 G	+3:50200232 540151100 G	A
645	1934 C	+3:50200233 540151101 C	
645	1935 C	+3:50200234 540151102 C	
646 T	1936 A	+3:50200235 540151103 A	T
646	1937 C	+3:50200236 540151104 C	
646	1938 T	+3:50200237 540151105 T	
647 E	1939 G	+3:50200238 540151106 G	E
647	1940 A	+3:50200239 540151107 A	
647	1941 G	+3:50200240 540151108 G	
648 N	1942 A	+3:50200241 540151109 A	N
648	1943 A	+3:50200242 540151110 A	
648	1944 C	+3:50200243 540151111 C	
649 N	1945 A	+3:50200244 540151112 A	N
649	1946 A	+3:50200245 540151113 A	
649	1947 C	+3:50200246 540151114 C	
650 F	1948 T	+3:50200247 540151115 T	F
650	1949 T	+3:50200248 540151116 T	
650	1950 T	+3:50200249 540151117 T	
651 K	1951 A	+3:50200250 540151118 A	K
651	1952 A	+3:50200251 540151119 A	
651	1953 G	+3:50200252 540151120 G	
652 H	1954 C	+3:50200253 540151121 C	H
652	1955 A	+3:50200254 540151122 A	
652	1956 C	+3:50200255 540151123 C	
653 V	1957 G	+3:50200256 540151124 G	V
653	1958 T	+3:50200257 540151125 T	
653	1959 C	+3:50200258 540151126 C	
654 V	1960 G	+3:50200259 540151127 G	V
654	1961 T	+3:50200260 540151128 T	
654	1962 C	+3:50200261 540151129 C	
655 T	1963 A	+3:50200262 540151130 A	T
655	1964 C	+3:50200263 540151131 C	
655	1965 A	+3:50200264 540151132 A	
656 R	1966 C	+3:50200265 540151133 C	R
656	1967 G	+3:50200266 540151134 G	
656	1968 A	+3:50200267 540151135 A	
657 V	1969 G	+3:50200268 540151136 G	V
657	1970 T	+3:50200269 540151137 T	
657	1971 G	+3:50200270 540151138 G	
658 Q	1972 C	+3:50200271 540151139 C	Q
658	1973 A	+3:50200272 540151140 A	
658	1974 G	+3:50200273 540151141 G	
659 L	1975 C	+3:50200274 540151142 C	L
659	1976 T	+3:50200275 540151143 T	
659	1977 G	+3:50200276 540151144 G	
660 H	1978 C	+3:50200277 540151145 C	H
660	1979 A	+3:50200278 540151146 A	
660	1980 T	+3:50200279 540151147 T	
661 V	1981 G	+3:50200280 540151148 G	V
661	1982 T	+3:50200281 540151149 T	
661	1983 A	+3:50200282 540151150 A	
662 L	1984 C	+3:50200283 540151151 C	L
662	1985 T	+3:50200284 540151152 T	
662	1986 G	+3:50200285 540151153 G	
663 G	1987 G	+3:50200286 540151154 G	G
663	1988 G	+3:50200287 540151155 G	
663	1989 C	+3:50200288 540151156 C	
664 R	1990 C	+3:50200289 540151157 C	R
664	1991 G	+3:50200290 540151158 G	
664	1992 G	+3:50200291 540151159 G	
665 D	1993 G	+3:50200292 540151160 G	D
665	1994 A	+3:50200293 540151161 A	
665	1995 C	+3:50200294 540151162 C	
666 A	1996 G	+3:50200295 540151163 G	A
666	1997 C	+3:50200296 540151164 C	
666	1998 C	+3:50200297 540151165 C	
667 V	1999 G	+3:50200298 540151166 G	V
667	2000 T	+3:50200299 540151167 T	
667	2001 C	+3:50200300 540151168 C	
668 H	2002 C	+3:50200301 540151169 C	H
668	2003 A	+3:50200302 540151170 A	
668	2004 T	+3:50200303 540151171 T	
669 A	2005 G	+3:50200304 540151172 G	A
669	2006 C	+3:50200305 540151173 C	
669	2007 T	+3:50200306 540151174 T	
670 A	2008 G	+3:50200307 540151175 G	A
670	2009 C	+3:50200308 540151176 C	
670	2010 C	+3:50200309 540151177 C	
671 L	2011 C	+3:50200310 540151178 C	L
671	2012 T	+3:50200311 540151179 T	
671	2013 C	+3:50200312 540151180 C	
672 F	2014 T	+3:50200313 540151181 T	F
672	2015 T	+3:50200314 540151182 T	
672	2016 C	+3:50200315 540151183 C	
673 P	2017 C	+3:50200316 540151184 C	P
673	2018 C	+3:50200317 540151185 C	
673	2019 A	+3:50200318 540151186 A	
674 P	2020 C	+3:50200319 540151187 C	P
674	2021 C	+3:50200320 540151188 C	
674	2022 A	+3:50200321 540151189 A	
675 L	2023 C	+3:50200322 540151190 C	L
675	2024 T	+3:50200323 540151191 T	
675	2025 G	+3:50200324 540151192 G	
676 S	2026 T	+3:50200325 540151193 T	S
676	2027 C	+3:50200326 540151194 C	
676	2028 C	+3:50200327 540151195 C	
677 M	2029 A	+3:50200328 540151196 A	M
677	2030 T	+3:50200329 540151197 T	
677	2031 G	+3:50200330 540151198 G	
678 S	2032 A	+3:50200331 540151199 A	S
678	2033 G	+3:50200332 540151200 G	
678	2034 C	+3:50200333 540151201 C	
679 A	2035 G	+3:50200334 540151202 G	A
679	2036 C	+3:50200335 540151203 C	
679	2037 C	+3:50200336 540151204 C	
680 P	2038 C	+3:50200337 540151205 C	P
680	2039 C	+3:50200338 540151206 C	
680	2040 G	+3:50200339 540151207 G	
681 P	2041 C	+3:50200340 540151208 C	P
681	2042 C	+3:50200341 540151209 C	
681	2043 A	+3:50200342 540151210 A	
682 P	2044 C	+3:50200343 540151211 C	P
682	2045 C	+3:50200344 540151212 C	
682	2046 C	+3:50200345 540151213 C	
683 P	2047 C	+3:50200346 540151214 C	P
683	2048 C	+3:50200347 540151215 C	
683	2049 A	+3:50200348 540151216 A	
684 G	2050 G	+3:50200349 540151217 G	G
684	2051 G	+3:50200350 540151218 G	
684	2052 C	+3:50200351 540151219 C	
685 A	2053 G	+3:50200352 540151220 G	A
685	2054 C	+3:50200353 540151221 C	
685	2055 A	+3:50200354 540151222 A	
686 G	2056 G	+3:50200355 540151223 G	G
686	2057 G	+3:50200356 540151224 G	
686	2058 C	+3:50200357 540151225 C	
687 P	2059 C	+3:50200358 540151226 C	P
687	2060 C	+3:50200359 540151227 C	
687	2061 C	+3:50200360 540151228 C	
688 P	2062 C	+3:50200361 540151229 C	P
688	2063 C	+3:50200362 540151230 C	
688	2064 A	+3:50200363 540151231 A	
689 T	2065 A	+3:50200364 540151232 A	T
689	2066 C	+3:50200365 540151233 C	
689	2067 G	+3:50200366 540151234 G	
690 P	2068 C	+3:50200367 540151235 C	P
690	2069 C	+3:50200368 540151236 C	
690	2070 T	+3:50200369 540151237 T	
691 P	2071 C	+3:50200370 540151238 C	P
691	2072 C	+3:50200371 540151239 C	
691	2073 T	+3:50200372 540151240 T	
692 Y	2074 T	+3:50200373 540151241 T	Y
692	2075 A	+3:50200374 540151242 A	
692	2076 C	+3:50200375 540151243 C	
693 Q	2077 C	+3:50200376 540151244 C	Q
693	2078 A	+3:50200377 540151245 A	
693	2079 G	+3:50200378 540151246 G	
694 E	2080 G	+3:50200379 540151247 G	E
694	2081 A	+3:50200380 540151248 A	
694	2082 G	+3:50200381 540151249 G	
695 L	2083 T	+3:50200382 540151250 T	L
695	2084 T	+3:50200383 540151251 T	
695	2085 A	+3:50200384 540151252 A	
696 A	2086 G	+3:50200385 540151253 G	A
696	2087 C	+3:50200386 540151254 C	
696	2088 C	+3:50200387 540151255 C	
697 Q	2089 C	+3:50200388 540151256 C	Q
697	2090 A	+3:50200389 540151257 A	
697	2091 G	+3:50200390 540151258 G	
698 L	2092 C	+3:50200391 540151259 C	L
698	2093 T	+3:50200392 540151260 T	
698	2094 G	+3:50200393 540151261 G	
699 L	2095 C	+3:50200394 540151262 C	L
699	2096 T	+3:50200395 540151263 T	
699	2097 G	+3:50200396 540151264 G	
700 A	2098 G	+3:50200397 540151265 G	A
700	2099 C	+3:50200398 540151266 C	
700	2100 C	+3:50200399 540151267 C	
701 Q	2101 C	+3:50200400 540151268 C	Q
701	2102 A	+3:50200401 540151269 A	
701	2103 G	+3:50200402 540151270 G	
702 P	2104 C	+3:50200403 540151271 C	P
702	2105 C	+3:50200404 540151272 C	
702	2106 A	+3:50200405 540151273 A	
703 E	2107 G	+3:50200406 540151274 G	E
703	2108 A	+3:50200407 540151275 A	
703	2109 A	+3:50200408 540151276 A	
704 V	2110 G	+3:50200409 540151277 G	V
704	2111 T	+3:50200410 540151278 T	
704	2112 G	+3:50200411 540151279 G	
705 G	2113 G	+3:50200412 540151280 G	G
705	2114 G	+3:50200413 540151281 G	
705	2115 C	+3:50200414 540151282 C	
706 L	2116 C	+3:50200415 540151283 C	L
706	2117 T	+3:50200416 540151284 T	
706	2118 C	+3:50200417 540151285 C	
707 I	2119 A	+3:50200418 540151286 A	I
707	2120 T	+3:50200419 540151287 T	
707	2121 C	+3:50200420 540151288 C	
708 H	2122 C	+3:50200421 540151289 C	H
708	2123 A	+3:50200422 540151290 A	
708	2124 C	+3:50200423 540151291 C	
709 Q	2125 C	+3:50200424 540151292 C	Q
709	2126 A	+3:50200425 540151293 A	
709	2127 G	+3:50200426 540151294 G	
710 Y	2128 T	+3:50200427 540151295 T	Y
710	2129 A	+3:50200428 540151296 A	
710	2130 C	+3:50200429 540151297 C	
711 C	2131 T	+3:50200430 540151298 T	C
711	2132 G	+3:50200431 540151299 G	
711	2133 C	+3:50200432 540151300 C	
712 Q	2134 C	+3:50200433 540151301 C	Q
712	2135 A	+3:50200434 540151302 A	
712	2136 G	+3:50200435 540151303 G	
713 G	2137 G	+3:50200436 540151304 G	G
713	2138 G	+3:50200437 540151305 G	
713	2139 T	+3:50200438 540151306 T	
714 Y	2140 T	+3:50200439 540151307 T	Y
714	2141 A	+3:50200440 540151308 A	
714	2142 C	+3:50200441 540151309 C	
715 W	2143 T	+3:50200442 540151310 T	W
715	2144 G	+3:50200443 540151311 G	
715	2145 G	+3:50200444 540151312 G	
716 R	2146 C	+3:50200445 540151313 C	R
716	2147 G	+3:50200446 540151314 G	
716	2148 C	+3:50200447 540151315 C	
717 H	2149 C	+3:50200448 540151316 C	H
717	2150 A	+3:50200449 540151317 A	
717	2151 T	+3:50200450 540151318 T	
718 V	2152 G	+3:50200451 540151319 G	V
718	2153 T	+3:50200452 540151320 T	
718	2154 G	+3:50200453 540151321 G	
719 P	2155 C	+3:50200454 540151322 C	P
719	2156 C	+3:50200455 540151323 C	
719	2157 C	+3:50200456 540151324 C	
720 P	2158 C	+3:50200457 540151325 C	P
720	2159 C	+3:50200458 540151326 C	
720	2160 C	+3:50200459 540151327 C	
721 S	2161 A	+3:50200460 540151328 A	S
721	2162 G	+3:50200461 540151329 G	
721	2163 C	+3:50200462 540151330 C	
722 P	2164 C	+3:50200463 540151331 C	P
722	2165 C	+3:50200464 540151332 C	
722	2166 C	+3:50200465 540151333 C	
723 R	2167 A	+3:50200466 540151334 A	R
723	2168 G	+3:50200467 540151335 G	
723	2169 G	+3:50200468 540151336 G	
724 E	2170 G	+3:50200469 540151337 G	E
724	2171 A	+3:50200470 540151338 A	
724	2172 G	+3:50200471 540151339 G	
725 A	2173 G	+3:50200472 540151340 G	A
725	2174 C	+3:50200473 540151341 C	
725	2175 T	+3:50200474 540151342 T	
726 P	2176 C	+3:50200475 540151343 C	P
726	2177 C	+3:50200476 540151344 C	
726	2178 A	+3:50200477 540151345 A	
727 G	2179 G	+3:50200478 540151346 G	G
727	2180 G	+3:50200479 540151347 G	
727	2181 G	+3:50200480 540151348 G	
728 A	2182 G	+3:50200481 540151349 G	A
728	2183 C	+3:50200482 540151350 C	
728	2184 A	+3:50200483 540151351 A	
729 P	2185 C	+3:50200484 540151352 C	P
729	2186 C	+3:50200485 540151353 C	
729	2187 C	+3:50200486 540151354 C	
730 R	2188 C	+3:50200487 540151355 C	R
730	2189 G	+3:50200488 540151356 G	
730	2190 G	+3:50200489 540151357 G	
731 S	2191 T	+3:50200490 540151358 T	S
731	2192 C	+3:50200491 540151359 C	
731	2193 T	+3:50200492 540151360 T	
732 P	2194 C	+3:50200493 540151361 C	P
732	2195 C	+3:50200494 540151362 C	
732	2196 T	+3:50200495 540151363 T	
733 E	2197 G	+3:50200496 540151364 G	E
733	2198 A	+3:50200497 540151365 A	
733	2199 G	+3:50200498 540151366 G	
734 P	2200 C	+3:50200499 540151367 C	P
734	2201 C	+3:50200500 540151368 C	
734	2202 C	+3:50200501 540151369 C	
735 Q	2203 C	+3:50200502 540151370 C	Q
735	2204 A	+3:50200503 540151371 A	
735	2205 G	+3:50200504 540151372 G	
736 D	2206 G	+3:50200505 540151373 G	D
736	2207 A	+3:50200506 540151374 A	
736	2208 C	+3:50200507 540151375 C	
737 Q	2209 C	+3:50200508 540151376 C	Q
737	2210 A	+3:50200509 540151377 A	
737	2211 G	+3:50200510 540151378 G	
738 K	2212 A	+3:50200511 540151379 A	K
738	2213 A	+3:50200512 540151380 A	
738	2214 A	+3:50200513 540151381 A	
739 K	2215 A	+3:50200514 540151382 A	K
739	2216 A	+3:50200515 540151383 A	
739	2217 G	+3:50200516 540151384 G	
740 P	2218 C	+3:50200517 540151385 C	P
740	2219 C	+3:50200518 540151386 C	
740	2220 C	+3:50200519 540151387 C	
741 R	2221 C	+3:50200520 540151388 C	R
741	2222 G	+3:50200521 540151389 G	
741	2223 G	+3:50200522 540151390 G	
742 N	2224 A	+3:50200523 540151391 A	N
742	2225 A	+3:50200524 540151392 A	
742	2226 C	+3:50200525 540151393 C	
743 R	2227 C	+3:50200526 540151394 C	R
743	2228 G	+3:50200527 540151395 G	
743	2229 C	+3:50200528 540151396 C	
744 R	2230 C	+3:50200529 540151397 C	R
744	2231 G	+3:50200530 540151398 G	
744	2232 G	+3:50200531 540151399 G	
745 H	2233 C	+3:50200532 540151400 C	H
745	2234 A	+3:50200533 540151401 A	
745	2235 C	+3:50200534 540151402 C	
746 H	2236 C	+3:50200535 540151403 C	H
746	2237 A	+3:50200536 540151404 A	
746	2238 C	+3:50200537 540151405 C	
747 P	2239 C	+3:50200538 540151406 C	P
747	2240 C	+3:50200539 540151407 C	
747	2241 T	+3:50200540 540151408 T	
748 P	2242 C	+3:50200541 540151409 C	P
748	2243 C	+3:50200542 540151410 C	
748	2244 G	+3:50200543 540151411 G	
749 D	2245 G	+3:50200544 540151412 G	D
749	2246 A	+3:50200545 540151413 A	
749	2247 C	+3:50200546 540151414 C	
750 T	2248 A	+3:50200547 540151415 A	T
750	2249 C	+3:50200548 540151416 C	
750	2250 A	+3:50200549 540151417 A	
>ENSP00000002829 
37 K	109 A	+3:50186226 540137094 A	T
37	110 A	+3:50186227 540137095 C	
37	111 A	+3:50186228 540137096 A	
38 E	112 G	+3:50186229 540137097 G	E
38	113 A	+3:50186230 540137098 A	
38	114 G	+3:50186231 540137099 G	
39 L	115 C	+3:50186232 540137100 C	L
39	116 T	+3:50186233 540137101 T	
39	117 G	+3:50186234 540137102 G	
40 K	118 A	+3:50186235 540137103 A	K
40	119 A	+3:50186236 540137104 A	
40	120 G	+3:50186237 540137105 G	
41 A	121 G	+3:50186238 540137106 G	A
41	122 C	+3:50186239 540137107 C	
41	123 C	+3:50186240 540137108 C	
42 T	124 A	+3:50186241 540137109 A	T
42	125 C	+3:50186242 540137110 C	
42	126 A	+3:50186243 540137111 A	
43 G	127 G	+3:50186244 540137112 G	G
43	128 G	+3:50186245 540137113 G	
43	129 C	+3:50186246 540137114 C	
44 T	130 A	+3:50186247 540137115 A	T
44	131 C	+3:50186248 540137116 C	
44	132 C	+3:50186249 540137117 C	
45 A	133 G	+3:50186250 540137118 G	A
45	134 C	+3:50186251 540137119 C	
45	135 C	+3:50186252 540137120 C	
46 H	136 C	+3:50186253 540137121 C	H
46	137 A	+3:50186254 540137122 A	
46	138 C	+3:50186255 540137123 C	
47 F	139 T	+3:50186256 540137124 T	F
47	140 T	+3:50186257 540137125 T	
47	141 C	+3:50186258 540137126 C	
48 F	142 T	+3:50186259 540137127 T	F
48	143 T	+3:50186260 540137128 T	
48	144 C	+3:50186261 540137129 C	
49 N	145 A	+3:50186262 540137130 A	N
49	146 A	+3:50186263 540137131 A	
49	147 C	+3:50186264 540137132 C	
50 F	148 T	+3:50186265 540137133 T	F
50	149 T	+3:50186266 540137134 T	
50	150 C	+3:50186267 540137135 C	
51 L	151 C	+3:50186268 540137136 C	L
51	152 T	+3:50186269 540137137 T	
51	153 G	+3:50186270 540137138 G	
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52	155 T	+3:50186272 540137140 T	
52	156 C	+3:50186273 540137141 C	
53 N	157 A	+3:50186274 540137142 A	N
53	158 A	+3:50186275 540137143 A	
53	159 C	+3:50186276 540137144 C	
54 T	160 A	+3:50186277 540137145 A	T
54	161 C	+3:50186278 540137146 C	
54	162 A	+3:50186279 540137147 A	
55 T	163 A	+3:50186280 540137148 A	T
55	164 C	+3:50186281 540137149 C	
55	165 C	+3:50186282 540137150 C	
56 D	166 G	+3:50186283 540137151 G	D
56	167 A	+3:50186284 540137152 A	
56	168 C	+3:50186285 540137153 C	
57 Y	169 T	+3:50186286 540137154 T	Y
57	170 A	+3:50186287 540137155 A	
57	171 C	+3:50186288 540137156 C	
58 R	172 C	+3:50186289 540137157 C	R
58	173 G	+3:50186290 540137158 G	
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59	176 T	+3:50186293 540137161 T	
59	177 C	+3:50186294 540137162 C	
60 L	178 T	+3:50186295 540137163 T	L
60	179 T	+3:50186296 540137164 T	
60	180 G	+3:50186297 540137165 G	
61 L	181 C	+3:50186298 540137166 C	L
61	182 T	+3:50186299 540137167 T	
61	183 C	+3:50186300 540137168 C	
62 K	184 A	+3:50186301 540137169 A	K
62	185 A	+3:50186302 540137170 A	
62	186 G	+3:50186303 540137171 G	
63 D	187 G	+3:50186304 540137172 G	D
63	188 A	+3:50186305 540137173 A	
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64 E	190 G	+3:50186307 540137175 G	E
64	191 A	+3:50186308 540137176 A	
64	192 G	+3:50186309 540137177 G	
65 D	193 G	+3:50186310 540137178 G	D
65	194 A	+3:50186311 540137179 A	
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66 H	196 C	+3:50186313 540137181 C	H
66	197 A	+3:50186314 540137182 A	
66	198 C	+3:50186315 540137183 C	
67 D	199 G	+3:50186316 540137184 G	D
67	200 A	+3:50186317 540137185 A	
67	201 C	+3:50186318 540137186 C	
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68	203 G	+3:50186320 540137188 G	
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69	206 T	+3:50186323 540137191 T	
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70	209 A	+3:50186326 540137194 A	
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71 V	211 G	+3:50186328 540137196 G	V
71	212 T	+3:50186329 540137197 T	
71	213 G	+3:50186330 540137198 G	
72 G	214 G	+3:50186331 540137199 G	G
72	215 G	+3:50186332 540137200 G	
72	216 C	+3:50186333 540137201 C	
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73	218 G	+3:50186335 540137203 G	
73	219 C	+3:50186336 540137204 C	
74 K	220 A	+3:50186337 540137205 A	K
74	221 A	+3:50186338 540137206 A	
74	222 G	+3:50186339 540137207 G	
75 D	223 G	+3:50186340 540137208 G	D
75	224 A	+3:50186341 540137209 A	
75	225 C	+3:50186342 540137210 C	
76 Y	226 T	+3:50186343 540137211 T	Y
76	227 A	+3:50186344 540137212 A	
76	228 C	+3:50186345 540137213 C	
77 V	229 G	+3:50186346 540137214 G	V
77	230 T	+3:50186347 540137215 T	
77	231 G	+3:50186348 540137216 G	
78 L	232 C	+3:50186349 540137217 C	L
78	233 T	+3:50186350 540137218 T	
78	234 G	+3:50186351 540137219 G	
79 S	235 T	+3:50186352 540137220 T	S
79	236 C	+3:50186353 540137221 C	
79	237 C	+3:50186354 540137222 C	
80 L	238 C	+3:50186355 540137223 C	L
80	239 T	+3:50186356 540137224 T	
80	240 G	+3:50186357 540137225 G	
81 D	241 G	+3:50186358 540137226 G	D
81	242 A	+3:50186359 540137227 A	
81	243 C	+3:50186360 540137228 C	
82 L	244 C	+3:50186361 540137229 C	L
82	245 T	+3:50186362 540137230 T	
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83 H	247 C	+3:50186364 540137232 C	H
83	248 A	+3:50186365 540137233 A	
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84 D	250 G	+3:50186367 540137235 G	D
84	251 A	+3:50186368 540137236 A	
84	252 C	+3:50186369 540137237 C	
85 I	253 A	+3:50186370 540137238 A	I
85	254 T	+3:50186371 540137239 T	
85	255 C	+3:50186372 540137240 C	
86 N	256 A	+3:50186373 540137241 A	N
86	257 A	+3:50186374 540137242 A	
86	258 C	+3:50186375 540137243 C	
87 R	259 C	+3:50186376 540137244 C	R
87	260 G	+3:50186377 540137245 G	
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88 E	262 G	+3:50186379 540137247 G	E
88	263 A	+3:50186380 540137248 A	
88	264 G	+3:50186381 540137249 G	
89 P	265 C	+3:50186382 540137250 C	P
89	266 C	+3:50186383 540137251 C	
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90 L	268 C	+3:50186385 540137253 C	L
90	269 T	+3:50186386 540137254 T	
90	270 C	+3:50186387 540137255 C	
91 I	271 A	+3:50186388 540137256 A	I
91	272 T	+3:50186389 540137257 T	
91	273 T	+3:50186390 540137258 T	
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92	275 T	+3:50186490 540137358 T	
92	276 A	+3:50186491 540137359 A	
93 H	277 C	+3:50186492 540137360 C	H
93	278 A	+3:50186493 540137361 A	
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94 W	280 T	+3:50186495 540137363 T	W
94	281 G	+3:50186496 540137364 G	
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95 A	283 G	+3:50186498 540137366 G	A
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96	287 C	+3:50186502 540137370 C	
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97 S	289 T	+3:50186504 540137372 T	S
97	290 C	+3:50186505 540137373 C	
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98 P	292 C	+3:50186507 540137375 C	P
98	293 C	+3:50186508 540137376 C	
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99 Q	295 C	+3:50186510 540137378 C	Q
99	296 A	+3:50186511 540137379 A	
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100	299 G	+3:50186514 540137382 G	
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101	302 T	+3:50186517 540137385 T	
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103	308 A	+3:50186523 540137391 A	
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104 C	310 T	+3:50186525 540137393 T	C
104	311 G	+3:50186526 540137394 G	
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105	314 T	+3:50186529 540137397 T	
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106	317 T	+3:50186532 540137400 T	
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107 S	319 T	+3:50186534 540137402 T	S
107	320 C	+3:50186535 540137403 C	
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109 K	325 A	+3:50186540 540137408 A	K
109	326 A	+3:50186541 540137409 A	
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110	329 A	+3:50186544 540137412 A	
110	330 T	+3:50186545 540137413 T	
111 V	331 G	+3:50186546 540137414 G	V
111	332 T	+3:50186547 540137415 T	
111	333 C	+3:50186548 540137416 C	
112 N	334 A	+3:50186549 540137417 A	N
112	335 A	+3:50186550 540137418 A	
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113 G	337 G	+3:50186668 540137536 G	G
113	338 G	+3:50186669 540137537 G	
113	339 C	+3:50186670 540137538 C	
114 E	340 G	+3:50186671 540137539 G	E
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115 C	343 T	+3:50186674 540137542 T	C
115	344 G	+3:50186675 540137543 G	
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118 F	352 T	+3:50186683 540137551 T	F
118	353 T	+3:50186684 540137552 T	
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119 V	355 G	+3:50186686 540137554 G	V
119	356 T	+3:50186687 540137555 T	
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122	365 T	+3:50186696 540137564 T	
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125	374 G	+3:50186705 540137573 G	
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128	383 C	+3:50186714 540137582 C	
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130	389 T	+3:50186720 540137588 T	
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131	393 T	+3:50186724 540137592 T	
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132	395 T	+3:50186726 540137594 T	
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133 C	397 T	+3:50186728 540137596 T	C
133	398 G	+3:50186729 540137597 G	
133	399 C	+3:50186730 540137598 C	
134 G	400 G	+3:50186731 540137599 G	G
134	401 G	+3:50186732 540137600 G	
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135 T	403 A	+3:50186734 540137602 A	T
135	404 C	+3:50186735 540137603 C	
135	405 A	+3:50186736 540137604 A	
136 G	406 G	+3:50186737 540137605 G	G
136	407 G	+3:50186738 540137606 G	
136	408 T	+3:50186739 540137607 T	
137 A	409 G	+3:50186740 540137608 G	A
137	410 C	+3:50186741 540137609 C	
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138	413 A	+3:50186744 540137612 A	
138	414 C	+3:50186745 540137613 C	
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139	416 A	+3:50186747 540137615 A	
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140 P	418 C	+3:50186749 540137617 C	P
140	419 C	+3:50186750 540137618 C	
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141	422 T	+3:50186753 540137621 T	
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143	428 C	+3:50186759 540137627 C	
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540	1619 T	+3:50198357 540149225 T	
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541 T	1621 A	+3:50198359 540149227 A	T
541	1622 C	+3:50198360 540149228 C	
541	1623 A	+3:50198361 540149229 A	
542 H	1624 C	+3:50198362 540149230 C	H
542	1625 A	+3:50198363 540149231 A	
542	1626 C	+3:50198364 540149232 C	
543 L	1627 C	+3:50198365 540149233 C	L
543	1628 T	+3:50198366 540149234 T	
543	1629 G	+3:50198367 540149235 G	
544 S	1630 A	+3:50198368 540149236 A	S
544	1631 G	+3:50198369 540149237 G	
544	1632 C	+3:50198370 540149238 C	
545 L	1633 C	+3:50198371 540149239 C	L
545	1634 T	+3:50198372 540149240 T	
545	1635 G	+3:50198373 540149241 G	
546 H	1636 C	+3:50198374 540149242 C	H
546	1637 A	+3:50198375 540149243 A	
546	1638 C	+3:50198376 540149244 C	
547 R	1639 C	+3:50198377 540149245 C	R
547	1640 G	+3:50198378 540149246 G	
547	1641 C	+3:50198379 540149247 C	
548 C	1642 T	+3:50198380 540149248 T	C
548	1643 G	+3:50198381 540149249 G	
548	1644 C	+3:50198382 540149250 C	
549 Q	1645 C	+3:50198383 540149251 C	Q
549	1646 A	+3:50198384 540149252 A	
549	1647 G	+3:50198385 540149253 G	
550 A	1648 G	+3:50198386 540149254 G	A
550	1649 C	+3:50198387 540149255 C	
550	1650 G	+3:50198388 540149256 G	
551 Y	1651 T	+3:50198389 540149257 T	Y
551	1652 A	+3:50198390 540149258 A	
551	1653 T	+3:50198391 540149259 T	
552 G	1654 G	+3:50198392 540149260 G	G
552	1655 G	+3:50198393 540149261 G	
552	1656 G	+3:50198394 540149262 G	
553 A	1657 G	+3:50198395 540149263 G	A
553	1658 C	+3:50198396 540149264 C	
553	1659 T	+3:50198397 540149265 T	
554 A	1660 G	+3:50198398 540149266 G	A
554	1661 C	+3:50198399 540149267 C	
554	1662 C	+3:50198400 540149268 C	
555 C	1663 T	+3:50198401 540149269 T	C
555	1664 G	+3:50198402 540149270 G	
555	1665 T	+3:50198403 540149271 T	
556 A	1666 G	+3:50198404 540149272 G	A
556	1667 C	+3:50198405 540149273 C	
556	1668 T	+3:50198406 540149274 T	
557 D	1669 G	+3:50198407 540149275 G	D
557	1670 A	+3:50198408 540149276 A	
557	1671 C	+3:50198409 540149277 C	
558 C	1672 T	+3:50198410 540149278 T	C
558	1673 G	+3:50198411 540149279 G	
558	1674 C	+3:50198412 540149280 C	
559 C	1675 T	+3:50198413 540149281 T	C
559	1676 G	+3:50198414 540149282 G	
559	1677 C	+3:50198415 540149283 C	
560 L	1678 C	+3:50198416 540149284 C	L
560	1679 T	+3:50198417 540149285 T	
560	1680 T	+3:50198418 540149286 T	
561 A	1681 G	+3:50198419 540149287 G	A
561	1682 C	+3:50198420 540149288 C	
561	1683 C	+3:50198421 540149289 C	
562 R	1684 C	+3:50198422 540149290 C	R
562	1685 G	+3:50198423 540149291 G	
562	1686 G	+3:50198424 540149292 G	
563 D	1687 G	+3:50198425 540149293 G	D
563	1688 A	+3:50198426 540149294 A	
563	1689 C	+3:50198427 540149295 C	
564 P	1690 C	+3:50198428 540149296 C	P
564	1691 C	+3:50198429 540149297 C	
564	1692 T	+3:50198430 540149298 T	
565 Y	1693 T	+3:50198431 540149299 T	Y
565	1694 A	+3:50198432 540149300 A	
565	1695 C	+3:50198433 540149301 C	
566 C	1696 T	+3:50198434 540149302 T	C
566	1697 G	+3:50198435 540149303 G	
566	1698 T	+3:50198436 540149304 T	
567 A	1699 G	+3:50198437 540149305 G	A
567	1700 C	+3:50198438 540149306 C	
567	1701 C	+3:50198439 540149307 C	
568 W	1702 T	+3:50198440 540149308 T	W
568	1703 G	+3:50198441 540149309 G	
568	1704 G	+3:50198442 540149310 G	
569 D	1705 G	+3:50198443 540149311 G	D
569	1706 A	+3:50198444 540149312 A	
569	1707 T	+3:50198445 540149313 T	
570 G	1708 G	+3:50198446 540149314 G	G
570	1709 G	+3:50198447 540149315 G	
570	1710 C	+3:50198448 540149316 C	
571 Q	1711 C	+3:50198449 540149317 C	Q
571	1712 A	+3:50198450 540149318 A	
571	1713 G	+3:50198451 540149319 G	
572 A	1714 G	+3:50198452 540149320 G	A
572	1715 C	+3:50198453 540149321 C	
572	1716 C	+3:50198454 540149322 C	
573 C	1717 T	+3:50198455 540149323 T	C
573	1718 G	+3:50198456 540149324 G	
573	1719 C	+3:50198457 540149325 C	
574 S	1720 T	+3:50198458 540149326 T	S
574	1721 C	+3:50198459 540149327 C	
574	1722 C	+3:50198460 540149328 C	
575 R	1723 C	+3:50198461 540149329 C	R
575	1724 G	+3:50198462 540149330 G	
575	1725 C	+3:50198463 540149331 C	
576 Y	1726 T	+3:50198464 540149332 T	Y
576	1727 A	+3:50198465 540149333 A	
576	1728 T	+3:50198466 540149334 T	
577 T	1729 A	+3:50198467 540149335 A	T
577	1730 C	+3:50198468 540149336 C	
577	1731 A	+3:50198469 540149337 A	
578 A	1732 G	+3:50198470 540149338 G	A
578	1733 C	+3:50198471 540149339 C	
578	1734 A	+3:50198472 540149340 A	
579 S	1735 T	+3:50198473 540149341 T	S
579	1736 C	+3:50198474 540149342 C	
579	1737 C	+3:50198475 540149343 C	
580 S	1738 T	+3:50198476 540149344 T	S
580	1739 C	+3:50198477 540149345 C	
580	1740 C	+3:50198478 540149346 C	
581 K	1741 A	+3:50198479 540149347 A	K
581	1742 A	+3:50198480 540149348 A	
581	1743 G	+3:50198481 540149349 G	
582 R	1744 A	+3:50198482 540149350 A	R
582	1745 G	+3:50198483 540149351 G	
582	1746 G	+3:50198718 540149586 G	
583 R	1747 C	+3:50198719 540149587 C	R
583	1748 G	+3:50198720 540149588 G	
583	1749 G	+3:50198721 540149589 G	
584 S	1750 A	+3:50198722 540149590 A	S
584	1751 G	+3:50198723 540149591 G	
584	1752 C	+3:50198724 540149592 C	
585 R	1753 C	+3:50198725 540149593 C	R
585	1754 G	+3:50198726 540149594 G	
585	1755 C	+3:50198727 540149595 C	
586 R	1756 C	+3:50198728 540149596 C	R
586	1757 G	+3:50198729 540149597 G	
586	1758 G	+3:50198730 540149598 G	
587 Q	1759 C	+3:50198731 540149599 C	Q
587	1760 A	+3:50198732 540149600 A	
587	1761 G	+3:50198733 540149601 G	
588 D	1762 G	+3:50198734 540149602 G	D
588	1763 A	+3:50198735 540149603 A	
588	1764 C	+3:50198736 540149604 C	
589 V	1765 G	+3:50198737 540149605 G	V
589	1766 T	+3:50198738 540149606 T	
589	1767 C	+3:50198739 540149607 C	
590 R	1768 C	+3:50198740 540149608 C	R
590	1769 G	+3:50198741 540149609 G	
590	1770 G	+3:50198742 540149610 G	
591 H	1771 C	+3:50198743 540149611 C	H
591	1772 A	+3:50198744 540149612 A	
591	1773 C	+3:50198745 540149613 C	
592 G	1774 G	+3:50198746 540149614 G	G
592	1775 G	+3:50198747 540149615 G	
592	1776 A	+3:50198748 540149616 A	
593 N	1777 A	+3:50198749 540149617 A	N
593	1778 A	+3:50198750 540149618 A	
593	1779 C	+3:50198751 540149619 C	
594 P	1780 C	+3:50198752 540149620 C	P
594	1781 C	+3:50198753 540149621 C	
594	1782 C	+3:50198754 540149622 C	
595 I	1783 A	+3:50198755 540149623 A	I
595	1784 T	+3:50198756 540149624 T	
595	1785 C	+3:50198757 540149625 C	
596 R	1786 A	+3:50198758 540149626 A	R
596	1787 G	+3:50198759 540149627 G	
596	1788 G	+3:50198760 540149628 G	
597 Q	1789 C	+3:50198761 540149629 C	Q
597	1790 A	+3:50198762 540149630 A	
597	1791 G	+3:50198763 540149631 G	
598 C	1792 T	+3:50198764 540149632 T	C
598	1793 G	+3:50198765 540149633 G	
598	1794 C	+3:50198766 540149634 C	
599 R	1795 C	+3:50198767 540149635 C	R
599	1796 G	+3:50198768 540149636 G	
599	1797 T	+3:50198769 540149637 T	
600 G	1798 G	+3:50198770 540149638 G	G
600	1799 G	+3:50198771 540149639 G	
600	1800 G	+3:50198772 540149640 G	
601 F	1801 T	+3:50198773 540149641 T	F
601	1802 T	+3:50198774 540149642 T	
601	1803 C	+3:50198775 540149643 C	
602 N	1804 A	+3:50198776 540149644 A	N
602	1805 A	+3:50198777 540149645 A	
602	1806 C	+3:50198778 540149646 C	
603 S	1807 T	+3:50198779 540149647 T	S
603	1808 C	+3:50198780 540149648 C	
603	1809 C	+3:50198781 540149649 C	
604 N	1810 A	+3:50198782 540149650 A	N
604	1811 A	+3:50198783 540149651 A	
604	1812 T	+3:50198784 540149652 T	
605 A	1813 G	+3:50198785 540149653 G	A
605	1814 C	+3:50199050 540149918 C	
605	1815 C	+3:50199051 540149919 C	
606 N	1816 A	+3:50199052 540149920 A	N
606	1817 A	+3:50199053 540149921 A	
606	1818 C	+3:50199054 540149922 C	
607 K	1819 A	+3:50199055 540149923 A	K
607	1820 A	+3:50199056 540149924 A	
607	1821 G	+3:50199057 540149925 G	
608 N	1822 A	+3:50199058 540149926 A	N
608	1823 A	+3:50199059 540149927 A	
608	1824 T	+3:50199060 540149928 T	
609 A	1825 G	+3:50199061 540149929 G	A
609	1826 C	+3:50199062 540149930 C	
609	1827 C	+3:50199063 540149931 C	
610 V	1828 G	+3:50199064 540149932 G	V
610	1829 T	+3:50199065 540149933 T	
610	1830 G	+3:50199066 540149934 G	
611 E	1831 G	+3:50199067 540149935 G	E
611	1832 A	+3:50199068 540149936 A	
611	1833 G	+3:50199069 540149937 G	
612 S	1834 T	+3:50199070 540149938 T	S
612	1835 C	+3:50199071 540149939 C	
612	1836 T	+3:50199072 540149940 T	
613 V	1837 G	+3:50199073 540149941 G	V
613	1838 T	+3:50199074 540149942 T	
613	1839 G	+3:50199075 540149943 G	
614 Q	1840 C	+3:50199076 540149944 C	Q
614	1841 A	+3:50199077 540149945 A	
614	1842 G	+3:50199078 540149946 G	
615 Y	1843 T	+3:50199079 540149947 T	Y
615	1844 A	+3:50199080 540149948 A	
615	1845 T	+3:50199081 540149949 T	
616 G	1846 G	+3:50199082 540149950 G	G
616	1847 G	+3:50199083 540149951 G	
616	1848 C	+3:50199084 540149952 C	
617 V	1849 G	+3:50199085 540149953 G	V
617	1850 T	+3:50199086 540149954 T	
617	1851 G	+3:50199087 540149955 G	
618 A	1852 G	+3:50199088 540149956 G	A
618	1853 C	+3:50199089 540149957 C	
618	1854 C	+3:50199090 540149958 C	
619 G	1855 G	+3:50199091 540149959 G	G
619	1856 G	+3:50199092 540149960 G	
619	1857 C	+3:50199093 540149961 C	
620 S	1858 A	+3:50199094 540149962 A	S
620	1859 G	+3:50199095 540149963 G	
620	1860 C	+3:50199096 540149964 C	
621 A	1861 G	+3:50199097 540149965 G	A
621	1862 C	+3:50199098 540149966 C	
621	1863 A	+3:50199099 540149967 A	
622 A	1864 G	+3:50199100 540149968 G	A
622	1865 C	+3:50199101 540149969 C	
622	1866 C	+3:50199102 540149970 C	
623 F	1867 T	+3:50199103 540149971 T	F
623	1868 T	+3:50199104 540149972 T	
623	1869 C	+3:50199105 540149973 C	
624 L	1870 C	+3:50199106 540149974 C	L
624	1871 T	+3:50199107 540149975 T	
624	1872 T	+3:50199108 540149976 T	
625 E	1873 G	+3:50199109 540149977 G	E
625	1874 A	+3:50199110 540149978 A	
625	1875 G	+3:50199111 540149979 G	
626 C	1876 T	+3:50199112 540149980 T	C
626	1877 G	+3:50199113 540149981 G	
626	1878 C	+3:50199114 540149982 C	
627 Q	1879 C	+3:50199115 540149983 C	Q
627	1880 A	+3:50199116 540149984 A	
627	1881 G	+3:50199117 540149985 G	
628 P	1882 C	+3:50199118 540149986 C	P
628	1883 C	+3:50199119 540149987 C	
628	1884 C	+3:50199120 540149988 C	
629 R	1885 C	+3:50199121 540149989 C	R
629	1886 G	+3:50199122 540149990 G	
629	1887 C	+3:50199123 540149991 C	
630 S	1888 T	+3:50199124 540149992 T	S
630	1889 C	+3:50199125 540149993 C	
630	1890 G	+3:50199126 540149994 G	
631 P	1891 C	+3:50199127 540149995 C	P
631	1892 C	+3:50199128 540149996 C	
631	1893 C	+3:50199129 540149997 C	
632 Q	1894 C	+3:50199130 540149998 C	Q
632	1895 A	+3:50199131 540149999 A	
632	1896 A	+3:50199132 540150000 A	
633 A	1897 G	+3:50199133 540150001 G	A
633	1898 C	+3:50199134 540150002 C	
633	1899 C	+3:50199135 540150003 C	
634 T	1900 A	+3:50199136 540150004 A	T
634	1901 C	+3:50199137 540150005 C	
634	1902 T	+3:50199138 540150006 T	
635 V	1903 G	+3:50199139 540150007 G	V
635	1904 T	+3:50199140 540150008 T	
635	1905 T	+3:50199141 540150009 T	
636 K	1906 A	+3:50199142 540150010 A	K
636	1907 A	+3:50199143 540150011 A	
636	1908 G	+3:50199144 540150012 G	
637 W	1909 T	+3:50199145 540150013 T	W
637	1910 G	+3:50199146 540150014 G	
637	1911 G	+3:50199147 540150015 G	
638 L	1912 C	+3:50199148 540150016 C	L
638	1913 T	+3:50199149 540150017 T	
638	1914 G	+3:50199150 540150018 G	
639 F	1915 T	+3:50199151 540150019 T	F
639	1916 T	+3:50199152 540150020 T	
639	1917 C	+3:50199153 540150021 C	
640 Q	1918 C	+3:50199154 540150022 C	Q
640	1919 A	+3:50199155 540150023 A	
640	1920 G	+3:50199156 540150024 G	
641 R	1921 C	+3:50199157 540150025 C	R
641	1922 G	+3:50199158 540150026 G	
641	1923 A	+3:50199159 540150027 A	
642 D	1924 G	+3:50199160 540150028 G	D
642	1925 A	+3:50199161 540150029 A	
642	1926 T	+3:50199162 540150030 T	
643 P	1927 C	+3:50199163 540150031 C	P
643	1928 C	+3:50199164 540150032 C	
643	1929 T	+3:50199165 540150033 T	
644 G	1930 G	+3:50199166 540150034 G	G
644	1931 G	+3:50199167 540150035 G	
644	1932 T	+3:50199168 540150036 T	
645 D	1933 G	+3:50199169 540150037 G	D
645	1934 A	+3:50199170 540150038 A	
645	1935 C	+3:50199171 540150039 C	
646 R	1936 C	+3:50199172 540150040 C	R
646	1937 G	+3:50199173 540150041 G	
646	1938 G	+3:50199174 540150042 G	
647 R	1939 C	+3:50199175 540150043 C	R
647	1940 G	+3:50199176 540150044 G	
647	1941 C	+3:50199177 540150045 C	
648 R	1942 C	+3:50199178 540150046 C	R
648	1943 G	+3:50199179 540150047 G	
648	1944 A	+3:50199180 540150048 A	
649 E	1945 G	+3:50199181 540150049 G	E
649	1946 A	+3:50199182 540150050 A	
649	1947 G	+3:50199183 540150051 G	
650 I	1948 A	+3:50200142 540151010 A	I
650	1949 T	+3:50200143 540151011 T	
650	1950 T	+3:50200144 540151012 T	
651 R	1951 C	+3:50200145 540151013 C	R
651	1952 G	+3:50200146 540151014 G	
651	1953 T	+3:50200147 540151015 T	
652 A	1954 G	+3:50200148 540151016 G	A
652	1955 C	+3:50200149 540151017 C	
652	1956 A	+3:50200150 540151018 A	
653 E	1957 G	+3:50200151 540151019 G	E
653	1958 A	+3:50200152 540151020 A	
653	1959 G	+3:50200153 540151021 G	
654 D	1960 G	+3:50200154 540151022 G	D
654	1961 A	+3:50200155 540151023 A	
654	1962 C	+3:50200156 540151024 C	
655 R	1963 C	+3:50200157 540151025 C	R
655	1964 G	+3:50200158 540151026 G	
655	1965 C	+3:50200159 540151027 C	
656 F	1966 T	+3:50200160 540151028 T	F
656	1967 T	+3:50200161 540151029 T	
656	1968 C	+3:50200162 540151030 C	
657 L	1969 C	+3:50200163 540151031 C	L
657	1970 T	+3:50200164 540151032 T	
657	1971 G	+3:50200165 540151033 G	
658 R	1972 C	+3:50200166 540151034 C	R
658	1973 G	+3:50200167 540151035 G	
658	1974 C	+3:50200168 540151036 C	
659 T	1975 A	+3:50200169 540151037 A	T
659	1976 C	+3:50200170 540151038 C	
659	1977 A	+3:50200171 540151039 A	
660 E	1978 G	+3:50200172 540151040 G	E
660	1979 A	+3:50200173 540151041 A	
660	1980 G	+3:50200174 540151042 G	
661 Q	1981 C	+3:50200175 540151043 C	Q
661	1982 A	+3:50200176 540151044 A	
661	1983 G	+3:50200177 540151045 G	
662 G	1984 G	+3:50200178 540151046 G	G
662	1985 G	+3:50200179 540151047 G	
662	1986 C	+3:50200180 540151048 C	
663 L	1987 T	+3:50200181 540151049 T	L
663	1988 T	+3:50200182 540151050 T	
663	1989 G	+3:50200183 540151051 G	
664 L	1990 T	+3:50200184 540151052 T	L
664	1991 T	+3:50200185 540151053 T	
664	1992 G	+3:50200186 540151054 G	
665 L	1993 C	+3:50200187 540151055 C	L
665	1994 T	+3:50200188 540151056 T	
665	1995 C	+3:50200189 540151057 C	
666 R	1996 C	+3:50200190 540151058 C	R
666	1997 G	+3:50200191 540151059 G	
666	1998 T	+3:50200192 540151060 T	
667 A	1999 G	+3:50200193 540151061 G	A
667	2000 C	+3:50200194 540151062 C	
667	2001 A	+3:50200195 540151063 A	
668 L	2002 C	+3:50200196 540151064 C	L
668	2003 T	+3:50200197 540151065 T	
668	2004 G	+3:50200198 540151066 G	
669 Q	2005 C	+3:50200199 540151067 C	Q
669	2006 A	+3:50200200 540151068 A	
669	2007 G	+3:50200201 540151069 G	
670 L	2008 C	+3:50200202 540151070 C	L
670	2009 T	+3:50200203 540151071 T	
670	2010 C	+3:50200204 540151072 C	
671 S	2011 A	+3:50200205 540151073 A	S
671	2012 G	+3:50200206 540151074 G	
671	2013 C	+3:50200207 540151075 C	
672 D	2014 G	+3:50200208 540151076 G	D
672	2015 A	+3:50200209 540151077 A	
672	2016 T	+3:50200210 540151078 T	
673 R	2017 C	+3:50200211 540151079 C	R
673	2018 G	+3:50200212 540151080 G	
673	2019 T	+3:50200213 540151081 T	
674 G	2020 G	+3:50200214 540151082 G	G
674	2021 G	+3:50200215 540151083 G	
674	2022 C	+3:50200216 540151084 C	
675 L	2023 C	+3:50200217 540151085 C	L
675	2024 T	+3:50200218 540151086 T	
675	2025 C	+3:50200219 540151087 C	
676 Y	2026 T	+3:50200220 540151088 T	Y
676	2027 A	+3:50200221 540151089 A	
676	2028 C	+3:50200222 540151090 C	
677 S	2029 T	+3:50200223 540151091 T	S
677	2030 C	+3:50200224 540151092 C	
677	2031 C	+3:50200225 540151093 C	
678 C	2032 T	+3:50200226 540151094 T	C
678	2033 G	+3:50200227 540151095 G	
678	2034 C	+3:50200228 540151096 C	
679 T	2035 A	+3:50200229 540151097 A	T
679	2036 C	+3:50200230 540151098 C	
679	2037 A	+3:50200231 540151099 A	
680 A	2038 G	+3:50200232 540151100 G	A
680	2039 C	+3:50200233 540151101 C	
680	2040 C	+3:50200234 540151102 C	
681 T	2041 A	+3:50200235 540151103 A	T
681	2042 C	+3:50200236 540151104 C	
681	2043 T	+3:50200237 540151105 T	
682 E	2044 G	+3:50200238 540151106 G	E
682	2045 A	+3:50200239 540151107 A	
682	2046 G	+3:50200240 540151108 G	
683 N	2047 A	+3:50200241 540151109 A	N
683	2048 A	+3:50200242 540151110 A	
683	2049 C	+3:50200243 540151111 C	
684 N	2050 A	+3:50200244 540151112 A	N
684	2051 A	+3:50200245 540151113 A	
684	2052 C	+3:50200246 540151114 C	
685 F	2053 T	+3:50200247 540151115 T	F
685	2054 T	+3:50200248 540151116 T	
685	2055 T	+3:50200249 540151117 T	
686 K	2056 A	+3:50200250 540151118 A	K
686	2057 A	+3:50200251 540151119 A	
686	2058 G	+3:50200252 540151120 G	
687 H	2059 C	+3:50200253 540151121 C	H
687	2060 A	+3:50200254 540151122 A	
687	2061 C	+3:50200255 540151123 C	
688 V	2062 G	+3:50200256 540151124 G	V
688	2063 T	+3:50200257 540151125 T	
688	2064 C	+3:50200258 540151126 C	
689 V	2065 G	+3:50200259 540151127 G	V
689	2066 T	+3:50200260 540151128 T	
689	2067 C	+3:50200261 540151129 C	
690 T	2068 A	+3:50200262 540151130 A	T
690	2069 C	+3:50200263 540151131 C	
690	2070 A	+3:50200264 540151132 A	
691 R	2071 C	+3:50200265 540151133 C	R
691	2072 G	+3:50200266 540151134 G	
691	2073 A	+3:50200267 540151135 A	
692 V	2074 G	+3:50200268 540151136 G	V
692	2075 T	+3:50200269 540151137 T	
692	2076 G	+3:50200270 540151138 G	
693 Q	2077 C	+3:50200271 540151139 C	Q
693	2078 A	+3:50200272 540151140 A	
693	2079 G	+3:50200273 540151141 G	
694 L	2080 C	+3:50200274 540151142 C	L
694	2081 T	+3:50200275 540151143 T	
694	2082 G	+3:50200276 540151144 G	
695 H	2083 C	+3:50200277 540151145 C	H
695	2084 A	+3:50200278 540151146 A	
695	2085 T	+3:50200279 540151147 T	
696 V	2086 G	+3:50200280 540151148 G	V
696	2087 T	+3:50200281 540151149 T	
696	2088 A	+3:50200282 540151150 A	
697 L	2089 C	+3:50200283 540151151 C	L
697	2090 T	+3:50200284 540151152 T	
697	2091 G	+3:50200285 540151153 G	
698 G	2092 G	+3:50200286 540151154 G	G
698	2093 G	+3:50200287 540151155 G	
698	2094 C	+3:50200288 540151156 C	
699 R	2095 C	+3:50200289 540151157 C	R
699	2096 G	+3:50200290 540151158 G	
699	2097 G	+3:50200291 540151159 G	
700 D	2098 G	+3:50200292 540151160 G	D
700	2099 A	+3:50200293 540151161 A	
700	2100 C	+3:50200294 540151162 C	
701 A	2101 G	+3:50200295 540151163 G	A
701	2102 C	+3:50200296 540151164 C	
701	2103 C	+3:50200297 540151165 C	
702 V	2104 G	+3:50200298 540151166 G	V
702	2105 T	+3:50200299 540151167 T	
702	2106 C	+3:50200300 540151168 C	
703 H	2107 C	+3:50200301 540151169 C	H
703	2108 A	+3:50200302 540151170 A	
703	2109 T	+3:50200303 540151171 T	
704 A	2110 G	+3:50200304 540151172 G	A
704	2111 C	+3:50200305 540151173 C	
704	2112 T	+3:50200306 540151174 T	
705 A	2113 G	+3:50200307 540151175 G	A
705	2114 C	+3:50200308 540151176 C	
705	2115 C	+3:50200309 540151177 C	
706 L	2116 C	+3:50200310 540151178 C	L
706	2117 T	+3:50200311 540151179 T	
706	2118 C	+3:50200312 540151180 C	
707 F	2119 T	+3:50200313 540151181 T	F
707	2120 T	+3:50200314 540151182 T	
707	2121 C	+3:50200315 540151183 C	
708 P	2122 C	+3:50200316 540151184 C	P
708	2123 C	+3:50200317 540151185 C	
708	2124 A	+3:50200318 540151186 A	
709 P	2125 C	+3:50200319 540151187 C	P
709	2126 C	+3:50200320 540151188 C	
709	2127 A	+3:50200321 540151189 A	
710 L	2128 C	+3:50200322 540151190 C	L
710	2129 T	+3:50200323 540151191 T	
710	2130 G	+3:50200324 540151192 G	
711 S	2131 T	+3:50200325 540151193 T	S
711	2132 C	+3:50200326 540151194 C	
711	2133 C	+3:50200327 540151195 C	
712 M	2134 A	+3:50200328 540151196 A	M
712	2135 T	+3:50200329 540151197 T	
712	2136 G	+3:50200330 540151198 G	
713 S	2137 A	+3:50200331 540151199 A	S
713	2138 G	+3:50200332 540151200 G	
713	2139 C	+3:50200333 540151201 C	
714 A	2140 G	+3:50200334 540151202 G	A
714	2141 C	+3:50200335 540151203 C	
714	2142 C	+3:50200336 540151204 C	
715 P	2143 C	+3:50200337 540151205 C	P
715	2144 C	+3:50200338 540151206 C	
715	2145 G	+3:50200339 540151207 G	
716 P	2146 C	+3:50200340 540151208 C	P
716	2147 C	+3:50200341 540151209 C	
716	2148 A	+3:50200342 540151210 A	
717 P	2149 C	+3:50200343 540151211 C	P
717	2150 C	+3:50200344 540151212 C	
717	2151 C	+3:50200345 540151213 C	
718 P	2152 C	+3:50200346 540151214 C	P
718	2153 C	+3:50200347 540151215 C	
718	2154 A	+3:50200348 540151216 A	
719 G	2155 G	+3:50200349 540151217 G	G
719	2156 G	+3:50200350 540151218 G	
719	2157 C	+3:50200351 540151219 C	
720 A	2158 G	+3:50200352 540151220 G	A
720	2159 C	+3:50200353 540151221 C	
720	2160 A	+3:50200354 540151222 A	
721 G	2161 G	+3:50200355 540151223 G	G
721	2162 G	+3:50200356 540151224 G	
721	2163 C	+3:50200357 540151225 C	
722 P	2164 C	+3:50200358 540151226 C	P
722	2165 C	+3:50200359 540151227 C	
722	2166 C	+3:50200360 540151228 C	
723 P	2167 C	+3:50200361 540151229 C	P
723	2168 C	+3:50200362 540151230 C	
723	2169 A	+3:50200363 540151231 A	
724 T	2170 A	+3:50200364 540151232 A	T
724	2171 C	+3:50200365 540151233 C	
724	2172 G	+3:50200366 540151234 G	
725 P	2173 C	+3:50200367 540151235 C	P
725	2174 C	+3:50200368 540151236 C	
725	2175 T	+3:50200369 540151237 T	
726 P	2176 C	+3:50200370 540151238 C	P
726	2177 C	+3:50200371 540151239 C	
726	2178 T	+3:50200372 540151240 T	
727 Y	2179 T	+3:50200373 540151241 T	Y
727	2180 A	+3:50200374 540151242 A	
727	2181 C	+3:50200375 540151243 C	
728 Q	2182 C	+3:50200376 540151244 C	Q
728	2183 A	+3:50200377 540151245 A	
728	2184 G	+3:50200378 540151246 G	
729 E	2185 G	+3:50200379 540151247 G	E
729	2186 A	+3:50200380 540151248 A	
729	2187 G	+3:50200381 540151249 G	
730 L	2188 T	+3:50200382 540151250 T	L
730	2189 T	+3:50200383 540151251 T	
730	2190 A	+3:50200384 540151252 A	
731 A	2191 G	+3:50200385 540151253 G	A
731	2192 C	+3:50200386 540151254 C	
731	2193 C	+3:50200387 540151255 C	
732 Q	2194 C	+3:50200388 540151256 C	Q
732	2195 A	+3:50200389 540151257 A	
732	2196 G	+3:50200390 540151258 G	
733 L	2197 C	+3:50200391 540151259 C	L
733	2198 T	+3:50200392 540151260 T	
733	2199 G	+3:50200393 540151261 G	
734 L	2200 C	+3:50200394 540151262 C	L
734	2201 T	+3:50200395 540151263 T	
734	2202 G	+3:50200396 540151264 G	
735 A	2203 G	+3:50200397 540151265 G	A
735	2204 C	+3:50200398 540151266 C	
735	2205 C	+3:50200399 540151267 C	
736 Q	2206 C	+3:50200400 540151268 C	Q
736	2207 A	+3:50200401 540151269 A	
736	2208 G	+3:50200402 540151270 G	
737 P	2209 C	+3:50200403 540151271 C	P
737	2210 C	+3:50200404 540151272 C	
737	2211 A	+3:50200405 540151273 A	
738 E	2212 G	+3:50200406 540151274 G	E
738	2213 A	+3:50200407 540151275 A	
738	2214 A	+3:50200408 540151276 A	
739 V	2215 G	+3:50200409 540151277 G	V
739	2216 T	+3:50200410 540151278 T	
739	2217 G	+3:50200411 540151279 G	
740 G	2218 G	+3:50200412 540151280 G	G
740	2219 G	+3:50200413 540151281 G	
740	2220 C	+3:50200414 540151282 C	
741 L	2221 C	+3:50200415 540151283 C	L
741	2222 T	+3:50200416 540151284 T	
741	2223 C	+3:50200417 540151285 C	
742 I	2224 A	+3:50200418 540151286 A	I
742	2225 T	+3:50200419 540151287 T	
742	2226 C	+3:50200420 540151288 C	
743 H	2227 C	+3:50200421 540151289 C	H
743	2228 A	+3:50200422 540151290 A	
743	2229 C	+3:50200423 540151291 C	
744 Q	2230 C	+3:50200424 540151292 C	Q
744	2231 A	+3:50200425 540151293 A	
744	2232 G	+3:50200426 540151294 G	
745 Y	2233 T	+3:50200427 540151295 T	Y
745	2234 A	+3:50200428 540151296 A	
745	2235 C	+3:50200429 540151297 C	
746 C	2236 T	+3:50200430 540151298 T	C
746	2237 G	+3:50200431 540151299 G	
746	2238 C	+3:50200432 540151300 C	
747 Q	2239 C	+3:50200433 540151301 C	Q
747	2240 A	+3:50200434 540151302 A	
747	2241 G	+3:50200435 540151303 G	
748 G	2242 G	+3:50200436 540151304 G	G
748	2243 G	+3:50200437 540151305 G	
748	2244 T	+3:50200438 540151306 T	
749 Y	2245 T	+3:50200439 540151307 T	Y
749	2246 A	+3:50200440 540151308 A	
749	2247 C	+3:50200441 540151309 C	
750 W	2248 T	+3:50200442 540151310 T	W
750	2249 G	+3:50200443 540151311 G	
750	2250 G	+3:50200444 540151312 G	
751 R	2251 C	+3:50200445 540151313 C	R
751	2252 G	+3:50200446 540151314 G	
751	2253 C	+3:50200447 540151315 C	
752 H	2254 C	+3:50200448 540151316 C	H
752	2255 A	+3:50200449 540151317 A	
752	2256 T	+3:50200450 540151318 T	
753 V	2257 G	+3:50200451 540151319 G	V
753	2258 T	+3:50200452 540151320 T	
753	2259 G	+3:50200453 540151321 G	
754 P	2260 C	+3:50200454 540151322 C	P
754	2261 C	+3:50200455 540151323 C	
754	2262 C	+3:50200456 540151324 C	
755 P	2263 C	+3:50200457 540151325 C	P
755	2264 C	+3:50200458 540151326 C	
755	2265 C	+3:50200459 540151327 C	
756 S	2266 A	+3:50200460 540151328 A	S
756	2267 G	+3:50200461 540151329 G	
756	2268 C	+3:50200462 540151330 C	
757 P	2269 C	+3:50200463 540151331 C	P
757	2270 C	+3:50200464 540151332 C	
757	2271 C	+3:50200465 540151333 C	
758 R	2272 A	+3:50200466 540151334 A	R
758	2273 G	+3:50200467 540151335 G	
758	2274 G	+3:50200468 540151336 G	
759 E	2275 G	+3:50200469 540151337 G	E
759	2276 A	+3:50200470 540151338 A	
759	2277 G	+3:50200471 540151339 G	
760 A	2278 G	+3:50200472 540151340 G	A
760	2279 C	+3:50200473 540151341 C	
760	2280 T	+3:50200474 540151342 T	
761 P	2281 C	+3:50200475 540151343 C	P
761	2282 C	+3:50200476 540151344 C	
761	2283 A	+3:50200477 540151345 A	
762 G	2284 G	+3:50200478 540151346 G	G
762	2285 G	+3:50200479 540151347 G	
762	2286 G	+3:50200480 540151348 G	
763 A	2287 G	+3:50200481 540151349 G	A
763	2288 C	+3:50200482 540151350 C	
763	2289 A	+3:50200483 540151351 A	
764 P	2290 C	+3:50200484 540151352 C	P
764	2291 C	+3:50200485 540151353 C	
764	2292 C	+3:50200486 540151354 C	
765 R	2293 C	+3:50200487 540151355 C	R
765	2294 G	+3:50200488 540151356 G	
765	2295 G	+3:50200489 540151357 G	
766 S	2296 T	+3:50200490 540151358 T	S
766	2297 C	+3:50200491 540151359 C	
766	2298 T	+3:50200492 540151360 T	
767 P	2299 C	+3:50200493 540151361 C	P
767	2300 C	+3:50200494 540151362 C	
767	2301 T	+3:50200495 540151363 T	
768 E	2302 G	+3:50200496 540151364 G	E
768	2303 A	+3:50200497 540151365 A	
768	2304 G	+3:50200498 540151366 G	
769 P	2305 C	+3:50200499 540151367 C	P
769	2306 C	+3:50200500 540151368 C	
769	2307 C	+3:50200501 540151369 C	
770 Q	2308 C	+3:50200502 540151370 C	Q
770	2309 A	+3:50200503 540151371 A	
770	2310 G	+3:50200504 540151372 G	
771 D	2311 G	+3:50200505 540151373 G	D
771	2312 A	+3:50200506 540151374 A	
771	2313 C	+3:50200507 540151375 C	
772 Q	2314 C	+3:50200508 540151376 C	Q
772	2315 A	+3:50200509 540151377 A	
772	2316 G	+3:50200510 540151378 G	
773 K	2317 A	+3:50200511 540151379 A	K
773	2318 A	+3:50200512 540151380 A	
773	2319 A	+3:50200513 540151381 A	
774 K	2320 A	+3:50200514 540151382 A	K
774	2321 A	+3:50200515 540151383 A	
774	2322 G	+3:50200516 540151384 G	
775 P	2323 C	+3:50200517 540151385 C	P
775	2324 C	+3:50200518 540151386 C	
775	2325 C	+3:50200519 540151387 C	
776 R	2326 C	+3:50200520 540151388 C	R
776	2327 G	+3:50200521 540151389 G	
776	2328 G	+3:50200522 540151390 G	
777 N	2329 A	+3:50200523 540151391 A	N
777	2330 A	+3:50200524 540151392 A	
777	2331 C	+3:50200525 540151393 C	
778 R	2332 C	+3:50200526 540151394 C	R
778	2333 G	+3:50200527 540151395 G	
778	2334 C	+3:50200528 540151396 C	
779 R	2335 C	+3:50200529 540151397 C	R
779	2336 G	+3:50200530 540151398 G	
779	2337 G	+3:50200531 540151399 G	
780 H	2338 C	+3:50200532 540151400 C	H
780	2339 A	+3:50200533 540151401 A	
780	2340 C	+3:50200534 540151402 C	
781 H	2341 C	+3:50200535 540151403 C	H
781	2342 A	+3:50200536 540151404 A	
781	2343 C	+3:50200537 540151405 C	
782 P	2344 C	+3:50200538 540151406 C	P
782	2345 C	+3:50200539 540151407 C	
782	2346 T	+3:50200540 540151408 T	
783 P	2347 C	+3:50200541 540151409 C	P
783	2348 C	+3:50200542 540151410 C	
783	2349 G	+3:50200543 540151411 G	
784 D	2350 G	+3:50200544 540151412 G	D
784	2351 A	+3:50200545 540151413 A	
784	2352 C	+3:50200546 540151414 C	
785 T	2353 A	+3:50200547 540151415 A	T
785	2354 C	+3:50200548 540151416 C	
785	2355 A	+3:50200549 540151417 A	
>ENSP00000003084 
16 F	46 T	+7:116931535 1349327151 T	Y
16	47 T	+7:116931536 1349327152 A	
16	48 T	+7:116931537 1349327153 T	
17 F	49 T	+7:116931538 1349327154 T	F
17	50 T	+7:116931539 1349327155 T	
17	51 T	+7:116931540 1349327156 T	
18 S	52 A	+7:116931541 1349327157 A	S
18	53 G	+7:116931542 1349327158 G	
18	54 C	+7:116931543 1349327159 C	
19 W	55 T	+7:116931544 1349327160 T	W
19	56 G	+7:116931545 1349327161 G	
19	57 G	+7:116931546 1349327162 G	
20 T	58 A	+7:116931547 1349327163 A	T
20	59 C	+7:116931548 1349327164 C	
20	60 C	+7:116931549 1349327165 C	
21 R	61 A	+7:116931550 1349327166 A	R
21	62 G	+7:116931551 1349327167 G	
21	63 A	+7:116931552 1349327168 A	
22 P	64 C	+7:116931553 1349327169 C	P
22	65 C	+7:116931554 1349327170 C	
22	66 A	+7:116931555 1349327171 A	
23 I	67 A	+7:116931556 1349327172 A	I
23	68 T	+7:116931557 1349327173 T	
23	69 T	+7:116931558 1349327174 T	
24 L	70 T	+7:116931559 1349327175 T	L
24	71 T	+7:116931560 1349327176 T	
24	72 G	+7:116931561 1349327177 G	
25 R	73 A	+7:116931562 1349327178 A	R
25	74 G	+7:116931563 1349327179 G	
25	75 G	+7:116931564 1349327180 G	
26 K	76 A	+7:116931565 1349327181 A	K
26	77 A	+7:116931566 1349327182 A	
26	78 A	+7:116931567 1349327183 A	
27 G	79 G	+7:116931568 1349327184 G	G
27	80 G	+7:116931569 1349327185 G	
27	81 A	+7:116931570 1349327186 A	
28 Y	82 T	+7:116931571 1349327187 T	Y
28	83 A	+7:116931572 1349327188 A	
28	84 C	+7:116931573 1349327189 C	
29 R	85 A	+7:116931574 1349327190 A	R
29	86 G	+7:116931575 1349327191 G	
29	87 A	+7:116931576 1349327192 A	
30 Q	88 C	+7:116931577 1349327193 C	Q
30	89 A	+7:116931578 1349327194 A	
30	90 G	+7:116931579 1349327195 G	
31 R	91 C	+7:116931580 1349327196 C	R
31	92 G	+7:116931581 1349327197 G	
31	93 C	+7:116931582 1349327198 C	
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288	863 T	+7:116963957 1349359573 T	
288	864 A	+7:116963958 1349359574 A	
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289	866 G	+7:116963960 1349359576 G	
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290	869 A	+7:116963963 1349359579 A	
290	870 A	+7:116967390 1349363006 A	
291 T	871 A	+7:116967391 1349363007 A	T
291	872 C	+7:116967392 1349363008 C	
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292 E	874 G	+7:116967394 1349363010 G	E
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293	878 T	+7:116967398 1349363014 T	
293	879 G	+7:116967399 1349363015 G	
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294	881 A	+7:116967401 1349363017 A	
294	882 A	+7:116967402 1349363018 A	
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295	884 T	+7:116967404 1349363020 T	
295	885 G	+7:116967405 1349363021 G	
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296	887 C	+7:116967407 1349363023 C	
296	888 T	+7:116967408 1349363024 T	
297 R	889 C	+7:116967409 1349363025 C	R
297	890 G	+7:116967410 1349363026 G	
297	891 G	+7:116967411 1349363027 G	
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298	893 A	+7:116967413 1349363029 A	
298	894 G	+7:116967414 1349363030 G	
299 A	895 G	+7:116967415 1349363031 G	A
299	896 C	+7:116967416 1349363032 C	
299	897 A	+7:116967417 1349363033 A	
300 A	898 G	+7:116967418 1349363034 G	A
300	899 C	+7:116967419 1349363035 C	
300	900 C	+7:116967420 1349363036 C	
301 Y	901 T	+7:116967421 1349363037 T	Y
301	902 A	+7:116967422 1349363038 A	
301	903 T	+7:116967423 1349363039 T	
302 V	904 G	+7:116967424 1349363040 G	V
302	905 T	+7:116967425 1349363041 T	
302	906 G	+7:116967426 1349363042 G	
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303	908 G	+7:116967428 1349363044 G	
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304 Y	910 T	+7:116967430 1349363046 T	Y
304	911 A	+7:116967431 1349363047 A	
304	912 C	+7:116967432 1349363048 C	
305 F	913 T	+7:116967433 1349363049 T	F
305	914 T	+7:116967434 1349363050 T	
305	915 C	+7:116967435 1349363051 C	
306 N	916 A	+7:116967436 1349363052 A	N
306	917 A	+7:116967437 1349363053 A	
306	918 T	+7:116967438 1349363054 T	
307 S	919 A	+7:116967439 1349363055 A	S
307	920 G	+7:116967440 1349363056 G	
307	921 C	+7:116967441 1349363057 C	
308 S	922 T	+7:116967442 1349363058 T	S
308	923 C	+7:116967443 1349363059 C	
308	924 A	+7:116967444 1349363060 A	
309 A	925 G	+7:116967445 1349363061 G	A
309	926 C	+7:116967446 1349363062 C	
309	927 C	+7:116967447 1349363063 C	
310 F	928 T	+7:116967448 1349363064 T	F
310	929 T	+7:116967449 1349363065 T	
310	930 C	+7:116967450 1349363066 C	
311 F	931 T	+7:116967451 1349363067 T	F
311	932 T	+7:116967452 1349363068 T	
311	933 C	+7:116967453 1349363069 C	
312 F	934 T	+7:116967454 1349363070 T	F
312	935 T	+7:116967455 1349363071 T	
312	936 C	+7:116967456 1349363072 C	
313 S	937 T	+7:116967457 1349363073 T	S
313	938 C	+7:116967458 1349363074 C	
313	939 A	+7:116967459 1349363075 A	
314 G	940 G	+7:116967460 1349363076 G	G
314	941 G	+7:116967461 1349363077 G	
314	942 G	+7:116967462 1349363078 G	
315 F	943 T	+7:116967463 1349363079 T	F
315	944 T	+7:116967464 1349363080 T	
315	945 C	+7:116967465 1349363081 C	
316 F	946 T	+7:116967466 1349363082 T	F
316	947 T	+7:116967467 1349363083 T	
316	948 T	+7:116967468 1349363084 T	
317 V	949 G	+7:116967469 1349363085 G	V
317	950 T	+7:116967470 1349363086 T	
317	951 G	+7:116967471 1349363087 G	
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318	953 T	+7:116967473 1349363089 T	
318	954 G	+7:116967474 1349363090 G	
319 F	955 T	+7:116967475 1349363091 T	F
319	956 T	+7:116967476 1349363092 T	
319	957 T	+7:116967477 1349363093 T	
320 L	958 T	+7:116967478 1349363094 T	L
320	959 T	+7:116967479 1349363095 T	
320	960 A	+7:116967480 1349363096 A	
321 S	961 T	+7:116967481 1349363097 T	S
321	962 C	+7:116967482 1349363098 C	
321	963 T	+7:116967483 1349363099 T	
322 V	964 G	+7:116967484 1349363100 G	V
322	965 T	+7:116967485 1349363101 T	
322	966 G	+7:116967486 1349363102 G	
323 L	967 C	+7:116967487 1349363103 C	L
323	968 T	+7:116967488 1349363104 T	
323	969 T	+7:116967489 1349363105 T	
324 P	970 C	+7:116967490 1349363106 C	P
324	971 C	+7:116967491 1349363107 C	
324	972 C	+7:116967492 1349363108 C	
325 Y	973 T	+7:116967493 1349363109 T	Y
325	974 A	+7:116967494 1349363110 A	
325	975 T	+7:116967495 1349363111 T	
326 A	976 G	+7:116967496 1349363112 G	A
326	977 C	+7:116967497 1349363113 C	
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327	980 T	+7:116967500 1349363116 T	
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328	983 T	+7:116967503 1349363119 T	
328	984 C	+7:116967504 1349363120 C	
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329	986 A	+7:116967506 1349363122 A	
329	987 A	+7:116967507 1349363123 A	
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331	992 T	+7:116967512 1349363128 T	
331	993 C	+7:116967513 1349363129 C	
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332	995 T	+7:116967515 1349363131 T	
332	996 C	+7:116967516 1349363132 C	
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333	998 T	+7:116967518 1349363134 T	
333	999 C	+7:116967519 1349363135 C	
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334	1001 G	+7:116967521 1349363137 G	
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335	1004 A	+7:116967524 1349363140 A	
335	1005 A	+7:116967525 1349363141 A	
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336	1007 T	+7:116967527 1349363143 T	
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337	1010 T	+7:116967530 1349363146 T	
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338	1013 C	+7:116967533 1349363149 C	
338	1014 C	+7:116967534 1349363150 C	
339 T	1015 A	+7:116967535 1349363151 A	T
339	1016 C	+7:116967536 1349363152 C	
339	1017 C	+7:116967537 1349363153 C	
340 I	1018 A	+7:116967538 1349363154 A	I
340	1019 T	+7:116967539 1349363155 T	
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341 S	1021 T	+7:116967541 1349363157 T	S
341	1022 C	+7:116967542 1349363158 C	
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342	1025 T	+7:116967545 1349363161 T	
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343 C	1027 T	+7:116967547 1349363163 T	C
343	1028 G	+7:116967548 1349363164 G	
343	1029 C	+7:116967549 1349363165 C	
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344	1031 T	+7:116967551 1349363167 T	
344	1032 T	+7:116967552 1349363168 T	
345 V	1033 G	+7:116967553 1349363169 G	V
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348	1043 T	+7:116967563 1349363179 T	
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350 V	1048 G	+7:116967568 1349363184 G	V
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351 T	1051 A	+7:116967571 1349363187 A	T
351	1052 C	+7:116967572 1349363188 C	
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352 R	1054 C	+7:116967574 1349363190 C	R
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353	1058 A	+7:116967578 1349363194 A	
353	1059 A	+7:116967579 1349363195 A	
354 F	1060 T	+7:116967580 1349363196 T	F
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354	1062 T	+7:116967582 1349363198 T	
355 P	1063 C	+7:116967583 1349363199 C	P
355	1064 C	+7:116967584 1349363200 C	
355	1065 C	+7:116967585 1349363201 C	
356 W	1066 T	+7:116967586 1349363202 T	W
356	1067 G	+7:116967587 1349363203 G	
356	1068 G	+7:116967588 1349363204 G	
357 A	1069 G	+7:116967589 1349363205 G	A
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358 V	1072 G	+7:116967592 1349363208 G	V
358	1073 T	+7:116967593 1349363209 T	
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359 Q	1075 C	+7:116967595 1349363211 C	Q
359	1076 A	+7:116967596 1349363212 A	
359	1077 A	+7:116967597 1349363213 A	
360 T	1078 A	+7:116967598 1349363214 A	T
360	1079 C	+7:116967599 1349363215 C	
360	1080 A	+7:116967600 1349363216 A	
361 W	1081 T	+7:116967601 1349363217 T	W
361	1082 G	+7:116967602 1349363218 G	
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362	1085 A	+7:116967605 1349363221 A	
362	1086 T	+7:116967606 1349363222 T	
363 D	1087 G	+7:116967607 1349363223 G	D
363	1088 A	+7:116967608 1349363224 A	
363	1089 C	+7:116967609 1349363225 C	
364 S	1090 T	+7:116967610 1349363226 T	S
364	1091 C	+7:116967611 1349363227 C	
364	1092 T	+7:116967612 1349363228 T	
365 L	1093 C	+7:116967613 1349363229 C	L
365	1094 T	+7:116967614 1349363230 T	
365	1095 T	+7:116967615 1349363231 T	
366 G	1096 G	+7:116967616 1349363232 G	G
366	1097 G	+7:116967617 1349363233 G	
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367 A	1099 G	+7:116967619 1349363235 G	A
367	1100 C	+7:116967620 1349363236 C	
367	1101 A	+7:116967621 1349363237 A	
368 I	1102 A	+7:116967622 1349363238 A	I
368	1103 T	+7:116967623 1349363239 T	
368	1104 A	+7:116967624 1349363240 A	
369 N	1105 A	+7:116967625 1349363241 A	N
369	1106 A	+7:116967626 1349363242 A	
369	1107 C	+7:116967627 1349363243 C	
370 K	1108 A	+7:116967628 1349363244 A	K
370	1109 A	+7:116967629 1349363245 A	
370	1110 A	+7:116967630 1349363246 A	
371 I	1111 A	+7:116967631 1349363247 A	I
371	1112 T	+7:116967632 1349363248 T	
371	1113 A	+7:116967633 1349363249 A	
372 Q	1114 C	+7:116967634 1349363250 C	Q
372	1115 A	+7:116967635 1349363251 A	
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373 D	1117 G	+7:116969306 1349364922 G	D
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374 F	1120 T	+7:116969309 1349364925 T	F
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375 L	1123 T	+7:116969312 1349364928 T	L
375	1124 T	+7:116969313 1349364929 T	
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376 Q	1126 C	+7:116969315 1349364931 C	Q
376	1127 A	+7:116969316 1349364932 A	
376	1128 A	+7:116969317 1349364933 A	
377 K	1129 A	+7:116969318 1349364934 A	K
377	1130 A	+7:116969319 1349364935 A	
377	1131 G	+7:116969320 1349364936 G	
378 Q	1132 C	+7:116969321 1349364937 C	Q
378	1133 A	+7:116969322 1349364938 A	
378	1134 A	+7:116969323 1349364939 A	
379 E	1135 G	+7:116969324 1349364940 G	E
379	1136 A	+7:116969325 1349364941 A	
379	1137 A	+7:116969326 1349364942 A	
380 Y	1138 T	+7:116969327 1349364943 T	Y
380	1139 A	+7:116969328 1349364944 A	
380	1140 T	+7:116969329 1349364945 T	
381 K	1141 A	+7:116969330 1349364946 A	K
381	1142 A	+7:116969331 1349364947 A	
381	1143 G	+7:116969332 1349364948 G	
382 T	1144 A	+7:116969333 1349364949 A	T
382	1145 C	+7:116969334 1349364950 C	
382	1146 A	+7:116969335 1349364951 A	
383 L	1147 T	+7:116969336 1349364952 T	L
383	1148 T	+7:116969337 1349364953 T	
383	1149 G	+7:116969338 1349364954 G	
384 E	1150 G	+7:116969339 1349364955 G	E
384	1151 A	+7:116969340 1349364956 A	
384	1152 A	+7:116969341 1349364957 A	
385 Y	1153 T	+7:116969342 1349364958 T	Y
385	1154 A	+7:116969343 1349364959 A	
385	1155 T	+7:116969344 1349364960 T	
386 N	1156 A	+7:116969345 1349364961 A	N
386	1157 A	+7:116969346 1349364962 A	
386	1158 C	+7:116969347 1349364963 C	
387 L	1159 T	+7:116969348 1349364964 T	L
387	1160 T	+7:116969349 1349364965 T	
387	1161 A	+7:116969350 1349364966 A	
388 T	1162 A	+7:116969351 1349364967 A	T
388	1163 C	+7:116969352 1349364968 C	
388	1164 G	+7:116969353 1349364969 G	
389 T	1165 A	+7:116969354 1349364970 A	T
389	1166 C	+7:116969355 1349364971 C	
389	1167 T	+7:116969356 1349364972 T	
390 T	1168 A	+7:116969357 1349364973 A	T
390	1169 C	+7:116969358 1349364974 C	
390	1170 A	+7:116969359 1349364975 A	
391 E	1171 G	+7:116969360 1349364976 G	E
391	1172 A	+7:116969361 1349364977 A	
391	1173 A	+7:116969362 1349364978 A	
392 V	1174 G	+7:116969363 1349364979 G	V
392	1175 T	+7:116969364 1349364980 T	
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393 V	1177 G	+7:116969366 1349364982 G	V
393	1178 T	+7:116969367 1349364983 T	
393	1179 G	+7:116969368 1349364984 G	
394 M	1180 A	+7:116969369 1349364985 A	M
394	1181 T	+7:116969370 1349364986 T	
394	1182 G	+7:116969371 1349364987 G	
395 E	1183 G	+7:116969372 1349364988 G	E
395	1184 A	+7:116969373 1349364989 A	
395	1185 G	+7:116969374 1349364990 G	
396 N	1186 A	+7:116969375 1349364991 A	N
396	1187 A	+7:116969376 1349364992 A	
396	1188 T	+7:116969377 1349364993 T	
397 V	1189 G	+7:116969378 1349364994 G	V
397	1190 T	+7:116969379 1349364995 T	
397	1191 A	+7:116969380 1349364996 A	
398 T	1192 A	+7:116969381 1349364997 A	T
398	1193 C	+7:116969382 1349364998 C	
398	1194 A	+7:116969383 1349364999 A	
399 A	1195 G	+7:116969384 1349365000 G	A
399	1196 C	+7:116969385 1349365001 C	
399	1197 C	+7:116969386 1349365002 C	
400 F	1198 T	+7:116969387 1349365003 T	F
400	1199 T	+7:116969388 1349365004 T	
400	1200 C	+7:116969389 1349365005 C	
401 W	1201 T	+7:116969390 1349365006 T	W
401	1202 G	+7:116969391 1349365007 G	
401	1203 G	+7:116969392 1349365008 G	
402 E	1204 G	+7:116969393 1349365009 G	E
402	1205 A	+7:116969394 1349365010 A	
402	1206 G	+7:116969395 1349365011 G	
403 E	1207 G	+7:116969396 1349365012 G	E
403	1208 A	+7:116969397 1349365013 A	
403	1209 G	+7:116969398 1349365014 G	
404 G	1210 G	+7:116975931 1349371547 G	G
404	1211 G	+7:116975932 1349371548 G	
404	1212 A	+7:116975933 1349371549 A	
405 F	1213 T	+7:116975934 1349371550 T	F
405	1214 T	+7:116975935 1349371551 T	
405	1215 T	+7:116975936 1349371552 T	
406 G	1216 G	+7:116975937 1349371553 G	G
406	1217 G	+7:116975938 1349371554 G	
406	1218 G	+7:116975939 1349371555 G	
407 E	1219 G	+7:116975940 1349371556 G	E
407	1220 A	+7:116975941 1349371557 A	
407	1221 A	+7:116975942 1349371558 A	
408 L	1222 T	+7:116975943 1349371559 T	L
408	1223 T	+7:116975944 1349371560 T	
408	1224 A	+7:116975945 1349371561 A	
409 F	1225 T	+7:116975946 1349371562 T	F
409	1226 T	+7:116975947 1349371563 T	
409	1227 T	+7:116975948 1349371564 T	
410 E	1228 G	+7:116975949 1349371565 G	E
410	1229 A	+7:116975950 1349371566 A	
410	1230 G	+7:116975951 1349371567 G	
411 K	1231 A	+7:116975952 1349371568 A	K
411	1232 A	+7:116975953 1349371569 A	
411	1233 A	+7:116975954 1349371570 A	
412 A	1234 G	+7:116975955 1349371571 G	A
412	1235 C	+7:116975956 1349371572 C	
412	1236 A	+7:116975957 1349371573 A	
413 K	1237 A	+7:116975958 1349371574 A	K
413	1238 A	+7:116975959 1349371575 A	
413	1239 A	+7:116975960 1349371576 A	
414 Q	1240 C	+7:116975961 1349371577 C	Q
414	1241 A	+7:116975962 1349371578 A	
414	1242 A	+7:116975963 1349371579 A	
415 N	1243 A	+7:116975964 1349371580 A	N
415	1244 A	+7:116975965 1349371581 A	
415	1245 C	+7:116975966 1349371582 C	
416 N	1246 A	+7:116975967 1349371583 A	N
416	1247 A	+7:116975968 1349371584 A	
416	1248 T	+7:116975969 1349371585 T	
417 N	1249 A	+7:116975970 1349371586 A	N
417	1250 A	+7:116975971 1349371587 A	
417	1251 C	+7:116975972 1349371588 C	
418 N	1252 A	+7:116975973 1349371589 A	N
418	1253 A	+7:116975974 1349371590 A	
418	1254 T	+7:116975975 1349371591 T	
419 R	1255 A	+7:116975976 1349371592 A	R
419	1256 G	+7:116975977 1349371593 G	
419	1257 A	+7:116975978 1349371594 A	
420 K	1258 A	+7:116975979 1349371595 A	K
420	1259 A	+7:116975980 1349371596 A	
420	1260 A	+7:116975981 1349371597 A	
421 T	1261 A	+7:116975982 1349371598 A	T
421	1262 C	+7:116975983 1349371599 C	
421	1263 T	+7:116975984 1349371600 T	
422 S	1264 T	+7:116975985 1349371601 T	S
422	1265 C	+7:116975986 1349371602 C	
422	1266 T	+7:116975987 1349371603 T	
423 N	1267 A	+7:116975988 1349371604 A	N
423	1268 A	+7:116975989 1349371605 A	
423	1269 T	+7:116975990 1349371606 T	
424 G	1270 G	+7:116975991 1349371607 G	G
424	1271 G	+7:116975992 1349371608 G	
424	1272 T	+7:116975993 1349371609 T	
425 D	1273 G	+7:116975994 1349371610 G	D
425	1274 A	+7:116975995 1349371611 A	
425	1275 T	+7:116975996 1349371612 T	
426 D	1276 G	+7:116975997 1349371613 G	D
426	1277 A	+7:116975998 1349371614 A	
426	1278 C	+7:116975999 1349371615 C	
427 S	1279 A	+7:116976000 1349371616 A	S
427	1280 G	+7:116976001 1349371617 G	
427	1281 C	+7:116976002 1349371618 C	
428 L	1282 C	+7:116976003 1349371619 C	L
428	1283 T	+7:116976004 1349371620 T	
428	1284 C	+7:116976005 1349371621 C	
429 F	1285 T	+7:116976006 1349371622 T	F
429	1286 T	+7:116976007 1349371623 T	
429	1287 C	+7:116976008 1349371624 C	
430 F	1288 T	+7:116976009 1349371625 T	F
430	1289 T	+7:116976010 1349371626 T	
430	1290 C	+7:116976011 1349371627 C	
431 S	1291 A	+7:116976012 1349371628 A	S
431	1292 G	+7:116976013 1349371629 G	
431	1293 T	+7:116976014 1349371630 T	
432 N	1294 A	+7:116976015 1349371631 A	N
432	1295 A	+7:116976016 1349371632 A	
432	1296 T	+7:116976017 1349371633 T	
433 F	1297 T	+7:116976018 1349371634 T	F
433	1298 T	+7:116976019 1349371635 T	
433	1299 C	+7:116976020 1349371636 C	
434 S	1300 T	+7:116976021 1349371637 T	S
434	1301 C	+7:116976022 1349371638 C	
434	1302 A	+7:116976023 1349371639 A	
435 L	1303 C	+7:116976024 1349371640 C	L
435	1304 T	+7:116976025 1349371641 T	
435	1305 T	+7:116976026 1349371642 T	
436 L	1306 C	+7:116976027 1349371643 C	L
436	1307 T	+7:116976028 1349371644 T	
436	1308 T	+7:116976029 1349371645 T	
437 G	1309 G	+7:116976030 1349371646 G	G
437	1310 G	+7:116976031 1349371647 G	
437	1311 T	+7:116976032 1349371648 T	
438 T	1312 A	+7:116976033 1349371649 A	T
438	1313 C	+7:116976034 1349371650 C	
438	1314 T	+7:116976035 1349371651 T	
439 P	1315 C	+7:116976036 1349371652 C	P
439	1316 C	+7:116976037 1349371653 C	
439	1317 T	+7:116976038 1349371654 T	
440 V	1318 G	+7:116976039 1349371655 G	V
440	1319 T	+7:116976040 1349371656 T	
440	1320 C	+7:116976041 1349371657 C	
441 L	1321 C	+7:116976042 1349371658 C	L
441	1322 T	+7:116976043 1349371659 T	
441	1323 G	+7:116976044 1349371660 G	
442 K	1324 A	+7:116976045 1349371661 A	K
442	1325 A	+7:116976046 1349371662 A	
442	1326 A	+7:116976047 1349371663 A	
443 D	1327 G	+7:116976048 1349371664 G	D
443	1328 A	+7:116976049 1349371665 A	
443	1329 T	+7:116976050 1349371666 T	
444 I	1330 A	+7:116976051 1349371667 A	I
444	1331 T	+7:116976052 1349371668 T	
444	1332 T	+7:116976053 1349371669 T	
445 N	1333 A	+7:116976054 1349371670 A	N
445	1334 A	+7:116976055 1349371671 A	
445	1335 T	+7:116976056 1349371672 T	
446 F	1336 T	+7:116976057 1349371673 T	F
446	1337 T	+7:116976058 1349371674 T	
446	1338 C	+7:116976059 1349371675 C	
447 K	1339 A	+7:116976060 1349371676 A	K
447	1340 A	+7:116976061 1349371677 A	
447	1341 G	+7:116976062 1349371678 G	
448 I	1342 A	+7:116976063 1349371679 A	I
448	1343 T	+7:116976064 1349371680 T	
448	1344 A	+7:116976065 1349371681 A	
449 E	1345 G	+7:116976066 1349371682 G	E
449	1346 A	+7:116976067 1349371683 A	
449	1347 A	+7:116976068 1349371684 A	
450 R	1348 A	+7:116976069 1349371685 A	R
450	1349 G	+7:116976070 1349371686 G	
450	1350 A	+7:116976071 1349371687 A	
451 G	1351 G	+7:116976072 1349371688 G	G
451	1352 G	+7:116976073 1349371689 G	
451	1353 A	+7:116976074 1349371690 A	
452 Q	1354 C	+7:116976075 1349371691 C	Q
452	1355 A	+7:116976076 1349371692 A	
452	1356 G	+7:116976077 1349371693 G	
453 L	1357 T	+7:116976078 1349371694 T	L
453	1358 T	+7:116976079 1349371695 T	
453	1359 G	+7:116976080 1349371696 G	
454 L	1360 T	+7:116976081 1349371697 T	L
454	1361 T	+7:116976082 1349371698 T	
454	1362 G	+7:116976083 1349371699 G	
455 A	1363 G	+7:116976084 1349371700 G	A
455	1364 C	+7:116976085 1349371701 C	
455	1365 G	+7:116976086 1349371702 G	
456 V	1366 G	+7:116976087 1349371703 G	V
456	1367 T	+7:116976088 1349371704 T	
456	1368 T	+7:116976089 1349371705 T	
457 A	1369 G	+7:116976090 1349371706 G	A
457	1370 C	+7:116976091 1349371707 C	
457	1371 T	+7:116976092 1349371708 T	
458 G	1372 G	+7:116976093 1349371709 G	G
458	1373 G	+7:116976094 1349371710 G	
458	1374 A	+7:116976095 1349371711 A	
459 S	1375 T	+7:116976096 1349371712 T	S
459	1376 C	+7:116976097 1349371713 C	
459	1377 C	+7:116976098 1349371714 C	
460 T	1378 A	+7:116976099 1349371715 A	T
460	1379 C	+7:116976100 1349371716 C	
460	1380 T	+7:116976101 1349371717 T	
461 G	1381 G	+7:116976102 1349371718 G	G
461	1382 G	+7:116976103 1349371719 G	
461	1383 A	+7:116976104 1349371720 A	
462 A	1384 G	+7:116976105 1349371721 G	A
462	1385 C	+7:116976106 1349371722 C	
462	1386 A	+7:116976107 1349371723 A	
463 G	1387 G	+7:116976108 1349371724 G	G
463	1388 G	+7:116976109 1349371725 G	
463	1389 C	+7:116976110 1349371726 C	
464 K	1390 A	+7:116976111 1349371727 A	K
464	1391 A	+7:116976112 1349371728 A	
464	1392 G	+7:116976113 1349371729 G	
465 T	1393 A	+7:116986754 1349382370 A	T
465	1394 C	+7:116986755 1349382371 C	
465	1395 T	+7:116986756 1349382372 T	
466 S	1396 T	+7:116986757 1349382373 T	S
466	1397 C	+7:116986758 1349382374 C	
466	1398 A	+7:116986759 1349382375 A	
467 L	1399 C	+7:116986760 1349382376 C	L
467	1400 T	+7:116986761 1349382377 T	
467	1401 T	+7:116986762 1349382378 T	
468 L	1402 C	+7:116986763 1349382379 C	L
468	1403 T	+7:116986764 1349382380 T	
468	1404 A	+7:116986765 1349382381 A	
469 M	1405 A	+7:116986766 1349382382 A	M
469	1406 T	+7:116986767 1349382383 T	
469	1407 G	+7:116986768 1349382384 G	
470 V	1408 G	+7:116986769 1349382385 G	V
470	1409 T	+7:116986770 1349382386 T	
470	1410 G	+7:116986771 1349382387 G	
471 I	1411 A	+7:116986772 1349382388 A	I
471	1412 T	+7:116986773 1349382389 T	
471	1413 T	+7:116986774 1349382390 T	
472 M	1414 A	+7:116986775 1349382391 A	M
472	1415 T	+7:116986776 1349382392 T	
472	1416 G	+7:116986777 1349382393 G	
473 G	1417 G	+7:116986778 1349382394 G	G
473	1418 G	+7:116986779 1349382395 G	
473	1419 A	+7:116986780 1349382396 A	
474 E	1420 G	+7:116986781 1349382397 G	E
474	1421 A	+7:116986782 1349382398 A	
474	1422 A	+7:116986783 1349382399 A	
475 L	1423 C	+7:116986784 1349382400 C	L
475	1424 T	+7:116986785 1349382401 T	
475	1425 G	+7:116986786 1349382402 G	
476 E	1426 G	+7:116986787 1349382403 G	E
476	1427 A	+7:116986788 1349382404 A	
476	1428 G	+7:116986789 1349382405 G	
477 P	1429 C	+7:116986790 1349382406 C	P
477	1430 C	+7:116986791 1349382407 C	
477	1431 T	+7:116986792 1349382408 T	
478 S	1432 T	+7:116986793 1349382409 T	S
478	1433 C	+7:116986794 1349382410 C	
478	1434 A	+7:116986795 1349382411 A	
479 E	1435 G	+7:116986796 1349382412 G	E
479	1436 A	+7:116986797 1349382413 A	
479	1437 G	+7:116986798 1349382414 G	
480 G	1438 G	+7:116986799 1349382415 G	G
480	1439 G	+7:116986800 1349382416 G	
480	1440 T	+7:116986801 1349382417 T	
481 K	1441 A	+7:116986802 1349382418 A	K
481	1442 A	+7:116986803 1349382419 A	
481	1443 A	+7:116986804 1349382420 A	
482 I	1444 A	+7:116986805 1349382421 A	I
482	1445 T	+7:116986806 1349382422 T	
482	1446 T	+7:116986807 1349382423 T	
483 K	1447 A	+7:116986808 1349382424 A	K
483	1448 A	+7:116986809 1349382425 A	
483	1449 G	+7:116986810 1349382426 G	
484 H	1450 C	+7:116986811 1349382427 C	H
484	1451 A	+7:116986812 1349382428 A	
484	1452 C	+7:116986813 1349382429 C	
485 S	1453 A	+7:116986814 1349382430 A	S
485	1454 G	+7:116986815 1349382431 G	
485	1455 T	+7:116986816 1349382432 T	
486 G	1456 G	+7:116986817 1349382433 G	G
486	1457 G	+7:116986818 1349382434 G	
486	1458 A	+7:116986819 1349382435 A	
487 R	1459 A	+7:116986820 1349382436 A	R
487	1460 G	+7:116986821 1349382437 G	
487	1461 A	+7:116986822 1349382438 A	
488 I	1462 A	+7:116986823 1349382439 A	I
488	1463 T	+7:116986824 1349382440 T	
488	1464 T	+7:116986825 1349382441 T	
489 S	1465 T	+7:116986826 1349382442 T	S
489	1466 C	+7:116986827 1349382443 C	
489	1467 A	+7:116986828 1349382444 A	
490 F	1468 T	+7:116986829 1349382445 T	F
490	1469 T	+7:116986830 1349382446 T	
490	1470 C	+7:116986831 1349382447 C	
491 C	1471 T	+7:116986832 1349382448 T	C
491	1472 G	+7:116986833 1349382449 G	
491	1473 T	+7:116986834 1349382450 T	
492 S	1474 T	+7:116986835 1349382451 T	S
492	1475 C	+7:116986836 1349382452 C	
492	1476 T	+7:116986837 1349382453 T	
493 Q	1477 C	+7:116986838 1349382454 C	Q
493	1478 A	+7:116986839 1349382455 A	
493	1479 G	+7:116986840 1349382456 G	
494 F	1480 T	+7:116986841 1349382457 T	F
494	1481 T	+7:116986842 1349382458 T	
494	1482 T	+7:116986843 1349382459 T	
495 S	1483 T	+7:116986844 1349382460 T	S
495	1484 C	+7:116986845 1349382461 C	
495	1485 C	+7:116986846 1349382462 C	
496 W	1486 T	+7:116986847 1349382463 T	W
496	1487 G	+7:116986848 1349382464 G	
496	1488 G	+7:116986849 1349382465 G	
497 I	1489 A	+7:116986850 1349382466 A	I
497	1490 T	+7:116986851 1349382467 T	
497	1491 T	+7:116986852 1349382468 T	
498 M	1492 A	+7:116986853 1349382469 A	M
498	1493 T	+7:116986854 1349382470 T	
498	1494 G	+7:116986855 1349382471 G	
499 P	1495 C	+7:116986856 1349382472 C	P
499	1496 C	+7:116986857 1349382473 C	
499	1497 T	+7:116986858 1349382474 T	
500 G	1498 G	+7:116986859 1349382475 G	G
500	1499 G	+7:116986860 1349382476 G	
500	1500 C	+7:116986861 1349382477 C	
501 T	1501 A	+7:116986862 1349382478 A	T
501	1502 C	+7:116986863 1349382479 C	
501	1503 C	+7:116986864 1349382480 C	
502 I	1504 A	+7:116986865 1349382481 A	I
502	1505 T	+7:116986866 1349382482 T	
502	1506 T	+7:116986867 1349382483 T	
503 K	1507 A	+7:116986868 1349382484 A	K
503	1508 A	+7:116986869 1349382485 A	
503	1509 A	+7:116986870 1349382486 A	
504 E	1510 G	+7:116986871 1349382487 G	E
504	1511 A	+7:116986872 1349382488 A	
504	1512 A	+7:116986873 1349382489 A	
505 N	1513 A	+7:116986874 1349382490 A	N
505	1514 A	+7:116986875 1349382491 A	
505	1515 T	+7:116986876 1349382492 T	
506 I	1516 A	+7:116986877 1349382493 A	I
506	1517 T	+7:116986878 1349382494 T	
506	1518 C	+7:116986879 1349382495 C	
507 I	1519 A	+7:116986880 1349382496 A	I
507	1520 T	+7:116986881 1349382497 T	
507	1521 C	+7:116986882 1349382498 C	
508 F	1522 T	+7:116986883 1349382499 T	F
508	1523 T	+7:116986884 1349382500 T	
508	1524 T	+7:116986885 1349382501 T	
509 G	1525 G	+7:116986886 1349382502 G	G
509	1526 G	+7:116986887 1349382503 G	
509	1527 T	+7:116986888 1349382504 T	
510 V	1528 G	+7:116986889 1349382505 G	V
510	1529 T	+7:116986890 1349382506 T	
510	1530 T	+7:116986891 1349382507 T	
511 S	1531 T	+7:116986892 1349382508 T	S
511	1532 C	+7:116986893 1349382509 C	
511	1533 C	+7:116986894 1349382510 C	
512 Y	1534 T	+7:116986895 1349382511 T	Y
512	1535 A	+7:116986896 1349382512 A	
512	1536 T	+7:116986897 1349382513 T	
513 D	1537 G	+7:116986898 1349382514 G	D
513	1538 A	+7:116986899 1349382515 A	
513	1539 T	+7:116986900 1349382516 T	
514 E	1540 G	+7:116986901 1349382517 G	E
514	1541 A	+7:116986902 1349382518 A	
514	1542 A	+7:116986903 1349382519 A	
515 Y	1543 T	+7:116986904 1349382520 T	Y
515	1544 A	+7:116986905 1349382521 A	
515	1545 T	+7:116986906 1349382522 T	
516 R	1546 A	+7:116986907 1349382523 A	R
516	1547 G	+7:116986908 1349382524 G	
516	1548 A	+7:116986909 1349382525 A	
517 Y	1549 T	+7:116986910 1349382526 T	Y
517	1550 A	+7:116986911 1349382527 A	
517	1551 C	+7:116986912 1349382528 C	
518 R	1552 A	+7:116986913 1349382529 A	R
518	1553 G	+7:116986914 1349382530 G	
518	1554 A	+7:116986915 1349382531 A	
519 S	1555 A	+7:116986916 1349382532 A	S
519	1556 G	+7:116986917 1349382533 G	
519	1557 C	+7:116986918 1349382534 C	
520 V	1558 G	+7:116986919 1349382535 G	V
520	1559 T	+7:116986920 1349382536 T	
520	1560 C	+7:116986921 1349382537 C	
521 I	1561 A	+7:116986922 1349382538 A	I
521	1562 T	+7:116986923 1349382539 T	
521	1563 C	+7:116986924 1349382540 C	
522 K	1564 A	+7:116986925 1349382541 A	K
522	1565 A	+7:116986926 1349382542 A	
522	1566 A	+7:116986927 1349382543 A	
523 A	1567 G	+7:116986928 1349382544 G	A
523	1568 C	+7:116986929 1349382545 C	
523	1569 A	+7:116986930 1349382546 A	
524 C	1570 T	+7:116986931 1349382547 T	C
524	1571 G	+7:116986932 1349382548 G	
524	1572 C	+7:116986933 1349382549 C	
525 Q	1573 C	+7:116986934 1349382550 C	Q
525	1574 A	+7:116986935 1349382551 A	
525	1575 A	+7:116986936 1349382552 A	
526 L	1576 C	+7:116986937 1349382553 C	L
526	1577 T	+7:116986938 1349382554 T	
526	1578 A	+7:116986939 1349382555 A	
527 E	1579 G	+7:116986940 1349382556 G	E
527	1580 A	+7:116986941 1349382557 A	
527	1581 A	+7:116986942 1349382558 A	
528 E	1582 G	+7:116986943 1349382559 G	E
528	1583 A	+7:116986944 1349382560 A	
528	1584 G	+7:116986945 1349382561 G	
529 D	1585 G	+7:117015029 1349410645 G	D
529	1586 A	+7:117015030 1349410646 A	
529	1587 C	+7:117015031 1349410647 C	
530 I	1588 A	+7:117015032 1349410648 A	I
530	1589 T	+7:117015033 1349410649 T	
530	1590 C	+7:117015034 1349410650 C	
531 S	1591 T	+7:117015035 1349410651 T	S
531	1592 C	+7:117015036 1349410652 C	
531	1593 C	+7:117015037 1349410653 C	
532 K	1594 A	+7:117015038 1349410654 A	K
532	1595 A	+7:117015039 1349410655 A	
532	1596 G	+7:117015040 1349410656 G	
533 F	1597 T	+7:117015041 1349410657 T	F
533	1598 T	+7:117015042 1349410658 T	
533	1599 T	+7:117015043 1349410659 T	
534 A	1600 G	+7:117015044 1349410660 G	A
534	1601 C	+7:117015045 1349410661 C	
534	1602 A	+7:117015046 1349410662 A	
535 E	1603 G	+7:117015047 1349410663 G	E
535	1604 A	+7:117015048 1349410664 A	
535	1605 G	+7:117015049 1349410665 G	
536 K	1606 A	+7:117015050 1349410666 A	K
536	1607 A	+7:117015051 1349410667 A	
536	1608 A	+7:117015052 1349410668 A	
537 D	1609 G	+7:117015053 1349410669 G	D
537	1610 A	+7:117015054 1349410670 A	
537	1611 C	+7:117015055 1349410671 C	
538 N	1612 A	+7:117015056 1349410672 A	N
538	1613 A	+7:117015057 1349410673 A	
538	1614 T	+7:117015058 1349410674 T	
539 I	1615 A	+7:117015059 1349410675 A	I
539	1616 T	+7:117015060 1349410676 T	
539	1617 A	+7:117015061 1349410677 A	
540 V	1618 G	+7:117015062 1349410678 G	V
540	1619 T	+7:117015063 1349410679 T	
540	1620 T	+7:117015064 1349410680 T	
541 L	1621 C	+7:117015065 1349410681 C	L
541	1622 T	+7:117015066 1349410682 T	
541	1623 T	+7:117015067 1349410683 T	
542 G	1624 G	+7:117015068 1349410684 G	G
542	1625 G	+7:117015069 1349410685 G	
542	1626 A	+7:117015070 1349410686 A	
543 E	1627 G	+7:117015071 1349410687 G	E
543	1628 A	+7:117015072 1349410688 A	
543	1629 A	+7:117015073 1349410689 A	
544 G	1630 G	+7:117015074 1349410690 G	G
544	1631 G	+7:117015075 1349410691 G	
544	1632 T	+7:117015076 1349410692 T	
545 G	1633 G	+7:117015077 1349410693 G	G
545	1634 G	+7:117015078 1349410694 G	
545	1635 A	+7:117015079 1349410695 A	
546 I	1636 A	+7:117015080 1349410696 A	I
546	1637 T	+7:117015081 1349410697 T	
546	1638 C	+7:117015082 1349410698 C	
547 T	1639 A	+7:117015083 1349410699 A	T
547	1640 C	+7:117015084 1349410700 C	
547	1641 A	+7:117015085 1349410701 A	
548 L	1642 C	+7:117015086 1349410702 C	L
548	1643 T	+7:117015087 1349410703 T	
548	1644 G	+7:117015088 1349410704 G	
549 S	1645 A	+7:117015089 1349410705 A	S
549	1646 G	+7:117015090 1349410706 G	
549	1647 T	+7:117015091 1349410707 T	
550 G	1648 G	+7:117015092 1349410708 G	G
550	1649 G	+7:117015093 1349410709 G	
550	1650 A	+7:117015094 1349410710 A	
551 G	1651 G	+7:117015095 1349410711 G	G
551	1652 G	+7:117015096 1349410712 G	
551	1653 T	+7:117015097 1349410713 T	
552 Q	1654 C	+7:117015098 1349410714 C	Q
552	1655 A	+7:117015099 1349410715 A	
552	1656 A	+7:117015100 1349410716 A	
553 R	1657 C	+7:117015101 1349410717 C	R
553	1658 G	+7:117015102 1349410718 G	
553	1659 A	+7:117015103 1349410719 A	
554 A	1660 G	+7:117015104 1349410720 G	A
554	1661 C	+7:117015105 1349410721 C	
554	1662 A	+7:117015106 1349410722 A	
555 R	1663 A	+7:117015107 1349410723 A	R
555	1664 G	+7:117015108 1349410724 G	
555	1665 A	+7:117015109 1349410725 A	
556 I	1666 A	+7:117015110 1349410726 A	I
556	1667 T	+7:117015111 1349410727 T	
556	1668 T	+7:117015112 1349410728 T	
557 S	1669 T	+7:117015113 1349410729 T	S
557	1670 C	+7:117015114 1349410730 C	
557	1671 T	+7:117015115 1349410731 T	
558 L	1672 T	+7:117015116 1349410732 T	L
558	1673 T	+7:117015117 1349410733 T	
558	1674 A	+7:117015118 1349410734 A	
559 A	1675 G	+7:117015119 1349410735 G	A
559	1676 C	+7:117015120 1349410736 C	
559	1677 A	+7:117015121 1349410737 A	
560 R	1678 A	+7:117015122 1349410738 A	R
560	1679 G	+7:117015123 1349410739 G	
560	1680 A	+7:117017643 1349413259 A	
561 A	1681 G	+7:117017644 1349413260 G	A
561	1682 C	+7:117017645 1349413261 C	
561	1683 A	+7:117017646 1349413262 A	
562 V	1684 G	+7:117017647 1349413263 G	V
562	1685 T	+7:117017648 1349413264 T	
562	1686 A	+7:117017649 1349413265 A	
563 Y	1687 T	+7:117017650 1349413266 T	Y
563	1688 A	+7:117017651 1349413267 A	
563	1689 C	+7:117017652 1349413268 C	
564 K	1690 A	+7:117017653 1349413269 A	K
564	1691 A	+7:117017654 1349413270 A	
564	1692 A	+7:117017655 1349413271 A	
565 D	1693 G	+7:117017656 1349413272 G	D
565	1694 A	+7:117017657 1349413273 A	
565	1695 T	+7:117017658 1349413274 T	
566 A	1696 G	+7:117017659 1349413275 G	A
566	1697 C	+7:117017660 1349413276 C	
566	1698 T	+7:117017661 1349413277 T	
567 D	1699 G	+7:117017662 1349413278 G	D
567	1700 A	+7:117017663 1349413279 A	
567	1701 T	+7:117017664 1349413280 T	
568 L	1702 T	+7:117017665 1349413281 T	L
568	1703 T	+7:117017666 1349413282 T	
568	1704 G	+7:117017667 1349413283 G	
569 Y	1705 T	+7:117017668 1349413284 T	Y
569	1706 A	+7:117017669 1349413285 A	
569	1707 T	+7:117017670 1349413286 T	
570 L	1708 T	+7:117017671 1349413287 T	L
570	1709 T	+7:117017672 1349413288 T	
570	1710 A	+7:117017673 1349413289 A	
571 L	1711 T	+7:117017674 1349413290 T	L
571	1712 T	+7:117017675 1349413291 T	
571	1713 A	+7:117017676 1349413292 A	
572 D	1714 G	+7:117017677 1349413293 G	D
572	1715 A	+7:117017678 1349413294 A	
572	1716 C	+7:117017679 1349413295 C	
573 S	1717 T	+7:117017680 1349413296 T	S
573	1718 C	+7:117017681 1349413297 C	
573	1719 T	+7:117017682 1349413298 T	
574 P	1720 C	+7:117017683 1349413299 C	P
574	1721 C	+7:117017684 1349413300 C	
574	1722 T	+7:117017685 1349413301 T	
575 F	1723 T	+7:117017686 1349413302 T	F
575	1724 T	+7:117017687 1349413303 T	
575	1725 T	+7:117017688 1349413304 T	
576 G	1726 G	+7:117017689 1349413305 G	G
576	1727 G	+7:117017690 1349413306 G	
576	1728 A	+7:117017691 1349413307 A	
577 Y	1729 T	+7:117017692 1349413308 T	Y
577	1730 A	+7:117017693 1349413309 A	
577	1731 C	+7:117017694 1349413310 C	
578 L	1732 C	+7:117017695 1349413311 C	L
578	1733 T	+7:117017696 1349413312 T	
578	1734 A	+7:117017697 1349413313 A	
579 D	1735 G	+7:117017698 1349413314 G	D
579	1736 A	+7:117017699 1349413315 A	
579	1737 T	+7:117017700 1349413316 T	
580 V	1738 G	+7:117017701 1349413317 G	V
580	1739 T	+7:117017702 1349413318 T	
580	1740 T	+7:117017703 1349413319 T	
581 L	1741 T	+7:117017704 1349413320 T	L
581	1742 T	+7:117017705 1349413321 T	
581	1743 A	+7:117017706 1349413322 A	
582 T	1744 A	+7:117017707 1349413323 A	T
582	1745 C	+7:117017708 1349413324 C	
582	1746 A	+7:117017709 1349413325 A	
583 E	1747 G	+7:117017710 1349413326 G	E
583	1748 A	+7:117017711 1349413327 A	
583	1749 A	+7:117017712 1349413328 A	
584 K	1750 A	+7:117017713 1349413329 A	K
584	1751 A	+7:117017714 1349413330 A	
584	1752 A	+7:117017715 1349413331 A	
585 E	1753 G	+7:117017716 1349413332 G	E
585	1754 A	+7:117017717 1349413333 A	
585	1755 A	+7:117017718 1349413334 A	
586 I	1756 A	+7:117017719 1349413335 A	I
586	1757 T	+7:117017720 1349413336 T	
586	1758 A	+7:117017721 1349413337 A	
587 F	1759 T	+7:117017722 1349413338 T	F
587	1760 T	+7:117017723 1349413339 T	
587	1761 T	+7:117017724 1349413340 T	
588 E	1762 G	+7:117017725 1349413341 G	E
588	1763 A	+7:117017726 1349413342 A	
588	1764 A	+7:117017727 1349413343 A	
589 S	1765 A	+7:117017728 1349413344 A	S
589	1766 G	+7:117017729 1349413345 G	
589	1767 C	+7:117019224 1349414840 C	
590 C	1768 T	+7:117019225 1349414841 T	C
590	1769 G	+7:117019226 1349414842 G	
590	1770 T	+7:117019227 1349414843 T	
591 V	1771 G	+7:117019228 1349414844 G	V
591	1772 T	+7:117019229 1349414845 T	
591	1773 C	+7:117019230 1349414846 C	
592 C	1774 T	+7:117019231 1349414847 T	C
592	1775 G	+7:117019232 1349414848 G	
592	1776 T	+7:117019233 1349414849 T	
593 K	1777 A	+7:117019234 1349414850 A	K
593	1778 A	+7:117019235 1349414851 A	
593	1779 A	+7:117019236 1349414852 A	
594 L	1780 C	+7:117019237 1349414853 C	L
594	1781 T	+7:117019238 1349414854 T	
594	1782 G	+7:117019239 1349414855 G	
595 M	1783 A	+7:117019240 1349414856 A	M
595	1784 T	+7:117019241 1349414857 T	
595	1785 G	+7:117019242 1349414858 G	
596 A	1786 G	+7:117019243 1349414859 G	A
596	1787 C	+7:117019244 1349414860 C	
596	1788 T	+7:117019245 1349414861 T	
597 N	1789 A	+7:117019246 1349414862 A	N
597	1790 A	+7:117019247 1349414863 A	
597	1791 C	+7:117019248 1349414864 C	
598 K	1792 A	+7:117019249 1349414865 A	K
598	1793 A	+7:117019250 1349414866 A	
598	1794 A	+7:117019251 1349414867 A	
599 T	1795 A	+7:117019252 1349414868 A	T
599	1796 C	+7:117019253 1349414869 C	
599	1797 T	+7:117019254 1349414870 T	
600 R	1798 A	+7:117019255 1349414871 A	R
600	1799 G	+7:117019256 1349414872 G	
600	1800 G	+7:117019257 1349414873 G	
601 I	1801 A	+7:117019258 1349414874 A	I
601	1802 T	+7:117019259 1349414875 T	
601	1803 T	+7:117019260 1349414876 T	
602 L	1804 T	+7:117019261 1349414877 T	L
602	1805 T	+7:117019262 1349414878 T	
602	1806 G	+7:117019263 1349414879 G	
603 V	1807 G	+7:117019264 1349414880 G	V
603	1808 T	+7:117019265 1349414881 T	
603	1809 C	+7:117019266 1349414882 C	
604 T	1810 A	+7:117019267 1349414883 A	T
604	1811 C	+7:117019268 1349414884 C	
604	1812 T	+7:117019269 1349414885 T	
605 S	1813 T	+7:117019270 1349414886 T	S
605	1814 C	+7:117019271 1349414887 C	
605	1815 T	+7:117019272 1349414888 T	
606 K	1816 A	+7:117019273 1349414889 A	K
606	1817 A	+7:117019274 1349414890 A	
606	1818 A	+7:117019275 1349414891 A	
607 M	1819 A	+7:117019276 1349414892 A	M
607	1820 T	+7:117019277 1349414893 T	
607	1821 G	+7:117019278 1349414894 G	
608 E	1822 G	+7:117019279 1349414895 G	E
608	1823 A	+7:117019280 1349414896 A	
608	1824 A	+7:117019281 1349414897 A	
609 H	1825 C	+7:117019282 1349414898 C	H
609	1826 A	+7:117019283 1349414899 A	
609	1827 T	+7:117019284 1349414900 T	
610 L	1828 T	+7:117019285 1349414901 T	L
610	1829 T	+7:117019286 1349414902 T	
610	1830 A	+7:117019287 1349414903 A	
611 K	1831 A	+7:117019288 1349414904 A	K
611	1832 A	+7:117019289 1349414905 A	
611	1833 G	+7:117019290 1349414906 G	
612 K	1834 A	+7:117019291 1349414907 A	K
612	1835 A	+7:117019292 1349414908 A	
612	1836 A	+7:117019293 1349414909 A	
613 A	1837 G	+7:117019294 1349414910 G	A
613	1838 C	+7:117019295 1349414911 C	
613	1839 T	+7:117019296 1349414912 T	
614 D	1840 G	+7:117019297 1349414913 G	D
614	1841 A	+7:117019298 1349414914 A	
614	1842 C	+7:117019299 1349414915 C	
615 K	1843 A	+7:117019300 1349414916 A	K
615	1844 A	+7:117019301 1349414917 A	
615	1845 A	+7:117019302 1349414918 A	
616 I	1846 A	+7:117019303 1349414919 A	I
616	1847 T	+7:117019304 1349414920 T	
616	1848 A	+7:117019305 1349414921 A	
617 L	1849 T	+7:117019306 1349414922 T	L
617	1850 T	+7:117019307 1349414923 T	
617	1851 A	+7:117019308 1349414924 A	
618 I	1852 A	+7:117019309 1349414925 A	I
618	1853 T	+7:117019310 1349414926 T	
618	1854 T	+7:117019311 1349414927 T	
619 L	1855 T	+7:117019312 1349414928 T	L
619	1856 T	+7:117019313 1349414929 T	
619	1857 G	+7:117019314 1349414930 G	
620 H	1858 C	+7:117019315 1349414931 C	H
620	1859 A	+7:117019316 1349414932 A	
620	1860 T	+7:117019317 1349414933 T	
621 E	1861 G	+7:117019318 1349414934 G	E
621	1862 A	+7:117019319 1349414935 A	
621	1863 A	+7:117019320 1349414936 A	
622 G	1864 G	+7:117019321 1349414937 G	G
622	1865 G	+7:117019322 1349414938 G	
622	1866 T	+7:117019323 1349414939 T	
623 S	1867 A	+7:117019324 1349414940 A	S
623	1868 G	+7:117019325 1349414941 G	
623	1869 C	+7:117019326 1349414942 C	
624 S	1870 A	+7:117019327 1349414943 A	S
624	1871 G	+7:117019328 1349414944 G	
624	1872 C	+7:117019329 1349414945 C	
625 Y	1873 T	+7:117019330 1349414946 T	Y
625	1874 A	+7:117019331 1349414947 A	
625	1875 T	+7:117019332 1349414948 T	
626 F	1876 T	+7:117019333 1349414949 T	F
626	1877 T	+7:117019334 1349414950 T	
626	1878 T	+7:117019335 1349414951 T	
627 Y	1879 T	+7:117019336 1349414952 T	Y
627	1880 A	+7:117019337 1349414953 A	
627	1881 T	+7:117019338 1349414954 T	
628 G	1882 G	+7:117019339 1349414955 G	G
628	1883 G	+7:117019340 1349414956 G	
628	1884 G	+7:117019341 1349414957 G	
629 T	1885 A	+7:117019342 1349414958 A	T
629	1886 C	+7:117019343 1349414959 C	
629	1887 A	+7:117019344 1349414960 A	
630 F	1888 T	+7:117019345 1349414961 T	F
630	1889 T	+7:117019346 1349414962 T	
630	1890 T	+7:117019347 1349414963 T	
631 S	1891 T	+7:117019348 1349414964 T	S
631	1892 C	+7:117019349 1349414965 C	
631	1893 A	+7:117019350 1349414966 A	
632 E	1894 G	+7:117019351 1349414967 G	E
632	1895 A	+7:117019352 1349414968 A	
632	1896 A	+7:117019353 1349414969 A	
633 L	1897 C	+7:117019354 1349414970 C	L
633	1898 T	+7:117019355 1349414971 T	
633	1899 C	+7:117019356 1349414972 C	
634 Q	1900 C	+7:117019357 1349414973 C	Q
634	1901 A	+7:117019358 1349414974 A	
634	1902 A	+7:117019359 1349414975 A	
635 N	1903 A	+7:117019360 1349414976 A	N
635	1904 A	+7:117019361 1349414977 A	
635	1905 T	+7:117019362 1349414978 T	
636 L	1906 C	+7:117019363 1349414979 C	L
636	1907 T	+7:117019364 1349414980 T	
636	1908 A	+7:117019365 1349414981 A	
637 Q	1909 C	+7:117019366 1349414982 C	Q
637	1910 A	+7:117019367 1349414983 A	
637	1911 G	+7:117019368 1349414984 G	
638 P	1912 C	+7:117019369 1349414985 C	P
638	1913 C	+7:117019370 1349414986 C	
638	1914 A	+7:117019371 1349414987 A	
639 D	1915 G	+7:117019372 1349414988 G	D
639	1916 A	+7:117019373 1349414989 A	
639	1917 C	+7:117019374 1349414990 C	
640 F	1918 T	+7:117019375 1349414991 T	F
640	1919 T	+7:117019376 1349414992 T	
640	1920 T	+7:117019377 1349414993 T	
641 S	1921 A	+7:117019378 1349414994 A	S
641	1922 G	+7:117019379 1349414995 G	
641	1923 C	+7:117019380 1349414996 C	
642 S	1924 T	+7:117019381 1349414997 T	S
642	1925 C	+7:117019382 1349414998 C	
642	1926 A	+7:117019383 1349414999 A	
643 K	1927 A	+7:117019384 1349415000 A	K
643	1928 A	+7:117019385 1349415001 A	
643	1929 A	+7:117019386 1349415002 A	
644 L	1930 C	+7:117019387 1349415003 C	L
644	1931 T	+7:117019388 1349415004 T	
644	1932 C	+7:117019389 1349415005 C	
645 M	1933 A	+7:117019390 1349415006 A	M
645	1934 T	+7:117019391 1349415007 T	
645	1935 G	+7:117019392 1349415008 G	
646 G	1936 G	+7:117019393 1349415009 G	G
646	1937 G	+7:117019394 1349415010 G	
646	1938 A	+7:117019395 1349415011 A	
647 C	1939 T	+7:117019396 1349415012 T	C
647	1940 G	+7:117019397 1349415013 G	
647	1941 T	+7:117019398 1349415014 T	
648 D	1942 G	+7:117019399 1349415015 G	D
648	1943 A	+7:117019400 1349415016 A	
648	1944 T	+7:117019401 1349415017 T	
649 S	1945 T	+7:117019402 1349415018 T	S
649	1946 C	+7:117019403 1349415019 C	
649	1947 T	+7:117019404 1349415020 T	
650 F	1948 T	+7:117019405 1349415021 T	F
650	1949 T	+7:117019406 1349415022 T	
650	1950 C	+7:117019407 1349415023 C	
651 D	1951 G	+7:117019408 1349415024 G	D
651	1952 A	+7:117019409 1349415025 A	
651	1953 C	+7:117019410 1349415026 C	
652 Q	1954 C	+7:117019411 1349415027 C	Q
652	1955 A	+7:117019412 1349415028 A	
652	1956 A	+7:117019413 1349415029 A	
653 F	1957 T	+7:117019414 1349415030 T	F
653	1958 T	+7:117019415 1349415031 T	
653	1959 T	+7:117019416 1349415032 T	
654 S	1960 A	+7:117019417 1349415033 A	S
654	1961 G	+7:117019418 1349415034 G	
654	1962 T	+7:117019419 1349415035 T	
655 A	1963 G	+7:117019420 1349415036 G	A
655	1964 C	+7:117019421 1349415037 C	
655	1965 A	+7:117019422 1349415038 A	
656 E	1966 G	+7:117019423 1349415039 G	E
656	1967 A	+7:117019424 1349415040 A	
656	1968 A	+7:117019425 1349415041 A	
657 R	1969 A	+7:117019426 1349415042 A	R
657	1970 G	+7:117019427 1349415043 G	
657	1971 A	+7:117019428 1349415044 A	
658 R	1972 A	+7:117019429 1349415045 A	R
658	1973 G	+7:117019430 1349415046 G	
658	1974 A	+7:117019431 1349415047 A	
659 N	1975 A	+7:117019432 1349415048 A	N
659	1976 A	+7:117019433 1349415049 A	
659	1977 T	+7:117019434 1349415050 T	
660 S	1978 T	+7:117019435 1349415051 T	S
660	1979 C	+7:117019436 1349415052 C	
660	1980 A	+7:117019437 1349415053 A	
661 I	1981 A	+7:117019438 1349415054 A	I
661	1982 T	+7:117019439 1349415055 T	
661	1983 C	+7:117019440 1349415056 C	
662 L	1984 C	+7:117019441 1349415057 C	L
662	1985 T	+7:117019442 1349415058 T	
662	1986 A	+7:117019443 1349415059 A	
663 T	1987 A	+7:117019444 1349415060 A	T
663	1988 C	+7:117019445 1349415061 C	
663	1989 T	+7:117019446 1349415062 T	
664 E	1990 G	+7:117019447 1349415063 G	E
664	1991 A	+7:117019448 1349415064 A	
664	1992 G	+7:117019449 1349415065 G	
665 T	1993 A	+7:117019450 1349415066 A	T
665	1994 C	+7:117019451 1349415067 C	
665	1995 C	+7:117019452 1349415068 C	
666 L	1996 T	+7:117019453 1349415069 T	L
666	1997 T	+7:117019454 1349415070 T	
666	1998 A	+7:117019455 1349415071 A	
667 H	1999 C	+7:117019456 1349415072 C	H
667	2000 A	+7:117019457 1349415073 A	
667	2001 C	+7:117019458 1349415074 C	
668 R	2002 C	+7:117019459 1349415075 C	R
668	2003 G	+7:117019460 1349415076 G	
668	2004 T	+7:117019461 1349415077 T	
669 F	2005 T	+7:117019462 1349415078 T	F
669	2006 T	+7:117019463 1349415079 T	
669	2007 C	+7:117019464 1349415080 C	
670 S	2008 T	+7:117019465 1349415081 T	S
670	2009 C	+7:117019466 1349415082 C	
670	2010 A	+7:117019467 1349415083 A	
671 L	2011 T	+7:117019468 1349415084 T	L
671	2012 T	+7:117019469 1349415085 T	
671	2013 A	+7:117019470 1349415086 A	
672 E	2014 G	+7:117019471 1349415087 G	E
672	2015 A	+7:117019472 1349415088 A	
672	2016 A	+7:117019473 1349415089 A	
673 G	2017 G	+7:117019474 1349415090 G	G
673	2018 G	+7:117019475 1349415091 G	
673	2019 A	+7:117019476 1349415092 A	
674 D	2020 G	+7:117019477 1349415093 G	D
674	2021 A	+7:117019478 1349415094 A	
674	2022 T	+7:117019479 1349415095 T	
675 A	2023 G	+7:117019480 1349415096 G	A
675	2024 C	+7:117019481 1349415097 C	
675	2025 T	+7:117019482 1349415098 T	
676 P	2026 C	+7:117019483 1349415099 C	P
676	2027 C	+7:117019484 1349415100 C	
676	2028 T	+7:117019485 1349415101 T	
677 V	2029 G	+7:117019486 1349415102 G	V
677	2030 T	+7:117019487 1349415103 T	
677	2031 C	+7:117019488 1349415104 C	
678 S	2032 T	+7:117019489 1349415105 T	S
678	2033 C	+7:117019490 1349415106 C	
678	2034 C	+7:117019491 1349415107 C	
679 W	2035 T	+7:117019492 1349415108 T	W
679	2036 G	+7:117019493 1349415109 G	
679	2037 G	+7:117019494 1349415110 G	
680 T	2038 A	+7:117019495 1349415111 A	T
680	2039 C	+7:117019496 1349415112 C	
680	2040 A	+7:117019497 1349415113 A	
681 E	2041 G	+7:117019498 1349415114 G	E
681	2042 A	+7:117019499 1349415115 A	
681	2043 A	+7:117019500 1349415116 A	
682 T	2044 A	+7:117019501 1349415117 A	T
682	2045 C	+7:117019502 1349415118 C	
682	2046 A	+7:117019503 1349415119 A	
683 K	2047 A	+7:117019504 1349415120 A	K
683	2048 A	+7:117019505 1349415121 A	
683	2049 A	+7:117019506 1349415122 A	
684 K	2050 A	+7:117019507 1349415123 A	K
684	2051 A	+7:117019508 1349415124 A	
684	2052 A	+7:117019509 1349415125 A	
685 Q	2053 C	+7:117019510 1349415126 C	Q
685	2054 A	+7:117019511 1349415127 A	
685	2055 A	+7:117019512 1349415128 A	
686 S	2056 T	+7:117019513 1349415129 T	S
686	2057 C	+7:117019514 1349415130 C	
686	2058 T	+7:117019515 1349415131 T	
687 F	2059 T	+7:117019516 1349415132 T	F
687	2060 T	+7:117019517 1349415133 T	
687	2061 T	+7:117019518 1349415134 T	
688 K	2062 A	+7:117019519 1349415135 A	K
688	2063 A	+7:117019520 1349415136 A	
688	2064 A	+7:117019521 1349415137 A	
689 Q	2065 C	+7:117019522 1349415138 C	Q
689	2066 A	+7:117019523 1349415139 A	
689	2067 G	+7:117019524 1349415140 G	
690 T	2068 A	+7:117019525 1349415141 A	T
690	2069 C	+7:117019526 1349415142 C	
690	2070 T	+7:117019527 1349415143 T	
691 G	2071 G	+7:117019528 1349415144 G	G
691	2072 G	+7:117019529 1349415145 G	
691	2073 A	+7:117019530 1349415146 A	
692 E	2074 G	+7:117019531 1349415147 G	E
692	2075 A	+7:117019532 1349415148 A	
692	2076 G	+7:117019533 1349415149 G	
693 F	2077 T	+7:117019534 1349415150 T	F
693	2078 T	+7:117019535 1349415151 T	
693	2079 T	+7:117019536 1349415152 T	
694 G	2080 G	+7:117019537 1349415153 G	G
694	2081 G	+7:117019538 1349415154 G	
694	2082 G	+7:117019539 1349415155 G	
695 E	2083 G	+7:117019540 1349415156 G	E
695	2084 A	+7:117019541 1349415157 A	
695	2085 A	+7:117019542 1349415158 A	
696 K	2086 A	+7:117019543 1349415159 A	K
696	2087 A	+7:117019544 1349415160 A	
696	2088 A	+7:117019545 1349415161 A	
697 R	2089 A	+7:117019546 1349415162 A	R
697	2090 G	+7:117019547 1349415163 G	
697	2091 G	+7:117019548 1349415164 G	
698 K	2092 A	+7:117019549 1349415165 A	K
698	2093 A	+7:117019550 1349415166 A	
698	2094 G	+7:117019551 1349415167 G	
699 N	2095 A	+7:117019552 1349415168 A	N
699	2096 A	+7:117019553 1349415169 A	
699	2097 T	+7:117019554 1349415170 T	
700 S	2098 T	+7:117019555 1349415171 T	S
700	2099 C	+7:117019556 1349415172 C	
700	2100 T	+7:117019557 1349415173 T	
701 I	2101 A	+7:117019558 1349415174 A	I
701	2102 T	+7:117019559 1349415175 T	
701	2103 T	+7:117019560 1349415176 T	
702 L	2104 C	+7:117019561 1349415177 C	L
702	2105 T	+7:117019562 1349415178 T	
702	2106 C	+7:117019563 1349415179 C	
703 N	2107 A	+7:117019564 1349415180 A	N
703	2108 A	+7:117019565 1349415181 A	
703	2109 T	+7:117019566 1349415182 T	
704 P	2110 C	+7:117019567 1349415183 C	P
704	2111 C	+7:117019568 1349415184 C	
704	2112 A	+7:117019569 1349415185 A	
705 I	2113 A	+7:117019570 1349415186 A	I
705	2114 T	+7:117019571 1349415187 T	
705	2115 C	+7:117019572 1349415188 C	
706 N	2116 A	+7:117019573 1349415189 A	N
706	2117 A	+7:117019574 1349415190 A	
706	2118 C	+7:117019575 1349415191 C	
707 S	2119 T	+7:117019576 1349415192 T	S
707	2120 C	+7:117019577 1349415193 C	
707	2121 T	+7:117019578 1349415194 T	
708 I	2122 A	+7:117019579 1349415195 A	I
708	2123 T	+7:117019580 1349415196 T	
708	2124 A	+7:117019581 1349415197 A	
709 R	2125 C	+7:117019582 1349415198 C	R
709	2126 G	+7:117019583 1349415199 G	
709	2127 A	+7:117019584 1349415200 A	
710 K	2128 A	+7:117019585 1349415201 A	K
710	2129 A	+7:117019586 1349415202 A	
710	2130 A	+7:117019587 1349415203 A	
711 F	2131 T	+7:117019588 1349415204 T	F
711	2132 T	+7:117019589 1349415205 T	
711	2133 T	+7:117019590 1349415206 T	
712 S	2134 T	+7:117019591 1349415207 T	S
712	2135 C	+7:117019592 1349415208 C	
712	2136 C	+7:117019593 1349415209 C	
713 I	2137 A	+7:117019594 1349415210 A	I
713	2138 T	+7:117019595 1349415211 T	
713	2139 T	+7:117019596 1349415212 T	
714 V	2140 G	+7:117019597 1349415213 G	V
714	2141 T	+7:117019598 1349415214 T	
714	2142 G	+7:117019599 1349415215 G	
715 Q	2143 C	+7:117019600 1349415216 C	Q
715	2144 A	+7:117019601 1349415217 A	
715	2145 A	+7:117019602 1349415218 A	
716 K	2146 A	+7:117019603 1349415219 A	K
716	2147 A	+7:117019604 1349415220 A	
716	2148 G	+7:117019605 1349415221 G	
717 T	2149 A	+7:117019606 1349415222 A	T
717	2150 C	+7:117019607 1349415223 C	
717	2151 T	+7:117019608 1349415224 T	
718 P	2152 C	+7:117019609 1349415225 C	P
718	2153 C	+7:117019610 1349415226 C	
718	2154 C	+7:117019611 1349415227 C	
719 L	2155 T	+7:117019612 1349415228 T	L
719	2156 T	+7:117019613 1349415229 T	
719	2157 A	+7:117019614 1349415230 A	
720 Q	2158 C	+7:117019615 1349415231 C	Q
720	2159 A	+7:117019616 1349415232 A	
720	2160 A	+7:117019617 1349415233 A	
721 M	2161 A	+7:117019618 1349415234 A	M
721	2162 T	+7:117019619 1349415235 T	
721	2163 G	+7:117019620 1349415236 G	
722 N	2164 A	+7:117019621 1349415237 A	N
722	2165 A	+7:117019622 1349415238 A	
722	2166 T	+7:117019623 1349415239 T	
723 G	2167 G	+7:117019624 1349415240 G	G
723	2168 G	+7:117019625 1349415241 G	
723	2169 C	+7:117019626 1349415242 C	
724 I	2170 A	+7:117019627 1349415243 A	I
724	2171 T	+7:117019628 1349415244 T	
724	2172 C	+7:117019629 1349415245 C	
725 E	2173 G	+7:117019630 1349415246 G	E
725	2174 A	+7:117019631 1349415247 A	
725	2175 A	+7:117019632 1349415248 A	
726 E	2176 G	+7:117019633 1349415249 G	E
726	2177 A	+7:117019634 1349415250 A	
726	2178 G	+7:117019635 1349415251 G	
727 D	2179 G	+7:117019636 1349415252 G	D
727	2180 A	+7:117019637 1349415253 A	
727	2181 T	+7:117019638 1349415254 T	
728 S	2182 T	+7:117019639 1349415255 T	S
728	2183 C	+7:117019640 1349415256 C	
728	2184 T	+7:117019641 1349415257 T	
729 D	2185 G	+7:117019642 1349415258 G	D
729	2186 A	+7:117019643 1349415259 A	
729	2187 T	+7:117019644 1349415260 T	
730 E	2188 G	+7:117019645 1349415261 G	E
730	2189 A	+7:117019646 1349415262 A	
730	2190 G	+7:117019647 1349415263 G	
731 P	2191 C	+7:117019648 1349415264 C	P
731	2192 C	+7:117019649 1349415265 C	
731	2193 T	+7:117019650 1349415266 T	
732 L	2194 T	+7:117019651 1349415267 T	L
732	2195 T	+7:117019652 1349415268 T	
732	2196 A	+7:117019653 1349415269 A	
733 E	2197 G	+7:117019654 1349415270 G	E
733	2198 A	+7:117019655 1349415271 A	
733	2199 G	+7:117019656 1349415272 G	
734 R	2200 A	+7:117019657 1349415273 A	R
734	2201 G	+7:117019658 1349415274 G	
734	2202 A	+7:117019659 1349415275 A	
735 R	2203 A	+7:117019660 1349415276 A	R
735	2204 G	+7:117019661 1349415277 G	
735	2205 G	+7:117019662 1349415278 G	
736 L	2206 C	+7:117019663 1349415279 C	L
736	2207 T	+7:117019664 1349415280 T	
736	2208 G	+7:117019665 1349415281 G	
737 S	2209 T	+7:117019666 1349415282 T	S
737	2210 C	+7:117019667 1349415283 C	
737	2211 C	+7:117019668 1349415284 C	
738 L	2212 T	+7:117019669 1349415285 T	L
738	2213 T	+7:117019670 1349415286 T	
738	2214 A	+7:117019671 1349415287 A	
739 V	2215 G	+7:117019672 1349415288 G	V
739	2216 T	+7:117019673 1349415289 T	
739	2217 A	+7:117019674 1349415290 A	
740 P	2218 C	+7:117019675 1349415291 C	P
740	2219 C	+7:117019676 1349415292 C	
740	2220 A	+7:117019677 1349415293 A	
741 D	2221 G	+7:117019678 1349415294 G	D
741	2222 A	+7:117019679 1349415295 A	
741	2223 T	+7:117019680 1349415296 T	
742 S	2224 T	+7:117019681 1349415297 T	S
742	2225 C	+7:117019682 1349415298 C	
742	2226 T	+7:117019683 1349415299 T	
743 E	2227 G	+7:117019684 1349415300 G	E
743	2228 A	+7:117019685 1349415301 A	
743	2229 G	+7:117019686 1349415302 G	
744 Q	2230 C	+7:117019687 1349415303 C	Q
744	2231 A	+7:117019688 1349415304 A	
744	2232 G	+7:117019689 1349415305 G	
745 G	2233 G	+7:117019690 1349415306 G	G
745	2234 G	+7:117019691 1349415307 G	
745	2235 A	+7:117019692 1349415308 A	
746 E	2236 G	+7:117019693 1349415309 G	E
746	2237 A	+7:117019694 1349415310 A	
746	2238 G	+7:117019695 1349415311 G	
747 A	2239 G	+7:117019696 1349415312 G	A
747	2240 C	+7:117019697 1349415313 C	
747	2241 G	+7:117019698 1349415314 G	
748 I	2242 A	+7:117019699 1349415315 A	I
748	2243 T	+7:117019700 1349415316 T	
748	2244 A	+7:117019701 1349415317 A	
749 L	2245 C	+7:117019702 1349415318 C	L
749	2246 T	+7:117019703 1349415319 T	
749	2247 G	+7:117019704 1349415320 G	
750 P	2248 C	+7:117019705 1349415321 C	P
750	2249 C	+7:117019706 1349415322 C	
750	2250 T	+7:117019707 1349415323 T	
751 R	2251 C	+7:117019708 1349415324 C	R
751	2252 G	+7:117019709 1349415325 G	
751	2253 C	+7:117019710 1349415326 C	
752 I	2254 A	+7:117019711 1349415327 A	I
752	2255 T	+7:117019712 1349415328 T	
752	2256 C	+7:117019713 1349415329 C	
753 S	2257 A	+7:117019714 1349415330 A	S
753	2258 G	+7:117019715 1349415331 G	
753	2259 C	+7:117019716 1349415332 C	
754 V	2260 G	+7:117019717 1349415333 G	V
754	2261 T	+7:117019718 1349415334 T	
754	2262 G	+7:117019719 1349415335 G	
755 I	2263 A	+7:117019720 1349415336 A	I
755	2264 T	+7:117019721 1349415337 T	
755	2265 C	+7:117019722 1349415338 C	
756 S	2266 A	+7:117019723 1349415339 A	S
756	2267 G	+7:117019724 1349415340 G	
756	2268 C	+7:117019725 1349415341 C	
757 T	2269 A	+7:117019726 1349415342 A	T
757	2270 C	+7:117019727 1349415343 C	
757	2271 T	+7:117019728 1349415344 T	
758 G	2272 G	+7:117019729 1349415345 G	G
758	2273 G	+7:117019730 1349415346 G	
758	2274 C	+7:117019731 1349415347 C	
759 P	2275 C	+7:117019732 1349415348 C	P
759	2276 C	+7:117019733 1349415349 C	
759	2277 C	+7:117019734 1349415350 C	
760 T	2278 A	+7:117019735 1349415351 A	T
760	2279 C	+7:117019736 1349415352 C	
760	2280 G	+7:117019737 1349415353 G	
761 L	2281 C	+7:117019738 1349415354 C	L
761	2282 T	+7:117019739 1349415355 T	
761	2283 T	+7:117019740 1349415356 T	
762 Q	2284 C	+7:117019741 1349415357 C	Q
762	2285 A	+7:117019742 1349415358 A	
762	2286 G	+7:117019743 1349415359 G	
763 A	2287 G	+7:117019744 1349415360 G	A
763	2288 C	+7:117019745 1349415361 C	
763	2289 A	+7:117019746 1349415362 A	
764 R	2290 C	+7:117019747 1349415363 C	R
764	2291 G	+7:117019748 1349415364 G	
764	2292 A	+7:117019749 1349415365 A	
765 R	2293 A	+7:117019750 1349415366 A	R
765	2294 G	+7:117019751 1349415367 G	
765	2295 G	+7:117019752 1349415368 G	
766 R	2296 A	+7:117019753 1349415369 A	R
766	2297 G	+7:117019754 1349415370 G	
766	2298 G	+7:117019755 1349415371 G	
767 Q	2299 C	+7:117019756 1349415372 C	Q
767	2300 A	+7:117019757 1349415373 A	
767	2301 G	+7:117019758 1349415374 G	
768 S	2302 T	+7:117019759 1349415375 T	S
768	2303 C	+7:117019760 1349415376 C	
768	2304 T	+7:117019761 1349415377 T	
769 V	2305 G	+7:117019762 1349415378 G	V
769	2306 T	+7:117019763 1349415379 T	
769	2307 C	+7:117019764 1349415380 C	
770 L	2308 C	+7:117019765 1349415381 C	L
770	2309 T	+7:117019766 1349415382 T	
770	2310 G	+7:117019767 1349415383 G	
771 N	2311 A	+7:117019768 1349415384 A	N
771	2312 A	+7:117019769 1349415385 A	
771	2313 C	+7:117019770 1349415386 C	
772 L	2314 C	+7:117019771 1349415387 C	L
772	2315 T	+7:117019772 1349415388 T	
772	2316 G	+7:117019773 1349415389 G	
773 M	2317 A	+7:117019774 1349415390 A	M
773	2318 T	+7:117019775 1349415391 T	
773	2319 G	+7:117019776 1349415392 G	
774 T	2320 A	+7:117019777 1349415393 A	T
774	2321 C	+7:117019778 1349415394 C	
774	2322 A	+7:117019779 1349415395 A	
775 H	2323 C	+7:117019780 1349415396 C	H
775	2324 A	+7:117019781 1349415397 A	
775	2325 C	+7:117019782 1349415398 C	
776 S	2326 T	+7:117019783 1349415399 T	S
776	2327 C	+7:117019784 1349415400 C	
776	2328 A	+7:117019785 1349415401 A	
777 V	2329 G	+7:117019786 1349415402 G	V
777	2330 T	+7:117019787 1349415403 T	
777	2331 T	+7:117019788 1349415404 T	
778 N	2332 A	+7:117019789 1349415405 A	N
778	2333 A	+7:117019790 1349415406 A	
778	2334 C	+7:117019791 1349415407 C	
779 Q	2335 C	+7:117019792 1349415408 C	Q
779	2336 A	+7:117019793 1349415409 A	
779	2337 A	+7:117019794 1349415410 A	
780 G	2338 G	+7:117019795 1349415411 G	G
780	2339 G	+7:117019796 1349415412 G	
780	2340 T	+7:117019797 1349415413 T	
781 Q	2341 C	+7:117019798 1349415414 C	Q
781	2342 A	+7:117019799 1349415415 A	
781	2343 G	+7:117019800 1349415416 G	
782 N	2344 A	+7:117019801 1349415417 A	N
782	2345 A	+7:117019802 1349415418 A	
782	2346 C	+7:117019803 1349415419 C	
783 I	2347 A	+7:117019804 1349415420 A	I
783	2348 T	+7:117019805 1349415421 T	
783	2349 T	+7:117019806 1349415422 T	
784 H	2350 C	+7:117019807 1349415423 C	H
784	2351 A	+7:117019808 1349415424 A	
784	2352 C	+7:117019809 1349415425 C	
785 R	2353 C	+7:117019810 1349415426 C	R
785	2354 G	+7:117019811 1349415427 G	
785	2355 A	+7:117019812 1349415428 A	
786 K	2356 A	+7:117019813 1349415429 A	K
786	2357 A	+7:117019814 1349415430 A	
786	2358 G	+7:117019815 1349415431 G	
787 T	2359 A	+7:117019816 1349415432 A	T
787	2360 C	+7:117019817 1349415433 C	
787	2361 A	+7:117019818 1349415434 A	
788 T	2362 A	+7:117019819 1349415435 A	T
788	2363 C	+7:117019820 1349415436 C	
788	2364 A	+7:117019821 1349415437 A	
789 A	2365 G	+7:117019822 1349415438 G	A
789	2366 C	+7:117019823 1349415439 C	
789	2367 A	+7:117019824 1349415440 A	
790 S	2368 T	+7:117019825 1349415441 T	S
790	2369 C	+7:117019826 1349415442 C	
790	2370 C	+7:117019827 1349415443 C	
791 T	2371 A	+7:117019828 1349415444 A	T
791	2372 C	+7:117019829 1349415445 C	
791	2373 A	+7:117019830 1349415446 A	
792 R	2374 C	+7:117019831 1349415447 C	R
792	2375 G	+7:117019832 1349415448 G	
792	2376 A	+7:117019833 1349415449 A	
793 K	2377 A	+7:117019834 1349415450 A	K
793	2378 A	+7:117019835 1349415451 A	
793	2379 A	+7:117019836 1349415452 A	
794 V	2380 G	+7:117019837 1349415453 G	V
794	2381 T	+7:117019838 1349415454 T	
794	2382 G	+7:117019839 1349415455 G	
795 S	2383 T	+7:117019840 1349415456 T	S
795	2384 C	+7:117019841 1349415457 C	
795	2385 A	+7:117019842 1349415458 A	
796 L	2386 C	+7:117019843 1349415459 C	L
796	2387 T	+7:117019844 1349415460 T	
796	2388 G	+7:117019845 1349415461 G	
797 A	2389 G	+7:117019846 1349415462 G	A
797	2390 C	+7:117019847 1349415463 C	
797	2391 C	+7:117019848 1349415464 C	
798 P	2392 C	+7:117019849 1349415465 C	P
798	2393 C	+7:117019850 1349415466 C	
798	2394 T	+7:117019851 1349415467 T	
799 Q	2395 C	+7:117019852 1349415468 C	Q
799	2396 A	+7:117019853 1349415469 A	
799	2397 G	+7:117019854 1349415470 G	
800 A	2398 G	+7:117019855 1349415471 G	A
800	2399 C	+7:117019856 1349415472 C	
800	2400 A	+7:117019857 1349415473 A	
801 N	2401 A	+7:117019858 1349415474 A	N
801	2402 A	+7:117019859 1349415475 A	
801	2403 C	+7:117019860 1349415476 C	
802 L	2404 T	+7:117019861 1349415477 T	L
802	2405 T	+7:117019862 1349415478 T	
802	2406 G	+7:117019863 1349415479 G	
803 T	2407 A	+7:117019864 1349415480 A	T
803	2408 C	+7:117019865 1349415481 C	
803	2409 T	+7:117019866 1349415482 T	
804 E	2410 G	+7:117019867 1349415483 G	E
804	2411 A	+7:117019868 1349415484 A	
804	2412 A	+7:117019869 1349415485 A	
805 L	2413 C	+7:117019870 1349415486 C	L
805	2414 T	+7:117019871 1349415487 T	
805	2415 G	+7:117019872 1349415488 G	
806 D	2416 G	+7:117019873 1349415489 G	D
806	2417 A	+7:117019874 1349415490 A	
806	2418 T	+7:117019875 1349415491 T	
807 I	2419 A	+7:117019876 1349415492 A	I
807	2420 T	+7:117019877 1349415493 T	
807	2421 A	+7:117019878 1349415494 A	
808 Y	2422 T	+7:117019879 1349415495 T	Y
808	2423 A	+7:117019880 1349415496 A	
808	2424 T	+7:117019881 1349415497 T	
809 S	2425 T	+7:117019882 1349415498 T	S
809	2426 C	+7:117019883 1349415499 C	
809	2427 A	+7:117019884 1349415500 A	
810 R	2428 A	+7:117019885 1349415501 A	R
810	2429 G	+7:117019886 1349415502 G	
810	2430 A	+7:117019887 1349415503 A	
811 R	2431 A	+7:117019888 1349415504 A	R
811	2432 G	+7:117019889 1349415505 G	
811	2433 G	+7:117019890 1349415506 G	
812 L	2434 T	+7:117019891 1349415507 T	L
812	2435 T	+7:117019892 1349415508 T	
812	2436 A	+7:117019893 1349415509 A	
813 S	2437 T	+7:117019894 1349415510 T	S
813	2438 C	+7:117019895 1349415511 C	
813	2439 T	+7:117019896 1349415512 T	
814 Q	2440 C	+7:117019897 1349415513 C	Q
814	2441 A	+7:117019898 1349415514 A	
814	2442 A	+7:117019899 1349415515 A	
815 E	2443 G	+7:117019900 1349415516 G	E
815	2444 A	+7:117019901 1349415517 A	
815	2445 A	+7:117019902 1349415518 A	
816 T	2446 A	+7:117019903 1349415519 A	T
816	2447 C	+7:117019904 1349415520 C	
816	2448 T	+7:117019905 1349415521 T	
817 G	2449 G	+7:117019906 1349415522 G	G
817	2450 G	+7:117019907 1349415523 G	
817	2451 C	+7:117019908 1349415524 C	
818 L	2452 T	+7:117019909 1349415525 T	L
818	2453 T	+7:117019910 1349415526 T	
818	2454 G	+7:117019911 1349415527 G	
819 E	2455 G	+7:117019912 1349415528 G	E
819	2456 A	+7:117019913 1349415529 A	
819	2457 A	+7:117019914 1349415530 A	
820 I	2458 A	+7:117019915 1349415531 A	I
820	2459 T	+7:117019916 1349415532 T	
820	2460 A	+7:117019917 1349415533 A	
821 S	2461 A	+7:117019918 1349415534 A	S
821	2462 G	+7:117019919 1349415535 G	
821	2463 T	+7:117019920 1349415536 T	
822 E	2464 G	+7:117019921 1349415537 G	E
822	2465 A	+7:117019922 1349415538 A	
822	2466 A	+7:117019923 1349415539 A	
823 E	2467 G	+7:117019924 1349415540 G	E
823	2468 A	+7:117019925 1349415541 A	
823	2469 A	+7:117019926 1349415542 A	
824 I	2470 A	+7:117019927 1349415543 A	I
824	2471 T	+7:117019928 1349415544 T	
824	2472 T	+7:117019929 1349415545 T	
825 N	2473 A	+7:117019930 1349415546 A	N
825	2474 A	+7:117019931 1349415547 A	
825	2475 C	+7:117019932 1349415548 C	
826 E	2476 G	+7:117019933 1349415549 G	E
826	2477 A	+7:117019934 1349415550 A	
826	2478 A	+7:117019935 1349415551 A	
827 E	2479 G	+7:117019936 1349415552 G	E
827	2480 A	+7:117019937 1349415553 A	
827	2481 A	+7:117019938 1349415554 A	
828 D	2482 G	+7:117019939 1349415555 G	D
828	2483 A	+7:117019940 1349415556 A	
828	2484 C	+7:117019941 1349415557 C	
829 L	2485 T	+7:117019942 1349415558 T	L
829	2486 T	+7:117019943 1349415559 T	
829	2487 A	+7:117019944 1349415560 A	
830 K	2488 A	+7:117019945 1349415561 A	K
830	2489 A	+7:117019946 1349415562 A	
830	2490 G	+7:117019947 1349415563 G	
831 E	2491 G	+7:117022220 1349417836 G	E
831	2492 A	+7:117022221 1349417837 A	
831	2493 G	+7:117022222 1349417838 G	
832 C	2494 T	+7:117022223 1349417839 T	C
832	2495 G	+7:117022224 1349417840 G	
832	2496 C	+7:117022225 1349417841 C	
833 F	2497 T	+7:117022226 1349417842 T	F
833	2498 T	+7:117022227 1349417843 T	
833	2499 T	+7:117022228 1349417844 T	
834 F	2500 T	+7:117022229 1349417845 T	F
834	2501 T	+7:117022230 1349417846 T	
834	2502 T	+7:117022231 1349417847 T	
835 D	2503 G	+7:117022232 1349417848 G	D
835	2504 A	+7:117022233 1349417849 A	
835	2505 T	+7:117022234 1349417850 T	
836 D	2506 G	+7:117022235 1349417851 G	D
836	2507 A	+7:117022236 1349417852 A	
836	2508 T	+7:117022237 1349417853 T	
837 M	2509 A	+7:117022238 1349417854 A	M
837	2510 T	+7:117022239 1349417855 T	
837	2511 G	+7:117022240 1349417856 G	
838 E	2512 G	+7:117022241 1349417857 G	E
838	2513 A	+7:117022242 1349417858 A	
838	2514 G	+7:117022243 1349417859 G	
839 S	2515 A	+7:117022244 1349417860 A	S
839	2516 G	+7:117022245 1349417861 G	
839	2517 C	+7:117022246 1349417862 C	
840 I	2518 A	+7:117022247 1349417863 A	I
840	2519 T	+7:117022248 1349417864 T	
840	2520 A	+7:117022249 1349417865 A	
841 P	2521 C	+7:117022250 1349417866 C	P
841	2522 C	+7:117022251 1349417867 C	
841	2523 A	+7:117022252 1349417868 A	
842 A	2524 G	+7:117022253 1349417869 G	A
842	2525 C	+7:117022254 1349417870 C	
842	2526 A	+7:117022255 1349417871 A	
843 V	2527 G	+7:117022256 1349417872 G	V
843	2528 T	+7:117022257 1349417873 T	
843	2529 G	+7:117022258 1349417874 G	
844 T	2530 A	+7:117022259 1349417875 A	T
844	2531 C	+7:117022260 1349417876 C	
844	2532 T	+7:117022261 1349417877 T	
845 T	2533 A	+7:117022262 1349417878 A	T
845	2534 C	+7:117022263 1349417879 C	
845	2535 A	+7:117022264 1349417880 A	
846 W	2536 T	+7:117022265 1349417881 T	W
846	2537 G	+7:117022266 1349417882 G	
846	2538 G	+7:117022267 1349417883 G	
847 N	2539 A	+7:117022268 1349417884 A	N
847	2540 A	+7:117022269 1349417885 A	
847	2541 C	+7:117022270 1349417886 C	
848 T	2542 A	+7:117022271 1349417887 A	T
848	2543 C	+7:117022272 1349417888 C	
848	2544 A	+7:117022273 1349417889 A	
849 Y	2545 T	+7:117022274 1349417890 T	Y
849	2546 A	+7:117022275 1349417891 A	
849	2547 C	+7:117022276 1349417892 C	
850 L	2548 C	+7:117022277 1349417893 C	L
850	2549 T	+7:117022278 1349417894 T	
850	2550 T	+7:117022279 1349417895 T	
851 R	2551 C	+7:117022280 1349417896 C	R
851	2552 G	+7:117022281 1349417897 G	
851	2553 A	+7:117022282 1349417898 A	
852 Y	2554 T	+7:117022283 1349417899 T	Y
852	2555 A	+7:117022284 1349417900 A	
852	2556 T	+7:117022285 1349417901 T	
853 I	2557 A	+7:117022286 1349417902 A	I
853	2558 T	+7:117022287 1349417903 T	
853	2559 T	+7:117022288 1349417904 T	
854 T	2560 A	+7:117022289 1349417905 A	T
854	2561 C	+7:117022290 1349417906 C	
854	2562 T	+7:117022291 1349417907 T	
855 V	2563 G	+7:117022292 1349417908 G	V
855	2564 T	+7:117022293 1349417909 T	
855	2565 C	+7:117022294 1349417910 C	
856 H	2566 C	+7:117022295 1349417911 C	H
856	2567 A	+7:117022296 1349417912 A	
856	2568 C	+7:117022297 1349417913 C	
857 K	2569 A	+7:117022298 1349417914 A	K
857	2570 A	+7:117022299 1349417915 A	
857	2571 G	+7:117022300 1349417916 G	
858 S	2572 A	+7:117022301 1349417917 A	S
858	2573 G	+7:117022302 1349417918 G	
858	2574 C	+7:117022303 1349417919 C	
859 L	2575 T	+7:117022304 1349417920 T	L
859	2576 T	+7:117022305 1349417921 T	
859	2577 A	+7:117022306 1349417922 A	
860 I	2578 A	+7:117022307 1349417923 A	I
860	2579 T	+7:117022308 1349417924 T	
860	2580 T	+7:117022309 1349417925 T	
861 F	2581 T	+7:117022310 1349417926 T	F
861	2582 T	+7:117022311 1349417927 T	
861	2583 T	+7:117022312 1349417928 T	
862 V	2584 G	+7:117022313 1349417929 G	V
862	2585 T	+7:117022314 1349417930 T	
862	2586 G	+7:117022315 1349417931 G	
863 L	2587 C	+7:117022316 1349417932 C	L
863	2588 T	+7:117022317 1349417933 T	
863	2589 A	+7:117022318 1349417934 A	
864 I	2590 A	+7:117022319 1349417935 A	I
864	2591 T	+7:117022320 1349417936 T	
864	2592 T	+7:117022321 1349417937 T	
865 W	2593 T	+7:117022322 1349417938 T	W
865	2594 G	+7:117022323 1349417939 G	
865	2595 G	+7:117022324 1349417940 G	
866 C	2596 T	+7:117022325 1349417941 T	C
866	2597 G	+7:117022326 1349417942 G	
866	2598 C	+7:117022327 1349417943 C	
867 L	2599 T	+7:117022328 1349417944 T	L
867	2600 T	+7:117022329 1349417945 T	
867	2601 A	+7:117022330 1349417946 A	
868 V	2602 G	+7:117022331 1349417947 G	V
868	2603 T	+7:117022332 1349417948 T	
868	2604 A	+7:117022333 1349417949 A	
869 I	2605 A	+7:117022334 1349417950 A	I
869	2606 T	+7:117022335 1349417951 T	
869	2607 T	+7:117022336 1349417952 T	
870 F	2608 T	+7:117022337 1349417953 T	F
870	2609 T	+7:117022338 1349417954 T	
870	2610 T	+7:117022339 1349417955 T	
871 L	2611 C	+7:117022340 1349417956 C	L
871	2612 T	+7:117022341 1349417957 T	
871	2613 G	+7:117022342 1349417958 G	
872 A	2614 G	+7:117022343 1349417959 G	A
872	2615 C	+7:117022344 1349417960 C	
872	2616 A	+7:117022345 1349417961 A	
873 E	2617 G	+7:117022346 1349417962 G	E
873	2618 A	+7:117022347 1349417963 A	
873	2619 G	+7:117022348 1349417964 G	
874 V	2620 G	+7:117030116 1349425732 G	V
874	2621 T	+7:117030117 1349425733 T	
874	2622 G	+7:117030118 1349425734 G	
875 A	2623 G	+7:117030119 1349425735 G	A
875	2624 C	+7:117030120 1349425736 C	
875	2625 T	+7:117030121 1349425737 T	
876 A	2626 G	+7:117030122 1349425738 G	A
876	2627 C	+7:117030123 1349425739 C	
876	2628 T	+7:117030124 1349425740 T	
877 S	2629 T	+7:117030125 1349425741 T	S
877	2630 C	+7:117030126 1349425742 C	
877	2631 T	+7:117030127 1349425743 T	
878 L	2632 T	+7:117030128 1349425744 T	L
878	2633 T	+7:117030129 1349425745 T	
878	2634 G	+7:117030130 1349425746 G	
879 V	2635 G	+7:117030131 1349425747 G	V
879	2636 T	+7:117030132 1349425748 T	
879	2637 T	+7:117030133 1349425749 T	
880 V	2638 G	+7:117030134 1349425750 G	V
880	2639 T	+7:117030135 1349425751 T	
880	2640 G	+7:117030136 1349425752 G	
881 L	2641 C	+7:117030137 1349425753 C	L
881	2642 T	+7:117030138 1349425754 T	
881	2643 G	+7:117030139 1349425755 G	
882 W	2644 T	+7:117030140 1349425756 T	W
882	2645 G	+7:117030141 1349425757 G	
882	2646 G	+7:117030142 1349425758 G	
883 L	2647 C	+7:117030143 1349425759 C	L
883	2648 T	+7:117030144 1349425760 T	
883	2649 C	+7:117030145 1349425761 C	
884 L	2650 C	+7:117030146 1349425762 C	L
884	2651 T	+7:117030147 1349425763 T	
884	2652 T	+7:117030148 1349425764 T	
885 G	2653 G	+7:117030149 1349425765 G	G
885	2654 G	+7:117030150 1349425766 G	
885	2655 A	+7:117030151 1349425767 A	
886 N	2656 A	+7:117030152 1349425768 A	N
886	2657 A	+7:117030153 1349425769 A	
886	2658 C	+7:117030822 1349426438 C	
887 T	2659 A	+7:117030823 1349426439 A	T
887	2660 C	+7:117030824 1349426440 C	
887	2661 T	+7:117030825 1349426441 T	
888 P	2662 C	+7:117030826 1349426442 C	P
888	2663 C	+7:117030827 1349426443 C	
888	2664 T	+7:117030828 1349426444 T	
889 L	2665 C	+7:117030829 1349426445 C	L
889	2666 T	+7:117030830 1349426446 T	
889	2667 T	+7:117030831 1349426447 T	
890 Q	2668 C	+7:117030832 1349426448 C	Q
890	2669 A	+7:117030833 1349426449 A	
890	2670 A	+7:117030834 1349426450 A	
891 D	2671 G	+7:117030835 1349426451 G	D
891	2672 A	+7:117030836 1349426452 A	
891	2673 C	+7:117030837 1349426453 C	
892 K	2674 A	+7:117030838 1349426454 A	K
892	2675 A	+7:117030839 1349426455 A	
892	2676 A	+7:117030840 1349426456 A	
893 G	2677 G	+7:117030841 1349426457 G	G
893	2678 G	+7:117030842 1349426458 G	
893	2679 G	+7:117030843 1349426459 G	
894 N	2680 A	+7:117030844 1349426460 A	N
894	2681 A	+7:117030845 1349426461 A	
894	2682 T	+7:117030846 1349426462 T	
895 S	2683 A	+7:117030847 1349426463 A	S
895	2684 G	+7:117030848 1349426464 G	
895	2685 T	+7:117030849 1349426465 T	
896 T	2686 A	+7:117030850 1349426466 A	T
896	2687 C	+7:117030851 1349426467 C	
896	2688 T	+7:117030852 1349426468 T	
897 H	2689 C	+7:117030853 1349426469 C	H
897	2690 A	+7:117030854 1349426470 A	
897	2691 T	+7:117030855 1349426471 T	
898 S	2692 A	+7:117030856 1349426472 A	S
898	2693 G	+7:117030857 1349426473 G	
898	2694 T	+7:117030858 1349426474 T	
899 R	2695 A	+7:117030859 1349426475 A	R
899	2696 G	+7:117030860 1349426476 G	
899	2697 A	+7:117030861 1349426477 A	
900 N	2698 A	+7:117030862 1349426478 A	N
900	2699 A	+7:117030863 1349426479 A	
900	2700 T	+7:117030864 1349426480 T	
901 N	2701 A	+7:117030865 1349426481 A	N
901	2702 A	+7:117030866 1349426482 A	
901	2703 C	+7:117030867 1349426483 C	
902 S	2704 A	+7:117030868 1349426484 A	S
902	2705 G	+7:117030869 1349426485 G	
902	2706 C	+7:117030870 1349426486 C	
903 Y	2707 T	+7:117030871 1349426487 T	Y
903	2708 A	+7:117030872 1349426488 A	
903	2709 T	+7:117030873 1349426489 T	
904 A	2710 G	+7:117030874 1349426490 G	A
904	2711 C	+7:117030875 1349426491 C	
904	2712 A	+7:117030876 1349426492 A	
905 V	2713 G	+7:117030877 1349426493 G	V
905	2714 T	+7:117030878 1349426494 T	
905	2715 G	+7:117030879 1349426495 G	
906 I	2716 A	+7:117030880 1349426496 A	I
906	2717 T	+7:117030881 1349426497 T	
906	2718 T	+7:117030882 1349426498 T	
907 I	2719 A	+7:117030883 1349426499 A	I
907	2720 T	+7:117030884 1349426500 T	
907	2721 C	+7:117030885 1349426501 C	
908 T	2722 A	+7:117030886 1349426502 A	T
908	2723 C	+7:117030887 1349426503 C	
908	2724 C	+7:117030888 1349426504 C	
909 S	2725 A	+7:117030889 1349426505 A	S
909	2726 G	+7:117030890 1349426506 G	
909	2727 C	+7:117030891 1349426507 C	
910 T	2728 A	+7:117030892 1349426508 A	T
910	2729 C	+7:117030893 1349426509 C	
910	2730 C	+7:117030894 1349426510 C	
911 S	2731 A	+7:117030895 1349426511 A	S
911	2732 G	+7:117030896 1349426512 G	
911	2733 T	+7:117030897 1349426513 T	
912 S	2734 T	+7:117030898 1349426514 T	S
912	2735 C	+7:117030899 1349426515 C	
912	2736 G	+7:117030900 1349426516 G	
913 Y	2737 T	+7:117030901 1349426517 T	Y
913	2738 A	+7:117030902 1349426518 A	
913	2739 T	+7:117030903 1349426519 T	
914 Y	2740 T	+7:117030904 1349426520 T	Y
914	2741 A	+7:117030905 1349426521 A	
914	2742 T	+7:117030906 1349426522 T	
915 V	2743 G	+7:117030907 1349426523 G	V
915	2744 T	+7:117030908 1349426524 T	
915	2745 G	+7:117030909 1349426525 G	
916 F	2746 T	+7:117030910 1349426526 T	F
916	2747 T	+7:117030911 1349426527 T	
916	2748 T	+7:117030912 1349426528 T	
917 Y	2749 T	+7:117030913 1349426529 T	Y
917	2750 A	+7:117030914 1349426530 A	
917	2751 C	+7:117030915 1349426531 C	
918 I	2752 A	+7:117030916 1349426532 A	I
918	2753 T	+7:117030917 1349426533 T	
918	2754 T	+7:117030918 1349426534 T	
919 Y	2755 T	+7:117030919 1349426535 T	Y
919	2756 A	+7:117030920 1349426536 A	
919	2757 C	+7:117030921 1349426537 C	
920 V	2758 G	+7:117030922 1349426538 G	V
920	2759 T	+7:117030923 1349426539 T	
920	2760 G	+7:117030924 1349426540 G	
921 G	2761 G	+7:117030925 1349426541 G	G
921	2762 G	+7:117030926 1349426542 G	
921	2763 A	+7:117030927 1349426543 A	
922 V	2764 G	+7:117030928 1349426544 G	V
922	2765 T	+7:117030929 1349426545 T	
922	2766 A	+7:117030930 1349426546 A	
923 A	2767 G	+7:117030931 1349426547 G	A
923	2768 C	+7:117030932 1349426548 C	
923	2769 C	+7:117030933 1349426549 C	
924 D	2770 G	+7:117030934 1349426550 G	D
924	2771 A	+7:117030935 1349426551 A	
924	2772 C	+7:117030936 1349426552 C	
925 T	2773 A	+7:117030937 1349426553 A	T
925	2774 C	+7:117030938 1349426554 C	
925	2775 T	+7:117030939 1349426555 T	
926 L	2776 T	+7:117030940 1349426556 T	L
926	2777 T	+7:117030941 1349426557 T	
926	2778 G	+7:117030942 1349426558 G	
927 L	2779 C	+7:117030943 1349426559 C	L
927	2780 T	+7:117030944 1349426560 T	
927	2781 T	+7:117030945 1349426561 T	
928 A	2782 G	+7:117030946 1349426562 G	A
928	2783 C	+7:117030947 1349426563 C	
928	2784 T	+7:117030948 1349426564 T	
929 M	2785 A	+7:117030949 1349426565 A	M
929	2786 T	+7:117030950 1349426566 T	
929	2787 G	+7:117030951 1349426567 G	
930 G	2788 G	+7:117030952 1349426568 G	G
930	2789 G	+7:117030953 1349426569 G	
930	2790 A	+7:117030954 1349426570 A	
931 F	2791 T	+7:117030955 1349426571 T	F
931	2792 T	+7:117030956 1349426572 T	
931	2793 C	+7:117030957 1349426573 C	
932 F	2794 T	+7:117030958 1349426574 T	F
932	2795 T	+7:117030959 1349426575 T	
932	2796 C	+7:117030960 1349426576 C	
933 R	2797 A	+7:117030961 1349426577 A	R
933	2798 G	+7:117030962 1349426578 G	
933	2799 A	+7:117030963 1349426579 A	
934 G	2800 G	+7:117030964 1349426580 G	G
934	2801 G	+7:117030965 1349426581 G	
934	2802 T	+7:117030966 1349426582 T	
935 L	2803 C	+7:117030967 1349426583 C	L
935	2804 T	+7:117030968 1349426584 T	
935	2805 A	+7:117030969 1349426585 A	
936 P	2806 C	+7:117030970 1349426586 C	P
936	2807 C	+7:117030971 1349426587 C	
936	2808 A	+7:117030972 1349426588 A	
937 L	2809 C	+7:117030973 1349426589 C	L
937	2810 T	+7:117030974 1349426590 T	
937	2811 G	+7:117030975 1349426591 G	
938 V	2812 G	+7:117030976 1349426592 G	V
938	2813 T	+7:117030977 1349426593 T	
938	2814 G	+7:117030978 1349426594 G	
939 H	2815 C	+7:117030979 1349426595 C	H
939	2816 A	+7:117030980 1349426596 A	
939	2817 T	+7:117030981 1349426597 T	
940 T	2818 A	+7:117030982 1349426598 A	T
940	2819 C	+7:117030983 1349426599 C	
940	2820 T	+7:117030984 1349426600 T	
941 L	2821 C	+7:117030985 1349426601 C	L
941	2822 T	+7:117030986 1349426602 T	
941	2823 A	+7:117030987 1349426603 A	
942 I	2824 A	+7:117030988 1349426604 A	I
942	2825 T	+7:117030989 1349426605 T	
942	2826 C	+7:117030990 1349426606 C	
943 T	2827 A	+7:117030991 1349426607 A	T
943	2828 C	+7:117030992 1349426608 C	
943	2829 A	+7:117030993 1349426609 A	
944 V	2830 G	+7:117030994 1349426610 G	V
944	2831 T	+7:117030995 1349426611 T	
944	2832 G	+7:117030996 1349426612 G	
945 S	2833 T	+7:117030997 1349426613 T	S
945	2834 C	+7:117030998 1349426614 C	
945	2835 G	+7:117030999 1349426615 G	
946 K	2836 A	+7:117031000 1349426616 A	K
946	2837 A	+7:117031001 1349426617 A	
946	2838 A	+7:117031002 1349426618 A	
947 I	2839 A	+7:117031003 1349426619 A	I
947	2840 T	+7:117031004 1349426620 T	
947	2841 T	+7:117031005 1349426621 T	
948 L	2842 T	+7:117031006 1349426622 T	L
948	2843 T	+7:117031007 1349426623 T	
948	2844 A	+7:117031008 1349426624 A	
949 H	2845 C	+7:117031009 1349426625 C	H
949	2846 A	+7:117031010 1349426626 A	
949	2847 C	+7:117031011 1349426627 C	
950 H	2848 C	+7:117031012 1349426628 C	H
950	2849 A	+7:117031013 1349426629 A	
950	2850 C	+7:117031014 1349426630 C	
951 K	2851 A	+7:117031015 1349426631 A	K
951	2852 A	+7:117031016 1349426632 A	
951	2853 A	+7:117031017 1349426633 A	
952 M	2854 A	+7:117031018 1349426634 A	M
952	2855 T	+7:117031019 1349426635 T	
952	2856 G	+7:117031020 1349426636 G	
953 L	2857 T	+7:117031021 1349426637 T	L
953	2858 T	+7:117031022 1349426638 T	
953	2859 A	+7:117031023 1349426639 A	
954 H	2860 C	+7:117031024 1349426640 C	H
954	2861 A	+7:117031025 1349426641 A	
954	2862 T	+7:117031026 1349426642 T	
955 S	2863 T	+7:117031027 1349426643 T	S
955	2864 C	+7:117031028 1349426644 C	
955	2865 T	+7:117031029 1349426645 T	
956 V	2866 G	+7:117031030 1349426646 G	V
956	2867 T	+7:117031031 1349426647 T	
956	2868 T	+7:117031032 1349426648 T	
957 L	2869 C	+7:117031033 1349426649 C	L
957	2870 T	+7:117031034 1349426650 T	
957	2871 T	+7:117031035 1349426651 T	
958 Q	2872 C	+7:117031036 1349426652 C	Q
958	2873 A	+7:117031037 1349426653 A	
958	2874 A	+7:117031038 1349426654 A	
959 A	2875 G	+7:117031039 1349426655 G	A
959	2876 C	+7:117031040 1349426656 C	
959	2877 A	+7:117031041 1349426657 A	
960 P	2878 C	+7:117031042 1349426658 C	P
960	2879 C	+7:117031043 1349426659 C	
960	2880 T	+7:117031044 1349426660 T	
961 M	2881 A	+7:117031045 1349426661 A	M
961	2882 T	+7:117031046 1349426662 T	
961	2883 G	+7:117031047 1349426663 G	
962 S	2884 T	+7:117031048 1349426664 T	S
962	2885 C	+7:117031049 1349426665 C	
962	2886 A	+7:117031050 1349426666 A	
963 T	2887 A	+7:117031051 1349426667 A	T
963	2888 C	+7:117031052 1349426668 C	
963	2889 C	+7:117031053 1349426669 C	
964 L	2890 C	+7:117031054 1349426670 C	L
964	2891 T	+7:117031055 1349426671 T	
964	2892 C	+7:117031056 1349426672 C	
965 N	2893 A	+7:117031057 1349426673 A	N
965	2894 A	+7:117031058 1349426674 A	
965	2895 C	+7:117031059 1349426675 C	
966 T	2896 A	+7:117031060 1349426676 A	T
966	2897 C	+7:117031061 1349426677 C	
966	2898 G	+7:117031062 1349426678 G	
967 L	2899 T	+7:117031063 1349426679 T	L
967	2900 T	+7:117031064 1349426680 T	
967	2901 G	+7:117031065 1349426681 G	
968 K	2902 A	+7:117031066 1349426682 A	K
968	2903 A	+7:117031067 1349426683 A	
968	2904 A	+7:117031068 1349426684 A	
969 A	2905 G	+7:117031069 1349426685 G	A
969	2906 C	+7:117031070 1349426686 C	
969	2907 A	+7:117031071 1349426687 A	
970 G	2908 G	+7:117031072 1349426688 G	G
970	2909 G	+7:117033964 1349429580 G	
970	2910 T	+7:117033965 1349429581 T	
971 G	2911 G	+7:117033966 1349429582 G	G
971	2912 G	+7:117033967 1349429583 G	
971	2913 G	+7:117033968 1349429584 G	
972 I	2914 A	+7:117033969 1349429585 A	I
972	2915 T	+7:117033970 1349429586 T	
972	2916 T	+7:117033971 1349429587 T	
973 L	2917 C	+7:117033972 1349429588 C	L
973	2918 T	+7:117033973 1349429589 T	
973	2919 T	+7:117033974 1349429590 T	
974 N	2920 A	+7:117033975 1349429591 A	N
974	2921 A	+7:117033976 1349429592 A	
974	2922 T	+7:117033977 1349429593 T	
975 R	2923 A	+7:117033978 1349429594 A	R
975	2924 G	+7:117033979 1349429595 G	
975	2925 A	+7:117033980 1349429596 A	
976 F	2926 T	+7:117033981 1349429597 T	F
976	2927 T	+7:117033982 1349429598 T	
976	2928 C	+7:117033983 1349429599 C	
977 S	2929 T	+7:117033984 1349429600 T	S
977	2930 C	+7:117033985 1349429601 C	
977	2931 C	+7:117033986 1349429602 C	
978 K	2932 A	+7:117033987 1349429603 A	K
978	2933 A	+7:117033988 1349429604 A	
978	2934 A	+7:117033989 1349429605 A	
979 D	2935 G	+7:117033990 1349429606 G	D
979	2936 A	+7:117033991 1349429607 A	
979	2937 T	+7:117033992 1349429608 T	
980 I	2938 A	+7:117033993 1349429609 A	I
980	2939 T	+7:117033994 1349429610 T	
980	2940 A	+7:117033995 1349429611 A	
981 A	2941 G	+7:117033996 1349429612 G	A
981	2942 C	+7:117033997 1349429613 C	
981	2943 A	+7:117033998 1349429614 A	
982 I	2944 A	+7:117033999 1349429615 A	I
982	2945 T	+7:117034000 1349429616 T	
982	2946 T	+7:117034001 1349429617 T	
983 L	2947 T	+7:117034002 1349429618 T	L
983	2948 T	+7:117034003 1349429619 T	
983	2949 G	+7:117034004 1349429620 G	
984 D	2950 G	+7:117034005 1349429621 G	D
984	2951 A	+7:117034006 1349429622 A	
984	2952 T	+7:117034007 1349429623 T	
985 D	2953 G	+7:117034008 1349429624 G	D
985	2954 A	+7:117034009 1349429625 A	
985	2955 C	+7:117034010 1349429626 C	
986 L	2956 C	+7:117034011 1349429627 C	L
986	2957 T	+7:117034012 1349429628 T	
986	2958 T	+7:117034013 1349429629 T	
987 L	2959 C	+7:117034014 1349429630 C	L
987	2960 T	+7:117034015 1349429631 T	
987	2961 G	+7:117034016 1349429632 G	
988 P	2962 C	+7:117034017 1349429633 C	P
988	2963 C	+7:117034018 1349429634 C	
988	2964 T	+7:117034019 1349429635 T	
989 L	2965 C	+7:117034020 1349429636 C	L
989	2966 T	+7:117034021 1349429637 T	
989	2967 T	+7:117034022 1349429638 T	
990 T	2968 A	+7:117034023 1349429639 A	T
990	2969 C	+7:117034024 1349429640 C	
990	2970 C	+7:117034025 1349429641 C	
991 I	2971 A	+7:117034026 1349429642 A	I
991	2972 T	+7:117034027 1349429643 T	
991	2973 A	+7:117034028 1349429644 A	
992 F	2974 T	+7:117034029 1349429645 T	F
992	2975 T	+7:117034030 1349429646 T	
992	2976 T	+7:117034031 1349429647 T	
993 D	2977 G	+7:117034032 1349429648 G	D
993	2978 A	+7:117034033 1349429649 A	
993	2979 C	+7:117034034 1349429650 C	
994 F	2980 T	+7:117034035 1349429651 T	F
994	2981 T	+7:117034036 1349429652 T	
994	2982 C	+7:117034037 1349429653 C	
995 I	2983 A	+7:117034038 1349429654 A	I
995	2984 T	+7:117034039 1349429655 T	
995	2985 C	+7:117034040 1349429656 C	
996 Q	2986 C	+7:117034041 1349429657 C	Q
996	2987 A	+7:117034042 1349429658 A	
996	2988 G	+7:117034043 1349429659 G	
997 L	2989 T	+7:117037809 1349433425 T	L
997	2990 T	+7:117037810 1349433426 T	
997	2991 G	+7:117037811 1349433427 G	
998 L	2992 T	+7:117037812 1349433428 T	L
998	2993 T	+7:117037813 1349433429 T	
998	2994 A	+7:117037814 1349433430 A	
999 L	2995 T	+7:117037815 1349433431 T	L
999	2996 T	+7:117037816 1349433432 T	
999	2997 A	+7:117037817 1349433433 A	
1000 I	2998 A	+7:117037818 1349433434 A	I
1000	2999 T	+7:117037819 1349433435 T	
1000	3000 T	+7:117037820 1349433436 T	
1001 V	3001 G	+7:117037821 1349433437 G	V
1001	3002 T	+7:117037822 1349433438 T	
1001	3003 G	+7:117037823 1349433439 G	
1002 I	3004 A	+7:117037824 1349433440 A	I
1002	3005 T	+7:117037825 1349433441 T	
1002	3006 T	+7:117037826 1349433442 T	
1003 G	3007 G	+7:117037827 1349433443 G	G
1003	3008 G	+7:117037828 1349433444 G	
1003	3009 A	+7:117037829 1349433445 A	
1004 A	3010 G	+7:117037830 1349433446 G	A
1004	3011 C	+7:117037831 1349433447 C	
1004	3012 T	+7:117037832 1349433448 T	
1005 I	3013 A	+7:117037833 1349433449 A	I
1005	3014 T	+7:117037834 1349433450 T	
1005	3015 A	+7:117037835 1349433451 A	
1006 A	3016 G	+7:117037836 1349433452 G	A
1006	3017 C	+7:117037837 1349433453 C	
1006	3018 A	+7:117037838 1349433454 A	
1007 V	3019 G	+7:117037839 1349433455 G	V
1007	3020 T	+7:117037840 1349433456 T	
1007	3021 T	+7:117037841 1349433457 T	
1008 V	3022 G	+7:117037842 1349433458 G	V
1008	3023 T	+7:117037843 1349433459 T	
1008	3024 C	+7:117037844 1349433460 C	
1009 A	3025 G	+7:117037845 1349433461 G	A
1009	3026 C	+7:117037846 1349433462 C	
1009	3027 A	+7:117037847 1349433463 A	
1010 V	3028 G	+7:117037848 1349433464 G	V
1010	3029 T	+7:117037849 1349433465 T	
1010	3030 T	+7:117037850 1349433466 T	
1011 L	3031 T	+7:117037851 1349433467 T	L
1011	3032 T	+7:117037852 1349433468 T	
1011	3033 A	+7:117037853 1349433469 A	
1012 Q	3034 C	+7:117037854 1349433470 C	Q
1012	3035 A	+7:117037855 1349433471 A	
1012	3036 A	+7:117037856 1349433472 A	
1013 P	3037 C	+7:117037857 1349433473 C	P
1013	3038 C	+7:117037858 1349433474 C	
1013	3039 C	+7:117037859 1349433475 C	
1014 Y	3040 T	+7:117037860 1349433476 T	Y
1014	3041 A	+7:117037861 1349433477 A	
1014	3042 C	+7:117037862 1349433478 C	
1015 I	3043 A	+7:117037863 1349433479 A	I
1015	3044 T	+7:117037864 1349433480 T	
1015	3045 C	+7:117037865 1349433481 C	
1016 F	3046 T	+7:117037866 1349433482 T	F
1016	3047 T	+7:117037867 1349433483 T	
1016	3048 T	+7:117037868 1349433484 T	
1017 V	3049 G	+7:117037869 1349433485 G	V
1017	3050 T	+7:117037870 1349433486 T	
1017	3051 T	+7:117037871 1349433487 T	
1018 A	3052 G	+7:117037872 1349433488 G	A
1018	3053 C	+7:117037873 1349433489 C	
1018	3054 A	+7:117037874 1349433490 A	
1019 T	3055 A	+7:117037875 1349433491 A	T
1019	3056 C	+7:117037876 1349433492 C	
1019	3057 A	+7:117037877 1349433493 A	
1020 V	3058 G	+7:117037878 1349433494 G	V
1020	3059 T	+7:117037879 1349433495 T	
1020	3060 G	+7:117037880 1349433496 G	
1021 P	3061 C	+7:117037881 1349433497 C	P
1021	3062 C	+7:117037882 1349433498 C	
1021	3063 A	+7:117037883 1349433499 A	
1022 V	3064 G	+7:117037884 1349433500 G	V
1022	3065 T	+7:117037885 1349433501 T	
1022	3066 G	+7:117037886 1349433502 G	
1023 I	3067 A	+7:117037887 1349433503 A	I
1023	3068 T	+7:117037888 1349433504 T	
1023	3069 A	+7:117037889 1349433505 A	
1024 V	3070 G	+7:117037890 1349433506 G	V
1024	3071 T	+7:117037891 1349433507 T	
1024	3072 G	+7:117037892 1349433508 G	
1025 A	3073 G	+7:117037893 1349433509 G	A
1025	3074 C	+7:117037894 1349433510 C	
1025	3075 T	+7:117037895 1349433511 T	
1026 F	3076 T	+7:117037896 1349433512 T	F
1026	3077 T	+7:117037897 1349433513 T	
1026	3078 T	+7:117037898 1349433514 T	
1027 I	3079 A	+7:117037899 1349433515 A	I
1027	3080 T	+7:117037900 1349433516 T	
1027	3081 T	+7:117037901 1349433517 T	
1028 M	3082 A	+7:117037902 1349433518 A	M
1028	3083 T	+7:117037903 1349433519 T	
1028	3084 G	+7:117037904 1349433520 G	
1029 L	3085 T	+7:117037905 1349433521 T	L
1029	3086 T	+7:117037906 1349433522 T	
1029	3087 G	+7:117037907 1349433523 G	
1030 R	3088 A	+7:117037908 1349433524 A	R
1030	3089 G	+7:117037909 1349433525 G	
1030	3090 A	+7:117037910 1349433526 A	
1031 A	3091 G	+7:117037911 1349433527 G	A
1031	3092 C	+7:117037912 1349433528 C	
1031	3093 A	+7:117037913 1349433529 A	
1032 Y	3094 T	+7:117037914 1349433530 T	Y
1032	3095 A	+7:117037915 1349433531 A	
1032	3096 T	+7:117037916 1349433532 T	
1033 F	3097 T	+7:117037917 1349433533 T	F
1033	3098 T	+7:117037918 1349433534 T	
1033	3099 C	+7:117037919 1349433535 C	
1034 L	3100 C	+7:117037920 1349433536 C	L
1034	3101 T	+7:117037921 1349433537 T	
1034	3102 C	+7:117037922 1349433538 C	
1035 Q	3103 C	+7:117037923 1349433539 C	Q
1035	3104 A	+7:117037924 1349433540 A	
1035	3105 A	+7:117037925 1349433541 A	
1036 T	3106 A	+7:117037926 1349433542 A	T
1036	3107 C	+7:117037927 1349433543 C	
1036	3108 C	+7:117037928 1349433544 C	
1037 S	3109 T	+7:117037929 1349433545 T	S
1037	3110 C	+7:117037930 1349433546 C	
1037	3111 A	+7:117037931 1349433547 A	
1038 Q	3112 C	+7:117037932 1349433548 C	Q
1038	3113 A	+7:117037933 1349433549 A	
1038	3114 G	+7:117037934 1349433550 G	
1039 Q	3115 C	+7:117037935 1349433551 C	Q
1039	3116 A	+7:117037936 1349433552 A	
1039	3117 A	+7:117037937 1349433553 A	
1040 L	3118 C	+7:117037938 1349433554 C	L
1040	3119 T	+7:117037939 1349433555 T	
1040	3120 C	+7:117037940 1349433556 C	
1041 K	3121 A	+7:117037941 1349433557 A	K
1041	3122 A	+7:117037942 1349433558 A	
1041	3123 A	+7:117037943 1349433559 A	
1042 Q	3124 C	+7:117037944 1349433560 C	Q
1042	3125 A	+7:117037945 1349433561 A	
1042	3126 A	+7:117037946 1349433562 A	
1043 L	3127 C	+7:117037947 1349433563 C	L
1043	3128 T	+7:117037948 1349433564 T	
1043	3129 G	+7:117037949 1349433565 G	
1044 E	3130 G	+7:117037950 1349433566 G	E
1044	3131 A	+7:117037951 1349433567 A	
1044	3132 A	+7:117037952 1349433568 A	
1045 S	3133 T	+7:117037953 1349433569 T	S
1045	3134 C	+7:117037954 1349433570 C	
1045	3135 T	+7:117037955 1349433571 T	
1046 E	3136 G	+7:117037956 1349433572 G	E
1046	3137 A	+7:117037957 1349433573 A	
1046	3138 A	+7:117037958 1349433574 A	
1047 G	3139 G	+7:117037959 1349433575 G	G
1047	3140 G	+7:117038871 1349434487 G	
1047	3141 C	+7:117038872 1349434488 C	
1048 R	3142 A	+7:117038873 1349434489 A	R
1048	3143 G	+7:117038874 1349434490 G	
1048	3144 G	+7:117038875 1349434491 G	
1049 S	3145 A	+7:117038876 1349434492 A	S
1049	3146 G	+7:117038877 1349434493 G	
1049	3147 T	+7:117038878 1349434494 T	
1050 P	3148 C	+7:117038879 1349434495 C	P
1050	3149 C	+7:117038880 1349434496 C	
1050	3150 A	+7:117038881 1349434497 A	
1051 I	3151 A	+7:117038882 1349434498 A	I
1051	3152 T	+7:117038883 1349434499 T	
1051	3153 T	+7:117038884 1349434500 T	
1052 F	3154 T	+7:117038885 1349434501 T	F
1052	3155 T	+7:117038886 1349434502 T	
1052	3156 C	+7:117038887 1349434503 C	
1053 T	3157 A	+7:117038888 1349434504 A	T
1053	3158 C	+7:117038889 1349434505 C	
1053	3159 T	+7:117038890 1349434506 T	
1054 H	3160 C	+7:117038891 1349434507 C	H
1054	3161 A	+7:117038892 1349434508 A	
1054	3162 T	+7:117038893 1349434509 T	
1055 L	3163 C	+7:117038894 1349434510 C	L
1055	3164 T	+7:117038895 1349434511 T	
1055	3165 T	+7:117038896 1349434512 T	
1056 V	3166 G	+7:117038897 1349434513 G	V
1056	3167 T	+7:117038898 1349434514 T	
1056	3168 T	+7:117038899 1349434515 T	
1057 T	3169 A	+7:117038900 1349434516 A	T
1057	3170 C	+7:117038901 1349434517 C	
1057	3171 A	+7:117038902 1349434518 A	
1058 S	3172 A	+7:117038903 1349434519 A	S
1058	3173 G	+7:117038904 1349434520 G	
1058	3174 C	+7:117038905 1349434521 C	
1059 L	3175 T	+7:117038906 1349434522 T	L
1059	3176 T	+7:117038907 1349434523 T	
1059	3177 A	+7:117038908 1349434524 A	
1060 K	3178 A	+7:117038909 1349434525 A	K
1060	3179 A	+7:117038910 1349434526 A	
1060	3180 A	+7:117038911 1349434527 A	
1061 G	3181 G	+7:117038912 1349434528 G	G
1061	3182 G	+7:117038913 1349434529 G	
1061	3183 A	+7:117038914 1349434530 A	
1062 L	3184 C	+7:117038915 1349434531 C	L
1062	3185 T	+7:117038916 1349434532 T	
1062	3186 A	+7:117038917 1349434533 A	
1063 W	3187 T	+7:117038918 1349434534 T	W
1063	3188 G	+7:117038919 1349434535 G	
1063	3189 G	+7:117038920 1349434536 G	
1064 T	3190 A	+7:117038921 1349434537 A	T
1064	3191 C	+7:117038922 1349434538 C	
1064	3192 A	+7:117038923 1349434539 A	
1065 L	3193 C	+7:117038924 1349434540 C	L
1065	3194 T	+7:117038925 1349434541 T	
1065	3195 T	+7:117038926 1349434542 T	
1066 R	3196 C	+7:117038927 1349434543 C	R
1066	3197 G	+7:117038928 1349434544 G	
1066	3198 T	+7:117038929 1349434545 T	
1067 A	3199 G	+7:117038930 1349434546 G	A
1067	3200 C	+7:117038931 1349434547 C	
1067	3201 C	+7:117038932 1349434548 C	
1068 F	3202 T	+7:117038933 1349434549 T	F
1068	3203 T	+7:117038934 1349434550 T	
1068	3204 C	+7:117038935 1349434551 C	
1069 G	3205 G	+7:117038936 1349434552 G	G
1069	3206 G	+7:117038937 1349434553 G	
1069	3207 A	+7:117038938 1349434554 A	
1070 R	3208 C	+7:117038939 1349434555 C	R
1070	3209 G	+7:117038940 1349434556 G	
1070	3210 G	+7:117038941 1349434557 G	
1071 Q	3211 C	+7:117038942 1349434558 C	Q
1071	3212 A	+7:117038943 1349434559 A	
1071	3213 G	+7:117038944 1349434560 G	
1072 P	3214 C	+7:117038945 1349434561 C	P
1072	3215 C	+7:117038946 1349434562 C	
1072	3216 T	+7:117038947 1349434563 T	
1073 Y	3217 T	+7:117038948 1349434564 T	Y
1073	3218 A	+7:117038949 1349434565 A	
1073	3219 C	+7:117038950 1349434566 C	
1074 F	3220 T	+7:117038951 1349434567 T	F
1074	3221 T	+7:117038952 1349434568 T	
1074	3222 T	+7:117038953 1349434569 T	
1075 E	3223 G	+7:117038954 1349434570 G	E
1075	3224 A	+7:117038955 1349434571 A	
1075	3225 A	+7:117038956 1349434572 A	
1076 T	3226 A	+7:117038957 1349434573 A	T
1076	3227 C	+7:117038958 1349434574 C	
1076	3228 T	+7:117038959 1349434575 T	
1077 L	3229 C	+7:117038960 1349434576 C	L
1077	3230 T	+7:117038961 1349434577 T	
1077	3231 G	+7:117038962 1349434578 G	
1078 F	3232 T	+7:117038963 1349434579 T	F
1078	3233 T	+7:117038964 1349434580 T	
1078	3234 C	+7:117038965 1349434581 C	
1079 H	3235 C	+7:117038966 1349434582 C	H
1079	3236 A	+7:117038967 1349434583 A	
1079	3237 C	+7:117038968 1349434584 C	
1080 K	3238 A	+7:117038969 1349434585 A	K
1080	3239 A	+7:117038970 1349434586 A	
1080	3240 A	+7:117038971 1349434587 A	
1081 A	3241 G	+7:117038972 1349434588 G	A
1081	3242 C	+7:117038973 1349434589 C	
1081	3243 T	+7:117038974 1349434590 T	
1082 L	3244 C	+7:117038975 1349434591 C	L
1082	3245 T	+7:117038976 1349434592 T	
1082	3246 G	+7:117038977 1349434593 G	
1083 N	3247 A	+7:117038978 1349434594 A	N
1083	3248 A	+7:117038979 1349434595 A	
1083	3249 T	+7:117038980 1349434596 T	
1084 L	3250 T	+7:117038981 1349434597 T	L
1084	3251 T	+7:117038982 1349434598 T	
1084	3252 A	+7:117038983 1349434599 A	
1085 H	3253 C	+7:117038984 1349434600 C	H
1085	3254 A	+7:117038985 1349434601 A	
1085	3255 T	+7:117038986 1349434602 T	
1086 T	3256 A	+7:117038987 1349434603 A	T
1086	3257 C	+7:117038988 1349434604 C	
1086	3258 T	+7:117038989 1349434605 T	
1087 A	3259 G	+7:117038990 1349434606 G	A
1087	3260 C	+7:117038991 1349434607 C	
1087	3261 C	+7:117038992 1349434608 C	
1088 N	3262 A	+7:117038993 1349434609 A	N
1088	3263 A	+7:117038994 1349434610 A	
1088	3264 C	+7:117038995 1349434611 C	
1089 W	3265 T	+7:117038996 1349434612 T	W
1089	3266 G	+7:117038997 1349434613 G	
1089	3267 G	+7:117038998 1349434614 G	
1090 F	3268 T	+7:117038999 1349434615 T	F
1090	3269 T	+7:117039000 1349434616 T	
1090	3270 C	+7:117039001 1349434617 C	
1091 L	3271 T	+7:117039002 1349434618 T	L
1091	3272 T	+7:117039003 1349434619 T	
1091	3273 G	+7:117039004 1349434620 G	
1092 Y	3274 T	+7:117039005 1349434621 T	Y
1092	3275 A	+7:117039006 1349434622 A	
1092	3276 C	+7:117039007 1349434623 C	
1093 L	3277 C	+7:117039008 1349434624 C	L
1093	3278 T	+7:117039009 1349434625 T	
1093	3279 G	+7:117039010 1349434626 G	
1094 S	3280 T	+7:117039011 1349434627 T	S
1094	3281 C	+7:117039012 1349434628 C	
1094	3282 A	+7:117039013 1349434629 A	
1095 T	3283 A	+7:117039014 1349434630 A	T
1095	3284 C	+7:117039015 1349434631 C	
1095	3285 A	+7:117039016 1349434632 A	
1096 L	3286 C	+7:117039017 1349434633 C	L
1096	3287 T	+7:117039018 1349434634 T	
1096	3288 G	+7:117039019 1349434635 G	
1097 R	3289 C	+7:117039020 1349434636 C	R
1097	3290 G	+7:117039021 1349434637 G	
1097	3291 C	+7:117039022 1349434638 C	
1098 W	3292 T	+7:117039023 1349434639 T	W
1098	3293 G	+7:117039024 1349434640 G	
1098	3294 G	+7:117039025 1349434641 G	
1099 F	3295 T	+7:117039026 1349434642 T	F
1099	3296 T	+7:117039027 1349434643 T	
1099	3297 C	+7:117039028 1349434644 C	
1100 Q	3298 C	+7:117039029 1349434645 C	Q
1100	3299 A	+7:117039030 1349434646 A	
1100	3300 A	+7:117039031 1349434647 A	
1101 M	3301 A	+7:117039032 1349434648 A	M
1101	3302 T	+7:117039033 1349434649 T	
1101	3303 G	+7:117039034 1349434650 G	
1102 R	3304 A	+7:117039035 1349434651 A	R
1102	3305 G	+7:117039036 1349434652 G	
1102	3306 A	+7:117039037 1349434653 A	
1103 I	3307 A	+7:117039038 1349434654 A	I
1103	3308 T	+7:117039039 1349434655 T	
1103	3309 A	+7:117039040 1349434656 A	
1104 E	3310 G	+7:117039041 1349434657 G	E
1104	3311 A	+7:117039042 1349434658 A	
1104	3312 A	+7:117039043 1349434659 A	
1105 M	3313 A	+7:117039044 1349434660 A	M
1105	3314 T	+7:117039045 1349434661 T	
1105	3315 G	+7:117039046 1349434662 G	
1106 I	3316 A	+7:117039047 1349434663 A	I
1106	3317 T	+7:117039048 1349434664 T	
1106	3318 T	+7:117039049 1349434665 T	
1107 F	3319 T	+7:117039050 1349434666 T	F
1107	3320 T	+7:117039051 1349434667 T	
1107	3321 T	+7:117039052 1349434668 T	
1108 V	3322 G	+7:117039053 1349434669 G	V
1108	3323 T	+7:117039054 1349434670 T	
1108	3324 C	+7:117039055 1349434671 C	
1109 I	3325 A	+7:117039056 1349434672 A	I
1109	3326 T	+7:117039057 1349434673 T	
1109	3327 C	+7:117039058 1349434674 C	
1110 F	3328 T	+7:117039059 1349434675 T	F
1110	3329 T	+7:117039060 1349434676 T	
1110	3330 C	+7:117039061 1349434677 C	
1111 F	3331 T	+7:117039062 1349434678 T	F
1111	3332 T	+7:117039063 1349434679 T	
1111	3333 C	+7:117039064 1349434680 C	
1112 I	3334 A	+7:117039065 1349434681 A	I
1112	3335 T	+7:117039066 1349434682 T	
1112	3336 T	+7:117039067 1349434683 T	
1113 A	3337 G	+7:117039068 1349434684 G	A
1113	3338 C	+7:117039069 1349434685 C	
1113	3339 T	+7:117039070 1349434686 T	
1114 V	3340 G	+7:117039071 1349434687 G	V
1114	3341 T	+7:117039072 1349434688 T	
1114	3342 T	+7:117039073 1349434689 T	
1115 T	3343 A	+7:117039074 1349434690 A	T
1115	3344 C	+7:117039075 1349434691 C	
1115	3345 C	+7:117039076 1349434692 C	
1116 F	3346 T	+7:117039077 1349434693 T	F
1116	3347 T	+7:117039078 1349434694 T	
1116	3348 C	+7:117039079 1349434695 C	
1117 I	3349 A	+7:117039080 1349434696 A	I
1117	3350 T	+7:117039081 1349434697 T	
1117	3351 T	+7:117039082 1349434698 T	
1118 S	3352 T	+7:117039083 1349434699 T	S
1118	3353 C	+7:117039084 1349434700 C	
1118	3354 C	+7:117039085 1349434701 C	
1119 I	3355 A	+7:117039086 1349434702 A	I
1119	3356 T	+7:117039087 1349434703 T	
1119	3357 T	+7:117039088 1349434704 T	
1120 L	3358 T	+7:117039089 1349434705 T	L
1120	3359 T	+7:117039090 1349434706 T	
1120	3360 A	+7:117039091 1349434707 A	
1121 T	3361 A	+7:117039092 1349434708 A	T
1121	3362 C	+7:117039093 1349434709 C	
1121	3363 A	+7:117039094 1349434710 A	
1122 T	3364 A	+7:117039095 1349434711 A	T
1122	3365 C	+7:117039096 1349434712 C	
1122	3366 A	+7:117039097 1349434713 A	
1123 G	3367 G	+7:117039098 1349434714 G	G
1123	3368 G	+7:117041903 1349437519 G	
1123	3369 A	+7:117041904 1349437520 A	
1124 E	3370 G	+7:117041905 1349437521 G	E
1124	3371 A	+7:117041906 1349437522 A	
1124	3372 A	+7:117041907 1349437523 A	
1125 G	3373 G	+7:117041908 1349437524 G	G
1125	3374 G	+7:117041909 1349437525 G	
1125	3375 A	+7:117041910 1349437526 A	
1126 E	3376 G	+7:117041911 1349437527 G	E
1126	3377 A	+7:117041912 1349437528 A	
1126	3378 A	+7:117041913 1349437529 A	
1127 G	3379 G	+7:117041914 1349437530 G	G
1127	3380 G	+7:117041915 1349437531 G	
1127	3381 A	+7:117041916 1349437532 A	
1128 R	3382 A	+7:117041917 1349437533 A	R
1128	3383 G	+7:117041918 1349437534 G	
1128	3384 A	+7:117041919 1349437535 A	
1129 V	3385 G	+7:117041920 1349437536 G	V
1129	3386 T	+7:117041921 1349437537 T	
1129	3387 T	+7:117041922 1349437538 T	
1130 G	3388 G	+7:117041923 1349437539 G	G
1130	3389 G	+7:117041924 1349437540 G	
1130	3390 T	+7:117041925 1349437541 T	
1131 I	3391 A	+7:117041926 1349437542 A	I
1131	3392 T	+7:117041927 1349437543 T	
1131	3393 T	+7:117041928 1349437544 T	
1132 I	3394 A	+7:117041929 1349437545 A	I
1132	3395 T	+7:117041930 1349437546 T	
1132	3396 C	+7:117041931 1349437547 C	
1133 L	3397 C	+7:117041932 1349437548 C	L
1133	3398 T	+7:117041933 1349437549 T	
1133	3399 G	+7:117041934 1349437550 G	
1134 T	3400 A	+7:117041935 1349437551 A	T
1134	3401 C	+7:117041936 1349437552 C	
1134	3402 T	+7:117041937 1349437553 T	
1135 L	3403 T	+7:117041938 1349437554 T	L
1135	3404 T	+7:117041939 1349437555 T	
1135	3405 A	+7:117041940 1349437556 A	
1136 A	3406 G	+7:117041941 1349437557 G	A
1136	3407 C	+7:117041942 1349437558 C	
1136	3408 C	+7:117041943 1349437559 C	
1137 M	3409 A	+7:117041944 1349437560 A	M
1137	3410 T	+7:117041945 1349437561 T	
1137	3411 G	+7:117041946 1349437562 G	
1138 N	3412 A	+7:117041947 1349437563 A	N
1138	3413 A	+7:117041948 1349437564 A	
1138	3414 T	+7:117041949 1349437565 T	
1139 I	3415 A	+7:117041950 1349437566 A	I
1139	3416 T	+7:117041951 1349437567 T	
1139	3417 C	+7:117041952 1349437568 C	
1140 M	3418 A	+7:117041953 1349437569 A	M
1140	3419 T	+7:117041954 1349437570 T	
1140	3420 G	+7:117041955 1349437571 G	
1141 S	3421 A	+7:117041956 1349437572 A	S
1141	3422 G	+7:117041957 1349437573 G	
1141	3423 T	+7:117041958 1349437574 T	
1142 T	3424 A	+7:117041959 1349437575 A	T
1142	3425 C	+7:117041960 1349437576 C	
1142	3426 A	+7:117041961 1349437577 A	
1143 L	3427 T	+7:117041962 1349437578 T	L
1143	3428 T	+7:117041963 1349437579 T	
1143	3429 G	+7:117041964 1349437580 G	
1144 Q	3430 C	+7:117041965 1349437581 C	Q
1144	3431 A	+7:117041966 1349437582 A	
1144	3432 G	+7:117041967 1349437583 G	
1145 W	3433 T	+7:117041968 1349437584 T	W
1145	3434 G	+7:117041969 1349437585 G	
1145	3435 G	+7:117041970 1349437586 G	
1146 A	3436 G	+7:117041971 1349437587 G	A
1146	3437 C	+7:117041972 1349437588 C	
1146	3438 T	+7:117041973 1349437589 T	
1147 V	3439 G	+7:117041974 1349437590 G	V
1147	3440 T	+7:117041975 1349437591 T	
1147	3441 A	+7:117041976 1349437592 A	
1148 N	3442 A	+7:117041977 1349437593 A	N
1148	3443 A	+7:117041978 1349437594 A	
1148	3444 C	+7:117041979 1349437595 C	
1149 S	3445 T	+7:117041980 1349437596 T	S
1149	3446 C	+7:117041981 1349437597 C	
1149	3447 C	+7:117041982 1349437598 C	
1150 S	3448 A	+7:117041983 1349437599 A	S
1150	3449 G	+7:117041984 1349437600 G	
1150	3450 C	+7:117041985 1349437601 C	
1151 I	3451 A	+7:117041986 1349437602 A	I
1151	3452 T	+7:117041987 1349437603 T	
1151	3453 A	+7:117041988 1349437604 A	
1152 D	3454 G	+7:117041989 1349437605 G	D
1152	3455 A	+7:117041990 1349437606 A	
1152	3456 T	+7:117041991 1349437607 T	
1153 V	3457 G	+7:117041992 1349437608 G	V
1153	3458 T	+7:117041993 1349437609 T	
1153	3459 G	+7:117041994 1349437610 G	
1154 D	3460 G	+7:117041995 1349437611 G	D
1154	3461 A	+7:117041996 1349437612 A	
1154	3462 T	+7:117041997 1349437613 T	
1155 S	3463 A	+7:117041998 1349437614 A	S
1155	3464 G	+7:117041999 1349437615 G	
1155	3465 C	+7:117042000 1349437616 C	
1156 L	3466 T	+7:117042001 1349437617 T	L
1156	3467 T	+7:117042002 1349437618 T	
1156	3468 G	+7:117042003 1349437619 G	
1157 M	3469 A	+7:117054812 1349450428 A	M
1157	3470 T	+7:117054813 1349450429 T	
1157	3471 G	+7:117054814 1349450430 G	
1158 R	3472 C	+7:117054815 1349450431 C	R
1158	3473 G	+7:117054816 1349450432 G	
1158	3474 A	+7:117054817 1349450433 A	
1159 S	3475 T	+7:117054818 1349450434 T	S
1159	3476 C	+7:117054819 1349450435 C	
1159	3477 T	+7:117054820 1349450436 T	
1160 V	3478 G	+7:117054821 1349450437 G	V
1160	3479 T	+7:117054822 1349450438 T	
1160	3480 G	+7:117054823 1349450439 G	
1161 S	3481 A	+7:117054824 1349450440 A	S
1161	3482 G	+7:117054825 1349450441 G	
1161	3483 C	+7:117054826 1349450442 C	
1162 R	3484 C	+7:117054827 1349450443 C	R
1162	3485 G	+7:117054828 1349450444 G	
1162	3486 A	+7:117054829 1349450445 A	
1163 V	3487 G	+7:117054830 1349450446 G	V
1163	3488 T	+7:117054831 1349450447 T	
1163	3489 C	+7:117054832 1349450448 C	
1164 F	3490 T	+7:117054833 1349450449 T	F
1164	3491 T	+7:117054834 1349450450 T	
1164	3492 T	+7:117054835 1349450451 T	
1165 K	3493 A	+7:117054836 1349450452 A	K
1165	3494 A	+7:117054837 1349450453 A	
1165	3495 G	+7:117054838 1349450454 G	
1166 F	3496 T	+7:117054839 1349450455 T	F
1166	3497 T	+7:117054840 1349450456 T	
1166	3498 C	+7:117054841 1349450457 C	
1167 I	3499 A	+7:117054842 1349450458 A	I
1167	3500 T	+7:117054843 1349450459 T	
1167	3501 T	+7:117054844 1349450460 T	
1168 D	3502 G	+7:117054845 1349450461 G	D
1168	3503 A	+7:117054846 1349450462 A	
1168	3504 C	+7:117054847 1349450463 C	
1169 M	3505 A	+7:117054848 1349450464 A	M
1169	3506 T	+7:117054849 1349450465 T	
1169	3507 G	+7:117054850 1349450466 G	
1170 P	3508 C	+7:117054851 1349450467 C	P
1170	3509 C	+7:117054852 1349450468 C	
1170	3510 A	+7:117054853 1349450469 A	
1171 T	3511 A	+7:117054854 1349450470 A	T
1171	3512 C	+7:117054855 1349450471 C	
1171	3513 A	+7:117054856 1349450472 A	
1172 E	3514 G	+7:117054857 1349450473 G	E
1172	3515 A	+7:117054858 1349450474 A	
1172	3516 A	+7:117054859 1349450475 A	
1173 G	3517 G	+7:117054860 1349450476 G	G
1173	3518 G	+7:117054861 1349450477 G	
1173	3519 T	+7:117054862 1349450478 T	
1174 K	3520 A	+7:117054863 1349450479 A	K
1174	3521 A	+7:117054864 1349450480 A	
1174	3522 A	+7:117054865 1349450481 A	
1175 P	3523 C	+7:117054866 1349450482 C	P
1175	3524 C	+7:117054867 1349450483 C	
1175	3525 T	+7:117054868 1349450484 T	
1176 T	3526 A	+7:117054869 1349450485 A	T
1176	3527 C	+7:117054870 1349450486 C	
1176	3528 C	+7:117054871 1349450487 C	
1177 K	3529 A	+7:117054872 1349450488 A	K
1177	3530 A	+7:117054873 1349450489 A	
1177	3531 G	+7:117054874 1349450490 G	
1178 S	3532 T	+7:117054875 1349450491 T	S
1178	3533 C	+7:117054876 1349450492 C	
1178	3534 A	+7:117054877 1349450493 A	
1179 T	3535 A	+7:117054878 1349450494 A	T
1179	3536 C	+7:117054879 1349450495 C	
1179	3537 C	+7:117054880 1349450496 C	
1180 K	3538 A	+7:117054881 1349450497 A	K
1180	3539 A	+7:117054882 1349450498 A	
1180	3540 A	+7:117054883 1349450499 A	
1181 P	3541 C	+7:117054884 1349450500 C	P
1181	3542 C	+7:117054885 1349450501 C	
1181	3543 A	+7:117054886 1349450502 A	
1182 Y	3544 T	+7:117054887 1349450503 T	Y
1182	3545 A	+7:117054888 1349450504 A	
1182	3546 C	+7:117054889 1349450505 C	
1183 K	3547 A	+7:117054890 1349450506 A	K
1183	3548 A	+7:117054891 1349450507 A	
1183	3549 G	+7:117054892 1349450508 G	
1184 N	3550 A	+7:117054893 1349450509 A	N
1184	3551 A	+7:117054894 1349450510 A	
1184	3552 T	+7:117054895 1349450511 T	
1185 G	3553 G	+7:117054896 1349450512 G	G
1185	3554 G	+7:117054897 1349450513 G	
1185	3555 C	+7:117054898 1349450514 C	
1186 Q	3556 C	+7:117054899 1349450515 C	Q
1186	3557 A	+7:117054900 1349450516 A	
1186	3558 A	+7:117054901 1349450517 A	
1187 L	3559 C	+7:117054902 1349450518 C	L
1187	3560 T	+7:117054903 1349450519 T	
1187	3561 C	+7:117054904 1349450520 C	
1188 S	3562 T	+7:117054905 1349450521 T	S
1188	3563 C	+7:117054906 1349450522 C	
1188	3564 G	+7:117054907 1349450523 G	
1189 K	3565 A	+7:117054908 1349450524 A	K
1189	3566 A	+7:117054909 1349450525 A	
1189	3567 A	+7:117054910 1349450526 A	
1190 V	3568 G	+7:117054911 1349450527 G	V
1190	3569 T	+7:117054912 1349450528 T	
1190	3570 T	+7:117054913 1349450529 T	
1191 M	3571 A	+7:117054914 1349450530 A	M
1191	3572 T	+7:117054915 1349450531 T	
1191	3573 G	+7:117054916 1349450532 G	
1192 I	3574 A	+7:117054917 1349450533 A	I
1192	3575 T	+7:117054918 1349450534 T	
1192	3576 T	+7:117054919 1349450535 T	
1193 I	3577 A	+7:117054920 1349450536 A	I
1193	3578 T	+7:117054921 1349450537 T	
1193	3579 T	+7:117054922 1349450538 T	
1194 E	3580 G	+7:117054923 1349450539 G	E
1194	3581 A	+7:117054924 1349450540 A	
1194	3582 G	+7:117054925 1349450541 G	
1195 N	3583 A	+7:117054926 1349450542 A	N
1195	3584 A	+7:117054927 1349450543 A	
1195	3585 T	+7:117054928 1349450544 T	
1196 S	3586 T	+7:117054929 1349450545 T	S
1196	3587 C	+7:117054930 1349450546 C	
1196	3588 A	+7:117054931 1349450547 A	
1197 H	3589 C	+7:117054932 1349450548 C	H
1197	3590 A	+7:117054933 1349450549 A	
1197	3591 C	+7:117054934 1349450550 C	
1198 V	3592 G	+7:117054935 1349450551 G	V
1198	3593 T	+7:117054936 1349450552 T	
1198	3594 G	+7:117054937 1349450553 G	
1199 K	3595 A	+7:117054938 1349450554 A	K
1199	3596 A	+7:117054939 1349450555 A	
1199	3597 G	+7:117054940 1349450556 G	
1200 K	3598 A	+7:117054941 1349450557 A	K
1200	3599 A	+7:117054942 1349450558 A	
1200	3600 A	+7:117054943 1349450559 A	
1201 D	3601 G	+7:117054944 1349450560 G	D
1201	3602 A	+7:117054945 1349450561 A	
1201	3603 T	+7:117054946 1349450562 T	
1202 D	3604 G	+7:117054947 1349450563 G	D
1202	3605 A	+7:117054948 1349450564 A	
1202	3606 C	+7:117054949 1349450565 C	
1203 I	3607 A	+7:117054950 1349450566 A	I
1203	3608 T	+7:117054951 1349450567 T	
1203	3609 C	+7:117054952 1349450568 C	
1204 W	3610 T	+7:117054953 1349450569 T	W
1204	3611 G	+7:117054954 1349450570 G	
1204	3612 G	+7:117054955 1349450571 G	
1205 P	3613 C	+7:117054956 1349450572 C	P
1205	3614 C	+7:117054957 1349450573 C	
1205	3615 C	+7:117054958 1349450574 C	
1206 S	3616 T	+7:117054959 1349450575 T	S
1206	3617 C	+7:117054960 1349450576 C	
1206	3618 A	+7:117054961 1349450577 A	
1207 G	3619 G	+7:117054962 1349450578 G	G
1207	3620 G	+7:117054963 1349450579 G	
1207	3621 G	+7:117054964 1349450580 G	
1208 G	3622 G	+7:117054965 1349450581 G	G
1208	3623 G	+7:117054966 1349450582 G	
1208	3624 C	+7:117054967 1349450583 C	
1209 Q	3625 C	+7:117054968 1349450584 C	Q
1209	3626 A	+7:117054969 1349450585 A	
1209	3627 A	+7:117054970 1349450586 A	
1210 M	3628 A	+7:117054971 1349450587 A	M
1210	3629 T	+7:117054972 1349450588 T	
1210	3630 G	+7:117054973 1349450589 G	
1211 T	3631 A	+7:117054974 1349450590 A	T
1211	3632 C	+7:117054975 1349450591 C	
1211	3633 T	+7:117054976 1349450592 T	
1212 V	3634 G	+7:117054977 1349450593 G	V
1212	3635 T	+7:117054978 1349450594 T	
1212	3636 C	+7:117054979 1349450595 C	
1213 K	3637 A	+7:117054980 1349450596 A	K
1213	3638 A	+7:117054981 1349450597 A	
1213	3639 A	+7:117054982 1349450598 A	
1214 D	3640 G	+7:117054983 1349450599 G	D
1214	3641 A	+7:117054984 1349450600 A	
1214	3642 T	+7:117054985 1349450601 T	
1215 L	3643 C	+7:117054986 1349450602 C	L
1215	3644 T	+7:117054987 1349450603 T	
1215	3645 C	+7:117054988 1349450604 C	
1216 T	3646 A	+7:117054989 1349450605 A	T
1216	3647 C	+7:117054990 1349450606 C	
1216	3648 A	+7:117054991 1349450607 A	
1217 A	3649 G	+7:117054992 1349450608 G	A
1217	3650 C	+7:117054993 1349450609 C	
1217	3651 A	+7:117054994 1349450610 A	
1218 K	3652 A	+7:117054995 1349450611 A	K
1218	3653 A	+7:117054996 1349450612 A	
1218	3654 A	+7:117054997 1349450613 A	
1219 Y	3655 T	+7:117054998 1349450614 T	Y
1219	3656 A	+7:117054999 1349450615 A	
1219	3657 C	+7:117055000 1349450616 C	
1220 T	3658 A	+7:117055001 1349450617 A	T
1220	3659 C	+7:117055002 1349450618 C	
1220	3660 A	+7:117055003 1349450619 A	
1221 E	3661 G	+7:117055004 1349450620 G	E
1221	3662 A	+7:117055005 1349450621 A	
1221	3663 A	+7:117055006 1349450622 A	
1222 G	3664 G	+7:117055007 1349450623 G	G
1222	3665 G	+7:117055008 1349450624 G	
1222	3666 T	+7:117055009 1349450625 T	
1223 G	3667 G	+7:117055010 1349450626 G	G
1223	3668 G	+7:117055011 1349450627 G	
1223	3669 A	+7:117055012 1349450628 A	
1224 N	3670 A	+7:117055013 1349450629 A	N
1224	3671 A	+7:117055014 1349450630 A	
1224	3672 T	+7:117055015 1349450631 T	
1225 A	3673 G	+7:117055016 1349450632 G	A
1225	3674 C	+7:117055017 1349450633 C	
1225	3675 C	+7:117055018 1349450634 C	
1226 I	3676 A	+7:117055019 1349450635 A	I
1226	3677 T	+7:117055020 1349450636 T	
1226	3678 A	+7:117055021 1349450637 A	
1227 L	3679 T	+7:117055022 1349450638 T	L
1227	3680 T	+7:117055023 1349450639 T	
1227	3681 A	+7:117055024 1349450640 A	
1228 E	3682 G	+7:117055025 1349450641 G	E
1228	3683 A	+7:117055026 1349450642 A	
1228	3684 G	+7:117055027 1349450643 G	
1229 N	3685 A	+7:117055028 1349450644 A	N
1229	3686 A	+7:117055029 1349450645 A	
1229	3687 C	+7:117055030 1349450646 C	
1230 I	3688 A	+7:117055031 1349450647 A	I
1230	3689 T	+7:117055032 1349450648 T	
1230	3690 T	+7:117055033 1349450649 T	
1231 S	3691 T	+7:117055034 1349450650 T	S
1231	3692 C	+7:117055035 1349450651 C	
1231	3693 C	+7:117055036 1349450652 C	
1232 F	3694 T	+7:117055037 1349450653 T	F
1232	3695 T	+7:117055038 1349450654 T	
1232	3696 C	+7:117055039 1349450655 C	
1233 S	3697 T	+7:117055040 1349450656 T	S
1233	3698 C	+7:117055041 1349450657 C	
1233	3699 A	+7:117055042 1349450658 A	
1234 I	3700 A	+7:117055043 1349450659 A	I
1234	3701 T	+7:117055044 1349450660 T	
1234	3702 A	+7:117055045 1349450661 A	
1235 S	3703 A	+7:117055046 1349450662 A	S
1235	3704 G	+7:117055047 1349450663 G	
1235	3705 T	+7:117055048 1349450664 T	
1236 P	3706 C	+7:117055049 1349450665 C	P
1236	3707 C	+7:117055050 1349450666 C	
1236	3708 T	+7:117055051 1349450667 T	
1237 G	3709 G	+7:117055052 1349450668 G	G
1237	3710 G	+7:117055053 1349450669 G	
1237	3711 C	+7:117055054 1349450670 C	
1238 Q	3712 C	+7:117055055 1349450671 C	Q
1238	3713 A	+7:117055056 1349450672 A	
1238	3714 G	+7:117055057 1349450673 G	
1239 R	3715 A	+7:117055058 1349450674 A	R
1239	3716 G	+7:117055059 1349450675 G	
1239	3717 G	+7:117055060 1349450676 G	
1240 V	3718 G	+7:117069728 1349465344 G	V
1240	3719 T	+7:117069729 1349465345 T	
1240	3720 G	+7:117069730 1349465346 G	
1241 G	3721 G	+7:117069731 1349465347 G	G
1241	3722 G	+7:117069732 1349465348 G	
1241	3723 C	+7:117069733 1349465349 C	
1242 L	3724 C	+7:117069734 1349465350 C	L
1242	3725 T	+7:117069735 1349465351 T	
1242	3726 C	+7:117069736 1349465352 C	
1243 L	3727 T	+7:117069737 1349465353 T	L
1243	3728 T	+7:117069738 1349465354 T	
1243	3729 G	+7:117069739 1349465355 G	
1244 G	3730 G	+7:117069740 1349465356 G	G
1244	3731 G	+7:117069741 1349465357 G	
1244	3732 A	+7:117069742 1349465358 A	
1245 R	3733 A	+7:117069743 1349465359 A	R
1245	3734 G	+7:117069744 1349465360 G	
1245	3735 A	+7:117069745 1349465361 A	
1246 T	3736 A	+7:117069746 1349465362 A	T
1246	3737 C	+7:117069747 1349465363 C	
1246	3738 T	+7:117069748 1349465364 T	
1247 G	3739 G	+7:117069749 1349465365 G	G
1247	3740 G	+7:117069750 1349465366 G	
1247	3741 A	+7:117069751 1349465367 A	
1248 S	3742 T	+7:117069752 1349465368 T	S
1248	3743 C	+7:117069753 1349465369 C	
1248	3744 A	+7:117069754 1349465370 A	
1249 G	3745 G	+7:117069755 1349465371 G	G
1249	3746 G	+7:117069756 1349465372 G	
1249	3747 G	+7:117069757 1349465373 G	
1250 K	3748 A	+7:117069758 1349465374 A	K
1250	3749 A	+7:117069759 1349465375 A	
1250	3750 G	+7:117069760 1349465376 G	
1251 S	3751 A	+7:117069761 1349465377 A	S
1251	3752 G	+7:117069762 1349465378 G	
1251	3753 T	+7:117069763 1349465379 T	
1252 T	3754 A	+7:117069764 1349465380 A	T
1252	3755 C	+7:117069765 1349465381 C	
1252	3756 T	+7:117069766 1349465382 T	
1253 L	3757 T	+7:117069767 1349465383 T	L
1253	3758 T	+7:117069768 1349465384 T	
1253	3759 G	+7:117069769 1349465385 G	
1254 L	3760 T	+7:117069770 1349465386 T	L
1254	3761 T	+7:117069771 1349465387 T	
1254	3762 A	+7:117069772 1349465388 A	
1255 S	3763 T	+7:117069773 1349465389 T	S
1255	3764 C	+7:117069774 1349465390 C	
1255	3765 A	+7:117069775 1349465391 A	
1256 A	3766 G	+7:117069776 1349465392 G	A
1256	3767 C	+7:117069777 1349465393 C	
1256	3768 T	+7:117069778 1349465394 T	
1257 F	3769 T	+7:117069779 1349465395 T	F
1257	3770 T	+7:117069780 1349465396 T	
1257	3771 T	+7:117069781 1349465397 T	
1258 L	3772 T	+7:117069782 1349465398 T	L
1258	3773 T	+7:117069783 1349465399 T	
1258	3774 G	+7:117069784 1349465400 G	
1259 R	3775 A	+7:117069785 1349465401 A	R
1259	3776 G	+7:117069786 1349465402 G	
1259	3777 A	+7:117069787 1349465403 A	
1260 L	3778 C	+7:117069788 1349465404 C	L
1260	3779 T	+7:117069789 1349465405 T	
1260	3780 A	+7:117069790 1349465406 A	
1261 L	3781 C	+7:117069791 1349465407 C	L
1261	3782 T	+7:117069792 1349465408 T	
1261	3783 G	+7:117069793 1349465409 G	
1262 N	3784 A	+7:117069794 1349465410 A	N
1262	3785 A	+7:117069795 1349465411 A	
1262	3786 C	+7:117069796 1349465412 C	
1263 T	3787 A	+7:117069797 1349465413 A	T
1263	3788 C	+7:117069798 1349465414 C	
1263	3789 T	+7:117069799 1349465415 T	
1264 E	3790 G	+7:117069800 1349465416 G	E
1264	3791 A	+7:117069801 1349465417 A	
1264	3792 A	+7:117069802 1349465418 A	
1265 G	3793 G	+7:117069803 1349465419 G	G
1265	3794 G	+7:117069804 1349465420 G	
1265	3795 A	+7:117069805 1349465421 A	
1266 E	3796 G	+7:117069806 1349465422 G	E
1266	3797 A	+7:117069807 1349465423 A	
1266	3798 A	+7:117069808 1349465424 A	
1267 I	3799 A	+7:117069809 1349465425 A	I
1267	3800 T	+7:117069810 1349465426 T	
1267	3801 C	+7:117069811 1349465427 C	
1268 Q	3802 C	+7:117069812 1349465428 C	Q
1268	3803 A	+7:117069813 1349465429 A	
1268	3804 G	+7:117069814 1349465430 G	
1269 I	3805 A	+7:117069815 1349465431 A	I
1269	3806 T	+7:117069816 1349465432 T	
1269	3807 C	+7:117069817 1349465433 C	
1270 D	3808 G	+7:117069818 1349465434 G	D
1270	3809 A	+7:117069819 1349465435 A	
1270	3810 T	+7:117069820 1349465436 T	
1271 G	3811 G	+7:117069821 1349465437 G	G
1271	3812 G	+7:117069822 1349465438 G	
1271	3813 T	+7:117069823 1349465439 T	
1272 V	3814 G	+7:117069824 1349465440 G	V
1272	3815 T	+7:117069825 1349465441 T	
1272	3816 G	+7:117069826 1349465442 G	
1273 S	3817 T	+7:117069827 1349465443 T	S
1273	3818 C	+7:117069828 1349465444 C	
1273	3819 T	+7:117069829 1349465445 T	
1274 W	3820 T	+7:117069830 1349465446 T	W
1274	3821 G	+7:117069831 1349465447 G	
1274	3822 G	+7:117069832 1349465448 G	
1275 D	3823 G	+7:117069833 1349465449 G	D
1275	3824 A	+7:117069834 1349465450 A	
1275	3825 T	+7:117069835 1349465451 T	
1276 S	3826 T	+7:117069836 1349465452 T	S
1276	3827 C	+7:117069837 1349465453 C	
1276	3828 A	+7:117069838 1349465454 A	
1277 I	3829 A	+7:117069839 1349465455 A	I
1277	3830 T	+7:117069840 1349465456 T	
1277	3831 A	+7:117069841 1349465457 A	
1278 T	3832 A	+7:117069842 1349465458 A	T
1278	3833 C	+7:117069843 1349465459 C	
1278	3834 T	+7:117069844 1349465460 T	
1279 L	3835 T	+7:117069845 1349465461 T	L
1279	3836 T	+7:117069846 1349465462 T	
1279	3837 G	+7:117069847 1349465463 G	
1280 Q	3838 C	+7:117069848 1349465464 C	Q
1280	3839 A	+7:117069849 1349465465 A	
1280	3840 A	+7:117069850 1349465466 A	
1281 Q	3841 C	+7:117069851 1349465467 C	Q
1281	3842 A	+7:117069852 1349465468 A	
1281	3843 G	+7:117069853 1349465469 G	
1282 W	3844 T	+7:117069854 1349465470 T	W
1282	3845 G	+7:117069855 1349465471 G	
1282	3846 G	+7:117069856 1349465472 G	
1283 R	3847 A	+7:117069857 1349465473 A	R
1283	3848 G	+7:117069858 1349465474 G	
1283	3849 G	+7:117069859 1349465475 G	
1284 K	3850 A	+7:117069860 1349465476 A	K
1284	3851 A	+7:117069861 1349465477 A	
1284	3852 A	+7:117069862 1349465478 A	
1285 A	3853 G	+7:117069863 1349465479 G	A
1285	3854 C	+7:117069864 1349465480 C	
1285	3855 C	+7:117069865 1349465481 C	
1286 F	3856 T	+7:117069866 1349465482 T	F
1286	3857 T	+7:117069867 1349465483 T	
1286	3858 T	+7:117069868 1349465484 T	
1287 G	3859 G	+7:117069869 1349465485 G	G
1287	3860 G	+7:117069870 1349465486 G	
1287	3861 A	+7:117069871 1349465487 A	
1288 V	3862 G	+7:117069872 1349465488 G	V
1288	3863 T	+7:117069873 1349465489 T	
1288	3864 G	+7:117069874 1349465490 G	
1289 I	3865 A	+7:117069875 1349465491 A	I
1289	3866 T	+7:117069876 1349465492 T	
1289	3867 A	+7:117069877 1349465493 A	
1290 P	3868 C	+7:117069878 1349465494 C	P
1290	3869 C	+7:117069879 1349465495 C	
1290	3870 A	+7:117069880 1349465496 A	
1291 Q	3871 C	+7:117069881 1349465497 C	Q
1291	3872 A	+7:117069882 1349465498 A	
1291	3873 G	+7:117069883 1349465499 G	
1292 K	3874 A	+7:117080132 1349475748 A	K
1292	3875 A	+7:117080133 1349475749 A	
1292	3876 A	+7:117080134 1349475750 A	
1293 V	3877 G	+7:117080135 1349475751 G	V
1293	3878 T	+7:117080136 1349475752 T	
1293	3879 A	+7:117080137 1349475753 A	
1294 F	3880 T	+7:117080138 1349475754 T	F
1294	3881 T	+7:117080139 1349475755 T	
1294	3882 T	+7:117080140 1349475756 T	
1295 I	3883 A	+7:117080141 1349475757 A	I
1295	3884 T	+7:117080142 1349475758 T	
1295	3885 T	+7:117080143 1349475759 T	
1296 F	3886 T	+7:117080144 1349475760 T	F
1296	3887 T	+7:117080145 1349475761 T	
1296	3888 T	+7:117080146 1349475762 T	
1297 S	3889 T	+7:117080147 1349475763 T	S
1297	3890 C	+7:117080148 1349475764 C	
1297	3891 T	+7:117080149 1349475765 T	
1298 G	3892 G	+7:117080150 1349475766 G	G
1298	3893 G	+7:117080151 1349475767 G	
1298	3894 A	+7:117080152 1349475768 A	
1299 T	3895 A	+7:117080153 1349475769 A	T
1299	3896 C	+7:117080154 1349475770 C	
1299	3897 A	+7:117080155 1349475771 A	
1300 F	3898 T	+7:117080156 1349475772 T	F
1300	3899 T	+7:117080157 1349475773 T	
1300	3900 T	+7:117080158 1349475774 T	
1301 R	3901 A	+7:117080159 1349475775 A	R
1301	3902 G	+7:117080160 1349475776 G	
1301	3903 A	+7:117080161 1349475777 A	
1302 K	3904 A	+7:117080162 1349475778 A	K
1302	3905 A	+7:117080163 1349475779 A	
1302	3906 A	+7:117080164 1349475780 A	
1303 N	3907 A	+7:117080165 1349475781 A	N
1303	3908 A	+7:117080166 1349475782 A	
1303	3909 C	+7:117080167 1349475783 C	
1304 L	3910 T	+7:117080168 1349475784 T	L
1304	3911 T	+7:117080169 1349475785 T	
1304	3912 G	+7:117080170 1349475786 G	
1305 D	3913 G	+7:117080171 1349475787 G	D
1305	3914 A	+7:117080172 1349475788 A	
1305	3915 T	+7:117080173 1349475789 T	
1306 P	3916 C	+7:117080174 1349475790 C	P
1306	3917 C	+7:117080175 1349475791 C	
1306	3918 C	+7:117080176 1349475792 C	
1307 Y	3919 T	+7:117080177 1349475793 T	Y
1307	3920 A	+7:117080178 1349475794 A	
1307	3921 T	+7:117080179 1349475795 T	
1308 E	3922 G	+7:117080180 1349475796 G	E
1308	3923 A	+7:117080181 1349475797 A	
1308	3924 A	+7:117080182 1349475798 A	
1309 Q	3925 C	+7:117080183 1349475799 C	Q
1309	3926 A	+7:117080184 1349475800 A	
1309	3927 G	+7:117080185 1349475801 G	
1310 W	3928 T	+7:117080186 1349475802 T	W
1310	3929 G	+7:117080187 1349475803 G	
1310	3930 G	+7:117080188 1349475804 G	
1311 S	3931 A	+7:117080189 1349475805 A	S
1311	3932 G	+7:117080190 1349475806 G	
1311	3933 T	+7:117080191 1349475807 T	
1312 D	3934 G	+7:117080192 1349475808 G	D
1312	3935 A	+7:117080193 1349475809 A	
1312	3936 T	+7:117080194 1349475810 T	
1313 Q	3937 C	+7:117080195 1349475811 C	Q
1313	3938 A	+7:117080196 1349475812 A	
1313	3939 A	+7:117080197 1349475813 A	
1314 E	3940 G	+7:117080198 1349475814 G	E
1314	3941 A	+7:117080199 1349475815 A	
1314	3942 A	+7:117080200 1349475816 A	
1315 I	3943 A	+7:117080201 1349475817 A	I
1315	3944 T	+7:117080202 1349475818 T	
1315	3945 A	+7:117080203 1349475819 A	
1316 W	3946 T	+7:117080204 1349475820 T	W
1316	3947 G	+7:117080205 1349475821 G	
1316	3948 G	+7:117080206 1349475822 G	
1317 K	3949 A	+7:117080207 1349475823 A	K
1317	3950 A	+7:117080208 1349475824 A	
1317	3951 A	+7:117080209 1349475825 A	
1318 V	3952 G	+7:117080210 1349475826 G	V
1318	3953 T	+7:117080211 1349475827 T	
1318	3954 T	+7:117080212 1349475828 T	
1319 A	3955 G	+7:117080213 1349475829 G	A
1319	3956 C	+7:117080214 1349475830 C	
1319	3957 A	+7:117080215 1349475831 A	
1320 D	3958 G	+7:117080216 1349475832 G	D
1320	3959 A	+7:117080217 1349475833 A	
1320	3960 T	+7:117080218 1349475834 T	
1321 E	3961 G	+7:117080219 1349475835 G	E
1321	3962 A	+7:117080220 1349475836 A	
1321	3963 G	+7:117080221 1349475837 G	
1322 V	3964 G	+7:117091978 1349487594 G	V
1322	3965 T	+7:117091979 1349487595 T	
1322	3966 T	+7:117091980 1349487596 T	
1323 G	3967 G	+7:117091981 1349487597 G	G
1323	3968 G	+7:117091982 1349487598 G	
1323	3969 G	+7:117091983 1349487599 G	
1324 L	3970 C	+7:117091984 1349487600 C	L
1324	3971 T	+7:117091985 1349487601 T	
1324	3972 C	+7:117091986 1349487602 C	
1325 R	3973 A	+7:117091987 1349487603 A	R
1325	3974 G	+7:117091988 1349487604 G	
1325	3975 A	+7:117091989 1349487605 A	
1326 S	3976 T	+7:117091990 1349487606 T	S
1326	3977 C	+7:117091991 1349487607 C	
1326	3978 T	+7:117091992 1349487608 T	
1327 V	3979 G	+7:117091993 1349487609 G	V
1327	3980 T	+7:117091994 1349487610 T	
1327	3981 G	+7:117091995 1349487611 G	
1328 I	3982 A	+7:117091996 1349487612 A	I
1328	3983 T	+7:117091997 1349487613 T	
1328	3984 A	+7:117091998 1349487614 A	
1329 E	3985 G	+7:117091999 1349487615 G	E
1329	3986 A	+7:117092000 1349487616 A	
1329	3987 A	+7:117092001 1349487617 A	
1330 Q	3988 C	+7:117092002 1349487618 C	Q
1330	3989 A	+7:117092003 1349487619 A	
1330	3990 G	+7:117092004 1349487620 G	
1331 F	3991 T	+7:117092005 1349487621 T	F
1331	3992 T	+7:117092006 1349487622 T	
1331	3993 T	+7:117092007 1349487623 T	
1332 P	3994 C	+7:117092008 1349487624 C	P
1332	3995 C	+7:117092009 1349487625 C	
1332	3996 T	+7:117092010 1349487626 T	
1333 G	3997 G	+7:117092011 1349487627 G	G
1333	3998 G	+7:117092012 1349487628 G	
1333	3999 G	+7:117092013 1349487629 G	
1334 K	4000 A	+7:117092014 1349487630 A	K
1334	4001 A	+7:117092015 1349487631 A	
1334	4002 G	+7:117092016 1349487632 G	
1335 L	4003 C	+7:117092017 1349487633 C	L
1335	4004 T	+7:117092018 1349487634 T	
1335	4005 T	+7:117092019 1349487635 T	
1336 D	4006 G	+7:117092020 1349487636 G	D
1336	4007 A	+7:117092021 1349487637 A	
1336	4008 C	+7:117092022 1349487638 C	
1337 F	4009 T	+7:117092023 1349487639 T	F
1337	4010 T	+7:117092024 1349487640 T	
1337	4011 T	+7:117092025 1349487641 T	
1338 V	4012 G	+7:117092026 1349487642 G	V
1338	4013 T	+7:117092027 1349487643 T	
1338	4014 C	+7:117092028 1349487644 C	
1339 L	4015 C	+7:117092029 1349487645 C	L
1339	4016 T	+7:117092030 1349487646 T	
1339	4017 T	+7:117092031 1349487647 T	
1340 V	4018 G	+7:117092032 1349487648 G	V
1340	4019 T	+7:117092033 1349487649 T	
1340	4020 G	+7:117092034 1349487650 G	
1341 D	4021 G	+7:117092035 1349487651 G	D
1341	4022 A	+7:117092036 1349487652 A	
1341	4023 T	+7:117092037 1349487653 T	
1342 G	4024 G	+7:117092038 1349487654 G	G
1342	4025 G	+7:117092039 1349487655 G	
1342	4026 G	+7:117092040 1349487656 G	
1343 G	4027 G	+7:117092041 1349487657 G	G
1343	4028 G	+7:117092042 1349487658 G	
1343	4029 C	+7:117092043 1349487659 C	
1344 C	4030 T	+7:117092044 1349487660 T	C
1344	4031 G	+7:117092045 1349487661 G	
1344	4032 T	+7:117092046 1349487662 T	
1345 V	4033 G	+7:117092047 1349487663 G	V
1345	4034 T	+7:117092048 1349487664 T	
1345	4035 C	+7:117092049 1349487665 C	
1346 L	4036 C	+7:117092050 1349487666 C	L
1346	4037 T	+7:117092051 1349487667 T	
1346	4038 A	+7:117092052 1349487668 A	
1347 S	4039 A	+7:117092053 1349487669 A	S
1347	4040 G	+7:117092054 1349487670 G	
1347	4041 C	+7:117092055 1349487671 C	
1348 H	4042 C	+7:117092056 1349487672 C	H
1348	4043 A	+7:117092057 1349487673 A	
1348	4044 T	+7:117092058 1349487674 T	
1349 G	4045 G	+7:117092059 1349487675 G	G
1349	4046 G	+7:117092060 1349487676 G	
1349	4047 C	+7:117092061 1349487677 C	
1350 H	4048 C	+7:117092062 1349487678 C	H
1350	4049 A	+7:117092063 1349487679 A	
1350	4050 C	+7:117092064 1349487680 C	
1351 K	4051 A	+7:117092065 1349487681 A	K
1351	4052 A	+7:117092066 1349487682 A	
1351	4053 G	+7:117092067 1349487683 G	
1352 Q	4054 C	+7:117092068 1349487684 C	Q
1352	4055 A	+7:117092069 1349487685 A	
1352	4056 G	+7:117092070 1349487686 G	
1353 L	4057 T	+7:117092071 1349487687 T	L
1353	4058 T	+7:117092072 1349487688 T	
1353	4059 G	+7:117092073 1349487689 G	
1354 M	4060 A	+7:117092074 1349487690 A	M
1354	4061 T	+7:117092075 1349487691 T	
1354	4062 G	+7:117092076 1349487692 G	
1355 C	4063 T	+7:117092077 1349487693 T	C
1355	4064 G	+7:117092078 1349487694 G	
1355	4065 C	+7:117092079 1349487695 C	
1356 L	4066 T	+7:117092080 1349487696 T	L
1356	4067 T	+7:117092081 1349487697 T	
1356	4068 G	+7:117092082 1349487698 G	
1357 A	4069 G	+7:117092083 1349487699 G	A
1357	4070 C	+7:117092084 1349487700 C	
1357	4071 T	+7:117092085 1349487701 T	
1358 R	4072 A	+7:117092086 1349487702 A	R
1358	4073 G	+7:117092087 1349487703 G	
1358	4074 A	+7:117092088 1349487704 A	
1359 S	4075 T	+7:117092089 1349487705 T	S
1359	4076 C	+7:117092090 1349487706 C	
1359	4077 T	+7:117092091 1349487707 T	
1360 V	4078 G	+7:117092092 1349487708 G	V
1360	4079 T	+7:117092093 1349487709 T	
1360	4080 T	+7:117092094 1349487710 T	
1361 L	4081 C	+7:117092095 1349487711 C	L
1361	4082 T	+7:117092096 1349487712 T	
1361	4083 C	+7:117092097 1349487713 C	
1362 S	4084 A	+7:117092098 1349487714 A	S
1362	4085 G	+7:117092099 1349487715 G	
1362	4086 T	+7:117092100 1349487716 T	
1363 K	4087 A	+7:117092101 1349487717 A	K
1363	4088 A	+7:117092102 1349487718 A	
1363	4089 G	+7:117092103 1349487719 G	
1364 A	4090 G	+7:117092104 1349487720 G	A
1364	4091 C	+7:117092105 1349487721 C	
1364	4092 G	+7:117092106 1349487722 G	
1365 K	4093 A	+7:117092107 1349487723 A	K
1365	4094 A	+7:117092108 1349487724 A	
1365	4095 G	+7:117092109 1349487725 G	
1366 I	4096 A	+7:117092110 1349487726 A	I
1366	4097 T	+7:117092111 1349487727 T	
1366	4098 C	+7:117092112 1349487728 C	
1367 L	4099 T	+7:117092113 1349487729 T	L
1367	4100 T	+7:117092114 1349487730 T	
1367	4101 G	+7:117092115 1349487731 G	
1368 L	4102 C	+7:117092116 1349487732 C	L
1368	4103 T	+7:117092117 1349487733 T	
1368	4104 G	+7:117092118 1349487734 G	
1369 L	4105 C	+7:117092119 1349487735 C	L
1369	4106 T	+7:117092120 1349487736 T	
1369	4107 T	+7:117092121 1349487737 T	
1370 D	4108 G	+7:117092122 1349487738 G	D
1370	4109 A	+7:117092123 1349487739 A	
1370	4110 T	+7:117092124 1349487740 T	
1371 E	4111 G	+7:117092125 1349487741 G	E
1371	4112 A	+7:117092126 1349487742 A	
1371	4113 A	+7:117092127 1349487743 A	
1372 P	4114 C	+7:117092128 1349487744 C	P
1372	4115 C	+7:117092129 1349487745 C	
1372	4116 C	+7:117092130 1349487746 C	
1373 S	4117 A	+7:117092131 1349487747 A	S
1373	4118 G	+7:117092132 1349487748 G	
1373	4119 T	+7:117092133 1349487749 T	
1374 A	4120 G	+7:117092134 1349487750 G	A
1374	4121 C	+7:117092135 1349487751 C	
1374	4122 T	+7:117092136 1349487752 T	
1375 H	4123 C	+7:117092137 1349487753 C	H
1375	4124 A	+7:117092138 1349487754 A	
1375	4125 T	+7:117092139 1349487755 T	
1376 L	4126 T	+7:117092140 1349487756 T	L
1376	4127 T	+7:117092141 1349487757 T	
1376	4128 G	+7:117092142 1349487758 G	
1377 D	4129 G	+7:117092143 1349487759 G	D
1377	4130 A	+7:117092144 1349487760 A	
1377	4131 T	+7:117092145 1349487761 T	
1378 P	4132 C	+7:117092146 1349487762 C	P
1378	4133 C	+7:117092147 1349487763 C	
1378	4134 A	+7:117092148 1349487764 A	
1379 V	4135 G	+7:117092149 1349487765 G	V
1379	4136 T	+7:117092150 1349487766 T	
1379	4137 A	+7:117092749 1349488365 A	
1380 T	4138 A	+7:117092750 1349488366 A	T
1380	4139 C	+7:117092751 1349488367 C	
1380	4140 A	+7:117092752 1349488368 A	
1381 Y	4141 T	+7:117092753 1349488369 T	Y
1381	4142 A	+7:117092754 1349488370 A	
1381	4143 C	+7:117092755 1349488371 C	
1382 Q	4144 C	+7:117092756 1349488372 C	Q
1382	4145 A	+7:117092757 1349488373 A	
1382	4146 A	+7:117092758 1349488374 A	
1383 I	4147 A	+7:117092759 1349488375 A	I
1383	4148 T	+7:117092760 1349488376 T	
1383	4149 A	+7:117092761 1349488377 A	
1384 I	4150 A	+7:117092762 1349488378 A	I
1384	4151 T	+7:117092763 1349488379 T	
1384	4152 T	+7:117092764 1349488380 T	
1385 R	4153 A	+7:117092765 1349488381 A	R
1385	4154 G	+7:117092766 1349488382 G	
1385	4155 A	+7:117092767 1349488383 A	
1386 R	4156 A	+7:117092768 1349488384 A	R
1386	4157 G	+7:117092769 1349488385 G	
1386	4158 A	+7:117092770 1349488386 A	
1387 T	4159 A	+7:117092771 1349488387 A	T
1387	4160 C	+7:117092772 1349488388 C	
1387	4161 T	+7:117092773 1349488389 T	
1388 L	4162 C	+7:117092774 1349488390 C	L
1388	4163 T	+7:117092775 1349488391 T	
1388	4164 A	+7:117092776 1349488392 A	
1389 K	4165 A	+7:117092777 1349488393 A	K
1389	4166 A	+7:117092778 1349488394 A	
1389	4167 A	+7:117092779 1349488395 A	
1390 Q	4168 C	+7:117092780 1349488396 C	Q
1390	4169 A	+7:117092781 1349488397 A	
1390	4170 A	+7:117092782 1349488398 A	
1391 A	4171 G	+7:117092783 1349488399 G	A
1391	4172 C	+7:117092784 1349488400 C	
1391	4173 A	+7:117092785 1349488401 A	
1392 F	4174 T	+7:117092786 1349488402 T	F
1392	4175 T	+7:117092787 1349488403 T	
1392	4176 T	+7:117092788 1349488404 T	
1393 A	4177 G	+7:117092789 1349488405 G	A
1393	4178 C	+7:117092790 1349488406 C	
1393	4179 T	+7:117092791 1349488407 T	
1394 D	4180 G	+7:117092792 1349488408 G	D
1394	4181 A	+7:117092793 1349488409 A	
1394	4182 T	+7:117092794 1349488410 T	
1395 C	4183 T	+7:117092795 1349488411 T	C
1395	4184 G	+7:117092796 1349488412 G	
1395	4185 C	+7:117092797 1349488413 C	
1396 T	4186 A	+7:117092798 1349488414 A	T
1396	4187 C	+7:117092799 1349488415 C	
1396	4188 A	+7:117092800 1349488416 A	
1397 V	4189 G	+7:117092801 1349488417 G	V
1397	4190 T	+7:117092802 1349488418 T	
1397	4191 A	+7:117092803 1349488419 A	
1398 I	4192 A	+7:117092804 1349488420 A	I
1398	4193 T	+7:117092805 1349488421 T	
1398	4194 T	+7:117092806 1349488422 T	
1399 L	4195 C	+7:117092807 1349488423 C	L
1399	4196 T	+7:117092808 1349488424 T	
1399	4197 C	+7:117092809 1349488425 C	
1400 C	4198 T	+7:117092810 1349488426 T	C
1400	4199 G	+7:117092811 1349488427 G	
1400	4200 T	+7:117092812 1349488428 T	
1401 E	4201 G	+7:117092813 1349488429 G	E
1401	4202 A	+7:117092814 1349488430 A	
1401	4203 A	+7:117092815 1349488431 A	
1402 H	4204 C	+7:117092816 1349488432 C	H
1402	4205 A	+7:117092817 1349488433 A	
1402	4206 C	+7:117092818 1349488434 C	
1403 R	4207 A	+7:117092819 1349488435 A	R
1403	4208 G	+7:117092820 1349488436 G	
1403	4209 G	+7:117092821 1349488437 G	
1404 I	4210 A	+7:117092822 1349488438 A	I
1404	4211 T	+7:117092823 1349488439 T	
1404	4212 A	+7:117092824 1349488440 A	
1405 E	4213 G	+7:117092825 1349488441 G	E
1405	4214 A	+7:117092826 1349488442 A	
1405	4215 A	+7:117092827 1349488443 A	
1406 A	4216 G	+7:117092828 1349488444 G	A
1406	4217 C	+7:117092829 1349488445 C	
1406	4218 A	+7:117092830 1349488446 A	
1407 M	4219 A	+7:117092831 1349488447 A	M
1407	4220 T	+7:117092832 1349488448 T	
1407	4221 G	+7:117092833 1349488449 G	
1408 L	4222 C	+7:117092834 1349488450 C	L
1408	4223 T	+7:117092835 1349488451 T	
1408	4224 G	+7:117092836 1349488452 G	
1409 E	4225 G	+7:117092837 1349488453 G	E
1409	4226 A	+7:117092838 1349488454 A	
1409	4227 A	+7:117092839 1349488455 A	
1410 C	4228 T	+7:117092840 1349488456 T	C
1410	4229 G	+7:117092841 1349488457 G	
1410	4230 C	+7:117092842 1349488458 C	
1411 Q	4231 C	+7:117092843 1349488459 C	Q
1411	4232 A	+7:117092844 1349488460 A	
1411	4233 A	+7:117092845 1349488461 A	
1412 Q	4234 C	+7:117092846 1349488462 C	Q
1412	4235 A	+7:117092847 1349488463 A	
1412	4236 A	+7:117092848 1349488464 A	
1413 F	4237 T	+7:117092849 1349488465 T	F
1413	4238 T	+7:117092850 1349488466 T	
1413	4239 T	+7:117092851 1349488467 T	
1414 L	4240 T	+7:117092852 1349488468 T	L
1414	4241 T	+7:117092853 1349488469 T	
1414	4242 G	+7:117092854 1349488470 G	
1415 V	4243 G	+7:117094198 1349489814 G	V
1415	4244 T	+7:117094199 1349489815 T	
1415	4245 C	+7:117094200 1349489816 C	
1416 I	4246 A	+7:117094201 1349489817 A	I
1416	4247 T	+7:117094202 1349489818 T	
1416	4248 A	+7:117094203 1349489819 A	
1417 E	4249 G	+7:117094204 1349489820 G	E
1417	4250 A	+7:117094205 1349489821 A	
1417	4251 A	+7:117094206 1349489822 A	
1418 E	4252 G	+7:117094207 1349489823 G	E
1418	4253 A	+7:117094208 1349489824 A	
1418	4254 G	+7:117094209 1349489825 G	
1419 N	4255 A	+7:117094210 1349489826 A	N
1419	4256 A	+7:117094211 1349489827 A	
1419	4257 C	+7:117094212 1349489828 C	
1420 K	4258 A	+7:117094213 1349489829 A	K
1420	4259 A	+7:117094214 1349489830 A	
1420	4260 A	+7:117094215 1349489831 A	
1421 V	4261 G	+7:117094216 1349489832 G	V
1421	4262 T	+7:117094217 1349489833 T	
1421	4263 G	+7:117094218 1349489834 G	
1422 R	4264 C	+7:117094219 1349489835 C	R
1422	4265 G	+7:117094220 1349489836 G	
1422	4266 G	+7:117094221 1349489837 G	
1423 Q	4267 C	+7:117094222 1349489838 C	Q
1423	4268 A	+7:117094223 1349489839 A	
1423	4269 G	+7:117094224 1349489840 G	
1424 Y	4270 T	+7:117094225 1349489841 T	Y
1424	4271 A	+7:117094226 1349489842 A	
1424	4272 C	+7:117094227 1349489843 C	
1425 D	4273 G	+7:117094228 1349489844 G	D
1425	4274 A	+7:117094229 1349489845 A	
1425	4275 T	+7:117094230 1349489846 T	
1426 S	4276 T	+7:117094231 1349489847 T	S
1426	4277 C	+7:117094232 1349489848 C	
1426	4278 C	+7:117094233 1349489849 C	
1427 I	4279 A	+7:117094234 1349489850 A	I
1427	4280 T	+7:117094235 1349489851 T	
1427	4281 C	+7:117094236 1349489852 C	
1428 Q	4282 C	+7:117094237 1349489853 C	Q
1428	4283 A	+7:117094238 1349489854 A	
1428	4284 G	+7:117094239 1349489855 G	
1429 K	4285 A	+7:117094240 1349489856 A	K
1429	4286 A	+7:117094241 1349489857 A	
1429	4287 A	+7:117094242 1349489858 A	
1430 L	4288 C	+7:117094243 1349489859 C	L
1430	4289 T	+7:117094244 1349489860 T	
1430	4290 G	+7:117094245 1349489861 G	
1431 L	4291 C	+7:117094246 1349489862 C	L
1431	4292 T	+7:117094247 1349489863 T	
1431	4293 G	+7:117094248 1349489864 G	
1432 N	4294 A	+7:117094249 1349489865 A	N
1432	4295 A	+7:117094250 1349489866 A	
1432	4296 C	+7:117094251 1349489867 C	
1433 E	4297 G	+7:117094252 1349489868 G	E
1433	4298 A	+7:117094253 1349489869 A	
1433	4299 G	+7:117094254 1349489870 G	
1434 R	4300 A	+7:117094255 1349489871 A	R
1434	4301 G	+7:117094256 1349489872 G	
1434	4302 G	+7:117094257 1349489873 G	
1435 S	4303 A	+7:117094258 1349489874 A	S
1435	4304 G	+7:117094259 1349489875 G	
1435	4305 C	+7:117094260 1349489876 C	
1436 L	4306 C	+7:117094261 1349489877 C	L
1436	4307 T	+7:117094262 1349489878 T	
1436	4308 C	+7:117094263 1349489879 C	
1437 F	4309 T	+7:117094264 1349489880 T	F
1437	4310 T	+7:117094265 1349489881 T	
1437	4311 C	+7:117094266 1349489882 C	
1438 R	4312 C	+7:117094267 1349489883 C	R
1438	4313 G	+7:117094268 1349489884 G	
1438	4314 G	+7:117094269 1349489885 G	
1439 Q	4315 C	+7:117094270 1349489886 C	Q
1439	4316 A	+7:117094271 1349489887 A	
1439	4317 A	+7:117094272 1349489888 A	
1440 A	4318 G	+7:117094273 1349489889 G	A
1440	4319 C	+7:117094274 1349489890 C	
1440	4320 C	+7:117094275 1349489891 C	
1441 I	4321 A	+7:117094276 1349489892 A	I
1441	4322 T	+7:117094277 1349489893 T	
1441	4323 C	+7:117094278 1349489894 C	
1442 S	4324 A	+7:117094279 1349489895 A	S
1442	4325 G	+7:117094280 1349489896 G	
1442	4326 C	+7:117094281 1349489897 C	
1443 P	4327 C	+7:117094282 1349489898 C	P
1443	4328 C	+7:117094283 1349489899 C	
1443	4329 C	+7:117094284 1349489900 C	
1444 S	4330 T	+7:117094285 1349489901 T	S
1444	4331 C	+7:117094286 1349489902 C	
1444	4332 C	+7:117094287 1349489903 C	
1445 D	4333 G	+7:117094288 1349489904 G	D
1445	4334 A	+7:117094289 1349489905 A	
1445	4335 C	+7:117094290 1349489906 C	
1446 R	4336 A	+7:117094291 1349489907 A	R
1446	4337 G	+7:117094292 1349489908 G	
1446	4338 G	+7:117094293 1349489909 G	
1447 V	4339 G	+7:117094294 1349489910 G	V
1447	4340 T	+7:117094295 1349489911 T	
1447	4341 G	+7:117094296 1349489912 G	
1448 K	4342 A	+7:117094297 1349489913 A	K
1448	4343 A	+7:117094298 1349489914 A	
1448	4344 G	+7:117094299 1349489915 G	
1449 L	4345 C	+7:117094300 1349489916 C	L
1449	4346 T	+7:117094301 1349489917 T	
1449	4347 C	+7:117094302 1349489918 C	
1450 F	4348 T	+7:117094303 1349489919 T	F
1450	4349 T	+7:117094304 1349489920 T	
1450	4350 T	+7:117094305 1349489921 T	
1451 P	4351 C	+7:117094306 1349489922 C	P
1451	4352 C	+7:117094307 1349489923 C	
1451	4353 C	+7:117094308 1349489924 C	
1452 H	4354 C	+7:117094309 1349489925 C	H
1452	4355 A	+7:117094310 1349489926 A	
1452	4356 C	+7:117094311 1349489927 C	
1453 R	4357 C	+7:117094312 1349489928 C	R
1453	4358 G	+7:117094313 1349489929 G	
1453	4359 G	+7:117094314 1349489930 G	
1454 N	4360 A	+7:117094315 1349489931 A	N
1454	4361 A	+7:117094316 1349489932 A	
1454	4362 C	+7:117094317 1349489933 C	
1455 S	4363 T	+7:117094318 1349489934 T	S
1455	4364 C	+7:117094319 1349489935 C	
1455	4365 A	+7:117094320 1349489936 A	
1456 S	4366 A	+7:117094321 1349489937 A	S
1456	4367 G	+7:117094322 1349489938 G	
1456	4368 C	+7:117094323 1349489939 C	
1457 K	4369 A	+7:117094324 1349489940 A	K
1457	4370 A	+7:117094325 1349489941 A	
1457	4371 G	+7:117094326 1349489942 G	
1458 C	4372 T	+7:117094327 1349489943 T	C
1458	4373 G	+7:117094328 1349489944 G	
1458	4374 C	+7:117094329 1349489945 C	
1459 K	4375 A	+7:117094330 1349489946 A	K
1459	4376 A	+7:117094331 1349489947 A	
1459	4377 G	+7:117094332 1349489948 G	
1460 S	4378 T	+7:117094333 1349489949 T	S
1460	4379 C	+7:117094334 1349489950 C	
1460	4380 T	+7:117094335 1349489951 T	
1461 K	4381 A	+7:117094336 1349489952 A	K
1461	4382 A	+7:117094337 1349489953 A	
1461	4383 G	+7:117094338 1349489954 G	
1462 P	4384 C	+7:117094339 1349489955 C	P
1462	4385 C	+7:117094340 1349489956 C	
1462	4386 C	+7:117094341 1349489957 C	
1463 Q	4387 C	+7:117094342 1349489958 C	Q
1463	4388 A	+7:117094343 1349489959 A	
1463	4389 G	+7:117094344 1349489960 G	
1464 I	4390 A	+7:117094345 1349489961 A	I
1464	4391 T	+7:117094346 1349489962 T	
1464	4392 T	+7:117094347 1349489963 T	
1465 A	4393 G	+7:117094348 1349489964 G	A
1465	4394 C	+7:117094349 1349489965 C	
1465	4395 T	+7:117094350 1349489966 T	
1466 A	4396 G	+7:117094351 1349489967 G	A
1466	4397 C	+7:117094352 1349489968 C	
1466	4398 T	+7:117094353 1349489969 T	
1467 L	4399 C	+7:117094354 1349489970 C	L
1467	4400 T	+7:117094355 1349489971 T	
1467	4401 G	+7:117094356 1349489972 G	
1468 K	4402 A	+7:117094357 1349489973 A	K
1468	4403 A	+7:117094358 1349489974 A	
1468	4404 A	+7:117094359 1349489975 A	
1469 E	4405 G	+7:117094360 1349489976 G	E
1469	4406 A	+7:117094361 1349489977 A	
1469	4407 G	+7:117094362 1349489978 G	
1470 E	4408 G	+7:117094363 1349489979 G	E
1470	4409 A	+7:117094364 1349489980 A	
1470	4410 G	+7:117094365 1349489981 G	
1471 T	4411 A	+7:117094366 1349489982 A	T
1471	4412 C	+7:117094367 1349489983 C	
1471	4413 A	+7:117094368 1349489984 A	
1472 E	4414 G	+7:117094369 1349489985 G	E
1472	4415 A	+7:117094370 1349489986 A	
1472	4416 A	+7:117094371 1349489987 A	
1473 E	4417 G	+7:117094372 1349489988 G	E
1473	4418 A	+7:117094373 1349489989 A	
1473	4419 A	+7:117094374 1349489990 A	
1474 E	4420 G	+7:117094375 1349489991 G	E
1474	4421 A	+7:117094376 1349489992 A	
1474	4422 G	+7:117094377 1349489993 G	
1475 V	4423 G	+7:117094378 1349489994 G	V
1475	4424 T	+7:117094379 1349489995 T	
1475	4425 G	+7:117094380 1349489996 G	
1476 Q	4426 C	+7:117094381 1349489997 C	Q
1476	4427 A	+7:117094382 1349489998 A	
1476	4428 A	+7:117094383 1349489999 A	
1477 D	4429 G	+7:117094384 1349490000 G	D
1477	4430 A	+7:117094385 1349490001 A	
1477	4431 T	+7:117094386 1349490002 T	
1478 T	4432 A	+7:117094387 1349490003 A	T
1478	4433 C	+7:117094388 1349490004 C	
1478	4434 A	+7:117094389 1349490005 A	
1479 R	4435 A	+7:117094390 1349490006 A	R
1479	4436 G	+7:117094391 1349490007 G	
1479	4437 G	+7:117094392 1349490008 G	
1480 L	4438 C	+7:117094393 1349490009 C	L
1480	4439 T	+7:117094394 1349490010 T	
1480	4440 T	+7:117094395 1349490011 T	
>ENSP00000265742 
96 N	286 A	+7:91762139 1324157755 A	N
96	287 A	+7:91762140 1324157756 A	
96	288 T	+7:91762141 1324157757 T	
97 V	289 G	+7:91762142 1324157758 G	V
97	290 T	+7:91762143 1324157759 T	
97	291 G	+7:91762144 1324157760 G	
98 K	292 A	+7:91762145 1324157761 A	K
98	293 A	+7:91762146 1324157762 A	
98	294 A	+7:91762147 1324157763 A	
99 D	295 G	+7:91762148 1324157764 G	D
99	296 A	+7:91762149 1324157765 A	
99	297 T	+7:91762150 1324157766 T	
100 V	298 G	+7:91762151 1324157767 G	V
100	299 T	+7:91762152 1324157768 T	
100	300 T	+7:91762153 1324157769 T	
101 A	301 G	+7:91762154 1324157770 G	A
101	302 C	+7:91762155 1324157771 C	
101	303 A	+7:91762156 1324157772 A	
102 E	304 G	+7:91762157 1324157773 G	E
102	305 A	+7:91762158 1324157774 A	
102	306 A	+7:91762159 1324157775 A	
103 V	307 G	+7:91762160 1324157776 G	V
103	308 T	+7:91762161 1324157777 T	
103	309 G	+7:91762162 1324157778 G	
104 F	310 T	+7:91762163 1324157779 T	F
104	311 T	+7:91762164 1324157780 T	
104	312 C	+7:91762165 1324157781 C	
105 Q	313 C	+7:91762166 1324157782 C	Q
105	314 A	+7:91762167 1324157783 A	
105	315 G	+7:91762168 1324157784 G	
106 K	316 A	+7:91762169 1324157785 A	K
106	317 A	+7:91762170 1324157786 A	
106	318 G	+7:91762171 1324157787 G	
107 W	319 T	+7:91762172 1324157788 T	W
107	320 G	+7:91762173 1324157789 G	
107	321 G	+7:91762174 1324157790 G	
108 L	322 C	+7:91762175 1324157791 C	L
108	323 T	+7:91762176 1324157792 T	
108	324 G	+7:91762177 1324157793 G	
109 K	325 A	+7:91762178 1324157794 A	K
109	326 A	+7:91762179 1324157795 A	
109	327 G	+7:91762180 1324157796 G	
110 I	328 A	+7:91762181 1324157797 A	I
110	329 T	+7:91762182 1324157798 T	
110	330 A	+7:91762183 1324157799 A	
111 E	331 G	+7:91762184 1324157800 G	E
111	332 A	+7:91762185 1324157801 A	
111	333 A	+7:91762186 1324157802 A	
112 G	334 G	+7:91762187 1324157803 G	G
112	335 G	+7:91762188 1324157804 G	
112	336 A	+7:91762189 1324157805 A	
113 K	337 A	+7:91762190 1324157806 A	K
113	338 A	+7:91762191 1324157807 A	
113	339 A	+7:91762192 1324157808 A	
114 K	340 A	+7:91762193 1324157809 A	K
114	341 A	+7:91762194 1324157810 A	
114	342 G	+7:91762195 1324157811 G	
115 C	343 T	+7:91762196 1324157812 T	C
115	344 G	+7:91762197 1324157813 G	
115	345 C	+7:91762198 1324157814 C	
116 H	346 C	+7:91762199 1324157815 C	H
116	347 A	+7:91762200 1324157816 A	
116	348 C	+7:91762201 1324157817 C	
117 C	349 T	+7:91762202 1324157818 T	C
117	350 G	+7:91762203 1324157819 G	
117	351 C	+7:91762204 1324157820 C	
118 L	352 C	+7:91762205 1324157821 C	L
118	353 T	+7:91762206 1324157822 T	
118	354 A	+7:91762207 1324157823 A	
119 S	355 T	+7:91762208 1324157824 T	S
119	356 C	+7:91762209 1324157825 C	
119	357 A	+7:91762210 1324157826 A	
120 E	358 G	+7:91762211 1324157827 G	E
120	359 A	+7:91762212 1324157828 A	
120	360 A	+7:91762213 1324157829 A	
121 K	361 A	+7:91762214 1324157830 A	K
121	362 A	+7:91762215 1324157831 A	
121	363 A	+7:91762216 1324157832 A	
122 T	364 A	+7:91762217 1324157833 A	T
122	365 C	+7:91762218 1324157834 C	
122	366 A	+7:91762219 1324157835 A	
123 K	367 A	+7:91762220 1324157836 A	K
123	368 A	+7:91762221 1324157837 A	
123	369 A	+7:91762222 1324157838 A	
124 Q	370 C	+7:91762223 1324157839 C	Q
124	371 A	+7:91762224 1324157840 A	
124	372 A	+7:91762225 1324157841 A	
125 N	373 A	+7:91762226 1324157842 A	N
125	374 A	+7:91762227 1324157843 A	
125	375 C	+7:91762228 1324157844 C	
126 M	376 A	+7:91762229 1324157845 A	M
126	377 T	+7:91762230 1324157846 T	
126	378 G	+7:91762231 1324157847 G	
127 G	379 G	+7:91762232 1324157848 G	G
127	380 G	+7:91762233 1324157849 G	
127	381 A	+7:91762234 1324157850 A	
128 N	382 A	+7:91762235 1324157851 A	N
128	383 A	+7:91762236 1324157852 A	
128	384 T	+7:91762237 1324157853 T	
129 T	385 A	+7:91762238 1324157854 A	T
129	386 C	+7:91762239 1324157855 C	
129	387 A	+7:91762240 1324157856 A	
130 T	388 A	+7:91762241 1324157857 A	T
130	389 C	+7:91762242 1324157858 C	
130	390 C	+7:91762243 1324157859 C	
131 T	391 A	+7:91762244 1324157860 A	T
131	392 C	+7:91762245 1324157861 C	
131	393 C	+7:91762246 1324157862 C	
132 K	394 A	+7:91762247 1324157863 A	K
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380 A	1138 G	+7:91795126 1324190742 G	A
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389	1167 G	+7:91810278 1324205894 G	
390 D	1168 G	+7:91810279 1324205895 G	D
390	1169 A	+7:91810280 1324205896 A	
390	1170 C	+7:91810281 1324205897 C	
391 R	1171 A	+7:91810282 1324205898 A	R
391	1172 G	+7:91810283 1324205899 G	
391	1173 G	+7:91810284 1324205900 G	
392 E	1174 G	+7:91810285 1324205901 G	E
392	1175 A	+7:91810286 1324205902 A	
392	1176 G	+7:91810287 1324205903 G	
393 K	1177 A	+7:91810288 1324205904 A	K
393	1178 A	+7:91810289 1324205905 A	
393	1179 A	+7:91810290 1324205906 A	
394 L	1180 T	+7:91810291 1324205907 T	L
394	1181 T	+7:91810292 1324205908 T	
394	1182 A	+7:91810293 1324205909 A	
395 L	1183 C	+7:91810294 1324205910 C	L
395	1184 T	+7:91810295 1324205911 T	
395	1185 T	+7:91810296 1324205912 T	
396 E	1186 G	+7:91810297 1324205913 G	E
396	1187 A	+7:91810298 1324205914 A	
396	1188 A	+7:91810299 1324205915 A	
397 A	1189 G	+7:91810300 1324205916 G	A
397	1190 C	+7:91810301 1324205917 C	
397	1191 T	+7:91810302 1324205918 T	
398 W	1192 T	+7:91810303 1324205919 T	W
398	1193 G	+7:91810304 1324205920 G	
398	1194 G	+7:91810305 1324205921 G	
399 M	1195 A	+7:91810306 1324205922 A	M
399	1196 T	+7:91810307 1324205923 T	
399	1197 G	+7:91810308 1324205924 G	
400 S	1198 T	+7:91810309 1324205925 T	S
400	1199 C	+7:91810310 1324205926 C	
400	1200 C	+7:91810311 1324205927 C	
401 N	1201 A	+7:91810312 1324205928 A	N
401	1202 A	+7:91810313 1324205929 A	
401	1203 C	+7:91810314 1324205930 C	
402 P	1204 C	+7:91810315 1324205931 C	P
402	1205 C	+7:91810316 1324205932 C	
402	1206 G	+7:91810317 1324205933 G	
403 E	1207 G	+7:91810318 1324205934 G	E
403	1208 A	+7:91810319 1324205935 A	
403	1209 G	+7:91810320 1324205936 G	
404 N	1210 A	+7:91810321 1324205937 A	N
404	1211 A	+7:91810322 1324205938 A	
404	1212 C	+7:91810323 1324205939 C	
405 C	1213 T	+7:91810324 1324205940 T	C
405	1214 G	+7:91810325 1324205941 G	
405	1215 C	+7:91810326 1324205942 C	
406 C	1216 T	+7:91810327 1324205943 T	C
406	1217 G	+7:91810328 1324205944 G	
406	1218 C	+7:91810329 1324205945 C	
407 Q	1219 C	+7:91810330 1324205946 C	Q
407	1220 A	+7:91810331 1324205947 A	
407	1221 A	+7:91810332 1324205948 A	
408 R	1222 C	+7:91810333 1324205949 C	R
408	1223 G	+7:91810334 1324205950 G	
408	1224 A	+7:91810335 1324205951 A	
409 S	1225 T	+7:91810336 1324205952 T	S
409	1226 C	+7:91810337 1324205953 C	
409	1227 A	+7:91810338 1324205954 A	
410 G	1228 G	+7:91810339 1324205955 G	G
410	1229 G	+7:91810340 1324205956 G	
410	1230 T	+7:91810341 1324205957 T	
411 V	1231 G	+7:91810342 1324205958 G	V
411	1232 T	+7:91810343 1324205959 T	
411	1233 T	+7:91810344 1324205960 T	
412 Q	1234 C	+7:91810345 1324205961 C	Q
412	1235 A	+7:91810346 1324205962 A	
412	1236 A	+7:91810347 1324205963 A	
413 M	1237 A	+7:91810348 1324205964 A	M
413	1238 T	+7:91810349 1324205965 T	
413	1239 G	+7:91810350 1324205966 G	
414 P	1240 C	+7:91810351 1324205967 C	P
414	1241 C	+7:91810352 1324205968 C	
414	1242 A	+7:91810353 1324205969 A	
415 T	1243 A	+7:91810354 1324205970 A	T
415	1244 C	+7:91810355 1324205971 C	
415	1245 T	+7:91810356 1324205972 T	
416 P	1246 C	+7:91810357 1324205973 C	P
416	1247 C	+7:91810358 1324205974 C	
416	1248 A	+7:91810359 1324205975 A	
417 P	1249 C	+7:91810360 1324205976 C	P
417	1250 C	+7:91810361 1324205977 C	
417	1251 A	+7:91810362 1324205978 A	
418 P	1252 C	+7:91810363 1324205979 C	P
418	1253 C	+7:91810364 1324205980 C	
418	1254 A	+7:91810365 1324205981 A	
419 S	1255 A	+7:91810366 1324205982 A	S
419	1256 G	+7:91810367 1324205983 G	
419	1257 T	+7:91810368 1324205984 T	
420 G	1258 G	+7:91810369 1324205985 G	G
420	1259 G	+7:91810370 1324205986 G	
420	1260 G	+7:91810371 1324205987 G	
421 Y	1261 T	+7:91810372 1324205988 T	Y
421	1262 A	+7:91810373 1324205989 A	
421	1263 T	+7:91810374 1324205990 T	
422 N	1264 A	+7:91810375 1324205991 A	N
422	1265 A	+7:91810376 1324205992 A	
422	1266 T	+7:91810377 1324205993 T	
423 A	1267 G	+7:91810378 1324205994 G	A
423	1268 C	+7:91810379 1324205995 C	
423	1269 C	+7:91810380 1324205996 C	
424 W	1270 T	+7:91810381 1324205997 T	W
424	1271 G	+7:91810382 1324205998 G	
424	1272 G	+7:91810383 1324205999 G	
425 D	1273 G	+7:91810384 1324206000 G	D
425	1274 A	+7:91810385 1324206001 A	
425	1275 C	+7:91810386 1324206002 C	
426 T	1276 A	+7:91810387 1324206003 A	T
426	1277 C	+7:91810388 1324206004 C	
426	1278 G	+7:91810389 1324206005 G	
427 L	1279 C	+7:91810390 1324206006 C	L
427	1280 T	+7:91810391 1324206007 T	
427	1281 C	+7:91810392 1324206008 C	
428 P	1282 C	+7:91810393 1324206009 C	P
428	1283 C	+7:91810394 1324206010 C	
428	1284 A	+7:91810395 1324206011 A	
429 S	1285 T	+7:91810396 1324206012 T	S
429	1286 C	+7:91810397 1324206013 C	
429	1287 T	+7:91810398 1324206014 T	
430 P	1288 C	+7:91810399 1324206015 C	P
430	1289 C	+7:91810400 1324206016 C	
430	1290 A	+7:91810401 1324206017 A	
431 R	1291 A	+7:91810402 1324206018 A	R
431	1292 G	+7:91810403 1324206019 G	
431	1293 A	+7:91810404 1324206020 A	
432 T	1294 A	+7:91810405 1324206021 A	T
432	1295 C	+7:91810406 1324206022 C	
432	1296 T	+7:91810407 1324206023 T	
433 P	1297 C	+7:91810408 1324206024 C	P
433	1298 C	+7:91810409 1324206025 C	
433	1299 A	+7:91810410 1324206026 A	
434 R	1300 A	+7:91810411 1324206027 A	R
434	1301 G	+7:91810412 1324206028 G	
434	1302 G	+7:91810413 1324206029 G	
435 T	1303 A	+7:91810414 1324206030 A	T
435	1304 C	+7:91810415 1324206031 C	
435	1305 T	+7:91810416 1324206032 T	
436 T	1306 A	+7:91810417 1324206033 A	T
436	1307 C	+7:91810418 1324206034 C	
436	1308 A	+7:91810419 1324206035 A	
437 R	1309 C	+7:91810420 1324206036 C	R
437	1310 G	+7:91810421 1324206037 G	
437	1311 C	+7:91810422 1324206038 C	
438 S	1312 T	+7:91810423 1324206039 T	S
438	1313 C	+7:91810424 1324206040 C	
438	1314 T	+7:91810425 1324206041 T	
439 S	1315 T	+7:91810426 1324206042 T	S
439	1316 C	+7:91810427 1324206043 C	
439	1317 T	+7:91810428 1324206044 T	
440 V	1318 G	+7:91810429 1324206045 G	V
440	1319 T	+7:91810430 1324206046 T	
440	1320 C	+7:91810431 1324206047 C	
441 T	1321 A	+7:91810432 1324206048 A	T
441	1322 C	+7:91810433 1324206049 C	
441	1323 C	+7:91810434 1324206050 C	
442 S	1324 T	+7:91810435 1324206051 T	S
442	1325 C	+7:91810436 1324206052 C	
442	1326 C	+7:91810437 1324206053 C	
443 P	1327 C	+7:91810438 1324206054 C	P
443	1328 C	+7:91810439 1324206055 C	
443	1329 A	+7:91810440 1324206056 A	
444 D	1330 G	+7:91810441 1324206057 G	D
444	1331 A	+7:91810442 1324206058 A	
444	1332 T	+7:91810443 1324206059 T	
445 E	1333 G	+7:91810444 1324206060 G	E
445	1334 A	+7:91810445 1324206061 A	
445	1335 A	+7:91810446 1324206062 A	
446 I	1336 A	+7:91810447 1324206063 A	I
446	1337 T	+7:91810448 1324206064 T	
446	1338 C	+7:91810449 1324206065 C	
447 S	1339 A	+7:91810450 1324206066 A	S
447	1340 G	+7:91810451 1324206067 G	
447	1341 C	+7:91810452 1324206068 C	
448 L	1342 T	+7:91810453 1324206069 T	L
448	1343 T	+7:91810454 1324206070 T	
448	1344 A	+7:91810455 1324206071 A	
449 S	1345 T	+7:91810456 1324206072 T	S
449	1346 C	+7:91810457 1324206073 C	
449	1347 T	+7:91810458 1324206074 T	
450 P	1348 C	+7:91810459 1324206075 C	P
450	1349 C	+7:91810460 1324206076 C	
450	1350 T	+7:91810461 1324206077 T	
451 G	1351 G	+7:91810462 1324206078 G	G
451	1352 G	+7:91810463 1324206079 G	
451	1353 G	+7:91810464 1324206080 G	
452 D	1354 G	+7:91810465 1324206081 G	D
452	1355 A	+7:91810466 1324206082 A	
452	1356 T	+7:91810467 1324206083 T	
453 L	1357 T	+7:91810468 1324206084 T	L
453	1358 T	+7:91810469 1324206085 T	
453	1359 A	+7:91810470 1324206086 A	
454 D	1360 G	+7:91810471 1324206087 G	D
454	1361 A	+7:91810472 1324206088 A	
454	1362 C	+7:91810473 1324206089 C	
455 T	1363 A	+7:91810474 1324206090 A	T
455	1364 C	+7:91810475 1324206091 C	
455	1365 C	+7:91810476 1324206092 C	
456 S	1366 A	+7:91810477 1324206093 A	S
456	1367 G	+7:91810478 1324206094 G	
456	1368 T	+7:91810479 1324206095 T	
457 L	1369 T	+7:91810480 1324206096 T	L
457	1370 T	+7:91810481 1324206097 T	
457	1371 G	+7:91810482 1324206098 G	
458 C	1372 T	+7:91812228 1324207844 T	C
458	1373 G	+7:91812229 1324207845 G	
458	1374 T	+7:91812230 1324207846 T	
459 D	1375 G	+7:91812231 1324207847 G	D
459	1376 A	+7:91812232 1324207848 A	
459	1377 C	+7:91812233 1324207849 C	
460 I	1378 A	+7:91812234 1324207850 A	I
460	1379 T	+7:91812235 1324207851 T	
460	1380 T	+7:91812236 1324207852 T	
461 C	1381 T	+7:91812237 1324207853 T	C
461	1382 G	+7:91812238 1324207854 G	
461	1383 T	+7:91812239 1324207855 T	
462 M	1384 A	+7:91812240 1324207856 A	M
462	1385 T	+7:91812241 1324207857 T	
462	1386 G	+7:91812242 1324207858 G	
463 C	1387 T	+7:91812243 1324207859 T	C
463	1388 G	+7:91812244 1324207860 G	
463	1389 C	+7:91812245 1324207861 C	
464 S	1390 A	+7:91812246 1324207862 A	S
464	1391 G	+7:91812247 1324207863 G	
464	1392 T	+7:91812248 1324207864 T	
465 I	1393 A	+7:91812249 1324207865 A	I
465	1394 T	+7:91812250 1324207866 T	
465	1395 C	+7:91812251 1324207867 C	
466 S	1396 T	+7:91812252 1324207868 T	S
466	1397 C	+7:91812253 1324207869 C	
466	1398 T	+7:91812254 1324207870 T	
467 V	1399 G	+7:91812255 1324207871 G	V
467	1400 T	+7:91812256 1324207872 T	
467	1401 A	+7:91812257 1324207873 A	
468 F	1402 T	+7:91812258 1324207874 T	F
468	1403 T	+7:91812259 1324207875 T	
468	1404 T	+7:91812260 1324207876 T	
469 E	1405 G	+7:91812261 1324207877 G	E
469	1406 A	+7:91812262 1324207878 A	
469	1407 A	+7:91812263 1324207879 A	
470 D	1408 G	+7:91812264 1324207880 G	D
470	1409 A	+7:91812265 1324207881 A	
470	1410 C	+7:91812266 1324207882 C	
471 P	1411 C	+7:91812267 1324207883 C	P
471	1412 C	+7:91812268 1324207884 C	
471	1413 T	+7:91812269 1324207885 T	
472 V	1414 G	+7:91812270 1324207886 G	V
472	1415 T	+7:91812271 1324207887 T	
472	1416 G	+7:91812272 1324207888 G	
473 D	1417 G	+7:91812273 1324207889 G	D
473	1418 A	+7:91812274 1324207890 A	
473	1419 T	+7:91812275 1324207891 T	
474 M	1420 A	+7:91812276 1324207892 A	M
474	1421 T	+7:91812277 1324207893 T	
474	1422 G	+7:91812278 1324207894 G	
475 P	1423 C	+7:91812279 1324207895 C	P
475	1424 C	+7:91812280 1324207896 C	
475	1425 C	+7:91812281 1324207897 C	
476 C	1426 T	+7:91812282 1324207898 T	C
476	1427 G	+7:91812283 1324207899 G	
476	1428 T	+7:91812284 1324207900 T	
477 G	1429 G	+7:91812285 1324207901 G	G
477	1430 G	+7:91812286 1324207902 G	
477	1431 A	+7:91812287 1324207903 A	
478 H	1432 C	+7:91812288 1324207904 C	H
478	1433 A	+7:91812289 1324207905 A	
478	1434 T	+7:91812290 1324207906 T	
479 D	1435 G	+7:91812291 1324207907 G	D
479	1436 A	+7:91812292 1324207908 A	
479	1437 C	+7:91812293 1324207909 C	
480 F	1438 T	+7:91812294 1324207910 T	F
480	1439 T	+7:91812295 1324207911 T	
480	1440 T	+7:91812296 1324207912 T	
481 C	1441 T	+7:91812297 1324207913 T	C
481	1442 G	+7:91812298 1324207914 G	
481	1443 T	+7:91812299 1324207915 T	
482 R	1444 A	+7:91812300 1324207916 A	R
482	1445 G	+7:91812301 1324207917 G	
482	1446 A	+7:91812302 1324207918 A	
483 G	1447 G	+7:91812303 1324207919 G	G
483	1448 G	+7:91812304 1324207920 G	
483	1449 A	+7:91812305 1324207921 A	
484 C	1450 T	+7:91812306 1324207922 T	C
484	1451 G	+7:91812307 1324207923 G	
484	1452 T	+7:91812308 1324207924 T	
485 W	1453 T	+7:91812309 1324207925 T	W
485	1454 G	+7:91812310 1324207926 G	
485	1455 G	+7:91812311 1324207927 G	
486 E	1456 G	+7:91812312 1324207928 G	E
486	1457 A	+7:91812313 1324207929 A	
486	1458 G	+7:91812314 1324207930 G	
487 S	1459 T	+7:91812315 1324207931 T	S
487	1460 C	+7:91812316 1324207932 C	
487	1461 G	+7:91818200 1324213816 G	
488 F	1462 T	+7:91818201 1324213817 T	F
488	1463 T	+7:91818202 1324213818 T	
488	1464 T	+7:91818203 1324213819 T	
489 L	1465 T	+7:91818204 1324213820 T	L
489	1466 T	+7:91818205 1324213821 T	
489	1467 G	+7:91818206 1324213822 G	
490 N	1468 A	+7:91818207 1324213823 A	N
490	1469 A	+7:91818208 1324213824 A	
490	1470 T	+7:91818209 1324213825 T	
491 L	1471 C	+7:91818210 1324213826 C	L
491	1472 T	+7:91818211 1324213827 T	
491	1473 G	+7:91818212 1324213828 G	
492 K	1474 A	+7:91818213 1324213829 A	K
492	1475 A	+7:91818214 1324213830 A	
492	1476 A	+7:91818215 1324213831 A	
493 I	1477 A	+7:91818216 1324213832 A	I
493	1478 T	+7:91818217 1324213833 T	
493	1479 T	+7:91818218 1324213834 T	
494 Q	1480 C	+7:91818219 1324213835 C	Q
494	1481 A	+7:91818220 1324213836 A	
494	1482 A	+7:91818221 1324213837 A	
495 E	1483 G	+7:91818222 1324213838 G	E
495	1484 A	+7:91818223 1324213839 A	
495	1485 A	+7:91818224 1324213840 A	
496 G	1486 G	+7:91818225 1324213841 G	G
496	1487 G	+7:91818226 1324213842 G	
496	1488 T	+7:91818227 1324213843 T	
497 E	1489 G	+7:91818228 1324213844 G	E
497	1490 A	+7:91818229 1324213845 A	
497	1491 A	+7:91818230 1324213846 A	
498 A	1492 G	+7:91818231 1324213847 G	A
498	1493 C	+7:91818232 1324213848 C	
498	1494 T	+7:91818233 1324213849 T	
499 H	1495 C	+7:91818234 1324213850 C	H
499	1496 A	+7:91818235 1324213851 A	
499	1497 C	+7:91818236 1324213852 C	
500 N	1498 A	+7:91818237 1324213853 A	N
500	1499 A	+7:91818238 1324213854 A	
500	1500 C	+7:91818239 1324213855 C	
501 I	1501 A	+7:91818240 1324213856 A	I
501	1502 T	+7:91818241 1324213857 T	
501	1503 T	+7:91818242 1324213858 T	
502 F	1504 T	+7:91818243 1324213859 T	F
502	1505 T	+7:91818244 1324213860 T	
502	1506 T	+7:91818245 1324213861 T	
503 C	1507 T	+7:91818246 1324213862 T	C
503	1508 G	+7:91818247 1324213863 G	
503	1509 C	+7:91818248 1324213864 C	
504 P	1510 C	+7:91818249 1324213865 C	P
504	1511 C	+7:91818250 1324213866 C	
504	1512 T	+7:91818251 1324213867 T	
505 A	1513 G	+7:91818252 1324213868 G	A
505	1514 C	+7:91818253 1324213869 C	
505	1515 A	+7:91818254 1324213870 A	
506 Y	1516 T	+7:91818255 1324213871 T	Y
506	1517 A	+7:91818256 1324213872 A	
506	1518 T	+7:91818257 1324213873 T	
507 D	1519 G	+7:91818258 1324213874 G	D
507	1520 A	+7:91818259 1324213875 A	
507	1521 T	+7:91818260 1324213876 T	
508 C	1522 T	+7:91818261 1324213877 T	C
508	1523 G	+7:91818262 1324213878 G	
508	1524 C	+7:91818263 1324213879 C	
509 F	1525 T	+7:91818264 1324213880 T	F
509	1526 T	+7:91818265 1324213881 T	
509	1527 C	+7:91818266 1324213882 C	
510 Q	1528 C	+7:91818267 1324213883 C	Q
510	1529 A	+7:91818268 1324213884 A	
510	1530 A	+7:91818269 1324213885 A	
511 L	1531 C	+7:91818270 1324213886 C	L
511	1532 T	+7:91818271 1324213887 T	
511	1533 T	+7:91818272 1324213888 T	
512 V	1534 G	+7:91818273 1324213889 G	V
512	1535 T	+7:91818274 1324213890 T	
512	1536 A	+7:91818275 1324213891 A	
513 P	1537 C	+7:91818276 1324213892 C	P
513	1538 C	+7:91818277 1324213893 C	
513	1539 T	+7:91818278 1324213894 T	
514 V	1540 G	+7:91818279 1324213895 G	V
514	1541 T	+7:91818280 1324213896 T	
514	1542 G	+7:91818281 1324213897 G	
515 D	1543 G	+7:91818282 1324213898 G	D
515	1544 A	+7:91818283 1324213899 A	
515	1545 T	+7:91818284 1324213900 T	
516 I	1546 A	+7:91818285 1324213901 A	I
516	1547 T	+7:91818286 1324213902 T	
516	1548 C	+7:91818287 1324213903 C	
517 I	1549 A	+7:91818288 1324213904 A	I
517	1550 T	+7:91818289 1324213905 T	
517	1551 A	+7:91818290 1324213906 A	
518 E	1552 G	+7:91818291 1324213907 G	E
518	1553 A	+7:91818292 1324213908 A	
518	1554 A	+7:91818293 1324213909 A	
519 S	1555 A	+7:91818294 1324213910 A	S
519	1556 G	+7:91818295 1324213911 G	
519	1557 T	+7:91818296 1324213912 T	
520 V	1558 G	+7:91818297 1324213913 G	V
520	1559 T	+7:91818298 1324213914 T	
520	1560 A	+7:91818299 1324213915 A	
521 V	1561 G	+7:91818300 1324213916 G	V
521	1562 T	+7:91818301 1324213917 T	
521	1563 T	+7:91818302 1324213918 T	
522 S	1564 T	+7:91818303 1324213919 T	S
522	1565 C	+7:91818304 1324213920 C	
522	1566 A	+7:91818305 1324213921 A	
523 K	1567 A	+7:91818306 1324213922 A	K
523	1568 A	+7:91818307 1324213923 A	
523	1569 G	+7:91818308 1324213924 G	
524 E	1570 G	+7:91818309 1324213925 G	E
524	1571 A	+7:91818310 1324213926 A	
524	1572 G	+7:91818311 1324213927 G	
525 M	1573 A	+7:91818312 1324213928 A	M
525	1574 T	+7:91818313 1324213929 T	
525	1575 G	+7:91818314 1324213930 G	
526 D	1576 G	+7:91818315 1324213931 G	D
526	1577 A	+7:91818316 1324213932 A	
526	1578 C	+7:91818317 1324213933 C	
527 K	1579 A	+7:91818318 1324213934 A	K
527	1580 A	+7:91818319 1324213935 A	
527	1581 A	+7:91818320 1324213936 A	
528 R	1582 C	+7:91818321 1324213937 C	R
528	1583 G	+7:91818322 1324213938 G	
528	1584 A	+7:91818323 1324213939 A	
529 Y	1585 T	+7:91818324 1324213940 T	Y
529	1586 A	+7:91818325 1324213941 A	
529	1587 C	+7:91818326 1324213942 C	
530 L	1588 C	+7:91818327 1324213943 C	L
530	1589 T	+7:91818328 1324213944 T	
530	1590 A	+7:91818329 1324213945 A	
531 Q	1591 C	+7:91818330 1324213946 C	Q
531	1592 A	+7:91818331 1324213947 A	
531	1593 G	+7:91818332 1324213948 G	
532 F	1594 T	+7:91818333 1324213949 T	F
532	1595 T	+7:91818334 1324213950 T	
532	1596 T	+7:91818335 1324213951 T	
533 D	1597 G	+7:91818336 1324213952 G	D
533	1598 A	+7:91818337 1324213953 A	
533	1599 T	+7:91818338 1324213954 T	
534 I	1600 A	+7:91818339 1324213955 A	I
534	1601 T	+7:91818340 1324213956 T	
534	1602 T	+7:91818341 1324213957 T	
535 K	1603 A	+7:91818342 1324213958 A	K
535	1604 A	+7:91818343 1324213959 A	
535	1605 G	+7:91818344 1324213960 G	
536 A	1606 G	+7:91819726 1324215342 G	A
536	1607 C	+7:91819727 1324215343 C	
536	1608 C	+7:91819728 1324215344 C	
537 F	1609 T	+7:91819729 1324215345 T	F
537	1610 T	+7:91819730 1324215346 T	
537	1611 T	+7:91819731 1324215347 T	
538 V	1612 G	+7:91819732 1324215348 G	V
538	1613 T	+7:91819733 1324215349 T	
538	1614 T	+7:91819734 1324215350 T	
539 E	1615 G	+7:91819735 1324215351 G	E
539	1616 A	+7:91819736 1324215352 A	
539	1617 A	+7:91819737 1324215353 A	
540 N	1618 A	+7:91819738 1324215354 A	N
540	1619 A	+7:91819739 1324215355 A	
540	1620 T	+7:91819740 1324215356 T	
541 N	1621 A	+7:91819741 1324215357 A	N
541	1622 A	+7:91819742 1324215358 A	
541	1623 T	+7:91819743 1324215359 T	
542 P	1624 C	+7:91819744 1324215360 C	P
542	1625 C	+7:91819745 1324215361 C	
542	1626 T	+7:91819746 1324215362 T	
543 A	1627 G	+7:91819747 1324215363 G	A
543	1628 C	+7:91819748 1324215364 C	
543	1629 C	+7:91819749 1324215365 C	
544 I	1630 A	+7:91819750 1324215366 A	I
544	1631 T	+7:91819751 1324215367 T	
544	1632 T	+7:91819752 1324215368 T	
545 K	1633 A	+7:91819753 1324215369 A	K
545	1634 A	+7:91819754 1324215370 A	
545	1635 A	+7:91819755 1324215371 A	
546 W	1636 T	+7:91819756 1324215372 T	W
546	1637 G	+7:91819757 1324215373 G	
546	1638 G	+7:91819758 1324215374 G	
547 C	1639 T	+7:91819759 1324215375 T	C
547	1640 G	+7:91819760 1324215376 G	
547	1641 T	+7:91819761 1324215377 T	
548 P	1642 C	+7:91819762 1324215378 C	P
548	1643 C	+7:91819763 1324215379 C	
548	1644 T	+7:91819764 1324215380 T	
549 T	1645 A	+7:91819765 1324215381 A	T
549	1646 C	+7:91819766 1324215382 C	
549	1647 T	+7:91819767 1324215383 T	
550 P	1648 C	+7:91819768 1324215384 C	P
550	1649 C	+7:91819769 1324215385 C	
550	1650 A	+7:91819770 1324215386 A	
551 G	1651 G	+7:91819771 1324215387 G	G
551	1652 G	+7:91819772 1324215388 G	
551	1653 C	+7:91819773 1324215389 C	
552 C	1654 T	+7:91819774 1324215390 T	C
552	1655 G	+7:91819775 1324215391 G	
552	1656 T	+7:91819776 1324215392 T	
553 D	1657 G	+7:91819777 1324215393 G	D
553	1658 A	+7:91819778 1324215394 A	
553	1659 C	+7:91819779 1324215395 C	
554 R	1660 A	+7:91819780 1324215396 A	R
554	1661 G	+7:91819781 1324215397 G	
554	1662 A	+7:91819782 1324215398 A	
555 A	1663 G	+7:91819783 1324215399 G	A
555	1664 C	+7:91819784 1324215400 C	
555	1665 A	+7:91819785 1324215401 A	
556 V	1666 G	+7:91819786 1324215402 G	V
556	1667 T	+7:91819787 1324215403 T	
556	1668 A	+7:91819788 1324215404 A	
557 R	1669 A	+7:91819789 1324215405 A	R
557	1670 G	+7:91819790 1324215406 G	
557	1671 A	+7:91819791 1324215407 A	
558 L	1672 C	+7:91819792 1324215408 C	L
558	1673 T	+7:91819793 1324215409 T	
558	1674 A	+7:91819794 1324215410 A	
559 T	1675 A	+7:91819795 1324215411 A	T
559	1676 C	+7:91819796 1324215412 C	
559	1677 G	+7:91819797 1324215413 G	
560 K	1678 A	+7:91819798 1324215414 A	K
560	1679 A	+7:91819799 1324215415 A	
560	1680 A	+7:91819800 1324215416 A	
561 Q	1681 C	+7:91819801 1324215417 C	Q
561	1682 A	+7:91819802 1324215418 A	
561	1683 A	+7:91819803 1324215419 A	
562 G	1684 G	+7:91819804 1324215420 G	G
562	1685 G	+7:91819805 1324215421 G	
562	1686 G	+7:91819806 1324215422 G	
563 S	1687 T	+7:91819807 1324215423 T	S
563	1688 C	+7:91819808 1324215424 C	
563	1689 A	+7:91819809 1324215425 A	
564 N	1690 A	+7:91819810 1324215426 A	N
564	1691 A	+7:91819811 1324215427 A	
564	1692 T	+7:91819812 1324215428 T	
565 T	1693 A	+7:91819813 1324215429 A	T
565	1694 C	+7:91819814 1324215430 C	
565	1695 A	+7:91819815 1324215431 A	
566 S	1696 T	+7:91819816 1324215432 T	S
566	1697 C	+7:91819817 1324215433 C	
566	1698 T	+7:91819818 1324215434 T	
567 G	1699 G	+7:91819819 1324215435 G	G
567	1700 G	+7:91819820 1324215436 G	
567	1701 A	+7:91819821 1324215437 A	
568 S	1702 T	+7:91819822 1324215438 T	S
568	1703 C	+7:91819823 1324215439 C	
568	1704 T	+7:91819824 1324215440 T	
569 D	1705 G	+7:91819825 1324215441 G	D
569	1706 A	+7:91819826 1324215442 A	
569	1707 T	+7:91819827 1324215443 T	
570 T	1708 A	+7:91819828 1324215444 A	T
570	1709 C	+7:91819829 1324215445 C	
570	1710 A	+7:91819830 1324215446 A	
571 L	1711 C	+7:91819831 1324215447 C	L
571	1712 T	+7:91819832 1324215448 T	
571	1713 C	+7:91819833 1324215449 C	
572 S	1714 A	+7:91819834 1324215450 A	S
572	1715 G	+7:91819835 1324215451 G	
572	1716 C	+7:91819836 1324215452 C	
573 F	1717 T	+7:91819837 1324215453 T	F
573	1718 T	+7:91819838 1324215454 T	
573	1719 C	+7:91819839 1324215455 C	
574 P	1720 C	+7:91819840 1324215456 C	P
574	1721 C	+7:91819841 1324215457 C	
574	1722 A	+7:91819842 1324215458 A	
575 L	1723 T	+7:91819843 1324215459 T	L
575	1724 T	+7:91819844 1324215460 T	
575	1725 G	+7:91819845 1324215461 G	
576 L	1726 C	+7:91819846 1324215462 C	L
576	1727 T	+7:91819847 1324215463 T	
576	1728 G	+7:91819848 1324215464 G	
577 R	1729 A	+7:91819849 1324215465 A	R
577	1730 G	+7:91819850 1324215466 G	
577	1731 A	+7:91819851 1324215467 A	
578 A	1732 G	+7:91819852 1324215468 G	A
578	1733 C	+7:91819853 1324215469 C	
578	1734 T	+7:91819854 1324215470 T	
579 P	1735 C	+7:91819855 1324215471 C	P
579	1736 C	+7:91819856 1324215472 C	
579	1737 T	+7:91819857 1324215473 T	
580 A	1738 G	+7:91819858 1324215474 G	A
580	1739 C	+7:91819859 1324215475 C	
580	1740 T	+7:91819860 1324215476 T	
581 V	1741 G	+7:91819861 1324215477 G	V
581	1742 T	+7:91819862 1324215478 T	
581	1743 T	+7:91819863 1324215479 T	
582 D	1744 G	+7:91819864 1324215480 G	D
582	1745 A	+7:91819865 1324215481 A	
582	1746 T	+7:91819866 1324215482 T	
583 C	1747 T	+7:91819867 1324215483 T	C
583	1748 G	+7:91819868 1324215484 G	
583	1749 T	+7:91819869 1324215485 T	
584 G	1750 G	+7:91819870 1324215486 G	G
584	1751 G	+7:91819871 1324215487 G	
584	1752 A	+7:91819872 1324215488 A	
585 K	1753 A	+7:91819873 1324215489 A	K
585	1754 A	+7:91819874 1324215490 A	
585	1755 A	+7:91819875 1324215491 A	
586 G	1756 G	+7:91819876 1324215492 G	G
586	1757 G	+7:91819877 1324215493 G	
586	1758 A	+7:91819878 1324215494 A	
587 H	1759 C	+7:91819879 1324215495 C	H
587	1760 A	+7:91819880 1324215496 A	
587	1761 C	+7:91819881 1324215497 C	
588 L	1762 C	+7:91819882 1324215498 C	L
588	1763 T	+7:91819883 1324215499 T	
588	1764 C	+7:91819884 1324215500 C	
589 F	1765 T	+7:91819885 1324215501 T	F
589	1766 T	+7:91819886 1324215502 T	
589	1767 C	+7:91819887 1324215503 C	
590 C	1768 T	+7:91819888 1324215504 T	C
590	1769 G	+7:91819889 1324215505 G	
590	1770 C	+7:91819890 1324215506 C	
591 W	1771 T	+7:91819891 1324215507 T	W
591	1772 G	+7:91819892 1324215508 G	
591	1773 G	+7:91829435 1324225051 G	
592 E	1774 G	+7:91829436 1324225052 G	E
592	1775 A	+7:91829437 1324225053 A	
592	1776 G	+7:91829438 1324225054 G	
593 C	1777 T	+7:91829439 1324225055 T	C
593	1778 G	+7:91829440 1324225056 G	
593	1779 C	+7:91829441 1324225057 C	
594 L	1780 C	+7:91829442 1324225058 C	L
594	1781 T	+7:91829443 1324225059 T	
594	1782 T	+7:91829444 1324225060 T	
595 G	1783 G	+7:91829445 1324225061 G	G
595	1784 G	+7:91829446 1324225062 G	
595	1785 T	+7:91829447 1324225063 T	
596 E	1786 G	+7:91829448 1324225064 G	E
596	1787 A	+7:91829449 1324225065 A	
596	1788 A	+7:91829450 1324225066 A	
597 A	1789 G	+7:91829451 1324225067 G	A
597	1790 C	+7:91829452 1324225068 C	
597	1791 A	+7:91829453 1324225069 A	
598 H	1792 C	+7:91829454 1324225070 C	H
598	1793 A	+7:91829455 1324225071 A	
598	1794 T	+7:91829456 1324225072 T	
599 E	1795 G	+7:91829457 1324225073 G	E
599	1796 A	+7:91829458 1324225074 A	
599	1797 G	+7:91829459 1324225075 G	
600 P	1798 C	+7:91829460 1324225076 C	P
600	1799 C	+7:91829461 1324225077 C	
600	1800 T	+7:91829462 1324225078 T	
601 C	1801 T	+7:91829463 1324225079 T	C
601	1802 G	+7:91829464 1324225080 G	
601	1803 T	+7:91829465 1324225081 T	
602 D	1804 G	+7:91829466 1324225082 G	D
602	1805 A	+7:91829467 1324225083 A	
602	1806 C	+7:91829468 1324225084 C	
603 C	1807 T	+7:91829469 1324225085 T	C
603	1808 G	+7:91829470 1324225086 G	
603	1809 C	+7:91829471 1324225087 C	
604 Q	1810 C	+7:91829472 1324225088 C	Q
604	1811 A	+7:91829473 1324225089 A	
604	1812 A	+7:91829474 1324225090 A	
605 T	1813 A	+7:91829475 1324225091 A	T
605	1814 C	+7:91829476 1324225092 C	
605	1815 A	+7:91829477 1324225093 A	
606 W	1816 T	+7:91829478 1324225094 T	W
606	1817 G	+7:91829479 1324225095 G	
606	1818 G	+7:91829480 1324225096 G	
607 K	1819 A	+7:91829481 1324225097 A	K
607	1820 A	+7:91829482 1324225098 A	
607	1821 G	+7:91829483 1324225099 G	
608 N	1822 A	+7:91829484 1324225100 A	N
608	1823 A	+7:91829485 1324225101 A	
608	1824 T	+7:91829486 1324225102 T	
609 W	1825 T	+7:91829487 1324225103 T	W
609	1826 G	+7:91829488 1324225104 G	
609	1827 G	+7:91829489 1324225105 G	
610 L	1828 C	+7:91829490 1324225106 C	L
610	1829 T	+7:91829491 1324225107 T	
610	1830 G	+7:91829492 1324225108 G	
611 Q	1831 C	+7:91829493 1324225109 C	Q
611	1832 A	+7:91829494 1324225110 A	
611	1833 A	+7:91829495 1324225111 A	
612 K	1834 A	+7:91829496 1324225112 A	K
612	1835 A	+7:91829497 1324225113 A	
612	1836 A	+7:91829498 1324225114 A	
613 I	1837 A	+7:91829499 1324225115 A	I
613	1838 T	+7:91829500 1324225116 T	
613	1839 A	+7:91829501 1324225117 A	
614 T	1840 A	+7:91829502 1324225118 A	T
614	1841 C	+7:91829503 1324225119 C	
614	1842 C	+7:91829504 1324225120 C	
615 E	1843 G	+7:91829505 1324225121 G	E
615	1844 A	+7:91829506 1324225122 A	
615	1845 A	+7:91829507 1324225123 A	
616 M	1846 A	+7:91829508 1324225124 A	M
616	1847 T	+7:91829509 1324225125 T	
616	1848 G	+7:91829510 1324225126 G	
617 K	1849 A	+7:91829511 1324225127 A	K
617	1850 A	+7:91829512 1324225128 A	
617	1851 A	+7:91829513 1324225129 A	
618 P	1852 C	+7:91829514 1324225130 C	P
618	1853 C	+7:91829515 1324225131 C	
618	1854 A	+7:91829516 1324225132 A	
619 E	1855 G	+7:91829517 1324225133 G	E
619	1856 A	+7:91829518 1324225134 A	
619	1857 A	+7:91829519 1324225135 A	
620 E	1858 G	+7:91829520 1324225136 G	E
620	1859 A	+7:91829521 1324225137 A	
620	1860 A	+7:91829522 1324225138 A	
621 L	1861 C	+7:91829523 1324225139 C	L
621	1862 T	+7:91838727 1324234343 T	
621	1863 T	+7:91838728 1324234344 T	
622 V	1864 G	+7:91838729 1324234345 G	V
622	1865 T	+7:91838730 1324234346 T	
622	1866 G	+7:91838731 1324234347 G	
623 G	1867 G	+7:91838732 1324234348 G	G
623	1868 G	+7:91838733 1324234349 G	
623	1869 A	+7:91838734 1324234350 A	
624 V	1870 G	+7:91838735 1324234351 G	V
624	1871 T	+7:91838736 1324234352 T	
624	1872 T	+7:91838737 1324234353 T	
625 S	1873 A	+7:91838738 1324234354 A	S
625	1874 G	+7:91838739 1324234355 G	
625	1875 T	+7:91838740 1324234356 T	
626 E	1876 G	+7:91838741 1324234357 G	E
626	1877 A	+7:91838742 1324234358 A	
626	1878 A	+7:91838743 1324234359 A	
627 A	1879 G	+7:91838744 1324234360 G	A
627	1880 C	+7:91838745 1324234361 C	
627	1881 C	+7:91838746 1324234362 C	
628 Y	1882 T	+7:91838747 1324234363 T	Y
628	1883 A	+7:91838748 1324234364 A	
628	1884 C	+7:91838749 1324234365 C	
629 E	1885 G	+7:91838750 1324234366 G	E
629	1886 A	+7:91838751 1324234367 A	
629	1887 G	+7:91838752 1324234368 G	
630 D	1888 G	+7:91838753 1324234369 G	D
630	1889 A	+7:91838754 1324234370 A	
630	1890 T	+7:91838755 1324234371 T	
631 A	1891 G	+7:91838756 1324234372 G	A
631	1892 C	+7:91838757 1324234373 C	
631	1893 C	+7:91838758 1324234374 C	
632 A	1894 G	+7:91838759 1324234375 G	A
632	1895 C	+7:91838760 1324234376 C	
632	1896 C	+7:91838761 1324234377 C	
633 N	1897 A	+7:91838762 1324234378 A	N
633	1898 A	+7:91838763 1324234379 A	
633	1899 T	+7:91838764 1324234380 T	
634 C	1900 T	+7:91838765 1324234381 T	C
634	1901 G	+7:91838766 1324234382 G	
634	1902 T	+7:91838767 1324234383 T	
635 L	1903 C	+7:91838768 1324234384 C	L
635	1904 T	+7:91838769 1324234385 T	
635	1905 C	+7:91838770 1324234386 C	
636 W	1906 T	+7:91838771 1324234387 T	W
636	1907 G	+7:91838772 1324234388 G	
636	1908 G	+7:91838773 1324234389 G	
637 L	1909 T	+7:91838774 1324234390 T	L
637	1910 T	+7:91838775 1324234391 T	
637	1911 A	+7:91838776 1324234392 A	
638 L	1912 T	+7:91838777 1324234393 T	L
638	1913 T	+7:91838778 1324234394 T	
638	1914 A	+7:91838779 1324234395 A	
639 T	1915 A	+7:91838780 1324234396 A	T
639	1916 C	+7:91838781 1324234397 C	
639	1917 T	+7:91838782 1324234398 T	
640 N	1918 A	+7:91838783 1324234399 A	N
640	1919 A	+7:91838784 1324234400 A	
640	1920 C	+7:91838785 1324234401 C	
641 S	1921 T	+7:91838786 1324234402 T	S
641	1922 C	+7:91838787 1324234403 C	
641	1923 C	+7:91838788 1324234404 C	
642 K	1924 A	+7:91838789 1324234405 A	K
642	1925 A	+7:91838790 1324234406 A	
642	1926 G	+7:91838791 1324234407 G	
643 P	1927 C	+7:91838792 1324234408 C	P
643	1928 C	+7:91838793 1324234409 C	
643	1929 T	+7:91838794 1324234410 T	
644 C	1930 T	+7:91838795 1324234411 T	C
644	1931 G	+7:91838796 1324234412 G	
644	1932 T	+7:91838797 1324234413 T	
645 A	1933 G	+7:91838798 1324234414 G	A
645	1934 C	+7:91838799 1324234415 C	
645	1935 C	+7:91838800 1324234416 C	
646 N	1936 A	+7:91838801 1324234417 A	N
646	1937 A	+7:91838802 1324234418 A	
646	1938 C	+7:91838803 1324234419 C	
647 C	1939 T	+7:91838804 1324234420 T	C
647	1940 G	+7:91838805 1324234421 G	
647	1941 T	+7:91838806 1324234422 T	
648 K	1942 A	+7:91838807 1324234423 A	K
648	1943 A	+7:91838808 1324234424 A	
648	1944 G	+7:91838809 1324234425 G	
649 S	1945 T	+7:91838810 1324234426 T	S
649	1946 C	+7:91838811 1324234427 C	
649	1947 T	+7:91838812 1324234428 T	
650 P	1948 C	+7:91838813 1324234429 C	P
650	1949 C	+7:91838814 1324234430 C	
650	1950 A	+7:91838815 1324234431 A	
651 I	1951 A	+7:91838816 1324234432 A	I
651	1952 T	+7:91838817 1324234433 T	
651	1953 A	+7:91838818 1324234434 A	
652 Q	1954 C	+7:91838819 1324234435 C	Q
652	1955 A	+7:91838820 1324234436 A	
652	1956 G	+7:91838821 1324234437 G	
653 K	1957 A	+7:91838822 1324234438 A	K
653	1958 A	+7:91838823 1324234439 A	
653	1959 G	+7:91838824 1324234440 G	
654 N	1960 A	+7:91838825 1324234441 A	N
654	1961 A	+7:91838826 1324234442 A	
654	1962 T	+7:91838827 1324234443 T	
655 E	1963 G	+7:91838828 1324234444 G	E
655	1964 A	+7:91838829 1324234445 A	
655	1965 A	+7:91838830 1324234446 A	
656 G	1966 G	+7:91838831 1324234447 G	G
656	1967 G	+7:91838832 1324234448 G	
656	1968 C	+7:91838833 1324234449 C	
657 C	1969 T	+7:91838834 1324234450 T	C
657	1970 G	+7:91838835 1324234451 G	
657	1971 C	+7:91838836 1324234452 C	
658 N	1972 A	+7:91838837 1324234453 A	N
658	1973 A	+7:91838838 1324234454 A	
658	1974 T	+7:91838839 1324234455 T	
659 H	1975 C	+7:91838840 1324234456 C	H
659	1976 A	+7:91838841 1324234457 A	
659	1977 C	+7:91838842 1324234458 C	
660 M	1978 A	+7:91838843 1324234459 A	M
660	1979 T	+7:91838844 1324234460 T	
660	1980 G	+7:91838845 1324234461 G	
661 Q	1981 C	+7:91838846 1324234462 C	Q
661	1982 A	+7:91838847 1324234463 A	
661	1983 G	+7:91838848 1324234464 G	
662 C	1984 T	+7:91838849 1324234465 T	C
662	1985 G	+7:91838850 1324234466 G	
662	1986 T	+7:91838851 1324234467 T	
663 A	1987 G	+7:91838852 1324234468 G	A
663	1988 C	+7:91838853 1324234469 C	
663	1989 T	+7:91838854 1324234470 T	
664 K	1990 A	+7:91838855 1324234471 A	K
664	1991 A	+7:91838856 1324234472 A	
664	1992 G	+7:91838857 1324234473 G	
665 C	1993 T	+7:91853759 1324249375 T	C
665	1994 G	+7:91853760 1324249376 G	
665	1995 C	+7:91853761 1324249377 C	
666 K	1996 A	+7:91853762 1324249378 A	K
666	1997 A	+7:91853763 1324249379 A	
666	1998 G	+7:91853764 1324249380 G	
667 Y	1999 T	+7:91853765 1324249381 T	Y
667	2000 A	+7:91853766 1324249382 A	
667	2001 T	+7:91853767 1324249383 T	
668 D	2002 G	+7:91853768 1324249384 G	D
668	2003 A	+7:91853769 1324249385 A	
668	2004 C	+7:91853770 1324249386 C	
669 F	2005 T	+7:91853771 1324249387 T	F
669	2006 T	+7:91853772 1324249388 T	
669	2007 T	+7:91853773 1324249389 T	
670 C	2008 T	+7:91853774 1324249390 T	C
670	2009 G	+7:91853775 1324249391 G	
670	2010 C	+7:91853776 1324249392 C	
671 W	2011 T	+7:91853777 1324249393 T	W
671	2012 G	+7:91853778 1324249394 G	
671	2013 G	+7:91853779 1324249395 G	
672 I	2014 A	+7:91853780 1324249396 A	I
672	2015 T	+7:91853781 1324249397 T	
672	2016 T	+7:91853782 1324249398 T	
673 C	2017 T	+7:91853783 1324249399 T	C
673	2018 G	+7:91853784 1324249400 G	
673	2019 C	+7:91853785 1324249401 C	
674 L	2020 C	+7:91853786 1324249402 C	L
674	2021 T	+7:91853787 1324249403 T	
674	2022 T	+7:91853788 1324249404 T	
675 E	2023 G	+7:91853789 1324249405 G	E
675	2024 A	+7:91853790 1324249406 A	
675	2025 A	+7:91853791 1324249407 A	
676 E	2026 G	+7:91853792 1324249408 G	E
676	2027 A	+7:91853793 1324249409 A	
676	2028 G	+7:91853794 1324249410 G	
677 W	2029 T	+7:91853795 1324249411 T	W
677	2030 G	+7:91853796 1324249412 G	
677	2031 G	+7:91853797 1324249413 G	
678 K	2032 A	+7:91853798 1324249414 A	K
678	2033 A	+7:91853799 1324249415 A	
678	2034 A	+7:91853800 1324249416 A	
679 K	2035 A	+7:91853801 1324249417 A	K
679	2036 A	+7:91853802 1324249418 A	
679	2037 A	+7:91853803 1324249419 A	
680 H	2038 C	+7:91853804 1324249420 C	H
680	2039 A	+7:91853805 1324249421 A	
680	2040 T	+7:91853806 1324249422 T	
681 S	2041 A	+7:91853807 1324249423 A	S
681	2042 G	+7:91853808 1324249424 G	
681	2043 T	+7:91853809 1324249425 T	
682 S	2044 T	+7:91853810 1324249426 T	S
682	2045 C	+7:91853811 1324249427 C	
682	2046 G	+7:91853812 1324249428 G	
683 S	2047 T	+7:91853813 1324249429 T	S
683	2048 C	+7:91853814 1324249430 C	
683	2049 C	+7:91853815 1324249431 C	
684 T	2050 A	+7:91853816 1324249432 A	T
684	2051 C	+7:91853817 1324249433 C	
684	2052 T	+7:91853818 1324249434 T	
685 G	2053 G	+7:91853819 1324249435 G	G
685	2054 G	+7:91853820 1324249436 G	
685	2055 A	+7:91853821 1324249437 A	
686 G	2056 G	+7:91853822 1324249438 G	G
686	2057 G	+7:91853823 1324249439 G	
686	2058 T	+7:91853824 1324249440 T	
687 Y	2059 T	+7:91853825 1324249441 T	Y
687	2060 A	+7:91853826 1324249442 A	
687	2061 T	+7:91853827 1324249443 T	
688 Y	2062 T	+7:91853828 1324249444 T	Y
688	2063 A	+7:91853829 1324249445 A	
688	2064 C	+7:91853830 1324249446 C	
689 R	2065 A	+7:91853831 1324249447 A	R
689	2066 G	+7:91853832 1324249448 G	
689	2067 A	+7:91853833 1324249449 A	
690 C	2068 T	+7:91853834 1324249450 T	C
690	2069 G	+7:91853835 1324249451 G	
690	2070 T	+7:91853836 1324249452 T	
691 T	2071 A	+7:91853837 1324249453 A	T
691	2072 C	+7:91853838 1324249454 C	
691	2073 T	+7:91853839 1324249455 T	
692 R	2074 C	+7:91853840 1324249456 C	R
692	2075 G	+7:91853841 1324249457 G	
692	2076 C	+7:91853842 1324249458 C	
693 Y	2077 T	+7:91853843 1324249459 T	Y
693	2078 A	+7:91853844 1324249460 A	
693	2079 T	+7:91853845 1324249461 T	
694 E	2080 G	+7:91853846 1324249462 G	E
694	2081 A	+7:91853847 1324249463 A	
694	2082 A	+7:91853848 1324249464 A	
695 V	2083 G	+7:91853849 1324249465 G	V
695	2084 T	+7:91853850 1324249466 T	
695	2085 C	+7:91853851 1324249467 C	
696 I	2086 A	+7:91853852 1324249468 A	I
696	2087 T	+7:91853853 1324249469 T	
696	2088 T	+7:91853854 1324249470 T	
697 Q	2089 C	+7:91853855 1324249471 C	Q
697	2090 A	+7:91853856 1324249472 A	
697	2091 A	+7:91853857 1324249473 A	
698 H	2092 C	+7:91853858 1324249474 C	H
698	2093 A	+7:91853859 1324249475 A	
698	2094 C	+7:91853860 1324249476 C	
699 V	2095 G	+7:91853861 1324249477 G	V
699	2096 T	+7:91853862 1324249478 T	
699	2097 G	+7:91853863 1324249479 G	
700 E	2098 G	+7:91853864 1324249480 G	E
700	2099 A	+7:91853865 1324249481 A	
700	2100 G	+7:91853866 1324249482 G	
701 E	2101 G	+7:91853867 1324249483 G	E
701	2102 A	+7:91853868 1324249484 A	
701	2103 G	+7:91853869 1324249485 G	
702 Q	2104 C	+7:91853870 1324249486 C	Q
702	2105 A	+7:91853871 1324249487 A	
702	2106 A	+7:91853872 1324249488 A	
703 S	2107 T	+7:91853873 1324249489 T	S
703	2108 C	+7:91853874 1324249490 C	
703	2109 C	+7:91853875 1324249491 C	
704 K	2110 A	+7:91853876 1324249492 A	K
704	2111 A	+7:91853877 1324249493 A	
704	2112 G	+7:91853878 1324249494 G	
705 E	2113 G	+7:91853879 1324249495 G	E
705	2114 A	+7:91853880 1324249496 A	
705	2115 A	+7:91853881 1324249497 A	
706 M	2116 A	+7:91853882 1324249498 A	M
706	2117 T	+7:91853883 1324249499 T	
706	2118 G	+7:91853884 1324249500 G	
707 T	2119 A	+7:91853885 1324249501 A	T
707	2120 C	+7:91853886 1324249502 C	
707	2121 T	+7:91853887 1324249503 T	
708 V	2122 G	+7:91853888 1324249504 G	V
708	2123 T	+7:91853889 1324249505 T	
708	2124 G	+7:91853890 1324249506 G	
709 E	2125 G	+7:91853891 1324249507 G	E
709	2126 A	+7:91853892 1324249508 A	
709	2127 G	+7:91853893 1324249509 G	
710 A	2128 G	+7:91855048 1324250664 G	A
710	2129 C	+7:91855049 1324250665 C	
710	2130 T	+7:91855050 1324250666 T	
711 E	2131 G	+7:91855051 1324250667 G	E
711	2132 A	+7:91855052 1324250668 A	
711	2133 G	+7:91855053 1324250669 G	
712 K	2134 A	+7:91855054 1324250670 A	K
712	2135 A	+7:91855055 1324250671 A	
712	2136 A	+7:91855056 1324250672 A	
713 K	2137 A	+7:91855057 1324250673 A	K
713	2138 A	+7:91855058 1324250674 A	
713	2139 A	+7:91855059 1324250675 A	
714 H	2140 C	+7:91855060 1324250676 C	H
714	2141 A	+7:91855061 1324250677 A	
714	2142 C	+7:91855062 1324250678 C	
715 K	2143 A	+7:91855063 1324250679 A	K
715	2144 A	+7:91855064 1324250680 A	
715	2145 A	+7:91855065 1324250681 A	
716 R	2146 C	+7:91855066 1324250682 C	R
716	2147 G	+7:91855067 1324250683 G	
716	2148 A	+7:91855068 1324250684 A	
717 F	2149 T	+7:91855069 1324250685 T	F
717	2150 T	+7:91855070 1324250686 T	
717	2151 T	+7:91855071 1324250687 T	
718 Q	2152 C	+7:91855072 1324250688 C	Q
718	2153 A	+7:91855073 1324250689 A	
718	2154 G	+7:91855074 1324250690 G	
719 E	2155 G	+7:91855075 1324250691 G	E
719	2156 A	+7:91855076 1324250692 A	
719	2157 A	+7:91855077 1324250693 A	
720 L	2158 C	+7:91855078 1324250694 C	L
720	2159 T	+7:91855079 1324250695 T	
720	2160 T	+7:91855080 1324250696 T	
721 D	2161 G	+7:91855081 1324250697 G	D
721	2162 A	+7:91855082 1324250698 A	
721	2163 C	+7:91855083 1324250699 C	
722 R	2164 A	+7:91855084 1324250700 A	R
722	2165 G	+7:91855085 1324250701 G	
722	2166 A	+7:91855086 1324250702 A	
723 F	2167 T	+7:91855087 1324250703 T	F
723	2168 T	+7:91855088 1324250704 T	
723	2169 T	+7:91855089 1324250705 T	
724 M	2170 A	+7:91855090 1324250706 A	M
724	2171 T	+7:91855091 1324250707 T	
724	2172 G	+7:91855092 1324250708 G	
725 H	2173 C	+7:91855093 1324250709 C	H
725	2174 A	+7:91855094 1324250710 A	
725	2175 C	+7:91855095 1324250711 C	
726 Y	2176 T	+7:91855096 1324250712 T	Y
726	2177 A	+7:91855097 1324250713 A	
726	2178 T	+7:91855098 1324250714 T	
727 Y	2179 T	+7:91855099 1324250715 T	Y
727	2180 A	+7:91855100 1324250716 A	
727	2181 T	+7:91855101 1324250717 T	
728 T	2182 A	+7:91855102 1324250718 A	T
728	2183 C	+7:91855103 1324250719 C	
728	2184 A	+7:91855104 1324250720 A	
729 R	2185 A	+7:91855105 1324250721 A	R
729	2186 G	+7:91855106 1324250722 G	
729	2187 A	+7:91855107 1324250723 A	
730 F	2188 T	+7:91855108 1324250724 T	F
730	2189 T	+7:91855109 1324250725 T	
730	2190 T	+7:91855110 1324250726 T	
731 K	2191 A	+7:91855111 1324250727 A	K
731	2192 A	+7:91855112 1324250728 A	
731	2193 A	+7:91855113 1324250729 A	
732 N	2194 A	+7:91855114 1324250730 A	N
732	2195 A	+7:91855115 1324250731 A	
732	2196 C	+7:91855116 1324250732 C	
733 H	2197 C	+7:91855117 1324250733 C	H
733	2198 A	+7:91855118 1324250734 A	
733	2199 T	+7:91855119 1324250735 T	
734 E	2200 G	+7:91855120 1324250736 G	E
734	2201 A	+7:91855121 1324250737 A	
734	2202 G	+7:91855122 1324250738 G	
735 H	2203 C	+7:91855123 1324250739 C	H
735	2204 A	+7:91855124 1324250740 A	
735	2205 T	+7:91855125 1324250741 T	
736 S	2206 A	+7:91855126 1324250742 A	S
736	2207 G	+7:91855127 1324250743 G	
736	2208 T	+7:91855128 1324250744 T	
737 Y	2209 T	+7:91855129 1324250745 T	Y
737	2210 A	+7:91855130 1324250746 A	
737	2211 T	+7:91855131 1324250747 T	
738 Q	2212 C	+7:91855132 1324250748 C	Q
738	2213 A	+7:91855133 1324250749 A	
738	2214 G	+7:91855134 1324250750 G	
739 L	2215 C	+7:91855225 1324250841 C	L
739	2216 T	+7:91855226 1324250842 T	
739	2217 A	+7:91855227 1324250843 A	
740 E	2218 G	+7:91855228 1324250844 G	E
740	2219 A	+7:91855229 1324250845 A	
740	2220 A	+7:91855230 1324250846 A	
741 Q	2221 C	+7:91855231 1324250847 C	Q
741	2222 A	+7:91855232 1324250848 A	
741	2223 A	+7:91855233 1324250849 A	
742 R	2224 C	+7:91855234 1324250850 C	R
742	2225 G	+7:91855235 1324250851 G	
742	2226 C	+7:91855236 1324250852 C	
743 L	2227 C	+7:91855237 1324250853 C	L
743	2228 T	+7:91855238 1324250854 T	
743	2229 T	+7:91855239 1324250855 T	
744 L	2230 C	+7:91855240 1324250856 C	L
744	2231 T	+7:91855241 1324250857 T	
744	2232 T	+7:91855242 1324250858 T	
745 K	2233 A	+7:91855243 1324250859 A	K
745	2234 A	+7:91855244 1324250860 A	
745	2235 A	+7:91855245 1324250861 A	
746 T	2236 A	+7:91855246 1324250862 A	T
746	2237 C	+7:91855247 1324250863 C	
746	2238 A	+7:91855248 1324250864 A	
747 A	2239 G	+7:91855249 1324250865 G	A
747	2240 C	+7:91855250 1324250866 C	
747	2241 C	+7:91855251 1324250867 C	
748 K	2242 A	+7:91855252 1324250868 A	K
748	2243 A	+7:91855253 1324250869 A	
748	2244 A	+7:91855254 1324250870 A	
749 E	2245 G	+7:91855255 1324250871 G	E
749	2246 A	+7:91855256 1324250872 A	
749	2247 A	+7:91855257 1324250873 A	
750 K	2248 A	+7:91855258 1324250874 A	K
750	2249 A	+7:91855259 1324250875 A	
750	2250 G	+7:91855260 1324250876 G	
751 M	2251 A	+7:91855261 1324250877 A	M
751	2252 T	+7:91855262 1324250878 T	
751	2253 G	+7:91855263 1324250879 G	
752 E	2254 G	+7:91855264 1324250880 G	E
752	2255 A	+7:91855265 1324250881 A	
752	2256 G	+7:91855266 1324250882 G	
753 Q	2257 C	+7:91855267 1324250883 C	Q
753	2258 A	+7:91855268 1324250884 A	
753	2259 A	+7:91855269 1324250885 A	
754 L	2260 T	+7:91855270 1324250886 T	L
754	2261 T	+7:91855271 1324250887 T	
754	2262 G	+7:91855272 1324250888 G	
755 S	2263 A	+7:91855273 1324250889 A	S
755	2264 G	+7:91855274 1324250890 G	
755	2265 C	+7:91855275 1324250891 C	
756 R	2266 A	+7:91855276 1324250892 A	R
756	2267 G	+7:91855277 1324250893 G	
756	2268 A	+7:91855278 1324250894 A	
757 A	2269 G	+7:91855279 1324250895 G	A
757	2270 C	+7:91855280 1324250896 C	
757	2271 T	+7:91855281 1324250897 T	
758 L	2272 C	+7:91855282 1324250898 C	L
758	2273 T	+7:91855283 1324250899 T	
758	2274 C	+7:91855284 1324250900 C	
759 K	2275 A	+7:91855285 1324250901 A	K
759	2276 A	+7:91855286 1324250902 A	
759	2277 A	+7:91855287 1324250903 A	
760 E	2278 G	+7:91855288 1324250904 G	E
760	2279 A	+7:91855289 1324250905 A	
760	2280 A	+7:91855290 1324250906 A	
761 T	2281 A	+7:91855291 1324250907 A	T
761	2282 C	+7:91857221 1324252837 C	
761	2283 T	+7:91857222 1324252838 T	
762 E	2284 G	+7:91857223 1324252839 G	E
762	2285 A	+7:91857224 1324252840 A	
762	2286 A	+7:91857225 1324252841 A	
763 G	2287 G	+7:91857226 1324252842 G	G
763	2288 G	+7:91857227 1324252843 G	
763	2289 A	+7:91857228 1324252844 A	
764 G	2290 G	+7:91857229 1324252845 G	G
764	2291 G	+7:91857230 1324252846 G	
764	2292 C	+7:91857231 1324252847 C	
765 C	2293 T	+7:91857232 1324252848 T	C
765	2294 G	+7:91857233 1324252849 G	
765	2295 T	+7:91857234 1324252850 T	
766 P	2296 C	+7:91857235 1324252851 C	P
766	2297 C	+7:91857236 1324252852 C	
766	2298 A	+7:91857237 1324252853 A	
767 D	2299 G	+7:91857238 1324252854 G	D
767	2300 A	+7:91857239 1324252855 A	
767	2301 T	+7:91857240 1324252856 T	
768 T	2302 A	+7:91857241 1324252857 A	T
768	2303 C	+7:91857242 1324252858 C	
768	2304 C	+7:91857243 1324252859 C	
769 T	2305 A	+7:91857244 1324252860 A	T
769	2306 C	+7:91857245 1324252861 C	
769	2307 T	+7:91857246 1324252862 T	
770 F	2308 T	+7:91857247 1324252863 T	F
770	2309 T	+7:91857248 1324252864 T	
770	2310 C	+7:91857249 1324252865 C	
771 I	2311 A	+7:91857250 1324252866 A	I
771	2312 T	+7:91857251 1324252867 T	
771	2313 T	+7:91857252 1324252868 T	
772 E	2314 G	+7:91857253 1324252869 G	E
772	2315 A	+7:91857254 1324252870 A	
772	2316 A	+7:91857255 1324252871 A	
773 D	2317 G	+7:91857256 1324252872 G	D
773	2318 A	+7:91857257 1324252873 A	
773	2319 T	+7:91857258 1324252874 T	
774 A	2320 G	+7:91857259 1324252875 G	A
774	2321 C	+7:91857260 1324252876 C	
774	2322 A	+7:91857261 1324252877 A	
775 V	2323 G	+7:91857262 1324252878 G	V
775	2324 T	+7:91857263 1324252879 T	
775	2325 T	+7:91857264 1324252880 T	
776 H	2326 C	+7:91857265 1324252881 C	H
776	2327 A	+7:91857266 1324252882 A	
776	2328 T	+7:91857267 1324252883 T	
777 V	2329 G	+7:91857268 1324252884 G	V
777	2330 T	+7:91857269 1324252885 T	
777	2331 G	+7:91857270 1324252886 G	
778 L	2332 C	+7:91857271 1324252887 C	L
778	2333 T	+7:91857272 1324252888 T	
778	2334 C	+7:91857273 1324252889 C	
779 L	2335 T	+7:91857274 1324252890 T	L
779	2336 T	+7:91857275 1324252891 T	
779	2337 A	+7:91857276 1324252892 A	
780 K	2338 A	+7:91857277 1324252893 A	K
780	2339 A	+7:91857278 1324252894 A	
780	2340 A	+7:91857279 1324252895 A	
781 T	2341 A	+7:91857280 1324252896 A	T
781	2342 C	+7:91857281 1324252897 C	
781	2343 T	+7:91857282 1324252898 T	
782 R	2344 C	+7:91857283 1324252899 C	R
782	2345 G	+7:91857284 1324252900 G	
782	2346 G	+7:91857285 1324252901 G	
783 R	2347 C	+7:91857286 1324252902 C	R
783	2348 G	+7:91857287 1324252903 G	
783	2349 C	+7:91857288 1324252904 C	
784 I	2350 A	+7:91857289 1324252905 A	I
784	2351 T	+7:91857290 1324252906 T	
784	2352 T	+7:91857291 1324252907 T	
785 L	2353 C	+7:91857292 1324252908 C	L
785	2354 T	+7:91857293 1324252909 T	
785	2355 C	+7:91857294 1324252910 C	
786 K	2356 A	+7:91857295 1324252911 A	K
786	2357 A	+7:91857296 1324252912 A	
786	2358 G	+7:91857297 1324252913 G	
787 C	2359 T	+7:91857298 1324252914 T	C
787	2360 G	+7:91857299 1324252915 G	
787	2361 T	+7:91857300 1324252916 T	
788 S	2362 T	+7:91857301 1324252917 T	S
788	2363 C	+7:91857302 1324252918 C	
788	2364 T	+7:91857303 1324252919 T	
789 Y	2365 T	+7:91857304 1324252920 T	Y
789	2366 A	+7:91857305 1324252921 A	
789	2367 T	+7:91857306 1324252922 T	
790 P	2368 C	+7:91857307 1324252923 C	P
790	2369 C	+7:91857308 1324252924 C	
790	2370 A	+7:91857309 1324252925 A	
791 Y	2371 T	+7:91857310 1324252926 T	Y
791	2372 A	+7:91857311 1324252927 A	
791	2373 T	+7:91857312 1324252928 T	
792 G	2374 G	+7:91857313 1324252929 G	G
792	2375 G	+7:91857314 1324252930 G	
792	2376 A	+7:91857315 1324252931 A	
793 F	2377 T	+7:91857316 1324252932 T	F
793	2378 T	+7:91857317 1324252933 T	
793	2379 T	+7:91857318 1324252934 T	
794 F	2380 T	+7:91857319 1324252935 T	F
794	2381 T	+7:91857320 1324252936 T	
794	2382 C	+7:91857321 1324252937 C	
795 L	2383 T	+7:91857322 1324252938 T	L
795	2384 T	+7:91857323 1324252939 T	
795	2385 G	+7:91857324 1324252940 G	
796 E	2386 G	+7:91857325 1324252941 G	E
796	2387 A	+7:91857326 1324252942 A	
796	2388 A	+7:91857327 1324252943 A	
797 P	2389 C	+7:91857328 1324252944 C	P
797	2390 C	+7:91857329 1324252945 C	
797	2391 T	+7:91857330 1324252946 T	
798 K	2392 A	+7:91857331 1324252947 A	K
798	2393 A	+7:91857332 1324252948 A	
798	2394 A	+7:91857333 1324252949 A	
799 S	2395 A	+7:91857334 1324252950 A	S
799	2396 G	+7:91857335 1324252951 G	
799	2397 C	+7:91857336 1324252952 C	
800 T	2398 A	+7:91857337 1324252953 A	T
800	2399 C	+7:91857338 1324252954 C	
800	2400 A	+7:91857339 1324252955 A	
801 K	2401 A	+7:91857340 1324252956 A	K
801	2402 A	+7:91857341 1324252957 A	
801	2403 G	+7:91857342 1324252958 G	
802 K	2404 A	+7:91857343 1324252959 A	K
802	2405 A	+7:91857344 1324252960 A	
802	2406 A	+7:91857345 1324252961 A	
803 E	2407 G	+7:91857346 1324252962 G	E
803	2408 A	+7:91857347 1324252963 A	
803	2409 A	+7:91857348 1324252964 A	
804 I	2410 A	+7:91857349 1324252965 A	I
804	2411 T	+7:91857350 1324252966 T	
804	2412 T	+7:91857351 1324252967 T	
805 F	2413 T	+7:91857352 1324252968 T	F
805	2414 T	+7:91857353 1324252969 T	
805	2415 T	+7:91857354 1324252970 T	
806 E	2416 G	+7:91857355 1324252971 G	E
806	2417 A	+7:91857356 1324252972 A	
806	2418 A	+7:91857357 1324252973 A	
807 L	2419 C	+7:91857358 1324252974 C	L
807	2420 T	+7:91857359 1324252975 T	
807	2421 A	+7:91857360 1324252976 A	
808 M	2422 A	+7:91857361 1324252977 A	M
808	2423 T	+7:91857362 1324252978 T	
808	2424 G	+7:91857363 1324252979 G	
809 Q	2425 C	+7:91857364 1324252980 C	Q
809	2426 A	+7:91857365 1324252981 A	
809	2427 A	+7:91857366 1324252982 A	
810 T	2428 A	+7:91858416 1324254032 A	T
810	2429 C	+7:91858417 1324254033 C	
810	2430 A	+7:91858418 1324254034 A	
811 D	2431 G	+7:91858419 1324254035 G	D
811	2432 A	+7:91858420 1324254036 A	
811	2433 C	+7:91858421 1324254037 C	
812 L	2434 C	+7:91858422 1324254038 C	L
812	2435 T	+7:91858423 1324254039 T	
812	2436 A	+7:91858424 1324254040 A	
813 E	2437 G	+7:91858425 1324254041 G	E
813	2438 A	+7:91858426 1324254042 A	
813	2439 A	+7:91858427 1324254043 A	
814 M	2440 A	+7:91858428 1324254044 A	M
814	2441 T	+7:91858429 1324254045 T	
814	2442 G	+7:91858430 1324254046 G	
815 V	2443 G	+7:91858431 1324254047 G	V
815	2444 T	+7:91858432 1324254048 T	
815	2445 C	+7:91858433 1324254049 C	
816 T	2446 A	+7:91858434 1324254050 A	T
816	2447 C	+7:91858435 1324254051 C	
816	2448 T	+7:91858436 1324254052 T	
817 E	2449 G	+7:91858437 1324254053 G	E
817	2450 A	+7:91858438 1324254054 A	
817	2451 A	+7:91858439 1324254055 A	
818 D	2452 G	+7:91858440 1324254056 G	D
818	2453 A	+7:91858441 1324254057 A	
818	2454 C	+7:91858442 1324254058 C	
819 L	2455 C	+7:91858443 1324254059 C	L
819	2456 T	+7:91858444 1324254060 T	
819	2457 T	+7:91858445 1324254061 T	
820 A	2458 G	+7:91858446 1324254062 G	A
820	2459 C	+7:91858447 1324254063 C	
820	2460 C	+7:91858448 1324254064 C	
821 Q	2461 C	+7:91858449 1324254065 C	Q
821	2462 A	+7:91858450 1324254066 A	
821	2463 G	+7:91858451 1324254067 G	
822 K	2464 A	+7:91858452 1324254068 A	K
822	2465 A	+7:91858453 1324254069 A	
822	2466 A	+7:91858454 1324254070 A	
823 V	2467 G	+7:91858455 1324254071 G	V
823	2468 T	+7:91858456 1324254072 T	
823	2469 C	+7:91858457 1324254073 C	
824 N	2470 A	+7:91858458 1324254074 A	N
824	2471 A	+7:91858459 1324254075 A	
824	2472 T	+7:91858460 1324254076 T	
825 R	2473 A	+7:91858461 1324254077 A	R
825	2474 G	+7:91858462 1324254078 G	
825	2475 G	+7:91858463 1324254079 G	
826 P	2476 C	+7:91858464 1324254080 C	P
826	2477 C	+7:91858465 1324254081 C	
826	2478 T	+7:91858466 1324254082 T	
827 Y	2479 T	+7:91858467 1324254083 T	Y
827	2480 A	+7:91858468 1324254084 A	
827	2481 C	+7:91858469 1324254085 C	
828 L	2482 C	+7:91858470 1324254086 C	L
828	2483 T	+7:91858471 1324254087 T	
828	2484 T	+7:91858472 1324254088 T	
829 R	2485 C	+7:91858473 1324254089 C	R
829	2486 G	+7:91858474 1324254090 G	
829	2487 C	+7:91858475 1324254091 C	
830 T	2488 A	+7:91858476 1324254092 A	T
830	2489 C	+7:91858477 1324254093 C	
830	2490 A	+7:91858478 1324254094 A	
831 P	2491 C	+7:91858479 1324254095 C	P
831	2492 C	+7:91858480 1324254096 C	
831	2493 C	+7:91858481 1324254097 C	
832 R	2494 C	+7:91858482 1324254098 C	R
832	2495 G	+7:91858483 1324254099 G	
832	2496 C	+7:91858484 1324254100 C	
833 H	2497 C	+7:91858485 1324254101 C	H
833	2498 A	+7:91858486 1324254102 A	
833	2499 C	+7:91858487 1324254103 C	
834 K	2500 A	+7:91858488 1324254104 A	K
834	2501 A	+7:91858489 1324254105 A	
834	2502 G	+7:91858490 1324254106 G	
835 I	2503 A	+7:91858491 1324254107 A	I
835	2504 T	+7:91858492 1324254108 T	
835	2505 C	+7:91858493 1324254109 C	
836 I	2506 A	+7:91858494 1324254110 A	I
836	2507 T	+7:91858495 1324254111 T	
836	2508 C	+7:91858496 1324254112 C	
837 K	2509 A	+7:91858497 1324254113 A	K
837	2510 A	+7:91858498 1324254114 A	
837	2511 A	+7:91858499 1324254115 A	
838 A	2512 G	+7:91858500 1324254116 G	A
838	2513 C	+7:91858501 1324254117 C	
838	2514 A	+7:91858502 1324254118 A	
839 A	2515 G	+7:91858503 1324254119 G	A
839	2516 C	+7:91858504 1324254120 C	
839	2517 A	+7:91858505 1324254121 A	
840 C	2518 T	+7:91858506 1324254122 T	C
840	2519 G	+7:91858507 1324254123 G	
840	2520 C	+7:91858508 1324254124 C	
841 L	2521 C	+7:91858509 1324254125 C	L
841	2522 T	+7:91858510 1324254126 T	
841	2523 T	+7:91858511 1324254127 T	
842 V	2524 G	+7:91858512 1324254128 G	V
842	2525 T	+7:91858513 1324254129 T	
842	2526 A	+7:91858514 1324254130 A	
843 Q	2527 C	+7:91858515 1324254131 C	Q
843	2528 A	+7:91858516 1324254132 A	
843	2529 G	+7:91858517 1324254133 G	
844 Q	2530 C	+7:91858518 1324254134 C	Q
844	2531 A	+7:91858519 1324254135 A	
844	2532 G	+7:91858520 1324254136 G	
845 K	2533 A	+7:91858521 1324254137 A	K
845	2534 A	+7:91858522 1324254138 A	
845	2535 G	+7:91858523 1324254139 G	
846 R	2536 A	+7:91858524 1324254140 A	R
846	2537 G	+7:91858525 1324254141 G	
846	2538 G	+7:91858526 1324254142 G	
847 Q	2539 C	+7:91858527 1324254143 C	Q
847	2540 A	+7:91858528 1324254144 A	
847	2541 A	+7:91858529 1324254145 A	
848 E	2542 G	+7:91858530 1324254146 G	E
848	2543 A	+7:91858531 1324254147 A	
848	2544 A	+7:91858532 1324254148 A	
849 F	2545 T	+7:91858533 1324254149 T	F
849	2546 T	+7:91858534 1324254150 T	
849	2547 C	+7:91858535 1324254151 C	
850 L	2548 C	+7:91858536 1324254152 C	L
850	2549 T	+7:91858537 1324254153 T	
850	2550 G	+7:91858538 1324254154 G	
851 A	2551 G	+7:91858539 1324254155 G	A
851	2552 C	+7:91858540 1324254156 C	
851	2553 A	+7:91858541 1324254157 A	
852 S	2554 T	+7:91858542 1324254158 T	S
852	2555 C	+7:91858543 1324254159 C	
852	2556 T	+7:91858544 1324254160 T	
853 V	2557 G	+7:91858545 1324254161 G	V
853	2558 T	+7:91858546 1324254162 T	
853	2559 G	+7:91858547 1324254163 G	
854 A	2560 G	+7:91858548 1324254164 G	A
854	2561 C	+7:91858549 1324254165 C	
854	2562 T	+7:91858550 1324254166 T	
855 R	2563 C	+7:91858551 1324254167 C	R
855	2564 G	+7:91858552 1324254168 G	
855	2565 G	+7:91858553 1324254169 G	
856 G	2566 G	+7:91858554 1324254170 G	G
856	2567 G	+7:91858555 1324254171 G	
856	2568 A	+7:91858556 1324254172 A	
857 V	2569 G	+7:91858557 1324254173 G	V
857	2570 T	+7:91858558 1324254174 T	
857	2571 A	+7:91858559 1324254175 A	
858 A	2572 G	+7:91858560 1324254176 G	A
858	2573 C	+7:91858561 1324254177 C	
858	2574 T	+7:91858562 1324254178 T	
859 P	2575 C	+7:91858563 1324254179 C	P
859	2576 C	+7:91858564 1324254180 C	
859	2577 T	+7:91858565 1324254181 T	
860 A	2578 G	+7:91858566 1324254182 G	A
860	2579 C	+7:91858567 1324254183 C	
860	2580 A	+7:91858568 1324254184 A	
861 D	2581 G	+7:91858569 1324254185 G	D
861	2582 A	+7:91858570 1324254186 A	
861	2583 C	+7:91858571 1324254187 C	
862 S	2584 T	+7:91858572 1324254188 T	S
862	2585 C	+7:91858573 1324254189 C	
862	2586 A	+7:91858574 1324254190 A	
863 P	2587 C	+7:91858575 1324254191 C	P
863	2588 C	+7:91858576 1324254192 C	
863	2589 A	+7:91858577 1324254193 A	
864 E	2590 G	+7:91858578 1324254194 G	E
864	2591 A	+7:91858579 1324254195 A	
864	2592 A	+7:91858580 1324254196 A	
865 A	2593 G	+7:91858581 1324254197 G	A
865	2594 C	+7:91858582 1324254198 C	
865	2595 T	+7:91858583 1324254199 T	
866 P	2596 C	+7:91858584 1324254200 C	P
866	2597 C	+7:91858585 1324254201 C	
866	2598 A	+7:91858586 1324254202 A	
867 R	2599 A	+7:91858587 1324254203 A	R
867	2600 G	+7:91858588 1324254204 G	
867	2601 G	+7:91858589 1324254205 G	
868 R	2602 C	+7:91858590 1324254206 C	R
868	2603 G	+7:91858591 1324254207 G	
868	2604 C	+7:91858592 1324254208 C	
869 S	2605 A	+7:91858593 1324254209 A	S
869	2606 G	+7:91858594 1324254210 G	
869	2607 C	+7:91859491 1324255107 C	
870 F	2608 T	+7:91859492 1324255108 T	F
870	2609 T	+7:91859493 1324255109 T	
870	2610 T	+7:91859494 1324255110 T	
871 A	2611 G	+7:91859495 1324255111 G	A
871	2612 C	+7:91859496 1324255112 C	
871	2613 T	+7:91859497 1324255113 T	
872 G	2614 G	+7:91859498 1324255114 G	G
872	2615 G	+7:91859499 1324255115 G	
872	2616 T	+7:91859500 1324255116 T	
873 G	2617 G	+7:91859501 1324255117 G	G
873	2618 G	+7:91859502 1324255118 G	
873	2619 A	+7:91859503 1324255119 A	
874 T	2620 A	+7:91859504 1324255120 A	T
874	2621 C	+7:91859505 1324255121 C	
874	2622 A	+7:91859506 1324255122 A	
875 W	2623 T	+7:91859507 1324255123 T	W
875	2624 G	+7:91859508 1324255124 G	
875	2625 G	+7:91859509 1324255125 G	
876 D	2626 G	+7:91859510 1324255126 G	D
876	2627 A	+7:91859511 1324255127 A	
876	2628 T	+7:91859512 1324255128 T	
877 W	2629 T	+7:91859513 1324255129 T	W
877	2630 G	+7:91859514 1324255130 G	
877	2631 G	+7:91859515 1324255131 G	
878 E	2632 G	+7:91859516 1324255132 G	E
878	2633 A	+7:91859517 1324255133 A	
878	2634 A	+7:91859518 1324255134 A	
879 Y	2635 T	+7:91859519 1324255135 T	Y
879	2636 A	+7:91859520 1324255136 A	
879	2637 T	+7:91859521 1324255137 T	
880 L	2638 T	+7:91859522 1324255138 T	L
880	2639 T	+7:91859523 1324255139 T	
880	2640 A	+7:91859524 1324255140 A	
881 G	2641 G	+7:91859525 1324255141 G	G
881	2642 G	+7:91859526 1324255142 G	
881	2643 A	+7:91859527 1324255143 A	
882 F	2644 T	+7:91859528 1324255144 T	F
882	2645 T	+7:91859529 1324255145 T	
882	2646 T	+7:91859530 1324255146 T	
883 A	2647 G	+7:91859531 1324255147 G	A
883	2648 C	+7:91859532 1324255148 C	
883	2649 A	+7:91859533 1324255149 A	
884 S	2650 T	+7:91859534 1324255150 T	S
884	2651 C	+7:91859535 1324255151 C	
884	2652 A	+7:91859536 1324255152 A	
885 P	2653 C	+7:91859537 1324255153 C	P
885	2654 C	+7:91859538 1324255154 C	
885	2655 A	+7:91859539 1324255155 A	
886 E	2656 G	+7:91859540 1324255156 G	E
886	2657 A	+7:91859541 1324255157 A	
886	2658 G	+7:91859542 1324255158 G	
887 E	2659 G	+7:91863615 1324259231 G	E
887	2660 A	+7:91863616 1324259232 A	
887	2661 A	+7:91863617 1324259233 A	
888 Y	2662 T	+7:91863618 1324259234 T	Y
888	2663 A	+7:91863619 1324259235 A	
888	2664 T	+7:91863620 1324259236 T	
889 A	2665 G	+7:91863621 1324259237 G	A
889	2666 C	+7:91863622 1324259238 C	
889	2667 T	+7:91863623 1324259239 T	
890 E	2668 G	+7:91863624 1324259240 G	E
890	2669 A	+7:91863625 1324259241 A	
890	2670 A	+7:91863626 1324259242 A	
891 F	2671 T	+7:91863627 1324259243 T	F
891	2672 T	+7:91863628 1324259244 T	
891	2673 T	+7:91863629 1324259245 T	
892 Q	2674 C	+7:91863630 1324259246 C	Q
892	2675 A	+7:91863631 1324259247 A	
892	2676 G	+7:91863632 1324259248 G	
893 Y	2677 T	+7:91863633 1324259249 T	Y
893	2678 A	+7:91863634 1324259250 A	
893	2679 T	+7:91863635 1324259251 T	
894 R	2680 C	+7:91863636 1324259252 C	R
894	2681 G	+7:91863637 1324259253 G	
894	2682 G	+7:91863638 1324259254 G	
895 R	2683 A	+7:91863639 1324259255 A	R
895	2684 G	+7:91863640 1324259256 G	
895	2685 G	+7:91863641 1324259257 G	
896 R	2686 A	+7:91863642 1324259258 A	R
896	2687 G	+7:91863643 1324259259 G	
896	2688 G	+7:91863644 1324259260 G	
897 H	2689 C	+7:91863645 1324259261 C	H
897	2690 A	+7:91863646 1324259262 A	
897	2691 C	+7:91863647 1324259263 C	
898 R	2692 A	+7:91863648 1324259264 A	R
898	2693 G	+7:91863649 1324259265 G	
898	2694 A	+7:91863650 1324259266 A	
899 Q	2695 C	+7:91863651 1324259267 C	Q
899	2696 A	+7:91863652 1324259268 A	
899	2697 A	+7:91863653 1324259269 A	
900 R	2698 C	+7:91863654 1324259270 C	R
900	2699 G	+7:91863655 1324259271 G	
900	2700 T	+7:91863656 1324259272 T	
901 R	2701 C	+7:91863657 1324259273 C	R
901	2702 G	+7:91863658 1324259274 G	
901	2703 T	+7:91863659 1324259275 T	
902 R	2704 C	+7:91863660 1324259276 C	R
902	2705 G	+7:91863661 1324259277 G	
902	2706 A	+7:91863662 1324259278 A	
903 G	2707 G	+7:91863663 1324259279 G	G
903	2708 G	+7:91863664 1324259280 G	
903	2709 A	+7:91863665 1324259281 A	
904 D	2710 G	+7:91863666 1324259282 G	D
904	2711 A	+7:91863667 1324259283 A	
904	2712 T	+7:91863668 1324259284 T	
905 V	2713 G	+7:91863669 1324259285 G	V
905	2714 T	+7:91863670 1324259286 T	
905	2715 T	+7:91863671 1324259287 T	
906 H	2716 C	+7:91863672 1324259288 C	H
906	2717 A	+7:91863673 1324259289 A	
906	2718 C	+7:91863674 1324259290 C	
907 S	2719 A	+7:91863675 1324259291 A	S
907	2720 G	+7:91863676 1324259292 G	
907	2721 T	+7:91863677 1324259293 T	
908 L	2722 C	+7:91863678 1324259294 C	L
908	2723 T	+7:91863679 1324259295 T	
908	2724 A	+7:91863680 1324259296 A	
909 L	2725 C	+7:91863681 1324259297 C	L
909	2726 T	+7:91863682 1324259298 T	
909	2727 C	+7:91863683 1324259299 C	
910 S	2728 A	+7:91863684 1324259300 A	S
910	2729 G	+7:91863685 1324259301 G	
910	2730 T	+7:91863686 1324259302 T	
911 N	2731 A	+7:91863687 1324259303 A	N
911	2732 A	+7:91863688 1324259304 A	
911	2733 T	+7:91863689 1324259305 T	
912 P	2734 C	+7:91863690 1324259306 C	P
912	2735 C	+7:91863691 1324259307 C	
912	2736 T	+7:91863692 1324259308 T	
913 P	2737 C	+7:91863693 1324259309 C	P
913	2738 C	+7:91863694 1324259310 C	
913	2739 A	+7:91863695 1324259311 A	
914 D	2740 G	+7:91863696 1324259312 G	D
914	2741 A	+7:91863697 1324259313 A	
914	2742 C	+7:91863698 1324259314 C	
915 P	2743 C	+7:91863699 1324259315 C	P
915	2744 C	+7:91863700 1324259316 C	
915	2745 T	+7:91863701 1324259317 T	
916 D	2746 G	+7:91863702 1324259318 G	D
916	2747 A	+7:91863703 1324259319 A	
916	2748 T	+7:91863704 1324259320 T	
917 E	2749 G	+7:91863705 1324259321 G	E
917	2750 A	+7:91863706 1324259322 A	
917	2751 G	+7:91863707 1324259323 G	
918 P	2752 C	+7:91863708 1324259324 C	P
918	2753 C	+7:91863709 1324259325 C	
918	2754 A	+7:91863710 1324259326 A	
919 S	2755 A	+7:91863711 1324259327 A	S
919	2756 G	+7:91863712 1324259328 G	
919	2757 T	+7:91863713 1324259329 T	
920 E	2758 G	+7:91863714 1324259330 G	E
920	2759 A	+7:91863715 1324259331 A	
920	2760 A	+7:91863716 1324259332 A	
921 S	2761 A	+7:91863717 1324259333 A	S
921	2762 G	+7:91863718 1324259334 G	
921	2763 C	+7:91863719 1324259335 C	
922 T	2764 A	+7:91863720 1324259336 A	T
922	2765 C	+7:91863721 1324259337 C	
922	2766 T	+7:91863722 1324259338 T	
923 L	2767 T	+7:91863723 1324259339 T	L
923	2768 T	+7:91863724 1324259340 T	
923	2769 A	+7:91863725 1324259341 A	
924 D	2770 G	+7:91863726 1324259342 G	D
924	2771 A	+7:91864973 1324260589 A	
924	2772 T	+7:91864974 1324260590 T	
925 I	2773 A	+7:91864975 1324260591 A	I
925	2774 T	+7:91864976 1324260592 T	
925	2775 T	+7:91864977 1324260593 T	
926 P	2776 C	+7:91864978 1324260594 C	P
926	2777 C	+7:91864979 1324260595 C	
926	2778 A	+7:91864980 1324260596 A	
927 E	2779 G	+7:91864981 1324260597 G	E
927	2780 A	+7:91864982 1324260598 A	
927	2781 A	+7:91864983 1324260599 A	
928 G	2782 G	+7:91864984 1324260600 G	G
928	2783 G	+7:91864985 1324260601 G	
928	2784 C	+7:91864986 1324260602 C	
929 G	2785 G	+7:91864987 1324260603 G	G
929	2786 G	+7:91864988 1324260604 G	
929	2787 C	+7:91864989 1324260605 C	
930 S	2788 A	+7:91864990 1324260606 A	S
930	2789 G	+7:91864991 1324260607 G	
930	2790 C	+7:91864992 1324260608 C	
931 S	2791 A	+7:91864993 1324260609 A	S
931	2792 G	+7:91864994 1324260610 G	
931	2793 C	+7:91864995 1324260611 C	
932 S	2794 A	+7:91864996 1324260612 A	S
932	2795 G	+7:91864997 1324260613 G	
932	2796 C	+7:91864998 1324260614 C	
933 R	2797 C	+7:91864999 1324260615 C	R
933	2798 G	+7:91865000 1324260616 G	
933	2799 C	+7:91865001 1324260617 C	
934 R	2800 A	+7:91865002 1324260618 A	R
934	2801 G	+7:91865003 1324260619 G	
934	2802 G	+7:91865004 1324260620 G	
935 P	2803 C	+7:91865005 1324260621 C	P
935	2804 C	+7:91865006 1324260622 C	
935	2805 T	+7:91865007 1324260623 T	
936 G	2806 G	+7:91865008 1324260624 G	G
936	2807 G	+7:91865009 1324260625 G	
936	2808 C	+7:91865010 1324260626 C	
937 T	2809 A	+7:91865011 1324260627 A	T
937	2810 C	+7:91865012 1324260628 C	
937	2811 A	+7:91865013 1324260629 A	
938 S	2812 T	+7:91865014 1324260630 T	S
938	2813 C	+7:91865015 1324260631 C	
938	2814 C	+7:91865016 1324260632 C	
939 V	2815 G	+7:91865017 1324260633 G	V
939	2816 T	+7:91865018 1324260634 T	
939	2817 G	+7:91865019 1324260635 G	
940 V	2818 G	+7:91865020 1324260636 G	V
940	2819 T	+7:91865021 1324260637 T	
940	2820 A	+7:91865022 1324260638 A	
941 S	2821 A	+7:91865023 1324260639 A	S
941	2822 G	+7:91865024 1324260640 G	
941	2823 T	+7:91865025 1324260641 T	
942 S	2824 T	+7:91865026 1324260642 T	S
942	2825 C	+7:91865027 1324260643 C	
942	2826 T	+7:91865028 1324260644 T	
943 A	2827 G	+7:91865029 1324260645 G	A
943	2828 C	+7:91865030 1324260646 C	
943	2829 A	+7:91865031 1324260647 A	
944 S	2830 T	+7:91865032 1324260648 T	S
944	2831 C	+7:91865033 1324260649 C	
944	2832 T	+7:91865034 1324260650 T	
945 M	2833 A	+7:91865035 1324260651 A	M
945	2834 T	+7:91865036 1324260652 T	
945	2835 G	+7:91865037 1324260653 G	
946 S	2836 A	+7:91865038 1324260654 A	S
946	2837 G	+7:91865039 1324260655 G	
946	2838 T	+7:91865040 1324260656 T	
947 V	2839 G	+7:91865041 1324260657 G	V
947	2840 T	+7:91865042 1324260658 T	
947	2841 G	+7:91865043 1324260659 G	
948 L	2842 C	+7:91865044 1324260660 C	L
948	2843 T	+7:91865045 1324260661 T	
948	2844 G	+7:91865046 1324260662 G	
949 H	2845 C	+7:91865047 1324260663 C	H
949	2846 A	+7:91865048 1324260664 A	
949	2847 C	+7:91865049 1324260665 C	
950 S	2848 A	+7:91865050 1324260666 A	S
950	2849 G	+7:91865051 1324260667 G	
950	2850 C	+7:91865052 1324260668 C	
951 S	2851 T	+7:91865053 1324260669 T	S
951	2852 C	+7:91865054 1324260670 C	
951	2853 T	+7:91865055 1324260671 T	
952 S	2854 T	+7:91865056 1324260672 T	S
952	2855 C	+7:91865057 1324260673 C	
952	2856 C	+7:91865058 1324260674 C	
953 L	2857 C	+7:91865059 1324260675 C	L
953	2858 T	+7:91865060 1324260676 T	
953	2859 G	+7:91865061 1324260677 G	
954 R	2860 C	+7:91865062 1324260678 C	R
954	2861 G	+7:91865063 1324260679 G	
954	2862 T	+7:91865064 1324260680 T	
955 D	2863 G	+7:91865065 1324260681 G	D
955	2864 A	+7:91865066 1324260682 A	
955	2865 C	+7:91865067 1324260683 C	
956 Y	2866 T	+7:91865068 1324260684 T	Y
956	2867 A	+7:91865069 1324260685 A	
956	2868 C	+7:91865070 1324260686 C	
957 T	2869 A	+7:91865071 1324260687 A	T
957	2870 C	+7:91865072 1324260688 C	
957	2871 C	+7:91865073 1324260689 C	
958 P	2872 C	+7:91865074 1324260690 C	P
958	2873 C	+7:91865075 1324260691 C	
958	2874 T	+7:91865076 1324260692 T	
959 A	2875 G	+7:91865077 1324260693 G	A
959	2876 C	+7:91865078 1324260694 C	
959	2877 C	+7:91865079 1324260695 C	
960 S	2878 A	+7:91865080 1324260696 A	S
960	2879 G	+7:91865081 1324260697 G	
960	2880 T	+7:91865082 1324260698 T	
961 R	2881 C	+7:91865083 1324260699 C	R
961	2882 G	+7:91865084 1324260700 G	
961	2883 C	+7:91865085 1324260701 C	
962 S	2884 T	+7:91865086 1324260702 T	S
962	2885 C	+7:91865087 1324260703 C	
962	2886 T	+7:91865088 1324260704 T	
963 E	2887 G	+7:91865089 1324260705 G	E
963	2888 A	+7:91865090 1324260706 A	
963	2889 A	+7:91865091 1324260707 A	
964 N	2890 A	+7:91865092 1324260708 A	N
964	2891 A	+7:91865093 1324260709 A	
964	2892 C	+7:91865094 1324260710 C	
965 Q	2893 C	+7:91865095 1324260711 C	Q
965	2894 A	+7:91865096 1324260712 A	
965	2895 G	+7:91865097 1324260713 G	
966 D	2896 G	+7:91865098 1324260714 G	D
966	2897 A	+7:91865099 1324260715 A	
966	2898 C	+7:91865100 1324260716 C	
967 S	2899 T	+7:91865101 1324260717 T	S
967	2900 C	+7:91865102 1324260718 C	
967	2901 T	+7:91865103 1324260719 T	
968 L	2902 C	+7:91865104 1324260720 C	L
968	2903 T	+7:91865105 1324260721 T	
968	2904 T	+7:91865106 1324260722 T	
969 Q	2905 C	+7:91865107 1324260723 C	Q
969	2906 A	+7:91865108 1324260724 A	
969	2907 G	+7:91865109 1324260725 G	
970 A	2908 G	+7:91865462 1324261078 G	A
970	2909 C	+7:91865463 1324261079 C	
970	2910 T	+7:91865464 1324261080 T	
971 L	2911 C	+7:91865465 1324261081 C	L
971	2912 T	+7:91865466 1324261082 T	
971	2913 G	+7:91865467 1324261083 G	
972 S	2914 A	+7:91865468 1324261084 A	S
972	2915 G	+7:91865469 1324261085 G	
972	2916 T	+7:91865470 1324261086 T	
973 S	2917 T	+7:91865471 1324261087 T	S
973	2918 C	+7:91865472 1324261088 C	
973	2919 C	+7:91865473 1324261089 C	
974 L	2920 T	+7:91865474 1324261090 T	L
974	2921 T	+7:91865475 1324261091 T	
974	2922 G	+7:91865476 1324261092 G	
975 D	2923 G	+7:91865477 1324261093 G	D
975	2924 A	+7:91865478 1324261094 A	
975	2925 T	+7:91865479 1324261095 T	
976 E	2926 G	+7:91865480 1324261096 G	E
976	2927 A	+7:91865481 1324261097 A	
976	2928 A	+7:91865482 1324261098 A	
977 D	2929 G	+7:91865483 1324261099 G	D
977	2930 A	+7:91865484 1324261100 A	
977	2931 C	+7:91865485 1324261101 C	
978 D	2932 G	+7:91865486 1324261102 G	D
978	2933 A	+7:91865487 1324261103 A	
978	2934 T	+7:91865488 1324261104 T	
979 P	2935 C	+7:91865489 1324261105 C	P
979	2936 C	+7:91865490 1324261106 C	
979	2937 C	+7:91865491 1324261107 C	
980 N	2938 A	+7:91865492 1324261108 A	N
980	2939 A	+7:91865493 1324261109 A	
980	2940 T	+7:91865494 1324261110 T	
981 I	2941 A	+7:91865495 1324261111 A	I
981	2942 T	+7:91865496 1324261112 T	
981	2943 A	+7:91865497 1324261113 A	
982 L	2944 C	+7:91865498 1324261114 C	L
982	2945 T	+7:91865499 1324261115 T	
982	2946 T	+7:91865500 1324261116 T	
983 L	2947 C	+7:91865501 1324261117 C	L
983	2948 T	+7:91865502 1324261118 T	
983	2949 T	+7:91865503 1324261119 T	
984 A	2950 G	+7:91865504 1324261120 G	A
984	2951 C	+7:91865505 1324261121 C	
984	2952 A	+7:91865506 1324261122 A	
985 I	2953 A	+7:91865507 1324261123 A	I
985	2954 T	+7:91865508 1324261124 T	
985	2955 A	+7:91865509 1324261125 A	
986 Q	2956 C	+7:91865510 1324261126 C	Q
986	2957 A	+7:91865511 1324261127 A	
986	2958 G	+7:91865512 1324261128 G	
987 L	2959 T	+7:91865513 1324261129 T	L
987	2960 T	+7:91865514 1324261130 T	
987	2961 A	+7:91865515 1324261131 A	
988 S	2962 T	+7:91865516 1324261132 T	S
988	2963 C	+7:91865517 1324261133 C	
988	2964 A	+7:91865518 1324261134 A	
989 L	2965 C	+7:91865519 1324261135 C	L
989	2966 T	+7:91865520 1324261136 T	
989	2967 G	+7:91865521 1324261137 G	
990 Q	2968 C	+7:91865522 1324261138 C	Q
990	2969 A	+7:91865523 1324261139 A	
990	2970 A	+7:91865524 1324261140 A	
991 E	2971 G	+7:91865525 1324261141 G	E
991	2972 A	+7:91865526 1324261142 A	
991	2973 G	+7:91865527 1324261143 G	
992 S	2974 T	+7:91865528 1324261144 T	S
992	2975 C	+7:91865529 1324261145 C	
992	2976 T	+7:91865530 1324261146 T	
993 G	2977 G	+7:91865531 1324261147 G	G
993	2978 G	+7:91865532 1324261148 G	
993	2979 G	+7:91865533 1324261149 G	
994 L	2980 C	+7:91865534 1324261150 C	L
994	2981 T	+7:91865535 1324261151 T	
994	2982 G	+7:91865536 1324261152 G	
995 A	2983 G	+7:91865537 1324261153 G	A
995	2984 C	+7:91865538 1324261154 C	
995	2985 C	+7:91865539 1324261155 C	
996 L	2986 C	+7:91865540 1324261156 C	L
996	2987 T	+7:91865541 1324261157 T	
996	2988 C	+7:91865542 1324261158 C	
997 D	2989 G	+7:91865543 1324261159 G	D
997	2990 A	+7:91865544 1324261160 A	
997	2991 T	+7:91865545 1324261161 T	
998 E	2992 G	+7:91865546 1324261162 G	E
998	2993 A	+7:91865547 1324261163 A	
998	2994 A	+7:91865548 1324261164 A	
999 E	2995 G	+7:91865549 1324261165 G	E
999	2996 A	+7:91865550 1324261166 A	
999	2997 A	+7:91865551 1324261167 A	
1000 T	2998 A	+7:91865552 1324261168 A	T
1000	2999 C	+7:91865553 1324261169 C	
1000	3000 T	+7:91865554 1324261170 T	
1001 R	3001 A	+7:91865555 1324261171 A	R
1001	3002 G	+7:91865556 1324261172 G	
1001	3003 A	+7:91865557 1324261173 A	
1002 D	3004 G	+7:91865558 1324261174 G	D
1002	3005 A	+7:91865559 1324261175 A	
1002	3006 C	+7:91865560 1324261176 C	
1003 F	3007 T	+7:91865561 1324261177 T	F
1003	3008 T	+7:91865562 1324261178 T	
1003	3009 C	+7:91865563 1324261179 C	
1004 L	3010 C	+7:91865564 1324261180 C	L
1004	3011 T	+7:91865565 1324261181 T	
1004	3012 C	+7:91865566 1324261182 C	
1005 S	3013 A	+7:91865567 1324261183 A	S
1005	3014 G	+7:91865568 1324261184 G	
1005	3015 T	+7:91865569 1324261185 T	
1006 N	3016 A	+7:91865570 1324261186 A	N
1006	3017 A	+7:91865571 1324261187 A	
1006	3018 T	+7:91865572 1324261188 T	
1007 E	3019 G	+7:91865573 1324261189 G	E
1007	3020 A	+7:91865574 1324261190 A	
1007	3021 A	+7:91865575 1324261191 A	
1008 A	3022 G	+7:91865576 1324261192 G	A
1008	3023 C	+7:91865577 1324261193 C	
1008	3024 A	+7:91865578 1324261194 A	
1009 S	3025 T	+7:91865579 1324261195 T	S
1009	3026 C	+7:91865580 1324261196 C	
1009	3027 C	+7:91865581 1324261197 C	
1010 L	3028 T	+7:91865582 1324261198 T	L
1010	3029 T	+7:91865583 1324261199 T	
1010	3030 A	+7:91865584 1324261200 A	
1011 G	3031 G	+7:91865585 1324261201 G	G
1011	3032 G	+7:91865586 1324261202 G	
1011	3033 T	+7:91865587 1324261203 T	
1012 A	3034 G	+7:91865588 1324261204 G	A
1012	3035 C	+7:91865589 1324261205 C	
1012	3036 G	+7:91865590 1324261206 G	
1013 I	3037 A	+7:91865591 1324261207 A	I
1013	3038 T	+7:91865592 1324261208 T	
1013	3039 A	+7:91865593 1324261209 A	
1014 G	3040 G	+7:91865594 1324261210 G	G
1014	3041 G	+7:91865595 1324261211 G	
1014	3042 C	+7:91865596 1324261212 C	
1015 T	3043 A	+7:91865597 1324261213 A	T
1015	3044 C	+7:91865598 1324261214 C	
1015	3045 T	+7:91865599 1324261215 T	
1016 S	3046 T	+7:91865600 1324261216 T	S
1016	3047 C	+7:91865601 1324261217 C	
1016	3048 T	+7:91865602 1324261218 T	
1017 L	3049 T	+7:91865603 1324261219 T	L
1017	3050 T	+7:91865604 1324261220 T	
1017	3051 A	+7:91865605 1324261221 A	
1018 P	3052 C	+7:91865606 1324261222 C	P
1018	3053 C	+7:91865607 1324261223 C	
1018	3054 T	+7:91865608 1324261224 T	
1019 S	3055 T	+7:91865609 1324261225 T	S
1019	3056 C	+7:91865610 1324261226 C	
1019	3057 C	+7:91865611 1324261227 C	
1020 R	3058 A	+7:91865612 1324261228 A	R
1020	3059 G	+7:91865613 1324261229 G	
1020	3060 G	+7:91865614 1324261230 G	
1021 L	3061 C	+7:91865615 1324261231 C	L
1021	3062 T	+7:91865616 1324261232 T	
1021	3063 G	+7:91865617 1324261233 G	
1022 D	3064 G	+7:91865618 1324261234 G	D
1022	3065 A	+7:91865619 1324261235 A	
1022	3066 C	+7:91865620 1324261236 C	
1023 S	3067 T	+7:91865621 1324261237 T	S
1023	3068 C	+7:91865622 1324261238 C	
1023	3069 T	+7:91865623 1324261239 T	
1024 V	3070 G	+7:91865624 1324261240 G	V
1024	3071 T	+7:91865625 1324261241 T	
1024	3072 C	+7:91865626 1324261242 C	
1025 P	3073 C	+7:91865627 1324261243 C	P
1025	3074 C	+7:91865628 1324261244 C	
1025	3075 C	+7:91865629 1324261245 C	
1026 R	3076 A	+7:91865630 1324261246 A	R
1026	3077 G	+7:91865631 1324261247 G	
1026	3078 A	+7:91865632 1324261248 A	
1027 N	3079 A	+7:91865633 1324261249 A	N
1027	3080 A	+7:91865634 1324261250 A	
1027	3081 T	+7:91865635 1324261251 T	
1028 T	3082 A	+7:91865636 1324261252 A	T
1028	3083 C	+7:91865637 1324261253 C	
1028	3084 A	+7:91865638 1324261254 A	
1029 D	3085 G	+7:91865639 1324261255 G	D
1029	3086 A	+7:91865640 1324261256 A	
1029	3087 T	+7:91865641 1324261257 T	
1030 S	3088 A	+7:91865642 1324261258 A	S
1030	3089 G	+7:91865643 1324261259 G	
1030	3090 C	+7:91865644 1324261260 C	
1031 P	3091 C	+7:91865645 1324261261 C	P
1031	3092 C	+7:91865646 1324261262 C	
1031	3093 T	+7:91865647 1324261263 T	
1032 R	3094 C	+7:91865648 1324261264 C	R
1032	3095 G	+7:91865649 1324261265 G	
1032	3096 G	+7:91865650 1324261266 G	
1033 A	3097 G	+7:91865651 1324261267 G	A
1033	3098 C	+7:91865652 1324261268 C	
1033	3099 T	+7:91865653 1324261269 T	
1034 A	3100 G	+7:91865654 1324261270 G	A
1034	3101 C	+7:91865655 1324261271 C	
1034	3102 A	+7:91865656 1324261272 A	
1035 L	3103 T	+7:91865657 1324261273 T	L
1035	3104 T	+7:91865658 1324261274 T	
1035	3105 G	+7:91865659 1324261275 G	
1036 S	3106 A	+7:91865660 1324261276 A	S
1036	3107 G	+7:91865661 1324261277 G	
1036	3108 C	+7:91865662 1324261278 C	
1037 S	3109 A	+7:91865663 1324261279 A	S
1037	3110 G	+7:91865664 1324261280 G	
1037	3111 C	+7:91865665 1324261281 C	
1038 S	3112 T	+7:91865666 1324261282 T	S
1038	3113 C	+7:91865667 1324261283 C	
1038	3114 T	+7:91865668 1324261284 T	
1039 E	3115 G	+7:91865669 1324261285 G	E
1039	3116 A	+7:91865670 1324261286 A	
1039	3117 G	+7:91865671 1324261287 G	
1040 L	3118 C	+7:91865672 1324261288 C	L
1040	3119 T	+7:91865673 1324261289 T	
1040	3120 T	+7:91865674 1324261290 T	
1041 L	3121 T	+7:91865675 1324261291 T	L
1041	3122 T	+7:91865676 1324261292 T	
1041	3123 G	+7:91865677 1324261293 G	
1042 E	3124 G	+7:91865678 1324261294 G	E
1042	3125 A	+7:91865679 1324261295 A	
1042	3126 A	+7:91865680 1324261296 A	
1043 L	3127 C	+7:91865681 1324261297 C	L
1043	3128 T	+7:91865682 1324261298 T	
1043	3129 T	+7:91865683 1324261299 T	
1044 G	3130 G	+7:91865684 1324261300 G	G
1044	3131 G	+7:91865685 1324261301 G	
1044	3132 T	+7:91865686 1324261302 T	
1045 D	3133 G	+7:91865687 1324261303 G	D
1045	3134 A	+7:91865688 1324261304 A	
1045	3135 C	+7:91865689 1324261305 C	
1046 S	3136 A	+7:91865690 1324261306 A	S
1046	3137 G	+7:91865691 1324261307 G	
1046	3138 C	+7:91865692 1324261308 C	
1047 L	3139 C	+7:91865693 1324261309 C	L
1047	3140 T	+7:91865694 1324261310 T	
1047	3141 C	+7:91865695 1324261311 C	
1048 M	3142 A	+7:91865696 1324261312 A	M
1048	3143 T	+7:91865697 1324261313 T	
1048	3144 G	+7:91865698 1324261314 G	
1049 R	3145 A	+7:91865699 1324261315 A	R
1049	3146 G	+7:91865700 1324261316 G	
1049	3147 A	+7:91865701 1324261317 A	
1050 L	3148 C	+7:91865702 1324261318 C	L
1050	3149 T	+7:91865703 1324261319 T	
1050	3150 A	+7:91865704 1324261320 A	
1051 G	3151 G	+7:91865705 1324261321 G	G
1051	3152 G	+7:91865706 1324261322 G	
1051	3153 A	+7:91865707 1324261323 A	
1052 A	3154 G	+7:91865708 1324261324 G	A
1052	3155 C	+7:91865709 1324261325 C	
1052	3156 A	+7:91865710 1324261326 A	
1053 E	3157 G	+7:91865711 1324261327 G	E
1053	3158 A	+7:91865712 1324261328 A	
1053	3159 G	+7:91865713 1324261329 G	
1054 N	3160 A	+7:91865714 1324261330 A	N
1054	3161 A	+7:91865715 1324261331 A	
1054	3162 T	+7:91865716 1324261332 T	
1055 D	3163 G	+7:91865717 1324261333 G	D
1055	3164 A	+7:91865718 1324261334 A	
1055	3165 C	+7:91865719 1324261335 C	
1056 P	3166 C	+7:91865720 1324261336 C	P
1056	3167 C	+7:91865721 1324261337 C	
1056	3168 A	+7:91865722 1324261338 A	
1057 F	3169 T	+7:91865723 1324261339 T	F
1057	3170 T	+7:91865724 1324261340 T	
1057	3171 T	+7:91865725 1324261341 T	
1058 S	3172 T	+7:91865726 1324261342 T	S
1058	3173 C	+7:91865727 1324261343 C	
1058	3174 A	+7:91865728 1324261344 A	
1059 T	3175 A	+7:91865729 1324261345 A	T
1059	3176 C	+7:91865730 1324261346 C	
1059	3177 T	+7:91865731 1324261347 T	
1060 D	3178 G	+7:91865732 1324261348 G	D
1060	3179 A	+7:91865733 1324261349 A	
1060	3180 C	+7:91865734 1324261350 C	
1061 T	3181 A	+7:91865735 1324261351 A	T
1061	3182 C	+7:91865736 1324261352 C	
1061	3183 C	+7:91865737 1324261353 C	
1062 L	3184 C	+7:91865738 1324261354 C	L
1062	3185 T	+7:91865739 1324261355 T	
1062	3186 G	+7:91865740 1324261356 G	
1063 S	3187 A	+7:91865741 1324261357 A	S
1063	3188 G	+7:91865742 1324261358 G	
1063	3189 C	+7:91865743 1324261359 C	
1064 S	3190 T	+7:91865744 1324261360 T	S
1064	3191 C	+7:91865745 1324261361 C	
1064	3192 A	+7:91865746 1324261362 A	
1065 H	3193 C	+7:91865747 1324261363 C	H
1065	3194 A	+7:91865748 1324261364 A	
1065	3195 C	+7:91865749 1324261365 C	
1066 P	3196 C	+7:91865750 1324261366 C	P
1066	3197 C	+7:91865751 1324261367 C	
1066	3198 T	+7:91865752 1324261368 T	
1067 L	3199 C	+7:91865753 1324261369 C	L
1067	3200 T	+7:91865754 1324261370 T	
1067	3201 C	+7:91865755 1324261371 C	
1068 S	3202 A	+7:91865756 1324261372 A	S
1068	3203 G	+7:91865757 1324261373 G	
1068	3204 T	+7:91865758 1324261374 T	
1069 E	3205 G	+7:91865759 1324261375 G	E
1069	3206 A	+7:91865760 1324261376 A	
1069	3207 G	+7:91865761 1324261377 G	
1070 A	3208 G	+7:91865762 1324261378 G	A
1070	3209 C	+7:91865763 1324261379 C	
1070	3210 A	+7:91865764 1324261380 A	
1071 R	3211 A	+7:91865765 1324261381 A	R
1071	3212 G	+7:91865766 1324261382 G	
1071	3213 A	+7:91865767 1324261383 A	
1072 S	3214 A	+7:91865768 1324261384 A	S
1072	3215 G	+7:91865769 1324261385 G	
1072	3216 T	+7:91865770 1324261386 T	
1073 D	3217 G	+7:91865771 1324261387 G	D
1073	3218 A	+7:91865772 1324261388 A	
1073	3219 T	+7:91865773 1324261389 T	
1074 F	3220 T	+7:91865774 1324261390 T	F
1074	3221 T	+7:91865775 1324261391 T	
1074	3222 C	+7:91865776 1324261392 C	
1075 C	3223 T	+7:91865777 1324261393 T	C
1075	3224 G	+7:91865778 1324261394 G	
1075	3225 T	+7:91865779 1324261395 T	
1076 P	3226 C	+7:91865780 1324261396 C	P
1076	3227 C	+7:91865781 1324261397 C	
1076	3228 C	+7:91865782 1324261398 C	
1077 S	3229 T	+7:91865783 1324261399 T	S
1077	3230 C	+7:91865784 1324261400 C	
1077	3231 A	+7:91865785 1324261401 A	
1078 S	3232 T	+7:91865786 1324261402 T	S
1078	3233 C	+7:91865787 1324261403 C	
1078	3234 T	+7:91865788 1324261404 T	
1079 S	3235 A	+7:91865789 1324261405 A	S
1079	3236 G	+7:91865790 1324261406 G	
1079	3237 T	+7:91865791 1324261407 T	
1080 D	3238 G	+7:91865792 1324261408 G	D
1080	3239 A	+7:91865793 1324261409 A	
1080	3240 T	+7:91865794 1324261410 T	
1081 P	3241 C	+7:91865795 1324261411 C	P
1081	3242 C	+7:91865796 1324261412 C	
1081	3243 T	+7:91865797 1324261413 T	
1082 D	3244 G	+7:91865798 1324261414 G	D
1082	3245 A	+7:91865799 1324261415 A	
1082	3246 C	+7:91865800 1324261416 C	
1083 S	3247 T	+7:91865801 1324261417 T	S
1083	3248 C	+7:91865802 1324261418 C	
1083	3249 A	+7:91865803 1324261419 A	
1084 A	3250 G	+7:91865804 1324261420 G	A
1084	3251 C	+7:91865805 1324261421 C	
1084	3252 T	+7:91865806 1324261422 T	
1085 G	3253 G	+7:91865807 1324261423 G	G
1085	3254 G	+7:91865808 1324261424 G	
1085	3255 C	+7:91865809 1324261425 C	
1086 Q	3256 C	+7:91865810 1324261426 C	Q
1086	3257 A	+7:91865811 1324261427 A	
1086	3258 G	+7:91865812 1324261428 G	
1087 D	3259 G	+7:91865813 1324261429 G	D
1087	3260 A	+7:91865814 1324261430 A	
1087	3261 C	+7:91865815 1324261431 C	
1088 P	3262 C	+7:91865816 1324261432 C	P
1088	3263 C	+7:91865817 1324261433 C	
1088	3264 C	+7:91865818 1324261434 C	
1089 N	3265 A	+7:91865819 1324261435 A	N
1089	3266 A	+7:91865820 1324261436 A	
1089	3267 C	+7:91865821 1324261437 C	
1090 I	3268 A	+7:91865822 1324261438 A	I
1090	3269 T	+7:91865823 1324261439 T	
1090	3270 C	+7:91865824 1324261440 C	
1091 N	3271 A	+7:91865825 1324261441 A	N
1091	3272 A	+7:91865826 1324261442 A	
1091	3273 T	+7:91865827 1324261443 T	
1092 D	3274 G	+7:91865828 1324261444 G	D
1092	3275 A	+7:91865829 1324261445 A	
1092	3276 C	+7:91865830 1324261446 C	
1093 N	3277 A	+7:91865831 1324261447 A	N
1093	3278 A	+7:91865832 1324261448 A	
1093	3279 T	+7:91865833 1324261449 T	
1094 L	3280 C	+7:91865834 1324261450 C	L
1094	3281 T	+7:91865835 1324261451 T	
1094	3282 T	+7:91865836 1324261452 T	
1095 L	3283 C	+7:91865837 1324261453 C	L
1095	3284 T	+7:91865838 1324261454 T	
1095	3285 C	+7:91865839 1324261455 C	
1096 G	3286 G	+7:91865840 1324261456 G	G
1096	3287 G	+7:91865841 1324261457 G	
1096	3288 C	+7:91865842 1324261458 C	
1097 N	3289 A	+7:91865843 1324261459 A	N
1097	3290 A	+7:91865844 1324261460 A	
1097	3291 C	+7:91865845 1324261461 C	
1098 I	3292 A	+7:91865846 1324261462 A	I
1098	3293 T	+7:91865847 1324261463 T	
1098	3294 C	+7:91865848 1324261464 C	
1099 M	3295 A	+7:91865849 1324261465 A	M
1099	3296 T	+7:91865850 1324261466 T	
1099	3297 G	+7:91865851 1324261467 G	
1100 A	3298 G	+7:91865852 1324261468 G	A
1100	3299 C	+7:91865853 1324261469 C	
1100	3300 T	+7:91865854 1324261470 T	
1101 W	3301 T	+7:91865855 1324261471 T	W
1101	3302 G	+7:91865856 1324261472 G	
1101	3303 G	+7:91865857 1324261473 G	
1102 F	3304 T	+7:91865858 1324261474 T	F
1102	3305 T	+7:91865859 1324261475 T	
1102	3306 T	+7:91865860 1324261476 T	
1103 H	3307 C	+7:91865861 1324261477 C	H
1103	3308 A	+7:91865862 1324261478 A	
1103	3309 T	+7:91865863 1324261479 T	
1104 D	3310 G	+7:91865864 1324261480 G	D
1104	3311 A	+7:91865865 1324261481 A	
1104	3312 C	+7:91865866 1324261482 C	
1105 M	3313 A	+7:91865867 1324261483 A	M
1105	3314 T	+7:91865868 1324261484 T	
1105	3315 G	+7:91865869 1324261485 G	
1106 N	3316 A	+7:91865870 1324261486 A	N
1106	3317 A	+7:91865871 1324261487 A	
1106	3318 C	+7:91865872 1324261488 C	
1107 P	3319 C	+7:91865873 1324261489 C	P
1107	3320 C	+7:91865874 1324261490 C	
1107	3321 T	+7:91865875 1324261491 T	
1108 Q	3322 C	+7:91865876 1324261492 C	Q
1108	3323 A	+7:91865877 1324261493 A	
1108	3324 G	+7:91865878 1324261494 G	
1109 S	3325 A	+7:91865879 1324261495 A	S
1109	3326 G	+7:91865880 1324261496 G	
1109	3327 T	+7:91865881 1324261497 T	
1110 I	3328 A	+7:91865882 1324261498 A	I
1110	3329 T	+7:91865883 1324261499 T	
1110	3330 T	+7:91865884 1324261500 T	
1111 A	3331 G	+7:91865885 1324261501 G	A
1111	3332 C	+7:91865886 1324261502 C	
1111	3333 C	+7:91865887 1324261503 C	
1112 L	3334 C	+7:91865888 1324261504 C	L
1112	3335 T	+7:91865889 1324261505 T	
1112	3336 G	+7:91865890 1324261506 G	
1113 I	3337 A	+7:91865891 1324261507 A	I
1113	3338 T	+7:91865892 1324261508 T	
1113	3339 T	+7:91865893 1324261509 T	
1114 P	3340 C	+7:91865894 1324261510 C	P
1114	3341 C	+7:91865895 1324261511 C	
1114	3342 T	+7:91865896 1324261512 T	
1115 P	3343 C	+7:91865897 1324261513 C	P
1115	3344 C	+7:91865898 1324261514 C	
1115	3345 A	+7:91865899 1324261515 A	
1116 A	3346 G	+7:91865900 1324261516 G	A
1116	3347 C	+7:91865901 1324261517 C	
1116	3348 A	+7:91865902 1324261518 A	
1117 T	3349 A	+7:91865903 1324261519 A	T
1117	3350 C	+7:91865904 1324261520 C	
1117	3351 T	+7:91865905 1324261521 T	
1118 T	3352 A	+7:91865906 1324261522 A	T
1118	3353 C	+7:91865907 1324261523 C	
1118	3354 A	+7:91865908 1324261524 A	
1119 E	3355 G	+7:91865909 1324261525 G	E
1119	3356 A	+7:91865910 1324261526 A	
1119	3357 A	+7:91865911 1324261527 A	
1120 I	3358 A	+7:91865912 1324261528 A	I
1120	3359 T	+7:91865913 1324261529 T	
1120	3360 C	+7:91865914 1324261530 C	
1121 S	3361 A	+7:91865915 1324261531 A	S
1121	3362 G	+7:91865916 1324261532 G	
1121	3363 T	+7:91865917 1324261533 T	
1122 A	3364 G	+7:91865918 1324261534 G	A
1122	3365 C	+7:91865919 1324261535 C	
1122	3366 A	+7:91865920 1324261536 A	
1123 D	3367 G	+7:91865921 1324261537 G	D
1123	3368 A	+7:91865922 1324261538 A	
1123	3369 T	+7:91865923 1324261539 T	
1124 S	3370 T	+7:91865924 1324261540 T	S
1124	3371 C	+7:91865925 1324261541 C	
1124	3372 C	+7:91865926 1324261542 C	
1125 Q	3373 C	+7:91865927 1324261543 C	Q
1125	3374 A	+7:91865928 1324261544 A	
1125	3375 G	+7:91865929 1324261545 G	
1126 L	3376 C	+7:91865930 1324261546 C	L
1126	3377 T	+7:91865931 1324261547 T	
1126	3378 C	+7:91865932 1324261548 C	
1127 P	3379 C	+7:91865933 1324261549 C	P
1127	3380 C	+7:91865934 1324261550 C	
1127	3381 C	+7:91865935 1324261551 C	
1128 C	3382 T	+7:91865936 1324261552 T	C
1128	3383 G	+7:91865937 1324261553 G	
1128	3384 T	+7:91865938 1324261554 T	
1129 I	3385 A	+7:91865939 1324261555 A	I
1129	3386 T	+7:91865940 1324261556 T	
1129	3387 C	+7:91865941 1324261557 C	
1130 K	3388 A	+7:91865942 1324261558 A	K
1130	3389 A	+7:91865943 1324261559 A	
1130	3390 A	+7:91865944 1324261560 A	
1131 D	3391 G	+7:91865945 1324261561 G	D
1131	3392 A	+7:91865946 1324261562 A	
1131	3393 T	+7:91865947 1324261563 T	
1132 G	3394 G	+7:91865948 1324261564 G	G
1132	3395 G	+7:91865949 1324261565 G	
1132	3396 G	+7:91865950 1324261566 G	
1133 S	3397 T	+7:91865951 1324261567 T	S
1133	3398 C	+7:91865952 1324261568 C	
1133	3399 A	+7:91865953 1324261569 A	
1134 E	3400 G	+7:91865954 1324261570 G	E
1134	3401 A	+7:91865955 1324261571 A	
1134	3402 A	+7:91865956 1324261572 A	
1135 G	3403 G	+7:91865957 1324261573 G	G
1135	3404 G	+7:91865958 1324261574 G	
1135	3405 T	+7:91865959 1324261575 T	
1136 V	3406 G	+7:91865960 1324261576 G	V
1136	3407 T	+7:91865961 1324261577 T	
1136	3408 G	+7:91865962 1324261578 G	
1137 K	3409 A	+7:91865963 1324261579 A	K
1137	3410 A	+7:91865964 1324261580 A	
1137	3411 G	+7:91865965 1324261581 G	
1138 D	3412 G	+7:91865966 1324261582 G	D
1138	3413 A	+7:91865967 1324261583 A	
1138	3414 T	+7:91865968 1324261584 T	
1139 V	3415 G	+7:91865969 1324261585 G	V
1139	3416 T	+7:91865970 1324261586 T	
1139	3417 G	+7:91865971 1324261587 G	
1140 E	3418 G	+7:91865972 1324261588 G	E
1140	3419 A	+7:91865973 1324261589 A	
1140	3420 A	+7:91865974 1324261590 A	
1141 L	3421 C	+7:91865975 1324261591 C	L
1141	3422 T	+7:91865976 1324261592 T	
1141	3423 G	+7:91865977 1324261593 G	
1142 V	3424 G	+7:91865978 1324261594 G	V
1142	3425 T	+7:91865979 1324261595 T	
1142	3426 G	+7:91865980 1324261596 G	
1143 L	3427 C	+7:91865981 1324261597 C	L
1143	3428 T	+7:91865982 1324261598 T	
1143	3429 G	+7:91865983 1324261599 G	
1144 P	3430 C	+7:91865984 1324261600 C	P
1144	3431 C	+7:91865985 1324261601 C	
1144	3432 A	+7:91865986 1324261602 A	
1145 E	3433 G	+7:91865987 1324261603 G	E
1145	3434 A	+7:91865988 1324261604 A	
1145	3435 A	+7:91865989 1324261605 A	
1146 D	3436 G	+7:91865990 1324261606 G	D
1146	3437 A	+7:91865991 1324261607 A	
1146	3438 T	+7:91865992 1324261608 T	
1147 S	3439 T	+7:91865993 1324261609 T	S
1147	3440 C	+7:91865994 1324261610 C	
1147	3441 A	+7:91865995 1324261611 A	
1148 M	3442 A	+7:91865996 1324261612 A	M
1148	3443 T	+7:91865997 1324261613 T	
1148	3444 G	+7:91865998 1324261614 G	
1149 F	3445 T	+7:91865999 1324261615 T	F
1149	3446 T	+7:91866000 1324261616 T	
1149	3447 T	+7:91866001 1324261617 T	
1150 E	3448 G	+7:91866002 1324261618 G	E
1150	3449 A	+7:91866003 1324261619 A	
1150	3450 A	+7:91866004 1324261620 A	
1151 D	3451 G	+7:91866005 1324261621 G	D
1151	3452 A	+7:91866006 1324261622 A	
1151	3453 T	+7:91866007 1324261623 T	
1152 A	3454 G	+7:91866008 1324261624 G	A
1152	3455 C	+7:91866009 1324261625 C	
1152	3456 C	+7:91866010 1324261626 C	
1153 S	3457 A	+7:91866011 1324261627 A	S
1153	3458 G	+7:91866012 1324261628 G	
1153	3459 T	+7:91866013 1324261629 T	
1154 V	3460 G	+7:91866014 1324261630 G	V
1154	3461 T	+7:91866015 1324261631 T	
1154	3462 C	+7:91866016 1324261632 C	
1155 S	3463 A	+7:91866017 1324261633 A	S
1155	3464 G	+7:91866018 1324261634 G	
1155	3465 T	+7:91866019 1324261635 T	
1156 E	3466 G	+7:91866020 1324261636 G	E
1156	3467 A	+7:91866021 1324261637 A	
1156	3468 A	+7:91866022 1324261638 A	
1157 G	3469 G	+7:91866023 1324261639 G	G
1157	3470 G	+7:91866024 1324261640 G	
1157	3471 T	+7:91866025 1324261641 T	
1158 R	3472 A	+7:91866026 1324261642 A	R
1158	3473 G	+7:91866027 1324261643 G	
1158	3474 A	+7:91866028 1324261644 A	
1159 G	3475 G	+7:91866029 1324261645 G	G
1159	3476 G	+7:91866030 1324261646 G	
1159	3477 A	+7:91866031 1324261647 A	
1160 T	3478 A	+7:91866032 1324261648 A	T
1160	3479 C	+7:91866033 1324261649 C	
1160	3480 C	+7:91866034 1324261650 C	
1161 Q	3481 C	+7:91866035 1324261651 C	Q
1161	3482 A	+7:91866036 1324261652 A	
1161	3483 G	+7:91866037 1324261653 G	
1162 I	3484 A	+7:91866038 1324261654 A	I
1162	3485 T	+7:91866039 1324261655 T	
1162	3486 A	+7:91866040 1324261656 A	
1163 E	3487 G	+7:91866041 1324261657 G	E
1163	3488 A	+7:91866042 1324261658 A	
1163	3489 A	+7:91866043 1324261659 A	
1164 E	3490 G	+7:91866044 1324261660 G	E
1164	3491 A	+7:91866045 1324261661 A	
1164	3492 A	+7:91866046 1324261662 A	
1165 N	3493 A	+7:91866047 1324261663 A	N
1165	3494 A	+7:91866048 1324261664 A	
1165	3495 T	+7:91866049 1324261665 T	
1166 P	3496 C	+7:91866050 1324261666 C	P
1166	3497 C	+7:91866051 1324261667 C	
1166	3498 T	+7:91866052 1324261668 T	
1167 L	3499 T	+7:91866053 1324261669 T	L
1167	3500 T	+7:91866054 1324261670 T	
1167	3501 G	+7:91866055 1324261671 G	
1168 E	3502 G	+7:91866056 1324261672 G	E
1168	3503 A	+7:91866057 1324261673 A	
1168	3504 A	+7:91866058 1324261674 A	
1169 E	3505 G	+7:91866059 1324261675 G	E
1169	3506 A	+7:91866060 1324261676 A	
1169	3507 A	+7:91866061 1324261677 A	
1170 N	3508 A	+7:91866062 1324261678 A	N
1170	3509 A	+7:91866063 1324261679 A	
1170	3510 T	+7:91866064 1324261680 T	
1171 I	3511 A	+7:91866065 1324261681 A	I
1171	3512 T	+7:91866066 1324261682 T	
1171	3513 T	+7:91866067 1324261683 T	
1172 L	3514 C	+7:91866068 1324261684 C	L
1172	3515 T	+7:91866069 1324261685 T	
1172	3516 G	+7:91866070 1324261686 G	
1173 A	3517 G	+7:91866071 1324261687 G	A
1173	3518 C	+7:91866072 1324261688 C	
1173	3519 G	+7:91866073 1324261689 G	
1174 G	3520 G	+7:91866074 1324261690 G	G
1174	3521 G	+7:91866075 1324261691 G	
1174	3522 G	+7:91866076 1324261692 G	
1175 E	3523 G	+7:91866077 1324261693 G	E
1175	3524 A	+7:91866078 1324261694 A	
1175	3525 A	+7:91866079 1324261695 A	
1176 A	3526 G	+7:91866080 1324261696 G	A
1176	3527 C	+7:91866081 1324261697 C	
1176	3528 A	+7:91866082 1324261698 A	
1177 A	3529 G	+7:91866083 1324261699 G	A
1177	3530 C	+7:91866084 1324261700 C	
1177	3531 A	+7:91866085 1324261701 A	
1178 S	3532 T	+7:91866086 1324261702 T	S
1178	3533 C	+7:91866087 1324261703 C	
1178	3534 T	+7:91866088 1324261704 T	
1179 Q	3535 C	+7:91866089 1324261705 C	Q
1179	3536 A	+7:91866090 1324261706 A	
1179	3537 A	+7:91866091 1324261707 A	
1180 A	3538 G	+7:91866092 1324261708 G	A
1180	3539 C	+7:91866093 1324261709 C	
1180	3540 T	+7:91866094 1324261710 T	
1181 G	3541 G	+7:91866095 1324261711 G	G
1181	3542 G	+7:91866096 1324261712 G	
1181	3543 T	+7:91866097 1324261713 T	
1182 D	3544 G	+7:91866098 1324261714 G	D
1182	3545 A	+7:91866099 1324261715 A	
1182	3546 C	+7:91866100 1324261716 C	
1183 S	3547 A	+7:91866101 1324261717 A	S
1183	3548 G	+7:91866102 1324261718 G	
1183	3549 T	+7:91866103 1324261719 T	
1184 G	3550 G	+7:91866104 1324261720 G	G
1184	3551 G	+7:91866105 1324261721 G	
1184	3552 T	+7:91866106 1324261722 T	
1185 N	3553 A	+7:91866107 1324261723 A	N
1185	3554 A	+7:91866108 1324261724 A	
1185	3555 C	+7:91866109 1324261725 C	
1186 E	3556 G	+7:91866110 1324261726 G	E
1186	3557 A	+7:91866111 1324261727 A	
1186	3558 G	+7:91866112 1324261728 G	
1187 A	3559 G	+7:91866113 1324261729 G	A
1187	3560 C	+7:91866114 1324261730 C	
1187	3561 A	+7:91866115 1324261731 A	
1188 A	3562 G	+7:91866116 1324261732 G	A
1188	3563 C	+7:91866117 1324261733 C	
1188	3564 C	+7:91866118 1324261734 C	
1189 N	3565 A	+7:91866119 1324261735 A	N
1189	3566 A	+7:91866120 1324261736 A	
1189	3567 C	+7:91866121 1324261737 C	
1190 R	3568 A	+7:91866122 1324261738 A	R
1190	3569 G	+7:91866123 1324261739 G	
1190	3570 A	+7:91866124 1324261740 A	
1191 G	3571 G	+7:91866125 1324261741 G	G
1191	3572 G	+7:91866126 1324261742 G	
1191	3573 A	+7:91866127 1324261743 A	
1192 D	3574 G	+7:91866128 1324261744 G	D
1192	3575 A	+7:91866129 1324261745 A	
1192	3576 T	+7:91866130 1324261746 T	
1193 G	3577 G	+7:91866131 1324261747 G	G
1193	3578 G	+7:91866132 1324261748 G	
1193	3579 T	+7:91866133 1324261749 T	
1194 S	3580 T	+7:91866134 1324261750 T	S
1194	3581 C	+7:91866135 1324261751 C	
1194	3582 A	+7:91866136 1324261752 A	
1195 D	3583 G	+7:91866137 1324261753 G	D
1195	3584 A	+7:91866138 1324261754 A	
1195	3585 T	+7:91866139 1324261755 T	
1196 V	3586 G	+7:91866140 1324261756 G	V
1196	3587 T	+7:91866141 1324261757 T	
1196	3588 T	+7:91866142 1324261758 T	
1197 S	3589 T	+7:91866143 1324261759 T	S
1197	3590 C	+7:91866144 1324261760 C	
1197	3591 A	+7:91866145 1324261761 A	
1198 S	3592 A	+7:91866146 1324261762 A	S
1198	3593 G	+7:91866147 1324261763 G	
1198	3594 T	+7:91866148 1324261764 T	
1199 Q	3595 C	+7:91866149 1324261765 C	Q
1199	3596 A	+7:91866150 1324261766 A	
1199	3597 A	+7:91866151 1324261767 A	
1200 T	3598 A	+7:91866152 1324261768 A	T
1200	3599 C	+7:91866153 1324261769 C	
1200	3600 A	+7:91866154 1324261770 A	
1201 P	3601 C	+7:91866155 1324261771 C	P
1201	3602 C	+7:91866156 1324261772 C	
1201	3603 T	+7:91866157 1324261773 T	
1202 Q	3604 C	+7:91866158 1324261774 C	Q
1202	3605 A	+7:91866159 1324261775 A	
1202	3606 A	+7:91866160 1324261776 A	
1203 T	3607 A	+7:91866161 1324261777 A	T
1203	3608 C	+7:91866162 1324261778 C	
1203	3609 C	+7:91866163 1324261779 C	
1204 S	3610 T	+7:91866164 1324261780 T	S
1204	3611 C	+7:91866165 1324261781 C	
1204	3612 A	+7:91866166 1324261782 A	
1205 S	3613 A	+7:91866167 1324261783 A	S
1205	3614 G	+7:91866168 1324261784 G	
1205	3615 T	+7:91866169 1324261785 T	
1206 D	3616 G	+7:91866170 1324261786 G	D
1206	3617 A	+7:91866171 1324261787 A	
1206	3618 C	+7:91866172 1324261788 C	
1207 W	3619 T	+7:91866173 1324261789 T	W
1207	3620 G	+7:91866174 1324261790 G	
1207	3621 G	+7:91866175 1324261791 G	
1208 L	3622 C	+7:91866176 1324261792 C	L
1208	3623 T	+7:91866177 1324261793 T	
1208	3624 T	+7:91866178 1324261794 T	
1209 E	3625 G	+7:91866179 1324261795 G	E
1209	3626 A	+7:91866180 1324261796 A	
1209	3627 A	+7:91866181 1324261797 A	
1210 Q	3628 C	+7:91866182 1324261798 C	Q
1210	3629 A	+7:91866183 1324261799 A	
1210	3630 A	+7:91866184 1324261800 A	
1211 V	3631 G	+7:91866185 1324261801 G	V
1211	3632 T	+7:91866186 1324261802 T	
1211	3633 A	+7:91866187 1324261803 A	
1212 H	3634 C	+7:91866188 1324261804 C	H
1212	3635 A	+7:91866189 1324261805 A	
1212	3636 T	+7:91866190 1324261806 T	
1213 L	3637 T	+7:91866191 1324261807 T	L
1213	3638 T	+7:91866192 1324261808 T	
1213	3639 A	+7:91866193 1324261809 A	
1214 V	3640 G	+7:91866194 1324261810 G	V
1214	3641 T	+7:91866195 1324261811 T	
1214	3642 G	+7:91866196 1324261812 G	
>ENSP00000003100 
1 M	1 A	-13:28196176 2108077949 A	M
1	2 T	-13:28196175 2108077948 T	
1	3 G	-13:28196174 2108077947 G	
2 A	4 G	-13:28196173 2108077946 G	A
2	5 C	-13:28196172 2108077945 C	
2	6 G	-13:28196171 2108077944 G	
3 A	7 G	-13:28196170 2108077943 G	A
3	8 C	-13:28196169 2108077942 C	
3	9 A	-13:28196168 2108077941 A	
4 A	10 G	-13:28196167 2108077940 G	A
4	11 C	-13:28196166 2108077939 C	
4	12 G	-13:28196165 2108077938 G	
5 A	13 G	-13:28196164 2108077937 G	A
5	14 C	-13:28196163 2108077936 C	
5	15 G	-13:28196162 2108077935 G	
6 G	16 G	-13:28196161 2108077934 G	G
6	17 G	-13:28196160 2108077933 G	
6	18 G	-13:28196159 2108077932 G	
7 M	19 A	-13:28196158 2108077931 A	M
7	20 T	-13:28196157 2108077930 T	
7	21 G	-13:28196156 2108077929 G	
8 L	22 Y	-13:28196155 2108077928 A	M
8	23 T	-13:28196154 2108077927 T	
8	24 G	-13:28196153 2108077926 G	
9 L	25 T	-13:28196152 2108077925 T	L
9	26 T	-13:28196151 2108077924 T	
9	27 G	-13:28196150 2108077923 G	
10 L	28 C	-13:28196149 2108077922 C	L
10	29 T	-13:28196148 2108077921 T	
10	30 G	-13:28196147 2108077920 G	
11 G	31 G	-13:28196146 2108077919 G	G
11	32 G	-13:28196145 2108077918 G	
11	33 C	-13:28196144 2108077917 C	
12 L	34 T	-13:28196143 2108077916 T	L
12	35 T	-13:28196142 2108077915 T	
12	36 G	-13:28196141 2108077914 G	
13 L	37 C	-13:28196140 2108077913 C	L
13	38 T	-13:28196139 2108077912 T	
13	39 G	-13:28196138 2108077911 G	
14 Q	40 C	-13:28196137 2108077910 C	Q
14	41 A	-13:28196136 2108077909 A	
14	42 G	-13:28196135 2108077908 G	
15 A	43 G	-13:28196134 2108077907 G	A
15	44 C	-13:28196133 2108077906 C	
15	45  	-13:28196132 2108077905 G	
15	45 G	-13:28196131 2108077904 G	G
16 G	46 G	-13:28196130 2108077903 G	
16	47 G	-13:28196129 2108077902 G	
16	48 T	-13:28196128 2108077901 T	W
17 G	49 G	-13:28196127 2108077900 G	
17	50 G	-13:28196126 2108077899 G	
17	51 G	-13:28196125 2108077898 G	V
18 S	52 T	-13:28196124 2108077897 T	
18	53 C	-13:28196123 2108077896 C	
18	54 G	-13:28196122 2108077895 G	G
19 V	55 G	-13:28196121 2108077894 G	
19	56 T	-13:28196120 2108077893 T	
19	57 G	-13:28196119 2108077892 G	A
20 L	58 C	-13:28196118 2108077891 C	
20	59 T	-13:28196117 2108077890 T	
20	60 G	-13:28196116 2108077889 G	G
21 G	61 G	-13:28196115 2108077888 G	
21	62 G	-13:28196114 2108077887 G	
21	63 C	-13:28196113 2108077886 C	P
22 Q	64 C	-13:28196112 2108077885 C	
22	65 A	-13:28196111 2108077884 A	
22	66 G	-13:28196110 2108077883 G	G
23 A	67 G	-13:28196109 2108077882 G	
23	68 C	-13:28196108 2108077881 C	
23	69 G	-13:28196107 2108077880 G	D
24 M	70 A	-13:28196106 2108077879 A	
24	71 T	-13:28196105 2108077878 T	
24	72 G	-13:28196104 2108077877 G	G
25 E	73 G	-13:28196103 2108077876 G	
25	74 A	-13:28196102 2108077875 A	
25	75 G	-13:28196101 2108077874 G	E
26 K	76 A	-13:28196100 2108077873 A	
26	77 A	-13:28196099 2108077872 A	
26	78 G	-13:28196098 2108077871 G	G
27 V	79 G	-13:28196097 2108077870 G	
27	80 T	-13:28196096 2108077869 T	
27	81 G	-13:28196095 2108077868 G	D
28 T	82 A	-13:28196094 2108077867 A	
28	83 C	-13:28196093 2108077866 C	
28	84 A	-13:28196092 2108077865 A	R
29 G	85 G	-13:28196091 2108077864 G	
29	86 G	-13:28196090 2108077863 G	
29	87 A	-13:28196089 2108077862 A	R
30 G	88 G	-13:28196088 2108077861 G	
30	89 G	-13:28196087 2108077860 G	
30	90 C	-13:28196086 2108077859 C	Q
31 N	91 A	-13:28196085 2108077858 A	
31	92 A	-13:28196084 2108077857 A	
31	93 C	-13:28196083 2108077856 C	P
32 L	94 C	-13:28196082 2108077855 C	
32	95 T	-13:28196081 2108077854 T	
32	96 C	-13:28196080 2108077853 C	L
33 L	97 T	-13:28196079 2108077852 T	
33	98 T	-13:28196078 2108077851 T	
33	99 G	-13:28196077 2108077850 G	V
34 S	100 T	-13:28196076 2108077849 T	
34	101 C	-13:28196075 2108077848 C	
34	102 C	-13:28196074 2108077847 C	H
35 M	103 A	-13:28196073 2108077846 A	
35	104 T	-13:28196072 2108077845 T	
35	105 G	-13:28196071 2108077844 G	A
36 L	106 C	-13:28196070 2108077843 C	
36	107 T	-13:28196069 2108077842 T	
36	108 G	-13:28196068 2108077841 G	A
37 L	109 C	-13:28196067 2108077840 C	
37	110 T	-13:28196066 2108077839 T	
37	111 G	-13:28196065 2108077838 G	D
38 I	112 A	-13:28196064 2108077837 A	
38	113 T	-13:28196063 2108077836 T	
38	114 C	-13:28196062 2108077835 C	R
39 A	115 G	-13:28196061 2108077834 G	
39	116 C	-13:28196060 2108077833 C	
39	117 C	-13:28196059 2108077832 C	L
40 C	118 T	-13:28196058 2108077831 T	
40	119 G	-13:28196057 2108077830 G	
40	120 C	-13:28196056 2108077829 C	H
41 A	121 G	-13:28196055 2108077828 A	
41	122 C	-13:28196054 2108077827 C	
41	123 C	-13:28196053 2108077826 C	L
42 F	124 T	-13:28196052 2108077825 T	
42	125 T	-13:28196051 2108077824 T	
42	126 C	-13:28196050 2108077823 C	H
43 T	127 A	-13:28196049 2108077822 A	
43	128 C	-13:28196048 2108077821 C	
43	129 C	-13:28196047 2108077820 C	P
44 L	130 C	-13:28196046 2108077819 C	
44	131 T	-13:28196045 2108077818 T	
44	132 C	-13:28196044 2108077817 C	Q
45 S	133 A	-13:28196043 2108077816 A	
45	134 G	-13:28196042 2108077815 G	
45	135 C	-13:28196041 2108077814 C	P
46 L	136 C	-13:28196040 2108077813 C	
46	137 T	-13:28196039 2108077812 T	
46	138 G	-13:28196038 2108077811 G	G
47 V	139 G	-13:28196037 2108077810 G	
47	140 T	-13:28196036 2108077809 T	
47	141 C	-13:28196035 2108077808 C	L
48 Y	142 T	-13:28196034 2108077807 T	
48	143 A	-13:28196033 2108077806 A	
48	144 C	-13:28196032 2108077805 C	P
49 L	145 C	-13:28196031 2108077804 C	
49	146 T	-13:28196030 2108077803 T	
49	147 G	-13:28196029 2108077802 G	V
50 I	148 A	-13:28196028 2108077801 T	
50	149 T	-13:28196027 2108077800 T	
50	150 C	-13:28196026 2108077799 C	P
51 R	151 C	-13:28196025 2108077798 C	
51	152 G	-13:28196024 2108077797 G	
51	153 T	-13:28196023 2108077796 T	S
52 L	154 C	-13:28196022 2108077795 C	
52	155 T	-13:28196021 2108077794 T	
52	156 G	-13:28196020 2108077793 G	G
53 A	157 G	-13:28196019 2108077792 G	
53	158 C	-13:28196018 2108077791 C	
53	159 C	-13:28196017 2108077790 C	R
54 A	160 G	-13:28196016 2108077789 G	
54	161 C	-13:28196015 2108077788 C	
54	162 C	-13:28196014 2108077787 C	R
55 G	163 G	-13:28196013 2108077786 G	
55	164 G	-13:28196012 2108077785 G	
55	165 C	-13:28196011 2108077784 C	P
56 H	166 C	-13:28196010 2108077783 C	
56	167 A	-13:28196009 2108077782 A	
56	168 C	-13:28196008 2108077781 C	L
57 L	169 T	-13:28196007 2108077780 T	
57	170 T	-13:28196006 2108077779 T	
57	171 G	-13:28196005 2108077778 G	G
58 V	172 G	-13:28196004 2108077777 G	
58	173 T	-13:28196003 2108077776 T	
58	174 C	-13:28196002 2108077775 C	P
59 Q	175 C	-13:28196001 2108077774 C	
59	176 A	-13:28196000 2108077773 A	
59	177 G	-13:28195999 2108077772 G	A
60 L	178 C	-13:28195998 2108077771 C	
60	179 T	-13:28195997 2108077770 T	
60	180 G	-13:28195996 2108077769 G	A
61 P	181 C	-13:28195995 2108077768 C	
61	182 C	-13:28195994 2108077767 C	
61	183 C	-13:28195993 2108077766 C	R
62 A	184 G	-13:28195992 2108077765 G	
62	185 C	-13:28195991 2108077764 C	
62	186 A	-13:28195990 2108077763 A	R
63 G	187 G	-13:28195989 2108077762 G	
63	188 G	-13:28195988 2108077761 G	
63	189 G	-13:28195987 2108077760 G	G
64 V	190 G	-13:28195986 2108077759 G	
64	191 T	-13:28195985 2108077758 C	
64	192 G	-13:28195984 2108077757 G	E
65 K	193 A	-13:28195983 2108077756 A	
65	194 A	-13:28195982 2108077755 A	
65	195 A	-13:28195981 2108077754 A	K
66 S	196 A	-13:28195980 2108077753 A	
66	197 G	-13:28195979 2108077752 G	
66	198 T	-13:28195978 2108077751 T	S
67 P	199 C	-13:28195977 2108077750 C	
67	200 C	-13:28195976 2108077749 C	
67	201 T	-13:28195975 2108077748 T	S
68 P	202 C	-13:28195974 2108077747 C	
68	203 C	-13:28195973 2108077746 C	
68	204 A	-13:28195972 2108077745 A	I
69 Y	205 T	-13:28195971 2108077744 T	
69	206 A	-13:28195970 2108077743 A	
69	207 C	-13:28195969 2108077742 C	R
70 I	208 A	-13:28195968 2108077741 G	
70	209 T	-13:28195967 2108077740 T	
70	210 T	-13:28195966 2108077739 T	F
71 F	211 T	-13:28195965 2108077738 T	
71	212 T	-13:28195964 2108077737 T	
71	213 C	-13:28195963 2108077736 C	L
72 S	214 T	-13:28195962 2108077735 T	
72	215 C	-13:28195961 2108077734 C	
72	216 C	-13:28195960 2108077733 C	P
73 P	217 C	-13:28195959 2108077732 C	
73	218 C	-13:28195958 2108077731 C	
73	219 A	-13:28195957 2108077730 A	S
74 I	220 A	-13:28195956 2108077729 G	
74	221 T	-13:28195955 2108077728 T	
74	222 T	-13:28195954 2108077727 T	S
75 P	223 C	-13:28195953 2108077726 C	
75	224 C	-13:28195952 2108077725 C	
75	225 A	-13:28195951 2108077724 A	I
76 F	226 T	-13:28195950 2108077723 T	
76	227 T	-13:28195949 2108077722 T	
76	228 C	-13:28195948 2108077721 C	P
77 L	229 C	-13:28195947 2108077720 C	
77	230 T	-13:28195946 2108077719 C	
77	231 T	-13:28195945 2108077718 T	W
78 G	232 G	-13:28195944 2108077717 G	
78	233 G	-13:28195943 2108077716 G	
78	234 G	-13:28195942 2108077715 G	A
79 H	235 C	-13:28195941 2108077714 C	
79	236 A	-13:28195940 2108077713 A	
79	237 T	-13:28195939 2108077712 T	C
80 A	238 G	-13:28195938 2108077711 G	
80	239 C	-13:28195937 2108077710 C	
80	240 C	-13:28195936 2108077709 C	H
81 I	241 A	-13:28195935 2108077708 A	
81	242 T	-13:28195934 2108077707 T	
81	243 A	-13:28195933 2108077706 A	S
82 A	244 G	-13:28195932 2108077705 G	
82	245 C	-13:28195931 2108077704 C	
82	246 A	-13:28195930 2108077703 A	I
83 F	247 T	-13:28195929 2108077702 T	
83	248 T	-13:28195928 2108077701 T	
83	249 T	-13:28195927 2108077700 T	W
84 G	250 G	-13:28195926 2108077699 G	
84	251 G	-13:28195925 2108077698 G	
84	252 G	-13:28195924 2108077697 G	E
85 K	253 A	-13:28195923 2108077696 A	
85	254 A	-13:28195922 2108077695 A	
85	255 A	-13:28195921 2108077694 A	K
86 S	256 A	-13:28195920 2108077693 A	
86	257 G	-13:28195919 2108077692 G	
86	258 T	-13:28195918 2108077691 T	S
87 P	259 C	-13:28195917 2108077690 C	
87	260 C	-13:28195916 2108077689 C	
87	261 A	-13:28195915 2108077688 A	S
88 I	262 A	-13:28195914 2108077687 G	
88	263 T	-13:28195913 2108077686 T	
88	264 T	-13:28195912 2108077685 T	*
89 E	265 G	-13:28195911 2108077684 G	
89	266 A	-13:28195910 2108077683 A	
89	267 A	-13:28195909 2108077682 A	
90 F	268 T	-13:28195908 2108077681 T	
90	269 T	-13:28195907 2108077680 T	
90	270 T	-13:28195906 2108077679 T	
91 L	271 C	-13:28195905 2108077678 C	
91	272 T	-13:28195904 2108077677 T	
91	273 A	-13:28195903 2108077676 A	
92 E	274 G	-13:28195902 2108077675 G	
92	275 A	-13:28195901 2108077674 A	
92	276 R	-13:28195900 2108077673  	
93 N	277 A	-13:28195900 2108077673 A	
93	278 A	-13:28195899 2108077672 A	
93	279 T	-13:28195898 2108077671 T	
94 A	280 G	-13:28195897 2108077670 G	
94	281 C	-13:28195896 2108077669 C	
94	282 A	-13:28195895 2108077668 A	
95 Y	283 T	-13:28195894 2108077667 T	
95	284 A	-13:28195893 2108077666 A	
95	285 T	-13:28195892 2108077665 T	
96 E	286 G	-13:28195891 2108077664 G	
96	287 A	-13:28195890 2108077663 A	
96	288 G	-13:28195889 2108077662 G	
97 K	289 A	-13:28195888 2108077661 A	
97	290 A	-13:28195887 2108077660 A	
97	291 G	-13:28195886 2108077659 G	
98 Y	292 T	-13:28195885 2108077658 T	
98	293 A	-13:28195884 2108077657 A	
98	294 T	-13:28195883 2108077656 T	
99 G	295 G	-13:28195882 2108077655 G	
99	296 G	-13:28195881 2108077654 G	
99	297 A	-13:28195880 2108077653 A	
100 P	298 C	-13:28195879 2108077652 C	
100	299 C	-13:28195878 2108077651 C	
100	300 T	-13:28195877 2108077650 T	
101 V	301 G	-13:28195876 2108077649 G	
101	302 T	-13:28195875 2108077648 T	
101	303 A	-13:28195874 2108077647 A	
102 F	304 T	-13:28195873 2108077646 T	
102	305 T	-13:28195872 2108077645 T	
102	306 T	-13:28195871 2108077644 T	
103 S	307 A	-13:28195870 2108077643 A	
103	308 G	-13:28195869 2108077642 G	
103	309 T	-13:28195868 2108077641 T	
104 F	310 T	-13:28195867 2108077640 T	
104	311 T	-13:28195866 2108077639 T	
104	312 T	-13:28195865 2108077638 T	
105 T	313 A	-13:28195864 2108077637 A	
105	314 C	-13:28195863 2108077636 C	
105	315 C	-13:28195862 2108077635 C	
106 M	316 A	-13:28195861 2108077634 A	
106	317 T	-13:28195860 2108077633 T	
106	318 G	-13:28195859 2108077632 G	
107 V	319 G	-13:28195858 2108077631 G	
107	320 T	-13:28195857 2108077630 T	
107	321 A	-13:28195856 2108077629 A	
108 G	322 G	-13:28195855 2108077628 G	
108	323 G	-13:28195854 2108077627 G	
108	324 C	-13:28195853 2108077626 C	
109 K	325 A	-13:28195852 2108077625 A	
109	326 A	-13:28195851 2108077624 A	
109	327 G	-13:28195850 2108077623 G	
110 T	328 A	-13:28195849 2108077622 A	
110	329 C	-13:28195848 2108077621 C	
110	330 A	-13:28195847 2108077620 A	
111 F	331 T	-13:28195846 2108077619 T	
111	332 T	-13:28195845 2108077618 T	
111	333 T	-13:28195844 2108077617 T	
112 T	334 A	-13:28195843 2108077616 A	
112	335 C	-13:28195842 2108077615 C	
112	336 T	-13:28195841 2108077614 T	
113 Y	337 T	-13:28195840 2108077613 T	
113	338 A	-13:28195839 2108077612 A	
113	339 C	-13:28195838 2108077611 C	
114 L	340 C	-13:28195837 2108077610 C	
114	341 T	-13:28195836 2108077609 T	
114	342 T	-13:28195835 2108077608 T	
115 L	343 C	-13:28195834 2108077607 C	
115	344 T	-13:28195833 2108077606 T	
115	345 G	-13:28195832 2108077605 G	
116 G	346 G	-13:28195831 2108077604 G	
116	347 G	-13:28195830 2108077603 G	
116	348 G	-13:28195829 2108077602 G	
117 S	349 A	-13:28195828 2108077601 A	
117	350 G	-13:28195827 2108077600 G	
117	351 T	-13:28195826 2108077599 T	
118 D	352 G	-13:28195825 2108077598 G	
118	353 A	-13:28195824 2108077597 A	
118	354 T	-13:28195823 2108077596 T	
119 A	355 G	-13:28195822 2108077595 G	
119	356 C	-13:28195821 2108077594 C	
119	357 T	-13:28195820 2108077593 T	
120 A	358 G	-13:28195819 2108077592 G	
120	359 C	-13:28195818 2108077591 C	
120	360 T	-13:28195817 2108077590 T	
121 A	361 G	-13:28195816 2108077589 G	
121	362 C	-13:28195815 2108077588 C	
121	363 G	-13:28195814 2108077587 G	
122 L	364 C	-13:28195813 2108077586 C	
122	365 T	-13:28195812 2108077585 T	
122	366 G	-13:28195811 2108077584 G	
123 L	367 C	-13:28195810 2108077583 C	
123	368 T	-13:28195809 2108077582 T	
123	369 T	-13:28195808 2108077581 T	
124 F	370 T	-13:28195807 2108077580 T	
124	371 T	-13:28195806 2108077579 T	
124	372 T	-13:28195805 2108077578 T	
125 N	373 A	-13:28195804 2108077577 A	
125	374 A	-13:28195803 2108077576 A	
125	375 T	-13:28195802 2108077575 T	
126 S	376 A	-13:28195801 2108077574 A	
126	377 G	-13:28195800 2108077573 G	
126	378 T	-13:28195799 2108077572 T	
127 K	379 A	-13:28195798 2108077571 A	
127	380 A	-13:28195797 2108077570 A	
127	381 A	-13:28195796 2108077569 A	
128 N	382 A	-13:28195795 2108077568 A	
128	383 A	-13:28195794 2108077567 A	
128	384 T	-13:28195793 2108077566 T	
129 E	385 G	-13:28195792 2108077565 G	
129	386 A	-13:28195791 2108077564 A	
129	387 A	-13:28195790 2108077563 A	
130 D	388 G	-13:28195789 2108077562 G	
130	389 A	-13:28195788 2108077561 A	
130	390 C	-13:28195787 2108077560 C	
131 L	391 C	-13:28195786 2108077559 C	
131	392 T	-13:28195785 2108077558 T	
131	393 G	-13:28195784 2108077557 G	
132 N	394 A	-13:28195783 2108077556 A	
132	395 A	-13:28195782 2108077555 A	
132	396 T	-13:28195781 2108077554 T	
133 A	397 G	-13:28195780 2108077553 G	
133	398 C	-13:28195779 2108077552 C	
133	399 A	-13:28195778 2108077551 A	
134 E	400 G	-13:28195777 2108077550 G	
134	401 A	-13:28195776 2108077549 A	
134	402 A	-13:28195775 2108077548 A	
135 D	403 G	-13:28195774 2108077547 G	
135	404 A	-13:28195773 2108077546 A	
135	405 T	-13:28195772 2108077545 T	
136 V	406 G	-13:28195771 2108077544 G	
136	407 T	-13:28195770 2108077543 T	
136	408 C	-13:28195769 2108077542 C	
137 Y	409 T	-13:28195768 2108077541 T	
137	410 A	-13:28195767 2108077540 A	
137	411 C	-13:28195766 2108077539 C	
138 S	412 A	-13:28195765 2108077538 A	
138	413 G	-13:28195764 2108077537 G	
138	414 T	-13:28195763 2108077536 T	
139 R	415 C	-13:28195762 2108077535 C	
139	416 G	-13:28195761 2108077534 A	
139	417 C	-13:28195760 2108077533 C	
140 L	418 C	-13:28195759 2108077532 C	
140	419 T	-13:28195758 2108077531 T	
140	420 G	-13:28195757 2108077530 G	
141 T	421 A	-13:28195756 2108077529 A	
141	422 C	-13:28195755 2108077528 C	
141	423 G	-13:28195754 2108077527 G	
142 T	424 A	-13:28195753 2108077526 A	
142	425 C	-13:28195752 2108077525 C	
142	426 A	-13:28195751 2108077524 A	
143 P	427 C	-13:28195750 2108077523 C	
143	428 C	-13:28195749 2108077522 C	
143	429 T	-13:28195748 2108077521 T	
144 V	430 G	-13:28195747 2108077520 G	
144	431 T	-13:28195746 2108077519 T	
144	432 G	-13:28195745 2108077518 G	
145 F	433 T	-13:28195744 2108077517 T	
145	434 T	-13:28195743 2108077516 T	
145	435 T	-13:28195742 2108077515 T	
146 G	436 G	-13:28195741 2108077514 G	
146	437 G	-13:28195740 2108077513 G	
146	438 G	-13:28195739 2108077512 G	
147 K	439 A	-13:28195738 2108077511 A	
147	440 A	-13:28195737 2108077510 A	
147	441 G	-13:28195736 2108077509 G	
148 G	442 G	-13:28195735 2108077508 G	
148	443 G	-13:28195734 2108077507 G	
148	444 A	-13:28195733 2108077506 A	
149 V	445 G	-13:28195732 2108077505 G	
149	446 T	-13:28195731 2108077504 T	
149	447 T	-13:28195730 2108077503 T	
150 A	448 G	-13:28195729 2108077502 G	
150	449 C	-13:28195728 2108077501 C	
150	450 A	-13:28195727 2108077500 A	
151 Y	451 T	-13:28195726 2108077499 T	
151	452 A	-13:28195725 2108077498 A	
151	453 C	-13:28195724 2108077497 C	
152 D	454 G	-13:28195723 2108077496 G	
152	455 A	-13:28195722 2108077495 A	
152	456 T	-13:28195721 2108077494 T	
153 V	457 G	-13:28195720 2108077493 G	
153	458 T	-13:28195719 2108077492 T	
153	459 G	-13:28195718 2108077491 G	
154 P	460 C	-13:28195717 2108077490 C	
154	461 C	-13:28195716 2108077489 C	
154	462 T	-13:28195715 2108077488 T	
155 N	463 A	-13:28195714 2108077487 A	
155	464 A	-13:28195713 2108077486 A	
155	465 T	-13:28195712 2108077485 T	
156 P	466 C	-13:28195711 2108077484 C	
156	467 C	-13:28195710 2108077483 C	
156	468 A	-13:28195709 2108077482 A	
157 V	469 G	-13:28195708 2108077481 G	
157	470 T	-13:28195707 2108077480 T	
157	471 T	-13:28195706 2108077479 T	
158 F	472 T	-13:28195705 2108077478 T	
158	473 T	-13:28195704 2108077477 T	
158	474 C	-13:28195703 2108077476 C	
159 L	475 T	-13:28195702 2108077475 T	
159	476 T	-13:28195701 2108077474 T	
159	477 G	-13:28195700 2108077473 G	
160 E	478 G	-13:28195699 2108077472 G	
160	479 A	-13:28195698 2108077471 A	
160	480 G	-13:28195697 2108077470 G	
161 Q	481 C	-13:28195696 2108077469 C	
161	482 A	-13:28195695 2108077468 A	
161	483 G	-13:28195694 2108077467 G	
162 K	484 A	-13:28195693 2108077466 A	
162	485 A	-13:28195692 2108077465 A	
162	486 G	-13:28195691 2108077464 G	
163 K	487 A	-13:28195690 2108077463 A	
163	488 A	-13:28195689 2108077462 A	
163	489 A	-13:28195688 2108077461 A	
164 M	490 A	-13:28195687 2108077460 A	
164	491 T	-13:28195686 2108077459 T	
164	492 G	-13:28195685 2108077458 G	
165 L	493 T	-13:28195684 2108077457 T	
165	494 T	-13:28195683 2108077456 T	
165	495 A	-13:28195682 2108077455 A	
166 K	496 A	-13:28195681 2108077454 A	
166	497 A	-13:28195680 2108077453 A	
166	498 A	-13:28195679 2108077452 A	
167 S	499 A	-13:28195678 2108077451 A	
167	500 G	-13:28195677 2108077450 G	
167	501 T	-13:28195676 2108077449 T	
168 G	502 G	-13:28195675 2108077448 G	
168	503 G	-13:28195674 2108077447 G	
168	504 C	-13:28195673 2108077446 C	
169 L	505 C	-13:28195672 2108077445 C	
169	506 T	-13:28195671 2108077444 T	
169	507 T	-13:28195670 2108077443 T	
170 N	508 A	-13:28195669 2108077442 A	
170	509 A	-13:28195668 2108077441 A	
170	510 C	-13:28195667 2108077440 C	
171 I	511 A	-13:28195666 2108077439 A	
171	512 T	-13:28195665 2108077438 A	
171	513 A	-13:28195664 2108077437 A	
172 A	514 G	-13:28195663 2108077436 G	
172	515 C	-13:28195662 2108077435 C	
172	516 C	-13:28195661 2108077434 C	
173 H	517 C	-13:28195660 2108077433 C	
173	518 A	-13:28195659 2108077432 A	
173	519 C	-13:28195658 2108077431 C	
174 F	520 T	-13:28195657 2108077430 T	
174	521 T	-13:28195656 2108077429 T	
174	522 T	-13:28195655 2108077428 T	
175 K	523 A	-13:28195654 2108077427 A	
175	524 A	-13:28195653 2108077426 A	
175	525 A	-13:28195652 2108077425 A	
176 Q	526 C	-13:28195651 2108077424 C	
176	527 A	-13:28195650 2108077423 A	
176	528 G	-13:28195649 2108077422 G	
177 H	529 C	-13:28195648 2108077421 C	
177	530 A	-13:28195647 2108077420 A	
177	531 T	-13:28195646 2108077419 T	
178 V	532 G	-13:28195523 2108077296 T	
178	533 T	-13:28195522 2108077295 A	
178	534 T	-13:28195521 2108077294 T	
179 S	535 A	-13:28195520 2108077293 A	
179	536 G	-13:28195519 2108077292 A	
179	537 T	-13:28195518 2108077291 T	
180 I	538 A	-13:28195517 2108077290 A	
180	539 T	-13:28195516 2108077289 A	
180	540 A	-13:28195515 2108077288 A	
181 I	541 A	-13:28195514 2108077287 A	
181	542 T	-13:28195513 2108077286 A	
181	543 A	-13:28195512 2108077285 A	
182	544  	-13:28195511 2108077284 A	
182	544  	-13:28195510 2108077283 A	
182	544  	-13:28195509 2108077282 A	
182	544  	-13:28195508 2108077281 A	
182	544  	-13:28195507 2108077280 A	
182	544  	-13:28195506 2108077279 A	
182 E	544 G	-13:28195505 2108077278 G	
182	545 A	-13:28195504 2108077277 A	
182	546 A	-13:28195503 2108077276 A	
183 K	547 A	-13:28195502 2108077275 A	
183	548 A	-13:28195501 2108077274 A	
183	549 A	-13:28195500 2108077273 A	
184 E	550 G	-13:28195499 2108077272 G	
184	551 A	-13:28195498 2108077271 A	
184	552 A	-13:28195497 2108077270 A	
185 T	553 A	-13:28195496 2108077269 A	
185	554 C	-13:28195495 2108077268 C	
185	555 A	-13:28195494 2108077267 A	
186 K	556 A	-13:28195493 2108077266 A	
186	557 A	-13:28195492 2108077265 A	
186	558 G	-13:28195491 2108077264 G	
187 E	559 G	-13:28195490 2108077263 G	
187	560 A	-13:28195489 2108077262 A	
187	561 G	-13:28195488 2108077261 G	
188 Y	562 T	-13:28195487 2108077260 T	
188	563 A	-13:28195486 2108077259 A	
188	564 C	-13:28195485 2108077258 C	
189 F	565 T	-13:28195484 2108077257 T	
189	566 T	-13:28195483 2108077256 T	
189	567 T	-13:28195482 2108077255 T	
190 E	568 G	-13:28195481 2108077254 C	
190	569 A	-13:28195480 2108077253 A	
190	570 G	-13:28195479 2108077252 G	
191 S	571 A	-13:28195478 2108077251 A	
191	572 G	-13:28195477 2108077250 G	
191	573 T	-13:28195476 2108077249 T	
192 W	574 T	-13:28195475 2108077248 T	
192	575 G	-13:28195474 2108077247 G	
192	576 G	-13:28195473 2108077246 G	
193 G	577 G	-13:28195472 2108077245 G	
193	578 G	-13:28195471 2108077244 G	
193	579 A	-13:28195470 2108077243 A	
194 E	580 G	-13:28195469 2108077242 G	
194	581 A	-13:28195468 2108077241 A	
194	582 A	-13:28195467 2108077240 A	
195 S	583 A	-13:28195466 2108077239 A	
195	584 G	-13:28195465 2108077238 G	
195	585 T	-13:28195464 2108077237 T	
196 G	586 G	-13:28195463 2108077236 G	
196	587 G	-13:28195462 2108077235 G	
196	588 A	-13:28195461 2108077234 A	
197 E	589 G	-13:28195460 2108077233 G	
197	590 A	-13:28195459 2108077232 A	
197	591 A	-13:28195458 2108077231 A	
198 K	592 A	-13:28195457 2108077230 A	
198	593 A	-13:28195456 2108077229 A	
198	594 A	-13:28195455 2108077228 A	
199 N	595 A	-13:28195454 2108077227 A	
199	596 A	-13:28195453 2108077226 A	
199	597 T	-13:28195452 2108077225 T	
200 V	598 G	-13:28195451 2108077224 G	
200	599 T	-13:28195450 2108077223 T	
200	600 G	-13:28195449 2108077222 G	
201 F	601 T	-13:28195448 2108077221 T	
201	602 T	-13:28195447 2108077220 T	
201	603 T	-13:28195446 2108077219 T	
202 E	604 G	-13:28195445 2108077218 G	
202	605 A	-13:28195444 2108077217 A	
202	606 A	-13:28195443 2108077216 A	
203 A	607 G	-13:28195442 2108077215 G	
203	608 C	-13:28195441 2108077214 C	
203	609 T	-13:28195440 2108077213 T	
204 L	610 C	-13:28195439 2108077212 C	
204	611 T	-13:28195438 2108077211 T	
204	612 T	-13:28195437 2108077210 T	
205 S	613 T	-13:28195436 2108077209 T	
205	614 C	-13:28195435 2108077208 C	
205	615 T	-13:28195434 2108077207 T	
206 E	616 G	-13:28195433 2108077206 G	
206	617 A	-13:28195432 2108077205 A	
206	618 G	-13:28195431 2108077204 G	
207 L	619 C	-13:28195430 2108077203 C	
207	620 T	-13:28195429 2108077202 T	
207	621 C	-13:28195428 2108077201 C	
208 I	622 A	-13:28195427 2108077200 A	
208	623 T	-13:28195426 2108077199 T	
208	624 A	-13:28195425 2108077198 A	
209 I	625 A	-13:28195424 2108077197 A	
209	626 T	-13:28195423 2108077196 T	
209	627 T	-13:28195422 2108077195 T	
210 L	628 T	-13:28195421 2108077194 T	
210	629 T	-13:28195420 2108077193 T	
210	630 A	-13:28195419 2108077192 A	
211 T	631 A	-13:28195418 2108077191 A	
211	632 C	-13:28195417 2108077190 C	
211	633 A	-13:28195416 2108077189 A	
212 A	634 G	-13:28195415 2108077188 G	
212	635 C	-13:28195414 2108077187 C	
212	636 T	-13:28195413 2108077186 T	
213 S	637 A	-13:28195412 2108077185 A	
213	638 G	-13:28195411 2108077184 G	
213	639 C	-13:28195410 2108077183 C	
214 H	640 C	-13:28195409 2108077182 C	
214	641 A	-13:28195408 2108077181 A	
214	642 C	-13:28195407 2108077180 C	
215 C	643 T	-13:28195406 2108077179 T	
215	644 G	-13:28195405 2108077178 G	
215	645 T	-13:28195404 2108077177 T	
216 L	646 T	-13:28195403 2108077176 T	
216	647 T	-13:28195402 2108077175 T	
216	648 G	-13:28195401 2108077174 G	
217 H	649 C	-13:28195400 2108077173 C	
217	650 A	-13:28195399 2108077172 A	
217	651 T	-13:28195398 2108077171 T	
218 G	652 G	-13:28195397 2108077170 G	
218	653 G	-13:28195396 2108077169 G	
218	654 A	-13:28195395 2108077168 A	
219 K	655 A	-13:28195394 2108077167 A	
219	656 A	-13:28195393 2108077166 A	
219	657 G	-13:28195392 2108077165 G	
220 E	658 G	-13:28195391 2108077164 G	
220	659 A	-13:28195390 2108077163 A	
220	660 A	-13:28195389 2108077162 A	
221 I	661 A	-13:28195388 2108077161 A	
221	662 T	-13:28195387 2108077160 T	
221	663 C	-13:28195386 2108077159 C	
222 R	664 A	-13:28195385 2108077158 A	
222	665 G	-13:28195384 2108077157 G	
222	666 A	-13:28195383 2108077156 A	
223 S	667 A	-13:28195382 2108077155 A	
223	668 G	-13:28195381 2108077154 G	
223	669 T	-13:28195380 2108077153 T	
224 Q	670 C	-13:28195379 2108077152 C	
224	671 A	-13:28195378 2108077151 A	
224	672 A	-13:28195377 2108077150 A	
225 L	673 C	-13:28195376 2108077149 C	
225	674 T	-13:28195375 2108077148 T	
225	675 C	-13:28195374 2108077147 C	
226 N	676 A	-13:28195373 2108077146 A	
226	677 A	-13:28195372 2108077145 A	
226	678 T	-13:28195371 2108077144 T	
227 E	679 G	-13:28195370 2108077143 G	
227	680 A	-13:28195369 2108077142 A	
227	681 A	-13:28195368 2108077141 A	
228 K	682 A	-13:28195367 2108077140 A	
228	683 A	-13:28195366 2108077139 A	
228	684 G	-13:28195365 2108077138 G	
229 V	685 G	-13:28195364 2108077137 G	
229	686 T	-13:28195363 2108077136 T	
229	687 A	-13:28195362 2108077135 A	
230 A	688 G	-13:28195361 2108077134 G	
230	689 C	-13:28195360 2108077133 C	
230	690 A	-13:28195359 2108077132 A	
231 Q	691 C	-13:28195358 2108077131 C	
231	692 A	-13:28195357 2108077130 A	
231	693 G	-13:28195356 2108077129 G	
232 L	694 C	-13:28195355 2108077128 C	
232	695 T	-13:28195354 2108077127 T	
232	696 G	-13:28195353 2108077126 G	
233 Y	697 T	-13:28195352 2108077125 T	
233	698 A	-13:28195351 2108077124 A	
233	699 T	-13:28195350 2108077123 T	
234 A	700 G	-13:28195349 2108077122 G	
234	701 C	-13:28195348 2108077121 C	
234	702 A	-13:28195347 2108077120 A	
235 D	703 G	-13:28195346 2108077119 G	
235	704 A	-13:28195345 2108077118 A	
235	705 T	-13:28195344 2108077117 T	
236 L	706 T	-13:28195343 2108077116 T	
236	707 T	-13:28195342 2108077115 T	
236	708 G	-13:28195341 2108077114 G	
237 D	709 G	-13:28195340 2108077113 G	
237	710 A	-13:28195339 2108077112 A	
237	711 T	-13:28195338 2108077111 T	
238 G	712 G	-13:28195337 2108077110 G	
238	713 G	-13:28195336 2108077109 G	
238	714 A	-13:28195335 2108077108 A	
239 G	715 G	-13:28195334 2108077107 G	
239	716 G	-13:28195333 2108077106 G	
239	717 T	-13:28195332 2108077105 T	
240 F	718 T	-13:28195331 2108077104 T	
240	719 T	-13:28195330 2108077103 T	
240	720 C	-13:28195329 2108077102 C	
241 S	721 A	-13:28195328 2108077101 A	
241	722 G	-13:28195327 2108077100 G	
241	723 C	-13:28195326 2108077099 C	
242 H	724 C	-13:28195325 2108077098 C	
242	725 A	-13:28195324 2108077097 A	
242	726 T	-13:28195323 2108077096 T	
243 A	727 G	-13:28195322 2108077095 G	
243	728 C	-13:28195321 2108077094 C	
243	729 A	-13:28195320 2108077093 A	
244 A	730 G	-13:28195319 2108077092 G	
244	731 C	-13:28195318 2108077091 C	
244	732 C	-13:28195317 2108077090 C	
245 W	733 T	-13:28195316 2108077089 T	
245	734 G	-13:28195315 2108077088 G	
245	735 G	-13:28195314 2108077087 G	
246 L	736 C	-13:28195313 2108077086 C	
246	737 T	-13:28195312 2108077085 T	
246	738 C	-13:28195311 2108077084 C	
247 L	739 T	-13:28195310 2108077083 T	
247	740 T	-13:28195309 2108077082 T	
247	741 A	-13:28195308 2108077081 A	
248 P	742 C	-13:28195307 2108077080 C	
248	743 C	-13:28195306 2108077079 C	
248	744 A	-13:28195305 2108077078 A	
249 G	745 G	-13:28195304 2108077077 G	
249	746 G	-13:28195303 2108077076 G	
249	747 T	-13:28195302 2108077075 T	
250 W	748 T	-13:28195301 2108077074 T	
250	749 G	-13:28195300 2108077073 G	
250	750 G	-13:28195299 2108077072 G	
251 L	751 C	-13:28195298 2108077071 C	
251	752 T	-13:28195297 2108077070 T	
251	753 G	-13:28195296 2108077069 G	
252 P	754 C	-13:28195295 2108077068 C	
252	755 C	-13:28195294 2108077067 C	
252	756 T	-13:28195293 2108077066 T	
253 L	757 T	-13:28195292 2108077065 T	
253	758 T	-13:28195291 2108077064 T	
253	759 G	-13:28195290 2108077063 G	
254 P	760 C	-13:28195289 2108077062 C	
254	761 C	-13:28195288 2108077061 C	
254	762 T	-13:28195287 2108077060 T	
255 S	763 A	-13:28195286 2108077059 A	
255	764 G	-13:28195285 2108077058 G	
255	765 T	-13:28195284 2108077057 T	
256 F	766 T	-13:28195283 2108077056 T	
256	767 T	-13:28195282 2108077055 T	
256	768 C	-13:28195281 2108077054 C	
257 R	769 A	-13:28195280 2108077053 A	
257	770 G	-13:28195279 2108077052 G	
257	771 A	-13:28195278 2108077051 A	
258 R	772 C	-13:28195277 2108077050 T	
258	773 G	-13:28195276 2108077049 G	
258	774 C	-13:28195275 2108077048 C	
259 R	775 A	-13:28195274 2108077047 A	
259	776 G	-13:28195273 2108077046 G	
259	777 G	-13:28195272 2108077045 G	
260 D	778 G	-13:28195271 2108077044 G	
260	779 A	-13:28195270 2108077043 A	
260	780 C	-13:28195269 2108077042 C	
261 R	781 A	-13:28195268 2108077041 A	
261	782 G	-13:28195267 2108077040 G	
261	783 A	-13:28195266 2108077039 A	
262 A	784 G	-13:28195265 2108077038 G	
262	785 C	-13:28195264 2108077037 C	
262	786 T	-13:28195263 2108077036 T	
263 H	787 C	-13:28195262 2108077035 C	
263	788 A	-13:28195261 2108077034 A	
263	789 T	-13:28195260 2108077033 T	
264 R	790 M	-13:28195259 2108077032 T	
264	791 G	-13:28195258 2108077031 G	
264	792 G	-13:28195257 2108077030 G	
265 E	793 G	-13:28195256 2108077029 G	
265	794 A	-13:28195255 2108077028 A	
265	795 A	-13:28195254 2108077027 A	
266 I	796 A	-13:28195253 2108077026 A	
266	797 T	-13:28195252 2108077025 T	
266	798 C	-13:28195251 2108077024 C	
267 K	799 A	-13:28195250 2108077023 A	
267	800 A	-13:28195249 2108077022 A	
267	801 G	-13:28195248 2108077021 G	
268 D	802 G	-13:28195247 2108077020 G	
268	803 A	-13:28195246 2108077019 A	
268	804 T	-13:28195245 2108077018 T	
269 I	805 A	-13:28195244 2108077017 A	
269	806 T	-13:28195243 2108077016 T	
269	807 T	-13:28195242 2108077015 T	
270 F	808 T	-13:28195241 2108077014 T	
270	809 T	-13:28195240 2108077013 T	
270	810 C	-13:28195239 2108077012 C	
271 Y	811 T	-13:28195238 2108077011 T	
271	812 A	-13:28195237 2108077010 A	
271	813 T	-13:28195236 2108077009 T	
272 K	814 A	-13:28195235 2108077008 A	
272	815 A	-13:28195234 2108077007 A	
272	816 G	-13:28195233 2108077006 G	
273 A	817 G	-13:28195232 2108077005 G	
273	818 C	-13:28195231 2108077004 C	
273	819 A	-13:28195230 2108077003 A	
274 I	820 A	-13:28195229 2108077002 A	
274	821 T	-13:28195228 2108077001 T	
274	822 C	-13:28195227 2108077000 C	
275 Q	823 C	-13:28195226 2108076999 C	
275	824 A	-13:28195225 2108076998 A	
275	825 G	-13:28195224 2108076997 G	
276 K	826 A	-13:28195223 2108076996 A	
276	827 A	-13:28195222 2108076995 A	
276	828 A	-13:28195221 2108076994 A	
277 R	829 C	-13:28195220 2108076993 C	
277	830 G	-13:28195219 2108076992 G	
277	831 C	-13:28195218 2108076991 C	
278 R	832 A	-13:28195217 2108076990 A	
278	833 G	-13:28195216 2108076989 G	
278	834 A	-13:28195215 2108076988 A	
279 Q	835 C	-13:28195214 2108076987 C	
279	836 A	-13:28195213 2108076986 A	
279	837 G	-13:28195212 2108076985 G	
280 S	838 T	-13:28195211 2108076984 T	
280	839 C	-13:28195210 2108076983 C	
280	840 T	-13:28195209 2108076982 T	
281 Q	841 C	-13:28195208 2108076981 C	
281	842 A	-13:28195207 2108076980 A	
281	843 A	-13:28195206 2108076979 A	
282 E	844 G	-13:28195205 2108076978 G	
282	845 A	-13:28195204 2108076977 A	
282	846 A	-13:28195203 2108076976 A	
283 K	847 A	-13:28195202 2108076975 A	
283	848 A	-13:28195201 2108076974 A	
283	849 A	-13:28195200 2108076973 A	
284 I	850 A	-13:28195199 2108076972 A	
284	851 T	-13:28195198 2108076971 T	
284	852 T	-13:28195197 2108076970 T	
285 D	853 G	-13:28195196 2108076969 G	
285	854 A	-13:28195195 2108076968 A	
285	855 T	-13:28195194 2108076967 T	
286 D	856 G	-13:28195193 2108076966 G	
286	857 A	-13:28195192 2108076965 A	
286	858 C	-13:28195191 2108076964 C	
287 I	859 A	-13:28195190 2108076963 A	
287	860 T	-13:28195189 2108076962 T	
287	861 T	-13:28195188 2108076961 T	
288 L	862 C	-13:28195187 2108076960 C	
288	863 T	-13:28195186 2108076959 T	
288	864 C	-13:28195185 2108076958 C	
289 Q	865 C	-13:28195184 2108076957 C	
289	866 A	-13:28195183 2108076956 A	
289	867 A	-13:28195182 2108076955 A	
290 T	868 A	-13:28195181 2108076954 A	
290	869 C	-13:28195180 2108076953 C	
290	870 T	-13:28195179 2108076952 T	
291 L	871 T	-13:28195178 2108076951 T	
291	872 T	-13:28195177 2108076950 T	
291	873 A	-13:28195176 2108076949 A	
292 L	874 C	-13:28195175 2108076948 C	
292	875 T	-13:28195174 2108076947 T	
292	876 A	-13:28195173 2108076946 A	
293 D	877 G	-13:28195172 2108076945 G	
293	878 A	-13:28195171 2108076944 A	
293	879 T	-13:28195170 2108076943 T	
294 A	880 G	-13:28195169 2108076942 G	
294	881 C	-13:28195168 2108076941 C	
294	882 T	-13:28195167 2108076940 T	
295 T	883 A	-13:28195166 2108076939 A	
295	884 C	-13:28195165 2108076938 C	
295	885 A	-13:28195164 2108076937 A	
296 Y	886 T	-13:28195163 2108076936 T	
296	887 A	-13:28195162 2108076935 A	
296	888 C	-13:28195161 2108076934 C	
297 K	889 A	-13:28195160 2108076933 A	
297	890 A	-13:28195159 2108076932 A	
297	891 G	-13:28195158 2108076931 G	
298 D	892 G	-13:28195157 2108076930 G	
298	893 A	-13:28195156 2108076929 A	
298	894 T	-13:28195155 2108076928 T	
299 G	895 G	-13:28195154 2108076927 G	
299	896 G	-13:28195153 2108076926 G	
299	897 G	-13:28195152 2108076925 G	
300 R	898 C	-13:28195151 2108076924 C	
300	899 G	-13:28195150 2108076923 G	
300	900 T	-13:28195149 2108076922 T	
301 P	901 C	-13:28195148 2108076921 C	
301	902 C	-13:28195147 2108076920 C	
301	903 T	-13:28195146 2108076919 T	
302 L	904 T	-13:28195145 2108076918 T	
302	905 T	-13:28195144 2108076917 T	
302	906 G	-13:28195143 2108076916 G	
303 T	907 A	-13:28195142 2108076915 A	
303	908 C	-13:28195141 2108076914 C	
303	909 T	-13:28195140 2108076913 T	
304 D	910 G	-13:28195139 2108076912 G	
304	911 A	-13:28195138 2108076911 A	
304	912 T	-13:28195137 2108076910 T	
305 D	913 G	-13:28195136 2108076909 G	
305	914 A	-13:28195135 2108076908 A	
305	915 T	-13:28195134 2108076907 T	
306 E	916 G	-13:28195133 2108076906 G	
306	917 A	-13:28195132 2108076905 A	
306	918 A	-13:28195131 2108076904 A	
307 V	919 G	-13:28195130 2108076903 G	
307	920 T	-13:28195129 2108076902 T	
307	921 A	-13:28195128 2108076901 A	
308 A	922 G	-13:28195127 2108076900 G	
308	923 C	-13:28195126 2108076899 C	
308	924 A	-13:28195125 2108076898 A	
309 G	925 G	-13:28195124 2108076897 G	
309	926 G	-13:28195123 2108076896 G	
309	927 G	-13:28195122 2108076895 G	
310 M	928 A	-13:28195121 2108076894 A	
310	929 T	-13:28195120 2108076893 T	
310	930 G	-13:28195119 2108076892 G	
311 L	931 C	-13:28195118 2108076891 C	
311	932 T	-13:28195117 2108076890 T	
311	933 T	-13:28195116 2108076889 T	
312 I	934 A	-13:28195115 2108076888 A	
312	935 T	-13:28195114 2108076887 T	
312	936 T	-13:28195113 2108076886 T	
313 G	937 G	-13:28195112 2108076885 G	
313	938 G	-13:28195111 2108076884 G	
313	939 A	-13:28195110 2108076883 A	
314 L	940 T	-13:28195109 2108076882 T	
314	941 T	-13:28195108 2108076881 T	
314	942 A	-13:28195107 2108076880 A	
315 L	943 C	-13:28195106 2108076879 C	
315	944 T	-13:28195105 2108076878 T	
315	945 C	-13:28195104 2108076877 C	
316 L	946 T	-13:28195103 2108076876 T	
316	947 T	-13:28195102 2108076875 T	
316	948 G	-13:28195101 2108076874 G	
317 A	949 G	-13:28195100 2108076873 G	
317	950 C	-13:28195099 2108076872 C	
317	951 A	-13:28195098 2108076871 A	
318 G	952 G	-13:28195097 2108076870 G	
318	953 G	-13:28195096 2108076869 G	
318	954 G	-13:28195095 2108076868 G	
319 Q	955 C	-13:28195094 2108076867 C	
319	956 A	-13:28195093 2108076866 A	
319	957 G	-13:28195092 2108076865 G	
320 H	958 C	-13:28195091 2108076864 C	
320	959 A	-13:28195090 2108076863 A	
320	960 T	-13:28195089 2108076862 T	
321 T	961 A	-13:28195088 2108076861 T	
321	962 C	-13:28195087 2108076860 C	
321	963 A	-13:28195086 2108076859 A	
322 S	964 T	-13:28195085 2108076858 T	
322	965 C	-13:28195084 2108076857 C	
322	966 C	-13:28195083 2108076856 C	
323 S	967 T	-13:28195082 2108076855 T	
323	968 C	-13:28195081 2108076854 C	
323	969 A	-13:28195080 2108076853 A	
324 T	970 A	-13:28195079 2108076852 A	
324	971 C	-13:28195078 2108076851 C	
324	972 T	-13:28195077 2108076850 T	
325 T	973 A	-13:28195076 2108076849 A	
325	974 C	-13:28195075 2108076848 C	
325	975 T	-13:28195074 2108076847 T	
326 S	976 A	-13:28195073 2108076846 A	
326	977 G	-13:28195072 2108076845 G	
326	978 T	-13:28195071 2108076844 T	
327 A	979 G	-13:28195070 2108076843 G	
327	980 C	-13:28195069 2108076842 C	
327	981 T	-13:28195068 2108076841 T	
328 W	982 T	-13:28195067 2108076840 T	
328	983 G	-13:28195066 2108076839 G	
328	984 G	-13:28195065 2108076838 G	
329 M	985 A	-13:28195064 2108076837 A	
329	986 T	-13:28195063 2108076836 T	
329	987 G	-13:28195062 2108076835 G	
330 G	988 G	-13:28195061 2108076834 G	
330	989 G	-13:28195060 2108076833 A	
330	990 C	-13:28195059 2108076832 C	
331 F	991 T	-13:28195058 2108076831 T	
331	992 T	-13:28195057 2108076830 T	
331	993 C	-13:28195056 2108076829 C	
332 F	994 T	-13:28195055 2108076828 T	
332	995 T	-13:28195054 2108076827 T	
332	996 T	-13:28195053 2108076826 T	
333 L	997 T	-13:28195052 2108076825 T	
333	998 T	-13:28195051 2108076824 T	
333	999 G	-13:28195050 2108076823 G	
334 A	1000 G	-13:28195049 2108076822 G	
334	1001 C	-13:28195048 2108076821 C	
334	1002 C	-13:28195047 2108076820 C	
335 R	1003 A	-13:28195046 2108076819 A	
335	1004 G	-13:28195045 2108076818 G	
335	1005 A	-13:28195044 2108076817 A	
336 D	1006 G	-13:28195043 2108076816 G	
336	1007 A	-13:28195042 2108076815 A	
336	1008 C	-13:28195041 2108076814 C	
337 K	1009 A	-13:28195040 2108076813 A	
337	1010 A	-13:28195039 2108076812 A	
337	1011 A	-13:28195038 2108076811 A	
338 T	1012 A	-13:28195037 2108076810 A	
338	1013 C	-13:28195036 2108076809 C	
338	1014 A	-13:28195035 2108076808 A	
339 L	1015 C	-13:28195034 2108076807 C	
339	1016 T	-13:28195033 2108076806 T	
339	1017 T	-13:28195032 2108076805 T	
340 Q	1018 C	-13:28195031 2108076804 C	
340	1019 A	-13:28195030 2108076803 A	
340	1020 A	-13:28195029 2108076802 A	
341 K	1021 A	-13:28195028 2108076801 G	
341	1022 A	-13:28195027 2108076800 A	
341	1023 A	-13:28195026 2108076799 A	
342 K	1024 A	-13:28195025 2108076798 A	
342	1025 A	-13:28195024 2108076797 A	
342	1026 A	-13:28195023 2108076796 A	
343 C	1027 T	-13:28195022 2108076795 T	
343	1028 G	-13:28195021 2108076794 G	
343	1029 T	-13:28195020 2108076793 T	
344 Y	1030 T	-13:28195019 2108076792 T	
344	1031 A	-13:28195018 2108076791 A	
344	1032 T	-13:28195017 2108076790 T	
345 L	1033 T	-13:28195016 2108076789 T	
345	1034 T	-13:28195015 2108076788 T	
345	1035 A	-13:28195014 2108076787 A	
346 E	1036 G	-13:28195013 2108076786 G	
346	1037 A	-13:28195012 2108076785 A	
346	1038 A	-13:28195011 2108076784 A	
347 Q	1039 C	-13:28195010 2108076783 C	
347	1040 A	-13:28195009 2108076782 A	
347	1041 G	-13:28195008 2108076781 G	
348 K	1042 A	-13:28195007 2108076780 A	
348	1043 A	-13:28195006 2108076779 A	
348	1044 A	-13:28195005 2108076778 A	
349 T	1045 A	-13:28195004 2108076777 A	
349	1046 C	-13:28195003 2108076776 C	
349	1047 A	-13:28195002 2108076775 A	
350 V	1048 G	-13:28195001 2108076774 G	
350	1049 T	-13:28195000 2108076773 T	
350	1050 C	-13:28194999 2108076772 C	
351 C	1051 T	-13:28194998 2108076771 T	
351	1052 G	-13:28194997 2108076770 G	
351	1053 T	-13:28194996 2108076769 T	
352 G	1054 G	-13:28194995 2108076768 G	
352	1055 G	-13:28194994 2108076767 G	
352	1056 A	-13:28194993 2108076766 A	
353 E	1057 G	-13:28194992 2108076765 G	
353	1058 A	-13:28194991 2108076764 A	
353	1059 G	-13:28194990 2108076763 G	
354 N	1060 A	-13:28194989 2108076762 A	
354	1061 A	-13:28194988 2108076761 A	
354	1062 T	-13:28194987 2108076760 T	
355 L	1063 C	-13:28194986 2108076759 C	
355	1064 T	-13:28194985 2108076758 T	
355	1065 G	-13:28194984 2108076757 G	
356 P	1066 C	-13:28194983 2108076756 C	
356	1067 C	-13:28194982 2108076755 C	
356	1068 T	-13:28194981 2108076754 T	
357 P	1069 C	-13:28194980 2108076753 C	
357	1070 C	-13:28194979 2108076752 C	
357	1071 T	-13:28194978 2108076751 T	
358 L	1072 T	-13:28194977 2108076750 T	
358	1073 T	-13:28194976 2108076749 T	
358	1074 A	-13:28194975 2108076748 A	
359 T	1075 A	-13:28194974 2108076747 A	
359	1076 C	-13:28194973 2108076746 C	
359	1077 T	-13:28194972 2108076745 T	
360 Y	1078 T	-13:28194971 2108076744 T	
360	1079 A	-13:28194970 2108076743 A	
360	1080 T	-13:28194969 2108076742 T	
361 D	1081 G	-13:28194968 2108076741 G	
361	1082 A	-13:28194967 2108076740 A	
361	1083 C	-13:28194966 2108076739 C	
362 Q	1084 C	-13:28194965 2108076738 C	
362	1085 A	-13:28194964 2108076737 A	
362	1086 A	-13:28194963 2108076736 A	
363 L	1087 C	-13:28194962 2108076735 C	
363	1088 T	-13:28194961 2108076734 T	
363	1089 C	-13:28194960 2108076733 C	
364 K	1090 A	-13:28194959 2108076732 A	
364	1091 A	-13:28194958 2108076731 A	
364	1092 G	-13:28194957 2108076730 G	
365 D	1093 G	-13:28194956 2108076729 G	
365	1094 A	-13:28194955 2108076728 A	
365	1095 T	-13:28194954 2108076727 T	
366 L	1096 C	-13:28194953 2108076726 C	
366	1097 T	-13:28194952 2108076725 T	
366	1098 A	-13:28194951 2108076724 A	
367 N	1099 A	-13:28194950 2108076723 A	
367	1100 A	-13:28194949 2108076722 A	
367	1101 T	-13:28194948 2108076721 T	
368 L	1102 T	-13:28194947 2108076720 T	
368	1103 T	-13:28194946 2108076719 T	
368	1104 A	-13:28194945 2108076718 A	
369 L	1105 C	-13:28194944 2108076717 C	
369	1106 T	-13:28194943 2108076716 T	
369	1107 T	-13:28194942 2108076715 T	
370 D	1108 G	-13:28194941 2108076714 G	
370	1109 A	-13:28194940 2108076713 A	
370	1110 T	-13:28194939 2108076712 T	
371 R	1111 C	-13:28194938 2108076711 C	
371	1112 G	-13:28194937 2108076710 G	
371	1113 C	-13:28194936 2108076709 C	
372 C	1114 T	-13:28194935 2108076708 T	
372	1115 G	-13:28194934 2108076707 G	
372	1116 T	-13:28194933 2108076706 T	
373 I	1117 A	-13:28194932 2108076705 A	
373	1118 T	-13:28194931 2108076704 T	
373	1119 A	-13:28194930 2108076703 A	
374 K	1120 A	-13:28194929 2108076702 A	
374	1121 A	-13:28194928 2108076701 A	
374	1122 A	-13:28194927 2108076700 A	
375 E	1123 G	-13:28194926 2108076699 G	
375	1124 A	-13:28194925 2108076698 A	
375	1125 A	-13:28194924 2108076697 A	
376 T	1126 A	-13:28194923 2108076696 A	
376	1127 C	-13:28194922 2108076695 C	
376	1128 A	-13:28194921 2108076694 A	
377 L	1129 T	-13:28194920 2108076693 T	
377	1130 T	-13:28194919 2108076692 T	
377	1131 A	-13:28194918 2108076691 A	
378 R	1132 A	-13:28194917 2108076690 A	
378	1133 G	-13:28194916 2108076689 G	
378	1134 A	-13:28194915 2108076688 A	
379 L	1135 C	-13:28194914 2108076687 C	
379	1136 T	-13:28194913 2108076686 T	
379	1137 T	-13:28194912 2108076685 T	
380 R	1138 A	-13:28194911 2108076684 A	
380	1139 G	-13:28194910 2108076683 G	
380	1140 A	-13:28194909 2108076682 A	
381 P	1141 C	-13:28194908 2108076681 C	
381	1142 C	-13:28194907 2108076680 C	
381	1143 T	-13:28194906 2108076679 T	
382 P	1144 C	-13:28194905 2108076678 C	
382	1145 C	-13:28194904 2108076677 C	
382	1146 T	-13:28194903 2108076676 T	
383 I	1147 A	-13:28194902 2108076675 A	
383	1148 T	-13:28194901 2108076674 T	
383	1149 A	-13:28194900 2108076673 A	
384 M	1150 A	-13:28194899 2108076672 A	
384	1151 T	-13:28194898 2108076671 T	
384	1152 G	-13:28194897 2108076670 G	
385 I	1153 A	-13:28194896 2108076669 A	
385	1154 T	-13:28194895 2108076668 T	
385	1155 C	-13:28194894 2108076667 C	
386 M	1156 A	-13:28194893 2108076666 A	
386	1157 T	-13:28194892 2108076665 T	
386	1158 G	-13:28194891 2108076664 G	
387 M	1159 A	-13:28194890 2108076663 A	
387	1160 T	-13:28194889 2108076662 T	
387	1161 G	-13:28194888 2108076661 G	
388 R	1162 A	-13:28194887 2108076660 A	
388	1163 G	-13:28194886 2108076659 G	
388	1164 A	-13:28194885 2108076658 A	
389 M	1165 A	-13:28194884 2108076657 A	
389	1166 T	-13:28194883 2108076656 T	
389	1167 G	-13:28194882 2108076655 G	
390 A	1168 G	-13:28194881 2108076654 G	
390	1169 C	-13:28194880 2108076653 C	
390	1170 C	-13:28194879 2108076652 C	
391 R	1171 A	-13:28194878 2108076651 A	
391	1172 G	-13:28194877 2108076650 G	
391	1173 A	-13:28194876 2108076649 A	
392 T	1174 A	-13:28194875 2108076648 A	
392	1175 C	-13:28194874 2108076647 C	
392	1176 T	-13:28194873 2108076646 T	
393 P	1177 C	-13:28194872 2108076645 C	
393	1178 C	-13:28194871 2108076644 C	
393	1179 T	-13:28194870 2108076643 T	
394 Q	1180 C	-13:28194869 2108076642 C	
394	1181 A	-13:28194868 2108076641 A	
394	1182 G	-13:28194867 2108076640 G	
395 T	1183 A	-13:28194866 2108076639 A	
395	1184 C	-13:28194865 2108076638 C	
395	1185 T	-13:28194864 2108076637 T	
396 V	1186 G	-13:28194863 2108076636 G	
396	1187 T	-13:28194862 2108076635 T	
396	1188 G	-13:28194861 2108076634 G	
397 A	1189 G	-13:28194860 2108076633 G	
397	1190 C	-13:28194859 2108076632 T	
397	1191 A	-13:28194858 2108076631 A	
398 G	1192 G	-13:28194857 2108076630 G	
398	1193 G	-13:28194856 2108076629 G	
398	1194 G	-13:28194855 2108076628 G	
399 Y	1195 T	-13:28194854 2108076627 T	
399	1196 A	-13:28194853 2108076626 A	
399	1197 T	-13:28194852 2108076625 T	
400 T	1198 A	-13:28194851 2108076624 A	
400	1199 C	-13:28194850 2108076623 C	
400	1200 C	-13:28194849 2108076622 C	
401 I	1201 A	-13:28194848 2108076621 A	
401	1202 T	-13:28194847 2108076620 T	
401	1203 T	-13:28194846 2108076619 T	
402 P	1204 C	-13:28194845 2108076618 C	
402	1205 C	-13:28194844 2108076617 C	
402	1206 T	-13:28194843 2108076616 T	
403 P	1207 C	-13:28194842 2108076615 C	
403	1208 C	-13:28194841 2108076614 C	
403	1209 A	-13:28194840 2108076613 A	
404 G	1210 G	-13:28194839 2108076612 G	
404	1211 G	-13:28194838 2108076611 G	
404	1212 A	-13:28194837 2108076610 A	
405 H	1213 C	-13:28194836 2108076609 C	
405	1214 A	-13:28194835 2108076608 A	
405	1215 T	-13:28194834 2108076607 T	
406 Q	1216 C	-13:28194833 2108076606 C	
406	1217 A	-13:28194832 2108076605 A	
406	1218 G	-13:28194831 2108076604 G	
407 V	1219 G	-13:28194830 2108076603 G	
407	1220 T	-13:28194829 2108076602 T	
407	1221 G	-13:28194828 2108076601 G	
408 C	1222 T	-13:28194827 2108076600 T	
408	1223 G	-13:28194826 2108076599 G	
408	1224 T	-13:28194825 2108076598 T	
409 V	1225 G	-13:28194824 2108076597 G	
409	1226 T	-13:28194823 2108076596 T	
409	1227 T	-13:28194822 2108076595 T	
410 S	1228 T	-13:28194821 2108076594 T	
410	1229 C	-13:28194820 2108076593 C	
410	1230 T	-13:28194819 2108076592 T	
411 P	1231 C	-13:28194818 2108076591 C	
411	1232 C	-13:28194817 2108076590 C	
411	1233 C	-13:28194816 2108076589 C	
412 T	1234 A	-13:28194815 2108076588 A	
412	1235 C	-13:28194814 2108076587 C	
412	1236 T	-13:28194813 2108076586 T	
413 V	1237 G	-13:28194812 2108076585 G	
413	1238 T	-13:28194811 2108076584 T	
413	1239 C	-13:28194810 2108076583 C	
414 N	1240 A	-13:28194809 2108076582 A	
414	1241 A	-13:28194808 2108076581 A	
414	1242 T	-13:28194807 2108076580 T	
415 Q	1243 C	-13:28194806 2108076579 C	
415	1244 A	-13:28194805 2108076578 A	
415	1245 A	-13:28194804 2108076577 A	
416 R	1246 A	-13:28194803 2108076576 A	
416	1247 G	-13:28194802 2108076575 G	
416	1248 A	-13:28194801 2108076574 A	
417 L	1249 C	-13:28194800 2108076573 C	
417	1250 T	-13:28194799 2108076572 C	
417	1251 T	-13:28194798 2108076571 T	
418 K	1252 A	-13:28194797 2108076570 A	
418	1253 A	-13:28194796 2108076569 A	
418	1254 A	-13:28194795 2108076568 A	
419 D	1255 G	-13:28194794 2108076567 G	
419	1256 A	-13:28194793 2108076566 A	
419	1257 C	-13:28194792 2108076565 C	
420 S	1258 T	-13:28194791 2108076564 T	
420	1259 C	-13:28194790 2108076563 C	
420	1260 A	-13:28194789 2108076562 A	
421 W	1261 T	-13:28194788 2108076561 T	
421	1262 G	-13:28194787 2108076560 G	
421	1263 G	-13:28194786 2108076559 G	
422 V	1264 G	-13:28194785 2108076558 G	
422	1265 T	-13:28194784 2108076557 T	
422	1266 A	-13:28194783 2108076556 A	
423 E	1267 G	-13:28194782 2108076555 G	
423	1268 A	-13:28194781 2108076554 A	
423	1269 A	-13:28194780 2108076553 A	
424 R	1270 C	-13:28194779 2108076552 C	
424	1271 G	-13:28194778 2108076551 G	
424	1272 C	-13:28194777 2108076550 C	
425 L	1273 C	-13:28194776 2108076549 C	
425	1274 T	-13:28194775 2108076548 T	
425	1275 G	-13:28194774 2108076547 G	
426 D	1276 G	-13:28194773 2108076546 G	
426	1277 A	-13:28194772 2108076545 A	
426	1278 C	-13:28194771 2108076544 C	
427 F	1279 T	-13:28194770 2108076543 T	
427	1280 T	-13:28194769 2108076542 T	
427	1281 T	-13:28194768 2108076541 T	
428 N	1282 A	-13:28194767 2108076540 A	
428	1283 A	-13:28194766 2108076539 A	
428	1284 T	-13:28194765 2108076538 T	
429 P	1285 C	-13:28194764 2108076537 C	
429	1286 C	-13:28194763 2108076536 C	
429	1287 T	-13:28194762 2108076535 T	
430 D	1288 G	-13:28194761 2108076534 G	
430	1289 A	-13:28194760 2108076533 A	
430	1290 T	-13:28194759 2108076532 T	
431 R	1291 C	-13:28194758 2108076531 T	
431	1292 G	-13:28194757 2108076530 G	
431	1293 C	-13:28194756 2108076529 C	
432 Y	1294 T	-13:28194755 2108076528 T	
432	1295 A	-13:28194754 2108076527 A	
432	1296 C	-13:28194753 2108076526 C	
433 L	1297 T	-13:28194752 2108076525 T	
433	1298 T	-13:28194751 2108076524 T	
433	1299 A	-13:28194750 2108076523 A	
434 Q	1300 C	-13:28194749 2108076522 C	
434	1301 A	-13:28194748 2108076521 A	
434	1302 G	-13:28194747 2108076520 G	
435 D	1303 G	-13:28194746 2108076519 G	
435	1304 A	-13:28194745 2108076518 A	
435	1305 T	-13:28194744 2108076517 T	
436 N	1306 A	-13:28194743 2108076516 A	
436	1307 A	-13:28194742 2108076515 A	
436	1308 C	-13:28194741 2108076514 C	
437 P	1309 C	-13:28194740 2108076513 C	
437	1310 C	-13:28194739 2108076512 C	
437	1311 A	-13:28194738 2108076511 A	
438 A	1312 G	-13:28194737 2108076510 G	
438	1313 C	-13:28194736 2108076509 C	
438	1314 A	-13:28194735 2108076508 A	
439 S	1315 T	-13:28194734 2108076507 T	
439	1316 C	-13:28194733 2108076506 C	
439	1317 A	-13:28194732 2108076505 A	
440 G	1318 G	-13:28194731 2108076504 G	
440	1319 G	-13:28194730 2108076503 G	
440	1320 G	-13:28194729 2108076502 G	
441 E	1321 G	-13:28194728 2108076501 G	
441	1322 A	-13:28194727 2108076500 A	
441	1323 A	-13:28194726 2108076499 A	
442 K	1324 A	-13:28194725 2108076498 A	
442	1325 A	-13:28194724 2108076497 A	
442	1326 G	-13:28194723 2108076496 G	
443 F	1327 T	-13:28194722 2108076495 T	
443	1328 T	-13:28194721 2108076494 T	
443	1329 T	-13:28194720 2108076493 T	
444 A	1330 G	-13:28194719 2108076492 G	
444	1331 C	-13:28194718 2108076491 C	
444	1332 C	-13:28194717 2108076490 C	
445 Y	1333 T	-13:28194716 2108076489 T	
445	1334 A	-13:28194715 2108076488 A	
445	1335 T	-13:28194714 2108076487 T	
446 V	1336 G	-13:28194713 2108076486 G	
446	1337 T	-13:28194712 2108076485 T	
446	1338 G	-13:28194711 2108076484 G	
447 P	1339 C	-13:28194710 2108076483 C	
447	1340 C	-13:28194709 2108076482 C	
447	1341 A	-13:28194708 2108076481 A	
448 F	1342 T	-13:28194707 2108076480 T	
448	1343 T	-13:28194706 2108076479 T	
448	1344 T	-13:28194705 2108076478 T	
449 G	1345 G	-13:28194704 2108076477 G	
449	1346 G	-13:28194703 2108076476 G	
449	1347 A	-13:28194702 2108076475 A	
450 A	1348 G	-13:28194701 2108076474 G	
450	1349 C	-13:28194700 2108076473 C	
450	1350 T	-13:28194699 2108076472 T	
451 G	1351 G	-13:28194698 2108076471 G	
451	1352 G	-13:28194697 2108076470 G	
451	1353 G	-13:28194696 2108076469 G	
452 R	1354 C	-13:28194695 2108076468 T	
452	1355 G	-13:28194694 2108076467 G	
452	1356 T	-13:28194693 2108076466 T	
453 H	1357 C	-13:28194692 2108076465 C	
453	1358 A	-13:28194691 2108076464 A	
453	1359 T	-13:28194690 2108076463 T	
454 R	1360 C	-13:28194689 2108076462 C	
454	1361 G	-13:28194688 2108076461 G	
454	1362 T	-13:28194687 2108076460 T	
455 C	1363 T	-13:28194686 2108076459 T	
455	1364 G	-13:28194685 2108076458 G	
455	1365 Y	-13:28194684 2108076457 A	
456 I	1366 A	-13:28194683 2108076456 A	
456	1367 T	-13:28194682 2108076455 T	
456	1368 T	-13:28194681 2108076454 T	
457 G	1369 G	-13:28194680 2108076453 G	
457	1370 G	-13:28194679 2108076452 G	
457	1371 G	-13:28194678 2108076451 G	
458 E	1372 G	-13:28194677 2108076450 G	
458	1373 A	-13:28194676 2108076449 A	
458	1374 A	-13:28194675 2108076448 A	
459 N	1375 A	-13:28194674 2108076447 A	
459	1376 A	-13:28194673 2108076446 A	
459	1377 T	-13:28194672 2108076445 T	
460 F	1378 T	-13:28194671 2108076444 T	
460	1379 T	-13:28194670 2108076443 T	
460	1380 T	-13:28194669 2108076442 T	
461 A	1381 G	-13:28194668 2108076441 G	
461	1382 C	-13:28194667 2108076440 C	
461	1383 C	-13:28194666 2108076439 C	
462 Y	1384 T	-13:28194665 2108076438 T	
462	1385 A	-13:28194664 2108076437 A	
462	1386 T	-13:28194663 2108076436 T	
463 V	1387 G	-13:28194662 2108076435 G	
463	1388 T	-13:28194661 2108076434 T	
463	1389 T	-13:28194660 2108076433 T	
464 Q	1390 C	-13:28194659 2108076432 C	
464	1391 A	-13:28194658 2108076431 A	
464	1392 A	-13:28194657 2108076430 A	
465 I	1393 A	-13:28194656 2108076429 A	
465	1394 T	-13:28194655 2108076428 T	
465	1395 T	-13:28194654 2108076427 T	
466 K	1396 A	-13:28194653 2108076426 A	
466	1397 A	-13:28194652 2108076425 A	
466	1398 G	-13:28194651 2108076424 G	
467 T	1399 A	-13:28194650 2108076423 A	
467	1400 C	-13:28194649 2108076422 C	
467	1401 A	-13:28194648 2108076421 A	
468 I	1402 A	-13:28194647 2108076420 A	
468	1403 T	-13:28194646 2108076419 T	
468	1404 T	-13:28194645 2108076418 T	
469 W	1405 T	-13:28194644 2108076417 T	
469	1406 G	-13:28194643 2108076416 G	
469	1407 G	-13:28194642 2108076415 G	
470 S	1408 T	-13:28194641 2108076414 T	
470	1409 C	-13:28194640 2108076413 C	
470	1410 C	-13:28194639 2108076412 C	
471 T	1411 A	-13:28194638 2108076411 A	
471	1412 C	-13:28194637 2108076410 C	
471	1413 T	-13:28194636 2108076409 T	
472 M	1414 A	-13:28194635 2108076408 A	
472	1415 T	-13:28194634 2108076407 T	
472	1416 G	-13:28194633 2108076406 G	
473 L	1417 C	-13:28194632 2108076405 C	
473	1418 T	-13:28194631 2108076404 T	
473	1419 T	-13:28194630 2108076403 T	
474 R	1420 C	-13:28194629 2108076402 C	
474	1421 G	-13:28194628 2108076401 G	
474	1422 T	-13:28194627 2108076400 T	
475 L	1423 T	-13:28194626 2108076399 T	
475	1424 T	-13:28194625 2108076398 T	
475	1425 A	-13:28194624 2108076397 A	
476 Y	1426 T	-13:28194623 2108076396 T	
476	1427 A	-13:28194622 2108076395 A	
476	1428 T	-13:28194621 2108076394 T	
477 E	1429 G	-13:28194620 2108076393 G	
477	1430 A	-13:28194619 2108076392 A	
477	1431 A	-13:28194618 2108076391 A	
478 F	1432 T	-13:28194617 2108076390 T	
478	1433 T	-13:28194616 2108076389 T	
478	1434 T	-13:28194615 2108076388 T	
479 D	1435 G	-13:28194614 2108076387 G	
479	1436 A	-13:28194613 2108076386 A	
479	1437 T	-13:28194612 2108076385 T	
480 L	1438 C	-13:28194611 2108076384 C	
480	1439 T	-13:28194610 2108076383 T	
480	1440 C	-13:28194609 2108076382 C	
481 I	1441 A	-13:28194608 2108076381 A	
481	1442 T	-13:28194607 2108076380 T	
481	1443 T	-13:28194606 2108076379 T	
482 D	1444 G	-13:28194605 2108076378 G	
482	1445 A	-13:28194604 2108076377 A	
482	1446 T	-13:28194603 2108076376 T	
483 G	1447 G	-13:28194602 2108076375 G	
483	1448 G	-13:28194601 2108076374 G	
483	1449 A	-13:28194600 2108076373 A	
484 Y	1450 T	-13:28194599 2108076372 T	
484	1451 A	-13:28194598 2108076371 A	
484	1452 T	-13:28194597 2108076370 T	
485 F	1453 T	-13:28194596 2108076369 T	
485	1454 T	-13:28194595 2108076368 T	
485	1455 T	-13:28194594 2108076367 T	
486 P	1456 C	-13:28194593 2108076366 C	
486	1457 C	-13:28194592 2108076365 C	
486	1458 C	-13:28194591 2108076364 C	
487 T	1459 A	-13:28194590 2108076363 A	
487	1460 C	-13:28194589 2108076362 T	
487	1461 C	-13:28194588 2108076361 C	
488 V	1462 G	-13:28194587 2108076360 G	
488	1463 T	-13:28194586 2108076359 T	
488	1464 G	-13:28194585 2108076358 G	
489 N	1465 A	-13:28194584 2108076357 A	
489	1466 A	-13:28194583 2108076356 A	
489	1467 T	-13:28194582 2108076355 T	
490 Y	1468 T	-13:28194581 2108076354 T	
490	1469 A	-13:28194580 2108076353 A	
490	1470 T	-13:28194579 2108076352 T	
491 T	1471 A	-13:28194578 2108076351 A	
491	1472 C	-13:28194577 2108076350 C	
491	1473 A	-13:28194576 2108076349 A	
492 T	1474 A	-13:28194575 2108076348 A	
492	1475 C	-13:28194574 2108076347 C	
492	1476 T	-13:28194573 2108076346 T	
493 M	1477 A	-13:28194572 2108076345 A	
493	1478 T	-13:28194571 2108076344 T	
493	1479 G	-13:28194570 2108076343 G	
494 I	1480 A	-13:28194569 2108076342 A	
494	1481 T	-13:28194568 2108076341 T	
494	1482 T	-13:28194567 2108076340 T	
495 H	1483 C	-13:28194566 2108076339 C	
495	1484 A	-13:28194565 2108076338 A	
495	1485 C	-13:28194564 2108076337 C	
496 T	1486 A	-13:28194563 2108076336 A	
496	1487 C	-13:28194562 2108076335 C	
496	1488 C	-13:28194561 2108076334 C	
497 P	1489 C	-13:28194560 2108076333 C	
497	1490 C	-13:28194559 2108076332 C	
497	1491 T	-13:28194558 2108076331 T	
498 E	1492 G	-13:28194557 2108076330 G	
498	1493 A	-13:28194556 2108076329 A	
498	1494 A	-13:28194555 2108076328 A	
499 N	1495 A	-13:28194554 2108076327 A	
499	1496 A	-13:28194553 2108076326 A	
499	1497 C	-13:28194552 2108076325 C	
500 P	1498 C	-13:28194551 2108076324 C	
500	1499 C	-13:28194550 2108076323 C	
500	1500 A	-13:28194549 2108076322 A	
501 V	1501 G	-13:28194548 2108076321 C	
501	1502 T	-13:28194547 2108076320 T	
501	1503 T	-13:28194546 2108076319 T	
502 I	1504 A	-13:28194545 2108076318 A	
502	1505 T	-13:28194544 2108076317 T	
502	1506 C	-13:28194543 2108076316 C	
503 R	1507 C	-13:28194542 2108076315 C	
503	1508 G	-13:28194541 2108076314 A	
503	1509 T	-13:28194540 2108076313 T	
504 Y	1510 T	-13:28194539 2108076312 T	
504	1511 A	-13:28194538 2108076311 A	
504	1512 C	-13:28194537 2108076310 C	
505 K	1513 A	-13:28194536 2108076309 A	
505	1514 A	-13:28194535 2108076308 A	
505	1515 A	-13:28194534 2108076307 A	
506 R	1516 C	-13:28194533 2108076306 C	
506	1517 G	-13:28194532 2108076305 G	
506	1518 A	-13:28194531 2108076304 A	
507 R	1519 A	-13:28194530 2108076303 A	
507	1520 G	-13:28194529 2108076302 G	
507	1521 A	-13:28194528 2108076301 A	
508 S	1522 T	-13:28194527 2108076300 T	
508	1523 C	-13:28194526 2108076299 C	
508	1524 A	-13:28194525 2108076298 A	
509 K	1525 A	-13:28194524 2108076297 A	
509	1526 A	-13:28194523 2108076296 A	
509	1527 A	-13:28194522 2108076295 A	
>ENSP00000378011 
1 M	1 A	-7:91709385 1324105001 A	M
1	2 T	-7:91709384 1324105000 T	
1	3 G	-7:91709383 1324104999 G	
2 G	4 G	-7:91709382 1324104998 G	G
2	5 G	-7:91709381 1324104997 G	
2	6 A	-7:91709380 1324104996 A	
3 N	7 A	-7:91709379 1324104995 A	N
3	8 A	-7:91709378 1324104994 A	
3	9 T	-7:91709377 1324104993 T	
4 P	10 C	-7:91709376 1324104992 C	P
4	11 C	-7:91709375 1324104991 C	
4	12 A	-7:91709374 1324104990 A	
5 E	13 G	-7:91709373 1324104989 G	E
5	14 A	-7:91709372 1324104988 A	
5	15 A	-7:91709371 1324104987 A	
6 N	16 A	-7:91709370 1324104986 A	N
6	17 A	-7:91709369 1324104985 A	
6	18 C	-7:91709368 1324104984 C	
7 I	19 A	-7:91709367 1324104983 A	I
7	20 T	-7:91709366 1324104982 T	
7	21 A	-7:91709365 1324104981 A	
8 E	22 G	-7:91709364 1324104980 G	E
8	23 A	-7:91709363 1324104979 A	
8	24 A	-7:91709362 1324104978 A	
9 D	25 G	-7:91709361 1324104977 G	D
9	26 A	-7:91709360 1324104976 A	
9	27 T	-7:91709359 1324104975 T	
10 A	28 G	-7:91709358 1324104974 G	A
10	29 C	-7:91709357 1324104973 C	
10	30 A	-7:91709356 1324104972 A	
11 Y	31 T	-7:91709355 1324104971 T	Y
11	32 A	-7:91709354 1324104970 A	
11	33 T	-7:91709353 1324104969 T	
12 V	34 G	-7:91709352 1324104968 G	V
12	35 T	-7:91709351 1324104967 T	
12	36 T	-7:91709350 1324104966 T	
13 A	37 G	-7:91709349 1324104965 G	A
13	38 C	-7:91709348 1324104964 C	
13	39 T	-7:91709347 1324104963 T	
14 V	40 G	-7:91709346 1324104962 G	V
14	41 T	-7:91709345 1324104961 T	
14	42 T	-7:91709344 1324104960 T	
15 I	43 A	-7:91709343 1324104959 A	I
15	44 T	-7:91709342 1324104958 T	
15	45 T	-7:91709341 1324104957 T	
16 R	46 C	-7:91709340 1324104956 C	R
16	47 G	-7:91709339 1324104955 G	
16	48 T	-7:91709338 1324104954 T	
17 P	49 C	-7:91709337 1324104953 C	P
17	50 C	-7:91709336 1324104952 C	
17	51 A	-7:91709335 1324104951 A	
18 K	52 A	-7:91709334 1324104950 A	K
18	53 A	-7:91709333 1324104949 A	
18	54 G	-7:91709332 1324104948 G	
19 N	55 A	-7:91709331 1324104947 A	N
19	56 A	-7:91709330 1324104946 A	
19	57 T	-7:91709329 1324104945 T	
20 T	58 A	-7:91709328 1324104944 A	T
20	59 C	-7:91709327 1324104943 C	
20	60 T	-7:91709326 1324104942 T	
21 A	61 G	-7:91709325 1324104941 G	A
21	62 C	-7:91709324 1324104940 C	
21	63 C	-7:91709323 1324104939 C	
22 S	64 A	-7:91709322 1324104938 A	S
22	65 G	-7:91709321 1324104937 G	
22	66 T	-7:91709320 1324104936 T	
23 L	67 C	-7:91709319 1324104935 C	L
23	68 T	-7:91709318 1324104934 T	
23	69 C	-7:91709317 1324104933 C	
24 N	70 A	-7:91709316 1324104932 A	N
24	71 A	-7:91709315 1324104931 A	
24	72 T	-7:91709314 1324104930 T	
25 S	73 T	-7:91709313 1324104929 T	S
25	74 C	-7:91709312 1324104928 C	
25	75 T	-7:91709311 1324104927 T	
26 R	76 C	-7:91709310 1324104926 C	R
26	77 G	-7:91709309 1324104925 G	
26	78 G	-7:91709308 1324104924 G	
27 E	79 G	-7:91709307 1324104923 G	E
27	80 A	-7:91709306 1324104922 A	
27	81 A	-7:91709305 1324104921 A	
28 Y	82 T	-7:91709304 1324104920 T	Y
28	83 A	-7:91709303 1324104919 A	
28	84 C	-7:91709302 1324104918 C	
29 R	85 A	-7:91709301 1324104917 A	R
29	86 G	-7:91709300 1324104916 G	
29	87 A	-7:91709299 1324104915 A	
30 A	88 G	-7:91709298 1324104914 G	A
30	89 C	-7:91709297 1324104913 C	
30	90 T	-7:91709296 1324104912 T	
31 K	91 A	-7:91709295 1324104911 A	K
31	92 A	-7:91709294 1324104910 A	
31	93 G	-7:91709293 1324104909 G	
32 S	94 T	-7:91709292 1324104908 T	S
32	95 C	-7:91709291 1324104907 C	
32	96 A	-7:91709290 1324104906 A	
33 Y	97 T	-7:91709289 1324104905 T	Y
33	98 A	-7:91709288 1324104904 A	
33	99 T	-7:91709287 1324104903 T	
34 E	100 G	-7:91709286 1324104902 G	E
34	101 A	-7:91709285 1324104901 A	
34	102 A	-7:91709284 1324104900 A	
35 I	103 A	-7:91708402 1324104018 A	I
35	104 T	-7:91708401 1324104017 T	
35	105 T	-7:91708400 1324104016 T	
36 L	106 T	-7:91708399 1324104015 T	L
36	107 T	-7:91708398 1324104014 T	
36	108 G	-7:91708397 1324104013 G	
37 L	109 T	-7:91708396 1324104012 T	L
37	110 T	-7:91708395 1324104011 T	
37	111 G	-7:91708394 1324104010 G	
38 H	112 C	-7:91708393 1324104009 C	H
38	113 A	-7:91708392 1324104008 A	
38	114 T	-7:91708391 1324104007 T	
39 E	115 G	-7:91708390 1324104006 G	E
39	116 A	-7:91708389 1324104005 A	
39	117 A	-7:91708388 1324104004 A	
40 V	118 G	-7:91708387 1324104003 G	V
40	119 T	-7:91708386 1324104002 T	
40	120 T	-7:91708385 1324104001 T	
41 P	121 C	-7:91708384 1324104000 C	P
41	122 C	-7:91708383 1324103999 C	
41	123 C	-7:91708382 1324103998 C	
42 I	124 A	-7:91708381 1324103997 A	I
42	125 T	-7:91708380 1324103996 T	
42	126 T	-7:91708379 1324103995 T	
43 E	127 G	-7:91708378 1324103994 G	E
43	128 A	-7:91708377 1324103993 A	
43	129 A	-7:91708376 1324103992 A	
44 G	130 G	-7:91708375 1324103991 G	G
44	131 G	-7:91708374 1324103990 G	
44	132 A	-7:91708373 1324103989 A	
45 Q	133 C	-7:91708372 1324103988 C	Q
45	134 A	-7:91708371 1324103987 A	
45	135 G	-7:91708370 1324103986 G	
46 K	136 A	-7:91708369 1324103985 A	K
46	137 A	-7:91708368 1324103984 A	
46	138 A	-7:91708367 1324103983 A	
47 K	139 A	-7:91708366 1324103982 A	K
47	140 A	-7:91708365 1324103981 A	
47	141 A	-7:91708364 1324103980 A	
48 K	142 A	-7:91708363 1324103979 A	K
48	143 A	-7:91708362 1324103978 A	
48	144 G	-7:91708361 1324103977 G	
49 R	145 A	-7:91708360 1324103976 A	R
49	146 G	-7:91708359 1324103975 G	
49	147 A	-7:91708358 1324103974 A	
50 K	148 A	-7:91708357 1324103973 A	K
50	149 A	-7:91708356 1324103972 A	
50	150 G	-7:91708355 1324103971 G	
51 K	151 A	-7:91708354 1324103970 A	K
51	152 A	-7:91708353 1324103969 A	
51	153 A	-7:91708352 1324103968 A	
52 V	154 G	-7:91708351 1324103967 G	V
52	155 T	-7:91708350 1324103966 T	
52	156 T	-7:91708349 1324103965 T	
53 L	157 T	-7:91708348 1324103964 T	L
53	158 T	-7:91708347 1324103963 T	
53	159 A	-7:91708346 1324103962 A	
54 L	160 T	-7:91708345 1324103961 T	L
54	161 T	-7:91708344 1324103960 T	
54	162 G	-7:91708343 1324103959 G	
55 E	163 G	-7:91708342 1324103958 G	E
55	164 A	-7:91708341 1324103957 A	
55	165 A	-7:91708340 1324103956 A	
56 T	166 A	-7:91708339 1324103955 A	T
56	167 C	-7:91708338 1324103954 C	
56	168 G	-7:91708337 1324103953 G	
57 K	169 A	-7:91708336 1324103952 A	K
57	170 A	-7:91708335 1324103951 A	
57	171 A	-7:91708334 1324103950 A	
58 L	172 C	-7:91708333 1324103949 C	L
58	173 T	-7:91708332 1324103948 T	
58	174 T	-7:91708331 1324103947 T	
59 Q	175 C	-7:91708330 1324103946 C	Q
59	176 A	-7:91708329 1324103945 A	
59	177 A	-7:91708328 1324103944 A	
60 G	178 G	-7:91708327 1324103943 G	G
60	179 G	-7:91708326 1324103942 G	
60	180 C	-7:91708325 1324103941 C	
61 N	181 A	-7:91708324 1324103940 A	N
61	182 A	-7:91708323 1324103939 A	
61	183 C	-7:91708322 1324103938 C	
62 S	184 A	-7:91708321 1324103937 A	S
62	185 G	-7:91708320 1324103936 G	
62	186 T	-7:91708319 1324103935 T	
63 E	187 G	-7:91708318 1324103934 G	E
63	188 A	-7:91708317 1324103933 A	
63	189 A	-7:91708316 1324103932 A	
64 I	190 A	-7:91708315 1324103931 A	I
64	191 T	-7:91708314 1324103930 T	
64	192 A	-7:91708313 1324103929 A	
65 T	193 A	-7:91708312 1324103928 A	T
65	194 C	-7:91708311 1324103927 C	
65	195 A	-7:91708310 1324103926 A	
66 Q	196 C	-7:91708309 1324103925 C	Q
66	197 A	-7:91708308 1324103924 A	
66	198 A	-7:91708307 1324103923 A	
67 G	199 G	-7:91708306 1324103922 G	G
67	200 G	-7:91708305 1324103921 G	
67	201 C	-7:91708304 1324103920 C	
68 I	202 A	-7:91708303 1324103919 A	I
68	203 T	-7:91708302 1324103918 T	
68	204 A	-7:91708301 1324103917 A	
69 L	205 T	-7:91708300 1324103916 T	L
69	206 T	-7:91708299 1324103915 T	
69	207 G	-7:91708298 1324103914 G	
70 D	208 G	-7:91708297 1324103913 G	D
70	209 A	-7:91708296 1324103912 A	
70	210 T	-7:91708295 1324103911 T	
71 Y	211 T	-7:91708294 1324103910 T	Y
71	212 A	-7:91708293 1324103909 A	
71	213 C	-7:91708292 1324103908 C	
72 V	214 G	-7:91708291 1324103907 G	V
72	215 T	-7:91708290 1324103906 T	
72	216 A	-7:91708289 1324103905 A	
73 V	217 G	-7:91708288 1324103904 G	V
73	218 T	-7:91708287 1324103903 T	
73	219 A	-7:91708286 1324103902 A	
74 E	220 G	-7:91708285 1324103901 G	E
74	221 A	-7:91708284 1324103900 A	
74	222 A	-7:91708283 1324103899 A	
75 T	223 A	-7:91708282 1324103898 A	T
75	224 C	-7:91708281 1324103897 C	
75	225 C	-7:91708280 1324103896 C	
76 T	226 A	-7:91708279 1324103895 A	T
76	227 C	-7:91708278 1324103894 C	
76	228 C	-7:91708277 1324103893 C	
77 K	229 A	-7:91708276 1324103892 A	K
77	230 A	-7:91708275 1324103891 A	
77	231 A	-7:91708274 1324103890 A	
78 P	232 C	-7:91708273 1324103889 C	P
78	233 C	-7:91708272 1324103888 C	
78	234 A	-7:91708271 1324103887 A	
79 I	235 A	-7:91708270 1324103886 A	I
79	236 T	-7:91708269 1324103885 T	
79	237 T	-7:91708268 1324103884 T	
80 S	238 T	-7:91708267 1324103883 T	S
80	239 C	-7:91708266 1324103882 C	
80	240 T	-7:91708265 1324103881 T	
81 P	241 C	-7:91708264 1324103880 C	P
81	242 C	-7:91708263 1324103879 C	
81	243 T	-7:91708262 1324103878 T	
82 A	244 G	-7:91708261 1324103877 G	A
82	245 C	-7:91708260 1324103876 C	
82	246 A	-7:91708259 1324103875 A	
83 N	247 A	-7:91708258 1324103874 A	N
83	248 A	-7:91708257 1324103873 A	
83	249 C	-7:91708256 1324103872 C	
84 Q	250 C	-7:91708255 1324103871 C	Q
84	251 A	-7:91708254 1324103870 A	
84	252 G	-7:91708253 1324103869 G	
85 G	253 G	-7:91708252 1324103868 G	G
85	254 G	-7:91708251 1324103867 G	
85	255 T	-7:91708250 1324103866 T	
86 I	256 A	-7:91708249 1324103865 A	I
86	257 T	-7:91708248 1324103864 T	
86	258 C	-7:91708247 1324103863 C	
87 R	259 A	-7:91708246 1324103862 A	R
87	260 G	-7:91708245 1324103861 G	
87	261 A	-7:91708244 1324103860 A	
88 G	262 G	-7:91708243 1324103859 G	G
88	263 G	-7:91705009 1324100625 G	
88	264 A	-7:91705008 1324100624 A	
89 K	265 A	-7:91705007 1324100623 A	K
89	266 A	-7:91705006 1324100622 A	
89	267 A	-7:91705005 1324100621 A	
90 R	268 C	-7:91705004 1324100620 C	R
90	269 G	-7:91705003 1324100619 G	
90	270 A	-7:91705002 1324100618 A	
91 V	271 G	-7:91705001 1324100617 G	V
91	272 T	-7:91705000 1324100616 T	
91	273 T	-7:91704999 1324100615 T	
92 V	274 G	-7:91704998 1324100614 G	V
92	275 T	-7:91704997 1324100613 T	
92	276 A	-7:91704996 1324100612 A	
93 L	277 C	-7:91704995 1324100611 C	L
93	278 T	-7:91704994 1324100610 T	
93	279 A	-7:91704993 1324100609 A	
94 M	280 A	-7:91704992 1324100608 A	M
94	281 T	-7:91704991 1324100607 T	
94	282 G	-7:91704990 1324100606 G	
95 K	283 A	-7:91704989 1324100605 A	K
95	284 A	-7:91704988 1324100604 A	
95	285 A	-7:91704987 1324100603 A	
96 K	286 A	-7:91704986 1324100602 A	K
96	287 A	-7:91704985 1324100601 A	
96	288 A	-7:91704984 1324100600 A	
97 F	289 T	-7:91704983 1324100599 T	F
97	290 T	-7:91704982 1324100598 T	
97	291 T	-7:91704981 1324100597 T	
98 P	292 C	-7:91704980 1324100596 C	P
98	293 C	-7:91704979 1324100595 C	
98	294 T	-7:91704978 1324100594 T	
99 L	295 C	-7:91704977 1324100593 C	L
99	296 T	-7:91704976 1324100592 T	
99	297 G	-7:91704975 1324100591 G	
100 D	298 G	-7:91704974 1324100590 G	D
100	299 A	-7:91704973 1324100589 A	
100	300 T	-7:91704972 1324100588 T	
101 G	301 G	-7:91704971 1324100587 G	G
101	302 G	-7:91704970 1324100586 G	
101	303 A	-7:91704969 1324100585 A	
102 E	304 G	-7:91704968 1324100584 G	E
102	305 A	-7:91704967 1324100583 A	
102	306 G	-7:91704966 1324100582 G	
103 K	307 A	-7:91704965 1324100581 A	K
103	308 A	-7:91704964 1324100580 A	
103	309 G	-7:91704963 1324100579 G	
104 M	310 A	-7:91704962 1324100578 A	M
104	311 T	-7:91704961 1324100577 T	
104	312 G	-7:91704960 1324100576 G	
105 G	313 G	-7:91704959 1324100575 G	G
105	314 G	-7:91704958 1324100574 G	
105	315 C	-7:91704957 1324100573 C	
106 R	316 A	-7:91704956 1324100572 A	R
106	317 G	-7:91704955 1324100571 G	
106	318 A	-7:91704954 1324100570 A	
107 E	319 G	-7:91704953 1324100569 G	E
107	320 A	-7:91704952 1324100568 A	
107	321 A	-7:91704951 1324100567 A	
108 A	322 G	-7:91704950 1324100566 G	A
108	323 C	-7:91704949 1324100565 C	
108	324 A	-7:91704948 1324100564 A	
109 S	325 T	-7:91704947 1324100563 T	S
109	326 C	-7:91704946 1324100562 C	
109	327 A	-7:91704945 1324100561 A	
110 L	328 T	-7:91704944 1324100560 T	L
110	329 T	-7:91704943 1324100559 T	
110	330 A	-7:91704942 1324100558 A	
111 F	331 T	-7:91704941 1324100557 T	F
111	332 T	-7:91704940 1324100556 T	
111	333 T	-7:91704939 1324100555 T	
112 I	334 A	-7:91704938 1324100554 A	I
112	335 T	-7:91704937 1324100553 T	
112	336 T	-7:91704936 1324100552 T	
113 V	337 G	-7:91704935 1324100551 G	V
113	338 T	-7:91704934 1324100550 T	
113	339 T	-7:91704933 1324100549 T	
114 P	340 C	-7:91704932 1324100548 C	P
114	341 C	-7:91704931 1324100547 C	
114	342 A	-7:91704930 1324100546 A	
115 S	343 T	-7:91704929 1324100545 T	S
115	344 C	-7:91704928 1324100544 C	
115	345 A	-7:91704927 1324100543 A	
116 V	346 G	-7:91704926 1324100542 G	V
116	347 T	-7:91704925 1324100541 T	
116	348 T	-7:91704924 1324100540 T	
117 V	349 G	-7:91704923 1324100539 G	V
117	350 T	-7:91704922 1324100538 T	
117	351 C	-7:91704921 1324100537 C	
118 K	352 A	-7:91704920 1324100536 A	K
118	353 A	-7:91704919 1324100535 A	
118	354 A	-7:91704918 1324100534 A	
119 D	355 G	-7:91704917 1324100533 G	D
119	356 A	-7:91703792 1324099408 A	
119	357 T	-7:91703791 1324099407 T	
120 N	358 A	-7:91703790 1324099406 A	N
120	359 A	-7:91703789 1324099405 A	
120	360 T	-7:91703788 1324099404 T	
121 T	361 A	-7:91703787 1324099403 A	T
121	362 C	-7:91703786 1324099402 C	
121	363 T	-7:91703785 1324099401 T	
122 K	364 A	-7:91703784 1324099400 A	K
122	365 A	-7:91703783 1324099399 A	
122	366 A	-7:91703782 1324099398 A	
123 Y	367 T	-7:91703781 1324099397 T	Y
123	368 A	-7:91703780 1324099396 A	
123	369 C	-7:91703779 1324099395 C	
124 T	370 A	-7:91703778 1324099394 A	T
124	371 C	-7:91703777 1324099393 C	
124	372 A	-7:91703776 1324099392 A	
125 Y	373 T	-7:91703775 1324099391 T	Y
125	374 A	-7:91703774 1324099390 A	
125	375 T	-7:91703773 1324099389 T	
126 T	376 A	-7:91703772 1324099388 A	T
126	377 C	-7:91703771 1324099387 C	
126	378 C	-7:91703770 1324099386 C	
127 P	379 C	-7:91703769 1324099385 C	P
127	380 C	-7:91703768 1324099384 C	
127	381 A	-7:91703767 1324099383 A	
128 G	382 G	-7:91703766 1324099382 G	G
128	383 G	-7:91703765 1324099381 G	
128	384 A	-7:91703764 1324099380 A	
129 C	385 T	-7:91703763 1324099379 T	C
129	386 G	-7:91703762 1324099378 G	
129	387 C	-7:91703761 1324099377 C	
130 P	388 C	-7:91703760 1324099376 C	P
130	389 C	-7:91703759 1324099375 C	
130	390 A	-7:91703758 1324099374 A	
131 I	391 A	-7:91703757 1324099373 A	I
131	392 T	-7:91703756 1324099372 T	
131	393 T	-7:91703755 1324099371 T	
132 F	394 T	-7:91703754 1324099370 T	F
132	395 T	-7:91703753 1324099369 T	
132	396 T	-7:91703752 1324099368 T	
133 Y	397 T	-7:91703751 1324099367 T	Y
133	398 A	-7:91703750 1324099366 A	
133	399 C	-7:91703749 1324099365 C	
134 C	400 T	-7:91703748 1324099364 T	C
134	401 G	-7:91703747 1324099363 G	
134	402 C	-7:91703746 1324099362 C	
135 L	403 T	-7:91703745 1324099361 T	L
135	404 T	-7:91703744 1324099360 T	
135	405 A	-7:91703743 1324099359 A	
136 Q	406 C	-7:91703742 1324099358 C	Q
136	407 A	-7:91703741 1324099357 A	
136	408 A	-7:91703740 1324099356 A	
137 D	409 G	-7:91703739 1324099355 G	D
137	410 A	-7:91703738 1324099354 A	
137	411 T	-7:91703737 1324099353 T	
138 I	412 A	-7:91703736 1324099352 A	I
138	413 T	-7:91703735 1324099351 T	
138	414 T	-7:91703734 1324099350 T	
139 M	415 A	-7:91703733 1324099349 A	M
139	416 T	-7:91703732 1324099348 T	
139	417 G	-7:91703731 1324099347 G	
140 R	418 C	-7:91703730 1324099346 C	R
140	419 G	-7:91703729 1324099345 G	
140	420 A	-7:91703728 1324099344 A	
141 V	421 G	-7:91703727 1324099343 G	V
141	422 T	-7:91703726 1324099342 T	
141	423 C	-7:91703725 1324099341 C	
142 C	424 T	-7:91703724 1324099340 T	C
142	425 G	-7:91703723 1324099339 G	
142	426 T	-7:91703722 1324099338 T	
143 S	427 A	-7:91703721 1324099337 A	S
143	428 G	-7:91703720 1324099336 G	
143	429 T	-7:91703719 1324099335 T	
144 E	430 G	-7:91703718 1324099334 G	E
144	431 A	-7:91703717 1324099333 A	
144	432 A	-7:91703716 1324099332 A	
145 S	433 T	-7:91703715 1324099331 T	S
145	434 C	-7:91703714 1324099330 C	
145	435 C	-7:91703713 1324099329 C	
146 S	436 A	-7:91703712 1324099328 A	S
146	437 G	-7:91703711 1324099327 G	
146	438 T	-7:91703710 1324099326 T	
147 T	439 A	-7:91703709 1324099325 A	T
147	440 C	-7:91703708 1324099324 C	
147	441 T	-7:91703707 1324099323 T	
148 H	442 C	-7:91703706 1324099322 C	H
148	443 A	-7:91703705 1324099321 A	
148	444 T	-7:91703704 1324099320 T	
149 F	445 T	-7:91703703 1324099319 T	F
149	446 T	-7:91703702 1324099318 T	
149	447 T	-7:91703701 1324099317 T	
150 A	448 G	-7:91703700 1324099316 G	A
150	449 C	-7:91703699 1324099315 C	
150	450 T	-7:91703698 1324099314 T	
151 T	451 A	-7:91703697 1324099313 A	T
151	452 C	-7:91703696 1324099312 C	
151	453 A	-7:91703695 1324099311 A	
152 L	454 C	-7:91703694 1324099310 C	L
152	455 T	-7:91703693 1324099309 T	
152	456 T	-7:91703692 1324099308 T	
153 T	457 A	-7:91703691 1324099307 A	T
153	458 C	-7:91703690 1324099306 C	
153	459 A	-7:91703689 1324099305 A	
154 A	460 G	-7:91703688 1324099304 G	A
154	461 C	-7:91703687 1324099303 C	
154	462 A	-7:91703686 1324099302 A	
155 R	463 A	-7:91703685 1324099301 A	R
155	464 G	-7:91703684 1324099300 G	
155	465 G	-7:91703683 1324099299 G	
156 M	466 A	-7:91703682 1324099298 A	M
156	467 T	-7:91703681 1324099297 T	
156	468 G	-7:91703680 1324099296 G	
157 L	469 T	-7:91703679 1324099295 T	L
157	470 T	-7:91703678 1324099294 T	
157	471 A	-7:91703677 1324099293 A	
158 I	472 A	-7:91703676 1324099292 A	I
158	473 T	-7:91703675 1324099291 T	
158	474 A	-7:91703674 1324099290 A	
159 A	475 G	-7:91703673 1324099289 G	A
159	476 C	-7:91703672 1324099288 C	
159	477 C	-7:91703671 1324099287 C	
160 L	478 T	-7:91703670 1324099286 T	L
160	479 T	-7:91703669 1324099285 T	
160	480 G	-7:91703668 1324099284 G	
161 D	481 G	-7:91703667 1324099283 G	D
161	482 A	-7:91703666 1324099282 A	
161	483 T	-7:91703665 1324099281 T	
162 K	484 A	-7:91703664 1324099280 A	K
162	485 A	-7:91703663 1324099279 A	
162	486 G	-7:91702896 1324098512 G	
163 W	487 T	-7:91702895 1324098511 T	W
163	488 G	-7:91702894 1324098510 G	
163	489 G	-7:91702893 1324098509 G	
164 L	490 T	-7:91702892 1324098508 T	L
164	491 T	-7:91702891 1324098507 T	
164	492 A	-7:91702890 1324098506 A	
165 D	493 G	-7:91702889 1324098505 G	D
165	494 A	-7:91702888 1324098504 A	
165	495 T	-7:91702887 1324098503 T	
166 E	496 G	-7:91702886 1324098502 G	E
166	497 A	-7:91702885 1324098501 A	
166	498 A	-7:91702884 1324098500 A	
167 R	499 C	-7:91702883 1324098499 C	R
167	500 G	-7:91702882 1324098498 G	
167	501 T	-7:91702881 1324098497 T	
168 H	502 C	-7:91702880 1324098496 C	H
168	503 A	-7:91702879 1324098495 A	
168	504 T	-7:91702878 1324098494 T	
169 A	505 G	-7:91702877 1324098493 G	A
169	506 C	-7:91702876 1324098492 C	
169	507 A	-7:91702875 1324098491 A	
170 Q	508 C	-7:91702874 1324098490 C	Q
170	509 A	-7:91702873 1324098489 A	
170	510 A	-7:91702872 1324098488 A	
171 S	511 T	-7:91702871 1324098487 T	S
171	512 C	-7:91702870 1324098486 C	
171	513 T	-7:91702869 1324098485 T	
172 H	514 C	-7:91702868 1324098484 C	H
172	515 A	-7:91702867 1324098483 A	
172	516 C	-7:91702866 1324098482 C	
173 F	517 T	-7:91702865 1324098481 T	F
173	518 T	-7:91702864 1324098480 T	
173	519 T	-7:91702863 1324098479 T	
174 I	520 A	-7:91702862 1324098478 A	I
174	521 T	-7:91702861 1324098477 T	
174	522 T	-7:91702860 1324098476 T	
175 P	523 C	-7:91702859 1324098475 C	P
175	524 C	-7:91702858 1324098474 C	
175	525 A	-7:91702857 1324098473 A	
176 A	526 G	-7:91702856 1324098472 G	A
176	527 C	-7:91702855 1324098471 C	
176	528 T	-7:91702854 1324098470 T	
177 L	529 T	-7:91702853 1324098469 T	L
177	530 T	-7:91702852 1324098468 T	
177	531 A	-7:91702851 1324098467 A	
178 F	532 T	-7:91702850 1324098466 T	F
178	533 T	-7:91702849 1324098465 T	
178	534 C	-7:91702848 1324098464 C	
179 R	535 C	-7:91702847 1324098463 C	R
179	536 G	-7:91702846 1324098462 G	
179	537 A	-7:91702845 1324098461 A	
180 P	538 C	-7:91702844 1324098460 C	P
180	539 C	-7:91702843 1324098459 C	
180	540 T	-7:91702842 1324098458 T	
181 S	541 T	-7:91702841 1324098457 T	S
181	542 C	-7:91702840 1324098456 C	
181	543 T	-7:91702839 1324098455 T	
182 P	544 C	-7:91702838 1324098454 C	P
182	545 C	-7:91702837 1324098453 C	
182	546 T	-7:91702836 1324098452 T	
183 L	547 C	-7:91702835 1324098451 C	L
183	548 T	-7:91702834 1324098450 T	
183	549 T	-7:91702833 1324098449 T	
184 E	550 G	-7:91702832 1324098448 G	E
184	551 A	-7:91702831 1324098447 A	
184	552 G	-7:91702830 1324098446 G	
185 R	553 C	-7:91702829 1324098445 C	R
185	554 G	-7:91702828 1324098444 G	
185	555 G	-7:91702827 1324098443 G	
186 I	556 A	-7:91702826 1324098442 A	I
186	557 T	-7:91702825 1324098441 T	
186	558 A	-7:91702824 1324098440 A	
187 K	559 A	-7:91702823 1324098439 A	K
187	560 A	-7:91702822 1324098438 A	
187	561 A	-7:91702821 1324098437 A	
188 T	562 A	-7:91702820 1324098436 A	T
188	563 C	-7:91702819 1324098435 C	
188	564 T	-7:91702818 1324098434 T	
189 N	565 A	-7:91702817 1324098433 A	N
189	566 A	-7:91702816 1324098432 A	
189	567 T	-7:91702815 1324098431 T	
190 V	568 G	-7:91702814 1324098430 G	V
190	569 T	-7:91702813 1324098429 T	
190	570 C	-7:91702812 1324098428 C	
191 I	571 A	-7:91702811 1324098427 A	I
191	572 T	-7:91702810 1324098426 T	
191	573 A	-7:91702809 1324098425 A	
192 N	574 A	-7:91702808 1324098424 A	N
192	575 A	-7:91702807 1324098423 A	
192	576 T	-7:91702806 1324098422 T	
193 P	577 C	-7:91702805 1324098421 C	P
193	578 C	-7:91702804 1324098420 C	
193	579 T	-7:91702803 1324098419 T	
194 A	580 G	-7:91702802 1324098418 G	A
194	581 C	-7:91702801 1324098417 C	
194	582 A	-7:91702800 1324098416 A	
195 Y	583 T	-7:91702799 1324098415 T	Y
195	584 A	-7:91702798 1324098414 A	
195	585 T	-7:91702797 1324098413 T	
196 A	586 G	-7:91702796 1324098412 G	A
196	587 C	-7:91702795 1324098411 C	
196	588 T	-7:91702794 1324098410 T	
197 T	589 A	-7:91702793 1324098409 A	T
197	590 C	-7:91702792 1324098408 C	
197	591 T	-7:91702791 1324098407 T	
198 E	592 G	-7:91702790 1324098406 G	E
198	593 A	-7:91702789 1324098405 A	
198	594 A	-7:91702788 1324098404 A	
199 S	595 T	-7:91702787 1324098403 T	S
199	596 C	-7:91702786 1324098402 C	
199	597 A	-7:91702785 1324098401 A	
200 G	598 G	-7:91702784 1324098400 G	G
200	599 G	-7:91702783 1324098399 G	
200	600 T	-7:91702782 1324098398 T	
201 Q	601 C	-7:91702781 1324098397 C	Q
201	602 A	-7:91702780 1324098396 A	
201	603 G	-7:91702779 1324098395 G	
202 T	604 A	-7:91702778 1324098394 A	T
202	605 C	-7:91702777 1324098393 C	
202	606 A	-7:91702776 1324098392 A	
203 E	607 G	-7:91702775 1324098391 G	E
203	608 A	-7:91702774 1324098390 A	
203	609 A	-7:91702773 1324098389 A	
204 N	610 A	-7:91702772 1324098388 A	N
204	611 A	-7:91702771 1324098387 A	
204	612 C	-7:91702770 1324098386 C	
205 S	613 T	-7:91702769 1324098385 T	S
205	614 C	-7:91702768 1324098384 C	
205	615 A	-7:91702767 1324098383 A	
206 L	616 C	-7:91702766 1324098382 C	L
206	617 T	-7:91702765 1324098381 T	
206	618 A	-7:91702764 1324098380 A	
207 H	619 C	-7:91702763 1324098379 C	H
207	620 A	-7:91702762 1324098378 A	
207	621 T	-7:91702761 1324098377 T	
208 M	622 A	-7:91702760 1324098376 A	M
208	623 T	-7:91702759 1324098375 T	
208	624 G	-7:91702758 1324098374 G	
209 G	625 G	-7:91702757 1324098373 G	G
209	626 G	-7:91702756 1324098372 G	
209	627 C	-7:91702755 1324098371 C	
210 Y	628 T	-7:91702754 1324098370 T	Y
210	629 A	-7:91702753 1324098369 A	
210	630 T	-7:91702752 1324098368 T	
211 S	631 A	-7:91702751 1324098367 A	S
211	632 G	-7:91702750 1324098366 G	
211	633 T	-7:91702749 1324098365 T	
212 A	634 G	-7:91702748 1324098364 G	A
212	635 C	-7:91702747 1324098363 C	
212	636 A	-7:91702746 1324098362 A	
213 L	637 C	-7:91702745 1324098361 C	L
213	638 T	-7:91702744 1324098360 T	
213	639 A	-7:91702743 1324098359 A	
214 E	640 G	-7:91702742 1324098358 G	E
214	641 A	-7:91702741 1324098357 A	
214	642 A	-7:91702740 1324098356 A	
215 I	643 A	-7:91702739 1324098355 A	I
215	644 T	-7:91702738 1324098354 T	
215	645 A	-7:91702737 1324098353 A	
216 K	646 A	-7:91702736 1324098352 A	K
216	647 A	-7:91702735 1324098351 A	
216	648 G	-7:91702734 1324098350 G	
217 S	649 A	-7:91702733 1324098349 A	S
217	650 G	-7:91702732 1324098348 G	
217	651 T	-7:91702731 1324098347 T	
218 K	652 A	-7:91702730 1324098346 A	K
218	653 A	-7:91702729 1324098345 A	
218	654 A	-7:91702728 1324098344 A	
219 M	655 A	-7:91702727 1324098343 A	M
219	656 T	-7:91702726 1324098342 T	
219	657 G	-7:91702725 1324098341 G	
220 L	658 T	-7:91702724 1324098340 T	L
220	659 T	-7:91702723 1324098339 T	
220	660 A	-7:91702722 1324098338 A	
221 A	661 G	-7:91702721 1324098337 G	A
221	662 C	-7:91702720 1324098336 C	
221	663 C	-7:91702719 1324098335 C	
222 L	664 C	-7:91702718 1324098334 C	L
222	665 T	-7:91702717 1324098333 T	
222	666 A	-7:91702716 1324098332 A	
223 E	667 G	-7:91702715 1324098331 G	E
223	668 A	-7:91702714 1324098330 A	
223	669 G	-7:91702713 1324098329 G	
224 K	670 A	-7:91702712 1324098328 A	K
224	671 A	-7:91702711 1324098327 A	
224	672 A	-7:91702710 1324098326 A	
225 A	673 G	-7:91702709 1324098325 G	A
225	674 C	-7:91702708 1324098324 C	
225	675 A	-7:91702707 1324098323 A	
226 D	676 G	-7:91702706 1324098322 G	D
226	677 A	-7:91702705 1324098321 A	
226	678 T	-7:91702704 1324098320 T	
227 T	679 A	-7:91702703 1324098319 A	T
227	680 C	-7:91702702 1324098318 C	
227	681 C	-7:91702701 1324098317 C	
228 C	682 T	-7:91702700 1324098316 T	C
228	683 G	-7:91702699 1324098315 G	
228	684 T	-7:91702698 1324098314 T	
229 I	685 A	-7:91702697 1324098313 A	I
229	686 T	-7:91702696 1324098312 T	
229	687 T	-7:91702695 1324098311 T	
230 Y	688 T	-7:91702694 1324098310 T	Y
230	689 A	-7:91702693 1324098309 A	
230	690 C	-7:91702692 1324098308 C	
231 N	691 A	-7:91702691 1324098307 A	N
231	692 A	-7:91702690 1324098306 A	
231	693 C	-7:91702689 1324098305 C	
232 P	694 C	-7:91702688 1324098304 C	P
232	695 C	-7:91702687 1324098303 C	
232	696 T	-7:91702686 1324098302 T	
233 L	697 T	-7:91702685 1324098301 T	L
233	698 T	-7:91702684 1324098300 T	
233	699 G	-7:91702683 1324098299 G	
234 F	700 T	-7:91702682 1324098298 T	F
234	701 T	-7:91702681 1324098297 T	
234	702 T	-7:91702680 1324098296 T	
235 G	703 G	-7:91702679 1324098295 G	G
235	704 G	-7:91702678 1324098294 G	
235	705 A	-7:91702677 1324098293 A	
236 S	706 T	-7:91702676 1324098292 T	S
236	707 C	-7:91702675 1324098291 C	
236	708 A	-7:91702674 1324098290 A	
237 D	709 G	-7:91702673 1324098289 G	D
237	710 A	-7:91702672 1324098288 A	
237	711 T	-7:91702671 1324098287 T	
238 L	712 C	-7:91702670 1324098286 C	L
238	713 T	-7:91702669 1324098285 T	
238	714 T	-7:91702668 1324098284 T	
239 Q	715 C	-7:91702667 1324098283 C	Q
239	716 A	-7:91702666 1324098282 A	
239	717 G	-7:91702665 1324098281 G	
240 Y	718 T	-7:91702664 1324098280 T	Y
240	719 A	-7:91702663 1324098279 A	
240	720 T	-7:91702662 1324098278 T	
241 T	721 A	-7:91702661 1324098277 A	T
241	722 C	-7:91702660 1324098276 C	
241	723 A	-7:91702659 1324098275 A	
242 N	724 A	-7:91702658 1324098274 A	N
242	725 A	-7:91702657 1324098273 A	
242	726 T	-7:91702656 1324098272 T	
243 R	727 C	-7:91702655 1324098271 C	R
243	728 G	-7:91702654 1324098270 G	
243	729 G	-7:91702653 1324098269 G	
244 V	730 G	-7:91702173 1324097789 G	V
244	731 T	-7:91702172 1324097788 T	
244	732 A	-7:91702171 1324097787 A	
245 D	733 G	-7:91702170 1324097786 G	D
245	734 A	-7:91702169 1324097785 A	
245	735 T	-7:91702168 1324097784 T	
246 K	736 A	-7:91702167 1324097783 A	K
246	737 A	-7:91702166 1324097782 A	
246	738 A	-7:91702165 1324097781 A	
247 V	739 G	-7:91702164 1324097780 G	V
247	740 T	-7:91702163 1324097779 T	
247	741 G	-7:91702162 1324097778 G	
248 V	742 G	-7:91702161 1324097777 G	V
248	743 T	-7:91702160 1324097776 T	
248	744 A	-7:91702159 1324097775 A	
249 I	745 A	-7:91702158 1324097774 A	I
249	746 T	-7:91702157 1324097773 T	
249	747 A	-7:91702156 1324097772 A	
250 N	748 A	-7:91702155 1324097771 A	N
250	749 A	-7:91702154 1324097770 A	
250	750 T	-7:91702153 1324097769 T	
251 P	751 C	-7:91702152 1324097768 C	P
251	752 C	-7:91702151 1324097767 C	
251	753 A	-7:91702150 1324097766 A	
252 Y	754 T	-7:91702149 1324097765 T	Y
252	755 A	-7:91702148 1324097764 A	
252	756 C	-7:91702147 1324097763 C	
253 F	757 T	-7:91702146 1324097762 T	F
253	758 T	-7:91702145 1324097761 T	
253	759 T	-7:91702144 1324097760 T	
254 G	760 G	-7:91702143 1324097759 G	G
254	761 G	-7:91702142 1324097758 G	
254	762 T	-7:91702141 1324097757 T	
255 L	763 C	-7:91702140 1324097756 C	L
255	764 T	-7:91702139 1324097755 T	
255	765 A	-7:91702138 1324097754 A	
256 G	766 G	-7:91702137 1324097753 G	G
256	767 G	-7:91702136 1324097752 G	
256	768 A	-7:91702135 1324097751 A	
257 A	769 G	-7:91702134 1324097750 G	A
257	770 C	-7:91702133 1324097749 C	
257	771 T	-7:91702132 1324097748 T	
258 P	772 C	-7:91702131 1324097747 C	P
258	773 C	-7:91702130 1324097746 C	
258	774 A	-7:91702129 1324097745 A	
259 D	775 G	-7:91702128 1324097744 G	D
259	776 A	-7:91702127 1324097743 A	
259	777 C	-7:91702126 1324097742 C	
260 Y	778 T	-7:91702125 1324097741 T	Y
260	779 A	-7:91702124 1324097740 A	
260	780 C	-7:91702123 1324097739 C	
261 S	781 T	-7:91702122 1324097738 T	S
261	782 C	-7:91702121 1324097737 C	
261	783 A	-7:91702120 1324097736 A	
262 K	784 A	-7:91702119 1324097735 A	K
262	785 A	-7:91702118 1324097734 A	
262	786 A	-7:91702117 1324097733 A	
263 I	787 A	-7:91702116 1324097732 A	I
263	788 T	-7:91702115 1324097731 T	
263	789 C	-7:91702114 1324097730 C	
264 Q	790 C	-7:91702113 1324097729 C	Q
264	791 A	-7:91702112 1324097728 A	
264	792 A	-7:91702111 1324097727 A	
265 I	793 A	-7:91702110 1324097726 A	I
265	794 T	-7:91702109 1324097725 T	
265	795 A	-7:91702108 1324097724 A	
266 P	796 C	-7:91702107 1324097723 C	P
266	797 C	-7:91702106 1324097722 C	
266	798 T	-7:91702105 1324097721 T	
267 K	799 A	-7:91702104 1324097720 A	K
267	800 A	-7:91702103 1324097719 A	
267	801 A	-7:91702102 1324097718 A	
268 Q	802 C	-7:91702101 1324097717 C	Q
268	803 A	-7:91702100 1324097716 A	
268	804 G	-7:91702099 1324097715 G	
269 E	805 G	-7:91702098 1324097714 G	E
269	806 A	-7:91702097 1324097713 A	
269	807 A	-7:91702096 1324097712 A	
270 K	808 A	-7:91702095 1324097711 A	K
270	809 A	-7:91702094 1324097710 A	
270	810 A	-7:91702093 1324097709 A	
271 W	811 T	-7:91702092 1324097708 T	W
271	812 G	-7:91702091 1324097707 G	
271	813 G	-7:91702090 1324097706 G	
272 Q	814 C	-7:91702089 1324097705 C	Q
272	815 A	-7:91702088 1324097704 A	
272	816 G	-7:91702087 1324097703 G	
273 R	817 A	-7:91702086 1324097702 A	R
273	818 G	-7:91702085 1324097701 G	
273	819 A	-7:91702084 1324097700 A	
274 S	820 A	-7:91702083 1324097699 A	S
274	821 G	-7:91702082 1324097698 G	
274	822 C	-7:91702081 1324097697 C	
275 M	823 A	-7:91702080 1324097696 A	M
275	824 T	-7:91702079 1324097695 T	
275	825 G	-7:91702078 1324097694 G	
276 S	826 A	-7:91702077 1324097693 A	S
276	827 G	-7:91702076 1324097692 G	
276	828 C	-7:91702075 1324097691 C	
277 S	829 A	-7:91702074 1324097690 A	S
277	830 G	-7:91702073 1324097689 G	
277	831 T	-7:91702072 1324097688 T	
278 V	832 G	-7:91702071 1324097687 G	V
278	833 T	-7:91702070 1324097686 T	
278	834 C	-7:91702069 1324097685 C	
279 T	835 A	-7:91702068 1324097684 A	T
279	836 C	-7:91702067 1324097683 C	
279	837 A	-7:91702066 1324097682 A	
280 E	838 G	-7:91702065 1324097681 G	E
280	839 A	-7:91702064 1324097680 A	
280	840 A	-7:91702063 1324097679 A	
281 D	841 G	-7:91702062 1324097678 G	D
281	842 A	-7:91702061 1324097677 A	
281	843 C	-7:91702060 1324097676 C	
282 K	844 A	-7:91702059 1324097675 A	K
282	845 A	-7:91702058 1324097674 A	
282	846 G	-7:91693932 1324089548 G	
283 Y	847 T	-7:91693931 1324089547 T	Y
283	848 A	-7:91693930 1324089546 A	
283	849 T	-7:91693929 1324089545 T	
284 G	850 G	-7:91693928 1324089544 G	G
284	851 G	-7:91693927 1324089543 G	
284	852 A	-7:91693926 1324089542 A	
285 K	853 A	-7:91693925 1324089541 A	K
285	854 A	-7:91693924 1324089540 A	
285	855 A	-7:91693923 1324089539 A	
286 V	856 G	-7:91693922 1324089538 G	V
286	857 T	-7:91693921 1324089537 T	
286	858 T	-7:91693920 1324089536 T	
287 E	859 G	-7:91693919 1324089535 G	E
287	860 A	-7:91693918 1324089534 A	
287	861 G	-7:91693917 1324089533 G	
288 A	862 G	-7:91693916 1324089532 G	A
288	863 C	-7:91693915 1324089531 C	
288	864 C	-7:91693914 1324089530 C	
289 T	865 A	-7:91693913 1324089529 A	T
289	866 C	-7:91693912 1324089528 C	
289	867 T	-7:91693911 1324089527 T	
290 R	868 C	-7:91693910 1324089526 C	R
290	869 G	-7:91693909 1324089525 G	
290	870 C	-7:91693908 1324089524 C	
291 I	871 A	-7:91693907 1324089523 A	I
291	872 T	-7:91693906 1324089522 T	
291	873 A	-7:91693905 1324089521 A	
292 L	874 T	-7:91693904 1324089520 T	L
292	875 T	-7:91693903 1324089519 T	
292	876 G	-7:91693902 1324089518 G	
293 L	877 T	-7:91693901 1324089517 T	L
293	878 T	-7:91693900 1324089516 T	
293	879 A	-7:91693899 1324089515 A	
294 E	880 G	-7:91693898 1324089514 G	E
294	881 A	-7:91693897 1324089513 A	
294	882 G	-7:91693896 1324089512 G	
295 K	883 A	-7:91693895 1324089511 A	K
295	884 A	-7:91693894 1324089510 A	
295	885 A	-7:91693893 1324089509 A	
296 G	886 G	-7:91693892 1324089508 G	G
296	887 G	-7:91693891 1324089507 G	
296	888 A	-7:91693890 1324089506 A	
297 K	889 A	-7:91693889 1324089505 A	K
297	890 A	-7:91693888 1324089504 A	
297	891 G	-7:91693887 1324089503 G	
298 C	892 T	-7:91693886 1324089502 T	C
298	893 G	-7:91693885 1324089501 G	
298	894 C	-7:91693884 1324089500 C	
299 N	895 A	-7:91693883 1324089499 A	N
299	896 A	-7:91693882 1324089498 A	
299	897 T	-7:91693881 1324089497 T	
300 P	898 C	-7:91693880 1324089496 C	P
300	899 C	-7:91693879 1324089495 C	
300	900 A	-7:91693878 1324089494 A	
301 N	901 A	-7:91693877 1324089493 A	N
301	902 A	-7:91693876 1324089492 A	
301	903 C	-7:91693875 1324089491 C	
302 L	904 C	-7:91693874 1324089490 C	L
302	905 T	-7:91693873 1324089489 T	
302	906 T	-7:91693872 1324089488 T	
303 L	907 T	-7:91693871 1324089487 T	L
303	908 T	-7:91693870 1324089486 T	
303	909 A	-7:91693869 1324089485 A	
304 N	910 A	-7:91693868 1324089484 A	N
304	911 A	-7:91693867 1324089483 A	
304	912 T	-7:91693866 1324089482 T	
305 G	913 G	-7:91693865 1324089481 G	G
305	914 G	-7:91693864 1324089480 G	
305	915 A	-7:91693863 1324089479 A	
306 Q	916 C	-7:91693862 1324089478 C	Q
306	917 A	-7:91693861 1324089477 A	
306	918 A	-7:91693860 1324089476 A	
307 L	919 C	-7:91693859 1324089475 C	L
307	920 T	-7:91693858 1324089474 T	
307	921 T	-7:91693857 1324089473 T	
308 S	922 A	-7:91693856 1324089472 A	S
308	923 G	-7:91693855 1324089471 G	
308	924 T	-7:91693854 1324089470 T	
309 S	925 T	-7:91693853 1324089469 T	S
309	926 C	-7:91693852 1324089468 C	
309	927 T	-7:91693851 1324089467 T	
310 P	928 C	-7:91693850 1324089466 C	P
310	929 C	-7:91693849 1324089465 C	
310	930 T	-7:91693848 1324089464 T	
311 L	931 C	-7:91693847 1324089463 C	L
311	932 T	-7:91693846 1324089462 T	
311	933 T	-7:91693845 1324089461 T	
312 H	934 C	-7:91693844 1324089460 C	H
312	935 A	-7:91693843 1324089459 A	
312	936 T	-7:91693842 1324089458 T	
313 F	937 T	-7:91693841 1324089457 T	F
313	938 T	-7:91693840 1324089456 T	
313	939 T	-7:91693839 1324089455 T	
314 A	940 G	-7:91693838 1324089454 G	A
314	941 C	-7:91693837 1324089453 C	
314	942 T	-7:91693836 1324089452 T	
315 A	943 G	-7:91693835 1324089451 G	A
315	944 C	-7:91693834 1324089450 C	
315	945 T	-7:91693833 1324089449 T	
316 G	946 G	-7:91693832 1324089448 G	G
316	947 G	-7:91693831 1324089447 G	
316	948 A	-7:91693830 1324089446 A	
317 G	949 G	-7:91693829 1324089445 G	G
317	950 G	-7:91693828 1324089444 G	
317	951 A	-7:91693827 1324089443 A	
318 G	952 G	-7:91693826 1324089442 G	G
318	953 G	-7:91693825 1324089441 G	
318	954 A	-7:91693824 1324089440 A	
319 H	955 C	-7:91693823 1324089439 C	H
319	956 A	-7:91693822 1324089438 A	
319	957 T	-7:91693821 1324089437 T	
320 A	958 G	-7:91693820 1324089436 G	A
320	959 C	-7:91693819 1324089435 C	
320	960 T	-7:91693818 1324089434 T	
321 E	961 G	-7:91693817 1324089433 G	E
321	962 A	-7:91693816 1324089432 A	
321	963 A	-7:91693815 1324089431 A	
322 I	964 A	-7:91693814 1324089430 A	I
322	965 T	-7:91693813 1324089429 T	
322	966 A	-7:91693812 1324089428 A	
323 V	967 G	-7:91693811 1324089427 G	V
323	968 T	-7:91693810 1324089426 T	
323	969 A	-7:91693809 1324089425 A	
324 Q	970 C	-7:91693808 1324089424 C	Q
324	971 A	-7:91693807 1324089423 A	
324	972 G	-7:91693806 1324089422 G	
325 I	973 A	-7:91693805 1324089421 A	I
325	974 T	-7:91693804 1324089420 T	
325	975 T	-7:91693803 1324089419 T	
326 L	976 C	-7:91693802 1324089418 C	L
326	977 T	-7:91693801 1324089417 T	
326	978 C	-7:91693800 1324089416 C	
327 L	979 C	-7:91693799 1324089415 C	L
327	980 T	-7:91693798 1324089414 T	
327	981 A	-7:91693797 1324089413 A	
328 N	982 A	-7:91693796 1324089412 A	N
328	983 A	-7:91693795 1324089411 A	
328	984 C	-7:91693794 1324089410 C	
329 H	985 C	-7:91693793 1324089409 C	H
329	986 A	-7:91693792 1324089408 A	
329	987 C	-7:91693791 1324089407 C	
330 P	988 C	-7:91693790 1324089406 C	P
330	989 C	-7:91693789 1324089405 C	
330	990 A	-7:91693788 1324089404 A	
331 E	991 G	-7:91693787 1324089403 G	E
331	992 A	-7:91693786 1324089402 A	
331	993 A	-7:91693785 1324089401 A	
332 T	994 A	-7:91693784 1324089400 A	T
332	995 C	-7:91693783 1324089399 C	
332	996 G	-7:91693782 1324089398 G	
333 D	997 G	-7:91693781 1324089397 G	D
333	998 A	-7:91693780 1324089396 A	
333	999 T	-7:91693779 1324089395 T	
334 R	1000 A	-7:91693778 1324089394 A	R
334	1001 G	-7:91693777 1324089393 G	
334	1002 A	-7:91693776 1324089392 A	
335 H	1003 C	-7:91693077 1324088693 C	H
335	1004 A	-7:91693076 1324088692 A	
335	1005 T	-7:91693075 1324088691 T	
336 I	1006 A	-7:91693074 1324088690 A	I
336	1007 T	-7:91693073 1324088689 T	
336	1008 A	-7:91693072 1324088688 A	
337 T	1009 A	-7:91693071 1324088687 A	T
337	1010 C	-7:91693070 1324088686 C	
337	1011 A	-7:91693069 1324088685 A	
338 D	1012 G	-7:91693068 1324088684 G	D
338	1013 A	-7:91693067 1324088683 A	
338	1014 C	-7:91693066 1324088682 C	
339 Q	1015 C	-7:91693065 1324088681 C	Q
339	1016 A	-7:91693064 1324088680 A	
339	1017 A	-7:91693063 1324088679 A	
340 Q	1018 C	-7:91693062 1324088678 C	Q
340	1019 A	-7:91693061 1324088677 A	
340	1020 A	-7:91693060 1324088676 A	
341 G	1021 G	-7:91693059 1324088675 G	G
341	1022 G	-7:91693058 1324088674 G	
341	1023 A	-7:91693057 1324088673 A	
342 R	1024 A	-7:91693056 1324088672 A	R
342	1025 G	-7:91693055 1324088671 G	
342	1026 A	-7:91693054 1324088670 A	
343 S	1027 T	-7:91693053 1324088669 T	S
343	1028 C	-7:91693052 1324088668 C	
343	1029 T	-7:91693051 1324088667 T	
344 P	1030 C	-7:91693050 1324088666 C	P
344	1031 C	-7:91693049 1324088665 C	
344	1032 A	-7:91693048 1324088664 A	
345 L	1033 T	-7:91693047 1324088663 T	L
345	1034 T	-7:91693046 1324088662 T	
345	1035 A	-7:91693045 1324088661 A	
346 N	1036 A	-7:91693044 1324088660 A	N
346	1037 A	-7:91693043 1324088659 A	
346	1038 T	-7:91693042 1324088658 T	
347 I	1039 A	-7:91693041 1324088657 A	I
347	1040 T	-7:91693040 1324088656 T	
347	1041 T	-7:91693039 1324088655 T	
348 C	1042 T	-7:91693038 1324088654 T	C
348	1043 G	-7:91693037 1324088653 G	
348	1044 T	-7:91693036 1324088652 T	
349 E	1045 G	-7:91693035 1324088651 G	E
349	1046 A	-7:91693034 1324088650 A	
349	1047 A	-7:91693033 1324088649 A	
350 E	1048 G	-7:91693032 1324088648 G	E
350	1049 A	-7:91693031 1324088647 A	
350	1050 A	-7:91693030 1324088646 A	
351 N	1051 A	-7:91693029 1324088645 A	N
351	1052 A	-7:91693028 1324088644 A	
351	1053 C	-7:91693027 1324088643 C	
352 K	1054 A	-7:91693026 1324088642 A	K
352	1055 A	-7:91693025 1324088641 A	
352	1056 A	-7:91693024 1324088640 A	
353 Q	1057 C	-7:91693023 1324088639 C	Q
353	1058 A	-7:91693022 1324088638 A	
353	1059 A	-7:91693021 1324088637 A	
354 N	1060 A	-7:91693020 1324088636 A	N
354	1061 A	-7:91693019 1324088635 A	
354	1062 C	-7:91693018 1324088634 C	
355 N	1063 A	-7:91693017 1324088633 A	N
355	1064 A	-7:91693016 1324088632 A	
355	1065 C	-7:91693015 1324088631 C	
356 W	1066 T	-7:91693014 1324088630 T	W
356	1067 G	-7:91693013 1324088629 G	
356	1068 G	-7:91693012 1324088628 G	
357 E	1069 G	-7:91693011 1324088627 G	E
357	1070 A	-7:91693010 1324088626 A	
357	1071 A	-7:91693009 1324088625 A	
358 E	1072 G	-7:91693008 1324088624 G	E
358	1073 A	-7:91693007 1324088623 A	
358	1074 A	-7:91693006 1324088622 A	
359 A	1075 G	-7:91693005 1324088621 G	A
359	1076 C	-7:91693004 1324088620 C	
359	1077 T	-7:91693003 1324088619 T	
360 A	1078 G	-7:91693002 1324088618 G	A
360	1079 C	-7:91693001 1324088617 C	
360	1080 A	-7:91693000 1324088616 A	
361 K	1081 A	-7:91692999 1324088615 A	K
361	1082 A	-7:91692998 1324088614 A	
361	1083 A	-7:91692997 1324088613 A	
362 L	1084 T	-7:91692996 1324088612 T	L
362	1085 T	-7:91692995 1324088611 T	
362	1086 G	-7:91692994 1324088610 G	
363 L	1087 T	-7:91692993 1324088609 T	L
363	1088 T	-7:91692992 1324088608 T	
363	1089 G	-7:91692991 1324088607 G	
364 K	1090 A	-7:91692990 1324088606 A	K
364	1091 A	-7:91692989 1324088605 A	
364	1092 G	-7:91692988 1324088604 G	
365 E	1093 G	-7:91692987 1324088603 G	E
365	1094 A	-7:91692986 1324088602 A	
365	1095 A	-7:91692985 1324088601 A	
366 A	1096 G	-7:91692984 1324088600 G	A
366	1097 C	-7:91692983 1324088599 C	
366	1098 A	-7:91692982 1324088598 A	
367 I	1099 A	-7:91692981 1324088597 A	I
367	1100 T	-7:91692980 1324088596 T	
367	1101 T	-7:91692979 1324088595 T	
368 N	1102 A	-7:91692978 1324088594 A	N
368	1103 A	-7:91692977 1324088593 A	
368	1104 C	-7:91692976 1324088592 C	
369 K	1105 A	-7:91692975 1324088591 A	K
369	1106 A	-7:91692974 1324088590 A	
369	1107 A	-7:91692973 1324088589 A	
370 P	1108 C	-7:91692972 1324088588 C	P
370	1109 C	-7:91692971 1324088587 C	
370	1110 A	-7:91692970 1324088586 A	
371 Y	1111 T	-7:91690228 1324085844 T	Y
371	1112 A	-7:91690227 1324085843 A	
371	1113 T	-7:91690226 1324085842 T	
372 E	1114 G	-7:91690225 1324085841 G	E
372	1115 A	-7:91690224 1324085840 A	
372	1116 A	-7:91690223 1324085839 A	
373 K	1117 A	-7:91690222 1324085838 A	K
373	1118 A	-7:91690221 1324085837 A	
373	1119 A	-7:91690220 1324085836 A	
374 V	1120 G	-7:91690219 1324085835 G	V
374	1121 T	-7:91690218 1324085834 T	
374	1122 T	-7:91690217 1324085833 T	
375 R	1123 C	-7:91690216 1324085832 C	R
375	1124 G	-7:91690215 1324085831 G	
375	1125 A	-7:91690214 1324085830 A	
376 I	1126 A	-7:91690213 1324085829 A	I
376	1127 T	-7:91690212 1324085828 T	
376	1128 A	-7:91690211 1324085827 A	
377 Y	1129 T	-7:91690210 1324085826 T	Y
377	1130 A	-7:91690209 1324085825 A	
377	1131 C	-7:91690208 1324085824 C	
378 R	1132 A	-7:91690207 1324085823 A	R
378	1133 G	-7:91690206 1324085822 G	
378	1134 A	-7:91690205 1324085821 A	
379 M	1135 A	-7:91690204 1324085820 A	M
379	1136 T	-7:91690203 1324085819 T	
379	1137 G	-7:91690202 1324085818 G	
380 D	1138 G	-7:91690201 1324085817 G	D
380	1139 A	-7:91690200 1324085816 A	
380	1140 T	-7:91690199 1324085815 T	
381 G	1141 G	-7:91690198 1324085814 G	G
381	1142 G	-7:91690197 1324085813 G	
381	1143 G	-7:91690196 1324085812 G	
382 S	1144 T	-7:91690195 1324085811 T	S
382	1145 C	-7:91690194 1324085810 C	
382	1146 A	-7:91690193 1324085809 A	
383 Y	1147 T	-7:91690192 1324085808 T	Y
383	1148 A	-7:91690191 1324085807 A	
383	1149 T	-7:91690190 1324085806 T	
384 R	1150 C	-7:91690189 1324085805 C	R
384	1151 G	-7:91690188 1324085804 G	
384	1152 T	-7:91690187 1324085803 T	
385 S	1153 T	-7:91690186 1324085802 T	S
385	1154 C	-7:91690185 1324085801 C	
385	1155 T	-7:91690184 1324085800 T	
386 V	1156 G	-7:91690183 1324085799 G	V
386	1157 T	-7:91690182 1324085798 T	
386	1158 T	-7:91690181 1324085797 T	
387 E	1159 G	-7:91690180 1324085796 G	E
387	1160 A	-7:91690179 1324085795 A	
387	1161 A	-7:91690178 1324085794 A	
388 L	1162 T	-7:91690177 1324085793 T	L
388	1163 T	-7:91690176 1324085792 T	
388	1164 G	-7:91690175 1324085791 G	
389 K	1165 A	-7:91690174 1324085790 A	K
389	1166 A	-7:91690173 1324085789 A	
389	1167 G	-7:91690172 1324085788 G	
390 H	1168 C	-7:91690171 1324085787 C	H
390	1169 A	-7:91690170 1324085786 A	
390	1170 T	-7:91690169 1324085785 T	
391 G	1171 G	-7:91690168 1324085784 G	G
391	1172 G	-7:91690167 1324085783 G	
391	1173 A	-7:91690166 1324085782 A	
392 N	1174 A	-7:91690165 1324085781 A	N
392	1175 A	-7:91690164 1324085780 A	
392	1176 T	-7:91690163 1324085779 T	
393 N	1177 A	-7:91690162 1324085778 A	N
393	1178 A	-7:91690161 1324085777 A	
393	1179 T	-7:91690160 1324085776 T	
394 T	1180 A	-7:91690159 1324085775 A	T
394	1181 C	-7:91690158 1324085774 C	
394	1182 C	-7:91690157 1324085773 C	
395 T	1183 A	-7:91690156 1324085772 A	T
395	1184 C	-7:91690155 1324085771 C	
395	1185 A	-7:91690154 1324085770 A	
396 V	1186 G	-7:91690153 1324085769 G	V
396	1187 T	-7:91690152 1324085768 T	
396	1188 G	-7:91690151 1324085767 G	
397 Q	1189 C	-7:91690150 1324085766 C	Q
397	1190 A	-7:91690149 1324085765 A	
397	1191 G	-7:91690148 1324085764 G	
398 Q	1192 C	-7:91690147 1324085763 C	Q
398	1193 A	-7:91690146 1324085762 A	
398	1194 G	-7:91690145 1324085761 G	
399 I	1195 A	-7:91690144 1324085760 A	I
399	1196 T	-7:91690143 1324085759 T	
399	1197 A	-7:91690142 1324085758 A	
400 M	1198 A	-7:91690141 1324085757 A	M
400	1199 T	-7:91690140 1324085756 T	
400	1200 G	-7:91690139 1324085755 G	
401 E	1201 G	-7:91690138 1324085754 G	E
401	1202 A	-7:91690137 1324085753 A	
401	1203 A	-7:91690136 1324085752 A	
402 G	1204 G	-7:91690135 1324085751 G	G
402	1205 G	-7:91690134 1324085750 G	
402	1206 A	-7:91690133 1324085749 A	
403 M	1207 A	-7:91690132 1324085748 A	M
403	1208 T	-7:91690131 1324085747 T	
403	1209 G	-7:91690130 1324085746 G	
404 R	1210 C	-7:91690129 1324085745 C	R
404	1211 G	-7:91690128 1324085744 G	
404	1212 T	-7:91690127 1324085743 T	
405 L	1213 C	-7:91690126 1324085742 C	L
405	1214 T	-7:91690125 1324085741 T	
405	1215 C	-7:91690124 1324085740 C	
406 S	1216 T	-7:91690123 1324085739 T	S
406	1217 C	-7:91690122 1324085738 C	
406	1218 T	-7:91690121 1324085737 T	
407 Q	1219 C	-7:91690120 1324085736 C	Q
407	1220 A	-7:91690119 1324085735 A	
407	1221 A	-7:91690118 1324085734 A	
408 E	1222 G	-7:91690117 1324085733 G	E
408	1223 A	-7:91690116 1324085732 A	
408	1224 A	-7:91690115 1324085731 A	
409 T	1225 A	-7:91690114 1324085730 A	T
409	1226 C	-7:91690113 1324085729 C	
409	1227 T	-7:91690112 1324085728 T	
410 Q	1228 C	-7:91690111 1324085727 C	Q
410	1229 A	-7:91690110 1324085726 A	
410	1230 G	-7:91690109 1324085725 G	
411 Q	1231 C	-7:91690108 1324085724 C	Q
411	1232 A	-7:91690107 1324085723 A	
411	1233 A	-7:91690106 1324085722 A	
412 Y	1234 T	-7:91690105 1324085721 T	Y
412	1235 A	-7:91690104 1324085720 A	
412	1236 T	-7:91690103 1324085719 T	
413 F	1237 T	-7:91690102 1324085718 T	F
413	1238 T	-7:91690101 1324085717 T	
413	1239 C	-7:91690100 1324085716 C	
414 T	1240 A	-7:91690099 1324085715 A	T
414	1241 C	-7:91690098 1324085714 C	
414	1242 T	-7:91690097 1324085713 T	
415 I	1243 A	-7:91690096 1324085712 A	I
415	1244 T	-7:91690095 1324085711 T	
415	1245 A	-7:91690094 1324085710 A	
416 W	1246 T	-7:91690093 1324085709 T	W
416	1247 G	-7:91690092 1324085708 G	
416	1248 G	-7:91690091 1324085707 G	
417 I	1249 A	-7:91690090 1324085706 A	I
417	1250 T	-7:91690089 1324085705 T	
417	1251 T	-7:91690088 1324085704 T	
418 C	1252 T	-7:91690087 1324085703 T	C
418	1253 G	-7:91690086 1324085702 G	
418	1254 T	-7:91690085 1324085701 T	
419 S	1255 T	-7:91690084 1324085700 T	S
419	1256 C	-7:91690083 1324085699 C	
419	1257 A	-7:91690082 1324085698 A	
420 E	1258 G	-7:91690081 1324085697 G	E
420	1259 A	-7:91690080 1324085696 A	
420	1260 A	-7:91690079 1324085695 A	
421 N	1261 A	-7:91690078 1324085694 A	N
421	1262 A	-7:91690077 1324085693 A	
421	1263 C	-7:91690076 1324085692 C	
422 L	1264 C	-7:91690075 1324085691 C	L
422	1265 T	-7:91690074 1324085690 T	
422	1266 C	-7:91690073 1324085689 C	
423 S	1267 A	-7:91690072 1324085688 A	S
423	1268 G	-7:91689303 1324084919 G	
423	1269 C	-7:91689302 1324084918 C	
424 L	1270 C	-7:91689301 1324084917 C	L
424	1271 T	-7:91689300 1324084916 T	
424	1272 T	-7:91689299 1324084915 T	
425 Q	1273 C	-7:91689298 1324084914 C	Q
425	1274 A	-7:91689297 1324084913 A	
425	1275 A	-7:91689296 1324084912 A	
426 L	1276 C	-7:91689295 1324084911 C	L
426	1277 T	-7:91689294 1324084910 T	
426	1278 C	-7:91689293 1324084909 C	
427 K	1279 A	-7:91689292 1324084908 A	K
427	1280 A	-7:91689291 1324084907 A	
427	1281 A	-7:91689290 1324084906 A	
428 P	1282 C	-7:91689289 1324084905 C	P
428	1283 C	-7:91689288 1324084904 C	
428	1284 A	-7:91689287 1324084903 A	
429 Y	1285 T	-7:91689286 1324084902 T	Y
429	1286 A	-7:91689285 1324084901 A	
429	1287 T	-7:91689284 1324084900 T	
430 H	1288 C	-7:91689283 1324084899 C	H
430	1289 A	-7:91689282 1324084898 A	
430	1290 T	-7:91689281 1324084897 T	
431 K	1291 A	-7:91689280 1324084896 A	K
431	1292 A	-7:91689279 1324084895 A	
431	1293 A	-7:91689278 1324084894 A	
432 P	1294 C	-7:91689277 1324084893 C	P
432	1295 C	-7:91689276 1324084892 C	
432	1296 C	-7:91689275 1324084891 C	
433 L	1297 T	-7:91689274 1324084890 T	L
433	1298 T	-7:91689273 1324084889 T	
433	1299 G	-7:91689272 1324084888 G	
434 Q	1300 C	-7:91689271 1324084887 C	Q
434	1301 A	-7:91689270 1324084886 A	
434	1302 A	-7:91689269 1324084885 A	
435 H	1303 C	-7:91689268 1324084884 C	H
435	1304 A	-7:91689267 1324084883 A	
435	1305 T	-7:91689266 1324084882 T	
436 V	1306 G	-7:91689265 1324084881 G	V
436	1307 T	-7:91689264 1324084880 T	
436	1308 T	-7:91689263 1324084879 T	
437 R	1309 C	-7:91689262 1324084878 C	R
437	1310 G	-7:91689261 1324084877 G	
437	1311 T	-7:91689260 1324084876 T	
438 D	1312 G	-7:91689259 1324084875 G	D
438	1313 A	-7:91689258 1324084874 A	
438	1314 C	-7:91689257 1324084873 C	
439 W	1315 T	-7:91689256 1324084872 T	W
439	1316 G	-7:91689255 1324084871 G	
439	1317 G	-7:91689254 1324084870 G	
440 P	1318 C	-7:91689253 1324084869 C	P
440	1319 C	-7:91689252 1324084868 C	
440	1320 A	-7:91689251 1324084867 A	
441 E	1321 G	-7:91689250 1324084866 G	E
441	1322 A	-7:91689249 1324084865 A	
441	1323 A	-7:91689248 1324084864 A	
442 I	1324 A	-7:91689247 1324084863 A	I
442	1325 T	-7:91689246 1324084862 T	
442	1326 A	-7:91689245 1324084861 A	
443 L	1327 C	-7:91689244 1324084860 C	L
443	1328 T	-7:91689243 1324084859 T	
443	1329 T	-7:91689242 1324084858 T	
444 A	1330 G	-7:91689241 1324084857 G	A
444	1331 C	-7:91689240 1324084856 C	
444	1332 T	-7:91689239 1324084855 T	
445 E	1333 G	-7:91689238 1324084854 G	E
445	1334 A	-7:91689237 1324084853 A	
445	1335 A	-7:91689236 1324084852 A	
446 L	1336 T	-7:91689235 1324084851 T	L
446	1337 T	-7:91689234 1324084850 T	
446	1338 G	-7:91689233 1324084849 G	
447 T	1339 A	-7:91689232 1324084848 A	T
447	1340 C	-7:91689231 1324084847 C	
447	1341 T	-7:91689230 1324084846 T	
448 N	1342 A	-7:91689229 1324084845 A	N
448	1343 A	-7:91689228 1324084844 A	
448	1344 T	-7:91689227 1324084843 T	
449 L	1345 C	-7:91689226 1324084842 C	L
449	1346 T	-7:91689225 1324084841 T	
449	1347 G	-7:91689224 1324084840 G	
450 D	1348 G	-7:91689223 1324084839 G	D
450	1349 A	-7:91689222 1324084838 A	
450	1350 T	-7:91689221 1324084837 T	
451 P	1351 C	-7:91689220 1324084836 C	P
451	1352 C	-7:91689219 1324084835 C	
451	1353 T	-7:91689218 1324084834 T	
452 Q	1354 C	-7:91689217 1324084833 C	Q
452	1355 A	-7:91689216 1324084832 A	
452	1356 A	-7:91689215 1324084831 A	
453 R	1357 A	-7:91689214 1324084830 A	R
453	1358 G	-7:91689213 1324084829 G	
453	1359 G	-7:91689212 1324084828 G	
454 E	1360 G	-7:91689211 1324084827 G	E
454	1361 A	-7:91689210 1324084826 A	
454	1362 A	-7:91689209 1324084825 A	
455 T	1363 A	-7:91689208 1324084824 A	T
455	1364 C	-7:91689207 1324084823 C	
455	1365 A	-7:91689206 1324084822 A	
456 P	1366 C	-7:91689205 1324084821 C	P
456	1367 C	-7:91689204 1324084820 C	
456	1368 T	-7:91689203 1324084819 T	
457 Q	1369 C	-7:91689202 1324084818 C	Q
457	1370 A	-7:91689201 1324084817 A	
457	1371 G	-7:91689200 1324084816 G	
458 L	1372 C	-7:91689199 1324084815 C	L
458	1373 T	-7:91689198 1324084814 T	
458	1374 T	-7:91689197 1324084813 T	
459 F	1375 T	-7:91689196 1324084812 T	F
459	1376 T	-7:91689195 1324084811 T	
459	1377 T	-7:91689194 1324084810 T	
460 L	1378 C	-7:91689193 1324084809 C	L
460	1379 T	-7:91689192 1324084808 T	
460	1380 A	-7:91689191 1324084807 A	
461 R	1381 A	-7:91689190 1324084806 A	R
461	1382 G	-7:91689189 1324084805 G	
461	1383 A	-7:91689188 1324084804 A	
462 R	1384 A	-7:91689187 1324084803 A	R
462	1385 G	-7:91689186 1324084802 G	
462	1386 A	-7:91689185 1324084801 A	
463 D	1387 G	-7:91689184 1324084800 G	D
463	1388 A	-7:91689183 1324084799 A	
463	1389 T	-7:91689182 1324084798 T	
464 V	1390 G	-7:91689181 1324084797 G	V
464	1391 T	-7:91689180 1324084796 T	
464	1392 G	-7:91689179 1324084795 G	
465 R	1393 A	-7:91689178 1324084794 A	R
465	1394 G	-7:91689177 1324084793 G	
465	1395 A	-7:91689176 1324084792 A	
466 L	1396 C	-7:91689175 1324084791 C	L
466	1397 T	-7:91689174 1324084790 T	
466	1398 T	-7:91689173 1324084789 T	
467 P	1399 C	-7:91689172 1324084788 C	P
467	1400 C	-7:91689171 1324084787 C	
467	1401 C	-7:91689170 1324084786 C	
468 L	1402 T	-7:91689169 1324084785 T	L
468	1403 T	-7:91689168 1324084784 T	
468	1404 G	-7:91689167 1324084783 G	
469 E	1405 G	-7:91689166 1324084782 G	E
469	1406 A	-7:91689165 1324084781 A	
469	1407 A	-7:91689164 1324084780 A	
470 V	1408 G	-7:91689163 1324084779 G	V
470	1409 T	-7:91689162 1324084778 T	
470	1410 T	-7:91689161 1324084777 T	
471 E	1411 G	-7:91689160 1324084776 G	E
471	1412 A	-7:91689159 1324084775 A	
471	1413 A	-7:91689158 1324084774 A	
472 K	1414 A	-7:91689157 1324084773 A	K
472	1415 A	-7:91689156 1324084772 A	
472	1416 A	-7:91689155 1324084771 A	
473 Q	1417 C	-7:91689154 1324084770 C	Q
473	1418 A	-7:91689153 1324084769 A	
473	1419 G	-7:91689152 1324084768 G	
474 I	1420 A	-7:91682027 1324077643 A	I
474	1421 T	-7:91682026 1324077642 T	
474	1422 T	-7:91682025 1324077641 T	
475 E	1423 G	-7:91682024 1324077640 G	E
475	1424 A	-7:91682023 1324077639 A	
475	1425 A	-7:91682022 1324077638 A	
476 D	1426 G	-7:91682021 1324077637 G	D
476	1427 A	-7:91682020 1324077636 A	
476	1428 C	-7:91682019 1324077635 C	
477 P	1429 C	-7:91682018 1324077634 C	P
477	1430 C	-7:91682017 1324077633 C	
477	1431 A	-7:91682016 1324077632 A	
478 L	1432 C	-7:91682015 1324077631 C	L
478	1433 T	-7:91682014 1324077630 T	
478	1434 A	-7:91682013 1324077629 A	
479 A	1435 G	-7:91682012 1324077628 G	A
479	1436 C	-7:91682011 1324077627 C	
479	1437 T	-7:91682010 1324077626 T	
480 I	1438 A	-7:91682009 1324077625 A	I
480	1439 T	-7:91682008 1324077624 T	
480	1440 T	-7:91682007 1324077623 T	
481 L	1441 C	-7:91682006 1324077622 C	L
481	1442 T	-7:91682005 1324077621 T	
481	1443 T	-7:91682004 1324077620 T	
482 I	1444 A	-7:91682003 1324077619 A	I
482	1445 T	-7:91682002 1324077618 T	
482	1446 T	-7:91682001 1324077617 T	
483 L	1447 C	-7:91682000 1324077616 C	L
483	1448 T	-7:91681999 1324077615 T	
483	1449 C	-7:91681998 1324077614 C	
484 F	1450 T	-7:91681997 1324077613 T	F
484	1451 T	-7:91681996 1324077612 T	
484	1452 T	-7:91681995 1324077611 T	
485 D	1453 G	-7:91681994 1324077610 G	D
485	1454 A	-7:91681993 1324077609 A	
485	1455 T	-7:91681992 1324077608 T	
486 E	1456 G	-7:91681991 1324077607 G	E
486	1457 A	-7:91681990 1324077606 A	
486	1458 A	-7:91681989 1324077605 A	
487 A	1459 G	-7:91681988 1324077604 G	A
487	1460 C	-7:91681987 1324077603 C	
487	1461 C	-7:91681986 1324077602 C	
488 R	1462 A	-7:91681985 1324077601 A	R
488	1463 G	-7:91681984 1324077600 G	
488	1464 A	-7:91681983 1324077599 A	
489 Y	1465 T	-7:91681982 1324077598 T	Y
489	1466 A	-7:91681981 1324077597 A	
489	1467 T	-7:91681980 1324077596 T	
490 N	1468 A	-7:91681979 1324077595 A	N
490	1469 A	-7:91681978 1324077594 A	
490	1470 T	-7:91681977 1324077593 T	
491 L	1471 T	-7:91681976 1324077592 T	L
491	1472 T	-7:91681975 1324077591 T	
491	1473 A	-7:91681974 1324077590 A	
492 L	1474 T	-7:91681973 1324077589 T	L
492	1475 T	-7:91681972 1324077588 T	
492	1476 G	-7:91681971 1324077587 G	
493 K	1477 A	-7:91681970 1324077586 A	K
493	1478 A	-7:91681969 1324077585 A	
493	1479 G	-7:91681968 1324077584 G	
494 G	1480 G	-7:91681967 1324077583 G	G
494	1481 G	-7:91681966 1324077582 G	
494	1482 C	-7:91681965 1324077581 C	
495 F	1483 T	-7:91681964 1324077580 T	F
495	1484 T	-7:91681963 1324077579 T	
495	1485 T	-7:91681962 1324077578 T	
496 Y	1486 T	-7:91681961 1324077577 T	Y
496	1487 A	-7:91681960 1324077576 A	
496	1488 T	-7:91681959 1324077575 T	
497 T	1489 A	-7:91681958 1324077574 A	T
497	1490 C	-7:91681957 1324077573 C	
497	1491 A	-7:91681956 1324077572 A	
498 A	1492 G	-7:91681955 1324077571 G	A
498	1493 C	-7:91681954 1324077570 C	
498	1494 T	-7:91681953 1324077569 T	
499 P	1495 C	-7:91681952 1324077568 C	P
499	1496 C	-7:91681951 1324077567 C	
499	1497 T	-7:91681950 1324077566 T	
500 D	1498 G	-7:91681949 1324077565 G	D
500	1499 A	-7:91681948 1324077564 A	
500	1500 T	-7:91681947 1324077563 T	
501 A	1501 G	-7:91681946 1324077562 G	A
501	1502 C	-7:91681945 1324077561 C	
501	1503 T	-7:91681944 1324077560 T	
502 K	1504 A	-7:91681943 1324077559 A	K
502	1505 A	-7:91681942 1324077558 A	
502	1506 G	-7:91681941 1324077557 G	
503 L	1507 C	-7:91681940 1324077556 C	L
503	1508 T	-7:91681939 1324077555 T	
503	1509 G	-7:91681938 1324077554 G	
504 I	1510 A	-7:91681937 1324077553 A	I
504	1511 T	-7:91681936 1324077552 T	
504	1512 A	-7:91681935 1324077551 A	
505 T	1513 A	-7:91681934 1324077550 A	T
505	1514 C	-7:91681933 1324077549 C	
505	1515 A	-7:91681932 1324077548 A	
506 L	1516 T	-7:91681931 1324077547 T	L
506	1517 T	-7:91681930 1324077546 T	
506	1518 G	-7:91681929 1324077545 G	
507 A	1519 G	-7:91681928 1324077544 G	A
507	1520 C	-7:91681927 1324077543 C	
507	1521 A	-7:91681926 1324077542 A	
508 S	1522 A	-7:91681925 1324077541 A	S
508	1523 G	-7:91681924 1324077540 G	
508	1524 T	-7:91681923 1324077539 T	
509 L	1525 C	-7:91681922 1324077538 C	L
509	1526 T	-7:91681921 1324077537 T	
509	1527 G	-7:91681920 1324077536 G	
510 L	1528 C	-7:91681919 1324077535 C	L
510	1529 T	-7:91681918 1324077534 T	
510	1530 T	-7:91681917 1324077533 T	
511 L	1531 T	-7:91681916 1324077532 T	L
511	1532 T	-7:91681915 1324077531 T	
511	1533 G	-7:91681914 1324077530 G	
512 Q	1534 C	-7:91681913 1324077529 C	Q
512	1535 A	-7:91681912 1324077528 A	
512	1536 A	-7:91681911 1324077527 A	
513 I	1537 A	-7:91681910 1324077526 A	I
513	1538 T	-7:91681909 1324077525 T	
513	1539 A	-7:91681908 1324077524 A	
514 V	1540 G	-7:91681907 1324077523 G	V
514	1541 T	-7:91681906 1324077522 T	
514	1542 C	-7:91681905 1324077521 C	
515 Y	1543 T	-7:91681904 1324077520 T	Y
515	1544 A	-7:91681903 1324077519 A	
515	1545 T	-7:91681902 1324077518 T	
516 G	1546 G	-7:91681901 1324077517 G	G
516	1547 G	-7:91681900 1324077516 G	
516	1548 A	-7:91681899 1324077515 A	
517 N	1549 A	-7:91681898 1324077514 A	N
517	1550 A	-7:91681897 1324077513 A	
517	1551 T	-7:91681896 1324077512 T	
518 Y	1552 T	-7:91681895 1324077511 T	Y
518	1553 A	-7:91681894 1324077510 A	
518	1554 T	-7:91681893 1324077509 T	
519 E	1555 G	-7:91681892 1324077508 G	E
519	1556 A	-7:91681891 1324077507 A	
519	1557 G	-7:91681890 1324077506 G	
520 S	1558 A	-7:91681889 1324077505 A	S
520	1559 G	-7:91681888 1324077504 G	
520	1560 T	-7:91681887 1324077503 T	
521 K	1561 A	-7:91681886 1324077502 A	K
521	1562 A	-7:91681885 1324077501 A	
521	1563 A	-7:91681884 1324077500 A	
522 K	1564 A	-7:91681883 1324077499 A	K
522	1565 A	-7:91681882 1324077498 A	
522	1566 A	-7:91681881 1324077497 A	
523 H	1567 C	-7:91681880 1324077496 C	H
523	1568 A	-7:91681879 1324077495 A	
523	1569 C	-7:91681878 1324077494 C	
524 K	1570 A	-7:91681877 1324077493 A	K
524	1571 A	-7:91681876 1324077492 A	
524	1572 G	-7:91681875 1324077491 G	
525 Q	1573 C	-7:91681874 1324077490 C	Q
525	1574 A	-7:91681873 1324077489 A	
525	1575 A	-7:91681872 1324077488 A	
526 G	1576 G	-7:91681871 1324077487 G	G
526	1577 G	-7:91681870 1324077486 G	
526	1578 T	-7:91681869 1324077485 T	
527 F	1579 T	-7:91681868 1324077484 T	F
527	1580 T	-7:91681867 1324077483 T	
527	1581 C	-7:91681866 1324077482 C	
528 L	1582 C	-7:91681865 1324077481 C	L
528	1583 T	-7:91681864 1324077480 T	
528	1584 A	-7:91681863 1324077479 A	
529 N	1585 A	-7:91681862 1324077478 A	N
529	1586 A	-7:91681861 1324077477 A	
529	1587 T	-7:91681229 1324076845 T	
530 E	1588 G	-7:91681228 1324076844 G	E
530	1589 A	-7:91681227 1324076843 A	
530	1590 A	-7:91681226 1324076842 A	
531 E	1591 G	-7:91681225 1324076841 G	E
531	1592 A	-7:91681224 1324076840 A	
531	1593 A	-7:91681223 1324076839 A	
532 N	1594 A	-7:91681222 1324076838 A	N
532	1595 A	-7:91681221 1324076837 A	
532	1596 T	-7:91681220 1324076836 T	
533 L	1597 C	-7:91681219 1324076835 C	L
533	1598 T	-7:91681218 1324076834 T	
533	1599 A	-7:91681217 1324076833 A	
534 K	1600 A	-7:91681216 1324076832 A	K
534	1601 A	-7:91681215 1324076831 A	
534	1602 A	-7:91681214 1324076830 A	
535 S	1603 T	-7:91681213 1324076829 T	S
535	1604 C	-7:91681212 1324076828 C	
535	1605 C	-7:91681211 1324076827 C	
536 I	1606 A	-7:91681210 1324076826 A	I
536	1607 T	-7:91681209 1324076825 T	
536	1608 C	-7:91681208 1324076824 C	
537 V	1609 G	-7:91681207 1324076823 G	V
537	1610 T	-7:91681206 1324076822 T	
537	1611 A	-7:91681205 1324076821 A	
538 P	1612 C	-7:91681204 1324076820 C	P
538	1613 C	-7:91681203 1324076819 C	
538	1614 T	-7:91681202 1324076818 T	
539 V	1615 G	-7:91681201 1324076817 G	V
539	1616 T	-7:91681200 1324076816 T	
539	1617 T	-7:91681199 1324076815 T	
540 T	1618 A	-7:91681198 1324076814 A	T
540	1619 C	-7:91681197 1324076813 C	
540	1620 C	-7:91681196 1324076812 C	
541 K	1621 A	-7:91681195 1324076811 A	K
541	1622 A	-7:91681194 1324076810 A	
541	1623 A	-7:91681193 1324076809 A	
542 L	1624 C	-7:91681192 1324076808 C	L
542	1625 T	-7:91681191 1324076807 T	
542	1626 G	-7:91681190 1324076806 G	
543 K	1627 A	-7:91681189 1324076805 A	K
543	1628 A	-7:91681188 1324076804 A	
543	1629 A	-7:91681187 1324076803 A	
544 S	1630 A	-7:91681186 1324076802 A	S
544	1631 G	-7:91681185 1324076801 G	
544	1632 T	-7:91681184 1324076800 T	
545 K	1633 A	-7:91681183 1324076799 A	K
545	1634 A	-7:91681182 1324076798 A	
545	1635 G	-7:91681181 1324076797 G	
546 A	1636 G	-7:91681180 1324076796 G	A
546	1637 C	-7:91681179 1324076795 C	
546	1638 A	-7:91681178 1324076794 A	
547 P	1639 C	-7:91681177 1324076793 C	P
547	1640 C	-7:91681176 1324076792 C	
547	1641 T	-7:91681175 1324076791 T	
548 H	1642 C	-7:91681174 1324076790 C	H
548	1643 A	-7:91681173 1324076789 A	
548	1644 C	-7:91681172 1324076788 C	
549 W	1645 T	-7:91681171 1324076787 T	W
549	1646 G	-7:91681170 1324076786 G	
549	1647 G	-7:91681169 1324076785 G	
550 T	1648 A	-7:91681168 1324076784 A	T
550	1649 C	-7:91681167 1324076783 C	
550	1650 A	-7:91681166 1324076782 A	
551 N	1651 A	-7:91681165 1324076781 A	N
551	1652 A	-7:91681164 1324076780 A	
551	1653 T	-7:91681163 1324076779 T	
552 R	1654 C	-7:91681162 1324076778 C	R
552	1655 G	-7:91681161 1324076777 G	
552	1656 C	-7:91681160 1324076776 C	
553 I	1657 A	-7:91681159 1324076775 A	I
553	1658 T	-7:91681158 1324076774 T	
553	1659 A	-7:91681157 1324076773 A	
554 L	1660 C	-7:91681156 1324076772 C	L
554	1661 T	-7:91681155 1324076771 T	
554	1662 T	-7:91681154 1324076770 T	
555 H	1663 C	-7:91681153 1324076769 C	H
555	1664 A	-7:91681152 1324076768 A	
555	1665 T	-7:91681151 1324076767 T	
556 E	1666 G	-7:91681150 1324076766 G	E
556	1667 A	-7:91681149 1324076765 A	
556	1668 A	-7:91681148 1324076764 A	
557 Y	1669 T	-7:91681147 1324076763 T	Y
557	1670 A	-7:91681146 1324076762 A	
557	1671 C	-7:91681145 1324076761 C	
558 K	1672 A	-7:91681144 1324076760 A	K
558	1673 A	-7:91681143 1324076759 A	
558	1674 G	-7:91681142 1324076758 G	
559 N	1675 A	-7:91680651 1324076267 A	N
559	1676 A	-7:91680650 1324076266 A	
559	1677 T	-7:91680649 1324076265 T	
560 L	1678 C	-7:91680648 1324076264 C	L
560	1679 T	-7:91680647 1324076263 T	
560	1680 C	-7:91680646 1324076262 C	
561 S	1681 A	-7:91680645 1324076261 A	S
561	1682 G	-7:91680644 1324076260 G	
561	1683 T	-7:91680643 1324076259 T	
562 T	1684 A	-7:91680642 1324076258 A	T
562	1685 C	-7:91680641 1324076257 C	
562	1686 A	-7:91680640 1324076256 A	
563 S	1687 A	-7:91680639 1324076255 A	S
563	1688 G	-7:91680638 1324076254 G	
563	1689 T	-7:91680637 1324076253 T	
564 E	1690 G	-7:91680636 1324076252 G	E
564	1691 A	-7:91680635 1324076251 A	
564	1692 A	-7:91680634 1324076250 A	
565 G	1693 G	-7:91680633 1324076249 G	G
565	1694 G	-7:91680632 1324076248 G	
565	1695 T	-7:91680631 1324076247 T	
566 V	1696 G	-7:91680630 1324076246 G	V
566	1697 T	-7:91680629 1324076245 T	
566	1698 C	-7:91680628 1324076244 C	
567 S	1699 A	-7:91680627 1324076243 A	S
567	1700 G	-7:91680626 1324076242 G	
567	1701 T	-7:91680625 1324076241 T	
568 K	1702 A	-7:91680624 1324076240 A	K
568	1703 A	-7:91680623 1324076239 A	
568	1704 A	-7:91680622 1324076238 A	
569 E	1705 G	-7:91680621 1324076237 G	E
569	1706 A	-7:91680620 1324076236 A	
569	1707 A	-7:91680619 1324076235 A	
570 M	1708 A	-7:91680618 1324076234 A	M
570	1709 T	-7:91680617 1324076233 T	
570	1710 G	-7:91680616 1324076232 G	
571 H	1711 C	-7:91680615 1324076231 C	H
571	1712 A	-7:91680614 1324076230 A	
571	1713 T	-7:91680613 1324076229 T	
572 H	1714 C	-7:91680612 1324076228 C	H
572	1715 A	-7:91680611 1324076227 A	
572	1716 C	-7:91680610 1324076226 C	
573 L	1717 C	-7:91680609 1324076225 C	L
573	1718 T	-7:91680608 1324076224 T	
573	1719 T	-7:91680607 1324076223 T	
574 Q	1720 C	-7:91680606 1324076222 C	Q
574	1721 A	-7:91680605 1324076221 A	
574	1722 G	-7:91680604 1324076220 G	
575 R	1723 C	-7:91680603 1324076219 C	R
575	1724 G	-7:91680602 1324076218 G	
575	1725 C	-7:91680601 1324076217 C	
576 M	1726 A	-7:91680600 1324076216 A	M
576	1727 T	-7:91680599 1324076215 T	
576	1728 G	-7:91680598 1324076214 G	
577 F	1729 T	-7:91680597 1324076213 T	F
577	1730 T	-7:91680596 1324076212 T	
577	1731 C	-7:91680595 1324076211 C	
578 L	1732 T	-7:91680594 1324076210 T	L
578	1733 T	-7:91680593 1324076209 T	
578	1734 A	-7:91680592 1324076208 A	
579 Q	1735 C	-7:91680591 1324076207 C	Q
579	1736 A	-7:91680590 1324076206 A	
579	1737 G	-7:91680589 1324076205 G	
580 N	1738 A	-7:91680588 1324076204 A	N
580	1739 A	-7:91680587 1324076203 A	
580	1740 T	-7:91680586 1324076202 T	
581 C	1741 T	-7:91680585 1324076201 T	C
581	1742 G	-7:91680584 1324076200 G	
581	1743 C	-7:91680583 1324076199 C	
582 W	1744 T	-7:91680582 1324076198 T	W
582	1745 G	-7:91680581 1324076197 G	
582	1746 G	-7:91680580 1324076196 G	
583 E	1747 G	-7:91680579 1324076195 G	E
583	1748 A	-7:91680578 1324076194 A	
583	1749 A	-7:91680577 1324076193 A	
584 I	1750 A	-7:91680576 1324076192 A	I
584	1751 T	-7:91680575 1324076191 T	
584	1752 T	-7:91680574 1324076190 T	
585 P	1753 C	-7:91680573 1324076189 C	P
585	1754 C	-7:91680572 1324076188 C	
585	1755 T	-7:91680571 1324076187 T	
586 T	1756 A	-7:91680570 1324076186 A	T
586	1757 C	-7:91680569 1324076185 C	
586	1758 T	-7:91680568 1324076184 T	
587 Y	1759 T	-7:91680567 1324076183 T	Y
587	1760 A	-7:91680566 1324076182 A	
587	1761 T	-7:91680565 1324076181 T	
588 G	1762 G	-7:91680564 1324076180 G	G
588	1763 G	-7:91680563 1324076179 G	
588	1764 A	-7:91680562 1324076178 A	
589 A	1765 G	-7:91680561 1324076177 G	A
589	1766 C	-7:91680560 1324076176 C	
589	1767 A	-7:91680559 1324076175 A	
590 A	1768 G	-7:91680558 1324076174 G	A
590	1769 C	-7:91680557 1324076173 C	
590	1770 A	-7:91680556 1324076172 A	
591 F	1771 T	-7:91680555 1324076171 T	F
591	1772 T	-7:91680554 1324076170 T	
591	1773 T	-7:91680553 1324076169 T	
592 F	1774 T	-7:91680552 1324076168 T	F
592	1775 T	-7:91680551 1324076167 T	
592	1776 C	-7:91680550 1324076166 C	
593 T	1777 A	-7:91680549 1324076165 A	T
593	1778 C	-7:91680548 1324076164 C	
593	1779 A	-7:91680547 1324076163 A	
594 G	1780 G	-7:91680546 1324076162 G	G
594	1781 G	-7:91680545 1324076161 G	
594	1782 A	-7:91680544 1324076160 A	
595 Q	1783 C	-7:91680543 1324076159 C	Q
595	1784 A	-7:91680542 1324076158 A	
595	1785 G	-7:91680541 1324076157 G	
596 I	1786 A	-7:91680540 1324076156 A	I
596	1787 T	-7:91680539 1324076155 T	
596	1788 A	-7:91680538 1324076154 A	
597 F	1789 T	-7:91680537 1324076153 T	F
597	1790 T	-7:91680536 1324076152 T	
597	1791 T	-7:91680535 1324076151 T	
598 T	1792 A	-7:91680534 1324076150 A	T
598	1793 C	-7:91680533 1324076149 C	
598	1794 A	-7:91680532 1324076148 A	
599 K	1795 A	-7:91680531 1324076147 A	K
599	1796 A	-7:91680530 1324076146 A	
599	1797 G	-7:91680529 1324076145 G	
600 A	1798 G	-7:91680528 1324076144 G	A
600	1799 C	-7:91680527 1324076143 C	
600	1800 A	-7:91680526 1324076142 A	
601 S	1801 A	-7:91680525 1324076141 A	S
601	1802 G	-7:91680524 1324076140 G	
601	1803 C	-7:91680523 1324076139 C	
602 P	1804 C	-7:91680522 1324076138 C	P
602	1805 C	-7:91680521 1324076137 C	
602	1806 C	-7:91680520 1324076136 C	
603 S	1807 A	-7:91680519 1324076135 A	S
603	1808 G	-7:91680518 1324076134 G	
603	1809 C	-7:91680517 1324076133 C	
604 N	1810 A	-7:91680516 1324076132 A	N
604	1811 A	-7:91680515 1324076131 A	
604	1812 T	-7:91680514 1324076130 T	
605 H	1813 C	-7:91680513 1324076129 C	H
605	1814 A	-7:91680512 1324076128 A	
605	1815 T	-7:91680511 1324076127 T	
606 K	1816 A	-7:91680510 1324076126 A	K
606	1817 A	-7:91680509 1324076125 A	
606	1818 A	-7:91680508 1324076124 A	
607 V	1819 G	-7:91680507 1324076123 G	V
607	1820 T	-7:91680506 1324076122 T	
607	1821 C	-7:91680505 1324076121 C	
608 I	1822 A	-7:91680504 1324076120 A	I
608	1823 T	-7:91680503 1324076119 T	
608	1824 C	-7:91680502 1324076118 C	
609 P	1825 C	-7:91680501 1324076117 C	P
609	1826 C	-7:91680500 1324076116 C	
609	1827 T	-7:91680499 1324076115 T	
610 V	1828 G	-7:91680498 1324076114 G	V
610	1829 T	-7:91680497 1324076113 T	
610	1830 G	-7:91680496 1324076112 G	
611 Y	1831 T	-7:91680495 1324076111 T	Y
611	1832 A	-7:91680494 1324076110 A	
611	1833 T	-7:91680493 1324076109 T	
612 V	1834 G	-7:91680492 1324076108 G	V
612	1835 T	-7:91680491 1324076107 T	
612	1836 A	-7:91680490 1324076106 A	
613 G	1837 G	-7:91680489 1324076105 G	G
613	1838 G	-7:91680488 1324076104 G	
613	1839 A	-7:91680487 1324076103 A	
614 V	1840 G	-7:91680486 1324076102 G	V
614	1841 T	-7:91680485 1324076101 T	
614	1842 G	-7:91680484 1324076100 G	
615 N	1843 A	-7:91680483 1324076099 A	N
615	1844 A	-7:91680482 1324076098 A	
615	1845 T	-7:91680481 1324076097 T	
616 I	1846 A	-7:91680480 1324076096 A	I
616	1847 T	-7:91680479 1324076095 T	
616	1848 A	-7:91680478 1324076094 A	
617 K	1849 A	-7:91680477 1324076093 A	K
617	1850 A	-7:91680476 1324076092 A	
617	1851 A	-7:91680475 1324076091 A	
618 G	1852 G	-7:91680474 1324076090 G	G
618	1853 G	-7:91680473 1324076089 G	
618	1854 A	-7:91680472 1324076088 A	
619 L	1855 C	-7:91680471 1324076087 C	L
619	1856 T	-7:91680470 1324076086 T	
619	1857 T	-7:91680469 1324076085 T	
620 H	1858 C	-7:91680468 1324076084 C	H
620	1859 A	-7:91680467 1324076083 A	
620	1860 T	-7:91680466 1324076082 T	
621 L	1861 C	-7:91680465 1324076081 C	L
621	1862 T	-7:91680464 1324076080 T	
621	1863 C	-7:91680463 1324076079 C	
622 L	1864 C	-7:91680462 1324076078 C	L
622	1865 T	-7:91680461 1324076077 T	
622	1866 C	-7:91680460 1324076076 C	
623 N	1867 A	-7:91680459 1324076075 A	N
623	1868 A	-7:91680458 1324076074 A	
623	1869 C	-7:91680457 1324076073 C	
624 M	1870 A	-7:91680456 1324076072 A	M
624	1871 T	-7:91680455 1324076071 T	
624	1872 G	-7:91680454 1324076070 G	
625 E	1873 G	-7:91680453 1324076069 G	E
625	1874 A	-7:91680452 1324076068 A	
625	1875 A	-7:91680451 1324076067 A	
626 T	1876 A	-7:91680450 1324076066 A	T
626	1877 C	-7:91680449 1324076065 C	
626	1878 T	-7:91680448 1324076064 T	
627 K	1879 A	-7:91680447 1324076063 A	K
627	1880 A	-7:91680446 1324076062 A	
627	1881 G	-7:91680445 1324076061 G	
>ENSP00000317061 
1 M	1 A	-7:91709385 1324105001 A	M
1	2 T	-7:91709384 1324105000 T	
1	3 G	-7:91709383 1324104999 G	
2 G	4 G	-7:91709382 1324104998 G	G
2	5 G	-7:91709381 1324104997 G	
2	6 A	-7:91709380 1324104996 A	
3 N	7 A	-7:91709379 1324104995 A	N
3	8 A	-7:91709378 1324104994 A	
3	9 T	-7:91709377 1324104993 T	
4 P	10 C	-7:91709376 1324104992 C	P
4	11 C	-7:91709375 1324104991 C	
4	12 A	-7:91709374 1324104990 A	
5 E	13 G	-7:91709373 1324104989 G	E
5	14 A	-7:91709372 1324104988 A	
5	15 A	-7:91709371 1324104987 A	
6 N	16 A	-7:91709370 1324104986 A	N
6	17 A	-7:91709369 1324104985 A	
6	18 C	-7:91709368 1324104984 C	
7 I	19 A	-7:91709367 1324104983 A	I
7	20 T	-7:91709366 1324104982 T	
7	21 A	-7:91709365 1324104981 A	
8 E	22 G	-7:91709364 1324104980 G	E
8	23 A	-7:91709363 1324104979 A	
8	24 A	-7:91709362 1324104978 A	
9 D	25 G	-7:91709361 1324104977 G	D
9	26 A	-7:91709360 1324104976 A	
9	27 T	-7:91709359 1324104975 T	
10 A	28 G	-7:91709358 1324104974 G	A
10	29 C	-7:91709357 1324104973 C	
10	30 A	-7:91709356 1324104972 A	
11 Y	31 T	-7:91709355 1324104971 T	Y
11	32 A	-7:91709354 1324104970 A	
11	33 T	-7:91709353 1324104969 T	
12 V	34 G	-7:91709352 1324104968 G	V
12	35 T	-7:91709351 1324104967 T	
12	36 T	-7:91709350 1324104966 T	
13 A	37 G	-7:91709349 1324104965 G	A
13	38 C	-7:91709348 1324104964 C	
13	39 T	-7:91709347 1324104963 T	
14 V	40 G	-7:91709346 1324104962 G	V
14	41 T	-7:91709345 1324104961 T	
14	42 T	-7:91709344 1324104960 T	
15 I	43 A	-7:91709343 1324104959 A	I
15	44 T	-7:91709342 1324104958 T	
15	45 T	-7:91709341 1324104957 T	
16 R	46 C	-7:91709340 1324104956 C	R
16	47 G	-7:91709339 1324104955 G	
16	48 T	-7:91709338 1324104954 T	
17 P	49 C	-7:91709337 1324104953 C	P
17	50 C	-7:91709336 1324104952 C	
17	51 A	-7:91709335 1324104951 A	
18 K	52 A	-7:91709334 1324104950 A	K
18	53 A	-7:91709333 1324104949 A	
18	54 G	-7:91709332 1324104948 G	
19 N	55 A	-7:91709331 1324104947 A	N
19	56 A	-7:91709330 1324104946 A	
19	57 T	-7:91709329 1324104945 T	
20 T	58 A	-7:91709328 1324104944 A	T
20	59 C	-7:91709327 1324104943 C	
20	60 T	-7:91709326 1324104942 T	
21 A	61 G	-7:91709325 1324104941 G	A
21	62 C	-7:91709324 1324104940 C	
21	63 C	-7:91709323 1324104939 C	
22 S	64 A	-7:91709322 1324104938 A	S
22	65 G	-7:91709321 1324104937 G	
22	66 T	-7:91709320 1324104936 T	
23 L	67 C	-7:91709319 1324104935 C	L
23	68 T	-7:91709318 1324104934 T	
23	69 C	-7:91709317 1324104933 C	
24 N	70 A	-7:91709316 1324104932 A	N
24	71 A	-7:91709315 1324104931 A	
24	72 T	-7:91709314 1324104930 T	
25 S	73 T	-7:91709313 1324104929 T	S
25	74 C	-7:91709312 1324104928 C	
25	75 T	-7:91709311 1324104927 T	
26 R	76 C	-7:91709310 1324104926 C	R
26	77 G	-7:91709309 1324104925 G	
26	78 G	-7:91709308 1324104924 G	
27 E	79 G	-7:91709307 1324104923 G	E
27	80 A	-7:91709306 1324104922 A	
27	81 A	-7:91709305 1324104921 A	
28 Y	82 T	-7:91709304 1324104920 T	Y
28	83 A	-7:91709303 1324104919 A	
28	84 C	-7:91709302 1324104918 C	
29 R	85 A	-7:91709301 1324104917 A	R
29	86 G	-7:91709300 1324104916 G	
29	87 A	-7:91709299 1324104915 A	
30 A	88 G	-7:91709298 1324104914 G	A
30	89 C	-7:91709297 1324104913 C	
30	90 T	-7:91709296 1324104912 T	
31 K	91 A	-7:91709295 1324104911 A	K
31	92 A	-7:91709294 1324104910 A	
31	93 G	-7:91709293 1324104909 G	
32 S	94 T	-7:91709292 1324104908 T	S
32	95 C	-7:91709291 1324104907 C	
32	96 A	-7:91709290 1324104906 A	
33 Y	97 T	-7:91709289 1324104905 T	Y
33	98 A	-7:91709288 1324104904 A	
33	99 T	-7:91709287 1324104903 T	
34 E	100 G	-7:91709286 1324104902 G	E
34	101 A	-7:91709285 1324104901 A	
34	102 A	-7:91709284 1324104900 A	
35 I	103 A	-7:91708402 1324104018 A	I
35	104 T	-7:91708401 1324104017 T	
35	105 T	-7:91708400 1324104016 T	
36 L	106 T	-7:91708399 1324104015 T	L
36	107 T	-7:91708398 1324104014 T	
36	108 G	-7:91708397 1324104013 G	
37 L	109 T	-7:91708396 1324104012 T	L
37	110 T	-7:91708395 1324104011 T	
37	111 G	-7:91708394 1324104010 G	
38 H	112 C	-7:91708393 1324104009 C	H
38	113 A	-7:91708392 1324104008 A	
38	114 T	-7:91708391 1324104007 T	
39 E	115 G	-7:91708390 1324104006 G	E
39	116 A	-7:91708389 1324104005 A	
39	117 A	-7:91708388 1324104004 A	
40 V	118 G	-7:91708387 1324104003 G	V
40	119 T	-7:91708386 1324104002 T	
40	120 T	-7:91708385 1324104001 T	
41 P	121 C	-7:91708384 1324104000 C	P
41	122 C	-7:91708383 1324103999 C	
41	123 C	-7:91708382 1324103998 C	
42 I	124 A	-7:91708381 1324103997 A	I
42	125 T	-7:91708380 1324103996 T	
42	126 T	-7:91708379 1324103995 T	
43 E	127 G	-7:91708378 1324103994 G	E
43	128 A	-7:91708377 1324103993 A	
43	129 A	-7:91708376 1324103992 A	
44 G	130 G	-7:91708375 1324103991 G	G
44	131 G	-7:91708374 1324103990 G	
44	132 A	-7:91708373 1324103989 A	
45 Q	133 C	-7:91708372 1324103988 C	Q
45	134 A	-7:91708371 1324103987 A	
45	135 G	-7:91708370 1324103986 G	
46 K	136 A	-7:91708369 1324103985 A	K
46	137 A	-7:91708368 1324103984 A	
46	138 A	-7:91708367 1324103983 A	
47 K	139 A	-7:91708366 1324103982 A	K
47	140 A	-7:91708365 1324103981 A	
47	141 A	-7:91708364 1324103980 A	
48 K	142 A	-7:91708363 1324103979 A	K
48	143 A	-7:91708362 1324103978 A	
48	144 G	-7:91708361 1324103977 G	
49 R	145 A	-7:91708360 1324103976 A	R
49	146 G	-7:91708359 1324103975 G	
49	147 A	-7:91708358 1324103974 A	
50 K	148 A	-7:91708357 1324103973 A	K
50	149 A	-7:91708356 1324103972 A	
50	150 G	-7:91708355 1324103971 G	
51 K	151 A	-7:91708354 1324103970 A	K
51	152 A	-7:91708353 1324103969 A	
51	153 A	-7:91708352 1324103968 A	
52 V	154 G	-7:91708351 1324103967 G	V
52	155 T	-7:91708350 1324103966 T	
52	156 T	-7:91708349 1324103965 T	
53 L	157 T	-7:91708348 1324103964 T	L
53	158 T	-7:91708347 1324103963 T	
53	159 A	-7:91708346 1324103962 A	
54 L	160 T	-7:91708345 1324103961 T	L
54	161 T	-7:91708344 1324103960 T	
54	162 G	-7:91708343 1324103959 G	
55 E	163 G	-7:91708342 1324103958 G	E
55	164 A	-7:91708341 1324103957 A	
55	165 A	-7:91708340 1324103956 A	
56 T	166 A	-7:91708339 1324103955 A	T
56	167 C	-7:91708338 1324103954 C	
56	168 G	-7:91708337 1324103953 G	
57 K	169 A	-7:91708336 1324103952 A	K
57	170 A	-7:91708335 1324103951 A	
57	171 A	-7:91708334 1324103950 A	
58 L	172 C	-7:91708333 1324103949 C	L
58	173 T	-7:91708332 1324103948 T	
58	174 T	-7:91708331 1324103947 T	
59 Q	175 C	-7:91708330 1324103946 C	Q
59	176 A	-7:91708329 1324103945 A	
59	177 A	-7:91708328 1324103944 A	
60 G	178 G	-7:91708327 1324103943 G	G
60	179 G	-7:91708326 1324103942 G	
60	180 C	-7:91708325 1324103941 C	
61 N	181 A	-7:91708324 1324103940 A	N
61	182 A	-7:91708323 1324103939 A	
61	183 C	-7:91708322 1324103938 C	
62 S	184 A	-7:91708321 1324103937 A	S
62	185 G	-7:91708320 1324103936 G	
62	186 T	-7:91708319 1324103935 T	
63 E	187 G	-7:91708318 1324103934 G	E
63	188 A	-7:91708317 1324103933 A	
63	189 A	-7:91708316 1324103932 A	
64 I	190 A	-7:91708315 1324103931 A	I
64	191 T	-7:91708314 1324103930 T	
64	192 A	-7:91708313 1324103929 A	
65 T	193 A	-7:91708312 1324103928 A	T
65	194 C	-7:91708311 1324103927 C	
65	195 A	-7:91708310 1324103926 A	
66 Q	196 C	-7:91708309 1324103925 C	Q
66	197 A	-7:91708308 1324103924 A	
66	198 A	-7:91708307 1324103923 A	
67 G	199 G	-7:91708306 1324103922 G	G
67	200 G	-7:91708305 1324103921 G	
67	201 C	-7:91708304 1324103920 C	
68 I	202 A	-7:91708303 1324103919 A	I
68	203 T	-7:91708302 1324103918 T	
68	204 A	-7:91708301 1324103917 A	
69 L	205 T	-7:91708300 1324103916 T	L
69	206 T	-7:91708299 1324103915 T	
69	207 G	-7:91708298 1324103914 G	
70 D	208 G	-7:91708297 1324103913 G	D
70	209 A	-7:91708296 1324103912 A	
70	210 T	-7:91708295 1324103911 T	
71 Y	211 T	-7:91708294 1324103910 T	Y
71	212 A	-7:91708293 1324103909 A	
71	213 C	-7:91708292 1324103908 C	
72 V	214 G	-7:91708291 1324103907 G	V
72	215 T	-7:91708290 1324103906 T	
72	216 A	-7:91708289 1324103905 A	
73 V	217 G	-7:91708288 1324103904 G	V
73	218 T	-7:91708287 1324103903 T	
73	219 A	-7:91708286 1324103902 A	
74 E	220 G	-7:91708285 1324103901 G	E
74	221 A	-7:91708284 1324103900 A	
74	222 A	-7:91708283 1324103899 A	
75 T	223 A	-7:91708282 1324103898 A	T
75	224 C	-7:91708281 1324103897 C	
75	225 C	-7:91708280 1324103896 C	
76 T	226 A	-7:91708279 1324103895 A	T
76	227 C	-7:91708278 1324103894 C	
76	228 C	-7:91708277 1324103893 C	
77 K	229 A	-7:91708276 1324103892 A	K
77	230 A	-7:91708275 1324103891 A	
77	231 A	-7:91708274 1324103890 A	
78 P	232 C	-7:91708273 1324103889 C	P
78	233 C	-7:91708272 1324103888 C	
78	234 A	-7:91708271 1324103887 A	
79 I	235 A	-7:91708270 1324103886 A	I
79	236 T	-7:91708269 1324103885 T	
79	237 T	-7:91708268 1324103884 T	
80 S	238 T	-7:91708267 1324103883 T	S
80	239 C	-7:91708266 1324103882 C	
80	240 T	-7:91708265 1324103881 T	
81 P	241 C	-7:91708264 1324103880 C	P
81	242 C	-7:91708263 1324103879 C	
81	243 T	-7:91708262 1324103878 T	
82 A	244 G	-7:91708261 1324103877 G	A
82	245 C	-7:91708260 1324103876 C	
82	246 A	-7:91708259 1324103875 A	
83 N	247 A	-7:91708258 1324103874 A	N
83	248 A	-7:91708257 1324103873 A	
83	249 C	-7:91708256 1324103872 C	
84 Q	250 C	-7:91708255 1324103871 C	Q
84	251 A	-7:91708254 1324103870 A	
84	252 G	-7:91708253 1324103869 G	
85 G	253 G	-7:91708252 1324103868 G	G
85	254 G	-7:91708251 1324103867 G	
85	255 T	-7:91708250 1324103866 T	
86 I	256 A	-7:91708249 1324103865 A	I
86	257 T	-7:91708248 1324103864 T	
86	258 C	-7:91708247 1324103863 C	
87 R	259 A	-7:91708246 1324103862 A	R
87	260 G	-7:91708245 1324103861 G	
87	261 A	-7:91708244 1324103860 A	
88 G	262 G	-7:91708243 1324103859 G	G
88	263 G	-7:91705009 1324100625 G	
88	264 A	-7:91705008 1324100624 A	
89 K	265 A	-7:91705007 1324100623 A	K
89	266 A	-7:91705006 1324100622 A	
89	267 A	-7:91705005 1324100621 A	
90 R	268 C	-7:91705004 1324100620 C	R
90	269 G	-7:91705003 1324100619 G	
90	270 A	-7:91705002 1324100618 A	
91 V	271 G	-7:91705001 1324100617 G	V
91	272 T	-7:91705000 1324100616 T	
91	273 T	-7:91704999 1324100615 T	
92 V	274 G	-7:91704998 1324100614 G	V
92	275 T	-7:91704997 1324100613 T	
92	276 A	-7:91704996 1324100612 A	
93 L	277 C	-7:91704995 1324100611 C	L
93	278 T	-7:91704994 1324100610 T	
93	279 A	-7:91704993 1324100609 A	
94 M	280 A	-7:91704992 1324100608 A	M
94	281 T	-7:91704991 1324100607 T	
94	282 G	-7:91704990 1324100606 G	
95 K	283 A	-7:91704989 1324100605 A	K
95	284 A	-7:91704988 1324100604 A	
95	285 A	-7:91704987 1324100603 A	
96 K	286 A	-7:91704986 1324100602 A	K
96	287 A	-7:91704985 1324100601 A	
96	288 A	-7:91704984 1324100600 A	
97 F	289 T	-7:91704983 1324100599 T	F
97	290 T	-7:91704982 1324100598 T	
97	291 T	-7:91704981 1324100597 T	
98 P	292 C	-7:91704980 1324100596 C	P
98	293 C	-7:91704979 1324100595 C	
98	294 T	-7:91704978 1324100594 T	
99 L	295 C	-7:91704977 1324100593 C	L
99	296 T	-7:91704976 1324100592 T	
99	297 G	-7:91704975 1324100591 G	
100 D	298 G	-7:91704974 1324100590 G	D
100	299 A	-7:91704973 1324100589 A	
100	300 T	-7:91704972 1324100588 T	
101 G	301 G	-7:91704971 1324100587 G	G
101	302 G	-7:91704970 1324100586 G	
101	303 A	-7:91704969 1324100585 A	
102 E	304 G	-7:91704968 1324100584 G	E
102	305 A	-7:91704967 1324100583 A	
102	306 G	-7:91704966 1324100582 G	
103 K	307 A	-7:91704965 1324100581 A	K
103	308 A	-7:91704964 1324100580 A	
103	309 G	-7:91704963 1324100579 G	
104 M	310 A	-7:91704962 1324100578 A	M
104	311 T	-7:91704961 1324100577 T	
104	312 G	-7:91704960 1324100576 G	
105 G	313 G	-7:91704959 1324100575 G	G
105	314 G	-7:91704958 1324100574 G	
105	315 C	-7:91704957 1324100573 C	
106 R	316 A	-7:91704956 1324100572 A	R
106	317 G	-7:91704955 1324100571 G	
106	318 A	-7:91704954 1324100570 A	
107 E	319 G	-7:91704953 1324100569 G	E
107	320 A	-7:91704952 1324100568 A	
107	321 A	-7:91704951 1324100567 A	
108 A	322 G	-7:91704950 1324100566 G	A
108	323 C	-7:91704949 1324100565 C	
108	324 A	-7:91704948 1324100564 A	
109 S	325 T	-7:91704947 1324100563 T	S
109	326 C	-7:91704946 1324100562 C	
109	327 A	-7:91704945 1324100561 A	
110 L	328 T	-7:91704944 1324100560 T	L
110	329 T	-7:91704943 1324100559 T	
110	330 A	-7:91704942 1324100558 A	
111 F	331 T	-7:91704941 1324100557 T	F
111	332 T	-7:91704940 1324100556 T	
111	333 T	-7:91704939 1324100555 T	
112 I	334 A	-7:91704938 1324100554 A	I
112	335 T	-7:91704937 1324100553 T	
112	336 T	-7:91704936 1324100552 T	
113 V	337 G	-7:91704935 1324100551 G	V
113	338 T	-7:91704934 1324100550 T	
113	339 T	-7:91704933 1324100549 T	
114 P	340 C	-7:91704932 1324100548 C	P
114	341 C	-7:91704931 1324100547 C	
114	342 A	-7:91704930 1324100546 A	
115 S	343 T	-7:91704929 1324100545 T	S
115	344 C	-7:91704928 1324100544 C	
115	345 A	-7:91704927 1324100543 A	
116 V	346 G	-7:91704926 1324100542 G	V
116	347 T	-7:91704925 1324100541 T	
116	348 T	-7:91704924 1324100540 T	
117 V	349 G	-7:91704923 1324100539 G	V
117	350 T	-7:91704922 1324100538 T	
117	351 C	-7:91704921 1324100537 C	
118 K	352 A	-7:91704920 1324100536 A	K
118	353 A	-7:91704919 1324100535 A	
118	354 A	-7:91704918 1324100534 A	
119 D	355 G	-7:91704917 1324100533 G	D
119	356 A	-7:91703792 1324099408 A	
119	357 T	-7:91703791 1324099407 T	
120 N	358 A	-7:91703790 1324099406 A	N
120	359 A	-7:91703789 1324099405 A	
120	360 T	-7:91703788 1324099404 T	
121 T	361 A	-7:91703787 1324099403 A	T
121	362 C	-7:91703786 1324099402 C	
121	363 T	-7:91703785 1324099401 T	
122 K	364 A	-7:91703784 1324099400 A	K
122	365 A	-7:91703783 1324099399 A	
122	366 A	-7:91703782 1324099398 A	
123 Y	367 T	-7:91703781 1324099397 T	Y
123	368 A	-7:91703780 1324099396 A	
123	369 C	-7:91703779 1324099395 C	
124 T	370 A	-7:91703778 1324099394 A	T
124	371 C	-7:91703777 1324099393 C	
124	372 A	-7:91703776 1324099392 A	
125 Y	373 T	-7:91703775 1324099391 T	Y
125	374 A	-7:91703774 1324099390 A	
125	375 T	-7:91703773 1324099389 T	
126 T	376 A	-7:91703772 1324099388 A	T
126	377 C	-7:91703771 1324099387 C	
126	378 C	-7:91703770 1324099386 C	
127 P	379 C	-7:91703769 1324099385 C	P
127	380 C	-7:91703768 1324099384 C	
127	381 A	-7:91703767 1324099383 A	
128 G	382 G	-7:91703766 1324099382 G	G
128	383 G	-7:91703765 1324099381 G	
128	384 A	-7:91703764 1324099380 A	
129 C	385 T	-7:91703763 1324099379 T	C
129	386 G	-7:91703762 1324099378 G	
129	387 C	-7:91703761 1324099377 C	
130 P	388 C	-7:91703760 1324099376 C	P
130	389 C	-7:91703759 1324099375 C	
130	390 A	-7:91703758 1324099374 A	
131 I	391 A	-7:91703757 1324099373 A	I
131	392 T	-7:91703756 1324099372 T	
131	393 T	-7:91703755 1324099371 T	
132 F	394 T	-7:91703754 1324099370 T	F
132	395 T	-7:91703753 1324099369 T	
132	396 T	-7:91703752 1324099368 T	
133 Y	397 T	-7:91703751 1324099367 T	Y
133	398 A	-7:91703750 1324099366 A	
133	399 C	-7:91703749 1324099365 C	
134 C	400 T	-7:91703748 1324099364 T	C
134	401 G	-7:91703747 1324099363 G	
134	402 C	-7:91703746 1324099362 C	
135 L	403 T	-7:91703745 1324099361 T	L
135	404 T	-7:91703744 1324099360 T	
135	405 A	-7:91703743 1324099359 A	
136 Q	406 C	-7:91703742 1324099358 C	Q
136	407 A	-7:91703741 1324099357 A	
136	408 A	-7:91703740 1324099356 A	
137 D	409 G	-7:91703739 1324099355 G	D
137	410 A	-7:91703738 1324099354 A	
137	411 T	-7:91703737 1324099353 T	
138 I	412 A	-7:91703736 1324099352 A	I
138	413 T	-7:91703735 1324099351 T	
138	414 T	-7:91703734 1324099350 T	
139 M	415 A	-7:91703733 1324099349 A	M
139	416 T	-7:91703732 1324099348 T	
139	417 G	-7:91703731 1324099347 G	
140 R	418 C	-7:91703730 1324099346 C	R
140	419 G	-7:91703729 1324099345 G	
140	420 A	-7:91703728 1324099344 A	
141 V	421 G	-7:91703727 1324099343 G	V
141	422 T	-7:91703726 1324099342 T	
141	423 C	-7:91703725 1324099341 C	
142 C	424 T	-7:91703724 1324099340 T	C
142	425 G	-7:91703723 1324099339 G	
142	426 T	-7:91703722 1324099338 T	
143 S	427 A	-7:91703721 1324099337 A	S
143	428 G	-7:91703720 1324099336 G	
143	429 T	-7:91703719 1324099335 T	
144 E	430 G	-7:91703718 1324099334 G	E
144	431 A	-7:91703717 1324099333 A	
144	432 A	-7:91703716 1324099332 A	
145 S	433 T	-7:91703715 1324099331 T	S
145	434 C	-7:91703714 1324099330 C	
145	435 C	-7:91703713 1324099329 C	
146 S	436 A	-7:91703712 1324099328 A	S
146	437 G	-7:91703711 1324099327 G	
146	438 T	-7:91703710 1324099326 T	
147 T	439 A	-7:91703709 1324099325 A	T
147	440 C	-7:91703708 1324099324 C	
147	441 T	-7:91703707 1324099323 T	
148 H	442 C	-7:91703706 1324099322 C	H
148	443 A	-7:91703705 1324099321 A	
148	444 T	-7:91703704 1324099320 T	
149 F	445 T	-7:91703703 1324099319 T	F
149	446 T	-7:91703702 1324099318 T	
149	447 T	-7:91703701 1324099317 T	
150 A	448 G	-7:91703700 1324099316 G	A
150	449 C	-7:91703699 1324099315 C	
150	450 T	-7:91703698 1324099314 T	
151 T	451 A	-7:91703697 1324099313 A	T
151	452 C	-7:91703696 1324099312 C	
151	453 A	-7:91703695 1324099311 A	
152 L	454 C	-7:91703694 1324099310 C	L
152	455 T	-7:91703693 1324099309 T	
152	456 T	-7:91703692 1324099308 T	
153 T	457 A	-7:91703691 1324099307 A	T
153	458 C	-7:91703690 1324099306 C	
153	459 A	-7:91703689 1324099305 A	
154 A	460 G	-7:91703688 1324099304 G	A
154	461 C	-7:91703687 1324099303 C	
154	462 A	-7:91703686 1324099302 A	
155 R	463 A	-7:91703685 1324099301 A	R
155	464 G	-7:91703684 1324099300 G	
155	465 G	-7:91703683 1324099299 G	
156 M	466 A	-7:91703682 1324099298 A	M
156	467 T	-7:91703681 1324099297 T	
156	468 G	-7:91703680 1324099296 G	
157 L	469 T	-7:91703679 1324099295 T	L
157	470 T	-7:91703678 1324099294 T	
157	471 A	-7:91703677 1324099293 A	
158 I	472 A	-7:91703676 1324099292 A	I
158	473 T	-7:91703675 1324099291 T	
158	474 A	-7:91703674 1324099290 A	
159 A	475 G	-7:91703673 1324099289 G	A
159	476 C	-7:91703672 1324099288 C	
159	477 C	-7:91703671 1324099287 C	
160 L	478 T	-7:91703670 1324099286 T	L
160	479 T	-7:91703669 1324099285 T	
160	480 G	-7:91703668 1324099284 G	
161 D	481 G	-7:91703667 1324099283 G	D
161	482 A	-7:91703666 1324099282 A	
161	483 T	-7:91703665 1324099281 T	
162 K	484 A	-7:91703664 1324099280 A	K
162	485 A	-7:91703663 1324099279 A	
162	486 G	-7:91702896 1324098512 G	
163 W	487 T	-7:91702895 1324098511 T	W
163	488 G	-7:91702894 1324098510 G	
163	489 G	-7:91702893 1324098509 G	
164 L	490 T	-7:91702892 1324098508 T	L
164	491 T	-7:91702891 1324098507 T	
164	492 A	-7:91702890 1324098506 A	
165 D	493 G	-7:91702889 1324098505 G	D
165	494 A	-7:91702888 1324098504 A	
165	495 T	-7:91702887 1324098503 T	
166 E	496 G	-7:91702886 1324098502 G	E
166	497 A	-7:91702885 1324098501 A	
166	498 A	-7:91702884 1324098500 A	
167 R	499 C	-7:91702883 1324098499 C	R
167	500 G	-7:91702882 1324098498 G	
167	501 T	-7:91702881 1324098497 T	
168 H	502 C	-7:91702880 1324098496 C	H
168	503 A	-7:91702879 1324098495 A	
168	504 T	-7:91702878 1324098494 T	
169 A	505 G	-7:91702877 1324098493 G	A
169	506 C	-7:91702876 1324098492 C	
169	507 A	-7:91702875 1324098491 A	
170 Q	508 C	-7:91702874 1324098490 C	Q
170	509 A	-7:91702873 1324098489 A	
170	510 A	-7:91702872 1324098488 A	
171 S	511 T	-7:91702871 1324098487 T	S
171	512 C	-7:91702870 1324098486 C	
171	513 T	-7:91702869 1324098485 T	
172 H	514 C	-7:91702868 1324098484 C	H
172	515 A	-7:91702867 1324098483 A	
172	516 C	-7:91702866 1324098482 C	
173 F	517 T	-7:91702865 1324098481 T	F
173	518 T	-7:91702864 1324098480 T	
173	519 T	-7:91702863 1324098479 T	
174 I	520 A	-7:91702862 1324098478 A	I
174	521 T	-7:91702861 1324098477 T	
174	522 T	-7:91702860 1324098476 T	
175 P	523 C	-7:91702859 1324098475 C	P
175	524 C	-7:91702858 1324098474 C	
175	525 A	-7:91702857 1324098473 A	
176 A	526 G	-7:91702856 1324098472 G	A
176	527 C	-7:91702855 1324098471 C	
176	528 T	-7:91702854 1324098470 T	
177 L	529 T	-7:91702853 1324098469 T	L
177	530 T	-7:91702852 1324098468 T	
177	531 A	-7:91702851 1324098467 A	
178 F	532 T	-7:91702850 1324098466 T	F
178	533 T	-7:91702849 1324098465 T	
178	534 C	-7:91702848 1324098464 C	
179 R	535 C	-7:91702847 1324098463 C	R
179	536 G	-7:91702846 1324098462 G	
179	537 A	-7:91702845 1324098461 A	
180 P	538 C	-7:91702844 1324098460 C	P
180	539 C	-7:91702843 1324098459 C	
180	540 T	-7:91702842 1324098458 T	
181 S	541 T	-7:91702841 1324098457 T	S
181	542 C	-7:91702840 1324098456 C	
181	543 T	-7:91702839 1324098455 T	
182 P	544 C	-7:91702838 1324098454 C	P
182	545 C	-7:91702837 1324098453 C	
182	546 T	-7:91702836 1324098452 T	
183 L	547 C	-7:91702835 1324098451 C	L
183	548 T	-7:91702834 1324098450 T	
183	549 T	-7:91702833 1324098449 T	
184 E	550 G	-7:91702832 1324098448 G	E
184	551 A	-7:91702831 1324098447 A	
184	552 G	-7:91702830 1324098446 G	
185 R	553 C	-7:91702829 1324098445 C	R
185	554 G	-7:91702828 1324098444 G	
185	555 G	-7:91702827 1324098443 G	
186 I	556 A	-7:91702826 1324098442 A	I
186	557 T	-7:91702825 1324098441 T	
186	558 A	-7:91702824 1324098440 A	
187 K	559 A	-7:91702823 1324098439 A	K
187	560 A	-7:91702822 1324098438 A	
187	561 A	-7:91702821 1324098437 A	
188 T	562 A	-7:91702820 1324098436 A	T
188	563 C	-7:91702819 1324098435 C	
188	564 T	-7:91702818 1324098434 T	
189 N	565 A	-7:91702817 1324098433 A	N
189	566 A	-7:91702816 1324098432 A	
189	567 T	-7:91702815 1324098431 T	
190 V	568 G	-7:91702814 1324098430 G	V
190	569 T	-7:91702813 1324098429 T	
190	570 C	-7:91702812 1324098428 C	
191 I	571 A	-7:91702811 1324098427 A	I
191	572 T	-7:91702810 1324098426 T	
191	573 A	-7:91702809 1324098425 A	
192 N	574 A	-7:91702808 1324098424 A	N
192	575 A	-7:91702807 1324098423 A	
192	576 T	-7:91702806 1324098422 T	
193 P	577 C	-7:91702805 1324098421 C	P
193	578 C	-7:91702804 1324098420 C	
193	579 T	-7:91702803 1324098419 T	
194 A	580 G	-7:91702802 1324098418 G	A
194	581 C	-7:91702801 1324098417 C	
194	582 A	-7:91702800 1324098416 A	
195 Y	583 T	-7:91702799 1324098415 T	Y
195	584 A	-7:91702798 1324098414 A	
195	585 T	-7:91702797 1324098413 T	
196 A	586 G	-7:91702796 1324098412 G	A
196	587 C	-7:91702795 1324098411 C	
196	588 T	-7:91702794 1324098410 T	
197 T	589 A	-7:91702793 1324098409 A	T
197	590 C	-7:91702792 1324098408 C	
197	591 T	-7:91702791 1324098407 T	
198 E	592 G	-7:91702790 1324098406 G	E
198	593 A	-7:91702789 1324098405 A	
198	594 A	-7:91702788 1324098404 A	
199 S	595 T	-7:91702787 1324098403 T	S
199	596 C	-7:91702786 1324098402 C	
199	597 A	-7:91702785 1324098401 A	
200 G	598 G	-7:91702784 1324098400 G	G
200	599 G	-7:91702783 1324098399 G	
200	600 T	-7:91702782 1324098398 T	
201 Q	601 C	-7:91702781 1324098397 C	Q
201	602 A	-7:91702780 1324098396 A	
201	603 G	-7:91702779 1324098395 G	
202 T	604 A	-7:91702778 1324098394 A	T
202	605 C	-7:91702777 1324098393 C	
202	606 A	-7:91702776 1324098392 A	
203 E	607 G	-7:91702775 1324098391 G	E
203	608 A	-7:91702774 1324098390 A	
203	609 A	-7:91702773 1324098389 A	
204 N	610 A	-7:91702772 1324098388 A	N
204	611 A	-7:91702771 1324098387 A	
204	612 C	-7:91702770 1324098386 C	
205 S	613 T	-7:91702769 1324098385 T	S
205	614 C	-7:91702768 1324098384 C	
205	615 A	-7:91702767 1324098383 A	
206 L	616 C	-7:91702766 1324098382 C	L
206	617 T	-7:91702765 1324098381 T	
206	618 A	-7:91702764 1324098380 A	
207 H	619 C	-7:91702763 1324098379 C	H
207	620 A	-7:91702762 1324098378 A	
207	621 T	-7:91702761 1324098377 T	
208 M	622 A	-7:91702760 1324098376 A	M
208	623 T	-7:91702759 1324098375 T	
208	624 G	-7:91702758 1324098374 G	
209 G	625 G	-7:91702757 1324098373 G	G
209	626 G	-7:91702756 1324098372 G	
209	627 C	-7:91702755 1324098371 C	
210 Y	628 T	-7:91702754 1324098370 T	Y
210	629 A	-7:91702753 1324098369 A	
210	630 T	-7:91702752 1324098368 T	
211 S	631 A	-7:91702751 1324098367 A	S
211	632 G	-7:91702750 1324098366 G	
211	633 T	-7:91702749 1324098365 T	
212 A	634 G	-7:91702748 1324098364 G	A
212	635 C	-7:91702747 1324098363 C	
212	636 A	-7:91702746 1324098362 A	
213 L	637 C	-7:91702745 1324098361 C	L
213	638 T	-7:91702744 1324098360 T	
213	639 A	-7:91702743 1324098359 A	
214 E	640 G	-7:91702742 1324098358 G	E
214	641 A	-7:91702741 1324098357 A	
214	642 A	-7:91702740 1324098356 A	
215 I	643 A	-7:91702739 1324098355 A	I
215	644 T	-7:91702738 1324098354 T	
215	645 A	-7:91702737 1324098353 A	
216 K	646 A	-7:91702736 1324098352 A	K
216	647 A	-7:91702735 1324098351 A	
216	648 G	-7:91702734 1324098350 G	
217 S	649 A	-7:91702733 1324098349 A	S
217	650 G	-7:91702732 1324098348 G	
217	651 T	-7:91702731 1324098347 T	
218 K	652 A	-7:91702730 1324098346 A	K
218	653 A	-7:91702729 1324098345 A	
218	654 A	-7:91702728 1324098344 A	
219 M	655 A	-7:91702727 1324098343 A	M
219	656 T	-7:91702726 1324098342 T	
219	657 G	-7:91702725 1324098341 G	
220 L	658 T	-7:91702724 1324098340 T	L
220	659 T	-7:91702723 1324098339 T	
220	660 A	-7:91702722 1324098338 A	
221 A	661 G	-7:91702721 1324098337 G	A
221	662 C	-7:91702720 1324098336 C	
221	663 C	-7:91702719 1324098335 C	
222 L	664 C	-7:91702718 1324098334 C	L
222	665 T	-7:91702717 1324098333 T	
222	666 A	-7:91702716 1324098332 A	
223 E	667 G	-7:91702715 1324098331 G	E
223	668 A	-7:91702714 1324098330 A	
223	669 G	-7:91702713 1324098329 G	
224 K	670 A	-7:91702712 1324098328 A	K
224	671 A	-7:91702711 1324098327 A	
224	672 A	-7:91702710 1324098326 A	
225 A	673 G	-7:91702709 1324098325 G	A
225	674 C	-7:91702708 1324098324 C	
225	675 A	-7:91702707 1324098323 A	
226 D	676 G	-7:91702706 1324098322 G	D
226	677 A	-7:91702705 1324098321 A	
226	678 T	-7:91702704 1324098320 T	
227 T	679 A	-7:91702703 1324098319 A	T
227	680 C	-7:91702702 1324098318 C	
227	681 C	-7:91702701 1324098317 C	
228 C	682 T	-7:91702700 1324098316 T	C
228	683 G	-7:91702699 1324098315 G	
228	684 T	-7:91702698 1324098314 T	
229 I	685 A	-7:91702697 1324098313 A	I
229	686 T	-7:91702696 1324098312 T	
229	687 T	-7:91702695 1324098311 T	
230 Y	688 T	-7:91702694 1324098310 T	Y
230	689 A	-7:91702693 1324098309 A	
230	690 C	-7:91702692 1324098308 C	
231 N	691 A	-7:91702691 1324098307 A	N
231	692 A	-7:91702690 1324098306 A	
231	693 C	-7:91702689 1324098305 C	
232 P	694 C	-7:91702688 1324098304 C	P
232	695 C	-7:91702687 1324098303 C	
232	696 T	-7:91702686 1324098302 T	
233 L	697 T	-7:91702685 1324098301 T	L
233	698 T	-7:91702684 1324098300 T	
233	699 G	-7:91702683 1324098299 G	
234 F	700 T	-7:91702682 1324098298 T	F
234	701 T	-7:91702681 1324098297 T	
234	702 T	-7:91702680 1324098296 T	
235 G	703 G	-7:91702679 1324098295 G	G
235	704 G	-7:91702678 1324098294 G	
235	705 A	-7:91702677 1324098293 A	
236 S	706 T	-7:91702676 1324098292 T	S
236	707 C	-7:91702675 1324098291 C	
236	708 A	-7:91702674 1324098290 A	
237 D	709 G	-7:91702673 1324098289 G	D
237	710 A	-7:91702672 1324098288 A	
237	711 T	-7:91702671 1324098287 T	
238 L	712 C	-7:91702670 1324098286 C	L
238	713 T	-7:91702669 1324098285 T	
238	714 T	-7:91702668 1324098284 T	
239 Q	715 C	-7:91702667 1324098283 C	Q
239	716 A	-7:91702666 1324098282 A	
239	717 G	-7:91702665 1324098281 G	
240 Y	718 T	-7:91702664 1324098280 T	Y
240	719 A	-7:91702663 1324098279 A	
240	720 T	-7:91702662 1324098278 T	
241 T	721 A	-7:91702661 1324098277 A	T
241	722 C	-7:91702660 1324098276 C	
241	723 A	-7:91702659 1324098275 A	
242 N	724 A	-7:91702658 1324098274 A	N
242	725 A	-7:91702657 1324098273 A	
242	726 T	-7:91702656 1324098272 T	
243 R	727 C	-7:91702655 1324098271 C	R
243	728 G	-7:91702654 1324098270 G	
243	729 G	-7:91702653 1324098269 G	
244 V	730 G	-7:91702173 1324097789 G	V
244	731 T	-7:91702172 1324097788 T	
244	732 A	-7:91702171 1324097787 A	
245 D	733 G	-7:91702170 1324097786 G	D
245	734 A	-7:91702169 1324097785 A	
245	735 T	-7:91702168 1324097784 T	
246 K	736 A	-7:91702167 1324097783 A	K
246	737 A	-7:91702166 1324097782 A	
246	738 A	-7:91702165 1324097781 A	
247 V	739 G	-7:91702164 1324097780 G	V
247	740 T	-7:91702163 1324097779 T	
247	741 G	-7:91702162 1324097778 G	
248 V	742 G	-7:91702161 1324097777 G	V
248	743 T	-7:91702160 1324097776 T	
248	744 A	-7:91702159 1324097775 A	
249 I	745 A	-7:91702158 1324097774 A	I
249	746 T	-7:91702157 1324097773 T	
249	747 A	-7:91702156 1324097772 A	
250 N	748 A	-7:91702155 1324097771 A	N
250	749 A	-7:91702154 1324097770 A	
250	750 T	-7:91702153 1324097769 T	
251 P	751 C	-7:91702152 1324097768 C	P
251	752 C	-7:91702151 1324097767 C	
251	753 A	-7:91702150 1324097766 A	
252 Y	754 T	-7:91702149 1324097765 T	Y
252	755 A	-7:91702148 1324097764 A	
252	756 C	-7:91702147 1324097763 C	
253 F	757 T	-7:91702146 1324097762 T	F
253	758 T	-7:91702145 1324097761 T	
253	759 T	-7:91702144 1324097760 T	
254 G	760 G	-7:91702143 1324097759 G	G
254	761 G	-7:91702142 1324097758 G	
254	762 T	-7:91702141 1324097757 T	
255 L	763 C	-7:91702140 1324097756 C	L
255	764 T	-7:91702139 1324097755 T	
255	765 A	-7:91702138 1324097754 A	
256 G	766 G	-7:91702137 1324097753 G	G
256	767 G	-7:91702136 1324097752 G	
256	768 A	-7:91702135 1324097751 A	
257 A	769 G	-7:91702134 1324097750 G	A
257	770 C	-7:91702133 1324097749 C	
257	771 T	-7:91702132 1324097748 T	
258 P	772 C	-7:91702131 1324097747 C	P
258	773 C	-7:91702130 1324097746 C	
258	774 A	-7:91702129 1324097745 A	
259 D	775 G	-7:91702128 1324097744 G	D
259	776 A	-7:91702127 1324097743 A	
259	777 C	-7:91702126 1324097742 C	
260 Y	778 T	-7:91702125 1324097741 T	Y
260	779 A	-7:91702124 1324097740 A	
260	780 C	-7:91702123 1324097739 C	
261 S	781 T	-7:91702122 1324097738 T	S
261	782 C	-7:91702121 1324097737 C	
261	783 A	-7:91702120 1324097736 A	
262 K	784 A	-7:91702119 1324097735 A	K
262	785 A	-7:91702118 1324097734 A	
262	786 A	-7:91702117 1324097733 A	
263 I	787 A	-7:91702116 1324097732 A	I
263	788 T	-7:91702115 1324097731 T	
263	789 C	-7:91702114 1324097730 C	
264 Q	790 C	-7:91702113 1324097729 C	Q
264	791 A	-7:91702112 1324097728 A	
264	792 A	-7:91702111 1324097727 A	
265 I	793 A	-7:91702110 1324097726 A	I
265	794 T	-7:91702109 1324097725 T	
265	795 A	-7:91702108 1324097724 A	
266 P	796 C	-7:91702107 1324097723 C	P
266	797 C	-7:91702106 1324097722 C	
266	798 T	-7:91702105 1324097721 T	
267 K	799 A	-7:91702104 1324097720 A	K
267	800 A	-7:91702103 1324097719 A	
267	801 A	-7:91702102 1324097718 A	
268 Q	802 C	-7:91702101 1324097717 C	Q
268	803 A	-7:91702100 1324097716 A	
268	804 G	-7:91702099 1324097715 G	
269 E	805 G	-7:91702098 1324097714 G	E
269	806 A	-7:91702097 1324097713 A	
269	807 A	-7:91702096 1324097712 A	
270 K	808 A	-7:91702095 1324097711 A	K
270	809 A	-7:91702094 1324097710 A	
270	810 A	-7:91702093 1324097709 A	
271 W	811 T	-7:91702092 1324097708 T	W
271	812 G	-7:91702091 1324097707 G	
271	813 G	-7:91702090 1324097706 G	
272 Q	814 C	-7:91702089 1324097705 C	Q
272	815 A	-7:91702088 1324097704 A	
272	816 G	-7:91702087 1324097703 G	
273 R	817 A	-7:91702086 1324097702 A	R
273	818 G	-7:91702085 1324097701 G	
273	819 A	-7:91702084 1324097700 A	
274 S	820 A	-7:91702083 1324097699 A	S
274	821 G	-7:91702082 1324097698 G	
274	822 C	-7:91702081 1324097697 C	
275 M	823 A	-7:91702080 1324097696 A	M
275	824 T	-7:91702079 1324097695 T	
275	825 G	-7:91702078 1324097694 G	
276 S	826 A	-7:91702077 1324097693 A	S
276	827 G	-7:91702076 1324097692 G	
276	828 C	-7:91702075 1324097691 C	
277 S	829 A	-7:91702074 1324097690 A	S
277	830 G	-7:91702073 1324097689 G	
277	831 T	-7:91702072 1324097688 T	
278 V	832 G	-7:91702071 1324097687 G	V
278	833 T	-7:91702070 1324097686 T	
278	834 C	-7:91702069 1324097685 C	
279 T	835 A	-7:91702068 1324097684 A	T
279	836 C	-7:91702067 1324097683 C	
279	837 A	-7:91702066 1324097682 A	
280 E	838 G	-7:91702065 1324097681 G	E
280	839 A	-7:91702064 1324097680 A	
280	840 A	-7:91702063 1324097679 A	
281 D	841 G	-7:91702062 1324097678 G	D
281	842 A	-7:91702061 1324097677 A	
281	843 C	-7:91702060 1324097676 C	
282 K	844 A	-7:91702059 1324097675 A	K
282	845 A	-7:91702058 1324097674 A	
282	846 G	-7:91693932 1324089548 G	
283 Y	847 T	-7:91693931 1324089547 T	Y
283	848 A	-7:91693930 1324089546 A	
283	849 T	-7:91693929 1324089545 T	
284 G	850 G	-7:91693928 1324089544 G	G
284	851 G	-7:91693927 1324089543 G	
284	852 A	-7:91693926 1324089542 A	
285 K	853 A	-7:91693925 1324089541 A	K
285	854 A	-7:91693924 1324089540 A	
285	855 A	-7:91693923 1324089539 A	
286 V	856 G	-7:91693922 1324089538 G	V
286	857 T	-7:91693921 1324089537 T	
286	858 T	-7:91693920 1324089536 T	
287 E	859 G	-7:91693919 1324089535 G	E
287	860 A	-7:91693918 1324089534 A	
287	861 G	-7:91693917 1324089533 G	
288 A	862 G	-7:91693916 1324089532 G	A
288	863 C	-7:91693915 1324089531 C	
288	864 C	-7:91693914 1324089530 C	
289 T	865 A	-7:91693913 1324089529 A	T
289	866 C	-7:91693912 1324089528 C	
289	867 T	-7:91693911 1324089527 T	
290 R	868 C	-7:91693910 1324089526 C	R
290	869 G	-7:91693909 1324089525 G	
290	870 C	-7:91693908 1324089524 C	
291 I	871 A	-7:91693907 1324089523 A	I
291	872 T	-7:91693906 1324089522 T	
291	873 A	-7:91693905 1324089521 A	
292 L	874 T	-7:91693904 1324089520 T	L
292	875 T	-7:91693903 1324089519 T	
292	876 G	-7:91693902 1324089518 G	
293 L	877 T	-7:91693901 1324089517 T	L
293	878 T	-7:91693900 1324089516 T	
293	879 A	-7:91693899 1324089515 A	
294 E	880 G	-7:91693898 1324089514 G	E
294	881 A	-7:91693897 1324089513 A	
294	882 G	-7:91693896 1324089512 G	
295 K	883 A	-7:91693895 1324089511 A	K
295	884 A	-7:91693894 1324089510 A	
295	885 A	-7:91693893 1324089509 A	
296 G	886 G	-7:91693892 1324089508 G	G
296	887 G	-7:91693891 1324089507 G	
296	888 A	-7:91693890 1324089506 A	
297 K	889 A	-7:91693889 1324089505 A	K
297	890 A	-7:91693888 1324089504 A	
297	891 G	-7:91693887 1324089503 G	
298 C	892 T	-7:91693886 1324089502 T	C
298	893 G	-7:91693885 1324089501 G	
298	894 C	-7:91693884 1324089500 C	
299 N	895 A	-7:91693883 1324089499 A	N
299	896 A	-7:91693882 1324089498 A	
299	897 T	-7:91693881 1324089497 T	
300 P	898 C	-7:91693880 1324089496 C	P
300	899 C	-7:91693879 1324089495 C	
300	900 A	-7:91693878 1324089494 A	
301 N	901 A	-7:91693877 1324089493 A	N
301	902 A	-7:91693876 1324089492 A	
301	903 C	-7:91693875 1324089491 C	
302 L	904 C	-7:91693874 1324089490 C	L
302	905 T	-7:91693873 1324089489 T	
302	906 T	-7:91693872 1324089488 T	
303 L	907 T	-7:91693871 1324089487 T	L
303	908 T	-7:91693870 1324089486 T	
303	909 A	-7:91693869 1324089485 A	
304 N	910 A	-7:91693868 1324089484 A	N
304	911 A	-7:91693867 1324089483 A	
304	912 T	-7:91693866 1324089482 T	
305 G	913 G	-7:91693865 1324089481 G	G
305	914 G	-7:91693864 1324089480 G	
305	915 A	-7:91693863 1324089479 A	
306 Q	916 C	-7:91693862 1324089478 C	Q
306	917 A	-7:91693861 1324089477 A	
306	918 A	-7:91693860 1324089476 A	
307 L	919 C	-7:91693859 1324089475 C	L
307	920 T	-7:91693858 1324089474 T	
307	921 T	-7:91693857 1324089473 T	
308 S	922 A	-7:91693856 1324089472 A	S
308	923 G	-7:91693855 1324089471 G	
308	924 T	-7:91693854 1324089470 T	
309 S	925 T	-7:91693853 1324089469 T	S
309	926 C	-7:91693852 1324089468 C	
309	927 T	-7:91693851 1324089467 T	
310 P	928 C	-7:91693850 1324089466 C	P
310	929 C	-7:91693849 1324089465 C	
310	930 T	-7:91693848 1324089464 T	
311 L	931 C	-7:91693847 1324089463 C	L
311	932 T	-7:91693846 1324089462 T	
311	933 T	-7:91693845 1324089461 T	
312 H	934 C	-7:91693844 1324089460 C	H
312	935 A	-7:91693843 1324089459 A	
312	936 T	-7:91693842 1324089458 T	
313 F	937 T	-7:91693841 1324089457 T	F
313	938 T	-7:91693840 1324089456 T	
313	939 T	-7:91693839 1324089455 T	
314 A	940 G	-7:91693838 1324089454 G	A
314	941 C	-7:91693837 1324089453 C	
314	942 T	-7:91693836 1324089452 T	
315 A	943 G	-7:91693835 1324089451 G	A
315	944 C	-7:91693834 1324089450 C	
315	945 T	-7:91693833 1324089449 T	
316 G	946 G	-7:91693832 1324089448 G	G
316	947 G	-7:91693831 1324089447 G	
316	948 A	-7:91693830 1324089446 A	
317 G	949 G	-7:91693829 1324089445 G	G
317	950 G	-7:91693828 1324089444 G	
317	951 A	-7:91693827 1324089443 A	
318 G	952 G	-7:91693826 1324089442 G	G
318	953 G	-7:91693825 1324089441 G	
318	954 A	-7:91693824 1324089440 A	
319 H	955 C	-7:91693823 1324089439 C	H
319	956 A	-7:91693822 1324089438 A	
319	957 T	-7:91693821 1324089437 T	
320 A	958 G	-7:91693820 1324089436 G	A
320	959 C	-7:91693819 1324089435 C	
320	960 T	-7:91693818 1324089434 T	
321 E	961 G	-7:91693817 1324089433 G	E
321	962 A	-7:91693816 1324089432 A	
321	963 A	-7:91693815 1324089431 A	
322 I	964 A	-7:91693814 1324089430 A	I
322	965 T	-7:91693813 1324089429 T	
322	966 A	-7:91693812 1324089428 A	
323 V	967 G	-7:91693811 1324089427 G	V
323	968 T	-7:91693810 1324089426 T	
323	969 A	-7:91693809 1324089425 A	
324 Q	970 C	-7:91693808 1324089424 C	Q
324	971 A	-7:91693807 1324089423 A	
324	972 G	-7:91693806 1324089422 G	
325 I	973 A	-7:91693805 1324089421 A	I
325	974 T	-7:91693804 1324089420 T	
325	975 T	-7:91693803 1324089419 T	
326 L	976 C	-7:91693802 1324089418 C	L
326	977 T	-7:91693801 1324089417 T	
326	978 C	-7:91693800 1324089416 C	
327 L	979 C	-7:91693799 1324089415 C	L
327	980 T	-7:91693798 1324089414 T	
327	981 A	-7:91693797 1324089413 A	
328 N	982 A	-7:91693796 1324089412 A	N
328	983 A	-7:91693795 1324089411 A	
328	984 C	-7:91693794 1324089410 C	
329 H	985 C	-7:91693793 1324089409 C	H
329	986 A	-7:91693792 1324089408 A	
329	987 C	-7:91693791 1324089407 C	
330 P	988 C	-7:91693790 1324089406 C	P
330	989 C	-7:91693789 1324089405 C	
330	990 A	-7:91693788 1324089404 A	
331 E	991 G	-7:91693787 1324089403 G	E
331	992 A	-7:91693786 1324089402 A	
331	993 A	-7:91693785 1324089401 A	
332 T	994 A	-7:91693784 1324089400 A	T
332	995 C	-7:91693783 1324089399 C	
332	996 G	-7:91693782 1324089398 G	
333 D	997 G	-7:91693781 1324089397 G	D
333	998 A	-7:91693780 1324089396 A	
333	999 T	-7:91693779 1324089395 T	
334 R	1000 A	-7:91693778 1324089394 A	R
334	1001 G	-7:91693777 1324089393 G	
334	1002 A	-7:91693776 1324089392 A	
335 H	1003 C	-7:91693077 1324088693 C	H
335	1004 A	-7:91693076 1324088692 A	
335	1005 T	-7:91693075 1324088691 T	
336 I	1006 A	-7:91693074 1324088690 A	I
336	1007 T	-7:91693073 1324088689 T	
336	1008 A	-7:91693072 1324088688 A	
337 T	1009 A	-7:91693071 1324088687 A	T
337	1010 C	-7:91693070 1324088686 C	
337	1011 A	-7:91693069 1324088685 A	
338 D	1012 G	-7:91693068 1324088684 G	D
338	1013 A	-7:91693067 1324088683 A	
338	1014 C	-7:91693066 1324088682 C	
339 Q	1015 C	-7:91693065 1324088681 C	Q
339	1016 A	-7:91693064 1324088680 A	
339	1017 A	-7:91693063 1324088679 A	
340 Q	1018 C	-7:91693062 1324088678 C	Q
340	1019 A	-7:91693061 1324088677 A	
340	1020 A	-7:91693060 1324088676 A	
341 G	1021 G	-7:91693059 1324088675 G	G
341	1022 G	-7:91693058 1324088674 G	
341	1023 A	-7:91693057 1324088673 A	
342 R	1024 A	-7:91693056 1324088672 A	R
342	1025 G	-7:91693055 1324088671 G	
342	1026 A	-7:91693054 1324088670 A	
343 S	1027 T	-7:91693053 1324088669 T	S
343	1028 C	-7:91693052 1324088668 C	
343	1029 T	-7:91693051 1324088667 T	
344 P	1030 C	-7:91693050 1324088666 C	P
344	1031 C	-7:91693049 1324088665 C	
344	1032 A	-7:91693048 1324088664 A	
345 L	1033 T	-7:91693047 1324088663 T	L
345	1034 T	-7:91693046 1324088662 T	
345	1035 A	-7:91693045 1324088661 A	
346 N	1036 A	-7:91693044 1324088660 A	N
346	1037 A	-7:91693043 1324088659 A	
346	1038 T	-7:91693042 1324088658 T	
347 I	1039 A	-7:91693041 1324088657 A	I
347	1040 T	-7:91693040 1324088656 T	
347	1041 T	-7:91693039 1324088655 T	
348 C	1042 T	-7:91693038 1324088654 T	C
348	1043 G	-7:91693037 1324088653 G	
348	1044 T	-7:91693036 1324088652 T	
349 E	1045 G	-7:91693035 1324088651 G	E
349	1046 A	-7:91693034 1324088650 A	
349	1047 A	-7:91693033 1324088649 A	
350 E	1048 G	-7:91693032 1324088648 G	E
350	1049 A	-7:91693031 1324088647 A	
350	1050 A	-7:91693030 1324088646 A	
351 N	1051 A	-7:91693029 1324088645 A	N
351	1052 A	-7:91693028 1324088644 A	
351	1053 C	-7:91693027 1324088643 C	
352 K	1054 A	-7:91693026 1324088642 A	K
352	1055 A	-7:91693025 1324088641 A	
352	1056 A	-7:91693024 1324088640 A	
353 Q	1057 C	-7:91693023 1324088639 C	Q
353	1058 A	-7:91693022 1324088638 A	
353	1059 A	-7:91693021 1324088637 A	
354 N	1060 A	-7:91693020 1324088636 A	N
354	1061 A	-7:91693019 1324088635 A	
354	1062 C	-7:91693018 1324088634 C	
355 N	1063 A	-7:91693017 1324088633 A	N
355	1064 A	-7:91693016 1324088632 A	
355	1065 C	-7:91693015 1324088631 C	
356 W	1066 T	-7:91693014 1324088630 T	W
356	1067 G	-7:91693013 1324088629 G	
356	1068 G	-7:91693012 1324088628 G	
357 E	1069 G	-7:91693011 1324088627 G	E
357	1070 A	-7:91693010 1324088626 A	
357	1071 A	-7:91693009 1324088625 A	
358 E	1072 G	-7:91693008 1324088624 G	E
358	1073 A	-7:91693007 1324088623 A	
358	1074 A	-7:91693006 1324088622 A	
359 A	1075 G	-7:91693005 1324088621 G	A
359	1076 C	-7:91693004 1324088620 C	
359	1077 T	-7:91693003 1324088619 T	
360 A	1078 G	-7:91693002 1324088618 G	A
360	1079 C	-7:91693001 1324088617 C	
360	1080 A	-7:91693000 1324088616 A	
361 K	1081 A	-7:91692999 1324088615 A	K
361	1082 A	-7:91692998 1324088614 A	
361	1083 A	-7:91692997 1324088613 A	
362 L	1084 T	-7:91692996 1324088612 T	L
362	1085 T	-7:91692995 1324088611 T	
362	1086 G	-7:91692994 1324088610 G	
363 L	1087 T	-7:91692993 1324088609 T	L
363	1088 T	-7:91692992 1324088608 T	
363	1089 G	-7:91692991 1324088607 G	
364 K	1090 A	-7:91692990 1324088606 A	K
364	1091 A	-7:91692989 1324088605 A	
364	1092 G	-7:91692988 1324088604 G	
365 E	1093 G	-7:91692987 1324088603 G	E
365	1094 A	-7:91692986 1324088602 A	
365	1095 A	-7:91692985 1324088601 A	
366 A	1096 G	-7:91692984 1324088600 G	A
366	1097 C	-7:91692983 1324088599 C	
366	1098 A	-7:91692982 1324088598 A	
367 I	1099 A	-7:91692981 1324088597 A	I
367	1100 T	-7:91692980 1324088596 T	
367	1101 T	-7:91692979 1324088595 T	
368 N	1102 A	-7:91692978 1324088594 A	N
368	1103 A	-7:91692977 1324088593 A	
368	1104 C	-7:91692976 1324088592 C	
369 K	1105 A	-7:91692975 1324088591 A	K
369	1106 A	-7:91692974 1324088590 A	
369	1107 A	-7:91692973 1324088589 A	
370 P	1108 C	-7:91692972 1324088588 C	P
370	1109 C	-7:91692971 1324088587 C	
370	1110 A	-7:91692970 1324088586 A	
371 Y	1111 T	-7:91690228 1324085844 T	Y
371	1112 A	-7:91690227 1324085843 A	
371	1113 T	-7:91690226 1324085842 T	
372 E	1114 G	-7:91690225 1324085841 G	E
372	1115 A	-7:91690224 1324085840 A	
372	1116 A	-7:91690223 1324085839 A	
373 K	1117 A	-7:91690222 1324085838 A	K
373	1118 A	-7:91690221 1324085837 A	
373	1119 A	-7:91690220 1324085836 A	
374 V	1120 G	-7:91690219 1324085835 G	V
374	1121 T	-7:91690218 1324085834 T	
374	1122 T	-7:91690217 1324085833 T	
375 R	1123 C	-7:91690216 1324085832 C	R
375	1124 G	-7:91690215 1324085831 G	
375	1125 A	-7:91690214 1324085830 A	
376 I	1126 A	-7:91690213 1324085829 A	I
376	1127 T	-7:91690212 1324085828 T	
376	1128 A	-7:91690211 1324085827 A	
377 Y	1129 T	-7:91690210 1324085826 T	Y
377	1130 A	-7:91690209 1324085825 A	
377	1131 C	-7:91690208 1324085824 C	
378 R	1132 A	-7:91690207 1324085823 A	R
378	1133 G	-7:91690206 1324085822 G	
378	1134 A	-7:91690205 1324085821 A	
379 M	1135 A	-7:91690204 1324085820 A	M
379	1136 T	-7:91690203 1324085819 T	
379	1137 G	-7:91690202 1324085818 G	
380 D	1138 G	-7:91690201 1324085817 G	D
380	1139 A	-7:91690200 1324085816 A	
380	1140 T	-7:91690199 1324085815 T	
381 G	1141 G	-7:91690198 1324085814 G	G
381	1142 G	-7:91690197 1324085813 G	
381	1143 G	-7:91690196 1324085812 G	
382 S	1144 T	-7:91690195 1324085811 T	S
382	1145 C	-7:91690194 1324085810 C	
382	1146 A	-7:91690193 1324085809 A	
383 Y	1147 T	-7:91690192 1324085808 T	Y
383	1148 A	-7:91690191 1324085807 A	
383	1149 T	-7:91690190 1324085806 T	
384 R	1150 C	-7:91690189 1324085805 C	R
384	1151 G	-7:91690188 1324085804 G	
384	1152 T	-7:91690187 1324085803 T	
385 S	1153 T	-7:91690186 1324085802 T	S
385	1154 C	-7:91690185 1324085801 C	
385	1155 T	-7:91690184 1324085800 T	
386 V	1156 G	-7:91690183 1324085799 G	V
386	1157 T	-7:91690182 1324085798 T	
386	1158 T	-7:91690181 1324085797 T	
387 E	1159 G	-7:91690180 1324085796 G	E
387	1160 A	-7:91690179 1324085795 A	
387	1161 A	-7:91690178 1324085794 A	
388 L	1162 T	-7:91690177 1324085793 T	L
388	1163 T	-7:91690176 1324085792 T	
388	1164 G	-7:91690175 1324085791 G	
389 K	1165 A	-7:91690174 1324085790 A	K
389	1166 A	-7:91690173 1324085789 A	
389	1167 G	-7:91690172 1324085788 G	
390 H	1168 C	-7:91690171 1324085787 C	H
390	1169 A	-7:91690170 1324085786 A	
390	1170 T	-7:91690169 1324085785 T	
391 G	1171 G	-7:91690168 1324085784 G	G
391	1172 G	-7:91690167 1324085783 G	
391	1173 A	-7:91690166 1324085782 A	
392 N	1174 A	-7:91690165 1324085781 A	N
392	1175 A	-7:91690164 1324085780 A	
392	1176 T	-7:91690163 1324085779 T	
393 N	1177 A	-7:91690162 1324085778 A	N
393	1178 A	-7:91690161 1324085777 A	
393	1179 T	-7:91690160 1324085776 T	
394 T	1180 A	-7:91690159 1324085775 A	T
394	1181 C	-7:91690158 1324085774 C	
394	1182 C	-7:91690157 1324085773 C	
395 T	1183 A	-7:91690156 1324085772 A	T
395	1184 C	-7:91690155 1324085771 C	
395	1185 A	-7:91690154 1324085770 A	
396 V	1186 G	-7:91690153 1324085769 G	V
396	1187 T	-7:91690152 1324085768 T	
396	1188 G	-7:91690151 1324085767 G	
397 Q	1189 C	-7:91690150 1324085766 C	Q
397	1190 A	-7:91690149 1324085765 A	
397	1191 G	-7:91690148 1324085764 G	
398 Q	1192 C	-7:91690147 1324085763 C	Q
398	1193 A	-7:91690146 1324085762 A	
398	1194 G	-7:91690145 1324085761 G	
399 I	1195 A	-7:91690144 1324085760 A	I
399	1196 T	-7:91690143 1324085759 T	
399	1197 A	-7:91690142 1324085758 A	
400 M	1198 A	-7:91690141 1324085757 A	M
400	1199 T	-7:91690140 1324085756 T	
400	1200 G	-7:91690139 1324085755 G	
401 E	1201 G	-7:91690138 1324085754 G	E
401	1202 A	-7:91690137 1324085753 A	
401	1203 A	-7:91690136 1324085752 A	
402 G	1204 G	-7:91690135 1324085751 G	G
402	1205 G	-7:91690134 1324085750 G	
402	1206 A	-7:91690133 1324085749 A	
403 M	1207 A	-7:91690132 1324085748 A	M
403	1208 T	-7:91690131 1324085747 T	
403	1209 G	-7:91690130 1324085746 G	
404 R	1210 C	-7:91690129 1324085745 C	R
404	1211 G	-7:91690128 1324085744 G	
404	1212 T	-7:91690127 1324085743 T	
405 L	1213 C	-7:91690126 1324085742 C	L
405	1214 T	-7:91690125 1324085741 T	
405	1215 C	-7:91690124 1324085740 C	
406 S	1216 T	-7:91690123 1324085739 T	S
406	1217 C	-7:91690122 1324085738 C	
406	1218 T	-7:91690121 1324085737 T	
407 Q	1219 C	-7:91690120 1324085736 C	Q
407	1220 A	-7:91690119 1324085735 A	
407	1221 A	-7:91690118 1324085734 A	
408 E	1222 G	-7:91690117 1324085733 G	E
408	1223 A	-7:91690116 1324085732 A	
408	1224 A	-7:91690115 1324085731 A	
409 T	1225 A	-7:91690114 1324085730 A	T
409	1226 C	-7:91690113 1324085729 C	
409	1227 T	-7:91690112 1324085728 T	
410 Q	1228 C	-7:91690111 1324085727 C	Q
410	1229 A	-7:91690110 1324085726 A	
410	1230 G	-7:91690109 1324085725 G	
411 Q	1231 C	-7:91690108 1324085724 C	Q
411	1232 A	-7:91690107 1324085723 A	
411	1233 A	-7:91690106 1324085722 A	
412 Y	1234 T	-7:91690105 1324085721 T	Y
412	1235 A	-7:91690104 1324085720 A	
412	1236 T	-7:91690103 1324085719 T	
413 F	1237 T	-7:91690102 1324085718 T	F
413	1238 T	-7:91690101 1324085717 T	
413	1239 C	-7:91690100 1324085716 C	
414 T	1240 A	-7:91690099 1324085715 A	T
414	1241 C	-7:91690098 1324085714 C	
414	1242 T	-7:91690097 1324085713 T	
415 I	1243 A	-7:91690096 1324085712 A	I
415	1244 T	-7:91690095 1324085711 T	
415	1245 A	-7:91690094 1324085710 A	
416 W	1246 T	-7:91690093 1324085709 T	W
416	1247 G	-7:91690092 1324085708 G	
416	1248 G	-7:91690091 1324085707 G	
417 I	1249 A	-7:91690090 1324085706 A	I
417	1250 T	-7:91690089 1324085705 T	
417	1251 T	-7:91690088 1324085704 T	
418 C	1252 T	-7:91690087 1324085703 T	C
418	1253 G	-7:91690086 1324085702 G	
418	1254 T	-7:91690085 1324085701 T	
419 S	1255 T	-7:91690084 1324085700 T	S
419	1256 C	-7:91690083 1324085699 C	
419	1257 A	-7:91690082 1324085698 A	
420 E	1258 G	-7:91690081 1324085697 G	E
420	1259 A	-7:91690080 1324085696 A	
420	1260 A	-7:91690079 1324085695 A	
421 N	1261 A	-7:91690078 1324085694 A	N
421	1262 A	-7:91690077 1324085693 A	
421	1263 C	-7:91690076 1324085692 C	
422 L	1264 C	-7:91690075 1324085691 C	L
422	1265 T	-7:91690074 1324085690 T	
422	1266 C	-7:91690073 1324085689 C	
423 S	1267 A	-7:91690072 1324085688 A	S
423	1268 G	-7:91689303 1324084919 G	
423	1269 C	-7:91689302 1324084918 C	
424 L	1270 C	-7:91689301 1324084917 C	L
424	1271 T	-7:91689300 1324084916 T	
424	1272 T	-7:91689299 1324084915 T	
425 Q	1273 C	-7:91689298 1324084914 C	Q
425	1274 A	-7:91689297 1324084913 A	
425	1275 A	-7:91689296 1324084912 A	
426 L	1276 C	-7:91689295 1324084911 C	L
426	1277 T	-7:91689294 1324084910 T	
426	1278 C	-7:91689293 1324084909 C	
427 K	1279 A	-7:91689292 1324084908 A	K
427	1280 A	-7:91689291 1324084907 A	
427	1281 A	-7:91689290 1324084906 A	
428 P	1282 C	-7:91689289 1324084905 C	P
428	1283 C	-7:91689288 1324084904 C	
428	1284 A	-7:91689287 1324084903 A	
429 Y	1285 T	-7:91689286 1324084902 T	Y
429	1286 A	-7:91689285 1324084901 A	
429	1287 T	-7:91689284 1324084900 T	
430 H	1288 C	-7:91689283 1324084899 C	H
430	1289 A	-7:91689282 1324084898 A	
430	1290 T	-7:91689281 1324084897 T	
431 K	1291 A	-7:91689280 1324084896 A	K
431	1292 A	-7:91689279 1324084895 A	
431	1293 A	-7:91689278 1324084894 A	
432 P	1294 C	-7:91689277 1324084893 C	P
432	1295 C	-7:91689276 1324084892 C	
432	1296 C	-7:91689275 1324084891 C	
433 L	1297 T	-7:91689274 1324084890 T	L
433	1298 T	-7:91689273 1324084889 T	
433	1299 G	-7:91689272 1324084888 G	
434 Q	1300 C	-7:91689271 1324084887 C	Q
434	1301 A	-7:91689270 1324084886 A	
434	1302 A	-7:91689269 1324084885 A	
435 H	1303 C	-7:91689268 1324084884 C	H
435	1304 A	-7:91689267 1324084883 A	
435	1305 T	-7:91689266 1324084882 T	
436 V	1306 G	-7:91689265 1324084881 G	V
436	1307 T	-7:91689264 1324084880 T	
436	1308 T	-7:91689263 1324084879 T	
437 R	1309 C	-7:91689262 1324084878 C	R
437	1310 G	-7:91689261 1324084877 G	
437	1311 T	-7:91689260 1324084876 T	
438 D	1312 G	-7:91689259 1324084875 G	D
438	1313 A	-7:91689258 1324084874 A	
438	1314 C	-7:91689257 1324084873 C	
439 W	1315 T	-7:91689256 1324084872 T	W
439	1316 G	-7:91689255 1324084871 G	
439	1317 G	-7:91689254 1324084870 G	
440 P	1318 C	-7:91689253 1324084869 C	P
440	1319 C	-7:91689252 1324084868 C	
440	1320 A	-7:91689251 1324084867 A	
441 E	1321 G	-7:91689250 1324084866 G	E
441	1322 A	-7:91689249 1324084865 A	
441	1323 A	-7:91689248 1324084864 A	
442 I	1324 A	-7:91689247 1324084863 A	I
442	1325 T	-7:91689246 1324084862 T	
442	1326 A	-7:91689245 1324084861 A	
443 L	1327 C	-7:91689244 1324084860 C	L
443	1328 T	-7:91689243 1324084859 T	
443	1329 T	-7:91689242 1324084858 T	
444 A	1330 G	-7:91689241 1324084857 G	A
444	1331 C	-7:91689240 1324084856 C	
444	1332 T	-7:91689239 1324084855 T	
445 E	1333 G	-7:91689238 1324084854 G	E
445	1334 A	-7:91689237 1324084853 A	
445	1335 A	-7:91689236 1324084852 A	
446 L	1336 T	-7:91689235 1324084851 T	L
446	1337 T	-7:91689234 1324084850 T	
446	1338 G	-7:91689233 1324084849 G	
447 T	1339 A	-7:91689232 1324084848 A	T
447	1340 C	-7:91689231 1324084847 C	
447	1341 T	-7:91689230 1324084846 T	
448 N	1342 A	-7:91689229 1324084845 A	N
448	1343 A	-7:91689228 1324084844 A	
448	1344 T	-7:91689227 1324084843 T	
449 L	1345 C	-7:91689226 1324084842 C	L
449	1346 T	-7:91689225 1324084841 T	
449	1347 G	-7:91689224 1324084840 G	
450 D	1348 G	-7:91689223 1324084839 G	D
450	1349 A	-7:91689222 1324084838 A	
450	1350 T	-7:91689221 1324084837 T	
451 P	1351 C	-7:91689220 1324084836 C	P
451	1352 C	-7:91689219 1324084835 C	
451	1353 T	-7:91689218 1324084834 T	
452 Q	1354 C	-7:91689217 1324084833 C	Q
452	1355 A	-7:91689216 1324084832 A	
452	1356 A	-7:91689215 1324084831 A	
453 R	1357 A	-7:91689214 1324084830 A	R
453	1358 G	-7:91689213 1324084829 G	
453	1359 G	-7:91689212 1324084828 G	
454 E	1360 G	-7:91689211 1324084827 G	E
454	1361 A	-7:91689210 1324084826 A	
454	1362 A	-7:91689209 1324084825 A	
455 T	1363 A	-7:91689208 1324084824 A	T
455	1364 C	-7:91689207 1324084823 C	
455	1365 A	-7:91689206 1324084822 A	
456 P	1366 C	-7:91689205 1324084821 C	P
456	1367 C	-7:91689204 1324084820 C	
456	1368 T	-7:91689203 1324084819 T	
457 Q	1369 C	-7:91689202 1324084818 C	Q
457	1370 A	-7:91689201 1324084817 A	
457	1371 G	-7:91689200 1324084816 G	
458 L	1372 C	-7:91689199 1324084815 C	L
458	1373 T	-7:91689198 1324084814 T	
458	1374 T	-7:91689197 1324084813 T	
459 F	1375 T	-7:91689196 1324084812 T	F
459	1376 T	-7:91689195 1324084811 T	
459	1377 T	-7:91689194 1324084810 T	
460 L	1378 C	-7:91689193 1324084809 C	L
460	1379 T	-7:91689192 1324084808 T	
460	1380 A	-7:91689191 1324084807 A	
461 R	1381 A	-7:91689190 1324084806 A	R
461	1382 G	-7:91689189 1324084805 G	
461	1383 A	-7:91689188 1324084804 A	
462 R	1384 A	-7:91689187 1324084803 A	R
462	1385 G	-7:91689186 1324084802 G	
462	1386 A	-7:91689185 1324084801 A	
463 D	1387 G	-7:91689184 1324084800 G	D
463	1388 A	-7:91689183 1324084799 A	
463	1389 T	-7:91689182 1324084798 T	
464 V	1390 G	-7:91689181 1324084797 G	V
464	1391 T	-7:91689180 1324084796 T	
464	1392 G	-7:91689179 1324084795 G	
465 R	1393 A	-7:91689178 1324084794 A	R
465	1394 G	-7:91689177 1324084793 G	
465	1395 A	-7:91689176 1324084792 A	
466 L	1396 C	-7:91689175 1324084791 C	L
466	1397 T	-7:91689174 1324084790 T	
466	1398 T	-7:91689173 1324084789 T	
467 P	1399 C	-7:91689172 1324084788 C	P
467	1400 C	-7:91689171 1324084787 C	
467	1401 C	-7:91689170 1324084786 C	
468 L	1402 T	-7:91689169 1324084785 T	L
468	1403 T	-7:91689168 1324084784 T	
468	1404 G	-7:91689167 1324084783 G	
469 E	1405 G	-7:91689166 1324084782 G	E
469	1406 A	-7:91689165 1324084781 A	
469	1407 A	-7:91689164 1324084780 A	
470 V	1408 G	-7:91689163 1324084779 G	V
470	1409 T	-7:91689162 1324084778 T	
470	1410 T	-7:91689161 1324084777 T	
471 E	1411 G	-7:91689160 1324084776 G	E
471	1412 A	-7:91689159 1324084775 A	
471	1413 A	-7:91689158 1324084774 A	
472 K	1414 A	-7:91689157 1324084773 A	K
472	1415 A	-7:91689156 1324084772 A	
472	1416 A	-7:91689155 1324084771 A	
473 Q	1417 C	-7:91689154 1324084770 C	Q
473	1418 A	-7:91689153 1324084769 A	
473	1419 G	-7:91689152 1324084768 G	
474 I	1420 A	-7:91682027 1324077643 A	I
474	1421 T	-7:91682026 1324077642 T	
474	1422 T	-7:91682025 1324077641 T	
475 E	1423 G	-7:91682024 1324077640 G	E
475	1424 A	-7:91682023 1324077639 A	
475	1425 A	-7:91682022 1324077638 A	
476 D	1426 G	-7:91682021 1324077637 G	D
476	1427 A	-7:91682020 1324077636 A	
476	1428 C	-7:91682019 1324077635 C	
477 P	1429 C	-7:91682018 1324077634 C	P
477	1430 C	-7:91682017 1324077633 C	
477	1431 A	-7:91682016 1324077632 A	
478 L	1432 C	-7:91682015 1324077631 C	L
478	1433 T	-7:91682014 1324077630 T	
478	1434 A	-7:91682013 1324077629 A	
479 A	1435 G	-7:91682012 1324077628 G	A
479	1436 C	-7:91682011 1324077627 C	
479	1437 T	-7:91682010 1324077626 T	
480 I	1438 A	-7:91682009 1324077625 A	I
480	1439 T	-7:91682008 1324077624 T	
480	1440 T	-7:91682007 1324077623 T	
481 L	1441 C	-7:91682006 1324077622 C	L
481	1442 T	-7:91682005 1324077621 T	
481	1443 T	-7:91682004 1324077620 T	
482 I	1444 A	-7:91682003 1324077619 A	I
482	1445 T	-7:91682002 1324077618 T	
482	1446 T	-7:91682001 1324077617 T	
483 L	1447 C	-7:91682000 1324077616 C	L
483	1448 T	-7:91681999 1324077615 T	
483	1449 C	-7:91681998 1324077614 C	
484 F	1450 T	-7:91681997 1324077613 T	F
484	1451 T	-7:91681996 1324077612 T	
484	1452 T	-7:91681995 1324077611 T	
485 D	1453 G	-7:91681994 1324077610 G	D
485	1454 A	-7:91681993 1324077609 A	
485	1455 T	-7:91681992 1324077608 T	
486 E	1456 G	-7:91681991 1324077607 G	E
486	1457 A	-7:91681990 1324077606 A	
486	1458 A	-7:91681989 1324077605 A	
487 A	1459 G	-7:91681988 1324077604 G	A
487	1460 C	-7:91681987 1324077603 C	
487	1461 C	-7:91681986 1324077602 C	
488 R	1462 A	-7:91681985 1324077601 A	R
488	1463 G	-7:91681984 1324077600 G	
488	1464 A	-7:91681983 1324077599 A	
489 Y	1465 T	-7:91681982 1324077598 T	Y
489	1466 A	-7:91681981 1324077597 A	
489	1467 T	-7:91681980 1324077596 T	
490 N	1468 A	-7:91681979 1324077595 A	N
490	1469 A	-7:91681978 1324077594 A	
490	1470 T	-7:91681977 1324077593 T	
491 L	1471 T	-7:91681976 1324077592 T	L
491	1472 T	-7:91681975 1324077591 T	
491	1473 A	-7:91681974 1324077590 A	
492 L	1474 T	-7:91681973 1324077589 T	L
492	1475 T	-7:91681972 1324077588 T	
492	1476 G	-7:91681971 1324077587 G	
493 K	1477 A	-7:91681970 1324077586 A	K
493	1478 A	-7:91681969 1324077585 A	
493	1479 G	-7:91681968 1324077584 G	
494 G	1480 G	-7:91681967 1324077583 G	G
494	1481 G	-7:91681966 1324077582 G	
494	1482 C	-7:91681965 1324077581 C	
495 F	1483 T	-7:91681964 1324077580 T	F
495	1484 T	-7:91681963 1324077579 T	
495	1485 T	-7:91681962 1324077578 T	
496 Y	1486 T	-7:91681961 1324077577 T	Y
496	1487 A	-7:91681960 1324077576 A	
496	1488 T	-7:91681959 1324077575 T	
497 T	1489 A	-7:91681958 1324077574 A	T
497	1490 C	-7:91681957 1324077573 C	
497	1491 A	-7:91681956 1324077572 A	
498 A	1492 G	-7:91681955 1324077571 G	A
498	1493 C	-7:91681954 1324077570 C	
498	1494 T	-7:91681953 1324077569 T	
499 P	1495 C	-7:91681952 1324077568 C	P
499	1496 C	-7:91681951 1324077567 C	
499	1497 T	-7:91681950 1324077566 T	
500 D	1498 G	-7:91681949 1324077565 G	D
500	1499 A	-7:91681948 1324077564 A	
500	1500 T	-7:91681947 1324077563 T	
501 A	1501 G	-7:91681946 1324077562 G	A
501	1502 C	-7:91681945 1324077561 C	
501	1503 T	-7:91681944 1324077560 T	
502 K	1504 A	-7:91681943 1324077559 A	K
502	1505 A	-7:91681942 1324077558 A	
502	1506 G	-7:91681941 1324077557 G	
503 L	1507 C	-7:91681940 1324077556 C	L
503	1508 T	-7:91681939 1324077555 T	
503	1509 G	-7:91681938 1324077554 G	
504 I	1510 A	-7:91681937 1324077553 A	I
504	1511 T	-7:91681936 1324077552 T	
504	1512 A	-7:91681935 1324077551 A	
505 T	1513 A	-7:91681934 1324077550 A	T
505	1514 C	-7:91681933 1324077549 C	
505	1515 A	-7:91681932 1324077548 A	
506 L	1516 T	-7:91681931 1324077547 T	L
506	1517 T	-7:91681930 1324077546 T	
506	1518 G	-7:91681929 1324077545 G	
507 A	1519 G	-7:91681928 1324077544 G	A
507	1520 C	-7:91681927 1324077543 C	
507	1521 A	-7:91681926 1324077542 A	
508 S	1522 A	-7:91681925 1324077541 A	S
508	1523 G	-7:91681924 1324077540 G	
508	1524 T	-7:91681923 1324077539 T	
509 L	1525 C	-7:91681922 1324077538 C	L
509	1526 T	-7:91681921 1324077537 T	
509	1527 G	-7:91681920 1324077536 G	
510 L	1528 C	-7:91681919 1324077535 C	L
510	1529 T	-7:91681918 1324077534 T	
510	1530 T	-7:91681917 1324077533 T	
511 L	1531 T	-7:91681916 1324077532 T	L
511	1532 T	-7:91681915 1324077531 T	
511	1533 G	-7:91681914 1324077530 G	
512 Q	1534 C	-7:91681913 1324077529 C	Q
512	1535 A	-7:91681912 1324077528 A	
512	1536 A	-7:91681911 1324077527 A	
513 I	1537 A	-7:91681910 1324077526 A	I
513	1538 T	-7:91681909 1324077525 T	
513	1539 A	-7:91681908 1324077524 A	
514 V	1540 G	-7:91681907 1324077523 G	V
514	1541 T	-7:91681906 1324077522 T	
514	1542 C	-7:91681905 1324077521 C	
515 Y	1543 T	-7:91681904 1324077520 T	Y
515	1544 A	-7:91681903 1324077519 A	
515	1545 T	-7:91681902 1324077518 T	
516 G	1546 G	-7:91681901 1324077517 G	G
516	1547 G	-7:91681900 1324077516 G	
516	1548 A	-7:91681899 1324077515 A	
517 N	1549 A	-7:91681898 1324077514 A	N
517	1550 A	-7:91681897 1324077513 A	
517	1551 T	-7:91681896 1324077512 T	
518 Y	1552 T	-7:91681895 1324077511 T	Y
518	1553 A	-7:91681894 1324077510 A	
518	1554 T	-7:91681893 1324077509 T	
519 E	1555 G	-7:91681892 1324077508 G	E
519	1556 A	-7:91681891 1324077507 A	
519	1557 G	-7:91681890 1324077506 G	
520 S	1558 A	-7:91681889 1324077505 A	S
520	1559 G	-7:91681888 1324077504 G	
520	1560 T	-7:91681887 1324077503 T	
521 K	1561 A	-7:91681886 1324077502 A	K
521	1562 A	-7:91681885 1324077501 A	
521	1563 A	-7:91681884 1324077500 A	
522 K	1564 A	-7:91681883 1324077499 A	K
522	1565 A	-7:91681882 1324077498 A	
522	1566 A	-7:91681881 1324077497 A	
523 H	1567 C	-7:91681880 1324077496 C	H
523	1568 A	-7:91681879 1324077495 A	
523	1569 C	-7:91681878 1324077494 C	
524 K	1570 A	-7:91681877 1324077493 A	K
524	1571 A	-7:91681876 1324077492 A	
524	1572 G	-7:91681875 1324077491 G	
525 Q	1573 C	-7:91681874 1324077490 C	Q
525	1574 A	-7:91681873 1324077489 A	
525	1575 A	-7:91681872 1324077488 A	
526 G	1576 G	-7:91681871 1324077487 G	G
526	1577 G	-7:91681870 1324077486 G	
526	1578 T	-7:91681869 1324077485 T	
527 F	1579 T	-7:91681868 1324077484 T	F
527	1580 T	-7:91681867 1324077483 T	
527	1581 C	-7:91681866 1324077482 C	
528 L	1582 C	-7:91681865 1324077481 C	L
528	1583 T	-7:91681864 1324077480 T	
528	1584 A	-7:91681863 1324077479 A	
529 N	1585 A	-7:91681862 1324077478 A	N
529	1586 A	-7:91681861 1324077477 A	
529	1587 T	-7:91681229 1324076845 T	
530 E	1588 G	-7:91681228 1324076844 G	E
530	1589 A	-7:91681227 1324076843 A	
530	1590 A	-7:91681226 1324076842 A	
531 E	1591 G	-7:91681225 1324076841 G	E
531	1592 A	-7:91681224 1324076840 A	
531	1593 A	-7:91681223 1324076839 A	
532 N	1594 A	-7:91681222 1324076838 A	N
532	1595 A	-7:91681221 1324076837 A	
532	1596 T	-7:91681220 1324076836 T	
533 L	1597 C	-7:91681219 1324076835 C	L
533	1598 T	-7:91681218 1324076834 T	
533	1599 A	-7:91681217 1324076833 A	
534 K	1600 A	-7:91681216 1324076832 A	K
534	1601 A	-7:91681215 1324076831 A	
534	1602 A	-7:91681214 1324076830 A	
535 S	1603 T	-7:91681213 1324076829 T	S
535	1604 C	-7:91681212 1324076828 C	
535	1605 C	-7:91681211 1324076827 C	
536 I	1606 A	-7:91681210 1324076826 A	I
536	1607 T	-7:91681209 1324076825 T	
536	1608 C	-7:91681208 1324076824 C	
537 V	1609 G	-7:91681207 1324076823 G	V
537	1610 T	-7:91681206 1324076822 T	
537	1611 A	-7:91681205 1324076821 A	
538 P	1612 C	-7:91681204 1324076820 C	P
538	1613 C	-7:91681203 1324076819 C	
538	1614 T	-7:91681202 1324076818 T	
539 V	1615 G	-7:91681201 1324076817 G	V
539	1616 T	-7:91681200 1324076816 T	
539	1617 T	-7:91681199 1324076815 T	
540 T	1618 A	-7:91681198 1324076814 A	T
540	1619 C	-7:91681197 1324076813 C	
540	1620 C	-7:91681196 1324076812 C	
541 K	1621 A	-7:91681195 1324076811 A	K
541	1622 A	-7:91681194 1324076810 A	
541	1623 A	-7:91681193 1324076809 A	
542 L	1624 C	-7:91681192 1324076808 C	L
542	1625 T	-7:91681191 1324076807 T	
542	1626 G	-7:91681190 1324076806 G	
543 K	1627 A	-7:91681189 1324076805 A	K
543	1628 A	-7:91681188 1324076804 A	
543	1629 A	-7:91681187 1324076803 A	
544 S	1630 A	-7:91681186 1324076802 A	S
544	1631 G	-7:91681185 1324076801 G	
544	1632 T	-7:91681184 1324076800 T	
545 K	1633 A	-7:91681183 1324076799 A	K
545	1634 A	-7:91681182 1324076798 A	
545	1635 G	-7:91681181 1324076797 G	
546 A	1636 G	-7:91681180 1324076796 G	A
546	1637 C	-7:91681179 1324076795 C	
546	1638 A	-7:91681178 1324076794 A	
547 P	1639 C	-7:91681177 1324076793 C	P
547	1640 C	-7:91681176 1324076792 C	
547	1641 T	-7:91681175 1324076791 T	
548 H	1642 C	-7:91681174 1324076790 C	H
548	1643 A	-7:91681173 1324076789 A	
548	1644 C	-7:91681172 1324076788 C	
549 W	1645 T	-7:91681171 1324076787 T	W
549	1646 G	-7:91681170 1324076786 G	
549	1647 G	-7:91681169 1324076785 G	
550 T	1648 A	-7:91681168 1324076784 A	T
550	1649 C	-7:91681167 1324076783 C	
550	1650 A	-7:91681166 1324076782 A	
551 N	1651 A	-7:91681165 1324076781 A	N
551	1652 A	-7:91681164 1324076780 A	
551	1653 T	-7:91681163 1324076779 T	
552 R	1654 C	-7:91681162 1324076778 C	R
552	1655 G	-7:91681161 1324076777 G	
552	1656 C	-7:91681160 1324076776 C	
553 I	1657 A	-7:91681159 1324076775 A	I
553	1658 T	-7:91681158 1324076774 T	
553	1659 A	-7:91681157 1324076773 A	
554 L	1660 C	-7:91681156 1324076772 C	L
554	1661 T	-7:91681155 1324076771 T	
554	1662 T	-7:91681154 1324076770 T	
555 H	1663 C	-7:91681153 1324076769 C	H
555	1664 A	-7:91681152 1324076768 A	
555	1665 T	-7:91681151 1324076767 T	
556 E	1666 G	-7:91681150 1324076766 G	E
556	1667 A	-7:91681149 1324076765 A	
556	1668 A	-7:91681148 1324076764 A	
557 Y	1669 T	-7:91681147 1324076763 T	Y
557	1670 A	-7:91681146 1324076762 A	
557	1671 C	-7:91681145 1324076761 C	
558 K	1672 A	-7:91681144 1324076760 A	K
558	1673 A	-7:91681143 1324076759 A	
558	1674 G	-7:91681142 1324076758 G	
559 N	1675 A	-7:91680651 1324076267 A	N
559	1676 A	-7:91680650 1324076266 A	
559	1677 T	-7:91680649 1324076265 T	
560 L	1678 C	-7:91680648 1324076264 C	L
560	1679 T	-7:91680647 1324076263 T	
560	1680 C	-7:91680646 1324076262 C	
561 S	1681 A	-7:91680645 1324076261 A	S
561	1682 G	-7:91680644 1324076260 G	
561	1683 T	-7:91680643 1324076259 T	
562 T	1684 A	-7:91680642 1324076258 A	T
562	1685 C	-7:91680641 1324076257 C	
562	1686 A	-7:91680640 1324076256 A	
563 S	1687 A	-7:91680639 1324076255 A	S
563	1688 G	-7:91680638 1324076254 G	
563	1689 T	-7:91680637 1324076253 T	
564 E	1690 G	-7:91680636 1324076252 G	E
564	1691 A	-7:91680635 1324076251 A	
564	1692 A	-7:91680634 1324076250 A	
565 G	1693 G	-7:91680633 1324076249 G	G
565	1694 G	-7:91680632 1324076248 G	
565	1695 T	-7:91680631 1324076247 T	
566 V	1696 G	-7:91680630 1324076246 G	V
566	1697 T	-7:91680629 1324076245 T	
566	1698 C	-7:91680628 1324076244 C	
567 S	1699 A	-7:91680627 1324076243 A	S
567	1700 G	-7:91680626 1324076242 G	
567	1701 T	-7:91680625 1324076241 T	
568 K	1702 A	-7:91680624 1324076240 A	K
568	1703 A	-7:91680623 1324076239 A	
568	1704 A	-7:91680622 1324076238 A	
569 E	1705 G	-7:91680621 1324076237 G	E
569	1706 A	-7:91680620 1324076236 A	
569	1707 A	-7:91680619 1324076235 A	
570 M	1708 A	-7:91680618 1324076234 A	M
570	1709 T	-7:91680617 1324076233 T	
570	1710 G	-7:91680616 1324076232 G	
571 H	1711 C	-7:91680615 1324076231 C	H
571	1712 A	-7:91680614 1324076230 A	
571	1713 T	-7:91680613 1324076229 T	
572 H	1714 C	-7:91680612 1324076228 C	H
572	1715 A	-7:91680611 1324076227 A	
572	1716 C	-7:91680610 1324076226 C	
573 L	1717 C	-7:91680609 1324076225 C	L
573	1718 T	-7:91680608 1324076224 T	
573	1719 T	-7:91680607 1324076223 T	
574 Q	1720 C	-7:91680606 1324076222 C	Q
574	1721 A	-7:91680605 1324076221 A	
574	1722 G	-7:91680604 1324076220 G	
575 R	1723 C	-7:91680603 1324076219 C	R
575	1724 G	-7:91680602 1324076218 G	
575	1725 C	-7:91680601 1324076217 C	
576 M	1726 A	-7:91680600 1324076216 A	M
576	1727 T	-7:91680599 1324076215 T	
576	1728 G	-7:91680598 1324076214 G	
577 F	1729 T	-7:91680597 1324076213 T	F
577	1730 T	-7:91680596 1324076212 T	
577	1731 C	-7:91680595 1324076211 C	
578 L	1732 T	-7:91680594 1324076210 T	L
578	1733 T	-7:91680593 1324076209 T	
578	1734 A	-7:91680592 1324076208 A	
579 Q	1735 C	-7:91680591 1324076207 C	Q
579	1736 A	-7:91680590 1324076206 A	
579	1737 G	-7:91680589 1324076205 G	
580 N	1738 A	-7:91680588 1324076204 A	N
580	1739 A	-7:91680587 1324076203 A	
580	1740 T	-7:91680586 1324076202 T	
581 C	1741 T	-7:91680585 1324076201 T	C
581	1742 G	-7:91680584 1324076200 G	
581	1743 C	-7:91680583 1324076199 C	
582 W	1744 T	-7:91680582 1324076198 T	W
582	1745 G	-7:91680581 1324076197 G	
582	1746 G	-7:91680580 1324076196 G	
583 E	1747 G	-7:91680579 1324076195 G	E
583	1748 A	-7:91680578 1324076194 A	
583	1749 A	-7:91680577 1324076193 A	
584 I	1750 A	-7:91680576 1324076192 A	I
584	1751 T	-7:91680575 1324076191 T	
584	1752 T	-7:91680574 1324076190 T	
585 P	1753 C	-7:91680573 1324076189 C	P
585	1754 C	-7:91680572 1324076188 C	
585	1755 T	-7:91680571 1324076187 T	
586 T	1756 A	-7:91680570 1324076186 A	T
586	1757 C	-7:91680569 1324076185 C	
586	1758 T	-7:91680568 1324076184 T	
587 Y	1759 T	-7:91680567 1324076183 T	Y
587	1760 A	-7:91680566 1324076182 A	
587	1761 T	-7:91680565 1324076181 T	
588 G	1762 G	-7:91680564 1324076180 G	G
588	1763 G	-7:91680563 1324076179 G	
588	1764 A	-7:91680562 1324076178 A	
589 A	1765 G	-7:91680561 1324076177 G	A
589	1766 C	-7:91680560 1324076176 C	
589	1767 A	-7:91680559 1324076175 A	
590 A	1768 G	-7:91680558 1324076174 G	A
590	1769 C	-7:91680557 1324076173 C	
590	1770 A	-7:91680556 1324076172 A	
591 F	1771 T	-7:91680555 1324076171 T	F
591	1772 T	-7:91680554 1324076170 T	
591	1773 T	-7:91680553 1324076169 T	
592 F	1774 T	-7:91680552 1324076168 T	F
592	1775 T	-7:91680551 1324076167 T	
592	1776 C	-7:91680550 1324076166 C	
593 T	1777 A	-7:91680549 1324076165 A	T
593	1778 C	-7:91680548 1324076164 C	
593	1779 A	-7:91680547 1324076163 A	
594 G	1780 G	-7:91680546 1324076162 G	G
594	1781 G	-7:91680545 1324076161 G	
594	1782 A	-7:91680544 1324076160 A	
595 Q	1783 C	-7:91680543 1324076159 C	Q
595	1784 A	-7:91680542 1324076158 A	
595	1785 G	-7:91680541 1324076157 G	
596 I	1786 A	-7:91680540 1324076156 A	I
596	1787 T	-7:91680539 1324076155 T	
596	1788 A	-7:91680538 1324076154 A	
597 F	1789 T	-7:91680537 1324076153 T	F
597	1790 T	-7:91680536 1324076152 T	
597	1791 T	-7:91680535 1324076151 T	
598 T	1792 A	-7:91680534 1324076150 A	T
598	1793 C	-7:91680533 1324076149 C	
598	1794 A	-7:91680532 1324076148 A	
599 K	1795 A	-7:91680531 1324076147 A	K
599	1796 A	-7:91680530 1324076146 A	
599	1797 G	-7:91680529 1324076145 G	
600 A	1798 G	-7:91680528 1324076144 G	A
600	1799 C	-7:91680527 1324076143 C	
600	1800 A	-7:91680526 1324076142 A	
601 S	1801 A	-7:91680525 1324076141 A	S
601	1802 G	-7:91680524 1324076140 G	
601	1803 C	-7:91680523 1324076139 C	
602 P	1804 C	-7:91680522 1324076138 C	P
602	1805 C	-7:91680521 1324076137 C	
602	1806 C	-7:91680520 1324076136 C	
603 S	1807 A	-7:91680519 1324076135 A	S
603	1808 G	-7:91680518 1324076134 G	
603	1809 C	-7:91680517 1324076133 C	
604 N	1810 A	-7:91680516 1324076132 A	N
604	1811 A	-7:91680515 1324076131 A	
604	1812 T	-7:91680514 1324076130 T	
605 H	1813 C	-7:91680513 1324076129 C	H
605	1814 A	-7:91680512 1324076128 A	
605	1815 T	-7:91680511 1324076127 T	
606 K	1816 A	-7:91680510 1324076126 A	K
606	1817 A	-7:91680509 1324076125 A	
606	1818 A	-7:91680508 1324076124 A	
607 V	1819 G	-7:91680507 1324076123 G	V
607	1820 T	-7:91680506 1324076122 T	
607	1821 C	-7:91680505 1324076121 C	
608 I	1822 A	-7:91680504 1324076120 A	I
608	1823 T	-7:91680503 1324076119 T	
608	1824 C	-7:91680502 1324076118 C	
609 P	1825 C	-7:91680501 1324076117 C	P
609	1826 C	-7:91680500 1324076116 C	
609	1827 T	-7:91680499 1324076115 T	
610 V	1828 G	-7:91680498 1324076114 G	V
610	1829 T	-7:91680497 1324076113 T	
610	1830 G	-7:91680496 1324076112 G	
611 Y	1831 T	-7:91680495 1324076111 T	Y
611	1832 A	-7:91680494 1324076110 A	
611	1833 T	-7:91680493 1324076109 T	
612 V	1834 G	-7:91680492 1324076108 G	V
612	1835 T	-7:91680491 1324076107 T	
612	1836 A	-7:91680490 1324076106 A	
613 G	1837 G	-7:91680489 1324076105 G	G
613	1838 G	-7:91680488 1324076104 G	
613	1839 A	-7:91680487 1324076103 A	
614 V	1840 G	-7:91680486 1324076102 G	V
614	1841 T	-7:91680485 1324076101 T	
614	1842 G	-7:91680484 1324076100 G	
615 N	1843 A	-7:91680483 1324076099 A	N
615	1844 A	-7:91680482 1324076098 A	
615	1845 T	-7:91680481 1324076097 T	
616 I	1846 A	-7:91680480 1324076096 A	I
616	1847 T	-7:91680479 1324076095 T	
616	1848 A	-7:91680478 1324076094 A	
617 K	1849 A	-7:91680477 1324076093 A	K
617	1850 A	-7:91680476 1324076092 A	
617	1851 A	-7:91680475 1324076091 A	
618 G	1852 G	-7:91680474 1324076090 G	G
618	1853 G	-7:91680473 1324076089 G	
618	1854 A	-7:91680472 1324076088 A	
619 L	1855 C	-7:91680471 1324076087 C	L
619	1856 T	-7:91680470 1324076086 T	
619	1857 T	-7:91680469 1324076085 T	
620 H	1858 C	-7:91680468 1324076084 C	H
620	1859 A	-7:91680467 1324076083 A	
620	1860 T	-7:91680466 1324076082 T	
621 L	1861 C	-7:91680465 1324076081 C	L
621	1862 T	-7:91680464 1324076080 T	
621	1863 C	-7:91680463 1324076079 C	
622 L	1864 C	-7:91680462 1324076078 C	L
622	1865 T	-7:91680461 1324076077 T	
622	1866 C	-7:91680460 1324076076 C	
623 N	1867 A	-7:91680459 1324076075 A	N
623	1868 A	-7:91680458 1324076074 A	
623	1869 C	-7:91680457 1324076073 C	
624 M	1870 A	-7:91680456 1324076072 A	M
624	1871 T	-7:91680455 1324076071 T	
624	1872 G	-7:91680454 1324076070 G	
625 E	1873 G	-7:91680453 1324076069 G	E
625	1874 A	-7:91680452 1324076068 A	
625	1875 A	-7:91680451 1324076067 A	
626 T	1876 A	-7:91680450 1324076066 A	T
626	1877 C	-7:91680449 1324076065 C	
626	1878 T	-7:91680448 1324076064 T	
627 K	1879 A	-7:91680447 1324076063 A	K
627	1880 A	-7:91680446 1324076062 A	
627	1881 G	-7:91680445 1324076061 G	
>ENSP00000378013 
1 M	1 A	-7:91709385 1324105001 A	M
1	2 T	-7:91709384 1324105000 T	
1	3 G	-7:91709383 1324104999 G	
2 G	4 G	-7:91709382 1324104998 G	G
2	5 G	-7:91709381 1324104997 G	
2	6 A	-7:91709380 1324104996 A	
3 N	7 A	-7:91709379 1324104995 A	N
3	8 A	-7:91709378 1324104994 A	
3	9 T	-7:91709377 1324104993 T	
4 P	10 C	-7:91709376 1324104992 C	P
4	11 C	-7:91709375 1324104991 C	
4	12 A	-7:91709374 1324104990 A	
5 E	13 G	-7:91709373 1324104989 G	E
5	14 A	-7:91709372 1324104988 A	
5	15 A	-7:91709371 1324104987 A	
6 N	16 A	-7:91709370 1324104986 A	N
6	17 A	-7:91709369 1324104985 A	
6	18 C	-7:91709368 1324104984 C	
7 I	19 A	-7:91709367 1324104983 A	I
7	20 T	-7:91709366 1324104982 T	
7	21 A	-7:91709365 1324104981 A	
8 E	22 G	-7:91709364 1324104980 G	E
8	23 A	-7:91709363 1324104979 A	
8	24 A	-7:91709362 1324104978 A	
9 D	25 G	-7:91709361 1324104977 G	D
9	26 A	-7:91709360 1324104976 A	
9	27 T	-7:91709359 1324104975 T	
10 A	28 G	-7:91709358 1324104974 G	A
10	29 C	-7:91709357 1324104973 C	
10	30 A	-7:91709356 1324104972 A	
11 Y	31 T	-7:91709355 1324104971 T	Y
11	32 A	-7:91709354 1324104970 A	
11	33 T	-7:91709353 1324104969 T	
12 V	34 G	-7:91709352 1324104968 G	V
12	35 T	-7:91709351 1324104967 T	
12	36 T	-7:91709350 1324104966 T	
13 A	37 G	-7:91709349 1324104965 G	A
13	38 C	-7:91709348 1324104964 C	
13	39 T	-7:91709347 1324104963 T	
14 V	40 G	-7:91709346 1324104962 G	V
14	41 T	-7:91709345 1324104961 T	
14	42 T	-7:91709344 1324104960 T	
15 I	43 A	-7:91709343 1324104959 A	I
15	44 T	-7:91709342 1324104958 T	
15	45 T	-7:91709341 1324104957 T	
16 R	46 C	-7:91709340 1324104956 C	R
16	47 G	-7:91709339 1324104955 G	
16	48 T	-7:91709338 1324104954 T	
17 P	49 C	-7:91709337 1324104953 C	P
17	50 C	-7:91709336 1324104952 C	
17	51 A	-7:91709335 1324104951 A	
18 K	52 A	-7:91709334 1324104950 A	K
18	53 A	-7:91709333 1324104949 A	
18	54 G	-7:91709332 1324104948 G	
19 N	55 A	-7:91709331 1324104947 A	N
19	56 A	-7:91709330 1324104946 A	
19	57 T	-7:91709329 1324104945 T	
20 T	58 A	-7:91709328 1324104944 A	T
20	59 C	-7:91709327 1324104943 C	
20	60 T	-7:91709326 1324104942 T	
21 A	61 G	-7:91709325 1324104941 G	A
21	62 C	-7:91709324 1324104940 C	
21	63 C	-7:91709323 1324104939 C	
22 S	64 A	-7:91709322 1324104938 A	S
22	65 G	-7:91709321 1324104937 G	
22	66 T	-7:91709320 1324104936 T	
23 L	67 C	-7:91709319 1324104935 C	L
23	68 T	-7:91709318 1324104934 T	
23	69 C	-7:91709317 1324104933 C	
24 N	70 A	-7:91709316 1324104932 A	N
24	71 A	-7:91709315 1324104931 A	
24	72 T	-7:91709314 1324104930 T	
25 S	73 T	-7:91709313 1324104929 T	S
25	74 C	-7:91709312 1324104928 C	
25	75 T	-7:91709311 1324104927 T	
26 R	76 C	-7:91709310 1324104926 C	R
26	77 G	-7:91709309 1324104925 G	
26	78 G	-7:91709308 1324104924 G	
27 E	79 G	-7:91709307 1324104923 G	E
27	80 A	-7:91709306 1324104922 A	
27	81 A	-7:91709305 1324104921 A	
28 Y	82 T	-7:91709304 1324104920 T	Y
28	83 A	-7:91709303 1324104919 A	
28	84 C	-7:91709302 1324104918 C	
29 R	85 A	-7:91709301 1324104917 A	R
29	86 G	-7:91709300 1324104916 G	
29	87 A	-7:91709299 1324104915 A	
30 A	88 G	-7:91709298 1324104914 G	A
30	89 C	-7:91709297 1324104913 C	
30	90 T	-7:91709296 1324104912 T	
31 K	91 A	-7:91709295 1324104911 A	K
31	92 A	-7:91709294 1324104910 A	
31	93 G	-7:91709293 1324104909 G	
32 S	94 T	-7:91709292 1324104908 T	S
32	95 C	-7:91709291 1324104907 C	
32	96 A	-7:91709290 1324104906 A	
33 Y	97 T	-7:91709289 1324104905 T	Y
33	98 A	-7:91709288 1324104904 A	
33	99 T	-7:91709287 1324104903 T	
34 E	100 G	-7:91709286 1324104902 G	E
34	101 A	-7:91709285 1324104901 A	
34	102 A	-7:91709284 1324104900 A	
35 I	103 A	-7:91708402 1324104018 A	I
35	104 T	-7:91708401 1324104017 T	
35	105 T	-7:91708400 1324104016 T	
36 L	106 T	-7:91708399 1324104015 T	L
36	107 T	-7:91708398 1324104014 T	
36	108 G	-7:91708397 1324104013 G	
37 L	109 T	-7:91708396 1324104012 T	L
37	110 T	-7:91708395 1324104011 T	
37	111 G	-7:91708394 1324104010 G	
38 H	112 C	-7:91708393 1324104009 C	H
38	113 A	-7:91708392 1324104008 A	
38	114 T	-7:91708391 1324104007 T	
39 E	115 G	-7:91708390 1324104006 G	E
39	116 A	-7:91708389 1324104005 A	
39	117 A	-7:91708388 1324104004 A	
40 V	118 G	-7:91708387 1324104003 G	V
40	119 T	-7:91708386 1324104002 T	
40	120 T	-7:91708385 1324104001 T	
41 P	121 C	-7:91708384 1324104000 C	P
41	122 C	-7:91708383 1324103999 C	
41	123 C	-7:91708382 1324103998 C	
42 I	124 A	-7:91708381 1324103997 A	I
42	125 T	-7:91708380 1324103996 T	
42	126 T	-7:91708379 1324103995 T	
43 E	127 G	-7:91708378 1324103994 G	E
43	128 A	-7:91708377 1324103993 A	
43	129 A	-7:91708376 1324103992 A	
44 G	130 G	-7:91708375 1324103991 G	G
44	131 G	-7:91708374 1324103990 G	
44	132 A	-7:91708373 1324103989 A	
45 Q	133 C	-7:91708372 1324103988 C	Q
45	134 A	-7:91708371 1324103987 A	
45	135 G	-7:91708370 1324103986 G	
46 K	136 A	-7:91708369 1324103985 A	K
46	137 A	-7:91708368 1324103984 A	
46	138 A	-7:91708367 1324103983 A	
47 K	139 A	-7:91708366 1324103982 A	K
47	140 A	-7:91708365 1324103981 A	
47	141 A	-7:91708364 1324103980 A	
48 K	142 A	-7:91708363 1324103979 A	K
48	143 A	-7:91708362 1324103978 A	
48	144 G	-7:91708361 1324103977 G	
49 R	145 A	-7:91708360 1324103976 A	R
49	146 G	-7:91708359 1324103975 G	
49	147 A	-7:91708358 1324103974 A	
50 K	148 A	-7:91708357 1324103973 A	K
50	149 A	-7:91708356 1324103972 A	
50	150 G	-7:91708355 1324103971 G	
51 K	151 A	-7:91708354 1324103970 A	K
51	152 A	-7:91708353 1324103969 A	
51	153 A	-7:91708352 1324103968 A	
52 V	154 G	-7:91708351 1324103967 G	V
52	155 T	-7:91708350 1324103966 T	
52	156 T	-7:91708349 1324103965 T	
53 L	157 T	-7:91708348 1324103964 T	L
53	158 T	-7:91708347 1324103963 T	
53	159 A	-7:91708346 1324103962 A	
54 L	160 T	-7:91708345 1324103961 T	L
54	161 T	-7:91708344 1324103960 T	
54	162 G	-7:91708343 1324103959 G	
55 E	163 G	-7:91708342 1324103958 G	E
55	164 A	-7:91708341 1324103957 A	
55	165 A	-7:91708340 1324103956 A	
56 T	166 A	-7:91708339 1324103955 A	T
56	167 C	-7:91708338 1324103954 C	
56	168 G	-7:91708337 1324103953 G	
57 K	169 A	-7:91708336 1324103952 A	K
57	170 A	-7:91708335 1324103951 A	
57	171 A	-7:91708334 1324103950 A	
58 L	172 C	-7:91708333 1324103949 C	L
58	173 T	-7:91708332 1324103948 T	
58	174 T	-7:91708331 1324103947 T	
59 Q	175 C	-7:91708330 1324103946 C	Q
59	176 A	-7:91708329 1324103945 A	
59	177 A	-7:91708328 1324103944 A	
60 G	178 G	-7:91708327 1324103943 G	G
60	179 G	-7:91708326 1324103942 G	
60	180 C	-7:91708325 1324103941 C	
61 N	181 A	-7:91708324 1324103940 A	N
61	182 A	-7:91708323 1324103939 A	
61	183 C	-7:91708322 1324103938 C	
62 S	184 A	-7:91708321 1324103937 A	S
62	185 G	-7:91708320 1324103936 G	
62	186 T	-7:91708319 1324103935 T	
63 E	187 G	-7:91708318 1324103934 G	E
63	188 A	-7:91708317 1324103933 A	
63	189 A	-7:91708316 1324103932 A	
64 I	190 A	-7:91708315 1324103931 A	I
64	191 T	-7:91708314 1324103930 T	
64	192 A	-7:91708313 1324103929 A	
65 T	193 A	-7:91708312 1324103928 A	T
65	194 C	-7:91708311 1324103927 C	
65	195 A	-7:91708310 1324103926 A	
66 Q	196 C	-7:91708309 1324103925 C	Q
66	197 A	-7:91708308 1324103924 A	
66	198 A	-7:91708307 1324103923 A	
67 G	199 G	-7:91708306 1324103922 G	G
67	200 G	-7:91708305 1324103921 G	
67	201 C	-7:91708304 1324103920 C	
68 I	202 A	-7:91708303 1324103919 A	I
68	203 T	-7:91708302 1324103918 T	
68	204 A	-7:91708301 1324103917 A	
69 L	205 T	-7:91708300 1324103916 T	L
69	206 T	-7:91708299 1324103915 T	
69	207 G	-7:91708298 1324103914 G	
70 D	208 G	-7:91708297 1324103913 G	D
70	209 A	-7:91708296 1324103912 A	
70	210 T	-7:91708295 1324103911 T	
71 Y	211 T	-7:91708294 1324103910 T	Y
71	212 A	-7:91708293 1324103909 A	
71	213 C	-7:91708292 1324103908 C	
72 V	214 G	-7:91708291 1324103907 G	V
72	215 T	-7:91708290 1324103906 T	
72	216 A	-7:91708289 1324103905 A	
73 V	217 G	-7:91708288 1324103904 G	V
73	218 T	-7:91708287 1324103903 T	
73	219 A	-7:91708286 1324103902 A	
74 E	220 G	-7:91708285 1324103901 G	E
74	221 A	-7:91708284 1324103900 A	
74	222 A	-7:91708283 1324103899 A	
75 T	223 A	-7:91708282 1324103898 A	T
75	224 C	-7:91708281 1324103897 C	
75	225 C	-7:91708280 1324103896 C	
76 T	226 A	-7:91708279 1324103895 A	T
76	227 C	-7:91708278 1324103894 C	
76	228 C	-7:91708277 1324103893 C	
77 K	229 A	-7:91708276 1324103892 A	K
77	230 A	-7:91708275 1324103891 A	
77	231 A	-7:91708274 1324103890 A	
78 P	232 C	-7:91708273 1324103889 C	P
78	233 C	-7:91708272 1324103888 C	
78	234 A	-7:91708271 1324103887 A	
79 I	235 A	-7:91708270 1324103886 A	I
79	236 T	-7:91708269 1324103885 T	
79	237 T	-7:91708268 1324103884 T	
80 S	238 T	-7:91708267 1324103883 T	S
80	239 C	-7:91708266 1324103882 C	
80	240 T	-7:91708265 1324103881 T	
81 P	241 C	-7:91708264 1324103880 C	P
81	242 C	-7:91708263 1324103879 C	
81	243 T	-7:91708262 1324103878 T	
82 A	244 G	-7:91708261 1324103877 G	A
82	245 C	-7:91708260 1324103876 C	
82	246 A	-7:91708259 1324103875 A	
83 N	247 A	-7:91708258 1324103874 A	N
83	248 A	-7:91708257 1324103873 A	
83	249 C	-7:91708256 1324103872 C	
84 Q	250 C	-7:91708255 1324103871 C	Q
84	251 A	-7:91708254 1324103870 A	
84	252 G	-7:91708253 1324103869 G	
85 G	253 G	-7:91708252 1324103868 G	G
85	254 G	-7:91708251 1324103867 G	
85	255 T	-7:91708250 1324103866 T	
86 I	256 A	-7:91708249 1324103865 A	I
86	257 T	-7:91708248 1324103864 T	
86	258 C	-7:91708247 1324103863 C	
87 R	259 A	-7:91708246 1324103862 A	R
87	260 G	-7:91708245 1324103861 G	
87	261 A	-7:91708244 1324103860 A	
88 G	262 G	-7:91708243 1324103859 G	G
88	263 G	-7:91705009 1324100625 G	
88	264 A	-7:91705008 1324100624 A	
89 K	265 A	-7:91705007 1324100623 A	K
89	266 A	-7:91705006 1324100622 A	
89	267 A	-7:91705005 1324100621 A	
90 R	268 C	-7:91705004 1324100620 C	R
90	269 G	-7:91705003 1324100619 G	
90	270 A	-7:91705002 1324100618 A	
91 V	271 G	-7:91705001 1324100617 G	V
91	272 T	-7:91705000 1324100616 T	
91	273 T	-7:91704999 1324100615 T	
92 V	274 G	-7:91704998 1324100614 G	V
92	275 T	-7:91704997 1324100613 T	
92	276 A	-7:91704996 1324100612 A	
93 L	277 C	-7:91704995 1324100611 C	L
93	278 T	-7:91704994 1324100610 T	
93	279 A	-7:91704993 1324100609 A	
94 M	280 A	-7:91704992 1324100608 A	M
94	281 T	-7:91704991 1324100607 T	
94	282 G	-7:91704990 1324100606 G	
95 K	283 A	-7:91704989 1324100605 A	K
95	284 A	-7:91704988 1324100604 A	
95	285 A	-7:91704987 1324100603 A	
96 K	286 A	-7:91704986 1324100602 A	K
96	287 A	-7:91704985 1324100601 A	
96	288 A	-7:91704984 1324100600 A	
97 F	289 T	-7:91704983 1324100599 T	F
97	290 T	-7:91704982 1324100598 T	
97	291 T	-7:91704981 1324100597 T	
98 P	292 C	-7:91704980 1324100596 C	P
98	293 C	-7:91704979 1324100595 C	
98	294 T	-7:91704978 1324100594 T	
99 L	295 C	-7:91704977 1324100593 C	L
99	296 T	-7:91704976 1324100592 T	
99	297 G	-7:91704975 1324100591 G	
100 D	298 G	-7:91704974 1324100590 G	D
100	299 A	-7:91704973 1324100589 A	
100	300 T	-7:91704972 1324100588 T	
101 G	301 G	-7:91704971 1324100587 G	G
101	302 G	-7:91704970 1324100586 G	
101	303 A	-7:91704969 1324100585 A	
102 E	304 G	-7:91704968 1324100584 G	E
102	305 A	-7:91704967 1324100583 A	
102	306 G	-7:91704966 1324100582 G	
103 K	307 A	-7:91704965 1324100581 A	K
103	308 A	-7:91704964 1324100580 A	
103	309 G	-7:91704963 1324100579 G	
104 M	310 A	-7:91704962 1324100578 A	M
104	311 T	-7:91704961 1324100577 T	
104	312 G	-7:91704960 1324100576 G	
105 G	313 G	-7:91704959 1324100575 G	G
105	314 G	-7:91704958 1324100574 G	
105	315 C	-7:91704957 1324100573 C	
106 R	316 A	-7:91704956 1324100572 A	R
106	317 G	-7:91704955 1324100571 G	
106	318 A	-7:91704954 1324100570 A	
107 E	319 G	-7:91704953 1324100569 G	E
107	320 A	-7:91704952 1324100568 A	
107	321 A	-7:91704951 1324100567 A	
108 A	322 G	-7:91704950 1324100566 G	A
108	323 C	-7:91704949 1324100565 C	
108	324 A	-7:91704948 1324100564 A	
109 S	325 T	-7:91704947 1324100563 T	S
109	326 C	-7:91704946 1324100562 C	
109	327 A	-7:91704945 1324100561 A	
110 L	328 T	-7:91704944 1324100560 T	L
110	329 T	-7:91704943 1324100559 T	
110	330 A	-7:91704942 1324100558 A	
111 F	331 T	-7:91704941 1324100557 T	F
111	332 T	-7:91704940 1324100556 T	
111	333 T	-7:91704939 1324100555 T	
112 I	334 A	-7:91704938 1324100554 A	I
112	335 T	-7:91704937 1324100553 T	
112	336 T	-7:91704936 1324100552 T	
113 V	337 G	-7:91704935 1324100551 G	V
113	338 T	-7:91704934 1324100550 T	
113	339 T	-7:91704933 1324100549 T	
114 P	340 C	-7:91704932 1324100548 C	P
114	341 C	-7:91704931 1324100547 C	
114	342 A	-7:91704930 1324100546 A	
115 S	343 T	-7:91704929 1324100545 T	S
115	344 C	-7:91704928 1324100544 C	
115	345 A	-7:91704927 1324100543 A	
116 V	346 G	-7:91704926 1324100542 G	V
116	347 T	-7:91704925 1324100541 T	
116	348 T	-7:91704924 1324100540 T	
117 V	349 G	-7:91704923 1324100539 G	V
117	350 T	-7:91704922 1324100538 T	
117	351 C	-7:91704921 1324100537 C	
118 K	352 A	-7:91704920 1324100536 A	K
118	353 A	-7:91704919 1324100535 A	
118	354 A	-7:91704918 1324100534 A	
119 D	355 G	-7:91704917 1324100533 G	D
119	356 A	-7:91703792 1324099408 A	
119	357 T	-7:91703791 1324099407 T	
120 N	358 A	-7:91703790 1324099406 A	N
120	359 A	-7:91703789 1324099405 A	
120	360 T	-7:91703788 1324099404 T	
121 T	361 A	-7:91703787 1324099403 A	T
121	362 C	-7:91703786 1324099402 C	
121	363 T	-7:91703785 1324099401 T	
122 K	364 A	-7:91703784 1324099400 A	K
122	365 A	-7:91703783 1324099399 A	
122	366 A	-7:91703782 1324099398 A	
123 Y	367 T	-7:91703781 1324099397 T	Y
123	368 A	-7:91703780 1324099396 A	
123	369 C	-7:91703779 1324099395 C	
124 T	370 A	-7:91703778 1324099394 A	T
124	371 C	-7:91703777 1324099393 C	
124	372 A	-7:91703776 1324099392 A	
125 Y	373 T	-7:91703775 1324099391 T	Y
125	374 A	-7:91703774 1324099390 A	
125	375 T	-7:91703773 1324099389 T	
126 T	376 A	-7:91703772 1324099388 A	T
126	377 C	-7:91703771 1324099387 C	
126	378 C	-7:91703770 1324099386 C	
127 P	379 C	-7:91703769 1324099385 C	P
127	380 C	-7:91703768 1324099384 C	
127	381 A	-7:91703767 1324099383 A	
128 G	382 G	-7:91703766 1324099382 G	G
128	383 G	-7:91703765 1324099381 G	
128	384 A	-7:91703764 1324099380 A	
129 C	385 T	-7:91703763 1324099379 T	C
129	386 G	-7:91703762 1324099378 G	
129	387 C	-7:91703761 1324099377 C	
130 P	388 C	-7:91703760 1324099376 C	P
130	389 C	-7:91703759 1324099375 C	
130	390 A	-7:91703758 1324099374 A	
131 I	391 A	-7:91703757 1324099373 A	I
131	392 T	-7:91703756 1324099372 T	
131	393 T	-7:91703755 1324099371 T	
132 F	394 T	-7:91703754 1324099370 T	F
132	395 T	-7:91703753 1324099369 T	
132	396 T	-7:91703752 1324099368 T	
133 Y	397 T	-7:91703751 1324099367 T	Y
133	398 A	-7:91703750 1324099366 A	
133	399 C	-7:91703749 1324099365 C	
134 C	400 T	-7:91703748 1324099364 T	C
134	401 G	-7:91703747 1324099363 G	
134	402 C	-7:91703746 1324099362 C	
135 L	403 T	-7:91703745 1324099361 T	L
135	404 T	-7:91703744 1324099360 T	
135	405 A	-7:91703743 1324099359 A	
136 Q	406 C	-7:91703742 1324099358 C	Q
136	407 A	-7:91703741 1324099357 A	
136	408 A	-7:91703740 1324099356 A	
137 D	409 G	-7:91703739 1324099355 G	D
137	410 A	-7:91703738 1324099354 A	
137	411 T	-7:91703737 1324099353 T	
138 I	412 A	-7:91703736 1324099352 A	I
138	413 T	-7:91703735 1324099351 T	
138	414 T	-7:91703734 1324099350 T	
139 M	415 A	-7:91703733 1324099349 A	M
139	416 T	-7:91703732 1324099348 T	
139	417 G	-7:91703731 1324099347 G	
140 R	418 C	-7:91703730 1324099346 C	R
140	419 G	-7:91703729 1324099345 G	
140	420 A	-7:91703728 1324099344 A	
141 V	421 G	-7:91703727 1324099343 G	V
141	422 T	-7:91703726 1324099342 T	
141	423 C	-7:91703725 1324099341 C	
142 C	424 T	-7:91703724 1324099340 T	C
142	425 G	-7:91703723 1324099339 G	
142	426 T	-7:91703722 1324099338 T	
143 S	427 A	-7:91703721 1324099337 A	S
143	428 G	-7:91703720 1324099336 G	
143	429 T	-7:91703719 1324099335 T	
144 E	430 G	-7:91703718 1324099334 G	E
144	431 A	-7:91703717 1324099333 A	
144	432 A	-7:91703716 1324099332 A	
145 S	433 T	-7:91703715 1324099331 T	S
145	434 C	-7:91703714 1324099330 C	
145	435 C	-7:91703713 1324099329 C	
146 S	436 A	-7:91703712 1324099328 A	S
146	437 G	-7:91703711 1324099327 G	
146	438 T	-7:91703710 1324099326 T	
147 T	439 A	-7:91703709 1324099325 A	T
147	440 C	-7:91703708 1324099324 C	
147	441 T	-7:91703707 1324099323 T	
148 H	442 C	-7:91703706 1324099322 C	H
148	443 A	-7:91703705 1324099321 A	
148	444 T	-7:91703704 1324099320 T	
149 F	445 T	-7:91703703 1324099319 T	F
149	446 T	-7:91703702 1324099318 T	
149	447 T	-7:91703701 1324099317 T	
150 A	448 G	-7:91703700 1324099316 G	A
150	449 C	-7:91703699 1324099315 C	
150	450 T	-7:91703698 1324099314 T	
151 T	451 A	-7:91703697 1324099313 A	T
151	452 C	-7:91703696 1324099312 C	
151	453 A	-7:91703695 1324099311 A	
152 L	454 C	-7:91703694 1324099310 C	L
152	455 T	-7:91703693 1324099309 T	
152	456 T	-7:91703692 1324099308 T	
153 T	457 A	-7:91703691 1324099307 A	T
153	458 C	-7:91703690 1324099306 C	
153	459 A	-7:91703689 1324099305 A	
154 A	460 G	-7:91703688 1324099304 G	A
154	461 C	-7:91703687 1324099303 C	
154	462 A	-7:91703686 1324099302 A	
155 R	463 A	-7:91703685 1324099301 A	R
155	464 G	-7:91703684 1324099300 G	
155	465 G	-7:91703683 1324099299 G	
156 M	466 A	-7:91703682 1324099298 A	M
156	467 T	-7:91703681 1324099297 T	
156	468 G	-7:91703680 1324099296 G	
157 L	469 T	-7:91703679 1324099295 T	L
157	470 T	-7:91703678 1324099294 T	
157	471 A	-7:91703677 1324099293 A	
158 I	472 A	-7:91703676 1324099292 A	I
158	473 T	-7:91703675 1324099291 T	
158	474 A	-7:91703674 1324099290 A	
159 A	475 G	-7:91703673 1324099289 G	A
159	476 C	-7:91703672 1324099288 C	
159	477 C	-7:91703671 1324099287 C	
160 L	478 T	-7:91703670 1324099286 T	L
160	479 T	-7:91703669 1324099285 T	
160	480 G	-7:91703668 1324099284 G	
161 D	481 G	-7:91703667 1324099283 G	D
161	482 A	-7:91703666 1324099282 A	
161	483 T	-7:91703665 1324099281 T	
162 K	484 A	-7:91703664 1324099280 A	K
162	485 A	-7:91703663 1324099279 A	
162	486 G	-7:91702896 1324098512 G	
163 W	487 T	-7:91702895 1324098511 T	W
163	488 G	-7:91702894 1324098510 G	
163	489 G	-7:91702893 1324098509 G	
164 L	490 T	-7:91702892 1324098508 T	L
164	491 T	-7:91702891 1324098507 T	
164	492 A	-7:91702890 1324098506 A	
165 D	493 G	-7:91702889 1324098505 G	D
165	494 A	-7:91702888 1324098504 A	
165	495 T	-7:91702887 1324098503 T	
166 E	496 G	-7:91702886 1324098502 G	E
166	497 A	-7:91702885 1324098501 A	
166	498 A	-7:91702884 1324098500 A	
167 R	499 C	-7:91702883 1324098499 C	R
167	500 G	-7:91702882 1324098498 G	
167	501 T	-7:91702881 1324098497 T	
168 H	502 C	-7:91702880 1324098496 C	H
168	503 A	-7:91702879 1324098495 A	
168	504 T	-7:91702878 1324098494 T	
169 A	505 G	-7:91702877 1324098493 G	A
169	506 C	-7:91702876 1324098492 C	
169	507 A	-7:91702875 1324098491 A	
170 Q	508 C	-7:91702874 1324098490 C	Q
170	509 A	-7:91702873 1324098489 A	
170	510 A	-7:91702872 1324098488 A	
171 S	511 T	-7:91702871 1324098487 T	S
171	512 C	-7:91702870 1324098486 C	
171	513 T	-7:91702869 1324098485 T	
172 H	514 C	-7:91702868 1324098484 C	H
172	515 A	-7:91702867 1324098483 A	
172	516 C	-7:91702866 1324098482 C	
173 F	517 T	-7:91702865 1324098481 T	F
173	518 T	-7:91702864 1324098480 T	
173	519 T	-7:91702863 1324098479 T	
174 I	520 A	-7:91702862 1324098478 A	I
174	521 T	-7:91702861 1324098477 T	
174	522 T	-7:91702860 1324098476 T	
175 P	523 C	-7:91702859 1324098475 C	P
175	524 C	-7:91702858 1324098474 C	
175	525 A	-7:91702857 1324098473 A	
176 A	526 G	-7:91702856 1324098472 G	A
176	527 C	-7:91702855 1324098471 C	
176	528 T	-7:91702854 1324098470 T	
177 L	529 T	-7:91702853 1324098469 T	L
177	530 T	-7:91702852 1324098468 T	
177	531 A	-7:91702851 1324098467 A	
178 F	532 T	-7:91702850 1324098466 T	F
178	533 T	-7:91702849 1324098465 T	
178	534 C	-7:91702848 1324098464 C	
179 R	535 C	-7:91702847 1324098463 C	R
179	536 G	-7:91702846 1324098462 G	
179	537 A	-7:91702845 1324098461 A	
180 P	538 C	-7:91702844 1324098460 C	P
180	539 C	-7:91702843 1324098459 C	
180	540 T	-7:91702842 1324098458 T	
181 S	541 T	-7:91702841 1324098457 T	S
181	542 C	-7:91702840 1324098456 C	
181	543 T	-7:91702839 1324098455 T	
182 P	544 C	-7:91702838 1324098454 C	P
182	545 C	-7:91702837 1324098453 C	
182	546 T	-7:91702836 1324098452 T	
183 L	547 C	-7:91702835 1324098451 C	L
183	548 T	-7:91702834 1324098450 T	
183	549 T	-7:91702833 1324098449 T	
184 E	550 G	-7:91702832 1324098448 G	E
184	551 A	-7:91702831 1324098447 A	
184	552 G	-7:91702830 1324098446 G	
185 R	553 C	-7:91702829 1324098445 C	R
185	554 G	-7:91702828 1324098444 G	
185	555 G	-7:91702827 1324098443 G	
186 I	556 A	-7:91702826 1324098442 A	I
186	557 T	-7:91702825 1324098441 T	
186	558 A	-7:91702824 1324098440 A	
187 K	559 A	-7:91702823 1324098439 A	K
187	560 A	-7:91702822 1324098438 A	
187	561 A	-7:91702821 1324098437 A	
188 T	562 A	-7:91702820 1324098436 A	T
188	563 C	-7:91702819 1324098435 C	
188	564 T	-7:91702818 1324098434 T	
189 N	565 A	-7:91702817 1324098433 A	N
189	566 A	-7:91702816 1324098432 A	
189	567 T	-7:91702815 1324098431 T	
190 V	568 G	-7:91702814 1324098430 G	V
190	569 T	-7:91702813 1324098429 T	
190	570 C	-7:91702812 1324098428 C	
191 I	571 A	-7:91702811 1324098427 A	I
191	572 T	-7:91702810 1324098426 T	
191	573 A	-7:91702809 1324098425 A	
192 N	574 A	-7:91702808 1324098424 A	N
192	575 A	-7:91702807 1324098423 A	
192	576 T	-7:91702806 1324098422 T	
193 P	577 C	-7:91702805 1324098421 C	P
193	578 C	-7:91702804 1324098420 C	
193	579 T	-7:91702803 1324098419 T	
194 A	580 G	-7:91702802 1324098418 G	A
194	581 C	-7:91702801 1324098417 C	
194	582 A	-7:91702800 1324098416 A	
195 Y	583 T	-7:91702799 1324098415 T	Y
195	584 A	-7:91702798 1324098414 A	
195	585 T	-7:91702797 1324098413 T	
196 A	586 G	-7:91702796 1324098412 G	A
196	587 C	-7:91702795 1324098411 C	
196	588 T	-7:91702794 1324098410 T	
197 T	589 A	-7:91702793 1324098409 A	T
197	590 C	-7:91702792 1324098408 C	
197	591 T	-7:91702791 1324098407 T	
198 E	592 G	-7:91702790 1324098406 G	E
198	593 A	-7:91702789 1324098405 A	
198	594 A	-7:91702788 1324098404 A	
199 S	595 T	-7:91702787 1324098403 T	S
199	596 C	-7:91702786 1324098402 C	
199	597 A	-7:91702785 1324098401 A	
200 G	598 G	-7:91702784 1324098400 G	G
200	599 G	-7:91702783 1324098399 G	
200	600 T	-7:91702782 1324098398 T	
201 Q	601 C	-7:91702781 1324098397 C	Q
201	602 A	-7:91702780 1324098396 A	
201	603 G	-7:91702779 1324098395 G	
202 T	604 A	-7:91702778 1324098394 A	T
202	605 C	-7:91702777 1324098393 C	
202	606 A	-7:91702776 1324098392 A	
203 E	607 G	-7:91702775 1324098391 G	E
203	608 A	-7:91702774 1324098390 A	
203	609 A	-7:91702773 1324098389 A	
204 N	610 A	-7:91702772 1324098388 A	N
204	611 A	-7:91702771 1324098387 A	
204	612 C	-7:91702770 1324098386 C	
205 S	613 T	-7:91702769 1324098385 T	S
205	614 C	-7:91702768 1324098384 C	
205	615 A	-7:91702767 1324098383 A	
206 L	616 C	-7:91702766 1324098382 C	L
206	617 T	-7:91702765 1324098381 T	
206	618 A	-7:91702764 1324098380 A	
207 H	619 C	-7:91702763 1324098379 C	H
207	620 A	-7:91702762 1324098378 A	
207	621 T	-7:91702761 1324098377 T	
208 M	622 A	-7:91702760 1324098376 A	M
208	623 T	-7:91702759 1324098375 T	
208	624 G	-7:91702758 1324098374 G	
209 G	625 G	-7:91702757 1324098373 G	G
209	626 G	-7:91702756 1324098372 G	
209	627 C	-7:91702755 1324098371 C	
210 Y	628 T	-7:91702754 1324098370 T	Y
210	629 A	-7:91702753 1324098369 A	
210	630 T	-7:91702752 1324098368 T	
211 S	631 A	-7:91702751 1324098367 A	S
211	632 G	-7:91702750 1324098366 G	
211	633 T	-7:91702749 1324098365 T	
212 A	634 G	-7:91702748 1324098364 G	A
212	635 C	-7:91702747 1324098363 C	
212	636 A	-7:91702746 1324098362 A	
213 L	637 C	-7:91702745 1324098361 C	L
213	638 T	-7:91702744 1324098360 T	
213	639 A	-7:91702743 1324098359 A	
214 E	640 G	-7:91702742 1324098358 G	E
214	641 A	-7:91702741 1324098357 A	
214	642 A	-7:91702740 1324098356 A	
215 I	643 A	-7:91702739 1324098355 A	I
215	644 T	-7:91702738 1324098354 T	
215	645 A	-7:91702737 1324098353 A	
216 K	646 A	-7:91702736 1324098352 A	K
216	647 A	-7:91702735 1324098351 A	
216	648 G	-7:91702734 1324098350 G	
217 S	649 A	-7:91702733 1324098349 A	S
217	650 G	-7:91702732 1324098348 G	
217	651 T	-7:91702731 1324098347 T	
218 K	652 A	-7:91702730 1324098346 A	K
218	653 A	-7:91702729 1324098345 A	
218	654 A	-7:91702728 1324098344 A	
219 M	655 A	-7:91702727 1324098343 A	M
219	656 T	-7:91702726 1324098342 T	
219	657 G	-7:91702725 1324098341 G	
220 L	658 T	-7:91702724 1324098340 T	L
220	659 T	-7:91702723 1324098339 T	
220	660 A	-7:91702722 1324098338 A	
221 A	661 G	-7:91702721 1324098337 G	A
221	662 C	-7:91702720 1324098336 C	
221	663 C	-7:91702719 1324098335 C	
222 L	664 C	-7:91702718 1324098334 C	L
222	665 T	-7:91702717 1324098333 T	
222	666 A	-7:91702716 1324098332 A	
223 E	667 G	-7:91702715 1324098331 G	E
223	668 A	-7:91702714 1324098330 A	
223	669 G	-7:91702713 1324098329 G	
224 K	670 A	-7:91702712 1324098328 A	K
224	671 A	-7:91702711 1324098327 A	
224	672 A	-7:91702710 1324098326 A	
225 A	673 G	-7:91702709 1324098325 G	A
225	674 C	-7:91702708 1324098324 C	
225	675 A	-7:91702707 1324098323 A	
226 D	676 G	-7:91702706 1324098322 G	D
226	677 A	-7:91702705 1324098321 A	
226	678 T	-7:91702704 1324098320 T	
227 T	679 A	-7:91702703 1324098319 A	T
227	680 C	-7:91702702 1324098318 C	
227	681 C	-7:91702701 1324098317 C	
228 C	682 T	-7:91702700 1324098316 T	C
228	683 G	-7:91702699 1324098315 G	
228	684 T	-7:91702698 1324098314 T	
229 I	685 A	-7:91702697 1324098313 A	I
229	686 T	-7:91702696 1324098312 T	
229	687 T	-7:91702695 1324098311 T	
230 Y	688 T	-7:91702694 1324098310 T	Y
230	689 A	-7:91702693 1324098309 A	
230	690 C	-7:91702692 1324098308 C	
231 N	691 A	-7:91702691 1324098307 A	N
231	692 A	-7:91702690 1324098306 A	
231	693 C	-7:91702689 1324098305 C	
232 P	694 C	-7:91702688 1324098304 C	P
232	695 C	-7:91702687 1324098303 C	
232	696 T	-7:91702686 1324098302 T	
233 L	697 T	-7:91702685 1324098301 T	L
233	698 T	-7:91702684 1324098300 T	
233	699 G	-7:91702683 1324098299 G	
234 F	700 T	-7:91702682 1324098298 T	F
234	701 T	-7:91702681 1324098297 T	
234	702 T	-7:91702680 1324098296 T	
235 G	703 G	-7:91702679 1324098295 G	G
235	704 G	-7:91702678 1324098294 G	
235	705 A	-7:91702677 1324098293 A	
236 S	706 T	-7:91702676 1324098292 T	S
236	707 C	-7:91702675 1324098291 C	
236	708 A	-7:91702674 1324098290 A	
237 D	709 G	-7:91702673 1324098289 G	D
237	710 A	-7:91702672 1324098288 A	
237	711 T	-7:91702671 1324098287 T	
238 L	712 C	-7:91702670 1324098286 C	L
238	713 T	-7:91702669 1324098285 T	
238	714 T	-7:91702668 1324098284 T	
239 Q	715 C	-7:91702667 1324098283 C	Q
239	716 A	-7:91702666 1324098282 A	
239	717 G	-7:91702665 1324098281 G	
240 Y	718 T	-7:91702664 1324098280 T	Y
240	719 A	-7:91702663 1324098279 A	
240	720 T	-7:91702662 1324098278 T	
241 T	721 A	-7:91702661 1324098277 A	T
241	722 C	-7:91702660 1324098276 C	
241	723 A	-7:91702659 1324098275 A	
242 N	724 A	-7:91702658 1324098274 A	N
242	725 A	-7:91702657 1324098273 A	
242	726 T	-7:91702656 1324098272 T	
243 R	727 C	-7:91702655 1324098271 C	R
243	728 G	-7:91702654 1324098270 G	
243	729 G	-7:91702653 1324098269 G	
244 V	730 G	-7:91702173 1324097789 G	V
244	731 T	-7:91702172 1324097788 T	
244	732 A	-7:91702171 1324097787 A	
245 D	733 G	-7:91702170 1324097786 G	D
245	734 A	-7:91702169 1324097785 A	
245	735 T	-7:91702168 1324097784 T	
246 K	736 A	-7:91702167 1324097783 A	K
246	737 A	-7:91702166 1324097782 A	
246	738 A	-7:91702165 1324097781 A	
247 V	739 G	-7:91702164 1324097780 G	V
247	740 T	-7:91702163 1324097779 T	
247	741 G	-7:91702162 1324097778 G	
248 V	742 G	-7:91702161 1324097777 G	V
248	743 T	-7:91702160 1324097776 T	
248	744 A	-7:91702159 1324097775 A	
249 I	745 A	-7:91702158 1324097774 A	I
249	746 T	-7:91702157 1324097773 T	
249	747 A	-7:91702156 1324097772 A	
250 N	748 A	-7:91702155 1324097771 A	N
250	749 A	-7:91702154 1324097770 A	
250	750 T	-7:91702153 1324097769 T	
251 P	751 C	-7:91702152 1324097768 C	P
251	752 C	-7:91702151 1324097767 C	
251	753 A	-7:91702150 1324097766 A	
252 Y	754 T	-7:91702149 1324097765 T	Y
252	755 A	-7:91702148 1324097764 A	
252	756 C	-7:91702147 1324097763 C	
253 F	757 T	-7:91702146 1324097762 T	F
253	758 T	-7:91702145 1324097761 T	
253	759 T	-7:91702144 1324097760 T	
254 G	760 G	-7:91702143 1324097759 G	G
254	761 G	-7:91702142 1324097758 G	
254	762 T	-7:91702141 1324097757 T	
255 L	763 C	-7:91702140 1324097756 C	L
255	764 T	-7:91702139 1324097755 T	
255	765 A	-7:91702138 1324097754 A	
256 G	766 G	-7:91702137 1324097753 G	G
256	767 G	-7:91702136 1324097752 G	
256	768 A	-7:91702135 1324097751 A	
257 A	769 G	-7:91702134 1324097750 G	A
257	770 C	-7:91702133 1324097749 C	
257	771 T	-7:91702132 1324097748 T	
258 P	772 C	-7:91702131 1324097747 C	P
258	773 C	-7:91702130 1324097746 C	
258	774 A	-7:91702129 1324097745 A	
259 D	775 G	-7:91702128 1324097744 G	D
259	776 A	-7:91702127 1324097743 A	
259	777 C	-7:91702126 1324097742 C	
260 Y	778 T	-7:91702125 1324097741 T	Y
260	779 A	-7:91702124 1324097740 A	
260	780 C	-7:91702123 1324097739 C	
261 S	781 T	-7:91702122 1324097738 T	S
261	782 C	-7:91702121 1324097737 C	
261	783 A	-7:91702120 1324097736 A	
262 K	784 A	-7:91702119 1324097735 A	K
262	785 A	-7:91702118 1324097734 A	
262	786 A	-7:91702117 1324097733 A	
263 I	787 A	-7:91702116 1324097732 A	I
263	788 T	-7:91702115 1324097731 T	
263	789 C	-7:91702114 1324097730 C	
264 Q	790 C	-7:91702113 1324097729 C	Q
264	791 A	-7:91702112 1324097728 A	
264	792 A	-7:91702111 1324097727 A	
265 I	793 A	-7:91702110 1324097726 A	I
265	794 T	-7:91702109 1324097725 T	
265	795 A	-7:91702108 1324097724 A	
266 P	796 C	-7:91702107 1324097723 C	P
266	797 C	-7:91702106 1324097722 C	
266	798 T	-7:91702105 1324097721 T	
267 K	799 A	-7:91702104 1324097720 A	K
267	800 A	-7:91702103 1324097719 A	
267	801 A	-7:91702102 1324097718 A	
268 Q	802 C	-7:91702101 1324097717 C	Q
268	803 A	-7:91702100 1324097716 A	
268	804 G	-7:91702099 1324097715 G	
269 E	805 G	-7:91702098 1324097714 G	E
269	806 A	-7:91702097 1324097713 A	
269	807 A	-7:91702096 1324097712 A	
270 K	808 A	-7:91702095 1324097711 A	K
270	809 A	-7:91702094 1324097710 A	
270	810 A	-7:91702093 1324097709 A	
271 W	811 T	-7:91702092 1324097708 T	W
271	812 G	-7:91702091 1324097707 G	
271	813 G	-7:91702090 1324097706 G	
272 Q	814 C	-7:91702089 1324097705 C	Q
272	815 A	-7:91702088 1324097704 A	
272	816 G	-7:91702087 1324097703 G	
273 R	817 A	-7:91702086 1324097702 A	R
273	818 G	-7:91702085 1324097701 G	
273	819 A	-7:91702084 1324097700 A	
274 S	820 A	-7:91702083 1324097699 A	S
274	821 G	-7:91702082 1324097698 G	
274	822 C	-7:91702081 1324097697 C	
275 M	823 A	-7:91702080 1324097696 A	M
275	824 T	-7:91702079 1324097695 T	
275	825 G	-7:91702078 1324097694 G	
276 S	826 A	-7:91702077 1324097693 A	S
276	827 G	-7:91702076 1324097692 G	
276	828 C	-7:91702075 1324097691 C	
277 S	829 A	-7:91702074 1324097690 A	S
277	830 G	-7:91702073 1324097689 G	
277	831 T	-7:91702072 1324097688 T	
278 V	832 G	-7:91702071 1324097687 G	V
278	833 T	-7:91702070 1324097686 T	
278	834 C	-7:91702069 1324097685 C	
279 T	835 A	-7:91702068 1324097684 A	T
279	836 C	-7:91702067 1324097683 C	
279	837 A	-7:91702066 1324097682 A	
280 E	838 G	-7:91702065 1324097681 G	E
280	839 A	-7:91702064 1324097680 A	
280	840 A	-7:91702063 1324097679 A	
281 D	841 G	-7:91702062 1324097678 G	D
281	842 A	-7:91702061 1324097677 A	
281	843 C	-7:91702060 1324097676 C	
282 K	844 A	-7:91702059 1324097675 A	K
282	845 A	-7:91702058 1324097674 A	
282	846 G	-7:91701842 1324097458 G	
283 E	847 G	-7:91701841 1324097457 G	E
283	848 A	-7:91701840 1324097456 A	
283	849 A	-7:91701839 1324097455 A	
284 R	850 C	-7:91701838 1324097454 C	R
284	851 G	-7:91701837 1324097453 G	
284	852 A	-7:91701836 1324097452 A	
285 Q	853 C	-7:91701835 1324097451 C	Q
285	854 A	-7:91701834 1324097450 A	
285	855 G	-7:91701833 1324097449 G	
286 W	856 T	-7:91701832 1324097448 T	W
286	857 G	-7:91701831 1324097447 G	
286	858 G	-7:91701830 1324097446 G	
287 V	859 G	-7:91701829 1324097445 G	V
287	860 T	-7:91701828 1324097444 T	
287	861 A	-7:91701827 1324097443 A	
288 D	862 G	-7:91701826 1324097442 G	D
288	863 A	-7:91701825 1324097441 A	
288	864 T	-7:91701824 1324097440 T	
289 D	865 G	-7:91701823 1324097439 G	D
289	866 A	-7:91701822 1324097438 A	
289	867 T	-7:91701821 1324097437 T	
290 F	868 T	-7:91701820 1324097436 T	F
290	869 T	-7:91701819 1324097435 T	
290	870 T	-7:91701818 1324097434 T	
291 P	871 C	-7:91701817 1324097433 C	P
291	872 C	-7:91701816 1324097432 C	
291	873 T	-7:91701815 1324097431 T	
292 L	874 C	-7:91701814 1324097430 C	L
292	875 T	-7:91701813 1324097429 T	
292	876 C	-7:91701812 1324097428 C	
293 H	877 C	-7:91701811 1324097427 C	H
293	878 A	-7:91701810 1324097426 A	
293	879 C	-7:91701809 1324097425 C	
294 R	880 C	-7:91701808 1324097424 C	R
294	881 G	-7:91701807 1324097423 G	
294	882 A	-7:91701806 1324097422 A	
295 S	883 A	-7:91701805 1324097421 A	S
295	884 G	-7:91701804 1324097420 G	
295	885 C	-7:91701803 1324097419 C	
296 A	886 G	-7:91701802 1324097418 G	A
296	887 C	-7:91701801 1324097417 C	
296	888 C	-7:91701800 1324097416 C	
297 C	889 T	-7:91701799 1324097415 T	C
297	890 G	-7:91701798 1324097414 G	
297	891 T	-7:91701797 1324097413 T	
298 E	892 G	-7:91701796 1324097412 G	E
298	893 A	-7:91701795 1324097411 A	
298	894 A	-7:91701794 1324097410 A	
299 G	895 G	-7:91701793 1324097409 G	G
299	896 G	-7:91701792 1324097408 G	
299	897 A	-7:91701791 1324097407 A	
300 D	898 G	-7:91701790 1324097406 G	D
300	899 A	-7:91701789 1324097405 A	
300	900 T	-7:91701788 1324097404 T	
301 S	901 T	-7:91701787 1324097403 T	S
301	902 C	-7:91701786 1324097402 C	
301	903 A	-7:91701785 1324097401 A	
302 E	904 G	-7:91701784 1324097400 G	E
302	905 A	-7:91701783 1324097399 A	
302	906 A	-7:91701782 1324097398 A	
303 L	907 T	-7:91701781 1324097397 T	L
303	908 T	-7:91701780 1324097396 T	
303	909 A	-7:91701779 1324097395 A	
304 L	910 C	-7:91701778 1324097394 C	L
304	911 T	-7:91701777 1324097393 T	
304	912 A	-7:91701776 1324097392 A	
305 S	913 A	-7:91701775 1324097391 A	S
305	914 G	-7:91701774 1324097390 G	
305	915 C	-7:91701773 1324097389 C	
306 R	916 C	-7:91701772 1324097388 C	R
306	917 G	-7:91701771 1324097387 G	
306	918 T	-7:91701770 1324097386 T	
307 L	919 C	-7:91701769 1324097385 C	L
307	920 T	-7:91701768 1324097384 T	
307	921 T	-7:91701767 1324097383 T	
308 L	922 C	-7:91701766 1324097382 C	L
308	923 T	-7:91701765 1324097381 T	
308	924 C	-7:91701764 1324097380 C	
309 S	925 A	-7:91701763 1324097379 A	S
309	926 G	-7:91701762 1324097378 G	
309	927 T	-7:91701761 1324097377 T	
310 E	928 G	-7:91701760 1324097376 G	E
310	929 A	-7:91701759 1324097375 A	
310	930 A	-7:91701758 1324097374 A	
311 R	931 A	-7:91701757 1324097373 A	R
311	932 G	-7:91701756 1324097372 G	
311	933 A	-7:91701755 1324097371 A	
312 F	934 T	-7:91701754 1324097370 T	F
312	935 T	-7:91701753 1324097369 T	
312	936 T	-7:91701752 1324097368 T	
313 S	937 T	-7:91701751 1324097367 T	S
313	938 C	-7:91701750 1324097366 C	
313	939 A	-7:91701749 1324097365 A	
314 V	940 G	-7:91701748 1324097364 G	V
314	941 T	-7:91701747 1324097363 T	
314	942 C	-7:91701746 1324097362 C	
315 N	943 A	-7:91701745 1324097361 A	N
315	944 A	-7:91701744 1324097360 A	
315	945 C	-7:91701743 1324097359 C	
316 Q	946 C	-7:91701742 1324097358 C	Q
316	947 A	-7:91701741 1324097357 A	
316	948 G	-7:91701740 1324097356 G	
317 L	949 T	-7:91701739 1324097355 T	L
317	950 T	-7:91701738 1324097354 T	
317	951 A	-7:91701737 1324097353 A	
318 D	952 G	-7:91701736 1324097352 G	D
318	953 A	-7:91701735 1324097351 A	
318	954 T	-7:91701734 1324097350 T	
319 S	955 A	-7:91701733 1324097349 A	S
319	956 G	-7:91701732 1324097348 G	
319	957 T	-7:91701731 1324097347 T	
320 D	958 G	-7:91701730 1324097346 G	D
320	959 A	-7:91701729 1324097345 A	
320	960 C	-7:91701728 1324097344 C	
321 H	961 C	-7:91701727 1324097343 C	H
321	962 A	-7:91701726 1324097342 A	
321	963 C	-7:91701725 1324097341 C	
322 W	964 T	-7:91701724 1324097340 T	W
322	965 G	-7:91701723 1324097339 G	
322	966 G	-7:91701722 1324097338 G	
323 A	967 G	-7:91701721 1324097337 G	A
323	968 C	-7:91701720 1324097336 C	
323	969 A	-7:91701719 1324097335 A	
324 P	970 C	-7:91701718 1324097334 C	P
324	971 C	-7:91701717 1324097333 C	
324	972 C	-7:91701716 1324097332 C	
325 I	973 A	-7:91701715 1324097331 A	I
325	974 T	-7:91701714 1324097330 T	
325	975 T	-7:91701713 1324097329 T	
326 H	976 C	-7:91701712 1324097328 C	H
326	977 A	-7:91701711 1324097327 A	
326	978 T	-7:91701710 1324097326 T	
327 Y	979 T	-7:91701709 1324097325 T	Y
327	980 A	-7:91701708 1324097324 A	
327	981 T	-7:91701707 1324097323 T	
328 A	982 G	-7:91701706 1324097322 G	A
328	983 C	-7:91701705 1324097321 C	
328	984 A	-7:91701704 1324097320 A	
329 C	985 T	-7:91701703 1324097319 T	C
329	986 G	-7:91701702 1324097318 G	
329	987 C	-7:91701701 1324097317 C	
330 W	988 T	-7:91701700 1324097316 T	W
330	989 G	-7:91701699 1324097315 G	
330	990 G	-7:91693932 1324089548 G	
331 Y	991 T	-7:91693931 1324089547 T	Y
331	992 A	-7:91693930 1324089546 A	
331	993 T	-7:91693929 1324089545 T	
332 G	994 G	-7:91693928 1324089544 G	G
332	995 G	-7:91693927 1324089543 G	
332	996 A	-7:91693926 1324089542 A	
333 K	997 A	-7:91693925 1324089541 A	K
333	998 A	-7:91693924 1324089540 A	
333	999 A	-7:91693923 1324089539 A	
334 V	1000 G	-7:91693922 1324089538 G	V
334	1001 T	-7:91693921 1324089537 T	
334	1002 T	-7:91693920 1324089536 T	
335 E	1003 G	-7:91693919 1324089535 G	E
335	1004 A	-7:91693918 1324089534 A	
335	1005 G	-7:91693917 1324089533 G	
336 A	1006 G	-7:91693916 1324089532 G	A
336	1007 C	-7:91693915 1324089531 C	
336	1008 C	-7:91693914 1324089530 C	
337 T	1009 A	-7:91693913 1324089529 A	T
337	1010 C	-7:91693912 1324089528 C	
337	1011 T	-7:91693911 1324089527 T	
338 R	1012 C	-7:91693910 1324089526 C	R
338	1013 G	-7:91693909 1324089525 G	
338	1014 C	-7:91693908 1324089524 C	
339 I	1015 A	-7:91693907 1324089523 A	I
339	1016 T	-7:91693906 1324089522 T	
339	1017 A	-7:91693905 1324089521 A	
340 L	1018 T	-7:91693904 1324089520 T	L
340	1019 T	-7:91693903 1324089519 T	
340	1020 G	-7:91693902 1324089518 G	
341 L	1021 T	-7:91693901 1324089517 T	L
341	1022 T	-7:91693900 1324089516 T	
341	1023 A	-7:91693899 1324089515 A	
342 E	1024 G	-7:91693898 1324089514 G	E
342	1025 A	-7:91693897 1324089513 A	
342	1026 G	-7:91693896 1324089512 G	
343 K	1027 A	-7:91693895 1324089511 A	K
343	1028 A	-7:91693894 1324089510 A	
343	1029 A	-7:91693893 1324089509 A	
344 G	1030 G	-7:91693892 1324089508 G	G
344	1031 G	-7:91693891 1324089507 G	
344	1032 A	-7:91693890 1324089506 A	
345 K	1033 A	-7:91693889 1324089505 A	K
345	1034 A	-7:91693888 1324089504 A	
345	1035 G	-7:91693887 1324089503 G	
346 C	1036 T	-7:91693886 1324089502 T	C
346	1037 G	-7:91693885 1324089501 G	
346	1038 C	-7:91693884 1324089500 C	
347 N	1039 A	-7:91693883 1324089499 A	N
347	1040 A	-7:91693882 1324089498 A	
347	1041 T	-7:91693881 1324089497 T	
348 P	1042 C	-7:91693880 1324089496 C	P
348	1043 C	-7:91693879 1324089495 C	
348	1044 A	-7:91693878 1324089494 A	
349 N	1045 A	-7:91693877 1324089493 A	N
349	1046 A	-7:91693876 1324089492 A	
349	1047 C	-7:91693875 1324089491 C	
350 L	1048 C	-7:91693874 1324089490 C	L
350	1049 T	-7:91693873 1324089489 T	
350	1050 T	-7:91693872 1324089488 T	
351 L	1051 T	-7:91693871 1324089487 T	L
351	1052 T	-7:91693870 1324089486 T	
351	1053 A	-7:91693869 1324089485 A	
352 N	1054 A	-7:91693868 1324089484 A	N
352	1055 A	-7:91693867 1324089483 A	
352	1056 T	-7:91693866 1324089482 T	
353 G	1057 G	-7:91693865 1324089481 G	G
353	1058 G	-7:91693864 1324089480 G	
353	1059 A	-7:91693863 1324089479 A	
354 Q	1060 C	-7:91693862 1324089478 C	Q
354	1061 A	-7:91693861 1324089477 A	
354	1062 A	-7:91693860 1324089476 A	
355 L	1063 C	-7:91693859 1324089475 C	L
355	1064 T	-7:91693858 1324089474 T	
355	1065 T	-7:91693857 1324089473 T	
356 S	1066 A	-7:91693856 1324089472 A	S
356	1067 G	-7:91693855 1324089471 G	
356	1068 T	-7:91693854 1324089470 T	
357 S	1069 T	-7:91693853 1324089469 T	S
357	1070 C	-7:91693852 1324089468 C	
357	1071 T	-7:91693851 1324089467 T	
358 P	1072 C	-7:91693850 1324089466 C	P
358	1073 C	-7:91693849 1324089465 C	
358	1074 T	-7:91693848 1324089464 T	
359 L	1075 C	-7:91693847 1324089463 C	L
359	1076 T	-7:91693846 1324089462 T	
359	1077 T	-7:91693845 1324089461 T	
360 H	1078 C	-7:91693844 1324089460 C	H
360	1079 A	-7:91693843 1324089459 A	
360	1080 T	-7:91693842 1324089458 T	
361 F	1081 T	-7:91693841 1324089457 T	F
361	1082 T	-7:91693840 1324089456 T	
361	1083 T	-7:91693839 1324089455 T	
362 A	1084 G	-7:91693838 1324089454 G	A
362	1085 C	-7:91693837 1324089453 C	
362	1086 T	-7:91693836 1324089452 T	
363 A	1087 G	-7:91693835 1324089451 G	A
363	1088 C	-7:91693834 1324089450 C	
363	1089 T	-7:91693833 1324089449 T	
364 G	1090 G	-7:91693832 1324089448 G	G
364	1091 G	-7:91693831 1324089447 G	
364	1092 A	-7:91693830 1324089446 A	
365 G	1093 G	-7:91693829 1324089445 G	G
365	1094 G	-7:91693828 1324089444 G	
365	1095 A	-7:91693827 1324089443 A	
366 G	1096 G	-7:91693826 1324089442 G	G
366	1097 G	-7:91693825 1324089441 G	
366	1098 A	-7:91693824 1324089440 A	
367 H	1099 C	-7:91693823 1324089439 C	H
367	1100 A	-7:91693822 1324089438 A	
367	1101 T	-7:91693821 1324089437 T	
368 A	1102 G	-7:91693820 1324089436 G	A
368	1103 C	-7:91693819 1324089435 C	
368	1104 T	-7:91693818 1324089434 T	
369 E	1105 G	-7:91693817 1324089433 G	E
369	1106 A	-7:91693816 1324089432 A	
369	1107 A	-7:91693815 1324089431 A	
370 I	1108 A	-7:91693814 1324089430 A	I
370	1109 T	-7:91693813 1324089429 T	
370	1110 A	-7:91693812 1324089428 A	
371 V	1111 G	-7:91693811 1324089427 G	V
371	1112 T	-7:91693810 1324089426 T	
371	1113 A	-7:91693809 1324089425 A	
372 Q	1114 C	-7:91693808 1324089424 C	Q
372	1115 A	-7:91693807 1324089423 A	
372	1116 G	-7:91693806 1324089422 G	
373 I	1117 A	-7:91693805 1324089421 A	I
373	1118 T	-7:91693804 1324089420 T	
373	1119 T	-7:91693803 1324089419 T	
374 L	1120 C	-7:91693802 1324089418 C	L
374	1121 T	-7:91693801 1324089417 T	
374	1122 C	-7:91693800 1324089416 C	
375 L	1123 C	-7:91693799 1324089415 C	L
375	1124 T	-7:91693798 1324089414 T	
375	1125 A	-7:91693797 1324089413 A	
376 N	1126 A	-7:91693796 1324089412 A	N
376	1127 A	-7:91693795 1324089411 A	
376	1128 C	-7:91693794 1324089410 C	
377 H	1129 C	-7:91693793 1324089409 C	H
377	1130 A	-7:91693792 1324089408 A	
377	1131 C	-7:91693791 1324089407 C	
378 P	1132 C	-7:91693790 1324089406 C	P
378	1133 C	-7:91693789 1324089405 C	
378	1134 A	-7:91693788 1324089404 A	
379 E	1135 G	-7:91693787 1324089403 G	E
379	1136 A	-7:91693786 1324089402 A	
379	1137 A	-7:91693785 1324089401 A	
380 T	1138 A	-7:91693784 1324089400 A	T
380	1139 C	-7:91693783 1324089399 C	
380	1140 G	-7:91693782 1324089398 G	
381 D	1141 G	-7:91693781 1324089397 G	D
381	1142 A	-7:91693780 1324089396 A	
381	1143 T	-7:91693779 1324089395 T	
382 R	1144 A	-7:91693778 1324089394 A	R
382	1145 G	-7:91693777 1324089393 G	
382	1146 A	-7:91693776 1324089392 A	
383 H	1147 C	-7:91693077 1324088693 C	H
383	1148 A	-7:91693076 1324088692 A	
383	1149 T	-7:91693075 1324088691 T	
384 I	1150 A	-7:91693074 1324088690 A	I
384	1151 T	-7:91693073 1324088689 T	
384	1152 A	-7:91693072 1324088688 A	
385 T	1153 A	-7:91693071 1324088687 A	T
385	1154 C	-7:91693070 1324088686 C	
385	1155 A	-7:91693069 1324088685 A	
386 D	1156 G	-7:91693068 1324088684 G	D
386	1157 A	-7:91693067 1324088683 A	
386	1158 C	-7:91693066 1324088682 C	
387 Q	1159 C	-7:91693065 1324088681 C	Q
387	1160 A	-7:91693064 1324088680 A	
387	1161 A	-7:91693063 1324088679 A	
388 Q	1162 C	-7:91693062 1324088678 C	Q
388	1163 A	-7:91693061 1324088677 A	
388	1164 A	-7:91693060 1324088676 A	
389 G	1165 G	-7:91693059 1324088675 G	G
389	1166 G	-7:91693058 1324088674 G	
389	1167 A	-7:91693057 1324088673 A	
390 R	1168 A	-7:91693056 1324088672 A	R
390	1169 G	-7:91693055 1324088671 G	
390	1170 A	-7:91693054 1324088670 A	
391 S	1171 T	-7:91693053 1324088669 T	S
391	1172 C	-7:91693052 1324088668 C	
391	1173 T	-7:91693051 1324088667 T	
392 P	1174 C	-7:91693050 1324088666 C	P
392	1175 C	-7:91693049 1324088665 C	
392	1176 A	-7:91693048 1324088664 A	
393 L	1177 T	-7:91693047 1324088663 T	L
393	1178 T	-7:91693046 1324088662 T	
393	1179 A	-7:91693045 1324088661 A	
394 N	1180 A	-7:91693044 1324088660 A	N
394	1181 A	-7:91693043 1324088659 A	
394	1182 T	-7:91693042 1324088658 T	
395 I	1183 A	-7:91693041 1324088657 A	I
395	1184 T	-7:91693040 1324088656 T	
395	1185 T	-7:91693039 1324088655 T	
396 C	1186 T	-7:91693038 1324088654 T	C
396	1187 G	-7:91693037 1324088653 G	
396	1188 T	-7:91693036 1324088652 T	
397 E	1189 G	-7:91693035 1324088651 G	E
397	1190 A	-7:91693034 1324088650 A	
397	1191 A	-7:91693033 1324088649 A	
398 E	1192 G	-7:91693032 1324088648 G	E
398	1193 A	-7:91693031 1324088647 A	
398	1194 A	-7:91693030 1324088646 A	
399 N	1195 A	-7:91693029 1324088645 A	N
399	1196 A	-7:91693028 1324088644 A	
399	1197 C	-7:91693027 1324088643 C	
400 K	1198 A	-7:91693026 1324088642 A	K
400	1199 A	-7:91693025 1324088641 A	
400	1200 A	-7:91693024 1324088640 A	
401 Q	1201 C	-7:91693023 1324088639 C	Q
401	1202 A	-7:91693022 1324088638 A	
401	1203 A	-7:91693021 1324088637 A	
402 N	1204 A	-7:91693020 1324088636 A	N
402	1205 A	-7:91693019 1324088635 A	
402	1206 C	-7:91693018 1324088634 C	
403 N	1207 A	-7:91693017 1324088633 A	N
403	1208 A	-7:91693016 1324088632 A	
403	1209 C	-7:91693015 1324088631 C	
404 W	1210 T	-7:91693014 1324088630 T	W
404	1211 G	-7:91693013 1324088629 G	
404	1212 G	-7:91693012 1324088628 G	
405 E	1213 G	-7:91693011 1324088627 G	E
405	1214 A	-7:91693010 1324088626 A	
405	1215 A	-7:91693009 1324088625 A	
406 E	1216 G	-7:91693008 1324088624 G	E
406	1217 A	-7:91693007 1324088623 A	
406	1218 A	-7:91693006 1324088622 A	
407 A	1219 G	-7:91693005 1324088621 G	A
407	1220 C	-7:91693004 1324088620 C	
407	1221 T	-7:91693003 1324088619 T	
408 A	1222 G	-7:91693002 1324088618 G	A
408	1223 C	-7:91693001 1324088617 C	
408	1224 A	-7:91693000 1324088616 A	
409 K	1225 A	-7:91692999 1324088615 A	K
409	1226 A	-7:91692998 1324088614 A	
409	1227 A	-7:91692997 1324088613 A	
410 L	1228 T	-7:91692996 1324088612 T	L
410	1229 T	-7:91692995 1324088611 T	
410	1230 G	-7:91692994 1324088610 G	
411 L	1231 T	-7:91692993 1324088609 T	L
411	1232 T	-7:91692992 1324088608 T	
411	1233 G	-7:91692991 1324088607 G	
412 K	1234 A	-7:91692990 1324088606 A	K
412	1235 A	-7:91692989 1324088605 A	
412	1236 G	-7:91692988 1324088604 G	
413 E	1237 G	-7:91692987 1324088603 G	E
413	1238 A	-7:91692986 1324088602 A	
413	1239 A	-7:91692985 1324088601 A	
414 A	1240 G	-7:91692984 1324088600 G	A
414	1241 C	-7:91692983 1324088599 C	
414	1242 A	-7:91692982 1324088598 A	
415 I	1243 A	-7:91692981 1324088597 A	I
415	1244 T	-7:91692980 1324088596 T	
415	1245 T	-7:91692979 1324088595 T	
416 N	1246 A	-7:91692978 1324088594 A	N
416	1247 A	-7:91692977 1324088593 A	
416	1248 C	-7:91692976 1324088592 C	
417 K	1249 A	-7:91692975 1324088591 A	K
417	1250 A	-7:91692974 1324088590 A	
417	1251 A	-7:91692973 1324088589 A	
418 P	1252 C	-7:91692972 1324088588 C	P
418	1253 C	-7:91692971 1324088587 C	
418	1254 A	-7:91692970 1324088586 A	
419 Y	1255 T	-7:91690228 1324085844 T	Y
419	1256 A	-7:91690227 1324085843 A	
419	1257 T	-7:91690226 1324085842 T	
420 E	1258 G	-7:91690225 1324085841 G	E
420	1259 A	-7:91690224 1324085840 A	
420	1260 A	-7:91690223 1324085839 A	
421 K	1261 A	-7:91690222 1324085838 A	K
421	1262 A	-7:91690221 1324085837 A	
421	1263 A	-7:91690220 1324085836 A	
422 V	1264 G	-7:91690219 1324085835 G	V
422	1265 T	-7:91690218 1324085834 T	
422	1266 T	-7:91690217 1324085833 T	
423 R	1267 C	-7:91690216 1324085832 C	R
423	1268 G	-7:91690215 1324085831 G	
423	1269 A	-7:91690214 1324085830 A	
424 I	1270 A	-7:91690213 1324085829 A	I
424	1271 T	-7:91690212 1324085828 T	
424	1272 A	-7:91690211 1324085827 A	
425 Y	1273 T	-7:91690210 1324085826 T	Y
425	1274 A	-7:91690209 1324085825 A	
425	1275 C	-7:91690208 1324085824 C	
426 R	1276 A	-7:91690207 1324085823 A	R
426	1277 G	-7:91690206 1324085822 G	
426	1278 A	-7:91690205 1324085821 A	
427 M	1279 A	-7:91690204 1324085820 A	M
427	1280 T	-7:91690203 1324085819 T	
427	1281 G	-7:91690202 1324085818 G	
428 D	1282 G	-7:91690201 1324085817 G	D
428	1283 A	-7:91690200 1324085816 A	
428	1284 T	-7:91690199 1324085815 T	
429 G	1285 G	-7:91690198 1324085814 G	G
429	1286 G	-7:91690197 1324085813 G	
429	1287 G	-7:91690196 1324085812 G	
430 S	1288 T	-7:91690195 1324085811 T	S
430	1289 C	-7:91690194 1324085810 C	
430	1290 A	-7:91690193 1324085809 A	
431 Y	1291 T	-7:91690192 1324085808 T	Y
431	1292 A	-7:91690191 1324085807 A	
431	1293 T	-7:91690190 1324085806 T	
432 R	1294 C	-7:91690189 1324085805 C	R
432	1295 G	-7:91690188 1324085804 G	
432	1296 T	-7:91690187 1324085803 T	
433 S	1297 T	-7:91690186 1324085802 T	S
433	1298 C	-7:91690185 1324085801 C	
433	1299 T	-7:91690184 1324085800 T	
434 V	1300 G	-7:91690183 1324085799 G	V
434	1301 T	-7:91690182 1324085798 T	
434	1302 T	-7:91690181 1324085797 T	
435 E	1303 G	-7:91690180 1324085796 G	E
435	1304 A	-7:91690179 1324085795 A	
435	1305 A	-7:91690178 1324085794 A	
436 L	1306 T	-7:91690177 1324085793 T	L
436	1307 T	-7:91690176 1324085792 T	
436	1308 G	-7:91690175 1324085791 G	
437 K	1309 A	-7:91690174 1324085790 A	K
437	1310 A	-7:91690173 1324085789 A	
437	1311 G	-7:91690172 1324085788 G	
438 H	1312 C	-7:91690171 1324085787 C	H
438	1313 A	-7:91690170 1324085786 A	
438	1314 T	-7:91690169 1324085785 T	
439 G	1315 G	-7:91690168 1324085784 G	G
439	1316 G	-7:91690167 1324085783 G	
439	1317 A	-7:91690166 1324085782 A	
440 N	1318 A	-7:91690165 1324085781 A	N
440	1319 A	-7:91690164 1324085780 A	
440	1320 T	-7:91690163 1324085779 T	
441 N	1321 A	-7:91690162 1324085778 A	N
441	1322 A	-7:91690161 1324085777 A	
441	1323 T	-7:91690160 1324085776 T	
442 T	1324 A	-7:91690159 1324085775 A	T
442	1325 C	-7:91690158 1324085774 C	
442	1326 C	-7:91690157 1324085773 C	
443 T	1327 A	-7:91690156 1324085772 A	T
443	1328 C	-7:91690155 1324085771 C	
443	1329 A	-7:91690154 1324085770 A	
444 V	1330 G	-7:91690153 1324085769 G	V
444	1331 T	-7:91690152 1324085768 T	
444	1332 G	-7:91690151 1324085767 G	
445 Q	1333 C	-7:91690150 1324085766 C	Q
445	1334 A	-7:91690149 1324085765 A	
445	1335 G	-7:91690148 1324085764 G	
446 Q	1336 C	-7:91690147 1324085763 C	Q
446	1337 A	-7:91690146 1324085762 A	
446	1338 G	-7:91690145 1324085761 G	
447 I	1339 A	-7:91690144 1324085760 A	I
447	1340 T	-7:91690143 1324085759 T	
447	1341 A	-7:91690142 1324085758 A	
448 M	1342 A	-7:91690141 1324085757 A	M
448	1343 T	-7:91690140 1324085756 T	
448	1344 G	-7:91690139 1324085755 G	
449 E	1345 G	-7:91690138 1324085754 G	E
449	1346 A	-7:91690137 1324085753 A	
449	1347 A	-7:91690136 1324085752 A	
450 G	1348 G	-7:91690135 1324085751 G	G
450	1349 G	-7:91690134 1324085750 G	
450	1350 A	-7:91690133 1324085749 A	
451 M	1351 A	-7:91690132 1324085748 A	M
451	1352 T	-7:91690131 1324085747 T	
451	1353 G	-7:91690130 1324085746 G	
452 R	1354 C	-7:91690129 1324085745 C	R
452	1355 G	-7:91690128 1324085744 G	
452	1356 T	-7:91690127 1324085743 T	
453 L	1357 C	-7:91690126 1324085742 C	L
453	1358 T	-7:91690125 1324085741 T	
453	1359 C	-7:91690124 1324085740 C	
454 S	1360 T	-7:91690123 1324085739 T	S
454	1361 C	-7:91690122 1324085738 C	
454	1362 T	-7:91690121 1324085737 T	
455 Q	1363 C	-7:91690120 1324085736 C	Q
455	1364 A	-7:91690119 1324085735 A	
455	1365 A	-7:91690118 1324085734 A	
456 E	1366 G	-7:91690117 1324085733 G	E
456	1367 A	-7:91690116 1324085732 A	
456	1368 A	-7:91690115 1324085731 A	
457 T	1369 A	-7:91690114 1324085730 A	T
457	1370 C	-7:91690113 1324085729 C	
457	1371 T	-7:91690112 1324085728 T	
458 Q	1372 C	-7:91690111 1324085727 C	Q
458	1373 A	-7:91690110 1324085726 A	
458	1374 G	-7:91690109 1324085725 G	
459 Q	1375 C	-7:91690108 1324085724 C	Q
459	1376 A	-7:91690107 1324085723 A	
459	1377 A	-7:91690106 1324085722 A	
460 Y	1378 T	-7:91690105 1324085721 T	Y
460	1379 A	-7:91690104 1324085720 A	
460	1380 T	-7:91690103 1324085719 T	
461 F	1381 T	-7:91690102 1324085718 T	F
461	1382 T	-7:91690101 1324085717 T	
461	1383 C	-7:91690100 1324085716 C	
462 T	1384 A	-7:91690099 1324085715 A	T
462	1385 C	-7:91690098 1324085714 C	
462	1386 T	-7:91690097 1324085713 T	
463 I	1387 A	-7:91690096 1324085712 A	I
463	1388 T	-7:91690095 1324085711 T	
463	1389 A	-7:91690094 1324085710 A	
464 W	1390 T	-7:91690093 1324085709 T	W
464	1391 G	-7:91690092 1324085708 G	
464	1392 G	-7:91690091 1324085707 G	
465 I	1393 A	-7:91690090 1324085706 A	I
465	1394 T	-7:91690089 1324085705 T	
465	1395 T	-7:91690088 1324085704 T	
466 C	1396 T	-7:91690087 1324085703 T	C
466	1397 G	-7:91690086 1324085702 G	
466	1398 T	-7:91690085 1324085701 T	
467 S	1399 T	-7:91690084 1324085700 T	S
467	1400 C	-7:91690083 1324085699 C	
467	1401 A	-7:91690082 1324085698 A	
468 E	1402 G	-7:91690081 1324085697 G	E
468	1403 A	-7:91690080 1324085696 A	
468	1404 A	-7:91690079 1324085695 A	
469 N	1405 A	-7:91690078 1324085694 A	N
469	1406 A	-7:91690077 1324085693 A	
469	1407 C	-7:91690076 1324085692 C	
470 L	1408 C	-7:91690075 1324085691 C	L
470	1409 T	-7:91690074 1324085690 T	
470	1410 C	-7:91690073 1324085689 C	
471 S	1411 A	-7:91690072 1324085688 A	S
471	1412 G	-7:91689303 1324084919 G	
471	1413 C	-7:91689302 1324084918 C	
472 L	1414 C	-7:91689301 1324084917 C	L
472	1415 T	-7:91689300 1324084916 T	
472	1416 T	-7:91689299 1324084915 T	
473 Q	1417 C	-7:91689298 1324084914 C	Q
473	1418 A	-7:91689297 1324084913 A	
473	1419 A	-7:91689296 1324084912 A	
474 L	1420 C	-7:91689295 1324084911 C	L
474	1421 T	-7:91689294 1324084910 T	
474	1422 C	-7:91689293 1324084909 C	
475 K	1423 A	-7:91689292 1324084908 A	K
475	1424 A	-7:91689291 1324084907 A	
475	1425 A	-7:91689290 1324084906 A	
476 P	1426 C	-7:91689289 1324084905 C	P
476	1427 C	-7:91689288 1324084904 C	
476	1428 A	-7:91689287 1324084903 A	
477 Y	1429 T	-7:91689286 1324084902 T	Y
477	1430 A	-7:91689285 1324084901 A	
477	1431 T	-7:91689284 1324084900 T	
478 H	1432 C	-7:91689283 1324084899 C	H
478	1433 A	-7:91689282 1324084898 A	
478	1434 T	-7:91689281 1324084897 T	
479 K	1435 A	-7:91689280 1324084896 A	K
479	1436 A	-7:91689279 1324084895 A	
479	1437 A	-7:91689278 1324084894 A	
480 P	1438 C	-7:91689277 1324084893 C	P
480	1439 C	-7:91689276 1324084892 C	
480	1440 C	-7:91689275 1324084891 C	
481 L	1441 T	-7:91689274 1324084890 T	L
481	1442 T	-7:91689273 1324084889 T	
481	1443 G	-7:91689272 1324084888 G	
482 Q	1444 C	-7:91689271 1324084887 C	Q
482	1445 A	-7:91689270 1324084886 A	
482	1446 A	-7:91689269 1324084885 A	
483 H	1447 C	-7:91689268 1324084884 C	H
483	1448 A	-7:91689267 1324084883 A	
483	1449 T	-7:91689266 1324084882 T	
484 V	1450 G	-7:91689265 1324084881 G	V
484	1451 T	-7:91689264 1324084880 T	
484	1452 T	-7:91689263 1324084879 T	
485 R	1453 C	-7:91689262 1324084878 C	R
485	1454 G	-7:91689261 1324084877 G	
485	1455 T	-7:91689260 1324084876 T	
486 D	1456 G	-7:91689259 1324084875 G	D
486	1457 A	-7:91689258 1324084874 A	
486	1458 C	-7:91689257 1324084873 C	
487 W	1459 T	-7:91689256 1324084872 T	W
487	1460 G	-7:91689255 1324084871 G	
487	1461 G	-7:91689254 1324084870 G	
488 P	1462 C	-7:91689253 1324084869 C	P
488	1463 C	-7:91689252 1324084868 C	
488	1464 A	-7:91689251 1324084867 A	
489 E	1465 G	-7:91689250 1324084866 G	E
489	1466 A	-7:91689249 1324084865 A	
489	1467 A	-7:91689248 1324084864 A	
490 I	1468 A	-7:91689247 1324084863 A	I
490	1469 T	-7:91689246 1324084862 T	
490	1470 A	-7:91689245 1324084861 A	
491 L	1471 C	-7:91689244 1324084860 C	L
491	1472 T	-7:91689243 1324084859 T	
491	1473 T	-7:91689242 1324084858 T	
492 A	1474 G	-7:91689241 1324084857 G	A
492	1475 C	-7:91689240 1324084856 C	
492	1476 T	-7:91689239 1324084855 T	
493 E	1477 G	-7:91689238 1324084854 G	E
493	1478 A	-7:91689237 1324084853 A	
493	1479 A	-7:91689236 1324084852 A	
494 L	1480 T	-7:91689235 1324084851 T	L
494	1481 T	-7:91689234 1324084850 T	
494	1482 G	-7:91689233 1324084849 G	
495 T	1483 A	-7:91689232 1324084848 A	T
495	1484 C	-7:91689231 1324084847 C	
495	1485 T	-7:91689230 1324084846 T	
496 N	1486 A	-7:91689229 1324084845 A	N
496	1487 A	-7:91689228 1324084844 A	
496	1488 T	-7:91689227 1324084843 T	
497 L	1489 C	-7:91689226 1324084842 C	L
497	1490 T	-7:91689225 1324084841 T	
497	1491 G	-7:91689224 1324084840 G	
498 D	1492 G	-7:91689223 1324084839 G	D
498	1493 A	-7:91689222 1324084838 A	
498	1494 T	-7:91689221 1324084837 T	
499 P	1495 C	-7:91689220 1324084836 C	P
499	1496 C	-7:91689219 1324084835 C	
499	1497 T	-7:91689218 1324084834 T	
500 Q	1498 C	-7:91689217 1324084833 C	Q
500	1499 A	-7:91689216 1324084832 A	
500	1500 A	-7:91689215 1324084831 A	
501 R	1501 A	-7:91689214 1324084830 A	R
501	1502 G	-7:91689213 1324084829 G	
501	1503 G	-7:91689212 1324084828 G	
502 E	1504 G	-7:91689211 1324084827 G	E
502	1505 A	-7:91689210 1324084826 A	
502	1506 A	-7:91689209 1324084825 A	
503 T	1507 A	-7:91689208 1324084824 A	T
503	1508 C	-7:91689207 1324084823 C	
503	1509 A	-7:91689206 1324084822 A	
504 P	1510 C	-7:91689205 1324084821 C	P
504	1511 C	-7:91689204 1324084820 C	
504	1512 T	-7:91689203 1324084819 T	
505 Q	1513 C	-7:91689202 1324084818 C	Q
505	1514 A	-7:91689201 1324084817 A	
505	1515 G	-7:91689200 1324084816 G	
506 L	1516 C	-7:91689199 1324084815 C	L
506	1517 T	-7:91689198 1324084814 T	
506	1518 T	-7:91689197 1324084813 T	
507 F	1519 T	-7:91689196 1324084812 T	F
507	1520 T	-7:91689195 1324084811 T	
507	1521 T	-7:91689194 1324084810 T	
508 L	1522 C	-7:91689193 1324084809 C	L
508	1523 T	-7:91689192 1324084808 T	
508	1524 A	-7:91689191 1324084807 A	
509 R	1525 A	-7:91689190 1324084806 A	R
509	1526 G	-7:91689189 1324084805 G	
509	1527 A	-7:91689188 1324084804 A	
510 R	1528 A	-7:91689187 1324084803 A	R
510	1529 G	-7:91689186 1324084802 G	
510	1530 A	-7:91689185 1324084801 A	
511 D	1531 G	-7:91689184 1324084800 G	D
511	1532 A	-7:91689183 1324084799 A	
511	1533 T	-7:91689182 1324084798 T	
512 V	1534 G	-7:91689181 1324084797 G	V
512	1535 T	-7:91689180 1324084796 T	
512	1536 G	-7:91689179 1324084795 G	
513 R	1537 A	-7:91689178 1324084794 A	R
513	1538 G	-7:91689177 1324084793 G	
513	1539 A	-7:91689176 1324084792 A	
514 L	1540 C	-7:91689175 1324084791 C	L
514	1541 T	-7:91689174 1324084790 T	
514	1542 T	-7:91689173 1324084789 T	
515 P	1543 C	-7:91689172 1324084788 C	P
515	1544 C	-7:91689171 1324084787 C	
515	1545 C	-7:91689170 1324084786 C	
516 L	1546 T	-7:91689169 1324084785 T	L
516	1547 T	-7:91689168 1324084784 T	
516	1548 G	-7:91689167 1324084783 G	
517 E	1549 G	-7:91689166 1324084782 G	E
517	1550 A	-7:91689165 1324084781 A	
517	1551 A	-7:91689164 1324084780 A	
518 V	1552 G	-7:91689163 1324084779 G	V
518	1553 T	-7:91689162 1324084778 T	
518	1554 T	-7:91689161 1324084777 T	
519 E	1555 G	-7:91689160 1324084776 G	E
519	1556 A	-7:91689159 1324084775 A	
519	1557 A	-7:91689158 1324084774 A	
520 K	1558 A	-7:91689157 1324084773 A	K
520	1559 A	-7:91689156 1324084772 A	
520	1560 A	-7:91689155 1324084771 A	
521 Q	1561 C	-7:91689154 1324084770 C	Q
521	1562 A	-7:91689153 1324084769 A	
521	1563 G	-7:91689152 1324084768 G	
522 I	1564 A	-7:91682027 1324077643 A	I
522	1565 T	-7:91682026 1324077642 T	
522	1566 T	-7:91682025 1324077641 T	
523 E	1567 G	-7:91682024 1324077640 G	E
523	1568 A	-7:91682023 1324077639 A	
523	1569 A	-7:91682022 1324077638 A	
524 D	1570 G	-7:91682021 1324077637 G	D
524	1571 A	-7:91682020 1324077636 A	
524	1572 C	-7:91682019 1324077635 C	
525 P	1573 C	-7:91682018 1324077634 C	P
525	1574 C	-7:91682017 1324077633 C	
525	1575 A	-7:91682016 1324077632 A	
526 L	1576 C	-7:91682015 1324077631 C	L
526	1577 T	-7:91682014 1324077630 T	
526	1578 A	-7:91682013 1324077629 A	
527 A	1579 G	-7:91682012 1324077628 G	A
527	1580 C	-7:91682011 1324077627 C	
527	1581 T	-7:91682010 1324077626 T	
528 I	1582 A	-7:91682009 1324077625 A	I
528	1583 T	-7:91682008 1324077624 T	
528	1584 T	-7:91682007 1324077623 T	
529 L	1585 C	-7:91682006 1324077622 C	L
529	1586 T	-7:91682005 1324077621 T	
529	1587 T	-7:91682004 1324077620 T	
530 I	1588 A	-7:91682003 1324077619 A	I
530	1589 T	-7:91682002 1324077618 T	
530	1590 T	-7:91682001 1324077617 T	
531 L	1591 C	-7:91682000 1324077616 C	L
531	1592 T	-7:91681999 1324077615 T	
531	1593 C	-7:91681998 1324077614 C	
532 F	1594 T	-7:91681997 1324077613 T	F
532	1595 T	-7:91681996 1324077612 T	
532	1596 T	-7:91681995 1324077611 T	
533 D	1597 G	-7:91681994 1324077610 G	D
533	1598 A	-7:91681993 1324077609 A	
533	1599 T	-7:91681992 1324077608 T	
534 E	1600 G	-7:91681991 1324077607 G	E
534	1601 A	-7:91681990 1324077606 A	
534	1602 A	-7:91681989 1324077605 A	
535 A	1603 G	-7:91681988 1324077604 G	A
535	1604 C	-7:91681987 1324077603 C	
535	1605 C	-7:91681986 1324077602 C	
536 R	1606 A	-7:91681985 1324077601 A	R
536	1607 G	-7:91681984 1324077600 G	
536	1608 A	-7:91681983 1324077599 A	
537 Y	1609 T	-7:91681982 1324077598 T	Y
537	1610 A	-7:91681981 1324077597 A	
537	1611 T	-7:91681980 1324077596 T	
538 N	1612 A	-7:91681979 1324077595 A	N
538	1613 A	-7:91681978 1324077594 A	
538	1614 T	-7:91681977 1324077593 T	
539 L	1615 T	-7:91681976 1324077592 T	L
539	1616 T	-7:91681975 1324077591 T	
539	1617 A	-7:91681974 1324077590 A	
540 L	1618 T	-7:91681973 1324077589 T	L
540	1619 T	-7:91681972 1324077588 T	
540	1620 G	-7:91681971 1324077587 G	
541 K	1621 A	-7:91681970 1324077586 A	K
541	1622 A	-7:91681969 1324077585 A	
541	1623 G	-7:91681968 1324077584 G	
542 G	1624 G	-7:91681967 1324077583 G	G
542	1625 G	-7:91681966 1324077582 G	
542	1626 C	-7:91681965 1324077581 C	
543 F	1627 T	-7:91681964 1324077580 T	F
543	1628 T	-7:91681963 1324077579 T	
543	1629 T	-7:91681962 1324077578 T	
544 Y	1630 T	-7:91681961 1324077577 T	Y
544	1631 A	-7:91681960 1324077576 A	
544	1632 T	-7:91681959 1324077575 T	
545 T	1633 A	-7:91681958 1324077574 A	T
545	1634 C	-7:91681957 1324077573 C	
545	1635 A	-7:91681956 1324077572 A	
546 A	1636 G	-7:91681955 1324077571 G	A
546	1637 C	-7:91681954 1324077570 C	
546	1638 T	-7:91681953 1324077569 T	
547 P	1639 C	-7:91681952 1324077568 C	P
547	1640 C	-7:91681951 1324077567 C	
547	1641 T	-7:91681950 1324077566 T	
548 D	1642 G	-7:91681949 1324077565 G	D
548	1643 A	-7:91681948 1324077564 A	
548	1644 T	-7:91681947 1324077563 T	
549 A	1645 G	-7:91681946 1324077562 G	A
549	1646 C	-7:91681945 1324077561 C	
549	1647 T	-7:91681944 1324077560 T	
550 K	1648 A	-7:91681943 1324077559 A	K
550	1649 A	-7:91681942 1324077558 A	
550	1650 G	-7:91681941 1324077557 G	
551 L	1651 C	-7:91681940 1324077556 C	L
551	1652 T	-7:91681939 1324077555 T	
551	1653 G	-7:91681938 1324077554 G	
552 I	1654 A	-7:91681937 1324077553 A	I
552	1655 T	-7:91681936 1324077552 T	
552	1656 A	-7:91681935 1324077551 A	
553 T	1657 A	-7:91681934 1324077550 A	T
553	1658 C	-7:91681933 1324077549 C	
553	1659 A	-7:91681932 1324077548 A	
554 L	1660 T	-7:91681931 1324077547 T	L
554	1661 T	-7:91681930 1324077546 T	
554	1662 G	-7:91681929 1324077545 G	
555 A	1663 G	-7:91681928 1324077544 G	A
555	1664 C	-7:91681927 1324077543 C	
555	1665 A	-7:91681926 1324077542 A	
556 S	1666 A	-7:91681925 1324077541 A	S
556	1667 G	-7:91681924 1324077540 G	
556	1668 T	-7:91681923 1324077539 T	
557 L	1669 C	-7:91681922 1324077538 C	L
557	1670 T	-7:91681921 1324077537 T	
557	1671 G	-7:91681920 1324077536 G	
558 L	1672 C	-7:91681919 1324077535 C	L
558	1673 T	-7:91681918 1324077534 T	
558	1674 T	-7:91681917 1324077533 T	
559 L	1675 T	-7:91681916 1324077532 T	L
559	1676 T	-7:91681915 1324077531 T	
559	1677 G	-7:91681914 1324077530 G	
560 Q	1678 C	-7:91681913 1324077529 C	Q
560	1679 A	-7:91681912 1324077528 A	
560	1680 A	-7:91681911 1324077527 A	
561 I	1681 A	-7:91681910 1324077526 A	I
561	1682 T	-7:91681909 1324077525 T	
561	1683 A	-7:91681908 1324077524 A	
562 V	1684 G	-7:91681907 1324077523 G	V
562	1685 T	-7:91681906 1324077522 T	
562	1686 C	-7:91681905 1324077521 C	
563 Y	1687 T	-7:91681904 1324077520 T	Y
563	1688 A	-7:91681903 1324077519 A	
563	1689 T	-7:91681902 1324077518 T	
564 G	1690 G	-7:91681901 1324077517 G	G
564	1691 G	-7:91681900 1324077516 G	
564	1692 A	-7:91681899 1324077515 A	
565 N	1693 A	-7:91681898 1324077514 A	N
565	1694 A	-7:91681897 1324077513 A	
565	1695 T	-7:91681896 1324077512 T	
566 Y	1696 T	-7:91681895 1324077511 T	Y
566	1697 A	-7:91681894 1324077510 A	
566	1698 T	-7:91681893 1324077509 T	
567 E	1699 G	-7:91681892 1324077508 G	E
567	1700 A	-7:91681891 1324077507 A	
567	1701 G	-7:91681890 1324077506 G	
568 S	1702 A	-7:91681889 1324077505 A	S
568	1703 G	-7:91681888 1324077504 G	
568	1704 T	-7:91681887 1324077503 T	
569 K	1705 A	-7:91681886 1324077502 A	K
569	1706 A	-7:91681885 1324077501 A	
569	1707 A	-7:91681884 1324077500 A	
570 K	1708 A	-7:91681883 1324077499 A	K
570	1709 A	-7:91681882 1324077498 A	
570	1710 A	-7:91681881 1324077497 A	
571 H	1711 C	-7:91681880 1324077496 C	H
571	1712 A	-7:91681879 1324077495 A	
571	1713 C	-7:91681878 1324077494 C	
572 K	1714 A	-7:91681877 1324077493 A	K
572	1715 A	-7:91681876 1324077492 A	
572	1716 G	-7:91681875 1324077491 G	
573 Q	1717 C	-7:91681874 1324077490 C	Q
573	1718 A	-7:91681873 1324077489 A	
573	1719 A	-7:91681872 1324077488 A	
574 G	1720 G	-7:91681871 1324077487 G	G
574	1721 G	-7:91681870 1324077486 G	
574	1722 T	-7:91681869 1324077485 T	
575 F	1723 T	-7:91681868 1324077484 T	F
575	1724 T	-7:91681867 1324077483 T	
575	1725 C	-7:91681866 1324077482 C	
576 L	1726 C	-7:91681865 1324077481 C	L
576	1727 T	-7:91681864 1324077480 T	
576	1728 A	-7:91681863 1324077479 A	
577 N	1729 A	-7:91681862 1324077478 A	N
577	1730 A	-7:91681861 1324077477 A	
577	1731 T	-7:91681229 1324076845 T	
578 E	1732 G	-7:91681228 1324076844 G	E
578	1733 A	-7:91681227 1324076843 A	
578	1734 A	-7:91681226 1324076842 A	
579 E	1735 G	-7:91681225 1324076841 G	E
579	1736 A	-7:91681224 1324076840 A	
579	1737 A	-7:91681223 1324076839 A	
580 N	1738 A	-7:91681222 1324076838 A	N
580	1739 A	-7:91681221 1324076837 A	
580	1740 T	-7:91681220 1324076836 T	
581 L	1741 C	-7:91681219 1324076835 C	L
581	1742 T	-7:91681218 1324076834 T	
581	1743 A	-7:91681217 1324076833 A	
582 K	1744 A	-7:91681216 1324076832 A	K
582	1745 A	-7:91681215 1324076831 A	
582	1746 A	-7:91681214 1324076830 A	
583 S	1747 T	-7:91681213 1324076829 T	S
583	1748 C	-7:91681212 1324076828 C	
583	1749 C	-7:91681211 1324076827 C	
584 I	1750 A	-7:91681210 1324076826 A	I
584	1751 T	-7:91681209 1324076825 T	
584	1752 C	-7:91681208 1324076824 C	
585 V	1753 G	-7:91681207 1324076823 G	V
585	1754 T	-7:91681206 1324076822 T	
585	1755 A	-7:91681205 1324076821 A	
586 P	1756 C	-7:91681204 1324076820 C	P
586	1757 C	-7:91681203 1324076819 C	
586	1758 T	-7:91681202 1324076818 T	
587 V	1759 G	-7:91681201 1324076817 G	V
587	1760 T	-7:91681200 1324076816 T	
587	1761 T	-7:91681199 1324076815 T	
588 T	1762 A	-7:91681198 1324076814 A	T
588	1763 C	-7:91681197 1324076813 C	
588	1764 C	-7:91681196 1324076812 C	
589 K	1765 A	-7:91681195 1324076811 A	K
589	1766 A	-7:91681194 1324076810 A	
589	1767 A	-7:91681193 1324076809 A	
590 L	1768 C	-7:91681192 1324076808 C	L
590	1769 T	-7:91681191 1324076807 T	
590	1770 G	-7:91681190 1324076806 G	
591 K	1771 A	-7:91681189 1324076805 A	K
591	1772 A	-7:91681188 1324076804 A	
591	1773 A	-7:91681187 1324076803 A	
592 S	1774 A	-7:91681186 1324076802 A	S
592	1775 G	-7:91681185 1324076801 G	
592	1776 T	-7:91681184 1324076800 T	
593 K	1777 A	-7:91681183 1324076799 A	K
593	1778 A	-7:91681182 1324076798 A	
593	1779 G	-7:91681181 1324076797 G	
594 A	1780 G	-7:91681180 1324076796 G	A
594	1781 C	-7:91681179 1324076795 C	
594	1782 A	-7:91681178 1324076794 A	
595 P	1783 C	-7:91681177 1324076793 C	P
595	1784 C	-7:91681176 1324076792 C	
595	1785 T	-7:91681175 1324076791 T	
596 H	1786 C	-7:91681174 1324076790 C	H
596	1787 A	-7:91681173 1324076789 A	
596	1788 C	-7:91681172 1324076788 C	
597 W	1789 T	-7:91681171 1324076787 T	W
597	1790 G	-7:91681170 1324076786 G	
597	1791 G	-7:91681169 1324076785 G	
598 T	1792 A	-7:91681168 1324076784 A	T
598	1793 C	-7:91681167 1324076783 C	
598	1794 A	-7:91681166 1324076782 A	
599 N	1795 A	-7:91681165 1324076781 A	N
599	1796 A	-7:91681164 1324076780 A	
599	1797 T	-7:91681163 1324076779 T	
600 R	1798 C	-7:91681162 1324076778 C	R
600	1799 G	-7:91681161 1324076777 G	
600	1800 C	-7:91681160 1324076776 C	
601 I	1801 A	-7:91681159 1324076775 A	I
601	1802 T	-7:91681158 1324076774 T	
601	1803 A	-7:91681157 1324076773 A	
602 L	1804 C	-7:91681156 1324076772 C	L
602	1805 T	-7:91681155 1324076771 T	
602	1806 T	-7:91681154 1324076770 T	
603 H	1807 C	-7:91681153 1324076769 C	H
603	1808 A	-7:91681152 1324076768 A	
603	1809 T	-7:91681151 1324076767 T	
604 E	1810 G	-7:91681150 1324076766 G	E
604	1811 A	-7:91681149 1324076765 A	
604	1812 A	-7:91681148 1324076764 A	
605 Y	1813 T	-7:91681147 1324076763 T	Y
605	1814 A	-7:91681146 1324076762 A	
605	1815 C	-7:91681145 1324076761 C	
606 K	1816 A	-7:91681144 1324076760 A	K
606	1817 A	-7:91681143 1324076759 A	
606	1818 G	-7:91681142 1324076758 G	
607 N	1819 A	-7:91680651 1324076267 A	N
607	1820 A	-7:91680650 1324076266 A	
607	1821 T	-7:91680649 1324076265 T	
608 L	1822 C	-7:91680648 1324076264 C	L
608	1823 T	-7:91680647 1324076263 T	
608	1824 C	-7:91680646 1324076262 C	
609 S	1825 A	-7:91680645 1324076261 A	S
609	1826 G	-7:91680644 1324076260 G	
609	1827 T	-7:91680643 1324076259 T	
610 T	1828 A	-7:91680642 1324076258 A	T
610	1829 C	-7:91680641 1324076257 C	
610	1830 A	-7:91680640 1324076256 A	
611 S	1831 A	-7:91680639 1324076255 A	S
611	1832 G	-7:91680638 1324076254 G	
611	1833 T	-7:91680637 1324076253 T	
612 E	1834 G	-7:91680636 1324076252 G	E
612	1835 A	-7:91680635 1324076251 A	
612	1836 A	-7:91680634 1324076250 A	
613 G	1837 G	-7:91680633 1324076249 G	G
613	1838 G	-7:91680632 1324076248 G	
613	1839 T	-7:91680631 1324076247 T	
614 V	1840 G	-7:91680630 1324076246 G	V
614	1841 T	-7:91680629 1324076245 T	
614	1842 C	-7:91680628 1324076244 C	
615 S	1843 A	-7:91680627 1324076243 A	S
615	1844 G	-7:91680626 1324076242 G	
615	1845 T	-7:91680625 1324076241 T	
616 K	1846 A	-7:91680624 1324076240 A	K
616	1847 A	-7:91680623 1324076239 A	
616	1848 A	-7:91680622 1324076238 A	
617 E	1849 G	-7:91680621 1324076237 G	E
617	1850 A	-7:91680620 1324076236 A	
617	1851 A	-7:91680619 1324076235 A	
618 M	1852 A	-7:91680618 1324076234 A	M
618	1853 T	-7:91680617 1324076233 T	
618	1854 G	-7:91680616 1324076232 G	
619 H	1855 C	-7:91680615 1324076231 C	H
619	1856 A	-7:91680614 1324076230 A	
619	1857 T	-7:91680613 1324076229 T	
620 H	1858 C	-7:91680612 1324076228 C	H
620	1859 A	-7:91680611 1324076227 A	
620	1860 C	-7:91680610 1324076226 C	
621 L	1861 C	-7:91680609 1324076225 C	L
621	1862 T	-7:91680608 1324076224 T	
621	1863 T	-7:91680607 1324076223 T	
622 Q	1864 C	-7:91680606 1324076222 C	Q
622	1865 A	-7:91680605 1324076221 A	
622	1866 G	-7:91680604 1324076220 G	
623 R	1867 C	-7:91680603 1324076219 C	R
623	1868 G	-7:91680602 1324076218 G	
623	1869 C	-7:91680601 1324076217 C	
624 M	1870 A	-7:91680600 1324076216 A	M
624	1871 T	-7:91680599 1324076215 T	
624	1872 G	-7:91680598 1324076214 G	
625 F	1873 T	-7:91680597 1324076213 T	F
625	1874 T	-7:91680596 1324076212 T	
625	1875 C	-7:91680595 1324076211 C	
626 L	1876 T	-7:91680594 1324076210 T	L
626	1877 T	-7:91680593 1324076209 T	
626	1878 A	-7:91680592 1324076208 A	
627 Q	1879 C	-7:91680591 1324076207 C	Q
627	1880 A	-7:91680590 1324076206 A	
627	1881 G	-7:91680589 1324076205 G	
628 N	1882 A	-7:91680588 1324076204 A	N
628	1883 A	-7:91680587 1324076203 A	
628	1884 T	-7:91680586 1324076202 T	
629 C	1885 T	-7:91680585 1324076201 T	C
629	1886 G	-7:91680584 1324076200 G	
629	1887 C	-7:91680583 1324076199 C	
630 W	1888 T	-7:91680582 1324076198 T	W
630	1889 G	-7:91680581 1324076197 G	
630	1890 G	-7:91680580 1324076196 G	
631 E	1891 G	-7:91680579 1324076195 G	E
631	1892 A	-7:91680578 1324076194 A	
631	1893 A	-7:91680577 1324076193 A	
632 I	1894 A	-7:91680576 1324076192 A	I
632	1895 T	-7:91680575 1324076191 T	
632	1896 T	-7:91680574 1324076190 T	
633 P	1897 C	-7:91680573 1324076189 C	P
633	1898 C	-7:91680572 1324076188 C	
633	1899 T	-7:91680571 1324076187 T	
634 T	1900 A	-7:91680570 1324076186 A	T
634	1901 C	-7:91680569 1324076185 C	
634	1902 T	-7:91680568 1324076184 T	
635 Y	1903 T	-7:91680567 1324076183 T	Y
635	1904 A	-7:91680566 1324076182 A	
635	1905 T	-7:91680565 1324076181 T	
636 G	1906 G	-7:91680564 1324076180 G	G
636	1907 G	-7:91680563 1324076179 G	
636	1908 A	-7:91680562 1324076178 A	
637 A	1909 G	-7:91680561 1324076177 G	A
637	1910 C	-7:91680560 1324076176 C	
637	1911 A	-7:91680559 1324076175 A	
638 A	1912 G	-7:91680558 1324076174 G	A
638	1913 C	-7:91680557 1324076173 C	
638	1914 A	-7:91680556 1324076172 A	
639 F	1915 T	-7:91680555 1324076171 T	F
639	1916 T	-7:91680554 1324076170 T	
639	1917 T	-7:91680553 1324076169 T	
640 F	1918 T	-7:91680552 1324076168 T	F
640	1919 T	-7:91680551 1324076167 T	
640	1920 C	-7:91680550 1324076166 C	
641 T	1921 A	-7:91680549 1324076165 A	T
641	1922 C	-7:91680548 1324076164 C	
641	1923 A	-7:91680547 1324076163 A	
642 G	1924 G	-7:91680546 1324076162 G	G
642	1925 G	-7:91680545 1324076161 G	
642	1926 A	-7:91680544 1324076160 A	
643 Q	1927 C	-7:91680543 1324076159 C	Q
643	1928 A	-7:91680542 1324076158 A	
643	1929 G	-7:91680541 1324076157 G	
644 I	1930 A	-7:91680540 1324076156 A	I
644	1931 T	-7:91680539 1324076155 T	
644	1932 A	-7:91680538 1324076154 A	
645 F	1933 T	-7:91680537 1324076153 T	F
645	1934 T	-7:91680536 1324076152 T	
645	1935 T	-7:91680535 1324076151 T	
646 T	1936 A	-7:91680534 1324076150 A	T
646	1937 C	-7:91680533 1324076149 C	
646	1938 A	-7:91680532 1324076148 A	
647 K	1939 A	-7:91680531 1324076147 A	K
647	1940 A	-7:91680530 1324076146 A	
647	1941 G	-7:91680529 1324076145 G	
648 A	1942 G	-7:91680528 1324076144 G	A
648	1943 C	-7:91680527 1324076143 C	
648	1944 A	-7:91680526 1324076142 A	
649 S	1945 A	-7:91680525 1324076141 A	S
649	1946 G	-7:91680524 1324076140 G	
649	1947 C	-7:91680523 1324076139 C	
650 P	1948 C	-7:91680522 1324076138 C	P
650	1949 C	-7:91680521 1324076137 C	
650	1950 C	-7:91680520 1324076136 C	
651 S	1951 A	-7:91680519 1324076135 A	S
651	1952 G	-7:91680518 1324076134 G	
651	1953 C	-7:91680517 1324076133 C	
652 N	1954 A	-7:91680516 1324076132 A	N
652	1955 A	-7:91680515 1324076131 A	
652	1956 T	-7:91680514 1324076130 T	
653 H	1957 C	-7:91680513 1324076129 C	H
653	1958 A	-7:91680512 1324076128 A	
653	1959 T	-7:91680511 1324076127 T	
654 K	1960 A	-7:91680510 1324076126 A	K
654	1961 A	-7:91680509 1324076125 A	
654	1962 A	-7:91680508 1324076124 A	
655 V	1963 G	-7:91680507 1324076123 G	V
655	1964 T	-7:91680506 1324076122 T	
655	1965 C	-7:91680505 1324076121 C	
656 I	1966 A	-7:91680504 1324076120 A	I
656	1967 T	-7:91680503 1324076119 T	
656	1968 C	-7:91680502 1324076118 C	
657 P	1969 C	-7:91680501 1324076117 C	P
657	1970 C	-7:91680500 1324076116 C	
657	1971 T	-7:91680499 1324076115 T	
658 V	1972 G	-7:91680498 1324076114 G	V
658	1973 T	-7:91680497 1324076113 T	
658	1974 G	-7:91680496 1324076112 G	
659 Y	1975 T	-7:91680495 1324076111 T	Y
659	1976 A	-7:91680494 1324076110 A	
659	1977 T	-7:91680493 1324076109 T	
660 V	1978 G	-7:91680492 1324076108 G	V
660	1979 T	-7:91680491 1324076107 T	
660	1980 A	-7:91680490 1324076106 A	
661 G	1981 G	-7:91680489 1324076105 G	G
661	1982 G	-7:91680488 1324076104 G	
661	1983 A	-7:91680487 1324076103 A	
662 V	1984 G	-7:91680486 1324076102 G	V
662	1985 T	-7:91680485 1324076101 T	
662	1986 G	-7:91680484 1324076100 G	
663 N	1987 A	-7:91680483 1324076099 A	N
663	1988 A	-7:91680482 1324076098 A	
663	1989 T	-7:91680481 1324076097 T	
664 I	1990 A	-7:91680480 1324076096 A	I
664	1991 T	-7:91680479 1324076095 T	
664	1992 A	-7:91680478 1324076094 A	
665 K	1993 A	-7:91680477 1324076093 A	K
665	1994 A	-7:91680476 1324076092 A	
665	1995 A	-7:91680475 1324076091 A	
666 G	1996 G	-7:91680474 1324076090 G	G
666	1997 G	-7:91680473 1324076089 G	
666	1998 A	-7:91680472 1324076088 A	
667 L	1999 C	-7:91680471 1324076087 C	L
667	2000 T	-7:91680470 1324076086 T	
667	2001 T	-7:91680469 1324076085 T	
668 H	2002 C	-7:91680468 1324076084 C	H
668	2003 A	-7:91680467 1324076083 A	
668	2004 T	-7:91680466 1324076082 T	
669 L	2005 C	-7:91680465 1324076081 C	L
669	2006 T	-7:91680464 1324076080 T	
669	2007 C	-7:91680463 1324076079 C	
670 L	2008 C	-7:91680462 1324076078 C	L
670	2009 T	-7:91680461 1324076077 T	
670	2010 C	-7:91680460 1324076076 C	
671 N	2011 A	-7:91680459 1324076075 A	N
671	2012 A	-7:91680458 1324076074 A	
671	2013 C	-7:91680457 1324076073 C	
672 M	2014 A	-7:91680456 1324076072 A	M
672	2015 T	-7:91680455 1324076071 T	
672	2016 G	-7:91680454 1324076070 G	
673 E	2017 G	-7:91680453 1324076069 G	E
673	2018 A	-7:91680452 1324076068 A	
673	2019 A	-7:91680451 1324076067 A	
674 T	2020 A	-7:91680450 1324076066 A	T
674	2021 C	-7:91680449 1324076065 C	
674	2022 T	-7:91680448 1324076064 T	
675 K	2023 A	-7:91680447 1324076063 A	K
675	2024 A	-7:91680446 1324076062 A	
675	2025 G	-7:91680445 1324076061 G	
>ENSP00000378015 
1 M	1 A	-7:91709385 1324105001 A	M
1	2 T	-7:91709384 1324105000 T	
1	3 G	-7:91709383 1324104999 G	
2 G	4 G	-7:91709382 1324104998 G	G
2	5 G	-7:91709381 1324104997 G	
2	6 A	-7:91709380 1324104996 A	
3 N	7 A	-7:91709379 1324104995 A	N
3	8 A	-7:91709378 1324104994 A	
3	9 T	-7:91709377 1324104993 T	
4 P	10 C	-7:91709376 1324104992 C	P
4	11 C	-7:91709375 1324104991 C	
4	12 A	-7:91709374 1324104990 A	
5 E	13 G	-7:91709373 1324104989 G	E
5	14 A	-7:91709372 1324104988 A	
5	15 A	-7:91709371 1324104987 A	
6 N	16 A	-7:91709370 1324104986 A	N
6	17 A	-7:91709369 1324104985 A	
6	18 C	-7:91709368 1324104984 C	
7 I	19 A	-7:91709367 1324104983 A	I
7	20 T	-7:91709366 1324104982 T	
7	21 A	-7:91709365 1324104981 A	
8 E	22 G	-7:91709364 1324104980 G	E
8	23 A	-7:91709363 1324104979 A	
8	24 A	-7:91709362 1324104978 A	
9 D	25 G	-7:91709361 1324104977 G	D
9	26 A	-7:91709360 1324104976 A	
9	27 T	-7:91709359 1324104975 T	
10 A	28 G	-7:91709358 1324104974 G	A
10	29 C	-7:91709357 1324104973 C	
10	30 A	-7:91709356 1324104972 A	
11 Y	31 T	-7:91709355 1324104971 T	Y
11	32 A	-7:91709354 1324104970 A	
11	33 T	-7:91709353 1324104969 T	
12 V	34 G	-7:91709352 1324104968 G	V
12	35 T	-7:91709351 1324104967 T	
12	36 T	-7:91709350 1324104966 T	
13 A	37 G	-7:91709349 1324104965 G	A
13	38 C	-7:91709348 1324104964 C	
13	39 T	-7:91709347 1324104963 T	
14 V	40 G	-7:91709346 1324104962 G	V
14	41 T	-7:91709345 1324104961 T	
14	42 T	-7:91709344 1324104960 T	
15 I	43 A	-7:91709343 1324104959 A	I
15	44 T	-7:91709342 1324104958 T	
15	45 T	-7:91709341 1324104957 T	
16 R	46 C	-7:91709340 1324104956 C	R
16	47 G	-7:91709339 1324104955 G	
16	48 T	-7:91709338 1324104954 T	
17 P	49 C	-7:91709337 1324104953 C	P
17	50 C	-7:91709336 1324104952 C	
17	51 A	-7:91709335 1324104951 A	
18 K	52 A	-7:91709334 1324104950 A	K
18	53 A	-7:91709333 1324104949 A	
18	54 G	-7:91709332 1324104948 G	
19 N	55 A	-7:91709331 1324104947 A	N
19	56 A	-7:91709330 1324104946 A	
19	57 T	-7:91709329 1324104945 T	
20 T	58 A	-7:91709328 1324104944 A	T
20	59 C	-7:91709327 1324104943 C	
20	60 T	-7:91709326 1324104942 T	
21 A	61 G	-7:91709325 1324104941 G	A
21	62 C	-7:91709324 1324104940 C	
21	63 C	-7:91709323 1324104939 C	
22 S	64 A	-7:91709322 1324104938 A	S
22	65 G	-7:91709321 1324104937 G	
22	66 T	-7:91709320 1324104936 T	
23 L	67 C	-7:91709319 1324104935 C	L
23	68 T	-7:91709318 1324104934 T	
23	69 C	-7:91709317 1324104933 C	
24 N	70 A	-7:91709316 1324104932 A	N
24	71 A	-7:91709315 1324104931 A	
24	72 T	-7:91709314 1324104930 T	
25 S	73 T	-7:91709313 1324104929 T	S
25	74 C	-7:91709312 1324104928 C	
25	75 T	-7:91709311 1324104927 T	
26 R	76 C	-7:91709310 1324104926 C	R
26	77 G	-7:91709309 1324104925 G	
26	78 G	-7:91709308 1324104924 G	
27 E	79 G	-7:91709307 1324104923 G	E
27	80 A	-7:91709306 1324104922 A	
27	81 A	-7:91709305 1324104921 A	
28 Y	82 T	-7:91709304 1324104920 T	Y
28	83 A	-7:91709303 1324104919 A	
28	84 C	-7:91709302 1324104918 C	
29 R	85 A	-7:91709301 1324104917 A	R
29	86 G	-7:91709300 1324104916 G	
29	87 A	-7:91709299 1324104915 A	
30 A	88 G	-7:91709298 1324104914 G	A
30	89 C	-7:91709297 1324104913 C	
30	90 T	-7:91709296 1324104912 T	
31 K	91 A	-7:91709295 1324104911 A	K
31	92 A	-7:91709294 1324104910 A	
31	93 G	-7:91709293 1324104909 G	
32 S	94 T	-7:91709292 1324104908 T	S
32	95 C	-7:91709291 1324104907 C	
32	96 A	-7:91709290 1324104906 A	
33 Y	97 T	-7:91709289 1324104905 T	Y
33	98 A	-7:91709288 1324104904 A	
33	99 T	-7:91709287 1324104903 T	
34 E	100 G	-7:91709286 1324104902 G	E
34	101 A	-7:91709285 1324104901 A	
34	102 A	-7:91709284 1324104900 A	
35 I	103 A	-7:91708402 1324104018 A	I
35	104 T	-7:91708401 1324104017 T	
35	105 T	-7:91708400 1324104016 T	
36 L	106 T	-7:91708399 1324104015 T	L
36	107 T	-7:91708398 1324104014 T	
36	108 G	-7:91708397 1324104013 G	
37 L	109 T	-7:91708396 1324104012 T	L
37	110 T	-7:91708395 1324104011 T	
37	111 G	-7:91708394 1324104010 G	
38 H	112 C	-7:91708393 1324104009 C	H
38	113 A	-7:91708392 1324104008 A	
38	114 T	-7:91708391 1324104007 T	
39 E	115 G	-7:91708390 1324104006 G	E
39	116 A	-7:91708389 1324104005 A	
39	117 A	-7:91708388 1324104004 A	
40 V	118 G	-7:91708387 1324104003 G	V
40	119 T	-7:91708386 1324104002 T	
40	120 T	-7:91708385 1324104001 T	
41 P	121 C	-7:91708384 1324104000 C	P
41	122 C	-7:91708383 1324103999 C	
41	123 C	-7:91708382 1324103998 C	
42 I	124 A	-7:91708381 1324103997 A	I
42	125 T	-7:91708380 1324103996 T	
42	126 T	-7:91708379 1324103995 T	
43 E	127 G	-7:91708378 1324103994 G	E
43	128 A	-7:91708377 1324103993 A	
43	129 A	-7:91708376 1324103992 A	
44 G	130 G	-7:91708375 1324103991 G	G
44	131 G	-7:91708374 1324103990 G	
44	132 A	-7:91708373 1324103989 A	
45 Q	133 C	-7:91708372 1324103988 C	Q
45	134 A	-7:91708371 1324103987 A	
45	135 G	-7:91708370 1324103986 G	
46 K	136 A	-7:91708369 1324103985 A	K
46	137 A	-7:91708368 1324103984 A	
46	138 A	-7:91708367 1324103983 A	
47 K	139 A	-7:91708366 1324103982 A	K
47	140 A	-7:91708365 1324103981 A	
47	141 A	-7:91708364 1324103980 A	
48 K	142 A	-7:91708363 1324103979 A	K
48	143 A	-7:91708362 1324103978 A	
48	144 G	-7:91708361 1324103977 G	
49 R	145 A	-7:91708360 1324103976 A	R
49	146 G	-7:91708359 1324103975 G	
49	147 A	-7:91708358 1324103974 A	
50 K	148 A	-7:91708357 1324103973 A	K
50	149 A	-7:91708356 1324103972 A	
50	150 G	-7:91708355 1324103971 G	
51 K	151 A	-7:91708354 1324103970 A	K
51	152 A	-7:91708353 1324103969 A	
51	153 A	-7:91708352 1324103968 A	
52 V	154 G	-7:91708351 1324103967 G	V
52	155 T	-7:91708350 1324103966 T	
52	156 T	-7:91708349 1324103965 T	
53 L	157 T	-7:91708348 1324103964 T	L
53	158 T	-7:91708347 1324103963 T	
53	159 A	-7:91708346 1324103962 A	
54 L	160 T	-7:91708345 1324103961 T	L
54	161 T	-7:91708344 1324103960 T	
54	162 G	-7:91708343 1324103959 G	
55 E	163 G	-7:91708342 1324103958 G	E
55	164 A	-7:91708341 1324103957 A	
55	165 A	-7:91708340 1324103956 A	
56 T	166 A	-7:91708339 1324103955 A	T
56	167 C	-7:91708338 1324103954 C	
56	168 G	-7:91708337 1324103953 G	
57 K	169 A	-7:91708336 1324103952 A	K
57	170 A	-7:91708335 1324103951 A	
57	171 A	-7:91708334 1324103950 A	
58 L	172 C	-7:91708333 1324103949 C	L
58	173 T	-7:91708332 1324103948 T	
58	174 T	-7:91708331 1324103947 T	
59 Q	175 C	-7:91708330 1324103946 C	Q
59	176 A	-7:91708329 1324103945 A	
59	177 A	-7:91708328 1324103944 A	
60 G	178 G	-7:91708327 1324103943 G	G
60	179 G	-7:91708326 1324103942 G	
60	180 C	-7:91708325 1324103941 C	
61 N	181 A	-7:91708324 1324103940 A	N
61	182 A	-7:91708323 1324103939 A	
61	183 C	-7:91708322 1324103938 C	
62 S	184 A	-7:91708321 1324103937 A	S
62	185 G	-7:91708320 1324103936 G	
62	186 T	-7:91708319 1324103935 T	
63 E	187 G	-7:91708318 1324103934 G	E
63	188 A	-7:91708317 1324103933 A	
63	189 A	-7:91708316 1324103932 A	
64 I	190 A	-7:91708315 1324103931 A	I
64	191 T	-7:91708314 1324103930 T	
64	192 A	-7:91708313 1324103929 A	
65 T	193 A	-7:91708312 1324103928 A	T
65	194 C	-7:91708311 1324103927 C	
65	195 A	-7:91708310 1324103926 A	
66 Q	196 C	-7:91708309 1324103925 C	Q
66	197 A	-7:91708308 1324103924 A	
66	198 A	-7:91708307 1324103923 A	
67 G	199 G	-7:91708306 1324103922 G	G
67	200 G	-7:91708305 1324103921 G	
67	201 C	-7:91708304 1324103920 C	
68 I	202 A	-7:91708303 1324103919 A	I
68	203 T	-7:91708302 1324103918 T	
68	204 A	-7:91708301 1324103917 A	
69 L	205 T	-7:91708300 1324103916 T	L
69	206 T	-7:91708299 1324103915 T	
69	207 G	-7:91708298 1324103914 G	
70 D	208 G	-7:91708297 1324103913 G	D
70	209 A	-7:91708296 1324103912 A	
70	210 T	-7:91708295 1324103911 T	
71 Y	211 T	-7:91708294 1324103910 T	Y
71	212 A	-7:91708293 1324103909 A	
71	213 C	-7:91708292 1324103908 C	
72 V	214 G	-7:91708291 1324103907 G	V
72	215 T	-7:91708290 1324103906 T	
72	216 A	-7:91708289 1324103905 A	
73 V	217 G	-7:91708288 1324103904 G	V
73	218 T	-7:91708287 1324103903 T	
73	219 A	-7:91708286 1324103902 A	
74 E	220 G	-7:91708285 1324103901 G	E
74	221 A	-7:91708284 1324103900 A	
74	222 A	-7:91708283 1324103899 A	
75 T	223 A	-7:91708282 1324103898 A	T
75	224 C	-7:91708281 1324103897 C	
75	225 C	-7:91708280 1324103896 C	
76 T	226 A	-7:91708279 1324103895 A	T
76	227 C	-7:91708278 1324103894 C	
76	228 C	-7:91708277 1324103893 C	
77 K	229 A	-7:91708276 1324103892 A	K
77	230 A	-7:91708275 1324103891 A	
77	231 A	-7:91708274 1324103890 A	
78 P	232 C	-7:91708273 1324103889 C	P
78	233 C	-7:91708272 1324103888 C	
78	234 A	-7:91708271 1324103887 A	
79 I	235 A	-7:91708270 1324103886 A	I
79	236 T	-7:91708269 1324103885 T	
79	237 T	-7:91708268 1324103884 T	
80 S	238 T	-7:91708267 1324103883 T	S
80	239 C	-7:91708266 1324103882 C	
80	240 T	-7:91708265 1324103881 T	
81 P	241 C	-7:91708264 1324103880 C	P
81	242 C	-7:91708263 1324103879 C	
81	243 T	-7:91708262 1324103878 T	
82 A	244 G	-7:91708261 1324103877 G	A
82	245 C	-7:91708260 1324103876 C	
82	246 A	-7:91708259 1324103875 A	
83 N	247 A	-7:91708258 1324103874 A	N
83	248 A	-7:91708257 1324103873 A	
83	249 C	-7:91708256 1324103872 C	
84 Q	250 C	-7:91708255 1324103871 C	Q
84	251 A	-7:91708254 1324103870 A	
84	252 G	-7:91708253 1324103869 G	
85 G	253 G	-7:91708252 1324103868 G	G
85	254 G	-7:91708251 1324103867 G	
85	255 T	-7:91708250 1324103866 T	
86 I	256 A	-7:91708249 1324103865 A	I
86	257 T	-7:91708248 1324103864 T	
86	258 C	-7:91708247 1324103863 C	
87 R	259 A	-7:91708246 1324103862 A	R
87	260 G	-7:91708245 1324103861 G	
87	261 A	-7:91708244 1324103860 A	
88 G	262 G	-7:91708243 1324103859 G	G
88	263 G	-7:91705009 1324100625 G	
88	264 A	-7:91705008 1324100624 A	
89 K	265 A	-7:91705007 1324100623 A	K
89	266 A	-7:91705006 1324100622 A	
89	267 A	-7:91705005 1324100621 A	
90 R	268 C	-7:91705004 1324100620 C	R
90	269 G	-7:91705003 1324100619 G	
90	270 A	-7:91705002 1324100618 A	
91 V	271 G	-7:91705001 1324100617 G	V
91	272 T	-7:91705000 1324100616 T	
91	273 T	-7:91704999 1324100615 T	
92 V	274 G	-7:91704998 1324100614 G	V
92	275 T	-7:91704997 1324100613 T	
92	276 A	-7:91704996 1324100612 A	
93 L	277 C	-7:91704995 1324100611 C	L
93	278 T	-7:91704994 1324100610 T	
93	279 A	-7:91704993 1324100609 A	
94 M	280 A	-7:91704992 1324100608 A	M
94	281 T	-7:91704991 1324100607 T	
94	282 G	-7:91704990 1324100606 G	
95 K	283 A	-7:91704989 1324100605 A	K
95	284 A	-7:91704988 1324100604 A	
95	285 A	-7:91704987 1324100603 A	
96 K	286 A	-7:91704986 1324100602 A	K
96	287 A	-7:91704985 1324100601 A	
96	288 A	-7:91704984 1324100600 A	
97 F	289 T	-7:91704983 1324100599 T	F
97	290 T	-7:91704982 1324100598 T	
97	291 T	-7:91704981 1324100597 T	
98 P	292 C	-7:91704980 1324100596 C	P
98	293 C	-7:91704979 1324100595 C	
98	294 T	-7:91704978 1324100594 T	
99 L	295 C	-7:91704977 1324100593 C	L
99	296 T	-7:91704976 1324100592 T	
99	297 G	-7:91704975 1324100591 G	
100 D	298 G	-7:91704974 1324100590 G	D
100	299 A	-7:91704973 1324100589 A	
100	300 T	-7:91704972 1324100588 T	
101 G	301 G	-7:91704971 1324100587 G	G
101	302 G	-7:91704970 1324100586 G	
101	303 A	-7:91704969 1324100585 A	
102 E	304 G	-7:91704968 1324100584 G	E
102	305 A	-7:91704967 1324100583 A	
102	306 G	-7:91704966 1324100582 G	
103 K	307 A	-7:91704965 1324100581 A	K
103	308 A	-7:91704964 1324100580 A	
103	309 G	-7:91704963 1324100579 G	
104 M	310 A	-7:91704962 1324100578 A	M
104	311 T	-7:91704961 1324100577 T	
104	312 G	-7:91704960 1324100576 G	
105 G	313 G	-7:91704959 1324100575 G	G
105	314 G	-7:91704958 1324100574 G	
105	315 C	-7:91704957 1324100573 C	
106 R	316 A	-7:91704956 1324100572 A	R
106	317 G	-7:91704955 1324100571 G	
106	318 A	-7:91704954 1324100570 A	
107 E	319 G	-7:91704953 1324100569 G	E
107	320 A	-7:91704952 1324100568 A	
107	321 A	-7:91704951 1324100567 A	
108 A	322 G	-7:91704950 1324100566 G	A
108	323 C	-7:91704949 1324100565 C	
108	324 A	-7:91704948 1324100564 A	
109 S	325 T	-7:91704947 1324100563 T	S
109	326 C	-7:91704946 1324100562 C	
109	327 A	-7:91704945 1324100561 A	
110 L	328 T	-7:91704944 1324100560 T	L
110	329 T	-7:91704943 1324100559 T	
110	330 A	-7:91704942 1324100558 A	
111 F	331 T	-7:91704941 1324100557 T	F
111	332 T	-7:91704940 1324100556 T	
111	333 T	-7:91704939 1324100555 T	
112 I	334 A	-7:91704938 1324100554 A	I
112	335 T	-7:91704937 1324100553 T	
112	336 T	-7:91704936 1324100552 T	
113 V	337 G	-7:91704935 1324100551 G	V
113	338 T	-7:91704934 1324100550 T	
113	339 T	-7:91704933 1324100549 T	
114 P	340 C	-7:91704932 1324100548 C	P
114	341 C	-7:91704931 1324100547 C	
114	342 A	-7:91704930 1324100546 A	
115 S	343 T	-7:91704929 1324100545 T	S
115	344 C	-7:91704928 1324100544 C	
115	345 A	-7:91704927 1324100543 A	
116 V	346 G	-7:91704926 1324100542 G	V
116	347 T	-7:91704925 1324100541 T	
116	348 T	-7:91704924 1324100540 T	
117 V	349 G	-7:91704923 1324100539 G	V
117	350 T	-7:91704922 1324100538 T	
117	351 C	-7:91704921 1324100537 C	
118 K	352 A	-7:91704920 1324100536 A	K
118	353 A	-7:91704919 1324100535 A	
118	354 A	-7:91704918 1324100534 A	
119 D	355 G	-7:91704917 1324100533 G	D
119	356 A	-7:91703792 1324099408 A	
119	357 T	-7:91703791 1324099407 T	
120 N	358 A	-7:91703790 1324099406 A	N
120	359 A	-7:91703789 1324099405 A	
120	360 T	-7:91703788 1324099404 T	
121 T	361 A	-7:91703787 1324099403 A	T
121	362 C	-7:91703786 1324099402 C	
121	363 T	-7:91703785 1324099401 T	
122 K	364 A	-7:91703784 1324099400 A	K
122	365 A	-7:91703783 1324099399 A	
122	366 A	-7:91703782 1324099398 A	
123 Y	367 T	-7:91703781 1324099397 T	Y
123	368 A	-7:91703780 1324099396 A	
123	369 C	-7:91703779 1324099395 C	
124 T	370 A	-7:91703778 1324099394 A	T
124	371 C	-7:91703777 1324099393 C	
124	372 A	-7:91703776 1324099392 A	
125 Y	373 T	-7:91703775 1324099391 T	Y
125	374 A	-7:91703774 1324099390 A	
125	375 T	-7:91703773 1324099389 T	
126 T	376 A	-7:91703772 1324099388 A	T
126	377 C	-7:91703771 1324099387 C	
126	378 C	-7:91703770 1324099386 C	
127 P	379 C	-7:91703769 1324099385 C	P
127	380 C	-7:91703768 1324099384 C	
127	381 A	-7:91703767 1324099383 A	
128 G	382 G	-7:91703766 1324099382 G	G
128	383 G	-7:91703765 1324099381 G	
128	384 A	-7:91703764 1324099380 A	
129 C	385 T	-7:91703763 1324099379 T	C
129	386 G	-7:91703762 1324099378 G	
129	387 C	-7:91703761 1324099377 C	
130 P	388 C	-7:91703760 1324099376 C	P
130	389 C	-7:91703759 1324099375 C	
130	390 A	-7:91703758 1324099374 A	
131 I	391 A	-7:91703757 1324099373 A	I
131	392 T	-7:91703756 1324099372 T	
131	393 T	-7:91703755 1324099371 T	
132 F	394 T	-7:91703754 1324099370 T	F
132	395 T	-7:91703753 1324099369 T	
132	396 T	-7:91703752 1324099368 T	
133 Y	397 T	-7:91703751 1324099367 T	Y
133	398 A	-7:91703750 1324099366 A	
133	399 C	-7:91703749 1324099365 C	
134 C	400 T	-7:91703748 1324099364 T	C
134	401 G	-7:91703747 1324099363 G	
134	402 C	-7:91703746 1324099362 C	
135 L	403 T	-7:91703745 1324099361 T	L
135	404 T	-7:91703744 1324099360 T	
135	405 A	-7:91703743 1324099359 A	
136 Q	406 C	-7:91703742 1324099358 C	Q
136	407 A	-7:91703741 1324099357 A	
136	408 A	-7:91703740 1324099356 A	
137 D	409 G	-7:91703739 1324099355 G	D
137	410 A	-7:91703738 1324099354 A	
137	411 T	-7:91703737 1324099353 T	
138 I	412 A	-7:91703736 1324099352 A	I
138	413 T	-7:91703735 1324099351 T	
138	414 T	-7:91703734 1324099350 T	
139 M	415 A	-7:91703733 1324099349 A	M
139	416 T	-7:91703732 1324099348 T	
139	417 G	-7:91703731 1324099347 G	
140 R	418 C	-7:91703730 1324099346 C	R
140	419 G	-7:91703729 1324099345 G	
140	420 A	-7:91703728 1324099344 A	
141 V	421 G	-7:91703727 1324099343 G	V
141	422 T	-7:91703726 1324099342 T	
141	423 C	-7:91703725 1324099341 C	
142 C	424 T	-7:91703724 1324099340 T	C
142	425 G	-7:91703723 1324099339 G	
142	426 T	-7:91703722 1324099338 T	
143 S	427 A	-7:91703721 1324099337 A	S
143	428 G	-7:91703720 1324099336 G	
143	429 T	-7:91703719 1324099335 T	
144 E	430 G	-7:91703718 1324099334 G	E
144	431 A	-7:91703717 1324099333 A	
144	432 A	-7:91703716 1324099332 A	
145 S	433 T	-7:91703715 1324099331 T	S
145	434 C	-7:91703714 1324099330 C	
145	435 C	-7:91703713 1324099329 C	
146 S	436 A	-7:91703712 1324099328 A	S
146	437 G	-7:91703711 1324099327 G	
146	438 T	-7:91703710 1324099326 T	
147 T	439 A	-7:91703709 1324099325 A	T
147	440 C	-7:91703708 1324099324 C	
147	441 T	-7:91703707 1324099323 T	
148 H	442 C	-7:91703706 1324099322 C	H
148	443 A	-7:91703705 1324099321 A	
148	444 T	-7:91703704 1324099320 T	
149 F	445 T	-7:91703703 1324099319 T	F
149	446 T	-7:91703702 1324099318 T	
149	447 T	-7:91703701 1324099317 T	
150 A	448 G	-7:91703700 1324099316 G	A
150	449 C	-7:91703699 1324099315 C	
150	450 T	-7:91703698 1324099314 T	
151 T	451 A	-7:91703697 1324099313 A	T
151	452 C	-7:91703696 1324099312 C	
151	453 A	-7:91703695 1324099311 A	
152 L	454 C	-7:91703694 1324099310 C	L
152	455 T	-7:91703693 1324099309 T	
152	456 T	-7:91703692 1324099308 T	
153 T	457 A	-7:91703691 1324099307 A	T
153	458 C	-7:91703690 1324099306 C	
153	459 A	-7:91703689 1324099305 A	
154 A	460 G	-7:91703688 1324099304 G	A
154	461 C	-7:91703687 1324099303 C	
154	462 A	-7:91703686 1324099302 A	
155 R	463 A	-7:91703685 1324099301 A	R
155	464 G	-7:91703684 1324099300 G	
155	465 G	-7:91703683 1324099299 G	
156 M	466 A	-7:91703682 1324099298 A	M
156	467 T	-7:91703681 1324099297 T	
156	468 G	-7:91703680 1324099296 G	
157 L	469 T	-7:91703679 1324099295 T	L
157	470 T	-7:91703678 1324099294 T	
157	471 A	-7:91703677 1324099293 A	
158 I	472 A	-7:91703676 1324099292 A	I
158	473 T	-7:91703675 1324099291 T	
158	474 A	-7:91703674 1324099290 A	
159 A	475 G	-7:91703673 1324099289 G	A
159	476 C	-7:91703672 1324099288 C	
159	477 C	-7:91703671 1324099287 C	
160 L	478 T	-7:91703670 1324099286 T	L
160	479 T	-7:91703669 1324099285 T	
160	480 G	-7:91703668 1324099284 G	
161 D	481 G	-7:91703667 1324099283 G	D
161	482 A	-7:91703666 1324099282 A	
161	483 T	-7:91703665 1324099281 T	
162 K	484 A	-7:91703664 1324099280 A	K
162	485 A	-7:91703663 1324099279 A	
162	486 G	-7:91702896 1324098512 G	
163 W	487 T	-7:91702895 1324098511 T	W
163	488 G	-7:91702894 1324098510 G	
163	489 G	-7:91702893 1324098509 G	
164 L	490 T	-7:91702892 1324098508 T	L
164	491 T	-7:91702891 1324098507 T	
164	492 A	-7:91702890 1324098506 A	
165 D	493 G	-7:91702889 1324098505 G	D
165	494 A	-7:91702888 1324098504 A	
165	495 T	-7:91702887 1324098503 T	
166 E	496 G	-7:91702886 1324098502 G	E
166	497 A	-7:91702885 1324098501 A	
166	498 A	-7:91702884 1324098500 A	
167 R	499 C	-7:91702883 1324098499 C	R
167	500 G	-7:91702882 1324098498 G	
167	501 T	-7:91702881 1324098497 T	
168 H	502 C	-7:91702880 1324098496 C	H
168	503 A	-7:91702879 1324098495 A	
168	504 T	-7:91702878 1324098494 T	
169 A	505 G	-7:91702877 1324098493 G	A
169	506 C	-7:91702876 1324098492 C	
169	507 A	-7:91702875 1324098491 A	
170 Q	508 C	-7:91702874 1324098490 C	Q
170	509 A	-7:91702873 1324098489 A	
170	510 A	-7:91702872 1324098488 A	
171 S	511 T	-7:91702871 1324098487 T	S
171	512 C	-7:91702870 1324098486 C	
171	513 T	-7:91702869 1324098485 T	
172 H	514 C	-7:91702868 1324098484 C	H
172	515 A	-7:91702867 1324098483 A	
172	516 C	-7:91702866 1324098482 C	
173 F	517 T	-7:91702865 1324098481 T	F
173	518 T	-7:91702864 1324098480 T	
173	519 T	-7:91702863 1324098479 T	
174 I	520 A	-7:91702862 1324098478 A	I
174	521 T	-7:91702861 1324098477 T	
174	522 T	-7:91702860 1324098476 T	
175 P	523 C	-7:91702859 1324098475 C	P
175	524 C	-7:91702858 1324098474 C	
175	525 A	-7:91702857 1324098473 A	
176 A	526 G	-7:91702856 1324098472 G	A
176	527 C	-7:91702855 1324098471 C	
176	528 T	-7:91702854 1324098470 T	
177 L	529 T	-7:91702853 1324098469 T	L
177	530 T	-7:91702852 1324098468 T	
177	531 A	-7:91702851 1324098467 A	
178 F	532 T	-7:91702850 1324098466 T	F
178	533 T	-7:91702849 1324098465 T	
178	534 C	-7:91702848 1324098464 C	
179 R	535 C	-7:91702847 1324098463 C	R
179	536 G	-7:91702846 1324098462 G	
179	537 A	-7:91702845 1324098461 A	
180 P	538 C	-7:91702844 1324098460 C	P
180	539 C	-7:91702843 1324098459 C	
180	540 T	-7:91702842 1324098458 T	
181 S	541 T	-7:91702841 1324098457 T	S
181	542 C	-7:91702840 1324098456 C	
181	543 T	-7:91702839 1324098455 T	
182 P	544 C	-7:91702838 1324098454 C	P
182	545 C	-7:91702837 1324098453 C	
182	546 T	-7:91702836 1324098452 T	
183 L	547 C	-7:91702835 1324098451 C	L
183	548 T	-7:91702834 1324098450 T	
183	549 T	-7:91702833 1324098449 T	
184 E	550 G	-7:91702832 1324098448 G	E
184	551 A	-7:91702831 1324098447 A	
184	552 G	-7:91702830 1324098446 G	
185 R	553 C	-7:91702829 1324098445 C	R
185	554 G	-7:91702828 1324098444 G	
185	555 G	-7:91702827 1324098443 G	
186 I	556 A	-7:91702826 1324098442 A	I
186	557 T	-7:91702825 1324098441 T	
186	558 A	-7:91702824 1324098440 A	
187 K	559 A	-7:91702823 1324098439 A	K
187	560 A	-7:91702822 1324098438 A	
187	561 A	-7:91702821 1324098437 A	
188 T	562 A	-7:91702820 1324098436 A	T
188	563 C	-7:91702819 1324098435 C	
188	564 T	-7:91702818 1324098434 T	
189 N	565 A	-7:91702817 1324098433 A	N
189	566 A	-7:91702816 1324098432 A	
189	567 T	-7:91702815 1324098431 T	
190 V	568 G	-7:91702814 1324098430 G	V
190	569 T	-7:91702813 1324098429 T	
190	570 C	-7:91702812 1324098428 C	
191 I	571 A	-7:91702811 1324098427 A	I
191	572 T	-7:91702810 1324098426 T	
191	573 A	-7:91702809 1324098425 A	
192 N	574 A	-7:91702808 1324098424 A	N
192	575 A	-7:91702807 1324098423 A	
192	576 T	-7:91702806 1324098422 T	
193 P	577 C	-7:91702805 1324098421 C	P
193	578 C	-7:91702804 1324098420 C	
193	579 T	-7:91702803 1324098419 T	
194 A	580 G	-7:91702802 1324098418 G	A
194	581 C	-7:91702801 1324098417 C	
194	582 A	-7:91702800 1324098416 A	
195 Y	583 T	-7:91702799 1324098415 T	Y
195	584 A	-7:91702798 1324098414 A	
195	585 T	-7:91702797 1324098413 T	
196 A	586 G	-7:91702796 1324098412 G	A
196	587 C	-7:91702795 1324098411 C	
196	588 T	-7:91702794 1324098410 T	
197 T	589 A	-7:91702793 1324098409 A	T
197	590 C	-7:91702792 1324098408 C	
197	591 T	-7:91702791 1324098407 T	
198 E	592 G	-7:91702790 1324098406 G	E
198	593 A	-7:91702789 1324098405 A	
198	594 A	-7:91702788 1324098404 A	
199 S	595 T	-7:91702787 1324098403 T	S
199	596 C	-7:91702786 1324098402 C	
199	597 A	-7:91702785 1324098401 A	
200 G	598 G	-7:91702784 1324098400 G	G
200	599 G	-7:91702783 1324098399 G	
200	600 T	-7:91702782 1324098398 T	
201 Q	601 C	-7:91702781 1324098397 C	Q
201	602 A	-7:91702780 1324098396 A	
201	603 G	-7:91702779 1324098395 G	
202 T	604 A	-7:91702778 1324098394 A	T
202	605 C	-7:91702777 1324098393 C	
202	606 A	-7:91702776 1324098392 A	
203 E	607 G	-7:91702775 1324098391 G	E
203	608 A	-7:91702774 1324098390 A	
203	609 A	-7:91702773 1324098389 A	
204 N	610 A	-7:91702772 1324098388 A	N
204	611 A	-7:91702771 1324098387 A	
204	612 C	-7:91702770 1324098386 C	
205 S	613 T	-7:91702769 1324098385 T	S
205	614 C	-7:91702768 1324098384 C	
205	615 A	-7:91702767 1324098383 A	
206 L	616 C	-7:91702766 1324098382 C	L
206	617 T	-7:91702765 1324098381 T	
206	618 A	-7:91702764 1324098380 A	
207 H	619 C	-7:91702763 1324098379 C	H
207	620 A	-7:91702762 1324098378 A	
207	621 T	-7:91702761 1324098377 T	
208 M	622 A	-7:91702760 1324098376 A	M
208	623 T	-7:91702759 1324098375 T	
208	624 G	-7:91702758 1324098374 G	
209 G	625 G	-7:91702757 1324098373 G	G
209	626 G	-7:91702756 1324098372 G	
209	627 C	-7:91702755 1324098371 C	
210 Y	628 T	-7:91702754 1324098370 T	Y
210	629 A	-7:91702753 1324098369 A	
210	630 T	-7:91702752 1324098368 T	
211 S	631 A	-7:91702751 1324098367 A	S
211	632 G	-7:91702750 1324098366 G	
211	633 T	-7:91702749 1324098365 T	
212 A	634 G	-7:91702748 1324098364 G	A
212	635 C	-7:91702747 1324098363 C	
212	636 A	-7:91702746 1324098362 A	
213 L	637 C	-7:91702745 1324098361 C	L
213	638 T	-7:91702744 1324098360 T	
213	639 A	-7:91702743 1324098359 A	
214 E	640 G	-7:91702742 1324098358 G	E
214	641 A	-7:91702741 1324098357 A	
214	642 A	-7:91702740 1324098356 A	
215 I	643 A	-7:91702739 1324098355 A	I
215	644 T	-7:91702738 1324098354 T	
215	645 A	-7:91702737 1324098353 A	
216 K	646 A	-7:91702736 1324098352 A	K
216	647 A	-7:91702735 1324098351 A	
216	648 G	-7:91702734 1324098350 G	
217 S	649 A	-7:91702733 1324098349 A	S
217	650 G	-7:91702732 1324098348 G	
217	651 T	-7:91702731 1324098347 T	
218 K	652 A	-7:91702730 1324098346 A	K
218	653 A	-7:91702729 1324098345 A	
218	654 A	-7:91702728 1324098344 A	
219 M	655 A	-7:91702727 1324098343 A	M
219	656 T	-7:91702726 1324098342 T	
219	657 G	-7:91702725 1324098341 G	
220 L	658 T	-7:91702724 1324098340 T	L
220	659 T	-7:91702723 1324098339 T	
220	660 A	-7:91702722 1324098338 A	
221 A	661 G	-7:91702721 1324098337 G	A
221	662 C	-7:91702720 1324098336 C	
221	663 C	-7:91702719 1324098335 C	
222 L	664 C	-7:91702718 1324098334 C	L
222	665 T	-7:91702717 1324098333 T	
222	666 A	-7:91702716 1324098332 A	
223 E	667 G	-7:91702715 1324098331 G	E
223	668 A	-7:91702714 1324098330 A	
223	669 G	-7:91702713 1324098329 G	
224 K	670 A	-7:91702712 1324098328 A	K
224	671 A	-7:91702711 1324098327 A	
224	672 A	-7:91702710 1324098326 A	
225 A	673 G	-7:91702709 1324098325 G	A
225	674 C	-7:91702708 1324098324 C	
225	675 A	-7:91702707 1324098323 A	
226 D	676 G	-7:91702706 1324098322 G	D
226	677 A	-7:91702705 1324098321 A	
226	678 T	-7:91702704 1324098320 T	
227 T	679 A	-7:91702703 1324098319 A	T
227	680 C	-7:91702702 1324098318 C	
227	681 C	-7:91702701 1324098317 C	
228 C	682 T	-7:91702700 1324098316 T	C
228	683 G	-7:91702699 1324098315 G	
228	684 T	-7:91702698 1324098314 T	
229 I	685 A	-7:91702697 1324098313 A	I
229	686 T	-7:91702696 1324098312 T	
229	687 T	-7:91702695 1324098311 T	
230 Y	688 T	-7:91702694 1324098310 T	Y
230	689 A	-7:91702693 1324098309 A	
230	690 C	-7:91702692 1324098308 C	
231 N	691 A	-7:91702691 1324098307 A	N
231	692 A	-7:91702690 1324098306 A	
231	693 C	-7:91702689 1324098305 C	
232 P	694 C	-7:91702688 1324098304 C	P
232	695 C	-7:91702687 1324098303 C	
232	696 T	-7:91702686 1324098302 T	
233 L	697 T	-7:91702685 1324098301 T	L
233	698 T	-7:91702684 1324098300 T	
233	699 G	-7:91702683 1324098299 G	
234 F	700 T	-7:91702682 1324098298 T	F
234	701 T	-7:91702681 1324098297 T	
234	702 T	-7:91702680 1324098296 T	
235 G	703 G	-7:91702679 1324098295 G	G
235	704 G	-7:91702678 1324098294 G	
235	705 A	-7:91702677 1324098293 A	
236 S	706 T	-7:91702676 1324098292 T	S
236	707 C	-7:91702675 1324098291 C	
236	708 A	-7:91702674 1324098290 A	
237 D	709 G	-7:91702673 1324098289 G	D
237	710 A	-7:91702672 1324098288 A	
237	711 T	-7:91702671 1324098287 T	
238 L	712 C	-7:91702670 1324098286 C	L
238	713 T	-7:91702669 1324098285 T	
238	714 T	-7:91702668 1324098284 T	
239 Q	715 C	-7:91702667 1324098283 C	Q
239	716 A	-7:91702666 1324098282 A	
239	717 G	-7:91702665 1324098281 G	
240 Y	718 T	-7:91702664 1324098280 T	Y
240	719 A	-7:91702663 1324098279 A	
240	720 T	-7:91702662 1324098278 T	
241 T	721 A	-7:91702661 1324098277 A	T
241	722 C	-7:91702660 1324098276 C	
241	723 A	-7:91702659 1324098275 A	
242 N	724 A	-7:91702658 1324098274 A	N
242	725 A	-7:91702657 1324098273 A	
242	726 T	-7:91702656 1324098272 T	
243 R	727 C	-7:91702655 1324098271 C	R
243	728 G	-7:91702654 1324098270 G	
243	729 G	-7:91702653 1324098269 G	
244 V	730 G	-7:91702173 1324097789 G	V
244	731 T	-7:91702172 1324097788 T	
244	732 A	-7:91702171 1324097787 A	
245 D	733 G	-7:91702170 1324097786 G	D
245	734 A	-7:91702169 1324097785 A	
245	735 T	-7:91702168 1324097784 T	
246 K	736 A	-7:91702167 1324097783 A	K
246	737 A	-7:91702166 1324097782 A	
246	738 A	-7:91702165 1324097781 A	
247 V	739 G	-7:91702164 1324097780 G	V
247	740 T	-7:91702163 1324097779 T	
247	741 G	-7:91702162 1324097778 G	
248 V	742 G	-7:91702161 1324097777 G	V
248	743 T	-7:91702160 1324097776 T	
248	744 A	-7:91702159 1324097775 A	
249 I	745 A	-7:91702158 1324097774 A	I
249	746 T	-7:91702157 1324097773 T	
249	747 A	-7:91702156 1324097772 A	
250 N	748 A	-7:91702155 1324097771 A	N
250	749 A	-7:91702154 1324097770 A	
250	750 T	-7:91702153 1324097769 T	
251 P	751 C	-7:91702152 1324097768 C	P
251	752 C	-7:91702151 1324097767 C	
251	753 A	-7:91702150 1324097766 A	
252 Y	754 T	-7:91702149 1324097765 T	Y
252	755 A	-7:91702148 1324097764 A	
252	756 C	-7:91702147 1324097763 C	
253 F	757 T	-7:91702146 1324097762 T	F
253	758 T	-7:91702145 1324097761 T	
253	759 T	-7:91702144 1324097760 T	
254 G	760 G	-7:91702143 1324097759 G	G
254	761 G	-7:91702142 1324097758 G	
254	762 T	-7:91702141 1324097757 T	
255 L	763 C	-7:91702140 1324097756 C	L
255	764 T	-7:91702139 1324097755 T	
255	765 A	-7:91702138 1324097754 A	
256 G	766 G	-7:91702137 1324097753 G	G
256	767 G	-7:91702136 1324097752 G	
256	768 A	-7:91702135 1324097751 A	
257 A	769 G	-7:91702134 1324097750 G	A
257	770 C	-7:91702133 1324097749 C	
257	771 T	-7:91702132 1324097748 T	
258 P	772 C	-7:91702131 1324097747 C	P
258	773 C	-7:91702130 1324097746 C	
258	774 A	-7:91702129 1324097745 A	
259 D	775 G	-7:91702128 1324097744 G	D
259	776 A	-7:91702127 1324097743 A	
259	777 C	-7:91702126 1324097742 C	
260 Y	778 T	-7:91702125 1324097741 T	Y
260	779 A	-7:91702124 1324097740 A	
260	780 C	-7:91702123 1324097739 C	
261 S	781 T	-7:91702122 1324097738 T	S
261	782 C	-7:91702121 1324097737 C	
261	783 A	-7:91702120 1324097736 A	
262 K	784 A	-7:91702119 1324097735 A	K
262	785 A	-7:91702118 1324097734 A	
262	786 A	-7:91702117 1324097733 A	
263 I	787 A	-7:91702116 1324097732 A	I
263	788 T	-7:91702115 1324097731 T	
263	789 C	-7:91702114 1324097730 C	
264 Q	790 C	-7:91702113 1324097729 C	Q
264	791 A	-7:91702112 1324097728 A	
264	792 A	-7:91702111 1324097727 A	
265 I	793 A	-7:91702110 1324097726 A	I
265	794 T	-7:91702109 1324097725 T	
265	795 A	-7:91702108 1324097724 A	
266 P	796 C	-7:91702107 1324097723 C	P
266	797 C	-7:91702106 1324097722 C	
266	798 T	-7:91702105 1324097721 T	
267 K	799 A	-7:91702104 1324097720 A	K
267	800 A	-7:91702103 1324097719 A	
267	801 A	-7:91702102 1324097718 A	
268 Q	802 C	-7:91702101 1324097717 C	Q
268	803 A	-7:91702100 1324097716 A	
268	804 G	-7:91702099 1324097715 G	
269 E	805 G	-7:91702098 1324097714 G	E
269	806 A	-7:91702097 1324097713 A	
269	807 A	-7:91702096 1324097712 A	
270 K	808 A	-7:91702095 1324097711 A	K
270	809 A	-7:91702094 1324097710 A	
270	810 A	-7:91702093 1324097709 A	
271 W	811 T	-7:91702092 1324097708 T	W
271	812 G	-7:91702091 1324097707 G	
271	813 G	-7:91702090 1324097706 G	
272 Q	814 C	-7:91702089 1324097705 C	Q
272	815 A	-7:91702088 1324097704 A	
272	816 G	-7:91702087 1324097703 G	
273 R	817 A	-7:91702086 1324097702 A	R
273	818 G	-7:91702085 1324097701 G	
273	819 A	-7:91702084 1324097700 A	
274 S	820 A	-7:91702083 1324097699 A	S
274	821 G	-7:91702082 1324097698 G	
274	822 C	-7:91702081 1324097697 C	
275 M	823 A	-7:91702080 1324097696 A	M
275	824 T	-7:91702079 1324097695 T	
275	825 G	-7:91702078 1324097694 G	
276 S	826 A	-7:91702077 1324097693 A	S
276	827 G	-7:91702076 1324097692 G	
276	828 C	-7:91702075 1324097691 C	
277 S	829 A	-7:91702074 1324097690 A	S
277	830 G	-7:91702073 1324097689 G	
277	831 T	-7:91702072 1324097688 T	
278 V	832 G	-7:91702071 1324097687 G	V
278	833 T	-7:91702070 1324097686 T	
278	834 C	-7:91702069 1324097685 C	
279 T	835 A	-7:91702068 1324097684 A	T
279	836 C	-7:91702067 1324097683 C	
279	837 A	-7:91702066 1324097682 A	
280 E	838 G	-7:91702065 1324097681 G	E
280	839 A	-7:91702064 1324097680 A	
280	840 A	-7:91702063 1324097679 A	
281 D	841 G	-7:91702062 1324097678 G	D
281	842 A	-7:91702061 1324097677 A	
281	843 C	-7:91702060 1324097676 C	
282 K	844 A	-7:91702059 1324097675 A	K
282	845 A	-7:91702058 1324097674 A	
282	846 G	-7:91701842 1324097458 G	
283 E	847 G	-7:91701841 1324097457 G	E
283	848 A	-7:91701840 1324097456 A	
283	849 A	-7:91701839 1324097455 A	
284 R	850 C	-7:91701838 1324097454 C	R
284	851 G	-7:91701837 1324097453 G	
284	852 A	-7:91701836 1324097452 A	
285 Q	853 C	-7:91701835 1324097451 C	Q
285	854 A	-7:91701834 1324097450 A	
285	855 G	-7:91701833 1324097449 G	
286 W	856 T	-7:91701832 1324097448 T	W
286	857 G	-7:91701831 1324097447 G	
286	858 G	-7:91701830 1324097446 G	
287 V	859 G	-7:91701829 1324097445 G	V
287	860 T	-7:91701828 1324097444 T	
287	861 A	-7:91701827 1324097443 A	
288 D	862 G	-7:91701826 1324097442 G	D
288	863 A	-7:91701825 1324097441 A	
288	864 T	-7:91701824 1324097440 T	
289 D	865 G	-7:91701823 1324097439 G	D
289	866 A	-7:91701822 1324097438 A	
289	867 T	-7:91701821 1324097437 T	
290 F	868 T	-7:91701820 1324097436 T	F
290	869 T	-7:91701819 1324097435 T	
290	870 T	-7:91701818 1324097434 T	
291 P	871 C	-7:91701817 1324097433 C	P
291	872 C	-7:91701816 1324097432 C	
291	873 T	-7:91701815 1324097431 T	
292 L	874 C	-7:91701814 1324097430 C	L
292	875 T	-7:91701813 1324097429 T	
292	876 C	-7:91701812 1324097428 C	
293 H	877 C	-7:91701811 1324097427 C	H
293	878 A	-7:91701810 1324097426 A	
293	879 C	-7:91701809 1324097425 C	
294 R	880 C	-7:91701808 1324097424 C	R
294	881 G	-7:91701807 1324097423 G	
294	882 A	-7:91701806 1324097422 A	
295 S	883 A	-7:91701805 1324097421 A	S
295	884 G	-7:91701804 1324097420 G	
295	885 C	-7:91701803 1324097419 C	
296 A	886 G	-7:91701802 1324097418 G	A
296	887 C	-7:91701801 1324097417 C	
296	888 C	-7:91701800 1324097416 C	
297 C	889 T	-7:91701799 1324097415 T	C
297	890 G	-7:91701798 1324097414 G	
297	891 T	-7:91701797 1324097413 T	
298 E	892 G	-7:91701796 1324097412 G	E
298	893 A	-7:91701795 1324097411 A	
298	894 A	-7:91701794 1324097410 A	
299 G	895 G	-7:91701793 1324097409 G	G
299	896 G	-7:91701792 1324097408 G	
299	897 A	-7:91701791 1324097407 A	
300 D	898 G	-7:91701790 1324097406 G	D
300	899 A	-7:91701789 1324097405 A	
300	900 T	-7:91701788 1324097404 T	
301 S	901 T	-7:91701787 1324097403 T	S
301	902 C	-7:91701786 1324097402 C	
301	903 A	-7:91701785 1324097401 A	
302 E	904 G	-7:91701784 1324097400 G	E
302	905 A	-7:91701783 1324097399 A	
302	906 A	-7:91701782 1324097398 A	
303 L	907 T	-7:91701781 1324097397 T	L
303	908 T	-7:91701780 1324097396 T	
303	909 A	-7:91701779 1324097395 A	
304 L	910 C	-7:91701778 1324097394 C	L
304	911 T	-7:91701777 1324097393 T	
304	912 A	-7:91701776 1324097392 A	
305 S	913 A	-7:91701775 1324097391 A	S
305	914 G	-7:91701774 1324097390 G	
305	915 C	-7:91701773 1324097389 C	
306 R	916 C	-7:91701772 1324097388 C	R
306	917 G	-7:91701771 1324097387 G	
306	918 T	-7:91701770 1324097386 T	
307 L	919 C	-7:91701769 1324097385 C	L
307	920 T	-7:91701768 1324097384 T	
307	921 T	-7:91701767 1324097383 T	
308 L	922 C	-7:91701766 1324097382 C	L
308	923 T	-7:91701765 1324097381 T	
308	924 C	-7:91701764 1324097380 C	
309 S	925 A	-7:91701763 1324097379 A	S
309	926 G	-7:91701762 1324097378 G	
309	927 T	-7:91701761 1324097377 T	
310 E	928 G	-7:91701760 1324097376 G	E
310	929 A	-7:91701759 1324097375 A	
310	930 A	-7:91701758 1324097374 A	
311 R	931 A	-7:91701757 1324097373 A	R
311	932 G	-7:91701756 1324097372 G	
311	933 A	-7:91701755 1324097371 A	
312 F	934 T	-7:91701754 1324097370 T	F
312	935 T	-7:91701753 1324097369 T	
312	936 T	-7:91701752 1324097368 T	
313 S	937 T	-7:91701751 1324097367 T	S
313	938 C	-7:91701750 1324097366 C	
313	939 A	-7:91701749 1324097365 A	
314 V	940 G	-7:91701748 1324097364 G	V
314	941 T	-7:91701747 1324097363 T	
314	942 C	-7:91701746 1324097362 C	
315 N	943 A	-7:91701745 1324097361 A	N
315	944 A	-7:91701744 1324097360 A	
315	945 C	-7:91701743 1324097359 C	
316 Q	946 C	-7:91701742 1324097358 C	Q
316	947 A	-7:91701741 1324097357 A	
316	948 G	-7:91701740 1324097356 G	
317 L	949 T	-7:91701739 1324097355 T	L
317	950 T	-7:91701738 1324097354 T	
317	951 A	-7:91701737 1324097353 A	
318 D	952 G	-7:91701736 1324097352 G	D
318	953 A	-7:91701735 1324097351 A	
318	954 T	-7:91701734 1324097350 T	
319 S	955 A	-7:91701733 1324097349 A	S
319	956 G	-7:91701732 1324097348 G	
319	957 T	-7:91701731 1324097347 T	
320 D	958 G	-7:91701730 1324097346 G	D
320	959 A	-7:91701729 1324097345 A	
320	960 C	-7:91701728 1324097344 C	
321 H	961 C	-7:91701727 1324097343 C	H
321	962 A	-7:91701726 1324097342 A	
321	963 C	-7:91701725 1324097341 C	
322 W	964 T	-7:91701724 1324097340 T	W
322	965 G	-7:91701723 1324097339 G	
322	966 G	-7:91701722 1324097338 G	
323 A	967 G	-7:91701721 1324097337 G	A
323	968 C	-7:91701720 1324097336 C	
323	969 A	-7:91701719 1324097335 A	
324 P	970 C	-7:91701718 1324097334 C	P
324	971 C	-7:91701717 1324097333 C	
324	972 C	-7:91701716 1324097332 C	
325 I	973 A	-7:91701715 1324097331 A	I
325	974 T	-7:91701714 1324097330 T	
325	975 T	-7:91701713 1324097329 T	
326 H	976 C	-7:91701712 1324097328 C	H
326	977 A	-7:91701711 1324097327 A	
326	978 T	-7:91701710 1324097326 T	
327 Y	979 T	-7:91701709 1324097325 T	Y
327	980 A	-7:91701708 1324097324 A	
327	981 T	-7:91701707 1324097323 T	
328 A	982 G	-7:91701706 1324097322 G	A
328	983 C	-7:91701705 1324097321 C	
328	984 A	-7:91701704 1324097320 A	
329 C	985 T	-7:91701703 1324097319 T	C
329	986 G	-7:91701702 1324097318 G	
329	987 C	-7:91701701 1324097317 C	
330 W	988 T	-7:91701700 1324097316 T	W
330	989 G	-7:91701699 1324097315 G	
330	990 G	-7:91693932 1324089548 G	
331 Y	991 T	-7:91693931 1324089547 T	Y
331	992 A	-7:91693930 1324089546 A	
331	993 T	-7:91693929 1324089545 T	
332 G	994 G	-7:91693928 1324089544 G	G
332	995 G	-7:91693927 1324089543 G	
332	996 A	-7:91693926 1324089542 A	
333 K	997 A	-7:91693925 1324089541 A	K
333	998 A	-7:91693924 1324089540 A	
333	999 A	-7:91693923 1324089539 A	
334 V	1000 G	-7:91693922 1324089538 G	V
334	1001 T	-7:91693921 1324089537 T	
334	1002 T	-7:91693920 1324089536 T	
335 E	1003 G	-7:91693919 1324089535 G	E
335	1004 A	-7:91693918 1324089534 A	
335	1005 G	-7:91693917 1324089533 G	
336 A	1006 G	-7:91693916 1324089532 G	A
336	1007 C	-7:91693915 1324089531 C	
336	1008 C	-7:91693914 1324089530 C	
337 T	1009 A	-7:91693913 1324089529 A	T
337	1010 C	-7:91693912 1324089528 C	
337	1011 T	-7:91693911 1324089527 T	
338 R	1012 C	-7:91693910 1324089526 C	R
338	1013 G	-7:91693909 1324089525 G	
338	1014 C	-7:91693908 1324089524 C	
339 I	1015 A	-7:91693907 1324089523 A	I
339	1016 T	-7:91693906 1324089522 T	
339	1017 A	-7:91693905 1324089521 A	
340 L	1018 T	-7:91693904 1324089520 T	L
340	1019 T	-7:91693903 1324089519 T	
340	1020 G	-7:91693902 1324089518 G	
341 L	1021 T	-7:91693901 1324089517 T	L
341	1022 T	-7:91693900 1324089516 T	
341	1023 A	-7:91693899 1324089515 A	
342 E	1024 G	-7:91693898 1324089514 G	E
342	1025 A	-7:91693897 1324089513 A	
342	1026 G	-7:91693896 1324089512 G	
343 K	1027 A	-7:91693895 1324089511 A	K
343	1028 A	-7:91693894 1324089510 A	
343	1029 A	-7:91693893 1324089509 A	
344 G	1030 G	-7:91693892 1324089508 G	G
344	1031 G	-7:91693891 1324089507 G	
344	1032 A	-7:91693890 1324089506 A	
345 K	1033 A	-7:91693889 1324089505 A	K
345	1034 A	-7:91693888 1324089504 A	
345	1035 G	-7:91693887 1324089503 G	
346 C	1036 T	-7:91693886 1324089502 T	C
346	1037 G	-7:91693885 1324089501 G	
346	1038 C	-7:91693884 1324089500 C	
347 N	1039 A	-7:91693883 1324089499 A	N
347	1040 A	-7:91693882 1324089498 A	
347	1041 T	-7:91693881 1324089497 T	
348 P	1042 C	-7:91693880 1324089496 C	P
348	1043 C	-7:91693879 1324089495 C	
348	1044 A	-7:91693878 1324089494 A	
349 N	1045 A	-7:91693877 1324089493 A	N
349	1046 A	-7:91693876 1324089492 A	
349	1047 C	-7:91693875 1324089491 C	
350 L	1048 C	-7:91693874 1324089490 C	L
350	1049 T	-7:91693873 1324089489 T	
350	1050 T	-7:91693872 1324089488 T	
351 L	1051 T	-7:91693871 1324089487 T	L
351	1052 T	-7:91693870 1324089486 T	
351	1053 A	-7:91693869 1324089485 A	
352 N	1054 A	-7:91693868 1324089484 A	N
352	1055 A	-7:91693867 1324089483 A	
352	1056 T	-7:91693866 1324089482 T	
353 G	1057 G	-7:91693865 1324089481 G	G
353	1058 G	-7:91693864 1324089480 G	
353	1059 A	-7:91693863 1324089479 A	
354 Q	1060 C	-7:91693862 1324089478 C	Q
354	1061 A	-7:91693861 1324089477 A	
354	1062 A	-7:91693860 1324089476 A	
355 L	1063 C	-7:91693859 1324089475 C	L
355	1064 T	-7:91693858 1324089474 T	
355	1065 T	-7:91693857 1324089473 T	
356 S	1066 A	-7:91693856 1324089472 A	S
356	1067 G	-7:91693855 1324089471 G	
356	1068 T	-7:91693854 1324089470 T	
357 S	1069 T	-7:91693853 1324089469 T	S
357	1070 C	-7:91693852 1324089468 C	
357	1071 T	-7:91693851 1324089467 T	
358 P	1072 C	-7:91693850 1324089466 C	P
358	1073 C	-7:91693849 1324089465 C	
358	1074 T	-7:91693848 1324089464 T	
359 L	1075 C	-7:91693847 1324089463 C	L
359	1076 T	-7:91693846 1324089462 T	
359	1077 T	-7:91693845 1324089461 T	
360 H	1078 C	-7:91693844 1324089460 C	H
360	1079 A	-7:91693843 1324089459 A	
360	1080 T	-7:91693842 1324089458 T	
361 F	1081 T	-7:91693841 1324089457 T	F
361	1082 T	-7:91693840 1324089456 T	
361	1083 T	-7:91693839 1324089455 T	
362 A	1084 G	-7:91693838 1324089454 G	A
362	1085 C	-7:91693837 1324089453 C	
362	1086 T	-7:91693836 1324089452 T	
363 A	1087 G	-7:91693835 1324089451 G	A
363	1088 C	-7:91693834 1324089450 C	
363	1089 T	-7:91693833 1324089449 T	
364 G	1090 G	-7:91693832 1324089448 G	G
364	1091 G	-7:91693831 1324089447 G	
364	1092 A	-7:91693830 1324089446 A	
365 G	1093 G	-7:91693829 1324089445 G	G
365	1094 G	-7:91693828 1324089444 G	
365	1095 A	-7:91693827 1324089443 A	
366 G	1096 G	-7:91693826 1324089442 G	G
366	1097 G	-7:91693825 1324089441 G	
366	1098 A	-7:91693824 1324089440 A	
367 H	1099 C	-7:91693823 1324089439 C	H
367	1100 A	-7:91693822 1324089438 A	
367	1101 T	-7:91693821 1324089437 T	
368 A	1102 G	-7:91693820 1324089436 G	A
368	1103 C	-7:91693819 1324089435 C	
368	1104 T	-7:91693818 1324089434 T	
369 E	1105 G	-7:91693817 1324089433 G	E
369	1106 A	-7:91693816 1324089432 A	
369	1107 A	-7:91693815 1324089431 A	
370 I	1108 A	-7:91693814 1324089430 A	I
370	1109 T	-7:91693813 1324089429 T	
370	1110 A	-7:91693812 1324089428 A	
371 V	1111 G	-7:91693811 1324089427 G	V
371	1112 T	-7:91693810 1324089426 T	
371	1113 A	-7:91693809 1324089425 A	
372 Q	1114 C	-7:91693808 1324089424 C	Q
372	1115 A	-7:91693807 1324089423 A	
372	1116 G	-7:91693806 1324089422 G	
373 I	1117 A	-7:91693805 1324089421 A	I
373	1118 T	-7:91693804 1324089420 T	
373	1119 T	-7:91693803 1324089419 T	
374 L	1120 C	-7:91693802 1324089418 C	L
374	1121 T	-7:91693801 1324089417 T	
374	1122 C	-7:91693800 1324089416 C	
375 L	1123 C	-7:91693799 1324089415 C	L
375	1124 T	-7:91693798 1324089414 T	
375	1125 A	-7:91693797 1324089413 A	
376 N	1126 A	-7:91693796 1324089412 A	N
376	1127 A	-7:91693795 1324089411 A	
376	1128 C	-7:91693794 1324089410 C	
377 H	1129 C	-7:91693793 1324089409 C	H
377	1130 A	-7:91693792 1324089408 A	
377	1131 C	-7:91693791 1324089407 C	
378 P	1132 C	-7:91693790 1324089406 C	P
378	1133 C	-7:91693789 1324089405 C	
378	1134 A	-7:91693788 1324089404 A	
379 E	1135 G	-7:91693787 1324089403 G	E
379	1136 A	-7:91693786 1324089402 A	
379	1137 A	-7:91693785 1324089401 A	
380 T	1138 A	-7:91693784 1324089400 A	T
380	1139 C	-7:91693783 1324089399 C	
380	1140 G	-7:91693782 1324089398 G	
381 D	1141 G	-7:91693781 1324089397 G	D
381	1142 A	-7:91693780 1324089396 A	
381	1143 T	-7:91693779 1324089395 T	
382 R	1144 A	-7:91693778 1324089394 A	R
382	1145 G	-7:91693777 1324089393 G	
382	1146 A	-7:91693776 1324089392 A	
383 H	1147 C	-7:91693077 1324088693 C	H
383	1148 A	-7:91693076 1324088692 A	
383	1149 T	-7:91693075 1324088691 T	
384 I	1150 A	-7:91693074 1324088690 A	I
384	1151 T	-7:91693073 1324088689 T	
384	1152 A	-7:91693072 1324088688 A	
385 T	1153 A	-7:91693071 1324088687 A	T
385	1154 C	-7:91693070 1324088686 C	
385	1155 A	-7:91693069 1324088685 A	
386 D	1156 G	-7:91693068 1324088684 G	D
386	1157 A	-7:91693067 1324088683 A	
386	1158 C	-7:91693066 1324088682 C	
387 Q	1159 C	-7:91693065 1324088681 C	Q
387	1160 A	-7:91693064 1324088680 A	
387	1161 A	-7:91693063 1324088679 A	
388 Q	1162 C	-7:91693062 1324088678 C	Q
388	1163 A	-7:91693061 1324088677 A	
388	1164 A	-7:91693060 1324088676 A	
389 G	1165 G	-7:91693059 1324088675 G	G
389	1166 G	-7:91693058 1324088674 G	
389	1167 A	-7:91693057 1324088673 A	
390 R	1168 A	-7:91693056 1324088672 A	R
390	1169 G	-7:91693055 1324088671 G	
390	1170 A	-7:91693054 1324088670 A	
391 S	1171 T	-7:91693053 1324088669 T	S
391	1172 C	-7:91693052 1324088668 C	
391	1173 T	-7:91693051 1324088667 T	
392 P	1174 C	-7:91693050 1324088666 C	P
392	1175 C	-7:91693049 1324088665 C	
392	1176 A	-7:91693048 1324088664 A	
393 L	1177 T	-7:91693047 1324088663 T	L
393	1178 T	-7:91693046 1324088662 T	
393	1179 A	-7:91693045 1324088661 A	
394 N	1180 A	-7:91693044 1324088660 A	N
394	1181 A	-7:91693043 1324088659 A	
394	1182 T	-7:91693042 1324088658 T	
395 I	1183 A	-7:91693041 1324088657 A	I
395	1184 T	-7:91693040 1324088656 T	
395	1185 T	-7:91693039 1324088655 T	
396 C	1186 T	-7:91693038 1324088654 T	C
396	1187 G	-7:91693037 1324088653 G	
396	1188 T	-7:91693036 1324088652 T	
397 E	1189 G	-7:91693035 1324088651 G	E
397	1190 A	-7:91693034 1324088650 A	
397	1191 A	-7:91693033 1324088649 A	
398 E	1192 G	-7:91693032 1324088648 G	E
398	1193 A	-7:91693031 1324088647 A	
398	1194 A	-7:91693030 1324088646 A	
399 N	1195 A	-7:91693029 1324088645 A	N
399	1196 A	-7:91693028 1324088644 A	
399	1197 C	-7:91693027 1324088643 C	
400 K	1198 A	-7:91693026 1324088642 A	K
400	1199 A	-7:91693025 1324088641 A	
400	1200 A	-7:91693024 1324088640 A	
401 Q	1201 C	-7:91693023 1324088639 C	Q
401	1202 A	-7:91693022 1324088638 A	
401	1203 A	-7:91693021 1324088637 A	
402 N	1204 A	-7:91693020 1324088636 A	N
402	1205 A	-7:91693019 1324088635 A	
402	1206 C	-7:91693018 1324088634 C	
403 N	1207 A	-7:91693017 1324088633 A	N
403	1208 A	-7:91693016 1324088632 A	
403	1209 C	-7:91693015 1324088631 C	
404 W	1210 T	-7:91693014 1324088630 T	W
404	1211 G	-7:91693013 1324088629 G	
404	1212 G	-7:91693012 1324088628 G	
405 E	1213 G	-7:91693011 1324088627 G	E
405	1214 A	-7:91693010 1324088626 A	
405	1215 A	-7:91693009 1324088625 A	
406 E	1216 G	-7:91693008 1324088624 G	E
406	1217 A	-7:91693007 1324088623 A	
406	1218 A	-7:91693006 1324088622 A	
407 A	1219 G	-7:91693005 1324088621 G	A
407	1220 C	-7:91693004 1324088620 C	
407	1221 T	-7:91693003 1324088619 T	
408 A	1222 G	-7:91693002 1324088618 G	A
408	1223 C	-7:91693001 1324088617 C	
408	1224 A	-7:91693000 1324088616 A	
409 K	1225 A	-7:91692999 1324088615 A	K
409	1226 A	-7:91692998 1324088614 A	
409	1227 A	-7:91692997 1324088613 A	
410 L	1228 T	-7:91692996 1324088612 T	L
410	1229 T	-7:91692995 1324088611 T	
410	1230 G	-7:91692994 1324088610 G	
411 L	1231 T	-7:91692993 1324088609 T	L
411	1232 T	-7:91692992 1324088608 T	
411	1233 G	-7:91692991 1324088607 G	
412 K	1234 A	-7:91692990 1324088606 A	K
412	1235 A	-7:91692989 1324088605 A	
412	1236 G	-7:91692988 1324088604 G	
413 E	1237 G	-7:91692987 1324088603 G	E
413	1238 A	-7:91692986 1324088602 A	
413	1239 A	-7:91692985 1324088601 A	
414 A	1240 G	-7:91692984 1324088600 G	A
414	1241 C	-7:91692983 1324088599 C	
414	1242 A	-7:91692982 1324088598 A	
415 I	1243 A	-7:91692981 1324088597 A	I
415	1244 T	-7:91692980 1324088596 T	
415	1245 T	-7:91692979 1324088595 T	
416 N	1246 A	-7:91692978 1324088594 A	N
416	1247 A	-7:91692977 1324088593 A	
416	1248 C	-7:91692976 1324088592 C	
417 K	1249 A	-7:91692975 1324088591 A	K
417	1250 A	-7:91692974 1324088590 A	
417	1251 A	-7:91692973 1324088589 A	
418 P	1252 C	-7:91692972 1324088588 C	P
418	1253 C	-7:91692971 1324088587 C	
418	1254 A	-7:91692970 1324088586 A	
419 Y	1255 T	-7:91690228 1324085844 T	Y
419	1256 A	-7:91690227 1324085843 A	
419	1257 T	-7:91690226 1324085842 T	
420 E	1258 G	-7:91690225 1324085841 G	E
420	1259 A	-7:91690224 1324085840 A	
420	1260 A	-7:91690223 1324085839 A	
421 K	1261 A	-7:91690222 1324085838 A	K
421	1262 A	-7:91690221 1324085837 A	
421	1263 A	-7:91690220 1324085836 A	
422 V	1264 G	-7:91690219 1324085835 G	V
422	1265 T	-7:91690218 1324085834 T	
422	1266 T	-7:91690217 1324085833 T	
423 R	1267 C	-7:91690216 1324085832 C	R
423	1268 G	-7:91690215 1324085831 G	
423	1269 A	-7:91690214 1324085830 A	
424 I	1270 A	-7:91690213 1324085829 A	I
424	1271 T	-7:91690212 1324085828 T	
424	1272 A	-7:91690211 1324085827 A	
425 Y	1273 T	-7:91690210 1324085826 T	Y
425	1274 A	-7:91690209 1324085825 A	
425	1275 C	-7:91690208 1324085824 C	
426 R	1276 A	-7:91690207 1324085823 A	R
426	1277 G	-7:91690206 1324085822 G	
426	1278 A	-7:91690205 1324085821 A	
427 M	1279 A	-7:91690204 1324085820 A	M
427	1280 T	-7:91690203 1324085819 T	
427	1281 G	-7:91690202 1324085818 G	
428 D	1282 G	-7:91690201 1324085817 G	D
428	1283 A	-7:91690200 1324085816 A	
428	1284 T	-7:91690199 1324085815 T	
429 G	1285 G	-7:91690198 1324085814 G	G
429	1286 G	-7:91690197 1324085813 G	
429	1287 G	-7:91690196 1324085812 G	
430 S	1288 T	-7:91690195 1324085811 T	S
430	1289 C	-7:91690194 1324085810 C	
430	1290 A	-7:91690193 1324085809 A	
431 Y	1291 T	-7:91690192 1324085808 T	Y
431	1292 A	-7:91690191 1324085807 A	
431	1293 T	-7:91690190 1324085806 T	
432 R	1294 C	-7:91690189 1324085805 C	R
432	1295 G	-7:91690188 1324085804 G	
432	1296 T	-7:91690187 1324085803 T	
433 S	1297 T	-7:91690186 1324085802 T	S
433	1298 C	-7:91690185 1324085801 C	
433	1299 T	-7:91690184 1324085800 T	
434 V	1300 G	-7:91690183 1324085799 G	V
434	1301 T	-7:91690182 1324085798 T	
434	1302 T	-7:91690181 1324085797 T	
435 E	1303 G	-7:91690180 1324085796 G	E
435	1304 A	-7:91690179 1324085795 A	
435	1305 A	-7:91690178 1324085794 A	
436 L	1306 T	-7:91690177 1324085793 T	L
436	1307 T	-7:91690176 1324085792 T	
436	1308 G	-7:91690175 1324085791 G	
437 K	1309 A	-7:91690174 1324085790 A	K
437	1310 A	-7:91690173 1324085789 A	
437	1311 G	-7:91690172 1324085788 G	
438 H	1312 C	-7:91690171 1324085787 C	H
438	1313 A	-7:91690170 1324085786 A	
438	1314 T	-7:91690169 1324085785 T	
439 G	1315 G	-7:91690168 1324085784 G	G
439	1316 G	-7:91690167 1324085783 G	
439	1317 A	-7:91690166 1324085782 A	
440 N	1318 A	-7:91690165 1324085781 A	N
440	1319 A	-7:91690164 1324085780 A	
440	1320 T	-7:91690163 1324085779 T	
441 N	1321 A	-7:91690162 1324085778 A	N
441	1322 A	-7:91690161 1324085777 A	
441	1323 T	-7:91690160 1324085776 T	
442 T	1324 A	-7:91690159 1324085775 A	T
442	1325 C	-7:91690158 1324085774 C	
442	1326 C	-7:91690157 1324085773 C	
443 T	1327 A	-7:91690156 1324085772 A	T
443	1328 C	-7:91690155 1324085771 C	
443	1329 A	-7:91690154 1324085770 A	
444 V	1330 G	-7:91690153 1324085769 G	V
444	1331 T	-7:91690152 1324085768 T	
444	1332 G	-7:91690151 1324085767 G	
445 Q	1333 C	-7:91690150 1324085766 C	Q
445	1334 A	-7:91690149 1324085765 A	
445	1335 G	-7:91690148 1324085764 G	
446 Q	1336 C	-7:91690147 1324085763 C	Q
446	1337 A	-7:91690146 1324085762 A	
446	1338 G	-7:91690145 1324085761 G	
447 I	1339 A	-7:91690144 1324085760 A	I
447	1340 T	-7:91690143 1324085759 T	
447	1341 A	-7:91690142 1324085758 A	
448 M	1342 A	-7:91690141 1324085757 A	M
448	1343 T	-7:91690140 1324085756 T	
448	1344 G	-7:91690139 1324085755 G	
449 E	1345 G	-7:91690138 1324085754 G	E
449	1346 A	-7:91690137 1324085753 A	
449	1347 A	-7:91690136 1324085752 A	
450 G	1348 G	-7:91690135 1324085751 G	G
450	1349 G	-7:91690134 1324085750 G	
450	1350 A	-7:91690133 1324085749 A	
451 M	1351 A	-7:91690132 1324085748 A	M
451	1352 T	-7:91690131 1324085747 T	
451	1353 G	-7:91690130 1324085746 G	
452 R	1354 C	-7:91690129 1324085745 C	R
452	1355 G	-7:91690128 1324085744 G	
452	1356 T	-7:91690127 1324085743 T	
453 L	1357 C	-7:91690126 1324085742 C	L
453	1358 T	-7:91690125 1324085741 T	
453	1359 C	-7:91690124 1324085740 C	
454 S	1360 T	-7:91690123 1324085739 T	S
454	1361 C	-7:91690122 1324085738 C	
454	1362 T	-7:91690121 1324085737 T	
455 Q	1363 C	-7:91690120 1324085736 C	Q
455	1364 A	-7:91690119 1324085735 A	
455	1365 A	-7:91690118 1324085734 A	
456 E	1366 G	-7:91690117 1324085733 G	E
456	1367 A	-7:91690116 1324085732 A	
456	1368 A	-7:91690115 1324085731 A	
457 T	1369 A	-7:91690114 1324085730 A	T
457	1370 C	-7:91690113 1324085729 C	
457	1371 T	-7:91690112 1324085728 T	
458 Q	1372 C	-7:91690111 1324085727 C	Q
458	1373 A	-7:91690110 1324085726 A	
458	1374 G	-7:91690109 1324085725 G	
459 Q	1375 C	-7:91690108 1324085724 C	Q
459	1376 A	-7:91690107 1324085723 A	
459	1377 A	-7:91690106 1324085722 A	
460 Y	1378 T	-7:91690105 1324085721 T	Y
460	1379 A	-7:91690104 1324085720 A	
460	1380 T	-7:91690103 1324085719 T	
461 F	1381 T	-7:91690102 1324085718 T	F
461	1382 T	-7:91690101 1324085717 T	
461	1383 C	-7:91690100 1324085716 C	
462 T	1384 A	-7:91690099 1324085715 A	T
462	1385 C	-7:91690098 1324085714 C	
462	1386 T	-7:91690097 1324085713 T	
463 I	1387 A	-7:91690096 1324085712 A	I
463	1388 T	-7:91690095 1324085711 T	
463	1389 A	-7:91690094 1324085710 A	
464 W	1390 T	-7:91690093 1324085709 T	W
464	1391 G	-7:91690092 1324085708 G	
464	1392 G	-7:91690091 1324085707 G	
465 I	1393 A	-7:91690090 1324085706 A	I
465	1394 T	-7:91690089 1324085705 T	
465	1395 T	-7:91690088 1324085704 T	
466 C	1396 T	-7:91690087 1324085703 T	C
466	1397 G	-7:91690086 1324085702 G	
466	1398 T	-7:91690085 1324085701 T	
467 S	1399 T	-7:91690084 1324085700 T	S
467	1400 C	-7:91690083 1324085699 C	
467	1401 A	-7:91690082 1324085698 A	
468 E	1402 G	-7:91690081 1324085697 G	E
468	1403 A	-7:91690080 1324085696 A	
468	1404 A	-7:91690079 1324085695 A	
469 N	1405 A	-7:91690078 1324085694 A	N
469	1406 A	-7:91690077 1324085693 A	
469	1407 C	-7:91690076 1324085692 C	
470 L	1408 C	-7:91690075 1324085691 C	L
470	1409 T	-7:91690074 1324085690 T	
470	1410 C	-7:91690073 1324085689 C	
471 S	1411 A	-7:91690072 1324085688 A	S
471	1412 G	-7:91689303 1324084919 G	
471	1413 C	-7:91689302 1324084918 C	
472 L	1414 C	-7:91689301 1324084917 C	L
472	1415 T	-7:91689300 1324084916 T	
472	1416 T	-7:91689299 1324084915 T	
473 Q	1417 C	-7:91689298 1324084914 C	Q
473	1418 A	-7:91689297 1324084913 A	
473	1419 A	-7:91689296 1324084912 A	
474 L	1420 C	-7:91689295 1324084911 C	L
474	1421 T	-7:91689294 1324084910 T	
474	1422 C	-7:91689293 1324084909 C	
475 K	1423 A	-7:91689292 1324084908 A	K
475	1424 A	-7:91689291 1324084907 A	
475	1425 A	-7:91689290 1324084906 A	
476 P	1426 C	-7:91689289 1324084905 C	P
476	1427 C	-7:91689288 1324084904 C	
476	1428 A	-7:91689287 1324084903 A	
477 Y	1429 T	-7:91689286 1324084902 T	Y
477	1430 A	-7:91689285 1324084901 A	
477	1431 T	-7:91689284 1324084900 T	
478 H	1432 C	-7:91689283 1324084899 C	H
478	1433 A	-7:91689282 1324084898 A	
478	1434 T	-7:91689281 1324084897 T	
479 K	1435 A	-7:91689280 1324084896 A	K
479	1436 A	-7:91689279 1324084895 A	
479	1437 A	-7:91689278 1324084894 A	
480 P	1438 C	-7:91689277 1324084893 C	P
480	1439 C	-7:91689276 1324084892 C	
480	1440 C	-7:91689275 1324084891 C	
481 L	1441 T	-7:91689274 1324084890 T	L
481	1442 T	-7:91689273 1324084889 T	
481	1443 G	-7:91689272 1324084888 G	
482 Q	1444 C	-7:91689271 1324084887 C	Q
482	1445 A	-7:91689270 1324084886 A	
482	1446 A	-7:91689269 1324084885 A	
483 H	1447 C	-7:91689268 1324084884 C	H
483	1448 A	-7:91689267 1324084883 A	
483	1449 T	-7:91689266 1324084882 T	
484 V	1450 G	-7:91689265 1324084881 G	V
484	1451 T	-7:91689264 1324084880 T	
484	1452 T	-7:91689263 1324084879 T	
485 R	1453 C	-7:91689262 1324084878 C	R
485	1454 G	-7:91689261 1324084877 G	
485	1455 T	-7:91689260 1324084876 T	
486 D	1456 G	-7:91689259 1324084875 G	D
486	1457 A	-7:91689258 1324084874 A	
486	1458 C	-7:91689257 1324084873 C	
487 W	1459 T	-7:91689256 1324084872 T	W
487	1460 G	-7:91689255 1324084871 G	
487	1461 G	-7:91689254 1324084870 G	
488 P	1462 C	-7:91689253 1324084869 C	P
488	1463 C	-7:91689252 1324084868 C	
488	1464 A	-7:91689251 1324084867 A	
489 E	1465 G	-7:91689250 1324084866 G	E
489	1466 A	-7:91689249 1324084865 A	
489	1467 A	-7:91689248 1324084864 A	
490 I	1468 A	-7:91689247 1324084863 A	I
490	1469 T	-7:91689246 1324084862 T	
490	1470 A	-7:91689245 1324084861 A	
491 L	1471 C	-7:91689244 1324084860 C	L
491	1472 T	-7:91689243 1324084859 T	
491	1473 T	-7:91689242 1324084858 T	
492 A	1474 G	-7:91689241 1324084857 G	A
492	1475 C	-7:91689240 1324084856 C	
492	1476 T	-7:91689239 1324084855 T	
493 E	1477 G	-7:91689238 1324084854 G	E
493	1478 A	-7:91689237 1324084853 A	
493	1479 A	-7:91689236 1324084852 A	
494 L	1480 T	-7:91689235 1324084851 T	L
494	1481 T	-7:91689234 1324084850 T	
494	1482 G	-7:91689233 1324084849 G	
495 T	1483 A	-7:91689232 1324084848 A	T
495	1484 C	-7:91689231 1324084847 C	
495	1485 T	-7:91689230 1324084846 T	
496 N	1486 A	-7:91689229 1324084845 A	N
496	1487 A	-7:91689228 1324084844 A	
496	1488 T	-7:91689227 1324084843 T	
497 L	1489 C	-7:91689226 1324084842 C	L
497	1490 T	-7:91689225 1324084841 T	
497	1491 G	-7:91689224 1324084840 G	
498 D	1492 G	-7:91689223 1324084839 G	D
498	1493 A	-7:91689222 1324084838 A	
498	1494 T	-7:91689221 1324084837 T	
499 P	1495 C	-7:91689220 1324084836 C	P
499	1496 C	-7:91689219 1324084835 C	
499	1497 T	-7:91689218 1324084834 T	
500 Q	1498 C	-7:91689217 1324084833 C	Q
500	1499 A	-7:91689216 1324084832 A	
500	1500 A	-7:91689215 1324084831 A	
501 R	1501 A	-7:91689214 1324084830 A	R
501	1502 G	-7:91689213 1324084829 G	
501	1503 G	-7:91689212 1324084828 G	
502 E	1504 G	-7:91689211 1324084827 G	E
502	1505 A	-7:91689210 1324084826 A	
502	1506 A	-7:91689209 1324084825 A	
503 T	1507 A	-7:91689208 1324084824 A	T
503	1508 C	-7:91689207 1324084823 C	
503	1509 A	-7:91689206 1324084822 A	
504 P	1510 C	-7:91689205 1324084821 C	P
504	1511 C	-7:91689204 1324084820 C	
504	1512 T	-7:91689203 1324084819 T	
505 Q	1513 C	-7:91689202 1324084818 C	Q
505	1514 A	-7:91689201 1324084817 A	
505	1515 G	-7:91689200 1324084816 G	
506 L	1516 C	-7:91689199 1324084815 C	L
506	1517 T	-7:91689198 1324084814 T	
506	1518 T	-7:91689197 1324084813 T	
507 F	1519 T	-7:91689196 1324084812 T	F
507	1520 T	-7:91689195 1324084811 T	
507	1521 T	-7:91689194 1324084810 T	
508 L	1522 C	-7:91689193 1324084809 C	L
508	1523 T	-7:91689192 1324084808 T	
508	1524 A	-7:91689191 1324084807 A	
509 R	1525 A	-7:91689190 1324084806 A	R
509	1526 G	-7:91689189 1324084805 G	
509	1527 A	-7:91689188 1324084804 A	
510 R	1528 A	-7:91689187 1324084803 A	R
510	1529 G	-7:91689186 1324084802 G	
510	1530 A	-7:91689185 1324084801 A	
511 D	1531 G	-7:91689184 1324084800 G	D
511	1532 A	-7:91689183 1324084799 A	
511	1533 T	-7:91689182 1324084798 T	
512 V	1534 G	-7:91689181 1324084797 G	V
512	1535 T	-7:91689180 1324084796 T	
512	1536 G	-7:91689179 1324084795 G	
513 R	1537 A	-7:91689178 1324084794 A	R
513	1538 G	-7:91689177 1324084793 G	
513	1539 A	-7:91689176 1324084792 A	
514 L	1540 C	-7:91689175 1324084791 C	L
514	1541 T	-7:91689174 1324084790 T	
514	1542 T	-7:91689173 1324084789 T	
515 P	1543 C	-7:91689172 1324084788 C	P
515	1544 C	-7:91689171 1324084787 C	
515	1545 C	-7:91689170 1324084786 C	
516 L	1546 T	-7:91689169 1324084785 T	L
516	1547 T	-7:91689168 1324084784 T	
516	1548 G	-7:91689167 1324084783 G	
517 E	1549 G	-7:91689166 1324084782 G	E
517	1550 A	-7:91689165 1324084781 A	
517	1551 A	-7:91689164 1324084780 A	
518 V	1552 G	-7:91689163 1324084779 G	V
518	1553 T	-7:91689162 1324084778 T	
518	1554 T	-7:91689161 1324084777 T	
519 E	1555 G	-7:91689160 1324084776 G	E
519	1556 A	-7:91689159 1324084775 A	
519	1557 A	-7:91689158 1324084774 A	
520 K	1558 A	-7:91689157 1324084773 A	K
520	1559 A	-7:91689156 1324084772 A	
520	1560 A	-7:91689155 1324084771 A	
521 Q	1561 C	-7:91689154 1324084770 C	Q
521	1562 A	-7:91689153 1324084769 A	
521	1563 G	-7:91689152 1324084768 G	
522 I	1564 A	-7:91682027 1324077643 A	I
522	1565 T	-7:91682026 1324077642 T	
522	1566 T	-7:91682025 1324077641 T	
523 E	1567 G	-7:91682024 1324077640 G	E
523	1568 A	-7:91682023 1324077639 A	
523	1569 A	-7:91682022 1324077638 A	
524 D	1570 G	-7:91682021 1324077637 G	D
524	1571 A	-7:91682020 1324077636 A	
524	1572 C	-7:91682019 1324077635 C	
525 P	1573 C	-7:91682018 1324077634 C	P
525	1574 C	-7:91682017 1324077633 C	
525	1575 A	-7:91682016 1324077632 A	
526 L	1576 C	-7:91682015 1324077631 C	L
526	1577 T	-7:91682014 1324077630 T	
526	1578 A	-7:91682013 1324077629 A	
527 A	1579 G	-7:91682012 1324077628 G	A
527	1580 C	-7:91682011 1324077627 C	
527	1581 T	-7:91682010 1324077626 T	
528 I	1582 A	-7:91682009 1324077625 A	I
528	1583 T	-7:91682008 1324077624 T	
528	1584 T	-7:91682007 1324077623 T	
529 L	1585 C	-7:91682006 1324077622 C	L
529	1586 T	-7:91682005 1324077621 T	
529	1587 T	-7:91682004 1324077620 T	
530 I	1588 A	-7:91682003 1324077619 A	I
530	1589 T	-7:91682002 1324077618 T	
530	1590 T	-7:91682001 1324077617 T	
531 L	1591 C	-7:91682000 1324077616 C	L
531	1592 T	-7:91681999 1324077615 T	
531	1593 C	-7:91681998 1324077614 C	
532 F	1594 T	-7:91681997 1324077613 T	F
532	1595 T	-7:91681996 1324077612 T	
532	1596 T	-7:91681995 1324077611 T	
533 D	1597 G	-7:91681994 1324077610 G	D
533	1598 A	-7:91681993 1324077609 A	
533	1599 T	-7:91681992 1324077608 T	
534 E	1600 G	-7:91681991 1324077607 G	E
534	1601 A	-7:91681990 1324077606 A	
534	1602 A	-7:91681989 1324077605 A	
535 A	1603 G	-7:91681988 1324077604 G	A
535	1604 C	-7:91681987 1324077603 C	
535	1605 C	-7:91681986 1324077602 C	
536 R	1606 A	-7:91681985 1324077601 A	R
536	1607 G	-7:91681984 1324077600 G	
536	1608 A	-7:91681983 1324077599 A	
537 Y	1609 T	-7:91681982 1324077598 T	Y
537	1610 A	-7:91681981 1324077597 A	
537	1611 T	-7:91681980 1324077596 T	
538 N	1612 A	-7:91681979 1324077595 A	N
538	1613 A	-7:91681978 1324077594 A	
538	1614 T	-7:91681977 1324077593 T	
539 L	1615 T	-7:91681976 1324077592 T	L
539	1616 T	-7:91681975 1324077591 T	
539	1617 A	-7:91681974 1324077590 A	
540 L	1618 T	-7:91681973 1324077589 T	L
540	1619 T	-7:91681972 1324077588 T	
540	1620 G	-7:91681971 1324077587 G	
541 K	1621 A	-7:91681970 1324077586 A	K
541	1622 A	-7:91681969 1324077585 A	
541	1623 G	-7:91681968 1324077584 G	
542 G	1624 G	-7:91681967 1324077583 G	G
542	1625 G	-7:91681966 1324077582 G	
542	1626 C	-7:91681965 1324077581 C	
543 F	1627 T	-7:91681964 1324077580 T	F
543	1628 T	-7:91681963 1324077579 T	
543	1629 T	-7:91681962 1324077578 T	
544 Y	1630 T	-7:91681961 1324077577 T	Y
544	1631 A	-7:91681960 1324077576 A	
544	1632 T	-7:91681959 1324077575 T	
545 T	1633 A	-7:91681958 1324077574 A	T
545	1634 C	-7:91681957 1324077573 C	
545	1635 A	-7:91681956 1324077572 A	
546 A	1636 G	-7:91681955 1324077571 G	A
546	1637 C	-7:91681954 1324077570 C	
546	1638 T	-7:91681953 1324077569 T	
547 P	1639 C	-7:91681952 1324077568 C	P
547	1640 C	-7:91681951 1324077567 C	
547	1641 T	-7:91681950 1324077566 T	
548 D	1642 G	-7:91681949 1324077565 G	D
548	1643 A	-7:91681948 1324077564 A	
548	1644 T	-7:91681947 1324077563 T	
549 A	1645 G	-7:91681946 1324077562 G	A
549	1646 C	-7:91681945 1324077561 C	
549	1647 T	-7:91681944 1324077560 T	
550 K	1648 A	-7:91681943 1324077559 A	K
550	1649 A	-7:91681942 1324077558 A	
550	1650 G	-7:91681941 1324077557 G	
551 L	1651 C	-7:91681940 1324077556 C	L
551	1652 T	-7:91681939 1324077555 T	
551	1653 G	-7:91681938 1324077554 G	
552 I	1654 A	-7:91681937 1324077553 A	I
552	1655 T	-7:91681936 1324077552 T	
552	1656 A	-7:91681935 1324077551 A	
553 T	1657 A	-7:91681934 1324077550 A	T
553	1658 C	-7:91681933 1324077549 C	
553	1659 A	-7:91681932 1324077548 A	
554 L	1660 T	-7:91681931 1324077547 T	L
554	1661 T	-7:91681930 1324077546 T	
554	1662 G	-7:91681929 1324077545 G	
555 A	1663 G	-7:91681928 1324077544 G	A
555	1664 C	-7:91681927 1324077543 C	
555	1665 A	-7:91681926 1324077542 A	
556 S	1666 A	-7:91681925 1324077541 A	S
556	1667 G	-7:91681924 1324077540 G	
556	1668 T	-7:91681923 1324077539 T	
557 L	1669 C	-7:91681922 1324077538 C	L
557	1670 T	-7:91681921 1324077537 T	
557	1671 G	-7:91681920 1324077536 G	
558 L	1672 C	-7:91681919 1324077535 C	L
558	1673 T	-7:91681918 1324077534 T	
558	1674 T	-7:91681917 1324077533 T	
559 L	1675 T	-7:91681916 1324077532 T	L
559	1676 T	-7:91681915 1324077531 T	
559	1677 G	-7:91681914 1324077530 G	
560 Q	1678 C	-7:91681913 1324077529 C	Q
560	1679 A	-7:91681912 1324077528 A	
560	1680 A	-7:91681911 1324077527 A	
561 I	1681 A	-7:91681910 1324077526 A	I
561	1682 T	-7:91681909 1324077525 T	
561	1683 A	-7:91681908 1324077524 A	
562 V	1684 G	-7:91681907 1324077523 G	V
562	1685 T	-7:91681906 1324077522 T	
562	1686 C	-7:91681905 1324077521 C	
563 Y	1687 T	-7:91681904 1324077520 T	Y
563	1688 A	-7:91681903 1324077519 A	
563	1689 T	-7:91681902 1324077518 T	
564 G	1690 G	-7:91681901 1324077517 G	G
564	1691 G	-7:91681900 1324077516 G	
564	1692 A	-7:91681899 1324077515 A	
565 N	1693 A	-7:91681898 1324077514 A	N
565	1694 A	-7:91681897 1324077513 A	
565	1695 T	-7:91681896 1324077512 T	
566 Y	1696 T	-7:91681895 1324077511 T	Y
566	1697 A	-7:91681894 1324077510 A	
566	1698 T	-7:91681893 1324077509 T	
567 E	1699 G	-7:91681892 1324077508 G	E
567	1700 A	-7:91681891 1324077507 A	
567	1701 G	-7:91681890 1324077506 G	
568 S	1702 A	-7:91681889 1324077505 A	S
568	1703 G	-7:91681888 1324077504 G	
568	1704 T	-7:91681887 1324077503 T	
569 K	1705 A	-7:91681886 1324077502 A	K
569	1706 A	-7:91681885 1324077501 A	
569	1707 A	-7:91681884 1324077500 A	
570 K	1708 A	-7:91681883 1324077499 A	K
570	1709 A	-7:91681882 1324077498 A	
570	1710 A	-7:91681881 1324077497 A	
571 H	1711 C	-7:91681880 1324077496 C	H
571	1712 A	-7:91681879 1324077495 A	
571	1713 C	-7:91681878 1324077494 C	
572 K	1714 A	-7:91681877 1324077493 A	K
572	1715 A	-7:91681876 1324077492 A	
572	1716 G	-7:91681875 1324077491 G	
573 Q	1717 C	-7:91681874 1324077490 C	Q
573	1718 A	-7:91681873 1324077489 A	
573	1719 A	-7:91681872 1324077488 A	
574 G	1720 G	-7:91681871 1324077487 G	G
574	1721 G	-7:91681870 1324077486 G	
574	1722 T	-7:91681869 1324077485 T	
575 F	1723 T	-7:91681868 1324077484 T	F
575	1724 T	-7:91681867 1324077483 T	
575	1725 C	-7:91681866 1324077482 C	
576 L	1726 C	-7:91681865 1324077481 C	L
576	1727 T	-7:91681864 1324077480 T	
576	1728 A	-7:91681863 1324077479 A	
577 N	1729 A	-7:91681862 1324077478 A	N
577	1730 A	-7:91681861 1324077477 A	
577	1731 T	-7:91681229 1324076845 T	
578 E	1732 G	-7:91681228 1324076844 G	E
578	1733 A	-7:91681227 1324076843 A	
578	1734 A	-7:91681226 1324076842 A	
579 E	1735 G	-7:91681225 1324076841 G	E
579	1736 A	-7:91681224 1324076840 A	
579	1737 A	-7:91681223 1324076839 A	
580 N	1738 A	-7:91681222 1324076838 A	N
580	1739 A	-7:91681221 1324076837 A	
580	1740 T	-7:91681220 1324076836 T	
581 L	1741 C	-7:91681219 1324076835 C	L
581	1742 T	-7:91681218 1324076834 T	
581	1743 A	-7:91681217 1324076833 A	
582 K	1744 A	-7:91681216 1324076832 A	K
582	1745 A	-7:91681215 1324076831 A	
582	1746 A	-7:91681214 1324076830 A	
583 S	1747 T	-7:91681213 1324076829 T	S
583	1748 C	-7:91681212 1324076828 C	
583	1749 C	-7:91681211 1324076827 C	
584 I	1750 A	-7:91681210 1324076826 A	I
584	1751 T	-7:91681209 1324076825 T	
584	1752 C	-7:91681208 1324076824 C	
585 V	1753 G	-7:91681207 1324076823 G	V
585	1754 T	-7:91681206 1324076822 T	
585	1755 A	-7:91681205 1324076821 A	
586 P	1756 C	-7:91681204 1324076820 C	P
586	1757 C	-7:91681203 1324076819 C	
586	1758 T	-7:91681202 1324076818 T	
587 V	1759 G	-7:91681201 1324076817 G	V
587	1760 T	-7:91681200 1324076816 T	
587	1761 T	-7:91681199 1324076815 T	
588 T	1762 A	-7:91681198 1324076814 A	T
588	1763 C	-7:91681197 1324076813 C	
588	1764 C	-7:91681196 1324076812 C	
589 K	1765 A	-7:91681195 1324076811 A	K
589	1766 A	-7:91681194 1324076810 A	
589	1767 A	-7:91681193 1324076809 A	
590 L	1768 C	-7:91681192 1324076808 C	L
590	1769 T	-7:91681191 1324076807 T	
590	1770 G	-7:91681190 1324076806 G	
591 K	1771 A	-7:91681189 1324076805 A	K
591	1772 A	-7:91681188 1324076804 A	
591	1773 A	-7:91681187 1324076803 A	
592 S	1774 A	-7:91681186 1324076802 A	S
592	1775 G	-7:91681185 1324076801 G	
592	1776 T	-7:91681184 1324076800 T	
593 K	1777 A	-7:91681183 1324076799 A	K
593	1778 A	-7:91681182 1324076798 A	
593	1779 G	-7:91681181 1324076797 G	
594 A	1780 G	-7:91681180 1324076796 G	A
594	1781 C	-7:91681179 1324076795 C	
594	1782 A	-7:91681178 1324076794 A	
595 P	1783 C	-7:91681177 1324076793 C	P
595	1784 C	-7:91681176 1324076792 C	
595	1785 T	-7:91681175 1324076791 T	
596 H	1786 C	-7:91681174 1324076790 C	H
596	1787 A	-7:91681173 1324076789 A	
596	1788 C	-7:91681172 1324076788 C	
597 W	1789 T	-7:91681171 1324076787 T	W
597	1790 G	-7:91681170 1324076786 G	
597	1791 G	-7:91681169 1324076785 G	
598 T	1792 A	-7:91681168 1324076784 A	T
598	1793 C	-7:91681167 1324076783 C	
598	1794 A	-7:91681166 1324076782 A	
599 N	1795 A	-7:91681165 1324076781 A	N
599	1796 A	-7:91681164 1324076780 A	
599	1797 T	-7:91681163 1324076779 T	
600 R	1798 C	-7:91681162 1324076778 C	R
600	1799 G	-7:91681161 1324076777 G	
600	1800 C	-7:91681160 1324076776 C	
601 I	1801 A	-7:91681159 1324076775 A	I
601	1802 T	-7:91681158 1324076774 T	
601	1803 A	-7:91681157 1324076773 A	
602 L	1804 C	-7:91681156 1324076772 C	L
602	1805 T	-7:91681155 1324076771 T	
602	1806 T	-7:91681154 1324076770 T	
603 H	1807 C	-7:91681153 1324076769 C	H
603	1808 A	-7:91681152 1324076768 A	
603	1809 T	-7:91681151 1324076767 T	
604 E	1810 G	-7:91681150 1324076766 G	E
604	1811 A	-7:91681149 1324076765 A	
604	1812 A	-7:91681148 1324076764 A	
605 Y	1813 T	-7:91681147 1324076763 T	Y
605	1814 A	-7:91681146 1324076762 A	
605	1815 C	-7:91681145 1324076761 C	
606 K	1816 A	-7:91681144 1324076760 A	K
606	1817 A	-7:91681143 1324076759 A	
606	1818 G	-7:91681142 1324076758 G	
607 N	1819 A	-7:91680651 1324076267 A	N
607	1820 A	-7:91680650 1324076266 A	
607	1821 T	-7:91680649 1324076265 T	
608 L	1822 C	-7:91680648 1324076264 C	L
608	1823 T	-7:91680647 1324076263 T	
608	1824 C	-7:91680646 1324076262 C	
609 S	1825 A	-7:91680645 1324076261 A	S
609	1826 G	-7:91680644 1324076260 G	
609	1827 T	-7:91680643 1324076259 T	
610 T	1828 A	-7:91680642 1324076258 A	T
610	1829 C	-7:91680641 1324076257 C	
610	1830 A	-7:91680640 1324076256 A	
611 S	1831 A	-7:91680639 1324076255 A	S
611	1832 G	-7:91680638 1324076254 G	
611	1833 T	-7:91680637 1324076253 T	
612 E	1834 G	-7:91680636 1324076252 G	E
612	1835 A	-7:91680635 1324076251 A	
612	1836 A	-7:91680634 1324076250 A	
613 G	1837 G	-7:91680633 1324076249 G	G
613	1838 G	-7:91680632 1324076248 G	
613	1839 T	-7:91680631 1324076247 T	
614 V	1840 G	-7:91680630 1324076246 G	V
614	1841 T	-7:91680629 1324076245 T	
614	1842 C	-7:91680628 1324076244 C	
615 S	1843 A	-7:91680627 1324076243 A	S
615	1844 G	-7:91680626 1324076242 G	
615	1845 T	-7:91680625 1324076241 T	
616 K	1846 A	-7:91680624 1324076240 A	K
616	1847 A	-7:91680623 1324076239 A	
616	1848 A	-7:91680622 1324076238 A	
617 E	1849 G	-7:91680621 1324076237 G	E
617	1850 A	-7:91680620 1324076236 A	
617	1851 A	-7:91680619 1324076235 A	
618 M	1852 A	-7:91680618 1324076234 A	M
618	1853 T	-7:91680617 1324076233 T	
618	1854 G	-7:91680616 1324076232 G	
619 H	1855 C	-7:91680615 1324076231 C	H
619	1856 A	-7:91680614 1324076230 A	
619	1857 T	-7:91680613 1324076229 T	
620 H	1858 C	-7:91680612 1324076228 C	H
620	1859 A	-7:91680611 1324076227 A	
620	1860 C	-7:91680610 1324076226 C	
621 L	1861 C	-7:91680609 1324076225 C	L
621	1862 T	-7:91680608 1324076224 T	
621	1863 T	-7:91680607 1324076223 T	
622 Q	1864 C	-7:91680606 1324076222 C	Q
622	1865 A	-7:91680605 1324076221 A	
622	1866 G	-7:91680604 1324076220 G	
623 R	1867 C	-7:91680603 1324076219 C	R
623	1868 G	-7:91680602 1324076218 G	
623	1869 C	-7:91680601 1324076217 C	
624 M	1870 A	-7:91680600 1324076216 A	M
624	1871 T	-7:91680599 1324076215 T	
624	1872 G	-7:91680598 1324076214 G	
625 F	1873 T	-7:91680597 1324076213 T	F
625	1874 T	-7:91680596 1324076212 T	
625	1875 C	-7:91680595 1324076211 C	
626 L	1876 T	-7:91680594 1324076210 T	L
626	1877 T	-7:91680593 1324076209 T	
626	1878 A	-7:91680592 1324076208 A	
627 Q	1879 C	-7:91680591 1324076207 C	Q
627	1880 A	-7:91680590 1324076206 A	
627	1881 G	-7:91680589 1324076205 G	
628 N	1882 A	-7:91680588 1324076204 A	N
628	1883 A	-7:91680587 1324076203 A	
628	1884 T	-7:91680586 1324076202 T	
629 C	1885 T	-7:91680585 1324076201 T	C
629	1886 G	-7:91680584 1324076200 G	
629	1887 C	-7:91680583 1324076199 C	
630 W	1888 T	-7:91680582 1324076198 T	W
630	1889 G	-7:91680581 1324076197 G	
630	1890 G	-7:91680580 1324076196 G	
631 E	1891 G	-7:91680579 1324076195 G	E
631	1892 A	-7:91680578 1324076194 A	
631	1893 A	-7:91680577 1324076193 A	
632 I	1894 A	-7:91680576 1324076192 A	I
632	1895 T	-7:91680575 1324076191 T	
632	1896 T	-7:91680574 1324076190 T	
633 P	1897 C	-7:91680573 1324076189 C	P
633	1898 C	-7:91680572 1324076188 C	
633	1899 T	-7:91680571 1324076187 T	
634 T	1900 A	-7:91680570 1324076186 A	T
634	1901 C	-7:91680569 1324076185 C	
634	1902 T	-7:91680568 1324076184 T	
635 Y	1903 T	-7:91680567 1324076183 T	Y
635	1904 A	-7:91680566 1324076182 A	
635	1905 T	-7:91680565 1324076181 T	
636 G	1906 G	-7:91680564 1324076180 G	G
636	1907 G	-7:91680563 1324076179 G	
636	1908 A	-7:91680562 1324076178 A	
637 A	1909 G	-7:91680561 1324076177 G	A
637	1910 C	-7:91680560 1324076176 C	
637	1911 A	-7:91680559 1324076175 A	
638 A	1912 G	-7:91680558 1324076174 G	A
638	1913 C	-7:91680557 1324076173 C	
638	1914 A	-7:91680556 1324076172 A	
639 F	1915 T	-7:91680555 1324076171 T	F
639	1916 T	-7:91680554 1324076170 T	
639	1917 T	-7:91680553 1324076169 T	
640 F	1918 T	-7:91680552 1324076168 T	F
640	1919 T	-7:91680551 1324076167 T	
640	1920 C	-7:91680550 1324076166 C	
641 T	1921 A	-7:91680549 1324076165 A	T
641	1922 C	-7:91680548 1324076164 C	
641	1923 A	-7:91680547 1324076163 A	
642 G	1924 G	-7:91680546 1324076162 G	G
642	1925 G	-7:91680545 1324076161 G	
642	1926 A	-7:91680544 1324076160 A	
643 Q	1927 C	-7:91680543 1324076159 C	Q
643	1928 A	-7:91680542 1324076158 A	
643	1929 G	-7:91680541 1324076157 G	
644 I	1930 A	-7:91680540 1324076156 A	I
644	1931 T	-7:91680539 1324076155 T	
644	1932 A	-7:91680538 1324076154 A	
645 F	1933 T	-7:91680537 1324076153 T	F
645	1934 T	-7:91680536 1324076152 T	
645	1935 T	-7:91680535 1324076151 T	
646 T	1936 A	-7:91680534 1324076150 A	T
646	1937 C	-7:91680533 1324076149 C	
646	1938 A	-7:91680532 1324076148 A	
647 K	1939 A	-7:91680531 1324076147 A	K
647	1940 A	-7:91680530 1324076146 A	
647	1941 G	-7:91680529 1324076145 G	
648 A	1942 G	-7:91680528 1324076144 G	A
648	1943 C	-7:91680527 1324076143 C	
648	1944 A	-7:91680526 1324076142 A	
649 S	1945 A	-7:91680525 1324076141 A	S
649	1946 G	-7:91680524 1324076140 G	
649	1947 C	-7:91680523 1324076139 C	
650 P	1948 C	-7:91680522 1324076138 C	P
650	1949 C	-7:91680521 1324076137 C	
650	1950 C	-7:91680520 1324076136 C	
651 S	1951 A	-7:91680519 1324076135 A	S
651	1952 G	-7:91680518 1324076134 G	
651	1953 C	-7:91680517 1324076133 C	
652 N	1954 A	-7:91680516 1324076132 A	N
652	1955 A	-7:91680515 1324076131 A	
652	1956 T	-7:91680514 1324076130 T	
653 H	1957 C	-7:91680513 1324076129 C	H
653	1958 A	-7:91680512 1324076128 A	
653	1959 T	-7:91680511 1324076127 T	
654 K	1960 A	-7:91680510 1324076126 A	K
654	1961 A	-7:91680509 1324076125 A	
654	1962 A	-7:91680508 1324076124 A	
655 V	1963 G	-7:91680507 1324076123 G	V
655	1964 T	-7:91680506 1324076122 T	
655	1965 C	-7:91680505 1324076121 C	
656 I	1966 A	-7:91680504 1324076120 A	I
656	1967 T	-7:91680503 1324076119 T	
656	1968 C	-7:91680502 1324076118 C	
657 P	1969 C	-7:91680501 1324076117 C	P
657	1970 C	-7:91680500 1324076116 C	
657	1971 T	-7:91680499 1324076115 T	
658 V	1972 G	-7:91680498 1324076114 G	V
658	1973 T	-7:91680497 1324076113 T	
658	1974 G	-7:91680496 1324076112 G	
659 Y	1975 T	-7:91680495 1324076111 T	Y
659	1976 A	-7:91680494 1324076110 A	
659	1977 T	-7:91680493 1324076109 T	
660 V	1978 G	-7:91680492 1324076108 G	V
660	1979 T	-7:91680491 1324076107 T	
660	1980 A	-7:91680490 1324076106 A	
661 G	1981 G	-7:91680489 1324076105 G	G
661	1982 G	-7:91680488 1324076104 G	
661	1983 A	-7:91680487 1324076103 A	
662 V	1984 G	-7:91680486 1324076102 G	V
662	1985 T	-7:91680485 1324076101 T	
662	1986 G	-7:91680484 1324076100 G	
663 N	1987 A	-7:91680483 1324076099 A	N
663	1988 A	-7:91680482 1324076098 A	
663	1989 T	-7:91680481 1324076097 T	
664 I	1990 A	-7:91680480 1324076096 A	I
664	1991 T	-7:91680479 1324076095 T	
664	1992 A	-7:91680478 1324076094 A	
665 K	1993 A	-7:91680477 1324076093 A	K
665	1994 A	-7:91680476 1324076092 A	
665	1995 A	-7:91680475 1324076091 A	
666 G	1996 G	-7:91680474 1324076090 G	G
666	1997 G	-7:91680473 1324076089 G	
666	1998 A	-7:91680472 1324076088 A	
667 L	1999 C	-7:91680471 1324076087 C	L
667	2000 T	-7:91680470 1324076086 T	
667	2001 T	-7:91680469 1324076085 T	
668 H	2002 C	-7:91680468 1324076084 C	H
668	2003 A	-7:91680467 1324076083 A	
668	2004 T	-7:91680466 1324076082 T	
669 L	2005 C	-7:91680465 1324076081 C	L
669	2006 T	-7:91680464 1324076080 T	
669	2007 C	-7:91680463 1324076079 C	
670 L	2008 C	-7:91680462 1324076078 C	L
670	2009 T	-7:91680461 1324076077 T	
670	2010 C	-7:91680460 1324076076 C	
671 N	2011 A	-7:91680459 1324076075 A	N
671	2012 A	-7:91680458 1324076074 A	
671	2013 C	-7:91680457 1324076073 C	
672 M	2014 A	-7:91680456 1324076072 A	M
672	2015 T	-7:91680455 1324076071 T	
672	2016 G	-7:91680454 1324076070 G	
673 E	2017 G	-7:91680453 1324076069 G	E
673	2018 A	-7:91680452 1324076068 A	
673	2019 A	-7:91680451 1324076067 A	
674 T	2020 A	-7:91680450 1324076066 A	T
674	2021 C	-7:91680449 1324076065 C	
674	2022 T	-7:91680448 1324076064 T	
675 K	2023 A	-7:91680447 1324076063 A	K
675	2024 A	-7:91680446 1324076062 A	
675	2025 G	-7:91680445 1324076061 G	
>ENSP00000344668 
1 M	1 A	-7:91709385 1324105001 A	M
1	2 T	-7:91709384 1324105000 T	
1	3 G	-7:91709383 1324104999 G	
2 G	4 G	-7:91709382 1324104998 G	G
2	5 G	-7:91709381 1324104997 G	
2	6 A	-7:91709380 1324104996 A	
3 N	7 A	-7:91709379 1324104995 A	N
3	8 A	-7:91709378 1324104994 A	
3	9 T	-7:91709377 1324104993 T	
4 P	10 C	-7:91709376 1324104992 C	P
4	11 C	-7:91709375 1324104991 C	
4	12 A	-7:91709374 1324104990 A	
5 E	13 G	-7:91709373 1324104989 G	E
5	14 A	-7:91709372 1324104988 A	
5	15 A	-7:91709371 1324104987 A	
6 N	16 A	-7:91709370 1324104986 A	N
6	17 A	-7:91709369 1324104985 A	
6	18 C	-7:91709368 1324104984 C	
7 I	19 A	-7:91709367 1324104983 A	I
7	20 T	-7:91709366 1324104982 T	
7	21 A	-7:91709365 1324104981 A	
8 E	22 G	-7:91709364 1324104980 G	E
8	23 A	-7:91709363 1324104979 A	
8	24 A	-7:91709362 1324104978 A	
9 D	25 G	-7:91709361 1324104977 G	D
9	26 A	-7:91709360 1324104976 A	
9	27 T	-7:91709359 1324104975 T	
10 A	28 G	-7:91709358 1324104974 G	A
10	29 C	-7:91709357 1324104973 C	
10	30 A	-7:91709356 1324104972 A	
11 Y	31 T	-7:91709355 1324104971 T	Y
11	32 A	-7:91709354 1324104970 A	
11	33 T	-7:91709353 1324104969 T	
12 V	34 G	-7:91709352 1324104968 G	V
12	35 T	-7:91709351 1324104967 T	
12	36 T	-7:91709350 1324104966 T	
13 A	37 G	-7:91709349 1324104965 G	A
13	38 C	-7:91709348 1324104964 C	
13	39 T	-7:91709347 1324104963 T	
14 V	40 G	-7:91709346 1324104962 G	V
14	41 T	-7:91709345 1324104961 T	
14	42 T	-7:91709344 1324104960 T	
15 I	43 A	-7:91709343 1324104959 A	I
15	44 T	-7:91709342 1324104958 T	
15	45 T	-7:91709341 1324104957 T	
16 R	46 C	-7:91709340 1324104956 C	R
16	47 G	-7:91709339 1324104955 G	
16	48 T	-7:91709338 1324104954 T	
17 P	49 C	-7:91709337 1324104953 C	P
17	50 C	-7:91709336 1324104952 C	
17	51 A	-7:91709335 1324104951 A	
18 K	52 A	-7:91709334 1324104950 A	K
18	53 A	-7:91709333 1324104949 A	
18	54 G	-7:91709332 1324104948 G	
19 N	55 A	-7:91709331 1324104947 A	N
19	56 A	-7:91709330 1324104946 A	
19	57 T	-7:91709329 1324104945 T	
20 T	58 A	-7:91709328 1324104944 A	T
20	59 C	-7:91709327 1324104943 C	
20	60 T	-7:91709326 1324104942 T	
21 A	61 G	-7:91709325 1324104941 G	A
21	62 C	-7:91709324 1324104940 C	
21	63 C	-7:91709323 1324104939 C	
22 S	64 A	-7:91709322 1324104938 A	S
22	65 G	-7:91709321 1324104937 G	
22	66 T	-7:91709320 1324104936 T	
23 L	67 C	-7:91709319 1324104935 C	L
23	68 T	-7:91709318 1324104934 T	
23	69 C	-7:91709317 1324104933 C	
24 N	70 A	-7:91709316 1324104932 A	N
24	71 A	-7:91709315 1324104931 A	
24	72 T	-7:91709314 1324104930 T	
25 S	73 T	-7:91709313 1324104929 T	S
25	74 C	-7:91709312 1324104928 C	
25	75 T	-7:91709311 1324104927 T	
26 R	76 C	-7:91709310 1324104926 C	R
26	77 G	-7:91709309 1324104925 G	
26	78 G	-7:91709308 1324104924 G	
27 E	79 G	-7:91709307 1324104923 G	E
27	80 A	-7:91709306 1324104922 A	
27	81 A	-7:91709305 1324104921 A	
28 Y	82 T	-7:91709304 1324104920 T	Y
28	83 A	-7:91709303 1324104919 A	
28	84 C	-7:91709302 1324104918 C	
29 R	85 A	-7:91709301 1324104917 A	R
29	86 G	-7:91709300 1324104916 G	
29	87 A	-7:91709299 1324104915 A	
30 A	88 G	-7:91709298 1324104914 G	A
30	89 C	-7:91709297 1324104913 C	
30	90 T	-7:91709296 1324104912 T	
31 K	91 A	-7:91709295 1324104911 A	K
31	92 A	-7:91709294 1324104910 A	
31	93 G	-7:91709293 1324104909 G	
32 S	94 T	-7:91709292 1324104908 T	S
32	95 C	-7:91709291 1324104907 C	
32	96 A	-7:91709290 1324104906 A	
33 Y	97 T	-7:91709289 1324104905 T	Y
33	98 A	-7:91709288 1324104904 A	
33	99 T	-7:91709287 1324104903 T	
34 E	100 G	-7:91709286 1324104902 G	E
34	101 A	-7:91709285 1324104901 A	
34	102 A	-7:91709284 1324104900 A	
35 I	103 A	-7:91708402 1324104018 A	I
35	104 T	-7:91708401 1324104017 T	
35	105 T	-7:91708400 1324104016 T	
36 L	106 T	-7:91708399 1324104015 T	L
36	107 T	-7:91708398 1324104014 T	
36	108 G	-7:91708397 1324104013 G	
37 L	109 T	-7:91708396 1324104012 T	L
37	110 T	-7:91708395 1324104011 T	
37	111 G	-7:91708394 1324104010 G	
38 H	112 C	-7:91708393 1324104009 C	H
38	113 A	-7:91708392 1324104008 A	
38	114 T	-7:91708391 1324104007 T	
39 E	115 G	-7:91708390 1324104006 G	E
39	116 A	-7:91708389 1324104005 A	
39	117 A	-7:91708388 1324104004 A	
40 V	118 G	-7:91708387 1324104003 G	V
40	119 T	-7:91708386 1324104002 T	
40	120 T	-7:91708385 1324104001 T	
41 P	121 C	-7:91708384 1324104000 C	P
41	122 C	-7:91708383 1324103999 C	
41	123 C	-7:91708382 1324103998 C	
42 I	124 A	-7:91708381 1324103997 A	I
42	125 T	-7:91708380 1324103996 T	
42	126 T	-7:91708379 1324103995 T	
43 E	127 G	-7:91708378 1324103994 G	E
43	128 A	-7:91708377 1324103993 A	
43	129 A	-7:91708376 1324103992 A	
44 G	130 G	-7:91708375 1324103991 G	G
44	131 G	-7:91708374 1324103990 G	
44	132 A	-7:91708373 1324103989 A	
45 Q	133 C	-7:91708372 1324103988 C	Q
45	134 A	-7:91708371 1324103987 A	
45	135 G	-7:91708370 1324103986 G	
46 K	136 A	-7:91708369 1324103985 A	K
46	137 A	-7:91708368 1324103984 A	
46	138 A	-7:91708367 1324103983 A	
47 K	139 A	-7:91708366 1324103982 A	K
47	140 A	-7:91708365 1324103981 A	
47	141 A	-7:91708364 1324103980 A	
48 K	142 A	-7:91708363 1324103979 A	K
48	143 A	-7:91708362 1324103978 A	
48	144 G	-7:91708361 1324103977 G	
49 R	145 A	-7:91708360 1324103976 A	R
49	146 G	-7:91708359 1324103975 G	
49	147 A	-7:91708358 1324103974 A	
50 K	148 A	-7:91708357 1324103973 A	K
50	149 A	-7:91708356 1324103972 A	
50	150 G	-7:91708355 1324103971 G	
51 K	151 A	-7:91708354 1324103970 A	K
51	152 A	-7:91708353 1324103969 A	
51	153 A	-7:91708352 1324103968 A	
52 V	154 G	-7:91708351 1324103967 G	V
52	155 T	-7:91708350 1324103966 T	
52	156 T	-7:91708349 1324103965 T	
53 L	157 T	-7:91708348 1324103964 T	L
53	158 T	-7:91708347 1324103963 T	
53	159 A	-7:91708346 1324103962 A	
54 L	160 T	-7:91708345 1324103961 T	L
54	161 T	-7:91708344 1324103960 T	
54	162 G	-7:91708343 1324103959 G	
55 E	163 G	-7:91708342 1324103958 G	E
55	164 A	-7:91708341 1324103957 A	
55	165 A	-7:91708340 1324103956 A	
56 T	166 A	-7:91708339 1324103955 A	T
56	167 C	-7:91708338 1324103954 C	
56	168 G	-7:91708337 1324103953 G	
57 K	169 A	-7:91708336 1324103952 A	K
57	170 A	-7:91708335 1324103951 A	
57	171 A	-7:91708334 1324103950 A	
58 L	172 C	-7:91708333 1324103949 C	L
58	173 T	-7:91708332 1324103948 T	
58	174 T	-7:91708331 1324103947 T	
59 Q	175 C	-7:91708330 1324103946 C	Q
59	176 A	-7:91708329 1324103945 A	
59	177 A	-7:91708328 1324103944 A	
60 G	178 G	-7:91708327 1324103943 G	G
60	179 G	-7:91708326 1324103942 G	
60	180 C	-7:91708325 1324103941 C	
61 N	181 A	-7:91708324 1324103940 A	N
61	182 A	-7:91708323 1324103939 A	
61	183 C	-7:91708322 1324103938 C	
62 S	184 A	-7:91708321 1324103937 A	S
62	185 G	-7:91708320 1324103936 G	
62	186 T	-7:91708319 1324103935 T	
63 E	187 G	-7:91708318 1324103934 G	E
63	188 A	-7:91708317 1324103933 A	
63	189 A	-7:91708316 1324103932 A	
64 I	190 A	-7:91708315 1324103931 A	I
64	191 T	-7:91708314 1324103930 T	
64	192 A	-7:91708313 1324103929 A	
65 T	193 A	-7:91708312 1324103928 A	T
65	194 C	-7:91708311 1324103927 C	
65	195 A	-7:91708310 1324103926 A	
66 Q	196 C	-7:91708309 1324103925 C	Q
66	197 A	-7:91708308 1324103924 A	
66	198 A	-7:91708307 1324103923 A	
67 G	199 G	-7:91708306 1324103922 G	G
67	200 G	-7:91708305 1324103921 G	
67	201 C	-7:91708304 1324103920 C	
68 I	202 A	-7:91708303 1324103919 A	I
68	203 T	-7:91708302 1324103918 T	
68	204 A	-7:91708301 1324103917 A	
69 L	205 T	-7:91708300 1324103916 T	L
69	206 T	-7:91708299 1324103915 T	
69	207 G	-7:91708298 1324103914 G	
70 D	208 G	-7:91708297 1324103913 G	D
70	209 A	-7:91708296 1324103912 A	
70	210 T	-7:91708295 1324103911 T	
71 Y	211 T	-7:91708294 1324103910 T	Y
71	212 A	-7:91708293 1324103909 A	
71	213 C	-7:91708292 1324103908 C	
72 V	214 G	-7:91708291 1324103907 G	V
72	215 T	-7:91708290 1324103906 T	
72	216 A	-7:91708289 1324103905 A	
73 V	217 G	-7:91708288 1324103904 G	V
73	218 T	-7:91708287 1324103903 T	
73	219 A	-7:91708286 1324103902 A	
74 E	220 G	-7:91708285 1324103901 G	E
74	221 A	-7:91708284 1324103900 A	
74	222 A	-7:91708283 1324103899 A	
75 T	223 A	-7:91708282 1324103898 A	T
75	224 C	-7:91708281 1324103897 C	
75	225 C	-7:91708280 1324103896 C	
76 T	226 A	-7:91708279 1324103895 A	T
76	227 C	-7:91708278 1324103894 C	
76	228 C	-7:91708277 1324103893 C	
77 K	229 A	-7:91708276 1324103892 A	K
77	230 A	-7:91708275 1324103891 A	
77	231 A	-7:91708274 1324103890 A	
78 P	232 C	-7:91708273 1324103889 C	P
78	233 C	-7:91708272 1324103888 C	
78	234 A	-7:91708271 1324103887 A	
79 I	235 A	-7:91708270 1324103886 A	I
79	236 T	-7:91708269 1324103885 T	
79	237 T	-7:91708268 1324103884 T	
80 S	238 T	-7:91708267 1324103883 T	S
80	239 C	-7:91708266 1324103882 C	
80	240 T	-7:91708265 1324103881 T	
81 P	241 C	-7:91708264 1324103880 C	P
81	242 C	-7:91708263 1324103879 C	
81	243 T	-7:91708262 1324103878 T	
82 A	244 G	-7:91708261 1324103877 G	A
82	245 C	-7:91708260 1324103876 C	
82	246 A	-7:91708259 1324103875 A	
83 N	247 A	-7:91708258 1324103874 A	N
83	248 A	-7:91708257 1324103873 A	
83	249 C	-7:91708256 1324103872 C	
84 Q	250 C	-7:91708255 1324103871 C	Q
84	251 A	-7:91708254 1324103870 A	
84	252 G	-7:91708253 1324103869 G	
85 G	253 G	-7:91708252 1324103868 G	G
85	254 G	-7:91708251 1324103867 G	
85	255 T	-7:91708250 1324103866 T	
86 I	256 A	-7:91708249 1324103865 A	I
86	257 T	-7:91708248 1324103864 T	
86	258 C	-7:91708247 1324103863 C	
87 R	259 A	-7:91708246 1324103862 A	R
87	260 G	-7:91708245 1324103861 G	
87	261 A	-7:91708244 1324103860 A	
88 G	262 G	-7:91708243 1324103859 G	G
88	263 G	-7:91705009 1324100625 G	
88	264 A	-7:91705008 1324100624 A	
89 K	265 A	-7:91705007 1324100623 A	K
89	266 A	-7:91705006 1324100622 A	
89	267 A	-7:91705005 1324100621 A	
90 R	268 C	-7:91705004 1324100620 C	R
90	269 G	-7:91705003 1324100619 G	
90	270 A	-7:91705002 1324100618 A	
91 V	271 G	-7:91705001 1324100617 G	V
91	272 T	-7:91705000 1324100616 T	
91	273 T	-7:91704999 1324100615 T	
92 V	274 G	-7:91704998 1324100614 G	V
92	275 T	-7:91704997 1324100613 T	
92	276 A	-7:91704996 1324100612 A	
93 L	277 C	-7:91704995 1324100611 C	L
93	278 T	-7:91704994 1324100610 T	
93	279 A	-7:91704993 1324100609 A	
94 M	280 A	-7:91704992 1324100608 A	M
94	281 T	-7:91704991 1324100607 T	
94	282 G	-7:91704990 1324100606 G	
95 K	283 A	-7:91704989 1324100605 A	K
95	284 A	-7:91704988 1324100604 A	
95	285 A	-7:91704987 1324100603 A	
96 K	286 A	-7:91704986 1324100602 A	K
96	287 A	-7:91704985 1324100601 A	
96	288 A	-7:91704984 1324100600 A	
97 F	289 T	-7:91704983 1324100599 T	F
97	290 T	-7:91704982 1324100598 T	
97	291 T	-7:91704981 1324100597 T	
98 P	292 C	-7:91704980 1324100596 C	P
98	293 C	-7:91704979 1324100595 C	
98	294 T	-7:91704978 1324100594 T	
99 L	295 C	-7:91704977 1324100593 C	L
99	296 T	-7:91704976 1324100592 T	
99	297 G	-7:91704975 1324100591 G	
100 D	298 G	-7:91704974 1324100590 G	D
100	299 A	-7:91704973 1324100589 A	
100	300 T	-7:91704972 1324100588 T	
101 G	301 G	-7:91704971 1324100587 G	G
101	302 G	-7:91704970 1324100586 G	
101	303 A	-7:91704969 1324100585 A	
102 E	304 G	-7:91704968 1324100584 G	E
102	305 A	-7:91704967 1324100583 A	
102	306 G	-7:91704966 1324100582 G	
103 K	307 A	-7:91704965 1324100581 A	K
103	308 A	-7:91704964 1324100580 A	
103	309 G	-7:91704963 1324100579 G	
104 M	310 A	-7:91704962 1324100578 A	M
104	311 T	-7:91704961 1324100577 T	
104	312 G	-7:91704960 1324100576 G	
105 G	313 G	-7:91704959 1324100575 G	G
105	314 G	-7:91704958 1324100574 G	
105	315 C	-7:91704957 1324100573 C	
106 R	316 A	-7:91704956 1324100572 A	R
106	317 G	-7:91704955 1324100571 G	
106	318 A	-7:91704954 1324100570 A	
107 E	319 G	-7:91704953 1324100569 G	E
107	320 A	-7:91704952 1324100568 A	
107	321 A	-7:91704951 1324100567 A	
108 A	322 G	-7:91704950 1324100566 G	A
108	323 C	-7:91704949 1324100565 C	
108	324 A	-7:91704948 1324100564 A	
109 S	325 T	-7:91704947 1324100563 T	S
109	326 C	-7:91704946 1324100562 C	
109	327 A	-7:91704945 1324100561 A	
110 L	328 T	-7:91704944 1324100560 T	L
110	329 T	-7:91704943 1324100559 T	
110	330 A	-7:91704942 1324100558 A	
111 F	331 T	-7:91704941 1324100557 T	F
111	332 T	-7:91704940 1324100556 T	
111	333 T	-7:91704939 1324100555 T	
112 I	334 A	-7:91704938 1324100554 A	I
112	335 T	-7:91704937 1324100553 T	
112	336 T	-7:91704936 1324100552 T	
113 V	337 G	-7:91704935 1324100551 G	V
113	338 T	-7:91704934 1324100550 T	
113	339 T	-7:91704933 1324100549 T	
114 P	340 C	-7:91704932 1324100548 C	P
114	341 C	-7:91704931 1324100547 C	
114	342 A	-7:91704930 1324100546 A	
115 S	343 T	-7:91704929 1324100545 T	S
115	344 C	-7:91704928 1324100544 C	
115	345 A	-7:91704927 1324100543 A	
116 V	346 G	-7:91704926 1324100542 G	V
116	347 T	-7:91704925 1324100541 T	
116	348 T	-7:91704924 1324100540 T	
117 V	349 G	-7:91704923 1324100539 G	V
117	350 T	-7:91704922 1324100538 T	
117	351 C	-7:91704921 1324100537 C	
118 K	352 A	-7:91704920 1324100536 A	K
118	353 A	-7:91704919 1324100535 A	
118	354 A	-7:91704918 1324100534 A	
119 D	355 G	-7:91704917 1324100533 G	D
119	356 A	-7:91703792 1324099408 A	
119	357 T	-7:91703791 1324099407 T	
120 N	358 A	-7:91703790 1324099406 A	N
120	359 A	-7:91703789 1324099405 A	
120	360 T	-7:91703788 1324099404 T	
121 T	361 A	-7:91703787 1324099403 A	T
121	362 C	-7:91703786 1324099402 C	
121	363 T	-7:91703785 1324099401 T	
122 K	364 A	-7:91703784 1324099400 A	K
122	365 A	-7:91703783 1324099399 A	
122	366 A	-7:91703782 1324099398 A	
123 Y	367 T	-7:91703781 1324099397 T	Y
123	368 A	-7:91703780 1324099396 A	
123	369 C	-7:91703779 1324099395 C	
124 T	370 A	-7:91703778 1324099394 A	T
124	371 C	-7:91703777 1324099393 C	
124	372 A	-7:91703776 1324099392 A	
125 Y	373 T	-7:91703775 1324099391 T	Y
125	374 A	-7:91703774 1324099390 A	
125	375 T	-7:91703773 1324099389 T	
126 T	376 A	-7:91703772 1324099388 A	T
126	377 C	-7:91703771 1324099387 C	
126	378 C	-7:91703770 1324099386 C	
127 P	379 C	-7:91703769 1324099385 C	P
127	380 C	-7:91703768 1324099384 C	
127	381 A	-7:91703767 1324099383 A	
128 G	382 G	-7:91703766 1324099382 G	G
128	383 G	-7:91703765 1324099381 G	
128	384 A	-7:91703764 1324099380 A	
129 C	385 T	-7:91703763 1324099379 T	C
129	386 G	-7:91703762 1324099378 G	
129	387 C	-7:91703761 1324099377 C	
130 P	388 C	-7:91703760 1324099376 C	P
130	389 C	-7:91703759 1324099375 C	
130	390 A	-7:91703758 1324099374 A	
131 I	391 A	-7:91703757 1324099373 A	I
131	392 T	-7:91703756 1324099372 T	
131	393 T	-7:91703755 1324099371 T	
132 F	394 T	-7:91703754 1324099370 T	F
132	395 T	-7:91703753 1324099369 T	
132	396 T	-7:91703752 1324099368 T	
133 Y	397 T	-7:91703751 1324099367 T	Y
133	398 A	-7:91703750 1324099366 A	
133	399 C	-7:91703749 1324099365 C	
134 C	400 T	-7:91703748 1324099364 T	C
134	401 G	-7:91703747 1324099363 G	
134	402 C	-7:91703746 1324099362 C	
135 L	403 T	-7:91703745 1324099361 T	L
135	404 T	-7:91703744 1324099360 T	
135	405 A	-7:91703743 1324099359 A	
136 Q	406 C	-7:91703742 1324099358 C	Q
136	407 A	-7:91703741 1324099357 A	
136	408 A	-7:91703740 1324099356 A	
137 D	409 G	-7:91703739 1324099355 G	D
137	410 A	-7:91703738 1324099354 A	
137	411 T	-7:91703737 1324099353 T	
138 I	412 A	-7:91703736 1324099352 A	I
138	413 T	-7:91703735 1324099351 T	
138	414 T	-7:91703734 1324099350 T	
139 M	415 A	-7:91703733 1324099349 A	M
139	416 T	-7:91703732 1324099348 T	
139	417 G	-7:91703731 1324099347 G	
140 R	418 C	-7:91703730 1324099346 C	R
140	419 G	-7:91703729 1324099345 G	
140	420 A	-7:91703728 1324099344 A	
141 V	421 G	-7:91703727 1324099343 G	V
141	422 T	-7:91703726 1324099342 T	
141	423 C	-7:91703725 1324099341 C	
142 C	424 T	-7:91703724 1324099340 T	C
142	425 G	-7:91703723 1324099339 G	
142	426 T	-7:91703722 1324099338 T	
143 S	427 A	-7:91703721 1324099337 A	S
143	428 G	-7:91703720 1324099336 G	
143	429 T	-7:91703719 1324099335 T	
144 E	430 G	-7:91703718 1324099334 G	E
144	431 A	-7:91703717 1324099333 A	
144	432 A	-7:91703716 1324099332 A	
145 S	433 T	-7:91703715 1324099331 T	S
145	434 C	-7:91703714 1324099330 C	
145	435 C	-7:91703713 1324099329 C	
146 S	436 A	-7:91703712 1324099328 A	S
146	437 G	-7:91703711 1324099327 G	
146	438 T	-7:91703710 1324099326 T	
147 T	439 A	-7:91703709 1324099325 A	T
147	440 C	-7:91703708 1324099324 C	
147	441 T	-7:91703707 1324099323 T	
148 H	442 C	-7:91703706 1324099322 C	H
148	443 A	-7:91703705 1324099321 A	
148	444 T	-7:91703704 1324099320 T	
149 F	445 T	-7:91703703 1324099319 T	F
149	446 T	-7:91703702 1324099318 T	
149	447 T	-7:91703701 1324099317 T	
150 A	448 G	-7:91703700 1324099316 G	A
150	449 C	-7:91703699 1324099315 C	
150	450 T	-7:91703698 1324099314 T	
151 T	451 A	-7:91703697 1324099313 A	T
151	452 C	-7:91703696 1324099312 C	
151	453 A	-7:91703695 1324099311 A	
152 L	454 C	-7:91703694 1324099310 C	L
152	455 T	-7:91703693 1324099309 T	
152	456 T	-7:91703692 1324099308 T	
153 T	457 A	-7:91703691 1324099307 A	T
153	458 C	-7:91703690 1324099306 C	
153	459 A	-7:91703689 1324099305 A	
154 A	460 G	-7:91703688 1324099304 G	A
154	461 C	-7:91703687 1324099303 C	
154	462 A	-7:91703686 1324099302 A	
155 R	463 A	-7:91703685 1324099301 A	R
155	464 G	-7:91703684 1324099300 G	
155	465 G	-7:91703683 1324099299 G	
156 M	466 A	-7:91703682 1324099298 A	M
156	467 T	-7:91703681 1324099297 T	
156	468 G	-7:91703680 1324099296 G	
157 L	469 T	-7:91703679 1324099295 T	L
157	470 T	-7:91703678 1324099294 T	
157	471 A	-7:91703677 1324099293 A	
158 I	472 A	-7:91703676 1324099292 A	I
158	473 T	-7:91703675 1324099291 T	
158	474 A	-7:91703674 1324099290 A	
159 A	475 G	-7:91703673 1324099289 G	A
159	476 C	-7:91703672 1324099288 C	
159	477 C	-7:91703671 1324099287 C	
160 L	478 T	-7:91703670 1324099286 T	L
160	479 T	-7:91703669 1324099285 T	
160	480 G	-7:91703668 1324099284 G	
161 D	481 G	-7:91703667 1324099283 G	D
161	482 A	-7:91703666 1324099282 A	
161	483 T	-7:91703665 1324099281 T	
162 K	484 A	-7:91703664 1324099280 A	K
162	485 A	-7:91703663 1324099279 A	
162	486 G	-7:91702896 1324098512 G	
163 W	487 T	-7:91702895 1324098511 T	W
163	488 G	-7:91702894 1324098510 G	
163	489 G	-7:91702893 1324098509 G	
164 L	490 T	-7:91702892 1324098508 T	L
164	491 T	-7:91702891 1324098507 T	
164	492 A	-7:91702890 1324098506 A	
165 D	493 G	-7:91702889 1324098505 G	D
165	494 A	-7:91702888 1324098504 A	
165	495 T	-7:91702887 1324098503 T	
166 E	496 G	-7:91702886 1324098502 G	E
166	497 A	-7:91702885 1324098501 A	
166	498 A	-7:91702884 1324098500 A	
167 R	499 C	-7:91702883 1324098499 C	R
167	500 G	-7:91702882 1324098498 G	
167	501 T	-7:91702881 1324098497 T	
168 H	502 C	-7:91702880 1324098496 C	H
168	503 A	-7:91702879 1324098495 A	
168	504 T	-7:91702878 1324098494 T	
169 A	505 G	-7:91702877 1324098493 G	A
169	506 C	-7:91702876 1324098492 C	
169	507 A	-7:91702875 1324098491 A	
170 Q	508 C	-7:91702874 1324098490 C	Q
170	509 A	-7:91702873 1324098489 A	
170	510 A	-7:91702872 1324098488 A	
171 S	511 T	-7:91702871 1324098487 T	S
171	512 C	-7:91702870 1324098486 C	
171	513 T	-7:91702869 1324098485 T	
172 H	514 C	-7:91702868 1324098484 C	H
172	515 A	-7:91702867 1324098483 A	
172	516 C	-7:91702866 1324098482 C	
173 F	517 T	-7:91702865 1324098481 T	F
173	518 T	-7:91702864 1324098480 T	
173	519 T	-7:91702863 1324098479 T	
174 I	520 A	-7:91702862 1324098478 A	I
174	521 T	-7:91702861 1324098477 T	
174	522 T	-7:91702860 1324098476 T	
175 P	523 C	-7:91702859 1324098475 C	P
175	524 C	-7:91702858 1324098474 C	
175	525 A	-7:91702857 1324098473 A	
176 A	526 G	-7:91702856 1324098472 G	A
176	527 C	-7:91702855 1324098471 C	
176	528 T	-7:91702854 1324098470 T	
177 L	529 T	-7:91702853 1324098469 T	L
177	530 T	-7:91702852 1324098468 T	
177	531 A	-7:91702851 1324098467 A	
178 F	532 T	-7:91702850 1324098466 T	F
178	533 T	-7:91702849 1324098465 T	
178	534 C	-7:91702848 1324098464 C	
179 R	535 C	-7:91702847 1324098463 C	R
179	536 G	-7:91702846 1324098462 G	
179	537 A	-7:91702845 1324098461 A	
180 P	538 C	-7:91702844 1324098460 C	P
180	539 C	-7:91702843 1324098459 C	
180	540 T	-7:91702842 1324098458 T	
181 S	541 T	-7:91702841 1324098457 T	S
181	542 C	-7:91702840 1324098456 C	
181	543 T	-7:91702839 1324098455 T	
182 P	544 C	-7:91702838 1324098454 C	P
182	545 C	-7:91702837 1324098453 C	
182	546 T	-7:91702836 1324098452 T	
183 L	547 C	-7:91702835 1324098451 C	L
183	548 T	-7:91702834 1324098450 T	
183	549 T	-7:91702833 1324098449 T	
184 E	550 G	-7:91702832 1324098448 G	E
184	551 A	-7:91702831 1324098447 A	
184	552 G	-7:91702830 1324098446 G	
185 R	553 C	-7:91702829 1324098445 C	R
185	554 G	-7:91702828 1324098444 G	
185	555 G	-7:91702827 1324098443 G	
186 I	556 A	-7:91702826 1324098442 A	I
186	557 T	-7:91702825 1324098441 T	
186	558 A	-7:91702824 1324098440 A	
187 K	559 A	-7:91702823 1324098439 A	K
187	560 A	-7:91702822 1324098438 A	
187	561 A	-7:91702821 1324098437 A	
188 T	562 A	-7:91702820 1324098436 A	T
188	563 C	-7:91702819 1324098435 C	
188	564 T	-7:91702818 1324098434 T	
189 N	565 A	-7:91702817 1324098433 A	N
189	566 A	-7:91702816 1324098432 A	
189	567 T	-7:91702815 1324098431 T	
190 V	568 G	-7:91702814 1324098430 G	V
190	569 T	-7:91702813 1324098429 T	
190	570 C	-7:91702812 1324098428 C	
191 I	571 A	-7:91702811 1324098427 A	I
191	572 T	-7:91702810 1324098426 T	
191	573 A	-7:91702809 1324098425 A	
192 N	574 A	-7:91702808 1324098424 A	N
192	575 A	-7:91702807 1324098423 A	
192	576 T	-7:91702806 1324098422 T	
193 P	577 C	-7:91702805 1324098421 C	P
193	578 C	-7:91702804 1324098420 C	
193	579 T	-7:91702803 1324098419 T	
194 A	580 G	-7:91702802 1324098418 G	A
194	581 C	-7:91702801 1324098417 C	
194	582 A	-7:91702800 1324098416 A	
195 Y	583 T	-7:91702799 1324098415 T	Y
195	584 A	-7:91702798 1324098414 A	
195	585 T	-7:91702797 1324098413 T	
196 A	586 G	-7:91702796 1324098412 G	A
196	587 C	-7:91702795 1324098411 C	
196	588 T	-7:91702794 1324098410 T	
197 T	589 A	-7:91702793 1324098409 A	T
197	590 C	-7:91702792 1324098408 C	
197	591 T	-7:91702791 1324098407 T	
198 E	592 G	-7:91702790 1324098406 G	E
198	593 A	-7:91702789 1324098405 A	
198	594 A	-7:91702788 1324098404 A	
199 S	595 T	-7:91702787 1324098403 T	S
199	596 C	-7:91702786 1324098402 C	
199	597 A	-7:91702785 1324098401 A	
200 G	598 G	-7:91702784 1324098400 G	G
200	599 G	-7:91702783 1324098399 G	
200	600 T	-7:91702782 1324098398 T	
201 Q	601 C	-7:91702781 1324098397 C	Q
201	602 A	-7:91702780 1324098396 A	
201	603 G	-7:91702779 1324098395 G	
202 T	604 A	-7:91702778 1324098394 A	T
202	605 C	-7:91702777 1324098393 C	
202	606 A	-7:91702776 1324098392 A	
203 E	607 G	-7:91702775 1324098391 G	E
203	608 A	-7:91702774 1324098390 A	
203	609 A	-7:91702773 1324098389 A	
204 N	610 A	-7:91702772 1324098388 A	N
204	611 A	-7:91702771 1324098387 A	
204	612 C	-7:91702770 1324098386 C	
205 S	613 T	-7:91702769 1324098385 T	S
205	614 C	-7:91702768 1324098384 C	
205	615 A	-7:91702767 1324098383 A	
206 L	616 C	-7:91702766 1324098382 C	L
206	617 T	-7:91702765 1324098381 T	
206	618 A	-7:91702764 1324098380 A	
207 H	619 C	-7:91702763 1324098379 C	H
207	620 A	-7:91702762 1324098378 A	
207	621 T	-7:91702761 1324098377 T	
208 M	622 A	-7:91702760 1324098376 A	M
208	623 T	-7:91702759 1324098375 T	
208	624 G	-7:91702758 1324098374 G	
209 G	625 G	-7:91702757 1324098373 G	G
209	626 G	-7:91702756 1324098372 G	
209	627 C	-7:91702755 1324098371 C	
210 Y	628 T	-7:91702754 1324098370 T	Y
210	629 A	-7:91702753 1324098369 A	
210	630 T	-7:91702752 1324098368 T	
211 S	631 A	-7:91702751 1324098367 A	S
211	632 G	-7:91702750 1324098366 G	
211	633 T	-7:91702749 1324098365 T	
212 A	634 G	-7:91702748 1324098364 G	A
212	635 C	-7:91702747 1324098363 C	
212	636 A	-7:91702746 1324098362 A	
213 L	637 C	-7:91702745 1324098361 C	L
213	638 T	-7:91702744 1324098360 T	
213	639 A	-7:91702743 1324098359 A	
214 E	640 G	-7:91702742 1324098358 G	E
214	641 A	-7:91702741 1324098357 A	
214	642 A	-7:91702740 1324098356 A	
215 I	643 A	-7:91702739 1324098355 A	I
215	644 T	-7:91702738 1324098354 T	
215	645 A	-7:91702737 1324098353 A	
216 K	646 A	-7:91702736 1324098352 A	K
216	647 A	-7:91702735 1324098351 A	
216	648 G	-7:91702734 1324098350 G	
217 S	649 A	-7:91702733 1324098349 A	S
217	650 G	-7:91702732 1324098348 G	
217	651 T	-7:91702731 1324098347 T	
218 K	652 A	-7:91702730 1324098346 A	K
218	653 A	-7:91702729 1324098345 A	
218	654 A	-7:91702728 1324098344 A	
219 M	655 A	-7:91702727 1324098343 A	M
219	656 T	-7:91702726 1324098342 T	
219	657 G	-7:91702725 1324098341 G	
220 L	658 T	-7:91702724 1324098340 T	L
220	659 T	-7:91702723 1324098339 T	
220	660 A	-7:91702722 1324098338 A	
221 A	661 G	-7:91702721 1324098337 G	A
221	662 C	-7:91702720 1324098336 C	
221	663 C	-7:91702719 1324098335 C	
222 L	664 C	-7:91702718 1324098334 C	L
222	665 T	-7:91702717 1324098333 T	
222	666 A	-7:91702716 1324098332 A	
223 E	667 G	-7:91702715 1324098331 G	E
223	668 A	-7:91702714 1324098330 A	
223	669 G	-7:91702713 1324098329 G	
224 K	670 A	-7:91702712 1324098328 A	K
224	671 A	-7:91702711 1324098327 A	
224	672 A	-7:91702710 1324098326 A	
225 A	673 G	-7:91702709 1324098325 G	A
225	674 C	-7:91702708 1324098324 C	
225	675 A	-7:91702707 1324098323 A	
226 D	676 G	-7:91702706 1324098322 G	D
226	677 A	-7:91702705 1324098321 A	
226	678 T	-7:91702704 1324098320 T	
227 T	679 A	-7:91702703 1324098319 A	T
227	680 C	-7:91702702 1324098318 C	
227	681 C	-7:91702701 1324098317 C	
228 C	682 T	-7:91702700 1324098316 T	C
228	683 G	-7:91702699 1324098315 G	
228	684 T	-7:91702698 1324098314 T	
229 I	685 A	-7:91702697 1324098313 A	I
229	686 T	-7:91702696 1324098312 T	
229	687 T	-7:91702695 1324098311 T	
230 Y	688 T	-7:91702694 1324098310 T	Y
230	689 A	-7:91702693 1324098309 A	
230	690 C	-7:91702692 1324098308 C	
231 N	691 A	-7:91702691 1324098307 A	N
231	692 A	-7:91702690 1324098306 A	
231	693 C	-7:91702689 1324098305 C	
232 P	694 C	-7:91702688 1324098304 C	P
232	695 C	-7:91702687 1324098303 C	
232	696 T	-7:91702686 1324098302 T	
233 L	697 T	-7:91702685 1324098301 T	L
233	698 T	-7:91702684 1324098300 T	
233	699 G	-7:91702683 1324098299 G	
234 F	700 T	-7:91702682 1324098298 T	F
234	701 T	-7:91702681 1324098297 T	
234	702 T	-7:91702680 1324098296 T	
235 G	703 G	-7:91702679 1324098295 G	G
235	704 G	-7:91702678 1324098294 G	
235	705 A	-7:91702677 1324098293 A	
236 S	706 T	-7:91702676 1324098292 T	S
236	707 C	-7:91702675 1324098291 C	
236	708 A	-7:91702674 1324098290 A	
237 D	709 G	-7:91702673 1324098289 G	D
237	710 A	-7:91702672 1324098288 A	
237	711 T	-7:91702671 1324098287 T	
238 L	712 C	-7:91702670 1324098286 C	L
238	713 T	-7:91702669 1324098285 T	
238	714 T	-7:91702668 1324098284 T	
239 Q	715 C	-7:91702667 1324098283 C	Q
239	716 A	-7:91702666 1324098282 A	
239	717 G	-7:91702665 1324098281 G	
240 Y	718 T	-7:91702664 1324098280 T	Y
240	719 A	-7:91702663 1324098279 A	
240	720 T	-7:91702662 1324098278 T	
241 T	721 A	-7:91702661 1324098277 A	T
241	722 C	-7:91702660 1324098276 C	
241	723 A	-7:91702659 1324098275 A	
242 N	724 A	-7:91702658 1324098274 A	N
242	725 A	-7:91702657 1324098273 A	
242	726 T	-7:91702656 1324098272 T	
243 R	727 C	-7:91702655 1324098271 C	R
243	728 G	-7:91702654 1324098270 G	
243	729 G	-7:91702653 1324098269 G	
244 V	730 G	-7:91702173 1324097789 G	V
244	731 T	-7:91702172 1324097788 T	
244	732 A	-7:91702171 1324097787 A	
245 D	733 G	-7:91702170 1324097786 G	D
245	734 A	-7:91702169 1324097785 A	
245	735 T	-7:91702168 1324097784 T	
246 K	736 A	-7:91702167 1324097783 A	K
246	737 A	-7:91702166 1324097782 A	
246	738 A	-7:91702165 1324097781 A	
247 V	739 G	-7:91702164 1324097780 G	V
247	740 T	-7:91702163 1324097779 T	
247	741 G	-7:91702162 1324097778 G	
248 V	742 G	-7:91702161 1324097777 G	V
248	743 T	-7:91702160 1324097776 T	
248	744 A	-7:91702159 1324097775 A	
249 I	745 A	-7:91702158 1324097774 A	I
249	746 T	-7:91702157 1324097773 T	
249	747 A	-7:91702156 1324097772 A	
250 N	748 A	-7:91702155 1324097771 A	N
250	749 A	-7:91702154 1324097770 A	
250	750 T	-7:91702153 1324097769 T	
251 P	751 C	-7:91702152 1324097768 C	P
251	752 C	-7:91702151 1324097767 C	
251	753 A	-7:91702150 1324097766 A	
252 Y	754 T	-7:91702149 1324097765 T	Y
252	755 A	-7:91702148 1324097764 A	
252	756 C	-7:91702147 1324097763 C	
253 F	757 T	-7:91702146 1324097762 T	F
253	758 T	-7:91702145 1324097761 T	
253	759 T	-7:91702144 1324097760 T	
254 G	760 G	-7:91702143 1324097759 G	G
254	761 G	-7:91702142 1324097758 G	
254	762 T	-7:91702141 1324097757 T	
255 L	763 C	-7:91702140 1324097756 C	L
255	764 T	-7:91702139 1324097755 T	
255	765 A	-7:91702138 1324097754 A	
256 G	766 G	-7:91702137 1324097753 G	G
256	767 G	-7:91702136 1324097752 G	
256	768 A	-7:91702135 1324097751 A	
257 A	769 G	-7:91702134 1324097750 G	A
257	770 C	-7:91702133 1324097749 C	
257	771 T	-7:91702132 1324097748 T	
258 P	772 C	-7:91702131 1324097747 C	P
258	773 C	-7:91702130 1324097746 C	
258	774 A	-7:91702129 1324097745 A	
259 D	775 G	-7:91702128 1324097744 G	D
259	776 A	-7:91702127 1324097743 A	
259	777 C	-7:91702126 1324097742 C	
260 Y	778 T	-7:91702125 1324097741 T	Y
260	779 A	-7:91702124 1324097740 A	
260	780 C	-7:91702123 1324097739 C	
261 S	781 T	-7:91702122 1324097738 T	S
261	782 C	-7:91702121 1324097737 C	
261	783 A	-7:91702120 1324097736 A	
262 K	784 A	-7:91702119 1324097735 A	K
262	785 A	-7:91702118 1324097734 A	
262	786 A	-7:91702117 1324097733 A	
263 I	787 A	-7:91702116 1324097732 A	I
263	788 T	-7:91702115 1324097731 T	
263	789 C	-7:91702114 1324097730 C	
264 Q	790 C	-7:91702113 1324097729 C	Q
264	791 A	-7:91702112 1324097728 A	
264	792 A	-7:91702111 1324097727 A	
265 I	793 A	-7:91702110 1324097726 A	I
265	794 T	-7:91702109 1324097725 T	
265	795 A	-7:91702108 1324097724 A	
266 P	796 C	-7:91702107 1324097723 C	P
266	797 C	-7:91702106 1324097722 C	
266	798 T	-7:91702105 1324097721 T	
267 K	799 A	-7:91702104 1324097720 A	K
267	800 A	-7:91702103 1324097719 A	
267	801 A	-7:91702102 1324097718 A	
268 Q	802 C	-7:91702101 1324097717 C	Q
268	803 A	-7:91702100 1324097716 A	
268	804 G	-7:91702099 1324097715 G	
269 E	805 G	-7:91702098 1324097714 G	E
269	806 A	-7:91702097 1324097713 A	
269	807 A	-7:91702096 1324097712 A	
270 K	808 A	-7:91702095 1324097711 A	K
270	809 A	-7:91702094 1324097710 A	
270	810 A	-7:91702093 1324097709 A	
271 W	811 T	-7:91702092 1324097708 T	W
271	812 G	-7:91702091 1324097707 G	
271	813 G	-7:91702090 1324097706 G	
272 Q	814 C	-7:91702089 1324097705 C	Q
272	815 A	-7:91702088 1324097704 A	
272	816 G	-7:91702087 1324097703 G	
273 R	817 A	-7:91702086 1324097702 A	R
273	818 G	-7:91702085 1324097701 G	
273	819 A	-7:91702084 1324097700 A	
274 S	820 A	-7:91702083 1324097699 A	S
274	821 G	-7:91702082 1324097698 G	
274	822 C	-7:91702081 1324097697 C	
275 M	823 A	-7:91702080 1324097696 A	M
275	824 T	-7:91702079 1324097695 T	
275	825 G	-7:91702078 1324097694 G	
276 S	826 A	-7:91702077 1324097693 A	S
276	827 G	-7:91702076 1324097692 G	
276	828 C	-7:91702075 1324097691 C	
277 S	829 A	-7:91702074 1324097690 A	S
277	830 G	-7:91702073 1324097689 G	
277	831 T	-7:91702072 1324097688 T	
278 V	832 G	-7:91702071 1324097687 G	V
278	833 T	-7:91702070 1324097686 T	
278	834 C	-7:91702069 1324097685 C	
279 T	835 A	-7:91702068 1324097684 A	T
279	836 C	-7:91702067 1324097683 C	
279	837 A	-7:91702066 1324097682 A	
280 E	838 G	-7:91702065 1324097681 G	E
280	839 A	-7:91702064 1324097680 A	
280	840 A	-7:91702063 1324097679 A	
281 D	841 G	-7:91702062 1324097678 G	D
281	842 A	-7:91702061 1324097677 A	
281	843 C	-7:91702060 1324097676 C	
282 K	844 A	-7:91702059 1324097675 A	K
282	845 A	-7:91702058 1324097674 A	
282	846 G	-7:91701842 1324097458 G	
283 E	847 G	-7:91701841 1324097457 G	E
283	848 A	-7:91701840 1324097456 A	
283	849 A	-7:91701839 1324097455 A	
284 R	850 C	-7:91701838 1324097454 C	R
284	851 G	-7:91701837 1324097453 G	
284	852 A	-7:91701836 1324097452 A	
285 Q	853 C	-7:91701835 1324097451 C	Q
285	854 A	-7:91701834 1324097450 A	
285	855 G	-7:91701833 1324097449 G	
286 W	856 T	-7:91701832 1324097448 T	W
286	857 G	-7:91701831 1324097447 G	
286	858 G	-7:91701830 1324097446 G	
287 V	859 G	-7:91701829 1324097445 G	V
287	860 T	-7:91701828 1324097444 T	
287	861 A	-7:91701827 1324097443 A	
288 D	862 G	-7:91701826 1324097442 G	D
288	863 A	-7:91701825 1324097441 A	
288	864 T	-7:91701824 1324097440 T	
289 D	865 G	-7:91701823 1324097439 G	D
289	866 A	-7:91701822 1324097438 A	
289	867 T	-7:91701821 1324097437 T	
290 F	868 T	-7:91701820 1324097436 T	F
290	869 T	-7:91701819 1324097435 T	
290	870 T	-7:91701818 1324097434 T	
291 P	871 C	-7:91701817 1324097433 C	P
291	872 C	-7:91701816 1324097432 C	
291	873 T	-7:91701815 1324097431 T	
292 L	874 C	-7:91701814 1324097430 C	L
292	875 T	-7:91701813 1324097429 T	
292	876 C	-7:91701812 1324097428 C	
293 H	877 C	-7:91701811 1324097427 C	H
293	878 A	-7:91701810 1324097426 A	
293	879 C	-7:91701809 1324097425 C	
294 R	880 C	-7:91701808 1324097424 C	R
294	881 G	-7:91701807 1324097423 G	
294	882 A	-7:91701806 1324097422 A	
295 S	883 A	-7:91701805 1324097421 A	S
295	884 G	-7:91701804 1324097420 G	
295	885 C	-7:91701803 1324097419 C	
296 A	886 G	-7:91701802 1324097418 G	A
296	887 C	-7:91701801 1324097417 C	
296	888 C	-7:91701800 1324097416 C	
297 C	889 T	-7:91701799 1324097415 T	C
297	890 G	-7:91701798 1324097414 G	
297	891 T	-7:91701797 1324097413 T	
298 E	892 G	-7:91701796 1324097412 G	E
298	893 A	-7:91701795 1324097411 A	
298	894 A	-7:91701794 1324097410 A	
299 G	895 G	-7:91701793 1324097409 G	G
299	896 G	-7:91701792 1324097408 G	
299	897 A	-7:91701791 1324097407 A	
300 D	898 G	-7:91701790 1324097406 G	D
300	899 A	-7:91701789 1324097405 A	
300	900 T	-7:91701788 1324097404 T	
301 S	901 T	-7:91701787 1324097403 T	S
301	902 C	-7:91701786 1324097402 C	
301	903 A	-7:91701785 1324097401 A	
302 E	904 G	-7:91701784 1324097400 G	E
302	905 A	-7:91701783 1324097399 A	
302	906 A	-7:91701782 1324097398 A	
303 L	907 T	-7:91701781 1324097397 T	L
303	908 T	-7:91701780 1324097396 T	
303	909 A	-7:91701779 1324097395 A	
304 L	910 C	-7:91701778 1324097394 C	L
304	911 T	-7:91701777 1324097393 T	
304	912 A	-7:91701776 1324097392 A	
305 S	913 A	-7:91701775 1324097391 A	S
305	914 G	-7:91701774 1324097390 G	
305	915 C	-7:91701773 1324097389 C	
306 R	916 C	-7:91701772 1324097388 C	R
306	917 G	-7:91701771 1324097387 G	
306	918 T	-7:91701770 1324097386 T	
307 L	919 C	-7:91701769 1324097385 C	L
307	920 T	-7:91701768 1324097384 T	
307	921 T	-7:91701767 1324097383 T	
308 L	922 C	-7:91701766 1324097382 C	L
308	923 T	-7:91701765 1324097381 T	
308	924 C	-7:91701764 1324097380 C	
309 S	925 A	-7:91701763 1324097379 A	S
309	926 G	-7:91701762 1324097378 G	
309	927 T	-7:91701761 1324097377 T	
310 E	928 G	-7:91701760 1324097376 G	E
310	929 A	-7:91701759 1324097375 A	
310	930 A	-7:91701758 1324097374 A	
311 R	931 A	-7:91701757 1324097373 A	R
311	932 G	-7:91701756 1324097372 G	
311	933 A	-7:91701755 1324097371 A	
312 F	934 T	-7:91701754 1324097370 T	F
312	935 T	-7:91701753 1324097369 T	
312	936 T	-7:91701752 1324097368 T	
313 S	937 T	-7:91701751 1324097367 T	S
313	938 C	-7:91701750 1324097366 C	
313	939 A	-7:91701749 1324097365 A	
314 V	940 G	-7:91701748 1324097364 G	V
314	941 T	-7:91701747 1324097363 T	
314	942 C	-7:91701746 1324097362 C	
315 N	943 A	-7:91701745 1324097361 A	N
315	944 A	-7:91701744 1324097360 A	
315	945 C	-7:91701743 1324097359 C	
316 Q	946 C	-7:91701742 1324097358 C	Q
316	947 A	-7:91701741 1324097357 A	
316	948 G	-7:91701740 1324097356 G	
317 L	949 T	-7:91701739 1324097355 T	L
317	950 T	-7:91701738 1324097354 T	
317	951 A	-7:91701737 1324097353 A	
318 D	952 G	-7:91701736 1324097352 G	D
318	953 A	-7:91701735 1324097351 A	
318	954 T	-7:91701734 1324097350 T	
319 S	955 A	-7:91701733 1324097349 A	S
319	956 G	-7:91701732 1324097348 G	
319	957 T	-7:91701731 1324097347 T	
320 D	958 G	-7:91701730 1324097346 G	D
320	959 A	-7:91701729 1324097345 A	
320	960 C	-7:91701728 1324097344 C	
321 H	961 C	-7:91701727 1324097343 C	H
321	962 A	-7:91701726 1324097342 A	
321	963 C	-7:91701725 1324097341 C	
322 W	964 T	-7:91701724 1324097340 T	W
322	965 G	-7:91701723 1324097339 G	
322	966 G	-7:91701722 1324097338 G	
323 A	967 G	-7:91701721 1324097337 G	A
323	968 C	-7:91701720 1324097336 C	
323	969 A	-7:91701719 1324097335 A	
324 P	970 C	-7:91701718 1324097334 C	P
324	971 C	-7:91701717 1324097333 C	
324	972 C	-7:91701716 1324097332 C	
325 I	973 A	-7:91701715 1324097331 A	I
325	974 T	-7:91701714 1324097330 T	
325	975 T	-7:91701713 1324097329 T	
326 H	976 C	-7:91701712 1324097328 C	H
326	977 A	-7:91701711 1324097327 A	
326	978 T	-7:91701710 1324097326 T	
327 Y	979 T	-7:91701709 1324097325 T	Y
327	980 A	-7:91701708 1324097324 A	
327	981 T	-7:91701707 1324097323 T	
328 A	982 G	-7:91701706 1324097322 G	A
328	983 C	-7:91701705 1324097321 C	
328	984 A	-7:91701704 1324097320 A	
329 C	985 T	-7:91701703 1324097319 T	C
329	986 G	-7:91701702 1324097318 G	
329	987 C	-7:91701701 1324097317 C	
330 W	988 T	-7:91701700 1324097316 T	W
330	989 G	-7:91701699 1324097315 G	
330	990 G	-7:91693932 1324089548 G	
331 Y	991 T	-7:91693931 1324089547 T	Y
331	992 A	-7:91693930 1324089546 A	
331	993 T	-7:91693929 1324089545 T	
332 G	994 G	-7:91693928 1324089544 G	G
332	995 G	-7:91693927 1324089543 G	
332	996 A	-7:91693926 1324089542 A	
333 K	997 A	-7:91693925 1324089541 A	K
333	998 A	-7:91693924 1324089540 A	
333	999 A	-7:91693923 1324089539 A	
334 V	1000 G	-7:91693922 1324089538 G	V
334	1001 T	-7:91693921 1324089537 T	
334	1002 T	-7:91693920 1324089536 T	
335 E	1003 G	-7:91693919 1324089535 G	E
335	1004 A	-7:91693918 1324089534 A	
335	1005 G	-7:91693917 1324089533 G	
336 A	1006 G	-7:91693916 1324089532 G	A
336	1007 C	-7:91693915 1324089531 C	
336	1008 C	-7:91693914 1324089530 C	
337 T	1009 A	-7:91693913 1324089529 A	T
337	1010 C	-7:91693912 1324089528 C	
337	1011 T	-7:91693911 1324089527 T	
338 R	1012 C	-7:91693910 1324089526 C	R
338	1013 G	-7:91693909 1324089525 G	
338	1014 C	-7:91693908 1324089524 C	
339 I	1015 A	-7:91693907 1324089523 A	I
339	1016 T	-7:91693906 1324089522 T	
339	1017 A	-7:91693905 1324089521 A	
340 L	1018 T	-7:91693904 1324089520 T	L
340	1019 T	-7:91693903 1324089519 T	
340	1020 G	-7:91693902 1324089518 G	
341 L	1021 T	-7:91693901 1324089517 T	L
341	1022 T	-7:91693900 1324089516 T	
341	1023 A	-7:91693899 1324089515 A	
342 E	1024 G	-7:91693898 1324089514 G	E
342	1025 A	-7:91693897 1324089513 A	
342	1026 G	-7:91693896 1324089512 G	
343 K	1027 A	-7:91693895 1324089511 A	K
343	1028 A	-7:91693894 1324089510 A	
343	1029 A	-7:91693893 1324089509 A	
344 G	1030 G	-7:91693892 1324089508 G	G
344	1031 G	-7:91693891 1324089507 G	
344	1032 A	-7:91693890 1324089506 A	
345 K	1033 A	-7:91693889 1324089505 A	K
345	1034 A	-7:91693888 1324089504 A	
345	1035 G	-7:91693887 1324089503 G	
346 C	1036 T	-7:91693886 1324089502 T	C
346	1037 G	-7:91693885 1324089501 G	
346	1038 C	-7:91693884 1324089500 C	
347 N	1039 A	-7:91693883 1324089499 A	N
347	1040 A	-7:91693882 1324089498 A	
347	1041 T	-7:91693881 1324089497 T	
348 P	1042 C	-7:91693880 1324089496 C	P
348	1043 C	-7:91693879 1324089495 C	
348	1044 A	-7:91693878 1324089494 A	
349 N	1045 A	-7:91693877 1324089493 A	N
349	1046 A	-7:91693876 1324089492 A	
349	1047 C	-7:91693875 1324089491 C	
350 L	1048 C	-7:91693874 1324089490 C	L
350	1049 T	-7:91693873 1324089489 T	
350	1050 T	-7:91693872 1324089488 T	
351 L	1051 T	-7:91693871 1324089487 T	L
351	1052 T	-7:91693870 1324089486 T	
351	1053 A	-7:91693869 1324089485 A	
352 N	1054 A	-7:91693868 1324089484 A	N
352	1055 A	-7:91693867 1324089483 A	
352	1056 T	-7:91693866 1324089482 T	
353 G	1057 G	-7:91693865 1324089481 G	G
353	1058 G	-7:91693864 1324089480 G	
353	1059 A	-7:91693863 1324089479 A	
354 Q	1060 C	-7:91693862 1324089478 C	Q
354	1061 A	-7:91693861 1324089477 A	
354	1062 A	-7:91693860 1324089476 A	
355 L	1063 C	-7:91693859 1324089475 C	L
355	1064 T	-7:91693858 1324089474 T	
355	1065 T	-7:91693857 1324089473 T	
356 S	1066 A	-7:91693856 1324089472 A	S
356	1067 G	-7:91693855 1324089471 G	
356	1068 T	-7:91693854 1324089470 T	
357 S	1069 T	-7:91693853 1324089469 T	S
357	1070 C	-7:91693852 1324089468 C	
357	1071 T	-7:91693851 1324089467 T	
358 P	1072 C	-7:91693850 1324089466 C	P
358	1073 C	-7:91693849 1324089465 C	
358	1074 T	-7:91693848 1324089464 T	
359 L	1075 C	-7:91693847 1324089463 C	L
359	1076 T	-7:91693846 1324089462 T	
359	1077 T	-7:91693845 1324089461 T	
360 H	1078 C	-7:91693844 1324089460 C	H
360	1079 A	-7:91693843 1324089459 A	
360	1080 T	-7:91693842 1324089458 T	
361 F	1081 T	-7:91693841 1324089457 T	F
361	1082 T	-7:91693840 1324089456 T	
361	1083 T	-7:91693839 1324089455 T	
362 A	1084 G	-7:91693838 1324089454 G	A
362	1085 C	-7:91693837 1324089453 C	
362	1086 T	-7:91693836 1324089452 T	
363 A	1087 G	-7:91693835 1324089451 G	A
363	1088 C	-7:91693834 1324089450 C	
363	1089 T	-7:91693833 1324089449 T	
364 G	1090 G	-7:91693832 1324089448 G	G
364	1091 G	-7:91693831 1324089447 G	
364	1092 A	-7:91693830 1324089446 A	
365 G	1093 G	-7:91693829 1324089445 G	G
365	1094 G	-7:91693828 1324089444 G	
365	1095 A	-7:91693827 1324089443 A	
366 G	1096 G	-7:91693826 1324089442 G	G
366	1097 G	-7:91693825 1324089441 G	
366	1098 A	-7:91693824 1324089440 A	
367 H	1099 C	-7:91693823 1324089439 C	H
367	1100 A	-7:91693822 1324089438 A	
367	1101 T	-7:91693821 1324089437 T	
368 A	1102 G	-7:91693820 1324089436 G	A
368	1103 C	-7:91693819 1324089435 C	
368	1104 T	-7:91693818 1324089434 T	
369 E	1105 G	-7:91693817 1324089433 G	E
369	1106 A	-7:91693816 1324089432 A	
369	1107 A	-7:91693815 1324089431 A	
370 I	1108 A	-7:91693814 1324089430 A	I
370	1109 T	-7:91693813 1324089429 T	
370	1110 A	-7:91693812 1324089428 A	
371 V	1111 G	-7:91693811 1324089427 G	V
371	1112 T	-7:91693810 1324089426 T	
371	1113 A	-7:91693809 1324089425 A	
372 Q	1114 C	-7:91693808 1324089424 C	Q
372	1115 A	-7:91693807 1324089423 A	
372	1116 G	-7:91693806 1324089422 G	
373 I	1117 A	-7:91693805 1324089421 A	I
373	1118 T	-7:91693804 1324089420 T	
373	1119 T	-7:91693803 1324089419 T	
374 L	1120 C	-7:91693802 1324089418 C	L
374	1121 T	-7:91693801 1324089417 T	
374	1122 C	-7:91693800 1324089416 C	
375 L	1123 C	-7:91693799 1324089415 C	L
375	1124 T	-7:91693798 1324089414 T	
375	1125 A	-7:91693797 1324089413 A	
376 N	1126 A	-7:91693796 1324089412 A	N
376	1127 A	-7:91693795 1324089411 A	
376	1128 C	-7:91693794 1324089410 C	
377 H	1129 C	-7:91693793 1324089409 C	H
377	1130 A	-7:91693792 1324089408 A	
377	1131 C	-7:91693791 1324089407 C	
378 P	1132 C	-7:91693790 1324089406 C	P
378	1133 C	-7:91693789 1324089405 C	
378	1134 A	-7:91693788 1324089404 A	
379 E	1135 G	-7:91693787 1324089403 G	E
379	1136 A	-7:91693786 1324089402 A	
379	1137 A	-7:91693785 1324089401 A	
380 T	1138 A	-7:91693784 1324089400 A	T
380	1139 C	-7:91693783 1324089399 C	
380	1140 G	-7:91693782 1324089398 G	
381 D	1141 G	-7:91693781 1324089397 G	D
381	1142 A	-7:91693780 1324089396 A	
381	1143 T	-7:91693779 1324089395 T	
382 R	1144 A	-7:91693778 1324089394 A	R
382	1145 G	-7:91693777 1324089393 G	
382	1146 A	-7:91693776 1324089392 A	
383 H	1147 C	-7:91693077 1324088693 C	H
383	1148 A	-7:91693076 1324088692 A	
383	1149 T	-7:91693075 1324088691 T	
384 I	1150 A	-7:91693074 1324088690 A	I
384	1151 T	-7:91693073 1324088689 T	
384	1152 A	-7:91693072 1324088688 A	
385 T	1153 A	-7:91693071 1324088687 A	T
385	1154 C	-7:91693070 1324088686 C	
385	1155 A	-7:91693069 1324088685 A	
386 D	1156 G	-7:91693068 1324088684 G	D
386	1157 A	-7:91693067 1324088683 A	
386	1158 C	-7:91693066 1324088682 C	
387 Q	1159 C	-7:91693065 1324088681 C	Q
387	1160 A	-7:91693064 1324088680 A	
387	1161 A	-7:91693063 1324088679 A	
388 Q	1162 C	-7:91693062 1324088678 C	Q
388	1163 A	-7:91693061 1324088677 A	
388	1164 A	-7:91693060 1324088676 A	
389 G	1165 G	-7:91693059 1324088675 G	G
389	1166 G	-7:91693058 1324088674 G	
389	1167 A	-7:91693057 1324088673 A	
390 R	1168 A	-7:91693056 1324088672 A	R
390	1169 G	-7:91693055 1324088671 G	
390	1170 A	-7:91693054 1324088670 A	
391 S	1171 T	-7:91693053 1324088669 T	S
391	1172 C	-7:91693052 1324088668 C	
391	1173 T	-7:91693051 1324088667 T	
392 P	1174 C	-7:91693050 1324088666 C	P
392	1175 C	-7:91693049 1324088665 C	
392	1176 A	-7:91693048 1324088664 A	
393 L	1177 T	-7:91693047 1324088663 T	L
393	1178 T	-7:91693046 1324088662 T	
393	1179 A	-7:91693045 1324088661 A	
394 N	1180 A	-7:91693044 1324088660 A	N
394	1181 A	-7:91693043 1324088659 A	
394	1182 T	-7:91693042 1324088658 T	
395 I	1183 A	-7:91693041 1324088657 A	I
395	1184 T	-7:91693040 1324088656 T	
395	1185 T	-7:91693039 1324088655 T	
396 C	1186 T	-7:91693038 1324088654 T	C
396	1187 G	-7:91693037 1324088653 G	
396	1188 T	-7:91693036 1324088652 T	
397 E	1189 G	-7:91693035 1324088651 G	E
397	1190 A	-7:91693034 1324088650 A	
397	1191 A	-7:91693033 1324088649 A	
398 E	1192 G	-7:91693032 1324088648 G	E
398	1193 A	-7:91693031 1324088647 A	
398	1194 A	-7:91693030 1324088646 A	
399 N	1195 A	-7:91693029 1324088645 A	N
399	1196 A	-7:91693028 1324088644 A	
399	1197 C	-7:91693027 1324088643 C	
400 K	1198 A	-7:91693026 1324088642 A	K
400	1199 A	-7:91693025 1324088641 A	
400	1200 A	-7:91693024 1324088640 A	
401 Q	1201 C	-7:91693023 1324088639 C	Q
401	1202 A	-7:91693022 1324088638 A	
401	1203 A	-7:91693021 1324088637 A	
402 N	1204 A	-7:91693020 1324088636 A	N
402	1205 A	-7:91693019 1324088635 A	
402	1206 C	-7:91693018 1324088634 C	
403 N	1207 A	-7:91693017 1324088633 A	N
403	1208 A	-7:91693016 1324088632 A	
403	1209 C	-7:91693015 1324088631 C	
404 W	1210 T	-7:91693014 1324088630 T	W
404	1211 G	-7:91693013 1324088629 G	
404	1212 G	-7:91693012 1324088628 G	
405 E	1213 G	-7:91693011 1324088627 G	E
405	1214 A	-7:91693010 1324088626 A	
405	1215 A	-7:91693009 1324088625 A	
406 E	1216 G	-7:91693008 1324088624 G	E
406	1217 A	-7:91693007 1324088623 A	
406	1218 A	-7:91693006 1324088622 A	
407 A	1219 G	-7:91693005 1324088621 G	A
407	1220 C	-7:91693004 1324088620 C	
407	1221 T	-7:91693003 1324088619 T	
408 A	1222 G	-7:91693002 1324088618 G	A
408	1223 C	-7:91693001 1324088617 C	
408	1224 A	-7:91693000 1324088616 A	
409 K	1225 A	-7:91692999 1324088615 A	K
409	1226 A	-7:91692998 1324088614 A	
409	1227 A	-7:91692997 1324088613 A	
410 L	1228 T	-7:91692996 1324088612 T	L
410	1229 T	-7:91692995 1324088611 T	
410	1230 G	-7:91692994 1324088610 G	
411 L	1231 T	-7:91692993 1324088609 T	L
411	1232 T	-7:91692992 1324088608 T	
411	1233 G	-7:91692991 1324088607 G	
412 K	1234 A	-7:91692990 1324088606 A	K
412	1235 A	-7:91692989 1324088605 A	
412	1236 G	-7:91692988 1324088604 G	
413 E	1237 G	-7:91692987 1324088603 G	E
413	1238 A	-7:91692986 1324088602 A	
413	1239 A	-7:91692985 1324088601 A	
414 A	1240 G	-7:91692984 1324088600 G	A
414	1241 C	-7:91692983 1324088599 C	
414	1242 A	-7:91692982 1324088598 A	
415 I	1243 A	-7:91692981 1324088597 A	I
415	1244 T	-7:91692980 1324088596 T	
415	1245 T	-7:91692979 1324088595 T	
416 N	1246 A	-7:91692978 1324088594 A	N
416	1247 A	-7:91692977 1324088593 A	
416	1248 C	-7:91692976 1324088592 C	
417 K	1249 A	-7:91692975 1324088591 A	K
417	1250 A	-7:91692974 1324088590 A	
417	1251 A	-7:91692973 1324088589 A	
418 P	1252 C	-7:91692972 1324088588 C	P
418	1253 C	-7:91692971 1324088587 C	
418	1254 A	-7:91692970 1324088586 A	
419 Y	1255 T	-7:91690228 1324085844 T	Y
419	1256 A	-7:91690227 1324085843 A	
419	1257 T	-7:91690226 1324085842 T	
420 E	1258 G	-7:91690225 1324085841 G	E
420	1259 A	-7:91690224 1324085840 A	
420	1260 A	-7:91690223 1324085839 A	
421 K	1261 A	-7:91690222 1324085838 A	K
421	1262 A	-7:91690221 1324085837 A	
421	1263 A	-7:91690220 1324085836 A	
422 V	1264 G	-7:91690219 1324085835 G	V
422	1265 T	-7:91690218 1324085834 T	
422	1266 T	-7:91690217 1324085833 T	
423 R	1267 C	-7:91690216 1324085832 C	R
423	1268 G	-7:91690215 1324085831 G	
423	1269 A	-7:91690214 1324085830 A	
424 I	1270 A	-7:91690213 1324085829 A	I
424	1271 T	-7:91690212 1324085828 T	
424	1272 A	-7:91690211 1324085827 A	
425 Y	1273 T	-7:91690210 1324085826 T	Y
425	1274 A	-7:91690209 1324085825 A	
425	1275 C	-7:91690208 1324085824 C	
426 R	1276 A	-7:91690207 1324085823 A	R
426	1277 G	-7:91690206 1324085822 G	
426	1278 A	-7:91690205 1324085821 A	
427 M	1279 A	-7:91690204 1324085820 A	M
427	1280 T	-7:91690203 1324085819 T	
427	1281 G	-7:91690202 1324085818 G	
428 D	1282 G	-7:91690201 1324085817 G	D
428	1283 A	-7:91690200 1324085816 A	
428	1284 T	-7:91690199 1324085815 T	
429 G	1285 G	-7:91690198 1324085814 G	G
429	1286 G	-7:91690197 1324085813 G	
429	1287 G	-7:91690196 1324085812 G	
430 S	1288 T	-7:91690195 1324085811 T	S
430	1289 C	-7:91690194 1324085810 C	
430	1290 A	-7:91690193 1324085809 A	
431 Y	1291 T	-7:91690192 1324085808 T	Y
431	1292 A	-7:91690191 1324085807 A	
431	1293 T	-7:91690190 1324085806 T	
432 R	1294 C	-7:91690189 1324085805 C	R
432	1295 G	-7:91690188 1324085804 G	
432	1296 T	-7:91690187 1324085803 T	
433 S	1297 T	-7:91690186 1324085802 T	S
433	1298 C	-7:91690185 1324085801 C	
433	1299 T	-7:91690184 1324085800 T	
434 V	1300 G	-7:91690183 1324085799 G	V
434	1301 T	-7:91690182 1324085798 T	
434	1302 T	-7:91690181 1324085797 T	
435 E	1303 G	-7:91690180 1324085796 G	E
435	1304 A	-7:91690179 1324085795 A	
435	1305 A	-7:91690178 1324085794 A	
436 L	1306 T	-7:91690177 1324085793 T	L
436	1307 T	-7:91690176 1324085792 T	
436	1308 G	-7:91690175 1324085791 G	
437 K	1309 A	-7:91690174 1324085790 A	K
437	1310 A	-7:91690173 1324085789 A	
437	1311 G	-7:91690172 1324085788 G	
438 H	1312 C	-7:91690171 1324085787 C	H
438	1313 A	-7:91690170 1324085786 A	
438	1314 T	-7:91690169 1324085785 T	
439 G	1315 G	-7:91690168 1324085784 G	G
439	1316 G	-7:91690167 1324085783 G	
439	1317 A	-7:91690166 1324085782 A	
440 N	1318 A	-7:91690165 1324085781 A	N
440	1319 A	-7:91690164 1324085780 A	
440	1320 T	-7:91690163 1324085779 T	
441 N	1321 A	-7:91690162 1324085778 A	N
441	1322 A	-7:91690161 1324085777 A	
441	1323 T	-7:91690160 1324085776 T	
442 T	1324 A	-7:91690159 1324085775 A	T
442	1325 C	-7:91690158 1324085774 C	
442	1326 C	-7:91690157 1324085773 C	
443 T	1327 A	-7:91690156 1324085772 A	T
443	1328 C	-7:91690155 1324085771 C	
443	1329 A	-7:91690154 1324085770 A	
444 V	1330 G	-7:91690153 1324085769 G	V
444	1331 T	-7:91690152 1324085768 T	
444	1332 G	-7:91690151 1324085767 G	
445 Q	1333 C	-7:91690150 1324085766 C	Q
445	1334 A	-7:91690149 1324085765 A	
445	1335 G	-7:91690148 1324085764 G	
446 Q	1336 C	-7:91690147 1324085763 C	Q
446	1337 A	-7:91690146 1324085762 A	
446	1338 G	-7:91690145 1324085761 G	
447 I	1339 A	-7:91690144 1324085760 A	I
447	1340 T	-7:91690143 1324085759 T	
447	1341 A	-7:91690142 1324085758 A	
448 M	1342 A	-7:91690141 1324085757 A	M
448	1343 T	-7:91690140 1324085756 T	
448	1344 G	-7:91690139 1324085755 G	
449 E	1345 G	-7:91690138 1324085754 G	E
449	1346 A	-7:91690137 1324085753 A	
449	1347 A	-7:91690136 1324085752 A	
450 G	1348 G	-7:91690135 1324085751 G	G
450	1349 G	-7:91690134 1324085750 G	
450	1350 A	-7:91690133 1324085749 A	
451 M	1351 A	-7:91690132 1324085748 A	M
451	1352 T	-7:91690131 1324085747 T	
451	1353 G	-7:91690130 1324085746 G	
452 R	1354 C	-7:91690129 1324085745 C	R
452	1355 G	-7:91690128 1324085744 G	
452	1356 T	-7:91690127 1324085743 T	
453 L	1357 C	-7:91690126 1324085742 C	L
453	1358 T	-7:91690125 1324085741 T	
453	1359 C	-7:91690124 1324085740 C	
454 S	1360 T	-7:91690123 1324085739 T	S
454	1361 C	-7:91690122 1324085738 C	
454	1362 T	-7:91690121 1324085737 T	
455 Q	1363 C	-7:91690120 1324085736 C	Q
455	1364 A	-7:91690119 1324085735 A	
455	1365 A	-7:91690118 1324085734 A	
456 E	1366 G	-7:91690117 1324085733 G	E
456	1367 A	-7:91690116 1324085732 A	
456	1368 A	-7:91690115 1324085731 A	
457 T	1369 A	-7:91690114 1324085730 A	T
457	1370 C	-7:91690113 1324085729 C	
457	1371 T	-7:91690112 1324085728 T	
458 Q	1372 C	-7:91690111 1324085727 C	Q
458	1373 A	-7:91690110 1324085726 A	
458	1374 G	-7:91690109 1324085725 G	
459 Q	1375 C	-7:91690108 1324085724 C	Q
459	1376 A	-7:91690107 1324085723 A	
459	1377 A	-7:91690106 1324085722 A	
460 Y	1378 T	-7:91690105 1324085721 T	Y
460	1379 A	-7:91690104 1324085720 A	
460	1380 T	-7:91690103 1324085719 T	
461 F	1381 T	-7:91690102 1324085718 T	F
461	1382 T	-7:91690101 1324085717 T	
461	1383 C	-7:91690100 1324085716 C	
462 T	1384 A	-7:91690099 1324085715 A	T
462	1385 C	-7:91690098 1324085714 C	
462	1386 T	-7:91690097 1324085713 T	
463 I	1387 A	-7:91690096 1324085712 A	I
463	1388 T	-7:91690095 1324085711 T	
463	1389 A	-7:91690094 1324085710 A	
464 W	1390 T	-7:91690093 1324085709 T	W
464	1391 G	-7:91690092 1324085708 G	
464	1392 G	-7:91690091 1324085707 G	
465 I	1393 A	-7:91690090 1324085706 A	I
465	1394 T	-7:91690089 1324085705 T	
465	1395 T	-7:91690088 1324085704 T	
466 C	1396 T	-7:91690087 1324085703 T	C
466	1397 G	-7:91690086 1324085702 G	
466	1398 T	-7:91690085 1324085701 T	
467 S	1399 T	-7:91690084 1324085700 T	S
467	1400 C	-7:91690083 1324085699 C	
467	1401 A	-7:91690082 1324085698 A	
468 E	1402 G	-7:91690081 1324085697 G	E
468	1403 A	-7:91690080 1324085696 A	
468	1404 A	-7:91690079 1324085695 A	
469 N	1405 A	-7:91690078 1324085694 A	N
469	1406 A	-7:91690077 1324085693 A	
469	1407 C	-7:91690076 1324085692 C	
470 L	1408 C	-7:91690075 1324085691 C	L
470	1409 T	-7:91690074 1324085690 T	
470	1410 C	-7:91690073 1324085689 C	
471 S	1411 A	-7:91690072 1324085688 A	S
471	1412 G	-7:91689303 1324084919 G	
471	1413 C	-7:91689302 1324084918 C	
472 L	1414 C	-7:91689301 1324084917 C	L
472	1415 T	-7:91689300 1324084916 T	
472	1416 T	-7:91689299 1324084915 T	
473 Q	1417 C	-7:91689298 1324084914 C	Q
473	1418 A	-7:91689297 1324084913 A	
473	1419 A	-7:91689296 1324084912 A	
474 L	1420 C	-7:91689295 1324084911 C	L
474	1421 T	-7:91689294 1324084910 T	
474	1422 C	-7:91689293 1324084909 C	
475 K	1423 A	-7:91689292 1324084908 A	K
475	1424 A	-7:91689291 1324084907 A	
475	1425 A	-7:91689290 1324084906 A	
476 P	1426 C	-7:91689289 1324084905 C	P
476	1427 C	-7:91689288 1324084904 C	
476	1428 A	-7:91689287 1324084903 A	
477 Y	1429 T	-7:91689286 1324084902 T	Y
477	1430 A	-7:91689285 1324084901 A	
477	1431 T	-7:91689284 1324084900 T	
478 H	1432 C	-7:91689283 1324084899 C	H
478	1433 A	-7:91689282 1324084898 A	
478	1434 T	-7:91689281 1324084897 T	
479 K	1435 A	-7:91689280 1324084896 A	K
479	1436 A	-7:91689279 1324084895 A	
479	1437 A	-7:91689278 1324084894 A	
480 P	1438 C	-7:91689277 1324084893 C	P
480	1439 C	-7:91689276 1324084892 C	
480	1440 C	-7:91689275 1324084891 C	
481 L	1441 T	-7:91689274 1324084890 T	L
481	1442 T	-7:91689273 1324084889 T	
481	1443 G	-7:91689272 1324084888 G	
482 Q	1444 C	-7:91689271 1324084887 C	Q
482	1445 A	-7:91689270 1324084886 A	
482	1446 A	-7:91689269 1324084885 A	
483 H	1447 C	-7:91689268 1324084884 C	H
483	1448 A	-7:91689267 1324084883 A	
483	1449 T	-7:91689266 1324084882 T	
484 V	1450 G	-7:91689265 1324084881 G	V
484	1451 T	-7:91689264 1324084880 T	
484	1452 T	-7:91689263 1324084879 T	
485 R	1453 C	-7:91689262 1324084878 C	R
485	1454 G	-7:91689261 1324084877 G	
485	1455 T	-7:91689260 1324084876 T	
486 D	1456 G	-7:91689259 1324084875 G	D
486	1457 A	-7:91689258 1324084874 A	
486	1458 C	-7:91689257 1324084873 C	
487 W	1459 T	-7:91689256 1324084872 T	W
487	1460 G	-7:91689255 1324084871 G	
487	1461 G	-7:91689254 1324084870 G	
488 P	1462 C	-7:91689253 1324084869 C	P
488	1463 C	-7:91689252 1324084868 C	
488	1464 A	-7:91689251 1324084867 A	
489 E	1465 G	-7:91689250 1324084866 G	E
489	1466 A	-7:91689249 1324084865 A	
489	1467 A	-7:91689248 1324084864 A	
490 I	1468 A	-7:91689247 1324084863 A	I
490	1469 T	-7:91689246 1324084862 T	
490	1470 A	-7:91689245 1324084861 A	
491 L	1471 C	-7:91689244 1324084860 C	L
491	1472 T	-7:91689243 1324084859 T	
491	1473 T	-7:91689242 1324084858 T	
492 A	1474 G	-7:91689241 1324084857 G	A
492	1475 C	-7:91689240 1324084856 C	
492	1476 T	-7:91689239 1324084855 T	
493 E	1477 G	-7:91689238 1324084854 G	E
493	1478 A	-7:91689237 1324084853 A	
493	1479 A	-7:91689236 1324084852 A	
494 L	1480 T	-7:91689235 1324084851 T	L
494	1481 T	-7:91689234 1324084850 T	
494	1482 G	-7:91689233 1324084849 G	
495 T	1483 A	-7:91689232 1324084848 A	T
495	1484 C	-7:91689231 1324084847 C	
495	1485 T	-7:91689230 1324084846 T	
496 N	1486 A	-7:91689229 1324084845 A	N
496	1487 A	-7:91689228 1324084844 A	
496	1488 T	-7:91689227 1324084843 T	
497 L	1489 C	-7:91689226 1324084842 C	L
497	1490 T	-7:91689225 1324084841 T	
497	1491 G	-7:91689224 1324084840 G	
498 D	1492 G	-7:91689223 1324084839 G	D
498	1493 A	-7:91689222 1324084838 A	
498	1494 T	-7:91689221 1324084837 T	
499 P	1495 C	-7:91689220 1324084836 C	P
499	1496 C	-7:91689219 1324084835 C	
499	1497 T	-7:91689218 1324084834 T	
500 Q	1498 C	-7:91689217 1324084833 C	Q
500	1499 A	-7:91689216 1324084832 A	
500	1500 A	-7:91689215 1324084831 A	
501 R	1501 A	-7:91689214 1324084830 A	R
501	1502 G	-7:91689213 1324084829 G	
501	1503 G	-7:91689212 1324084828 G	
502 E	1504 G	-7:91689211 1324084827 G	E
502	1505 A	-7:91689210 1324084826 A	
502	1506 A	-7:91689209 1324084825 A	
503 T	1507 A	-7:91689208 1324084824 A	T
503	1508 C	-7:91689207 1324084823 C	
503	1509 A	-7:91689206 1324084822 A	
504 P	1510 C	-7:91689205 1324084821 C	P
504	1511 C	-7:91689204 1324084820 C	
504	1512 T	-7:91689203 1324084819 T	
505 Q	1513 C	-7:91689202 1324084818 C	Q
505	1514 A	-7:91689201 1324084817 A	
505	1515 G	-7:91689200 1324084816 G	
506 L	1516 C	-7:91689199 1324084815 C	L
506	1517 T	-7:91689198 1324084814 T	
506	1518 T	-7:91689197 1324084813 T	
507 F	1519 T	-7:91689196 1324084812 T	F
507	1520 T	-7:91689195 1324084811 T	
507	1521 T	-7:91689194 1324084810 T	
508 L	1522 C	-7:91689193 1324084809 C	L
508	1523 T	-7:91689192 1324084808 T	
508	1524 A	-7:91689191 1324084807 A	
509 R	1525 A	-7:91689190 1324084806 A	R
509	1526 G	-7:91689189 1324084805 G	
509	1527 A	-7:91689188 1324084804 A	
510 R	1528 A	-7:91689187 1324084803 A	R
510	1529 G	-7:91689186 1324084802 G	
510	1530 A	-7:91689185 1324084801 A	
511 D	1531 G	-7:91689184 1324084800 G	D
511	1532 A	-7:91689183 1324084799 A	
511	1533 T	-7:91689182 1324084798 T	
512 V	1534 G	-7:91689181 1324084797 G	V
512	1535 T	-7:91689180 1324084796 T	
512	1536 G	-7:91689179 1324084795 G	
513 R	1537 A	-7:91689178 1324084794 A	R
513	1538 G	-7:91689177 1324084793 G	
513	1539 A	-7:91689176 1324084792 A	
514 L	1540 C	-7:91689175 1324084791 C	L
514	1541 T	-7:91689174 1324084790 T	
514	1542 T	-7:91689173 1324084789 T	
515 P	1543 C	-7:91689172 1324084788 C	P
515	1544 C	-7:91689171 1324084787 C	
515	1545 C	-7:91689170 1324084786 C	
516 L	1546 T	-7:91689169 1324084785 T	L
516	1547 T	-7:91689168 1324084784 T	
516	1548 G	-7:91689167 1324084783 G	
517 E	1549 G	-7:91689166 1324084782 G	E
517	1550 A	-7:91689165 1324084781 A	
517	1551 A	-7:91689164 1324084780 A	
518 V	1552 G	-7:91689163 1324084779 G	V
518	1553 T	-7:91689162 1324084778 T	
518	1554 T	-7:91689161 1324084777 T	
519 E	1555 G	-7:91689160 1324084776 G	E
519	1556 A	-7:91689159 1324084775 A	
519	1557 A	-7:91689158 1324084774 A	
520 K	1558 A	-7:91689157 1324084773 A	K
520	1559 A	-7:91689156 1324084772 A	
520	1560 A	-7:91689155 1324084771 A	
521 Q	1561 C	-7:91689154 1324084770 C	Q
521	1562 A	-7:91689153 1324084769 A	
521	1563 G	-7:91689152 1324084768 G	
522 I	1564 A	-7:91682027 1324077643 A	I
522	1565 T	-7:91682026 1324077642 T	
522	1566 T	-7:91682025 1324077641 T	
523 E	1567 G	-7:91682024 1324077640 G	E
523	1568 A	-7:91682023 1324077639 A	
523	1569 A	-7:91682022 1324077638 A	
524 D	1570 G	-7:91682021 1324077637 G	D
524	1571 A	-7:91682020 1324077636 A	
524	1572 C	-7:91682019 1324077635 C	
525 P	1573 C	-7:91682018 1324077634 C	P
525	1574 C	-7:91682017 1324077633 C	
525	1575 A	-7:91682016 1324077632 A	
526 L	1576 C	-7:91682015 1324077631 C	L
526	1577 T	-7:91682014 1324077630 T	
526	1578 A	-7:91682013 1324077629 A	
527 A	1579 G	-7:91682012 1324077628 G	A
527	1580 C	-7:91682011 1324077627 C	
527	1581 T	-7:91682010 1324077626 T	
528 I	1582 A	-7:91682009 1324077625 A	I
528	1583 T	-7:91682008 1324077624 T	
528	1584 T	-7:91682007 1324077623 T	
529 L	1585 C	-7:91682006 1324077622 C	L
529	1586 T	-7:91682005 1324077621 T	
529	1587 T	-7:91682004 1324077620 T	
530 I	1588 A	-7:91682003 1324077619 A	I
530	1589 T	-7:91682002 1324077618 T	
530	1590 T	-7:91682001 1324077617 T	
531 L	1591 C	-7:91682000 1324077616 C	L
531	1592 T	-7:91681999 1324077615 T	
531	1593 C	-7:91681998 1324077614 C	
532 F	1594 T	-7:91681997 1324077613 T	F
532	1595 T	-7:91681996 1324077612 T	
532	1596 T	-7:91681995 1324077611 T	
533 D	1597 G	-7:91681994 1324077610 G	D
533	1598 A	-7:91681993 1324077609 A	
533	1599 T	-7:91681992 1324077608 T	
534 E	1600 G	-7:91681991 1324077607 G	E
534	1601 A	-7:91681990 1324077606 A	
534	1602 A	-7:91681989 1324077605 A	
535 A	1603 G	-7:91681988 1324077604 G	A
535	1604 C	-7:91681987 1324077603 C	
535	1605 C	-7:91681986 1324077602 C	
536 R	1606 A	-7:91681985 1324077601 A	R
536	1607 G	-7:91681984 1324077600 G	
536	1608 A	-7:91681983 1324077599 A	
537 Y	1609 T	-7:91681982 1324077598 T	Y
537	1610 A	-7:91681981 1324077597 A	
537	1611 T	-7:91681980 1324077596 T	
538 N	1612 A	-7:91681979 1324077595 A	N
538	1613 A	-7:91681978 1324077594 A	
538	1614 T	-7:91681977 1324077593 T	
539 L	1615 T	-7:91681976 1324077592 T	L
539	1616 T	-7:91681975 1324077591 T	
539	1617 A	-7:91681974 1324077590 A	
540 L	1618 T	-7:91681973 1324077589 T	L
540	1619 T	-7:91681972 1324077588 T	
540	1620 G	-7:91681971 1324077587 G	
541 K	1621 A	-7:91681970 1324077586 A	K
541	1622 A	-7:91681969 1324077585 A	
541	1623 G	-7:91681968 1324077584 G	
542 G	1624 G	-7:91681967 1324077583 G	G
542	1625 G	-7:91681966 1324077582 G	
542	1626 C	-7:91681965 1324077581 C	
543 F	1627 T	-7:91681964 1324077580 T	F
543	1628 T	-7:91681963 1324077579 T	
543	1629 T	-7:91681962 1324077578 T	
544 Y	1630 T	-7:91681961 1324077577 T	Y
544	1631 A	-7:91681960 1324077576 A	
544	1632 T	-7:91681959 1324077575 T	
545 T	1633 A	-7:91681958 1324077574 A	T
545	1634 C	-7:91681957 1324077573 C	
545	1635 A	-7:91681956 1324077572 A	
546 A	1636 G	-7:91681955 1324077571 G	A
546	1637 C	-7:91681954 1324077570 C	
546	1638 T	-7:91681953 1324077569 T	
547 P	1639 C	-7:91681952 1324077568 C	P
547	1640 C	-7:91681951 1324077567 C	
547	1641 T	-7:91681950 1324077566 T	
548 D	1642 G	-7:91681949 1324077565 G	D
548	1643 A	-7:91681948 1324077564 A	
548	1644 T	-7:91681947 1324077563 T	
549 A	1645 G	-7:91681946 1324077562 G	A
549	1646 C	-7:91681945 1324077561 C	
549	1647 T	-7:91681944 1324077560 T	
550 K	1648 A	-7:91681943 1324077559 A	K
550	1649 A	-7:91681942 1324077558 A	
550	1650 G	-7:91681941 1324077557 G	
551 L	1651 C	-7:91681940 1324077556 C	L
551	1652 T	-7:91681939 1324077555 T	
551	1653 G	-7:91681938 1324077554 G	
552 I	1654 A	-7:91681937 1324077553 A	I
552	1655 T	-7:91681936 1324077552 T	
552	1656 A	-7:91681935 1324077551 A	
553 T	1657 A	-7:91681934 1324077550 A	T
553	1658 C	-7:91681933 1324077549 C	
553	1659 A	-7:91681932 1324077548 A	
554 L	1660 T	-7:91681931 1324077547 T	L
554	1661 T	-7:91681930 1324077546 T	
554	1662 G	-7:91681929 1324077545 G	
555 A	1663 G	-7:91681928 1324077544 G	A
555	1664 C	-7:91681927 1324077543 C	
555	1665 A	-7:91681926 1324077542 A	
556 S	1666 A	-7:91681925 1324077541 A	S
556	1667 G	-7:91681924 1324077540 G	
556	1668 T	-7:91681923 1324077539 T	
557 L	1669 C	-7:91681922 1324077538 C	L
557	1670 T	-7:91681921 1324077537 T	
557	1671 G	-7:91681920 1324077536 G	
558 L	1672 C	-7:91681919 1324077535 C	L
558	1673 T	-7:91681918 1324077534 T	
558	1674 T	-7:91681917 1324077533 T	
559 L	1675 T	-7:91681916 1324077532 T	L
559	1676 T	-7:91681915 1324077531 T	
559	1677 G	-7:91681914 1324077530 G	
560 Q	1678 C	-7:91681913 1324077529 C	Q
560	1679 A	-7:91681912 1324077528 A	
560	1680 A	-7:91681911 1324077527 A	
561 I	1681 A	-7:91681910 1324077526 A	I
561	1682 T	-7:91681909 1324077525 T	
561	1683 A	-7:91681908 1324077524 A	
562 V	1684 G	-7:91681907 1324077523 G	V
562	1685 T	-7:91681906 1324077522 T	
562	1686 C	-7:91681905 1324077521 C	
563 Y	1687 T	-7:91681904 1324077520 T	Y
563	1688 A	-7:91681903 1324077519 A	
563	1689 T	-7:91681902 1324077518 T	
564 G	1690 G	-7:91681901 1324077517 G	G
564	1691 G	-7:91681900 1324077516 G	
564	1692 A	-7:91681899 1324077515 A	
565 N	1693 A	-7:91681898 1324077514 A	N
565	1694 A	-7:91681897 1324077513 A	
565	1695 T	-7:91681896 1324077512 T	
566 Y	1696 T	-7:91681895 1324077511 T	Y
566	1697 A	-7:91681894 1324077510 A	
566	1698 T	-7:91681893 1324077509 T	
567 E	1699 G	-7:91681892 1324077508 G	E
567	1700 A	-7:91681891 1324077507 A	
567	1701 G	-7:91681890 1324077506 G	
568 S	1702 A	-7:91681889 1324077505 A	S
568	1703 G	-7:91681888 1324077504 G	
568	1704 T	-7:91681887 1324077503 T	
569 K	1705 A	-7:91681886 1324077502 A	K
569	1706 A	-7:91681885 1324077501 A	
569	1707 A	-7:91681884 1324077500 A	
570 K	1708 A	-7:91681883 1324077499 A	K
570	1709 A	-7:91681882 1324077498 A	
570	1710 A	-7:91681881 1324077497 A	
571 H	1711 C	-7:91681880 1324077496 C	H
571	1712 A	-7:91681879 1324077495 A	
571	1713 C	-7:91681878 1324077494 C	
572 K	1714 A	-7:91681877 1324077493 A	K
572	1715 A	-7:91681876 1324077492 A	
572	1716 G	-7:91681875 1324077491 G	
573 Q	1717 C	-7:91681874 1324077490 C	Q
573	1718 A	-7:91681873 1324077489 A	
573	1719 A	-7:91681872 1324077488 A	
574 G	1720 G	-7:91681871 1324077487 G	G
574	1721 G	-7:91681870 1324077486 G	
574	1722 T	-7:91681869 1324077485 T	
575 F	1723 T	-7:91681868 1324077484 T	F
575	1724 T	-7:91681867 1324077483 T	
575	1725 C	-7:91681866 1324077482 C	
576 L	1726 C	-7:91681865 1324077481 C	L
576	1727 T	-7:91681864 1324077480 T	
576	1728 A	-7:91681863 1324077479 A	
577 N	1729 A	-7:91681862 1324077478 A	N
577	1730 A	-7:91681861 1324077477 A	
577	1731 T	-7:91681229 1324076845 T	
578 E	1732 G	-7:91681228 1324076844 G	E
578	1733 A	-7:91681227 1324076843 A	
578	1734 A	-7:91681226 1324076842 A	
579 E	1735 G	-7:91681225 1324076841 G	E
579	1736 A	-7:91681224 1324076840 A	
579	1737 A	-7:91681223 1324076839 A	
580 N	1738 A	-7:91681222 1324076838 A	N
580	1739 A	-7:91681221 1324076837 A	
580	1740 T	-7:91681220 1324076836 T	
581 L	1741 C	-7:91681219 1324076835 C	L
581	1742 T	-7:91681218 1324076834 T	
581	1743 A	-7:91681217 1324076833 A	
582 K	1744 A	-7:91681216 1324076832 A	K
582	1745 A	-7:91681215 1324076831 A	
582	1746 A	-7:91681214 1324076830 A	
583 S	1747 T	-7:91681213 1324076829 T	S
583	1748 C	-7:91681212 1324076828 C	
583	1749 C	-7:91681211 1324076827 C	
584 I	1750 A	-7:91681210 1324076826 A	I
584	1751 T	-7:91681209 1324076825 T	
584	1752 C	-7:91681208 1324076824 C	
585 V	1753 G	-7:91681207 1324076823 G	V
585	1754 T	-7:91681206 1324076822 T	
585	1755 A	-7:91681205 1324076821 A	
586 P	1756 C	-7:91681204 1324076820 C	P
586	1757 C	-7:91681203 1324076819 C	
586	1758 T	-7:91681202 1324076818 T	
587 V	1759 G	-7:91681201 1324076817 G	V
587	1760 T	-7:91681200 1324076816 T	
587	1761 T	-7:91681199 1324076815 T	
588 T	1762 A	-7:91681198 1324076814 A	T
588	1763 C	-7:91681197 1324076813 C	
588	1764 C	-7:91681196 1324076812 C	
589 K	1765 A	-7:91681195 1324076811 A	K
589	1766 A	-7:91681194 1324076810 A	
589	1767 A	-7:91681193 1324076809 A	
590 L	1768 C	-7:91681192 1324076808 C	L
590	1769 T	-7:91681191 1324076807 T	
590	1770 G	-7:91681190 1324076806 G	
591 K	1771 A	-7:91681189 1324076805 A	K
591	1772 A	-7:91681188 1324076804 A	
591	1773 A	-7:91681187 1324076803 A	
592 S	1774 A	-7:91681186 1324076802 A	S
592	1775 G	-7:91681185 1324076801 G	
592	1776 T	-7:91681184 1324076800 T	
593 K	1777 A	-7:91681183 1324076799 A	K
593	1778 A	-7:91681182 1324076798 A	
593	1779 G	-7:91681181 1324076797 G	
594 A	1780 G	-7:91681180 1324076796 G	A
594	1781 C	-7:91681179 1324076795 C	
594	1782 A	-7:91681178 1324076794 A	
595 P	1783 C	-7:91681177 1324076793 C	P
595	1784 C	-7:91681176 1324076792 C	
595	1785 T	-7:91681175 1324076791 T	
596 H	1786 C	-7:91681174 1324076790 C	H
596	1787 A	-7:91681173 1324076789 A	
596	1788 C	-7:91681172 1324076788 C	
597 W	1789 T	-7:91681171 1324076787 T	W
597	1790 G	-7:91681170 1324076786 G	
597	1791 G	-7:91681169 1324076785 G	
598 T	1792 A	-7:91681168 1324076784 A	T
598	1793 C	-7:91681167 1324076783 C	
598	1794 A	-7:91681166 1324076782 A	
599 N	1795 A	-7:91681165 1324076781 A	N
599	1796 A	-7:91681164 1324076780 A	
599	1797 T	-7:91681163 1324076779 T	
600 R	1798 C	-7:91681162 1324076778 C	R
600	1799 G	-7:91681161 1324076777 G	
600	1800 C	-7:91681160 1324076776 C	
601 I	1801 A	-7:91681159 1324076775 A	I
601	1802 T	-7:91681158 1324076774 T	
601	1803 A	-7:91681157 1324076773 A	
602 L	1804 C	-7:91681156 1324076772 C	L
602	1805 T	-7:91681155 1324076771 T	
602	1806 T	-7:91681154 1324076770 T	
603 H	1807 C	-7:91681153 1324076769 C	H
603	1808 A	-7:91681152 1324076768 A	
603	1809 T	-7:91681151 1324076767 T	
604 E	1810 G	-7:91681150 1324076766 G	E
604	1811 A	-7:91681149 1324076765 A	
604	1812 A	-7:91681148 1324076764 A	
605 Y	1813 T	-7:91681147 1324076763 T	Y
605	1814 A	-7:91681146 1324076762 A	
605	1815 C	-7:91681145 1324076761 C	
606 K	1816 A	-7:91681144 1324076760 A	K
606	1817 A	-7:91681143 1324076759 A	
606	1818 G	-7:91681142 1324076758 G	
607 N	1819 A	-7:91680651 1324076267 A	N
607	1820 A	-7:91680650 1324076266 A	
607	1821 T	-7:91680649 1324076265 T	
608 L	1822 C	-7:91680648 1324076264 C	L
608	1823 T	-7:91680647 1324076263 T	
608	1824 C	-7:91680646 1324076262 C	
609 S	1825 A	-7:91680645 1324076261 A	S
609	1826 G	-7:91680644 1324076260 G	
609	1827 T	-7:91680643 1324076259 T	
610 T	1828 A	-7:91680642 1324076258 A	T
610	1829 C	-7:91680641 1324076257 C	
610	1830 A	-7:91680640 1324076256 A	
611 S	1831 A	-7:91680639 1324076255 A	S
611	1832 G	-7:91680638 1324076254 G	
611	1833 T	-7:91680637 1324076253 T	
612 E	1834 G	-7:91680636 1324076252 G	E
612	1835 A	-7:91680635 1324076251 A	
612	1836 A	-7:91680634 1324076250 A	
613 G	1837 G	-7:91680633 1324076249 G	G
613	1838 G	-7:91680632 1324076248 G	
613	1839 T	-7:91680631 1324076247 T	
614 V	1840 G	-7:91680630 1324076246 G	V
614	1841 T	-7:91680629 1324076245 T	
614	1842 C	-7:91680628 1324076244 C	
615 S	1843 A	-7:91680627 1324076243 A	S
615	1844 G	-7:91680626 1324076242 G	
615	1845 T	-7:91680625 1324076241 T	
616 K	1846 A	-7:91680624 1324076240 A	K
616	1847 A	-7:91680623 1324076239 A	
616	1848 A	-7:91680622 1324076238 A	
617 E	1849 G	-7:91680621 1324076237 G	E
617	1850 A	-7:91680620 1324076236 A	
617	1851 A	-7:91680619 1324076235 A	
618 M	1852 A	-7:91680618 1324076234 A	M
618	1853 T	-7:91680617 1324076233 T	
618	1854 G	-7:91680616 1324076232 G	
619 H	1855 C	-7:91680615 1324076231 C	H
619	1856 A	-7:91680614 1324076230 A	
619	1857 T	-7:91680613 1324076229 T	
620 H	1858 C	-7:91680612 1324076228 C	H
620	1859 A	-7:91680611 1324076227 A	
620	1860 C	-7:91680610 1324076226 C	
621 L	1861 C	-7:91680609 1324076225 C	L
621	1862 T	-7:91680608 1324076224 T	
621	1863 T	-7:91680607 1324076223 T	
622 Q	1864 C	-7:91680606 1324076222 C	Q
622	1865 A	-7:91680605 1324076221 A	
622	1866 G	-7:91680604 1324076220 G	
623 R	1867 C	-7:91680603 1324076219 C	R
623	1868 G	-7:91680602 1324076218 G	
623	1869 C	-7:91680601 1324076217 C	
624 M	1870 A	-7:91680600 1324076216 A	M
624	1871 T	-7:91680599 1324076215 T	
624	1872 G	-7:91680598 1324076214 G	
625 F	1873 T	-7:91680597 1324076213 T	F
625	1874 T	-7:91680596 1324076212 T	
625	1875 C	-7:91680595 1324076211 C	
626 L	1876 T	-7:91680594 1324076210 T	L
626	1877 T	-7:91680593 1324076209 T	
626	1878 A	-7:91680592 1324076208 A	
627 Q	1879 C	-7:91680591 1324076207 C	Q
627	1880 A	-7:91680590 1324076206 A	
627	1881 G	-7:91680589 1324076205 G	
628 N	1882 A	-7:91680588 1324076204 A	N
628	1883 A	-7:91680587 1324076203 A	
628	1884 T	-7:91680586 1324076202 T	
629 C	1885 T	-7:91680585 1324076201 T	C
629	1886 G	-7:91680584 1324076200 G	
629	1887 C	-7:91680583 1324076199 C	
630 W	1888 T	-7:91680582 1324076198 T	W
630	1889 G	-7:91680581 1324076197 G	
630	1890 G	-7:91680580 1324076196 G	
631 E	1891 G	-7:91680579 1324076195 G	E
631	1892 A	-7:91680578 1324076194 A	
631	1893 A	-7:91680577 1324076193 A	
632 I	1894 A	-7:91680576 1324076192 A	I
632	1895 T	-7:91680575 1324076191 T	
632	1896 T	-7:91680574 1324076190 T	
633 P	1897 C	-7:91680573 1324076189 C	P
633	1898 C	-7:91680572 1324076188 C	
633	1899 T	-7:91680571 1324076187 T	
634 T	1900 A	-7:91680570 1324076186 A	T
634	1901 C	-7:91680569 1324076185 C	
634	1902 T	-7:91680568 1324076184 T	
635 Y	1903 T	-7:91680567 1324076183 T	Y
635	1904 A	-7:91680566 1324076182 A	
635	1905 T	-7:91680565 1324076181 T	
636 G	1906 G	-7:91680564 1324076180 G	G
636	1907 G	-7:91680563 1324076179 G	
636	1908 A	-7:91680562 1324076178 A	
637 A	1909 G	-7:91680561 1324076177 G	A
637	1910 C	-7:91680560 1324076176 C	
637	1911 A	-7:91680559 1324076175 A	
638 A	1912 G	-7:91680558 1324076174 G	A
638	1913 C	-7:91680557 1324076173 C	
638	1914 A	-7:91680556 1324076172 A	
639 F	1915 T	-7:91680555 1324076171 T	F
639	1916 T	-7:91680554 1324076170 T	
639	1917 T	-7:91680553 1324076169 T	
640 F	1918 T	-7:91680552 1324076168 T	F
640	1919 T	-7:91680551 1324076167 T	
640	1920 C	-7:91680550 1324076166 C	
641 T	1921 A	-7:91680549 1324076165 A	T
641	1922 C	-7:91680548 1324076164 C	
641	1923 A	-7:91680547 1324076163 A	
642 G	1924 G	-7:91680546 1324076162 G	G
642	1925 G	-7:91680545 1324076161 G	
642	1926 A	-7:91680544 1324076160 A	
643 Q	1927 C	-7:91680543 1324076159 C	Q
643	1928 A	-7:91680542 1324076158 A	
643	1929 G	-7:91680541 1324076157 G	
644 I	1930 A	-7:91680540 1324076156 A	I
644	1931 T	-7:91680539 1324076155 T	
644	1932 A	-7:91680538 1324076154 A	
645 F	1933 T	-7:91680537 1324076153 T	F
645	1934 T	-7:91680536 1324076152 T	
645	1935 T	-7:91680535 1324076151 T	
646 T	1936 A	-7:91680534 1324076150 A	T
646	1937 C	-7:91680533 1324076149 C	
646	1938 A	-7:91680532 1324076148 A	
647 K	1939 A	-7:91680531 1324076147 A	K
647	1940 A	-7:91680530 1324076146 A	
647	1941 G	-7:91680529 1324076145 G	
648 A	1942 G	-7:91680528 1324076144 G	A
648	1943 C	-7:91680527 1324076143 C	
648	1944 A	-7:91680526 1324076142 A	
649 S	1945 A	-7:91680525 1324076141 A	S
649	1946 G	-7:91680524 1324076140 G	
649	1947 C	-7:91680523 1324076139 C	
650 P	1948 C	-7:91680522 1324076138 C	P
650	1949 C	-7:91680521 1324076137 C	
650	1950 C	-7:91680520 1324076136 C	
651 S	1951 A	-7:91680519 1324076135 A	S
651	1952 G	-7:91680518 1324076134 G	
651	1953 C	-7:91680517 1324076133 C	
652 N	1954 A	-7:91680516 1324076132 A	N
652	1955 A	-7:91680515 1324076131 A	
652	1956 T	-7:91680514 1324076130 T	
653 H	1957 C	-7:91680513 1324076129 C	H
653	1958 A	-7:91680512 1324076128 A	
653	1959 T	-7:91680511 1324076127 T	
654 K	1960 A	-7:91680510 1324076126 A	K
654	1961 A	-7:91680509 1324076125 A	
654	1962 A	-7:91680508 1324076124 A	
655 V	1963 G	-7:91680507 1324076123 G	V
655	1964 T	-7:91680506 1324076122 T	
655	1965 C	-7:91680505 1324076121 C	
656 I	1966 A	-7:91680504 1324076120 A	I
656	1967 T	-7:91680503 1324076119 T	
656	1968 C	-7:91680502 1324076118 C	
657 P	1969 C	-7:91680501 1324076117 C	P
657	1970 C	-7:91680500 1324076116 C	
657	1971 T	-7:91680499 1324076115 T	
658 V	1972 G	-7:91680498 1324076114 G	V
658	1973 T	-7:91680497 1324076113 T	
658	1974 G	-7:91680496 1324076112 G	
659 Y	1975 T	-7:91680495 1324076111 T	Y
659	1976 A	-7:91680494 1324076110 A	
659	1977 T	-7:91680493 1324076109 T	
660 V	1978 G	-7:91680492 1324076108 G	V
660	1979 T	-7:91680491 1324076107 T	
660	1980 A	-7:91680490 1324076106 A	
661 G	1981 G	-7:91680489 1324076105 G	G
661	1982 G	-7:91680488 1324076104 G	
661	1983 A	-7:91680487 1324076103 A	
662 V	1984 G	-7:91680486 1324076102 G	V
662	1985 T	-7:91680485 1324076101 T	
662	1986 G	-7:91680484 1324076100 G	
663 N	1987 A	-7:91680483 1324076099 A	N
663	1988 A	-7:91680482 1324076098 A	
663	1989 T	-7:91680481 1324076097 T	
664 I	1990 A	-7:91680480 1324076096 A	I
664	1991 T	-7:91680479 1324076095 T	
664	1992 A	-7:91680478 1324076094 A	
665 K	1993 A	-7:91680477 1324076093 A	K
665	1994 A	-7:91680476 1324076092 A	
665	1995 A	-7:91680475 1324076091 A	
666 G	1996 G	-7:91680474 1324076090 G	G
666	1997 G	-7:91680473 1324076089 G	
666	1998 A	-7:91680472 1324076088 A	
667 L	1999 C	-7:91680471 1324076087 C	L
667	2000 T	-7:91680470 1324076086 T	
667	2001 T	-7:91680469 1324076085 T	
668 H	2002 C	-7:91680468 1324076084 C	H
668	2003 A	-7:91680467 1324076083 A	
668	2004 T	-7:91680466 1324076082 T	
669 L	2005 C	-7:91680465 1324076081 C	L
669	2006 T	-7:91680464 1324076080 T	
669	2007 C	-7:91680463 1324076079 C	
670 L	2008 C	-7:91680462 1324076078 C	L
670	2009 T	-7:91680461 1324076077 T	
670	2010 C	-7:91680460 1324076076 C	
671 N	2011 A	-7:91680459 1324076075 A	N
671	2012 A	-7:91680458 1324076074 A	
671	2013 C	-7:91680457 1324076073 C	
672 M	2014 A	-7:91680456 1324076072 A	M
672	2015 T	-7:91680455 1324076071 T	
672	2016 G	-7:91680454 1324076070 G	
673 E	2017 G	-7:91680453 1324076069 G	E
673	2018 A	-7:91680452 1324076068 A	
673	2019 A	-7:91680451 1324076067 A	
674 T	2020 A	-7:91680450 1324076066 A	T
674	2021 C	-7:91680449 1324076065 C	
674	2022 T	-7:91680448 1324076064 T	
675 K	2023 A	-7:91680447 1324076063 A	K
675	2024 A	-7:91680446 1324076062 A	
675	2025 G	-7:91680445 1324076061 G	
>ENSP00000351284 
1 M	1 A	-12:912485 1948504724 A	M
1	2 T	-12:912484 1948504723 T	
1	3 G	-12:912483 1948504722 G	
2 S	4 T	-12:912482 1948504721 T	S
2	5 C	-12:912481 1948504720 C	
2	6 T	-12:912480 1948504719 T	
3 G	7 G	-12:912479 1948504718 G	G
3	8 G	-12:912478 1948504717 G	
3	9 G	-12:912477 1948504716 G	
4 T	10 A	-12:912476 1948504715 A	T
4	11 C	-12:912475 1948504714 C	
4	12 T	-12:912474 1948504713 T	
5 E	13 G	-12:912473 1948504712 G	E
5	14 A	-12:912472 1948504711 A	
5	15 G	-12:912471 1948504710 G	
6 E	16 G	-12:912470 1948504709 G	E
6	17 A	-12:912469 1948504708 A	
6	18 A	-12:912468 1948504707 A	
7 A	19 G	-12:912467 1948504706 G	A
7	20 C	-12:912466 1948504705 C	
7	21 A	-12:912465 1948504704 A	
8 I	22 A	-12:912464 1948504703 A	I
8	23 T	-12:912463 1948504702 T	
8	24 T	-12:912462 1948504701 T	
9 L	25 C	-12:912461 1948504700 C	L
9	26 T	-12:912460 1948504699 T	
9	27 T	-12:912459 1948504698 T	
10 G	28 G	-12:912458 1948504697 G	G
10	29 G	-12:912457 1948504696 G	
10	30 A	-12:912456 1948504695 A	
11 G	31 G	-12:912455 1948504694 G	G
11	32 G	-12:912454 1948504693 G	
11	33 A	-12:912453 1948504692 A	
12 R	34 C	-12:912452 1948504691 C	R
12	35 G	-12:912451 1948504690 G	
12	36 T	-12:912450 1948504689 T	
13 D	37 G	-12:912449 1948504688 G	D
13	38 A	-12:912448 1948504687 A	
13	39 C	-12:912447 1948504686 C	
14 S	40 A	-12:912446 1948504685 A	S
14	41 G	-12:912445 1948504684 G	
14	42 C	-12:912444 1948504683 C	
15 H	43 C	-12:912443 1948504682 C	H
15	44 A	-12:912442 1948504681 A	
15	45 T	-12:912441 1948504680 T	
16 P	46 C	-12:912440 1948504679 C	P
16	47 C	-12:912439 1948504678 C	
16	48 T	-12:912438 1948504677 T	
17 A	49 G	-12:912437 1948504676 G	A
17	50 C	-12:912436 1948504675 C	
17	51 T	-12:912435 1948504674 T	
18 A	52 G	-12:912434 1948504673 G	A
18	53 C	-12:912433 1948504672 C	
18	54 T	-12:912432 1948504671 T	
19 G	55 G	-12:912431 1948504670 G	G
19	56 G	-12:912430 1948504669 G	
19	57 C	-12:912429 1948504668 C	
20 G	58 G	-12:912428 1948504667 G	G
20	59 G	-12:912427 1948504666 G	
20	60 C	-12:912426 1948504665 C	
21 G	61 G	-12:912425 1948504664 G	G
21	62 G	-12:912424 1948504663 G	
21	63 C	-12:912423 1948504662 C	
22 S	64 T	-12:912422 1948504661 T	S
22	65 C	-12:912421 1948504660 C	
22	66 A	-12:912420 1948504659 A	
23 V	67 G	-12:912419 1948504658 G	V
23	68 T	-12:912418 1948504657 T	
23	69 G	-12:912417 1948504656 G	
24 L	70 T	-12:912416 1948504655 T	L
24	71 T	-12:912415 1948504654 T	
24	72 A	-12:912414 1948504653 A	
25 C	73 T	-12:912413 1948504652 T	C
25	74 G	-12:912412 1948504651 G	
25	75 C	-12:912411 1948504650 C	
26 F	76 T	-12:912410 1948504649 T	F
26	77 T	-12:912409 1948504648 T	
26	78 T	-12:912408 1948504647 T	
27 G	79 G	-12:912407 1948504646 G	G
27	80 G	-12:912406 1948504645 G	
27	81 A	-12:912405 1948504644 A	
28 Q	82 C	-12:912404 1948504643 C	Q
28	83 A	-12:912403 1948504642 A	
28	84 G	-12:912402 1948504641 G	
29 C	85 T	-12:910748 1948502987 T	C
29	86 G	-12:910747 1948502986 G	
29	87 C	-12:910746 1948502985 C	
30 Q	88 C	-12:910745 1948502984 C	Q
30	89 A	-12:910744 1948502983 A	
30	90 G	-12:910743 1948502982 G	
31 Y	91 T	-12:910742 1948502981 T	Y
31	92 A	-12:910741 1948502980 A	
31	93 C	-12:910740 1948502979 C	
32 T	94 A	-12:910739 1948502978 A	T
32	95 C	-12:910738 1948502977 C	
32	96 A	-12:910737 1948502976 A	
33 A	97 G	-12:910736 1948502975 G	A
33	98 C	-12:910735 1948502974 C	
33	99 A	-12:910734 1948502973 A	
34 E	100 G	-12:910733 1948502972 G	E
34	101 A	-12:910732 1948502971 A	
34	102 A	-12:910731 1948502970 A	
35 E	103 G	-12:910730 1948502969 G	E
35	104 A	-12:910729 1948502968 A	
35	105 G	-12:910728 1948502967 G	
36 Y	106 T	-12:910727 1948502966 T	Y
36	107 A	-12:910726 1948502965 A	
36	108 C	-12:910725 1948502964 C	
37 Q	109 C	-12:910724 1948502963 C	Q
37	110 A	-12:910723 1948502962 A	
37	111 G	-12:910722 1948502961 G	
38 A	112 G	-12:910721 1948502960 G	A
38	113 C	-12:910720 1948502959 C	
38	114 C	-12:910719 1948502958 C	
39 I	115 A	-12:910718 1948502957 A	I
39	116 T	-12:910717 1948502956 T	
39	117 C	-12:910716 1948502955 C	
40 Q	118 C	-12:910715 1948502954 C	Q
40	119 A	-12:910714 1948502953 A	
40	120 G	-12:910713 1948502952 G	
41 K	121 A	-12:910712 1948502951 A	K
41	122 A	-12:910711 1948502950 A	
41	123 G	-12:910710 1948502949 G	
42 A	124 G	-12:910709 1948502948 G	A
42	125 C	-12:910708 1948502947 C	
42	126 C	-12:910707 1948502946 C	
43 L	127 C	-12:910706 1948502945 C	L
43	128 T	-12:910705 1948502944 T	
43	129 G	-12:910704 1948502943 G	
44 R	130 A	-12:910703 1948502942 A	R
44	131 G	-12:910702 1948502941 G	
44	132 G	-12:910701 1948502940 G	
45 Q	133 C	-12:910700 1948502939 C	Q
45	134 A	-12:910699 1948502938 A	
45	135 G	-12:910698 1948502937 G	
46 R	136 A	-12:910697 1948502936 A	R
46	137 G	-12:910696 1948502935 G	
46	138 G	-12:910695 1948502934 G	
47 L	139 C	-12:910694 1948502933 C	L
47	140 T	-12:910693 1948502932 T	
47	141 G	-12:910692 1948502931 G	
48 G	142 G	-12:910691 1948502930 G	G
48	143 G	-12:910690 1948502929 G	
48	144 C	-12:910689 1948502928 C	
49 P	145 C	-12:910688 1948502927 C	P
49	146 C	-12:910687 1948502926 C	
49	147 A	-12:910686 1948502925 A	
50 E	148 G	-12:910685 1948502924 G	E
50	149 A	-12:910684 1948502923 A	
50	150 A	-12:910683 1948502922 A	
51 Y	151 T	-12:910682 1948502921 T	Y
51	152 A	-12:910681 1948502920 A	
51	153 C	-12:910680 1948502919 C	
52 I	154 A	-12:910679 1948502918 A	I
52	155 T	-12:910678 1948502917 T	
52	156 A	-12:910677 1948502916 A	
53 S	157 A	-12:910676 1948502915 A	S
53	158 G	-12:910675 1948502914 G	
53	159 T	-12:910674 1948502913 T	
54 S	160 A	-12:910673 1948502912 A	S
54	161 G	-12:910672 1948502911 G	
54	162 C	-12:910671 1948502910 C	
55 R	163 C	-12:910670 1948502909 C	R
55	164 G	-12:910669 1948502908 G	
55	165 C	-12:910668 1948502907 C	
56 M	166 A	-12:910667 1948502906 A	M
56	167 T	-12:910666 1948502905 T	
56	168 G	-12:910665 1948502904 G	
57 A	169 G	-12:910664 1948502903 G	A
57	170 C	-12:910663 1948502902 C	
57	171 T	-12:910662 1948502901 T	
58 G	172 G	-12:910661 1948502900 G	G
58	173 G	-12:910660 1948502899 G	
58	174 C	-12:910659 1948502898 C	
59 G	175 G	-12:910658 1948502897 G	G
59	176 G	-12:910657 1948502896 G	
59	177 A	-12:910656 1948502895 A	
60 G	178 G	-12:910655 1948502894 G	G
60	179 G	-12:910654 1948502893 G	
60	180 C	-12:910653 1948502892 C	
61 Q	181 C	-12:910652 1948502891 C	Q
61	182 A	-12:910651 1948502890 A	
61	183 G	-12:910650 1948502889 G	
62 K	184 A	-12:910649 1948502888 A	K
62	185 A	-12:910648 1948502887 A	
62	186 G	-12:910647 1948502886 G	
63 V	187 G	-12:909571 1948501810 G	V
63	188 T	-12:909570 1948501809 T	
63	189 G	-12:909569 1948501808 G	
64 C	190 T	-12:909568 1948501807 T	C
64	191 G	-12:909567 1948501806 G	
64	192 C	-12:909566 1948501805 C	
65 Y	193 T	-12:909565 1948501804 T	Y
65	194 A	-12:909564 1948501803 A	
65	195 C	-12:909563 1948501802 C	
66 I	196 A	-12:909562 1948501801 A	I
66	197 T	-12:909561 1948501800 T	
66	198 T	-12:909560 1948501799 T	
67 E	199 G	-12:909559 1948501798 G	E
67	200 A	-12:909558 1948501797 A	
67	201 G	-12:909557 1948501796 G	
68 G	202 G	-12:909556 1948501795 G	G
68	203 G	-12:909555 1948501794 G	
68	204 T	-12:909554 1948501793 T	
69 H	205 C	-12:909553 1948501792 C	H
69	206 A	-12:909552 1948501791 A	
69	207 T	-12:909551 1948501790 T	
70 R	208 C	-12:909550 1948501789 C	R
70	209 G	-12:909549 1948501788 G	
70	210 G	-12:909548 1948501787 G	
71 V	211 G	-12:909547 1948501786 G	V
71	212 T	-12:909546 1948501785 T	
71	213 A	-12:909545 1948501784 A	
72 I	214 A	-12:909544 1948501783 A	I
72	215 T	-12:909543 1948501782 T	
72	216 T	-12:909542 1948501781 T	
73 N	217 A	-12:909541 1948501780 A	N
73	218 A	-12:909540 1948501779 A	
73	219 T	-12:909539 1948501778 T	
74 L	220 C	-12:909538 1948501777 C	L
74	221 T	-12:909537 1948501776 T	
74	222 G	-12:909536 1948501775 G	
75 A	223 G	-12:909535 1948501774 G	A
75	224 C	-12:909534 1948501773 C	
75	225 C	-12:909533 1948501772 C	
76 N	226 A	-12:909532 1948501771 A	N
76	227 A	-12:909531 1948501770 A	
76	228 T	-12:909530 1948501769 T	
77 E	229 G	-12:909529 1948501768 G	E
77	230 A	-12:909528 1948501767 A	
77	231 G	-12:909527 1948501766 G	
78 M	232 A	-12:909526 1948501765 A	M
78	233 T	-12:909525 1948501764 T	
78	234 G	-12:909524 1948501763 G	
79 F	235 T	-12:909523 1948501762 T	F
79	236 T	-12:909522 1948501761 T	
79	237 T	-12:909521 1948501760 T	
80 G	238 G	-12:909520 1948501759 G	G
80	239 G	-12:909519 1948501758 G	
80	240 T	-12:909518 1948501757 T	
81 Y	241 T	-12:909517 1948501756 T	Y
81	242 A	-12:909516 1948501755 A	
81	243 C	-12:909515 1948501754 C	
82 N	244 A	-12:909514 1948501753 A	N
82	245 A	-12:909513 1948501752 A	
82	246 T	-12:909512 1948501751 T	
83 G	247 G	-12:909511 1948501750 G	G
83	248 G	-12:909510 1948501749 G	
83	249 C	-12:909509 1948501748 C	
84 W	250 T	-12:909508 1948501747 T	W
84	251 G	-12:909507 1948501746 G	
84	252 G	-12:909506 1948501745 G	
85 A	253 G	-12:909505 1948501744 G	A
85	254 C	-12:909504 1948501743 C	
85	255 A	-12:909503 1948501742 A	
86 H	256 C	-12:909502 1948501741 C	H
86	257 A	-12:909501 1948501740 A	
86	258 C	-12:909500 1948501739 C	
87 S	259 T	-12:909499 1948501738 T	S
87	260 C	-12:909498 1948501737 C	
87	261 C	-12:909497 1948501736 C	
88 I	262 A	-12:909496 1948501735 A	I
88	263 T	-12:909495 1948501734 T	
88	264 C	-12:909494 1948501733 C	
89 T	265 A	-12:909493 1948501732 A	T
89	266 C	-12:909492 1948501731 C	
89	267 G	-12:909491 1948501730 G	
90 Q	268 C	-12:909490 1948501729 C	Q
90	269 A	-12:909489 1948501728 A	
90	270 G	-12:909488 1948501727 G	
91 Q	271 C	-12:909487 1948501726 C	Q
91	272 A	-12:909486 1948501725 A	
91	273 G	-12:909485 1948501724 G	
92 N	274 A	-12:909484 1948501723 A	N
92	275 A	-12:909483 1948501722 A	
92	276 T	-12:909482 1948501721 T	
93 V	277 G	-12:909481 1948501720 G	V
93	278 T	-12:909480 1948501719 T	
93	279 G	-12:909479 1948501718 G	
94 D	280 G	-12:909478 1948501717 G	D
94	281 A	-12:909313 1948501552 A	
94	282 T	-12:909312 1948501551 T	
95 F	283 T	-12:909311 1948501550 T	F
95	284 T	-12:909310 1948501549 T	
95	285 T	-12:909309 1948501548 T	
96 V	286 G	-12:909308 1948501547 G	V
96	287 T	-12:909307 1948501546 T	
96	288 T	-12:909306 1948501545 T	
97 D	289 G	-12:909305 1948501544 G	D
97	290 A	-12:909304 1948501543 A	
97	291 C	-12:909303 1948501542 C	
98 L	292 C	-12:909302 1948501541 C	L
98	293 T	-12:909301 1948501540 T	
98	294 C	-12:909300 1948501539 C	
99 N	295 A	-12:909299 1948501538 A	N
99	296 A	-12:909298 1948501537 A	
99	297 C	-12:909297 1948501536 C	
100 N	298 A	-12:909296 1948501535 A	N
100	299 A	-12:909295 1948501534 A	
100	300 T	-12:909294 1948501533 T	
101 G	301 G	-12:909293 1948501532 G	G
101	302 G	-12:909292 1948501531 G	
101	303 C	-12:909291 1948501530 C	
102 K	304 A	-12:909290 1948501529 A	K
102	305 A	-12:909289 1948501528 A	
102	306 G	-12:909288 1948501527 G	
103 F	307 T	-12:909287 1948501526 T	F
103	308 T	-12:909286 1948501525 T	
103	309 C	-12:909285 1948501524 C	
104 Y	310 T	-12:909284 1948501523 T	Y
104	311 A	-12:909283 1948501522 A	
104	312 C	-12:909282 1948501521 C	
105 V	313 G	-12:909281 1948501520 G	V
105	314 T	-12:909280 1948501519 T	
105	315 G	-12:909279 1948501518 G	
106 G	316 G	-12:909278 1948501517 G	G
106	317 G	-12:909277 1948501516 G	
106	318 A	-12:909276 1948501515 A	
107 V	319 G	-12:909275 1948501514 G	V
107	320 T	-12:909274 1948501513 T	
107	321 C	-12:909273 1948501512 C	
108 C	322 T	-12:909272 1948501511 T	C
108	323 G	-12:909271 1948501510 G	
108	324 T	-12:909270 1948501509 T	
109 A	325 G	-12:909269 1948501508 G	A
109	326 C	-12:909268 1948501507 C	
109	327 A	-12:909267 1948501506 A	
110 F	328 T	-12:909266 1948501505 T	F
110	329 T	-12:909265 1948501504 T	
110	330 T	-12:909264 1948501503 T	
111 V	331 G	-12:909263 1948501502 G	V
111	332 T	-12:909262 1948501501 T	
111	333 G	-12:909261 1948501500 G	
112 R	334 A	-12:909260 1948501499 A	R
112	335 G	-12:909259 1948501498 G	
112	336 G	-12:909258 1948501497 G	
113 V	337 G	-12:909257 1948501496 G	V
113	338 T	-12:909256 1948501495 T	
113	339 C	-12:909255 1948501494 C	
114 Q	340 C	-12:909254 1948501493 C	Q
114	341 A	-12:909253 1948501492 A	
114	342 G	-12:909252 1948501491 G	
115 L	343 C	-12:909251 1948501490 C	L
115	344 T	-12:909250 1948501489 T	
115	345 G	-12:909249 1948501488 G	
116 K	346 A	-12:909248 1948501487 A	K
116	347 A	-12:909247 1948501486 A	
116	348 G	-12:909246 1948501485 G	
117 D	349 G	-12:906690 1948498929 G	D
117	350 A	-12:906689 1948498928 A	
117	351 T	-12:906688 1948498927 T	
118 G	352 G	-12:906687 1948498926 G	G
118	353 G	-12:906686 1948498925 G	
118	354 T	-12:906685 1948498924 T	
119 S	355 T	-12:906684 1948498923 T	S
119	356 C	-12:906683 1948498922 C	
119	357 A	-12:906682 1948498921 A	
120 Y	358 T	-12:906681 1948498920 T	Y
120	359 A	-12:906680 1948498919 A	
120	360 T	-12:906679 1948498918 T	
121 H	361 C	-12:906678 1948498917 C	H
121	362 A	-12:906677 1948498916 A	
121	363 T	-12:906676 1948498915 T	
122 E	364 G	-12:906675 1948498914 G	E
122	365 A	-12:906674 1948498913 A	
122	366 A	-12:906673 1948498912 A	
123 D	367 G	-12:906672 1948498911 G	D
123	368 A	-12:906671 1948498910 A	
123	369 T	-12:906670 1948498909 T	
124 V	370 G	-12:906669 1948498908 G	V
124	371 T	-12:906668 1948498907 T	
124	372 T	-12:906667 1948498906 T	
125 G	373 G	-12:906666 1948498905 G	G
125	374 G	-12:906665 1948498904 G	
125	375 T	-12:906664 1948498903 T	
126 Y	376 T	-12:906663 1948498902 T	Y
126	377 A	-12:906662 1948498901 A	
126	378 T	-12:906661 1948498900 T	
127 G	379 G	-12:906660 1948498899 G	G
127	380 G	-12:906659 1948498898 G	
127	381 T	-12:906658 1948498897 T	
128 V	382 G	-12:906657 1948498896 G	V
128	383 T	-12:906656 1948498895 T	
128	384 T	-12:906655 1948498894 T	
129 S	385 A	-12:906654 1948498893 A	S
129	386 G	-12:906653 1948498892 G	
129	387 T	-12:906652 1948498891 T	
130 E	388 G	-12:906651 1948498890 G	E
130	389 A	-12:906650 1948498889 A	
130	390 G	-12:906649 1948498888 G	
131 G	391 G	-12:906648 1948498887 G	G
131	392 G	-12:906647 1948498886 G	
131	393 C	-12:906646 1948498885 C	
132 L	394 C	-12:906645 1948498884 C	L
132	395 T	-12:906644 1948498883 T	
132	396 C	-12:906643 1948498882 C	
133 K	397 A	-12:906642 1948498881 A	K
133	398 A	-12:906641 1948498880 A	
133	399 G	-12:906640 1948498879 G	
134 S	400 T	-12:906639 1948498878 T	S
134	401 C	-12:906638 1948498877 C	
134	402 C	-12:906637 1948498876 C	
135 K	403 A	-12:906636 1948498875 A	K
135	404 A	-12:906635 1948498874 A	
135	405 G	-12:906634 1948498873 G	
136 A	406 G	-12:906633 1948498872 G	A
136	407 C	-12:906632 1948498871 C	
136	408 T	-12:906631 1948498870 T	
137 L	409 T	-12:906630 1948498869 T	L
137	410 T	-12:906629 1948498868 T	
137	411 A	-12:906628 1948498867 A	
138 S	412 T	-12:906627 1948498866 T	S
138	413 C	-12:906626 1948498865 C	
138	414 T	-12:906625 1948498864 T	
139 L	415 T	-12:906624 1948498863 T	L
139	416 T	-12:906623 1948498862 T	
139	417 G	-12:906622 1948498861 G	
140 E	418 G	-12:906621 1948498860 G	E
140	419 A	-12:906620 1948498859 A	
140	420 G	-12:906619 1948498858 G	
141 K	421 A	-12:906618 1948498857 A	K
141	422 A	-12:906617 1948498856 A	
141	423 G	-12:906616 1948498855 G	
142 A	424 G	-12:906615 1948498854 G	A
142	425 C	-12:906614 1948498853 C	
142	426 A	-12:906613 1948498852 A	
143 R	427 A	-12:906612 1948498851 A	R
143	428 G	-12:906611 1948498850 G	
143	429 G	-12:906610 1948498849 G	
144 K	430 A	-12:906609 1948498848 A	K
144	431 A	-12:906608 1948498847 A	
144	432 G	-12:906607 1948498846 G	
145 E	433 G	-12:906606 1948498845 G	E
145	434 A	-12:906605 1948498844 A	
145	435 G	-12:906604 1948498843 G	
146 A	436 G	-12:906603 1948498842 G	A
146	437 C	-12:906602 1948498841 C	
146	438 G	-12:906601 1948498840 G	
147 V	439 G	-12:906600 1948498839 G	V
147	440 T	-12:906599 1948498838 T	
147	441 G	-12:906598 1948498837 G	
148 T	442 A	-12:906597 1948498836 A	T
148	443 C	-12:906596 1948498835 C	
148	444 A	-12:906595 1948498834 A	
149 D	445 G	-12:906594 1948498833 G	D
149	446 A	-12:906593 1948498832 A	
149	447 C	-12:906592 1948498831 C	
150 G	448 G	-12:906591 1948498830 G	G
150	449 G	-12:906590 1948498829 G	
150	450 G	-12:906589 1948498828 G	
151 L	451 C	-12:906588 1948498827 C	L
151	452 T	-12:906587 1948498826 T	
151	453 G	-12:906586 1948498825 G	
152 K	454 A	-12:906585 1948498824 A	K
152	455 A	-12:906584 1948498823 A	
152	456 G	-12:906583 1948498822 G	
153 R	457 C	-12:906582 1948498821 C	R
153	458 G	-12:906581 1948498820 G	
153	459 A	-12:906580 1948498819 A	
154 A	460 G	-12:906579 1948498818 G	A
154	461 C	-12:906578 1948498817 C	
154	462 C	-12:906577 1948498816 C	
155 L	463 C	-12:906576 1948498815 C	L
155	464 T	-12:906575 1948498814 T	
155	465 C	-12:906574 1948498813 C	
156 R	466 A	-12:906573 1948498812 A	R
156	467 G	-12:906572 1948498811 G	
156	468 G	-12:904952 1948497191 G	
157 S	469 A	-12:904951 1948497190 A	S
157	470 G	-12:904950 1948497189 G	
157	471 T	-12:904949 1948497188 T	
158 F	472 T	-12:904948 1948497187 T	F
158	473 T	-12:904947 1948497186 T	
158	474 T	-12:904946 1948497185 T	
159 G	475 G	-12:904945 1948497184 G	G
159	476 G	-12:904944 1948497183 G	
159	477 G	-12:904943 1948497182 G	
160 N	478 A	-12:904942 1948497181 A	N
160	479 A	-12:904941 1948497180 A	
160	480 T	-12:904940 1948497179 T	
161 A	481 G	-12:904939 1948497178 G	A
161	482 C	-12:904938 1948497177 C	
161	483 A	-12:904937 1948497176 A	
162 L	484 C	-12:904936 1948497175 C	L
162	485 T	-12:904935 1948497174 T	
162	486 T	-12:904934 1948497173 T	
163 G	487 G	-12:904933 1948497172 G	G
163	488 G	-12:904932 1948497171 G	
163	489 A	-12:904931 1948497170 A	
164 N	490 A	-12:904930 1948497169 A	N
164	491 A	-12:904929 1948497168 A	
164	492 C	-12:904928 1948497167 C	
165 C	493 T	-12:904927 1948497166 T	C
165	494 G	-12:904926 1948497165 G	
165	495 T	-12:904925 1948497164 T	
166 I	496 A	-12:904924 1948497163 A	I
166	497 T	-12:904923 1948497162 T	
166	498 T	-12:904922 1948497161 T	
167 L	499 C	-12:904921 1948497160 C	L
167	500 T	-12:904920 1948497159 T	
167	501 G	-12:904919 1948497158 G	
168 D	502 G	-12:904918 1948497157 G	D
168	503 A	-12:904917 1948497156 A	
168	504 C	-12:904916 1948497155 C	
169 K	505 A	-12:904915 1948497154 A	K
169	506 A	-12:904914 1948497153 A	
169	507 A	-12:904913 1948497152 A	
170 D	508 G	-12:904912 1948497151 G	D
170	509 A	-12:904911 1948497150 A	
170	510 C	-12:904910 1948497149 C	
171 Y	511 T	-12:904909 1948497148 T	Y
171	512 A	-12:904908 1948497147 A	
171	513 C	-12:904907 1948497146 C	
172 L	514 C	-12:904906 1948497145 C	L
172	515 T	-12:904905 1948497144 T	
172	516 G	-12:904904 1948497143 G	
173 R	517 A	-12:904903 1948497142 A	R
173	518 G	-12:904902 1948497141 G	
173	519 A	-12:904901 1948497140 A	
174 S	520 T	-12:904900 1948497139 T	S
174	521 C	-12:904899 1948497138 C	
174	522 A	-12:904898 1948497137 A	
175 L	523 C	-12:904897 1948497136 C	L
175	524 T	-12:904896 1948497135 T	
175	525 A	-12:904895 1948497134 A	
176 N	526 A	-12:904894 1948497133 A	N
176	527 A	-12:904893 1948497132 A	
176	528 T	-12:904892 1948497131 T	
177 K	529 A	-12:904891 1948497130 A	K
177	530 A	-12:904890 1948497129 A	
177	531 G	-12:904889 1948497128 G	
178 L	532 C	-12:904888 1948497127 C	L
178	533 T	-12:904887 1948497126 T	
178	534 T	-12:904886 1948497125 T	
179 P	535 C	-12:904885 1948497124 C	P
179	536 C	-12:904884 1948497123 C	
179	537 A	-12:904883 1948497122 A	
180 R	538 C	-12:904882 1948497121 C	R
180	539 G	-12:904881 1948497120 G	
180	540 C	-12:904880 1948497119 C	
181 Q	541 C	-12:904879 1948497118 C	Q
181	542 A	-12:904878 1948497117 A	
181	543 G	-12:904877 1948497116 G	
182 L	544 T	-12:896247 1948488486 T	L
182	545 T	-12:896246 1948488485 T	
182	546 G	-12:896245 1948488484 G	
183 P	547 C	-12:896244 1948488483 C	P
183	548 C	-12:896243 1948488482 C	
183	549 T	-12:896242 1948488481 T	
184 L	550 C	-12:896241 1948488480 C	L
184	551 T	-12:896240 1948488479 T	
184	552 T	-12:896239 1948488478 T	
185 E	553 G	-12:896238 1948488477 G	E
185	554 A	-12:896237 1948488476 A	
185	555 A	-12:896236 1948488475 A	
186 V	556 G	-12:896235 1948488474 G	V
186	557 T	-12:896234 1948488473 T	
186	558 G	-12:896233 1948488472 G	
187 D	559 G	-12:896232 1948488471 G	D
187	560 A	-12:896231 1948488470 A	
187	561 T	-12:896230 1948488469 T	
188 L	562 T	-12:896229 1948488468 T	L
188	563 T	-12:896228 1948488467 T	
188	564 A	-12:896227 1948488466 A	
189 T	565 A	-12:896226 1948488465 A	T
189	566 C	-12:896225 1948488464 C	
189	567 T	-12:896224 1948488463 T	
190 K	568 A	-12:896223 1948488462 A	K
190	569 A	-12:896222 1948488461 A	
190	570 A	-12:896221 1948488460 A	
191 A	571 G	-12:896220 1948488459 G	A
191	572 C	-12:896219 1948488458 C	
191	573 G	-12:896218 1948488457 G	
192 K	574 A	-12:896217 1948488456 A	K
192	575 A	-12:896216 1948488455 A	
192	576 G	-12:896215 1948488454 G	
193 R	577 A	-12:896214 1948488453 A	R
193	578 G	-12:896213 1948488452 G	
193	579 A	-12:896212 1948488451 A	
194 Q	580 C	-12:896211 1948488450 C	Q
194	581 A	-12:896210 1948488449 A	
194	582 A	-12:896209 1948488448 A	
195 D	583 G	-12:896208 1948488447 G	D
195	584 A	-12:896207 1948488446 A	
195	585 T	-12:896206 1948488445 T	
196 L	586 C	-12:896205 1948488444 C	L
196	587 T	-12:896204 1948488443 T	
196	588 T	-12:896203 1948488442 T	
197 E	589 G	-12:896202 1948488441 G	E
197	590 A	-12:896201 1948488440 A	
197	591 A	-12:896200 1948488439 A	
198 P	592 C	-12:896199 1948488438 C	P
198	593 C	-12:896198 1948488437 C	
198	594 G	-12:896197 1948488436 G	
199 S	595 T	-12:896196 1948488435 T	S
199	596 C	-12:896195 1948488434 C	
199	597 T	-12:896194 1948488433 T	
200 V	598 G	-12:896193 1948488432 G	V
200	599 T	-12:896192 1948488431 T	
200	600 G	-12:896191 1948488430 G	
201 E	601 G	-12:896190 1948488429 G	E
201	602 A	-12:896189 1948488428 A	
201	603 G	-12:896188 1948488427 G	
202 E	604 G	-12:896187 1948488426 G	E
202	605 A	-12:896186 1948488425 A	
202	606 G	-12:896185 1948488424 G	
203 A	607 G	-12:896184 1948488423 G	A
203	608 C	-12:896183 1948488422 C	
203	609 A	-12:896182 1948488421 A	
204 R	610 A	-12:896181 1948488420 A	R
204	611 G	-12:896180 1948488419 G	
204	612 A	-12:896179 1948488418 A	
205 Y	613 T	-12:896178 1948488417 T	Y
205	614 A	-12:896177 1948488416 A	
205	615 C	-12:896176 1948488415 C	
206 N	616 A	-12:896175 1948488414 A	N
206	617 A	-12:896174 1948488413 A	
206	618 C	-12:896173 1948488412 C	
207 S	619 A	-12:896172 1948488411 A	S
207	620 G	-12:896171 1948488410 G	
207	621 C	-12:896170 1948488409 C	
208 C	622 T	-12:896169 1948488408 T	C
208	623 G	-12:896168 1948488407 G	
208	624 C	-12:896167 1948488406 C	
209 R	625 C	-12:896166 1948488405 C	R
209	626 G	-12:896165 1948488404 G	
209	627 A	-12:896164 1948488403 A	
210 P	628 C	-12:896163 1948488402 C	P
210	629 C	-12:896162 1948488401 C	
210	630 G	-12:896161 1948488400 G	
211 N	631 A	-12:896160 1948488399 A	N
211	632 A	-12:896159 1948488398 A	
211	633 C	-12:896158 1948488397 C	
212 M	634 A	-12:896157 1948488396 A	M
212	635 T	-12:896156 1948488395 T	
212	636 G	-12:896155 1948488394 G	
213 A	637 G	-12:896154 1948488393 G	A
213	638 C	-12:896153 1948488392 C	
213	639 C	-12:896152 1948488391 C	
214 L	640 C	-12:896151 1948488390 C	L
214	641 T	-12:896150 1948488389 T	
214	642 G	-12:896149 1948488388 G	
215 G	643 G	-12:896148 1948488387 G	G
215	644 G	-12:896147 1948488386 G	
215	645 A	-12:896146 1948488385 A	
216 H	646 C	-12:896145 1948488384 C	H
216	647 A	-12:896144 1948488383 A	
216	648 C	-12:896143 1948488382 C	
217 P	649 C	-12:896142 1948488381 C	P
217	650 C	-12:896141 1948488380 C	
217	651 A	-12:896140 1948488379 A	
218 Q	652 C	-12:896139 1948488378 C	Q
218	653 A	-12:896138 1948488377 A	
218	654 G	-12:896137 1948488376 G	
219 L	655 C	-12:896136 1948488375 C	L
219	656 T	-12:896135 1948488374 T	
219	657 G	-12:896134 1948488373 G	
220 Q	658 C	-12:896133 1948488372 C	Q
220	659 A	-12:896132 1948488371 A	
220	660 G	-12:896131 1948488370 G	
221 Q	661 C	-12:896130 1948488369 C	Q
221	662 A	-12:896129 1948488368 A	
221	663 G	-12:896128 1948488367 G	
222 V	664 G	-12:896127 1948488366 G	V
222	665 T	-12:896126 1948488365 T	
222	666 G	-12:896125 1948488364 G	
223 T	667 A	-12:896124 1948488363 A	T
223	668 C	-12:896123 1948488362 C	
223	669 C	-12:896122 1948488361 C	
224 S	670 T	-12:896121 1948488360 T	S
224	671 C	-12:896120 1948488359 C	
224	672 C	-12:896119 1948488358 C	
225 P	673 C	-12:896118 1948488357 C	P
225	674 C	-12:896117 1948488356 C	
225	675 T	-12:896116 1948488355 T	
226 S	676 T	-12:896115 1948488354 T	S
226	677 C	-12:896114 1948488353 C	
226	678 C	-12:896113 1948488352 C	
227 R	679 A	-12:896112 1948488351 A	R
227	680 G	-12:896111 1948488350 G	
227	681 A	-12:896110 1948488349 A	
228 P	682 C	-12:896109 1948488348 C	P
228	683 C	-12:896108 1948488347 C	
228	684 C	-12:896107 1948488346 C	
229 S	685 A	-12:896106 1948488345 A	S
229	686 G	-12:896105 1948488344 G	
229	687 C	-12:896104 1948488343 C	
230 H	688 C	-12:896103 1948488342 C	H
230	689 A	-12:896102 1948488341 A	
230	690 T	-12:896101 1948488340 T	
231 A	691 G	-12:896100 1948488339 G	A
231	692 C	-12:896099 1948488338 C	
231	693 T	-12:896098 1948488337 T	
232 V	694 G	-12:896097 1948488336 G	V
232	695 T	-12:896096 1948488335 T	
232	696 G	-12:896095 1948488334 G	
233 I	697 A	-12:896094 1948488333 A	I
233	698 T	-12:896093 1948488332 T	
233	699 A	-12:896092 1948488331 A	
234 P	700 C	-12:896091 1948488330 C	P
234	701 C	-12:896090 1948488329 C	
234	702 G	-12:896089 1948488328 G	
235 A	703 G	-12:896088 1948488327 G	A
235	704 C	-12:896087 1948488326 C	
235	705 G	-12:896086 1948488325 G	
236 D	706 G	-12:896085 1948488324 G	D
236	707 A	-12:896084 1948488323 A	
236	708 C	-12:896083 1948488322 C	
237 Q	709 C	-12:896082 1948488321 C	Q
237	710 A	-12:896081 1948488320 A	
237	711 G	-12:896080 1948488319 G	
238 D	712 G	-12:896079 1948488318 G	D
238	713 A	-12:896078 1948488317 A	
238	714 C	-12:896077 1948488316 C	
239 C	715 T	-12:896076 1948488315 T	C
239	716 G	-12:896075 1948488314 G	
239	717 C	-12:896074 1948488313 C	
240 S	718 A	-12:896073 1948488312 A	S
240	719 G	-12:896072 1948488311 G	
240	720 C	-12:896071 1948488310 C	
241 S	721 T	-12:896070 1948488309 T	S
241	722 C	-12:896069 1948488308 C	
241	723 C	-12:896068 1948488307 C	
242 R	724 C	-12:896067 1948488306 C	R
242	725 G	-12:896066 1948488305 G	
242	726 A	-12:895910 1948488149 A	
243 S	727 A	-12:895909 1948488148 A	S
243	728 G	-12:895908 1948488147 G	
243	729 C	-12:895907 1948488146 C	
244 L	730 C	-12:895906 1948488145 C	L
244	731 T	-12:895905 1948488144 T	
244	732 G	-12:895904 1948488143 G	
245 S	733 A	-12:895903 1948488142 A	S
245	734 G	-12:895902 1948488141 G	
245	735 C	-12:895901 1948488140 C	
246 S	736 T	-12:895900 1948488139 T	S
246	737 C	-12:895899 1948488138 C	
246	738 A	-12:895898 1948488137 A	
247 S	739 T	-12:895897 1948488136 T	S
247	740 C	-12:895896 1948488135 C	
247	741 C	-12:895895 1948488134 C	
248 A	742 G	-12:895894 1948488133 G	A
248	743 C	-12:895893 1948488132 C	
248	744 C	-12:895892 1948488131 C	
249 V	745 G	-12:895891 1948488130 G	V
249	746 T	-12:895890 1948488129 T	
249	747 G	-12:895889 1948488128 G	
250 E	748 G	-12:895888 1948488127 G	E
250	749 A	-12:895887 1948488126 A	
250	750 G	-12:895886 1948488125 G	
251 S	751 A	-12:895885 1948488124 A	S
251	752 G	-12:895884 1948488123 G	
251	753 C	-12:895883 1948488122 C	
252 E	754 G	-12:895882 1948488121 G	E
252	755 A	-12:895881 1948488120 A	
252	756 G	-12:895880 1948488119 G	
253 A	757 G	-12:895879 1948488118 G	A
253	758 C	-12:895878 1948488117 C	
253	759 C	-12:895877 1948488116 C	
254 T	760 A	-12:895876 1948488115 A	T
254	761 C	-12:895875 1948488114 C	
254	762 G	-12:895874 1948488113 G	
255 H	763 C	-12:895873 1948488112 C	H
255	764 A	-12:895872 1948488111 A	
255	765 C	-12:895871 1948488110 C	
256 Q	766 C	-12:895870 1948488109 C	Q
256	767 A	-12:895869 1948488108 A	
256	768 G	-12:895868 1948488107 G	
257 R	769 C	-12:895867 1948488106 C	R
257	770 G	-12:895866 1948488105 G	
257	771 G	-12:895865 1948488104 G	
258 K	772 A	-12:895864 1948488103 A	K
258	773 A	-12:895863 1948488102 A	
258	774 G	-12:895862 1948488101 G	
259 L	775 C	-12:895861 1948488100 C	L
259	776 T	-12:895860 1948488099 T	
259	777 C	-12:895859 1948488098 C	
260 R	778 C	-12:895858 1948488097 C	R
260	779 G	-12:895857 1948488096 G	
260	780 G	-12:895856 1948488095 G	
261 Q	781 C	-12:895855 1948488094 C	Q
261	782 A	-12:895854 1948488093 A	
261	783 G	-12:895853 1948488092 G	
262 K	784 A	-12:895852 1948488091 A	K
262	785 A	-12:895851 1948488090 A	
262	786 G	-12:895850 1948488089 G	
263 Q	787 C	-12:895849 1948488088 C	Q
263	788 A	-12:895848 1948488087 A	
263	789 G	-12:895847 1948488086 G	
264 L	790 C	-12:895846 1948488085 C	L
264	791 T	-12:895845 1948488084 T	
264	792 G	-12:895844 1948488083 G	
265 Q	793 C	-12:895843 1948488082 C	Q
265	794 A	-12:895842 1948488081 A	
265	795 G	-12:895841 1948488080 G	
266 Q	796 C	-12:895840 1948488079 C	Q
266	797 A	-12:895839 1948488078 A	
266	798 G	-12:895838 1948488077 G	
267 Q	799 C	-12:895837 1948488076 C	Q
267	800 A	-12:895836 1948488075 A	
267	801 G	-12:895835 1948488074 G	
268 F	802 T	-12:895834 1948488073 T	F
268	803 T	-12:895833 1948488072 T	
268	804 C	-12:895832 1948488071 C	
269 R	805 C	-12:895831 1948488070 C	R
269	806 G	-12:895830 1948488069 G	
269	807 G	-12:895829 1948488068 G	
270 E	808 G	-12:895828 1948488067 G	E
270	809 A	-12:895827 1948488066 A	
270	810 G	-12:895826 1948488065 G	
271 R	811 C	-12:895825 1948488064 C	R
271	812 G	-12:895824 1948488063 G	
271	813 G	-12:895823 1948488062 G	
272 M	814 A	-12:895822 1948488061 A	M
272	815 T	-12:895821 1948488060 T	
272	816 G	-12:895820 1948488059 G	
273 E	817 G	-12:895819 1948488058 G	E
273	818 A	-12:895818 1948488057 A	
273	819 G	-12:895817 1948488056 G	
274 K	820 A	-12:895816 1948488055 A	K
274	821 A	-12:895815 1948488054 A	
274	822 G	-12:895814 1948488053 G	
275 Q	823 C	-12:895813 1948488052 C	Q
275	824 A	-12:895812 1948488051 A	
275	825 G	-12:895811 1948488050 G	
276 Q	826 C	-12:895810 1948488049 C	Q
276	827 A	-12:895809 1948488048 A	
276	828 G	-12:895808 1948488047 G	
277 V	829 G	-12:895807 1948488046 G	V
277	830 T	-12:895806 1948488045 T	
277	831 T	-12:895805 1948488044 T	
278 R	832 C	-12:895804 1948488043 C	R
278	833 G	-12:895803 1948488042 G	
278	834 A	-12:895802 1948488041 A	
279 V	835 G	-12:895801 1948488040 G	V
279	836 T	-12:895800 1948488039 T	
279	837 C	-12:895799 1948488038 C	
280 S	838 T	-12:895798 1948488037 T	S
280	839 C	-12:895797 1948488036 C	
280	840 C	-12:895796 1948488035 C	
281 T	841 A	-12:895795 1948488034 A	T
281	842 C	-12:895794 1948488033 C	
281	843 G	-12:895793 1948488032 G	
282 P	844 C	-12:895792 1948488031 C	P
282	845 C	-12:895791 1948488030 C	
282	846 G	-12:895790 1948488029 G	
283 S	847 T	-12:895789 1948488028 T	S
283	848 C	-12:895788 1948488027 C	
283	849 A	-12:895787 1948488026 A	
284 A	850 G	-12:895786 1948488025 G	A
284	851 C	-12:895785 1948488024 C	
284	852 T	-12:895784 1948488023 T	
285 E	853 G	-12:895783 1948488022 G	E
285	854 A	-12:895782 1948488021 A	
285	855 G	-12:895781 1948488020 G	
286 K	856 A	-12:895780 1948488019 A	K
286	857 A	-12:895779 1948488018 A	
286	858 G	-12:895778 1948488017 G	
287 S	859 A	-12:895777 1948488016 A	S
287	860 G	-12:895776 1948488015 G	
287	861 T	-12:895775 1948488014 T	
288 E	862 G	-12:895774 1948488013 G	E
288	863 A	-12:895773 1948488012 A	
288	864 G	-12:895772 1948488011 G	
289 A	865 G	-12:895771 1948488010 G	A
289	866 C	-12:893959 1948486198 C	
289	867 A	-12:893958 1948486197 A	
290 A	868 G	-12:893957 1948486196 G	A
290	869 C	-12:893956 1948486195 C	
290	870 G	-12:893955 1948486194 G	
291 P	871 C	-12:893954 1948486193 C	P
291	872 C	-12:893953 1948486192 C	
291	873 T	-12:893952 1948486191 T	
292 P	874 C	-12:893951 1948486190 C	P
292	875 C	-12:893950 1948486189 C	
292	876 G	-12:893949 1948486188 G	
293 A	877 G	-12:893948 1948486187 G	A
293	878 C	-12:893947 1948486186 C	
293	879 C	-12:893946 1948486185 C	
294 P	880 C	-12:893945 1948486184 C	P
294	881 C	-12:893944 1948486183 C	
294	882 T	-12:893943 1948486182 T	
295 P	883 C	-12:893942 1948486181 C	P
295	884 C	-12:893941 1948486180 C	
295	885 T	-12:893940 1948486179 T	
296 V	886 G	-12:893939 1948486178 G	V
296	887 T	-12:893938 1948486177 T	
296	888 G	-12:893937 1948486176 G	
297 T	889 A	-12:893936 1948486175 A	T
297	890 C	-12:893935 1948486174 C	
297	891 G	-12:893934 1948486173 G	
298 H	892 C	-12:893933 1948486172 C	H
298	893 A	-12:893932 1948486171 A	
298	894 C	-12:893931 1948486170 C	
299 S	895 A	-12:893930 1948486169 A	S
299	896 G	-12:893929 1948486168 G	
299	897 C	-12:893928 1948486167 C	
300 T	898 A	-12:893927 1948486166 A	T
300	899 C	-12:893926 1948486165 C	
300	900 T	-12:893925 1948486164 T	
301 P	901 C	-12:893924 1948486163 C	P
301	902 C	-12:893923 1948486162 C	
301	903 T	-12:893922 1948486161 T	
302 V	904 G	-12:893921 1948486160 G	V
302	905 T	-12:893920 1948486159 T	
302	906 A	-12:893919 1948486158 A	
303 T	907 A	-12:893918 1948486157 A	T
303	908 C	-12:893917 1948486156 C	
303	909 T	-12:893916 1948486155 T	
304 V	910 G	-12:893915 1948486154 G	V
304	911 T	-12:893914 1948486153 T	
304	912 C	-12:893913 1948486152 C	
305 S	913 T	-12:893912 1948486151 T	S
305	914 C	-12:893911 1948486150 C	
305	915 A	-12:893910 1948486149 A	
306 E	916 G	-12:893909 1948486148 G	E
306	917 A	-12:893908 1948486147 A	
306	918 A	-12:893907 1948486146 A	
307 P	919 C	-12:893906 1948486145 C	P
307	920 C	-12:893905 1948486144 C	
307	921 A	-12:893904 1948486143 A	
308 L	922 C	-12:893903 1948486142 C	L
308	923 T	-12:893902 1948486141 T	
308	924 C	-12:893901 1948486140 C	
309 L	925 C	-12:893900 1948486139 C	L
309	926 T	-12:893899 1948486138 T	
309	927 G	-12:893898 1948486137 G	
310 E	928 G	-12:893897 1948486136 G	E
310	929 A	-12:893896 1948486135 A	
310	930 G	-12:893895 1948486134 G	
311 K	931 A	-12:893894 1948486133 A	K
311	932 A	-12:893893 1948486132 A	
311	933 A	-12:893892 1948486131 A	
312 D	934 G	-12:893891 1948486130 G	D
312	935 A	-12:893890 1948486129 A	
312	936 C	-12:893889 1948486128 C	
313 F	937 T	-12:893888 1948486127 T	F
313	938 T	-12:893887 1948486126 T	
313	939 C	-12:893886 1948486125 C	
314 L	940 C	-12:893885 1948486124 C	L
314	941 T	-12:893884 1948486123 T	
314	942 T	-12:893883 1948486122 T	
315 A	943 G	-12:893882 1948486121 G	A
315	944 C	-12:893881 1948486120 C	
315	945 A	-12:893880 1948486119 A	
316 G	946 G	-12:893879 1948486118 G	G
316	947 G	-12:893878 1948486117 G	
316	948 A	-12:893877 1948486116 A	
317 V	949 G	-12:893876 1948486115 G	V
317	950 T	-12:893875 1948486114 T	
317	951 G	-12:893874 1948486113 G	
318 T	952 A	-12:893873 1948486112 A	T
318	953 C	-12:893872 1948486111 C	
318	954 T	-12:893871 1948486110 T	
319 Q	955 C	-12:893870 1948486109 C	Q
319	956 A	-12:893869 1948486108 A	
319	957 A	-12:893868 1948486107 A	
320 E	958 G	-12:893867 1948486106 G	E
320	959 A	-12:893866 1948486105 A	
320	960 A	-12:893865 1948486104 A	
321 L	961 T	-12:893864 1948486103 T	L
321	962 T	-12:893863 1948486102 T	
321	963 A	-12:893862 1948486101 A	
322 I	964 A	-12:893861 1948486100 A	I
322	965 T	-12:893860 1948486099 T	
322	966 C	-12:893859 1948486098 C	
323 K	967 A	-12:893858 1948486097 A	K
323	968 A	-12:893548 1948485787 A	
323	969 G	-12:893547 1948485786 G	
324 T	970 A	-12:893546 1948485785 A	T
324	971 C	-12:893545 1948485784 C	
324	972 T	-12:893544 1948485783 T	
325 L	973 C	-12:893543 1948485782 C	L
325	974 T	-12:893542 1948485781 T	
325	975 T	-12:893541 1948485780 T	
326 E	976 G	-12:893540 1948485779 G	E
326	977 A	-12:893539 1948485778 A	
326	978 A	-12:893538 1948485777 A	
327 D	979 G	-12:893537 1948485776 G	D
327	980 A	-12:893536 1948485775 A	
327	981 C	-12:893535 1948485774 C	
328 N	982 A	-12:893534 1948485773 A	N
328	983 A	-12:893533 1948485772 A	
328	984 C	-12:893532 1948485771 C	
329 S	985 T	-12:893531 1948485770 T	S
329	986 C	-12:893530 1948485769 C	
329	987 T	-12:893529 1948485768 T	
330 E	988 G	-12:893528 1948485767 G	E
330	989 A	-12:893527 1948485766 A	
330	990 A	-12:893526 1948485765 A	
331 K	991 A	-12:893525 1948485764 A	K
331	992 A	-12:893524 1948485763 A	
331	993 G	-12:893523 1948485762 G	
332 W	994 T	-12:893522 1948485761 T	W
332	995 G	-12:893521 1948485760 G	
332	996 G	-12:893520 1948485759 G	
333 A	997 G	-12:893519 1948485758 G	A
333	998 C	-12:893518 1948485757 C	
333	999 T	-12:893517 1948485756 T	
334 V	1000 G	-12:893516 1948485755 G	V
334	1001 T	-12:893515 1948485754 T	
334	1002 G	-12:893514 1948485753 G	
335 T	1003 A	-12:893513 1948485752 A	T
335	1004 C	-12:893512 1948485751 C	
335	1005 T	-12:893511 1948485750 T	
336 P	1006 C	-12:893510 1948485749 C	P
336	1007 C	-12:893509 1948485748 C	
336	1008 C	-12:893508 1948485747 C	
337 D	1009 G	-12:893507 1948485746 G	D
337	1010 A	-12:893506 1948485745 A	
337	1011 T	-12:893505 1948485744 T	
338 A	1012 G	-12:893504 1948485743 G	A
338	1013 C	-12:893503 1948485742 C	
338	1014 A	-12:893502 1948485741 A	
339 G	1015 G	-12:893501 1948485740 G	G
339	1016 G	-12:893500 1948485739 G	
339	1017 G	-12:893499 1948485738 G	
340 D	1018 G	-12:893498 1948485737 G	D
340	1019 A	-12:893497 1948485736 A	
340	1020 T	-12:893496 1948485735 T	
341 G	1021 G	-12:893495 1948485734 G	G
341	1022 G	-12:893494 1948485733 G	
341	1023 T	-12:893493 1948485732 T	
342 V	1024 G	-12:893492 1948485731 G	V
342	1025 T	-12:893491 1948485730 T	
342	1026 G	-12:893490 1948485729 G	
343 V	1027 G	-12:893489 1948485728 G	V
343	1028 T	-12:893488 1948485727 T	
343	1029 C	-12:893487 1948485726 C	
344 K	1030 A	-12:893486 1948485725 A	K
344	1031 A	-12:893485 1948485724 A	
344	1032 G	-12:893484 1948485723 G	
345 P	1033 C	-12:893483 1948485722 C	P
345	1034 C	-12:893482 1948485721 C	
345	1035 C	-12:893481 1948485720 C	
346 S	1036 T	-12:893480 1948485719 T	S
346	1037 C	-12:893479 1948485718 C	
346	1038 G	-12:893478 1948485717 G	
347 S	1039 T	-12:893477 1948485716 T	S
347	1040 C	-12:893476 1948485715 C	
347	1041 T	-12:893475 1948485714 T	
348 R	1042 A	-12:893474 1948485713 A	R
348	1043 G	-12:893473 1948485712 G	
348	1044 A	-12:893472 1948485711 A	
349 A	1045 G	-12:893471 1948485710 G	A
349	1046 C	-12:893470 1948485709 C	
349	1047 A	-12:893469 1948485708 A	
350 D	1048 G	-12:893468 1948485707 G	D
350	1049 A	-12:893467 1948485706 A	
350	1050 C	-12:893466 1948485705 C	
351 P	1051 C	-12:893465 1948485704 C	P
351	1052 C	-12:893464 1948485703 C	
351	1053 A	-12:893463 1948485702 A	
352 A	1054 G	-12:893462 1948485701 G	A
352	1055 C	-12:893461 1948485700 C	
352	1056 C	-12:893460 1948485699 C	
353 Q	1057 C	-12:893459 1948485698 C	Q
353	1058 A	-12:893458 1948485697 A	
353	1059 G	-12:893457 1948485696 G	
354 T	1060 A	-12:893456 1948485695 A	T
354	1061 C	-12:893455 1948485694 C	
354	1062 C	-12:893454 1948485693 C	
355 S	1063 T	-12:893453 1948485692 T	S
355	1064 C	-12:893452 1948485691 C	
355	1065 T	-12:893451 1948485690 T	
356 D	1066 G	-12:893450 1948485689 G	D
356	1067 A	-12:893449 1948485688 A	
356	1068 C	-12:893448 1948485687 C	
357 T	1069 A	-12:893447 1948485686 A	T
357	1070 C	-12:893446 1948485685 C	
357	1071 A	-12:893445 1948485684 A	
358 L	1072 T	-12:893444 1948485683 T	L
358	1073 T	-12:893443 1948485682 T	
358	1074 A	-12:893442 1948485681 A	
359 A	1075 G	-12:893441 1948485680 G	A
359	1076 C	-12:893440 1948485679 C	
359	1077 C	-12:893439 1948485678 C	
360 L	1078 T	-12:893438 1948485677 T	L
360	1079 T	-12:893437 1948485676 T	
360	1080 G	-12:893436 1948485675 G	
361 N	1081 A	-12:893435 1948485674 A	N
361	1082 A	-12:893434 1948485673 A	
361	1083 C	-12:893433 1948485672 C	
362 N	1084 A	-12:893432 1948485671 A	N
362	1085 A	-12:893431 1948485670 A	
362	1086 C	-12:893430 1948485669 C	
363 Q	1087 C	-12:893429 1948485668 C	Q
363	1088 A	-12:893428 1948485667 A	
363	1089 G	-12:893427 1948485666 G	
364 M	1090 A	-12:893426 1948485665 A	M
364	1091 T	-12:893425 1948485664 T	
364	1092 G	-12:893424 1948485663 G	
365 V	1093 G	-12:893423 1948485662 G	V
365	1094 T	-12:893422 1948485661 T	
365	1095 G	-12:893421 1948485660 G	
366 T	1096 A	-12:893420 1948485659 A	T
366	1097 C	-12:893419 1948485658 C	
366	1098 C	-12:893418 1948485657 C	
367 Q	1099 C	-12:893417 1948485656 C	Q
367	1100 A	-12:893416 1948485655 A	
367	1101 G	-12:893415 1948485654 G	
368 N	1102 A	-12:893414 1948485653 A	N
368	1103 A	-12:893413 1948485652 A	
368	1104 C	-12:893412 1948485651 C	
369 R	1105 A	-12:893411 1948485650 A	R
369	1106 G	-12:893410 1948485649 G	
369	1107 G	-12:893409 1948485648 G	
370 T	1108 A	-12:893408 1948485647 A	T
370	1109 C	-12:893407 1948485646 C	
370	1110 T	-12:893406 1948485645 T	
371 P	1111 C	-12:893405 1948485644 C	P
371	1112 C	-12:893404 1948485643 C	
371	1113 A	-12:893403 1948485642 A	
372 H	1114 C	-12:893402 1948485641 C	H
372	1115 A	-12:893401 1948485640 A	
372	1116 C	-12:893400 1948485639 C	
373 S	1117 A	-12:893399 1948485638 A	S
373	1118 G	-12:893398 1948485637 G	
373	1119 C	-12:893397 1948485636 C	
374 V	1120 G	-12:893396 1948485635 G	V
374	1121 T	-12:893395 1948485634 T	
374	1122 T	-12:893394 1948485633 T	
375 C	1123 T	-12:893393 1948485632 T	C
375	1124 G	-12:893392 1948485631 G	
375	1125 C	-12:893391 1948485630 C	
376 H	1126 C	-12:893390 1948485629 C	H
376	1127 A	-12:893389 1948485628 A	
376	1128 C	-12:893388 1948485627 C	
377 Q	1129 C	-12:893387 1948485626 C	Q
377	1130 A	-12:893386 1948485625 A	
377	1131 G	-12:893385 1948485624 G	
378 K	1132 A	-12:893384 1948485623 A	K
378	1133 A	-12:893383 1948485622 A	
378	1134 A	-12:893382 1948485621 A	
379 P	1135 C	-12:893381 1948485620 C	P
379	1136 C	-12:893380 1948485619 C	
379	1137 A	-12:893379 1948485618 A	
380 Q	1138 C	-12:893378 1948485617 C	Q
380	1139 A	-12:893377 1948485616 A	
380	1140 A	-12:893376 1948485615 A	
381 A	1141 G	-12:893375 1948485614 G	A
381	1142 C	-12:893374 1948485613 C	
381	1143 A	-12:893373 1948485612 A	
382 K	1144 A	-12:893372 1948485611 A	K
382	1145 A	-12:893371 1948485610 A	
382	1146 A	-12:893370 1948485609 A	
383 S	1147 T	-12:893369 1948485608 T	S
383	1148 C	-12:893368 1948485607 C	
383	1149 T	-12:893367 1948485606 T	
384 G	1150 G	-12:893366 1948485605 G	G
384	1151 G	-12:893365 1948485604 G	
384	1152 A	-12:893364 1948485603 A	
385 S	1153 T	-12:893363 1948485602 T	S
385	1154 C	-12:893362 1948485601 C	
385	1155 T	-12:893361 1948485600 T	
386 W	1156 T	-12:893360 1948485599 T	W
386	1157 G	-12:893359 1948485598 G	
386	1158 G	-12:893358 1948485597 G	
387 D	1159 G	-12:893357 1948485596 G	D
387	1160 A	-12:893356 1948485595 A	
387	1161 C	-12:893355 1948485594 C	
388 L	1162 C	-12:893354 1948485593 C	L
388	1163 T	-12:893353 1948485592 T	
388	1164 C	-12:893352 1948485591 C	
389 Q	1165 C	-12:893351 1948485590 C	Q
389	1166 A	-12:893350 1948485589 A	
389	1167 A	-12:893349 1948485588 A	
390 T	1168 A	-12:893348 1948485587 A	T
390	1169 C	-12:893347 1948485586 C	
390	1170 T	-12:893346 1948485585 T	
391 Y	1171 T	-12:893345 1948485584 T	Y
391	1172 A	-12:893344 1948485583 A	
391	1173 T	-12:893343 1948485582 T	
392 S	1174 A	-12:893342 1948485581 A	S
392	1175 G	-12:893341 1948485580 G	
392	1176 C	-12:893340 1948485579 C	
393 A	1177 G	-12:893339 1948485578 G	A
393	1178 C	-12:893338 1948485577 C	
393	1179 T	-12:893337 1948485576 T	
394 D	1180 G	-12:893336 1948485575 G	D
394	1181 A	-12:893335 1948485574 A	
394	1182 C	-12:893334 1948485573 C	
395 Q	1183 C	-12:893333 1948485572 C	Q
395	1184 A	-12:893332 1948485571 A	
395	1185 A	-12:893331 1948485570 A	
396 R	1186 C	-12:893330 1948485569 C	R
396	1187 G	-12:893329 1948485568 G	
396	1188 C	-12:893328 1948485567 C	
397 T	1189 A	-12:893327 1948485566 A	T
397	1190 C	-12:893326 1948485565 C	
397	1191 A	-12:893325 1948485564 A	
398 T	1192 A	-12:893324 1948485563 A	T
398	1193 C	-12:893323 1948485562 C	
398	1194 A	-12:893322 1948485561 A	
399 G	1195 G	-12:893321 1948485560 G	G
399	1196 G	-12:893320 1948485559 G	
399	1197 T	-12:893319 1948485558 T	
400 N	1198 A	-12:893318 1948485557 A	S
400	1199 A	-12:893317 1948485556 G	
400	1200 C	-12:893316 1948485555 C	
401 W	1201 T	-12:893315 1948485554 A	R
401	1202 G	-12:893314 1948485553 G	
401	1203 G	-12:893313 1948485552 A	
>ENSP00000228345 
1 M	1 A	-12:912485 1948504724 A	M
1	2 T	-12:912484 1948504723 T	
1	3 G	-12:912483 1948504722 G	
2 S	4 T	-12:912482 1948504721 T	S
2	5 C	-12:912481 1948504720 C	
2	6 T	-12:912480 1948504719 T	
3 G	7 G	-12:912479 1948504718 G	G
3	8 G	-12:912478 1948504717 G	
3	9 G	-12:912477 1948504716 G	
4 T	10 A	-12:912476 1948504715 A	T
4	11 C	-12:912475 1948504714 C	
4	12 T	-12:912474 1948504713 T	
5 E	13 G	-12:912473 1948504712 G	E
5	14 A	-12:912472 1948504711 A	
5	15 G	-12:912471 1948504710 G	
6 E	16 G	-12:912470 1948504709 G	E
6	17 A	-12:912469 1948504708 A	
6	18 A	-12:912468 1948504707 A	
7 A	19 G	-12:912467 1948504706 G	A
7	20 C	-12:912466 1948504705 C	
7	21 A	-12:912465 1948504704 A	
8 I	22 A	-12:912464 1948504703 A	I
8	23 T	-12:912463 1948504702 T	
8	24 T	-12:912462 1948504701 T	
9 L	25 C	-12:912461 1948504700 C	L
9	26 T	-12:912460 1948504699 T	
9	27 T	-12:912459 1948504698 T	
10 G	28 G	-12:912458 1948504697 G	G
10	29 G	-12:912457 1948504696 G	
10	30 A	-12:912456 1948504695 A	
11 G	31 G	-12:912455 1948504694 G	G
11	32 G	-12:912454 1948504693 G	
11	33 A	-12:912453 1948504692 A	
12 R	34 C	-12:912452 1948504691 C	R
12	35 G	-12:912451 1948504690 G	
12	36 T	-12:912450 1948504689 T	
13 D	37 G	-12:912449 1948504688 G	D
13	38 A	-12:912448 1948504687 A	
13	39 C	-12:912447 1948504686 C	
14 S	40 A	-12:912446 1948504685 A	S
14	41 G	-12:912445 1948504684 G	
14	42 C	-12:912444 1948504683 C	
15 H	43 C	-12:912443 1948504682 C	H
15	44 A	-12:912442 1948504681 A	
15	45 T	-12:912441 1948504680 T	
16 P	46 C	-12:912440 1948504679 C	P
16	47 C	-12:912439 1948504678 C	
16	48 T	-12:912438 1948504677 T	
17 A	49 G	-12:912437 1948504676 G	A
17	50 C	-12:912436 1948504675 C	
17	51 T	-12:912435 1948504674 T	
18 A	52 G	-12:912434 1948504673 G	A
18	53 C	-12:912433 1948504672 C	
18	54 T	-12:912432 1948504671 T	
19 G	55 G	-12:912431 1948504670 G	G
19	56 G	-12:912430 1948504669 G	
19	57 C	-12:912429 1948504668 C	
20 G	58 G	-12:912428 1948504667 G	G
20	59 G	-12:912427 1948504666 G	
20	60 C	-12:912426 1948504665 C	
21 G	61 G	-12:912425 1948504664 G	G
21	62 G	-12:912424 1948504663 G	
21	63 C	-12:912423 1948504662 C	
22 S	64 T	-12:912422 1948504661 T	S
22	65 C	-12:912421 1948504660 C	
22	66 A	-12:912420 1948504659 A	
23 V	67 G	-12:912419 1948504658 G	V
23	68 T	-12:912418 1948504657 T	
23	69 G	-12:912417 1948504656 G	
24 L	70 T	-12:912416 1948504655 T	L
24	71 T	-12:912415 1948504654 T	
24	72 A	-12:912414 1948504653 A	
25 C	73 T	-12:912413 1948504652 T	C
25	74 G	-12:912412 1948504651 G	
25	75 C	-12:912411 1948504650 C	
26 F	76 T	-12:912410 1948504649 T	F
26	77 T	-12:912409 1948504648 T	
26	78 T	-12:912408 1948504647 T	
27 G	79 G	-12:912407 1948504646 G	G
27	80 G	-12:912406 1948504645 G	
27	81 A	-12:912405 1948504644 A	
28 Q	82 C	-12:912404 1948504643 C	Q
28	83 A	-12:912403 1948504642 A	
28	84 G	-12:912402 1948504641 G	
29 C	85 T	-12:910748 1948502987 T	C
29	86 G	-12:910747 1948502986 G	
29	87 C	-12:910746 1948502985 C	
30 Q	88 C	-12:910745 1948502984 C	Q
30	89 A	-12:910744 1948502983 A	
30	90 G	-12:910743 1948502982 G	
31 Y	91 T	-12:910742 1948502981 T	Y
31	92 A	-12:910741 1948502980 A	
31	93 C	-12:910740 1948502979 C	
32 T	94 A	-12:910739 1948502978 A	T
32	95 C	-12:910738 1948502977 C	
32	96 A	-12:910737 1948502976 A	
33 A	97 G	-12:910736 1948502975 G	A
33	98 C	-12:910735 1948502974 C	
33	99 A	-12:910734 1948502973 A	
34 E	100 G	-12:910733 1948502972 G	E
34	101 A	-12:910732 1948502971 A	
34	102 A	-12:910731 1948502970 A	
35 E	103 G	-12:910730 1948502969 G	E
35	104 A	-12:910729 1948502968 A	
35	105 G	-12:910728 1948502967 G	
36 Y	106 T	-12:910727 1948502966 T	Y
36	107 A	-12:910726 1948502965 A	
36	108 C	-12:910725 1948502964 C	
37 Q	109 C	-12:910724 1948502963 C	Q
37	110 A	-12:910723 1948502962 A	
37	111 G	-12:910722 1948502961 G	
38 A	112 G	-12:910721 1948502960 G	A
38	113 C	-12:910720 1948502959 C	
38	114 C	-12:910719 1948502958 C	
39 I	115 A	-12:910718 1948502957 A	I
39	116 T	-12:910717 1948502956 T	
39	117 C	-12:910716 1948502955 C	
40 Q	118 C	-12:910715 1948502954 C	Q
40	119 A	-12:910714 1948502953 A	
40	120 G	-12:910713 1948502952 G	
41 K	121 A	-12:910712 1948502951 A	K
41	122 A	-12:910711 1948502950 A	
41	123 G	-12:910710 1948502949 G	
42 A	124 G	-12:910709 1948502948 G	A
42	125 C	-12:910708 1948502947 C	
42	126 C	-12:910707 1948502946 C	
43 L	127 C	-12:910706 1948502945 C	L
43	128 T	-12:910705 1948502944 T	
43	129 G	-12:910704 1948502943 G	
44 R	130 A	-12:910703 1948502942 A	R
44	131 G	-12:910702 1948502941 G	
44	132 G	-12:910701 1948502940 G	
45 Q	133 C	-12:910700 1948502939 C	Q
45	134 A	-12:910699 1948502938 A	
45	135 G	-12:910698 1948502937 G	
46 R	136 A	-12:910697 1948502936 A	R
46	137 G	-12:910696 1948502935 G	
46	138 G	-12:910695 1948502934 G	
47 L	139 C	-12:910694 1948502933 C	L
47	140 T	-12:910693 1948502932 T	
47	141 G	-12:910692 1948502931 G	
48 G	142 G	-12:910691 1948502930 G	G
48	143 G	-12:910690 1948502929 G	
48	144 C	-12:910689 1948502928 C	
49 P	145 C	-12:910688 1948502927 C	P
49	146 C	-12:910687 1948502926 C	
49	147 A	-12:910686 1948502925 A	
50 E	148 G	-12:910685 1948502924 G	E
50	149 A	-12:910684 1948502923 A	
50	150 A	-12:910683 1948502922 A	
51 Y	151 T	-12:910682 1948502921 T	Y
51	152 A	-12:910681 1948502920 A	
51	153 C	-12:910680 1948502919 C	
52 I	154 A	-12:910679 1948502918 A	I
52	155 T	-12:910678 1948502917 T	
52	156 A	-12:910677 1948502916 A	
53 S	157 A	-12:910676 1948502915 A	S
53	158 G	-12:910675 1948502914 G	
53	159 T	-12:910674 1948502913 T	
54 S	160 A	-12:910673 1948502912 A	S
54	161 G	-12:910672 1948502911 G	
54	162 C	-12:910671 1948502910 C	
55 R	163 C	-12:910670 1948502909 C	R
55	164 G	-12:910669 1948502908 G	
55	165 C	-12:910668 1948502907 C	
56 M	166 A	-12:910667 1948502906 A	M
56	167 T	-12:910666 1948502905 T	
56	168 G	-12:910665 1948502904 G	
57 A	169 G	-12:910664 1948502903 G	A
57	170 C	-12:910663 1948502902 C	
57	171 T	-12:910662 1948502901 T	
58 G	172 G	-12:910661 1948502900 G	G
58	173 G	-12:910660 1948502899 G	
58	174 C	-12:910659 1948502898 C	
59 G	175 G	-12:910658 1948502897 G	G
59	176 G	-12:910657 1948502896 G	
59	177 A	-12:910656 1948502895 A	
60 G	178 G	-12:910655 1948502894 G	G
60	179 G	-12:910654 1948502893 G	
60	180 C	-12:910653 1948502892 C	
61 Q	181 C	-12:910652 1948502891 C	Q
61	182 A	-12:910651 1948502890 A	
61	183 G	-12:910650 1948502889 G	
62 K	184 A	-12:910649 1948502888 A	K
62	185 A	-12:910648 1948502887 A	
62	186 G	-12:910647 1948502886 G	
63 V	187 G	-12:909571 1948501810 G	V
63	188 T	-12:909570 1948501809 T	
63	189 G	-12:909569 1948501808 G	
64 C	190 T	-12:909568 1948501807 T	C
64	191 G	-12:909567 1948501806 G	
64	192 C	-12:909566 1948501805 C	
65 Y	193 T	-12:909565 1948501804 T	Y
65	194 A	-12:909564 1948501803 A	
65	195 C	-12:909563 1948501802 C	
66 I	196 A	-12:909562 1948501801 A	I
66	197 T	-12:909561 1948501800 T	
66	198 T	-12:909560 1948501799 T	
67 E	199 G	-12:909559 1948501798 G	E
67	200 A	-12:909558 1948501797 A	
67	201 G	-12:909557 1948501796 G	
68 G	202 G	-12:909556 1948501795 G	G
68	203 G	-12:909555 1948501794 G	
68	204 T	-12:909554 1948501793 T	
69 H	205 C	-12:909553 1948501792 C	H
69	206 A	-12:909552 1948501791 A	
69	207 T	-12:909551 1948501790 T	
70 R	208 C	-12:909550 1948501789 C	R
70	209 G	-12:909549 1948501788 G	
70	210 G	-12:909548 1948501787 G	
71 V	211 G	-12:909547 1948501786 G	V
71	212 T	-12:909546 1948501785 T	
71	213 A	-12:909545 1948501784 A	
72 I	214 A	-12:909544 1948501783 A	I
72	215 T	-12:909543 1948501782 T	
72	216 T	-12:909542 1948501781 T	
73 N	217 A	-12:909541 1948501780 A	N
73	218 A	-12:909540 1948501779 A	
73	219 T	-12:909539 1948501778 T	
74 L	220 C	-12:909538 1948501777 C	L
74	221 T	-12:909537 1948501776 T	
74	222 G	-12:909536 1948501775 G	
75 A	223 G	-12:909535 1948501774 G	A
75	224 C	-12:909534 1948501773 C	
75	225 C	-12:909533 1948501772 C	
76 N	226 A	-12:909532 1948501771 A	N
76	227 A	-12:909531 1948501770 A	
76	228 T	-12:909530 1948501769 T	
77 E	229 G	-12:909529 1948501768 G	E
77	230 A	-12:909528 1948501767 A	
77	231 G	-12:909527 1948501766 G	
78 M	232 A	-12:909526 1948501765 A	M
78	233 T	-12:909525 1948501764 T	
78	234 G	-12:909524 1948501763 G	
79 F	235 T	-12:909523 1948501762 T	F
79	236 T	-12:909522 1948501761 T	
79	237 T	-12:909521 1948501760 T	
80 G	238 G	-12:909520 1948501759 G	G
80	239 G	-12:909519 1948501758 G	
80	240 T	-12:909518 1948501757 T	
81 Y	241 T	-12:909517 1948501756 T	Y
81	242 A	-12:909516 1948501755 A	
81	243 C	-12:909515 1948501754 C	
82 N	244 A	-12:909514 1948501753 A	N
82	245 A	-12:909513 1948501752 A	
82	246 T	-12:909512 1948501751 T	
83 G	247 G	-12:909511 1948501750 G	G
83	248 G	-12:909510 1948501749 G	
83	249 C	-12:909509 1948501748 C	
84 W	250 T	-12:909508 1948501747 T	W
84	251 G	-12:909507 1948501746 G	
84	252 G	-12:909506 1948501745 G	
85 A	253 G	-12:909505 1948501744 G	A
85	254 C	-12:909504 1948501743 C	
85	255 A	-12:909503 1948501742 A	
86 H	256 C	-12:909502 1948501741 C	H
86	257 A	-12:909501 1948501740 A	
86	258 C	-12:909500 1948501739 C	
87 S	259 T	-12:909499 1948501738 T	S
87	260 C	-12:909498 1948501737 C	
87	261 C	-12:909497 1948501736 C	
88 I	262 A	-12:909496 1948501735 A	I
88	263 T	-12:909495 1948501734 T	
88	264 C	-12:909494 1948501733 C	
89 T	265 A	-12:909493 1948501732 A	T
89	266 C	-12:909492 1948501731 C	
89	267 G	-12:909491 1948501730 G	
90 Q	268 C	-12:909490 1948501729 C	Q
90	269 A	-12:909489 1948501728 A	
90	270 G	-12:909488 1948501727 G	
91 Q	271 C	-12:909487 1948501726 C	Q
91	272 A	-12:909486 1948501725 A	
91	273 G	-12:909485 1948501724 G	
92 N	274 A	-12:909484 1948501723 A	N
92	275 A	-12:909483 1948501722 A	
92	276 T	-12:909482 1948501721 T	
93 V	277 G	-12:909481 1948501720 G	V
93	278 T	-12:909480 1948501719 T	
93	279 G	-12:909479 1948501718 G	
94 D	280 G	-12:909478 1948501717 G	D
94	281 A	-12:909313 1948501552 A	
94	282 T	-12:909312 1948501551 T	
95 F	283 T	-12:909311 1948501550 T	F
95	284 T	-12:909310 1948501549 T	
95	285 T	-12:909309 1948501548 T	
96 V	286 G	-12:909308 1948501547 G	V
96	287 T	-12:909307 1948501546 T	
96	288 T	-12:909306 1948501545 T	
97 D	289 G	-12:909305 1948501544 G	D
97	290 A	-12:909304 1948501543 A	
97	291 C	-12:909303 1948501542 C	
98 L	292 C	-12:909302 1948501541 C	L
98	293 T	-12:909301 1948501540 T	
98	294 C	-12:909300 1948501539 C	
99 N	295 A	-12:909299 1948501538 A	N
99	296 A	-12:909298 1948501537 A	
99	297 C	-12:909297 1948501536 C	
100 N	298 A	-12:909296 1948501535 A	N
100	299 A	-12:909295 1948501534 A	
100	300 T	-12:909294 1948501533 T	
101 G	301 G	-12:909293 1948501532 G	G
101	302 G	-12:909292 1948501531 G	
101	303 C	-12:909291 1948501530 C	
102 K	304 A	-12:909290 1948501529 A	K
102	305 A	-12:909289 1948501528 A	
102	306 G	-12:909288 1948501527 G	
103 F	307 T	-12:909287 1948501526 T	F
103	308 T	-12:909286 1948501525 T	
103	309 C	-12:909285 1948501524 C	
104 Y	310 T	-12:909284 1948501523 T	Y
104	311 A	-12:909283 1948501522 A	
104	312 C	-12:909282 1948501521 C	
105 V	313 G	-12:909281 1948501520 G	V
105	314 T	-12:909280 1948501519 T	
105	315 G	-12:909279 1948501518 G	
106 G	316 G	-12:909278 1948501517 G	G
106	317 G	-12:909277 1948501516 G	
106	318 A	-12:909276 1948501515 A	
107 V	319 G	-12:909275 1948501514 G	V
107	320 T	-12:909274 1948501513 T	
107	321 C	-12:909273 1948501512 C	
108 C	322 T	-12:909272 1948501511 T	C
108	323 G	-12:909271 1948501510 G	
108	324 T	-12:909270 1948501509 T	
109 A	325 G	-12:909269 1948501508 G	A
109	326 C	-12:909268 1948501507 C	
109	327 A	-12:909267 1948501506 A	
110 F	328 T	-12:909266 1948501505 T	F
110	329 T	-12:909265 1948501504 T	
110	330 T	-12:909264 1948501503 T	
111 V	331 G	-12:909263 1948501502 G	V
111	332 T	-12:909262 1948501501 T	
111	333 G	-12:909261 1948501500 G	
112 R	334 A	-12:909260 1948501499 A	R
112	335 G	-12:909259 1948501498 G	
112	336 G	-12:909258 1948501497 G	
113 V	337 G	-12:909257 1948501496 G	V
113	338 T	-12:909256 1948501495 T	
113	339 C	-12:909255 1948501494 C	
114 Q	340 C	-12:909254 1948501493 C	Q
114	341 A	-12:909253 1948501492 A	
114	342 G	-12:909252 1948501491 G	
115 L	343 C	-12:909251 1948501490 C	L
115	344 T	-12:909250 1948501489 T	
115	345 G	-12:909249 1948501488 G	
116 K	346 A	-12:909248 1948501487 A	K
116	347 A	-12:909247 1948501486 A	
116	348 G	-12:909246 1948501485 G	
117 D	349 G	-12:906690 1948498929 G	D
117	350 A	-12:906689 1948498928 A	
117	351 T	-12:906688 1948498927 T	
118 G	352 G	-12:906687 1948498926 G	G
118	353 G	-12:906686 1948498925 G	
118	354 T	-12:906685 1948498924 T	
119 S	355 T	-12:906684 1948498923 T	S
119	356 C	-12:906683 1948498922 C	
119	357 A	-12:906682 1948498921 A	
120 Y	358 T	-12:906681 1948498920 T	Y
120	359 A	-12:906680 1948498919 A	
120	360 T	-12:906679 1948498918 T	
121 H	361 C	-12:906678 1948498917 C	H
121	362 A	-12:906677 1948498916 A	
121	363 T	-12:906676 1948498915 T	
122 E	364 G	-12:906675 1948498914 G	E
122	365 A	-12:906674 1948498913 A	
122	366 A	-12:906673 1948498912 A	
123 D	367 G	-12:906672 1948498911 G	D
123	368 A	-12:906671 1948498910 A	
123	369 T	-12:906670 1948498909 T	
124 V	370 G	-12:906669 1948498908 G	V
124	371 T	-12:906668 1948498907 T	
124	372 T	-12:906667 1948498906 T	
125 G	373 G	-12:906666 1948498905 G	G
125	374 G	-12:906665 1948498904 G	
125	375 T	-12:906664 1948498903 T	
126 Y	376 T	-12:906663 1948498902 T	Y
126	377 A	-12:906662 1948498901 A	
126	378 T	-12:906661 1948498900 T	
127 G	379 G	-12:906660 1948498899 G	G
127	380 G	-12:906659 1948498898 G	
127	381 T	-12:906658 1948498897 T	
128 V	382 G	-12:906657 1948498896 G	V
128	383 T	-12:906656 1948498895 T	
128	384 T	-12:906655 1948498894 T	
129 S	385 A	-12:906654 1948498893 A	S
129	386 G	-12:906653 1948498892 G	
129	387 T	-12:906652 1948498891 T	
130 E	388 G	-12:906651 1948498890 G	E
130	389 A	-12:906650 1948498889 A	
130	390 G	-12:906649 1948498888 G	
131 G	391 G	-12:906648 1948498887 G	G
131	392 G	-12:906647 1948498886 G	
131	393 C	-12:906646 1948498885 C	
132 L	394 C	-12:906645 1948498884 C	L
132	395 T	-12:906644 1948498883 T	
132	396 C	-12:906643 1948498882 C	
133 K	397 A	-12:906642 1948498881 A	K
133	398 A	-12:906641 1948498880 A	
133	399 G	-12:906640 1948498879 G	
134 S	400 T	-12:906639 1948498878 T	S
134	401 C	-12:906638 1948498877 C	
134	402 C	-12:906637 1948498876 C	
135 K	403 A	-12:906636 1948498875 A	K
135	404 A	-12:906635 1948498874 A	
135	405 G	-12:906634 1948498873 G	
136 A	406 G	-12:906633 1948498872 G	A
136	407 C	-12:906632 1948498871 C	
136	408 T	-12:906631 1948498870 T	
137 L	409 T	-12:906630 1948498869 T	L
137	410 T	-12:906629 1948498868 T	
137	411 A	-12:906628 1948498867 A	
138 S	412 T	-12:906627 1948498866 T	S
138	413 C	-12:906626 1948498865 C	
138	414 T	-12:906625 1948498864 T	
139 L	415 T	-12:906624 1948498863 T	L
139	416 T	-12:906623 1948498862 T	
139	417 G	-12:906622 1948498861 G	
140 E	418 G	-12:906621 1948498860 G	E
140	419 A	-12:906620 1948498859 A	
140	420 G	-12:906619 1948498858 G	
141 K	421 A	-12:906618 1948498857 A	K
141	422 A	-12:906617 1948498856 A	
141	423 G	-12:906616 1948498855 G	
142 A	424 G	-12:906615 1948498854 G	A
142	425 C	-12:906614 1948498853 C	
142	426 A	-12:906613 1948498852 A	
143 R	427 A	-12:906612 1948498851 A	R
143	428 G	-12:906611 1948498850 G	
143	429 G	-12:906610 1948498849 G	
144 K	430 A	-12:906609 1948498848 A	K
144	431 A	-12:906608 1948498847 A	
144	432 G	-12:906607 1948498846 G	
145 E	433 G	-12:906606 1948498845 G	E
145	434 A	-12:906605 1948498844 A	
145	435 G	-12:906604 1948498843 G	
146 A	436 G	-12:906603 1948498842 G	A
146	437 C	-12:906602 1948498841 C	
146	438 G	-12:906601 1948498840 G	
147 V	439 G	-12:906600 1948498839 G	V
147	440 T	-12:906599 1948498838 T	
147	441 G	-12:906598 1948498837 G	
148 T	442 A	-12:906597 1948498836 A	T
148	443 C	-12:906596 1948498835 C	
148	444 A	-12:906595 1948498834 A	
149 D	445 G	-12:906594 1948498833 G	D
149	446 A	-12:906593 1948498832 A	
149	447 C	-12:906592 1948498831 C	
150 G	448 G	-12:906591 1948498830 G	G
150	449 G	-12:906590 1948498829 G	
150	450 G	-12:906589 1948498828 G	
151 L	451 C	-12:906588 1948498827 C	L
151	452 T	-12:906587 1948498826 T	
151	453 G	-12:906586 1948498825 G	
152 K	454 A	-12:906585 1948498824 A	K
152	455 A	-12:906584 1948498823 A	
152	456 G	-12:906583 1948498822 G	
153 R	457 C	-12:906582 1948498821 C	R
153	458 G	-12:906581 1948498820 G	
153	459 A	-12:906580 1948498819 A	
154 A	460 G	-12:906579 1948498818 G	A
154	461 C	-12:906578 1948498817 C	
154	462 C	-12:906577 1948498816 C	
155 L	463 C	-12:906576 1948498815 C	L
155	464 T	-12:906575 1948498814 T	
155	465 C	-12:906574 1948498813 C	
156 R	466 A	-12:906573 1948498812 A	R
156	467 G	-12:906572 1948498811 G	
156	468 G	-12:906373 1948498612 G	
157 L	469 C	-12:906372 1948498611 C	L
157	470 T	-12:906371 1948498610 T	
157	471 T	-12:906370 1948498609 T	
158 P	472 C	-12:906369 1948498608 C	P
158	473 C	-12:906368 1948498607 C	
158	474 C	-12:906367 1948498606 C	
159 L	475 T	-12:906366 1948498605 T	L
159	476 T	-12:906365 1948498604 T	
159	477 G	-12:906364 1948498603 G	
160 L	478 C	-12:906363 1948498602 C	L
160	479 T	-12:906362 1948498601 T	
160	480 G	-12:906361 1948498600 G	
161 G	481 G	-12:906360 1948498599 G	G
161	482 G	-12:906359 1948498598 G	
161	483 A	-12:906358 1948498597 A	
162 V	484 G	-12:906357 1948498596 G	V
162	485 T	-12:906356 1948498595 T	
162	486 A	-12:906355 1948498594 A	
163 S	487 A	-12:906354 1948498593 A	S
163	488 G	-12:906353 1948498592 G	
163	489 T	-12:906352 1948498591 T	
164 G	490 G	-12:906351 1948498590 G	G
164	491 G	-12:906350 1948498589 G	
164	492 T	-12:906349 1948498588 T	
165 R	493 A	-12:906348 1948498587 A	R
165	494 G	-12:906347 1948498586 G	
165	495 A	-12:906346 1948498585 A	
166 I	496 A	-12:906345 1948498584 A	I
166	497 T	-12:906344 1948498583 T	
166	498 C	-12:906343 1948498582 C	
167 L	499 C	-12:906342 1948498581 C	L
167	500 T	-12:906341 1948498580 T	
167	501 G	-12:906340 1948498579 G	
168 Y	502 T	-12:906339 1948498578 T	Y
168	503 A	-12:906338 1948498577 A	
168	504 C	-12:906337 1948498576 C	
169 S	505 T	-12:906336 1948498575 T	S
169	506 C	-12:906335 1948498574 C	
169	507 T	-12:906334 1948498573 T	
170 L	508 C	-12:906333 1948498572 C	L
170	509 T	-12:906332 1948498571 T	
170	510 C	-12:906331 1948498570 C	
171 F	511 T	-12:906330 1948498569 T	F
171	512 T	-12:906329 1948498568 T	
171	513 C	-12:906328 1948498567 C	
172 S	514 T	-12:906327 1948498566 T	S
172	515 C	-12:906326 1948498565 C	
172	516 C	-12:906325 1948498564 C	
173 V	517 G	-12:906324 1948498563 G	V
173	518 T	-12:906323 1948498562 T	
173	519 G	-12:906322 1948498561 G	
174 H	520 C	-12:906321 1948498560 C	H
174	521 A	-12:906320 1948498559 A	
174	522 C	-12:906319 1948498558 C	
175 S	523 T	-12:906318 1948498557 T	S
175	524 C	-12:906317 1948498556 C	
175	525 A	-12:906316 1948498555 A	
176 V	526 G	-12:906315 1948498554 G	V
176	527 T	-12:906314 1948498553 T	
176	528 C	-12:906313 1948498552 C	
177 M	529 A	-12:906312 1948498551 A	M
177	530 T	-12:906311 1948498550 T	
177	531 G	-12:906310 1948498549 G	
178 C	532 T	-12:906309 1948498548 T	C
178	533 G	-12:906308 1948498547 G	
178	534 T	-12:906307 1948498546 T	
179 A	535 G	-12:906306 1948498545 G	A
179	536 C	-12:906305 1948498544 C	
179	537 C	-12:906304 1948498543 C	
180 G	538 G	-12:906303 1948498542 G	G
180	539 G	-12:906302 1948498541 G	
180	540 A	-12:906301 1948498540 A	
181 G	541 G	-12:906300 1948498539 G	G
181	542 G	-12:906299 1948498538 G	
181	543 C	-12:906298 1948498537 C	
182 L	544 C	-12:906297 1948498536 C	L
182	545 T	-12:906296 1948498535 T	
182	546 T	-12:906295 1948498534 T	
183 P	547 C	-12:906294 1948498533 C	P
183	548 C	-12:906293 1948498532 C	
183	549 C	-12:906292 1948498531 C	
184 T	550 A	-12:906291 1948498530 A	T
184	551 C	-12:906290 1948498529 C	
184	552 T	-12:906289 1948498528 T	
185 P	553 C	-12:906288 1948498527 C	P
185	554 C	-12:906287 1948498526 C	
185	555 T	-12:906286 1948498525 T	
186 T	556 A	-12:906285 1948498524 A	T
186	557 C	-12:906284 1948498523 C	
186	558 T	-12:906283 1948498522 T	
187 A	559 G	-12:906282 1948498521 G	A
187	560 C	-12:906281 1948498520 C	
187	561 G	-12:906280 1948498519 G	
188 S	562 A	-12:906279 1948498518 A	S
188	563 G	-12:906278 1948498517 G	
188	564 T	-12:906277 1948498516 T	
189 A	565 G	-12:906276 1948498515 G	A
189	566 C	-12:906275 1948498514 C	
189	567 A	-12:906274 1948498513 A	
190 Q	568 C	-12:906273 1948498512 C	Q
190	569 A	-12:906272 1948498511 A	
190	570 G	-12:906271 1948498510 G	
191 T	571 A	-12:906270 1948498509 A	T
191	572 C	-12:906269 1948498508 C	
191	573 A	-12:906268 1948498507 A	
192 A	574 G	-12:906267 1948498506 G	A
192	575 C	-12:906266 1948498505 C	
192	576 A	-12:906265 1948498504 A	
193 P	577 C	-12:906264 1948498503 C	P
193	578 C	-12:906263 1948498502 C	
193	579 C	-12:906262 1948498501 C	
194 S	580 T	-12:906261 1948498500 T	S
194	581 C	-12:906260 1948498499 C	
194	582 C	-12:906259 1948498498 C	
195 S	583 T	-12:906258 1948498497 T	S
195	584 C	-12:906257 1948498496 C	
195	585 T	-12:906256 1948498495 T	
196 P	586 C	-12:906255 1948498494 C	P
196	587 C	-12:906254 1948498493 C	
196	588 G	-12:906253 1948498492 G	
197 C	589 T	-12:906252 1948498491 T	C
197	590 G	-12:906251 1948498490 G	
197	591 C	-12:906250 1948498489 C	
198 S	592 T	-12:906249 1948498488 T	S
198	593 C	-12:906248 1948498487 C	
198	594 C	-12:906247 1948498486 C	
199 S	595 T	-12:906246 1948498485 T	S
199	596 C	-12:906245 1948498484 C	
199	597 A	-12:906244 1948498483 A	
200 A	598 G	-12:906243 1948498482 G	A
200	599 C	-12:906242 1948498481 C	
200	600 A	-12:906241 1948498480 A	
201 V	601 G	-12:906240 1948498479 G	V
201	602 T	-12:906239 1948498478 T	
201	603 C	-12:906238 1948498477 C	
202 L	604 C	-12:906237 1948498476 C	L
202	605 T	-12:906236 1948498475 T	
202	606 C	-12:906235 1948498474 C	
203 R	607 C	-12:906234 1948498473 C	R
203	608 G	-12:906233 1948498472 G	
203	609 C	-12:906232 1948498471 C	
204 Y	610 T	-12:906231 1948498470 T	Y
204	611 A	-12:906230 1948498469 A	
204	612 C	-12:906229 1948498468 C	
205 A	613 G	-12:906228 1948498467 G	A
205	614 C	-12:906227 1948498466 C	
205	615 A	-12:906226 1948498465 A	
206 Q	616 C	-12:906225 1948498464 C	Q
206	617 A	-12:906224 1948498463 A	
206	618 G	-12:906223 1948498462 G	
>ENSP00000380407 
1 M	1 A	-12:912485 1948504724 A	M
1	2 T	-12:912484 1948504723 T	
1	3 G	-12:912483 1948504722 G	
2 S	4 T	-12:912482 1948504721 T	S
2	5 C	-12:912481 1948504720 C	
2	6 T	-12:912480 1948504719 T	
3 G	7 G	-12:912479 1948504718 G	G
3	8 G	-12:912478 1948504717 G	
3	9 G	-12:912477 1948504716 G	
4 T	10 A	-12:912476 1948504715 A	T
4	11 C	-12:912475 1948504714 C	
4	12 T	-12:912474 1948504713 T	
5 E	13 G	-12:912473 1948504712 G	E
5	14 A	-12:912472 1948504711 A	
5	15 G	-12:912471 1948504710 G	
6 E	16 G	-12:912470 1948504709 G	E
6	17 A	-12:912469 1948504708 A	
6	18 A	-12:912468 1948504707 A	
7 A	19 G	-12:912467 1948504706 G	A
7	20 C	-12:912466 1948504705 C	
7	21 A	-12:912465 1948504704 A	
8 I	22 A	-12:912464 1948504703 A	I
8	23 T	-12:912463 1948504702 T	
8	24 T	-12:912462 1948504701 T	
9 L	25 C	-12:912461 1948504700 C	L
9	26 T	-12:912460 1948504699 T	
9	27 T	-12:912459 1948504698 T	
10 G	28 G	-12:912458 1948504697 G	G
10	29 G	-12:912457 1948504696 G	
10	30 A	-12:912456 1948504695 A	
11 G	31 G	-12:912455 1948504694 G	G
11	32 G	-12:912454 1948504693 G	
11	33 A	-12:912453 1948504692 A	
12 R	34 C	-12:912452 1948504691 C	R
12	35 G	-12:912451 1948504690 G	
12	36 T	-12:912450 1948504689 T	
13 D	37 G	-12:912449 1948504688 G	D
13	38 A	-12:912448 1948504687 A	
13	39 C	-12:912447 1948504686 C	
14 S	40 A	-12:912446 1948504685 A	S
14	41 G	-12:912445 1948504684 G	
14	42 C	-12:912444 1948504683 C	
15 H	43 C	-12:912443 1948504682 C	H
15	44 A	-12:912442 1948504681 A	
15	45 T	-12:912441 1948504680 T	
16 P	46 C	-12:912440 1948504679 C	P
16	47 C	-12:912439 1948504678 C	
16	48 T	-12:912438 1948504677 T	
17 A	49 G	-12:912437 1948504676 G	A
17	50 C	-12:912436 1948504675 C	
17	51 T	-12:912435 1948504674 T	
18 A	52 G	-12:912434 1948504673 G	A
18	53 C	-12:912433 1948504672 C	
18	54 T	-12:912432 1948504671 T	
19 G	55 G	-12:912431 1948504670 G	G
19	56 G	-12:912430 1948504669 G	
19	57 C	-12:912429 1948504668 C	
20 G	58 G	-12:912428 1948504667 G	G
20	59 G	-12:912427 1948504666 G	
20	60 C	-12:912426 1948504665 C	
21 G	61 G	-12:912425 1948504664 G	G
21	62 G	-12:912424 1948504663 G	
21	63 C	-12:912423 1948504662 C	
22 S	64 T	-12:912422 1948504661 T	S
22	65 C	-12:912421 1948504660 C	
22	66 A	-12:912420 1948504659 A	
23 V	67 G	-12:912419 1948504658 G	V
23	68 T	-12:912418 1948504657 T	
23	69 G	-12:912417 1948504656 G	
24 L	70 T	-12:912416 1948504655 T	L
24	71 T	-12:912415 1948504654 T	
24	72 A	-12:912414 1948504653 A	
25 C	73 T	-12:912413 1948504652 T	C
25	74 G	-12:912412 1948504651 G	
25	75 C	-12:912411 1948504650 C	
26 F	76 T	-12:912410 1948504649 T	F
26	77 T	-12:912409 1948504648 T	
26	78 T	-12:912408 1948504647 T	
27 G	79 G	-12:912407 1948504646 G	G
27	80 G	-12:912406 1948504645 G	
27	81 A	-12:912405 1948504644 A	
28 Q	82 C	-12:912404 1948504643 C	Q
28	83 A	-12:912403 1948504642 A	
28	84 G	-12:912402 1948504641 G	
29 C	85 T	-12:910748 1948502987 T	C
29	86 G	-12:910747 1948502986 G	
29	87 C	-12:910746 1948502985 C	
30 Q	88 C	-12:910745 1948502984 C	Q
30	89 A	-12:910744 1948502983 A	
30	90 G	-12:910743 1948502982 G	
31 Y	91 T	-12:910742 1948502981 T	Y
31	92 A	-12:910741 1948502980 A	
31	93 C	-12:910740 1948502979 C	
32 T	94 A	-12:910739 1948502978 A	T
32	95 C	-12:910738 1948502977 C	
32	96 A	-12:910737 1948502976 A	
33 A	97 G	-12:910736 1948502975 G	A
33	98 C	-12:910735 1948502974 C	
33	99 A	-12:910734 1948502973 A	
34 E	100 G	-12:910733 1948502972 G	E
34	101 A	-12:910732 1948502971 A	
34	102 A	-12:910731 1948502970 A	
35 E	103 G	-12:910730 1948502969 G	E
35	104 A	-12:910729 1948502968 A	
35	105 G	-12:910728 1948502967 G	
36 Y	106 T	-12:910727 1948502966 T	Y
36	107 A	-12:910726 1948502965 A	
36	108 C	-12:910725 1948502964 C	
37 Q	109 C	-12:910724 1948502963 C	Q
37	110 A	-12:910723 1948502962 A	
37	111 G	-12:910722 1948502961 G	
38 A	112 G	-12:910721 1948502960 G	A
38	113 C	-12:910720 1948502959 C	
38	114 C	-12:910719 1948502958 C	
39 I	115 A	-12:910718 1948502957 A	I
39	116 T	-12:910717 1948502956 T	
39	117 C	-12:910716 1948502955 C	
40 Q	118 C	-12:910715 1948502954 C	Q
40	119 A	-12:910714 1948502953 A	
40	120 G	-12:910713 1948502952 G	
41 K	121 A	-12:910712 1948502951 A	K
41	122 A	-12:910711 1948502950 A	
41	123 G	-12:910710 1948502949 G	
42 A	124 G	-12:910709 1948502948 G	A
42	125 C	-12:910708 1948502947 C	
42	126 C	-12:910707 1948502946 C	
43 L	127 C	-12:910706 1948502945 C	L
43	128 T	-12:910705 1948502944 T	
43	129 G	-12:910704 1948502943 G	
44 R	130 A	-12:910703 1948502942 A	R
44	131 G	-12:910702 1948502941 G	
44	132 G	-12:910701 1948502940 G	
45 Q	133 C	-12:910700 1948502939 C	Q
45	134 A	-12:910699 1948502938 A	
45	135 G	-12:910698 1948502937 G	
46 R	136 A	-12:910697 1948502936 A	R
46	137 G	-12:910696 1948502935 G	
46	138 G	-12:910695 1948502934 G	
47 L	139 C	-12:910694 1948502933 C	L
47	140 T	-12:910693 1948502932 T	
47	141 G	-12:910692 1948502931 G	
48 G	142 G	-12:910691 1948502930 G	G
48	143 G	-12:910690 1948502929 G	
48	144 C	-12:910689 1948502928 C	
49 P	145 C	-12:910688 1948502927 C	P
49	146 C	-12:910687 1948502926 C	
49	147 A	-12:910686 1948502925 A	
50 E	148 G	-12:910685 1948502924 G	E
50	149 A	-12:910684 1948502923 A	
50	150 A	-12:910683 1948502922 A	
51 Y	151 T	-12:910682 1948502921 T	Y
51	152 A	-12:910681 1948502920 A	
51	153 C	-12:910680 1948502919 C	
52 I	154 A	-12:910679 1948502918 A	I
52	155 T	-12:910678 1948502917 T	
52	156 A	-12:910677 1948502916 A	
53 S	157 A	-12:910676 1948502915 A	S
53	158 G	-12:910675 1948502914 G	
53	159 T	-12:910674 1948502913 T	
54 S	160 A	-12:910673 1948502912 A	S
54	161 G	-12:910672 1948502911 G	
54	162 C	-12:910671 1948502910 C	
55 R	163 C	-12:910670 1948502909 C	R
55	164 G	-12:910669 1948502908 G	
55	165 C	-12:910668 1948502907 C	
56 M	166 A	-12:910667 1948502906 A	M
56	167 T	-12:910666 1948502905 T	
56	168 G	-12:910665 1948502904 G	
57 A	169 G	-12:910664 1948502903 G	A
57	170 C	-12:910663 1948502902 C	
57	171 T	-12:910662 1948502901 T	
58 G	172 G	-12:910661 1948502900 G	G
58	173 G	-12:910660 1948502899 G	
58	174 C	-12:910659 1948502898 C	
59 G	175 G	-12:910658 1948502897 G	G
59	176 G	-12:910657 1948502896 G	
59	177 A	-12:910656 1948502895 A	
60 G	178 G	-12:910655 1948502894 G	G
60	179 G	-12:910654 1948502893 G	
60	180 C	-12:910653 1948502892 C	
61 Q	181 C	-12:910652 1948502891 C	Q
61	182 A	-12:910651 1948502890 A	
61	183 G	-12:910650 1948502889 G	
62 K	184 A	-12:910649 1948502888 A	K
62	185 A	-12:910648 1948502887 A	
62	186 G	-12:910647 1948502886 G	
63 V	187 G	-12:909571 1948501810 G	V
63	188 T	-12:909570 1948501809 T	
63	189 G	-12:909569 1948501808 G	
64 C	190 T	-12:909568 1948501807 T	C
64	191 G	-12:909567 1948501806 G	
64	192 C	-12:909566 1948501805 C	
65 Y	193 T	-12:909565 1948501804 T	Y
65	194 A	-12:909564 1948501803 A	
65	195 C	-12:909563 1948501802 C	
66 I	196 A	-12:909562 1948501801 A	I
66	197 T	-12:909561 1948501800 T	
66	198 T	-12:909560 1948501799 T	
67 E	199 G	-12:909559 1948501798 G	E
67	200 A	-12:909558 1948501797 A	
67	201 G	-12:909557 1948501796 G	
68 G	202 G	-12:909556 1948501795 G	G
68	203 G	-12:909555 1948501794 G	
68	204 T	-12:909554 1948501793 T	
69 H	205 C	-12:909553 1948501792 C	H
69	206 A	-12:909552 1948501791 A	
69	207 T	-12:909551 1948501790 T	
70 R	208 C	-12:909550 1948501789 C	R
70	209 G	-12:909549 1948501788 G	
70	210 G	-12:909548 1948501787 G	
71 V	211 G	-12:909547 1948501786 G	V
71	212 T	-12:909546 1948501785 T	
71	213 A	-12:909545 1948501784 A	
72 I	214 A	-12:909544 1948501783 A	I
72	215 T	-12:909543 1948501782 T	
72	216 T	-12:909542 1948501781 T	
73 N	217 A	-12:909541 1948501780 A	N
73	218 A	-12:909540 1948501779 A	
73	219 T	-12:909539 1948501778 T	
74 L	220 C	-12:909538 1948501777 C	L
74	221 T	-12:909537 1948501776 T	
74	222 G	-12:909536 1948501775 G	
75 A	223 G	-12:909535 1948501774 G	A
75	224 C	-12:909534 1948501773 C	
75	225 C	-12:909533 1948501772 C	
76 N	226 A	-12:909532 1948501771 A	N
76	227 A	-12:909531 1948501770 A	
76	228 T	-12:909530 1948501769 T	
77 E	229 G	-12:909529 1948501768 G	E
77	230 A	-12:909528 1948501767 A	
77	231 G	-12:909527 1948501766 G	
78 M	232 A	-12:909526 1948501765 A	M
78	233 T	-12:909525 1948501764 T	
78	234 G	-12:909524 1948501763 G	
79 F	235 T	-12:909523 1948501762 T	F
79	236 T	-12:909522 1948501761 T	
79	237 T	-12:909521 1948501760 T	
80 G	238 G	-12:909520 1948501759 G	G
80	239 G	-12:909519 1948501758 G	
80	240 T	-12:909518 1948501757 T	
81 Y	241 T	-12:909517 1948501756 T	Y
81	242 A	-12:909516 1948501755 A	
81	243 C	-12:909515 1948501754 C	
82 N	244 A	-12:909514 1948501753 A	N
82	245 A	-12:909513 1948501752 A	
82	246 T	-12:909512 1948501751 T	
83 G	247 G	-12:909511 1948501750 G	G
83	248 G	-12:909510 1948501749 G	
83	249 C	-12:909509 1948501748 C	
84 W	250 T	-12:909508 1948501747 T	W
84	251 G	-12:909507 1948501746 G	
84	252 G	-12:909506 1948501745 G	
85 A	253 G	-12:909505 1948501744 G	A
85	254 C	-12:909504 1948501743 C	
85	255 A	-12:909503 1948501742 A	
86 H	256 C	-12:909502 1948501741 C	H
86	257 A	-12:909501 1948501740 A	
86	258 C	-12:909500 1948501739 C	
87 S	259 T	-12:909499 1948501738 T	S
87	260 C	-12:909498 1948501737 C	
87	261 C	-12:909497 1948501736 C	
88 I	262 A	-12:909496 1948501735 A	I
88	263 T	-12:909495 1948501734 T	
88	264 C	-12:909494 1948501733 C	
89 T	265 A	-12:909493 1948501732 A	T
89	266 C	-12:909492 1948501731 C	
89	267 G	-12:909491 1948501730 G	
90 Q	268 C	-12:909490 1948501729 C	Q
90	269 A	-12:909489 1948501728 A	
90	270 G	-12:909488 1948501727 G	
91 Q	271 C	-12:909487 1948501726 C	Q
91	272 A	-12:909486 1948501725 A	
91	273 G	-12:909485 1948501724 G	
92 N	274 A	-12:909484 1948501723 A	N
92	275 A	-12:909483 1948501722 A	
92	276 T	-12:909482 1948501721 T	
93 V	277 G	-12:909481 1948501720 G	V
93	278 T	-12:909480 1948501719 T	
93	279 G	-12:909479 1948501718 G	
94 D	280 G	-12:909478 1948501717 G	D
94	281 A	-12:909313 1948501552 A	
94	282 T	-12:909312 1948501551 T	
95 F	283 T	-12:909311 1948501550 T	F
95	284 T	-12:909310 1948501549 T	
95	285 T	-12:909309 1948501548 T	
96 V	286 G	-12:909308 1948501547 G	V
96	287 T	-12:909307 1948501546 T	
96	288 T	-12:909306 1948501545 T	
97 D	289 G	-12:909305 1948501544 G	D
97	290 A	-12:909304 1948501543 A	
97	291 C	-12:909303 1948501542 C	
98 L	292 C	-12:909302 1948501541 C	L
98	293 T	-12:909301 1948501540 T	
98	294 C	-12:909300 1948501539 C	
99 N	295 A	-12:909299 1948501538 A	N
99	296 A	-12:909298 1948501537 A	
99	297 C	-12:909297 1948501536 C	
100 N	298 A	-12:909296 1948501535 A	N
100	299 A	-12:909295 1948501534 A	
100	300 T	-12:909294 1948501533 T	
101 G	301 G	-12:909293 1948501532 G	G
101	302 G	-12:909292 1948501531 G	
101	303 C	-12:909291 1948501530 C	
102 K	304 A	-12:909290 1948501529 A	K
102	305 A	-12:909289 1948501528 A	
102	306 G	-12:909288 1948501527 G	
103 F	307 T	-12:909287 1948501526 T	F
103	308 T	-12:909286 1948501525 T	
103	309 C	-12:909285 1948501524 C	
104 Y	310 T	-12:909284 1948501523 T	Y
104	311 A	-12:909283 1948501522 A	
104	312 C	-12:909282 1948501521 C	
105 V	313 G	-12:909281 1948501520 G	V
105	314 T	-12:909280 1948501519 T	
105	315 G	-12:909279 1948501518 G	
106 G	316 G	-12:909278 1948501517 G	G
106	317 G	-12:909277 1948501516 G	
106	318 A	-12:909276 1948501515 A	
107 V	319 G	-12:909275 1948501514 G	V
107	320 T	-12:909274 1948501513 T	
107	321 C	-12:909273 1948501512 C	
108 C	322 T	-12:909272 1948501511 T	C
108	323 G	-12:909271 1948501510 G	
108	324 T	-12:909270 1948501509 T	
109 A	325 G	-12:909269 1948501508 G	A
109	326 C	-12:909268 1948501507 C	
109	327 A	-12:909267 1948501506 A	
110 F	328 T	-12:909266 1948501505 T	F
110	329 T	-12:909265 1948501504 T	
110	330 T	-12:909264 1948501503 T	
111 V	331 G	-12:909263 1948501502 G	V
111	332 T	-12:909262 1948501501 T	
111	333 G	-12:909261 1948501500 G	
112 R	334 A	-12:909260 1948501499 A	R
112	335 G	-12:909259 1948501498 G	
112	336 G	-12:909258 1948501497 G	
113 V	337 G	-12:909257 1948501496 G	V
113	338 T	-12:909256 1948501495 T	
113	339 C	-12:909255 1948501494 C	
114 Q	340 C	-12:909254 1948501493 C	Q
114	341 A	-12:909253 1948501492 A	
114	342 G	-12:909252 1948501491 G	
115 L	343 C	-12:909251 1948501490 C	L
115	344 T	-12:909250 1948501489 T	
115	345 G	-12:909249 1948501488 G	
116 K	346 A	-12:909248 1948501487 A	K
116	347 A	-12:909247 1948501486 A	
116	348 G	-12:909246 1948501485 G	
117 V	349 G	-12:909245 1948501484 G	V
117	350 T	-12:909244 1948501483 T	
117	351 G	-12:909243 1948501482 G	
118 R	352 A	-12:909242 1948501481 A	R
118	353 G	-12:909241 1948501480 G	
118	354 G	-12:909240 1948501479 G	
119 G	355 G	-12:909239 1948501478 G	G
119	356 G	-12:909238 1948501477 G	
119	357 A	-12:909237 1948501476 A	
120 W	358 T	-12:909236 1948501475 T	W
120	359 G	-12:909235 1948501474 G	
120	360 G	-12:909234 1948501473 G	
121 S	361 A	-12:909233 1948501472 A	S
121	362 G	-12:909232 1948501471 G	
121	363 T	-12:909231 1948501470 T	
122 R	364 A	-12:909230 1948501469 A	R
122	365 G	-12:909229 1948501468 G	
122	366 A	-12:909228 1948501467 A	
123 P	367 C	-12:909227 1948501466 C	P
123	368 C	-12:909226 1948501465 C	
123	369 T	-12:909225 1948501464 T	
124 A	370 G	-12:909224 1948501463 G	A
124	371 C	-12:909223 1948501462 C	
124	372 T	-12:909222 1948501461 T	
125 A	373 G	-12:909221 1948501460 G	A
125	374 C	-12:909220 1948501459 C	
125	375 C	-12:909219 1948501458 C	
126 R	376 C	-12:909218 1948501457 C	R
126	377 G	-12:909217 1948501456 G	
126	378 G	-12:909216 1948501455 G	
127 K	379 A	-12:909215 1948501454 A	K
127	380 A	-12:909214 1948501453 A	
127	381 G	-12:909213 1948501452 G	
128 D	382 G	-12:909212 1948501451 G	D
128	383 A	-12:909211 1948501450 A	
128	384 T	-12:909210 1948501449 T	
129 Q	385 C	-12:909209 1948501448 C	Q
129	386 A	-12:909208 1948501447 A	
129	387 G	-12:909207 1948501446 G	
130 W	388 T	-12:909206 1948501445 T	W
130	389 G	-12:909205 1948501444 G	
130	390 G	-12:909204 1948501443 G	
131 V	391 G	-12:909203 1948501442 G	V
131	392 T	-12:909202 1948501441 T	
131	393 G	-12:909201 1948501440 G	
132 V	394 G	-12:909200 1948501439 G	V
132	395 T	-12:909199 1948501438 T	
132	396 A	-12:909198 1948501437 A	
133 G	397 G	-12:909197 1948501436 G	G
133	398 G	-12:909196 1948501435 G	
133	399 A	-12:909195 1948501434 A	
134 E	400 G	-12:909194 1948501433 G	E
134	401 A	-12:909193 1948501432 A	
134	402 A	-12:909192 1948501431 A	
>ENSP00000378040 
1 M	1 A	-11:63808416 1876948271 A	M
1	2 T	-11:63808415 1876948270 T	
1	3 G	-11:63808414 1876948269 G	
2 F	4 T	-11:63808413 1876948268 T	F
2	5 T	-11:63808412 1876948267 T	
2	6 C	-11:63808411 1876948266 C	
3 Q	7 C	-11:63808410 1876948265 C	Q
3	8 A	-11:63808409 1876948264 A	
3	9 G	-11:63808408 1876948263 G	
4 I	10 A	-11:63808407 1876948262 A	I
4	11 T	-11:63808406 1876948261 T	
4	12 C	-11:63808405 1876948260 C	
5 P	13 C	-11:63808404 1876948259 C	P
5	14 C	-11:63808403 1876948258 C	
5	15 A	-11:63808402 1876948257 A	
6 E	16 G	-11:63808401 1876948256 G	E
6	17 A	-11:63808400 1876948255 A	
6	18 G	-11:63808399 1876948254 G	
7 F	19 T	-11:63808398 1876948253 T	F
7	20 T	-11:63808397 1876948252 T	
7	21 T	-11:63808396 1876948251 T	
8 E	22 G	-11:63808395 1876948250 G	E
8	23 A	-11:63808394 1876948249 A	
8	24 G	-11:63808393 1876948248 G	
9 P	25 C	-11:63808392 1876948247 C	P
9	26 C	-11:63808391 1876948246 C	
9	27 G	-11:63808390 1876948245 G	
10 S	28 A	-11:63808389 1876948244 A	S
10	29 G	-11:63808388 1876948243 G	
10	30 T	-11:63808387 1876948242 T	
11 E	31 G	-11:63808386 1876948241 G	E
11	32 A	-11:63808385 1876948240 A	
11	33 G	-11:63808384 1876948239 G	
12 Q	34 C	-11:63808383 1876948238 C	Q
12	35 A	-11:63808382 1876948237 A	
12	36 G	-11:63808381 1876948236 G	
13 E	37 G	-11:63808380 1876948235 G	E
13	38 A	-11:63808379 1876948234 A	
13	39 A	-11:63808378 1876948233 A	
14 D	40 G	-11:63808377 1876948232 G	D
14	41 A	-11:63808376 1876948231 A	
14	42 C	-11:63808375 1876948230 C	
15 S	43 T	-11:63808374 1876948229 T	S
15	44 C	-11:63808373 1876948228 C	
15	45 C	-11:63808372 1876948227 C	
16 S	46 A	-11:63808371 1876948226 A	S
16	47 G	-11:63808370 1876948225 G	
16	48 C	-11:63808369 1876948224 C	
17 S	49 T	-11:63808368 1876948223 T	S
17	50 C	-11:63808367 1876948222 C	
17	51 T	-11:63808366 1876948221 T	
18 A	52 G	-11:63808365 1876948220 G	A
18	53 C	-11:63808364 1876948219 C	
18	54 A	-11:63808363 1876948218 A	
19 E	55 G	-11:63808362 1876948217 G	E
19	56 A	-11:63808361 1876948216 A	
19	57 G	-11:63808360 1876948215 G	
20 R	58 A	-11:63808359 1876948214 A	R
20	59 G	-11:63808358 1876948213 G	
20	60 G	-11:63808357 1876948212 G	
21 G	61 G	-11:63808356 1876948211 G	G
21	62 G	-11:63808355 1876948210 G	
21	63 C	-11:63808354 1876948209 C	
22 L	64 C	-11:63808353 1876948208 C	L
22	65 T	-11:63808352 1876948207 T	
22	66 G	-11:63808351 1876948206 G	
23 G	67 G	-11:63808350 1876948205 G	G
23	68 G	-11:63808349 1876948204 G	
23	69 C	-11:63808348 1876948203 C	
24 P	70 C	-11:63808347 1876948202 C	P
24	71 C	-11:63808346 1876948201 C	
24	72 C	-11:63808345 1876948200 C	
25 S	73 A	-11:63808344 1876948199 A	S
25	74 G	-11:63808343 1876948198 G	
25	75 C	-11:63808342 1876948197 C	
26 P	76 C	-11:63808341 1876948196 C	P
26	77 C	-11:63808340 1876948195 C	
26	78 C	-11:63808339 1876948194 C	
27 A	79 G	-11:63808338 1876948193 G	A
27	80 C	-11:63808337 1876948192 C	
27	81 A	-11:63808336 1876948191 A	
28 G	82 G	-11:63808335 1876948190 G	G
28	83 G	-11:63808334 1876948189 G	
28	84 G	-11:63808333 1876948188 G	
29 D	85 G	-11:63808332 1876948187 G	D
29	86 A	-11:63808331 1876948186 A	
29	87 C	-11:63808330 1876948185 C	
30 G	88 G	-11:63808329 1876948184 G	G
30	89 G	-11:63808328 1876948183 G	
30	90 G	-11:63808327 1876948182 G	
31 P	91 C	-11:63808326 1876948181 C	P
31	92 C	-11:63808325 1876948180 C	
31	93 C	-11:63808324 1876948179 C	
32 S	94 T	-11:63808323 1876948178 T	S
32	95 C	-11:63808322 1876948177 C	
32	96 A	-11:63808321 1876948176 A	
33 G	97 G	-11:63808320 1876948175 G	G
33	98 G	-11:63808319 1876948174 G	
33	99 C	-11:63808318 1876948173 C	
34 S	100 T	-11:63808317 1876948172 T	S
34	101 C	-11:63808316 1876948171 C	
34	102 C	-11:63808315 1876948170 C	
35 G	103 G	-11:63808314 1876948169 G	G
35	104 G	-11:63808313 1876948168 G	
35	105 C	-11:63808312 1876948167 C	
36 K	106 A	-11:63808311 1876948166 A	K
36	107 A	-11:63808310 1876948165 A	
36	108 G	-11:63808309 1876948164 G	
37 H	109 C	-11:63808308 1876948163 C	H
37	110 A	-11:63808307 1876948162 A	
37	111 T	-11:63808306 1876948161 T	
38 H	112 C	-11:63808305 1876948160 C	H
38	113 A	-11:63808304 1876948159 A	
38	114 T	-11:63808303 1876948158 T	
39 R	115 C	-11:63808302 1876948157 C	R
39	116 G	-11:63808301 1876948156 G	
39	117 C	-11:63808300 1876948155 C	
40 Q	118 C	-11:63808299 1876948154 C	Q
40	119 A	-11:63808298 1876948153 A	
40	120 G	-11:63808297 1876948152 G	
41 A	121 G	-11:63808296 1876948151 G	A
41	122 C	-11:63808295 1876948150 C	
41	123 C	-11:63808294 1876948149 C	
42 P	124 C	-11:63808293 1876948148 C	P
42	125 C	-11:63808292 1876948147 C	
42	126 A	-11:63808291 1876948146 A	
43 G	127 G	-11:63808290 1876948145 G	G
43	128 G	-11:63808289 1876948144 G	
43	129 C	-11:63808288 1876948143 C	
44 L	130 C	-11:63808287 1876948142 C	L
44	131 T	-11:63808286 1876948141 T	
44	132 C	-11:63808285 1876948140 C	
45 L	133 C	-11:63808284 1876948139 C	L
45	134 T	-11:63808283 1876948138 T	
45	135 G	-11:63808282 1876948137 G	
46 W	136 T	-11:63808281 1876948136 T	W
46	137 G	-11:63808280 1876948135 G	
46	138 G	-11:63808279 1876948134 G	
47 D	139 G	-11:63808278 1876948133 G	D
47	140 A	-11:63808277 1876948132 A	
47	141 C	-11:63808276 1876948131 C	
48 A	142 G	-11:63808275 1876948130 G	A
48	143 C	-11:63808274 1876948129 C	
48	144 C	-11:63808273 1876948128 C	
49 S	145 A	-11:63808272 1876948127 A	S
49	146 G	-11:63808271 1876948126 G	
49	147 T	-11:63808270 1876948125 T	
50 H	148 C	-11:63808269 1876948124 C	H
50	149 A	-11:63808268 1876948123 A	
50	150 C	-11:63808267 1876948122 C	
51 Q	151 C	-11:63808266 1876948121 C	Q
51	152 A	-11:63808265 1876948120 A	
51	153 G	-11:63808264 1876948119 G	
52 Q	154 C	-11:63808263 1876948118 C	Q
52	155 A	-11:63808262 1876948117 A	
52	156 G	-11:63808261 1876948116 G	
53 E	157 G	-11:63808260 1876948115 G	E
53	158 A	-11:63808259 1876948114 A	
53	159 G	-11:63808258 1876948113 G	
54 Q	160 C	-11:63808257 1876948112 C	Q
54	161 A	-11:63808256 1876948111 A	
54	162 G	-11:63808255 1876948110 G	
55 P	163 C	-11:63808254 1876948109 C	P
55	164 C	-11:63808253 1876948108 C	
55	165 A	-11:63808252 1876948107 A	
56 T	166 A	-11:63808251 1876948106 A	T
56	167 C	-11:63808250 1876948105 C	
56	168 C	-11:63808249 1876948104 C	
57 S	169 A	-11:63808248 1876948103 A	S
57	170 G	-11:63808247 1876948102 G	
57	171 C	-11:63808246 1876948101 C	
58 S	172 A	-11:63808245 1876948100 A	S
58	173 G	-11:63808244 1876948099 G	
58	174 C	-11:63808243 1876948098 C	
59 S	175 A	-11:63808242 1876948097 A	S
59	176 G	-11:63808241 1876948096 G	
59	177 C	-11:63808240 1876948095 C	
60 H	178 C	-11:63808239 1876948094 C	H
60	179 A	-11:63808238 1876948093 A	
60	180 T	-11:63808237 1876948092 T	
61 H	181 C	-11:63808236 1876948091 C	H
61	182 A	-11:63808235 1876948090 A	
61	183 T	-11:63808234 1876948089 T	
62 G	184 G	-11:63808233 1876948088 G	G
62	185 G	-11:63808232 1876948087 G	
62	186 A	-11:63808231 1876948086 A	
63 G	187 G	-11:63808230 1876948085 G	G
63	188 G	-11:63795851 1876935706 G	
63	189 C	-11:63795850 1876935705 C	
64 A	190 G	-11:63795849 1876935704 G	A
64	191 C	-11:63795848 1876935703 C	
64	192 T	-11:63795847 1876935702 T	
65 G	193 G	-11:63795846 1876935701 G	G
65	194 G	-11:63795845 1876935700 G	
65	195 G	-11:63795844 1876935699 G	
66 A	196 G	-11:63795843 1876935698 G	A
66	197 C	-11:63795842 1876935697 C	
66	198 T	-11:63795841 1876935696 T	
67 V	199 G	-11:63795840 1876935695 G	V
67	200 T	-11:63795839 1876935694 T	
67	201 G	-11:63795838 1876935693 G	
68 E	202 G	-11:63795837 1876935692 G	E
68	203 A	-11:63795836 1876935691 A	
68	204 G	-11:63795835 1876935690 G	
69 I	205 A	-11:63795834 1876935689 A	I
69	206 T	-11:63795833 1876935688 T	
69	207 C	-11:63795832 1876935687 C	
70 R	208 C	-11:63795831 1876935686 C	R
70	209 G	-11:63795830 1876935685 G	
70	210 G	-11:63795829 1876935684 G	
71 S	211 A	-11:63795828 1876935683 A	S
71	212 G	-11:63795827 1876935682 G	
71	213 T	-11:63795826 1876935681 T	
72 R	214 C	-11:63795825 1876935680 C	R
72	215 G	-11:63795824 1876935679 G	
72	216 C	-11:63795823 1876935678 C	
73 H	217 C	-11:63795822 1876935677 C	H
73	218 A	-11:63795821 1876935676 A	
73	219 C	-11:63795820 1876935675 C	
74 S	220 A	-11:63795819 1876935674 A	S
74	221 G	-11:63795818 1876935673 G	
74	222 C	-11:63795817 1876935672 C	
75 S	223 T	-11:63795816 1876935671 T	S
75	224 C	-11:63795815 1876935670 C	
75	225 C	-11:63795814 1876935669 C	
76 Y	226 T	-11:63795813 1876935668 T	Y
76	227 A	-11:63795812 1876935667 A	
76	228 C	-11:63795811 1876935666 C	
77 P	229 C	-11:63795810 1876935665 C	P
77	230 C	-11:63795809 1876935664 C	
77	231 C	-11:63795808 1876935663 C	
78 A	232 G	-11:63795807 1876935662 G	A
78	233 C	-11:63795806 1876935661 C	
78	234 G	-11:63795805 1876935660 G	
79 G	235 G	-11:63795804 1876935659 G	G
79	236 G	-11:63795803 1876935658 G	
79	237 G	-11:63795802 1876935657 G	
80 T	238 A	-11:63795801 1876935656 A	T
80	239 C	-11:63795800 1876935655 C	
80	240 G	-11:63795799 1876935654 G	
81 E	241 G	-11:63795798 1876935653 G	E
81	242 A	-11:63795797 1876935652 A	
81	243 G	-11:63795796 1876935651 G	
82 D	244 G	-11:63795795 1876935650 G	D
82	245 A	-11:63795794 1876935649 A	
82	246 C	-11:63795793 1876935648 C	
83 D	247 G	-11:63795792 1876935647 G	D
83	248 A	-11:63795791 1876935646 A	
83	249 C	-11:63795790 1876935645 C	
84 E	250 G	-11:63795789 1876935644 G	E
84	251 A	-11:63795788 1876935643 A	
84	252 A	-11:63795787 1876935642 A	
85 G	253 G	-11:63795786 1876935641 G	G
85	254 G	-11:63795785 1876935640 G	
85	255 G	-11:63795784 1876935639 G	
86 M	256 A	-11:63795783 1876935638 A	M
86	257 T	-11:63795782 1876935637 T	
86	258 G	-11:63795781 1876935636 G	
87 G	259 G	-11:63795780 1876935635 G	G
87	260 G	-11:63795779 1876935634 G	
87	261 G	-11:63795778 1876935633 G	
88 E	262 G	-11:63795777 1876935632 G	E
88	263 A	-11:63795776 1876935631 A	
88	264 G	-11:63795775 1876935630 G	
89 E	265 G	-11:63795774 1876935629 G	E
89	266 A	-11:63795773 1876935628 A	
89	267 G	-11:63795772 1876935627 G	
90 P	268 C	-11:63795771 1876935626 C	P
90	269 C	-11:63795770 1876935625 C	
90	270 C	-11:63795769 1876935624 C	
91 S	271 A	-11:63795768 1876935623 A	S
91	272 G	-11:63795767 1876935622 G	
91	273 C	-11:63795766 1876935621 C	
92 P	274 C	-11:63795765 1876935620 C	P
92	275 C	-11:63795764 1876935619 C	
92	276 C	-11:63795763 1876935618 C	
93 F	277 T	-11:63795762 1876935617 T	F
93	278 T	-11:63795761 1876935616 T	
93	279 T	-11:63795760 1876935615 T	
94 R	280 C	-11:63795759 1876935614 C	R
94	281 G	-11:63795758 1876935613 G	
94	282 G	-11:63795757 1876935612 G	
95 G	283 G	-11:63795756 1876935611 G	G
95	284 G	-11:63795755 1876935610 G	
95	285 C	-11:63795754 1876935609 C	
96 R	286 C	-11:63795753 1876935608 C	R
96	287 G	-11:63795752 1876935607 G	
96	288 C	-11:63795751 1876935606 C	
97 S	289 T	-11:63795750 1876935605 T	S
97	290 C	-11:63795749 1876935604 C	
97	291 G	-11:63795748 1876935603 G	
98 R	292 C	-11:63795747 1876935602 C	R
98	293 G	-11:63795746 1876935601 G	
98	294 C	-11:63795745 1876935600 C	
99 S	295 T	-11:63795744 1876935599 T	S
99	296 C	-11:63795743 1876935598 C	
99	297 G	-11:63795742 1876935597 G	
100 A	298 G	-11:63795741 1876935596 G	A
100	299 C	-11:63795740 1876935595 C	
100	300 G	-11:63795739 1876935594 G	
101 P	301 C	-11:63795738 1876935593 C	P
101	302 C	-11:63795737 1876935592 C	
101	303 C	-11:63795736 1876935591 C	
102 P	304 C	-11:63795735 1876935590 C	P
102	305 C	-11:63795734 1876935589 C	
102	306 C	-11:63795733 1876935588 C	
103 N	307 A	-11:63795732 1876935587 A	N
103	308 A	-11:63795731 1876935586 A	
103	309 C	-11:63795730 1876935585 C	
104 L	310 C	-11:63795729 1876935584 C	L
104	311 T	-11:63795728 1876935583 T	
104	312 C	-11:63795727 1876935582 C	
105 W	313 T	-11:63795726 1876935581 T	W
105	314 G	-11:63795725 1876935580 G	
105	315 G	-11:63795724 1876935579 G	
106 A	316 G	-11:63795723 1876935578 G	A
106	317 C	-11:63795722 1876935577 C	
106	318 A	-11:63795721 1876935576 A	
107 A	319 G	-11:63795720 1876935575 G	A
107	320 C	-11:63795719 1876935574 C	
107	321 A	-11:63795718 1876935573 A	
108 Q	322 C	-11:63795717 1876935572 C	Q
108	323 A	-11:63795716 1876935571 A	
108	324 G	-11:63795715 1876935570 G	
109 R	325 C	-11:63795714 1876935569 C	R
109	326 G	-11:63795713 1876935568 G	
109	327 C	-11:63795712 1876935567 C	
110 Y	328 T	-11:63795711 1876935566 T	Y
110	329 A	-11:63795710 1876935565 A	
110	330 T	-11:63795709 1876935564 T	
111 G	331 G	-11:63795708 1876935563 G	G
111	332 G	-11:63795707 1876935562 G	
111	333 C	-11:63795706 1876935561 C	
112 R	334 C	-11:63795705 1876935560 C	R
112	335 G	-11:63795704 1876935559 G	
112	336 C	-11:63795703 1876935558 C	
113 E	337 G	-11:63795702 1876935557 G	E
113	338 A	-11:63795701 1876935556 A	
113	339 G	-11:63795700 1876935555 G	
114 L	340 C	-11:63795699 1876935554 C	L
114	341 T	-11:63795698 1876935553 T	
114	342 C	-11:63795697 1876935552 C	
115 R	343 C	-11:63795696 1876935551 C	R
115	344 G	-11:63795695 1876935550 G	
115	345 G	-11:63795694 1876935549 G	
116 R	346 A	-11:63795693 1876935548 A	R
116	347 G	-11:63795692 1876935547 G	
116	348 G	-11:63795691 1876935546 G	
117 M	349 A	-11:63795690 1876935545 A	M
117	350 T	-11:63795689 1876935544 T	
117	351 G	-11:63795688 1876935543 G	
118 S	352 A	-11:63795687 1876935542 A	S
118	353 G	-11:63795686 1876935541 G	
118	354 T	-11:63795685 1876935540 T	
119 D	355 G	-11:63795684 1876935539 G	D
119	356 A	-11:63795683 1876935538 A	
119	357 C	-11:63795682 1876935537 C	
120 E	358 G	-11:63795681 1876935536 G	E
120	359 A	-11:63795680 1876935535 A	
120	360 G	-11:63795679 1876935534 G	
121 F	361 T	-11:63795678 1876935533 T	F
121	362 T	-11:63795677 1876935532 T	
121	363 T	-11:63795676 1876935531 T	
122 V	364 G	-11:63795675 1876935530 G	V
122	365 T	-11:63795674 1876935529 T	
122	366 G	-11:63795673 1876935528 G	
123 D	367 G	-11:63795672 1876935527 G	D
123	368 A	-11:63795671 1876935526 A	
123	369 C	-11:63795670 1876935525 C	
124 S	370 T	-11:63795669 1876935524 T	S
124	371 C	-11:63795668 1876935523 C	
124	372 C	-11:63795667 1876935522 C	
125 F	373 T	-11:63795666 1876935521 T	F
125	374 T	-11:63795665 1876935520 T	
125	375 T	-11:63795664 1876935519 T	
>ENSP00000309103 
1 M	1 A	-11:63808416 1876948271 A	M
1	2 T	-11:63808415 1876948270 T	
1	3 G	-11:63808414 1876948269 G	
2 F	4 T	-11:63808413 1876948268 T	F
2	5 T	-11:63808412 1876948267 T	
2	6 C	-11:63808411 1876948266 C	
3 Q	7 C	-11:63808410 1876948265 C	Q
3	8 A	-11:63808409 1876948264 A	
3	9 G	-11:63808408 1876948263 G	
4 I	10 A	-11:63808407 1876948262 A	I
4	11 T	-11:63808406 1876948261 T	
4	12 C	-11:63808405 1876948260 C	
5 P	13 C	-11:63808404 1876948259 C	P
5	14 C	-11:63808403 1876948258 C	
5	15 A	-11:63808402 1876948257 A	
6 E	16 G	-11:63808401 1876948256 G	E
6	17 A	-11:63808400 1876948255 A	
6	18 G	-11:63808399 1876948254 G	
7 F	19 T	-11:63808398 1876948253 T	F
7	20 T	-11:63808397 1876948252 T	
7	21 T	-11:63808396 1876948251 T	
8 E	22 G	-11:63808395 1876948250 G	E
8	23 A	-11:63808394 1876948249 A	
8	24 G	-11:63808393 1876948248 G	
9 P	25 C	-11:63808392 1876948247 C	P
9	26 C	-11:63808391 1876948246 C	
9	27 G	-11:63808390 1876948245 G	
10 S	28 A	-11:63808389 1876948244 A	S
10	29 G	-11:63808388 1876948243 G	
10	30 T	-11:63808387 1876948242 T	
11 E	31 G	-11:63808386 1876948241 G	E
11	32 A	-11:63808385 1876948240 A	
11	33 G	-11:63808384 1876948239 G	
12 Q	34 C	-11:63808383 1876948238 C	Q
12	35 A	-11:63808382 1876948237 A	
12	36 G	-11:63808381 1876948236 G	
13 E	37 G	-11:63808380 1876948235 G	E
13	38 A	-11:63808379 1876948234 A	
13	39 A	-11:63808378 1876948233 A	
14 D	40 G	-11:63808377 1876948232 G	D
14	41 A	-11:63808376 1876948231 A	
14	42 C	-11:63808375 1876948230 C	
15 S	43 T	-11:63808374 1876948229 T	S
15	44 C	-11:63808373 1876948228 C	
15	45 C	-11:63808372 1876948227 C	
16 S	46 A	-11:63808371 1876948226 A	S
16	47 G	-11:63808370 1876948225 G	
16	48 C	-11:63808369 1876948224 C	
17 S	49 T	-11:63808368 1876948223 T	S
17	50 C	-11:63808367 1876948222 C	
17	51 T	-11:63808366 1876948221 T	
18 A	52 G	-11:63808365 1876948220 G	A
18	53 C	-11:63808364 1876948219 C	
18	54 A	-11:63808363 1876948218 A	
19 E	55 G	-11:63808362 1876948217 G	E
19	56 A	-11:63808361 1876948216 A	
19	57 G	-11:63808360 1876948215 G	
20 R	58 A	-11:63808359 1876948214 A	R
20	59 G	-11:63808358 1876948213 G	
20	60 G	-11:63808357 1876948212 G	
21 G	61 G	-11:63808356 1876948211 G	G
21	62 G	-11:63808355 1876948210 G	
21	63 C	-11:63808354 1876948209 C	
22 L	64 C	-11:63808353 1876948208 C	L
22	65 T	-11:63808352 1876948207 T	
22	66 G	-11:63808351 1876948206 G	
23 G	67 G	-11:63808350 1876948205 G	G
23	68 G	-11:63808349 1876948204 G	
23	69 C	-11:63808348 1876948203 C	
24 P	70 C	-11:63808347 1876948202 C	P
24	71 C	-11:63808346 1876948201 C	
24	72 C	-11:63808345 1876948200 C	
25 S	73 A	-11:63808344 1876948199 A	S
25	74 G	-11:63808343 1876948198 G	
25	75 C	-11:63808342 1876948197 C	
26 P	76 C	-11:63808341 1876948196 C	P
26	77 C	-11:63808340 1876948195 C	
26	78 C	-11:63808339 1876948194 C	
27 A	79 G	-11:63808338 1876948193 G	A
27	80 C	-11:63808337 1876948192 C	
27	81 A	-11:63808336 1876948191 A	
28 G	82 G	-11:63808335 1876948190 G	G
28	83 G	-11:63808334 1876948189 G	
28	84 G	-11:63808333 1876948188 G	
29 D	85 G	-11:63808332 1876948187 G	D
29	86 A	-11:63808331 1876948186 A	
29	87 C	-11:63808330 1876948185 C	
30 G	88 G	-11:63808329 1876948184 G	G
30	89 G	-11:63808328 1876948183 G	
30	90 G	-11:63808327 1876948182 G	
31 P	91 C	-11:63808326 1876948181 C	P
31	92 C	-11:63808325 1876948180 C	
31	93 C	-11:63808324 1876948179 C	
32 S	94 T	-11:63808323 1876948178 T	S
32	95 C	-11:63808322 1876948177 C	
32	96 A	-11:63808321 1876948176 A	
33 G	97 G	-11:63808320 1876948175 G	G
33	98 G	-11:63808319 1876948174 G	
33	99 C	-11:63808318 1876948173 C	
34 S	100 T	-11:63808317 1876948172 T	S
34	101 C	-11:63808316 1876948171 C	
34	102 C	-11:63808315 1876948170 C	
35 G	103 G	-11:63808314 1876948169 G	G
35	104 G	-11:63808313 1876948168 G	
35	105 C	-11:63808312 1876948167 C	
36 K	106 A	-11:63808311 1876948166 A	K
36	107 A	-11:63808310 1876948165 A	
36	108 G	-11:63808309 1876948164 G	
37 H	109 C	-11:63808308 1876948163 C	H
37	110 A	-11:63808307 1876948162 A	
37	111 T	-11:63808306 1876948161 T	
38 H	112 C	-11:63808305 1876948160 C	H
38	113 A	-11:63808304 1876948159 A	
38	114 T	-11:63808303 1876948158 T	
39 R	115 C	-11:63808302 1876948157 C	R
39	116 G	-11:63808301 1876948156 G	
39	117 C	-11:63808300 1876948155 C	
40 Q	118 C	-11:63808299 1876948154 C	Q
40	119 A	-11:63808298 1876948153 A	
40	120 G	-11:63808297 1876948152 G	
41 A	121 G	-11:63808296 1876948151 G	A
41	122 C	-11:63808295 1876948150 C	
41	123 C	-11:63808294 1876948149 C	
42 P	124 C	-11:63808293 1876948148 C	P
42	125 C	-11:63808292 1876948147 C	
42	126 A	-11:63808291 1876948146 A	
43 G	127 G	-11:63808290 1876948145 G	G
43	128 G	-11:63808289 1876948144 G	
43	129 C	-11:63808288 1876948143 C	
44 L	130 C	-11:63808287 1876948142 C	L
44	131 T	-11:63808286 1876948141 T	
44	132 C	-11:63808285 1876948140 C	
45 L	133 C	-11:63808284 1876948139 C	L
45	134 T	-11:63808283 1876948138 T	
45	135 G	-11:63808282 1876948137 G	
46 W	136 T	-11:63808281 1876948136 T	W
46	137 G	-11:63808280 1876948135 G	
46	138 G	-11:63808279 1876948134 G	
47 D	139 G	-11:63808278 1876948133 G	D
47	140 A	-11:63808277 1876948132 A	
47	141 C	-11:63808276 1876948131 C	
48 A	142 G	-11:63808275 1876948130 G	A
48	143 C	-11:63808274 1876948129 C	
48	144 C	-11:63808273 1876948128 C	
49 S	145 A	-11:63808272 1876948127 A	S
49	146 G	-11:63808271 1876948126 G	
49	147 T	-11:63808270 1876948125 T	
50 H	148 C	-11:63808269 1876948124 C	H
50	149 A	-11:63808268 1876948123 A	
50	150 C	-11:63808267 1876948122 C	
51 Q	151 C	-11:63808266 1876948121 C	Q
51	152 A	-11:63808265 1876948120 A	
51	153 G	-11:63808264 1876948119 G	
52 Q	154 C	-11:63808263 1876948118 C	Q
52	155 A	-11:63808262 1876948117 A	
52	156 G	-11:63808261 1876948116 G	
53 E	157 G	-11:63808260 1876948115 G	E
53	158 A	-11:63808259 1876948114 A	
53	159 G	-11:63808258 1876948113 G	
54 Q	160 C	-11:63808257 1876948112 C	Q
54	161 A	-11:63808256 1876948111 A	
54	162 G	-11:63808255 1876948110 G	
55 P	163 C	-11:63808254 1876948109 C	P
55	164 C	-11:63808253 1876948108 C	
55	165 A	-11:63808252 1876948107 A	
56 T	166 A	-11:63808251 1876948106 A	T
56	167 C	-11:63808250 1876948105 C	
56	168 C	-11:63808249 1876948104 C	
57 S	169 A	-11:63808248 1876948103 A	S
57	170 G	-11:63808247 1876948102 G	
57	171 C	-11:63808246 1876948101 C	
58 S	172 A	-11:63808245 1876948100 A	S
58	173 G	-11:63808244 1876948099 G	
58	174 C	-11:63808243 1876948098 C	
59 S	175 A	-11:63808242 1876948097 A	S
59	176 G	-11:63808241 1876948096 G	
59	177 C	-11:63808240 1876948095 C	
60 H	178 C	-11:63808239 1876948094 C	H
60	179 A	-11:63808238 1876948093 A	
60	180 T	-11:63808237 1876948092 T	
61 H	181 C	-11:63808236 1876948091 C	H
61	182 A	-11:63808235 1876948090 A	
61	183 T	-11:63808234 1876948089 T	
62 G	184 G	-11:63808233 1876948088 G	G
62	185 G	-11:63808232 1876948087 G	
62	186 A	-11:63808231 1876948086 A	
63 G	187 G	-11:63808230 1876948085 G	G
63	188 G	-11:63795851 1876935706 G	
63	189 C	-11:63795850 1876935705 C	
64 A	190 G	-11:63795849 1876935704 G	A
64	191 C	-11:63795848 1876935703 C	
64	192 T	-11:63795847 1876935702 T	
65 G	193 G	-11:63795846 1876935701 G	G
65	194 G	-11:63795845 1876935700 G	
65	195 G	-11:63795844 1876935699 G	
66 A	196 G	-11:63795843 1876935698 G	A
66	197 C	-11:63795842 1876935697 C	
66	198 T	-11:63795841 1876935696 T	
67 V	199 G	-11:63795840 1876935695 G	V
67	200 T	-11:63795839 1876935694 T	
67	201 G	-11:63795838 1876935693 G	
68 E	202 G	-11:63795837 1876935692 G	E
68	203 A	-11:63795836 1876935691 A	
68	204 G	-11:63795835 1876935690 G	
69 I	205 A	-11:63795834 1876935689 A	I
69	206 T	-11:63795833 1876935688 T	
69	207 C	-11:63795832 1876935687 C	
70 R	208 C	-11:63795831 1876935686 C	R
70	209 G	-11:63795830 1876935685 G	
70	210 G	-11:63795829 1876935684 G	
71 S	211 A	-11:63795828 1876935683 A	S
71	212 G	-11:63795827 1876935682 G	
71	213 T	-11:63795826 1876935681 T	
72 R	214 C	-11:63795825 1876935680 C	R
72	215 G	-11:63795824 1876935679 G	
72	216 C	-11:63795823 1876935678 C	
73 H	217 C	-11:63795822 1876935677 C	H
73	218 A	-11:63795821 1876935676 A	
73	219 C	-11:63795820 1876935675 C	
74 S	220 A	-11:63795819 1876935674 A	S
74	221 G	-11:63795818 1876935673 G	
74	222 C	-11:63795817 1876935672 C	
75 S	223 T	-11:63795816 1876935671 T	S
75	224 C	-11:63795815 1876935670 C	
75	225 C	-11:63795814 1876935669 C	
76 Y	226 T	-11:63795813 1876935668 T	Y
76	227 A	-11:63795812 1876935667 A	
76	228 C	-11:63795811 1876935666 C	
77 P	229 C	-11:63795810 1876935665 C	P
77	230 C	-11:63795809 1876935664 C	
77	231 C	-11:63795808 1876935663 C	
78 A	232 G	-11:63795807 1876935662 G	A
78	233 C	-11:63795806 1876935661 C	
78	234 G	-11:63795805 1876935660 G	
79 G	235 G	-11:63795804 1876935659 G	G
79	236 G	-11:63795803 1876935658 G	
79	237 G	-11:63795802 1876935657 G	
80 T	238 A	-11:63795801 1876935656 A	T
80	239 C	-11:63795800 1876935655 C	
80	240 G	-11:63795799 1876935654 G	
81 E	241 G	-11:63795798 1876935653 G	E
81	242 A	-11:63795797 1876935652 A	
81	243 G	-11:63795796 1876935651 G	
82 D	244 G	-11:63795795 1876935650 G	D
82	245 A	-11:63795794 1876935649 A	
82	246 C	-11:63795793 1876935648 C	
83 D	247 G	-11:63795792 1876935647 G	D
83	248 A	-11:63795791 1876935646 A	
83	249 C	-11:63795790 1876935645 C	
84 E	250 G	-11:63795789 1876935644 G	E
84	251 A	-11:63795788 1876935643 A	
84	252 A	-11:63795787 1876935642 A	
85 G	253 G	-11:63795786 1876935641 G	G
85	254 G	-11:63795785 1876935640 G	
85	255 G	-11:63795784 1876935639 G	
86 M	256 A	-11:63795783 1876935638 A	M
86	257 T	-11:63795782 1876935637 T	
86	258 G	-11:63795781 1876935636 G	
87 G	259 G	-11:63795780 1876935635 G	G
87	260 G	-11:63795779 1876935634 G	
87	261 G	-11:63795778 1876935633 G	
88 E	262 G	-11:63795777 1876935632 G	E
88	263 A	-11:63795776 1876935631 A	
88	264 G	-11:63795775 1876935630 G	
89 E	265 G	-11:63795774 1876935629 G	E
89	266 A	-11:63795773 1876935628 A	
89	267 G	-11:63795772 1876935627 G	
90 P	268 C	-11:63795771 1876935626 C	P
90	269 C	-11:63795770 1876935625 C	
90	270 C	-11:63795769 1876935624 C	
91 S	271 A	-11:63795768 1876935623 A	S
91	272 G	-11:63795767 1876935622 G	
91	273 C	-11:63795766 1876935621 C	
92 P	274 C	-11:63795765 1876935620 C	P
92	275 C	-11:63795764 1876935619 C	
92	276 C	-11:63795763 1876935618 C	
93 F	277 T	-11:63795762 1876935617 T	F
93	278 T	-11:63795761 1876935616 T	
93	279 T	-11:63795760 1876935615 T	
94 R	280 C	-11:63795759 1876935614 C	R
94	281 G	-11:63795758 1876935613 G	
94	282 G	-11:63795757 1876935612 G	
95 G	283 G	-11:63795756 1876935611 G	G
95	284 G	-11:63795755 1876935610 G	
95	285 C	-11:63795754 1876935609 C	
96 R	286 C	-11:63795753 1876935608 C	R
96	287 G	-11:63795752 1876935607 G	
96	288 C	-11:63795751 1876935606 C	
97 S	289 T	-11:63795750 1876935605 T	S
97	290 C	-11:63795749 1876935604 C	
97	291 G	-11:63795748 1876935603 G	
98 R	292 C	-11:63795747 1876935602 C	R
98	293 G	-11:63795746 1876935601 G	
98	294 C	-11:63795745 1876935600 C	
99 S	295 T	-11:63795744 1876935599 T	S
99	296 C	-11:63795743 1876935598 C	
99	297 G	-11:63795742 1876935597 G	
100 A	298 G	-11:63795741 1876935596 G	A
100	299 C	-11:63795740 1876935595 C	
100	300 G	-11:63795739 1876935594 G	
101 P	301 C	-11:63795738 1876935593 C	P
101	302 C	-11:63795737 1876935592 C	
101	303 C	-11:63795736 1876935591 C	
102 P	304 C	-11:63795735 1876935590 C	P
102	305 C	-11:63795734 1876935589 C	
102	306 C	-11:63795733 1876935588 C	
103 N	307 A	-11:63795732 1876935587 A	N
103	308 A	-11:63795731 1876935586 A	
103	309 C	-11:63795730 1876935585 C	
104 L	310 C	-11:63795729 1876935584 C	L
104	311 T	-11:63795728 1876935583 T	
104	312 C	-11:63795727 1876935582 C	
105 W	313 T	-11:63795726 1876935581 T	W
105	314 G	-11:63795725 1876935580 G	
105	315 G	-11:63795724 1876935579 G	
106 A	316 G	-11:63795723 1876935578 G	A
106	317 C	-11:63795722 1876935577 C	
106	318 A	-11:63795721 1876935576 A	
107 A	319 G	-11:63795720 1876935575 G	A
107	320 C	-11:63795719 1876935574 C	
107	321 A	-11:63795718 1876935573 A	
108 Q	322 C	-11:63795717 1876935572 C	Q
108	323 A	-11:63795716 1876935571 A	
108	324 G	-11:63795715 1876935570 G	
109 R	325 C	-11:63795714 1876935569 C	R
109	326 G	-11:63795713 1876935568 G	
109	327 C	-11:63795712 1876935567 C	
110 Y	328 T	-11:63795711 1876935566 T	Y
110	329 A	-11:63795710 1876935565 A	
110	330 T	-11:63795709 1876935564 T	
111 G	331 G	-11:63795708 1876935563 G	G
111	332 G	-11:63795707 1876935562 G	
111	333 C	-11:63795706 1876935561 C	
112 R	334 C	-11:63795705 1876935560 C	R
112	335 G	-11:63795704 1876935559 G	
112	336 C	-11:63795703 1876935558 C	
113 E	337 G	-11:63795702 1876935557 G	E
113	338 A	-11:63795701 1876935556 A	
113	339 G	-11:63795700 1876935555 G	
114 L	340 C	-11:63795699 1876935554 C	L
114	341 T	-11:63795698 1876935553 T	
114	342 C	-11:63795697 1876935552 C	
115 R	343 C	-11:63795696 1876935551 C	R
115	344 G	-11:63795695 1876935550 G	
115	345 G	-11:63795694 1876935549 G	
116 R	346 A	-11:63795693 1876935548 A	R
116	347 G	-11:63795692 1876935547 G	
116	348 G	-11:63795691 1876935546 G	
117 M	349 A	-11:63795690 1876935545 A	M
117	350 T	-11:63795689 1876935544 T	
117	351 G	-11:63795688 1876935543 G	
118 S	352 A	-11:63795687 1876935542 A	S
118	353 G	-11:63795686 1876935541 G	
118	354 T	-11:63795685 1876935540 T	
119 D	355 G	-11:63795684 1876935539 G	D
119	356 A	-11:63795683 1876935538 A	
119	357 C	-11:63795682 1876935537 C	
120 E	358 G	-11:63795681 1876935536 G	E
120	359 A	-11:63795680 1876935535 A	
120	360 G	-11:63795679 1876935534 G	
121 F	361 T	-11:63795678 1876935533 T	F
121	362 T	-11:63795677 1876935532 T	
121	363 T	-11:63795676 1876935531 T	
122 V	364 G	-11:63795675 1876935530 G	V
122	365 T	-11:63795674 1876935529 T	
122	366 G	-11:63795673 1876935528 G	
123 D	367 G	-11:63795672 1876935527 G	D
123	368 A	-11:63795671 1876935526 A	
123	369 C	-11:63795670 1876935525 C	
124 S	370 T	-11:63795669 1876935524 T	S
124	371 C	-11:63795668 1876935523 C	
124	372 C	-11:63795667 1876935522 C	
125 F	373 T	-11:63795666 1876935521 T	F
125	374 T	-11:63795665 1876935520 T	
125	375 T	-11:63795664 1876935519 T	
>ENSP00000378039 
1 M	1 A	-11:63808416 1876948271 A	M
1	2 T	-11:63808415 1876948270 T	
1	3 G	-11:63808414 1876948269 G	
2 F	4 T	-11:63808413 1876948268 T	F
2	5 T	-11:63808412 1876948267 T	
2	6 C	-11:63808411 1876948266 C	
3 Q	7 C	-11:63808410 1876948265 C	Q
3	8 A	-11:63808409 1876948264 A	
3	9 G	-11:63808408 1876948263 G	
4 I	10 A	-11:63808407 1876948262 A	I
4	11 T	-11:63808406 1876948261 T	
4	12 C	-11:63808405 1876948260 C	
5 P	13 C	-11:63808404 1876948259 C	P
5	14 C	-11:63808403 1876948258 C	
5	15 A	-11:63808402 1876948257 A	
6 E	16 G	-11:63808401 1876948256 G	E
6	17 A	-11:63808400 1876948255 A	
6	18 G	-11:63808399 1876948254 G	
7 F	19 T	-11:63808398 1876948253 T	F
7	20 T	-11:63808397 1876948252 T	
7	21 T	-11:63808396 1876948251 T	
8 E	22 G	-11:63808395 1876948250 G	E
8	23 A	-11:63808394 1876948249 A	
8	24 G	-11:63808393 1876948248 G	
9 P	25 C	-11:63808392 1876948247 C	P
9	26 C	-11:63808391 1876948246 C	
9	27 G	-11:63808390 1876948245 G	
10 S	28 A	-11:63808389 1876948244 A	S
10	29 G	-11:63808388 1876948243 G	
10	30 T	-11:63808387 1876948242 T	
11 E	31 G	-11:63808386 1876948241 G	E
11	32 A	-11:63808385 1876948240 A	
11	33 G	-11:63808384 1876948239 G	
12 Q	34 C	-11:63808383 1876948238 C	Q
12	35 A	-11:63808382 1876948237 A	
12	36 G	-11:63808381 1876948236 G	
13 E	37 G	-11:63808380 1876948235 G	E
13	38 A	-11:63808379 1876948234 A	
13	39 A	-11:63808378 1876948233 A	
14 D	40 G	-11:63808377 1876948232 G	D
14	41 A	-11:63808376 1876948231 A	
14	42 C	-11:63808375 1876948230 C	
15 S	43 T	-11:63808374 1876948229 T	S
15	44 C	-11:63808373 1876948228 C	
15	45 C	-11:63808372 1876948227 C	
16 S	46 A	-11:63808371 1876948226 A	S
16	47 G	-11:63808370 1876948225 G	
16	48 C	-11:63808369 1876948224 C	
17 S	49 T	-11:63808368 1876948223 T	S
17	50 C	-11:63808367 1876948222 C	
17	51 T	-11:63808366 1876948221 T	
18 A	52 G	-11:63808365 1876948220 G	A
18	53 C	-11:63808364 1876948219 C	
18	54 A	-11:63808363 1876948218 A	
19 E	55 G	-11:63808362 1876948217 G	E
19	56 A	-11:63808361 1876948216 A	
19	57 G	-11:63808360 1876948215 G	
20 R	58 A	-11:63808359 1876948214 A	R
20	59 G	-11:63808358 1876948213 G	
20	60 G	-11:63808357 1876948212 G	
21 G	61 G	-11:63808356 1876948211 G	G
21	62 G	-11:63808355 1876948210 G	
21	63 C	-11:63808354 1876948209 C	
22 L	64 C	-11:63808353 1876948208 C	L
22	65 T	-11:63808352 1876948207 T	
22	66 G	-11:63808351 1876948206 G	
23 G	67 G	-11:63808350 1876948205 G	G
23	68 G	-11:63808349 1876948204 G	
23	69 C	-11:63808348 1876948203 C	
24 P	70 C	-11:63808347 1876948202 C	P
24	71 C	-11:63808346 1876948201 C	
24	72 C	-11:63808345 1876948200 C	
25 S	73 A	-11:63808344 1876948199 A	S
25	74 G	-11:63808343 1876948198 G	
25	75 C	-11:63808342 1876948197 C	
26 P	76 C	-11:63808341 1876948196 C	P
26	77 C	-11:63808340 1876948195 C	
26	78 C	-11:63808339 1876948194 C	
27 A	79 G	-11:63808338 1876948193 G	A
27	80 C	-11:63808337 1876948192 C	
27	81 A	-11:63808336 1876948191 A	
28 G	82 G	-11:63808335 1876948190 G	G
28	83 G	-11:63808334 1876948189 G	
28	84 G	-11:63808333 1876948188 G	
29 D	85 G	-11:63808332 1876948187 G	D
29	86 A	-11:63808331 1876948186 A	
29	87 C	-11:63808330 1876948185 C	
30 G	88 G	-11:63808329 1876948184 G	G
30	89 G	-11:63808328 1876948183 G	
30	90 G	-11:63808327 1876948182 G	
31 P	91 C	-11:63808326 1876948181 C	P
31	92 C	-11:63808325 1876948180 C	
31	93 C	-11:63808324 1876948179 C	
32 S	94 T	-11:63808323 1876948178 T	S
32	95 C	-11:63808322 1876948177 C	
32	96 A	-11:63808321 1876948176 A	
33 G	97 G	-11:63808320 1876948175 G	G
33	98 G	-11:63808319 1876948174 G	
33	99 C	-11:63808318 1876948173 C	
34 S	100 T	-11:63808317 1876948172 T	S
34	101 C	-11:63808316 1876948171 C	
34	102 C	-11:63808315 1876948170 C	
35 G	103 G	-11:63808314 1876948169 G	G
35	104 G	-11:63808313 1876948168 G	
35	105 C	-11:63808312 1876948167 C	
36 K	106 A	-11:63808311 1876948166 A	K
36	107 A	-11:63808310 1876948165 A	
36	108 G	-11:63808309 1876948164 G	
37 H	109 C	-11:63808308 1876948163 C	H
37	110 A	-11:63808307 1876948162 A	
37	111 T	-11:63808306 1876948161 T	
38 H	112 C	-11:63808305 1876948160 C	H
38	113 A	-11:63808304 1876948159 A	
38	114 T	-11:63808303 1876948158 T	
39 R	115 C	-11:63808302 1876948157 C	R
39	116 G	-11:63808301 1876948156 G	
39	117 C	-11:63808300 1876948155 C	
40 Q	118 C	-11:63808299 1876948154 C	Q
40	119 A	-11:63808298 1876948153 A	
40	120 G	-11:63808297 1876948152 G	
41 A	121 G	-11:63808296 1876948151 G	A
41	122 C	-11:63808295 1876948150 C	
41	123 C	-11:63808294 1876948149 C	
42 P	124 C	-11:63808293 1876948148 C	P
42	125 C	-11:63808292 1876948147 C	
42	126 A	-11:63808291 1876948146 A	
43 G	127 G	-11:63808290 1876948145 G	G
43	128 G	-11:63808289 1876948144 G	
43	129 C	-11:63808288 1876948143 C	
44 L	130 C	-11:63808287 1876948142 C	L
44	131 T	-11:63808286 1876948141 T	
44	132 C	-11:63808285 1876948140 C	
45 L	133 C	-11:63808284 1876948139 C	L
45	134 T	-11:63808283 1876948138 T	
45	135 G	-11:63808282 1876948137 G	
46 W	136 T	-11:63808281 1876948136 T	W
46	137 G	-11:63808280 1876948135 G	
46	138 G	-11:63808279 1876948134 G	
47 D	139 G	-11:63808278 1876948133 G	D
47	140 A	-11:63808277 1876948132 A	
47	141 C	-11:63808276 1876948131 C	
48 A	142 G	-11:63808275 1876948130 G	A
48	143 C	-11:63808274 1876948129 C	
48	144 C	-11:63808273 1876948128 C	
49 S	145 A	-11:63808272 1876948127 A	S
49	146 G	-11:63808271 1876948126 G	
49	147 T	-11:63808270 1876948125 T	
50 H	148 C	-11:63808269 1876948124 C	H
50	149 A	-11:63808268 1876948123 A	
50	150 C	-11:63808267 1876948122 C	
51 Q	151 C	-11:63808266 1876948121 C	Q
51	152 A	-11:63808265 1876948120 A	
51	153 G	-11:63808264 1876948119 G	
52 Q	154 C	-11:63808263 1876948118 C	Q
52	155 A	-11:63808262 1876948117 A	
52	156 G	-11:63808261 1876948116 G	
53 E	157 G	-11:63808260 1876948115 G	E
53	158 A	-11:63808259 1876948114 A	
53	159 G	-11:63808258 1876948113 G	
54 Q	160 C	-11:63808257 1876948112 C	Q
54	161 A	-11:63808256 1876948111 A	
54	162 G	-11:63808255 1876948110 G	
55 P	163 C	-11:63808254 1876948109 C	P
55	164 C	-11:63808253 1876948108 C	
55	165 A	-11:63808252 1876948107 A	
56 T	166 A	-11:63808251 1876948106 A	T
56	167 C	-11:63808250 1876948105 C	
56	168 C	-11:63808249 1876948104 C	
57 S	169 A	-11:63808248 1876948103 A	S
57	170 G	-11:63808247 1876948102 G	
57	171 C	-11:63808246 1876948101 C	
58 S	172 A	-11:63808245 1876948100 A	S
58	173 G	-11:63808244 1876948099 G	
58	174 C	-11:63808243 1876948098 C	
59 S	175 A	-11:63808242 1876948097 A	S
59	176 G	-11:63808241 1876948096 G	
59	177 C	-11:63808240 1876948095 C	
60 H	178 C	-11:63808239 1876948094 C	H
60	179 A	-11:63808238 1876948093 A	
60	180 T	-11:63808237 1876948092 T	
61 H	181 C	-11:63808236 1876948091 C	H
61	182 A	-11:63808235 1876948090 A	
61	183 T	-11:63808234 1876948089 T	
62 G	184 G	-11:63808233 1876948088 G	G
62	185 G	-11:63808232 1876948087 G	
62	186 A	-11:63808231 1876948086 A	
63 G	187 G	-11:63808230 1876948085 G	G
63	188 G	-11:63801091 1876940946 G	
63	189 G	-11:63801090 1876940945 G	
64 R	190 A	-11:63801089 1876940944 A	R
64	191 G	-11:63801088 1876940943 G	
64	192 A	-11:63801087 1876940942 A	
65 T	193 A	-11:63801086 1876940941 A	T
65	194 C	-11:63801085 1876940940 C	
65	195 T	-11:63801084 1876940939 T	
66 S	196 T	-11:63801083 1876940938 T	S
66	197 C	-11:63801082 1876940937 C	
66	198 G	-11:63801081 1876940936 G	
67 Y	199 T	-11:63801080 1876940935 T	Y
67	200 A	-11:63801079 1876940934 A	
67	201 T	-11:63801078 1876940933 T	
68 S	202 T	-11:63801077 1876940932 T	S
68	203 C	-11:63801076 1876940931 C	
68	204 T	-11:63801075 1876940930 T	
69 P	205 C	-11:63801074 1876940929 C	P
69	206 C	-11:63801073 1876940928 C	
69	207 T	-11:63801072 1876940927 T	
70 S	208 T	-11:63801071 1876940926 T	S
70	209 C	-11:63801070 1876940925 C	
70	210 T	-11:63801069 1876940924 T	
71 W	211 T	-11:63801068 1876940923 T	W
71	212 G	-11:63801067 1876940922 G	
71	213 G	-11:63801066 1876940921 G	
72 E	214 G	-11:63801065 1876940920 G	E
72	215 A	-11:63801064 1876940919 A	
72	216 A	-11:63801063 1876940918 A	
73 S	217 T	-11:63801062 1876940917 T	S
73	218 C	-11:63801061 1876940916 C	
73	219 T	-11:63801060 1876940915 T	
74 E	220 G	-11:63801059 1876940914 G	E
74	221 A	-11:63801058 1876940913 A	
74	222 G	-11:63801057 1876940912 G	
75 D	223 G	-11:63801056 1876940911 G	D
75	224 A	-11:63801055 1876940910 A	
75	225 C	-11:63801054 1876940909 C	
76 S	226 T	-11:63801053 1876940908 T	S
76	227 C	-11:63801052 1876940907 C	
76	228 T	-11:63801051 1876940906 T	
77 E	229 G	-11:63801050 1876940905 G	E
77	230 A	-11:63801049 1876940904 A	
77	231 A	-11:63801048 1876940903 A	
78 N	232 A	-11:63801047 1876940902 A	N
78	233 A	-11:63801046 1876940901 A	
78	234 T	-11:63801045 1876940900 T	
79 P	235 C	-11:63801044 1876940899 C	P
79	236 C	-11:63801043 1876940898 C	
79	237 C	-11:63801042 1876940897 C	
80 S	238 A	-11:63801041 1876940896 A	S
80	239 G	-11:63801040 1876940895 G	
80	240 T	-11:63801039 1876940894 T	
81 A	241 G	-11:63801038 1876940893 G	A
81	242 C	-11:63801037 1876940892 C	
81	243 A	-11:63801036 1876940891 A	
82 G	244 G	-11:63801035 1876940890 G	G
82	245 G	-11:63801034 1876940889 G	
82	246 G	-11:63801033 1876940888 G	
83 M	247 A	-11:63801032 1876940887 A	M
83	248 T	-11:63801031 1876940886 T	
83	249 G	-11:63801030 1876940885 G	
84 L	250 C	-11:63801029 1876940884 C	L
84	251 T	-11:63801028 1876940883 T	
84	252 C	-11:63801027 1876940882 C	
85 A	253 G	-11:63801026 1876940881 G	A
85	254 C	-11:63801025 1876940880 C	
85	255 G	-11:63801024 1876940879 G	
86 E	256 G	-11:63801023 1876940878 G	E
86	257 A	-11:63801022 1876940877 A	
86	258 A	-11:63801021 1876940876 A	
87 A	259 G	-11:63801020 1876940875 G	A
87	260 C	-11:63801019 1876940874 C	
87	261 A	-11:63801018 1876940873 A	
88 S	262 T	-11:63801017 1876940872 T	S
88	263 C	-11:63801016 1876940871 C	
88	264 A	-11:63801015 1876940870 A	
89 A	265 G	-11:63801014 1876940869 G	A
89	266 C	-11:63801013 1876940868 C	
89	267 A	-11:63801012 1876940867 A	
90 G	268 G	-11:63801011 1876940866 G	G
90	269 G	-11:63801010 1876940865 G	
90	270 G	-11:63801009 1876940864 G	
91 M	271 A	-11:63801008 1876940863 A	M
91	272 T	-11:63801007 1876940862 T	
91	273 G	-11:63801006 1876940861 G	
92 S	274 T	-11:63801005 1876940860 T	S
92	275 C	-11:63801004 1876940859 C	
92	276 C	-11:63801003 1876940858 C	
93 A	277 G	-11:63801002 1876940857 G	A
93	278 C	-11:63801001 1876940856 C	
93	279 C	-11:63801000 1876940855 C	
94 P	280 C	-11:63800999 1876940854 C	P
94	281 C	-11:63800998 1876940853 C	
94	282 A	-11:63800997 1876940852 A	
95 A	283 G	-11:63800996 1876940851 G	A
95	284 C	-11:63800995 1876940850 C	
95	285 C	-11:63800994 1876940849 C	
96 A	286 G	-11:63800993 1876940848 G	A
96	287 C	-11:63800992 1876940847 C	
96	288 T	-11:63800991 1876940846 T	
97 D	289 G	-11:63800990 1876940845 G	D
97	290 A	-11:63800989 1876940844 A	
97	291 C	-11:63800988 1876940843 C	
98 S	292 T	-11:63800987 1876940842 T	S
98	293 C	-11:63800986 1876940841 C	
98	294 A	-11:63800985 1876940840 A	
99 E	295 G	-11:63800984 1876940839 G	E
99	296 A	-11:63800983 1876940838 A	
99	297 A	-11:63800982 1876940837 A	
100 A	298 G	-11:63800981 1876940836 G	A
100	299 C	-11:63800980 1876940835 C	
100	300 C	-11:63800979 1876940834 C	
101 Q	301 C	-11:63800978 1876940833 C	Q
101	302 A	-11:63800977 1876940832 A	
101	303 A	-11:63800976 1876940831 A	
102 H	304 C	-11:63800975 1876940830 C	H
102	305 A	-11:63800974 1876940829 A	
102	306 C	-11:63800973 1876940828 C	
103 A	307 G	-11:63800972 1876940827 G	A
103	308 C	-11:63800971 1876940826 C	
103	309 A	-11:63800970 1876940825 A	
104 E	310 G	-11:63800969 1876940824 G	E
104	311 A	-11:63800968 1876940823 A	
104	312 G	-11:63800967 1876940822 G	
105 N	313 A	-11:63800966 1876940821 A	N
105	314 A	-11:63800965 1876940820 A	
105	315 T	-11:63800964 1876940819 T	
106 V	316 G	-11:63800963 1876940818 G	V
106	317 T	-11:63800962 1876940817 T	
106	318 A	-11:63800961 1876940816 A	
107 K	319 A	-11:63800960 1876940815 A	K
107	320 A	-11:63800959 1876940814 A	
107	321 G	-11:63800958 1876940813 G	
108 L	322 C	-11:63800957 1876940812 C	L
108	323 T	-11:63800956 1876940811 T	
108	324 A	-11:63800955 1876940810 A	
109 E	325 G	-11:63800954 1876940809 G	E
109	326 A	-11:63800953 1876940808 A	
109	327 G	-11:63800952 1876940807 G	
BioPerl-1.007002/t/data/gmap_f9-reverse-strand.txt000444000766000024     54053013155576321 21764 0ustar00cjfieldsstaff000000000000>NM_004448 Homo sapiens v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) (ERBB2), transcript variant 1, mRNA. 4624 bp, mRNA, linear, PRI 20-DEC-2004 md5:8064b90c82e72ea2e5fba8d53f7d44d5
1335	1 T	-17:35138441 2524669948 T	
1335	2 A	-17:35138440 2524669947 A	
1335	3 G	-17:35138439 2524669946 G	
1335	4 C	-17:35138438 2524669945 C	
1335 S	5 T	-17:35138437 2524669944 T	
1335	6 G	-17:35138436 2524669943 G	
1335	7 T	-17:35138435 2524669942 T	
1335 N	8 T	-17:35138434 2524669941 T	
1335	9 T	-17:35138433 2524669940 T	
1335	10 T	-17:35138432 2524669939 T	
1335 E	11 C	-17:35138431 2524669938 C	
1335	12 C	-17:35138430 2524669937 C	
1335	13 A	-17:35138429 2524669936 A	
1335 L	14 A	-17:35138428 2524669935 A	
1335	15 A	-17:35138427 2524669934 A	
1335	16 A	-17:35138426 2524669933 A	
1335 I	17 T	-17:35138425 2524669932 T	
1335	18 A	-17:35138424 2524669931 A	
1335	19 T	-17:35138423 2524669930 T	
1335 Y	20 A	-17:35138422 2524669929 A	
1335	21 T	-17:35138421 2524669928 T	
1335	22 T	-17:35138420 2524669927 T	
1335 K	23 T	-17:35138419 2524669926 T	
1335	24 G	-17:35138418 2524669925 G	
1335	25 C	-17:35138417 2524669924 C	
1335 C	26 A	-17:35138416 2524669923 A	
1335	27 A	-17:35138415 2524669922 A	
1335	28 A	-17:35138414 2524669921 A	
1335 I	29 T	-17:35138413 2524669920 T	
1335	30 G	-17:35138412 2524669919 G	
1335	31 G	-17:35138411 2524669918 G	
1335 S	32 A	-17:35138410 2524669917 A	
1335	33 C	-17:35138409 2524669916 C	
1335	34 A	-17:35138408 2524669915 A	
1335 L	35 A	-17:35138407 2524669914 A	
1335	36 A	-17:35138406 2524669913 A	
1335	37 G	-17:35138405 2524669912 G	
1335 T	38 T	-17:35138404 2524669911 T	
1335	39 G	-17:35138403 2524669910 G	
1335	40 G	-17:35138402 2524669909 G	
1335 P	41 G	-17:35138401 2524669908 G	
1335	42 T	-17:35138400 2524669907 T	
1335	43 G	-17:35138399 2524669906 G	
1335 T	44 T	-17:35138398 2524669905 T	
1335	45 G	-17:35138397 2524669904 G	
1335	46 G	-17:35138396 2524669903 G	
1335 S	47 A	-17:35138395 2524669902 A	
1335	48 G	-17:35138394 2524669901 G	
1335	49 A	-17:35138393 2524669900 A	
1335 F	50 A	-17:35138392 2524669899 A	
1335	51 G	-17:35138391 2524669898 G	
1335	52 G	-17:35138390 2524669897 G	
1335 S	53 A	-17:35138389 2524669896 A	
1335	54 C	-17:35138388 2524669895 C	
1335	55 C	-17:35138387 2524669894 C	
1335 G	56 C	-17:35138386 2524669893 C	
1335	57 C	-17:35138385 2524669892 C	
1335	58 C	-17:35138384 2524669891 C	
1335 G	59 C	-17:35138383 2524669890 C	
1335	60 A	-17:35138382 2524669889 A	
1335	61 C	-17:35138381 2524669888 C	
1335 C	62 A	-17:35138380 2524669887 A	
1335	63 C	-17:35138379 2524669886 C	
1335	64 T	-17:35138378 2524669885 T	
1335 K	65 T	-17:35138377 2524669884 T	
1335	66 G	-17:35138376 2524669883 G	
1335	67 C	-17:35138375 2524669882 C	
1335 G	68 C	-17:35138374 2524669881 C	
1335	69 T	-17:35138373 2524669880 T	
1335	70 C	-17:35138372 2524669879 C	
1335 G	71 C	-17:35138371 2524669878 C	
1335	72 C	-17:35138370 2524669877 C	
1335	73 C	-17:35138369 2524669876 C	
1335 W	74 A	-17:35138368 2524669875 A	
1335	75 T	-17:35138367 2524669874 T	
1335	76 A	-17:35138366 2524669873 A	
1335 V	77 C	-17:35138365 2524669872 C	
1335	78 A	-17:35138364 2524669871 A	
1335	79 A	-17:35138363 2524669870 A	
1335 V	80 C	-17:35138362 2524669869 C	
1335	81 A	-17:35138361 2524669868 A	
1335	82 C	-17:35138360 2524669867 C	
1335 G	83 C	-17:35138359 2524669866 C	
1335	84 C	-17:35138358 2524669865 C	
1335	85 A	-17:35138357 2524669864 A	
1335 M	86 T	-17:35138356 2524669863 T	
1335	87 T	-17:35138355 2524669862 T	
1335	88 C	-17:35138354 2524669861 C	
1335 R	89 T	-17:35138353 2524669860 T	
1335	90 C	-17:35138352 2524669859 C	
1335	91 C	-17:35138351 2524669858 C	
1335 G	92 C	-17:35138350 2524669857 C	
1335	93 C	-17:35138349 2524669856 C	
1335	94 C	-17:35138348 2524669855 C	
1335 R	95 T	-17:35138347 2524669854 T	
1335	96 G	-17:35138346 2524669853 G	
1335	97 G	-17:35138345 2524669852 G	
1335 P	98 G	-17:35138344 2524669851 G	
1335	99 T	-17:35138343 2524669850 T	
1335	100 C	-17:35138342 2524669849 C	
1335 R	101 T	-17:35138341 2524669848 T	
1335	102 T	-17:35138340 2524669847 T	
1335	103 T	-17:35138339 2524669846 T	
1335 *	104 A	-17:35138338 2524669845 A	
1335	105 T	-17:35138337 2524669844 T	
1335	106 T	-17:35138336 2524669843 T	
1335 K	107 T	-17:35138335 2524669842 T	
1335	108 C	-17:35138334 2524669841 C	
1335	109 A	-17:35138333 2524669840 A	
1335 M	110 T	-17:35138332 2524669839 T	
1335	111 C	-17:35138331 2524669838 C	
1335	112 T	-17:35138330 2524669837 T	
1335 K	113 T	-17:35138329 2524669836 T	
1335	114 T	-17:35138328 2524669835 T	
1335	115 A	-17:35138327 2524669834 A	
1335 L	116 A	-17:35138326 2524669833 A	
1335	117 A	-17:35138325 2524669832 A	
1335	118 A	-17:35138324 2524669831 A	
1335 F	119 A	-17:35138323 2524669830 A	
1335	120 A	-17:35138322 2524669829 A	
1335	121 A	-17:35138321 2524669828 A	
1335 V	122 C	-17:35138320 2524669827 C	
1335	123 A	-17:35138319 2524669826 A	
1335	124 A	-17:35138318 2524669825 A	
1335 F	125 A	-17:35138317 2524669824 A	
1335	126 A	-17:35138316 2524669823 A	
1335	127 C	-17:35138315 2524669822 C	
1335 C	128 A	-17:35138314 2524669821 A	
1335	129 A	-17:35138313 2524669820 A	
1335	130 A	-17:35138312 2524669819 A	
1335 F	131 A	-17:35138311 2524669818 A	
1335	132 A	-17:35138310 2524669817 A	
1335	133 A	-17:35138309 2524669816 A	
1335 F	134 A	-17:35138308 2524669815 A	
1335	135 G	-17:35138307 2524669814 G	
1335	136 T	-17:35138306 2524669813 T	
1335 Y	137 A	-17:35138305 2524669812 A	
1335	138 A	-17:35138304 2524669811 A	
1335	139 A	-17:35138303 2524669810 A	
1335 F	140 A	-17:35138302 2524669809 A	
1335	141 A	-17:35138301 2524669808 A	
1335	142 C	-17:35138300 2524669807 C	
1335 S	143 T	-17:35138299 2524669806 T	
1335	144 A	-17:35138298 2524669805 A	
1335	145 A	-17:35138297 2524669804 A	
1335 F	146 A	-17:35138296 2524669803 A	
1335	147 C	-17:35138295 2524669802 C	
1335	148 A	-17:35138294 2524669801 A	
1335 L	149 G	-17:35138293 2524669800 G	
1335	150 A	-17:35138292 2524669799 A	
1335	151 A	-17:35138291 2524669798 A	
1335 F	152 A	-17:35138290 2524669797 A	
1335	153 A	-17:35138289 2524669796 A	
1335	154 G	-17:35138288 2524669795 G	
1335 A	155 C	-17:35138287 2524669794 C	
1335	156 A	-17:35138286 2524669793 A	
1335	157 C	-17:35138285 2524669792 C	
1335 S	158 T	-17:35138284 2524669791 T	
1335	159 C	-17:35138283 2524669790 C	
1335	160 T	-17:35138282 2524669789 T	
1335 Q	161 G	-17:35138281 2524669788 G	
1335	162 T	-17:35138280 2524669787 T	
1335	163 A	-17:35138279 2524669786 A	
1335 V	164 C	-17:35138278 2524669785 C	
1335	165 A	-17:35138277 2524669784 A	
1335	166 A	-17:35138276 2524669783 A	
1335 F	167 A	-17:35138275 2524669782 A	
1335	168 G	-17:35138274 2524669781 G	
1335	169 C	-17:35138273 2524669780 C	
1335 G	170 C	-17:35138272 2524669779 C	
1335	171 T	-17:35138271 2524669778 T	
1335	172 G	-17:35138270 2524669777 G	
1335 P	173 G	-17:35138269 2524669776 G	
1335	174 A	-17:35138268 2524669775 A	
1335	175 T	-17:35138267 2524669774 T	
1335 Y	176 A	-17:35138266 2524669773 A	
1335	177 C	-17:35138265 2524669772 C	
1335	178 T	-17:35138264 2524669771 T	
1335 Q	179 G	-17:35138263 2524669770 G	
1335	180 A	-17:35138262 2524669769 A	
1335	181 C	-17:35138261 2524669768 C	
1335 C	182 A	-17:35138260 2524669767 A	
1335	183 C	-17:35138259 2524669766 C	
1335	184 C	-17:35138258 2524669765 C	
1335 W	185 A	-17:35138257 2524669764 A	
1335	186 T	-17:35138256 2524669763 T	
1335	187 T	-17:35138255 2524669762 T	
1335 Q	188 G	-17:35138254 2524669761 G	
1335	189 C	-17:35138253 2524669760 C	
1335	190 T	-17:35138252 2524669759 T	
1335 Q	191 G	-17:35138251 2524669758 G	
1335	192 T	-17:35138250 2524669757 T	
1335	193 T	-17:35138249 2524669756 T	
1335 E	194 C	-17:35138248 2524669755 C	
1335	195 C	-17:35138247 2524669754 C	
1335	196 T	-17:35138246 2524669753 T	
1335 K	197 T	-17:35138245 2524669752 T	
1335	198 C	-17:35138244 2524669751 C	
1335	199 C	-17:35138243 2524669750 C	
1335 R	200 T	-17:35138242 2524669749 T	
1335	201 C	-17:35138241 2524669748 C	
1335	202 A	-17:35138240 2524669747 A	
1335 M	203 T	-17:35138239 2524669746 T	
1335	204 G	-17:35138238 2524669745 G	
1335	205 G	-17:35138237 2524669744 G	
1335 P	206 G	-17:35138236 2524669743 G	
1335	207 G	-17:35138235 2524669742 G	
1335	208 G	-17:35138234 2524669741 G	
1335 P	209 G	-17:35138233 2524669740 G	
1335	210 C	-17:35138232 2524669739 C	
1335	211 A	-17:35138231 2524669738 A	
1335 L	212 G	-17:35138230 2524669737 G	
1335	213 T	-17:35138229 2524669736 T	
1335	214 A	-17:35138228 2524669735 A	
1335 V	215 C	-17:35138227 2524669734 C	
1335	216 T	-17:35138226 2524669733 T	
1335	217 A	-17:35138225 2524669732 A	
1335 L	218 G	-17:35138224 2524669731 G	
1335	219 G	-17:35138223 2524669730 G	
1335	220 T	-17:35138222 2524669729 T	
1335 N	221 T	-17:35138221 2524669728 T	
1335	222 T	-17:35138220 2524669727 T	
1335	223 C	-17:35138219 2524669726 C	
1335 *	224 A	-17:35138218 2524669725 A	
1335	225 G	-17:35138217 2524669724 G	
1335	226 G	-17:35138216 2524669723 G	
1335 P	227 G	-17:35138215 2524669722 G	
1335	228 A	-17:35138214 2524669721 A	
1335	229 C	-17:35138213 2524669720 C	
1335 C	230 A	-17:35138212 2524669719 A	
1335	231 G	-17:35138211 2524669718 G	
1335	232 T	-17:35138210 2524669717 T	
1335 D	233 C	-17:35138209 2524669716 C	
1335	234 T	-17:35138208 2524669715 T	
1335	235 C	-17:35138207 2524669714 C	
1335 R	236 T	-17:35138206 2524669713 T	
1335	237 G	-17:35138205 2524669712 G	
1335	238 A	-17:35138204 2524669711 A	
1335 F	239 A	-17:35138203 2524669710 A	
1335	240 T	-17:35138202 2524669709 T	
1335	241 G	-17:35138201 2524669708 G	
1335 P	242 G	-17:35138200 2524669707 G	
1335	243 G	-17:35138199 2524669706 G	
1335	244 T	-17:35138198 2524669705 T	
1335 D	245 C	-17:35138197 2524669704 C	
1335	246 G	-17:35138196 2524669703 G	
1335	247 C	-17:35138195 2524669702 C	
1335 S	248 T	-17:35138194 2524669701 T	
1335	249 T	-17:35138193 2524669700 T	
1335	250 T	-17:35138192 2524669699 T	
1335 K	251 T	-17:35138191 2524669698 T	
1335	252 G	-17:35138190 2524669697 G	
1335	253 T	-17:35138189 2524669696 T	
1335 N	254 T	-17:35138188 2524669695 T	
1335	255 C	-17:35138187 2524669694 C	
1335	256 T	-17:35138186 2524669693 T	
1335 K	257 T	-17:35138185 2524669692 T	
1335	258 A	-17:35138184 2524669691 A	
1335	259 G	-17:35138183 2524669690 G	
1335 S	260 A	-17:35138182 2524669689 A	
1335	261 C	-17:35138181 2524669688 C	
1335	262 A	-17:35138180 2524669687 A	
1335 V	263 C	-17:35138179 2524669686 C	
1335	264 T	-17:35138178 2524669685 T	
1335	265 C	-17:35138177 2524669684 C	
1335 G	266 C	-17:35138176 2524669683 C	
1335	267 C	-17:35138175 2524669682 C	
1335	268 T	-17:35138174 2524669681 T	
1335 K	269 T	-17:35138173 2524669680 T	
1335	270 A	-17:35138172 2524669679 A	
1335	271 G	-17:35138171 2524669678 G	
1335 P	272 G	-17:35138170 2524669677 G	
1335	273 G	-17:35138169 2524669676 G	
1335	274 C	-17:35138168 2524669675 C	
1335 G	275 C	-17:35138167 2524669674 C	
1335	276 G	-17:35138166 2524669673 G	
1335	277 C	-17:35138165 2524669672 C	
1335 S	278 T	-17:35138164 2524669671 T	
1335	279 T	-17:35138163 2524669670 T	
1335	280 C	-17:35138162 2524669669 C	
1335 G	281 C	-17:35138161 2524669668 C	
1335	282 C	-17:35138160 2524669667 C	
1335	283 C	-17:35138159 2524669666 C	
1335 R	284 T	-17:35138158 2524669665 T	
1335	285 C	-17:35138157 2524669664 C	
1335	286 T	-17:35138156 2524669663 T	
1335 E	287 C	-17:35138155 2524669662 C	
1335	288 A	-17:35138154 2524669661 A	
1335	289 G	-17:35138153 2524669660 G	
1335 P	290 G	-17:35138152 2524669659 G	
1335	291 C	-17:35138151 2524669658 C	
1335	292 C	-17:35138150 2524669657 C	
1335 W	293 A	-17:35138149 2524669656 A	
1335	294 G	-17:35138148 2524669655 G	
1335	295 C	-17:35138147 2524669654 C	
1335 S	296 T	-17:35138146 2524669653 T	
1335	297 T	-17:35138145 2524669652 T	
1335	298 C	-17:35138144 2524669651 C	
1335 G	299 C	-17:35138143 2524669650 C	
1335	300 C	-17:35138142 2524669649 C	
1335	301 T	-17:35138141 2524669648 T	
1335 *	302 A	-17:35138140 2524669647 A	
1335	303 A	-17:35138139 2524669646 A	
1335	304 G	-17:35138138 2524669645 G	
1335 P	305 G	-17:35138137 2524669644 G	
1335	306 C	-17:35138136 2524669643 C	
1335	307 T	-17:35138135 2524669642 T	
1335 K	308 T	-17:35138134 2524669641 T	
1335	309 T	-17:35138133 2524669640 T	
1335	310 C	-17:35138132 2524669639 C	
1335 *	311 A	-17:35138131 2524669638 A	
1335	312 G	-17:35138130 2524669637 G	
1335	313 T	-17:35138129 2524669636 T	
1335 Y	314 A	-17:35138128 2524669635 A	
1335	315 C	-17:35138127 2524669634 C	
1335	316 C	-17:35138126 2524669633 C	
1335 G	317 C	-17:35138125 2524669632 C	
1335	318 A	-17:35138124 2524669631 A	
1335	319 G	-17:35138123 2524669630 G	
1335 P	320 G	-17:35138122 2524669629 G	
1335	321 A	-17:35138121 2524669628 A	
1335	322 T	-17:35138120 2524669627 T	
1335 D	323 C	-17:35138119 2524669626 C	
1335	324 T	-17:35138118 2524669625 T	
1335	325 G	-17:35138117 2524669624 G	
1335 P	326 G	-17:35138116 2524669623 G	
1335	327 A	-17:35138115 2524669622 A	
1335	328 A	-17:35138114 2524669621 A	
1335 L	329 G	-17:35138113 2524669620 G	
1335	330 G	-17:35138112 2524669619 G	
1335	331 A	-17:35138111 2524669618 A	
1335 F	332 A	-17:35138110 2524669617 A	
1335	333 A	-17:35138109 2524669616 A	
1335	334 G	-17:35138108 2524669615 G	
1335 P	335 G	-17:35138107 2524669614 G	
1335	336 G	-17:35138106 2524669613 G	
1335	337 C	-17:35138105 2524669612 C	
1335 G	338 C	-17:35138104 2524669611 C	
1335	339 A	-17:35138103 2524669610 A	
1335	340 A	-17:35138102 2524669609 A	
1335 L	341 G	-17:35138101 2524669608 G	
1335	342 C	-17:35138100 2524669607 C	
1335	343 T	-17:35138099 2524669606 T	
1335 Q	344 G	-17:35138098 2524669605 G	
1335	345 G	-17:35138097 2524669604 G	
1335	346 G	-17:35138096 2524669603 G	
1335 A	347 C	-17:35138095 2524669602 C	
1335	348 T	-17:35138094 2524669601 T	
1335	349 G	-17:35138093 2524669600 G	
1335 T	350 T	-17:35138092 2524669599 T	
1335	351 G	-17:35138091 2524669598 G	
1335	352 G	-17:35138090 2524669597 G	
1335 A	353 C	-17:35138089 2524669596 C	
1335	354 A	-17:35138088 2524669595 A	
1335	355 T	-17:35138087 2524669594 T	
1335 D	356 C	-17:35138086 2524669593 C	
1335	357 C	-17:35138085 2524669592 C	
1335	358 A	-17:35138084 2524669591 A	
1335 V	359 C	-17:35138083 2524669590 C	
1335	360 T	-17:35138082 2524669589 T	
1335	361 G	-17:35138081 2524669588 G	
1335 P	362 G	-17:35138080 2524669587 G	
1335	363 A	-17:35138079 2524669586 A	
1335	364 C	-17:35138078 2524669585 C	
1335 G	365 C	-17:35138077 2524669584 C	
1335	366 C	-17:35138076 2524669583 C	
1335	367 T	-17:35138075 2524669582 T	
1335 *	368 A	-17:35138074 2524669581 A	
1335	369 G	-17:35138073 2524669580 G	
1335	370 A	-17:35138072 2524669579 A	
1335 L	371 G	-17:35138071 2524669578 G	
1335	372 T	-17:35138070 2524669577 T	
1335	373 C	-17:35138069 2524669576 C	
1335 R	374 T	-17:35138068 2524669575 T	
1335	375 C	-17:35138067 2524669574 C	
1335	376 A	-17:35138066 2524669573 A	
1335 M	377 T	-17:35138065 2524669572 T	
1335	378 T	-17:35138064 2524669571 T	
1335	379 G	-17:35138063 2524669570 G	
1335 P	380 G	-17:35138062 2524669569 G	
1335	381 G	-17:35138061 2524669568 G	
1335	382 C	-17:35138060 2524669567 C	
1335 C	383 A	-17:35138059 2524669566 A	
1335	384 G	-17:35138058 2524669565 G	
1335	385 G	-17:35138057 2524669564 G	
1335 P	386 G	-17:35138056 2524669563 G	
1335	387 C	-17:35138055 2524669562 C	
1335	388 C	-17:35138054 2524669561 C	
1335 R	389 T	-17:35138053 2524669560 T	
1335	390 C	-17:35138052 2524669559 C	
1335	391 A	-17:35138051 2524669558 A	
1335 L	392 G	-17:35138050 2524669557 G	
1335	393 A	-17:35138049 2524669556 A	
1335	394 A	-17:35138048 2524669555 A	
1335 I	395 T	-17:35138047 2524669554 T	
1335	396 C	-17:35138046 2524669553 C	
1335	397 C	-17:35138045 2524669552 C	
1335 W	398 A	-17:35138044 2524669551 A	
1335	399 C	-17:35138043 2524669550 C	
1335	400 A	-17:35138042 2524669549 A	
1335 L	401 A	-17:35138041 2524669548 A	
1335	402 A	-17:35138040 2524669547 A	
1335	403 G	-17:35138039 2524669546 G	
1335 S	404 A	-17:35138038 2524669545 A	
1335	405 C	-17:35138037 2524669544 C	
1335	406 T	-17:35138036 2524669543 T	
1335 E	407 C	-17:35138035 2524669542 C	
1335	408 C	-17:35138034 2524669541 C	
1335	409 C	-17:35138033 2524669540 C	
1335 G	410 C	-17:35138032 2524669539 C	
1335	411 A	-17:35138031 2524669538 A	
1335	412 G	-17:35138030 2524669537 G	
1335 T	413 T	-17:35138029 2524669536 T	
1335	414 G	-17:35138028 2524669535 G	
1335	415 C	-17:35138027 2524669534 C	
1335 S	416 T	-17:35138026 2524669533 T	
1335	417 G	-17:35138025 2524669532 G	
1335	418 T	-17:35138024 2524669531 T	
1335 N	419 T	-17:35138023 2524669530 T	
1335	420 C	-17:35138022 2524669529 C	
1335	421 C	-17:35138021 2524669528 C	
1335 R	422 T	-17:35138020 2524669527 T	
1335	423 C	-17:35138019 2524669526 C	
1335	424 T	-17:35138018 2524669525 T	
1335 K	425 T	-17:35138017 2524669524 T	
1335	426 C	-17:35138016 2524669523 C	
1335	427 C	-17:35138015 2524669522 C	
1335 W	428 A	-17:35138014 2524669521 A	
1335	429 A	-17:35138013 2524669520 A	
1335	430 C	-17:35138012 2524669519 C	
1335 R	431 G	-17:35138011 2524669518 G	
1335	432 A	-17:35138010 2524669517 A	
1335	433 G	-17:35138009 2524669516 G	
1335 P	434 G	-17:35138008 2524669515 G	
1335	435 C	-17:35138007 2524669514 C	
1335	436 T	-17:35138006 2524669513 T	
1335 Q	437 G	-17:35138005 2524669512 G	
1335	438 G	-17:35138004 2524669511 G	
1335	439 A	-17:35138003 2524669510 A	
1335 V	440 C	-17:35138002 2524669509 C	
1335	441 C	-17:35138001 2524669508 C	
1335	442 C	-17:35138000 2524669507 C	
1335 G	443 C	-17:35137999 2524669506 C	
1335	444 T	-17:35137998 2524669505 T	
1335	445 T	-17:35137997 2524669504 T	
1335 E	446 C	-17:35137996 2524669503 C	
1335	447 C	-17:35137995 2524669502 C	
1335	448 A	-17:35137994 2524669501 A	
1335 L	449 G	-17:35137993 2524669500 G	
1335	450 C	-17:35137992 2524669499 C	
1335	451 C	-17:35137991 2524669498 C	
1335 W	452 A	-17:35137990 2524669497 A	
1335	453 T	-17:35137989 2524669496 T	
1335	454 C	-17:35137988 2524669495 C	
1335 R	455 T	-17:35137987 2524669494 T	
1335	456 G	-17:35137986 2524669493 G	
1335	457 G	-17:35137985 2524669492 G	
1335 P	458 G	-17:35137984 2524669491 G	
1335	459 A	-17:35137983 2524669490 A	
1335	460 A	-17:35137982 2524669489 A	
1335 V	461 C	-17:35137981 2524669488 C	
1335	462 T	-17:35137980 2524669487 T	
1335	463 C	-17:35137979 2524669486 C	
1335 *	464 A	-17:35137978 2524669485 A	
1335	465 A	-17:35137977 2524669484 A	
1335	466 G	-17:35137976 2524669483 G	
1335 A	467 C	-17:35137975 2524669482 C	
1335	468 A	-17:35137974 2524669481 A	
1335	469 G	-17:35137973 2524669480 G	
1335 P	470 G	-17:35137972 2524669479 G	
1335	471 A	-17:35137971 2524669478 A	
1335	472 A	-17:35137970 2524669477 A	
1335 L	473 G	-17:35137969 2524669476 G	
1335	474 G	-17:35137968 2524669475 G	
1335	475 A	-17:35137967 2524669474 A	
1335 F	476 A	-17:35137966 2524669473 A	
1335	477 G	-17:35137965 2524669472 G	
1335	478 G	-17:35137964 2524669471 G	
1335 T	479 T	-17:35137963 2524669470 T	
1335	480 T	-17:35137962 2524669469 T	
1335	481 C	-17:35137961 2524669468 C	
1335 G	482 C	-17:35137960 2524669467 C	
1335	483 T	-17:35137959 2524669466 T	
1335	484 T	-17:35137958 2524669465 T	
1335 *	485 A	-17:35137957 2524669464 A	
1335	486 G	-17:35137956 2524669463 G	
1335	487 G	-17:35137955 2524669462 G	
1335 S	488 A	-17:35137954 2524669461 A	
1335	489 C	-17:35137953 2524669460 C	
1335	490 A	-17:35137952 2524669459 A	
1335 L	491 G	-17:35137951 2524669458 G	
1335	492 G	-17:35137950 2524669457 G	
1335	493 T	-17:35137949 2524669456 T	
1335 N	494 T	-17:35137948 2524669455 T	
1335	495 C	-17:35137947 2524669454 C	
1335	496 C	-17:35137946 2524669453 C	
1335 R	497 T	-17:35137945 2524669452 T	
1335	498 G	-17:35137944 2524669451 G	
1335	499 G	-17:35137943 2524669450 G	
1335 A	500 C	-17:35137942 2524669449 C	
1335	501 A	-17:35137941 2524669448 A	
1335	502 T	-17:35137940 2524669447 T	
1335 H	503 G	-17:35137939 2524669446 G	
1335	504 G	-17:35137938 2524669445 G	
1335	505 C	-17:35137937 2524669444 C	
1335 C	506 A	-17:35137936 2524669443 A	
1335	507 G	-17:35137935 2524669442 G	
1335	508 G	-17:35137934 2524669441 G	
1335 T	509 T	-17:35137933 2524669440 T	
1335	510 T	-17:35137932 2524669439 T	
1335	511 C	-17:35137931 2524669438 C	
1335 G	512 C	-17:35137930 2524669437 C	
1335	513 C	-17:35137929 2524669436 C	
1335	514 C	-17:35137928 2524669435 C	
1335 R	515 T	-17:35137927 2524669434 T	
1335	516 G	-17:35137926 2524669433 G	
1335	517 G	-17:35137925 2524669432 G	
1335 S	518 A	-17:35137924 2524669431 A	
1335	519 A	-17:35137923 2524669430 A	
1335	520 G	-17:35137922 2524669429 G	
1335 T	521 T	-17:35137921 2524669428 T	
1335	522 G	-17:35137920 2524669427 G	
1335	523 G	-17:35137919 2524669426 G	
1335 T	524 T	-17:35137918 2524669425 T	
1335	525 C	-17:35137917 2524669424 C	
1335	526 G	-17:35137916 2524669423 G	
1335 P	527 G	-17:35137915 2524669422 G	
1335	528 A	-17:35137914 2524669421 A	
1335	529 G	-17:35137913 2524669420 G	
1335 P	530 G	-17:35137912 2524669419 G	
1335	531 G	-17:35137911 2524669418 G	
1335	532 C	-17:35137910 2524669417 C	
1335 G	533 C	-17:35137909 2524669416 C	
1335	534 C	-17:35137908 2524669415 C	
1335	535 T	-17:35137907 2524669414 T	
1335 E	536 C	-17:35137906 2524669413 C	
1335	537 C	-17:35137905 2524669412 C	
1335	538 C	-17:35137904 2524669411 C	
1335 W	539 A	-17:35137903 2524669410 A	
1335	540 C	-17:35137902 2524669409 C	
1335	541 C	-17:35137901 2524669408 C	
1335 R	542 T	-17:35137900 2524669407 T	
1335	543 C	-17:35137899 2524669406 C	
1335	544 T	-17:35137898 2524669405 T	
1335 K	545 T	-17:35137897 2524669404 T	
1335	546 G	-17:35137896 2524669403 G	
1335	547 A	-17:35137895 2524669402 A	
1335 I	548 T	-17:35137894 2524669401 T	
1335	549 G	-17:35137893 2524669400 G	
1335	550 C	-17:35137892 2524669399 C	
1335 G	551 C	-17:35137891 2524669398 C	
1335	552 A	-17:35137890 2524669397 A	
1335	553 G	-17:35137889 2524669396 G	
1335 A	554 C	-17:35137888 2524669395 C	
1335	555 A	-17:35137887 2524669394 A	
1335	556 G	-17:35137886 2524669393 G	
1335 S	557 A	-17:35137885 2524669392 A	
1335	558 A	-17:35137884 2524669391 A	
1335	559 G	-17:35137883 2524669390 G	
1335 T	560 T	-17:35137882 2524669389 T	
1335	561 C	-17:35137881 2524669388 C	
1335	562 A	-17:35137880 2524669387 A	
1335 L	563 G	-17:35137879 2524669386 G	
1335	564 G	-17:35137878 2524669385 G	
1335	565 C	-17:35137877 2524669384 C	
1335 G	566 C	-17:35137876 2524669383 C	
1335	567 T	-17:35137875 2524669382 T	
1335	568 T	-17:35137874 2524669381 T	
1335 E	569 C	-17:35137873 2524669380 C	
1335	570 C	-17:35137872 2524669379 C	
1335	571 C	-17:35137871 2524669378 C	
1335 R	572 T	-17:35137870 2524669377 T	
1335	573 G	-17:35137869 2524669376 G	
1335	574 C	-17:35137868 2524669375 C	
1335 S	575 T	-17:35137867 2524669374 T	
1335	576 C	-17:35137866 2524669373 C	
1335	577 C	-17:35137865 2524669372 C	
1335 G	578 C	-17:35137864 2524669371 C	
1335	579 T	-17:35137863 2524669370 T	
1335	580 G	-17:35137862 2524669369 G	
1335 S	581 A	-17:35137861 2524669368 A	
1335	582 G	-17:35137860 2524669367 G	
1335	583 G	-17:35137859 2524669366 G	
1335 S	584 A	-17:35137858 2524669365 A	
1335	585 C	-17:35137857 2524669364 C	
1335	586 A	-17:35137856 2524669363 A	
1335 V	587 C	-17:35137855 2524669362 C	
1335	588 A	-17:35137854 2524669361 A	
1335	589 T	-17:35137853 2524669360 T	
1335 D	590 C	-17:35137852 2524669359 C	
1335	591 A	-17:35137851 2524669358 A	
1335	592 G	-17:35137850 2524669357 G	
1335 P	593 G	-17:35137849 2524669356 G	
1335	594 G	-17:35137848 2524669355 G	
1335	595 C	-17:35137847 2524669354 C	
1335 S	596 T	-17:35137846 2524669353 T	
1335	597 T	-17:35137845 2524669352 T	
1335	598 C	-17:35137844 2524669351 C	
1335 R	599 T	-17:35137843 2524669350 T	
1335	600 G	-17:35137842 2524669349 G	
1335	601 C	-17:35137841 2524669348 C	
1335 R	602 G	-17:35137840 2524669347 G	
1335	603 G	-17:35137839 2524669346 G	
1335	604 A	-17:35137838 2524669345 A	
1335 V	605 C	-17:35137837 2524669344 C	
1335	606 T	-17:35137836 2524669343 T	
1335	607 T	-17:35137835 2524669342 T	
1335 Q	608 G	-17:35137834 2524669341 G	
1335	609 G	-17:35137833 2524669340 G	
1335	610 C	-17:35137832 2524669339 C	
1335 G	611 C	-17:35137831 2524669338 C	
1335	612 T	-17:35137830 2524669337 T	
1335	613 T	-17:35137829 2524669336 T	
1335 E	614 C	-17:35137828 2524669335 C	
1335	615 T	-17:35137827 2524669334 T	
1335	616 G	-17:35137826 2524669333 G	
1335 P	617 G	-17:35137825 2524669332 G	
1335	618 T	-17:35137824 2524669331 T	
1335	619 T	-17:35137823 2524669330 T	
1335 E	620 C	-17:35137822 2524669329 C	
1335	621 A	-17:35137821 2524669328 A	*
1334	622 C	-17:35137820 2524669327 C	
1334 C	623 A	-17:35137819 2524669326 A	
1334	624 C	-17:35137818 2524669325 C	V
1333	625 T	-17:35137817 2524669324 T	
1333 Q	626 G	-17:35137816 2524669323 G	
1333	627 G	-17:35137815 2524669322 G	P
1332	628 C	-17:35137814 2524669321 C	
1332 C	629 A	-17:35137813 2524669320 A	
1332	630 C	-17:35137812 2524669319 C	V
1331	631 G	-17:35137811 2524669318 G	
1331 T	632 T	-17:35137810 2524669317 T	
1331	633 C	-17:35137809 2524669316 C	D
1330	634 C	-17:35137808 2524669315 C	
1330 W	635 A	-17:35137807 2524669314 A	
1330	636 G	-17:35137806 2524669313 G	L
1329	637 A	-17:35137805 2524669312 A	
1329 V	638 C	-17:35137804 2524669311 C	
1329	639 C	-17:35137803 2524669310 C	G
1328	640 C	-17:35137802 2524669309 C	
1328 W	641 A	-17:35137801 2524669308 A	
1328	642 G	-17:35137800 2524669307 G	L
1327	643 G	-17:35137799 2524669306 G	
1327 T	644 T	-17:35137798 2524669305 T	
1327	645 A	-17:35137797 2524669304 A	Y
1326	646 C	-17:35137796 2524669303 C	
1326 S	647 T	-17:35137795 2524669302 T	
1326	648 C	-17:35137794 2524669301 C	E
1325	649 T	-17:35137793 2524669300 T	
1325 Q	650 G	-17:35137792 2524669299 G	
1325	651 G	-17:35137791 2524669298 G	P
1324	652 G	-17:35137790 2524669297 G	
1324 T	653 T	-17:35137789 2524669296 T	
1324	654 T	-17:35137788 2524669295 T	N
1323	655 C	-17:35137787 2524669294 C	
1323 R	656 T	-17:35137786 2524669293 T	
1323	657 C	-17:35137785 2524669292 C	E
1322	658 T	-17:35137784 2524669291 T	
1322 Q	659 G	-17:35137783 2524669290 G	
1322	660 C	-17:35137782 2524669289 C	A
1321	661 C	-17:35137781 2524669288 C	
1321 R	662 G	-17:35137780 2524669287 G	
1321	663 T	-17:35137779 2524669286 T	T
1320	664 A	-17:35137778 2524669285 A	
1320 L	665 G	-17:35137777 2524669284 G	
1320	666 G	-17:35137776 2524669283 G	P
1319	667 T	-17:35137775 2524669282 T	
1319 H	668 G	-17:35137774 2524669281 G	
1319	669 T	-17:35137773 2524669280 T	T
1318	670 C	-17:35137772 2524669279 C	
1318 G	671 C	-17:35137771 2524669278 C	
1318	672 C	-17:35137770 2524669277 C	G
1317	673 T	-17:35137769 2524669276 T	
1317 K	674 T	-17:35137768 2524669275 T	
1317	675 T	-17:35137767 2524669274 T	K
1316	676 G	-17:35137766 2524669273 G	
1316 S	677 A	-17:35137765 2524669272 A	
1316	678 A	-17:35137764 2524669271 A	F
1315	679 G	-17:35137763 2524669270 G	
1315 P	680 G	-17:35137762 2524669269 G	
1315	681 T	-17:35137761 2524669268 T	T
1314	682 G	-17:35137760 2524669267 G	
1314 A	683 C	-17:35137759 2524669266 C	
1314	684 T	-17:35137758 2524669265 T	S
1313	685 G	-17:35137757 2524669264 G	
1313 P	686 G	-17:35137756 2524669263 G	
1313	687 G	-17:35137755 2524669262 G	P
1312	688 T	-17:35137754 2524669261 T	
1312 H	689 G	-17:35137753 2524669260 G	
1312	690 G	-17:35137752 2524669259 G	P
1311	691 A	-17:35137751 2524669258 A	
1311 L	692 G	-17:35137750 2524669257 G	
1311	693 C	-17:35137749 2524669256 C	A
1310	694 C	-17:35137748 2524669255 C	
1310 G	695 C	-17:35137747 2524669254 C	
1310	696 C	-17:35137746 2524669253 C	G
1309	697 C	-17:35137745 2524669252 C	
1309 G	698 C	-17:35137744 2524669251 C	
1309	699 G	-17:35137743 2524669250 G	R
1308	700 C	-17:35137742 2524669249 C	
1308 S	701 T	-17:35137741 2524669248 T	
1308	702 C	-17:35137740 2524669247 C	E
1307	703 T	-17:35137739 2524669246 T	
1307 Q	704 G	-17:35137738 2524669245 G	
1307	705 G	-17:35137737 2524669244 G	P
1306	706 T	-17:35137736 2524669243 T	
1306 H	707 G	-17:35137735 2524669242 G	
1306	708 G	-17:35137734 2524669241 G	P
1305	709 G	-17:35137733 2524669240 G	
1305 T	710 T	-17:35137732 2524669239 T	
1305	711 C	-17:35137731 2524669238 C	D
1304	712 C	-17:35137730 2524669237 C	
1304 R	713 T	-17:35137729 2524669236 T	
1304	714 G	-17:35137728 2524669235 G	Q
1303	715 G	-17:35137727 2524669234 G	
1303 T	716 T	-17:35137726 2524669233 T	
1303	717 C	-17:35137725 2524669232 C	D
1302	718 C	-17:35137724 2524669231 C	
1302 G	719 C	-17:35137723 2524669230 C	
1302	720 A	-17:35137722 2524669229 A	W
1301	721 G	-17:35137721 2524669228 G	
1301 T	722 T	-17:35137720 2524669227 T	
1301	723 A	-17:35137719 2524669226 A	Y
1300	724 A	-17:35137718 2524669225 A	
1300 I	725 T	-17:35137717 2524669224 T	
1300	726 A	-17:35137716 2524669223 A	Y
1299	727 G	-17:35137715 2524669222 G	
1299 S	728 A	-17:35137714 2524669221 A	
1299	729 G	-17:35137713 2524669220 G	L
1298	730 G	-17:35137712 2524669219 G	
1298 T	731 T	-17:35137711 2524669218 T	
1298	732 T	-17:35137710 2524669217 T	N
1297	733 G	-17:35137709 2524669216 G	
1297 T	734 T	-17:35137708 2524669215 T	
1297	735 C	-17:35137707 2524669214 C	D
1296	736 G	-17:35137706 2524669213 G	
1296 S	737 A	-17:35137705 2524669212 A	
1296	738 A	-17:35137704 2524669211 A	F
1295	739 G	-17:35137703 2524669210 G	
1295 P	740 G	-17:35137702 2524669209 G	
1295	741 C	-17:35137701 2524669208 C	A
1294	742 T	-17:35137700 2524669207 T	
1294 Q	743 G	-17:35137699 2524669206 G	
1294	744 G	-17:35137698 2524669205 G	P
1293	745 G	-17:35137697 2524669204 G	
1293 A	746 C	-17:35137696 2524669203 C	
1293	747 T	-17:35137695 2524669202 T	S
1292	748 G	-17:35137694 2524669201 G	
1292 S	749 A	-17:35137693 2524669200 A	
1292	750 A	-17:35137692 2524669199 A	F
1291	751 G	-17:35137691 2524669198 G	
1291 P	752 G	-17:35137690 2524669197 G	
1291	753 C	-17:35137689 2524669196 C	A
1290	754 A	-17:35137688 2524669195 A	
1290 L	755 G	-17:35137687 2524669194 G	
1290	756 G	-17:35137686 2524669193 G	P
1289	757 A	-17:35137685 2524669192 A	
1289 L	758 G	-17:35137684 2524669191 G	
1289	759 G	-17:35137683 2524669190 G	P
1288	760 A	-17:35137682 2524669189 A	
1288 L	761 G	-17:35137681 2524669188 G	
1288	762 G	-17:35137680 2524669187 G	P
1287	763 G	-17:35137679 2524669186 G	
1287 T	764 T	-17:35137678 2524669185 T	
1287	765 G	-17:35137677 2524669184 G	H
1286	766 G	-17:35137676 2524669183 G	
1286 P	767 G	-17:35137675 2524669182 G	
1286	768 G	-17:35137674 2524669181 G	P
1285	769 C	-17:35137673 2524669180 C	
1285 S	770 T	-17:35137672 2524669179 T	
1285	771 G	-17:35137671 2524669178 G	Q
1284	772 A	-17:35137670 2524669177 A	
1284 L	773 G	-17:35137669 2524669176 G	
1284	774 G	-17:35137668 2524669175 G	P
1283	775 G	-17:35137667 2524669174 G	
1283 P	776 G	-17:35137666 2524669173 G	
1283	777 C	-17:35137665 2524669172 C	A
1282	778 A	-17:35137664 2524669171 A	
1282 L	779 G	-17:35137663 2524669170 G	
1282	780 C	-17:35137662 2524669169 C	A
1281	781 T	-17:35137661 2524669168 T	
1281 E	782 C	-17:35137660 2524669167 C	
1281	783 C	-17:35137659 2524669166 C	G
1280	784 T	-17:35137658 2524669165 T	
1280 E	785 C	-17:35137657 2524669164 C	
1280	786 C	-17:35137656 2524669163 C	G
1279	787 C	-17:35137655 2524669162 C	
1279 R	788 T	-17:35137654 2524669161 T	
1279	789 G	-17:35137653 2524669160 G	Q
1278	790 G	-17:35137652 2524669159 G	
1278 P	791 G	-17:35137651 2524669158 G	
1278	792 G	-17:35137650 2524669157 G	P
1277	793 T	-17:35137649 2524669156 T	
1277 H	794 G	-17:35137648 2524669155 G	
1277	795 T	-17:35137647 2524669154 T	T
1276	796 C	-17:35137646 2524669153 C	
1276 *	797 A	-17:35137645 2524669152 A	
1276	798 A	-17:35137644 2524669151 A	L
1275	799 G	-17:35137643 2524669150 G	
1275 T	800 T	-17:35137642 2524669149 T	
1275	801 A	-17:35137641 2524669148 A	Y
1274	802 C	-17:35137640 2524669147 C	
1274 S	803 T	-17:35137639 2524669146 T	
1274	804 C	-17:35137638 2524669145 C	E
1273	805 G	-17:35137637 2524669144 G	
1273 P	806 G	-17:35137636 2524669143 G	
1273	807 G	-17:35137635 2524669142 G	P
1272	808 G	-17:35137634 2524669141 G	
1272 T	809 T	-17:35137633 2524669140 T	
1272	810 T	-17:35137632 2524669139 T	N
1271	811 C	-17:35137631 2524669138 C	
1271 R	812 T	-17:35137630 2524669137 T	
1271	813 C	-17:35137629 2524669136 C	E
1270	814 C	-17:35137628 2524669135 C	
1270 W	815 A	-17:35137627 2524669134 A	
1270	816 C	-17:35137626 2524669133 C	V
1269	817 G	-17:35137625 2524669132 G	
1269 P	818 G	-17:35137624 2524669131 G	
1269	819 C	-17:35137623 2524669130 C	A
1268	820 A	-17:35137622 2524669129 A	
1268 V	821 C	-17:35137621 2524669128 C	
1268	822 C	-17:35137620 2524669127 C	G
1267	823 C	-17:35137619 2524669126 C	
1267 G	824 C	-17:35137618 2524669125 C	
1267	825 C	-17:35137617 2524669124 C	G
1266	826 A	-17:35137616 2524669123 A	
1266 L	827 A	-17:35137615 2524669122 A	
1266	828 A	-17:35137614 2524669121 A	F
1265	829 G	-17:35137613 2524669120 G	
1265 P	830 G	-17:35137612 2524669119 G	
1265	831 C	-17:35137611 2524669118 C	A
1264	832 A	-17:35137610 2524669117 A	
1264 L	833 A	-17:35137609 2524669116 A	
1264	834 A	-17:35137608 2524669115 A	F
1263	835 A	-17:35137607 2524669114 A	
1263 F	836 A	-17:35137606 2524669113 A	
1263	837 C	-17:35137605 2524669112 C	V
1262	838 G	-17:35137604 2524669111 G	
1262 T	839 T	-17:35137603 2524669110 T	
1262	840 C	-17:35137602 2524669109 C	D
1261	841 T	-17:35137601 2524669108 T	
1261 K	842 T	-17:35137600 2524669107 T	
1261	843 T	-17:35137599 2524669106 T	K
1260	844 G	-17:35137598 2524669105 G	
1260 S	845 A	-17:35137597 2524669104 A	
1260	846 C	-17:35137596 2524669103 C	V
1259	847 G	-17:35137595 2524669102 G	
1259 S	848 A	-17:35137594 2524669101 A	
1259	849 C	-17:35137593 2524669100 C	V
1258	850 C	-17:35137592 2524669099 C	
1258 G	851 C	-17:35137591 2524669098 C	
1258	852 C	-17:35137590 2524669097 C	G
1257	853 A	-17:35137589 2524669096 A	
1257 M	854 T	-17:35137588 2524669095 T	
1257	855 T	-17:35137587 2524669094 T	N
1256	856 C	-17:35137586 2524669093 C	
1256 R	857 T	-17:35137585 2524669092 T	
1256	858 T	-17:35137584 2524669091 T	K
1255	859 C	-17:35137583 2524669090 C	
1255 G	860 C	-17:35137582 2524669089 C	
1255	861 C	-17:35137581 2524669088 C	G
1254	862 T	-17:35137580 2524669087 T	
1254 Q	863 G	-17:35137579 2524669086 G	
1254	864 G	-17:35137578 2524669085 G	P
1253	865 G	-17:35137577 2524669084 G	
1253 P	866 G	-17:35137576 2524669083 G	
1253	867 A	-17:35137575 2524669082 A	S
1252	868 G	-17:35137574 2524669081 G	
1252 S	869 A	-17:35137573 2524669080 A	
1252	870 G	-17:35137572 2524669079 G	L
1251	871 A	-17:35137571 2524669078 A	
1251 L	872 G	-17:35137570 2524669077 G	
1251	873 T	-17:35137569 2524669076 T	T
1250	874 C	-17:35137568 2524669075 C	
1250 R	875 T	-17:35137567 2524669074 T	
1250	876 T	-17:35137566 2524669073 T	K
1249	877 G	-17:35137565 2524669072 G	
1249 P	878 G	-17:35137564 2524669071 G	
1249	879 G	-17:35137563 2524669070 G	P
1248	880 C	-17:35137562 2524669069 C	
1248 G	881 C	-17:35137561 2524669068 C	
1248	882 T	-17:35137560 2524669067 T	R
1247	883 T	-17:35137559 2524669066 T	
1247 K	884 T	-17:35137558 2524669065 T	
1247	885 C	-17:35137557 2524669064 C	E
1246	886 C	-17:35137556 2524669063 C	
1246 W	887 A	-17:35137555 2524669062 A	
1246	888 G	-17:35137554 2524669061 G	L
1245	889 A	-17:35137553 2524669060 A	
1245 L	890 G	-17:35137552 2524669059 G	
1245	891 T	-17:35137551 2524669058 T	T
1244	892 G	-17:35137550 2524669057 G	
1244 P	893 G	-17:35137549 2524669056 G	
1244	894 C	-17:35137548 2524669055 C	A
1243	895 A	-17:35137547 2524669054 A	
1243 V	896 C	-17:35137546 2524669053 C	
1243	897 C	-17:35137545 2524669052 C	G
1242	898 A	-17:35137544 2524669051 A	
1242 L	899 G	-17:35137543 2524669050 G	
1242	900 C	-17:35137542 2524669049 C	A
1241	901 A	-17:35137541 2524669048 A	
1241 L	902 G	-17:35137540 2524669047 G	
1241	903 G	-17:35137539 2524669046 G	P
1240	904 T	-17:35137538 2524669045 T	
1240 D	905 C	-17:35137537 2524669044 C	
1240	906 G	-17:35137536 2524669043 G	R
1239	907 G	-17:35137535 2524669042 G	
1239 P	908 G	-17:35137534 2524669041 G	
1239	909 C	-17:35137533 2524669040 C	A
1238	910 A	-17:35137532 2524669039 A	
1238 L	911 G	-17:35137531 2524669038 G	
1238	912 C	-17:35137530 2524669037 C	A
1237	913 A	-17:35137529 2524669036 A	
1237 L	914 G	-17:35137528 2524669035 G	
1237	915 G	-17:35137527 2524669034 G	P
1236	916 C	-17:35137526 2524669033 C	
1236 C	917 A	-17:35137525 2524669032 A	
1236	918 G	-17:35137524 2524669031 G	L
1235	919 A	-17:35137523 2524669030 A	
1235 L	920 G	-17:35137522 2524669029 G	
1235	921 G	-17:35137521 2524669028 G	P
1234	922 G	-17:35137520 2524669027 G	
1234 A	923 C	-17:35137519 2524669026 C	
1234	924 C	-17:35137518 2524669025 C	G
1233	925 C	-17:35137517 2524669024 C	
1233 R	926 T	-17:35137516 2524669023 T	
1233	927 C	-17:35137515 2524669022 C	E
1232	928 T	-17:35137514 2524669021 T	
1232 E	929 C	-17:35137513 2524669020 C	
1232	930 G	-17:35137512 2524669019 G	R
1231	931 G	-17:35137511 2524669018 G	
1231 P	932 G	-17:35137510 2524669017 G	
1231	933 G	-17:35137509 2524669016 G	P
1230	934 C	-17:35137508 2524669015 C	
1230 R	935 G	-17:35137507 2524669014 G	
1230	936 A	-17:35137506 2524669013 A	S
1229	937 A	-17:35137505 2524669012 A	
1229 L	938 G	-17:35137504 2524669011 G	
1229	939 G	-17:35137503 2524669010 G	P
1228	940 G	-17:35137502 2524669009 G	
1228 P	941 G	-17:35137501 2524669008 G	
1228	942 G	-17:35137500 2524669007 G	P
1227	943 C	-17:35137499 2524669006 C	
1227 S	944 T	-17:35137498 2524669005 T	
1227	945 G	-17:35137497 2524669004 G	Q
1226	946 G	-17:35137496 2524669003 G	
1226 P	947 G	-17:35137495 2524669002 G	
1226	948 G	-17:35137494 2524669001 G	P
1225	949 C	-17:35137493 2524669000 C	
1225 G	950 C	-17:35137492 2524668999 C	
1225	951 G	-17:35137491 2524668998 G	R
1224	952 A	-17:35137490 2524668997 A	
1224 F	953 A	-17:35137489 2524668996 A	
1224	954 C	-17:35137488 2524668995 C	V
1223	955 A	-17:35137487 2524668994 A	
1223 M	956 T	-17:35137486 2524668993 T	
1223	957 C	-17:35137485 2524668992 C	D
1222	958 T	-17:35137484 2524668991 T	
1222 Q	959 G	-17:35137483 2524668990 G	
1222	960 G	-17:35137482 2524668989 G	P
1221	961 C	-17:35137481 2524668988 C	
1221 S	962 T	-17:35137480 2524668987 T	
1221	963 G	-17:35137479 2524668986 G	Q
1220	964 G	-17:35137478 2524668985 G	
1220 T	965 T	-17:35137477 2524668984 T	
1220	966 T	-17:35137476 2524668983 T	N
1219	967 C	-17:35137475 2524668982 C	
1219 *	968 A	-17:35137474 2524668981 A	
1219	969 C	-17:35137473 2524668980 C	V
1218	970 A	-17:35137472 2524668979 A	
1218 M	971 T	-17:35137471 2524668978 T	
1218	972 A	-17:35137470 2524668977 A	Y
1217	973 T	-17:35137469 2524668976 T	
1217 N	974 T	-17:35137468 2524668975 T	
1217	975 C	-17:35137326 2524668833 C	E
1216	976 A	-17:35137325 2524668832 A	
1216 L	977 G	-17:35137324 2524668831 G	
1216	978 G	-17:35137323 2524668830 G	P
1215	979 C	-17:35137322 2524668829 C	
1215 S	980 T	-17:35137321 2524668828 T	
1215	981 G	-17:35137320 2524668827 G	Q
1214	982 G	-17:35137319 2524668826 G	
1214 P	983 G	-17:35137318 2524668825 G	
1214	984 G	-17:35137317 2524668824 G	P
1213	985 G	-17:35137316 2524668823 G	
1213 A	986 C	-17:35137315 2524668822 C	
1213	987 T	-17:35137314 2524668821 T	S
1212	988 G	-17:35137313 2524668820 G	
1212 A	989 C	-17:35137312 2524668819 C	
1212	990 A	-17:35137311 2524668818 A	C
1211	991 G	-17:35137310 2524668817 G	
1211 P	992 G	-17:35137309 2524668816 G	
1211	993 T	-17:35137308 2524668815 T	T
1210	994 C	-17:35137307 2524668814 C	
1210 *	995 A	-17:35137306 2524668813 A	
1210	996 G	-17:35137305 2524668812 G	L
1209	997 G	-17:35137304 2524668811 G	
1209 P	998 G	-17:35137303 2524668810 G	
1209	999 G	-17:35137302 2524668809 G	P
1208	1000 G	-17:35137301 2524668808 G	
1208 P	1001 G	-17:35137300 2524668807 G	
1208	1002 C	-17:35137299 2524668806 C	A
1207	1003 A	-17:35137298 2524668805 A	
1207 L	1004 A	-17:35137297 2524668804 A	
1207	1005 C	-17:35137296 2524668803 C	V
1206	1006 G	-17:35137295 2524668802 G	
1206 T	1007 T	-17:35137294 2524668801 T	
1206	1008 A	-17:35137293 2524668800 A	Y
1205	1009 G	-17:35137292 2524668799 G	
1205 A	1010 C	-17:35137291 2524668798 C	
1205	1011 C	-17:35137290 2524668797 C	G
1204	1012 A	-17:35137289 2524668796 A	
1204 M	1013 T	-17:35137288 2524668795 T	
1204	1014 C	-17:35137287 2524668794 C	D
1203	1015 A	-17:35137286 2524668793 A	
1203 L	1016 G	-17:35137285 2524668792 G	
1203	1017 T	-17:35137284 2524668791 T	T
1202	1018 C	-17:35137283 2524668790 C	
1202 R	1019 T	-17:35137282 2524668789 T	
1202	1020 C	-17:35137281 2524668788 C	E
1201	1021 A	-17:35137280 2524668787 A	
1201 L	1022 G	-17:35137279 2524668786 G	
1201	1023 A	-17:35137278 2524668785 A	S
1200	1024 G	-17:35137277 2524668784 G	
1200 P	1025 G	-17:35137276 2524668783 G	
1200	1026 G	-17:35137275 2524668782 G	P
1199	1027 C	-17:35137274 2524668781 C	
1199 C	1028 A	-17:35137273 2524668780 A	
1199	1029 G	-17:35137272 2524668779 G	L
1198	1030 G	-17:35137271 2524668778 G	
1198 P	1031 G	-17:35137270 2524668777 G	
1198	1032 G	-17:35137269 2524668776 G	P
1197	1033 T	-17:35137268 2524668775 T	
1197 Y	1034 A	-17:35137267 2524668774 A	
1197	1035 C	-17:35137266 2524668773 C	V
1196	1036 T	-17:35137265 2524668772 T	
1196 Q	1037 G	-17:35137264 2524668771 G	
1196	1038 T	-17:35137263 2524668770 T	T
1195	1039 G	-17:35137262 2524668769 G	
1195 P	1040 G	-17:35137261 2524668768 G	
1195	1041 G	-17:35137260 2524668767 G	P
1194	1042 G	-17:35137259 2524668766 G	
1194 T	1043 T	-17:35137258 2524668765 T	
1194	1044 C	-17:35137257 2524668764 C	D
1193	1045 C	-17:35137256 2524668763 C	
1193 R	1046 T	-17:35137255 2524668762 T	
1193	1047 C	-17:35137254 2524668761 C	E
1192	1048 A	-17:35137253 2524668760 A	
1192 V	1049 C	-17:35137252 2524668759 C	
1192	1050 T	-17:35137251 2524668758 T	S
1191	1051 G	-17:35137250 2524668757 G	
1191 T	1052 T	-17:35137249 2524668756 T	
1191	1053 A	-17:35137248 2524668755 A	Y
1190	1054 C	-17:35137247 2524668754 C	
1190 G	1055 C	-17:35137246 2524668753 C	
1190	1056 G	-17:35137245 2524668752 G	R
1189	1057 C	-17:35137244 2524668751 C	
1189 S	1058 T	-17:35137243 2524668750 T	
1189	1059 G	-17:35137242 2524668749 G	Q
1188	1060 T	-17:35137241 2524668748 T	
1188 Y	1061 A	-17:35137240 2524668747 A	
1188	1062 G	-17:35137239 2524668746 G	L
1187	1063 A	-17:35137238 2524668745 A	
1187 L	1064 G	-17:35137237 2524668744 G	
1187	1065 G	-17:35137236 2524668743 G	P
1186	1066 G	-17:35137235 2524668742 G	
1186 A	1067 C	-17:35137234 2524668741 C	
1186	1068 T	-17:35137233 2524668740 T	S
1185	1069 G	-17:35137232 2524668739 G	
1185 P	1070 G	-17:35137231 2524668738 G	
1185	1071 G	-17:35137230 2524668737 G	P
1184	1072 G	-17:35137229 2524668736 G	
1184 T	1073 T	-17:35137228 2524668735 T	
1184	1074 C	-17:35137227 2524668734 C	D
1183	1075 A	-17:35137226 2524668733 A	
1183 M	1076 T	-17:35137225 2524668732 T	
1183	1077 G	-17:35137224 2524668731 G	H
1182	1078 T	-17:35137223 2524668730 T	
1182 H	1079 G	-17:35137222 2524668729 G	
1182	1080 T	-17:35137221 2524668728 T	T
1181	1081 G	-17:35137220 2524668727 G	
1181 P	1082 G	-17:35137219 2524668726 G	
1181	1083 G	-17:35137218 2524668725 G	P
1180	1084 G	-17:35137217 2524668724 G	
1180 S	1085 A	-17:35137216 2524668723 A	
1180	1086 G	-17:35137215 2524668722 G	L
1179	1087 G	-17:35137214 2524668721 G	
1179 A	1088 C	-17:35137213 2524668720 C	
1179	1089 T	-17:35137212 2524668719 T	S
1178	1090 T	-17:35137211 2524668718 T	
1178 K	1091 T	-17:35137210 2524668717 T	
1178	1092 G	-17:35137209 2524668716 G	Q
1177	1093 C	-17:35137208 2524668715 C	
1177 C	1094 A	-17:35137207 2524668714 A	
1177	1095 G	-17:35137206 2524668713 G	L
1176	1096 C	-17:35137205 2524668712 C	
1176 G	1097 C	-17:35137204 2524668711 C	
1176	1098 C	-17:35137203 2524668710 C	G
1175	1099 C	-17:35137202 2524668709 C	
1175 R	1100 T	-17:35137201 2524668708 T	
1175	1101 T	-17:35137200 2524668707 T	K
1174	1102 G	-17:35137199 2524668706 G	
1174 P	1103 G	-17:35137198 2524668705 G	
1174	1104 C	-17:35137197 2524668704 C	A
1173	1105 T	-17:35137196 2524668703 T	
1173 Q	1106 G	-17:35137195 2524668702 G	
1173	1107 C	-17:35137194 2524668701 C	A
1172	1108 C	-17:35137193 2524668700 C	
1172 G	1109 C	-17:35137192 2524668699 C	
1172	1110 C	-17:35137191 2524668698 C	G
1171	1111 C	-17:35137190 2524668697 C	
1171 W	1112 A	-17:35137189 2524668696 A	
1171	1113 T	-17:35137188 2524668695 T	M
1170	1114 T	-17:35137187 2524668694 T	
1170 E	1115 C	-17:35137186 2524668693 C	
1170	1116 C	-17:35137185 2524668692 C	G
1169	1117 C	-17:35137184 2524668691 C	
1169 W	1118 A	-17:35137183 2524668690 A	
1169	1119 G	-17:35137182 2524668689 G	L
1168	1120 G	-17:35137181 2524668688 G	
1168 T	1121 T	-17:35137180 2524668687 T	
1168	1122 C	-17:35137179 2524668686 C	D
1167	1123 A	-17:35137178 2524668685 A	
1167 V	1124 C	-17:35137177 2524668684 C	
1167	1125 C	-17:35137176 2524668683 C	G
1166	1126 A	-17:35137175 2524668682 A	
1166 M	1127 T	-17:35137174 2524668681 T	
1166	1128 C	-17:35137173 2524668680 C	D
1165	1129 A	-17:35137172 2524668679 A	
1165 L	1130 A	-17:35137171 2524668678 A	
1165	1131 A	-17:35137170 2524668677 A	F
1164	1132 T	-17:35137169 2524668676 T	
1164 Y	1133 A	-17:35137168 2524668675 A	
1164	1134 C	-17:35137167 2524668674 C	V
1163	1135 A	-17:35137166 2524668673 A	
1163 M	1136 T	-17:35137165 2524668672 T	
1163	1137 C	-17:35137164 2524668671 C	D
1162	1138 G	-17:35137163 2524668670 G	
1162 P	1139 G	-17:35137162 2524668669 G	
1162	1140 A	-17:35137161 2524668668 A	S
1161	1141 G	-17:35137160 2524668667 G	
1161 A	1142 C	-17:35137159 2524668666 C	
1161	1143 C	-17:35137158 2524668665 C	G
1160	1144 A	-17:35137157 2524668664 A	
1160 L	1145 G	-17:35137156 2524668663 G	
1160	1146 C	-17:35137155 2524668662 C	A
1159	1147 C	-17:35137154 2524668661 C	
1159 G	1148 C	-17:35137153 2524668660 C	
1159	1149 C	-17:35137152 2524668659 C	G
1158	1150 T	-17:35137151 2524668658 T	
1158 K	1151 T	-17:35137150 2524668657 T	
1158	1152 C	-17:35137149 2524668656 C	E
1157	1153 G	-17:35137148 2524668655 G	
1157 P	1154 G	-17:35137147 2524668654 G	
1157	1155 A	-17:35137146 2524668653 A	S
1156	1156 G	-17:35137145 2524668652 G	
1156 P	1157 G	-17:35137144 2524668651 G	
1156	1158 G	-17:35137143 2524668650 G	P
1155	1159 T	-17:35137142 2524668649 T	
1155 H	1160 G	-17:35137141 2524668648 G	
1155	1161 C	-17:35137140 2524668647 C	A
1154	1162 C	-17:35137139 2524668646 C	
1154 W	1163 A	-17:35137138 2524668645 A	
1154	1164 G	-17:35137137 2524668644 G	L
1153	1165 T	-17:35137136 2524668643 T	
1153 H	1166 G	-17:35137135 2524668642 G	
1153	1167 G	-17:35137134 2524668641 G	P
1152	1168 A	-17:35137133 2524668640 A	
1152 L	1169 G	-17:35137132 2524668639 G	
1152	1170 A	-17:35137131 2524668638 A	S
1151	1171 C	-17:35137130 2524668637 C	
1151 G	1172 C	-17:35137129 2524668636 C	
1151	1173 T	-17:35137128 2524668635 T	R
1150	1174 G	-17:35137127 2524668634 G	
1150 P	1175 G	-17:35137126 2524668633 G	
1150	1176 G	-17:35137125 2524668632 G	P
1149	1177 G	-17:35137124 2524668631 G	
1149 P	1178 G	-17:35137123 2524668630 G	
1149	1179 C	-17:35137122 2524668629 C	A
1148	1180 C	-17:35137121 2524668628 C	
1148 R	1181 T	-17:35137120 2524668627 T	
1148	1182 C	-17:35137119 2524668626 C	E
1147	1183 C	-17:35137118 2524668625 C	
1147 R	1184 T	-17:35137117 2524668624 T	
1147	1185 C	-17:35137116 2524668623 C	E
1146	1186 T	-17:35137115 2524668622 T	
1146 K	1187 T	-17:35137114 2524668621 T	
1146	1188 C	-17:35137113 2524668620 C	E
1145	1189 A	-17:35137112 2524668619 A	
1145 L	1190 G	-17:35137111 2524668618 G	
1145	1191 A	-17:35137110 2524668617 A	S
1144	1192 G	-17:35137109 2524668616 G	
1144 P	1193 G	-17:35137108 2524668615 G	
1144	1194 G	-17:35137107 2524668614 G	P
1143	1195 C	-17:35137106 2524668613 C	
1143 S	1196 T	-17:35137105 2524668612 T	
1143	1197 C	-17:35137104 2524668611 C	E
1142	1198 C	-17:35137103 2524668610 C	
1142 W	1199 A	-17:35137102 2524668609 A	
1142	1200 G	-17:35137101 2524668608 G	L
1141	1201 C	-17:35137100 2524668607 C	
1141 G	1202 C	-17:35137099 2524668606 C	
1141	1203 C	-17:35137098 2524668605 C	G
1140	1204 T	-17:35137097 2524668604 T	
1140 *	1205 A	-17:35137096 2524668603 A	
1140	1206 G	-17:35137095 2524668602 G	L
1139	1207 T	-17:35137094 2524668601 T	
1139 H	1208 G	-17:35137093 2524668600 G	
1139	1209 T	-17:35137092 2524668599 T	T
1138	1210 C	-17:35137091 2524668598 C	
1138 *	1211 A	-17:35137090 2524668597 A	
1138	1212 G	-17:35137089 2524668596 G	L
1137	1213 G	-17:35137088 2524668595 G	
1137 T	1214 T	-17:35137087 2524668594 T	
1137	1215 C	-17:35137086 2524668593 C	D
1136	1216 C	-17:35137085 2524668592 C	
1136 G	1217 C	-17:35137084 2524668591 C	
1136	1218 C	-17:35137083 2524668590 C	G
1135	1219 A	-17:35137082 2524668589 A	
1135 V	1220 C	-17:35137081 2524668588 C	
1135	1221 C	-17:35137080 2524668587 C	G
1134	1222 G	-17:35137079 2524668586 G	
1134 A	1223 C	-17:35137078 2524668585 C	
1134	1224 C	-17:35137077 2524668584 C	G
1133	1225 A	-17:35137076 2524668583 A	
1133 V	1226 C	-17:35137075 2524668582 C	
1133	1227 T	-17:35137074 2524668581 T	S
1132	1228 C	-17:35136782 2524668289 C	
1132 G	1229 C	-17:35136781 2524668288 C	
1132	1230 T	-17:35136780 2524668287 T	R
1131	1231 G	-17:35136779 2524668286 G	
1131 P	1232 G	-17:35136778 2524668285 G	
1131	1233 T	-17:35136777 2524668284 T	T
1130	1234 A	-17:35136776 2524668283 A	
1130 L	1235 G	-17:35136775 2524668282 G	
1130	1236 A	-17:35136774 2524668281 A	S
1129	1237 T	-17:35136773 2524668280 T	
1129 H	1238 G	-17:35136772 2524668279 G	
1129	1239 A	-17:35136771 2524668278 A	S
1128	1240 G	-17:35136770 2524668277 G	
1128 A	1241 C	-17:35136769 2524668276 C	
1128	1242 T	-17:35136768 2524668275 T	S
1127	1243 G	-17:35136767 2524668274 G	
1127 A	1244 C	-17:35136766 2524668273 C	
1127	1245 G	-17:35136765 2524668272 G	R
1126	1246 G	-17:35136764 2524668271 G	
1126 T	1247 T	-17:35136763 2524668270 T	
1126	1248 G	-17:35136762 2524668269 G	H
1125	1249 C	-17:35136761 2524668268 C	
1125 G	1250 C	-17:35136760 2524668267 C	
1125	1251 T	-17:35136759 2524668266 T	R
1124	1252 G	-17:35136758 2524668265 G	
1124 T	1253 T	-17:35136757 2524668264 T	
1124	1254 G	-17:35136756 2524668263 G	H
1123	1255 G	-17:35136755 2524668262 G	
1123 T	1256 T	-17:35136754 2524668261 T	
1123	1257 G	-17:35136753 2524668260 G	H
1122	1258 G	-17:35136752 2524668259 G	
1122 S	1259 A	-17:35136751 2524668258 A	
1122	1260 C	-17:35136750 2524668257 C	V
1121	1261 C	-17:35136749 2524668256 C	
1121 W	1262 A	-17:35136748 2524668255 A	
1121	1263 T	-17:35136747 2524668254 T	M
1120	1264 G	-17:35136746 2524668253 G	
1120 A	1265 C	-17:35136745 2524668252 C	
1120	1266 C	-17:35136744 2524668251 C	G
1119	1267 C	-17:35136743 2524668250 C	
1119 G	1268 C	-17:35136742 2524668249 C	
1119	1269 C	-17:35136741 2524668248 C	G
1118	1270 A	-17:35136740 2524668247 A	
1118 L	1271 G	-17:35136739 2524668246 G	
1118	1272 C	-17:35136738 2524668245 C	A
1117	1273 G	-17:35136737 2524668244 G	
1117 A	1274 C	-17:35136736 2524668243 C	
1117	1275 C	-17:35136735 2524668242 C	G
1116	1276 C	-17:35136734 2524668241 C	
1116 R	1277 G	-17:35136733 2524668240 G	
1116	1278 G	-17:35136732 2524668239 G	P
1115	1279 G	-17:35136731 2524668238 G	
1115 P	1280 G	-17:35136730 2524668237 G	
1115	1281 C	-17:35136729 2524668236 C	A
1114	1282 A	-17:35136728 2524668235 A	
1114 L	1283 G	-17:35136727 2524668234 G	
1114	1284 G	-17:35136726 2524668233 G	P
1113	1285 G	-17:35136725 2524668232 G	
1113 T	1286 T	-17:35136724 2524668231 T	
1113	1287 C	-17:35136723 2524668230 C	D
1112	1288 T	-17:35136722 2524668229 T	
1112 Q	1289 G	-17:35136721 2524668228 G	
1112	1290 G	-17:35136720 2524668227 G	P
1111	1291 A	-17:35136719 2524668226 A	
1111 V	1292 C	-17:35136718 2524668225 C	
1111	1293 A	-17:35136717 2524668224 A	C
1110	1294 G	-17:35136716 2524668223 G	
1110 S	1295 A	-17:35136715 2524668222 A	
1110	1296 A	-17:35136714 2524668221 A	F
1109	1297 G	-17:35136713 2524668220 G	
1109 S	1298 A	-17:35136712 2524668219 A	
1109	1299 A	-17:35136711 2524668218 A	F
1108	1300 G	-17:35136710 2524668217 G	
1108 A	1301 C	-17:35136709 2524668216 C	
1108	1302 C	-17:35136708 2524668215 C	G
1107	1303 C	-17:35136707 2524668214 C	
1107 R	1304 T	-17:35136706 2524668213 T	
1107	1305 G	-17:35136705 2524668212 G	Q
1106	1306 C	-17:35136704 2524668211 C	
1106 S	1307 T	-17:35136703 2524668210 T	
1106	1308 G	-17:35136702 2524668209 G	Q
1105	1309 G	-17:35136701 2524668208 G	
1105 P	1310 G	-17:35136700 2524668207 G	
1105	1311 G	-17:35136699 2524668206 G	P
1104	1312 T	-17:35136698 2524668205 T	
1104 Y	1313 A	-17:35136697 2524668204 A	
1104	1314 C	-17:35136696 2524668203 C	V
1103	1315 C	-17:35136695 2524668202 C	
1103 W	1316 A	-17:35136694 2524668201 A	
1103	1317 G	-17:35136693 2524668200 G	L
1102	1318 A	-17:35136692 2524668199 A	
1102 I	1319 T	-17:35136691 2524668198 T	
1102	1320 A	-17:35136690 2524668197 A	Y
1101	1321 C	-17:35136689 2524668196 C	
1101 S	1322 T	-17:35136688 2524668195 T	
1101	1323 C	-17:35136687 2524668194 C	E
1100	1324 C	-17:35136686 2524668193 C	
1100 R	1325 T	-17:35136685 2524668192 T	
1100	1326 C	-17:35136684 2524668191 C	E
1099	1327 A	-17:35136683 2524668190 A	
1099 L	1328 G	-17:35136682 2524668189 G	
1099	1329 C	-17:35136681 2524668188 C	A
1098	1330 A	-17:35136680 2524668187 A	
1098 M	1331 T	-17:35136679 2524668186 T	
1098	1332 C	-17:35136678 2524668185 C	D
1097	1333 C	-17:35136677 2524668184 C	
1097 W	1334 A	-17:35136676 2524668183 A	
1097	1335 C	-17:35136675 2524668182 C	V
1096	1336 C	-17:35136674 2524668181 C	
1096 W	1337 A	-17:35136673 2524668180 A	
1096	1338 G	-17:35136672 2524668179 G	L
1095	1339 G	-17:35136671 2524668178 G	
1095 T	1340 T	-17:35136670 2524668177 T	
1095	1341 C	-17:35136669 2524668176 C	D
1094	1342 C	-17:35136668 2524668175 C	
1094 G	1343 C	-17:35136667 2524668174 C	
1094	1344 C	-17:35136666 2524668173 C	G
1093	1345 C	-17:35136665 2524668172 C	
1093 W	1346 A	-17:35136664 2524668171 A	
1093	1347 T	-17:35136663 2524668170 T	M
1092	1348 G	-17:35136662 2524668169 G	
1092 T	1349 T	-17:35136661 2524668168 T	
1092	1350 C	-17:35136660 2524668167 C	D
1091	1351 A	-17:35136659 2524668166 A	
1091 M	1352 T	-17:35136658 2524668165 T	
1091	1353 C	-17:35136657 2524668164 C	D
1090	1354 G	-17:35136656 2524668163 G	
1090 T	1355 T	-17:35136655 2524668162 T	
1090	1356 C	-17:35136654 2524668161 C	D
1089	1357 C	-17:35136653 2524668160 C	
1089 R	1358 T	-17:35136652 2524668159 T	
1089	1359 C	-17:35136651 2524668158 C	E
1088	1360 C	-17:35136650 2524668157 C	
1088 W	1361 A	-17:35136649 2524668156 A	
1088	1362 G	-17:35136648 2524668155 G	L
1087	1363 C	-17:35136647 2524668154 C	
1087 C	1364 A	-17:35136646 2524668153 A	
1087	1365 G	-17:35136645 2524668152 G	L
1086	1366 T	-17:35136644 2524668151 T	
1086 H	1367 G	-17:35136643 2524668150 G	
1086	1368 A	-17:35136642 2524668149 A	S
1085	1369 G	-17:35136641 2524668148 G	
1085 A	1370 C	-17:35136640 2524668147 C	
1085	1371 G	-17:35136639 2524668146 G	R
1084	1372 G	-17:35136638 2524668145 G	
1084 T	1373 T	-17:35136637 2524668144 T	
1084	1374 A	-17:35136636 2524668143 A	Y
1083	1375 G	-17:35136635 2524668142 G	
1083 S	1376 A	-17:35136634 2524668141 A	
1083	1377 A	-17:35136633 2524668140 A	F
1082	1378 G	-17:35136632 2524668139 G	
1082 P	1379 G	-17:35136631 2524668138 G	
1082	1380 T	-17:35136630 2524668137 T	T
1081	1381 G	-17:35136629 2524668136 G	
1081 A	1382 C	-17:35136628 2524668135 C	
1081	1383 T	-17:35136627 2524668134 T	S
1080	1384 G	-17:35136626 2524668133 G	
1080 T	1385 T	-17:35136625 2524668132 T	
1080	1386 C	-17:35136624 2524668131 C	D
1079	1387 C	-17:35136623 2524668130 C	
1079 W	1388 A	-17:35136622 2524668129 A	
1079	1389 A	-17:35136621 2524668128 A	L
1078	1390 G	-17:35136620 2524668127 G	
1078 P	1391 G	-17:35136619 2524668126 G	
1078	1392 G	-17:35136618 2524668125 G	P
1077	1393 A	-17:35136617 2524668124 A	
1077 V	1394 C	-17:35136616 2524668123 C	
1077	1395 T	-17:35136615 2524668122 T	S
1076	1396 G	-17:35136614 2524668121 G	
1076 P	1397 G	-17:35136613 2524668120 G	
1076	1398 C	-17:35136612 2524668119 C	A
1075	1399 T	-17:35136611 2524668118 T	
1075 Q	1400 G	-17:35136610 2524668117 G	
1075	1401 G	-17:35136609 2524668116 G	P
1074	1402 G	-17:35136608 2524668115 G	
1074 A	1403 C	-17:35136607 2524668114 C	
1074	1404 C	-17:35136606 2524668113 C	G
1073	1405 C	-17:35136605 2524668112 C	
1073 W	1406 A	-17:35136604 2524668111 A	
1073	1407 A	-17:35136603 2524668110 A	L
1072	1408 G	-17:35136602 2524668109 G	
1072 T	1409 T	-17:35136601 2524668108 T	
1072	1410 C	-17:35136600 2524668107 C	D
1071	1411 C	-17:35136599 2524668106 C	
1071 R	1412 T	-17:35136598 2524668105 T	
1071	1413 C	-17:35136597 2524668104 C	E
1070	1414 A	-17:35136596 2524668103 A	
1070 M	1415 T	-17:35136595 2524668102 T	
1070	1416 T	-17:35136594 2524668101 T	N
1069	1417 C	-17:35136438 2524667945 C	
1069 R	1418 T	-17:35136437 2524667944 T	
1069	1419 G	-17:35136436 2524667943 G	Q
1068	1420 G	-17:35136435 2524667942 G	
1068 S	1421 A	-17:35136434 2524667941 A	
1068	1422 T	-17:35136433 2524667940 T	I
1067	1423 G	-17:35136432 2524667939 G	
1067 S	1424 A	-17:35136431 2524667938 A	
1067	1425 C	-17:35136430 2524667937 C	V
1066	1426 C	-17:35136429 2524667936 C	
1066 W	1427 A	-17:35136428 2524667935 A	
1066	1428 C	-17:35136427 2524667934 C	V
1065	1429 A	-17:35136426 2524667933 A	
1065 L	1430 A	-17:35136425 2524667932 A	
1065	1431 A	-17:35136424 2524667931 A	F
1064	1432 G	-17:35136423 2524667930 G	
1064 A	1433 C	-17:35136422 2524667929 C	
1064	1434 G	-17:35136421 2524667928 G	R
1063	1435 C	-17:35136420 2524667927 C	
1063 S	1436 T	-17:35136419 2524667926 T	
1063	1437 G	-17:35136418 2524667925 G	Q
1062	1438 G	-17:35136417 2524667924 G	
1062 P	1439 G	-17:35136416 2524667923 G	
1062	1440 G	-17:35136415 2524667922 G	P
1061	1441 G	-17:35136414 2524667921 G	
1061 T	1442 T	-17:35136413 2524667920 T	
1061	1443 C	-17:35136412 2524667919 C	D
1060	1444 C	-17:35136411 2524667918 C	
1060 G	1445 C	-17:35136410 2524667917 C	
1060	1446 T	-17:35136409 2524667916 T	R
1059	1447 G	-17:35136408 2524667915 G	
1059 P	1448 G	-17:35136407 2524667914 G	
1059	1449 C	-17:35136406 2524667913 C	A
1058	1450 C	-17:35136405 2524667912 C	
1058 W	1451 A	-17:35136404 2524667911 A	
1058	1452 T	-17:35136403 2524667910 T	M
1057	1453 G	-17:35136402 2524667909 G	
1057 A	1454 C	-17:35136401 2524667908 C	
1057	1455 G	-17:35136400 2524667907 G	R
1056	1456 G	-17:35136399 2524667906 G	
1056 P	1457 G	-17:35136398 2524667905 G	
1056	1458 A	-17:35136397 2524667904 A	S
1055	1459 G	-17:35136396 2524667903 G	
1055 S	1460 A	-17:35136395 2524667902 A	
1055	1461 A	-17:35136394 2524667901 A	F
1054	1462 T	-17:35136393 2524667900 T	
1054 N	1463 T	-17:35136392 2524667899 T	
1054	1464 C	-17:35136391 2524667898 C	E
1053	1465 A	-17:35136390 2524667897 A	
1053 L	1466 G	-17:35136389 2524667896 G	
1053	1467 A	-17:35136388 2524667895 A	S
1052	1468 C	-17:35136387 2524667894 C	
1052 C	1469 A	-17:35136386 2524667893 A	
1052	1470 C	-17:35136385 2524667892 C	V
1051	1471 C	-17:35136384 2524667891 C	
1051 W	1472 A	-17:35136383 2524667890 A	
1051	1473 A	-17:35136382 2524667889 A	L
1050	1474 C	-17:35136381 2524667888 C	
1050 S	1475 T	-17:35136380 2524667887 T	
1050	1476 C	-17:35136379 2524667886 C	E
1049	1477 C	-17:35136378 2524667885 C	
1049 G	1478 C	-17:35136377 2524667884 C	
1049	1479 G	-17:35136376 2524667883 G	R
1048	1480 G	-17:35136375 2524667882 G	
1048 S	1481 A	-17:35136374 2524667881 A	
1048	1482 A	-17:35136373 2524667880 A	F
1047	1483 T	-17:35136372 2524667879 T	
1047 D	1484 C	-17:35136371 2524667878 C	
1047	1485 T	-17:35136370 2524667877 T	R
1046	1486 T	-17:35136369 2524667876 T	
1046 Q	1487 G	-17:35136368 2524667875 G	
1046	1488 G	-17:35136367 2524667874 G	P
1045	1489 C	-17:35136366 2524667873 C	
1045 G	1490 C	-17:35136365 2524667872 C	
1045	1491 G	-17:35136364 2524667871 G	R
1044	1492 A	-17:35136363 2524667870 A	
1044 V	1493 C	-17:35136362 2524667869 C	
1044	1494 A	-17:35136361 2524667868 A	C
1043	1495 T	-17:35136360 2524667867 T	
1043 N	1496 T	-17:35136359 2524667866 T	
1043	1497 C	-17:35136358 2524667865 C	E
1042	1498 A	-17:35136357 2524667864 A	
1042 L	1499 G	-17:35136356 2524667863 G	
1042	1500 A	-17:35136355 2524667862 A	S
1041	1501 G	-17:35136354 2524667861 G	
1041 T	1502 T	-17:35136353 2524667860 T	
1041	1503 C	-17:35136352 2524667859 C	D
1040	1504 A	-17:35136351 2524667858 A	
1040 L	1505 A	-17:35136350 2524667857 A	
1040	1506 T	-17:35136349 2524667856 T	I
1039	1507 C	-17:35136348 2524667855 C	
1039 *	1508 A	-17:35136347 2524667854 A	
1039	1509 T	-17:35136346 2524667853 T	M
1038	1510 C	-17:35136345 2524667852 C	
1038 G	1511 C	-17:35136344 2524667851 C	
1038	1512 A	-17:35136343 2524667850 A	W
1037	1513 A	-17:35136342 2524667849 A	
1037 V	1514 C	-17:35136341 2524667848 C	
1037	1515 A	-17:35135632 2524667139 A	C
1036	1516 T	-17:35135631 2524667138 T	
1036 N	1517 T	-17:35135630 2524667137 T	
1036	1518 T	-17:35135629 2524667136 T	K
1035	1519 G	-17:35135628 2524667135 G	
1035 S	1520 A	-17:35135627 2524667134 A	
1035	1521 C	-17:35135626 2524667133 C	V
1034	1522 C	-17:35135625 2524667132 C	
1034 W	1523 A	-17:35135624 2524667131 A	
1034	1524 T	-17:35135623 2524667130 T	M
1033	1525 G	-17:35135622 2524667129 G	
1033 S	1526 A	-17:35135621 2524667128 A	
1033	1527 T	-17:35135620 2524667127 T	I
1032	1528 C	-17:35135619 2524667126 C	
1032 *	1529 A	-17:35135618 2524667125 A	
1032	1530 T	-17:35135617 2524667124 T	M
1031	1531 G	-17:35135616 2524667123 G	
1031 T	1532 T	-17:35135615 2524667122 T	
1031	1533 A	-17:35135614 2524667121 A	Y
1030	1534 G	-17:35135613 2524667120 G	
1030 S	1535 A	-17:35135612 2524667119 A	
1030	1536 C	-17:35135611 2524667118 C	V
1029	1537 A	-17:35135610 2524667117 A	
1029 M	1538 T	-17:35135609 2524667116 T	
1029	1539 C	-17:35135608 2524667115 C	D
1028	1540 A	-17:35135607 2524667114 A	
1028 L	1541 A	-17:35135606 2524667113 A	
1028	1542 T	-17:35135605 2524667112 T	I
1027	1543 G	-17:35135604 2524667111 G	
1027 P	1544 G	-17:35135603 2524667110 G	
1027	1545 T	-17:35135602 2524667109 T	T
1026	1546 G	-17:35135601 2524667108 G	
1026 A	1547 C	-17:35135600 2524667107 C	
1026	1548 A	-17:35135599 2524667106 A	C
1025	1549 G	-17:35135598 2524667105 G	
1025 S	1550 A	-17:35135597 2524667104 A	
1025	1551 T	-17:35135596 2524667103 T	I
1024	1552 G	-17:35135595 2524667102 G	
1024 P	1553 G	-17:35135594 2524667101 G	
1024	1554 G	-17:35135593 2524667100 G	P
1023	1555 G	-17:35135592 2524667099 G	
1023 P	1556 G	-17:35135591 2524667098 G	
1023	1557 G	-17:35135590 2524667097 G	P
1022	1558 C	-17:35135589 2524667096 C	
1022 S	1559 T	-17:35135588 2524667095 T	
1022	1560 G	-17:35135587 2524667094 G	Q
1021	1561 G	-17:35135586 2524667093 G	
1021 P	1562 G	-17:35135585 2524667092 G	
1021	1563 G	-17:35135584 2524667091 G	P
1020	1564 C	-17:35135583 2524667090 C	
1020 C	1565 A	-17:35135582 2524667089 A	
1020	1566 G	-17:35135581 2524667088 G	L
1019	1567 C	-17:35135580 2524667087 C	
1019 G	1568 C	-17:35135579 2524667086 C	
1019	1569 G	-17:35135578 2524667085 G	R
1018	1570 C	-17:35135577 2524667084 C	
1018 S	1571 T	-17:35135576 2524667083 T	
1018	1572 C	-17:35135575 2524667082 C	E
1017	1573 C	-17:35135574 2524667081 C	
1017 G	1574 C	-17:35135573 2524667080 C	
1017	1575 C	-17:35135572 2524667079 C	G
1016	1576 C	-17:35135571 2524667078 C	
1016 R	1577 T	-17:35135570 2524667077 T	
1016	1578 T	-17:35135569 2524667076 T	K
1015	1579 T	-17:35135568 2524667075 T	
1015 K	1580 T	-17:35135567 2524667074 T	
1015	1581 C	-17:35135566 2524667073 C	E
1014	1582 C	-17:35135565 2524667072 C	
1014 W	1583 A	-17:35135564 2524667071 A	
1014	1584 G	-17:35135563 2524667070 G	L
1013	1585 C	-17:35135562 2524667069 C	
1013 C	1586 A	-17:35135561 2524667068 A	
1013	1587 G	-17:35135560 2524667067 G	L
1012	1588 G	-17:35135559 2524667066 G	
1012 T	1589 T	-17:35135558 2524667065 T	
1012	1590 C	-17:35135557 2524667064 C	D
1011	1591 A	-17:35135556 2524667063 A	
1011 L	1592 G	-17:35135555 2524667062 G	
1011	1593 G	-17:35135554 2524667061 G	P
1010	1594 G	-17:35135553 2524667060 G	
1010 S	1595 A	-17:35135552 2524667059 A	
1010	1596 T	-17:35135551 2524667058 T	I
1009	1597 C	-17:35135550 2524667057 C	
1009 R	1598 T	-17:35135549 2524667056 T	
1009	1599 C	-17:35135548 2524667055 C	E
1008	1600 C	-17:35135547 2524667054 C	
1008 G	1601 C	-17:35135546 2524667053 C	
1008	1602 G	-17:35135545 2524667052 G	R
1007	1603 G	-17:35135544 2524667051 G	
1007 P	1604 G	-17:35135543 2524667050 G	
1007	1605 C	-17:35135542 2524667049 C	A
1006	1606 T	-17:35135541 2524667048 T	
1006 Q	1607 G	-17:35135540 2524667047 G	
1006	1608 G	-17:35135539 2524667046 G	P
1005	1609 G	-17:35135538 2524667045 G	
1005 S	1610 A	-17:35135537 2524667044 A	
1005	1611 T	-17:35135536 2524667043 T	I
1004	1612 C	-17:35135535 2524667042 C	
1004 G	1613 C	-17:35135534 2524667041 C	
1004	1614 C	-17:35135533 2524667040 C	G
1003	1615 A	-17:35135532 2524667039 A	
1003 M	1616 T	-17:35135531 2524667038 T	
1003	1617 C	-17:35135530 2524667037 C	D
1002	1618 G	-17:35135529 2524667036 G	
1002 T	1619 T	-17:35135528 2524667035 T	
1002	1620 A	-17:35135527 2524667034 A	Y
1001	1621 A	-17:35135526 2524667033 A	
1001 L	1622 G	-17:35135525 2524667032 G	
1001	1623 G	-17:35135524 2524667031 G	P
1000	1624 T	-17:35135523 2524667030 T	
1000 N	1625 T	-17:35135522 2524667029 T	
1000	1626 T	-17:35135521 2524667028 T	K
999	1627 G	-17:35135520 2524667027 G	
999 P	1628 G	-17:35135519 2524667026 G	
999	1629 C	-17:35135518 2524667025 C	A
998	1630 C	-17:35135517 2524667024 C	
998 G	1631 C	-17:35135516 2524667023 C	
998	1632 C	-17:35135515 2524667022 C	G
997	1633 A	-17:35135514 2524667021 A	
997 L	1634 A	-17:35135513 2524667020 A	
997	1635 A	-17:35135512 2524667019 A	F
996	1636 A	-17:35135511 2524667018 A	
996 L	1637 G	-17:35135510 2524667017 G	
996	1638 T	-17:35135509 2524667016 T	T
995	1639 C	-17:35135508 2524667015 C	
995 *	1640 A	-17:35135507 2524667014 A	
995	1641 T	-17:35135506 2524667013 T	M
994	1642 C	-17:35135505 2524667012 C	
994 *	1643 A	-17:35135504 2524667011 A	
994	1644 G	-17:35135503 2524667010 G	L
993	1645 C	-17:35135502 2524667009 C	
993 S	1646 T	-17:35135501 2524667008 T	
993	1647 C	-17:35135500 2524667007 C	E
992	1648 C	-17:35135499 2524667006 C	
992 G	1649 C	-17:35135498 2524667005 C	
992	1650 A	-17:35135497 2524667004 A	W
991	1651 C	-17:35135496 2524667003 C	
991 C	1652 A	-17:35135495 2524667002 A	
991	1653 C	-17:35135494 2524667001 C	V
990	1654 A	-17:35135493 2524667000 A	
990 L	1655 G	-17:35135492 2524666999 G	
990	1656 T	-17:35135491 2524666998 T	T
989	1657 C	-17:35135490 2524666997 C	
989 *	1658 A	-17:35135489 2524666996 A	
989	1659 C	-17:35135488 2524666995 C	V
988	1660 A	-17:35135487 2524666994 A	
988 V	1661 C	-17:35135486 2524666993 C	
988	1662 C	-17:35135181 2524666688 C	G
987	1663 A	-17:35135180 2524666687 A	
987 M	1664 T	-17:35135179 2524666686 T	
987	1665 A	-17:35135178 2524666685 A	Y
986	1666 A	-17:35135177 2524666684 A	
986 V	1667 C	-17:35135176 2524666683 C	
986	1668 T	-17:35135175 2524666682 T	S
985	1669 C	-17:35135174 2524666681 C	
985 G	1670 C	-17:35135173 2524666680 C	
985	1671 A	-17:35135172 2524666679 A	W
984	1672 C	-17:35135171 2524666678 C	
984 C	1673 A	-17:35135170 2524666677 A	
984	1674 C	-17:35135169 2524666676 C	V
983	1675 A	-17:35135168 2524666675 A	
983 M	1676 T	-17:35135167 2524666674 T	
983	1677 C	-17:35135166 2524666673 C	D
982	1678 A	-17:35135165 2524666672 A	
982 V	1679 C	-17:35135164 2524666671 C	
982	1680 T	-17:35135163 2524666670 T	S
981	1681 C	-17:35135162 2524666669 C	
981 R	1682 T	-17:35135161 2524666668 T	
981	1683 G	-17:35135160 2524666667 G	Q
980	1684 G	-17:35135159 2524666666 G	
980 T	1685 T	-17:35135158 2524666665 T	
980	1686 G	-17:35135157 2524666664 G	H
979	1687 G	-17:35135156 2524666663 G	
979 P	1688 G	-17:35135155 2524666662 G	
979	1689 T	-17:35135154 2524666661 T	T
978	1690 G	-17:35135153 2524666660 G	
978 S	1691 A	-17:35135152 2524666659 A	
978	1692 A	-17:35135151 2524666658 A	F
977	1693 C	-17:35135150 2524666657 C	
977 G	1694 C	-17:35135149 2524666656 C	
977	1695 G	-17:35135148 2524666655 G	R
976	1696 C	-17:35135147 2524666654 C	
976 G	1697 C	-17:35135146 2524666653 C	
976	1698 G	-17:35135145 2524666652 G	R
975	1699 G	-17:35135144 2524666651 G	
975 A	1700 C	-17:35135143 2524666650 C	
975	1701 G	-17:35135142 2524666649 G	R
974	1702 G	-17:35135141 2524666648 G	
974 S	1703 A	-17:35135140 2524666647 A	
974	1704 G	-17:35135139 2524666646 G	L
973	1705 A	-17:35135138 2524666645 A	
973 F	1706 A	-17:35135137 2524666644 A	
973	1707 T	-17:35135136 2524666643 T	I
972	1708 G	-17:35135135 2524666642 G	
972 P	1709 G	-17:35135134 2524666641 G	
972	1710 A	-17:35135133 2524666640 A	S
971	1711 C	-17:35135132 2524666639 C	
971 S	1712 T	-17:35135131 2524666638 T	
971	1713 C	-17:35135130 2524666637 C	E
970	1714 C	-17:35135129 2524666636 C	
970 W	1715 A	-17:35135128 2524666635 A	
970	1716 G	-17:35135127 2524666634 G	L
969	1717 C	-17:35135126 2524666633 C	
969 R	1718 G	-17:35135125 2524666632 G	
969	1719 C	-17:35135124 2524666631 C	A
968	1720 C	-17:35135123 2524666630 C	
968 W	1721 A	-17:35135122 2524666629 A	
968	1722 T	-17:35135121 2524666628 T	M
967	1723 C	-17:35135120 2524666627 C	
967 G	1724 C	-17:35135119 2524666626 C	
967	1725 A	-17:35135118 2524666625 A	W
966	1726 C	-17:35135117 2524666624 C	
966 S	1727 T	-17:35135116 2524666623 T	
966	1728 T	-17:35135115 2524666622 T	K
965	1729 G	-17:35135114 2524666621 G	
965 S	1730 A	-17:35135113 2524666620 A	
965	1731 T	-17:35135112 2524666619 T	I
964	1732 G	-17:35135111 2524666618 G	
964 P	1733 G	-17:35135110 2524666617 G	
964	1734 G	-17:35135109 2524666616 G	P
963	1735 C	-17:35135108 2524666615 C	
963 C	1736 A	-17:35135107 2524666614 A	
963	1737 C	-17:35135106 2524666613 C	V
962	1738 C	-17:35134983 2524666490 C	
962 R	1739 T	-17:35134982 2524666489 T	
962	1740 T	-17:35134981 2524666488 T	K
961	1741 G	-17:35134980 2524666487 G	
961 A	1742 C	-17:35134979 2524666486 C	
961	1743 C	-17:35134978 2524666485 C	G
960	1744 C	-17:35134977 2524666484 C	
960 G	1745 C	-17:35134976 2524666483 C	
960	1746 C	-17:35134975 2524666482 C	G
959	1747 A	-17:35134974 2524666481 A	
959 M	1748 T	-17:35134973 2524666480 T	
959	1749 C	-17:35134972 2524666479 C	D
958	1750 T	-17:35134971 2524666478 T	
958 Q	1751 G	-17:35134970 2524666477 G	
958	1752 C	-17:35134969 2524666476 C	A
957	1753 A	-17:35134968 2524666475 A	
957 M	1754 T	-17:35134967 2524666474 T	
957	1755 G	-17:35134966 2524666473 G	H
956	1756 G	-17:35134965 2524666472 G	
956 T	1757 T	-17:35134964 2524666471 T	
956	1758 A	-17:35134963 2524666470 A	Y
955	1759 C	-17:35134962 2524666469 C	
955 S	1760 T	-17:35134961 2524666468 T	
955	1761 C	-17:35134960 2524666467 C	E
954	1762 T	-17:35134959 2524666466 T	
954 Q	1763 G	-17:35134958 2524666465 G	
954	1764 T	-17:35134957 2524666464 T	T
953	1765 C	-17:35134956 2524666463 C	
953 R	1766 T	-17:35134955 2524666462 T	
953	1767 C	-17:35134954 2524666461 C	E
952	1768 G	-17:35134953 2524666460 G	
952 T	1769 T	-17:35134952 2524666459 T	
952	1770 C	-17:35134951 2524666458 C	D
951	1771 A	-17:35134950 2524666457 A	
951 L	1772 A	-17:35134949 2524666456 A	
951	1773 T	-17:35134948 2524666455 T	I
950	1774 G	-17:35134947 2524666454 G	
950 T	1775 T	-17:35134946 2524666453 T	
950	1776 C	-17:35134945 2524666452 C	D
949	1777 C	-17:35134944 2524666451 C	
949 W	1778 A	-17:35134943 2524666450 A	
949	1779 G	-17:35134942 2524666449 G	L
948	1780 C	-17:35134941 2524666448 C	
948 C	1781 A	-17:35134940 2524666447 A	
948	1782 G	-17:35134939 2524666446 G	L
947	1783 C	-17:35134938 2524666445 C	
947 G	1784 C	-17:35134937 2524666444 C	
947	1785 G	-17:35134936 2524666443 G	R
946	1786 A	-17:35134935 2524666442 A	
946 L	1787 G	-17:35134934 2524666441 G	
946	1788 C	-17:35134933 2524666440 C	A
945	1789 C	-17:35134932 2524666439 C	
945 W	1790 A	-17:35134931 2524666438 A	
945	1791 G	-17:35134930 2524666437 G	L
944	1792 C	-17:35134929 2524666436 C	
944 G	1793 C	-17:35134928 2524666435 C	
944	1794 C	-17:35134927 2524666434 C	G
943	1795 G	-17:35134926 2524666433 G	
943 S	1796 A	-17:35134925 2524666432 A	
943	1797 A	-17:35134924 2524666431 A	F
942	1798 G	-17:35134923 2524666430 G	
942 T	1799 T	-17:35134922 2524666429 T	
942	1800 C	-17:35134921 2524666428 C	D
941	1801 T	-17:35134920 2524666427 T	
941 Q	1802 G	-17:35134919 2524666426 G	
941	1803 T	-17:35134918 2524666425 T	T
940	1804 A	-17:35134917 2524666424 A	
940 L	1805 A	-17:35134916 2524666423 A	
940	1806 T	-17:35134915 2524666422 T	I
939	1807 T	-17:35134914 2524666421 T	
939 K	1808 T	-17:35134913 2524666420 T	
939	1809 T	-17:35134912 2524666419 T	K
938	1810 G	-17:35134911 2524666418 G	
938 S	1811 A	-17:35134910 2524666417 A	
938	1812 C	-17:35134909 2524666416 C	V
937	1813 A	-17:35134908 2524666415 A	
937 M	1814 T	-17:35134907 2524666414 T	
937	1815 G	-17:35134906 2524666413 G	H
936	1816 G	-17:35134905 2524666412 G	
936 T	1817 T	-17:35134904 2524666411 T	
936	1818 T	-17:35134903 2524666410 T	N
935	1819 G	-17:35134902 2524666409 G	
935 P	1820 G	-17:35134901 2524666408 G	
935	1821 G	-17:35134900 2524666407 G	P
934	1822 A	-17:35134899 2524666406 A	
934 V	1823 C	-17:35134898 2524666405 C	
934	1824 T	-17:35134897 2524666404 T	S
933	1825 C	-17:35134896 2524666403 C	
933 R	1826 T	-17:35134895 2524666402 T	
933	1827 T	-17:35134894 2524666401 T	K
932	1828 G	-17:35134893 2524666400 G	
932 S	1829 A	-17:35134892 2524666399 A	
932	1830 C	-17:35134891 2524666398 C	V
931	1831 C	-17:35134890 2524666397 C	
931 W	1832 A	-17:35134889 2524666396 A	
931	1833 G	-17:35134888 2524666395 G	L
930	1834 C	-17:35134887 2524666394 C	
930 C	1835 A	-17:35134886 2524666393 A	
930	1836 C	-17:35134885 2524666392 C	V
929	1837 G	-17:35134884 2524666391 G	
929 T	1838 T	-17:35134883 2524666390 T	
929	1839 T	-17:35134882 2524666389 T	N
928	1840 C	-17:35134881 2524666388 C	
928 G	1841 C	-17:35134880 2524666387 C	
928	1842 G	-17:35134879 2524666386 G	R
927	1843 A	-17:35134878 2524666385 A	
927 L	1844 G	-17:35134877 2524666384 G	
927	1845 C	-17:35134876 2524666383 C	A
926	1846 G	-17:35134875 2524666382 G	
926 P	1847 G	-17:35134874 2524666381 G	
926	1848 C	-17:35134873 2524666380 C	A
925	1849 C	-17:35134872 2524666379 C	
925 W	1850 A	-17:35134871 2524666378 A	
925	1851 A	-17:35134870 2524666377 A	L
924	1852 G	-17:35134869 2524666376 G	
924 T	1853 T	-17:35134868 2524666375 T	
924	1854 C	-17:35134867 2524666374 C	D
923	1855 C	-17:35134866 2524666373 C	
923 G	1856 C	-17:35134865 2524666372 C	
923	1857 T	-17:35134864 2524666371 T	R
922	1858 G	-17:35134863 2524666370 G	
922 T	1859 T	-17:35134862 2524666369 T	
922	1860 G	-17:35134861 2524666368 G	H
921	1861 T	-17:35134860 2524666367 T	
921 Y	1862 A	-17:35134859 2524666366 A	
921	1863 C	-17:35134858 2524666365 C	V
920	1864 G	-17:35134857 2524666364 G	
920 S	1865 A	-17:35134856 2524666363 A	
920	1866 G	-17:35134855 2524666362 G	L
919	1867 C	-17:35134854 2524666361 C	
919 G	1868 C	-17:35134853 2524666360 C	
919	1869 G	-17:35134852 2524666359 G	R
918	1870 C	-17:35134851 2524666358 C	
918 C	1871 A	-17:35134850 2524666357 A	
918	1872 C	-17:35134849 2524666356 C	V
917	1873 A	-17:35134848 2524666355 A	
917 M	1874 T	-17:35134847 2524666354 T	
917	1875 C	-17:35134846 2524666353 C	D
916	1876 C	-17:35134845 2524666352 C	
916 R	1877 T	-17:35134844 2524666351 T	
916	1878 C	-17:35134843 2524666350 C	E
915	1879 C	-17:35134842 2524666349 C	
915 W	1880 A	-17:35134841 2524666348 A	
915	1881 G	-17:35134840 2524666347 G	L
914	1882 G	-17:35134839 2524666346 G	
914 T	1883 T	-17:35134838 2524666345 T	
914	1884 A	-17:35134837 2524666344 A	Y
913	1885 G	-17:35134836 2524666343 G	
913 A	1886 C	-17:35134835 2524666342 C	
913	1887 T	-17:35134834 2524666341 T	S
912	1888 C	-17:35134833 2524666340 C	
912 *	1889 A	-17:35134832 2524666339 A	
912	1890 T	-17:35134831 2524666338 T	M
911	1891 C	-17:35134830 2524666337 C	
911 G	1892 C	-17:35134829 2524666336 C	
911	1893 C	-17:35134828 2524666335 C	G
910	1894 C	-17:35134690 2524666197 C	
910 R	1895 T	-17:35134689 2524666196 T	
910	1896 T	-17:35134688 2524666195 T	K
909	1897 G	-17:35134687 2524666194 G	
909 P	1898 G	-17:35134686 2524666193 G	
909	1899 C	-17:35134685 2524666192 C	A
908	1900 A	-17:35134684 2524666191 A	
908 L	1901 A	-17:35134683 2524666190 A	
908	1902 T	-17:35134682 2524666189 T	I
907	1903 C	-17:35134681 2524666188 C	
907 R	1904 T	-17:35134680 2524666187 T	
907	1905 G	-17:35134679 2524666186 G	Q
906	1906 C	-17:35134678 2524666185 C	
906 C	1907 A	-17:35134677 2524666184 A	
906	1908 T	-17:35134676 2524666183 T	M
905	1909 A	-17:35134675 2524666182 A	
905 V	1910 C	-17:35134674 2524666181 C	
905	1911 A	-17:35134673 2524666180 A	C
904	1912 C	-17:35134672 2524666179 C	
904 G	1913 C	-17:35134671 2524666178 C	
904	1914 A	-17:35134670 2524666177 A	W
903	1915 G	-17:35134669 2524666176 G	
903 T	1916 T	-17:35134668 2524666175 T	
903	1917 T	-17:35134667 2524666174 T	N
902	1918 C	-17:35134666 2524666173 C	
902 *	1919 A	-17:35134665 2524666172 A	
902	1920 G	-17:35134664 2524666171 G	L
901	1921 C	-17:35134663 2524666170 C	
901 C	1922 A	-17:35134662 2524666169 A	
901	1923 G	-17:35134661 2524666168 G	L
900	1924 G	-17:35134660 2524666167 G	
900 T	1925 T	-17:35134659 2524666166 T	
900	1926 C	-17:35134658 2524666165 C	D
899	1927 C	-17:35134657 2524666164 C	
899 R	1928 T	-17:35134656 2524666163 T	
899	1929 G	-17:35134655 2524666162 G	Q
898	1930 G	-17:35134654 2524666161 G	
898 P	1931 G	-17:35134653 2524666160 G	
898	1932 A	-17:35134652 2524666159 A	S
897	1933 G	-17:35134651 2524666158 G	
897 A	1934 C	-17:35134650 2524666157 C	
897	1935 C	-17:35134649 2524666156 C	G
896	1936 C	-17:35134648 2524666155 C	
896 W	1937 A	-17:35134647 2524666154 A	
896	1938 G	-17:35134646 2524666153 G	L
895	1939 G	-17:35134645 2524666152 G	
895 A	1940 C	-17:35134644 2524666151 C	
895	1941 G	-17:35134643 2524666150 G	R
894	1942 T	-17:35134642 2524666149 T	
894 D	1943 C	-17:35134641 2524666148 C	
894	1944 C	-17:35134640 2524666147 C	G
893	1945 G	-17:35134639 2524666146 G	
893 A	1946 C	-17:35134638 2524666145 C	
893	1947 G	-17:35134637 2524666144 G	R
892	1948 G	-17:35134636 2524666143 G	
892 T	1949 T	-17:35134635 2524666142 T	
892	1950 T	-17:35134634 2524666141 T	N
891	1951 T	-17:35134633 2524666140 T	
891 K	1952 T	-17:35134632 2524666139 T	
891	1953 C	-17:35134631 2524666138 C	E
890	1954 C	-17:35134630 2524666137 C	
890 G	1955 C	-17:35134629 2524666136 C	
890	1956 G	-17:35134628 2524666135 G	R
889	1957 G	-17:35134627 2524666134 G	
889 S	1958 A	-17:35134626 2524666133 A	
889	1959 C	-17:35134625 2524666132 C	V
888	1960 A	-17:35134624 2524666131 A	
888 M	1961 T	-17:35134623 2524666130 T	
888	1962 G	-17:35134622 2524666129 G	H
887	1963 G	-17:35134621 2524666128 G	
887 T	1964 T	-17:35134620 2524666127 T	
887	1965 C	-17:35134619 2524666126 C	D
886	1966 T	-17:35134618 2524666125 T	
886 *	1967 A	-17:35134617 2524666124 A	
886	1968 A	-17:35134616 2524666123 A	L
885	1969 G	-17:35134615 2524666122 G	
885 S	1970 A	-17:35134614 2524666121 A	
885	1971 G	-17:35134613 2524666120 G	L
884	1972 G	-17:35134612 2524666119 G	
884 A	1973 C	-17:35134611 2524666118 C	
884	1974 A	-17:35134610 2524666117 A	C
883	1975 G	-17:35134609 2524666116 G	
883 A	1976 C	-17:35134608 2524666115 C	
883	1977 C	-17:35134607 2524666114 C	G
882	1978 A	-17:35134606 2524666113 A	
882 M	1979 T	-17:35134605 2524666112 T	
882	1980 A	-17:35134604 2524666111 A	Y
881	1981 G	-17:35134603 2524666110 G	
881 P	1982 G	-17:35134602 2524666109 G	
881	1983 G	-17:35134601 2524666108 G	P
880	1984 C	-17:35134600 2524666107 C	
880 C	1985 A	-17:35134599 2524666106 A	
880	1986 T	-17:35134598 2524666105 T	M
879	1987 A	-17:35134597 2524666104 A	
879 L	1988 A	-17:35134596 2524666103 A	
879	1989 G	-17:35134595 2524666102 G	L
878	1990 C	-17:35134594 2524666101 C	
878 S	1991 T	-17:35134593 2524666100 T	
878	1992 G	-17:35134592 2524666099 G	Q
877	1993 T	-17:35134591 2524666098 T	
877 H	1994 G	-17:35134590 2524666097 G	
877	1995 T	-17:35134589 2524666096 T	T
876	1996 C	-17:35134588 2524666095 C	
876 *	1997 A	-17:35134587 2524666094 A	
876	1998 C	-17:35134586 2524666093 C	V
875	1999 C	-17:35134585 2524666092 C	
875 W	2000 A	-17:35134584 2524666091 A	
875	2001 G	-17:35134583 2524666090 G	L
874	2002 C	-17:35134582 2524666089 C	
874 S	2003 T	-17:35134581 2524666088 T	
874	2004 G	-17:35134580 2524666087 G	Q
873	2005 C	-17:35134579 2524666086 C	
873 C	2006 A	-17:35134578 2524666085 A	
873	2007 C	-17:35134577 2524666084 C	V
872	2008 C	-17:35134576 2524666083 C	
872 R	2009 G	-17:35134575 2524666082 G	
872	2010 T	-17:35134574 2524666081 T	T
871	2011 G	-17:35134573 2524666080 G	
871 P	2012 G	-17:35134572 2524666079 G	
871	2013 A	-17:35134571 2524666078 A	S
870	2014 T	-17:35134570 2524666077 T	
870 H	2015 G	-17:35134569 2524666076 G	
870	2016 T	-17:35134568 2524666075 T	T
869	2017 C	-17:35134567 2524666074 C	
869 *	2018 A	-17:35134566 2524666073 A	
869	2019 G	-17:35134565 2524666072 G	L
868	2020 G	-17:35134564 2524666071 G	
868 A	2021 C	-17:35134563 2524666070 C	
868	2022 A	-17:35134562 2524666069 A	C
867	2023 G	-17:35134561 2524666068 G	
867 S	2024 A	-17:35134560 2524666067 A	
867	2025 T	-17:35134559 2524666066 T	I
866	2026 G	-17:35134558 2524666065 G	
866 A	2027 C	-17:35134557 2524666064 C	
866	2028 C	-17:35134556 2524666063 C	G
865	2029 C	-17:35134555 2524666062 C	
865 W	2030 A	-17:35134554 2524666061 A	
865	2031 G	-17:35134553 2524666060 G	L
864	2032 A	-17:35134552 2524666059 A	
864 F	2033 A	-17:35134551 2524666058 A	
864	2034 G	-17:35134550 2524666057 G	L
863	2035 G	-17:35134549 2524666056 G	
863 A	2036 C	-17:35134548 2524666055 C	
863	2037 G	-17:35134547 2524666054 G	R
862	2038 G	-17:35134546 2524666053 G	
862 P	2039 G	-17:35134545 2524666052 G	
862	2040 A	-17:35134544 2524666051 A	S
861	2041 G	-17:35134543 2524666050 G	
861 S	2042 A	-17:35134542 2524666049 A	
861	2043 C	-17:35134541 2524666048 C	V
860	2044 A	-17:35134540 2524666047 A	
860 M	2045 T	-17:35134539 2524666046 T	
860	2046 A	-17:35134538 2524666045 A	Y
859	2047 T	-17:35134537 2524666044 T	
859 H	2048 G	-17:35134536 2524666043 G	
859	2049 G	-17:35134535 2524666042 G	P
858	2050 G	-17:35134534 2524666041 G	
858 P	2051 G	-17:35134533 2524666040 G	
858	2052 A	-17:35134532 2524666039 A	S
857	2053 G	-17:35134531 2524666038 G	
857 A	2054 C	-17:35134530 2524666037 C	
857	2055 C	-17:35134529 2524666036 C	G
856	2056 C	-17:35134528 2524666035 C	
856 W	2057 A	-17:35134527 2524666034 A	
856	2058 C	-17:35134526 2524666033 C	V
855	2059 A	-17:35134525 2524666032 A	
855 V	2060 C	-17:35134524 2524666031 C	
855	2061 C	-17:35134523 2524666030 C	G
854	2062 A	-17:35134522 2524666029 A	
854 L	2063 G	-17:35134521 2524666028 G	
854	2064 C	-17:35134520 2524666027 C	A
853	2065 C	-17:35134519 2524666026 C	
853 W	2066 A	-17:35134518 2524666025 A	
853	2067 T	-17:35134517 2524666024 T	M
852	2068 C	-17:35134516 2524666023 C	
852 *	2069 A	-17:35134515 2524666022 A	
852	2070 C	-17:35134514 2524666021 C	V
851	2071 G	-17:35134513 2524666020 G	
851 T	2072 T	-17:35134512 2524666019 T	
851	2073 A	-17:35134511 2524666018 A	Y
850	2074 T	-17:35134510 2524666017 T	
850 H	2075 G	-17:35134509 2524666016 G	
850	2076 C	-17:35134508 2524666015 C	A
849	2077 T	-17:35134507 2524666014 T	
849 K	2078 T	-17:35134506 2524666013 T	
849	2079 C	-17:35134505 2524666012 C	E
848	2080 G	-17:35133789 2524665296 G	
848 T	2081 T	-17:35133788 2524665295 T	
848	2082 C	-17:35133787 2524665294 C	D
847	2083 T	-17:35133786 2524665293 T	
847 *	2084 A	-17:35133785 2524665292 A	
847	2085 A	-17:35133784 2524665291 A	L
846	2086 G	-17:35133783 2524665290 G	
846 S	2087 A	-17:35133782 2524665289 A	
846	2088 T	-17:35133781 2524665288 T	I
845	2089 T	-17:35133780 2524665287 T	
845 K	2090 T	-17:35133779 2524665286 T	
845	2091 C	-17:35133778 2524665285 C	E
844	2092 T	-17:35133777 2524665284 T	
844 K	2093 T	-17:35133776 2524665283 T	
844	2094 T	-17:35133775 2524665282 T	K
843	2095 G	-17:35133774 2524665281 G	
843 T	2096 T	-17:35133773 2524665280 T	
843	2097 T	-17:35133772 2524665279 T	N
842	2098 G	-17:35133771 2524665278 G	
842 P	2099 G	-17:35133770 2524665277 G	
842	2100 C	-17:35133769 2524665276 C	A
841	2101 T	-17:35133768 2524665275 T	
841 K	2102 T	-17:35133767 2524665274 T	
841	2103 T	-17:35133766 2524665273 T	K
840	2104 G	-17:35133765 2524665272 G	
840 P	2105 G	-17:35133764 2524665271 G	
840	2106 G	-17:35133763 2524665270 G	P
839	2107 G	-17:35133762 2524665269 G	
839 P	2108 G	-17:35133761 2524665268 G	
839	2109 A	-17:35133760 2524665267 A	S
838	2110 T	-17:35133759 2524665266 T	
838 H	2111 G	-17:35133758 2524665265 G	
838	2112 T	-17:35133757 2524665264 T	T
837	2113 G	-17:35133756 2524665263 G	
837 T	2114 T	-17:35133755 2524665262 T	
837	2115 T	-17:35133754 2524665261 T	N
836	2116 T	-17:35133753 2524665260 T	
836 K	2117 T	-17:35133752 2524665259 T	
836	2118 C	-17:35133751 2524665258 C	E
835	2119 C	-17:35133750 2524665257 C	
835 G	2120 C	-17:35133749 2524665256 C	
835	2121 T	-17:35133748 2524665255 T	R
834	2122 C	-17:35133747 2524665254 C	
834 *	2123 A	-17:35133746 2524665253 A	
834	2124 A	-17:35133745 2524665252 A	L
833	2125 C	-17:35133744 2524665251 C	
833 C	2126 A	-17:35133743 2524665250 A	
833	2127 C	-17:35133742 2524665249 C	V
832	2128 T	-17:35133741 2524665248 T	
832 K	2129 T	-17:35133740 2524665247 T	
832	2130 T	-17:35133739 2524665246 T	K
831	2131 G	-17:35133738 2524665245 G	
831 S	2132 A	-17:35133737 2524665244 A	
831	2133 T	-17:35133736 2524665243 T	I
830	2134 G	-17:35133735 2524665242 G	
830 P	2135 G	-17:35133734 2524665241 G	
830	2136 C	-17:35133733 2524665240 C	A
829	2137 C	-17:35133732 2524665239 C	
829 W	2138 A	-17:35133731 2524665238 A	
829	2139 C	-17:35133730 2524665237 C	V
828	2140 T	-17:35133729 2524665236 T	
828 Q	2141 G	-17:35133728 2524665235 G	
828	2142 G	-17:35133727 2524665234 G	P
827	2143 A	-17:35133726 2524665233 A	
827 F	2144 A	-17:35133725 2524665232 A	
827	2145 T	-17:35133724 2524665231 T	I
826	2146 T	-17:35133723 2524665230 T	
826 K	2147 T	-17:35133722 2524665229 T	
826	2148 T	-17:35133721 2524665228 T	K
825	2149 C	-17:35133720 2524665227 C	
825 *	2150 A	-17:35133719 2524665226 A	
825	2151 C	-17:35133718 2524665225 C	V
824	2152 A	-17:35133717 2524665224 A	
824 M	2153 T	-17:35133716 2524665223 T	
824	2154 T	-17:35133715 2524665222 T	N
823	2155 C	-17:35133714 2524665221 C	
823 R	2156 T	-17:35133713 2524665220 T	
823	2157 C	-17:35133712 2524665219 C	E
822	2158 C	-17:35133711 2524665218 C	
822 G	2159 C	-17:35133710 2524665217 C	
822	2160 C	-17:35133709 2524665216 C	G
821	2161 A	-17:35133708 2524665215 A	
821 M	2162 T	-17:35133707 2524665214 T	
821	2163 C	-17:35133706 2524665213 C	D
820	2164 A	-17:35133705 2524665212 A	
820 L	2165 G	-17:35133704 2524665211 G	
820	2166 G	-17:35133703 2524665210 G	P
819	2167 G	-17:35133702 2524665209 G	
819 S	2168 A	-17:35133701 2524665208 A	
819	2169 T	-17:35133700 2524665207 T	I
818	2170 C	-17:35133699 2524665206 C	
818 G	2171 C	-17:35133698 2524665205 C	
818	2172 A	-17:35133697 2524665204 A	W
817	2173 G	-17:35133696 2524665203 G	
817 S	2174 A	-17:35133695 2524665202 A	
817	2175 T	-17:35133694 2524665201 T	I
816	2176 G	-17:35133693 2524665200 G	
816 A	2177 C	-17:35133692 2524665199 C	
816	2178 C	-17:35133691 2524665198 C	G
815	2179 C	-17:35133439 2524664946 C	
815 R	2180 T	-17:35133438 2524664945 T	
815	2181 T	-17:35133437 2524664944 T	K
814	2182 G	-17:35133436 2524664943 G	
814 T	2183 T	-17:35133435 2524664942 T	
814	2184 A	-17:35133434 2524664941 A	Y
813	2185 G	-17:35133433 2524664940 G	
813 S	2186 A	-17:35133432 2524664939 A	
813	2187 C	-17:35133431 2524664938 C	V
812	2188 T	-17:35133430 2524664937 T	
812 Q	2189 G	-17:35133429 2524664936 G	
812	2190 T	-17:35133428 2524664935 T	T
811	2191 G	-17:35133427 2524664934 G	
811 A	2192 C	-17:35133426 2524664933 C	
811	2193 C	-17:35133425 2524664932 C	G
810	2194 A	-17:35133424 2524664931 A	
810 L	2195 A	-17:35133423 2524664930 A	
810	2196 A	-17:35133422 2524664929 A	F
809	2197 A	-17:35133421 2524664928 A	
809 L	2198 G	-17:35133420 2524664927 G	
809	2199 C	-17:35133419 2524664926 C	A
808	2200 G	-17:35133418 2524664925 G	
808 A	2201 C	-17:35133417 2524664924 C	
808	2202 C	-17:35133416 2524664923 C	G
807	2203 A	-17:35133415 2524664922 A	
807 L	2204 G	-17:35133414 2524664921 G	
807	2205 A	-17:35133413 2524664920 A	S
806	2206 T	-17:35133412 2524664919 T	
806 D	2207 C	-17:35133411 2524664918 C	
806	2208 C	-17:35133410 2524664917 C	G
805	2209 A	-17:35133409 2524664916 A	
805 L	2210 A	-17:35133408 2524664915 A	
805	2211 G	-17:35133407 2524664914 G	L
804	2212 C	-17:35133406 2524664913 C	
804 C	2213 A	-17:35133405 2524664912 A	
804	2214 C	-17:35133404 2524664911 C	V
803	2215 C	-17:35133403 2524664910 C	
803 R	2216 T	-17:35133402 2524664909 T	
803	2217 T	-17:35133401 2524664908 T	K
802	2218 C	-17:35133400 2524664907 C	
802 *	2219 A	-17:35133399 2524664906 A	
802	2220 C	-17:35133398 2524664905 C	V
801	2221 C	-17:35133397 2524664904 C	
801 R	2222 T	-17:35133396 2524664903 T	
801	2223 T	-17:35133395 2524664902 T	K
800	2224 C	-17:35133394 2524664901 C	
800 G	2225 C	-17:35133393 2524664900 C	
800	2226 T	-17:35133392 2524664899 T	R
799	2227 C	-17:35133391 2524664898 C	
799 *	2228 A	-17:35133390 2524664897 A	
799	2229 G	-17:35133389 2524664896 G	L
798	2230 C	-17:35133388 2524664895 C	
798 S	2231 T	-17:35133387 2524664894 T	
798	2232 C	-17:35133386 2524664893 C	E
797	2233 C	-17:35133385 2524664892 C	
797 R	2234 G	-17:35133384 2524664891 G	
797	2235 T	-17:35133383 2524664890 T	T
796	2236 C	-17:35133382 2524664889 C	
796 R	2237 T	-17:35133381 2524664888 T	
796	2238 C	-17:35133380 2524664887 C	E
795	2239 T	-17:35133379 2524664886 T	
795 K	2240 T	-17:35133378 2524664885 T	
795	2241 T	-17:35133377 2524664884 T	K
794	2242 C	-17:35133376 2524664883 C	
794 *	2243 A	-17:35133375 2524664882 A	
794	2244 G	-17:35133374 2524664881 G	L
793	2245 G	-17:35133373 2524664880 G	
793 S	2246 A	-17:35133372 2524664879 A	
793	2247 T	-17:35133371 2524664878 T	I
792	2248 C	-17:35133370 2524664877 C	
792 G	2249 C	-17:35133369 2524664876 C	
792	2250 G	-17:35133368 2524664875 G	R
791	2251 C	-17:35133367 2524664874 C	
791 C	2252 A	-17:35133366 2524664873 A	
791	2253 T	-17:35133365 2524664872 T	M
790	2254 C	-17:35133364 2524664871 C	
790 R	2255 T	-17:35133363 2524664870 T	
790	2256 G	-17:35133362 2524664869 G	Q
789	2257 C	-17:35133361 2524664868 C	
789 R	2258 G	-17:35133360 2524664867 G	
789	2259 C	-17:35133359 2524664866 C	A
788	2260 C	-17:35133358 2524664865 C	
788 R	2261 T	-17:35133357 2524664864 T	
788	2262 G	-17:35133356 2524664863 G	Q
787	2263 G	-17:35133355 2524664862 G	
787 T	2264 T	-17:35133354 2524664861 T	
787	2265 T	-17:35133353 2524664860 T	N
786	2266 G	-17:35133352 2524664859 G	
786 P	2267 G	-17:35133351 2524664858 G	
786	2268 G	-17:35133350 2524664857 G	P
785	2269 C	-17:35133349 2524664856 C	
785 C	2270 A	-17:35133348 2524664855 A	
785	2271 T	-17:35133347 2524664854 T	M
784	2272 C	-17:35133346 2524664853 C	
784 R	2273 G	-17:35133345 2524664852 G	
784	2274 C	-17:35133344 2524664851 C	A
783	2275 T	-17:35133343 2524664850 T	
783 E	2276 C	-17:35133342 2524664849 C	
783	2277 C	-17:35133341 2524664848 C	G
782	2278 G	-17:35133340 2524664847 G	
782 A	2279 C	-17:35133339 2524664846 C	
782	2280 T	-17:35133338 2524664845 T	S
781	2281 A	-17:35133337 2524664844 A	
781 L	2282 G	-17:35133336 2524664843 G	
781	2283 G	-17:35133335 2524664842 G	P
780	2284 T	-17:35133334 2524664841 T	
780 H	2285 G	-17:35133333 2524664840 G	
780	2286 T	-17:35133332 2524664839 T	T
779	2287 C	-17:35133331 2524664838 C	
779 *	2288 A	-17:35133330 2524664837 A	
779	2289 G	-17:35133329 2524664836 G	L
778	2290 C	-17:35133328 2524664835 C	
778 R	2291 G	-17:35133327 2524664834 G	
778	2292 G	-17:35133326 2524664833 G	P
777	2293 C	-17:35133325 2524664832 C	
777 S	2294 T	-17:35133324 2524664831 T	
777	2295 C	-17:35133323 2524664830 C	E
776	2296 C	-17:35133322 2524664829 C	
776 W	2297 A	-17:35133321 2524664828 A	
776	2298 C	-17:35133320 2524664827 C	V
775	2299 C	-17:35133319 2524664826 C	
775 W	2300 A	-17:35133318 2524664825 A	
775	2301 G	-17:35133317 2524664824 G	L
774	2302 C	-17:35133236 2524664743 C	
774 S	2303 T	-17:35133235 2524664742 T	
774	2304 C	-17:35133234 2524664741 C	E
773	2305 C	-17:35133233 2524664740 C	
773 R	2306 G	-17:35133232 2524664739 G	
773	2307 T	-17:35133231 2524664738 T	T
772	2308 T	-17:35133230 2524664737 T	
772 K	2309 T	-17:35133229 2524664736 T	
772	2310 C	-17:35133228 2524664735 C	E
771	2311 C	-17:35133227 2524664734 C	
771 R	2312 T	-17:35133226 2524664733 T	
771	2313 G	-17:35133225 2524664732 G	Q
770	2314 C	-17:35133224 2524664731 C	
770 C	2315 A	-17:35133223 2524664730 A	
770	2316 G	-17:35133222 2524664729 G	L
769	2317 C	-17:35133221 2524664728 C	
769 C	2318 A	-17:35133220 2524664727 A	
769	2319 G	-17:35133219 2524664726 G	L
768	2320 T	-17:35133218 2524664725 T	
768 D	2321 C	-17:35133217 2524664724 C	
768	2322 T	-17:35133216 2524664723 T	R
767	2323 C	-17:35133215 2524664722 C	
767 G	2324 C	-17:35133214 2524664721 C	
767	2325 G	-17:35133213 2524664720 G	R
766	2326 C	-17:35133212 2524664719 C	
766 C	2327 A	-17:35133211 2524664718 A	
766	2328 T	-17:35133210 2524664717 T	M
765	2329 C	-17:35133209 2524664716 C	
765 R	2330 G	-17:35133208 2524664715 G	
765	2331 T	-17:35133207 2524664714 T	T
764	2332 G	-17:35133206 2524664713 G	
764 T	2333 T	-17:35133205 2524664712 T	
764	2334 A	-17:35133204 2524664711 A	Y
763	2335 C	-17:35133203 2524664710 C	
763 S	2336 T	-17:35133202 2524664709 T	
763	2337 T	-17:35133201 2524664708 T	K
762	2338 C	-17:35133200 2524664707 C	
762 G	2339 C	-17:35133199 2524664706 C	
762	2340 G	-17:35133198 2524664705 G	R
761	2341 G	-17:35133197 2524664704 G	
761 S	2342 A	-17:35133196 2524664703 A	
761	2343 T	-17:35133195 2524664702 T	I
760	2344 C	-17:35133194 2524664701 C	
760 R	2345 T	-17:35133193 2524664700 T	
760	2346 T	-17:35133192 2524664699 T	K
759	2347 C	-17:35133191 2524664698 C	
759 R	2348 T	-17:35133190 2524664697 T	
759	2349 G	-17:35133189 2524664696 G	Q
758	2350 C	-17:35133188 2524664695 C	
758 S	2351 T	-17:35133187 2524664694 T	
758	2352 G	-17:35133186 2524664693 G	Q
757	2353 C	-17:35133185 2524664692 C	
757 G	2354 C	-17:35133184 2524664691 C	
757	2355 G	-17:35133183 2524664690 G	R
756	2356 T	-17:35133182 2524664689 T	
756 D	2357 C	-17:35133181 2524664688 C	
756	2358 G	-17:35133180 2524664687 G	R
755	2359 C	-17:35133179 2524664686 C	
755 S	2360 T	-17:35133178 2524664685 T	
755	2361 T	-17:35133177 2524664684 T	K
754	2362 G	-17:35133176 2524664683 G	
754 S	2363 A	-17:35133175 2524664682 A	
754	2364 T	-17:35133174 2524664681 T	I
753	2365 G	-17:35133173 2524664680 G	
753 S	2366 A	-17:35133172 2524664679 A	
753	2367 G	-17:35133171 2524664678 G	L
752	2368 G	-17:35133170 2524664677 G	
752 S	2369 A	-17:35133169 2524664676 A	
752	2370 T	-17:35133168 2524664675 T	I
751	2371 C	-17:35133167 2524664674 C	
751 G	2372 C	-17:35133166 2524664673 C	
751	2373 C	-17:35133165 2524664672 C	G
750	2374 A	-17:35133164 2524664671 A	
750 L	2375 A	-17:35133163 2524664670 A	
750	2376 A	-17:35133162 2524664669 A	F
749	2377 G	-17:35133161 2524664668 G	
749 S	2378 A	-17:35133160 2524664667 A	
749	2379 C	-17:35133159 2524664666 C	V
748	2380 C	-17:35133158 2524664665 C	
748 W	2381 A	-17:35133157 2524664664 A	
748	2382 C	-17:35133156 2524664663 C	V
747	2383 C	-17:35133155 2524664662 C	
747 G	2384 C	-17:35133154 2524664661 C	
747	2385 C	-17:35133153 2524664660 C	G
746	2386 C	-17:35133152 2524664659 C	
746 W	2387 A	-17:35133151 2524664658 A	
746	2388 A	-17:35133150 2524664657 A	L
745	2389 G	-17:35133149 2524664656 G	
745 S	2390 A	-17:35133148 2524664655 A	
745	2391 C	-17:35133147 2524664654 C	V
744	2392 C	-17:35133146 2524664653 C	
744 W	2393 A	-17:35133145 2524664652 A	
744	2394 C	-17:35133144 2524664651 C	V
743	2395 G	-17:35133143 2524664650 G	
743 S	2396 A	-17:35133142 2524664649 A	
743	2397 C	-17:35133141 2524664648 C	V
742	2398 C	-17:35133140 2524664647 C	
742 W	2399 A	-17:35133139 2524664646 A	
742	2400 G	-17:35133138 2524664645 G	L
741	2401 C	-17:35133137 2524664644 C	
741 C	2402 A	-17:35133136 2524664643 A	
741	2403 G	-17:35133135 2524664642 G	L
740	2404 A	-17:35133134 2524664641 A	
740 F	2405 A	-17:35133133 2524664640 A	
740	2406 T	-17:35133132 2524664639 T	I
739	2407 G	-17:35133131 2524664638 G	
739 A	2408 C	-17:35133130 2524664637 C	
739	2409 C	-17:35133129 2524664636 C	G
738	2410 A	-17:35133128 2524664635 A	
738 L	2411 A	-17:35133127 2524664634 A	
738	2412 C	-17:35133126 2524664633 C	V
737	2413 C	-17:35133125 2524664632 C	
737 W	2414 A	-17:35133124 2524664631 A	
737	2415 C	-17:35133123 2524664630 C	V
736	2416 C	-17:35133122 2524664629 C	
736 R	2417 G	-17:35133121 2524664628 G	
736	2418 C	-17:35133120 2524664627 C	A
735	2419 A	-17:35133119 2524664626 A	
735 L	2420 G	-17:35133118 2524664625 G	
735	2421 A	-17:35133117 2524664624 A	S
734	2422 G	-17:35133116 2524664623 G	
734 S	2423 A	-17:35133115 2524664622 A	
734	2424 T	-17:35133114 2524664621 T	I
733	2425 G	-17:35133113 2524664620 G	
733 S	2426 A	-17:35133112 2524664619 A	
733	2427 T	-17:35133111 2524664618 T	I
732	2428 G	-17:35133110 2524664617 G	
732 P	2429 G	-17:35133109 2524664616 G	
732	2430 A	-17:35133108 2524664615 A	S
731	2431 C	-17:35133107 2524664614 C	
731 R	2432 G	-17:35133106 2524664613 G	
731	2433 T	-17:35133105 2524664612 T	T
730	2434 C	-17:35133104 2524664611 C	
730 *	2435 A	-17:35133103 2524664610 A	
730	2436 G	-17:35133102 2524664609 G	L
729	2437 A	-17:35133101 2524664608 A	
729 L	2438 G	-17:35133100 2524664607 G	
729	2439 G	-17:35133099 2524664606 G	P
728	2440 G	-17:35133098 2524664605 G	
728 A	2441 C	-17:35129613 2524661120 C	
728	2442 T	-17:35129612 2524661119 T	S
727	2443 G	-17:35129611 2524661118 G	
727 P	2444 G	-17:35129610 2524661117 G	
727	2445 C	-17:35129609 2524661116 C	A
726	2446 T	-17:35129608 2524661115 T	
726 E	2447 C	-17:35129607 2524661114 C	
726	2448 T	-17:35129606 2524661113 T	R
725	2449 C	-17:35129605 2524661112 C	
725 R	2450 T	-17:35129604 2524661111 T	
725	2451 G	-17:35129603 2524661110 G	Q
724	2452 C	-17:35129602 2524661109 C	
724 S	2453 T	-17:35129601 2524661108 T	
724	2454 C	-17:35129600 2524661107 C	E
723	2455 G	-17:35129599 2524661106 G	
723 P	2456 G	-17:35129598 2524661105 G	
723	2457 C	-17:35129597 2524661104 C	A
722	2458 G	-17:35129596 2524661103 G	
722 P	2459 G	-17:35129595 2524661102 G	
722	2460 G	-17:35129594 2524661101 G	P
721	2461 G	-17:35129593 2524661100 G	
721 A	2462 C	-17:35129592 2524661099 C	
721	2463 A	-17:35129591 2524661098 A	C
720	2464 G	-17:35129590 2524661097 G	
720 A	2465 C	-17:35129589 2524661096 C	
720	2466 C	-17:35129588 2524661095 C	G
719	2467 C	-17:35129587 2524661094 C	
719 R	2468 T	-17:35129586 2524661093 T	
719	2469 T	-17:35129585 2524661092 T	K
718	2470 G	-17:35129584 2524661091 G	
718 T	2471 T	-17:35129583 2524661090 T	
718	2472 C	-17:35129582 2524661089 C	D
717	2473 A	-17:35129581 2524661088 A	
717 M	2474 T	-17:35129580 2524661087 T	
717	2475 C	-17:35129579 2524661086 C	D
716	2476 C	-17:35129578 2524661085 C	
716 W	2477 A	-17:35129577 2524661084 A	
716	2478 G	-17:35129576 2524661083 G	L
715	2479 G	-17:35129575 2524661082 G	
715 T	2480 T	-17:35129574 2524661081 T	
715	2481 C	-17:35129573 2524661080 C	D
714	2482 C	-17:35129572 2524661079 C	
714 W	2483 A	-17:35129571 2524661078 A	
714	2484 C	-17:35129570 2524661077 C	V
713	2485 A	-17:35129569 2524661076 A	
713 V	2486 C	-17:35129568 2524661075 C	
713	2487 A	-17:35129567 2524661074 A	C
712	2488 G	-17:35129566 2524661073 G	
712 P	2489 G	-17:35127259 2524658766 G	
712	2490 A	-17:35127258 2524658765 A	S
711	2491 G	-17:35127257 2524658764 G	
711 T	2492 T	-17:35127256 2524658763 T	
711	2493 G	-17:35127255 2524658762 G	H
710	2494 G	-17:35127254 2524658761 G	
710 P	2495 G	-17:35127253 2524658760 G	
710	2496 T	-17:35127252 2524658759 T	T
709	2497 G	-17:35127251 2524658758 G	
709 A	2498 C	-17:35127250 2524658757 C	
709	2499 A	-17:35127249 2524658756 A	C
708	2500 G	-17:35127248 2524658755 G	
708 T	2501 T	-17:35127247 2524658754 T	
708	2502 T	-17:35127246 2524658753 T	N
707	2503 G	-17:35127245 2524658752 G	
707 S	2504 A	-17:35127244 2524658751 A	
707	2505 T	-17:35127243 2524658750 T	I
706	2506 G	-17:35127242 2524658749 G	
706 P	2507 G	-17:35127241 2524658748 G	
706	2508 G	-17:35127240 2524658747 G	P
705	2509 G	-17:35127239 2524658746 G	
705 A	2510 C	-17:35127238 2524658745 C	
705	2511 A	-17:35127237 2524658744 A	C
704	2512 A	-17:35127236 2524658743 A	
704 L	2513 G	-17:35127235 2524658742 G	
704	2514 G	-17:35127234 2524658741 G	P
703	2515 C	-17:35127233 2524658740 C	
703 S	2516 T	-17:35127232 2524658739 T	
703	2517 G	-17:35127231 2524658738 G	Q
702	2518 G	-17:35127230 2524658737 G	
702 A	2519 C	-17:35127229 2524658736 C	
702	2520 A	-17:35127228 2524658735 A	C
701	2521 T	-17:35127227 2524658734 T	
701 H	2522 G	-17:35127226 2524658733 G	
701	2523 C	-17:35127225 2524658732 C	A
700	2524 G	-17:35127224 2524658731 G	
700 A	2525 C	-17:35127223 2524658730 C	
700	2526 C	-17:35127222 2524658729 C	G
699	2527 C	-17:35127221 2524658728 C	
699 R	2528 T	-17:35127220 2524658727 T	
699	2529 C	-17:35127219 2524658726 C	E
698	2530 C	-17:35127218 2524658725 C	
698 R	2531 T	-17:35127217 2524658724 T	
698	2532 C	-17:35127216 2524658723 C	E
697	2533 A	-17:35127215 2524658722 A	
697 M	2534 T	-17:35127214 2524658721 T	
697	2535 C	-17:35127213 2524658720 C	D
696	2536 T	-17:35127212 2524658719 T	
696 Q	2537 G	-17:35127211 2524658718 G	
696	2538 G	-17:35127210 2524658717 G	P
695	2539 A	-17:35127209 2524658716 A	
695 F	2540 A	-17:35127208 2524658715 A	
695	2541 A	-17:35127207 2524658714 A	F
694	2542 C	-17:35127206 2524658713 C	
694 S	2543 T	-17:35127205 2524658712 T	
694	2544 T	-17:35127204 2524658711 T	K
693	2545 C	-17:35127203 2524658710 C	
693 G	2546 C	-17:35127202 2524658709 C	
693	2547 A	-17:35127201 2524658708 A	W
692	2548 G	-17:35127200 2524658707 G	
692 S	2549 A	-17:35127199 2524658706 A	
692	2550 T	-17:35127198 2524658705 T	I
691	2551 G	-17:35127197 2524658704 G	
691 P	2552 G	-17:35127196 2524658703 G	
691	2553 G	-17:35127195 2524658702 G	P
690	2554 C	-17:35127194 2524658701 C	
690 C	2555 A	-17:35127193 2524658700 A	
690	2556 T	-17:35127192 2524658699 T	M
689	2557 G	-17:35127191 2524658698 G	
689 T	2558 T	-17:35127190 2524658697 T	
689	2559 A	-17:35127189 2524658696 A	Y
688	2560 G	-17:35127188 2524658695 G	
688 P	2561 G	-17:35127187 2524658694 G	
688	2562 A	-17:35127186 2524658693 A	S
687	2563 G	-17:35127185 2524658692 G	
687 S	2564 A	-17:35127184 2524658691 A	
687	2565 G	-17:35127183 2524658690 G	L
686	2566 G	-17:35127182 2524658689 G	
686 T	2567 T	-17:35127181 2524658688 T	
686	2568 C	-17:35127180 2524658687 C	D
685	2569 A	-17:35127179 2524658686 A	
685 L	2570 G	-17:35127178 2524658685 G	
685	2571 G	-17:35127177 2524658684 G	P
684	2572 T	-17:35127176 2524658683 T	
684 N	2573 T	-17:35127175 2524658682 T	
684	2574 T	-17:35127174 2524658681 T	K
683	2575 C	-17:35127173 2524658680 C	
683 *	2576 A	-17:35127172 2524658679 A	
683	2577 C	-17:35127171 2524658678 C	V
682	2578 A	-17:35127170 2524658677 A	
682 V	2579 C	-17:35127169 2524658676 C	
682	2580 C	-17:35127168 2524658675 C	G
681	2581 G	-17:35127167 2524658674 G	
681 A	2582 C	-17:35127166 2524658673 C	
681	2583 T	-17:35127165 2524658672 T	S
680	2584 G	-17:35127164 2524658671 G	
680 P	2585 G	-17:35127163 2524658670 G	
680	2586 G	-17:35127162 2524658669 G	P
679	2587 G	-17:35127161 2524658668 G	
679 A	2588 C	-17:35127160 2524658667 C	
679	2589 A	-17:35127159 2524658666 A	C
678	2590 G	-17:35127158 2524658665 G	
678 A	2591 C	-17:35127157 2524658664 C	
678	2592 G	-17:35127156 2524658663 G	R
677	2593 G	-17:35127155 2524658662 G	
677 P	2594 G	-17:35127154 2524658661 G	
677	2595 C	-17:35127153 2524658660 C	A
676	2596 C	-17:35127152 2524658659 C	
676 W	2597 A	-17:35127151 2524658658 A	
676	2598 C	-17:35127150 2524658657 C	V
675	2599 G	-17:35127149 2524658656 G	
675 A	2600 C	-17:35127148 2524658655 C	
675	2601 A	-17:35127147 2524658654 A	C
674	2602 G	-17:35127146 2524658653 G	
674 S	2603 A	-17:35127145 2524658652 A	
674	2604 A	-17:35127144 2524658651 A	F
673	2605 G	-17:35127143 2524658650 G	
673 P	2606 G	-17:35127142 2524658649 G	
673	2607 G	-17:35127141 2524658648 G	P
672	2608 A	-17:35127140 2524658647 A	
672 L	2609 G	-17:35127139 2524658646 G	
672	2610 G	-17:35127138 2524658645 G	P
671	2611 G	-17:35127137 2524658644 G	
671 T	2612 T	-17:35127136 2524658643 T	
671	2613 C	-17:35127135 2524658642 C	D
670	2614 C	-17:35127134 2524658641 C	
670 R	2615 T	-17:35127133 2524658640 T	
670	2616 T	-17:35127132 2524658639 T	K
669	2617 A	-17:35127131 2524658638 A	
669 I	2618 T	-17:35127130 2524658637 T	
669	2619 A	-17:35127129 2524658636 A	Y
668	2620 G	-17:35127128 2524658635 G	
668 T	2621 T	-17:35127127 2524658634 T	
668	2622 G	-17:35127126 2524658633 G	H
667	2623 G	-17:35127125 2524658632 G	
667 P	2624 G	-17:35127124 2524658631 G	
667	2625 C	-17:35127123 2524658630 C	A
666	2626 A	-17:35127122 2524658629 A	
666 V	2627 C	-17:35127121 2524658628 C	
666	2628 A	-17:35127120 2524658627 A	C
665	2629 G	-17:35127119 2524658626 G	
665 P	2630 G	-17:35127118 2524658625 G	
665	2631 C	-17:35127117 2524658624 C	A
664	2632 C	-17:35127116 2524658623 C	
664 W	2633 A	-17:35127115 2524658622 A	
664	2634 C	-17:35127114 2524658621 C	V
663	2635 A	-17:35127113 2524658620 A	
663 V	2636 C	-17:35127112 2524658619 C	
663	2637 A	-17:35127111 2524658618 A	C
662	2638 C	-17:35127110 2524658617 C	
662 S	2639 T	-17:35127109 2524658616 T	
662	2640 G	-17:35127108 2524658615 G	Q
661	2641 G	-17:35127107 2524658614 G	
661 T	2642 T	-17:35127106 2524658613 T	
661	2643 C	-17:35127105 2524658612 C	D
660	2644 A	-17:35127104 2524658611 A	
660 L	2645 G	-17:35127103 2524658610 G	
660	2646 C	-17:35127102 2524658609 C	A
659	2647 C	-17:35127101 2524658608 C	
659 R	2648 T	-17:35127100 2524658607 T	
659	2649 C	-17:35127099 2524658606 C	E
658	2650 C	-17:35126384 2524657891 C	
658 R	2651 G	-17:35126383 2524657890 G	
658	2652 G	-17:35126382 2524657889 G	P
657	2653 T	-17:35126381 2524657888 T	
657 D	2654 C	-17:35126380 2524657887 C	
657	2655 C	-17:35126379 2524657886 C	G
656	2656 A	-17:35126378 2524657885 A	
656 L	2657 A	-17:35126377 2524657884 A	
656	2658 A	-17:35126376 2524657883 A	F
655	2659 A	-17:35126375 2524657882 A	
655 V	2660 C	-17:35126374 2524657881 C	
655	2661 A	-17:35126373 2524657880 A	C
654	2662 G	-17:35126372 2524657879 G	
654 P	2663 G	-17:35126371 2524657878 G	
654	2664 T	-17:35126370 2524657877 T	T
653	2665 C	-17:35126369 2524657876 C	
653 *	2666 A	-17:35126368 2524657875 A	
653	2667 C	-17:35126367 2524657874 C	V
652	2668 T	-17:35126366 2524657873 T	
652 Q	2669 G	-17:35126365 2524657872 G	
652	2670 A	-17:35126364 2524657871 A	S
651	2671 G	-17:35126363 2524657870 G	
651 A	2672 C	-17:35126362 2524657869 C	
651	2673 C	-17:35126361 2524657868 C	G
650	2674 A	-17:35126360 2524657867 A	
650 M	2675 T	-17:35126359 2524657866 T	
650	2676 T	-17:35126358 2524657865 T	N
649	2677 C	-17:35126357 2524657864 C	
649 R	2678 T	-17:35126356 2524657863 T	
649	2679 G	-17:35126355 2524657862 G	Q
648	2680 G	-17:35126354 2524657861 G	
648 P	2681 G	-17:35126353 2524657860 G	
648	2682 G	-17:35126352 2524657859 G	P
647	2683 C	-17:35126351 2524657858 C	
647 S	2684 T	-17:35126350 2524657857 T	
647	2685 G	-17:35126349 2524657856 G	Q
646	2686 A	-17:35126348 2524657855 A	
646 V	2687 C	-17:35126347 2524657854 C	
646	2688 A	-17:35126346 2524657853 A	C
645	2689 C	-17:35126345 2524657852 C	
645 S	2690 T	-17:35126344 2524657851 T	
645	2691 C	-17:35126343 2524657850 C	E
644	2692 A	-17:35126342 2524657849 A	
644 L	2693 G	-17:35126341 2524657848 G	
644	2694 G	-17:35126340 2524657847 G	P
643	2695 G	-17:35126339 2524657846 G	
643 T	2696 T	-17:35126338 2524657845 T	
643	2697 G	-17:35126337 2524657844 G	H
642	2698 G	-17:35126336 2524657843 G	
642 A	2699 C	-17:35126335 2524657842 C	
642	2700 A	-17:35126334 2524657841 A	C
641	2701 C	-17:35126333 2524657840 C	
641 R	2702 G	-17:35126332 2524657839 G	
641	2703 G	-17:35126331 2524657838 G	P
640	2704 C	-17:35126330 2524657837 C	
640 C	2705 A	-17:35126329 2524657836 A	
640	2706 A	-17:35126328 2524657835 A	L
639	2707 A	-17:35126327 2524657834 A	
639 V	2708 C	-17:35126326 2524657833 C	
639	2709 A	-17:35126325 2524657832 A	C
638	2710 G	-17:35126324 2524657831 G	
638 T	2711 T	-17:35126323 2524657830 T	
638	2712 G	-17:35126322 2524657829 G	H
637	2713 C	-17:35126321 2524657828 C	
637 G	2714 C	-17:35126320 2524657827 C	
637	2715 T	-17:35126319 2524657826 T	R
636	2716 G	-17:35126318 2524657825 G	
636 P	2717 G	-17:35126317 2524657824 G	
636	2718 C	-17:35126316 2524657823 C	A
635	2719 A	-17:35126315 2524657822 A	
635 M	2720 T	-17:35126314 2524657821 T	
635	2721 T	-17:35126313 2524657820 T	N
634	2722 C	-17:35126312 2524657819 C	
634 *	2723 A	-17:35126311 2524657818 A	
634	2724 C	-17:35126310 2524657817 C	V
633	2725 A	-17:35126309 2524657816 A	
633 M	2726 T	-17:35126308 2524657815 T	
633	2727 A	-17:35126307 2524657814 A	Y
632	2728 C	-17:35126306 2524657813 C	
632 S	2729 T	-17:35126305 2524657812 T	
632	2730 C	-17:35126304 2524657811 C	E
631	2731 C	-17:35126303 2524657810 C	
631 G	2732 C	-17:35126302 2524657809 C	
631	2733 T	-17:35126301 2524657808 T	R
630	2734 G	-17:35126300 2524657807 G	
630 P	2735 G	-17:35126299 2524657806 G	
630	2736 G	-17:35126298 2524657805 G	P
629	2737 G	-17:35126297 2524657804 G	
629 S	2738 A	-17:35126296 2524657803 A	
629	2739 G	-17:35126295 2524657802 G	L
628	2740 C	-17:35126294 2524657801 C	
628 G	2741 C	-17:35126212 2524657719 C	
628	2742 C	-17:35126211 2524657718 C	G
627	2743 C	-17:35126210 2524657717 C	
627 R	2744 T	-17:35126209 2524657716 T	
627	2745 G	-17:35126208 2524657715 G	Q
626	2746 C	-17:35126207 2524657714 C	
626 C	2747 A	-17:35126206 2524657713 A	
626	2748 G	-17:35126205 2524657712 G	L
625	2749 T	-17:35126204 2524657711 T	
625 Y	2750 A	-17:35126203 2524657710 A	
625	2751 C	-17:35126202 2524657709 C	V
624	2752 T	-17:35126201 2524657708 T	
624 E	2753 C	-17:35126200 2524657707 C	
624	2754 G	-17:35126199 2524657706 G	R
623	2755 G	-17:35126198 2524657705 G	
623 A	2756 C	-17:35126197 2524657704 C	
623	2757 A	-17:35126196 2524657703 A	C
622	2758 T	-17:35126195 2524657702 T	
622 N	2759 T	-17:35126194 2524657701 T	
622	2760 C	-17:35126193 2524657700 C	E
621	2761 C	-17:35126192 2524657699 C	
621 R	2762 T	-17:35126191 2524657698 T	
621	2763 C	-17:35126190 2524657697 C	E
620	2764 C	-17:35126189 2524657696 C	
620 W	2765 A	-17:35126188 2524657695 A	
620	2766 C	-17:35126187 2524657694 C	V
619	2767 G	-17:35126186 2524657693 G	
619 A	2768 C	-17:35126185 2524657692 C	
619	2769 A	-17:35126184 2524657691 A	C
618	2770 C	-17:35126183 2524657690 C	
618 S	2771 T	-17:35126182 2524657689 T	
618	2772 C	-17:35126181 2524657688 C	E
617	2773 C	-17:35126180 2524657687 C	
617 R	2774 T	-17:35126179 2524657686 T	
617	2775 G	-17:35126178 2524657685 G	Q
616	2776 G	-17:35126177 2524657684 G	
616 A	2777 C	-17:35126176 2524657683 C	
616	2778 C	-17:35126175 2524657682 C	G
615	2779 C	-17:35126174 2524657681 C	
615 G	2780 C	-17:35126173 2524657680 C	
615	2781 G	-17:35126172 2524657679 G	R
614	2782 A	-17:35126171 2524657678 A	
614 F	2783 A	-17:35126170 2524657677 A	
614	2784 G	-17:35126169 2524657676 G	L
613	2785 G	-17:35126168 2524657675 G	
613 S	2786 A	-17:35126167 2524657674 A	
613	2787 A	-17:35126166 2524657673 A	F
612	2788 C	-17:35126165 2524657672 C	
612 S	2789 T	-17:35126164 2524657671 T	
612	2790 G	-17:35126163 2524657670 G	Q
611	2791 G	-17:35126162 2524657669 G	
611 A	2792 C	-17:35126161 2524657668 C	
611	2793 T	-17:35126160 2524657667 T	S
610	2794 G	-17:35126159 2524657666 G	
610 A	2795 C	-17:35126158 2524657665 C	
610	2796 A	-17:35126157 2524657664 A	C
609	2797 G	-17:35126156 2524657663 G	
609 T	2798 T	-17:35126155 2524657662 T	
609	2799 T	-17:35126154 2524657661 T	N
608	2800 G	-17:35126153 2524657660 G	
608 S	2801 A	-17:35126152 2524657659 A	
608	2802 C	-17:35126151 2524657658 C	V
607	2803 A	-17:35126150 2524657657 A	
607 V	2804 C	-17:35126149 2524657656 C	
607	2805 A	-17:35126148 2524657655 A	C
606	2806 C	-17:35126147 2524657654 C	
606 S	2807 T	-17:35126146 2524657653 T	
606	2808 G	-17:35126145 2524657652 G	Q
605	2809 G	-17:35126144 2524657651 G	
605 P	2810 G	-17:35126143 2524657650 G	
605	2811 T	-17:35126142 2524657649 T	T
604	2812 G	-17:35126141 2524657648 G	
604 P	2813 G	-17:35126140 2524657647 G	
604	2814 G	-17:35126139 2524657646 G	P
603	2815 C	-17:35126138 2524657645 C	
603 G	2816 C	-17:35126137 2524657644 C	
603	2817 C	-17:35126136 2524657643 C	G
602	2818 T	-17:35126135 2524657642 T	
602 Q	2819 G	-17:35126134 2524657641 G	
602	2820 G	-17:35126133 2524657640 G	P
601	2821 A	-17:35126132 2524657639 A	
601 V	2822 C	-17:35126131 2524657638 C	
601	2823 C	-17:35126130 2524657637 C	G
600	2824 C	-17:35126129 2524657636 C	
600 G	2825 C	-17:35126128 2524657635 C	
600	2826 A	-17:35126127 2524657634 A	W
599	2827 G	-17:35126126 2524657633 G	
599 A	2828 C	-17:35126125 2524657632 C	
599	2829 A	-17:35126124 2524657631 A	C
598	2830 G	-17:35126123 2524657630 G	
598 T	2831 T	-17:35126122 2524657629 T	
598	2832 G	-17:35126121 2524657628 G	H
597	2833 C	-17:35126120 2524657627 C	
597 G	2834 C	-17:35126119 2524657626 C	
597	2835 C	-17:35126118 2524657625 C	G
596	2836 T	-17:35126117 2524657624 T	
596 E	2837 C	-17:35126116 2524657623 C	
596	2838 G	-17:35126115 2524657622 G	R
595	2839 G	-17:35126114 2524657621 G	
595 P	2840 G	-17:35126113 2524657620 G	
595	2841 C	-17:35126112 2524657619 C	A
594	2842 G	-17:35126111 2524657618 G	
594 A	2843 C	-17:35126110 2524657617 C	
594	2844 A	-17:35126109 2524657616 A	C
593	2845 C	-17:35126108 2524657615 C	
593 C	2846 A	-17:35126107 2524657614 A	
593	2847 G	-17:35126106 2524657613 G	L
592	2848 C	-17:35126105 2524657612 C	
592 S	2849 T	-17:35126104 2524657611 T	
592	2850 G	-17:35126103 2524657610 G	Q
591	2851 G	-17:35126102 2524657609 G	
591 T	2852 T	-17:35126101 2524657608 T	
591	2853 G	-17:35126100 2524657607 G	H
590	2854 G	-17:35126099 2524657606 G	
590 A	2855 C	-17:35126098 2524657605 C	
590	2856 A	-17:35126097 2524657604 A	C
589	2857 G	-17:35126096 2524657603 G	
589 P	2858 G	-17:35126095 2524657602 G	
589	2859 C	-17:35126094 2524657601 C	A
588	2860 C	-17:35126093 2524657600 C	
588 W	2861 A	-17:35126092 2524657599 A	
588	2862 G	-17:35126091 2524657598 G	L
587	2863 G	-17:35126090 2524657597 G	
587 A	2864 C	-17:35126089 2524657596 C	
587	2865 C	-17:35126088 2524657595 C	G
586	2866 C	-17:35126087 2524657594 C	
586 R	2867 T	-17:35126086 2524657593 T	
586	2868 C	-17:35126085 2524657592 C	E
585	2869 G	-17:35126084 2524657591 G	
585 A	2870 C	-17:35126083 2524657590 C	
585	2871 C	-17:35126082 2524657589 C	G
584	2872 C	-17:35126081 2524657588 C	
584 W	2873 A	-17:35126080 2524657587 A	
584	2874 C	-17:35125718 2524657225 C	V
583	2875 A	-17:35125717 2524657224 A	
583 V	2876 C	-17:35125716 2524657223 C	
583	2877 A	-17:35125715 2524657222 A	C
582	2878 C	-17:35125714 2524657221 C	
582 S	2879 T	-17:35125713 2524657220 T	
582	2880 C	-17:35125712 2524657219 C	E
581	2881 G	-17:35125711 2524657218 G	
581 T	2882 T	-17:35125710 2524657217 T	
581	2883 C	-17:35125709 2524657216 C	D
580	2884 C	-17:35125708 2524657215 C	
580 R	2885 T	-17:35125707 2524657214 T	
580	2886 C	-17:35125706 2524657213 C	E
579	2887 T	-17:35125705 2524657212 T	
579 Q	2888 G	-17:35125704 2524657211 G	
579	2889 G	-17:35125703 2524657210 G	P
578	2890 C	-17:35125702 2524657209 C	
578 G	2891 C	-17:35125701 2524657208 C	
578	2892 G	-17:35125700 2524657207 G	R
577	2893 G	-17:35125699 2524657206 G	
577 T	2894 T	-17:35125698 2524657205 T	
577	2895 T	-17:35125697 2524657204 T	N
576	2896 G	-17:35125696 2524657203 G	
576 P	2897 G	-17:35125695 2524657202 G	
576	2898 C	-17:35125694 2524657201 C	A
575	2899 A	-17:35125693 2524657200 A	
575 L	2900 G	-17:35125692 2524657199 G	
575	2901 T	-17:35125691 2524657198 T	T
574	2902 G	-17:35125690 2524657197 G	
574 T	2903 T	-17:35125689 2524657196 T	
574	2904 G	-17:35125688 2524657195 G	H
573	2905 G	-17:35125687 2524657194 G	
573 S	2906 A	-17:35125686 2524657193 A	
573	2907 G	-17:35125685 2524657192 G	L
572	2908 C	-17:35125684 2524657191 C	
572 C	2909 A	-17:35125683 2524657190 A	
572	2910 G	-17:35125682 2524657189 G	L
571	2911 A	-17:35125681 2524657188 A	
571 L	2912 G	-17:35125680 2524657187 G	
571	2913 C	-17:35125679 2524657186 C	A
570	2914 T	-17:35125678 2524657185 T	
570 K	2915 T	-17:35125677 2524657184 T	
570	2916 G	-17:35125676 2524657183 G	Q
569	2917 G	-17:35125675 2524657182 G	
569 T	2918 T	-17:35125674 2524657181 T	
569	2919 G	-17:35125673 2524657180 G	H
568	2920 C	-17:35125672 2524657179 C	
568 R	2921 G	-17:35125671 2524657178 G	
568	2922 G	-17:35125670 2524657177 G	P
567	2923 G	-17:35125669 2524657176 G	
567 T	2924 T	-17:35125668 2524657175 T	
567	2925 T	-17:35125667 2524657174 T	N
566	2926 C	-17:35125666 2524657173 C	
566 G	2927 C	-17:35125665 2524657172 C	
566	2928 G	-17:35125664 2524657171 G	R
565	2929 A	-17:35125663 2524657170 A	
565 F	2930 A	-17:35125662 2524657169 A	
565	2931 A	-17:35125661 2524657168 A	F
564	2932 G	-17:35125660 2524657167 G	
564 S	2933 A	-17:35125659 2524657166 A	
564	2934 G	-17:35125658 2524657165 G	L
563	2935 C	-17:35125657 2524657164 C	
563 S	2936 T	-17:35125656 2524657163 T	
563	2937 G	-17:35125655 2524657162 G	Q
562	2938 G	-17:35125654 2524657161 G	
562 T	2939 T	-17:35125653 2524657160 T	
562	2940 C	-17:35125652 2524657159 C	D
561	2941 C	-17:35125651 2524657158 C	
561 G	2942 C	-17:35125650 2524657157 C	
561	2943 A	-17:35125649 2524657156 A	W
560	2944 G	-17:35125648 2524657155 G	
560 P	2945 G	-17:35125647 2524657154 G	
560	2946 G	-17:35125646 2524657153 G	P
559	2947 C	-17:35125645 2524657152 C	
559 C	2948 A	-17:35125644 2524657151 A	
559	2949 C	-17:35125643 2524657150 C	V
558	2950 C	-17:35125642 2524657149 C	
558 R	2951 G	-17:35125641 2524657148 G	
558	2952 T	-17:35125640 2524657147 T	T
557	2953 G	-17:35125639 2524657146 G	
557 T	2954 T	-17:35125638 2524657145 T	
557	2955 G	-17:35125637 2524657144 G	H
556	2956 C	-17:35125636 2524657143 C	
556 C	2957 A	-17:35125635 2524657142 A	
556	2958 C	-17:35125634 2524657141 C	V
555	2959 G	-17:35125633 2524657140 G	
555 S	2960 A	-17:35125632 2524657139 A	
555	2961 A	-17:35125631 2524657138 A	F
554	2962 G	-17:35125630 2524657137 G	
554 A	2963 C	-17:35125629 2524657136 C	
554	2964 A	-17:35125628 2524657135 A	C
553	2965 G	-17:35125627 2524657134 G	
553 S	2966 A	-17:35125626 2524657133 A	
553	2967 G	-17:35125625 2524657132 G	L
552	2968 G	-17:35125624 2524657131 G	
552 T	2969 T	-17:35125623 2524657130 T	
552	2970 G	-17:35125622 2524657129 G	H
551	2971 G	-17:35125621 2524657128 G	
551 P	2972 G	-17:35125620 2524657127 G	
551	2973 T	-17:35125619 2524657126 T	T
550	2974 G	-17:35125618 2524657125 G	
550 T	2975 T	-17:35125617 2524657124 T	
550	2976 T	-17:35125616 2524657123 T	N
549	2977 A	-17:35125615 2524657122 A	
549 I	2978 T	-17:35125614 2524657121 T	
549	2979 G	-17:35125613 2524657120 G	H
548	2980 G	-17:35125612 2524657119 G	
548 T	2981 T	-17:35125611 2524657118 T	
548	2982 G	-17:35125610 2524657117 G	H
547	2983 G	-17:35125609 2524657116 G	
547 S	2984 A	-17:35125608 2524657115 A	
547	2985 T	-17:35125607 2524657114 T	I
546	2986 G	-17:35125606 2524657113 G	
546 S	2987 A	-17:35125605 2524657112 A	
546	2988 G	-17:35125604 2524657111 G	L
545	2989 G	-17:35125603 2524657110 G	
545 P	2990 G	-17:35125602 2524657109 G	
545	2991 C	-17:35125601 2524657108 C	A
544	2992 C	-17:35125600 2524657107 C	
544 W	2993 A	-17:35125599 2524657106 A	
544	2994 G	-17:35125598 2524657105 G	L
543	2995 T	-17:35125597 2524657104 T	
543 D	2996 C	-17:35125596 2524657103 C	
543	2997 C	-17:35125595 2524657102 C	G
542	2998 A	-17:35125594 2524657101 A	
542 V	2999 C	-17:35125593 2524657100 C	
542	3000 T	-17:35125592 2524657099 T	S
541	3001 G	-17:35125591 2524657098 G	
541 A	3002 C	-17:35125590 2524657097 C	
541	3003 C	-17:35125589 2524657096 C	G
540	3004 C	-17:35125588 2524657095 C	
540 W	3005 A	-17:35125587 2524657094 A	
540	3006 G	-17:35125586 2524657093 G	L
539	3007 T	-17:35125585 2524657092 T	
539 N	3008 T	-17:35125584 2524657091 T	
539	3009 C	-17:35125583 2524657090 C	E
538	3010 C	-17:35125582 2524657089 C	
538 G	3011 C	-17:35125581 2524657088 C	
538	3012 T	-17:35125580 2524657087 T	R
537	3013 C	-17:35125579 2524657086 C	
537 *	3014 A	-17:35125578 2524657085 A	
537	3015 G	-17:35125577 2524657084 G	L
536	3016 T	-17:35125576 2524657083 T	
536 H	3017 G	-17:35125575 2524657082 G	
536	3018 A	-17:35125574 2524657081 A	S
535	3019 G	-17:35125573 2524657080 G	
535 A	3020 C	-17:35125572 2524657079 C	
535	3021 G	-17:35125571 2524657078 G	R
534	3022 C	-17:35125570 2524657077 C	
534 C	3023 A	-17:35125569 2524657076 A	
534	3024 G	-17:35125568 2524657075 G	L
533	3025 C	-17:35125567 2524657074 C	
533 G	3026 C	-17:35125566 2524657073 C	
533	3027 C	-17:35125565 2524657072 C	G
532	3028 C	-17:35125564 2524657071 C	
532 W	3029 A	-17:35125563 2524657070 A	
532	3030 G	-17:35125562 2524657069 G	L
531	3031 C	-17:35125561 2524657068 C	
531 G	3032 C	-17:35125560 2524657067 C	
531	3033 A	-17:35125559 2524657066 A	W
530	3034 G	-17:35125558 2524657065 G	
530 A	3035 C	-17:35125557 2524657064 C	
530	3036 T	-17:35125556 2524657063 T	S
529	3037 G	-17:35125555 2524657062 G	
529 S	3038 A	-17:35125554 2524657061 A	
529	3039 T	-17:35125553 2524657060 T	I
528	3040 G	-17:35125552 2524657059 G	
528 A	3041 C	-17:35125551 2524657058 C	
528	3042 C	-17:35125550 2524657057 C	G
527	3043 C	-17:35125549 2524657056 C	
527 W	3044 A	-17:35125548 2524657055 A	
527	3045 G	-17:35125547 2524657054 G	L
526	3046 C	-17:35125546 2524657053 C	
526 G	3047 C	-17:35125545 2524657052 C	
526	3048 C	-17:35125544 2524657051 C	G
525	3049 T	-17:35125543 2524657050 T	
525 K	3050 T	-17:35125542 2524657049 T	
525	3051 G	-17:35125541 2524657048 G	Q
524	3052 C	-17:35125540 2524657047 C	
524 C	3053 A	-17:35125539 2524657046 A	
524	3054 G	-17:35125538 2524657045 G	L
523	3055 G	-17:35125537 2524657044 G	
523 P	3056 G	-17:35125536 2524657043 G	
523	3057 T	-17:35125535 2524657042 T	T
522	3058 C	-17:35125534 2524657041 C	
522 *	3059 A	-17:35125533 2524657040 A	
522	3060 G	-17:35125532 2524657039 G	L
521	3061 C	-17:35125531 2524657038 C	
521 R	3062 G	-17:35125530 2524657037 G	
521	3063 A	-17:35125529 2524657036 A	S
520	3064 G	-17:35125528 2524657035 G	
520 T	3065 T	-17:35125527 2524657034 T	
520	3066 A	-17:35125526 2524657033 A	Y
519	3067 G	-17:35125525 2524657032 G	
519 P	3068 G	-17:35125524 2524657031 G	
519	3069 C	-17:35125523 2524657030 C	A
518	3070 G	-17:35125522 2524657029 G	
518 A	3071 C	-17:35125521 2524657028 C	
518	3072 C	-17:35125520 2524657027 C	G
517	3073 A	-17:35125519 2524657026 A	
517 M	3074 T	-17:35125315 2524656822 T	
517	3075 T	-17:35125314 2524656821 T	N
516	3076 G	-17:35125313 2524656820 G	
516 T	3077 T	-17:35125312 2524656819 T	
516	3078 G	-17:35125311 2524656818 G	H
515	3079 C	-17:35125310 2524656817 C	
515 C	3080 A	-17:35125309 2524656816 A	
515	3081 G	-17:35125308 2524656815 G	L
514	3082 A	-17:35125307 2524656814 A	
514 F	3083 A	-17:35125306 2524656813 A	
514	3084 T	-17:35125305 2524656812 T	I
513	3085 T	-17:35125304 2524656811 T	
513 E	3086 C	-17:35125303 2524656810 C	
513	3087 G	-17:35125302 2524656809 G	R
512	3088 T	-17:35125301 2524656808 T	
512 D	3089 C	-17:35125300 2524656807 C	
512	3090 C	-17:35125299 2524656806 C	G
511	3091 C	-17:35125298 2524656805 C	
511 G	3092 C	-17:35125297 2524656804 C	
511	3093 G	-17:35125296 2524656803 G	R
510	3094 G	-17:35125295 2524656802 G	
510 S	3095 A	-17:35125294 2524656801 A	
510	3096 T	-17:35125293 2524656800 T	I
509	3097 T	-17:35125292 2524656799 T	
509 *	3098 A	-17:35125291 2524656798 A	
509	3099 C	-17:35125290 2524656797 C	V
508	3100 T	-17:35125289 2524656796 T	
508 K	3101 T	-17:35125288 2524656795 T	
508	3102 G	-17:35125287 2524656794 G	Q
507	3103 C	-17:35125286 2524656793 C	
507 C	3104 A	-17:35125285 2524656792 A	
507	3105 G	-17:35125284 2524656791 G	L
506	3106 G	-17:35125283 2524656790 G	
506 T	3107 T	-17:35125282 2524656789 T	
506	3108 T	-17:35125281 2524656788 T	N
505	3109 C	-17:35125280 2524656787 C	
505 R	3110 T	-17:35125279 2524656786 T	
505	3111 G	-17:35125278 2524656785 G	Q
504	3112 G	-17:35125277 2524656784 G	
504 S	3113 A	-17:35125276 2524656783 A	
504	3114 A	-17:35125275 2524656782 A	F
503	3115 G	-17:35125274 2524656781 G	
503 S	3116 A	-17:35125273 2524656780 A	
503	3117 C	-17:35125272 2524656779 C	V
502	3118 G	-17:35125271 2524656778 G	
502 A	3119 C	-17:35125270 2524656777 C	
502	3120 T	-17:35125269 2524656776 T	S
501	3121 G	-17:35125268 2524656775 G	
501 S	3122 A	-17:35125267 2524656774 A	
501	3123 G	-17:35125266 2524656773 G	L
500	3124 G	-17:35125265 2524656772 G	
500 T	3125 T	-17:35125264 2524656771 T	
500	3126 C	-17:35125263 2524656770 C	D
499	3127 A	-17:35125262 2524656769 A	
499 L	3128 G	-17:35125261 2524656768 G	
499	3129 G	-17:35125260 2524656767 G	P
498	3130 C	-17:35125259 2524656766 C	
498 C	3131 A	-17:35125258 2524656765 A	
498	3132 G	-17:35125257 2524656764 G	L
497	3133 G	-17:35125256 2524656763 G	
497 A	3134 C	-17:35125255 2524656762 C	
497	3135 T	-17:35125254 2524656761 T	S
496	3136 G	-17:35125253 2524656760 G	
496 T	3137 T	-17:35125252 2524656759 T	
496	3138 C	-17:35125251 2524656758 C	D
495	3139 C	-17:35125250 2524656757 C	
495 R	3140 G	-17:35125249 2524656756 G	
495	3141 G	-17:35125248 2524656755 G	P
494	3142 C	-17:35125247 2524656754 C	
494 G	3143 C	-17:35125246 2524656753 C	
494	3144 A	-17:35125245 2524656752 A	W
493	3145 T	-17:35125244 2524656751 T	
493 H	3146 G	-17:35125243 2524656750 G	
493	3147 C	-17:35125242 2524656749 C	A
492	3148 T	-17:35125241 2524656748 T	
492 Q	3149 G	-17:35125240 2524656747 G	
492	3150 A	-17:35125239 2524656746 A	S
491	3151 G	-17:35125238 2524656745 G	
491 S	3152 A	-17:35125237 2524656744 A	
491	3153 T	-17:35125236 2524656743 T	I
490	3154 G	-17:35125235 2524656742 G	
490 T	3155 T	-17:35125234 2524656741 T	
490	3156 A	-17:35125233 2524656740 A	Y
489	3157 T	-17:35125232 2524656739 T	
489 Y	3158 A	-17:35125231 2524656738 A	
489	3159 G	-17:35125230 2524656737 G	L
488	3160 G	-17:35125229 2524656736 G	
488 T	3161 T	-17:35125228 2524656735 T	
488	3162 A	-17:35125227 2524656734 A	Y
487	3163 A	-17:35125226 2524656733 A	
487 V	3164 C	-17:35125225 2524656732 C	
487	3165 C	-17:35125138 2524656645 C	G
486	3166 T	-17:35125137 2524656644 T	
486 Q	3167 G	-17:35125136 2524656643 G	
486	3168 T	-17:35125135 2524656642 T	T
485	3169 G	-17:35125134 2524656641 G	
485 S	3170 A	-17:35125133 2524656640 A	
485	3171 T	-17:35125132 2524656639 T	I
484	3172 C	-17:35125131 2524656638 C	
484 R	3173 T	-17:35125130 2524656637 T	
484	3174 C	-17:35125129 2524656636 C	E
483	3175 T	-17:35125128 2524656635 T	
483 K	3176 T	-17:35125127 2524656634 T	
483	3177 C	-17:35125126 2524656633 C	E
482	3178 C	-17:35125125 2524656632 C	
482 W	3179 A	-17:35125124 2524656631 A	
482	3180 G	-17:35125123 2524656630 G	L
481	3181 A	-17:35125122 2524656629 A	
481 L	3182 G	-17:35125121 2524656628 G	
481	3183 T	-17:35125120 2524656627 T	T
480	3184 C	-17:35125119 2524656626 C	
480 R	3185 T	-17:35125118 2524656625 T	
480	3186 C	-17:35125117 2524656624 C	E
479	3187 A	-17:35125116 2524656623 A	
479 L	3188 A	-17:35125115 2524656622 A	
479	3189 A	-17:35125114 2524656621 A	F
478	3190 C	-17:35125113 2524656620 C	
478 C	3191 A	-17:35125112 2524656619 A	
478	3192 C	-17:35125111 2524656618 C	V
477	3193 T	-17:35125110 2524656617 T	
477 K	3194 T	-17:35125109 2524656616 T	
477	3195 G	-17:35125108 2524656615 G	Q
476	3196 G	-17:35125107 2524656614 G	
476 S	3197 A	-17:35125106 2524656613 A	
476	3198 G	-17:35125105 2524656612 G	L
475	3199 C	-17:35125104 2524656611 C	
475 S	3200 T	-17:35125103 2524656610 T	
475	3201 G	-17:35125102 2524656609 G	Q
474	3202 C	-17:35125101 2524656608 C	
474 S	3203 T	-17:35125100 2524656607 T	
474	3204 C	-17:35125099 2524656606 C	E
473	3205 T	-17:35125098 2524656605 T	
473 Q	3206 G	-17:35125097 2524656604 G	
473	3207 G	-17:35125096 2524656603 G	P
472	3208 C	-17:35125095 2524656602 C	
472 S	3209 T	-17:35125094 2524656601 T	
472	3210 G	-17:35125093 2524656600 G	Q
471	3211 G	-17:35125092 2524656599 G	
471 S	3212 A	-17:35125091 2524656598 A	
471	3213 G	-17:35125090 2524656597 G	L
470	3214 C	-17:35125089 2524656596 C	
470 R	3215 G	-17:35125088 2524656595 G	
470	3216 G	-17:35125087 2524656594 G	P
469	3217 G	-17:35125086 2524656593 G	
469 P	3218 G	-17:35125085 2524656592 G	
469	3219 C	-17:35125084 2524656591 C	A
468	3220 A	-17:35125083 2524656590 A	
468 L	3221 G	-17:35125082 2524656589 G	
468	3222 T	-17:35125081 2524656588 T	T
467	3223 G	-17:35125080 2524656587 G	
467 T	3224 T	-17:35125079 2524656586 T	
467	3225 T	-17:35125078 2524656585 T	N
466	3226 G	-17:35125077 2524656584 G	
466 P	3227 G	-17:35125076 2524656583 G	
466	3228 A	-17:35125075 2524656582 A	S
465	3229 G	-17:35125074 2524656581 G	
465 P	3230 G	-17:35125073 2524656580 G	
465	3231 C	-17:35125072 2524656579 C	A
464	3232 T	-17:35125071 2524656578 T	
464 Q	3233 G	-17:35125070 2524656577 G	
464	3234 G	-17:35125069 2524656576 G	P
463	3235 G	-17:35125068 2524656575 G	
463 T	3236 T	-17:35125067 2524656574 T	
463	3237 C	-17:35125066 2524656573 C	D
462	3238 C	-17:35125065 2524656572 C	
462 G	3239 C	-17:35122227 2524653734 C	
462	3240 C	-17:35122226 2524653733 C	G
461	3241 A	-17:35122225 2524653732 A	
461 M	3242 T	-17:35122224 2524653731 T	
461	3243 C	-17:35122223 2524653730 C	D
460	3244 A	-17:35122222 2524653729 A	
460 L	3245 A	-17:35122221 2524653728 A	
460	3246 A	-17:35122220 2524653727 A	F
459	3247 G	-17:35122219 2524653726 G	
459 A	3248 C	-17:35122218 2524653725 C	
459	3249 T	-17:35122217 2524653724 T	S
458	3250 C	-17:35122216 2524653723 C	
458 R	3251 T	-17:35122215 2524653722 T	
458	3252 C	-17:35122214 2524653721 C	E
457	3253 C	-17:35122213 2524653720 C	
457 R	3254 G	-17:35122212 2524653719 G	
457	3255 G	-17:35122211 2524653718 G	P
456	3256 C	-17:35122210 2524653717 C	
456 C	3257 A	-17:35122209 2524653716 A	
456	3258 G	-17:35122208 2524653715 G	L
455	3259 A	-17:35122207 2524653714 A	
455 F	3260 A	-17:35122206 2524653713 A	
455	3261 A	-17:35122205 2524653712 A	F
454	3262 T	-17:35122204 2524653711 T	
454 H	3263 G	-17:35122203 2524653710 G	
454	3264 C	-17:35122202 2524653709 C	A
453	3265 C	-17:35122201 2524653708 C	
453 W	3266 A	-17:35122200 2524653707 A	
453	3267 G	-17:35122199 2524653706 G	L
452	3268 G	-17:35122198 2524653705 G	
452 A	3269 C	-17:35122197 2524653704 C	
452	3270 T	-17:35122196 2524653703 T	S
451	3271 C	-17:35122195 2524653702 C	
451 G	3272 C	-17:35122194 2524653701 C	
451	3273 C	-17:35122193 2524653700 C	G
450	3274 A	-17:35122192 2524653699 A	
450 L	3275 A	-17:35122191 2524653698 A	
450	3276 A	-17:35122190 2524653697 A	F
449	3277 G	-17:35122189 2524653696 G	
449 S	3278 A	-17:35122188 2524653695 A	
449	3279 T	-17:35122187 2524653694 T	I
448	3280 C	-17:35122186 2524653693 C	
448 R	3281 T	-17:35122185 2524653692 T	
448	3282 T	-17:35122184 2524653691 T	K
447	3283 C	-17:35122183 2524653690 C	
447 R	3284 T	-17:35122182 2524653689 T	
447	3285 T	-17:35122181 2524653688 T	K
446	3286 G	-17:35122180 2524653687 G	
446 A	3287 C	-17:35122179 2524653686 C	
446	3288 A	-17:35122178 2524653685 A	C
445	3289 G	-17:35122177 2524653684 G	
445 A	3290 C	-17:35122176 2524653683 C	
445	3291 C	-17:35122175 2524653682 C	G
444	3292 A	-17:35122174 2524653681 A	
444 L	3293 G	-17:35122173 2524653680 G	
444	3294 C	-17:35122172 2524653679 C	A
443	3295 A	-17:35122171 2524653678 A	
443 L	3296 A	-17:35122170 2524653677 A	
443	3297 A	-17:35122169 2524653676 A	F
442	3298 C	-17:35122168 2524653675 C	
442 S	3299 T	-17:35122167 2524653674 T	
442	3300 C	-17:35122166 2524653673 C	E
441	3301 C	-17:35122165 2524653672 C	
441 R	3302 T	-17:35122164 2524653671 T	
441	3303 G	-17:35122163 2524653670 G	Q
440	3304 G	-17:35122162 2524653669 G	
440 S	3305 A	-17:35122161 2524653668 A	
440	3306 T	-17:35122160 2524653667 T	I
439	3307 A	-17:35122159 2524653666 A	
439 I	3308 T	-17:35122158 2524653665 T	
439	3309 T	-17:35122157 2524653664 T	N
438	3310 G	-17:35122156 2524653663 G	
438 P	3311 G	-17:35122155 2524653662 G	
438	3312 C	-17:35122154 2524653661 C	A
437	3313 A	-17:35122153 2524653660 A	
437 V	3314 C	-17:35122152 2524653659 C	
437	3315 T	-17:35122151 2524653658 T	S
436	3316 G	-17:35122150 2524653657 G	
436 P	3317 G	-17:35122149 2524653656 G	
436	3318 T	-17:35122148 2524653655 T	T
435	3319 A	-17:35122147 2524653654 A	
435 L	3320 A	-17:35122146 2524653653 A	
435	3321 C	-17:35122145 2524653652 C	V
434	3322 T	-17:35122144 2524653651 T	
434 Q	3323 G	-17:35122143 2524653650 G	
434	3324 C	-17:35122142 2524653649 C	A
433	3325 C	-17:35122141 2524653648 C	
433 G	3326 C	-17:35122140 2524653647 C	
433	3327 T	-17:35122139 2524653646 T	R
432	3328 C	-17:35122138 2524653645 C	
432 *	3329 A	-17:35122137 2524653644 A	
432	3330 C	-17:35122136 2524653643 C	V
431	3331 C	-17:35122135 2524653642 C	
431 R	3332 T	-17:35122134 2524653641 T	
431	3333 C	-17:35122133 2524653640 C	E
430	3334 T	-17:35122132 2524653639 T	
430 E	3335 C	-17:35122131 2524653638 C	
430	3336 G	-17:35122130 2524653637 G	R
429	3337 C	-17:35122129 2524653636 C	
429 C	3338 A	-17:35122128 2524653635 A	
429	3339 A	-17:35122127 2524653634 A	L
428	3340 G	-17:35122126 2524653633 G	
428 T	3341 T	-17:35122125 2524653632 T	
428	3342 G	-17:35122124 2524653631 G	H
427	3343 C	-17:35122123 2524653630 C	
427 S	3344 T	-17:35122122 2524653629 T	
427	3345 C	-17:35122121 2524653628 C	E
426	3346 C	-17:35122120 2524653627 C	
426 W	3347 A	-17:35122119 2524653626 A	
426	3348 T	-17:35122118 2524653625 T	M
425	3349 G	-17:35122117 2524653624 G	
425 A	3350 C	-17:35122116 2524653623 C	
425	3351 C	-17:35122115 2524653622 C	G
424	3352 C	-17:35122114 2524653621 C	
424 W	3353 A	-17:35122113 2524653620 A	
424	3354 G	-17:35122112 2524653619 G	L
423	3355 A	-17:35122111 2524653618 A	
423 V	3356 C	-17:35122110 2524653617 C	
423	3357 C	-17:35122109 2524653616 C	G
422	3358 A	-17:35122108 2524653615 A	
422 M	3359 T	-17:35122107 2524653614 T	
422	3360 A	-17:35122106 2524653613 A	Y
421	3361 G	-17:35122105 2524653612 G	
421 A	3362 C	-17:35122104 2524653611 C	
421	3363 A	-17:35122103 2524653610 A	C
420	3364 C	-17:35122102 2524653609 C	
420 C	3365 A	-17:35122101 2524653608 A	
420	3366 C	-17:35121826 2524653333 C	V
419	3367 T	-17:35121825 2524653332 T	
419 E	3368 C	-17:35121824 2524653331 C	
419	3369 G	-17:35121823 2524653330 G	R
418	3370 G	-17:35121822 2524653329 G	
418 P	3371 G	-17:35121821 2524653328 G	
418	3372 C	-17:35121820 2524653327 C	A
417	3373 A	-17:35121819 2524653326 A	
417 V	3374 C	-17:35121818 2524653325 C	
417	3375 A	-17:35121817 2524653324 A	C
416	3376 G	-17:35121816 2524653323 G	
416 P	3377 G	-17:35121815 2524653322 G	
416	3378 G	-17:35121814 2524653321 G	P
415	3379 C	-17:35121813 2524653320 C	
415 S	3380 T	-17:35121812 2524653319 T	
415	3381 T	-17:35121811 2524653318 T	K
414	3382 G	-17:35121810 2524653317 G	
414 A	3383 C	-17:35121809 2524653316 C	
414	3384 T	-17:35121808 2524653315 T	S
413	3385 G	-17:35121807 2524653314 G	
413 A	3386 C	-17:35121806 2524653313 C	
413	3387 A	-17:35121805 2524653312 A	C
412	3388 C	-17:35121804 2524653311 C	
412 S	3389 T	-17:35121803 2524653310 T	
412	3390 T	-17:35121802 2524653309 T	K
411	3391 C	-17:35121801 2524653308 C	
411 R	3392 T	-17:35121800 2524653307 T	
411	3393 C	-17:35121799 2524653306 C	E
410	3394 A	-17:35121798 2524653305 A	
410 V	3395 C	-17:35121797 2524653304 C	
410	3396 A	-17:35121796 2524653303 A	C
409	3397 C	-17:35121795 2524653302 C	
409 G	3398 C	-17:35121794 2524653301 C	
409	3399 G	-17:35121793 2524653300 G	R
408	3400 C	-17:35121792 2524653299 C	
408 S	3401 T	-17:35121791 2524653298 T	
408	3402 G	-17:35121790 2524653297 G	Q
407	3403 T	-17:35121789 2524653296 T	
407 H	3404 G	-17:35121788 2524653295 G	
407	3405 T	-17:35121787 2524653294 T	T
406	3406 T	-17:35121786 2524653293 T	
406 E	3407 C	-17:35121785 2524653292 C	
406	3408 C	-17:35121784 2524653291 C	G
405	3409 A	-17:35121783 2524653290 A	
405 M	3410 T	-17:35121782 2524653289 T	
405	3411 C	-17:35121781 2524653288 C	D
404	3412 C	-17:35121780 2524653287 C	
404 R	3413 T	-17:35121779 2524653286 T	
404	3414 C	-17:35121778 2524653285 C	E
403	3415 T	-17:35121777 2524653284 T	
403 Q	3416 G	-17:35121776 2524653283 G	
403	3417 C	-17:35121775 2524653282 C	A
402	3418 T	-17:35121774 2524653281 T	
402 Q	3419 G	-17:35121773 2524653280 G	
402	3420 T	-17:35121772 2524653279 T	T
401	3421 C	-17:35121771 2524653278 C	
401 *	3422 A	-17:35121770 2524653277 A	
401	3423 C	-17:35121769 2524653276 C	V
400	3424 C	-17:35121768 2524653275 C	
400 R	3425 T	-17:35121767 2524653274 T	
400	3426 C	-17:35121766 2524653273 C	E
399	3427 T	-17:35121765 2524653272 T	
399 K	3428 T	-17:35121764 2524653271 T	
399	3429 G	-17:35121763 2524653270 G	Q
398	3430 G	-17:35121762 2524653269 G	
398 T	3431 T	-17:35121761 2524653268 T	
398	3432 T	-17:35121760 2524653267 T	N
397	3433 G	-17:35121759 2524653266 G	
397 T	3434 T	-17:35121758 2524653265 T	
397	3435 G	-17:35121757 2524653264 G	H
396	3436 C	-17:35121756 2524653263 C	
396 C	3437 A	-17:35121755 2524653262 A	
396	3438 G	-17:35121754 2524653261 G	L
395	3439 G	-17:35121753 2524653260 G	
395 P	3440 G	-17:35121752 2524653259 G	
395	3441 G	-17:35121751 2524653258 G	P
394	3442 G	-17:35121750 2524653257 G	
394 A	3443 C	-17:35121749 2524653256 C	
394	3444 A	-17:35121748 2524653255 A	C
393	3445 G	-17:35121747 2524653254 G	
393 S	3446 A	-17:35121746 2524653253 A	
393	3447 C	-17:35121745 2524653252 C	V
392	3448 G	-17:35121744 2524653251 G	
392 S	3449 A	-17:35121743 2524653250 A	
392	3450 G	-17:35121742 2524653249 G	L
391	3451 G	-17:35121741 2524653248 G	
391 P	3452 G	-17:35121740 2524653247 G	
391	3453 T	-17:35121739 2524653246 T	T
390	3454 G	-17:35121738 2524653245 G	
390 A	3455 C	-17:35121737 2524653244 C	
390	3456 A	-17:35121736 2524653243 A	C
389	3457 G	-17:35121735 2524653242 G	
389 P	3458 G	-17:35121734 2524653241 G	
389	3459 A	-17:35121733 2524653240 A	S
388	3460 T	-17:35121732 2524653239 T	
388 D	3461 C	-17:35121731 2524653238 C	
388	3462 C	-17:35121730 2524653237 C	G
387	3463 C	-17:35121729 2524653236 C	
387 W	3464 A	-17:35121728 2524653235 A	
387	3465 C	-17:35121727 2524653234 C	V
386	3466 G	-17:35121726 2524653233 G	
386 T	3467 T	-17:35121725 2524653232 T	
386	3468 C	-17:35121724 2524653231 C	D
385	3469 C	-17:35121723 2524653230 C	
385 R	3470 G	-17:35121722 2524653229 G	
385	3471 T	-17:35121721 2524653228 T	T
384	3472 A	-17:35121720 2524653227 A	
384 L	3473 G	-17:35121719 2524653226 G	
384	3474 A	-17:35121718 2524653225 A	S
383	3475 A	-17:35121717 2524653224 A	
383 F	3476 A	-17:35121716 2524653223 A	
383	3477 G	-17:35121715 2524653222 G	L
382	3478 G	-17:35121714 2524653221 G	
382 T	3479 T	-17:35121713 2524653220 T	
382	3480 A	-17:35121712 2524653219 A	Y
381	3481 G	-17:35121711 2524653218 G	
381 T	3482 T	-17:35121710 2524653217 T	
381	3483 T	-17:35121709 2524653216 T	N
380	3484 G	-17:35121708 2524653215 G	
380 T	3485 T	-17:35121707 2524653214 T	
380	3486 A	-17:35120260 2524651767 A	Y
379	3487 G	-17:35120259 2524651766 G	
379 P	3488 G	-17:35120258 2524651765 G	
379	3489 G	-17:35120257 2524651764 G	P
378	3490 A	-17:35120256 2524651763 A	
378 V	3491 C	-17:35120255 2524651762 C	
378	3492 A	-17:35120254 2524651761 A	C
377	3493 G	-17:35120253 2524651760 G	
377 P	3494 G	-17:35120252 2524651759 G	
377	3495 C	-17:35120251 2524651758 C	A
376	3496 A	-17:35120250 2524651757 A	
376 L	3497 G	-17:35120249 2524651756 G	
376	3498 T	-17:35120248 2524651755 T	T
375	3499 C	-17:35120247 2524651754 C	
375 *	3500 A	-17:35120246 2524651753 A	
375	3501 C	-17:35120245 2524651752 C	V
374	3502 A	-17:35120244 2524651751 A	
374 V	3503 C	-17:35120243 2524651750 C	
374	3504 A	-17:35120242 2524651749 A	C
373	3505 G	-17:35120241 2524651748 G	
373 A	3506 C	-17:35120240 2524651747 C	
373	3507 T	-17:35120239 2524651746 T	S
372	3508 G	-17:35120238 2524651745 G	
372 P	3509 G	-17:35120237 2524651744 G	
372	3510 C	-17:35120236 2524651743 C	A
371	3511 G	-17:35120235 2524651742 G	
371 A	3512 C	-17:35120234 2524651741 C	
371	3513 C	-17:35120233 2524651740 C	G
370	3514 G	-17:35120232 2524651739 G	
370 S	3515 A	-17:35120231 2524651738 A	
370	3516 A	-17:35120230 2524651737 A	F
369	3517 T	-17:35120229 2524651736 T	
369 H	3518 G	-17:35120228 2524651735 G	
369	3519 T	-17:35120227 2524651734 T	T
368	3520 A	-17:35120226 2524651733 A	
368 I	3521 T	-17:35120225 2524651732 T	
368	3522 A	-17:35120224 2524651731 A	Y
367	3523 C	-17:35120223 2524651730 C	
367 G	3524 C	-17:35120222 2524651729 C	
367	3525 G	-17:35120221 2524651728 G	R
366	3526 G	-17:35120220 2524651727 G	
366 A	3527 C	-17:35120219 2524651726 C	
366	3528 C	-17:35120218 2524651725 C	G
365	3529 C	-17:35120217 2524651724 C	
365 R	3530 T	-17:35120216 2524651723 T	
365	3531 C	-17:35120215 2524651722 C	E
364	3532 G	-17:35120214 2524651721 G	
364 P	3533 G	-17:35120213 2524651720 G	
364	3534 G	-17:35120212 2524651719 G	P
363	3535 A	-17:35120211 2524651718 A	
363 I	3536 T	-17:35120210 2524651717 T	
363	3537 T	-17:35120209 2524651716 T	N
362	3538 G	-17:35120208 2524651715 G	
362 P	3539 G	-17:35120207 2524651714 G	
362	3540 G	-17:35120206 2524651713 G	P
361	3541 C	-17:35120205 2524651712 C	
361 C	3542 A	-17:35120204 2524651711 A	
361	3543 T	-17:35120203 2524651710 T	M
360	3544 G	-17:35120202 2524651709 G	
360 P	3545 G	-17:35120201 2524651708 G	
360	3546 A	-17:35120200 2524651707 A	S
359	3547 C	-17:35120199 2524651706 C	
359 S	3548 T	-17:35120198 2524651705 T	
359	3549 C	-17:35120197 2524651704 C	E
358	3550 A	-17:35120196 2524651703 A	
358 L	3551 A	-17:35120195 2524651702 A	
358	3552 A	-17:35120194 2524651701 A	F
357	3553 C	-17:35120193 2524651700 C	
357 R	3554 G	-17:35120192 2524651699 G	
357	3555 T	-17:35120191 2524651698 T	T
356	3556 G	-17:35120190 2524651697 G	
356 T	3557 T	-17:35120189 2524651696 T	
356	3558 C	-17:35120188 2524651695 C	D
355	3559 T	-17:35120187 2524651694 T	
355 Q	3560 G	-17:35120186 2524651693 G	
355	3561 T	-17:35120185 2524651692 T	T
354	3562 G	-17:35120184 2524651691 G	
354 T	3563 T	-17:35120183 2524651690 T	
354	3564 T	-17:35120182 2524651689 T	N
353	3565 G	-17:35120181 2524651688 G	
353 T	3566 T	-17:35120180 2524651687 T	
353	3567 A	-17:35120179 2524651686 A	Y
352	3568 G	-17:35120178 2524651685 G	
352 P	3569 G	-17:35120177 2524651684 G	
352	3570 T	-17:35120176 2524651683 T	T
351	3571 G	-17:35120175 2524651682 G	
351 S	3572 A	-17:35120174 2524651681 A	
351	3573 C	-17:35120173 2524651680 C	V
350	3574 C	-17:35120172 2524651679 C	
350 W	3575 A	-17:35120171 2524651678 A	
350	3576 G	-17:35120170 2524651677 G	L
349	3577 G	-17:35120169 2524651676 G	
349 P	3578 G	-17:35120168 2524651675 G	
349	3579 C	-17:35120167 2524651674 C	A
348	3580 T	-17:35120166 2524651673 T	
348 Q	3581 G	-17:35120165 2524651672 G	
348	3582 G	-17:35120164 2524651671 G	P
347	3583 G	-17:35120163 2524651670 G	
347 A	3584 C	-17:35120162 2524651669 C	
347	3585 A	-17:35120161 2524651668 A	C
346	3586 G	-17:35120160 2524651667 G	
346 T	3587 T	-17:35120159 2524651666 T	
346	3588 G	-17:35120158 2524651665 G	H
345	3589 C	-17:35120157 2524651664 C	
345 C	3590 A	-17:35120156 2524651663 A	
345	3591 G	-17:35120155 2524651662 G	L
344	3592 C	-17:35120154 2524651661 C	
344 S	3593 T	-17:35120153 2524651660 T	
344	3594 C	-17:35120152 2524651659 C	E
343	3595 A	-17:35120151 2524651658 A	
343 V	3596 C	-17:35120150 2524651657 C	
343	3597 A	-17:35120149 2524651656 A	C
342	3598 G	-17:35120148 2524651655 G	
342 S	3599 A	-17:35120147 2524651654 A	
342	3600 T	-17:35120146 2524651653 T	I
341	3601 G	-17:35120145 2524651652 G	
341 A	3602 C	-17:35120144 2524651651 C	
341	3603 C	-17:35120143 2524651650 C	G
340	3604 A	-17:35120142 2524651649 A	
340 V	3605 C	-17:35120141 2524651648 C	
340	3606 T	-17:35120140 2524651647 T	S
339	3607 G	-17:35120139 2524651646 G	
339 T	3608 T	-17:35120138 2524651645 T	
339	3609 G	-17:35120137 2524651644 G	H
338	3610 G	-17:35120136 2524651643 G	
338 T	3611 T	-17:35120135 2524651642 T	
338	3612 T	-17:35120134 2524651641 T	N
337	3613 G	-17:35120133 2524651640 G	
337 S	3614 A	-17:35120132 2524651639 A	
337	3615 A	-17:35120131 2524651638 A	F
336	3616 G	-17:35120130 2524651637 G	
336 T	3617 T	-17:35120129 2524651636 T	
336	3618 G	-17:35120128 2524651635 G	H
335	3619 G	-17:35120127 2524651634 G	
335 S	3620 A	-17:35120126 2524651633 A	
335	3621 G	-17:35120125 2524651632 G	L
334	3622 G	-17:35120124 2524651631 G	
334 A	3623 C	-17:35120123 2524651630 C	
334	3624 A	-17:35120122 2524651629 A	C
333	3625 G	-17:35120121 2524651628 G	
333 P	3626 G	-17:35120120 2524651627 G	
333	3627 C	-17:35120119 2524651626 C	A
332	3628 C	-17:35119980 2524651487 C	
332 W	3629 A	-17:35119979 2524651486 A	
332	3630 G	-17:35119978 2524651485 G	L
331	3631 G	-17:35119977 2524651484 G	
331 A	3632 C	-17:35119976 2524651483 C	
331	3633 A	-17:35119975 2524651482 A	C
330	3634 G	-17:35119974 2524651481 G	
330 T	3635 T	-17:35119973 2524651480 T	
330	3636 C	-17:35119972 2524651479 C	D
329	3637 A	-17:35119971 2524651478 A	
329 L	3638 G	-17:35119970 2524651477 G	
329	3639 A	-17:35119969 2524651476 A	S
328	3640 G	-17:35119968 2524651475 G	
328 T	3641 T	-17:35119967 2524651474 T	
328	3642 G	-17:35119966 2524651473 G	H
327	3643 C	-17:35119965 2524651472 C	
327 S	3644 T	-17:35119964 2524651471 T	
327	3645 T	-17:35119963 2524651470 T	K
326	3646 G	-17:35119962 2524651469 G	
326 P	3647 G	-17:35119961 2524651468 G	
326	3648 G	-17:35119960 2524651467 G	P
325	3649 G	-17:35119959 2524651466 G	
325 A	3650 C	-17:35119958 2524651465 C	
325	3651 C	-17:35119957 2524651464 C	G
324	3652 C	-17:35119956 2524651463 C	
324 R	3653 G	-17:35119955 2524651462 G	
324	3654 T	-17:35119954 2524651461 T	T
323	3655 G	-17:35119953 2524651460 G	
323 A	3656 C	-17:35119952 2524651459 C	
323	3657 A	-17:35119951 2524651458 A	C
322	3658 G	-17:35119950 2524651457 G	
322 A	3659 C	-17:35119949 2524651456 C	
322	3660 C	-17:35119948 2524651455 C	G
321	3661 G	-17:35119947 2524651454 G	
321 P	3662 G	-17:35119946 2524651453 G	
321	3663 C	-17:35119945 2524651452 C	A
320	3664 A	-17:35119944 2524651451 A	
320 L	3665 G	-17:35119943 2524651450 G	
320	3666 C	-17:35119942 2524651449 C	A
319	3667 A	-17:35119941 2524651448 A	
319 V	3668 C	-17:35119940 2524651447 C	
319	3669 A	-17:35119939 2524651446 A	C
318	3670 C	-17:35119938 2524651445 C	
318 S	3671 T	-17:35119937 2524651444 T	
318	3672 G	-17:35119936 2524651443 G	Q
317	3673 C	-17:35119935 2524651442 C	
317 S	3674 T	-17:35119934 2524651441 T	
317	3675 C	-17:35119933 2524651440 C	E
316	3676 A	-17:35119932 2524651439 A	
316 M	3677 T	-17:35119931 2524651438 T	
316	3678 G	-17:35119930 2524651437 G	H
315	3679 G	-17:35119929 2524651436 G	
315 A	3680 C	-17:35119928 2524651435 C	
315	3681 A	-17:35119927 2524651434 A	C
314	3682 G	-17:35119926 2524651433 G	
314 A	3683 C	-17:35119925 2524651432 C	
314	3684 A	-17:35119924 2524651431 A	C
313	3685 G	-17:35119923 2524651430 G	
313 T	3686 T	-17:35119922 2524651429 T	
313	3687 C	-17:35119921 2524651428 C	D
312	3688 A	-17:35119920 2524651427 A	
312 L	3689 G	-17:35119919 2524651426 G	
312	3690 T	-17:35119918 2524651425 T	T
311	3691 G	-17:35119917 2524651424 G	
311 P	3692 G	-17:35119916 2524651423 G	
311	3693 G	-17:35119915 2524651422 G	P
310	3694 C	-17:35119914 2524651421 C	
310 C	3695 A	-17:35119913 2524651420 A	
310	3696 G	-17:35119912 2524651419 G	L
309	3697 T	-17:35119911 2524651418 T	
309 H	3698 G	-17:35119910 2524651417 G	
309	3699 G	-17:35119909 2524651416 G	P
308	3700 C	-17:35119908 2524651415 C	
308 G	3701 C	-17:35119907 2524651414 C	
308	3702 C	-17:35119906 2524651413 C	G
307	3703 C	-17:35119905 2524651412 C	
307 R	3704 T	-17:35119904 2524651411 T	
307	3705 T	-17:35119903 2524651410 T	K
306	3706 G	-17:35119902 2524651409 G	
306 A	3707 C	-17:35119901 2524651408 C	
306	3708 A	-17:35119900 2524651407 A	C
305	3709 G	-17:35119899 2524651406 G	
305 A	3710 C	-17:35119898 2524651405 C	
305	3711 G	-17:35119897 2524651404 G	R
304	3712 G	-17:35119896 2524651403 G	
304 P	3713 G	-17:35119895 2524651402 G	
304	3714 C	-17:35119894 2524651401 C	A
303	3715 A	-17:35119893 2524651400 A	
303 V	3716 C	-17:35119892 2524651399 C	
303	3717 A	-17:35119891 2524651398 A	C
302	3718 G	-17:35119890 2524651397 G	
302 A	3719 C	-17:35119889 2524651396 C	
302	3720 C	-17:35119888 2524651395 C	G
301	3721 A	-17:35119887 2524651394 A	
301 V	3722 C	-17:35119886 2524651393 C	
301	3723 C	-17:35119885 2524651392 C	G
300	3724 G	-17:35119884 2524651391 G	
300 P	3725 G	-17:35119883 2524651390 G	
300	3726 C	-17:35119882 2524651389 C	A
299	3727 A	-17:35119881 2524651388 A	
299 V	3728 C	-17:35119880 2524651387 C	
299	3729 A	-17:35119879 2524651386 A	C
298	3730 G	-17:35119878 2524651385 G	
298 S	3731 A	-17:35119877 2524651384 A	
298	3732 C	-17:35119876 2524651383 C	V
297	3733 A	-17:35119875 2524651382 A	
297 L	3734 G	-17:35119874 2524651381 G	
297	3735 T	-17:35119873 2524651380 T	T
296	3736 G	-17:35119872 2524651379 G	
296 A	3737 C	-17:35119871 2524651378 C	
296	3738 G	-17:35119870 2524651377 G	R
295	3739 C	-17:35119869 2524651376 C	
295 R	3740 G	-17:35119868 2524651375 G	
295	3741 T	-17:35119867 2524651374 T	T
294	3742 C	-17:35119866 2524651373 C	
294 *	3743 A	-17:35119865 2524651372 A	
294	3744 G	-17:35119660 2524651167 G	L
293	3745 G	-17:35119659 2524651166 G	
293 A	3746 C	-17:35119658 2524651165 C	
293	3747 T	-17:35119657 2524651164 T	S
292	3748 C	-17:35119656 2524651163 C	
292 R	3749 T	-17:35119655 2524651162 T	
292	3750 G	-17:35119654 2524651161 G	Q
291	3751 A	-17:35119653 2524651160 A	
291 V	3752 C	-17:35119652 2524651159 C	
291	3753 A	-17:35119651 2524651158 A	C
290	3754 A	-17:35119650 2524651157 A	
290 I	3755 T	-17:35119649 2524651156 T	
290	3756 C	-17:35119648 2524651155 C	D
289	3757 C	-17:35119647 2524651154 C	
289 R	3758 T	-17:35119646 2524651153 T	
289	3759 C	-17:35119645 2524651152 C	E
288	3760 A	-17:35119644 2524651151 A	
288 L	3761 G	-17:35119643 2524651150 G	
288	3762 A	-17:35119642 2524651149 A	S
287	3763 A	-17:35119641 2524651148 A	
287 V	3764 C	-17:35119640 2524651147 C	
287	3765 T	-17:35119639 2524651146 T	S
286	3766 C	-17:35119638 2524651145 C	
286 R	3767 T	-17:35119637 2524651144 T	
286	3768 C	-17:35119636 2524651143 C	E
285	3769 T	-17:35119635 2524651142 T	
285 E	3770 C	-17:35119634 2524651141 C	
285	3771 C	-17:35119633 2524651140 C	G
284	3772 C	-17:35119632 2524651139 C	
284 G	3773 C	-17:35119631 2524651138 C	
284	3774 A	-17:35119630 2524651137 A	W
283	3775 G	-17:35119629 2524651136 G	
283 A	3776 C	-17:35119628 2524651135 C	
283	3777 A	-17:35119627 2524651134 A	C
282	3778 G	-17:35119626 2524651133 G	
282 A	3779 C	-17:35119625 2524651132 C	
282	3780 G	-17:35119624 2524651131 G	R
281	3781 G	-17:35119623 2524651130 G	
281 P	3782 G	-17:35119622 2524651129 G	
281	3783 A	-17:35119621 2524651128 A	S
280	3784 G	-17:35119620 2524651127 G	
280 A	3785 C	-17:35119619 2524651126 C	
280	3786 C	-17:35119618 2524651125 C	G
279	3787 C	-17:35119617 2524651124 C	
279 R	3788 T	-17:35119616 2524651123 T	
279	3789 T	-17:35119615 2524651122 T	K
278	3790 A	-17:35119614 2524651121 A	
278 V	3791 C	-17:35119613 2524651120 C	
278	3792 A	-17:35119612 2524651119 A	C
277	3793 C	-17:35119611 2524651118 C	
277 C	3794 A	-17:35119610 2524651117 A	
277	3795 T	-17:35119609 2524651116 T	M
276	3796 C	-17:35119608 2524651115 C	
276 R	3797 G	-17:35119607 2524651114 G	
276	3798 G	-17:35119606 2524651113 G	P
275	3799 A	-17:35119605 2524651112 A	
275 L	3800 G	-17:35119604 2524651111 G	
275	3801 A	-17:35119603 2524651110 A	S
274	3802 A	-17:35119602 2524651109 A	
274 V	3803 C	-17:35119601 2524651108 C	
274	3804 A	-17:35119600 2524651107 A	C
273	3805 G	-17:35119599 2524651106 G	
273 P	3806 G	-17:35119598 2524651105 G	
273	3807 G	-17:35119597 2524651104 G	P
272	3808 G	-17:35119596 2524651103 G	
272 T	3809 T	-17:35119595 2524651102 T	
272	3810 G	-17:35119594 2524651101 G	H
271	3811 G	-17:35119593 2524651100 G	
271 A	3812 C	-17:35119592 2524651099 C	
271	3813 A	-17:35119231 2524650738 A	C
270	3814 G	-17:35119230 2524650737 G	
270 P	3815 G	-17:35119229 2524650736 G	
270	3816 C	-17:35119228 2524650735 C	A
269	3817 C	-17:35119227 2524650734 C	
269 G	3818 C	-17:35119226 2524650733 C	
269	3819 G	-17:35119225 2524650732 G	R
268	3820 A	-17:35119224 2524650731 A	
268 L	3821 G	-17:35119223 2524650730 G	
268	3822 A	-17:35119222 2524650729 A	S
267	3823 G	-17:35119221 2524650728 G	
267 A	3824 C	-17:35119220 2524650727 C	
267	3825 G	-17:35119219 2524650726 G	R
266	3826 G	-17:35119218 2524650725 G	
266 T	3827 T	-17:35119217 2524650724 T	
266	3828 T	-17:35119216 2524650723 T	N
265	3829 G	-17:35119215 2524650722 G	
265 P	3830 G	-17:35119214 2524650721 G	
265	3831 T	-17:35119213 2524650720 T	T
264	3832 G	-17:35119212 2524650719 G	
264 T	3833 T	-17:35119211 2524650718 T	
264	3834 C	-17:35119210 2524650717 C	D
263	3835 T	-17:35119209 2524650716 T	
263 *	3836 A	-17:35119208 2524650715 A	
263	3837 T	-17:35119207 2524650714 T	I
262	3838 C	-17:35119206 2524650713 C	
262 *	3839 A	-17:35119205 2524650712 A	
262	3840 G	-17:35119204 2524650711 G	L
261	3841 T	-17:35119203 2524650710 T	
261 H	3842 G	-17:35119202 2524650709 G	
261	3843 T	-17:35119201 2524650708 T	T
260	3844 G	-17:35119200 2524650707 G	
260 S	3845 A	-17:35119199 2524650706 A	
260	3846 G	-17:35119198 2524650705 G	L
259	3847 A	-17:35119197 2524650704 A	
259 L	3848 G	-17:35119196 2524650703 G	
259	3849 C	-17:35119195 2524650702 C	A
258	3850 C	-17:35119194 2524650701 C	
258 W	3851 A	-17:35119193 2524650700 A	
258	3852 G	-17:35119192 2524650699 G	L
257	3853 C	-17:35119191 2524650698 C	
257 S	3854 T	-17:35119190 2524650697 T	
257	3855 G	-17:35119189 2524650696 G	Q
256	3856 G	-17:35119188 2524650695 G	
256 T	3857 T	-17:35119187 2524650694 T	
256	3858 T	-17:35119186 2524650693 T	N
255	3859 G	-17:35119185 2524650692 G	
255 T	3860 T	-17:35119184 2524650691 T	
255	3861 T	-17:35119183 2524650690 T	N
254	3862 C	-17:35119182 2524650689 C	
254 R	3863 T	-17:35119181 2524650688 T	
254	3864 T	-17:35119180 2524650687 T	K
253	3865 G	-17:35119179 2524650686 G	
253 T	3866 T	-17:35119178 2524650685 T	
253	3867 G	-17:35119177 2524650684 G	H
252	3868 G	-17:35119176 2524650683 G	
252 S	3869 A	-17:35119175 2524650682 A	
252	3870 A	-17:35119174 2524650681 A	F
251	3871 G	-17:35119173 2524650680 G	
251 S	3872 A	-17:35119172 2524650679 A	
251	3873 T	-17:35119171 2524650678 T	I
250	3874 G	-17:35119170 2524650677 G	
250 T	3875 T	-17:35119169 2524650676 T	
250	3876 C	-17:35119168 2524650675 C	D
249	3877 C	-17:35119167 2524650674 C	
249 R	3878 T	-17:35119166 2524650673 T	
249	3879 T	-17:35119165 2524650672 T	K
248	3880 C	-17:35119164 2524650671 C	
248 G	3881 C	-17:35119163 2524650670 C	
248	3882 A	-17:35119162 2524650669 A	W
247	3883 C	-17:35119161 2524650668 C	
247 C	3884 A	-17:35119160 2524650667 A	
247	3885 A	-17:35119159 2524650666 A	L
246	3886 A	-17:35119158 2524650665 A	
246 F	3887 A	-17:35119157 2524650664 A	
246	3888 T	-17:35119156 2524650663 T	I
245	3889 C	-17:35119155 2524650662 C	
245 R	3890 G	-17:35119154 2524650661 G	
245	3891 T	-17:35119153 2524650660 T	T
244	3892 G	-17:35119152 2524650659 G	
244 T	3893 T	-17:35119151 2524650658 T	
244	3894 C	-17:35119150 2524650657 C	D
243	3895 C	-17:35119149 2524650656 C	
243 R	3896 T	-17:35119148 2524650655 T	
243	3897 G	-17:35119147 2524650654 G	Q
242	3898 G	-17:35119146 2524650653 G	
242 T	3899 T	-17:35119145 2524650652 T	
242	3900 A	-17:35119144 2524650651 A	Y
241	3901 G	-17:35119143 2524650650 G	
241 A	3902 C	-17:35119142 2524650649 C	
241	3903 A	-17:35119141 2524650648 A	C
240	3904 G	-17:35119140 2524650647 G	
240 S	3905 A	-17:35119139 2524650646 A	
240	3906 G	-17:35119138 2524650645 G	L
239	3907 C	-17:35119137 2524650644 C	
239 S	3908 T	-17:35119136 2524650643 T	
239	3909 G	-17:35119135 2524650642 G	Q
238	3910 G	-17:35119134 2524650641 G	
238 P	3911 G	-17:35119133 2524650640 G	
238	3912 G	-17:35119132 2524650639 G	P
237	3913 G	-17:35119131 2524650638 G	
237 T	3914 T	-17:35119130 2524650637 T	
237	3915 T	-17:35119129 2524650636 T	N
236	3916 C	-17:35119128 2524650635 C	
236 G	3917 C	-17:35119127 2524650634 C	
236	3918 G	-17:35119126 2524650633 G	R
235	3919 C	-17:35119125 2524650632 C	
235 S	3920 T	-17:35119124 2524650631 T	
235	3921 G	-17:35119123 2524650630 G	Q
234	3922 G	-17:35119122 2524650629 G	
234 S	3923 A	-17:35119121 2524650628 A	
234	3924 T	-17:35119120 2524650627 T	I
233	3925 C	-17:35119119 2524650626 C	
233 *	3926 A	-17:35119118 2524650625 A	
233	3927 A	-17:35119117 2524650624 A	L
232	3928 G	-17:35119116 2524650623 G	
232 S	3929 A	-17:35119115 2524650622 A	
232	3930 C	-17:35119114 2524650621 C	V
231	3931 C	-17:35119113 2524650620 C	
231 G	3932 C	-17:35119112 2524650619 C	
231	3933 C	-17:35119111 2524650618 C	G
230	3934 T	-17:35119110 2524650617 T	
230 E	3935 C	-17:35119109 2524650616 C	
230	3936 C	-17:35119108 2524650615 C	G
229	3937 T	-17:35119107 2524650614 T	
229 K	3938 T	-17:35119106 2524650613 T	
229	3939 T	-17:35119105 2524650612 T	K
228	3940 C	-17:35119104 2524650611 C	
228 *	3941 A	-17:35119103 2524650610 A	
228	3942 A	-17:35119102 2524650609 A	L
227	3943 G	-17:35119101 2524650608 G	
227 S	3944 A	-17:35119100 2524650607 A	
227	3945 T	-17:35119099 2524650606 T	I
226	3946 C	-17:35119098 2524650605 C	
226 R	3947 T	-17:35119097 2524650604 T	
226	3948 C	-17:35118313 2524649820 C	E
225	3949 T	-17:35118312 2524649819 T	
225 Q	3950 G	-17:35118311 2524649818 G	
225	3951 T	-17:35118310 2524649817 T	T
224	3952 G	-17:35118309 2524649816 G	
224 S	3953 A	-17:35118308 2524649815 A	
224	3954 G	-17:35118307 2524649814 G	L
223	3955 G	-17:35118306 2524649813 G	
223 A	3956 C	-17:35118305 2524649812 C	
223	3957 T	-17:35118304 2524649811 T	S
222	3958 T	-17:35118303 2524649810 T	
222 E	3959 C	-17:35118302 2524649809 C	
222	3960 G	-17:35118301 2524649808 G	R
221	3961 A	-17:35118300 2524649807 A	
221 F	3962 A	-17:35118299 2524649806 A	
221	3963 G	-17:35118298 2524649805 G	L
220	3964 C	-17:35118297 2524649804 C	
220 S	3965 T	-17:35118296 2524649803 T	
220	3966 G	-17:35118295 2524649802 G	Q
219	3967 C	-17:35118294 2524649801 C	
219 C	3968 A	-17:35118293 2524649800 A	
219	3969 G	-17:35118292 2524649799 G	L
218	3970 C	-17:35118291 2524649798 C	
218 S	3971 T	-17:35118290 2524649797 T	
218	3972 C	-17:35118289 2524649796 C	E
217	3973 C	-17:35118288 2524649795 C	
217 G	3974 C	-17:35118287 2524649794 C	
217	3975 G	-17:35118286 2524649793 G	R
216	3976 C	-17:35118285 2524649792 C	
216 C	3977 A	-17:35118284 2524649791 A	
216	3978 G	-17:35118283 2524649790 G	L
215	3979 G	-17:35118282 2524649789 G	
215 A	3980 C	-17:35118281 2524649788 C	
215	3981 C	-17:35118280 2524649787 C	G
214	3982 T	-17:35118279 2524649786 T	
214 E	3983 C	-17:35118278 2524649785 C	
214	3984 C	-17:35118277 2524649784 C	G
213	3985 T	-17:35118276 2524649783 T	
213 Q	3986 G	-17:35118275 2524649782 G	
213	3987 G	-17:35118274 2524649781 G	P
212	3988 G	-17:35118273 2524649780 G	
212 P	3989 G	-17:35118272 2524649779 G	
212	3990 A	-17:35118271 2524649778 A	S
211	3991 G	-17:35118270 2524649777 G	
211 P	3992 G	-17:35118269 2524649776 G	
211	3993 C	-17:35118268 2524649775 C	A
210	3994 C	-17:35118267 2524649774 C	
210 G	3995 C	-17:35118266 2524649773 C	
210	3996 C	-17:35118265 2524649772 C	G
209	3997 T	-17:35118264 2524649771 T	
209 Q	3998 G	-17:35118263 2524649770 G	
209	3999 T	-17:35118262 2524649769 T	T
208	4000 G	-17:35118261 2524649768 G	
208 S	4001 A	-17:35118260 2524649767 A	
208	4002 C	-17:35118259 2524649766 C	V
207	4003 A	-17:35118258 2524649765 A	
207 L	4004 G	-17:35118257 2524649764 G	
207	4005 G	-17:35118256 2524649763 G	P
206	4006 G	-17:35118255 2524649762 G	
206 P	4007 G	-17:35118254 2524649761 G	
206	4008 T	-17:35118253 2524649760 T	T
205	4009 G	-17:35118252 2524649759 G	
205 P	4010 G	-17:35118251 2524649758 G	
205	4011 T	-17:35118250 2524649757 T	T
204	4012 A	-17:35118249 2524649756 A	
204 I	4013 T	-17:35118248 2524649755 T	
204	4014 T	-17:35118247 2524649754 T	N
203	4015 G	-17:35118246 2524649753 G	
203 T	4016 T	-17:35118245 2524649752 T	
203	4017 T	-17:35118244 2524649751 T	N
202	4018 C	-17:35118243 2524649750 C	
202 *	4019 A	-17:35118242 2524649749 A	
202	4020 G	-17:35118241 2524649748 G	L
201	4021 C	-17:35118240 2524649747 C	
201 R	4022 G	-17:35118239 2524649746 G	
201	4023 G	-17:35118238 2524649745 G	P
200	4024 G	-17:35118237 2524649744 G	
200 T	4025 T	-17:35118236 2524649743 T	
200	4026 C	-17:35118235 2524649742 C	D
199	4027 T	-17:35118234 2524649741 T	
199 E	4028 C	-17:35118233 2524649740 C	
199	4029 C	-17:35118232 2524649739 C	G
198	4030 A	-17:35118231 2524649738 A	
198 M	4031 T	-17:35118230 2524649737 T	
198	4032 T	-17:35118229 2524649736 T	N
197	4033 G	-17:35118228 2524649735 G	
197 T	4034 T	-17:35118227 2524649734 T	
197	4035 C	-17:35118226 2524649733 C	D
196	4036 T	-17:35118225 2524649732 T	
196 *	4037 A	-17:35118224 2524649731 A	
196	4038 G	-17:35118223 2524649730 G	L
195	4039 C	-17:35118222 2524649729 C	
195 C	4040 A	-17:35118221 2524649728 A	
195	4041 C	-17:35118220 2524649727 C	V
194	4042 G	-17:35118219 2524649726 G	
194 P	4043 G	-17:35118218 2524649725 G	
194	4044 C	-17:35118217 2524649724 C	A
193	4045 C	-17:35118216 2524649723 C	
193 W	4046 A	-17:35118215 2524649722 A	
193	4047 G	-17:35118214 2524649721 G	L
192	4048 G	-17:35118213 2524649720 G	
192 P	4049 G	-17:35118212 2524649719 G	
192	4050 C	-17:35118211 2524649718 C	A
191	4051 A	-17:35118210 2524649717 A	
191 M	4052 T	-17:35118209 2524649716 T	
191	4053 A	-17:35118208 2524649715 A	Y
190	4054 G	-17:35118207 2524649714 G	
190 T	4055 T	-17:35118206 2524649713 T	
190	4056 T	-17:35118205 2524649712 T	N
189	4057 G	-17:35118204 2524649711 G	
189 T	4058 T	-17:35118203 2524649710 T	
189	4059 C	-17:35118202 2524649709 C	D
188	4060 C	-17:35118201 2524649708 C	
188 R	4061 T	-17:35118200 2524649707 T	
188	4062 C	-17:35118199 2524649706 C	E
187	4063 A	-17:35118198 2524649705 A	
187 L	4064 A	-17:35118197 2524649704 A	
187	4065 A	-17:35118196 2524649703 A	F
186	4066 G	-17:35118195 2524649702 G	
186 S	4067 A	-17:35118194 2524649701 A	
186	4068 G	-17:35118193 2524649700 G	L
185	4069 C	-17:35118192 2524649699 C	
185 S	4070 T	-17:35118191 2524649698 T	
185	4071 G	-17:35118190 2524649697 G	Q
184	4072 G	-17:35118189 2524649696 G	
184 P	4073 G	-17:35118188 2524649695 G	
184	4074 T	-17:35118187 2524649694 T	T
183	4075 G	-17:35118186 2524649693 G	
183 A	4076 C	-17:35118185 2524649692 C	
183	4077 C	-17:35118184 2524649691 C	G
182	4078 T	-17:35118183 2524649690 T	
182 E	4079 C	-17:35118182 2524649689 C	
182	4080 G	-17:35118181 2524649688 G	R
181	4081 C	-17:35118180 2524649687 C	
181 C	4082 A	-17:35118179 2524649686 A	
181	4083 C	-17:35118178 2524649685 C	V
180	4084 A	-17:35118177 2524649684 A	
180 L	4085 A	-17:35118176 2524649683 A	
180	4086 T	-17:35118175 2524649682 T	I
179	4087 C	-17:35118174 2524649681 C	
179 G	4088 C	-17:35118173 2524649680 C	
179	4089 G	-17:35118172 2524649679 G	R
178	4090 C	-17:35118171 2524649678 C	
178 C	4091 A	-17:35118170 2524649677 A	
178	4092 G	-17:35118169 2524649676 G	L
177	4093 C	-17:35118168 2524649675 C	
177 G	4094 C	-17:35118167 2524649674 C	
177	4095 T	-17:35118166 2524649673 T	R
176	4096 C	-17:35118165 2524649672 C	
176 R	4097 T	-17:35118164 2524649671 T	
176	4098 G	-17:35118163 2524649670 G	Q
175	4099 C	-17:35118162 2524649669 C	
175 C	4100 A	-17:35118161 2524649668 A	
175	4101 G	-17:35118160 2524649667 G	L
174	4102 T	-17:35118159 2524649666 T	
174 H	4103 G	-17:35118158 2524649665 G	
174	4104 G	-17:35118157 2524649664 G	P
173	4105 G	-17:35118156 2524649663 G	
173 S	4106 A	-17:35118155 2524649662 A	
173	4107 C	-17:35118154 2524649661 C	V
172	4108 C	-17:35118153 2524649660 C	
172 R	4109 T	-17:35118152 2524649659 T	
172	4110 G	-17:35118151 2524649658 G	Q
171	4111 C	-17:35118150 2524649657 C	
171 G	4112 C	-17:35118149 2524649656 C	
171	4113 T	-17:35118148 2524649655 T	R
170	4114 C	-17:35118147 2524649654 C	
170 *	4115 A	-17:35118146 2524649653 A	
170	4116 C	-17:35118145 2524649652 C	V
169	4117 T	-17:35118144 2524649651 T	
169 K	4118 T	-17:35118143 2524649650 T	
169	4119 G	-17:35118142 2524649649 G	Q
168	4120 G	-17:35118141 2524649648 G	
168 T	4121 T	-17:35118140 2524649647 T	
168	4122 T	-17:35118139 2524649646 T	N
167	4123 G	-17:35118138 2524649645 G	
167 T	4124 T	-17:35118137 2524649644 T	
167	4125 G	-17:35118136 2524649643 G	H
166	4126 A	-17:35118135 2524649642 A	
166 L	4127 G	-17:35118134 2524649641 G	
166	4128 C	-17:35118133 2524649640 C	A
165	4129 G	-17:35118132 2524649639 G	
165 S	4130 A	-17:35118131 2524649638 A	
165	4131 T	-17:35118130 2524649637 T	I
164	4132 G	-17:35118129 2524649636 G	
164 S	4133 A	-17:35118128 2524649635 A	
164	4134 G	-17:35118127 2524649634 G	L
163	4135 C	-17:35118126 2524649633 C	
163 C	4136 A	-17:35118125 2524649632 A	
163	4137 C	-17:35118124 2524649631 C	V
162	4138 G	-17:35118123 2524649630 G	
162 T	4139 T	-17:35118122 2524649629 T	
162	4140 A	-17:35118121 2524649628 A	Y
161	4141 G	-17:35118120 2524649627 G	
161 A	4142 C	-17:35118119 2524649626 C	
161	4143 C	-17:35118118 2524649625 C	G
160	4144 C	-17:35118117 2524649624 C	
160 R	4145 T	-17:35118116 2524649623 T	
160	4146 G	-17:35118115 2524649622 G	Q
159	4147 C	-17:35118114 2524649621 C	
159 C	4148 A	-17:35118113 2524649620 A	
159	4149 C	-17:35118112 2524649619 C	V
158	4150 C	-17:35118111 2524649618 C	
158 R	4151 T	-17:35118110 2524649617 T	
158	4152 C	-17:35118109 2524649616 C	E
157	4153 C	-17:35118108 2524649615 C	
157 R	4154 T	-17:35118107 2524649614 T	
157	4155 G	-17:35118106 2524649613 G	Q
156	4156 G	-17:35118105 2524649612 G	
156 S	4157 A	-17:35118104 2524649611 A	
156	4158 T	-17:35118103 2524649610 T	I
155	4159 A	-17:35118102 2524649609 A	
155 I	4160 T	-17:35118101 2524649608 T	
155	4161 C	-17:35118100 2524649607 C	D
154	4162 C	-17:35116920 2524648427 C	
154 R	4163 T	-17:35116919 2524648426 T	
154	4164 G	-17:35116918 2524648425 G	Q
153	4165 C	-17:35116917 2524648424 C	
153 C	4166 A	-17:35116916 2524648423 A	
153	4167 G	-17:35116915 2524648422 G	L
152	4168 G	-17:35116914 2524648421 G	
152 S	4169 A	-17:35116913 2524648420 A	
152	4170 A	-17:35116912 2524648419 A	F
151	4171 G	-17:35116911 2524648418 G	
151 P	4172 G	-17:35116910 2524648417 G	
151	4173 A	-17:35116909 2524648416 A	S
150	4174 C	-17:35116908 2524648415 C	
150 C	4175 A	-17:35116907 2524648414 A	
150	4176 G	-17:35116906 2524648413 G	L
149	4177 G	-17:35116905 2524648412 G	
149 A	4178 C	-17:35116904 2524648411 C	
149	4179 T	-17:35116903 2524648410 T	S
148	4180 G	-17:35116902 2524648409 G	
148 P	4181 G	-17:35116901 2524648408 G	
148	4182 C	-17:35116900 2524648407 C	A
147	4183 A	-17:35116899 2524648406 A	
147 M	4184 T	-17:35116898 2524648405 T	
147	4185 T	-17:35116897 2524648404 T	N
146	4186 G	-17:35116896 2524648403 G	
146 P	4187 G	-17:35116895 2524648402 G	
146	4188 T	-17:35116894 2524648401 T	T
145	4189 G	-17:35116893 2524648400 G	
145 P	4190 G	-17:35116892 2524648399 G	
145	4191 G	-17:35116891 2524648398 G	P
144	4192 C	-17:35116890 2524648397 C	
144 C	4193 A	-17:35116889 2524648396 A	
144	4194 G	-17:35116888 2524648395 G	L
143	4195 G	-17:35116887 2524648394 G	
143 T	4196 T	-17:35116886 2524648393 T	
143	4197 A	-17:35116885 2524648392 A	Y
142	4198 G	-17:35116884 2524648391 G	
142 P	4199 G	-17:35116883 2524648390 G	
142	4200 T	-17:35116882 2524648389 T	T
141	4201 G	-17:35116881 2524648388 G	
141 S	4202 A	-17:35116880 2524648387 A	
141	4203 G	-17:35116879 2524648386 G	L
140	4204 T	-17:35116878 2524648385 T	
140 N	4205 T	-17:35116877 2524648384 T	
140	4206 C	-17:35116876 2524648383 C	E
139	4207 C	-17:35116875 2524648382 C	
139 W	4208 A	-17:35116874 2524648381 A	
139	4209 G	-17:35116873 2524648380 G	L
138	4210 G	-17:35116872 2524648379 G	
138 T	4211 T	-17:35116871 2524648378 T	
138	4212 T	-17:35116870 2524648377 T	N
137	4213 T	-17:35116869 2524648376 T	
137 E	4214 C	-17:35116868 2524648375 C	
137	4215 C	-17:35116867 2524648374 C	G
136	4216 C	-17:35116866 2524648373 C	
136 R	4217 T	-17:35116865 2524648372 T	
136	4218 G	-17:35116864 2524648371 G	Q
135	4219 C	-17:35116863 2524648370 C	
135 C	4220 A	-17:35116862 2524648369 A	
135	4221 C	-17:35116861 2524648368 C	V
134	4222 C	-17:35116860 2524648367 C	
134 W	4223 A	-17:35116859 2524648366 A	
134	4224 C	-17:35116858 2524648365 C	V
133	4225 C	-17:35116857 2524648364 C	
133 R	4226 T	-17:35116856 2524648363 T	
133	4227 G	-17:35116855 2524648362 G	Q
132	4228 G	-17:35116854 2524648361 G	
132 A	4229 C	-17:35116853 2524648360 C	
132	4230 A	-17:35116852 2524648359 A	C
131	4231 G	-17:35116851 2524648358 G	
131 A	4232 C	-17:35116850 2524648357 C	
131	4233 C	-17:35116849 2524648356 C	G
130	4234 C	-17:35116848 2524648355 C	
130 R	4235 T	-17:35116847 2524648354 T	
130	4236 G	-17:35116846 2524648353 G	Q
129	4237 G	-17:35116845 2524648352 G	
129 T	4238 T	-17:35116844 2524648351 T	
129	4239 A	-17:35116843 2524648350 A	Y
128	4240 G	-17:35116842 2524648349 G	
128 S	4241 A	-17:35116841 2524648348 A	
128	4242 G	-17:35116840 2524648347 G	L
127	4243 G	-17:35116839 2524648346 G	
127 T	4244 T	-17:35116838 2524648345 T	
127	4245 G	-17:35116837 2524648344 G	H
126	4246 G	-17:35116836 2524648343 G	
126 A	4247 C	-17:35116835 2524648342 C	
126	4248 G	-17:35116834 2524648341 G	R
125	4249 G	-17:35116833 2524648340 G	
125 S	4250 A	-17:35116832 2524648339 A	
125	4251 G	-17:35116831 2524648338 G	L
124	4252 C	-17:35116830 2524648337 C	
124 C	4253 A	-17:35116829 2524648336 A	
124	4254 T	-17:35116828 2524648335 T	M
123	4255 G	-17:35116827 2524648334 G	
123 T	4256 T	-17:35116826 2524648333 T	
123	4257 C	-17:35116825 2524648332 C	D
122	4258 C	-17:35116824 2524648331 C	
122 W	4259 A	-17:35116823 2524648330 A	
122	4260 G	-17:35116822 2524648329 G	L
121	4261 G	-17:35116821 2524648328 G	
121 T	4262 T	-17:35116820 2524648327 T	
121	4263 G	-17:35116819 2524648326 G	H
120	4264 G	-17:35116818 2524648325 G	
120 P	4265 G	-17:35116817 2524648324 G	
120	4266 T	-17:35116816 2524648323 T	T
119	4267 C	-17:35116815 2524648322 C	
119 R	4268 T	-17:35116814 2524648321 T	
119	4269 C	-17:35116813 2524648320 C	E
118	4270 G	-17:35116812 2524648319 G	
118 P	4271 G	-17:35116811 2524648318 G	
118	4272 G	-17:35116810 2524648317 G	P
117	4273 A	-17:35116809 2524648316 A	
117 V	4274 C	-17:35116808 2524648315 C	
117	4275 T	-17:35116807 2524648314 T	S
116	4276 G	-17:35116806 2524648313 G	
116 P	4277 G	-17:35116805 2524648312 G	
116	4278 C	-17:35116804 2524648311 C	A
115	4279 A	-17:35116803 2524648310 A	
115 L	4280 G	-17:35116802 2524648309 G	
115	4281 G	-17:35116801 2524648308 G	P
114	4282 G	-17:35116800 2524648307 G	
114 S	4283 A	-17:35116799 2524648306 A	
114	4284 G	-17:35116798 2524648305 G	L
113	4285 C	-17:35116797 2524648304 C	
113 G	4286 C	-17:35116796 2524648303 C	
113	4287 G	-17:35116795 2524648302 G	R
112	4288 C	-17:35116794 2524648301 C	
112 C	4289 A	-17:35116793 2524648300 A	
112	4290 G	-17:35116792 2524648299 G	L
111	4291 C	-17:35116791 2524648298 C	
111 S	4292 T	-17:35116790 2524648297 T	
111	4293 T	-17:35116789 2524648296 T	K
110	4294 C	-17:35116788 2524648295 C	
110 *	4295 A	-17:35116787 2524648294 A	
110	4296 T	-17:35116786 2524648293 T	M
109	4297 G	-17:35116785 2524648292 G	
109 T	4298 T	-17:35116784 2524648291 T	
109	4299 C	-17:35116783 2524648290 C	D
108	4300 T	-17:35116782 2524648289 T	
108 Q	4301 G	-17:35116781 2524648288 G	
108	4302 T	-17:35116780 2524648287 T	T
107	4303 G	-17:35116779 2524648286 G	
107 A	4304 C	-17:35116778 2524648285 C	
107	4305 C	-17:35116777 2524648284 C	G
106	4306 G	-17:35116776 2524648283 G	
106 P	4307 G	-17:35116775 2524648282 G	
106	4308 T	-17:35116774 2524648281 T	T
105	4309 G	-17:35116773 2524648280 G	
105 A	4310 C	-17:35116772 2524648279 C	
105	4311 A	-17:35116771 2524648278 A	C
104	4312 C	-17:35116770 2524648277 C	
104 C	4313 A	-17:35116769 2524648276 A	
104	4314 C	-17:35110090 2524641597 C	V
103	4315 T	-17:35110089 2524641596 T	
103 K	4316 T	-17:35110088 2524641595 T	
103	4317 G	-17:35110087 2524641594 G	Q
102	4318 G	-17:35110086 2524641593 G	
102 P	4319 G	-17:35110085 2524641592 G	
102	4320 T	-17:35110084 2524641591 T	T
101	4321 G	-17:35110083 2524641590 G	
101 A	4322 C	-17:35110082 2524641589 C	
101	4323 T	-17:35110081 2524641588 T	S
100	4324 C	-17:35110080 2524641587 C	
100 R	4325 G	-17:35110079 2524641586 G	
100	4326 C	-17:35110078 2524641585 C	A
99	4327 G	-17:35110077 2524641584 G	
99 P	4328 G	-17:35110076 2524641583 G	
99	4329 C	-17:35110075 2524641582 C	A
98	4330 T	-17:35110074 2524641581 T	
98 E	4331 C	-17:35110073 2524641580 C	
98	4332 C	-17:35110072 2524641579 C	G
97	4333 G	-17:35110071 2524641578 G	
97 P	4334 G	-17:35110070 2524641577 G	
97	4335 G	-17:35110069 2524641576 G	P
96	4336 G	-17:35110068 2524641575 G	
96 P	4337 G	-17:35110067 2524641574 G	
96	4338 G	-17:35110066 2524641573 G	P
95	4339 C	-17:35110065 2524641572 C	
95 C	4340 A	-17:35110064 2524641571 A	
95	4341 A	-17:35110063 2524641570 A	L
94	4342 G	-17:35110062 2524641569 G	
94 S	4343 A	-17:35110061 2524641568 A	
94	4344 G	-17:35110060 2524641567 G	L
93	4345 G	-17:35110059 2524641566 G	
93 P	4346 G	-17:35110058 2524641565 G	
93	4347 C	-17:35110057 2524641564 C	A
92	4348 G	-17:35110056 2524641563 G	
92 S	4349 A	-17:35110055 2524641562 A	
92	4350 G	-17:35110054 2524641561 G	L
91	4351 G	-17:35110053 2524641560 G	
91 S	4352 A	-17:35110052 2524641559 A	
91	4353 G	-17:35110051 2524641558 G	L
90	4354 G	-17:35110050 2524641557 G	
90 S	4355 A	-17:35110049 2524641556 A	
90	4356 G	-17:35110048 2524641555 G	L
89	4357 C	-17:35110047 2524641554 C	
89 G	4358 C	-17:35110046 2524641553 C	
89	4359 C	-17:35110045 2524641552 C	G
88	4360 C	-17:35110044 2524641551 C	
88 G	4361 C	-17:35110043 2524641550 C	
88	4362 A	-17:35110042 2524641549 A	W
87	4363 G	-17:35110041 2524641548 G	
87 A	4364 C	-17:35110040 2524641547 C	
87	4365 G	-17:35110039 2524641546 G	R
86	4366 G	-17:35110038 2524641545 G	
86 A	4367 C	-17:35110037 2524641544 C	
86	4368 A	-17:35110036 2524641543 A	C
85	4369 C	-17:35110035 2524641542 C	
85 C	4370 A	-17:35110034 2524641541 A	
85	4371 A	-17:35110033 2524641540 A	L
84	4372 G	-17:35110032 2524641539 G	
84 P	4373 G	-17:35110031 2524641538 G	
84	4374 C	-17:35110030 2524641537 C	A
83	4375 C	-17:35110029 2524641536 C	
83 R	4376 G	-17:35110028 2524641535 G	
83	4377 C	-17:35110027 2524641534 C	A
82	4378 C	-17:35110026 2524641533 C	
82 W	4379 A	-17:35110025 2524641532 A	
82	4380 G	-17:35110024 2524641531 G	L
81	4381 C	-17:35110023 2524641530 C	
81 S	4382 T	-17:35110022 2524641529 T	
81	4383 C	-17:35110021 2524641528 C	E
80	4384 C	-17:35110020 2524641527 C	
80 W	4385 A	-17:35110019 2524641526 A	
80	4386 T	-17:35110018 2524641525 T	M
79	4387 G	-17:35110017 2524641524 G	
79 P	4388 G	-17:35110016 2524641523 G	
79	4389 T	-17:35110015 2524641522 T	T
78	4390 G	-17:35110014 2524641521 G	
78 A	4391 C	-17:35110013 2524641520 C	
78	4392 T	-17:35110012 2524641519 T	S
77	4393 C	-17:35110011 2524641518 C	
77 *	4394 A	-17:35110010 2524641517 A	
77	4395 C	-17:35110009 2524641516 C	V
76	4396 T	-17:35110008 2524641515 T	
76 Q	4397 G	-17:35110007 2524641514 G	
76	4398 C	-17:35110006 2524641513 C	A
75	4399 G	-17:35110005 2524641512 G	
75 P	4400 G	-17:35110004 2524641511 G	
75	4401 C	-17:35110003 2524641510 C	A
74	4402 T	-17:35110002 2524641509 T	
74 E	4403 C	-17:35110001 2524641508 C	
74	4404 C	-17:35110000 2524641507 C	G
73	4405 G	-17:35109999 2524641506 G	
73 P	4406 G	-17:35109998 2524641505 G	
73	4407 C	-17:35109997 2524641504 C	A
72	4408 C	-17:35109996 2524641503 C	
72 G	4409 C	-17:35109995 2524641502 C	
72	4410 C	-17:35109994 2524641501 C	G
71	4411 A	-17:35109993 2524641500 A	
71 M	4412 T	-17:35109992 2524641499 T	
71	4413 G	-17:35109991 2524641498 G	H
70	4414 G	-17:35109990 2524641497 G	
70 A	4415 C	-17:35109989 2524641496 C	
70	4416 T	-17:35109988 2524641495 T	S
69	4417 C	-17:35109987 2524641494 C	
69 G	4418 C	-17:35109986 2524641493 C	
69	4419 G	-17:35109985 2524641492 G	R
68	4420 G	-17:35109984 2524641491 G	
68 A	4421 C	-17:35109983 2524641490 C	
68	4422 T	-17:35109982 2524641489 T	S
67	4423 G	-17:35109981 2524641488 G	
67 P	4424 G	-17:35109980 2524641487 G	
67	4425 A	-17:35109979 2524641486 A	S
66	4426 C	-17:35109978 2524641485 C	
66 G	4427 C	-17:35109977 2524641484 C	
66	4428 C	-17:35109976 2524641483 C	G
65	4429 G	-17:35109975 2524641482 G	
65 P	4430 G	-17:35109974 2524641481 G	
65	4431 C	-17:35109973 2524641480 C	A
64	4432 T	-17:35109972 2524641479 T	
64 Q	4433 G	-17:35109971 2524641478 G	
64	4434 G	-17:35109970 2524641477 G	P
63	4435 G	-17:35109969 2524641476 G	
63 S	4436 A	-17:35109968 2524641475 A	
63	4437 G	-17:35109967 2524641474 G	L
62	4438 G	-17:35109966 2524641473 G	
62 P	4439 G	-17:35109965 2524641472 G	
62	4440 C	-17:35109964 2524641471 C	A
61	4441 G	-17:35109963 2524641470 G	
61 A	4442 C	-17:35109962 2524641469 C	
61	4443 G	-17:35109961 2524641468 G	R
60	4444 G	-17:35109960 2524641467 G	
60 P	4445 G	-17:35109959 2524641466 G	
60	4446 G	-17:35109958 2524641465 G	P
59	4447 C	-17:35109957 2524641464 C	
59 R	4448 G	-17:35109956 2524641463 G	
59	4449 C	-17:35109955 2524641462 C	A
58	4450 G	-17:35109954 2524641461 G	
58 P	4451 G	-17:35109953 2524641460 G	
58	4452 G	-17:35109952 2524641459 G	P
57	4453 G	-17:35109951 2524641458 G	
57 T	4454 T	-17:35109950 2524641457 T	
57	4455 G	-17:35109949 2524641456 G	H
56	4456 C	-17:35109948 2524641455 C	
56 S	4457 T	-17:35109947 2524641454 T	
56	4458 G	-17:35109946 2524641453 G	Q
55	4459 C	-17:35109945 2524641452 C	
55 R	4460 G	-17:35109944 2524641451 G	
55	4461 A	-17:35109943 2524641450 A	S
54	4462 G	-17:35109942 2524641449 G	
54 P	4463 G	-17:35109941 2524641448 G	
54	4464 G	-17:35109940 2524641447 G	P
53	4465 G	-17:35109939 2524641446 G	
53 T	4466 T	-17:35109938 2524641445 T	
53	4467 G	-17:35109937 2524641444 G	H
52	4468 G	-17:35109936 2524641443 G	
52 P	4469 G	-17:35109935 2524641442 G	
52	4470 G	-17:35109934 2524641441 G	P
51	4471 G	-17:35109933 2524641440 G	
51 A	4472 C	-17:35109932 2524641439 C	
51	4473 C	-17:35109931 2524641438 C	G
50	4474 G	-17:35109930 2524641437 G	
50 P	4475 G	-17:35109929 2524641436 G	
50	4476 G	-17:35109928 2524641435 G	P
49	4477 C	-17:35109927 2524641434 C	
49 R	4478 G	-17:35109926 2524641433 G	
49	4479 C	-17:35109925 2524641432 C	A
48	4480 G	-17:35109924 2524641431 G	
48 A	4481 C	-17:35109923 2524641430 C	
48	4482 G	-17:35109922 2524641429 G	R
47	4483 G	-17:35109921 2524641428 G	
47 A	4484 C	-17:35109920 2524641427 C	
47	4485 G	-17:35109919 2524641426 G	R
46	4486 C	-17:35109918 2524641425 C	
46 C	4487 A	-17:35109917 2524641424 A	
46	4488 G	-17:35109916 2524641423 G	L
45	4489 T	-17:35109915 2524641422 T	
45 Y	4490 A	-17:35109914 2524641421 A	
45	4491 A	-17:35109913 2524641420 A	L
44	4492 A	-17:35109912 2524641419 A	
44 L	4493 G	-17:35109911 2524641418 G	
44	4494 G	-17:35109910 2524641417 G	P
43	4495 G	-17:35109909 2524641416 G	
43 A	4496 C	-17:35109908 2524641415 C	
43	4497 C	-17:35109907 2524641414 C	G
42	4498 C	-17:35109906 2524641413 C	
42 G	4499 C	-17:35109905 2524641412 C	
42	4500 G	-17:35109904 2524641411 G	R
41	4501 T	-17:35109903 2524641410 T	
41 H	4502 G	-17:35109902 2524641409 G	
41	4503 G	-17:35109901 2524641408 G	P
40	4504 G	-17:35109900 2524641407 G	
40 S	4505 A	-17:35109899 2524641406 A	
40	4506 A	-17:35109898 2524641405 A	F
39	4507 G	-17:35109897 2524641404 G	
39 P	4508 G	-17:35109896 2524641403 G	
39	4509 G	-17:35109895 2524641402 G	P
38	4510 G	-17:35109894 2524641401 G	
38 A	4511 C	-17:35109893 2524641400 C	
38	4512 G	-17:35109892 2524641399 G	R
37	4513 C	-17:35109891 2524641398 C	
37 R	4514 G	-17:35109890 2524641397 G	
37	4515 C	-17:35109889 2524641396 C	A
36	4516 G	-17:35109888 2524641395 G	
36 P	4517 G	-17:35109887 2524641394 G	
36	4518 C	-17:35109886 2524641393 C	A
35	4519 T	-17:35109885 2524641392 T	
35 Q	4520 G	-17:35109884 2524641391 G	
35	4521 C	-17:35109883 2524641390 C	A
34	4522 C	-17:35109882 2524641389 C	
34 G	4523 C	-17:35109881 2524641388 C	
34	4524 G	-17:35109880 2524641387 G	R
33	4525 G	-17:35109879 2524641386 G	
33 P	4526 G	-17:35109878 2524641385 G	
33	4527 G	-17:35109877 2524641384 G	P
32	4528 G	-17:35109876 2524641383 G	
32 P	4529 G	-17:35109875 2524641382 G	
32	4530 C	-17:35109874 2524641381 C	A
31	4531 T	-17:35109873 2524641380 T	
31 E	4532 C	-17:35109872 2524641379 C	
31	4533 C	-17:35109871 2524641378 C	G
30	4534 C	-17:35109870 2524641377 C	
30 G	4535 C	-17:35109869 2524641376 C	
30	4536 T	-17:35109868 2524641375 T	R
29	4537 G	-17:35109867 2524641374 G	
29 P	4538 G	-17:35109866 2524641373 G	
29	4539 T	-17:35109865 2524641372 T	T
28	4540 T	-17:35109864 2524641371 T	
28 K	4541 T	-17:35109863 2524641370 T	
28	4542 C	-17:35109862 2524641369 C	E
27	4543 T	-17:35109861 2524641368 T	
27 E	4544 C	-17:35109860 2524641367 C	
27	4545 C	-17:35109859 2524641366 C	G
26	4546 G	-17:35109858 2524641365 G	
26 P	4547 G	-17:35109857 2524641364 G	
26	4548 T	-17:35109856 2524641363 T	T
25	4549 C	-17:35109855 2524641362 C	
25 G	4550 C	-17:35109854 2524641361 C	
25	4551 C	-17:35109853 2524641360 C	G
24	4552 A	-17:35109852 2524641359 A	
24 L	4553 A	-17:35109851 2524641358 A	
24	4554 T	-17:35109850 2524641357 T	I
23	4555 G	-17:35109849 2524641356 G	
23 P	4556 G	-17:35109848 2524641355 G	
23	4557 A	-17:35109847 2524641354 A	S
22	4558 G	-17:35109846 2524641353 G	
22 P	4559 G	-17:35109845 2524641352 G	
22	4560 G	-17:35109844 2524641351 G	P
21	4561 G	-17:35109843 2524641350 G	
21	4562  	-17:35109842 2524641349 A	
21 S	4562 A	-17:35109841 2524641348 A	F
20	4563 T	-17:35109840 2524641347 T	
20	4564 C	-17:35109839 2524641346 C	
20 R	4565 T	-17:35109838 2524641345 T	R
19	4566 C	-17:35109837 2524641344 C	
19	4567 A	-17:35109836 2524641343 A	
19 L	4568 G	-17:35109835 2524641342 G	L
18	4569 C	-17:35109834 2524641341 C	
18	4570 T	-17:35109833 2524641340 T	
18 K	4571 T	-17:35109832 2524641339 T	K
17	4572 C	-17:35109831 2524641338 C	
17	4573 A	-17:35109830 2524641337 A	
17 V	4574 C	-17:35109829 2524641336 C	V
16	4575 A	-17:35109828 2524641335 A	
16	4576 A	-17:35109827 2524641334 A	
16 V	4577 C	-17:35109826 2524641333 C	V
15	4578 T	-17:35109825 2524641332 T	
15	4579 T	-17:35109824 2524641331 T	
15 E	4580 C	-17:35109823 2524641330 C	E
14	4581 A	-17:35109822 2524641329 A	
14	4582 T	-17:35109821 2524641328 T	
14 N	4583 T	-17:35109820 2524641327 T	N
13	4584 C	-17:35109819 2524641326 C	
13	4585 T	-17:35109818 2524641325 T	
13 K	4586 T	-17:35109817 2524641324 T	K
12	4587 A	-17:35109816 2524641323 A	
12	4588 T	-17:35109815 2524641322 T	
12 Y	4589 A	-17:35109814 2524641321 A	Y
11	4590 C	-17:35109813 2524641320 C	
11	4591 T	-17:35109812 2524641319 T	
11 K	4592 T	-17:35109811 2524641318 T	K
10	4593 C	-17:35109810 2524641317 C	
10	4594 C	-17:35109809 2524641316 C	
10 R	4595 T	-17:35109808 2524641315 T	R
9	4596 C	-17:35109807 2524641314 C	
9	4597 A	-17:35109806 2524641313 A	
9 L	4598 A	-17:35109805 2524641312 A	L
8	4599 G	-17:35109804 2524641311 G	
8	4600 C	-17:35109803 2524641310 C	
8 C	4601 A	-17:35109802 2524641309 A	C
7	4602 G	-17:35109801 2524641308 G	
7	4603 C	-17:35109800 2524641307 C	
7 G	4604 C	-17:35109799 2524641306 C	G
6	4605 C	-17:35109798 2524641305 C	
6	4606 T	-17:35109797 2524641304 T	
6 E	4607 C	-17:35109796 2524641303 C	E
5	4608 C	-17:35109795 2524641302 C	
5	4609 T	-17:35109794 2524641301 T	
5 E	4610 C	-17:35109793 2524641300 C	E
4	4611 C	-17:35109792 2524641299 C	
4	4612 T	-17:35109791 2524641298 T	
4 E	4613 C	-17:35109790 2524641297 C	E
3	4614 C	-17:35109789 2524641296 C	
3	4615 A	-17:35109788 2524641295 A	
3 V	4616 C	-17:35109787 2524641294 C	V
2	4617 C	-17:35109786 2524641293 C	
2	4618 T	-17:35109785 2524641292 T	
2 E	4619 C	-17:35109784 2524641291 C	E
1	4620 C	-17:35109783 2524641290 C	
1	4621 T	-17:35109782 2524641289 T	
1 E	4622 C	-17:35109781 2524641288 C	E
0	4623 C	-17:35109780 2524641287 C	
BioPerl-1.007002/t/data/gmap_f9.txt000444000766000024     53270513155576321 17027 0ustar00cjfieldsstaff000000000000>NM_004448   Homo sapiens v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) (ERBB2), transcript variant 1, mRNA. 4624 bp, mRNA, linear, PRI 20-DEC-2004
0	1 G	+17:35109780 2524641287 G	
1 E	2 G	+17:35109781 2524641288 G	E
1	3 A	+17:35109782 2524641289 A	
1	4 G	+17:35109783 2524641290 G	
2 E	5 G	+17:35109784 2524641291 G	E
2	6 A	+17:35109785 2524641292 A	
2	7 G	+17:35109786 2524641293 G	
3 V	8 G	+17:35109787 2524641294 G	V
3	9 T	+17:35109788 2524641295 T	
3	10 G	+17:35109789 2524641296 G	
4 E	11 G	+17:35109790 2524641297 G	E
4	12 A	+17:35109791 2524641298 A	
4	13 G	+17:35109792 2524641299 G	
5 E	14 G	+17:35109793 2524641300 G	E
5	15 A	+17:35109794 2524641301 A	
5	16 G	+17:35109795 2524641302 G	
6 E	17 G	+17:35109796 2524641303 G	E
6	18 A	+17:35109797 2524641304 A	
6	19 G	+17:35109798 2524641305 G	
7 G	20 G	+17:35109799 2524641306 G	G
7	21 G	+17:35109800 2524641307 G	
7	22 C	+17:35109801 2524641308 C	
8 C	23 T	+17:35109802 2524641309 T	C
8	24 G	+17:35109803 2524641310 G	
8	25 C	+17:35109804 2524641311 C	
9 L	26 T	+17:35109805 2524641312 T	L
9	27 T	+17:35109806 2524641313 T	
9	28 G	+17:35109807 2524641314 G	
10 R	29 A	+17:35109808 2524641315 A	R
10	30 G	+17:35109809 2524641316 G	
10	31 G	+17:35109810 2524641317 G	
11 K	32 A	+17:35109811 2524641318 A	K
11	33 A	+17:35109812 2524641319 A	
11	34 G	+17:35109813 2524641320 G	
12 Y	35 T	+17:35109814 2524641321 T	Y
12	36 A	+17:35109815 2524641322 A	
12	37 T	+17:35109816 2524641323 T	
13 K	38 A	+17:35109817 2524641324 A	K
13	39 A	+17:35109818 2524641325 A	
13	40 G	+17:35109819 2524641326 G	
14 N	41 A	+17:35109820 2524641327 A	N
14	42 A	+17:35109821 2524641328 A	
14	43 T	+17:35109822 2524641329 T	
15 E	44 G	+17:35109823 2524641330 G	E
15	45 A	+17:35109824 2524641331 A	
15	46 A	+17:35109825 2524641332 A	
16 V	47 G	+17:35109826 2524641333 G	V
16	48 T	+17:35109827 2524641334 T	
16	49 T	+17:35109828 2524641335 T	
17 V	50 G	+17:35109829 2524641336 G	V
17	51 T	+17:35109830 2524641337 T	
17	52 G	+17:35109831 2524641338 G	
18 K	53 A	+17:35109832 2524641339 A	K
18	54 A	+17:35109833 2524641340 A	
18	55 G	+17:35109834 2524641341 G	
19 L	56 C	+17:35109835 2524641342 C	L
19	57 T	+17:35109836 2524641343 T	
19	58 G	+17:35109837 2524641344 G	
20 R	59 A	+17:35109838 2524641345 A	R
20	60 G	+17:35109839 2524641346 G	
20	61 A	+17:35109840 2524641347 A	
21	62  	+17:35109841 2524641348 T	F
21 S	62 T	+17:35109842 2524641349 T	
21	63 C	+17:35109843 2524641350 C	
22	64 C	+17:35109844 2524641351 C	P
22 P	65 C	+17:35109845 2524641352 C	
22	66 C	+17:35109846 2524641353 C	
23	67 T	+17:35109847 2524641354 T	S
23 P	68 C	+17:35109848 2524641355 C	
23	69 C	+17:35109849 2524641356 C	
24	70 A	+17:35109850 2524641357 A	I
24 L	71 T	+17:35109851 2524641358 T	
24	72 T	+17:35109852 2524641359 T	
25	73 G	+17:35109853 2524641360 G	G
25 G	74 G	+17:35109854 2524641361 G	
25	75 G	+17:35109855 2524641362 G	
26	76 A	+17:35109856 2524641363 A	T
26 P	77 C	+17:35109857 2524641364 C	
26	78 C	+17:35109858 2524641365 C	
27	79 G	+17:35109859 2524641366 G	G
27 E	80 G	+17:35109860 2524641367 G	
27	81 A	+17:35109861 2524641368 A	
28	82 G	+17:35109862 2524641369 G	E
28 K	83 A	+17:35109863 2524641370 A	
28	84 A	+17:35109864 2524641371 A	
29	85 A	+17:35109865 2524641372 A	T
29 P	86 C	+17:35109866 2524641373 C	
29	87 C	+17:35109867 2524641374 C	
30	88 A	+17:35109868 2524641375 A	R
30 G	89 G	+17:35109869 2524641376 G	
30	90 G	+17:35109870 2524641377 G	
31	91 G	+17:35109871 2524641378 G	G
31 E	92 G	+17:35109872 2524641379 G	
31	93 A	+17:35109873 2524641380 A	
32	94 G	+17:35109874 2524641381 G	A
32 P	95 C	+17:35109875 2524641382 C	
32	96 C	+17:35109876 2524641383 C	
33	97 C	+17:35109877 2524641384 C	P
33 P	98 C	+17:35109878 2524641385 C	
33	99 C	+17:35109879 2524641386 C	
34	100 C	+17:35109880 2524641387 C	R
34 G	101 G	+17:35109881 2524641388 G	
34	102 G	+17:35109882 2524641389 G	
35	103 G	+17:35109883 2524641390 G	A
35 Q	104 C	+17:35109884 2524641391 C	
35	105 A	+17:35109885 2524641392 A	
36	106 G	+17:35109886 2524641393 G	A
36 P	107 C	+17:35109887 2524641394 C	
36	108 C	+17:35109888 2524641395 C	
37	109 G	+17:35109889 2524641396 G	A
37 R	110 C	+17:35109890 2524641397 C	
37	111 G	+17:35109891 2524641398 G	
38	112 C	+17:35109892 2524641399 C	R
38 A	113 G	+17:35109893 2524641400 G	
38	114 C	+17:35109894 2524641401 C	
39	115 C	+17:35109895 2524641402 C	P
39 P	116 C	+17:35109896 2524641403 C	
39	117 C	+17:35109897 2524641404 C	
40	118 T	+17:35109898 2524641405 T	F
40 S	119 T	+17:35109899 2524641406 T	
40	120 C	+17:35109900 2524641407 C	
41	121 C	+17:35109901 2524641408 C	P
41 H	122 C	+17:35109902 2524641409 C	
41	123 A	+17:35109903 2524641410 A	
42	124 C	+17:35109904 2524641411 C	R
42 G	125 G	+17:35109905 2524641412 G	
42	126 G	+17:35109906 2524641413 G	
43	127 G	+17:35109907 2524641414 G	G
43 A	128 G	+17:35109908 2524641415 G	
43	129 C	+17:35109909 2524641416 C	
44	130 C	+17:35109910 2524641417 C	P
44 L	131 C	+17:35109911 2524641418 C	
44	132 T	+17:35109912 2524641419 T	
45	133 T	+17:35109913 2524641420 T	L
45 Y	134 T	+17:35109914 2524641421 T	
45	135 A	+17:35109915 2524641422 A	
46	136 C	+17:35109916 2524641423 C	L
46 C	137 T	+17:35109917 2524641424 T	
46	138 G	+17:35109918 2524641425 G	
47	139 C	+17:35109919 2524641426 C	R
47 A	140 G	+17:35109920 2524641427 G	
47	141 C	+17:35109921 2524641428 C	
48	142 C	+17:35109922 2524641429 C	R
48 A	143 G	+17:35109923 2524641430 G	
48	144 C	+17:35109924 2524641431 C	
49	145 G	+17:35109925 2524641432 G	A
49 R	146 C	+17:35109926 2524641433 C	
49	147 G	+17:35109927 2524641434 G	
50	148 C	+17:35109928 2524641435 C	P
50 P	149 C	+17:35109929 2524641436 C	
50	150 C	+17:35109930 2524641437 C	
51	151 G	+17:35109931 2524641438 G	G
51 A	152 G	+17:35109932 2524641439 G	
51	153 C	+17:35109933 2524641440 C	
52	154 C	+17:35109934 2524641441 C	P
52 P	155 C	+17:35109935 2524641442 C	
52	156 C	+17:35109936 2524641443 C	
53	157 C	+17:35109937 2524641444 C	H
53 T	158 A	+17:35109938 2524641445 A	
53	159 C	+17:35109939 2524641446 C	
54	160 C	+17:35109940 2524641447 C	P
54 P	161 C	+17:35109941 2524641448 C	
54	162 C	+17:35109942 2524641449 C	
55	163 T	+17:35109943 2524641450 T	S
55 R	164 C	+17:35109944 2524641451 C	
55	165 G	+17:35109945 2524641452 G	
56	166 C	+17:35109946 2524641453 C	Q
56 S	167 A	+17:35109947 2524641454 A	
56	168 G	+17:35109948 2524641455 G	
57	169 C	+17:35109949 2524641456 C	H
57 T	170 A	+17:35109950 2524641457 A	
57	171 C	+17:35109951 2524641458 C	
58	172 C	+17:35109952 2524641459 C	P
58 P	173 C	+17:35109953 2524641460 C	
58	174 C	+17:35109954 2524641461 C	
59	175 G	+17:35109955 2524641462 G	A
59 R	176 C	+17:35109956 2524641463 C	
59	177 G	+17:35109957 2524641464 G	
60	178 C	+17:35109958 2524641465 C	P
60 P	179 C	+17:35109959 2524641466 C	
60	180 C	+17:35109960 2524641467 C	
61	181 C	+17:35109961 2524641468 C	R
61 A	182 G	+17:35109962 2524641469 G	
61	183 C	+17:35109963 2524641470 C	
62	184 G	+17:35109964 2524641471 G	A
62 P	185 C	+17:35109965 2524641472 C	
62	186 C	+17:35109966 2524641473 C	
63	187 C	+17:35109967 2524641474 C	L
63 S	188 T	+17:35109968 2524641475 T	
63	189 C	+17:35109969 2524641476 C	
64	190 C	+17:35109970 2524641477 C	P
64 Q	191 C	+17:35109971 2524641478 C	
64	192 A	+17:35109972 2524641479 A	
65	193 G	+17:35109973 2524641480 G	A
65 P	194 C	+17:35109974 2524641481 C	
65	195 C	+17:35109975 2524641482 C	
66	196 G	+17:35109976 2524641483 G	G
66 G	197 G	+17:35109977 2524641484 G	
66	198 G	+17:35109978 2524641485 G	
67	199 T	+17:35109979 2524641486 T	S
67 P	200 C	+17:35109980 2524641487 C	
67	201 C	+17:35109981 2524641488 C	
68	202 A	+17:35109982 2524641489 A	S
68 A	203 G	+17:35109983 2524641490 G	
68	204 C	+17:35109984 2524641491 C	
69	205 C	+17:35109985 2524641492 C	R
69 G	206 G	+17:35109986 2524641493 G	
69	207 G	+17:35109987 2524641494 G	
70	208 A	+17:35109988 2524641495 A	S
70 A	209 G	+17:35109989 2524641496 G	
70	210 C	+17:35109990 2524641497 C	
71	211 C	+17:35109991 2524641498 C	H
71 M	212 A	+17:35109992 2524641499 A	
71	213 T	+17:35109993 2524641500 T	
72	214 G	+17:35109994 2524641501 G	G
72 G	215 G	+17:35109995 2524641502 G	
72	216 G	+17:35109996 2524641503 G	
73	217 G	+17:35109997 2524641504 G	A
73 P	218 C	+17:35109998 2524641505 C	
73	219 C	+17:35109999 2524641506 C	
74	220 G	+17:35110000 2524641507 G	G
74 E	221 G	+17:35110001 2524641508 G	
74	222 A	+17:35110002 2524641509 A	
75	223 G	+17:35110003 2524641510 G	A
75 P	224 C	+17:35110004 2524641511 C	
75	225 C	+17:35110005 2524641512 C	
76	226 G	+17:35110006 2524641513 G	A
76 Q	227 C	+17:35110007 2524641514 C	
76	228 A	+17:35110008 2524641515 A	
77	229 G	+17:35110009 2524641516 G	V
77 *	230 T	+17:35110010 2524641517 T	
77	231 G	+17:35110011 2524641518 G	
78	232 A	+17:35110012 2524641519 A	S
78	233 G	+17:35110013 2524641520 G	
78	234 C	+17:35110014 2524641521 C	
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79	236 C	+17:35110016 2524641523 C	
79	237 C	+17:35110017 2524641524 C	
80	238 A	+17:35110018 2524641525 A	M
80	239 T	+17:35110019 2524641526 T	
80	240 G	+17:35110020 2524641527 G	
81	241 G	+17:35110021 2524641528 G	E
81	242 A	+17:35110022 2524641529 A	
81	243 G	+17:35110023 2524641530 G	
82	244 C	+17:35110024 2524641531 C	L
82	245 T	+17:35110025 2524641532 T	
82	246 G	+17:35110026 2524641533 G	
83	247 G	+17:35110027 2524641534 G	A
83	248 C	+17:35110028 2524641535 C	
83	249 G	+17:35110029 2524641536 G	
84	250 G	+17:35110030 2524641537 G	A
84	251 C	+17:35110031 2524641538 C	
84	252 C	+17:35110032 2524641539 C	
85	253 T	+17:35110033 2524641540 T	L
85	254 T	+17:35110034 2524641541 T	
85	255 G	+17:35110035 2524641542 G	
86	256 T	+17:35110036 2524641543 T	C
86	257 G	+17:35110037 2524641544 G	
86	258 C	+17:35110038 2524641545 C	
87	259 C	+17:35110039 2524641546 C	R
87	260 G	+17:35110040 2524641547 G	
87	261 C	+17:35110041 2524641548 C	
88	262 T	+17:35110042 2524641549 T	W
88	263 G	+17:35110043 2524641550 G	
88	264 G	+17:35110044 2524641551 G	
89	265 G	+17:35110045 2524641552 G	G
89	266 G	+17:35110046 2524641553 G	
89	267 G	+17:35110047 2524641554 G	
90	268 C	+17:35110048 2524641555 C	L
90	269 T	+17:35110049 2524641556 T	
90	270 C	+17:35110050 2524641557 C	
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91	272 T	+17:35110052 2524641559 T	
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92	274 C	+17:35110054 2524641561 C	L
92	275 T	+17:35110055 2524641562 T	
92	276 C	+17:35110056 2524641563 C	
93	277 G	+17:35110057 2524641564 G	A
93	278 C	+17:35110058 2524641565 C	
93	279 C	+17:35110059 2524641566 C	
94	280 C	+17:35110060 2524641567 C	L
94	281 T	+17:35110061 2524641568 T	
94	282 C	+17:35110062 2524641569 C	
95	283 T	+17:35110063 2524641570 T	L
95	284 T	+17:35110064 2524641571 T	
95	285 G	+17:35110065 2524641572 G	
96	286 C	+17:35110066 2524641573 C	P
96	287 C	+17:35110067 2524641574 C	
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97	290 C	+17:35110070 2524641577 C	
97	291 C	+17:35110071 2524641578 C	
98	292 G	+17:35110072 2524641579 G	G
98	293 G	+17:35110073 2524641580 G	
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99	295 G	+17:35110075 2524641582 G	A
99	296 C	+17:35110076 2524641583 C	
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100	298 G	+17:35110078 2524641585 G	A
100	299 C	+17:35110079 2524641586 C	
100	300 G	+17:35110080 2524641587 G	
101	301 A	+17:35110081 2524641588 A	S
101	302 G	+17:35110082 2524641589 G	
101	303 C	+17:35110083 2524641590 C	
102	304 A	+17:35110084 2524641591 A	T
102	305 C	+17:35110085 2524641592 C	
102	306 C	+17:35110086 2524641593 C	
103	307 C	+17:35110087 2524641594 C	Q
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350	1048 C	+17:35120170 2524651677 C	L
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351	1051 G	+17:35120173 2524651680 G	V
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354	1060 A	+17:35120182 2524651689 A	N
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355	1063 A	+17:35120185 2524651692 A	T
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355	1065 A	+17:35120187 2524651694 A	
356	1066 G	+17:35120188 2524651695 G	D
356	1067 A	+17:35120189 2524651696 A	
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357	1069 A	+17:35120191 2524651698 A	T
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358	1072 T	+17:35120194 2524651701 T	F
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363	1087 A	+17:35120209 2524651716 A	N
363	1088 A	+17:35120210 2524651717 A	
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383	1149 T	+17:35121717 2524653224 T	
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417	1250 G	+17:35121818 2524653325 G	
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517	1549 A	+17:35125314 2524656821 A	N
517	1550 A	+17:35125315 2524656822 A	
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518	1552 G	+17:35125520 2524657027 G	G
518	1553 G	+17:35125521 2524657028 G	
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519	1556 C	+17:35125524 2524657031 C	
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520	1558 T	+17:35125526 2524657033 T	Y
520	1559 A	+17:35125527 2524657034 A	
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531	1591 T	+17:35125559 2524657066 T	W
531	1592 G	+17:35125560 2524657067 G	
531	1593 G	+17:35125561 2524657068 G	
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533	1598 G	+17:35125566 2524657073 G	
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541	1621 G	+17:35125589 2524657096 G	G
541	1622 G	+17:35125590 2524657097 G	
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543	1627 G	+17:35125595 2524657102 G	G
543	1628 G	+17:35125596 2524657103 G	
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547	1640 T	+17:35125608 2524657115 T	
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548	1642 C	+17:35125610 2524657117 C	H
548	1643 A	+17:35125611 2524657118 A	
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549	1645 C	+17:35125613 2524657120 C	H
549	1646 A	+17:35125614 2524657121 A	
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550	1648 A	+17:35125616 2524657123 A	N
550	1649 A	+17:35125617 2524657124 A	
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551	1651 A	+17:35125619 2524657126 A	T
551	1652 C	+17:35125620 2524657127 C	
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552	1655 A	+17:35125623 2524657130 A	
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554	1661 G	+17:35125629 2524657136 G	
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555	1664 T	+17:35125632 2524657139 T	
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559	1676 T	+17:35125644 2524657151 T	
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560	1678 C	+17:35125646 2524657153 C	P
560	1679 C	+17:35125647 2524657154 C	
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561	1682 G	+17:35125650 2524657157 G	
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562	1685 A	+17:35125653 2524657160 A	
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563	1688 A	+17:35125656 2524657163 A	
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565	1693 T	+17:35125661 2524657168 T	F
565	1694 T	+17:35125662 2524657169 T	
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566	1697 G	+17:35125665 2524657172 G	
566	1698 G	+17:35125666 2524657173 G	
567	1699 A	+17:35125667 2524657174 A	N
567	1700 A	+17:35125668 2524657175 A	
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569	1705 C	+17:35125673 2524657180 C	H
569	1706 A	+17:35125674 2524657181 A	
569	1707 C	+17:35125675 2524657182 C	
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577	1729 A	+17:35125697 2524657204 A	N
577	1730 A	+17:35125698 2524657205 A	
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578	1732 C	+17:35125700 2524657207 C	R
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579	1735 C	+17:35125703 2524657210 C	P
579	1736 C	+17:35125704 2524657211 C	
579	1737 A	+17:35125705 2524657212 A	
580	1738 G	+17:35125706 2524657213 G	E
580	1739 A	+17:35125707 2524657214 A	
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581	1741 G	+17:35125709 2524657216 G	D
581	1742 A	+17:35125710 2524657217 A	
581	1743 C	+17:35125711 2524657218 C	
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582	1745 A	+17:35125713 2524657220 A	
582	1746 G	+17:35125714 2524657221 G	
583	1747 T	+17:35125715 2524657222 T	C
583	1748 G	+17:35125716 2524657223 G	
583	1749 T	+17:35125717 2524657224 T	
584	1750 G	+17:35125718 2524657225 G	V
584	1751 T	+17:35126080 2524657587 T	
584	1752 G	+17:35126081 2524657588 G	
585	1753 G	+17:35126082 2524657589 G	G
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586	1757 A	+17:35126086 2524657593 A	
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588	1762 C	+17:35126091 2524657598 C	L
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605	1813 A	+17:35126142 2524657649 A	T
605	1814 C	+17:35126143 2524657650 C	
605	1815 C	+17:35126144 2524657651 C	
606	1816 C	+17:35126145 2524657652 C	Q
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608	1822 G	+17:35126151 2524657658 G	V
608	1823 T	+17:35126152 2524657659 T	
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609	1825 A	+17:35126154 2524657661 A	N
609	1826 A	+17:35126155 2524657662 A	
609	1827 C	+17:35126156 2524657663 C	
610	1828 T	+17:35126157 2524657664 T	C
610	1829 G	+17:35126158 2524657665 G	
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611	1831 A	+17:35126160 2524657667 A	S
611	1832 G	+17:35126161 2524657668 G	
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612	1834 C	+17:35126163 2524657670 C	Q
612	1835 A	+17:35126164 2524657671 A	
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613	1837 T	+17:35126166 2524657673 T	F
613	1838 T	+17:35126167 2524657674 T	
613	1839 C	+17:35126168 2524657675 C	
614	1840 C	+17:35126169 2524657676 C	L
614	1841 T	+17:35126170 2524657677 T	
614	1842 T	+17:35126171 2524657678 T	
615	1843 C	+17:35126172 2524657679 C	R
615	1844 G	+17:35126173 2524657680 G	
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616	1846 G	+17:35126175 2524657682 G	G
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617	1849 C	+17:35126178 2524657685 C	Q
617	1850 A	+17:35126179 2524657686 A	
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618	1852 G	+17:35126181 2524657688 G	E
618	1853 A	+17:35126182 2524657689 A	
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619	1855 T	+17:35126184 2524657691 T	C
619	1856 G	+17:35126185 2524657692 G	
619	1857 C	+17:35126186 2524657693 C	
620	1858 G	+17:35126187 2524657694 G	V
620	1859 T	+17:35126188 2524657695 T	
620	1860 G	+17:35126189 2524657696 G	
621	1861 G	+17:35126190 2524657697 G	E
621	1862 A	+17:35126191 2524657698 A	
621	1863 G	+17:35126192 2524657699 G	
622	1864 G	+17:35126193 2524657700 G	E
622	1865 A	+17:35126194 2524657701 A	
622	1866 A	+17:35126195 2524657702 A	
623	1867 T	+17:35126196 2524657703 T	C
623	1868 G	+17:35126197 2524657704 G	
623	1869 C	+17:35126198 2524657705 C	
624	1870 C	+17:35126199 2524657706 C	R
624	1871 G	+17:35126200 2524657707 G	
624	1872 A	+17:35126201 2524657708 A	
625	1873 G	+17:35126202 2524657709 G	V
625	1874 T	+17:35126203 2524657710 T	
625	1875 A	+17:35126204 2524657711 A	
626	1876 C	+17:35126205 2524657712 C	L
626	1877 T	+17:35126206 2524657713 T	
626	1878 G	+17:35126207 2524657714 G	
627	1879 C	+17:35126208 2524657715 C	Q
627	1880 A	+17:35126209 2524657716 A	
627	1881 G	+17:35126210 2524657717 G	
628	1882 G	+17:35126211 2524657718 G	G
628	1883 G	+17:35126212 2524657719 G	
628	1884 G	+17:35126294 2524657801 G	
629	1885 C	+17:35126295 2524657802 C	L
629	1886 T	+17:35126296 2524657803 T	
629	1887 C	+17:35126297 2524657804 C	
630	1888 C	+17:35126298 2524657805 C	P
630	1889 C	+17:35126299 2524657806 C	
630	1890 C	+17:35126300 2524657807 C	
631	1891 A	+17:35126301 2524657808 A	R
631	1892 G	+17:35126302 2524657809 G	
631	1893 G	+17:35126303 2524657810 G	
632	1894 G	+17:35126304 2524657811 G	E
632	1895 A	+17:35126305 2524657812 A	
632	1896 G	+17:35126306 2524657813 G	
633	1897 T	+17:35126307 2524657814 T	Y
633	1898 A	+17:35126308 2524657815 A	
633	1899 T	+17:35126309 2524657816 T	
634	1900 G	+17:35126310 2524657817 G	V
634	1901 T	+17:35126311 2524657818 T	
634	1902 G	+17:35126312 2524657819 G	
635	1903 A	+17:35126313 2524657820 A	N
635	1904 A	+17:35126314 2524657821 A	
635	1905 T	+17:35126315 2524657822 T	
636	1906 G	+17:35126316 2524657823 G	A
636	1907 C	+17:35126317 2524657824 C	
636	1908 C	+17:35126318 2524657825 C	
637	1909 A	+17:35126319 2524657826 A	R
637	1910 G	+17:35126320 2524657827 G	
637	1911 G	+17:35126321 2524657828 G	
638	1912 C	+17:35126322 2524657829 C	H
638	1913 A	+17:35126323 2524657830 A	
638	1914 C	+17:35126324 2524657831 C	
639	1915 T	+17:35126325 2524657832 T	C
639	1916 G	+17:35126326 2524657833 G	
639	1917 T	+17:35126327 2524657834 T	
640	1918 T	+17:35126328 2524657835 T	L
640	1919 T	+17:35126329 2524657836 T	
640	1920 G	+17:35126330 2524657837 G	
641	1921 C	+17:35126331 2524657838 C	P
641	1922 C	+17:35126332 2524657839 C	
641	1923 G	+17:35126333 2524657840 G	
642	1924 T	+17:35126334 2524657841 T	C
642	1925 G	+17:35126335 2524657842 G	
642	1926 C	+17:35126336 2524657843 C	
643	1927 C	+17:35126337 2524657844 C	H
643	1928 A	+17:35126338 2524657845 A	
643	1929 C	+17:35126339 2524657846 C	
644	1930 C	+17:35126340 2524657847 C	P
644	1931 C	+17:35126341 2524657848 C	
644	1932 T	+17:35126342 2524657849 T	
645	1933 G	+17:35126343 2524657850 G	E
645	1934 A	+17:35126344 2524657851 A	
645	1935 G	+17:35126345 2524657852 G	
646	1936 T	+17:35126346 2524657853 T	C
646	1937 G	+17:35126347 2524657854 G	
646	1938 T	+17:35126348 2524657855 T	
647	1939 C	+17:35126349 2524657856 C	Q
647	1940 A	+17:35126350 2524657857 A	
647	1941 G	+17:35126351 2524657858 G	
648	1942 C	+17:35126352 2524657859 C	P
648	1943 C	+17:35126353 2524657860 C	
648	1944 C	+17:35126354 2524657861 C	
649	1945 C	+17:35126355 2524657862 C	Q
649	1946 A	+17:35126356 2524657863 A	
649	1947 G	+17:35126357 2524657864 G	
650	1948 A	+17:35126358 2524657865 A	N
650	1949 A	+17:35126359 2524657866 A	
650	1950 T	+17:35126360 2524657867 T	
651	1951 G	+17:35126361 2524657868 G	G
651	1952 G	+17:35126362 2524657869 G	
651	1953 C	+17:35126363 2524657870 C	
652	1954 T	+17:35126364 2524657871 T	S
652	1955 C	+17:35126365 2524657872 C	
652	1956 A	+17:35126366 2524657873 A	
653	1957 G	+17:35126367 2524657874 G	V
653	1958 T	+17:35126368 2524657875 T	
653	1959 G	+17:35126369 2524657876 G	
654	1960 A	+17:35126370 2524657877 A	T
654	1961 C	+17:35126371 2524657878 C	
654	1962 C	+17:35126372 2524657879 C	
655	1963 T	+17:35126373 2524657880 T	C
655	1964 G	+17:35126374 2524657881 G	
655	1965 T	+17:35126375 2524657882 T	
656	1966 T	+17:35126376 2524657883 T	F
656	1967 T	+17:35126377 2524657884 T	
656	1968 T	+17:35126378 2524657885 T	
657	1969 G	+17:35126379 2524657886 G	G
657	1970 G	+17:35126380 2524657887 G	
657	1971 A	+17:35126381 2524657888 A	
658	1972 C	+17:35126382 2524657889 C	P
658	1973 C	+17:35126383 2524657890 C	
658	1974 G	+17:35126384 2524657891 G	
659	1975 G	+17:35127099 2524658606 G	E
659	1976 A	+17:35127100 2524658607 A	
659	1977 G	+17:35127101 2524658608 G	
660	1978 G	+17:35127102 2524658609 G	A
660	1979 C	+17:35127103 2524658610 C	
660	1980 T	+17:35127104 2524658611 T	
661	1981 G	+17:35127105 2524658612 G	D
661	1982 A	+17:35127106 2524658613 A	
661	1983 C	+17:35127107 2524658614 C	
662	1984 C	+17:35127108 2524658615 C	Q
662	1985 A	+17:35127109 2524658616 A	
662	1986 G	+17:35127110 2524658617 G	
663	1987 T	+17:35127111 2524658618 T	C
663	1988 G	+17:35127112 2524658619 G	
663	1989 T	+17:35127113 2524658620 T	
664	1990 G	+17:35127114 2524658621 G	V
664	1991 T	+17:35127115 2524658622 T	
664	1992 G	+17:35127116 2524658623 G	
665	1993 G	+17:35127117 2524658624 G	A
665	1994 C	+17:35127118 2524658625 C	
665	1995 C	+17:35127119 2524658626 C	
666	1996 T	+17:35127120 2524658627 T	C
666	1997 G	+17:35127121 2524658628 G	
666	1998 T	+17:35127122 2524658629 T	
667	1999 G	+17:35127123 2524658630 G	A
667	2000 C	+17:35127124 2524658631 C	
667	2001 C	+17:35127125 2524658632 C	
668	2002 C	+17:35127126 2524658633 C	H
668	2003 A	+17:35127127 2524658634 A	
668	2004 C	+17:35127128 2524658635 C	
669	2005 T	+17:35127129 2524658636 T	Y
669	2006 A	+17:35127130 2524658637 A	
669	2007 T	+17:35127131 2524658638 T	
670	2008 A	+17:35127132 2524658639 A	K
670	2009 A	+17:35127133 2524658640 A	
670	2010 G	+17:35127134 2524658641 G	
671	2011 G	+17:35127135 2524658642 G	D
671	2012 A	+17:35127136 2524658643 A	
671	2013 C	+17:35127137 2524658644 C	
672	2014 C	+17:35127138 2524658645 C	P
672	2015 C	+17:35127139 2524658646 C	
672	2016 T	+17:35127140 2524658647 T	
673	2017 C	+17:35127141 2524658648 C	P
673	2018 C	+17:35127142 2524658649 C	
673	2019 C	+17:35127143 2524658650 C	
674	2020 T	+17:35127144 2524658651 T	F
674	2021 T	+17:35127145 2524658652 T	
674	2022 C	+17:35127146 2524658653 C	
675	2023 T	+17:35127147 2524658654 T	C
675	2024 G	+17:35127148 2524658655 G	
675	2025 C	+17:35127149 2524658656 C	
676	2026 G	+17:35127150 2524658657 G	V
676	2027 T	+17:35127151 2524658658 T	
676	2028 G	+17:35127152 2524658659 G	
677	2029 G	+17:35127153 2524658660 G	A
677	2030 C	+17:35127154 2524658661 C	
677	2031 C	+17:35127155 2524658662 C	
678	2032 C	+17:35127156 2524658663 C	R
678	2033 G	+17:35127157 2524658664 G	
678	2034 C	+17:35127158 2524658665 C	
679	2035 T	+17:35127159 2524658666 T	C
679	2036 G	+17:35127160 2524658667 G	
679	2037 C	+17:35127161 2524658668 C	
680	2038 C	+17:35127162 2524658669 C	P
680	2039 C	+17:35127163 2524658670 C	
680	2040 C	+17:35127164 2524658671 C	
681	2041 A	+17:35127165 2524658672 A	S
681	2042 G	+17:35127166 2524658673 G	
681	2043 C	+17:35127167 2524658674 C	
682	2044 G	+17:35127168 2524658675 G	G
682	2045 G	+17:35127169 2524658676 G	
682	2046 T	+17:35127170 2524658677 T	
683	2047 G	+17:35127171 2524658678 G	V
683	2048 T	+17:35127172 2524658679 T	
683	2049 G	+17:35127173 2524658680 G	
684	2050 A	+17:35127174 2524658681 A	K
684	2051 A	+17:35127175 2524658682 A	
684	2052 A	+17:35127176 2524658683 A	
685	2053 C	+17:35127177 2524658684 C	P
685	2054 C	+17:35127178 2524658685 C	
685	2055 T	+17:35127179 2524658686 T	
686	2056 G	+17:35127180 2524658687 G	D
686	2057 A	+17:35127181 2524658688 A	
686	2058 C	+17:35127182 2524658689 C	
687	2059 C	+17:35127183 2524658690 C	L
687	2060 T	+17:35127184 2524658691 T	
687	2061 C	+17:35127185 2524658692 C	
688	2062 T	+17:35127186 2524658693 T	S
688	2063 C	+17:35127187 2524658694 C	
688	2064 C	+17:35127188 2524658695 C	
689	2065 T	+17:35127189 2524658696 T	Y
689	2066 A	+17:35127190 2524658697 A	
689	2067 C	+17:35127191 2524658698 C	
690	2068 A	+17:35127192 2524658699 A	M
690	2069 T	+17:35127193 2524658700 T	
690	2070 G	+17:35127194 2524658701 G	
691	2071 C	+17:35127195 2524658702 C	P
691	2072 C	+17:35127196 2524658703 C	
691	2073 C	+17:35127197 2524658704 C	
692	2074 A	+17:35127198 2524658705 A	I
692	2075 T	+17:35127199 2524658706 T	
692	2076 C	+17:35127200 2524658707 C	
693	2077 T	+17:35127201 2524658708 T	W
693	2078 G	+17:35127202 2524658709 G	
693	2079 G	+17:35127203 2524658710 G	
694	2080 A	+17:35127204 2524658711 A	K
694	2081 A	+17:35127205 2524658712 A	
694	2082 G	+17:35127206 2524658713 G	
695	2083 T	+17:35127207 2524658714 T	F
695	2084 T	+17:35127208 2524658715 T	
695	2085 T	+17:35127209 2524658716 T	
696	2086 C	+17:35127210 2524658717 C	P
696	2087 C	+17:35127211 2524658718 C	
696	2088 A	+17:35127212 2524658719 A	
697	2089 G	+17:35127213 2524658720 G	D
697	2090 A	+17:35127214 2524658721 A	
697	2091 T	+17:35127215 2524658722 T	
698	2092 G	+17:35127216 2524658723 G	E
698	2093 A	+17:35127217 2524658724 A	
698	2094 G	+17:35127218 2524658725 G	
699	2095 G	+17:35127219 2524658726 G	E
699	2096 A	+17:35127220 2524658727 A	
699	2097 G	+17:35127221 2524658728 G	
700	2098 G	+17:35127222 2524658729 G	G
700	2099 G	+17:35127223 2524658730 G	
700	2100 C	+17:35127224 2524658731 C	
701	2101 G	+17:35127225 2524658732 G	A
701	2102 C	+17:35127226 2524658733 C	
701	2103 A	+17:35127227 2524658734 A	
702	2104 T	+17:35127228 2524658735 T	C
702	2105 G	+17:35127229 2524658736 G	
702	2106 C	+17:35127230 2524658737 C	
703	2107 C	+17:35127231 2524658738 C	Q
703	2108 A	+17:35127232 2524658739 A	
703	2109 G	+17:35127233 2524658740 G	
704	2110 C	+17:35127234 2524658741 C	P
704	2111 C	+17:35127235 2524658742 C	
704	2112 T	+17:35127236 2524658743 T	
705	2113 T	+17:35127237 2524658744 T	C
705	2114 G	+17:35127238 2524658745 G	
705	2115 C	+17:35127239 2524658746 C	
706	2116 C	+17:35127240 2524658747 C	P
706	2117 C	+17:35127241 2524658748 C	
706	2118 C	+17:35127242 2524658749 C	
707	2119 A	+17:35127243 2524658750 A	I
707	2120 T	+17:35127244 2524658751 T	
707	2121 C	+17:35127245 2524658752 C	
708	2122 A	+17:35127246 2524658753 A	N
708	2123 A	+17:35127247 2524658754 A	
708	2124 C	+17:35127248 2524658755 C	
709	2125 T	+17:35127249 2524658756 T	C
709	2126 G	+17:35127250 2524658757 G	
709	2127 C	+17:35127251 2524658758 C	
710	2128 A	+17:35127252 2524658759 A	T
710	2129 C	+17:35127253 2524658760 C	
710	2130 C	+17:35127254 2524658761 C	
711	2131 C	+17:35127255 2524658762 C	H
711	2132 A	+17:35127256 2524658763 A	
711	2133 C	+17:35127257 2524658764 C	
712	2134 T	+17:35127258 2524658765 T	S
712	2135 C	+17:35127259 2524658766 C	
712	2136 C	+17:35129566 2524661073 C	
713	2137 T	+17:35129567 2524661074 T	C
713	2138 G	+17:35129568 2524661075 G	
713	2139 T	+17:35129569 2524661076 T	
714	2140 G	+17:35129570 2524661077 G	V
714	2141 T	+17:35129571 2524661078 T	
714	2142 G	+17:35129572 2524661079 G	
715	2143 G	+17:35129573 2524661080 G	D
715	2144 A	+17:35129574 2524661081 A	
715	2145 C	+17:35129575 2524661082 C	
716	2146 C	+17:35129576 2524661083 C	L
716	2147 T	+17:35129577 2524661084 T	
716	2148 G	+17:35129578 2524661085 G	
717	2149 G	+17:35129579 2524661086 G	D
717	2150 A	+17:35129580 2524661087 A	
717	2151 T	+17:35129581 2524661088 T	
718	2152 G	+17:35129582 2524661089 G	D
718	2153 A	+17:35129583 2524661090 A	
718	2154 C	+17:35129584 2524661091 C	
719	2155 A	+17:35129585 2524661092 A	K
719	2156 A	+17:35129586 2524661093 A	
719	2157 G	+17:35129587 2524661094 G	
720	2158 G	+17:35129588 2524661095 G	G
720	2159 G	+17:35129589 2524661096 G	
720	2160 C	+17:35129590 2524661097 C	
721	2161 T	+17:35129591 2524661098 T	C
721	2162 G	+17:35129592 2524661099 G	
721	2163 C	+17:35129593 2524661100 C	
722	2164 C	+17:35129594 2524661101 C	P
722	2165 C	+17:35129595 2524661102 C	
722	2166 C	+17:35129596 2524661103 C	
723	2167 G	+17:35129597 2524661104 G	A
723	2168 C	+17:35129598 2524661105 C	
723	2169 C	+17:35129599 2524661106 C	
724	2170 G	+17:35129600 2524661107 G	E
724	2171 A	+17:35129601 2524661108 A	
724	2172 G	+17:35129602 2524661109 G	
725	2173 C	+17:35129603 2524661110 C	Q
725	2174 A	+17:35129604 2524661111 A	
725	2175 G	+17:35129605 2524661112 G	
726	2176 A	+17:35129606 2524661113 A	R
726	2177 G	+17:35129607 2524661114 G	
726	2178 A	+17:35129608 2524661115 A	
727	2179 G	+17:35129609 2524661116 G	A
727	2180 C	+17:35129610 2524661117 C	
727	2181 C	+17:35129611 2524661118 C	
728	2182 A	+17:35129612 2524661119 A	S
728	2183 G	+17:35129613 2524661120 G	
728	2184 C	+17:35133098 2524664605 C	
729	2185 C	+17:35133099 2524664606 C	P
729	2186 C	+17:35133100 2524664607 C	
729	2187 T	+17:35133101 2524664608 T	
730	2188 C	+17:35133102 2524664609 C	L
730	2189 T	+17:35133103 2524664610 T	
730	2190 G	+17:35133104 2524664611 G	
731	2191 A	+17:35133105 2524664612 A	T
731	2192 C	+17:35133106 2524664613 C	
731	2193 G	+17:35133107 2524664614 G	
732	2194 T	+17:35133108 2524664615 T	S
732	2195 C	+17:35133109 2524664616 C	
732	2196 C	+17:35133110 2524664617 C	
733	2197 A	+17:35133111 2524664618 A	I
733	2198 T	+17:35133112 2524664619 T	
733	2199 C	+17:35133113 2524664620 C	
734	2200 A	+17:35133114 2524664621 A	I
734	2201 T	+17:35133115 2524664622 T	
734	2202 C	+17:35133116 2524664623 C	
735	2203 T	+17:35133117 2524664624 T	S
735	2204 C	+17:35133118 2524664625 C	
735	2205 T	+17:35133119 2524664626 T	
736	2206 G	+17:35133120 2524664627 G	A
736	2207 C	+17:35133121 2524664628 C	
736	2208 G	+17:35133122 2524664629 G	
737	2209 G	+17:35133123 2524664630 G	V
737	2210 T	+17:35133124 2524664631 T	
737	2211 G	+17:35133125 2524664632 G	
738	2212 G	+17:35133126 2524664633 G	V
738	2213 T	+17:35133127 2524664634 T	
738	2214 T	+17:35133128 2524664635 T	
739	2215 G	+17:35133129 2524664636 G	G
739	2216 G	+17:35133130 2524664637 G	
739	2217 C	+17:35133131 2524664638 C	
740	2218 A	+17:35133132 2524664639 A	I
740	2219 T	+17:35133133 2524664640 T	
740	2220 T	+17:35133134 2524664641 T	
741	2221 C	+17:35133135 2524664642 C	L
741	2222 T	+17:35133136 2524664643 T	
741	2223 G	+17:35133137 2524664644 G	
742	2224 C	+17:35133138 2524664645 C	L
742	2225 T	+17:35133139 2524664646 T	
742	2226 G	+17:35133140 2524664647 G	
743	2227 G	+17:35133141 2524664648 G	V
743	2228 T	+17:35133142 2524664649 T	
743	2229 C	+17:35133143 2524664650 C	
744	2230 G	+17:35133144 2524664651 G	V
744	2231 T	+17:35133145 2524664652 T	
744	2232 G	+17:35133146 2524664653 G	
745	2233 G	+17:35133147 2524664654 G	V
745	2234 T	+17:35133148 2524664655 T	
745	2235 C	+17:35133149 2524664656 C	
746	2236 T	+17:35133150 2524664657 T	L
746	2237 T	+17:35133151 2524664658 T	
746	2238 G	+17:35133152 2524664659 G	
747	2239 G	+17:35133153 2524664660 G	G
747	2240 G	+17:35133154 2524664661 G	
747	2241 G	+17:35133155 2524664662 G	
748	2242 G	+17:35133156 2524664663 G	V
748	2243 T	+17:35133157 2524664664 T	
748	2244 G	+17:35133158 2524664665 G	
749	2245 G	+17:35133159 2524664666 G	V
749	2246 T	+17:35133160 2524664667 T	
749	2247 C	+17:35133161 2524664668 C	
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764	2290 T	+17:35133204 2524664711 T	Y
764	2291 A	+17:35133205 2524664712 A	
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766	2296 A	+17:35133210 2524664717 A	M
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784	2352 G	+17:35133346 2524664853 G	
785	2353 A	+17:35133347 2524664854 A	M
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787	2359 A	+17:35133353 2524664860 A	N
787	2360 A	+17:35133354 2524664861 A	
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788	2362 C	+17:35133356 2524664863 C	Q
788	2363 A	+17:35133357 2524664864 A	
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790	2368 C	+17:35133362 2524664869 C	Q
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795	2383 A	+17:35133377 2524664884 A	K
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810	2430 T	+17:35133424 2524664931 T	
811	2431 G	+17:35133425 2524664932 G	G
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811	2433 C	+17:35133427 2524664934 C	
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814	2440 T	+17:35133434 2524664941 T	Y
814	2441 A	+17:35133435 2524664942 A	
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815	2443 A	+17:35133437 2524664944 A	K
815	2444 A	+17:35133438 2524664945 A	
815	2445 G	+17:35133439 2524664946 G	
816	2446 G	+17:35133691 2524665198 G	G
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818	2452 T	+17:35133697 2524665204 T	W
818	2453 G	+17:35133698 2524665205 G	
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819	2456 T	+17:35133701 2524665208 T	
819	2457 C	+17:35133702 2524665209 C	
820	2458 C	+17:35133703 2524665210 C	P
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821	2461 G	+17:35133706 2524665213 G	D
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822	2464 G	+17:35133709 2524665216 G	G
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822	2466 G	+17:35133711 2524665218 G	
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823	2469 G	+17:35133714 2524665221 G	
824	2470 A	+17:35133715 2524665222 A	N
824	2471 A	+17:35133716 2524665223 A	
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825	2473 G	+17:35133718 2524665225 G	V
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827	2479 A	+17:35133724 2524665231 A	I
827	2480 T	+17:35133725 2524665232 T	
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828	2482 C	+17:35133727 2524665234 C	P
828	2483 C	+17:35133728 2524665235 C	
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829	2486 T	+17:35133731 2524665238 T	
829	2487 G	+17:35133732 2524665239 G	
830	2488 G	+17:35133733 2524665240 G	A
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831	2492 T	+17:35133737 2524665244 T	
831	2493 C	+17:35133738 2524665245 C	
832	2494 A	+17:35133739 2524665246 A	K
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835	2503 A	+17:35133748 2524665255 A	R
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836	2508 A	+17:35133753 2524665260 A	
837	2509 A	+17:35133754 2524665261 A	N
837	2510 A	+17:35133755 2524665262 A	
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838	2512 A	+17:35133757 2524665264 A	T
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839	2515 T	+17:35133760 2524665267 T	S
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843	2527 A	+17:35133772 2524665279 A	N
843	2528 A	+17:35133773 2524665280 A	
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844	2530 A	+17:35133775 2524665282 A	K
844	2531 A	+17:35133776 2524665283 A	
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847	2539 T	+17:35133784 2524665291 T	L
847	2540 T	+17:35133785 2524665292 T	
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848	2543 A	+17:35133788 2524665295 A	
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851	2552 A	+17:35134512 2524666019 A	
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864	2590 C	+17:35134550 2524666057 C	L
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866	2596 G	+17:35134556 2524666063 G	G
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872	2614 A	+17:35134574 2524666081 A	T
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876	2626 G	+17:35134586 2524666093 G	V
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877	2630 C	+17:35134590 2524666097 C	
877	2631 A	+17:35134591 2524666098 A	
878	2632 C	+17:35134592 2524666099 C	Q
878	2633 A	+17:35134593 2524666100 A	
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879	2636 T	+17:35134596 2524666103 T	
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880	2638 A	+17:35134598 2524666105 A	M
880	2639 T	+17:35134599 2524666106 T	
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881	2642 C	+17:35134602 2524666109 C	
881	2643 C	+17:35134603 2524666110 C	
882	2644 T	+17:35134604 2524666111 T	Y
882	2645 A	+17:35134605 2524666112 A	
882	2646 T	+17:35134606 2524666113 T	
883	2647 G	+17:35134607 2524666114 G	G
883	2648 G	+17:35134608 2524666115 G	
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884	2650 T	+17:35134610 2524666117 T	C
884	2651 G	+17:35134611 2524666118 G	
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885	2653 C	+17:35134613 2524666120 C	L
885	2654 T	+17:35134614 2524666121 T	
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886	2656 T	+17:35134616 2524666123 T	L
886	2657 T	+17:35134617 2524666124 T	
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887	2660 A	+17:35134620 2524666127 A	
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888	2663 A	+17:35134623 2524666130 A	
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889	2666 T	+17:35134626 2524666133 T	
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890	2668 C	+17:35134628 2524666135 C	R
890	2669 G	+17:35134629 2524666136 G	
890	2670 G	+17:35134630 2524666137 G	
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891	2672 A	+17:35134632 2524666139 A	
891	2673 A	+17:35134633 2524666140 A	
892	2674 A	+17:35134634 2524666141 A	N
892	2675 A	+17:35134635 2524666142 A	
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893	2678 G	+17:35134638 2524666145 G	
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895	2684 G	+17:35134644 2524666151 G	
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898	2693 C	+17:35134653 2524666160 C	
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899	2695 C	+17:35134655 2524666162 C	Q
899	2696 A	+17:35134656 2524666163 A	
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900	2699 A	+17:35134659 2524666166 A	
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901	2702 T	+17:35134662 2524666169 T	
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902	2705 T	+17:35134665 2524666172 T	
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903	2707 A	+17:35134667 2524666174 A	N
903	2708 A	+17:35134668 2524666175 A	
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904	2710 T	+17:35134670 2524666177 T	W
904	2711 G	+17:35134671 2524666178 G	
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905	2714 G	+17:35134674 2524666181 G	
905	2715 T	+17:35134675 2524666182 T	
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908	2723 T	+17:35134683 2524666190 T	
908	2724 T	+17:35134684 2524666191 T	
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910	2728 A	+17:35134688 2524666195 A	K
910	2729 A	+17:35134689 2524666196 A	
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913	2737 A	+17:35134834 2524666341 A	S
913	2738 G	+17:35134835 2524666342 G	
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914	2741 A	+17:35134838 2524666345 A	
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915	2743 C	+17:35134840 2524666347 C	L
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916	2746 G	+17:35134843 2524666350 G	E
916	2747 A	+17:35134844 2524666351 A	
916	2748 G	+17:35134845 2524666352 G	
917	2749 G	+17:35134846 2524666353 G	D
917	2750 A	+17:35134847 2524666354 A	
917	2751 T	+17:35134848 2524666355 T	
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918	2753 T	+17:35134850 2524666357 T	
918	2754 G	+17:35134851 2524666358 G	
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919	2757 G	+17:35134854 2524666361 G	
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921	2762 T	+17:35134859 2524666366 T	
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922	2764 C	+17:35134861 2524666368 C	H
922	2765 A	+17:35134862 2524666369 A	
922	2766 C	+17:35134863 2524666370 C	
923	2767 A	+17:35134864 2524666371 A	R
923	2768 G	+17:35134865 2524666372 G	
923	2769 G	+17:35134866 2524666373 G	
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926	2776 G	+17:35134873 2524666380 G	A
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926	2778 C	+17:35134875 2524666382 C	
927	2779 G	+17:35134876 2524666383 G	A
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928	2783 G	+17:35134880 2524666387 G	
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929	2786 A	+17:35134883 2524666390 A	
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930	2788 G	+17:35134885 2524666392 G	V
930	2789 T	+17:35134886 2524666393 T	
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931	2792 T	+17:35134889 2524666396 T	
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932	2795 T	+17:35134892 2524666399 T	
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933	2797 A	+17:35134894 2524666401 A	K
933	2798 A	+17:35134895 2524666402 A	
933	2799 G	+17:35134896 2524666403 G	
934	2800 A	+17:35134897 2524666404 A	S
934	2801 G	+17:35134898 2524666405 G	
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935	2803 C	+17:35134900 2524666407 C	P
935	2804 C	+17:35134901 2524666408 C	
935	2805 C	+17:35134902 2524666409 C	
936	2806 A	+17:35134903 2524666410 A	N
936	2807 A	+17:35134904 2524666411 A	
936	2808 C	+17:35134905 2524666412 C	
937	2809 C	+17:35134906 2524666413 C	H
937	2810 A	+17:35134907 2524666414 A	
937	2811 T	+17:35134908 2524666415 T	
938	2812 G	+17:35134909 2524666416 G	V
938	2813 T	+17:35134910 2524666417 T	
938	2814 C	+17:35134911 2524666418 C	
939	2815 A	+17:35134912 2524666419 A	K
939	2816 A	+17:35134913 2524666420 A	
939	2817 A	+17:35134914 2524666421 A	
940	2818 A	+17:35134915 2524666422 A	I
940	2819 T	+17:35134916 2524666423 T	
940	2820 T	+17:35134917 2524666424 T	
941	2821 A	+17:35134918 2524666425 A	T
941	2822 C	+17:35134919 2524666426 C	
941	2823 A	+17:35134920 2524666427 A	
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942	2825 A	+17:35134922 2524666429 A	
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943	2827 T	+17:35134924 2524666431 T	F
943	2828 T	+17:35134925 2524666432 T	
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944	2831 G	+17:35134928 2524666435 G	
944	2832 G	+17:35134929 2524666436 G	
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947	2839 C	+17:35134936 2524666443 C	R
947	2840 G	+17:35134937 2524666444 G	
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949	2846 T	+17:35134943 2524666450 T	
949	2847 G	+17:35134944 2524666451 G	
950	2848 G	+17:35134945 2524666452 G	D
950	2849 A	+17:35134946 2524666453 A	
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951	2851 A	+17:35134948 2524666455 A	I
951	2852 T	+17:35134949 2524666456 T	
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955	2864 A	+17:35134961 2524666468 A	
955	2865 G	+17:35134962 2524666469 G	
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957	2869 C	+17:35134966 2524666473 C	H
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962	2885 A	+17:35134982 2524666489 A	
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978	2932 T	+17:35135151 2524666658 T	F
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979	2935 A	+17:35135154 2524666661 A	T
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979	2937 C	+17:35135156 2524666663 C	
980	2938 C	+17:35135157 2524666664 C	H
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981	2941 C	+17:35135160 2524666667 C	Q
981	2942 A	+17:35135161 2524666668 A	
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984	2951 T	+17:35135170 2524666677 T	
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985	2953 T	+17:35135172 2524666679 T	W
985	2954 G	+17:35135173 2524666680 G	
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987	2959 T	+17:35135178 2524666685 T	Y
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998	2994 G	+17:35135517 2524667024 G	
999	2995 G	+17:35135518 2524667025 G	A
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999	2997 C	+17:35135520 2524667027 C	
1000	2998 A	+17:35135521 2524667028 A	K
1000	2999 A	+17:35135522 2524667029 A	
1000	3000 A	+17:35135523 2524667030 A	
1001	3001 C	+17:35135524 2524667031 C	P
1001	3002 C	+17:35135525 2524667032 C	
1001	3003 T	+17:35135526 2524667033 T	
1002	3004 T	+17:35135527 2524667034 T	Y
1002	3005 A	+17:35135528 2524667035 A	
1002	3006 C	+17:35135529 2524667036 C	
1003	3007 G	+17:35135530 2524667037 G	D
1003	3008 A	+17:35135531 2524667038 A	
1003	3009 T	+17:35135532 2524667039 T	
1004	3010 G	+17:35135533 2524667040 G	G
1004	3011 G	+17:35135534 2524667041 G	
1004	3012 G	+17:35135535 2524667042 G	
1005	3013 A	+17:35135536 2524667043 A	I
1005	3014 T	+17:35135537 2524667044 T	
1005	3015 C	+17:35135538 2524667045 C	
1006	3016 C	+17:35135539 2524667046 C	P
1006	3017 C	+17:35135540 2524667047 C	
1006	3018 A	+17:35135541 2524667048 A	
1007	3019 G	+17:35135542 2524667049 G	A
1007	3020 C	+17:35135543 2524667050 C	
1007	3021 C	+17:35135544 2524667051 C	
1008	3022 C	+17:35135545 2524667052 C	R
1008	3023 G	+17:35135546 2524667053 G	
1008	3024 G	+17:35135547 2524667054 G	
1009	3025 G	+17:35135548 2524667055 G	E
1009	3026 A	+17:35135549 2524667056 A	
1009	3027 G	+17:35135550 2524667057 G	
1010	3028 A	+17:35135551 2524667058 A	I
1010	3029 T	+17:35135552 2524667059 T	
1010	3030 C	+17:35135553 2524667060 C	
1011	3031 C	+17:35135554 2524667061 C	P
1011	3032 C	+17:35135555 2524667062 C	
1011	3033 T	+17:35135556 2524667063 T	
1012	3034 G	+17:35135557 2524667064 G	D
1012	3035 A	+17:35135558 2524667065 A	
1012	3036 C	+17:35135559 2524667066 C	
1013	3037 C	+17:35135560 2524667067 C	L
1013	3038 T	+17:35135561 2524667068 T	
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1014	3041 T	+17:35135564 2524667071 T	
1014	3042 G	+17:35135565 2524667072 G	
1015	3043 G	+17:35135566 2524667073 G	E
1015	3044 A	+17:35135567 2524667074 A	
1015	3045 A	+17:35135568 2524667075 A	
1016	3046 A	+17:35135569 2524667076 A	K
1016	3047 A	+17:35135570 2524667077 A	
1016	3048 G	+17:35135571 2524667078 G	
1017	3049 G	+17:35135572 2524667079 G	G
1017	3050 G	+17:35135573 2524667080 G	
1017	3051 G	+17:35135574 2524667081 G	
1018	3052 G	+17:35135575 2524667082 G	E
1018	3053 A	+17:35135576 2524667083 A	
1018	3054 G	+17:35135577 2524667084 G	
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1019	3056 G	+17:35135579 2524667086 G	
1019	3057 G	+17:35135580 2524667087 G	
1020	3058 C	+17:35135581 2524667088 C	L
1020	3059 T	+17:35135582 2524667089 T	
1020	3060 G	+17:35135583 2524667090 G	
1021	3061 C	+17:35135584 2524667091 C	P
1021	3062 C	+17:35135585 2524667092 C	
1021	3063 C	+17:35135586 2524667093 C	
1022	3064 C	+17:35135587 2524667094 C	Q
1022	3065 A	+17:35135588 2524667095 A	
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1023	3068 C	+17:35135591 2524667098 C	
1023	3069 C	+17:35135592 2524667099 C	
1024	3070 C	+17:35135593 2524667100 C	P
1024	3071 C	+17:35135594 2524667101 C	
1024	3072 C	+17:35135595 2524667102 C	
1025	3073 A	+17:35135596 2524667103 A	I
1025	3074 T	+17:35135597 2524667104 T	
1025	3075 C	+17:35135598 2524667105 C	
1026	3076 T	+17:35135599 2524667106 T	C
1026	3077 G	+17:35135600 2524667107 G	
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1027	3079 A	+17:35135602 2524667109 A	T
1027	3080 C	+17:35135603 2524667110 C	
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1028	3082 A	+17:35135605 2524667112 A	I
1028	3083 T	+17:35135606 2524667113 T	
1028	3084 T	+17:35135607 2524667114 T	
1029	3085 G	+17:35135608 2524667115 G	D
1029	3086 A	+17:35135609 2524667116 A	
1029	3087 T	+17:35135610 2524667117 T	
1030	3088 G	+17:35135611 2524667118 G	V
1030	3089 T	+17:35135612 2524667119 T	
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1031	3091 T	+17:35135614 2524667121 T	Y
1031	3092 A	+17:35135615 2524667122 A	
1031	3093 C	+17:35135616 2524667123 C	
1032	3094 A	+17:35135617 2524667124 A	M
1032	3095 T	+17:35135618 2524667125 T	
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1033	3097 A	+17:35135620 2524667127 A	I
1033	3098 T	+17:35135621 2524667128 T	
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1034	3100 A	+17:35135623 2524667130 A	M
1034	3101 T	+17:35135624 2524667131 T	
1034	3102 G	+17:35135625 2524667132 G	
1035	3103 G	+17:35135626 2524667133 G	V
1035	3104 T	+17:35135627 2524667134 T	
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1036	3106 A	+17:35135629 2524667136 A	K
1036	3107 A	+17:35135630 2524667137 A	
1036	3108 A	+17:35135631 2524667138 A	
1037	3109 T	+17:35135632 2524667139 T	C
1037	3110 G	+17:35136341 2524667848 G	
1037	3111 T	+17:35136342 2524667849 T	
1038	3112 T	+17:35136343 2524667850 T	W
1038	3113 G	+17:35136344 2524667851 G	
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1039	3115 A	+17:35136346 2524667853 A	M
1039	3116 T	+17:35136347 2524667854 T	
1039	3117 G	+17:35136348 2524667855 G	
1040	3118 A	+17:35136349 2524667856 A	I
1040	3119 T	+17:35136350 2524667857 T	
1040	3120 T	+17:35136351 2524667858 T	
1041	3121 G	+17:35136352 2524667859 G	D
1041	3122 A	+17:35136353 2524667860 A	
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1042	3124 T	+17:35136355 2524667862 T	S
1042	3125 C	+17:35136356 2524667863 C	
1042	3126 T	+17:35136357 2524667864 T	
1043	3127 G	+17:35136358 2524667865 G	E
1043	3128 A	+17:35136359 2524667866 A	
1043	3129 A	+17:35136360 2524667867 A	
1044	3130 T	+17:35136361 2524667868 T	C
1044	3131 G	+17:35136362 2524667869 G	
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1048	3142 T	+17:35136373 2524667880 T	F
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1049	3146 G	+17:35136377 2524667884 G	
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1051	3151 T	+17:35136382 2524667889 T	L
1051	3152 T	+17:35136383 2524667890 T	
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1052	3154 G	+17:35136385 2524667892 G	V
1052	3155 T	+17:35136386 2524667893 T	
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1054	3160 G	+17:35136391 2524667898 G	E
1054	3161 A	+17:35136392 2524667899 A	
1054	3162 A	+17:35136393 2524667900 A	
1055	3163 T	+17:35136394 2524667901 T	F
1055	3164 T	+17:35136395 2524667902 T	
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1056	3166 T	+17:35136397 2524667904 T	S
1056	3167 C	+17:35136398 2524667905 C	
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1057	3169 C	+17:35136400 2524667907 C	R
1057	3170 G	+17:35136401 2524667908 G	
1057	3171 C	+17:35136402 2524667909 C	
1058	3172 A	+17:35136403 2524667910 A	M
1058	3173 T	+17:35136404 2524667911 T	
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1060	3178 A	+17:35136409 2524667916 A	R
1060	3179 G	+17:35136410 2524667917 G	
1060	3180 G	+17:35136411 2524667918 G	
1061	3181 G	+17:35136412 2524667919 G	D
1061	3182 A	+17:35136413 2524667920 A	
1061	3183 C	+17:35136414 2524667921 C	
1062	3184 C	+17:35136415 2524667922 C	P
1062	3185 C	+17:35136416 2524667923 C	
1062	3186 C	+17:35136417 2524667924 C	
1063	3187 C	+17:35136418 2524667925 C	Q
1063	3188 A	+17:35136419 2524667926 A	
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1064	3191 G	+17:35136422 2524667929 G	
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1065	3193 T	+17:35136424 2524667931 T	F
1065	3194 T	+17:35136425 2524667932 T	
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1066	3196 G	+17:35136427 2524667934 G	V
1066	3197 T	+17:35136428 2524667935 T	
1066	3198 G	+17:35136429 2524667936 G	
1067	3199 G	+17:35136430 2524667937 G	V
1067	3200 T	+17:35136431 2524667938 T	
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1068	3202 A	+17:35136433 2524667940 A	I
1068	3203 T	+17:35136434 2524667941 T	
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1069	3205 C	+17:35136436 2524667943 C	Q
1069	3206 A	+17:35136437 2524667944 A	
1069	3207 G	+17:35136438 2524667945 G	
1070	3208 A	+17:35136594 2524668101 A	N
1070	3209 A	+17:35136595 2524668102 A	
1070	3210 T	+17:35136596 2524668103 T	
1071	3211 G	+17:35136597 2524668104 G	E
1071	3212 A	+17:35136598 2524668105 A	
1071	3213 G	+17:35136599 2524668106 G	
1072	3214 G	+17:35136600 2524668107 G	D
1072	3215 A	+17:35136601 2524668108 A	
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1073	3217 T	+17:35136603 2524668110 T	L
1073	3218 T	+17:35136604 2524668111 T	
1073	3219 G	+17:35136605 2524668112 G	
1074	3220 G	+17:35136606 2524668113 G	G
1074	3221 G	+17:35136607 2524668114 G	
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1075	3223 C	+17:35136609 2524668116 C	P
1075	3224 C	+17:35136610 2524668117 C	
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1076	3226 G	+17:35136612 2524668119 G	A
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1076	3228 C	+17:35136614 2524668121 C	
1077	3229 A	+17:35136615 2524668122 A	S
1077	3230 G	+17:35136616 2524668123 G	
1077	3231 T	+17:35136617 2524668124 T	
1078	3232 C	+17:35136618 2524668125 C	P
1078	3233 C	+17:35136619 2524668126 C	
1078	3234 C	+17:35136620 2524668127 C	
1079	3235 T	+17:35136621 2524668128 T	L
1079	3236 T	+17:35136622 2524668129 T	
1079	3237 G	+17:35136623 2524668130 G	
1080	3238 G	+17:35136624 2524668131 G	D
1080	3239 A	+17:35136625 2524668132 A	
1080	3240 C	+17:35136626 2524668133 C	
1081	3241 A	+17:35136627 2524668134 A	S
1081	3242 G	+17:35136628 2524668135 G	
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1082	3244 A	+17:35136630 2524668137 A	T
1082	3245 C	+17:35136631 2524668138 C	
1082	3246 C	+17:35136632 2524668139 C	
1083	3247 T	+17:35136633 2524668140 T	F
1083	3248 T	+17:35136634 2524668141 T	
1083	3249 C	+17:35136635 2524668142 C	
1084	3250 T	+17:35136636 2524668143 T	Y
1084	3251 A	+17:35136637 2524668144 A	
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1085	3253 C	+17:35136639 2524668146 C	R
1085	3254 G	+17:35136640 2524668147 G	
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1086	3256 T	+17:35136642 2524668149 T	S
1086	3257 C	+17:35136643 2524668150 C	
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1087	3259 C	+17:35136645 2524668152 C	L
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1088	3263 T	+17:35136649 2524668156 T	
1088	3264 G	+17:35136650 2524668157 G	
1089	3265 G	+17:35136651 2524668158 G	E
1089	3266 A	+17:35136652 2524668159 A	
1089	3267 G	+17:35136653 2524668160 G	
1090	3268 G	+17:35136654 2524668161 G	D
1090	3269 A	+17:35136655 2524668162 A	
1090	3270 C	+17:35136656 2524668163 C	
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1091	3272 A	+17:35136658 2524668165 A	
1091	3273 T	+17:35136659 2524668166 T	
1092	3274 G	+17:35136660 2524668167 G	D
1092	3275 A	+17:35136661 2524668168 A	
1092	3276 C	+17:35136662 2524668169 C	
1093	3277 A	+17:35136663 2524668170 A	M
1093	3278 T	+17:35136664 2524668171 T	
1093	3279 G	+17:35136665 2524668172 G	
1094	3280 G	+17:35136666 2524668173 G	G
1094	3281 G	+17:35136667 2524668174 G	
1094	3282 G	+17:35136668 2524668175 G	
1095	3283 G	+17:35136669 2524668176 G	D
1095	3284 A	+17:35136670 2524668177 A	
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1096	3286 C	+17:35136672 2524668179 C	L
1096	3287 T	+17:35136673 2524668180 T	
1096	3288 G	+17:35136674 2524668181 G	
1097	3289 G	+17:35136675 2524668182 G	V
1097	3290 T	+17:35136676 2524668183 T	
1097	3291 G	+17:35136677 2524668184 G	
1098	3292 G	+17:35136678 2524668185 G	D
1098	3293 A	+17:35136679 2524668186 A	
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1099	3295 G	+17:35136681 2524668188 G	A
1099	3296 C	+17:35136682 2524668189 C	
1099	3297 T	+17:35136683 2524668190 T	
1100	3298 G	+17:35136684 2524668191 G	E
1100	3299 A	+17:35136685 2524668192 A	
1100	3300 G	+17:35136686 2524668193 G	
1101	3301 G	+17:35136687 2524668194 G	E
1101	3302 A	+17:35136688 2524668195 A	
1101	3303 G	+17:35136689 2524668196 G	
1102	3304 T	+17:35136690 2524668197 T	Y
1102	3305 A	+17:35136691 2524668198 A	
1102	3306 T	+17:35136692 2524668199 T	
1103	3307 C	+17:35136693 2524668200 C	L
1103	3308 T	+17:35136694 2524668201 T	
1103	3309 G	+17:35136695 2524668202 G	
1104	3310 G	+17:35136696 2524668203 G	V
1104	3311 T	+17:35136697 2524668204 T	
1104	3312 A	+17:35136698 2524668205 A	
1105	3313 C	+17:35136699 2524668206 C	P
1105	3314 C	+17:35136700 2524668207 C	
1105	3315 C	+17:35136701 2524668208 C	
1106	3316 C	+17:35136702 2524668209 C	Q
1106	3317 A	+17:35136703 2524668210 A	
1106	3318 G	+17:35136704 2524668211 G	
1107	3319 C	+17:35136705 2524668212 C	Q
1107	3320 A	+17:35136706 2524668213 A	
1107	3321 G	+17:35136707 2524668214 G	
1108	3322 G	+17:35136708 2524668215 G	G
1108	3323 G	+17:35136709 2524668216 G	
1108	3324 C	+17:35136710 2524668217 C	
1109	3325 T	+17:35136711 2524668218 T	F
1109	3326 T	+17:35136712 2524668219 T	
1109	3327 C	+17:35136713 2524668220 C	
1110	3328 T	+17:35136714 2524668221 T	F
1110	3329 T	+17:35136715 2524668222 T	
1110	3330 C	+17:35136716 2524668223 C	
1111	3331 T	+17:35136717 2524668224 T	C
1111	3332 G	+17:35136718 2524668225 G	
1111	3333 T	+17:35136719 2524668226 T	
1112	3334 C	+17:35136720 2524668227 C	P
1112	3335 C	+17:35136721 2524668228 C	
1112	3336 A	+17:35136722 2524668229 A	
1113	3337 G	+17:35136723 2524668230 G	D
1113	3338 A	+17:35136724 2524668231 A	
1113	3339 C	+17:35136725 2524668232 C	
1114	3340 C	+17:35136726 2524668233 C	P
1114	3341 C	+17:35136727 2524668234 C	
1114	3342 T	+17:35136728 2524668235 T	
1115	3343 G	+17:35136729 2524668236 G	A
1115	3344 C	+17:35136730 2524668237 C	
1115	3345 C	+17:35136731 2524668238 C	
1116	3346 C	+17:35136732 2524668239 C	P
1116	3347 C	+17:35136733 2524668240 C	
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1117	3349 G	+17:35136735 2524668242 G	G
1117	3350 G	+17:35136736 2524668243 G	
1117	3351 C	+17:35136737 2524668244 C	
1118	3352 G	+17:35136738 2524668245 G	A
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1119	3355 G	+17:35136741 2524668248 G	G
1119	3356 G	+17:35136742 2524668249 G	
1119	3357 G	+17:35136743 2524668250 G	
1120	3358 G	+17:35136744 2524668251 G	G
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1120	3360 C	+17:35136746 2524668253 C	
1121	3361 A	+17:35136747 2524668254 A	M
1121	3362 T	+17:35136748 2524668255 T	
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1122	3364 G	+17:35136750 2524668257 G	V
1122	3365 T	+17:35136751 2524668258 T	
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1123	3367 C	+17:35136753 2524668260 C	H
1123	3368 A	+17:35136754 2524668261 A	
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1126	3376 C	+17:35136762 2524668269 C	H
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1127	3380 G	+17:35136766 2524668273 G	
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1128	3382 A	+17:35136768 2524668275 A	S
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1130	3388 T	+17:35136774 2524668281 T	S
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1131	3392 C	+17:35136778 2524668285 C	
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1134	3400 G	+17:35137077 2524668584 G	G
1134	3401 G	+17:35137078 2524668585 G	
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1136	3407 G	+17:35137084 2524668591 G	
1136	3408 G	+17:35137085 2524668592 G	
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1138	3413 T	+17:35137090 2524668597 T	
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1139	3416 C	+17:35137093 2524668600 C	
1139	3417 A	+17:35137094 2524668601 A	
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1145	3435 T	+17:35137112 2524668619 T	
1146	3436 G	+17:35137113 2524668620 G	E
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1147	3439 G	+17:35137116 2524668623 G	E
1147	3440 A	+17:35137117 2524668624 A	
1147	3441 G	+17:35137118 2524668625 G	
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1148	3443 A	+17:35137120 2524668627 A	
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1149	3447 C	+17:35137124 2524668631 C	
1150	3448 C	+17:35137125 2524668632 C	P
1150	3449 C	+17:35137126 2524668633 C	
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1153	3458 C	+17:35137135 2524668642 C	
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1154	3460 C	+17:35137137 2524668644 C	L
1154	3461 T	+17:35137138 2524668645 T	
1154	3462 G	+17:35137139 2524668646 G	
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1156	3466 C	+17:35137143 2524668650 C	P
1156	3467 C	+17:35137144 2524668651 C	
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1157	3470 C	+17:35137147 2524668654 C	
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1158	3473 A	+17:35137150 2524668657 A	
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1159	3476 G	+17:35137153 2524668660 G	
1159	3477 G	+17:35137154 2524668661 G	
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1161	3482 G	+17:35137159 2524668666 G	
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1162	3485 C	+17:35137162 2524668669 C	
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1163	3488 A	+17:35137165 2524668672 A	
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1164	3490 G	+17:35137167 2524668674 G	V
1164	3491 T	+17:35137168 2524668675 T	
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1165	3493 T	+17:35137170 2524668677 T	F
1165	3494 T	+17:35137171 2524668678 T	
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1171	3512 T	+17:35137189 2524668696 T	
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1178	3532 C	+17:35137209 2524668716 C	Q
1178	3533 A	+17:35137210 2524668717 A	
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1181	3541 C	+17:35137218 2524668725 C	P
1181	3542 C	+17:35137219 2524668726 C	
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1182	3545 C	+17:35137222 2524668729 C	
1182	3546 A	+17:35137223 2524668730 A	
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1183	3548 A	+17:35137225 2524668732 A	
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1184	3551 A	+17:35137228 2524668735 A	
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1185	3553 C	+17:35137230 2524668737 C	P
1185	3554 C	+17:35137231 2524668738 C	
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1186	3556 A	+17:35137233 2524668740 A	S
1186	3557 G	+17:35137234 2524668741 G	
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1187	3559 C	+17:35137236 2524668743 C	P
1187	3560 C	+17:35137237 2524668744 C	
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1188	3562 C	+17:35137239 2524668746 C	L
1188	3563 T	+17:35137240 2524668747 T	
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1189	3565 C	+17:35137242 2524668749 C	Q
1189	3566 A	+17:35137243 2524668750 A	
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1190	3568 C	+17:35137245 2524668752 C	R
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1190	3570 G	+17:35137247 2524668754 G	
1191	3571 T	+17:35137248 2524668755 T	Y
1191	3572 A	+17:35137249 2524668756 A	
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1192	3575 G	+17:35137252 2524668759 G	
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1193	3577 G	+17:35137254 2524668761 G	E
1193	3578 A	+17:35137255 2524668762 A	
1193	3579 G	+17:35137256 2524668763 G	
1194	3580 G	+17:35137257 2524668764 G	D
1194	3581 A	+17:35137258 2524668765 A	
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1195	3583 C	+17:35137260 2524668767 C	P
1195	3584 C	+17:35137261 2524668768 C	
1195	3585 C	+17:35137262 2524668769 C	
1196	3586 A	+17:35137263 2524668770 A	T
1196	3587 C	+17:35137264 2524668771 C	
1196	3588 A	+17:35137265 2524668772 A	
1197	3589 G	+17:35137266 2524668773 G	V
1197	3590 T	+17:35137267 2524668774 T	
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1198	3593 C	+17:35137270 2524668777 C	
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1199	3595 C	+17:35137272 2524668779 C	L
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1202	3606 G	+17:35137283 2524668790 G	
1203	3607 A	+17:35137284 2524668791 A	T
1203	3608 C	+17:35137285 2524668792 C	
1203	3609 T	+17:35137286 2524668793 T	
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1204	3611 A	+17:35137288 2524668795 A	
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1206	3616 T	+17:35137293 2524668800 T	Y
1206	3617 A	+17:35137294 2524668801 A	
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1207	3619 G	+17:35137296 2524668803 G	V
1207	3620 T	+17:35137297 2524668804 T	
1207	3621 T	+17:35137298 2524668805 T	
1208	3622 G	+17:35137299 2524668806 G	A
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1209	3625 C	+17:35137302 2524668809 C	P
1209	3626 C	+17:35137303 2524668810 C	
1209	3627 C	+17:35137304 2524668811 C	
1210	3628 C	+17:35137305 2524668812 C	L
1210	3629 T	+17:35137306 2524668813 T	
1210	3630 G	+17:35137307 2524668814 G	
1211	3631 A	+17:35137308 2524668815 A	T
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1212	3635 G	+17:35137312 2524668819 G	
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1213	3638 G	+17:35137315 2524668822 G	
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1214	3640 C	+17:35137317 2524668824 C	P
1214	3641 C	+17:35137318 2524668825 C	
1214	3642 C	+17:35137319 2524668826 C	
1215	3643 C	+17:35137320 2524668827 C	Q
1215	3644 A	+17:35137321 2524668828 A	
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1217	3649 G	+17:35137326 2524668833 G	E
1217	3650 A	+17:35137468 2524668975 A	
1217	3651 A	+17:35137469 2524668976 A	
1218	3652 T	+17:35137470 2524668977 T	Y
1218	3653 A	+17:35137471 2524668978 A	
1218	3654 T	+17:35137472 2524668979 T	
1219	3655 G	+17:35137473 2524668980 G	V
1219	3656 T	+17:35137474 2524668981 T	
1219	3657 G	+17:35137475 2524668982 G	
1220	3658 A	+17:35137476 2524668983 A	N
1220	3659 A	+17:35137477 2524668984 A	
1220	3660 C	+17:35137478 2524668985 C	
1221	3661 C	+17:35137479 2524668986 C	Q
1221	3662 A	+17:35137480 2524668987 A	
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1222	3664 C	+17:35137482 2524668989 C	P
1222	3665 C	+17:35137483 2524668990 C	
1222	3666 A	+17:35137484 2524668991 A	
1223	3667 G	+17:35137485 2524668992 G	D
1223	3668 A	+17:35137486 2524668993 A	
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1224	3670 G	+17:35137488 2524668995 G	V
1224	3671 T	+17:35137489 2524668996 T	
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1225	3674 G	+17:35137492 2524668999 G	
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1226	3678 C	+17:35137496 2524669003 C	
1227	3679 C	+17:35137497 2524669004 C	Q
1227	3680 A	+17:35137498 2524669005 A	
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1228	3682 C	+17:35137500 2524669007 C	P
1228	3683 C	+17:35137501 2524669008 C	
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1229	3685 C	+17:35137503 2524669010 C	P
1229	3686 C	+17:35137504 2524669011 C	
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1230	3688 T	+17:35137506 2524669013 T	S
1230	3689 C	+17:35137507 2524669014 C	
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1231	3691 C	+17:35137509 2524669016 C	P
1231	3692 C	+17:35137510 2524669017 C	
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1232	3694 C	+17:35137512 2524669019 C	R
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1233	3697 G	+17:35137515 2524669022 G	E
1233	3698 A	+17:35137516 2524669023 A	
1233	3699 G	+17:35137517 2524669024 G	
1234	3700 G	+17:35137518 2524669025 G	G
1234	3701 G	+17:35137519 2524669026 G	
1234	3702 C	+17:35137520 2524669027 C	
1235	3703 C	+17:35137521 2524669028 C	P
1235	3704 C	+17:35137522 2524669029 C	
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1236	3706 C	+17:35137524 2524669031 C	L
1236	3707 T	+17:35137525 2524669032 T	
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1237	3710 C	+17:35137528 2524669035 C	
1237	3711 T	+17:35137529 2524669036 T	
1238	3712 G	+17:35137530 2524669037 G	A
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1238	3714 T	+17:35137532 2524669039 T	
1239	3715 G	+17:35137533 2524669040 G	A
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1239	3717 C	+17:35137535 2524669042 C	
1240	3718 C	+17:35137536 2524669043 C	R
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1241	3723 T	+17:35137541 2524669048 T	
1242	3724 G	+17:35137542 2524669049 G	A
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1242	3726 T	+17:35137544 2524669051 T	
1243	3727 G	+17:35137545 2524669052 G	G
1243	3728 G	+17:35137546 2524669053 G	
1243	3729 T	+17:35137547 2524669054 T	
1244	3730 G	+17:35137548 2524669055 G	A
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1245	3733 A	+17:35137551 2524669058 A	T
1245	3734 C	+17:35137552 2524669059 C	
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1246	3736 C	+17:35137554 2524669061 C	L
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1247	3739 G	+17:35137557 2524669064 G	E
1247	3740 A	+17:35137558 2524669065 A	
1247	3741 A	+17:35137559 2524669066 A	
1248	3742 A	+17:35137560 2524669067 A	R
1248	3743 G	+17:35137561 2524669068 G	
1248	3744 G	+17:35137562 2524669069 G	
1249	3745 C	+17:35137563 2524669070 C	P
1249	3746 C	+17:35137564 2524669071 C	
1249	3747 C	+17:35137565 2524669072 C	
1250	3748 A	+17:35137566 2524669073 A	K
1250	3749 A	+17:35137567 2524669074 A	
1250	3750 G	+17:35137568 2524669075 G	
1251	3751 A	+17:35137569 2524669076 A	T
1251	3752 C	+17:35137570 2524669077 C	
1251	3753 T	+17:35137571 2524669078 T	
1252	3754 C	+17:35137572 2524669079 C	L
1252	3755 T	+17:35137573 2524669080 T	
1252	3756 C	+17:35137574 2524669081 C	
1253	3757 T	+17:35137575 2524669082 T	S
1253	3758 C	+17:35137576 2524669083 C	
1253	3759 C	+17:35137577 2524669084 C	
1254	3760 C	+17:35137578 2524669085 C	P
1254	3761 C	+17:35137579 2524669086 C	
1254	3762 A	+17:35137580 2524669087 A	
1255	3763 G	+17:35137581 2524669088 G	G
1255	3764 G	+17:35137582 2524669089 G	
1255	3765 G	+17:35137583 2524669090 G	
1256	3766 A	+17:35137584 2524669091 A	K
1256	3767 A	+17:35137585 2524669092 A	
1256	3768 G	+17:35137586 2524669093 G	
1257	3769 A	+17:35137587 2524669094 A	N
1257	3770 A	+17:35137588 2524669095 A	
1257	3771 T	+17:35137589 2524669096 T	
1258	3772 G	+17:35137590 2524669097 G	G
1258	3773 G	+17:35137591 2524669098 G	
1258	3774 G	+17:35137592 2524669099 G	
1259	3775 G	+17:35137593 2524669100 G	V
1259	3776 T	+17:35137594 2524669101 T	
1259	3777 C	+17:35137595 2524669102 C	
1260	3778 G	+17:35137596 2524669103 G	V
1260	3779 T	+17:35137597 2524669104 T	
1260	3780 C	+17:35137598 2524669105 C	
1261	3781 A	+17:35137599 2524669106 A	K
1261	3782 A	+17:35137600 2524669107 A	
1261	3783 A	+17:35137601 2524669108 A	
1262	3784 G	+17:35137602 2524669109 G	D
1262	3785 A	+17:35137603 2524669110 A	
1262	3786 C	+17:35137604 2524669111 C	
1263	3787 G	+17:35137605 2524669112 G	V
1263	3788 T	+17:35137606 2524669113 T	
1263	3789 T	+17:35137607 2524669114 T	
1264	3790 T	+17:35137608 2524669115 T	F
1264	3791 T	+17:35137609 2524669116 T	
1264	3792 T	+17:35137610 2524669117 T	
1265	3793 G	+17:35137611 2524669118 G	A
1265	3794 C	+17:35137612 2524669119 C	
1265	3795 C	+17:35137613 2524669120 C	
1266	3796 T	+17:35137614 2524669121 T	F
1266	3797 T	+17:35137615 2524669122 T	
1266	3798 T	+17:35137616 2524669123 T	
1267	3799 G	+17:35137617 2524669124 G	G
1267	3800 G	+17:35137618 2524669125 G	
1267	3801 G	+17:35137619 2524669126 G	
1268	3802 G	+17:35137620 2524669127 G	G
1268	3803 G	+17:35137621 2524669128 G	
1268	3804 T	+17:35137622 2524669129 T	
1269	3805 G	+17:35137623 2524669130 G	A
1269	3806 C	+17:35137624 2524669131 C	
1269	3807 C	+17:35137625 2524669132 C	
1270	3808 G	+17:35137626 2524669133 G	V
1270	3809 T	+17:35137627 2524669134 T	
1270	3810 G	+17:35137628 2524669135 G	
1271	3811 G	+17:35137629 2524669136 G	E
1271	3812 A	+17:35137630 2524669137 A	
1271	3813 G	+17:35137631 2524669138 G	
1272	3814 A	+17:35137632 2524669139 A	N
1272	3815 A	+17:35137633 2524669140 A	
1272	3816 C	+17:35137634 2524669141 C	
1273	3817 C	+17:35137635 2524669142 C	P
1273	3818 C	+17:35137636 2524669143 C	
1273	3819 C	+17:35137637 2524669144 C	
1274	3820 G	+17:35137638 2524669145 G	E
1274	3821 A	+17:35137639 2524669146 A	
1274	3822 G	+17:35137640 2524669147 G	
1275	3823 T	+17:35137641 2524669148 T	Y
1275	3824 A	+17:35137642 2524669149 A	
1275	3825 C	+17:35137643 2524669150 C	
1276	3826 T	+17:35137644 2524669151 T	L
1276	3827 T	+17:35137645 2524669152 T	
1276	3828 G	+17:35137646 2524669153 G	
1277	3829 A	+17:35137647 2524669154 A	T
1277	3830 C	+17:35137648 2524669155 C	
1277	3831 A	+17:35137649 2524669156 A	
1278	3832 C	+17:35137650 2524669157 C	P
1278	3833 C	+17:35137651 2524669158 C	
1278	3834 C	+17:35137652 2524669159 C	
1279	3835 C	+17:35137653 2524669160 C	Q
1279	3836 A	+17:35137654 2524669161 A	
1279	3837 G	+17:35137655 2524669162 G	
1280	3838 G	+17:35137656 2524669163 G	G
1280	3839 G	+17:35137657 2524669164 G	
1280	3840 A	+17:35137658 2524669165 A	
1281	3841 G	+17:35137659 2524669166 G	G
1281	3842 G	+17:35137660 2524669167 G	
1281	3843 A	+17:35137661 2524669168 A	
1282	3844 G	+17:35137662 2524669169 G	A
1282	3845 C	+17:35137663 2524669170 C	
1282	3846 T	+17:35137664 2524669171 T	
1283	3847 G	+17:35137665 2524669172 G	A
1283	3848 C	+17:35137666 2524669173 C	
1283	3849 C	+17:35137667 2524669174 C	
1284	3850 C	+17:35137668 2524669175 C	P
1284	3851 C	+17:35137669 2524669176 C	
1284	3852 T	+17:35137670 2524669177 T	
1285	3853 C	+17:35137671 2524669178 C	Q
1285	3854 A	+17:35137672 2524669179 A	
1285	3855 G	+17:35137673 2524669180 G	
1286	3856 C	+17:35137674 2524669181 C	P
1286	3857 C	+17:35137675 2524669182 C	
1286	3858 C	+17:35137676 2524669183 C	
1287	3859 C	+17:35137677 2524669184 C	H
1287	3860 A	+17:35137678 2524669185 A	
1287	3861 C	+17:35137679 2524669186 C	
1288	3862 C	+17:35137680 2524669187 C	P
1288	3863 C	+17:35137681 2524669188 C	
1288	3864 T	+17:35137682 2524669189 T	
1289	3865 C	+17:35137683 2524669190 C	P
1289	3866 C	+17:35137684 2524669191 C	
1289	3867 T	+17:35137685 2524669192 T	
1290	3868 C	+17:35137686 2524669193 C	P
1290	3869 C	+17:35137687 2524669194 C	
1290	3870 T	+17:35137688 2524669195 T	
1291	3871 G	+17:35137689 2524669196 G	A
1291	3872 C	+17:35137690 2524669197 C	
1291	3873 C	+17:35137691 2524669198 C	
1292	3874 T	+17:35137692 2524669199 T	F
1292	3875 T	+17:35137693 2524669200 T	
1292	3876 C	+17:35137694 2524669201 C	
1293	3877 A	+17:35137695 2524669202 A	S
1293	3878 G	+17:35137696 2524669203 G	
1293	3879 C	+17:35137697 2524669204 C	
1294	3880 C	+17:35137698 2524669205 C	P
1294	3881 C	+17:35137699 2524669206 C	
1294	3882 A	+17:35137700 2524669207 A	
1295	3883 G	+17:35137701 2524669208 G	A
1295	3884 C	+17:35137702 2524669209 C	
1295	3885 C	+17:35137703 2524669210 C	
1296	3886 T	+17:35137704 2524669211 T	F
1296	3887 T	+17:35137705 2524669212 T	
1296	3888 C	+17:35137706 2524669213 C	
1297	3889 G	+17:35137707 2524669214 G	D
1297	3890 A	+17:35137708 2524669215 A	
1297	3891 C	+17:35137709 2524669216 C	
1298	3892 A	+17:35137710 2524669217 A	N
1298	3893 A	+17:35137711 2524669218 A	
1298	3894 C	+17:35137712 2524669219 C	
1299	3895 C	+17:35137713 2524669220 C	L
1299	3896 T	+17:35137714 2524669221 T	
1299	3897 C	+17:35137715 2524669222 C	
1300	3898 T	+17:35137716 2524669223 T	Y
1300	3899 A	+17:35137717 2524669224 A	
1300	3900 T	+17:35137718 2524669225 T	
1301	3901 T	+17:35137719 2524669226 T	Y
1301	3902 A	+17:35137720 2524669227 A	
1301	3903 C	+17:35137721 2524669228 C	
1302	3904 T	+17:35137722 2524669229 T	W
1302	3905 G	+17:35137723 2524669230 G	
1302	3906 G	+17:35137724 2524669231 G	
1303	3907 G	+17:35137725 2524669232 G	D
1303	3908 A	+17:35137726 2524669233 A	
1303	3909 C	+17:35137727 2524669234 C	
1304	3910 C	+17:35137728 2524669235 C	Q
1304	3911 A	+17:35137729 2524669236 A	
1304	3912 G	+17:35137730 2524669237 G	
1305	3913 G	+17:35137731 2524669238 G	D
1305	3914 A	+17:35137732 2524669239 A	
1305	3915 C	+17:35137733 2524669240 C	
1306	3916 C	+17:35137734 2524669241 C	P
1306	3917 C	+17:35137735 2524669242 C	
1306	3918 A	+17:35137736 2524669243 A	
1307	3919 C	+17:35137737 2524669244 C	P
1307	3920 C	+17:35137738 2524669245 C	
1307	3921 A	+17:35137739 2524669246 A	
1308	3922 G	+17:35137740 2524669247 G	E
1308	3923 A	+17:35137741 2524669248 A	
1308	3924 G	+17:35137742 2524669249 G	
1309	3925 C	+17:35137743 2524669250 C	R
1309	3926 G	+17:35137744 2524669251 G	
1309	3927 G	+17:35137745 2524669252 G	
1310	3928 G	+17:35137746 2524669253 G	G
1310	3929 G	+17:35137747 2524669254 G	
1310	3930 G	+17:35137748 2524669255 G	
1311	3931 G	+17:35137749 2524669256 G	A
1311	3932 C	+17:35137750 2524669257 C	
1311	3933 T	+17:35137751 2524669258 T	
1312	3934 C	+17:35137752 2524669259 C	P
1312	3935 C	+17:35137753 2524669260 C	
1312	3936 A	+17:35137754 2524669261 A	
1313	3937 C	+17:35137755 2524669262 C	P
1313	3938 C	+17:35137756 2524669263 C	
1313	3939 C	+17:35137757 2524669264 C	
1314	3940 A	+17:35137758 2524669265 A	S
1314	3941 G	+17:35137759 2524669266 G	
1314	3942 C	+17:35137760 2524669267 C	
1315	3943 A	+17:35137761 2524669268 A	T
1315	3944 C	+17:35137762 2524669269 C	
1315	3945 C	+17:35137763 2524669270 C	
1316	3946 T	+17:35137764 2524669271 T	F
1316	3947 T	+17:35137765 2524669272 T	
1316	3948 C	+17:35137766 2524669273 C	
1317	3949 A	+17:35137767 2524669274 A	K
1317	3950 A	+17:35137768 2524669275 A	
1317	3951 A	+17:35137769 2524669276 A	
1318	3952 G	+17:35137770 2524669277 G	G
1318	3953 G	+17:35137771 2524669278 G	
1318	3954 G	+17:35137772 2524669279 G	
1319	3955 A	+17:35137773 2524669280 A	T
1319	3956 C	+17:35137774 2524669281 C	
1319	3957 A	+17:35137775 2524669282 A	
1320	3958 C	+17:35137776 2524669283 C	P
1320	3959 C	+17:35137777 2524669284 C	
1320	3960 T	+17:35137778 2524669285 T	
1321	3961 A	+17:35137779 2524669286 A	T
1321	3962 C	+17:35137780 2524669287 C	
1321	3963 G	+17:35137781 2524669288 G	
1322	3964 G	+17:35137782 2524669289 G	A
1322	3965 C	+17:35137783 2524669290 C	
1322	3966 A	+17:35137784 2524669291 A	
1323	3967 G	+17:35137785 2524669292 G	E
1323	3968 A	+17:35137786 2524669293 A	
1323	3969 G	+17:35137787 2524669294 G	
1324	3970 A	+17:35137788 2524669295 A	N
1324	3971 A	+17:35137789 2524669296 A	
1324	3972 C	+17:35137790 2524669297 C	
1325	3973 C	+17:35137791 2524669298 C	P
1325	3974 C	+17:35137792 2524669299 C	
1325	3975 A	+17:35137793 2524669300 A	
1326	3976 G	+17:35137794 2524669301 G	E
1326	3977 A	+17:35137795 2524669302 A	
1326	3978 G	+17:35137796 2524669303 G	
1327	3979 T	+17:35137797 2524669304 T	Y
1327	3980 A	+17:35137798 2524669305 A	
1327	3981 C	+17:35137799 2524669306 C	
1328	3982 C	+17:35137800 2524669307 C	L
1328	3983 T	+17:35137801 2524669308 T	
1328	3984 G	+17:35137802 2524669309 G	
1329	3985 G	+17:35137803 2524669310 G	G
1329	3986 G	+17:35137804 2524669311 G	
1329	3987 T	+17:35137805 2524669312 T	
1330	3988 C	+17:35137806 2524669313 C	L
1330	3989 T	+17:35137807 2524669314 T	
1330	3990 G	+17:35137808 2524669315 G	
1331	3991 G	+17:35137809 2524669316 G	D
1331	3992 A	+17:35137810 2524669317 A	
1331	3993 C	+17:35137811 2524669318 C	
1332	3994 G	+17:35137812 2524669319 G	V
1332	3995 T	+17:35137813 2524669320 T	
1332	3996 G	+17:35137814 2524669321 G	
1333	3997 C	+17:35137815 2524669322 C	P
1333	3998 C	+17:35137816 2524669323 C	
1333	3999 A	+17:35137817 2524669324 A	
1334	4000 G	+17:35137818 2524669325 G	V
1334	4001 T	+17:35137819 2524669326 T	
1334	4002 G	+17:35137820 2524669327 G	
1335	4003 T	+17:35137821 2524669328 T	*
1335	4004 G	+17:35137822 2524669329 G	
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1335	4006 A	+17:35137824 2524669331 A	
1335	4007 C	+17:35137825 2524669332 C	
1335	4008 C	+17:35137826 2524669333 C	
1335	4009 A	+17:35137827 2524669334 A	
1335	4010 G	+17:35137828 2524669335 G	
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1335	4013 G	+17:35137831 2524669338 G	
1335	4014 G	+17:35137832 2524669339 G	
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1335	4016 C	+17:35137834 2524669341 C	
1335	4017 A	+17:35137835 2524669342 A	
1335	4018 A	+17:35137836 2524669343 A	
1335	4019 G	+17:35137837 2524669344 G	
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1335	4021 C	+17:35137839 2524669346 C	
1335	4022 C	+17:35137840 2524669347 C	
1335	4023 G	+17:35137841 2524669348 G	
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1335	4025 A	+17:35137843 2524669350 A	
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1335	4027 A	+17:35137845 2524669352 A	
1335	4028 A	+17:35137846 2524669353 A	
1335	4029 G	+17:35137847 2524669354 G	
1335	4030 C	+17:35137848 2524669355 C	
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1335	4032 C	+17:35137850 2524669357 C	
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1335	4050 G	+17:35137868 2524669375 G	
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1335	4066 T	+17:35137884 2524669391 T	
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1335	4069 T	+17:35137887 2524669394 T	
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1335	4080 A	+17:35137898 2524669405 A	
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1335	4083 G	+17:35137901 2524669408 G	
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1335	4085 T	+17:35137903 2524669410 T	
1335	4086 G	+17:35137904 2524669411 G	
1335	4087 G	+17:35137905 2524669412 G	
1335	4088 G	+17:35137906 2524669413 G	
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1335	4091 G	+17:35137909 2524669416 G	
1335	4092 G	+17:35137910 2524669417 G	
1335	4093 C	+17:35137911 2524669418 C	
1335	4094 C	+17:35137912 2524669419 C	
1335	4095 C	+17:35137913 2524669420 C	
1335	4096 T	+17:35137914 2524669421 T	
1335	4097 C	+17:35137915 2524669422 C	
1335	4098 C	+17:35137916 2524669423 C	
1335	4099 G	+17:35137917 2524669424 G	
1335	4100 A	+17:35137918 2524669425 A	
1335	4101 C	+17:35137919 2524669426 C	
1335	4102 C	+17:35137920 2524669427 C	
1335	4103 A	+17:35137921 2524669428 A	
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1335	4107 C	+17:35137925 2524669432 C	
1335	4108 C	+17:35137926 2524669433 C	
1335	4109 A	+17:35137927 2524669434 A	
1335	4110 G	+17:35137928 2524669435 G	
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1335	4491 T	+17:35138309 2524669816 T	
1335	4492 T	+17:35138310 2524669817 T	
1335	4493 T	+17:35138311 2524669818 T	
1335	4494 T	+17:35138312 2524669819 T	
1335	4495 T	+17:35138313 2524669820 T	
1335	4496 T	+17:35138314 2524669821 T	
1335	4497 G	+17:35138315 2524669822 G	
1335	4498 T	+17:35138316 2524669823 T	
1335	4499 T	+17:35138317 2524669824 T	
1335	4500 T	+17:35138318 2524669825 T	
1335	4501 T	+17:35138319 2524669826 T	
1335	4502 G	+17:35138320 2524669827 G	
1335	4503 T	+17:35138321 2524669828 T	
1335	4504 T	+17:35138322 2524669829 T	
1335	4505 T	+17:35138323 2524669830 T	
1335	4506 T	+17:35138324 2524669831 T	
1335	4507 T	+17:35138325 2524669832 T	
1335	4508 T	+17:35138326 2524669833 T	
1335	4509 T	+17:35138327 2524669834 T	
1335	4510 A	+17:35138328 2524669835 A	
1335	4511 A	+17:35138329 2524669836 A	
1335	4512 A	+17:35138330 2524669837 A	
1335	4513 G	+17:35138331 2524669838 G	
1335	4514 A	+17:35138332 2524669839 A	
1335	4515 T	+17:35138333 2524669840 T	
1335	4516 G	+17:35138334 2524669841 G	
1335	4517 A	+17:35138335 2524669842 A	
1335	4518 A	+17:35138336 2524669843 A	
1335	4519 A	+17:35138337 2524669844 A	
1335	4520 T	+17:35138338 2524669845 T	
1335	4521 A	+17:35138339 2524669846 A	
1335	4522 A	+17:35138340 2524669847 A	
1335	4523 A	+17:35138341 2524669848 A	
1335	4524 G	+17:35138342 2524669849 G	
1335	4525 A	+17:35138343 2524669850 A	
1335	4526 C	+17:35138344 2524669851 C	
1335	4527 C	+17:35138345 2524669852 C	
1335	4528 C	+17:35138346 2524669853 C	
1335	4529 A	+17:35138347 2524669854 A	
1335	4530 G	+17:35138348 2524669855 G	
1335	4531 G	+17:35138349 2524669856 G	
1335	4532 G	+17:35138350 2524669857 G	
1335	4533 G	+17:35138351 2524669858 G	
1335	4534 G	+17:35138352 2524669859 G	
1335	4535 A	+17:35138353 2524669860 A	
1335	4536 G	+17:35138354 2524669861 G	
1335	4537 A	+17:35138355 2524669862 A	
1335	4538 A	+17:35138356 2524669863 A	
1335	4539 T	+17:35138357 2524669864 T	
1335	4540 G	+17:35138358 2524669865 G	
1335	4541 G	+17:35138359 2524669866 G	
1335	4542 G	+17:35138360 2524669867 G	
1335	4543 T	+17:35138361 2524669868 T	
1335	4544 G	+17:35138362 2524669869 G	
1335	4545 T	+17:35138363 2524669870 T	
1335	4546 T	+17:35138364 2524669871 T	
1335	4547 G	+17:35138365 2524669872 G	
1335	4548 T	+17:35138366 2524669873 T	
1335	4549 A	+17:35138367 2524669874 A	
1335	4550 T	+17:35138368 2524669875 T	
1335	4551 G	+17:35138369 2524669876 G	
1335	4552 G	+17:35138370 2524669877 G	
1335	4553 G	+17:35138371 2524669878 G	
1335	4554 G	+17:35138372 2524669879 G	
1335	4555 A	+17:35138373 2524669880 A	
1335	4556 G	+17:35138374 2524669881 G	
1335	4557 G	+17:35138375 2524669882 G	
1335	4558 C	+17:35138376 2524669883 C	
1335	4559 A	+17:35138377 2524669884 A	
1335	4560 A	+17:35138378 2524669885 A	
1335	4561 G	+17:35138379 2524669886 G	
1335	4562 T	+17:35138380 2524669887 T	
1335	4563 G	+17:35138381 2524669888 G	
1335	4564 T	+17:35138382 2524669889 T	
1335	4565 G	+17:35138383 2524669890 G	
1335	4566 G	+17:35138384 2524669891 G	
1335	4567 G	+17:35138385 2524669892 G	
1335	4568 G	+17:35138386 2524669893 G	
1335	4569 G	+17:35138387 2524669894 G	
1335	4570 G	+17:35138388 2524669895 G	
1335	4571 T	+17:35138389 2524669896 T	
1335	4572 C	+17:35138390 2524669897 C	
1335	4573 C	+17:35138391 2524669898 C	
1335	4574 T	+17:35138392 2524669899 T	
1335	4575 T	+17:35138393 2524669900 T	
1335	4576 C	+17:35138394 2524669901 C	
1335	4577 T	+17:35138395 2524669902 T	
1335	4578 C	+17:35138396 2524669903 C	
1335	4579 C	+17:35138397 2524669904 C	
1335	4580 A	+17:35138398 2524669905 A	
1335	4581 C	+17:35138399 2524669906 C	
1335	4582 A	+17:35138400 2524669907 A	
1335	4583 C	+17:35138401 2524669908 C	
1335	4584 C	+17:35138402 2524669909 C	
1335	4585 C	+17:35138403 2524669910 C	
1335	4586 A	+17:35138404 2524669911 A	
1335	4587 C	+17:35138405 2524669912 C	
1335	4588 T	+17:35138406 2524669913 T	
1335	4589 T	+17:35138407 2524669914 T	
1335	4590 T	+17:35138408 2524669915 T	
1335	4591 G	+17:35138409 2524669916 G	
1335	4592 T	+17:35138410 2524669917 T	
1335	4593 C	+17:35138411 2524669918 C	
1335	4594 C	+17:35138412 2524669919 C	
1335	4595 A	+17:35138413 2524669920 A	
1335	4596 T	+17:35138414 2524669921 T	
1335	4597 T	+17:35138415 2524669922 T	
1335	4598 T	+17:35138416 2524669923 T	
1335	4599 G	+17:35138417 2524669924 G	
1335	4600 C	+17:35138418 2524669925 C	
1335	4601 A	+17:35138419 2524669926 A	
1335	4602 A	+17:35138420 2524669927 A	
1335	4603 A	+17:35138421 2524669928 A	
1335	4604 T	+17:35138422 2524669929 T	
1335	4605 A	+17:35138423 2524669930 A	
1335	4606 T	+17:35138424 2524669931 T	
1335	4607 A	+17:35138425 2524669932 A	
1335	4608 T	+17:35138426 2524669933 T	
1335	4609 T	+17:35138427 2524669934 T	
1335	4610 T	+17:35138428 2524669935 T	
1335	4611 T	+17:35138429 2524669936 T	
1335	4612 G	+17:35138430 2524669937 G	
1335	4613 G	+17:35138431 2524669938 G	
1335	4614 A	+17:35138432 2524669939 A	
1335	4615 A	+17:35138433 2524669940 A	
1335	4616 A	+17:35138434 2524669941 A	
1335	4617 A	+17:35138435 2524669942 A	
1335	4618 C	+17:35138436 2524669943 C	
1335	4619 A	+17:35138437 2524669944 A	
1335	4620 G	+17:35138438 2524669945 G	
1335	4621 C	+17:35138439 2524669946 C	
1335	4622 T	+17:35138440 2524669947 T	
1335	4623 A	+17:35138441 2524669948 A	
BioPerl-1.007002/t/data/headerless.psl000444000766000024        66313155576321 17514 0ustar00cjfieldsstaff000000000000psLayout version 4 DNA DNA

match mis-  rep.  N's Q gap Q gap T gap T gap strand Q         Q    Q     Q   T         T    T     T   block blockSizes  qStarts  tStarts
      match match     count bases count bases        name      size start end name      size start end count
---------------------------------------------------------------------------------------------------------------------------------------------------------------
BioPerl-1.007002/t/data/hg16_chroms.gff000444000766000024       302113155576321 17470 0ustar00cjfieldsstaff000000000000##sequence-region chr1 1 246127941
##sequence-region chr2 1 243615958
##sequence-region chr3 1 199344050
##sequence-region chr4 1 191731959
##sequence-region chr5 1 181034922
##sequence-region chr6 1 170914576
##sequence-region chr7 1 158545518
##sequence-region chr8 1 146308819
##sequence-region chr9 1 136372045
##sequence-region chrM 1 16571
##sequence-region chrX 1 153692391
##sequence-region chrY 1 50286555
##sequence-region chr1_random 1 6515988
##sequence-region chr2_random 1 1104831
##sequence-region chr3_random 1 749256
##sequence-region chr4_random 1 648024
##sequence-region chr5_random 1 143687
##sequence-region chr6_random 1 2055751
##sequence-region chr7_random 1 632637
##sequence-region chr8_random 1 1499381
##sequence-region chr9_random 1 2766341
##sequence-region chrX_random 1 3403558
##sequence-region chr10 1 135037215
##sequence-region chr11 1 134482954
##sequence-region chr12 1 132078379
##sequence-region chr13 1 113042980
##sequence-region chr14 1 105311216
##sequence-region chr15 1 100256656
##sequence-region chr16 1 90041932
##sequence-region chr17 1 81860266
##sequence-region chr18 1 76115139
##sequence-region chr19 1 63811651
##sequence-region chr20 1 63741868
##sequence-region chr21 1 46976097
##sequence-region chr22 1 49396972
##sequence-region chr10_random 1 1043775
##sequence-region chr13_random 1 189598
##sequence-region chr15_random 1 1132826
##sequence-region chr17_random 1 2549222
##sequence-region chr18_random 1 4262
##sequence-region chr19_random 1 92689
##sequence-region chrUn_random 1 3349625
BioPerl-1.007002/t/data/hmmpfam.out000444000766000024       367113155576321 17055 0ustar00cjfieldsstaff000000000000hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:                 pfam
Sequence file:            /home/birney/src/wise2/example/road.pep
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query:  roa1_drome  

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
SEED                                                    146.1    6.3e-40   2

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
SEED       1/2      33   103 ..     1    77 []    71.2  2.2e-17
SEED       2/2     124   193 ..     1    77 []    75.5  1.1e-18

Alignments of top-scoring domains:
SEED: domain 1 of 2, from 33 to 103: score 71.2, E = 2.2e-17
                   *->lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGf
                      lf+g+L + +t+e Lk++F+k G iv++ +++D     + t++s+Gf
  roa1_drome    33    LFIGGLDYRTTDENLKAHFEKWGNIVDVVVMKD-----PRTKRSRGF 74   

                   aFVeFeseedAekAlealnG.kelggrklrv<-*
                   +F+++  ++  + A +    +++++gr+++    
  roa1_drome    75 GFITYSHSSMIDEAQK--SRpHKIDGRVVEP    103  

SEED: domain 2 of 2, from 124 to 193: score 75.5, E = 1.1e-18
                   *->lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGf
                      lfVg L  d +e+ ++d+F++fG iv+i+iv+D     ketgk +Gf
  roa1_drome   124    LFVGALKDDHDEQSIRDYFQHFGNIVDINIVID-----KETGKKRGF 165  

                   aFVeFeseedAekAlealnGkelggrklrv<-*
                   aFVeF++++ ++k +     ++l+g+ + v   
  roa1_drome   166 AFVEFDDYDPVDKVVL--KQHQLNGKMVDV    193  

//
BioPerl-1.007002/t/data/hmmpfam_HSPdashline.txt000444000766000024       721413155576321 21304 0ustar00cjfieldsstaff000000000000hmmpfam - search one or more sequences against HMM database
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:                 trans_db
Sequence file:            megaplasmid.fasta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query sequence: lcl|gi|340783625|Plus1
Accession:      [none]
Description:    megaplasmid, complete sequence [UNKNOWN]

Scores for sequence family classification (score includes all domains):
Model                Description                        Score    E-value  N 
--------             -----------                        -----    ------- ---
IS66_ORF3.uniq                                          -30.0    1.7e-15   1

Parsed for domains:
Model                Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------             ------- ----- -----    ----- -----      -----  -------
IS66_ORF3.uniq         1/1   60792 61184 ..     1   558 []   -30.0  1.7e-15

Alignments of top-scoring domains:
IS66_ORF3.uniq: domain 1 of 1, from 60792 to 61184: score -30.0, E = 1.7e-15
                   *->mSSPLDLSLFPNLmtevvkmnaalpddlslLkAalqkqQavvea..l
                          L  S FP + +      aa+p+ l +    l    + v  + +
  lcl|gi|340 60792    SCTGLWDSEFPPVFPVNGSQRAATPF-LPVGPDELSSPPSSVLXscY 60837

                   dakianleelIEkLka.qldkLRRmkFGkrSEKkRhkLeldiaQiekale
                   d  +     l  +L ++q   LR    ++r                    
  lcl|gi|340 60838 DFPLCQSLSLCFRLGFpQALALRVRQRAPRGCH----------------- 60870

                   dLEddLnetqaeiaeaekkieaPAssppkeaPiaskPesPRqerkRkPLP
                         +  +a+    +      A+ +p++            + +   LP
  lcl|gi|340 60871 ------AHRRARGLFFTDTPHPVAVPRPQR----------DLTGSLVTLP 60904

                   eeLPReerRlePestvCPcggGqLkriGEDvsEqLDlvpaaFeVIqTvRp
                   + +P  e    P + + P             + + D vp+  +       
  lcl|gi|340 60905 APMPCSET---PVESQHPGH-----------TGRSDAVPTPNTMKTS--- 60937

                   KyACrqCdtiVQAPaPakpIErGiptaGLLArvlVSKyaEHlPLYRQsEI
                                                                     
  lcl|gi|340     - -------------------------------------------------- -    

                   yaRqGVeiaRstLadWVgrtgarLaPLvdALaeyVLkeGklHADeTPVqV
                         +i  s L   V++ + r                           
  lcl|gi|340 60938 ------AIMISGLIHGVSARCLRF-------------------------- 60955

                   LaPGnkKTKTGyLWAYvRDDRnagsSlppaVvfayspdRkGEHaqvhLae
                        k   TG      R D     Slp+ +    +  R G        e
  lcl|gi|340 60956 -----KRSVTG-----PRQD-----SLPADGL---RLCREG-------VE 60980

                   ysGkLqaDAyaGYnalyesgRVGGDpikEAgCwAHaRRKifDlhvrnpSe
                    sG      +   +   +           ++ wAH RR ++D+    pS+
  lcl|gi|340 60981 PSGSQXKVSVTSILLSRTXP---------VASWAHVRRHFYDVNQGAPSP 61021

                   lteEALerIaaLYeIEaeIRGspaEdRlavRqelSvPlvkslseWLtaqr
                    ++ AL rI +LYeIEaeI   p+E+    Rq+++ Pl+ s+  WL   r
  lcl|gi|340 61022 VAQTALLRIHELYEIEAEIKDDPPEQKMLARQQRAAPLLESFWTWLNDTR 61071

                   KtlsrgseLAKALaYlLnrWdALtryldDGqVpIDNNivENAiRrvAlGR
                     +  +s+ AKA  Y+L+rW ALt+yl+ G+  IDNN vE A+R vA+GR
  lcl|gi|340 61072 AQVAPKSAIAKAIGYALKRWKALTLYLQEGHLGIDNNPVERALRGVAIGR 61121

                   kNyLFaGSDrGGeraAliySLIgTCKmNgVePyaYLrdVltrLadwplnk
                   kN+LFaG D GGeraA++y LI TCK+NgVeP aYL+dVl++L++wp  +
  lcl|gi|340 61122 KNFLFAGNDAGGERAAAFYTLIETCKLNGVEPFAYLCDVLEKLPTWPNKR 61171

                   DideLLPWayasai<-*
                     +eLLPW++       
  lcl|gi|340 61172 -LHELLPWNWKNLT    61184

//
BioPerl-1.007002/t/data/hmmpfam_cs.out000444000766000024      7054413155576321 17565 0ustar00cjfieldsstaff000000000000hmmpfam - search one or more sequences against HMM database
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:                 ../Shared/Pfam_fs
Sequence file:            single_porphyra_AA.fa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query sequence: gi|90819130|dbj|BAE92499.1|
Accession:      [none]
Description:    glutamate synthase [Porphyra yezoensis]

Scores for sequence family classification (score includes all domains):
Model           Description                             Score    E-value  N 
--------        -----------                             -----    ------- ---
Glu_synthase    Conserved region in glutamate synthas   858.6   3.6e-255   2
GATase_2        Glutamine amidotransferases class-II    731.8   3.9e-226   1
Glu_syn_central Glutamate synthase central domain       649.1   7.9e-213   1
GXGXG           GXGXG motif                             367.3   2.7e-107   1
HdeA            hns-dependent expression protein A (H     9.6      0.015   1
GDC-P           Glycine cleavage system P-protein         7.1      0.086   1
Cache_1         Cache domain                              7.0       0.14   1
IBN_N           Importin-beta N-terminal domain           8.2       0.17   1
DUF1200         Protein of unknown function (DUF1200)     6.7       0.42   1
cobW            CobW/HypB/UreG, nucleotide-binding do     5.1       0.45   1
PUF             Pumilio-family RNA binding repeat         6.5       0.47   1
Arch_flagellin  Archaebacterial flagellin                 4.1       0.66   1
FMN_dh          FMN-dependent dehydrogenase               3.2       0.89   1
RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4             4.6        1.4   1
DUF477          Domain of unknown function (DUF477)       3.8        1.7   1
FRG1            FRG1-like family                          0.2        1.7   1
DUF1393         Protein of unknown function (DUF1393)     3.1          2   1
tRNA_anti       OB-fold nucleic acid binding domain       4.9          2   1
SelT            Selenoprotein T                           3.1        2.2   1
RNase_PH_C      3' exoribonuclease family, domain 2       4.2        2.3   1
Pencillinase_R  Penicillinase repressor                   3.9        2.5   1
Hormone_4       Neurohypophysial hormones, N-terminal     4.4        2.5   1
DSRB            Dextransucrase DSRB                       2.7        2.7   1
FtsK_SpoIIIE    FtsK/SpoIIIE family                       2.6        3.1   1
UBA             UBA/TS-N domain                           4.2        3.1   1
DUF1981         Domain of unknown function (DUF1981)      3.6        3.3   1
Gla             Vitamin K-dependent carboxylation/gam     4.0        3.5   1
Scm3            Centromere protein Scm3                   2.2        3.5   1
Ribosomal_S6    Ribosomal protein S6                      3.3        3.7   1
Cystatin        Cystatin domain                           2.4        3.9   1
Phage_prot_Gp6  Phage portal protein, SPP1 Gp6-like       1.0          4   1
DUF1976         Domain of unknown function (DUF1976)     -1.5        4.3   1
DUF37           Domain of unknown function DUF37          3.0        4.5   1
Flavodoxin_NdrI NrdI Flavodoxin like                      2.1        4.6   1
Bac_rhodopsin   Bacteriorhodopsin                         0.9        4.9   1
Nitro_FeMo-Co   Dinitrogenase iron-molybdenum cofacto     2.1        5.3   1
MoCF_biosynth   Probable molybdopterin binding domain     1.3        5.6   1
PaaA_PaaC       Phenylacetic acid catabolic protein       0.4        5.6   1
Albicidin_res   Albicidin resistance domain               1.7        5.7   1
DUF1514         Protein of unknown function (DUF1514)     3.5        5.7   1
T5orf172        T5orf172 domain                           2.0        6.1   1
Nup133_N        Nup133 N terminal like                   -0.6        6.5   1
BicD            Microtubule-associated protein Bicaud    -1.6        6.8   1
Sel1            Sel1 repeat                               2.5          7   1
CAP_C           DE   Adenylate cyclase associated (CA     1.3        7.4   1
Colicin         Colicin pore forming domain               1.4        7.5   1
MADF_DNA_bdg    Alcohol dehydrogenase transcription f     1.8        8.2   1
DUF258          Protein of unknown function, DUF258       0.3        8.3   1
PspB            Phage shock protein B                     0.4        8.4   1
GspM            General secretion pathway, M protein      1.0        8.6   1
Coq4            Coenzyme Q (ubiquinone) biosynthesis     -0.3        9.1   1
P22_AR_N        P22_AR N-terminal domain                 -0.2        9.5   1
C1_2            C1 domain                                 1.1        9.6   1
Phage_Mu_P      Bacteriophage Mu P protein               -0.4         10   1

Parsed for domains:
Model           Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------        ------- ----- -----    ----- -----      -----  -------
GATase_2          1/1      34   404 ..     1   385 []   731.8 3.9e-226
FRG1              1/1      88   107 ..   151   173 ..     0.2      1.7
C1_2              1/1     191   210 ..     9    27 ..     1.1      9.6
MADF_DNA_bdg      1/1     235   261 ..    57    95 .]     1.8      8.2
PaaA_PaaC         1/1     258   269 ..     1    13 [.     0.4      5.6
Albicidin_res     1/1     274   289 ..    50    65 ..     1.7      5.7
UBA               1/1     311   331 ..    18    38 .]     4.2      3.1
Gla               1/1     342   357 ..    27    42 .]     4.0      3.5
RNA_pol_Rpb2_4    1/1     369   381 ..     1    13 [.     4.6      1.4
MoCF_biosynth     1/1     371   396 ..    23    49 ..     1.3      5.6
DUF1200           1/1     389   401 ..     1    13 [.     6.7     0.42
Nup133_N          1/1     397   419 ..   475   498 .]    -0.6      6.5
DUF1976           1/1     428   448 ..  1296  1319 .]    -1.5      4.3
Bac_rhodopsin     1/1     445   472 ..   219   250 .]     0.9      4.9
Coq4              1/1     459   481 ..    60    82 ..    -0.3      9.1
Glu_syn_central   1/1     478   773 ..     1   301 []   649.1 7.9e-213
Flavodoxin_NdrI   1/1     488   497 ..   122   131 .]     2.1      4.6
P22_AR_N          1/1     524   541 ..   110   126 .]    -0.2      9.5
Cache_1           1/1     537   557 ..     1    23 [.     7.0     0.14
Glu_synthase      1/2     650   676 ..   297   323 ..     1.3        3
HdeA              1/1     727   749 ..    58    79 .]     9.6    0.015
Sel1              1/1     729   745 ..    32    49 .]     2.5        7
DUF1981           1/1     765   787 ..    62    88 .]     3.6      3.3
tRNA_anti         1/1     818   839 ..    54    85 .]     4.9        2
Cystatin          1/1     826   859 ..     1    38 [.     2.4      3.9
RNase_PH_C        1/1     827   846 ..    64    84 .]     4.2      2.3
Glu_synthase      2/2     830  1216 ..     1   412 []   857.3   9e-255
DUF258            1/1     839   860 ..   282   305 .]     0.3      8.3
Pencillinase_R    1/1     856   894 ..    84   118 .]     3.9      2.5
SelT              1/1     872   885 ..    96   111 .]     3.1      2.2
Nitro_FeMo-Co     1/1     879   897 ..    87   105 .]     2.1      5.3
DUF37             1/1     927   934 ..    61    68 .]     3.0      4.5
Scm3              1/1     953   963 ..   103   113 .]     2.2      3.5
cobW              1/1    1038  1058 ..   202   222 .]     5.1     0.45
Arch_flagellin    1/1    1050  1072 ..   197   219 .]     4.1     0.66
DUF1393           1/1    1055  1068 ..     1    14 [.     3.1        2
FtsK_SpoIIIE      1/1    1107  1143 ..   163   198 ..     2.6      3.1
FMN_dh            1/1    1109  1148 ..   291   330 ..     3.2     0.89
DSRB              1/1    1120  1134 ..     1    16 [.     2.7      2.7
Phage_Mu_P        1/1    1122  1131 ..     1    10 [.    -0.4       10
Hormone_4         1/1    1168  1176 ..     1     9 []     4.4      2.5
GDC-P             1/1    1205  1225 ..    10    30 ..     7.1    0.086
PspB              1/1    1268  1276 ..     1     9 [.     0.4      8.4
T5orf172          1/1    1271  1293 ..    35    58 ..     2.0      6.1
CAP_C             1/1    1283  1292 ..   161   170 .]     1.3      7.4
GXGXG             1/1    1290  1485 ..     1   228 []   367.3 2.7e-107
DUF1514           1/1    1453  1469 ..    50    66 .]     3.5      5.7
Colicin           1/1    1456  1467 ..   192   203 .]     1.4      7.5
Ribosomal_S6      1/1    1461  1481 ..    16    36 ..     3.3      3.7
BicD              1/1    1465  1481 ..     1    17 [.    -1.6      6.8
PUF               1/1    1470  1486 ..    19    35 .]     6.5     0.47
DUF477            1/1    1472  1495 ..     1    24 [.     3.8      1.7
Phage_prot_Gp6    1/1    1479  1492 ..     1    14 [.     1.0        4
IBN_N             1/1    1498  1516 ..     1    20 [.     8.2     0.17
GspM              1/1    1506  1520 ..     1    15 [.     1.0      8.6

Alignments of top-scoring domains:
GATase_2: domain 1 of 1, from 34 to 404: score 731.8, E = 3.9e-226
                CS    EEEEEEEEETSSHSBHHHHHHHHHHHHHGGGGSSCSTTSSCECEEEE
                   *->CGvlGfiAhikgkpshkivedaleaLerLeHRGavgADgktGDGAGI
                      CGv GfiA+ ++ ++hkiv +aleaL+++eHRGa++AD ++GDGAGI
  gi|9081913    34    CGV-GFIADVNNVANHKIVVQALEALTCMEHRGACSADRDSGDGAGI 79   

                CS EEECTCCCHHHHHHHCT----S GC-EEEEEEE-SSHHHHHHHHHHHHHH
                   ltqiPdgFFrevakelGieLpe.gqYAVGmvFLPqdelaraearkifEki
                    t+iP+++F++  ++++i++ ++   +VGm+FLP   l+    + i+E +
  gi|9081913    80 TTAIPWNLFQKSLQNQNIKFEQnDSVGVGMLFLPAHKLKES--KLIIETV 127  

                CS HHHTT-EEEEEEE--B-GGGS-HHHHHC--EEEEEEEE-TT--HHHHHHC
                   aeeeGLeVLGWReVPvnnsvLGetAlatePvIeQvFvgapsgdgedfErr
                   ++ee+Le++GWR VP+  +vLG++A  + P++eQvF+ +++ +++ +E++
  gi|9081913   128 LKEENLEIIGWRLVPTVQEVLGKQAYLNKPHVEQVFCKSSNLSKDRLEQQ 177  

                CS EEEEECHSCHHHHTHHH.    BEEEEEESSEEEEEECC-GGGHHHHBHG
                   LyviRkrieksivaenvn....fYiCSLSsrTIVYKGMLtseQLgqFYpD
                   L+++Rk+iek+i+  + +  ++fYiCSLS++TIVYKGM++s++LgqFY+D
  gi|9081913   178 LFLVRKKIEKYIGINGKDwaheFYICSLSCYTIVYKGMMRSAVLGQFYQD 227  

                CS GGSTTEEBSEEEEEECESSSSSCTGGGSSCEEECCCTTCEEEEEEEEETT
                   LqderfeSalAivHsRFSTNTfPsWplAQPfRVnslwgggivlAHNGEIN
                   L++++++S++Ai+H+RFSTNT+P+WplAQP+R         ++ HNGEIN
  gi|9081913   228 LYHSEYTSSFAIYHRRFSTNTMPKWPLAQPMR---------FVSHNGEIN 268  

                CS THHHHHHHHHHTSCCCSSTTCGHHHHCC-SSS-TTSCHHHHHHHHHHHHH
                   TlrgNrnwMraRegvlksplFgddldkLkPIvneggSDSaalDnvlEllv
                   Tl gN nwM++Re +l+s++++d++++LkPI n+++SDSa+lD ++Ell+
  gi|9081913   269 TLLGNLNWMQSREPLLQSKVWKDRIHELKPITNKDNSDSANLDAAVELLI 318  

                CS HTT--HHHHHHHHS----TT-GGGTST-HHHHHHHHHHHHHHCCHCCEEE
                   raGRslpeAlMMlIPEAWqnnpdmdkdrpekraFYeylsglmEPWDGPAa
                   ++GRs++eAlM+l+PEA+qn+pd   +++e+ +FYey+sgl+EPWDGPA+
  gi|9081913   319 ASGRSPEEALMILVPEAFQNQPDFA-NNTEISDFYEYYSGLQEPWDGPAL 367  

                CS EEEETSSEEEEEEETTTSCESEEEEEEEEEE.TTEEEEEESSC   
                   lvftDGryavgAtLDRNGLTRPaRygiTrdldkDglvvvaSEa<-*
                   +vft+G++ +gAtLDRNGL RPaRy+iT    kD+lv+v+SE+   
  gi|9081913   368 VVFTNGKV-IGATLDRNGL-RPARYVIT----KDNLVIVSSES    404  

FRG1: domain 1 of 1, from 88 to 107: score 0.2, E = 1.7
                   *->FQkfKvDLqdrklrinekDkkel<-*
                      FQk+   Lq+  +  +++D+ ++   
  gi|9081913    88    FQKS---LQNQNIKFEQNDSVGV    107  

C1_2: domain 1 of 1, from 191 to 210: score 1.1, E = 9.6
                   *->idgfyg...fYsCkkccddftl<-*
                      i+g+++ ++fY C+  c  +t+   
  gi|9081913   191    INGKDWaheFYICSLSC--YTI    210  

MADF_DNA_bdg: domain 1 of 1, from 235 to 261: score 1.8, E = 8.2
                   *->drYrrelrkirqgnsegsstgsgesykskWryyeelsFL<-*
                      +++  ++r+               ++ +kW+++  ++F    
  gi|9081913   235    SSFAIYHRRFS------------TNTMPKWPLAQPMRFV    261  

PaaA_PaaC: domain 1 of 1, from 258 to 269: score 0.4, E = 5.6
                CS    X............   
                   *->MYnFvEHGGvint<-*
                      M  Fv H G int   
  gi|9081913   258    M-RFVSHNGEINT    269  

Albicidin_res: domain 1 of 1, from 274 to 289: score 1.7, E = 5.7
                   *->LrlmharEPsLrkgtG<-*
                      L+ m+ rEP L+ +++   
  gi|9081913   274    LNWMQSREPLLQSKVW    289  

UBA: domain 1 of 1, from 311 to 331: score 4.2, E = 3.1
                CS    HHHHHHHHHTTT-HHHHHHHH   
                   *->eeakkALeatngnverAvewL<-*
                      ++a++ L a++ ++e+A+++L   
  gi|9081913   311    DAAVELLIASGRSPEEALMIL    331  

Gla: domain 1 of 1, from 342 to 357: score 4.0, E = 3.5
                CS    CSSHHHHHHHHHHCTC   
                   *->fednegtkefwrkYfg<-*
                      f++n+++  f++ Y g   
  gi|9081913   342    FANNTEISDFYEYYSG    357  

RNA_pol_Rpb2_4: domain 1 of 1, from 369 to 381: score 4.6, E = 1.4
                CS    EEETTEEEEEESS   
                   *->VYvNGklvGthrn<-*
                      V+ NGk++G + +   
  gi|9081913   369    VFTNGKVIGATLD    381  

MoCF_biosynth: domain 1 of 1, from 371 to 396: score 1.3, E = 5.6
                CS    CHHHHHHHHHHHTTTCEEEEEEEE-SS   
                   *->tNgpmLaalLresaGaevirygiVpDd<-*
                      tNg+ + a L +  G  ++ry+i +D+   
  gi|9081913   371    TNGKVIGATLDR-NGLRPARYVITKDN    396  

DUF1200: domain 1 of 1, from 389 to 401: score 6.7, E = 0.42
                   *->kYvltedtLlIks<-*
                      +Yv+t+d L+I+s   
  gi|9081913   389    RYVITKDNLVIVS    401  

Nup133_N: domain 1 of 1, from 397 to 419: score -0.6, E = 6.5
                   *->lylltrnsGvvrIeHaleedstne<-*
                      l++ + +sGvv++e +  + s  +   
  gi|9081913   397    LVIVSSESGVVQVE-PGNVKSKGR    419  

DUF1976: domain 1 of 1, from 428 to 448: score -1.5, E = 4.3
                   *->VsvYiyFkevtdnksLsEysVtyk<-*
                      V++++   ++++nk ++  sVt k   
  gi|9081913   428    VDIFS--HKILNNKEIK-TSVTTK    448  

Bac_rhodopsin: domain 1 of 1, from 445 to 472: score 0.9, E = 4.9
                CS    HHHHHHHHHHHHHHHHHCHHHTC---------   
                   *->vvAKVgFgfilLrsravlertvavgsalaage<-*
                      v++K+++g +l ++r++le  +   + l+++    
  gi|9081913   445    VTTKIPYGELLTDARQILE--HK--PFLSDQQ    472  

Coq4: domain 1 of 1, from 459 to 481: score -0.3, E = 9.1
                   *->rrILkEkPRissetldlkkLrkL<-*
                      r+IL  kP  s  ++d kkL +L   
  gi|9081913   459    RQILEHKPFLSDQQVDIKKLMQL    481  

Glu_syn_central: domain 1 of 1, from 478 to 773: score 649.1, E = 7.9e-213
                CS    HHHHHHCTT--HHHHHCTCHHHHHHSS--EE-S---S--CCC-SS--
                   *->llrrQkAFGYTyEdvelvllPMAetGkEalGSMGdDtPLAVLSekpr
                      l+++Q+AFGYT+Edvelv+++MA+++kE++++MGdD+PL +LSek++
  gi|9081913   478    LMQLQTAFGYTNEDVELVIEHMASQAKEPTFCMGDDIPLSILSEKSH 524  

                CS -GGGCEEE----SSS----TTTTGGG-B--EEES--S-TTS-SGGGC-CE
                   lLYdYFKQlFAQVTNPPIDPIREelVMSLetylGpegNlLeptpeqarrl
                   +LYdYFKQ+FAQVTNP+IDP+RE+lVMSL+ ++G+++NlL+  p+ a+++
  gi|9081913   525 ILYDYFKQRFAQVTNPAIDPLRESLVMSLAIQIGHKSNLLDDQPTLAKHI 574  

                CS EESSSB--HHHHHH.HHHH....CCCCEEEEESEEESTTSTTCHHHHHHH
                   kLesPILsnselekmlknidairegfkaatIditFdveeGvdgLeaaLdr
                   kLesP+++++el++ + +     +++++  I+++F  e+G++ ++  + +
  gi|9081913   575 KLESPVINEGELNA-IFE-----SKLSCIRINTLFQLEDGPKNFKQQIQQ 618  

                CS HHHHHHHHHHCT-SEEEEESTCG--CTTEEE--HHHHHHHHHHHHHCTT-
                   lceeAeeAirsGaniivLSDRndildeervaIPaLLAvGAVHhHLIrkgL
                   lce A++Ai +G ni+vLSD+n+ ld+e+v+IP+LLAvGAVHhHLI kgL
  gi|9081913   619 LCENASQAILDGNNILVLSDKNNSLDSEKVSIPPLLAVGAVHHHLINKGL 668  

                CS CCC-EEEEEESS--SHHHHHHHHCTT-SEEEEHCCHHHHHHHHCCCCCCC
                   RtkvslvVETGEaREvHHFAvLiGYGAsAInPYLAyETirdWWlirrGll
                   R+ +s+ VET++++++HHFA+LiGYGAsAI+PYLA+ET r+WW + ++++
  gi|9081913   669 RQEASILVETAQCWSTHHFACLIGYGASAICPYLAFETARHWWSNPKTKM 718  

                CS CHTTTS- T--HHHHHHHHHHHHHHHHHHHHHCTT--BHHHHCCS--EEE
                   lmskGkl.elsleeavkNYrkAiekGlLKIMSKMGISTlqSYrGAQIFEA
                   lmskG+l++++++ea++NY+kA+e+GlLKI+SKMGIS+l+SY+GAQIFE+
  gi|9081913   719 LMSKGRLpACNIQEAQANYKKAVEAGLLKILSKMGISLLSSYHGAQIFEI 768  

                CS SSB-H   
                   vGLsk<-*
                   +GL++   
  gi|9081913   769 LGLGS    773  

Flavodoxin_NdrI: domain 1 of 1, from 488 to 497: score 2.1, E = 4.6
                CS    -HHHHHHHHH   
                   *->TneDVerVrk<-*
                      TneDVe V +   
  gi|9081913   488    TNEDVELVIE    497  

P22_AR_N: domain 1 of 1, from 524 to 541: score -0.2, E = 9.5
                   *->dVLydYWtrkGkAv..NPR<-*
                      ++LydY+  + +A  +NP+   
  gi|9081913   524    HILYDYFK-QRFAQvtNPA    541  

Cache_1: domain 1 of 1, from 537 to 557: score 7.0, E = 0.14
                   *->wTePYvdaalktgdlViTiaqPv<-*
                      +T+P++d +  +++lV ++a+++   
  gi|9081913   537    VTNPAIDPL--RESLVMSLAIQI    557  

Glu_synthase: domain 1 of 2, from 650 to 676: score 1.3, E = 3
                CS    --HHHHHHHHHHHHHCTT-CCCSEEEE   
                   *->lPwelgLaevhqtLvengLRdrVsLia<-*
                      +P  l++ +vh  L++ gLR + s+ +   
  gi|9081913   650    IPPLLAVGAVHHHLINKGLRQEASILV    676  

HdeA: domain 1 of 1, from 727 to 749: score 9.6, E = 0.015
                   *->ACk.QdkkAsFkdKvkaEldKvk<-*
                      AC  Q+ +A++k+ v+a l K+    
  gi|9081913   727    ACNiQEAQANYKKAVEAGLLKIL    749  

Sel1: domain 1 of 1, from 729 to 745: score 2.5, E = 7
                CS    .HHH.HHHHHHHHHHTT-   
                   *->DyekeAlkwyekAAeqGn<-*
                      ++++ A + y+kA e+G    
  gi|9081913   729    NIQE-AQANYKKAVEAGL    745  

DUF1981: domain 1 of 1, from 765 to 787: score 3.6, E = 3.3
                   *->iFgvltlaakeesesivklAfqiid.qi<-*
                      iF++l+l++       v+lAf+ +++qi   
  gi|9081913   765    IFEILGLGSEV-----VNLAFKGTTsQI    787  

tRNA_anti: domain 1 of 1, from 818 to 839: score 4.9, E = 2
                CS    EEEEEEETTSSTSTCTCTT..EEEEEEEEEEE   
                   *->tGkvkkrpggeqNnlkTGeKAlelvveeievl<-*
                      +G v+ rpgge          ++++ +e+      
  gi|9081913   818    YGFVQYRPGGE----------YHINNPEMSKA    839  

Cystatin: domain 1 of 1, from 826 to 859: score 2.4, E = 3.9
                CS    ECEEEEET.STSHHHHHHHHHHHHHHHHHSSSSEEEEE   
                   *->GglspvdpNendpevqealdfAlakyNeksndnylfel<-*
                      Gg   +++    pe  +al+ A+  yN +  +ny++ l   
  gi|9081913   826    GGEYHINN----PEMSKALHQAVRGYNPEYYNNYQSLL    859  

RNase_PH_C: domain 1 of 1, from 827 to 846: score 4.2, E = 2.3
                CS    SSSS.B.HHHHHHHHHHHHHH   
                   *->GkgnglteelleealelAkeg<-*
                      G +++++ +++ +al++A+ g   
  gi|9081913   827    G-EYHINNPEMSKALHQAVRG    846  

Glu_synthase: domain 2 of 2, from 830 to 1216: score 857.3, E = 9e-255
                CS    -SS-HHHHHHHHHHHHC--T-HHHHHHHHHHHHTS.-S-SGGGGEEE
                   *->hrnepeviktlqkavqvpveskpsydkYreplnertpigalrdlLef
                      h n+pe++k l++av+    +   y +Y+ +l +r p++alrdlL++
  gi|9081913   830    HINNPEMSKALHQAVRG--YNPEYYNNYQSLLQNR-PPTALRDLLKL 873  

                CS --SS--......--GGGS--HHHHHTTEEEEEB-CTTC-HHHHHHHHHHH
                   kyaeepldtdkiipieevepaleikkrfctgaMSyGALSeeAheALAiAm
                    ++++p      i+i+eve+++ i + fctg+MS+GALS+e+he+LAiAm
  gi|9081913   874 QSNRAP------ISIDEVESIEDILQKFCTGGMSLGALSRETHETLAIAM 917  

                CS HHCT-EEEETTT---GGGCSB-TTS-T S BTTSTT--S--TT-B---SE
                   nriGtksNtGEGGedperlkpaadlds.G.SpTlpHLkGLqnednarSAI
                   nriG+ksN+GEGGedp r+k + d++s+G+Sp lpHLkGL+n+d+a+SAI
  gi|9081913   918 NRIGGKSNSGEGGEDPVRFKILNDVNSsGtSPLLPHLKGLKNGDTASSAI 967  

                CS EEE-TT-TT--............HHHHCC-SEEEEE---TTSTTT--EE-
                   kQvASGRFGVtkRnGefWeefkRseYLvnAdalEIKiAQGAKPGeGGhLP
                   kQ+ASGRFGVt            +eYL+nA++lEIKiAQGAKPGeGG+LP
  gi|9081913   968 KQIASGRFGVT------------PEYLMNAKQLEIKIAQGAKPGEGGQLP 1005 

                CS GGG--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-.TTS
                   GeKVspeIAriRnstPGvgliSPpPHHDIysiEDLaqLIydLkeindpkA
                   G+K+sp+IA +R ++PGv liSPpPHHDIysiEDL+qLI+dL++in pkA
  gi|9081913  1006 GKKISPYIATLRKCKPGVPLISPPPHHDIYSIEDLSQLIFDLHQIN-PKA 1054 

                CS EEEEEEE-STTHHHHHHH...HHHTT-SEEEEE-TT---SSEECCHHHHC
                   pisVKLVsehgvgtiaaGhmqvakAnADiIlIdGhdGGTGASpktsikha
                   +isVKLVse g+gtiaaG   vak+nADiI+I+GhdGGTGASp++sikha
  gi|9081913  1055 KISVKLVSEIGIGTIAAG---VAKGNADIIQISGHDGGTGASPLSSIKHA 1101 

                CS ---HHHHHHHHHHHHHCTT-CCCSEEEEESS--SHHHHHHHHHCT-SEEE
                   GlPwelgLaevhqtLvengLRdrVsLiadGGLrTGaDVakAaaLGAdavg
                   G PwelgL+evhq+L en+LRdrV+L++dGGLrTG D+++Aa++GA+++g
  gi|9081913  1102 GSPWELGLSEVHQLLAENQLRDRVTLRVDGGLRTGSDIVLAAIMGAEEFG 1151 

                CS -SHHHHHHCT--S---CCCT--TTSSS---CCHH..CT----HHHHHHHH
                   iGTaaLiAlGCimaRvCHtntCPvGvATQDPeLrKrlkfegaperVvNyf
                   +GT+a+iA+GCimaR+CHtn+CPvGvATQ++eLr   +f g+pe +vN+f
  gi|9081913  1152 FGTVAMIATGCIMARICHTNKCPVGVATQREELR--ARFSGVPEALVNFF 1199 

                CS HHHHHHHHHHHHHHT-S   
                   iflaeEvrellaqlGfr<-*
                   +f+  Evre+la+lG++   
  gi|9081913  1200 LFIGNEVREILASLGYK    1216 

DUF258: domain 1 of 1, from 839 to 860: score 0.3, E = 8.3
                CS    HHHHHHHCTSS-HHHHHHHHHHHH   
                   *->AVkaAveeGeIseeRYesYlklle<-*
                      A+ +Av    +++e Y++Y+ ll+   
  gi|9081913   839    ALHQAVR--GYNPEYYNNYQSLLQ    860  

Pencillinase_R: domain 1 of 1, from 856 to 894: score 3.9, E = 2.5
                CS    XXXXXXXXXXXXXXXXXXX    XXXXXXXXXXXXXXXX   
                   *->drlfggsvgalvanfleee....klSeddieeLrelLde<-*
                      + l++++++ ++ ++l+ ++++ ++S d++e ++++L++   
  gi|9081913   856    QSLLQNRPPTALRDLLKLQsnraPISIDEVESIEDILQK    894  

SelT: domain 1 of 1, from 872 to 885: score 3.1, E = 2.2
                   *->KLqtGrvYAPPtpqEL<-*
                      KLq++r   P++++E+   
  gi|9081913   872    KLQSNRA--PISIDEV    885  

Nitro_FeMo-Co: domain 1 of 1, from 879 to 897: score 2.1, E = 5.3
                CS    EEE-TTSSBHHHHHHHHHC   
                   *->pikagegetieeaiealqe<-*
                      pi   e e+ie+ + ++ +   
  gi|9081913   879    PISIDEVESIEDILQKFCT    897  

DUF37: domain 1 of 1, from 927 to 934: score 3.0, E = 4.5
                   *->hpGGyDPV<-*
                      ++GG DPV   
  gi|9081913   927    GEGGEDPV    934  

Scm3: domain 1 of 1, from 953 to 963: score 2.2, E = 3.5
                   *->HLraLeteddi<-*
                      HL++L+++d++   
  gi|9081913   953    HLKGLKNGDTA    963  

cobW: domain 1 of 1, from 1038 to 1058: score 5.1, E = 0.45
                CS    ...HHHHHHHHHH-SSS-EEE   
                   *->adlekleadlrrlnpeapiip<-*
                      +dl++l+ dl+++np+a+i     
  gi|9081913  1038    EDLSQLIFDLHQINPKAKISV    1058 

Arch_flagellin: domain 1 of 1, from 1050 to 1072: score 4.1, E = 0.66
                   *->inpstkvrgeVvpenGapgtief<-*
                      inp  k+++++v+e+G+ ++      
  gi|9081913  1050    INPKAKISVKLVSEIGIGTIAAG    1072 

DUF1393: domain 1 of 1, from 1055 to 1068: score 3.1, E = 2
                   *->klSvKtVVAiGIGA<-*
                      k+SvK V  iGIG+   
  gi|9081913  1055    KISVKLVSEIGIGT    1068 

FtsK_SpoIIIE: domain 1 of 1, from 1107 to 1143: score 2.6, E = 3.1
                   *->lviDnydeLaeenlL.ervtsLknqGlsygvhvmata<-*
                      l++ + ++L +en+L++rvt+ + +Gl +g +++++a   
  gi|9081913  1107    LGLSEVHQLLAENQLrDRVTLRVDGGLRTGSDIVLAA    1143 

FMN_dh: domain 1 of 1, from 1109 to 1148: score 3.2, E = 0.89
                CS    HHHHHHHHHCHHTTTSSEEEEESS-SSHHHHHHHHHHTSS   
                   *->LpeVvPIlkeaAvkgdieVllDgGvRRGtDVlKALALGAr<-*
                      L eV  +l e  + +++   +DgG R+G+D++ A  +GA+   
  gi|9081913  1109    LSEVHQLLAENQLRDRVTLRVDGGLRTGSDIVLAAIMGAE    1148 

DSRB: domain 1 of 1, from 1120 to 1134: score 2.7, E = 2.7
                   *->mKvndrvtvKtDGgpR<-*
                       ++ drvt + DGg R   
  gi|9081913  1120    -QLRDRVTLRVDGGLR    1134 

Phage_Mu_P: domain 1 of 1, from 1122 to 1131: score -0.4, E = 10
                   *->sntVtLrvgG<-*
                       ++VtLrv+G   
  gi|9081913  1122    RDRVTLRVDG    1131 

Hormone_4: domain 1 of 1, from 1168 to 1176: score 4.4, E = 2.5
                CS    X-TT--TT-   
                   *->CyirnCPrG<-*
                      C  + CP+G   
  gi|9081913  1168    CHTNKCPVG    1176 

GDC-P: domain 1 of 1, from 1205 to 1225: score 7.1, E = 0.086
                   *->eqqeMLstiGlssLddLidat<-*
                      e++e+L+++G++sLdd ++++   
  gi|9081913  1205    EVREILASLGYKSLDDITGQN    1225 

PspB: domain 1 of 1, from 1268 to 1276: score 0.4, E = 8.4
                   *->MsaffLagP<-*
                      M+ ++La+P   
  gi|9081913  1268    MDDDILAIP    1276 

T5orf172: domain 1 of 1, from 1271 to 1293: score 2.0, E = 6.1
                   *->dvvalievedaraklEklLHkrFk<-*
                      d+ a+ ev++a  klE+++ k+Fk   
  gi|9081913  1271    DILAIPEVSNAI-KLETEITKHFK    1293 

CAP_C: domain 1 of 1, from 1283 to 1292: score 1.3, E = 7.4
                CS    EEEEEE----   
                   *->KLvTevveha<-*
                      KL+Te++ h    
  gi|9081913  1283    KLETEITKHF    1292 

GXGXG: domain 1 of 1, from 1290 to 1485: score 367.3, E = 2.7e-107
                CS    EEEEE-TT--STTHHHHHHHHHHCTTTS.S-TTCEEEEEEEEE-TTT
                   *->keeaiiNtdrlvgtrlsgeiakkygeegalpkdtgkivfnGsAGqsf
                      k+++i Nt+r+vgtrlsg iak yg+ g + k+ +k++f+GsAGqsf
  gi|9081913  1290    KHFKIANTNRTVGTRLSGIIAKNYGNTG-F-KGLIKLNFYGSAGQSF 1334 

                CS TTT-BTTEEEEEEEEE-S.TTTTT-ECCEEEEE--TT-.......SS-GG
                   GafmagGvtLeleGdAnddyvGkgmsGGeIvikgnagdpvGnnMdageyv
                   Gaf+a+G++L l+G+And yvGkgm+GG+Ivi+++ag         +e +
  gi|9081913  1335 GAFLASGINLKLMGEAND-YVGKGMNGGSIVIVPPAGT-------IYEDN 1376 

                CS GSEEC-SSTTTT--CEEEEESSEE-TTTTTT-.....CCEEEEESEB.-S
                   gnviaGNtclyGatGGkifiaGdAGerfgvrnkayKdsgatiVveGvaGd
                   ++vi+GNtclyGatGG++f++G+AGerf+vrn     s a+ VveGv Gd
  gi|9081913  1377 NQVIIGNTCLYGATGGYLFAQGQAGERFAVRN-----SLAESVVEGV-GD 1420 

                CS STTTT-EEEEEEESS-B-SSBTTT--CCEEEEE-TTS.......THHHHB
                   hggEYMtGGtivVlGdaGrnvGagMtGGiaYvlgeiedfsyMiatlpgkv
                   h++EYMtGG+ivVlG+aGrnvGagMtGG+aY+l+e+e        + ++v
  gi|9081913  1421 HACEYMTGGVIVVLGKAGRNVGAGMTGGLAYFLDEDE-------NFIDRV 1463 

                CS -CCCEEEE...ES-S......CCHHHHHHHH   
                   nleiVeledlkrievkrkklLpegekqlkel<-*
                   n+eiV+ +   r+ +      ++ge+qlk+l   
  gi|9081913  1464 NSEIVKIQ---RVIT------KAGEEQLKNL    1485 

DUF1514: domain 1 of 1, from 1453 to 1469: score 3.5, E = 5.7
                   *->LeeyrieveRikkevkk<-*
                      L e+++ ++R++ e+ k   
  gi|9081913  1453    LDEDENFIDRVNSEIVK    1469 

Colicin: domain 1 of 1, from 1456 to 1467: score 1.4, E = 7.5
                CS    SHHHHHHHHHCH   
                   *->DdkfveklNkli<-*
                      D++f++ +N +i   
  gi|9081913  1456    DENFIDRVNSEI    1467 

Ribosomal_S6: domain 1 of 1, from 1461 to 1481: score 3.3, E = 3.7
                CS    CCHHHHHHHHHHHHHCTT-EE   
                   *->EqvkqeiekYqkvLtnngAei<-*
                      ++v++ei k+q+v+t++g+e+   
  gi|9081913  1461    DRVNSEIVKIQRVITKAGEEQ    1481 

BicD: domain 1 of 1, from 1465 to 1481: score -1.6, E = 6.8
                   *->gqaysnqrkvAkdGeer<-*
                       + +++qr+ +k Gee+   
  gi|9081913  1465    SEIVKIQRVITKAGEEQ    1481 

PUF: domain 1 of 1, from 1470 to 1486: score 6.5, E = 0.47
                   *->lQkllevateeqkqlil<-*
                      +Q+++++a+eeq ++++   
  gi|9081913  1470    IQRVITKAGEEQLKNLI    1486 

DUF477: domain 1 of 1, from 1472 to 1495: score 3.8, E = 1.7
                   *->gtLspserarLeqalaalEqktga<-*
                      ++++++  ++L   ++  ++ktg+   
  gi|9081913  1472    RVITKAGEEQLKNLIENHAAKTGS    1495 

Phage_prot_Gp6: domain 1 of 1, from 1479 to 1492: score 1.0, E = 4
                   *->eEmikkFidkHklr<-*
                      eE +k++i+ H+++   
  gi|9081913  1479    EEQLKNLIENHAAK    1492 

IBN_N: domain 1 of 1, from 1498 to 1516: score 8.2, E = 0.17
                CS    HHHHHHHHHCCTHHCHHHHH   
                   *->AEkqLeqlekqklPgfllaL<-*
                      A++ Le+++++ lP+f++ +   
  gi|9081913  1498    AHTILEKWNSY-LPQFWQVV    1516 

GspM: domain 1 of 1, from 1506 to 1520: score 1.0, E = 8.6
                CS    XXXXXXXXXXXXXXX   
                   *->mneLqawWqgrspRE<-*
                      ++ L ++Wq ++p+E   
  gi|9081913  1506    NSYLPQFWQVVPPSE    1520 

//
BioPerl-1.007002/t/data/hmmpfam_fake.out000555000766000024       523013155576321 20037 0ustar00cjfieldsstaff000000000000hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:                 pfam
Sequence file:            /home/birney/src/wise2/example/road.pep
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query:  roa1_drome  

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
SEED                                                    146.1    6.3e-40   2
TEST                                                      5.0        7.2   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
SEED       1/2      33   103 ..     1    77 []    71.2  2.2e-17
SEED       2/2     124   194 ..     1    77 []    75.5  1.1e-18

Alignments of top-scoring domains:
SEED: domain 1 of 2, from 33 to 103: score 71.2, E = 2.2e-17
                   *->lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGf
                      lf+g+L + +t+e Lk++F+k G iv++ +++D     + t++s+Gf
  roa1_drome    33    LFIGGLDYRTTDENLKAHFEKWGNIVDVVVMKD-----PRTKRSRGF 74   

                   aFVeFeseedAekAlealnG.kelggrklrv<-*
                   +F+++  ++  + A +    +++++gr+++    
  roa1_drome    75 GFITYSHSSMIDEAQK--SRpHKIDGRVVEP    103  

SEED: domain 2 of 2, from 124 to 194: score 75.5, E = 1.1e-18
                   *->lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGf
                      lfVg L  d +e+ ++d+F++fG iv+i+iv+D     ketgk +Gf
  roa1_drome   124    LFVGALKDDHDEQSIRDYFQHFGNIVDINIVID-----KETGKKRGF 165  

                   aFVeFeseedAekAlealnGkelggrklrv<-*
                   aFVeF++++ ++k +     ++l+g+ + v   
  roa1_drome   166 AFVEFDDYDPVDKVVL-QKQHQLNGKMVDV    194  

//
Query:  roa2_drome  

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
SEED                                                    146.1    6.3e-40   2

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
SEED       1/2      33   103 ..     1    77 []    71.2  2.2e-17
SEED       2/2     124   194 ..     1    77 []    75.5  1.1e-18
//BioPerl-1.007002/t/data/hmmpfam_multiresult.out000444000766000024      1151113155576321 21536 0ustar00cjfieldsstaff000000000000hmmpfam - search one or more sequences against HMM database
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:                 testInput.hmm
Sequence file:            testInput.fasta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query sequence: Test
Accession:      [none]
Description:    [none]

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
TEST                                                    184.7    2.5e-56   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
TEST       1/1       8    97 .]     1    95 []   184.7  2.5e-56

Alignments of top-scoring domains:
TEST: domain 1 of 1, from 8 to 97: score 184.7, E = 2.5e-56
                   *->svfqqqqssksttgstvtAiAiAigYRYRYRAvtWnsGsLssGvnDn
                      sv+qqqq+  +    +vtAiAiAigYRYRYRAv Wn GsLs G nDn
        Test     8    SVYQQQQGGSA----MVTAIAIAIGYRYRYRAVVWNKGSLSTGTNDN 50   

                   DnDqqsdgLYtiYYsvtvpssslpsqtviHHHaHkasstkiiikiePr<-
                   DnDq +d LYtiYYsvtv +ss+p q+v+HHHaH+asstkiiiki P   
        Test    51 DNDQAAD-LYTIYYSVTVSASSWPGQSVTHHHAHPASSTKIIIKIAPS   97   

                   *
                    
        Test     -   -    

//
Sequence 0

Query sequence: lcl|gi|340783625|Plus1
Accession:      [none]
Description:    megaplasmid, complete sequence [UNKNOWN]

Scores for sequence family classification (score includes all domains):
Model                Description                        Score    E-value  N 
--------             -----------                        -----    ------- ---
IS66_ORF3.uniq                                          -30.0    1.7e-15   1

Parsed for domains:
Model                Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------             ------- ----- -----    ----- -----      -----  -------
IS66_ORF3.uniq         1/1   60792 61184 ..     1   558 []   -30.0  1.7e-15

Alignments of top-scoring domains:
IS66_ORF3.uniq: domain 1 of 1, from 60792 to 61184: score -30.0, E = 1.7e-15
                   *->mSSPLDLSLFPNLmtevvkmnaalpddlslLkAalqkqQavvea..l
                          L  S FP + +      aa+p+ l +    l    + v  + +
  lcl|gi|340 60792    SCTGLWDSEFPPVFPVNGSQRAATPF-LPVGPDELSSPPSSVLXscY 60837

                   dakianleelIEkLka.qldkLRRmkFGkrSEKkRhkLeldiaQiekale
                   d  +     l  +L ++q   LR    ++r                    
  lcl|gi|340 60838 DFPLCQSLSLCFRLGFpQALALRVRQRAPRGCH----------------- 60870

                   dLEddLnetqaeiaeaekkieaPAssppkeaPiaskPesPRqerkRkPLP
                         +  +a+    +      A+ +p++            + +   LP
  lcl|gi|340 60871 ------AHRRARGLFFTDTPHPVAVPRPQR----------DLTGSLVTLP 60904

                   eeLPReerRlePestvCPcggGqLkriGEDvsEqLDlvpaaFeVIqTvRp
                   + +P  e    P + + P             + + D vp+  +       
  lcl|gi|340 60905 APMPCSET---PVESQHPGH-----------TGRSDAVPTPNTMKTS--- 60937

                   KyACrqCdtiVQAPaPakpIErGiptaGLLArvlVSKyaEHlPLYRQsEI
                                                                     
  lcl|gi|340     - -------------------------------------------------- -    

                   yaRqGVeiaRstLadWVgrtgarLaPLvdALaeyVLkeGklHADeTPVqV
                         +i  s L   V++ + r                           
  lcl|gi|340 60938 ------AIMISGLIHGVSARCLRF-------------------------- 60955

                   LaPGnkKTKTGyLWAYvRDDRnagsSlppaVvfayspdRkGEHaqvhLae
                        k   TG      R D     Slp+ +    +  R G        e
  lcl|gi|340 60956 -----KRSVTG-----PRQD-----SLPADGL---RLCREG-------VE 60980

                   ysGkLqaDAyaGYnalyesgRVGGDpikEAgCwAHaRRKifDlhvrnpSe
                    sG      +   +   +           ++ wAH RR ++D+    pS+
  lcl|gi|340 60981 PSGSQXKVSVTSILLSRTXP---------VASWAHVRRHFYDVNQGAPSP 61021

                   lteEALerIaaLYeIEaeIRGspaEdRlavRqelSvPlvkslseWLtaqr
                    ++ AL rI +LYeIEaeI   p+E+    Rq+++ Pl+ s+  WL   r
  lcl|gi|340 61022 VAQTALLRIHELYEIEAEIKDDPPEQKMLARQQRAAPLLESFWTWLNDTR 61071

                   KtlsrgseLAKALaYlLnrWdALtryldDGqVpIDNNivENAiRrvAlGR
                     +  +s+ AKA  Y+L+rW ALt+yl+ G+  IDNN vE A+R vA+GR
  lcl|gi|340 61072 AQVAPKSAIAKAIGYALKRWKALTLYLQEGHLGIDNNPVERALRGVAIGR 61121

                   kNyLFaGSDrGGeraAliySLIgTCKmNgVePyaYLrdVltrLadwplnk
                   kN+LFaG D GGeraA++y LI TCK+NgVeP aYL+dVl++L++wp  +
  lcl|gi|340 61122 KNFLFAGNDAGGERAAAFYTLIETCKLNGVEPFAYLCDVLEKLPTWPNKR 61171

                   DideLLPWayasai<-*
                     +eLLPW++       
  lcl|gi|340 61172 -LHELLPWNWKNLT    61184

//
Sequence 1
BioPerl-1.007002/t/data/hmmscan.out000444000766000024      2732613155576321 17101 0ustar00cjfieldsstaff000000000000# hmmscan :: search sequence(s) against a profile database
# HMMER 3.0 (March 2010); http://hmmer.org/
# Copyright (C) 2010 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             BA000019.orf1.fasta
# target HMM database:             /data/biodata/HMMerDB/Pfam.hmm
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       BA000019.orf1  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-30  105.2   0.3    6.7e-30  105.0   0.2    1.0  1  Peripla_BP_2    Periplasmic binding protein
  ------ inclusion threshold ------
      0.036   14.7   0.0       0.09   13.4   0.0    1.7  1  DUF2726         Protein of unknown function (DUF2726)
      0.039   14.1   0.3      0.049   13.8   0.2    1.1  1  Pfam-B_1590     
       0.22   12.5   0.0       0.33   12.0   0.0    1.3  1  Pfam-B_6580     
       0.25   12.1   0.2       0.37   11.5   0.2    1.2  1  Calpain_III     Calpain large subunit, domain III
       0.42   11.5   1.2        1.7    9.5   0.1    2.3  3  MHCassoc_trimer Class II MHC-associated invariant chain trim
        1.2    9.2   2.2        1.3    9.1   1.5    1.1  1  DUF3498         Domain of unknown function (DUF3498)


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.2   1.5e-33   6.7e-30      59     236 ..       2     173 ..       1     175 [. 0.93

  Alignments for each domain:
  == domain 1    score: 105.0 bits;  conditional E-value: 1.5e-33
   Peripla_BP_2  59 lkPDlvivsafgalvseieellelgipvvavessstaeslleqirllgellgeedeaeelvaelesridavkaridsl.kpktvlvfgyadegikv 153
                    lkPDl+i+ +++   ++i+++l++ +p+v v+  s+  s+++ +r ++++l+ee++++ + +++++ri+++++r  +  ++ +v+v+g+++ +ik+
  BA000019.orf1   2 LKPDLIIGREYQ---KNIYNQLSNFAPTVLVDWGSF-TSFQDNFRYIAQVLNEEEQGKLVLQQYQKRIRDLQDRMGERlQKIEVSVIGFSGQSIKS 93 
                    8***********...********************9.*****************************************999999999999997777 PP

   Peripla_BP_2 154 vfgsgswvgdlldaaggeni.iaeakgseseeisaEqilaadpdviivsgrgedtktgveelkenplwaelpAvkngrvyllds 236
                    ++  +  ++++ld+ag++ i i++++++ + eis+E+++++d+dv++v       k+ +   ++nplw +l+Avk+++vy++++
  BA000019.orf1  94 LNR-DAVFNQVLDDAGIKRIsIQKNQQERYLEISIENLNKYDADVLFVINE---SKEQLYPDLKNPLWHHLRAVKKQQVYVVNQ 173
                    776.5678999999****99777777*************************...77777777899***************9976 PP

>> DUF2726  Protein of unknown function (DUF2726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     2e-05      0.09      79     112 ..      86     119 ..      79     130 .. 0.75

  Alignments for each domain:
  == domain 1    score: 13.4 bits;  conditional E-value: 2e-05
        DUF2726  79 ashkqgkaekrDalkeealekAgipllrvkakks 112
                    +s ++ k  +rDa+++++l+ Agi+ + +++ ++
  BA000019.orf1  86 FSGQSIKSLNRDAVFNQVLDDAGIKRISIQKNQQ 119
                    4555777999****************99954433 PP

>> Pfam-B_1590  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.1e-05     0.049       6     102 ..      78     169 ..      74     195 .. 0.75

  Alignments for each domain:
  == domain 1    score: 13.8 bits;  conditional E-value: 1.1e-05
    Pfam-B_1590   6 risafinlfiGqsvsrktivnail.slleqkGflkrswnkinlpctyvnlsieriskfdflpilskikgkeisyklyGeteWqtidklLlnvnkhk 100
                    +i   +  f Gqs++  +  +a++  +l++ G  + s +k n    y+++sie+++k+d   ++   + ke +y  + +  W+++      v+k++
  BA000019.orf1  78 KIEVSVIGFSGQSIKSLNR-DAVFnQVLDDAGIKRISIQK-NQQERYLEISIENLNKYDADVLFVINESKEQLYPDLKNPLWHHLR----AVKKQQ 167
                    5666666789999876554.34441578999999999988.56789*************98888888899****999999997654....444444 PP

    Pfam-B_1590 101 af 102
                    ++
  BA000019.orf1 168 VY 169
                    44 PP

>> Pfam-B_6580  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.2e-05      0.33      36      89 ..      70     124 ..      61     139 .. 0.83

  Alignments for each domain:
  == domain 1    score: 12.0 bits;  conditional E-value: 7.2e-05
    Pfam-B_6580  36 ewLedrlataaaAalvldalqseelpr.alqrelLeaigakavvlrkdqtrrlla 89 
                    +++ +rl+++++  +   +   + l+r a+ +++L+ +g+k + ++k+q+ r l 
  BA000019.orf1  70 DRMGERLQKIEVSVIGFSGQSIKSLNRdAVFNQVLDDAGIKRISIQKNQQERYLE 124
                    5677889999999999999988888862699******************999764 PP

>> Calpain_III  Calpain large subunit, domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   8.1e-05      0.37      25      91 ..      35     102 ..      31     129 .. 0.75

  Alignments for each domain:
  == domain 1    score: 11.5 bits;  conditional E-value: 8.1e-05
    Calpain_III  25 etfltNPqfrlslkepddedctvliaLmqknrrkkrkk.geenltigfavykv.kkkekeldkeffkkn 91 
                     +f +N  +  ++ +++++  +++++ +qk+ r ++   ge++  i+++v+   +++ k+l+++++ ++
  BA000019.orf1  35 TSFQDNFRYIAQVLNEEEQ-GKLVLQQYQKRIRDLQDRmGERLQKIEVSVIGFsGQSIKSLNRDAVFNQ 102
                    48999**********9987.7999999999988776655888888999998887777788888766555 PP

>> MHCassoc_trimer  Class II MHC-associated invariant chain trimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.3     2e+04      41      49 ..      29      37 ..      27      41 .. 0.78
   2 ?    0.1   0.0      0.35   1.6e+03       4      36 ..      51      81 ..      49      96 .. 0.74
   3 ?    9.5   0.1   0.00038       1.7       9      43 ..     139     176 ..     131     178 .. 0.73

  Alignments for each domain:
  == domain 1    score: -3.5 bits;  conditional E-value: 4.3
                     HHHHHHHHH CS
  MHCassoc_trimer 41 vdWksfEsW 49
                     vdW sf s+
    BA000019.orf1 29 VDWGSFTSF 37
                     689999886 PP

  == domain 2    score: 0.1 bits;  conditional E-value: 0.35
                     HHHHHHHHHHH-TT---------HHHHHHHHHH CS
  MHCassoc_trimer  4 edqvkhLllksdPkkvfPqlketlleNLksLKk 36
                     e+q k  l++ +  k   +l++ + e L+++  
    BA000019.orf1 51 EEQGKLVLQQYQ--KRIRDLQDRMGERLQKIEV 81
                     556666677777..7789999999999998765 PP

  == domain 3    score: 9.5 bits;  conditional E-value: 0.00038
                      HHHHHH-TT---------HHHHHHHHHHH....S-HHHH CS
  MHCassoc_trimer   9 hLllksdPkkvfPqlketlleNLksLKkt....mdevdW 43 
                        + +s+ ++++P+lk+ l + L++ Kk+    ++++dW
    BA000019.orf1 139 FVINESK-EQLYPDLKNPLWHHLRAVKKQqvyvVNQSDW 176
                      5556666.899****************973443456666 PP

>> DUF3498  Domain of unknown function (DUF3498)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.5   0.00029       1.3     395     425 ..      43      73 ..      35     137 .. 0.81

  Alignments for each domain:
  == domain 1    score: 9.1 bits;  conditional E-value: 0.00029
                    ------------------------------- CS
        DUF3498 395 yErRLlsQeeQaqklLleYqaRLedseeRLR 425
                    y +  l  eeQ + +L++Yq+R+ d ++R+ 
  BA000019.orf1  43 YIAQVLNEEEQGKLVLQQYQKRIRDLQDRMG 73 
                    66788999*****************999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues)
Target model(s):                       31912  (6698792 nodes)
Passed MSV filter:                      1891  (0.0592567); expected 638.2 (0.02)
Passed bias filter:                     1237  (0.0387628); expected 638.2 (0.02)
Passed Vit filter:                       100  (0.00313362); expected 31.9 (0.001)
Passed Fwd filter:                         7  (0.000219353); expected 0.3 (1e-05)
Initial search space (Z):              31912  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.74u 0.55s 00:00:01.29 Elapsed: 00:00:07.01
# Mc/sec: 189.21
//
Query:       lcl|Test_ID.1|P1  [L=463]
Description: 281521..282909 
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-06   19.9   1.5    4.3e-06   18.9   1.0    1.4  1  IS4.original 
    2.3e-06   19.7   1.5    4.3e-06   18.8   1.0    1.4  1  IS4.original 


Domain annotation for each model (and alignments):
>> IS4.original  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.0   8.9e-08   4.3e-06     315     353 ..     335     369 ..     318     391 .. 0.75

  Alignments for each domain:
  == domain 1    score: 18.9 bits;  conditional E-value: 8.9e-08
      IS4.original 315 filatnlddeldaediaelYrlRwqiElfFrelKsllgl 353
                         lat+  +el+ae+i+ lY +Rw+iE +F+ lK   ++
  lcl|Test_ID.1|P1 335 LLLATE--TELSAEEILRLYARRWGIEPLFHNLKR--WW 369
                       345555..**************************7..44 PP

>> IS4.original  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   1.0     9e-08   4.3e-06     315     353 ..     335     369 ..     318     391 .. 0.75

  Alignments for each domain:
  == domain 1    score: 18.8 bits;  conditional E-value: 9e-08
      IS4.original 315 filatnlddeldaediaelYrlRwqiElfFrelKsllgl 353
                         lat+  +el+ae+i+ lY +Rw+iE +F+ lK   ++
  lcl|Test_ID.1|P1 335 LLLATE--TELSAEEILRLYARRWGIEPLFHNLKR--WW 369
                       345555..**************************7..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues)
Target model(s):                          96  (37031 nodes)
Passed MSV filter:                        16  (0.166667); expected 1.9 (0.02)
Passed bias filter:                       16  (0.166667); expected 1.9 (0.02)
Passed Vit filter:                         9  (0.09375); expected 0.1 (0.001)
Passed Fwd filter:                         2  (0.0208333); expected 0.0 (1e-05)
Initial search space (Z):                 96  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.03u 0.02s 00:00:00.04 Elapsed: 00:00:00.06
# Mc/sec: 276.54
//
BioPerl-1.007002/t/data/hmmscan_multi_domain.out000444000766000024      1555713155576321 21645 0ustar00cjfieldsstaff000000000000# hmmscan :: search sequence(s) against a profile database
# HMMER 3.0 (March 2010); http://hmmer.org/
# Copyright (C) 2010 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             BA000019.orf37.fasta
# target HMM database:             /data/biodata/HMMerDB/Pfam-A.hmm
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       BA000019.orf37  [L=1418]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-32  111.0  11.8    7.6e-20   71.3   2.3    6.4  6  PPC             Bacterial pre-peptidase C-terminal domain
    4.7e-13   47.9  92.9     0.0022   17.8   3.3   10.0  3  HemolysinCabind Hemolysin-type calcium-binding repeat (2 cop


Domain annotation for each model (and alignments):
>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.16   9.3e+02       4      59 ..     117     183 ..      84     192 .. 0.58
   2 ?   -0.6   0.0      0.36   2.1e+03      12      58 ..     347     388 ..     311     397 .. 0.46
   3 !   71.3   2.3   1.3e-23   7.6e-20       1      69 [.     470     549 ..     470     550 .. 0.95
   4 ?   -3.2   0.1         2   1.2e+04      15      25 ..     582     603 ..     567     626 .. 0.51
   5 ?   -1.1   0.6       0.5     3e+03      13      36 ..     987    1019 ..     974    1072 .. 0.49
   6 !   54.4   1.0   2.4e-18   1.4e-14       1      69 [.    1087    1168 ..    1087    1169 .. 0.85

  Alignments for each domain:
  == domain 1    score: 0.5 bits;  conditional E-value: 0.16
                     EEEE--S----EEEEEECTSS...EEEEE.EEEES.E.SSSSTTC--...-B--SEEEEEESS..... CS
             PPC   4 vykfevpaggsltididggsg...dldLy.lldgngp.slaaydans...apsgndeyiefta....p 59 
                     + +f+++ag+ ++i  d++s     ++L  +++++ +  ++ +  n+   +  gn+++++ft     p
  BA000019.orf37 117 TATFTLEAGDDYSIG-DSSSEvtfYASLEeVPTPSVTpEISLSVENAtisEAEGNTTTLRFTLseppP 183
                     446667777766665.4444222222244455555322222222222233455566777777755544 PP

  == domain 2    score: -0.6 bits;  conditional E-value: 0.36
                     ---EEEEEECTSSEEEEEEEEES.ESSSSTTC---B--SEEEEEESS CS
             PPC  12 ggsltididggsgdldLylldgngpslaaydansapsgndeyiefta 58 
                     g  +++  + g+ dl+++   +  +   ++d  +    +de++ f+ 
  BA000019.orf37 347 GEIVAVR-SDGF-DLKITAKSATIQLPIQADGVA---ESDEQVVFSL 388
                     1112222.2233.444444444444444433333...2556666665 PP

  == domain 3    score: 71.3 bits;  conditional E-value: 1.3e-23
                     -EEEEEE--S----EEEEEECTSS......EEEEEEEEES.ESSSSTTC--.....-B--SEEEEEESS.----EEEEEE CS
             PPC   1 dvDvykfevpaggsltididggsg......dldLylldgngpslaaydans.....apsgndeyieftapqaGtYyvaVs 69 
                     dvD+yk+e++ag++++id+d++++      d++L+l+d +g+ la++d+ +     + sg ++yieftap++G+Yyv+V+
  BA000019.orf37 470 DVDFYKVELKAGDTIKIDTDSNQFadgrkvDTWLRLFDVSGTELASNDDGAapnevFDSGFQSYIEFTAPSDGVYYVGVT 549
                     8******************999999***99999******************8888877789*****************96 PP

  == domain 4    score: -3.2 bits;  conditional E-value: 2
                     EEEEEECTSS...........E CS
             PPC  15 ltididggsg...........d 25 
                     l+i++++ +g           +
  BA000019.orf37 582 LNISLNNPTGfvagateippgN 603
                     5555555544333333333331 PP

  == domain 5    score: -1.1 bits;  conditional E-value: 0.5
                      --.EEEEEECTSS.....EEEEEEEEES....E CS
             PPC   13 gs.ltididggsg.....dldLylldgng...p 36  
                      +  l+++i + ++      ++ +ll g+g   +
  BA000019.orf37  987 TAsLSVAIANDNIaegveTATVTLLAGDGyqiN 1019
                      444777775555555665444555555542221 PP

  == domain 6    score: 54.4 bits;  conditional E-value: 2.4e-18
                      -EEEEEE--S----EEEEEECTSSEEE.....EEEEEES.E.....SSSSTTC--...-B--SEEEEEESS.----EEEEEE CS
             PPC    1 dvDvykfevpaggsltididggsgdld.....Lylldgngp.....slaaydans...apsgndeyieftapqaGtYyvaVs 69  
                      dvD+yk+++++g +l+i++d   +d++     L+++d++g+     + ++++a++   ++  nd+y+efta ++GtYyv++s
  BA000019.orf37 1087 DVDLYKVNLKVGEKLSINVDAAEIDSKllyaqLRVFDAEGNelaktDFDDFQAAPdevFSAFNDPYLEFTAETTGTYYVGIS 1168
                      8***********************9999788888*****96222225555777777777777******************98 PP

>> HemolysinCabind  Hemolysin-type calcium-binding repeat (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.5    0.0026        16       2      13 ..    1214    1225 ..    1213    1225 .. 0.89
   2 !   10.8   3.1   6.8e-05      0.41       1      18 []    1231    1248 ..    1231    1248 .. 0.95
   3 !   11.4   2.4   4.3e-05      0.26       4      18 .]    1243    1257 ..    1240    1257 .. 0.91

  Alignments for each domain:
  == domain 1    score: 5.9 bits;  conditional E-value: 0.0026
                       ---S-EEEE--- CS
  HemolysinCabind    2 GgaGnDtLyGga 13  
                       G++G+DtL G++
   BA000019.orf37 1214 GTSGDDTLIGTD 1225
                       99*******986 PP

  == domain 2    score: 10.8 bits;  conditional E-value: 6.8e-05
                       E---S-EEEE---S-EEE CS
  HemolysinCabind    1 yGgaGnDtLyGgaGnDtl 18  
                       +G++GnD+Ly  +G+D+l
   BA000019.orf37 1231 FGNGGNDILYARGGDDKL 1248
                       69**************87 PP

  == domain 3    score: 11.4 bits;  conditional E-value: 4.3e-05
                       -S-EEEE---S-EEE CS
  HemolysinCabind    4 aGnDtLyGgaGnDtl 18  
                       +G+D L+GgaG+D l
   BA000019.orf37 1243 GGDDKLFGGAGDDLL 1257
                       6************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1418 residues)
Target model(s):                       11912  (2158902 nodes)
Passed MSV filter:                       231  (0.0193922); expected 238.2 (0.02)
Passed bias filter:                      133  (0.0111652); expected 238.2 (0.02)
Passed Vit filter:                        15  (0.00125923); expected 11.9 (0.001)
Passed Fwd filter:                         2  (0.000167898); expected 0.1 (1e-05)
Initial search space (Z):              11912  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.17s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 7849.55
//
BioPerl-1.007002/t/data/hmmscan_qry_stop.txt000444000766000024       754713155576321 21034 0ustar00cjfieldsstaff000000000000# hmmscan :: search sequence(s) against a profile database
# HMMER 3.0 (March 2010); http://hmmer.org/
# Copyright (C) 2010 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             FQ377874.faa
# target HMM database:             HMM_Profiles.hmm
# output directed to file:         FQ377874.txt
# number of worker threads:        8
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|328801650|gb|CBW53803.1|  [L=243]
Description: IS1296 A transposase protein B [Mycoplasma mycoides subsp. capri LC str. 95010]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                    -----------
    2.3e-88  289.2  12.7    3.8e-88  288.5   8.8    1.3  1  IS3_IS150_ORF2.curated      


Domain annotation for each model (and alignments):
>> IS3_IS150_ORF2.curated  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.5   8.8   7.6e-89   3.8e-88     145     386 ..       4     236 ..       1     238 [. 0.94

  Alignments for each domain:
  == domain 1    score: 288.5 bits;  conditional E-value: 7.6e-89
       IS3_IS150_ORF2.curated 145 eiyhrhrgrYGYRRitlaLrlSEkrGkqiNhKrvqrLMkelgLkSv.iRvKk.kyrsyrgevgivadNlLqRqFkadkPnek 224
                                   i+ ++ + YGYRR++++L      G  +NhK++ rL kelg      R K  +y sy+g+vg+ adN+L R+F +   n k
  gi|328801650|gb|CBW53803.1|   4 DIFSKSFETYGYRRLKITLK---SKGYIVNHKKILRLTKELGVQCIkFRTKNgRYSSYKGTVGKIADNVLKRNFHSLQAN-K 81 
                                  69999***************...*******************87642344434**********************99998.5 PP

       IS3_IS150_ORF2.curated 225 W.vTDVTEFkvgggkKlYLSpIlDLFNrEIisyslserpdaklVkktLerAlkklgpdevpvlHSPRLLSDqGwqYqskay. 304
                                    +TDVTEFkv+ g+KlYLSpI+DL+N EIisys  + p+++l+  +L++Alkk+ ++ +++ HS     DqG++Yq+  + 
  gi|328801650|gb|CBW53803.1|  82 L*CTDVTEFKVN-GQKLYLSPIIDLYNDEIISYSIQTNPNLNLTNSMLDKALKKVKNTNGLLIHS-----DQGFHYQH--Is 155
                                  788*********.****************************************************.....******98..75 PP

       IS3_IS150_ORF2.curated 305 .remLeeqGirqSMSRKGnclDNavmEsffgtLKsEifygnlkkFeslddLeraItdYIey.YNheRIhlKLkgltPveYRt 384
                                   + +Lee  i qSMSRKGnclDNa +E+ffg LK Ei+y   +k++s+++L++ I+ YI y YN+ RI++KLkgl+Pv+ R 
  gi|328801650|gb|CBW53803.1| 156 *AKKLEENNITQSMSRKGNCLDNAIIENFFGLLKQEIYY--GEKYNSVEELTKRIHKYI-Y*YNNIRIKEKLKGLSPVQFRK 234
                                  6689***********************************..67****************.*********************9 PP

       IS3_IS150_ORF2.curated 385 qr 386
                                  q+
  gi|328801650|gb|CBW53803.1| 235 QS 236
                                  97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues)
Target model(s):                         116  (57162 nodes)
Passed MSV filter:                        38  (0.327586); expected 2.3 (0.02)
Passed bias filter:                       38  (0.327586); expected 2.3 (0.02)
Passed Vit filter:                        31  (0.267241); expected 0.1 (0.001)
Passed Fwd filter:                         1  (0.198276); expected 0.0 (1e-05)
Initial search space (Z):                116  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.91u 0.30s 00:00:01.20 Elapsed: 00:00:01.71
# Mc/sec: 8.09
//
BioPerl-1.007002/t/data/hmmscan_sec_struct.out000444000766000024      1676613155576321 21345 0ustar00cjfieldsstaff000000000000# hmmscan :: search sequence(s) against a profile database
# HMMER 3.0 (March 2010); http://hmmer.org/
# Copyright (C) 2010 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             BA000019.orf8.fasta
# target HMM database:             Pfam-A.hmm
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       BA000019.orf8  [L=348]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.7e-11   41.3   0.0    1.5e-09   37.0   0.0    2.5  2  HTH_AraC   Bacterial regulatory helix-turn-helix proteins, Ara
    3.8e-12   38.2  11.9    5.9e-08   25.0   2.5    2.9  2  PKSI-KS_m3 
      0.023   13.9   0.0       0.54    9.5   0.0    2.3  2  DUF746     Domain of Unknown Function (DUF746)

Domain annotation for each model (and alignments):
>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.038   2.3e+02      10      36 ..     251     277 ..     242     278 .. 0.80
   2 !   37.0   0.0   2.6e-13   1.5e-09       8      41 ..     298     332 ..     295     333 .. 0.94

  Alignments for each domain:
  == domain 1    score: 1.5 bits;  conditional E-value: 0.038
                    -HHHHHHHHTS-HHHHHHHHHHH---- CS
       HTH_AraC  10 siadiAeevgfSpsyfsrlFkkytGvt 36 
                    s+ +++++vg++  +++r F+ ++  t
  BA000019.orf8 251 SLMELSRQVGLNDCTLKRGFRLVFDTT 277
                    66689999999999*******999877 PP

  == domain 2    score: 37.0 bits;  conditional E-value: 2.6e-13
                    .--HHHHHHHHTS.-HHHHHHHHHHH----HHHHH CS
       HTH_AraC   8 nwsiadiAeevgf.SpsyfsrlFkkytGvtPsqyr 41 
                    +++i++ A++vgf S+syf+++F+k++G++P++++
  BA000019.orf8 298 EINISQAARRVGFsSRSYFATAFRKKFGINPKEFL 332
                    5789*****************************97 PP

>> PKSI-KS_m3  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   2.5   3.6e-09   5.9e-08       1      16 []     538     553 ..     538     553 .. 0.99
   2 !   17.4   0.9     9e-07   1.5e-05       1      15 [.    1672    1686 ..    1672    1687 .. 0.96

  Alignments for each domain:
  == domain 1    score: 25.0 bits;  conditional E-value: 3.6e-09
      PKSI-KS_m3   1 GPSvtVDTACSSSLvA 16 
                     GPSvtVDT CSSSLvA
  AM746336.orf22 538 GPSVTVDTLCSSSLVA 553
                     9**************9 PP

  == domain 2    score: 17.4 bits;  conditional E-value: 9e-07
      PKSI-KS_m3    1 GPSvtVDTACSSSLv 15  
                      GP +++D ACSS Lv
  AM746336.orf22 1672 GPNLVIDSACSSALV 1686
                      9*************9 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   9.1e-05      0.54       4      32 ..     240     268 ..     237     275 .. 0.85
   2 ?    1.8   0.0     0.022   1.3e+02      13      28 ..     298     313 ..     293     319 .. 0.87

  Alignments for each domain:
  == domain 1    score: 9.5 bits;  conditional E-value: 9.1e-05
         DUF746   4 rllIrlLsqplslaeaadqlgtdegiiak 32 
                    + lIr L  p sl+e+++q+g+   + ++
  BA000019.orf8 240 EILIRNLENPPSLMELSRQVGLNDCTLKR 268
                    579******************98766655 PP

  == domain 2    score: 1.8 bits;  conditional E-value: 0.022
         DUF746  13 plslaeaadqlgtdeg 28 
                    ++ + +aa+++g +++
  BA000019.orf8 298 EINISQAARRVGFSSR 313
                    6899********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues)
Target model(s):                       11912  (2158902 nodes)
Passed MSV filter:                       248  (0.0208193); expected 238.2 (0.02)
Passed bias filter:                      220  (0.0184688); expected 238.2 (0.02)
Passed Vit filter:                        19  (0.00159503); expected 11.9 (0.001)
Passed Fwd filter:                         2  (0.000167898); expected 0.1 (1e-05)
Initial search space (Z):              11912  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.24u 0.15s 00:00:00.39 Elapsed: 00:00:00.27
# Mc/sec: 2782.58
//
Query:       lcl|aorf_00010|P1  [L=132]
Description: IS481.original transposase
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model               Description
    ------- ------ -----    ------- ------ -----   ---- --  --------            -----------
    3.4e-40  130.0   0.4    3.8e-40  129.9   0.3    1.0  1  IS481.original.hmm  


Domain annotation for each model (and alignments):
>> IS481.original.hmm  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   0.3   6.6e-42   3.8e-40     127     281 ..       7     130 ..       2     132 .] 0.97

  Alignments for each domain:
  == domain 1    score: 129.9 bits;  conditional E-value: 6.6e-42
  IS481.original.hmm 127 kRYErdhPgeLvhmDvkklgripdgGgvkighRwrgrtrgrgkrtnqsrnrglgkayvitaiDDhSRfayaeilsd 202
                         +++E++hP +L+++D++++g+i + G+                            +y++t++D++S+   ++++++
   lcl|aorf_00010|P1   7 GEIETAHPSYLGSQDTFYVGNITGAGR----------------------------IYQQTFVDTYSKWDSTKLYTT 54 
                         579*******************88888............................********************* PP

  IS481.original.hmm 203 ettttaadfllraaayfygkigeeiitrvlTDnGaayrskkrsakhdFqealaelGIkhilTrprsPqTNGKiERF 278
                         +t++taad l++ ++ f+   ++++i r lTD+ ++y+sk   ++ d+  +la ++I+h++T++++PqTN ++ RF
   lcl|aorf_00010|P1  55 KTPITAADLLNDRVLSFFA-EQGMGIIRLLTDRSTEYCSKA--ETQDYELCLALNDIEHTKTKVYHPQTNDICRRF 127
                         *******************.********************8..********************************* PP

  IS481.original.hmm 279 hrT 281
                         h+ 
   lcl|aorf_00010|P1 128 HKA 130
                         *95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues)
Target model(s):                         116  (57162 nodes)
Passed MSV filter:                         4  (0.0344828); expected 2.3 (0.02)
Passed bias filter:                        4  (0.0344828); expected 2.3 (0.02)
Passed Vit filter:                         3  (0.0258621); expected 0.1 (0.001)
Passed Fwd filter:                         1  (0.0172414); expected 0.0 (1e-05)
Initial search space (Z):                116  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 117.90
//
BioPerl-1.007002/t/data/hmmsearch.out000555000766000024     45151413155576321 17445 0ustar00cjfieldsstaff000000000000hmmsearch - search a sequence database with a profile HMM
HMMER 2.0 (June 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
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HMM file:                 HMM [SEED]
Sequence database:        HMM.dbtemp.29591
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Query HMM:  SEED  
  [HMM has been calibrated; E-values are empirical estimates]

Scores for complete sequences (score includes all domains):
Sequence   Description                                  Score    E-value  N 
--------   -----------                                  -----    ------- ---
PAB2_ARATH P42731 POLYADENYLATE-BINDING PROTEIN 2 (PO   393.8   6.1e-114   4
Q13310     Q13310 INDUCIBLE POLY(A)-BINDING PROTEIN.    385.6   1.8e-111   4
Q93004     Q93004 POLY(A)-BINDING PROTEIN.              384.2   4.6e-111   4
PABP_MOUSE P29341 POLYADENYLATE-BINDING PROTEIN (POLY   383.5   7.5e-111   4
O22173     O22173 PUTATIVE POLY(A)-BINDING PROTEIN.     371.0   4.3e-107   4
P87135     P87135 POLYADENYLATE-BINDING PROTEIN PABPP   370.6   5.7e-107   4
PABP_SCHPO P31209 POLYADENYLATE-BINDING PROTEIN (POLY   370.6   5.7e-107   4
PABP_YEAST P04147 POLYADENYLATE-BINDING PROTEIN, CYTO   364.7   3.5e-105   4
PABP_HUMAN P11940 POLYADENYLATE-BINDING PROTEIN (POLY   364.2   4.7e-105   4
PABP_XENLA P20965 POLYADENYLATE-BINDING PROTEIN (POLY   362.6   1.5e-104   4
P93616     P93616 POLY(A)-BINDING PROTEIN.              362.1   2.1e-104   4
Q62029     Q62029 POLY A BINDING PROTEIN 2 (POLYA BIN   356.6   9.3e-103   4
PAB5_ARATH Q05196 POLYADENYLATE-BINDING PROTEIN 5 (PO   354.4   4.4e-102   4
Q39953     Q39953 POLY(A)-MRNA BINDING PROTEIN.         348.3     3e-100   4
PABP_DROME P21187 POLYADENYLATE-BINDING PROTEIN (POLY   342.4    1.8e-98   4
Q15097     Q15097 POLYADENYLATE BINDING PROTEIN II.     333.6    7.8e-96   4
Q19581     Q19581 F18H3.3B.                             329.1    1.8e-94   4
Q19579     Q19579 F18H3.3A.                             329.1    1.8e-94   4
Q17350     Q17350 POLYADENYLATE-BINDING PROTEIN.        328.4      3e-94   4
Q92227     Q92227 PUTATIVE POLY(A)-BINDING PROTEIN FA   324.6    3.9e-93   4
O04319     O04319 POLY(A)-BINDING PROTEIN ISOLOG.       292.2    2.3e-83   4
TIA1_MOUSE P52912 NUCLEOLYSIN TIA-1 (RNA BINDING PROT   288.1    3.9e-82   3
TIA1_HUMAN P31483 NUCLEOLYSIN TIA-1.                    285.7      2e-81   3
Q27335     Q27335 POLY(A) BINDING PROTEIN.              280.8    6.3e-80   4
Q12926     Q12926 ELAV-LIKE NEURONAL PROTEIN 1.         271.3    4.5e-77   3
Q13235     Q13235 ELAV-LIKE NEURONAL PROTEIN 2 HEL-N2   271.3    4.5e-77   3
NUCL_CHICK P15771 NUCLEOLIN (PROTEIN C23).              270.9      6e-77   4
Q60899     Q60899 HU-ANTIGEN D (NERVOUS SYSTEM-SPECIF   270.3    8.9e-77   3
Q24474     Q24474 RNA-BINDING PROTEIN.                  268.9    2.3e-76   3
HUD_MOUSE  Q61701 PARANEOPLASTIC ENCEPHALOMYELITIS AN   268.7    2.7e-76   3
HUD_HUMAN  P26378 PARANEOPLASTIC ENCEPHALOMYELITIS AN   268.7    2.7e-76   3
HUD_RAT    O09032 PARANEOPLASTIC ENCEPHALOMYELITIS AN   268.7    2.7e-76   3
O13620     O13620 HYPOTHETICAL 93.7 KD PROTEIN.         267.3    7.1e-76   5
Q91585     Q91585 RIBONUCLEOPROTEIN.                    267.3    7.2e-76   3
Q60900     Q60900 HU-ANTIGEN C (MHUC-L).                262.0    2.8e-74   3
Q91583     Q91583 RIBONUCLEOPROTEIN.                    261.9      3e-74   3
TIAR_HUMAN Q01085 NUCLEOLYSIN TIAR (TIA-1 RELATED PRO   261.8    3.2e-74   3
Q91584     Q91584 RIBONUCLEOPROTEIN.                    261.5    3.9e-74   3
Q90409     Q90409 RIBONUCLEOPROTEIN.                    260.6    7.4e-74   3
P79736     P79736 ELAV/HUC HOMOLOG.                     260.0    1.1e-73   3
Q91903     Q91903 XEL-1.                                259.2    1.9e-73   3
Q06106     Q06106 SIMILAR TO POLYADENYLATE-BINDING PR   258.2      4e-73   5
Q24473     Q24473 RNA-BINDING PROTEIN.                  256.8    1.1e-72   3
Q26293     Q26293 RRM9 (FRAGMENT).                      255.9      2e-72   3
Q14576     Q14576 (HUC).                                255.2    3.1e-72   3
Q16135     Q16135 NEURON-SPECIFIC RNA RECOGNITION MOT   254.2    6.2e-72   3
GBP2_YEAST P25555 SINGLE-STRAND TELOMERIC DNA-BINDING   253.6    9.6e-72   3
Q91582     Q91582 RIBONUCLEOPROTEIN.                    253.2    1.3e-71   3
Q15717     Q15717 HUR RNA BINDING PROTEIN.              250.3    9.7e-71   3
Q20084     Q20084 F35H8.5.                              247.9    4.9e-70   3
PUB1_YEAST P32588 NUCLEAR AND CYTOPLASMIC POLYADENYLA   247.8    5.3e-70   3
TIAR_MOUSE P70318 NUCLEOLYSIN TIAR (TIA-1 RELATED PRO   243.5    1.1e-68   3
Q06459     Q06459 NUCLEOLIN.                            242.4    2.3e-68   4
ELAV_DROVI P23241 ELAV PROTEIN.                         241.8    3.3e-68   3
ELAV_DROME P16914 ELAV PROTEIN (EMBRYONIC LETHAL ABNO   241.8    3.3e-68   3
NUCL_XENLA P20397 NUCLEOLIN (PROTEIN C23).              240.9    6.4e-68   4
P70372     P70372 ELAV G HOMOLOG.                       238.8    2.8e-67   3
HRB1_YEAST P38922 HRB1 PROTEIN (TOM34 PROTEIN).         228.9    2.5e-64   3
NUCL_MESAU P08199 NUCLEOLIN (PROTEIN C23).              225.1    3.5e-63   4
ROM_HUMAN  P52272 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   224.6    5.3e-63   3
NUCL_MOUSE P09405 NUCLEOLIN (PROTEIN C23).              223.4    1.2e-62   4
NUCL_RAT   P13383 NUCLEOLIN (PROTEIN C23).              223.1    1.5e-62   4
Q09959     Q09959 HYPOTHETICAL 49.8 KD PROTEIN C18A3.   221.0    6.4e-62   3
Q08212     Q08212 NUCLEOLYSIN TIAR HOMOLOG (TIA-1 REL   220.3      1e-61   3
Q91579     Q91579 RIBONUCLEOPROTEIN.                    213.1    1.5e-59   3
P93843     P93843 DNA BINDING PROTEIN ACBF.             208.7      3e-58   3
NUCL_HUMAN P19338 NUCLEOLIN (PROTEIN C23).              207.1    9.4e-58   4
Q40270     Q40270 RNA-BINDING PROTEIN PRECURSOR.        207.0      1e-57   2
RO31_NICSY P19683 CHLOROPLAST 31 KD RIBONUCLEOPROTEIN   206.3    1.7e-57   2
RO28_SPIOL P28644 CHLOROPLAST 28 KD RIBONUCLEOPROTEIN   205.8    2.4e-57   2
PES4_YEAST P39684 PES4 PROTEIN (DNA POLYMERASE EPSILO   203.3    1.3e-56   4
P92871     P92871 RNA-BINDING PROTEIN 2 (RNA-BINDING    202.5    2.4e-56   2
Q39209     Q39209 RNA BINDING PROTEIN (FRAGMENT).       202.5    2.4e-56   2
Q43350     Q43350 CP31 PRECURSOR.                       202.5    2.4e-56   2
RO31_ARATH Q04836 CHLOROPLAST 31 KD RIBONUCLEOPROTEIN   202.5    2.4e-56   2
RO28_NICSY P19682 CHLOROPLAST 28 KD RIBONUCLEOPROTEIN   200.0    1.3e-55   2
O18409     O18409 TESTIS-SPECIFIC RNP-TYPE RNA BINDIN   199.8    1.5e-55   3
O02374     O02374 BRUNO.                                199.8    1.5e-55   3
Q41834     Q41834 NUCLEIC ACID-BINDING PROTEIN PRECUR   199.7    1.6e-55   2
Q15164     Q15164 POLYADENYLATE BINDING PROTEIN II (F   199.7    1.6e-55   2
NSR1_YEAST P27476 NUCLEAR LOCALIZATION SEQUENCE BINDI   199.0    2.6e-55   2
Q08935     Q08935 CHLOROPLAST 29 KD RIBONUCLEOPROTEIN   198.0    5.3e-55   2
O24306     O24306 RIBONUCLEOPROTEIN.                    197.0    1.1e-54   2
O23798     O23798 PS16 PROTEIN.                         195.8    2.3e-54   2
NOP4_YEAST P37838 NUCLEOLAR PROTEIN NOP4 (NUCLEOLAR P   194.4    6.3e-54   4
Q39062     Q39062 CHLOROPLAST RNA-BINDING PROTEIN CP3   190.4      1e-52   2
Q39061     Q39061 CHLOROPLAST RNA-BINDING PROTEIN CP3   190.4      1e-52   2
RO30_NICPL P49313 CHLOROPLAST 30 KD RIBONUCLEOPROTEIN   189.6    1.8e-52   2
Q08948     Q08948 CHLOROPLAST 33 KD RIBONUCLEOPROTEIN   189.5    1.9e-52   2
RO33_NICSY P19684 CHLOROPLAST 33 KD RIBONUCLEOPROTEIN   188.9    2.9e-52   2
Q99628     Q99628 SIAH BINDING PROTEIN 1 (FRAGMENT).    188.9      3e-52   3
Q43349     Q43349 CP29.                                 188.8      3e-52   2
Q41367     Q41367 24 KDA RNA BINDING PROTEIN (FRAGMEN   188.8    3.1e-52   2
GAR2_SCHPO P41891 GAR2 PROTEIN.                         188.0    5.4e-52   2
O13707     O13707 PRE-RIBOPSOMAL PARTICLE ASSEMBLY PR   188.0    5.4e-52   2
RO31_NICPL P49314 CHLOROPLAST 31 KD RIBONUCLEOPROTEIN   187.3      9e-52   2
Q08937     Q08937 CHLOROPLAST 29 KD RIBONUCLEOPROTEIN   186.9    1.1e-51   2
Q01491     Q01491 COLONY 1.                             184.8    4.8e-51   4
Q17385     Q17385 ELAV-TYPE RIBONUCLEOPROTEIN.          183.7    1.1e-50   3
MODU_DROME P13469 DNA-BINDING PROTEIN MODULO.           182.8      2e-50   4
O17310     O17310 SEX-LETHAL PROTEIN.                   182.3    2.7e-50   2
O17309     O17309 SEX-LETHAL PROTEIN (FRAGMENT).        182.3    2.7e-50   2
YHH5_YEAST P38760 HYPOTHETICAL 75.9 KD PROTEIN IN SPO   181.3    5.4e-50   3
NAM8_YEAST Q00539 NAM8 PROTEIN.                         181.3    5.5e-50   3
P70055     P70055 RNA BINDING PROTEIN ETR-3.            180.3    1.1e-49   3
Q92879     Q92879 CUG-BP/HNAB50.                        177.5    7.6e-49   3
ROA1_RAT   P04256 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   177.3    8.9e-49   2
ROA1_MOUSE P49312 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   177.3    8.9e-49   2
ROA1_HUMAN P09651 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   177.3    8.9e-49   2
ROA1_BOVIN P09867 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   177.3    8.9e-49   2
Q99141     Q99141 SEX-LETHAL PROTEIN, ALTERNATIVELY S   177.0    1.1e-48   2
SXLF_DROME P19339 SEX-LETHAL PROTEIN, FEMALE-SPECIFIC   177.0    1.1e-48   2
Q24668     Q24668 SEX-LETHAL GENE.                      177.0    1.1e-48   2
O13845     O13845 HYPOTHETICAL 69.4 KD PROTEIN.         176.6    1.4e-48   3
Q92950     Q92950 ETR-3.                                176.6    1.5e-48   3
Q60668     Q60668 AU-RICH ELEMENT RNA-BINDING PROTEIN   175.3    3.5e-48   2
SP49_HUMAN Q15427 SPLICEOSOME ASSOCIATED PROTEIN 49 (   173.8      1e-47   2
SQD_DROME  Q08473 RNA-BINDING PROTEIN SQUID (HETEROGE   173.5    1.2e-47   2
O15187     O15187 T-CLUSTER BINDING PROTEIN.            173.4    1.3e-47   2
Q12771     Q12771 P37 AUF1 RNA-BINDING PROTEIN.         172.9    1.9e-47   2
Q14103     Q14103 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   172.9    1.9e-47   2
Q14100     Q14100 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   172.9    1.9e-47   2
Q14102     Q14102 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   172.9    1.9e-47   2
Q14101     Q14101 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   172.9    1.9e-47   2
Q39568     Q39568 GBP1P.                                172.8    2.1e-47   2
PR24_YEAST P49960 U4/U6 SNRNA-ASSOCIATED SPLICING FAC   172.6    2.3e-47   3
CABA_MOUSE Q99020 CARG-BINDING FACTOR-A (CBF-A).        171.7    4.4e-47   2
ROA1_MACMU Q28521 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   171.1    6.4e-47   2
Q93194     Q93194 C07A4.1.                              170.8    8.3e-47   2
O01671     O01671 SEX-LETHAL PROTEIN.                   169.9    1.5e-46   2
Q14498     Q14498 SPLICING FACTOR.                      169.5      2e-46   3
Q14499     Q14499 SPLICING FACTOR.                      169.5      2e-46   3
Q01858     Q01858 EII BINDING PROTEIN (HETEROGENEOUS    169.3    2.2e-46   2
Q63568     Q63568 POLYPYRIMIDINE TRACT BINDING PROTEI   169.1    2.6e-46   4
PTB_RAT    Q00438 POLYPYRIMIDINE TRACT-BINDING PROTEI   169.1    2.6e-46   4
Q08940     Q08940 PUTATIVE CHLOROPLAST 33 KD RIBONUCL   167.7    6.9e-46   2
Q90602     Q90602 SINGLE STRANDED D BOX BINDING FACTO   167.4    8.2e-46   2
NGR1_YEAST P32831 NEGATIVE GROWTH REGULATORY PROTEIN    165.5    3.1e-45   3
ROA1_XENLA P17130 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   165.1    4.2e-45   2
Q60901     Q60901 HU-ANTIGEN C (MHUC-S) (FRAGMENT).     164.8    5.1e-45   2
PTB_HUMAN  P26599 POLYPYRIMIDINE TRACT-BINDING PROTEI   163.6    1.1e-44   4
Q39675     Q39675 (CEBP-1).                             163.1    1.7e-44   2
O14979     O14979 A+U-RICH ELEMENT RNA BINDING FACTOR   160.3    1.2e-43   2
Q99729     Q99729 ABBP-1.                               160.1    1.3e-43   2
Q04150     Q04150 HETEROGENEOUS RIBONUCLEOPROTEIN C (   160.1    1.3e-43   2
Q00880     Q00880 CUTINASE NEGATIVE ACTING PROTEIN.     160.0    1.4e-43   2
Q17352     Q17352 RRM-TYPE RNA BINDING PROTEIN.         159.2    2.5e-43   2
YP85_CAEEL Q09442 HYPOTHETICAL 40.9 KD PROTEIN C08B11   159.2    2.5e-43   2
Q41124     Q41124 CHLOROPLAST RNA BINDING PROTEIN PRE   158.9      3e-43   2
NAB4_YEAST Q99383 NUCLEAR POLYADENYLATED RNA-BINDING    158.8    3.3e-43   2
O22791     O22791 PUTATIVE RIBONUCLEOPROTEIN.           158.4    4.2e-43   2
ROA2_HUMAN P22626 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   157.2    9.9e-43   2
RO32_XENLA P51992 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   156.1    2.1e-42   2
Q90626     Q90626 RIBONUCLEOPROTEIN.                    156.1    2.1e-42   2
O23093     O23093 SIMILAR TO NUCLEOLIN PROTEIN.         155.1    4.3e-42   3
Q23795     Q23795 HNRNP PROTEIN.                        154.6    6.2e-42   2
RB27_DROME P48809 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   154.4    6.7e-42   2
Q17201     Q17201 BMSQD-2.                              154.4    7.2e-42   2
Q17200     Q17200 BMSQD-1.                              154.4    7.2e-42   2
PTB_PIG    Q29099 POLYPYRIMIDINE TRACT-BINDING PROTEI   154.3    7.3e-42   4
Q90407     Q90407 RIBONUCLEOPROTEIN (FRAGMENT).         153.8      1e-41   2
Q15584     Q15584 HTGR 1 MRNA.                          152.8    2.1e-41   2
RO31_XENLA P51968 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   151.9    3.8e-41   2
O04240     O04240 RNA- OR SSDNA-BINDING PROTEIN (FRAG   151.9    3.8e-41   2
RO22_XENLA P51990 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   151.9    3.9e-41   2
Q61474     Q61474 MUSASHI-1 HOMOLOG (RNA-BINDING PROT   151.6    4.9e-41   2
RO21_XENLA P51989 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   151.1    6.6e-41   2
ROA3_HUMAN P51991 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   150.5      1e-40   2
Q60690     Q60690 MYELIN BASIC PROTEIN EXPRESSION FAC   149.1    2.7e-40   2
Q91807     Q91807 NERVOUS SYSTEM-SPECIFIC RNA-BINDING   148.8    3.4e-40   2
Q91920     Q91920 RIBONUCLEOPROTEIN.                    148.8    3.4e-40   2
O08752     O08752 MLARK.                                148.8    3.4e-40   2
Q22037     Q22037 HNRNP LIKE PROTEIN.                   148.8    3.4e-40   2
Q91808     Q91808 NERVOUS SYSTEM-SPECIFIC RNA-BINDING   148.7    3.5e-40   2
ROA1_SCHAM P21522 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   147.5    8.3e-40   2
O02916     O02916 HLARK.                                147.4      9e-40   2
Q24486     Q24486 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   147.2      1e-39   2
RB87_DROME P48810 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   147.2      1e-39   2
Q24847     Q24847 SURFACE ANTIGEN.                      146.6    1.5e-39   2
ROA1_DROME P07909 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   146.1    2.2e-39   2
Q99361     Q99361 HETEROGENEOUS RIBONUCLEOPROTEIN A1    146.1    2.2e-39   2
Q24360     Q24360 NUCLEAR RIBONUCLEOPROTEIN.            146.1    2.2e-39   2
Q24359     Q24359 NUCLEAR RIBONUCLEOPROTEIN.            146.1    2.2e-39   2
O22855     O22855 HYPOTHETICAL PROTEIN.                 145.2      4e-39   3
Q24409     Q24409 MUSASHI.                              145.2    4.1e-39   2
Q13151     Q13151 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   145.1    4.4e-39   2
Q21911     Q21911 R10E9.1.                              144.8    5.3e-39   2
SR55_DROME P26686 SERINE-ARGININE PROTEIN 55 (SRP55)    144.8    5.6e-39   2
Q24252     Q24252 52-KD BRACKETING PROTEIN.             144.8    5.6e-39   2
Q23796     Q23796 HNRNP PROTEIN.                        144.2    7.9e-39   2
SP33_HUMAN Q07955 PRE-MRNA SPLICING FACTOR SF2, P33 S   142.6    2.5e-38   2
O04425     O04425 FLOWERING TIME CONTROL PROTEIN FCA.   140.4    1.1e-37   2
O23475     O23475 FCA GAMMA.                            140.4    1.1e-37   2
RB97_DROME Q02926 RIBONUCLEOPROTEIN RB97D.              139.7    1.9e-37   2
Q41042     Q41042 PROTEIN LOCALIZED IN THE NUCLEOLI.    139.4    2.2e-37   2
SR75_HUMAN Q08170 PRE-MRNA SPLICING FACTOR SRP75.       138.8    3.5e-37   2
U2AF_HUMAN P26368 SPLICING FACTOR U2AF 65 KD SUBUNIT    138.0    5.8e-37   3
U2AF_MOUSE P26369 SPLICING FACTOR U2AF 65 KD SUBUNIT    138.0    5.8e-37   3
Q13809     Q13809 ALTERNATIVE SPLICING FACTOR.          137.7    7.4e-37   2
YG5B_YEAST P53316 HYPOTHETICAL 89.5 KD PROTEIN IN MGA   136.4    1.8e-36   3
Q15020     Q15020 ORF.                                  136.3      2e-36   2
Q13242     Q13242 SPLICING FACTOR, ARGININE/SERINE RI   136.3      2e-36   2
P92966     P92966 SPLICING FACTOR.                      133.6    1.3e-35   2
O23189     O23189 RNA-BINDING PROTEIN HOMOLOG.          132.7    2.4e-35   3
Q26692     Q26692 TBRRM1.                               132.7    2.5e-35   3
Q13245     Q13245 SRP55-3 PRE-MRNA SPLICING FACTOR (F   132.6    2.6e-35   2
Q13247     Q13247 SRP55-1 PRE-MRNA SPLICING FACTOR.     132.6    2.6e-35   2
MSSP_HUMAN P29558 SINGLE-STRANDED DNA-BINDING PROTEIN   131.9      4e-35   2
O23212     O23212 SPLICING FACTOR HOMOLOG.              129.4    2.4e-34   2
CL4_RAT    Q09167 INSULIN-INDUCED GROWTH RESPONSE PRO   128.8    3.6e-34   2
Q13243     Q13243 SRP40-1 PRE-MRNA SPLICING FACTOR.     128.8    3.6e-34   2
P92965     P92965 ARGININE/SERINE-RICH SPLICING FACTO   128.2    5.5e-34   2
RU1A_HUMAN P09012 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN    127.6    7.9e-34   2
Q27199     Q27199 NUCLEOLAR PHOSPHOPROTEIN.             127.2    1.1e-33   2
Q14869     Q14869 MSSP-2 MRNA.                          126.6    1.6e-33   2
Q15433     Q15433 SCR2.                                 126.6    1.6e-33   2
Q26658     Q26658 ACTIVATOR PROTEIN.                    126.2    2.1e-33   2
Q19335     Q19335 HYPOTHETICAL PROTEIN F11A10.2.        125.5    3.6e-33   2
NONA_DROME Q04047 NO-ON-TRANSIENT A PROTEIN.            125.4    3.7e-33   2
RU1A_XENLA P45429 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN    125.4    3.8e-33   2
PSF_HUMAN  P23246 PTB-ASSOCIATED SPLICING FACTOR (PSF   124.6    6.3e-33   2
Q62189     Q62189 SMALL NUCLEAR RNA.                    124.4    7.3e-33   2
PTB_MOUSE  P17225 POLYPYRIMIDINE TRACT-BINDING PROTEI   124.3    7.9e-33   4
P92964     P92964 SPLICING FACTOR.                      124.2    8.8e-33   2
O00201     O00201 NUCLEAR MATRIX PROTEIN 55.            123.7    1.3e-32   2
Q12786     Q12786 54 KDA PROTEIN.                       123.7    1.3e-32   2
O35737     O35737 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   123.6    1.3e-32   3
ROH1_HUMAN P31943 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   123.6    1.3e-32   3
P90727     P90727 SPLICING FACTOR U2AF65.               122.5    2.8e-32   3
Q24024     Q24024 TESTIS-SPECIFIC-RRM-PROTEIN.          122.3    3.1e-32   2
ROH2_HUMAN P55795 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   121.6    5.2e-32   3
Q24534     Q24534 SPLICEOSOMAL PROTEIN.                 120.7    9.9e-32   2
P70333     P70333 MURINE HOMOLOG OF HUMAN FTP-3.        120.6      1e-31   3
P78814     P78814 FISSION YEAST (FRAGMENT).             120.5    1.1e-31   2
Q24261     Q24261 BJ6 PROTEIN.                          120.2    1.4e-31   2
Q15434     Q15434 SCR3.                                 120.2    1.4e-31   2
O13759     O13759 RNA BINDING POST-TRANSCRIPTIONAL RE   120.0    1.5e-31   2
Q94901     Q94901 RNA-BINDING PROTEIN LARK.             120.0    1.6e-31   2
Q91581     Q91581 POLYADENYLATION FACTOR 64 KDA SUBUN   119.7      2e-31   1
CST2_HUMAN P33240 CLEAVAGE STIMULATION FACTOR, 64 KD    119.7      2e-31   1
NOP3_YEAST Q01560 NUCLEOLAR PROTEIN 3 (MITOCHONDRIAL    119.5    2.2e-31   2
Q24562     Q24562 RNA BINDING PROTEIN.                  118.7      4e-31   3
Q40363     Q40363 NUM1 PROTEIN.                         118.5    4.6e-31   2
Q63887     Q63887 NONO.                                 117.2    1.1e-30   2
RU2B_HUMAN P08579 U2 SMALL NUCLEAR RIBONUCLEOPROTEIN    116.7    1.5e-30   2
Q24113     Q24113 NO-ON TRANSIENT A-LIKE PROTEIN (FRA   116.3      2e-30   2
Q17430     Q17430 B0035.12.                             114.6    6.5e-30   2
RU1A_DROME P43332 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN    114.3    8.1e-30   2
Q61413     Q61413 COLD INDUCIBLE RNA-BINDING PROTEIN    114.2    8.9e-30   1
Q14011     Q14011 GLYCINE-RICH RNA BINDING PROTEIN CI   114.2    9.1e-30   1
P93486     P93486 GLYCINE-RICH RNA-BINDING PROTEIN PS   114.1    9.6e-30   1
YHC4_YEAST P38741 HYPOTHETICAL 80.1 KD PROTEIN IN SNF   113.6    1.4e-29   2
GRP_DAUCA  Q03878 GLYCINE-RICH RNA-BINDING PROTEIN.     113.4    1.6e-29   1
GR10_BRANA Q05966 GLYCINE-RICH RNA-BINDING PROTEIN 10   113.0      2e-29   1
ROG_HUMAN  P38159 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   113.0      2e-29   1
O23288     O23288 RIBONUCLEOPROTEIN HOMOLOG.            111.4      6e-29   2
O24106     O24106 RNA-BINDING PROTEIN.                  110.9    8.9e-29   1
Q40426     Q40426 RNA-BINDING GLYCINE-RICH PROTEIN-1    110.4    1.2e-28   1
O04070     O04070 SGRP-1 PROTEIN.                       110.3    1.3e-28   1
Q41518     Q41518 SINGLE-STRANDED NUCLEIC ACID BINDIN   110.3    1.3e-28   1
O24601     O24601 GLYCINE-RICH RNA BINDING PROTEIN 2.   110.2    1.4e-28   1
O24188     O24188 OSGRP2.                               110.2    1.4e-28   1
Q39105     Q39105 GLYCINE-RICH RNA-BINDING PROTEIN (F   109.8    1.8e-28   1
RNPL_HUMAN P98179 PUTATIVE RNA-BINDING PROTEIN RNPL.    108.8    3.6e-28   1
GRP1_SINAL P49310 GLYCINE-RICH RNA-BINDING PROTEIN GR   108.6    4.4e-28   1
Q40052     Q40052 GLYCINE RICH PROTEIN, RNA BINDING P   108.6    4.4e-28   1
O23793     O23793 RNA BINDING PROTEIN.                  108.1    6.1e-28   1
Q40437     Q40437 RGP-3 (FRAGMENT).                     108.1    6.1e-28   1
GRP8_ARATH Q03251 GLYCINE-RICH RNA-BINDING PROTEIN 8    107.9    7.1e-28   1
GRP2_SINAL P49311 GLYCINE-RICH RNA-BINDING PROTEIN GR   107.8    7.3e-28   1
O22314     O22314 ASF/SF2 HOMOLOG.                      107.6    8.4e-28   2
O22315     O22315 ASF/SF2 HOMOLOG.                      107.6    8.4e-28   2
Q40425     Q40425 RNA-BINDING GRICINE-RICH PROTEIN-1    106.7    1.6e-27   1
GRP2_SORVU Q99070 GLYCINE-RICH RNA-BINDING PROTEIN 2.   106.5    1.8e-27   1
RT19_ARATH P39697 MITOCHONDRIAL 40S RIBOSOMAL PROTEIN   106.4    1.9e-27   1
O35326     O35326 HRS.                                  106.2    2.2e-27   2
O35479     O35479 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   106.2    2.2e-27   1
Q40427     Q40427 RNA-BINDING GLYCINE-RICH PROTEIN-1    106.0    2.6e-27   1
Q41453     Q41453 PUTATIVE GLYCINE RICH RNA BINDING P   105.6    3.4e-27   1
YA2B_SCHPO Q09702 HYPOTHETICAL 57.8 KD PROTEIN C2F7.1   105.4    3.8e-27   4
U2AF_SCHPO P36629 SPLICING FACTOR U2AF LARGE SUBUNIT.   105.3    4.3e-27   2
O24187     O24187 OSGRP1.                               105.2    4.4e-27   1
O22390     O22390 GLYCINE-RICH PROTEIN.                 105.2    4.6e-27   1
GRP7_ARATH Q03250 GLYCINE-RICH RNA-BINDING PROTEIN 7.   105.2    4.6e-27   1
HS49_YEAST Q99181 HSH49 PROTEIN.                        104.7    6.2e-27   2
Q40436     Q40436 RNA-BINDING GLYCINE RICH PROTEIN (R   103.7    1.3e-26   1
GRPA_MAIZE P10979 GLYCINE-RICH RNA-BINDING, ABSCISIC    103.7    1.3e-26   1
Q21900     Q21900 R10E4.2.                              103.7    1.3e-26   2
O22385     O22385 GLYCINE-RICH PROTEIN.                 103.6    1.3e-26   1
P90978     P90978 U2AF65.                               103.3    1.6e-26   3
Q42412     Q42412 RNA-BINDING PROTEIN RZ-1.             102.8    2.3e-26   1
YIS1_YEAST P40561 HYPOTHETICAL 29.0 KD PROTEIN IN BET   102.7    2.5e-26   1
O22653     O22653 GLYCINE-RICH RNA-BINDING PROTEIN.     102.4    3.2e-26   1
P90699     P90699 PUTATIVE RNA BINDING PROTEIN.         102.1    3.9e-26   1
Q64283     Q64283 SILICA-INDUCED PROTEIN 41 (SIG41).    101.9    4.3e-26   1
Q15815     Q15815 HTRA2-BETA.                           101.9    4.3e-26   1
O22703     O22703 PUTATIVE RNA-BINDING PROTEIN.         101.6    5.6e-26   1
O22384     O22384 GLYCINE-RICH PROTEIN.                 101.4    6.1e-26   1
Q43472     Q43472 LOW TEMPERATURE-RESPONSIVE RNA-BIND   101.4    6.4e-26   1
GRF1_HUMAN Q12849 G-RICH SEQUENCE FACTOR-1 (GRSF-1).    100.6    1.1e-25   3
Q15376     Q15376 Y-CHROMOSOME RNA RECOGNITION MOTIF    100.2    1.4e-25   1
Q15414     Q15414 RNA BINDING MOTIF PROTEIN 1, RELATE   100.2    1.4e-25   1
Q09542     Q09542 HYPOTHETICAL 60.3 KD PROTEIN F25B5.   100.0    1.7e-25   2
O24184     O24184 GLYCINE-RICH RNA-BINDING PROTEIN.      99.9    1.8e-25   1
YNR5_YEAST P53883 HYPOTHETICAL 45.7 KD PROTEIN IN RPS    99.7      2e-25   2
Q39244     Q39244 U1SNRNP-SPECIFIC PROTEIN.              99.6    2.2e-25   2
Q62093     Q62093 PR264/SC35.                            99.6    2.2e-25   1
SC35_CHICK P30352 SPLICING FACTOR SC35 (SC-35) (SPLIC    99.6    2.2e-25   1
Q44555     Q44555 RNA-BINDING PROTEIN.                   99.5    2.3e-25   1
Q15415     Q15415 YRRM2.                                 99.3    2.6e-25   1
RN15_YEAST P25299 MRNA 3'-END PROCESSING PROTEIN RNA1    98.9    3.7e-25   1
O25501     O25501 SS-DNA BINDING PROTEIN 12RNP2 PRECU    95.0    5.3e-24   1
Q19706     Q19706 F22B5.2.                               95.0    5.3e-24   1
Q39201     Q39201 RIBONUCLEOPROTEIN.                     94.9    5.7e-24   2
ROF_HUMAN  P52597 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO    94.8    5.9e-24   3
Q23120     Q23120 W02B12.2.                              94.7    6.7e-24   2
O22905     O22905 FCA GAMMA ISOLOG.                      94.5    7.3e-24   2
Q44560     Q44560 RBPA1 PROTEIN.                         94.5    7.7e-24   1
Q90408     Q90408 RIBONUCLEOPROTEIN (FRAGMENT).          93.9    1.2e-23   1
Q08374     Q08374 RNA-BINDING PROTEIN RBPA.              93.7    1.3e-23   1
Q13148     Q13148 TAR DNA-BINDING PROTEIN-43.            93.7    1.3e-23   2
Q13595     Q13595 TRANSFORMER-2 ALPHA.                   93.5    1.5e-23   1
Q60990     Q60990 RBM.                                   92.9    2.3e-23   1
TRA2_DROME P19018 TRANSFORMER-2 SEX-DETERMINING PROTE    92.8    2.4e-23   1
O13741     O13741 HYPOTHETICAL 49.4 KD PROTEIN.          92.4    3.3e-23   2
P70807     P70807 RNA-BINDING PROTEIN.                   92.3    3.4e-23   1
P73557     P73557 RNA-BINDING PROTEIN.                   91.8      5e-23   1
Q23121     Q23121 W02B12.3.                              91.5      6e-23   2
O35698     O35698 RNA-BINDING PROTEIN.                   90.8      1e-22   1
O15414     O15414 CAGH4.                                 90.5    1.2e-22   1
Q44556     Q44556 RNA-BINDING PROTEIN.                   90.3    1.4e-22   1
Q21323     Q21323 SIMILAR TO U1 SMALL NUCLEAR RIBONUC    90.3    1.4e-22   2
RN24_SCHPO Q09100 RNA-BINDING PROTEIN RNP24.             90.1    1.6e-22   2
O02008     O02008 TRANSFORMER-2 PROTEIN ISOFORM 272.     90.0    1.7e-22   1
O02009     O02009 TRANSFORMER-2 PROTEIN ISOFORM 225.     90.0    1.7e-22   1
YDC1_SCHPO Q10422 HYPOTHETICAL 33.6 KD PROTEIN C25G10    89.7    2.1e-22   1
Q44554     Q44554 RNA-BINDING PROTEIN RBPB.              89.3    2.8e-22   1
SC35_HUMAN Q01130 SPLICING FACTOR SC35 (SC-35) (SPLIC    89.1    3.1e-22   1
YIS5_YEAST P40565 HYPOTHETICAL 17.1 KD PROTEIN IN BET    88.9    3.6e-22   1
Q41498     Q41498 U1SNRNP-SPECIFIC PROTEIN, U1A.         88.4      5e-22   2
Q41810     Q41810 GLYCINE-RICH PROTEIN.                  88.2    6.1e-22   1
Q46349     Q46349 RNA-BINDING PROTEIN.                   87.8      8e-22   1
O22922     O22922 SPLICEOSOMAL PROTEIN U2B ISOLOG.       87.7    8.1e-22   2
Q53322     Q53322 SS-DNA BINDING PROTEIN 12RNP2.         87.2    1.1e-21   1
Q55343     Q55343 12KDA RNA-BINDING.                     86.9    1.4e-21   1
RU17_HUMAN P08621 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN     86.9    1.5e-21   1
Q99377     Q99377 SMALL NUCLEAR RIBONUCLEOPROTEIN (U1    86.9    1.5e-21   1
Q62376     Q62376 U1RNA-ASSOCIATED 70-KDA PROTEIN (FR    86.9    1.5e-21   1
P78493     P78493 68 KDA (U1) RIBONUCLEOPROTEIN (U1).    86.9    1.5e-21   1
Q57014     Q57014 HYPOTHETICAL 11.0 KD PROTEIN.          86.1    2.5e-21   1
Q41499     Q41499 SPLICEOSOMAL PROTEIN.                  86.0    2.7e-21   2
RU17_DROME P17133 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN     85.8    3.1e-21   1
Q62019     Q62019 16 KDA PROTEIN.                        84.8    6.3e-21   2
Q18999     Q18999 HYPOTHETICAL PROTEIN D2089.4.          84.0    1.1e-20   4
O22851     O22851 SMALL NUCLEAR RIBONUCLEOPROTEIN ISO    83.9    1.2e-20   1
O00320     O00320 F25451_2.                              83.9    1.2e-20   1
RU17_XENLA P09406 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN     83.4    1.7e-20   1
Q94467     Q94467 SSRNA-BINDING PROTEIN.                 83.3    1.7e-20   1
O08831     O08831 SRP20 GENE.                            82.8    2.5e-20   1
X16_HUMAN  P23152 PRE-MRNA SPLICING FACTOR SRP20 (X16    82.8    2.5e-20   1
P91414     P91414 SIMILARITY TO RNA RECOGNITION MOTIF    82.5      3e-20   1
Q42404     Q42404 U1 SNRNP 70K PROTEIN.                  82.4    3.2e-20   1
ROC_RAT    P17132 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO    81.7    5.2e-20   1
Q55345     Q55345 RNA-BINDING PROTEIN.                   81.7    5.4e-20   1
YDB2_SCHPO Q10355 HYPOTHETICAL 24.4 KD PROTEIN C22E12    81.7    5.4e-20   1
O18352     O18352 RNA BINDING PROTEIN.                   81.5    6.2e-20   1
Q18318     Q18318 SIMILAR TO RNA-BINDING PROTEIN.        81.4    6.7e-20   1
P93396     P93396 TRANSFORMER-SR RIBONUCLEOPROTEIN (F    81.4    6.8e-20   1
Q09511     Q09511 PROBABLE SPLICING FACTOR SC35 (PR26    80.8    9.8e-20   1
Q15351     Q15351 SEB4B (FRAGMENT).                      80.8      1e-19   1
Q15350     Q15350 SEB4D (FRAGMENT).                      80.8      1e-19   1
YD3D_SCHPO Q10277 HYPOTHETICAL 59.1 KD PROTEIN C13G7.    80.7    1.1e-19   2
O23866     O23866 MEI2-LIKE PROTEIN.                     80.5    1.2e-19   2
Q60399     Q60399 C23 NUCLEOLIN, GLYCINE RICH REGION     80.5    1.3e-19   1
Q55342     Q55342 RNA-BINDING PROTEIN.                   80.3    1.4e-19   1
Q62176     Q62176 SEB4.                                  80.2    1.5e-19   1
Q21832     Q21832 R07E5.14.                              80.2    1.5e-19   1
Q38915     Q38915 RNA-BINDING PROTEIN.                   79.7    2.1e-19   2
Q16629     Q16629 SPLICING FACTOR, ARGININE/SERINE-RI    79.6    2.4e-19   1
RNP1_YEAST P32385 RIBONUCLEOPROTEIN-1.                   79.0    3.5e-19   1
YQOC_CAEEL Q09301 HYPOTHETICAL 21.6 KD PROTEIN EEED8.    79.0    3.6e-19   1
Q16662     Q16662 SRP40-2.                               78.8    3.9e-19   1
P78795     P78795 FISSION YEAST (FRAGMENT).              78.8      4e-19   1
YQO4_CAEEL Q09295 HYPOTHETICAL 26.2 KD PROTEIN EEED8.    78.5      5e-19   1
Q55341     Q55341 21KDA RNA-BINDING PROTEIN, 12RNP1.     78.4    5.4e-19   1
Q53321     Q53321 SS-DNA BINDING PROTEIN 12RNP1.         78.4    5.4e-19   1
O14801     O14801 EUKARYOTIC TRANSLATION INITIATION F    78.0      7e-19   1
EWS_MOUSE  Q61545 RNA-BINDING PROTEIN EWS.               77.9    7.2e-19   1
Q18409     Q18409 SIMILAR TO PRE-MRNA SPLICING FACTOR    77.9    7.7e-19   1
O14875     O14875 RNA BINDING PROTEIN.                   77.5    9.9e-19   1
EWS_HUMAN  Q01844 RNA-BINDING PROTEIN EWS.               77.4      1e-18   1
O14327     O14327 RNA BINDING PROTEIN.                   77.4    1.1e-18   1
O13829     O13829 PUTATIVE SMALL NUCLEAR RIBONUCLEOPR    77.4    1.1e-18   1
O00425     O00425 PUTATIVE RNA BINDING PROTEIN KOC (K    76.4    2.1e-18   2
Q61954     Q61954 NEOSIN (FRAGMENT).                     76.3    2.3e-18   2
YNL0_YEAST P53927 HYPOTHETICAL 25.4 KD PROTEIN IN CYB    75.8    3.2e-18   1
SSB1_YEAST P10080 SINGLE-STRANDED NUCLEIC ACID-BINDIN    75.6    3.6e-18   2
O35935     O35935 POLY(A) BINDING PROTEIN II.            75.5      4e-18   1
Q28165     Q28165 POLYA BINDING PROTEIN II.              75.5      4e-18   1
Q99730     Q99730 TAT-SF1.                               75.2      5e-18   2
Q27926     Q27926 RNA BINDING PROTEIN.                   75.1    5.3e-18   1
Q16560     Q16560 U1-SNRNP BINDING PROTEIN HOMOLOG.      74.8    6.3e-18   1
Q55765     Q55765 HYPOTHETICAL 16.6 KD PROTEIN.          74.8    6.5e-18   1
O23146     O23146 HNRNP-LIKE PROTEIN.                    74.1      1e-17   1
O35335     O35335 RNA BINDING PROTEIN.                   74.1      1e-17   1
Q22030     Q22030 R74.5.                                 73.0    2.3e-17   1
Q10572     Q10572 44.4 KD RNA-BINDING PROTEIN IN FOX-    72.7    2.8e-17   1
Q22304     Q22304 SIMILAR TO C. ELEGANS PROTEIN R74.5    72.7    2.8e-17   1
Q21155     Q21155 SIMILAR TO RNA BINDING PROTEINS.       72.6    2.9e-17   1
Q22318     Q22318 T07F10.3.                              72.1    4.2e-17   2
Q93233     Q93233 C17E4.5.                               72.0    4.3e-17   1
Q02427     Q02427 RNA BINDING PROTEIN 1.                 71.9    4.7e-17   1
Q13244     Q13244 SRP55-2 PRE-MRNA SPLICING FACTOR.      71.8      5e-17   1
Q15287     Q15287 RNA-BINDING PROTEIN.                   71.4    6.7e-17   1
Q13344     Q13344 FUS-LIKE PROTEIN (FRAGMENT).           71.3    7.4e-17   1
FUS_HUMAN  P35637 RNA-BINDING PROTEIN FUS/TLS.           71.3    7.4e-17   1
FUS_BOVIN  Q28009 RNA-BINDING PROTEIN FUS/TLS (NUCLEA    71.3    7.4e-17   1
Q62826     Q62826 M4 PROTEIN HOMOLOG.                    71.3    7.5e-17   1
Q24491     Q24491 RNA BINDING PROTEIN.                   70.8    1.1e-16   1
O04432     O04432 GLYCINE-RICH PROTEIN.                  70.3    1.5e-16   1
Q08208     Q08208 CHROMOSOME XV READING FRAME ORF YOL    70.0    1.8e-16   1
Q27294     Q27294 RNA BINDING PROTEIN CABEZA.            69.6    2.3e-16   1
O14369     O14369 PUTATIVE RNA-BINDING PROTEIN.          68.5    5.2e-16   1
YSO5_CAEEL Q10130 HYPOTHETICAL 98.0 KD PROTEIN F56D1.    66.9    1.5e-15   1
ROC_HUMAN  P07910 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO    66.4    2.1e-15   1
Q92751     Q92751 HTAFII68.                              66.2    2.5e-15   1
Q92804     Q92804 PUTATIVE RNA BINDING PROTEIN RBP56.    66.2    2.5e-15   1
WHI3_YEAST P34761 WHI3 PROTEIN.                          65.4    4.4e-15   1
CB20_XENLA P52299 20 KD NUCLEAR CAP BINDING PROTEIN (    65.3    4.5e-15   1
CB20_HUMAN P52298 20 KD NUCLEAR CAP BINDING PROTEIN (    64.1      1e-14   1
O23131     O23131 CONTAINS PROCITE 'RNP1' PUTATIVE RN    64.0    1.1e-14   1
Q21322     Q21322 SIMILAR TO U1 SMALL NUCLEAR RIBONUC    64.0    1.2e-14   2
O42254     O42254 ZIPCODE-BINDING PROTEIN.               63.8    1.3e-14   2
Q92909     Q92909 DAZLA.                                 63.6    1.5e-14   1
Q92904     Q92904 RNA BINDING PROTEIN.                   63.6    1.5e-14   1
Q95192     Q95192 RNA-BINDING PROTEIN.                   63.6    1.5e-14   1
IF4B_HUMAN P23588 EUKARYOTIC TRANSLATION INITIATION F    63.5    1.6e-14   1
Q93594     Q93594 F26A3.2.                               63.4    1.8e-14   1
Q19018     Q19018 MEC-8 GENE.                            63.2      2e-14   2
Q22039     Q22039 MEC-8 PROTEIN.                         63.2      2e-14   2
ROC_XENLA  P19600 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO    63.0    2.2e-14   1
O15396     O15396 DAZLA PROTEIN.                         62.1    4.4e-14   1
O13674     O13674 HYPOTHETICAL 73.9 KD PROTEIN.          61.8    5.2e-14   3
O23646     O23646 RSZP22 PROTEIN.                        61.3    7.5e-14   1
Q23287     Q23287 SIMILARITY TO 2 RNA RECOGNITION MOT    61.2    7.9e-14   1
P90871     P90871 HYPOTHETICAL PROTEIN F39H2.2 IN CHR    61.1    8.7e-14   1
O15042     O15042 KIAA0332 (FRAGMENT).                   60.7    1.1e-13   1
YSX2_CAEEL Q10021 HYPOTHETICAL 24.0 KD PROTEIN T28D9.    60.7    1.1e-13   1
Q64368     Q64368 DAZ-LIKE AUTOSOMAL (RNA RECOGNITION    60.3    1.5e-13   1
Q09331     Q09331 CSX1+ (FRAGMENT).                      60.1    1.7e-13   1
Q14151     Q14151 KIAA0138 PROTEIN.                      60.1    1.7e-13   1
Q22412     Q22412 T11G6.8.                               60.0    1.8e-13   1
Q09335     Q09335 CSX1+ (FRAGMENT).                      59.9      2e-13   1
Q64012     Q64012 MERC=RNA-BINDING PROTEIN {ALTERNATI    59.7    2.2e-13   1
Q15056     Q15056 MRNA (KIAA0038) FOR ORF, PARTIAL CD    59.5    2.6e-13   1
Q42215     Q42215 NAM8 PROTEIN (FRAGMENT).               59.5    2.6e-13   1
Q09584     Q09584 HYPOTHETICAL 36.0 KD PROTEIN K04G7.    59.4    2.7e-13   1
Q14924     Q14924 NCBP INTERACTING PROTEIN 1.            59.3      3e-13   1
Q20414     Q20414 F44G4.4.                               59.0    3.6e-13   2
MLO3_SCHPO Q09330 MLO3 PROTEIN.                          59.0    3.6e-13   1
GRP1_SORVU Q99069 GLYCINE-RICH RNA-BINDING PROTEIN 1     58.9    3.9e-13   1
RU17_YEAST Q00916 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN     58.9      4e-13   1
O08583     O08583 TRANSCRIPTIONAL COACTIVATOR ALY (AL    58.7    4.6e-13   1
Q14730     Q14730 LA 4.1 PROTEIN (FRAGMENT).             58.4    5.4e-13   1
Q91017     Q91017 GIZZARD PTB-ASSOCIATED SPLICING FAC    58.2    6.2e-13   1
LA_HUMAN   P05455 LUPUS LA PROTEIN (SJOGREN SYNDROME     58.2    6.5e-13   1
Q15367     Q15367 RIBONUCLEOPROTEIN (LA) (FRAGMENT).     58.2    6.5e-13   1
Q08920     Q08920 CHROMOSOME XVI READING FRAME ORF YP    57.2    1.3e-12   1
Q22135     Q22135 T04A8.6.                               56.1    2.7e-12   1
O23645     O23645 RSZP21 PROTEIN.                        55.9    3.1e-12   1
ARP2_PLAFA P13824 CLUSTERED-ASPARAGINE-RICH PROTEIN (    55.6    3.9e-12   2
P97855     P97855 RAS-GTPASE-ACTIVATING PROTEIN SH3-D    55.5      4e-12   1
Q24207     Q24207 BOULE PROTEIN.                         55.5    4.2e-12   1
O14797     O14797 HRS (FRAGMENT).                        55.4    4.5e-12   2
Q62150     Q62150 RIBONUCLEIC ACID BINDING PROTEIN S1    55.2    4.9e-12   1
Q13283     Q13283 GAP SH3 BINDING PROTEIN.               54.2      1e-11   1
Q22708     Q22708 ZK1067.6 (FRAGMENT).                   54.1    1.1e-11   2
Q14136     Q14136 KIAA0122 PROTEIN (FRAGMENT).           54.1    1.1e-11   2
Q04067     Q04067 D9461.16P.                             54.0    1.2e-11   1
Q62379     Q62379 U2-SNRNP B'' (PRNP31) (FRAGMENT).      53.7    1.5e-11   1
Q18724     Q18724 HYPOTHETICAL PROTEIN C50B8.1.          53.3    1.9e-11   1
ROL_HUMAN  P14866 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO    52.7    2.8e-11   3
Q15424     Q15424 SCAFFOLD ATTACHMENT FACTOR (FRAGMEN    52.3    3.7e-11   1
P97379     P97379 RAS-GTPASE-ACTIVATING PROTEIN SH3-D    52.2      4e-11   1
SRP1_SCHPO Q10193 SRP1 PROTEIN.                          51.1    8.9e-11   1
RDP_MOUSE  P19426 RD PROTEIN (WL623).                    50.2    1.7e-10   1
RDP_HUMAN  P18615 RD PROTEIN.                            50.2    1.7e-10   1
LA_BOVIN   P10881 LUPUS LA PROTEIN HOMOLOG (SJOGREN S    49.8    2.1e-10   1
LA_RAT     P38656 LUPUS LA PROTEIN HOMOLOG (SJOGREN S    49.8    2.2e-10   1
LU15_HUMAN P52756 PUTATIVE TUMOR SUPPRESSOR LUCA15.      49.5    2.7e-10   2
O15237     O15237 MSSP-2 (FRAGMENT).                     49.4    2.8e-10   1
O15236     O15236 MSSP-2 (FRAGMENT).                     49.4    2.8e-10   1
O14102     O14102 SPLICOSOME ASSOIATED PROTEIN (FRAGM    49.3    3.1e-10   1
Q62378     Q62378 U2-SNRNP B'' (PRNP11) (FRAGMENT).      49.1    3.4e-10   1
Q15380     Q15380 Y-CHROMOSOME RNA RECOGNITION MOTIF     48.9    3.9e-10   1
U2AG_HUMAN Q01081 SPLICING FACTOR U2AF 35 KD SUBUNIT     48.7    4.6e-10   1
YFK2_YEAST P43607 HYPOTHETICAL 31.9 KD PROTEIN IN RPL    48.5    5.4e-10   1
IF32_YEAST P06103 EUKARYOTIC TRANSLATION INITIATION F    48.0    7.6e-10   1
LA_MOUSE   P32067 LUPUS LA PROTEIN HOMOLOG (SJOGREN S    47.6    9.8e-10   1
CPO_DROME  Q01617 PUTATIVE COUCH POTATO PROTEIN.         47.3    1.2e-09   1
Q17175     Q17175 50KDA LECTIN.                          46.6      2e-09   1
Q13117     Q13117 PUTATIVE RNA BINDING DAZ PROTEIN.      46.1    2.8e-09   1
O13801     O13801 HYPOTHETICAL 66.4 KD PROTEIN.          45.5    4.3e-09   1
RU1A_YEAST P32605 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN     45.3    4.9e-09   1
Q12159     Q12159 RNA ANNEALING PROTEIN YRA1P.           45.2    5.2e-09   1
NAB3_YEAST P38996 NUCLEAR POLYADENYLATED RNA-BINDING     44.7    7.5e-09   1
Q08925     Q08925 CHROMOSOME XVI READING FRAME ORF YP    44.1    1.1e-08   4
Q18601     Q18601 SIMILAR TO HETEROGENEOUS RIBONUCLEO    44.0    1.2e-08   2
Q63627     Q63627 CTD-BINDING SR-LIKE PROTEIN RA4 (FR    44.0    1.2e-08   1
O15758     O15758 RNA BINDING PROTEIN.                   43.9    1.3e-08   2
MEI2_SCHPO P08965 MEI2 PROTEIN.                          43.8    1.4e-08   1
Q23161     Q23161 W04D2.6 (FRAGMENT).                    43.3      2e-08   1
O13649     O13649 SPLICEOSOMAL PROTEIN.                  43.0    2.4e-08   1
P90797     P90797 HYPOTHETICAL PROTEIN D2089.1 (FRAGM    42.9    2.5e-08   1
Q07655     Q07655 CHROMOSOME IV READING FRAME ORF YDL    42.8    2.7e-08   1
O15759     O15759 RNA BINDING PROTEIN.                   42.8    2.7e-08   2
RN12_YEAST P32843 RNA12 PROTEIN.                         42.8    2.8e-08   1
Q07034     Q07034 RNA BINDING PROTEIN.                   42.3    3.9e-08   1
Q24375     Q24375 LA RIBONUCLEOPROTEIN.                  40.7    1.1e-07   1
O18219     O18219 Y57G11A.5.                             40.6    1.2e-07   1
Q15686     Q15686 HU1-70K-LIKE PROTEIN (216 AA) (FRAG    40.4    1.5e-07   1
Q15364     Q15364 RIBONUCLEOPROTEIN ANTIGEN.             40.4    1.5e-07   1
D111_ARATH P42698 DNA-DAMAGE-REPAIR/TOLERATION PROTEI    40.4    1.5e-07   1
LAB_XENLA  P28049 LUPUS LA PROTEIN HOMOLOG B.            39.8    2.2e-07   1
LA_DROME   P40796 LA PROTEIN HOMOLOG.                    38.3      6e-07   1
YAG3_SCHPO Q09868 HYPOTHETICAL 62.1 KD PROTEIN C12G12    38.2    6.8e-07   1
LAA_XENLA  P28048 LUPUS LA PROTEIN HOMOLOG A.            37.7    9.1e-07   1
Q92516     Q92516 WS-1/TYPE2.                            37.5    1.1e-06   1
Q92517     Q92517 WS-1/TYPE3.                            37.5    1.1e-06   1
Q93062     Q93062 WS-1/TYPE4.                            37.5    1.1e-06   1
Q63623     Q63623 CTD-BINDING SR-LIKE PROTEIN RA8.       37.2    1.3e-06   1
Q10667     Q10667 RNA-BINDING PROTEIN RNP-1.             36.7    1.9e-06   1
YN26_YEAST P53830 HYPOTHETICAL 32.3 KD PROTEIN IN SEC    36.0    3.1e-06   2
P92204     P92204 ANON-66DA PROTEIN.                     35.8    3.5e-06   1
Q93733     Q93733 C17E4.11 (FRAGMENT).                   35.5    4.5e-06   1
MAT3_RAT   P43244 MATRIN 3.                              35.4    4.7e-06   2
O35833     O35833 MATRIN 3.                              35.4    4.7e-06   2
P87216     P87216 VIP1 PROTEIN.                          35.2    5.2e-06   1
Q16630     Q16630 HPBRII-4 MRNA.                         34.8    7.2e-06   1
P87126     P87126 HYPOTHETICAL 46.4 KD PROTEIN.          34.4    8.9e-06   1
Q18265     Q18265 SIMILAR TO NUCLEOLIN.                  34.4    9.2e-06   1
YAS9_SCHPO Q10145 HYPOTHETICAL 82.4 KD PROTEIN C3H8.0    34.2    1.1e-05   1
YQOA_CAEEL Q09299 HYPOTHETICAL 76.5 KD PROTEIN EEED8.    33.1    2.4e-05   1
O01806     O01806 SIMILARITY TO AN RNA RECOGNITION MO    32.9    2.5e-05   1
YIS9_YEAST P40567 HYPOTHETICAL 12.8 KD PROTEIN IN PRI    32.9    2.7e-05   1
Q18220     Q18220 COSMID C26E6.                          32.3      4e-05   1
Q18219     Q18219 COSMID C26E6.                          32.3      4e-05   1
ROU2_HUMAN P07029 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO    31.8    5.6e-05   1
Q60745     Q60745 RIBONUCLEOPROTEIN (FRAGMENT).          31.5    6.9e-05   2
IF32_HUMAN P55884 EUKARYOTIC TRANSLATION INITIATION F    31.4    7.4e-05   1
Q41988     Q41988 GLYCINE-RICH RNA-BINDING PROTEIN (F    31.0    9.7e-05   1
YBF1_YEAST P34217 HYPOTHETICAL 73.8 KD PROTEIN IN SAS    30.9     0.0001   1
U2AG_DROME Q94535 SPLICING FACTOR U2AF 35 KD SUBUNIT     29.0    0.00038   1
U2AG_SCHPO Q09176 SPLICING FACTOR U2AF 23 KD SUBUNIT     28.9    0.00043   1
IF32_SCHPO Q10425 PROBABLE EUKARYOTIC TRANSLATION INI    28.3    0.00063   1
PRT1_PICAN P12806 PUTATIVE PRT1 PROTEIN.                 28.2    0.00068   1
P70501     P70501 S1-1 PROTEIN.                          27.6     0.0011   2
P87058     P87058 SLA1P.                                 27.4     0.0012   1
ARP_YEAST  P32770 ARP PROTEIN.                           27.3     0.0012   1
O13362     O13362 LA AUTOANTIGEN HOMOLOG.                27.3     0.0013   1
MAT3_HUMAN P43243 MATRIN 3 (FRAGMENT).                   27.0     0.0015   1
O04554     O04554 T7N9.7.                                26.9     0.0016   1
Q26457     Q26457 LA AUTOANTIGEN HOMOLOG.                26.2     0.0026   1
O15047     O15047 KIAA0339.                              25.8     0.0035   1
NOT4_YEAST P34909 GENERAL NEGATIVE REGULATOR OF TRANS    25.7     0.0039   1
JSN1_YEAST P47135 JSN1 PROTEIN.                          24.6     0.0081   1
YAC4_SCHPO Q09818 PUTATIVE GENERAL NEGATIVE REGULATOR    24.6     0.0083   1
P97343     P97343 PROTEIN KINASE.                        24.4     0.0094   1
Q63285     Q63285 KIS PROTEIN (PAM COOH-TERMINAL INTE    24.4     0.0094   1
O18254     O18254 Y57G11C.9.                             24.3     0.0099   1
YLF1_CAEEL Q03571 HYPOTHETICAL 42.4 KD PROTEIN C40H1.    24.3       0.01   2
Q18717     Q18717 SIMILAR TO S. CEREVISIAE GENERAL NE    23.6      0.016   1
YKV4_YEAST P36036 HYPOTHETICAL 23.8 KD PROTEIN IN URA    23.0       0.02   1
Q08287     Q08287 CHROMOSOME XV READING FRAME ORF YOL    22.5      0.022   1
IF4B_YEAST P34167 EUKARYOTIC TRANSLATION INITIATION F    22.4      0.023   1
Q05519     Q05519 ARGININE-RICH 54 KD NUCLEAR PROTEIN    22.3      0.023   1
Q26273     Q26273 RNA RECOGNITION MOTIF-TYPE RNA-BIND    22.3      0.023   1
Q14966     Q14966 NUCLEAR PROTEIN, NP220.                22.2      0.024   1
P87143     P87143 HYPOTHETICAL 64.4 KD PROTEIN.          21.9      0.025   2
Q20966     Q20966 F58B3.7.                               21.4      0.028   1
Q24433     Q24433 OVARIAN PROTEIN.                       21.3      0.029   1
P91156     P91156 SIMILARITY TO HUMAN HETEROGENEOUS N    21.1       0.03   1
Q04142     Q04142 HYPOTHETICAL PROTEIN (FRAGMENT).       20.6      0.035   1
Q12221     Q12221 HYPOTHETICAL 119.5 KD PROTEIN YPR03    20.6      0.035   1
Q93021     Q93021 PUTATIVE TUMOR SUPPRESSOR.             19.5      0.044   1
NRD1_YEAST P53617 NRD1 PROTEIN.                          18.9      0.051   1
Q93237     Q93237 C17E4.11 (FRAGMENT).                   18.4      0.057   1
O01159     O01159 D2089.1 (FRAGMENT).                    16.8      0.083   1
YAX9_SCHPO Q10200 HYPOTHETICAL 57.1 KD PROTEIN C13F4.    16.7      0.084   1
Q61464     Q61464 NUCLEAR PROTEIN, NP220.                16.1      0.098   2
Q21351     Q21351 K08F4.2.                               15.9        0.1   1
LAH1_YEAST P33399 LA PROTEIN HOMOLOG.                    15.8        0.1   1
Q06477     Q06477 INTERFERON RESPONSE ELEMENT-BINDING    14.5       0.14   1
U2R1_HUMAN Q15695 U2 SMALL NUCLEAR RIBONUCLEOPROTEIN     14.1       0.15   1
U2R2_HUMAN Q15696 U2 SMALL NUCLEAR RIBONUCLEOPROTEIN     14.1       0.15   1
U2R2_MOUSE Q62377 U2 SMALL NUCLEAR RIBONUCLEOPROTEIN     13.4       0.18   1
YN8T_YEAST P53741 HYPOTHETICAL 57.7 KD PROTEIN IN LYS    13.2       0.19   1
O35404     O35404 SYNAPTOJANIN 2 (FRAGMENT).             13.1       0.19   1
U2R1_MOUSE Q64707 U2 SMALL NUCLEAR RIBONUCLEOPROTEIN     13.1        0.2   1
Q23391     Q23391 ZK1067.6 (FRAGMENT).                   12.9        0.2   1
Q10458     Q10458 SLA1 (FRAGMENT).                       12.6       0.22   1
P78332     P78332 G16 PROTEIN (FRAGMENT).                12.1       0.24   1
Q18937     Q18937 HYPOTHETICAL PROTEIN D1046.1.          12.0       0.25   1
O23612     O23612 HYPOTHETICAL 34.5 KD PROTEIN.          11.5       0.28   1
Q23953     Q23953 D34 IMMUNODOMINANT ANTIGEN.            11.5       0.28   1
Q26548     Q26548 CYCLOPHYLIN-LIKE PROTEIN TRANS-SPLI    11.2        0.3   1
O15056     O15056 KIAA0348.                              11.1       0.31   1
P70166     P70166 CYTOPLASMIC POLYADENYLATION ELEMENT    10.6       0.35   1
BF41_MOUSE P28659 BRAIN PROTEIN F41.                     10.6       0.35   1
Q24527     Q24527 MRNA SMOOTH FOR POLYPEPTIDE (HOMOLO    10.5       0.35   1
O18964     O18964 SYNAPTOJANIN.                          10.2       0.38   1
Q62504     Q62504 COCHLEAR MRNA (CLONE 28D2) (FRAGMEN     9.2       0.48   1
Q91572     Q91572 CYTOPLASMIC POLYADENYLATION ELEMENT     9.1       0.49   2
YQO1_CAEEL Q09293 HYPOTHETICAL 69.9 KD PROTEIN EEED8.     8.8       0.53   1
Q17561     Q17561 C01F6.5.                                8.7       0.54   1
YHS7_YEAST P38833 HYPOTHETICAL 27.1 KD PROTEIN IN NDT     8.6       0.55   1
Q14206     Q14206 ZAKI-4 MRNA IN HUMAN SKIN FIBROBLAS     8.6       0.55   1
O04526     O04526 F20P5.8.                                7.9       0.65   1
Q17860     Q17860 SIMILAR TO DIACYLGLYCEROL KINASE.       7.3       0.75   1
Q92615     Q92615 MYELOBLAST KIAA0217 (FRAGMENT).         7.3       0.75   1
O22794     O22794 PUTATIVE SPLICING FACTOR U2AF LARGE     6.6       0.87   2
YMC7_CAEEL P53806 HYPOTHETICAL 26.6 KD PROTEIN F54E7.     5.6        1.1   1
Q12046     Q12046 CHROMOSOME IV READING FRAME ORF YDL     5.1        1.2   1
Q07623     Q07623 CHROMOSOME IV READING FRAME ORF YDL     5.1        1.2   1
Q10954     Q10954 HYPOTHETICAL 78.8 KD PROTEIN B0336.     4.9        1.3   1
Q26276     Q26276 RNA RECOGNITION MOTIF-TYPE RNA-BIND     4.4        1.5   1
O01835     O01835 SIMILARITY TO XENOPUS CYTOPLASMIC P     4.2        1.5   1
O01691     O01691 SIMILAR TO A HUMAN PUTATIVE TUMOR S     4.0        1.6   1
Q23452     Q23452 F07A11.6 (FRAGMENT).                    3.9        1.6   1
ROAB_ARTSA P80350 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO     3.8        1.7   1
YN8V_YEAST P53743 HYPOTHETICAL 36.4 KD PROTEIN IN POP     3.2        1.9   1
Q26279     Q26279 RNA RECOGNITION MOTIF-TYPE RNA-BIND     2.9        2.1   1
Q18317     Q18317 SIMILAR TO C. ELEGANS PROTEIN C40H1     2.6        2.2   1
MUD2_YEAST P36084 SPLICING FACTOR MUD2.                   1.9        2.6   1
Q21559     Q21559 M18.7.                                  1.2        3.1   1
O29092     O29092 ACYL-COA DEHYDROGENASE, SHORT CHAIN     0.9        3.3   1
YG3Q_YEAST P39927 HYPOTHETICAL 47.0 KD PROTEIN IN CYS    -0.2        4.3   1
P70221     P70221 ORF2 PRODUCT (FRAGMENT).               -0.3        4.3   1
Y051_NPVAC P41455 HYPOTHETICAL 37.5 KD PROTEIN IN LEF    -0.9          5   1
YHR9_YEAST P38827 HYPOTHETICAL 123.9 KD PROTEIN IN OR    -1.2        5.4   1
O35847     O35847 ADAPT78.                               -2.7        7.6   1
HIPO_CAMJE P45493 HIPPURATE HYDROLASE (EC 3.5.1.32) (    -3.7        9.4   1
Q60701     Q60701 SPLICING FACTOR, ARGININE/SERINE-RI    -3.7        9.5   1
Q24424     Q24424 RNA BINDING PROTEIN (FRAGMENT).        -3.9         10   1
BLSA_HUMAN Q02832 B-LYMPHOCYTE ANTIGEN PRECURSOR (B-L    -4.2         11   1
XE7_HUMAN  Q02040 PROTEIN XE7.                           -4.2         11   1
YAQ2_SCHPO Q10103 HYPOTHETICAL 108.7 KD PROTEIN C18G6    -6.5         18   1
O00583     O00583 DOWN SYNDROME CRITICAL REGION 1 PRO    -6.7         19   1
O13838     O13838 HYPOTHETICAL 40.3 KD PROTEIN.          -7.5         23   1
O05954     O05954 UDP-MURNAC-TRIPEPTIDE SYNTHETASE.      -7.6         23   1
YM28_YEAST Q03790 HYPOTHETICAL 52.6 KD PROTEIN IN IMP    -8.1         26   1
Q19944     Q19944 F31F6.3.                               -8.7         30   1
Q26274     Q26274 RNA RECOGNITION MOTIF-TYPE RNA-BIND    -8.9         32   1
O01886     O01886 SIMILARITY TO THE PEPTIDASE FAMILY     -9.2         34   1
Q19164     Q19164 HYPOTHETICAL PROTEIN F07D3.3.          -9.2         34   1
ASM4_YEAST Q05166 ASM4 PROTEIN.                          -9.5         37   1
Y117_HUMAN P42696 HYPOTHETICAL PROTEIN KIAA0117 (HAL8   -10.0         41   1
O00582     O00582 DOWN SYNDROME CRITICAL REGION 1 PRO   -10.0         41   1
O28580     O28580 PHOSPHORIBOSYLFORMYLGLYCINAMIDINE C   -10.9         50   1
O35309     O35309 NMI.                                  -11.2         54   1
O29837     O29837 SIGNAL-TRANSDUCING HISTIDINE KINASE   -11.7         61   1
Q47952     Q47952 PRE-HGBA PRECURSOR.                   -12.8         78   1
Q08646     Q08646 CHROMOSOME XV READING FRAME ORF YOR   -13.0         82   1
Q47957     Q47957 HEMOGLOBIN-BINDING PROTEIN.           -13.1         84   1
Q58954     Q58954 HYPOTHETICAL 21.3 KD PROTEIN 1559.    -13.2         86   1
Q26278     Q26278 RNA RECOGNITION MOTIF-TYPE RNA-BIND   -13.5         92   1
Q13287     Q13287 HOU.                                  -14.9    1.3e+02   1
TKTC_METJA Q58092 PUTATIVE TRANSKETOLASE C-TERMINAL S   -15.0    1.3e+02   1
PR06_YEAST P19735 PRE-MRNA SPLICING FACTOR PRP6.        -15.1    1.3e+02   1
KHK_HUMAN  P50053 KETOHEXOKINASE (EC 2.7.1.3) (HEPATI   -15.5    1.5e+02   1
PUR5_METJA Q57656 PROBABLE PHOSPHORIBOSYLFORMYLGLYCIN   -15.8    1.6e+02   1
O31824     O31824 YNGD PROTEIN.                         -15.9    1.6e+02   1
Q92518     Q92518 WS-1/TYPE5 (FRAGMENT).                -16.0    1.6e+02   1
YD33_SCHPO Q10267 HYPOTHETICAL 30.9 KD PROTEIN C13G7.   -16.1    1.7e+02   1
Q09135     Q09135 HETEROGENEOUS NUCLEAR RIBONUCLEOPRO   -16.1    1.7e+02   1
O30057     O30057 HYPOTHETICAL 32.2 KD PROTEIN.         -16.3    1.8e+02   1
Q42378     Q42378 U1 SNRNP 70K TRUNCATED PROTEIN.       -16.7    1.9e+02   1
Q42482     Q42482 X P.DELTOIDES HYBRID WOUND RESPONSI   -16.8      2e+02   1
O35002     O35002 PUTATIVE PROTEASE.                    -17.0    2.1e+02   1
PGDS_RAT   P20786 ALPHA PLATELET-DERIVED GROWTH FACTO   -17.1    2.1e+02   1
YY08_METJA Q60307 HYPOTHETICAL PROTEIN MJECS08.         -17.2    2.2e+02   1
Q48827     Q48827 MAJOR OUTER MEMBRANE PROTEIN PRECUR   -17.8    2.5e+02   1
Q23637     Q23637 ZK856.3.                              -17.9    2.5e+02   1
Q48639     Q48639 BGLR.                                 -17.9    2.5e+02   1
VJ01_VACCC P21032 PROTEIN J1.                           -18.3    2.8e+02   1
HBA_ARAAR  P01996 HEMOGLOBIN ALPHA-A CHAIN.             -18.4    2.8e+02   1
YAB9_SCHPO Q09809 HYPOTHETICAL 90.9 KD PROTEIN C2G11.   -18.4    2.8e+02   1
P94393     P94393 HOMOLOGUE OF HYPOTHETICAL PROTEIN H   -18.7    3.1e+02   1
Q26271     Q26271 RNA RECOGNITION MOTIF-TYPE RNA-BIND   -18.9    3.2e+02   1
Q96423     Q96423 CYTOCHROME P450.                      -18.9    3.2e+02   1
O00373     O00373 L1 ELEMENT L1.24 P40.                 -19.3    3.5e+02   1
YHB0_YEAST P38748 HYPOTHETICAL 67.5 KD PROTEIN IN PRP   -19.4    3.6e+02   1
VJ01_VACCV P07616 PROTEIN J1 (PROTEIN F7).              -19.4    3.6e+02   1
SYH_METJA  Q58406 HISTIDYL-TRNA SYNTHETASE (EC 6.1.1.   -19.8    3.9e+02   1
Q12452     Q12452 ORF YLR100W.                          -20.0    4.1e+02   1
Q46102     Q46102 CDTC.                                 -20.2    4.3e+02   1
O17002     O17002 T23B12.7 PROTEIN.                     -20.3    4.4e+02   1
Q19942     Q19942 F31F6.1.                              -20.3    4.5e+02   1
PHYA_SOLTU P30733 PHYTOCHROME A.                        -20.4    4.5e+02   1
P75023     P75023 CARBOXYL-TERMINAL PROTEASE.           -20.4    4.5e+02   1
SYF_METJA  Q57911 PROBABLE PHENYLALANYL-TRNA SYNTHETA   -20.4    4.6e+02   1
Y447_METJA Q57889 HYPOTHETICAL PROTEIN MJ0447.          -20.6    4.7e+02   1
Y383_METJA Q57828 HYPOTHETICAL PROTEIN MJ0383.          -20.6    4.8e+02   1
Q94172     Q94172 SIMILAR TO EF-HAND CALCIUM BINDING    -20.8      5e+02   1
CHLL_CHLRE Q00469 PROTOCHLOROPHYLLIDE REDUCTASE IRON-   -20.9      5e+02   1
Q61283     Q61283 ALPHA-1 ANTITRYPSIN 1-2 PRECURSOR (   -20.9    5.1e+02   1
A1A2_MOUSE P22599 ALPHA-1 ANTITRYPSIN 2 PRECURSOR (AL   -20.9    5.1e+02   1
Q00898     Q00898 ALPHA-1 ANTITRYPSIN 1-5 PRECURSOR (   -20.9    5.1e+02   1
Q00897     Q00897 ALPHA-1 ANTITRYPSIN 1-4 PRECURSOR (   -20.9    5.1e+02   1
Q85381     Q85381 HOMOLOG OF VACCINIA VIRUS CDS J1R.    -21.0    5.2e+02   1
VJ01_VARV  P33004 PROTEIN J1.                           -21.0    5.2e+02   1
O34784     O34784 DNA-BINDING PROTEIN.                  -21.0    5.2e+02   1
MENE_HAEIN P44565 O-SUCCINYLBENZOIC ACID--COA LIGASE    -21.1    5.3e+02   1
T2C2_CHVP1 P31117 TYPE II RESTRICTION ENZYME CVIAII (   -21.2    5.4e+02   1
CARA_BACSU P25993 CARBAMOYL-PHOSPHATE SYNTHASE, PYRIM   -21.2    5.4e+02   1
SFCA_ECOLI P26616 PROBABLE MALATE OXIDOREDUCTASE (NAD   -21.2    5.5e+02   1
Q23267     Q23267 PROBABLE CARBOXYLESTERASE ZC376.3 I   -21.5    5.8e+02   1
DDLA_ECOLI P23844 D-ALANINE--D-ALANINE LIGASE A (EC 6   -21.5    5.8e+02   1
KLP1_CHLRE P46870 KINESIN-LIKE PROTEIN KLP1.            -21.5    5.8e+02   1
Q26272     Q26272 RNA RECOGNITION MOTIF-TYPE RNA-BIND   -21.7    6.1e+02   1
CPC3_RABIT P00182 CYTOCHROME P450 IIC3 (EC 1.14.14.1)   -22.0    6.6e+02   1
O29409     O29409 CONSERVED HYPOTHETICAL PROTEIN.       -22.0    6.6e+02   1
O34925     O34925 PURINE NUCLEOSIDE PHOSPHORYLASE.      -22.2    6.9e+02   1
Q26281     Q26281 RNA RECOGNITION MOTIF-TYPE RNA-BIND   -22.4    7.2e+02   1
Q25988     Q25988 (CLONE PNM5) ORF (FRAGMENT).          -22.4    7.2e+02   1
META_ECOLI P07623 HOMOSERINE O-SUCCINYLTRANSFERASE (E   -22.5    7.3e+02   1
O04614     O04614 SIMILARITY TO NEBULIN.                -22.8    7.8e+02   1
Q51350     Q51350 PVDS.                                 -22.8    7.9e+02   1
P95425     P95425 PVDS.                                 -22.8    7.9e+02   1
P75431     P75431 TYPE 1 RESTRICTION ENZYME.            -22.9      8e+02   1
O00364     O00364 L1 ELEMENT L1.14 P40.                 -22.9      8e+02   1
PRE1_STAAU P03857 PLASMID RECOMBINATION ENZYME (MOBIL   -22.9    8.1e+02   1
Q96515     Q96515 AR192.                                -23.0    8.2e+02   1
O27761     O27761 PHOSPHATE-BINDING PROTEIN PSTS HOMO   -23.1    8.4e+02   1
Q51783     Q51783 IRON REGULATED TRANSCRIPTION ACTIVA   -23.2    8.6e+02   1
Q00896     Q00896 ALPHA-1 ANTITRYPSIN 1-3 PRECURSOR (   -23.4      9e+02   1
A1A1_MOUSE P07758 ALPHA-1 ANTITRYPSIN 1 PRECURSOR (AL   -23.4      9e+02   1
Q20445     Q20445 F46B6.3.                              -23.5    9.3e+02   1
YNC8_CAEEL P34541 HYPOTHETICAL 15.3 KD PROTEIN R05D3.   -23.5    9.3e+02   1
Q57721     Q57721 HYPOTHETICAL 12.0 KD PROTEIN 0273.    -23.5    9.3e+02   1
Y556_METJA Q57976 HYPOTHETICAL PROTEIN MJ0556.          -23.7    9.7e+02   1
O28372     O28372 LSU RIBOSOMAL PROTEIN L19E (RPL19E)   -23.8    9.8e+02   1
O00376     O00376 L1 ELEMENT L1.33 P40.                 -23.8    9.9e+02   1
O00374     O00374 L1 ELEMENT L1.25 P40 AND PUTATIVE P   -23.8    9.9e+02   1
O00371     O00371 L1 ELEMENT L1.21 P40 AND PUTATIVE P   -23.8    9.9e+02   1
O00361     O00361 L1 ELEMENT L1.8 P40 AND PUTATIVE P1   -23.8    9.9e+02   1
Q15605     Q15605 ORF1 CODES FOR A 40 KDA PRODUCT.      -23.8    9.9e+02   1
O00377     O00377 L1 ELEMENT L1.39 P40 AND PUTATIVE P   -23.8    9.9e+02   1
O00365     O00365 L1 ELEMENT L1.15 P40 AND PUTATIVE P   -23.8    9.9e+02   1
Q12880     Q12880 RETROTRANSPOSABLE L1 ELEMENT LRE2 F   -23.8    9.9e+02   1
O00369     O00369 L1 ELEMENT L1.20 P40 AND PUTATIVE P   -23.8    9.9e+02   1

Parsed for domains:
Sequence   Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------   ------- ----- -----    ----- -----      -----  -------
Q91581       1/1      18    89 ..     1    77 []   119.7    2e-31
CST2_HUMAN   1/1      18    89 ..     1    77 []   119.7    2e-31
Q61413       1/1       8    79 ..     1    77 []   114.2  8.9e-30
Q14011       1/1       8    79 ..     1    77 []   114.2  9.1e-30
P93486       1/1      38   109 ..     1    77 []   114.1  9.6e-30
GRP_DAUCA    1/1       8    79 ..     1    77 []   113.4  1.6e-29
Q14498       2/3     252   323 ..     1    77 []   113.3  1.7e-29
Q14499       2/3     252   323 ..     1    77 []   113.3  1.7e-29
GR10_BRANA   1/1       8    79 ..     1    77 []   113.0    2e-29
ROG_HUMAN    1/1      10    81 ..     1    77 []   113.0    2e-29
Q15097       3/4     168   238 ..     1    77 []   111.8  4.5e-29
Q93004       3/4     193   263 ..     1    77 []   111.8  4.5e-29
PABP_MOUSE   3/4     193   263 ..     1    77 []   111.2  7.2e-29
O24106       1/1       8    79 ..     1    77 []   110.9  8.9e-29
Q40426       1/1       8    79 ..     1    77 []   110.4  1.2e-28
O04070       1/1       9    80 ..     1    77 []   110.3  1.3e-28
Q41518       1/1       8    79 ..     1    77 []   110.3  1.3e-28
O24601       1/1      10    81 ..     1    77 []   110.2  1.4e-28
O24188       1/1      39   110 ..     1    77 []   110.2  1.4e-28
Q39105       1/1      18    89 ..     1    77 []   109.8  1.8e-28
RO28_SPIOL   2/2     151   222 ..     1    77 []   109.5  2.2e-28
O22173       3/4     227   297 ..     1    77 []   109.4  2.5e-28
PAB2_ARATH   3/4     217   287 ..     1    77 []   109.1    3e-28
RNPL_HUMAN   1/1       8    79 ..     1    77 []   108.8  3.6e-28
GRP1_SINAL   1/1      10    81 ..     1    77 []   108.6  4.4e-28
Q40052       1/1       8    79 ..     1    77 []   108.6  4.4e-28
Q40270       2/2     207   278 ..     1    77 []   108.1  5.9e-28
Q15164       1/2       4    74 ..     1    77 []   108.1  5.9e-28
Q13310       3/4     193   263 ..     1    77 []   108.1  5.9e-28
O23793       1/1      40   111 ..     1    77 []   108.1  6.1e-28
Q40437       1/1      40   111 ..     1    77 []   108.1  6.1e-28
Q41834       2/2     221   292 ..     1    77 []   108.0  6.3e-28
GRP8_ARATH   1/1       8    79 ..     1    77 []   107.9  7.1e-28
GRP2_SINAL   1/1      10    81 ..     1    77 []   107.8  7.3e-28
TIA1_MOUSE   2/3     108   179 ..     1    77 []   107.7  8.2e-28
O24306       2/2     208   279 ..     1    77 []   107.5  9.4e-28
RO31_NICSY   2/2     232   303 ..     1    77 []   107.5  9.4e-28
P92871       2/2     232   303 ..     1    77 []   107.4  9.7e-28
Q39209       2/2     227   298 ..     1    77 []   107.4  9.7e-28
Q43350       2/2     231   302 ..     1    77 []   107.4  9.7e-28
RO31_ARATH   2/2     246   317 ..     1    77 []   107.4  9.7e-28
P93616       3/4     213   283 ..     1    77 []   106.9  1.4e-27
Q40425       1/1       8    79 ..     1    77 []   106.7  1.6e-27
GRP2_SORVU   1/1      10    81 ..     1    77 []   106.5  1.8e-27
P87135       3/4     263   333 ..     1    77 []   106.5  1.9e-27
PABP_SCHPO   3/4     249   319 ..     1    77 []   106.5  1.9e-27
RT19_ARATH   1/1      33   104 ..     1    77 []   106.4  1.9e-27
O35479       1/1      10    81 ..     1    77 []   106.2  2.2e-27
Q40427       1/1       8    79 ..     1    77 []   106.0  2.6e-27
Q41453       1/1       8    79 ..     1    77 []   105.6  3.4e-27
O24187       1/1      10    81 ..     1    77 []   105.2  4.4e-27
O22390       1/1      10    81 ..     1    77 []   105.2  4.6e-27
GRP7_ARATH   1/1      10    81 ..     1    77 []   105.2  4.6e-27
TIA1_HUMAN   2/3      97   168 ..     1    77 []   104.9  5.5e-27
Q08935       2/2     190   261 ..     1    77 []   104.7  6.3e-27
RO30_NICPL   2/2     196   267 ..     1    77 []   104.7  6.3e-27
Q39953       3/4     206   276 ..     1    77 []   104.0    1e-26
Q39061       1/2     118   189 ..     1    77 []   103.7  1.3e-26
Q39062       1/2     110   181 ..     1    77 []   103.7  1.3e-26
Q40436       1/1      42   113 ..     1    77 []   103.7  1.3e-26
GRPA_MAIZE   1/1      10    81 ..     1    77 []   103.7  1.3e-26
O22385       1/1      10    81 ..     1    77 []   103.6  1.3e-26
RO28_NICSY   2/2     193   264 ..     1    77 []   103.6  1.4e-26
GAR2_SCHPO   2/2     368   438 ..     1    77 []   103.2  1.8e-26
O13707       2/2     368   438 ..     1    77 []   103.2  1.8e-26
O23798       2/2     211   282 ..     1    77 []   102.9  2.1e-26
Q42412       1/1       8    79 ..     1    77 []   102.8  2.3e-26
YIS1_YEAST   1/1      66   136 ..     1    77 []   102.7  2.5e-26
O22653       1/1       9    80 ..     1    77 []   102.4  3.2e-26
P90699       1/1       5    76 ..     1    77 []   102.1  3.9e-26
Q15815       1/1     120   191 ..     1    77 []   101.9  4.3e-26
Q64283       1/1     120   191 ..     1    77 []   101.9  4.3e-26
RO33_NICSY   1/2     116   187 ..     1    77 []   101.8  4.8e-26
Q08948       1/2     111   182 ..     1    77 []   101.8  4.8e-26
Q08940       1/2     105   176 ..     1    77 []   101.8  4.8e-26
O22703       1/1      14    85 ..     1    77 []   101.6  5.6e-26
O22384       1/1      10    81 ..     1    77 []   101.4  6.1e-26
Q43472       1/1       8    79 ..     1    77 []   101.4  6.4e-26
Q62029       3/4     193   263 ..     1    77 []   100.9  8.7e-26
Q09959       2/3     177   248 ..     1    77 []   100.8  9.7e-26
Q15376       1/1      10    80 ..     1    77 []   100.2  1.4e-25
Q15414       1/1      10    80 ..     1    77 []   100.2  1.4e-25
Q24474       1/3     112   183 ..     1    77 []   100.1  1.5e-25
Q26293       1/3     112   183 ..     1    77 []   100.1  1.5e-25
Q24473       1/3     112   183 ..     1    77 []   100.1  1.5e-25
O24184       1/1      10    81 ..     1    77 []    99.9  1.8e-25
PABP_YEAST   2/4     127   197 ..     1    77 []    99.8  1.9e-25
Q92227       3/4     225   295 ..     1    77 []    99.6  2.2e-25
SC35_CHICK   1/1      16    87 ..     1    77 []    99.6  2.2e-25
Q62093       1/1      16    87 ..     1    77 []    99.6  2.2e-25
NSR1_YEAST   1/2     170   241 ..     1    77 []    99.5  2.3e-25
NSR1_YEAST   2/2     269   340 ..     1    77 []    99.5  2.3e-25
Q44555       1/1       3    74 ..     1    77 []    99.5  2.3e-25
PABP_HUMAN   1/4      13    84 ..     1    77 []    99.4  2.6e-25
Q93004       1/4      13    84 ..     1    77 []    99.4  2.6e-25
PABP_MOUSE   1/4      13    84 ..     1    77 []    99.4  2.6e-25
Q15415       1/1      10    80 ..     1    77 []    99.3  2.6e-25
TIA1_HUMAN   1/3       9    78 ..     1    77 []    99.2  2.8e-25
TIA1_MOUSE   1/3       9    78 ..     1    77 []    99.2  2.8e-25
Q13235       1/3      41   112 ..     1    77 []    99.2  2.8e-25
Q12926       1/3      41   112 ..     1    77 []    99.2  2.8e-25
Q60899       1/3      41   112 ..     1    77 []    99.2  2.8e-25
RO31_NICPL   2/2     210   281 ..     1    77 []    98.9  3.5e-25
RN15_YEAST   1/1      20    91 ..     1    77 []    98.9  3.7e-25
RO31_NICSY   1/2     138   209 ..     1    77 []    98.8  3.8e-25
Q40270       1/2     113   184 ..     1    77 []    98.7    4e-25
O17309       1/2      97   168 ..     1    77 []    98.6  4.3e-25
O17310       1/2     104   175 ..     1    77 []    98.6  4.3e-25
PABP_XENLA   1/4      13    84 ..     1    77 []    98.5  4.7e-25
TIAR_HUMAN   2/3      99   170 ..     1    77 []    98.5  4.8e-25
O15187       1/2      60   131 ..     1    77 []    98.5  4.8e-25
TIAR_MOUSE   2/3     116   187 ..     1    77 []    98.5  4.8e-25
PAB2_ARATH   2/4     126   196 ..     1    77 []    98.3  5.4e-25
Q08937       2/2     209   280 ..     1    77 []    98.3  5.4e-25
Q13310       1/4      13    84 ..     1    77 []    98.3  5.5e-25
Q91584       1/3      36   107 ..     1    77 []    98.1  6.1e-25
P79736       1/3      40   111 ..     1    77 []    98.1  6.1e-25
PES4_YEAST   1/4      93   164 ..     1    77 []    97.8  7.8e-25
ELAV_DROME   3/3     404   475 ..     1    77 []    97.5  9.4e-25
ELAV_DROVI   3/3     440   511 ..     1    77 []    97.5  9.4e-25
PAB2_ARATH   4/4     320   390 ..     1    77 []    97.5  9.6e-25
Q60900       1/3      41   112 ..     1    77 []    97.3    1e-24
Q16135       1/3      32   103 ..     1    77 []    97.3    1e-24
Q41367       1/2      40   111 ..     1    77 []    96.5  1.9e-24
RO28_NICSY   1/2      99   170 ..     1    77 []    96.4    2e-24
SQD_DROME    1/2      58   128 ..     1    77 []    96.3  2.1e-24
RO28_SPIOL   1/2      57   128 ..     1    77 []    96.2  2.3e-24
HUD_HUMAN    1/3      48   119 ..     1    77 []    96.2  2.3e-24
HUD_MOUSE    1/3      53   124 ..     1    77 []    96.2  2.3e-24
HUD_RAT      1/3      41   112 ..     1    77 []    96.2  2.3e-24
Q91585       1/3      48   119 ..     1    77 []    96.2  2.3e-24
Q90409       1/3      46   117 ..     1    77 []    96.2  2.3e-24
PUB1_YEAST   2/3     163   234 ..     1    77 []    95.7  3.2e-24
P93616       4/4     316   386 ..     1    77 []    95.6  3.6e-24
P92871       1/2     138   209 ..     1    77 []    95.4  4.1e-24
RO31_ARATH   1/2     152   223 ..     1    77 []    95.4  4.1e-24
Q39209       1/2     133   204 ..     1    77 []    95.4  4.1e-24
Q43350       1/2     137   208 ..     1    77 []    95.4  4.1e-24
PABP_XENLA   3/4     193   263 ..     1    77 []    95.3  4.2e-24
PABP_DROME   3/4     183   254 ..     1    77 []    95.3  4.4e-24
Q24668       1/2     121   192 ..     1    77 []    95.2  4.5e-24
SXLF_DROME   1/2     127   198 ..     1    77 []    95.2  4.5e-24
Q99141       1/2     119   190 ..     1    77 []    95.2  4.5e-24
Q39568       1/2      13    83 ..     1    77 []    95.1  4.9e-24
O25501       1/1       4    74 ..     1    77 []    95.0  5.3e-24
Q19706       1/1     178   249 ..     1    77 []    95.0  5.3e-24
Q13235       3/3     265   336 ..     1    77 []    94.8    6e-24
Q12926       3/3     278   349 ..     1    77 []    94.8    6e-24
PABP_YEAST   3/4     220   290 ..     1    77 []    94.8  6.2e-24
Q43349       2/2     251   322 ..     1    77 []    94.6    7e-24
Q43349       1/2     101   172 ..     1    77 []    94.5  7.6e-24
Q44560       1/1       3    74 ..     1    77 []    94.5  7.7e-24
Q13310       4/4     296   365 ..     1    77 []    94.2  9.5e-24
Q15164       2/2     107   176 ..     1    77 []    94.2  9.5e-24
Q14100       1/2      11    81 ..     1    77 []    93.9  1.1e-23
Q12771       1/2      78   148 ..     1    77 []    93.9  1.1e-23
Q01858       1/2      78   148 ..     1    77 []    93.9  1.1e-23
Q14101       1/2      99   169 ..     1    77 []    93.9  1.1e-23
Q60668       1/2      68   138 ..     1    77 []    93.9  1.1e-23
Q14103       1/2      99   169 ..     1    77 []    93.9  1.1e-23
Q14102       1/2       8    78 ..     1    77 []    93.9  1.1e-23
Q91584       3/3     267   338 ..     1    77 []    93.9  1.2e-23
P79736       3/3     264   335 ..     1    77 []    93.9  1.2e-23
Q90408       1/1     102   173 ..     1    77 []    93.9  1.2e-23
Q91583       3/3     308   379 ..     1    77 []    93.8  1.2e-23
Q60899       3/3     279   350 ..     1    77 []    93.8  1.2e-23
Q91903       3/3     308   379 ..     1    77 []    93.8  1.2e-23
Q08374       1/1       3    74 ..     1    77 []    93.7  1.3e-23
Q08935       1/2      89   160 ..     1    77 []    93.7  1.3e-23
Q08212       2/3      97   168 ..     1    77 []    93.7  1.3e-23
Q20084       1/3      44   115 ..     1    77 []    93.6  1.4e-23
Q13595       1/1     121   192 ..     1    77 []    93.5  1.5e-23
O22173       2/4     136   206 ..     1    77 []    93.4  1.6e-23
Q41367       2/2     137   208 ..     1    77 []    93.3  1.7e-23
Q93194       1/2      29   100 ..     1    77 []    93.1    2e-23
Q91585       3/3     285   356 ..     1    77 []    93.1    2e-23
Q90409       3/3     286   357 ..     1    77 []    93.1    2e-23
HUD_RAT      3/3     292   363 ..     1    77 []    93.1    2e-23
HUD_HUMAN    3/3     299   370 ..     1    77 []    93.1    2e-23
HUD_MOUSE    3/3     304   375 ..     1    77 []    93.1    2e-23
PAB5_ARATH   3/4     227   297 ..     1    77 []    93.0  2.1e-23
O01671       1/2      66   137 ..     1    77 []    93.0  2.1e-23
Q60990       1/1      10    81 ..     1    77 []    92.9  2.3e-23
O23798       1/2     117   188 ..     1    77 []    92.9  2.3e-23
TRA2_DROME   1/1      99   170 ..     1    77 []    92.8  2.4e-23
Q14576       1/3      41   112 ..     1    77 []    92.8  2.4e-23
Q41124       2/2     206   277 ..     1    77 []    92.7  2.5e-23
PABP_DROME   1/4       4    75 ..     1    77 []    92.7  2.5e-23
Q19579       4/4     345   415 ..     1    77 []    92.6  2.9e-23
Q19581       4/4     345   415 ..     1    77 []    92.6  2.9e-23
Q13310       2/4     101   170 ..     1    77 []    92.5  3.1e-23
NOP4_YEAST   1/4      28    98 ..     1    77 []    92.4  3.2e-23
P70807       1/1       3    74 ..     1    77 []    92.3  3.4e-23
Q24473       3/3     363   434 ..     1    77 []    92.2  3.6e-23
Q26293       3/3     363   434 ..     1    77 []    92.2  3.6e-23
Q24474       3/3     358   429 ..     1    77 []    92.2  3.6e-23
Q60901       2/2     194   265 ..     1    77 []    92.2  3.7e-23
Q60900       3/3     286   357 ..     1    77 []    92.2  3.7e-23
SP49_HUMAN   2/2     102   174 ..     1    77 []    92.1  3.8e-23
PAB2_ARATH   1/4      38   109 ..     1    77 []    92.1  3.9e-23
PABP_YEAST   4/4     323   393 ..     1    77 []    92.0  4.2e-23
ROA1_MOUSE   2/2     106   176 ..     1    77 []    92.0  4.2e-23
ROA1_BOVIN   2/2     106   176 ..     1    77 []    92.0  4.2e-23
ROA1_HUMAN   2/2     106   176 ..     1    77 []    92.0  4.2e-23
ROA1_RAT     2/2     106   176 ..     1    77 []    92.0  4.2e-23
P70372       1/3      22    93 ..     1    77 []    91.9  4.7e-23
PABP_XENLA   2/4     101   170 ..     1    77 []    91.8  4.8e-23
Q15097       2/4      76   145 ..     1    77 []    91.8    5e-23
PABP_MOUSE   2/4     101   170 ..     1    77 []    91.8    5e-23
PABP_HUMAN   2/4     101   170 ..     1    77 []    91.8    5e-23
Q93004       2/4     101   170 ..     1    77 []    91.8    5e-23
P73557       1/1       3    74 ..     1    77 []    91.8    5e-23
P87135       1/4      82   153 ..     1    77 []    91.7  5.2e-23
PABP_SCHPO   1/4      68   139 ..     1    77 []    91.7  5.2e-23
HRB1_YEAST   1/3     138   207 ..     1    77 []    91.7  5.3e-23
Q41834       1/2     127   198 ..     1    77 []    91.7  5.4e-23
Q62029       1/4      13    84 ..     1    77 []    91.6  5.5e-23
Q15717       1/3      22    93 ..     1    77 []    91.5  6.1e-23
Q99628       1/3     113   184 ..     1    77 []    91.2  7.5e-23
PABP_HUMAN   3/4     193   260 ..     1    77 []    91.2  7.6e-23
CABA_MOUSE   1/2      77   147 ..     1    77 []    90.8  9.4e-23
O35698       1/1      10    81 ..     1    77 []    90.8    1e-22
O22173       4/4     330   400 ..     1    77 []    90.7    1e-22
Q91582       3/3     246   317 ..     1    77 []    90.6  1.1e-22
O15414       1/1     275   346 ..     1    77 []    90.5  1.2e-22
Q91582       1/3      22    93 ..     1    77 []    90.3  1.3e-22
Q44556       1/1       3    74 ..     1    77 []    90.3  1.4e-22
PAB5_ARATH   4/4     330   400 ..     1    77 []    90.3  1.4e-22
Q14576       3/3     278   349 ..     1    77 []    90.0  1.6e-22
O02008       1/1     107   178 ..     1    77 []    90.0  1.7e-22
O02009       1/1      60   131 ..     1    77 []    90.0  1.7e-22
Q39675       1/2     114   185 ..     1    77 []    89.9  1.8e-22
Q62029       2/4     101   170 ..     1    77 []    89.8  1.9e-22
Q08937       1/2      89   160 ..     1    77 []    89.8    2e-22
Q23795       1/2      42   112 ..     1    77 []    89.8    2e-22
YDC1_SCHPO   1/1     103   174 ..     1    77 []    89.7  2.1e-22
O24306       1/2     111   182 ..     1    77 []    89.7  2.1e-22
PABP_SCHPO   2/4     156   226 ..     1    77 []    89.6  2.2e-22
P87135       2/4     170   240 ..     1    77 []    89.6  2.2e-22
RO31_NICPL   1/2      90   161 ..     1    77 []    89.6  2.3e-22
ROA1_MACMU   2/2     106   176 ..     1    77 []    89.6  2.3e-22
PABP_SCHPO   4/4     352   422 ..     1    77 []    89.5  2.4e-22
P87135       4/4     366   436 ..     1    77 []    89.5  2.4e-22
Q99729       1/2      70   140 ..     1    77 []    89.4  2.6e-22
Q04150       1/2      70   140 ..     1    77 []    89.4  2.6e-22
Q44554       1/1       3    74 ..     1    77 []    89.3  2.8e-22
NAM8_YEAST   2/3     165   237 ..     1    77 []    89.3  2.8e-22
SC35_HUMAN   1/1      16    87 ..     1    77 []    89.1  3.1e-22
YIS5_YEAST   1/1      33   104 ..     1    77 []    88.9  3.6e-22
PABP_DROME   2/4      92   162 ..     1    77 []    88.7  4.2e-22
Q17350       4/4     319   389 ..     1    77 []    88.5  4.6e-22
GBP2_YEAST   1/3     124   193 ..     1    77 []    88.5  4.7e-22
TIAR_HUMAN   1/3      11    80 ..     1    77 []    88.4    5e-22
Q41810       1/1      10    81 ..     1    77 []    88.2  6.1e-22
Q91583       1/3      68   140 ..     1    77 []    88.1  6.5e-22
ROA1_XENLA   2/2     107   177 ..     1    77 []    87.8    8e-22
Q46349       1/1       3    74 ..     1    77 []    87.8    8e-22
P93616       1/4      34   105 ..     1    77 []    87.7  8.4e-22
Q08948       2/2     214   285 ..     1    77 []    87.6  8.7e-22
Q15097       4/4     271   340 ..     1    77 []    87.5  9.7e-22
Q93004       4/4     296   365 ..     1    77 []    87.5  9.7e-22
PABP_MOUSE   4/4     296   365 ..     1    77 []    87.5  9.7e-22
PABP_HUMAN   4/4     293   362 ..     1    77 []    87.5  9.7e-22
Q91579       3/3     379   450 ..     1    77 []    87.4    1e-21
PAB5_ARATH   2/4     134   204 ..     1    77 []    87.4    1e-21
Q53322       1/1       2    73 ..     1    77 []    87.2  1.1e-21
Q15717       3/3     246   317 ..     1    77 []    87.2  1.2e-21
RO33_NICSY   2/2     219   290 ..     1    77 []    87.0  1.3e-21
Q55343       1/1       3    74 ..     1    77 []    86.9  1.4e-21
Q99377       1/1     105   176 ..     1    77 []    86.9  1.5e-21
Q62376       1/1      35   106 ..     1    77 []    86.9  1.5e-21
P78493       1/1     105   176 ..     1    77 []    86.9  1.5e-21
RU17_HUMAN   1/1     282   353 ..     1    77 []    86.9  1.5e-21
Q39062       2/2     213   284 ..     1    77 []    86.7  1.6e-21
Q39061       2/2     221   292 ..     1    77 []    86.7  1.6e-21
O13620       2/5     325   396 ..     1    77 []    86.7  1.7e-21
Q15584       2/2     495   564 ..     1    77 []    86.5  1.9e-21
ROM_HUMAN    3/3     655   724 ..     1    77 []    86.5  1.9e-21
GBP2_YEAST   2/3     221   291 ..     1    77 []    86.5  1.9e-21
Q91920       1/2      23    93 ..     1    77 []    86.5    2e-21
Q57014       1/1       3    74 ..     1    77 []    86.1  2.5e-21
Q39953       1/4      28    99 ..     1    77 []    86.0  2.7e-21
RU17_DROME   1/1     104   175 ..     1    77 []    85.8  3.1e-21
Q39953       2/4     116   186 ..     1    77 []    85.8  3.2e-21
RO30_NICPL   1/2      89   160 ..     1    77 []    85.5  3.9e-21
Q91903       1/3      68   140 ..     1    77 []    85.5  3.9e-21
SR55_DROME   1/2       5    68 ..     1    77 []    85.5    4e-21
Q24252       1/2       6    69 ..     1    77 []    85.5    4e-21
Q24534       2/2     121   193 ..     1    77 []    85.4    4e-21
PABP_YEAST   1/4      39   110 ..     1    77 []    85.4    4e-21
Q23796       1/2       6    69 ..     1    77 []    85.4  4.1e-21
PUB1_YEAST   1/3      76   146 ..     1    77 []    85.4  4.1e-21
NAB4_YEAST   1/2     161   230 ..     1    77 []    85.4  4.2e-21
ROA1_RAT     1/2      15    85 ..     1    77 []    85.1  4.9e-21
ROA1_BOVIN   1/2      15    85 ..     1    77 []    85.1  4.9e-21
ROA1_MOUSE   1/2      15    85 ..     1    77 []    85.1  4.9e-21
ROA1_HUMAN   1/2      15    85 ..     1    77 []    85.1  4.9e-21
Q90602       1/2      92   162 ..     1    77 []    85.1    5e-21
PAB5_ARATH   1/4      47   117 ..     1    77 []    85.0  5.6e-21
O13707       1/2     265   336 ..     1    77 []    84.7  6.5e-21
GAR2_SCHPO   1/2     265   336 ..     1    77 []    84.7  6.5e-21
Q13242       1/2      16    84 ..     1    77 []    84.6  7.3e-21
Q90407       2/2     165   236 ..     1    77 []    84.5  7.7e-21
Q90602       2/2     176   246 ..     1    77 []    84.4    8e-21
O04240       2/2     210   281 ..     1    77 []    84.3  8.7e-21
Q60668       2/2     153   225 ..     1    77 []    84.3    9e-21
Q92879       3/3     399   470 ..     1    77 []    84.1    1e-20
Q17350       2/4     122   192 ..     1    77 []    84.0    1e-20
O22851       1/1      60   131 ..     1    77 []    83.9  1.2e-20
O17310       2/2     190   263 ..     1    77 []    83.9  1.2e-20
O17309       2/2     183   256 ..     1    77 []    83.9  1.2e-20
O00320       1/1     242   313 ..     1    77 []    83.9  1.2e-20
YP85_CAEEL   2/2     102   174 ..     1    77 []    83.8  1.2e-20
Q17352       2/2     112   184 ..     1    77 []    83.8  1.2e-20
P93843       3/3     297   362 ..     1    77 []    83.7  1.3e-20
P70372       3/3     246   317 ..     1    77 []    83.7  1.4e-20
O22314       1/2       9    77 ..     1    77 []    83.6  1.4e-20
Q39201       1/2       9    77 ..     1    77 []    83.6  1.4e-20
O22315       1/2       9    77 ..     1    77 []    83.6  1.4e-20
Q61474       1/2      22    92 ..     1    77 []    83.6  1.5e-20
NGR1_YEAST   2/3     194   266 ..     1    77 []    83.5  1.5e-20
RO21_XENLA   2/2     102   172 ..     1    77 []    83.5  1.6e-20
RU17_XENLA   1/1     105   179 ..     1    77 []    83.4  1.7e-20
Q94467       1/1     202   272 ..     1    77 []    83.3  1.7e-20
CABA_MOUSE   2/2     161   231 ..     1    77 []    83.3  1.7e-20
Q90626       2/2     159   229 ..     1    77 []    83.1    2e-20
Q17350       1/4      34   105 ..     1    77 []    83.0  2.2e-20
PABP_XENLA   4/4     296   365 ..     1    77 []    82.9  2.2e-20
O22173       1/4      48   119 ..     1    77 []    82.9  2.2e-20
O08831       1/1      12    78 ..     1    77 []    82.8  2.5e-20
X16_HUMAN    1/1      12    78 ..     1    77 []    82.8  2.5e-20
Q62029       4/4     296   365 ..     1    77 []    82.6  2.8e-20
RO22_XENLA   2/2     102   172 ..     1    77 []    82.6  2.8e-20
NOP3_YEAST   1/2     127   190 ..     1    77 []    82.6  2.9e-20
U2AF_SCHPO   1/2     312   383 ..     1    77 []    82.6    3e-20
Q17385       3/3     501   572 ..     1    77 []    82.5    3e-20
P91414       1/1     335   406 ..     1    77 []    82.5    3e-20
MSSP_HUMAN   1/2      31   102 ..     1    77 []    82.5    3e-20
Q42404       1/1     140   211 ..     1    77 []    82.4  3.2e-20
O23288       2/2     107   177 ..     1    77 []    82.1  4.1e-20
Q91808       1/2      22    92 ..     1    77 []    82.0  4.3e-20
Q91807       1/2      22    92 ..     1    77 []    82.0  4.3e-20
O18409       3/3     726   797 ..     1    77 []    82.0  4.3e-20
O02374       3/3     522   593 ..     1    77 []    82.0  4.3e-20
P70055       3/3     455   526 ..     1    77 []    82.0  4.4e-20
O14979       1/2       1    71 [.     1    77 []    81.9  4.8e-20
Q24668       2/2     207   280 ..     1    77 []    81.8    5e-20
SXLF_DROME   2/2     213   286 ..     1    77 []    81.8    5e-20
Q99141       2/2     205   278 ..     1    77 []    81.8    5e-20
Q14100       2/2      96   168 ..     1    77 []    81.7  5.2e-20
Q14103       2/2     184   256 ..     1    77 []    81.7  5.2e-20
Q12771       2/2     163   235 ..     1    77 []    81.7  5.2e-20
ROC_RAT      1/1      36   108 ..     1    77 []    81.7  5.2e-20
Q14102       2/2      93   165 ..     1    77 []    81.7  5.2e-20
Q14101       2/2     184   256 ..     1    77 []    81.7  5.2e-20
Q55345       1/1       3    74 ..     1    77 []    81.7  5.4e-20
YDB2_SCHPO   1/1      32   102 ..     1    77 []    81.7  5.4e-20
SP49_HUMAN   1/2      15    86 ..     1    77 []    81.7  5.5e-20
Q19579       1/4      59   130 ..     1    77 []    81.7  5.5e-20
Q19581       1/4      59   130 ..     1    77 []    81.7  5.5e-20
Q60690       2/2     360   429 ..     1    77 []    81.6  5.6e-20
TIA1_HUMAN   3/3     205   270 ..     1    77 []    81.6  5.8e-20
ROA2_HUMAN   2/2     114   184 ..     1    77 []    81.6  5.9e-20
O18352       1/1     728   798 ..     1    77 []    81.5  6.2e-20
ROA1_MACMU   1/2      15    85 ..     1    77 []    81.4  6.4e-20
Q26658       2/2     101   171 ..     1    77 []    81.4  6.5e-20
Q18318       1/1      40   111 ..     1    77 []    81.4  6.7e-20
Q16135       3/3     269   340 ..     1    77 []    81.4  6.7e-20
Q19581       3/4     240   310 ..     1    77 []    81.4  6.8e-20
Q19579       3/4     240   310 ..     1    77 []    81.4  6.8e-20
P93396       1/1      68   139 ..     1    77 []    81.4  6.8e-20
O22791       2/2     112   182 ..     1    77 []    81.3  7.2e-20
TIA1_MOUSE   3/3     216   281 ..     1    77 []    81.2  7.4e-20
Q00880       2/2     358   429 ..     1    77 []    81.2  7.5e-20
O23212       2/2     358   429 ..     1    77 []    80.9  9.4e-20
Q92227       1/4      44   115 ..     1    77 []    80.9  9.6e-20
Q09511       1/1      21    92 ..     1    77 []    80.8  9.8e-20
Q15351       1/1      27    97 ..     1    77 []    80.8    1e-19
Q15350       1/1      26    96 ..     1    77 []    80.8    1e-19
U2AF_MOUSE   2/3     261   332 ..     1    77 []    80.6  1.1e-19
U2AF_HUMAN   2/3     261   332 ..     1    77 []    80.6  1.1e-19
Q99628       2/3     210   281 ..     1    77 []    80.6  1.2e-19
Q60399       1/1      52   120 ..     1    77 []    80.5  1.3e-19
NUCL_MOUSE   4/4     570   638 ..     1    77 []    80.5  1.3e-19
NUCL_MESAU   4/4     573   641 ..     1    77 []    80.5  1.3e-19
NUCL_RAT     4/4     576   644 ..     1    77 []    80.5  1.3e-19
Q17430       2/2     685   755 ..     1    77 []    80.5  1.3e-19
Q55342       1/1       3    74 ..     1    77 []    80.3  1.4e-19
Q91583       2/3     155   226 ..     1    77 []    80.3  1.4e-19
Q91903       2/3     155   226 ..     1    77 []    80.3  1.4e-19
Q62176       1/1      34   104 ..     1    77 []    80.2  1.5e-19
Q21832       1/1      57   128 ..     1    77 []    80.2  1.5e-19
YHH5_YEAST   3/3     315   384 ..     1    77 []    80.1  1.6e-19
HUD_MOUSE    2/3     139   210 ..     1    77 []    79.9  1.9e-19
HUD_RAT      2/3     127   198 ..     1    77 []    79.9  1.9e-19
HUD_HUMAN    2/3     134   205 ..     1    77 []    79.9  1.9e-19
RO32_XENLA   2/2     120   190 ..     1    77 []    79.7  2.1e-19
Q20084       3/3     376   446 ..     1    77 []    79.7  2.2e-19
Q41042       1/2     357   426 ..     1    77 []    79.6  2.3e-19
Q16629       1/1      13    79 ..     1    77 []    79.6  2.4e-19
Q17350       3/4     215   284 ..     1    77 []    79.6  2.4e-19
NUCL_CHICK   4/4     555   623 ..     1    77 []    79.5  2.4e-19
PES4_YEAST   3/4     305   374 ..     1    77 []    79.4  2.6e-19
Q19335       2/2     477   548 ..     1    77 []    79.4  2.6e-19
GBP2_YEAST   3/3     351   421 ..     1    77 []    79.4  2.7e-19
Q00880       1/2     253   324 ..     1    77 []    79.3  2.8e-19
RB27_DROME   1/2       9    79 ..     1    77 []    79.3  2.8e-19
RNP1_YEAST   1/1      37   109 ..     1    77 []    79.0  3.5e-19
YQOC_CAEEL   1/1      63   133 ..     1    77 []    79.0  3.6e-19
Q92950       3/3     407   478 ..     1    77 []    79.0  3.6e-19
SP33_HUMAN   1/2      17    85 ..     1    77 []    78.9  3.7e-19
Q13809       1/2      18    86 ..     1    77 []    78.9  3.7e-19
SQD_DROME    2/2     138   208 ..     1    77 []    78.8  3.9e-19
Q13243       1/2       6    69 ..     1    77 []    78.8  3.9e-19
O35326       1/2       6    69 ..     1    77 []    78.8  3.9e-19
CL4_RAT      1/2       6    69 ..     1    77 []    78.8  3.9e-19
Q16662       1/1       6    69 ..     1    77 []    78.8  3.9e-19
O14979       2/2      86   158 ..     1    77 []    78.8    4e-19
P78795       1/1      51   122 ..     1    77 []    78.8    4e-19
HRB1_YEAST   3/3     353   423 ..     1    77 []    78.8  4.1e-19
Q13151       2/2     100   170 ..     1    77 []    78.7  4.3e-19
Q17201       2/2     125   195 ..     1    77 []    78.6  4.4e-19
Q17200       2/2     125   195 ..     1    77 []    78.6  4.4e-19
YQO4_CAEEL   1/1     103   173 ..     1    77 []    78.5    5e-19
Q91585       2/3     134   205 ..     1    77 []    78.4  5.1e-19
Q53321       1/1       2    73 ..     1    77 []    78.4  5.4e-19
Q55341       1/1       3    74 ..     1    77 []    78.4  5.4e-19
Q93194       2/2     131   196 ..     1    77 []    78.1  6.5e-19
Q27335       1/4      11    81 ..     1    77 []    78.0  6.9e-19
O14801       1/1     241   312 ..     1    77 []    78.0    7e-19
NGR1_YEAST   3/3     362   427 ..     1    77 []    78.0  7.1e-19
EWS_MOUSE    1/1     362   441 ..     1    77 []    77.9  7.2e-19
Q18409       1/1       5    71 ..     1    77 []    77.9  7.7e-19
Q01858       2/2     163   235 ..     1    77 []    77.7  8.7e-19
Q39568       2/2     145   215 ..     1    77 []    77.6  8.9e-19
P93616       2/4     122   192 ..     1    77 []    77.6  9.5e-19
Q19579       2/4     147   217 ..     1    77 []    77.5  9.5e-19
Q19581       2/4     147   217 ..     1    77 []    77.5  9.5e-19
O14875       1/1      10    80 ..     1    77 []    77.5  9.9e-19
O04319       3/4     204   274 ..     1    77 []    77.5    1e-18
Q17201       1/2      45   115 ..     1    77 []    77.4    1e-18
Q17200       1/2      45   115 ..     1    77 []    77.4    1e-18
O22791       1/2       8    77 ..     1    77 []    77.4    1e-18
Q12926       2/3     127   198 ..     1    77 []    77.4    1e-18
Q13235       2/3     127   198 ..     1    77 []    77.4    1e-18
Q60899       2/3     127   198 ..     1    77 []    77.4    1e-18
EWS_HUMAN    1/1     363   442 ..     1    77 []    77.4    1e-18
O14327       1/1      57   127 ..     1    77 []    77.4  1.1e-18
O13829       1/1     102   173 ..     1    77 []    77.4  1.1e-18
ROA3_HUMAN   2/2     128   198 ..     1    77 []    77.3  1.1e-18
Q22037       1/2      25    95 ..     1    77 []    77.2  1.2e-18
Q14869       1/2      31   102 ..     1    77 []    77.2  1.2e-18
Q15433       1/2      64   135 ..     1    77 []    77.2  1.2e-18
Q92227       2/4     132   202 ..     1    77 []    77.2  1.2e-18
ROA1_XENLA   1/2      16    86 ..     1    77 []    77.0  1.4e-18
O01671       2/2     152   224 ..     1    77 []    77.0  1.4e-18
ROA1_SCHAM   1/2      19    89 ..     1    77 []    76.9  1.5e-18
Q24409       2/2     265   335 ..     1    77 []    76.9  1.5e-18
Q24474       2/3     198   269 ..     1    77 []    76.7  1.7e-18
Q24847       2/2     188   259 ..     1    77 []    76.5  1.9e-18
Q39953       4/4     309   379 ..     1    77 []    76.5    2e-18
Q21911       1/2      47   117 ..     1    77 []    76.4  2.1e-18
Q15020       2/2     803   873 ..     1    77 []    76.3  2.2e-18
O04319       2/4     114   183 ..     1    77 []    76.2  2.4e-18
RO31_XENLA   1/2      29    99 ..     1    77 []    76.0  2.8e-18
RO32_XENLA   1/2      29    99 ..     1    77 []    76.0  2.8e-18
O08752       2/2      80   143 ..     1    77 []    76.0  2.8e-18
YNL0_YEAST   1/1      93   164 ..     1    77 []    75.8  3.2e-18
RO31_XENLA   2/2     120   190 ..     1    77 []    75.8  3.3e-18
YP85_CAEEL   1/2      15    86 ..     1    77 []    75.6  3.6e-18
Q17352       1/2      25    96 ..     1    77 []    75.6  3.6e-18
Q16135       2/3     118   190 ..     1    77 []    75.6  3.8e-18
Q24360       2/2     119   189 ..     1    77 []    75.5  3.8e-18
ROA1_DROME   2/2     124   194 ..     1    77 []    75.5  3.8e-18
Q24359       2/2     120   190 ..     1    77 []    75.5  3.8e-18
Q99361       2/2     123   193 ..     1    77 []    75.5  3.8e-18
Q24486       2/2     117   187 ..     1    77 []    75.5  3.9e-18
RB87_DROME   2/2     117   187 ..     1    77 []    75.5  3.9e-18
O35935       1/1     170   240 ..     1    77 []    75.5    4e-18
Q28165       1/1     174   244 ..     1    77 []    75.5    4e-18
O04319       4/4     306   376 ..     1    77 []    75.3  4.4e-18
RB27_DROME   2/2      98   168 ..     1    77 []    75.3  4.5e-18
SR75_HUMAN   1/2       4    67 ..     1    77 []    75.3  4.5e-18
ROA2_HUMAN   1/2      23    93 ..     1    77 []    75.3  4.6e-18
NONA_DROME   1/2     304   369 ..     1    77 []    75.2  4.8e-18
Q27926       1/1      98   168 ..     1    77 []    75.1  5.3e-18
YHH5_YEAST   1/3     113   184 ..     1    77 []    75.0  5.6e-18
ELAV_DROME   1/3     151   235 ..     1    77 []    75.0  5.7e-18
ELAV_DROVI   1/3     187   271 ..     1    77 []    75.0  5.7e-18
O15187       2/2     168   233 ..     1    77 []    74.9  5.9e-18
TIAR_MOUSE   3/3     224   289 ..     1    77 []    74.9  5.9e-18
TIAR_HUMAN   3/3     207   272 ..     1    77 []    74.9  5.9e-18
Q12786       1/2      76   141 ..     1    77 []    74.9    6e-18
O00201       1/2      76   141 ..     1    77 []    74.9    6e-18
Q90626       1/2      75   145 ..     1    77 []    74.8  6.3e-18
Q16560       1/1      53   124 ..     1    77 []    74.8  6.3e-18
Q55765       1/1       5    77 ..     1    77 []    74.8  6.5e-18
PABP_DROME   4/4     287   357 ..     1    77 []    74.8  6.6e-18
Q20084       2/3     130   201 ..     1    77 []    74.6  7.1e-18
O02916       2/2      80   143 ..     1    77 []    74.6  7.2e-18
O13845       2/3     342   412 ..     1    77 []    74.6  7.3e-18
NAB4_YEAST   2/2     245   315 ..     1    77 []    74.4  8.6e-18
RB97_DROME   1/2      34   104 ..     1    77 []    74.3  9.2e-18
O23146       1/1      51   121 ..     1    77 []    74.1    1e-17
O35335       1/1       6    69 ..     1    77 []    74.1    1e-17
O13845       1/3     242   312 ..     1    77 []    73.6  1.5e-17
NAM8_YEAST   3/3     315   380 ..     1    77 []    73.4  1.6e-17
Q92227       4/4     328   449 ..     1    77 []    73.3  1.8e-17
ROA3_HUMAN   1/2      37   107 ..     1    77 []    73.3  1.8e-17
Q04150       2/2     154   225 ..     1    77 []    73.1  2.1e-17
Q99729       2/2     154   225 ..     1    77 []    73.1  2.1e-17
Q39675       2/2     210   281 ..     1    77 []    73.1  2.1e-17
Q22030       1/1     102   171 ..     1    77 []    73.0  2.3e-17
Q61954       1/2      26    89 ..     1    77 []    72.9  2.4e-17
O02916       1/2       4    67 ..     1    77 []    72.9  2.4e-17
O08752       1/2       4    67 ..     1    77 []    72.9  2.4e-17
Q22304       1/1     194   263 ..     1    77 []    72.7  2.8e-17
Q10572       1/1     155   224 ..     1    77 []    72.7  2.8e-17
Q24847       1/2       4    74 ..     1    77 []    72.7  2.8e-17
Q14576       2/3     127   198 ..     1    77 []    72.7  2.8e-17
Q21155       1/1     150   222 ..     1    77 []    72.6  2.9e-17
Q60900       2/3     127   198 ..     1    77 []    72.6  2.9e-17
Q60901       1/2      42   113 ..     1    77 []    72.6  2.9e-17
RB87_DROME   1/2      26    96 ..     1    77 []    72.5  3.1e-17
Q24486       1/2      26    96 ..     1    77 []    72.5  3.1e-17
RU1A_XENLA   1/2      12    84 ..     1    77 []    72.5  3.2e-17
Q91582       2/3     108   179 ..     1    77 []    72.3  3.6e-17
ROM_HUMAN    1/3      73   144 ..     1    77 []    72.1  4.1e-17
Q06459       3/4     468   534 ..     1    77 []    72.1  4.3e-17
Q93233       1/1      80   150 ..     1    77 []    72.0  4.3e-17
P78814       1/2       2    65 ..     1    77 []    72.0  4.4e-17
O23189       1/3      65   136 ..     1    77 []    72.0  4.5e-17
NUCL_XENLA   4/4     504   572 ..     1    77 []    71.9  4.6e-17
Q02427       1/1      13    79 ..     1    77 []    71.9  4.7e-17
Q13247       1/2       4    67 ..     1    77 []    71.8    5e-17
Q13244       1/1       4    67 ..     1    77 []    71.8    5e-17
Q13245       1/2       4    67 ..     1    77 []    71.8    5e-17
Q22037       2/2     116   186 ..     1    77 []    71.7  5.5e-17
Q15717       2/3     108   179 ..     1    77 []    71.7  5.6e-17
Q90409       2/3     132   206 ..     1    77 []    71.5  6.1e-17
Q63887       1/2      78   143 ..     1    77 []    71.5  6.5e-17
RU1A_HUMAN   1/2      12    84 ..     1    77 []    71.4  6.6e-17
Q15287       1/1     163   235 ..     1    77 []    71.4  6.7e-17
O23475       2/2     213   284 ..     1    77 []    71.4    7e-17
O04425       2/2     213   284 ..     1    77 []    71.4    7e-17
FUS_BOVIN    1/1     273   352 ..     1    77 []    71.3  7.4e-17
FUS_HUMAN    1/1     287   366 ..     1    77 []    71.3  7.4e-17
Q13344       1/1     290   369 ..     1    77 []    71.3  7.4e-17
Q62826       1/1      12    83 ..     1    77 []    71.3  7.5e-17
Q99361       1/2      32   102 ..     1    77 []    71.2  7.9e-17
Q24359       1/2      29    99 ..     1    77 []    71.2  7.9e-17
ROA1_DROME   1/2      33   103 ..     1    77 []    71.2  7.9e-17
Q24360       1/2      28    98 ..     1    77 []    71.2  7.9e-17
YHC4_YEAST   2/2     348   415 ..     1    77 []    71.2    8e-17
Q62019       2/2      80   143 ..     1    77 []    71.1  8.1e-17
Q23121       1/2       5    68 ..     1    77 []    70.9  9.3e-17
ROA1_SCHAM   2/2     110   180 ..     1    77 []    70.9  9.6e-17
Q27199       2/2     357   425 ..     1    77 []    70.8  9.9e-17
Q24491       1/1       9    75 ..     1    77 []    70.8  1.1e-16
O13741       2/2     272   343 ..     1    77 []    70.7  1.1e-16
NUCL_XENLA   3/4     416   482 ..     1    77 []    70.6  1.2e-16
Q15434       1/2      58   129 ..     1    77 []    70.4  1.3e-16
Q27335       4/4     290   362 ..     1    77 []    70.4  1.3e-16
Q06459       4/4     556   624 ..     1    77 []    70.3  1.5e-16
O04432       1/1      10   117 ..     1    77 []    70.3  1.5e-16
P92966       1/2       4    69 ..     1    77 []    70.2  1.5e-16
Q06106       5/5     765   835 ..     1    77 []    70.2  1.6e-16
Q24562       2/3     209   280 ..     1    77 []    70.2  1.6e-16
TIAR_MOUSE   1/3      11    97 ..     1    77 []    70.1  1.7e-16
Q24261       1/2     304   369 ..     1    77 []    70.0  1.8e-16
Q08208       1/1     281   351 ..     1    77 []    70.0  1.8e-16
Q91584       2/3     122   194 ..     1    77 []    69.9  1.9e-16
NUCL_CHICK   3/4     463   530 ..     1    77 []    69.9  1.9e-16
P92965       1/2       4    69 ..     1    77 []    69.7  2.3e-16
Q27294       1/1     121   200 ..     1    77 []    69.6  2.3e-16
Q06106       2/5     347   418 ..     1    77 []    69.6  2.4e-16
Q09542       1/2     118   182 ..     1    77 []    69.4  2.6e-16
ELAV_DROME   2/3     250   322 ..     1    77 []    69.4  2.7e-16
ELAV_DROVI   2/3     286   358 ..     1    77 []    69.4  2.7e-16
Q90407       1/2      27    99 ..     1    77 []    69.4  2.8e-16
O23475       1/2     122   194 ..     1    77 []    69.0  3.5e-16
O04425       1/2     122   194 ..     1    77 []    69.0  3.5e-16
RO22_XENLA   1/2      11    81 ..     1    77 []    69.0  3.6e-16
Q24409       1/2     177   247 ..     1    77 []    68.7  4.5e-16
Q21911       2/2     136   206 ..     1    77 []    68.6  4.6e-16
O14369       1/1      96   164 ..     1    77 []    68.5  5.2e-16
P79736       2/3     126   197 ..     1    77 []    68.4  5.2e-16
Q62189       1/2      18    90 ..     1    77 []    68.3  5.7e-16
YG5B_YEAST   1/3     197   268 ..     1    77 []    68.2  6.3e-16
Q61474       2/2     111   181 ..     1    77 []    68.0  7.1e-16
NUCL_CHICK   2/4     373   440 ..     1    77 []    68.0  7.3e-16
P93843       2/3     179   251 ..     1    77 []    67.9  7.5e-16
Q60690       1/2      87   157 ..     1    77 []    67.8    8e-16
O02374       1/3     153   225 ..     1    77 []    67.8    8e-16
O18409       1/3     357   429 ..     1    77 []    67.8    8e-16
Q27335       2/4      98   168 ..     1    77 []    67.7  8.6e-16
Q08212       1/3       9    77 ..     1    77 []    67.7  8.9e-16
O04240       1/2     119   190 ..     1    77 []    67.7  8.9e-16
NUCL_MOUSE   3/4     488   555 ..     1    77 []    67.6  9.3e-16
Q40363       1/2     378   447 ..     1    77 []    67.5    1e-15
NUCL_HUMAN   3/4     487   554 ..     1    77 []    67.4  1.1e-15
RO21_XENLA   1/2      11    81 ..     1    77 []    67.3  1.1e-15
Q24113       1/2     279   344 ..     1    77 []    67.3  1.1e-15
YNR5_YEAST   2/2     241   312 ..     1    77 []    67.1  1.4e-15
NUCL_RAT     3/4     490   557 ..     1    77 []    66.9  1.5e-15
YSO5_CAEEL   1/1     440   511 ..     1    77 []    66.9  1.5e-15
PUB1_YEAST   3/3     342   407 ..     1    77 []    66.6  1.8e-15
Q13151       1/2       9    79 ..     1    77 []    66.5    2e-15
NUCL_MESAU   3/4     487   554 ..     1    77 []    66.5    2e-15
RB97_DROME   2/2     125   196 ..     1    77 []    66.4  2.1e-15
NUCL_XENLA   2/4     326   393 ..     1    77 []    66.4  2.1e-15
ROC_HUMAN    1/1      18    82 ..     1    77 []    66.4  2.1e-15
Q91807       2/2     111   181 ..     1    77 []    66.4  2.1e-15
Q15584       1/2      46   116 ..     1    77 []    66.4  2.1e-15
ROM_HUMAN    2/3     206   276 ..     1    77 []    66.4  2.1e-15
Q91808       2/2     111   181 ..     1    77 []    66.3  2.3e-15
Q41124       1/2     115   186 ..     1    77 []    66.2  2.5e-15
Q92804       1/1     236   315 ..     1    77 []    66.2  2.5e-15
Q92751       1/1     233   312 ..     1    77 []    66.2  2.5e-15
Q21900       1/2      83   154 ..     1    77 []    66.0  2.8e-15
Q23795       2/2     122   192 ..     1    77 []    65.9  3.1e-15
Q08940       2/2     208   280 ..     1    77 []    65.8  3.2e-15
WHI3_YEAST   1/1     540   614 ..     1    77 []    65.4  4.4e-15
CB20_XENLA   1/1      34   105 ..     1    77 []    65.3  4.5e-15
P90727       2/3     284   354 ..     1    77 []    65.1  5.2e-15
PSF_HUMAN    1/2     299   364 ..     1    77 []    65.1  5.3e-15
Q01491       1/4     312   380 ..     1    77 []    65.1  5.4e-15
NUCL_HUMAN   4/4     573   639 ..     1    77 []    65.1  5.5e-15
O23093       3/3     320   389 ..     1    77 []    65.0  5.7e-15
P92964       2/2      95   159 ..     1    77 []    64.8  6.4e-15
Q09959       3/3     283   347 ..     1    77 []    64.6  7.3e-15
PR24_YEAST   3/3     212   284 ..     1    77 []    64.6  7.3e-15
Q27335       3/4     186   260 ..     1    77 []    64.6  7.3e-15
Q24473       2/3     198   274 ..     1    77 []    64.4  8.4e-15
O22855       2/3     252   316 ..     1    77 []    64.3  9.2e-15
P92966       2/2      98   162 ..     1    77 []    64.3  9.5e-15
CB20_HUMAN   1/1      42   113 ..     1    77 []    64.1    1e-14
Q91579       1/3       9    83 ..     1    77 []    64.1  1.1e-14
O23131       1/1      30   100 ..     1    77 []    64.0  1.1e-14
SP33_HUMAN   2/2     122   186 ..     1    77 []    63.6  1.5e-14
Q92904       1/1      42   110 ..     1    77 []    63.6  1.5e-14
Q92909       1/1      42   110 ..     1    77 []    63.6  1.5e-14
Q95192       1/1      42   110 ..     1    77 []    63.6  1.5e-14
Q26293       2/3     198   274 ..     1    77 []    63.5  1.6e-14
IF4B_HUMAN   1/1      98   168 ..     1    77 []    63.5  1.6e-14
Q06459       2/4     378   445 ..     1    77 []    63.5  1.6e-14
SR75_HUMAN   2/2     106   172 ..     1    77 []    63.4  1.8e-14
Q93594       1/1      39   110 ..     1    77 []    63.4  1.8e-14
P70372       2/3     108   179 ..     1    77 []    63.3  1.9e-14
O04319       1/4      23    94 ..     1    77 []    63.2    2e-14
RU2B_HUMAN   1/2       9    81 ..     1    77 []    63.1  2.1e-14
ROC_XENLA    1/1      19    83 ..     1    77 []    63.0  2.2e-14
P92964       1/2       4    69 ..     1    77 []    62.6    3e-14
O15396       1/1      42   110 ..     1    77 []    62.1  4.4e-14
Q01491       3/4     479   549 ..     1    77 []    62.0  4.5e-14
Q94901       1/2       9    72 ..     1    77 []    61.7  5.4e-14
Q17385       2/3     144   215 ..     1    77 []    61.7  5.6e-14
Q91920       2/2     112   182 ..     1    77 []    61.6  6.1e-14
P92965       2/2      99   163 ..     1    77 []    61.5  6.4e-14
Q24024       2/2     138   208 ..     1    77 []    61.5  6.5e-14
Q91579       2/3      97   168 ..     1    77 []    61.5  6.6e-14
NUCL_CHICK   1/4     283   352 ..     1    77 []    61.4  6.9e-14
O23646       1/1       4    66 ..     1    77 []    61.3  7.5e-14
HS49_YEAST   1/2      11    83 ..     1    77 []    61.3  7.6e-14
Q23287       1/1      53   122 ..     1    77 []    61.2  7.9e-14
P90871       1/1     173   244 ..     1    77 []    61.1  8.7e-14
Q24024       1/2      34   104 ..     1    77 []    60.9  9.9e-14
Q94901       2/2      88   151 ..     1    77 []    60.7  1.1e-13
O15042       1/1     275   349 ..     1    77 []    60.7  1.1e-13
YSX2_CAEEL   1/1       4    67 ..     1    77 []    60.7  1.1e-13
RU1A_DROME   1/2       9    81 ..     1    77 []    60.6  1.2e-13
O13620       4/5     621   697 ..     1    77 []    60.6  1.2e-13
Q13245       2/2     112   178 ..     1    77 []    60.5  1.2e-13
Q13247       2/2     112   178 ..     1    77 []    60.5  1.2e-13
SSB1_YEAST   1/2      39   114 ..     1    77 []    60.4  1.3e-13
Q64368       1/1      42   110 ..     1    77 []    60.3  1.5e-13
HRB1_YEAST   2/3     238   308 ..     1    77 []    60.3  1.5e-13
Q13148       1/2     106   175 ..     1    77 []    60.2  1.5e-13
Q27199       1/2     265   335 ..     1    77 []    60.2  1.6e-13
O13759       1/2     184   256 ..     1    77 []    60.1  1.7e-13
Q09331       1/1      24    96 ..     1    77 []    60.1  1.7e-13
Q14151       1/1     409   480 ..     1    77 []    60.1  1.7e-13
Q41042       2/2     453   527 ..     1    77 []    60.0  1.8e-13
Q22412       1/1     237   307 ..     1    77 []    60.0  1.8e-13
Q15020       1/2     706   777 ..     1    77 []    60.0  1.8e-13
O13759       2/2     299   364 ..     1    77 []    59.9    2e-13
Q09335       1/1      31    96 ..     1    77 []    59.9    2e-13
Q64012       1/1      23    87 ..     1    77 []    59.7  2.2e-13
Q23120       1/2       4    67 ..     1    77 []    59.7  2.2e-13
O22855       1/3      20    85 ..     1    77 []    59.7  2.3e-13
PSF_HUMAN    2/2     373   443 ..     1    77 []    59.6  2.4e-13
Q15056       1/1      46   115 ..     1    77 []    59.5  2.6e-13
Q42215       1/1       5    77 ..     1    77 []    59.5  2.6e-13
Q09584       1/1     105   172 ..     1    77 []    59.4  2.7e-13
NUCL_HUMAN   2/4     394   460 ..     1    77 []    59.3  2.9e-13
Q14924       1/1      42   113 ..     1    77 []    59.3    3e-13
MLO3_SCHPO   1/1      57   129 ..     1    77 []    59.0  3.6e-13
Q08212       3/3     223   289 ..     1    77 []    58.9  3.8e-13
GRP1_SORVU   1/1       1    60 [.     1    77 []    58.9  3.9e-13
ROH1_HUMAN   2/3     113   183 ..     1    77 []    58.9    4e-13
O35737       2/3     113   183 ..     1    77 []    58.9    4e-13
RU17_YEAST   1/1     109   183 ..     1    77 []    58.9    4e-13
Q13809       2/2     123   187 ..     1    77 []    58.7  4.4e-13
O08583       1/1     107   177 ..     1    77 []    58.7  4.6e-13
Q23796       2/2     118   184 ..     1    77 []    58.5  5.1e-13
NOP4_YEAST   3/4     292   378 ..     1    77 []    58.5  5.3e-13
Q06106       4/5     665   741 ..     1    77 []    58.4  5.4e-13
Q24252       2/2     122   188 ..     1    77 []    58.4  5.4e-13
SR55_DROME   2/2     116   182 ..     1    77 []    58.4  5.4e-13
Q14730       1/1       1    70 [.     1    77 []    58.4  5.4e-13
Q91017       1/1      26    96 ..     1    77 []    58.2  6.2e-13
LA_HUMAN     1/1     113   182 ..     1    77 []    58.2  6.5e-13
Q15367       1/1      60   129 ..     1    77 []    58.2  6.5e-13
MODU_DROME   3/4     342   410 ..     1    77 []    58.1  6.7e-13
RN24_SCHPO   2/2     230   295 ..     1    77 []    57.8  8.2e-13
Q26692       3/3     207   271 ..     1    77 []    57.8  8.3e-13
O13620       5/5     723   793 ..     1    77 []    57.6  9.4e-13
O23189       3/3     341   410 ..     1    77 []    57.6  9.6e-13
O23093       1/3     118   215 ..     1    77 []    57.5  1.1e-12
ROH2_HUMAN   2/3     113   183 ..     1    77 []    57.4  1.1e-12
P70333       2/3     113   183 ..     1    77 []    57.4  1.1e-12
Q08920       1/1      48   119 ..     1    77 []    57.2  1.3e-12
PR24_YEAST   2/3     119   190 ..     1    77 []    57.1  1.3e-12
P93843       1/3      86   157 ..     1    77 []    57.1  1.4e-12
Q92950       2/3     110   181 ..     1    77 []    56.6  1.9e-12
P70055       2/3     152   223 ..     1    77 []    56.6  1.9e-12
RU1A_HUMAN   2/2     210   277 ..     1    77 []    56.6  1.9e-12
Q62189       2/2     215   282 ..     1    77 []    56.6  1.9e-12
Q22135       1/1      34   105 ..     1    77 []    56.1  2.7e-12
O23645       1/1       4    68 ..     1    77 []    55.9  3.1e-12
Q09959       1/3      48   156 ..     1    77 []    55.7  3.6e-12
P97855       1/1     340   400 ..     1    77 []    55.5    4e-12
Q24207       1/1      35   105 ..     1    77 []    55.5  4.2e-12
Q62150       1/1     162   234 ..     1    77 []    55.2  4.9e-12
O14797       1/2       6    66 ..     1    77 []    55.0    6e-12
ARP2_PLAFA   2/2     364   438 ..     1    77 []    55.0    6e-12
Q13283       1/1     342   402 ..     1    77 []    54.2    1e-11
Q39244       1/2      20    92 ..     1    77 []    54.1  1.1e-11
Q04067       1/1     193   265 ..     1    77 []    54.0  1.2e-11
RU1A_DROME   2/2     144   211 ..     1    77 []    53.8  1.4e-11
Q62379       1/1      51   118 ..     1    77 []    53.7  1.5e-11
RU2B_HUMAN   2/2     153   220 ..     1    77 []    53.7  1.5e-11
NUCL_RAT     2/4     398   464 ..     1    77 []    53.5  1.6e-11
Q18724       1/1      27    97 ..     1    77 []    53.3  1.9e-11
ROF_HUMAN    2/3     113   183 ..     1    77 []    53.2    2e-11
RU1A_XENLA   2/2     210   277 ..     1    77 []    53.1  2.2e-11
MODU_DROME   2/4     260   326 ..     1    77 []    52.8  2.6e-11
Q15424       1/1     357   428 ..     1    77 []    52.3  3.7e-11
Q26692       2/3     127   191 ..     1    77 []    52.3  3.9e-11
Q41498       1/2      25    97 ..     1    77 []    52.2  3.9e-11
P97379       1/1     300   371 ..     1    77 []    52.2    4e-11
NUCL_MESAU   2/4     395   461 ..     1    77 []    52.1  4.3e-11
NUCL_MOUSE   2/4     396   462 ..     1    77 []    52.0  4.6e-11
Q92879       2/3     110   181 ..     1    77 []    51.8  5.5e-11
YG5B_YEAST   3/3     542   633 ..     1    77 []    51.8  5.5e-11
Q40363       2/2     477   552 ..     1    77 []    51.6    6e-11
Q13242       2/2     113   177 ..     1    77 []    51.6  6.3e-11
GRF1_HUMAN   2/3     196   265 ..     1    77 []    51.5  6.7e-11
Q38915       1/2     152   220 ..     1    77 []    51.3  7.4e-11
SRP1_SCHPO   1/1       9    81 ..     1    77 []    51.1  8.9e-11
PR24_YEAST   1/3      43   111 ..     1    77 []    50.8  1.1e-10
Q13243       2/2     110   176 ..     1    77 []    50.7  1.1e-10
CL4_RAT      2/2     110   176 ..     1    77 []    50.7  1.1e-10
NONA_DROME   2/2     378   448 ..     1    77 []    50.2  1.6e-10
Q24261       2/2     378   448 ..     1    77 []    50.2  1.6e-10
RDP_MOUSE    1/1     268   331 ..     1    77 []    50.2  1.7e-10
RDP_HUMAN    1/1     264   327 ..     1    77 []    50.2  1.7e-10
O02374       2/3     240   306 ..     1    77 []    50.1  1.8e-10
O18409       2/3     444   510 ..     1    77 []    50.1  1.8e-10
Q15097       1/4       1    59 [.     1    77 []    49.9  1.9e-10
PTB_MOUSE    2/4     185   252 ..     1    77 []    49.9  2.1e-10
PTB_PIG      2/4     186   253 ..     1    77 []    49.9  2.1e-10
PTB_HUMAN    2/4     186   253 ..     1    77 []    49.9  2.1e-10
PTB_RAT      2/4     185   252 ..     1    77 []    49.9  2.1e-10
Q63568       2/4     185   252 ..     1    77 []    49.9  2.1e-10
LA_BOVIN     1/1     113   182 ..     1    77 []    49.8  2.1e-10
LA_RAT       1/1     113   182 ..     1    77 []    49.8  2.2e-10
Q15434       2/2     137   207 ..     1    77 []    49.7  2.2e-10
PTB_HUMAN    3/4     339   406 ..     1    77 []    49.6  2.5e-10
O15236       1/1       9    79 ..     1    77 []    49.4  2.8e-10
Q15433       2/2     143   213 ..     1    77 []    49.4  2.8e-10
O15237       1/1       9    79 ..     1    77 []    49.4  2.8e-10
MSSP_HUMAN   2/2     110   180 ..     1    77 []    49.4  2.8e-10
Q14869       2/2     110   180 ..     1    77 []    49.4  2.8e-10
Q21323       1/2      10    82 ..     1    77 []    49.3    3e-10
O14102       1/1       1    66 [.     1    77 []    49.3  3.1e-10
Q62378       1/1      25    92 ..     1    77 []    49.1  3.4e-10
Q24113       2/2     352   422 ..     1    77 []    49.1  3.5e-10
Q14499       1/3     155   225 ..     1    77 []    49.0  3.6e-10
Q14498       1/3     155   225 ..     1    77 []    49.0  3.6e-10
Q15380       1/1      10    75 ..     1    77 []    48.9  3.9e-10
O00201       2/2     150   220 ..     1    77 []    48.9    4e-10
Q12786       2/2     150   220 ..     1    77 []    48.9    4e-10
O23212       1/2     238   314 ..     1    77 []    48.9    4e-10
U2AG_HUMAN   1/1      67   142 ..     1    77 []    48.7  4.6e-10
YFK2_YEAST   1/1      20   100 ..     1    77 []    48.5  5.4e-10
P78814       2/2      96   162 ..     1    77 []    48.4  5.7e-10
PTB_RAT      3/4     363   430 ..     1    77 []    48.2  6.3e-10
Q63568       3/4     364   431 ..     1    77 []    48.2  6.3e-10
O22905       2/2     213   284 ..     1    77 []    48.0  7.3e-10
U2AF_HUMAN   1/3     151   226 ..     1    77 []    48.0  7.3e-10
U2AF_MOUSE   1/3     151   226 ..     1    77 []    48.0  7.3e-10
IF32_YEAST   1/1      79   157 ..     1    77 []    48.0  7.6e-10
P90978       2/3     292   362 ..     1    77 []    47.9  7.9e-10
LA_MOUSE     1/1     113   182 ..     1    77 []    47.6  9.8e-10
Q19335       1/2     374   461 ..     1    77 []    47.6    1e-09
CPO_DROME    1/1     453   526 ..     1    77 []    47.3  1.2e-09
Q06459       1/4     286   355 ..     1    77 []    47.2  1.3e-09
Q17175       1/1       7    79 ..     1    77 []    46.6    2e-09
O22905       1/2     112   184 ..     1    77 []    46.5  2.1e-09
Q26658       1/2       8    79 ..     1    77 []    46.3  2.4e-09
HS49_YEAST   2/2     110   180 ..     1    77 []    46.1  2.8e-09
Q13117       1/1      42   110 ..     1    77 []    46.1  2.8e-09
Q63887       2/2     152   218 ..     1    77 []    46.1  2.9e-09
Q39244       2/2     179   245 ..     1    77 []    45.5  4.2e-09
O13801       1/1     246   317 ..     1    77 []    45.5  4.3e-09
O13674       1/3     301   356 ..     1    77 []    45.4  4.4e-09
RU1A_YEAST   1/1     229   294 ..     1    77 []    45.3  4.9e-09
Q41499       2/2     159   226 ..     1    77 []    45.3    5e-09
Q12159       1/1      80   151 ..     1    77 []    45.2  5.2e-09
O22922       2/2     160   227 ..     1    77 []    45.1  5.5e-09
NUCL_XENLA   1/4     234   303 ..     1    77 []    45.1  5.6e-09
YD3D_SCHPO   1/2      81   153 ..     1    77 []    45.0  5.8e-09
NAB3_YEAST   1/1     332   396 ..     1    77 []    44.7  7.5e-09
Q63627       1/1     424   491 ..     1    77 []    44.0  1.2e-08
MEI2_SCHPO   1/1     197   265 ..     1    77 []    43.8  1.4e-08
Q24562       1/3      95   170 ..     1    77 []    43.6  1.6e-08
Q06106       1/5       4    89 ..     1    77 []    43.6  1.6e-08
Q23161       1/1      59   129 ..     1    77 []    43.3    2e-08
O13649       1/1       6    78 ..     1    77 []    43.0  2.4e-08
P90797       1/1      66   136 ..     1    77 []    42.9  2.5e-08
Q07655       1/1     535   612 ..     1    77 []    42.8  2.7e-08
RN12_YEAST   1/1     200   267 ..     1    77 []    42.8  2.8e-08
O22922       1/2      12    84 ..     1    77 []    42.6  3.1e-08
YHC4_YEAST   1/2      95   167 ..     1    77 []    42.4  3.6e-08
Q07034       1/1     332   396 ..     1    77 []    42.3  3.9e-08
Q22318       2/2     179   249 ..     1    77 []    41.8  5.4e-08
Q92879       1/3      18    92 ..     1    77 []    41.7    6e-08
P70055       1/3      60   134 ..     1    77 []    41.6  6.1e-08
O13620       1/5       4    78 ..     1    77 []    41.4  7.3e-08
Q22708       1/2      16    85 ..     1    77 []    41.3  7.7e-08
MODU_DROME   4/4     422   484 ..     1    77 []    41.2  8.5e-08
P90978       1/3     185   260 ..     1    77 []    41.0  9.5e-08
Q92950       1/3      18    92 ..     1    77 []    41.0  9.7e-08
Q21323       2/2     145   212 ..     1    77 []    40.9    1e-07
P90727       1/3     177   252 ..     1    77 []    40.9    1e-07
O23866       1/2     188   254 ..     1    77 []    40.9  1.1e-07
Q41499       1/2      13    85 ..     1    77 []    40.8  1.1e-07
Q24375       1/1     151   225 ..     1    77 []    40.7  1.1e-07
O18219       1/1      19    96 ..     1    77 []    40.6  1.2e-07
Q15686       1/1     155   215 ..     1    77 []    40.4  1.5e-07
Q15364       1/1     105   165 ..     1    77 []    40.4  1.5e-07
D111_ARATH   1/1     281   360 ..     1    77 []    40.4  1.5e-07
Q21322       2/2     129   196 ..     1    77 []    39.9    2e-07
LAB_XENLA    1/1     112   183 ..     1    77 []    39.8  2.2e-07
O23866       2/2     273   339 ..     1    77 []    39.7  2.4e-07
PTB_MOUSE    1/4      60   127 ..     1    77 []    39.5  2.7e-07
Q17385       1/3      57   129 ..     1    77 []    39.4  2.9e-07
O00425       1/2       4    70 ..     1    77 []    39.2  3.3e-07
PTB_RAT      1/4      60   127 ..     1    77 []    39.2  3.4e-07
Q63568       1/4      60   127 ..     1    77 []    39.2  3.4e-07
PTB_PIG      1/4      61   128 ..     1    77 []    38.9    4e-07
NUCL_MESAU   1/4     309   378 ..     1    77 []    38.5  5.3e-07
LA_DROME     1/1     151   225 ..     1    77 []    38.3    6e-07
Q01491       2/4     388   458 ..     1    77 []    38.3  6.3e-07
YA2B_SCHPO   2/4     208   274 ..     1    77 []    38.3  6.4e-07
Q99730       1/2     135   213 ..     1    77 []    38.2  6.6e-07
PTB_PIG      3/4     365   432 ..     1    77 []    38.2  6.7e-07
YAG3_SCHPO   1/1     234   305 ..     1    77 []    38.2  6.8e-07
LAA_XENLA    1/1     113   182 ..     1    77 []    37.7  9.1e-07
Q21900       2/2     164   236 ..     1    77 []    37.6  9.7e-07
NOP4_YEAST   2/4     149   220 ..     1    77 []    37.6  9.8e-07
Q93062       1/1      26    93 ..     1    77 []    37.5  1.1e-06
Q92516       1/1      26    93 ..     1    77 []    37.5  1.1e-06
Q92517       1/1      26    93 ..     1    77 []    37.5  1.1e-06
ROH1_HUMAN   3/3     291   359 ..     1    77 []    37.3  1.2e-06
O35737       3/3     291   359 ..     1    77 []    37.3  1.2e-06
O00425       2/2      83   151 ..     1    77 []    37.2  1.3e-06
Q63623       1/1     479   546 ..     1    77 []    37.2  1.3e-06
PTB_HUMAN    1/4      61   128 ..     1    77 []    37.1  1.4e-06
MODU_DROME   1/4     177   246 ..     1    77 []    37.0  1.5e-06
Q99730       2/2     266   344 ..     1    77 []    36.9  1.6e-06
NOP3_YEAST   2/2     202   270 ..     1    77 []    36.8  1.7e-06
Q10667       1/1       5    67 ..     1    77 []    36.7  1.9e-06
O23093       2/3     224   299 ..     1    77 []    36.3  2.4e-06
YA2B_SCHPO   4/4     416   482 ..     1    77 []    36.3  2.5e-06
Q41498       2/2     181   248 ..     1    77 []    36.2  2.7e-06
P92204       1/1     168   231 ..     1    77 []    35.8  3.5e-06
NUCL_MOUSE   1/4     310   379 ..     1    77 []    35.8  3.5e-06
YD3D_SCHPO   2/2     367   436 ..     1    77 []    35.7  3.8e-06
Q22039       1/2      33   105 ..     1    77 []    35.5  4.5e-06
Q93733       1/1      33   105 ..     1    77 []    35.5  4.5e-06
Q19018       1/2      33   105 ..     1    77 []    35.5  4.5e-06
P87216       1/1       5    71 ..     1    77 []    35.2  5.2e-06
Q24534       1/2      15   105 ..     1    77 []    35.2  5.3e-06
Q23120       2/2     114   181 ..     1    77 []    34.9  6.7e-06
PES4_YEAST   2/4     181   249 ..     1    77 []    34.8  6.8e-06
Q16630       1/1      83   156 ..     1    77 []    34.8  7.2e-06
Q17430       1/2     595   663 ..     1    77 []    34.7  7.4e-06
Q20414       1/2     175   244 ..     1    77 []    34.6  7.9e-06
ROF_HUMAN    3/3     291   359 ..     1    77 []    34.5  8.4e-06
P87126       1/1     194   261 ..     1    77 []    34.4  8.9e-06
Q18265       1/1     300   379 ..     1    77 []    34.4  9.2e-06
YAS9_SCHPO   1/1     365   429 ..     1    77 []    34.2  1.1e-05
NUCL_RAT     1/4     312   381 ..     1    77 []    34.0  1.2e-05
P70333       3/3     291   359 ..     1    77 []    34.0  1.2e-05
ROH2_HUMAN   3/3     291   359 ..     1    77 []    34.0  1.2e-05
Q13148       2/2     193   257 ..     1    77 []    33.4  1.9e-05
YNR5_YEAST   1/2     127   214 ..     1    77 []    33.1  2.2e-05
YQOA_CAEEL   1/1     114   196 ..     1    77 []    33.1  2.4e-05
O42254       2/2      83   151 ..     1    77 []    33.0  2.4e-05
O01806       1/1     112   182 ..     1    77 []    32.9  2.5e-05
YIS9_YEAST   1/1      30   101 ..     1    77 []    32.9  2.7e-05
Q18999       3/4     392   459 ..     1    77 []    32.7  3.1e-05
RN24_SCHPO   1/2     107   196 ..     1    77 []    32.3  3.9e-05
Q18220       1/1     420   491 ..     1    77 []    32.3    4e-05
Q18219       1/1     420   491 ..     1    77 []    32.3    4e-05
YHH5_YEAST   2/3     201   269 ..     1    77 []    31.9  5.2e-05
PTB_MOUSE    4/4     452   520 ..     1    77 []    31.8  5.5e-05
PTB_RAT      4/4     480   548 ..     1    77 []    31.8  5.5e-05
Q63568       4/4     481   549 ..     1    77 []    31.8  5.5e-05
ROU2_HUMAN   1/1     174   224 ..     1    77 []    31.8  5.6e-05
IF32_HUMAN   1/1     195   271 ..     1    77 []    31.4  7.4e-05
Q41988       1/1      18    66 .]     1    77 []    31.0  9.7e-05
Q06106       3/5     534   599 ..     1    77 []    30.9   0.0001
YBF1_YEAST   1/1      87   158 ..     1    77 []    30.9   0.0001
O42254       1/2       4    70 ..     1    77 []    30.7  0.00012
Q09542       2/2     191   261 ..     1    77 []    30.6  0.00013
Q22318       1/2      91   161 ..     1    77 []    30.3  0.00016
ROH2_HUMAN   1/3      13    85 ..     1    77 []    30.2  0.00017
LU15_HUMAN   1/2     100   173 ..     1    77 []    29.9   0.0002
O23288       1/2       8    72 ..     1    77 []    29.6  0.00026
Q18601       1/2      37    97 ..     1    77 []    29.4   0.0003
P70333       1/3      13    85 ..     1    77 []    29.3  0.00032
U2AG_DROME   1/1      51   144 ..     1    77 []    29.0  0.00038
YN26_YEAST   1/2      47   125 ..     1    77 []    29.0  0.00039
U2AG_SCHPO   1/1      73   136 ..     1    77 []    28.9  0.00043
GRF1_HUMAN   1/3      96   168 ..     1    77 []    28.7  0.00048
O13845       3/3     509   586 ..     1    77 []    28.7  0.00049
Q14136       1/2     212   285 ..     1    77 []    28.4  0.00058
Q38915       2/2     249   318 ..     1    77 []    28.4   0.0006
IF32_SCHPO   1/1      41   124 ..     1    77 []    28.3  0.00063
NUCL_HUMAN   1/4     308   377 ..     1    77 []    28.2  0.00066
PRT1_PICAN   1/1      39   115 ..     1    77 []    28.2  0.00068
ROL_HUMAN    1/3      73   140 ..     1    77 []    27.8   0.0009
Q19018       2/2     230   298 ..     1    77 []    27.7  0.00096
Q22039       2/2     230   298 ..     1    77 []    27.7  0.00096
O35737       1/3      13    85 ..     1    77 []    27.5   0.0011
ROH1_HUMAN   1/3      13    85 ..     1    77 []    27.5   0.0011
P87058       1/1     156   238 ..     1    77 []    27.4   0.0012
PTB_PIG      4/4     482   550 ..     1    77 []    27.3   0.0012
ARP_YEAST    1/1     228   317 ..     1    77 []    27.3   0.0012
O13362       1/1     156   238 ..     1    77 []    27.3   0.0013
O35326       2/2     110   177 ..     1    77 []    27.2   0.0013
PTB_HUMAN    4/4     456   524 ..     1    77 []    27.0   0.0015
MAT3_HUMAN   1/1      70   138 ..     1    77 []    27.0   0.0015
O35833       2/2     498   566 ..     1    77 []    27.0   0.0015
MAT3_RAT     2/2     498   566 ..     1    77 []    27.0   0.0015
O04554       1/1     353   421 ..     1    77 []    26.9   0.0016
Q26457       1/1     143   219 ..     1    77 []    26.2   0.0026
Q20414       2/2     261   333 ..     1    77 []    26.1   0.0029
O15047       1/1      96   167 ..     1    77 []    25.8   0.0035
NOT4_YEAST   1/1     139   227 ..     1    77 []    25.7   0.0039
Q14136       2/2     383   459 ..     1    77 []    25.6   0.0041
YA2B_SCHPO   1/4     117   183 ..     1    77 []    25.5   0.0045
P70501       2/2     225   302 ..     1    77 []    25.0   0.0064
JSN1_YEAST   1/1     342   421 ..     1    77 []    24.6   0.0081
YAC4_SCHPO   1/1     118   197 ..     1    77 []    24.6   0.0083
P97343       1/1     344   400 ..     1    77 []    24.4   0.0094
Q63285       1/1     345   401 ..     1    77 []    24.4   0.0094
O18254       1/1      52   118 ..     1    77 []    24.3   0.0099
Q08925       4/4     524   599 ..     1    77 []    24.3     0.01
Q21322       1/2      10    77 ..     1    77 []    24.1    0.012
Q26692       1/3       6    69 ..     1    77 []    24.1    0.012
O22314       2/2     121   192 ..     1    77 []    24.0    0.013
O22315       2/2     121   192 ..     1    77 []    24.0    0.013
Q18717       1/1     110   188 ..     1    77 []    23.6    0.016
O15759       1/2      77   140 ..     1    77 []    23.3    0.019
O15758       1/2      59   122 ..     1    77 []    23.3    0.019
O13620       3/5     508   573 ..     1    77 []    23.1    0.019
Q60745       1/2       1    61 [.     1    77 []    23.1    0.019
YKV4_YEAST   1/1      66   133 ..     1    77 []    23.0     0.02
U2AF_SCHPO   2/2     440   504 ..     1    77 []    22.8    0.021
Q08287       1/1       9    78 ..     1    77 []    22.5    0.022
IF4B_YEAST   1/1     103   178 ..     1    77 []    22.4    0.023
Q05519       1/1      35   107 ..     1    77 []    22.3    0.023
Q26273       1/1       1    44 []     1    77 []    22.3    0.023
O13741       1/2     166   257 ..     1    77 []    22.2    0.023
Q14966       1/1     678   746 ..     1    77 []    22.2    0.024
ROL_HUMAN    2/3     163   232 ..     1    77 []    22.2    0.024
O15758       2/2     140   204 ..     1    77 []    21.5    0.028
Q20966       1/1     276   358 ..     1    77 []    21.4    0.028
Q24433       1/1     578   654 ..     1    77 []    21.3    0.029
O22855       3/3     363   431 ..     1    77 []    21.2     0.03
P91156       1/1     275   342 ..     1    77 []    21.1     0.03
Q12221       1/1     318   397 ..     1    77 []    20.6    0.035
Q04142       1/1     318   397 ..     1    77 []    20.6    0.035
GRF1_HUMAN   3/3     347   415 ..     1    77 []    20.4    0.036
O15759       2/2     158   222 ..     1    77 []    20.4    0.036
Q23121       2/2     131   197 ..     1    77 []    20.1    0.038
LU15_HUMAN   2/2     233   310 ..     1    77 []    19.5    0.044
Q93021       1/1     117   194 ..     1    77 []    19.5    0.044
Q01491       4/4     595   665 ..     1    77 []    19.3    0.047
NRD1_YEAST   1/1     341   404 ..     1    77 []    18.9    0.051
SSB1_YEAST   2/2     188   269 ..     1    77 []    18.8    0.053
Q18999       1/4     120   193 ..     1    77 []    18.7    0.053
NAM8_YEAST   1/3      56   140 ..     1    77 []    18.5    0.055
Q93237       1/1       1    68 [.     1    77 []    18.4    0.057
Q18999       4/4     509   577 ..     1    77 []    18.3    0.058
YG5B_YEAST   2/3     297   413 ..     1    77 []    17.7    0.068
Q99628       3/3     446   526 ..     1    77 []    17.2    0.075
O01159       1/1      12    85 ..     1    77 []    16.8    0.083
YAX9_SCHPO   1/1     137   205 ..     1    77 []    16.7    0.084
P90727       3/3     391   474 ..     1    77 []    16.5    0.089
O13674       3/3     502   568 ..     1    77 []    15.9      0.1
Q21351       1/1     392   472 ..     1    77 []    15.9      0.1
LAH1_YEAST   1/1     125   211 ..     1    77 []    15.8      0.1
Q18601       2/2     128   195 ..     1    77 []    14.6     0.14
Q06477       1/1      62   128 ..     1    77 []    14.5     0.14
P90978       3/3     399   482 ..     1    77 []    14.4     0.14
Q18999       2/4     203   270 ..     1    77 []    14.3     0.15
U2R2_HUMAN   1/1     240   299 ..     1    77 []    14.1     0.15
U2R1_HUMAN   1/1     245   304 ..     1    77 []    14.1     0.15
P87143       1/2      73   146 ..     1    77 []    13.7     0.17
Q62019       1/2       3    67 ..     1    77 []    13.6     0.17
U2R2_MOUSE   1/1     236   303 ..     1    77 []    13.4     0.18
YN8T_YEAST   1/1     420   482 ..     1    77 []    13.2     0.19
O35404       1/1     877   948 ..     1    77 []    13.1     0.19
YLF1_CAEEL   2/2     180   244 ..     1    77 []    13.1      0.2
U2R1_MOUSE   1/1     215   290 ..     1    77 []    13.1      0.2
Q23391       1/1     179   249 ..     1    77 []    12.9      0.2
Q08925       3/4     433   499 ..     1    77 []    12.9     0.21
Q22708       2/2     124   199 ..     1    77 []    12.8     0.21
Q10458       1/1       3    77 ..     1    77 []    12.6     0.22
P78332       1/1     386   459 ..     1    77 []    12.1     0.24
Q61464       1/2     678   746 ..     1    77 []    12.0     0.25
Q18937       1/1      86   161 ..     1    77 []    12.0     0.25
O23612       1/1       4    82 ..     1    77 []    11.5     0.28
Q23953       1/1     250   313 ..     1    77 []    11.5     0.28
Q26548       1/1       1    43 [.     1    77 []    11.2      0.3
Q39201       2/2     121   192 ..     1    77 []    11.2      0.3
YLF1_CAEEL   1/2      60   144 ..     1    77 []    11.2      0.3
O15056       1/1     509   580 ..     1    77 []    11.1     0.31
U2AF_MOUSE   3/3     400   461 ..     1    77 []    10.8     0.33
U2AF_HUMAN   3/3     400   461 ..     1    77 []    10.8     0.33
P70166       1/1     312   402 ..     1    77 []    10.6     0.35
BF41_MOUSE   1/1       1    55 [.     1    77 []    10.6     0.35
Q24527       1/1      82   151 ..     1    77 []    10.5     0.35
O18964       1/1     907   966 ..     1    77 []    10.2     0.38
Q62504       1/1     124   193 ..     1    77 []     9.2     0.48
NOP4_YEAST   4/4     464   585 ..     1    77 []     9.1     0.49
Q91572       1/2     315   392 ..     1    77 []     9.1     0.49
YQO1_CAEEL   1/1     269   341 ..     1    77 []     8.8     0.53
Q17561       1/1      74   142 ..     1    77 []     8.7     0.54
Q60745       2/2     128   174 .]     1    77 []     8.6     0.55
YHS7_YEAST   1/1     159   231 ..     1    77 []     8.6     0.55
Q14206       1/1      13    78 ..     1    77 []     8.6     0.55
O35833       1/2     400   468 ..     1    77 []     8.3     0.59
MAT3_RAT     1/2     400   468 ..     1    77 []     8.3     0.59
P87143       2/2     211   288 ..     1    77 []     8.2      0.6
O04526       1/1     189   266 ..     1    77 []     7.9     0.65
Q08925       1/4     203   269 ..     1    77 []     7.4     0.73
Q17860       1/1     458   529 ..     1    77 []     7.3     0.75
Q92615       1/1     173   241 ..     1    77 []     7.3     0.75
Q14498       3/3     441   497 ..     1    77 []     7.2     0.77
Q14499       3/3     447   503 ..     1    77 []     7.2     0.77
YN26_YEAST   2/2     188   260 ..     1    77 []     7.1     0.77
ROF_HUMAN    1/3      13    85 ..     1    77 []     7.0     0.79
YA2B_SCHPO   3/4     325   391 ..     1    77 []     6.5     0.91
O22794       1/2     212   277 ..     1    77 []     6.4     0.91
Q08925       2/4     294   366 ..     1    77 []     5.9        1
Q24562       3/3     341   403 ..     1    77 []     5.8      1.1
YMC7_CAEEL   1/1      32   102 ..     1    77 []     5.6      1.1
Q12046       1/1     137   214 ..     1    77 []     5.1      1.2
Q07623       1/1      80   150 ..     1    77 []     5.1      1.2
Q10954       1/1     368   435 ..     1    77 []     4.9      1.3
Q26276       1/1       1    44 []     1    77 []     4.4      1.5
O01835       1/1     297   390 ..     1    77 []     4.2      1.5
PES4_YEAST   4/4     395   466 ..     1    77 []     4.2      1.5
Q61464       2/2     904   971 ..     1    77 []     4.1      1.6
O01691       1/1     109   179 ..     1    77 []     4.0      1.6
NGR1_YEAST   1/3      36   159 ..     1    77 []     4.0      1.6
Q23452       1/1     213   280 ..     1    77 []     3.9      1.6
ARP2_PLAFA   1/2      26   107 ..     1    77 []     3.9      1.6
ROAB_ARTSA   1/1      36    95 ..     1    77 []     3.8      1.7
Q61954       2/2     102   153 .]     1    77 []     3.3      1.9
YN8V_YEAST   1/1     116   199 ..     1    77 []     3.2      1.9
PTB_MOUSE    3/4     337   413 ..     1    77 []     3.1        2
O23189       2/3     155   254 ..     1    77 []     3.1        2
Q26279       1/1       1    44 []     1    77 []     2.9      2.1
ROL_HUMAN    3/3     353   420 ..     1    77 []     2.9      2.1
Q18317       1/1     277   347 ..     1    77 []     2.6      2.2
P70501       1/2      60   127 ..     1    77 []     2.6      2.2
MUD2_YEAST   1/1     425   510 ..     1    77 []     1.9      2.6
Q21559       1/1      76   144 ..     1    77 []     1.2      3.1
O29092       1/1     362   435 ..     1    77 []     0.9      3.3
O14797       2/2     107   173 ..     1    77 []     0.6      3.5
O13674       2/3     411   477 ..     1    77 []     0.6      3.5
O22794       2/2     375   460 ..     1    77 []     0.2      3.9
Q91572       2/2     434   504 ..     1    77 []     0.0        4
YG3Q_YEAST   1/1      22    90 ..     1    77 []    -0.2      4.3
P70221       1/1     128   194 ..     1    77 []    -0.3      4.3
Y051_NPVAC   1/1     225   284 ..     1    77 []    -0.9        5
YHR9_YEAST   1/1     250   335 ..     1    77 []    -1.2      5.4
O35847       1/1      17    83 ..     1    77 []    -2.7      7.6
HIPO_CAMJE   1/1     254   322 ..     1    77 []    -3.7      9.4
Q60701       1/1      85   143 ..     1    77 []    -3.7      9.5
Q24424       1/1       2    43 .]     1    77 []    -3.9       10
BLSA_HUMAN   1/1     149   248 ..     1    77 []    -4.2       11
XE7_HUMAN    1/1     149   248 ..     1    77 []    -4.2       11
YAQ2_SCHPO   1/1     313   388 ..     1    77 []    -6.5       18
O00583       1/1      22    83 ..     1    77 []    -6.7       19
O13838       1/1     172   248 ..     1    77 []    -7.5       23
O05954       1/1     285   364 ..     1    77 []    -7.6       23
YM28_YEAST   1/1     253   342 ..     1    77 []    -8.1       26
Q19944       1/1     131   197 ..     1    77 []    -8.7       30
Q26274       1/1       1    44 []     1    77 []    -8.9       32
O01886       1/1      37   121 ..     1    77 []    -9.2       34
Q19164       1/1      14    84 ..     1    77 []    -9.2       34
ASM4_YEAST   1/1     271   384 ..     1    77 []    -9.5       37
Y117_HUMAN   1/1     189   227 .]     1    77 []   -10.0       41
O00582       1/1      22    83 ..     1    77 []   -10.0       41
O28580       1/1     244   322 ..     1    77 []   -10.9       50
O35309       1/1     160   233 ..     1    77 []   -11.2       54
O29837       1/1     267   359 ..     1    77 []   -11.7       61
Q47952       1/1     101   196 ..     1    77 []   -12.8       78
Q08646       1/1     284   354 ..     1    77 []   -13.0       82
Q47957       1/1     101   188 ..     1    77 []   -13.1       84
Q58954       1/1      21    96 ..     1    77 []   -13.2       86
Q26278       1/1       1    44 []     1    77 []   -13.5       92
Q13287       1/1     159   233 ..     1    77 []   -14.9  1.3e+02
TKTC_METJA   1/1     139   200 ..     1    77 []   -15.0  1.3e+02
PR06_YEAST   1/1     599   668 ..     1    77 []   -15.1  1.3e+02
KHK_HUMAN    1/1     166   223 ..     1    77 []   -15.5  1.5e+02
PUR5_METJA   1/1     258   322 ..     1    77 []   -15.8  1.6e+02
O31824       1/1      57   130 ..     1    77 []   -15.9  1.6e+02
Q92518       1/1       2    48 ..     1    77 []   -16.0  1.6e+02
YD33_SCHPO   1/1      14    90 ..     1    77 []   -16.1  1.7e+02
Q09135       1/1      44    93 ..     1    77 []   -16.1  1.7e+02
O30057       1/1     159   244 ..     1    77 []   -16.3  1.8e+02
Q42378       1/1     140   193 ..     1    77 []   -16.7  1.9e+02
Q42482       1/1      20    76 ..     1    77 []   -16.8    2e+02
O35002       1/1     186   249 ..     1    77 []   -17.0  2.1e+02
PGDS_RAT     1/1     447   515 ..     1    77 []   -17.1  2.1e+02
YY08_METJA   1/1     879   966 ..     1    77 []   -17.2  2.2e+02
Q48827       1/1     113   175 ..     1    77 []   -17.8  2.5e+02
Q23637       1/1     311   382 ..     1    77 []   -17.9  2.5e+02
Q48639       1/1      46   120 ..     1    77 []   -17.9  2.5e+02
VJ01_VACCC   1/1      70   126 ..     1    77 []   -18.3  2.8e+02
HBA_ARAAR    1/1      13    93 ..     1    77 []   -18.4  2.8e+02
YAB9_SCHPO   1/1     241   300 ..     1    77 []   -18.4  2.8e+02
P94393       1/1     303   365 ..     1    77 []   -18.7  3.1e+02
Q26271       1/1       1    39 []     1    77 []   -18.9  3.2e+02
Q96423       1/1      42   105 ..     1    77 []   -18.9  3.2e+02
O00373       1/1     181   248 ..     1    77 []   -19.3  3.5e+02
YHB0_YEAST   1/1     115   191 ..     1    77 []   -19.4  3.6e+02
VJ01_VACCV   1/1      70   126 ..     1    77 []   -19.4  3.6e+02
SYH_METJA    1/1     329   397 ..     1    77 []   -19.8  3.9e+02
Q12452       1/1      50   101 ..     1    77 []   -20.0  4.1e+02
Q46102       1/1      39   109 ..     1    77 []   -20.2  4.3e+02
O17002       1/1     192   242 ..     1    77 []   -20.3  4.4e+02
Q19942       1/1     125   197 ..     1    77 []   -20.3  4.5e+02
PHYA_SOLTU   1/1     822   898 ..     1    77 []   -20.4  4.5e+02
P75023       1/1     228   280 ..     1    77 []   -20.4  4.5e+02
SYF_METJA    1/1      84   188 ..     1    77 []   -20.4  4.6e+02
Y447_METJA   1/1      76   149 ..     1    77 []   -20.6  4.7e+02
Y383_METJA   1/1     182   261 ..     1    77 []   -20.6  4.8e+02
Q94172       1/1      32   112 ..     1    77 []   -20.8    5e+02
CHLL_CHLRE   1/1     172   245 ..     1    77 []   -20.9    5e+02
Q00898       1/1     136   190 ..     1    77 []   -20.9  5.1e+02
Q00897       1/1     136   190 ..     1    77 []   -20.9  5.1e+02
A1A2_MOUSE   1/1     136   190 ..     1    77 []   -20.9  5.1e+02
Q61283       1/1     125   179 ..     1    77 []   -20.9  5.1e+02
Q85381       1/1      70   137 ..     1    77 []   -21.0  5.2e+02
VJ01_VARV    1/1      70   137 ..     1    77 []   -21.0  5.2e+02
O34784       1/1     466   555 ..     1    77 []   -21.0  5.2e+02
MENE_HAEIN   1/1     340   416 ..     1    77 []   -21.1  5.3e+02
T2C2_CHVP1   1/1     220   286 ..     1    77 []   -21.2  5.4e+02
CARA_BACSU   1/1     100   156 ..     1    77 []   -21.2  5.4e+02
SFCA_ECOLI   1/1      84   158 ..     1    77 []   -21.2  5.5e+02
Q23267       1/1     351   414 ..     1    77 []   -21.5  5.8e+02
DDLA_ECOLI   1/1     120   200 ..     1    77 []   -21.5  5.8e+02
KLP1_CHLRE   1/1     171   249 ..     1    77 []   -21.5  5.8e+02
Q26272       1/1       1    43 []     1    77 []   -21.7  6.1e+02
CPC3_RABIT   1/1      38   101 ..     1    77 []   -22.0  6.6e+02
O29409       1/1     236   296 ..     1    77 []   -22.0  6.6e+02
O34925       1/1      71   150 ..     1    77 []   -22.2  6.9e+02
Q26281       1/1       1    39 [.     1    77 []   -22.4  7.2e+02
Q25988       1/1       2    73 ..     1    77 []   -22.4  7.2e+02
META_ECOLI   1/1      38   112 ..     1    77 []   -22.5  7.3e+02
O04614       1/1      39   117 ..     1    77 []   -22.8  7.8e+02
P95425       1/1      70   137 ..     1    77 []   -22.8  7.9e+02
Q51350       1/1      70   137 ..     1    77 []   -22.8  7.9e+02
P75431       1/1       1    78 [.     1    77 []   -22.9    8e+02
O00364       1/1     181   249 ..     1    77 []   -22.9    8e+02
PRE1_STAAU   1/1      89   166 ..     1    77 []   -22.9  8.1e+02
Q96515       1/1     181   253 ..     1    77 []   -23.0  8.2e+02
O27761       1/1     110   225 ..     1    77 []   -23.1  8.4e+02
Q51783       1/1      70   137 ..     1    77 []   -23.2  8.6e+02
A1A1_MOUSE   1/1     136   190 ..     1    77 []   -23.4    9e+02
Q00896       1/1     136   190 ..     1    77 []   -23.4    9e+02
Q20445       1/1      11   106 ..     1    77 []   -23.5  9.3e+02
YNC8_CAEEL   1/1       3    52 ..     1    77 []   -23.5  9.3e+02
Q57721       1/1       1    62 [.     1    77 []   -23.5  9.3e+02
Y556_METJA   1/1     101   181 ..     1    77 []   -23.7  9.7e+02
O28372       1/1      29    98 ..     1    77 []   -23.8  9.8e+02
O00376       1/1     181   249 ..     1    77 []   -23.8  9.9e+02
O00361       1/1     181   249 ..     1    77 []   -23.8  9.9e+02
O00371       1/1     181   249 ..     1    77 []   -23.8  9.9e+02
O00377       1/1     181   249 ..     1    77 []   -23.8  9.9e+02
Q15605       1/1     181   249 ..     1    77 []   -23.8  9.9e+02
Q12880       1/1     181   249 ..     1    77 []   -23.8  9.9e+02
O00369       1/1     181   249 ..     1    77 []   -23.8  9.9e+02
O00374       1/1     181   249 ..     1    77 []   -23.8  9.9e+02
O00365       1/1     181   249 ..     1    77 []   -23.8  9.9e+02

Histogram of all scores:
score    obs    exp  (one = represents 6 sequences)
-----    ---    ---
  -67      2      0|=                                                          
  -66      0      0|                                                           
  -65      0      0|                                                           
  -64      1      0|=                                                          
  -63      0      0|                                                           
  -62      4      0|=                                                          
  -61      2      0|=                                                          
  -60      5      0|=                                                          
  -59     12      0|==                                                         
  -58      3      0|=                                                          
  -57      5      0|=                                                          
  -56      7      3|*=                                                         
  -55     16     12|=*=                                                        
  -54     16     30|=== *                                                      
  -53     20     61|====      *                                                
  -52     37    103|=======          *                                         
  -51     42    148|=======                 *                                  
  -50     48    188|========                       *                           
  -49     42    216|=======                            *                       
  -48     71    231|============                          *                    
  -47     61    232|===========                           *                    
  -46     64    222|===========                         *                      
  -45     96    204|================                 *                         
  -44     96    183|================              *                            
  -43    100    159|=================         *                                
  -42     92    136|================      *                                    
  -41     97    114|================= *                                        
  -40    112     95|===============*===                                        
  -39    109     78|============*======                                        
  -38     95     64|==========*=====                                           
  -37    108     52|========*=========                                         
  -36     86     42|======*========                                            
  -35     92     33|=====*==========                                           
  -34     89     27|====*==========                                            
  -33     81     21|===*==========                                             
  -32     61     17|==*========                                                
  -31     64     13|==*========                                                
  -30     34     11|=*====                                                     
  -29     25      8|=*===                                                      
  -28     33      7|=*====                                                     
  -27     14      5|*==                                                        
  -26     30      4|*====                                                      
  -25     25      3|*====                                                      
  -24     22      2|*===                                                       
  -23     13      2|*==                                                        
  -22      9      1|*=                                                         
  -21     16      1|*==                                                        
  -20      5      1|*                                                          
  -19      6      0|=                                                          
  -18      5      0|=                                                          
  -17      6      0|=                                                          
  -16      6      0|=                                                          
  -15      1      0|=                                                          
  -14      4      0|=                                                          
  -13      1      0|=                                                          
  -12      2      0|=                                                          
  -11      2      0|=                                                          
  -10      4      0|=                                                          
   -9      3      0|=                                                          
   -8      2      0|=                                                          
   -7      2      0|=                                                          
   -6      0      0|                                                           
   -5      2      0|=                                                          
   -4      3      0|=                                                          
   -3      1      0|=                                                          
   -2      1      0|=                                                          
   -1      3      0|=                                                          
    0      1      0|=                                                          
    1      2      0|=                                                          
    2      2      0|=                                                          
    3      3      0|=                                                          
    4      4      0|=                                                          
    5      3      0|=                                                          
    6      1      0|=                                                          
    7      3      0|=                                                          
    8      4      0|=                                                          
    9      2      0|=                                                          
   10      4      0|=                                                          
   11      5      0|=                                                          
   12      3      0|=                                                          
   13      4      0|=                                                          
   14      3      0|=                                                          
   15      2      0|=                                                          
   16      3      0|=                                                          
   17      0      0|                                                           
   18      2      0|=                                                          
   19      1      0|=                                                          
   20      2      0|=                                                          
   21      4      0|=                                                          
   22      6      0|=                                                          
   23      1      0|=                                                          
   24      6      0|=                                                          
   25      2      0|=                                                          
   26      2      0|=                                                          
   27      5      0|=                                                          
   28      3      0|=                                                          
   29      1      0|=                                                          
   30      1      0|=                                                          
   31      4      0|=                                                          
   32      4      0|=                                                          
   33      1      0|=                                                          
   34      4      0|=                                                          
   35      6      0|=                                                          
   36      1      0|=                                                          
   37      5      0|=                                                          
   38      2      0|=                                                          
   39      1      0|=                                                          
   40      5      0|=                                                          
   41      0      0|                                                           
   42      6      0|=                                                          
   43      5      0|=                                                          
   44      2      0|=                                                          
   45      3      0|=                                                          
   46      2      0|=                                                          
   47      3      0|=                                                          
   48      3      0|=                                                          
   49      7      0|==                                                         
   50      2      0|=                                                          
   51      1      0|=                                                          
   52      3      0|=                                                          
   53      2      0|=                                                          
   54      4      0|=                                                          
   55      6      0|=                                                          
   56      1      0|=                                                          
   57      1      0|=                                                          
   58      7      0|==                                                         
   59      8      0|==                                                         
   60      6      0|=                                                          
   61      4      0|=                                                          
   62      1      0|=                                                          
   63     10      0|==                                                         
   64      2      0|=                                                          
   65      2      0|=                                                          
   66      4      0|=                                                          
   67      0      0|                                                           
   68      1      0|=                                                          
   69      2      0|=                                                          
   70      2      0|=                                                          
   71      7      0|==                                                         
   72      6      0|=                                                          
   73      0      0|                                                           
   74      4      0|=                                                          
   75      6      0|=                                                          
   76      2      0|=                                                          
   77      7      0|==                                                         
   78      6      0|=                                                          
   79      3      0|=                                                          
   80      9      0|==                                                         
   81      6      0|=                                                          
   82      4      0|=                                                          
   83      5      0|=                                                          
   84      1      0|=                                                          
   85      1      0|=                                                          
   86      7      0|==                                                         
   87      3      0|=                                                          
   88      3      0|=                                                          
   89      5      0|=                                                          
   90      5      0|=                                                          
   91      2      0|=                                                          
   92      4      0|=                                                          
   93      4      0|=                                                          
>  94    318      -|=====================================================      


% Statistical details of theoretical EVD fit:
              mu =   -46.9346
          lambda =     0.2314
chi-sq statistic =  1898.6975
  P(chi-square)  =          0

Whole sequence top hits:
tophits_s report:
     Total hits:           751
     Satisfying E cutoff:  751
     Total memory:         117K

Domain top hits:
tophits_s report:
     Total hits:           1215
     Satisfying E cutoff:  1215
     Total memory:         618K
BioPerl-1.007002/t/data/hmmsearch3.out000444000766000024       233713155576321 17460 0ustar00cjfieldsstaff000000000000# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.0 (March 2010); http://hmmer.org/
# Copyright (C) 2010 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  Kv9.hmm
# target sequence database:        /home/pboutet/Desktop/databases/nr_May26
# max ASCII text line length:      unlimited
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       Kv9  [M=481]
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                              Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   1.1e-260  874.4   2.2   1.2e-260  874.3   1.5    1.0  1  gi|281344220|gb|EFB19804.1|           hypothetical protein PANDA_002980 [Ailuropoda melanoleuca]
   2.2e-259  870.1   2.8   2.5e-259  869.9   1.9    1.0  1  gi|296224438|ref|XP_002758060.1|      PREDICTED: potassium voltage-gated channel subfamily S member 3 [Callithrix jacchus]
//
BioPerl-1.007002/t/data/hmmsearch3_multi.out000444000766000024      3364313155576321 20716 0ustar00cjfieldsstaff000000000000# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.0 (March 2010); http://hmmer.org/
# Copyright (C) 2010 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  Pfam-A.hmm
# target sequence database:        test_seqs.seq_raw.txt
# output directed to file:         hmmsearch.output.txt
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       1-cysPrx_C  [M=40]
Accession:   PF10417.4
Description: C-terminal domain of 1-Cys peroxiredoxin
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each sequence (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (40 nodes)
Target sequences:                          3  (2141 residues)
Passed MSV filter:                         0  (0); expected 0.1 (0.02)
Passed bias filter:                        0  (0); expected 0.1 (0.02)
Passed Vit filter:                         0  (0); expected 0.0 (0.001)
Passed Fwd filter:                         0  (0); expected 0.0 (1e-05)
Initial search space (Z):                  3  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 14.27
//
Query:       DUF4229  [M=69]
Accession:   PF14012.1
Description: Protein of unknown function (DUF4229)
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------             -----------
  ------ inclusion threshold ------
          3  -17.8  37.0      0.019    3.0   2.5    4.3  5  lcl|Protein_ID1.3|M3 complement(48376..51420)


Domain annotation for each sequence (and alignments):
>> lcl|Protein_ID1.3|M3  complement(48376..51420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   1.7         1         3      34      40 ..     305     311 ..     277     337 .. 0.55
   2 ?    2.6   2.1    0.0084     0.025      12      50 ..     382     418 ..     374     422 .. 0.69
   3 ?   -1.1   0.6      0.12      0.36       4      36 ..     841     874 ..     841     882 .. 0.52
   4 ?    3.0   2.5    0.0064     0.019       7      59 ..     872     925 ..     870     929 .. 0.90
   5 ?   -0.7   0.9     0.087      0.26      31      50 ..     972     991 ..     937    1001 .. 0.56

  Alignments for each domain:
  == domain 1    score: -4.3 bits;  conditional E-value: 1
               DUF4229  34 laallAl 40 
                           la+l A+
  lcl|Protein_ID1.3|M3 305 LAILSAI 311
                           3333332 PP

  == domain 2    score: 2.6 bits;  conditional E-value: 0.0084
               DUF4229  12 fvvllavlvllgvligllvplllaallAlvvalplSfll 50 
                           + v ++   l gv   l +p+  a++++++ +++lS  +
  lcl|Protein_ID1.3|M3 382 VFVPMF--SLTGVPRYLFIPMAEAVIFGMLSSFVLSQTF 418
                           333333..34455555449*****************776 PP

  == domain 3    score: -1.1 bits;  conditional E-value: 0.12
               DUF4229   4 YtalRlglfvvllav..lvllgvligllvplllaa 36 
                           Y +l lgl++ + ++  lv+++ + +l+ p++++ 
  lcl|Protein_ID1.3|M3 841 YRGLSLGLVASIILIyfLVVVNFESWLD-PFVIIT 874
                           5566688888777774344444444444.554443 PP

  == domain 4    score: 3.0 bits;  conditional E-value: 0.0064
               DUF4229   7 lRlglfvvllavlvllgvligll.vplllaallAlvvalplSflllrklRrrat 59 
                           +  +l ++l++++++l + +  l vp l  a++ + va + S+l+ +  R+r++
  lcl|Protein_ID1.3|M3 872 IITALPAALAGIVWMLYLTGTTLsVPALTGAIMCMGVATANSILVISFARERLA 925
                           56789999******9999999889*********************999999875 PP

  == domain 5    score: -0.7 bits;  conditional E-value: 0.087
               DUF4229  31 plllaallAlvvalplSfll 50 
                           pl  a++ +l++a +  +++
  lcl|Protein_ID1.3|M3 972 PLGRAVIGGLLLATIATLIF 991
                           55555555555554444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (69 nodes)
Target sequences:                          3  (2141 residues)
Passed MSV filter:                         1  (0.333333); expected 0.1 (0.02)
Passed bias filter:                        1  (0.333333); expected 0.1 (0.02)
Passed Vit filter:                         1  (0.333333); expected 0.0 (0.001)
Passed Fwd filter:                         1  (0.333333); expected 0.0 (1e-05)
Initial search space (Z):                  3  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 16.41
//
Query:       ACR_tran  [M=1021]
Accession:   PF00873.14
Description: AcrB/AcrD/AcrF family
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------             -----------
   9.3e-189  616.9  10.5   1.2e-188  616.6   7.2    1.0  1  lcl|Protein_ID1.3|M3 complement(48376..51420)


Domain annotation for each sequence (and alignments):
>> lcl|Protein_ID1.3|M3  complement(48376..51420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  616.6   7.2  3.9e-189  1.2e-188      71    1021 .]      11    1000 ..       2    1000 .. 0.93

  Alignments for each domain:
  == domain 1    score: 616.6 bits;  conditional E-value: 3.9e-189
                            S-TTEEEEEEEETTSEEEEEEEESTTS-HHHHHHHHHHHHHHHGGGS-HHHHHH-EEEEEEECCECEEEEEEESSSTS-HHHHHHHH CS
              ACR_tran   71 gldglkyvsSqSseglssitvtFedgtdidiArqqvqnrlqeaknkLPeevqepgiskiktssseilvlavtskdgsltktdlrdla 157 
                             ++ +++++SqS  g   + + F+ + di  A+ qv++  q + +++P ++++p i   +++  +il+la++sk   l++  + dl 
  lcl|Protein_ID1.3|M3   11 TVNDIEHIESQSLFGYGIVKIFFQPDVDIRTANAQVTAISQTVLKQMPPGITPPLILNYNAATVPILQLALSSK--VLSEDRIFDLG 95  
                            578899********************************************************************..*********** PP

                            HHCTHHHHHTSTTEEEEEESS.--EEEEEEE-HHHHHCTT--HHHHHHHHHHHSSB-EEEECTT-SB-EEEE-SB---SCCHHCT-E CS
              ACR_tran  158 esnikdqlsrveGVgdvqliGgsekavriwldpqklaklgltltdvvsalkeqnvqvaaGqlegqqeelliraqgrlqsaediekii 244 
                            ++ i++ql+ v G +    +Gg+ ++++i ldpq++++ +++++dv++al++qn   + G+ +  + e+++++++   +   ++++ 
  lcl|Protein_ID1.3|M3   96 QNFIRPQLATVRGSAVPSPYGGKVRQIQIDLDPQAMQSKRVSPDDVARALSQQNLVLSPGTEKIGSFEYNVKINDSPDEFTLLNNLP 182 
                            *************************************************************************************** PP

                            EEETTSEEEEHHHCEEEEEEESSSS-EEEETTCEEEEEEEEEETTSBHHHHHHHHHHHHHCCGGGSSTTEEEEEEEESHHHHHHHHH CS
              ACR_tran  245 vksqdgskvrlrDvAkvelgaeeeriaatlngkpavllavkklpganaievvkavkekleelketlPegveivvvydttefvrasie 331 
                            +k+  g  + ++DvA+v +g   + ++++ +g   vl+++ k     ++++++  ke +++lketlP+++ ++vv d++ fv+++i+
  lcl|Protein_ID1.3|M3  183 IKNVGGVTIFIHDVAHVRDGFPPQINVVRDDGRRSVLMTILKNGATSTLDIIQGTKELIPKLKETLPNNLVLKVVGDQSIFVKSAIS 269 
                            *************************************************************************************** PP

                            HHHHHHHHHHHHHHHHHHHHHSSHCCCHHHHHHHHHHHHHHHHHHHHTT--EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSS CS
              ACR_tran  332 eVvktlleaivLvvlvlflFLqnlratlipaiavPlsllgtfavlkalglsiNlltlfgLvlAiGlvvDdAiVvvEnverkleeege 418 
                             Vv +  +a +L  ++++lFL+++r+t+i+ +++Pl++l ++++l++ g ++N++tl+gL+lA+G++vDdA Vv+En+  +le+ g+
  lcl|Protein_ID1.3|M3  270 GVVREGTIAGILTSVMILLFLGSWRSTIIISMSIPLAILSAIIFLSLTGNTLNVMTLGGLALAVGMLVDDATVVIENINHHLEM-GK 355 
                            ************************************************************************************.** PP

                            -HHHHHHHHHHHHCCHHHHHHHHHHHHCCGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCS----TT-CC...... CS
              ACR_tran  419 kpleaalksmkeiegalvaialvllavfvPilflgGveGklfrqfaltivlaillsvlvaltltPalcallLkarkeekek...... 499 
                               +a++ ++++i  + + ++l++++vfvP+++l+Gv   lf ++a ++++ +l s +++ t++P ++  lLk + ++ ++      
  lcl|Protein_ID1.3|M3  356 PTTKAIIDAARQIIQPALVSTLSICIVFVPMFSLTGVPRYLFIPMAEAVIFGMLSSFVLSQTFVPTVANKLLKYQTQHFKHehhtda 442 
                            *************************************************************************8776544446799* PP

                            ........................CHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHH.HHHHHCCS-BESS----TSEE CS
              ACR_tran  500 ........................gffrefnrlfdalerrYekllekvlrhravvllvalllvvg.slllfvripkeflPeedegvl 561 
                                                    ++ + f++ f ++   Y+ +l++ l hr+  ++++l +v++ ++ lf+ ++k+f+Pe d g++
  lcl|Protein_ID1.3|M3  443 hrpehdpnfkvhrsvkasifqffiNIQQGFEKRFTKVRLVYRSILHFALDHRKKFITLFLGFVIVsCVTLFPLLGKNFFPEVDSGDM 529 
                            *******************9655555578*************************999999887775899****************** PP

                            EEEEE-STTC-HHHHHHHHHHHHHHHH...TTTTEEEEEEEESESSSS..E........CTTEEEEEEEE--CTTS-SCCCSHHHHH CS
              ACR_tran  562 vtsvqlppgvsleqtekvlkqvekilk...ekpevesvfavtGfafagdta........gqnsakvfisLkpekerkeeektveali 637 
                             ++++++ g+ +e+t+k  + +e++++    ++e + ++   G + +g +         g++ +++ i+L ++      ++  ++ +
  lcl|Protein_ID1.3|M3  530 KIHIRVQVGTRIEETAKQFDLIENTIRrlvPQNELDTIVDNIGLSVSGINTaysstgtiGPQDGDILIHLNEN------HHPTKEYM 610 
                            ************************8875446889999999999888774331111111134445555555444......45688999 PP

                            HHHHHHC.CTSTSSEEEEEE-SSSCCCSSSSSEEEEEEE.TSSSCHHHHHHHHHHHHHHHCCSTTEECEEESS-S-EEEEEEEE-HH CS
              ACR_tran  638 erlrkel.ekikganvellapiqlreletlsgvrlelqvklfgddleaLseareqllaalkqlpeladvrseqqedepqlqvkidre 723 
                            ++lr+ l ++++g++ +++ p +++ +    gv + ++  + g ++++  + ++++l+ ++++p++ad+r++q ++ pq++v+idr 
  lcl|Protein_ID1.3|M3  611 KKLRETLpRAFPGVS-FAFLPADITSQILNFGVPAPIDIRVDGPNHDNNLKFVRAILKDIRNVPGIADLRVQQATNYPQFNVDIDRS 696 
                            999999945678887.7888999*999************************************************************ PP

                            HHHHCTB-HHHHHHHHHHHHT-..EEEEEEEETTE...EEEEEEEE-GGGSSSGGGGCC-EEEETTSE.EEECGGCEEEEEEEE-SE CS
              ACR_tran  724 kaaalGvsiadinetlstalgg..syvndfieegr...vvkvvvqleedlrsspedlkklyvrnkkgk.mvplsavakieeekgpns 804 
                            +a+++G++  di + l + l g  +++ +f  +++    + +v+q+++ + +s+ dl+++++++k++  m  l+ + +ie+ ++ + 
  lcl|Protein_ID1.3|M3  697 QAKNYGLTEGDITNSLVATLAGtsQVAPTFWLNNKngvSYPIVIQMPQYKINSLADLANIPITTKESSsMQVLGGLGSIERDQSDSV 783 
                            ************8877666655434556776544422279***********************998764889*************** PP

                            EEEETTCEEEEEEEEESTTS...-HHHHHHHHHHCCTT..SSTTEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCTSSST CS
              ACR_tran  805 ierenglrsveisgevaegd...slgeaeeavekiakqvklPagvgiewtglseqeqeagnsllllvalalllvflvLaalyeslsd 888 
                            i+++n ++s+ i ++++ +d   ++g++e+++++ +++  lP+gv+++ +g+    q ++  l+l ++++++l++++  + +es++d
  lcl|Protein_ID1.3|M3  784 ISHYNIKPSFDIFASLQGRDlgsISGDIETIIQHHHQE--LPKGVSVKLQGQVPIMQDSYRGLSLGLVASIILIYFLVVVNFESWLD 868 
                            ****************8876222578999999999888..*********************************************** PP

                            CHHHHTTHHHHHHHHHHHHHHTT--BSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTTBHHHHHHHHHHHHCHHHHHHHHHHHHH CS
              ACR_tran  889 pllvlltvPlalvGallalllrglelsviaqvGlilliGlavkNailivefakelrekeglsleeAileaaklRLrPiLMTalaail 975 
                            p+++++ +P al+G +  l+l+g++lsv a+ G i+ +G+a  N il+++fa+e  +   ++  +A+lea+ +R+rP+LMTa a+++
  lcl|Protein_ID1.3|M3  869 PFVIITALPAALAGIVWMLYLTGTTLSVPALTGAIMCMGVATANSILVISFARERLA-IVKDSTQAALEAGYTRFRPVLMTASAMLI 954 
                            *********************************************************.888899*********************** PP

                            CCHHHHTT-STTHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHH CS
              ACR_tran  976 GvlPLalstGaGselqqplgivvlGGlvtstvLtlllvPvlYvlva 1021
                            G++P+al+ G+G e   plg +v+GGl+++t+ tl +vPv++ +v+
  lcl|Protein_ID1.3|M3  955 GMIPMALGLGDGGEQNAPLGRAVIGGLLLATIATLIFVPVVFSVVH 1000
                            ******************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1021 nodes)
Target sequences:                          3  (2141 residues)
Passed MSV filter:                         1  (0.333333); expected 0.1 (0.02)
Passed bias filter:                        1  (0.333333); expected 0.1 (0.02)
Passed Vit filter:                         1  (0.333333); expected 0.0 (0.001)
Passed Fwd filter:                         1  (0.333333); expected 0.0 (1e-05)
Initial search space (Z):                  3  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.17u 0.03s 00:00:00.20 Elapsed: 00:00:00.19
# Mc/sec: 11.27
//
BioPerl-1.007002/t/data/hs_est.est2genome000444000766000024       171213155576321 20150 0ustar00cjfieldsstaff000000000000Note Best alignment is between forward est and forward genome, and splice  sites imply forward gene
Exon       119 100.0   695   813 HSHNRNPA         1   119 hs_est        
+Intron    -20   0.0   814  1376 HSHNRNPA    
Exon       117 100.0  1377  1493 HSHNRNPA       120   236 hs_est        
+Intron    -20   0.0  1494  1788 HSHNRNPA    
Exon       144  99.3  1789  1935 HSHNRNPA       237   382 hs_est        
+Intron    -20   0.0  1936  2083 HSHNRNPA    
Exon        97 100.0  2084  2180 HSHNRNPA       383   479 hs_est        

Span       417  99.8   695  2180 HSHNRNPA         1   479 hs_est        

Segment    119 100.0   695   813 HSHNRNPA         1   119 hs_est        
Segment    117 100.0  1377  1493 HSHNRNPA       120   236 hs_est        
Segment      4 100.0  1789  1792 HSHNRNPA       237   240 hs_est        
Segment    142 100.0  1794  1935 HSHNRNPA       241   382 hs_est        
Segment     97 100.0  2084  2180 HSHNRNPA       383   479 hs_est        
BioPerl-1.007002/t/data/hs_fugu.newick000444000766000024         7213155576321 17471 0ustar00cjfieldsstaff000000000000((ENSP00000263374,SINFRUP00000082596),SINFRUP0000006110);
BioPerl-1.007002/t/data/hs_owlmonkey.aln000444000766000024       146513155576321 20110 0ustar00cjfieldsstaff000000000000CLUSTAL W (1.82) multiple sequence alignment


human           gtctgttccaagggcctttgcgtcaggtggg--ctcagggtt-------ccagggtggct
owlmonkey       gtctgttccaagggccttcgagccagtctgggccccagggctgccccactcggggttcca
                ****************** * * ***   **  * ***** *        * ****  * 

human           ggacc-ccaggccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgg
owlmonkey       gagcagttggaccccaggtct-cagc-gggagggtgtggctgggctc-tgaagcatttgg
                *  *     * ****** *** **** ******  ************ ******** ***

human           gggtgagcccaggggccccaaggcagggcacctggccttcagcctgcctcagccctgcct
owlmonkey       g--tgagcccaggggctc-agggcagggcacctg-ccttcagcg-gcctcagcc-tgcct
                *  ************* * * ************* ********  ********* *****

human           gtctcccag
owlmonkey       gtctcccag
                *********
BioPerl-1.007002/t/data/hs_owlmonkey.fas000444000766000024        60313155576321 20060 0ustar00cjfieldsstaff000000000000>human 
GTCTGTTCCAAGGGCCTTTGCGTCAGGTGGGCTCAGGGTTCCAGGGTGGC
TGGACCCCAGGCCCCAGCTCTGCAGCAGGGAGGACGTGGCTGGGCTCGTG
AAGCATGTGGGGGTGAGCCCAGGGGCCCCAAGGCAGGGCACCTGGCCTTC
AGCCTGCCTCAGCCCTGCCTGTCTCCCAG
>owlmonkey 
GTCTGTTCCAAGGGCCTTCGAGCCAGTCTGGGCCCCAGGGCTGCCCCACT
CGGGGTTCCAGAGCAGTTGGACCCCAGGTCTCAGCGGGAGGGTGTGGCTG
GGCTCTGAAGCATTTGGGTGAGCCCAGGGGCTCAGGGCAGGGCACCTGCC
TTCAGCGGCCTCAGCCTGCCTGTCTCCCAG
BioPerl-1.007002/t/data/hs_owlmonkey.fasta000444000766000024        64013155576321 20406 0ustar00cjfieldsstaff000000000000>human
GTCTGTTCCAAGGGCCTTTGCGTCAGG-TGGGC-TCAGGGTT---------------CCAGGGTGGCTGG
ACCCCAGGCCCCAGCTCTGCAGCAGGGAGGACGTGGCTGGGCTCGTGAAGCATGTGGGGGTGAGCCCAGG
GGCCCCAAGGCAGGGCACCTGGCCTTCAGCCTGCCTCAGCCCTGCCTGTCTCCCAG
>owlmonkey
GTCTGTTCCAAGGGCCTTCGAGCCAGTCTGGGCCCCAGGGCTGCCCCACTCGGGGTTCCAGAGCAGTTGG
ACCCCAGGTCTCAGC---------GGGAGGGTGTGGCTGGGCTC-TGAAGCATTT--GGGTGAGCCCAGG
GGCTC-AGGGCAGGGCACCTG-CCTTCAGC-GGCCTCAGC-CTGCCTGTCTCCCAG
BioPerl-1.007002/t/data/hsinsulin.blastcl3.blastn000444000766000024      4537513155576321 21655 0ustar00cjfieldsstaff000000000000BLASTN 2.2.6 [Apr-09-2003]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= human 
         (179 letters)

Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
or phase 0, 1 or 2 HTGS sequences)
           1,787,533 sequences; -24,016,349 total letters

Searching... please wait.. done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gb|J00265.1|HUMINS01 Human insulin gene, complete cds                 355  2e-95
emb|V00565.1|HSINSU Human gene for preproinsulin, from chromosom...   355  2e-95
gb|M10039.1|HUMINSPR Human alpha-type insulin gene and 5' flanki...   355  2e-95
gb|L15440.1|HUMINSTHIG Homo sapiens tyrosine hydroxylase (TH) ge...   355  2e-95
gb|AC132217.15| Homo sapiens chromosome 11, clone RP11-889I17, c...   347  4e-93
gb|AC130303.8| Homo sapiens chromosome 11, clone RP4-539G11, com...   347  4e-93
gb|AY138590.1|AY138589S2 Homo sapiens insulin (INS) gene, exons ...   347  4e-93
emb|AJ009655.1|HSA9655 Homo sapiens ins gene, partial                 347  4e-93
gb|AY137497.1|AY137496S2 Pan troglodytes insulin precursor (INS)...   339  9e-91
emb|X61089.1|PTPPINS P.troglodytes gene for preproinsulin             315  1e-83
gb|AY137500.1|AY137498S3 Gorilla gorilla insulin precursor (INS)...   262  2e-67
gb|AY137503.1|AY137501S3 Pongo pygmaeus insulin precursor (INS) ...   222  1e-55
emb|X61092.1|CEPPINS C.aethiops gene for preproinsulin                129  2e-27

>gb|J00265.1|HUMINS01 Human insulin gene, complete cds
          Length = 4044

 Score =  355 bits (179), Expect = 2e-95
 Identities = 179/179 (100%)
 Strand = Plus / Plus

                                                                        
Query: 1    gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2228 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 2287

                                                                        
Query: 61   gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2288 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 2347

                                                                       
Query: 121  aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
            |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2348 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 2406


>emb|V00565.1|HSINSU Human gene for preproinsulin, from chromosome 11. Includes a highly
            polymorphic region upstream from the insulin gene
            containing tandemly repeated sequences
          Length = 4992

 Score =  355 bits (179), Expect = 2e-95
 Identities = 179/179 (100%)
 Strand = Plus / Plus

                                                                        
Query: 1    gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2228 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 2287

                                                                        
Query: 61   gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2288 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 2347

                                                                       
Query: 121  aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
            |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2348 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 2406


>gb|M10039.1|HUMINSPR Human alpha-type insulin gene and 5' flanking polymorphic region
          Length = 3943

 Score =  355 bits (179), Expect = 2e-95
 Identities = 179/179 (100%)
 Strand = Plus / Plus

                                                                        
Query: 1    gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2503 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 2562

                                                                        
Query: 61   gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2563 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 2622

                                                                       
Query: 121  aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
            |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2623 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 2681


>gb|L15440.1|HUMINSTHIG Homo sapiens tyrosine hydroxylase (TH) gene, 3' end; insulin (INS)
            gene, complete cds; insulin-like growth factor 2 (IGF2)
            gene, 5' end
          Length = 12565

 Score =  355 bits (179), Expect = 2e-95
 Identities = 179/179 (100%)
 Strand = Plus / Plus

                                                                        
Query: 1    gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4289 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 4348

                                                                        
Query: 61   gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4349 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 4408

                                                                       
Query: 121  aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
            |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4409 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 4467


>gb|AC132217.15| Homo sapiens chromosome 11, clone RP11-889I17, complete sequence
          Length = 170027

 Score =  347 bits (175), Expect = 4e-93
 Identities = 178/179 (99%)
 Strand = Plus / Plus

                                                                         
Query: 1     gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
             ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Sbjct: 86461 gtctgttccaagggcctttgcgtcaggtgggctcaggattccagggtggctggaccccag 86520

                                                                         
Query: 61    gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86521 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 86580

                                                                        
Query: 121   aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
             |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86581 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 86639


>gb|AC130303.8| Homo sapiens chromosome 11, clone RP4-539G11, complete sequence
          Length = 171366

 Score =  347 bits (175), Expect = 4e-93
 Identities = 178/179 (99%)
 Strand = Plus / Plus

                                                                          
Query: 1      gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 127800 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 127859

                                                                          
Query: 61     gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 127860 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 127919

                                                                         
Query: 121    aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
              ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
Sbjct: 127920 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtcacccag 127978


>gb|AY138590.1|AY138589S2 Homo sapiens insulin (INS) gene, exons 1, 2, 3, and complete cds;
           and insulin-like growth factor (IGF2) gene, exon 1
          Length = 4233

 Score =  347 bits (175), Expect = 4e-93
 Identities = 178/179 (99%)
 Strand = Plus / Plus

                                                                       
Query: 1   gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 378 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 437

                                                                       
Query: 61  gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 438 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 497

                                                                      
Query: 121 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
           ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
Sbjct: 498 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtcacccag 556


>emb|AJ009655.1|HSA9655 Homo sapiens ins gene, partial
          Length = 1393

 Score =  347 bits (175), Expect = 4e-93
 Identities = 178/179 (99%)
 Strand = Plus / Plus

                                                                       
Query: 1   gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6   gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 65

                                                                       
Query: 61  gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
           ||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 66  gccccagctgtgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 125

                                                                      
Query: 121 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 126 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 184


>gb|AY137497.1|AY137496S2 Pan troglodytes insulin precursor (INS) gene, complete cds
          Length = 4124

 Score =  339 bits (171), Expect = 9e-91
 Identities = 177/179 (98%)
 Strand = Plus / Plus

                                                                       
Query: 1   gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 338 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 397

                                                                       
Query: 61  gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
           ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Sbjct: 398 gccccagctctgcagcagggaggacgtggctgggctcttgaagcatgtgggggtgagccc 457

                                                                      
Query: 121 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
           |||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Sbjct: 458 aggggccccaaggcagggcacctggccttcagccggcctcagccctgcctgtctcccag 516


>emb|X61089.1|PTPPINS P.troglodytes gene for preproinsulin
          Length = 2483

 Score =  315 bits (159), Expect = 1e-83
 Identities = 175/179 (97%), Gaps = 1/179 (0%)
 Strand = Plus / Plus

                                                                        
Query: 1    gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1028 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 1087

                                                                        
Query: 61   gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
            ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Sbjct: 1088 gccccagctctgcagcagggaggacgtggctgggctcttgaagcatgtgggggtgagccc 1147

                                                                       
Query: 121  aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
            |||||||||||||||||||| || |||||||||| ||||||||||||||||||||||||
Sbjct: 1148 aggggccccaaggcagggcagct-gccttcagccggcctcagccctgcctgtctcccag 1205


>gb|AY137500.1|AY137498S3 Gorilla gorilla insulin precursor (INS) gene, complete cds
          Length = 4146

 Score =  262 bits (132), Expect = 2e-67
 Identities = 141/144 (97%)
 Strand = Plus / Plus

                                                                       
Query: 36  gggttccagggtggctggaccccaggccccagctctgcagcagggaggacgtggctgggc 95
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 389 gggttccagggtggctggaccccaggccccagctctgcagcagggaggacgtggctgggc 448

                                                                       
Query: 96  tcgtgaagcatgtgggggtgagcccaggggccccaaggcagggcacctggccttcagcct 155
           || |||||||||||||||||||||||||||||||||||||||||| ||||||||||||| 
Sbjct: 449 tcttgaagcatgtgggggtgagcccaggggccccaaggcagggcaactggccttcagccg 508

                                   
Query: 156 gcctcagccctgcctgtctcccag 179
           ||||||||||||||||||||||||
Sbjct: 509 gcctcagccctgcctgtctcccag 532


>gb|AY137503.1|AY137501S3 Pongo pygmaeus insulin precursor (INS) gene, complete cds
          Length = 4126

 Score =  222 bits (112), Expect = 1e-55
 Identities = 136/144 (94%)
 Strand = Plus / Plus

                                                                       
Query: 36  gggttccagggtggctggaccccaggccccagctctgcagcagggaggacgtggctgggc 95
           ||||||||||||||||||||||||||| ||||||||||||| ||||||||||||||||||
Sbjct: 384 gggttccagggtggctggaccccaggctccagctctgcagctgggaggacgtggctgggc 443

                                                                       
Query: 96  tcgtgaagcatgtgggggtgagcccaggggccccaaggcagggcacctggccttcagcct 155
           || |||||||| ||||||||||||||||||||||| ||||||||||||||||||||||| 
Sbjct: 444 tcttgaagcatttgggggtgagcccaggggccccagggcagggcacctggccttcagccg 503

                                   
Query: 156 gcctcagccctgcctgtctcccag 179
            ||||||| |||||||||||||||
Sbjct: 504 acctcagctctgcctgtctcccag 527


>emb|X61092.1|CEPPINS C.aethiops gene for preproinsulin
          Length = 1909

 Score =  129 bits (65), Expect = 2e-27
 Identities = 86/93 (92%)
 Strand = Plus / Plus

                                                                       
Query: 36  gggttccagggtggctggaccccaggccccagctctgcagcagggaggacgtggctgggc 95
           ||||||||||||||||||||||||||||||||||||||| |||||||||| |||||||||
Sbjct: 514 gggttccagggtggctggaccccaggccccagctctgcaacagggaggacatggctgggc 573

                                            
Query: 96  tcgtgaagcatgtgggggtgagcccaggggccc 128
           || |||||| | || |||||| |||||||||||
Sbjct: 574 tcttgaagcgtttgagggtgaacccaggggccc 606


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
  or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Jul 31, 2003  1:26 AM
  Number of letters in database: 192,913,178
  Number of sequences in database:  1,867,771
  
Lambda     K      H
    1.37    0.711     0.00 

Gapped
Lambda     K      H
    1.37    0.711 7.29e-304 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 1,670,626
Number of Sequences: 1867771
Number of extensions: 1670626
Number of successful extensions: 118444
Number of sequences better than 1.0e-20: 13
Number of HSP's better than  0.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 118410
Number of HSP's gapped (non-prelim): 33
length of query: 179
length of database: 8,782,847,770
effective HSP length: 20
effective length of query: 159
effective length of database: 8,745,492,350
effective search space: 1390533283650
effective search space used: 1390533283650
T: 0
A: 0
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 54 (107.5 bits)

Query= owlmonkey 
         (180 letters)

Searching... please wait.. done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gb|J02989.1|ATRINS Owl monkey (A.trivirgatus) insulin gene, comp...   357  4e-96

>gb|J02989.1|ATRINS Owl monkey (A.trivirgatus) insulin gene, complete cds
          Length = 2113

 Score =  357 bits (180), Expect = 4e-96
 Identities = 180/180 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   gtctgttccaagggccttcgagccagtctgggccccagggctgccccactcggggttcca 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 551 gtctgttccaagggccttcgagccagtctgggccccagggctgccccactcggggttcca 610

                                                                       
Query: 61  gagcagttggaccccaggtctcagcgggagggtgtggctgggctctgaagcatttgggtg 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 611 gagcagttggaccccaggtctcagcgggagggtgtggctgggctctgaagcatttgggtg 670

                                                                       
Query: 121 agcccaggggctcagggcagggcacctgccttcagcggcctcagcctgcctgtctcccag 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 671 agcccaggggctcagggcagggcacctgccttcagcggcctcagcctgcctgtctcccag 730


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
  or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Jul 31, 2003  1:26 AM
  Number of letters in database: 192,913,178
  Number of sequences in database:  1,867,771
  
Lambda     K      H
    1.37    0.711     0.00 

Gapped
Lambda     K      H
    1.37    0.711 7.29e-304 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 910,717
Number of Sequences: 1867771
Number of extensions: 910717
Number of successful extensions: 72147
Number of sequences better than 1.0e-20: 1
Number of HSP's better than  0.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 72146
Number of HSP's gapped (non-prelim): 1
length of query: 180
length of database: 8,782,847,770
effective HSP length: 20
effective length of query: 160
effective length of database: 8,745,492,350
effective search space: 1399278776000
effective search space used: 1399278776000
T: 0
A: 0
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 54 (107.5 bits)
BioPerl-1.007002/t/data/humor.maf000444000766000024     10217113155576321 16551 0ustar00cjfieldsstaff000000000000##maf version=1 scoring=zero
a
s NM_006987 0 5000 - 5000 gcacagcctttactccctgactgcgtttatattctgcctctcccgtgcctgttggtccttggggacGGCCCTCCGGCAGGTTCTGGCCTCAGGA--------CCCCGCACCAGCCCCGGCC-----GTGCCAGCTGCCCTCCCACTGGCCTGGCCCAGCTCTCCAGAGAGGCTTCATGCAGCCAGTTCCCCAGGGAACACCGTTGCCCACACGTTGCTAATGT-TAAAACATGAATTTATTGCATCTGTAGCATCTTACCTTGAGCACGGCTTCTTTCAATGCTTTTATTTTGCAATTATAG----GTTTATTTTCTTCCTT-----TCCTCTCTCTTGAGCTTTTTAAGGTGTTTTCTGTCACTCAGCTGGAGACTTTAAATTTCCTATTTATATTAATTATCAAATTA------TTTCATATATGA---GTCATTCAGCTCAGCCCTTTTTGGCTCCTTCTTGCAACTCTTACTTGTGGATTTATTGGGCAGTTCAGCGCCTACTTTCATG------------------------GGCAGA---CTCAACTGGCGA----GATTTTAACTGGAGGGTGAGAGATGTCCT------------GGCCACGGGGCCCTGTTG-----------------------CTCACAGTC--------------------------------------CCTGGATCAGAGGA--TGGTGCC---------------------GGATGGGCAGGTGCTGAGGATGCACATACCGCCCTCGGGTTA--------GCACCGAAGGTTCTTGTGTCAGACGTGAGGCTTCCTTCCTGGGTTCTTTCTGGCTGCGCTAGTCCAGAAGACCAGCAAACCCGAGATGGTCTGAGGTGGACGATGGAGCCTGAATGGAGAGCCTGGGGCGTGAGCCAG-GGTCTGGGATACCCTGGGACAGAGTTAGATGCCCCTGCAGACGTGGATGAGCGGCTGAAGACTAAGGGAGCAGGTCACACGTGGTGACAGACAGGAGAGGCTGCTGTGCCATCCAGGGGCTGGGGAAGGAGCCCCCG-TGGAGAGGCTCCATTTCGGCCACGTGGCTGCTGCAGACAACCGGGAGTCAGCGTCGGCACAAACACGGGTGCCTCGAAAGAGAGCAGTGCCGGCC-TGGTGTCTCCGGGCCCAGCTGCCACTGGCACAGGCCTCCGAAGGGGCAGGAGCAGGAGCAGGAGCAGAAAGCGCACA-TCAGGGCTcatgctgtgcctgtgaagatgtcgggcacgtccgttagtgtgtgtggtgcgcggtcgcctgtgaagacgactgttagtgtgtgtggtgcgtggtcgcctgtgaagacgactgttagtatgtgtggtctacggtcgcctgtgaagacgactgttagtatctgtggtgcgcggtcgcctgtgaagacgactgttagtatgtgtggtctatggtcgcctgtgaagacgactgttagtatctgtggtgcgcggtcgcctgtgaagacgactgttagtaagtgtggtgcgcggtcgcctgtgaagacgactgttagtaagtgtggtgcgcggtcgcctgtgaagacgtctgttagtaagtgtggtgcgcggtcgcctgtgaagacgactgttagtAAGTGTG-GTGCGCGGTCGCCTGTGAAGACGACTGTTAGTAAGTGTGGTGCGCGGTCGCCTGTGAAGACGACTGTTAGTGTG----GTGCGCGGTCGCCTGTGAAGACGACTGTTAGTAAGTGTGGTGCGCGGTCGCCTGTGAAGACGACTGTTAGTAAGTGTGGTGCGCGGTCGCCTGTGAAGACGTCTGTTAGTAAGTGTGGTGCGCGGTCGCCTGTGAAGACGACTGTTAGTATGTGTGGTGCGCGGTCGCCTGTGAAGACGACTGTTAGTATGTGTGGTGCGCGGTCGCCTGTGAAGACGACTGTTAGCAAGTGTGGTGCGCGGTCGTCTGTGAAGACGACTGTTAGCAAGTGTGGTGCGCGGTCGCCTGTGAAGACGACTGTTAGCAAGTGTGGTGCGCGGTCGCCTGTGAAGACGACTGTTAGCAAGTGTGGTGCGCGGTCGCCTGTGAAGACGACTGTTAGTATGTGTGGTGCACggtcgcctgtgaagatgtcttttagtaagtgtggtgcacggtcgcctgtgaagacgactgttagtatgtgtggtgcacggtcgcctgtgaagacgactgttagtaagtgtggtgcgcggtcgcctgtgaagacgactgttagtaagtgtggtgcgcggtcgcctgtgaagatgactgttagtaagtgtggtgcacggtcacaCCTTCCCACACAGTGCAGGTGACttactcagggctctggatggcaaatgacaa----ggacccaattcaaactagcataagcaaaaaggcagctctgtgggcctggca-cctggggatcaaaacagtcgttcaggcacggctggatccagccattgaccatgggtatgaggtgactcaccttcatctctcagctctgtttagctgcaccggcagacaggccgtttc-aagggggagccaggtggctactggccatcgtgagctagtgccg-------tgcttaccgtcccag---------------------------------------------acagtgggtt---tattgca--------------caggaactctggcaag--accccaggaggactcagtatggctgggtctgggtcacatgcccagccctgagccaattaccctgccttgggggtgg-----------ggctattctaattggtcaTCCTCATCACATTCACCCAGGAAGAAGGGGAAGG-AGGGGCTGTTTCTCTTGCCCAGGAAGACTGGGCGTGACTACTTTGACCTGAAGAGTTATTCTCAAAAAGGAAAGGAATGCTGGGTAGACAAAATATATGCCCATTGCAGAAGGCCAGCAGGGGCCCCTGGCCTTCGCTTTGCTAAAGGTGGC-----------------AGGTGCACA--GCTGTCCGGACCCTGGAGCTCAGTGTGAGGAGTGTAAAGGTGTAGAAGGTGCCGTCTGTGCAGCAGTGTGGCGGCGTTCTGCCTTTCTCAGCTGAATGGAAGACAAACACTCAGGCCTCTTCACACCTTCGTGACTGGTCCCCCCTGGACCTTTGCGCAGAGCTGGCCTTTC--------CATGAAGCAAACTCTGGGCACATGTGGAA-----ACCAGCCTCTTGCTGCCATGCCTGCCCCAGGGACTGACCAGGGTCGGCTCCAGTCACTGACATAGTTTATCACATCTCTTTGGCCTCTGGTCTCTGGATCCACACCTCTGGCTCTGACGTCTGCATCGAGCCCCTGTCCCTGCTGGGTTCA-AGTCTCTTTTCCAGAAGCTTCACTTGGCTCGAGGCTCCACTTGAT-TTGGTG-TCATTTGC-GTTTCTGAGCTTGGTCCTCCCGACCTGTGGTCCTGCCAGGGGAAGAGCAGCGTGGCCTGGCTGGACCCTGGCAAAGGAGGCTTCTCTTCTGCATTTCTTCTACACGGAGTGCATGAGCAGGACAAAGACCAGCTGATTCCTGCAGGCCTGGGGCTGTGGTGTGCGGGTCTCCCACAGGCCTTGGtatgtgtgtggtgtgtggtcccgcacactcagagatggcttccagcacattccacactttctttctttctttcttttttttttgagtcggagtctcgctctgttgcccaggctggagtgcagtggcgcgatctcggctcactgcaagctccgccttccgggttcaagcgattctcctgcctcagcctcccgagtagttgggacgacagttgcccacgaccatgtctggccaagcctcagccttcccaagtgctagggttacaggcgtgagccactatgcctggcctacccatgaattttattttattttttaaattttaaggcgaggtctcactctgtcacctaggctggagtacggtggctagatcatggctcacagcagcctcaaactcctagactccagccaccctcccacctcagcctcctgaatggctggggctacagacatttgccaccacacctggctaatttttgtattttcagtagagatgggtttttactatgttggccaggctggtctcgaactcctgaccttaggtgatccacccgcctcggcctctggagtagctggggttacaggagtgagccaccgtgccagtcctccttccaccctttcatataaccagcagcgcatatcagcacttctcaacatctttactgcaggacCTTTTCTTCAAATGAAGTCTTACCTGGAAGCCTGAcagatgacgaggaaaaagctgagttgctctgggttgggctgtaataacccccttgttcccagccccctgcttctgcttgcacggtcctgaagaggggctccacacccctggctccttggaacccagtttgttgggttataataaccggccttgttcccagccccctgcttcgcctgtacagtcctgaagagggtctccacaccccTGGCTCCTTGGAACCCAGTTTGAG-------AGCCTCTTGGCAATTATATCCATCTGTCTGTCTCTCTTGTGGTAGCACCTGCTGCTGCTCCCCATGGGGAAAGGTTGCTGATGGTGTTTATTTTTTTTTTAAGCATGAAAACATTTTCTTTTTTCTATCAGTAGCTTGTTTGCACTATGAAAAGGTCAACAGAGAGATCCTTGTCATCTTCCttctccctgcaggagggtgtcagggtgtaagtgctccctcgctgtgcaggggttcatttcattcatttcatTACCCTTGCCCTCCTCGAGGTACCTCCGGGAAGCTGTTCCATTTACACATCTGTCAAGTTCTCTGTGCGTCAATTTGCCTTGCTCCTGAAGAGCCACACCCAAAAGGGGCCCCACTCCAGGCAGCGGGGCTTCAGGAAGCGATGAGATGCT---GACGCAGGCCCCGTGCACCACCACTGCTG----CCTGTAAGGGCTGTTTTGGATACAGAAAATGTGCCCTTTCTAACC--------CAAAAAA------------------------------------------------------------------------------------------------------------------------------TGCTTGAAATGTGTAAAAGTGGCCAGACT---AACAGTCCCAAAGAGGGCTGC---------CCTCTAAGAGGAAGCGTCCCAAATCTGT---TCAGTTTTAGAGACTACGTGACTGGG------GTACG-------TGGTGGGGCCTTACCAGACATCCACG---------AGGAGAATCCAGGCCTTGGTTTGGCTCCAGCTGGGCCTGCCTGGTGGCTGCCACTTATTGACTTAAGTCCCAGTGATTCAGCTCCTCATCTGGAACACCTCGGGTCACCCCCG
s mm3       0 3424 + 3424 ..................................................................GACCCCCCTGTACCCACTGGCCTAAGGAGCAACCCCACCCACAGCAGCTCTGGCCCTGTCATGCCAACCACTGTCCCACTGACCCAGACTACCCCTG-AGAAGGACATTGTACAGCTAAGTCACAGAGTAACACTGC----------------ATGTGTAACACAAGCGTGTGTT-----TGTAACAT---GCCTTCACCAAGGTTTCTTCTAATGCTTTTGTTTTGCAGTTCTAGCTGTTTTCATTTCCCTCCTTGGATCTTCTCTCTCTTGAACTTTTTAAAGTGTCATA-GTCTATAAGTTAGCAACTTCA--CTCCTTACGTGTATTAATTGTCAAATTACTTATTTTTTCTATGTGAATTGCTGTTTA------TCATCTTTGCCTCCTTTTTGCAAACTTTACGTATTCGGGGATTAAGCATTTTAGCATTTGCTCTTCTATTTAGAGACTGAGCAAGCAGTGATGGCGGAGCCCTGTGCTGGTGA-TGCATTTTGGGCTGGGAAGAGAATTCTACCTTTAGCAAAGC-AAGGCCA-TGGCCTCTGCTGTCAGTATATGATGGACGTTCATTCTGACTGTCTAGCTTCCTTCTTCAGGTGTAAGTAATCATGTCGTCCTCCTGGAGAAGATAAATTGGTCCCTGCGCCTCCCTCCTTAGGAAAGGACTGGCAGGTGCTTAAG------------CCAGTGTGTTAAGCCAGGAGCACTCAGAATCCT---GTCAGCAACCCTGCTTCTTTGTCATGATCATTCTAGGCGCACTT-TCTGGAAGATGAG--------GGGTGGTCAGAAGTGGATGACAGAGTCTCCACGTACAACCTTGGAGATAGGCCAG-GGTGTGGGATGAGCCTGGGATCTCTTGGGGATCATTGGAGACATAGGTGTA-ATTTGAAGA------GAGCAGGTCATAT-----------------------------TATCCAGG---------------------AGCTGGAGCTCTCTTTGGGCCCCATAGCTACAGCAGAAGCGCAA-AGTTAGCCAAAGAATGAACACTGGAGGTTGAAAGGAAGGTGATCTCTGCCATGGCATCTCGGAGTC----------------AGGCCTCAGAGG----ACAGTTAGCTGCAGGAGCAGACAGCTCTCC-CCAAAGCT......................................................................................................................................................................................................................................................................................................................................................................................................AAGTGAGCGTGTGCAGTGCATTCAGAAGAACAGAATGAGCGTGTGCAGTGTGCAGTGCATTCAGAAGAACAGAGTGAGCGTGTGCAGTGTGCACTGCATTCAGAAGAACAGAGTGAGCGTGTGCAGTGTGCACTGCATTCAGAAGAACAGAGTGAGC--GTGTGCAGCGCATTCA-----GAAGAACAGAGTGAGCGTGTGCAGTGTGCAGCGCATTCAGAAGAACAGAGTGAGCGTGTGCAGTGCAT-------TCAGAAGAACAGAGTGAGCGTGTGCAGTGTGCACTGCATTCAGAAGAACAGAGTGAGCGTGTGCAGTGTGCAGTGCATTCAGGAGAACAGAGTGAGCGTGTGCAGTGTGCACTGCATTCAGAAGAACAGAGTGAGCATGTGCAGTGTGCAGTGCATTCAGAAGAACAGAGTGAGCGTGTGCAGTGTGCAGTGCATTCAGAAGAACAGAGTGAGCGTGTGCAGTGTGC..........................................................................................................................................................................................................................AGGTGATTTTCTCAGAGTTC---ATGATCAATCACAAATACGACTccagctcaaactacctgaagcaaaaatgggactctgcgagtctggcaaactgggaaccataaaagtgggtcaggcttggctgcacccagtgactgacaatatcttcaggcgtattcgcctccttccgtcgacttctctaagcatggtttc-agcctggcagtttctgagaggcagcaagatggccgcAGGATTTCCCACACCAGCACCATCAACACTGTTTGCTTCCCACACTGCCACCTATCCACTGCTCACTTCCCACGTGGACACTACACACCAAGATGCTGTCTGTACCGCAGCTCACTGTCACAAAAGGTACACTTTCCAGTAACCCAGGGAAGACACACCTTGGC-----CTAGGTCACATATACAGCCTTGAGCCAGCCACTCT--CCAGGAAGTGGAGGAGGGTGATGGACATCTTAATAGGTCCCTC-AGTCATGTCCACCCCCAAGGAGGAGGAAGCAGGGAACAGTTTCTTTTCTCCAGGAGGTC--GACATGGTTAGTTAAACCTAAAGA-------------AGGAA------GCTGGGCAGGCAAGATGGGTCTCCATCACCTAGAGCTAGCAGAGGCCTCTGGCCTTTGCTTTGCTAAAG-TAGAGTTGTCTTTCCAGCCTAAGATGCACACAGTTGTCTGGATCTTGGTGCT........................AAGGCTGTCATCTGCTTAGCATTGCCACAG--TTCTGGGGTATACAGT----------GTGAACCCT-AGCAATCTTCAAGCCTTCTTGTGAGGGGCATCGTAGGCCTTCTCATGGAGG----CTTCCCACCACCCTGTGTGGGCAATCC----CTCACATGGAACCTTCACAAGCAGTAAGCAGCTATGCTTG-----GGG--------GAAATAGCTTT--TCCCTAACATGCTT------GTGTCCCAGGATGCTGGCCCCTAG-----CACCACTTGCTCT-----TTGC-------ACCTCTCCTTGCCAGGCTCATGGTCTCTTTG--AGATGCTCATCTTGGCTCAGATCACAACCAGATGTTGGTG-TTACCTATAGTTTGTGGACA-GGTCCATCTGGTAGGTGGAGCTGC-AGGGAATGGACAGAGCAGCCAGGCTGGGCCCCGACAAAGGAGGC................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTCTTCTTCAAGTGGAGTCTTATCTGGAAAGCTGA.............................................................................................................................................................................................................aGGCTCCTTGGAACCCCGATTGAGGATTGAGAAGTGTTGGGTGGCTATGCTCATTGGTCTCTC-----------AGAATCGTTTTTTACCTCCCTGGGGATAAGGTTGCTG--------------------------GAAAACATTTTCTTCCTTC----ACTAGATTGTCTGT--TATGAAAAGGTCACTTGTGATCTCCTTGTCATCCTCC.......................................................................TGCCCCTGTGCTGGGCTAGCTGCCTTTGGGGATTTGTTCTTCTACTGCACTGCTCAAGTGGTCAGGGCCTCAGTTTCCCTTCTTCCCAAGAAGCCAGAGCCA---GAGGCTCCACTGCAGGC-----GACTCTGGTAAGCTCTGTGATGCTCACAACTTGGGCCCTG----CCAGGACGGATAATAACTTTTGAGAAATGTCT-------AAAAGCTAAGTCCTTTCTAACAACAACAGACAAACAAACCCTTCAGTGCTGGCAGGTCCCTcatgtttataattccaatcactgtgaaggatgaagcagtaagatcctgggttctaggccagcctgggctactcagcaagatcctgtctcaagaaatgacaaaTGTTTCCAATTTGTAT--GTGTCCAGACTGAAAACACATCCGCGAGGGGATGTAAGCTTCTGCCTTGGGTGGGAAATACCCCACAATTGTCTGTCAGCTGCTGCCACTGTGGGACTTGGTCTCCAGTACAATAGTGCTGGGGTGGCTTGGCCCGGCTTCCCTGCACTAGGGAGAGAGAATCCAGGCCTGGGTTTGGCTCCAACTGGGCCTTGCAGG--GCTGTTACTTATTGAGTTAAGTCAGAGTGGCTCAAATGTTGATATGCAGCACCT-GGGTCACCCTTG
s rn3       0 1951 + 1951 ..................................................................................................................................................................................................................................................................................................................................................GAGCTTTTTAAAGTGTCAGA-GC----AAGTTATCAACTTCA--TTCCCTATGAGTATTAATTATCAAATTACTTACGTTTCCTATATAAATTGCCATTTA------TCATCTTTGCCTCTTTCTTGCAAACTTTGCGTGTTCGTGGATTAAGCAATTTAGCGTTTGCTTTTCTGTTTAGAGAGTGAGCAAGCAGTGATGGCGGAGCCCCGTGCTGGTGCCTGCAGTGTGGGCTGGGAGGAGAAGGCTAACTTTAGCAAAGCGAAGGTCA-GGGCCTCTGCTGTCAGTATGTGATGGACAGCCATTCTACCTGTCCAGCTTCCTTCTTCAGGTATAAGTAATCACGTCATCCTCCTGGAGAAGATAA-CTGGCCCCTGCCCCTTCGTCCTTAGGAAAGGACTGACTGGTGCTTAAG------------CCAGTGTGTTAAGCCAGGGGCACTCAGGGTCCT---GTCAGCAAGGCTGTTTCTTTGCAGTGATCATTCTGGGTGCAGTC-TCTGGAAGACAAG--------GGGTGGTCAGAAGTGGATGGCACAGTCTCAGTGTACAACCTGGGAGATGGGCCCGAGGTCTGGGAT---------CTCTCTTGGGGATCATTGGAGACATAGGTGTG-ATTTGAAGA------GA-CAGGTCAGAC-----------------------------CATCCCGGGACCACAGAGAAAGCACATGGAGCTGGATCTCTCTTTGGGCCCCATGGCTACAGCAGAAGAGCAA-AG----------AATGAACACTGGAGATTGGAGGGA------TCTCTGCCATGGTGTCTCTCAGCC----------------AGACCTCAGAGG----AGAGTTAGCTGCAGGAACAGACAGCTCCCCACCAGAGCT..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTTCTCCATTCTGCCTAGGTGATTTTCTCAGAGTTC---GTGATCAATCACAAATAAGAGTCCAGCTCAAA--------AGCAGAAATGGGACTCTGTGAGTCTGGCAACCTGGGAACTGTAAAAGTGGGTCAGGCTTGGCTGCACCCAGTGACTGACAATATCTTCAGGCATATTTGTCTTCTTCTGTTGGCTTCCCTAAGCATCATTTCCAGACTGGCTGCTTCTGAGAGGGGGCAAGATGGCCACAGGATTTCCCATGCCAGCACCACCAGCACTGTTTGCTCCCCACG---------------------------------------------ACAACACTGT---TACCACAGCTCACCGTCATGAAAGGTATACTTCTCAGTAACCCAGAGAAGACAAACCCTGGC-----CTAGGTCACCTG--CAGCCTTGGGCCAGCCACTCT--CCAGGAAGTGGAAGAGGGTGATGGATATCTTAATAGGTTCTCC-AGTCATGTCCAACCCTAAGGAGGAAGAAGC--------------------CAGGAGGAC--AACCTGGTTACTTAATCCTGAAGA-------------AGGAA------GCTGGGCAGGCAAGATGGTTGTCCTTCACCTAGAGCTAGCAGAAGCCCCTGGCCTTTGCTTTGCTAAAGGTAGAATTGTCTTCCCAGCCCAAGATGCACA--GCTGTCTGGACCTTGGTGC------TGCAGGGTTGAA-----TTAAGGCTATGATCTGCTTAGCATTGCCACAG--TTCTGGGGTACACAGT----------GTGAACGCT-AGTAATCTTCATGCTTTTGCGTAAAGGGCATCTTAGGCCTTCTCATGGAGG----CTTCC--------TGTGTGGGAAATCC----CTCACACGGCACCTTCACATGTGATAAGCTGCTATGCTTG-----GGG--------AAAATAGCTTT--TCCCTAACATGCTT------GTGTCCCAGGATGCTGGTCC-TAG-----CACCCCTTGGCCT-----CTGC------TACCTCTCCTTGCCAGGGTCACAGTCTCTTTG--GGATGCTACTCTCAGCTCAGATTTCAACCGGATGTTGGGGGTCACCTCTAGTTTGTGAACA-AGTCTATTTTGTGGGTGGACATGC-AGGGACGGGACAGAGCTGCCAGGCTGAGCCCTGACAAAGGAGGCACC----CGGTATGGCTTCGGAGCTCTCTGCACGCGCACAGCAA----CTTCCTAGTCTTGCTGCTCTGTGGCAGCTGCA--------CCCCACAAGCCCTGG.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AAGTTCCTTGGAACCCCATTTGAG-------AAGCTCTGGGTGATTGTGTCCATTGGTCTCTC...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

a
s NM_018289 0 5000 + 5000 tttgtccatgttggtcaggctggtctcgaactccccacctcaggtgatccacccacctcggcctcccagagtgctgggattacaggcgtgagccaccgtgcccagcctggaagttgttttttttGAGCCCAGCTCATTTGTGAAAATATCACGTGCTCCTTATTTTCATACCCAAATTTCTCATATCCATAAACTTCCACATTTTATTTCTGTCAGAAGTATACAATCTCTTTCTAGATTTCCACCTCCTGTCAAAGGTATTTCCTTCTTTTGTTTGACATAAATGAATCAATCTAGTCTGTTATTACTTA----AAGAAGTT--------TTTTAAAACCCA----------------------------------------------------------------GTGTGT----------------------------------------------------------------CAACCTATCTCTC--------------------------------------------------------------------------------------------------------------------------------------------------------------TGCTCTTTTAACTTCCTTTACTTCTTTGTACTGCATAACTCTCCTAAACTCAAACTTATATTATTAGTAGCTT----ATCTGCAAAGAGGGAGAAGGGGTATCATGGAGTTGGGAGCTCCAGAGGAGGCAAAGGTTTTGGGTCACGGGAGAGTGCCATTGAGAACGGACAATGGATGCTGAGAAGGACAATGAGAATCAGTGGAAATAAGGCAACAGGAATTTGTGCTGAACATGGTCACCCTGGTTTCATGATTCTCCACAACAATATGGGAAGCTCAGAGGCAAAGAAAAAAACAAAAAACAAAAAACAGAGAGACCAGGGCTGATGGCAGGCATGGtaaacct-ggtcatgcccctcctctgcttacagtccgtcagaggcttcccattccttcaagaagaccttccagatccttcaccgtccggcagtgcccatttctccagcttcctcgtgtatcactctcccttgggctttcaaacttccatcaccctggccgactcttttcatactcatggcttttgcacattctgttccttttatctatgtgttatcttcacttccaacccttggcttcagcttaaaaa--tcacttcctcagaaaagcctttcctggccgggcttgatggctcacacccgtaatcccagcagttagggaggtcaaggcaggcggatcacctgaggtcaggagttcaagaccagcatggccaacatggagaaaccccgtctctactaaaaatacaaaaattagccgggtgtggtggcgtatgcctgtaatcccagctactcaggaggctgaggcaggcgaatcacttgaatccaggaggcggaggttgcggtgagccgaggtcgcgccattgcactccagcctgggcaacaagagagaaactctgtctcaaaaaaaaaaaaaaaaaagaaaaaaagaaaaagaaaaagaaagaaaaggctttcctgacccctaatccaatcagaactctaaccatatagtctctcaacatgtgctttacttctcttttatcggatctatcacaattatatgtttatttgtacaaatgcccttttcatacatagaaatagctctgtagaggcaagcatggggtctattttgttcactgctgaattcccggcacctagcttgagtacctgtcgctaacaggaacaggtgttcaataaatgtattgactagcttaatgaaCGGCAGGAAGACTtaggtatacggccttaggcaaatttttattttgttgcttgttttaactagatcttca-tctccta-tctgttagatgggtatagtaataaaaactaacaacctc--agaattgctgtgtgaattaaaagagacaatgcatgtaacatgcttcgaatggtacctgtcatatagtaagggctaggaaattttccttcttattATCATCATTAAAAATAAGCTCTCTgagcaaacagaactctcatacattgctggtagcaatgtgaaagtgatacagccactttggaaaacagtttaccagtttcttagaaagttaaacacagacatatcatataacacagcaatcccacatctacatatttacccaagtgacatgaaaacttatgttcacacaaaaatctgtacatgaatgtttatagcagctttattcataattgccaaaaactggaaa-aacccatatgtccttcaa-ccaggga-ctagataaacaaatagtggtgtattcatctagtggaataccagcaagaagacatgaa-ccacagatacatgcaacaacatggatgaattttagatactttatgacagatgaaagaagcca-gactgaaaaggtgtcatactgtatgattccatc-----------tatatgatattctggaaatatcaaaactatagggacaggccaggcgtggtggctcatgcctgtaaccccagcactttgggagcctgatgctggcagatcacctgaggtcaggagtttgagaccatcctgggcaacatgatgaaaccctgtctctactaaaaatacaaaaattagccaggtgtggtggcacgtgcctgtcatcccagctactcaggaggctgaggcaggagaatcgcttgaacccgggaggcggaggttgcagtgagctgagattgcaccactgcactccagcctgggtgatagagcgagactccgtctcaaaaaaacaaaaacaaaaacaaaaactatagggacagaaatcaagtcagtggttgccagtggatggggtgaggcaagagggaatttggggga--atgaaattgtcctataactagattgtggtagtagttacatggttatatacatttatttattttgttttattattgttttcttattatttgtttgtttgttttgagatggagtcttgctctgtcacccaggctggagtgcaatggtgcaatcttggctcactgcaacctccacctctcgggttcaagtgattctgtgcaccaccacggccagctacgttttgtatttttagtagatagagacgggttttaccatgttggccaggctggtctcgaacccctgacctcaagtgatctggcagcctcggcctccccacgtgctgggattataggcgtgagtcaccatgcccagtcgtttatacacatttatcaaaactca----ctgcatcataaattgcaag-agtaaattttactgtatgtaaatatcttaatTTTTTAAAGGAAAAAAAAAGTCCAAAATAAGTAGCTATAATTACCTTTTCCTTTTAGAAAAAGGCATTCATATTTTCTGAGCATGAGAGAACTACAGG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTCATTGTAGACATTTGGGAAAATGTACAAAGGATGTACATTCATCACGTGCAGAAAAGTAATATTTCCTTGCTGTGAGCTTT--ATTGGCACAG-------------------------------------------------------------------------------------------AATACACacaaagctgggaccatgctatgcattttttaaatgaaattatacattttgctttctgaaatatattgtgcatat-ttttcatgtcattaa----ttttcaaaatcatgattttatgaatcaataatattctatgtttacttaagagacagagtctccctttgtggcccaggctggagtgcagtggcgcaaaggaatcattcctcactgcagcctcaaactcctgggctcaagcgatcctcagtggtgggatgagatctagacccctgatattcaatctcagaaagtcaataattccctgcctcagcctcctgagtagctggggctgcaggcctgtgccactgcaccaggttcaatgtatattttattttgtctttTTTTTCTTTTTTTAATGTATATTTTTTAGCA---TTCCTTTGTTGTTAGAAATTACATTGtttatata--------------------------------------------------attattatttgtcaattaaaaa----------taaaagaaaaaatCATACTGCTCCTATTTTTTACTTTGAGCAACTCTGATAACA-------------ACAACAAAAAAAAGTTCAGTGGGGCCAACGCGTTTCCCTCCTGGAGTTTCCCG--GTTCACCTGGTGGAGCGGGTCCTCCTTGGGCTGCAATTCCCTCCTTCTTTTCAGTGTCTGCAGGAAAGGTGGTTTCACAGGGTGATCGGTGATCTGGCTTATTTGTTCCTTTGTGGGGGTAAGGGCTGGGCACCTCACTATTTCCTGTATTACCAGCTTGAATTTACATCGCGCTGTTAATGTTTAATCCTCTCCACATCGA----------CGCGGGGTag-------taatttgttccaagtcacacaacttatcaatggtggactattcaggacttagatcccggatattcaacctcag----tAAACGTCTCCCCAGCTCCAGGGCGCTGCGTCATCTGGCTTTAAAAAAACGTTTCTggccgggcgcagtagctcacgcctgtcatcccagcactttgggaggccgaggcgggcggatcacgaggtcaagagttcgagaccagcctggccaacatggtgaaacctcgtctccactaaaaatacaaaaattagctgggcgtggtggcgggcgcctgtaatcccagctactcgggaggctgagacaggagaatcgcttgaacccagcaggcggggttgcagtgagccgagatcgcgccgttgcactccagcctgggcaacaagtaagactccgtctcaaaaaaaaaaaaaaaaaaaaaaaagaCGTTTCTCCCCA------TAAGGAGGCTGCAGTCACCTCGAAAAGCTTCTGCGCAGAGCCCGGCGCACGGGGAATTTCTATCGAGTGG----GCACTGTCCCGTCCTACGAATGTCCTTGGCGACATCGCCACTCGCCAGCTGGGATCACGTCGCCCCCG-TGGCCGGGG-ACACCCGCTGCCACTGACCGAGGGGGCCCCGGGAGCTGAGAGGTCGCCG-CTGCGCTGCCCGCGGAGGCTGTGGGCTGCGGTTGGCGACGCCG-CAGGGCTG-ACTTTCATCCGGGCGTCCT-GCTGGA-GGCCAGACCCTACCCCAACCTCGGGGTCCTCAGTGCGGGGCGCGCCTTGGG-GAGGGAAGAGGCCCCGCCCATCCTAAGGACGCGCTGAGGCCACGCGGGGCCGCCGGGATACTGCGTTGCCCGGGAGACACCT---GACGTGACAGGAACGCC-GCCAGTCTCAGTCCGCCGTGATCCCACAGTTCCCCGGT-CCCGGAAGTGCCCTGGCCTGCCGGAAGTGCcggagcggctgacagagcggctgacggagcCGGGCTCACCAGGTCGCTGCCGCGAGGGAGTTGCTGTGCTGGGGCCTGGGT
s mm3       0 3181 + 3181 ............................................................................................................................AAGCCCAGTTCATTTGTGAGACTATCACACGCTC---ATTTTCATAGACAAATTATTCTTCTCTATAAACTTCCCCCTTATATTTATCTTTAAAACATAACATCTGTTTTT----------CTCCAGCCAAAGTTATTTCCTG-TTTTGCTTATTATAAA-----CAGCTTGGCCTATTGTTGCTTATCCTAATGCATTAAAAAACTTTTAAAATTAca..........................................................................................................................................................................................................................................................................................................................................................................................ATTTGCAATTAAAGACAATATAATA-TATAATGGAGTTGGGAGCTTCAGAAGGAAGAATGGTTTCCAGTTGTAGCAGATA-----TAACCACTGAAAATGGATACACAAGAGGACAAC------CAGCAAGAACCAGACAGTGTGAATGCAGCCTGGACATAGTAGCCTTGGTTTCA-GACTCTCTGTAAGAGTGCAGGAAGCTCAGACACAGAGAAAAAAACC------------CAGAGGGCC--------ATGACAG---CAGTGAGCCTAGGTCA--CCACTCCTC-GCCTCCAGTCTTTCAAAGGCTATCCATTTCCCTAGGACAGCTCTC---AACACTAAGGAGCTGGCTCCACCCAGTTCTTTAGCCTCTACTCCAACC--TCTGCTCTTGACTTTCAAAACTCTTT--------TCAAGTCTTTTCTTCCCTATGGCTCT-GCACATATTGTTACTTGGGTTT--GTCATGCCTTCTCTTCCGAA---TTgcttcagcttaaaaa--tcactctcttggagaaagcttcccc...........................................................................................................................................................................................................................................................................................................................................gcattccgcaccc-------------------------acactctctcagtgtgcactgtcctgacctagcttgggacttatcacgattacatctttatt-gtatgaatgccatctccttacatgaagttagatgtga--tgacaggcgtttgatgtatctggttctttgctgaat--tcagcaccgagcataggtgcctgtcatcagcaggaacaggtgttgaatacatttattaattgagtgaaGGAGCAACAGAA-------GCCAGAGGGTCTAGGG--------TGCTTGGTT---TGTTTGAACCAGCTctccattctctca-tctgttaaattgggattatggtaa----ttaaactct---ggaactgctttgtggattaa--gagtcaaggc-tgtagtatgcttggtatg-tacatgacatatagcaagcattaggaaacattagct---attatCACCATTAAAAGGAAACTCT--gagtatctgaaactcttagacactgtcagtaggaatgtgaaaataacac-----cctt-------------------ccttataattgtaaacacagacagaccataccacttagcaatcttactcctaggcatacacttaagcgaatgaaaaactta------cagaaaactttagacaggaacgtttatagcagctttattcacaacgtctcagaatttaaaacaactcggatgttttccaaatcaccta-gtagatagacaaat---------------caacgga------gcaagaa---acaaa-ctgatggcacaaataataacacagatgaatcacagatccacgatgctaagtgagagaagacaagagtcaaaaggtgacatgctgtaggactccattcctggagaatttatatgacattctggaaa.........................................................................................................................................................................................................................................................................................................................................................GCCAGTGATTTGCAgacaatagagtg-ggtgtgaagga-----ggggatgatggaagtgtctcc--gccggactgtgct-gtgctgacacgatgaca....................................................................................................................................................................................................................................................................................................................acatgcatttatcaaagctcatgtacagcactggaaaccggaaacggctaatctcactgcatgcaaat-tctatctaatttaaaaTAGAAAAATAAGGCACGATAA--AACTGCACATTCCTGTTCCTTCAAGAAgACAGCACCTATGGTTTCTGATAATAAAAGTACCATATGGAGAAAAAAAAAAAAAAAagctgggcagtggtggcgcatgcctttagtcccagcacttgggaggcagaggcaggcagatttctgagttcgaggccagcctggtctacagagtgagttccaggacagccaaggctacacagagaaaccctgtcttgaaaaacaaacaaacaaacaaacaaacaCAAAAAAAAGTACCATATGTTGATTGTAGATGTGTGGGAAAATAAAGAAAAAATATA--------------------------TTTCCCTGTCATTTGCTTTTGGTTGAGACAG-------------------------------------------------------------------------------------------..............................................TAAATATTCTGCTTTCTGAAATACACTGTGCATATATCGCTATGTCATTAAATAATTGTCAAAATAATACTTTTATGAGTCAATA...........................................................................................................................................................................................................................................................----------------------------------TGTTGCTGTTGCTAAAACTTATACTACTCACACATTTTTGGGGGGCAAACTAAAACAACAATAAAATTCCATTCCTAAAACTATAATGTTTTTTAAAAACTAAAAA----------AAAAAAAGCAAATTATATTATTCCTGA-----------AGCAATTTTTATAAAACTATATGTACGGAAAAAAAAAAAAAAGTTCAGCAGGGCCAGATACTCCTCTGTCGAGGTTTTCACAATGTTGAACTGGTAAGGCAACCCTTCCCTTGGCTGCAATTCCATCATT-GTTCCAGTGCCTGCTGGAAAAGCGGTTCCACAGGGCTATC-------TGGCTCCTCT----TTTTGTAATGTACGCGGCTAAACACCCTAACATTTCCTGTACTACCTGCCTAAGTTTGCATAATACT-TCCATATTTAATG-TCACCCCATCTAACGTAGTGTAAGCAGGGCAGATGGGAATACTTTGTTCAAGATCATA-AGGTTATCAAGGGTGTA--AATAAGGATGTACAGCCCGGACATTCGGTCTCAAAAACCAAACACTTCCCA---------GCGTTGGGTCGCT----------------TTTCT................................................................................................................................................................................................................................................................................................................CCTTACTCCCCACCCTAGCGAGGAGGCTTCAGACAA----------TTCTGCCCAG--------------TAGATCCTTATCTAAGGAGCAGAAGCTCTCCCAAACCTCAAATGTCTTTGGCAACACTGCCACTTACCAGCTGGGGTCATTTCACTCCCGATGGCAGGGGGACACAGACTGCCCTAGACCAAGGGGATCCAGCGAGCGGGTTGCACGTTGGCTTCATGGCCAGCGGGGCTTATTGCCCATCCATTGGGACACTGCCGTGGCTA-CCGCTCTCTGGGGCGCCCG--------GGC--GACACTAC------------GGCGCTGGTGGGGGATGCGCCCTGGGCGAAGAAGAGAGGGCTTTCAATCTTAAGAACCCGCCGCGTGCGAACAGGGAACTTGAGGTTAAGGGTTGTCTGGAGATTTTCCAGGGACTTGACAGCCATGCCTGCGGAAGTCAGTCCTCCGCTATCCCAGAGTCCCCCGGTTCCCGGAAGTGCCCAGTTCT-CCGGAAGTGCCAGGCTAGCCGAGTAAGTAGC-----------GGCTCCCTCGAGCCCCGTACCTGGAGGCTTGCTCTTCTGGGGTCCTGGT
s rn3       0 3320 + 3320 ............................................................................................................................AAGCCCAGTTCATTTGTGAGACTATCACATGCTC---ATTTTCATATACAAATTATTCTTATCTGTAAATATCCACATTATATTTATCTTAAAAACATACCATCTGTTTTT----------CTCCAGCCAAAGGTATTTCCTG-TTTTGCTTATTATGAA-----CAGCTTGGCCTATTGTTACTTATCCTAATGCATT--------TCTAAAATTACATTTATTTATTTACTTATATTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTGCTCCCTGAACTGCATATCAAGACCCTATTCAGTGGACTCGCAGGCAGTTAGGGAACTGTGTGCAGCCTGTCTCTGAAGAAATATAAGAGTGAGGTGGAGGCAAATTATGATATTTGGTTCTCTCCTTTTACCATGTGGGTTCAGGGACCATACTCAGGTCACTAGGCTTGGTGGCAAGTGTCTTTCCCACTGAGCCATTGGCCACAACAGTTTTTAAATCTAGGGTCTACCTGTGTTCTTTTAAAACAGCTTACTTTTT---ATTTTACAAACCCCCTACATT-GAACTTGCATT--TGATA--TT----ATTGTTAAAGACAATCTAATG-------------GAGAACTTCAGAGGGAAGAGTGGTTTCGAGTTGTAGCAGATAG----TGACCGCTAAAAATGGATACGCAAAAGGACAAC------CAGCAAGAACTAGAC--TGTGAATGTGGGTTGGGCATGGTGGCCTTCATTCCA-GGCTCTCTGTAACAGTGCAGGAAGCTCAGAAACAGAGAAAGAAAAA------------CAGAGGACCCTGAGCTGATGACAG---CAGTGAACCTGGGTCA--CCACTCCTC-ACCT--AGTCCTTCAGAAGCTATCCATTTCCCTATGACAACTC-----AACACTAAGCATCCGGCTCCACCCAATTCTTTAGCCTCTGCTTGTACC--TCTACTCTTGACTTTCAAAACTCCAT-GTCCTAGCTGTGTCTTTTCTTCCTCATGTCTCT-GCTCACATTGCTACTTTGGTTT--GTCATGCCTTCTCTTCCAAA---TTGCTTCAGCTTAAAAAAATCATTTCCTTTGAGAAAGCTTCCCC........................................................................................................................................................................................................................................................................................................................AAAG---------------GCATTCCACGCCC-------------------------GCACTCTCTCAGTGTGCACTGTCCTTACCTGGCTTGGGACCTATCACAATCACATCTCTATT-GTGTGACTACTATCTCCTTATGTGAAGCTAGCTTTGAGATGGCAGGCATATGATGTATCCAGCTCTTTGCTGAAT--CCAGCAGCCAGCATAGGTGCCTGTCATCAN---------GNGTTCAGTATATTAATTANNTGGGTGAATGAGCGACANNN-------GCCATANGATCTNGNGC-------TGTTTTGTT---TGTCTGAACCAGCTCTCCACTCNCNNNNTNTNNTAAGTTGNGANNATGGTNA----NNNNAANCTNNNGNNNCTACTTTGTGGATTAA--GAGTCAAGGC-TGTAGTATGCCTGGTATG-TGCATGACATATAGTAAGCATTAGGAAACATCCGCT---ATTATGGCCATTAAAAGGAAACTCTCTGAGTATCTGAAACTCTTAGACATTGTCAGTAGGAATGTGAAAATAATAC-----CCT--------------------CCTTATAATTGTAAACACAGACAGACCTTACCACTTAGCAGTCTTACTTCTAGGCATACACTTCAGCAAACAAAAAACTTA------CACAAAACTGTAGACAGGAATGTTTATAGCAGCTTTATTCACAACTTCTCAGAATTTAAAACAATG-------TTTCCAAATCACCTAAGTAGATAAACAAAT---------------CAAAGGA------GCAAGAA---ACAAAACTGATGACACAAATAATAATGTGGATGGATCACAGATCCATTACGCTAAGTGAGAGAAGACA-GAGTCGAAAGGTGACATGCTATAGGTCTCCATTCATGTAGAACTTATATGACATTCCGGAAA.........................................................................................................................................................................................................................................................................................................................................................ACCAGAGATTTCCAGACAATAGAGTG-GGTGTGAAGAAAAGTAGGGGATGATGGAAATATCTCA--ATTGGACTGTGGT-GTGCTGAGATGACAACATGCATTTAAT.................................................................................................................................................................................................................................................................................................................................................................................................................................................GACGGCACCTATAGTTTCTGATAATAAAACTACCGTATG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCATTATAGACATGTGGGAAAATAAAGAAAAAATAT----------------------------TTCCTTGTCATTTGCTTTTGGTTGAGAAAGTAAATTCCATATCCACCTACCCTCCATCTTCCAAGGGTTGGGATTAAATATAGACTTATACCATCACACCCAGCCAAATTTGCTCTCAAAAAATAAATA--------------------------------------------TTCTGCTTTCTGAAATACACTGTGTATACATTCCCATGTTATTAAATAATTTTCAAAACAATG---TTATGAGTCAATG...........................................................................................................................................................................................................................................................CTCTGCACTTCTGCAATTATATTTTTTAAGCAGTTTCTTTGGTTGCTAAAAATTATACTACTTACACATTTTTTTGG------------------CAAA---------CCAAAACAAAATTCCATTCCTAATACTGCAATTTTTTTTAATGAAAAGAGCAAATTATATTATTCCTGC-----------AGAAATTTCGATAAAACTATATGTCAG--AAAAAAAAAAAAAGTTCAGCAGGGCCAGATACTCCTTGGTCGAGGGTTTCACAATGTCAAACTGGTAAGGCAACCCTTCCCTTGGCTGCAATTCCCTCATT-GTTCCAGTACCTGCTGGAAAAGCCGTTCCACAGGGCGATC-------TGGCTCCTCT----TTTTGTGATGTAGGAGGCTAAACACCCTAACATTTCCTGTACTACCTGCCTAAGTTTGCATAATACT-TCCATATTTAATGCTCACCCCATCTAACGTAGTGTACGCAGGGCAGATGGGAGTACTTTGTTCAAGGTCGTA-AGGTTATCAAGGGTGTA--AACAAGGATGTACAGCTTGGACGTCCAGTCTCAAAAATCAAACACTTTCCT---------GCGTTGAGTCATTTTCCC................................................................................................................................................................................................................................................................................................................................CCCTACTCCCCACCCTAGTGAGGAGGCTTCAGACAA----------TTTTGCGCAG--------------GGGATCCTTATCTAAG------ACACTCCCCCAAACTTCATATGCCCTTGGCAACACCGCCACTTACCAGC--GAGTCATTTCACCCGCTATGGTAGGGGGTCACAGACTGTTCCAGACCAAGGGGATCCAGCGAGTGGGTTGTATGTTGGCTTCGTTGCCAGAGGGGCTTACTGCCCATCCATTGAGACACTGACGGGGCCAACCGCTCTCTGGGGCGCCCCCGCTCTCCAGC--GACACTAC------------GGCGCCGGTGGGAGACGCGCCCTGGGCGAGGTGGGGAGGGTTCCCAATCTTAAGAACCCGCCGCGTGCGGCCAGGGAACCTGTGGTTAAGGGTTATCTGGAGATTTTCCAGGGATTTGACTGCCATG---GCTGAAGTCAGTCCTCCGCTATCCCAGAGTCCCCCGGTTCCCGGAAGTGCCCGACTCT-CCGGAAGTGCCGGGCTAGACGAGCGAGTAGC-----------GGCTTTCTCGAGCCCTGTACCTGGAGGATTGCAATTCTGGGGTCCTGGT
BioPerl-1.007002/t/data/humts1.pal000444000766000024       375613155576321 16622 0ustar00cjfieldsstaff000000000000Palindromes of:  HUMTS1 
Sequence length is: 18596 
Start at position: 1
End at position: 18596
Minimum length of Palindromes is: 10 
Maximum length of Palindromes is: 100 
Maximum gap between elements is: 100 
Number of mismatches allowed in Palindrome: 0



Palindromes:
126   caaaaaaaaaaaaaaaa   142
      |||||||||||||||||
217   gtttttttttttttttt   201

127   aaaaaaaaaaaaaaaa   142
      ||||||||||||||||
215   tttttttttttttttt   200

127   aaaaaaaaaaaaaaaa   142
      ||||||||||||||||
214   tttttttttttttttt   199

127   aaaaaaaaaaaaaaaa   142
      ||||||||||||||||
213   tttttttttttttttt   198

127   aaaaaaaaaaaaaaaa   142
      ||||||||||||||||
212   tttttttttttttttt   197

127   aaaaaaaaaaaaaaaa   142
      ||||||||||||||||
211   tttttttttttttttt   196

127   aaaaaaaaaaaaaaaa   142
      ||||||||||||||||
210   tttttttttttttttt   195

127   aaaaaaaaaaaaaaaa   142
      ||||||||||||||||
209   tttttttttttttttt   194

127   aaaaaaaaaaaaaaaa   142
      ||||||||||||||||
208   tttttttttttttttt   193

127   aaaaaaaaaaaaaaaa   142
      ||||||||||||||||
207   tttttttttttttttt   192

127   aaaaaaaaaaaaaaaa   142
      ||||||||||||||||
206   tttttttttttttttt   191

127   aaaaaaaaaaaaaaaa   142
      ||||||||||||||||
205   tttttttttttttttt   190

127   aaaaaaaaaaaaaaaagaccgccagggct   155
      |||||||||||||||||||||||||||||
204   ttttttttttttttttctggcggtcccga   176

2278  catttttaac  2287
      ||||||||||
2351  gtaaaaattg  2342

3960  agcccagacc  3969
      ||||||||||
4056  tcgggtctgg  4047

4367  gattgagaaa  4376
      ||||||||||
4449  ctaactcttt  4440

4368  attgagaaat  4377
      ||||||||||
4399  taactcttta  4390

4387  gaaatttctc  4396
      ||||||||||
4411  ctttaaagag  4402

4408  tttctttgatt  4418
      |||||||||||
4456  aaagaaactaa  4446

4428  tttctttgatt  4438
      |||||||||||
4456  aaagaaactaa  4446

6809  cataggcatg  6818
      ||||||||||
6839  gtatccgtac  6830

11270 atgtttccaa 11279
      ||||||||||
11339 tacaaaggtt 11330

14171 ttacctgaat 14180
      ||||||||||
14208 aatggactta 14199




BioPerl-1.007002/t/data/hybrid2.gff3000444000766000024       101513155576321 16777 0ustar00cjfieldsstaff000000000000##gff-version 3
chr17	UCSC	mRNA	62467934	62469545	.	-	.	ID=A00469;Dbxref=AFFX-U133:205840_x_at,Locuslink:2688,Genbank-mRNA:A00469,Swissprot:P01241,PFAM:PF00103,AFFX-U95:1332_f_at,Swissprot:SOMA_HUMAN;Note=growth%20hormone%201;Alias=GH1
chr17	UCSC	CDS	62468039	62468236	.	-	1	Parent=A00469
chr17	UCSC	CDS	62468490	62468654	.	-	2	Parent=A00469
chr17	UCSC	CDS	62468747	62468866	.	-	1	Parent=A00469
chr17	UCSC	CDS	62469076	62469236	.	-	1	Parent=A00469
chr17	UCSC	CDS	62469497	62469506	.	-	0	Parent=A00469
>A00469
GATTACA
GATTACA
BioPerl-1.007002/t/data/ids-with-spaces.phy000444000766000024       606213155576321 20422 0ustar00cjfieldsstaff00000000000018  162
A BAD ID  MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A57307    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A61002    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A65082    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A1895     MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARLLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A53685    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A9694     MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A13531    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A21170    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A17451    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A30004    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A34040    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A38189    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A72804    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A42101    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLXXXQVQP
A45935    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A76877    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
A49905    MTRPRTDAIHHHVVVNAPIERAFAVFTTRFGDFKPREHNLLAIPITETVFECHAGGHIYDRGVDGSVCKWARVLVYEPPSRVLFTWDIGPTWRPETDLAKTSEVEVRFTAQSAETTRVDLEHRHLDRHGPGWESVADGVDSEAGWPLYLRRYTDLLCIQVQP
BioPerl-1.007002/t/data/in.fasta000444000766000024       401013155576321 16311 0ustar00cjfieldsstaff000000000000FASTA searches a protein or DNA sequence data bank
 version 35.03 Feb. 18, 2008
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query: fake.fa
  1>>>TM1000020|total:2746_L:1626_-3:439_0:279_+3:402 32 nt - 32 nt
Library: /home/va473/databases/contaminants/contaminants.fasta 1055411 residues in  2012 sequences

1055411 residues in  2016 sequences
Statistics:  Expectation_n fit: rho(ln(x))= 0.9735+/-0.00348; mu= 31.8193+/- 0.161
 mean_var=45.4281+/-12.600, 0's: 0 Z-trim: 6  B-trim: 532 in 2/40
 Lambda= 0.190288
Algorithm: FASTA (3.5 Sept 2006) [optimized]
Parameters: +5/-4 matrix (5:-4) ktup: 2
 join: 65, opt: 50, open/ext: -100/-4, width:  16
 Scan time:  0.230

The best scores are:                                      opt bits E(2016)
DQ345959.1 | Symbols:  | chloroplast | Gossypi (160301) [r]  142 50.2 2.7e-08

>>DQ345959.1 | Symbols:  | chloroplast | Gossypium hirsu  (160301 nt)
rev-comp initn: 141 init1: 141 opt: 142  Z-score: 196.2  bits: 50.2 E(): 2.7e-08
banded Smith-Waterman score: 142; 93.8% identity (93.8% similar) in 32 nt overlap (32-1:31483-31514)

                                      30        20        10       
TM100-                               GCCGGTGCTCTGACCAATTGAACTAGAATC
                                     : ::::::::::::::::::::::: ::::
DQ3459 GGCTCGAACCCGCAGCTTCCGCCTTGACAGGGCGGTGCTCTGACCAATTGAACTACAATC
          31460     31470     31480     31490     31500     31510  

                                                                   
TM100- CC                                                          
       ::                                                          
DQ3459 CCAGGGAAATAAAGAAAAGTGTACAACAGAGATAGTCTTATGATTTCATTCATTTTCTAT
          31520     31530     31540     31550     31560     31570  



32 residues in 1 query   sequences
1055411 residues in 2012 library sequences
 Tcomplib [35.03] (4 proc)
 start: Sun Jul  6 00:14:21 2008 done: Sun Jul  6 00:14:21 2008
 Total Scan time:  0.230 Total Display time:  0.010

Function used was FASTA [version 35.03 Feb. 18, 2008]

BioPerl-1.007002/t/data/insulin.water000444000766000024       271113155576321 17416 0ustar00cjfieldsstaff000000000000########################################
# Program:  water
# Rundate:  Tue Feb 12 21:26:34 2002
# Report_file: hs_insulin.water
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: hs_insulin
# 2: 
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 194
# Identity:     160/194 (82.5%)
# Similarity:   160/194 (82.5%)
# Gaps:          21/194 (10.8%)
# Score: 690.0
# 
#
#=======================================

hs_insulin         1 gtctgttccaagggcctttgcgtcaggtgggctcaggg------------     38
                     ||||||||||||||||||.|||||||||||||||||||            
                   1 gtctgttccaagggccttcgcgtcaggtgggctcagggctgcccacttgg     50

hs_insulin        39 -----ccagggtggctggaccccaggccccagctctgcagcagggaggac     83
                          ||||||||||||||||||||||||||||||||||.||||||||||
                  51 gggttccagggtggctggaccccaggccccagctctgcaacagggaggac    100

hs_insulin        84 gtggctgggctcgtgaagcatgtgggggtgagcccaggggccccaaggca    133
                     .|||||||||||.||||||.|.||.||||||.|||||||| ||||.||||
                 101 atggctgggctcttgaagcgtttgagggtgaacccagggg-cccagggca    149

hs_insulin       134 gggcacctggccttcagcctgcctcagccctgcctgtctcccag    177
                      ||||||||||| |||||..||||||| .|||||||||||.|||
                 150 -ggcacctggcc-tcagctggcctcag-gctgcctgtctctcag    190


#---------------------------------------
#---------------------------------------
BioPerl-1.007002/t/data/interpro.xml000444000766000024     45602613155576321 17331 0ustar00cjfieldsstaff000000000000



  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  


  Kringle
  

Kringles are autonomous structural domains, found throughout the blood clotting and fibrinolytic proteins. Kringle domains are believed to play a role in binding mediators (e.g., membranes, other proteins or phospholipids), and in the regulation of proteolytic activity [, , ]. 
Kringle domains [, , ] are characterised by a triple loop, 3-disulphide bridge structure, whose  conformation is defined by a number of hydrogen bonds and small pieces of  anti-parallel beta-sheet. They are found in a varying number  of  copies  in some plasma proteins including prothrombin and urokinase-type plasminogen activator, which are serine proteases belonging to MEROPS peptidase family S1A.


Steroid or nuclear hormone receptors (4A nuclear receptor, NRs) constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands []. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner [, ]. In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity.


NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed 'orphan' receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members.


  
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Patthy L.
      Evolution of the proteases of blood coagulation and fibrinolysis by assembly from modules.
      
      Cell
      
      1985
    
    
      Patthy L, Trexler M, Vali Z, Banyai L, Varadi A.
      Kringles: modules specialized for protein binding. Homology of the gelatin-binding region of fibronectin with the kringle structures of proteases.
      
      FEBS Lett.
      
      1984
    
    
      McMullen BA, Fujikawa K.
      Amino acid sequence of the heavy chain of human alpha-factor XIIa (activated Hageman factor).
      
      J. Biol. Chem.
      
      1985
    
    
      Ikeo K, Takahashi K, Gojobori T.
      Evolutionary origin of numerous kringles in human and simian apolipoprotein(a).
      
      FEBS Lett.
      
      1991
    
    
      De Vos P, Schmitt J, Verhoeven G, Stunnenberg HG.
      Human androgen receptor expressed in HeLa cells activates transcription in vitro.
      
      Nucleic Acids Res.
      
      1994
    
    
      Schwabe JW, Teichmann SA.
      Nuclear receptors: the evolution of diversity.
      
      Sci. STKE
      
      2004
    
    
      Atkinson RA, Williams RJ.
      Solution structure of the kringle 4 domain from human plasminogen by 1H nuclear magnetic resonance spectroscopy and distance geometry.
      
      J. Mol. Biol.
      
      1990
    
    
      Castellino FJ, Beals JM.
      The genetic relationships between the kringle domains of human plasminogen, prothrombin, tissue plasminogen activator, urokinase, and coagulation factor XII.
      
      J. Mol. Evol.
      
      1987
    
    
      Nishikawa J, Kitaura M, Imagawa M, Nishihara T.
      Vitamin D receptor contains multiple dimerization interfaces that are functionally different.
      
      Nucleic Acids Res.
      
      1995
    
  
  
    
  
  
    
  
  
    
  
  
    
    
    
    
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  


  Retinoid X receptor
  

Steroid or nuclear hormone receptors (4A nuclear receptor, NRs) constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands []. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner [, ]. In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity.


NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed 'orphan' receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members.


The retinoic acid (retinoid X) receptor consists of 3 functional and 
               structural domains: an N-terminal (modulatory) domain; a DNA binding domain
               that mediates specific binding to target DNA sequences (ligand-responsive
               elements); and a hormone binding domain. The N-terminal domain differs 
               between retinoic acid isoforms; the small highly-conserved DNA-binding
               domain (~65 residues) occupies the central portion of the protein; and 
               the ligand binding domain lies at the receptor C terminus.


Synonym(s): 2B nuclear receptor


  
    
      Molecular Function
      DNA binding
    
    
      Molecular Function
      ligand-dependent nuclear receptor activity
    
    
      Molecular Function
      steroid binding
    
    
      Cellular Component
      nucleus
    
    
      Biological Process
      regulation of transcription, DNA-dependent
    
    
      Molecular Function
      zinc ion binding
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Nishikawa J, Kitaura M, Imagawa M, Nishihara T.
      Vitamin D receptor contains multiple dimerization interfaces that are functionally different.
      
      Nucleic Acids Res.
      
      1995
    
    
      De Vos P, Schmitt J, Verhoeven G, Stunnenberg HG.
      Human androgen receptor expressed in HeLa cells activates transcription in vitro.
      
      Nucleic Acids Res.
      
      1994
    
    
      Schwabe JW, Teichmann SA.
      Nuclear receptors: the evolution of diversity.
      
      Sci. STKE
      
      2004
    
  
  
    
  
  
    
    
  
  
    
  
  
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
  


  Helix-turn-helix, AraC type
  

Many bacterial transcription regulation proteins bind DNA through a
'helix-turn-helix' (HTH) motif. One major subfamily of these proteins [, ] is related to the arabinose 
operon regulatory protein AraC [], . Except for celD [], all of these proteins seem to be positive transcriptional factors.


Although the sequences belonging to this family differ somewhat in length, in nearly every case the HTH motif is situated towards the C terminus in the third quarter of most of the sequences. The minimal DNA binding domain spans roughly 100 residues and comprises two HTH subdomains; the classical HTH domain and another HTH subdomain with similarity to the classical HTH domain but with an insertion of one residue in the turn-region. The  N-terminal and  central regions of these proteins are presumed to interact with effector molecules and may be involved in dimerisation [].


The known structure of MarA () shows that the AraC domain is alpha helical and shows the two HTH subdomains both bind the major groove of the DNA. The two HTH subdomains are separated by only 27
angstroms, which causes the cognate DNA to bend.


  
    
      Molecular Function
      transcription factor activity
    
    
      Cellular Component
      intracellular
    
    
      Biological Process
      regulation of transcription, DNA-dependent
    
    
      Molecular Function
      sequence-specific DNA binding
    
  
  
    
      
    
  
  
    
      Parker LL, Hall BG.
      Characterization and nucleotide sequence of the cryptic cel operon of Escherichia coli K12.
      
      Genetics
      
      1990
    
    
      Henikoff S, Wallace JC, Brown JP.
      Finding protein similarities with nucleotide sequence databases.
      
      Meth. Enzymol.
      
      1990
    
    
      Gallegos MT, Michan C, Ramos JL.
      The XylS/AraC family of regulators.
      
      Nucleic Acids Res.
      
      1993
    
    
      Bustos SA, Schleif RF.
      Functional domains of the AraC protein.
      
      Proc. Natl. Acad. Sci. U.S.A.
      
      1993
    
  
  
    
  
  
    
    
  
  
    
    
    
    
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
  


  Metallothionein, vertebrate
  

Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, nickel, etc. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, ]. An empirical classification into three classes has been proposed by Fowler and coworkers [] and Kojima []. Members of class I are defined to include polypeptides related in the positions of their cysteines to equine MT-1B, and include mammalian MTs as well as from crustaceans and molluscs. Class II groups MTs from a variety of species, including sea urchins,
fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units [].


This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Consequently, all class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. This system subdivides the MT superfamily into families, subfamilies, subgroups, and isolated isoforms and alleles. 


The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects []: e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. The inclusion of a MT within a family presupposes that its amino acid sequence is alignable with that of all members. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range: e.g., Family 1: vertebrate MTs [see http://www.bioc.unizh.ch/mtpage/protali.html]. 


 The members of family 1 are recognised by the sequence pattern K-x(1,2)-C-C-x-C-C-P-x(2)-C located at the beginning of the third exon. 
The taxonomic range of the members extends to vertebrates. 
Known characteristics: 60 to 68 AAs; 20 Cys (21 in one case), 19 of them are totally conserved; the protein sequence is divided into two structural domains, containing 9 and 11 Cys all binding 3 and 4 bivalent metal ions, respectively. The gene is composed of 3 exons, 2 introns and the splicing sites are conserved. Family 1 includes subfamilies: m1, m2, m3, m4, m, a, a1, a2, b, ba, t, all of them hit the same InterPro entry. 



  
    
      Molecular Function
      metal ion binding
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Kagi JH, Kojima Y.
      Chemistry and biochemistry of metallothionein.
      
      Experientia Suppl.
      
      1987
    
    
      Kagi JH.
      Overview of metallothionein.
      
      Meth. Enzymol.
      
      1991
    
    
      Kojima Y.
      Definitions and nomenclature of metallothioneins.
      
      Meth. Enzymol.
      
      1991
    
    
      Fowler BA, Hildebrand CE, Kojima Y, Webb M.
      Nomenclature of metallothionein.
      
      Experientia Suppl.
      
      1987
    
  
  
    
  
  
    
    
  
  
    
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
  


  Tubby, C-terminal
  

 Tubby, an autosomal recessive mutation, mapping to mouse  chromosome 7, was recently found to be the result of a splicing defect in a novel gene with unknown function. This  mutation  maps to the tub gene [, ]. The mouse  tubby mutation is  the  cause  of  maturity-onset  obesity, insulin resistance and  sensory  deficits. By contrast with the rapid juvenile-onset weight gain seen in diabetes (db) and obese (ob) mice, obesity in tubby mice develops gradually, and strongly resembles the late-onset obesity observed in the human population. Excessive deposition of adipose tissue  culminates in a two-fold increase of body weight. Tubby mice also suffer retinal degeneration and neurosensory hearing loss. The tripartite character of the tubby phenotype is highly similar to human obesity syndromes, such as Alstrom and Bardet-Biedl. Although these phenotypes indicate a vital role for tubby proteins, no biochemical function has yet been ascribed to any family member [], although it has been suggested that the phenotypic features of tubby mice may be the result of cellular apoptosis triggered by expression of the mutated tub gene. TUB is the founding-member of the tubby-like proteins, the TULPs. TULPs are found in multicellular organisms from both the plant and animal kingdoms. Ablation of members of this protein family cause disease phenotypes that are indicative of their importance in nervous-system function and development [].


Mammalian TUB is a hydrophilic protein of ~500 residues. The N-terminal () portion of the protein is conserved neither in length nor sequence, but, in TUB, contains the nuclear localisation signal and may have transcriptional-activation activity. The C-terminal 250 residues are highly conserved. The C-terminal extremity contains a cysteine residue that might play an important role in the normal functioning of these proteins. The crystal structure of the C-terminal core domain from mouse tubby has been determined to 1.9A resolution. This domain is arranged as a 12-stranded, all anti-parallel, closed beta-barrel that surrounds a central alpha helix, (which is at the extreme carboxyl terminus of the protein) that forms most of the hydrophobic core. Structural analyses suggest that TULPs constitute a unique family of bipartite transcription factors [].


  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Kleyn PW, Fan W, Kovats SG, Lee JJ, Pulido JC, Wu Y, Berkemeier LR, Misumi DJ, Holmgren L, Charlat O, Woolf EA, Tayber O, Brody T, Shu P, Hawkins F, Kennedy B, Baldini L, Ebeling C, Alperin GD, Deeds J, Lakey ND, Culpepper J, Chen H, Glucksmann-Kuis MA, Carlson GA, Duyk GM, Moore KJ.
      Identification and characterization of the mouse obesity gene tubby: a member of a novel gene family.
      
      Cell
      
      1996
    
    
      Noben-Trauth K, Naggert JK, North MA, Nishina PM.
      A candidate gene for the mouse mutation tubby.
      
      Nature
      
      1996
    
    
      Boggon TJ, Shan WS, Santagata S, Myers SC, Shapiro L.
      Implication of tubby proteins as transcription factors by structure-based functional analysis.
      
      Science
      
      1999
    
    
      Carroll K, Gomez C, Shapiro L.
      Tubby proteins: the plot thickens.
      
      Nat. Rev. Mol. Cell Biol.
      
      2004
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
    
  
  
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  


  C2 calcium-dependent membrane targeting
  
The C2 domain is a Ca2+-dependent membrane-targeting module found in many cellular proteins involved in signal transduction or membrane trafficking. C2 domains are unique among membrane targeting domains in that they show wide range of lipid selectivity for the major components of cell membranes, including phosphatidylserine and phosphatidylcholine. This C2 domain is about  116  amino-acid  residues and is located between the two copies of
the C1 domain in Protein Kinase C (that bind phorbol esters and diacylglycerol) (see )
and the  protein  kinase  catalytic  domain  (see ).  Regions with
significant homology [] to  the C2-domain have been found in many proteins.
The C2  domain  is  thought  to  be involved in calcium-dependent phospholipid
binding [] and in membrane targetting processes such as subcellular localisation. 
The 3D  structure  of  the
C2 domain of synaptotagmin has been reported
[], the domain forms an eight-stranded beta sandwich constructed around a 
conserved 4-stranded motif, designated a C2 key []. Calcium binds in
a cup-shaped depression formed by the N- and C-terminal loops of the
C2-key motif. Structural analyses of several C2 domains have shown them to consist of similar ternary structures in which three Ca2+-binding loops are located at the end of an 8 stranded antiparallel beta sandwich. 


  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Sutton RB, Davletov BA, Berghuis AM, Sudhof TC, Sprang SR.
      Structure of the first C2 domain of synaptotagmin I: a novel Ca2+/phospholipid-binding fold.
      
      Cell
      
      1995
    
    
      Davletov BA, Sudhof TC.
      A single C2 domain from synaptotagmin I is sufficient for high affinity Ca2+/phospholipid binding.
      
      J. Biol. Chem.
      
      1993
    
    
      Brose N, Hofmann K, Hata Y, Sudhof TC.
      Mammalian homologues of Caenorhabditis elegans unc-13 gene define novel family of C2-domain proteins.
      
      J. Biol. Chem.
      
      1995
    
  
  
    
  
  
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  


  Protein phosphatase 2A, regulatory subunit PR55
  
Protein phosphatase 2A (PP2A) is a serine/threonine phosphatase implicated 
in many cellular processes, including the regulation of metabolic enzymes 
and proteins involved in signal transduction [, ]. PP2A is a trimer
composed of a 36 kDa catalytic subunit, a 65 kDa regulatory subunit 
(subunit A) and a variable third subunit (subunit B) [, ]. 

One form of the third subunit is a 55 kDa protein (PR55), which exists in
Drosophila melanogaster and yeast, and has up to three forms in mammals [, ]. PR55 may act
as a substrate recognition unit, or may help to target the enzyme to the
correct subcellular location [].


  
    
      Cellular Component
      protein phosphatase type 2A complex
    
    
      Biological Process
      signal transduction
    
    
      Molecular Function
      protein phosphatase type 2A regulator activity
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Mayer RE, Hendrix P, Cron P, Matthies R, Stone SR, Goris J, Merlevede W, Hofsteenge J, Hemmings BA.
      Structure of the 55-kDa regulatory subunit of protein phosphatase 2A: evidence for a neuronal-specific isoform.
      
      Biochemistry
      
      1991
    
    
      Pallas DC, Weller W, Jaspers S, Miller TB, Lane WS, Roberts TM.
      The third subunit of protein phosphatase 2A (PP2A), a 55-kilodalton protein which is apparently substituted for by T antigens in complexes with the 36- and 63-kilodalton PP2A subunits, bears little resemblance to T antigens.
      
      J. Virol.
      
      1992
    
  
  
    
    
    
    
    
  
  
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  


  Proteinase inhibitor I25, cystatin
  

Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site.  Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. 


The cystatins are cysteine proteinase inhibitors belonging to MEROPS inhibitor family I25, clan IH [, , ]. They mainly inhibit peptidases belonging to peptidase families C1 (papain family) and  C13 (legumain family).  The cystatin family includes:


    

  • 
The Type 1 cystatins, which are intracellular cystatins that are present in the cytosol of many cell types, but can also appear in body fluids at significant concentrations. They are single-chain polypeptides of about 100 residues, which have neither disulphide bonds nor carbohydrate side chains. 
    • 

  • The Type 2 cystatins, which are mainly extracellular secreted polypeptides synthesised with a 19-28 residue signal peptide. They are broadly distributed  and found in most body fluids. 
    • 

  • The Type 3 cystatins, which are multidomain proteins. The mammalian representatives of this group are the kininogens. There are three different kininogens in mammals: H- (high molecular mass, ) and L- (low molecular mass) kininogen which are found in a number of species, and T-kininogen that is found only in rat. 
    • 

  • Unclassified cystatins. These are cystatin-like proteins found in a range of organisms: plant phytocystatins, fetuin in mammals, insect cystatins and a puff adder venom cystatin which inhibits metalloproteases  of the MEROPS peptidase family M12 (astacin/adamalysin). Also a number of the cystatins-like proteins have been shown to be devoid of inhibitory activity. 
    • 
    


All true cystatins inhibit cysteine peptidases of the papain family (MEROPS peptidase family C1), and some also inhibit legumain family enzymes (MEROPS peptidase family C13). These peptidases play key roles in physiological processes, such as intracellular protein degradation (cathepsins B, H and L), are pivotal in the remodelling of bone (cathepsin K), and may be important in the control of antigen presentation (cathepsin S, mammalian legumain). Moreover, the activities of such peptidases are increased in pathophysiological conditions, such as cancer metastasis and inflammation. Additionally, such peptidases are essential for several pathogenic parasites and bacteria. Thus in animals cystatins not only have capacity to regulate normal body processes and perhaps cause disease when down-regulated, but in other organisms may also participate in defence against biotic and abiotic stress. 


  
    
      Molecular Function
      cysteine-type endopeptidase inhibitor activity
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Turk V, Bode W.
      The cystatins: protein inhibitors of cysteine proteinases.
      
      FEBS Lett.
      
      1991
    
    
      Rawlings ND, Barrett AJ.
      Evolution of proteins of the cystatin superfamily.
      
      J. Mol. Evol.
      
      1990
    
    
      Abrahamson M, Alvarez-Fernandez M, Nathanson CM.
      Cystatins.
      
      Biochem. Soc. Symp.
      
      2003
    
  
  
    
  
  
    
    
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  


  Ubiquitin-activating enzyme, E1-like
  

The post-translational attachment of ubiquitin () to proteins (ubiquitinylation) alters the function, location or trafficking of a protein, or targets it to the 26S proteasome for degradation [, , ]. Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2, ), and a ubiquitin ligase (E3, , ), which work sequentially in a cascade []. The E1 enzyme is responsible for activating ubiquitin, the first step in ubiquitinylation. The E1 enzyme hydrolyses ATP and adenylates the C-terminal glycine residue of ubiquitin, and then links this residue to the active site cysteine of E1, yielding a ubiquitin-thioester and free AMP. To be fully active, E1 must non-covalently bind to and adenylate a second ubiquitin molecule. The E1 enzyme can then transfer the thioester-linked ubiquitin molecule to a cysteine residue on the ubiquitin-conjugating enzyme, E2, in an ATP-dependent reaction.


  
    
      Biological Process
      protein modification process
    
    
      Molecular Function
      small protein activating enzyme activity
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Burger AM, Seth AK.
      The ubiquitin-mediated protein degradation pathway in cancer: therapeutic implications.
      
      Eur. J. Cancer
      
      2004
    
    
      Passmore LA, Barford D.
      Getting into position: the catalytic mechanisms of protein ubiquitylation.
      
      Biochem. J.
      
      2004
    
    
      Pickart CM, Fushman D.
      Polyubiquitin chains: polymeric protein signals.
      
      
      2004
    
    
      Sun L, Chen ZJ.
      The novel functions of ubiquitination in signaling.
      
      Curr. Opin. Cell Biol.
      
      2004
    
  
  
    
    
    
    
  
  
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  


  Retroviral VpR/VpX protein
  
Human immunodeficiency virus (HIV) is the human retrovirus associated with AIDS (acquired immune deficiency syndrome), and SIV its simian counterpart. Three main groups of primate lentivirus are known, designated Human immunodeficiency virus 1 (HIV-1), Human immunodeficiency virus 2 (HIV-2)/Simian immunodeficiency virus - mac (SIVMAC)/Simian immunodeficiency virus - sm (SIVSM) and Simian immunodeficiency virus - agm (SIVAGM). Simian immunodeficiency virus - mnd (SIVMND) has been suggested to represent a fourth distinct group []. These groups are believed to have diverged from a common ancestor long before the spread of AIDS in humans. Genetic variation in HIV-1 and HIV-2 has been studied extensively, and the nucleotide sequences reported for several strains [].
 ORF analysis has revealed two open reading frames, yielding the so-called R- and X-ORF proteins, whose functions are unknown, but which show a high degree of              sequence similarity.


  
    
      
    
  
  
    
      Hasegawa A, Tsujimoto H, Maki N, Ishikawa K, Miura T, Fukasawa M, Miki K, Hayami M.
      Genomic divergence of HIV-2 from Ghana.
      
      AIDS Res. Hum. Retroviruses
      
      1989
    
    
      Tsujimoto H, Hasegawa A, Maki N, Fukasawa M, Miura T, Speidel S, Cooper RW, Moriyama EN, Gojobori T, Hayami M.
      Sequence of a novel simian immunodeficiency virus from a wild-caught African mandrill.
      
      Nature
      
      1989
    
  
  
    
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  


  Peptidase M7, snapalysin
  

In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:


    
 
  • Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.
    • 

  • Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.
    • 



In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and  binding. 


Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. 
Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases [].


This group of metallopeptidases belong to the MEROPS peptidase family M7 (snapalysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA.


With a molecular weight of around 16kDa, Streptomyces extracellular neutral protease is one of the smallest known proteases []; it is capable of hydrolysing milk proteins []. The enzyme is synthesised as a proenzyme with a signal peptide, a propeptide and an active domain that contains the conserved HEXXH motif characteristic of metalloproteases. Although family M7 shows active site sequence similarity to other members, it differs in one major respect: the third zinc ligand appears to be an aspartate residue rather than the usual histidine.


  
    
      Molecular Function
      metalloendopeptidase activity
    
    
      Cellular Component
      extracellular region
    
    
      Biological Process
      proteolysis
    
    
      Molecular Function
      zinc ion binding
    
  
  
    
      
    
  
  
    
      Rawlings ND, Barrett AJ.
      Evolutionary families of metallopeptidases.
      
      Meth. Enzymol.
      
      1995
    
  
  
    
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
  
  
    
  


  PAS
  

PAS domains are involved in many signalling proteins where they
are used as a signal sensor domain. PAS domains appear in archaea,
bacteria and eukaryotes. Several PAS-domain proteins are known to
detect their signal by way of an associated cofactor. Haeme,
flavin, and a 4-hydroxycinnamyl chromophore are used in different
proteins. The PAS domain was named after three proteins that it
occurs in: 


  • Per- period circadian protein
    • 

  • Arnt- Ah receptor nuclear translocator protein
    • 

  • Sim-  single-minded protein.
    • 

    PAS domains are often associated with
PAC domains .  It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold.  The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs [].  In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand [].
Probably the most surprising identification of a PAS domain was that in
EAG-like K+-channels [].
    
    
  
    
      Molecular Function
      signal transducer activity
    
    
      Biological Process
      signal transduction
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Zhulin IB, Taylor BL, Dixon R.
      PAS domain S-boxes in Archaea, Bacteria and sensors for oxygen and redox.
      
      Trends Biochem. Sci.
      
      1997
    
    
      Hefti MH, Francoijs KJ, de Vries SC, Dixon R, Vervoort J.
      The PAS fold. A redefinition of the PAS domain based upon structural prediction.
      
      Eur. J. Biochem.
      
      2004
    
    
      Amezcua CA, Harper SM, Rutter J, Gardner KH.
      Structure and interactions of PAS kinase N-terminal PAS domain: model for intramolecular kinase regulation.
      
      Structure
      
      2002
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
  
    

  Fimbrial biogenesis outer membrane usher protein
  
In Gram-negative bacteria the biogenesis of fimbriae (or pili) requires a two-
component assembly  and  transport  system  which is composed of a periplasmic
chaperone (see )  and  an  outer  membrane  protein which has been
termed a  molecular  'usher'  [, , ]. 
    The usher protein is rather large (from 86 to
100 Kd) and seems to be mainly composed  of  membrane-spanning  beta-sheets, a
structure reminiscent  of  porins.  
Although the degree of sequence similarity of these proteins is not very high
they  share a number of characteristics. One of these is the presence of two pairs
of cysteines, the first one located in the N-terminal part and the second
at the  C-terminal  extremity that are probably involved in disulphide bonds.
The best conserved region is located in the central part of these proteins.
    
    
  
    
      Molecular Function
      transporter activity
    
    
      Biological Process
      transport
    
    
      Cellular Component
      membrane
    
  
  
    
      
    
  
  
    
      Schifferli DM, Alrutz MA.
      Permissive linker insertion sites in the outer membrane protein of 987P fimbriae of Escherichia coli.
      
      J. Bacteriol.
      
      1994
    
    
      Jacob-Dubuisson F, Striker R, Hultgren SJ.
      Chaperone-assisted self-assembly of pili independent of cellular energy.
      
      J. Biol. Chem.
      
      1994
    
    
      Van Rosmalen M, Saier MH Jr.
      Structural and evolutionary relationships between two families of bacterial extracytoplasmic chaperone proteins which function cooperatively in fimbrial assembly.
      
      Res. Microbiol.
      
      1993
    
  
  
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
    
  
  
    
    
    
    
    
    
    
  
    

  P2Y4 purinoceptor
  

    G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). 
    

    The rhodopsin-like GPCRs themselves represent a widespread protein family that includes hormone, neurotransmitter and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide-binding (G) proteins. Although their activating ligands vary widely in structure and character, the amino acid sequences of the receptors are very similar and are believed to adopt a common structural framework comprising 7
transmembrane (TM) helices [, , ].
    

    In addition to their role in energy metabolism, purines (especially
adenosine and adenine nucleotides) produce a wide range of pharmacological
effects mediated by activation of cell surface receptors []. ATP is a
co-transmitter in sympathetic nerves in the autonomic nervous system,
where it exerts an important physiological role in the regulation of
smooth muscle activity, stimulating relaxation of intestinal smooth muscle
and contraction of the bladder. Receptors for adenine nucleotides are
involved in a number of other physiological pathways, including stimulation
of platelet activation by ADP, which is released from the vascular
endothelium following injury. ATP has excitatory effects in the CNS [].
Distinct receptors exist for adenosine. The main effects of adenosine in
the periphery include vasodilation, bronchoconstriction, immunosuppression,
inhibition of platelet aggregation, cardiac depression, stimulation of
nociceptive afferents, inhibition of neurotransmitter release, and
inhibition of the release of hormones. In the CNS, adenosine exerts a
pre- and post-synaptic depressant action, reducing motor activity,
depressing respiration, inducing sleep and relieving anxiety. The
physiological role of adenosine is believed to be to adjust energy demands
in line with oxygen supply [].
    

    Purinoceptors have been classified as P1 or P2, depending on their
preference for adenosine or adenine nucleotides respectively. Adenosine
receptors (P1 purinoceptors) are characterised by their affinity for
adenosine and by the ability of methylxanthines to act as antagonists [].
Adenosine has very low affinity for P2 purinoceptors.
    

    The P2Y receptor is found in smooth muscle (e.g., taeni caeci) and in
vascular tissue, where it induces vasodilation through endothelium-dependent
release of nitric oxide. The receptor activates phosphoinositide metabolism
through a pertussis-toxin-insensitive G-protein, probably belonging to
the Gi/Go class [].
    

    A new subtype of P2 purinoceptors has been isolated []. Its deduced amino acid sequence is consistent with a GPCR that is 51% identical to the human P2Y2 receptor and 35% identical to the chicken P2Y1 receptor []. P2Y4 is expressed in the placenta, with low levels in the lung and vascular smoothmuscle.  In cells stably expressing the receptor, UTP and UDP have been shown to stimulate the formation of inositol phosphates with equivalent potency and maximal effect, while ATP behaves as a partial agonist, and ADP is almost inactive []. The receptor is thus a new member of the P2 purinergic receptor family that functionally behaves as a pyrimidinergic receptor [].  P2Y4 can couple to both Gi and Gq proteins to activate phospholipase C [].
    
    
  
    
      Biological Process
      G-protein coupled receptor protein signaling pathway
    
    
      Cellular Component
      integral to membrane
    
    
      Molecular Function
      purinergic nucleotide receptor activity, G-protein coupled
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Birnbaumer L.
      G proteins in signal transduction.
      
      Annu. Rev. Pharmacol. Toxicol.
      
      1990
    
    
      Casey PJ, Gilman AG.
      G protein involvement in receptor-effector coupling.
      
      J. Biol. Chem.
      
      1988
    
    
      Communi D, Pirotton S, Parmentier M, Boeynaems JM.
      Cloning and functional expression of a human uridine nucleotide receptor.
      
      J. Biol. Chem.
      
      1995
    
    
      Attwood TK, Findlay JB.
      Design of a discriminating fingerprint for G-protein-coupled receptors.
      
      Protein Eng.
      
      1993
    
    
      Communi D, Janssens R, Suarez-Huerta N, Robaye B, Boeynaems JM.
      Advances in signalling by extracellular nucleotides. the role and transduction mechanisms of P2Y receptors.
      
      Cell. Signal.
      
      2000
    
    
      Attwood TK, Findlay JB.
      Fingerprinting G-protein-coupled receptors.
      
      Protein Eng.
      
      1994
    
    
      Watson S, Arkinstall S.
      Adenosine and adenine nucleotides.
      ISBN:0127384405
      
      1994
    
  
  
    
  
  
    
    
  
  
    
    
  
  
    
    
    
    
    
  
    

  Anaphylatoxin/fibulin
  

    Complement components C3, C4 and C5 are large glycoproteins that have important functions in the immune response and host defence []. They have a wide variety of biological activities and are proteolytically activated by cleavage at a specific site, forming a- and b-fragments []. A-fragments form distinct structural domains of approximately 76 amino acids, coded for by a single exon within the complement protein gene. The C3a, C4a and C5a components are referred to as anaphylatoxins [, ]: they cause smooth muscle contraction, histamine release from mast cells, and enhanced vascular permeability []. They also mediate chemotaxis, inflammation, and generation of cytotoxic oxygen radicals []. The proteins are highly hydrophilic, with a mainly alpha-helical structure held together by 3 disulphide bridges [].
    

     Fibulins are secreted glycoproteins that become incorporated into a fibrillar extracellular matrix when expressed by cultured cells or added exogenously to cell monolayers [, ]. The five known members of the family share an elongated structure and many calcium-binding sites, owing to the presence of tandem arrays of epidermal growth factor-like domains. They have overlapping binding sites for several basement-membrane proteins, tropoelastin, fibrillin, fibronectin and proteoglycans, and they participate in diverse supramolecular structures. The amino-terminal domain I of fibulin consists of three anaphylatoxin-like (AT) modules, each approximately 40 residues long and containing four or six cysteines. The structure of an AT module was determined for the complement-derived anaphylatoxin C3a, and  was found to be a compact alpha-helical fold that is stabilised by three disulphide bridges in the pattern Cys1-4, Cys2-5 and Cys3-6 (where Cys is cysteine). The bulk of the remaining portion of the fibulin molecule is a series of nine EGF-like repeats []. 
    
    
  
    
      Cellular Component
      extracellular region
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Gennaro R, Simonic T, Negri A, Mottola C, Secchi C, Ronchi S, Romeo D.
      C5a fragment of bovine complement. Purification, bioassays, amino-acid sequence and other structural studies.
      
      Eur. J. Biochem.
      
      1986
    
    
      Ogata RT, Rosa PA, Zepf NE.
      Sequence of the gene for murine complement component C4.
      
      J. Biol. Chem.
      
      1989
    
    
      Argraves WS, Tran H, Burgess WH, Dickerson K.
      Fibulin is an extracellular matrix and plasma glycoprotein with repeated domain structure.
      
      J. Cell Biol.
      
      1990
    
    
      Timpl R, Sasaki T, Kostka G, Chu ML.
      Fibulins: a versatile family of extracellular matrix proteins.
      
      Nat. Rev. Mol. Cell Biol.
      
      2003
    
    
      Pan TC, Sasaki T, Zhang RZ, Fassler R, Timpl R, Chu ML.
      Structure and expression of fibulin-2, a novel extracellular matrix protein with multiple EGF-like repeats and consensus motifs for calcium binding.
      
      J. Cell Biol.
      
      1993
    
    
      Fritzinger DC, Petrella EC, Connelly MB, Bredehorst R, Vogel CW.
      Primary structure of cobra complement component C3.
      
      J. Immunol.
      
      1992
    
  
  
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
  
  
    
  
    

  Hok/gef cell toxic protein
  
The hok/gef family of Gram-negative bacterial proteins are toxic to cells
when over-expressed, killing the cells from within by interfering with a
vital function in the cell membrane []. Some family members (flm) increase the stability of unstable RNA [], some (pnd) induce the degradation of stable RNA at higher than optimum growth temperatures [], while others affect the release of cellular magnesium by membrane alterations []. The
proteins are short (50-70 residues), consisting of an N-terminal hydrophobic (possibly membrane spanning) domain, and a C-terminal periplasmic region, which contains the toxic domain. The C-terminal region contains a conserved cysteine residue that mediates homo-dimerisation in the gef protein, although dimerisation is not necessary for the toxic effect [].

  
    
      Cellular Component
      membrane
    
  
  
    
      
    
  
  
    
      Sakikawa T, Akimoto S, Ohnishi Y.
      The pnd gene in E. coli plasmid R16: nucleotide sequence and gene expression leading to cell Mg2+ release and stable RNA degradation.
      
      Biochim. Biophys. Acta
      
      1989
    
    
      Golub EI, Panzer HA.
      The F factor of Escherichia coli carries a locus of stable plasmid inheritance stm, similar to the parB locus of plasmid RI.
      
      Mol. Gen. Genet.
      
      1988
    
    
      Poulsen LK, Refn A, Molin S, Andersson P.
      Topographic analysis of the toxic Gef protein from Escherichia coli.
      
      Mol. Microbiol.
      
      1991
    
  
  
    
  
  
    
    
    
  
  
    
    
    
    
  
  
    
    
    
  


  Carboxyl transferase
  

    Members in this domain include biotin dependent carboxylases
[, ].
The carboxyl transferase domain carries out the following reaction;
transcarboxylation from biotin to an acceptor molecule. There are
two recognised types of carboxyl transferase. One of them uses acyl-CoA
and the other uses 2-oxo acid as the acceptor molecule of carbon dioxide.  
All of the members in this family utilise acyl-CoA as the acceptor
molecule.
    
    
  
    
      Molecular Function
      ligase activity
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Toh H, Kondo H, Tanabe T.
      Molecular evolution of biotin-dependent carboxylases.
      
      Eur. J. Biochem.
      
      1993
    
    
      Thornton CG, Kumar GK, Haase FC, Phillips NF, Woo SB, Park VM, Magner WJ, Shenoy BC, Wood HG, Samols D.
      Primary structure of the monomer of the 12S subunit of transcarboxylase as deduced from DNA and characterization of the product expressed in Escherichia coli.
      
      J. Bacteriol.
      
      1993
    
  
  
    
    
  
  
    
    
    
  
  
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  Phosphofructokinase
  
The enzyme-catalysed transfer of a phosphoryl group from ATP is an
important reaction in a wide variety of biological processes []. One
enzyme that utilises this reaction is phosphofructokinase (PFK), which
catalyses the phosphorylation of fructose-6-phosphate to fructose-1,6-
bisphosphate, a key regulatory step in the glycolytic pathway [, ]. 
PFK exists as a homotetramer in bacteria and mammals (where each monomer
possesses 2 similar domains), and as an octomer in yeast (where there are
4 alpha- (PFK1) and 4 beta-chains (PFK2), the latter, like the mammalian
monomers, possessing 2 similar domains []). 
    PFK is ~300 amino acids in length, and structural studies of the
bacterial enzyme have shown it comprises two similar (alpha/beta) lobes: one involved in
ATP binding and the other housing both the substrate-binding site and the allosteric site (a regulatory binding site distinct from the active site, but that affects enzyme
activity). The identical tetramer subunits  adopt 2 
different conformations: in a 'closed' state, the bound magnesium ion
bridges the phosphoryl groups of the enzyme products (ADP and fructose-1,6-
bisphosphate); and in an 'open' state, the magnesium ion binds only the ADP
[], as the 2 products are now further apart. These conformations are
thought to be successive stages of a reaction pathway that requires subunit
closure to bring the 2 molecules sufficiently close to react [].
    

    Deficiency in PFK leads to glycogenosis type VII (Tauri's disease), an
autosomal recessive disorder characterised by severe nausea, vomiting,
muscle cramps and myoglobinuria in response to bursts of intense or
vigorous exercise []. Sufferers are usually able to lead a reasonably
ordinary life by learning to adjust activity levels [].
    
    
  
    
      Molecular Function
      6-phosphofructokinase activity
    
    
      Cellular Component
      6-phosphofructokinase complex
    
    
      Biological Process
      glycolysis
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Raben N, Exelbert R, Spiegel R, Sherman JB, Nakajima H, Plotz P, Heinisch J.
      Functional expression of human mutant phosphofructokinase in yeast: genetic defects in French Canadian and Swiss patients with phosphofructokinase deficiency.
      
      Am. J. Hum. Genet.
      
      1995
    
    
      Shirakihara Y, Evans PR.
      Crystal structure of the complex of phosphofructokinase from Escherichia coli with its reaction products.
      
      J. Mol. Biol.
      
      1988
    
    
      Hellinga HW, Evans PR.
      Mutations in the active site of Escherichia coli phosphofructokinase.
      
      Nature
      
      1987
    
    
      Wegener G, Krause U.
      Different modes of activating phosphofructokinase, a key regulatory enzyme of glycolysis, in working vertebrate muscle.
      
      Biochem. Soc. Trans.
      
      2002
    
  
  
    
    
    
    
    
    
  
  
    
    
  
  
    
  
  
    
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
  
    

  Frizzled cysteine-rich domain
  
The Frizzled CRD (cysteine rich domain) is conserved in diverse proteins including several receptor tyrosine kinases
[, , ].
In Drosophila melanogaster, members of the Frizzled family of tissue-polarity genes encode proteins that appear to function as cell-surface receptors for Wnts. The Frizzled genes belong to the seven transmembrane class of receptors (7TMR) and have in their extracellular region a cysteine-rich domain that has been implicated as the Wnt binding domain. Sequence similarity between the cysteine-rich domain of Frizzled and several receptor tyrosine kinases, which have roles in development, include the muscle-specific receptor tyrosine kinase (MuSK), the neuronal specific kinase (NSK2), and ROR1 and ROR2.
The structure of this domain is known and is composed mainly of alpha helices.
This domain contains ten conserved cysteines that form five disulphide bridges.

  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Xu YK, Nusse R.
      The Frizzled CRD domain is conserved in diverse proteins including several receptor tyrosine kinases.
      
      Curr. Biol.
      
      1998
    
    
      Saldanha J, Singh J, Mahadevan D.
      Identification of a Frizzled-like cysteine rich domain in the extracellular region of developmental receptor tyrosine kinases.
      
      Protein Sci.
      
      1998
    
    
      Rehn M, Pihlajaniemi T, Hofmann K, Bucher P.
      The frizzled motif: in how many different protein families does it occur?
      
      Trends Biochem. Sci.
      
      1998
    
  
  
    
  
  
    
  
  
    
    
    
  
  
    
    
  
  
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  


  Alkylbase DNA glycosidase, conserved site
  

    Alkylbase DNA glycosidases [] are  DNA repair  enzymes  that hydrolyse the deoxyribose N-glycosidic bond to excise various alkylated bases from a damaged DNA polymer. In Escherichia coli there  are two alkylbase DNA glycosidases: one (gene tag) which is constitutively expressed and  which is specific for the removal of 3-methyladenine (), and one (gene alkA) which is induced during adaptation to alkylation and which can remove a variety of alkylation products (). Tag and alkA do not share any region of sequence similarity. In yeast there is  an alkylbase DNA glycosidase (gene MAG1) [, ], which can remove 3-methyladenine or 7-methyladenine and which is structurally related to alkA. MAG and alkA are both proteins of about 300 amino acid residues.  While the C- and N-terminal ends appear to be unrelated, there is a central region of about 130 residues which is well conserved.
    
    
  
    
      Molecular Function
      alkylbase DNA N-glycosylase activity
    
    
      Biological Process
      DNA repair
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Lindahl T, Sedgwick B, Sekiguchi M, Nakabeppu Y.
      Regulation and expression of the adaptive response to alkylating agents.
      
      Annu. Rev. Biochem.
      
      1988
    
    
      Berdal KG, Bjoras M, Bjelland S, Seeberg E.
      Cloning and expression in Escherichia coli of a gene for an alkylbase DNA glycosylase from Saccharomyces cerevisiae; a homologue to the bacterial alkA gene.
      
      EMBO J.
      
      1990
    
    
      Chen J, Derfler B, Samson L.
      Saccharomyces cerevisiae 3-methyladenine DNA glycosylase has homology to the AlkA glycosylase of E. coli and is induced in response to DNA alkylation damage.
      
      EMBO J.
      
      1990
    
  
  
    
    
  
  
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
  
    

  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  

    
BioPerl-1.007002/t/data/interpro_ebi.xml000444000766000024       322313155576321 20073 0ustar00cjfieldsstaff000000000000

  
    
	 
	 
		
		
		  
		  
		  
		  
		  
		  
		  
		  
		  
		  
		
	 
  
    

  

	 
		
		
		  
			 
		  
		

		
		  
			 
		  
		

   
	 
  

BioPerl-1.007002/t/data/interpro_relationship.xml000444000766000024    160671113155576321 22131 0ustar00cjfieldsstaff000000000000



  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  


  Kringle
  

    Kringles are autonomous structural domains, found throughout the blood clotting and fibrinolytic proteins. Kringle domains are believed to play a role in binding mediators (e.g., membranes, other proteins or phospholipids), and in the regulation of proteolytic activity [, , ]. 
Kringle domains [, , ] are characterised by a triple loop, 3-disulphide bridge structure, whose  conformation is defined by a number of hydrogen bonds and small pieces of  anti-parallel beta-sheet. They are found in a varying number  of  copies  in some plasma proteins including prothrombin and urokinase-type plasminogen activator, which are serine proteases belonging to MEROPS peptidase family S1A.
    

    Steroid or nuclear hormone receptors (4A nuclear receptor, NRs) constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands []. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner [, ]. In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity.
    

    NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed 'orphan' receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members.
    
    
  
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Patthy L.
      Evolution of the proteases of blood coagulation and fibrinolysis by assembly from modules.
      
      Cell
      
      1985
    
    
      Patthy L, Trexler M, Vali Z, Banyai L, Varadi A.
      Kringles: modules specialized for protein binding. Homology of the gelatin-binding region of fibronectin with the kringle structures of proteases.
      
      FEBS Lett.
      
      1984
    
    
      McMullen BA, Fujikawa K.
      Amino acid sequence of the heavy chain of human alpha-factor XIIa (activated Hageman factor).
      
      J. Biol. Chem.
      
      1985
    
    
      Ikeo K, Takahashi K, Gojobori T.
      Evolutionary origin of numerous kringles in human and simian apolipoprotein(a).
      
      FEBS Lett.
      
      1991
    
    
      De Vos P, Schmitt J, Verhoeven G, Stunnenberg HG.
      Human androgen receptor expressed in HeLa cells activates transcription in vitro.
      
      Nucleic Acids Res.
      
      1994
    
    
      Schwabe JW, Teichmann SA.
      Nuclear receptors: the evolution of diversity.
      
      Sci. STKE
      
      2004
    
    
      Atkinson RA, Williams RJ.
      Solution structure of the kringle 4 domain from human plasminogen by 1H nuclear magnetic resonance spectroscopy and distance geometry.
      
      J. Mol. Biol.
      
      1990
    
    
      Castellino FJ, Beals JM.
      The genetic relationships between the kringle domains of human plasminogen, prothrombin, tissue plasminogen activator, urokinase, and coagulation factor XII.
      
      J. Mol. Evol.
      
      1987
    
    
      Nishikawa J, Kitaura M, Imagawa M, Nishihara T.
      Vitamin D receptor contains multiple dimerization interfaces that are functionally different.
      
      Nucleic Acids Res.
      
      1995
    
  
  
    
  
  
    
  
  
    
  
  
    
    
    
    
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  
    

  Retinoid X receptor
  

    Steroid or nuclear hormone receptors (4A nuclear receptor, NRs) constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands []. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner [, ]. In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity.
    

    NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed 'orphan' receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members.
    

    The retinoic acid (retinoid X) receptor consists of 3 functional and 
               structural domains: an N-terminal (modulatory) domain; a DNA binding domain
               that mediates specific binding to target DNA sequences (ligand-responsive
               elements); and a hormone binding domain. The N-terminal domain differs 
               between retinoic acid isoforms; the small highly-conserved DNA-binding
               domain (~65 residues) occupies the central portion of the protein; and 
               the ligand binding domain lies at the receptor C terminus.
    

    Synonym(s): 2B nuclear receptor
    
    
  
    
      Molecular Function
      DNA binding
    
    
      Molecular Function
      ligand-dependent nuclear receptor activity
    
    
      Molecular Function
      steroid binding
    
    
      Cellular Component
      nucleus
    
    
      Biological Process
      regulation of transcription, DNA-dependent
    
    
      Molecular Function
      zinc ion binding
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Nishikawa J, Kitaura M, Imagawa M, Nishihara T.
      Vitamin D receptor contains multiple dimerization interfaces that are functionally different.
      
      Nucleic Acids Res.
      
      1995
    
    
      De Vos P, Schmitt J, Verhoeven G, Stunnenberg HG.
      Human androgen receptor expressed in HeLa cells activates transcription in vitro.
      
      Nucleic Acids Res.
      
      1994
    
    
      Schwabe JW, Teichmann SA.
      Nuclear receptors: the evolution of diversity.
      
      Sci. STKE
      
      2004
    
  
  
    
  
  
    
    
  
  
    
  
  
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
  
    

  Helix-turn-helix, AraC type
  

    Many bacterial transcription regulation proteins bind DNA through a
'helix-turn-helix' (HTH) motif. One major subfamily of these proteins [, ] is related to the arabinose 
operon regulatory protein AraC [], . Except for celD [], all of these proteins seem to be positive transcriptional factors.
    

    Although the sequences belonging to this family differ somewhat in length, in nearly every case the HTH motif is situated towards the C terminus in the third quarter of most of the sequences. The minimal DNA binding domain spans roughly 100 residues and comprises two HTH subdomains; the classical HTH domain and another HTH subdomain with similarity to the classical HTH domain but with an insertion of one residue in the turn-region. The  N-terminal and  central regions of these proteins are presumed to interact with effector molecules and may be involved in dimerisation [].
    

    The known structure of MarA () shows that the AraC domain is alpha helical and shows the two HTH subdomains both bind the major groove of the DNA. The two HTH subdomains are separated by only 27
angstroms, which causes the cognate DNA to bend.
    
    
  
    
      Molecular Function
      transcription factor activity
    
    
      Cellular Component
      intracellular
    
    
      Biological Process
      regulation of transcription, DNA-dependent
    
    
      Molecular Function
      sequence-specific DNA binding
    
  
  
    
      
    
  
  
    
      Parker LL, Hall BG.
      Characterization and nucleotide sequence of the cryptic cel operon of Escherichia coli K12.
      
      Genetics
      
      1990
    
    
      Henikoff S, Wallace JC, Brown JP.
      Finding protein similarities with nucleotide sequence databases.
      
      Meth. Enzymol.
      
      1990
    
    
      Gallegos MT, Michan C, Ramos JL.
      The XylS/AraC family of regulators.
      
      Nucleic Acids Res.
      
      1993
    
    
      Bustos SA, Schleif RF.
      Functional domains of the AraC protein.
      
      Proc. Natl. Acad. Sci. U.S.A.
      
      1993
    
  
  
    
  
  
    
    
  
  
    
    
    
    
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
  
    

  Metallothionein, vertebrate
  

    Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, nickel, etc. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, ]. An empirical classification into three classes has been proposed by Fowler and coworkers [] and Kojima []. Members of class I are defined to include polypeptides related in the positions of their cysteines to equine MT-1B, and include mammalian MTs as well as from crustaceans and molluscs. Class II groups MTs from a variety of species, including sea urchins,
fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units [].
    

    This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Consequently, all class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. This system subdivides the MT superfamily into families, subfamilies, subgroups, and isolated isoforms and alleles. 
    

    The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects []: e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. The inclusion of a MT within a family presupposes that its amino acid sequence is alignable with that of all members. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range: e.g., Family 1: vertebrate MTs [see http://www.bioc.unizh.ch/mtpage/protali.html]. 
    

     The members of family 1 are recognised by the sequence pattern K-x(1,2)-C-C-x-C-C-P-x(2)-C located at the beginning of the third exon. 
The taxonomic range of the members extends to vertebrates. 
Known characteristics: 60 to 68 AAs; 20 Cys (21 in one case), 19 of them are totally conserved; the protein sequence is divided into two structural domains, containing 9 and 11 Cys all binding 3 and 4 bivalent metal ions, respectively. The gene is composed of 3 exons, 2 introns and the splicing sites are conserved. Family 1 includes subfamilies: m1, m2, m3, m4, m, a, a1, a2, b, ba, t, all of them hit the same InterPro entry. 

    
    
  
    
      Molecular Function
      metal ion binding
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Kagi JH, Kojima Y.
      Chemistry and biochemistry of metallothionein.
      
      Experientia Suppl.
      
      1987
    
    
      Kagi JH.
      Overview of metallothionein.
      
      Meth. Enzymol.
      
      1991
    
    
      Kojima Y.
      Definitions and nomenclature of metallothioneins.
      
      Meth. Enzymol.
      
      1991
    
    
      Fowler BA, Hildebrand CE, Kojima Y, Webb M.
      Nomenclature of metallothionein.
      
      Experientia Suppl.
      
      1987
    
  
  
    
  
  
    
    
  
  
    
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
  
    

  Tubby, C-terminal
  

     Tubby, an autosomal recessive mutation, mapping to mouse  chromosome 7, was recently found to be the result of a splicing defect in a novel gene with unknown function. This  mutation  maps to the tub gene [, ]. The mouse  tubby mutation is  the  cause  of  maturity-onset  obesity, insulin resistance and  sensory  deficits. By contrast with the rapid juvenile-onset weight gain seen in diabetes (db) and obese (ob) mice, obesity in tubby mice develops gradually, and strongly resembles the late-onset obesity observed in the human population. Excessive deposition of adipose tissue  culminates in a two-fold increase of body weight. Tubby mice also suffer retinal degeneration and neurosensory hearing loss. The tripartite character of the tubby phenotype is highly similar to human obesity syndromes, such as Alstrom and Bardet-Biedl. Although these phenotypes indicate a vital role for tubby proteins, no biochemical function has yet been ascribed to any family member [], although it has been suggested that the phenotypic features of tubby mice may be the result of cellular apoptosis triggered by expression of the mutated tub gene. TUB is the founding-member of the tubby-like proteins, the TULPs. TULPs are found in multicellular organisms from both the plant and animal kingdoms. Ablation of members of this protein family cause disease phenotypes that are indicative of their importance in nervous-system function and development [].
    

    Mammalian TUB is a hydrophilic protein of ~500 residues. The N-terminal () portion of the protein is conserved neither in length nor sequence, but, in TUB, contains the nuclear localisation signal and may have transcriptional-activation activity. The C-terminal 250 residues are highly conserved. The C-terminal extremity contains a cysteine residue that might play an important role in the normal functioning of these proteins. The crystal structure of the C-terminal core domain from mouse tubby has been determined to 1.9A resolution. This domain is arranged as a 12-stranded, all anti-parallel, closed beta-barrel that surrounds a central alpha helix, (which is at the extreme carboxyl terminus of the protein) that forms most of the hydrophobic core. Structural analyses suggest that TULPs constitute a unique family of bipartite transcription factors [].
    
    
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Kleyn PW, Fan W, Kovats SG, Lee JJ, Pulido JC, Wu Y, Berkemeier LR, Misumi DJ, Holmgren L, Charlat O, Woolf EA, Tayber O, Brody T, Shu P, Hawkins F, Kennedy B, Baldini L, Ebeling C, Alperin GD, Deeds J, Lakey ND, Culpepper J, Chen H, Glucksmann-Kuis MA, Carlson GA, Duyk GM, Moore KJ.
      Identification and characterization of the mouse obesity gene tubby: a member of a novel gene family.
      
      Cell
      
      1996
    
    
      Noben-Trauth K, Naggert JK, North MA, Nishina PM.
      A candidate gene for the mouse mutation tubby.
      
      Nature
      
      1996
    
    
      Boggon TJ, Shan WS, Santagata S, Myers SC, Shapiro L.
      Implication of tubby proteins as transcription factors by structure-based functional analysis.
      
      Science
      
      1999
    
    
      Carroll K, Gomez C, Shapiro L.
      Tubby proteins: the plot thickens.
      
      Nat. Rev. Mol. Cell Biol.
      
      2004
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
    
  
  
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  C2 calcium-dependent membrane targeting
  
The C2 domain is a Ca2+-dependent membrane-targeting module found in many cellular proteins involved in signal transduction or membrane trafficking. C2 domains are unique among membrane targeting domains in that they show wide range of lipid selectivity for the major components of cell membranes, including phosphatidylserine and phosphatidylcholine. This C2 domain is about  116  amino-acid  residues and is located between the two copies of
the C1 domain in Protein Kinase C (that bind phorbol esters and diacylglycerol) (see )
and the  protein  kinase  catalytic  domain  (see ).  Regions with
significant homology [] to  the C2-domain have been found in many proteins.
The C2  domain  is  thought  to  be involved in calcium-dependent phospholipid
binding [] and in membrane targetting processes such as subcellular localisation. 
    The 3D  structure  of  the
C2 domain of synaptotagmin has been reported
[], the domain forms an eight-stranded beta sandwich constructed around a 
conserved 4-stranded motif, designated a C2 key []. Calcium binds in
a cup-shaped depression formed by the N- and C-terminal loops of the
C2-key motif. Structural analyses of several C2 domains have shown them to consist of similar ternary structures in which three Ca2+-binding loops are located at the end of an 8 stranded antiparallel beta sandwich. 
    
    
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Sutton RB, Davletov BA, Berghuis AM, Sudhof TC, Sprang SR.
      Structure of the first C2 domain of synaptotagmin I: a novel Ca2+/phospholipid-binding fold.
      
      Cell
      
      1995
    
    
      Davletov BA, Sudhof TC.
      A single C2 domain from synaptotagmin I is sufficient for high affinity Ca2+/phospholipid binding.
      
      J. Biol. Chem.
      
      1993
    
    
      Brose N, Hofmann K, Hata Y, Sudhof TC.
      Mammalian homologues of Caenorhabditis elegans unc-13 gene define novel family of C2-domain proteins.
      
      J. Biol. Chem.
      
      1995
    
  
  
    
  
  
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  
    

  Protein phosphatase 2A, regulatory subunit PR55
  
Protein phosphatase 2A (PP2A) is a serine/threonine phosphatase implicated 
in many cellular processes, including the regulation of metabolic enzymes 
and proteins involved in signal transduction [, ]. PP2A is a trimer
composed of a 36 kDa catalytic subunit, a 65 kDa regulatory subunit 
(subunit A) and a variable third subunit (subunit B) [, ]. 

    One form of the third subunit is a 55 kDa protein (PR55), which exists in
Drosophila melanogaster and yeast, and has up to three forms in mammals [, ]. PR55 may act
as a substrate recognition unit, or may help to target the enzyme to the
correct subcellular location [].
    
    
  
    
      Cellular Component
      protein phosphatase type 2A complex
    
    
      Biological Process
      signal transduction
    
    
      Molecular Function
      protein phosphatase type 2A regulator activity
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Mayer RE, Hendrix P, Cron P, Matthies R, Stone SR, Goris J, Merlevede W, Hofsteenge J, Hemmings BA.
      Structure of the 55-kDa regulatory subunit of protein phosphatase 2A: evidence for a neuronal-specific isoform.
      
      Biochemistry
      
      1991
    
    
      Pallas DC, Weller W, Jaspers S, Miller TB, Lane WS, Roberts TM.
      The third subunit of protein phosphatase 2A (PP2A), a 55-kilodalton protein which is apparently substituted for by T antigens in complexes with the 36- and 63-kilodalton PP2A subunits, bears little resemblance to T antigens.
      
      J. Virol.
      
      1992
    
  
  
    
    
    
    
    
  
  
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  Proteinase inhibitor I25, cystatin
  

    Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site.  Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. 
    

    The cystatins are cysteine proteinase inhibitors belonging to MEROPS inhibitor family I25, clan IH [, , ]. They mainly inhibit peptidases belonging to peptidase families C1 (papain family) and  C13 (legumain family).  The cystatin family includes:
    

      

    • 
The Type 1 cystatins, which are intracellular cystatins that are present in the cytosol of many cell types, but can also appear in body fluids at significant concentrations. They are single-chain polypeptides of about 100 residues, which have neither disulphide bonds nor carbohydrate side chains. 
      • 

    • The Type 2 cystatins, which are mainly extracellular secreted polypeptides synthesised with a 19-28 residue signal peptide. They are broadly distributed  and found in most body fluids. 
      • 

    • The Type 3 cystatins, which are multidomain proteins. The mammalian representatives of this group are the kininogens. There are three different kininogens in mammals: H- (high molecular mass, ) and L- (low molecular mass) kininogen which are found in a number of species, and T-kininogen that is found only in rat. 
      • 

    • Unclassified cystatins. These are cystatin-like proteins found in a range of organisms: plant phytocystatins, fetuin in mammals, insect cystatins and a puff adder venom cystatin which inhibits metalloproteases  of the MEROPS peptidase family M12 (astacin/adamalysin). Also a number of the cystatins-like proteins have been shown to be devoid of inhibitory activity. 
      • 
    
    

    All true cystatins inhibit cysteine peptidases of the papain family (MEROPS peptidase family C1), and some also inhibit legumain family enzymes (MEROPS peptidase family C13). These peptidases play key roles in physiological processes, such as intracellular protein degradation (cathepsins B, H and L), are pivotal in the remodelling of bone (cathepsin K), and may be important in the control of antigen presentation (cathepsin S, mammalian legumain). Moreover, the activities of such peptidases are increased in pathophysiological conditions, such as cancer metastasis and inflammation. Additionally, such peptidases are essential for several pathogenic parasites and bacteria. Thus in animals cystatins not only have capacity to regulate normal body processes and perhaps cause disease when down-regulated, but in other organisms may also participate in defence against biotic and abiotic stress. 
    
    
  
    
      Molecular Function
      cysteine-type endopeptidase inhibitor activity
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Turk V, Bode W.
      The cystatins: protein inhibitors of cysteine proteinases.
      
      FEBS Lett.
      
      1991
    
    
      Rawlings ND, Barrett AJ.
      Evolution of proteins of the cystatin superfamily.
      
      J. Mol. Evol.
      
      1990
    
    
      Abrahamson M, Alvarez-Fernandez M, Nathanson CM.
      Cystatins.
      
      Biochem. Soc. Symp.
      
      2003
    
  
  
    
  
  
    
    
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  
    

  Ubiquitin-activating enzyme, E1-like
  

    The post-translational attachment of ubiquitin () to proteins (ubiquitinylation) alters the function, location or trafficking of a protein, or targets it to the 26S proteasome for degradation [, , ]. Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2, ), and a ubiquitin ligase (E3, , ), which work sequentially in a cascade []. The E1 enzyme is responsible for activating ubiquitin, the first step in ubiquitinylation. The E1 enzyme hydrolyses ATP and adenylates the C-terminal glycine residue of ubiquitin, and then links this residue to the active site cysteine of E1, yielding a ubiquitin-thioester and free AMP. To be fully active, E1 must non-covalently bind to and adenylate a second ubiquitin molecule. The E1 enzyme can then transfer the thioester-linked ubiquitin molecule to a cysteine residue on the ubiquitin-conjugating enzyme, E2, in an ATP-dependent reaction.
    
    
  
    
      Biological Process
      protein modification process
    
    
      Molecular Function
      small protein activating enzyme activity
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Burger AM, Seth AK.
      The ubiquitin-mediated protein degradation pathway in cancer: therapeutic implications.
      
      Eur. J. Cancer
      
      2004
    
    
      Passmore LA, Barford D.
      Getting into position: the catalytic mechanisms of protein ubiquitylation.
      
      Biochem. J.
      
      2004
    
    
      Pickart CM, Fushman D.
      Polyubiquitin chains: polymeric protein signals.
      
      
      2004
    
    
      Sun L, Chen ZJ.
      The novel functions of ubiquitination in signaling.
      
      Curr. Opin. Cell Biol.
      
      2004
    
  
  
    
    
    
    
  
  
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  Retroviral VpR/VpX protein
  
Human immunodeficiency virus (HIV) is the human retrovirus associated with AIDS (acquired immune deficiency syndrome), and SIV its simian counterpart. Three main groups of primate lentivirus are known, designated Human immunodeficiency virus 1 (HIV-1), Human immunodeficiency virus 2 (HIV-2)/Simian immunodeficiency virus - mac (SIVMAC)/Simian immunodeficiency virus - sm (SIVSM) and Simian immunodeficiency virus - agm (SIVAGM). Simian immunodeficiency virus - mnd (SIVMND) has been suggested to represent a fourth distinct group []. These groups are believed to have diverged from a common ancestor long before the spread of AIDS in humans. Genetic variation in HIV-1 and HIV-2 has been studied extensively, and the nucleotide sequences reported for several strains [].
     ORF analysis has revealed two open reading frames, yielding the so-called R- and X-ORF proteins, whose functions are unknown, but which show a high degree of              sequence similarity.
    
    
  
    
      
    
  
  
    
      Hasegawa A, Tsujimoto H, Maki N, Ishikawa K, Miura T, Fukasawa M, Miki K, Hayami M.
      Genomic divergence of HIV-2 from Ghana.
      
      AIDS Res. Hum. Retroviruses
      
      1989
    
    
      Tsujimoto H, Hasegawa A, Maki N, Fukasawa M, Miura T, Speidel S, Cooper RW, Moriyama EN, Gojobori T, Hayami M.
      Sequence of a novel simian immunodeficiency virus from a wild-caught African mandrill.
      
      Nature
      
      1989
    
  
  
    
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  
    

  Peptidase M7, snapalysin
  

    In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:
    

      
 
    • Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.
      • 

    • Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.
      • 

    

    In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and  binding. 
    

    Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. 
Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases [].
    

    This group of metallopeptidases belong to the MEROPS peptidase family M7 (snapalysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA.
    

    With a molecular weight of around 16kDa, Streptomyces extracellular neutral protease is one of the smallest known proteases []; it is capable of hydrolysing milk proteins []. The enzyme is synthesised as a proenzyme with a signal peptide, a propeptide and an active domain that contains the conserved HEXXH motif characteristic of metalloproteases. Although family M7 shows active site sequence similarity to other members, it differs in one major respect: the third zinc ligand appears to be an aspartate residue rather than the usual histidine.
    
    
  
    
      Molecular Function
      metalloendopeptidase activity
    
    
      Cellular Component
      extracellular region
    
    
      Biological Process
      proteolysis
    
    
      Molecular Function
      zinc ion binding
    
  
  
    
      
    
  
  
    
      Rawlings ND, Barrett AJ.
      Evolutionary families of metallopeptidases.
      
      Meth. Enzymol.
      
      1995
    
  
  
    
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
  
  
    
  
    

  PAS
  

    PAS domains are involved in many signalling proteins where they
are used as a signal sensor domain. PAS domains appear in archaea,
bacteria and eukaryotes. Several PAS-domain proteins are known to
detect their signal by way of an associated cofactor. Haeme,
flavin, and a 4-hydroxycinnamyl chromophore are used in different
proteins. The PAS domain was named after three proteins that it
occurs in: 
    

  • Per- period circadian protein
    • 

  • Arnt- Ah receptor nuclear translocator protein
    • 

  • Sim-  single-minded protein.
    • 

    PAS domains are often associated with
PAC domains .  It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold.  The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs [].  In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand [].
Probably the most surprising identification of a PAS domain was that in
EAG-like K+-channels [].
    
    
  
    
      Molecular Function
      signal transducer activity
    
    
      Biological Process
      signal transduction
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Zhulin IB, Taylor BL, Dixon R.
      PAS domain S-boxes in Archaea, Bacteria and sensors for oxygen and redox.
      
      Trends Biochem. Sci.
      
      1997
    
    
      Hefti MH, Francoijs KJ, de Vries SC, Dixon R, Vervoort J.
      The PAS fold. A redefinition of the PAS domain based upon structural prediction.
      
      Eur. J. Biochem.
      
      2004
    
    
      Amezcua CA, Harper SM, Rutter J, Gardner KH.
      Structure and interactions of PAS kinase N-terminal PAS domain: model for intramolecular kinase regulation.
      
      Structure
      
      2002
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
  
    

  Fimbrial biogenesis outer membrane usher protein
  
In Gram-negative bacteria the biogenesis of fimbriae (or pili) requires a two-
component assembly  and  transport  system  which is composed of a periplasmic
chaperone (see )  and  an  outer  membrane  protein which has been
termed a  molecular  'usher'  [, , ]. 
    The usher protein is rather large (from 86 to
100 Kd) and seems to be mainly composed  of  membrane-spanning  beta-sheets, a
structure reminiscent  of  porins.  
Although the degree of sequence similarity of these proteins is not very high
they  share a number of characteristics. One of these is the presence of two pairs
of cysteines, the first one located in the N-terminal part and the second
at the  C-terminal  extremity that are probably involved in disulphide bonds.
The best conserved region is located in the central part of these proteins.
    
    
  
    
      Molecular Function
      transporter activity
    
    
      Biological Process
      transport
    
    
      Cellular Component
      membrane
    
  
  
    
      
    
  
  
    
      Schifferli DM, Alrutz MA.
      Permissive linker insertion sites in the outer membrane protein of 987P fimbriae of Escherichia coli.
      
      J. Bacteriol.
      
      1994
    
    
      Jacob-Dubuisson F, Striker R, Hultgren SJ.
      Chaperone-assisted self-assembly of pili independent of cellular energy.
      
      J. Biol. Chem.
      
      1994
    
    
      Van Rosmalen M, Saier MH Jr.
      Structural and evolutionary relationships between two families of bacterial extracytoplasmic chaperone proteins which function cooperatively in fimbrial assembly.
      
      Res. Microbiol.
      
      1993
    
  
  
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
    
  
  
    
    
    
    
    
    
    
  
    

  P2Y4 purinoceptor
  

    G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). 
    

    The rhodopsin-like GPCRs themselves represent a widespread protein family that includes hormone, neurotransmitter and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide-binding (G) proteins. Although their activating ligands vary widely in structure and character, the amino acid sequences of the receptors are very similar and are believed to adopt a common structural framework comprising 7
transmembrane (TM) helices [, , ].
    

    In addition to their role in energy metabolism, purines (especially
adenosine and adenine nucleotides) produce a wide range of pharmacological
effects mediated by activation of cell surface receptors []. ATP is a
co-transmitter in sympathetic nerves in the autonomic nervous system,
where it exerts an important physiological role in the regulation of
smooth muscle activity, stimulating relaxation of intestinal smooth muscle
and contraction of the bladder. Receptors for adenine nucleotides are
involved in a number of other physiological pathways, including stimulation
of platelet activation by ADP, which is released from the vascular
endothelium following injury. ATP has excitatory effects in the CNS [].
Distinct receptors exist for adenosine. The main effects of adenosine in
the periphery include vasodilation, bronchoconstriction, immunosuppression,
inhibition of platelet aggregation, cardiac depression, stimulation of
nociceptive afferents, inhibition of neurotransmitter release, and
inhibition of the release of hormones. In the CNS, adenosine exerts a
pre- and post-synaptic depressant action, reducing motor activity,
depressing respiration, inducing sleep and relieving anxiety. The
physiological role of adenosine is believed to be to adjust energy demands
in line with oxygen supply [].
    

    Purinoceptors have been classified as P1 or P2, depending on their
preference for adenosine or adenine nucleotides respectively. Adenosine
receptors (P1 purinoceptors) are characterised by their affinity for
adenosine and by the ability of methylxanthines to act as antagonists [].
Adenosine has very low affinity for P2 purinoceptors.
    

    The P2Y receptor is found in smooth muscle (e.g., taeni caeci) and in
vascular tissue, where it induces vasodilation through endothelium-dependent
release of nitric oxide. The receptor activates phosphoinositide metabolism
through a pertussis-toxin-insensitive G-protein, probably belonging to
the Gi/Go class [].
    

    A new subtype of P2 purinoceptors has been isolated []. Its deduced amino acid sequence is consistent with a GPCR that is 51% identical to the human P2Y2 receptor and 35% identical to the chicken P2Y1 receptor []. P2Y4 is expressed in the placenta, with low levels in the lung and vascular smoothmuscle.  In cells stably expressing the receptor, UTP and UDP have been shown to stimulate the formation of inositol phosphates with equivalent potency and maximal effect, while ATP behaves as a partial agonist, and ADP is almost inactive []. The receptor is thus a new member of the P2 purinergic receptor family that functionally behaves as a pyrimidinergic receptor [].  P2Y4 can couple to both Gi and Gq proteins to activate phospholipase C [].
    
    
  
    
      Biological Process
      G-protein coupled receptor protein signaling pathway
    
    
      Cellular Component
      integral to membrane
    
    
      Molecular Function
      purinergic nucleotide receptor activity, G-protein coupled
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Birnbaumer L.
      G proteins in signal transduction.
      
      Annu. Rev. Pharmacol. Toxicol.
      
      1990
    
    
      Casey PJ, Gilman AG.
      G protein involvement in receptor-effector coupling.
      
      J. Biol. Chem.
      
      1988
    
    
      Communi D, Pirotton S, Parmentier M, Boeynaems JM.
      Cloning and functional expression of a human uridine nucleotide receptor.
      
      J. Biol. Chem.
      
      1995
    
    
      Attwood TK, Findlay JB.
      Design of a discriminating fingerprint for G-protein-coupled receptors.
      
      Protein Eng.
      
      1993
    
    
      Communi D, Janssens R, Suarez-Huerta N, Robaye B, Boeynaems JM.
      Advances in signalling by extracellular nucleotides. the role and transduction mechanisms of P2Y receptors.
      
      Cell. Signal.
      
      2000
    
    
      Attwood TK, Findlay JB.
      Fingerprinting G-protein-coupled receptors.
      
      Protein Eng.
      
      1994
    
    
      Watson S, Arkinstall S.
      Adenosine and adenine nucleotides.
      ISBN:0127384405
      
      1994
    
  
  
    
  
  
    
    
  
  
    
    
  
  
    
    
    
    
    
  
    

  Anaphylatoxin/fibulin
  

    Complement components C3, C4 and C5 are large glycoproteins that have important functions in the immune response and host defence []. They have a wide variety of biological activities and are proteolytically activated by cleavage at a specific site, forming a- and b-fragments []. A-fragments form distinct structural domains of approximately 76 amino acids, coded for by a single exon within the complement protein gene. The C3a, C4a and C5a components are referred to as anaphylatoxins [, ]: they cause smooth muscle contraction, histamine release from mast cells, and enhanced vascular permeability []. They also mediate chemotaxis, inflammation, and generation of cytotoxic oxygen radicals []. The proteins are highly hydrophilic, with a mainly alpha-helical structure held together by 3 disulphide bridges [].
    

     Fibulins are secreted glycoproteins that become incorporated into a fibrillar extracellular matrix when expressed by cultured cells or added exogenously to cell monolayers [, ]. The five known members of the family share an elongated structure and many calcium-binding sites, owing to the presence of tandem arrays of epidermal growth factor-like domains. They have overlapping binding sites for several basement-membrane proteins, tropoelastin, fibrillin, fibronectin and proteoglycans, and they participate in diverse supramolecular structures. The amino-terminal domain I of fibulin consists of three anaphylatoxin-like (AT) modules, each approximately 40 residues long and containing four or six cysteines. The structure of an AT module was determined for the complement-derived anaphylatoxin C3a, and  was found to be a compact alpha-helical fold that is stabilised by three disulphide bridges in the pattern Cys1-4, Cys2-5 and Cys3-6 (where Cys is cysteine). The bulk of the remaining portion of the fibulin molecule is a series of nine EGF-like repeats []. 
    
    
  
    
      Cellular Component
      extracellular region
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Gennaro R, Simonic T, Negri A, Mottola C, Secchi C, Ronchi S, Romeo D.
      C5a fragment of bovine complement. Purification, bioassays, amino-acid sequence and other structural studies.
      
      Eur. J. Biochem.
      
      1986
    
    
      Ogata RT, Rosa PA, Zepf NE.
      Sequence of the gene for murine complement component C4.
      
      J. Biol. Chem.
      
      1989
    
    
      Argraves WS, Tran H, Burgess WH, Dickerson K.
      Fibulin is an extracellular matrix and plasma glycoprotein with repeated domain structure.
      
      J. Cell Biol.
      
      1990
    
    
      Timpl R, Sasaki T, Kostka G, Chu ML.
      Fibulins: a versatile family of extracellular matrix proteins.
      
      Nat. Rev. Mol. Cell Biol.
      
      2003
    
    
      Pan TC, Sasaki T, Zhang RZ, Fassler R, Timpl R, Chu ML.
      Structure and expression of fibulin-2, a novel extracellular matrix protein with multiple EGF-like repeats and consensus motifs for calcium binding.
      
      J. Cell Biol.
      
      1993
    
    
      Fritzinger DC, Petrella EC, Connelly MB, Bredehorst R, Vogel CW.
      Primary structure of cobra complement component C3.
      
      J. Immunol.
      
      1992
    
  
  
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
  
  
    
  
    

  Hok/gef cell toxic protein
  
The hok/gef family of Gram-negative bacterial proteins are toxic to cells
when over-expressed, killing the cells from within by interfering with a
vital function in the cell membrane []. Some family members (flm) increase the stability of unstable RNA [], some (pnd) induce the degradation of stable RNA at higher than optimum growth temperatures [], while others affect the release of cellular magnesium by membrane alterations []. The
proteins are short (50-70 residues), consisting of an N-terminal hydrophobic (possibly membrane spanning) domain, and a C-terminal periplasmic region, which contains the toxic domain. The C-terminal region contains a conserved cysteine residue that mediates homo-dimerisation in the gef protein, although dimerisation is not necessary for the toxic effect [].

  
    
      Cellular Component
      membrane
    
  
  
    
      
    
  
  
    
      Sakikawa T, Akimoto S, Ohnishi Y.
      The pnd gene in E. coli plasmid R16: nucleotide sequence and gene expression leading to cell Mg2+ release and stable RNA degradation.
      
      Biochim. Biophys. Acta
      
      1989
    
    
      Golub EI, Panzer HA.
      The F factor of Escherichia coli carries a locus of stable plasmid inheritance stm, similar to the parB locus of plasmid RI.
      
      Mol. Gen. Genet.
      
      1988
    
    
      Poulsen LK, Refn A, Molin S, Andersson P.
      Topographic analysis of the toxic Gef protein from Escherichia coli.
      
      Mol. Microbiol.
      
      1991
    
  
  
    
  
  
    
    
    
  
  
    
    
    
    
  
  
    
    
    
  


  Carboxyl transferase
  

    Members in this domain include biotin dependent carboxylases
[, ].
The carboxyl transferase domain carries out the following reaction;
transcarboxylation from biotin to an acceptor molecule. There are
two recognised types of carboxyl transferase. One of them uses acyl-CoA
and the other uses 2-oxo acid as the acceptor molecule of carbon dioxide.  
All of the members in this family utilise acyl-CoA as the acceptor
molecule.
    
    
  
    
      Molecular Function
      ligase activity
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Toh H, Kondo H, Tanabe T.
      Molecular evolution of biotin-dependent carboxylases.
      
      Eur. J. Biochem.
      
      1993
    
    
      Thornton CG, Kumar GK, Haase FC, Phillips NF, Woo SB, Park VM, Magner WJ, Shenoy BC, Wood HG, Samols D.
      Primary structure of the monomer of the 12S subunit of transcarboxylase as deduced from DNA and characterization of the product expressed in Escherichia coli.
      
      J. Bacteriol.
      
      1993
    
  
  
    
    
  
  
    
    
    
  
  
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  Phosphofructokinase
  
The enzyme-catalysed transfer of a phosphoryl group from ATP is an
important reaction in a wide variety of biological processes []. One
enzyme that utilises this reaction is phosphofructokinase (PFK), which
catalyses the phosphorylation of fructose-6-phosphate to fructose-1,6-
bisphosphate, a key regulatory step in the glycolytic pathway [, ]. 
PFK exists as a homotetramer in bacteria and mammals (where each monomer
possesses 2 similar domains), and as an octomer in yeast (where there are
4 alpha- (PFK1) and 4 beta-chains (PFK2), the latter, like the mammalian
monomers, possessing 2 similar domains []). 
    PFK is ~300 amino acids in length, and structural studies of the
bacterial enzyme have shown it comprises two similar (alpha/beta) lobes: one involved in
ATP binding and the other housing both the substrate-binding site and the allosteric site (a regulatory binding site distinct from the active site, but that affects enzyme
activity). The identical tetramer subunits  adopt 2 
different conformations: in a 'closed' state, the bound magnesium ion
bridges the phosphoryl groups of the enzyme products (ADP and fructose-1,6-
bisphosphate); and in an 'open' state, the magnesium ion binds only the ADP
[], as the 2 products are now further apart. These conformations are
thought to be successive stages of a reaction pathway that requires subunit
closure to bring the 2 molecules sufficiently close to react [].
    

    Deficiency in PFK leads to glycogenosis type VII (Tauri's disease), an
autosomal recessive disorder characterised by severe nausea, vomiting,
muscle cramps and myoglobinuria in response to bursts of intense or
vigorous exercise []. Sufferers are usually able to lead a reasonably
ordinary life by learning to adjust activity levels [].
    
    
  
    
      Molecular Function
      6-phosphofructokinase activity
    
    
      Cellular Component
      6-phosphofructokinase complex
    
    
      Biological Process
      glycolysis
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Raben N, Exelbert R, Spiegel R, Sherman JB, Nakajima H, Plotz P, Heinisch J.
      Functional expression of human mutant phosphofructokinase in yeast: genetic defects in French Canadian and Swiss patients with phosphofructokinase deficiency.
      
      Am. J. Hum. Genet.
      
      1995
    
    
      Shirakihara Y, Evans PR.
      Crystal structure of the complex of phosphofructokinase from Escherichia coli with its reaction products.
      
      J. Mol. Biol.
      
      1988
    
    
      Hellinga HW, Evans PR.
      Mutations in the active site of Escherichia coli phosphofructokinase.
      
      Nature
      
      1987
    
    
      Wegener G, Krause U.
      Different modes of activating phosphofructokinase, a key regulatory enzyme of glycolysis, in working vertebrate muscle.
      
      Biochem. Soc. Trans.
      
      2002
    
  
  
    
    
    
    
    
    
  
  
    
    
  
  
    
  
  
    
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
  
    

  Frizzled cysteine-rich domain
  
The Frizzled CRD (cysteine rich domain) is conserved in diverse proteins including several receptor tyrosine kinases
[, , ].
In Drosophila melanogaster, members of the Frizzled family of tissue-polarity genes encode proteins that appear to function as cell-surface receptors for Wnts. The Frizzled genes belong to the seven transmembrane class of receptors (7TMR) and have in their extracellular region a cysteine-rich domain that has been implicated as the Wnt binding domain. Sequence similarity between the cysteine-rich domain of Frizzled and several receptor tyrosine kinases, which have roles in development, include the muscle-specific receptor tyrosine kinase (MuSK), the neuronal specific kinase (NSK2), and ROR1 and ROR2.
The structure of this domain is known and is composed mainly of alpha helices.
This domain contains ten conserved cysteines that form five disulphide bridges.

  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Xu YK, Nusse R.
      The Frizzled CRD domain is conserved in diverse proteins including several receptor tyrosine kinases.
      
      Curr. Biol.
      
      1998
    
    
      Saldanha J, Singh J, Mahadevan D.
      Identification of a Frizzled-like cysteine rich domain in the extracellular region of developmental receptor tyrosine kinases.
      
      Protein Sci.
      
      1998
    
    
      Rehn M, Pihlajaniemi T, Hofmann K, Bucher P.
      The frizzled motif: in how many different protein families does it occur?
      
      Trends Biochem. Sci.
      
      1998
    
  
  
    
  
  
    
  
  
    
    
    
  
  
    
    
  
  
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  


  Melatonin receptor
  

    G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). 
    

    The rhodopsin-like GPCRs themselves represent a widespread protein family that includes hormone, neurotransmitter and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide-binding (G) proteins. Although their activating ligands vary widely in structure and character, the amino acid sequences of the receptors are very similar and are believed to adopt a common structural framework comprising 7
transmembrane (TM) helices [, , ].
    

    Melatonin is secreted by the pineal gland during darkness []. It regulates
a variety of neuroendocrine functions and is thought to play an essential
role in circadian rhythms. Drugs that modify the action of melatonin,
and hence influence circadian cycles, are of clinical interest (for example,
in the treatment of jet-lag). Melatonin receptors are found in the
retina, in the pars tuberalis of the pituitary, and in discrete areas of
the brain. The receptor inhibits adenylyl cyclase via a pertussis-toxin-sensitive G-protein, probably of the Gi/Go class [].
    
    
  
    
      Biological Process
      G-protein coupled receptor protein signaling pathway
    
    
      Molecular Function
      melatonin receptor activity
    
    
      Cellular Component
      integral to membrane
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Birnbaumer L.
      G proteins in signal transduction.
      
      Annu. Rev. Pharmacol. Toxicol.
      
      1990
    
    
      Casey PJ, Gilman AG.
      G protein involvement in receptor-effector coupling.
      
      J. Biol. Chem.
      
      1988
    
    
      Attwood TK, Findlay JB.
      Design of a discriminating fingerprint for G-protein-coupled receptors.
      
      Protein Eng.
      
      1993
    
    
      Attwood TK, Findlay JB.
      Fingerprinting G-protein-coupled receptors.
      
      Protein Eng.
      
      1994
    
    
      Watson S, Arkinstall S.
      Melatonin.
      ISBN:0127384405
      
      1994
    
  
  
    
  
  
    
    
    
  
  
    
  
  
    
    
  
  
    
    
    
    
    
  
  
    
    
    
  
    

  Guanine-specific ribonuclease N1/T1
  

    Ribonuclease N1 (RNase N1) is a guanine-specific ribonuclease from fungi.  RNase T1 and other bacteria RNases are related.
    

    The enzyme hydrolyses the phosphodiester bonds in RNA and oligoribonucleotides [], resulting in 3'-nucleoside monophosphates via 2',3'-cyclophosphate intermediates.
    
    
  
    
      Molecular Function
      RNA binding
    
    
      Molecular Function
      endoribonuclease activity
    
  
  
    
      
    
    
      
    
  
  
    
      Buckle AM, Fersht AR.
      Subsite binding in an RNase: structure of a barnase-tetranucleotide complex at 1.76-A resolution.
      
      Biochemistry
      
      1994
    
  
  
    
  
  
    
  
  
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
  
  
    
  
    

  Chloroperoxidase
  

    Chloroperoxidase (CPO), also known as Heme haloperoxidase, is a ~250 residue heme-containing glycoprotein that is secreted by various fungi. Chloroperoxidase was first identified  in Caldariomyces fumago where it catalyzes the hydrogen
peroxide-dependent chlorination of cyclopentanedione during the biosynthesis
of the antibiotic caldarioymcin. Additionally, heme haloperoxidase catalyzes
the iodination and bromination of a wide range of substrates. Besides
performing  H2O2-dependent  halogenation reactions, the enzyme catalyzes
dehydrogenation reactions. Chloroperoxidase also functions as a catalase, facilitating the decomposition of hydrogen peroxide to oxygen and water. Furthermore, chloroperoxidase catalyzes P450-like oxygen insertion reactions. The capability of chloroperoxidase to perform these diverse reactions makes it one of the most versatile of all known heme proteins [, ].
    

    Despite functional similarities with other heme enzymes, chloroperoxidase
folds into a novel tertiary structure dominated by eight helical segments []. Structurally, chloroperoxidase is unique, but it shares
features with both peroxidases and P450 enzymes. As in cytochrome P450
enzymes, the proximal heme ligand is a cysteine,
but similar to peroxidases, the distal side of the heme is polar. However,
unlike other peroxidases, the normally conserved distal arginine is lacking
and the catalytic acid base is a glutamic acid and not a histidine [].
    
    
  
    
      Molecular Function
      peroxidase activity
    
  
  
    
      
    
  
  
    
      Sundaramoorthy M, Terner J, Poulos TL.
      The crystal structure of chloroperoxidase: a heme peroxidase--cytochrome P450 functional hybrid.
      
      Structure
      
      1995
    
    
      Kuhnel K, Blankenfeldt W, Terner J, Schlichting I.
      Crystal structures of chloroperoxidase with its bound substrates and complexed with formate, acetate, and nitrate.
      
      J. Biol. Chem.
      
      2006
    
    
      Manoj KM, Hager LP.
      Chloroperoxidase, a janus enzyme.
      
      Biochemistry
      
      2008
    
    
      Hofrichter M, Ullrich R.
      Heme-thiolate haloperoxidases: versatile biocatalysts with biotechnological and environmental significance.
      
      Appl. Microbiol. Biotechnol.
      
      2006
    
  
  
    
    
    
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
  
    

  Uncharacterised protein family, PPE protein
  
This mycobacterial family is named after a conserved amino-terminal region of about 180
amino acids, the PPE motif. The carboxy termini of proteins belonging to the PPE family are variable, and on the basis of this region at least three groups can be distinguished. The MPTR subgroup is characterised by tandem copies of a motif NXGXGNXG. The second subgroup contains a conserved motif at about position 350.
The third group shares only similarity in the amino terminal region.
The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis [].

  
    
      
    
  
  
    
      Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE 3rd, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quail MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG.
      Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.
      
      Nature
      
      1998
    
  
  
    
  
  
    
    
  
  
    
    
  
  
    
    
  


  1-(5-Phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR) carboxylase
  

    Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE.
PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain []. The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme [].
    
    
  
    
      Molecular Function
      phosphoribosylaminoimidazole carboxylase activity
    
    
      Biological Process
      'de novo' IMP biosynthetic process
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Meyer E, Kappock TJ, Osuji C, Stubbe J.
      Evidence for the direct transfer of the carboxylate of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to generate 4-carboxy-5-aminoimidazole ribonucleotide catalyzed by Escherichia coli PurE, an N5-CAIR mutase.
      
      Biochemistry
      
      1999
    
    
      Mathews II, Kappock TJ, Stubbe J, Ealick SE.
      Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway.
      
      Structure
      
      1999
    
  
  
    
  
  
    
    
    
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  Phosphotransferase system, phosphocarrier HPr protein-like
  

    This entry represents a structural domain found in both the histidine-containing phosphocarrier protein HPr, as well as its structural homologues, which includes the catabolite repression protein Crh found in Bacillus subtilis. This domain has a alpha+beta structure found in two layers with an overall architecture of an open faced beta-sandwich in which a beta-sheet is packed against three alpha-helices. 
    

    The histidine-containing phosphocarrier  protein (HPr) is a central component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), which  transfers metabolic carbohydrates across the cell membrane in many bacterial  species [, ]. PTS catalyses the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is as follows: a phosphoryl group from phosphoenolpyruvate  (PEP) is transferred to Enzyme I (EI) of the PTS, which in turn transfers it to the phosphoryl carrier protein (HPr) [, ]. Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease complex (enzymes EII/EIII). 
    

    HPr [, ] is a small cytoplasmic protein of 70 to 90 amino acid residues. In some bacteria, HPr is a domain in a larger protein that includes a EIII(Fru) (IIA) domain and in some cases also the EI domain. A conserved histidine in the N-terminal section of HPr serves as an acceptor for the phosphoryl group of EI. In the central part of HPr, there is a conserved serine which (in Gram-positive bacteria only) is phosphorylated by an ATP-dependent protein kinase; a process which probably play a regulatory role in sugar transport. Regulatory phosphorylation at the conserved Ser residue does not appear to  induce large structural changes to the HPr domain, in particular in the region of the active site [, ].
    
    
  
    
      Molecular Function
      sugar:hydrogen symporter activity
    
    
      Biological Process
      phosphoenolpyruvate-dependent sugar phosphotransferase system
    
  
  
    
      
    
  
  
    
      Meadow ND, Fox DK, Roseman S.
      The bacterial phosphoenolpyruvate: glycose phosphotransferase system.
      
      Annu. Rev. Biochem.
      
      1990
    
    
      van Nuland NA, Boelens R, Scheek RM, Robillard GT.
      High-resolution structure of the phosphorylated form of the histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from NMR-NOE data.
      
      J. Mol. Biol.
      
      1995
    
    
      Postma PW, Lengeler JW, Jacobson GR.
      Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria.
      
      Microbiol. Rev.
      
      1993
    
    
      Herzberg O, Reddy P, Sutrina S, Saier MH Jr, Reizer J, Kapadia G.
      Structure of the histidine-containing phosphocarrier protein HPr from Bacillus subtilis at 2.0-A resolution.
      
      Proc. Natl. Acad. Sci. U.S.A.
      
      1992
    
    
      Sridharan S, Razvi A, Scholtz JM, Sacchettini JC.
      The HPr proteins from the thermophile Bacillus stearothermophilus can form domain-swapped dimers.
      
      J. Mol. Biol.
      
      2005
    
    
      Audette GF, Engelmann R, Hengstenberg W, Deutscher J, Hayakawa K, Quail JW, Delbaere LT.
      The 1.9 A resolution structure of phospho-serine 46 HPr from Enterococcus faecalis.
      
      J. Mol. Biol.
      
      2000
    
    
      Reizer J, Hoischen C, Reizer A, Pham TN, Saier MH Jr.
      Sequence analyses and evolutionary relationships among the energy-coupling proteins Enzyme I and HPr of the bacterial phosphoenolpyruvate: sugar phosphotransferase system.
      
      Protein Sci.
      
      1993
    
    
      Liao DI, Herzberg O.
      Refined structures of the active Ser83-->Cys and impaired Ser46-->Asp histidine-containing phosphocarrier proteins.
      
      Structure
      
      1994
    
  
  
    
  
  
    
    
  
  
    
    
  
  
    
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
  
  
    
  
    

  Low-density lipoprotein receptor, class B (YWTD) repeat
  

     The low-density lipoprotein receptor (LDLR) is the major cholesterol-carrying lipoprotein of plasma, acting to regulate cholesterol homeostasis in mammalian cells. The LDL receptor binds LDL and transports it into cells by acidic endocytosis. In order to be internalized, the receptor-ligand complex must first cluster into clathrin-coated pits. Once inside the cell, the LDLR separates from its ligand, which is degraded in the lysosomes, while the receptor returns to the cell surface []. The internal dissociation of the LDLR with its ligand is mediated by proton pumps within the walls of the endosome that lower the pH. The LDLR is a multi-domain protein, containing: 
    

    
      
      
        
    • The ligand-binding domain contains seven or eight 40-amino acid LDLR class A (cysteine-rich) repeats, each of which contains a coordinated calcium ion and six cysteine residues involved in disulphide bond formation []. Similar domains have been found in other extracellular and membrane proteins []. 
      • 
      
    
    
    

    
      
      
        
    • The second conserved region contains two EGF repeats, followed by six LDLR class B (YWTD) repeats, and another EGF repeat. The LDLR class B repeats each contain a conserved YWTD motif, and is predicted to form a beta-propeller structure []. This region is critical for ligand release and recycling of the receptor [].
      • 
      
    
    
    

    
      
      
        
    • The third domain is rich in serine and threonine residues and contains clustered O-linked carbohydrate chains.
      • 
      
    
    
    

    
      
      
        
    • The fourth domain is the hydrophobic transmembrane region.
      • 
      
    
    
    

    
      
      
        
    • The fifth domain is the cytoplasmic tail that directs the receptor to clathrin-coated pits.
      • 
      
    
    
    

    LDLR is closely related in structure to several other receptors, including LRP1, LRP1b, megalin/LRP2, VLDL receptor, lipoprotein receptor, MEGF7/LRP4, and LRP8/apolipoprotein E receptor2); these proteins participate in a wide range of physiological processes, including the regulation of lipid metabolism, protection against atherosclerosis, neurodevelopment, and transport of nutrients and vitamins [].
    

    This entry represents the LDLR classB (YWTD) repeat, the structure of which has been solved []. The six YWTD repeats together fold into a six-bladed beta-propeller. Each blade of the propeller consists of four antiparallel beta-strands; the innermost strand of each blade is labeled 1 and the outermost strand, 4. The sequence repeats are offset with respect to the blades of the propeller, such that any given 40-residue YWTD repeat spans strands 24 of one propeller blade and strand 1 of the subsequent blade. This offset ensures circularization of the propeller because the last strand of the final sequence repeat acts as an innermost strand 1 of the blade that harbors strands 24 from the first sequence repeat. The repeat is found in a variety of proteins that include, vitellogenin receptor from Drosophila melanogaster, low-density lipoprotein (LDL) receptor [], preproepidermal growth factor, and nidogen (entactin).
    
    
  
    
      Cellular Component
      membrane
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Yamamoto T, Davis CG, Brown MS, Schneider WJ, Casey ML, Goldstein JL, Russell DW.
      The human LDL receptor: a cysteine-rich protein with multiple Alu sequences in its mRNA.
      
      Cell
      
      1984
    
    
      Springer TA.
      An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases, epidermal growth factor precursor, and extracellular matrix components.
      
      J. Mol. Biol.
      
      1998
    
    
      Daly NL, Scanlon MJ, Djordjevic JT, Kroon PA, Smith R.
      Three-dimensional structure of a cysteine-rich repeat from the low-density lipoprotein receptor.
      
      Proc. Natl. Acad. Sci. U.S.A.
      
      1995
    
    
      May P, Woldt E, Matz RL, Boucher P.
      The LDL receptor-related protein (LRP) family: an old family of proteins with new physiological functions.
      
      Ann. Med.
      
      2007
    
    
      Brown MS, Goldstein JL.
      A receptor-mediated pathway for cholesterol homeostasis.
      
      Science
      
      1986
    
    
      Davis CG, Goldstein JL, Sudhof TC, Anderson RG, Russell DW, Brown MS.
      Acid-dependent ligand dissociation and recycling of LDL receptor mediated by growth factor homology region.
      
      Nature
      
      1987
    
    
      Jeon H, Meng W, Takagi J, Eck MJ, Springer TA, Blacklow SC.
      Implications for familial hypercholesterolemia from the structure of the LDL receptor YWTD-EGF domain pair.
      
      Nat. Struct. Biol.
      
      2001
    
  
  
    
    
    
  
  
    
    
    
  
  
    
    
    
  
  
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  Laminin B type IV
  

    Laminins represent a distinct family of extracellular matrix proteins present only in basement membranes in almost every animal tissue. They are heterotrimeric molecules composed of alpha, beta and gamma subunits  (formerly A, B1, and B2, respectively []) and form a cruciform structure consisting of 3 short arms, each formed by a different chain, and a long arm composed of all 3 chains, [, ]. Most of the globular domains of the short arms correspond to one of two different motifs, the 200-residue laminin N-terminal (domain VI) (LN) module and the 250-residue laminin domain IV (L4) module [].  All alpha chains share a unique C-terminal G domain which consists of five laminin G modules. The laminins can self-assemble, bind to other matrix macromolecules, and have unique and shared cell interactions mediated by integrins, dystroglycan, and other receptors.  There are at least 14 laminin isoforms that regulate a variety of cellular functions including cell adhesion, migration, proliferation, signalling and differentiation [, , ].
    

    The laminin B domain (also known as domain IV) is an extracellular module of unknown function. It is found in a number of different proteins that include, heparan sulphate proteoglycan from basement membrane, a laminin-like protein from Caenorhabditis elegans and laminin. Laminin IV domain is not found in short laminin chains (alpha4 or beta3). 
    
    
  
    
      Biological Process
      cell adhesion
    
    
      Cellular Component
      extracellular matrix
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Beck K, Hunter I, Engel J.
      Structure and function of laminin: anatomy of a multidomain glycoprotein.
      
      FASEB J.
      
      1990
    
    
      Burgeson RE, Chiquet M, Deutzmann R, Ekblom P, Engel J, Kleinman H, Martin GR, Meneguzzi G, Paulsson M, Sanes J.
      A new nomenclature for the laminins.
      
      Matrix Biol.
      
      1994
    
    
      Timpl R, Brown JC.
      The laminins.
      
      Matrix Biol.
      
      1994
    
    
      Schulze B, Mann K, Poschl E, Yamada Y, Timpl R.
      Structural and functional analysis of the globular domain IVa of the laminin alpha 1 chain and its impact on an adjacent RGD site.
      
      Biochem. J.
      
      1996
    
    
      Tunggal P, Smyth N, Paulsson M, Ott MC.
      Laminins: structure and genetic regulation.
      
      Microsc. Res. Tech.
      
      2000
    
    
      Aumailley M, Smyth N.
      The role of laminins in basement membrane function.
      
      J. Anat.
      
      1998
    
  
  
    
  
  
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  
    

  Alkylbase DNA glycosidase, conserved site
  

    Alkylbase DNA glycosidases [] are  DNA repair  enzymes  that hydrolyse the deoxyribose N-glycosidic bond to excise various alkylated bases from a damaged DNA polymer. In Escherichia coli there  are two alkylbase DNA glycosidases: one (gene tag) which is constitutively expressed and  which is specific for the removal of 3-methyladenine (), and one (gene alkA) which is induced during adaptation to alkylation and which can remove a variety of alkylation products (). Tag and alkA do not share any region of sequence similarity. In yeast there is  an alkylbase DNA glycosidase (gene MAG1) [, ], which can remove 3-methyladenine or 7-methyladenine and which is structurally related to alkA. MAG and alkA are both proteins of about 300 amino acid residues.  While the C- and N-terminal ends appear to be unrelated, there is a central region of about 130 residues which is well conserved.
    
    
  
    
      Molecular Function
      alkylbase DNA N-glycosylase activity
    
    
      Biological Process
      DNA repair
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Lindahl T, Sedgwick B, Sekiguchi M, Nakabeppu Y.
      Regulation and expression of the adaptive response to alkylating agents.
      
      Annu. Rev. Biochem.
      
      1988
    
    
      Berdal KG, Bjoras M, Bjelland S, Seeberg E.
      Cloning and expression in Escherichia coli of a gene for an alkylbase DNA glycosylase from Saccharomyces cerevisiae; a homologue to the bacterial alkA gene.
      
      EMBO J.
      
      1990
    
    
      Chen J, Derfler B, Samson L.
      Saccharomyces cerevisiae 3-methyladenine DNA glycosylase has homology to the AlkA glycosylase of E. coli and is induced in response to DNA alkylation damage.
      
      EMBO J.
      
      1990
    
  
  
    
    
  
  
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
  
    

  Peptidase A26, omptin
  

    In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:
    

      
 
    • Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.
      • 

    • Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.
      • 

    

    In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and  binding. 
    

    Aspartic endopeptidases   of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ].
    

    Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases.
All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure.
    

    This group of aspartic peptidases  belongs to the MEROPS family A26 (clan AF). The omptin family, comprises a number of novel outer membrane-associated
serine proteases that are distinct from trypsin-like proteases in that 
they cleave polypeptides between two basically-charged amino acids []. The enzyme is sensitive to the serine protease inhibitor diisopropylfluoro-phosphate, to divalent cations such as Cu2+, Zn2+ and Fe2+ [], and is
temperature regulated, activity decreasing at lower temperatures [, ]. Temperature regulation is most prominently shown in the Yersinia pestis
coagulase/fibrinolysin protein, where coagulase activity is prevalent 
below 30 degrees Celsius, and fibrinolysin (protease) activity is prevalent
above this point, the optimum temperature being 37 degrees []. It is possible that this assists in 'flea blockage' and transmission of the bacteria to animals [].
    

    The Escherichia coli OmpT has previously been classified as a serine protease with Ser(99) and His(212) as active site residues. The X-ray structure of the enzyme is inconsistent with this classification, and the involvement of a nucleophilic water molecule that is activated by the Asp(210)/His(212) catalytic dyad classifies this as a aspartic endopeptidase where activity is also strongly dependent on Asp(83) and Asp(85). Both may function in binding of the water molecule and/or oxyanion stabilisation. The proposed mechanism implies a novel proteolytic catalytic site [, ].
    
    
  
    
      Molecular Function
      endopeptidase activity
    
    
      Biological Process
      proteolysis
    
    
      Cellular Component
      cell outer membrane
    
  
  
    
      
    
  
  
    
      Sugimura K, Nishihara T.
      Purification, characterization, and primary structure of Escherichia coli protease VII with specificity for paired basic residues: identity of protease VII and OmpT.
      
      J. Bacteriol.
      
      1988
    
    
      Kaufmann A, Stierhof YD, Henning U.
      New outer membrane-associated protease of Escherichia coli K-12.
      
      J. Bacteriol.
      
      1994
    
    
      McDonough KA, Falkow S.
      A Yersinia pestis-specific DNA fragment encodes temperature-dependent coagulase and fibrinolysin-associated phenotypes.
      
      Mol. Microbiol.
      
      1989
    
    
      Szecsi PB.
      The aspartic proteases.
      
      Scand. J. Clin. Lab. Invest. Suppl.
      
      1992
    
    
      Kramer RA, Vandeputte-Rutten L, de Roon GJ, Gros P, Dekker N, Egmond MR.
      Identification of essential acidic residues of outer membrane protease OmpT supports a novel active site.
      
      FEBS Lett.
      
      2001
    
    
      Bardy SL, Jarrell KF.
      Cleavage of preflagellins by an aspartic acid signal peptidase is essential for flagellation in the archaeon Methanococcus voltae.
      
      Mol. Microbiol.
      
      2003
    
    
      Vandeputte-Rutten L, Kramer RA, Kroon J, Dekker N, Egmond MR, Gros P.
      Crystal structure of the outer membrane protease OmpT from Escherichia coli suggests a novel catalytic site.
      
      EMBO J.
      
      2001
    
    
      Ng SY, Chaban B, Jarrell KF.
      Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications.
      
      J. Mol. Microbiol. Biotechnol.
      
      2006
    
    
      LaPointe CF, Taylor RK.
      The type 4 prepilin peptidases comprise a novel family of aspartic acid proteases.
      
      J. Biol. Chem.
      
      2000
    
  
  
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
  
  
    
    
    
  
  
    
  
    

  SsrA-binding protein
  

    This entry represents SsrA-binding protein (aka small protein B or SmpB), which is a unique RNA-binding protein that is conserved throughout the bacterial kingdom and is an essential component of the SsrA quality-control system. Tight recognition of codon-anticodon pairings by the ribosome ensures the accuracy and fidelity of protein synthesis. In eubacteria, translational surveillance and ribosome rescue are performed by the 'tmRNA-SmpB' system (transfer messenger RNA-small protein B). SmpB binds specifically to the ssrA RNA (tmRNA) and is required for stable association of ssrA with ribosomes. SsrA RNA recognises ribosomes stalled on defective messages and acts to mediate the addition of a short peptide tag to the C terminus of the partially synthesised nascent polypeptide chain. Within a stalled ribosome, SmpB interacts with the three universally conserved bases G530, A1492 and A1493 that form the 30S subunit decoding centre, in which canonical codon-anticodon pairing occurs []. The SsrA-tagged protein is then degraded by C-terminal-specific proteases. Formation of an SmpB-SsrA complex appears to be critical in mediating SsrA activity after aminoacylation with alanine but prior to the transpeptidation reaction that couples this alanine to the nascent chain []. The SmpB protein has functional and structural similarities with initiation factor 1, and is proposed to be a functional mimic of the pairing between a codon and an anticodon. 
    
    
  
    
      Molecular Function
      RNA binding
    
    
      Biological Process
      translation
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Karzai AW, Susskind MM, Sauer RT.
      SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA).
      
      EMBO J.
      
      1999
    
    
      Nonin-Lecomte S, Germain-Amiot N, Gillet R, Hallier M, Ponchon L, Dardel F, Felden B.
      Ribosome hijacking: a role for small protein B during trans-translation.
      
      EMBO Rep.
      
      2009
    
  
  
    
  
  
    
    
    
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
  
    

  Cell division/GTP binding protein
  

    Septins constitute a eukaryotic family of guanine nucleotide-binding proteins, most of which polymerise to form filaments []. Members of the family were first identified by genetic screening for Saccharomyces cerevisiae (Baker's yeast) mutants defective in cytokinesis []. Temperature-sensitive mutations in four genes, CDC3, CDC10, CDC11 and CDC12, were found to cause cell-cycle arrest and defects in bud growth and cytokinesis. The protein products of these genes localise at the division plane between mother and daughter cells, indicating a role in mother-daughter separation during cytokinesis []. Members of the family were therefore termed septins to reflect their role in septation and cell division. The identification of septin homologues in higher eukaryotes, which localise to the cleavage furrow in dividing cells, supports an orthologous function in cytokinesis. Septins have since been identified in most eukaryotes, except plants [].
    

    Septins are approximately 40-50 kDa in molecular mass, and typically comprise a conserved central core domain (more than 35% sequence identity between mammalian and yeast homologues) flanked by more divergent N- and C-termini. Most septins possess a P-loop motif in their N-terminal domain (which is characteristic of GTP-binding proteins), and a predicted C-terminal coiled-coil domain [].
    

    A number of septin interaction partners have been identified in yeast, many of which are components of the budding site selection machinery, kinase cascades or of the ubiquitination pathway. It has been proposed that septins may act as a scaffold that provides an interaction  matrix for other proteins [, ]. In mammals, septins have been shown to regulate vesicle dynamics []. Mammalian septins have also been implicated in a variety of other cellular processes, including apoptosis, carcinogenesis and neurodegeneration [].
    

    This entry represents a variety of septins and homologous sequences involved in the cell division process.
    
    
  
    
      Molecular Function
      GTP binding
    
    
      Biological Process
      cell cycle
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Haarer BK, Pringle JR.
      Immunofluorescence localization of the Saccharomyces cerevisiae CDC12 gene product to the vicinity of the 10-nm filaments in the mother-bud neck.
      
      Mol. Cell. Biol.
      
      1987
    
    
      Hartwell LH.
      Genetic control of the cell division cycle in yeast. IV. Genes controlling bud emergence and cytokinesis.
      
      Exp. Cell Res.
      
      1971
    
    
      Kinoshita M, Kumar S, Mizoguchi A, Ide C, Kinoshita A, Haraguchi T, Hiraoka Y, Noda M.
      Nedd5, a mammalian septin, is a novel cytoskeletal component interacting with actin-based structures.
      
      Genes Dev.
      
      1997
    
    
      Field CM, Kellogg D.
      Septins: cytoskeletal polymers or signalling GTPases?
      
      Trends Cell Biol.
      
      1999
    
    
      Kinoshita M.
      The septins.
      
      Genome Biol.
      
      2003
    
    
      Longtine MS, Theesfeld CL, McMillan JN, Weaver E, Pringle JR, Lew DJ.
      Septin-dependent assembly of a cell cycle-regulatory module in Saccharomyces cerevisiae.
      
      Mol. Cell. Biol.
      
      2000
    
    
      Kinoshita M, Noda M.
      Roles of septins in the mammalian cytokinesis machinery.
      
      Cell Struct. Funct.
      
      2001
    
  
  
    
  
  
    
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  
    

  Ribosomal protein L18e
  

    Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ].  About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. 
    

    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ].
    

    Members of this family are large subunit ribosomal proteins which are found in the Eukaryota and Archaea. These proteins have 115 to 187 amino-acid residues. The family consists of:
      

    • Vertebrate L18 (known as L14 in Xenopus) []
      • 

    • Plant L18
      • 

    • Yeast L18 (Rp28)
      • 

    • 
          Haloarcula marismortui (Halobacterium marismortui) HL29
      • 

    • 
          Sulfolobus acidocaldarius HL29e
      • 
      
    

    
    
  
    
      Molecular Function
      structural constituent of ribosome
    
    
      Cellular Component
      intracellular
    
    
      Cellular Component
      ribosome
    
    
      Biological Process
      translation
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Puder M, Barnard GF, Staniunas RJ, Steele GD Jr, Chen LB.
      Nucleotide and deduced amino acid sequence of human ribosomal protein L18.
      
      Biochim. Biophys. Acta
      
      1993
    
    
      Ramakrishnan V, Moore PB.
      Atomic structures at last: the ribosome in 2000.
      
      Curr. Opin. Struct. Biol.
      
      2001
    
    
      Maguire BA, Zimmermann RA.
      The ribosome in focus.
      
      Cell
      
      2001
    
    
      Chandra Sanyal S, Liljas A.
      The end of the beginning: structural studies of ribosomal proteins.
      
      Curr. Opin. Struct. Biol.
      
      2000
    
  
  
    
  
  
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  Acute myeloid leukemia 1 protein (AML 1)/Runt
  
The AML1 gene is rearranged by the t(8;21) translocation in acute myeloid
               leukemia []. The gene is highly similar to the Drosophila melanogaster segmentation 
               gene runt and to the mouse transcription factor PEBP2 alpha subunit gene [].
               The region of shared similarity, known as the Runt domain, is responsible 
               for DNA-binding and protein-protein interaction. 
    
     In addition to the highly-conserved Runt domain, the AML-1 gene product
               carries a putative ATP-binding site (GRSGRGKS), and has a C-terminal region
               rich in proline and serine residues. The protein (known as acute myeloid 
               leukemia 1 protein, oncogene AML-1, core-binding factor (CBF), alpha-B 
               subunit, etc.) binds to the core site, 5'-pygpyggt-3', of a number of
               enhancers and promoters. 
    

    The protein is a heterodimer of alpha- and beta-subunits. The alpha-subunit
               binds DNA as a monomer, and appears to have a role in the development of
               normal hematopoiesis. CBF is a nuclear protein expressed in numerous tissue
               types, except brain and heart; highest levels have been found to occur in 
               thymus, bone marrow and peripheral blood.
    
    
  
    
      Molecular Function
      DNA binding
    
    
      Molecular Function
      ATP binding
    
    
      Cellular Component
      nucleus
    
    
      Biological Process
      regulation of transcription, DNA-dependent
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Miyoshi H, Ohira M, Shimizu K, Mitani K, Hirai H, Imai T, Yokoyama K, Soeda E, Ohki M.
      Alternative splicing and genomic structure of the AML1 gene involved in acute myeloid leukemia.
      
      Nucleic Acids Res.
      
      1995
    
  
  
    
  
  
    
    
  
  
    
    
  
  
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
  
  
    
  
    

  S-adenosyl-L-homocysteine hydrolase
  

    S-adenosyl-L-homocysteine hydrolase () (AdoHcyase) is an enzyme of the activated methyl cycle, responsible for the reversible hydration of S-adenosyl-L-homocysteine into adenosine and homocysteine. AdoHcyase is an ubiquitous enzyme which binds and requires NAD+ as a cofactor. AdoHcyase is a highly conserved protein [] of about 430 to 470 amino acids. The family contains a glycine-rich region in the central part of AdoHcyase, which is thought to be involved in NAD-binding.
    
    
  
    
      Molecular Function
      adenosylhomocysteinase activity
    
    
      Biological Process
      one-carbon metabolic process
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Sganga MW, Aksamit RR, Cantoni GL, Bauer CE.
      Mutational and nucleotide sequence analysis of S-adenosyl-L-homocysteine hydrolase from Rhodobacter capsulatus.
      
      Proc. Natl. Acad. Sci. U.S.A.
      
      1992
    
  
  
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  Uncharacterised lipoprotein MG045
  

      Mycoplasma genitalium has the smallest known genome of any free-living organism. Its complete genome sequence has been determined by whole-genome random sequencing and assembly []. Only 470 putative coding regions were identified, including genes for DNA replication, transcription and translation, DNA repair, cellular transport and energy metabolism []. A hypothetical protein from the MG045 gene [] has a homologue of similarly unknown function in M.pneumoniae; these, in turn, share regions of similarity with a family of putative lipoproteins from Ureaplasma parvum and Ureaplasma urealyticum. 
    
    
  
    
      Cellular Component
      membrane
    
  
  
    
      
    
  
  
    
      Peterson SN, Hu PC, Bott KF, Hutchison CA 3rd.
      A survey of the Mycoplasma genitalium genome by using random sequencing.
      
      J. Bacteriol.
      
      1993
    
    
      Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, Fritchman RD, Weidman JF, Small KV, Sandusky M, Fuhrmann J, Nguyen D, Utterback TR, Saudek DM, Phillips CA, Merrick JM, Tomb JF, Dougherty BA, Bott KF, Hu PC, Lucier TS, Peterson SN, Smith HO, Hutchison CA 3rd, Venter JC.
      The minimal gene complement of Mycoplasma genitalium.
      
      Science
      
      1995
    
  
  
    
  
  
    
  
  
    
  
    

  Peptidase A24A, prepilin type IV
  

    In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:
    

      
 
    • Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.
      • 

    • Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.
      • 

    

    In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and  binding. 
    

    Aspartic endopeptidases   of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ].
    

    Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases.
All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure.
    

    This group of aspartic endopeptidases belong to MEROPS peptidase family A24 (type IV prepilin peptidase family, clan AD), subfamily A24A.
    

    Bacteria produce a number of protein precursors that undergo post-translational methylation and proteolysis prior to secretion as active
proteins. Type IV prepilin leader peptidases are enzymes that mediate this type of post-translational modification. Type IV pilin is a protein found on the surface of Pseudomonas aeruginosa, Neisseria gonorrhoeae and other Gram-negative
pathogens. Pilin subunits attach the infecting organism to the surface of
host epithelial cells. They are synthesised as prepilin subunits, which
differ from mature pilin by virtue of containing a 6-8 residue leader
peptide consisting of charged amino acids. Mature type IV pilins also
contain a methylated N-terminal phenylalanine residue.
    

     The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin    precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of                        Gram-negative pathogens. Following removal of the leader peptides, the same  enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue []. 
    
    
  
    
      Molecular Function
      aspartic-type endopeptidase activity
    
    
      Cellular Component
      membrane
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Szecsi PB.
      The aspartic proteases.
      
      Scand. J. Clin. Lab. Invest. Suppl.
      
      1992
    
    
      Bardy SL, Jarrell KF.
      Cleavage of preflagellins by an aspartic acid signal peptidase is essential for flagellation in the archaeon Methanococcus voltae.
      
      Mol. Microbiol.
      
      2003
    
    
      Lory S, Strom MS.
      Structure-function relationship of type-IV prepilin peptidase of Pseudomonas aeruginosa--a review.
      
      Gene
      
      1997
    
    
      LaPointe CF, Taylor RK.
      The type 4 prepilin peptidases comprise a novel family of aspartic acid proteases.
      
      J. Biol. Chem.
      
      2000
    
    
      Ng SY, Chaban B, Jarrell KF.
      Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications.
      
      J. Mol. Microbiol. Biotechnol.
      
      2006
    
  
  
    
  
  
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  Neurokinin NK1 receptor
  

    G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). 
    

    The rhodopsin-like GPCRs themselves represent a widespread protein family that includes hormone, neurotransmitter and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide-binding (G) proteins. Although their activating ligands vary widely in structure and character, the amino acid sequences of the receptors are very similar and are believed to adopt a common structural framework comprising 7
transmembrane (TM) helices [, , ].
    

    Neuropeptide receptors are present in very small quantities in the cell
and are embedded tightly in the plasma membrane. The neuropeptides exhibit
a high degree of functional diversity through both regulation of peptide
production and through peptide-receptor interaction []. The mammalian
tachykinin system consists of 3 distinct peptides: substance P, substance
K and neuromedin K. All possess a common spectrum of biological activities,
including sensory transmission in the nervous system and contraction/
relaxation of peripheral smooth muscles, and each interacts with a
specific receptor type.
    

    In the brain, high concentrations of the NK1 receptor are found in striatum,
olfactory bulb, dendate gyrus, locus coeruleus and spinal chord []. In
peripheral tissues NK1 receptors are found in smooth muscle (e.g., ileum
and bladder), enteric neurons, secretory glands (e.g. parotid), cells of
the immune system and vascular endothelium. NK1 receptors activate the
phosphoinositide pathway through a pertussis-toxin-insensitive G-protein [].
    
    
  
    
      Molecular Function
      tachykinin receptor activity
    
    
      Cellular Component
      plasma membrane
    
    
      Biological Process
      G-protein coupled receptor protein signaling pathway
    
    
      Cellular Component
      integral to membrane
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Birnbaumer L.
      G proteins in signal transduction.
      
      Annu. Rev. Pharmacol. Toxicol.
      
      1990
    
    
      Casey PJ, Gilman AG.
      G protein involvement in receptor-effector coupling.
      
      J. Biol. Chem.
      
      1988
    
    
      Yokota Y, Sasai Y, Tanaka K, Fujiwara T, Tsuchida K, Shigemoto R, Kakizuka A, Ohkubo H, Nakanishi S.
      Molecular characterization of a functional cDNA for rat substance P receptor.
      
      J. Biol. Chem.
      
      1989
    
    
      Attwood TK, Findlay JB.
      Design of a discriminating fingerprint for G-protein-coupled receptors.
      
      Protein Eng.
      
      1993
    
    
      Attwood TK, Findlay JB.
      Fingerprinting G-protein-coupled receptors.
      
      Protein Eng.
      
      1994
    
    
      Yip J, Chahl LA.
      Localization of tachykinin receptors and Fos-like immunoreactivity induced by substance P in guinea-pig brain.
      
      Clin. Exp. Pharmacol. Physiol.
      
      2000
    
    
      Gilbert R, Ryan JS, Horackova M, Smith FM, Kelly ME.
      Actions of substance P on membrane potential and ionic currents in guinea pig stellate ganglion neurons.
      
      Am. J. Physiol.
      
      1998
    
  
  
    
  
  
    
  
  
    
    
  
  
    
    
    
    
    
  
    

  Helix-turn-helix motif, lambda-like repressor
  
Helix-turn-helix (HTH) motifs are found in all known DNA binding proteins
that regulate gene expression. The motif consists of approximately 20 
residues and is characterised by 2 alpha-helices, which make intimate 
contacts with the DNA and are joined by a short turn. The second helix of 
the HTH motif binds to DNA via a number of hydrogen bonds and hydrophobic 
interactions, which occur between specific side chains and the exposed 
bases and thymine methyl groups within the major groove of the DNA []. The
first helix helps to stabilise the structure []. 

    The HTH motif is very similar in sequence and structure to the N-terminal 
region of the lamda [] and other repressor proteins, and has also been 
identified in many other DNA-binding proteins on the basis of sequence and 
structural similarity []. One of the principal differences between HTH 
motifs in these different proteins arises from the stereochemical 
requirement for glycine in the turn, which is needed to avoid steric 
interference of the beta-carbon with the main chain: for cro and other 
repressors the Gly appears to be mandatory, while for many of the homeotic
and other DNA-binding proteins the requirement is relaxed.
    
    
  
    
      Molecular Function
      transcription factor activity
    
    
      Cellular Component
      nucleus
    
    
      Biological Process
      regulation of transcription, DNA-dependent
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Pabo CO, Sauer RT.
      Protein-DNA recognition.
      
      Annu. Rev. Biochem.
      
      1984
    
    
      Brennan RG, Matthews BW.
      The helix-turn-helix DNA binding motif.
      
      J. Biol. Chem.
      
      1989
    
    
      Sauer RT, Yocum RR, Doolittle RF, Lewis M, Pabo CO.
      Homology among DNA-binding proteins suggests use of a conserved super-secondary structure.
      
      Nature
      
      1982
    
  
  
    
  
  
    
    
    
    
    
    
    
    
  
  
    
  
  
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  IQ calmodulin-binding region
  

    Calmodulin (CaM) is recognised as a major calcium sensor and orchestrator of  regulatory events through its interaction with a diverse group of cellular proteins. Three classes of recognition motifs exist for many of the known CaM binding proteins; the IQ motif as a consensus for Ca2+-independent binding and two related motifs for Ca2+-dependent binding, termed
18-14 and 1-5-10 based on the position of conserved hydrophobic residues [].
    

    The regulatory domain of scallop myosin is a three-chain protein complex that
 switches on this motor in response to Ca2+ binding. Side-chain interactions link the two light chains in tandem to adjacent segments of the heavy chain bearing the IQ-sequence motif. The Ca2+-binding site is a novel EF-hand motif on the  essential light chain and is stabilised by linkages involving the heavy chain and both light chains, accounting for the requirement of all three chains for Ca2+ binding and regulation in the intact myosin molecule [].
    
    
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Rhoads AR, Friedberg F.
      Sequence motifs for calmodulin recognition.
      
      FASEB J.
      
      1997
    
    
      Xie X, Harrison DH, Schlichting I, Sweet RM, Kalabokis VN, Szent-Gyorgyi AG, Cohen C.
      Structure of the regulatory domain of scallop myosin at 2.8 A resolution.
      
      Nature
      
      1994
    
  
  
    
  
  
    
    
    
    
    
    
    
    
  
  
    
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  Electron transfer flavoprotein, beta-subunit, conserved site
  
The electron  transfer flavoprotein (ETF) [, ]
serves as a  specific electron
acceptor for various mitochondrial dehydrogenases.  ETF transfers electrons to
the  main  respiratory chain  via  ETF-ubiquinone  oxidoreductase.  ETF  is an
heterodimer that consist of  an  alpha  and  a beta subunit and which bind one
molecule of FAD per dimer. A similar system also exists in some bacteria.
The beta  subunit  of  ETF  is  a protein of about 28 Kd which is structurally
related to  the  bacterial  nitrogen  fixation protein fixA which could play a
role in a redox process and feed electrons to ferredoxin.
The beta subunit protein is distantly related to and forms a
heterodimer with the alpha subunit .

  
    
      Molecular Function
      electron carrier activity
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Finocchiaro G, Ikeda Y, Ito M, Tanaka K.
      Biosynthesis, molecular cloning and sequencing of electron transfer flavoprotein.
      
      Prog. Clin. Biol. Res.
      
      1990
    
    
      Tsai MH, Saier MH Jr.
      Phylogenetic characterization of the ubiquitous electron transfer flavoprotein families ETF-alpha and ETF-beta.
      
      Res. Microbiol.
      
      1995
    
  
  
    
    
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  


  Potex/carlavirus coat protein
  

    Potexviruses and Carlaviruses are plant-infecting viruses whose genome consist of a single-stranded RNA molecule encapsided in a coat protein. The genome of many Potexviruses is known  and their coat protein sequence has been shown to be rather well conserved []. The same observation applies to the coat protein of a variety of Carlaviruses whose sequences are related to those of Potexviruses [, ]. The coat proteins of Potexviruses and of Carlaviruses
contain from 190 to 300 amino acid residues. The best conserved region of these coat proteins is located in the central part.
    
    
  
    
      Molecular Function
      structural molecule activity
    
    
      Cellular Component
      viral capsid
    
  
  
    
      
    
  
  
    
      MacKenzie DJ, Tremaine JH, Stace-Smith R.
      Organization and interviral homologies of the 3'-terminal portion of potato virus S RNA.
      
      J. Gen. Virol.
      
      1989
    
    
      Abouhaidar MG, Lai R.
      Nucleotide sequence of the 3'-terminal region of clover yellow mosaic virus RNA.
      
      J. Gen. Virol.
      
      1989
    
    
      Henderson J, Gibbs MJ, Edwards ML, Clarke VA, Gardner KA, Cooper JI.
      Partial nucleotide sequence of poplar mosaic virus RNA confirms its classification as a carlavirus.
      
      J. Gen. Virol.
      
      1992
    
  
  
    
    
    
  
  
    
    
    
    
  
  
    
  
    

  Pyrimidine-nucleoside phosphorylase
  

    Two highly similar activities are represented in this group: thymidine phosphorylase (TP, gene deoA, ) and pyrimidine-nucleoside phosphorylase (PyNP, gene pdp, ). Both are dimeric enzymes that function in the salvage pathway to catalyse the reversible phosphorolysis of pyrimidine nucleosides to the free base and sugar moieties. In the case of thymidine phosphorylase, thymidine (and to a lesser extent, 2'-deoxyuridine) is lysed to produce thymine (or uracil) and 2'-deoxyribose-1-phosphate. Pyrimidine-nucleoside phosphorylase performs the analogous reaction on thymidine (to produce the same products) and uridine (to produce uracil and ribose-1-phosphate). PyNP is typically the only pyrimidine nucleoside phosphorylase encoded by Gram positive bacteria, while eukaryotes and proteobacteria encode two: TP, and the unrelated uridine phosphorylase. In humans, TP was originally characterised as platelet-derived endothelial cell growth factor and gliostatin []. Structurally, the enzymes are homodimers, each composed of a rigid all alpha-helix lobe and a mixed alpha-helix/beta-sheet lobe, which are connected by a flexible hinge [, ]. Prior to substrate binding, the lobes are separated by a large cleft. A functional active site and subsequent catalysis occurs upon closing of the cleft. The active site, composed of a phosphate binding site and a (deoxy)ribonucleotide binding site within the cleft region, is highly conserved between the two enzymes of this group. Active site residues (Escherichia coli DeoA numbering) include the phosphate binding Lys84 and Ser86 (close to a glycine-rich loop), Ser113, and Thr123, and the pyrimidine nucleoside-binding Arg171, Ser186, and Lys190. Sequence comparison between the active site residues for both enzymes reveals only one difference [], which has been proposed to partially mediate substrate specificity. In TP, position 111 is a methionine, while the analogous position in PyNP is lysine. It should be noted that the uncharacterised archaeal members of this family differ in a number of respects from either of the characterised activities. The residue at position 108 is lysine, indicating the activity might be PyNP-like (though the determinants of substrate specificity have not been fully elucidated). Position 171 is glutamate (negative charge side chain) rather than arginine (positive charge side chain). In addition, a large loop that may "lock in" the substrates within the active site is much smaller than in the characterised members. It is not clear what effect these and other differences have on activity and specificity.
    
    
  
    
      Biological Process
      pyrimidine base metabolic process
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Griffiths L, Stratford IJ.
      Platelet-derived endothelial cell growth factor thymidine phosphorylase in tumour growth and response to therapy.
      
      Br. J. Cancer
      
      1997
    
    
      Pugmire MJ, Cook WJ, Jasanoff A, Walter MR, Ealick SE.
      Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase.
      
      J. Mol. Biol.
      
      1998
    
    
      Pugmire MJ, Ealick SE.
      The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation.
      
      Structure
      
      1998
    
  
  
    
    
  
  
    
    
    
    
    
  
  
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
  
  
    
    
  
    

  Ribosomal protein L31e
  

    Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ].  About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. 
    

    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ].
    

    A number of eukaryotic and archaebacterial large subunit ribosomal
proteins can be grouped on the basis of sequence similarities.
These proteins have 87 to 128 amino-acid residues. This family consists of:

  • Yeast L34
    • 

  • Archaeal L31 []
    • 

  • Plants L31
    • 

  • Mammalian L31 []
    • 
    
    
    
  
    
      Molecular Function
      structural constituent of ribosome
    
    
      Cellular Component
      intracellular
    
    
      Cellular Component
      ribosome
    
    
      Biological Process
      translation
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Bergmann U, Arndt E.
      Evidence for an additional archaebacterial gene cluster in Halobacterium marismortui encoding ribosomal proteins HL46e and HL30.
      
      Biochim. Biophys. Acta
      
      1990
    
    
      Tanaka T, Kuwano Y, Kuzumaki T, Ishikawa K, Ogata K.
      Nucleotide sequence of cloned cDNA specific for rat ribosomal protein L31.
      
      Eur. J. Biochem.
      
      1987
    
    
      Ramakrishnan V, Moore PB.
      Atomic structures at last: the ribosome in 2000.
      
      Curr. Opin. Struct. Biol.
      
      2001
    
    
      Maguire BA, Zimmermann RA.
      The ribosome in focus.
      
      Cell
      
      2001
    
    
      Chandra Sanyal S, Liljas A.
      The end of the beginning: structural studies of ribosomal proteins.
      
      Curr. Opin. Struct. Biol.
      
      2000
    
  
  
    
  
  
    
    
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  Restriction endonuclease, type I, S subunit, EcoBI
  

    There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below:
    

    
      
      

    • Type I enzymes () cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase () activities.
      • 

    • Type II enzymes () cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.
      • 

    • Type III enzymes () cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it);  S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase ().
      • 

    • Type IV enzymes target methylated DNA.
      • 

    
    
    

    Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (), methylase () and ATPase activities [, ]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID.
    

    This entry represents the S subunit of type I restriction endonucleases such as EcoBI and EcoKI (), which recognise the DNA sequence 5' TGAN(8)TGCT and 5'-AACN(6)GTGC, respectively [, ]. The M and S subunits together form a methyltransferase that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. In the presence of the R subunit the complex can also act as an endonuclease, binding to the same target sequence but cutting the DNA some distance from this site. Whether the DNA is cut or modified depends on the methylation state of the target sequence: when the target site is unmodified, the DNA is cut; when the target site is hemi-methylated, the complex acts as a maintenance methyltransferase to modify the DNA, methylating both strands []. Most of the proteins in this family have two copies of the domain.
    
    
  
    
      Molecular Function
      DNA binding
    
    
      Biological Process
      DNA modification
    
  
  
    
      
    
    
      
    
  
  
    
      Janscak P, Bickle TA.
      The DNA recognition subunit of the type IB restriction-modification enzyme EcoAI tolerates circular permutions of its polypeptide chain.
      
      J. Mol. Biol.
      
      1998
    
    
      Sistla S, Rao DN.
      S-Adenosyl-L-methionine-dependent restriction enzymes.
      
      Crit. Rev. Biochem. Mol. Biol.
      
      2004
    
    
      Bourniquel AA, Bickle TA.
      Complex restriction enzymes: NTP-driven molecular motors.
      
      Biochimie
      
      2002
    
    
      Williams RJ.
      Restriction endonucleases: classification, properties, and applications.
      
      Mol. Biotechnol.
      
      2003
    
    
      Kasarjian JK, Kodama Y, Iida M, Matsuda K, Ryu J.
      Four new type I restriction enzymes identified in Escherichia coli clinical isolates.
      
      Nucleic Acids Res.
      
      2005
    
    
      Cajthamlova K, Sisakova E, Weiser J, Weiserova M.
      Phosphorylation of Type IA restriction-modification complex enzyme EcoKI on the HsdR subunit.
      
      FEMS Microbiol. Lett.
      
      2007
    
  
  
    
  
  
    
  
  
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
  
    

  Ribulose-phosphate 3-epimerase
  
Ribulose-phosphate 3-epimerase () (also known as pentose-5-phosphate 3-epimerase or PPE) is  the enzyme  that  converts D-ribulose 5-phosphate into D-xylulose 5-phosphate in  Calvin's  reductive  pentose  phosphate  cycle.  In Ralstonia eutropha (Alcaligenes eutrophus) two  copies of the gene coding for PPE are known [], one is  chromosomally  encoded , the other one is on a plasmid . PPE has  been  found  in  a  wide  range of bacteria, archaebacteria, fungi and plants. All the proteins have from 209 to 241 amino acid residues. The enzyme has a TIM barrel structure.

  
    
      Molecular Function
      ribulose-phosphate 3-epimerase activity
    
    
      Biological Process
      carbohydrate metabolic process
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Kusian B, Yoo JG, Bednarski R, Bowien B.
      The Calvin cycle enzyme pentose-5-phosphate 3-epimerase is encoded within the cfx operons of the chemoautotroph Alcaligenes eutrophus.
      
      J. Bacteriol.
      
      1992
    
  
  
    
  
  
    
    
    
    
    
  
  
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  


  Interleukin 8B receptor
  

    G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). 
    

    The rhodopsin-like GPCRs themselves represent a widespread protein family that includes hormone, neurotransmitter and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide-binding (G) proteins. Although their activating ligands vary widely in structure and character, the amino acid sequences of the receptors are very similar and are believed to adopt a common structural framework comprising 7
transmembrane (TM) helices [, , ].
    

    Interleukin-8 (IL8) is a pro-inflammatory cytokine involved in the cellular
response to inflammation, being a powerful chemoattractant for neutrophils
[]. There are 2 similar cell surface receptors for IL8: type 1 (IL-8RA) is
a high affinity receptor for IL8 alone; while type 2 (IL-8RB) is a high
affinity receptor for IL8, growth related gene (GRO) and neutrophil-activating protein-2 (NAP-2). The affinity of type 1 receptors for IL8 is
higher than that of type 2 receptors [, ]. The receptors are coupled to
Bordetella pertussis toxin-sensitive GTP-binding proteins []. Signal
transduction depends on the activation of a phospholipase C specific for
phosphatidylinositol-4,5-bisphosphate, producing 2 second messengers:
inositol triphosphate and diacylglycerol []. Inositol triphosphate induces
a rise in the levels of cytosolic free calcium, while diacylglycerol
activates protein kinase C, leading to activation of neutrophils [].
    

    IL8RB receptors are found in high density in neutrophils, monocytes,
basophils, and melanoma cells, and in lower density in T-cells. IL8
has been reported to stimulate the phosphoinositide pathway through an
uncharacterised G-protein; pertussis toxin also inhibits several of its
actions []. The IL8RB receptor shares around 80% similarity with the
IL8RA receptor.
    
    
  
    
      Molecular Function
      interleukin-8 receptor activity
    
    
      Biological Process
      chemotaxis
    
    
      Cellular Component
      integral to membrane
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Birnbaumer L.
      G proteins in signal transduction.
      
      Annu. Rev. Pharmacol. Toxicol.
      
      1990
    
    
      Baggiolini M, Clark-Lewis I.
      Interleukin-8, a chemotactic and inflammatory cytokine.
      
      FEBS Lett.
      
      1992
    
    
      Mollereau C, Muscatelli F, Mattei MG, Vassart G, Parmentier M.
      The high-affinity interleukin 8 receptor gene (IL8RA) maps to the 2q33-q36 region of the human genome: cloning of a pseudogene (IL8RBP) for the low-affinity receptor.
      
      Genomics
      
      1993
    
    
      Casey PJ, Gilman AG.
      G protein involvement in receptor-effector coupling.
      
      J. Biol. Chem.
      
      1988
    
    
      Attwood TK, Findlay JB.
      Design of a discriminating fingerprint for G-protein-coupled receptors.
      
      Protein Eng.
      
      1993
    
    
      Attwood TK, Findlay JB.
      Fingerprinting G-protein-coupled receptors.
      
      Protein Eng.
      
      1994
    
    
      Holmes WE, Lee J, Kuang WJ, Rice GC, Wood WI.
      Structure and functional expression of a human interleukin-8 receptor.
      
      Science
      
      1991
    
    
      Watson S, Arkinstall S.
      Chemokines.
      ISBN:0127384405
      
      1994
    
  
  
    
  
  
    
  
  
    
    
  
  
    
    
    
    
    
  
    

  Zinc finger, AN1-type
  

    Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [].  Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. 
    

    This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 , a ubiquitin-like
protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms.
    

    Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include:
    

    

      

    • Ascidian posterior end mark 6 (pem-6) protein  [].
      • 

    • Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis [].
      • 

    • Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 [].
      • 

    
    
    

    More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
    
    
  
    
      Molecular Function
      zinc ion binding
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Linnen JM, Bailey CP, Weeks DL.
      Two related localized mRNAs from Xenopus laevis encode ubiquitin-like fusion proteins.
      
      Gene
      
      1993
    
    
      Matthews JM, Sunde M.
      Zinc fingers--folds for many occasions.
      
      IUBMB Life
      
      2002
    
    
      Satou Y, Satoh N.
      Posterior end mark 2 (pem-2), pem-4, pem-5, and pem-6: maternal genes with localized mRNA in the ascidian embryo.
      
      Dev. Biol.
      
      1997
    
    
      Duan W, Sun B, Li TW, Tan BJ, Lee MK, Teo TS.
      Cloning and characterization of AWP1, a novel protein that associates with serine/threonine kinase PRK1 in vivo.
      
      Gene
      
      2000
    
    
      Liepinsh E, Leonchiks A, Sharipo A, Guignard L, Otting G.
      Solution structure of the R3H domain from human Smubp-2.
      
      J. Mol. Biol.
      
      2003
    
    
      Gamsjaeger R, Liew CK, Loughlin FE, Crossley M, Mackay JP.
      Sticky fingers: zinc-fingers as protein-recognition motifs.
      
      Trends Biochem. Sci.
      
      2007
    
    
      Hall TM.
      Multiple modes of RNA recognition by zinc finger proteins.
      
      Curr. Opin. Struct. Biol.
      
      2005
    
    
      Brown RS.
      Zinc finger proteins: getting a grip on RNA.
      
      Curr. Opin. Struct. Biol.
      
      2005
    
    
      Klug A.
      Zinc finger peptides for the regulation of gene expression.
      
      J. Mol. Biol.
      
      1999
    
    
      Laity JH, Lee BM, Wright PE.
      Zinc finger proteins: new insights into structural and functional diversity.
      
      Curr. Opin. Struct. Biol.
      
      2001
    
    
      McDowall J.
      Protein of the Month: Zinc Fingers.
      http://www.ebi.ac.uk/interpro/potm/2007_3/Page1.htm
      2007
    
    
      Huang J, Teng L, Li L, Liu T, Li L, Chen D, Xu LG, Zhai Z, Shu HB.
      ZNF216 Is an A20-like and IkappaB kinase gamma-interacting inhibitor of NFkappaB activation.
      
      J. Biol. Chem.
      
      2004
    
    
      Vij S, Tyagi AK.
      Genome-wide analysis of the stress associated protein (SAP) gene family containing A20/AN1 zinc-finger(s) in rice and their phylogenetic relationship with Arabidopsis.
      
      Mol. Genet. Genomics
      
      2006
    
  
  
    
    
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  NUDIX hydrolase, NudL, conserved site
  

    Nudix hydrolases, which are commonly found in all kingdoms of life, are pyrophosphohydrolases predominantly acting on substrates that contain a nucleotide diphosphate linked to another moiety X [, ]. These substrates include nucleoside triphosphates, nucleotide sugars, dinucleoside polyphosphates, dinucleotide coenzymes and capped RNAs. In some cases, phosphohydrolase activity has been observed with nucleoside diphopshates and some non-nucletoide substrates. These enzymes posses an almost universally conserved, charateristic twenty-three-amino acid motif, Gx(5)Ex(5)[UA]xREx(2)EExGU (where U is an aliphatic, hydrophobic amino acid residue), necessary for catalytic activity. Some members of this family protect cells by degrading potentially mutagenic oxidised nucleotides, while others control the levels of metabolic intermediates and signalling compounds.
     

    This entry represents a number of proteins which contain the characteristic Nudix domain. One of the characterised protein in this entry, PCD1, is a peroxisomal coenzyme A (CoA) diphosphatase catalysing the cleavage of coenzyme A into ADP and phosphopantetheine, with a strong preference for oxidised CoA disulphide as its substrate []. PCD1 may function, therefore, to maintain the capacity for beta-oxidation of fatty acids. It has also been shown to degrade oxo-dGTP and so may also be involved in protecting the cell from mutagenic oxidised nucleotides [].
    
    
  
    
      Molecular Function
      magnesium ion binding
    
    
      Biological Process
      nucleoside diphosphate metabolic process
    
    
      Molecular Function
      hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
    
    
      Molecular Function
      manganese ion binding
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Bessman MJ, Frick DN, O'Handley SF.
      The MutT proteins or "Nudix" hydrolases, a family of versatile, widely distributed, "housecleaning" enzymes.
      
      J. Biol. Chem.
      
      1996
    
    
      McLennan AG.
      The Nudix hydrolase superfamily.
      
      Cell. Mol. Life Sci.
      
      2006
    
    
      Nunoshiba T, Ishida R, Sasaki M, Iwai S, Nakabeppu Y, Yamamoto K.
      A novel Nudix hydrolase for oxidized purine nucleoside triphosphates encoded by ORFYLR151c (PCD1 gene) in Saccharomyces cerevisiae.
      
      Nucleic Acids Res.
      
      2004
    
    
      Cartwright JL, Gasmi L, Spiller DG, McLennan AG.
      The Saccharomyces cerevisiae PCD1 gene encodes a peroxisomal nudix hydrolase active toward coenzyme A and its derivatives.
      
      J. Biol. Chem.
      
      2000
    
  
  
    
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  BCCT transporter
  

    These  prokaryotic transport proteins belong to a family known as BCCT (for Betaine /
Carnitine / Choline Transporters) and are specific for compounds containing
a quaternary nitrogen atom. The BCCT proteins contain 12 transmembrane regions
and are energized by proton symport. They contain a conserved region with four
tryptophans in their central region [].
    
    
  
    
      Molecular Function
      transporter activity
    
    
      Biological Process
      transport
    
    
      Cellular Component
      membrane
    
  
  
    
      
    
  
  
    
      Kappes RM, Kempf B, Bremer E.
      Three transport systems for the osmoprotectant glycine betaine operate in Bacillus subtilis: characterization of OpuD.
      
      J. Bacteriol.
      
      1996
    
  
  
    
  
  
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
    
  
    

  SWAP/Surp
  
SWAP is derived from the Suppressor-of-White-APricot splicing
                       regulator from Drosophila melanogaster. The domain is found in regulators responsible for pervasive, nonsex-specific alternative pre-mRNA
                       splicing characteristics and has been found in splicing regulatory proteins []. These ancient, conserved
                       SWAP proteins share a colinearly arrayed series of novel
                       sequence motifs [].

  
    
      Molecular Function
      RNA binding
    
    
      Biological Process
      RNA processing
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Denhez F, Lafyatis R.
      Conservation of regulated alternative splicing and identification of functional domains in vertebrate homologs to the Drosophila splicing regulator, suppressor-of-white-apricot.
      
      J. Biol. Chem.
      
      1994
    
    
      Spikes DA, Kramer J, Bingham PM, Van Doren K.
      SWAP pre-mRNA splicing regulators are a novel, ancient protein family sharing a highly conserved sequence motif with the prp21 family of constitutive splicing proteins.
      
      Nucleic Acids Res.
      
      1994
    
  
  
    
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  


  Thymidylate kinase-like
  

    Thymidylate kinase (; dTMP kinase) catalyzes the phosphorylation of  thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) in the presence of ATP and magnesium: 
    

ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate 


    Thymidylate kinase is an ubiquitous enzyme of about 25 Kd and is important in the dTTP synthesis pathway for DNA synthesis. The function of dTMP kinase in eukaryotes comes from the study of a cell cycle mutant, cdc8, in Saccharomyces cerevisiae. Structural and functional analyses suggest that the cDNA codes for authentic human dTMP kinase. The mRNA levels and enzyme activities corresponded to cell cycle progression and cell growth stages[]. 
    

    This entry reprsents known and predicted kinases, and related enzymes such as UMP-CMP kinase.
    
    
  
    
      Molecular Function
      ATP binding
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Huang SH, Tang A, Drisco B, Zhang SQ, Seeger R, Li C, Jong A.
      Human dTMP kinase: gene expression and enzymatic activity coinciding with cell cycle progression and cell growth.
      
      DNA Cell Biol.
      
      1994
    
  
  
    
    
  
  
    
  
  
    
  
  
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
  
    

  NLP/P60
  

    The Escherichia coli  NLPC/Listeria P60 domain occurs at the C terminus of a number of different bacterial and viral proteins. The viral proteins are either described as tail assembly proteins or Gp19. In bacteria, the proteins are variously described as being putative tail component of prophage, invasin, invasion associated protein, putative lipoprotein, cell wall hydrolase, or putative endopeptidase. 
    

    The E. coli NLPC/Listeria P60 domain is contained within the boundaries of the cysteine peptidase domain that defines the MEROPS peptidase family C40 (clan C-). A type example being dipeptidyl-peptidase VI from Bacillus sphaericus and gamma-glutamyl-diamino acid-endopeptidase precursor from Lactococcus lactis . This group also contains proteins classified as non-peptidase homologues in that they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the C40 family.

    
    
  
    
      
    
    
      
    
  
  
  
    
  
  
    
  
  
    
    
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  Obesity factor
  
Leptin, a metabolic monitor of food intake and energy need, is expressed
by the ob obesity gene. The protein may function as part of a signalling
pathway from adipose tissue that acts to regulate the size of the body
fat depot [], the hormone effectively turning the brain's appetite
message off when it senses that the body is satiated. Obese humans have
high levels of the protein, suggesting a similarity to type II (adult
onset) diabetes, in which sufferers over-produce insulin, but can't respond
to it metabolically - they have become insulin resistant. Similarly, it is
thought that obese individuals may be leptin resistant.

  
    
      Molecular Function
      hormone activity
    
    
      Cellular Component
      extracellular region
    
    
      Biological Process
      signal transduction
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Zhang Y, Proenca R, Maffei M, Barone M, Leopold L, Friedman JM.
      Positional cloning of the mouse obese gene and its human homologue.
      
      Nature
      
      1994
    
  
  
    
  
  
    
    
    
    
    
  
  
    
    
  
  
    
    
    
  
  
    
    
    
    
    
  


  Antenna complex, alpha/beta subunit
  
In photosynthetic bacteria the antenna complexes function as light-harvesting
systems that absorb light radiation and transfer the  excitation energy to the
reaction centres. The  antenna complexes  are  generally composed of two
polypeptides (alpha and beta chains); two  or three bacteriochlorophyll (BChl)
molecules and some carotenoids [, ].
Both the  alpha and the beta chains of antenna complexes are small proteins of
42 to  68  residues which share a three-domain organisation. They are composed
of a  N-terminal  hydrophilic  cytoplasmic  domain followed by a transmembrane
region and  a  C-terminal hydrophilic periplasmic domain. In the transmembrane
region of  both  chains  there is a conserved histidine which is most probably
involved in  the binding of the magnesium atom of a bacteriochlorophyll group.
The beta  chains contain an additional conserved histidine which is located at
the C-terminal extremity  of the  cytoplasmic domain and which is also thought
to be involved in bacteriochlorophyll-binding.

  
    
      Cellular Component
      integral to membrane
    
    
      Biological Process
      photosynthesis, light reaction
    
    
      Cellular Component
      plasma membrane light-harvesting complex
    
    
      Molecular Function
      electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
    
  
  
    
      
    
  
  
    
      Wagner-Huber R, Brunisholz RA, Bissig I, Frank G, Suter F, Zuber H.
      The primary structure of the antenna polypeptides of Ectothiorhodospira halochloris and Ectothiorhodospira halophila. Four core-type antenna polypeptides in E. halochloris and E. halophila.
      
      Eur. J. Biochem.
      
      1992
    
    
      Brunisholz RA, Zuber H.
      Structure, function and organization of antenna polypeptides and antenna complexes from the three families of Rhodospirillaneae.
      
      J. Photochem. Photobiol. B, Biol.
      
      1992
    
  
  
    
    
  
  
    
  
  
    
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  
  
    
    
  


  Flagellar FliF M-ring protein
  
This family corresponds to the FliF protein. FliF is the major protein
of the M-ring in bacterial flagellar basal body [].
The basal body consists of four rings (L,P,S and M) surrounding the
flagellar rod, which is believed to transmit motor rotation to the filament 
[]. 
The M ring is integral to the inner membrane of the cell, and may be
connected to the rod via the S (supramembrane) ring, which lies just distal
to it. The L and P rings reside in the outer membrane and periplasmic space,
respectively.
FliF lacks a signal peptide and is predicted to have considerable 
alpha-helical structure, including an N-terminal sequence that is likely
to be membrane-spanning []. Overall, however, FliF has a relatively
hydrophilic sequence, with a high charge density, especially towards its 
C terminus [].

  
    
      Biological Process
      ciliary or flagellar motility
    
    
      Molecular Function
      motor activity
    
    
      Cellular Component
      bacterial-type flagellum basal body, MS ring
    
  
  
    
      
    
  
  
    
      Jones CJ, Homma M, Macnab RM.
      L-, P-, and M-ring proteins of the flagellar basal body of Salmonella typhimurium: gene sequences and deduced protein sequences.
      
      J. Bacteriol.
      
      1989
    
    
      Homma M, Kutsukake K, Hasebe M, Iino T, Macnab RM.
      FlgB, FlgC, FlgF and FlgG. A family of structurally related proteins in the flagellar basal body of Salmonella typhimurium.
      
      J. Mol. Biol.
      
      1990
    
  
  
    
    
  
  
    
    
  
  
    
  
  
    
    
    
    
    
    
  


  GPCR, family 3, extracellular calcium-sensing receptor-related
  

    G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). 
    

    The metabotropic glutamate receptors are functionally and pharmacologically distinct from the ionotropic glutamate receptors. They are coupled to G-proteins and stimulate the inositol phosphate/Ca2+ intracellular signalling pathway [, , , ]. At least eight sub-types of metabotropic receptor (MGR1-8) have been identified in cloning studies. The sub-types differ in their agonist pharmacology and signal transduction pathways [].
    

    The calcium-sensing receptor (CaSR) is an integral membrane protein that
senses changes in the extracellular concentration of calcium ions. The
activity of the receptor is mediated by a G-protein that activates a
phosphatidyl-inositol-calcium second messenger system. The sequences of the
receptors show a high degree of similarity to the TM signature that
characterises the metabotropic glutamate receptors. In addition, the
sequences contain a large extracellular domain that includes clusters of
acidic amino acid residues, which may be involved in calcium binding [].
Defects in CaSR that result in reduced activity of the receptor cause
familial hypocalciuric hypercalcemia (FHH) and neonatal severe hyperparathyroidism (NSHPT), inherited conditions characterised by altered calcium
homeostasis [, ]. FHH-affected individuals exhibit mild or modest hypercalcemia, relative hypocalciuria and inappropriately normal PTH levels. By
contrast, NSHPT is a rare autosomal recessive life-threatening disorder
characterised by high serum calcium concentrations, skeletal demineralisation and parathyroid hyperplasia. In addition, defects resulting from
receptor activation at subnormal Ca2+ levels cause autosomal dominant
hypocalcemia [].
    

    This entry represents the extracellular calcium-sensing receptors and related proteins in GPCR family 3, such as the taste receptors.
    
    
  
    
      Molecular Function
      G-protein coupled receptor activity
    
    
      Biological Process
      G-protein coupled receptor protein signaling pathway
    
    
      Cellular Component
      integral to membrane
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Ward BK, Stuckey BG, Gutteridge DH, Laing NG, Pullan PT, Ratajczak T.
      A novel mutation (L174R) in the Ca2+-sensing receptor gene associated with familial hypocalciuric hypercalcemia.
      
      Hum. Mutat.
      
      1997
    
    
      Abe T, Sugihara H, Nawa H, Shigemoto R, Mizuno N, Nakanishi S.
      Molecular characterization of a novel metabotropic glutamate receptor mGluR5 coupled to inositol phosphate/Ca2+ signal transduction.
      
      J. Biol. Chem.
      
      1992
    
    
      Pearce SH, Trump D, Wooding C, Besser GM, Chew SL, Grant DB, Heath DA, Hughes IA, Paterson CR, Whyte MP.
      Calcium-sensing receptor mutations in familial benign hypercalcemia and neonatal hyperparathyroidism.
      
      J. Clin. Invest.
      
      1995
    
    
      Pollak MR, Brown EM, Estep HL, McLaine PN, Kifor O, Park J, Hebert SC, Seidman CE, Seidman JG.
      Autosomal dominant hypocalcaemia caused by a Ca(2+)-sensing receptor gene mutation.
      
      Nat. Genet.
      
      1994
    
    
      Brown EM, Gamba G, Riccardi D, Lombardi M, Butters R, Kifor O, Sun A, Hediger MA, Lytton J, Hebert SC.
      Cloning and characterization of an extracellular Ca(2+)-sensing receptor from bovine parathyroid.
      
      Nature
      
      1993
    
    
      Attwood TK, Findlay JB.
      Fingerprinting G-protein-coupled receptors.
      
      Protein Eng.
      
      1994
    
    
      Watson S, Arkinstall S.
      Glutamate.
      ISBN:0127384405
      
      1994
    
    
      Houamed KM, Kuijper JL, Gilbert TL, Haldeman BA, O'Hara PJ, Mulvihill ER, Almers W, Hagen FS.
      Cloning, expression, and gene structure of a G protein-coupled glutamate receptor from rat brain.
      
      Science
      
      1991
    
    
      Masu M, Tanabe Y, Tsuchida K, Shigemoto R, Nakanishi S.
      Sequence and expression of a metabotropic glutamate receptor.
      
      Nature
      
      1991
    
    
      Tanabe Y, Masu M, Ishii T, Shigemoto R, Nakanishi S.
      A family of metabotropic glutamate receptors.
      
      Neuron
      
      1992
    
  
  
    
  
  
    
  
  
    
  
  
    
  
  
    
    
  
  
    
    
    
    
    
  
  
    
  
    

  Envelope glycoprotein M, flavivirus
  

    Flaviviruses are small enveloped viruses with virions comprised of
three proteins called C, M and E [, , ]. The envelope glycoprotein M is made as a precursor, called prM. The precursor portion of the protein is the signal peptide for the proteins entry into the membrane. prM is cleaved to form M in a late-stage cleavage event.  Associated with this cleavage is a change in the infectivity and fusion activity of the virus.
    
    
  
    
      Cellular Component
      viral capsid
    
    
      Biological Process
      viral infectious cycle
    
  
  
    
      
    
  
  
    
      Heinz FX, Auer G, Stiasny K, Holzmann H, Mandl C, Guirakhoo F, Kunz C.
      The interactions of the flavivirus envelope proteins: implications for virus entry and release.
      
      Arch. Virol. Suppl.
      
      1994
    
    
      Konishi E, Mason PW.
      Proper maturation of the Japanese encephalitis virus envelope glycoprotein requires cosynthesis with the premembrane protein.
      
      J. Virol.
      
      1993
    
    
      Schalich J, Allison SL, Stiasny K, Mandl CW, Kunz C, Heinz FX.
      Recombinant subviral particles from tick-borne encephalitis virus are fusogenic and provide a model system for studying flavivirus envelope glycoprotein functions.
      
      J. Virol.
      
      1996
    
  
  
    
  
  
    
  
  
    
    
    
    
    
    
  
  
    
  
    

  Pectinesterase, catalytic
  

    Pectinesterase  (pectin methylesterase) catalyses the de-esterification of pectin into pectate and methanol. Pectin is one of the main components of the plant cell wall. In plants, pectinesterase plays an important role in cell wall metabolism during fruit ripening. In plant bacterial pathogens such as Erwinia carotovora  and  in fungal pathogens  such as Aspergillus niger, pectinesterase is involved in maceration and soft-rotting of plant tissue. Plant pectinesterases are regulated by pectinesterase inhibitors, which are ineffective against microbial enzymes [].
    

    Prokaryotic and eukaryotic pectinesterases share a few regions of sequence similarity. The crystal structure of pectinesterase from Erwinia chrysanthemi revealed a beta-helix structure similar to that found in pectinolytic enzymes, though it is different from most structures of esterases []. The putative catalytic residues are in a similar location to those of the active site and substrate-binding cleft of pectate lyase.
    
    
  
    
      Cellular Component
      cell wall
    
    
      Molecular Function
      pectinesterase activity
    
    
      Biological Process
      cell wall modification
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Di Matteo A, Giovane A, Raiola A, Camardella L, Bonivento D, De Lorenzo G, Cervone F, Bellincampi D, Tsernoglou D.
      Structural basis for the interaction between pectin methylesterase and a specific inhibitor protein.
      
      Plant Cell
      
      2005
    
    
      Jenkins J, Mayans O, Smith D, Worboys K, Pickersgill RW.
      Three-dimensional structure of Erwinia chrysanthemi pectin methylesterase reveals a novel esterase active site.
      
      J. Mol. Biol.
      
      2001
    
  
  
    
  
  
    
  
  
    
  
  
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
  
    

  Immunodeficiency lentiviral matrix, N-terminal
  

    Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different.
    

    This entry represents matrix proteins from immunodeficiency lentiviruses, such as Human immunodeficiency virus (HIV) and Simian immunodeficiency virus (SIV-cpz) []. The structure of the HIV protein consists of 5 alpha helices, a short 3.10 helix and a 3-stranded mixed beta-sheet [].
    
    
  
    
      Molecular Function
      structural molecule activity
    
  
  
    
      
    
  
  
    
      Massiah MA, Starich MR, Paschall C, Summers MF, Christensen AM, Sundquist WI.
      Three-dimensional structure of the human immunodeficiency virus type 1 matrix protein.
      
      J. Mol. Biol.
      
      1994
    
    
      Conte MR, Matthews S.
      Retroviral matrix proteins: a structural perspective.
      
      Virology
      
      1998
    
    
      Freed EO.
      HIV-1 replication.
      
      Somat. Cell Mol. Genet.
      
      2001
    
  
  
    
  
  
    
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  
    

  Platelet-derived growth factor (PDGF)
  
Platelet-derived growth factor (PDGF) [, ] is a potent mitogen  for  cells of
mesenchymal  origin,  including  smooth  muscle  cells and glial  cells.  In both mouse and human, the PDGF signalling network consists of four ligands, PDGFA-D, and two receptors, PDGFRalpha and PDGFRbeta. All PDGFs function as secreted, disulphide-linked
homodimers, but only PDGFA and B can form functional heterodimers. PDGFRs also function as homo- and heterodimers. All known PDGFs have characteristic `PDGF domains',
which include eight conserved cysteines that are involved in inter- and intramolecular bonds.
Alternate splicing of the A chain  transcript  can give rise to  two different
forms that differ only in their C-terminal extremity. The transforming protein
of Woolly monkey sarcoma virus (WMSV) (Simian sarcoma virus), encoded by the v-sis oncogene,  is derived from the B chain of PDGF.

    PDGFs are mitogenic during early developmental stages, driving the proliferation of undifferentiated mesenchyme and some progenitor populations. During later maturation stages, PDGF signalling has been implicated in tissue remodelling and cellular differentiation, and in inductive events involved in patterning and morphogenesis. In addition to driving
mesenchymal proliferation, PDGFs have been shown to direct the migration, differentiation and function of a variety of specialised mesenchymal and migratory cell types, both during development and in the
adult animal []. Other growth factors in this family include vascular endothelial growth factors B and C (VEGF-B, VEGF-C) [, ] which are active in angiogenesis and endothelial cell growth, and placenta growth factor (PlGF) which is also active in angiogenesis []. 
    

    PDGF is  structurally  related  to a number of other growth factors which also form disulphide-linked homo- or heterodimers.
    
    
  
    
      Molecular Function
      growth factor activity
    
    
      Cellular Component
      membrane
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Hannink M, Donoghue DJ.
      Structure and function of platelet-derived growth factor (PDGF) and related proteins.
      
      Biochim. Biophys. Acta
      
      1989
    
    
      Heldin CH.
      Structural and functional studies on platelet-derived growth factor.
      
      EMBO J.
      
      1992
    
    
      Joukov V, Pajusola K, Kaipainen A, Chilov D, Lahtinen I, Kukk E, Saksela O, Kalkkinen N, Alitalo K.
      A novel vascular endothelial growth factor, VEGF-C, is a ligand for the Flt4 (VEGFR-3) and KDR (VEGFR-2) receptor tyrosine kinases.
      
      EMBO J.
      
      1996
    
    
      Maglione D, Guerriero V, Viglietto G, Ferraro MG, Aprelikova O, Alitalo K, Del Vecchio S, Lei KJ, Chou JY, Persico MG.
      Two alternative mRNAs coding for the angiogenic factor, placenta growth factor (PlGF), are transcribed from a single gene of chromosome 14.
      
      Oncogene
      
      1993
    
    
      Olofsson B, Pajusola K, Kaipainen A, von Euler G, Joukov V, Saksela O, Orpana A, Pettersson RF, Alitalo K, Eriksson U.
      Vascular endothelial growth factor B, a novel growth factor for endothelial cells.
      
      Proc. Natl. Acad. Sci. U.S.A.
      
      1996
    
    
      Hoch RV, Soriano P.
      Roles of PDGF in animal development.
      
      Development
      
      2003
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  Alpha/beta hydrolase fold-1
  

    The alpha/beta hydrolase fold [] is common to a number of hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is an alpha/beta-sheet (rather than a barrel), containing 8 strands connected by helices []. The enzymes are believed to have diverged from a common ancestor, preserving the arrangement of the catalytic residues. All have a catalytic triad, the elements of which are borne on loops, which are the best conserved structural features of the fold. Esterase (EST) from Pseudomonas putida is a member of the alpha/beta hydrolase fold superfamily of enzymes [].
    

    In most of the family members the beta-strands are parallels, but some have an inversion of the first strands, which gives it an antiparallel orientation. The catalytic triad residues are presented on loops. One of these is the nucleophile elbow and is the most conserved feature of the fold. Some other members lack one or all of the catalytic residues. Some members are therefore inactive but others are involved in surface recognition. The ESTHER database [] gathers and annotates all the published information related to gene and protein sequences of this superfamily [].
    

    This entry represents fold-1 of alpha/beta hydrolase.
    
    
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J.
      The alpha/beta hydrolase fold.
      
      Protein Eng.
      
      1992
    
    
      Elmi F, Lee HT, Huang JY, Hsieh YC, Wang YL, Chen YJ, Shaw SY, Chen CJ.
      Stereoselective esterase from Pseudomonas putida IFO12996 reveals alpha/beta hydrolase folds for D-beta-acetylthioisobutyric acid synthesis.
      
      J. Bacteriol.
      
      2005
    
  
  
    
    
  
  
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
  
    

  Apolipoprotein A1/A4/E
  

     Exchangeable apolipoproteins (apoA, apoC and apoE) have the same genomic structure and are members of a multi-gene family that probably evolved from a common ancestral gene. This entry includes the ApoA1, ApoA4 and ApoE proteins. ApoA1 and ApoA4 are part of the APOA1/C3/A4/A5 gene cluster on chromosome 11 []. Apolipoproteins function in lipid transport as structural components of lipoprotein particles, cofactors for enzymes and ligands for cell-surface receptors. In particular, apoA1 is the major protein component of high-density lipoproteins; apoA4 is thought to act primarily in intestinal lipid absorption; and apoE is a blood plasma protein that mediates the transport and uptake of cholesterol and lipid by way of its high affinity interaction with different cellular receptors, including the low-density lipoprotein (LDL) receptor. Recent findings with apoA1 and apoE suggest that the tertiary structures of these two members of the human exchangeable apolipoprotein gene family are related []. The three-dimensional structure of the LDL receptor-binding domain of apoE indicates that the protein forms an unusually elongated four-helix bundle that may be stabilised by a tightly packed hydrophobic core that includes leucine zipper-type interactions and by numerous salt bridges on the mostly charged surface. Basic amino acids important for LDL receptor binding are clustered into a surface patch on one long helix [].
    
    
  
    
      Cellular Component
      extracellular region
    
    
      Biological Process
      lipid transport
    
    
      Molecular Function
      lipid binding
    
    
      Biological Process
      lipoprotein metabolic process
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Wilson C, Wardell MR, Weisgraber KH, Mahley RW, Agard DA.
      Three-dimensional structure of the LDL receptor-binding domain of human apolipoprotein E.
      
      Science
      
      1991
    
    
      Fullerton SM, Buchanan AV, Sonpar VA, Taylor SL, Smith JD, Carlson CS, Salomaa V, Stengard JH, Boerwinkle E, Clark AG, Nickerson DA, Weiss KM.
      The effects of scale: variation in the APOA1/C3/A4/A5 gene cluster.
      
      Hum. Genet.
      
      2004
    
    
      Saito H, Lund-Katz S, Phillips MC.
      Contributions of domain structure and lipid interaction to the functionality of exchangeable human apolipoproteins.
      
      Prog. Lipid Res.
      
      2004
    
  
  
    
  
  
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
  
    

  K-Cl co-transporter
  

    The K-Cl co-transporter (KCC) mediates the coupled movement of K+ and Cl-
ions across the plasma membrane of many animal cells. This transport is
involved in the regulatory volume decrease in response to cell swelling in
red blood cells, and has been proposed to play a role in the vectorial
movement of Cl- across kidney epithelia. The transport process involves one
for one electroneutral movement of K+ together with Cl-, and, in all
known mammalian cells, the net movement is outward [].
    

    In neurones, it appears to play a unique role in maintaining low
intracellular Cl-concentration, which is required for the functioning of Cl-
dependent fast synaptic inhibition, mediated by certain neurotransmitters,
such as gamma-aminobutyric acid (GABA) and glycine.
    

    Two isoforms of the K-Cl co-transporter have been described, termed KCC1 and
KCC2, containing 1085 and 1116 amino acids, respectively. They are both
predicted to have 12 transmembrane (TM) regions in a central hydrophobic
domain, together with hydrophilic N- and C-termini that are likely
cytoplasmic. Comparison of their sequences with those of other
ion-transporting membrane proteins reveals that they are part of a new
superfamily of cation-chloride co-transporters, which includes the Na-Cl and
Na-K-2Cl co-transporters. KCC1 is widely expressed in human tissues, while
KCC2 is expressed only in brain neurones, making it likely that this is the
isoform responsible for maintaining low Cl- concentration in neurones [, ].
    
    
  
    
      Molecular Function
      transporter activity
    
    
      Biological Process
      ion transport
    
    
      Cellular Component
      membrane
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Gillen CM, Brill S, Payne JA, Forbush B 3rd.
      Molecular cloning and functional expression of the K-Cl cotransporter from rabbit, rat, and human. A new member of the cation-chloride cotransporter family.
      
      J. Biol. Chem.
      
      1996
    
    
      Payne JA, Stevenson TJ, Donaldson LF.
      Molecular characterization of a putative K-Cl cotransporter in rat brain. A neuronal-specific isoform.
      
      J. Biol. Chem.
      
      1996
    
    
      Rivera C, Voipio J, Payne JA, Ruusuvuori E, Lahtinen H, Lamsa K, Pirvola U, Saarma M, Kaila K.
      The K+/Cl- co-transporter KCC2 renders GABA hyperpolarizing during neuronal maturation.
      
      Nature
      
      1999
    
  
  
    
  
  
    
  
  
    
    
  
  
    
  
  
    
  
  
    
    
    
    
    
    
    
  
  
    
  
    

  Ribosomal protein L39e
  

    Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ].  About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. 
    

    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ].
    

    A number of eukaryotic and archaebacterial large subunit ribosomal proteins can be grouped on the basis of sequence similarities.
These proteins are very basic. About 50 residues long, they are the smallest
proteins of eukaryotic-type ribosomes.
    
    
  
    
      Molecular Function
      structural constituent of ribosome
    
    
      Cellular Component
      intracellular
    
    
      Cellular Component
      ribosome
    
    
      Biological Process
      translation
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Ramakrishnan V, Moore PB.
      Atomic structures at last: the ribosome in 2000.
      
      Curr. Opin. Struct. Biol.
      
      2001
    
    
      Maguire BA, Zimmermann RA.
      The ribosome in focus.
      
      Cell
      
      2001
    
    
      Chandra Sanyal S, Liljas A.
      The end of the beginning: structural studies of ribosomal proteins.
      
      Curr. Opin. Struct. Biol.
      
      2000
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  High mobility group protein HMG14/HMG17
  

    High mobility group (HMG) proteins constitute a family of relatively low molecular weight non-histone components in chromatin. HMG14 and HMG17 are highly-similar proteins of about 100 amino acid residues; the sequence of chicken HMG14 is almost as similar to chicken HMG17 as it is to mammalian HMG14 polypeptides []. The proteins bind to the inner side of the nucleosomal DNA, altering the interaction between the DNA and the histone octamer. It is thought that they may be involved in the process that confers specific chromatin conformations to transcribable regions in the genome [].
    

    The SMART signature describes a nucleosomal binding domain, which facilitates binding of proteins to nucleosomes in chromatin. The domain is most commonly found in the high mobility group (HMG) proteins, HMG14 and HMG17, however, it is also found in other proteins which bind to nucleosomes, e.g. NBP-45. NBP-45 is a nucleosomal binding protein, first identified in mice [], which is related to HMG14 and HMG17. NBP-45 binds specifically to nucleosome core particles, and can function as a transcriptional activator. These findings led to the suggestion that this domain, common to NBP-45, HMG14 and HMG17 is responsible for binding of the proteins to nucleosomes in chromatin.
    
    
  
    
      Cellular Component
      chromatin
    
    
      Molecular Function
      DNA binding
    
    
      Cellular Component
      nucleus
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Dodgson JB, Browne DL, Black AJ.
      Chicken chromosomal protein HMG-14 and HMG-17 cDNA clones: isolation, characterization and sequence comparison.
      
      Gene
      
      1988
    
    
      Landsman D, Soares N, Gonzalez FJ, Bustin M.
      Chromosomal protein HMG-17. Complete human cDNA sequence and evidence for a multigene family.
      
      J. Biol. Chem.
      
      1986
    
    
      Shirakawa H, Landsman D, Postnikov YV, Bustin M.
      NBP-45, a novel nucleosomal binding protein with a tissue-specific and developmentally regulated expression.
      
      J. Biol. Chem.
      
      2000
    
  
  
    
    
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
  
    

  Peptidase C3, picornavirus core protein 2A
  

    In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:
    

      
 
    • Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.
      • 

    • Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.
      • 

    

    In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and  binding. 
    

    Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures.  These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. 
    

    This domain defines cysteine peptidases belong to MEROPS peptidase family C3 (picornain, clan PA(C)), subfamilies 3CA and 3CB. The protein fold of this peptidase domain for members of this family resembles that of the serine peptidase, chymotrypsin [], the type example for clan PA.
    

    Picornaviral proteins are expressed as a single polyprotein
which is cleaved by the viral 3C cysteine protease []. The poliovirus polyprotein is selectively cleaved between the Gln-|-Gly bond. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.

    
    
  
    
      Biological Process
      proteolysis
    
    
      Molecular Function
      peptidase activity
    
    
      Biological Process
      viral reproduction
    
  
  
    
      
    
  
  
    
      Zoll J, van Kuppeveld FJ, Galama JM, Melchers WJ.
      Genetic analysis of mengovirus protein 2A: its function in polyprotein processing and virus reproduction.
      
      J. Gen. Virol.
      
      1998
    
    
      Allaire M, Chernaia MM, Malcolm BA, James MN.
      Picornaviral 3C cysteine proteinases have a fold similar to chymotrypsin-like serine proteinases.
      
      Nature
      
      1994
    
    
      Barrett AJ, Rawlings ND.
      Evolutionary lines of cysteine peptidases.
      
      Biol. Chem.
      
      2001
    
  
  
    
    
  
  
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  
    

  SEA
  
SEA is an extracellular domain associated with
                       O-glycosylation [].
Proteins found to contain SEA-modules include, agrin, enterokinase, 63 kDa Strongylocentrotus purpuratus (Purple sea urchin)
 sperm protein, perlecan (heparan sulphate proteoglycan core, mucin 1 and the cell surface antigen, 114/A10, and two functionally uncharacterised,
                       probably extracellular, Caenorhabditis elegans proteins. Despite the functional
                       diversity of these adhesive proteins, a common denominator seems to be their
                       existence in heavily glycosylated environments. In addition, the better characterised
                       proteins all contain O-glycosidic-linked carbohydrates such as
                       heparan sulphate that contribute considerably to their molecular masses. The common
                       module might regulate or assist binding to neighbouring carbohydrate moieties.

    Enterokinase, the initiator of intestinal digestion, is a
             mosaic protease composed of a distinctive assortment of
             domains []. 
    
    
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Kitamoto Y, Yuan X, Wu Q, McCourt DW, Sadler JE.
      Enterokinase, the initiator of intestinal digestion, is a mosaic protease composed of a distinctive assortment of domains.
      
      Proc. Natl. Acad. Sci. U.S.A.
      
      1994
    
    
      Bork P, Patthy L.
      The SEA module: a new extracellular domain associated with O-glycosylation.
      
      Protein Sci.
      
      1995
    
  
  
    
    
    
    
    
  
  
    
    
    
  
  
    
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  Fibronectin, type I
  

    Fibronectin type I repeats are one of the three repeats found in the fibronectin protein.
               Fibronectin is a plasma protein that binds cell surfaces and various compounds
               including collagen, fibrin, heparin, DNA, and actin. Type I domain (FN1) is approximately
               40 residues in length. Four conserved cysteines are involved in disulphide bonds. The 3D
               structure of the FN1 domain has been determined [, , ]. It consists of two antiparallel
               beta-sheets, first a double-stranded one, that is linked by a disulphide bond to a
               triple-stranded beta-sheet. The second conserved disulphide bridge links the C-terminal
               adjacent strands of the domain.
    

                   In human tissue plasminogen activator chain A the FN1 domain together with the
               following epidermal growth factor (EGF)-like domain are involved in
               fibrin-binding []. It has been suggested that these two modules form a single structural
               and functional unit []. The two domains keep their specific tertiary structure, but interact
               intimately to bury a hydrophobic core; the inter-module linker makes up the third strand of
               the EGF-module's major beta-sheet.
    
    
  
    
      Cellular Component
      extracellular region
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Bennett WF, Paoni NF, Keyt BA, Botstein D, Jones AJ, Presta L, Wurm FM, Zoller MJ.
      High resolution analysis of functional determinants on human tissue-type plasminogen activator.
      
      J. Biol. Chem.
      
      1991
    
    
      Downing AK, Driscoll PC, Harvey TS, Dudgeon TJ, Smith BO, Baron M, Campbell ID.
      Solution structure of the fibrin binding finger domain of tissue-type plasminogen activator determined by 1H nuclear magnetic resonance.
      
      J. Mol. Biol.
      
      1992
    
    
      Baron M, Norman D, Willis A, Campbell ID.
      Structure of the fibronectin type 1 module.
      
      Nature
      
      1990
    
    
      Smith BO, Downing AK, Driscoll PC, Dudgeon TJ, Campbell ID.
      The solution structure and backbone dynamics of the fibronectin type I and epidermal growth factor-like pair of modules of tissue-type plasminogen activator.
      
      Structure
      
      1995
    
  
  
    
    
  
  
    
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
  
    

  PE N-terminal
  
This family is named after a PE motif near to the amino
terminus.  The carboxyl terminus of this family
are variable and fall into several classes.  The
largest class of PE proteins is the highly repetitive
PGRS class which have a high glycine content.
The function of these proteins is uncertain but it
has been suggested that they may be related to
antigenic variation of Mycobacterium tuberculosis [].

  
    
      
    
  
  
    
      Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE 3rd, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quail MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG.
      Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.
      
      Nature
      
      1998
    
  
  
    
  
  
    
    
  
  
    
    
  
  
    
  


  Bacterial DNA recombination protein RuvA
  

    In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB.
    
    
  
    
      Molecular Function
      DNA helicase activity
    
    
      Biological Process
      DNA repair
    
    
      Biological Process
      DNA recombination
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Yamada K, Miyata T, Tsuchiya D, Oyama T, Fujiwara Y, Ohnishi T, Iwasaki H, Shinagawa H, Ariyoshi M, Mayanagi K, Morikawa K.
      Crystal structure of the RuvA-RuvB complex: a structural basis for the Holliday junction migrating motor machinery.
      
      Mol. Cell
      
      2002
    
  
  
    
    
    
    
  
  
    
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
  
    

  NUDIX hydrolase domain
  
MutT is a small bacterial protein (~12-15Kd) involved in the GO system []
               responsible for removing an oxidatively damaged form of guanine (8-hydroxy-
               guanine or 7,8-dihydro-8-oxoguanine) from DNA and the nucleotide pool.
               8-oxo-dGTP is inserted opposite dA and dC residues of template DNA with near equal efficiency, leading to A.T to G.C transversions. MutT
 specifically degrades 8-oxo-dGTP to the monophosphate, with the concomitant
 release of pyrophosphate. A short conserved N-terminal region of mutT 
               (designated the MutT domain) is also found in a variety of other
               prokaryotic, viral and eukaryotic proteins [, , , ].
           
    The generic name `NUDIX hydrolases' (NUcleoside DIphosphate linked
               to some other moiety X) has been coined for this domain family []. The
               family can be divided into a number of subgroups, of which MutT anti-
               mutagenic activity represents only one type; most of the rest hydrolyse
               diverse nucleoside diphosphate derivatives (including ADP-ribose, GDP-
               mannose, TDP-glucose, NADH, UDP-sugars, dNTP and NTP).
    
    
  
    
      Molecular Function
      hydrolase activity
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Michaels ML, Miller JH.
      The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7,8-dihydro-8-oxoguanine).
      
      J. Bacteriol.
      
      1992
    
    
      Sakumi K, Furuichi M, Tsuzuki T, Kakuma T, Kawabata S, Maki H, Sekiguchi M.
      Cloning and expression of cDNA for a human enzyme that hydrolyzes 8-oxo-dGTP, a mutagenic substrate for DNA synthesis.
      
      J. Biol. Chem.
      
      1993
    
    
      Mejean V, Salles C, Bullions LC, Bessman MJ, Claverys JP.
      Characterization of the mutX gene of Streptococcus pneumoniae as a homologue of Escherichia coli mutT, and tentative definition of a catalytic domain of the dGTP pyrophosphohydrolases.
      
      Mol. Microbiol.
      
      1994
    
    
      Koonin EV.
      A highly conserved sequence motif defining the family of MutT-related proteins from eubacteria, eukaryotes and viruses.
      
      Nucleic Acids Res.
      
      1993
    
    
      Bessman MJ, Frick DN, O'Handley SF.
      The MutT proteins or "Nudix" hydrolases, a family of versatile, widely distributed, "housecleaning" enzymes.
      
      J. Biol. Chem.
      
      1996
    
    
      McLennan AG.
      The MutT motif family of nucleotide phosphohydrolases in man and human pathogens (review).
      
      Int. J. Mol. Med.
      
      1999
    
  
  
    
  
  
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
  
  
    
    
  
  
    
    
  
  
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
  
    

  Biotin/lipoyl attachment
  
The biotin / lipoyl attachment domain has a conserved lysine residue that binds biotin or lipoic acid. Biotin plays a  catalytic role in  some carboxyl transfer reactions and is covalently attached,  via  an  amide  bond,  to  a  lysine  residue in enzymes requiring this coenzyme []. E2 acyltransferases have an essential cofactor, lipoic acid, which is covalently bound  via an amide linkage to a lysine group []. The lipoic acid cofactor is found in a variety of proteins that include, H-protein of the glycine cleavage system (GCS), mammalian and yeast pyruvate dehydrogenases and fast migrating protein (FMP) (gene acoC) from Ralstonia eutropha (Alcaligenes eutrophus).

  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Russell GC, Guest JR.
      Sequence similarities within the family of dihydrolipoamide acyltransferases and discovery of a previously unidentified fungal enzyme.
      
      Biochim. Biophys. Acta
      
      1991
    
    
      Shenoy BC, Xie Y, Park VL, Kumar GK, Beegen H, Wood HG, Samols D.
      The importance of methionine residues for the catalysis of the biotin enzyme, transcarboxylase. Analysis by site-directed mutagenesis.
      
      J. Biol. Chem.
      
      1992
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
  
  
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  


  Flagellar motor switch protein FliG
  

    The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the 
direction of flagellar rotation and hence controls swimming behaviour [].
The switch is a complex apparatus that responds to signals transduced by the
chemotaxis sensory signalling system during chemotactic behaviour []. CheY,
the chemotaxis response regulator, is believed to act directly on the switch
to induce tumbles in the swimming pattern, but no physical interactions of 
CheY and switch proteins have yet been demonstrated. 
    

    The switch complex comprises at least three proteins - FliG, FliM and FliN.
It has been shown that FliG interacts with FliM, FliM interacts with itself,
and FliM interacts with FliN []. Several residues within the middle third
of FliG appear to be strongly involved in the FliG-FliM interaction, with
residues near the N- or C-termini being less important []. Such clustering
suggests that FliG-FliM interaction plays a central role in switching.
     

    Analysis of the FliG, FliM and FliN sequences shows that none are especially
hydrophobic or appear to be integral membrane proteins []. This result is
consistent with other evidence suggesting that the proteins may be 
peripheral to the membrane, possibly mounted on the basal body M ring [, ]. FliG is present in about 25 copies per flagellum.  This structure of the
C-terminal domain is known, this domain functions
specifically in motor rotation [].
    
    
  
    
      Biological Process
      ciliary or flagellar motility
    
    
      Molecular Function
      motor activity
    
    
      Biological Process
      chemotaxis
    
    
      Cellular Component
      bacterial-type flagellum
    
  
  
    
      
    
  
  
    
      Roman SJ, Frantz BB, Matsumura P.
      Gene sequence, overproduction, purification and determination of the wild-type level of the Escherichia coli flagellar switch protein FliG.
      
      Gene
      
      1993
    
    
      Kihara M, Homma M, Kutsukake K, Macnab RM.
      Flagellar switch of Salmonella typhimurium: gene sequences and deduced protein sequences.
      
      J. Bacteriol.
      
      1989
    
    
      Marykwas DL, Berg HC.
      A mutational analysis of the interaction between FliG and FliM, two components of the flagellar motor of Escherichia coli.
      
      J. Bacteriol.
      
      1996
    
    
      Francis NR, Irikura VM, Yamaguchi S, DeRosier DJ, Macnab RM.
      Localization of the Salmonella typhimurium flagellar switch protein FliG to the cytoplasmic M-ring face of the basal body.
      
      Proc. Natl. Acad. Sci. U.S.A.
      
      1992
    
    
      Lloyd SA, Whitby FG, Blair DF, Hill CP.
      Structure of the C-terminal domain of FliG, a component of the rotor in the bacterial flagellar motor.
      
      Nature
      
      1999
    
  
  
    
  
  
    
    
    
  
  
    
    
  
  
    
    
    
    
  
  
    
    
    
  
    

  Huntingtin
  
Huntington's disease (HD) is a mid-life onset, inherited, neurodegenerative
disorder characterised by motor impairment, involuntary movements (chorea),
psychiatric disorders and dementia []. The disease results from the
expansion of a polyglutamine-encoding CAG repeat in a gene of unknown
function. Moderate expansion of glutamine-coding CAG repeats has been
found in other neurological diseases (e.g. spinobulbar muscular atrophy
and Machado-Joseph disease), in all of which the pathological mechanism
linked to the expansion of the polyglutamine tract in the protein remains
a mystery.

    The HD transcript is highly conserved, significant differences, as already
noted, occurring in the N-terminal Gln-repeat region. Huntingtin normally
contains 10-35 repeats, but shows 36-120 repeats in the disease form.
Migration differences between normal and mutated huntingtin in a denaturing
polyacrylamide gel suggest that the poly-Gln stretch disrupts the protein
conformation. This finding is consistent with the observation that
Gln repeats may form tightly-linked beta-sheets that could act as polar
zippers [].
    
    
  
    
      Cellular Component
      nucleus
    
    
      Cellular Component
      cytoplasm
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Baxendale S, Abdulla S, Elgar G, Buck D, Berks M, Micklem G, Durbin R, Bates G, Brenner S, Beck S.
      Comparative sequence analysis of the human and pufferfish Huntington's disease genes.
      
      Nat. Genet.
      
      1995
    
    
      Perutz MF, Johnson T, Suzuki M, Finch JT.
      Glutamine repeats as polar zippers: their possible role in inherited neurodegenerative diseases.
      
      Proc. Natl. Acad. Sci. U.S.A.
      
      1994
    
  
  
    
    
  
  
    
    
  
  
    
  
  
    
    
    
    
    
    
    
    
  
    
    
BioPerl-1.007002/t/data/interpro_sample.xml000444000766000024     16724713155576321 20676 0ustar00cjfieldsstaff000000000000



  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  


  Kringle
  

    Kringles are autonomous structural domains, found throughout the blood clotting and fibrinolytic proteins. Kringle domains are believed to play a role in binding mediators (e.g., membranes, other proteins or phospholipids), and in the regulation of proteolytic activity [, , ]. 
Kringle domains [, , ] are characterised by a triple loop, 3-disulphide bridge structure, whose  conformation is defined by a number of hydrogen bonds and small pieces of  anti-parallel beta-sheet. They are found in a varying number  of  copies  in some plasma proteins including prothrombin and urokinase-type plasminogen activator, which are serine proteases belonging to MEROPS peptidase family S1A.
    

    Steroid or nuclear hormone receptors (4A nuclear receptor, NRs) constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands []. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner [, ]. In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity.
    

    NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed 'orphan' receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members.
    
    
  
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Patthy L.
      Evolution of the proteases of blood coagulation and fibrinolysis by assembly from modules.
      
      Cell
      
      1985
    
    
      Patthy L, Trexler M, Vali Z, Banyai L, Varadi A.
      Kringles: modules specialized for protein binding. Homology of the gelatin-binding region of fibronectin with the kringle structures of proteases.
      
      FEBS Lett.
      
      1984
    
    
      McMullen BA, Fujikawa K.
      Amino acid sequence of the heavy chain of human alpha-factor XIIa (activated Hageman factor).
      
      J. Biol. Chem.
      
      1985
    
    
      Ikeo K, Takahashi K, Gojobori T.
      Evolutionary origin of numerous kringles in human and simian apolipoprotein(a).
      
      FEBS Lett.
      
      1991
    
    
      De Vos P, Schmitt J, Verhoeven G, Stunnenberg HG.
      Human androgen receptor expressed in HeLa cells activates transcription in vitro.
      
      Nucleic Acids Res.
      
      1994
    
    
      Schwabe JW, Teichmann SA.
      Nuclear receptors: the evolution of diversity.
      
      Sci. STKE
      
      2004
    
    
      Atkinson RA, Williams RJ.
      Solution structure of the kringle 4 domain from human plasminogen by 1H nuclear magnetic resonance spectroscopy and distance geometry.
      
      J. Mol. Biol.
      
      1990
    
    
      Castellino FJ, Beals JM.
      The genetic relationships between the kringle domains of human plasminogen, prothrombin, tissue plasminogen activator, urokinase, and coagulation factor XII.
      
      J. Mol. Evol.
      
      1987
    
    
      Nishikawa J, Kitaura M, Imagawa M, Nishihara T.
      Vitamin D receptor contains multiple dimerization interfaces that are functionally different.
      
      Nucleic Acids Res.
      
      1995
    
  
  
    
  
  
    
  
  
    
  
  
    
    
    
    
    
    
    
  
  
    
    
    
    
  
  
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  
    

  Retinoid X receptor
  

    Steroid or nuclear hormone receptors (4A nuclear receptor, NRs) constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands []. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner [, ]. In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity.
    

    NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed 'orphan' receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members.
    

    The retinoic acid (retinoid X) receptor consists of 3 functional and 
               structural domains: an N-terminal (modulatory) domain; a DNA binding domain
               that mediates specific binding to target DNA sequences (ligand-responsive
               elements); and a hormone binding domain. The N-terminal domain differs 
               between retinoic acid isoforms; the small highly-conserved DNA-binding
               domain (~65 residues) occupies the central portion of the protein; and 
               the ligand binding domain lies at the receptor C terminus.
    

    Synonym(s): 2B nuclear receptor
    
    
  
    
      Molecular Function
      DNA binding
    
    
      Molecular Function
      ligand-dependent nuclear receptor activity
    
    
      Molecular Function
      steroid binding
    
    
      Cellular Component
      nucleus
    
    
      Biological Process
      regulation of transcription, DNA-dependent
    
    
      Molecular Function
      zinc ion binding
    
  
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Nishikawa J, Kitaura M, Imagawa M, Nishihara T.
      Vitamin D receptor contains multiple dimerization interfaces that are functionally different.
      
      Nucleic Acids Res.
      
      1995
    
    
      De Vos P, Schmitt J, Verhoeven G, Stunnenberg HG.
      Human androgen receptor expressed in HeLa cells activates transcription in vitro.
      
      Nucleic Acids Res.
      
      1994
    
    
      Schwabe JW, Teichmann SA.
      Nuclear receptors: the evolution of diversity.
      
      Sci. STKE
      
      2004
    
  
  
    
  
  
    
    
  
  
    
  
  
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
  
    

  Helix-turn-helix, AraC type
  

    Many bacterial transcription regulation proteins bind DNA through a
'helix-turn-helix' (HTH) motif. One major subfamily of these proteins [, ] is related to the arabinose 
operon regulatory protein AraC [], . Except for celD [], all of these proteins seem to be positive transcriptional factors.
    

    Although the sequences belonging to this family differ somewhat in length, in nearly every case the HTH motif is situated towards the C terminus in the third quarter of most of the sequences. The minimal DNA binding domain spans roughly 100 residues and comprises two HTH subdomains; the classical HTH domain and another HTH subdomain with similarity to the classical HTH domain but with an insertion of one residue in the turn-region. The  N-terminal and  central regions of these proteins are presumed to interact with effector molecules and may be involved in dimerisation [].
    

    The known structure of MarA () shows that the AraC domain is alpha helical and shows the two HTH subdomains both bind the major groove of the DNA. The two HTH subdomains are separated by only 27
angstroms, which causes the cognate DNA to bend.
    
    
  
    
      Molecular Function
      transcription factor activity
    
    
      Cellular Component
      intracellular
    
    
      Biological Process
      regulation of transcription, DNA-dependent
    
    
      Molecular Function
      sequence-specific DNA binding
    
  
  
    
      
    
  
  
    
      Parker LL, Hall BG.
      Characterization and nucleotide sequence of the cryptic cel operon of Escherichia coli K12.
      
      Genetics
      
      1990
    
    
      Henikoff S, Wallace JC, Brown JP.
      Finding protein similarities with nucleotide sequence databases.
      
      Meth. Enzymol.
      
      1990
    
    
      Gallegos MT, Michan C, Ramos JL.
      The XylS/AraC family of regulators.
      
      Nucleic Acids Res.
      
      1993
    
    
      Bustos SA, Schleif RF.
      Functional domains of the AraC protein.
      
      Proc. Natl. Acad. Sci. U.S.A.
      
      1993
    
  
  
    
  
  
    
    
  
  
    
    
    
    
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
  
    

  Metallothionein, vertebrate
  

    Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, nickel, etc. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, ]. An empirical classification into three classes has been proposed by Fowler and coworkers [] and Kojima []. Members of class I are defined to include polypeptides related in the positions of their cysteines to equine MT-1B, and include mammalian MTs as well as from crustaceans and molluscs. Class II groups MTs from a variety of species, including sea urchins,
fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units [].
    

    This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Consequently, all class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. This system subdivides the MT superfamily into families, subfamilies, subgroups, and isolated isoforms and alleles. 
    

    The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects []: e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. The inclusion of a MT within a family presupposes that its amino acid sequence is alignable with that of all members. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range: e.g., Family 1: vertebrate MTs [see http://www.bioc.unizh.ch/mtpage/protali.html]. 
    

     The members of family 1 are recognised by the sequence pattern K-x(1,2)-C-C-x-C-C-P-x(2)-C located at the beginning of the third exon. 
The taxonomic range of the members extends to vertebrates. 
Known characteristics: 60 to 68 AAs; 20 Cys (21 in one case), 19 of them are totally conserved; the protein sequence is divided into two structural domains, containing 9 and 11 Cys all binding 3 and 4 bivalent metal ions, respectively. The gene is composed of 3 exons, 2 introns and the splicing sites are conserved. Family 1 includes subfamilies: m1, m2, m3, m4, m, a, a1, a2, b, ba, t, all of them hit the same InterPro entry. 

    
    
  
    
      Molecular Function
      metal ion binding
    
  
  
    
      
    
    
      
    
    
      
    
  
  
    
      Kagi JH, Kojima Y.
      Chemistry and biochemistry of metallothionein.
      
      Experientia Suppl.
      
      1987
    
    
      Kagi JH.
      Overview of metallothionein.
      
      Meth. Enzymol.
      
      1991
    
    
      Kojima Y.
      Definitions and nomenclature of metallothioneins.
      
      Meth. Enzymol.
      
      1991
    
    
      Fowler BA, Hildebrand CE, Kojima Y, Webb M.
      Nomenclature of metallothionein.
      
      Experientia Suppl.
      
      1987
    
  
  
    
  
  
    
    
  
  
    
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
  
    

  Tubby, C-terminal
  

     Tubby, an autosomal recessive mutation, mapping to mouse  chromosome 7, was recently found to be the result of a splicing defect in a novel gene with unknown function. This  mutation  maps to the tub gene [, ]. The mouse  tubby mutation is  the  cause  of  maturity-onset  obesity, insulin resistance and  sensory  deficits. By contrast with the rapid juvenile-onset weight gain seen in diabetes (db) and obese (ob) mice, obesity in tubby mice develops gradually, and strongly resembles the late-onset obesity observed in the human population. Excessive deposition of adipose tissue  culminates in a two-fold increase of body weight. Tubby mice also suffer retinal degeneration and neurosensory hearing loss. The tripartite character of the tubby phenotype is highly similar to human obesity syndromes, such as Alstrom and Bardet-Biedl. Although these phenotypes indicate a vital role for tubby proteins, no biochemical function has yet been ascribed to any family member [], although it has been suggested that the phenotypic features of tubby mice may be the result of cellular apoptosis triggered by expression of the mutated tub gene. TUB is the founding-member of the tubby-like proteins, the TULPs. TULPs are found in multicellular organisms from both the plant and animal kingdoms. Ablation of members of this protein family cause disease phenotypes that are indicative of their importance in nervous-system function and development [].
    

    Mammalian TUB is a hydrophilic protein of ~500 residues. The N-terminal () portion of the protein is conserved neither in length nor sequence, but, in TUB, contains the nuclear localisation signal and may have transcriptional-activation activity. The C-terminal 250 residues are highly conserved. The C-terminal extremity contains a cysteine residue that might play an important role in the normal functioning of these proteins. The crystal structure of the C-terminal core domain from mouse tubby has been determined to 1.9A resolution. This domain is arranged as a 12-stranded, all anti-parallel, closed beta-barrel that surrounds a central alpha helix, (which is at the extreme carboxyl terminus of the protein) that forms most of the hydrophobic core. Structural analyses suggest that TULPs constitute a unique family of bipartite transcription factors [].
    
    
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Kleyn PW, Fan W, Kovats SG, Lee JJ, Pulido JC, Wu Y, Berkemeier LR, Misumi DJ, Holmgren L, Charlat O, Woolf EA, Tayber O, Brody T, Shu P, Hawkins F, Kennedy B, Baldini L, Ebeling C, Alperin GD, Deeds J, Lakey ND, Culpepper J, Chen H, Glucksmann-Kuis MA, Carlson GA, Duyk GM, Moore KJ.
      Identification and characterization of the mouse obesity gene tubby: a member of a novel gene family.
      
      Cell
      
      1996
    
    
      Noben-Trauth K, Naggert JK, North MA, Nishina PM.
      A candidate gene for the mouse mutation tubby.
      
      Nature
      
      1996
    
    
      Boggon TJ, Shan WS, Santagata S, Myers SC, Shapiro L.
      Implication of tubby proteins as transcription factors by structure-based functional analysis.
      
      Science
      
      1999
    
    
      Carroll K, Gomez C, Shapiro L.
      Tubby proteins: the plot thickens.
      
      Nat. Rev. Mol. Cell Biol.
      
      2004
    
  
  
    
  
  
    
    
    
    
  
  
    
    
    
    
    
  
  
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
    

  C2 calcium-dependent membrane targeting
  
The C2 domain is a Ca2+-dependent membrane-targeting module found in many cellular proteins involved in signal transduction or membrane trafficking. C2 domains are unique among membrane targeting domains in that they show wide range of lipid selectivity for the major components of cell membranes, including phosphatidylserine and phosphatidylcholine. This C2 domain is about  116  amino-acid  residues and is located between the two copies of
the C1 domain in Protein Kinase C (that bind phorbol esters and diacylglycerol) (see )
and the  protein  kinase  catalytic  domain  (see ).  Regions with
significant homology [] to  the C2-domain have been found in many proteins.
The C2  domain  is  thought  to  be involved in calcium-dependent phospholipid
binding [] and in membrane targetting processes such as subcellular localisation. 
    The 3D  structure  of  the
C2 domain of synaptotagmin has been reported
[], the domain forms an eight-stranded beta sandwich constructed around a 
conserved 4-stranded motif, designated a C2 key []. Calcium binds in
a cup-shaped depression formed by the N- and C-terminal loops of the
C2-key motif. Structural analyses of several C2 domains have shown them to consist of similar ternary structures in which three Ca2+-binding loops are located at the end of an 8 stranded antiparallel beta sandwich. 
    
    
  
    
      
    
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Sutton RB, Davletov BA, Berghuis AM, Sudhof TC, Sprang SR.
      Structure of the first C2 domain of synaptotagmin I: a novel Ca2+/phospholipid-binding fold.
      
      Cell
      
      1995
    
    
      Davletov BA, Sudhof TC.
      A single C2 domain from synaptotagmin I is sufficient for high affinity Ca2+/phospholipid binding.
      
      J. Biol. Chem.
      
      1993
    
    
      Brose N, Hofmann K, Hata Y, Sudhof TC.
      Mammalian homologues of Caenorhabditis elegans unc-13 gene define novel family of C2-domain proteins.
      
      J. Biol. Chem.
      
      1995
    
  
  
    
  
  
    
  
  
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
  
  
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
  
    

  Kringle-like fold
  

    This entry represents proteins displaying a Kringle-like structure, which consists of a nearly all-beta, disulphide-rich fold. Proteins displaying this fold include both Kringle modules as well as fibronectin type II modules, the latter displaying a shorter two-disulphide version of the Kringle module.
    

     Kringle modules occur in blood clotting and fibrinolytic proteins, such as plasminogen, prothrombin, meizothrombin, and urokinase-type plasminogen activator, as well as in apolipoprotein and hepatocyte growth factor. Kringle domains are believed to play a role in binding mediators (e.g., membranes, other proteins or phospholipids), and in the regulation of proteolytic activity [, ].
    

    Fibronectin type II modules occur in fibronectin, as well as in gelatinase A (MMP-2), gelatinase B (MMP-9), and the collagen-binding domain of PDC-109. Fibronectin is a multi-domain glycoprotein, found in a soluble form in plasma, and in an insoluble form in loose connective tissue and basement membranes, that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin []. Fibronectins are involved in a number of important functions e.g., wound healing; cell adhesion; blood coagulation; cell differentiation and migration; maintenance of the cellular cytoskeleton; and tumour metastasis. Gelatinases A and B are members of the matrix metalloproteinase family that act as neutral proteinases in the breakdown and remodelling of the extracellular matrix. These gelatinases play important roles in the pathogenesis of inflammation, infection and in neoplastic diseases []. In gelatinase A, the three fibronectin-like modules are inserted within a catalytic domain, these modules acting to target the enzyme to matrix macromolecules [].
    
    
  
    
      
    
    
      
    
    
      
    
    
      
    
  
  
    
      Skorstengaard K, Jensen MS, Sahl P, Petersen TE, Magnusson S.
      Complete primary structure of bovine plasma fibronectin.
      
      Eur. J. Biochem.
      
      1986
    
    
      Patthy L, Trexler M, Vali Z, Banyai L, Varadi A.
      Kringles: modules specialized for protein binding. Homology of the gelatin-binding region of fibronectin with the kringle structures of proteases.
      
      FEBS Lett.
      
      1984
    
    
      Atkinson RA, Williams RJ.
      Solution structure of the kringle 4 domain from human plasminogen by 1H nuclear magnetic resonance spectroscopy and distance geometry.
      
      J. Mol. Biol.
      
      1990
    
    
      Chakrabarti S, Patel KD.
      Matrix metalloproteinase-2 (MMP-2) and MMP-9 in pulmonary pathology.
      
      Exp. Lung Res.
      
      2005
    
    
      Hornebeck W, Bellon G, Emonard H.
      Fibronectin type II (FnII)-like modules regulate gelatinase A activity.
      
      Pathol. Biol.
      
      2005
    
  
  
    
    
  
  
    
    
  
  
    
    
  
  
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
    
    
    
    
    
    
    
    
    
    
    
  
  
    
    
  
    

  
  

    
BioPerl-1.007002/t/data/interpro_short.xml000444000766000024     10172613155576321 20542 0ustar00cjfieldsstaff000000000000



  
    
    
    
    
    
    
    
    
    
    
  
  
    Kringle
    
Kringles are autonomous structural domains, found throughout the blood 
               clotting and fibrinolytic proteins.
Kringle domains are believed to play a role in binding mediators (e.g., membranes,
other proteins or phospholipids), and in the regulation of proteolytic activity
, , . 
Kringle domains , ,  are characterised by a triple loop, 3-disulphide bridge structure, whose  conformation is defined by a number of hydrogen bonds and small pieces of  anti-parallel beta-sheet. They are found in a varying number  of  copies,  in some serine proteases and
plasma proteins.
    
      Blood coagulation factor XII (Hageman factor) (1 copy)
      Urokinase-type plasminogen activator (1 copy)
      Hepatocyte growth factor (HGF) (4 copies)
      Hepatocyte growth factor activator  (1 copy) 
      
				
Plasminogen (5 copies)
      
      
				
Hepatocyte growth factor like protein (4 copies) 
			
      
				
Thrombin (2 copies)
      
      
				
Tissue plasminogen activator (TPA) (2 copies)
      
      
				
Apolipoprotein A (38 copies)
      
    
    
      
	Fujikawa K., McMullen B.A.
	Primary structure of the heavy chain of human factor XIIa.
	
	J. Biol. Chem.
	
	1985
      
      
	Patthy L., Trexler M., Vali V., Banyai L., Varadi A.
	Kringles: Modules specialized for protein binding.
	
	FEBS Lett.
	
	1984
      
      
	Atkinson R.A., Williams R.J.P.
	Solution structure of the kringle 4 domain from human plasminogen by 1H nuclear magnetic resonance spectroscopy and distance geometry.
	
	J. Mol. Biol.
	
	1990
      
      
	Castellino F.J., Beals J.M.
	The genetic relationships between the kringle domains of human plasminogen, prothrombin, tissue plasminogen activator, urokinase, and coagulation factor XII.
	
	J. Mol. Evol.
	
	1987
      
      
	Patthy L.
	Evolution of the proteases of blood coagulation and fibrinolysis by assembly from modules.
	
	Cell
	
	1985
      
      
	Takahashi K., Ikeo K., Gojobori T.
	Evolutionary origin of numerous kringles in human and simian apolipoprotein(a).
	
	FEBS Lett.
	
	1991
      
      
	Friezner Degen S.J., Stuart L.A., Han S., Jamison C.S.
	Characterization of the mouse cDNA and gene coding for a hepatocyte growth factor-like protein: expression during development.
	
	Biochemistry
	
	1991
      
      
	Miyazawa K., Shimomura T., Kitamura A., Kondo J., Morimoto Y., Kitamura N.
	Molecular cloning and sequence analysis of the cDNA for a human serine protease reponsible for activation of hepatocyte growth factor. Structural similarity of the protease precursor to blood coagulation factor XII.
	
	J. Biol. Chem.
	
	1993
      
    
    
      
      
      
      
      
      
    
    
      
      
    
  
  
    Cdc20/Fizzy
    
<p>The Cdc20/Fizzy region is almost always associated with the G-protein beta WD-40 repeat (). Ubiquitin-mediated proteolysis due to the anaphase-promoting complex/cyclosome
 (APC/C) is essential for separation of sister chromatids, requiring degradation of the anaphase inhibitor Pds1, and for exit from mitosis, requiring inactivation of cyclin B  Cdk1 kinases . In yeast Cdc20 is required for two microtubule-dependent processes, nuclear movements prior to anaphase and chromosome separation. APC(Cdc20) allows activation of Cdc14 and promotes exit from mitosis by mediating proteolysis of Pds1  and the S phase cyclin Clb5 in the yeast Saccharomyces cerevisiae. </p>
<p>This domain is also found in a number of, as yet, uncharacterised proteins. These include a mammalian protein, p55CDC, that is present in dividing cells and is
      associated with protein kinase activity.</p>

    
      
				Cell division control protein (Cdc20) from S. cerevisiae
      
      
				A hypothetical protein from S. pombe
      
    
    
      
	Shirayama M., Toth A., Galova M., Nasmyth K.
	APC(Cdc20) promotes exit from mitosis by destroying the anaphase inhibitor Pds1 and cyclin Clb5.
	
	Nature
	
	1999
      
    
    
      
      
    
    
      
    
  
  
    Retinoid X receptor
    
Steroid or nuclear hormone receptors (4A nuclear receptor, NRs) constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner , . In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity.

NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed "orphan" receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members.


<p>The retinoic acid (retinoid X) receptor consists of 3 functional and 
               structural domains: an N-terminal (modulatory) domain; a DNA binding domain
               that mediates specific binding to target DNA sequences (ligand-responsive
               elements); and a hormone binding domain. The N-terminal domain differs 
               between retinoic acid isoforms; the small highly-conserved DNA-binding
               domain (~65 residues) occupies the central portion of the protein; and 
               the ligand binding domain lies at the receptor C-terminus.</p>
<p>Synonym(s): 2B nuclear receptor</p>

    
      
	Molecular Function
	DNA binding
      
      
	Molecular Function
	ligand-dependent nuclear receptor
      
      
	Molecular Function
	steroid binding
      
      
	Cellular Component
	nucleus
      
      
	Biological Process
	regulation of transcription
      
    
    
      
				
			
      
				
			
      
				
			
      
				
			
      
				
			
      
				
			
    
    
      
	Nishihara T., Nishikawa J.-I., Kitaura M., Imagawa M.
	Vitamin D receptor contains multiple dimerisation interfaces that are functionally different.
	
	Nucleic Acids Res.
	
	1995
      
      
	Schmitt J., De Vos P., Verhoeven G., Stunnenberg H.G.
	Human androgen receptor expressed in HeLa cells activates transcription in vitro.
	
	Nucleic Acids Res.
	
	1994
      
    
    
      
    
    
      
    
    
      
    
  
  
    Saposin type B
    
Saposins are small lysosomal proteins that serve as activators of various
lysosomal lipid-degrading enzymes . They probably act by isolating the
lipid substrate from the membrane surroundings, thus making it more 
accessible to the soluble degradative enzymes. All mammalian saposins
are synthesized as a single precursor molecule (prosaposin) which contains
four Saposin-B domains, yielding the active saposins after proteolytic
cleavage, and two Saposin-A domains that are removed in the activation
reaction. 
The Saposin-B domains also occur in other 
proteins, many of them active in the lysis of membranes , . <p>The 3D-structure of NK-lysin has recently been determined  and found to
be very different from the one predicted in .
A group of plant aspartic proteases related to cyprosin. These proteins
have a peculiar SAP-B domain where the two halves are 'swapped' .</p>

    
      
				Mammalian Acyloxyacyl-hydrolase
      
      
				Plant aspartic proteinase
      
      
				Mammalian acid sphingomyelinase
      
      
				Nonpathogenic pore-forming peptide from entamoeba
      
      
				Saposins Sap-A, Sap-B, Sap-C, Sap-D
      
    
    
      
	O'Hara P.J., Munford R.S., Sheppard P.O.
	Saposin-like proteins (SAPLIP) carry out diverse functions on a common backbone structure.
	
	J. Lipid Res.
	
	1995
      
      
	Ponting C.P.
	Acid sphingomyelinase possesses a domain homologous to its activator proteins: saposins B and D.
	
	Protein Sci.
	
	1994
      
      
	Hofmann K., Tschopp J.
	Cytotoxic T cells: more weapons for new targets?
	
	Trends Microbiol.
	
	1996
      
      
	Liepinsh E., Otting G., Andersson M., Ruysschaert J.M.
	Saposin fold revealed by the NMR structure of NK-lysin.
	
	Nat. Struct. Biol.
	
	1997
      
      
	Ponting C.P., Russell R.B.
	Swaposins: circular permutations within genes encoding saposin homologues.
	
	Trends Biochem. Sci.
	
	1995
      
    
    
      
    
    
      
      
      
    
    
      
    
  
  
    Helix-turn-helix, AraC type 
    
<p>Many bacterial transcription regulation proteins bind DNA through a
'helix-turn-helix' (HTH) motif. One major subfamily of these proteins ,  is related to the arabinose 
operon regulatory protein AraC , .
Except for celD , all of these proteins seem to be positive transcriptional factors.</p>

<p>Although the sequences belonging to this family differ somewhat in length, in nearly every case the HTH motif is situated towards the C-terminus in the third quarter of most of the sequences. The minimal DNA binding domain spans roughly 100 residues and comprises two HTH subdomains; the classical HTH domain and another HTH subdomain with similarity to the classical HTH domain but with an insertion of one residue in the turn-region. The  N-terminal and  central regions of these proteins are presumed
            to interact  with  effector molecules and may be involved in dimerization .</p>

<p>The known structure of MarA () shows that the AraC domain is alpha helical and shows the two HTH subdomains both bind the major groove of the DNA. The two HTH subdomains are separated by only 27
angstroms, which causes the cognate DNA to bend.</p>

    
      
	Molecular Function
	transcription factor
      
      
	Cellular Component
	intracellular
      
      
	Biological Process
	regulation of transcription
      
    
    
      
				Virulence regulon transcriptional activator
      
      
				mmsAB peron regulatory  protein
      
      
				
			
      
				Transcription regulator
      
      
				Regulatory factor of blood coagulation
      
      
				CelD, the Escherichia coli cel operon repressor.
      
      
				AdaA, a Bacillus subtilis  bifunctional protein  that   acts  both  as  a transcriptional activator of the ada operon and as a methylphosphotriester-DNA alkyltransferase.
      
      
				AraC, the arabinose operon regulatory  protein, which activates the transcription of the araBAD genes.
      
      
				MarA,  which  may  be  a transcriptional activator of genes involved in the multiple antibiotic resistance (mar) phenotype.
      
    
    
      
	Gallegos M.-T., Michan C., Ramos J.L.
	The XylS/AraC family of regulators.
	
	Nucleic Acids Res.
	
	1993
      
      
	Henikoff S., Wallace J.C., Brown J.P.
	Finding protein similarities with nucleotide sequence databases.
	
	Meth. Enzymol.
	
	1990
      
      
	Parker L.L., Hall B.G.
	Characterisation and nucleotide sequence of the cryptic cel operon of Escherichia coli K12.
	
	Genetics
	
	1990
      
      
	Bustos S.A., Schleif R.F.
	Functional domains of the AraC protein.
	
	Proc. Natl. Acad. Sci. U.S.A.
	
	1993
      
    
    
      
      
      
      
      
    
    
      
      
    
  
	
		Cysteine proteases inhibitor
		
Members of this family are inhibitors of cysteine  proteases , , , which are found in the tissues and body fluids of animals, as well as in plants. They can be grouped into three distinct but related families. These are the type 1 cystatins (or stefins), type 2 cystatins, and the kininogens.
<p>Kininogen is the precursor  of  the  active  peptide  bradykinin that  plays a role in blood coagulation by  helping  to  position optimally prekallikrein and factor XI next  to factor XII. They  are  also  inhibitors  of  cysteine  proteases. Structurally,  kininogens  are  made  of  three  contiguous type-2 cystatin domains, followed  by an  additional  domain  (of  variable  length)  which contains  the  sequence of bradykinin.  The  first  of  the  three cystatin domains seems to have lost its inhibitory activity.</p>

		
			
				Molecular Function
				cysteine protease inhibitor
			
		
		
			
				Cysteine proteinase inhibitor of rice
      
			
				Mammalian fetuin
      
			
				Type 2 cystatin
      
			
				Potato  multicystatin, an eight-domain cysteine proteinase inhibitor
      
			
				Kininogen
      
			
				Type 1 cystatin
      
			
				Sarcocystatin A from the flesh fish
      
		
		
			
				Barrett A.J.
				Trends Biochem. Sci.
				
				1987
			
			
				Rawlings N.D., Barrett A.J.
				Evolution of proteins of the cystatin superfamily.
				
				J. Mol. Evol.
				
				1990
			
			
				Bode W., Turk V.
				The cystatins: protein inhibitors of cysteine proteinases.
				
				FEBS Lett.
				
				1991
			
		
		
			
			
			
			
		
		
			
			
			
		
		
			
			
		
		
			
		
	
	
		Integrins alpha chain
		
Integrins ,  are a large family of cell surface receptors that mediate cell
to cell as well as cell to matrix adhesion. Some integrins recognize the R-G-D
sequence in their extracellular matrix protein ligand. Structurally, integrins
consist of a dimer of an alpha and a beta chain.  Each  subunit  has  a  large
N-terminal extracellular domain followed by a transmembrane domain and a short
C-terminal cytoplasmic  region.    Some    alpha  subunits   are cleaved post-
translationally to produce  a  heavy  and a  light chain linked by a disulfide
bond. Integrin alpha chains  share a  conserved sequence which is found at
the  beginning  of  the  cytoplasmic  domain,  just   after  the  end  of  the
transmembrane region. The exact pairing of alpha- and beta-subunits determines
ligand specificity, localisation and function. Within the N-terminal domain of alpha subunits, seven sequence repeats, each
of approximately 60 amino acids, have been found . It has been predicted 
that these repeats assume a beta-propeller fold. The domains contain seven 
four-stranded beta-sheets arranged in a torus around a pseudosymmetry axis
. Integrin ligands and a putative Mg<sup>2+</sup> ion are predicted to bind to the
upper face of the propeller, in a manner analogous to the way in which the
trimeric G-protein beta subunit (G beta) (which also has a beta-propeller
fold) binds the G protein alpha subunit .

		
			
				Molecular Function
				cell adhesion receptor
			
			
				Biological Process
				cell adhesion
			
			
				Biological Process
				cell-matrix adhesion
			
			
				Cellular Component
				integrin
			
		
		
			
				The alpha-6 chain (VLA-6) which,  with  the beta-1  chain, forms a platelet laminin receptor.
      
			
				The alpha-8 chain which, with the  beta-1 chain  plays  a  possible role in cell-cell interactions during axon-growth and fasciculation.
      
			
				The alpha-5 chain (VLA-5) (CD49e) which,  with  the beta-1 chain,  forms  a receptor specific to fibronectin.
      
			
				The Drosophila position-specific antigen 2 alpha chain (PS2).
      
			
				The alpha-3 chain (VLA-3) (Galactoprotein B3).
      
			
				The alpha-1 chain (VLA-1) (CD49a)  which,  with the beta-1 chain, acts as a receptor for laminin and collagen.
      
			
				The alpha-4 chain (VLA-4) (CD49d)  which,  with the beta-1 chain, interacts with vascular cell adhesion protein 1 (VCAM-1).
      
			
				The alpha-2 chain (VLA-2) (CD49b)  which,  with the beta-1 chain, acts as a receptor that binds collagen.
      
		
		
			
				Hynes R.O.
				Integrins: a family of cell surface receptors.
				
				Cell
				
				1987
			
			
				Albelda S.M., Buck C.A.
				Integrins and other cell adhesion molecules.
				
				FASEB J.
				
				1990
			
			
				Springer T.A., Corbi A.L., Miller L.J., O'Connor K., Larson R.S.
				cDNA cloning and complete primary structure of the alpha subunit of a leukocyte adhesion glycoprotein, p150,95.
				
				EMBO J.
				
				1987
			
			
				Springer T.A.
				Folding of the N-terminal, ligand-binding region of integrin alpha-subunits into a beta-propeller domain.
				
				Proc. Natl. Acad. Sci. U.S.A.
				
				1997
			
		
		
			
			
			
			
			
			
		
		
			
			
			
		
		
			
			
		
	
  
    
    
    
    
    
  

BioPerl-1.007002/t/data/intrablock-comment.nex000444000766000024       104313155576321 21172 0ustar00cjfieldsstaff000000000000#NEXUS

BEGIN TAXA;
[block-level comment in the TAXA block]
      dimensions ntax=8;
      taxlabels A B C D E F G H;  
END;

BEGIN CHARACTERS;
[block-level comment in the CHARACTERS block]

      dimensions nchar=5;
      format datatype=protein missing=? gap=-;
      charlabels 1 2 3 4 5;
      matrix
A     --ONE
B     --ONE
C     TWO--
D     THREE
E     F-OUR
F     FIVE-
G     SIX--
H     SEVEN;
END;

BEGIN TREES;
[block-level comment in the TREES block]

       tree ladder = (((((((A:1,B:1):1,C:2):1,D:3):1,E:4):1,F:5):1,G:6):1,H:7);
END;BioPerl-1.007002/t/data/little.largemultifasta000444000766000024       207613155576321 21300 0ustar00cjfieldsstaff000000000000>Human: 72.0:1018606-3386002; 73.0:0-14850845; 74.0:0-83355922; SPECIAL_hsApr2003_3.0:0-414023;
CATCTCTGACTGTGGTCACACACCTGTGCATGCATGCTCCTGACGTCATGCACTGCATGCTGCAACTGCTGCATGCATGCA
>Mouse: 72.0:1018606-3386002; 73.0:0-14850845; 74.0:0-83355922; SPECIAL_hsApr2003_3.0:0-414023;
TATCTCTGACTGTGGTCACACACCTGTGCATGCATGCTCCTGACGTCATGCACTGCATGCTGCAACTGCTGCATGCATGCA
>Rat: 72.0:1018606-3386002; 73.0:0-14850845; 74.0:0-83355922; SPECIAL_hsApr2003_3.0:0-414023;
TTTCTCTGACTGTGGTCACACACCTGTGCATGCATGCTCCTGACGTCATGCACTGCATGCTGCAACTGCTGCATGCATGCA
>Whatever: 72.0:1018606-3386002; 73.0:0-14850845; 74.0:0-83355922; SPECIAL_hsApr2003_3.0:0-414023;
CATCTCTGACTGTGGTCACACACCTGTGCATGCATGCTCCTGACGTCATGCACTGCATGCTGCAACTGCTGCATGCATGCA
>Extraterrestrial: 72.0:1018606-3386002; 73.0:0-14850845; 74.0:0-83355922; SPECIAL_hsApr2003_3.0:0-414023;
CCCCCCTGACTGTGGTCACACACCTGTGCATGCATGCTCCTGACGTCATGCACTGCATGCTGCAACTGCTGCATGCATGCA
>GeorgeWBush: 72.0:1018606-3386002; 73.0:0-14850845; 74.0:0-83355922; SPECIAL_hsApr2003_3.0:0-414023;
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
BioPerl-1.007002/t/data/long-names.nex000444000766000024       114713155576321 17447 0ustar00cjfieldsstaff000000000000#NEXUS

BEGIN TAXA;
      dimensions ntax=8;
      taxlabels A B C D E F SupercalifragilisticexpialidociousOTU H;  
END;

BEGIN CHARACTERS;
      dimensions nchar=5;
      charlabels SupercalifragilisticexpialidociousLabel Two Three
      Four Five;
      format datatype=protein missing=? gap=-;
      matrix
A     --ONE
B     --ONE
C     TWO--
D     THREE
E     F-OUR
F     FIVE-
SupercalifragilisticexpialidociousOTU     SIX--
H     SEVEN;
END;

BEGIN TREES;
       tree SupercalifragilisticexpialidociousTree = (((((((A:1,B:1):1,C:2):1,D:3):1,E:4):1,F:5):1,SupercalifragilisticexpialidociousOTU:6):1,H:7);
END;
BioPerl-1.007002/t/data/longnames.aln000444000766000024      2044313155576321 17372 0ustar00cjfieldsstaff000000000000CLUSTAL W (1.82) multiple sequence alignment


Spar_21273             -------------MPFAQIVIGPPGSGKSTYCN------GCSQFFNAIGRHSQVVNMDPA
YOR262W                -------------MPFAQIVIGPPGSGKSTYCN------GCSQFFNAIGRHSQVVNMDPA
Smik_Contig1103.1      -------------MPFAQIVIGPPGSGKSTYCN------GCSQFFNAIGRHSQVVNMDPA
Skud_Contig1703.7      -------------MPFAQIVIGPPGSGKSTYCN------GCSQFFNAIGRHSQVVNMDPA
Sbay_Contig635.43      -------------MPFAQIVIGPPGSGKSTYCN------GCSQFFNAIGRHSQVVNMDPA
Scas_Contig692.20      -------------MPFAQIVIGPPGSGKSTYCN------GCSQFFNAIGRHGQIVNMDPA
Sklu_Contig2277.4      -------------MPFGQIVIGPPGSGKSTYCN------GCSQFFNAVGRHAQVINMDPA
AAL117C                -------------MAYGQIVIGPPGSGKSTYCN------GCSQFFNAIGRHARIVNMDPA
SPAC144.07c            -------------MPFCQVVVGPPGSGKSTYCF------GMYQLLSAIGRSSIIVNLDPA
MG06110.4              -----------------------------------------MGFLGAIGRACSVVNLDPA
NCU09745.1             ----------------------------------MTSPLPVQQFMGAIGRQCSVVNLDPA
FG05298.1              -------------MPFAQLVLGSPGCGKSTYCDGIQLTGQVHQFLGAIGRACSVVNLDPA
AN2438.1               ------------------------------------------------------------
183.m01790             MDDKELEIPVEHSTAFGQLVTGPPGAGKSTYCH------GLHQFLTAIGRPVHIINLDPA
                                                                                   

Spar_21273             NDALPYPCAVDIRDFITLEEIMQEQQLGPNGGLVYAVESLDKSIDLFILQIKSLV--EEE
YOR262W                NDALPYPCAVDIRDFITLEEIMQEQQLGPNGGLMYAVESLDNSIDLFILQIKSLV--EEE
Smik_Contig1103.1      NDALPYPCAVDIRDFITLEEIMQEQQLGPNGGLMYAVESLDKSIDLFLLQIKSLV--EEE
Skud_Contig1703.7      NDALPYPCAVDIRDFITLEEVMQEQQLGPNGGLMYAVESLDNSIDLFILQIKSLV--EEE
Sbay_Contig635.43      NDALPYPCAVDIRDFITLEEIMKEQHLGPNGGLMYAVESLDKSIDLFILQIKSLV--EEE
Scas_Contig692.20      NDALPYPCAVDIRDFVTLEEIMQEQQLGPNGGLMYAVESLDESIDLFILQIKSLV--QEE
Sklu_Contig2277.4      NDSLPYPCAVDIRDFITLEEIMTEQQLGPNGGLMYALESLDKSIDLFVLQIKSLV--QDE
AAL117C                NDSLPYQCDVDIRDFITLEEIMNEQHLGPNGGLVYAFESVEHSLSLFALQIKTLV--KDE
SPAC144.07c            NDFIKYPCAIDIRKVLDVEMIQKDYDLGPNGALIYAMEAIEYHVEWLLKELK-----KHR
MG06110.4              NDHTSYPCALDIRNLVTLEEIMGDDNLGPNGGILYAIEELEHNFEWLEDGLK-----ELG
NCU09745.1             NDHTNYPCALDIRDLVTLEEIMADDKLGPNGGILYALEELENNMEWLENGLK-----ELG
FG05298.1              NDHTNYPAALDIRSLIKLEEIMKDDKLGPNGGILYALEELEHNFEWLEEGLK-----EFS
AN2438.1               ---------------------MSEDQLGPNGGVLYALEELEENFDFLEEGLK-----ELG
183.m01790             VPNPPYPCSINITELITLESVMEEYNLGPNGAMLYCIEFLEANFDWLVERLDEVLAEEGG
                                              : .*****.::*..* ::  .. :   :.     :  

Spar_21273             KAYLVFDCPGQVELFTHHSSLFSIFKKMEKELDMRFCVVNLIDCFYMTSPSQYISILLLA
YOR262W                KAYLVFDCPGQVELFTHHSSLFNIFKKMEKELDIRFCVVNLIDCFYMTSPSQYISILLLA
Smik_Contig1103.1      KAYLVFDCPGQVELFTHHSSLFNIFKKMEKELDMRFCVINLIDCFYMTSPSQYVSILLLA
Skud_Contig1703.7      KAYLVFDCPGQVELFTHHSSLFSIFKKMEKELDMRFCVVNLIDCFYMTSPSQYVSILLLA
Sbay_Contig635.43      KAYVVFDCPGQVELFTHHSSLFSIFKKLEKELDMRFCVVNLIDCFYMTSPSQYVSILLLA
Scas_Contig692.20      KAYLVFDCPGQVELFTHHSSLFKIFKKLEKELDMRFCVVNLIDSFYITSPSQYVSILLLA
Sklu_Contig2277.4      HAYVVFDCPGQVELFTHHSSLFRIFKKLERELDMRLCVVNLIDCFYITSPSQYVSILLLA
AAL117C                NAYLVFDCPGQVELFTHHSALSKIFQQLVRDLDLRVCVVNLMDSIYITSPSQYVSVLLLA
SPAC144.07c            DSYVIFDCPGQVELFTNHNSLQKIIKTLEKELDYRPVSVQLVDAYCCTNPSAYVSALLVC
MG06110.4              DDYILFDCPGQVELYTHHNSLRNIFFKLQK-LGYRLVVVHLSDSICLTQPSLYISNLLLA
NCU09745.1             EDYVLFDCPGQVELYTHHNSLRNIFYRLQK-LGYRLVVVHLSDCFCLTQPSLYISNVLLS
FG05298.1              EDYILFDCPGQVELYTHHNSLRNIFYKLQK-IGFRLVSVHLSDSFCLTQPSLYVSNVLLS
AN2438.1               EDYIIFDCPGQVEIFTHHSSLRNIFFKIQK-MGYRLIVLHLIDSYNLTLPSMYISSLILC
183.m01790             NGYVVFDTPGQAELWTNHDSLKNVVEKLVK-MDYRLAAVHLSDAHYITDASKFISVVLLA
                       . *::** ***.*::*:*.:*  :.  : : :. *   ::* *.   * .* ::* :::.

Spar_21273             LRSMLMMDLPHINVFSKIDMLKSYGELPFRLDYYTEVQDLDYLEPYIEKEGSSVLGKKYS
YOR262W                LRSMLMMDLPHINVFSKIDMLKSYGELPFRLDYYTEVQDLDYLEPYIEKEGSSVLGKKYS
Smik_Contig1103.1      LRSMLMMDLPHINVFSKIDMLKSYGELPFRLDYYTEVQDLDYLEPYIEKEGSSVLGKKYN
Skud_Contig1703.7      LRSMLMMDLPHINVFSKIDMLKSYGELPFRLDYYTEVQELDHLEPYIEKEGSSVLGKKYS
Sbay_Contig635.43      LRSMLMMDLPHINVFSKIDKLKSYGELPFRLDYYTEVQDLDYLEPYIEKEGSGALGKRYS
Scas_Contig692.20      LRSMLMMDLPQINVFSKIDMLKSYGELPFRLDYYTEVQDLDYLQPFIEKESSSVLGRRYS
Sklu_Contig2277.4      LRSMLMMDLPHINVFSKIDLLKSYGELPFRLDYYTEVQELDYLKPHIDKEGSSVLGRKYS
AAL117C                LRSMLMMDLPHINVLSKIDMLSSYGDLPFRLDYYTEVQDLEYLQPHIEREHKGAKALRYR
SPAC144.07c            LKGMLQLDMPHVNILSKADLLCTYGTLPMKLDFFTEVQDLSYLAPLLDRDKR---LQRYS
MG06110.4              LRAMLQMDLSHVNVLTKIDKVSSYDRLAFNLDFYTEVHDLSYLLPELEAENPSLRSEKFA
NCU09745.1             LRAMLQMDLPHINVLTKIDKISSYDPLPFNLDYYTEVQDLRYLMPSLDAESPALKKGKFT
FG05298.1              LRAMIQMDMPHINILSKIDKVADYDELPFNLDYYTDVDDLTYLTPHLETESPALRSEKFG
AN2438.1               LRAMLQMDLPHLNVLTKIDNLSNYTSLPFNLDFYTEVQDLTYLLPHLEAESSRLSHEKFG
183.m01790             LRAMLQMEMPHLNVLSKIDLISTYGELPFDLSYYTEVQDLSYLLGSLDSDPR---TAKYH
                       *:.*: :::.::*:::* * :  *  *.: *.::*:*.:* :*   :: :       :: 

Spar_21273             KLTETIKELVSDFNLVSFEVLSVDDKESMINLQGVIDKANGYIFGAS---EVGG------
YOR262W                KLTETIKELVSDFNLVSFEVLSVDDKESMINLQGVIDKANGYIFGAS---EVGG------
Smik_Contig1103.1      KLTDAIKELVSDFNLVSFEVLSVDDKESMINLQGVIDKANGYIFGAS---EVGG------
Skud_Contig1703.7      KLTETIKELVSDFNLVSFEVLSVDDKESMINLQGVIDKANGYIFGAS---EVGG------
Sbay_Contig635.43      KLTETISELVSDFNLVSFEVLAVDDKESMINLQGVIDKANGYIFGAS---EVGG------
Scas_Contig692.20      KLTETISELVSDFNLVSFEVLAVDDKQSMINLQSVVDKANGYIFGAS---EVGG------
Sklu_Contig2277.4      RLTETISELVSDFNLVSFEVLCVDDKQSMINLQSIVDKANGYIFGVS---EIGG------
AAL117C                RLTEAIGEVVSDFNLVAFEVLCVDDKQSMINLQSAIDKANGYIFGAS---EVGG------
SPAC144.07c            DLNKAICELVEDFNLVSFEVVAVENKASMLRVLRKIDQAGGYAYGST---EIGG------
MG06110.4              KLNRAVANLIEDFGLVRFEVLAVENKKSMMHLLRVLDRANGYVFGGA---EGAN------
NCU09745.1             KLNEAVANMVEQFGLVSFEVLAVENKKSMMHLLRVIDRASGYVFGGA---EGTN------
FG05298.1              KLNEAIANLIESYGLVRYEVLAVENKKSMMHILRVIDRAGGYVFGSA---EGAN------
AN2438.1               ALNNAIITLIEEFGLVGFETLAVEDKKSMMNLLRAIDRASGYVFGPA---EGAN------
183.m01790             KLNKALVELIEGFSLVGFQTLAVEDKESMLNIVRLVDKMTGYIFIPSGDLEGTNAINTQA
                        *. ::  ::. :.** ::.:.*::* **:.:   :*:  ** :  :   *  .      

Spar_21273             --DTVWAEASREGA-LLANYDIQDRWIDNKEKYDKEEEEKRAALLKEQELQNKAVDVNEE
YOR262W                --DTVWAEASREGA-LIANYDIQDRWIDNKEKYDKEEEEKRTALLKEQELQNKAVDVNEE
Smik_Contig1103.1      --DTVWAEASREGA-LLTSYDIQDRWIDNKEKYDKEEEEKRVILLKEQELQNKAVDVNED
Skud_Contig1703.7      --DTVWAEASREGA-LLENYDIQDRWIDNKETYDKEEQEKRASLLKEQELQNKTVDVKEE
Sbay_Contig635.43      --DTVWAEASREGA-LLASYDIQDRWIDNKEKYDKEEQEKRAAMVKEQELQNKEVNVDEE
Scas_Contig692.20      --DTVWAEATREGA-MMVNYDIQDRWIDNKEKYDEEERKRQEEQAKEQNMQEKEVDVDNE
Sklu_Contig2277.4      --DTVWAEATRQGS-AIANYDIQERWIDNKDMYDREEQEKREQLLKEEELQNKEVDVDKG
AAL117C                --DTVWAEATRQGT-AAIEYDIQDRWIDNKDFYDKEEEARRKKLLEEHELLEKEVDVNQD
SPAC144.07c            --DAVWVNAVRQGGDPLQGISPQERWIDKKEEYDK----------YEWELEQK--STMDE
MG06110.4              --DTVWQVAMRNEGSLMGVQDIQERWIDNKEAYDEMEQREWEEQVKAQEAMAEADAAAAE
NCU09745.1             --DTVWQVAMRNESSLPDALDIQERWIDSKEEYDEMERKEEEEQEKLRAEQARAAEEAGL
FG05298.1              --DTVWSVAMRNESSMLGVQDIQERWIDQKVEYDQMEREAEEEQARIQEEQAMEMEQSQP
AN2438.1               --DSVWQVAVREGMGSMDIRDIQERWIDAKDEYDELERRQREEEIKNHQQAATYQAGNED
183.m01790             LFGSAMSSAKLTGRAGGDVRDVQERWMDNKEAWDEWEKKEWKREAEIRAQMGTGIPEGMK
                         .:.   *           . *:**:* *  :*.                         

Spar_21273             DEWENALKEWEEKQGTDFVR--------------
YOR262W                DEWENALKEWEEKQGMDFVR--------------
Smik_Contig1103.1      DEWESALKEWEEKQGMDFVR--------------
Skud_Contig1703.7      DEWENALKEWEEKQDTEFVR--------------
Sbay_Contig635.43      DEWENALNDWEEKQGTDFVR--------------
Scas_Contig692.20      DEWEKALKDWEEKQGTGYVR--------------
Sklu_Contig2277.4      DEWENALKEWEEKQGMSYVK--------------
AAL117C                DEWERAVKEWESQHSVNFVK--------------
SPAC144.07c            DENEG-----------------------------
MG06110.4              -EG-----DDDLMGGPGAR---------------
NCU09745.1             GDGSVPGVAPQFTSGSGIRVTLSLVAAFTKYSDL
FG05298.1              PPAPTGGMDPDFGDMTVPKDSGIKVVRK------
AN2438.1               DDDDN---DYEFGRRMPVPDSGVKVMRK------
183.m01790             GGED--------AESTGI----------------
                                                         
BioPerl-1.007002/t/data/longnames.dnd000444000766000024        62513155576321 17325 0ustar00cjfieldsstaff000000000000((Smik_Contig1103.1:0.02476,YOR262W:0.00522):0.00550,((((((((((MG06110.4:0.12375,NCU09745.1:0.16183):0.02603,FG05298.1:0.20399):0.07667,AN2438.1:0.28559):0.09760,183.m01790:0.50030):0.11832,SPAC144.07c:0.38280):0.24654,AAL117C:0.17383):0.05813,Sklu_Contig2277.4:0.08437):0.01525,Scas_Contig692.20:0.06952):0.03306,Sbay_Contig635.43:0.03348):0.02127,Skud_Contig1703.7:0.02261):0.00422,Spar_21273:0.00359);
BioPerl-1.007002/t/data/lucy.info000444000766000024        10113155576321 16471 0ustar00cjfieldsstaff000000000000TaLr1010B10R	CLR	86	505	CLB	11	577	CLN	11	577	CLZ	0	0	CLV	86	523
BioPerl-1.007002/t/data/lucy.qual000444000766000024       530013155576321 16526 0ustar00cjfieldsstaff000000000000>TaLr1010B10R
0 0 0 0 0 0 0 0 0 0 15 16 25 32 39 39 34 34 34 32 
32 29 34 26 26 29 29 32 34 39 35 35 35 39 39 35 35 
35 35 35 35 39 40 40 40 40 40 45 45 45 40 40 51 51 
51 45 51 51 51 40 40 42 46 45 45 56 45 45 40 40 40 
40 40 40 40 40 40 40 40 40 40 40 40 45 45 51 51 51 
51 42 43 43 56 46 51 40 35 35 35 35 35 35 35 37 40 
40 40 42 56 44 56 50 56 56 56 46 46 42 42 42 46 37 
37 34 30 30 42 50 42 40 40 45 45 45 45 40 40 40 40 
42 50 42 43 43 43 42 42 42 56 50 43 56 40 40 37 37 
37 43 40 40 40 41 41 41 41 41 41 41 50 56 56 50 50 
50 56 50 50 50 56 56 56 42 46 46 42 42 42 43 43 56 
56 56 43 43 41 41 41 41 41 41 51 51 56 56 56 50 50 
50 46 45 45 45 41 41 41 41 44 45 41 43 43 46 41 56 
56 56 51 45 45 45 45 41 41 42 41 41 41 41 41 43 43 
42 42 56 51 43 43 41 38 38 38 42 43 43 56 56 46 42 
42 42 42 56 50 50 42 42 42 50 50 41 41 42 42 43 42 
42 41 37 35 38 40 40 38 38 38 40 40 40 41 42 42 42 
42 42 42 41 41 41 41 41 43 38 40 38 40 40 43 50 50 
35 35 30 33 32 35 41 41 35 35 32 35 40 41 44 45 45 
41 40 37 37 35 37 41 42 42 42 42 41 40 40 40 40 40 
42 43 56 42 40 35 35 35 37 40 40 40 42 42 42 42 42 
42 36 35 35 35 36 39 42 42 42 42 37 35 35 35 32 32 
32 40 40 40 40 42 56 50 56 50 50 50 56 43 40 40 40 
40 36 42 37 48 33 33 33 35 35 32 32 32 32 37 42 34 
31 31 35 33 33 33 39 35 37 35 32 32 33 33 37 35 35 
36 35 35 37 44 42 48 48 44 44 42 33 31 24 24 30 24 
31 28 29 31 31 36 30 33 33 42 30 34 34 36 36 34 34 
34 30 36 30 30 28 25 25 29 29 29 35 32 35 35 35 35 
35 33 40 40 32 29 25 23 23 23 19 19 19 20 17 17 17 
25 25 33 33 35 40 33 35 35 37 37 35 42 42 42 40 40 
56 56 56 56 47 47 42 40 40 30 30 21 22 22 27 27 28 
28 26 26 24 16 12 9 14 13 14 16 22 22 19 12 10 12 
9 9 11 13 12 21 25 25 29 24 25 28 28 28 27 24 11 11 
10 17 20 29 26 25 25 18 18 18 24 19 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 
BioPerl-1.007002/t/data/lucy.seq000444000766000024       212513155576321 16356 0ustar00cjfieldsstaff000000000000>TaLr1010B10R 0 0 0 86 505
ATACGCCAAGCTCGAAATTAACCCTCACTAAAGGGAACAAAAGCTGGAGC
TCGCGCGCCTGCAGGTCGACACTAGTGGATCCAAAGAATTCGGCACGAGA
CCTACCCGTTCGTCAAGGAGGGTGTGTCCAACGGAACCCTCAAGCTCGTT
GGCGGCCACTACGACTTCGTCTCCGGCAAGTTCGAGACATGGGAGCAGTA
AATCTTCCCCACCGGTTAACTCCTATATATACATGCGAATACAAACGCGT
ACATATATCAAGATATCGTCCGACCGTCCGACCGACCGATGTGAATCCAA
TGCCATGGAGTGCGTACTCGTTATTTTCCAGTACTGGATGCCGGGATGGC
CCGATGTGAATTCGCCATAAGCAATAGAACCTTTTTTCTTTTACCATTTT
CTGACGAGGAATTGTACTACCATGTGATGCATAATTTGATCGTCCTGTGA
TCAAAAGACATCATATATAAGTTTAATAATATTTTCATGAACAGTTTACC
CTTTTAAAAAAAAAAAAAAAAAACTCGAGAGTACTTTTAGAGCGGCCGCG
GGCCCATCGATTTTCCACCCGGGTGGGGTACCAGGTAAGTGTACCCAATT
CGCCCTATAGTGAGTCGTATTACAATTCACTGGCCGGCGTTTTACAACGG
CGGGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTTGAGCACA
TTCCCCTTTTGCCAGGTTGGCGTAATAACAAAAGAGAGCCCGAACCGATC
GCCCTTTCCAACAAGTTGGGCAACTTGAATGGGTGAATGGAGAATCCAAA
TTTTTAAGTGGTGTAAAGGGTGTTAAACTCACTGGGATCCTTAAAGGGTT
GGGGTGATTATAAAAAACACAAACGCCCAAAGCGTTATATTCCAGGCCCC
CTCAGGTCCCTTAACAGGGCTGTGTGATGGGTCATTAAACCGCCCCCTAC
CCACCATTTCGTAGAAGAGGGTTTAACTTGCGTTTTAAAAAGAAAACTCT
CACACCCCTCTCCTCCTCGGACCCTGGAGAACAATAAATAGAAAAGGCGA
CGTTGTTTCG
BioPerl-1.007002/t/data/lucy.stderr000444000766000024        10013155576321 17040 0ustar00cjfieldsstaff000000000000lucy: ==> dropping TaLr1011A07R
TaLr1010B10R has PolyA (right).
BioPerl-1.007002/t/data/lysozyme6.protml000444000766000024      2135113155576321 20132 0ustar00cjfieldsstaff000000000000
Relative Substitution Rate Matrix
  Ala  157  163  241  172  165  314  519   65  108   92  110  135   41  574 1135 1343   26   42  869
  157  Arg  132   45  306  897   94  407  951   72  110 1951  125   20  209  293  191  382   70   51
  163  132  Asn 1602   93  225  169  229 1178  145   40  747   94   22   35 1464  683    8  207   48
  241   45 1602  Asp   31  152 2260  375  301   34   18   83   54   10   37  170  123   17  134   93
  172  306   93   31  Cys   27   16  166  217   46   49   15  120  206   37  639  140  339  641  188
  165  897  225  152   27  Gln 1010   69 1683   23  210  887  132   14  472  161  154   52   76   54
  314   94  169 2260   16 1010  Glu  332   72   33   29  515   50   13   56   91   97   35   19  138
  519  407  229  375  166   69  332  Gly   60   16   21   81   38   15   62  554   94  167   16  141
   65  951 1178  301  217 1683   72   60  His   54  160  157   95  136  335  217  140   39 1746   36
  108   72  145   34   46   23   33   16   54  Ile  699   61 1410  236   29  120  758   41   92 2869
   92  110   40   18   49  210   29   21  160  699  Leu   44 1115  751  311  174   80  161   72  525
  110 1951  747   83   15  887  515   81  157   61   44  Lys  182    7   64  140  286   27   26   37
  135  125   94   54  120  132   50   38   95 1410 1115  182  Met  128   47   82  606   60   55  882
   41   20   22   10  206   14   13   15  136  236  751    7  128  Phe   44  280   41  165 1660  179
  574  209   35   37   37  472   56   62  335   29  311   64   47   44  Pro  808  342   21   34   62
 1135  293 1464  170  639  161   91  554  217  120  174  140   82  280  808  Ser 1387   93  186  120
 1343  191  683  123  140  154   97   94  140  758   80  286  606   41  342 1387  Thr   24   60  338
   26  382    8   17  339   52   35  167   39   41  161   27   60  165   21   93   24  Trp  229   73
   42   70  207  134  641   76   19   16 1746   92   72   26   55 1660   34  186   60  229  Tyr   50
  869   51   48   93  188   54  138  141   36 2869  525   37  882  179   62  120  338   73   50  Val

Transition Probability Matrix (x1.0e7)  1PAM
-124462    2710    2370    4235    1163    2282    6582   12978     505    1898
   4091 -103605    1921     795    2070   12423    1971   10170    7387    1259
   4243    2279 -128302   28151     629    3124    3536    5717    9155    2554
   6271     780   23279 -105722     211    2112   47338    9373    2339     601
   4477    5280    1352     549  -55626     380     338    4139    1689     803
   4285   15453    3276    2678     185 -104892   21160    1731   13083     412
   8175    1621    2452   39703     109   13993  -95728    8311     559     586
  13504    7009    3322    6587    1119     959    6963  -62944     468     285
   1689   16381   17115    5289    1469   23322    1506    1506 -113378     955
   2810    1235    2112     601     309     325     699     406     422 -129830
   2386    1903     585     316     334    2915     603     520    1244   12290
   2864   33618   10853    1460     100   12284   10795    2033    1217    1074
   3520    2147    1373     950     810    1830    1056     950     739   24779
   1077     338     317     169    1394     190     275     380    1056    4139
  14924    3594     513     646     248    6543    1176    1540    2600     513
  29541    5056   21278    2987    4322    2228    1910   13846    1689    2106
  34935    3293    9922    2162     945    2133    2033    2348    1088   13315
    664    6577     121     302    2293     724     724    4163     302     724
   1082    1214    3009    2349    4329    1056     396     396   13569    1610
  22603     883     704    1625    1267     742    2893    3533     282   50403

   2819    2194    1097     560    9885   26472   26768     121     450   19374
   3396   38891    1010     265    3594    6841    3810    1805     762    1143
   1238   14891     766     295     609   34143   13614      39    2240    1080
    552    1657     439     130     634    3964    2453      81    1446    2063
   1521     296     971    2788     634   14910    2788    1605    6927    4181
   6469   17678    1071     185    8138    3750    3070     247     824    1195
    886   10273     409     177     967    2125    1935     163     204    3079
    639    1621     308     205    1062   12911    1872     788     171    3151
   4922    3122     771    1836    5766    5068    2791     184   18878     808
  21508    1218   11436    3184     504    2794   15108     195     991   63973
 -67412     873    9041   10146    5365    4047    1597     761     780   11706
   1346  -90530    1475     100    1102    3264    5698     129     286     830
  34282    3625 -113124    1725     810    1901   12073     282     598   19675
  23082     148    1035  -64432     760    6526     824     781   17951    3991
   9574    1275     381     596  -71654   18849    6824      99     364    1391
   5338    2791     661    3783   13932 -144242   27644     441    2008    2681
   2463    5698    4911     558    5899   32329 -132323     115     644    7531
   4948     543     483    2233     362    2172     483  -31919    2474    1629
   2217     528     449   22438     581    4329    1188    1082  -62933    1109
  16140     742    7155    2419    1075    2803    6732     346     538 -122884

Transition Probability Matrix (x1.0e5)  1PAM
      Ala   Arg   Asn   Asp   Cys   Gln   Glu   Gly   His   Ile   Leu   Lys   Met   Phe   Pro   Ser   Thr   Trp   Tyr   Val
Ala 98755    27    24    42    12    23    66   130     5    19    28    22    11     6    99   265   268     1     4   194
Arg    41 98964    19     8    21   124    20   102    74    13    34   389    10     3    36    68    38    18     8    11
Asn    42    23 98717   282     6    31    35    57    92    26    12   149     8     3     6   341   136     0    22    11
Asp    63     8   233 98943     2    21   473    94    23     6     6    17     4     1     6    40    25     1    14    21
Cys    45    53    14     5 99444     4     3    41    17     8    15     3    10    28     6   149    28    16    69    42
Gln    43   155    33    27     2 98951   212    17   131     4    65   177    11     2    81    37    31     2     8    12
Glu    82    16    25   397     1   140 99043    83     6     6     9   103     4     2    10    21    19     2     2    31
Gly   135    70    33    66    11    10    70 99371     5     3     6    16     3     2    11   129    19     8     2    32
His    17   164   171    53    15   233    15    15 98866    10    49    31     8    18    58    51    28     2   189     8
Ile    28    12    21     6     3     3     7     4     4 98702   215    12   114    32     5    28   151     2    10   640
Leu    24    19     6     3     3    29     6     5    12   123 99326     9    90   101    54    40    16     8     8   117
Lys    29   336   109    15     1   123   108    20    12    11    13 99095    15     1    11    33    57     1     3     8
Met    35    21    14    10     8    18    11    10     7   248   343    36 98869    17     8    19   121     3     6   197
Phe    11     3     3     2    14     2     3     4    11    41   231     1    10 99356     8    65     8     8   180    40
Pro   149    36     5     6     2    65    12    15    26     5    96    13     4     6 99283   188    68     1     4    14
Ser   295    51   213    30    43    22    19   138    17    21    53    28     7    38   139 98558   276     4    20    27
Thr   349    33    99    22     9    21    20    23    11   133    25    57    49     6    59   323 98677     1     6    75
Trp     7    66     1     3    23     7     7    42     3     7    49     5     5    22     4    22     5 99681    25    16
Tyr    11    12    30    23    43    11     4     4   136    16    22     5     4   224     6    43    12    11 99371    11
Val   226     9     7    16    13     7    29    35     3   504   161     7    72    24    11    28    67     3     5 98771
Pai 0.077 0.051 0.043 0.052 0.020 0.041 0.062 0.074 0.023 0.052 0.091 0.059 0.024 0.040 0.051 0.069 0.059 0.014 0.032 0.066

Amino Acid Frequencies
         Model    Data       
  1  A   0.077   0.091
  2  R   0.051   0.062
  3  N   0.043   0.081
  4  D   0.052   0.063
  5  C   0.020   0.062
  6  Q   0.041   0.042
  7  E   0.062   0.035
  8  G   0.074   0.073
  9  H   0.023   0.018
 10  I   0.052   0.044
 11  L   0.091   0.063
 12  K   0.059   0.066
 13  M   0.024   0.010
 14  F   0.040   0.019
 15  P   0.051   0.019
 16  S   0.069   0.068
 17  T   0.059   0.039
 18  W   0.014   0.039
 19  Y   0.032   0.045
 20  V   0.066   0.062
5 / 50  JTT model  approx ln L -1047.8 ... -1056.8  diff 9.0
29	-1047.8 ((((Bosta2,Preen),Homsa),Papan),Equca,Ratno1);
7	-1048.1 ((((Bosta2,Preen),Papan),Homsa),Equca,Ratno1);
3	-1053.3 ((((Bosta2,Preen),Equca),Homsa),Papan,Ratno1);
2	-1056.8 (((Bosta2,(Preen,Papan)),Homsa),Equca,Ratno1);
9	-1056.8 ((Bosta2,(Preen,(Papan,Homsa))),Equca,Ratno1);
BioPerl-1.007002/t/data/lysozyme6.simple.protml000444000766000024        45013155576321 21357 0ustar00cjfieldsstaff0000000000005 / 50  JTT model  approx ln L -1047.8 ... -1056.8  diff 9.0
((((Bosta2,Preen),Homsa),Papan),Equca,Ratno1);
((((Bosta2,Preen),Papan),Homsa),Equca,Ratno1);
((((Bosta2,Preen),Equca),Homsa),Papan,Ratno1);
(((Bosta2,(Preen,Papan)),Homsa),Equca,Ratno1);
((Bosta2,(Preen,(Papan,Homsa))),Equca,Ratno1);
BioPerl-1.007002/t/data/mapmaker.out000444000766000024       272213155576321 17221 0ustar00cjfieldsstaff000000000000************************************************************************
* Output from:                                Tue Aug 29 19:27:07 2001 *
*                                                                      *
*                             MAPMAKER/EXP                             *
*                            (version 3.0b)                            *
*                                                                      *
************************************************************************

data from 'P:\Chad1.TXT' are loaded
  F2 backcross data  (30 individuals, 18 loci)
'photo' is on: file is 'P:\Chad1.OUT'

12> cent kos
centimorgan function: Kosambi

13> map
===============================================================================
Map:                        
  Markers          Distance 
    1  chad1         0.0 cM
    2  chad2         0.0 cM
    3  chad3         3.3 cM
    4  chad4        10.1 cM
    5  chad5         6.7 cM
    6  chad6        13.7 cM
    7  chad7        10.1 cM
    8  chad8         3.4 cM
    9  chad9        21.7 cM
   10  chad10       21.7 cM
   11  chad11        0.0 cM
   12  chad12        3.3 cM
   13  chad13        3.3 cM
   14  chad14        0.0 cM
   15  chad15       10.1 cM
   16  chad16        0.0 cM
   17  chad17        0.0 cM
   18  chad18     ----------
                   107.8 cM   18 markers   log-likelihood= -50.67
===============================================================================

14> photo off
BioPerl-1.007002/t/data/mapmaker.txt000444000766000024        77413155576321 17216 0ustar00cjfieldsstaff000000000000Map:
  mapname=THE_NAME_OF_MAP
  Markers          Distance 
  1  bnl5.62a         35.3 cM coremarker
  2  npi406           15.6 cM EST
  3  npi439a          27.2 cM
  4  dpg11            30.7 cM ssr
  5  bnl7.21a           33 cM
  6  bnl23b            8.6 cM coremarker
  7  umc58           107.9 cM
  8  npi605a          26.5 cM EST
  9  npi120             19 cM ssr
  10  npi615           19.5 cM coremarker
  11  npi407             14 cM
  12  npi241a          45.2 cM
  13  bnl6.32       ---------- RflP
BioPerl-1.007002/t/data/mast.dat000444000766000024     50640713155576321 16402 0ustar00cjfieldsstaff000000000000********************************************************************************
MAST - Motif Alignment and Search Tool
********************************************************************************
	MAST version 3.0 (Release date: 2002/04/02 00:11:59)

	For further information on how to interpret these results or to get
	a copy of the MAST software please access http://meme.sdsc.edu.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
	If you use this program in your research, please cite:

	Timothy L. Bailey and Michael Gribskov,
	"Combining evidence using p-values: application to sequence homology
	searches", Bioinformatics, 14(48-54), 1998.
********************************************************************************


********************************************************************************
DATABASE AND MOTIFS
********************************************************************************
	DATABASE /home/sao/applications/mask_db/upstream.masked (nucleotide)
	Last updated on Mon Jul 28 14:24:33 2003
	Database contains 35386 sequences, 70745108 residues

	Reverse complement strands are not scored.

	MOTIFS acro1.set.fasta.conserved.25.meme (nucleotide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  2    21   ATGAAAAGCAGTGATTCACAG
	  3    21   AGTGCCCTGGGCCTTTAAGAG
	  4    23   AGGAGAGAGCTCACACCTCTCCC
	  8    21   AACTTCAAAATGTCTCTTTGA

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     2     3     4
	----- ----- ----- -----
	   3   0.20
	   4   0.32  0.17
	   8   0.20  0.23  0.23
	No overly similar pairs (correlation > 0.60) found.

	Random model letter frequencies (from /home/sao/proj_motif/model.bckg):
	A 0.264 C 0.241 G 0.237 T 0.258 
********************************************************************************


********************************************************************************
SECTION I: HIGH-SCORING SEQUENCES
********************************************************************************
SEQUENCE NAME                      DESCRIPTION                   E-VALUE  LENGTH
-------------                      -----------                   -------- ------
NM_148937                          ENSMUSG00000026173               1e-19   2000
NM_080688                          ENSRNOG00000016361             9.5e-18   2000
NM_032726                          ENSG00000115556                7.2e-17   2000
NM_006422                          ENSG00000111254                1.5e-06   2000
NM_011775                          ENSMUSG00000030911             7.7e-06   2000
NM_013455                          ENSMUSG00000022622              0.0015   2000
NM_009581                          ENSMUSG00000042554              0.0045   2000
NM_022915                          ENSG00000135900                  0.034   2000
NM_012490                          ENSRNOG00000013584               0.044   2000
NM_146726                          ENSMUSG00000047041               0.075   2000
NM_003460                          ENSG00000103310                   0.11   2000
NM_029236                          ENSMUSG00000037525                0.14   2000
NM_012069                          ENSG00000101892                    0.2   2000
NM_007868                          ENSMUSG00000025065                 0.2   2000
NM_006805                          ENSG00000177733                   0.21   2000
NM_012038                          ENSMUSG00000019005                0.27   2000
NM_176924                          ENSMUSG00000047730                0.27   2000
NM_053967                          ENSRNOG00000007231                0.28   2000
NM_022484                          ENSG00000146802                   0.31   2000
NM_016106                          ENSG00000092108                    0.4   2000
NM_016163                          ENSG00000092108                    0.4   2000
NM_021475                          ENSMUSG00000022057                0.57   2000
NM_013462                          ENSMUSG00000031489                0.74   2000
NM_002227                          ENSG00000162434                   0.83   2000
NM_000717                          ENSG00000167434                   0.97   2000
NM_147080                          ENSMUSG00000044506                   1   2000
NM_001097                          ENSG00000100312                    1.1   2000
NM_023662                          ENSMUSG00000031592                 1.1   2000
NM_026576                          ENSMUSG00000016984                 1.4   2000
NM_021757                          ENSRNOG00000006655                 1.6   2000
NM_019794                          ENSMUSG00000031701                 1.7   2000
NM_019343                          ENSRNOG00000003618                 1.7   2000
NM_144715                          ENSG00000163576                    1.9   2000
NM_010510                          ENSMUSG00000048806                   2   2000
NM_009241                          ENSMUSG00000029682                 2.1   2000
NM_014783                          ENSG00000175306                    2.1   2000
NM_006056                          ENSG00000171596                    2.5   2000
NM_175619                          ENSG00000182223                    2.7   2000
NM_000994                          ENSG00000144713                    2.7   2000
NM_031922                          ENSG00000135597                    2.7   2000
NM_007260                          ENSG00000011009                    2.8   2000
NM_011839                          ENSMUSG00000046212                 2.9   2000
NM_009531                          ENSMUSG00000030094                 3.5   2000
NM_011717                          ENSMUSG00000024050                 3.5   2000
NM_011291                          ENSMUSG00000025922                 3.5   2000
NM_000324                          ENSG00000112077                    3.6   2000
NM_026408                          ENSMUSG00000024534                 3.7   2000
NM_026065                          ENSMUSG00000009550                 3.7   2000
NM_010324                          ENSMUSG00000025190                 3.7   2000
NM_028381                          ENSMUSG00000003208                 3.8   2000
NM_033030                          ENSG00000152430                    3.8   2000
NM_003215                          ENSG00000135605                    3.9   2000
NM_172893                          ENSMUSG00000038507                   4   2000
NM_133867                          ENSMUSG00000040600                 4.1   2000
NM_027877                          ENSMUSG00000024906                 4.1   2000
NM_011937                          ENSMUSG00000024437                 4.2   2000
NM_024993                          ENSG00000176204                    4.2   2000
NM_002578                          ENSG00000077264                    4.3   2000
NM_021763                          ENSRNOG00000010533                 4.3   2000
NM_016957                          ENSMUSG00000051601                 4.4   2000
NM_172499                          ENSMUSG00000041945                 4.4   2000
NM_021470                          ENSMUSG00000029130                 4.9   2000
NM_177001                          ENSMUSG00000047433                 4.9   2000
NM_021836                          ENSRNOG00000003678                 4.9   2000
NM_011167                          ENSMUSG00000021345                 5.1   2000
NM_020610                          ENSMUSG00000031019                 5.2   2000
NM_026838                          ENSMUSG00000031253                 5.3   2000
NM_153270                          ENSG00000185915                    5.3   2000
NM_013255                          ENSG00000128585                    5.3   2000
NM_031817                          ENSRNOG00000015326                 5.4   2000
NM_172801                          ENSMUSG00000050201                 5.5   2000
NM_033072                          ENSMUSG00000025409                 5.6   2000
NM_177229                          ENSMUSG00000047113                 5.7   2000
NM_026776                          ENSMUSG00000035120                 5.7   2000
NM_027279                          ENSMUSG00000041396                 5.8   2000
NM_052828                          ENSG00000137394                    6.1   2000
NM_153189                          ENSG00000106304                    6.2   2000
NM_003117                          ENSG00000106304                    6.2   2000
NM_004490                          ENSG00000115290                    6.2   2000
NM_153784                          ENSMUSG00000043782                 6.3   2000
NM_011741                          ENSMUSG00000037327                 6.4   2000
NM_002192                          ENSG00000122641                    6.6   2000
NM_031249                          ENSMUSG00000050614                 6.6   2000
NM_016704                          ENSMUSG00000022181                 6.6   2000
NM_146140                          ENSMUSG00000044528                 6.7   2000
NM_026856                          ENSMUSG00000049606                 6.8   2000
NM_153572                          ENSMUSG00000041298                 6.9   2000
NM_024251                          ENSMUSG00000030051                 7.6   2000
NM_176831                          ENSMUSG00000009768                 7.6   2000
NM_172599                          ENSMUSG00000037526                 7.9   2000
NM_028539                          ENSMUSG00000048409                 8.1   2000
NM_025781                          ENSMUSG00000031953                 8.3   2000
NM_174924                          ENSG00000169340                    8.4   2000
NM_007003                          ENSG00000101951                    8.4   2000
NM_028604                          ENSMUSG00000019792                 8.5   2000
NM_013166                          ENSRNOG00000012460                 8.5   2000
NM_153399                          ENSMUSG00000040566                 8.5   2000
NM_173084                          ENSG00000175447                    8.6   2000
NM_009412                          ENSMUSG00000027506                 8.6   2000
NM_005565                          ENSG00000043462                    9.3   2000
NM_145514                          ENSMUSG00000038733                 9.4   2000
NM_000319                          ENSG00000139197                    9.5   2000
NM_139063                          ENSMUSG00000038982                 9.6   2000
NM_009980                          ENSMUSG00000030970                 9.8   2000

********************************************************************************



********************************************************************************
SECTION II: MOTIF DIAGRAMS
********************************************************************************
SEQUENCE NAME                      E-VALUE   MOTIF DIAGRAM
-------------                      --------  -------------
NM_148937                             1e-19  46_[2]_195_<3>_17_[4]_967_[4]_687
NM_080688                           9.5e-18  681_[3]_998_[2]_195_[3]_17_[4]_23
NM_032726                           7.2e-17  73_[4]_1628_[2]_163_[3]_15_[4]_33
NM_006422                           1.5e-06  94_[4]_71_[4]_105_[8]_1062_[2]_
                                             361_[8]_198
NM_011775                           7.7e-06  624_[8]_512_[3]_141_[4]_86_[2]_
                                             74_[2]_456
NM_013455                            0.0015  993_[2]_532_[8]_433
NM_009581                            0.0045  117_[4]_262_[2]_1577
NM_022915                             0.034  1378_[4]_250_[8]_71_[2]_236
NM_012490                             0.044  147_[2]_694_[3]_618_[2]_40_[8]_417
NM_146726                             0.075  1067_[3]_139_[2]_267_[8]_98_[4]_
                                             41_[2]_281
NM_003460                              0.11  592_[3]_571_[8]_71_[4]_701
NM_029236                              0.14  263_[8]_1004_[2]_661_[4]_7
NM_012069                               0.2  141_[8]_153_[8]_732_[4]_243_[2]_
                                             117_[2]_108_[2]_378
NM_007868                               0.2  493_[4]_136_[8]_522_[8]_89_[3]_
                                             4_[8]_362_[4]_39_[8]_45_[8]_138
NM_006805                              0.21  281_[8]_1075_[2]_78_[3]_3_[8]_
                                             431_[4]_25
NM_012038                              0.27  740_[8]_146_[2]_221_[8]_418_[3]_
                                             50_[8]_239_[8]_60
NM_176924                              0.27  396_[3]_1539_[4]_21
NM_053967                              0.28  148_[8]_19_[4]_799_[8]_969
NM_022484                              0.31  111_[8]_178_[4]_108_[8]_1293_
                                             [8]_224
NM_016106                               0.4  673_[2]_899_[8]_47_[3]_275_[4]_20
NM_016163                               0.4  673_[2]_899_[8]_47_[3]_275_[4]_20
NM_021475                              0.57  634_[8]_527_[8]_364_[2]_102_[8]_289
NM_013462                              0.74  333_[3]_255_[3]_593_[8]_146_[2]_589
NM_002227                              0.83  582_[8]_356_[8]_911_[4]_86
NM_000717                              0.97  167_[3]_131_[8]_772_[2]_251_[4]_593
NM_147080                                 1  355_[2]_292_[3]_909_[3]_5_[8]_
                                             243_[4]_89
NM_001097                               1.1  1490_[8]_489
NM_023662                               1.1  705_[8]_239_[3]_630_[8]_47_[8]_
                                             124_[4]_148
NM_026576                               1.4  435_[4]_299_[2]_565_[8]_367_[8]_248
NM_021757                               1.6  436_[3]_117_[2]_304_[4]_1041_[8]_16
NM_019794                               1.7  682_[8]_57_[3]_237_[8]_102_[4]_836
NM_019343                               1.7  228_[8]_40_[3]_58_[2]_655_[8]_
                                             70_[4]_241_[3]_580
NM_144715                               1.9  5_[3]_464_[4]_57_[3]_606_[8]_782
NM_010510                                 2  86_[3]_1326_[2]_153_[2]_277_[8]_74
NM_009241                               2.1  208_[2]_1224_[3]_294_[4]_209
NM_014783                               2.1  419_[3]_585_[8]_774_[2]_159
NM_006056                               2.5  724_[2]_641_[8]_593
NM_175619                               2.7  563_[2]_38_[4]_167_[8]_36_[8]_1110
NM_000994                               2.7  327_[4]_87_[8]_302_[8]_944_[8]_254
NM_031922                               2.7  396_[4]_58_[8]_92_[8]_253_[8]_
                                             418_[2]_676
NM_007260                               2.8  711_[8]_915_[2]_332
NM_011839                               2.9  111_[8]_61_[8]_414_[8]_491_[4]_
                                             211_[8]_213_[3]_64_[8]_286
NM_009531                               3.5  90_[8]_729_[2]_1002_[3]_87_[2]_8
NM_011717                               3.5  146_[8]_277_[8]_589_[4]_152_[2]_750
NM_011291                               3.5  678_[3]_299_[2]_435_[8]_161_[4]_
                                             317_[4]_1
NM_000324                               3.6  1220_[8]_55_[3]_105_[2]_557
NM_026408                               3.7  28_[2]_151_[4]_27_[4]_227_[4]_
                                             311_[8]_220_[2]_904
NM_026065                               3.7  107_[8]_176_[3]_286_[4]_735_[8]_610
NM_010324                               3.7  605_[2]_42_[2]_1105_[3]_185
NM_028381                               3.8  34_[8]_1159_[3]_6_[2]_433_[2]_284
NM_033030                               3.8  189_[3]_218_[8]_1213_[8]_53_[2]_
                                             3_[4]_170_[3]_26
NM_003215                               3.9  97_[8]_88_[3]_758_[4]_369_[2]_602
NM_172893                                 4  44_[3]_340_[2]_74_[3]_791_[3]_
                                             133_[3]_130_[8]_362
NM_133867                               4.1  769_[3]_282_[2]_761_[4]_123
NM_027877                               4.1  114_[8]_370_[2]_57_[8]_1295_[4]_78
NM_011937                               4.2  418_[4]_623_[4]_913
NM_024993                               4.2  98_[3]_552_[8]_192_[3]_111_[4]_961
NM_002578                               4.3  434_[2]_359_[2]_704_[3]_440
NM_021763                               4.3  788_[2]_130_[2]_361_[2]_173_[4]_462
NM_016957                               4.4  421_[8]_591_[3]_430_[8]_473_[8]_1
NM_172499                               4.4  686_[3]_176_[3]_34_[8]_806_[4]_212
NM_021470                               4.9  621_[4]_380_[8]_256_[2]_244_[4]_411
NM_177001                               4.9  548_[2]_1093_[3]_317
NM_021836                               4.9  1433_[4]_61_[8]_462
NM_011167                               5.1  175_[2]_314_[3]_577_[4]_584_[3]_
                                             160_[3]_83
NM_020610                               5.2  1245_[4]_285_[2]_29_[3]_376
NM_026838                               5.3  8_[2]_55_[3]_1012_[3]_538_[2]_
                                             45_[2]_106_[8]_110
NM_153270                               5.3  38_[8]_66_[4]_175_[3]_1026_[8]_609
NM_013255                               5.3  141_[3]_111_[8]_1249_[4]_122_
                                             [8]_81_[4]_187
NM_031817                               5.4  72_[8]_1324_[8]_97_[2]_444
NM_172801                               5.5  499_[3]_72_[2]_367_[8]_486_[2]_492
NM_033072                               5.6  460_[2]_458_[3]_190_[8]_399_[3]_409
NM_177229                               5.7  412_[2]_472_[8]_74_[4]_977
NM_026776                               5.7  519_[4]_464_[2]_158_[3]_794
NM_027279                               5.8  60_[2]_237_[8]_1023_[4]_615
NM_052828                               6.1  814_[2]_215_[8]_137_[4]_737_[2]_11
NM_153189                               6.2  352_[3]_1004_[8]_602
NM_003117                               6.2  352_[3]_1004_[8]_602
NM_004490                               6.2  677_[3]_153_[3]_257_[2]_576_[8]_253
NM_153784                               6.3  120_[8]_1007_[2]_521_[8]_134_
                                             [3]_134
NM_011741                               6.4  1899_[2]_80
NM_002192                               6.6  28_[4]_183_[3]_96_[8]_1046_[4]_
                                             202_[8]_126_[8]_147_[2]_21
NM_031249                               6.6  502_[8]_158_[4]_247_[2]_97_[3]_
                                             473_[8]_72_[4]_321
NM_016704                               6.6  587_[8]_93_[3]_219_[2]_432_[4]_583
NM_146140                               6.7  443_[2]_103_[3]_254_[8]_99_[3]_
                                             23_[8]_386_[4]_98_[4]_443
NM_026856                               6.8  397_[3]_368_[8]_269_[2]_170_[4]_
                                             199_[2]_457_[2]_12
NM_153572                               6.9  97_[2]_458_[4]_196_[3]_861_[8]_
                                             102_[4]_156_[8]
NM_024251                               7.6  73_[2]_64_[4]_508_[8]_658_[4]_609
NM_176831                               7.6  44_[8]_733_[3]_368_[2]_99_[8]_672
NM_172599                               7.9  1166_[2]_279_[8]_391_[8]_101
NM_028539                               8.1  226_[4]_1039_[2]_60_[8]_182_[8]_407
NM_025781                               8.3  55_[2]_61_[8]_123_[8]_23_[4]_
                                             823_[2]_624_[3]_163
NM_174924                               8.4  779_[3]_64_[4]_957_[2]_135
NM_007003                               8.4  311_[4]_68_[2]_1483_[4]_71
NM_028604                               8.5  577_[8]_511_[3]_310_[4]_356_[4]_158
NM_013166                               8.5  605_[8]_749_[2]_604
NM_153399                               8.5  39_[2]_895_[4]_1022
NM_173084                               8.6  201_[2]_643_[8]_634_[3]_459
NM_009412                               8.6  125_[8]_526_[2]_87_[2]_483_[8]_
                                             83_[4]_70_[8]_498
NM_005565                               9.3  878_[8]_563_[2]_409_[8]_87
NM_145514                               9.4  314_[3]_436_[8]_635_[8]_521_[8]_10
NM_000319                               9.5  118_[2]_227_[3]_160_[8]_1250_
                                             [4]_159
NM_139063                               9.6  622_[4]_876_[4]_203_[2]_232
NM_009980                               9.8  437_[3]_1109_[8]_62_[2]_308_[8]

********************************************************************************



********************************************************************************
SECTION III: ANNOTATED SEQUENCES
********************************************************************************


NM_148937
  ENSMUSG00000026173
  LENGTH = 2000  COMBINED P-VALUE = 2.87e-24  E-VALUE =    1e-19
  DIAGRAM: 46_[2]_195_[3]_17_[4]_967_[4]_687

                                                   [2]
                                                   2.9e-13
                                                   ATGAAAAGCAGTGATTCACAG
                                                   +++++++++++++++++++++
1    GAATTGAGGGCAAAAACAGCGGTATTCCACACAGACTCTGAGCAGAATGAAAAGCAGTGATTCACAGCACACTGC

                                          [3]
                                          1.9e-13
                                          AGTGCCCTGGGCCTTTAAGAG
                                          +++++++++++++++++++++
226  TTCTGCAACCCCACCCCCACAATTCCTCCTGTTGACCAGTGCCCTGGGCCTTTAAGAGTTGGATAGGCTGGACCT

     [4]
     2.6e-13
     AGGAGAGAGCTCACACCTCTCCC
     +++++++++++++++++++++++
301  AGGAGAGCGCTCACACCTCTCCCCACCCCACTCCTCCTCTCTGGCTGTAACTCTGCCAGTTTACAGCAGCAAACT

                    [4]
                    3.6e-05
                    AGGAGAGAGCTCACACCTCTCCC
                    +++  +++ +++++ ++++++++
1276 CACTTTATATGAAACAGGTTAGCCATAACCCTTCTCAGAAGTGAGAACATAGACAAAATAGCTCTCTTCCTTCCT


NM_080688
  ENSRNOG00000016361
  LENGTH = 2000  COMBINED P-VALUE = 2.67e-22  E-VALUE =  9.5e-18
  DIAGRAM: 681_[3]_998_[2]_195_[3]_17_[4]_23


           [3]
           9.1e-05
           AGTGCCCTGGGCCTTTAAGAG
           ++ + + +  +++++++++++
676  TGTTACAAAGTTGTAATTCATTAAAAGATGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                                                       [2]
                                                       2.9e-13
                                                       ATGAAAAGCAGTGATTCACAG
                                                       +++++++++++++++++++++
1651 AGATGAAATGAGGGCAAAAACAGTGGTATTCCACACAGACTCCGACCAGAATGAAAAGCAGTGATTCACAGAGCA

                                              [3]
                                              4.9e-12
                                              AGTGCCCTGGGCCTTTAAGAG
                                              +++++++++++++++++++++
1876 CCTTTTCTGTCACTCCACCCCCACAACTCCTCCTGTTGACCAGTGCTCTGGGCCTTTAAGAGTTAGATAGGCTGG

         [4]
         7.7e-13
         AGGAGAGAGCTCACACCTCTCCC
         +++++++++++++++++++++++
1951 ACCTAGGAAAGCGCTCACACCTCTCCCCACTCCACTCCTCTCTGGCTGTA


NM_032726
  ENSG00000115556
  LENGTH = 2000  COMBINED P-VALUE = 2.04e-21  E-VALUE =  7.2e-17
  DIAGRAM: 73_[4]_1628_[2]_163_[3]_15_[4]_33

                                                                              [4
                                                                              6.
                                                                              AG
                                                                              +
1    GAAGAATACTGTTGTATTCATGGGAACATTGAAACAGAATATTTGAGATCTAGACTCTCCCAGAAAATCCACTAT

     ]
     7e-06
     GAGAGAGCTCACACCTCTCCC
     +++ ++ +++++ ++++++++
76   GAGTGATAACACCCCTCACAGATTACCCAAGAGGGAAGGAGGTTGGGCAGCATTAAATTGATGCAAATAGTGACT

                                                                               [
                                                                               2
                                                                               A
                                                                               +
1651 GTGGAAACAGACACTATGGAAAGGAGCCAGATTAAATAAGGGCAAAAACAGCCGTATTACATGCAGGAACCAGAA

     2]
     .9e-13
     TGAAAAGCAGTGATTCACAG
     ++++++++++++++++++++
1726 TGAAAAGCAGTGATTCACAGAGCACTGCAACTGAGGACACTCCCTTCACTTTGAGAGCTACTGCGGGATTGGGGT

                                      [3]                                 [4]
                                      4.2e-11                             2.1e-1
                                      AGTGCCCTGGGCCTTTAAGAG               AGGAGA
                                      ++++ ++++++++++++++++                +++++
1876 CCACCCCACCCCCACTACTCCCTCACATTGACCAGTGTCCTGGGCCTTTAAGAGTTGGATGGGCTGGACTGGAGA

     
     2
     GAGCTCACACCTCTCCC
     +++++++++++++++++
1951 GAGCTCACACCTCTCCCCTTCTTACTGCTTCCCTCCGGCTATAACTTGCC


NM_006422
  ENSG00000111254
  LENGTH = 2000  COMBINED P-VALUE = 4.16e-11  E-VALUE =  1.5e-06
  DIAGRAM: 94_[4]_71_[4]_105_[8]_1062_[2]_361_[8]_198


                        [4]
                        3.6e-05
                        AGGAGAGAGCTCACACCTCTCCC
                        ++ ++ +++++ +++++  ++++
76   GATCAGCAGGACTGTCTCCAGCACGGAGCTGACACTGTTCAGCTGCCTCAACTGGTAGACGCTCCCAAGAAGTCA

                                           [4]
                                           1.0e-11
                                           AGGAGAGAGCTCACACCTCTCCC
                                           +++++++++++++++++++++++
151  GAGGCAGCTGTCGGGGCGGAGGTGTCCATGACCTCCCCAGGACAGAGCAAAAACTTCTCCCTCAAGAACACAAAC

                     [8]
                     2.3e-09
                     AACTTCAAAATGTCTCTTTGA
                      ++++++ +++++++++++++
301  CACTTATATTGTACAATACTTCAGACTGTTTTTTTTAAATACATAAAACTTTATGTTAAAAAACTCTATTAACAT

                                                      [2]
                                                      3.7e-05
                                                      ATGAAAAGCAGTGATTCACAG
                                                      + ++++ ++++ +++ ++ +
1351 CCAGGAAAGACAAATATATAAGGAGTTGCCAGAGTTGAGGAGGTCCTCCAAGAGACCCAGAGATACAGAAAGAAA

                                                             [8]
                                                             4.9e-06
                                                             AACTTCAAAATGTCTCTTT
                                                             ++  + ++++++  ++ ++
1726 TCAGGATGATTTTGATTGAATAATTCAAAAGTATCTTCTGATTTTCATGGTTATAAAAGGTTAAAATGAATTCTT

     
     
     GA
     ++
1801 GATAAACTGTGGCTTATTTTAAGAGAATAGTTTAAATAAGGAAGCTGCAAATTGTGACACAGACAGGGGACAGGC


NM_011775
  ENSMUSG00000030911
  LENGTH = 2000  COMBINED P-VALUE = 2.18e-10  E-VALUE =  7.7e-06
  DIAGRAM: 624_[8]_512_[3]_141_[4]_86_[2]_74_[2]_456


                             [8]
                             3.2e-09
                             AACTTCAAAATGTCTCTTTGA
                             +++++ +++++++++++++++
601  ATTTGAACCTCTTCCCAATTACAGAGATTAAAAATGTTTTTTGGAGGGGGGAGATCATATTTTCTAGTCAAAGGT

                                     [3]
                                     4.0e-05
                                     AGTGCCCTGGGCCTTTAAGAG
                                      +++++ +++ + +++++++
1126 AAAAATACACATGTCAAGCTTTGGCATCGAGAGGTGCTGTGGACATTTAAGAAGTTATTAGGCCATGGAGGATGA

                                                 [4]
                                                 2.9e-05
                                                 AGGAGAGAGCTCACACCTCTCCC
                                                  +++++ + +++ ++  +++ ++
1276 ATGATGGGACCATCCAGGCTTGGACTTGAGCATCAACAGGAAGGTGGAAAACAATCCCAAATCATCCCCAAAGCC

        [2]
        4.0e-05
        ATGAAAAGCAGTGATTCACAG
         +  +++ ++++++++++ ++
1426 TGTGTCCAAGTAAGGGACTCAAACACAGAGGACTCTTAAGTGTACTGTCAGGTGGGCTGCAGCTAAACCCTATTG

                            [2]
                            7.5e-10
                            ATGAAAAGCAGTGATTCACAG
                            ++++++  +++++++++++++
1501 AACATACATGACATGTGTCGGGTATAAGACTAAGGGATTCACAGAATCTCAGATAGGAGATTTACCTTCTCTTGT


NM_013455
  ENSMUSG00000022622
  LENGTH = 2000  COMBINED P-VALUE = 4.27e-08  E-VALUE =   0.0015
  DIAGRAM: 993_[2]_532_[8]_433


                       [2]
                       1.4e-05
                       ATGAAAAGCAGTGATTCACAG
                       + +++++ ++++ ++++ +++
976  CGGGCCTTGATGTGGAAAAAAAAAAACAGTTATTCTCACATATGGAGAAAGGAAGTCTGCTTTCTGATGCTTAGG

                                                   [8]
                                                   1.7e-12
                                                   AACTTCAAAATGTCTCTTTGA
                                                   +++++++++++++++++++++
1501 ACTCAGCAGTGGGCAAGAAGGTAGGCTTTGAAGTCATAAGTCAAGCAACTTCAAAATGGCTCTTTGAAAGTGTTC


NM_009581
  ENSMUSG00000042554
  LENGTH = 2000  COMBINED P-VALUE = 1.26e-07  E-VALUE =   0.0045
  DIAGRAM: 117_[4]_262_[2]_1577


                                               [4]
                                               2.6e-09
                                               AGGAGAGAGCTCACACCTCTCCC
                                               ++++++++ ++ ++++++++ ++
76   CACACTTTCGTTCTGAATTTACGTTTATAGGGATGAAACTTCAGGAAAGAAAAGACACTTCATAGTGTAGAAACA

                                [2]
                                5.9e-09
                                ATGAAAAGCAGTGATTCACAG
                                + ++++++++++++++++ ++
376  NNNNNNNNNNNNNTCCCAGAAAGCATAAAAGGAGCAAGTGATTCATAGACTGCTTGCTTTCTGCAGGTGCAAACA


NM_022915
  ENSG00000135900
  LENGTH = 2000  COMBINED P-VALUE = 9.57e-07  E-VALUE =    0.034
  DIAGRAM: 1378_[4]_250_[8]_71_[2]_236


                                 [4]
                                 5.2e-06
                                 AGGAGAGAGCTCACACCTCTCCC
                                 ++++++++ +++ ++ + ++  +
1351 AAAAATTGTACTGTATTAACAGTTTGGTAGGAAAGCAATAGAATTACATTGTTAAAGAGTGTTAACATAAAGAAG

      [8]
      1.1e-08
      AACTTCAAAATGTCTCTTTGA
      +++++ ++++++++++ +++
1651 TAAATTAAAAATGTTTTCTTTTTTTGAGGATTTAAATGTTTCCTTAACCTGAAAGCGAAACAGATTTTTGTTTGT

                       [2]
                       5.3e-06
                       ATGAAAAGCAGTGATTCACAG
                         +++++++++ ++ + ++++
1726 TTTGCTGTAACGAGAGAGGAAGGAACAAGAGAGTGACAGGGTGAAGCAACTTCTCCCAGAAACTTTTGGGCGCAA


NM_012490
  ENSRNOG00000013584
  LENGTH = 2000  COMBINED P-VALUE = 1.25e-06  E-VALUE =    0.044
  DIAGRAM: 147_[2]_694_[3]_618_[2]_40_[8]_417


                                                                             [2]
                                                                             9.4
                                                                             ATG
                                                                              ++
76   TTACTGGAGATATGCTTATAGCCCAAGAGGGAGGATGAGACCTTCTAGTCACTTACAGAGGAAAGACAAAACCTA

     
     e-05
     AAAAGCAGTGATTCACAG
     ++++++++++ +++ ++
151  GAAAGCAGTGCTTCTCAACCTTCCTTTTTTTTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                                          [3]
                                          4.2e-05
                                          AGTGCCCTGGGCCTTTAAGAG
                                          ++ +++ ++++++++ + + +
826  AGAACGTGTGACAAGGTGCCACGCAGAAGAAAGAAATAAGACCTTGGGCCCTGATGTGGAAAAGAACAGTTCTCA

      [2]                                                          [8]
      6.0e-05                                                      7.2e-11
      ATGAAAAGCAGTGATTCACAG                                        AACTTCAAAATGT
        +++++ + +++++ + +++                                        +++++++++++++
1501 TCAAGAAGTATGTGATACTCAGAAATGGGCAAGAAGGTAGGCTTTGAAATCATAAGTCAAGAAACTTCAAAATGG

     
     
     CTCTTTGA
     +++ ++++
1576 CTCCTTGAAAGTGTTCTGGTAAACCCCCCCCCCCCCACGCCCCTGTACTGATGATCCCATCAGTCAGCAGAACCC


NM_146726
  ENSMUSG00000047041
  LENGTH = 2000  COMBINED P-VALUE = 2.12e-06  E-VALUE =    0.075
  DIAGRAM: 1067_[3]_139_[2]_267_[8]_98_[4]_41_[2]_281


                      [3]
                      5.6e-05
                      AGTGCCCTGGGCCTTTAAGAG
                      + +   ++++++ +++++++
1051 AGTTGTCAACAATTACTATTTAGATGGGCTCTTAAAATAATCTTTTATGGAACTCATGAGTTGGTGCCAAACAAC

                                [2]
                                8.0e-05
                                ATGAAAAGCAGTGATTCACAG
                                + ++++++++ +  +  ++++
1201 TGGGACTAGTGAGATCATGGACCTTAGAAAAGAAGCAATTTCCGACACTTTGCTAGGCCAGCATTAATTCCTTAC

                    [8]
                    5.0e-05
                    AACTTCAAAATGTCTCTTTGA
                     + ++++++++ + +++ ++
1501 AGGCTTTTGTAATCATGTTTCAAAATTTATTTCTTTAATGGTTATTCAAATTTTTGAACAATGGGCTTAGGTAGA

                                                                [4]
                                                                2.3e-07
                                                                AGGAGAGAGCTCACAC
                                                                 ++++++++++  ++
1576 AGCATAGGGACTGAGCAGCTGCTTAATTAGAGAATAGCAGTGACTTGAACTCTCAGAAATGGACAGAGAAGCAAG

                                                     [2]
                                                     1.4e-07
     CTCTCCC                                         ATGAAAAGCAGTGATTCACAG
     + +++++                                         + +++++++ +++++ ++ ++
1651 CACACACACAATATAAAACTGAACAGAATGGTAAGTGGCAGAACAGAGAGAAAAAGAGGTGATACATAGAAAGAC


NM_003460
  ENSG00000103310
  LENGTH = 2000  COMBINED P-VALUE = 3.14e-06  E-VALUE =     0.11
  DIAGRAM: 592_[3]_571_[8]_71_[4]_701


                                                                        [3]
                                                                        1.5e-09
                                                                        AGTGCCCT
                                                                        ++++++ +
526  TTAGTTATGATATACAATGCAACTTGATAAAGTCACACAGAATTTTGAATCTAAAACTATTTAGCAGAATGCCTT

     
     
     GGGCCTTTAAGAG
     ++ ++++++++++
601  GGATCCTTAAAAGAAGGTCCAAAGAAGGCTTTTGATGAGACAATTTGAGCTTTTGACCCTATTACTCTAGAAATG

                                                                [8]
                                                                7.4e-06
                                                                AACTTCAAAATGTCTC
                                                                +++++  ++++ ++++
1126 AGCTGACATTTAAATCCAGCCACTAGAAGCTTTCATCACTTATTCTTCCTGCCATACGTAGATTTGAAATATTTC

     
     
     TTTGA
      +++
1201 CTTGCAAAAATTTTAGACTCAAGTTTTCTAGAATACAAGTGAATTTCCATATATCTTGAAGGTCTCTAAGAGCTG

      [4]
      6.3e-05
      AGGAGAGAGCTCACACCTCTCCC
      ++ + + ++++ +++++  +++
1276 CAGTATAAAGCAGACACTAGTCATGTTGATGACATAATTACTTAGAATAAGACTGGCTACCCTCAGGACGAAGGC


NM_029236
  ENSMUSG00000037525
  LENGTH = 2000  COMBINED P-VALUE = 3.92e-06  E-VALUE =     0.14
  DIAGRAM: 263_[8]_1004_[2]_661_[4]_7


                                           [8]
                                           7.8e-06
                                           AACTTCAAAATGTCTCTTTGA
                                            ++++ +++++++++  +++
226  TCTTTTCCCATCCTTCCATTCCCACTGTCTCCTAACCCTGATTTAAAATGTTTGGTGGCCCTCAAACTGAACATG

                  [2]
                  1.0e-05
                  ATGAAAAGCAGTGATTCACAG
                  + ++ +++++ ++ + ++ ++
1276 AAATATATAAACTAAGACAGCCAAGGCTACATAGATACCTTGTCTTAAAAGACAAACAAATAAACAAAAAGTCCC

                         [4]
                         6.6e-09
                         AGGAGAGAGCTCACACCTCTCCC
                         ++++++++ ++ ++++  +++++
1951 AGAAACCAGATCAGATTTTAAGGAGAGCAAAGAAACGACACAGCCTTTTT


NM_012069
  ENSG00000101892
  LENGTH = 2000  COMBINED P-VALUE = 5.75e-06  E-VALUE =      0.2
  DIAGRAM: 141_[8]_153_[8]_732_[4]_243_[2]_117_[2]_108_[2]_378


                                                                       [8]
                                                                       3.3e-06
                                                                       AACTTCAAA
                                                                       + +++++++
76   ACCTGTGCCCAAGAAATGAGCATGTAGTTTTCTAGACTTTAATAATGTGCCCCCGAATCTGCTGTTATATTCAAA

     
     
     ATGTCTCTTTGA
      + ++++ +++
151  GTCTCTCCTTTCTCCCTCCCCTTGTCCCTTTGTAGCCACTGCTTCATTTGCATCCGCATTAGCCACTTGTGGCTC

                    [8]
                    7.5e-07
                    AACTTCAAAATGTCTCTTTGA
                    ++++++++++ + +++ +++
301  TAGTGTTTTGAGTGTAAATTCATACAGATTTCTGTCTTCAACATCCTATGGGATTTGGTTATTTTACCCCACCCA

                       [4]
                       7.1e-07
                       AGGAGAGAGCTCACACCTCTCCC
                       +++++ ++ ++++++++ ++ ++
1051 ATGGGGTTTGATTTGTGAAGGAAGGATCACAAACTCCATCCAGGCCTTTTAGCCACCCAGGCTCCAGTAGGGTGG

                                                                [2]
                                                                3.7e-06
                                                                ATGAAAAGCAGTGATT
                                                                +++++ ++++++++++
1276 GGATAAATATAGATCTCAACCACTACAGAAATTTGGCCAGGATTTGGAGGGGTGTGTGTATGAGGGGCAGTGACT

     
     
     CACAG
      +  +
1351 GATGGGGCCACTCTGACATGTGGGCTAGAAAAAGGCTTCCTTATGTCCAAGACCCTCTTTGGGGCAGGGAGGAAT

                                                    [2]
                                                    7.7e-06
                                                    ATGAAAAGCAGTGATTCACAG
                                                    + +++   ++ +++++ ++++
1426 GAAGTAGGAGCCTGGCTTCTAAAATCAGAAAGAATAATCCACATTTTAAGAAGCTCATGGATTGACACAAATAAG

                               [2]
                               3.7e-05
                               ATGAAAAGCAGTGATTCACAG
                               + ++++++++++ ++++   +
1576 TCCTTTTGCATGAGATCAGCCTTATGAAAAAAGCAAGTTATTCTTGGCCATCTCCCCTCACCCCCAACTCCCACC


NM_007868
  ENSMUSG00000025065
  LENGTH = 2000  COMBINED P-VALUE = 5.78e-06  E-VALUE =      0.2
  DIAGRAM: 493_[4]_136_[8]_522_[8]_89_[3]_4_[8]_362_[4]_39_[8]_45_[8]_138


                                                [4]
                                                2.2e-05
                                                AGGAGAGAGCTCACACCTCTCCC
                                                 +++++ +  +  +++++++ +
451  TTCTACCTTGCACACAAACTTCTGCATTTAAAGTGACTGTGGCTGGAAACATGAGCCACTTCTTCAAGATTACTA

                                                         [8]
                                                         1.0e-07
                                                         AACTTCAAAATGTCTCTTTGA
                                                         +++++++ ++++  +++++ +
601  AGGGGAGGGAAGGAATTTTTTTTCAGTCACACAGATCAATTCAATTTGTCGGAGCTTCAGAATGAATTTTTAAAT

                                                                           [8]
                                                                           5.5e-
                                                                           AACTT
                                                                           +++
1126 CTATGCAACAGGATCAGTGCTGTAGTCCCCGGTTCAAGCTGAAAATGTTGCACAGGAAGACATATCATGTAAAGG

     
     05
     CAAAATGTCTCTTTGA
      ++ +++ ++++++++
1201 TATTATGATTTTTTTATCTGTGTCTATACAAACAGAACTTAATGTCATAACTCTTGTCATAACCCTTACCAAGGT

                                   [3]                      [8]
                                   1.1e-06                  6.3e-05
                                   AGTGCCCTGGGCCTTTAAGAG    AACTTCAAAATGTCTCTTTG
                                   ++++  +++++  ++++++ +     ++++  ++++  ++ ++++
1276 CCTATGGACTCTTTACCTGTCAAGTCTGAAAATATGATGGTATTTTAAATGGGAATGCTTAGTAATCATTGTTTG

     
     
     A
     +
1351 ATGTTGATGTATCTATGATGCCATAGTACCAAGGTGAACTGCTGTCCGTTTTCAAGAAGATGCTCTTGTCTCATT

                                                                    [4]
                                                                    1.9e-05
                                                                    AGGAGAGAGCTC
                                                                    ++++++ + +++
1651 AAATTATAAAATGTGCTATCTGTATATTAATTCTATTATATAATTATAATAACTTGGCAAGGCAGGACACCAAAA

                                                       [8]
                                                       5.6e-05
     ACACCTCTCCC                                       AACTTCAAAATGTCTCTTTGA
     +++ +  ++++                                        ++ + +++++ ++++++++
1726 ACATTATTCAGGACATATTTTCTTGTTAGTTGCCAAGATAGAATTTCTTTGAACTAATAATTTTTTTTTTTTTTT

                                              [8]
                                              3.9e-05
                                              AACTTCAAAATGTCTCTTTGA
                                               +++++  +++++ ++++ +
1801 AGTTCTTCAAATTCACATTCCCAGCAAGTCTCTTTGTTTGGTAATTCTGAATGTGTTTTATTGCTTTCTGGTAGG


NM_006805
  ENSG00000177733
  LENGTH = 2000  COMBINED P-VALUE = 5.92e-06  E-VALUE =     0.21
  DIAGRAM: 281_[8]_1075_[2]_78_[3]_3_[8]_431_[4]_25


                                                             [8]
                                                             2.5e-05
                                                             AACTTCAAAATGTCTCTTT
                                                             ++++++ ++ + +  ++++
226  TAAAAAATGGTTCNNNNNNNNNNNNNNNNNNNNNNNNNNNGCCCAATCTTTCAGAAAGCTTCTTAGTATAGCTTT

     
     
     GA
     ++
301  GAGCCTTCAACGTCAACATGTAAGTCAAATATTTAAGTTAAATATTAACATCAAGTTAAGCATACTAGATTAAAA

                                [2]
                                6.2e-05
                                ATGAAAAGCAGTGATTCACAG
                                  +++++ ++ + +++ ++++
1351 GACCTCTTAAGTTTCTCTAAGTACACATCAAGAATAAAGAATTAACACGTAAAGTCTTAAACAAATATCCCTTAA

                                                        [3]
                                                        2.0e-06
                                                        AGTGCCCTGGGCCTTTAAGAG
                                                        ++ ++ +++ ++ +++++++
1426 AAAACGGTACGGAATGGATCCTAGAAAAAAAATGTTAGACATGTACGGTCAAACACAATGATTTATTAAAAATAA

     [8]
     1.6e-07
     AACTTCAAAATGTCTCTTTGA
     +++ + ++++++ ++++++++
1501 AACGTAAAAATGATTTTTGTACATATGCTTCCAAATTTCAGGCATGGGATCCAAGTAGATTTCATAGAAAACGCT

       [4]
       1.5e-05
       AGGAGAGAGCTCACACCTCTCCC
        +++++++++++ + ++  + ++
1951 GTTGGAAAGAGCTACCCCTATAGCCACTCCCAGGCATTTTAAATTTTCTT


NM_012038
  ENSMUSG00000019005
  LENGTH = 2000  COMBINED P-VALUE = 7.63e-06  E-VALUE =     0.27
  DIAGRAM: 740_[8]_146_[2]_221_[8]_418_[3]_50_[8]_239_[8]_60


                                                                      [8]
                                                                      3.4e-06
                                                                      AACTTCAAAA
                                                                      +++  +++++
676  GAGGACACACATGGCTTTTCTTCAGTGCTGAGCGGGACAGTCTACACTAATAAAAAAGAGGACTAAAAAGCAAAC

     
     
     TGTCTCTTTGA
     +++ ++++++
751  TGGATTTTTGTTCACACAGCATCTACATCTTCTAAAAAGAACGAGTGGCATGGAGGAGCCGAGCAGTGGTGGCAC

            [2]
            1.0e-07
            ATGAAAAGCAGTGATTCACAG
            + ++ ++++++++++ +++++
901  GGGTTCCAGGATAGCCAGGGATACACAGAAAATCCTGTCTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                             [8]
                             6.7e-05
                             AACTTCAAAATGTCTCTTTGA
                              + ++  + ++++++++++++
1126 CTATTCCCTGCTCTTATCTTGCTGTGTTTTCTTCTGTTTCTTGGAGTTTGACATTCATGAGTGTGTCGTCTGTCT

                  [3]
                  1.0e-05
                  AGTGCCCTGGGCCTTTAAGAG
                  ++++++ +++ +++   ++++
1576 GCACTCCATTAAAAGTGCTTTGGATCAAGGAAAGAATGCTGCAGTGTTTGATAAAAGGAAGCATGGGCTCTACAC

              [8]
              1.3e-05
              AACTTCAAAATGTCTCTTTGA
               ++++ +++  + ++++ ++
1651 AAGTTAGTTTAATTAAAAGGGATTTTGTGTTTTTGTTTTGTGGTCACAGCGCCTGCCCCTGAGAGGCTTAATAGC

                                                 [8]
                                                 6.1e-05
                                                 AACTTCAAAATGTCTCTTTGA
                                                  ++++  ++ +   +++++++
1876 GTCAGTTTTATTCCATCCTGAAAAATAAAAAGTAGCATGCCTTTTACTTTGAATTTAATCTTGGATGACCCCACT


NM_176924
  ENSMUSG00000047730
  LENGTH = 2000  COMBINED P-VALUE = 7.76e-06  E-VALUE =     0.27
  DIAGRAM: 396_[3]_1539_[4]_21


                          [3]
                          1.2e-05
                          AGTGCCCTGGGCCTTTAAGAG
                          ++++ +++++ + +++ +++
376  GAAATTTTATATTTAATTTTTAATAGCATGGATTTTTTAAAAATGTCTGTTGCAACTAGTTCAGAGACTTCAAGC

           [4]
           2.0e-09
           AGGAGAGAGCTCACACCTCTCCC
           ++++++++ +++++++   ++ +
1951 GTCTGAAGGAGAGATCACACACGAGTCTGACCACTGTCACCTCTCTGCAG


NM_053967
  ENSRNOG00000007231
  LENGTH = 2000  COMBINED P-VALUE = 7.90e-06  E-VALUE =     0.28
  DIAGRAM: 148_[8]_19_[4]_799_[8]_969


                                                                              [8
                                                                              2.
                                                                              AA
                                                                              ++
76   NNNGTTCTTTTTACATAGTGTATTCTGCTGTCACTTCCCCCTCCAACTCCTCCCAGATCTTTCTCACATACCTAA

     ]                                     [4]
     7e-10                                 5.6e-05
     CTTCAAAATGTCTCTTTGA                   AGGAGAGAGCTCACACCTCTCCC
     ++++++++++++++++++                    ++ ++++ ++++++ +++++ ++
151  CTTCATACTGTCTCTTTTTCTTCCTCTCTTTAAAAAACAGAAGAGTGAAAAACCTTCAAACTNNNNNNNNNNNNN

                                        [8]
                                        5.3e-05
                                        AACTTCAAAATGTCTCTTTGA
                                        +++   ++++++ +++ +++
976  TATAGAAGATGGTAGGGGCAAGGGACACTCTTACTAACAATATAATGATTTATTGTTTTATTAGATTTATTATTG


NM_022484
  ENSG00000146802
  LENGTH = 2000  COMBINED P-VALUE = 8.65e-06  E-VALUE =     0.31
  DIAGRAM: 111_[8]_178_[4]_108_[8]_1293_[8]_224


                                         [8]
                                         1.4e-05
                                         AACTTCAAAATGTCTCTTTGA
                                          ++++ + +++ +  +++++
76   AATCTACCCACTAATGCATTAAATATAAGTGCATTTTAATTAAGACTTTAATTTTTTTAAAGCATAACTGGTCAT

               [4]
               1.7e-05
               AGGAGAGAGCTCACACCTCTCCC
                ++ ++++++++ +++++  + +
301  TGAAAAGTCATGGGGAGAGAAAGAACTTGGCTCCTTATTTATTTTGCAACAGTGTGTATGCTATTNNNNNNNNNN

                                                                       [8]
                                                                       6.6e-10
                                                                       AACTTCAAA
                                                                       +++++++++
376  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTAAAATAAATAAATAATGGTTAAAAAAAGAAAATAAATTCATA

     
     
     ATGTCTCTTTGA
     ++++++++++++
451  CTGTTTTTTTTATTCTATTGAAAAAAAAGATGATGTTTTTAGAGCTAGTGGTTTTGTGGTTTTAGCAAGGTATCA

                                   [8]
                                   5.0e-05
                                   AACTTCAAAATGTCTCTTTGA
                                    ++++ + + +  +++++++
1726 CAAATAGCTGAGAAATTTAAAAGGAGATTTTACTTAACATTAACTTTTTTTAAGCTAAAAGCTCATAATTTTAAC


NM_016106
  ENSG00000092108
  LENGTH = 2000  COMBINED P-VALUE = 1.12e-05  E-VALUE =      0.4
  DIAGRAM: 673_[2]_899_[8]_47_[3]_275_[4]_20


                                                                              [2
                                                                              7.
                                                                              AT
                                                                              +
601  NNNNNNNNNNNNNNAGAGATTATGTAATAAGATAACCTGTTTTAAATGTCACAAAAATAAATTTTTATTAATGAA

     ]
     3e-08
     GAAAAGCAGTGATTCACAG
     +++++++++++ +++++++
676  AAAAGCCAGTGTTTCACACTATAAAACAATATATAATCGTTAGGCTAACCATTTCATTTATATAATTGTGAAAGT

                       [8]
                       3.2e-05
                       AACTTCAAAATGTCTCTTTGA
                       +++ + ++++++++ + +++
1576 CACTGAGAAACGAGAGCTAACGTTAAAATGTTGCCTGTGTTTCAGGAGCTTCATTTACTTCAGTCCTGTGGTCCT

                [3]
                1.9e-05
                AGTGCCCTGGGCCTTTAAGAG
                ++ + +++   ++++++++ +
1651 TATACTCCTAGAGCATTATCACCCTTTAAGTGCTCTGTAAGTCACCAAACCAACAGTTCAGTAATTAGGTTCTTA

            [4]
            1.4e-05
            AGGAGAGAGCTCACACCTCTCCC
             ++ +++ +++  +++ +++ ++
1951 TCCGGGGCGGTAAGGGCAGCCACGTCATCCCCCCGCTCCGCTCCCCAGCC


NM_016163
  ENSG00000092108
  LENGTH = 2000  COMBINED P-VALUE = 1.12e-05  E-VALUE =      0.4
  DIAGRAM: 673_[2]_899_[8]_47_[3]_275_[4]_20


                                                                              [2
                                                                              7.
                                                                              AT
                                                                              +
601  NNNNNNNNNNNNNNAGAGATTATGTAATAAGATAACCTGTTTTAAATGTCACAAAAATAAATTTTTATTAATGAA

     ]
     3e-08
     GAAAAGCAGTGATTCACAG
     +++++++++++ +++++++
676  AAAAGCCAGTGTTTCACACTATAAAACAATATATAATCGTTAGGCTAACCATTTCATTTATATAATTGTGAAAGT

                       [8]
                       3.2e-05
                       AACTTCAAAATGTCTCTTTGA
                       +++ + ++++++++ + +++
1576 CACTGAGAAACGAGAGCTAACGTTAAAATGTTGCCTGTGTTTCAGGAGCTTCATTTACTTCAGTCCTGTGGTCCT

                [3]
                1.9e-05
                AGTGCCCTGGGCCTTTAAGAG
                ++ + +++   ++++++++ +
1651 TATACTCCTAGAGCATTATCACCCTTTAAGTGCTCTGTAAGTCACCAAACCAACAGTTCAGTAATTAGGTTCTTA

            [4]
            1.4e-05
            AGGAGAGAGCTCACACCTCTCCC
             ++ +++ +++  +++ +++ ++
1951 TCCGGGGCGGTAAGGGCAGCCACGTCATCCCCCCGCTCCGCTCCCCAGCC


NM_021475
  ENSMUSG00000022057
  LENGTH = 2000  COMBINED P-VALUE = 1.62e-05  E-VALUE =     0.57
  DIAGRAM: 634_[8]_527_[8]_364_[2]_102_[8]_289


                                       [8]
                                       3.1e-08
                                       AACTTCAAAATGTCTCTTTGA
                                       +++++ +++ +++ ++ +++
601  TCAGTGTGTGTGTGTAATCTATCCAATAATTCATAAATTAATAGTGGATTCTTGCCTTTCCGGTTATGCACATCC

                                                              [8]
                                                              1.9e-05
                                                              AACTTCAAAATGTCTCTT
                                                               +++  + +++++++++
1126 ACTGATAGATCAAGAACGAATTGAGGAACAAGACCTTAGTATCAGACCCACCCTCTGTACTCAACAATGGCTCTC

     
     
     TGA
     +++
1201 TGAACTATTTTATGACTCTAGTAATAACTACCTACCCTAAATAATTTCATAGAAGACATCACATTGTTGATTTGG

                                                                        [2]
                                                                        2.0e-06
                                                                        ATGAAAAG
                                                                        +++++++
1501 GGACTCAACAGATTATATATAGTAATGTATAAGCATAAAAATGTACATATGTGCGCAATAATAATTGATAAAAGA

     
     
     CAGTGATTCACAG
     ++ +++  +++++
1576 AAAGGAGACACAGTTTTGAAGAAGAGTGGGGAAGGATATATAGGAAAGTTTGAAGGGAGAGAAGGGAAGGTAGAG

                                             [8]
                                             3.1e-05
                                             AACTTCAAAATGTCTCTTTGA
                                             +++ +++++ ++   +++++
1651 ATATTGTAATTAAAATATAATTTCAAAAATAAGCAACAACAACATCAAAGTGAGCCTTGTCATGATAAAATCTAT


NM_013462
  ENSMUSG00000031489
  LENGTH = 2000  COMBINED P-VALUE = 2.08e-05  E-VALUE =     0.74
  DIAGRAM: 333_[3]_255_[3]_593_[8]_146_[2]_589


                                      [3]
                                      8.3e-05
                                      AGTGCCCTGGGCCTTTAAGAG
                                      ++++++++++++ +++  +
301  TCTTTGCTCTTGGAGTTAAAAAAGAGCCAGTGCAATACTCTGGTCACTTCCATAGAACCTCCCCACACCCCACCC

              [3]
              5.6e-07
              AGTGCCCTGGGCCTTTAAGAG
              +++++++++  ++++++ +
601  TCTCAAACCAGTGCCCTGAACCTTTAGATACACAGGCACACAAAACTGAAGCAAAGTGTTTGCTGATGTCAATGA

                            [8]
                            1.4e-06
                            AACTTCAAAATGTCTCTTTGA
                            +++ +++++++ ++++++++
1201 CCATAGTGAGGAGACAGGGATGAAACCTCAAACTTTTTTTTTTTCCTGGATTCCTGCTCTCAAACTAACCAGAGA

                                             [2]
                                             2.7e-05
                                             ATGAAAAGCAGTGATTCACAG
                                             +  + +++++++++++  +++
1351 GGAGGGAGGGGTGCTCTCTTTTCCCTAAGCATACAGCACAAACATAGGCAGGGACTGGCAGGCCTCCAAGGCCAT


NM_002227
  ENSG00000162434
  LENGTH = 2000  COMBINED P-VALUE = 2.34e-05  E-VALUE =     0.83
  DIAGRAM: 582_[8]_356_[8]_911_[4]_86


                                                              [8]
                                                              7.0e-05
                                                              AACTTCAAAATGTCTCTT
                                                              +++   ++++++++ +++
526  AGTGGTGTTTGTTTGTTTGTTAGTAGTAAGGACCGTAACCCACCCCTTCCTCCCCCCAAAACTATACTGTTATTT

     
     
     TGA
     ++
601  TTCTATGTAAGCAAATTGTTTGAAATGCTTTGAAAATGAAATCTTAATATTAAAAGGCATATGCATGTAAAGTCT

                                                                [8]
                                                                1.5e-05
                                                                AACTTCAAAATGTCTC
                                                                ++++  +++++++++
901  TAATCGTTCACATTGAATCAATGACTAAACATTTTTGATTACCCAGCTACCTCCAAGCAAACTGAAAACTGTCTA

     
     
     TTTGA
      ++++
976  GTGGATCCTGAAGTCCATAGTGCCTCTAGCCGGGTCTTTCAAGTGTTGCACCACAGGGTGATGATTGATGGTAAA

                     [4]
                     2.3e-09
                     AGGAGAGAGCTCACACCTCTCCC
                      +++++++ +++++++++++  +
1876 GAGTTCAGTGACTTTTTGGACAGAACACAAACTTCTTTCATTAGAAATTTTTAAAAAATGACTTGGGCATTTGTT


NM_000717
  ENSG00000167434
  LENGTH = 2000  COMBINED P-VALUE = 2.75e-05  E-VALUE =     0.97
  DIAGRAM: 167_[3]_131_[8]_772_[2]_251_[4]_593


                      [3]
                      1.1e-05
                      AGTGCCCTGGGCCTTTAAGAG
                      + ++  +++  +++ ++++++
151  GCTCTGTGGTGCCCATAATTAAGATGCACCCATAAGAGAGTGTATAGCTTTACCCCTCCCGCATTCCTCAGAGGG

                        [8]
                        1.0e-07
                        AACTTCAAAATGTCTCTTTGA
                        +++++ +++ +++ ++ ++++
301  GGGGGGCCTGAATGCAATGAACTTTAAAGTGGATCATTGATCAACAGTCCCTTAACCCCACCAAAGTTTCCCAAG

                                                                   [2]
                                                                   8.0e-05
                                                                   ATGAAAAGCAGTG
                                                                     +++++++++++
1051 CCAAATGTTGGAGCCGCCCTTAAGGGAACTTCCCCTGGACTCCTCTGGAGGTCTTGCCAGATGGGAGAACCAGGG

     
     
     ATTCACAG
      + ++  +
1126 GTCCATTCAGACCCCAGTCTCTTCTCTTCCCATCTCATCTCTCCACCTGGGGGGCTCAAAGAACCTAGCTCCTCC

                                       [4]
                                       2.2e-05
                                       AGGAGAGAGCTCACACCTCTCCC
                                       ++++++ ++++ + +    ++++
1351 GTCTGCTTAGAAATTAAGTTTGGAGCAGCCTGGGAGGAAATAGAAGAGATGAGACCCAGAGAATCAATGGCCACT


NM_147080
  ENSMUSG00000044506
  LENGTH = 2000  COMBINED P-VALUE = 2.87e-05  E-VALUE =        1
  DIAGRAM: 355_[2]_292_[3]_909_[3]_5_[8]_243_[4]_89


                                                            [2]
                                                            6.4e-06
                                                            ATGAAAAGCAGTGATTCACA
                                                              ++++++++ +++++ + +
301  ATGAAAATAAGTATTTAAAAGCATCCAGAATCAAAGAATAAAAATAATTAGTAATGGAAGAGGAATTGATTGAAA

     
     
     G
     +
376  CTGAAACTAGTCATTGCCCTCTAATGTCCATTGAACAAAAGACATTTATAAGTATAGAAGAATAATTCATTAAAA

                                                                         [3]
                                                                         5.6e-07
                                                                         AGTGCCC
                                                                         +++++++
601  TGTAACCTTCTAATTCTTTATCAATAATTATTAGATATTATTATGGAATTAATGGAATTAACATAAAGAATGCTA

     
     
     TGGGCCTTTAAGAG
     ++ ++ ++++++ +
676  TGATTTTTTAAAGGTTTTATTTATTTATTGTATATAAATATACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGC

                            [3]                       [8]
                            2.7e-05                   2.9e-05
                            AGTGCCCTGGGCCTTTAAGAG     AACTTCAAAATGTCTCTTTGA
                            + ++ + +  ++ +++++++      ++++   + ++++++++++++
1576 ATGTTTGCTTGTTTGTTTGTTTGATTGTTTTAATCTATTAAGACTTTGAAACTGTCTGATGTTTTTTGTATGCAC

                  [4]
                  1.8e-05
                  AGGAGAGAGCTCACACCTCTCCC
                  +++ ++ + ++++++ ++ + ++
1876 CACTATCCTTCACAGGTAATATCTAACATTTGTTAGAACATCCTGAATGTGACATTTAACGTTTGCTTCTTTCCA


NM_001097
  ENSG00000100312
  LENGTH = 2000  COMBINED P-VALUE = 2.98e-05  E-VALUE =      1.1
  DIAGRAM: 1490_[8]_489


                                                                      [8]
                                                                      3.0e-10
                                                                      AACTTCAAAA
                                                                      ++++++++++
1426 TAATAGGAGACCTTGTGATATTCAGCAACGGACAGGAAGGTGGGCTTTGCAGTTGTAAATTAGGAAAATTCAAAA

     
     
     TGTCTCTTTGA
     ++ ++++++++
1501 TGACTCTTGGAAAAGTGTGTTGATAGCATTCACTTGGAAGAGGAAAAGAAAACTTCCCCAACAACAATTAAGGAT


NM_023662
  ENSMUSG00000031592
  LENGTH = 2000  COMBINED P-VALUE = 3.09e-05  E-VALUE =      1.1
  DIAGRAM: 705_[8]_239_[3]_630_[8]_47_[8]_124_[4]_148


                                   [8]
                                   3.0e-05
                                   AACTTCAAAATGTCTCTTTGA
                                   ++ ++ ++ +++ ++++ +++
676  GTTGAATTTTATGTCACTATTTTTAGATAAAATTTTAATATGATTCTAGTAAAATTATCTGCCTGTTAAAGTTTA

                                                                      [3]
                                                                      1.0e-05
                                                                      AGTGCCCTGG
                                                                      ++++++++
901  CGGCCTCTGAGCCTCTGCTTCCGTGTCAGCTTCTATTTCTCCTCTCTGATCCAGGCATCATATTTAGTACCCTTA

     
     
     GCCTTTAAGAG
     ++ ++++ + +
976  GTTTTTATATGTATATGTACTCCATGGGGTGTATTGCTAGGGTTGTCCGCACTTCTAATTCTAGTGCTTGGGGCT

                                              [8]
                                              1.2e-05
                                              AACTTCAAAATGTCTCTTTGA
                                               + ++ +++ +++ ++ +++
1576 TATAATGTGTATATCATGTAGATCAATTTATCTGTGATACGTGTTTGATAGTGTATTCTTTTATATTTTTGGTTG

                                       [8]
                                       5.0e-06
                                       AACTTCAAAATGTCTCTTTGA
                                       ++++  +++ +++ ++ ++++
1651 TGAGCCTAGCCTTTAACAGCTGAGCCATCTCTCCAGCTCGATAGTGTATTCTTTAAGATAAGTGTTTGAAAGATT

                                  [4]
                                  1.9e-07
                                  AGGAGAGAGCTCACACCTCTCCC
                                  ++++++++ ++ ++ ++  + ++
1801 AACCTGATGACCTCAGATCACACAGTGGCAGGAGAGAACTGACTCCAGATAGTTGCTCTGACCTCTGCACACATG


NM_026576
  ENSMUSG00000016984
  LENGTH = 2000  COMBINED P-VALUE = 3.89e-05  E-VALUE =      1.4
  DIAGRAM: 435_[4]_299_[2]_565_[8]_367_[8]_248


                                                                 [4]
                                                                 2.0e-05
                                                                 AGGAGAGAGCTCACA
                                                                   ++++++ ++++++
376  AGAGGGGTAGCCTGCTGGACCAGCACATCTCCACTATCCAGAAGTGTTTTTATGTTTCCTTAGAAAGATAACACA

     
     
     CCTCTCCC
       ++++
451  AGTCACTTAGTATCAATTTCAGTGAGGATGGTCAGGTATAAATTTCAAAAAAAAAAACCAAAAAACAAAAAAACA

            [2]
            2.4e-06
            ATGAAAAGCAGTGATTCACAG
            + ++ ++++++++ + +++++
751  GAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCGAAAAACCNNNNNNNNNNNNNNNNNNNNNNNNN

                                                                         [8]
                                                                         3.2e-07
                                                                         AACTTCA
                                                                          ++++ +
1276 TGGAAAGATTAGTTAGTTCTTTAAGATAAAGAATGTATGTAAGTACTGCTAACAAGCAGCCTTTAATGTACTTTA

     
     
     AAATGTCTCTTTGA
     ++ +++++++ ++
1351 AAGTGTTTCTGTGCCTTCCAGTTATTTTAAGTACGAACAGACTGAAGCAAGTCATGCAACAGTTAAGATTGTCTC

           [8]
           6.1e-05
           AACTTCAAAATGTCTCTTTGA
            ++ + ++++ + +++++++
1726 ATTACTTACATAATAAAGCTTTTTTTTTCTTTTTGCTAAACTAGACTTAATGCCTAGTCTGTGGGTTTCCTAACA


NM_021757
  ENSRNOG00000006655
  LENGTH = 2000  COMBINED P-VALUE = 4.60e-05  E-VALUE =      1.6
  DIAGRAM: 436_[3]_117_[2]_304_[4]_1041_[8]_16


                                                                  [3]
                                                                  2.4e-05
                                                                  AGTGCCCTGGGCCT
                                                                  ++++ ++   ++++
376  ATTTGGTAACCTTGCCCTAGTAATCTAGTGTTTCCTTTCAGAGAGTACTAGGAAATGTTGAAATGTCACAATCCA

     
     
     TTAAGAG
     +++++
451  TTAAATAAATGAGCCCTGTATGGACAGGACATTTGGGTTAGTTTTCAGGATTAAAGAGTAAATATGCCGTGCACT

                                                      [2]
                                                      2.0e-06
                                                      ATGAAAAGCAGTGATTCACAG
                                                      +  ++ ++++ ++++++++++
526  GTGACTGTATGTGTCAGGTTACTCCCGGAAAGCTGTTTCCTAGAAATGTAGCAGGACAAAGGATTCACAGAGCTT

                                                                               [
                                                                               6
                                                                               A
                                                                               +
826  CTTTGTGACAAGTTCCAACAGCACTAATCCTATCAGTTGTCTTCTCTGCTTCTTTACTAGTATCTAACTATTGCA

     4]
     .6e-05
     GGAGAGAGCTCACACCTCTCCC
     + +++ + + +++++  +++ +
901  GAACAAAACCCACACAACACTCAGCCTTCCCTGAAGACGTATCAGCATCTGCTGGAGATTCCTGGAAAACACATC

                  [8]
                  1.1e-06
                  AACTTCAAAATGTCTCTTTGA
                  ++++  +++++++++ +++++
1951 ATTTTACTACTAAAACTATAAACTGTTTATTTTAGAAATCAAACACAGGT


NM_019794
  ENSMUSG00000031701
  LENGTH = 2000  COMBINED P-VALUE = 4.85e-05  E-VALUE =      1.7
  DIAGRAM: 682_[8]_57_[3]_237_[8]_102_[4]_836


            [8]
            4.2e-06
            AACTTCAAAATGTCTCTTTGA
             ++++++ ++ +  ++ ++++
676  AAGTATATACTTCAGAAGGAATTGTTGAAATGAAGGGTAAGAAACTGGAATCAGGGCTGGTGCATTTCTAGGCTG

               [3]
               7.5e-07
               AGTGCCCTGGGCCTTTAAGAG
               + +++++++  + +++ ++++
751  AGCTAATTGAATTGCCCTGAATTCTTCAAAGGCAGCCTAGAATACAACAGCAAATCTTTTGTCTCAAAACAAGTA

                                                [8]
                                                7.5e-05
                                                AACTTCAAAATGTCTCTTTGA
                                                ++++  ++++++ +++ + +
976  AACATATGAAAGGATACATGAACATTAGTCATCAGGGAAACACAAATCAAAACTGCTTTCTATCCATGGGAGAGG

                     [4]
                     1.0e-05
                     AGGAGAGAGCTCACACCTCTCCC
                     ++  ++++++++ + ++ +++++
1126 AGAGAGATGGTTCAGTAGTGAAGAGCACCAGCTACTCACCCAAAGGACAGGAGTTCAAATCCCAGCACCCACATG


NM_019343
  ENSRNOG00000003618
  LENGTH = 2000  COMBINED P-VALUE = 4.94e-05  E-VALUE =      1.7
  DIAGRAM: 228_[8]_40_[3]_58_[2]_655_[8]_70_[4]_241_[3]_580


        [8]                                                          [3]
        1.3e-05                                                      3.3e-05
        AACTTCAAAATGTCTCTTTGA                                        AGTGCCCTGGG
         ++++ ++++++ ++ +++++                                        + ++ + +  +
226  CTTGGCTTTAAAATGCTTGTTTGATTATTTTCTCCTTTCAAAGGTTGAAAAGCACAGAACTTTCATTGTCTTAAT

                                                                         [2]
                                                                         7.8e-05
     CCTTTAAGAG                                                          ATGAAAA
     + ++++++                                                            + +++++
301  CTTTTAAACATAAGAAAGAGTTGAGGGTAAGGGCAAAAAAAATGCATGCAACTATTGTTAATAAGGAAAAGGAAA

     
     
     GCAGTGATTCACAG
     ++ ++ ++ ++ ++
376  CATGGAACACAGACACAAAGAGGAACTTATCCTTCATTGTCTACACCATGCTATACACTTCTTTCCAAACCTTAG

                                                                          [8]
                                                                          7.0e-0
                                                                          AACTTC
                                                                          ++++
976  CAAGAGAAGCAGAAATGTTGTAAACGCGGCAAGCTTTCGTGCTGACACTTGCAAAGCCTAAGTAGCTGAAAATCT

     
     5
     AAAATGTCTCTTTGA
     +  + +++++ ++++
1051 AGCAGGGTTCCTTGAGAGTTGATTCCTAATCTTCTCTAATATCATCGATTTGATAAAGAGTTGCTGCGGGTTAGA

               [4]
               1.1e-07
               AGGAGAGAGCTCACACCTCTCCC
               ++++++++ +++ +++++ +  +
1126 CCTTGCTCAAAGGACAGAAATCTCACTTGATTCTATCTCTTGTTAAAGCCTGTAGGGGTGGTGAGTGAGCCCTTG

                                                      [3]
                                                      6.2e-05
                                                      AGTGCCCTGGGCCTTTAAGAG
                                                      + +++  +++++ + ++++ +
1351 AAAAAATAATGAATGAGGTTGATTTTTCTCTACAGATTTTCTATTTGCTATTACATTGGTCACATAAGCGATTTA


NM_144715
  ENSG00000163576
  LENGTH = 2000  COMBINED P-VALUE = 5.47e-05  E-VALUE =      1.9
  DIAGRAM: 5_[3]_464_[4]_57_[3]_606_[8]_782

          [3]
          3.6e-06
          AGTGCCCTGGGCCTTTAAGAG
          ++++ + ++ ++++ ++++++
1    TTTCAAATGTCGTGCTCCAATAAGAGAAGACAGTATACATAAAGTAGATTTTTAGGCCAGATATAGTAAATGCAT

                                             [4]
                                             3.9e-05
                                             AGGAGAGAGCTCACACCTCTCCC
                                                ++++  ++++++++++++++
451  CTATGGTCTTCCCAGTGAGAAGCAGCTCAAGACGCAGCTGCTTAAAGGAAACACACCTCTCCCCAGGTCTTCCAA

                                                  [3]
                                                  2.1e-05
                                                  AGTGCCCTGGGCCTTTAAGAG
                                                  + + ++ +++ + +++++
526  ACACCTTGGCTGAAACTAGGCAGAAGCAGAAAAAAGGGAGAGAGAATTTCCTTGGATTTTTAACTCACTGGACAC

                                                                             [8]
                                                                             3.6
                                                                             AAC
                                                                             +++
1126 TGATGACTTAAGCCAAACGTGTTAAGAAAGCATGAGTTTAGAGATCATTTGGAAAAGATTGCTTATTCCCCAAAC

     
     e-07
     TTCAAAATGTCTCTTTGA
      + ++++++++++ +++
1201 CTTATAATGTTTTCTTTTGTCTTGTTTTTGCTGTCTTAAAAGCTTTCAATTTGTGGTTTTTAATATATGGAAAGA


NM_010510
  ENSMUSG00000048806
  LENGTH = 2000  COMBINED P-VALUE = 5.54e-05  E-VALUE =        2
  DIAGRAM: 86_[3]_1326_[2]_153_[2]_277_[8]_74


                [3]
                3.5e-07
                AGTGCCCTGGGCCTTTAAGAG
                ++++  +++++++++ ++ ++
76   ATGAAGACACAAATGTGCTGGTTCTTAAACAGCACCACACAGATGCCTTTCTGTCTTTTATGGTGCTGTACTTAA

             [2]
             4.3e-07
             ATGAAAAGCAGTGATTCACAG
             + + +++++++++++  ++++
1426 CAGATGTGAAGTGAAGAAGGGACAGACACCCTCAGCTTCCCCAGGGGATCATGAGGAGCAAGATAAAGGCATTTA

                                     [2]
                                     4.4e-05
                                     ATGAAAAGCAGTGATTCACAG
                                     +  ++++++ +++++ ++  +
1576 ATCATTTCCCTGATGGCAAAGGTTTTGGGGTAAATAAAAGAGGTGATACATTCCTCTGTCTGGCCACCCTAAATG

                                   [8]
                                   8.8e-05
                                   AACTTCAAAATGTCTCTTTGA
                                    ++++ + ++ +   + ++++
1876 CCAGAAACTATACTACTTTTTTTAAAGGAGTACTTTACAAAGAACCCTTTATAAGAAGTGTCCAGCAATTATTAA


NM_009241
  ENSMUSG00000029682
  LENGTH = 2000  COMBINED P-VALUE = 5.89e-05  E-VALUE =      2.1
  DIAGRAM: 208_[2]_1224_[3]_294_[4]_209


                                                               [2]
                                                               2.5e-05
                                                               ATGAAAAGCAGTGATTC
                                                               + ++++  ++++ ++++
151  CATAGTTATTATCAATGCTTCCACCATGCCTATGCAATAAAGTCACTATAAAACCTTGAAAGAATTAAGGAATTC

     
     
     ACAG
      +++
226  TCAGGTCATAGATCTTGTGAAGATTTCTGGATCGAGGTTCACCTGGGGAAGGTTTGAAGCTTTAACTAGCTTCTC

                                 [3]
                                 2.1e-08
                                 AGTGCCCTGGGCCTTTAAGAG
                                 +++++++++ ++++ ++++ +
1426 AAGTTCCAGGACACCCAGGGAATTTAACAATACCATGATCCAATAAATGAGTCAACGAACAATCAAACAAACAAA

                                                [4]
                                                4.3e-05
                                                AGGAGAGAGCTCACACCTCTCCC
                                                + + ++++ +++ ++++ ++  +
1726 TCTAAAATACTGATAGATACAGGACCCTATATATCTGGGAATGAAGTAAGAAAAATAACTACATTCAGTTTTCTG


NM_014783
  ENSG00000175306
  LENGTH = 2000  COMBINED P-VALUE = 5.94e-05  E-VALUE =      2.1
  DIAGRAM: 419_[3]_585_[8]_774_[2]_159


                                                 [3]
                                                 9.5e-09
                                                 AGTGCCCTGGGCCTTTAAGAG
                                                 + ++ +++++++++++++++
376  CTTTAAAAAAGGATCACGACGTAGAAAAAGACACAACACTGAAGATTGTCATGGGTCTTTAAGAAAAGGAAATTT

                                                       [8]
                                                       3.9e-05
                                                       AACTTCAAAATGTCTCTTTGA
                                                       +++  +++++++ ++++ ++
976  CTTTTCTTTGGATTGGGAAGGGTAAAATATCCGAAGATTTGAACTCCAAAAGAAACAAAATGATTCTATGCAAAC

                         [2]
                         6.5e-05
                         ATGAAAAGCAGTGATTCACAG
                           ++++++++++++  + ++
1801 CCGCCCCAAAAACTGGCCTTGAAGGAACAAGTGAAACTCATCCTGCTTTTCATGTTTGCTGGGTTTGCCCGTTAC


NM_006056
  ENSG00000171596
  LENGTH = 2000  COMBINED P-VALUE = 7.19e-05  E-VALUE =      2.5
  DIAGRAM: 724_[2]_641_[8]_593


                                                      [2]
                                                      1.8e-09
                                                      ATGAAAAGCAGTGATTCACAG
                                                      ++++++++++++++++ ++++
676  CATCCCTGTTTCTCAAGGGGTGAGTTCAGATCTGCTATTCCCGTTTTCCATGGGAACCAGTGACTGACAGGACCT

                                         [8]
                                         6.3e-05
                                         AACTTCAAAATGTCTCTTTGA
                                         +++++   ++ +++++ +++
1351 CTCAGGGGCAGCACTCAGGTGCTCACGGCTCTGCACAGCTTTTCACAGGCTCCTTTCTCTGCAGAATCTCCCTGT


NM_175619
  ENSG00000182223
  LENGTH = 2000  COMBINED P-VALUE = 7.51e-05  E-VALUE =      2.7
  DIAGRAM: 563_[2]_38_[4]_167_[8]_36_[8]_1110


                                           [2]
                                           1.0e-06
                                           ATGAAAAGCAGTGATTCACAG
                                           + ++++++++ ++ +  ++++
526  GAAGATGAAGATACAGATATTTCTTATAAAAAACTAAAAGAAGAGGAAATGGCAGACACTTCCTATGGCACAGTG

                           [4]
                           3.3e-07
                           AGGAGAGAGCTCACACCTCTCCC
                            +++++ ++++++ +++++++ +
601  AAAGCAGAAAATATAATAATGATGGAAACCGCTCAGACTTCTCTCTAAATGTGGAGATACACAGGAGCTTCTATC

                                                                   [8]
                                                                   9.7e-05
                                                                   AACTTCAAAATGT
                                                                   +++++  ++++
751  TCATACATGTAACAATTCTGATCTTTTTAAGGTTCACTGGTGTATTAACCAAACGTTGTCACAAATTACAAATCA

                                                 [8]
                                                 6.5e-05
     CTCTTTGA                                    AACTTCAAAATGTCTCTTTGA
      +  ++++                                     ++++ ++  ++++++++ +
826  ATGCTGTAATATAATTTGCACCTGGAATGGCTAACGTGAAGCCTGAATTAAATGTGGTTTTTAGTTTTTACCATC


NM_000994
  ENSG00000144713
  LENGTH = 2000  COMBINED P-VALUE = 7.57e-05  E-VALUE =      2.7
  DIAGRAM: 327_[4]_87_[8]_302_[8]_944_[8]_254


                                [4]
                                4.8e-07
                                AGGAGAGAGCTCACACCTCTCCC
                                +++++  ++++ +++++ +++ +
301  AGGCTGTGCTGTCAGCTGTAAAAGATCAGGAGGCAGCAGACACCACTCTGGTTTCTTCACTGCATTCAGCAATGC

                                                                   [8]
                                                                   1.7e-06
                                                                   AACTTCAAAATGT
                                                                   ++++++++++ ++
376  CTGAAGTTAGTGCTCAGGCCGGGCATCTCAAAAGAAAAGATACTTGAGTTATTCACATTTTAAAATTCAAAACGG

     
     
     CTCTTTGA
     +++ +++
451  TTCATTTTTAAGTGGCAGTGATGAATCAGAAATTTGGAAGATGATACGGGTTTCTTTTTTCCAGGGAGGAGGAAT

               [8]
               1.0e-05
               AACTTCAAAATGTCTCTTTGA
               ++++++ ++ +  +++ +++
751  AATAAAGATTAGATTCTAAGTTACTTCTTTCCTCTGCACGACTCGTCTCCAATTGTTAATCNNNNNNNNNNNNNN

     [8]
     8.4e-05
     AACTTCAAAATGTCTCTTTGA
     ++  + + ++++ ++  +++
1726 AGGCTAAGAATGACTACTTGTGGCTTGGGAGCCACAAGCTTCTTCAAGTGTCTCAGAACCTACCTGGTGTGAGGG


NM_031922
  ENSG00000135597
  LENGTH = 2000  COMBINED P-VALUE = 7.61e-05  E-VALUE =      2.7
  DIAGRAM: 396_[4]_58_[8]_92_[8]_253_[8]_418_[2]_676


                          [4]
                          3.0e-05
                          AGGAGAGAGCTCACACCTCTCCC
                          +  +++++ +++ ++++ ++ ++
376  GAATGTACTCCTCTAGAGAGCATTAAAGATATACCACTACAAAGTACTAAAAAGTTTTCTATAATTTTTAAGTGT

                                [8]
                                2.5e-05
                                AACTTCAAAATGTCTCTTTGA
                                +++++ ++ +  + +++++++
451  TATTTATTGGAAGGCTAAATTCTAAGAAGCTTTAACAAATATTTTTGACATTGTTAAATTAGAAGGCTATTTTTA

                                                                      [8]
                                                                      2.0e-07
                                                                      AACTTCAAAA
                                                                       ++ + ++++
526  AAAAGCATATTTTAAAAAACAAAACTAAATGGAAACAGCAAAACTTGCTTGTAATGAAATACAGCTGAGTAAAAA

     
     
     TGTCTCTTTGA
     +++++++++++
601  TGTTTCTTTGAAAACAAAGACACTCAGAAAAACAGGTGTTGAGTAGTTTCCTGGGCCTTTAATGCTTTAAATTTA

                                            [8]
                                            9.3e-05
                                            AACTTCAAAATGTCTCTTTGA
                                             + ++ ++ ++ ++++ +++
826  CAAAGTCTATCGGTGCAGTTTAGGACTGTGAATCTATAGTATTTAAACATTTTTTCTTTCAGAAATGAAAATACA

                                 [2]
                                 8.7e-06
                                 ATGAAAAGCAGTGATTCACAG
                                 + +++++++  + +++++ ++
1276 AAGTTTTAAAACAATACTTAAAAAAATTAAGAAAGGCCATTACTCATACCTATTTCATAAGTTTACATGACTGCT


NM_007260
  ENSG00000011009
  LENGTH = 2000  COMBINED P-VALUE = 7.96e-05  E-VALUE =      2.8
  DIAGRAM: 711_[8]_915_[2]_332


                                         [8]
                                         4.6e-07
                                         AACTTCAAAATGTCTCTTTGA
                                         +++++  +++++++++ +++
676  CTCTGGGCCTGGGGGAAAGTGCTTTGTTGAGCTTCCAACTTTGTACTGTTTTCTTTTTCTNNNNNNNNNNNNNNN

                                                                             [2]
                                                                             3.5
                                                                             ATG
                                                                             +++
1576 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGTTCAGAGTGTGTCATTCCATTCATGATCCTGGAATAGGGCATG

     
     e-07
     AAAAGCAGTGATTCACAG
     ++++++++++ +  ++++
1651 AAAGCCAGTGGCAGACACCCGAGGCCTTAAGAGGTGTGTCCCATGAGGATGGGAAGGTGGTAAAGTTTATGCAAA


NM_011839
  ENSMUSG00000046212
  LENGTH = 2000  COMBINED P-VALUE = 8.15e-05  E-VALUE =      2.9
  DIAGRAM: 111_[8]_61_[8]_414_[8]_491_[4]_211_[8]_213_[3]_64_[8]_286


                                         [8]
                                         7.8e-06
                                         AACTTCAAAATGTCTCTTTGA
                                         +++++  ++ + ++++++++
76   TTCTTTGAAGCTATTTGTTCTTTTATAGGAAGCTGTAGCTTTTAAGTTTTTTTTGTCTTTCTGTAGCATAATTAC

                                                [8]
                                                9.3e-05
                                                AACTTCAAAATGTCTCTTTGA
                                                + +++ ++ +++   +++++
151  ATTAGTTTTCTTTCTCTGTTGCTTGTAAAACATAAGATATTTTACCTTAATCATGAAATTTGTCTTGTACTGAAA

                                 [8]
                                 2.4e-05
                                 AACTTCAAAATGTCTCTTTGA
                                 +++++++ ++  ++++ ++ +
601  CAAACATACTCCTTTGAAAATTTTCTTAAAATTCAGACCTTCTCCTTAAGAGGATAAATTGTTTTATTGTTCAAA

                    [4]
                    4.7e-07
                    AGGAGAGAGCTCACACCTCTCCC
                     ++ ++++ ++++++++  +  +
1126 TCAAATCTTGTCCTTTGGCCAGAAAACAAACCAGTTTCTTTAGGATATTTTCAGTTTTCCTAATTATTTTTTATT

                             [8]
                             2.3e-06
                             AACTTCAAAATGTCTCTTTGA
                             +++++++++++  ++++++ +
1351 GTTTTAAGACCTTTATATATAGGTAGATTCAAAATAATTTTTGAAATTTAATTAAAATGATACTGTTTATTGCAT

                                      [3]
                                      6.5e-05
                                      AGTGCCCTGGGCCTTTAAGAG
                                       +++ + +  +++++++++++
1576 AACTTAAAAAGAATAGTTGAAGAAAGAGCATGACATGACTTCATTCTTTAAAAGCAATTTTAAAAACATTTAGAA

                                                [8]
                                                1.4e-05
                                                AACTTCAAAATGTCTCTTTGA
                                                ++ ++ +++  ++++++++++
1651 CTAGATTTTAAAAAACCTTACAGCATTAAAAAAATCCTGATATAATTTTAAATAGGCTTTTTTATTATTTTAAAT


NM_009531
  ENSMUSG00000030094
  LENGTH = 2000  COMBINED P-VALUE = 9.75e-05  E-VALUE =      3.5
  DIAGRAM: 90_[8]_729_[2]_1002_[3]_87_[2]_8


                    [8]
                    5.5e-07
                    AACTTCAAAATGTCTCTTTGA
                     +++ ++ + ++++++++++
76   CCGGCCTCAAGCAGTTGCTGCAGAGTGGTTCTTTTTGCATTTAATGCCCATCACTATCCTCATCCCAAATAAAAT

                    [2]
                    7.6e-05
                    ATGAAAAGCAGTGATTCACAG
                     + ++++ ++ +++++++  +
826  CTACTTTGTCTTGGCTTTAAAGTAAATGACTCATGCTTCATGAACATTGAGAATGTGTCAGAAGCATGATGCACA

                                                                    [3]
                                                                    1.9e-05
                                                                    AGTGCCCTGGGC
                                                                    ++++++++++++
1801 CTCTGACAAAAGAGCAGCAGGCAGTACTGGAAACCTGACTCAGGAAGGCAGGCCTGAAAAGCAAATGCCCTGGGT

     
     
     CTTTAAGAG
     ++  + +++
1876 CTGAAGGAGAGGAAAGCAAGCGTTGTGAACGGCACTAAAGGAAGATTTGTCTCAGTGCTCCAGTACCCATAATTT

                          [2]
                          2.7e-06
                          ATGAAAAGCAGTGATTCACAG
                          + +++++ ++ ++++  + +
1951 CCCAGTGAGTTCTATTTAAAAACAGAAATAAAGGACAGATAAGGCATTGT


NM_011717
  ENSMUSG00000024050
  LENGTH = 2000  COMBINED P-VALUE = 9.76e-05  E-VALUE =      3.5
  DIAGRAM: 146_[8]_277_[8]_589_[4]_152_[2]_750


                                                                            [8]
                                                                            9.5e
                                                                            AACT
                                                                             +++
76   ATAGCCAAAACTGTTCTTCACAATTTAGTTGGGGCAGGGGAGGTAGAGAAGTATAGATTAGGCTGTTGCTGTGAT

     
     -05
     TCAAAATGTCTCTTTGA
     + +++  + ++ ++++
151  TAAAAGGGCTTGTTTTTACCATTTGTCCAGATACAATGTCCTGACGATAATTTCTCCCCACTTTTGCAAAAGAAA

                                                                          [8]
                                                                          1.1e-0
                                                                          AACTTC
                                                                          ++ ++
376  GCACTTGGTGTGATTTCACCCAAGGTCTTGTTTAATTTCTGATGTCCTCACAGGTTGAGCTTAGCCTAAAAGTTA

     
     6
     AAAATGTCTCTTTGA
     + + +++++++++++
451  AGATTGTTTCTTTGAGACCATGGAGTGGTTTAAGCAAAGACTTAAGCTATGCTCAGGAGTTTTAGGAAAAGGTCT

         [4]
         1.4e-05
         AGGAGAGAGCTCACACCTCTCCC
         ++++++ + ++ ++ +++ + ++
1051 AAGTAGGAGATAACAGAATCTTATTACCTTAGAAATGTTCAGTAAACATTAGCTGAGCAAGAAAATAGCATTGTT

                                  [2]
                                  2.4e-06
                                  ATGAAAAGCAGTGATTCACAG
                                  + ++ ++++++++ + +++++
1201 TTTGAGGCCAGCCTAGTTTATAGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTTGAAAAGCAAAA


NM_011291
  ENSMUSG00000025922
  LENGTH = 2000  COMBINED P-VALUE = 9.78e-05  E-VALUE =      3.5
  DIAGRAM: 678_[3]_299_[2]_435_[8]_161_[4]_317_[4]_1


        [3]
        2.5e-05
        AGTGCCCTGGGCCTTTAAGAG
        + ++ +  ++ ++++ ++ +
676  GATATTATCTAGGACCATCAACAAGAGAAATTACTTCATAACCGGACAAGAACTTTCCACCAACAGTACCCAAGG

                            [2]
                            2.4e-06
                            ATGAAAAGCAGTGATTCACAG
                            + ++ ++++++++ + +++++
976  AGCCTGGTCTATAAGTAAGTTCCAGGACAGCCAGGGTTACACAGAGAAACCCCCAAAAGAAAAACAAAAACCCCA

                                  [8]
                                  3.8e-06
                                  AACTTCAAAATGTCTCTTTGA
                                  ++++  +++++++  +++++
1426 GAAAAGCCTTTAACAAGTTGTCTTTCAAAAACTATAAACTGGAACTTTGCACATCATAGGCTGTTGATCTGACTG

                                                                  [4]
                                                                  3.7e-05
                                                                  AGGAGAGAGCTCAC
                                                                  + + ++ + +++++
1576 TGCCAAGCTGTGACTGTTTATTAACTGACCAGATTACAAAAATACAATGGGTGACACCTGAAAGGGAAAAAACAC

     
     
     ACCTCTCCC
     ++   + ++
1651 ACGAGTTAGAGACTGTCTTCCAAGCCGCACATCAGCACCCCCCCGTAAAGGAGCACACTTCCATTAAAGACACAT

                               [4]
                               9.6e-05
                               AGGAGAGAGCTCACACCTCTCCC
                               +  +++ + +++ +++++++ ++
1951 CGATTGCCAGAAATAGATTCTGTCTCAAAAAACAACACTAACTTCTTACC


NM_000324
  ENSG00000112077
  LENGTH = 2000  COMBINED P-VALUE = 1.01e-04  E-VALUE =      3.6
  DIAGRAM: 1220_[8]_55_[3]_105_[2]_557


                         [8]
                         1.6e-07
                         AACTTCAAAATGTCTCTTTGA
                           +++ ++++++ ++++++++
1201 NNNNNNNNNNNNNTTTGATTTTCTTAAAAATGATTTTTTGACGATGTCAGTTATCTTTTCTAAAATTTAACTTTT

                          [3]
                          2.0e-06
                          AGTGCCCTGGGCCTTTAAGAG
                          + ++ + ++ ++ +++++++
1276 TACAACATTCTATAATGAGACATTAACTTGATTTTTTAAAAATAGCAAATACATGATAAATATTTAAATTGAGTG

                                                                             [2]
                                                                             6.3
                                                                             ATG
                                                                             + +
1351 TGGACTAAATATGAAGTGTGTGTGTGTGCACCTGTGTGCTTGTTACTGACATGAATTCCAACTACCAAAGAAAGG

     
     e-05
     AAAAGCAGTGATTCACAG
     ++++ ++  ++++ +
1426 AGAGTCAAAGACTGATGNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGACATTTTATGCAAAATAGACTTTGATCA


NM_026408
  ENSMUSG00000024534
  LENGTH = 2000  COMBINED P-VALUE = 1.05e-04  E-VALUE =      3.7
  DIAGRAM: 28_[2]_151_[4]_27_[4]_227_[4]_311_[8]_220_[2]_904

                                 [2]
                                 3.6e-05
                                 ATGAAAAGCAGTGATTCACAG
                                 +  +++++++   ++ +++++
1    TAGGAGAAGCAAACCAGCAAACAGTCCAAACAAAAGCAAACACACACAGTCTATGTGGGAAAGTGTATACAAGCC

                                                       [4]
                                                       5.6e-06
                                                       AGGAGAGAGCTCACACCTCTCCC
                                                       ++++++ + ++++++  ++++ +
151  GAAAAAAAAAGTAACAAAAGGACTATAAAAAATAGTAGGGGAAATAACTGAGGAAACATCACAAAGATCTCTGCC

                              [4]
                              2.0e-06
                              AGGAGAGAGCTCACACCTCTCCC
                               ++ ++++ +++ + ++++++++
226  TTACACTGTGGCTTGCTGGTTGCTGTGGTCAGAAAAACCTCTTCACCCCCAGGCAATCTATTTTCTGCACATACA

                                                       [4]
                                                       9.1e-05
                                                       AGGAGAGAGCTCACACCTCTCCC
                                                       + + ++++++++++ ++  + ++
451  CAATGAAGTCAGGAGGGCAGGAACTGACATTTCTACTCTTGTCTAGCTCCACGTCAGAGAAAACGCCAATTCCAT

              [8]
              5.8e-07
              AACTTCAAAATGTCTCTTTGA
               ++++ ++++++++++ +++
826  TAGGGAGGAGGATTAAAACTGTCTTCTGGTGACATTCAAGGCTGTCATTTCTAGGGGTGCCATTTACTTATGGTA

                              [2]
                              7.3e-05
                              ATGAAAAGCAGTGATTCACAG
                               +++ +++++++ ++ ++  +
1051 CTTTCTTACTGGCAGTGTATTTTCTGTGACAGGCAGGCATACATCCCTCTGCCAGCACCCAGGTAGTATTGGATT


NM_026065
  ENSMUSG00000009550
  LENGTH = 2000  COMBINED P-VALUE = 1.05e-04  E-VALUE =      3.7
  DIAGRAM: 107_[8]_176_[3]_286_[4]_735_[8]_610


                                     [8]
                                     1.7e-06
                                     AACTTCAAAATGTCTCTTTGA
                                      +++  ++++++++++++ ++
76   GAATGGGGGATGAGCCAAAAGACACAGACAAGTGCTATAAAATGTCTTTTAGACTTTAGTGACCAATTCCACTCA

         [3]
         8.7e-05
         AGTGCCCTGGGCCTTTAAGAG
          + + + +++++ +  ++++
301  TTTTGGCATTTTGGTTTAAAAAAAAAAACCCAGAGATATTAGAATACTATTTTCATGTTTTGGTTTTACTCTCAG

                [4]
                3.0e-07
                AGGAGAGAGCTCACACCTCTCCC
                  ++++++++++++++++ ++++
601  ATTAAGACTTCCTGACAGAGATCAAACCTGTCCCAAAGAACTGGACACCCCAAGCAGCAAGACCTAGTCTACCCA

                        [8]
                        5.2e-05
                        AACTTCAAAATGTCTCTTTGA
                          + +++++++++ +++ +++
1351 ACTGATGATGTAAAAATAGTTAATCATACTGGATTTATGACAATAAGTAACTGGGCTGTGCAGGGTGGATCACTC


NM_010324
  ENSMUSG00000025190
  LENGTH = 2000  COMBINED P-VALUE = 1.06e-04  E-VALUE =      3.7
  DIAGRAM: 605_[2]_42_[2]_1105_[3]_185


          [2]                                                            [2]
          8.1e-05                                                        1.6e-07
          ATGAAAAGCAGTGATTCACAG                                          ATGAAAA
          + +++++++++ + +   +++                                          + ++ ++
601  CCAGCACGGGAGGCAGAGGCAGGCAGATTTCTGAGTTTAAGGCCAGCCTGGTTTACAGAGTGAGTTCCAGGACAG

     
     
     GCAGTGATTCACAG
      +++++++ +++++
676  TCAGGGATACACAGAGAGACCCTGTCTCAAAAAAAAAAAAAAAAAAAAAAAAGGTGGGGGGTGGTTACTGGGTAG

                                                                          [3]
                                                                          2.4e-0
                                                                          AGTGCC
                                                                          +  + +
1726 ATACACTAGGGACATAGCAGCTCCAGCGGTGACGGAAAGAGCTGGTATTCTAGAATCCCTCTAAATGATATCATC

     
     6
     CTGGGCCTTTAAGAG
     ++ +++ +++++++
1801 CTAGTTTCTTAAGAAAATGGCTGGTGTCTGAACGATAAACCTACAAAAGCAACATGGACTTACAGCCTGGATCCT


NM_028381
  ENSMUSG00000003208
  LENGTH = 2000  COMBINED P-VALUE = 1.06e-04  E-VALUE =      3.8
  DIAGRAM: 34_[8]_1159_[3]_6_[2]_433_[2]_284

                                       [8]
                                       2.5e-06
                                       AACTTCAAAATGTCTCTTTGA
                                       +++++ + +++  +++++++
1    GACGTGCACCACCACCCAATAGGAATTACTATTAAAATTAAGAATTCCTCTTTGCCCATTTTAAATTTTTAAATA

                   [3]                        [2]
                   8.3e-05                    4.6e-05
                   AGTGCCCTGGGCCTTTAAGAG      ATGAAAAGCAGTGATTCACAG
                   +  + +++++++ ++ +++ +      + ++ +++++++  + +++++
1201 TTTCTGAGTTCGAGACCAGCCTGGTCTATAAAGTGAGTTCCAGAACAGCCAGGACCACACAGAGAAACCCTGTCT

                                                  [2]
                                                  1.7e-07
                                                  ATGAAAAGCAGTGATTCACAG
                                                  + ++ ++++++++++ +++++
1651 GATCTCCTTTAGTTTGTGACCACCCTGAGCTACATAGTGAGTTACAGGACAGCCAGGGACACACAGTGAGACTCT


NM_033030
  ENSG00000152430
  LENGTH = 2000  COMBINED P-VALUE = 1.07e-04  E-VALUE =      3.8
  DIAGRAM: 189_[3]_218_[8]_1213_[8]_53_[2]_3_[4]_170_[3]_26


                                            [3]
                                            6.2e-05
                                            AGTGCCCTGGGCCTTTAAGAG
                                            + ++  ++ ++++++ ++++
151  NNNNNNNNNNNNNNNNNNNNNNNGTAACATGTTTGGGCTATTAAGCTAGGCCATGAAGAAGGCTGTATGATATCC

                                                          [8]
                                                          8.8e-05
                                                          AACTTCAAAATGTCTCTTTGA
                                                           +++ ++++++   +++++
376  GTTGTGGAAGAAACACACTTGGGTATCAATTATCATCAAAATTCCTTATCCAATAATACATAATTAATTTTTATT

                 [8]
                 5.4e-07
                 AACTTCAAAATGTCTCTTTGA
                  ++++ ++++++ +++++ +
1651 TTAAAAGTATTATAATTAAAAATGATTCTTATCCTAAATATGAAAATAAATATCAAATAATATGAAACATAACAT

                [2]                     [4]
                3.1e-05                 1.3e-05
                ATGAAAAGCAGTGATTCACAG   AGGAGAGAGCTCACACCTCTCCC
                +++++++ ++ + ++ ++ ++   ++ +++ + ++ +++++++++
1726 CTAATTGTTTGATAAGAAAAAATAACACAAAGCAGAGAAAATAAAAGACACCTCACTATTCCCAATGTGGTTATT

        [3]
        4.3e-05
        AGTGCCCTGGGCCTTTAAGAG
        ++++   ++ +  +++++
1951 CTGAGTATGGTGAGGTATTAACTAACACTAAGTTTCACAACGGGCAGCTT


NM_003215
  ENSG00000135605
  LENGTH = 2000  COMBINED P-VALUE = 1.11e-04  E-VALUE =      3.9
  DIAGRAM: 97_[8]_88_[3]_758_[4]_369_[2]_602


                           [8]
                           9.6e-06
                           AACTTCAAAATGTCTCTTTGA
                            +++++++++++ ++   ++
76   ACAGTCTCATTCTAAAAACAAGTACTTCATACTGATTGCATTTCTACACACACATATGCAGATTTCTGGACACTC

                                                             [3]
                                                             1.3e-06
                                                             AGTGCCCTGGGCCTTTAAG
                                                             +  +++ ++++++++++++
151  TTTCTGTTTTTCTTTCATTTATGTTCTCAATGCTGAACCTTTATTAGAATTACATCATCACTGTGGTTCTTTAAA

     
     
     AG
     
226  TAAGAAACAAAACTCTGTCACAACATCTGAGGAAATTATCTTTTAATGTCCCCAAGCTCTATGCCTTGGAAAAAA

               [4]
               3.5e-05
               AGGAGAGAGCTCACACCTCTCCC
                +++++++  ++ ++  + +++
976  TTCATCCCACTGGAAAGCATAACCATGTGTCAACTAATTAACAGAGCAACTTTAATGAAGACACAGCATATTCTA

                                [2]
                                8.8e-05
                                ATGAAAAGCAGTGATTCACAG
                                  +++ ++++  + ++ ++++
1351 TGGGATGGGAGGAGGGAAGGTCAGGAAGGAAGGAGAAAAGGCTGACAGTGATAGTAAGGTAGAGTGTGCCAGGAC


NM_172893
  ENSMUSG00000038507
  LENGTH = 2000  COMBINED P-VALUE = 1.14e-04  E-VALUE =        4
  DIAGRAM: 44_[3]_340_[2]_74_[3]_791_[3]_133_[3]_130_[8]_362

                                                 [3]
                                                 4.0e-07
                                                 AGTGCCCTGGGCCTTTAAGAG
                                                  +++++ +++++ ++++++++
1    ATGTATATAGACACTCAGCCTCCAAAGTAGCTCCAAAGCCTCATTATACTTTGGTTTTTTAAAAGGACAGAGAAA

                                   [2]
                                   9.7e-05
                                   ATGAAAAGCAGTGATTCACAG
                                     +++++    +++++++ ++
376  CAAAGAACAGAGGGGGTTGTAAGTGCAAGAGGGGAAATTGAGGATTCAAACTGCCATCAAGGGACAGGAGTCCAG

                                                       [3]
                                                       7.3e-06
                                                       AGTGCCCTGGGCCTTTAAGAG
                                                        +++++  ++++++ ++++ +
451  TGATTCTAATGCAGTCCTGTCCCTATTCACAACAGACAAGGCAAGGCAGGTATGCCTGGGGTCTATAAATGAAGA

                                          [3]
                                          1.5e-05
                                          AGTGCCCTGGGCCTTTAAGAG
                                          ++ +++++ +++ + ++++ +
1276 ATTGGGTCCAAAACAGGAATCCCTCATCAGTGAGATTAACACCCTTGTTTAATAAAGGGTCTGGGATAGTCTCCT

                                              [3]
                                              6.1e-05
                                              AGTGCCCTGGGCCTTTAAGAG
                                              ++++++  + ++++ + ++++
1426 CTTGATTTTGAACTTCCTAGTCTCCAAAACCTTGAACAATAAATACCTAGTGTCCATTAAAGCCACTCCGTTTAT

                                               [8]
                                               1.4e-06
                                               AACTTCAAAATGTCTCTTTGA
                                                ++++++ + +++++++++
1576 TCTTAAAAACAGACATCAAAAAAATAAACTCCAGTCTTCATCTACTTCAGATTGTCTTTTTATTTCCATACTCTC


NM_133867
  ENSMUSG00000040600
  LENGTH = 2000  COMBINED P-VALUE = 1.16e-04  E-VALUE =      4.1
  DIAGRAM: 769_[3]_282_[2]_761_[4]_123


                        [3]
                        4.0e-07
                        AGTGCCCTGGGCCTTTAAGAG
                        ++++  ++ +++++++++++
751  AAACCCAGCCTGAGAATGGAATATGATTGGCCTTTAAGAATAAATAAACAAATTAAGGCTATTCAAACCTGAAAG

                           [2]
                           4.4e-06
                           ATGAAAAGCAGTGATTCACAG
                             ++++++++ ++++ ++  +
1051 ACATCATCTCTCACTTGGTCCTGAGGAAGCCAAGGACACATTCCTGACTGCAGGCTATAGTTATATGATCTGTGG

                                                           [4]
                                                           1.3e-05
                                                           AGGAGAGAGCTCACACCTCTC
                                                            + +++++ ++  +++++ ++
1801 GCCACACCTGAGGTCAGAGGCCAACAAGGAAGAAGCTGGAGAGCAGGGGTCTCGGGTAAAGCTCTGGCACCTGTC

     
     
     CC
     ++
1876 AGCACAGACACTTCCTCAGGTCCACTACCGTGCTGTGCGGTTGGTGGCCTGAAAGGCCTCTCCACCCTCTAGAGT


NM_027877
  ENSMUSG00000024906
  LENGTH = 2000  COMBINED P-VALUE = 1.17e-04  E-VALUE =      4.1
  DIAGRAM: 114_[8]_370_[2]_57_[8]_1295_[4]_78


                                            [8]
                                            9.1e-05
                                            AACTTCAAAATGTCTCTTTGA
                                            +++    ++ ++++++++++
76   AAAAATGACCTGAATATAATTCTCTACTTTCTTTATCCCAGAAATTAAGTGGTTTTTTGTTCTTTATGGTTCCTG

                                                            [2]
                                                            2.4e-06
                                                            ATGAAAAGCAGTGATTCACA
                                                            + ++ ++++++++ + ++++
451  CAGAGGCAGGCGGATTTCTGAGTGCGAGGCAAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTACACA

                                                               [8]
                                                               7.9e-07
     G                                                         AACTTCAAAATGTCTCT
     +                                                         ++++++ + ++++++++
526  GAGAAACCCTGTCTTGAAAAATCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAACTTCTTTATGTTTCT

     
     
     TTGA
     ++++
601  TTTACGATACAGGAAAAGGAATACTTCAATTTAATTCCAGAGTTGATAGGTTTATGATCATTTTAGCACAAAGAC

                             [4]
                             4.9e-05
                             AGGAGAGAGCTCACACCTCTCCC
                             ++ +++ + ++++++    ++ +
1876 GCGCTGTCCTCCTTTTTAACAGTCAGTACACAAAAAAAAAGAGTCTGCTCTCGAATTTTTGGGTGAGAGGAAAGG


NM_011937
  ENSMUSG00000024437
  LENGTH = 2000  COMBINED P-VALUE = 1.19e-04  E-VALUE =      4.2
  DIAGRAM: 418_[4]_623_[4]_913


                                                [4]
                                                8.3e-05
                                                AGGAGAGAGCTCACACCTCTCCC
                                                ++  ++++++++ + +++ +++
376  CATGATGGGCACTATGGTGACATGCAGCCTGGCACTGGGCAGTAGTTGAGAGCTACAGCCTGACCTGCNNNNNNN

                   [4]
                   1.1e-09
                   AGGAGAGAGCTCACACCTCTCCC
                   ++++++++++++ ++++++++++
1051 AAGGTAGGTGAGAAAGGACAGAGATACAACTTCACAGTGTACCCCAACATATGGGGCCATTCTTAATCAATGGGA


NM_024993
  ENSG00000176204
  LENGTH = 2000  COMBINED P-VALUE = 1.19e-04  E-VALUE =      4.2
  DIAGRAM: 98_[3]_552_[8]_192_[3]_111_[4]_961


                            [3]
                            6.4e-06
                            AGTGCCCTGGGCCTTTAAGAG
                             + + +++++++++++++++
76   AAAAGTCTTAGAACCCCAGTTCTCAAATCCTGGTTCTTTAAGAATGTTTCTTTCTTCTTGGTGATTCTTAAACAT

                                                                            [8]
                                                                            3.1e
                                                                            AACT
                                                                              ++
601  ATATGCTATCAAAGAGCAATTATATTTTCCAACTGTTAACTAGCATTAGAAAGGGCAACATCTTTAATTACTCAT

     
     -06
     TCAAAATGTCTCTTTGA
     + +++++++++++++ +
676  TAAAACTGTCTTTTGAAAGAGTGATCATCTAAAATCAGATACTAAAACATTATATTGCCAGAATTTAACCTCTCT

                                                                [3]
                                                                5.3e-05
                                                                AGTGCCCTGGGCCTTT
                                                                + ++ ++++ ++++ +
826  CAATTTACATCCAGCATTACTTATTGACAAGTTTGAAATTTGTGACTATTTGTCTGCTCACTAACATGATCCTGT

     
     
     AAGAG
     +++ +
901  AAGTGATCTTTTAAATTAAATAATCAGAAACCGGGTCCAAATTTATTCTTATAAAAACAAAAATAATATAACATG

                                              [4]
                                              1.1e-05
                                              AGGAGAGAGCTCACACCTCTCCC
                                                  ++++ ++++++++++++ +
976  GAAGGTACACCTTTATTTGAGGCTGTTACAGAAAGGGAGGATACCCAGAACTCAAACCTCTCTCCTTTTATTTAT


NM_002578
  ENSG00000077264
  LENGTH = 2000  COMBINED P-VALUE = 1.20e-04  E-VALUE =      4.3
  DIAGRAM: 434_[2]_359_[2]_704_[3]_440


                                                                [2]
                                                                7.8e-05
                                                                ATGAAAAGCAGTGATT
                                                                  ++++++++ ++++
376  CATGATGTAACTTAGAGTGCATTACTGAGAGTAATAAACATACTATAACCACTAAAGGGCCGGAAAGCATTGATA

     
     
     CACAG
      + +
451  GATAATTTTTCAGCACAACAGTTAATGAGTAGACCCCTGTTTTTGTTTTTATTGTTCTTAGGTTTGTTCATAGTA

                                                                     [2]
                                                                     2.5e-05
                                                                     ATGAAAAGCAG
                                                                     ++++++++++
751  TGGAGACAGAAACATTCCCTTGGGGAGTTCATGCTTTTCCAGTTTACTTTATCCTCCCAGGGGAATGAAAACCAA

     
     
     TGATTCACAG
       ++ + +++
826  ATATACTCAGATGTAGACACAAGATACTAAAGAATAATGAACTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                                            [3]
                                            1.1e-08
                                            AGTGCCCTGGGCCTTTAAGAG
                                            + ++ +++++++++++++++
1501 ACACCAAGGACATCTCGATGTTAAAGCAGCTAACAAGTCATTGTTATGGGCCATTAAAAATCAACAGCCAAACCT


NM_021763
  ENSRNOG00000010533
  LENGTH = 2000  COMBINED P-VALUE = 1.21e-04  E-VALUE =      4.3
  DIAGRAM: 788_[2]_130_[2]_361_[2]_173_[4]_462


                                           [2]
                                           2.5e-05
                                           ATGAAAAGCAGTGATTCACAG
                                           + +++++ ++ +++++ + ++
751  GAGACTGCATGTGTTCAGCGCCTGAGAGATTCAGACTGAGAAGAAACAATGACTTAGAGGATGGCAGAGTAAGAG

                                            [2]
                                            5.9e-08
                                            ATGAAAAGCAGTGATTCACAG
                                            +++++++++  ++++++++++
901  TTGAGGCCAGGGCAAGTGGATACTGCAGCAGCCACTTTAATAAGAAGACAGGATTCACACAGAGGCACACTCGGA

                                                   [2]
                                                   1.5e-05
                                                   ATGAAAAGCAGTGATTCACAG
                                                   ++++++ ++++++ + ++++
1276 AAGATTACATCACTGAGGAACCACAGTAGACACGCCAACCACATACATAAGACCAAGTGCTGCACAAGTAACCCA

                    [4]
                    8.0e-06
                    AGGAGAGAGCTCACACCTCTCCC
                    ++++++ + ++++++ + +++++
1501 AGGTGTGGTTTTATGAGGACAAAAAAAAAATCCCTCCGTTACAGAGGAATTGCGTCATCTGTAGGAGTTTCTTCA


NM_016957
  ENSMUSG00000051601
  LENGTH = 2000  COMBINED P-VALUE = 1.23e-04  E-VALUE =      4.4
  DIAGRAM: 421_[8]_591_[3]_430_[8]_473_[8]_1


                                                   [8]
                                                   2.4e-06
                                                   AACTTCAAAATGTCTCTTTGA
                                                   ++++++++ ++++ ++ +++
376  TATCTCACTTAGGGTGATATTCTCAAGATCCATCCATTTGCCTGCAAAATTCATGATGTATTGTTGTTTTGTTTT

                                                               [3]
                                                               3.1e-08
                                                               AGTGCCCTGGGCCTTTA
                                                               ++++++ ++  ++++++
976  TGACCACAGTGTAAGACCTATCTCAGAGTTGTTTTGATTTGCTTTTCCCTGATGACTAAGTACTTTGAATCTTTA

     
     
     AGAG
     ++ +
1051 AGTGCTTCTTGGCCATTCAAGATTCCTATCTTGTGAATTCTCTGTTTAGCTCTCTGCCCCATTTTTAAAATTGGG

                                                                [8]
                                                                3.8e-05
                                                                AACTTCAAAATGTCTC
                                                                 ++++ + ++++ +++
1426 ATTTATTAATTTGAGACCTCTCAAATTTTTGGATGTAGACACTTAACCATTAATCTTGCCACTTAAGACTGCCTT

     
     
     TTTGA
       +++
1501 CATTATGTCCCATAGATTTTGGTATGTTCTGGTTTTATTTTCATTCATTTCTAGGACTTTTAACATTTCATTCTT

                                 [8]
                                 1.3e-05
                                 AACTTCAAAATGTCTCTTTGA
                                  ++++ +   + ++++++++
1951 TATGGCTGATTTTGGAGAAAAATGTGTGTGCTTTAGTGTTTTTTTTTTTT


NM_172499
  ENSMUSG00000041945
  LENGTH = 2000  COMBINED P-VALUE = 1.24e-04  E-VALUE =      4.4
  DIAGRAM: 686_[3]_176_[3]_34_[8]_806_[4]_212


                [3]
                3.3e-05
                AGTGCCCTGGGCCTTTAAGAG
                ++++++++++++ +   ++
676  TTAAAAAATAAAGTGCTATGGTTTTAAGAATACAAACATGGCTTTGATAAGCATTTGAAAGAAAAGTCCACTGTC

                                                               [3]
                                                               7.7e-08
                                                               AGTGCCCTGGGCCTTTA
                                                                +++++ ++++++++++
826  CTCTCTGAGGCTCATCTCCGTGACATTCAGATGCTGTGTGAGGACATGGCACTGGTGCCATGCTTTGGTCCTTTA

                                           [8]
                                           8.6e-06
     AGAG                                  AACTTCAAAATGTCTCTTTGA
     ++++                                  +++++ +++ ++  ++  ++
901  AGAGTTCTTAGCGCCTGTGTTAAATTCACAGTGGAAACAACTTAAAAGTGAATTGGTTTTCTCACAGCCAGAGAG

                                             [4]
                                             6.9e-05
                                             AGGAGAGAGCTCACACCTCTCCC
                                             +++ + ++  + ++ ++++++++
1726 CTGCCTTTCCCTAAGAGCAAATGTTAACTCTACTGTGCCCAGGTGGGAAGAGAAGCCTCTCAGGCAAGCTTCTGA


NM_021470
  ENSMUSG00000029130
  LENGTH = 2000  COMBINED P-VALUE = 1.38e-04  E-VALUE =      4.9
  DIAGRAM: 621_[4]_380_[8]_256_[2]_244_[4]_411


                          [4]
                          4.2e-05
                          AGGAGAGAGCTCACACCTCTCCC
                          ++++++   ++  +++++ + +
601  AAAATAAGAAGCCCATAACTCAGGACAATAAAGCAACTTGTTAAAATTCAGACATCCAAAGAGTTAAATGTAGGT

                                                      [8]
                                                      2.5e-07
                                                      AACTTCAAAATGTCTCTTTGA
                                                      +++++ ++++++ +++++++
976  TTAAGTGGAGTTTAAAATTATATTGTTCCAGAGACTTATCATGTGTACCAGATTTATAATGACTTTTGGGACTTC

                               [2]
                               5.3e-06
                               ATGAAAAGCAGTGATTCACAG
                                +++++++++ ++ ++++ ++
1276 AGCGCGGGGATGCAGACTTAAGAGGGGTAGGAGGCAATGTCTCAGAGTGCAGAAGGCCAGGAGCCGCAAGGACAC

                                                                       [4]
                                                                       5.5e-05
                                                                       AGGAGAGAG
                                                                       +++ ++ ++
1501 AGGGCGGATGGCGACGCCACACAGCTCGCAAAACAGTCGAGGGGCCGTTATCAAGTCTTTCGACTGAGGGGACAG

     
     
     CTCACACCTCTCCC
     ++++++ + +++ +
1576 CAAAAAGCGCACTCCAAAGAGCCGCACGGGTCAGCGCATCCTCGGGACGCATCACGCAGCCTGGCTGGAGGGCAG


NM_177001
  ENSMUSG00000047433
  LENGTH = 2000  COMBINED P-VALUE = 1.39e-04  E-VALUE =      4.9
  DIAGRAM: 548_[2]_1093_[3]_317


                            [2]
                            7.3e-08
                            ATGAAAAGCAGTGATTCACAG
                            + ++++++++ +++ ++++++
526  CACAGATGAAGAAACTGAGAGCCAGAAAAAGAAATGAGTCACACAACTAGAGACAAACCCAGTCACTTAGAAACT

                 [3]
                 4.7e-06
                 AGTGCCCTGGGCCTTTAAGAG
                 ++ +++++++++++++ +  +
1651 AAAAAAACTAACAACACTCTGGTCCCTTCATTGAAGCCAGGGATAACTGCAGAAACTCTCATCTTGGAACACCCA


NM_021836
  ENSRNOG00000003678
  LENGTH = 2000  COMBINED P-VALUE = 1.39e-04  E-VALUE =      4.9
  DIAGRAM: 1433_[4]_61_[8]_462


             [4]
             9.4e-07
             AGGAGAGAGCTCACACCTCTCCC
             ++++++++ +++ ++ ++  +++
1426 TACCCGAAAGGAGAGAACTACAAACTGCCCCGGGCTTGGGGCAGCCCAATCTTCTCCCTCCATCCGCCCAGCTTG

                      [8]
                      3.6e-07
                      AACTTCAAAATGTCTCTTTGA
                      +++++ ++++ + +++++++
1501 GAAGAAAGAGACCACAGAAATTAATAAAGACTTTTTTTTTACTTAAATAGATTCAATAAAAAGTCAAACACACAC


NM_011167
  ENSMUSG00000021345
  LENGTH = 2000  COMBINED P-VALUE = 1.43e-04  E-VALUE =      5.1
  DIAGRAM: 175_[2]_314_[3]_577_[4]_584_[3]_160_[3]_83


                              [2]
                              4.1e-05
                              ATGAAAAGCAGTGATTCACAG
                                +++++ ++++++  ++++
151  AAGGGACAGCACATGCTGGTAAGGATGGGAAATAAGGGAAACACATCTCCATTAATGGTGGAAGTACAAACCTGT

                                                                 [3]
                                                                 1.5e-05
                                                                 AGTGCCCTGGGCCTT
                                                                 +  ++++++ ++++
451  ATTCTAATATTAAAAACAGACATCCTGAATTTTGCAGGCAAATGGATGGAACTTGATAATATCACCCTGAGTCAG

     
     
     TAAGAG
     + ++ +
526  TTAGTGCAGACACAAAAATAAATGCATTGTATGCAATCACTTTTAATTGGACATTATACATAACGTGTAGGATAA

                                                               [4]
                                                               4.8e-06
                                                               AGGAGAGAGCTCACACC
                                                                + +++++++ ++++++
1051 ACAAAAGATTGAGGGAATATCCAACCAATGCTTTGCCCAACTTGAAACCTATCCTATTGGAAAAGAGCCAACACC

     
     
     TCTCCC
     + ++++
1126 TGACACTATTAATGATATTCTGCTATGCTTTCAGACAGGAGCCTGAGAAACTGCATCCAGCAGATGACAGAAATA

                                                                      [3]
                                                                      2.9e-05
                                                                      AGTGCCCTGG
                                                                      ++++ + +
1651 AAGGTTATAGTTGGACTTATGACACATACTGAAGAGATCATCACTAACTGATATTTGCATCCTAAAATAATTTTA

     
     
     GCCTTTAAGAG
     ++ +++++++
1726 TTTTTTAAAAATCAAGTTTTGGGGTATCTCAGACATGAATACAGTGTATTTTTATCATCTCTAGTCTTTGCCTCC

                          [3]
                          5.4e-07
                          AGTGCCCTGGGCCTTTAAGAG
                          ++++ +++++   ++++++++
1876 TGGTTTCCAAAGGACAGCCTGAATGTTATGGAGTATTAAAAGTTTTATAATTCTGATTAGGATACATGTATCAGC


NM_020610
  ENSMUSG00000031019
  LENGTH = 2000  COMBINED P-VALUE = 1.48e-04  E-VALUE =      5.2
  DIAGRAM: 1245_[4]_285_[2]_29_[3]_376


                                                  [4]
                                                  9.6e-05
                                                  AGGAGAGAGCTCACACCTCTCCC
                                                  +++ ++ + ++++ ++++  +++
1201 TGGATTGATTAATAAAAAGCAAATTCTTGGAAGAAGCAGAGAAATAGGCCACAAATAAGACCTGGCAGTGTCAAA

                                                          [2]
                                                          7.3e-07
                                                          ATGAAAAGCAGTGATTCACAG
                                                          + ++++++++ + +++ + ++
1501 CACATGCGCACACGCTTCAGGCTGCAATTATGCTTCTGAAGTGCTGAAATGAGAAAGAAACAAATAATTGATAGC

                                 [3]
                                 1.2e-05
                                 AGTGCCCTGGGCCTTTAAGAG
                                 + ++ + +++++ ++ +++ +
1576 AAATTCAAAGGAGTTAATCTGAAGGCAAATTAACTTGGGTTTTAAAATGTCTCATGTATACATCTATAATCCTAG


NM_026838
  ENSMUSG00000031253
  LENGTH = 2000  COMBINED P-VALUE = 1.49e-04  E-VALUE =      5.3
  DIAGRAM: 8_[2]_55_[3]_1012_[3]_538_[2]_45_[2]_106_[8]_110

             [2]
             2.5e-06
             ATGAAAAGCAGTGATTCACAG
             + ++ ++++++++ + +++++
1    TGAGTTCCAGGACAGCAAGGGCTACACAGAGAAACCGTGCCTTGGAAAAAACAAACAAACAAACAAGCAGCAACA

              [3]
              1.0e-05
              AGTGCCCTGGGCCTTTAAGAG
              ++ ++++++ ++++++ + +
76   ACAACAATAAAAACCCTGATTCTTTCACAATTGTATAGAGATCTTAAAATTTTTCCTGTTACACACATATATTAT

                                                                        [3]
                                                                        4.1e-05
                                                                        AGTGCCCT
                                                                        + ++ +
1051 TGAATAGCCCTCCATCCAAGACAGCTGAAAAACAGCTTAGCAATAAATATCACCTTGCCATGGATAGATTATTTA

     
     
     GGGCCTTTAAGAG
     + ++ +++ ++++
1126 GATTTATTTAAAGAACCTTTCAGAAAAGCCTCCCTAGGCATGCTTTCCTTCCATTCATAGTATGGGAAATTAATC

                               [2]
                               7.2e-06
                               ATGAAAAGCAGTGATTCACAG
                               +++++++++++++ + + +++
1651 TTTCAATCCCGATGTCATGCTGAGTCATAAAAAGCAGTGTTCCTCAGAAGTCCTCTCTGGAGGTCCTATGCTAGT

                      [2]
                      5.9e-05
                      ATGAAAAGCAGTGATTCACAG
                       + ++++++++++++   +++
1726 CATCACTCCACCCAGAGCTTGAAACCAGTGACAGTCACACTTCCCCTCTTCTGCAGCAGACAGCACTAGCTCCTC

                                                                          [8]
                                                                          5.2e-0
                                                                          AACTTC
                                                                          +++++
1801 TAATCCTCTTGCTTCCCCCTCCCCCAACCATTTCTTGGGGAATAACAAATATAGCTTTGGGGATAATATAGCTTT

     
     6
     AAAATGTCTCTTTGA
     ++ + + +++++++
1876 AAGACGACTTTTGGCAAATGTAAATGTCCTAACATCTGGGCAGTGTTACCAGAATCCCGGAGGCCCTGACAGACC


NM_153270
  ENSG00000185915
  LENGTH = 2000  COMBINED P-VALUE = 1.50e-04  E-VALUE =      5.3
  DIAGRAM: 38_[8]_66_[4]_175_[3]_1026_[8]_609

                                           [8]
                                           4.2e-07
                                           AACTTCAAAATGTCTCTTTGA
                                           +++++ ++++++++ + ++++
1    TCCTTTACTATTCTATATCCTAAAATCTACTTCTAATCAGCTTTATACTGTTGCCTGTACAGCTCAGTGAATGTA

                                                       [4]
                                                       4.6e-06
                                                       AGGAGAGAGCTCACACCTCTCCC
                                                       ++++++ ++ +++++++ +++++
76   CTTTCATCTTTAAGAGTTCAGATATATGCCAGTGAATATTTTTGCTGTAGAGGAGAAAGTAAAAACTCCACAGCG

                            [3]
                            2.1e-05
                            AGTGCCCTGGGCCTTTAAGAG
                            ++++ + +  ++ +++++++
301  GTATGGAATTTTGGGTCCAGTGTAATATTTTTATCATTTAAAAAGAACTCTATTTGTAAAAACATTTATTTACTG

                         [8]
                         7.7e-05
                         AACTTCAAAATGTCTCTTTGA
                          ++++  + ++ ++++++++
1351 CTTTCTAGATTAAAAAAAAGTGCTTAGAGATTTTTTTTTTCCTTCTCAGTTCCATATTTATATCAAACCATCAGA


NM_013255
  ENSG00000128585
  LENGTH = 2000  COMBINED P-VALUE = 1.51e-04  E-VALUE =      5.3
  DIAGRAM: 141_[3]_111_[8]_1249_[4]_122_[8]_81_[4]_187


                                                                       [3]
                                                                       1.0e-05
                                                                       AGTGCCCTG
                                                                       + ++ ++++
76   GCCTCTGTTAAACAGTTTAGAAGGGTATTGAAAGTCACCAAAAGGATTTAAGCTTAAGAAGAACTAATTAACATG

     
     
     GGCCTTTAAGAG
      ++ +++++++
151  TGTTTTTAAAAAAGATTGCTCAGGAACTATGTCTGGAAAAGAACAAGGACTTGACTTACATTAAGGTAAGAAGTG

                                                     [8]
                                                     2.0e-05
                                                     AACTTCAAAATGTCTCTTTGA
                                                       +++ +++ +++++ ++++
226  GAATTATAAAATCTGGGGCCCAAAGGAATTGGAGTGAGTTAATTCCTCCCCTTTAAAGTGTCTATTTTCTTCAAA

                                                [4]
                                                7.3e-05
                                                AGGAGAGAGCTCACACCTCTCCC
                                                ++++++++ ++  + ++ ++ ++
1501 TGGAAGGCGGGGACAAGACATTTAAAACCAGGACCACTCCAGGAGGACAGCACATTAGCTACTGCCCTCCAGCTC

                                           [8]
                                           2.1e-05
                                           AACTTCAAAATGTCTCTTTGA
                                           ++++ +++  +++++++ ++
1651 TTCCAACTTGGTCTTCTTATTTTCCCTTCCTGCTCCATAACTACAACGTGTTTCTGTTCGTAATCATCTCGGCTT

                                                                      [4]
                                                                      3.1e-07
                                                                      AGGAGAGAGC
                                                                       +++++++++
1726 TTCCTTACCTCTGCTTGTAAGAAAAGTCCTTTGCGCCATTCCCCTCCAAGCCCCAGGGAAGGGCCTGGAAAGCGC

     
     
     TCACACCTCTCCC
     + ++++++++ ++
1801 TTACACCTCAGACCCAGTGTCGGTCAGCCGTCAAGGAGCGAGCGACGTGGGAAACCCTGAGATAGGACATTGGCC


NM_031817
  ENSRNOG00000015326
  LENGTH = 2000  COMBINED P-VALUE = 1.52e-04  E-VALUE =      5.4
  DIAGRAM: 72_[8]_1324_[8]_97_[2]_444

                                                                             [8]
                                                                             9.0
                                                                             AAC
                                                                             +++
1    TAATACCAATTTTTTTCTTTTTTTTCAGTTGCCAGATGTATACTTTGGGTTTTTGTTAAGGATTATTTTTTAAAA

     
     e-09
     TTCAAAATGTCTCTTTGA
     ++ +++ +++ +++++++
76   TTAAAAGTGTATTTTGTAATTTAGAAGGAATTTAACAATTTTTAGACTTCAAAATTGAGAATTTTCACTTTTTAG

                                                                        [8]
                                                                        7.9e-05
                                                                        AACTTCAA
                                                                        +++++ +
1351 CATCTGCTAATTGTACCTTGTCTGAAACTTTACTGTGTGTTTTTGGATTCCTTGTACTGGCATACACAGATTTAC

     
     
     AATGTCTCTTTGA
     + + ++++ +++
1426 ATTTGTTCCTTTTTTTAATCACGAGTCCTGTGAAGCATAAGTAAAAGAATTCACACAACAGTTTGAATATTCACC

                                        [2]
                                        3.1e-05
                                        ATGAAAAGCAGTGATTCACAG
                                        + +++ + +++++++ ++ +
1501 TTAAAGCTTACTTAAAATACTTTTAAAATGAACTGAAGAACATAAGTGATACAGATGGGAGGAGGCTACAGCTCA


NM_172801
  ENSMUSG00000050201
  LENGTH = 2000  COMBINED P-VALUE = 1.56e-04  E-VALUE =      5.5
  DIAGRAM: 499_[3]_72_[2]_367_[8]_486_[2]_492


                                                      [3]
                                                      4.6e-05
                                                      AGTGCCCTGGGCCTTTAAGAG
                                                       +++ ++++++++++ ++++
451  AGTTGGAGATGATAATGTTTAAGTAAACATGCTCAAGGCAGCCCTTCAAGGTGGCATGGGTCATGAAAAAACAAC

                                                                        [2]
                                                                        1.0e-05
                                                                        ATGAAAAG
                                                                        + ++ +++
526  ACTCAGGGAGTAGGGACAGGCAGGTCTCTGTGAGTTCAAGACCAGTCTGGTCTACAGTATGAGTTCCAGGATAGC

     
     
     CAGTGATTCACAG
     ++ ++ + ++ ++
601  CAAGGCTACATAGTGAGATTCTGTCTAGTAAGTAGATGAGAATAAAATAATGTACCATAATAGAGAGAGAAAAGA

          [8]
          9.3e-07
          AACTTCAAAATGTCTCTTTGA
           ++++ ++++++   + +++
976  NNNNGTACTTTAAAATGAAATCTTTCAAAATGAAAGAAAGAAAACTGCATTTCCTGTCTTTCCCAATAGCCAGCC

                                                                   [2]
                                                                   2.4e-06
                                                                   ATGAAAAGCAGTG
                                                                   + ++ ++++++++
1426 CTCGGGCGACAGGGGTGGGCAGATCTGTGTTCGAGGCCAGCCTGGCCTACCAAGCAAGTTCTAGGACAGCCAGGG

     
     
     ATTCACAG
      + +++++
1501 CTACACAGAGAAACCCTGTCTCAAAAAAACAATAACAAAAGTCAGATGATGGAGAAAATGTCCTCTAAGTAAGTC


NM_033072
  ENSMUSG00000025409
  LENGTH = 2000  COMBINED P-VALUE = 1.58e-04  E-VALUE =      5.6
  DIAGRAM: 460_[2]_458_[3]_190_[8]_399_[3]_409


               [2]
               2.4e-06
               ATGAAAAGCAGTGATTCACAG
               + ++ ++++++++ + +++++
451  ACAGAGTTCCAGGACAGCCAGGGCTACACAGATAAAGTCTCGAAAAAAGAGAGAGAGTTTCTTCTGGGTGTTCCT

                                            [3]
                                            8.9e-05
                                            AGTGCCCTGGGCCTTTAAGAG
                                            + ++ +   + ++++++++ +
901  CCTCTAACGTCTGTCTCTGGCCGAGTCTAACACTGTACAACTGTCTCTGACCATTAAATGCTGTTGTACCGTGGA

                              [8]
                              6.3e-06
                              AACTTCAAAATGTCTCTTTGA
                              +++++ + + ++++++   ++
1126 GAGTTTCAAAATATTCTCATCTGTTAAATTAAGAGTGTCTCCCATAGAAAAGCAGTGGAGGCCCCACAGGGCAAG

                                                                           [3]
                                                                           7.3e-
                                                                           AGTGC
                                                                           + +++
1501 TCTGTGCTTTGAGCAACCTGAGCCAGAGGCAGAGGGGTGCTAGTGGGAATCGGGGAGATGCATGATGCTTATTGC

     
     06
     CCTGGGCCTTTAAGAG
     ++++  +++++ +  +
1576 TCTGTACCTTTCACTGGGAAGGAGGGCAGCAGCCAACAGTAGCTCACAGGTTTGTAAACTGAGCCTGCTAGCTTT


NM_177229
  ENSMUSG00000047113
  LENGTH = 2000  COMBINED P-VALUE = 1.60e-04  E-VALUE =      5.7
  DIAGRAM: 412_[2]_472_[8]_74_[4]_977


                                          [2]
                                          2.5e-06
                                          ATGAAAAGCAGTGATTCACAG
                                          + ++ ++++++++ + +++++
376  TGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGAACAGCCAGGGCTACACAGAGAAACCCTGTCTCGAA

          [8]
          8.9e-07
          AACTTCAAAATGTCTCTTTGA
           ++++ +++++++ ++  ++
901  ACGTCTGCTTTAAAATGTATTCAGGTAAGAAAATTTCTTAAGCCTCTTATCAAAGATATTAGCAATTAATACCTT

                              [4]
                              3.0e-05
                              AGGAGAGAGCTCACACCTCTCCC
                                 ++++++++++++ +  ++ +
976  TATGGTAACTAAATTTCAGACTAACTTTACAGAGAACAAATCAGTCTCAGCATTGTCCTCTGAGGATTCTGGCAG


NM_026776
  ENSMUSG00000035120
  LENGTH = 2000  COMBINED P-VALUE = 1.61e-04  E-VALUE =      5.7
  DIAGRAM: 519_[4]_464_[2]_158_[3]_794


                                                                          [4]
                                                                          4.5e-0
                                                                          AGGAGA
                                                                           +++++
451  GTGTGTCTGAAGACAACTACAGTGTACTCACATATCTAAAATAGATATATCTTTAAAAAAAACAGACCATGGACA

     
     5
     GAGCTCACACCTCTCCC
      +++++++++ + + +
526  CAGCACACACATGTAATCTCAGTTCTCAGAAGGTTGAGGCAGTGGGATTAAAGGCTGAGCTCTGGGATAAAGGTG

                                    [2]
                                    4.5e-06
                                    ATGAAAAGCAGTGATTCACAG
                                      ++++  +++++++++ +++
976  TTTGGAGCTATGAATTAAACATTGTGACAGAGAGAGATTAAGGGATTCTCACAATAATTCTTCAGGGAACAGAAA

                                                                 [3]
                                                                 2.7e-07
                                                                 AGTGCCCTGGGCCTT
                                                                 ++++++++  +++++
1126 TAAAGGTGAGCATCTCCTAGCAGCCCAAGGTCAGCCTTCTTTTCAATACACCTTTTGTTTAGTGCTCTTATCCCT

     
     
     TAAGAG
     ++++ +
1201 TAAATGGGTTCATATTGCATGTCAGGTCAGAAGACTCCCAAACTTGTATTTCTAGATCCAACAAGGCTCCCCTGA


NM_027279
  ENSMUSG00000041396
  LENGTH = 2000  COMBINED P-VALUE = 1.63e-04  E-VALUE =      5.8
  DIAGRAM: 60_[2]_237_[8]_1023_[4]_615

                                                                 [2]
                                                                 2.4e-06
                                                                 ATGAAAAGCAGTGAT
                                                                 + ++ ++++++++ +
1    GGAGTCAGAGGCAGGCGGATTTCTGAGTTCGAGGGCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCT

     
     
     TCACAG
      +++++
76   ACACAGAGAAACCCTGTCTTGAAAAAACAAAACAAACAAACAAACAAAAAAAGATTGATAAAAAGGTTCCTGTAA

                       [8]
                       1.1e-05
                       AACTTCAAAATGTCTCTTTGA
                       ++ ++++ +++++ +++++ +
301  ATAGGGAACCTTGGAGACAAGTTCAGACTGTGTTTTTAAAATTAAGCCACATATAAAAGAGGGAGGTTTGGAGTT

                 [4]
                 3.2e-06
                 AGGAGAGAGCTCACACCTCTCCC
                 + + ++++ +++ ++++ ++ ++
1351 AGATGTGGTACCACGGAAGAACTACAACTACATCCTTCAGCTCTCACGCTTCATCCAGATACTGAGCACCAGCGC


NM_052828
  ENSG00000137394
  LENGTH = 2000  COMBINED P-VALUE = 1.72e-04  E-VALUE =      6.1
  DIAGRAM: 814_[2]_215_[8]_137_[4]_737_[2]_11


                                                                     [2]
                                                                     6.5e-05
                                                                     ATGAAAAGCAG
                                                                       ++ ++++ +
751  AAAGTGACAGCTAGCAATTTCTGCATCCCAGATGGAGTTAATGTCACCAAGAGAACTTGTACTAGGAGTAGGAGG

     
     
     TGATTCACAG
      ++++ ++++
826  AGACTGACAGCCCCCAGGGTCTCTCCTCAGGAGAGAATTCAGTTATACTGAAGATGCCTTCCAGGCCCCCCTTGG

     [8]
     5.9e-06
     AACTTCAAAATGTCTCTTTGA
     +++++++ ++ ++ ++  +++
1051 AGATTCAGAAGGGATCCATGATGAATGTGTCATTAGTTGGCAAGAAGAGCAGACACAGAGAGAATCAGAGATGCA

             [4]
             1.8e-05
             AGGAGAGAGCTCACACCTCTCCC
              ++++  +++ + +++++++ ++
1201 CGCTTCTTTGGACTTCGAGCCCACTTCTTACCGGTAGGTCCTGGGCATACAACATACCACTNNNNNNNNNNNNNN

                       [2]
                       3.0e-07
                       ATGAAAAGCAGTGATTCACAG
                         ++++++++++ +++ ++++
1951 CAAGTAAAATTACCCTAGGGGAGAAGCAGGTACTGACAGACCAACATGAG


NM_153189
  ENSG00000106304
  LENGTH = 2000  COMBINED P-VALUE = 1.74e-04  E-VALUE =      6.2
  DIAGRAM: 352_[3]_1004_[8]_602


                                                         [3]
                                                         5.3e-09
                                                         AGTGCCCTGGGCCTTTAAGAG
                                                         + +++ ++++++ ++++++++
301  AAAATACTTGTAAATATTTTTGCTTTAGGAGAAAATATGTGCTTTCAGGGATATTACGCTGGTCTCTTAAAAGTT

                                [8]
                                4.0e-05
                                AACTTCAAAATGTCTCTTTGA
                                + +++ +++ +++ +++ ++
1351 AAGTTTGTTCTGGCAAACTATTTTCTAACATTAAAATTGTATTTGTTTCCACTTTTTATTTGAGAAACAGTATGA


NM_003117
  ENSG00000106304
  LENGTH = 2000  COMBINED P-VALUE = 1.74e-04  E-VALUE =      6.2
  DIAGRAM: 352_[3]_1004_[8]_602


                                                         [3]
                                                         5.3e-09
                                                         AGTGCCCTGGGCCTTTAAGAG
                                                         + +++ ++++++ ++++++++
301  AAAATACTTGTAAATATTTTTGCTTTAGGAGAAAATATGTGCTTTCAGGGATATTACGCTGGTCTCTTAAAAGTT

                                [8]
                                4.0e-05
                                AACTTCAAAATGTCTCTTTGA
                                + +++ +++ +++ +++ ++
1351 AAGTTTGTTCTGGCAAACTATTTTCTAACATTAAAATTGTATTTGTTTCCACTTTTTATTTGAGAAACAGTATGA


NM_004490
  ENSG00000115290
  LENGTH = 2000  COMBINED P-VALUE = 1.74e-04  E-VALUE =      6.2
  DIAGRAM: 677_[3]_153_[3]_257_[2]_576_[8]_253


       [3]
       2.3e-05
       AGTGCCCTGGGCCTTTAAGAG
       +++++++ ++++++++  +++
676  GAAATACTCAGGGCCATTCTGAGAGGTTGAAAAAGGCAAGTGTGTTTACTCATGCTGTTCTACTTAGAAGTCCTG

                               [3]
                               2.4e-05
                               AGTGCCCTGGGCCTTTAAGAG
                               ++++   +   +++++++++
826  TAGCAATTAGGCTTGCATTAGCTAAAAGTAAGTTAAATCTTTAAAAATTCAATAAATAATTCTTTTTCAGTTATT

         [2]
         1.3e-06
         ATGAAAAGCAGTGATTCACAG
         ++++++++++  ++ ++++++
1126 AAAAATGGGAACAAAAGAATCACAGAATCTAAAAACTATTCCCAGATGGTCTCGAAGAAGTGATAAGGAAGGTTA

      [8]
      3.6e-06
      AACTTCAAAATGTCTCTTTGA
       ++++++++++ ++++++ +
1726 ATAATTCAAAATAGTTTTTAGTTTCATTAACAGGTTGTGGATAGTTTCTTTTAATTGATAAGTTATTATCATATT


NM_153784
  ENSMUSG00000043782
  LENGTH = 2000  COMBINED P-VALUE = 1.78e-04  E-VALUE =      6.3
  DIAGRAM: 120_[8]_1007_[2]_521_[8]_134_[3]_134


                                                  [8]
                                                  3.0e-05
                                                  AACTTCAAAATGTCTCTTTGA
                                                   +++++ ++++  +++++++
76   CTCCCAAATGCTGGGATTAAAGGTGTACGCTGCCACCACCTGGCCTACTTCCTACTTCCTTTTTTTTTTTTTTTT

                            [2]
                            5.0e-06
                            ATGAAAAGCAGTGATTCACAG
                            ++++++ ++ ++ ++ +++++
1126 AATTTGAGGCCATCCTGTGACACATGAGACCCTGTCACACACACATCCCAAAAATGGCACCGCACACATTCACTG

                                             [8]
                                             2.9e-05
                                             AACTTCAAAATGTCTCTTTGA
                                              +++  ++++ ++++++ +++
1651 TAGATGCTGCTTCCTTAGGGTGTTACAAAAGAAAAAAAATTACTATAAAAGGGCTTTCTTAGTGGAGGGCTTACC

                                                  [3]
                                                  4.6e-07
                                                  AGTGCCCTGGGCCTTTAAGAG
                                                  ++ +  ++++ ++++++++++
1801 GTAGATCTGCACATAGTAGGTGTTCAATTAATGTTCCCAGTAAGAAGCAAGATGGATCTTTAAGAGGATGGATGT


NM_011741
  ENSMUSG00000037327
  LENGTH = 2000  COMBINED P-VALUE = 1.81e-04  E-VALUE =      6.4
  DIAGRAM: 1899_[2]_80


                             [2]
                             9.6e-10
                             ATGAAAAGCAGTGATTCACAG
                             + +++++++++++++++++++
1876 GAGTTCAATCCCCACGTCCCACAAAGGAAAGGAAGTGACTCACACAAACTGTCTTCTCAGGACACGCAAGTGGCA


NM_002192
  ENSG00000122641
  LENGTH = 2000  COMBINED P-VALUE = 1.86e-04  E-VALUE =      6.6
  DIAGRAM: 28_[4]_183_[3]_96_[8]_1046_[4]_202_[8]_126_[8]_147_[2]_21

                                 [4]
                                 1.4e-05
                                 AGGAGAGAGCTCACACCTCTCCC
                                 ++++++++ +++ +++++ +
1    ATAGTATACCAACTTAGTATATTTTTCAAGGAGAGCTAAACCACCTTTTGTAATGTTTGGTTTCTCACTGTTATC

              [3]
              4.7e-06
              AGTGCCCTGGGCCTTTAAGAG
              ++ +++++++ + ++ +++++
226  TGTAAAAATAGGGCTCTGGATTTTCAAAAGCACATACATGAATAATTTATTAGCTATTCCAGGCAAGCTAAGTAC

                                                        [8]
                                                        7.0e-05
                                                        AACTTCAAAATGTCTCTTTGA
                                                        +++   ++  ++++++++++
301  TAGAATAAACTAGATAAAAACTTGGCTTTAAGCATGTACTTTGATATTTATAAAACAAAGGTGTTTTTTTTTCAT

                                                                         [4]
                                                                         5.2e-05
                                                                         AGGAGAG
                                                                         ++  +++
1351 NNNNNNNNNNNNNNNNNNNNNNNNNNGCTATTTTGTGTGCTGTAGCAGTTCTTTTATAGCTCACATTAAGTGCAG

     
     
     AGCTCACACCTCTCCC
     + ++ +++++ +++++
1426 CTCTTAAACCCCACCCCCACCCCCAACCAAAGAAAATACTTGTTAAATAAGGATTAGACAGGTCAAACACCATTG

                                                                         [8]
                                                                         6.1e-05
                                                                         AACTTCA
                                                                          ++   +
1576 ATGGACAAACATATTCCTTTCAAGTATCTCTCCTTGAAGAAAATAAAAATTAATCAGATTACTTCCAATACAAAA

     
     
     AAATGTCTCTTTGA
     ++ + ++++++++
1651 AAGTCTCTCTTTTTGTTCTCTCTCAGGTAAACAGTTTCAAACCTATTAGGTTGCATAGTTCTAAGATCATAAGCA

                                                                      [8]
                                                                      4.9e-05
                                                                      AACTTCAAAA
                                                                      ++ ++  +++
1726 CCTTAACGAAATGTAACTTGGTATTCTTTTTTCCTTGATCTTTCATTCTTTCCATACTTGTTCTCAATTTTTTAA

     
     
     TGTCTCTTTGA
     ++++ +++++
1801 TGTTGTTTGTTTTGTTTTGTTGCAAAAGTGGTACAGAAAAAGGAAGTGTGACCACCTGCACACGATTGTTCTTTT

             [2]
             5.7e-06
             ATGAAAAGCAGTGATTCACAG
             + +++ + +++++ + +++++
1951 TGATATACACAGAGATAAGTGTCACACAGACATACCTTATGACCTGGGTA


NM_031249
  ENSMUSG00000050614
  LENGTH = 2000  COMBINED P-VALUE = 1.86e-04  E-VALUE =      6.6
  DIAGRAM: 502_[8]_158_[4]_247_[2]_97_[3]_473_[8]_72_[4]_321


                                                         [8]
                                                         1.2e-05
                                                         AACTTCAAAATGTCTCTTTGA
                                                          ++++ ++  ++  + +++++
451  GGATGTCCTGGAAGTATCCCAAGTGCTAGGATTAAAGATGAGCCGCCATGCCTAATTTATGGTGAATGTTTTATT

           [4]
           1.8e-05
           AGGAGAGAGCTCACACCTCTCCC
            + +++ ++++ +++++ ++ ++
676  CAAATTTGAAGACAGCTTAAACTACATACACAGTGAATTTTTCAGGCCAACCTGGGCTGTAGAAGGGCCCTGTAT

                                                        [2]
                                                        3.6e-06
                                                        ATGAAAAGCAGTGATTCACAG
                                                        + ++ ++++++++ + +++++
901  GTAGGTGGATCTCTTGAGTTCAACGCCAGCCTCATCTACAGACTAAGTTCTAGGGCAGCCAGGGCTACACAGACA

                        [3]
                        2.4e-05
                        AGTGCCCTGGGCCTTTAAGAG
                        + ++   + +++++++ +++
1051 CCAAGTTAAAACAGTGAAAATTATGTTTGGTCATTTAAAATAAAATGGCAGTATTTAAAGTACAAAACTGGCAAG

                                                                    [8]
                                                                    4.2e-05
                                                                    AACTTCAAAATG
                                                                     ++++  ++++
1501 TTTAATGTTGTTAAGCTATTTTAAGGGATAAATAACAATATTTTTACCTCATAATATTGGATATAATTTTAAATA

     
     
     TCTCTTTGA
     +++++ +++
1576 TTTCTATTATCCTACACTAAACGAAAGCTGTGAAAACACATTAAGCCTTAAATCAGCTTCCGGCTTGCGGTTTCC

           [4]
           4.4e-05
           AGGAGAGAGCTCACACCTCTCCC
            ++++ ++ ++ +++ +   +++
1651 CGCCGGTGGAACGCAATGAAAACAGCCCCGAGTGTGTGGAAACACAGACGCTGCCGGTTACCCCATGGAAGCCCG


NM_016704
  ENSMUSG00000022181
  LENGTH = 2000  COMBINED P-VALUE = 1.87e-04  E-VALUE =      6.6
  DIAGRAM: 587_[8]_93_[3]_219_[2]_432_[4]_583


                                                                   [8]
                                                                   8.2e-05
                                                                   AACTTCAAAATGT
                                                                   +++++++ + +++
526  AGATTCTGCTGAAAGAATACCCTGATATAGCTGTCTCTTGTGAGGCTATGCCAGTTCCTGGCAAATTCAGAGTGG

     
     
     CTCTTTGA
      +  +
601  ATGCTCACAGTCGTCTATAGGATGGAACACAGGGTCCCCAATGGAGGAGCTAGAGAAAGCACCCAAGGAGCTGAA

                               [3]
                               1.0e-05
                               AGTGCCCTGGGCCTTTAAGAG
                               ++ ++++++  + + + ++
676  GGGGTCTGCAACCCTATAGGTGAAACAACACTATGAACTAATCAGTACCCCCAGAGCTCGTGTCTCTAGCTGCAT

                                              [2]
                                              3.4e-07
                                              ATGAAAAGCAGTGATTCACAG
                                              + ++++++++ ++ + +++++
901  TTGGAATAGCATTTGAAATGTAAATGAAGAAAATATCTAATAAAAAAGGAAATGGCACACAGGCTGATAGTGTCA

                                                 [4]
                                                 6.9e-05
                                                 AGGAGAGAGCTCACACCTCTCCC
                                                 ++++++++ ++++++    +++
1351 GGATTTTCTTGGCAGAATCACTTGGTTTTGAATCTATTGTCACTAGGAGAGAAAAAAAATGGTTCCTAACTGAAT


NM_146140
  ENSMUSG00000044528
  LENGTH = 2000  COMBINED P-VALUE = 1.88e-04  E-VALUE =      6.7
  DIAGRAM: 443_[2]_103_[3]_254_[8]_99_[3]_23_[8]_386_[4]_98_[4]_443


                                                                         [2]
                                                                         1.3e-05
                                                                         ATGAAAA
                                                                         + + +++
376  AACCCCCATACCAGGCTGGAGGAATCACCCCAGTAAGAGGAGGAAAAAAGGCCCCAGAACTGAACATCAGATGAG

     
     
     GCAGTGATTCACAG
      ++ ++++ +++ +
451  TCAATGACACACCCACTCCCATTGTTAGGAGTCCCACAAAAACCCCAAGCCAAACCACCATAGCAAGTATGGGGA

                                               [3]
                                               9.4e-05
                                               AGTGCCCTGGGCCTTTAAGAG
                                                   +++++ +++++++ +++
526  TGAGGGAATGCAGATCCATGTATTCCCTGTGATTGGCGCTCATTCTCTCTGAGTCCTTAGGAGCCCAGCTTAGTT

                      [8]
                      2.3e-05
                      AACTTCAAAATGTCTCTTTGA
                      ++++++++ +++ +++ + +
826  CCGTATTTTCCTCTGGAAAATTCAAGATGCCTTCTATTGATACAATCTCCAAGCTAAATAAACAAGGTTCTATTT

                                                                   [3]
                                                                   1.3e-05
                                                                   AGTGCCCTGGGCC
                                                                   ++ +++ ++ +++
901  ATACTGCGCTATGCTATGTAGCGAACTGAAGGATGACGATAAATCTCAGCACTCTAACGATAAACGCTTTGTTTC

                                    [8]
                                    4.9e-05
     TTTAAGAG                       AACTTCAAAATGTCTCTTTGA
     +++ +++                        ++++ ++++++ + +  +++
976  TTTTAAAAGGGCCTGTAGCGTTATTCGTCTGAACTGCATACTTTATACTTTCACCCATCATTCCTCTCCGTAAGG

                                                                    [4]
                                                                    9.1e-05
                                                                    AGGAGAGAGCTC
                                                                    +  ++++++++
1351 TTCTGAAACTGCTTCTTTGCATTGGTGTTGCCAGGTCTGACTGATTTAACATAGAGACAGCACAATACAGCGCTG

     
     
     ACACCTCTCCC
     + + + +++ +
1426 AGAATACTCTGGTTCCACTCAGGATTTAAATCGTGGCTACTGATATTTATTAGACCTGTGGTGATAATAATGGCA

                                       [4]
                                       4.4e-06
                                       AGGAGAGAGCTCACACCTCTCCC
                                       ++++++++++++ +     ++++
1501 GGCATGGTGTGTCACAAAGAGGTGGGTGGGGAAAAGGAGAGAGAAACAGAGAGACAGAGGCAAAGACAAAAAACA


NM_026856
  ENSMUSG00000049606
  LENGTH = 2000  COMBINED P-VALUE = 1.93e-04  E-VALUE =      6.8
  DIAGRAM: 397_[3]_368_[8]_269_[2]_170_[4]_199_[2]_457_[2]_12


                           [3]
                           6.5e-05
                           AGTGCCCTGGGCCTTTAAGAG
                           ++++  +++++++++  ++
376  GTTTAGACATAGTACTACCCAGAGTGGGCTGGGCCCTCTAATATTAATCAATAAGACGCCCCCAGACCAATCTGA

                                         [8]
                                         4.9e-07
                                         AACTTCAAAATGTCTCTTTGA
                                         +++ +++ + ++++++ +++
751  TCAACACAAGCCTATACCCAACATTATAAATACTGAAAACTCAGAGTGTTTCCTTTTTGAACCAGGAGCGAGGCA

                               [2]
                               4.0e-05
                               ATGAAAAGCAGTGATTCACAG
                               ++++++++++ +++   ++ +
1051 AAGAGATGGTTCCTAAAAAGTAAATAATGGAAGGAAAGGAGATACGGAGGAAAAGAGGGGAGGAGAGGTGGGGGT

                                                                        [4]
                                                                        2.9e-05
                                                                        AGGAGAGA
                                                                        ++++++ +
1201 TTAATTCTGAACTATGTGGCTATACTAATTCTTCCTGCATTCCTATACATTGATAGCTGTCATGATTAGGAAAAA

     
     
     GCTCACACCTCTCCC
      ++++++  +++ +
1276 AAAAAAAAGTCATAATTAAATCTAAGAGGCTCTAAAAATTCCAAGTCTTCCAACTAGGAATCCTGTCAATTTTTT

                                                                     [2]
                                                                     5.7e-05
                                                                     ATGAAAAGCAG
                                                                     + +++++ +++
1426 GCACACTGGTGTAGTCAGTCTCAGAAGGGCTTGAAATGGAGGATTCTGAGTTCAAAGCCAGCCCAGGGAAATCAG

     
     
     TGATTCACAG
     +++  + + +
1501 TGAGACCCTCCCCAAACAAACAGAGCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCA

                      [2]
                      2.2e-05
                      ATGAAAAGCAGTGATTCACAG
                      + ++ +++++ ++ ++++++
1951 TTTCCCATGAAATAAAAAAAATAACAAATGTTTCACATTAGAGGCACTGT


NM_153572
  ENSMUSG00000041298
  LENGTH = 2000  COMBINED P-VALUE = 1.94e-04  E-VALUE =      6.9
  DIAGRAM: 97_[2]_458_[4]_196_[3]_861_[8]_102_[4]_156_[8]


                           [2]
                           1.4e-05
                           ATGAAAAGCAGTGATTCACAG
                           +++++++++++ + +++ +++
76   ATAAATAAAAGCAAGTTTGTTCATGGAAGGAAGAGTCTCTCAGTCTAATTTTAAAATTAGTCCCATTACAAATGT

                                                        [4]
                                                        9.6e-05
                                                        AGGAGAGAGCTCACACCTCTCCC
                                                         ++ ++ +++ +++++++ ++++
526  AGACCTTGGTAGTGAGCTTCAGGATCAAGCTAACAGCTCAGTGGGGGAGAGGGGTAAACGACAAAACCTGTCAGT

                                                  [3]
                                                  9.7e-06
                                                  AGTGCCCTGGGCCTTTAAGAG
                                                   ++++++ + ++ ++++++++
751  ATTTATAGGTTTTAGTAAGAAAAAGGGGTCAAATATCTTAAGCAACATACTAGGAGTTTTTAAAAGTGCCTCTAA

                                [8]
                                7.2e-05
                                AACTTCAAAATGTCTCTTTGA
                                +++++ ++++  + ++  +++
1651 ACTCTAACAGGAAGTATTAGATTCTAGAGATTTAAAAATTATTCCTGAAGAACTTGTGATCATTCCACTCAAAGT

     [4]
     8.2e-06
     AGGAGAGAGCTCACACCTCTCCC
      + +++++++++ + +++++ ++
1801 TGCACAGAGCTACCCCTTCAGCCCGGGCCACTGGCTCTCTTATTCTGTACACAAGTATGAGGTTTGGTAGCCTGG

                                  [8]
                                  1.7e-05
                                  AACTTCAAAATGTCTCTTTGA
                                  ++++++ + ++ ++++++++
1951 GGCCTTCAAGTGAAGATTCCTCTGATTAAAACTTCCAGATTTTTTTTTTT


NM_024251
  ENSMUSG00000030051
  LENGTH = 2000  COMBINED P-VALUE = 2.14e-04  E-VALUE =      7.6
  DIAGRAM: 73_[2]_64_[4]_508_[8]_658_[4]_609

                                                                              [2
                                                                              2.
                                                                              AT
     
1    TTTCAACATCCTTGAATTTATACTGAGTGGAAGGGTTAAAGGACCCCTTAAAGATTGAGTCAGTGCAGGATGGGA

     ]
     8e-08
     GAAAAGCAGTGATTCACAG
     +++++ ++ ++++++++++
76   AGAAGTCAAGGACTCACAGGTTCACCAACCCCTCCACAATAGAAGGTGTGAGTGTTAATCTTGCTTTGTCACTTG

             [4]
             6.9e-05
             AGGAGAGAGCTCACACCTCTCCC
              ++ +  +++++++++++ + ++
151  ACTGGACCTGGGGTTAGCTAAAACCTGTGCCTCTGGGCAGGGCTGTGAGGGTGTTTCCCTGAAGGACGGACTTGG

                   [8]
                   4.6e-05
                   AACTTCAAAATGTCTCTTTGA
                   + +++ ++ ++++++++ ++
676  CTGATAATAGAGAAATATTTATTCTGTCTTTCTTCAGTTTAAGTAAATTTAACCCTGTGCAATTACATGGAGAGA

                       [4]
                       3.7e-05
                       AGGAGAGAGCTCACACCTCTCCC
                       +   ++++++++ ++++++++++
1351 GAGGCCAGAACCCTATCCACAGCAGAGAACGCACCTCTCAGGTGACCCTCTGAGAAGACAGTGGCTTGAAGCTTC


NM_176831
  ENSMUSG00000009768
  LENGTH = 2000  COMBINED P-VALUE = 2.15e-04  E-VALUE =      7.6
  DIAGRAM: 44_[8]_733_[3]_368_[2]_99_[8]_672

                                                 [8]
                                                 7.9e-07
                                                 AACTTCAAAATGTCTCTTTGA
                                                 ++++++++++++ ++++ +++
1    CTCTATGCAAAAAAACCCTCGCTTGAGAGCTGCAAAATACACTCAGATTCAAACTGCCTCTGTGATTTGTTTCTG

                                                     [3]
                                                     3.9e-05
                                                     AGTGCCCTGGGCCTTTAAGAG
                                                     +++++++  +++++++++++
751  CACTTACGTGCAATGTTGCTCTCTGTTACCTGGTCAACCGTAGCCTGAAATACCAAAGTTCATTAAAACGATCCA

                                                                   [2]
                                                                   2.3e-06
                                                                   ATGAAAAGCAGTG
                                                                   + ++ ++++++++
1126 TCGAGAAGCAGAGACGGGAGGCTCTCCGAGTTCCAAGCTACTCTGGTATAAAGAGGAAGTTCAGGACAGCCAGGG

     
     
     ATTCACAG
     ++ ++ ++
1201 ATACAAAGAGAAACCTTGTCTCGAGACAACAAAACAAAACAACAGAAAGTCTAAGTTCTTGACTTGATACAATTT

                                     [8]
                                     7.7e-05
                                     AACTTCAAAATGTCTCTTTGA
                                     ++++   ++++++ +++ ++
1276 TAAAGTTGTATGTTGAGTTCACACAAGTTTTTAAATATTTACTGTATCTGTTTTGTATGTGTGTACACATGCAGA


NM_172599
  ENSMUSG00000037526
  LENGTH = 2000  COMBINED P-VALUE = 2.22e-04  E-VALUE =      7.9
  DIAGRAM: 1166_[2]_279_[8]_391_[8]_101


                                              [2]
                                              2.4e-06
                                              ATGAAAAGCAGTGATTCACAG
                                              + ++ ++++++++ + +++++
1126 TTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCT

                                              [8]
                                              2.9e-05
                                              AACTTCAAAATGTCTCTTTGA
                                              ++ + +++++ ++ ++ ++++
1426 TCCATATCACCTGGAAGCTACTGCTGCCTGTCGGAGAGATTAGTTACAAAAAGGATTCTTGAGAGCTTGCCGACT

        [8]
        2.7e-07
        AACTTCAAAATGTCTCTTTGA
          +++ +++++++ ++ ++++
1876 ACATTCTTTAAAATGTATCCTTTAATTTCTATGAAGTACTCCAGGTTAGCTTGCACTTTTGCTGCTACCATCAAT


NM_028539
  ENSMUSG00000048409
  LENGTH = 2000  COMBINED P-VALUE = 2.30e-04  E-VALUE =      8.1
  DIAGRAM: 226_[4]_1039_[2]_60_[8]_182_[8]_407


      [4]
      5.2e-06
      AGGAGAGAGCTCACACCTCTCCC
       +++++ + +++ + ++  ++ +
226  GTGGAGAAAACTACAGCTAGTCTCGAGTATGACCAGGGGATGTGTGATTCTCTGACTTTAACATGAATTTGGAAA

                  [2]
                  2.4e-06
                  ATGAAAAGCAGTGATTCACAG
                  + ++ ++++++++ + +++++
1276 CTCTATGAGTTTCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTTGACCCCCCATCTTCCCCCCCAAAAAGG

                        [8]
                        7.9e-05
                        AACTTCAAAATGTCTCTTTGA
                         +  +  +++++++++ ++++
1351 TGAAACTAAAAATTTCATCTGTCTTCAAATGGTTCCTTTAAAACTGCACTCAGGAAACAGGCATCAGGGCATATG

                                                                             [8]
                                                                             7.0
                                                                             AAC
                                                                              ++
1501 CTCTGAAAACAGATAAAGGTGAGTCTGTGTGCTTGGAATGTAGTTCAGTTGGTAGACTGCTTGCCTAGCTTATAA

     
     e-06
     TTCAAAATGTCTCTTTGA
     ++ ++ ++ +++++++++
1576 TTAATCCTAGCTCTTGGAAAGCAGGAGCAGGAGGACCAGAAGTTTGACAGTATCTTCAGCCAGTGGGAGATCTAG


NM_025781
  ENSMUSG00000031953
  LENGTH = 2000  COMBINED P-VALUE = 2.35e-04  E-VALUE =      8.3
  DIAGRAM: 55_[2]_61_[8]_123_[8]_23_[4]_823_[2]_624_[3]_163

                                                            [2]
                                                            9.4e-06
                                                            ATGAAAAGCAGTGATTCACA
                                                            + +  +++++ ++++ ++ +
1    GAGAAAGGAAGACTGCCACAAATTCAAGGCCAGCCTGGGCTTCATGAAGAGATGGAGGCTAGCCAAGGATACATA

                                                                   [8]
                                                                   7.0e-05
     G                                                             AACTTCAAAATGT
     +                                                              ++++ +++ +
76   GCAAGACATTGCATCAAATGAAATCTAAAAACAAACAAACAAATCAAGGTTCCCAACGCAAAGAATTTAAAGTAA

     
     
     CTCTTTGA
     ++++++
151  TTCTTTATTGATAATAAACATTTATACTAGCATTAGAAATGTCAGTAGAAAAATAATATTTAAATAAATCTCTAA

                                                             [8]
                                                             1.0e-05
                                                             AACTTCAAAATGTCTCTTT
                                                             +++ + ++++++ ++++ +
226  TGTACAAAGATTTGATCATTTTGACTATAGCAGTTAAGTGCAATAACCTAATATAAAAAGTTAAACTGATTTTGG

                              [4]
                              2.0e-05
     GA                       AGGAGAGAGCTCACACCTCTCCC
     +                        + ++++++ +++ ++ ++++++
301  TCATAACCAGCCCTACACAGTACACAAGAAAGAAATACAAGTTCACAAAACCTTCTGCGCGTGGACCATTAATGG

                                                   [2]
                                                   4.3e-05
                                                   ATGAAAAGCAGTGATTCACAG
                                                   + ++++++++   ++ +++++
1126 CAGAGAAACCTGTCTCCNNNNNNNNNNNNNNNNNNNNNNNNNNNCCAGAAAAACCACACACACACACCCCCAAAA

                     [3]
                     1.2e-05
                     AGTGCCCTGGGCCTTTAAGAG
                     ++ + + +++ + +++++++
1801 GTGCAAGTGCCCACAGAGAGTCTTGGATATTTAAAAAGAAATTTTATTTATGTGTGACGTGAACAGCATGTAGAG


NM_174924
  ENSG00000169340
  LENGTH = 2000  COMBINED P-VALUE = 2.36e-04  E-VALUE =      8.4
  DIAGRAM: 779_[3]_64_[4]_957_[2]_135


                                  [3]
                                  1.4e-07
                                  AGTGCCCTGGGCCTTTAAGAG
                                  ++ +++++++++ ++++++++
751  AATTAGACAAGGTGATGTTGCAAGTGCTTAAGGCTATGGGTTTTTAAAAGATAGCCTCAGTGATTGCATGGAATA

                                            [4]
                                            4.1e-05
                                            AGGAGAGAGCTCACACCTCTCCC
                                             ++ ++++ ++++ +++  + ++
826  TGGAGGGGTTTGGGATGGGGGCTGGGAGGGAGGCACAGAGGGGCAGCAAAAAGACCAGTTAGGAGACTTCAGCTG

                                                 [2]
                                                 8.3e-06
                                                 ATGAAAAGCAGTGATTCACAG
                                                 +  +++++++ ++++ + +++
1801 TTCTTCTAAGACTGCACCAACCAGGAAAAAGAGGTCATGAGTAAAACAGAGCCAAGGACACTCAGAGGCTTTATT


NM_007003
  ENSG00000101951
  LENGTH = 2000  COMBINED P-VALUE = 2.37e-04  E-VALUE =      8.4
  DIAGRAM: 311_[4]_68_[2]_1483_[4]_71


                [4]
                6.9e-05
                AGGAGAGAGCTCACACCTCTCCC
                ++++++ + ++ ++ +++  +++
301  GCACCAGGTGCAGGAGACCTATGACCCCTAGCACTGCCTTTTATCTGCTGGGTTCCCCTTGGAGAACCATATATC

                                [2]
                                1.9e-05
                                ATGAAAAGCAGTGATTCACAG
                                + ++++++++ + ++ +  ++
376  TTTGGAGCCCCAGAACATGCTGGTTGCACAAGAACAAAGCACACTTACTGTCTGAGAGGAAGGCTGGTGGTGTGG

                                    [4]
                                    1.4e-07
                                    AGGAGAGAGCTCACACCTCTCCC
                                     +++++++ +++ +++ + ++++
1876 GGCACAGAGCCTCTAGGAGGCGGGAGAGGGCTGGAAAGACAACCCACGTGACACACCCCCGAGGTTTGGGATTGG


NM_028604
  ENSMUSG00000019792
  LENGTH = 2000  COMBINED P-VALUE = 2.39e-04  E-VALUE =      8.5
  DIAGRAM: 577_[8]_511_[3]_310_[4]_356_[4]_158


                                                         [8]
                                                         1.1e-06
                                                         AACTTCAAAATGTCTCTTTGA
                                                         +++ ++++++++++++ +++
526  GAGTTTTCTCAAAGCGGAAGAAGTAGAAGTCCTGAGTTACCTCCCAGAGCTGAACCTCAAACTGTTTTATTGCTC

                                                                [3]
                                                                1.8e-06
                                                                AGTGCCCTGGGCCTTT
                                                                +  + + +++++ +++
1051 GCTCTGTAACTTCTGTAGGAAGTAAAGGCTCGTTTTGTAGGTAACAAAGTTTGAGGGCAATCATTTTGGGTTTTT

     
     
     AAGAG
      ++++
1126 GAGAGTGGGTTTCTCTTCAGGTAGCTCTGTCTGTACTGGATATCTCTCTGTAGAGCAGGCTGGCTTCAAAGTCAA

                    [4]
                    9.6e-05
                    AGGAGAGAGCTCACACCTCTCCC
                    +   ++++ ++ +++++++++++
1426 GAACTTACTAATAAAAAATAAGAAAATAAACCTCACAGCTGATGCTCAAAAGATTTCAATTAATAATAATAAAAG

                        [4]
                        8.3e-05
                        AGGAGAGAGCTCACACCTCTCCC
                        ++++++++++++  +  +  + +
1801 AAATCAGGAGCACATGACAAGGAGAGCGCAACTAAATGCCTGACCTCTGCACAGCATTGGTCATTTGTGGCTCCT


NM_013166
  ENSRNOG00000012460
  LENGTH = 2000  COMBINED P-VALUE = 2.40e-04  E-VALUE =      8.5
  DIAGRAM: 605_[8]_749_[2]_604


          [8]
          2.0e-07
          AACTTCAAAATGTCTCTTTGA
            +++ + +++++++++++++
601  TGAGATTCTTAAGAATGTTTCTTGGATCAATCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                              [2]
                              7.0e-06
                              ATGAAAAGCAGTGATTCACAG
                               +++++++++ ++++ +  ++
1351 AAGGTCTCTTGGGTTTTAAAGATAAGTAAAAACAAATGATACTGACAAATTCTGGATTCACAGTGTACAGGCCTC


NM_153399
  ENSMUSG00000040566
  LENGTH = 2000  COMBINED P-VALUE = 2.41e-04  E-VALUE =      8.5
  DIAGRAM: 39_[2]_895_[4]_1022

                                            [2]
                                            1.5e-06
                                            ATGAAAAGCAGTGATTCACAG
                                            + ++++++++ ++++  +  +
1    NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGGGAAAGAAAGGATAGATTCTCTACCTCCCCCTTC

                                                            [4]
                                                            7.6e-07
                                                            AGGAGAGAGCTCACACCTCT
                                                            ++++++++ +++++++++ +
901  CCAGGTGAAAGGGTTTGAGGATATTTGATTCCTTCCAAGCGTGAACCATTGGAGCAGGAAAGCACACACACTTGA

     
     
     CCC
      +
976  GAAGAGTTGTCTATCTGACCCCAGCCCCCCTGTCTCTTCTGGGAATGTGCTCAGGGGAAGGCAGTGCAAGTGCTA


NM_173084
  ENSG00000175447
  LENGTH = 2000  COMBINED P-VALUE = 2.43e-04  E-VALUE =      8.6
  DIAGRAM: 201_[2]_643_[8]_634_[3]_459


                                                        [2]
                                                        1.7e-06
                                                        ATGAAAAGCAGTGATTCACAG
                                                        ++++++++++++ +++++ +
151  CATACATCAACTTTTGCAATCTTCCTGCTGGTAAAAATACAAAACAGCAGCATAAGAACCAGTTACTCATATACT

                                             [8]
                                             2.7e-06
                                             AACTTCAAAATGTCTCTTTGA
                                              ++  ++ +++++++++++++
826  GTTTATGTGCAATCTGTAGGGCCAGGAGCATAGTCTAATCTGACCCAGAATGTCTTTTTGATTTGATATAGGTAA

                         [3]
                         3.2e-05
                         AGTGCCCTGGGCCTTTAAGAG
                         +  + ++++ ++ + +++++
1501 TTGCAGACCAAGTTACCAACATGATTCTGTTCTAATAAGAATGAGTTTTTAATCCAAGAACTGATTTGACTGACG


NM_009412
  ENSMUSG00000027506
  LENGTH = 2000  COMBINED P-VALUE = 2.44e-04  E-VALUE =      8.6
  DIAGRAM: 125_[8]_526_[2]_87_[2]_483_[8]_83_[4]_70_[8]_498


                                                       [8]
                                                       9.7e-05
                                                       AACTTCAAAATGTCTCTTTGA
                                                       +++++ ++ ++ ++++ ++++
76   TTCTCCTTCTCTCCACTTAATCATTTTCCTCATATGAAATCTCTATACAAAACTTGAAGATTTCTTATTTAAAAA

                                                                             [2]
                                                                             9.8
                                                                             ATG
                                                                             + +
601  CTCTGAAAAAGGCTTTAGGTCACTCCAAGCTTGGCAGTTAACATTTGGCATGGACACTGGTAAAACCACAATAGA

     
     e-07
     AAAAGCAGTGATTCACAG
     +++++++++ ++  + ++
676  GAAAGAAGTAACAGATACAACCTCATAGGCCATAAACATACACAGCAAAGGAAGCAGGAGTGAGTCAGGAGTGAC

                                   [2]
                                   1.3e-05
                                   ATGAAAAGCAGTGATTCACAG
                                    ++++++++  ++++++++++
751  CACAGTTAACAGAGGGGCTTAGCAGAGCCACTGGGAAGCTTTGACTCACAGCCCCGACAGTTCTTAGAGTGGGAA

              [8]
              5.6e-05
              AACTTCAAAATGTCTCTTTGA
              +++++ ++  +   +++++++
1276 ATTTACCTGAAATTAAATTTTAATCTTGTAAAAAAATGTGTGAGAATGGTATAATAAATAACTGATAAGCATATT

                                           [4]
                                           1.4e-05
                                           AGGAGAGAGCTCACACCTCTCCC
                                           +++ +++++++  + ++ +++ +
1351 TGAGCTCAAATAGATGTAGCTACAAATGACAGTTACCAAGGCAAGAGCAGGACCCACACTCTCCCCACTGGAAGT

                                                             [8]
                                                             1.2e-05
                                                             AACTTCAAAATGTCTCTTT
                                                              ++++ +  +++++ + ++
1426 TTGAGTGTCTGCATGTTTTTAATTTACAGAACTATAGAACTGCATACACACCTGTCTACTTTAGTCTGGTGTCTT

     
     
     GA
     ++
1501 TAGAAACCCAAGATATGGTCCTCACAGAACTGTTTATCCGAGAAAAAAAATGTAGCTGGTAGTTTCTCCTTTGAA


NM_005565
  ENSG00000043462
  LENGTH = 2000  COMBINED P-VALUE = 2.62e-04  E-VALUE =      9.3
  DIAGRAM: 878_[8]_563_[2]_409_[8]_87


                                                          [8]
                                                          7.2e-05
                                                          AACTTCAAAATGTCTCTTTGA
                                                          +++ + ++++++   +++++
826  CAGTCATAGCCATGGAACAGAACATCTTAATCCTGATGGCACTTTCCACTAATAGACTTAAAATGAGCTTTGGTT

                                          [2]
                                          3.9e-05
                                          ATGAAAAGCAGTGATTCACAG
                                            ++++++++ +++++  +++
1426 TTGTGCAATAACAACCAAGGTCCCAAAGGGAAAAACTTGAAGAACAACTGATTGTCACTATTTGGCTGAATACCA

                      [8]
                      1.1e-08
                      AACTTCAAAATGTCTCTTTGA
                      +++++ ++++++++++ +++
1876 ACCAAAGTCTCATCCCTAAATTTAAAATGTTTTCTTTTGGTATTTGTAGTTTAAATTTTCTTTAAGACAAAAATA


NM_145514
  ENSMUSG00000038733
  LENGTH = 2000  COMBINED P-VALUE = 2.67e-04  E-VALUE =      9.4
  DIAGRAM: 314_[3]_436_[8]_635_[8]_521_[8]_10


                   [3]
                   1.9e-05
                   AGTGCCCTGGGCCTTTAAGAG
                   ++ +  ++++++ ++ ++++
301  TTCTCTGATTTTCTAAAGTGATGGTCTCTGAAAAATGAAGCTTAAAGGAATCTTTTCCATTACCCATTTGAATTA

                          [8]
                          8.6e-05
                          AACTTCAAAATGTCTCTTTGA
                          ++++   ++ +  +++++++
751  ATGTTAGATATAGGGTCTTCAAAATGACAAGTCACTTTTTTTCCATAAAGGAAACATTCCCGTAAACTAAAAGGG

       [8]
       2.1e-05
       AACTTCAAAATGTCTCTTTGA
        +++++ ++++ + +++++ +
1426 AATACTTCTTAATTTATTTTTAAAAAATTGTGCTGTTAACCCTTTTACGGGGCAACAACTATGTGAAAAGTACAA

                        [8]
                        5.6e-08
                        AACTTCAAAATGTCTCTTTGA
                         +++++++++++++++++++
1951 AAATGTTTGGCCCCAATCGGGCTTCAAAATGGTTCTTTTTTTTTTTTTTT


NM_000319
  ENSG00000139197
  LENGTH = 2000  COMBINED P-VALUE = 2.68e-04  E-VALUE =      9.5
  DIAGRAM: 118_[2]_227_[3]_160_[8]_1250_[4]_159


                                                [2]
                                                2.2e-05
                                                ATGAAAAGCAGTGATTCACAG
                                                + +++ ++++ ++ + +++++
76   GGGTGTAGAAGTGGGGCCTCTGAAAGAGGGCGAAAAGGCAAGGAAAAGGAGAAATGTTGCACAGTCTTATGGTCT

                                                                       [3]
                                                                       3.9e-05
                                                                       AGTGCCCTG
                                                                       + ++++++
301  CCTGCTGCCTGCCTGCCTCCGCTCATGCACCCTGGGCTGGGATGGTACTTCTGTTCGTCTGGCATTATTGCCCTT

     
     
     GGCCTTTAAGAG
     +++++++ +  +
376  GGTCATTTACCGGCAGCCCTGGGCCCCTCCTTGCTCTTCTCCATGACACTAGGACTCCCTTGGTCTTGAAGCTGG

                           [8]
                           1.0e-05
                           AACTTCAAAATGTCTCTTTGA
                            ++++ +++   +++++++++
526  CTTGAGGCTTAGTCTTATTCCGTGATTAAAAGCATTTCTTGTATGTTTGTCCTTTCCCAGCCTGGAGTGATGGGA

                       [4]
                       3.2e-06
                       AGGAGAGAGCTCACACCTCTCCC
                       +++++++++ ++  +++++ + +
1801 GCCTTTGAGGGGGGCGGCAGGAGAGAGTACCGACCTCCCTCGAACTCCTGGCAGAGGTGGGGGTCGCAGCAAAAG


NM_139063
  ENSMUSG00000038982
  LENGTH = 2000  COMBINED P-VALUE = 2.71e-04  E-VALUE =      9.6
  DIAGRAM: 622_[4]_876_[4]_203_[2]_232


                           [4]
                           2.6e-08
                           AGGAGAGAGCTCACACCTCTCCC
                           ++++++++ ++ ++ +  +++++
601  GTCCCCAGAGTCCACATGGCAGAGGAGAGAACTGACTCGACTCCCACAAATTATCCTCTGATCTCCACACGTGTG

                          [4]
                          1.9e-06
                          AGGAGAGAGCTCACACCTCTCCC
                           +++++++  + +++++++  ++
1501 ACAAAACTGAGGACATTAACATGGAAAGCTTAGAAACTTCGTCCTGGTCCACACCCTTAGAAAGGCGTATGCTGT

                           [2]
                           3.8e-05
                           ATGAAAAGCAGTGATTCACAG
                           + +++ +++ +++++ ++ ++
1726 AGTGGTCACTAACGACATTCCAAAAAGTGCCTGTGATACAAAGGGGATTTTCACTTGCGGCTCCCTCCCCTCCCT


NM_009980
  ENSMUSG00000030970
  LENGTH = 2000  COMBINED P-VALUE = 2.78e-04  E-VALUE =      9.8
  DIAGRAM: 437_[3]_1109_[8]_62_[2]_308_[8]


                                                                   [3]
                                                                   9.4e-05
                                                                   AGTGCCCTGGGCC
                                                                    ++  + +++ +
376  CTGACCACACATAATTTGATAGGTACCCATTCTTCCCTGTGGGAAAGAATTAAAGAAGGCTCCATTTCTTGGACT

     
     
     TTTAAGAG
     +++++++
451  CTTAAGATAGGAATGGGGCTTTCATTAGTTTCTCTAGCAGACTGCTGGCTGTGAAATGGCCAACCCCTTTGGGAA

                                                                        [8]
                                                                        4.2e-05
                                                                        AACTTCAA
                                                                         + ++ ++
1501 AAATACAGTAACGATAACTCACACTAAAACAAAACATTTCTGATAGCCATTATTTTTCTGTTTGGGACAGTTTAA

     
     
     AATGTCTCTTTGA
     + + ++++++++
1576 AGTTTTTTTTTTCTTTTGTGTCACAAAAACAGGAATGTACCTATACAAAGGCTCAAAATAGGCCATCTTTAAAAA

     [2]
     1.6e-06
     ATGAAAAGCAGTGATTCACAG
       ++++++++ +++++++++
1651 CAAAAAGGCAATGATTCACAAAAGACTATGAATAGAACATGTAACTAGCTGATACAAATCTAATAGGATTTGTTA

                                  [8]
                                  4.9e-07
                                  AACTTCAAAATGTCTCTTTGA
                                  +++++ +++++ ++++ +++
1951 AAATAGATTTGAGTACAAACAGCTTGTGAAACTTAATACTTTTTTCTTTT

********************************************************************************


CPU: crick
Time 67.670000 secs.

mast acro1.set.fasta.conserved.25.meme -m 2 -m 3 -m 4 -m 8 -text -brief -remcorr -norc -stdout -d /home/sao/applications/mask_db/upstream.masked -bfile /home/sao/proj_motif/model.bckg
BioPerl-1.007002/t/data/masta.dat000555000766000024       373313155576321 16500 0ustar00cjfieldsstaff000000000000>m1seq                     pos 1311
CAGAAAAATTGAATTCCCACCCCCC
CAGAAAAATTGAATTCCCACCCCCC
CCTTAAAATAAAATCCCCACCACCA
CAGACAAAGACATTCCACAGCTCCC
CAGAAAAATTGAATTCCCACCCCCC
CAGAAAAATTGAATTCCCACCCCCC
CCTTAAAATAAAATCCCCACCACCA
CAGACAAAGACATTCCACAGCTCCC
>m1logs
  -865    208   -865   -865 
   156      8   -865   -865 
  -865   -865    157     -4 
   156   -865   -865     -4 
   156      8   -865   -865 
   197   -865   -865   -865 
   197   -865   -865   -865 
   197   -865   -865   -865 
  -865   -865     -1    154 
    97   -865   -865     96 
    -3      8     99   -865 
   197   -865   -865   -865 
   156   -865   -865     -4 
  -865   -865   -865    196 
  -865    108   -865     96 
  -865    208   -865   -865 
    -3    166   -865   -865 
  -865    208   -865   -865 
   197   -865   -865   -865 
  -865    166     -1   -865 
  -865    208   -865   -865 
    -3    108   -865     -4 
  -865    208   -865   -865 
  -865    208   -865   -865 
    -3    166   -865   -865 
>m1freq
 0.000635  0.998096  0.000629  0.000640 
 0.748765  0.249966  0.000629  0.000640 
 0.000635  0.000589  0.748759  0.250017 
 0.748765  0.000589  0.000629  0.250017 
 0.748765  0.249966  0.000629  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.000635  0.000589  0.250006  0.748770 
 0.499388  0.000589  0.000629  0.499393 
 0.250012  0.249966  0.499382  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.748765  0.000589  0.000629  0.250017 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.499343  0.000629  0.499393 
 0.000635  0.998096  0.000629  0.000640 
 0.250012  0.748719  0.000629  0.000640 
 0.000635  0.998096  0.000629  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.000635  0.748719  0.250006  0.000640 
 0.000635  0.998096  0.000629  0.000640 
 0.250012  0.499343  0.000629  0.250017 
 0.000635  0.998096  0.000629  0.000640 
 0.000635  0.998096  0.000629  0.000640 
 0.250012  0.748719  0.000629  0.000640 

BioPerl-1.007002/t/data/match.output000555000766000024    360751613155576321 17353 0ustar00cjfieldsstaff000000000000Search for sites by WeightMatrix library: ../../cgi-bin/data/matrix.dat
Sequence file: default.seq.EXAMPLE
Site selection profile: minSUM_good104.prf prf to minimize sum of both errors, high qual.


Inspecting sequence ID   RNTATFL

 V$MYOD_01              |     4338 (+) |  1.000 |  0.945 | atcCAGGTggtg
 V$MYOD_01              |     7390 (+) |  1.000 |  0.932 | gtcCAGGTggta
 V$MYOD_01              |     8503 (+) |  1.000 |  0.941 | ggaCAGGTgcgg
 V$MYOD_01              |     8767 (-) |  1.000 |  0.937 | cagcACCTGgga
 V$E47_01               |       33 (-) |  0.693 |  0.779 | gtgaacAACTTcaga
 V$E47_01               |       40 (+) |  0.934 |  0.858 | acttCAGATgtcatt
 V$E47_01               |      122 (-) |  0.924 |  0.753 | ctggctAACTGctca
 V$E47_01               |      143 (-) |  0.703 |  0.776 | ccagacATTTGctca
 V$E47_01               |      670 (+) |  0.712 |  0.753 | actgTAGCTgctctt
 V$E47_01               |      715 (+) |  0.934 |  0.829 | tttaCAGATggttgt
 V$E47_01               |     1025 (+) |  0.924 |  0.854 | ttggCAGTTgaatca
 V$E47_01               |     1124 (+) |  0.769 |  0.812 | tatgCACGTgtgttc
 V$E47_01               |     1174 (+) |  0.703 |  0.765 | aaagGAGATgggcac
 V$E47_01               |     1355 (-) |  1.000 |  0.860 | tgggtcACCTGatgc
 V$E47_01               |     1390 (+) |  1.000 |  0.930 | agggCAGGTgaggag
 V$E47_01               |     1482 (+) |  0.703 |  0.750 | ctggCAGAGggaggg
 V$E47_01               |     1678 (+) |  0.769 |  0.753 | ccttCGGGTgtcagc
 V$E47_01               |     1707 (-) |  0.703 |  0.760 | agcaccCTCTGcctt
 V$E47_01               |     1783 (-) |  1.000 |  0.927 | tggagcACCTGccat
 V$E47_01               |     1857 (-) |  0.924 |  0.823 | agagccAACTGaaga
 V$E47_01               |     1968 (+) |  1.000 |  0.807 | tgagCAGGTtggcct
 V$E47_01               |     2005 (-) |  0.703 |  0.773 | ctatacATCTCctga
 V$E47_01               |     2423 (+) |  0.769 |  0.753 | atcaCAGGGgttggg
 V$E47_01               |     2544 (+) |  1.000 |  0.755 | ataaCAGGTttctgt
 V$E47_01               |     2580 (-) |  0.693 |  0.780 | tacaacAAATGcagt
 V$E47_01               |     2642 (-) |  1.000 |  0.761 | cccctgACCTGcgta
 V$E47_01               |     2771 (+) |  0.769 |  0.768 | tccgCATGTgagatt
 V$E47_01               |     2824 (+) |  0.924 |  0.842 | tgtcCAGTTgtctgc
 V$E47_01               |     2834 (+) |  0.703 |  0.755 | tctgCAAATggcatc
 V$E47_01               |     2968 (+) |  0.934 |  0.898 | acggCAGATgcgcag
 V$E47_01               |     3007 (+) |  0.769 |  0.820 | tgcgCAGGCgtctcg
 V$E47_01               |     3049 (-) |  1.000 |  0.819 | ggacatACCTGcgag
 V$E47_01               |     3295 (-) |  0.703 |  0.787 | gtgaacATCTCcatg
 V$E47_01               |     3555 (+) |  0.712 |  0.768 | ttagTAGCTgtgtgg
 V$E47_01               |     3607 (+) |  0.924 |  0.766 | tctgCAGTTttcaaa
 V$E47_01               |     3899 (+) |  1.000 |  0.748 | atcaCAGGTattaat
 V$E47_01               |     4041 (+) |  0.769 |  0.806 | ccagCAGGGggaaat
 V$E47_01               |     4116 (+) |  0.934 |  0.825 | ttccCAGATgttaaa
 V$E47_01               |     4184 (+) |  0.703 |  0.756 | tgagCAGAAggctgc
 V$E47_01               |     4337 (+) |  1.000 |  0.871 | catcCAGGTggtgga
 V$E47_01               |     4350 (+) |  0.769 |  0.797 | gaggCAGGAggatca
 V$E47_01               |     4525 (-) |  0.693 |  0.770 | gacaacAAATGcgtc
 V$E47_01               |     4563 (-) |  0.712 |  0.799 | ggacacAGTTGcggt
 V$E47_01               |     4564 (+) |  0.924 |  0.807 | gacaCAGTTgcggtt
 V$E47_01               |     4589 (-) |  0.769 |  0.807 | tcctccTCCTGcccg
 V$E47_01               |     4645 (-) |  0.769 |  0.781 | cccggcACCTTctct
 V$E47_01               |     4736 (+) |  0.703 |  0.761 | ctcgCTGATggtcct
 V$E47_01               |     4763 (-) |  0.712 |  0.757 | ggtcccAGCAGcgag
 V$E47_01               |     4809 (+) |  0.693 |  0.767 | ctggCATTTgttacc
 V$E47_01               |     4902 (-) |  0.693 |  0.756 | ttggccAAGTGcatg
 V$E47_01               |     4956 (+) |  0.712 |  0.760 | tctgCAGCAggaagt
 V$E47_01               |     4979 (-) |  1.000 |  0.748 | gcccctACCTGtccg
 V$E47_01               |     5056 (+) |  1.000 |  0.787 | taagCAGGTagtgag
 V$E47_01               |     5125 (+) |  0.934 |  0.844 | gaaaCAGATggtgcg
 V$E47_01               |     5286 (+) |  0.934 |  0.838 | ggctCAGATgggcta
 V$E47_01               |     5493 (-) |  0.703 |  0.758 | ccttccCTCTGctcc
 V$E47_01               |     5871 (-) |  0.703 |  0.773 | tggaccATCTCctgc
 V$E47_01               |     5874 (-) |  0.769 |  0.784 | accatcTCCTGctgg
 V$E47_01               |     6033 (-) |  0.934 |  0.839 | ggacccATCTGgtgc
 V$E47_01               |     6061 (-) |  0.769 |  0.779 | ccctgcACGTGctgc
 V$E47_01               |     6062 (+) |  0.769 |  0.785 | cctgCACGTgctgcc
 V$E47_01               |     6152 (-) |  0.769 |  0.778 | tggctcTCCTGcctc
 V$E47_01               |     6259 (-) |  0.934 |  0.907 | tgtcccATCTGccga
 V$E47_01               |     6494 (+) |  0.934 |  0.877 | attgCAGATgcggcc
 V$E47_01               |     6656 (+) |  0.934 |  0.813 | caaaCAGATgaagat
 V$E47_01               |     6779 (+) |  0.934 |  0.784 | acagCAGATctaatg
 V$E47_01               |     6842 (-) |  0.924 |  0.821 | actgccAACTGgtga
 V$E47_01               |     6985 (+) |  0.769 |  0.750 | ttagCTGGTgaggag
 V$E47_01               |     7006 (+) |  0.769 |  0.802 | aaggCAGGCggatgt
 V$E47_01               |     7010 (+) |  0.703 |  0.783 | caggCGGATgtttcc
 V$E47_01               |     7025 (-) |  0.943 |  0.803 | tgcatcAGCTGaaga
 V$E47_01               |     7026 (+) |  0.943 |  0.808 | gcatCAGCTgaagag
 V$E47_01               |     7112 (+) |  0.769 |  0.774 | accaCATGTgtgcaa
 V$E47_01               |     7160 (+) |  0.712 |  0.774 | cctgGAGCTggcgtt
 V$E47_01               |     7172 (+) |  0.934 |  0.912 | gttgCAGATggtccc
 V$E47_01               |     7389 (+) |  1.000 |  0.864 | tgtcCAGGTggtaga
 V$E47_01               |     7509 (+) |  0.934 |  0.826 | gtgtCAGATggcctg
 V$E47_01               |     7531 (+) |  0.924 |  0.831 | gttaCAGTTggttgt
 V$E47_01               |     7545 (-) |  0.924 |  0.828 | tgagccAACTGtgta
 V$E47_01               |     7587 (-) |  0.693 |  0.780 | tcaaacAAATGctct
 V$E47_01               |     7617 (-) |  0.712 |  0.759 | ctctccAGCCGcctg
 V$E47_01               |     7677 (-) |  0.943 |  0.856 | gctcacAGCTGtaaa
 V$E47_01               |     7678 (+) |  0.943 |  0.860 | ctcaCAGCTgtaaag
 V$E47_01               |     7710 (+) |  0.703 |  0.753 | gaggCAGAAggatca
 V$E47_01               |     7722 (+) |  0.924 |  0.753 | tcagCAGTTtgggcc
 V$E47_01               |     7810 (-) |  0.693 |  0.754 | aacgacAACTCcaaa
 V$E47_01               |     8166 (+) |  1.000 |  0.801 | gaggCAGGTagcacc
 V$E47_01               |     8238 (+) |  0.934 |  0.798 | caccCAGATgaaggt
 V$E47_01               |     8244 (+) |  0.769 |  0.820 | gatgAAGGTgtgttc
 V$E47_01               |     8274 (-) |  0.943 |  0.893 | tgatgcAGCTGccct
 V$E47_01               |     8275 (+) |  0.943 |  0.892 | gatgCAGCTgccctg
 V$E47_01               |     8301 (-) |  0.703 |  0.772 | atgcccCTCTGccct
 V$E47_01               |     8345 (-) |  0.769 |  0.791 | tggaccACTTGccaa
 V$E47_01               |     8355 (-) |  0.769 |  0.757 | gccaacCCCTGtgca
 V$E47_01               |     8367 (-) |  0.712 |  0.775 | gcagccTGCTGctct
 V$E47_01               |     8387 (-) |  1.000 |  0.752 | ctgtatACCTGaagc
 V$E47_01               |     8418 (-) |  0.943 |  0.830 | gtaagcAGCTGttct
 V$E47_01               |     8419 (+) |  0.943 |  0.933 | taagCAGCTgttcta
 V$E47_01               |     8501 (-) |  0.712 |  0.807 | agggacAGGTGcggg
 V$E47_01               |     8502 (+) |  1.000 |  0.865 | gggaCAGGTgcggga
 V$E47_01               |     8518 (-) |  0.712 |  0.782 | actcacAGATGcttc
 V$E47_01               |     8519 (+) |  0.934 |  0.809 | ctcaCAGATgcttca
 V$E47_01               |     8749 (-) |  0.769 |  0.748 | gcccacACCTTgtcc
 V$E47_01               |     8765 (-) |  1.000 |  0.836 | cccagcACCTGggag
 V$E47_01               |     8766 (+) |  0.712 |  0.773 | ccagCACCTgggagg
 V$E47_01               |     8788 (+) |  0.703 |  0.775 | aaagAAGATgtagag
 V$E47_01               |     8806 (-) |  0.712 |  0.787 | ggggccAGCTTctgg
 V$E47_01               |     8967 (+) |  1.000 |  0.889 | gaacCAGGTgtggtg
 V$E47_01               |     8982 (-) |  0.769 |  0.751 | gtacacACCTTtaat
 V$E47_01               |     8998 (+) |  0.703 |  0.769 | ccagCACATggaggc
 V$E47_01               |     9008 (+) |  0.769 |  0.771 | gaggCAGGGgcaggc
 V$E47_01               |     9018 (+) |  0.934 |  0.782 | caggCAGATctttgt
 V$E47_01               |     9245 (-) |  0.943 |  0.788 | taggagAGCTGctca
 V$E47_01               |     9338 (-) |  0.769 |  0.761 | gaggacCCCTGaagt
 V$E47_01               |     9598 (+) |  0.693 |  0.757 | ccagCATTTgggaag
 V$E47_01               |    10617 (+) |  0.693 |  0.765 | gaggGAGTTgtagaa
 V$E47_01               |    10692 (-) |  0.769 |  0.762 | ggcaacACCCGtgtt
 V$E47_01               |    10886 (-) |  0.769 |  0.763 | cactgcACATGcgca
 V$E47_01               |    11001 (-) |  1.000 |  0.779 | cagattACCTGcttt
 V$E47_01               |    11072 (-) |  0.943 |  0.768 | gttacaAGCTGctct
 V$E47_01               |    11544 (+) |  0.703 |  0.749 | atggTAGATgggtat
 V$E47_01               |    11707 (-) |  0.924 |  0.910 | caccccAACTGccct
 V$E47_01               |    11805 (+) |  0.769 |  0.792 | ttggAAGGTggccca
 V$E47_01               |    11958 (-) |  1.000 |  0.848 | gactgcACCTGagct
 V$E47_01               |    11959 (+) |  0.712 |  0.754 | actgCACCTgagctc
 V$VMYB_01              |       36 (+) |  0.790 |  0.786 | aacAACTTca
 V$VMYB_01              |       69 (-) |  0.904 |  0.888 | taCTGTTgtt
 V$VMYB_01              |      125 (+) |  0.938 |  0.893 | gctAACTGct
 V$VMYB_01              |      161 (-) |  1.000 |  0.916 | ctCCGTTccc
 V$VMYB_01              |      452 (-) |  0.904 |  0.856 | gtCTGTTttg
 V$VMYB_01              |      570 (+) |  0.852 |  0.792 | ataAACGTct
 V$VMYB_01              |      580 (-) |  0.904 |  0.838 | acCTGTTgaa
 V$VMYB_01              |      589 (+) |  0.904 |  0.878 | attAACAGac
 V$VMYB_01              |      790 (+) |  0.910 |  0.865 | cttAACCGct
 V$VMYB_01              |      858 (-) |  0.852 |  0.798 | gaTCGTTgcc
 V$VMYB_01              |      984 (-) |  0.938 |  0.899 | caCAGTTaat
 V$VMYB_01              |     1027 (-) |  0.938 |  0.869 | ggCAGTTgaa
 V$VMYB_01              |     1057 (+) |  0.790 |  0.785 | aacAACTTta
 V$VMYB_01              |     1140 (+) |  0.910 |  0.854 | taaAACCGtt
 V$VMYB_01              |     1143 (-) |  1.000 |  0.966 | aaCCGTTact
 V$VMYB_01              |     1461 (-) |  0.852 |  0.798 | ggACGTTtct
 V$VMYB_01              |     1526 (-) |  0.904 |  0.865 | agCTGTTttt
 V$VMYB_01              |     1860 (+) |  0.938 |  0.887 | gccAACTGaa
 V$VMYB_01              |     2375 (-) |  0.938 |  0.877 | caCAGTTttc
 V$VMYB_01              |     2543 (+) |  0.904 |  0.898 | aatAACAGgt
 V$VMYB_01              |     2553 (-) |  0.904 |  0.880 | ttCTGTTgtg
 V$VMYB_01              |     2679 (-) |  1.000 |  0.930 | acCCGTTgca
 V$VMYB_01              |     2826 (-) |  0.938 |  0.905 | tcCAGTTgtc
 V$VMYB_01              |     2865 (+) |  0.904 |  0.837 | ctgAACAGaa
 V$VMYB_01              |     3345 (-) |  0.904 |  0.845 | tcCTGTTcat
 V$VMYB_01              |     3400 (-) |  0.938 |  0.923 | tcCAGTTata
 V$VMYB_01              |     3443 (+) |  0.904 |  0.866 | ggtAACAGtt
 V$VMYB_01              |     3446 (-) |  0.938 |  0.903 | aaCAGTTaat
 V$VMYB_01              |     3510 (-) |  0.904 |  0.870 | tgCTGTTaga
 V$VMYB_01              |     3546 (-) |  0.904 |  0.876 | ttCTGTTctt
 V$VMYB_01              |     3576 (-) |  0.790 |  0.795 | gcAAGTTatt
 V$VMYB_01              |     3609 (-) |  0.938 |  0.891 | tgCAGTTttc
 V$VMYB_01              |     3621 (-) |  0.852 |  0.797 | atGCGTTtat
 V$VMYB_01              |     3815 (-) |  0.852 |  0.799 | caTCGTTttc
 V$VMYB_01              |     3999 (+) |  0.852 |  0.841 | aacAACGAta
 V$VMYB_01              |     4214 (-) |  0.938 |  0.890 | ctCAGTTaaa
 V$VMYB_01              |     4319 (+) |  0.938 |  0.875 | taaAACTGgg
 V$VMYB_01              |     4371 (-) |  0.790 |  0.791 | taAAGTTatc
 V$VMYB_01              |     4537 (+) |  0.904 |  0.840 | gtcAACAGcc
 V$VMYB_01              |     4566 (-) |  0.938 |  0.872 | caCAGTTgcg
 V$VMYB_01              |     4572 (-) |  0.910 |  0.875 | tgCGGTTaga
 V$VMYB_01              |     4942 (+) |  0.938 |  0.848 | ctgAACTGgg
 V$VMYB_01              |     5096 (-) |  0.762 |  0.785 | ttGGGTTatt
 V$VMYB_01              |     5124 (+) |  0.904 |  0.837 | ggaAACAGat
 V$VMYB_01              |     5149 (-) |  0.938 |  0.856 | ggCAGTTtac
 V$VMYB_01              |     5279 (+) |  0.904 |  0.878 | aacAACAGgc
 V$VMYB_01              |     5322 (-) |  0.910 |  0.833 | atCGGTTcag
 V$VMYB_01              |     5727 (+) |  0.938 |  0.865 | ctaAACTGga
 V$VMYB_01              |     6107 (-) |  0.904 |  0.849 | tcCTGTTgac
 V$VMYB_01              |     6386 (+) |  0.938 |  0.868 | acgAACTGgc
 V$VMYB_01              |     6403 (+) |  0.852 |  0.800 | cagAACGCtc
 V$VMYB_01              |     6541 (+) |  1.000 |  0.928 | acaAACGGct
 V$VMYB_01              |     6571 (-) |  0.938 |  0.911 | caCAGTTatg
 V$VMYB_01              |     6655 (+) |  0.904 |  0.833 | gcaAACAGat
 V$VMYB_01              |     6775 (+) |  0.904 |  0.861 | caaAACAGca
 V$VMYB_01              |     6845 (+) |  0.938 |  0.872 | gccAACTGgt
 V$VMYB_01              |     6976 (+) |  0.852 |  0.796 | aggAACGAct
 V$VMYB_01              |     7168 (-) |  0.852 |  0.807 | tgGCGTTgca
 V$VMYB_01              |     7185 (+) |  1.000 |  0.911 | ccgAACGGcc
 V$VMYB_01              |     7491 (-) |  0.904 |  0.867 | gtCTGTTctt
 V$VMYB_01              |     7521 (+) |  0.938 |  0.868 | ctgAACTGaa
 V$VMYB_01              |     7533 (-) |  0.938 |  0.895 | taCAGTTggt
 V$VMYB_01              |     7548 (+) |  0.938 |  0.868 | gccAACTGtg
 V$VMYB_01              |     7600 (+) |  0.938 |  0.853 | ctgAACTGct
 V$VMYB_01              |     7724 (-) |  0.938 |  0.858 | agCAGTTtgg
 V$VMYB_01              |     7807 (+) |  0.852 |  0.841 | aacAACGAca
 V$VMYB_01              |     7930 (-) |  0.852 |  0.799 | atTCGTTtgt
 V$VMYB_01              |     7966 (-) |  0.790 |  0.785 | taTAGTTgtt
 V$VMYB_01              |     8003 (-) |  0.904 |  0.855 | gcCTGTTggt
 V$VMYB_01              |     8197 (-) |  0.904 |  0.831 | gcCTGTTtcc
 V$VMYB_01              |     8215 (-) |  0.938 |  0.880 | ctCAGTTctg
 V$VMYB_01              |     8424 (-) |  0.904 |  0.847 | agCTGTTcta
 V$VMYB_01              |     8673 (-) |  0.910 |  0.866 | acCGGTTagg
 V$VMYB_01              |     8723 (+) |  0.938 |  0.901 | aagAACTGta
 V$VMYB_01              |     8729 (+) |  0.852 |  0.813 | tgtAACGTcg
 V$VMYB_01              |     8840 (+) |  0.904 |  0.866 | caaAACAGaa
 V$VMYB_01              |     8845 (+) |  1.000 |  0.934 | cagAACGGtt
 V$VMYB_01              |     8848 (-) |  0.910 |  0.828 | aaCGGTTtaa
 V$VMYB_01              |     8890 (+) |  0.852 |  0.784 | tcaAACGTac
 V$VMYB_01              |     8901 (+) |  0.904 |  0.846 | acaAACAGat
 V$VMYB_01              |     9117 (+) |  0.910 |  0.865 | aaaAACCGgg
 V$VMYB_01              |     9133 (-) |  0.938 |  0.910 | ttCAGTTttt
 V$VMYB_01              |     9175 (+) |  0.852 |  0.799 | atgAACGCca
 V$VMYB_01              |     9316 (-) |  0.852 |  0.795 | agGCGTTggg
 V$VMYB_01              |     9431 (+) |  0.904 |  0.908 | aatAACAGga
 V$VMYB_01              |     9562 (-) |  0.910 |  0.856 | gtCGGTTtct
 V$VMYB_01              |     9763 (+) |  0.904 |  0.850 | gaaAACAGtc
 V$VMYB_01              |     9814 (+) |  0.790 |  0.786 | agtAACTTca
 V$VMYB_01              |    10056 (+) |  0.938 |  0.907 | aagAACTGaa
 V$VMYB_01              |    10061 (+) |  0.910 |  0.823 | ctgAACCGgg
 V$VMYB_01              |    10159 (-) |  0.852 |  0.814 | tgTCGTTttc
 V$VMYB_01              |    10195 (-) |  0.938 |  0.884 | gtCAGTTctg
 V$VMYB_01              |    10308 (+) |  0.938 |  0.888 | tttAACTGtt
 V$VMYB_01              |    10311 (-) |  0.904 |  0.864 | aaCTGTTttt
 V$VMYB_01              |    10399 (+) |  0.852 |  0.784 | atgAACGAgg
 V$VMYB_01              |    10441 (+) |  0.852 |  0.798 | tgcAACGTct
 V$VMYB_01              |    10663 (+) |  0.904 |  0.849 | gtcAACAGga
 V$VMYB_01              |    10965 (-) |  0.904 |  0.840 | gcCTGTTgga
 V$VMYB_01              |    11037 (-) |  0.904 |  0.874 | caCTGTTgtt
 V$VMYB_01              |    11056 (+) |  0.852 |  0.808 | gttAACGTtg
 V$VMYB_01              |    11058 (-) |  0.852 |  0.827 | taACGTTgtg
 V$VMYB_01              |    11068 (-) |  0.938 |  0.900 | atCAGTTaca
 V$VMYB_01              |    11097 (-) |  0.904 |  0.819 | caCTGTTtaa
 V$VMYB_01              |    11106 (+) |  0.852 |  0.815 | aagAACGAct
 V$VMYB_01              |    11138 (-) |  0.938 |  0.882 | ctCAGTTttg
 V$VMYB_01              |    11217 (+) |  0.938 |  0.852 | ttgAACTGcc
 V$VMYB_01              |    11225 (-) |  0.938 |  0.867 | ccCAGTTtgt
 V$VMYB_01              |    11235 (+) |  0.938 |  0.900 | tctAACTGga
 V$VMYB_01              |    11304 (+) |  0.852 |  0.852 | aatAACGAct
 V$VMYB_01              |    11353 (+) |  0.852 |  0.785 | tcgAACGAga
 V$VMYB_01              |    11494 (-) |  0.910 |  0.853 | tgCGGTTgaa
 V$VMYB_01              |    11517 (-) |  1.000 |  0.961 | taCCGTTgtc
 V$VMYB_01              |    11654 (-) |  0.904 |  0.869 | taCTGTTaac
 V$VMYB_01              |    11710 (+) |  0.938 |  0.873 | cccAACTGcc
 V$VMYB_01              |    11762 (+) |  0.904 |  0.869 | gttAACAGga
 V$VMYB_01              |    11831 (+) |  0.904 |  0.855 | agaAACAGca
 V$VMYB_01              |    11921 (+) |  0.852 |  0.795 | cccAACGCcc
 V$CMYB_01              |       63 (+) |  0.988 |  0.917 | cataattactGTTGTtga
 V$CMYB_01              |      574 (+) |  0.989 |  0.882 | acgtctacctGTTGAatt
 V$CMYB_01              |      715 (+) |  0.988 |  0.876 | tttacagatgGTTGTgag
 V$CMYB_01              |      733 (+) |  0.989 |  0.862 | ccaccacgtgGTTGCtgg
 V$CMYB_01              |      788 (-) |  0.895 |  0.861 | ctcTTAACcgctgagcca
 V$CMYB_01              |     1021 (+) |  0.989 |  0.930 | gtgattggcaGTTGAatc
 V$CMYB_01              |     1858 (-) |  1.000 |  0.899 | gagCCAACtgaagaaggg
 V$CMYB_01              |     2547 (+) |  0.988 |  0.893 | acaggtttctGTTGTgaa
 V$CMYB_01              |     2673 (+) |  0.989 |  0.874 | ctcttaacccGTTGCatc
 V$CMYB_01              |     2820 (+) |  0.988 |  0.907 | gctctgtccaGTTGTctg
 V$CMYB_01              |     3235 (-) |  1.000 |  0.869 | cagCCAACattcccagcc
 V$CMYB_01              |     3504 (+) |  0.906 |  0.863 | ctaccctgctGTTAGagg
 V$CMYB_01              |     4535 (-) |  0.989 |  0.940 | gcgTCAACagcctcttag
 V$CMYB_01              |     4560 (+) |  0.989 |  0.921 | gctggacacaGTTGCggt
 V$CMYB_01              |     5277 (-) |  0.988 |  0.931 | ccaACAACaggctcagat
 V$CMYB_01              |     6101 (+) |  0.989 |  0.878 | gatcagtcctGTTGAcca
 V$CMYB_01              |     6843 (-) |  1.000 |  0.908 | ctgCCAACtggtgagcac
 V$CMYB_01              |     7183 (-) |  0.880 |  0.874 | tccCGAACggccacgggg
 V$CMYB_01              |     7527 (+) |  1.000 |  0.940 | tgaagttacaGTTGGttg
 V$CMYB_01              |     7531 (+) |  0.988 |  0.860 | gttacagttgGTTGTgag
 V$CMYB_01              |     7546 (-) |  1.000 |  0.905 | gagCCAACtgtgtagatg
 V$CMYB_01              |     7960 (+) |  0.988 |  0.859 | ccagactataGTTGTttg
 V$CMYB_01              |     7997 (+) |  1.000 |  0.929 | cactgtgcctGTTGGtgt
 V$CMYB_01              |     9556 (+) |  0.869 |  0.866 | tcgcctgtcgGTTTCtgg
 V$CMYB_01              |    10401 (+) |  1.000 |  0.858 | gaacgaggtgGTTGGcat
 V$CMYB_01              |    10661 (-) |  0.989 |  0.875 | atgTCAACaggaggatcc
 V$CMYB_01              |    10690 (-) |  0.989 |  0.863 | ctgGCAACacccgtgttt
 V$CMYB_01              |    10959 (+) |  1.000 |  0.913 | gtctgtgcctGTTGGagc
 V$CMYB_01              |    11031 (+) |  0.988 |  0.938 | tcctaccactGTTGTtgg
 V$CMYB_01              |    11488 (+) |  0.989 |  0.907 | ttggaatgcgGTTGAatt
 V$CMYB_01              |    11511 (+) |  0.988 |  0.923 | ggatattaccGTTGTccg
 V$CMYB_01              |    11708 (-) |  1.000 |  0.960 | accCCAACtgccctccac
 V$CMYB_01              |    11919 (-) |  1.000 |  0.872 | ggcCCAACgcccattggc
 V$AP4_01               |     7025 (+) |  1.000 |  0.865 | tgcatCAGCTgaagagtt
 V$MEF2_01              |      627 (-) |  1.000 |  0.755 | acacttttTTTTAaac
 V$MEF2_01              |     1157 (-) |  0.800 |  0.747 | gtagttctTTTTCaaa
 V$MEF2_01              |     2405 (+) |  1.000 |  0.755 | cctTAAAAaaaacaaa
 V$MEF2_01              |     2527 (-) |  1.000 |  0.757 | catattacTTTTAgag
 V$MEF2_01              |     3753 (-) |  0.800 |  0.730 | ttagtcatTCTTAaaa
 V$MEF2_01              |     4219 (+) |  0.800 |  0.747 | ttaAAAAAataaattc
 V$MEF2_01              |     4422 (+) |  1.000 |  0.736 | gtcTAAAAaaaaaaaa
 V$MEF2_01              |     5097 (-) |  0.600 |  0.763 | tgggttatTATTTgtg
 V$MEF2_01              |     5806 (+) |  0.800 |  0.731 | aaaAAAAAatagccct
 V$MEF2_01              |     7637 (-) |  0.800 |  0.797 | agaattatTTTAAaaa
 V$MEF2_01              |     8486 (-) |  0.600 |  0.749 | ggggttatTTTCTaca
 V$MEF2_01              |     8697 (+) |  0.800 |  0.763 | ttcTGAAAataccatc
 V$MEF2_01              |     9833 (-) |  1.000 |  0.799 | agggataaTTTTAaag
 V$MEF2_01              |    11297 (+) |  0.800 |  0.746 | aaaTAATAataacgac
 V$ELK1_01              |      606 (-) |  0.933 |  0.849 | ttaaaCATCCtgtcgt
 V$ELK1_01              |      921 (-) |  1.000 |  0.804 | tagcaCTTCCacgaaa
 V$ELK1_01              |     1455 (+) |  0.900 |  0.812 | tgagccGGACGtttct
 V$ELK1_01              |     1726 (-) |  0.933 |  0.785 | gggctCATCCtgaact
 V$ELK1_01              |     1735 (-) |  1.000 |  0.873 | ctgaaCTTCCtataga
 V$ELK1_01              |     2151 (-) |  1.000 |  0.824 | ccttcCTTCCtcttcc
 V$ELK1_01              |     2157 (-) |  1.000 |  0.773 | ttcctCTTCCtttcct
 V$ELK1_01              |     2201 (-) |  1.000 |  0.812 | tctttCTTCCtttctt
 V$ELK1_01              |     2682 (-) |  0.933 |  0.773 | cgttgCATCCtggtca
 V$ELK1_01              |     2703 (-) |  1.000 |  0.803 | ttctcCTTCCtcttcc
 V$ELK1_01              |     2985 (-) |  1.000 |  0.867 | atctaCTTCCgctcct
 V$ELK1_01              |     3029 (-) |  1.000 |  0.876 | accgaCTTCCgctcca
 V$ELK1_01              |     3338 (-) |  0.900 |  0.812 | atttcCCTCCtgttca
 V$ELK1_01              |     4147 (-) |  0.900 |  0.776 | tggtgCCTCCcatttg
 V$ELK1_01              |     4332 (-) |  0.933 |  0.779 | ggtgaCATCCaggtgg
 V$ELK1_01              |     4350 (+) |  0.900 |  0.794 | gaggcaGGAGGatcag
 V$ELK1_01              |     4959 (+) |  1.000 |  0.879 | gcagcaGGAAGtcagg
 V$ELK1_01              |     5728 (+) |  1.000 |  0.852 | taaactGGAAGccata
 V$ELK1_01              |     6085 (-) |  0.775 |  0.787 | tgtgaGTTCCtgtgtg
 V$ELK1_01              |     6272 (+) |  1.000 |  0.778 | gaagaaGGAAGcctct
 V$ELK1_01              |     6518 (+) |  0.775 |  0.830 | agaacaCGAAGttcac
 V$ELK1_01              |     6795 (-) |  1.000 |  0.815 | tggctCTTCCtcccct
 V$ELK1_01              |     6855 (-) |  0.900 |  0.792 | gagcaCGTCCagaccg
 V$ELK1_01              |     6874 (+) |  1.000 |  0.849 | cttataGGAAGcacca
 V$ELK1_01              |     7009 (+) |  0.933 |  0.773 | gcaggcGGATGtttcc
 V$ELK1_01              |     7227 (+) |  1.000 |  0.931 | ccagcaGGAAGttcat
 V$ELK1_01              |     7981 (+) |  1.000 |  0.801 | ttcaagGGAAGgactt
 V$ELK1_01              |     8078 (-) |  1.000 |  0.836 | agaaaCTTCCtataca
 V$ELK1_01              |     8155 (-) |  1.000 |  0.779 | attagCTTCCagaggc
 V$ELK1_01              |     8190 (-) |  0.775 |  0.775 | ttgctCTGCCtgtttc
 V$ELK1_01              |     9432 (+) |  1.000 |  0.931 | ataacaGGAAGcccaa
 V$ELK1_01              |     9465 (+) |  0.933 |  0.904 | tgtacaGGATGttcta
 V$ELK1_01              |    10009 (+) |  0.900 |  0.792 | gggactGGAGGtatag
 V$ELK1_01              |    10071 (+) |  1.000 |  0.774 | tcttctGGAAGggcag
 V$ELK1_01              |    10254 (+) |  1.000 |  0.870 | tgtgcaGGAAGtgatt
 V$ELK1_01              |    10664 (+) |  0.900 |  0.836 | tcaacaGGAGGatcca
 V$ELK1_01              |    10841 (+) |  1.000 |  0.794 | atcgcaGGAAGaagcc
 V$SP1_01               |      118 (+) |  0.962 |  0.923 | gaGGCTGgct
 V$SP1_01               |     1380 (+) |  0.911 |  0.915 | tgGGCGAggt
 V$SP1_01               |     3245 (-) |  0.962 |  0.932 | tccCAGCCca
 V$SP1_01               |     4823 (+) |  1.000 |  0.965 | caGGCGGggt
 V$SP1_01               |     5077 (+) |  0.962 |  0.923 | gaGGCTGgct
 V$SP1_01               |     5514 (-) |  0.972 |  0.925 | tccCTGCCtt
 V$SP1_01               |     5895 (-) |  1.000 |  0.938 | ggcCCGCCcc
 V$SP1_01               |     8121 (-) |  0.972 |  0.943 | accCTGCCtg
 V$SP1_01               |     8404 (-) |  0.962 |  0.917 | agcCAGCCcg
 V$SP1_01               |     9008 (+) |  0.972 |  0.919 | gaGGCAGggg
 V$SP1_01               |     9014 (+) |  0.972 |  0.923 | ggGGCAGgca
 V$SP1_01               |     9683 (+) |  0.909 |  0.915 | gaGGGGGggt
 V$SP1_01               |    11847 (+) |  0.894 |  0.918 | ggGGTGGggt
 P$O2_01                |     1566 (-) |  0.800 |  0.849 | aatctacggggAATGC
 I$CF2II_01             |      656 (+) |  1.000 |  0.973 | tTATATata
 I$CF2II_01             |      657 (-) |  1.000 |  0.973 | tatATATAa
 I$CF2II_02             |      656 (+) |  1.000 |  0.945 | tTATATata
 I$CF2II_02             |      657 (-) |  1.000 |  0.945 | tatATATAa
 I$CF2II_02             |     4578 (-) |  1.000 |  0.894 | tagATATAg
 F$REPCAR1_01           |     7619 (+) |  0.886 |  0.874 | ctcCAGCCgcctggcgg
 F$ABF1_01              |     2908 (+) |  0.988 |  0.904 | ccacatctctgtggACGGAccc
 F$ABF1_01              |     3708 (+) |  0.978 |  0.917 | cttgatcaatatttACGGGtga
 I$E74A_01              |     4958 (+) |  0.947 |  0.908 | tgcagcAGGAAgtcagg
 I$E74A_01              |     5469 (-) |  0.947 |  0.930 | tactatTTCCTgatttt
 V$ATF_01               |       35 (-) |  0.800 |  0.802 | gaacaaCTTCAgat
 V$ATF_01               |     1236 (-) |  0.800 |  0.800 | ctttgaCATCAggg
 V$ATF_01               |     1443 (-) |  0.800 |  0.804 | tagtgaAGTCActg
 V$ATF_01               |     1458 (+) |  0.800 |  0.797 | gccGGACGtttctc
 V$ATF_01               |     1839 (-) |  1.000 |  0.923 | tggggtCGTCAaca
 V$ATF_01               |     2963 (+) |  1.000 |  0.930 | cagTGACGgcagat
 V$ATF_01               |     2963 (-) |  0.800 |  0.800 | cagtgaCGGCAgat
 V$ATF_01               |     3069 (-) |  0.800 |  0.804 | tagctaGGTCAcag
 V$ATF_01               |     4530 (-) |  1.000 |  0.921 | caaatgCGTCAaca
 V$ATF_01               |     4861 (-) |  0.800 |  0.799 | gagggaGGTCAgca
 V$ATF_01               |     5818 (+) |  0.800 |  0.801 | cccTGGCGtggcac
 V$ATF_01               |     7988 (-) |  0.800 |  0.808 | gaaggaCTTCActg
 V$ATF_01               |     8208 (+) |  0.800 |  0.811 | ctcTGACCtcagtt
 V$ATF_01               |     8320 (-) |  1.000 |  0.932 | cttctgCGTCAgcg
 V$ATF_01               |     8609 (-) |  1.000 |  0.905 | tcattcCGTCAatc
 V$ATF_01               |     8728 (+) |  0.800 |  0.803 | ctgTAACGtcgggg
 V$ATF_01               |     9174 (-) |  0.800 |  0.800 | catgaaCGCCAcag
 V$ATF_01               |     9344 (+) |  0.800 |  0.808 | cccTGAAGtctctt
 V$ATF_01               |    11108 (-) |  0.800 |  0.806 | gaacgaCTTCAgat
 V$ATF_01               |    11315 (+) |  1.000 |  0.949 | cggTGACGacgatg
 V$ATF_01               |    11330 (+) |  1.000 |  0.912 | tgaTGACGatgtaa
 I$DFD_01               |       46 (+) |  1.000 |  0.997 | gatgtcATTACttggg
 I$DFD_01               |       61 (+) |  1.000 |  0.999 | gccataATTACtgttg
 I$DFD_01               |      174 (+) |  1.000 |  0.996 | gctggcATTACtaccc
 I$DFD_01               |      493 (+) |  0.991 |  0.988 | tgcaacATTATtatat
 I$DFD_01               |      583 (+) |  0.996 |  0.986 | tgttgaATTAAcagac
 I$DFD_01               |      984 (-) |  0.996 |  0.983 | cacagTTAATaatttt
 I$DFD_01               |      987 (-) |  0.991 |  0.991 | agttaATAATtttcat
 I$DFD_01               |     1900 (+) |  0.991 |  0.987 | tattttATTATtttat
 I$DFD_01               |     1990 (+) |  0.991 |  0.981 | accaagATTATctggc
 I$DFD_01               |     2524 (+) |  1.000 |  0.996 | ttacatATTACtttta
 I$DFD_01               |     3103 (-) |  0.991 |  0.990 | ctataCTAATttccat
 I$DFD_01               |     3121 (+) |  0.996 |  0.992 | ggctatATTAAtttac
 I$DFD_01               |     3123 (-) |  0.996 |  0.996 | ctataTTAATttacat
 I$DFD_01               |     3409 (-) |  0.996 |  0.983 | aaaagTTAATgattct
 I$DFD_01               |     3446 (-) |  0.996 |  0.983 | aacagTTAATaaaaca
 I$DFD_01               |     3729 (+) |  0.991 |  0.991 | actaaaATTATtattt
 I$DFD_01               |     3732 (+) |  0.991 |  0.988 | aaaattATTATttcta
 I$DFD_01               |     3871 (-) |  0.996 |  0.982 | aggagTTAATacaagc
 I$DFD_01               |     3902 (+) |  0.996 |  0.993 | acaggtATTAAtaaag
 I$DFD_01               |     3904 (-) |  0.996 |  0.992 | aggtaTTAATaaagct
 I$DFD_01               |     4026 (+) |  0.996 |  0.996 | catggaATTAAtattc
 I$DFD_01               |     4028 (-) |  0.996 |  0.992 | tggaaTTAATattcca
 I$DFD_01               |     4056 (-) |  0.991 |  0.991 | aggcaATAATtaaaat
 I$DFD_01               |     4246 (+) |  1.000 |  0.997 | gattgtATTACttggt
 I$DFD_01               |     4443 (+) |  0.996 |  0.996 | cacacaATTAAtattc
 I$DFD_01               |     4445 (-) |  0.996 |  0.993 | cacaaTTAATattcat
 I$DFD_01               |     4710 (-) |  1.000 |  0.989 | cttggGTAATtcactg
 I$DFD_01               |     5003 (+) |  1.000 |  0.986 | ccttgtATTACccatt
 I$DFD_01               |     5097 (+) |  0.991 |  0.988 | tgggttATTATttgtg
 I$DFD_01               |     5584 (-) |  0.991 |  0.987 | ggataATAATaaaata
 I$DFD_01               |     5786 (-) |  0.991 |  0.991 | atgaaATAATtaaata
 I$DFD_01               |     6806 (+) |  1.000 |  0.986 | cccctcATTACcttct
 I$DFD_01               |     6954 (+) |  0.991 |  0.988 | ctgtccATTATtctgg
 I$DFD_01               |     7351 (-) |  0.996 |  0.986 | acatgTTAATcatggg
 I$DFD_01               |     7398 (+) |  1.000 |  0.999 | ggtagaATTACtgaag
 I$DFD_01               |     7634 (+) |  0.991 |  0.991 | ggtagaATTATtttaa
 I$DFD_01               |     7826 (+) |  0.996 |  0.986 | caaacaATTAAcccac
 I$DFD_01               |     8681 (-) |  1.000 |  0.989 | ggaagGTAATtagcct
 I$DFD_01               |     8950 (+) |  0.991 |  0.991 | tttaaaATTAGtaggg
 I$DFD_01               |     9748 (+) |  0.996 |  0.992 | caatatATTAAtattg
 I$DFD_01               |     9750 (-) |  0.996 |  0.992 | atataTTAATattgaa
 I$DFD_01               |     9928 (-) |  1.000 |  0.989 | tatggGTAATttgcat
 I$DFD_01               |    10124 (+) |  0.991 |  0.990 | aataaaATTAGttaag
 I$DFD_01               |    10136 (+) |  0.991 |  0.991 | taagaaATTATtatta
 I$DFD_01               |    10139 (+) |  0.991 |  0.987 | gaaattATTATtattg
 I$DFD_01               |    10142 (+) |  0.991 |  0.987 | attattATTATtgttg
 I$DFD_01               |    10169 (+) |  0.991 |  0.987 | gtccttATTAGtgtgt
 I$DFD_01               |    10913 (-) |  0.991 |  0.988 | tgcaaATAATagtcta
 I$DFD_01               |    10998 (+) |  1.000 |  0.990 | aatcagATTACctgct
 I$DFD_01               |    11198 (+) |  0.991 |  0.991 | tgattgATTATtaatt
 I$DFD_01               |    11201 (+) |  0.996 |  0.993 | ttgattATTAAtttgt
 I$DFD_01               |    11203 (-) |  0.996 |  0.996 | gattaTTAATttgttt
 I$DFD_01               |    11294 (-) |  0.991 |  0.987 | aagaaATAATaataac
 I$DFD_01               |    11297 (-) |  0.991 |  0.988 | aaataATAATaacgac
 I$DFD_01               |    11509 (+) |  1.000 |  0.986 | gtggatATTACcgttg
 I$DFD_01               |    11691 (-) |  0.996 |  0.986 | taaagTTAATcactgt
 I$FTZ_01               |       63 (-) |  0.800 |  0.834 | cATAATtactgt
 I$FTZ_01               |      467 (-) |  0.800 |  0.815 | cTTATTtgacac
 I$FTZ_01               |      790 (-) |  0.800 |  0.790 | cTTAACcgctga
 I$FTZ_01               |     2596 (+) |  1.000 |  0.777 | ctgactATTAAa
 I$FTZ_01               |     2947 (+) |  0.800 |  0.777 | ctgcctATTACg
 I$FTZ_01               |     3127 (-) |  1.000 |  0.778 | aTTAATttacat
 I$FTZ_01               |     3272 (+) |  0.800 |  0.790 | gatgccATTATg
 I$FTZ_01               |     3306 (+) |  0.800 |  0.819 | catgtaGTTAAg
 I$FTZ_01               |     3366 (-) |  0.800 |  0.785 | cTGAATagccta
 I$FTZ_01               |     3430 (-) |  1.000 |  0.971 | cTTAATtgactt
 I$FTZ_01               |     3499 (-) |  0.800 |  0.826 | cTTAACtaccct
 I$FTZ_01               |     3861 (+) |  0.800 |  0.831 | gtaccaTTTAAg
 I$FTZ_01               |     3906 (+) |  0.800 |  0.797 | gtattaATAAAg
 I$FTZ_01               |     4026 (+) |  1.000 |  0.794 | catggaATTAAt
 I$FTZ_01               |     4058 (+) |  1.000 |  0.807 | gcaataATTAAa
 I$FTZ_01               |     4295 (-) |  0.800 |  0.779 | cTAAATttgacc
 I$FTZ_01               |     4443 (+) |  1.000 |  0.820 | cacacaATTAAt
 I$FTZ_01               |     4548 (-) |  0.800 |  0.780 | cTTAGTtttgat
 I$FTZ_01               |     5010 (+) |  1.000 |  0.907 | ttacccATTAAg
 I$FTZ_01               |     5318 (-) |  0.800 |  0.788 | cTTCATcggttc
 I$FTZ_01               |     5434 (-) |  0.800 |  0.794 | cTTTATttgtat
 I$FTZ_01               |     5788 (+) |  1.000 |  0.810 | gaaataATTAAa
 I$FTZ_01               |     5964 (+) |  0.800 |  0.783 | agtgttTTTAAg
 I$FTZ_01               |     6190 (+) |  0.800 |  0.820 | cacccaTTTAAg
 I$FTZ_01               |     6458 (-) |  0.800 |  0.787 | cTTATTtcctga
 I$FTZ_01               |     6589 (+) |  0.800 |  0.848 | aaaacaAATAAg
 I$FTZ_01               |     7060 (-) |  1.000 |  0.937 | cTTAATttgttt
 I$FTZ_01               |     7826 (+) |  1.000 |  0.835 | caaacaATTAAc
 I$FTZ_01               |     8634 (+) |  0.800 |  0.797 | agcttaTTTAAg
 I$FTZ_01               |     8704 (+) |  0.800 |  0.790 | aataccATCAAg
 I$FTZ_01               |     8854 (+) |  1.000 |  0.911 | ttaaaaATTAAg
 I$FTZ_01               |     8920 (+) |  0.800 |  0.780 | ctcggaATTCAg
 I$FTZ_01               |     8991 (-) |  1.000 |  0.792 | tTTAATtccagc
 I$FTZ_01               |     9907 (-) |  0.800 |  0.820 | cTTACTtactgg
 I$FTZ_01               |     9911 (-) |  0.800 |  0.785 | cTTACTggattt
 I$FTZ_01               |    10128 (+) |  0.800 |  0.814 | aaattaGTTAAg
 I$FTZ_01               |    10504 (+) |  0.800 |  0.832 | aagtcaATTATg
 I$FTZ_01               |    10813 (-) |  0.800 |  0.808 | cTAAATcgcagt
 I$FTZ_01               |    11124 (-) |  0.800 |  0.778 | cTTAACtcgctg
 I$FTZ_01               |    11155 (+) |  0.800 |  0.787 | atgaaaATGAAg
 I$FTZ_01               |    11196 (-) |  0.800 |  0.818 | cTTGATtgatta
 I$FTZ_01               |    11207 (-) |  1.000 |  0.798 | aTTAATttgttt
 I$FTZ_01               |    11272 (+) |  1.000 |  0.943 | aaggaaATTAAg
 I$FTZ_01               |    11419 (+) |  0.800 |  0.785 | atttctATTTAg
 I$FTZ_01               |    11684 (+) |  0.800 |  0.846 | agaccaATAAAg
 I$FTZ_01               |    11695 (-) |  1.000 |  0.787 | gTTAATcactgt
 I$KR_01                |     1595 (+) |  1.000 |  0.923 | actGGGTTtg
 I$KR_01                |     2676 (-) |  1.000 |  1.000 | ttAACCCgtt
 I$KR_01                |     6439 (-) |  1.000 |  0.948 | tcAACCCagt
 I$KR_01                |     6747 (-) |  1.000 |  0.923 | aaAACCCact
 I$KR_01                |     7833 (-) |  1.000 |  0.966 | ttAACCCact
 I$KR_01                |     8484 (+) |  1.000 |  0.941 | aggGGGTTat
 I$HB_01                |      220 (-) |  1.000 |  0.983 | tTTTTTtttc
 I$HB_01                |     1532 (-) |  1.000 |  0.981 | tTTTTTgttc
 I$HB_01                |     2515 (+) |  1.000 |  0.969 | gaaaAAAAAt
 I$HB_01                |     2900 (-) |  1.000 |  0.975 | tTTTTTatcc
 I$HB_01                |     4425 (+) |  1.000 |  0.968 | taaaAAAAAa
 I$HB_01                |     4491 (+) |  1.000 |  0.981 | gaacAAAAAa
 I$HB_01                |     5801 (+) |  1.000 |  0.974 | acaaAAAAAa
 I$HB_01                |     5802 (+) |  1.000 |  0.976 | caaaAAAAAa
 I$HB_01                |     6825 (-) |  1.000 |  0.983 | tTTTTTatgt
 I$HB_01                |     7051 (-) |  1.000 |  0.969 | aTTTTTtttc
 I$HB_01                |    10337 (-) |  1.000 |  0.968 | gTTTTTattg
 I$HB_01                |    11469 (-) |  1.000 |  0.974 | tTTTTTattt
 I$HB_01                |    11503 (-) |  1.000 |  0.968 | aTTTTTgtgg
 V$E2F_01               |     1718 (-) |  0.800 |  0.757 | cctTTTCCgggctca
 V$E2F_01               |     5772 (+) |  1.000 |  0.783 | aaggagaGAAAAata
 V$E2F_01               |     6125 (-) |  1.000 |  0.816 | ttgTTTTCtcggcgt
 V$E2F_01               |     7087 (-) |  0.800 |  0.766 | tgcTTTGCgcgcacc
 V$E2F_01               |     8544 (+) |  1.000 |  0.819 | gggccgaGAAAAtga
 V$E2F_01               |     9119 (+) |  1.000 |  0.808 | aaaccggGAAAAcct
 V$E2F_01               |    10161 (-) |  1.000 |  0.761 | tcgTTTTCgtcctta
 V$E2F_01               |    10827 (-) |  1.000 |  0.776 | gccTTTTCaggccca
 V$ELK1_02              |      404 (+) |  1.000 |  0.921 | caaggCGGAAtggg
 V$ELK1_02              |     1718 (-) |  1.000 |  0.955 | ccttTTCCGggctc
 V$ELK1_02              |     2563 (-) |  1.000 |  0.946 | aaatTTCCGtaagt
 V$ELK1_02              |     2766 (-) |  1.000 |  0.918 | tagaTTCCGcatgt
 V$ELK1_02              |     2846 (-) |  1.000 |  0.921 | atcaTTCCGtcctt
 V$ELK1_02              |     2987 (-) |  1.000 |  0.958 | ctacTTCCGctcct
 V$ELK1_02              |     3031 (-) |  1.000 |  0.961 | cgacTTCCGctcca
 V$ELK1_02              |     3161 (-) |  1.000 |  0.919 | tccaTTCCGcctgt
 V$ELK1_02              |     4959 (+) |  0.938 |  0.939 | gcagcAGGAAgtca
 V$ELK1_02              |     5471 (-) |  0.938 |  0.918 | ctatTTCCTgattt
 V$ELK1_02              |     5728 (+) |  0.924 |  0.918 | taaacTGGAAgcca
 V$ELK1_02              |     6087 (-) |  0.938 |  0.918 | tgagTTCCTgtgtg
 V$ELK1_02              |     6459 (-) |  0.938 |  0.922 | ttatTTCCTgataa
 V$ELK1_02              |     7227 (+) |  0.938 |  0.943 | ccagcAGGAAgttc
 V$ELK1_02              |     8608 (-) |  1.000 |  0.921 | atcaTTCCGtcaat
 V$ELK1_02              |     8917 (+) |  1.000 |  0.923 | atactCGGAAttca
 V$ELK1_02              |     9432 (+) |  0.938 |  0.928 | ataacAGGAAgccc
 V$ELK1_02              |    10254 (+) |  0.938 |  0.939 | tgtgcAGGAAgtga
 V$ELK1_02              |    10841 (+) |  0.938 |  0.919 | atcgcAGGAAgaag
 F$ABAA_01              |     3129 (+) |  1.000 |  0.983 | taatttaCATTCccacaac
 F$HSF_01               |     1160 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |     1538 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |     1748 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     2871 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     3545 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |     3550 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |     3693 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     4680 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |     5185 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |     5662 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     6404 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     6518 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     6914 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     7412 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     7495 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |     7695 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     7805 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     8181 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     8219 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |     8428 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |     8534 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     8724 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     8846 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     8966 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     9364 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |     9404 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |     9475 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |     9534 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |     9780 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |    10051 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |    10057 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |    10199 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |    10773 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |    11107 (+) |  1.000 |  1.000 | AGAAC
 F$HSF_01               |    11233 (-) |  1.000 |  1.000 | GTTCT
 F$HSF_01               |    11885 (-) |  1.000 |  1.000 | GTTCT
 F$MATA1_01             |      349 (-) |  1.000 |  0.962 | ttctaCATCA
 F$MATA1_01             |     9800 (-) |  1.000 |  0.996 | atgtaCATCA
 F$MATALPHA2_01         |        7 (+) |  1.000 |  0.974 | gCATGTacaa
 F$MATALPHA2_01         |        9 (-) |  0.950 |  0.921 | atgtACAAGt
 F$MATALPHA2_01         |       15 (-) |  1.000 |  0.956 | aagtACATGt
 F$MATALPHA2_01         |       19 (+) |  1.000 |  0.977 | aCATGTgaat
 F$MATALPHA2_01         |       78 (+) |  0.905 |  0.895 | tGATGTtgat
 F$MATALPHA2_01         |      273 (+) |  0.950 |  0.918 | cCTTGTgcat
 F$MATALPHA2_01         |      322 (+) |  0.950 |  0.915 | tCCTGTgctg
 F$MATALPHA2_01         |      349 (-) |  0.905 |  0.901 | ttctACATCa
 F$MATALPHA2_01         |      421 (+) |  0.950 |  0.927 | gCTTGTccaa
 F$MATALPHA2_01         |      485 (-) |  0.916 |  0.886 | gtcaACATTg
 F$MATALPHA2_01         |      544 (+) |  0.950 |  0.914 | gCTTGTgttt
 F$MATALPHA2_01         |      580 (+) |  0.950 |  0.925 | aCCTGTtgaa
 F$MATALPHA2_01         |      606 (-) |  0.905 |  0.891 | ttaaACATCc
 F$MATALPHA2_01         |      613 (+) |  0.950 |  0.930 | tCCTGTcgta
 F$MATALPHA2_01         |      618 (-) |  1.000 |  0.920 | tcgtACATGa
 F$MATALPHA2_01         |      637 (-) |  0.916 |  0.898 | ttaaACATTt
 F$MATALPHA2_01         |      837 (-) |  0.950 |  0.919 | taaaACAAGt
 F$MATALPHA2_01         |      879 (-) |  0.972 |  0.891 | acaaACACGa
 F$MATALPHA2_01         |      935 (-) |  0.950 |  0.909 | aaccACAAGt
 F$MATALPHA2_01         |      963 (-) |  0.950 |  0.950 | atttACAGGa
 F$MATALPHA2_01         |      999 (+) |  1.000 |  0.903 | tCATGTgggg
 F$MATALPHA2_01         |     1129 (+) |  0.972 |  0.928 | aCGTGTgttc
 F$MATALPHA2_01         |     1153 (+) |  0.905 |  0.886 | tTATGTagtt
 F$MATALPHA2_01         |     1237 (-) |  0.905 |  0.914 | tttgACATCa
 F$MATALPHA2_01         |     1267 (+) |  0.972 |  0.937 | cCGTGTgtac
 F$MATALPHA2_01         |     1282 (-) |  0.950 |  0.921 | gatgACAGGg
 F$MATALPHA2_01         |     1298 (+) |  0.950 |  0.912 | aCCTGTgtag
 F$MATALPHA2_01         |     1421 (-) |  0.972 |  0.893 | tgagACACGc
 F$MATALPHA2_01         |     1628 (+) |  1.000 |  0.958 | gCATGTccag
 F$MATALPHA2_01         |     1772 (+) |  0.950 |  0.910 | gCCTGTcctc
 F$MATALPHA2_01         |     1796 (-) |  0.950 |  0.947 | attcACAGGa
 F$MATALPHA2_01         |     2358 (+) |  0.950 |  0.915 | aCTTGTattt
 F$MATALPHA2_01         |     2422 (-) |  0.950 |  0.923 | aatcACAGGg
 F$MATALPHA2_01         |     2522 (-) |  0.905 |  0.886 | aattACATAt
 F$MATALPHA2_01         |     2543 (-) |  0.950 |  0.925 | aataACAGGt
 F$MATALPHA2_01         |     2615 (+) |  1.000 |  0.965 | cCATGTgtat
 F$MATALPHA2_01         |     2774 (+) |  1.000 |  0.920 | gCATGTgaga
 F$MATALPHA2_01         |     3131 (-) |  0.916 |  0.908 | atttACATTc
 F$MATALPHA2_01         |     3169 (+) |  0.950 |  0.924 | gCCTGTacat
 F$MATALPHA2_01         |     3171 (-) |  0.916 |  0.897 | ctgtACATTa
 F$MATALPHA2_01         |     3305 (+) |  1.000 |  0.956 | cCATGTagtt
 F$MATALPHA2_01         |     3345 (+) |  0.950 |  0.935 | tCCTGTtcat
 F$MATALPHA2_01         |     3457 (-) |  0.950 |  0.912 | aaacACAGGg
 F$MATALPHA2_01         |     3640 (-) |  1.000 |  0.958 | taccACATGg
 F$MATALPHA2_01         |     3694 (-) |  0.950 |  0.923 | gaacACAAGa
 F$MATALPHA2_01         |     3743 (-) |  0.916 |  0.896 | ttctACATTt
 F$MATALPHA2_01         |     3877 (-) |  0.950 |  0.923 | taatACAAGc
 F$MATALPHA2_01         |     3898 (-) |  0.950 |  0.915 | catcACAGGt
 F$MATALPHA2_01         |     3925 (-) |  0.916 |  0.910 | aattACATTa
 F$MATALPHA2_01         |     3941 (+) |  0.950 |  0.920 | aCTTGTtcat
 F$MATALPHA2_01         |     4070 (+) |  0.905 |  0.901 | aTATGTaaaa
 F$MATALPHA2_01         |     4077 (+) |  0.916 |  0.890 | aAATGTatac
 F$MATALPHA2_01         |     4121 (+) |  0.905 |  0.900 | aGATGTtaaa
 F$MATALPHA2_01         |     4399 (-) |  0.950 |  0.904 | caagACAGGt
 F$MATALPHA2_01         |     4418 (+) |  0.950 |  0.927 | cCTTGTctaa
 F$MATALPHA2_01         |     4698 (+) |  0.905 |  0.890 | tGATGTccta
 F$MATALPHA2_01         |     4893 (+) |  1.000 |  0.908 | cCATGTtcct
 F$MATALPHA2_01         |     5003 (+) |  0.950 |  0.920 | cCTTGTatta
 F$MATALPHA2_01         |     5210 (+) |  0.950 |  0.923 | tCTTGTgctt
 F$MATALPHA2_01         |     5239 (-) |  1.000 |  0.968 | gattACATGg
 F$MATALPHA2_01         |     5249 (-) |  1.000 |  0.974 | gttcACATGt
 F$MATALPHA2_01         |     5253 (+) |  1.000 |  0.950 | aCATGTggtc
 F$MATALPHA2_01         |     5279 (-) |  0.950 |  0.914 | aacaACAGGc
 F$MATALPHA2_01         |     5364 (-) |  0.972 |  0.930 | aaacACACGg
 F$MATALPHA2_01         |     5605 (-) |  0.950 |  0.932 | taacACAAGa
 F$MATALPHA2_01         |     6006 (+) |  0.972 |  0.943 | aCGTGTccaa
 F$MATALPHA2_01         |     6107 (+) |  0.950 |  0.932 | tCCTGTtgac
 F$MATALPHA2_01         |     6123 (+) |  0.950 |  0.914 | gCTTGTtttc
 F$MATALPHA2_01         |     6394 (+) |  0.950 |  0.912 | gCCTGTgttc
 F$MATALPHA2_01         |     6517 (-) |  0.972 |  0.944 | aagaACACGa
 F$MATALPHA2_01         |     6829 (+) |  0.905 |  0.889 | tTATGTgcta
 F$MATALPHA2_01         |     6892 (-) |  0.950 |  0.933 | taagACAAGa
 F$MATALPHA2_01         |     6913 (-) |  0.950 |  0.908 | gagaACAAGg
 F$MATALPHA2_01         |     7111 (-) |  1.000 |  0.958 | taccACATGt
 F$MATALPHA2_01         |     7115 (+) |  1.000 |  0.897 | aCATGTgtgc
 F$MATALPHA2_01         |     7347 (-) |  1.000 |  0.970 | ttcaACATGt
 F$MATALPHA2_01         |     7351 (+) |  1.000 |  0.979 | aCATGTtaat
 F$MATALPHA2_01         |     7736 (-) |  0.950 |  0.918 | catcACAGGc
 F$MATALPHA2_01         |     8102 (+) |  0.950 |  0.898 | tCCTGTcaca
 F$MATALPHA2_01         |     8149 (-) |  0.916 |  0.895 | gaaaACATTa
 F$MATALPHA2_01         |     8361 (+) |  0.950 |  0.909 | cCCTGTgcag
 F$MATALPHA2_01         |     8495 (-) |  0.950 |  0.926 | ttctACAGGg
 F$MATALPHA2_01         |     8756 (+) |  0.950 |  0.907 | cCTTGTcctc
 F$MATALPHA2_01         |     8999 (-) |  1.000 |  0.944 | cagcACATGg
 F$MATALPHA2_01         |     9051 (-) |  1.000 |  0.962 | gtctACATGg
 F$MATALPHA2_01         |     9370 (-) |  0.950 |  0.929 | tatcACAGGg
 F$MATALPHA2_01         |     9431 (-) |  0.950 |  0.940 | aataACAGGa
 F$MATALPHA2_01         |     9464 (-) |  0.950 |  0.927 | ctgtACAGGa
 F$MATALPHA2_01         |     9517 (+) |  1.000 |  0.969 | cCATGTccaa
 F$MATALPHA2_01         |     9588 (+) |  0.950 |  0.923 | cCCTGTaatc
 F$MATALPHA2_01         |     9710 (+) |  0.877 |  0.890 | tGGTGTaaaa
 F$MATALPHA2_01         |     9737 (+) |  0.916 |  0.903 | tAATGTccat
 F$MATALPHA2_01         |     9798 (+) |  0.916 |  0.890 | aAATGTacat
 F$MATALPHA2_01         |     9800 (-) |  0.905 |  0.896 | atgtACATCa
 F$MATALPHA2_01         |     9805 (-) |  0.905 |  0.889 | catcACATAa
 F$MATALPHA2_01         |     9940 (+) |  1.000 |  0.906 | gCATGTatgt
 F$MATALPHA2_01         |     9944 (+) |  0.905 |  0.894 | gTATGTtata
 F$MATALPHA2_01         |    10251 (+) |  0.950 |  0.912 | gCTTGTgcag
 F$MATALPHA2_01         |    10420 (-) |  0.887 |  0.899 | tttaACACTa
 F$MATALPHA2_01         |    10659 (+) |  0.916 |  0.915 | tAATGTcaac
 F$MATALPHA2_01         |    10663 (-) |  0.950 |  0.932 | gtcaACAGGa
 F$MATALPHA2_01         |    10700 (+) |  0.972 |  0.942 | cCGTGTttat
 F$MATALPHA2_01         |    10756 (+) |  0.972 |  0.930 | cCGTGTgttt
 F$MATALPHA2_01         |    10803 (+) |  0.950 |  0.918 | cCTTGTgcat
 F$MATALPHA2_01         |    10888 (-) |  1.000 |  0.957 | ctgcACATGc
 F$MATALPHA2_01         |    10934 (+) |  0.950 |  0.930 | tCTTGTggac
 F$MATALPHA2_01         |    11336 (+) |  0.905 |  0.896 | cGATGTaaat
 F$MATALPHA2_01         |    11762 (-) |  0.950 |  0.946 | gttaACAGGa
 V$CETS1P54_01          |      609 (-) |  0.974 |  0.964 | aacaTCCTGt
 V$CETS1P54_01          |     1458 (+) |  1.000 |  0.968 | gCCGGAcgtt
 V$CETS1P54_01          |     4962 (+) |  0.974 |  0.973 | gCAGGAagtc
 V$CETS1P54_01          |     7230 (+) |  0.974 |  0.972 | gCAGGAagtt
 V$CETS1P54_01          |     9435 (+) |  0.974 |  0.967 | aCAGGAagcc
 V$CETS1P54_01          |     9468 (+) |  0.974 |  0.964 | aCAGGAtgtt
 V$CETS1P54_01          |    10257 (+) |  0.974 |  0.973 | gCAGGAagtg
 V$P53_01               |        1 (-) |  0.785 |  0.632 | gttcatgcatgtaCAAGTac
 V$P53_01               |     1626 (+) |  0.879 |  0.634 | caGCATGtccagcctttcct
 V$P53_01               |     2971 (+) |  0.785 |  0.694 | gcAGATGcgcaggcatctac
 V$P53_01               |     2971 (-) |  0.785 |  0.694 | gcagatgcgcaggCATCTac
 V$P53_01               |     7991 (+) |  0.570 |  0.630 | ggACTTCactgtgcctgttg
 V$P53_01               |     9385 (-) |  0.785 |  0.645 | tgtcagcccctggAATGTgg
 V$VMAF_01              |       72 (+) |  0.874 |  0.700 | tgttGTTGAtgttgatagg
 V$VMAF_01              |       78 (+) |  0.874 |  0.756 | tgatGTTGAtagggcctat
 V$VMAF_01              |      128 (-) |  0.653 |  0.734 | aactgctcagTCAATccag
 V$VMAF_01              |      295 (+) |  0.580 |  0.718 | ttttACAGActgagctatc
 V$VMAF_01              |      395 (+) |  0.645 |  0.727 | atttGCCAAcaaggcggaa
 V$VMAF_01              |      476 (-) |  0.874 |  0.714 | cacttacaagTCAACattg
 V$VMAF_01              |     1224 (+) |  0.910 |  0.702 | ttctGATGActgctttgac
 V$VMAF_01              |     1231 (-) |  0.642 |  0.756 | gactgctttgACATCaggg
 V$VMAF_01              |     1250 (-) |  0.910 |  0.721 | cagcattctgTCATCatcc
 V$VMAF_01              |     1278 (+) |  0.910 |  0.780 | ctggGATGAcagggacctg
 V$VMAF_01              |     1349 (-) |  0.870 |  0.797 | cttgcctgggTCACCtgat
 V$VMAF_01              |     1615 (-) |  0.732 |  0.728 | ggtctcgtggACAGCatgt
 V$VMAF_01              |     1678 (-) |  1.000 |  0.726 | ccttcgggtgTCAGCtcag
 V$VMAF_01              |     1837 (-) |  0.874 |  0.713 | attggggtcgTCAACacaa
 V$VMAF_01              |     2328 (-) |  0.718 |  0.760 | tcttgctatgTGACCctac
 V$VMAF_01              |     2929 (+) |  1.000 |  0.763 | cttaGCTGAttgcgaagtc
 V$VMAF_01              |     2936 (-) |  0.801 |  0.801 | gattgcgaagTCTGCctat
 V$VMAF_01              |     2973 (-) |  0.642 |  0.716 | agatgcgcagGCATCtact
 V$VMAF_01              |     3067 (-) |  0.642 |  0.701 | tatagctaggTCACAgggt
 V$VMAF_01              |     3208 (-) |  0.600 |  0.736 | gtatgctaggCAAGCactt
 V$VMAF_01              |     3224 (-) |  1.000 |  0.742 | cttttaccagTCAGCcaac
 V$VMAF_01              |     3341 (-) |  0.910 |  0.708 | tccctcctgtTCATCagac
 V$VMAF_01              |     3941 (+) |  0.723 |  0.714 | acttGTTCAttcagccatc
 V$VMAF_01              |     4398 (-) |  1.000 |  0.748 | ccaagacaggTCAGCcaca
 V$VMAF_01              |     4528 (-) |  0.874 |  0.702 | aacaaatgcgTCAACagcc
 V$VMAF_01              |     4788 (+) |  1.000 |  0.752 | gattGCTGActtgcataat
 V$VMAF_01              |     4859 (-) |  1.000 |  0.781 | ctgagggaggTCAGCagca
 V$VMAF_01              |     4966 (-) |  1.000 |  0.728 | gaagtcaggcTCAGCccct
 V$VMAF_01              |     4994 (+) |  0.801 |  0.738 | aatgGCAGAccttgtatta
 V$VMAF_01              |     5076 (+) |  0.747 |  0.725 | agagGCTGGctctgactgg
 V$VMAF_01              |     5235 (+) |  0.763 |  0.705 | gaacGATTAcatgggttca
 V$VMAF_01              |     5257 (-) |  0.910 |  0.803 | gtggtcacagTCATCctgg
 V$VMAF_01              |     5267 (-) |  0.621 |  0.712 | tcatcctgggCCAACaaca
 V$VMAF_01              |     5310 (-) |  0.910 |  0.742 | aatggcttctTCATCggtt
 V$VMAF_01              |     6047 (-) |  0.732 |  0.712 | cagccctgtgACAGCcctg
 V$VMAF_01              |     6067 (+) |  0.732 |  0.752 | acgtGCTGCcacagtctct
 V$VMAF_01              |     6289 (+) |  0.910 |  0.931 | tgatGATGActgagcaggg
 V$VMAF_01              |     6493 (+) |  0.801 |  0.720 | gattGCAGAtgcggccaca
 V$VMAF_01              |     6524 (+) |  0.723 |  0.715 | cgaaGTTCAccctggagac
 V$VMAF_01              |     6642 (-) |  0.801 |  0.794 | ggcacctcagTCTGCaaac
 V$VMAF_01              |     6693 (+) |  1.000 |  0.774 | gagtGCTGAagtagagaga
 V$VMAF_01              |     7019 (-) |  1.000 |  0.789 | gtttcctgcaTCAGCtgaa
 V$VMAF_01              |     7162 (+) |  0.747 |  0.761 | tggaGCTGGcgttgcagat
 V$VMAF_01              |     7295 (+) |  1.000 |  0.757 | ccaaGCTGAgagagtaagg
 V$VMAF_01              |     7603 (+) |  1.000 |  0.714 | aactGCTGAgccatctctc
 V$VMAF_01              |     7603 (-) |  0.657 |  0.756 | aactgctgagCCATCtctc
 V$VMAF_01              |     7712 (-) |  1.000 |  0.709 | ggcagaaggaTCAGCagtt
 V$VMAF_01              |     8122 (-) |  0.801 |  0.798 | ccctgcctggTCTGCtttc
 V$VMAF_01              |     8268 (+) |  0.910 |  0.801 | acctGATGAtgcagctgcc
 V$VMAF_01              |     8277 (+) |  0.732 |  0.733 | tgcaGCTGCcctggctccc
 V$VMAF_01              |     8318 (-) |  1.000 |  0.889 | agcttctgcgTCAGCgcca
 V$VMAF_01              |     8396 (-) |  0.747 |  0.742 | tgaagccaagCCAGCccgg
 V$VMAF_01              |     8409 (-) |  0.853 |  0.711 | gcccggcctgTAAGCagct
 V$VMAF_01              |     8581 (-) |  0.607 |  0.727 | tggggcaaagGCAACatct
 V$VMAF_01              |     9033 (-) |  0.732 |  0.704 | gagttcaaggGCAGCctgg
 V$VMAF_01              |     9042 (-) |  0.676 |  0.738 | ggcagcctggTCTACatgg
 V$VMAF_01              |     9071 (-) |  0.732 |  0.767 | gctagccaggGCAGCatag
 V$VMAF_01              |     9265 (-) |  0.732 |  0.742 | cagggcagcgACAGCcacc
 V$VMAF_01              |     9284 (-) |  1.000 |  0.748 | aagctgagagTCAGCttgt
 V$VMAF_01              |     9377 (-) |  1.000 |  0.750 | gggagagctgTCAGCccct
 V$VMAF_01              |     9546 (-) |  0.671 |  0.728 | tcctgcgtagTCGCCtgtc
 V$VMAF_01              |     9583 (-) |  0.763 |  0.738 | tatagccctgTAATCccag
 V$VMAF_01              |     9608 (+) |  1.000 |  0.742 | ggaaGCTGAggtgggagga
 V$VMAF_01              |     9631 (-) |  1.000 |  0.861 | gagttcaaggTCAGCttgg
 V$VMAF_01              |    10030 (-) |  0.870 |  0.709 | agtttgtgagTCACCgtgt
 V$VMAF_01              |    10269 (-) |  0.848 |  0.749 | ttttgccggcTGAGCaatc
 V$VMAF_01              |    10278 (-) |  0.910 |  0.752 | ctgagcaatcTCATCaggc
 V$VMAF_01              |    10422 (-) |  0.712 |  0.708 | taacactaagTCTTCgcaa
 V$VMAF_01              |    10628 (+) |  0.648 |  0.704 | agaaAGTGActgaggaaga
 V$VMAF_01              |    10814 (-) |  0.789 |  0.728 | taaatcgcagTCCGCcttt
 V$VMAF_01              |    11047 (-) |  0.718 |  0.723 | ggttcctttgTTAACgttg
 V$VMAF_01              |    11052 (+) |  0.718 |  0.709 | ctttGTTAAcgttgtgatc
 V$VMAF_01              |    11056 (-) |  0.758 |  0.729 | gttaacgttgTGATCagtt
 V$VMAF_01              |    11150 (+) |  0.910 |  0.725 | ctctGATGAaaatgaagct
 V$VMAF_01              |    11312 (+) |  0.870 |  0.759 | ctacGGTGAcgacgatgat
 V$VMAF_01              |    11315 (+) |  0.712 |  0.708 | cggtGACGAcgatgatgat
 V$VMAF_01              |    11324 (+) |  0.910 |  0.717 | cgatGATGAtgacgatgta
 V$VMAF_01              |    11327 (+) |  0.910 |  0.849 | tgatGATGAcgatgtaaat
 V$VMAF_01              |    11450 (+) |  0.870 |  0.729 | ttttGGTGAatcagtgaaa
 V$VMAF_01              |    11696 (-) |  0.870 |  0.757 | ttaatcactgTCACCccaa
 F$GCN4_01              |     1345 (-) |  0.829 |  0.847 | aaggcttgcctgGGTCAcctgatgctc
 F$GCN4_01              |     3925 (-) |  1.000 |  0.856 | aattacattatcAGTCActtgttcatt
 F$GCN4_01              |     4524 (-) |  0.829 |  0.856 | agacaacaaatgCGTCAacagcctctt
 F$GCN4_01              |     6407 (+) |  1.000 |  0.847 | acgctcagaaTGACTcctctggctttc
 F$GCN4_01              |     6547 (-) |  1.000 |  0.849 | ggctgaggtaagAGTCAtggttgccac
 F$GCN4_01              |     8314 (-) |  0.829 |  0.846 | ctgcagcttctgCGTCAgcgccagtat
 F$GCN4_01              |     9312 (-) |  0.829 |  0.852 | agggaggcgttgGGTCAgagcctctgg
 F$GCN4_01              |    10026 (-) |  1.000 |  0.971 | ccgtagtttgtgAGTCAccgtgtgggt
 V$CREB_01              |     2966 (+) |  1.000 |  0.879 | TGACGgca
 V$CREB_01              |     8612 (-) |  1.000 |  0.869 | ttcCGTCA
 V$CREBP1_01            |     3440 (-) |  0.831 |  0.891 | ttaGGTAA
 V$CREBP1_01            |     4273 (+) |  0.831 |  0.891 | TTACCtaa
 V$CREBP1CJUN_01        |       45 (-) |  0.848 |  0.781 | agATGTCa
 V$CREBP1CJUN_01        |     1239 (+) |  0.848 |  0.891 | tGACATca
 V$CREBP1CJUN_01        |     1239 (-) |  0.780 |  0.842 | tgACATCa
 V$CREBP1CJUN_01        |     1416 (+) |  0.780 |  0.821 | tGCCGTga
 V$CREBP1CJUN_01        |     1446 (+) |  0.780 |  0.842 | tGAAGTca
 V$CREBP1CJUN_01        |     1446 (-) |  0.840 |  0.885 | tgAAGTCa
 V$CREBP1CJUN_01        |     2966 (+) |  0.780 |  0.842 | tGACGGca
 V$CREBP1CJUN_01        |     2966 (-) |  0.780 |  0.842 | tgACGGCa
 V$CREBP1CJUN_01        |     3291 (+) |  0.780 |  0.821 | tGAGGTga
 V$CREBP1CJUN_01        |     4334 (+) |  0.848 |  0.778 | tGACATcc
 V$CREBP1CJUN_01        |     4864 (-) |  0.844 |  0.776 | ggAGGTCa
 V$CREBP1CJUN_01        |     6550 (+) |  0.780 |  0.817 | tGAGGTaa
 V$CREBP1CJUN_01        |     7527 (+) |  0.780 |  0.842 | tGAAGTta
 V$CREBP1CJUN_01        |     7582 (-) |  0.844 |  0.866 | tcAGGTCa
 V$CREBP1CJUN_01        |     7882 (-) |  0.840 |  0.776 | agAAGTCa
 V$CREBP1CJUN_01        |     8211 (+) |  0.844 |  0.888 | tGACCTca
 V$CREBP1CJUN_01        |     8211 (-) |  0.780 |  0.842 | tgACCTCa
 V$CREBP1CJUN_01        |     8266 (+) |  0.844 |  0.866 | tGACCTga
 V$CREBP1CJUN_01        |     8612 (-) |  0.780 |  0.817 | ttCCGTCa
 V$CREBP1CJUN_01        |     8731 (-) |  1.000 |  0.862 | taACGTCg
 V$CREBP1CJUN_01        |     9816 (-) |  0.780 |  0.842 | taACTTCa
 V$CREBP1CJUN_01        |     9844 (-) |  0.840 |  0.885 | taAAGTCa
 V$CREBP1CJUN_01        |    10502 (-) |  0.840 |  0.776 | aaAAGTCa
 V$CREBP1CJUN_01        |    10659 (-) |  0.848 |  0.891 | taATGTCa
 V$CREBP1CJUN_01        |    11783 (+) |  0.780 |  0.817 | tGATGTaa
 V$SOX5_01              |      947 (+) |  1.000 |  0.992 | ggaACAATga
 V$SOX5_01              |     3143 (+) |  1.000 |  0.996 | acaACAATat
 V$SOX5_01              |     7331 (+) |  1.000 |  0.995 | ggaACAATag
 V$SOX5_01              |     7826 (+) |  1.000 |  0.994 | caaACAATta
 V$SOX5_01              |     8556 (+) |  1.000 |  0.995 | tgaACAATgt
 V$SOX5_01              |     9744 (+) |  1.000 |  0.874 | catACAATat
 V$SOX5_01              |     9780 (+) |  1.000 |  0.991 | agaACAATtt
 V$SOX5_01              |    10149 (-) |  1.000 |  0.996 | ttATTGTtgt
 V$SOX5_01              |    10341 (-) |  1.000 |  0.997 | ttATTGTttt
 V$SOX5_01              |    10459 (+) |  1.000 |  0.996 | tcaACAATgc
 V$SOX5_01              |    10855 (-) |  1.000 |  0.872 | ccATTGTaga
 I$DL_01                |      330 (+) |  0.906 |  0.816 | tggaaATTCCc
 I$DL_01                |      330 (-) |  1.000 |  0.924 | tGGAAAttccc
 I$DL_01                |     1667 (+) |  0.906 |  0.801 | tggagATTCCt
 I$DL_01                |     1716 (+) |  1.000 |  0.773 | tgcctTTTCCg
 I$DL_01                |     1825 (-) |  0.897 |  0.764 | gGGAAGacacc
 I$DL_01                |     1953 (+) |  1.000 |  0.779 | ggaacTTTCCt
 I$DL_01                |     3048 (-) |  0.766 |  0.763 | gGGACAtacct
 I$DL_01                |     3154 (+) |  0.897 |  0.797 | tggagGTTCCa
 I$DL_01                |     3321 (+) |  1.000 |  0.825 | ggcctTTTCCt
 I$DL_01                |     4613 (-) |  0.766 |  0.809 | aGGTAAaacca
 I$DL_01                |     4637 (-) |  0.806 |  0.854 | aGCAAAatccc
 I$DL_01                |     4713 (+) |  0.671 |  0.771 | gggtaATTCAc
 I$DL_01                |     4884 (-) |  0.897 |  0.774 | tGGAACattcc
 I$DL_01                |     4949 (+) |  0.766 |  0.782 | gggacTTTCTg
 I$DL_01                |     5164 (+) |  0.766 |  0.782 | gggacTTTCAc
 I$DL_01                |     6135 (+) |  0.897 |  0.763 | ggcgtCTTCCa
 I$DL_01                |     6204 (+) |  0.671 |  0.768 | ggggtATGCCa
 I$DL_01                |     6708 (-) |  0.766 |  0.773 | gAGAAAagcca
 I$DL_01                |     6744 (-) |  0.766 |  0.766 | tTGAAAaccca
 I$DL_01                |     6795 (+) |  0.897 |  0.845 | tggctCTTCCt
 I$DL_01                |     6879 (-) |  0.897 |  0.829 | aGGAAGcacca
 I$DL_01                |     7001 (-) |  1.000 |  0.772 | tGGAAAaggca
 I$DL_01                |     7015 (+) |  1.000 |  0.809 | ggatgTTTCCt
 I$DL_01                |     8700 (-) |  0.806 |  0.791 | tGAAAAtacca
 I$DL_01                |     9123 (-) |  0.766 |  0.804 | cGGGAAaacct
 I$DL_01                |     9124 (-) |  1.000 |  0.761 | gGGAAAacctt
 I$DL_01                |     9580 (-) |  0.671 |  0.773 | tGGTATagccc
 I$DL_01                |    10640 (-) |  0.897 |  0.761 | aGGAAGacacc
 I$DL_01                |    10691 (-) |  0.766 |  0.810 | tGGCAAcaccc
 I$DL_01                |    10741 (+) |  0.766 |  0.767 | gggggTTTCAg
 I$DL_01                |    10846 (-) |  0.897 |  0.805 | aGGAAGaagcc
 I$DL_01                |    11087 (+) |  0.806 |  0.815 | gggaaTTTTCc
 I$DL_01                |    11088 (+) |  1.000 |  0.832 | ggaatTTTCCa
 I$DL_01                |    11477 (+) |  1.000 |  0.811 | ttgttTTTCCc
 I$SN_02                |       32 (-) |  0.972 |  0.930 | tgtgAACAActtca
 I$SN_02                |      440 (-) |  0.972 |  0.951 | tttaATCAGgttgt
 I$SN_02                |      577 (+) |  1.000 |  0.909 | tctacCTGTTgaat
 I$SN_02                |      636 (-) |  0.953 |  0.908 | tttaAACATttatt
 I$SN_02                |      731 (-) |  0.924 |  0.905 | agccACCACgtggt
 I$SN_02                |      735 (+) |  0.924 |  0.908 | accacGTGGTtgct
 I$SN_02                |      836 (-) |  0.972 |  0.886 | ataaAACAAgttaa
 I$SN_02                |     1195 (+) |  0.953 |  0.900 | gaaagCTGGTtata
 I$SN_02                |     1358 (+) |  0.972 |  0.886 | gtcacCTGATgctc
 I$SN_02                |     1523 (+) |  1.000 |  0.889 | tagagCTGTTtttt
 I$SN_02                |     1966 (-) |  0.972 |  0.933 | tttgAGCAGgttgg
 I$SN_02                |     2542 (-) |  1.000 |  0.893 | gaatAACAGgtttc
 I$SN_02                |     2579 (-) |  0.972 |  0.921 | ttacAACAAatgca
 I$SN_02                |     3442 (-) |  1.000 |  0.916 | aggtAACAGttaat
 I$SN_02                |     3641 (+) |  0.905 |  0.912 | accacATGGTggaa
 I$SN_02                |     3938 (+) |  0.972 |  0.895 | gtcacTTGTTcatt
 I$SN_02                |     4118 (+) |  0.953 |  0.921 | cccagATGTTaaaa
 I$SN_02                |     4524 (-) |  0.972 |  0.904 | agacAACAAatgcg
 I$SN_02                |     4811 (+) |  0.972 |  0.939 | ggcatTTGTTacca
 I$SN_02                |     5054 (-) |  0.972 |  0.951 | tctaAGCAGgtagt
 I$SN_02                |     5123 (-) |  1.000 |  0.945 | aggaAACAGatggt
 I$SN_02                |     5252 (+) |  0.924 |  0.902 | cacatGTGGTcaca
 I$SN_02                |     6064 (+) |  0.943 |  0.935 | tgcacGTGCTgcca
 I$SN_02                |     6596 (+) |  0.924 |  0.890 | ataagGTGGTgcta
 I$SN_02                |     6654 (-) |  1.000 |  0.958 | tgcaAACAGatgaa
 I$SN_02                |     6920 (+) |  0.943 |  0.907 | aggaaTTGATtgta
 I$SN_02                |     7346 (-) |  0.953 |  0.908 | tttcAACATgttaa
 I$SN_02                |     7391 (+) |  0.924 |  0.897 | tccagGTGGTagaa
 I$SN_02                |     7426 (+) |  0.972 |  0.902 | tttatTTGTTttta
 I$SN_02                |     7586 (-) |  0.972 |  0.897 | gtcaAACAAatgct
 I$SN_02                |     7590 (+) |  0.924 |  0.899 | aacaaATGCTctga
 I$SN_02                |     7922 (-) |  0.943 |  0.884 | aggtATCAAttcgt
 I$SN_02                |     8181 (+) |  0.972 |  0.927 | agaacTTGTTtgct
 I$SN_02                |     8417 (-) |  0.972 |  0.958 | tgtaAGCAGctgtt
 I$SN_02                |     8421 (+) |  1.000 |  0.904 | agcagCTGTTctag
 I$SN_02                |     8521 (+) |  0.924 |  0.894 | cacagATGCTtcaa
 I$SN_02                |     8764 (-) |  0.943 |  0.918 | tcccAGCACctggg
 I$SN_02                |     8965 (-) |  0.953 |  0.880 | gagaACCAGgtgtg
 I$SN_02                |     8996 (-) |  0.943 |  0.906 | ttccAGCACatgga
 I$SN_02                |     9536 (-) |  0.972 |  0.906 | aacaAACAAgtcct
 I$SN_02                |     9596 (-) |  0.924 |  0.901 | tcccAGCATttggg
 I$SN_02                |    10308 (+) |  1.000 |  0.923 | tttaaCTGTTttta
 I$SN_02                |    10374 (+) |  0.953 |  0.899 | tcaaaATGTTgcaa
 I$SN_02                |    10995 (-) |  0.972 |  0.924 | tggaATCAGattac
 I$SN_02                |    11064 (-) |  0.972 |  0.921 | tgtgATCAGttaca
 I$SN_02                |    11208 (+) |  0.972 |  0.909 | ttaatTTGTTtgaa
 I$SN_02                |    11740 (-) |  0.924 |  0.888 | tctcACCAAatgac
 I$SN_02                |    11777 (+) |  0.943 |  0.894 | gatacTTGATgtaa
 F$GCR1_01              |     4963 (-) |  1.000 |  0.934 | caGGAAGtc
 F$GCR1_01              |     5732 (-) |  1.000 |  0.967 | ctGGAAGcc
 F$GCR1_01              |     6276 (-) |  1.000 |  0.956 | aaGGAAGcc
 F$GCR1_01              |     8158 (+) |  1.000 |  0.935 | agCTTCCag
 F$GCR1_01              |     9436 (-) |  1.000 |  0.967 | caGGAAGcc
 F$GCR1_01              |    10639 (-) |  1.000 |  0.967 | gaGGAAGac
 F$ADR1_01              |      105 (+) |  1.000 |  0.996 | gGGGGT
 F$ADR1_01              |      972 (-) |  1.000 |  0.997 | ACCCCt
 F$ADR1_01              |     1187 (-) |  1.000 |  0.996 | ACCCCc
 F$ADR1_01              |     1612 (+) |  1.000 |  0.996 | gGGGGT
 F$ADR1_01              |     1695 (+) |  1.000 |  0.997 | aGGGGT
 F$ADR1_01              |     1839 (+) |  1.000 |  1.000 | tGGGGT
 F$ADR1_01              |     2428 (+) |  1.000 |  0.997 | aGGGGT
 F$ADR1_01              |     2641 (-) |  1.000 |  0.997 | ACCCCt
 F$ADR1_01              |     4827 (+) |  1.000 |  0.999 | cGGGGT
 F$ADR1_01              |     6000 (+) |  1.000 |  1.000 | tGGGGT
 F$ADR1_01              |     6203 (+) |  1.000 |  0.999 | cGGGGT
 F$ADR1_01              |     7197 (+) |  1.000 |  0.996 | gGGGGT
 F$ADR1_01              |     7957 (-) |  1.000 |  1.000 | ACCCCa
 F$ADR1_01              |     8359 (-) |  1.000 |  0.997 | ACCCCt
 F$ADR1_01              |     8485 (+) |  1.000 |  0.996 | gGGGGT
 F$ADR1_01              |     8737 (+) |  1.000 |  0.999 | cGGGGT
 F$ADR1_01              |     9342 (-) |  1.000 |  0.997 | ACCCCt
 F$ADR1_01              |     9687 (+) |  1.000 |  0.996 | gGGGGT
 F$ADR1_01              |    10741 (+) |  1.000 |  0.996 | gGGGGT
 F$ADR1_01              |    11616 (+) |  1.000 |  0.997 | aGGGGT
 F$ADR1_01              |    11708 (-) |  1.000 |  1.000 | ACCCCa
 F$ADR1_01              |    11824 (+) |  1.000 |  1.000 | tGGGGT
 F$ADR1_01              |    11846 (+) |  1.000 |  0.996 | gGGGGT
 F$ADR1_01              |    11851 (+) |  1.000 |  1.000 | tGGGGT
 F$ADR1_01              |    11859 (+) |  1.000 |  0.996 | gGGGGT
 V$NFKAPPAB50_01        |      105 (+) |  0.856 |  0.804 | GGGGGtggcc
 V$NFKAPPAB50_01        |      331 (+) |  0.630 |  0.790 | GGAAAttccc
 V$NFKAPPAB50_01        |      331 (-) |  0.864 |  0.845 | ggaaaTTCCC
 V$NFKAPPAB50_01        |     1183 (+) |  0.845 |  0.828 | GGGCAccccc
 V$NFKAPPAB50_01        |     1183 (-) |  0.856 |  0.893 | gggcaCCCCC
 V$NFKAPPAB50_01        |     1202 (-) |  0.845 |  0.795 | ggttaTACCC
 V$NFKAPPAB50_01        |     3393 (+) |  0.766 |  0.781 | GAGGAtctcc
 V$NFKAPPAB50_01        |     6205 (+) |  0.845 |  0.780 | GGGTAtgcca
 V$NFKAPPAB50_01        |    10114 (-) |  1.000 |  0.780 | tgccaTCCCC
 V$NFKAPPAB65_01        |      330 (+) |  0.862 |  0.900 | tggaaATTCC
 V$NFKAPPAB65_01        |      331 (-) |  1.000 |  1.000 | GGAAAttccc
 V$NFKAPPAB65_01        |     1667 (+) |  0.862 |  0.891 | tggagATTCC
 V$CREL_01              |      331 (-) |  1.000 |  0.990 | GGAAAttccc
 V$NFKAPPAB_01          |      331 (-) |  1.000 |  1.000 | ggaaaTTCCC
 V$NFKAPPAB_01          |     3048 (+) |  0.986 |  0.930 | GGGACatacc
 V$NMYC_01              |      734 (+) |  1.000 |  0.993 | caccACGTGgtt
 V$NMYC_01              |      734 (-) |  1.000 |  0.993 | cacCACGTggtt
 V$NMYC_01              |     1125 (-) |  1.000 |  0.988 | atgCACGTgtgt
 V$NMYC_01              |     6063 (+) |  1.000 |  0.986 | ctgcACGTGctg
 V$NMYC_01              |     6063 (-) |  1.000 |  0.987 | ctgCACGTgctg
 V$MYOGNF1_01           |      110 (+) |  0.900 |  0.622 | tggccagtgaggCTGGCtaactgctcagt
 V$MYOGNF1_01           |      306 (+) |  0.616 |  0.626 | gagctatctctcCTAGTcctgtgctggaa
 V$MYOGNF1_01           |      415 (-) |  0.728 |  0.635 | gggtgagcttgtCCAAAataccacgttta
 V$MYOGNF1_01           |      451 (+) |  1.000 |  0.623 | tgtctgttttggTTGGCttatttgacact
 V$MYOGNF1_01           |      710 (+) |  0.779 |  0.708 | atctctttacagATGGTtgtgagccacca
 V$MYOGNF1_01           |      720 (-) |  0.851 |  0.623 | agatggttgtgaGCCACcacgtggttgct
 V$MYOGNF1_01           |      857 (+) |  0.715 |  0.629 | cgatcgttgcccTTAGAaatgcacaaaca
 V$MYOGNF1_01           |      873 (-) |  0.715 |  0.628 | aaatgcacaaacACGAAatgggacagact
 V$MYOGNF1_01           |      991 (+) |  0.762 |  0.665 | aataattttcatGTGGGgacgcacctata
 V$MYOGNF1_01           |     1361 (+) |  0.817 |  0.671 | acctgatgctcgTTTGCagtgggcgaggt
 V$MYOGNF1_01           |     1371 (-) |  0.687 |  0.679 | cgtttgcagtggGCGAGgtagggcaggtg
 V$MYOGNF1_01           |     2306 (+) |  0.929 |  0.675 | tgtctgtgtgttTTGGAtacagtcttgct
 V$MYOGNF1_01           |     2988 (-) |  0.929 |  0.672 | tacttccgctccTCCAAggtgcgcaggcg
 V$MYOGNF1_01           |     3225 (-) |  1.000 |  0.638 | ttttaccagtcaGCCAAcattcccagccc
 V$MYOGNF1_01           |     3273 (+) |  0.911 |  0.673 | atgccattatgaTTGGGatgaggtgaaca
 V$MYOGNF1_01           |     3307 (+) |  1.000 |  0.632 | atgtagttaagaTTGGCcttttcctgatt
 V$MYOGNF1_01           |     3388 (-) |  0.829 |  0.637 | gccctgaggatcTCCAGttataaaagtta
 V$MYOGNF1_01           |     3588 (+) |  0.911 |  0.651 | actctcctatgtTTGGGtttctgcagttt
 V$MYOGNF1_01           |     3667 (+) |  0.668 |  0.675 | cacagacttagaATTGCcaagtgccaaga
 V$MYOGNF1_01           |     3677 (-) |  1.000 |  0.705 | gaattgccaagtGCCAAgaacacaagaga
 V$MYOGNF1_01           |     3755 (+) |  0.637 |  0.623 | agtcattcttaaAAGGCaatgctccttcc
 V$MYOGNF1_01           |     4129 (+) |  0.715 |  0.636 | aaacccagaatcTAGGTgtggtgcctccc
 V$MYOGNF1_01           |     4263 (-) |  0.715 |  0.667 | gttaggatgcttACCTAagcacacattag
 V$MYOGNF1_01           |     4542 (+) |  0.746 |  0.648 | cagcctcttagtTTTGAtgctggacacag
 V$MYOGNF1_01           |     4718 (+) |  1.000 |  0.623 | attcactgtgatTTGGCcctcgctgatgg
 V$MYOGNF1_01           |     4731 (+) |  0.779 |  0.673 | tggccctcgctgATGGTcctctcccctct
 V$MYOGNF1_01           |     4890 (+) |  1.000 |  0.702 | attccatgttccTTGGCcaagtgcatgct
 V$MYOGNF1_01           |     4969 (-) |  0.698 |  0.657 | gtcaggctcagcCCCTAcctgtccgaatg
 V$MYOGNF1_01           |     5106 (-) |  0.746 |  0.719 | atttgtgagtgcTCAAAaggaaacagatg
 V$MYOGNF1_01           |     5145 (-) |  0.715 |  0.716 | cctaggcagtttACGAAaagggactttca
 V$MYOGNF1_01           |     5630 (-) |  0.665 |  0.674 | cactgggataaaGACAAaataaaaagaag
 V$MYOGNF1_01           |     5726 (-) |  0.851 |  0.625 | actaaactggaaGCCATaatatagacgca
 V$MYOGNF1_01           |     5858 (+) |  0.779 |  0.631 | agttggtttcccATGGAccatctcctgct
 V$MYOGNF1_01           |     5874 (+) |  0.817 |  0.732 | accatctcctgcTGGGCatggggcccgcc
 V$MYOGNF1_01           |     5879 (+) |  0.762 |  0.633 | ctcctgctgggcATGGGgcccgcccctaa
 V$MYOGNF1_01           |     5884 (-) |  0.718 |  0.679 | gctgggcatgggGCCCGcccctaagagta
 V$MYOGNF1_01           |     6169 (-) |  0.746 |  0.665 | cttctgcagggtTCCCAgagacacccatt
 V$MYOGNF1_01           |     6575 (-) |  0.746 |  0.663 | gttatgcaaaacACAAAacaaataaggtg
 V$MYOGNF1_01           |     6717 (+) |  0.597 |  0.630 | cacaacctttaaAGGGTgagcagcccttt
 V$MYOGNF1_01           |     6931 (-) |  0.911 |  0.641 | gtatgtgcagtaCCCAAgtgatactgtcc
 V$MYOGNF1_01           |     7336 (-) |  0.597 |  0.626 | aatagacacattTCAACatgttaatcatg
 V$MYOGNF1_01           |     7379 (-) |  0.829 |  0.672 | atattgcttgtgTCCAGgtggtagaatta
 V$MYOGNF1_01           |     7490 (+) |  0.929 |  0.693 | cgtctgttcttcTTGGAgggtgtcagatg
 V$MYOGNF1_01           |     7526 (+) |  0.929 |  0.813 | ctgaagttacagTTGGTtgtgagccaact
 V$MYOGNF1_01           |     7536 (-) |  1.000 |  0.626 | agttggttgtgaGCCAActgtgtagatgc
 V$MYOGNF1_01           |     7937 (+) |  0.746 |  0.696 | tgtgtgtttagtTTTGAgataccccagac
 V$MYOGNF1_01           |     7947 (-) |  0.811 |  0.633 | gttttgagatacCCCAGactatagttgtt
 V$MYOGNF1_01           |     8332 (+) |  0.829 |  0.636 | cgccagtatttgCTGGAccacttgccaac
 V$MYOGNF1_01           |     8426 (+) |  0.817 |  0.660 | ctgttctagagcTTTGCaacccgcatcct
 V$MYOGNF1_01           |     8826 (-) |  0.929 |  0.677 | tcgatgttcaaaACCAAaacagaacggtt
 V$MYOGNF1_01           |     8827 (-) |  0.728 |  0.628 | cgatgttcaaaaCCAAAacagaacggttt
 V$MYOGNF1_01           |     9045 (+) |  0.851 |  0.623 | agcctggtctacATGGCaagttccaggct
 V$MYOGNF1_01           |     9309 (+) |  0.911 |  0.667 | aggagggaggcgTTGGGtcagagcctctg
 V$MYOGNF1_01           |     9364 (+) |  0.597 |  0.623 | gttctctatcacAGGGAgagctgtcagcc
 V$MYOGNF1_01           |     9389 (+) |  0.779 |  0.702 | agcccctggaatGTGGTtctatgtctaga
 V$MYOGNF1_01           |     9838 (+) |  0.687 |  0.647 | taattttaaagtCAGGCaggcagcattaa
 V$MYOGNF1_01           |     9903 (+) |  0.829 |  0.718 | aagacttacttaCTGGAtttttgcctatg
 V$MYOGNF1_01           |     9918 (+) |  0.746 |  0.655 | gatttttgcctaTGGGTaatttgcatgta
 V$MYOGNF1_01           |    10481 (-) |  0.646 |  0.622 | accagccacataTCAAGgatcaaaagtca
 V$MYOGNF1_01           |    10501 (+) |  0.851 |  0.627 | caaaagtcaattATGGCtgtagccattat
 V$MYOGNF1_01           |    10645 (-) |  0.698 |  0.626 | gacacccagtgtCCTAAtgtcaacaggag
 V$MYOGNF1_01           |    10753 (+) |  0.817 |  0.636 | gatccgtgtgttTGGGCactagaactctg
 V$MYOGNF1_01           |    10878 (-) |  0.634 |  0.663 | ggtgggagcactGCACAtgcgcagagacg
 V$MYOGNF1_01           |    10958 (+) |  0.929 |  0.623 | ggtctgtgcctgTTGGAgcaaggagcctg
 V$MYOGNF1_01           |    11083 (-) |  0.779 |  0.664 | ctctgggaatttTCCACtgtttaaagaac
 V$MYOGNF1_01           |    11234 (-) |  0.929 |  0.656 | ttctaactggagTCCAAaactctgtggtg
 V$MYOGNF1_01           |    11252 (-) |  1.000 |  0.630 | actctgtggtgtGCCAAgaaaaggaaatt
 V$MYOGNF1_01           |    11279 (-) |  0.817 |  0.699 | ttaaggcataggGCAAAgaaataataata
 V$MYOGNF1_01           |    11415 (+) |  0.787 |  0.706 | ctgcatttctatTTAGCtatccgcatact
 V$MYOGNF1_01           |    11476 (+) |  0.929 |  0.622 | tttgtttttcccTTGGAatgcggttgaat
 V$MYOGNF1_01           |    11574 (-) |  0.829 |  0.645 | tcattgcttataTCCAGgagtgagactag
 V$MYOGNF1_01           |    11761 (-) |  0.829 |  0.623 | agttaacaggatTCCAGatacttgatgta
 V$MYOGNF1_01           |    11787 (-) |  0.811 |  0.674 | gtaaggacaaatCCCAGattggaaggtgg
 V$MYOGNF1_01           |    11793 (+) |  0.929 |  0.662 | acaaatcccagaTTGGAaggtggcccagg
 V$MYOGNF1_01           |    11845 (+) |  0.762 |  0.626 | ggggggtggggtATGGGggtaggtccggg
 V$MYOGNF1_01           |    11915 (-) |  0.817 |  0.651 | ttcgggcccaacGCCCAttggctgaaact
 V$YY1_01               |      522 (-) |  0.922 |  0.925 | ttttaaaaATGATgggt
 V$YY1_01               |      714 (-) |  1.000 |  0.963 | ctttacagATGGTtgtg
 V$YY1_01               |      798 (+) |  0.998 |  0.955 | ctgaGCCATttctccag
 V$YY1_01               |      882 (-) |  0.996 |  0.944 | aacacgaaATGGGacag
 V$YY1_01               |     1173 (-) |  0.996 |  0.949 | gaaaggagATGGGcacc
 V$YY1_01               |     1658 (-) |  1.000 |  0.970 | cttggcaaATGGAgatt
 V$YY1_01               |     1883 (+) |  0.996 |  0.975 | gcctCCCATtttatatt
 V$YY1_01               |     2610 (+) |  0.998 |  0.940 | aagaGCCATgtgtatgc
 V$YY1_01               |     2833 (-) |  0.998 |  0.963 | gtctgcaaATGGCatca
 V$YY1_01               |     3145 (-) |  1.000 |  0.974 | aacaatatATGGAggtt
 V$YY1_01               |     3300 (+) |  1.000 |  0.980 | catcTCCATgtagttaa
 V$YY1_01               |     3375 (-) |  0.996 |  0.956 | ctaatcatATGGGgccc
 V$YY1_01               |     3638 (-) |  1.000 |  0.938 | cctaccacATGGTggaa
 V$YY1_01               |     3836 (+) |  1.000 |  0.920 | aattTCCATtctcataa
 V$YY1_01               |     3859 (+) |  1.000 |  0.982 | cagtACCATttaaggag
 V$YY1_01               |     3983 (+) |  1.000 |  0.966 | agacACCATctcatgaa
 V$YY1_01               |     4106 (+) |  1.000 |  0.990 | aacaTCCATtttcccag
 V$YY1_01               |     4151 (+) |  0.996 |  0.950 | gcctCCCATttgtaatc
 V$YY1_01               |     4888 (+) |  1.000 |  0.973 | acatTCCATgttccttg
 V$YY1_01               |     5124 (-) |  1.000 |  0.942 | ggaaacagATGGTgcgg
 V$YY1_01               |     5237 (-) |  0.996 |  0.954 | acgattacATGGGttca
 V$YY1_01               |     5285 (-) |  0.996 |  0.932 | aggctcagATGGGctag
 V$YY1_01               |     5303 (-) |  0.998 |  0.979 | catccaaaATGGCttct
 V$YY1_01               |     5443 (+) |  0.998 |  0.969 | tattGCCATataacctt
 V$YY1_01               |     5870 (+) |  1.000 |  0.938 | atggACCATctcctgct
 V$YY1_01               |     6032 (+) |  0.996 |  0.937 | aggaCCCATctggtgca
 V$YY1_01               |     6188 (+) |  0.996 |  0.960 | gacaCCCATttaagccg
 V$YY1_01               |     6258 (+) |  0.996 |  0.947 | ttgtCCCATctgccgaa
 V$YY1_01               |     6992 (-) |  1.000 |  0.955 | gtgaggagATGGAaaag
 V$YY1_01               |     7171 (-) |  1.000 |  0.943 | cgttgcagATGGTcccg
 V$YY1_01               |     7508 (-) |  0.998 |  0.943 | ggtgtcagATGGCctga
 V$YY1_01               |     7608 (+) |  0.998 |  0.951 | ctgaGCCATctctccag
 V$YY1_01               |     8572 (-) |  0.996 |  0.968 | ttgattaaATGGGgcaa
 V$YY1_01               |     8997 (-) |  1.000 |  0.944 | tccagcacATGGAggca
 V$YY1_01               |     9049 (-) |  0.998 |  0.956 | tggtctacATGGCaagt
 V$YY1_01               |     9512 (+) |  0.996 |  0.938 | tttcCCCATgtccaaca
 V$YY1_01               |    10103 (+) |  0.998 |  0.974 | ctgaGCCATcttgccat
 V$YY1_01               |    10384 (+) |  1.000 |  0.979 | gcaaTCCATataaaaat
 V$YY1_01               |    11342 (+) |  0.998 |  0.917 | aaatGCCATtatcgaac
 V$YY1_01               |    11536 (-) |  1.000 |  0.935 | tcccacatATGGTagat
 V$YY1_01               |    11543 (-) |  0.996 |  0.966 | tatggtagATGGGtatt
 V$YY1_01               |    11720 (+) |  1.000 |  0.982 | ctccACCATtttctcaa
 I$SN_01                |     1785 (-) |  1.000 |  0.948 | gagcACCTGccat
 I$SN_01                |     8502 (+) |  1.000 |  0.983 | gggaCAGGTgcgg
 I$SN_01                |    11960 (-) |  1.000 |  0.939 | ctgcACCTGagct
 V$IRF1_01              |      224 (-) |  0.978 |  0.879 | tttttcctTTTTG
 V$IRF1_01              |      900 (-) |  0.811 |  0.861 | cttttcacTTTCT
 V$IRF1_01              |     1956 (-) |  0.934 |  0.882 | actttcctTTTTT
 V$IRF1_01              |     2508 (+) |  0.934 |  0.882 | AAAAAgggaaaaa
 V$IRF1_01              |     5942 (+) |  1.000 |  0.858 | GAAAAgtaaaatt
 V$IRF1_01              |     7848 (+) |  0.978 |  0.869 | CAAAAgcgacagc
 V$IRF1_01              |     8834 (+) |  0.978 |  0.857 | CAAAAccaaaaca
 V$IRF1_01              |     9104 (+) |  0.978 |  0.873 | CAAAAgcaaaaca
 F$PHO4_01              |     1125 (+) |  1.000 |  0.979 | atgCACGTgtgt
 V$TAL1BETAE47_01       |       39 (+) |  1.000 |  0.877 | aacttCAGATgtcatt
 V$TAL1BETAE47_01       |      714 (+) |  1.000 |  0.972 | ctttaCAGATggttgt
 V$TAL1BETAE47_01       |     1355 (-) |  0.894 |  0.809 | tgggtcACCTGatgct
 V$TAL1BETAE47_01       |     1358 (+) |  0.780 |  0.794 | gtcacCTGATgctcgt
 V$TAL1BETAE47_01       |     1707 (-) |  0.780 |  0.791 | agcaccCTCTGccttt
 V$TAL1BETAE47_01       |     1783 (-) |  0.894 |  0.837 | tggagcACCTGccatt
 V$TAL1BETAE47_01       |     1857 (-) |  0.885 |  0.814 | agagccAACTGaagaa
 V$TAL1BETAE47_01       |     2823 (+) |  0.885 |  0.814 | ctgtcCAGTTgtctgc
 V$TAL1BETAE47_01       |     2967 (+) |  1.000 |  0.847 | gacggCAGATgcgcag
 V$TAL1BETAE47_01       |     3638 (+) |  0.780 |  0.828 | cctacCACATggtgga
 V$TAL1BETAE47_01       |     3697 (+) |  0.780 |  0.807 | cacaaGAGATgcttga
 V$TAL1BETAE47_01       |     3984 (-) |  0.780 |  0.815 | gacaccATCTCatgaa
 V$TAL1BETAE47_01       |     4115 (+) |  1.000 |  0.939 | tttccCAGATgttaaa
 V$TAL1BETAE47_01       |     4336 (+) |  0.894 |  0.883 | acatcCAGGTggtgga
 V$TAL1BETAE47_01       |     4358 (+) |  0.780 |  0.802 | aggatCAGAAgtttaa
 V$TAL1BETAE47_01       |     4563 (+) |  0.885 |  0.791 | ggacaCAGTTgcggtt
 V$TAL1BETAE47_01       |     4735 (+) |  0.780 |  0.793 | cctcgCTGATggtcct
 V$TAL1BETAE47_01       |     5124 (+) |  1.000 |  0.994 | ggaaaCAGATggtgcg
 V$TAL1BETAE47_01       |     5285 (+) |  1.000 |  0.884 | aggctCAGATgggcta
 V$TAL1BETAE47_01       |     5616 (-) |  0.780 |  0.799 | accaacATCTAataca
 V$TAL1BETAE47_01       |     5871 (-) |  0.780 |  0.816 | tggaccATCTCctgct
 V$TAL1BETAE47_01       |     5980 (-) |  0.780 |  0.787 | gataacTTCTGgatta
 V$TAL1BETAE47_01       |     6033 (-) |  1.000 |  0.915 | ggacccATCTGgtgca
 V$TAL1BETAE47_01       |     6259 (-) |  1.000 |  0.881 | tgtcccATCTGccgaa
 V$TAL1BETAE47_01       |     6493 (+) |  1.000 |  0.843 | gattgCAGATgcggcc
 V$TAL1BETAE47_01       |     6655 (+) |  1.000 |  0.895 | gcaaaCAGATgaagat
 V$TAL1BETAE47_01       |     6842 (-) |  0.885 |  0.850 | actgccAACTGgtgag
 V$TAL1BETAE47_01       |     7025 (+) |  0.882 |  0.786 | tgcatCAGCTgaagag
 V$TAL1BETAE47_01       |     7025 (-) |  0.882 |  0.827 | tgcatcAGCTGaagag
 V$TAL1BETAE47_01       |     7171 (+) |  1.000 |  0.946 | cgttgCAGATggtccc
 V$TAL1BETAE47_01       |     7388 (+) |  0.894 |  0.887 | gtgtcCAGGTggtaga
 V$TAL1BETAE47_01       |     7508 (+) |  1.000 |  0.897 | ggtgtCAGATggcctg
 V$TAL1BETAE47_01       |     7530 (+) |  0.885 |  0.892 | agttaCAGTTggttgt
 V$TAL1BETAE47_01       |     7545 (-) |  0.885 |  0.841 | tgagccAACTGtgtag
 V$TAL1BETAE47_01       |     7587 (+) |  0.780 |  0.808 | tcaaaCAAATgctctg
 V$TAL1BETAE47_01       |     7677 (+) |  0.882 |  0.812 | gctcaCAGCTgtaaag
 V$TAL1BETAE47_01       |     7677 (-) |  0.882 |  0.811 | gctcacAGCTGtaaag
 V$TAL1BETAE47_01       |     8237 (+) |  1.000 |  0.856 | acaccCAGATgaaggt
 V$TAL1BETAE47_01       |     8265 (+) |  0.780 |  0.792 | ttgacCTGATgatgca
 V$TAL1BETAE47_01       |     8418 (+) |  0.882 |  0.870 | gtaagCAGCTgttcta
 V$TAL1BETAE47_01       |     8418 (-) |  0.882 |  0.879 | gtaagcAGCTGttcta
 V$TAL1BETAE47_01       |     8501 (+) |  0.894 |  0.803 | agggaCAGGTgcggga
 V$TAL1BETAE47_01       |     8518 (+) |  1.000 |  0.935 | actcaCAGATgcttca
 V$TAL1BETAE47_01       |     8590 (-) |  0.780 |  0.803 | ggcaacATCTTtaata
 V$TAL1BETAE47_01       |     8765 (-) |  0.894 |  0.848 | cccagcACCTGggagg
 V$TAL1BETAE47_01       |     8809 (-) |  0.780 |  0.791 | gccagcTTCTGgtact
 V$TAL1BETAE47_01       |     8966 (+) |  0.894 |  0.826 | agaacCAGGTgtggtg
 V$TAL1BETAE47_01       |    10709 (-) |  0.780 |  0.806 | tgaaacATCTCtgcgt
 V$TAL1BETAE47_01       |    11536 (+) |  0.780 |  0.819 | tcccaCATATggtaga
 V$TAL1BETAE47_01       |    11707 (-) |  0.885 |  0.803 | caccccAACTGccctc
 V$TAL1ALPHAE47_01      |       39 (+) |  1.000 |  0.868 | aacttCAGATgtcatt
 V$TAL1ALPHAE47_01      |      143 (-) |  0.810 |  0.769 | ccagacATTTGctcat
 V$TAL1ALPHAE47_01      |      714 (+) |  1.000 |  0.968 | ctttaCAGATggttgt
 V$TAL1ALPHAE47_01      |      732 (+) |  0.696 |  0.768 | gccacCACGTggttgc
 V$TAL1ALPHAE47_01      |      732 (-) |  0.696 |  0.769 | gccaccACGTGgttgc
 V$TAL1ALPHAE47_01      |     1024 (+) |  0.875 |  0.760 | attggCAGTTgaatca
 V$TAL1ALPHAE47_01      |     1173 (+) |  0.772 |  0.743 | gaaagGAGATgggcac
 V$TAL1ALPHAE47_01      |     1192 (+) |  0.655 |  0.745 | caggaAAGCTggttat
 V$TAL1ALPHAE47_01      |     1259 (-) |  0.772 |  0.788 | gtcatcATCCGtgtgt
 V$TAL1ALPHAE47_01      |     1355 (-) |  0.886 |  0.790 | tgggtcACCTGatgct
 V$TAL1ALPHAE47_01      |     1358 (+) |  0.772 |  0.786 | gtcacCTGATgctcgt
 V$TAL1ALPHAE47_01      |     1389 (+) |  0.886 |  0.777 | tagggCAGGTgaggag
 V$TAL1ALPHAE47_01      |     1658 (+) |  0.810 |  0.750 | cttggCAAATggagat
 V$TAL1ALPHAE47_01      |     1707 (-) |  0.772 |  0.790 | agcaccCTCTGccttt
 V$TAL1ALPHAE47_01      |     1783 (-) |  0.886 |  0.837 | tggagcACCTGccatt
 V$TAL1ALPHAE47_01      |     1857 (-) |  0.875 |  0.796 | agagccAACTGaagaa
 V$TAL1ALPHAE47_01      |     1873 (-) |  1.000 |  0.763 | gggaggATCTGcctcc
 V$TAL1ALPHAE47_01      |     1993 (-) |  1.000 |  0.769 | aagattATCTGgctat
 V$TAL1ALPHAE47_01      |     2580 (+) |  0.810 |  0.766 | tacaaCAAATgcagta
 V$TAL1ALPHAE47_01      |     2611 (-) |  0.810 |  0.791 | agagccATGTGtatgc
 V$TAL1ALPHAE47_01      |     2626 (+) |  0.810 |  0.785 | ctaggCAAATgctcta
 V$TAL1ALPHAE47_01      |     2726 (-) |  0.772 |  0.755 | ataatcTTCTGccttt
 V$TAL1ALPHAE47_01      |     2823 (+) |  0.875 |  0.802 | ctgtcCAGTTgtctgc
 V$TAL1ALPHAE47_01      |     2833 (+) |  0.810 |  0.761 | gtctgCAAATggcatc
 V$TAL1ALPHAE47_01      |     2906 (-) |  0.772 |  0.745 | atccacATCTCtgtgg
 V$TAL1ALPHAE47_01      |     2967 (+) |  1.000 |  0.853 | gacggCAGATgcgcag
 V$TAL1ALPHAE47_01      |     3295 (-) |  0.772 |  0.777 | gtgaacATCTCcatgt
 V$TAL1ALPHAE47_01      |     3375 (+) |  0.818 |  0.767 | ctaatCATATggggcc
 V$TAL1ALPHAE47_01      |     3375 (-) |  0.818 |  0.794 | ctaatcATATGgggcc
 V$TAL1ALPHAE47_01      |     3638 (+) |  0.810 |  0.841 | cctacCACATggtgga
 V$TAL1ALPHAE47_01      |     3638 (-) |  0.704 |  0.773 | cctaccACATGgtgga
 V$TAL1ALPHAE47_01      |     3697 (+) |  0.772 |  0.803 | cacaaGAGATgcttga
 V$TAL1ALPHAE47_01      |     3984 (-) |  0.772 |  0.805 | gacaccATCTCatgaa
 V$TAL1ALPHAE47_01      |     4115 (+) |  1.000 |  0.941 | tttccCAGATgttaaa
 V$TAL1ALPHAE47_01      |     4152 (-) |  0.810 |  0.780 | cctcccATTTGtaatc
 V$TAL1ALPHAE47_01      |     4183 (+) |  0.772 |  0.753 | ctgagCAGAAggctgc
 V$TAL1ALPHAE47_01      |     4336 (+) |  0.886 |  0.872 | acatcCAGGTggtgga
 V$TAL1ALPHAE47_01      |     4358 (+) |  0.772 |  0.789 | aggatCAGAAgtttaa
 V$TAL1ALPHAE47_01      |     4509 (-) |  0.772 |  0.782 | aacaacATCAGaccaa
 V$TAL1ALPHAE47_01      |     4525 (+) |  0.810 |  0.768 | gacaaCAAATgcgtca
 V$TAL1ALPHAE47_01      |     4563 (+) |  0.875 |  0.792 | ggacaCAGTTgcggtt
 V$TAL1ALPHAE47_01      |     4735 (+) |  0.772 |  0.785 | cctcgCTGATggtcct
 V$TAL1ALPHAE47_01      |     4750 (-) |  0.772 |  0.754 | tctcccCTCTGtaggt
 V$TAL1ALPHAE47_01      |     4808 (-) |  0.810 |  0.779 | tctggcATTTGttacc
 V$TAL1ALPHAE47_01      |     4924 (+) |  1.000 |  0.786 | acttaCAGATcatgga
 V$TAL1ALPHAE47_01      |     5124 (+) |  1.000 |  0.994 | ggaaaCAGATggtgcg
 V$TAL1ALPHAE47_01      |     5124 (-) |  0.701 |  0.757 | ggaaacAGATGgtgcg
 V$TAL1ALPHAE47_01      |     5249 (+) |  0.704 |  0.778 | gttcaCATGTggtcac
 V$TAL1ALPHAE47_01      |     5249 (-) |  0.810 |  0.772 | gttcacATGTGgtcac
 V$TAL1ALPHAE47_01      |     5285 (+) |  1.000 |  0.871 | aggctCAGATgggcta
 V$TAL1ALPHAE47_01      |     5616 (-) |  0.772 |  0.791 | accaacATCTAataca
 V$TAL1ALPHAE47_01      |     5871 (-) |  0.772 |  0.805 | tggaccATCTCctgct
 V$TAL1ALPHAE47_01      |     5980 (-) |  0.772 |  0.786 | gataacTTCTGgatta
 V$TAL1ALPHAE47_01      |     6033 (+) |  0.701 |  0.748 | ggaccCATCTggtgca
 V$TAL1ALPHAE47_01      |     6033 (-) |  1.000 |  0.907 | ggacccATCTGgtgca
 V$TAL1ALPHAE47_01      |     6112 (+) |  0.772 |  0.766 | ttgacCAGAGggcttg
 V$TAL1ALPHAE47_01      |     6259 (-) |  1.000 |  0.884 | tgtcccATCTGccgaa
 V$TAL1ALPHAE47_01      |     6283 (+) |  0.772 |  0.749 | cctctCTGATgatgac
 V$TAL1ALPHAE47_01      |     6493 (+) |  1.000 |  0.845 | gattgCAGATgcggcc
 V$TAL1ALPHAE47_01      |     6632 (+) |  0.772 |  0.746 | gcaccCAGAAggcacc
 V$TAL1ALPHAE47_01      |     6655 (+) |  1.000 |  0.894 | gcaaaCAGATgaagat
 V$TAL1ALPHAE47_01      |     6842 (+) |  0.693 |  0.753 | actgcCAACTggtgag
 V$TAL1ALPHAE47_01      |     6842 (-) |  0.875 |  0.829 | actgccAACTGgtgag
 V$TAL1ALPHAE47_01      |     7009 (+) |  0.772 |  0.785 | gcaggCGGATgtttcc
 V$TAL1ALPHAE47_01      |     7025 (+) |  0.883 |  0.778 | tgcatCAGCTgaagag
 V$TAL1ALPHAE47_01      |     7025 (-) |  0.883 |  0.821 | tgcatcAGCTGaagag
 V$TAL1ALPHAE47_01      |     7109 (+) |  0.810 |  0.768 | tgtacCACATgtgtgc
 V$TAL1ALPHAE47_01      |     7109 (-) |  0.704 |  0.774 | tgtaccACATGtgtgc
 V$TAL1ALPHAE47_01      |     7111 (-) |  0.810 |  0.775 | taccacATGTGtgcaa
 V$TAL1ALPHAE47_01      |     7171 (+) |  1.000 |  0.938 | cgttgCAGATggtccc
 V$TAL1ALPHAE47_01      |     7388 (+) |  0.886 |  0.874 | gtgtcCAGGTggtaga
 V$TAL1ALPHAE47_01      |     7485 (-) |  0.772 |  0.768 | gcgcacGTCTGttctt
 V$TAL1ALPHAE47_01      |     7508 (+) |  1.000 |  0.890 | ggtgtCAGATggcctg
 V$TAL1ALPHAE47_01      |     7530 (+) |  0.875 |  0.884 | agttaCAGTTggttgt
 V$TAL1ALPHAE47_01      |     7545 (-) |  0.875 |  0.831 | tgagccAACTGtgtag
 V$TAL1ALPHAE47_01      |     7553 (+) |  0.772 |  0.754 | ctgtgTAGATgctgga
 V$TAL1ALPHAE47_01      |     7575 (-) |  0.772 |  0.756 | atccccATCAGgtcaa
 V$TAL1ALPHAE47_01      |     7587 (+) |  0.810 |  0.836 | tcaaaCAAATgctctg
 V$TAL1ALPHAE47_01      |     7609 (-) |  0.772 |  0.772 | tgagccATCTCtccag
 V$TAL1ALPHAE47_01      |     7677 (+) |  0.883 |  0.820 | gctcaCAGCTgtaaag
 V$TAL1ALPHAE47_01      |     7677 (-) |  0.883 |  0.819 | gctcacAGCTGtaaag
 V$TAL1ALPHAE47_01      |     7883 (-) |  0.810 |  0.753 | gaagtcATTTGgtttt
 V$TAL1ALPHAE47_01      |     8217 (+) |  0.772 |  0.771 | cagttCTGATgttggc
 V$TAL1ALPHAE47_01      |     8237 (+) |  1.000 |  0.849 | acaccCAGATgaaggt
 V$TAL1ALPHAE47_01      |     8265 (+) |  0.772 |  0.787 | ttgacCTGATgatgca
 V$TAL1ALPHAE47_01      |     8274 (+) |  0.883 |  0.776 | tgatgCAGCTgccctg
 V$TAL1ALPHAE47_01      |     8274 (-) |  0.883 |  0.766 | tgatgcAGCTGccctg
 V$TAL1ALPHAE47_01      |     8315 (-) |  0.772 |  0.754 | tgcagcTTCTGcgtca
 V$TAL1ALPHAE47_01      |     8345 (-) |  0.696 |  0.744 | tggaccACTTGccaac
 V$TAL1ALPHAE47_01      |     8418 (+) |  0.883 |  0.872 | gtaagCAGCTgttcta
 V$TAL1ALPHAE47_01      |     8418 (-) |  0.883 |  0.885 | gtaagcAGCTGttcta
 V$TAL1ALPHAE47_01      |     8501 (+) |  0.886 |  0.808 | agggaCAGGTgcggga
 V$TAL1ALPHAE47_01      |     8518 (+) |  1.000 |  0.940 | actcaCAGATgcttca
 V$TAL1ALPHAE47_01      |     8590 (-) |  0.772 |  0.812 | ggcaacATCTTtaata
 V$TAL1ALPHAE47_01      |     8667 (-) |  0.658 |  0.761 | caaaccACCGGttagg
 V$TAL1ALPHAE47_01      |     8765 (-) |  0.886 |  0.842 | cccagcACCTGggagg
 V$TAL1ALPHAE47_01      |     8809 (-) |  0.772 |  0.784 | gccagcTTCTGgtact
 V$TAL1ALPHAE47_01      |     8966 (+) |  0.886 |  0.818 | agaacCAGGTgtggtg
 V$TAL1ALPHAE47_01      |     8966 (-) |  0.693 |  0.762 | agaaccAGGTGtggtg
 V$TAL1ALPHAE47_01      |     8997 (+) |  0.810 |  0.769 | tccagCACATggaggc
 V$TAL1ALPHAE47_01      |     9017 (+) |  1.000 |  0.783 | gcaggCAGATctttgt
 V$TAL1ALPHAE47_01      |     9148 (+) |  0.818 |  0.772 | agacaCATATgtgagt
 V$TAL1ALPHAE47_01      |     9148 (-) |  0.818 |  0.775 | agacacATATGtgagt
 V$TAL1ALPHAE47_01      |     9327 (-) |  0.772 |  0.768 | cagagcCTCTGgagga
 V$TAL1ALPHAE47_01      |     9497 (-) |  1.000 |  0.771 | tagaaaATCTGaaagt
 V$TAL1ALPHAE47_01      |     9597 (-) |  0.810 |  0.789 | cccagcATTTGggaag
 V$TAL1ALPHAE47_01      |    10095 (-) |  0.772 |  0.774 | cttaacCTCTGagcca
 V$TAL1ALPHAE47_01      |    10104 (-) |  0.772 |  0.750 | tgagccATCTTgccat
 V$TAL1ALPHAE47_01      |    10709 (-) |  0.772 |  0.810 | tgaaacATCTCtgcgt
 V$TAL1ALPHAE47_01      |    11367 (-) |  1.000 |  0.753 | gattctATCTGtgctt
 V$TAL1ALPHAE47_01      |    11536 (+) |  0.818 |  0.852 | tcccaCATATggtaga
 V$TAL1ALPHAE47_01      |    11536 (-) |  0.818 |  0.776 | tcccacATATGgtaga
 V$TAL1ALPHAE47_01      |    11619 (+) |  0.772 |  0.751 | ggtacCAGAAggaccc
 V$TAL1ALPHAE47_01      |    11707 (-) |  0.875 |  0.802 | caccccAACTGccctc
 V$TAL1ALPHAE47_01      |    11733 (-) |  0.772 |  0.780 | tcaaacATCTCaccaa
 V$TAL1ALPHAE47_01      |    11741 (+) |  0.810 |  0.754 | ctcacCAAATgactag
 V$TAL1ALPHAE47_01      |    11770 (+) |  1.000 |  0.762 | gattcCAGATacttga
 V$TAL1ALPHAE47_01      |    11958 (-) |  0.886 |  0.763 | gactgcACCTGagctc
 I$HAIRY_01             |     5818 (-) |  1.000 |  0.887 | ccctgGCGTGgcac
 I$HAIRY_01             |    10866 (-) |  1.000 |  0.902 | atgcaGCGTGgtgg
 V$YY1_02               |       56 (+) |  1.000 |  0.853 | cttggGCCATaattactgtt
 V$YY1_02               |      199 (+) |  0.908 |  0.761 | acaccACCATgcctggtatt
 V$YY1_02               |      383 (+) |  1.000 |  0.765 | gagatGCCATtcatttgcca
 V$YY1_02               |      403 (-) |  0.881 |  0.777 | acaaggcggaATGGGtgagc
 V$YY1_02               |      523 (-) |  0.881 |  0.810 | tttaaaaatgATGGGtgatg
 V$YY1_02               |      712 (-) |  0.908 |  0.807 | ctctttacagATGGTtgtga
 V$YY1_02               |      797 (+) |  1.000 |  0.799 | gctgaGCCATttctccagcc
 V$YY1_02               |      880 (-) |  0.881 |  0.772 | caaacacgaaATGGGacaga
 V$YY1_02               |     1171 (-) |  0.881 |  0.805 | aagaaaggagATGGGcaccc
 V$YY1_02               |     1788 (+) |  1.000 |  0.802 | cacctGCCATtcacaggatt
 V$YY1_02               |     1882 (+) |  0.881 |  0.796 | tgcctCCCATtttatattta
 V$YY1_02               |     2450 (-) |  1.000 |  0.793 | tggtagcgctATGGCctagc
 V$YY1_02               |     2609 (+) |  1.000 |  0.815 | caagaGCCATgtgtatgcta
 V$YY1_02               |     2831 (-) |  1.000 |  0.809 | ttgtctgcaaATGGCatcat
 V$YY1_02               |     3143 (-) |  0.881 |  0.772 | acaacaatatATGGAggttc
 V$YY1_02               |     3156 (+) |  0.881 |  0.760 | gaggtTCCATtccgcctgta
 V$YY1_02               |     3270 (+) |  1.000 |  0.853 | gtgatGCCATtatgattggg
 V$YY1_02               |     3519 (+) |  0.780 |  0.765 | aggagGCCACcttggcccga
 V$YY1_02               |     3636 (-) |  0.908 |  0.808 | tacctaccacATGGTggaat
 V$YY1_02               |     3949 (+) |  1.000 |  0.837 | attcaGCCATcctactgagc
 V$YY1_02               |     4105 (+) |  0.881 |  0.795 | aaacaTCCATtttcccagat
 V$YY1_02               |     4150 (+) |  0.881 |  0.788 | tgcctCCCATttgtaatcct
 V$YY1_02               |     4733 (-) |  0.908 |  0.763 | gccctcgctgATGGTcctct
 V$YY1_02               |     4887 (+) |  0.881 |  0.781 | aacatTCCATgttccttggc
 V$YY1_02               |     4985 (-) |  1.000 |  0.844 | acctgtccgaATGGCagacc
 V$YY1_02               |     5122 (-) |  0.908 |  0.797 | aaggaaacagATGGTgcggt
 V$YY1_02               |     5283 (-) |  0.881 |  0.774 | acaggctcagATGGGctagc
 V$YY1_02               |     5296 (+) |  1.000 |  0.820 | ggctaGCCATccaaaatggc
 V$YY1_02               |     5301 (-) |  1.000 |  0.880 | gccatccaaaATGGCttctt
 V$YY1_02               |     5442 (+) |  1.000 |  0.824 | gtattGCCATataacctttt
 V$YY1_02               |     5733 (+) |  1.000 |  0.762 | tggaaGCCATaatatagacg
 V$YY1_02               |     5869 (+) |  0.908 |  0.785 | catggACCATctcctgctgg
 V$YY1_02               |     6031 (+) |  0.881 |  0.780 | taggaCCCATctggtgcagc
 V$YY1_02               |     6257 (+) |  0.881 |  0.774 | tttgtCCCATctgccgaaga
 V$YY1_02               |     6891 (-) |  0.780 |  0.770 | gtaagacaagAGGGCataag
 V$YY1_02               |     6960 (-) |  0.881 |  0.787 | attattctggATGGAaagga
 V$YY1_02               |     6990 (-) |  0.881 |  0.770 | tggtgaggagATGGAaaagg
 V$YY1_02               |     7169 (-) |  0.908 |  0.802 | ggcgttgcagATGGTcccga
 V$YY1_02               |     7506 (-) |  1.000 |  0.853 | agggtgtcagATGGCctgaa
 V$YY1_02               |     7607 (+) |  1.000 |  0.844 | gctgaGCCATctctccagcc
 V$YY1_02               |     7729 (+) |  1.000 |  0.799 | tttggGCCATcacaggctgg
 V$YY1_02               |     8649 (-) |  0.908 |  0.761 | acaattcccaATGGTtttca
 V$YY1_02               |     8702 (+) |  0.908 |  0.774 | aaaatACCATcaaggagtct
 V$YY1_02               |     8995 (-) |  0.881 |  0.761 | attccagcacATGGAggcag
 V$YY1_02               |     9047 (-) |  1.000 |  0.828 | cctggtctacATGGCaagtt
 V$YY1_02               |    10102 (+) |  1.000 |  0.902 | tctgaGCCATcttgccatcc
 V$YY1_02               |    10110 (+) |  1.000 |  0.833 | atcttGCCATccccaataaa
 V$YY1_02               |    10503 (-) |  1.000 |  0.810 | aaagtcaattATGGCtgtag
 V$YY1_02               |    10517 (+) |  1.000 |  0.764 | ctgtaGCCATtataggaggc
 V$YY1_02               |    10849 (+) |  1.000 |  0.768 | aagaaGCCATtgtagagatg
 V$YY1_02               |    11341 (+) |  1.000 |  0.800 | taaatGCCATtatcgaacga
 V$YY1_02               |    11534 (-) |  0.908 |  0.756 | aatcccacatATGGTagatg
 V$YY1_02               |    11541 (-) |  0.881 |  0.785 | catatggtagATGGGtattc
 V$YY1_02               |    11719 (+) |  0.908 |  0.794 | cctccACCATtttctcaaac
 V$TAL1BETAITF2_01      |      714 (+) |  1.000 |  0.954 | ctttaCAGATggttgt
 V$TAL1BETAITF2_01      |     5124 (+) |  1.000 |  0.997 | ggaaaCAGATggtgcg
 V$TAL1BETAITF2_01      |     6033 (-) |  1.000 |  0.907 | ggacccATCTGgtgca
 V$TAL1BETAITF2_01      |     7171 (+) |  1.000 |  0.916 | cgttgCAGATggtccc
 V$TAL1BETAITF2_01      |     8518 (+) |  1.000 |  0.905 | actcaCAGATgcttca
 V$E47_02               |       39 (+) |  0.866 |  0.833 | aacttCAGATgtcatt
 V$E47_02               |      284 (+) |  0.836 |  0.843 | caagtCAAGTgtttta
 V$E47_02               |      714 (+) |  0.866 |  0.855 | ctttaCAGATggttgt
 V$E47_02               |      732 (+) |  0.845 |  0.834 | gccacCACGTggttgc
 V$E47_02               |      732 (-) |  0.845 |  0.835 | gccaccACGTGgttgc
 V$E47_02               |     1123 (+) |  0.845 |  0.825 | gtatgCACGTgtgttc
 V$E47_02               |     1123 (-) |  0.845 |  0.819 | gtatgcACGTGtgttc
 V$E47_02               |     1355 (-) |  1.000 |  0.903 | tgggtcACCTGatgct
 V$E47_02               |     1389 (+) |  1.000 |  0.898 | tagggCAGGTgaggag
 V$E47_02               |     1783 (-) |  1.000 |  0.960 | tggagcACCTGccatt
 V$E47_02               |     2422 (+) |  0.766 |  0.817 | aatcaCAGGGgttggg
 V$E47_02               |     2611 (+) |  0.842 |  0.823 | agagcCATGTgtatgc
 V$E47_02               |     2823 (+) |  0.866 |  0.832 | ctgtcCAGTTgtctgc
 V$E47_02               |     2967 (+) |  0.866 |  0.824 | gacggCAGATgcgcag
 V$E47_02               |     3638 (-) |  0.842 |  0.837 | cctaccACATGgtgga
 V$E47_02               |     3898 (+) |  1.000 |  0.822 | catcaCAGGTattaat
 V$E47_02               |     4115 (+) |  0.866 |  0.880 | tttccCAGATgttaaa
 V$E47_02               |     4336 (+) |  1.000 |  0.939 | acatcCAGGTggtgga
 V$E47_02               |     4563 (+) |  0.866 |  0.824 | ggacaCAGTTgcggtt
 V$E47_02               |     5124 (+) |  0.866 |  0.861 | ggaaaCAGATggtgcg
 V$E47_02               |     5249 (+) |  0.842 |  0.850 | gttcaCATGTggtcac
 V$E47_02               |     6061 (+) |  0.845 |  0.841 | ccctgCACGTgctgcc
 V$E47_02               |     6061 (-) |  0.845 |  0.817 | ccctgcACGTGctgcc
 V$E47_02               |     6259 (-) |  0.866 |  0.814 | tgtcccATCTGccgaa
 V$E47_02               |     6493 (+) |  0.866 |  0.819 | gattgCAGATgcggcc
 V$E47_02               |     6655 (+) |  0.866 |  0.824 | gcaaaCAGATgaagat
 V$E47_02               |     6842 (-) |  0.866 |  0.815 | actgccAACTGgtgag
 V$E47_02               |     6940 (+) |  0.836 |  0.820 | gtaccCAAGTgatact
 V$E47_02               |     7025 (+) |  0.891 |  0.826 | tgcatCAGCTgaagag
 V$E47_02               |     7025 (-) |  0.891 |  0.849 | tgcatcAGCTGaagag
 V$E47_02               |     7109 (-) |  0.842 |  0.844 | tgtaccACATGtgtgc
 V$E47_02               |     7111 (+) |  0.842 |  0.840 | taccaCATGTgtgcaa
 V$E47_02               |     7171 (+) |  0.866 |  0.858 | cgttgCAGATggtccc
 V$E47_02               |     7388 (+) |  1.000 |  0.943 | gtgtcCAGGTggtaga
 V$E47_02               |     7530 (+) |  0.866 |  0.855 | agttaCAGTTggttgt
 V$E47_02               |     7545 (-) |  0.866 |  0.816 | tgagccAACTGtgtag
 V$E47_02               |     7677 (+) |  0.891 |  0.881 | gctcaCAGCTgtaaag
 V$E47_02               |     7677 (-) |  0.891 |  0.873 | gctcacAGCTGtaaag
 V$E47_02               |     8274 (+) |  0.891 |  0.840 | tgatgCAGCTgccctg
 V$E47_02               |     8274 (-) |  0.891 |  0.842 | tgatgcAGCTGccctg
 V$E47_02               |     8345 (-) |  0.836 |  0.834 | tggaccACTTGccaac
 V$E47_02               |     8355 (-) |  0.766 |  0.816 | gccaacCCCTGtgcag
 V$E47_02               |     8418 (+) |  0.891 |  0.912 | gtaagCAGCTgttcta
 V$E47_02               |     8418 (-) |  0.891 |  0.888 | gtaagcAGCTGttcta
 V$E47_02               |     8501 (+) |  1.000 |  0.919 | agggaCAGGTgcggga
 V$E47_02               |     8518 (+) |  0.866 |  0.865 | actcaCAGATgcttca
 V$E47_02               |     8765 (-) |  1.000 |  0.947 | cccagcACCTGggagg
 V$E47_02               |     8966 (+) |  1.000 |  0.938 | agaacCAGGTgtggtg
 V$E47_02               |     8997 (-) |  0.842 |  0.830 | tccagcACATGgaggc
 V$E47_02               |    10692 (-) |  0.766 |  0.817 | ggcaacACCCGtgttt
 V$E47_02               |    11958 (-) |  1.000 |  0.913 | gactgcACCTGagctc
 V$CP2_01               |        7 (+) |  0.936 |  0.798 | gcatgtACAAG
 V$CP2_01               |      103 (-) |  1.000 |  0.877 | CTGGGggtggc
 V$CP2_01               |      136 (+) |  0.961 |  0.798 | agtcaaTCCAG
 V$CP2_01               |      274 (-) |  0.936 |  0.818 | CTTGTgcatgc
 V$CP2_01               |      329 (-) |  0.961 |  0.766 | CTGGAaattcc
 V$CP2_01               |      475 (+) |  0.936 |  0.762 | acacttACAAG
 V$CP2_01               |      747 (-) |  1.000 |  0.770 | CTGGGaattga
 V$CP2_01               |     1184 (+) |  1.000 |  0.798 | ggcaccCCCAG
 V$CP2_01               |     1200 (-) |  0.987 |  0.881 | CTGGTtatacc
 V$CP2_01               |     1329 (+) |  1.000 |  0.822 | tcactcCCCAG
 V$CP2_01               |     1349 (-) |  0.923 |  0.754 | CTTGCctgggt
 V$CP2_01               |     1583 (+) |  0.974 |  0.762 | tggagaGCCAG
 V$CP2_01               |     1596 (-) |  1.000 |  0.889 | CTGGGtttggg
 V$CP2_01               |     1637 (+) |  0.897 |  0.774 | gcctttCCTAG
 V$CP2_01               |     1939 (+) |  0.871 |  0.758 | gccttgGCTAG
 V$CP2_01               |     1941 (-) |  0.948 |  0.806 | CTTGGctaggc
 V$CP2_01               |     2001 (-) |  0.974 |  0.774 | CTGGCtataca
 V$CP2_01               |     2290 (-) |  0.884 |  0.798 | CTAGTttttgt
 V$CP2_01               |     2462 (+) |  0.923 |  0.873 | ggcctaGCAAG
 V$CP2_01               |     2465 (-) |  0.871 |  0.810 | CTAGCaagcgc
 V$CP2_01               |     2483 (-) |  1.000 |  0.838 | CTGGGttcggt
 V$CP2_01               |     2650 (-) |  0.714 |  0.761 | CTGCGtaatgc
 V$CP2_01               |     2758 (+) |  0.858 |  0.770 | tctacaTCTAG
 V$CP2_01               |     2765 (-) |  0.858 |  0.837 | CTAGAttccgc
 V$CP2_01               |     2795 (-) |  0.987 |  0.750 | CTGGTcttctc
 V$CP2_01               |     2820 (+) |  0.961 |  0.877 | gctctgTCCAG
 V$CP2_01               |     2995 (+) |  0.948 |  0.857 | gctcctCCAAG
 V$CP2_01               |     3039 (+) |  0.714 |  0.812 | gctccaCCCGG
 V$CP2_01               |     3065 (+) |  0.871 |  0.810 | ggtataGCTAG
 V$CP2_01               |     3266 (-) |  0.948 |  0.893 | CTTGGtgatgc
 V$CP2_01               |     3942 (-) |  0.936 |  0.798 | CTTGTtcattc
 V$CP2_01               |     3970 (-) |  0.974 |  0.762 | CTGGCtgtatg
 V$CP2_01               |     4126 (+) |  1.000 |  0.770 | ttaaaaCCCAG
 V$CP2_01               |     4133 (+) |  0.858 |  0.770 | ccagaaTCTAG
 V$CP2_01               |     4140 (-) |  0.897 |  0.794 | CTAGGtgtggt
 V$CP2_01               |     4197 (+) |  0.910 |  0.814 | gcaagtTCAAG
 V$CP2_01               |     4241 (-) |  1.000 |  0.790 | CTGGGgattgt
 V$CP2_01               |     4256 (-) |  0.948 |  0.770 | CTTGGttgtta
 V$CP2_01               |     4324 (-) |  1.000 |  0.869 | CTGGGtctggt
 V$CP2_01               |     4330 (-) |  0.987 |  0.750 | CTGGTgacatc
 V$CP2_01               |     4333 (+) |  0.961 |  0.821 | gtgacaTCCAG
 V$CP2_01               |     4560 (+) |  0.714 |  0.761 | gctggaCACAG
 V$CP2_01               |     4604 (-) |  0.923 |  0.762 | CTTGCtggaag
 V$CP2_01               |     4736 (-) |  0.871 |  0.766 | CTCGCtgatgg
 V$CP2_01               |     4767 (+) |  0.871 |  0.766 | ccagcaGCGAG
 V$CP2_01               |     4779 (-) |  0.961 |  0.814 | CTGGAtaaaga
 V$CP2_01               |     4809 (-) |  0.974 |  0.754 | CTGGCatttgt
 V$CP2_01               |     4947 (-) |  1.000 |  0.770 | CTGGGactttc
 V$CP2_01               |     5004 (-) |  0.936 |  0.750 | CTTGTattacc
 V$CP2_01               |     5030 (-) |  1.000 |  0.790 | CTGGGatgctc
 V$CP2_01               |     5081 (-) |  0.974 |  0.853 | CTGGCtctgac
 V$CP2_01               |     5091 (-) |  0.987 |  0.893 | CTGGTttgggt
 V$CP2_01               |     5139 (+) |  0.897 |  0.857 | ggtcaaCCTAG
 V$CP2_01               |     5526 (+) |  0.961 |  0.798 | ctcctaTCCAG
 V$CP2_01               |     5553 (+) |  0.884 |  0.750 | tctctcACTAG
 V$CP2_01               |     5564 (+) |  0.987 |  0.750 | aaaacaACCAG
 V$CP2_01               |     5694 (-) |  0.884 |  0.766 | CTAGTtcatac
 V$CP2_01               |     5885 (-) |  1.000 |  0.790 | CTGGGcatggg
 V$CP2_01               |     5920 (+) |  0.871 |  0.810 | tccccaGCGAG
 V$CP2_01               |     5988 (-) |  0.961 |  0.834 | CTGGAttaggg
 V$CP2_01               |     6041 (-) |  0.987 |  0.770 | CTGGTgcagcc
 V$CP2_01               |     6124 (-) |  0.936 |  0.817 | CTTGTtttctc
 V$CP2_01               |     6151 (-) |  0.974 |  0.762 | CTGGCtctcct
 V$CP2_01               |     6206 (+) |  0.948 |  0.758 | ggtatgCCAAG
 V$CP2_01               |     6240 (-) |  0.974 |  0.921 | CTGGCtacggc
 V$CP2_01               |     6391 (-) |  0.974 |  0.786 | CTGGCctgtgt
 V$CP2_01               |     6437 (+) |  1.000 |  0.921 | ggtcaaCCCAG
 V$CP2_01               |     6490 (-) |  0.961 |  0.786 | CTGGAttgcag
 V$CP2_01               |     6629 (+) |  1.000 |  0.833 | ggggcaCCCAG
 V$CP2_01               |     6794 (-) |  0.974 |  0.873 | CTGGCtcttcc
 V$CP2_01               |     6850 (-) |  0.987 |  0.802 | CTGGTgagcac
 V$CP2_01               |     6862 (+) |  0.897 |  0.806 | tccagaCCGAG
 V$CP2_01               |     6937 (+) |  0.714 |  0.761 | gcagtaCCCAA
 V$CP2_01               |     6966 (-) |  0.961 |  0.766 | CTGGAtggaaa
 V$CP2_01               |     7161 (-) |  0.961 |  0.865 | CTGGAgctggc
 V$CP2_01               |     7629 (-) |  0.974 |  0.762 | CTGGCggtaga
 V$CP2_01               |     7686 (+) |  0.974 |  0.774 | tgtaaaGCCAG
 V$CP2_01               |     7844 (-) |  0.974 |  0.822 | CTGGCaaaagc
 V$CP2_01               |     8036 (-) |  0.923 |  0.861 | CTTGCtgggcc
 V$CP2_01               |     8040 (-) |  1.000 |  0.770 | CTGGGccttga
 V$CP2_01               |     8097 (-) |  1.000 |  0.838 | CTGGGtcctgt
 V$CP2_01               |     8133 (-) |  0.701 |  0.753 | CTGCTttctgc
 V$CP2_01               |     8172 (+) |  0.987 |  0.802 | ggtagcACCAG
 V$CP2_01               |     8185 (-) |  0.936 |  0.849 | CTTGTttgctc
 V$CP2_01               |     8234 (+) |  1.000 |  0.877 | cccacaCCCAG
 V$CP2_01               |     8327 (+) |  0.974 |  0.774 | gtcagcGCCAG
 V$CP2_01               |     8399 (+) |  0.974 |  0.806 | agccaaGCCAG
 V$CP2_01               |     8452 (+) |  0.948 |  0.758 | cctaagCCAAG
 V$CP2_01               |     8817 (-) |  0.987 |  0.750 | CTGGTactctc
 V$CP2_01               |     8963 (+) |  0.987 |  0.869 | gggagaACCAG
 V$CP2_01               |     9060 (+) |  0.961 |  0.845 | gcaagtTCCAG
 V$CP2_01               |     9069 (+) |  0.974 |  0.794 | aggctaGCCAG
 V$CP2_01               |     9072 (-) |  0.871 |  0.822 | CTAGCcagggc
 V$CP2_01               |     9189 (+) |  0.910 |  0.766 | gaccacTCAAG
 V$CP2_01               |     9219 (+) |  0.923 |  0.822 | gcaaagGCAAG
 V$CP2_01               |     9229 (+) |  0.961 |  0.766 | gttagcTCCAG
 V$CP2_01               |     9272 (+) |  0.688 |  0.752 | gcgacaGCCAC
 V$CP2_01               |     9276 (+) |  0.948 |  0.766 | cagccaCCAAG
 V$CP2_01               |     9298 (-) |  0.936 |  0.790 | CTTGTgtgccc
 V$CP2_01               |     9394 (-) |  0.961 |  0.798 | CTGGAatgtgg
 V$CP2_01               |     9438 (+) |  0.948 |  0.778 | ggaagcCCAAG
 V$CP2_01               |     9520 (+) |  0.936 |  0.770 | tgtccaACAAG
 V$CP2_01               |     9535 (+) |  0.936 |  0.861 | gaacaaACAAG
 V$CP2_01               |     9570 (-) |  1.000 |  0.857 | CTGGGtgtggt
 V$CP2_01               |     9915 (-) |  0.961 |  0.766 | CTGGAtttttg
 V$CP2_01               |    10007 (-) |  1.000 |  0.770 | CTGGGactgga
 V$CP2_01               |    10228 (+) |  0.897 |  0.762 | gtggaaCCTAG
 V$CP2_01               |    10235 (-) |  0.897 |  0.758 | CTAGGttggtg
 V$CP2_01               |    10248 (-) |  0.688 |  0.808 | CAGGCttgtgc
 V$CP2_01               |    10513 (-) |  0.688 |  0.764 | ATGGCtgtagc
 V$CP2_01               |    10781 (+) |  1.000 |  0.838 | gtcggaCCCAG
 V$CP2_01               |    10969 (+) |  0.923 |  0.790 | gttggaGCAAG
 V$CP2_01               |    11219 (+) |  1.000 |  0.802 | gaactgCCCAG
 V$CP2_01               |    11580 (+) |  0.961 |  0.766 | cttataTCCAG
 V$CP2_01               |    11793 (+) |  1.000 |  0.770 | acaaatCCCAG
 V$DELTAEF1_01          |      374 (-) |  1.000 |  0.985 | tctAGGTGaga
 V$DELTAEF1_01          |     1357 (+) |  1.000 |  0.987 | ggtCACCTgat
 V$DELTAEF1_01          |     1392 (-) |  1.000 |  0.982 | ggcAGGTGagg
 V$DELTAEF1_01          |     3290 (-) |  1.000 |  0.985 | atgAGGTGaac
 V$DELTAEF1_01          |     6596 (-) |  1.000 |  0.985 | ataAGGTGgtg
 V$DELTAEF1_01          |     7391 (-) |  1.000 |  0.980 | tccAGGTGgta
 V$DELTAEF1_01          |     9613 (-) |  1.000 |  0.985 | ctgAGGTGgga
 V$DELTAEF1_01          |    11960 (+) |  1.000 |  0.991 | ctgCACCTgag
 V$CETS1P54_02          |      223 (-) |  0.993 |  0.965 | ttttTTCCTtttt
 V$CETS1P54_02          |      326 (+) |  0.983 |  0.968 | gtgcTGGAAattc
 V$CETS1P54_02          |      608 (-) |  0.971 |  0.972 | aaacATCCTgtcg
 V$CETS1P54_02          |      766 (+) |  0.983 |  0.957 | cctcTGGAAgagt
 V$CETS1P54_02          |     1558 (+) |  0.983 |  0.969 | cttcTGGAAatct
 V$CETS1P54_02          |     1718 (-) |  1.000 |  0.966 | ccttTTCCGggct
 V$CETS1P54_02          |     1737 (-) |  0.993 |  0.971 | gaacTTCCTatag
 V$CETS1P54_02          |     1948 (+) |  0.983 |  0.960 | aggcTGGAActtt
 V$CETS1P54_02          |     2159 (-) |  0.993 |  0.963 | cctcTTCCTttcc
 V$CETS1P54_02          |     2203 (-) |  0.993 |  0.964 | tttcTTCCTttct
 V$CETS1P54_02          |     2563 (-) |  1.000 |  0.977 | aaatTTCCGtaag
 V$CETS1P54_02          |     2987 (-) |  1.000 |  0.979 | ctacTTCCGctcc
 V$CETS1P54_02          |     3031 (-) |  1.000 |  0.977 | cgacTTCCGctcc
 V$CETS1P54_02          |     3323 (-) |  0.993 |  0.965 | ccttTTCCTgatt
 V$CETS1P54_02          |     3835 (-) |  0.983 |  0.971 | aaatTTCCAttct
 V$CETS1P54_02          |     3852 (-) |  0.960 |  0.963 | aaatATCCAgtac
 V$CETS1P54_02          |     4622 (-) |  0.971 |  0.960 | caatATCCTttgg
 V$CETS1P54_02          |     4686 (+) |  0.993 |  0.959 | tggcAGGAAactt
 V$CETS1P54_02          |     4960 (+) |  0.993 |  0.974 | cagcAGGAAgtca
 V$CETS1P54_02          |     5119 (+) |  0.993 |  0.962 | caaaAGGAAacag
 V$CETS1P54_02          |     5471 (-) |  0.993 |  0.980 | ctatTTCCTgatt
 V$CETS1P54_02          |     5729 (+) |  0.983 |  0.963 | aaacTGGAAgcca
 V$CETS1P54_02          |     6087 (-) |  0.993 |  0.982 | tgagTTCCTgtgt
 V$CETS1P54_02          |     6459 (-) |  0.993 |  0.979 | ttatTTCCTgata
 V$CETS1P54_02          |     7017 (-) |  0.993 |  0.958 | atgtTTCCTgcat
 V$CETS1P54_02          |     7228 (+) |  0.993 |  0.978 | cagcAGGAAgttc
 V$CETS1P54_02          |     7245 (+) |  0.993 |  0.965 | tctcAGGAAaaag
 V$CETS1P54_02          |     8080 (-) |  0.993 |  0.971 | aaacTTCCTatac
 V$CETS1P54_02          |     8157 (-) |  0.983 |  0.957 | tagcTTCCAgagg
 V$CETS1P54_02          |     8909 (+) |  0.993 |  0.956 | attcAGGAAtact
 V$CETS1P54_02          |     8992 (-) |  0.983 |  0.957 | ttaaTTCCAgcac
 V$CETS1P54_02          |     9061 (-) |  0.983 |  0.960 | caagTTCCAggct
 V$CETS1P54_02          |     9433 (+) |  0.993 |  0.971 | taacAGGAAgccc
 V$CETS1P54_02          |     9466 (+) |  0.971 |  0.972 | gtacAGGATgttc
 V$CETS1P54_02          |     9872 (+) |  0.993 |  0.961 | aatgAGGAAatca
 V$CETS1P54_02          |    10255 (+) |  0.993 |  0.974 | gtgcAGGAAgtga
 V$CETS1P54_02          |    10587 (-) |  0.993 |  0.971 | caatTTCCTatat
 V$CETS1P54_02          |    10842 (+) |  0.993 |  0.960 | tcgcAGGAAgaag
 V$CETS1P54_02          |    11269 (+) |  0.993 |  0.981 | gaaaAGGAAatta
 V$GATA1_01             |       82 (+) |  1.000 |  0.990 | gttGATAGgg
 V$GATA1_01             |       91 (-) |  1.000 |  0.990 | gcCTATCttc
 V$GATA1_01             |      137 (-) |  0.997 |  0.982 | gtCAATCcag
 V$GATA1_01             |      536 (+) |  0.993 |  0.989 | ggtGATGCgc
 V$GATA1_01             |      608 (-) |  0.990 |  0.982 | aaACATCctg
 V$GATA1_01             |     1113 (+) |  0.987 |  0.982 | gctGATTTgt
 V$GATA1_01             |     1177 (+) |  1.000 |  0.995 | ggaGATGGgc
 V$GATA1_01             |     1239 (-) |  0.990 |  0.983 | tgACATCagg
 V$GATA1_01             |     1362 (+) |  0.993 |  0.988 | cctGATGCtc
 V$GATA1_01             |     1668 (+) |  0.990 |  0.985 | ggaGATTCct
 V$GATA1_01             |     1805 (-) |  0.988 |  0.981 | atTCATCagg
 V$GATA1_01             |     1995 (-) |  0.988 |  0.982 | gaTTATCtgg
 V$GATA1_01             |     2007 (-) |  0.990 |  0.982 | atACATCtcc
 V$GATA1_01             |     2933 (+) |  0.997 |  0.992 | gctGATTGcg
 V$GATA1_01             |     2971 (+) |  0.993 |  0.987 | gcaGATGCgc
 V$GATA1_01             |     3083 (+) |  0.990 |  0.984 | ggtGATTCta
 V$GATA1_01             |     3269 (+) |  0.993 |  0.986 | ggtGATGCca
 V$GATA1_01             |     3297 (-) |  0.990 |  0.984 | gaACATCtcc
 V$GATA1_01             |     3329 (+) |  0.990 |  0.984 | cctGATTCta
 V$GATA1_01             |     3393 (-) |  0.988 |  0.982 | gaGGATCtcc
 V$GATA1_01             |     3986 (-) |  1.000 |  0.983 | caCCATCtca
 V$GATA1_01             |     4119 (+) |  0.990 |  0.983 | ccaGATGTta
 V$GATA1_01             |     4243 (+) |  0.997 |  0.989 | gggGATTGta
 V$GATA1_01             |     4374 (-) |  0.988 |  0.983 | agTTATCtgg
 V$GATA1_01             |     4639 (-) |  0.987 |  0.985 | caAAATCccg
 V$GATA1_01             |     4739 (+) |  1.000 |  0.993 | gctGATGGtc
 V$GATA1_01             |     5040 (+) |  0.997 |  0.989 | cagGATTGct
 V$GATA1_01             |     5335 (+) |  1.000 |  0.994 | gccGATAGtt
 V$GATA1_01             |     5345 (-) |  0.993 |  0.983 | ttGCATCccc
 V$GATA1_01             |     5371 (+) |  0.987 |  0.984 | cggGATTTct
 V$GATA1_01             |     5477 (+) |  0.987 |  0.983 | cctGATTTtt
 V$GATA1_01             |     5527 (-) |  1.000 |  0.987 | tcCTATCcag
 V$GATA1_01             |     5533 (+) |  0.990 |  0.982 | ccaGATTCac
 V$GATA1_01             |     5841 (-) |  0.993 |  0.988 | agGCATCtcc
 V$GATA1_01             |     5873 (-) |  1.000 |  0.994 | gaCCATCtcc
 V$GATA1_01             |     5977 (+) |  0.988 |  0.984 | ggtGATAAct
 V$GATA1_01             |     5995 (+) |  1.000 |  0.983 | aggGATGGgg
 V$GATA1_01             |     6035 (-) |  1.000 |  0.996 | acCCATCtgg
 V$GATA1_01             |     6261 (-) |  1.000 |  0.992 | tcCCATCtgc
 V$GATA1_01             |     6373 (+) |  0.987 |  0.986 | cgaGATTTgg
 V$GATA1_01             |     6479 (+) |  0.988 |  0.982 | cagGATGAgg
 V$GATA1_01             |     6490 (+) |  0.997 |  0.983 | ctgGATTGca
 V$GATA1_01             |     6497 (+) |  0.993 |  0.989 | gcaGATGCgg
 V$GATA1_01             |     6753 (-) |  1.000 |  0.982 | caCTATCcct
 V$GATA1_01             |     6966 (+) |  1.000 |  0.983 | ctgGATGGaa
 V$GATA1_01             |     6996 (+) |  1.000 |  0.990 | ggaGATGGaa
 V$GATA1_01             |     7013 (+) |  0.990 |  0.983 | gcgGATGTtt
 V$GATA1_01             |     7024 (-) |  0.993 |  0.986 | ctGCATCagc
 V$GATA1_01             |     7152 (-) |  0.993 |  0.991 | ccGTATCtcc
 V$GATA1_01             |     7175 (+) |  1.000 |  0.992 | gcaGATGGtc
 V$GATA1_01             |     7557 (+) |  0.993 |  0.981 | gtaGATGCtg
 V$GATA1_01             |     7571 (-) |  0.987 |  0.984 | ccAAATCccc
 V$GATA1_01             |     7577 (-) |  1.000 |  0.998 | ccCCATCagg
 V$GATA1_01             |     7717 (-) |  0.988 |  0.982 | aaGGATCagc
 V$GATA1_01             |     8241 (+) |  0.988 |  0.982 | ccaGATGAag
 V$GATA1_01             |     8269 (+) |  0.988 |  0.985 | cctGATGAtg
 V$GATA1_01             |     8272 (+) |  0.993 |  0.983 | gatGATGCag
 V$GATA1_01             |     8706 (-) |  1.000 |  0.987 | taCCATCaag
 V$GATA1_01             |     9419 (-) |  1.000 |  0.981 | aaCTATCcca
 V$GATA1_01             |     9622 (+) |  0.995 |  0.987 | gagGATCGgg
 V$GATA1_01             |     9622 (-) |  0.988 |  0.983 | gaGGATCggg
 V$GATA1_01             |    10106 (-) |  1.000 |  0.992 | agCCATCttg
 V$GATA1_01             |    10114 (-) |  1.000 |  0.992 | tgCCATCccc
 V$GATA1_01             |    10286 (-) |  0.988 |  0.983 | tcTCATCagg
 V$GATA1_01             |    10792 (+) |  0.990 |  0.984 | gggGATGTga
 V$GATA1_01             |    10837 (-) |  1.000 |  0.982 | gcCCATCgca
 V$GATA1_01             |    11196 (+) |  0.997 |  0.984 | cttGATTGat
 V$GATA1_01             |    11429 (-) |  1.000 |  0.993 | agCTATCcgc
 V$GATA1_01             |    11547 (+) |  1.000 |  0.988 | gtaGATGGgt
 V$GATA1_01             |    11774 (+) |  0.993 |  0.988 | ccaGATACtt
 V$GATA1_01             |    11800 (+) |  0.997 |  0.991 | ccaGATTGga
 V$GATA2_01             |       82 (+) |  1.000 |  0.983 | gttGATAGgg
 V$GATA2_01             |       91 (-) |  1.000 |  0.993 | gcCTATCttc
 V$GATA2_01             |      307 (-) |  1.000 |  0.994 | agCTATCtct
 V$GATA2_01             |      566 (+) |  0.992 |  0.983 | ggaGATAAac
 V$GATA2_01             |     1177 (+) |  0.987 |  0.983 | ggaGATGGgc
 V$GATA2_01             |     1995 (-) |  0.992 |  0.986 | gaTTATCtgg
 V$GATA2_01             |     3178 (-) |  0.994 |  0.983 | ttATATCccc
 V$GATA2_01             |     3930 (-) |  0.992 |  0.984 | caTTATCagt
 V$GATA2_01             |     3953 (-) |  0.987 |  0.982 | agCCATCcta
 V$GATA2_01             |     3977 (+) |  1.000 |  0.986 | tatGATAGac
 V$GATA2_01             |     3986 (-) |  0.987 |  0.982 | caCCATCtca
 V$GATA2_01             |     4374 (-) |  0.992 |  0.990 | agTTATCtgg
 V$GATA2_01             |     4622 (-) |  0.994 |  0.984 | caATATCctt
 V$GATA2_01             |     4739 (+) |  0.987 |  0.981 | gctGATGGtc
 V$GATA2_01             |     5335 (+) |  1.000 |  0.995 | gccGATAGtt
 V$GATA2_01             |     5633 (+) |  0.992 |  0.984 | tggGATAAag
 V$GATA2_01             |     5873 (-) |  0.987 |  0.982 | gaCCATCtcc
 V$GATA2_01             |     5977 (+) |  0.992 |  0.990 | ggtGATAAct
 V$GATA2_01             |     6035 (-) |  0.987 |  0.982 | acCCATCtgg
 V$GATA2_01             |     6753 (-) |  1.000 |  0.993 | caCTATCcct
 V$GATA2_01             |     6947 (+) |  0.995 |  0.987 | agtGATACtg
 V$GATA2_01             |     7152 (-) |  0.995 |  0.992 | ccGTATCtcc
 V$GATA2_01             |     7175 (+) |  0.987 |  0.982 | gcaGATGGtc
 V$GATA2_01             |     7266 (-) |  0.994 |  0.985 | aaATATCcta
 V$GATA2_01             |     7512 (+) |  0.987 |  0.983 | tcaGATGGcc
 V$GATA2_01             |     7577 (-) |  0.987 |  0.983 | ccCCATCagg
 V$GATA2_01             |     7611 (-) |  0.987 |  0.981 | agCCATCtct
 V$GATA2_01             |     7733 (-) |  0.987 |  0.983 | ggCCATCaca
 V$GATA2_01             |     7788 (-) |  0.992 |  0.986 | aaTTATCcca
 V$GATA2_01             |     7951 (+) |  0.995 |  0.991 | tgaGATACcc
 V$GATA2_01             |     8062 (-) |  0.992 |  0.982 | gtTTATCtgg
 V$GATA2_01             |     9367 (-) |  1.000 |  0.990 | ctCTATCaca
 V$GATA2_01             |     9419 (-) |  1.000 |  0.994 | aaCTATCcca
 V$GATA2_01             |     9732 (+) |  0.992 |  0.984 | tatGATAAtg
 V$GATA2_01             |     9833 (+) |  0.992 |  0.984 | aggGATAAtt
 V$GATA2_01             |    10106 (-) |  0.987 |  0.982 | agCCATCttg
 V$GATA2_01             |    10114 (-) |  0.987 |  0.984 | tgCCATCccc
 V$GATA2_01             |    11369 (-) |  1.000 |  0.985 | ttCTATCtgt
 V$GATA2_01             |    11429 (-) |  1.000 |  0.999 | agCTATCcgc
 V$GATA2_01             |    11774 (+) |  0.995 |  0.989 | ccaGATACtt
 V$GATA3_01             |       83 (+) |  1.000 |  0.993 | ttGATAGgg
 V$GATA3_01             |     6753 (-) |  1.000 |  0.992 | caCTATCcc
 V$GATA3_01             |     7798 (+) |  0.985 |  0.979 | aaGATAAag
 V$GATA3_01             |     9367 (-) |  1.000 |  0.992 | ctCTATCac
 V$EVI1_01              |     2178 (-) |  0.889 |  0.813 | ccttcttTTCTTctct
 V$EVI1_01              |     2791 (-) |  0.922 |  0.823 | ttagctgGTCTTctct
 V$EVI1_01              |     5652 (+) |  0.889 |  0.776 | aaagAAGAAaagaaca
 V$EVI1_04              |    11572 (-) |  0.907 |  0.783 | tATCATtgcttatat
 V$MZF1_01              |     1002 (+) |  1.000 |  0.996 | tgtGGGGA
 V$MZF1_01              |     1333 (-) |  1.000 |  0.979 | TCCCCagg
 V$MZF1_01              |     1497 (+) |  1.000 |  0.995 | gggGGGGA
 V$MZF1_01              |     2432 (+) |  1.000 |  0.983 | gttGGGGA
 V$MZF1_01              |     3183 (-) |  1.000 |  0.996 | TCCCCcct
 V$MZF1_01              |     3781 (-) |  1.000 |  0.996 | TCCCCcct
 V$MZF1_01              |     4045 (+) |  1.000 |  0.979 | cagGGGGA
 V$MZF1_01              |     4240 (+) |  1.000 |  0.981 | gctGGGGA
 V$MZF1_01              |     4752 (-) |  1.000 |  0.994 | TCCCCtct
 V$MZF1_01              |     5350 (-) |  1.000 |  0.994 | TCCCCtct
 V$MZF1_01              |     5461 (-) |  1.000 |  0.996 | TCCCCaca
 V$MZF1_01              |     5490 (-) |  1.000 |  0.980 | TCCCCttc
 V$MZF1_01              |     5920 (-) |  1.000 |  0.981 | TCCCCagc
 V$MZF1_01              |     6805 (-) |  1.000 |  0.990 | TCCCCtca
 V$MZF1_01              |     7576 (-) |  1.000 |  0.985 | TCCCCatc
 V$MZF1_01              |     8204 (-) |  1.000 |  0.994 | TCCCCtct
 V$MZF1_01              |     9514 (-) |  1.000 |  0.983 | TCCCCatg
 V$MZF1_01              |     9977 (+) |  1.000 |  0.983 | tatGGGGA
 V$MZF1_01              |    10119 (-) |  1.000 |  0.985 | TCCCCaat
 V$MZF1_01              |    10789 (+) |  1.000 |  0.979 | cagGGGGA
 V$MZF1_02              |     1176 (+) |  0.898 |  0.873 | aggagATGGGcac
 V$MZF1_02              |     1488 (+) |  1.000 |  0.897 | gagggAGGGGggg
 V$MZF1_02              |     2639 (-) |  1.000 |  0.856 | ctaCCCCTgacct
 V$MZF1_02              |     3183 (-) |  1.000 |  0.916 | tccCCCCTctctt
 V$MZF1_02              |     3890 (-) |  0.857 |  0.877 | ttgACCCTcatca
 V$MZF1_02              |     4041 (+) |  1.000 |  0.876 | ccagcAGGGGgaa
 V$MZF1_02              |     4301 (-) |  0.857 |  0.869 | ttgACCCTcaata
 V$MZF1_02              |     4750 (-) |  1.000 |  0.904 | tctCCCCTctgta
 V$MZF1_02              |     5348 (-) |  1.000 |  0.871 | catCCCCTctttg
 V$MZF1_02              |     5489 (-) |  0.875 |  0.862 | atcCCCTTccctc
 V$MZF1_02              |     5994 (+) |  0.898 |  0.860 | tagggATGGGgta
 V$MZF1_02              |     6803 (-) |  1.000 |  0.881 | cctCCCCTcatta
 V$MZF1_02              |     8141 (+) |  0.844 |  0.858 | tgctgAGGGAaaa
 V$MZF1_02              |     8202 (-) |  1.000 |  0.970 | tttCCCCTctgac
 V$MZF1_02              |     8301 (-) |  1.000 |  0.937 | atgCCCCTctgcc
 V$MZF1_02              |     9008 (+) |  1.000 |  0.866 | gaggcAGGGGcag
 V$MZF1_02              |     9679 (+) |  1.000 |  0.876 | agtggAGGGGggg
 V$MZF1_02              |     9924 (+) |  0.898 |  0.859 | tgcctATGGGtaa
 V$MZF1_02              |    11546 (+) |  0.898 |  0.863 | ggtagATGGGtat
 V$MZF1_02              |    11611 (+) |  1.000 |  0.866 | gagaaAGGGGtac
 V$ZID_01               |     1851 (-) |  1.000 |  0.898 | cacaataGAGCCa
 V$IK1_01               |     2378 (-) |  1.000 |  0.955 | agttTTCCCagag
 V$IK1_01               |     3134 (-) |  1.000 |  0.966 | tacaTTCCCacaa
 V$IK1_01               |     3240 (-) |  1.000 |  0.948 | aacaTTCCCagcc
 V$IK1_01               |     6176 (-) |  1.000 |  0.946 | agggTTCCCagag
 V$IK1_01               |     8649 (-) |  1.000 |  0.955 | acaaTTCCCaatg
 V$IK1_01               |    11083 (+) |  1.000 |  0.959 | ctctGGGAAtttt
 V$IK2_01               |      163 (-) |  1.000 |  0.986 | ccgtTCCCAatg
 V$IK2_01               |      191 (-) |  1.000 |  0.958 | tgccTCCCAcac
 V$IK2_01               |      745 (+) |  1.000 |  0.978 | tgcTGGGAattg
 V$IK2_01               |      888 (+) |  1.000 |  0.962 | aaaTGGGAcaga
 V$IK2_01               |     1276 (+) |  1.000 |  0.983 | ctcTGGGAtgac
 V$IK2_01               |     1821 (+) |  0.969 |  0.962 | ttcAGGGAagac
 V$IK2_01               |     1882 (-) |  1.000 |  0.955 | tgccTCCCAttt
 V$IK2_01               |     2021 (+) |  1.000 |  0.973 | tgcTGGGAttaa
 V$IK2_01               |     2379 (-) |  1.000 |  0.993 | gtttTCCCAgag
 V$IK2_01               |     2712 (-) |  1.000 |  0.986 | ctctTCCCAaat
 V$IK2_01               |     3135 (-) |  1.000 |  0.979 | acatTCCCAcaa
 V$IK2_01               |     3241 (-) |  1.000 |  0.979 | acatTCCCAgcc
 V$IK2_01               |     3283 (+) |  1.000 |  0.977 | gatTGGGAtgag
 V$IK2_01               |     4113 (-) |  1.000 |  0.980 | atttTCCCAgat
 V$IK2_01               |     4150 (-) |  1.000 |  0.955 | tgccTCCCAttt
 V$IK2_01               |     4761 (-) |  1.000 |  0.961 | taggTCCCAgca
 V$IK2_01               |     4830 (+) |  0.969 |  0.959 | ggtAGGGAacga
 V$IK2_01               |     4945 (+) |  1.000 |  0.960 | aacTGGGActtt
 V$IK2_01               |     5028 (+) |  1.000 |  0.969 | gacTGGGAtgct
 V$IK2_01               |     5229 (+) |  1.000 |  0.983 | gacTGGGAacga
 V$IK2_01               |     5368 (+) |  0.978 |  0.959 | acaCGGGAtttc
 V$IK2_01               |     5510 (-) |  0.969 |  0.962 | ggttTCCCTgcc
 V$IK2_01               |     5630 (+) |  1.000 |  0.975 | cacTGGGAtaaa
 V$IK2_01               |     5710 (-) |  1.000 |  0.983 | ggaaTCCCAcaa
 V$IK2_01               |     5862 (-) |  1.000 |  0.988 | ggttTCCCAtgg
 V$IK2_01               |     6177 (-) |  1.000 |  0.992 | gggtTCCCAgag
 V$IK2_01               |     6257 (-) |  1.000 |  0.961 | tttgTCCCAtct
 V$IK2_01               |     7446 (+) |  1.000 |  0.955 | gtgTGGGAgtgt
 V$IK2_01               |     7698 (+) |  1.000 |  0.961 | actTGGGAggta
 V$IK2_01               |     7789 (-) |  1.000 |  0.977 | attaTCCCAaag
 V$IK2_01               |     8143 (+) |  0.969 |  0.964 | ctgAGGGAaaac
 V$IK2_01               |     8229 (-) |  1.000 |  0.958 | tggcTCCCAcac
 V$IK2_01               |     8650 (-) |  1.000 |  0.987 | caatTCCCAatg
 V$IK2_01               |     8760 (-) |  1.000 |  0.963 | gtccTCCCAgca
 V$IK2_01               |     8771 (+) |  1.000 |  0.963 | accTGGGAggcc
 V$IK2_01               |     9120 (+) |  0.978 |  0.971 | aacCGGGAaaac
 V$IK2_01               |     9257 (+) |  1.000 |  0.956 | tcaTGGGAcagg
 V$IK2_01               |     9420 (-) |  1.000 |  0.968 | actaTCCCAtaa
 V$IK2_01               |     9592 (-) |  1.000 |  0.981 | gtaaTCCCAgca
 V$IK2_01               |     9603 (+) |  1.000 |  0.985 | attTGGGAagct
 V$IK2_01               |    10005 (+) |  1.000 |  0.962 | ctcTGGGActgg
 V$IK2_01               |    10611 (+) |  1.000 |  0.958 | gtgTGGGAggga
 V$IK2_01               |    10877 (+) |  1.000 |  0.963 | tggTGGGAgcac
 V$IK2_01               |    11083 (+) |  1.000 |  0.980 | ctcTGGGAattt
 V$IK2_01               |    11532 (-) |  1.000 |  0.972 | caaaTCCCAcat
 V$IK2_01               |    11794 (-) |  1.000 |  0.972 | caaaTCCCAgat
 V$IK3_01               |      162 (-) |  1.000 |  0.794 | tccgTTCCCaatg
 V$IK3_01               |      326 (+) |  0.887 |  0.737 | gtgcTGGAAattc
 V$IK3_01               |      327 (+) |  0.778 |  0.815 | tgctGGAAAttcc
 V$IK3_01               |      332 (-) |  1.000 |  0.870 | gaaaTTCCCtcag
 V$IK3_01               |      745 (+) |  1.000 |  0.871 | tgctGGGAAttga
 V$IK3_01               |      923 (-) |  0.887 |  0.746 | gcacTTCCAcgaa
 V$IK3_01               |      942 (+) |  0.915 |  0.784 | agttAGGAAcaat
 V$IK3_01               |     1132 (-) |  0.915 |  0.845 | tgtgTTCCTaaaa
 V$IK3_01               |     1189 (+) |  0.915 |  0.773 | ccccAGGAAagct
 V$IK3_01               |     1203 (-) |  0.778 |  0.733 | gttaTACCCattg
 V$IK3_01               |     1558 (+) |  0.887 |  0.742 | cttcTGGAAatct
 V$IK3_01               |     1570 (+) |  1.000 |  0.904 | tacgGGGAAtgca
 V$IK3_01               |     1637 (-) |  0.915 |  0.763 | gcctTTCCTagtg
 V$IK3_01               |     1669 (-) |  0.915 |  0.797 | gagaTTCCTcctt
 V$IK3_01               |     1737 (-) |  0.915 |  0.753 | gaacTTCCTatag
 V$IK3_01               |     1793 (-) |  0.778 |  0.762 | gccaTTCACagga
 V$IK3_01               |     1821 (+) |  1.000 |  0.873 | ttcaGGGAAgaca
 V$IK3_01               |     2021 (+) |  0.778 |  0.743 | tgctGGGATtaaa
 V$IK3_01               |     2378 (-) |  1.000 |  0.873 | agttTTCCCagag
 V$IK3_01               |     2399 (-) |  0.915 |  0.781 | tgctTTCCTtaaa
 V$IK3_01               |     2509 (+) |  1.000 |  0.771 | aaaaGGGAAaaaa
 V$IK3_01               |     2536 (+) |  0.778 |  0.767 | tttaGAGAAtaac
 V$IK3_01               |     2562 (-) |  0.778 |  0.737 | gaaaTTTCCgtaa
 V$IK3_01               |     2711 (-) |  1.000 |  0.796 | cctcTTCCCaaat
 V$IK3_01               |     2766 (-) |  0.887 |  0.735 | tagaTTCCGcatg
 V$IK3_01               |     2783 (-) |  0.915 |  0.754 | attcTTCCTtagc
 V$IK3_01               |     2846 (-) |  0.887 |  0.754 | atcaTTCCGtcct
 V$IK3_01               |     3134 (-) |  1.000 |  0.872 | tacaTTCCCacaa
 V$IK3_01               |     3156 (-) |  0.887 |  0.750 | gaggTTCCAttcc
 V$IK3_01               |     3240 (-) |  1.000 |  0.892 | aacaTTCCCagcc
 V$IK3_01               |     3336 (-) |  1.000 |  0.747 | ctatTTCCCtcct
 V$IK3_01               |     3676 (-) |  0.778 |  0.753 | agaaTTGCCaagt
 V$IK3_01               |     3776 (-) |  1.000 |  0.738 | ctccTTCCCccct
 V$IK3_01               |     4024 (+) |  0.887 |  0.747 | ctcaTGGAAttaa
 V$IK3_01               |     4035 (-) |  0.887 |  0.785 | aataTTCCAgcag
 V$IK3_01               |     4112 (-) |  1.000 |  0.822 | cattTTCCCagat
 V$IK3_01               |     4161 (-) |  0.693 |  0.735 | tgtaATCCTagta
 V$IK3_01               |     4392 (-) |  0.887 |  0.789 | tgagTTCCAagac
 V$IK3_01               |     4686 (+) |  0.915 |  0.737 | tggcAGGAAactt
 V$IK3_01               |     4830 (+) |  1.000 |  0.794 | ggtaGGGAAcgag
 V$IK3_01               |     4880 (+) |  0.887 |  0.772 | gctcTGGAAcatt
 V$IK3_01               |     4887 (-) |  0.887 |  0.789 | aacaTTCCAtgtt
 V$IK3_01               |     4894 (-) |  0.915 |  0.782 | catgTTCCTtggc
 V$IK3_01               |     4945 (+) |  0.778 |  0.753 | aactGGGACtttc
 V$IK3_01               |     4960 (+) |  0.915 |  0.734 | cagcAGGAAgtca
 V$IK3_01               |     5006 (-) |  0.778 |  0.737 | tgtaTTACCcatt
 V$IK3_01               |     5229 (+) |  1.000 |  0.837 | gactGGGAAcgat
 V$IK3_01               |     5421 (-) |  1.000 |  0.795 | atctTTCCCtcca
 V$IK3_01               |     5441 (-) |  0.778 |  0.744 | tgtaTTGCCatat
 V$IK3_01               |     5456 (-) |  1.000 |  0.796 | ccttTTCCCcaca
 V$IK3_01               |     5491 (-) |  1.000 |  0.740 | ccccTTCCCtctg
 V$IK3_01               |     5509 (-) |  1.000 |  0.838 | aggtTTCCCtgcc
 V$IK3_01               |     5519 (-) |  0.915 |  0.750 | gcctTTCCTccta
 V$IK3_01               |     5705 (+) |  0.915 |  0.871 | acttAGGAAtccc
 V$IK3_01               |     5709 (-) |  0.778 |  0.758 | aggaATCCCacaa
 V$IK3_01               |     5861 (-) |  1.000 |  0.796 | tggtTTCCCatgg
 V$IK3_01               |     5915 (-) |  1.000 |  0.751 | ttgtTTCCCcagc
 V$IK3_01               |     6087 (-) |  0.915 |  0.760 | tgagTTCCTgtgt
 V$IK3_01               |     6137 (-) |  0.887 |  0.773 | cgtcTTCCAtgcc
 V$IK3_01               |     6176 (-) |  1.000 |  0.863 | agggTTCCCagag
 V$IK3_01               |     6201 (+) |  0.778 |  0.776 | gccgGGGTAtgcc
 V$IK3_01               |     6206 (-) |  0.665 |  0.736 | ggtaTGCCAaggt
 V$IK3_01               |     6273 (+) |  0.915 |  0.751 | aagaAGGAAgcct
 V$IK3_01               |     6315 (-) |  1.000 |  0.774 | ctacTTCCCtgac
 V$IK3_01               |     6797 (-) |  0.915 |  0.757 | gctcTTCCTcccc
 V$IK3_01               |     6875 (+) |  0.915 |  0.761 | ttatAGGAAgcac
 V$IK3_01               |     6916 (+) |  0.915 |  0.771 | aacaAGGAAttga
 V$IK3_01               |     6972 (+) |  0.915 |  0.766 | ggaaAGGAAcgac
 V$IK3_01               |     7016 (-) |  0.778 |  0.750 | gatgTTTCCtgca
 V$IK3_01               |     7228 (+) |  0.915 |  0.743 | cagcAGGAAgttc
 V$IK3_01               |     7245 (+) |  0.915 |  0.749 | tctcAGGAAaaag
 V$IK3_01               |     7326 (+) |  0.887 |  0.742 | cgtcTGGAAcaat
 V$IK3_01               |     7952 (-) |  0.778 |  0.737 | gagaTACCCcaga
 V$IK3_01               |     7982 (+) |  1.000 |  0.819 | tcaaGGGAAggac
 V$IK3_01               |     8070 (-) |  0.665 |  0.737 | ggtaTTGCAgaaa
 V$IK3_01               |     8080 (-) |  0.915 |  0.739 | aaacTTCCTatac
 V$IK3_01               |     8143 (+) |  1.000 |  0.822 | ctgaGGGAAaaca
 V$IK3_01               |     8608 (-) |  0.887 |  0.779 | atcaTTCCGtcaa
 V$IK3_01               |     8649 (-) |  1.000 |  0.849 | acaaTTCCCaatg
 V$IK3_01               |     8676 (+) |  0.915 |  0.741 | ggttAGGAAggta
 V$IK3_01               |     8909 (+) |  0.915 |  0.860 | attcAGGAAtact
 V$IK3_01               |     8918 (+) |  0.887 |  0.846 | tactCGGAAttca
 V$IK3_01               |     8992 (-) |  0.887 |  0.740 | ttaaTTCCAgcac
 V$IK3_01               |     9120 (+) |  1.000 |  0.893 | aaccGGGAAaacc
 V$IK3_01               |     9159 (-) |  0.915 |  0.819 | tgagTTCCTaaga
 V$IK3_01               |     9300 (-) |  0.778 |  0.756 | tgtgTGCCCagga
 V$IK3_01               |     9361 (-) |  0.778 |  0.734 | agtgTTCTCtatc
 V$IK3_01               |     9391 (+) |  0.887 |  0.760 | ccccTGGAAtgtg
 V$IK3_01               |     9433 (+) |  0.915 |  0.798 | taacAGGAAgccc
 V$IK3_01               |     9509 (-) |  1.000 |  0.769 | aagtTTCCCcatg
 V$IK3_01               |     9591 (-) |  0.778 |  0.795 | tgtaATCCCagca
 V$IK3_01               |     9603 (+) |  1.000 |  0.779 | atttGGGAAgctg
 V$IK3_01               |     9872 (+) |  0.915 |  0.743 | aatgAGGAAatca
 V$IK3_01               |    10115 (-) |  0.778 |  0.755 | gccaTCCCCaata
 V$IK3_01               |    10636 (+) |  0.915 |  0.769 | actgAGGAAgaca
 V$IK3_01               |    10688 (+) |  0.778 |  0.770 | ctctGGCAAcacc
 V$IK3_01               |    10842 (+) |  0.915 |  0.737 | tcgcAGGAAgaag
 V$IK3_01               |    10877 (+) |  0.778 |  0.754 | tggtGGGAGcact
 V$IK3_01               |    10991 (+) |  0.887 |  0.749 | gcccTGGAAtcag
 V$IK3_01               |    11083 (+) |  1.000 |  0.875 | ctctGGGAAtttt
 V$IK3_01               |    11479 (-) |  1.000 |  0.811 | gtttTTCCCttgg
 V$IK3_01               |    11485 (+) |  0.887 |  0.814 | ccctTGGAAtgcg
 V$IK3_01               |    11768 (-) |  0.887 |  0.831 | aggaTTCCAgata
 P$ATHB1_01             |     4057 (-) |  1.000 |  0.978 | ggcaATAATtaaaa
 I$ABDB_01              |       46 (-) |  0.769 |  0.802 | gatgtcATTACttg
 I$ABDB_01              |       58 (-) |  0.745 |  0.819 | tgggccATAATtac
 I$ABDB_01              |      174 (-) |  0.769 |  0.793 | gctggcATTACtac
 I$ABDB_01              |      385 (-) |  0.799 |  0.853 | gatgccATTCAttt
 I$ABDB_01              |      396 (-) |  0.684 |  0.793 | tttgccAACAAggc
 I$ABDB_01              |      564 (-) |  1.000 |  0.842 | taggagATAAAcgt
 I$ABDB_01              |      618 (+) |  0.771 |  0.817 | tcgTACATgacact
 I$ABDB_01              |     1790 (-) |  0.799 |  0.853 | cctgccATTCAcag
 I$ABDB_01              |     1840 (-) |  0.813 |  0.835 | ggggtcGTCAAcac
 I$ABDB_01              |     1975 (-) |  0.779 |  0.812 | gttggcCTCAAact
 I$ABDB_01              |     2022 (-) |  0.960 |  0.816 | gctgggATTAAagg
 I$ABDB_01              |     2661 (+) |  0.951 |  0.936 | actTTGATgacact
 I$ABDB_01              |     2736 (+) |  1.000 |  0.954 | gccTTTATgccttt
 I$ABDB_01              |     2979 (-) |  0.790 |  0.806 | gcaggcATCTActt
 I$ABDB_01              |     3272 (-) |  0.705 |  0.792 | gatgccATTATgat
 I$ABDB_01              |     3401 (-) |  1.000 |  0.856 | ccagttATAAAagt
 I$ABDB_01              |     3472 (+) |  0.862 |  0.819 | tgaTTTACtgccta
 I$ABDB_01              |     3843 (-) |  1.000 |  0.807 | attctcATAAAata
 I$ABDB_01              |     3902 (-) |  0.960 |  0.802 | acaggtATTAAtaa
 I$ABDB_01              |     3916 (+) |  1.000 |  0.789 | agcTTTATgaatta
 I$ABDB_01              |     4026 (-) |  0.960 |  0.831 | catggaATTAAtat
 I$ABDB_01              |     4199 (+) |  0.789 |  0.846 | aagTTCAAggcttg
 I$ABDB_01              |     4332 (-) |  0.790 |  0.819 | ggtgacATCCAggt
 I$ABDB_01              |     4453 (+) |  0.932 |  0.814 | ataTTCATttcaca
 I$ABDB_01              |     4694 (+) |  0.951 |  0.909 | aacTTGATgtccta
 I$ABDB_01              |     5010 (-) |  0.960 |  0.824 | ttacccATTAAgcc
 I$ABDB_01              |     5298 (-) |  0.790 |  0.847 | ctagccATCCAaaa
 I$ABDB_01              |     5438 (+) |  0.839 |  0.798 | attTGTATtgccat
 I$ABDB_01              |     5444 (-) |  0.839 |  0.893 | attgccATATAacc
 I$ABDB_01              |     5483 (+) |  0.951 |  0.794 | tttTTGATcccctt
 I$ABDB_01              |     5631 (-) |  1.000 |  0.831 | actgggATAAAgac
 I$ABDB_01              |     5735 (-) |  0.745 |  0.815 | gaagccATAATata
 I$ABDB_01              |     6139 (+) |  0.758 |  0.795 | tctTCCATgcctct
 I$ABDB_01              |     6193 (+) |  0.857 |  0.861 | ccaTTTAAgccggg
 I$ABDB_01              |     6444 (+) |  0.741 |  0.829 | ccaGTCATggcaaa
 I$ABDB_01              |     6759 (+) |  1.000 |  0.840 | cccTTTATaccatg
 I$ABDB_01              |     6825 (+) |  1.000 |  0.791 | tttTTTATgtgcta
 I$ABDB_01              |     6836 (+) |  0.862 |  0.811 | ctaTTTACtgccaa
 I$ABDB_01              |     6900 (-) |  0.754 |  0.793 | gagggcATAAGtgg
 I$ABDB_01              |     7200 (-) |  0.932 |  0.828 | ggtgctATGAAttg
 I$ABDB_01              |     7438 (+) |  1.000 |  0.793 | tatTTTATgtgtgg
 I$ABDB_01              |     7656 (+) |  0.839 |  0.835 | tttTGTATgccagg
 I$ABDB_01              |     7681 (-) |  0.862 |  0.795 | acagctGTAAAgcc
 I$ABDB_01              |     7731 (-) |  0.759 |  0.840 | tgggccATCACagg
 I$ABDB_01              |     7920 (-) |  0.951 |  0.799 | ttaggtATCAAttc
 I$ABDB_01              |     8258 (-) |  0.786 |  0.815 | cgtggcATTGAcct
 I$ABDB_01              |     8466 (+) |  0.683 |  0.790 | tcaTCTAAggcaaa
 I$ABDB_01              |     8868 (-) |  0.826 |  0.827 | tctggcATAGAata
 I$ABDB_01              |     8989 (+) |  0.960 |  0.844 | cctTTAATtccagc
 I$ABDB_01              |     9051 (+) |  0.771 |  0.838 | gtcTACATggcaag
 I$ABDB_01              |     9403 (+) |  0.826 |  0.842 | ggtTCTATgtctag
 I$ABDB_01              |     9422 (-) |  1.000 |  0.833 | tatcccATAAAtaa
 I$ABDB_01              |     9717 (+) |  0.951 |  0.797 | aaaTTGATctcttt
 I$ABDB_01              |     9772 (-) |  0.826 |  0.879 | catgccATAGAaca
 I$ABDB_01              |     9840 (+) |  0.816 |  0.823 | attTTAAAgtcagg
 I$ABDB_01              |     9857 (-) |  0.857 |  0.806 | gcagcaTTAAAgaa
 I$ABDB_01              |     9875 (-) |  0.951 |  0.826 | gaggaaATCAAttt
 I$ABDB_01              |     9897 (+) |  0.816 |  0.831 | tttTTAAAgactta
 I$ABDB_01              |    10214 (-) |  0.790 |  0.816 | agtggcATCTAaga
 I$ABDB_01              |    10450 (+) |  1.000 |  0.842 | tctTTTATatcaac
 I$ABDB_01              |    10507 (+) |  0.745 |  0.829 | tcaATTATggctgt
 I$ABDB_01              |    10519 (-) |  0.705 |  0.806 | gtagccATTATagg
 I$ABDB_01              |    11175 (+) |  0.733 |  0.812 | atcTTTTTggctgc
 I$ABDB_01              |    11272 (-) |  0.960 |  0.844 | aaggaaATTAAggc
 I$ABDB_01              |    11338 (+) |  0.799 |  0.810 | atgTAAATgccatt
 I$ABDB_01              |    11343 (-) |  0.705 |  0.802 | aatgccATTATcga
 I$ABDB_01              |    11667 (+) |  0.932 |  0.800 | attTTCATaaccaa
 I$ABDB_01              |    11693 (+) |  0.960 |  0.817 | aagTTAATcactgt
 I$BRCZ1_01             |     2407 (+) |  1.000 |  0.902 | ttaaaaaaaACAAAaaat
 I$BRCZ1_01             |     5792 (+) |  1.000 |  0.894 | taattaaatACAAAaaaa
 I$BRCZ1_01             |     6578 (+) |  1.000 |  0.899 | atgcaaaacACAAAacaa
 I$BRCZ1_01             |     7426 (-) |  1.000 |  0.912 | tttaTTTGTttttatttt
 I$BRCZ1_01             |     7769 (+) |  1.000 |  0.897 | tctcaaaaaACAAAacaa
 I$BRCZ1_01             |    11472 (-) |  1.000 |  0.914 | tttaTTTGTttttccctt
 I$BRCZ2_01             |      311 (+) |  0.948 |  0.865 | atctctcCTAGTcctg
 I$BRCZ2_01             |     1637 (+) |  0.948 |  0.871 | gcctttcCTAGTgcta
 I$BRCZ2_01             |     1648 (+) |  0.940 |  0.852 | tgctaatCTACTtggc
 I$BRCZ2_01             |     2283 (+) |  0.948 |  0.945 | ttctcttCTAGTtttt
 I$BRCZ2_01             |     2717 (-) |  1.000 |  0.870 | cccaAATAGataatct
 I$BRCZ2_01             |     3083 (+) |  1.000 |  0.933 | ggtgattCTATTtttc
 I$BRCZ2_01             |     3101 (+) |  0.940 |  0.850 | atctataCTAATttcc
 I$BRCZ2_01             |     3329 (+) |  1.000 |  0.856 | cctgattCTATTtccc
 I$BRCZ2_01             |     3365 (-) |  1.000 |  0.851 | actgAATAGcctaatc
 I$BRCZ2_01             |     3587 (+) |  0.887 |  0.858 | aactctcCTATGtttg
 I$BRCZ2_01             |     3738 (+) |  0.841 |  0.850 | attatttCTACAtttt
 I$BRCZ2_01             |     3800 (-) |  1.000 |  0.907 | acagAATAGaaaaaac
 I$BRCZ2_01             |     4079 (+) |  0.901 |  0.901 | atgtataCTATAtttt
 I$BRCZ2_01             |     4161 (+) |  0.948 |  0.850 | tgtaatcCTAGTattc
 I$BRCZ2_01             |     5464 (+) |  1.000 |  0.854 | ccacataCTATTtcct
 I$BRCZ2_01             |     5809 (-) |  1.000 |  0.925 | aaaaAATAGccctggc
 I$BRCZ2_01             |     6247 (+) |  1.000 |  0.929 | cggctttCTATTtgtc
 I$BRCZ2_01             |     6600 (+) |  1.000 |  0.875 | ggtggtgCTATTtgct
 I$BRCZ2_01             |     6829 (+) |  1.000 |  0.883 | ttatgtgCTATTtact
 I$BRCZ2_01             |     7042 (+) |  1.000 |  0.957 | tagttgaCTATTtttt
 I$BRCZ2_01             |     7217 (-) |  0.940 |  0.907 | aaaaAGTAGgccagca
 I$BRCZ2_01             |     7332 (-) |  1.000 |  0.871 | gaacAATAGacacatt
 I$BRCZ2_01             |     8952 (-) |  0.940 |  0.879 | taaaATTAGtagggag
 I$BRCZ2_01             |     9527 (-) |  0.948 |  0.875 | caagACTAGaacaaac
 I$BRCZ2_01             |    10126 (-) |  0.940 |  0.907 | taaaATTAGttaagaa
 I$BRCZ2_01             |    10916 (-) |  1.000 |  0.903 | aaatAATAGtctagcg
 I$BRCZ2_01             |    11416 (+) |  1.000 |  0.905 | tgcatttCTATTtagc
 I$BRCZ2_01             |    11440 (+) |  1.000 |  0.901 | tacttatCTATTttgg
 I$BRCZ2_01             |    11748 (-) |  0.948 |  0.882 | aatgACTAGaaagagt
 I$BRCZ2_01             |    11897 (-) |  1.000 |  0.897 | aaccAATAGcacgaag
 I$BRCZ3_01             |      835 (+) |  0.939 |  0.906 | tataaAACAAgttaa
 I$BRCZ3_01             |     1034 (+) |  0.939 |  0.853 | gaatcAACAAagcag
 I$BRCZ3_01             |     1089 (+) |  1.000 |  0.908 | tggtcAACTAaaatt
 I$BRCZ3_01             |     1144 (-) |  0.851 |  0.846 | accgtTACTTtatgt
 I$BRCZ3_01             |     1153 (-) |  1.000 |  0.854 | ttatgTAGTTctttt
 I$BRCZ3_01             |     1895 (-) |  0.834 |  0.861 | atattTATTTtatta
 I$BRCZ3_01             |     1903 (-) |  0.834 |  0.855 | tttatTATTTtattt
 I$BRCZ3_01             |     2286 (-) |  1.000 |  0.953 | tcttcTAGTTtttgt
 I$BRCZ3_01             |     2410 (+) |  0.939 |  0.924 | aaaaaAACAAaaaat
 I$BRCZ3_01             |     2601 (+) |  0.879 |  0.887 | tattaAACCAagagc
 I$BRCZ3_01             |     3101 (+) |  0.849 |  0.850 | atctaTACTAatttc
 I$BRCZ3_01             |     3124 (-) |  0.851 |  0.856 | tatatTAATTtacat
 I$BRCZ3_01             |     3254 (-) |  0.879 |  0.855 | acttaTGGTTttctt
 I$BRCZ3_01             |     3305 (-) |  1.000 |  0.847 | ccatgTAGTTaagat
 I$BRCZ3_01             |     3656 (+) |  0.851 |  0.863 | cagtaAAGTAacaca
 I$BRCZ3_01             |     3994 (+) |  0.939 |  0.868 | catgaAACAAcgata
 I$BRCZ3_01             |     4487 (+) |  0.939 |  0.846 | ttttgAACAAaaaac
 I$BRCZ3_01             |     4494 (+) |  0.939 |  0.927 | caaaaAACAAaacaa
 I$BRCZ3_01             |     4499 (+) |  0.939 |  0.927 | aacaaAACAAaacaa
 I$BRCZ3_01             |     4504 (+) |  0.939 |  0.892 | aacaaAACAAcatca
 I$BRCZ3_01             |     4545 (-) |  1.000 |  0.947 | cctctTAGTTttgat
 I$BRCZ3_01             |     4614 (+) |  0.879 |  0.857 | ggtaaAACCAatatc
 I$BRCZ3_01             |     4661 (-) |  0.939 |  0.903 | ggactTTGTTttgct
 I$BRCZ3_01             |     4673 (-) |  1.000 |  0.854 | gctcaTAGTTctgtg
 I$BRCZ3_01             |     5335 (-) |  1.000 |  0.927 | gccgaTAGTTttgca
 I$BRCZ3_01             |     5378 (-) |  1.000 |  0.979 | tctttTAGTTttatt
 I$BRCZ3_01             |     5384 (-) |  0.834 |  0.852 | agtttTATTTtacct
 I$BRCZ3_01             |     5561 (+) |  0.939 |  0.873 | tagaaAACAAccagg
 I$BRCZ3_01             |     5610 (+) |  0.879 |  0.850 | caagaAACCAacatc
 I$BRCZ3_01             |     5690 (-) |  1.000 |  0.873 | cccacTAGTTcatac
 I$BRCZ3_01             |     5832 (+) |  0.939 |  0.880 | tgtgaAACAAggcat
 I$BRCZ3_01             |     5856 (-) |  0.879 |  0.847 | tgagtTGGTTtccca
 I$BRCZ3_01             |     5906 (-) |  1.000 |  0.917 | aagagTAGTTtgttt
 I$BRCZ3_01             |     5910 (-) |  0.939 |  0.889 | gtagtTTGTTtcccc
 I$BRCZ3_01             |     5940 (+) |  0.851 |  0.853 | gagaaAAGTAaaatt
 I$BRCZ3_01             |     6120 (-) |  0.939 |  0.897 | agggcTTGTTttctc
 I$BRCZ3_01             |     6586 (+) |  0.939 |  0.910 | cacaaAACAAataag
 I$BRCZ3_01             |     7037 (-) |  1.000 |  0.903 | agagtTAGTTgacta
 I$BRCZ3_01             |     7061 (-) |  0.939 |  0.903 | ttaatTTGTTtttgt
 I$BRCZ3_01             |     7067 (-) |  0.939 |  0.904 | tgtttTTGTTtgtgt
 I$BRCZ3_01             |     7209 (+) |  0.939 |  0.861 | aattgAACAAaaagt
 I$BRCZ3_01             |     7426 (-) |  0.939 |  0.907 | tttatTTGTTtttat
 I$BRCZ3_01             |     7564 (+) |  0.879 |  0.854 | ctggaAACCAaatcc
 I$BRCZ3_01             |     7585 (+) |  0.939 |  0.895 | ggtcaAACAAatgct
 I$BRCZ3_01             |     7772 (+) |  0.939 |  0.927 | caaaaAACAAaacaa
 I$BRCZ3_01             |     7777 (+) |  0.939 |  0.923 | aacaaAACAAaaatt
 I$BRCZ3_01             |     7819 (+) |  0.939 |  0.894 | tccaaAACAAacaat
 I$BRCZ3_01             |     7823 (+) |  0.939 |  0.881 | aaacaAACAAttaac
 I$BRCZ3_01             |     7887 (-) |  0.879 |  0.871 | tcattTGGTTtttat
 I$BRCZ3_01             |     7927 (-) |  0.879 |  0.849 | tcaatTCGTTtgtgt
 I$BRCZ3_01             |     7940 (-) |  1.000 |  0.959 | gtgttTAGTTttgag
 I$BRCZ3_01             |     7963 (-) |  1.000 |  0.872 | gactaTAGTTgtttg
 I$BRCZ3_01             |     7966 (-) |  0.939 |  0.873 | tatagTTGTTtgttt
 I$BRCZ3_01             |     7970 (-) |  0.939 |  0.900 | gttgtTTGTTtttca
 I$BRCZ3_01             |     8055 (-) |  1.000 |  0.972 | aggtcTAGTTtatct
 I$BRCZ3_01             |     8181 (-) |  0.939 |  0.893 | agaacTTGTTtgctc
 I$BRCZ3_01             |     8832 (+) |  0.879 |  0.869 | ttcaaAACCAaaaca
 I$BRCZ3_01             |     8931 (+) |  1.000 |  0.984 | gtataAACTAaagca
 I$BRCZ3_01             |     9108 (+) |  0.939 |  0.914 | agcaaAACAAaaaac
 I$BRCZ3_01             |     9414 (+) |  1.000 |  0.938 | tagaaAACTAtccca
 I$BRCZ3_01             |     9535 (+) |  0.939 |  0.894 | gaacaAACAAgtcct
 I$BRCZ3_01             |     9784 (-) |  0.939 |  0.854 | caattTTGTTcagta
 I$BRCZ3_01             |    10024 (-) |  1.000 |  0.898 | gaccgTAGTTtgtga
 I$BRCZ3_01             |    10127 (-) |  1.000 |  0.875 | aaaatTAGTTaagaa
 I$BRCZ3_01             |    10323 (-) |  0.834 |  0.848 | attttTATTTtatag
 I$BRCZ3_01             |    10330 (-) |  1.000 |  0.940 | ttttaTAGTTtttat
 I$BRCZ3_01             |    10339 (-) |  0.939 |  0.891 | ttttaTTGTTttaat
 I$BRCZ3_01             |    11185 (-) |  0.939 |  0.885 | ctgccTTGTTtcttg
 I$BRCZ3_01             |    11208 (-) |  0.939 |  0.895 | ttaatTTGTTtgaac
 I$BRCZ3_01             |    11472 (-) |  0.939 |  0.910 | tttatTTGTTtttcc
 I$BRCZ3_01             |    11630 (-) |  0.879 |  0.858 | gacccTCGTTtaaat
 I$BRCZ3_01             |    11878 (-) |  1.000 |  0.863 | ggactTAGTTctcac
 I$BRCZ3_01             |    11935 (+) |  1.000 |  0.918 | gctgaAACTAtttca
 I$BRCZ4_01             |      221 (-) |  0.936 |  0.926 | tttttTTTCCttt
 I$BRCZ4_01             |      631 (-) |  0.974 |  0.926 | tttttTTTAAaca
 I$BRCZ4_01             |      647 (-) |  1.000 |  0.916 | attcaTTTATtat
 I$BRCZ4_01             |     1893 (-) |  1.000 |  0.967 | ttataTTTATttt
 I$BRCZ4_01             |     1898 (-) |  1.000 |  0.941 | tttatTTTATtat
 I$BRCZ4_01             |     2360 (-) |  1.000 |  0.959 | ttgtaTTTATttt
 I$BRCZ4_01             |     2404 (+) |  0.974 |  0.917 | tccTTAAAaaaaa
 I$BRCZ4_01             |     4003 (+) |  1.000 |  0.917 | acgATAAAtaaat
 I$BRCZ4_01             |     4421 (+) |  0.961 |  0.917 | tgtCTAAAaaaaa
 I$BRCZ4_01             |     5393 (-) |  1.000 |  0.933 | ttaccTTTATatt
 I$BRCZ4_01             |     5645 (+) |  1.000 |  0.942 | aaaATAAAaagaa
 I$BRCZ4_01             |     5792 (+) |  0.974 |  0.942 | taaTTAAAtacaa
 I$BRCZ4_01             |     6670 (-) |  0.961 |  0.934 | ttttaTTTAGctt
 I$BRCZ4_01             |     7052 (-) |  0.948 |  0.942 | tttttTTTCTtaa
 I$BRCZ4_01             |     7431 (-) |  1.000 |  0.950 | ttgttTTTATttt
 I$BRCZ4_01             |     8930 (+) |  1.000 |  0.933 | agtATAAActaaa
 I$BRCZ4_01             |    10321 (-) |  1.000 |  0.926 | atattTTTATttt
 I$BRCZ4_01             |    10326 (-) |  1.000 |  0.916 | tttatTTTATagt
 V$PBX1_01              |     1050 (+) |  1.000 |  0.956 | aaaAATCAa
 V$PBX1_01              |     3908 (+) |  0.948 |  0.943 | attAATAAa
 V$PBX1_01              |    10340 (-) |  0.948 |  0.948 | tTTATTgtt
 V$PBX1_01              |    11197 (-) |  1.000 |  1.000 | tTGATTgat
 V$PBX1_01              |    11201 (-) |  1.000 |  0.968 | tTGATTatt
 V$PBX1_01              |    11686 (+) |  0.948 |  0.950 | accAATAAa
 V$PAX6_01              |      473 (-) |  0.660 |  0.705 | tgacacttacaAGTCAacatt
 V$PAX6_01              |      525 (-) |  0.722 |  0.770 | taaaaatgatgGGTGAtgcgc
 V$PAX6_01              |      711 (+) |  0.688 |  0.689 | tctctTTACAgatggttgtga
 V$PAX6_01              |      908 (-) |  0.682 |  0.707 | tttctttcatgCGTAGcactt
 V$PAX6_01              |     1339 (+) |  0.749 |  0.756 | gggctTAAGGcttgcctgggt
 V$PAX6_01              |     2462 (-) |  0.812 |  0.723 | ggcctagcaagCGCGAaggcc
 V$PAX6_01              |     2519 (+) |  0.688 |  0.687 | aaaaaTTACAtattactttta
 V$PAX6_01              |     2735 (+) |  0.802 |  0.697 | tgcctTTATGcctttttcttt
 V$PAX6_01              |     2870 (-) |  0.735 |  0.687 | cagaactccacCGTGTatgcg
 V$PAX6_01              |     3464 (+) |  0.842 |  0.742 | gggccTCATGatttactgcct
 V$PAX6_01              |     3697 (-) |  0.832 |  0.729 | cacaagagatgCTTGAtcaat
 V$PAX6_01              |     3714 (-) |  0.722 |  0.695 | caatatttacgGGTGActaaa
 V$PAX6_01              |     3715 (+) |  0.960 |  0.855 | aatatTTACGggtgactaaaa
 V$PAX6_01              |     3751 (-) |  0.792 |  0.784 | ttttagtcattCTTAAaaggc
 V$PAX6_01              |     3863 (-) |  0.665 |  0.709 | accatttaaggAGTTAataca
 V$PAX6_01              |     3864 (+) |  0.749 |  0.713 | ccattTAAGGagttaatacaa
 V$PAX6_01              |     3907 (-) |  0.763 |  0.742 | tattaataaagCTTTAtgaat
 V$PAX6_01              |     3915 (+) |  0.802 |  0.745 | aagctTTATGaattacattat
 V$PAX6_01              |     4091 (-) |  0.604 |  0.687 | ttttactgattCTAAAacatc
 V$PAX6_01              |     4283 (-) |  0.778 |  0.693 | acacattagacCCTAAatttg
 V$PAX6_01              |     4306 (-) |  0.802 |  0.750 | cctcaatactgCATAAaactg
 V$PAX6_01              |     4525 (-) |  0.925 |  0.829 | gacaacaaatgCGTCAacagc
 V$PAX6_01              |     5166 (+) |  0.735 |  0.764 | gacttTCACTtgtgactgtgt
 V$PAX6_01              |     5182 (+) |  0.644 |  0.702 | tgtgtTCTAGcaggatttgtc
 V$PAX6_01              |     5376 (+) |  0.604 |  0.711 | tttctTTTAGttttattttac
 V$PAX6_01              |     6426 (-) |  0.647 |  0.689 | tggctttcatcGGTCAaccca
 V$PAX6_01              |     6570 (-) |  0.613 |  0.701 | ccacagttatgCAAAAcacaa
 V$PAX6_01              |     6720 (-) |  0.722 |  0.687 | aacctttaaagGGTGAgcagc
 V$PAX6_01              |     6721 (+) |  0.763 |  0.694 | accttTAAAGggtgagcagcc
 V$PAX6_01              |     7017 (+) |  0.673 |  0.758 | atgttTCCTGcatcagctgaa
 V$PAX6_01              |     7028 (-) |  0.665 |  0.684 | atcagctgaagAGTTAgttga
 V$PAX6_01              |     7029 (+) |  0.757 |  0.690 | tcagcTGAAGagttagttgac
 V$PAX6_01              |     7071 (+) |  0.613 |  0.735 | tttgtTTGTGtatgagtgctt
 V$PAX6_01              |     7415 (+) |  0.763 |  0.794 | actttTAAAGgtttatttgtt
 V$PAX6_01              |     7682 (-) |  0.630 |  0.716 | cagctgtaaagCCAGAacttg
 V$PAX6_01              |     7915 (+) |  0.778 |  0.739 | tttacTTAGGtatcaattcgt
 V$PAX6_01              |     8465 (-) |  0.613 |  0.688 | ctcatctaaggCAAAAataag
 V$PAX6_01              |     8518 (-) |  0.757 |  0.753 | actcacagatgCTTCAagaac
 V$PAX6_01              |     8537 (-) |  0.812 |  0.697 | acacagtgggcCGAGAaaatg
 V$PAX6_01              |     9112 (-) |  0.831 |  0.715 | aaacaaaaaacCGGGAaaacc
 V$PAX6_01              |     9163 (-) |  0.842 |  0.722 | ttcctaagatgCATGAacgcc
 V$PAX6_01              |     9765 (-) |  0.561 |  0.698 | aaacagtcatgCCATAgaaca
 V$PAX6_01              |     9896 (+) |  0.763 |  0.761 | tttttTAAAGacttacttact
 V$PAX6_01              |    10267 (+) |  0.756 |  0.695 | attttTGCCGgctgagcaatc
 V$PAX6_01              |    10337 (+) |  0.584 |  0.702 | gttttTATTGttttaattcaa
 V$PAX6_01              |    10746 (-) |  0.735 |  0.723 | tttcagtgatcCGTGTgtttg
 V$PAX6_01              |    11099 (+) |  0.763 |  0.709 | ctgttTAAAGaacgacttcag
 V$PAX6_01              |    11156 (-) |  0.589 |  0.705 | tgaaaatgaagCTGCAgagat
 V$PAX6_01              |    11190 (+) |  0.654 |  0.711 | ttgttTCTTGattgattatta
 V$PAX6_01              |    11397 (+) |  0.688 |  0.719 | attttGTACGcatttattctg
 V$PAX6_01              |    11448 (+) |  0.579 |  0.708 | tatttTGGTGaatcagtgaaa
 V$PAX6_01              |    11941 (-) |  0.647 |  0.683 | actatttcaagGGTCAggact
 V$PAX6_01              |    11942 (+) |  0.832 |  0.709 | ctattTCAAGggtcaggactg
 V$PAX2_01              |      133 (+) |  0.979 |  0.767 | ctcaGTCAAtccagacatt
 V$PAX2_01              |      134 (-) |  0.822 |  0.803 | tcagtcaatcCAGACattt
 V$PAX2_01              |      283 (+) |  0.979 |  0.839 | gcaaGTCAAgtgttttaca
 V$PAX2_01              |      520 (-) |  0.893 |  0.744 | gattttaaaaATGATgggt
 V$PAX2_01              |      527 (-) |  0.902 |  0.783 | aaaatgatggGTGATgcgc
 V$PAX2_01              |      613 (+) |  0.825 |  0.770 | tcctGTCGTacatgacact
 V$PAX2_01              |      614 (-) |  0.991 |  0.875 | cctgtcgtacATGACactt
 V$PAX2_01              |      644 (+) |  0.857 |  0.798 | tttaTTCATttattatata
 V$PAX2_01              |      909 (+) |  0.857 |  0.757 | ttctTTCATgcgtagcact
 V$PAX2_01              |      939 (+) |  0.847 |  0.784 | acaaGTTAGgaacaatgat
 V$PAX2_01              |     1087 (+) |  0.979 |  0.798 | tttgGTCAActaaaatttg
 V$PAX2_01              |     1219 (-) |  0.991 |  0.767 | ggagtttctgATGACtgct
 V$PAX2_01              |     1258 (+) |  0.893 |  0.756 | tgtcATCATccgtgtgtac
 V$PAX2_01              |     1273 (-) |  0.991 |  0.768 | gtactctgggATGACaggg
 V$PAX2_01              |     1817 (+) |  0.837 |  0.808 | ggtgTTCAGggaagacacc
 V$PAX2_01              |     2327 (-) |  1.000 |  0.763 | gtcttgctatGTGACccta
 V$PAX2_01              |     2586 (-) |  0.970 |  0.759 | aaatgcagtaCTGACtatt
 V$PAX2_01              |     2635 (-) |  0.970 |  0.819 | tgctctacccCTGACctgc
 V$PAX2_01              |     2666 (-) |  0.856 |  0.759 | gatgacactcTTAACccgt
 V$PAX2_01              |     2961 (+) |  0.826 |  0.744 | tacaGTGACggcagatgcg
 V$PAX2_01              |     3038 (-) |  0.833 |  0.761 | cgctccacccGGGACatac
 V$PAX2_01              |     3199 (+) |  0.819 |  0.767 | ctgcCTCAAgtatgctagg
 V$PAX2_01              |     3229 (+) |  0.970 |  0.784 | accaGTCAGccaacattcc
 V$PAX2_01              |     3308 (+) |  0.856 |  0.762 | tgtaGTTAAgattggcctt
 V$PAX2_01              |     3464 (+) |  0.831 |  0.779 | gggcCTCATgatttactgc
 V$PAX2_01              |     3699 (-) |  0.881 |  0.821 | caagagatgcTTGATcaat
 V$PAX2_01              |     3708 (+) |  0.881 |  0.780 | cttgATCAAtatttacggg
 V$PAX2_01              |     3716 (-) |  1.000 |  0.862 | atatttacggGTGACtaaa
 V$PAX2_01              |     3752 (+) |  0.991 |  0.832 | tttaGTCATtcttaaaagg
 V$PAX2_01              |     3880 (-) |  0.979 |  0.772 | tacaagctccTTGACcctc
 V$PAX2_01              |     3916 (-) |  0.797 |  0.745 | agctttatgaATTACatta
 V$PAX2_01              |     3928 (-) |  0.826 |  0.762 | tacattatcaGTCACttgt
 V$PAX2_01              |     3934 (+) |  1.000 |  0.794 | atcaGTCACttgttcattc
 V$PAX2_01              |     3988 (+) |  0.831 |  0.760 | ccatCTCATgaaacaacga
 V$PAX2_01              |     4403 (+) |  0.970 |  0.783 | acagGTCAGccacaacctt
 V$PAX2_01              |     4461 (-) |  0.970 |  0.747 | ttcacactgaCTGACcagc
 V$PAX2_01              |     4552 (-) |  0.813 |  0.800 | gttttgatgcTGGACacag
 V$PAX2_01              |     4687 (-) |  0.881 |  0.754 | ggcaggaaacTTGATgtcc
 V$PAX2_01              |     4783 (-) |  0.970 |  0.752 | ataaagattgCTGACttgc
 V$PAX2_01              |     4845 (-) |  0.805 |  0.763 | atcctgagacTTCACtgag
 V$PAX2_01              |     4864 (+) |  0.970 |  0.749 | ggagGTCAGcagcaaagct
 V$PAX2_01              |     4928 (+) |  0.893 |  0.746 | acagATCATggagactgaa
 V$PAX2_01              |     4965 (+) |  0.970 |  0.746 | ggaaGTCAGgctcagcccc
 V$PAX2_01              |     5034 (+) |  0.810 |  0.751 | gatgCTCAGgattgctgtg
 V$PAX2_01              |     5062 (+) |  0.796 |  0.756 | ggtaGTGAGagatgagagg
 V$PAX2_01              |     5166 (+) |  0.866 |  0.796 | gactTTCACttgtgactgt
 V$PAX2_01              |     5167 (-) |  1.000 |  0.843 | actttcacttGTGACtgtg
 V$PAX2_01              |     5468 (-) |  0.872 |  0.796 | atactatttcCTGATtttt
 V$PAX2_01              |     5968 (-) |  0.902 |  0.742 | tttttaagtgGTGATaact
 V$PAX2_01              |     6281 (-) |  0.893 |  0.751 | agcctctctgATGATgact
 V$PAX2_01              |     6288 (-) |  0.810 |  0.779 | ctgatgatgaCTGAGcagg
 V$PAX2_01              |     6313 (-) |  0.970 |  0.812 | atctacttccCTGACtgaa
 V$PAX2_01              |     6345 (+) |  0.866 |  0.750 | ttctTTCACgaaagctcag
 V$PAX2_01              |     6443 (+) |  0.991 |  0.820 | cccaGTCATggcaaactta
 V$PAX2_01              |     6456 (-) |  0.872 |  0.817 | aacttatttcCTGATaaaa
 V$PAX2_01              |     6556 (+) |  0.991 |  0.822 | aagaGTCATggttgccaca
 V$PAX2_01              |     6571 (+) |  0.868 |  0.798 | cacaGTTATgcaaaacaca
 V$PAX2_01              |     6760 (-) |  0.857 |  0.762 | cctttataccATGAAcaaa
 V$PAX2_01              |     7323 (+) |  0.822 |  0.755 | gtacGTCTGgaacaataga
 V$PAX2_01              |     7951 (-) |  0.822 |  0.764 | tgagatacccCAGACtata
 V$PAX2_01              |     8037 (-) |  0.979 |  0.791 | ttgctgggccTTGACtcga
 V$PAX2_01              |     8102 (+) |  1.000 |  0.752 | tcctGTCACacactctccc
 V$PAX2_01              |     8200 (-) |  0.970 |  0.762 | tgtttcccctCTGACctca
 V$PAX2_01              |     8385 (-) |  0.837 |  0.753 | atctgtatacCTGAAgcca
 V$PAX2_01              |     8564 (+) |  0.843 |  0.762 | gtccGTCTTtgattaaatg
 V$PAX2_01              |     8612 (+) |  0.979 |  0.754 | ttccGTCAAtcactttgag
 V$PAX2_01              |     8706 (+) |  0.881 |  0.749 | taccATCAAggagtctgaa
 V$PAX2_01              |     8906 (+) |  0.837 |  0.752 | cagaTTCAGgaatactcgg
 V$PAX2_01              |     9165 (-) |  0.857 |  0.777 | cctaagatgcATGAAcgcc
 V$PAX2_01              |     9252 (+) |  0.831 |  0.777 | gctgCTCATgggacagggc
 V$PAX2_01              |     9336 (-) |  0.837 |  0.755 | tggaggacccCTGAAgtct
 V$PAX2_01              |     9518 (-) |  0.843 |  0.768 | catgtccaacAAGACtaga
 V$PAX2_01              |     9541 (+) |  0.825 |  0.748 | acaaGTCCTgcgtagtcgc
 V$PAX2_01              |     9766 (+) |  0.991 |  0.822 | aacaGTCATgccatagaac
 V$PAX2_01              |     9844 (+) |  0.970 |  0.819 | taaaGTCAGgcaggcagca
 V$PAX2_01              |    10184 (+) |  0.837 |  0.743 | tgtgTTCAGcagtcagttc
 V$PAX2_01              |    10191 (+) |  0.970 |  0.747 | agcaGTCAGttctgtcctt
 V$PAX2_01              |    10242 (+) |  0.970 |  0.853 | ggtgGTCAGgcttgtgcag
 V$PAX2_01              |    10286 (+) |  0.872 |  0.751 | tctcATCAGgcttcggaca
 V$PAX2_01              |    10468 (-) |  0.831 |  0.756 | catctcacttTAGACcagc
 V$PAX2_01              |    10488 (+) |  0.881 |  0.843 | acatATCAAggatcaaaag
 V$PAX2_01              |    10502 (+) |  0.979 |  0.798 | aaaaGTCAAttatggctgt
 V$PAX2_01              |    10623 (-) |  1.000 |  0.772 | gttgtagaaaGTGACtgag
 V$PAX2_01              |    11062 (-) |  0.806 |  0.752 | gttgtgatcaGTTACaagc
 V$PAX2_01              |    11064 (+) |  0.872 |  0.744 | tgtgATCAGttacaagctg
 V$PAX2_01              |    11187 (-) |  0.881 |  0.795 | gccttgtttcTTGATtgat
 V$PAX2_01              |    11191 (-) |  0.881 |  0.772 | tgtttcttgaTTGATtatt
 V$PAX2_01              |    11569 (+) |  0.893 |  0.766 | tcttATCATtgcttatatc
 V$PAX2_01              |    11663 (-) |  0.868 |  0.742 | cacaattttcATAACcaaa
 V$PAX2_01              |    11772 (-) |  0.881 |  0.789 | ttccagatacTTGATgtaa
 V$PAX2_01              |    11942 (+) |  0.846 |  0.827 | ctatTTCAAgggtcaggac
 V$PAX2_01              |    11949 (+) |  0.970 |  0.793 | aaggGTCAGgactgcacct
 V$S8_01                |       61 (-) |  1.000 |  0.969 | gccaTAATTactgttg
 V$S8_01                |     3428 (-) |  1.000 |  0.993 | tgctTAATTgacttag
 V$S8_01                |     4056 (+) |  1.000 |  0.972 | aggcaatAATTAaaat
 V$S8_01                |     4058 (-) |  1.000 |  0.981 | gcaaTAATTaaaatat
 V$S8_01                |     4441 (+) |  1.000 |  0.987 | accacacAATTAatat
 V$S8_01                |     5786 (+) |  1.000 |  0.984 | atgaaatAATTAaata
 V$S8_01                |     5788 (-) |  1.000 |  0.986 | gaaaTAATTaaataca
 V$S8_01                |     7824 (+) |  1.000 |  0.991 | aacaaacAATTAaccc
 V$S8_01                |     8681 (+) |  1.000 |  0.985 | ggaaggtAATTAgcct
 V$S8_01                |     8683 (-) |  1.000 |  0.982 | aaggTAATTagccttt
 V$S8_01                |    10502 (+) |  1.000 |  0.990 | aaaagtcAATTAtggc
 V$CDP_02               |      648 (+) |  0.703 |  0.777 | ttcATTTAttatata
 V$CDP_02               |     1107 (+) |  0.773 |  0.809 | gaaATCGCtgatttg
 V$CDP_02               |     1751 (-) |  0.912 |  0.912 | acactgaTCTATaag
 V$CDP_02               |     1754 (+) |  0.773 |  0.805 | ctgATCTAtaagcct
 V$CDP_02               |     2719 (+) |  0.912 |  0.908 | caaATAGAtaatctt
 V$CDP_02               |     3095 (-) |  0.912 |  0.819 | tttcgaaTCTATact
 V$CDP_02               |     3706 (-) |  0.930 |  0.911 | tgcttgaTCAATatt
 V$CDP_02               |     3999 (+) |  0.773 |  0.813 | aacAACGAtaaataa
 V$CDP_02               |     4103 (-) |  0.907 |  0.811 | taaaacaTCCATttt
 V$CDP_02               |     5233 (+) |  0.773 |  0.810 | gggAACGAttacatg
 V$CDP_02               |     5316 (-) |  0.773 |  0.789 | ttcttcaTCGGTtca
 V$CDP_02               |     6428 (-) |  0.773 |  0.797 | gctttcaTCGGTcaa
 V$CDP_02               |     6431 (+) |  0.773 |  0.805 | ttcATCGGtcaaccc
 V$CDP_02               |     6921 (+) |  0.930 |  0.831 | ggaATTGAttgtatg
 V$CDP_02               |     7372 (+) |  0.930 |  0.809 | agaATTGAtattgct
 V$CDP_02               |     7920 (-) |  0.930 |  0.813 | ttaggtaTCAATtcg
 V$CDP_02               |     9716 (+) |  0.930 |  0.833 | aaaATTGAtctcttt
 V$CDP_02               |     9875 (-) |  0.930 |  0.837 | gaggaaaTCAATtta
 V$CDP_02               |    10381 (-) |  0.907 |  0.825 | gttgcaaTCCATata
 V$CDP_02               |    11194 (-) |  0.773 |  0.801 | ttcttgaTTGATtat
 V$CDP_02               |    11197 (+) |  0.930 |  0.943 | ttgATTGAttattaa
 V$CDP_02               |    11346 (-) |  0.773 |  0.797 | gccattaTCGAAcga
 V$CDP_02               |    11439 (-) |  0.912 |  0.912 | atacttaTCTATttt
 V$CDP_02               |    11693 (-) |  0.703 |  0.779 | aagttaaTCACTgtc
 V$CLOX_01              |    11197 (+) |  0.941 |  0.947 | ttgATTGAttattaa
 V$CDPCR1_01            |      856 (-) |  0.858 |  0.888 | acgaTCGTTg
 V$CDPCR1_01            |     3709 (-) |  0.929 |  0.869 | ttgaTCAATa
 V$CDPCR1_01            |     6923 (+) |  0.929 |  0.918 | aATTGAttgt
 V$CDPCR1_01            |     7923 (-) |  0.929 |  0.868 | ggtaTCAATt
 V$CDPCR1_01            |     9718 (+) |  0.929 |  0.885 | aATTGAtctc
 V$CDPCR1_01            |     9878 (-) |  0.929 |  0.865 | gaaaTCAATt
 V$CDPCR1_01            |    10384 (-) |  0.910 |  0.917 | gcaaTCCATa
 V$CDPCR3_01            |       62 (-) |  1.000 |  0.845 | CCATAattactgttg
 V$CDPCR3_01            |     1008 (+) |  0.745 |  0.676 | gacgcacctaTATGT
 V$CDPCR3_01            |     1015 (-) |  0.980 |  0.696 | CTATAtgtgattggc
 V$CDPCR3_01            |     1471 (-) |  0.996 |  0.727 | CAATAtttgctctgg
 V$CDPCR3_01            |     1735 (+) |  0.980 |  0.700 | ctgaacttccTATAG
 V$CDPCR3_01            |     1759 (-) |  0.980 |  0.683 | CTATAagcctctcgc
 V$CDPCR3_01            |     1853 (-) |  0.996 |  0.746 | CAATAgagccaactg
 V$CDPCR3_01            |     2005 (-) |  0.980 |  0.703 | CTATAcatctcctga
 V$CDPCR3_01            |     2615 (-) |  0.795 |  0.701 | CCATGtgtatgctag
 V$CDPCR3_01            |     3051 (-) |  0.745 |  0.714 | ACATAcctgcgagtg
 V$CDPCR3_01            |     3057 (+) |  0.980 |  0.774 | ctgcgagtggTATAG
 V$CDPCR3_01            |     3103 (-) |  0.980 |  0.705 | CTATActaatttcca
 V$CDPCR3_01            |     3123 (-) |  0.980 |  0.695 | CTATAttaatttaca
 V$CDPCR3_01            |     3141 (-) |  0.745 |  0.713 | CCACAacaatatatg
 V$CDPCR3_01            |     3142 (+) |  1.000 |  0.860 | cacaacaataTATGG
 V$CDPCR3_01            |     3147 (-) |  0.996 |  0.774 | CAATAtatggaggtt
 V$CDPCR3_01            |     3247 (+) |  1.000 |  0.702 | ccagcccactTATGG
 V$CDPCR3_01            |     3276 (-) |  0.786 |  0.684 | CCATTatgattggga
 V$CDPCR3_01            |     3372 (+) |  1.000 |  0.754 | agcctaatcaTATGG
 V$CDPCR3_01            |     3711 (+) |  0.745 |  0.691 | gatcaatattTACGG
 V$CDPCR3_01            |     3714 (-) |  0.996 |  0.904 | CAATAtttacgggtg
 V$CDPCR3_01            |     4004 (-) |  0.998 |  0.710 | CGATAaataaatatt
 V$CDPCR3_01            |     4086 (-) |  0.980 |  0.680 | CTATAttttactgat
 V$CDPCR3_01            |     4316 (-) |  0.745 |  0.691 | GCATAaaactgggtc
 V$CDPCR3_01            |     4447 (-) |  0.781 |  0.693 | CAATTaatattcatt
 V$CDPCR3_01            |     4572 (+) |  0.980 |  0.709 | tgcggttagaTATAG
 V$CDPCR3_01            |     4622 (-) |  0.996 |  0.777 | CAATAtcctttgggt
 V$CDPCR3_01            |     4674 (+) |  0.745 |  0.685 | ctcatagttcTGTGG
 V$CDPCR3_01            |     4781 (-) |  0.743 |  0.752 | GGATAaagattgctg
 V$CDPCR3_01            |     5085 (+) |  0.745 |  0.689 | ctctgactggTTTGG
 V$CDPCR3_01            |     5337 (-) |  0.998 |  0.765 | CGATAgttttgcatc
 V$CDPCR3_01            |     5433 (+) |  0.996 |  0.688 | actttatttgTATTG
 V$CDPCR3_01            |     5448 (-) |  1.000 |  0.682 | CCATAtaaccttttc
 V$CDPCR3_01            |     5466 (-) |  0.745 |  0.704 | ACATActatttcctg
 V$CDPCR3_01            |     6143 (-) |  0.795 |  0.687 | CCATGcctctggctc
 V$CDPCR3_01            |     6866 (+) |  0.980 |  0.836 | gaccgaggctTATAG
 V$CDPCR3_01            |     6958 (-) |  0.786 |  0.757 | CCATTattctggatg
 V$CDPCR3_01            |     7335 (-) |  0.996 |  0.699 | CAATAgacacatttc
 V$CDPCR3_01            |     7370 (+) |  0.996 |  0.781 | aaagaattgaTATTG
 V$CDPCR3_01            |     7928 (-) |  0.781 |  0.818 | CAATTcgtttgtgtg
 V$CDPCR3_01            |     7956 (+) |  0.980 |  0.729 | taccccagacTATAG
 V$CDPCR3_01            |     7965 (-) |  0.980 |  0.854 | CTATAgttgtttgtt
 V$CDPCR3_01            |     8087 (-) |  0.980 |  0.840 | CTATAcagctctggg
 V$CDPCR3_01            |     8241 (-) |  0.745 |  0.704 | CCAGAtgaaggtgtg
 V$CDPCR3_01            |     8560 (-) |  0.791 |  0.733 | CAATGtccgtctttg
 V$CDPCR3_01            |     8650 (-) |  0.781 |  0.674 | CAATTcccaatggtt
 V$CDPCR3_01            |     9236 (-) |  0.745 |  0.705 | CCAGAgccctaggag
 V$CDPCR3_01            |     9426 (-) |  1.000 |  0.715 | CCATAaataacagga
 V$CDPCR3_01            |     9748 (-) |  0.996 |  0.678 | CAATAtattaatatt
 V$CDPCR3_01            |     9749 (+) |  0.996 |  0.766 | aatatattaaTATTG
 V$CDPCR3_01            |     9784 (-) |  0.781 |  0.690 | CAATTttgttcagta
 V$CDPCR3_01            |     9967 (+) |  1.000 |  0.687 | ttctggttccTATGG
 V$CDPCR3_01            |    10123 (-) |  0.996 |  0.746 | CAATAaaattagtta
 V$CDPCR3_01            |    10140 (+) |  0.996 |  0.757 | aaattattatTATTG
 V$CDPCR3_01            |    10171 (-) |  0.745 |  0.765 | CCTTAttagtgtgtg
 V$CDPCR3_01            |    10389 (-) |  1.000 |  0.675 | CCATAtaaaaatgaa
 V$CDPCR3_01            |    10502 (+) |  1.000 |  0.697 | aaaagtcaatTATGG
 V$CDPCR3_01            |    10697 (+) |  0.745 |  0.737 | cacccgtgttTATGA
 V$CDPCR3_01            |    10726 (+) |  0.996 |  0.681 | ctgtagctttTATTG
 V$CDPCR3_01            |    11170 (+) |  0.745 |  0.735 | cagagatcttTTTGG
 V$CDPCR3_01            |    11437 (-) |  0.745 |  0.676 | GCATActtatctatt
 V$CDPCR3_01            |    11533 (+) |  1.000 |  0.679 | aaatcccacaTATGG
 V$CDPCR3_01            |    11800 (-) |  0.745 |  0.690 | CCAGAttggaaggtg
 V$CDPCR3HD_01          |     1754 (-) |  0.983 |  0.964 | ctgATCTAta
 V$CDPCR3HD_01          |     2721 (+) |  0.983 |  0.911 | aaTAGATaat
 V$CDPCR3HD_01          |     2982 (-) |  0.983 |  0.861 | ggcATCTAct
 V$CDPCR3HD_01          |     3098 (-) |  0.983 |  0.951 | cgaATCTAta
 V$CDPCR3HD_01          |     3709 (-) |  0.996 |  0.952 | ttgATCAAta
 V$CDPCR3HD_01          |     4106 (-) |  0.983 |  0.937 | aacATCCAtt
 V$CDPCR3HD_01          |     5484 (+) |  0.996 |  0.870 | ttTTGATccc
 V$CDPCR3HD_01          |     6097 (+) |  0.983 |  0.858 | tgTGGATcag
 V$CDPCR3HD_01          |     6310 (-) |  0.983 |  0.862 | ctgATCTAct
 V$CDPCR3HD_01          |     6783 (-) |  0.983 |  0.855 | cagATCTAat
 V$CDPCR3HD_01          |     6923 (+) |  0.996 |  0.944 | aaTTGATtgt
 V$CDPCR3HD_01          |     7374 (+) |  0.996 |  0.927 | aaTTGATatt
 V$CDPCR3HD_01          |     7923 (-) |  0.996 |  0.957 | ggtATCAAtt
 V$CDPCR3HD_01          |     8380 (+) |  0.996 |  0.867 | ctTTGATctg
 V$CDPCR3HD_01          |     9718 (+) |  0.996 |  0.986 | aaTTGATctc
 V$CDPCR3HD_01          |     9878 (-) |  0.996 |  0.959 | gaaATCAAtt
 V$CDPCR3HD_01          |    10217 (-) |  0.983 |  0.850 | ggcATCTAag
 V$CDPCR3HD_01          |    10384 (-) |  0.983 |  0.952 | gcaATCCAta
 V$CDPCR3HD_01          |    10672 (-) |  0.983 |  0.851 | aggATCCAca
 V$CDPCR3HD_01          |    11199 (+) |  0.996 |  0.934 | gaTTGATtat
 V$CDPCR3HD_01          |    11442 (-) |  0.983 |  0.931 | cttATCTAtt
 V$CDPCR3HD_01          |    11546 (+) |  0.983 |  0.861 | ggTAGATggg
 V$NRF2_01              |     3032 (-) |  1.000 |  0.946 | gaCTTCCgct
 V$CEBPB_01             |      333 (-) |  0.965 |  0.928 | aaATTCCctcagac
 V$CEBPB_01             |      489 (-) |  1.000 |  0.956 | acATTGCaacatta
 V$CEBPB_01             |      803 (-) |  0.996 |  0.951 | ccATTTCtccagcc
 V$CEBPB_01             |     1100 (+) |  0.996 |  0.975 | aatttgaGAAATcg
 V$CEBPB_01             |     1463 (-) |  0.966 |  0.972 | acGTTTCtcaatat
 V$CEBPB_01             |     2368 (-) |  0.976 |  0.935 | atTTTGCcacagtt
 V$CEBPB_01             |     2555 (+) |  0.996 |  0.979 | ctgttgtGAAATtt
 V$CEBPB_01             |     2564 (+) |  0.965 |  0.929 | aatttccGTAAGta
 V$CEBPB_01             |     2564 (-) |  0.941 |  0.927 | aaTTTCCgtaagta
 V$CEBPB_01             |     2712 (-) |  0.950 |  0.939 | ctCTTCCcaaatag
 V$CEBPB_01             |     2803 (-) |  0.965 |  0.947 | ctCTTACtgaacac
 V$CEBPB_01             |     3424 (-) |  0.970 |  0.952 | tgGTTGCttaattg
 V$CEBPB_01             |     3437 (+) |  0.950 |  0.943 | gacttagGTAACag
 V$CEBPB_01             |     3569 (+) |  0.985 |  0.966 | gcctttgGCAAGtt
 V$CEBPB_01             |     3644 (+) |  0.965 |  0.942 | acatggtGGAATca
 V$CEBPB_01             |     3739 (-) |  0.996 |  0.955 | ttATTTCtacattt
 V$CEBPB_01             |     4207 (-) |  0.985 |  0.939 | ggCTTGCctcagtt
 V$CEBPB_01             |     4270 (-) |  0.965 |  0.943 | tgCTTACctaagca
 V$CEBPB_01             |     4708 (+) |  0.981 |  0.963 | gacttggGTAATtc
 V$CEBPB_01             |     4795 (-) |  0.985 |  0.981 | gaCTTGCataatct
 V$CEBPB_01             |     5152 (+) |  0.972 |  0.955 | agtttacGAAAAgg
 V$CEBPB_01             |     5152 (-) |  0.956 |  0.928 | agTTTACgaaaagg
 V$CEBPB_01             |     5456 (-) |  0.972 |  0.945 | ccTTTTCcccacat
 V$CEBPB_01             |     5471 (-) |  0.996 |  0.928 | ctATTTCctgattt
 V$CEBPB_01             |     6547 (+) |  0.965 |  0.927 | ggctgagGTAAGag
 V$CEBPB_01             |     6564 (-) |  0.970 |  0.926 | tgGTTGCcacagtt
 V$CEBPB_01             |     6573 (+) |  0.976 |  0.958 | cagttatGCAAAac
 V$CEBPB_01             |     6608 (-) |  0.976 |  0.964 | taTTTGCtaaactc
 V$CEBPB_01             |     7054 (-) |  0.972 |  0.968 | ttTTTTCttaattt
 V$CEBPB_01             |     7343 (-) |  0.996 |  0.964 | acATTTCaacatgt
 V$CEBPB_01             |     7402 (-) |  0.981 |  0.936 | gaATTACtgaagaa
 V$CEBPB_01             |     8071 (-) |  1.000 |  0.961 | gtATTGCagaaact
 V$CEBPB_01             |     8578 (+) |  0.976 |  0.949 | aaatgggGCAAAgg
 V$CEBPB_01             |     8623 (+) |  0.972 |  0.956 | actttgaGAAAAgc
 V$CEBPB_01             |     8693 (-) |  0.981 |  0.945 | gcCTTTCtgaaaat
 V$CEBPB_01             |     8907 (+) |  0.965 |  0.948 | agattcaGGAATac
 V$CEBPB_01             |     9098 (-) |  0.965 |  0.944 | tgCTTACaaaagca
 V$CEBPB_01             |     9509 (-) |  0.966 |  0.943 | aaGTTTCcccatgt
 V$CEBPB_01             |     9601 (+) |  0.950 |  0.954 | gcatttgGGAAGct
 V$CEBPB_01             |     9707 (+) |  0.956 |  0.929 | tggtggtGTAAAat
 V$CEBPB_01             |     9789 (+) |  0.956 |  0.931 | ttgttcaGTAAAtg
 V$CEBPB_01             |     9871 (+) |  0.996 |  0.956 | gaatgagGAAATca
 V$CEBPB_01             |    10070 (+) |  0.950 |  0.931 | gtcttctGGAAGgg
 V$CEBPB_01             |    10132 (+) |  0.996 |  0.971 | tagttaaGAAATta
 V$CEBPB_01             |    10369 (-) |  0.981 |  0.980 | atCTTTCaaaatgt
 V$CEBPB_01             |    10377 (+) |  1.000 |  0.962 | aaatgttGCAATcc
 V$CEBPB_01             |    10622 (+) |  0.981 |  0.933 | agttgtaGAAAGtg
 V$CEBPB_01             |    10703 (+) |  0.966 |  0.948 | tgtttatGAAACat
 V$CEBPB_01             |    10968 (+) |  0.985 |  0.928 | tgttggaGCAAGga
 V$CEBPB_01             |    11666 (-) |  0.972 |  0.964 | aaTTTTCataacca
 V$CEBPB_01             |    11726 (-) |  0.972 |  0.947 | caTTTTCtcaaaca
 V$CEBPB_01             |    11780 (+) |  0.965 |  0.925 | acttgatGTAAGga
 I$ELF1_01              |      929 (-) |  1.000 |  0.940 | ccacgAAACCacaagt
 I$ELF1_01              |     1137 (-) |  1.000 |  0.922 | tcctaAAACCgttact
 I$ELF1_01              |     2600 (-) |  1.000 |  0.919 | ctattAAACCaagagc
 I$ELF1_01              |     3254 (+) |  1.000 |  0.914 | acttatGGTTTtcttg
 I$ELF1_01              |     4124 (-) |  1.000 |  0.909 | tgttaAAACCcagaat
 I$ELF1_01              |     4434 (-) |  1.000 |  0.929 | aaaaaAAACCacacaa
 I$ELF1_01              |     4613 (-) |  1.000 |  0.931 | aggtaAAACCaatatc
 I$ELF1_01              |     5609 (-) |  1.000 |  0.904 | acaagAAACCaacatc
 I$ELF1_01              |     6743 (-) |  1.000 |  0.922 | tttgaAAACCcactat
 I$ELF1_01              |     7887 (+) |  1.000 |  0.919 | tcatttGGTTTttatt
 I$ELF1_01              |     8064 (+) |  0.966 |  0.948 | ttatctGGTATtgcag
 I$ELF1_01              |     8655 (+) |  1.000 |  0.934 | cccaatGGTTTtcaaa
 I$ELF1_01              |     8700 (-) |  0.966 |  0.904 | tgaaaATACCatcaag
 I$ELF1_01              |     8831 (-) |  1.000 |  0.997 | gttcaAAACCaaaaca
 I$ELF1_01              |     8845 (+) |  1.000 |  0.941 | cagaacGGTTTaaaaa
 I$ELF1_01              |     9114 (-) |  1.000 |  0.922 | acaaaAAACCgggaaa
 I$ELF1_01              |     9705 (+) |  0.966 |  0.906 | ggtggtGGTGTaaaat
 I$ELF1_01              |    10938 (+) |  0.966 |  0.958 | gtggacGGTGTtgtag
 I$ELF1_01              |    11548 (+) |  0.966 |  0.918 | tagatgGGTATtcaac
 V$CREB_02              |     1842 (-) |  1.000 |  0.949 | ggtCGTCAacac
 V$CREB_02              |     2962 (+) |  1.000 |  0.886 | acagTGACGgca
 V$CREB_02              |     4533 (-) |  1.000 |  0.963 | atgCGTCAacag
 V$CREB_02              |     8323 (-) |  1.000 |  0.956 | ctgCGTCAgcgc
 V$CREB_02              |     8612 (-) |  1.000 |  0.883 | ttcCGTCAatca
 V$CREB_02              |    11314 (+) |  1.000 |  0.948 | acggTGACGacg
 V$CREB_02              |    11329 (+) |  1.000 |  0.944 | atgaTGACGatg
 V$TAXCREB_01           |     1278 (+) |  0.780 |  0.782 | ctgggaTGACAggga
 V$TAXCREB_01           |     1841 (-) |  1.000 |  0.854 | gggtCGTCAacacaa
 V$TAXCREB_01           |     3285 (+) |  0.780 |  0.791 | ttgggaTGAGGtgaa
 V$TAXCREB_01           |     4532 (-) |  1.000 |  0.844 | aatgCGTCAacagcc
 V$TAXCREB_01           |     5149 (+) |  0.906 |  0.782 | ggcagtTTACGaaaa
 V$TAXCREB_01           |     6433 (-) |  0.780 |  0.826 | catcGGTCAacccag
 V$TAXCREB_01           |     8322 (-) |  1.000 |  0.900 | tctgCGTCAgcgcca
 V$TAXCREB_01           |     8611 (-) |  1.000 |  0.811 | attcCGTCAatcact
 V$TAXCREB_01           |     9381 (-) |  0.780 |  0.801 | gagcTGTCAgcccct
 V$TAXCREB_01           |    11312 (+) |  1.000 |  0.793 | ctacggTGACGacga
 V$TAXCREB_01           |    11700 (-) |  0.780 |  0.786 | tcacTGTCAccccaa
 V$TAXCREB_02           |       23 (-) |  0.600 |  0.631 | gtgaatgtgTGTGAa
 V$TAXCREB_02           |      407 (-) |  0.600 |  0.672 | ggcggaatgGGTGAg
 V$TAXCREB_02           |      566 (-) |  0.800 |  0.622 | ggagataaaCGTCTa
 V$TAXCREB_02           |      722 (-) |  0.600 |  0.673 | atggttgtgAGCCAc
 V$TAXCREB_02           |      798 (+) |  0.600 |  0.664 | cTGAGCcatttctcc
 V$TAXCREB_02           |     1703 (+) |  0.800 |  0.686 | aTGAAGcaccctctg
 V$TAXCREB_02           |     1767 (+) |  0.600 |  0.631 | cTCTCGcctgtcctc
 V$TAXCREB_02           |     1875 (-) |  0.600 |  0.734 | gaggatctgCCTCCc
 V$TAXCREB_02           |     1971 (-) |  0.800 |  0.629 | gcaggttggCCTCAa
 V$TAXCREB_02           |     2001 (-) |  0.600 |  0.620 | ctggctataCATCTc
 V$TAXCREB_02           |     2435 (-) |  0.600 |  0.664 | ggggatttaGCTCAg
 V$TAXCREB_02           |     2644 (-) |  0.800 |  0.644 | cctgacctgCGTAAt
 V$TAXCREB_02           |     2880 (-) |  0.600 |  0.655 | ccgtgtatgCGTACt
 V$TAXCREB_02           |     3006 (-) |  0.800 |  0.646 | gtgcgcaggCGTCTc
 V$TAXCREB_02           |     3485 (+) |  0.800 |  0.629 | aTGAGGcagaatagc
 V$TAXCREB_02           |     3699 (-) |  0.600 |  0.624 | caagagatgCTTGAt
 V$TAXCREB_02           |     3890 (+) |  0.800 |  0.642 | tTGACCctcatcaca
 V$TAXCREB_02           |     4143 (-) |  0.600 |  0.642 | ggtgtggtgCCTCCc
 V$TAXCREB_02           |     4204 (-) |  0.800 |  0.638 | caaggcttgCCTCAg
 V$TAXCREB_02           |     4527 (-) |  1.000 |  0.673 | caacaaatgCGTCAa
 V$TAXCREB_02           |     4832 (-) |  0.600 |  0.633 | tagggaacgAGTGAt
 V$TAXCREB_02           |     4969 (+) |  0.600 |  0.675 | gTCAGGctcagcccc
 V$TAXCREB_02           |     5678 (+) |  0.600 |  0.646 | cAGACAcagagaccc
 V$TAXCREB_02           |     5747 (+) |  0.800 |  0.646 | tAGACGcaaaggacc
 V$TAXCREB_02           |     5891 (+) |  0.600 |  0.622 | aTGGGGcccgcccct
 V$TAXCREB_02           |     6000 (-) |  0.600 |  0.683 | tggggtacgTGTCCa
 V$TAXCREB_02           |     6258 (+) |  0.600 |  0.631 | tTGTCCcatctgccg
 V$TAXCREB_02           |     6327 (+) |  0.800 |  0.692 | cTGAAGcacacactg
 V$TAXCREB_02           |     6550 (-) |  0.800 |  0.710 | tgaggtaagAGTCAt
 V$TAXCREB_02           |     6575 (+) |  0.600 |  0.631 | gTTATGcaaaacaca
 V$TAXCREB_02           |     7338 (+) |  0.600 |  0.620 | tAGACAcatttcaac
 V$TAXCREB_02           |     7538 (-) |  0.600 |  0.666 | ttggttgtgAGCCAa
 V$TAXCREB_02           |     7608 (+) |  0.600 |  0.675 | cTGAGCcatctctcc
 V$TAXCREB_02           |     7845 (-) |  0.800 |  0.631 | tggcaaaagCGACAg
 V$TAXCREB_02           |     8104 (+) |  0.600 |  0.651 | cTGTCAcacactctc
 V$TAXCREB_02           |     8106 (+) |  0.600 |  0.657 | gTCACAcactctccc
 V$TAXCREB_02           |     8273 (+) |  0.800 |  0.743 | aTGATGcagctgccc
 V$TAXCREB_02           |     8317 (-) |  1.000 |  0.741 | cagcttctgCGTCAg
 V$TAXCREB_02           |     8395 (+) |  0.800 |  0.644 | cTGAAGccaagccag
 V$TAXCREB_02           |     8746 (+) |  0.600 |  0.624 | gTGGCCcacaccttg
 V$TAXCREB_02           |     8805 (-) |  0.600 |  0.629 | gggggccagCTTCTg
 V$TAXCREB_02           |     9123 (-) |  0.800 |  0.620 | cgggaaaacCTTCAg
 V$TAXCREB_02           |     9168 (+) |  0.600 |  0.629 | aAGATGcatgaacgc
 V$TAXCREB_02           |     9315 (-) |  0.800 |  0.752 | gaggcgttgGGTCAg
 V$TAXCREB_02           |     9376 (-) |  0.800 |  0.631 | agggagagcTGTCAg
 V$TAXCREB_02           |     9923 (-) |  0.600 |  0.640 | ttgcctatgGGTAAt
 V$TAXCREB_02           |    10029 (-) |  0.800 |  0.695 | tagtttgtgAGTCAc
 V$TAXCREB_02           |    10637 (+) |  0.800 |  0.672 | cTGAGGaagacaccc
 V$TAXCREB_02           |    10708 (+) |  0.600 |  0.657 | aTGAAAcatctctgc
 V$TAXCREB_02           |    10741 (-) |  0.600 |  0.699 | gggggtttcAGTGAt
 V$CEBPA_01             |      393 (-) |  0.922 |  0.930 | tcatttgCCAACaa
 V$CEBPA_01             |      420 (-) |  0.920 |  0.931 | agcttgtCCAAAat
 V$CEBPA_01             |      489 (+) |  1.000 |  0.941 | acATTGCaacatta
 V$CEBPA_01             |     1085 (+) |  0.920 |  0.930 | atTTTGGtcaacta
 V$CEBPA_01             |     1100 (+) |  0.909 |  0.921 | aaTTTGAgaaatcg
 V$CEBPA_01             |     1100 (-) |  0.929 |  0.934 | aatttgaGAAATcg
 V$CEBPA_01             |     1161 (-) |  0.909 |  0.921 | ttcttttTCAAAga
 V$CEBPA_01             |     1463 (-) |  0.932 |  0.938 | acgtttcTCAATat
 V$CEBPA_01             |     1656 (+) |  0.917 |  0.924 | taCTTGGcaaatgg
 V$CEBPA_01             |     2368 (+) |  0.977 |  0.921 | atTTTGCcacagtt
 V$CEBPA_01             |     2555 (-) |  0.929 |  0.934 | ctgttgtGAAATtt
 V$CEBPA_01             |     2564 (-) |  0.940 |  0.933 | aatttccGTAAGta
 V$CEBPA_01             |     2803 (+) |  0.940 |  0.932 | ctCTTACtgaacac
 V$CEBPA_01             |     2935 (+) |  1.000 |  0.926 | tgATTGCgaagtct
 V$CEBPA_01             |     3424 (+) |  0.979 |  0.973 | tgGTTGCttaattg
 V$CEBPA_01             |     3437 (-) |  0.945 |  0.945 | gacttagGTAACag
 V$CEBPA_01             |     3569 (-) |  0.974 |  0.972 | gcctttgGCAAGtt
 V$CEBPA_01             |     3677 (+) |  1.000 |  0.920 | gaATTGCcaagtgc
 V$CEBPA_01             |     3706 (-) |  0.932 |  0.942 | tgcttgaTCAATat
 V$CEBPA_01             |     4270 (+) |  0.940 |  0.947 | tgCTTACctaagca
 V$CEBPA_01             |     4708 (+) |  0.917 |  0.922 | gaCTTGGgtaattc
 V$CEBPA_01             |     4708 (-) |  0.966 |  0.962 | gacttggGTAATtc
 V$CEBPA_01             |     4795 (+) |  0.974 |  0.973 | gaCTTGCataatct
 V$CEBPA_01             |     4899 (+) |  0.917 |  0.922 | tcCTTGGccaagtg
 V$CEBPA_01             |     4899 (-) |  0.917 |  0.925 | tccttggCCAAGtg
 V$CEBPA_01             |     5152 (+) |  0.943 |  0.946 | agTTTACgaaaagg
 V$CEBPA_01             |     5355 (+) |  0.909 |  0.923 | tcTTTGAcaaaaca
 V$CEBPA_01             |     5442 (+) |  1.000 |  0.922 | gtATTGCcatataa
 V$CEBPA_01             |     6564 (+) |  0.979 |  0.920 | tgGTTGCcacagtt
 V$CEBPA_01             |     6573 (-) |  0.977 |  0.971 | cagttatGCAAAac
 V$CEBPA_01             |     6608 (+) |  0.977 |  0.974 | taTTTGCtaaactc
 V$CEBPA_01             |     7116 (-) |  1.000 |  0.922 | catgtgtGCAATgc
 V$CEBPA_01             |     7208 (+) |  0.932 |  0.937 | gaATTGAacaaaaa
 V$CEBPA_01             |     7402 (+) |  0.966 |  0.955 | gaATTACtgaagaa
 V$CEBPA_01             |     8071 (+) |  1.000 |  0.984 | gtATTGCagaaact
 V$CEBPA_01             |     8907 (-) |  0.929 |  0.926 | agattcaGGAATac
 V$CEBPA_01             |     9098 (+) |  0.940 |  0.949 | tgCTTACaaaagca
 V$CEBPA_01             |     9447 (-) |  0.943 |  0.951 | aggtttaCCAATct
 V$CEBPA_01             |     9789 (-) |  0.943 |  0.937 | ttgttcaGTAAAtg
 V$CEBPA_01             |    10128 (+) |  0.909 |  0.920 | aaATTAGttaagaa
 V$CEBPA_01             |    10132 (-) |  0.929 |  0.935 | tagttaaGAAATta
 V$CEBPA_01             |    10275 (-) |  1.000 |  0.924 | cggctgaGCAATct
 V$CEBPA_01             |    10377 (-) |  1.000 |  0.937 | aaatgttGCAATcc
 V$CEBPA_01             |    10430 (-) |  1.000 |  0.925 | agtcttcGCAATgc
 V$CEBPA_01             |    10703 (-) |  0.908 |  0.922 | tgtttatGAAACat
 V$CEBPA_01             |    11449 (+) |  0.920 |  0.922 | atTTTGGtgaatca
 V$CEBPA_01             |    11666 (+) |  0.906 |  0.921 | aaTTTTCataacca
 V$CEBPB_02             |      489 (+) |  1.000 |  0.919 | acaTTGCAacatta
 V$CEBPB_02             |     1085 (+) |  0.842 |  0.886 | attTTGGTcaacta
 V$CEBPB_02             |     1100 (-) |  0.861 |  0.889 | aatttgAGAAAtcg
 V$CEBPB_02             |     1463 (+) |  0.861 |  0.884 | acgTTTCTcaatat
 V$CEBPB_02             |     2368 (+) |  0.994 |  0.913 | attTTGCCacagtt
 V$CEBPB_02             |     2555 (-) |  0.865 |  0.890 | ctgttgTGAAAttt
 V$CEBPB_02             |     3424 (+) |  0.996 |  0.981 | tggTTGCTtaattg
 V$CEBPB_02             |     3437 (-) |  0.882 |  0.894 | gacttaGGTAAcag
 V$CEBPB_02             |     3569 (-) |  0.994 |  0.954 | gcctttGGCAAgtt
 V$CEBPB_02             |     4207 (+) |  0.994 |  0.915 | ggcTTGCCtcagtt
 V$CEBPB_02             |     4270 (+) |  0.882 |  0.888 | tgcTTACCtaagca
 V$CEBPB_02             |     4708 (-) |  0.882 |  0.899 | gacttgGGTAAttc
 V$CEBPB_02             |     4795 (+) |  1.000 |  0.970 | gacTTGCAtaatct
 V$CEBPB_02             |     5152 (+) |  0.888 |  0.885 | agtTTACGaaaagg
 V$CEBPB_02             |     5442 (+) |  0.994 |  0.886 | gtaTTGCCatataa
 V$CEBPB_02             |     6564 (+) |  0.994 |  0.913 | tggTTGCCacagtt
 V$CEBPB_02             |     6573 (-) |  1.000 |  0.985 | cagttaTGCAAaac
 V$CEBPB_02             |     6608 (+) |  0.996 |  0.970 | tatTTGCTaaactc
 V$CEBPB_02             |     7054 (+) |  0.861 |  0.886 | tttTTTCTtaattt
 V$CEBPB_02             |     8071 (+) |  1.000 |  0.955 | gtaTTGCAgaaact
 V$CEBPB_02             |     8578 (-) |  0.994 |  0.923 | aaatggGGCAAagg
 V$CEBPB_02             |     8936 (-) |  0.996 |  0.884 | aactaaAGCAActt
 V$CEBPB_02             |     9098 (+) |  0.888 |  0.889 | tgcTTACAaaagca
 V$CEBPB_02             |    10132 (-) |  0.861 |  0.883 | tagttaAGAAAtta
 V$CEBPB_02             |    10377 (-) |  1.000 |  0.924 | aaatgtTGCAAtcc
 V$CEBPB_02             |    10686 (-) |  0.994 |  0.894 | gactctGGCAAcac
 V$CEBPB_02             |    10968 (-) |  0.996 |  0.916 | tgttggAGCAAgga
 V$CEBPB_02             |    11284 (-) |  0.994 |  0.889 | gcatagGGCAAaga
 V$MYCMAX_01            |      733 (+) |  1.000 |  0.989 | ccacCACGTggttg
 V$MYCMAX_01            |      733 (-) |  1.000 |  0.989 | ccaccACGTGgttg
 V$MYCMAX_01            |     1124 (+) |  1.000 |  0.866 | tatgCACGTgtgtt
 V$MYCMAX_01            |     1124 (-) |  1.000 |  0.866 | tatgcACGTGtgtt
 V$MYCMAX_01            |     6062 (+) |  1.000 |  0.899 | cctgCACGTgctgc
 V$MYCMAX_01            |     6062 (-) |  1.000 |  0.899 | cctgcACGTGctgc
 V$MAX_01               |      733 (+) |  1.000 |  0.992 | ccacCACGTggttg
 V$MAX_01               |      733 (-) |  1.000 |  0.992 | ccaccACGTGgttg
 V$MAX_01               |     1124 (+) |  1.000 |  0.937 | tatgCACGTgtgtt
 V$MAX_01               |     1124 (-) |  1.000 |  0.937 | tatgcACGTGtgtt
 V$MAX_01               |     6062 (+) |  1.000 |  0.957 | cctgCACGTgctgc
 V$MAX_01               |     6062 (-) |  1.000 |  0.957 | cctgcACGTGctgc
 I$DL_02                |      898 (-) |  1.000 |  0.939 | gacTTTTCact
 I$DL_02                |     1548 (+) |  1.000 |  0.889 | actGAAAActc
 I$DL_02                |     1717 (-) |  1.000 |  0.896 | gccTTTTCcgg
 I$DL_02                |     2377 (-) |  1.000 |  0.962 | cagTTTTCcca
 I$DL_02                |     2501 (+) |  1.000 |  0.880 | tccGAAAAaaa
 I$DL_02                |     2512 (+) |  1.000 |  0.939 | aggGAAAAaaa
 I$DL_02                |     2750 (-) |  1.000 |  0.937 | ttcTTTTCtct
 I$DL_02                |     3259 (-) |  1.000 |  0.912 | tggTTTTCttg
 I$DL_02                |     4111 (-) |  1.000 |  0.950 | ccaTTTTCcca
 I$DL_02                |     5455 (-) |  1.000 |  0.920 | accTTTTCccc
 I$DL_02                |     5776 (+) |  1.000 |  0.958 | agaGAAAAata
 I$DL_02                |     5939 (+) |  1.000 |  0.946 | ggaGAAAAgta
 I$DL_02                |     6125 (-) |  1.000 |  0.944 | ttgTTTTCtcg
 I$DL_02                |     6707 (+) |  1.000 |  0.990 | agaGAAAAgcc
 I$DL_02                |     6743 (+) |  1.000 |  0.899 | tttGAAAAccc
 I$DL_02                |     7867 (+) |  1.000 |  0.898 | ttaGAAAAgct
 I$DL_02                |     7976 (-) |  1.000 |  0.891 | tgtTTTTCaag
 I$DL_02                |     8146 (+) |  1.000 |  0.927 | aggGAAAAcat
 I$DL_02                |     8548 (+) |  1.000 |  0.950 | cgaGAAAAtga
 I$DL_02                |     8627 (+) |  1.000 |  0.980 | tgaGAAAAgct
 I$DL_02                |     8660 (-) |  1.000 |  0.896 | tggTTTTCaaa
 I$DL_02                |     8698 (+) |  1.000 |  0.877 | tctGAAAAtac
 I$DL_02                |     9123 (+) |  1.000 |  0.980 | cggGAAAAcct
 I$DL_02                |     9413 (+) |  1.000 |  0.881 | ctaGAAAActa
 I$DL_02                |     9496 (+) |  1.000 |  0.895 | ataGAAAAtct
 I$DL_02                |    10827 (-) |  1.000 |  0.876 | gccTTTTCagg
 I$DL_02                |    11478 (-) |  1.000 |  0.989 | tgtTTTTCcct
 I$DL_02                |    11725 (-) |  1.000 |  0.950 | ccaTTTTCtca
 V$USF_01               |      285 (+) |  0.812 |  0.843 | aagtCAAGTgtttt
 V$USF_01               |      285 (-) |  0.812 |  0.843 | aagtcAAGTGtttt
 V$USF_01               |      733 (+) |  1.000 |  0.991 | ccacCACGTggttg
 V$USF_01               |      733 (-) |  1.000 |  0.991 | ccaccACGTGgttg
 V$USF_01               |     1124 (+) |  1.000 |  0.962 | tatgCACGTgtgtt
 V$USF_01               |     1124 (-) |  1.000 |  0.962 | tatgcACGTGtgtt
 V$USF_01               |     1356 (+) |  0.812 |  0.850 | gggtCACCTgatgc
 V$USF_01               |     1356 (-) |  0.812 |  0.850 | gggtcACCTGatgc
 V$USF_01               |     3639 (+) |  0.822 |  0.853 | ctacCACATggtgg
 V$USF_01               |     3639 (-) |  0.822 |  0.853 | ctaccACATGgtgg
 V$USF_01               |     3936 (+) |  0.812 |  0.843 | cagtCACTTgttca
 V$USF_01               |     3936 (-) |  0.812 |  0.843 | cagtcACTTGttca
 V$USF_01               |     6062 (+) |  1.000 |  0.971 | cctgCACGTgctgc
 V$USF_01               |     6062 (-) |  1.000 |  0.971 | cctgcACGTGctgc
 V$USF_02               |      285 (+) |  0.915 |  0.935 | aagtCAAGTgtttt
 V$USF_02               |      285 (-) |  0.915 |  0.935 | aagtcAAGTGtttt
 V$USF_02               |      733 (+) |  1.000 |  0.994 | ccacCACGTggttg
 V$USF_02               |      733 (-) |  1.000 |  0.994 | ccaccACGTGgttg
 V$USF_02               |     1124 (+) |  1.000 |  0.962 | tatgCACGTgtgtt
 V$USF_02               |     1124 (-) |  1.000 |  0.962 | tatgcACGTGtgtt
 V$USF_02               |     1356 (+) |  0.935 |  0.947 | gggtCACCTgatgc
 V$USF_02               |     1356 (-) |  0.935 |  0.947 | gggtcACCTGatgc
 V$USF_02               |     1784 (+) |  0.935 |  0.945 | ggagCACCTgccat
 V$USF_02               |     1784 (-) |  0.935 |  0.945 | ggagcACCTGccat
 V$USF_02               |     3639 (+) |  0.938 |  0.950 | ctacCACATggtgg
 V$USF_02               |     3639 (-) |  0.938 |  0.950 | ctaccACATGgtgg
 V$USF_02               |     3936 (+) |  0.915 |  0.933 | cagtCACTTgttca
 V$USF_02               |     3936 (-) |  0.915 |  0.933 | cagtcACTTGttca
 V$USF_02               |     5250 (+) |  0.938 |  0.938 | ttcaCATGTggtca
 V$USF_02               |     5250 (-) |  0.938 |  0.938 | ttcacATGTGgtca
 V$USF_02               |     6062 (+) |  1.000 |  0.972 | cctgCACGTgctgc
 V$USF_02               |     6062 (-) |  1.000 |  0.972 | cctgcACGTGctgc
 V$USF_02               |     7110 (+) |  0.938 |  0.936 | gtacCACATgtgtg
 V$USF_02               |     7110 (-) |  0.938 |  0.936 | gtaccACATGtgtg
 V$USF_02               |     8967 (+) |  0.935 |  0.934 | gaacCAGGTgtggt
 V$USF_02               |     8967 (-) |  0.935 |  0.934 | gaaccAGGTGtggt
 V$MYCMAX_02            |      734 (+) |  1.000 |  0.984 | cacCACGTggtt
 V$MYCMAX_02            |      734 (-) |  1.000 |  0.964 | caccACGTGgtt
 V$MYCMAX_02            |     1125 (+) |  1.000 |  0.942 | atgCACGTgtgt
 V$MYCMAX_02            |     1125 (-) |  1.000 |  0.929 | atgcACGTGtgt
 V$MYCMAX_02            |     3640 (+) |  0.941 |  0.921 | tacCACATggtg
 V$MYCMAX_02            |     5251 (-) |  0.941 |  0.953 | tcacATGTGgtc
 V$MYCMAX_02            |     6063 (-) |  1.000 |  0.960 | ctgcACGTGctg
 V$MYCMAX_02            |     7111 (+) |  0.941 |  0.946 | tacCACATgtgt
 V$MYCMAX_02            |     8999 (+) |  0.941 |  0.919 | cagCACATggag
 V$PBX1_02              |    11194 (-) |  1.000 |  0.982 | ttcttGATTGattat
 F$MCM1_01              |     7574 (+) |  0.867 |  0.895 | aatCCCCAtcaggtca
 V$GATA1_02             |       80 (+) |  0.993 |  0.979 | atgtTGATAgggcc
 V$GATA1_02             |       89 (-) |  1.000 |  0.970 | gggccTATCTtcgc
 V$GATA1_02             |      305 (-) |  1.000 |  0.944 | tgagcTATCTctcc
 V$GATA1_02             |      564 (+) |  1.000 |  0.951 | taggAGATAaacgt
 V$GATA1_02             |     1993 (-) |  1.000 |  0.950 | aagatTATCTggct
 V$GATA1_02             |     2316 (+) |  0.986 |  0.942 | ttttGGATAcagtc
 V$GATA1_02             |     2720 (+) |  1.000 |  0.955 | aaatAGATAatctt
 V$GATA1_02             |     3928 (-) |  0.993 |  0.962 | tacatTATCAgtca
 V$GATA1_02             |     3975 (+) |  0.993 |  0.934 | tgtaTGATAgacac
 V$GATA1_02             |     4372 (-) |  1.000 |  0.935 | aaagtTATCTggct
 V$GATA1_02             |     4575 (+) |  1.000 |  0.945 | ggttAGATAtagtc
 V$GATA1_02             |     4620 (-) |  0.986 |  0.956 | accaaTATCCtttg
 V$GATA1_02             |     4777 (+) |  0.986 |  0.945 | gtctGGATAaagat
 V$GATA1_02             |     5333 (+) |  0.991 |  0.948 | gcgcCGATAgtttt
 V$GATA1_02             |     5525 (-) |  0.986 |  0.969 | cctccTATCCagat
 V$GATA1_02             |     5580 (+) |  0.986 |  0.943 | taaaGGATAataat
 V$GATA1_02             |     5631 (+) |  0.986 |  0.937 | actgGGATAaagac
 V$GATA1_02             |     5975 (+) |  0.993 |  0.935 | gtggTGATAacttc
 V$GATA1_02             |     6463 (+) |  0.993 |  0.941 | ttccTGATAaaatg
 V$GATA1_02             |     6751 (-) |  0.986 |  0.969 | cccacTATCCcttt
 V$GATA1_02             |     6945 (+) |  0.993 |  0.959 | caagTGATActgtc
 V$GATA1_02             |     7150 (-) |  1.000 |  0.975 | cgccgTATCTcctg
 V$GATA1_02             |     7308 (+) |  0.986 |  0.940 | gtaaGGATAtagaa
 V$GATA1_02             |     7373 (+) |  0.993 |  0.957 | gaatTGATAttgct
 V$GATA1_02             |     7786 (-) |  0.986 |  0.939 | aaaatTATCCcaaa
 V$GATA1_02             |     7795 (+) |  1.000 |  0.955 | ccaaAGATAaagaa
 V$GATA1_02             |     7900 (+) |  0.993 |  0.947 | atttTGATAttagc
 V$GATA1_02             |     7949 (+) |  1.000 |  0.938 | tttgAGATAcccca
 V$GATA1_02             |     8060 (-) |  1.000 |  0.944 | tagttTATCTggta
 V$GATA1_02             |     8602 (-) |  0.993 |  0.950 | aatatTATCAttcc
 V$GATA1_02             |     9365 (-) |  0.993 |  0.948 | ttctcTATCAcagg
 V$GATA1_02             |     9417 (-) |  0.986 |  0.941 | aaaacTATCCcata
 V$GATA1_02             |     9730 (+) |  0.993 |  0.956 | tgtaTGATAatgtc
 V$GATA1_02             |     9831 (+) |  0.986 |  0.942 | gaagGGATAatttt
 V$GATA1_02             |    10486 (-) |  0.993 |  0.958 | ccacaTATCAagga
 V$GATA1_02             |    10592 (-) |  0.993 |  0.952 | tcctaTATCAaaaa
 V$GATA1_02             |    11346 (-) |  0.991 |  0.961 | gccatTATCGaacg
 V$GATA1_02             |    11367 (-) |  1.000 |  0.952 | gattcTATCTgtgc
 V$GATA1_02             |    11439 (-) |  1.000 |  0.963 | atactTATCTattt
 V$GATA1_02             |    11507 (+) |  0.986 |  0.936 | ttgtGGATAttacc
 V$GATA1_02             |    11567 (-) |  0.993 |  0.973 | actctTATCAttgc
 V$GATA1_02             |    11772 (+) |  1.000 |  0.960 | ttccAGATActtga
 V$GATA1_04             |       81 (+) |  0.991 |  0.956 | tgtTGATAgggcc
 V$GATA1_04             |       89 (-) |  1.000 |  0.962 | gggccTATCTtcg
 V$GATA1_04             |      305 (-) |  1.000 |  0.959 | tgagcTATCTctc
 V$GATA1_04             |      565 (+) |  1.000 |  0.979 | aggAGATAaacgt
 V$GATA1_04             |     1993 (-) |  1.000 |  0.981 | aagatTATCTggc
 V$GATA1_04             |     2721 (+) |  1.000 |  0.967 | aatAGATAatctt
 V$GATA1_04             |     3928 (-) |  0.991 |  0.974 | tacatTATCAgtc
 V$GATA1_04             |     3976 (+) |  0.991 |  0.954 | gtaTGATAgacac
 V$GATA1_04             |     4372 (-) |  1.000 |  0.983 | aaagtTATCTggc
 V$GATA1_04             |     5976 (+) |  0.991 |  0.962 | tggTGATAacttc
 V$GATA1_04             |     6464 (+) |  0.991 |  0.976 | tccTGATAaaatg
 V$GATA1_04             |     7150 (-) |  1.000 |  0.952 | cgccgTATCTcct
 V$GATA1_04             |     7796 (+) |  1.000 |  0.972 | caaAGATAaagaa
 V$GATA1_04             |     8060 (-) |  1.000 |  0.987 | tagttTATCTggt
 V$GATA1_04             |     8602 (-) |  0.991 |  0.963 | aatatTATCAttc
 V$GATA1_04             |     9365 (-) |  0.991 |  0.947 | ttctcTATCAcag
 V$GATA1_04             |     9731 (+) |  0.991 |  0.964 | gtaTGATAatgtc
 V$GATA1_04             |    11367 (-) |  1.000 |  0.963 | gattcTATCTgtg
 V$GATA1_04             |    11439 (-) |  1.000 |  0.982 | atactTATCTatt
 V$GATA1_04             |    11567 (-) |  0.991 |  0.970 | actctTATCAttg
 V$GATA1_04             |    11773 (+) |  1.000 |  0.949 | tccAGATActtga
 V$HFH1_01              |      568 (-) |  1.000 |  0.842 | agaTAAACgtct
 V$HFH1_01              |      604 (-) |  1.000 |  0.843 | tttTAAACatcc
 V$HFH1_01              |      635 (-) |  1.000 |  0.873 | tttTAAACattt
 V$HFH1_01              |     2410 (-) |  0.841 |  0.852 | aaaAAAACaaaa
 V$HFH1_01              |     4008 (-) |  0.790 |  0.835 | aaaTAAATattc
 V$HFH1_01              |     5718 (-) |  0.841 |  0.845 | acaAAAACacta
 V$HFH1_01              |     7064 (+) |  0.841 |  0.834 | atttGTTTTtgt
 V$HFH1_01              |     7070 (+) |  0.853 |  0.846 | ttttGTTTGtgt
 V$HFH1_01              |     7421 (+) |  1.000 |  0.893 | aaagGTTTAttt
 V$HFH1_01              |     7429 (+) |  0.841 |  0.844 | atttGTTTTtat
 V$HFH1_01              |     7823 (-) |  0.853 |  0.893 | aaaCAAACaatt
 V$HFH1_01              |     7938 (+) |  1.000 |  0.903 | gtgtGTTTAgtt
 V$HFH1_01              |     7969 (+) |  0.853 |  0.862 | agttGTTTGttt
 V$HFH1_01              |     8058 (+) |  1.000 |  0.869 | tctaGTTTAtct
 V$HFH1_01              |     8553 (-) |  0.790 |  0.848 | aaaTGAACaatg
 V$HFH1_01              |    10311 (+) |  0.841 |  0.858 | aactGTTTTtat
 V$HFH1_01              |    10456 (-) |  0.790 |  0.842 | ataTCAACaatg
 V$HFH1_01              |    10700 (+) |  1.000 |  0.865 | ccgtGTTTAtga
 V$HFH1_01              |    11097 (+) |  1.000 |  0.861 | cactGTTTAaag
 V$HFH1_01              |    11467 (+) |  0.790 |  0.847 | aattTTTTAttt
 V$HFH1_01              |    11575 (+) |  0.790 |  0.842 | cattGCTTAtat
 V$FOXD3_01             |      215 (+) |  0.906 |  0.921 | taTTTTTttttt
 V$FOXD3_01             |     1893 (+) |  0.944 |  0.918 | ttATATTtattt
 V$FOXD3_01             |     1905 (+) |  0.948 |  0.916 | taTTATTttatt
 V$FOXD3_01             |     2410 (-) |  1.000 |  0.949 | aaaaaAACAAaa
 V$FOXD3_01             |     2414 (-) |  0.906 |  0.937 | aaacaAAAAAtc
 V$FOXD3_01             |     4008 (-) |  0.944 |  0.958 | aaataAATATtc
 V$FOXD3_01             |     4221 (-) |  0.948 |  0.917 | aaaaaAATAAat
 V$FOXD3_01             |     5805 (-) |  0.906 |  0.921 | aaaaaAAAAAta
 V$FOXD3_01             |     7047 (+) |  0.884 |  0.912 | gaCTATTttttt
 V$FOXD3_01             |     7425 (+) |  0.948 |  0.931 | gtTTATTtgttt
 V$FOXD3_01             |     7781 (-) |  0.901 |  0.929 | aaacaAAAATta
 V$FOXD3_01             |     7823 (-) |  1.000 |  0.997 | aaacaAACAAtt
 V$FOXD3_01             |     7969 (+) |  1.000 |  0.937 | agTTGTTtgttt
 V$FOXD3_01             |     8553 (-) |  1.000 |  0.929 | aaatgAACAAtg
 V$FOXD3_01             |    11203 (+) |  0.948 |  0.915 | gaTTATTaattt
 V$FOXD3_01             |    11293 (-) |  0.948 |  0.938 | aaagaAATAAta
 V$FOXD3_01             |    11467 (+) |  0.906 |  0.929 | aaTTTTTtattt
 V$FOXD3_01             |    11471 (+) |  0.948 |  0.926 | ttTTATTtgttt
 V$HNF3B_01             |      210 (+) |  1.000 |  0.903 | cctggTATTTttttt
 V$HNF3B_01             |      212 (+) |  0.930 |  0.898 | tggtaTTTTTttttt
 V$HNF3B_01             |      213 (+) |  0.930 |  0.918 | ggtatTTTTTttttt
 V$HNF3B_01             |      503 (+) |  1.000 |  0.894 | ttataTATTTgtctt
 V$HNF3B_01             |      847 (-) |  1.000 |  0.938 | taaatAAATAcgatc
 V$HNF3B_01             |      954 (-) |  1.000 |  0.906 | tgatcAAATAtttac
 V$HNF3B_01             |     1469 (+) |  1.000 |  0.910 | ctcaaTATTTgctct
 V$HNF3B_01             |     1524 (+) |  1.000 |  0.917 | agagcTGTTTttttg
 V$HNF3B_01             |     1891 (+) |  1.000 |  0.945 | ttttaTATTTatttt
 V$HNF3B_01             |     1895 (+) |  1.000 |  0.907 | atattTATTTtatta
 V$HNF3B_01             |     1903 (+) |  1.000 |  0.938 | tttatTATTTtattt
 V$HNF3B_01             |     2358 (+) |  1.000 |  0.910 | acttgTATTTatttt
 V$HNF3B_01             |     2409 (-) |  1.000 |  0.928 | aaaaaAAACAaaaaa
 V$HNF3B_01             |     2413 (-) |  0.930 |  0.910 | aaaacAAAAAatcac
 V$HNF3B_01             |     3452 (-) |  1.000 |  0.894 | taataAAACAcaggg
 V$HNF3B_01             |     4007 (-) |  1.000 |  0.966 | taaatAAATAttctg
 V$HNF3B_01             |     4220 (-) |  1.000 |  0.923 | taaaaAAATAaattc
 V$HNF3B_01             |     4429 (-) |  0.930 |  0.890 | aaaaaAAAAAaaacc
 V$HNF3B_01             |     4430 (-) |  0.930 |  0.894 | aaaaaAAAAAaacca
 V$HNF3B_01             |     4498 (-) |  1.000 |  0.925 | aaacaAAACAaaaca
 V$HNF3B_01             |     4503 (-) |  1.000 |  0.893 | aaacaAAACAacatc
 V$HNF3B_01             |     5121 (-) |  1.000 |  0.900 | aaaggAAACAgatgg
 V$HNF3B_01             |     5590 (-) |  1.000 |  0.913 | taataAAATAtaata
 V$HNF3B_01             |     5717 (-) |  1.000 |  0.896 | cacaaAAACActaaa
 V$HNF3B_01             |     5792 (-) |  1.000 |  0.927 | taattAAATAcaaaa
 V$HNF3B_01             |     5805 (-) |  0.930 |  0.894 | aaaaaAAAAAtagcc
 V$HNF3B_01             |     5807 (-) |  1.000 |  0.930 | aaaaaAAATAgccct
 V$HNF3B_01             |     6589 (-) |  1.000 |  0.928 | aaaacAAATAaggtg
 V$HNF3B_01             |     7045 (+) |  1.000 |  0.953 | ttgacTATTTttttt
 V$HNF3B_01             |     7068 (+) |  1.000 |  0.901 | gttttTGTTTgtgta
 V$HNF3B_01             |     7423 (+) |  1.000 |  0.943 | aggttTATTTgtttt
 V$HNF3B_01             |     7776 (-) |  1.000 |  0.896 | aaacaAAACAaaaat
 V$HNF3B_01             |     7780 (-) |  0.930 |  0.904 | aaaacAAAAAttatc
 V$HNF3B_01             |     7822 (-) |  1.000 |  0.966 | aaaacAAACAattaa
 V$HNF3B_01             |     7936 (+) |  1.000 |  0.916 | ttgtgTGTTTagttt
 V$HNF3B_01             |     7967 (+) |  1.000 |  0.926 | atagtTGTTTgtttt
 V$HNF3B_01             |     9534 (-) |  1.000 |  0.906 | agaacAAACAagtcc
 V$HNF3B_01             |    10309 (+) |  1.000 |  0.920 | ttaacTGTTTttata
 V$HNF3B_01             |    10317 (+) |  1.000 |  0.890 | ttttaTATTTttatt
 V$HNF3B_01             |    10319 (+) |  0.930 |  0.894 | ttataTTTTTatttt
 V$HNF3B_01             |    10340 (+) |  1.000 |  0.896 | tttatTGTTTtaatt
 V$HNF3B_01             |    10911 (-) |  1.000 |  0.905 | tatgcAAATAatagt
 V$HNF3B_01             |    11292 (-) |  1.000 |  0.928 | caaagAAATAataat
 V$HNF3B_01             |    11464 (+) |  0.930 |  0.908 | tgaaaTTTTTtattt
 V$HNF3B_01             |    11465 (+) |  0.930 |  0.891 | gaaatTTTTTatttg
 V$HNF3B_01             |    11469 (+) |  1.000 |  0.938 | tttttTATTTgtttt
 V$HNF3B_01             |    11674 (-) |  0.930 |  0.895 | taaccAAAAAagacc
 V$HNF1_01              |      987 (+) |  1.000 |  0.948 | aGTTAAtaattttca
 V$HNF1_01              |     2535 (-) |  0.918 |  0.820 | ttttagagaATAACa
 V$HNF1_01              |     3412 (+) |  1.000 |  0.916 | aGTTAAtgattctgg
 V$HNF1_01              |     3449 (+) |  1.000 |  0.815 | aGTTAAtaaaacaca
 V$HNF1_01              |     4056 (-) |  0.788 |  0.823 | aggcaataaTTAAAa
 V$HNF1_01              |     5099 (+) |  0.918 |  0.884 | gGTTATtatttgtga
 V$HNF1_01              |     5786 (-) |  0.788 |  0.812 | atgaaataaTTAAAt
 V$HNF1_01              |     7354 (+) |  1.000 |  0.867 | tGTTAAtcatgggca
 V$HNF1_01              |     7824 (-) |  1.000 |  0.909 | aacaaacaaTTAACc
 V$HNF1_01              |     8488 (+) |  0.918 |  0.849 | gGTTATtttctacag
 V$HNF1_01              |     8852 (-) |  0.788 |  0.809 | gtttaaaaaTTAAGa
 V$HNF1_01              |    11694 (+) |  1.000 |  0.886 | aGTTAAtcactgtca
 V$HNF4_01              |     7082 (-) |  1.000 |  0.864 | atgagtgCTTTGcgcgcac
 V$HNF4_01              |     8373 (-) |  1.000 |  0.934 | tgctgctCTTTGatctgta
 V$HNF4_01              |     8579 (+) |  1.000 |  0.884 | aatggggCAAAGgcaacat
 V$OCT1_01              |     2622 (+) |  0.784 |  0.845 | tatgcTAGGCaaatgctct
 V$OCT1_01              |     2829 (+) |  0.784 |  0.848 | agttgTCTGCaaatggcat
 V$OCT1_01              |     3099 (+) |  0.784 |  0.819 | gaatcTATACtaatttcca
 V$OCT1_01              |     3838 (-) |  0.831 |  0.819 | tttccattcTCATAaaata
 V$OCT1_01              |     4066 (+) |  0.837 |  0.806 | taaaaTATGTaaaatgtat
 V$OCT1_01              |     4791 (-) |  1.000 |  0.864 | tgctgacttGCATAatctc
 V$OCT1_01              |     5439 (-) |  0.834 |  0.829 | tttgtattgCCATAtaacc
 V$OCT1_01              |     6203 (+) |  1.000 |  0.838 | cggggTATGCcaaggtttc
 V$OCT1_01              |     6572 (+) |  1.000 |  0.890 | acagtTATGCaaaacacaa
 V$OCT1_01              |     9727 (+) |  0.831 |  0.848 | ctttgTATGAtaatgtcca
 V$OCT1_01              |     9931 (-) |  0.822 |  0.880 | gggtaatttGCATGtatgt
 V$OCT1_01              |    10906 (+) |  1.000 |  0.970 | gctacTATGCaaataatag
 V$OCT1_01              |    11662 (-) |  0.831 |  0.881 | acacaatttTCATAaccaa
 V$OCT1_02              |        2 (-) |  0.809 |  0.792 | ttcatGCATGtacaa
 V$OCT1_02              |      641 (+) |  0.992 |  0.827 | acattTATTCattta
 V$OCT1_02              |      869 (+) |  0.814 |  0.769 | ttagaAATGCacaaa
 V$OCT1_02              |      957 (+) |  0.758 |  0.777 | tcaaaTATTTacagg
 V$OCT1_02              |     1119 (+) |  1.000 |  0.854 | ttgtgTATGCacgtg
 V$OCT1_02              |     1466 (-) |  0.753 |  0.776 | tttctCAATAtttgc
 V$OCT1_02              |     2001 (+) |  0.940 |  0.813 | ctggcTATACatctc
 V$OCT1_02              |     2315 (-) |  0.942 |  0.783 | gttttGGATAcagtc
 V$OCT1_02              |     2521 (-) |  0.766 |  0.793 | aaattACATAttact
 V$OCT1_02              |     2537 (-) |  0.992 |  0.775 | ttagaGAATAacagg
 V$OCT1_02              |     2582 (+) |  0.814 |  0.768 | caacaAATGCagtac
 V$OCT1_02              |     2593 (-) |  0.753 |  0.778 | gtactGACTAttaaa
 V$OCT1_02              |     2617 (+) |  1.000 |  0.801 | atgtgTATGCtaggc
 V$OCT1_02              |     2736 (+) |  1.000 |  0.777 | gccttTATGCctttt
 V$OCT1_02              |     2880 (+) |  1.000 |  0.803 | ccgtgTATGCgtact
 V$OCT1_02              |     2890 (-) |  0.805 |  0.817 | gtactGCATCttttt
 V$OCT1_02              |     2900 (+) |  0.942 |  0.788 | tttttTATCCacatc
 V$OCT1_02              |     2944 (-) |  0.761 |  0.785 | agtctGCCTAttacg
 V$OCT1_02              |     2953 (-) |  0.992 |  0.769 | attacGAATAcagtg
 V$OCT1_02              |     3176 (+) |  0.942 |  0.810 | cattaTATCCcccct
 V$OCT1_02              |     3204 (+) |  1.000 |  0.824 | tcaagTATGCtaggc
 V$OCT1_02              |     3363 (-) |  0.992 |  0.850 | ccactGAATAgccta
 V$OCT1_02              |     3577 (+) |  0.992 |  0.826 | caagtTATTCaactc
 V$OCT1_02              |     3709 (-) |  0.753 |  0.778 | ttgatCAATAtttac
 V$OCT1_02              |     3712 (+) |  0.758 |  0.784 | atcaaTATTTacggg
 V$OCT1_02              |     3850 (+) |  0.942 |  0.918 | taaaaTATCCagtac
 V$OCT1_02              |     4007 (-) |  0.758 |  0.812 | taaatAAATAttctg
 V$OCT1_02              |     4010 (+) |  0.992 |  0.905 | ataaaTATTCtgctc
 V$OCT1_02              |     4029 (-) |  0.753 |  0.805 | ggaatTAATAttcca
 V$OCT1_02              |     4032 (+) |  0.992 |  0.911 | attaaTATTCcagca
 V$OCT1_02              |     4050 (+) |  0.761 |  0.783 | ggaaaTAGGCaataa
 V$OCT1_02              |     4066 (+) |  0.766 |  0.786 | taaaaTATGTaaaat
 V$OCT1_02              |     4076 (-) |  0.940 |  0.841 | aaaatGTATActata
 V$OCT1_02              |     4103 (+) |  0.752 |  0.775 | taaaaCATCCatttt
 V$OCT1_02              |     4167 (+) |  0.992 |  0.878 | cctagTATTCaggag
 V$OCT1_02              |     4311 (-) |  1.000 |  0.835 | atactGCATAaaact
 V$OCT1_02              |     4446 (-) |  0.753 |  0.809 | acaatTAATAttcat
 V$OCT1_02              |     4449 (+) |  0.992 |  0.965 | attaaTATTCatttc
 V$OCT1_02              |     4473 (-) |  0.814 |  0.768 | gaccaGCATTtttct
 V$OCT1_02              |     4620 (+) |  0.942 |  0.868 | accaaTATCCtttgg
 V$OCT1_02              |     4776 (-) |  0.942 |  0.791 | agtctGGATAaagat
 V$OCT1_02              |     4795 (-) |  1.000 |  0.918 | gacttGCATAatctc
 V$OCT1_02              |     4884 (+) |  0.802 |  0.787 | tggaaCATTCcatgt
 V$OCT1_02              |     5525 (+) |  0.942 |  0.789 | cctccTATCCagatt
 V$OCT1_02              |     5579 (-) |  0.942 |  0.794 | ctaaaGGATAataat
 V$OCT1_02              |     5780 (+) |  0.761 |  0.785 | aaaaaTATGAaataa
 V$OCT1_02              |     6203 (+) |  1.000 |  0.801 | cggggTATGCcaagg
 V$OCT1_02              |     6468 (+) |  0.814 |  0.770 | gataaAATGCtcagg
 V$OCT1_02              |     6572 (+) |  1.000 |  0.834 | acagtTATGCaaaac
 V$OCT1_02              |     6751 (+) |  0.942 |  0.786 | cccacTATCCcttta
 V$OCT1_02              |     6899 (-) |  1.000 |  0.779 | agaggGCATAagtgg
 V$OCT1_02              |     6957 (+) |  0.992 |  0.826 | tccatTATTCtggat
 V$OCT1_02              |     7042 (-) |  0.753 |  0.780 | tagttGACTAttttt
 V$OCT1_02              |     7264 (+) |  0.942 |  0.865 | taaaaTATCCtaaaa
 V$OCT1_02              |     7307 (-) |  0.942 |  0.809 | agtaaGGATAtagaa
 V$OCT1_02              |     7656 (+) |  1.000 |  0.771 | ttttgTATGCcaggc
 V$OCT1_02              |     7786 (+) |  0.942 |  0.790 | aaaatTATCCcaaag
 V$OCT1_02              |     8083 (+) |  0.940 |  0.787 | cttccTATACagctc
 V$OCT1_02              |     8384 (-) |  0.940 |  0.779 | gatctGTATAcctga
 V$OCT1_02              |     8596 (-) |  0.753 |  0.780 | atcttTAATAttatc
 V$OCT1_02              |     8867 (-) |  1.000 |  0.771 | ctctgGCATAgaata
 V$OCT1_02              |     8872 (-) |  0.992 |  0.932 | gcataGAATAttcta
 V$OCT1_02              |     8875 (+) |  0.992 |  0.934 | tagaaTATTCtagaa
 V$OCT1_02              |     8910 (-) |  0.992 |  0.852 | ttcagGAATActcgg
 V$OCT1_02              |     9079 (-) |  1.000 |  0.828 | gggcaGCATAgtgaa
 V$OCT1_02              |     9138 (-) |  0.992 |  0.833 | tttttGAATAagaca
 V$OCT1_02              |     9165 (+) |  0.805 |  0.819 | cctaaGATGCatgaa
 V$OCT1_02              |     9417 (+) |  0.942 |  0.787 | aaaacTATCCcataa
 V$OCT1_02              |     9751 (-) |  0.753 |  0.780 | tatatTAATAttgaa
 V$OCT1_02              |     9754 (+) |  0.753 |  0.782 | attaaTATTGaaaac
 V$OCT1_02              |     9830 (-) |  0.942 |  0.791 | agaagGGATAatttt
 V$OCT1_02              |     9912 (-) |  0.756 |  0.778 | ttactGGATTtttgc
 V$OCT1_02              |     9939 (-) |  0.749 |  0.777 | tgcatGTATGttata
 V$OCT1_02              |     9956 (-) |  0.749 |  0.774 | accctGTATGtttct
 V$OCT1_02              |    10906 (+) |  1.000 |  0.888 | gctacTATGCaaata
 V$OCT1_02              |    11084 (-) |  0.806 |  0.791 | tctggGAATTttcca
 V$OCT1_02              |    11198 (-) |  0.753 |  0.784 | tgattGATTAttaat
 V$OCT1_02              |    11279 (-) |  1.000 |  0.777 | ttaagGCATAgggca
 V$OCT1_02              |    11412 (-) |  0.814 |  0.771 | attctGCATTtctat
 V$OCT1_02              |    11432 (-) |  1.000 |  0.835 | tatccGCATActtat
 V$OCT1_02              |    11496 (-) |  0.806 |  0.817 | cggttGAATTtttgt
 V$OCT1_02              |    11506 (-) |  0.942 |  0.925 | tttgtGGATAttacc
 V$OCT1_02              |    11548 (-) |  0.709 |  0.773 | tagatGGGTAttcaa
 V$OCT1_02              |    11551 (+) |  0.992 |  0.857 | atgggTATTCaacca
 V$OCT1_02              |    11579 (+) |  0.942 |  0.864 | gcttaTATCCaggag
 V$OCT1_03              |       47 (-) |  1.000 |  0.995 | atgtcATTACttg
 V$OCT1_03              |       61 (+) |  0.996 |  0.988 | gccATAATtactg
 V$OCT1_03              |       62 (-) |  1.000 |  0.992 | ccataATTACtgt
 V$OCT1_03              |      175 (-) |  1.000 |  0.936 | ctggcATTACtac
 V$OCT1_03              |      438 (+) |  0.982 |  0.980 | cgtTTAATcaggt
 V$OCT1_03              |      494 (-) |  0.996 |  0.943 | gcaacATTATtat
 V$OCT1_03              |      497 (-) |  0.996 |  0.991 | acattATTATata
 V$OCT1_03              |      650 (-) |  0.996 |  0.986 | catttATTATata
 V$OCT1_03              |      710 (-) |  0.934 |  0.936 | atctcTTTACaga
 V$OCT1_03              |      959 (-) |  0.934 |  0.932 | aaataTTTACagg
 V$OCT1_03              |      986 (+) |  0.982 |  0.977 | cagTTAATaattt
 V$OCT1_03              |      989 (+) |  0.996 |  0.940 | ttaATAATtttca
 V$OCT1_03              |     1647 (+) |  0.985 |  0.931 | gtgCTAATctact
 V$OCT1_03              |     1901 (-) |  0.996 |  0.989 | attttATTATttt
 V$OCT1_03              |     1991 (-) |  0.996 |  0.942 | ccaagATTATctg
 V$OCT1_03              |     2518 (-) |  1.000 |  0.945 | aaaaaATTACata
 V$OCT1_03              |     2525 (-) |  1.000 |  0.945 | tacatATTACttt
 V$OCT1_03              |     2573 (-) |  0.934 |  0.933 | aagtaTTTACaac
 V$OCT1_03              |     2651 (+) |  1.000 |  0.937 | tgcGTAATgcact
 V$OCT1_03              |     2723 (+) |  0.996 |  0.941 | tagATAATcttct
 V$OCT1_03              |     2898 (-) |  0.930 |  0.930 | tctttTTTATcca
 V$OCT1_03              |     2948 (-) |  1.000 |  0.948 | tgcctATTACgaa
 V$OCT1_03              |     3172 (-) |  0.996 |  0.940 | tgtacATTATatc
 V$OCT1_03              |     3273 (-) |  0.996 |  0.948 | atgccATTATgat
 V$OCT1_03              |     3372 (+) |  0.985 |  0.983 | agcCTAATcatat
 V$OCT1_03              |     3411 (+) |  0.982 |  0.975 | aagTTAATgattc
 V$OCT1_03              |     3428 (+) |  0.982 |  0.930 | tgcTTAATtgact
 V$OCT1_03              |     3448 (+) |  0.982 |  0.974 | cagTTAATaaaac
 V$OCT1_03              |     3626 (+) |  0.996 |  0.943 | tttATAATagtac
 V$OCT1_03              |     3714 (-) |  0.934 |  0.931 | caataTTTACggg
 V$OCT1_03              |     3730 (-) |  0.996 |  0.941 | ctaaaATTATtat
 V$OCT1_03              |     3733 (-) |  0.996 |  0.989 | aaattATTATttc
 V$OCT1_03              |     3827 (+) |  0.996 |  0.991 | ttcATAATaaatt
 V$OCT1_03              |     3906 (+) |  0.982 |  0.975 | gtaTTAATaaagc
 V$OCT1_03              |     3921 (-) |  1.000 |  0.934 | tatgaATTACatt
 V$OCT1_03              |     3926 (-) |  0.996 |  0.945 | attacATTATcag
 V$OCT1_03              |     4058 (+) |  0.996 |  0.989 | gcaATAATtaaaa
 V$OCT1_03              |     4059 (-) |  0.982 |  0.975 | caataATTAAaat
 V$OCT1_03              |     4159 (+) |  1.000 |  0.936 | tttGTAATcctag
 V$OCT1_03              |     4247 (-) |  1.000 |  0.935 | attgtATTACttg
 V$OCT1_03              |     4282 (-) |  0.985 |  0.932 | cacacATTAGacc
 V$OCT1_03              |     4444 (-) |  0.982 |  0.933 | acacaATTAAtat
 V$OCT1_03              |     4712 (+) |  1.000 |  0.934 | tggGTAATtcact
 V$OCT1_03              |     4799 (+) |  0.996 |  0.941 | tgcATAATctctg
 V$OCT1_03              |     5004 (-) |  1.000 |  0.934 | cttgtATTACcca
 V$OCT1_03              |     5011 (-) |  0.982 |  0.934 | tacccATTAAgcc
 V$OCT1_03              |     5098 (-) |  0.996 |  0.984 | gggttATTATttg
 V$OCT1_03              |     5235 (-) |  1.000 |  0.945 | gaacgATTACatg
 V$OCT1_03              |     5411 (-) |  0.982 |  0.978 | atcttATTAAatc
 V$OCT1_03              |     5583 (+) |  0.996 |  0.991 | aggATAATaataa
 V$OCT1_03              |     5586 (+) |  0.996 |  0.991 | ataATAATaaaat
 V$OCT1_03              |     5596 (+) |  0.996 |  0.939 | aatATAATataac
 V$OCT1_03              |     5634 (+) |  0.930 |  0.931 | gggATAAAgacaa
 V$OCT1_03              |     5738 (+) |  0.996 |  0.943 | gccATAATataga
 V$OCT1_03              |     5788 (+) |  0.996 |  0.990 | gaaATAATtaaat
 V$OCT1_03              |     5789 (-) |  0.982 |  0.976 | aaataATTAAata
 V$OCT1_03              |     6807 (-) |  1.000 |  0.995 | ccctcATTACctt
 V$OCT1_03              |     6834 (-) |  0.934 |  0.930 | tgctaTTTACtgc
 V$OCT1_03              |     6955 (-) |  0.996 |  0.942 | tgtccATTATtct
 V$OCT1_03              |     7058 (+) |  0.982 |  0.932 | ttcTTAATttgtt
 V$OCT1_03              |     7257 (-) |  0.982 |  0.978 | gtctcATTAAaat
 V$OCT1_03              |     7353 (+) |  0.982 |  0.978 | atgTTAATcatgg
 V$OCT1_03              |     7399 (-) |  1.000 |  0.933 | gtagaATTACtga
 V$OCT1_03              |     7784 (-) |  0.996 |  0.940 | caaaaATTATccc
 V$OCT1_03              |     7827 (-) |  0.982 |  0.932 | aaacaATTAAccc
 V$OCT1_03              |     7903 (-) |  0.985 |  0.931 | ttgatATTAGctt
 V$OCT1_03              |     8150 (-) |  0.985 |  0.933 | aaaacATTAGctt
 V$OCT1_03              |     8570 (-) |  0.982 |  0.975 | ctttgATTAAatg
 V$OCT1_03              |     8600 (-) |  0.996 |  0.943 | ttaatATTATcat
 V$OCT1_03              |     8683 (+) |  1.000 |  0.989 | aagGTAATtagcc
 V$OCT1_03              |     8684 (-) |  0.985 |  0.978 | aggtaATTAGcct
 V$OCT1_03              |     8855 (-) |  0.982 |  0.930 | taaaaATTAAgac
 V$OCT1_03              |     8951 (-) |  0.985 |  0.933 | ttaaaATTAGtag
 V$OCT1_03              |     9589 (+) |  1.000 |  0.934 | cctGTAATcccag
 V$OCT1_03              |     9733 (+) |  0.996 |  0.942 | atgATAATgtcca
 V$OCT1_03              |     9752 (+) |  0.982 |  0.930 | ataTTAATattga
 V$OCT1_03              |     9834 (+) |  0.996 |  0.943 | gggATAATtttaa
 V$OCT1_03              |     9930 (+) |  1.000 |  0.945 | tggGTAATttgca
 V$OCT1_03              |    10125 (-) |  0.985 |  0.932 | ataaaATTAGtta
 V$OCT1_03              |    10137 (-) |  0.996 |  0.942 | aagaaATTATtat
 V$OCT1_03              |    10140 (-) |  0.996 |  0.990 | aaattATTATtat
 V$OCT1_03              |    10143 (-) |  0.996 |  0.989 | ttattATTATtgt
 V$OCT1_03              |    10170 (-) |  0.985 |  0.980 | tccttATTAGtgt
 V$OCT1_03              |    10505 (-) |  0.996 |  0.942 | agtcaATTATggc
 V$OCT1_03              |    10520 (-) |  0.996 |  0.944 | tagccATTATagg
 V$OCT1_03              |    10655 (+) |  0.985 |  0.935 | gtcCTAATgtcaa
 V$OCT1_03              |    10700 (-) |  0.930 |  0.931 | ccgtgTTTATgaa
 V$OCT1_03              |    10915 (+) |  0.996 |  0.942 | caaATAATagtct
 V$OCT1_03              |    10999 (-) |  1.000 |  0.948 | atcagATTACctg
 V$OCT1_03              |    11199 (-) |  0.996 |  0.987 | gattgATTATtaa
 V$OCT1_03              |    11202 (-) |  0.982 |  0.974 | tgattATTAAttt
 V$OCT1_03              |    11205 (+) |  0.982 |  0.930 | ttaTTAATttgtt
 V$OCT1_03              |    11296 (+) |  0.996 |  0.990 | gaaATAATaataa
 V$OCT1_03              |    11299 (+) |  0.996 |  0.991 | ataATAATaacga
 V$OCT1_03              |    11344 (-) |  0.996 |  0.946 | atgccATTATcga
 V$OCT1_03              |    11387 (-) |  0.982 |  0.977 | aacttATTAAatt
 V$OCT1_03              |    11510 (-) |  1.000 |  0.942 | tggatATTACcgt
 V$OCT1_03              |    11693 (+) |  0.982 |  0.974 | aagTTAATcactg
 V$OCT1_04              |      352 (+) |  0.877 |  0.874 | tacatcagATTCAaatcctttct
 V$OCT1_04              |      988 (-) |  0.952 |  0.913 | gttaataattTTCATgtggggac
 V$OCT1_04              |     3104 (-) |  0.948 |  0.933 | tatactaattTCCATgcggctat
 V$OCT1_04              |     3124 (-) |  0.961 |  0.954 | tatattaattTACATtcccacaa
 V$OCT1_04              |     3830 (-) |  0.948 |  0.946 | ataataaattTCCATtctcataa
 V$OCT1_04              |     4056 (+) |  0.829 |  0.873 | aggcaataATTAAaatatgtaaa
 V$OCT1_04              |     4064 (+) |  0.961 |  0.899 | attaaaatATGTAaaatgtatac
 V$OCT1_04              |     4446 (-) |  0.952 |  0.895 | acaattaataTTCATttcacact
 V$OCT1_04              |     5336 (-) |  1.000 |  0.906 | ccgatagtttTGCATcccctctt
 V$OCT1_04              |     5398 (-) |  0.952 |  0.897 | tttatattttTTCATcttattaa
 V$OCT1_04              |     5431 (-) |  0.847 |  0.879 | ccactttattTGTATtgccatat
 V$OCT1_04              |     6570 (+) |  1.000 |  0.935 | ccacagttATGCAaaacacaaaa
 V$OCT1_04              |     9929 (-) |  1.000 |  0.956 | atgggtaattTGCATgtatgtta
 V$OCT1_04              |    10904 (+) |  1.000 |  0.959 | acgctactATGCAaataatagtc
 V$OCT1_04              |    11147 (+) |  0.952 |  0.922 | gtactctgATGAAaatgaagctg
 V$OCT1_04              |    11330 (+) |  0.961 |  0.941 | tgatgacgATGTAaatgccatta
 V$OCT1_04              |    11660 (-) |  0.952 |  0.949 | taacacaattTTCATaaccaaaa
 V$AHR_01               |     1423 (-) |  1.000 |  0.812 | agaCACGCaatcagtggc
 V$AHR_01               |     5813 (+) |  1.000 |  0.799 | aatagccctgGCGTGgca
 V$AHR_01               |     6348 (-) |  0.800 |  0.805 | tttCACGAaagctcaggg
 V$AHR_01               |     7160 (+) |  0.800 |  0.801 | cctggagctgGCGTTgca
 V$AHR_01               |     9065 (-) |  0.800 |  0.828 | ttcCAGGCtagccagggc
 I$BCD_01               |     2025 (+) |  1.000 |  1.000 | ggGATTAa
 V$LYF1_01              |      193 (-) |  1.000 |  0.890 | ccTCCCAca
 V$LYF1_01              |     1277 (+) |  1.000 |  0.878 | tcTGGGAtg
 V$LYF1_01              |     2381 (-) |  1.000 |  0.905 | ttTCCCAga
 V$LYF1_01              |     2714 (-) |  1.000 |  0.956 | ctTCCCAaa
 V$LYF1_01              |     3284 (+) |  1.000 |  0.862 | atTGGGAtg
 V$LYF1_01              |     4115 (-) |  1.000 |  0.905 | ttTCCCAga
 V$LYF1_01              |     5993 (+) |  0.861 |  0.843 | ttAGGGAtg
 V$LYF1_01              |     6179 (-) |  1.000 |  0.840 | gtTCCCAga
 V$LYF1_01              |     7269 (-) |  0.859 |  0.852 | taTCCTAaa
 V$LYF1_01              |     7699 (+) |  1.000 |  0.921 | ctTGGGAgg
 V$LYF1_01              |     7791 (-) |  1.000 |  0.951 | taTCCCAaa
 V$LYF1_01              |     8115 (-) |  1.000 |  0.842 | tcTCCCAcc
 V$LYF1_01              |     8762 (-) |  1.000 |  0.869 | ccTCCCAgc
 V$LYF1_01              |     8772 (+) |  1.000 |  0.859 | ccTGGGAgg
 V$LYF1_01              |     8960 (+) |  0.861 |  0.844 | gtAGGGAga
 V$LYF1_01              |     9422 (-) |  1.000 |  0.852 | taTCCCAta
 V$LYF1_01              |     9604 (+) |  1.000 |  0.956 | ttTGGGAag
 V$LYF1_01              |    10612 (+) |  1.000 |  0.890 | tgTGGGAgg
 V$LYF1_01              |    11084 (+) |  1.000 |  0.840 | tcTGGGAat
 F$NIT2_01              |      310 (+) |  1.000 |  0.996 | TATCTc
 F$NIT2_01              |      567 (-) |  1.000 |  0.996 | gAGATA
 F$NIT2_01              |     2723 (-) |  1.000 |  1.000 | tAGATA
 F$NIT2_01              |     4578 (-) |  1.000 |  1.000 | tAGATA
 F$NIT2_01              |     7155 (+) |  1.000 |  0.996 | TATCTc
 F$NIT2_01              |     7952 (-) |  1.000 |  0.996 | gAGATA
 F$NIT2_01              |    11444 (+) |  1.000 |  1.000 | TATCTa
 V$PAX5_01              |     6306 (-) |  0.988 |  0.824 | ggcactgatctacttCCCTGactgaagc
 V$PAX5_01              |     7672 (+) |  0.965 |  0.858 | tggtggctCACAGctgtaaagccagaac
 V$PAX5_01              |    10848 (+) |  0.999 |  0.826 | gaagaagcCATTGtagagatgcagcgtg
 V$PAX5_02              |      406 (+) |  0.711 |  0.690 | aggcggaatgggtGAGCTtgtccaaaat
 V$PAX5_02              |      527 (+) |  0.866 |  0.658 | aaaatgatgggtgATGCGcttgtgtttt
 V$PAX5_02              |      533 (-) |  1.000 |  0.718 | atgggtgatgCGCTTgtgttttaacctt
 V$PAX5_02              |      661 (+) |  0.657 |  0.659 | tataagtacactgTAGCTgctcttcaga
 V$PAX5_02              |      670 (-) |  0.738 |  0.634 | actgtagctgCTCTTcagacacaccaga
 V$PAX5_02              |      691 (+) |  0.657 |  0.646 | caccagaagagggCATCGgatctcttta
 V$PAX5_02              |      702 (-) |  0.738 |  0.637 | ggcatcggatCTCTTtacagatggttgt
 V$PAX5_02              |      799 (+) |  0.657 |  0.679 | tgagccatttctcCAGCCcgacactttt
 V$PAX5_02              |      856 (-) |  0.738 |  0.713 | acgatcgttgCCCTTagaaatgcacaaa
 V$PAX5_02              |      903 (+) |  0.866 |  0.683 | ttcactttctttcATGCGtagcacttcc
 V$PAX5_02              |      964 (-) |  0.657 |  0.648 | tttacaggacCCCTAagcatcacagtta
 V$PAX5_02              |      965 (+) |  0.738 |  0.723 | ttacaggacccctAAGCAtcacagttaa
 V$PAX5_02              |     1000 (-) |  0.839 |  0.642 | catgtggggaCGCACctatatgtgattg
 V$PAX5_02              |     1130 (+) |  0.738 |  0.676 | cgtgtgttcctaaAACCGttactttatg
 V$PAX5_02              |     1178 (-) |  0.611 |  0.707 | gagatgggcaCCCCCaggaaagctggtt
 V$PAX5_02              |     1391 (+) |  0.711 |  0.704 | gggcaggtgaggaGAGTGggtccattgc
 V$PAX5_02              |     1418 (-) |  0.785 |  0.638 | ccgtgagacaCGCAAtcagtggcaatag
 V$PAX5_02              |     1443 (+) |  0.711 |  0.686 | tagtgaagtcactGAGCCggacgtttct
 V$PAX5_02              |     1939 (-) |  0.657 |  0.724 | gccttggctaGGCTGgaactttcctttt
 V$PAX5_02              |     2022 (+) |  0.711 |  0.631 | gctgggattaaagGAGTGtaccactgta
 V$PAX5_02              |     2033 (-) |  0.657 |  0.710 | aggagtgtacCACTGtacctggcttctc
 V$PAX5_02              |     2096 (-) |  0.657 |  0.662 | ctctctgtctCTCTGtctctctctctct
 V$PAX5_02              |     2104 (-) |  0.711 |  0.685 | ctctctgtctCTCTCtctctctctctct
 V$PAX5_02              |     2321 (-) |  0.657 |  0.659 | gatacagtctTGCTAtgtgaccctacgc
 V$PAX5_02              |     2331 (-) |  0.657 |  0.628 | tgctatgtgaCCCTAcgctcttctcaaa
 V$PAX5_02              |     2446 (-) |  0.919 |  0.709 | tcagtggtagCGCTAtggcctagcaagc
 V$PAX5_02              |     2457 (+) |  1.000 |  0.682 | gctatggcctagcAAGCGcgaaggccct
 V$PAX5_02              |     2663 (-) |  0.738 |  0.710 | tttgatgacaCTCTTaacccgttgcatc
 V$PAX5_02              |     2688 (-) |  0.711 |  0.689 | atcctggtcaCACTCttctccttcctct
 V$PAX5_02              |     2849 (+) |  0.711 |  0.713 | attccgtcctttaGAGCTgaacagaact
 V$PAX5_02              |     2968 (-) |  0.785 |  0.652 | acggcagatgCGCAGgcatctacttccg
 V$PAX5_02              |     2999 (+) |  0.900 |  0.698 | ctccaaggtgcgcAGGCGtctcggcagt
 V$PAX5_02              |     3028 (-) |  0.973 |  0.640 | caccgacttcCGCTCcacccgggacata
 V$PAX5_02              |     3487 (-) |  0.738 |  0.682 | gaggcagaatAGCTTaactaccctgctg
 V$PAX5_02              |     3709 (+) |  0.604 |  0.639 | ttgatcaatatttACGGGtgactaaaat
 V$PAX5_02              |     3764 (-) |  0.711 |  0.633 | taaaaggcaaTGCTCcttcccccctttt
 V$PAX5_02              |     3906 (-) |  0.738 |  0.629 | gtattaataaAGCTTtatgaattacatt
 V$PAX5_02              |     4520 (+) |  0.866 |  0.655 | accaagacaacaaATGCGtcaacagcct
 V$PAX5_02              |     4564 (-) |  0.738 |  0.664 | gacacagttgCGGTTagatatagtctcc
 V$PAX5_02              |     4758 (+) |  0.919 |  0.685 | ctgtaggtcccagCAGCGagtctggata
 V$PAX5_02              |     4963 (-) |  0.711 |  0.640 | caggaagtcaGGCTCagcccctacctgt
 V$PAX5_02              |     5026 (-) |  0.711 |  0.670 | gggactgggaTGCTCaggattgctgtgg
 V$PAX5_02              |     5069 (-) |  0.657 |  0.628 | agagatgagaGGCTGgctctgactggtt
 V$PAX5_02              |     5242 (-) |  0.604 |  0.630 | tacatgggttCACATgtggtcacagtca
 V$PAX5_02              |     5308 (+) |  0.657 |  0.722 | aaaatggcttcttCATCGgttcagtgcg
 V$PAX5_02              |     5482 (-) |  0.738 |  0.644 | ttttttgatcCCCTTccctctgctccca
 V$PAX5_02              |     5682 (-) |  0.657 |  0.631 | cacagagaccCACTAgttcatacactta
 V$PAX5_02              |     5808 (+) |  0.819 |  0.713 | aaaaaaatagcccTGGCGtggcactgtg
 V$PAX5_02              |     5857 (-) |  0.604 |  0.662 | gagttggtttCCCATggaccatctcctg
 V$PAX5_02              |     5889 (-) |  0.873 |  0.669 | gcatggggccCGCCCctaagagtagttt
 V$PAX5_02              |     5911 (+) |  0.919 |  0.717 | tagtttgtttcccCAGCGagactccctt
 V$PAX5_02              |     6215 (-) |  0.973 |  0.690 | aggtttctcaCGCTCtgcatgctgtctg
 V$PAX5_02              |     6232 (-) |  0.657 |  0.716 | catgctgtctGGCTAcggctttctattt
 V$PAX5_02              |     6398 (-) |  0.973 |  0.669 | gtgttcagaaCGCTCagaatgactcctc
 V$PAX5_02              |     6586 (+) |  0.638 |  0.631 | cacaaaacaaataAGGTGgtgctatttg
 V$PAX5_02              |     6715 (+) |  0.738 |  0.630 | gccacaacctttaAAGGGtgagcagccc
 V$PAX5_02              |     6933 (+) |  0.738 |  0.631 | atgtgcagtacccAAGTGatactgtcca
 V$PAX5_02              |     7080 (+) |  0.839 |  0.657 | gtatgagtgctttGCGCGcacctagtct
 V$PAX5_02              |     7275 (+) |  0.657 |  0.639 | aaaataagacccaTAGAGtaccaagctg
 V$PAX5_02              |     7474 (-) |  0.839 |  0.646 | gagtgtgctaCGCGCacgtctgttcttc
 V$PAX5_02              |     7492 (+) |  0.711 |  0.637 | tctgttcttcttgGAGGGtgtcagatgg
 V$PAX5_02              |     7838 (+) |  1.000 |  0.630 | ccacttctggcaaAAGCGacagcgtaca
 V$PAX5_02              |     8195 (-) |  0.638 |  0.675 | ctgcctgtttCCCCTctgacctcagttc
 V$PAX5_02              |     8283 (-) |  0.738 |  0.664 | tgccctggctCCCTTcgcatgcccctct
 V$PAX5_02              |     8340 (-) |  0.738 |  0.656 | tttgctggacCACTTgccaacccctgtg
 V$PAX5_02              |     8385 (+) |  0.738 |  0.650 | atctgtatacctgAAGCCaagccagccc
 V$PAX5_02              |     8421 (+) |  0.711 |  0.669 | agcagctgttctaGAGCTttgcaacccg
 V$PAX5_02              |     8496 (+) |  0.839 |  0.684 | tctacagggacagGTGCGggacactcac
 V$PAX5_02              |     8813 (-) |  0.711 |  0.644 | gcttctggtaCTCTCgatgttcaaaacc
 V$PAX5_02              |     9083 (-) |  0.711 |  0.644 | agcatagtgaAGCTCtgcttacaaaagc
 V$PAX5_02              |     9094 (+) |  0.738 |  0.675 | gctctgcttacaaAAGCAaaacaaaaaa
 V$PAX5_02              |     9170 (-) |  0.819 |  0.637 | gatgcatgaaCGCCAcagagaccactca
 V$PAX5_02              |     9323 (-) |  0.657 |  0.644 | gggtcagagcCTCTGgaggacccctgaa
 V$PAX5_02              |     9576 (-) |  0.611 |  0.638 | gtggtggtatAGCCCtgtaatcccagca
 V$PAX5_02              |     9603 (+) |  0.638 |  0.643 | atttgggaagctgAGGTGggaggatcgg
 V$PAX5_02              |    10051 (+) |  0.738 |  0.679 | gttctaagaactgAACCGggtcttctgg
 V$PAX5_02              |    10213 (+) |  0.711 |  0.660 | cagtggcatctaaGAGTGgaacctaggt
 V$PAX5_02              |    10240 (-) |  0.738 |  0.690 | ttggtggtcaGGCTTgtgcaggaagtga
 V$PAX5_02              |    10265 (-) |  0.638 |  0.644 | tgatttttgcCGGCTgagcaatctcatc
 V$PAX5_02              |    10549 (+) |  0.819 |  0.668 | aagtatgtacagcCGGCGgtacagcgtt
 V$PAX5_02              |    10667 (+) |  0.657 |  0.663 | acaggaggatccaCAGCAggactctggc
 V$PAX5_02              |    10822 (+) |  0.638 |  0.631 | agtccgccttttcAGGCCcatcgcagga
 V$PAX5_02              |    10856 (+) |  0.919 |  0.670 | cattgtagagatgCAGCGtggtggtggg
 V$PAX5_02              |    10895 (-) |  0.919 |  0.652 | tgcgcagagaCGCTActatgcaaataat
 V$PAX5_02              |    10914 (+) |  0.919 |  0.647 | gcaaataatagtcTAGCGcctcttgtgg
 V$PAX5_02              |    11155 (-) |  0.657 |  0.643 | atgaaaatgaAGCTGcagagatcttttt
 V$PAX5_02              |    11326 (-) |  0.657 |  0.635 | atgatgatgaCGATGtaaatgccattat
 V$PAX5_02              |    11578 (+) |  0.711 |  0.652 | tgcttatatccagGAGTGagactagagt
 V$PAX5_02              |    11602 (+) |  0.738 |  0.631 | gagtgcacagagaAAGGGgtaccagaag
 V$PAX5_02              |    11882 (-) |  0.711 |  0.640 | ttagttctcaCTCTCaaccaatagcacg
 V$PAX5_02              |    11905 (+) |  0.611 |  0.635 | gcacgaaggcttcGGGCCcaacgcccat
 V$BRN2_01              |      498 (-) |  1.000 |  0.912 | cattATTATatatttg
 V$BRN2_01              |      647 (-) |  0.993 |  0.928 | attcATTTAttatata
 V$BRN2_01              |      651 (-) |  1.000 |  0.932 | atttATTATatataag
 V$BRN2_01              |     1886 (-) |  1.000 |  0.913 | tcccATTTTatattta
 V$BRN2_01              |     2519 (-) |  1.000 |  0.899 | aaaaATTACatattac
 V$BRN2_01              |     2719 (+) |  1.000 |  0.906 | caaatagATAATcttc
 V$BRN2_01              |     2765 (-) |  0.917 |  0.921 | ctagATTCCgcatgtg
 V$BRN2_01              |     2949 (-) |  1.000 |  0.929 | gcctATTACgaataca
 V$BRN2_01              |     2950 (+) |  0.904 |  0.865 | cctattaCGAATacag
 V$BRN2_01              |     3823 (+) |  1.000 |  0.944 | tcaattcATAATaaat
 V$BRN2_01              |     3827 (+) |  0.993 |  0.940 | ttcataaTAAATttcc
 V$BRN2_01              |     4051 (+) |  0.917 |  0.874 | gaaatagGCAATaatt
 V$BRN2_01              |     4069 (+) |  1.000 |  0.918 | aatatgtAAAATgtat
 V$BRN2_01              |     4154 (-) |  0.987 |  0.907 | tcccATTTGtaatcct
 V$BRN2_01              |     4155 (+) |  1.000 |  0.960 | cccatttGTAATccta
 V$BRN2_01              |     5005 (-) |  1.000 |  0.929 | ttgtATTACccattaa
 V$BRN2_01              |     5301 (+) |  1.000 |  0.962 | gccatccAAAATggct
 V$BRN2_01              |     5781 (+) |  1.000 |  0.917 | aaaatatGAAATaatt
 V$BRN2_01              |     5842 (+) |  0.904 |  0.896 | ggcatctCCAATgttg
 V$BRN2_01              |     5988 (-) |  0.987 |  0.973 | ctggATTAGggatggg
 V$BRN2_01              |     6490 (-) |  0.917 |  0.920 | ctggATTGCagatgcg
 V$BRN2_01              |     6959 (-) |  0.917 |  0.929 | cattATTCTggatgga
 V$BRN2_01              |     7311 (+) |  0.917 |  0.869 | aggatatAGAATgtac
 V$BRN2_01              |     8593 (+) |  0.993 |  0.948 | aacatctTTAATatta
 V$BRN2_01              |     8648 (-) |  0.917 |  0.910 | gacaATTCCcaatggt
 V$BRN2_01              |     8649 (+) |  0.904 |  0.860 | acaattcCCAATggtt
 V$BRN2_01              |     9485 (-) |  0.987 |  0.926 | ctttATTTGcaataga
 V$BRN2_01              |     9486 (+) |  0.917 |  0.865 | tttatttGCAATagaa
 V$BRN2_01              |     9493 (+) |  1.000 |  0.915 | gcaatagAAAATctga
 V$BRN2_01              |     9881 (-) |  0.993 |  0.907 | atcaATTTAaaattct
 V$BRN2_01              |     9882 (+) |  1.000 |  0.909 | tcaatttAAAATtctt
 V$BRN2_01              |     9926 (+) |  1.000 |  0.920 | cctatggGTAATttgc
 V$BRN2_01              |    10115 (+) |  0.904 |  0.936 | gccatccCCAATaaaa
 V$BRN2_01              |    10455 (+) |  0.917 |  0.878 | tatatcaACAATgcat
 V$BRN2_01              |    10585 (-) |  1.000 |  0.912 | ttcaATTTCctatatc
 V$BRN2_01              |    11196 (-) |  0.911 |  0.870 | cttgATTGAttattaa
 V$BRN2_01              |    11200 (-) |  1.000 |  0.929 | attgATTATtaatttg
 V$BRN2_01              |    11201 (+) |  0.993 |  0.909 | ttgattaTTAATttgt
 V$BRN2_01              |    11408 (-) |  0.917 |  0.894 | atttATTCTgcatttc
 V$BRN2_01              |    11464 (-) |  1.000 |  0.885 | tgaaATTTTttatttg
 V$BRN2_01              |    11572 (-) |  0.917 |  0.867 | tatcATTGCttatatc
 V$HSF1_01              |     1953 (-) |  0.974 |  0.976 | ggaacTTTCC
 V$HSF1_01              |     4885 (+) |  0.976 |  0.969 | GGAACattcc
 V$HSF1_01              |     4885 (-) |  0.977 |  0.978 | ggaacATTCC
 V$HSF1_01              |     8078 (+) |  0.997 |  0.970 | AGAAActtcc
 V$HSF1_01              |     8876 (+) |  1.000 |  0.986 | AGAATattct
 V$HSF1_01              |     8876 (-) |  1.000 |  0.986 | agaatATTCT
 V$HSF2_01              |     1953 (+) |  0.996 |  0.986 | GGAACtttcc
 V$HSF2_01              |     1953 (-) |  0.995 |  0.986 | ggaacTTTCC
 V$HSF2_01              |     2561 (+) |  0.990 |  0.982 | TGAAAtttcc
 V$HSF2_01              |     2561 (-) |  0.995 |  0.982 | tgaaaTTTCC
 V$HSF2_01              |     2781 (-) |  0.997 |  0.977 | agattCTTCC
 V$HSF2_01              |     4885 (+) |  0.996 |  0.987 | GGAACattcc
 V$HSF2_01              |     4885 (-) |  0.999 |  0.988 | ggaacATTCC
 V$HSF2_01              |     7015 (-) |  0.995 |  0.969 | ggatgTTTCC
 V$HSF2_01              |     7715 (+) |  0.998 |  0.968 | AGAAGgatca
 V$HSF2_01              |     8078 (+) |  0.996 |  0.986 | AGAAActtcc
 V$HSF2_01              |     8078 (-) |  0.997 |  0.993 | agaaaCTTCC
 V$HSF2_01              |     8524 (-) |  0.992 |  0.974 | agatgCTTCA
 V$HSF2_01              |     8876 (+) |  1.000 |  0.996 | AGAATattct
 V$HSF2_01              |     8876 (-) |  1.000 |  0.996 | agaatATTCT
 V$HSF2_01              |     8914 (+) |  0.999 |  0.968 | GGAATactcg
 V$HSF2_01              |    10709 (+) |  0.990 |  0.973 | TGAAAcatct
 V$HSF2_01              |    11088 (+) |  0.999 |  0.987 | GGAATtttcc
 V$HSF2_01              |    11088 (-) |  0.995 |  0.986 | ggaatTTTCC
 P$SBF1_01              |      520 (-) |  1.000 |  0.921 | gatTTTAAaaatga
 P$SBF1_01              |      983 (+) |  1.000 |  0.934 | tcacagTTAATaat
 P$SBF1_01              |     2401 (+) |  1.000 |  0.924 | ctttccTTAAAaaa
 P$SBF1_01              |     3307 (+) |  0.934 |  0.922 | atgtagTTAAGatt
 P$SBF1_01              |     3445 (+) |  1.000 |  0.941 | taacagTTAATaaa
 P$SBF1_01              |     4059 (+) |  1.000 |  0.924 | caataaTTAAAata
 P$SBF1_01              |     7257 (+) |  1.000 |  0.924 | gtctcaTTAAAata
 P$SBF1_01              |    10305 (-) |  1.000 |  0.915 | tttTTTAActgttt
 P$SBF1_01              |    10417 (-) |  1.000 |  0.939 | attTTTAAcactaa
 P$AG_01                |      164 (+) |  0.967 |  0.775 | cgttCCCAAtgctggcat
 P$AG_01                |      165 (+) |  0.878 |  0.858 | gttcCCAATgctggcatt
 P$AG_01                |     1134 (+) |  0.994 |  0.776 | tgttCCTAAaaccgttac
 P$AG_01                |     1551 (-) |  0.875 |  0.790 | gaaaactctTCTGGaaat
 P$AG_01                |     2381 (+) |  0.875 |  0.768 | tttcCCAGAgctgagagt
 P$AG_01                |     2713 (+) |  0.967 |  0.813 | tcttCCCAAatagataat
 P$AG_01                |     2714 (+) |  1.000 |  0.809 | cttcCCAAAtagataatc
 P$AG_01                |     2785 (+) |  0.915 |  0.786 | tcttCCTTAgctggtctt
 P$AG_01                |     3638 (+) |  0.881 |  0.771 | cctaCCACAtggtggaat
 P$AG_01                |     3860 (+) |  0.798 |  0.780 | agtaCCATTtaaggagtt
 P$AG_01                |     4394 (+) |  0.840 |  0.795 | agttCCAAGacaggtcag
 P$AG_01                |     5009 (+) |  0.845 |  0.807 | attaCCCATtaagccacg
 P$AG_01                |     5984 (-) |  0.994 |  0.825 | acttctggaTTAGGgatg
 P$AG_01                |     6266 (+) |  0.971 |  0.846 | tctgCCGAAgaaggaagc
 P$AG_01                |     6369 (-) |  1.000 |  0.784 | taagcgagaTTTGGtaga
 P$AG_01                |     7573 (-) |  0.869 |  0.788 | aaatccccaTCAGGtcaa
 P$AG_01                |     7834 (-) |  0.875 |  0.856 | taacccactTCTGGcaaa
 P$AG_01                |     8135 (-) |  0.875 |  0.770 | gctttctgcTGAGGgaaa
 P$AG_01                |     8462 (-) |  0.915 |  0.785 | ggtctcatcTAAGGcaaa
 P$AG_01                |     9595 (-) |  1.000 |  0.851 | atcccagcaTTTGGgaag
 P$AG_01                |    11442 (-) |  1.000 |  0.795 | cttatctatTTTGGtgaa
 P$AG_01                |    11534 (+) |  0.881 |  0.858 | aatcCCACAtatggtaga
 P$AG_01                |    11534 (-) |  0.920 |  0.875 | aatcccacaTATGGtaga
 P$AG_01                |    11673 (+) |  1.000 |  0.774 | ataaCCAAAaaagaccaa
 P$AG_01                |    11795 (-) |  0.878 |  0.773 | aaatcccagATTGGaagg
 V$SRF_01               |    11534 (+) |  0.812 |  0.772 | aatcCCACAtatggtaga
 F$STRE_01              |     1609 (+) |  1.000 |  1.000 | tcAGGGGg
 F$STRE_01              |     8482 (+) |  1.000 |  0.999 | taAGGGGg
 V$ARP1_01              |       50 (+) |  0.811 |  0.727 | tcattACTTGggccat
 V$ARP1_01              |      254 (+) |  0.721 |  0.698 | tgtaaGGTTGaactca
 V$ARP1_01              |      698 (-) |  0.833 |  0.746 | agagggCATCGgatct
 V$ARP1_01              |      791 (+) |  0.833 |  0.805 | ttaacCGCTGagccat
 V$ARP1_01              |      952 (-) |  0.789 |  0.701 | aatgatCAAATattta
 V$ARP1_01              |     1126 (+) |  0.693 |  0.703 | tgcacGTGTGttccta
 V$ARP1_01              |     1239 (-) |  0.924 |  0.734 | tgacatCAGGGcagca
 V$ARP1_01              |     1604 (-) |  0.924 |  0.820 | ggggctCAGGGggtct
 V$ARP1_01              |     1688 (-) |  0.924 |  0.737 | tcagctCAGGGgtaga
 V$ARP1_01              |     2038 (+) |  0.833 |  0.731 | tgtacCACTGtacctg
 V$ARP1_01              |     2411 (-) |  0.820 |  0.705 | aaaaaaCAAAAaatca
 V$ARP1_01              |     2638 (+) |  0.924 |  0.718 | tctacCCCTGacctgc
 V$ARP1_01              |     2677 (+) |  0.909 |  0.752 | taaccCGTTGcatcct
 V$ARP1_01              |     3072 (-) |  0.882 |  0.767 | ctaggtCACAGggtga
 V$ARP1_01              |     3456 (-) |  0.924 |  0.767 | aaaacaCAGGGcctca
 V$ARP1_01              |     3523 (+) |  1.000 |  0.725 | ggccaCCTTGgcccga
 V$ARP1_01              |     3661 (-) |  0.882 |  0.715 | aagtaaCACAGactta
 V$ARP1_01              |     3685 (-) |  0.843 |  0.726 | aagtgcCAAGAacaca
 V$ARP1_01              |     4020 (-) |  0.924 |  0.726 | tgctctCATGGaatta
 V$ARP1_01              |     4198 (-) |  1.000 |  0.719 | caagttCAAGGcttgc
 V$ARP1_01              |     4357 (-) |  0.744 |  0.732 | gaggatCAGAAgttta
 V$ARP1_01              |     5213 (+) |  0.744 |  0.704 | tgtgcTTCTGagcgga
 V$ARP1_01              |     5238 (-) |  0.924 |  0.801 | cgattaCATGGgttca
 V$ARP1_01              |     5315 (-) |  0.833 |  0.741 | cttcttCATCGgttca
 V$ARP1_01              |     5479 (+) |  0.820 |  0.819 | tgattTTTTGatcccc
 V$ARP1_01              |     5826 (+) |  0.882 |  0.736 | tggcaCTGTGaaacaa
 V$ARP1_01              |     6045 (+) |  0.924 |  0.700 | tgcagCCCTGtgacag
 V$ARP1_01              |     6207 (-) |  1.000 |  0.701 | gtatgcCAAGGtttct
 V$ARP1_01              |     6556 (-) |  0.924 |  0.699 | aagagtCATGGttgcc
 V$ARP1_01              |     6763 (+) |  0.924 |  0.732 | ttataCCATGaacaaa
 V$ARP1_01              |     7125 (-) |  1.000 |  0.721 | aatgctCAAGGaggcc
 V$ARP1_01              |     7234 (-) |  0.833 |  0.790 | gaagttCATCGtctca
 V$ARP1_01              |     7601 (+) |  0.676 |  0.819 | tgaacTGCTGagccat
 V$ARP1_01              |     8203 (+) |  0.901 |  0.747 | ttcccCTCTGacctca
 V$ARP1_01              |     8258 (+) |  0.909 |  0.708 | cgtggCATTGacctga
 V$ARP1_01              |     8266 (+) |  0.676 |  0.706 | tgaccTGATGatgcag
 V$ARP1_01              |     8302 (+) |  0.901 |  0.731 | tgcccCTCTGccctgc
 V$ARP1_01              |     8453 (-) |  1.000 |  0.763 | ctaagcCAAGGtctca
 V$ARP1_01              |     8526 (-) |  0.843 |  0.724 | atgcttCAAGAacaca
 V$ARP1_01              |     8706 (-) |  1.000 |  0.719 | taccatCAAGGagtct
 V$ARP1_01              |     9032 (-) |  1.000 |  0.711 | tgagttCAAGGgcagc
 V$ARP1_01              |     9090 (+) |  0.901 |  0.731 | tgaagCTCTGcttaca
 V$ARP1_01              |     9190 (-) |  0.843 |  0.706 | accactCAAGAgagca
 V$ARP1_01              |     9259 (-) |  0.924 |  0.705 | atgggaCAGGGcagcg
 V$ARP1_01              |     9294 (+) |  0.725 |  0.734 | tcagcTTGTGtgccca
 V$ARP1_01              |     9321 (-) |  0.901 |  0.802 | ttgggtCAGAGcctct
 V$ARP1_01              |     9339 (+) |  0.924 |  0.701 | aggacCCCTGaagtct
 V$ARP1_01              |     9387 (+) |  0.924 |  0.765 | tcagcCCCTGgaatgt
 V$ARP1_01              |     9713 (+) |  0.721 |  0.698 | tgtaaAATTGatctct
 V$ARP1_01              |    10096 (+) |  0.901 |  0.836 | ttaacCTCTGagccat
 V$ARP1_01              |    10349 (-) |  0.977 |  0.806 | ttaattCAAAGtgtca
 V$ARP1_01              |    10357 (-) |  0.901 |  0.781 | aagtgtCAGAGaatct
 V$ARP1_01              |    10495 (-) |  0.820 |  0.722 | aaggatCAAAAgtcaa
 V$ARP1_01              |    10979 (+) |  0.882 |  0.703 | ggagcCTGTGtggccc
 V$ARP1_01              |    10987 (+) |  0.924 |  0.725 | tgtggCCCTGgaatca
 V$ARP1_01              |    11456 (+) |  0.814 |  0.797 | tgaatCAGTGaaattt
 V$ARP1_01              |    11924 (-) |  0.833 |  0.737 | aacgccCATTGgctga
 V$ARP1_01              |    11949 (-) |  0.767 |  0.779 | aagggtCAGGActgca
 V$RORA1_01             |     1074 (+) |  1.000 |  0.968 | atgtgtaGGTCAt
 V$RORA1_01             |     9632 (+) |  1.000 |  0.976 | agttcaaGGTCAg
 V$COUP_01              |      946 (-) |  0.919 |  0.857 | aggaacaatGATCA
 V$COUP_01              |     3567 (+) |  0.796 |  0.817 | TGGCCtttggcaag
 V$COUP_01              |     7119 (-) |  0.919 |  0.858 | gtgtgcaatGCTCA
 V$COUP_01              |     8376 (+) |  0.697 |  0.813 | TGCTCtttgatctg
 V$COUP_01              |    10489 (-) |  0.919 |  0.831 | catatcaagGATCA
 V$COUP_01              |    10496 (-) |  0.701 |  0.834 | aggatcaaaAGTCA
 V$COUP_01              |    10799 (+) |  0.919 |  0.870 | TGAGCcttgtgcat
 V$COUP_01              |    11943 (-) |  1.000 |  0.875 | tatttcaagGGTCA
 V$OCT1_05              |      992 (+) |  0.934 |  0.917 | ataaTTTTCatgtg
 V$OCT1_05              |     3108 (+) |  0.934 |  0.905 | ctaaTTTCCatgcg
 V$OCT1_05              |     3128 (+) |  0.918 |  0.887 | ttaaTTTACattcc
 V$OCT1_05              |     6575 (-) |  1.000 |  0.875 | gttatGCAAAacac
 V$OCT1_05              |     7350 (-) |  0.852 |  0.890 | aacatGTTAAtcat
 V$OCT1_05              |     9933 (+) |  1.000 |  0.933 | gtaaTTTGCatgta
 V$OCT1_05              |    10909 (-) |  1.000 |  0.964 | actatGCAAAtaat
 V$OCT1_05              |    11664 (+) |  0.934 |  0.899 | acaaTTTTCataac
 V$OCT1_06              |       18 (-) |  0.901 |  0.936 | tacaTGTGAatgtg
 V$OCT1_06              |       44 (-) |  1.000 |  0.911 | cagaTGTCAttact
 V$OCT1_06              |      278 (-) |  0.964 |  0.897 | tgcaTGCAAgtcaa
 V$OCT1_06              |      357 (+) |  0.865 |  0.888 | cagatTCAAAtcct
 V$OCT1_06              |      383 (-) |  0.964 |  0.900 | gagaTGCCAttcat
 V$OCT1_06              |      498 (+) |  0.946 |  0.922 | cattaTTATAtatt
 V$OCT1_06              |      621 (-) |  0.982 |  0.922 | tacaTGACActttt
 V$OCT1_06              |      750 (-) |  0.911 |  0.891 | ggaaTTGAActcag
 V$OCT1_06              |      820 (+) |  0.946 |  0.911 | cacttTTTAAtact
 V$OCT1_06              |      907 (+) |  0.982 |  0.920 | ctttcTTTCAtgcg
 V$OCT1_06              |      979 (-) |  0.964 |  0.899 | agcaTCACAgttaa
 V$OCT1_06              |      992 (+) |  0.982 |  0.930 | ataatTTTCAtgtg
 V$OCT1_06              |     2355 (+) |  0.911 |  0.913 | caaacTTGTAttta
 V$OCT1_06              |     2519 (+) |  1.000 |  0.950 | aaaaaTTACAtatt
 V$OCT1_06              |     3108 (+) |  0.946 |  0.950 | ctaatTTCCAtgcg
 V$OCT1_06              |     3128 (+) |  1.000 |  0.907 | ttaatTTACAttcc
 V$OCT1_06              |     3270 (-) |  0.964 |  0.897 | gtgaTGCCAttatg
 V$OCT1_06              |     3834 (+) |  0.946 |  0.889 | taaatTTCCAttct
 V$OCT1_06              |     3923 (-) |  0.946 |  0.912 | tgaaTTACAttatc
 V$OCT1_06              |     4061 (-) |  0.946 |  0.889 | ataaTTAAAatatg
 V$OCT1_06              |     4315 (-) |  0.928 |  0.902 | tgcaTAAAActggg
 V$OCT1_06              |     4793 (+) |  0.964 |  0.888 | ctgacTTGCAtaat
 V$OCT1_06              |     4886 (+) |  0.946 |  0.891 | gaacaTTCCAtgtt
 V$OCT1_06              |     5026 (+) |  0.946 |  0.891 | gggacTGGGAtgct
 V$OCT1_06              |     5619 (-) |  0.982 |  0.900 | aacaTCTAAtacac
 V$OCT1_06              |     5783 (-) |  0.982 |  0.901 | aataTGAAAtaatt
 V$OCT1_06              |     5790 (+) |  0.964 |  0.931 | aataaTTAAAtaca
 V$OCT1_06              |     5948 (+) |  0.928 |  0.888 | taaaaTTTTAtttg
 V$OCT1_06              |     6666 (-) |  0.865 |  0.889 | aagaTTTTAtttag
 V$OCT1_06              |     6783 (-) |  0.982 |  0.919 | cagaTCTAAtgctg
 V$OCT1_06              |     7259 (+) |  0.865 |  0.896 | ctcatTAAAAtatc
 V$OCT1_06              |     7342 (-) |  0.964 |  0.917 | cacaTTTCAacatg
 V$OCT1_06              |     7897 (+) |  0.964 |  0.899 | tttatTTTGAtatt
 V$OCT1_06              |     9933 (+) |  0.964 |  0.922 | gtaatTTGCAtgta
 V$OCT1_06              |    10109 (+) |  0.946 |  0.891 | catctTGCCAtccc
 V$OCT1_06              |    10211 (+) |  0.964 |  0.922 | cacagTGGCAtcta
 V$OCT1_06              |    10217 (-) |  0.982 |  0.928 | ggcaTCTAAgagtg
 V$OCT1_06              |    10466 (-) |  0.982 |  0.908 | tgcaTCTCActtta
 V$OCT1_06              |    10808 (-) |  0.982 |  0.911 | tgcaTCTAAatcgc
 V$OCT1_06              |    10814 (-) |  0.928 |  0.902 | taaaTCGCAgtccg
 V$OCT1_06              |    11341 (-) |  0.964 |  0.922 | taaaTGCCAttatc
 V$OCT1_06              |    11389 (-) |  0.946 |  0.907 | cttaTTAAAttttg
 V$OCT1_06              |    11634 (+) |  0.964 |  0.907 | ctcgtTTAAAtgta
 V$OCT1_06              |    11794 (-) |  0.946 |  0.891 | caaaTCCCAgattg
 I$HSF_04               |     8876 (+) |  1.000 |  0.985 | agaatatTCTAGaat
 F$HSF_04               |     8876 (+) |  1.000 |  0.998 | agaatatTCTAGaat
 V$AP1FJ_Q2             |       44 (-) |  0.975 |  0.934 | cagatGTCATt
 V$AP1FJ_Q2             |      132 (-) |  0.963 |  0.949 | gctcaGTCAAt
 V$AP1FJ_Q2             |     1077 (-) |  0.975 |  0.952 | tgtagGTCATt
 V$AP1FJ_Q2             |     1086 (-) |  0.963 |  0.946 | ttttgGTCAAc
 V$AP1FJ_Q2             |     1228 (+) |  0.975 |  0.960 | gATGACtgctt
 V$AP1FJ_Q2             |     1254 (-) |  0.975 |  0.960 | attctGTCATc
 V$AP1FJ_Q2             |     1353 (-) |  1.000 |  0.976 | cctggGTCACc
 V$AP1FJ_Q2             |     1445 (-) |  1.000 |  0.973 | gtgaaGTCACt
 V$AP1FJ_Q2             |     1682 (-) |  0.983 |  0.950 | cgggtGTCAGc
 V$AP1FJ_Q2             |     2595 (+) |  0.983 |  0.945 | aCTGACtatta
 V$AP1FJ_Q2             |     2666 (+) |  0.975 |  0.935 | gATGACactct
 V$AP1FJ_Q2             |     2689 (-) |  1.000 |  0.938 | tcctgGTCACa
 V$AP1FJ_Q2             |     2964 (+) |  1.000 |  0.956 | aGTGACggcag
 V$AP1FJ_Q2             |     3071 (-) |  1.000 |  0.960 | gctagGTCACa
 V$AP1FJ_Q2             |     3228 (-) |  0.983 |  0.948 | taccaGTCAGc
 V$AP1FJ_Q2             |     3434 (+) |  0.963 |  0.947 | aTTGACttagg
 V$AP1FJ_Q2             |     3725 (+) |  1.000 |  0.994 | gGTGACtaaaa
 V$AP1FJ_Q2             |     3751 (-) |  0.975 |  0.966 | ttttaGTCATt
 V$AP1FJ_Q2             |     3933 (-) |  1.000 |  0.986 | tatcaGTCACt
 V$AP1FJ_Q2             |     4332 (+) |  1.000 |  0.971 | gGTGACatcca
 V$AP1FJ_Q2             |     4466 (+) |  0.983 |  0.966 | aCTGACtgacc
 V$AP1FJ_Q2             |     4532 (-) |  0.963 |  0.952 | aatgcGTCAAc
 V$AP1FJ_Q2             |     4792 (+) |  0.983 |  0.950 | gCTGACttgca
 V$AP1FJ_Q2             |     4863 (-) |  0.983 |  0.949 | gggagGTCAGc
 V$AP1FJ_Q2             |     4964 (-) |  0.983 |  0.954 | aggaaGTCAGg
 V$AP1FJ_Q2             |     5176 (+) |  1.000 |  0.951 | tGTGACtgtgt
 V$AP1FJ_Q2             |     5255 (-) |  1.000 |  0.955 | atgtgGTCACa
 V$AP1FJ_Q2             |     5261 (-) |  0.975 |  0.943 | tcacaGTCATc
 V$AP1FJ_Q2             |     6053 (+) |  1.000 |  0.947 | tGTGACagccc
 V$AP1FJ_Q2             |     6293 (+) |  0.975 |  0.965 | gATGACtgagc
 V$AP1FJ_Q2             |     6322 (+) |  0.983 |  0.953 | cCTGACtgaag
 V$AP1FJ_Q2             |     6415 (+) |  0.975 |  0.952 | aATGACtcctc
 V$AP1FJ_Q2             |     6433 (-) |  0.963 |  0.935 | catcgGTCAAc
 V$AP1FJ_Q2             |     7506 (-) |  0.983 |  0.943 | agggtGTCAGa
 V$AP1FJ_Q2             |     7881 (-) |  0.975 |  0.955 | tagaaGTCATt
 V$AP1FJ_Q2             |     8322 (-) |  0.983 |  0.972 | tctgcGTCAGc
 V$AP1FJ_Q2             |     8611 (-) |  0.963 |  0.943 | attccGTCAAt
 V$AP1FJ_Q2             |     9288 (-) |  0.983 |  0.952 | tgagaGTCAGc
 V$AP1FJ_Q2             |     9320 (-) |  0.983 |  0.945 | gttggGTCAGa
 V$AP1FJ_Q2             |     9381 (-) |  0.983 |  0.949 | gagctGTCAGc
 V$AP1FJ_Q2             |     9635 (-) |  0.983 |  0.940 | tcaagGTCAGc
 V$AP1FJ_Q2             |     9843 (-) |  0.983 |  0.936 | ttaaaGTCAGg
 V$AP1FJ_Q2             |    10034 (-) |  1.000 |  0.995 | tgtgaGTCACc
 V$AP1FJ_Q2             |    10190 (-) |  0.983 |  0.951 | cagcaGTCAGt
 V$AP1FJ_Q2             |    10241 (-) |  0.983 |  0.940 | tggtgGTCAGg
 V$AP1FJ_Q2             |    10632 (+) |  1.000 |  0.980 | aGTGACtgagg
 V$AP1FJ_Q2             |    11316 (+) |  1.000 |  0.974 | gGTGACgacga
 V$AP1FJ_Q2             |    11331 (+) |  0.975 |  0.936 | gATGACgatgt
 V$AP1FJ_Q2             |    11700 (-) |  1.000 |  0.955 | tcactGTCACc
 V$AP1FJ_Q2             |    11748 (+) |  0.975 |  0.938 | aATGACtagaa
 V$AP1_Q2               |      132 (-) |  1.000 |  0.950 | gctcAGTCAat
 V$AP1_Q2               |      480 (-) |  1.000 |  0.938 | tacaAGTCAac
 V$AP1_Q2               |     1228 (+) |  1.000 |  0.961 | gaTGACTgctt
 V$AP1_Q2               |     1254 (-) |  0.967 |  0.946 | attcTGTCAtc
 V$AP1_Q2               |     1353 (-) |  0.962 |  0.950 | cctgGGTCAcc
 V$AP1_Q2               |     1445 (-) |  1.000 |  0.948 | gtgaAGTCAct
 V$AP1_Q2               |     2595 (+) |  1.000 |  0.954 | acTGACTatta
 V$AP1_Q2               |     3228 (-) |  1.000 |  0.957 | taccAGTCAgc
 V$AP1_Q2               |     3434 (+) |  1.000 |  0.950 | atTGACTtagg
 V$AP1_Q2               |     3725 (+) |  1.000 |  0.989 | ggTGACTaaaa
 V$AP1_Q2               |     3751 (-) |  1.000 |  0.972 | ttttAGTCAtt
 V$AP1_Q2               |     3933 (-) |  1.000 |  0.982 | tatcAGTCAct
 V$AP1_Q2               |     4332 (+) |  0.967 |  0.941 | ggTGACAtcca
 V$AP1_Q2               |     4466 (+) |  1.000 |  0.960 | acTGACTgacc
 V$AP1_Q2               |     4532 (-) |  0.967 |  0.941 | aatgCGTCAac
 V$AP1_Q2               |     4792 (+) |  1.000 |  0.955 | gcTGACTtgca
 V$AP1_Q2               |     5261 (-) |  1.000 |  0.957 | tcacAGTCAtc
 V$AP1_Q2               |     6293 (+) |  1.000 |  0.967 | gaTGACTgagc
 V$AP1_Q2               |     6415 (+) |  1.000 |  0.944 | aaTGACTcctc
 V$AP1_Q2               |     7044 (+) |  1.000 |  0.941 | gtTGACTattt
 V$AP1_Q2               |     7881 (-) |  1.000 |  0.955 | tagaAGTCAtt
 V$AP1_Q2               |     8322 (-) |  0.967 |  0.967 | tctgCGTCAgc
 V$AP1_Q2               |     9288 (-) |  1.000 |  0.960 | tgagAGTCAgc
 V$AP1_Q2               |    10034 (-) |  1.000 |  0.991 | tgtgAGTCAcc
 V$AP1_Q2               |    10190 (-) |  1.000 |  0.946 | cagcAGTCAgt
 V$AP1_Q2               |    10632 (+) |  1.000 |  0.973 | agTGACTgagg
 V$AP1_Q2               |    11316 (+) |  0.967 |  0.953 | ggTGACGacga
 V$AP1_Q2               |    11700 (-) |  0.967 |  0.939 | tcacTGTCAcc
 V$AP1_Q2               |    11748 (+) |  1.000 |  0.945 | aaTGACTagaa
 V$AP1_Q6               |      132 (-) |  1.000 |  0.971 | gctcAGTCAat
 V$AP1_Q6               |     1228 (+) |  1.000 |  0.939 | gaTGACTgctt
 V$AP1_Q6               |     1353 (-) |  0.938 |  0.942 | cctgGGTCAcc
 V$AP1_Q6               |     1445 (-) |  1.000 |  0.938 | gtgaAGTCAct
 V$AP1_Q6               |     3434 (+) |  1.000 |  0.973 | atTGACTtagg
 V$AP1_Q6               |     3725 (+) |  1.000 |  0.986 | ggTGACTaaaa
 V$AP1_Q6               |     3751 (-) |  1.000 |  0.983 | ttttAGTCAtt
 V$AP1_Q6               |     3933 (-) |  1.000 |  0.977 | tatcAGTCAct
 V$AP1_Q6               |     4466 (+) |  1.000 |  0.977 | acTGACTgacc
 V$AP1_Q6               |     4532 (-) |  0.941 |  0.939 | aatgCGTCAac
 V$AP1_Q6               |     4964 (-) |  1.000 |  0.938 | aggaAGTCAgg
 V$AP1_Q6               |     6293 (+) |  1.000 |  0.981 | gaTGACTgagc
 V$AP1_Q6               |     6322 (+) |  1.000 |  0.976 | ccTGACTgaag
 V$AP1_Q6               |     6415 (+) |  1.000 |  0.954 | aaTGACTcctc
 V$AP1_Q6               |     6555 (-) |  1.000 |  0.943 | taagAGTCAtg
 V$AP1_Q6               |     7881 (-) |  1.000 |  0.938 | tagaAGTCAtt
 V$AP1_Q6               |     8046 (+) |  1.000 |  0.939 | ctTGACTcgag
 V$AP1_Q6               |     8322 (-) |  0.941 |  0.944 | tctgCGTCAgc
 V$AP1_Q6               |     9288 (-) |  1.000 |  0.946 | tgagAGTCAgc
 V$AP1_Q6               |     9320 (-) |  0.938 |  0.937 | gttgGGTCAga
 V$AP1_Q6               |    10034 (-) |  1.000 |  0.999 | tgtgAGTCAcc
 V$AP1_Q6               |    10190 (-) |  1.000 |  0.935 | cagcAGTCAgt
 V$AP1_Q6               |    10632 (+) |  1.000 |  0.978 | agTGACTgagg
 V$AP1_Q6               |    11748 (+) |  1.000 |  0.934 | aaTGACTagaa
 V$AP4_Q5               |     7028 (+) |  1.000 |  0.984 | atCAGCTgaa
 V$AP4_Q5               |     7028 (-) |  1.000 |  0.976 | atcAGCTGaa
 V$AP4_Q5               |     7680 (+) |  1.000 |  0.987 | caCAGCTgta
 V$AP4_Q5               |     8277 (-) |  1.000 |  0.978 | tgcAGCTGcc
 V$AP4_Q5               |     8421 (+) |  1.000 |  0.985 | agCAGCTgtt
 V$AP4_Q5               |     8421 (-) |  1.000 |  0.983 | agcAGCTGtt
 V$AP4_Q6               |     7680 (+) |  1.000 |  0.976 | caCAGCTgta
 V$AP4_Q6               |     8421 (-) |  1.000 |  0.954 | agcAGCTGtt
 V$CREB_Q2              |     2964 (+) |  1.000 |  0.895 | agTGACGgcaga
 V$CREB_Q2              |     4531 (-) |  1.000 |  0.915 | aaatgCGTCAac
 V$CREB_Q2              |     8321 (-) |  1.000 |  0.942 | ttctgCGTCAgc
 V$CREB_Q2              |     8610 (-) |  1.000 |  0.909 | cattcCGTCAat
 V$CREB_Q2              |    11316 (+) |  1.000 |  0.892 | ggTGACGacgat
 V$CREB_Q4              |     1840 (-) |  1.000 |  0.876 | ggggtCGTCAac
 V$CREB_Q4              |     2964 (+) |  1.000 |  0.930 | agTGACGgcaga
 V$CREB_Q4              |     4531 (-) |  1.000 |  0.891 | aaatgCGTCAac
 V$CREB_Q4              |     8321 (-) |  1.000 |  0.914 | ttctgCGTCAgc
 V$CREB_Q4              |     8610 (-) |  1.000 |  0.914 | cattcCGTCAat
 V$CREB_Q4              |    11316 (+) |  1.000 |  0.901 | ggTGACGacgat
 V$CREB_Q4              |    11331 (+) |  1.000 |  0.863 | gaTGACGatgta
 V$CREBP1_Q2            |     2964 (+) |  1.000 |  0.877 | agTGACGgcaga
 V$E2_Q6                |    11305 (+) |  1.000 |  0.930 | ataacgactaCGGTGa
 P$GBP_Q6               |     6002 (-) |  1.000 |  0.955 | gggtACGTGtcc
 P$GBP_Q6               |    10441 (-) |  0.980 |  0.953 | tgcaACGTCtct
 V$MYB_Q6               |      125 (+) |  1.000 |  0.975 | gctAACTGct
 V$MYB_Q6               |      452 (-) |  0.964 |  0.952 | gtCTGTTttg
 V$MYB_Q6               |      589 (+) |  0.964 |  0.955 | attAACAGac
 V$MYB_Q6               |      841 (-) |  0.979 |  0.954 | acAAGTTaaa
 V$MYB_Q6               |      858 (-) |  0.955 |  0.948 | gaTCGTTgcc
 V$MYB_Q6               |      939 (-) |  0.979 |  0.956 | acAAGTTagg
 V$MYB_Q6               |      984 (-) |  1.000 |  0.967 | caCAGTTaat
 V$MYB_Q6               |     1027 (-) |  1.000 |  0.995 | ggCAGTTgaa
 V$MYB_Q6               |     1143 (-) |  0.980 |  0.948 | aaCCGTTact
 V$MYB_Q6               |     1316 (+) |  0.968 |  0.965 | cctAACTCcc
 V$MYB_Q6               |     1368 (-) |  0.955 |  0.952 | gcTCGTTtgc
 V$MYB_Q6               |     1461 (-) |  0.959 |  0.951 | ggACGTTtct
 V$MYB_Q6               |     1735 (+) |  0.979 |  0.975 | ctgAACTTcc
 V$MYB_Q6               |     1860 (+) |  1.000 |  0.961 | gccAACTGaa
 V$MYB_Q6               |     1952 (+) |  0.979 |  0.964 | tggAACTTtc
 V$MYB_Q6               |     1982 (+) |  0.968 |  0.954 | tcaAACTCac
 V$MYB_Q6               |     2354 (+) |  0.979 |  0.951 | tcaAACTTgt
 V$MYB_Q6               |     2375 (-) |  1.000 |  0.964 | caCAGTTttc
 V$MYB_Q6               |     2393 (-) |  0.968 |  0.959 | gaGAGTTgct
 V$MYB_Q6               |     2679 (-) |  0.980 |  0.953 | acCCGTTgca
 V$MYB_Q6               |     2826 (-) |  1.000 |  0.966 | tcCAGTTgtc
 V$MYB_Q6               |     3400 (-) |  1.000 |  0.961 | tcCAGTTata
 V$MYB_Q6               |     3409 (-) |  0.979 |  0.950 | aaAAGTTaat
 V$MYB_Q6               |     3446 (-) |  1.000 |  0.971 | aaCAGTTaat
 V$MYB_Q6               |     3499 (+) |  0.975 |  0.973 | cttAACTAcc
 V$MYB_Q6               |     3576 (-) |  0.979 |  0.973 | gcAAGTTatt
 V$MYB_Q6               |     3584 (+) |  0.968 |  0.960 | ttcAACTCtc
 V$MYB_Q6               |     3609 (-) |  1.000 |  0.961 | tgCAGTTttc
 V$MYB_Q6               |     4197 (-) |  0.979 |  0.973 | gcAAGTTcaa
 V$MYB_Q6               |     4214 (-) |  1.000 |  0.964 | ctCAGTTaaa
 V$MYB_Q6               |     4319 (+) |  1.000 |  0.966 | taaAACTGgg
 V$MYB_Q6               |     4364 (-) |  0.979 |  0.951 | agAAGTTtaa
 V$MYB_Q6               |     4391 (-) |  0.968 |  0.952 | gtGAGTTcca
 V$MYB_Q6               |     4537 (+) |  0.964 |  0.964 | gtcAACAGcc
 V$MYB_Q6               |     4566 (-) |  1.000 |  0.967 | caCAGTTgcg
 V$MYB_Q6               |     4920 (+) |  0.979 |  0.969 | cacAACTTac
 V$MYB_Q6               |     4942 (+) |  1.000 |  0.973 | ctgAACTGgg
 V$MYB_Q6               |     5149 (-) |  1.000 |  0.995 | ggCAGTTtac
 V$MYB_Q6               |     5279 (+) |  0.964 |  0.961 | aacAACAGgc
 V$MYB_Q6               |     5338 (-) |  0.975 |  0.964 | gaTAGTTttg
 V$MYB_Q6               |     5693 (-) |  0.975 |  0.951 | acTAGTTcat
 V$MYB_Q6               |     5727 (+) |  1.000 |  0.966 | ctaAACTGga
 V$MYB_Q6               |     5980 (+) |  0.979 |  0.953 | gatAACTTct
 V$MYB_Q6               |     6011 (+) |  0.968 |  0.958 | tccAACTCtc
 V$MYB_Q6               |     6086 (-) |  0.968 |  0.954 | gtGAGTTcct
 V$MYB_Q6               |     6386 (+) |  1.000 |  0.993 | acgAACTGgc
 V$MYB_Q6               |     6524 (-) |  0.979 |  0.951 | cgAAGTTcac
 V$MYB_Q6               |     6541 (+) |  0.980 |  0.952 | acaAACGGct
 V$MYB_Q6               |     6571 (-) |  1.000 |  0.966 | caCAGTTatg
 V$MYB_Q6               |     6845 (+) |  1.000 |  0.978 | gccAACTGgt
 V$MYB_Q6               |     7040 (-) |  0.975 |  0.969 | gtTAGTTgac
 V$MYB_Q6               |     7185 (+) |  0.980 |  0.975 | ccgAACGGcc
 V$MYB_Q6               |     7233 (-) |  0.979 |  0.973 | ggAAGTTcat
 V$MYB_Q6               |     7491 (-) |  0.964 |  0.950 | gtCTGTTctt
 V$MYB_Q6               |     7521 (+) |  1.000 |  0.959 | ctgAACTGaa
 V$MYB_Q6               |     7533 (-) |  1.000 |  0.960 | taCAGTTggt
 V$MYB_Q6               |     7548 (+) |  1.000 |  0.969 | gccAACTGtg
 V$MYB_Q6               |     7600 (+) |  1.000 |  0.975 | ctgAACTGct
 V$MYB_Q6               |     7694 (+) |  0.979 |  0.949 | cagAACTTgg
 V$MYB_Q6               |     7724 (-) |  1.000 |  0.973 | agCAGTTtgg
 V$MYB_Q6               |     8003 (-) |  0.964 |  0.962 | gcCTGTTggt
 V$MYB_Q6               |     8078 (+) |  0.979 |  0.970 | agaAACTTcc
 V$MYB_Q6               |     8180 (+) |  0.979 |  0.953 | cagAACTTgt
 V$MYB_Q6               |     8197 (-) |  0.964 |  0.959 | gcCTGTTtcc
 V$MYB_Q6               |     8215 (-) |  1.000 |  0.963 | ctCAGTTctg
 V$MYB_Q6               |     8723 (+) |  1.000 |  0.955 | aagAACTGta
 V$MYB_Q6               |     8845 (+) |  0.980 |  0.948 | cagAACGGtt
 V$MYB_Q6               |     8942 (+) |  0.979 |  0.949 | agcAACTTtt
 V$MYB_Q6               |     9031 (-) |  0.968 |  0.955 | gtGAGTTcaa
 V$MYB_Q6               |     9060 (-) |  0.979 |  0.969 | gcAAGTTcca
 V$MYB_Q6               |     9133 (-) |  1.000 |  0.954 | ttCAGTTttt
 V$MYB_Q6               |     9158 (-) |  0.968 |  0.954 | gtGAGTTcct
 V$MYB_Q6               |     9225 (-) |  0.979 |  0.976 | gcAAGTTagc
 V$MYB_Q6               |     9416 (+) |  0.975 |  0.964 | gaaAACTAtc
 V$MYB_Q6               |     9507 (-) |  0.979 |  0.967 | gaAAGTTtcc
 V$MYB_Q6               |     9562 (-) |  0.968 |  0.954 | gtCGGTTtct
 V$MYB_Q6               |     9629 (-) |  0.968 |  0.961 | ggGAGTTcaa
 V$MYB_Q6               |     9763 (+) |  0.964 |  0.953 | gaaAACAGtc
 V$MYB_Q6               |    10056 (+) |  1.000 |  0.954 | aagAACTGaa
 V$MYB_Q6               |    10195 (-) |  1.000 |  0.986 | gtCAGTTctg
 V$MYB_Q6               |    10308 (+) |  1.000 |  0.969 | tttAACTGtt
 V$MYB_Q6               |    10619 (-) |  0.968 |  0.961 | ggGAGTTgta
 V$MYB_Q6               |    10965 (-) |  0.964 |  0.960 | gcCTGTTgga
 V$MYB_Q6               |    11068 (-) |  1.000 |  0.964 | atCAGTTaca
 V$MYB_Q6               |    11124 (+) |  0.968 |  0.968 | cttAACTCgc
 V$MYB_Q6               |    11138 (-) |  1.000 |  0.963 | ctCAGTTttg
 V$MYB_Q6               |    11217 (+) |  1.000 |  0.991 | ttgAACTGcc
 V$MYB_Q6               |    11225 (-) |  1.000 |  0.969 | ccCAGTTtgt
 V$MYB_Q6               |    11235 (+) |  1.000 |  0.962 | tctAACTGga
 V$MYB_Q6               |    11710 (+) |  1.000 |  0.997 | cccAACTGcc
 V$MYOD_Q6              |     1027 (-) |  0.984 |  0.980 | ggcAGTTGaa
 V$MYOD_Q6              |     1392 (-) |  1.000 |  0.991 | ggcAGGTGag
 V$MYOD_Q6              |     1786 (+) |  1.000 |  0.998 | agCACCTgcc
 V$MYOD_Q6              |     2970 (-) |  0.989 |  0.988 | ggcAGATGcg
 V$MYOD_Q6              |     5127 (-) |  0.989 |  0.962 | aacAGATGgt
 V$MYOD_Q6              |     6262 (+) |  0.989 |  0.988 | ccCATCTgcc
 V$MYOD_Q6              |     7511 (-) |  0.989 |  0.987 | gtcAGATGgc
 V$MYOD_Q6              |     8277 (+) |  0.989 |  0.989 | tgCAGCTgcc
 V$MYOD_Q6              |     8421 (+) |  0.989 |  0.962 | agCAGCTgtt
 V$MYOD_Q6              |     8504 (-) |  1.000 |  0.998 | gacAGGTGcg
 V$MYOD_Q6              |    11710 (+) |  0.984 |  0.984 | ccCAACTgcc
 V$NFY_Q6               |     1021 (-) |  1.000 |  0.945 | gtgATTGGcag
 V$NFY_Q6               |     4618 (+) |  1.000 |  0.951 | aaaCCAATatc
 V$NFY_Q6               |     9451 (+) |  1.000 |  0.946 | ttaCCAATctc
 V$NFY_Q6               |    11684 (+) |  1.000 |  0.951 | agaCCAATaaa
 V$NFY_Q6               |    11896 (+) |  1.000 |  0.962 | caaCCAATagc
 V$NFY_Q6               |    11928 (-) |  1.000 |  0.955 | cccATTGGctg
 V$SRF_Q6               |    11536 (+) |  0.948 |  0.942 | tcCCACAtatggta
 V$USF_Q6               |      735 (+) |  0.987 |  0.940 | aCCACGtggt
 V$USF_Q6               |      735 (-) |  0.987 |  0.940 | accaCGTGGt
 V$USF_Q6               |     1616 (-) |  0.987 |  0.934 | gtctCGTGGa
 V$USF_Q6               |     3938 (+) |  0.945 |  0.929 | gTCACTtgtt
 V$USF_Q6               |     5021 (+) |  0.987 |  0.969 | gCCACGggac
 V$USF_Q6               |     6049 (-) |  0.945 |  0.939 | gcccTGTGAc
 V$USF_Q6               |     7192 (+) |  0.987 |  0.942 | gCCACGgggg
 V$AP1_Q4               |      132 (-) |  1.000 |  0.957 | gctcAGTCAat
 V$AP1_Q4               |     1353 (-) |  0.935 |  0.938 | cctgGGTCAcc
 V$AP1_Q4               |     1445 (-) |  1.000 |  0.940 | gtgaAGTCAct
 V$AP1_Q4               |     3434 (+) |  1.000 |  0.955 | atTGACTtagg
 V$AP1_Q4               |     3725 (+) |  1.000 |  0.992 | ggTGACTaaaa
 V$AP1_Q4               |     3751 (-) |  1.000 |  0.973 | ttttAGTCAtt
 V$AP1_Q4               |     3933 (-) |  1.000 |  0.985 | tatcAGTCAct
 V$AP1_Q4               |     4466 (+) |  1.000 |  0.969 | acTGACTgacc
 V$AP1_Q4               |     6293 (+) |  1.000 |  0.970 | gaTGACTgagc
 V$AP1_Q4               |     6322 (+) |  1.000 |  0.948 | ccTGACTgaag
 V$AP1_Q4               |    10034 (-) |  1.000 |  0.994 | tgtgAGTCAcc
 V$AP1_Q4               |    10632 (+) |  1.000 |  0.987 | agTGACTgagg
 V$AP2_Q6               |      100 (-) |  0.992 |  0.979 | cgcctGGGGGtg
 V$AP2_Q6               |     1186 (+) |  0.992 |  0.893 | caCCCCCaggaa
 V$AP2_Q6               |     1332 (+) |  0.934 |  0.907 | ctCCCCAgggct
 V$AP2_Q6               |     1332 (-) |  0.905 |  0.872 | ctcccCAGGGct
 V$AP2_Q6               |     1483 (-) |  0.953 |  0.862 | tggcaGAGGGag
 V$AP2_Q6               |     1676 (-) |  0.942 |  0.894 | ctcctTCGGGtg
 V$AP2_Q6               |     1709 (+) |  0.953 |  0.857 | caCCCTCtgcct
 V$AP2_Q6               |     4598 (+) |  1.000 |  0.854 | tgCCCGCttgct
 V$AP2_Q6               |     5887 (-) |  0.934 |  0.854 | gggcaTGGGGcc
 V$AP2_Q6               |     7190 (-) |  0.923 |  0.861 | cggccACGGGgg
 V$AP2_Q6               |     7191 (-) |  0.944 |  0.893 | ggccaCGGGGgt
 V$AP2_Q6               |    10786 (-) |  0.992 |  0.866 | acccaGGGGGat
 V$AP2_Q6               |    11866 (-) |  0.992 |  0.902 | ggtccGGGGGag
 V$AP2_Q6               |    11911 (-) |  0.942 |  0.855 | aggctTCGGGcc
 V$AP2_Q6               |    11926 (+) |  0.892 |  0.884 | cgCCCATtggct
 V$CEBP_Q2              |      420 (-) |  0.936 |  0.934 | agcttgtCCAAAat
 V$CEBP_Q2              |      489 (+) |  1.000 |  0.968 | acATTGCaacatta
 V$CEBP_Q2              |     1085 (+) |  0.936 |  0.933 | atTTTGGtcaacta
 V$CEBP_Q2              |     1463 (-) |  0.944 |  0.944 | acgtttcTCAATat
 V$CEBP_Q2              |     2368 (+) |  0.984 |  0.942 | atTTTGCcacagtt
 V$CEBP_Q2              |     2555 (+) |  0.936 |  0.936 | ctGTTGTgaaattt
 V$CEBP_Q2              |     3424 (+) |  0.987 |  0.981 | tgGTTGCttaattg
 V$CEBP_Q2              |     3569 (-) |  0.984 |  0.968 | gcctttgGCAAGtt
 V$CEBP_Q2              |     3578 (-) |  0.931 |  0.936 | aagttatTCAACtc
 V$CEBP_Q2              |     3706 (-) |  0.944 |  0.938 | tgcttgaTCAATat
 V$CEBP_Q2              |     4207 (+) |  0.984 |  0.945 | ggCTTGCctcagtt
 V$CEBP_Q2              |     4708 (+) |  0.936 |  0.942 | gaCTTGGgtaattc
 V$CEBP_Q2              |     4795 (+) |  0.984 |  0.980 | gaCTTGCataatct
 V$CEBP_Q2              |     5442 (+) |  1.000 |  0.948 | gtATTGCcatataa
 V$CEBP_Q2              |     6564 (+) |  0.987 |  0.942 | tgGTTGCcacagtt
 V$CEBP_Q2              |     6573 (-) |  0.984 |  0.981 | cagttatGCAAAac
 V$CEBP_Q2              |     6608 (+) |  0.984 |  0.971 | taTTTGCtaaactc
 V$CEBP_Q2              |     7208 (+) |  0.944 |  0.941 | gaATTGAacaaaaa
 V$CEBP_Q2              |     8071 (+) |  1.000 |  0.984 | gtATTGCagaaact
 V$CEBP_Q2              |     8468 (-) |  0.984 |  0.938 | atctaagGCAAAaa
 V$CEBP_Q2              |     8578 (-) |  0.984 |  0.939 | aaatgggGCAAAgg
 V$CEBP_Q2              |     8936 (-) |  0.987 |  0.950 | aactaaaGCAACtt
 V$CEBP_Q2              |     9138 (+) |  0.928 |  0.934 | ttTTTGAataagac
 V$CEBP_Q2              |     9447 (-) |  0.952 |  0.944 | aggtttaCCAATct
 V$CEBP_Q2              |     9488 (+) |  0.984 |  0.944 | taTTTGCaatagaa
 V$CEBP_Q2              |    10377 (-) |  1.000 |  0.965 | aaatgttGCAATcc
 V$CEBP_Q2              |    10686 (-) |  0.987 |  0.933 | gactctgGCAACac
 V$CEBP_Q2              |    10968 (-) |  0.984 |  0.942 | tgttggaGCAAGga
 V$CEBP_Q2              |    11284 (-) |  0.984 |  0.933 | gcataggGCAAAga
 V$ER_Q6                |     1078 (-) |  1.000 |  0.928 | gtaGGTCAttttggtcaac
 V$ER_Q6                |     1087 (-) |  1.000 |  0.928 | tttGGTCAactaaaatttg
 V$ER_Q6                |     1354 (-) |  1.000 |  0.935 | ctgGGTCAcctgatgctcg
 V$ER_Q6                |     2327 (+) |  1.000 |  0.908 | gtcttgctatgTGACCcta
 V$ER_Q6                |     2635 (+) |  1.000 |  0.904 | tgctctaccccTGACCtgc
 V$ER_Q6                |     2690 (-) |  1.000 |  0.947 | cctGGTCAcactcttctcc
 V$ER_Q6                |     3072 (-) |  1.000 |  0.931 | ctaGGTCAcagggtgattc
 V$ER_Q6                |     3880 (+) |  1.000 |  0.914 | tacaagctcctTGACCctc
 V$ER_Q6                |     4291 (+) |  1.000 |  0.910 | gaccctaaattTGACCctc
 V$ER_Q6                |     4403 (-) |  1.000 |  0.922 | acaGGTCAgccacaacctt
 V$ER_Q6                |     5136 (-) |  1.000 |  0.909 | tgcGGTCAacctaggcagt
 V$ER_Q6                |     5256 (-) |  1.000 |  0.931 | tgtGGTCAcagtcatcctg
 V$ER_Q6                |     6102 (+) |  1.000 |  0.926 | atcagtcctgtTGACCaga
 V$ER_Q6                |     7582 (-) |  1.000 |  0.906 | tcaGGTCAaacaaatgctc
 V$ER_Q6                |     8255 (+) |  1.000 |  0.916 | gttcgtggcatTGACCtga
 V$ER_Q6                |     9321 (-) |  1.000 |  0.928 | ttgGGTCAgagcctctgga
 V$ER_Q6                |     9636 (-) |  1.000 |  0.950 | caaGGTCAgcttgggctac
 V$GR_Q6                |        8 (-) |  0.984 |  0.872 | catGTACAagtacatgtga
 V$GR_Q6                |       14 (-) |  0.984 |  0.909 | caaGTACAtgtgaatgtgt
 V$GR_Q6                |       32 (-) |  1.000 |  0.883 | tgtGAACAacttcagatgt
 V$GR_Q6                |      224 (+) |  0.864 |  0.859 | tttttccttttTGTCTttt
 V$GR_Q6                |      265 (+) |  0.986 |  0.870 | actcaggtcctTGTGCatg
 V$GR_Q6                |      314 (+) |  0.986 |  0.910 | tctcctagtccTGTGCtgg
 V$GR_Q6                |      413 (+) |  0.989 |  0.887 | atgggtgagctTGTCCaaa
 V$GR_Q6                |      538 (+) |  0.875 |  0.851 | tgatgcgcttgTGTTTtaa
 V$GR_Q6                |      605 (+) |  0.882 |  0.850 | tttaaacatccTGTCGtac
 V$GR_Q6                |      663 (-) |  0.984 |  0.924 | taaGTACActgtagctgct
 V$GR_Q6                |      874 (-) |  0.986 |  0.898 | aatGCACAaacacgaaatg
 V$GR_Q6                |      890 (-) |  0.989 |  0.904 | atgGGACAgacttttcact
 V$GR_Q6                |      945 (-) |  1.000 |  0.881 | tagGAACAatgatcaaata
 V$GR_Q6                |     1009 (+) |  0.865 |  0.871 | acgcacctataTGTGAttg
 V$GR_Q6                |     1123 (+) |  1.000 |  0.901 | gtatgcacgtgTGTTCcta
 V$GR_Q6                |     1145 (+) |  0.876 |  0.878 | ccgttactttaTGTAGttc
 V$GR_Q6                |     1247 (+) |  0.869 |  0.873 | gggcagcattcTGTCAtca
 V$GR_Q6                |     1261 (+) |  0.984 |  0.961 | catcatccgtgTGTACtct
 V$GR_Q6                |     1526 (+) |  1.000 |  0.948 | agctgttttttTGTTCtaa
 V$GR_Q6                |     1620 (+) |  0.989 |  0.902 | cgtggacagcaTGTCCagc
 V$GR_Q6                |     1620 (-) |  0.989 |  0.905 | cgtGGACAgcatgtccagc
 V$GR_Q6                |     1746 (-) |  1.000 |  0.934 | ataGAACActgatctataa
 V$GR_Q6                |     1764 (+) |  0.989 |  0.908 | agcctctcgccTGTCCtcc
 V$GR_Q6                |     1808 (+) |  1.000 |  0.881 | catcagggtggTGTTCagg
 V$GR_Q6                |     2027 (+) |  0.984 |  0.869 | gattaaaggagTGTACcac
 V$GR_Q6                |     2035 (+) |  0.984 |  0.878 | gagtgtaccacTGTACctg
 V$GR_Q6                |     2301 (+) |  0.861 |  0.847 | gtgtgtgtctgTGTGTttt
 V$GR_Q6                |     2303 (+) |  0.875 |  0.875 | gtgtgtctgtgTGTTTtgg
 V$GR_Q6                |     2411 (-) |  0.875 |  0.853 | aaaAAACAaaaaatcacag
 V$GR_Q6                |     2545 (+) |  0.892 |  0.862 | taacaggtttcTGTTGtga
 V$GR_Q6                |     2579 (-) |  0.892 |  0.866 | ttaCAACAaatgcagtact
 V$GR_Q6                |     2808 (-) |  1.000 |  0.913 | actGAACAccgtgctctgt
 V$GR_Q6                |     2813 (+) |  0.989 |  0.903 | acaccgtgctcTGTCCagt
 V$GR_Q6                |     2864 (-) |  1.000 |  0.916 | gctGAACAgaactccaccg
 V$GR_Q6                |     3022 (-) |  0.984 |  0.927 | gcaGTACAccgacttccgc
 V$GR_Q6                |     3046 (-) |  0.989 |  0.890 | ccgGGACAtacctgcgagt
 V$GR_Q6                |     3161 (+) |  0.984 |  0.889 | tccattccgccTGTACatt
 V$GR_Q6                |     3170 (-) |  0.984 |  0.897 | cctGTACAttatatccccc
 V$GR_Q6                |     3294 (-) |  1.000 |  0.883 | ggtGAACAtctccatgtag
 V$GR_Q6                |     3337 (+) |  1.000 |  0.904 | tatttccctccTGTTCatc
 V$GR_Q6                |     3454 (-) |  0.875 |  0.880 | ataAAACAcagggcctcat
 V$GR_Q6                |     3538 (+) |  1.000 |  0.962 | aggtttggttcTGTTCttt
 V$GR_Q6                |     3691 (-) |  1.000 |  0.955 | caaGAACAcaagagatgct
 V$GR_Q6                |     3795 (-) |  0.989 |  0.906 | tctGGACAgaatagaaaaa
 V$GR_Q6                |     3933 (+) |  1.000 |  0.881 | tatcagtcactTGTTCatt
 V$GR_Q6                |     4134 (+) |  0.878 |  0.851 | cagaatctaggTGTGGtgc
 V$GR_Q6                |     4150 (+) |  0.863 |  0.859 | tgcctcccattTGTAAtcc
 V$GR_Q6                |     4278 (-) |  0.986 |  0.962 | taaGCACAcattagaccct
 V$GR_Q6                |     4439 (-) |  0.878 |  0.857 | aaaCCACAcaattaatatt
 V$GR_Q6                |     4488 (-) |  1.000 |  0.909 | tttGAACAaaaaacaaaac
 V$GR_Q6                |     4495 (-) |  0.875 |  0.853 | aaaAAACAaaacaaaacaa
 V$GR_Q6                |     4524 (-) |  0.892 |  0.868 | agaCAACAaatgcgtcaac
 V$GR_Q6                |     4560 (-) |  0.989 |  0.907 | gctGGACAcagttgcggtt
 V$GR_Q6                |     4690 (+) |  0.989 |  0.946 | aggaaacttgaTGTCCtag
 V$GR_Q6                |     4883 (-) |  1.000 |  0.885 | ctgGAACAttccatgttcc
 V$GR_Q6                |     4885 (+) |  1.000 |  0.877 | ggaacattccaTGTTCctt
 V$GR_Q6                |     4977 (+) |  0.989 |  0.880 | cagcccctaccTGTCCgaa
 V$GR_Q6                |     5173 (+) |  1.000 |  0.959 | acttgtgactgTGTTCtag
 V$GR_Q6                |     5202 (+) |  0.986 |  0.932 | ctgtggcctctTGTGCttc
 V$GR_Q6                |     5361 (-) |  0.875 |  0.870 | acaAAACAcacgggatttc
 V$GR_Q6                |     5602 (-) |  0.879 |  0.870 | ataTAACAcaagaaaccaa
 V$GR_Q6                |     5660 (-) |  1.000 |  0.953 | aaaGAACAcaataagagac
 V$GR_Q6                |     5998 (+) |  0.989 |  0.882 | gatggggtacgTGTCCaac
 V$GR_Q6                |     6248 (+) |  0.989 |  0.914 | ggctttctattTGTCCcat
 V$GR_Q6                |     6329 (-) |  0.986 |  0.967 | gaaGCACAcactggatttc
 V$GR_Q6                |     6388 (+) |  1.000 |  0.917 | gaactggcctgTGTTCaga
 V$GR_Q6                |     6516 (-) |  1.000 |  0.955 | aaaGAACAcgaagttcacc
 V$GR_Q6                |     6580 (-) |  0.875 |  0.846 | gcaAAACAcaaaacaaata
 V$GR_Q6                |     6769 (-) |  1.000 |  0.906 | catGAACAaaacagcagat
 V$GR_Q6                |     6821 (+) |  0.986 |  0.941 | tcccttttttaTGTGCtat
 V$GR_Q6                |     6912 (-) |  1.000 |  0.923 | ggaGAACAaggaattgatt
 V$GR_Q6                |     6923 (+) |  0.986 |  0.898 | aattgattgtaTGTGCagt
 V$GR_Q6                |     6944 (+) |  0.989 |  0.889 | ccaagtgatacTGTCCatt
 V$GR_Q6                |     7056 (+) |  0.875 |  0.849 | ttttcttaattTGTTTttg
 V$GR_Q6                |     7098 (+) |  0.984 |  0.895 | cacctagtctgTGTACcac
 V$GR_Q6                |     7109 (+) |  0.986 |  0.909 | tgtaccacatgTGTGCaat
 V$GR_Q6                |     7210 (-) |  1.000 |  0.936 | attGAACAaaaagtaggcc
 V$GR_Q6                |     7311 (+) |  0.984 |  0.869 | aggatatagaaTGTACgtc
 V$GR_Q6                |     7329 (-) |  1.000 |  0.886 | ctgGAACAatagacacatt
 V$GR_Q6                |     7378 (+) |  0.989 |  0.910 | gatattgcttgTGTCCagg
 V$GR_Q6                |     7421 (+) |  0.875 |  0.854 | aaaggtttattTGTTTtta
 V$GR_Q6                |     7466 (+) |  0.986 |  0.935 | caggatttgagTGTGCtac
 V$GR_Q6                |     7483 (+) |  1.000 |  0.959 | acgcgcacgtcTGTTCttc
 V$GR_Q6                |     7778 (-) |  0.875 |  0.857 | acaAAACAaaaattatccc
 V$GR_Q6                |     7803 (-) |  1.000 |  0.931 | aaaGAACAacgacaactcc
 V$GR_Q6                |     7858 (-) |  0.984 |  0.881 | agcGTACActtagaaaagc
 V$GR_Q6                |     7989 (+) |  0.986 |  0.887 | aaggacttcacTGTGCctg
 V$GR_Q6                |     8243 (+) |  1.000 |  0.891 | agatgaaggtgTGTTCgtg
 V$GR_Q6                |     8353 (+) |  0.986 |  0.882 | ttgccaaccccTGTGCagc
 V$GR_Q6                |     8416 (+) |  1.000 |  0.931 | ctgtaagcagcTGTTCtag
 V$GR_Q6                |     8500 (-) |  0.989 |  0.868 | cagGGACAggtgcgggaca
 V$GR_Q6                |     8511 (-) |  0.989 |  0.873 | gcgGGACActcacagatgc
 V$GR_Q6                |     8532 (-) |  1.000 |  0.996 | caaGAACAcagtgggccga
 V$GR_Q6                |     8552 (+) |  0.989 |  0.864 | aaaatgaacaaTGTCCgtc
 V$GR_Q6                |     8554 (-) |  1.000 |  0.903 | aatGAACAatgtccgtctt
 V$GR_Q6                |     8748 (+) |  0.989 |  0.936 | ggcccacacctTGTCCtcc
 V$GR_Q6                |     8819 (+) |  1.000 |  0.908 | ggtactctcgaTGTTCaaa
 V$GR_Q6                |     8839 (-) |  0.875 |  0.871 | ccaAAACAgaacggtttaa
 V$GR_Q6                |     8896 (-) |  0.878 |  0.878 | gtaCCACAaacagattcag
 V$GR_Q6                |     8964 (+) |  0.878 |  0.852 | ggagaaccaggTGTGGtgg
 V$GR_Q6                |     8979 (-) |  0.984 |  0.889 | gtgGTACAcacctttaatt
 V$GR_Q6                |     8998 (-) |  0.986 |  0.925 | ccaGCACAtggaggcaggg
 V$GR_Q6                |     9259 (-) |  0.989 |  0.866 | atgGGACAgggcagcgaca
 V$GR_Q6                |     9291 (+) |  0.986 |  0.902 | gagtcagcttgTGTGCcca
 V$GR_Q6                |     9352 (+) |  1.000 |  0.961 | tctcttctcagTGTTCtct
 V$GR_Q6                |     9454 (+) |  0.984 |  0.868 | ccaatctctgcTGTACagg
 V$GR_Q6                |     9463 (+) |  1.000 |  0.952 | gctgtacaggaTGTTCtag
 V$GR_Q6                |     9463 (-) |  0.984 |  0.899 | gctGTACAggatgttctag
 V$GR_Q6                |     9509 (+) |  0.989 |  0.903 | aagtttccccaTGTCCaac
 V$GR_Q6                |     9532 (-) |  1.000 |  0.963 | ctaGAACAaacaagtcctg
 V$GR_Q6                |     9564 (+) |  0.878 |  0.847 | cggtttctgggTGTGGtgg
 V$GR_Q6                |     9729 (+) |  0.989 |  0.895 | ttgtatgataaTGTCCata
 V$GR_Q6                |     9778 (-) |  1.000 |  0.942 | ataGAACAattttgttcag
 V$GR_Q6                |     9779 (+) |  1.000 |  0.923 | tagaacaatttTGTTCagt
 V$GR_Q6                |     9790 (+) |  0.984 |  0.885 | tgttcagtaaaTGTACatc
 V$GR_Q6                |     9799 (-) |  0.984 |  0.866 | aatGTACAtcacataagta
 V$GR_Q6                |     9936 (+) |  0.879 |  0.846 | atttgcatgtaTGTTAtaa
 V$GR_Q6                |    10175 (+) |  1.000 |  0.916 | attagtgtgtgTGTTCagc
 V$GR_Q6                |    10192 (+) |  0.989 |  0.950 | gcagtcagttcTGTCCttc
 V$GR_Q6                |    10243 (+) |  0.986 |  0.879 | gtggtcaggctTGTGCagg
 V$GR_Q6                |    10297 (-) |  0.989 |  0.871 | ttcGGACAttttttaactg
 V$GR_Q6                |    10543 (+) |  0.984 |  0.902 | actctaaagtaTGTACagc
 V$GR_Q6                |    10552 (-) |  0.984 |  0.887 | tatGTACAgccggcggtac
 V$GR_Q6                |    10564 (-) |  0.984 |  0.869 | gcgGTACAgcgtttgcttt
 V$GR_Q6                |    10643 (+) |  0.989 |  0.960 | aagacacccagTGTCCtaa
 V$GR_Q6                |    10795 (+) |  0.986 |  0.874 | gatgtgagcctTGTGCatc
 V$GR_Q6                |    10887 (-) |  0.986 |  0.863 | actGCACAtgcgcagagac
 V$GR_Q6                |    10951 (+) |  0.986 |  0.919 | tagctgcggtcTGTGCctg
 V$GR_Q6                |    11135 (+) |  0.984 |  0.937 | gcactcagtttTGTACtct
 V$GR_Q6                |    11221 (+) |  1.000 |  0.980 | actgcccagttTGTTCtaa
 V$GR_Q6                |    11245 (+) |  0.878 |  0.853 | gtccaaaactcTGTGGtgt
 V$GR_Q6                |    11250 (+) |  0.986 |  0.862 | aaactctgtggTGTGCcaa
 V$GR_Q6                |    11365 (+) |  0.986 |  0.975 | atgattctatcTGTGCttt
 V$GR_Q6                |    11390 (+) |  0.984 |  0.878 | ttattaaatttTGTACgca
 V$GR_Q6                |    11467 (+) |  0.875 |  0.847 | aattttttattTGTTTttc
 V$GR_Q6                |    11512 (+) |  0.989 |  0.852 | gatattaccgtTGTCCgta
 V$GR_Q6                |    11603 (-) |  0.986 |  0.902 | agtGCACAgagaaaggggt
 V$GR_Q6                |    11641 (+) |  0.984 |  0.937 | aaatgtatttcTGTACtgt
 V$GR_Q6                |    11788 (-) |  0.989 |  0.943 | taaGGACAaatcccagatt
 V$NF1_Q6               |      388 (-) |  1.000 |  0.957 | gccattcatttGCCAAca
 V$NF1_Q6               |      461 (+) |  1.000 |  0.954 | ggTTGGCttatttgacac
 V$NF1_Q6               |     1023 (+) |  1.000 |  0.958 | gaTTGGCagttgaatcaa
 V$NF1_Q6               |     1657 (+) |  1.000 |  0.963 | acTTGGCaaatggagatt
 V$NF1_Q6               |     1849 (-) |  1.000 |  0.952 | aacacaatagaGCCAAct
 V$NF1_Q6               |     1940 (+) |  1.000 |  0.959 | ccTTGGCtaggctggaac
 V$NF1_Q6               |     1974 (+) |  1.000 |  0.974 | ggTTGGCctcaaactcac
 V$NF1_Q6               |     3226 (-) |  1.000 |  0.959 | tttaccagtcaGCCAAca
 V$NF1_Q6               |     3317 (+) |  1.000 |  0.966 | gaTTGGCcttttcctgat
 V$NF1_Q6               |     3528 (+) |  1.000 |  0.962 | ccTTGGCccgaggtttgg
 V$NF1_Q6               |     3571 (+) |  1.000 |  0.964 | ctTTGGCaagttattcaa
 V$NF1_Q6               |     3671 (-) |  1.000 |  0.952 | gacttagaattGCCAAgt
 V$NF1_Q6               |     3678 (-) |  1.000 |  0.977 | aattgccaagtGCCAAga
 V$NF1_Q6               |     4728 (+) |  1.000 |  0.958 | atTTGGCcctcgctgatg
 V$NF1_Q6               |     4894 (-) |  1.000 |  0.968 | catgttccttgGCCAAgt
 V$NF1_Q6               |     4900 (+) |  1.000 |  0.970 | ccTTGGCcaagtgcatgc
 V$NF1_Q6               |     5265 (-) |  1.000 |  0.958 | agtcatcctggGCCAAca
 V$NF1_Q6               |     6200 (-) |  1.000 |  0.968 | agccggggtatGCCAAgg
 V$NF1_Q6               |     6834 (-) |  1.000 |  0.961 | tgctatttactGCCAAct
 V$NF1_Q6               |     7537 (-) |  1.000 |  0.990 | gttggttgtgaGCCAAct
 V$NF1_Q6               |     8226 (+) |  1.000 |  0.973 | tgTTGGCtcccacaccca
 V$NF1_Q6               |     8344 (-) |  1.000 |  0.979 | ctggaccacttGCCAAcc
 V$NF1_Q6               |     8389 (-) |  1.000 |  0.960 | gtatacctgaaGCCAAgc
 V$NF1_Q6               |     8446 (-) |  1.000 |  0.958 | ccgcatcctaaGCCAAgg
 V$NF1_Q6               |    10410 (+) |  1.000 |  0.957 | ggTTGGCatttttaacac
 V$NF1_Q6               |    11179 (+) |  1.000 |  0.955 | ttTTGGCtgccttgtttc
 V$NF1_Q6               |    11253 (-) |  1.000 |  0.969 | ctctgtggtgtGCCAAga
 V$NF1_Q6               |    11930 (+) |  1.000 |  0.963 | caTTGGCtgaaactattt
 V$NFKB_Q6              |      328 (+) |  0.863 |  0.857 | gcTGGAAattccct
 V$NFKB_Q6              |      329 (-) |  1.000 |  0.974 | ctggaaaTTCCCtc
 V$NFKB_Q6              |     1004 (+) |  1.000 |  0.875 | tgGGGACgcaccta
 V$NFKB_Q6              |     1951 (+) |  0.805 |  0.866 | ctGGAACtttcctt
 V$NFKB_Q6              |     3046 (+) |  1.000 |  0.889 | ccGGGACatacctg
 V$NFKB_Q6              |     4947 (+) |  1.000 |  0.866 | ctGGGACtttctgc
 V$OCT1_Q6              |      992 (-) |  0.893 |  0.918 | ataaTTTTCatgtgg
 V$OCT1_Q6              |     2831 (+) |  1.000 |  0.855 | ttgtctGCAAAtggc
 V$OCT1_Q6              |     3108 (-) |  0.888 |  0.917 | ctaaTTTCCatgcgg
 V$OCT1_Q6              |     3128 (-) |  0.909 |  0.930 | ttaaTTTACattccc
 V$OCT1_Q6              |     3834 (-) |  0.888 |  0.874 | taaaTTTCCattctc
 V$OCT1_Q6              |     5340 (-) |  1.000 |  0.875 | tagtTTTGCatcccc
 V$OCT1_Q6              |     5435 (-) |  0.838 |  0.884 | tttaTTTGTattgcc
 V$OCT1_Q6              |     6574 (+) |  1.000 |  0.927 | agttatGCAAAacac
 V$OCT1_Q6              |     6966 (+) |  0.888 |  0.861 | ctggatGGAAAggaa
 V$OCT1_Q6              |     7349 (+) |  0.792 |  0.860 | caacatGTTAAtcat
 V$OCT1_Q6              |     9486 (-) |  1.000 |  0.884 | tttaTTTGCaataga
 V$OCT1_Q6              |     9933 (-) |  1.000 |  0.996 | gtaaTTTGCatgtat
 V$OCT1_Q6              |    10408 (-) |  0.883 |  0.859 | gtggTTGGCattttt
 V$OCT1_Q6              |    10908 (+) |  1.000 |  0.981 | tactatGCAAAtaat
 V$OCT1_Q6              |    11151 (+) |  0.893 |  0.902 | tctgatGAAAAtgaa
 V$OCT1_Q6              |    11334 (+) |  0.909 |  0.903 | gacgatGTAAAtgcc
 V$OCT1_Q6              |    11664 (-) |  0.893 |  0.882 | acaaTTTTCataacc
 V$SP1_Q6               |     1487 (+) |  0.927 |  0.911 | agagGGAGGgggg
 V$SP1_Q6               |     1492 (+) |  0.904 |  0.902 | gaggGGGGGggga
 V$SP1_Q6               |     1493 (+) |  0.904 |  0.907 | agggGGGGGggag
 V$SP1_Q6               |     5894 (-) |  1.000 |  0.956 | gggcCCGCCccta
 V$SP1_Q6               |    11845 (+) |  0.915 |  0.922 | ggggGGTGGggta
 V$SP1_Q6               |    11870 (+) |  0.927 |  0.912 | cgggGGAGGgact
 F$ABF_C                |     2911 (+) |  0.931 |  0.954 | cATCTCtgtggacgg
 F$ABF_C                |     3711 (+) |  0.906 |  0.944 | gATCAAtatttacgg
 F$ABF_C                |     6859 (-) |  0.719 |  0.861 | acgtccagaCCGAGg
 F$ABF_C                |     6889 (-) |  0.796 |  0.878 | acgtaagacAAGAGg
 F$ABF_C                |     7859 (-) |  0.714 |  0.827 | gcgtacactTAGAAa
 F$ABF_C                |     9318 (-) |  0.714 |  0.826 | gcgttgggtCAGAGc
 F$ABF_C                |    10026 (-) |  0.877 |  0.909 | ccgtagtttGTGAGt
 F$ABF_C                |    11914 (+) |  0.719 |  0.832 | cTTCGGgcccaacgc
 V$AP1_C                |      133 (+) |  1.000 |  0.880 | ctcAGTCAa
 V$AP1_C                |      133 (-) |  0.808 |  0.864 | cTCAGTcaa
 V$AP1_C                |      440 (+) |  0.964 |  0.894 | tttAATCAg
 V$AP1_C                |      644 (+) |  0.955 |  0.876 | tttATTCAt
 V$AP1_C                |      644 (-) |  0.808 |  0.852 | tTTATTcat
 V$AP1_C                |     1032 (+) |  0.964 |  0.956 | ttgAATCAa
 V$AP1_C                |     1032 (-) |  0.955 |  0.949 | tTGAATcaa
 V$AP1_C                |     3435 (+) |  0.808 |  0.864 | ttgACTTAg
 V$AP1_C                |     3435 (-) |  1.000 |  0.880 | tTGACTtag
 V$AP1_C                |     3471 (-) |  0.964 |  0.861 | aTGATTtac
 V$AP1_C                |     3580 (+) |  0.955 |  0.874 | gttATTCAa
 V$AP1_C                |     3726 (+) |  0.833 |  0.867 | gtgACTAAa
 V$AP1_C                |     3726 (-) |  1.000 |  0.904 | gTGACTaaa
 V$AP1_C                |     3752 (+) |  1.000 |  0.907 | tttAGTCAt
 V$AP1_C                |     3752 (-) |  0.833 |  0.869 | tTTAGTcat
 V$AP1_C                |     3922 (-) |  0.955 |  0.854 | aTGAATtac
 V$AP1_C                |     3934 (+) |  1.000 |  0.884 | atcAGTCAc
 V$AP1_C                |     3934 (-) |  0.808 |  0.854 | aTCAGTcac
 V$AP1_C                |     3946 (+) |  0.955 |  0.864 | ttcATTCAg
 V$AP1_C                |     4467 (+) |  0.808 |  0.850 | ctgACTGAc
 V$AP1_C                |     4467 (-) |  1.000 |  0.897 | cTGACTgac
 V$AP1_C                |     4715 (+) |  0.955 |  0.851 | gtaATTCAc
 V$AP1_C                |     6294 (+) |  0.808 |  0.868 | atgACTGAg
 V$AP1_C                |     6294 (-) |  1.000 |  0.884 | aTGACTgag
 V$AP1_C                |     6323 (-) |  1.000 |  0.895 | cTGACTgaa
 V$AP1_C                |     7355 (+) |  0.964 |  0.885 | gttAATCAt
 V$AP1_C                |     8323 (+) |  0.788 |  0.852 | ctgCGTCAg
 V$AP1_C                |     8572 (-) |  0.964 |  0.879 | tTGATTaaa
 V$AP1_C                |     8616 (+) |  0.964 |  0.858 | gtcAATCAc
 V$AP1_C                |     9141 (+) |  0.808 |  0.864 | ttgAATAAg
 V$AP1_C                |     9141 (-) |  0.955 |  0.873 | tTGAATaag
 V$AP1_C                |     9321 (+) |  0.788 |  0.850 | ttgGGTCAg
 V$AP1_C                |    10035 (+) |  1.000 |  0.983 | gtgAGTCAc
 V$AP1_C                |    10035 (-) |  0.989 |  0.976 | gTGAGTcac
 V$AP1_C                |    10633 (+) |  0.808 |  0.866 | gtgACTGAg
 V$AP1_C                |    10633 (-) |  1.000 |  0.881 | gTGACTgag
 V$AP1_C                |    11197 (-) |  0.964 |  0.859 | tTGATTgat
 V$AP1_C                |    11455 (+) |  0.964 |  0.974 | gtgAATCAg
 V$AP1_C                |    11455 (-) |  0.955 |  0.952 | gTGAATcag
 V$AP1_C                |    11695 (+) |  0.964 |  0.882 | gttAATCAc
 V$CEBP_C               |      323 (+) |  0.893 |  0.817 | cctgtgctGGAAAttccc
 V$CEBP_C               |      330 (-) |  0.944 |  0.900 | tggaaATTCCctcagaca
 V$CEBP_C               |      486 (-) |  1.000 |  0.822 | tcaacATTGCaacattat
 V$CEBP_C               |      800 (-) |  0.955 |  0.848 | gagccATTTCtccagccc
 V$CEBP_C               |      921 (-) |  0.941 |  0.819 | tagcaCTTCCacgaaacc
 V$CEBP_C               |     1099 (+) |  0.955 |  0.811 | aaatttgaGAAATcgctg
 V$CEBP_C               |     1130 (-) |  0.903 |  0.894 | cgtgtGTTCCtaaaaccg
 V$CEBP_C               |     1460 (-) |  0.914 |  0.838 | cggacGTTTCtcaatatt
 V$CEBP_C               |     1556 (+) |  0.955 |  0.838 | ctcttctgGAAATctacg
 V$CEBP_C               |     1818 (+) |  0.941 |  0.834 | gtgttcagGGAAGacacc
 V$CEBP_C               |     2365 (-) |  0.949 |  0.844 | tttatTTTGCcacagttt
 V$CEBP_C               |     2396 (-) |  0.951 |  0.843 | agttgCTTTCcttaaaaa
 V$CEBP_C               |     2554 (+) |  0.955 |  0.862 | tctgttgtGAAATttccg
 V$CEBP_C               |     2561 (-) |  0.893 |  0.818 | tgaaaTTTCCgtaagtat
 V$CEBP_C               |     2563 (+) |  0.982 |  0.817 | aaatttccGTAAGtattt
 V$CEBP_C               |     2573 (-) |  0.935 |  0.806 | aagtaTTTACaacaaatg
 V$CEBP_C               |     2709 (-) |  0.941 |  0.810 | ttcctCTTCCcaaataga
 V$CEBP_C               |     2800 (-) |  0.982 |  0.893 | cttctCTTACtgaacacc
 V$CEBP_C               |     3132 (-) |  0.944 |  0.824 | tttacATTCCcacaacaa
 V$CEBP_C               |     3320 (-) |  0.904 |  0.847 | tggccTTTTCctgattct
 V$CEBP_C               |     3436 (+) |  0.945 |  0.873 | tgacttagGTAACagtta
 V$CEBP_C               |     3568 (+) |  0.996 |  0.940 | ggcctttgGCAAGttatt
 V$CEBP_C               |     3599 (-) |  0.914 |  0.810 | tttggGTTTCtgcagttt
 V$CEBP_C               |     3643 (+) |  0.944 |  0.815 | cacatggtGGAATcagta
 V$CEBP_C               |     3921 (-) |  0.985 |  0.857 | tatgaATTACattatcag
 V$CEBP_C               |     4021 (+) |  0.944 |  0.832 | gctctcatGGAATtaata
 V$CEBP_C               |     4204 (-) |  0.996 |  0.843 | caaggCTTGCctcagtta
 V$CEBP_C               |     4267 (-) |  0.982 |  0.853 | ggatgCTTACctaagcac
 V$CEBP_C               |     4390 (-) |  0.903 |  0.834 | agtgaGTTCCaagacagg
 V$CEBP_C               |     4602 (+) |  0.941 |  0.861 | cgcttgctGGAAGgtaaa
 V$CEBP_C               |     4707 (+) |  0.985 |  0.966 | agacttggGTAATtcact
 V$CEBP_C               |     4792 (-) |  0.996 |  0.871 | gctgaCTTGCataatctc
 V$CEBP_C               |     4896 (-) |  0.792 |  0.824 | tgttcCTTGGccaagtgc
 V$CEBP_C               |     4948 (-) |  0.951 |  0.837 | tgggaCTTTCtgcagcag
 V$CEBP_C               |     5149 (-) |  0.935 |  0.820 | ggcagTTTACgaaaaggg
 V$CEBP_C               |     5439 (-) |  1.000 |  0.845 | tttgtATTGCcatataac
 V$CEBP_C               |     5912 (-) |  0.914 |  0.860 | agtttGTTTCcccagcga
 V$CEBP_C               |     6342 (-) |  0.951 |  0.813 | gatttCTTTCacgaaagc
 V$CEBP_C               |     6546 (+) |  0.982 |  0.898 | cggctgagGTAAGagtca
 V$CEBP_C               |     6572 (+) |  0.949 |  0.917 | acagttatGCAAAacaca
 V$CEBP_C               |     6605 (-) |  0.949 |  0.884 | tgctaTTTGCtaaactcc
 V$CEBP_C               |     6872 (+) |  0.941 |  0.818 | ggcttataGGAAGcacca
 V$CEBP_C               |     7051 (-) |  0.904 |  0.809 | attttTTTTCttaatttg
 V$CEBP_C               |     7243 (+) |  0.904 |  0.820 | cgtctcagGAAAAagtct
 V$CEBP_C               |     7326 (+) |  0.770 |  0.832 | cgtctggaACAATagaca
 V$CEBP_C               |     7340 (-) |  0.955 |  0.824 | gacacATTTCaacatgtt
 V$CEBP_C               |     7558 (+) |  0.893 |  0.812 | tagatgctGGAAAccaaa
 V$CEBP_C               |     8068 (-) |  1.000 |  0.816 | ctggtATTGCagaaactt
 V$CEBP_C               |     8071 (+) |  0.914 |  0.801 | gtattgcaGAAACttcct
 V$CEBP_C               |     8140 (+) |  0.893 |  0.838 | ctgctgagGGAAAacatt
 V$CEBP_C               |     8488 (-) |  0.904 |  0.838 | ggttaTTTTCtacaggga
 V$CEBP_C               |     8577 (+) |  0.949 |  0.806 | taaatgggGCAAAggcaa
 V$CEBP_C               |     8606 (-) |  0.944 |  0.807 | ttatcATTCCgtcaatca
 V$CEBP_C               |     8693 (+) |  0.904 |  0.818 | gcctttctGAAAAtacca
 V$CEBP_C               |     8906 (+) |  0.944 |  0.832 | cagattcaGGAATactcg
 V$CEBP_C               |     8990 (-) |  0.944 |  0.826 | ctttaATTCCagcacatg
 V$CEBP_C               |     9095 (-) |  0.982 |  0.803 | ctctgCTTACaaaagcaa
 V$CEBP_C               |     9506 (-) |  0.914 |  0.818 | tgaaaGTTTCcccatgtc
 V$CEBP_C               |     9600 (+) |  0.941 |  0.833 | agcatttgGGAAGctgag
 V$CEBP_C               |     9870 (+) |  0.955 |  0.916 | agaatgagGAAATcaatt
 V$CEBP_C               |    10069 (+) |  0.941 |  0.847 | ggtcttctGGAAGggcag
 V$CEBP_C               |    10131 (+) |  0.955 |  0.812 | ttagttaaGAAATtatta
 V$CEBP_C               |    10252 (+) |  0.941 |  0.848 | cttgtgcaGGAAGtgatt
 V$CEBP_C               |    10366 (-) |  0.951 |  0.849 | agaatCTTTCaaaatgtt
 V$CEBP_C               |    10376 (+) |  1.000 |  0.915 | aaaatgttGCAATccata
 V$CEBP_C               |    10621 (+) |  0.951 |  0.860 | gagttgtaGAAAGtgact
 V$CEBP_C               |    10685 (+) |  0.959 |  0.866 | ggactctgGCAACacccg
 V$CEBP_C               |    10967 (+) |  0.996 |  0.829 | ctgttggaGCAAGgagcc
 V$CEBP_C               |    11149 (+) |  0.904 |  0.812 | actctgatGAAAAtgaag
 V$CEBP_C               |    11283 (+) |  0.949 |  0.831 | ggcataggGCAAAgaaat
 V$CEBP_C               |    11642 (-) |  0.955 |  0.819 | aatgtATTTCtgtactgt
 B$CRP_C                |       25 (+) |  1.000 |  0.814 | gaatgtgTGTGAacaacttcagatgt
 B$CRP_C                |     3886 (-) |  1.000 |  0.828 | ctccttgaccctcaTCACAggtatta
 B$CRP_C                |     4136 (+) |  0.716 |  0.783 | gaatctaGGTGTggtgcctcccattt
 V$GATA_C               |       84 (+) |  0.959 |  0.957 | tGATAGggcct
 V$GATA_C               |       88 (-) |  0.959 |  0.963 | agggcCTATCt
 V$GATA_C               |      304 (-) |  0.959 |  0.912 | ctgagCTATCt
 V$GATA_C               |      568 (+) |  1.000 |  0.959 | aGATAAacgtc
 V$GATA_C               |     1992 (-) |  1.000 |  0.940 | caagaTTATCt
 V$GATA_C               |     2320 (+) |  0.953 |  0.915 | gGATACagtct
 V$GATA_C               |     2724 (+) |  1.000 |  0.942 | aGATAAtcttc
 V$GATA_C               |     2899 (-) |  1.000 |  0.956 | cttttTTATCc
 V$GATA_C               |     3927 (-) |  1.000 |  0.938 | ttacaTTATCa
 V$GATA_C               |     3979 (+) |  0.959 |  0.927 | tGATAGacacc
 V$GATA_C               |     4004 (+) |  1.000 |  0.946 | cGATAAataaa
 V$GATA_C               |     4371 (-) |  1.000 |  0.943 | taaagTTATCt
 V$GATA_C               |     4579 (+) |  0.951 |  0.920 | aGATATagtct
 V$GATA_C               |     4781 (+) |  1.000 |  0.959 | gGATAAagatt
 V$GATA_C               |     5524 (-) |  0.959 |  0.935 | tcctcCTATCc
 V$GATA_C               |     5584 (+) |  1.000 |  0.942 | gGATAAtaata
 V$GATA_C               |     5635 (+) |  1.000 |  0.964 | gGATAAagaca
 V$GATA_C               |     5979 (+) |  1.000 |  0.943 | tGATAActtct
 V$GATA_C               |     6467 (+) |  1.000 |  0.945 | tGATAAaatgc
 V$GATA_C               |     7149 (-) |  0.953 |  0.944 | gcgccGTATCt
 V$GATA_C               |     7312 (+) |  0.951 |  0.915 | gGATATagaat
 V$GATA_C               |     7785 (-) |  1.000 |  0.936 | aaaaaTTATCc
 V$GATA_C               |     7799 (+) |  1.000 |  0.965 | aGATAAagaac
 V$GATA_C               |     7953 (+) |  0.953 |  0.907 | aGATACcccag
 V$GATA_C               |     8059 (-) |  1.000 |  0.956 | ctagtTTATCt
 V$GATA_C               |     8601 (-) |  1.000 |  0.937 | taataTTATCa
 V$GATA_C               |     9364 (-) |  0.959 |  0.922 | gttctCTATCa
 V$GATA_C               |     9734 (+) |  1.000 |  0.942 | tGATAAtgtcc
 V$GATA_C               |     9835 (+) |  1.000 |  0.935 | gGATAAtttta
 V$GATA_C               |    10451 (-) |  0.951 |  0.912 | cttttATATCa
 V$GATA_C               |    10485 (-) |  0.951 |  0.928 | gccacATATCa
 V$GATA_C               |    10591 (-) |  0.951 |  0.909 | ttcctATATCa
 V$GATA_C               |    11345 (-) |  1.000 |  0.930 | tgccaTTATCg
 V$GATA_C               |    11366 (-) |  0.959 |  0.927 | tgattCTATCt
 V$GATA_C               |    11426 (-) |  0.959 |  0.906 | tttagCTATCc
 V$GATA_C               |    11438 (-) |  1.000 |  0.989 | catacTTATCt
 V$GATA_C               |    11566 (-) |  1.000 |  0.981 | aactcTTATCa
 V$GATA_C               |    11578 (-) |  0.951 |  0.913 | tgcttATATCc
 F$GCN4_C               |      134 (-) |  1.000 |  0.814 | tcAGTCAatc
 F$GCN4_C               |      358 (-) |  0.892 |  0.832 | agATTCAaat
 F$GCN4_C               |      622 (+) |  0.777 |  0.770 | acaTGACAct
 F$GCN4_C               |      729 (-) |  0.777 |  0.792 | tgAGCCAcca
 F$GCN4_C               |      799 (-) |  0.777 |  0.837 | tgAGCCAttt
 F$GCN4_C               |     1030 (+) |  0.892 |  0.868 | agtTGAATca
 F$GCN4_C               |     1033 (-) |  0.922 |  0.888 | tgAATCAaca
 F$GCN4_C               |     1227 (+) |  1.000 |  0.795 | tgaTGACTgc
 F$GCN4_C               |     1309 (-) |  0.777 |  0.787 | agAGTCCcct
 F$GCN4_C               |     1355 (-) |  0.777 |  0.794 | tgGGTCAcct
 F$GCN4_C               |     1447 (-) |  1.000 |  0.816 | gaAGTCActg
 F$GCN4_C               |     1586 (-) |  0.777 |  0.768 | agAGCCAgca
 F$GCN4_C               |     1684 (-) |  0.777 |  0.769 | ggTGTCAgct
 F$GCN4_C               |     1803 (-) |  0.892 |  0.879 | ggATTCAtca
 F$GCN4_C               |     1857 (-) |  0.777 |  0.777 | agAGCCAact
 F$GCN4_C               |     2594 (+) |  1.000 |  0.799 | tacTGACTat
 F$GCN4_C               |     2611 (-) |  0.777 |  0.770 | agAGCCAtgt
 F$GCN4_C               |     2665 (+) |  0.777 |  0.797 | tgaTGACAct
 F$GCN4_C               |     2843 (-) |  0.699 |  0.770 | ggCATCAttc
 F$GCN4_C               |     3082 (+) |  0.922 |  0.891 | gggTGATTct
 F$GCN4_C               |     3328 (+) |  0.922 |  0.845 | tccTGATTct
 F$GCN4_C               |     3415 (+) |  0.922 |  0.933 | taaTGATTct
 F$GCN4_C               |     3433 (+) |  1.000 |  0.815 | aatTGACTta
 F$GCN4_C               |     3578 (+) |  0.699 |  0.768 | aagTTATTca
 F$GCN4_C               |     3651 (-) |  0.922 |  0.903 | ggAATCAgta
 F$GCN4_C               |     3724 (+) |  1.000 |  0.793 | gggTGACTaa
 F$GCN4_C               |     3753 (-) |  1.000 |  0.836 | ttAGTCAttc
 F$GCN4_C               |     3872 (-) |  0.777 |  0.804 | ggAGTTAata
 F$GCN4_C               |     3935 (-) |  1.000 |  0.825 | tcAGTCActt
 F$GCN4_C               |     4094 (+) |  0.922 |  0.904 | tacTGATTct
 F$GCN4_C               |     4147 (+) |  0.777 |  0.783 | tggTGCCTcc
 F$GCN4_C               |     4465 (+) |  1.000 |  0.809 | cacTGACTga
 F$GCN4_C               |     4534 (-) |  0.777 |  0.782 | tgCGTCAaca
 F$GCN4_C               |     4839 (-) |  0.777 |  0.788 | cgAGTGAtcc
 F$GCN4_C               |     5079 (+) |  0.777 |  0.769 | ggcTGGCTct
 F$GCN4_C               |     5263 (-) |  1.000 |  0.798 | acAGTCAtcc
 F$GCN4_C               |     5535 (-) |  0.892 |  0.900 | agATTCActc
 F$GCN4_C               |     5536 (+) |  0.777 |  0.806 | gatTCACTct
 F$GCN4_C               |     6143 (+) |  0.777 |  0.770 | ccaTGCCTct
 F$GCN4_C               |     6185 (-) |  0.777 |  0.785 | agAGACAccc
 F$GCN4_C               |     6292 (+) |  1.000 |  0.805 | tgaTGACTga
 F$GCN4_C               |     6414 (+) |  1.000 |  0.990 | gaaTGACTcc
 F$GCN4_C               |     6557 (-) |  1.000 |  0.932 | agAGTCAtgg
 F$GCN4_C               |     6792 (+) |  0.777 |  0.768 | tgcTGGCTct
 F$GCN4_C               |     7037 (-) |  0.777 |  0.801 | agAGTTAgtt
 F$GCN4_C               |     7043 (+) |  1.000 |  0.777 | agtTGACTat
 F$GCN4_C               |     7545 (-) |  0.777 |  0.785 | tgAGCCAact
 F$GCN4_C               |     7609 (-) |  0.777 |  0.807 | tgAGCCAtct
 F$GCN4_C               |     7637 (-) |  0.699 |  0.773 | agAATTAttt
 F$GCN4_C               |     7672 (+) |  0.777 |  0.792 | tggTGGCTca
 F$GCN4_C               |     7883 (-) |  1.000 |  0.828 | gaAGTCAttt
 F$GCN4_C               |     8045 (+) |  1.000 |  0.900 | cctTGACTcg
 F$GCN4_C               |     8226 (+) |  0.777 |  0.773 | tgtTGGCTcc
 F$GCN4_C               |     8324 (-) |  0.777 |  0.778 | tgCGTCAgcg
 F$GCN4_C               |     8617 (-) |  0.922 |  0.768 | tcAATCActt
 F$GCN4_C               |     8861 (+) |  0.777 |  0.768 | ttaAGACTct
 F$GCN4_C               |     8886 (-) |  0.922 |  0.852 | agAATCAaac
 F$GCN4_C               |     8907 (-) |  0.892 |  0.823 | agATTCAgga
 F$GCN4_C               |     9290 (-) |  1.000 |  0.933 | agAGTCAgct
 F$GCN4_C               |     9767 (-) |  1.000 |  0.769 | acAGTCAtgc
 F$GCN4_C               |    10033 (+) |  0.892 |  0.847 | ttgTGAGTca
 F$GCN4_C               |    10036 (-) |  1.000 |  0.957 | tgAGTCAccg
 F$GCN4_C               |    10104 (-) |  0.777 |  0.807 | tgAGCCAtct
 F$GCN4_C               |    10192 (-) |  1.000 |  0.800 | gcAGTCAgtt
 F$GCN4_C               |    10366 (-) |  0.699 |  0.771 | agAATCTttc
 F$GCN4_C               |    10503 (-) |  1.000 |  0.807 | aaAGTCAatt
 F$GCN4_C               |    10631 (+) |  1.000 |  0.825 | aagTGACTga
 F$GCN4_C               |    10682 (+) |  0.777 |  0.769 | gcaGGACTct
 F$GCN4_C               |    10996 (-) |  0.922 |  0.846 | ggAATCAgat
 F$GCN4_C               |    11363 (+) |  0.922 |  0.875 | gcaTGATTct
 F$GCN4_C               |    11453 (+) |  0.892 |  0.876 | tggTGAATca
 F$GCN4_C               |    11456 (-) |  0.922 |  0.914 | tgAATCAgtg
 F$GCN4_C               |    11696 (-) |  0.922 |  0.768 | ttAATCActg
 F$GCN4_C               |    11747 (+) |  1.000 |  0.820 | aaaTGACTag
 F$GCN4_C               |    11759 (-) |  0.777 |  0.774 | agAGTTAaca
 V$GRE_C                |      296 (+) |  0.722 |  0.771 | tttacagactGAGCTa
 V$GRE_C                |      761 (-) |  0.978 |  0.740 | cAGGACctctggaaga
 V$GRE_C                |     1147 (+) |  0.714 |  0.734 | gttactttatGTAGTt
 V$GRE_C                |     1263 (+) |  0.952 |  0.746 | tcatccgtgtGTACTc
 V$GRE_C                |     1399 (-) |  0.741 |  0.755 | gAGGAGagtgggtcca
 V$GRE_C                |     1591 (-) |  0.960 |  0.738 | cAGCACtgggtttggg
 V$GRE_C                |     1621 (-) |  0.741 |  0.786 | gTGGACagcatgtcca
 V$GRE_C                |     1622 (+) |  0.741 |  0.792 | tggacagcatGTCCAg
 V$GRE_C                |     1631 (+) |  0.741 |  0.730 | tgtccagcctTTCCTa
 V$GRE_C                |     1785 (-) |  0.960 |  0.730 | gAGCACctgccattca
 V$GRE_C                |     2591 (-) |  0.952 |  0.776 | cAGTACtgactattaa
 V$GRE_C                |     2810 (+) |  0.762 |  0.798 | tgaacaccgtGCTCTg
 V$GRE_C                |     2844 (+) |  0.978 |  0.743 | gcatcattccGTCCTt
 V$GRE_C                |     3023 (-) |  0.952 |  0.800 | cAGTACaccgacttcc
 V$GRE_C                |     3171 (-) |  0.714 |  0.742 | cTGTACattatatccc
 V$GRE_C                |     3521 (-) |  0.741 |  0.731 | gAGGCCaccttggccc
 V$GRE_C                |     3540 (+) |  1.000 |  0.760 | gtttggttctGTTCTt
 V$GRE_C                |     3692 (-) |  1.000 |  0.741 | aAGAACacaagagatg
 V$GRE_C                |     3965 (-) |  0.960 |  0.824 | gAGCACtggctgtatg
 V$GRE_C                |     4073 (+) |  0.714 |  0.741 | tgtaaaatgtATACTa
 V$GRE_C                |     4279 (-) |  0.960 |  0.842 | aAGCACacattagacc
 V$GRE_C                |     4670 (+) |  1.000 |  0.738 | tttgctcataGTTCTg
 V$GRE_C                |     4692 (+) |  0.978 |  0.817 | gaaacttgatGTCCTa
 V$GRE_C                |     5175 (+) |  1.000 |  0.759 | ttgtgactgtGTTCTa
 V$GRE_C                |     5204 (+) |  0.960 |  0.774 | gtggcctcttGTGCTt
 V$GRE_C                |     5661 (-) |  1.000 |  0.783 | aAGAACacaataagag
 V$GRE_C                |     6330 (-) |  0.960 |  0.798 | aAGCACacactggatt
 V$GRE_C                |     6517 (-) |  1.000 |  0.877 | aAGAACacgaagttca
 V$GRE_C                |     6913 (-) |  1.000 |  0.758 | gAGAACaaggaattga
 V$GRE_C                |     7468 (+) |  0.960 |  0.744 | ggatttgagtGTGCTa
 V$GRE_C                |     7531 (+) |  0.762 |  0.740 | gttacagttgGTTGTg
 V$GRE_C                |     7804 (-) |  1.000 |  0.751 | aAGAACaacgacaact
 V$GRE_C                |     8418 (+) |  1.000 |  0.820 | gtaagcagctGTTCTa
 V$GRE_C                |     8533 (-) |  1.000 |  0.880 | aAGAACacagtgggcc
 V$GRE_C                |     8750 (+) |  0.978 |  0.853 | cccacaccttGTCCTc
 V$GRE_C                |     8845 (-) |  1.000 |  0.758 | cAGAACggtttaaaaa
 V$GRE_C                |     8871 (+) |  0.762 |  0.767 | ggcatagaatATTCTa
 V$GRE_C                |     8965 (-) |  1.000 |  0.789 | gAGAACcaggtgtggt
 V$GRE_C                |     8966 (+) |  0.722 |  0.742 | agaaccaggtGTGGTg
 V$GRE_C                |     8999 (-) |  0.960 |  0.738 | cAGCACatggaggcag
 V$GRE_C                |     9354 (+) |  1.000 |  0.782 | tcttctcagtGTTCTc
 V$GRE_C                |     9440 (-) |  0.722 |  0.746 | aAGCCCaaggtttacc
 V$GRE_C                |     9464 (-) |  0.714 |  0.758 | cTGTACaggatgttct
 V$GRE_C                |     9465 (+) |  1.000 |  0.959 | tgtacaggatGTTCTa
 V$GRE_C                |     9533 (-) |  1.000 |  0.748 | tAGAACaaacaagtcc
 V$GRE_C                |     9779 (-) |  1.000 |  0.739 | tAGAACaattttgttc
 V$GRE_C                |     9950 (-) |  0.762 |  0.760 | tATAACaccctgtatg
 V$GRE_C                |    10062 (+) |  0.762 |  0.769 | tgaaccgggtCTTCTg
 V$GRE_C                |    10079 (-) |  0.741 |  0.732 | aAGGGCagccagtgct
 V$GRE_C                |    10080 (+) |  0.960 |  0.763 | agggcagccaGTGCTc
 V$GRE_C                |    10189 (+) |  1.000 |  0.750 | tcagcagtcaGTTCTg
 V$GRE_C                |    10194 (+) |  0.978 |  0.740 | agtcagttctGTCCTt
 V$GRE_C                |    10298 (-) |  0.741 |  0.738 | tCGGACattttttaac
 V$GRE_C                |    10566 (+) |  0.722 |  0.825 | ggtacagcgtTTGCTt
 V$GRE_C                |    10645 (+) |  0.978 |  0.852 | gacacccagtGTCCTa
 V$GRE_C                |    10683 (-) |  0.978 |  0.732 | cAGGACtctggcaaca
 V$GRE_C                |    10883 (-) |  0.960 |  0.750 | gAGCACtgcacatgcg
 V$GRE_C                |    11072 (+) |  0.762 |  0.830 | gttacaagctGCTCTg
 V$GRE_C                |    11223 (+) |  1.000 |  0.848 | tgcccagtttGTTCTa
 V$GRE_C                |    11367 (+) |  0.960 |  0.796 | gattctatctGTGCTt
 V$HNF1_C               |      387 (+) |  0.670 |  0.805 | tGCCATtcatttgccaa
 V$HNF1_C               |      985 (-) |  0.750 |  0.808 | acagttaataaTTTTCa
 V$HNF1_C               |      987 (+) |  1.000 |  0.880 | aGTTAAtaattttcatg
 V$HNF1_C               |     3412 (+) |  1.000 |  0.821 | aGTTAAtgattctggtt
 V$HNF1_C               |     4056 (+) |  0.816 |  0.837 | aGGCAAtaattaaaata
 V$HNF1_C               |     6834 (+) |  0.796 |  0.792 | tGCTATttactgccaac
 V$HNF1_C               |     8145 (-) |  0.942 |  0.825 | gagggaaaacaTTAGCt
 V$HNF1_C               |     9876 (+) |  0.771 |  0.795 | aGGAAAtcaatttaaaa
 V$HNF1_C               |    10298 (-) |  1.000 |  0.819 | tcggacattttTTAACt
 V$HNF1_C               |    11694 (+) |  1.000 |  0.857 | aGTTAAtcactgtcacc
 V$NFKB_C               |      330 (-) |  0.973 |  0.983 | tggaaaTTCCCt
 V$NFKB_C               |     1952 (+) |  0.760 |  0.851 | tGGAACtttcct
 V$NFKB_C               |     4637 (-) |  0.977 |  0.867 | agcaaaATCCCg
 V$NFKB_C               |     4948 (+) |  1.000 |  0.870 | tGGGACtttctg
 V$NFKB_C               |     5163 (+) |  1.000 |  0.878 | aGGGACtttcac
 V$NFKB_C               |    11086 (+) |  0.973 |  0.868 | tGGGAAttttcc
 V$NFKB_C               |    11087 (+) |  0.737 |  0.854 | gGGAATtttcca
 V$NFY_C                |      458 (+) |  0.800 |  0.811 | ttTGGTTggcttat
 V$NFY_C                |      529 (+) |  0.800 |  0.789 | aaTGATGggtgatg
 V$NFY_C                |     1020 (+) |  1.000 |  0.893 | tgTGATTggcagtt
 V$NFY_C                |     1113 (+) |  1.000 |  0.785 | gcTGATTtgtgtat
 V$NFY_C                |     1424 (-) |  1.000 |  0.794 | gacacgcAATCAgt
 V$NFY_C                |     1789 (-) |  0.800 |  0.785 | acctgccATTCAca
 V$NFY_C                |     2933 (+) |  1.000 |  0.816 | gcTGATTgcgaagt
 V$NFY_C                |     3225 (-) |  0.800 |  0.834 | ttttaccAGTCAgc
 V$NFY_C                |     3280 (+) |  1.000 |  0.851 | taTGATTgggatga
 V$NFY_C                |     5086 (+) |  0.800 |  0.817 | tcTGACTggtttgg
 V$NFY_C                |     9186 (-) |  0.800 |  0.780 | agagaccACTCAag
 V$NFY_C                |     9449 (-) |  0.800 |  0.814 | gtttaccAATCTct
 V$NFY_C                |    10759 (+) |  0.800 |  0.797 | tgTGTTTgggcact
 V$NFY_C                |    11196 (+) |  1.000 |  0.855 | ctTGATTgattatt
 V$NFY_C                |    11800 (+) |  0.800 |  0.776 | ccAGATTggaaggt
 V$OCT_C                |      279 (-) |  0.761 |  0.835 | gcatGCAAGtcaa
 V$OCT_C                |      992 (+) |  0.884 |  0.901 | ataaTTTTCatgt
 V$OCT_C                |     2626 (-) |  1.000 |  0.830 | ctagGCAAAtgct
 V$OCT_C                |     3108 (+) |  0.859 |  0.896 | ctaaTTTCCatgc
 V$OCT_C                |     3128 (+) |  0.859 |  0.882 | ttaaTTTACattc
 V$OCT_C                |     3834 (+) |  0.859 |  0.822 | taaaTTTCCattc
 V$OCT_C                |     4793 (+) |  0.761 |  0.855 | ctgaCTTGCataa
 V$OCT_C                |     5340 (+) |  1.000 |  0.814 | tagtTTTGCatcc
 V$OCT_C                |     5435 (+) |  0.761 |  0.817 | tttaTTTGTattg
 V$OCT_C                |     5748 (-) |  1.000 |  0.799 | agacGCAAAggac
 V$OCT_C                |     6576 (-) |  1.000 |  0.900 | ttatGCAAAacac
 V$OCT_C                |     6968 (-) |  0.859 |  0.810 | ggatGGAAAggaa
 V$OCT_C                |     7351 (-) |  0.742 |  0.822 | acatGTTAAtcat
 V$OCT_C                |     9486 (+) |  1.000 |  0.819 | tttaTTTGCaata
 V$OCT_C                |     9731 (-) |  0.767 |  0.801 | gtatGATAAtgtc
 V$OCT_C                |     9933 (+) |  1.000 |  0.965 | gtaaTTTGCatgt
 V$OCT_C                |    10910 (-) |  1.000 |  0.983 | ctatGCAAAtaat
 V$OCT_C                |    11153 (-) |  0.884 |  0.886 | tgatGAAAAtgaa
 V$OCT_C                |    11336 (-) |  0.859 |  0.809 | cgatGTAAAtgcc
 V$OCT_C                |    11664 (+) |  0.884 |  0.852 | acaaTTTTCataa
 V$PADS_C               |      933 (-) |  1.000 |  0.957 | gaaACCACa
 V$PADS_C               |     3359 (-) |  1.000 |  0.952 | cagACCACt
 V$PADS_C               |     5049 (+) |  1.000 |  0.953 | tGTGGTcta
 V$PADS_C               |     9187 (-) |  1.000 |  0.993 | gagACCACt
 F$RAP1_C               |     3595 (-) |  1.000 |  0.969 | tatgttTGGGTttc
 V$SRF_C                |     3860 (-) |  0.871 |  0.886 | agtaCCATTtaagga
 V$SRF_C                |     3863 (+) |  0.925 |  0.893 | accattTAAGGagtt
 V$SRF_C                |    11534 (-) |  0.836 |  0.882 | aatcCCACAtatggt
 V$SRF_C                |    11537 (+) |  1.000 |  0.874 | cccacaTATGGtaga
 V$TATA_C               |      239 (-) |  1.000 |  0.885 | tTTTTAaatc
 V$TATA_C               |      294 (-) |  1.000 |  0.923 | gTTTTAcaga
 V$TATA_C               |      502 (-) |  0.853 |  0.811 | aTTATAtatt
 V$TATA_C               |      521 (+) |  1.000 |  0.889 | atttTAAAAa
 V$TATA_C               |      521 (-) |  1.000 |  0.886 | aTTTTAaaaa
 V$TATA_C               |      550 (-) |  1.000 |  0.837 | gTTTTAacct
 V$TATA_C               |      558 (-) |  0.790 |  0.833 | cTTTTCtagg
 V$TATA_C               |      603 (-) |  1.000 |  0.903 | tTTTTAaaca
 V$TATA_C               |      634 (-) |  1.000 |  0.903 | tTTTTAaaca
 V$TATA_C               |      655 (-) |  0.853 |  0.811 | aTTATAtata
 V$TATA_C               |      657 (+) |  0.853 |  0.817 | tataTATAAg
 V$TATA_C               |      823 (-) |  1.000 |  0.828 | tTTTTAatac
 V$TATA_C               |      831 (+) |  0.853 |  0.881 | actaTATAAa
 V$TATA_C               |      833 (+) |  1.000 |  0.926 | tataTAAAAc
 V$TATA_C               |     1061 (+) |  1.000 |  0.950 | acttTAAAAt
 V$TATA_C               |     1136 (+) |  1.000 |  0.818 | ttccTAAAAc
 V$TATA_C               |     1743 (+) |  0.841 |  0.867 | cctaTAGAAc
 V$TATA_C               |     1890 (-) |  1.000 |  0.927 | aTTTTAtatt
 V$TATA_C               |     1901 (-) |  1.000 |  0.870 | aTTTTAttat
 V$TATA_C               |     1909 (-) |  1.000 |  0.867 | aTTTTAtttg
 V$TATA_C               |     2404 (+) |  1.000 |  0.911 | tcctTAAAAa
 V$TATA_C               |     2534 (-) |  1.000 |  0.929 | cTTTTAgaga
 V$TATA_C               |     2599 (+) |  0.790 |  0.827 | actaTTAAAc
 V$TATA_C               |     2901 (-) |  1.000 |  0.885 | tTTTTAtcca
 V$TATA_C               |     3404 (+) |  1.000 |  0.936 | gttaTAAAAg
 V$TATA_C               |     3451 (+) |  1.000 |  0.869 | ttaaTAAAAc
 V$TATA_C               |     3727 (+) |  1.000 |  0.814 | tgacTAAAAt
 V$TATA_C               |     3750 (-) |  1.000 |  0.816 | tTTTTAgtca
 V$TATA_C               |     3760 (+) |  1.000 |  0.851 | ttctTAAAAg
 V$TATA_C               |     3846 (+) |  1.000 |  0.889 | ctcaTAAAAt
 V$TATA_C               |     4062 (+) |  1.000 |  0.822 | taatTAAAAt
 V$TATA_C               |     4071 (+) |  1.000 |  0.857 | tatgTAAAAt
 V$TATA_C               |     4090 (-) |  1.000 |  0.863 | aTTTTActga
 V$TATA_C               |     4099 (+) |  1.000 |  0.859 | attcTAAAAc
 V$TATA_C               |     4123 (+) |  1.000 |  0.822 | atgtTAAAAc
 V$TATA_C               |     4216 (+) |  1.000 |  0.823 | cagtTAAAAa
 V$TATA_C               |     4315 (+) |  1.000 |  0.903 | tgcaTAAAAc
 V$TATA_C               |     4421 (+) |  1.000 |  0.877 | tgtcTAAAAa
 V$TATA_C               |     4423 (+) |  0.790 |  0.830 | tctaAAAAAa
 V$TATA_C               |     5385 (-) |  1.000 |  0.866 | gTTTTAtttt
 V$TATA_C               |     5439 (-) |  0.841 |  0.810 | tTTGTAttgc
 V$TATA_C               |     5447 (+) |  0.853 |  0.836 | gccaTATAAc
 V$TATA_C               |     5559 (+) |  0.790 |  0.827 | actaGAAAAc
 V$TATA_C               |     5576 (-) |  0.841 |  0.830 | cTTCTAaagg
 V$TATA_C               |     5589 (+) |  1.000 |  0.870 | ataaTAAAAt
 V$TATA_C               |     5645 (+) |  1.000 |  0.869 | aaaaTAAAAa
 V$TATA_C               |     5765 (+) |  1.000 |  0.817 | agggTAAAAg
 V$TATA_C               |     5952 (-) |  1.000 |  0.867 | aTTTTAtttg
 V$TATA_C               |     5968 (-) |  1.000 |  0.844 | tTTTTAagtg
 V$TATA_C               |     6466 (+) |  1.000 |  0.868 | ctgaTAAAAt
 V$TATA_C               |     6510 (+) |  1.000 |  0.872 | caaaTAAAAg
 V$TATA_C               |     6669 (-) |  1.000 |  0.867 | aTTTTAttta
 V$TATA_C               |     6826 (-) |  1.000 |  0.889 | tTTTTAtgtg
 V$TATA_C               |     7260 (+) |  1.000 |  0.889 | tcatTAAAAt
 V$TATA_C               |     7270 (+) |  1.000 |  0.819 | atccTAAAAt
 V$TATA_C               |     7416 (-) |  1.000 |  0.956 | cTTTTAaagg
 V$TATA_C               |     7434 (-) |  1.000 |  0.869 | tTTTTAtttt
 V$TATA_C               |     7439 (-) |  1.000 |  0.886 | aTTTTAtgtg
 V$TATA_C               |     7643 (+) |  1.000 |  0.889 | atttTAAAAa
 V$TATA_C               |     7643 (-) |  1.000 |  0.886 | aTTTTAaaaa
 V$TATA_C               |     7895 (-) |  1.000 |  0.869 | tTTTTAtttt
 V$TATA_C               |     8851 (+) |  1.000 |  0.903 | ggttTAAAAa
 V$TATA_C               |     8948 (+) |  1.000 |  0.886 | ttttTAAAAt
 V$TATA_C               |     8948 (-) |  1.000 |  0.889 | tTTTTAaaat
 V$TATA_C               |     9412 (+) |  0.790 |  0.827 | tctaGAAAAc
 V$TATA_C               |     9493 (+) |  0.841 |  0.810 | gcaaTAGAAa
 V$TATA_C               |     9711 (+) |  1.000 |  0.874 | ggtgTAAAAt
 V$TATA_C               |     9742 (+) |  0.841 |  0.827 | tccaTACAAt
 V$TATA_C               |     9775 (+) |  0.841 |  0.826 | gccaTAGAAc
 V$TATA_C               |     9825 (-) |  1.000 |  0.860 | aTTTTAgaag
 V$TATA_C               |     9840 (-) |  1.000 |  0.950 | aTTTTAaagt
 V$TATA_C               |     9884 (+) |  1.000 |  0.883 | aattTAAAAt
 V$TATA_C               |     9897 (-) |  1.000 |  0.953 | tTTTTAaaga
 V$TATA_C               |    10122 (+) |  1.000 |  0.934 | ccaaTAAAAt
 V$TATA_C               |    10306 (-) |  1.000 |  0.823 | tTTTTAactg
 V$TATA_C               |    10316 (-) |  1.000 |  0.930 | tTTTTAtatt
 V$TATA_C               |    10324 (-) |  1.000 |  0.869 | tTTTTAtttt
 V$TATA_C               |    10329 (-) |  1.000 |  0.994 | aTTTTAtagt
 V$TATA_C               |    10338 (-) |  1.000 |  0.936 | tTTTTAttgt
 V$TATA_C               |    10346 (-) |  1.000 |  0.821 | gTTTTAattc
 V$TATA_C               |    10388 (+) |  0.853 |  0.840 | tccaTATAAa
 V$TATA_C               |    10390 (+) |  1.000 |  0.930 | cataTAAAAa
 V$TATA_C               |    10418 (-) |  1.000 |  0.826 | tTTTTAacac
 V$TATA_C               |    10451 (-) |  1.000 |  0.933 | cTTTTAtatc
 V$TATA_C               |    10732 (-) |  1.000 |  0.939 | cTTTTAttgg
 V$TATA_C               |    11470 (-) |  1.000 |  0.869 | tTTTTAtttg
 V$USF_C                |       19 (-) |  0.929 |  0.940 | acATGTGa
 V$USF_C                |      736 (+) |  1.000 |  0.996 | cCACGTgg
 V$USF_C                |      736 (-) |  1.000 |  0.996 | ccACGTGg
 V$USF_C                |      999 (-) |  0.929 |  0.943 | tcATGTGg
 V$USF_C                |     1127 (+) |  1.000 |  0.992 | gCACGTgt
 V$USF_C                |     1127 (-) |  1.000 |  0.995 | gcACGTGt
 V$USF_C                |     1393 (-) |  0.918 |  0.934 | gcAGGTGa
 V$USF_C                |     2615 (-) |  0.929 |  0.937 | ccATGTGt
 V$USF_C                |     2774 (-) |  0.929 |  0.942 | gcATGTGa
 V$USF_C                |     3642 (+) |  0.929 |  0.941 | cCACATgg
 V$USF_C                |     4340 (-) |  0.918 |  0.933 | ccAGGTGg
 V$USF_C                |     5251 (+) |  0.929 |  0.940 | tCACATgt
 V$USF_C                |     5253 (-) |  0.929 |  0.943 | acATGTGg
 V$USF_C                |     6065 (+) |  1.000 |  0.994 | gCACGTgc
 V$USF_C                |     6065 (-) |  1.000 |  0.994 | gcACGTGc
 V$USF_C                |     7113 (+) |  0.929 |  0.943 | cCACATgt
 V$USF_C                |     7115 (-) |  0.929 |  0.939 | acATGTGt
 V$USF_C                |     7392 (-) |  0.918 |  0.933 | ccAGGTGg
 V$USF_C                |     9001 (+) |  0.929 |  0.935 | gCACATgg
 V$USF_C                |    10890 (+) |  0.929 |  0.939 | gCACATgc
 P$MYBPH3_01            |     1139 (+) |  0.984 |  0.972 | ctaaaaCCGTTac
 P$MYBPH3_01            |    10309 (-) |  0.967 |  0.963 | ttAACTGttttta
 P$MYBPH3_02            |     7036 (+) |  1.000 |  0.933 | aagagtTAGTTga
 V$SREBP1_02            |      195 (+) |  0.600 |  0.747 | tcCCACAccac
 V$SREBP1_02            |      532 (-) |  1.000 |  0.782 | gatgGGTGAtg
 V$SREBP1_02            |      780 (-) |  0.800 |  0.790 | gtcgGGTGCtc
 V$SREBP1_02            |     1278 (-) |  0.800 |  0.764 | ctggGATGAca
 V$SREBP1_02            |     1327 (+) |  0.800 |  0.747 | tcTCACTcccc
 V$SREBP1_02            |     2336 (+) |  0.800 |  0.764 | tgTGACCctac
 V$SREBP1_02            |     3181 (+) |  0.800 |  0.790 | taTCCCCcctc
 V$SREBP1_02            |     3232 (+) |  0.800 |  0.752 | agTCAGCcaac
 V$SREBP1_02            |     3245 (+) |  0.600 |  0.747 | tcCCAGCccac
 V$SREBP1_02            |     3290 (-) |  1.000 |  0.747 | atgaGGTGAac
 V$SREBP1_02            |     4144 (-) |  0.800 |  0.752 | gtgtGGTGCct
 V$SREBP1_02            |     4328 (-) |  1.000 |  0.764 | gtctGGTGAca
 V$SREBP1_02            |     5135 (-) |  0.800 |  0.747 | gtgcGGTCAac
 V$SREBP1_02            |     5424 (+) |  0.600 |  0.747 | ttTCCCTccac
 V$SREBP1_02            |     5763 (-) |  0.800 |  0.747 | gtagGGTAAaa
 V$SREBP1_02            |     6437 (+) |  0.800 |  0.764 | ggTCAACccag
 V$SREBP1_02            |     6992 (-) |  0.800 |  0.782 | gtgaGGAGAtg
 V$SREBP1_02            |     7831 (+) |  0.600 |  0.778 | aaTTAACccac
 V$SREBP1_02            |     8542 (-) |  0.600 |  0.747 | gtggGCCGAga
 V$SREBP1_02            |     8664 (+) |  0.600 |  0.747 | ttTCAAAccac
 V$SREBP1_02            |     8741 (-) |  0.800 |  0.764 | gtgtGGTGGcc
 V$SREBP1_02            |     8960 (-) |  0.800 |  0.747 | gtagGGAGAac
 V$SREBP1_02            |     8974 (-) |  0.800 |  0.790 | gtgtGGTGGta
 V$SREBP1_02            |     9320 (-) |  0.800 |  0.747 | gttgGGTCAga
 V$SREBP1_02            |     9574 (-) |  0.800 |  0.790 | gtgtGGTGGta
 V$SREBP1_02            |     9618 (-) |  0.600 |  0.790 | gtggGAGGAtc
 V$SREBP1_02            |     9686 (-) |  0.800 |  0.782 | ggggGGTGGtg
 V$SREBP1_02            |     9709 (-) |  0.600 |  0.747 | gtggTGTAAaa
 V$SREBP1_02            |    10876 (-) |  0.600 |  0.747 | gtggTGGGAgc
 V$SREBP1_02            |    11257 (-) |  0.600 |  0.764 | gtggTGTGCca
 V$SREBP1_02            |    11704 (+) |  1.000 |  0.869 | tgTCACCccaa
 V$SREBP1_02            |    11823 (-) |  1.000 |  0.852 | ttggGGTGAga
 V$HAND1E47_01          |       39 (-) |  0.853 |  0.812 | aactTCAGAtgtcatt
 V$HAND1E47_01          |      114 (+) |  0.856 |  0.841 | cagtgagGCTGGctaa
 V$HAND1E47_01          |      139 (-) |  1.000 |  0.939 | caatCCAGAcatttgc
 V$HAND1E47_01          |      203 (+) |  0.868 |  0.837 | caccatgCCTGGtatt
 V$HAND1E47_01          |      240 (+) |  1.000 |  0.904 | ttttaaaTCTGGgctg
 V$HAND1E47_01          |      295 (-) |  0.859 |  0.816 | ttttACAGActgagct
 V$HAND1E47_01          |      352 (-) |  0.853 |  0.814 | tacaTCAGAttcaaat
 V$HAND1E47_01          |      446 (+) |  0.859 |  0.820 | caggttgTCTGTtttg
 V$HAND1E47_01          |      589 (-) |  0.859 |  0.831 | attaACAGActtactt
 V$HAND1E47_01          |      680 (-) |  0.853 |  0.820 | ctctTCAGAcacacca
 V$HAND1E47_01          |      689 (-) |  1.000 |  0.882 | cacaCCAGAagagggc
 V$HAND1E47_01          |      739 (+) |  0.856 |  0.814 | cgtggttGCTGGgaat
 V$HAND1E47_01          |      761 (+) |  1.000 |  0.906 | caggaccTCTGGaaga
 V$HAND1E47_01          |     1270 (+) |  1.000 |  0.903 | tgtgtacTCTGGgatg
 V$HAND1E47_01          |     1286 (+) |  0.868 |  0.829 | acagggaCCTGGacct
 V$HAND1E47_01          |     1474 (+) |  1.000 |  0.908 | tatttgcTCTGGcaga
 V$HAND1E47_01          |     1553 (+) |  1.000 |  0.921 | aaactctTCTGGaaat
 V$HAND1E47_01          |     1873 (+) |  0.871 |  0.832 | gggaggaTCTGCctcc
 V$HAND1E47_01          |     1943 (+) |  0.856 |  0.825 | tggctagGCTGGaact
 V$HAND1E47_01          |     1993 (+) |  1.000 |  0.933 | aagattaTCTGGctat
 V$HAND1E47_01          |     2043 (+) |  0.868 |  0.841 | cactgtaCCTGGcttc
 V$HAND1E47_01          |     2076 (+) |  0.859 |  0.819 | gtctctgTCTGTctct
 V$HAND1E47_01          |     2301 (+) |  0.859 |  0.834 | gtgtgtgTCTGTgtgt
 V$HAND1E47_01          |     2381 (-) |  1.000 |  0.892 | tttcCCAGAgctgaga
 V$HAND1E47_01          |     2726 (+) |  0.871 |  0.816 | ataatctTCTGCcttt
 V$HAND1E47_01          |     2827 (+) |  0.871 |  0.844 | ccagttgTCTGCaaat
 V$HAND1E47_01          |     2939 (+) |  0.871 |  0.837 | tgcgaagTCTGCctat
 V$HAND1E47_01          |     2967 (-) |  0.871 |  0.833 | gacgGCAGAtgcgcag
 V$HAND1E47_01          |     3226 (-) |  0.868 |  0.826 | tttaCCAGTcagccaa
 V$HAND1E47_01          |     3243 (-) |  0.856 |  0.824 | attcCCAGCccactta
 V$HAND1E47_01          |     3354 (-) |  0.859 |  0.819 | tcagACAGAccactga
 V$HAND1E47_01          |     3397 (-) |  0.868 |  0.809 | atctCCAGTtataaaa
 V$HAND1E47_01          |     3415 (+) |  1.000 |  0.918 | taatgatTCTGGttgc
 V$HAND1E47_01          |     3600 (+) |  0.871 |  0.828 | ttgggttTCTGCagtt
 V$HAND1E47_01          |     3664 (-) |  0.859 |  0.810 | taacACAGActtagaa
 V$HAND1E47_01          |     3788 (+) |  1.000 |  0.889 | tttttctTCTGGacag
 V$HAND1E47_01          |     3854 (-) |  0.868 |  0.827 | atatCCAGTaccattt
 V$HAND1E47_01          |     4115 (-) |  1.000 |  0.920 | tttcCCAGAtgttaaa
 V$HAND1E47_01          |     4129 (-) |  1.000 |  0.929 | aaacCCAGAatctagg
 V$HAND1E47_01          |     4322 (+) |  1.000 |  0.940 | aactgggTCTGGtgac
 V$HAND1E47_01          |     4372 (+) |  1.000 |  0.930 | aaagttaTCTGGctac
 V$HAND1E47_01          |     4771 (+) |  1.000 |  0.956 | cagcgagTCTGGataa
 V$HAND1E47_01          |     4801 (+) |  1.000 |  0.926 | cataatcTCTGGcatt
 V$HAND1E47_01          |     4818 (-) |  0.868 |  0.816 | gttaCCAGGcggggta
 V$HAND1E47_01          |     4875 (+) |  1.000 |  0.899 | gcaaagcTCTGGaaca
 V$HAND1E47_01          |     4939 (+) |  0.868 |  0.811 | agactgaACTGGgact
 V$HAND1E47_01          |     4994 (-) |  0.871 |  0.852 | aatgGCAGAccttgta
 V$HAND1E47_01          |     5022 (+) |  0.868 |  0.848 | ccacgggACTGGgatg
 V$HAND1E47_01          |     5073 (+) |  0.856 |  0.849 | atgagagGCTGGctct
 V$HAND1E47_01          |     5083 (+) |  0.868 |  0.813 | ggctctgACTGGtttg
 V$HAND1E47_01          |     5223 (+) |  0.868 |  0.844 | agcggagACTGGgaac
 V$HAND1E47_01          |     5529 (-) |  1.000 |  0.942 | ctatCCAGAttcactc
 V$HAND1E47_01          |     5567 (-) |  0.868 |  0.827 | acaaCCAGGcttctaa
 V$HAND1E47_01          |     5673 (-) |  0.859 |  0.848 | agagACAGAcacagag
 V$HAND1E47_01          |     5724 (+) |  0.868 |  0.811 | acactaaACTGGaagc
 V$HAND1E47_01          |     5980 (+) |  1.000 |  0.912 | gataactTCTGGatta
 V$HAND1E47_01          |     6033 (+) |  1.000 |  0.890 | ggacccaTCTGGtgca
 V$HAND1E47_01          |     6112 (-) |  1.000 |  0.872 | ttgaCCAGAgggcttg
 V$HAND1E47_01          |     6143 (+) |  1.000 |  0.930 | ccatgccTCTGGctct
 V$HAND1E47_01          |     6179 (-) |  1.000 |  0.913 | gttcCCAGAgacaccc
 V$HAND1E47_01          |     6232 (+) |  1.000 |  0.940 | catgctgTCTGGctac
 V$HAND1E47_01          |     6417 (+) |  1.000 |  0.913 | tgactccTCTGGcttt
 V$HAND1E47_01          |     6440 (-) |  0.868 |  0.812 | caacCCAGTcatggca
 V$HAND1E47_01          |     6482 (+) |  0.868 |  0.837 | gatgaggACTGGattg
 V$HAND1E47_01          |     6493 (-) |  0.871 |  0.844 | gattGCAGAtgcggcc
 V$HAND1E47_01          |     6632 (-) |  1.000 |  0.886 | gcacCCAGAaggcacc
 V$HAND1E47_01          |     6645 (+) |  0.871 |  0.826 | acctcagTCTGCaaac
 V$HAND1E47_01          |     6778 (-) |  0.871 |  0.813 | aacaGCAGAtctaatg
 V$HAND1E47_01          |     6859 (-) |  1.000 |  0.914 | acgtCCAGAccgaggc
 V$HAND1E47_01          |     6958 (+) |  1.000 |  0.895 | ccattatTCTGGatgg
 V$HAND1E47_01          |     7135 (-) |  1.000 |  0.890 | gaggCCAGAagagggc
 V$HAND1E47_01          |     7159 (+) |  0.856 |  0.827 | tcctggaGCTGGcgtt
 V$HAND1E47_01          |     7171 (-) |  0.871 |  0.808 | cgttGCAGAtggtccc
 V$HAND1E47_01          |     7321 (+) |  1.000 |  0.948 | atgtacgTCTGGaaca
 V$HAND1E47_01          |     7556 (+) |  0.856 |  0.811 | tgtagatGCTGGaaac
 V$HAND1E47_01          |     7617 (-) |  0.856 |  0.826 | ctctCCAGCcgcctgg
 V$HAND1E47_01          |     7621 (+) |  0.868 |  0.818 | ccagccgCCTGGcggt
 V$HAND1E47_01          |     7661 (-) |  0.868 |  0.839 | tatgCCAGGcatggtg
 V$HAND1E47_01          |     7689 (-) |  1.000 |  0.917 | aaagCCAGAacttggg
 V$HAND1E47_01          |     7737 (+) |  0.856 |  0.808 | atcacagGCTGGctac
 V$HAND1E47_01          |     7836 (+) |  1.000 |  0.912 | acccactTCTGGcaaa
 V$HAND1E47_01          |     7956 (-) |  1.000 |  0.918 | taccCCAGActatagt
 V$HAND1E47_01          |     8060 (+) |  1.000 |  0.941 | tagtttaTCTGGtatt
 V$HAND1E47_01          |     8072 (-) |  0.871 |  0.830 | tattGCAGAaacttcc
 V$HAND1E47_01          |     8089 (+) |  1.000 |  0.884 | atacagcTCTGGgtcc
 V$HAND1E47_01          |     8125 (+) |  0.871 |  0.819 | tgcctggTCTGCtttc
 V$HAND1E47_01          |     8159 (-) |  1.000 |  0.923 | gcttCCAGAggcaggt
 V$HAND1E47_01          |     8175 (-) |  1.000 |  0.889 | agcaCCAGAacttgtt
 V$HAND1E47_01          |     8237 (-) |  1.000 |  0.911 | acacCCAGAtgaaggt
 V$HAND1E47_01          |     8402 (-) |  0.856 |  0.819 | caagCCAGCccggcct
 V$HAND1E47_01          |     8518 (-) |  0.859 |  0.825 | actcACAGAtgcttca
 V$HAND1E47_01          |     8712 (+) |  0.853 |  0.825 | caaggagTCTGAagaa
 V$HAND1E47_01          |     8765 (+) |  0.868 |  0.817 | cccagcaCCTGGgagg
 V$HAND1E47_01          |     8809 (+) |  1.000 |  0.929 | gccagctTCTGGtact
 V$HAND1E47_01          |     8861 (+) |  1.000 |  0.939 | ttaagacTCTGGcata
 V$HAND1E47_01          |     8901 (-) |  0.859 |  0.819 | acaaACAGAttcagga
 V$HAND1E47_01          |     9017 (-) |  0.871 |  0.811 | gcagGCAGAtctttgt
 V$HAND1E47_01          |     9040 (+) |  0.868 |  0.808 | agggcagCCTGGtcta
 V$HAND1E47_01          |     9063 (-) |  0.868 |  0.834 | agttCCAGGctagcca
 V$HAND1E47_01          |     9232 (-) |  1.000 |  0.919 | agctCCAGAgccctag
 V$HAND1E47_01          |     9327 (+) |  1.000 |  0.902 | cagagccTCTGGagga
 V$HAND1E47_01          |     9386 (+) |  0.868 |  0.818 | gtcagccCCTGGaatg
 V$HAND1E47_01          |     9497 (+) |  0.853 |  0.810 | tagaaaaTCTGAaagt
 V$HAND1E47_01          |     9562 (+) |  1.000 |  0.920 | gtcggttTCTGGgtgt
 V$HAND1E47_01          |     9961 (+) |  1.000 |  0.919 | gtatgttTCTGGttcc
 V$HAND1E47_01          |     9999 (+) |  1.000 |  0.905 | taggtccTCTGGgact
 V$HAND1E47_01          |    10005 (+) |  0.868 |  0.837 | ctctgggACTGGaggt
 V$HAND1E47_01          |    10067 (+) |  1.000 |  0.908 | cgggtctTCTGGaagg
 V$HAND1E47_01          |    10478 (-) |  0.856 |  0.827 | tagaCCAGCcacatat
 V$HAND1E47_01          |    10682 (+) |  1.000 |  0.932 | gcaggacTCTGGcaac
 V$HAND1E47_01          |    10986 (+) |  0.868 |  0.825 | gtgtggcCCTGGaatc
 V$HAND1E47_01          |    11077 (+) |  1.000 |  0.901 | aagctgcTCTGGgaat
 V$HAND1E47_01          |    11112 (-) |  0.853 |  0.822 | gactTCAGAtccctta
 V$HAND1E47_01          |    11407 (+) |  0.871 |  0.811 | catttatTCTGCattt
 V$HAND1E47_01          |    11619 (-) |  1.000 |  0.897 | ggtaCCAGAaggaccc
 V$HAND1E47_01          |    11770 (-) |  1.000 |  0.959 | gattCCAGAtacttga
 V$HAND1E47_01          |    11796 (-) |  1.000 |  0.929 | aatcCCAGAttggaag
 V$STAT_01              |      927 (+) |  0.933 |  0.936 | TTCCAcgaa
 V$STAT_01              |      927 (-) |  0.780 |  0.866 | ttccACGAA
 V$STAT_01              |     1136 (+) |  0.956 |  0.906 | TTCCTaaaa
 V$STAT_01              |     1559 (-) |  0.824 |  0.878 | ttctGGAAA
 V$STAT_01              |     1821 (-) |  1.000 |  0.969 | ttcaGGGAA
 V$STAT_01              |     2403 (+) |  0.956 |  0.890 | TTCCTtaaa
 V$STAT_01              |     2566 (+) |  0.824 |  0.881 | TTTCCgtaa
 V$STAT_01              |     3138 (+) |  1.000 |  0.933 | TTCCCacaa
 V$STAT_01              |     3844 (+) |  0.854 |  0.883 | TTCTCataa
 V$STAT_01              |     4605 (+) |  0.780 |  0.866 | TTGCTggaa
 V$STAT_01              |     4605 (-) |  0.933 |  0.908 | ttgcTGGAA
 V$STAT_01              |     6875 (-) |  0.956 |  0.945 | ttatAGGAA
 V$STAT_01              |     7842 (-) |  0.824 |  0.878 | ttctGGCAA
 V$STAT_01              |     8612 (+) |  0.948 |  0.886 | TTCCGtcaa
 V$STAT_01              |    10052 (-) |  0.809 |  0.868 | ttctAAGAA
 V$STAT3_01             |      921 (-) |  0.775 |  0.829 | tagcacttccaCGAAAccaca
 P$P_01                 |     3637 (+) |  1.000 |  0.997 | acCTACCac
 P$P_01                 |    10236 (-) |  0.992 |  0.988 | taGGTTGgt
 P$P_01                 |    11860 (-) |  1.000 |  0.998 | ggGGTAGgt
 V$VMYB_02              |     1144 (-) |  1.000 |  0.990 | aCCGTTact
 V$VMYB_02              |    11518 (-) |  1.000 |  0.977 | aCCGTTgtc
 N$SKN1_02              |     8604 (+) |  1.000 |  0.987 | tattATCATtcc
 N$SKN1_02              |     9730 (-) |  1.000 |  0.983 | tgtATGATaatg
 V$MEF2_02              |     2526 (-) |  0.829 |  0.797 | acatatTACTTttagagaataa
 V$MEF2_02              |     3085 (-) |  1.000 |  0.898 | tgattcTATTTttcgaatctat
 V$MEF2_02              |     3734 (-) |  1.000 |  0.793 | aattatTATTTctacattttta
 V$MEF2_02              |     3997 (+) |  1.000 |  0.800 | gaaacaacgatAAATAaatatt
 V$MEF2_02              |     5801 (+) |  1.000 |  0.832 | acaaaaaaaaaAAATAgccctg
 V$MEF2_02              |     6249 (-) |  1.000 |  0.795 | gctttcTATTTgtcccatctgc
 V$MEF2_02              |     6831 (-) |  1.000 |  0.815 | atgtgcTATTTactgccaactg
 V$MEF2_02              |     7044 (-) |  1.000 |  0.822 | gttgacTATTTtttttcttaat
 V$MEF2_02              |     8692 (+) |  1.000 |  0.814 | agcctttctgaAAATAccatca
 V$MEF2_02              |     8944 (+) |  0.838 |  0.823 | caactttttaaAATTAgtaggg
 V$MEF2_02              |     9402 (-) |  0.803 |  0.834 | tggttcTATGTctagaaaacta
 V$MEF2_02              |     9419 (+) |  1.000 |  0.806 | aactatcccatAAATAacagga
 V$MEF2_02              |    10118 (+) |  0.838 |  0.809 | atccccaataaAATTAgttaag
 V$MEF2_02              |    10316 (-) |  1.000 |  0.826 | tttttaTATTTttattttatag
 V$MEF2_02              |    10908 (+) |  0.853 |  0.816 | tactatgcaaaTAATAgtctag
 V$MEF2_02              |    11746 (+) |  0.766 |  0.798 | caaatgactagAAAGAgttaac
 V$MEF2_02              |    11937 (-) |  1.000 |  0.867 | tgaaacTATTTcaagggtcagg
 V$MEF2_03              |      956 (-) |  1.000 |  0.828 | atcaaaTATTTacaggacccct
 V$MEF2_03              |     3085 (-) |  1.000 |  0.869 | tgattcTATTTttcgaatctat
 V$MEF2_03              |     6831 (-) |  1.000 |  0.794 | atgtgcTATTTactgccaactg
 V$MEF2_03              |     8692 (+) |  1.000 |  0.844 | agcctttctgaAAATAccatca
 V$MEF2_03              |     9402 (-) |  0.843 |  0.877 | tggttcTATGTctagaaaacta
 V$MEF2_03              |    11937 (-) |  1.000 |  0.886 | tgaaacTATTTcaagggtcagg
 V$MEF2_04              |      513 (-) |  0.615 |  0.674 | gtcttcTGATTttaaaaatgat
 V$MEF2_04              |      956 (-) |  1.000 |  0.707 | atcaaaTATTTacaggacccct
 V$MEF2_04              |     1158 (-) |  0.815 |  0.675 | tagttcTTTTTcaaagaaagga
 V$MEF2_04              |     1890 (-) |  1.000 |  0.669 | attttaTATTTattttattatt
 V$MEF2_04              |     1957 (-) |  0.815 |  0.707 | ctttccTTTTTtgagcaggttg
 V$MEF2_04              |     2285 (-) |  0.796 |  0.662 | ctcttcTAGTTtttgtgtgtgt
 V$MEF2_04              |     2399 (+) |  0.815 |  0.683 | tgctttccttaAAAAAaacaaa
 V$MEF2_04              |     2526 (-) |  0.796 |  0.661 | acatatTACTTttagagaataa
 V$MEF2_04              |     2828 (+) |  0.796 |  0.655 | cagttgtctgcAAATGgcatca
 V$MEF2_04              |     3085 (-) |  1.000 |  0.839 | tgattcTATTTttcgaatctat
 V$MEF2_04              |     3118 (-) |  0.796 |  0.659 | tgcggcTATATtaatttacatt
 V$MEF2_04              |     3723 (+) |  0.796 |  0.715 | cgggtgactaaAATTAttattt
 V$MEF2_04              |     3742 (-) |  0.796 |  0.683 | tttctaCATTTttagtcattct
 V$MEF2_04              |     4417 (+) |  0.815 |  0.711 | accttgtctaaAAAAAaaaaaa
 V$MEF2_04              |     4479 (-) |  0.815 |  0.656 | cattttTCTTTtgaacaaaaaa
 V$MEF2_04              |     5431 (-) |  1.000 |  0.676 | ccacttTATTTgtattgccata
 V$MEF2_04              |     5795 (+) |  0.815 |  0.659 | ttaaatacaaaAAAAAaaaata
 V$MEF2_04              |     6249 (-) |  1.000 |  0.734 | gctttcTATTTgtcccatctgc
 V$MEF2_04              |     6500 (+) |  1.000 |  0.692 | gatgcggccacAAATAaaagaa
 V$MEF2_04              |     6646 (+) |  0.818 |  0.654 | cctcagtctgcAAACAgatgaa
 V$MEF2_04              |     6831 (-) |  1.000 |  0.680 | atgtgcTATTTactgccaactg
 V$MEF2_04              |     6926 (-) |  0.796 |  0.675 | tgattgTATGTgcagtacccaa
 V$MEF2_04              |     7266 (+) |  0.611 |  0.689 | aaatatcctaaAATAAgaccca
 V$MEF2_04              |     7765 (+) |  0.818 |  0.669 | agggtctcaaaAAACAaaacaa
 V$MEF2_04              |     8692 (+) |  1.000 |  0.750 | agcctttctgaAAATAccatca
 V$MEF2_04              |     8892 (+) |  0.818 |  0.682 | aaacgtaccacAAACAgattca
 V$MEF2_04              |     8944 (+) |  0.796 |  0.712 | caactttttaaAATTAgtaggg
 V$MEF2_04              |     9402 (-) |  0.796 |  0.802 | tggttcTATGTctagaaaacta
 V$MEF2_04              |     9419 (+) |  1.000 |  0.671 | aactatcccatAAATAacagga
 V$MEF2_04              |     9483 (+) |  0.796 |  0.684 | tactttatttgCAATAgaaaat
 V$MEF2_04              |     9720 (-) |  0.815 |  0.694 | ttgatcTCTTTgtatgataatg
 V$MEF2_04              |     9890 (-) |  0.815 |  0.660 | aaattcTTTTTtaaagacttac
 V$MEF2_04              |    10316 (-) |  1.000 |  0.677 | tttttaTATTTttattttatag
 V$MEF2_04              |    10908 (+) |  0.796 |  0.657 | tactatgcaaaTAATAgtctag
 V$MEF2_04              |    11094 (-) |  0.818 |  0.690 | ttccacTGTTTaaagaacgact
 V$MEF2_04              |    11442 (-) |  1.000 |  0.683 | cttatcTATTTtggtgaatcag
 V$MEF2_04              |    11660 (-) |  0.796 |  0.657 | taacacAATTTtcataaccaaa
 V$MEF2_04              |    11746 (+) |  0.815 |  0.712 | caaatgactagAAAGAgttaac
 V$MEF2_04              |    11937 (-) |  1.000 |  0.745 | tgaaacTATTTcaagggtcagg
 V$AHRARNT_01           |     1423 (-) |  1.000 |  0.927 | agaCACGCaatcagtg
 V$AHRARNT_01           |     5815 (+) |  1.000 |  0.929 | tagccctgGCGTGgca
 V$AHRARNT_01           |    10713 (+) |  1.000 |  0.926 | acatctctGCGTGctg
 V$ARNT_01              |      431 (-) |  1.000 |  0.916 | aatacCACGTttaatc
 V$ARNT_01              |      732 (+) |  1.000 |  0.961 | gccaccACGTGgttgc
 V$ARNT_01              |      732 (-) |  1.000 |  0.975 | gccacCACGTggttgc
 V$ARNT_01              |     1123 (+) |  1.000 |  0.983 | gtatgcACGTGtgttc
 V$ARNT_01              |     1123 (-) |  1.000 |  0.974 | gtatgCACGTgtgttc
 V$ARNT_01              |     1613 (+) |  0.831 |  0.838 | ggggtcTCGTGgacag
 V$ARNT_01              |     5364 (-) |  0.831 |  0.839 | aaacaCACGGgatttc
 V$ARNT_01              |     6000 (+) |  1.000 |  0.883 | tggggtACGTGtccaa
 V$ARNT_01              |     6061 (+) |  1.000 |  0.950 | ccctgcACGTGctgcc
 V$ARNT_01              |     6061 (-) |  1.000 |  0.971 | ccctgCACGTgctgcc
 V$ARNT_01              |     6853 (-) |  1.000 |  0.883 | gtgagCACGTccagac
 V$ARNT_01              |     6883 (-) |  1.000 |  0.886 | agcacCACGTaagaca
 V$ARNT_01              |     7189 (-) |  0.831 |  0.827 | acggcCACGGgggtgc
 V$ARNT_01              |     7483 (-) |  1.000 |  0.890 | acgcgCACGTctgttc
 V$AHRARNT_02           |     1419 (-) |  1.000 |  0.804 | cgtgagaCACGCaatcagt
 V$AHRARNT_02           |     1573 (+) |  0.800 |  0.770 | ggggaatGCATGgagagcc
 V$AHRARNT_02           |     6216 (-) |  1.000 |  0.855 | ggtttctCACGCtctgcat
 V$AHRARNT_02           |     8101 (-) |  0.800 |  0.778 | gtcctgtCACACactctcc
 V$BARBIE_01            |     1170 (+) |  0.979 |  0.940 | aaagAAAGGagatgg
 V$BARBIE_01            |     5427 (-) |  0.966 |  0.929 | ccctccACTTTattt
 V$BARBIE_01            |     6243 (-) |  1.000 |  0.923 | gctacgGCTTTctat
 V$BARBIE_01            |     6716 (-) |  0.979 |  0.919 | ccacaaCCTTTaaag
 V$NKX25_01             |      288 (+) |  1.000 |  1.000 | tcAAGTG
 V$NKX25_01             |      346 (-) |  1.000 |  0.897 | CACTTct
 V$NKX25_01             |      476 (-) |  1.000 |  0.939 | CACTTac
 V$NKX25_01             |      628 (-) |  1.000 |  0.897 | CACTTtt
 V$NKX25_01             |      820 (-) |  1.000 |  0.897 | CACTTtt
 V$NKX25_01             |      905 (-) |  1.000 |  0.897 | CACTTtc
 V$NKX25_01             |      924 (-) |  1.000 |  0.897 | CACTTcc
 V$NKX25_01             |     2660 (-) |  1.000 |  0.886 | CACTTtg
 V$NKX25_01             |     3204 (+) |  0.891 |  0.903 | tcAAGTA
 V$NKX25_01             |     3222 (-) |  1.000 |  0.897 | CACTTtt
 V$NKX25_01             |     3253 (-) |  1.000 |  0.939 | CACTTat
 V$NKX25_01             |     3683 (+) |  1.000 |  0.942 | ccAAGTG
 V$NKX25_01             |     3940 (-) |  1.000 |  0.953 | CACTTgt
 V$NKX25_01             |     4694 (-) |  0.869 |  0.884 | AACTTga
 V$NKX25_01             |     4906 (+) |  1.000 |  0.942 | ccAAGTG
 V$NKX25_01             |     5172 (-) |  1.000 |  0.953 | CACTTgt
 V$NKX25_01             |     5432 (-) |  1.000 |  0.944 | CACTTta
 V$NKX25_01             |     5704 (-) |  1.000 |  0.928 | CACTTag
 V$NKX25_01             |     5971 (+) |  1.000 |  0.986 | ttAAGTG
 V$NKX25_01             |     6906 (+) |  1.000 |  0.939 | atAAGTG
 V$NKX25_01             |     6944 (+) |  1.000 |  0.942 | ccAAGTG
 V$NKX25_01             |     7839 (-) |  1.000 |  0.897 | CACTTct
 V$NKX25_01             |     7864 (-) |  1.000 |  0.928 | CACTTag
 V$NKX25_01             |     8350 (-) |  1.000 |  0.953 | CACTTgc
 V$NKX25_01             |     8622 (-) |  1.000 |  0.886 | CACTTtg
 V$NKX25_01             |     9676 (+) |  1.000 |  0.897 | agAAGTG
 V$NKX25_01             |    10260 (+) |  1.000 |  0.897 | ggAAGTG
 V$NKX25_01             |    10355 (+) |  1.000 |  0.886 | caAAGTG
 V$NKX25_01             |    10473 (-) |  1.000 |  0.944 | CACTTta
 V$NKX25_01             |    10629 (+) |  1.000 |  0.897 | gaAAGTG
 V$NKX25_01             |    11779 (-) |  0.891 |  0.903 | TACTTga
 V$PPARA_01             |      370 (+) |  0.748 |  0.685 | tttctctaggtGAGAGatgc
 V$PPARA_01             |     2454 (-) |  0.939 |  0.709 | agcgCTATGgcctagcaagc
 V$PPARA_01             |     2621 (+) |  0.625 |  0.715 | gtatgctaggcAAATGctct
 V$PPARA_01             |     3067 (+) |  0.899 |  0.702 | tatagctaggtCACAGggtg
 V$PPARA_01             |     3435 (+) |  0.773 |  0.759 | ttgacttaggtAACAGttaa
 V$PPARA_01             |     3525 (-) |  0.751 |  0.740 | ccacCTTGGcccgaggtttg
 V$PPARA_01             |     3567 (-) |  1.000 |  0.675 | tggcCTTTGgcaagttattc
 V$PPARA_01             |     4049 (+) |  0.564 |  0.702 | gggaaataggcAATAAttaa
 V$PPARA_01             |     4555 (+) |  0.899 |  0.695 | ttgatgctggaCACAGttgc
 V$PPARA_01             |     4803 (-) |  0.899 |  0.680 | taatCTCTGgcatttgttac
 V$PPARA_01             |     4896 (-) |  0.751 |  0.673 | tgttCCTTGgccaagtgcat
 V$PPARA_01             |     5453 (-) |  0.875 |  0.761 | taacCTTTTccccacatact
 V$PPARA_01             |     6813 (-) |  0.625 |  0.723 | ttacCTTCTcccttttttat
 V$PPARA_01             |     7785 (+) |  1.000 |  0.682 | aaaaattatccCAAAGataa
 V$PPARA_01             |     7909 (-) |  0.875 |  0.713 | ttagCTTTTacttaggtatc
 V$PPARA_01             |     8204 (-) |  0.899 |  0.713 | tcccCTCTGacctcagttct
 V$PPARA_01             |     8211 (-) |  0.649 |  0.713 | tgacCTCAGttctgatgttg
 V$PPARA_01             |     8303 (-) |  0.899 |  0.673 | gcccCTCTGccctgcagctt
 V$PPARA_01             |     8465 (+) |  0.751 |  0.688 | ctcatctaaggCAAAAataa
 V$PPARA_01             |     8556 (-) |  0.690 |  0.715 | tgaaCAATGtccgtctttga
 V$PPARA_01             |     8575 (+) |  1.000 |  0.733 | attaaatggggCAAAGgcaa
 V$PPARA_01             |     9986 (+) |  0.564 |  0.681 | cagaagagggtATTAGgtcc
 V$PPARA_01             |    10097 (-) |  0.899 |  0.709 | taacCTCTGagccatcttgc
 V$PPARA_01             |    10196 (-) |  0.649 |  0.680 | tcagTTCTGtccttccacag
 V$PPARA_01             |    11014 (+) |  0.748 |  0.728 | ttagggtaggaGAGAGatcc
 V$PPARA_01             |    11274 (+) |  0.939 |  0.733 | ggaaattaaggCATAGggca
 V$PPARA_01             |    11281 (+) |  1.000 |  0.687 | aaggcatagggCAAAGaaat
 V$PPARA_01             |    11937 (+) |  0.751 |  0.689 | tgaaactatttCAAGGgtca
 V$EGR1_01              |     2975 (+) |  0.809 |  0.778 | atgcGCAGGcat
 V$EGR1_01              |     3006 (+) |  0.809 |  0.894 | gtgcGCAGGcgt
 V$EGR1_01              |     7444 (+) |  1.000 |  0.844 | atgtGTGGGagt
 V$EGR1_01              |     9211 (-) |  0.945 |  0.894 | gctCCTACgcaa
 V$EGR1_01              |    10609 (+) |  1.000 |  0.823 | gtgtGTGGGagg
 V$EGR1_01              |    11867 (+) |  0.885 |  0.785 | gtccGGGGGagg
 V$EGR2_01              |      193 (-) |  1.000 |  0.812 | cctCCCACacca
 V$EGR2_01              |     7444 (+) |  1.000 |  0.862 | atgtGTGGGagt
 V$EGR2_01              |     8115 (-) |  1.000 |  0.784 | tctCCCACcctg
 V$EGR2_01              |     8231 (-) |  1.000 |  0.792 | gctCCCACaccc
 V$EGR2_01              |     9211 (-) |  0.970 |  0.903 | gctCCTACgcaa
 V$EGR2_01              |    10609 (+) |  1.000 |  0.859 | gtgtGTGGGagg
 V$EGR2_01              |    11015 (+) |  0.970 |  0.770 | taggGTAGGaga
 V$EGR2_01              |    11839 (+) |  1.000 |  0.805 | cagaGTGGGggg
 F$PACC_01              |     7621 (-) |  0.976 |  0.941 | ccagccgcCTGGCggta
 V$OCT1_07              |      588 (-) |  1.000 |  0.864 | AATTAacagact
 V$OCT1_07              |      994 (-) |  0.930 |  0.867 | AATTTtcatgtg
 V$OCT1_07              |     2521 (-) |  0.705 |  0.825 | AAATTacatatt
 V$OCT1_07              |     3102 (+) |  1.000 |  0.899 | tctatacTAATT
 V$OCT1_07              |     3110 (-) |  0.930 |  0.876 | AATTTccatgcg
 V$OCT1_07              |     3122 (+) |  1.000 |  0.884 | gctatatTAATT
 V$OCT1_07              |     3130 (-) |  0.930 |  0.876 | AATTTacattcc
 V$OCT1_07              |     3836 (-) |  0.930 |  0.880 | AATTTccattct
 V$OCT1_07              |     4063 (-) |  1.000 |  0.888 | AATTAaaatatg
 V$OCT1_07              |     4069 (+) |  0.705 |  0.825 | aatatgtAAAAT
 V$OCT1_07              |     4448 (-) |  1.000 |  0.827 | AATTAatattca
 V$OCT1_07              |     9730 (+) |  0.776 |  0.866 | tgtatgaTAATG
 V$OCT1_07              |     9738 (-) |  0.705 |  0.835 | AATGTccataca
 V$OCT1_07              |     9935 (-) |  0.930 |  0.891 | AATTTgcatgta
 V$OCT1_07              |    10909 (+) |  0.705 |  0.828 | actatgcAAATA
 V$OCT1_07              |    11666 (-) |  0.930 |  0.938 | AATTTtcataac
 V$GFI1_01              |      237 (+) |  0.960 |  0.938 | tctttttaAATCTgggctgtaagg
 V$GFI1_01              |     1104 (-) |  1.000 |  0.946 | tgagaaatcgcTGATTtgtgtatg
 V$GFI1_01              |     1423 (+) |  1.000 |  0.923 | agacacgcAATCAgtggcaatagt
 V$GFI1_01              |     2414 (+) |  1.000 |  0.971 | aaacaaaaAATCAcaggggttggg
 V$GFI1_01              |     4634 (+) |  0.940 |  0.931 | ggtagcaaAATCCcggcaccttct
 V$GFI1_01              |     4715 (-) |  1.000 |  0.982 | gtaattcactgTGATTtggccctc
 V$GFI1_01              |     8562 (-) |  1.000 |  0.918 | atgtccgtcttTGATTaaatgggg
 V$GFI1_01              |     9448 (+) |  0.960 |  0.918 | ggtttaccAATCTctgctgtacag
 V$GFI1_01              |     9872 (+) |  1.000 |  0.917 | aatgaggaAATCAatttaaaattc
 V$GFI1_01              |    10254 (-) |  1.000 |  0.941 | tgtgcaggaagTGATTtttgccgg
 V$GFI1_01              |    10808 (+) |  0.939 |  0.932 | tgcatctaAATCGcagtccgcctt
 V$GFI1_01              |    11450 (+) |  1.000 |  0.923 | ttttggtgAATCAgtgaaattttt
 V$GFI1_01              |    11690 (+) |  1.000 |  0.942 | ataaagttAATCActgtcacccca
 V$GFI1_01              |    11788 (+) |  0.940 |  0.922 | taaggacaAATCCcagattggaag
 V$TATA_01              |      496 (-) |  0.936 |  0.916 | aacattatTATATat
 V$TATA_01              |      503 (+) |  0.936 |  0.896 | ttATATAtttgtctt
 V$TATA_01              |      636 (-) |  1.000 |  0.870 | tttaaacaTTTATtc
 V$TATA_01              |      644 (-) |  1.000 |  0.864 | tttattcaTTTATta
 V$TATA_01              |      649 (-) |  0.936 |  0.917 | tcatttatTATATat
 V$TATA_01              |      651 (-) |  0.936 |  0.902 | atttattaTATATaa
 V$TATA_01              |      656 (+) |  0.936 |  0.907 | ttATATAtaagtaca
 V$TATA_01              |      658 (+) |  0.936 |  0.929 | atATATAagtacact
 V$TATA_01              |      825 (-) |  0.936 |  0.874 | tttaatacTATATaa
 V$TATA_01              |      832 (+) |  0.936 |  0.938 | ctATATAaaacaagt
 V$TATA_01              |      834 (+) |  1.000 |  0.971 | atATAAAacaagtta
 V$TATA_01              |      848 (+) |  1.000 |  0.875 | aaATAAAtacgatcg
 V$TATA_01              |     1744 (+) |  0.884 |  0.884 | ctATAGAacactgat
 V$TATA_01              |     1884 (-) |  1.000 |  0.980 | cctcccatTTTATat
 V$TATA_01              |     1890 (-) |  1.000 |  0.866 | attttataTTTATtt
 V$TATA_01              |     1895 (-) |  1.000 |  0.873 | atatttatTTTATta
 V$TATA_01              |     1903 (-) |  1.000 |  0.875 | tttattatTTTATtt
 V$TATA_01              |     2005 (+) |  0.884 |  0.865 | ctATACAtctcctga
 V$TATA_01              |     2357 (-) |  1.000 |  0.872 | aacttgtaTTTATtt
 V$TATA_01              |     2731 (-) |  1.000 |  0.875 | cttctgccTTTATgc
 V$TATA_01              |     2895 (-) |  1.000 |  0.899 | gcatctttTTTATcc
 V$TATA_01              |     3094 (-) |  0.884 |  0.866 | ttttcgaaTCTATac
 V$TATA_01              |     3405 (+) |  1.000 |  0.976 | ttATAAAagttaatg
 V$TATA_01              |     3452 (+) |  1.000 |  0.882 | taATAAAacacaggg
 V$TATA_01              |     3618 (-) |  1.000 |  0.938 | caaatgcgTTTATaa
 V$TATA_01              |     3831 (+) |  1.000 |  0.858 | taATAAAtttccatt
 V$TATA_01              |     3847 (+) |  1.000 |  0.883 | tcATAAAatatccag
 V$TATA_01              |     4004 (+) |  1.000 |  0.873 | cgATAAAtaaatatt
 V$TATA_01              |     4008 (+) |  1.000 |  0.866 | aaATAAAtattctgc
 V$TATA_01              |     4225 (+) |  1.000 |  0.861 | aaATAAAttctcagg
 V$TATA_01              |     4316 (+) |  1.000 |  0.898 | gcATAAAactgggtc
 V$TATA_01              |     4781 (+) |  1.000 |  0.859 | ggATAAAgattgctg
 V$TATA_01              |     5379 (-) |  1.000 |  0.878 | cttttagtTTTATtt
 V$TATA_01              |     5390 (-) |  1.000 |  0.944 | attttaccTTTATat
 V$TATA_01              |     5590 (+) |  1.000 |  0.871 | taATAAAatataata
 V$TATA_01              |     5635 (+) |  1.000 |  0.863 | ggATAAAgacaaaat
 V$TATA_01              |     5646 (+) |  1.000 |  0.893 | aaATAAAaagaagaa
 V$TATA_01              |     5946 (-) |  1.000 |  0.872 | agtaaaatTTTATtt
 V$TATA_01              |     6467 (+) |  1.000 |  0.884 | tgATAAAatgctcag
 V$TATA_01              |     6511 (+) |  1.000 |  0.890 | aaATAAAagaacacg
 V$TATA_01              |     6663 (-) |  1.000 |  0.877 | atgaagatTTTATtt
 V$TATA_01              |     6754 (-) |  1.000 |  0.957 | actatcccTTTATac
 V$TATA_01              |     6820 (-) |  1.000 |  0.902 | ctccctttTTTATgt
 V$TATA_01              |     7314 (+) |  0.884 |  0.877 | atATAGAatgtacgt
 V$TATA_01              |     7428 (-) |  1.000 |  0.892 | tatttgttTTTATtt
 V$TATA_01              |     7433 (-) |  1.000 |  0.886 | gtttttatTTTATgt
 V$TATA_01              |     7889 (-) |  1.000 |  0.895 | atttggttTTTATtt
 V$TATA_01              |     8380 (-) |  0.884 |  0.859 | ctttgatcTGTATac
 V$TATA_01              |     8931 (+) |  1.000 |  0.933 | gtATAAActaaagca
 V$TATA_01              |     9426 (+) |  1.000 |  0.889 | ccATAAAtaacagga
 V$TATA_01              |    10123 (+) |  1.000 |  0.883 | caATAAAattagtta
 V$TATA_01              |    10310 (-) |  1.000 |  0.985 | taactgttTTTATat
 V$TATA_01              |    10318 (-) |  1.000 |  0.886 | tttatattTTTATtt
 V$TATA_01              |    10323 (-) |  1.000 |  0.975 | atttttatTTTATag
 V$TATA_01              |    10332 (-) |  1.000 |  0.894 | ttatagttTTTATtg
 V$TATA_01              |    10391 (+) |  1.000 |  0.984 | atATAAAaatgaacg
 V$TATA_01              |    10445 (-) |  1.000 |  0.985 | acgtctctTTTATat
 V$TATA_01              |    10697 (-) |  1.000 |  0.860 | cacccgtgTTTATga
 V$TATA_01              |    10726 (-) |  1.000 |  0.897 | ctgtagctTTTATtg
 V$TATA_01              |    11401 (-) |  1.000 |  0.881 | tgtacgcaTTTATtc
 V$TATA_01              |    11464 (-) |  1.000 |  0.884 | tgaaatttTTTATtt
 V$CAAT_01              |      108 (+) |  0.950 |  0.927 | ggtggCCAGTga
 V$CAAT_01              |     1022 (-) |  1.000 |  0.938 | tgATTGGcagtt
 V$CAAT_01              |     5088 (-) |  0.950 |  0.938 | tgACTGGtttgg
 V$CAAT_01              |     6439 (+) |  0.950 |  0.923 | tcaacCCAGTca
 V$CAAT_01              |    11682 (+) |  1.000 |  0.938 | aaagaCCAATaa
 V$CAAT_01              |    11894 (+) |  1.000 |  0.923 | ctcaaCCAATag
 V$CAAT_01              |    11929 (-) |  1.000 |  0.950 | ccATTGGctgaa
 V$GC_01                |     1487 (+) |  0.956 |  0.907 | agagGGAGGggggg
 V$GC_01                |     1491 (+) |  0.935 |  0.884 | ggagGGGGGgggga
 V$GC_01                |     1492 (+) |  0.935 |  0.906 | gaggGGGGGgggag
 V$GC_01                |     1493 (+) |  0.935 |  0.903 | agggGGGGGggagg
 V$GC_01                |     1495 (+) |  0.935 |  0.876 | ggggGGGGGaggga
 V$GC_01                |     1498 (+) |  0.956 |  0.879 | ggggGGAGGgaggg
 V$GC_01                |     1870 (+) |  0.956 |  0.876 | gaagGGAGGatctg
 V$GC_01                |     3037 (-) |  0.954 |  0.896 | ccgctCCACCcggg
 V$GC_01                |     5893 (-) |  1.000 |  0.939 | ggggcCCGCCccta
 V$GC_01                |     9617 (+) |  0.956 |  0.874 | ggtgGGAGGatcgg
 V$GC_01                |     9683 (+) |  0.935 |  0.870 | gaggGGGGGtggtg
 V$GC_01                |     9686 (+) |  0.954 |  0.885 | ggggGGTGGtggtg
 V$GC_01                |    11845 (+) |  0.954 |  0.931 | ggggGGTGGggtat
 V$GC_01                |    11870 (+) |  0.956 |  0.919 | cgggGGAGGgactt
 V$HLF_01               |     3439 (-) |  1.000 |  0.896 | cttagGTAAC
 V$HLF_01               |     6575 (+) |  0.892 |  0.885 | GTTATgcaaa
 V$HLF_01               |     8008 (-) |  1.000 |  0.893 | ttggtGTAAC
 V$OLF1_01              |     1327 (+) |  1.000 |  0.882 | tctcacTCCCCagggcttaagg
 V$STAF_01              |     6631 (+) |  1.000 |  0.833 | ggcACCCAgaaggcacctcagt
 V$STAF_02              |     5502 (+) |  1.000 |  0.897 | tgcTCCCAggtttccctgcct
 I$CROC_01              |      846 (+) |  1.000 |  0.952 | ttaaaTAAATacgatc
 I$CROC_01              |     1891 (-) |  1.000 |  0.991 | ttttatATTTAtttta
 I$CROC_01              |     2358 (-) |  1.000 |  0.966 | acttgtATTTAttttg
 I$CROC_01              |     4002 (+) |  1.000 |  0.949 | aacgaTAAATaaatat
 I$CROC_01              |     4006 (+) |  1.000 |  0.983 | ataaaTAAATattctg
 I$CROC_01              |     9424 (+) |  1.000 |  0.928 | tcccaTAAATaacagg
 V$XFD1_01              |      709 (-) |  1.000 |  0.864 | gatctcTTTACaga
 V$XFD1_01              |      843 (+) |  0.917 |  0.874 | aagTTAAAtaaata
 V$XFD1_01              |      847 (+) |  0.959 |  0.920 | taaATAAAtacgat
 V$XFD1_01              |      958 (-) |  1.000 |  0.930 | caaataTTTACagg
 V$XFD1_01              |     1892 (-) |  0.959 |  0.914 | tttataTTTATttt
 V$XFD1_01              |     2359 (-) |  0.959 |  0.914 | cttgtaTTTATttt
 V$XFD1_01              |     2572 (-) |  1.000 |  0.906 | taagtaTTTACaac
 V$XFD1_01              |     3713 (-) |  1.000 |  0.923 | tcaataTTTACggg
 V$XFD1_01              |     4003 (+) |  0.959 |  0.864 | acgATAAAtaaata
 V$XFD1_01              |     4007 (+) |  0.959 |  0.927 | taaATAAAtattct
 V$XFD1_01              |     4780 (+) |  0.959 |  0.859 | tggATAAAgattgc
 V$XFD1_01              |     5792 (+) |  0.917 |  0.887 | taaTTAAAtacaaa
 V$XFD1_01              |     6669 (-) |  0.917 |  0.894 | attttaTTTAGctt
 V$XFD1_01              |     6822 (-) |  0.959 |  0.880 | ccctttTTTATgtg
 V$XFD1_01              |     6833 (-) |  1.000 |  0.890 | gtgctaTTTACtgc
 V$XFD1_01              |     8634 (-) |  0.917 |  0.859 | agcttaTTTAAgaa
 V$XFD1_01              |     9425 (+) |  0.959 |  0.883 | cccATAAAtaacag
 V$XFD1_01              |    10302 (-) |  0.917 |  0.867 | acatttTTTAActg
 V$XFD1_01              |    10312 (-) |  0.959 |  0.880 | actgttTTTATatt
 V$XFD1_01              |    10390 (+) |  0.959 |  0.874 | catATAAAaatgaa
 V$XFD1_01              |    10699 (-) |  0.959 |  0.859 | cccgtgTTTATgaa
 V$XFD1_01              |    11420 (-) |  0.917 |  0.867 | tttctaTTTAGcta
 V$XFD1_01              |    11466 (-) |  0.959 |  0.894 | aaatttTTTATttg
 V$XFD2_01              |       77 (-) |  0.781 |  0.839 | ttgatgTTGATagg
 V$XFD2_01              |      603 (+) |  0.877 |  0.898 | tttTTAAAcatcct
 V$XFD2_01              |      634 (+) |  0.877 |  0.911 | tttTTAAAcattta
 V$XFD2_01              |      847 (+) |  1.000 |  0.868 | taaATAAAtacgat
 V$XFD2_01              |      958 (-) |  0.901 |  0.848 | caaataTTTACagg
 V$XFD2_01              |     1892 (-) |  1.000 |  0.908 | tttataTTTATttt
 V$XFD2_01              |     2359 (-) |  1.000 |  0.882 | cttgtaTTTATttt
 V$XFD2_01              |     2897 (-) |  1.000 |  0.837 | atctttTTTATcca
 V$XFD2_01              |     4003 (+) |  1.000 |  0.874 | acgATAAAtaaata
 V$XFD2_01              |     4007 (+) |  1.000 |  0.889 | taaATAAAtattct
 V$XFD2_01              |     4780 (+) |  1.000 |  0.839 | tggATAAAgattgc
 V$XFD2_01              |     5645 (+) |  1.000 |  0.872 | aaaATAAAaagaag
 V$XFD2_01              |     6822 (-) |  1.000 |  0.839 | ccctttTTTATgtg
 V$XFD2_01              |     7428 (-) |  0.781 |  0.848 | tatttgTTTTTatt
 V$XFD2_01              |     7430 (-) |  1.000 |  0.872 | tttgttTTTATttt
 V$XFD2_01              |     7798 (+) |  1.000 |  0.858 | aagATAAAgaacaa
 V$XFD2_01              |     7891 (-) |  1.000 |  0.871 | ttggttTTTATttt
 V$XFD2_01              |     7937 (-) |  0.877 |  0.873 | tgtgtgTTTAGttt
 V$XFD2_01              |     8930 (+) |  1.000 |  0.840 | agtATAAActaaag
 V$XFD2_01              |     9425 (+) |  1.000 |  0.854 | cccATAAAtaacag
 V$XFD2_01              |    10312 (-) |  1.000 |  0.886 | actgttTTTATatt
 V$XFD2_01              |    10320 (-) |  1.000 |  0.892 | tatattTTTATttt
 V$XFD2_01              |    10334 (-) |  1.000 |  0.858 | atagttTTTATtgt
 V$XFD2_01              |    10390 (+) |  1.000 |  0.904 | catATAAAaatgaa
 V$XFD2_01              |    10699 (-) |  1.000 |  0.914 | cccgtgTTTATgaa
 V$XFD2_01              |    11096 (-) |  0.877 |  0.892 | ccactgTTTAAaga
 V$XFD2_01              |    11466 (-) |  1.000 |  0.859 | aaatttTTTATttg
 V$XFD3_01              |       30 (+) |  0.917 |  0.913 | tgtGTGAAcaactt
 V$XFD3_01              |      482 (+) |  0.959 |  0.852 | caaGTCAAcattgc
 V$XFD3_01              |     1843 (+) |  0.959 |  0.845 | gtcGTCAAcacaat
 V$XFD3_01              |     4215 (+) |  0.917 |  0.861 | tcaGTTAAaaaaat
 V$XFD3_01              |     4534 (+) |  0.959 |  0.881 | tgcGTCAAcagcct
 V$XFD3_01              |    10131 (+) |  0.917 |  0.849 | ttaGTTAAgaaatt
 V$XFD3_01              |    10660 (+) |  0.959 |  0.858 | aatGTCAAcaggag
 V$XFD3_01              |    11051 (-) |  0.917 |  0.870 | cctttgTTAACgtt
 V$XFD3_01              |    11653 (-) |  0.917 |  0.869 | gtactgTTAACaca
 V$XFD3_01              |    11655 (+) |  0.917 |  0.858 | actGTTAAcacaat
 V$XFD3_01              |    11759 (+) |  0.917 |  0.850 | agaGTTAAcaggat
 I$GCM_01               |     8442 (+) |  1.000 |  0.995 | caacCCGCAtcct
 V$AML1_01              |      936 (-) |  1.000 |  1.000 | ACCACa
 V$AML1_01              |     3641 (-) |  1.000 |  1.000 | ACCACa
 V$AML1_01              |     4145 (+) |  1.000 |  1.000 | tGTGGT
 V$AML1_01              |     4441 (-) |  1.000 |  1.000 | ACCACa
 V$AML1_01              |     4572 (+) |  0.949 |  0.956 | tGCGGT
 V$AML1_01              |     5049 (+) |  1.000 |  1.000 | tGTGGT
 V$AML1_01              |     5136 (+) |  0.949 |  0.956 | tGCGGT
 V$AML1_01              |     5256 (+) |  1.000 |  1.000 | tGTGGT
 V$AML1_01              |     7112 (-) |  1.000 |  1.000 | ACCACa
 V$AML1_01              |     8742 (+) |  1.000 |  1.000 | tGTGGT
 V$AML1_01              |     8898 (-) |  1.000 |  1.000 | ACCACa
 V$AML1_01              |     8975 (+) |  1.000 |  1.000 | tGTGGT
 V$AML1_01              |     9400 (+) |  1.000 |  1.000 | tGTGGT
 V$AML1_01              |     9575 (+) |  1.000 |  1.000 | tGTGGT
 V$AML1_01              |    10955 (+) |  0.949 |  0.956 | tGCGGT
 V$AML1_01              |    11256 (+) |  1.000 |  1.000 | tGTGGT
 V$AML1_01              |    11494 (+) |  0.949 |  0.956 | tGCGGT
 V$P53_02               |     1346 (+) |  0.982 |  0.969 | aggCTTGCct
 V$P53_02               |     4206 (+) |  0.982 |  0.969 | aggCTTGCct
 V$P53_02               |     4401 (-) |  0.965 |  0.972 | agACAGGtca
 F$MAT1MC_01            |     1034 (-) |  1.000 |  0.886 | gaatcaaCAAAGcagcaa
 F$MAT1MC_01            |     7802 (-) |  0.800 |  0.867 | taaagaaCAACGacaact
 F$MAT1MC_01            |    11046 (+) |  1.000 |  0.885 | tggttcCTTTGttaacgt
 F$MAT1MC_02            |     1850 (-) |  1.000 |  0.960 | acACAATaga
 F$MAT1MC_02            |     7332 (-) |  1.000 |  0.975 | gaACAATaga
 F$MAT1MC_02            |    10340 (+) |  1.000 |  0.957 | tttATTGTtt
 V$LMO2COM_01           |     1785 (-) |  1.000 |  0.981 | gagcACCTGcca
 V$LMO2COM_01           |     4338 (+) |  1.000 |  0.975 | atcCAGGTggtg
 V$LMO2COM_01           |     7390 (+) |  1.000 |  0.973 | gtcCAGGTggta
 V$LMO2COM_01           |     8503 (+) |  1.000 |  0.986 | ggaCAGGTgcgg
 V$LMO2COM_01           |     8767 (-) |  1.000 |  0.985 | cagcACCTGgga
 V$LMO2COM_01           |     8968 (+) |  1.000 |  0.973 | aacCAGGTgtgg
 V$LMO2COM_01           |    11960 (-) |  1.000 |  0.986 | ctgcACCTGagc
 V$LMO2COM_02           |       83 (+) |  0.985 |  0.980 | tTGATAggg
 V$LMO2COM_02           |     7152 (-) |  1.000 |  0.993 | ccgTATCTc
 V$RFX1_01              |      484 (+) |  1.000 |  0.876 | agtcaacattGCAACat
 V$RFX1_01              |      741 (-) |  1.000 |  0.879 | tgGTTGCtgggaattga
 V$RFX1_01              |     4816 (-) |  0.992 |  0.917 | ttGTTACcaggcggggt
 V$RFX1_01              |     4875 (+) |  0.982 |  0.881 | gcaaagctctGGAACat
 V$RFX1_01              |     4895 (-) |  0.982 |  0.911 | atGTTCCttggccaagt
 V$RFX1_01              |     5224 (+) |  0.982 |  0.899 | gcggagactgGGAACga
 V$RFX1_01              |     5509 (-) |  0.982 |  0.898 | agGTTTCcctgcctttc
 V$RFX1_01              |     5825 (+) |  0.982 |  0.916 | gtggcactgtGAAACaa
 V$RFX1_01              |     5861 (-) |  0.982 |  0.875 | tgGTTTCccatggacca
 V$RFX1_01              |     6967 (+) |  0.982 |  0.869 | tggatggaaaGGAACga
 V$RFX1_01              |     8069 (+) |  0.982 |  0.867 | tggtattgcaGAAACtt
 V$RFX1_01              |     8431 (+) |  1.000 |  0.905 | ctagagctttGCAACcc
 V$RFX1_01              |     8581 (+) |  1.000 |  0.868 | tggggcaaagGCAACat
 V$RFX1_01              |     9160 (-) |  0.982 |  0.904 | gaGTTCCtaagatgcat
 V$RFX1_01              |     9509 (-) |  0.982 |  0.870 | aaGTTTCcccatgtcca
 V$RFX1_01              |     9564 (-) |  0.982 |  0.883 | cgGTTTCtgggtgtggt
 V$RFX1_01              |    10432 (+) |  1.000 |  0.908 | tcttcgcaatGCAACgt
 V$RFX1_01              |    10530 (+) |  1.000 |  0.925 | aggaggccgtGCAACtc
 V$RFX1_01              |    10683 (+) |  1.000 |  0.877 | caggactctgGCAACac
 V$RFX1_01              |    10743 (-) |  0.982 |  0.889 | ggGTTTCagtgatccgt
 V$RFX1_01              |    11046 (-) |  0.982 |  0.905 | tgGTTCCtttgttaacg
 V$RFX1_02              |      163 (-) |  0.982 |  0.898 | ccGTTCCcaatgctggca
 V$RFX1_02              |      483 (+) |  1.000 |  0.903 | aagtcaacattGCAACat
 V$RFX1_02              |      860 (-) |  1.000 |  0.823 | tcGTTGCccttagaaatg
 V$RFX1_02              |      936 (+) |  0.982 |  0.823 | accacaagttaGGAACaa
 V$RFX1_02              |     1133 (-) |  0.982 |  0.828 | gtGTTCCtaaaaccgtta
 V$RFX1_02              |     1145 (-) |  0.992 |  0.825 | ccGTTACtttatgtagtt
 V$RFX1_02              |     1220 (-) |  0.982 |  0.833 | gaGTTTCtgatgactgct
 V$RFX1_02              |     2395 (-) |  1.000 |  0.838 | gaGTTGCtttccttaaaa
 V$RFX1_02              |     2549 (-) |  0.982 |  0.891 | agGTTTCtgttgtgaaat
 V$RFX1_02              |     2681 (-) |  1.000 |  0.824 | ccGTTGCatcctggtcac
 V$RFX1_02              |     3424 (-) |  1.000 |  0.896 | tgGTTGCttaattgactt
 V$RFX1_02              |     3433 (+) |  0.992 |  0.901 | aattgacttagGTAACag
 V$RFX1_02              |     3602 (-) |  0.982 |  0.870 | ggGTTTCtgcagttttca
 V$RFX1_02              |     3652 (+) |  0.992 |  0.849 | gaatcagtaaaGTAACac
 V$RFX1_02              |     3986 (+) |  0.982 |  0.834 | caccatctcatGAAACaa
 V$RFX1_02              |     4824 (+) |  0.982 |  0.860 | aggcggggtagGGAACga
 V$RFX1_02              |     4895 (-) |  0.982 |  0.845 | atGTTCCttggccaagtg
 V$RFX1_02              |     5114 (+) |  0.982 |  0.840 | gtgctcaaaagGAAACag
 V$RFX1_02              |     5223 (+) |  0.982 |  0.829 | agcggagactgGGAACga
 V$RFX1_02              |     5509 (-) |  0.982 |  0.829 | agGTTTCcctgcctttcc
 V$RFX1_02              |     5602 (+) |  0.982 |  0.905 | atataacacaaGAAACca
 V$RFX1_02              |     5861 (-) |  0.982 |  0.897 | tgGTTTCccatggaccat
 V$RFX1_02              |     5915 (-) |  0.982 |  0.909 | ttGTTTCcccagcgagac
 V$RFX1_02              |     6088 (-) |  0.982 |  0.819 | gaGTTCCtgtgtggatca
 V$RFX1_02              |     6177 (-) |  0.982 |  0.934 | ggGTTCCcagagacaccc
 V$RFX1_02              |     6215 (-) |  0.982 |  0.883 | agGTTTCtcacgctctgc
 V$RFX1_02              |     6564 (-) |  1.000 |  0.940 | tgGTTGCcacagttatgc
 V$RFX1_02              |     6966 (+) |  0.982 |  0.838 | ctggatggaaaGGAACga
 V$RFX1_02              |     7017 (-) |  0.982 |  0.844 | atGTTTCctgcatcagct
 V$RFX1_02              |     7170 (-) |  1.000 |  0.887 | gcGTTGCagatggtcccg
 V$RFX1_02              |     7320 (+) |  0.982 |  0.850 | aatgtacgtctGGAACaa
 V$RFX1_02              |     7529 (-) |  0.992 |  0.841 | aaGTTACagttggttgtg
 V$RFX1_02              |     7556 (+) |  0.982 |  0.820 | tgtagatgctgGAAACca
 V$RFX1_02              |     8068 (+) |  0.982 |  0.854 | ctggtattgcaGAAACtt
 V$RFX1_02              |     8199 (-) |  0.982 |  0.873 | ctGTTTCccctctgacct
 V$RFX1_02              |     8580 (+) |  1.000 |  0.955 | atggggcaaagGCAACat
 V$RFX1_02              |     8932 (+) |  1.000 |  0.883 | tataaactaaaGCAACtt
 V$RFX1_02              |     9509 (-) |  0.982 |  0.836 | aaGTTTCcccatgtccaa
 V$RFX1_02              |     9804 (+) |  0.992 |  0.908 | acatcacataaGTAACtt
 V$RFX1_02              |     9970 (-) |  0.982 |  0.904 | tgGTTCCtatggggatca
 V$RFX1_02              |    10379 (-) |  1.000 |  0.831 | atGTTGCaatccatataa
 V$RFX1_02              |    10529 (+) |  1.000 |  0.853 | taggaggccgtGCAACtc
 V$RFX1_02              |    10682 (+) |  1.000 |  0.912 | gcaggactctgGCAACac
 V$RFX1_02              |    11046 (-) |  0.982 |  0.891 | tgGTTCCtttgttaacgt
 V$RFX1_02              |    11070 (-) |  0.992 |  0.827 | caGTTACaagctgctctg
 V$RFX1_02              |    11190 (-) |  0.982 |  0.845 | ttGTTTCttgattgatta
 I$ZESTE_Q2             |     2012 (+) |  1.000 |  0.946 | tctcctGAGTGctggg
 I$ZESTE_Q2             |     5106 (+) |  1.000 |  0.946 | atttgtGAGTGctcaa
 I$ZESTE_Q2             |     6619 (+) |  1.000 |  0.934 | ctccgtGAGTGgggca
 I$ZESTE_Q2             |     7078 (+) |  1.000 |  0.952 | gtgtatGAGTGctttg
 I$ZESTE_Q2             |     7468 (+) |  1.000 |  0.994 | ggatttGAGTGtgcta
 I$ZESTE_Q2             |     8019 (+) |  1.000 |  0.947 | tttagtGAGTGtcaga
 I$ZESTE_Q2             |     8512 (-) |  1.000 |  0.937 | cgggaCACTCacagat
 I$ZESTE_Q2             |     9187 (-) |  1.000 |  0.989 | gagacCACTCaagaga
 I$ZESTE_Q2             |    11131 (-) |  1.000 |  0.950 | cgctgCACTCagtttt
 V$TCF11MAFG_01         |      125 (-) |  0.941 |  0.926 | gctaactgctcaGTCAAtccag
 V$TCF11MAFG_01         |      525 (-) |  0.741 |  0.740 | taaaaatgatggGTGATgcgct
 V$TCF11MAFG_01         |      580 (+) |  0.784 |  0.730 | acctgTTGAAttaacagactta
 V$TCF11MAFG_01         |      723 (+) |  0.833 |  0.764 | tggttGTGAGccaccacgtggt
 V$TCF11MAFG_01         |      790 (-) |  0.741 |  0.753 | cttaaccgctgaGCCATttctc
 V$TCF11MAFG_01         |     1027 (+) |  0.784 |  0.760 | ggcagTTGAAtcaacaaagcag
 V$TCF11MAFG_01         |     1228 (-) |  0.741 |  0.779 | gatgactgctttGACATcaggg
 V$TCF11MAFG_01         |     2325 (-) |  0.704 |  0.779 | cagtcttgctatGTGACcctac
 V$TCF11MAFG_01         |     2455 (+) |  0.741 |  0.764 | gcgctATGGCctagcaagcgcg
 V$TCF11MAFG_01         |     2813 (-) |  0.682 |  0.728 | acaccgtgctctGTCCAgttgt
 V$TCF11MAFG_01         |     2970 (-) |  0.741 |  0.747 | ggcagatgcgcaGGCATctact
 V$TCF11MAFG_01         |     3064 (-) |  0.963 |  0.792 | tggtatagctagGTCACagggt
 V$TCF11MAFG_01         |     3366 (-) |  0.844 |  0.738 | ctgaatagcctaATCATatggg
 V$TCF11MAFG_01         |     3480 (+) |  0.870 |  0.744 | tgcctATGAGgcagaatagctt
 V$TCF11MAFG_01         |     3700 (-) |  0.784 |  0.817 | aagagatgcttgATCAAtattt
 V$TCF11MAFG_01         |     3744 (-) |  1.000 |  0.771 | tctacatttttaGTCATtctta
 V$TCF11MAFG_01         |     3834 (-) |  0.870 |  0.719 | taaatttccattCTCATaaaat
 V$TCF11MAFG_01         |     3926 (-) |  0.963 |  0.755 | attacattatcaGTCACttgtt
 V$TCF11MAFG_01         |     3938 (-) |  0.777 |  0.758 | gtcacttgttcaTTCAGccatc
 V$TCF11MAFG_01         |     4190 (-) |  0.784 |  0.728 | gaaggctgcaagTTCAAggctt
 V$TCF11MAFG_01         |     4462 (+) |  0.933 |  0.816 | tcacaCTGACtgaccagcattt
 V$TCF11MAFG_01         |     4843 (+) |  0.803 |  0.715 | tgatcCTGAGacttcactgagg
 V$TCF11MAFG_01         |     5307 (-) |  0.844 |  0.774 | caaaatggcttcTTCATcggtt
 V$TCF11MAFG_01         |     5353 (+) |  0.941 |  0.812 | cctctTTGACaaaacacacggg
 V$TCF11MAFG_01         |     6289 (+) |  1.000 |  0.911 | tgatgATGACtgagcagggcac
 V$TCF11MAFG_01         |     6975 (+) |  0.741 |  0.718 | aaggaACGACttagctggtgag
 V$TCF11MAFG_01         |     7600 (-) |  0.741 |  0.847 | ctgaactgctgaGCCATctctc
 V$TCF11MAFG_01         |     7666 (-) |  0.833 |  0.760 | caggcatggtggCTCACagctg
 V$TCF11MAFG_01         |     8265 (+) |  0.777 |  0.763 | ttgacCTGATgatgcagctgcc
 V$TCF11MAFG_01         |     8268 (+) |  0.844 |  0.741 | acctgATGATgcagctgccctg
 V$TCF11MAFG_01         |     8315 (-) |  0.933 |  0.795 | tgcagcttctgcGTCAGcgcca
 V$TCF11MAFG_01         |     9313 (-) |  0.933 |  0.733 | gggaggcgttggGTCAGagcct
 V$TCF11MAFG_01         |     9543 (-) |  0.704 |  0.718 | aagtcctgcgtaGTCGCctgtc
 V$TCF11MAFG_01         |     9628 (-) |  0.933 |  0.733 | cgggagttcaagGTCAGcttgg
 V$TCF11MAFG_01         |     9836 (-) |  0.933 |  0.716 | gataattttaaaGTCAGgcagg
 V$TCF11MAFG_01         |    10027 (-) |  0.963 |  0.779 | cgtagtttgtgaGTCACcgtgt
 V$TCF11MAFG_01         |    10628 (+) |  0.963 |  0.806 | agaaaGTGACtgaggaagacac
 V$TCF11MAFG_01         |    11156 (+) |  0.844 |  0.792 | tgaaaATGAAgctgcagagatc
 V$TCF11MAFG_01         |    11327 (+) |  1.000 |  0.790 | tgatgATGACgatgtaaatgcc
 V$TCF11MAFG_01         |    11447 (-) |  0.777 |  0.762 | ctattttggtgaATCAGtgaaa
 V$TCF11_01             |       49 (+) |  1.000 |  0.986 | GTCATtacttggg
 V$TCF11_01             |      464 (-) |  0.887 |  0.883 | tggcttatTTGAC
 V$TCF11_01             |      485 (+) |  0.887 |  0.887 | GTCAAcattgcaa
 V$TCF11_01             |      522 (-) |  0.887 |  0.887 | ttttaaaaATGAT
 V$TCF11_01             |      616 (-) |  1.000 |  0.992 | tgtcgtacATGAC
 V$TCF11_01             |      945 (-) |  0.887 |  0.887 | taggaacaATGAT
 V$TCF11_01             |     1082 (+) |  1.000 |  0.999 | GTCATtttggtca
 V$TCF11_01             |     1091 (+) |  0.887 |  0.882 | GTCAActaaaatt
 V$TCF11_01             |     1221 (-) |  1.000 |  0.983 | agtttctgATGAC
 V$TCF11_01             |     1259 (+) |  1.000 |  0.995 | GTCATcatccgtg
 V$TCF11_01             |     1275 (-) |  1.000 |  0.985 | actctgggATGAC
 V$TCF11_01             |     1358 (+) |  0.905 |  0.892 | GTCACctgatgct
 V$TCF11_01             |     1450 (+) |  0.905 |  0.902 | GTCACtgagccgg
 V$TCF11_01             |     1729 (+) |  0.883 |  0.882 | CTCATcctgaact
 V$TCF11_01             |     2329 (-) |  0.905 |  0.902 | cttgctatGTGAC
 V$TCF11_01             |     2659 (-) |  1.000 |  0.995 | gcactttgATGAC
 V$TCF11_01             |     2694 (+) |  0.905 |  0.902 | GTCACactcttct
 V$TCF11_01             |     2957 (-) |  0.905 |  0.906 | cgaatacaGTGAC
 V$TCF11_01             |     3076 (+) |  0.905 |  0.891 | GTCACagggtgat
 V$TCF11_01             |     3273 (-) |  0.887 |  0.888 | atgccattATGAT
 V$TCF11_01             |     3427 (-) |  0.887 |  0.884 | ttgcttaaTTGAC
 V$TCF11_01             |     3468 (+) |  0.883 |  0.883 | CTCATgatttact
 V$TCF11_01             |     3718 (-) |  0.905 |  0.891 | atttacggGTGAC
 V$TCF11_01             |     3756 (+) |  1.000 |  0.997 | GTCATtcttaaaa
 V$TCF11_01             |     3882 (-) |  0.887 |  0.883 | caagctccTTGAC
 V$TCF11_01             |     3938 (+) |  0.905 |  0.893 | GTCACttgttcat
 V$TCF11_01             |     3970 (-) |  0.887 |  0.885 | ctggctgtATGAT
 V$TCF11_01             |     4293 (-) |  0.887 |  0.886 | ccctaaatTTGAC
 V$TCF11_01             |     4325 (-) |  0.905 |  0.891 | tgggtctgGTGAC
 V$TCF11_01             |     4932 (+) |  0.887 |  0.883 | ATCATggagactg
 V$TCF11_01             |     5140 (+) |  0.887 |  0.887 | GTCAAcctaggca
 V$TCF11_01             |     5169 (-) |  0.905 |  0.892 | tttcacttGTGAC
 V$TCF11_01             |     5260 (+) |  0.905 |  0.900 | GTCACagtcatcc
 V$TCF11_01             |     5266 (+) |  1.000 |  0.999 | GTCATcctgggcc
 V$TCF11_01             |     5350 (-) |  0.887 |  0.883 | tcccctctTTGAC
 V$TCF11_01             |     6046 (-) |  0.905 |  0.892 | gcagccctGTGAC
 V$TCF11_01             |     6286 (-) |  1.000 |  0.994 | ctctgatgATGAC
 V$TCF11_01             |     6408 (-) |  1.000 |  0.998 | cgctcagaATGAC
 V$TCF11_01             |     6447 (+) |  1.000 |  0.983 | GTCATggcaaact
 V$TCF11_01             |     6560 (+) |  1.000 |  0.997 | GTCATggttgcca
 V$TCF11_01             |     7037 (-) |  0.887 |  0.883 | agagttagTTGAC
 V$TCF11_01             |     7886 (+) |  1.000 |  0.986 | GTCATttggtttt
 V$TCF11_01             |     8106 (+) |  0.905 |  0.899 | GTCACacactctc
 V$TCF11_01             |     9293 (+) |  0.882 |  0.884 | GTCAGcttgtgtg
 V$TCF11_01             |     9640 (+) |  0.882 |  0.883 | GTCAGcttgggct
 V$TCF11_01             |     9725 (-) |  0.887 |  0.883 | ctctttgtATGAT
 V$TCF11_01             |     9770 (+) |  1.000 |  0.985 | GTCATgccataga
 V$TCF11_01             |     9865 (-) |  0.883 |  0.883 | aaagaagaATGAG
 V$TCF11_01             |    10039 (+) |  0.905 |  0.906 | GTCACcgtgtggg
 V$TCF11_01             |    10246 (+) |  0.882 |  0.883 | GTCAGgcttgtgc
 V$TCF11_01             |    10506 (+) |  0.887 |  0.884 | GTCAAttatggct
 V$TCF11_01             |    10625 (-) |  0.905 |  0.903 | tgtagaaaGTGAC
 V$TCF11_01             |    11309 (-) |  0.905 |  0.906 | cgactacgGTGAC
 V$TCF11_01             |    11318 (-) |  0.887 |  0.884 | tgacgacgATGAT
 V$TCF11_01             |    11321 (-) |  0.887 |  0.886 | cgacgatgATGAT
 V$TCF11_01             |    11324 (-) |  1.000 |  0.994 | cgatgatgATGAC
 V$TCF11_01             |    11357 (-) |  0.887 |  0.885 | acgagagcATGAT
 V$TCF11_01             |    11705 (+) |  0.905 |  0.892 | GTCACcccaactg
 V$TCF11_01             |    11741 (-) |  1.000 |  0.987 | ctcaccaaATGAC
 V$NFY_01               |     1018 (-) |  1.000 |  0.959 | tatgtgATTGGcagtt
 V$NFY_01               |     3278 (-) |  1.000 |  0.934 | attatgATTGGgatga
 V$NFY_01               |    11682 (+) |  1.000 |  0.945 | aaagaCCAATaaagtt
 V$NFY_01               |    11894 (+) |  1.000 |  0.941 | ctcaaCCAATagcacg
 V$NFY_01               |    11925 (-) |  1.000 |  0.974 | acgcccATTGGctgaa
 F$HAP234_01            |     1018 (-) |  1.000 |  0.956 | tatgtgATTGGcagtt
 F$HAP234_01            |    10731 (-) |  1.000 |  0.975 | gcttttATTGGggggt
 V$HFH3_01              |      212 (+) |  0.981 |  0.925 | tggTATTTttttt
 V$HFH3_01              |      214 (+) |  0.931 |  0.890 | gtaTTTTTttttt
 V$HFH3_01              |      228 (+) |  0.931 |  0.906 | tccTTTTTgtctt
 V$HFH3_01              |      505 (+) |  0.981 |  0.942 | ataTATTTgtctt
 V$HFH3_01              |      847 (-) |  0.981 |  0.976 | taaatAAATAcga
 V$HFH3_01              |      876 (-) |  1.000 |  0.915 | tgcacAAACAcga
 V$HFH3_01              |     1526 (+) |  1.000 |  0.932 | agcTGTTTttttg
 V$HFH3_01              |     1893 (+) |  0.981 |  0.966 | ttaTATTTatttt
 V$HFH3_01              |     2291 (+) |  0.931 |  0.908 | tagTTTTTgtgtg
 V$HFH3_01              |     2360 (+) |  0.981 |  0.966 | ttgTATTTatttt
 V$HFH3_01              |     2409 (-) |  1.000 |  0.938 | aaaaaAAACAaaa
 V$HFH3_01              |     2413 (-) |  0.931 |  0.934 | aaaacAAAAAatc
 V$HFH3_01              |     4007 (-) |  0.981 |  0.980 | taaatAAATAttc
 V$HFH3_01              |     4220 (-) |  0.981 |  0.930 | taaaaAAATAaat
 V$HFH3_01              |     4425 (-) |  0.931 |  0.896 | taaaaAAAAAaaa
 V$HFH3_01              |     4431 (-) |  0.931 |  0.891 | aaaaaAAAAAacc
 V$HFH3_01              |     4478 (+) |  0.931 |  0.891 | gcaTTTTTctttt
 V$HFH3_01              |     5102 (+) |  0.981 |  0.890 | tatTATTTgtgag
 V$HFH3_01              |     5434 (+) |  0.981 |  0.946 | cttTATTTgtatt
 V$HFH3_01              |     5645 (-) |  0.931 |  0.927 | aaaatAAAAAgaa
 V$HFH3_01              |     5717 (-) |  1.000 |  0.915 | cacaaAAACActa
 V$HFH3_01              |     5777 (-) |  0.981 |  0.894 | gagaaAAATAtga
 V$HFH3_01              |     5792 (-) |  0.981 |  0.893 | taattAAATAcaa
 V$HFH3_01              |     5798 (-) |  0.931 |  0.917 | aatacAAAAAaaa
 V$HFH3_01              |     5807 (-) |  0.981 |  0.928 | aaaaaAAATAgcc
 V$HFH3_01              |     6506 (-) |  0.981 |  0.893 | gccacAAATAaaa
 V$HFH3_01              |     6589 (-) |  0.981 |  0.961 | aaaacAAATAagg
 V$HFH3_01              |     6823 (+) |  0.931 |  0.898 | cctTTTTTatgtg
 V$HFH3_01              |     7047 (+) |  0.981 |  0.925 | gacTATTTttttt
 V$HFH3_01              |     7064 (+) |  1.000 |  0.914 | attTGTTTttgtt
 V$HFH3_01              |     7066 (+) |  0.931 |  0.929 | ttgTTTTTgtttg
 V$HFH3_01              |     7070 (+) |  1.000 |  0.974 | tttTGTTTgtgta
 V$HFH3_01              |     7425 (+) |  0.981 |  0.973 | gttTATTTgtttt
 V$HFH3_01              |     7429 (+) |  1.000 |  0.920 | attTGTTTttatt
 V$HFH3_01              |     7431 (+) |  0.931 |  0.928 | ttgTTTTTatttt
 V$HFH3_01              |     7771 (-) |  1.000 |  0.897 | tcaaaAAACAaaa
 V$HFH3_01              |     7780 (-) |  0.931 |  0.931 | aaaacAAAAAtta
 V$HFH3_01              |     7798 (-) |  0.931 |  0.905 | aagatAAAGAaca
 V$HFH3_01              |     7822 (-) |  1.000 |  0.979 | aaaacAAACAatt
 V$HFH3_01              |     7892 (+) |  0.931 |  0.930 | tggTTTTTatttt
 V$HFH3_01              |     7938 (+) |  1.000 |  0.901 | gtgTGTTTagttt
 V$HFH3_01              |     7969 (+) |  1.000 |  0.982 | agtTGTTTgtttt
 V$HFH3_01              |     8783 (-) |  0.931 |  0.902 | gagacAAAGAaga
 V$HFH3_01              |     8898 (-) |  1.000 |  0.908 | accacAAACAgat
 V$HFH3_01              |     9111 (-) |  0.931 |  0.937 | aaaacAAAAAacc
 V$HFH3_01              |     9425 (-) |  0.981 |  0.894 | cccatAAATAaca
 V$HFH3_01              |     9534 (-) |  1.000 |  0.921 | agaacAAACAagt
 V$HFH3_01              |     9723 (+) |  0.931 |  0.910 | atcTCTTTgtatg
 V$HFH3_01              |    10311 (+) |  1.000 |  0.928 | aacTGTTTttata
 V$HFH3_01              |    10313 (+) |  0.931 |  0.905 | ctgTTTTTatatt
 V$HFH3_01              |    10319 (+) |  0.981 |  0.910 | ttaTATTTttatt
 V$HFH3_01              |    10321 (+) |  0.931 |  0.925 | ataTTTTTatttt
 V$HFH3_01              |    10390 (-) |  0.931 |  0.912 | catatAAAAAtga
 V$HFH3_01              |    10700 (+) |  1.000 |  0.906 | ccgTGTTTatgaa
 V$HFH3_01              |    10911 (-) |  0.981 |  0.906 | tatgcAAATAata
 V$HFH3_01              |    11292 (-) |  0.981 |  0.920 | caaagAAATAata
 V$HFH3_01              |    11467 (+) |  0.931 |  0.921 | aatTTTTTatttg
 V$HFH3_01              |    11471 (+) |  0.981 |  0.969 | tttTATTTgtttt
 V$HFH3_01              |    11643 (+) |  0.981 |  0.910 | atgTATTTctgta
 V$FREAC2_01            |      601 (+) |  1.000 |  0.887 | acttttTAAACatcct
 V$FREAC2_01            |      632 (+) |  1.000 |  0.890 | ttttttTAAACattta
 V$FREAC2_01            |      958 (-) |  0.855 |  0.850 | caaatATTTAcaggac
 V$FREAC2_01            |     2572 (-) |  0.855 |  0.847 | taagtATTTAcaacaa
 V$FREAC2_01            |     3713 (-) |  0.855 |  0.856 | tcaatATTTAcgggtg
 V$FREAC2_01            |     7937 (-) |  1.000 |  0.915 | tgtgtGTTTAgttttg
 V$FREAC2_01            |    10699 (-) |  1.000 |  0.913 | cccgtGTTTAtgaaac
 V$FREAC2_01            |    11096 (-) |  1.000 |  0.886 | ccactGTTTAaagaac
 V$FREAC3_01            |     3713 (-) |  1.000 |  0.866 | tcaataTTTACgggtg
 V$FREAC4_01            |       28 (+) |  0.831 |  0.766 | tgtgtgTGAACaactt
 V$FREAC4_01            |      480 (+) |  0.840 |  0.802 | tacaagTCAACattgc
 V$FREAC4_01            |      579 (-) |  0.840 |  0.761 | tacctGTTGAattaac
 V$FREAC4_01            |      601 (+) |  1.000 |  0.765 | acttttTAAACatcct
 V$FREAC4_01            |      632 (+) |  1.000 |  0.780 | ttttttTAAACattta
 V$FREAC4_01            |      709 (-) |  0.792 |  0.781 | gatctCTTTAcagatg
 V$FREAC4_01            |     1031 (+) |  0.840 |  0.750 | gttgaaTCAACaaagc
 V$FREAC4_01            |     1049 (+) |  0.840 |  0.763 | caaaaaTCAACaactt
 V$FREAC4_01            |     1266 (-) |  0.792 |  0.808 | tccgtGTGTActctgg
 V$FREAC4_01            |     3290 (+) |  0.831 |  0.786 | atgaggTGAACatctc
 V$FREAC4_01            |     3450 (+) |  0.792 |  0.752 | gttaatAAAACacagg
 V$FREAC4_01            |     4076 (-) |  0.792 |  0.754 | aaaatGTATActatat
 V$FREAC4_01            |     4266 (-) |  0.792 |  0.850 | aggatGCTTAcctaag
 V$FREAC4_01            |     4532 (+) |  0.840 |  0.767 | aatgcgTCAACagcct
 V$FREAC4_01            |     5119 (+) |  0.792 |  0.832 | caaaagGAAACagatg
 V$FREAC4_01            |     5558 (+) |  0.792 |  0.753 | cactagAAAACaacca
 V$FREAC4_01            |     5912 (-) |  0.792 |  0.779 | agtttGTTTCcccagc
 V$FREAC4_01            |     6106 (-) |  0.840 |  0.785 | gtcctGTTGAccagag
 V$FREAC4_01            |     6122 (-) |  0.792 |  0.751 | ggcttGTTTTctcggc
 V$FREAC4_01            |     7820 (+) |  0.792 |  0.749 | ccaaaaCAAACaatta
 V$FREAC4_01            |     7937 (-) |  1.000 |  0.855 | tgtgtGTTTAgttttg
 V$FREAC4_01            |     8183 (-) |  0.792 |  0.772 | aacttGTTTGctctgc
 V$FREAC4_01            |     8384 (-) |  0.792 |  0.767 | gatctGTATAcctgaa
 V$FREAC4_01            |     9094 (-) |  0.792 |  0.814 | gctctGCTTAcaaaag
 V$FREAC4_01            |     9444 (-) |  1.000 |  0.765 | ccaagGTTTAccaatc
 V$FREAC4_01            |    10453 (+) |  0.840 |  0.759 | tttataTCAACaatgc
 V$FREAC4_01            |    10658 (+) |  0.840 |  0.869 | ctaatgTCAACaggag
 V$FREAC4_01            |    10699 (-) |  1.000 |  0.798 | cccgtGTTTAtgaaac
 V$FREAC4_01            |    11051 (-) |  0.831 |  0.809 | cctttGTTAAcgttgt
 V$FREAC4_01            |    11096 (-) |  1.000 |  0.812 | ccactGTTTAaagaac
 V$FREAC4_01            |    11653 (+) |  0.831 |  0.787 | gtactgTTAACacaat
 V$FREAC4_01            |    11653 (-) |  0.831 |  0.801 | gtactGTTAAcacaat
 V$FREAC4_01            |    11757 (+) |  0.831 |  0.767 | aaagagTTAACaggat
 V$FREAC7_01            |       71 (-) |  0.814 |  0.848 | ctgttgTTGATgttga
 V$FREAC7_01            |      211 (-) |  0.832 |  0.832 | ctggtaTTTTTttttt
 V$FREAC7_01            |      504 (-) |  0.848 |  0.840 | tatataTTTGTcttct
 V$FREAC7_01            |      565 (+) |  1.000 |  0.858 | aggagATAAAcgtcta
 V$FREAC7_01            |      601 (+) |  0.832 |  0.836 | actttTTAAAcatcct
 V$FREAC7_01            |      632 (+) |  0.832 |  0.845 | tttttTTAAAcattta
 V$FREAC7_01            |      638 (-) |  1.000 |  0.835 | taaacaTTTATtcatt
 V$FREAC7_01            |      646 (-) |  1.000 |  0.832 | tattcaTTTATtatat
 V$FREAC7_01            |      841 (+) |  0.832 |  0.830 | acaagTTAAAtaaata
 V$FREAC7_01            |      845 (+) |  1.000 |  0.960 | gttaaATAAAtacgat
 V$FREAC7_01            |      874 (+) |  0.848 |  0.862 | aatgcACAAAcacgaa
 V$FREAC7_01            |     1049 (+) |  0.814 |  0.833 | caaaaATCAAcaactt
 V$FREAC7_01            |     1525 (-) |  0.832 |  0.847 | gagctgTTTTTttgtt
 V$FREAC7_01            |     1892 (-) |  1.000 |  0.965 | tttataTTTATtttat
 V$FREAC7_01            |     2359 (-) |  1.000 |  0.954 | cttgtaTTTATtttgc
 V$FREAC7_01            |     2407 (+) |  0.832 |  0.862 | ttaaaAAAAAcaaaaa
 V$FREAC7_01            |     2572 (-) |  0.848 |  0.833 | taagtaTTTACaacaa
 V$FREAC7_01            |     2897 (-) |  1.000 |  0.918 | atctttTTTATccaca
 V$FREAC7_01            |     3620 (-) |  1.000 |  0.843 | aatgcgTTTATaatag
 V$FREAC7_01            |     3713 (-) |  0.848 |  0.830 | tcaataTTTACgggtg
 V$FREAC7_01            |     3805 (+) |  0.832 |  0.839 | atagaAAAAAcatcgt
 V$FREAC7_01            |     4001 (+) |  1.000 |  0.943 | caacgATAAAtaaata
 V$FREAC7_01            |     4005 (+) |  1.000 |  0.959 | gataaATAAAtattct
 V$FREAC7_01            |     4218 (+) |  0.832 |  0.831 | gttaaAAAAAtaaatt
 V$FREAC7_01            |     4222 (+) |  1.000 |  0.837 | aaaaaATAAAttctca
 V$FREAC7_01            |     4491 (+) |  0.832 |  0.842 | gaacaAAAAAcaaaac
 V$FREAC7_01            |     4778 (+) |  1.000 |  0.913 | tctggATAAAgattgc
 V$FREAC7_01            |     5101 (-) |  0.848 |  0.831 | ttattaTTTGTgagtg
 V$FREAC7_01            |     5433 (-) |  0.848 |  0.843 | actttaTTTGTattgc
 V$FREAC7_01            |     5632 (+) |  1.000 |  0.904 | ctgggATAAAgacaaa
 V$FREAC7_01            |     5643 (+) |  1.000 |  0.921 | acaaaATAAAaagaag
 V$FREAC7_01            |     5715 (+) |  0.832 |  0.845 | cccacAAAAAcactaa
 V$FREAC7_01            |     5775 (+) |  0.832 |  0.834 | gagagAAAAAtatgaa
 V$FREAC7_01            |     5790 (+) |  0.832 |  0.836 | aataaTTAAAtacaaa
 V$FREAC7_01            |     5962 (-) |  0.832 |  0.829 | ccagtgTTTTTaagtg
 V$FREAC7_01            |     6251 (-) |  0.848 |  0.830 | tttctaTTTGTcccat
 V$FREAC7_01            |     6587 (+) |  0.848 |  0.845 | acaaaACAAAtaaggt
 V$FREAC7_01            |     6669 (-) |  0.832 |  0.838 | attttaTTTAGctttt
 V$FREAC7_01            |     6822 (-) |  1.000 |  0.927 | ccctttTTTATgtgct
 V$FREAC7_01            |     6833 (-) |  0.848 |  0.829 | gtgctaTTTACtgcca
 V$FREAC7_01            |     7063 (-) |  0.832 |  0.854 | aatttgTTTTTgtttg
 V$FREAC7_01            |     7069 (-) |  0.848 |  0.869 | tttttgTTTGTgtatg
 V$FREAC7_01            |     7420 (-) |  1.000 |  0.866 | taaaggTTTATttgtt
 V$FREAC7_01            |     7424 (-) |  0.848 |  0.852 | ggtttaTTTGTtttta
 V$FREAC7_01            |     7428 (-) |  0.832 |  0.859 | tatttgTTTTTatttt
 V$FREAC7_01            |     7430 (-) |  1.000 |  0.925 | tttgttTTTATtttat
 V$FREAC7_01            |     7769 (+) |  0.832 |  0.847 | tctcaAAAAAcaaaac
 V$FREAC7_01            |     7796 (+) |  1.000 |  0.920 | caaagATAAAgaacaa
 V$FREAC7_01            |     7820 (+) |  0.848 |  0.855 | ccaaaACAAAcaatta
 V$FREAC7_01            |     7891 (-) |  1.000 |  0.926 | ttggttTTTATtttga
 V$FREAC7_01            |     7937 (-) |  0.832 |  0.844 | tgtgtgTTTAGttttg
 V$FREAC7_01            |     7968 (-) |  0.848 |  0.863 | tagttgTTTGTttttc
 V$FREAC7_01            |     8057 (-) |  1.000 |  0.859 | gtctagTTTATctggt
 V$FREAC7_01            |     8472 (+) |  0.832 |  0.829 | aaggcAAAAAtaaggg
 V$FREAC7_01            |     8896 (+) |  0.848 |  0.850 | gtaccACAAAcagatt
 V$FREAC7_01            |     8928 (+) |  1.000 |  0.856 | tcagtATAAActaaag
 V$FREAC7_01            |     9423 (+) |  1.000 |  0.954 | atcccATAAAtaacag
 V$FREAC7_01            |     9532 (+) |  0.848 |  0.846 | ctagaACAAAcaagtc
 V$FREAC7_01            |     9960 (-) |  0.832 |  0.843 | tgtatgTTTCTggttc
 V$FREAC7_01            |    10310 (-) |  0.832 |  0.853 | taactgTTTTTatatt
 V$FREAC7_01            |    10312 (-) |  1.000 |  0.928 | actgttTTTATatttt
 V$FREAC7_01            |    10318 (-) |  0.832 |  0.841 | tttataTTTTTatttt
 V$FREAC7_01            |    10320 (-) |  1.000 |  0.926 | tatattTTTATtttat
 V$FREAC7_01            |    10334 (-) |  1.000 |  0.914 | atagttTTTATtgttt
 V$FREAC7_01            |    10388 (+) |  1.000 |  0.934 | tccatATAAAaatgaa
 V$FREAC7_01            |    10453 (+) |  0.814 |  0.846 | tttatATCAAcaatgc
 V$FREAC7_01            |    10699 (-) |  1.000 |  0.966 | cccgtgTTTATgaaac
 V$FREAC7_01            |    11096 (-) |  0.832 |  0.833 | ccactgTTTAAagaac
 V$FREAC7_01            |    11187 (-) |  0.832 |  0.845 | gccttgTTTCTtgatt
 V$FREAC7_01            |    11466 (-) |  1.000 |  0.927 | aaatttTTTATttgtt
 V$FREAC7_01            |    11470 (-) |  0.848 |  0.847 | tttttaTTTGTttttc
 V$FREAC7_01            |    11474 (-) |  0.832 |  0.843 | tatttgTTTTTccctt
 V$FREAC7_01            |    11642 (-) |  0.832 |  0.832 | aatgtaTTTCTgtact
 V$HFH8_01              |      603 (-) |  1.000 |  0.867 | tttttAAACAtcc
 V$HFH8_01              |      634 (-) |  1.000 |  0.867 | tttttAAACAttt
 V$HFH8_01              |      847 (-) |  0.892 |  0.908 | taaatAAATAcga
 V$HFH8_01              |      876 (-) |  1.000 |  0.906 | tgcacAAACAcga
 V$HFH8_01              |     1526 (+) |  1.000 |  0.904 | agcTGTTTttttg
 V$HFH8_01              |     1893 (+) |  0.892 |  0.901 | ttaTATTTatttt
 V$HFH8_01              |     2360 (+) |  0.892 |  0.900 | ttgTATTTatttt
 V$HFH8_01              |     2409 (-) |  1.000 |  0.898 | aaaaaAAACAaaa
 V$HFH8_01              |     2898 (+) |  0.870 |  0.872 | tctTTTTTatcca
 V$HFH8_01              |     3807 (-) |  1.000 |  0.883 | agaaaAAACAtcg
 V$HFH8_01              |     4003 (-) |  0.892 |  0.869 | acgatAAATAaat
 V$HFH8_01              |     4007 (-) |  0.892 |  0.910 | taaatAAATAttc
 V$HFH8_01              |     4493 (-) |  1.000 |  0.872 | acaaaAAACAaaa
 V$HFH8_01              |     4780 (-) |  0.870 |  0.872 | tggatAAAGAttg
 V$HFH8_01              |     5434 (+) |  0.892 |  0.841 | cttTATTTgtatt
 V$HFH8_01              |     5634 (-) |  0.870 |  0.861 | gggatAAAGAcaa
 V$HFH8_01              |     5645 (-) |  0.870 |  0.881 | aaaatAAAAAgaa
 V$HFH8_01              |     5717 (-) |  1.000 |  0.902 | cacaaAAACActa
 V$HFH8_01              |     5963 (+) |  1.000 |  0.887 | cagTGTTTttaag
 V$HFH8_01              |     6589 (-) |  0.892 |  0.838 | aaaacAAATAagg
 V$HFH8_01              |     6823 (+) |  0.870 |  0.896 | cctTTTTTatgtg
 V$HFH8_01              |     7064 (+) |  1.000 |  0.896 | attTGTTTttgtt
 V$HFH8_01              |     7070 (+) |  1.000 |  0.923 | tttTGTTTgtgta
 V$HFH8_01              |     7425 (+) |  0.892 |  0.838 | gttTATTTgtttt
 V$HFH8_01              |     7429 (+) |  1.000 |  0.901 | attTGTTTttatt
 V$HFH8_01              |     7431 (+) |  0.870 |  0.883 | ttgTTTTTatttt
 V$HFH8_01              |     7771 (-) |  1.000 |  0.880 | tcaaaAAACAaaa
 V$HFH8_01              |     7798 (-) |  0.870 |  0.878 | aagatAAAGAaca
 V$HFH8_01              |     7822 (-) |  1.000 |  0.919 | aaaacAAACAatt
 V$HFH8_01              |     7892 (+) |  0.870 |  0.883 | tggTTTTTatttt
 V$HFH8_01              |     7938 (+) |  1.000 |  0.877 | gtgTGTTTagttt
 V$HFH8_01              |     7969 (+) |  1.000 |  0.919 | agtTGTTTgtttt
 V$HFH8_01              |     7973 (+) |  1.000 |  0.876 | gttTGTTTttcaa
 V$HFH8_01              |     8898 (-) |  1.000 |  0.884 | accacAAACAgat
 V$HFH8_01              |     9425 (-) |  0.892 |  0.885 | cccatAAATAaca
 V$HFH8_01              |     9534 (-) |  1.000 |  0.905 | agaacAAACAagt
 V$HFH8_01              |     9961 (+) |  1.000 |  0.867 | gtaTGTTTctggt
 V$HFH8_01              |    10311 (+) |  1.000 |  0.904 | aacTGTTTttata
 V$HFH8_01              |    10313 (+) |  0.870 |  0.887 | ctgTTTTTatatt
 V$HFH8_01              |    10321 (+) |  0.870 |  0.885 | ataTTTTTatttt
 V$HFH8_01              |    10335 (+) |  0.870 |  0.857 | tagTTTTTattgt
 V$HFH8_01              |    10390 (-) |  0.870 |  0.897 | catatAAAAAtga
 V$HFH8_01              |    10455 (-) |  0.783 |  0.834 | tatatCAACAatg
 V$HFH8_01              |    10700 (+) |  1.000 |  0.966 | ccgTGTTTatgaa
 V$HFH8_01              |    11097 (+) |  1.000 |  0.861 | cacTGTTTaaaga
 V$HFH8_01              |    11188 (+) |  1.000 |  0.882 | cctTGTTTcttga
 V$HFH8_01              |    11467 (+) |  0.870 |  0.899 | aatTTTTTatttg
 V$HFH8_01              |    11471 (+) |  0.892 |  0.837 | tttTATTTgtttt
 V$HFH8_01              |    11475 (+) |  1.000 |  0.877 | attTGTTTttccc
 V$HFH8_01              |    11828 (-) |  1.000 |  0.861 | gtgagAAACAgca
 V$NFAT_Q6              |      223 (-) |  1.000 |  0.995 | tttTTTCCtttt
 V$NFAT_Q6              |      327 (+) |  1.000 |  0.969 | tgctGGAAAttc
 V$NFAT_Q6              |     1190 (+) |  1.000 |  0.969 | cccaGGAAAgct
 V$NFAT_Q6              |     1559 (+) |  1.000 |  0.967 | ttctGGAAAtct
 V$NFAT_Q6              |     1637 (-) |  1.000 |  0.962 | gccTTTCCtagt
 V$NFAT_Q6              |     1718 (-) |  1.000 |  0.956 | cctTTTCCgggc
 V$NFAT_Q6              |     1955 (-) |  1.000 |  0.975 | aacTTTCCtttt
 V$NFAT_Q6              |     2164 (-) |  1.000 |  0.962 | tccTTTCCttct
 V$NFAT_Q6              |     2172 (-) |  1.000 |  0.967 | ttcTTTCCttct
 V$NFAT_Q6              |     2378 (-) |  1.000 |  0.966 | agtTTTCCcaga
 V$NFAT_Q6              |     2399 (-) |  1.000 |  0.965 | tgcTTTCCttaa
 V$NFAT_Q6              |     2510 (+) |  1.000 |  0.974 | aaagGGAAAaaa
 V$NFAT_Q6              |     2563 (-) |  1.000 |  0.948 | aaaTTTCCgtaa
 V$NFAT_Q6              |     3109 (-) |  1.000 |  0.964 | taaTTTCCatgc
 V$NFAT_Q6              |     3323 (-) |  1.000 |  0.982 | cctTTTCCtgat
 V$NFAT_Q6              |     3336 (-) |  1.000 |  0.946 | ctaTTTCCctcc
 V$NFAT_Q6              |     3835 (-) |  1.000 |  0.973 | aaaTTTCCattc
 V$NFAT_Q6              |     4046 (+) |  1.000 |  0.950 | agggGGAAAtag
 V$NFAT_Q6              |     4112 (-) |  1.000 |  0.968 | catTTTCCcaga
 V$NFAT_Q6              |     4687 (+) |  1.000 |  0.969 | ggcaGGAAActt
 V$NFAT_Q6              |     5120 (+) |  1.000 |  0.979 | aaaaGGAAAcag
 V$NFAT_Q6              |     5421 (-) |  1.000 |  0.944 | atcTTTCCctcc
 V$NFAT_Q6              |     5456 (-) |  1.000 |  0.959 | cctTTTCCccac
 V$NFAT_Q6              |     5471 (-) |  1.000 |  0.969 | ctaTTTCCtgat
 V$NFAT_Q6              |     5509 (-) |  1.000 |  0.946 | aggTTTCCctgc
 V$NFAT_Q6              |     5519 (-) |  1.000 |  0.963 | gccTTTCCtcct
 V$NFAT_Q6              |     5861 (-) |  1.000 |  0.961 | tggTTTCCcatg
 V$NFAT_Q6              |     5915 (-) |  1.000 |  0.955 | ttgTTTCCccag
 V$NFAT_Q6              |     6459 (-) |  1.000 |  0.969 | ttaTTTCCtgat
 V$NFAT_Q6              |     6968 (+) |  1.000 |  0.957 | ggatGGAAAgga
 V$NFAT_Q6              |     6998 (+) |  1.000 |  0.981 | agatGGAAAagg
 V$NFAT_Q6              |     7017 (-) |  1.000 |  0.973 | atgTTTCCtgca
 V$NFAT_Q6              |     7246 (+) |  1.000 |  0.991 | ctcaGGAAAaag
 V$NFAT_Q6              |     7562 (+) |  1.000 |  0.968 | tgctGGAAAcca
 V$NFAT_Q6              |     8144 (+) |  1.000 |  0.966 | tgagGGAAAaca
 V$NFAT_Q6              |     8199 (-) |  1.000 |  0.956 | ctgTTTCCcctc
 V$NFAT_Q6              |     9121 (+) |  1.000 |  0.964 | accgGGAAAacc
 V$NFAT_Q6              |     9509 (-) |  1.000 |  0.951 | aagTTTCCccat
 V$NFAT_Q6              |     9873 (+) |  1.000 |  0.968 | atgaGGAAAtca
 V$NFAT_Q6              |    10587 (-) |  1.000 |  0.979 | caaTTTCCtata
 V$NFAT_Q6              |    11090 (-) |  1.000 |  0.998 | aatTTTCCactg
 V$NFAT_Q6              |    11270 (+) |  1.000 |  0.977 | aaaaGGAAAtta
 V$NFAT_Q6              |    11479 (-) |  1.000 |  0.978 | gttTTTCCcttg
 F$DDE1_B               |      796 (-) |  1.000 |  0.928 | cGCTGAgcc
 F$DDE1_B               |     1484 (-) |  0.943 |  0.908 | gGCAGAggg
 F$DDE1_B               |     1711 (+) |  0.943 |  0.908 | cccTCTGCc
 F$DDE1_B               |     3231 (+) |  1.000 |  0.899 | cagTCAGCc
 F$DDE1_B               |     4181 (-) |  1.000 |  0.990 | gGCTGAgca
 F$DDE1_B               |     4405 (+) |  1.000 |  0.946 | aggTCAGCc
 F$DDE1_B               |     4973 (+) |  1.000 |  0.992 | ggcTCAGCc
 F$DDE1_B               |     4997 (-) |  0.943 |  0.901 | gGCAGAcct
 F$DDE1_B               |     6225 (+) |  0.943 |  0.899 | cgcTCTGCa
 F$DDE1_B               |     6547 (-) |  1.000 |  0.946 | gGCTGAggt
 F$DDE1_B               |     7606 (-) |  1.000 |  0.937 | tGCTGAgcc
 F$DDE1_B               |     8141 (-) |  1.000 |  0.899 | tGCTGAggg
 F$DDE1_B               |     8191 (+) |  0.943 |  0.944 | tgcTCTGCc
 F$DDE1_B               |     8305 (+) |  0.943 |  0.908 | cccTCTGCc
 F$DDE1_B               |     9093 (+) |  0.943 |  0.901 | agcTCTGCt
 F$DDE1_B               |     9611 (-) |  1.000 |  0.901 | aGCTGAggt
 F$DDE1_B               |     9638 (+) |  1.000 |  0.901 | aggTCAGCt
 F$DDE1_B               |    10276 (-) |  1.000 |  0.990 | gGCTGAgca
 F$STRE_B               |     1610 (+) |  1.000 |  1.000 | cAGGGGg
 F$STRE_B               |     4045 (+) |  1.000 |  1.000 | cAGGGGg
 F$STRE_B               |    10789 (+) |  1.000 |  1.000 | cAGGGGg
 V$ATATA_B              |      658 (+) |  0.972 |  0.953 | atataTAAGT
 V$ATATA_B              |     8637 (+) |  0.926 |  0.938 | ttattTAAGA
 V$BEL1_B               |     7704 (-) |  1.000 |  0.892 | gaggtagaggcagaaggaTCAGCagttt
 V$LDSPOLYA_B           |      508 (+) |  0.966 |  0.907 | tattTGTCTtctgatt
 V$LDSPOLYA_B           |      874 (-) |  0.972 |  0.898 | aatgcacAAACAcgaa
 V$LDSPOLYA_B           |     1266 (+) |  1.000 |  0.920 | tccgTGTGTactctgg
 V$LDSPOLYA_B           |     3452 (-) |  1.000 |  0.939 | taataaaACACAgggc
 V$LDSPOLYA_B           |     3559 (+) |  1.000 |  0.919 | tagcTGTGTggccttt
 V$LDSPOLYA_B           |     3659 (-) |  1.000 |  0.911 | taaagtaACACAgact
 V$LDSPOLYA_B           |     5119 (-) |  0.972 |  0.908 | caaaaggAAACAgatg
 V$LDSPOLYA_B           |     5600 (-) |  1.000 |  0.899 | taatataACACAagaa
 V$LDSPOLYA_B           |     5658 (-) |  1.000 |  0.928 | gaaaagaACACAataa
 V$LDSPOLYA_B           |     5668 (-) |  0.966 |  0.906 | caataagAGACAgaca
 V$LDSPOLYA_B           |     7332 (-) |  0.966 |  0.921 | gaacaatAGACAcatt
 V$LDSPOLYA_B           |     7935 (+) |  1.000 |  0.905 | tttgTGTGTttagttt
 V$LDSPOLYA_B           |     7937 (+) |  0.972 |  0.908 | tgtgTGTTTagttttg
 V$LDSPOLYA_B           |    10178 (+) |  1.000 |  0.924 | agtgTGTGTgttcagc
 V$LPOLYA_B             |     3910 (+) |  1.000 |  0.993 | tAATAAag
 V$LPOLYA_B             |    11688 (+) |  1.000 |  1.000 | cAATAAag
 V$MTATA_B              |      233 (-) |  0.951 |  0.835 | tttgtcttTTTAAatct
 V$MTATA_B              |      238 (+) |  0.951 |  0.928 | ctttTTAAAtctgggct
 V$MTATA_B              |      288 (-) |  0.901 |  0.859 | tcaagtgtTTTACagac
 V$MTATA_B              |      515 (-) |  0.951 |  0.860 | cttctgatTTTAAaaat
 V$MTATA_B              |      520 (+) |  0.951 |  0.856 | gattTTAAAaatgatgg
 V$MTATA_B              |      566 (+) |  1.000 |  0.809 | ggagATAAAcgtctacc
 V$MTATA_B              |      597 (-) |  0.951 |  0.867 | acttacttTTTAAacat
 V$MTATA_B              |      602 (+) |  0.951 |  0.872 | ctttTTAAAcatcctgt
 V$MTATA_B              |      628 (-) |  0.951 |  0.860 | cactttttTTTAAacat
 V$MTATA_B              |      633 (+) |  0.951 |  0.853 | ttttTTAAAcatttatt
 V$MTATA_B              |      707 (-) |  0.901 |  0.846 | cggatctcTTTACagat
 V$MTATA_B              |      830 (+) |  0.877 |  0.811 | tactATATAaaacaagt
 V$MTATA_B              |      832 (+) |  1.000 |  0.906 | ctatATAAAacaagtta
 V$MTATA_B              |      846 (+) |  1.000 |  0.806 | ttaaATAAAtacgatcg
 V$MTATA_B              |      956 (-) |  0.901 |  0.820 | atcaaataTTTACagga
 V$MTATA_B              |     1055 (-) |  0.951 |  0.828 | tcaacaacTTTAAaata
 V$MTATA_B              |     1060 (+) |  0.951 |  0.853 | aactTTAAAataagatg
 V$MTATA_B              |     1144 (-) |  1.000 |  0.815 | accgttacTTTATgtag
 V$MTATA_B              |     1742 (+) |  0.846 |  0.827 | tcctATAGAacactgat
 V$MTATA_B              |     1750 (-) |  0.846 |  0.823 | aacactgaTCTATaagc
 V$MTATA_B              |     1757 (+) |  0.801 |  0.810 | atctATAAGcctctcgc
 V$MTATA_B              |     1884 (-) |  1.000 |  0.913 | cctcccatTTTATattt
 V$MTATA_B              |     2003 (+) |  0.846 |  0.825 | ggctATACAtctcctga
 V$MTATA_B              |     2570 (-) |  0.901 |  0.860 | cgtaagtaTTTACaaca
 V$MTATA_B              |     2850 (-) |  0.901 |  0.811 | ttccgtccTTTAGagct
 V$MTATA_B              |     3398 (-) |  0.827 |  0.809 | tctccagtTATAAaagt
 V$MTATA_B              |     3403 (+) |  1.000 |  0.893 | agttATAAAagttaatg
 V$MTATA_B              |     3450 (+) |  1.000 |  0.860 | gttaATAAAacacaggg
 V$MTATA_B              |     3618 (-) |  1.000 |  0.857 | caaatgcgTTTATaata
 V$MTATA_B              |     3845 (+) |  1.000 |  0.812 | tctcATAAAatatccag
 V$MTATA_B              |     3908 (+) |  1.000 |  0.833 | attaATAAAgctttatg
 V$MTATA_B              |     3911 (-) |  1.000 |  0.838 | aataaagcTTTATgaat
 V$MTATA_B              |     4070 (+) |  0.901 |  0.810 | atatGTAAAatgtatac
 V$MTATA_B              |     4098 (+) |  0.901 |  0.836 | gattCTAAAacatccat
 V$MTATA_B              |     4314 (+) |  1.000 |  0.867 | ctgcATAAAactgggtc
 V$MTATA_B              |     4361 (-) |  0.951 |  0.847 | atcagaagTTTAAagtt
 V$MTATA_B              |     4366 (+) |  0.951 |  0.842 | aagtTTAAAgttatctg
 V$MTATA_B              |     4779 (+) |  1.000 |  0.810 | ctggATAAAgattgctg
 V$MTATA_B              |     5390 (-) |  1.000 |  0.841 | attttaccTTTATattt
 V$MTATA_B              |     5413 (+) |  0.951 |  0.816 | cttaTTAAAtctttccc
 V$MTATA_B              |     5427 (-) |  1.000 |  0.814 | ccctccacTTTATttgt
 V$MTATA_B              |     6465 (+) |  1.000 |  0.814 | cctgATAAAatgctcag
 V$MTATA_B              |     6716 (-) |  0.951 |  0.872 | ccacaaccTTTAAaggg
 V$MTATA_B              |     6721 (+) |  0.951 |  0.872 | acctTTAAAgggtgagc
 V$MTATA_B              |     6754 (-) |  1.000 |  0.880 | actatcccTTTATacca
 V$MTATA_B              |     6759 (+) |  0.827 |  0.817 | ccctTTATAccatgaac
 V$MTATA_B              |     6820 (-) |  1.000 |  0.824 | ctccctttTTTATgtgc
 V$MTATA_B              |     6866 (-) |  0.801 |  0.816 | gaccgaggCTTATagga
 V$MTATA_B              |     7410 (-) |  0.951 |  0.843 | gaagaactTTTAAaggt
 V$MTATA_B              |     7415 (+) |  0.951 |  0.841 | acttTTAAAggtttatt
 V$MTATA_B              |     7637 (-) |  0.951 |  0.844 | agaattatTTTAAaaat
 V$MTATA_B              |     7642 (+) |  0.951 |  0.833 | tattTTAAAaatgcttt
 V$MTATA_B              |     7683 (+) |  0.901 |  0.854 | agctGTAAAgccagaac
 V$MTATA_B              |     7797 (+) |  1.000 |  0.811 | aaagATAAAgaacaacg
 V$MTATA_B              |     8085 (+) |  0.846 |  0.862 | tcctATACAgctctggg
 V$MTATA_B              |     8845 (-) |  0.951 |  0.906 | cagaacggTTTAAaaat
 V$MTATA_B              |     8850 (+) |  0.951 |  0.864 | cggtTTAAAaattaaga
 V$MTATA_B              |     8929 (+) |  1.000 |  0.880 | cagtATAAActaaagca
 V$MTATA_B              |     8942 (-) |  0.951 |  0.867 | agcaacttTTTAAaatt
 V$MTATA_B              |     8947 (+) |  0.951 |  0.853 | ctttTTAAAattagtag
 V$MTATA_B              |     9424 (+) |  1.000 |  0.820 | tcccATAAAtaacagga
 V$MTATA_B              |     9710 (+) |  0.901 |  0.823 | tggtGTAAAattgatct
 V$MTATA_B              |     9819 (-) |  0.901 |  0.845 | cttcaaatTTTAGaagg
 V$MTATA_B              |     9834 (-) |  0.951 |  0.859 | gggataatTTTAAagtc
 V$MTATA_B              |     9839 (+) |  0.951 |  0.849 | aattTTAAAgtcaggca
 V$MTATA_B              |     9878 (-) |  0.951 |  0.829 | gaaatcaaTTTAAaatt
 V$MTATA_B              |     9883 (+) |  0.951 |  0.851 | caatTTAAAattctttt
 V$MTATA_B              |     9891 (-) |  0.951 |  0.858 | aattctttTTTAAagac
 V$MTATA_B              |     9896 (+) |  0.951 |  0.877 | ttttTTAAAgacttact
 V$MTATA_B              |     9947 (+) |  0.819 |  0.811 | tgttATAACaccctgta
 V$MTATA_B              |    10017 (+) |  0.846 |  0.821 | aggtATAGAccgtagtt
 V$MTATA_B              |    10310 (-) |  1.000 |  0.851 | taactgttTTTATattt
 V$MTATA_B              |    10323 (-) |  1.000 |  0.855 | atttttatTTTATagtt
 V$MTATA_B              |    10389 (+) |  1.000 |  0.934 | ccatATAAAaatgaacg
 V$MTATA_B              |    10445 (-) |  1.000 |  0.882 | acgtctctTTTATatca
 V$MTATA_B              |    10468 (-) |  0.901 |  0.837 | catctcacTTTAGacca
 V$MTATA_B              |    10697 (-) |  1.000 |  0.831 | cacccgtgTTTATgaaa
 V$MTATA_B              |    10809 (+) |  0.901 |  0.889 | gcatCTAAAtcgcagtc
 V$MTATA_B              |    11094 (-) |  0.951 |  0.853 | ttccactgTTTAAagaa
 V$MTATA_B              |    11099 (+) |  0.951 |  0.897 | ctgtTTAAAgaacgact
 V$MTATA_B              |    11336 (+) |  0.901 |  0.810 | cgatGTAAAtgccatta
 V$MTATA_B              |    11630 (-) |  0.951 |  0.856 | gaccctcgTTTAAatgt
 V$MTATA_B              |    11635 (+) |  0.951 |  0.827 | tcgtTTAAAtgtatttc
 V$MUSCLE_INI_B         |      100 (-) |  1.000 |  0.875 | cgcctggGGGTGgccagtgag
 V$MUSCLE_INI_B         |      191 (+) |  0.930 |  0.877 | tgcctcccaCACCAccatgcc
 V$MUSCLE_INI_B         |     1274 (-) |  0.932 |  0.856 | tactctgGGATGacagggacc
 V$MUSCLE_INI_B         |     1321 (+) |  0.985 |  0.869 | ctcccttctCACTCcccaggg
 V$MUSCLE_INI_B         |     1823 (+) |  1.000 |  0.855 | cagggaagaCACCCattgggg
 V$MUSCLE_INI_B         |     2011 (-) |  0.985 |  0.903 | atctcctGAGTGctgggatta
 V$MUSCLE_INI_B         |     4328 (+) |  0.932 |  0.858 | gtctggtgaCATCCaggtggt
 V$MUSCLE_INI_B         |     5036 (-) |  0.901 |  0.854 | tgctcagGATTGctgtggtct
 V$MUSCLE_INI_B         |     5816 (-) |  0.981 |  0.900 | agccctgGCGTGgcactgtga
 V$MUSCLE_INI_B         |     6522 (+) |  1.000 |  0.857 | cacgaagttCACCCtggagac
 V$MUSCLE_INI_B         |     6624 (+) |  1.000 |  0.872 | tgagtggggCACCCagaaggc
 V$MUSCLE_INI_B         |     7192 (-) |  1.000 |  0.875 | gccacggGGGTGctatgaatt
 V$MUSCLE_INI_B         |     8229 (+) |  1.000 |  0.907 | tggctcccaCACCCagatgaa
 V$MUSCLE_INI_B         |     8732 (-) |  1.000 |  0.917 | aacgtcgGGGTGtggtggccc
 V$MUSCLE_INI_B         |     8734 (-) |  0.974 |  0.862 | cgtcgggGTGTGgtggcccac
 V$MUSCLE_INI_B         |     9183 (+) |  0.985 |  0.883 | cacagagacCACTCaagagag
 V$MUSCLE_INI_B         |     9271 (+) |  0.930 |  0.859 | agcgacagcCACCAagctgag
 V$MUSCLE_INI_B         |     9390 (-) |  0.917 |  0.855 | gcccctgGAATGtggttctat
 V$MUSCLE_INI_B         |     9565 (-) |  1.000 |  0.862 | ggtttctGGGTGtggtggtat
 V$MUSCLE_INI_B         |     9682 (-) |  1.000 |  0.879 | ggaggggGGGTGgtggtggtg
 V$MUSCLE_INI_B         |    10867 (-) |  0.930 |  0.904 | tgcagcgTGGTGgtgggagca
 V$MUSCLE_INI_B         |    11814 (-) |  0.915 |  0.873 | ggcccagGGTTGgggtgagaa
 V$MUSCLE_INI_B         |    11834 (-) |  0.985 |  0.892 | aacagcaGAGTGgggggtggg
 V$MUSCLE_INI_B         |    11841 (-) |  1.000 |  0.869 | gagtgggGGGTGgggtatggg
 V$MYCMAX_B             |      735 (+) |  1.000 |  0.948 | aCCACGtggt
 V$MYCMAX_B             |      735 (-) |  1.000 |  0.948 | accaCGTGGt
 V$MYCMAX_B             |     2614 (+) |  0.958 |  0.933 | gCCATGtgta
 V$MYCMAX_B             |     7192 (+) |  1.000 |  0.938 | gCCACGgggg
 V$MINI19_B             |     2011 (-) |  0.998 |  0.866 | atctcctGAGTGctgggatta
 V$MINI19_B             |     6224 (-) |  0.986 |  0.851 | acgctctGCATGctgtctggc
 V$MINI19_B             |     6647 (+) |  0.953 |  0.856 | ctcagtctgCAAACagatgaa
 V$MINI19_B             |     8229 (+) |  0.998 |  0.851 | tggctcccaCACCCagatgaa
 V$MINI19_B             |     9183 (+) |  0.998 |  0.847 | cacagagacCACTCaagagag
 V$MINI19_B             |     9565 (-) |  0.998 |  0.866 | ggtttctGGGTGtggtggtat
 V$MINI19_B             |    10979 (-) |  0.995 |  0.845 | ggagcctGTGTGgccctggaa
 V$MINI19_B             |    11814 (-) |  0.955 |  0.847 | ggcccagGGTTGgggtgagaa
 V$MINI20_B             |     2011 (-) |  0.949 |  0.867 | atctcctgagTGCTGggatta
 V$MINI20_B             |     4848 (+) |  0.960 |  0.858 | ctgagaCTTCActgagggagg
 V$MINI20_B             |     6647 (+) |  0.944 |  0.855 | ctcagtCTGCAaacagatgaa
 V$MINI20_B             |     9390 (-) |  0.937 |  0.867 | gcccctggaaTGTGGttctat
 V$MINI20_B             |    11814 (-) |  1.000 |  0.857 | ggcccagggtTGGGGtgagaa
 V$PAX3_B               |     1138 (-) |  0.868 |  0.881 | cctaaaacCGTTActttatgt
 V$PAX3_B               |     2956 (-) |  0.772 |  0.811 | acgaatacAGTGAcggcagat
 V$PAX3_B               |     2958 (+) |  0.904 |  0.797 | gaatacagTGACGgcagatgc
 V$PAX3_B               |     5919 (-) |  0.818 |  0.812 | ttccccagCGAGActcccttg
 V$PAX3_B               |     6214 (+) |  1.000 |  0.856 | aaggtttcTCACGctctgcat
 V$PAX3_B               |     6553 (+) |  0.797 |  0.813 | ggtaagagTCATGgttgccac
 V$PAX3_B               |    10239 (+) |  0.772 |  0.801 | gttggtggTCAGGcttgtgca
 V$WHN_B                |    10900 (+) |  1.000 |  0.992 | agaGACGCtac
 V$ZF5_B                |      812 (-) |  0.888 |  0.756 | caGCCCGacactt
 V$ZF5_B                |     1004 (+) |  0.919 |  0.816 | tggggaCGCACct
 V$ZF5_B                |     1005 (-) |  0.841 |  0.756 | ggGGACGcaccta
 V$ZF5_B                |     1125 (-) |  0.922 |  0.792 | atGCACGtgtgtt
 V$ZF5_B                |     1366 (-) |  0.888 |  0.787 | atGCTCGtttgca
 V$ZF5_B                |     1404 (-) |  0.738 |  0.750 | gaGTGGGtccatt
 V$ZF5_B                |     1587 (-) |  0.753 |  0.749 | gaGCCAGcactgg
 V$ZF5_B                |     2340 (+) |  0.919 |  0.768 | accctaCGCTCtt
 V$ZF5_B                |     2466 (-) |  0.786 |  0.779 | taGCAAGcgcgaa
 V$ZF5_B                |     2470 (-) |  1.000 |  0.845 | aaGCGCGaaggcc
 V$ZF5_B                |     2811 (+) |  0.922 |  0.769 | gaacacCGTGCtc
 V$ZF5_B                |     2883 (+) |  0.841 |  0.820 | tgtatgCGTACtg
 V$ZF5_B                |     2918 (-) |  0.841 |  0.769 | gtGGACGgaccct
 V$ZF5_B                |     2974 (+) |  0.738 |  0.745 | gatgcgCAGGCat
 V$ZF5_B                |     3004 (-) |  0.919 |  0.758 | agGTGCGcaggcg
 V$ZF5_B                |     3069 (-) |  0.753 |  0.747 | taGCTAGgtcaca
 V$ZF5_B                |     3964 (+) |  0.753 |  0.770 | tgagcaCTGGCtg
 V$ZF5_B                |     4389 (-) |  0.783 |  0.755 | taGTGAGttccaa
 V$ZF5_B                |     4597 (-) |  0.888 |  0.811 | ctGCCCGcttgct
 V$ZF5_B                |     4598 (+) |  0.786 |  0.759 | tgcccgCTTGCtg
 V$ZF5_B                |     4730 (+) |  0.864 |  0.782 | ttggccCTCGCtg
 V$ZF5_B                |     4771 (-) |  0.864 |  0.764 | caGCGAGtctgga
 V$ZF5_B                |     4907 (+) |  0.771 |  0.792 | caagtgCATGCtc
 V$ZF5_B                |     5075 (+) |  0.753 |  0.763 | gagaggCTGGCtc
 V$ZF5_B                |     5108 (-) |  0.783 |  0.757 | ttGTGAGtgctca
 V$ZF5_B                |     5132 (+) |  0.807 |  0.763 | atggtgCGGTCaa
 V$ZF5_B                |     5220 (-) |  0.919 |  0.749 | ctGAGCGgagact
 V$ZF5_B                |     5329 (-) |  0.919 |  0.845 | caGTGCGccgata
 V$ZF5_B                |     5893 (+) |  0.919 |  0.779 | ggggccCGCCCct
 V$ZF5_B                |     5894 (-) |  0.888 |  0.802 | ggGCCCGccccta
 V$ZF5_B                |     5924 (-) |  0.864 |  0.798 | caGCGAGactccc
 V$ZF5_B                |     6062 (+) |  0.922 |  0.839 | cctgcaCGTGCtg
 V$ZF5_B                |     6063 (-) |  0.922 |  0.797 | ctGCACGtgctgc
 V$ZF5_B                |     6219 (+) |  0.919 |  0.751 | ttctcaCGCTCtg
 V$ZF5_B                |     6329 (+) |  0.768 |  0.761 | gaagcaCACACtg
 V$ZF5_B                |     6381 (+) |  0.807 |  0.777 | ggtagaCGAACtg
 V$ZF5_B                |     6402 (+) |  0.919 |  0.794 | tcagaaCGCTCag
 V$ZF5_B                |     6403 (-) |  0.841 |  0.814 | caGAACGctcaga
 V$ZF5_B                |     6498 (+) |  0.807 |  0.750 | cagatgCGGCCac
 V$ZF5_B                |     6627 (+) |  0.768 |  0.747 | gtggggCACCCag
 V$ZF5_B                |     6854 (+) |  0.841 |  0.792 | tgagcaCGTCCag
 V$ZF5_B                |     6855 (-) |  0.922 |  0.846 | gaGCACGtccaga
 V$ZF5_B                |     7088 (+) |  1.000 |  0.798 | gctttgCGCGCac
 V$ZF5_B                |     7090 (+) |  0.919 |  0.782 | tttgcgCGCACct
 V$ZF5_B                |     7091 (-) |  1.000 |  0.925 | ttGCGCGcaccta
 V$ZF5_B                |     7143 (-) |  0.738 |  0.762 | aaGAGGGcgccgt
 V$ZF5_B                |     7145 (-) |  0.919 |  0.808 | gaGGGCGccgtat
 V$ZF5_B                |     7478 (+) |  1.000 |  0.790 | gtgctaCGCGCac
 V$ZF5_B                |     7480 (+) |  0.919 |  0.750 | gctacgCGCACgt
 V$ZF5_B                |     7739 (+) |  0.753 |  0.756 | cacaggCTGGCta
 V$ZF5_B                |     7854 (+) |  0.841 |  0.757 | cgacagCGTACac
 V$ZF5_B                |     7870 (+) |  0.783 |  0.765 | gaaaagCTCACta
 V$ZF5_B                |     8030 (+) |  0.786 |  0.775 | tcagagCTTGCtg
 V$ZF5_B                |     8403 (-) |  0.753 |  0.768 | aaGCCAGcccggc
 V$ZF5_B                |     8407 (-) |  0.888 |  0.794 | caGCCCGgcctgt
 V$ZF5_B                |     9012 (+) |  0.738 |  0.759 | caggggCAGGCag
 V$ZF5_B                |     9156 (-) |  0.783 |  0.751 | atGTGAGttccta
 V$ZF5_B                |     9197 (-) |  0.783 |  0.790 | aaGAGAGcaccaa
 V$ZF5_B                |    10084 (-) |  0.753 |  0.769 | caGCCAGtgctct
 V$ZF5_B                |    10242 (+) |  0.738 |  0.751 | ggtggtCAGGCtt
 V$ZF5_B                |    10531 (+) |  0.922 |  0.832 | ggaggcCGTGCaa
 V$ZF5_B                |    10532 (-) |  0.807 |  0.757 | gaGGCCGtgcaac
 V$ZF5_B                |    10716 (+) |  0.922 |  0.802 | tctctgCGTGCtg
 V$ZF5_B                |    10821 (-) |  0.807 |  0.789 | caGTCCGcctttt
 V$ZF5_B                |    10951 (+) |  0.807 |  0.764 | tagctgCGGTCtg
 V$ZF5_B                |    11023 (-) |  0.783 |  0.753 | gaGAGAGatccta
 V$ZF5_B                |    11106 (-) |  0.841 |  0.779 | aaGAACGacttca
 V$ZF5_B                |    11400 (-) |  0.841 |  0.766 | ttGTACGcattta
 V$ZF5_B                |    11600 (-) |  0.768 |  0.766 | taGAGTGcacaga
 V$ZF5_B                |    11903 (-) |  0.922 |  0.788 | taGCACGaaggct
 F$GCR1_B               |     5728 (-) |  1.000 |  0.940 | taaactGGAAGcca
 V$ATF_B                |     1236 (-) |  0.800 |  0.835 | ctttgaCATCAg
 V$ATF_B                |     1238 (+) |  0.800 |  0.834 | tTGACAtcaggg
 V$ATF_B                |     1445 (+) |  0.800 |  0.840 | gTGAAGtcactg
 V$ATF_B                |     2963 (-) |  0.800 |  0.840 | cagtgaCGGCAg
 V$ATF_B                |     2965 (+) |  1.000 |  0.853 | gTGACGgcagat
 V$ATF_B                |     4530 (-) |  1.000 |  0.834 | caaatgCGTCAa
 V$ATF_B                |     8208 (-) |  0.800 |  0.835 | ctctgaCCTCAg
 V$ATF_B                |     8609 (-) |  1.000 |  0.835 | tcattcCGTCAa
 V$ATF_B                |    11317 (+) |  1.000 |  0.838 | gTGACGacgatg
 V$ETS1_B               |      604 (-) |  0.943 |  0.908 | ttttaaacATCCTgt
 V$ETS1_B               |     1733 (-) |  1.000 |  0.915 | tcctgaacTTCCTat
 V$ETS1_B               |     2149 (-) |  1.000 |  0.899 | ttccttccTTCCTct
 V$ETS1_B               |     2701 (-) |  1.000 |  0.894 | tcttctccTTCCTct
 V$ETS1_B               |     4962 (+) |  1.000 |  0.957 | gcAGGAAgtcaggct
 V$ETS1_B               |     5467 (-) |  1.000 |  0.915 | catactatTTCCTga
 V$ETS1_B               |     6083 (-) |  1.000 |  0.907 | tctgtgagTTCCTgt
 V$ETS1_B               |     6455 (-) |  1.000 |  0.925 | aaacttatTTCCTga
 V$ETS1_B               |     6793 (-) |  1.000 |  0.901 | gctggctcTTCCTcc
 V$ETS1_B               |     7230 (+) |  1.000 |  0.976 | gcAGGAAgttcatcg
 V$ETS1_B               |     8076 (-) |  1.000 |  0.940 | gcagaaacTTCCTat
 V$ETS1_B               |     9435 (+) |  1.000 |  0.919 | acAGGAAgcccaagg
 V$ETS1_B               |     9468 (+) |  0.943 |  0.924 | acAGGATgttctagc
 V$ETS1_B               |     9874 (+) |  1.000 |  0.893 | tgAGGAAatcaattt
 V$ETS1_B               |    10257 (+) |  1.000 |  0.986 | gcAGGAAgtgatttt
 V$ETS1_B               |    10844 (+) |  1.000 |  0.899 | gcAGGAAgaagccat
 V$ETS2_B               |      606 (-) |  0.880 |  0.860 | ttaaacATCCTgtc
 V$ETS2_B               |     1190 (+) |  1.000 |  0.830 | cccAGGAAagctgg
 V$ETS2_B               |     1667 (-) |  1.000 |  0.800 | tggagaTTCCTcct
 V$ETS2_B               |     1735 (-) |  1.000 |  0.858 | ctgaacTTCCTata
 V$ETS2_B               |     2007 (-) |  0.861 |  0.814 | atacatCTCCTgag
 V$ETS2_B               |     2143 (-) |  1.000 |  0.829 | tctctcTTCCTtcc
 V$ETS2_B               |     2147 (-) |  1.000 |  0.833 | tcttccTTCCTtcc
 V$ETS2_B               |     2151 (-) |  1.000 |  0.846 | ccttccTTCCTctt
 V$ETS2_B               |     2157 (-) |  1.000 |  0.826 | ttcctcTTCCTttc
 V$ETS2_B               |     2201 (-) |  1.000 |  0.844 | tctttcTTCCTttc
 V$ETS2_B               |     2682 (-) |  0.880 |  0.812 | cgttgcATCCTggt
 V$ETS2_B               |     2703 (-) |  1.000 |  0.845 | ttctccTTCCTctt
 V$ETS2_B               |     2781 (-) |  1.000 |  0.822 | agattcTTCCTtag
 V$ETS2_B               |     3321 (-) |  1.000 |  0.839 | ggccttTTCCTgat
 V$ETS2_B               |     3338 (-) |  0.861 |  0.823 | atttccCTCCTgtt
 V$ETS2_B               |     4687 (+) |  1.000 |  0.887 | ggcAGGAAacttga
 V$ETS2_B               |     4961 (+) |  1.000 |  0.936 | agcAGGAAgtcagg
 V$ETS2_B               |     5058 (+) |  0.785 |  0.800 | agcAGGTAgtgaga
 V$ETS2_B               |     5120 (+) |  1.000 |  0.847 | aaaAGGAAacagat
 V$ETS2_B               |     5190 (+) |  0.880 |  0.833 | agcAGGATttgtct
 V$ETS2_B               |     5263 (-) |  0.880 |  0.810 | acagtcATCCTggg
 V$ETS2_B               |     5469 (-) |  1.000 |  0.913 | tactatTTCCTgat
 V$ETS2_B               |     5873 (-) |  0.861 |  0.822 | gaccatCTCCTgct
 V$ETS2_B               |     6085 (-) |  1.000 |  0.892 | tgtgagTTCCTgtg
 V$ETS2_B               |     6274 (+) |  1.000 |  0.865 | agaAGGAAgcctct
 V$ETS2_B               |     6457 (-) |  1.000 |  0.937 | acttatTTCCTgat
 V$ETS2_B               |     6795 (-) |  1.000 |  0.846 | tggctcTTCCTccc
 V$ETS2_B               |     6876 (+) |  1.000 |  0.863 | tatAGGAAgcacca
 V$ETS2_B               |     6917 (+) |  1.000 |  0.841 | acaAGGAAttgatt
 V$ETS2_B               |     6973 (+) |  1.000 |  0.816 | gaaAGGAAcgactt
 V$ETS2_B               |     7015 (-) |  1.000 |  0.891 | ggatgtTTCCTgca
 V$ETS2_B               |     7152 (-) |  0.861 |  0.811 | ccgtatCTCCTgga
 V$ETS2_B               |     7229 (+) |  1.000 |  0.953 | agcAGGAAgttcat
 V$ETS2_B               |     7246 (+) |  1.000 |  0.842 | ctcAGGAAaaagtc
 V$ETS2_B               |     7464 (+) |  0.880 |  0.841 | tgcAGGATttgagt
 V$ETS2_B               |     8078 (-) |  1.000 |  0.903 | agaaacTTCCTata
 V$ETS2_B               |     8677 (+) |  1.000 |  0.813 | gttAGGAAggtaat
 V$ETS2_B               |     8910 (+) |  1.000 |  0.806 | ttcAGGAAtactcg
 V$ETS2_B               |     9434 (+) |  1.000 |  0.915 | aacAGGAAgcccaa
 V$ETS2_B               |     9467 (+) |  0.880 |  0.872 | tacAGGATgttcta
 V$ETS2_B               |     9539 (-) |  0.861 |  0.817 | aaacaaGTCCTgcg
 V$ETS2_B               |     9873 (+) |  1.000 |  0.867 | atgAGGAAatcaat
 V$ETS2_B               |     9906 (-) |  0.785 |  0.821 | acttacTTACTgga
 V$ETS2_B               |    10256 (+) |  1.000 |  0.982 | tgcAGGAAgtgatt
 V$ETS2_B               |    10585 (-) |  1.000 |  0.842 | ttcaatTTCCTata
 V$ETS2_B               |    10637 (+) |  1.000 |  0.806 | ctgAGGAAgacacc
 V$ETS2_B               |    10843 (+) |  1.000 |  0.879 | cgcAGGAAgaagcc
 V$ETS2_B               |    11270 (+) |  1.000 |  0.828 | aaaAGGAAattaag
 V$GABP_B               |      692 (+) |  0.800 |  0.824 | accAGAAGaggg
 V$GABP_B               |      768 (+) |  1.000 |  0.906 | tctGGAAGagta
 V$GABP_B               |      922 (-) |  1.000 |  0.888 | agcaCTTCCacg
 V$GABP_B               |     1554 (-) |  0.800 |  0.799 | aactCTTCTgga
 V$GABP_B               |     1717 (-) |  0.800 |  0.814 | gcctTTTCCggg
 V$GABP_B               |     1736 (-) |  1.000 |  0.804 | tgaaCTTCCtat
 V$GABP_B               |     2144 (-) |  1.000 |  0.842 | ctctCTTCCttc
 V$GABP_B               |     2158 (-) |  1.000 |  0.863 | tcctCTTCCttt
 V$GABP_B               |     2710 (-) |  1.000 |  0.849 | tcctCTTCCcaa
 V$GABP_B               |     2986 (-) |  1.000 |  0.826 | tctaCTTCCgct
 V$GABP_B               |     3030 (-) |  1.000 |  0.823 | ccgaCTTCCgct
 V$GABP_B               |     4607 (+) |  1.000 |  0.820 | gctGGAAGgtaa
 V$GABP_B               |     4962 (+) |  1.000 |  0.821 | gcaGGAAGtcag
 V$GABP_B               |     5490 (-) |  1.000 |  0.858 | tcccCTTCCctc
 V$GABP_B               |     5731 (+) |  1.000 |  0.807 | actGGAAGccat
 V$GABP_B               |     6796 (-) |  1.000 |  0.891 | ggctCTTCCtcc
 V$GABP_B               |     7138 (+) |  0.800 |  0.820 | gccAGAAGaggg
 V$GABP_B               |     7230 (+) |  1.000 |  0.870 | gcaGGAAGttca
 V$GABP_B               |     7837 (-) |  0.800 |  0.825 | cccaCTTCTggc
 V$GABP_B               |     8156 (-) |  1.000 |  0.813 | ttagCTTCCaga
 V$GABP_B               |     8191 (-) |  0.800 |  0.813 | tgctCTGCCtgt
 V$GABP_B               |     9374 (+) |  0.800 |  0.804 | acaGGGAGagct
 V$GABP_B               |     9435 (+) |  1.000 |  0.859 | acaGGAAGccca
 V$GABP_B               |    10074 (+) |  1.000 |  0.933 | tctGGAAGggca
 V$GABP_B               |    10257 (+) |  1.000 |  0.914 | gcaGGAAGtgat
 V$GABP_B               |    10844 (+) |  1.000 |  0.822 | gcaGGAAGaagc
 V$OCT1_B               |     5342 (-) |  1.000 |  0.940 | gtttTGCATc
 V$OCT1_B               |     6577 (+) |  1.000 |  0.953 | tATGCAaaac
 V$OCT1_B               |     9935 (-) |  1.000 |  0.992 | aattTGCATg
 V$OCT1_B               |    10911 (+) |  1.000 |  1.000 | tATGCAaata
 V$OCT1_B               |    11666 (-) |  0.821 |  0.881 | aattTTCATa
 P$RAV1_01              |       68 (-) |  1.000 |  0.951 | ttacTGTTGttg
 P$RAV1_01              |      492 (+) |  1.000 |  0.972 | ttgCAACAttat
 P$RAV1_01              |     1035 (+) |  1.000 |  0.941 | aatCAACAaagc
 P$RAV1_01              |     1845 (+) |  1.000 |  0.953 | cgtCAACAcaat
 P$RAV1_01              |     2552 (-) |  1.000 |  0.970 | tttcTGTTGtga
 P$RAV1_01              |     2579 (+) |  1.000 |  0.951 | ttaCAACAaatg
 P$RAV1_01              |     3141 (+) |  1.000 |  0.940 | ccaCAACAatat
 P$RAV1_01              |     3236 (+) |  1.000 |  0.937 | agcCAACAttcc
 P$RAV1_01              |     4524 (+) |  1.000 |  0.952 | agaCAACAaatg
 P$RAV1_01              |     4680 (-) |  0.947 |  0.949 | gttcTGTGGcag
 P$RAV1_01              |     5199 (-) |  0.947 |  0.938 | tgtcTGTGGcct
 P$RAV1_01              |     6504 (+) |  0.947 |  0.935 | cggCCACAaata
 P$RAV1_01              |     8222 (-) |  1.000 |  0.936 | ctgaTGTTGgct
 P$RAV1_01              |     8589 (+) |  1.000 |  0.950 | aggCAACAtctt
 P$RAV1_01              |     9179 (+) |  0.947 |  0.940 | acgCCACAgaga
 P$RAV1_01              |    10149 (-) |  1.000 |  0.942 | ttatTGTTGttg
 P$RAV1_01              |    10376 (-) |  1.000 |  0.965 | aaaaTGTTGcaa
 P$RAV1_01              |    10483 (+) |  0.947 |  0.937 | cagCCACAtatc
 P$RAV1_01              |    10691 (+) |  1.000 |  0.937 | tggCAACAcccg
 P$RAV1_01              |    11036 (-) |  1.000 |  0.938 | ccacTGTTGttg
 P$RAV1_02              |       98 (+) |  0.969 |  0.964 | ttcGCCTGgggg
 P$RAV1_02              |      442 (-) |  1.000 |  0.921 | taatCAGGTtgt
 P$RAV1_02              |     1358 (+) |  1.000 |  0.998 | gtcACCTGatgc
 P$RAV1_02              |     1390 (-) |  1.000 |  0.987 | agggCAGGTgag
 P$RAV1_02              |     1606 (-) |  0.967 |  0.967 | ggctCAGGGggt
 P$RAV1_02              |     1690 (-) |  0.967 |  0.963 | agctCAGGGgta
 P$RAV1_02              |     1769 (+) |  0.969 |  0.959 | ctcGCCTGtcct
 P$RAV1_02              |     1777 (+) |  0.972 |  0.968 | tccTCCTGgagc
 P$RAV1_02              |     1786 (+) |  1.000 |  0.983 | agcACCTGccat
 P$RAV1_02              |     2011 (+) |  0.972 |  0.969 | atcTCCTGagtg
 P$RAV1_02              |     2423 (-) |  0.967 |  0.954 | atcaCAGGGgtt
 P$RAV1_02              |     2640 (+) |  0.967 |  0.963 | tacCCCTGacct
 P$RAV1_02              |     3007 (-) |  0.969 |  0.954 | tgcgCAGGCgtc
 P$RAV1_02              |     3166 (+) |  0.969 |  0.954 | tccGCCTGtaca
 P$RAV1_02              |     3342 (+) |  0.972 |  0.955 | cccTCCTGttca
 P$RAV1_02              |     4041 (-) |  0.967 |  0.952 | ccagCAGGGgga
 P$RAV1_02              |     4172 (-) |  0.972 |  0.965 | tattCAGGAggc
 P$RAV1_02              |     4337 (-) |  1.000 |  0.988 | catcCAGGTggt
 P$RAV1_02              |     4350 (-) |  0.972 |  0.962 | gaggCAGGAgga
 P$RAV1_02              |     4592 (+) |  0.972 |  0.957 | tccTCCTGcccg
 P$RAV1_02              |     4819 (-) |  0.969 |  0.960 | ttacCAGGCggg
 P$RAV1_02              |     5877 (+) |  0.972 |  0.960 | atcTCCTGctgg
 P$RAV1_02              |     6155 (+) |  0.972 |  0.964 | ctcTCCTGcctc
 P$RAV1_02              |     7006 (-) |  0.969 |  0.957 | aaggCAGGCgga
 P$RAV1_02              |     7156 (+) |  0.972 |  0.972 | atcTCCTGgagc
 P$RAV1_02              |     7389 (-) |  1.000 |  0.989 | tgtcCAGGTggt
 P$RAV1_02              |     7624 (+) |  0.969 |  0.959 | gccGCCTGgcgg
 P$RAV1_02              |     8358 (+) |  0.967 |  0.953 | aacCCCTGtgca
 P$RAV1_02              |     8390 (+) |  1.000 |  0.922 | tatACCTGaagc
 P$RAV1_02              |     8502 (-) |  1.000 |  0.983 | gggaCAGGTgcg
 P$RAV1_02              |     8768 (+) |  1.000 |  0.987 | agcACCTGggag
 P$RAV1_02              |     8967 (-) |  1.000 |  0.991 | gaacCAGGTgtg
 P$RAV1_02              |     9008 (-) |  0.967 |  0.955 | gaggCAGGGgca
 P$RAV1_02              |     9304 (-) |  0.972 |  0.963 | tgccCAGGAggg
 P$RAV1_02              |     9341 (+) |  0.967 |  0.962 | gacCCCTGaagt
 P$RAV1_02              |     9389 (+) |  0.967 |  0.959 | agcCCCTGgaat
 P$RAV1_02              |     9555 (+) |  0.969 |  0.956 | gtcGCCTGtcgg
 P$RAV1_02              |    10664 (-) |  0.972 |  0.956 | tcaaCAGGAgga
 P$RAV1_02              |    10785 (-) |  0.967 |  0.963 | gaccCAGGGgga
 P$RAV1_02              |    11584 (-) |  0.972 |  0.962 | tatcCAGGAgtg
 P$RAV1_02              |    11961 (+) |  1.000 |  0.991 | tgcACCTGagct
 P$GAMYB_01             |      591 (+) |  0.937 |  0.947 | TAACAgac
 P$GAMYB_01             |      721 (-) |  1.000 |  0.943 | gatGGTTG
 P$GAMYB_01             |     1027 (-) |  0.978 |  0.982 | ggcAGTTG
 P$GAMYB_01             |     4539 (+) |  0.980 |  0.983 | CAACAgcc
 P$GAMYB_01             |     5281 (+) |  0.980 |  0.968 | CAACAggc
 P$GAMYB_01             |     7040 (-) |  0.978 |  0.935 | gttAGTTG
 P$GAMYB_01             |     7537 (-) |  1.000 |  0.953 | gttGGTTG
 P$GAMYB_01             |     8003 (-) |  0.980 |  0.968 | gccTGTTG
 P$GAMYB_01             |    10407 (-) |  1.000 |  0.953 | ggtGGTTG
 P$GAMYB_01             |    10965 (-) |  0.980 |  0.968 | gccTGTTG
 P$GAMYB_01             |    11494 (-) |  1.000 |  0.948 | tgcGGTTG
 P$GAMYB_01             |    11712 (+) |  0.978 |  0.982 | CAACTgcc
 P$GAMYB_01             |    11923 (+) |  0.988 |  0.935 | CAACGccc
 V$GATA1_05             |      448 (-) |  0.800 |  0.802 | ggTTGTCtgt
 V$GATA1_05             |      566 (+) |  1.000 |  0.942 | ggaGATAAac
 V$GATA1_05             |     1258 (-) |  0.800 |  0.803 | tgTCATCatc
 V$GATA1_05             |     1995 (-) |  1.000 |  0.948 | gaTTATCtgg
 V$GATA1_05             |     2722 (+) |  1.000 |  0.929 | ataGATAAtc
 V$GATA1_05             |     2902 (-) |  1.000 |  0.940 | ttTTATCcac
 V$GATA1_05             |     3930 (-) |  1.000 |  0.945 | caTTATCagt
 V$GATA1_05             |     4002 (+) |  1.000 |  0.932 | aacGATAAat
 V$GATA1_05             |     4374 (-) |  1.000 |  0.978 | agTTATCtgg
 V$GATA1_05             |     4779 (+) |  1.000 |  0.918 | ctgGATAAag
 V$GATA1_05             |     4817 (-) |  0.800 |  0.816 | tgTTACCagg
 V$GATA1_05             |     5582 (+) |  1.000 |  0.932 | aagGATAAta
 V$GATA1_05             |     5633 (+) |  1.000 |  0.917 | tggGATAAag
 V$GATA1_05             |     5977 (+) |  1.000 |  0.961 | ggtGATAAct
 V$GATA1_05             |     6465 (+) |  1.000 |  0.974 | cctGATAAaa
 V$GATA1_05             |     7788 (-) |  1.000 |  0.905 | aaTTATCcca
 V$GATA1_05             |     7797 (+) |  1.000 |  0.941 | aaaGATAAag
 V$GATA1_05             |     8062 (-) |  1.000 |  0.959 | gtTTATCtgg
 V$GATA1_05             |     8604 (-) |  1.000 |  0.949 | taTTATCatt
 V$GATA1_05             |     9732 (+) |  1.000 |  0.927 | tatGATAAtg
 V$GATA1_05             |     9833 (+) |  1.000 |  0.908 | aggGATAAtt
 V$GATA1_05             |    11064 (-) |  0.800 |  0.818 | tgTGATCagt
 V$GATA1_05             |    11348 (-) |  1.000 |  0.914 | caTTATCgaa
 V$GATA1_05             |    11441 (-) |  1.000 |  0.937 | acTTATCtat
 V$GATA1_05             |    11569 (-) |  1.000 |  0.960 | tcTTATCatt
 V$GATA1_05             |    11655 (+) |  0.800 |  0.818 | actGTTAAca
 V$GATA1_06             |      153 (-) |  0.839 |  0.820 | gcTCATCtct
 V$GATA1_06             |      566 (+) |  1.000 |  0.938 | ggaGATAAac
 V$GATA1_06             |     1699 (+) |  0.839 |  0.819 | gtaGATGAag
 V$GATA1_06             |     1753 (-) |  0.850 |  0.828 | acTGATCtat
 V$GATA1_06             |     1995 (-) |  1.000 |  0.949 | gaTTATCtgg
 V$GATA1_06             |     2722 (+) |  1.000 |  0.953 | ataGATAAtc
 V$GATA1_06             |     2902 (-) |  1.000 |  0.918 | ttTTATCcac
 V$GATA1_06             |     3930 (-) |  1.000 |  0.922 | caTTATCagt
 V$GATA1_06             |     4002 (+) |  1.000 |  0.900 | aacGATAAat
 V$GATA1_06             |     4374 (-) |  1.000 |  0.949 | agTTATCtgg
 V$GATA1_06             |     4779 (+) |  1.000 |  0.912 | ctgGATAAag
 V$GATA1_06             |     4801 (-) |  0.839 |  0.830 | caTAATCtct
 V$GATA1_06             |     4928 (+) |  0.850 |  0.841 | acaGATCAtg
 V$GATA1_06             |     5069 (+) |  0.839 |  0.858 | agaGATGAga
 V$GATA1_06             |     5407 (-) |  0.839 |  0.835 | ttTCATCtta
 V$GATA1_06             |     5582 (+) |  1.000 |  0.928 | aagGATAAta
 V$GATA1_06             |     5633 (+) |  1.000 |  0.897 | tggGATAAag
 V$GATA1_06             |     5977 (+) |  1.000 |  0.886 | ggtGATAAct
 V$GATA1_06             |     6465 (+) |  1.000 |  0.941 | cctGATAAaa
 V$GATA1_06             |     6659 (+) |  0.839 |  0.834 | acaGATGAag
 V$GATA1_06             |     7788 (-) |  1.000 |  0.871 | aaTTATCcca
 V$GATA1_06             |     7797 (+) |  1.000 |  0.972 | aaaGATAAag
 V$GATA1_06             |     8062 (-) |  1.000 |  0.952 | gtTTATCtgg
 V$GATA1_06             |     8241 (+) |  0.839 |  0.831 | ccaGATGAag
 V$GATA1_06             |     8381 (-) |  0.850 |  0.862 | ttTGATCtgt
 V$GATA1_06             |     8464 (-) |  0.839 |  0.844 | tcTCATCtaa
 V$GATA1_06             |     8604 (-) |  1.000 |  0.939 | taTTATCatt
 V$GATA1_06             |     9719 (-) |  0.850 |  0.820 | atTGATCtct
 V$GATA1_06             |     9732 (+) |  1.000 |  0.904 | tatGATAAtg
 V$GATA1_06             |     9833 (+) |  1.000 |  0.887 | aggGATAAtt
 V$GATA1_06             |    11348 (-) |  1.000 |  0.907 | caTTATCgaa
 V$GATA1_06             |    11441 (-) |  1.000 |  0.958 | acTTATCtat
 V$GATA1_06             |    11569 (-) |  1.000 |  0.948 | tcTTATCatt
 V$GATA2_02             |       82 (+) |  0.833 |  0.815 | gttGATAGgg
 V$GATA2_02             |       91 (-) |  0.833 |  0.826 | gcCTATCttc
 V$GATA2_02             |      153 (-) |  0.813 |  0.813 | gcTCATCtct
 V$GATA2_02             |      307 (-) |  0.833 |  0.821 | agCTATCtct
 V$GATA2_02             |      566 (+) |  1.000 |  0.961 | ggaGATAAac
 V$GATA2_02             |      952 (+) |  0.819 |  0.799 | aatGATCAaa
 V$GATA2_02             |     1065 (+) |  0.785 |  0.794 | taaAATAAga
 V$GATA2_02             |     1258 (-) |  0.813 |  0.795 | tgTCATCatc
 V$GATA2_02             |     1649 (-) |  0.813 |  0.807 | gcTAATCtac
 V$GATA2_02             |     1699 (+) |  0.813 |  0.792 | gtaGATGAag
 V$GATA2_02             |     1753 (-) |  0.819 |  0.819 | acTGATCtat
 V$GATA2_02             |     1995 (-) |  1.000 |  0.954 | gaTTATCtgg
 V$GATA2_02             |     2181 (-) |  0.785 |  0.796 | tcTTTTCttc
 V$GATA2_02             |     2186 (-) |  0.785 |  0.801 | tcTTCTCtct
 V$GATA2_02             |     2663 (+) |  0.813 |  0.793 | tttGATGAca
 V$GATA2_02             |     2722 (+) |  1.000 |  0.961 | ataGATAAtc
 V$GATA2_02             |     2751 (-) |  0.785 |  0.801 | tcTTTTCtct
 V$GATA2_02             |     2799 (-) |  0.785 |  0.794 | tcTTCTCtta
 V$GATA2_02             |     2902 (-) |  1.000 |  0.943 | ttTTATCcac
 V$GATA2_02             |     3178 (-) |  0.845 |  0.801 | ttATATCccc
 V$GATA2_02             |     3309 (+) |  0.785 |  0.796 | gtaGTTAAga
 V$GATA2_02             |     3374 (-) |  0.813 |  0.794 | ccTAATCata
 V$GATA2_02             |     3895 (-) |  0.813 |  0.795 | ccTCATCaca
 V$GATA2_02             |     3930 (-) |  1.000 |  0.950 | caTTATCagt
 V$GATA2_02             |     4002 (+) |  1.000 |  0.944 | aacGATAAat
 V$GATA2_02             |     4357 (+) |  0.819 |  0.796 | gagGATCAga
 V$GATA2_02             |     4374 (-) |  1.000 |  0.967 | agTTATCtgg
 V$GATA2_02             |     4577 (+) |  0.845 |  0.819 | ttaGATATag
 V$GATA2_02             |     4779 (+) |  1.000 |  0.931 | ctgGATAAag
 V$GATA2_02             |     4801 (-) |  0.813 |  0.793 | caTAATCtct
 V$GATA2_02             |     4928 (+) |  0.819 |  0.798 | acaGATCAtg
 V$GATA2_02             |     5069 (+) |  0.813 |  0.828 | agaGATGAga
 V$GATA2_02             |     5236 (+) |  0.813 |  0.793 | aacGATTAca
 V$GATA2_02             |     5407 (-) |  0.813 |  0.801 | ttTCATCtta
 V$GATA2_02             |     5527 (-) |  0.833 |  0.807 | tcCTATCcag
 V$GATA2_02             |     5582 (+) |  1.000 |  0.944 | aagGATAAta
 V$GATA2_02             |     5633 (+) |  1.000 |  0.931 | tggGATAAag
 V$GATA2_02             |     5655 (+) |  0.785 |  0.796 | gaaGAAAAga
 V$GATA2_02             |     5977 (+) |  1.000 |  0.954 | ggtGATAAct
 V$GATA2_02             |     6309 (-) |  0.819 |  0.814 | acTGATCtac
 V$GATA2_02             |     6465 (+) |  1.000 |  0.959 | cctGATAAaa
 V$GATA2_02             |     6550 (+) |  0.785 |  0.794 | tgaGGTAAga
 V$GATA2_02             |     6659 (+) |  0.813 |  0.797 | acaGATGAag
 V$GATA2_02             |     6892 (+) |  0.785 |  0.794 | taaGACAAga
 V$GATA2_02             |     6947 (+) |  0.833 |  0.797 | agtGATACtg
 V$GATA2_02             |     7152 (-) |  0.833 |  0.830 | ccGTATCtcc
 V$GATA2_02             |     7274 (+) |  0.785 |  0.794 | taaAATAAga
 V$GATA2_02             |     7310 (+) |  0.845 |  0.795 | aagGATATag
 V$GATA2_02             |     7375 (+) |  0.845 |  0.807 | attGATATtg
 V$GATA2_02             |     7788 (-) |  1.000 |  0.923 | aaTTATCcca
 V$GATA2_02             |     7797 (+) |  1.000 |  0.969 | aaaGATAAag
 V$GATA2_02             |     7902 (+) |  0.845 |  0.810 | tttGATATta
 V$GATA2_02             |     7922 (-) |  0.833 |  0.805 | agGTATCaat
 V$GATA2_02             |     7951 (+) |  0.833 |  0.812 | tgaGATACcc
 V$GATA2_02             |     8062 (-) |  1.000 |  0.959 | gtTTATCtgg
 V$GATA2_02             |     8381 (-) |  0.819 |  0.813 | ttTGATCtgt
 V$GATA2_02             |     8464 (-) |  0.813 |  0.820 | tcTCATCtaa
 V$GATA2_02             |     8604 (-) |  1.000 |  0.961 | taTTATCatt
 V$GATA2_02             |     9367 (-) |  0.833 |  0.794 | ctCTATCaca
 V$GATA2_02             |     9719 (-) |  0.819 |  0.800 | atTGATCtct
 V$GATA2_02             |     9732 (+) |  1.000 |  0.943 | tatGATAAtg
 V$GATA2_02             |     9833 (+) |  1.000 |  0.931 | aggGATAAtt
 V$GATA2_02             |     9980 (+) |  0.819 |  0.796 | gggGATCAga
 V$GATA2_02             |    10131 (+) |  0.785 |  0.794 | ttaGTTAAga
 V$GATA2_02             |    10286 (-) |  0.813 |  0.806 | tcTCATCagg
 V$GATA2_02             |    10454 (-) |  0.845 |  0.817 | ttATATCaac
 V$GATA2_02             |    10488 (-) |  0.845 |  0.821 | acATATCaag
 V$GATA2_02             |    10594 (-) |  0.845 |  0.804 | ctATATCaaa
 V$GATA2_02             |    11000 (+) |  0.813 |  0.793 | tcaGATTAcc
 V$GATA2_02             |    11064 (+) |  0.819 |  0.797 | tgtGATCAgt
 V$GATA2_02             |    11064 (-) |  0.819 |  0.806 | tgTGATCagt
 V$GATA2_02             |    11348 (-) |  1.000 |  0.935 | caTTATCgaa
 V$GATA2_02             |    11369 (-) |  0.833 |  0.826 | ttCTATCtgt
 V$GATA2_02             |    11441 (-) |  1.000 |  0.985 | acTTATCtat
 V$GATA2_02             |    11509 (+) |  0.845 |  0.796 | gtgGATATta
 V$GATA2_02             |    11569 (-) |  1.000 |  0.985 | tcTTATCatt
 V$GATA2_02             |    11581 (-) |  0.845 |  0.799 | ttATATCcag
 V$GATA2_02             |    11774 (+) |  0.833 |  0.802 | ccaGATACtt
 V$GATA2_03             |     2902 (-) |  1.000 |  0.912 | ttTTATCcac
 V$GATA2_03             |     3178 (-) |  0.954 |  0.905 | ttATATCccc
 V$GATA2_03             |     5069 (+) |  0.871 |  0.908 | agaGATGAga
 V$GATA2_03             |     5582 (+) |  1.000 |  0.931 | aagGATAAta
 V$GATA2_03             |     6465 (+) |  1.000 |  0.944 | cctGATAAaa
 V$GATA2_03             |     8381 (-) |  0.908 |  0.920 | ttTGATCtgt
 V$GATA2_03             |     8604 (-) |  1.000 |  0.943 | taTTATCatt
 V$GATA2_03             |    11369 (-) |  0.942 |  0.945 | ttCTATCtgt
 V$GATA2_03             |    11569 (-) |  1.000 |  0.947 | tcTTATCatt
 V$GATA3_02             |      566 (+) |  1.000 |  0.950 | ggaGATAAac
 V$GATA3_02             |     1995 (-) |  1.000 |  0.931 | gaTTATCtgg
 V$GATA3_02             |     2722 (+) |  1.000 |  0.936 | ataGATAAtc
 V$GATA3_02             |     2902 (-) |  1.000 |  0.933 | ttTTATCcac
 V$GATA3_02             |     3930 (-) |  1.000 |  0.916 | caTTATCagt
 V$GATA3_02             |     4002 (+) |  1.000 |  0.919 | aacGATAAat
 V$GATA3_02             |     4374 (-) |  1.000 |  0.937 | agTTATCtgg
 V$GATA3_02             |     5069 (+) |  0.917 |  0.926 | agaGATGAga
 V$GATA3_02             |     5407 (-) |  0.917 |  0.902 | ttTCATCtta
 V$GATA3_02             |     5582 (+) |  1.000 |  0.949 | aagGATAAta
 V$GATA3_02             |     5633 (+) |  1.000 |  0.919 | tggGATAAag
 V$GATA3_02             |     5977 (+) |  1.000 |  0.928 | ggtGATAAct
 V$GATA3_02             |     6465 (+) |  1.000 |  0.942 | cctGATAAaa
 V$GATA3_02             |     7788 (-) |  1.000 |  0.921 | aaTTATCcca
 V$GATA3_02             |     7797 (+) |  1.000 |  0.949 | aaaGATAAag
 V$GATA3_02             |     8062 (-) |  1.000 |  0.929 | gtTTATCtgg
 V$GATA3_02             |     8381 (-) |  0.928 |  0.914 | ttTGATCtgt
 V$GATA3_02             |     8604 (-) |  1.000 |  0.956 | taTTATCatt
 V$GATA3_02             |     9719 (-) |  0.928 |  0.899 | atTGATCtct
 V$GATA3_02             |     9732 (+) |  1.000 |  0.914 | tatGATAAtg
 V$GATA3_02             |     9833 (+) |  1.000 |  0.928 | aggGATAAtt
 V$GATA3_02             |    11348 (-) |  1.000 |  0.905 | caTTATCgaa
 V$GATA3_02             |    11441 (-) |  1.000 |  0.943 | acTTATCtat
 V$GATA3_02             |    11569 (-) |  1.000 |  0.957 | tcTTATCatt
 V$GATA3_03             |       43 (+) |  0.955 |  0.900 | tcaGATGTca
 V$GATA3_03             |      242 (-) |  0.968 |  0.926 | ttAAATCtgg
 V$GATA3_03             |      706 (-) |  0.915 |  0.913 | tcGGATCtct
 V$GATA3_03             |      952 (+) |  0.977 |  0.926 | aatGATCAaa
 V$GATA3_03             |     4119 (+) |  0.955 |  0.927 | ccaGATGTta
 V$GATA3_03             |     5069 (+) |  0.932 |  0.926 | agaGATGAga
 V$GATA3_03             |     5407 (-) |  0.932 |  0.903 | ttTCATCtta
 V$GATA3_03             |     5417 (-) |  0.968 |  0.964 | ttAAATCttt
 V$GATA3_03             |     5582 (+) |  0.958 |  0.900 | aagGATAAta
 V$GATA3_03             |     6665 (+) |  0.968 |  0.944 | gaaGATTTta
 V$GATA3_03             |     6782 (+) |  1.000 |  0.956 | gcaGATCTaa
 V$GATA3_03             |     7902 (+) |  0.981 |  0.905 | tttGATATta
 V$GATA3_03             |     8381 (-) |  0.977 |  0.968 | ttTGATCtgt
 V$GATA3_03             |     8604 (-) |  0.958 |  0.922 | taTTATCatt
 V$GATA3_03             |    10495 (+) |  0.977 |  0.904 | aagGATCAaa
 V$GATA3_03             |    11026 (+) |  0.915 |  0.931 | agaGATCCta
 V$GATA3_03             |    11064 (-) |  0.977 |  0.906 | tgTGATCagt
 V$GATA3_03             |    11116 (-) |  1.000 |  0.912 | tcAGATCcct
 V$GATA3_03             |    11171 (+) |  1.000 |  0.915 | agaGATCTtt
 V$GATA3_03             |    11369 (-) |  0.896 |  0.905 | ttCTATCtgt
 V$GATA3_03             |    11569 (-) |  0.958 |  0.904 | tcTTATCatt
 P$DOF1_01              |     7799 (+) |  1.000 |  0.988 | agaTAAAGaac
 P$DOF1_01              |     8936 (+) |  1.000 |  0.998 | aacTAAAGcaa
 P$DOF2_01              |     1038 (+) |  1.000 |  0.985 | caacAAAGCag
 P$DOF2_01              |     2398 (-) |  1.000 |  0.984 | ttGCTTTcctt
 P$DOF2_01              |     3910 (+) |  1.000 |  0.996 | taatAAAGCtt
 P$DOF2_01              |     3915 (-) |  1.000 |  0.996 | aaGCTTTatga
 P$DOF2_01              |     6677 (-) |  1.000 |  0.990 | taGCTTTtgaa
 P$DOF2_01              |     6708 (+) |  1.000 |  0.989 | gagaAAAGCca
 P$DOF2_01              |     7652 (-) |  1.000 |  0.990 | atGCTTTtgta
 P$DOF2_01              |     7685 (+) |  1.000 |  0.997 | ctgtAAAGCca
 P$DOF2_01              |     7846 (+) |  1.000 |  0.988 | ggcaAAAGCga
 P$DOF2_01              |     7868 (+) |  1.000 |  0.991 | tagaAAAGCtc
 P$DOF2_01              |     7910 (-) |  1.000 |  0.993 | taGCTTTtact
 P$DOF2_01              |     8628 (+) |  1.000 |  0.987 | gagaAAAGCtt
 P$DOF2_01              |     8936 (+) |  1.000 |  0.998 | aactAAAGCaa
 P$DOF2_01              |     9102 (+) |  1.000 |  0.991 | tacaAAAGCaa
 P$DOF2_01              |    10729 (-) |  1.000 |  0.994 | taGCTTTtatt
 P$DOF2_01              |    11009 (-) |  1.000 |  0.997 | ctGCTTTaggg
 P$DOF3_01              |     2027 (+) |  0.992 |  0.988 | gattAAAGGag
 P$DOF3_01              |     2199 (-) |  0.992 |  0.987 | ttTCTTTcttc
 P$DOF3_01              |     2271 (-) |  0.992 |  0.987 | ttTCTTTcttc
 P$DOF3_01              |     2398 (-) |  1.000 |  0.990 | ttGCTTTcctt
 P$DOF3_01              |     2506 (+) |  0.992 |  0.986 | aaaaAAAGGga
 P$DOF3_01              |     2749 (-) |  0.992 |  0.992 | ttTCTTTtctc
 P$DOF3_01              |     5518 (-) |  0.992 |  0.988 | tgCCTTTcctc
 P$DOF3_01              |     5940 (+) |  0.994 |  0.994 | gagaAAAGTaa
 P$DOF3_01              |     6426 (-) |  1.000 |  0.995 | tgGCTTTcatc
 P$DOF3_01              |     6708 (+) |  1.000 |  0.999 | gagaAAAGCca
 P$DOF3_01              |     7086 (-) |  1.000 |  0.989 | gtGCTTTgcgc
 P$DOF3_01              |     7652 (-) |  1.000 |  0.989 | atGCTTTtgta
 P$DOF3_01              |     7846 (+) |  1.000 |  0.990 | ggcaAAAGCga
 P$DOF3_01              |     7868 (+) |  1.000 |  0.988 | tagaAAAGCtc
 P$DOF3_01              |     8133 (-) |  1.000 |  0.987 | ctGCTTTctgc
 P$DOF3_01              |     8377 (-) |  0.992 |  0.987 | gcTCTTTgatc
 P$DOF3_01              |     8628 (+) |  1.000 |  0.994 | gagaAAAGCtt
 P$DOF3_01              |     8936 (+) |  1.000 |  0.993 | aactAAAGCaa
 P$DOF3_01              |     9102 (+) |  1.000 |  0.992 | tacaAAAGCaa
 P$DOF3_01              |    10576 (-) |  1.000 |  0.990 | ttGCTTTggtt
 P$DOF3_01              |    10729 (-) |  1.000 |  0.991 | taGCTTTtatt
 P$CDC5_01              |      794 (-) |  1.000 |  0.982 | accGCTGAgcc
 P$CDC5_01              |     4973 (+) |  1.000 |  0.869 | ggcTCAGCccc
 P$EMBP1_Q2             |      735 (+) |  1.000 |  0.929 | acCACGTggt
 P$EMBP1_Q2             |      735 (-) |  1.000 |  0.929 | accACGTGgt
 P$EMBP1_Q2             |     6003 (-) |  1.000 |  0.906 | ggtACGTGtc
 P$TAF1_Q2              |      735 (+) |  1.000 |  0.983 | accACGTGgt
 P$TAF1_Q2              |      735 (-) |  1.000 |  0.983 | acCACGTggt
 P$CPRF2_Q2             |      735 (+) |  1.000 |  0.998 | acCACGTggt
 P$CPRF2_Q2             |      735 (-) |  1.000 |  0.998 | accACGTGgt
 P$O2_02                |      434 (+) |  1.000 |  0.959 | acCACGTtta
 P$O2_02                |      434 (-) |  0.919 |  0.896 | accACGTTta
 P$O2_02                |      571 (+) |  0.919 |  0.879 | taAACGTcta
 P$O2_02                |      571 (-) |  0.946 |  0.890 | taaACGTCta
 P$O2_02                |      735 (+) |  1.000 |  0.990 | acCACGTggt
 P$O2_02                |      735 (-) |  1.000 |  0.990 | accACGTGgt
 P$O2_02                |     1126 (+) |  1.000 |  0.949 | tgCACGTgtg
 P$O2_02                |     1126 (-) |  1.000 |  0.944 | tgcACGTGtg
 P$O2_02                |     1460 (+) |  0.946 |  0.872 | cgGACGTttc
 P$O2_02                |     1460 (-) |  0.919 |  0.861 | cggACGTTtc
 P$O2_02                |     6003 (+) |  0.924 |  0.874 | ggTACGTgtc
 P$O2_02                |     6003 (-) |  1.000 |  0.936 | ggtACGTGtc
 P$O2_02                |     6064 (+) |  1.000 |  0.941 | tgCACGTgct
 P$O2_02                |     6064 (-) |  1.000 |  0.936 | tgcACGTGct
 P$O2_02                |     6856 (+) |  1.000 |  0.928 | agCACGTcca
 P$O2_02                |     6856 (-) |  0.946 |  0.892 | agcACGTCca
 P$O2_02                |     6886 (+) |  1.000 |  0.977 | acCACGTaag
 P$O2_02                |     6886 (-) |  0.924 |  0.901 | accACGTAag
 P$O2_02                |     7322 (+) |  0.924 |  0.872 | tgTACGTctg
 P$O2_02                |     7322 (-) |  0.946 |  0.887 | tgtACGTCtg
 P$O2_02                |     7486 (+) |  1.000 |  0.934 | cgCACGTctg
 P$O2_02                |     7486 (-) |  0.946 |  0.892 | cgcACGTCtg
 P$O2_02                |     8730 (+) |  0.919 |  0.891 | gtAACGTcgg
 P$O2_02                |     8730 (-) |  0.946 |  0.916 | gtaACGTCgg
 P$O2_02                |     8891 (+) |  0.919 |  0.860 | caAACGTacc
 P$O2_02                |    10442 (+) |  0.919 |  0.898 | gcAACGTctc
 P$O2_02                |    10442 (-) |  0.946 |  0.895 | gcaACGTCtc
 P$O2_02                |    11057 (+) |  0.919 |  0.884 | ttAACGTtgt
 P$O2_02                |    11057 (-) |  0.919 |  0.893 | ttaACGTTgt
 P$TGA1A_Q2             |     1126 (+) |  1.000 |  0.981 | tgCACGTgtg
 P$TGA1A_Q2             |     1126 (-) |  1.000 |  0.981 | tgcACGTGtg
 P$TGA1A_Q2             |     7486 (+) |  1.000 |  0.986 | cgCACGTctg
 P$TGA1A_Q2             |     7486 (-) |  0.992 |  0.980 | cgcACGTCtg
 V$PAX4_04              |       28 (-) |  0.797 |  0.773 | tgtgtgtgaacaacttcagatgtcaTTACT
 V$PAX4_04              |      534 (-) |  0.943 |  0.778 | tgggtgatgcgcttgtgttttaaccTTTTC
 V$PAX4_04              |     1510 (-) |  0.936 |  0.780 | ggagggagggaggtagagctgttttTTTGT
 V$PAX4_04              |     1878 (-) |  0.936 |  0.768 | gatctgcctcccattttatatttatTTTAT
 V$PAX4_04              |     2519 (+) |  1.000 |  0.765 | AAAAAttacatattacttttagagaataac
 V$PAX4_04              |     4430 (+) |  1.000 |  0.776 | AAAAAaaaaaaaccacacaattaatattca
 V$PAX4_04              |     4434 (+) |  1.000 |  0.818 | AAAAAaaaccacacaattaatattcatttc
 V$PAX4_04              |     4493 (+) |  0.936 |  0.846 | ACAAAaaacaaaacaaaacaacatcagacc
 V$PAX4_04              |     5082 (-) |  0.936 |  0.768 | tggctctgactggtttgggttattaTTTGT
 V$PAX4_04              |     5805 (+) |  1.000 |  0.799 | AAAAAaaaaatagccctggcgtggcactgt
 V$PAX4_04              |     7030 (-) |  1.000 |  0.779 | cagctgaagagttagttgactatttTTTTT
 V$PAX4_04              |     7785 (+) |  1.000 |  0.816 | AAAAAttatcccaaagataaagaacaacga
 V$PAX4_04              |     7923 (-) |  0.887 |  0.799 | ggtatcaattcgtttgtgtgtttagTTTTG
 V$PAX4_04              |     8856 (+) |  1.000 |  0.835 | AAAAAttaagactctggcatagaatattct
 V$PAX4_04              |     9416 (+) |  0.943 |  0.767 | GAAAActatcccataaataacaggaagccc
 V$PAX4_04              |     9461 (-) |  0.936 |  0.764 | ctgctgtacaggatgttctagctacTTTAT
 V$PAX4_04              |     9703 (-) |  0.936 |  0.784 | gtggtggtggtgtaaaattgatctcTTTGT
 V$PAX4_04              |    10243 (-) |  1.000 |  0.805 | gtggtcaggcttgtgcaggaagtgaTTTTT
 V$PAX4_04              |    11187 (-) |  0.936 |  0.817 | gccttgtttcttgattgattattaaTTTGT
 V$PAX4_04              |    11295 (+) |  0.950 |  0.779 | AGAAAtaataataacgactacggtgacgac
 V$PAX4_04              |    11374 (-) |  0.936 |  0.771 | tctgtgctttgaaaacttattaaatTTTGT
 V$PAX4_04              |    11452 (-) |  0.809 |  0.779 | ttggtgaatcagtgaaattttttatTTGTT
 V$PAX4_04              |    11677 (+) |  0.823 |  0.774 | CCAAAaaagaccaataaagttaatcactgt
 F$FACBCA_Q2            |      362 (+) |  0.853 |  0.899 | tcaaatcctttctctagGTGAGagat
 F$FACBCA_Q2            |      362 (-) |  0.989 |  0.849 | tcaaATCCTttctctaggtgagagat
 F$FACBCA_Q2            |      952 (+) |  0.930 |  0.810 | aatgatcaaatatttacAGGACccct
 F$FACBCA_Q2            |      952 (-) |  0.808 |  0.845 | aatgATCAAatatttacaggacccct
 F$FACBCA_Q2            |     1272 (-) |  0.806 |  0.802 | tgtaCTCTGggatgacagggacctgg
 F$FACBCA_Q2            |     1473 (-) |  0.691 |  0.797 | atatTTGCTctggcagagggaggggg
 F$FACBCA_Q2            |     1718 (+) |  0.786 |  0.804 | ccttttccgggctcatcCTGAActtc
 F$FACBCA_Q2            |     1718 (-) |  0.933 |  0.809 | ccttTTCCGggctcatcctgaacttc
 F$FACBCA_Q2            |     1737 (+) |  0.830 |  0.874 | gaacttcctatagaacaCTGATctat
 F$FACBCA_Q2            |     2016 (-) |  0.677 |  0.813 | ctgaGTGCTgggattaaaggagtgta
 F$FACBCA_Q2            |     2419 (+) |  1.000 |  0.827 | aaaaatcacaggggttgGGGATttag
 F$FACBCA_Q2            |     2419 (-) |  0.853 |  0.873 | aaaaATCACaggggttggggatttag
 F$FACBCA_Q2            |     2496 (+) |  0.956 |  0.858 | tcagctccgaaaaaaaaGGGAAaaaa
 F$FACBCA_Q2            |     2496 (-) |  0.977 |  0.891 | tcagCTCCGaaaaaaaagggaaaaaa
 F$FACBCA_Q2            |     2902 (+) |  0.896 |  0.879 | ttttatccacatctctgTGGACggac
 F$FACBCA_Q2            |     2902 (-) |  0.955 |  0.878 | ttttATCCAcatctctgtggacggac
 F$FACBCA_Q2            |     2992 (+) |  0.724 |  0.796 | tccgctcctccaaggtgCGCAGgcgt
 F$FACBCA_Q2            |     3031 (+) |  0.941 |  0.936 | cgacttccgctccacccGGGACatac
 F$FACBCA_Q2            |     3031 (-) |  0.933 |  0.857 | cgacTTCCGctccacccgggacatac
 F$FACBCA_Q2            |     3374 (+) |  0.830 |  0.803 | cctaatcatatggggccCTGAGgatc
 F$FACBCA_Q2            |     3986 (+) |  0.842 |  0.793 | caccatctcatgaaacaACGATaaat
 F$FACBCA_Q2            |     4227 (-) |  0.699 |  0.826 | ataaATTCTcagggctggggattgta
 F$FACBCA_Q2            |     4742 (+) |  0.665 |  0.800 | gatggtcctctcccctcTGTAGgtcc
 F$FACBCA_Q2            |     6256 (+) |  0.773 |  0.853 | atttgtcccatctgccgAAGAAggaa
 F$FACBCA_Q2            |     6256 (-) |  0.941 |  0.809 | atttGTCCCatctgccgaagaaggaa
 F$FACBCA_Q2            |     6355 (-) |  0.830 |  0.819 | aaagCTCAGggtactaagcgagattt
 F$FACBCA_Q2            |     6753 (+) |  0.798 |  0.842 | cactatccctttataccATGAAcaaa
 F$FACBCA_Q2            |     6959 (-) |  0.699 |  0.847 | cattATTCTggatggaaaggaacgac
 F$FACBCA_Q2            |     8228 (+) |  0.798 |  0.817 | ttggctcccacacccagATGAAggtg
 F$FACBCA_Q2            |     8228 (-) |  1.000 |  0.847 | ttggCTCCCacacccagatgaaggtg
 F$FACBCA_Q2            |     9453 (+) |  0.989 |  0.822 | accaatctctgctgtacAGGATgttc
 F$FACBCA_Q2            |     9453 (-) |  0.829 |  0.883 | accaATCTCtgctgtacaggatgttc
 F$FACBCA_Q2            |     9664 (+) |  0.955 |  0.788 | ccttgtctcaaaagaagTGGAGgggg
 F$FACBCA_Q2            |     9664 (-) |  0.770 |  0.842 | ccttGTCTCaaaagaagtggaggggg
 F$FACBCA_Q2            |     9969 (+) |  0.762 |  0.837 | ctggttcctatggggatCAGAAgagg
 F$FACBCA_Q2            |     9969 (-) |  0.945 |  0.839 | ctggTTCCTatggggatcagaagagg
 F$FACBCA_Q2            |    11531 (+) |  0.783 |  0.802 | gcaaatcccacatatggTAGATgggt
 F$FACBCA_Q2            |    11531 (-) |  1.000 |  0.798 | gcaaATCCCacatatggtagatgggt
 F$FACBCA_Q2            |    11737 (-) |  0.853 |  0.819 | acatCTCACcaaatgactagaaagag
 F$FACBALL_Q2           |      190 (-) |  0.822 |  0.821 | gtgcctcccacaccaccaTGCCTggt
 F$FACBALL_Q2           |      283 (+) |  0.920 |  0.805 | gcaAGTCAagtgttttacagactgag
 F$FACBALL_Q2           |      309 (+) |  0.882 |  0.785 | ctaTCTCTcctagtcctgtgctggaa
 F$FACBALL_Q2           |      362 (+) |  0.992 |  0.870 | tcaAATCCtttctctaggtgagagat
 F$FACBALL_Q2           |      362 (-) |  0.939 |  0.884 | tcaaatcctttctctaggTGAGAgat
 F$FACBALL_Q2           |      952 (+) |  0.935 |  0.877 | aatGATCAaatatttacaggacccct
 F$FACBALL_Q2           |      952 (-) |  0.976 |  0.860 | aatgatcaaatatttacaGGACCcct
 F$FACBALL_Q2           |     1272 (+) |  0.874 |  0.830 | tgtACTCTgggatgacagggacctgg
 F$FACBALL_Q2           |     1272 (-) |  0.976 |  0.795 | tgtactctgggatgacagGGACCtgg
 F$FACBALL_Q2           |     1322 (+) |  0.871 |  0.818 | tccCTTCTcactccccagggcttaag
 F$FACBALL_Q2           |     1428 (-) |  0.928 |  0.793 | cgcaatcagtggcaatagTGAAGtca
 F$FACBALL_Q2           |     1672 (-) |  0.781 |  0.791 | attcctccttcgggtgtcAGCTCagg
 F$FACBALL_Q2           |     1683 (+) |  0.928 |  0.806 | gggTGTCAgctcaggggtagatgaag
 F$FACBALL_Q2           |     1709 (+) |  0.871 |  0.843 | cacCCTCTgccttttccgggctcatc
 F$FACBALL_Q2           |     1718 (+) |  0.996 |  0.840 | cctTTTCCgggctcatcctgaacttc
 F$FACBALL_Q2           |     1718 (-) |  0.931 |  0.875 | ccttttccgggctcatccTGAACttc
 F$FACBALL_Q2           |     1737 (+) |  0.985 |  0.853 | gaaCTTCCtatagaacactgatctat
 F$FACBALL_Q2           |     1737 (-) |  0.935 |  0.899 | gaacttcctatagaacacTGATCtat
 F$FACBALL_Q2           |     1926 (+) |  0.871 |  0.803 | gtaTGTCTatgtagccttggctaggc
 F$FACBALL_Q2           |     1985 (-) |  0.903 |  0.792 | aactcaccaagattatctGGCTAtac
 F$FACBALL_Q2           |     2016 (-) |  0.988 |  0.803 | ctgagtgctgggattaaaGGAGTgta
 F$FACBALL_Q2           |     2419 (+) |  0.935 |  0.873 | aaaAATCAcaggggttggggatttag
 F$FACBALL_Q2           |     2419 (-) |  0.992 |  0.875 | aaaaatcacaggggttggGGATTtag
 F$FACBALL_Q2           |     2496 (+) |  0.988 |  0.868 | tcaGCTCCgaaaaaaaagggaaaaaa
 F$FACBALL_Q2           |     2496 (-) |  0.996 |  0.914 | tcagctccgaaaaaaaagGGAAAaaa
 F$FACBALL_Q2           |     2902 (+) |  1.000 |  0.906 | tttTATCCacatctctgtggacggac
 F$FACBALL_Q2           |     2902 (-) |  0.974 |  0.864 | ttttatccacatctctgtGGACGgac
 F$FACBALL_Q2           |     2987 (+) |  0.985 |  0.830 | ctaCTTCCgctcctccaaggtgcgca
 F$FACBALL_Q2           |     2995 (+) |  0.985 |  0.856 | gctCCTCCaaggtgcgcaggcgtctc
 F$FACBALL_Q2           |     2995 (-) |  0.891 |  0.841 | gctcctccaaggtgcgcaGGCGTctc
 F$FACBALL_Q2           |     3003 (+) |  0.805 |  0.794 | aagGTGCGcaggcgtctcggcagtac
 F$FACBALL_Q2           |     3031 (+) |  0.985 |  0.961 | cgaCTTCCgctccacccgggacatac
 F$FACBALL_Q2           |     3031 (-) |  0.985 |  0.866 | cgacttccgctccacccgGGACAtac
 F$FACBALL_Q2           |     3040 (-) |  0.842 |  0.793 | ctccacccgggacataccTGCGAgtg
 F$FACBALL_Q2           |     3270 (+) |  0.891 |  0.840 | gtgATGCCattatgattgggatgagg
 F$FACBALL_Q2           |     3270 (-) |  0.989 |  0.857 | gtgatgccattatgattgGGATGagg
 F$FACBALL_Q2           |     3349 (+) |  0.932 |  0.793 | gttCATCAgacagaccactgaatagc
 F$FACBALL_Q2           |     3349 (-) |  0.931 |  0.801 | gttcatcagacagaccacTGAATagc
 F$FACBALL_Q2           |     3374 (+) |  0.935 |  0.857 | cctAATCAtatggggccctgaggatc
 F$FACBALL_Q2           |     3374 (-) |  0.928 |  0.796 | cctaatcatatggggcccTGAGGatc
 F$FACBALL_Q2           |     3502 (-) |  0.985 |  0.809 | aactaccctgctgttagaGGAGGcca
 F$FACBALL_Q2           |     3946 (-) |  0.931 |  0.794 | ttcattcagccatcctacTGAGCact
 F$FACBALL_Q2           |     3986 (+) |  0.875 |  0.805 | cacCATCTcatgaaacaacgataaat
 F$FACBALL_Q2           |     3986 (-) |  0.915 |  0.795 | caccatctcatgaaacaaCGATAaat
 F$FACBALL_Q2           |     4039 (-) |  0.899 |  0.789 | ttccagcagggggaaataGGCAAtaa
 F$FACBALL_Q2           |     4334 (+) |  0.989 |  0.846 | tgaCATCCaggtggtggaggcaggag
 F$FACBALL_Q2           |     4334 (-) |  0.888 |  0.816 | tgacatccaggtggtggaGGCAGgag
 F$FACBALL_Q2           |     4392 (-) |  0.774 |  0.789 | tgagttccaagacaggtcAGCCAcaa
 F$FACBALL_Q2           |     4584 (-) |  0.809 |  0.789 | tagtctcctcctcctgccCGCTTgct
 F$FACBALL_Q2           |     4807 (+) |  0.831 |  0.804 | ctcTGGCAtttgttaccaggcggggt
 F$FACBALL_Q2           |     4867 (+) |  0.835 |  0.838 | ggtCAGCAgcaaagctctggaacatt
 F$FACBALL_Q2           |     4974 (+) |  0.892 |  0.790 | gctCAGCCcctacctgtccgaatggc
 F$FACBALL_Q2           |     4974 (-) |  0.902 |  0.792 | gctcagcccctacctgtcCGAATggc
 F$FACBALL_Q2           |     5049 (-) |  0.939 |  0.785 | tgtggtctaagcaggtagTGAGAgat
 F$FACBALL_Q2           |     5256 (+) |  0.920 |  0.785 | tgtGGTCAcagtcatcctgggccaac
 F$FACBALL_Q2           |     5500 (+) |  0.988 |  0.820 | tctGCTCCcaggtttccctgcctttc
 F$FACBALL_Q2           |     5500 (-) |  0.822 |  0.821 | tctgctcccaggtttcccTGCCTttc
 F$FACBALL_Q2           |     5921 (+) |  0.806 |  0.852 | cccCAGCGagactcccttggagaaaa
 F$FACBALL_Q2           |     6055 (-) |  0.831 |  0.787 | tgacagccctgcacgtgcTGCCAcag
 F$FACBALL_Q2           |     6069 (+) |  0.888 |  0.784 | gtgCTGCCacagtctctgtgagttcc
 F$FACBALL_Q2           |     6069 (-) |  0.931 |  0.821 | gtgctgccacagtctctgTGAGTtcc
 F$FACBALL_Q2           |     6128 (+) |  0.911 |  0.788 | tttTCTCGgcgtcttccatgcctctg
 F$FACBALL_Q2           |     6160 (+) |  0.985 |  0.819 | ctgCCTCCtcttctgcagggttccca
 F$FACBALL_Q2           |     6256 (+) |  0.985 |  0.859 | attTGTCCcatctgccgaagaaggaa
 F$FACBALL_Q2           |     6256 (-) |  0.871 |  0.846 | atttgtcccatctgccgaAGAAGgaa
 F$FACBALL_Q2           |     6277 (+) |  0.894 |  0.797 | aggAAGCCtctctgatgatgactgag
 F$FACBALL_Q2           |     6277 (-) |  0.920 |  0.804 | aggaagcctctctgatgaTGACTgag
 F$FACBALL_Q2           |     6355 (+) |  0.931 |  0.822 | aaaGCTCAgggtactaagcgagattt
 F$FACBALL_Q2           |     6355 (-) |  0.911 |  0.838 | aaagctcagggtactaagCGAGAttt
 F$FACBALL_Q2           |     6434 (+) |  0.920 |  0.810 | atcGGTCAacccagtcatggcaaact
 F$FACBALL_Q2           |     6753 (+) |  1.000 |  0.866 | cacTATCCctttataccatgaacaaa
 F$FACBALL_Q2           |     6753 (-) |  0.931 |  0.863 | cactatccctttataccaTGAACaaa
 F$FACBALL_Q2           |     6816 (+) |  0.996 |  0.840 | cctTCTCCcttttttatgtgctattt
 F$FACBALL_Q2           |     6816 (-) |  0.846 |  0.814 | ccttctcccttttttatgTGCTAttt
 F$FACBALL_Q2           |     6862 (-) |  0.985 |  0.821 | tccagaccgaggcttataGGAAGcac
 F$FACBALL_Q2           |     6881 (-) |  0.871 |  0.801 | gaagcaccacgtaagacaAGAGGgca
 F$FACBALL_Q2           |     6959 (-) |  0.988 |  0.823 | cattattctggatggaaaGGAACgac
 F$FACBALL_Q2           |     7016 (-) |  0.928 |  0.784 | gatgtttcctgcatcagcTGAAGagt
 F$FACBALL_Q2           |     7294 (+) |  0.781 |  0.804 | accAAGCTgagagagtaaggatatag
 F$FACBALL_Q2           |     7294 (-) |  1.000 |  0.793 | accaagctgagagagtaaGGATAtag
 F$FACBALL_Q2           |     7613 (+) |  0.882 |  0.829 | ccaTCTCTccagccgcctggcggtag
 F$FACBALL_Q2           |     7729 (-) |  0.903 |  0.797 | tttgggccatcacaggctGGCTAcat
 F$FACBALL_Q2           |     8025 (+) |  0.928 |  0.841 | gagTGTCAgagcttgctgggccttga
 F$FACBALL_Q2           |     8025 (-) |  0.879 |  0.808 | gagtgtcagagcttgctgGGCCTtga
 F$FACBALL_Q2           |     8112 (+) |  0.996 |  0.797 | cacTCTCCcaccctgcctggtctgct
 F$FACBALL_Q2           |     8157 (-) |  0.777 |  0.803 | tagcttccagaggcaggtAGCACcag
 F$FACBALL_Q2           |     8228 (+) |  0.988 |  0.832 | ttgGCTCCcacacccagatgaaggtg
 F$FACBALL_Q2           |     8228 (-) |  0.928 |  0.896 | ttggctcccacacccagaTGAAGgtg
 F$FACBALL_Q2           |     8292 (+) |  0.900 |  0.782 | tccCTTCGcatgcccctctgccctgc
 F$FACBALL_Q2           |     8298 (+) |  0.891 |  0.787 | cgcATGCCcctctgccctgcagcttc
 F$FACBALL_Q2           |     8306 (-) |  0.834 |  0.793 | cctctgccctgcagcttcTGCGTcag
 F$FACBALL_Q2           |     8328 (+) |  0.891 |  0.845 | tcaGCGCCagtatttgctggaccact
 F$FACBALL_Q2           |     8328 (-) |  0.976 |  0.810 | tcagcgccagtatttgctGGACCact
 F$FACBALL_Q2           |     8365 (+) |  0.892 |  0.784 | gtgCAGCCtgctgctctttgatctgt
 F$FACBALL_Q2           |     8365 (-) |  0.935 |  0.800 | gtgcagcctgctgctcttTGATCtgt
 F$FACBALL_Q2           |     8395 (+) |  0.894 |  0.850 | ctgAAGCCaagccagcccggcctgta
 F$FACBALL_Q2           |     8395 (-) |  0.879 |  0.837 | ctgaagccaagccagcccGGCCTgta
 F$FACBALL_Q2           |     8616 (+) |  0.935 |  0.783 | gtcAATCActttgagaaaagcttatt
 F$FACBALL_Q2           |     8706 (-) |  0.874 |  0.800 | taccatcaaggagtctgaAGAACtgt
 F$FACBALL_Q2           |     8775 (-) |  0.875 |  0.828 | gggaggccgagacaaagaAGATGtag
 F$FACBALL_Q2           |     8828 (-) |  0.874 |  0.818 | gatgttcaaaaccaaaacAGAACggt
 F$FACBALL_Q2           |     8992 (+) |  0.988 |  0.813 | ttaATTCCagcacatggaggcagggg
 F$FACBALL_Q2           |     8992 (-) |  0.888 |  0.837 | ttaattccagcacatggaGGCAGggg
 F$FACBALL_Q2           |     9041 (+) |  0.892 |  0.827 | gggCAGCCtggtctacatggcaagtt
 F$FACBALL_Q2           |     9041 (-) |  0.899 |  0.785 | gggcagcctggtctacatGGCAAgtt
 F$FACBALL_Q2           |     9061 (+) |  0.988 |  0.790 | caaGTTCCaggctagccagggcagca
 F$FACBALL_Q2           |     9236 (-) |  0.838 |  0.813 | ccagagccctaggagagcTGCTCatg
 F$FACBALL_Q2           |     9292 (+) |  0.778 |  0.847 | agtCAGCTtgtgtgcccaggagggag
 F$FACBALL_Q2           |     9329 (-) |  0.928 |  0.797 | gagcctctggaggaccccTGAAGtct
 F$FACBALL_Q2           |     9378 (+) |  0.781 |  0.829 | ggaGAGCTgtcagcccctggaatgtg
 F$FACBALL_Q2           |     9420 (-) |  0.985 |  0.805 | actatcccataaataacaGGAAGccc
 F$FACBALL_Q2           |     9453 (+) |  0.878 |  0.875 | accAATCTctgctgtacaggatgttc
 F$FACBALL_Q2           |     9453 (-) |  0.989 |  0.834 | accaatctctgctgtacaGGATGttc
 F$FACBALL_Q2           |     9488 (-) |  0.939 |  0.803 | tatttgcaatagaaaatcTGAAAgtt
 F$FACBALL_Q2           |     9664 (+) |  0.871 |  0.804 | cctTGTCTcaaaagaagtggaggggg
 F$FACBALL_Q2           |     9664 (-) |  0.985 |  0.828 | ccttgtctcaaaagaagtGGAGGggg
 F$FACBALL_Q2           |     9963 (+) |  0.882 |  0.791 | atgTTTCTggttcctatggggatcag
 F$FACBALL_Q2           |     9969 (+) |  0.988 |  0.818 | ctgGTTCCtatggggatcagaagagg
 F$FACBALL_Q2           |     9969 (-) |  0.871 |  0.891 | ctggttcctatggggatcAGAAGagg
 F$FACBALL_Q2           |    10242 (+) |  0.920 |  0.828 | ggtGGTCAggcttgtgcaggaagtga
 F$FACBALL_Q2           |    10781 (-) |  0.931 |  0.835 | gtcggacccagggggatgTGAGCctt
 F$FACBALL_Q2           |    10832 (-) |  0.871 |  0.786 | ttcaggcccatcgcaggaAGAAGcca
 F$FACBALL_Q2           |    10849 (-) |  0.831 |  0.832 | aagaagccattgtagagaTGCAGcgt
 F$FACBALL_Q2           |    11116 (+) |  0.992 |  0.800 | tcaGATCCcttaactcgctgcactca
 F$FACBALL_Q2           |    11116 (-) |  0.834 |  0.814 | tcagatcccttaactcgcTGCACtca
 F$FACBALL_Q2           |    11348 (-) |  0.935 |  0.797 | cattatcgaacgagagcaTGATTcta
 F$FACBALL_Q2           |    11479 (+) |  0.996 |  0.805 | gttTTTCCcttggaatgcggttgaat
 F$FACBALL_Q2           |    11531 (-) |  0.875 |  0.818 | gcaaatcccacatatggtAGATGggt
 F$FACBALL_Q2           |    11666 (-) |  0.863 |  0.802 | aattttcataaccaaaaaAGACCaat
 F$FACBALL_Q2           |    11737 (+) |  0.939 |  0.782 | acaTCTCAccaaatgactagaaagag
 F$FACBALL_Q2           |    11737 (-) |  0.882 |  0.807 | acatctcaccaaatgactAGAAAgag
 F$FACBALL_Q2           |    11890 (-) |  0.900 |  0.786 | cactctcaaccaatagcaCGAAGgct
 P$AGL3_01              |     3143 (-) |  1.000 |  0.881 | acaacaataTATGGaggt
 P$AGL3_01              |     3590 (-) |  0.989 |  0.887 | tctcctatgTTTGGgttt
 P$AGL3_01              |     3860 (+) |  0.963 |  0.877 | agtaCCATTtaaggagtt
 P$AGL3_01              |    11534 (+) |  0.940 |  0.916 | aatcCCACAtatggtaga
 P$AGL3_01              |    11534 (-) |  1.000 |  0.886 | aatcccacaTATGGtaga
 P$AGL3_02              |     3590 (-) |  0.998 |  0.879 | tctcctatgTTTGGgttt
 P$AGL3_02              |    11534 (+) |  0.959 |  0.923 | aatcCCACAtatggtaga
 P$AGL3_02              |    11534 (-) |  1.000 |  0.874 | aatcccacaTATGGtaga
 V$MSX1_01              |        8 (-) |  0.897 |  0.863 | cATGTAcaa
 V$MSX1_01              |       14 (-) |  0.901 |  0.866 | cAAGTAcat
 V$MSX1_01              |       15 (+) |  0.897 |  0.863 | aagTACATg
 V$MSX1_01              |       21 (+) |  0.873 |  0.847 | atgTGAATg
 V$MSX1_01              |       51 (+) |  0.901 |  0.891 | catTACTTg
 V$MSX1_01              |      124 (+) |  0.988 |  0.884 | ggcTAACTg
 V$MSX1_01              |      373 (+) |  0.849 |  0.863 | ctcTAGGTg
 V$MSX1_01              |      476 (-) |  0.988 |  0.927 | cACTTAcaa
 V$MSX1_01              |      618 (+) |  0.897 |  0.864 | tcgTACATg
 V$MSX1_01              |      642 (-) |  0.996 |  0.874 | cATTTAttc
 V$MSX1_01              |      650 (-) |  0.996 |  0.885 | cATTTAtta
 V$MSX1_01              |      671 (+) |  0.849 |  0.895 | ctgTAGCTg
 V$MSX1_01              |      986 (-) |  0.988 |  0.887 | cAGTTAata
 V$MSX1_01              |     1013 (+) |  0.936 |  0.860 | accTATATg
 V$MSX1_01              |     1015 (+) |  0.928 |  0.903 | ctaTATGTg
 V$MSX1_01              |     1019 (+) |  0.877 |  0.850 | atgTGATTg
 V$MSX1_01              |     1430 (+) |  0.865 |  0.859 | caaTCAGTg
 V$MSX1_01              |     1430 (-) |  0.877 |  0.883 | cAATCAgtg
 V$MSX1_01              |     1471 (+) |  0.940 |  0.911 | caaTATTTg
 V$MSX1_01              |     1795 (-) |  0.873 |  0.912 | cATTCAcag
 V$MSX1_01              |     1910 (+) |  0.940 |  0.854 | tttTATTTg
 V$MSX1_01              |     1961 (+) |  0.853 |  0.858 | cctTTTTTg
 V$MSX1_01              |     2045 (+) |  0.889 |  0.922 | ctgTACCTg
 V$MSX1_01              |     2068 (+) |  0.806 |  0.865 | ctgTCTCTg
 V$MSX1_01              |     2074 (+) |  0.806 |  0.865 | ctgTCTCTg
 V$MSX1_01              |     2331 (+) |  0.928 |  0.854 | tgcTATGTg
 V$MSX1_01              |     2719 (-) |  0.940 |  0.862 | cAAATAgat
 V$MSX1_01              |     2789 (+) |  0.849 |  0.856 | cctTAGCTg
 V$MSX1_01              |     2803 (+) |  0.900 |  0.899 | ctcTTACTg
 V$MSX1_01              |     2880 (+) |  0.814 |  0.871 | ccgTGTATg
 V$MSX1_01              |     2928 (+) |  0.849 |  0.856 | cctTAGCTg
 V$MSX1_01              |     2963 (-) |  0.865 |  0.907 | cAGTGAcgg
 V$MSX1_01              |     3147 (+) |  0.936 |  0.908 | caaTATATg
 V$MSX1_01              |     3253 (-) |  0.988 |  0.945 | cACTTAtgg
 V$MSX1_01              |     3402 (-) |  0.988 |  0.880 | cAGTTAtaa
 V$MSX1_01              |     3411 (+) |  0.908 |  0.871 | aagTTAATg
 V$MSX1_01              |     3429 (+) |  1.000 |  0.885 | gctTAATTg
 V$MSX1_01              |     3448 (-) |  0.988 |  0.887 | cAGTTAata
 V$MSX1_01              |     3865 (-) |  0.996 |  0.958 | cATTTAagg
 V$MSX1_01              |     4216 (-) |  0.988 |  0.887 | cAGTTAaaa
 V$MSX1_01              |     4447 (-) |  1.000 |  0.896 | cAATTAata
 V$MSX1_01              |     4465 (+) |  0.865 |  0.875 | cacTGACTg
 V$MSX1_01              |     4465 (-) |  0.865 |  0.906 | cACTGActg
 V$MSX1_01              |     4857 (-) |  0.865 |  0.875 | cACTGAggg
 V$MSX1_01              |     4981 (+) |  0.889 |  0.891 | cccTACCTg
 V$MSX1_01              |     5060 (-) |  0.889 |  0.891 | cAGGTAgtg
 V$MSX1_01              |     5085 (+) |  0.865 |  0.875 | ctcTGACTg
 V$MSX1_01              |     5102 (+) |  0.940 |  0.854 | tatTATTTg
 V$MSX1_01              |     5434 (+) |  0.940 |  0.919 | cttTATTTg
 V$MSX1_01              |     5465 (-) |  0.928 |  0.885 | cACATActa
 V$MSX1_01              |     5544 (+) |  0.841 |  0.858 | ctcTTTCTg
 V$MSX1_01              |     5668 (-) |  0.912 |  0.907 | cAATAAgag
 V$MSX1_01              |     5678 (-) |  0.806 |  0.865 | cAGACAcag
 V$MSX1_01              |     5704 (-) |  0.988 |  0.896 | cACTTAgga
 V$MSX1_01              |     5953 (+) |  0.940 |  0.854 | tttTATTTg
 V$MSX1_01              |     5969 (+) |  0.988 |  0.887 | tttTAAGTg
 V$MSX1_01              |     6078 (+) |  0.806 |  0.865 | cagTCTCTg
 V$MSX1_01              |     6194 (-) |  0.996 |  0.882 | cATTTAagc
 V$MSX1_01              |     6252 (+) |  0.940 |  0.862 | ttcTATTTg
 V$MSX1_01              |     6321 (+) |  0.865 |  0.875 | cccTGACTg
 V$MSX1_01              |     6333 (-) |  0.806 |  0.865 | cACACActg
 V$MSX1_01              |     6445 (-) |  0.865 |  0.859 | cAGTCAtgg
 V$MSX1_01              |     6510 (-) |  0.940 |  0.854 | cAAATAaaa
 V$MSX1_01              |     6573 (-) |  0.988 |  0.869 | cAGTTAtgc
 V$MSX1_01              |     6593 (-) |  0.940 |  0.919 | cAAATAagg
 V$MSX1_01              |     6605 (+) |  0.940 |  0.862 | tgcTATTTg
 V$MSX1_01              |     6621 (+) |  0.865 |  0.907 | ccgTGAGTg
 V$MSX1_01              |     6904 (+) |  0.988 |  0.869 | gcaTAAGTg
 V$MSX1_01              |     6929 (+) |  0.928 |  0.885 | ttgTATGTg
 V$MSX1_01              |     7830 (-) |  1.000 |  0.885 | cAATTAacc
 V$MSX1_01              |     7864 (-) |  0.988 |  0.895 | cACTTAgaa
 V$MSX1_01              |     7965 (+) |  0.861 |  0.856 | ctaTAGTTg
 V$MSX1_01              |     8017 (+) |  0.900 |  0.892 | cctTTAGTg
 V$MSX1_01              |     8263 (-) |  0.873 |  0.847 | cATTGAcct
 V$MSX1_01              |     8335 (+) |  0.940 |  0.958 | cagTATTTg
 V$MSX1_01              |     8467 (-) |  0.857 |  0.861 | cATCTAagg
 V$MSX1_01              |     8517 (-) |  0.865 |  0.906 | cACTCAcag
 V$MSX1_01              |     8566 (+) |  0.818 |  0.873 | ccgTCTTTg
 V$MSX1_01              |     8574 (+) |  0.996 |  0.882 | gatTAAATg
 V$MSX1_01              |     8618 (-) |  0.877 |  0.850 | cAATCActt
 V$MSX1_01              |     8900 (-) |  0.841 |  0.889 | cACAAAcag
 V$MSX1_01              |     9135 (+) |  0.853 |  0.897 | cagTTTTTg
 V$MSX1_01              |     9485 (+) |  0.940 |  0.919 | cttTATTTg
 V$MSX1_01              |     9564 (+) |  0.841 |  0.889 | cggTTTCTg
 V$MSX1_01              |     9794 (+) |  0.996 |  0.997 | cagTAAATg
 V$MSX1_01              |     9794 (-) |  0.900 |  0.891 | cAGTAAatg
 V$MSX1_01              |    10307 (+) |  0.988 |  0.887 | tttTAACTg
 V$MSX1_01              |    10390 (-) |  0.936 |  0.851 | cATATAaaa
 V$MSX1_01              |    10508 (-) |  1.000 |  0.953 | cAATTAtgg
 V$MSX1_01              |    10732 (+) |  0.912 |  0.900 | cttTTATTg
 V$MSX1_01              |    10915 (-) |  0.940 |  0.854 | cAAATAata
 V$MSX1_01              |    10957 (+) |  0.806 |  0.865 | cggTCTGTg
 V$MSX1_01              |    11070 (-) |  0.988 |  0.927 | cAGTTAcaa
 V$MSX1_01              |    11234 (+) |  0.988 |  0.895 | ttcTAACTg
 V$MSX1_01              |    11338 (+) |  0.996 |  0.932 | atgTAAATg
 V$MSX1_01              |    11369 (+) |  0.928 |  0.854 | ttcTATCTg
 V$MSX1_01              |    11407 (-) |  0.996 |  0.874 | cATTTAttc
 V$MSX1_01              |    11471 (+) |  0.940 |  0.854 | tttTATTTg
 V$MSX1_01              |    11539 (-) |  0.928 |  0.903 | cACATAtgg
 V$MSX1_01              |    11637 (+) |  0.996 |  0.882 | gttTAAATg
 V$MSX1_01              |    11775 (-) |  0.928 |  0.885 | cAGATActt
 P$ABF1_02              |      728 (-) |  1.000 |  0.762 | gtgagccaccaCGTGGttgctggga
 V$AMEF2_Q6             |      627 (-) |  1.000 |  0.825 | acacttttTTTTAaacat
 V$AMEF2_Q6             |     2403 (+) |  1.000 |  0.879 | ttcctTAAAAaaaacaaa
 V$AMEF2_Q6             |     3801 (+) |  0.885 |  0.825 | cagaaTAGAAaaaacatc
 V$AMEF2_Q6             |     4420 (+) |  1.000 |  0.820 | ttgtcTAAAAaaaaaaaa
 V$AMEF2_Q6             |     4779 (+) |  0.885 |  0.830 | ctggaTAAAGattgctga
 V$AMEF2_Q6             |     8850 (+) |  1.000 |  0.830 | cggttTAAAAattaagac
 V$AMEF2_Q6             |     9833 (-) |  1.000 |  0.868 | agggataaTTTTAaagtc
 V$AMEF2_Q6             |    10411 (-) |  1.000 |  0.882 | gttggcatTTTTAacact
 V$MMEF2_Q6             |      234 (-) |  1.000 |  0.880 | ttgtctTTTTAaatct
 V$MMEF2_Q6             |      520 (+) |  1.000 |  0.883 | gatttTAAAAatgatg
 V$MMEF2_Q6             |      598 (-) |  1.000 |  0.880 | cttactTTTTAaacat
 V$MMEF2_Q6             |      629 (-) |  1.000 |  0.943 | acttttTTTTAaacat
 V$MMEF2_Q6             |     2403 (+) |  1.000 |  0.926 | ttcctTAAAAaaaaca
 V$MMEF2_Q6             |     2896 (-) |  1.000 |  0.896 | catcttTTTTAtccac
 V$MMEF2_Q6             |     3745 (-) |  1.000 |  0.885 | ctacatTTTTAgtcat
 V$MMEF2_Q6             |     4420 (+) |  1.000 |  0.912 | ttgtcTAAAAaaaaaa
 V$MMEF2_Q6             |     7259 (+) |  1.000 |  0.902 | ctcatTAAAAtatcct
 V$MMEF2_Q6             |     7642 (+) |  1.000 |  0.890 | tatttTAAAAatgctt
 V$MMEF2_Q6             |     8633 (-) |  0.943 |  0.877 | aagcttATTTAagaag
 V$MMEF2_Q6             |     8850 (+) |  1.000 |  0.923 | cggttTAAAAattaag
 V$MMEF2_Q6             |     9710 (+) |  1.000 |  0.878 | tggtgTAAAAttgatc
 V$MMEF2_Q6             |     9835 (-) |  1.000 |  0.895 | ggataaTTTTAaagtc
 V$MMEF2_Q6             |     9892 (-) |  1.000 |  0.922 | attcttTTTTAaagac
 V$MMEF2_Q6             |    10389 (+) |  1.000 |  0.902 | ccataTAAAAatgaac
 V$MMEF2_Q6             |    10413 (-) |  1.000 |  0.923 | tggcatTTTTAacact
 V$SOX9_B1              |      945 (+) |  1.000 |  0.963 | taggaACAATgatc
 V$SOX9_B1              |     7329 (+) |  1.000 |  0.978 | ctggaACAATagac
 V$SOX9_B1              |     8554 (+) |  1.000 |  0.956 | aatgaACAATgtcc
 V$SOX9_B1              |    10147 (-) |  1.000 |  0.943 | tattATTGTtgttg
 V$SOX9_B1              |    10339 (-) |  1.000 |  0.950 | ttttATTGTtttaa
 V$SOX9_B1              |    10457 (+) |  1.000 |  0.952 | tatcaACAATgcat
 V$HNF4_01_B            |      856 (-) |  0.800 |  0.804 | acgatCGTTGccctt
 V$HNF4_01_B            |     3566 (-) |  1.000 |  0.865 | gtggcCTTTGgcaag
 V$HNF4_01_B            |     4723 (-) |  0.800 |  0.815 | ctgtgATTTGgccct
 V$HNF4_01_B            |     5452 (-) |  0.800 |  0.806 | ataacCTTTTcccca
 V$HNF4_01_B            |     7084 (-) |  1.000 |  0.835 | gagtgCTTTGcgcgc
 V$HNF4_01_B            |     8375 (-) |  1.000 |  0.894 | ctgctCTTTGatctg
 V$HNF4_01_B            |     8581 (+) |  1.000 |  0.918 | tggggCAAAGgcaac
 V$HNF4_01_B            |    10496 (+) |  0.800 |  0.819 | aggatCAAAAgtcaa
 V$HNF4_01_B            |    11287 (+) |  1.000 |  0.825 | tagggCAAAGaaata
 V$HNF4_01_B            |    11789 (+) |  0.800 |  0.818 | aaggaCAAATcccag
 V$AREB6_01             |      265 (-) |  1.000 |  0.923 | actCAGGTccttg
 V$AREB6_01             |      575 (+) |  1.000 |  0.939 | cgtctACCTGttg
 V$AREB6_01             |     1293 (+) |  1.000 |  0.950 | cctggACCTGtgt
 V$AREB6_01             |     1356 (+) |  1.000 |  0.908 | gggtcACCTGatg
 V$AREB6_01             |     1391 (-) |  1.000 |  0.945 | gggCAGGTgagga
 V$AREB6_01             |     1784 (+) |  1.000 |  0.900 | ggagcACCTGcca
 V$AREB6_01             |     1969 (-) |  1.000 |  0.905 | gagCAGGTtggcc
 V$AREB6_01             |     2044 (+) |  1.000 |  0.962 | actgtACCTGgct
 V$AREB6_01             |     2643 (+) |  1.000 |  0.947 | ccctgACCTGcgt
 V$AREB6_01             |     3050 (+) |  1.000 |  0.959 | gacatACCTGcga
 V$AREB6_01             |     3900 (-) |  1.000 |  0.941 | tcaCAGGTattaa
 V$AREB6_01             |     4338 (-) |  1.000 |  0.918 | atcCAGGTggtgg
 V$AREB6_01             |     4401 (-) |  1.000 |  0.947 | agaCAGGTcagcc
 V$AREB6_01             |     4980 (+) |  1.000 |  0.964 | cccctACCTGtcc
 V$AREB6_01             |     5057 (-) |  1.000 |  0.923 | aagCAGGTagtga
 V$AREB6_01             |     7390 (-) |  1.000 |  0.905 | gtcCAGGTggtag
 V$AREB6_01             |     7580 (-) |  1.000 |  0.909 | catCAGGTcaaac
 V$AREB6_01             |     8167 (-) |  1.000 |  0.939 | aggCAGGTagcac
 V$AREB6_01             |     8263 (+) |  1.000 |  0.912 | cattgACCTGatg
 V$AREB6_01             |     8388 (+) |  1.000 |  0.947 | tgtatACCTGaag
 V$AREB6_01             |     8503 (-) |  1.000 |  0.952 | ggaCAGGTgcggg
 V$AREB6_01             |     8766 (+) |  1.000 |  0.914 | ccagcACCTGgga
 V$AREB6_01             |     8968 (-) |  1.000 |  0.939 | aacCAGGTgtggt
 V$AREB6_01             |    11002 (+) |  1.000 |  0.930 | agattACCTGctt
 V$AREB6_01             |    11959 (+) |  1.000 |  0.953 | actgcACCTGagc
 V$AREB6_02             |     1357 (+) |  1.000 |  0.978 | ggtCACCTgatg
 V$AREB6_02             |     1391 (-) |  1.000 |  0.978 | gggcAGGTGagg
 V$AREB6_02             |     3289 (-) |  1.000 |  0.973 | gatgAGGTGaac
 V$AREB6_02             |     8503 (-) |  1.000 |  0.979 | ggacAGGTGcgg
 V$AREB6_02             |     8984 (+) |  1.000 |  0.983 | acaCACCTttaa
 V$AREB6_02             |    11960 (+) |  1.000 |  0.971 | ctgCACCTgagc
 V$AREB6_03             |     1125 (+) |  0.852 |  0.877 | atgCACGTgtgt
 V$AREB6_03             |     1357 (+) |  1.000 |  0.907 | ggtCACCTgatg
 V$AREB6_03             |     1391 (-) |  1.000 |  0.922 | gggcAGGTGagg
 V$AREB6_03             |     1785 (+) |  1.000 |  0.958 | gagCACCTgcca
 V$AREB6_03             |     4338 (-) |  1.000 |  0.929 | atccAGGTGgtg
 V$AREB6_03             |     7390 (-) |  1.000 |  0.924 | gtccAGGTGgta
 V$AREB6_03             |     8503 (-) |  1.000 |  0.994 | ggacAGGTGcgg
 V$AREB6_03             |     8520 (-) |  0.852 |  0.875 | tcacAGATGctt
 V$AREB6_03             |     8767 (+) |  1.000 |  0.984 | cagCACCTggga
 V$AREB6_03             |     8968 (-) |  1.000 |  0.969 | aaccAGGTGtgg
 V$AREB6_03             |    11960 (+) |  1.000 |  0.972 | ctgCACCTgagc
 V$CART1_01             |       62 (+) |  1.000 |  0.850 | ccaTAATTactgttgttg
 V$CART1_01             |      834 (-) |  0.783 |  0.757 | atataaaacaAGTTAaat
 V$CART1_01             |      839 (-) |  0.854 |  0.754 | aaacaagttaAATAAata
 V$CART1_01             |      987 (+) |  0.924 |  0.757 | agtTAATAattttcatgt
 V$CART1_01             |      990 (+) |  1.000 |  0.827 | taaTAATTttcatgtggg
 V$CART1_01             |     1201 (+) |  0.778 |  0.799 | tggTTATAcccattgctt
 V$CART1_01             |     1361 (+) |  0.797 |  0.733 | accTGATGctcgtttgca
 V$CART1_01             |     1890 (+) |  0.778 |  0.788 | attTTATAtttattttat
 V$CART1_01             |     1904 (+) |  0.854 |  0.738 | ttaTTATTttatttgaga
 V$CART1_01             |     1985 (-) |  0.933 |  0.765 | aactcaccaaGATTAtct
 V$CART1_01             |     2512 (-) |  1.000 |  0.831 | agggaaaaaaAATTAcat
 V$CART1_01             |     2519 (-) |  0.924 |  0.749 | aaaaattacaTATTActt
 V$CART1_01             |     2591 (-) |  0.924 |  0.800 | cagtactgacTATTAaac
 V$CART1_01             |     2652 (+) |  0.951 |  0.805 | gcgTAATGcactttgatg
 V$CART1_01             |     3082 (+) |  0.847 |  0.744 | gggTGATTctatttttcg
 V$CART1_01             |     3106 (+) |  1.000 |  0.829 | tacTAATTtccatgcggc
 V$CART1_01             |     3126 (+) |  1.000 |  0.929 | tatTAATTtacattccca
 V$CART1_01             |     3279 (+) |  0.847 |  0.789 | ttaTGATTgggatgaggt
 V$CART1_01             |     3328 (+) |  0.847 |  0.747 | tccTGATTctatttccct
 V$CART1_01             |     3402 (+) |  0.778 |  0.768 | cagTTATAaaagttaatg
 V$CART1_01             |     3402 (-) |  0.783 |  0.772 | cagttataaaAGTTAatg
 V$CART1_01             |     3406 (-) |  0.839 |  0.735 | tataaaagttAATGAttc
 V$CART1_01             |     3415 (+) |  0.847 |  0.752 | taaTGATTctggttgctt
 V$CART1_01             |     3429 (+) |  1.000 |  0.750 | gctTAATTgacttaggta
 V$CART1_01             |     3707 (+) |  0.779 |  0.798 | gctTGATCaatatttacg
 V$CART1_01             |     3724 (-) |  1.000 |  0.812 | gggtgactaaAATTAtta
 V$CART1_01             |     3897 (-) |  0.924 |  0.757 | tcatcacaggTATTAata
 V$CART1_01             |     3907 (+) |  0.924 |  0.786 | tatTAATAaagctttatg
 V$CART1_01             |     3920 (-) |  0.951 |  0.766 | ttatgaattaCATTAtca
 V$CART1_01             |     4059 (+) |  1.000 |  0.842 | caaTAATTaaaatatgta
 V$CART1_01             |     4448 (+) |  0.924 |  0.878 | aatTAATAttcatttcac
 V$CART1_01             |     5005 (-) |  0.951 |  0.816 | ttgtattaccCATTAagc
 V$CART1_01             |     5433 (+) |  0.854 |  0.852 | actTTATTtgtattgcca
 V$CART1_01             |     5578 (-) |  0.854 |  0.740 | tctaaaggatAATAAtaa
 V$CART1_01             |     5581 (-) |  0.854 |  0.749 | aaaggataatAATAAaat
 V$CART1_01             |     6585 (-) |  0.854 |  0.754 | acacaaaacaAATAAggt
 V$CART1_01             |     6669 (+) |  0.854 |  0.742 | attTTATTtagcttttga
 V$CART1_01             |     6949 (-) |  0.951 |  0.829 | tgatactgtcCATTAttc
 V$CART1_01             |     7059 (+) |  1.000 |  0.828 | tctTAATTtgtttttgtt
 V$CART1_01             |     7251 (-) |  0.951 |  0.801 | gaaaaagtctCATTAaaa
 V$CART1_01             |     7257 (+) |  0.839 |  0.748 | gtcTCATTaaaatatcct
 V$CART1_01             |     7348 (-) |  0.847 |  0.743 | tcaacatgttAATCAtgg
 V$CART1_01             |     7424 (+) |  0.854 |  0.739 | ggtTTATTtgtttttatt
 V$CART1_01             |     7570 (-) |  0.797 |  0.806 | accaaatcccCATCAggt
 V$CART1_01             |     7778 (-) |  1.000 |  0.834 | acaaaacaaaAATTAtcc
 V$CART1_01             |     7884 (+) |  0.839 |  0.732 | aagTCATTtggtttttat
 V$CART1_01             |     7895 (+) |  0.854 |  0.741 | tttTTATTttgatattag
 V$CART1_01             |     8678 (-) |  1.000 |  0.741 | ttaggaaggtAATTAgcc
 V$CART1_01             |     8684 (+) |  1.000 |  0.838 | aggTAATTagcctttctg
 V$CART1_01             |     8945 (-) |  1.000 |  0.766 | aactttttaaAATTAgta
 V$CART1_01             |     9164 (-) |  0.790 |  0.769 | tcctaagatgCATGAacg
 V$CART1_01             |     9484 (+) |  0.854 |  0.765 | actTTATTtgcaatagaa
 V$CART1_01             |     9734 (+) |  0.951 |  0.803 | tgaTAATGtccatacaat
 V$CART1_01             |     9795 (-) |  0.797 |  0.807 | agtaaatgtaCATCAcat
 V$CART1_01             |     9862 (-) |  0.839 |  0.735 | attaaagaagAATGAgga
 V$CART1_01             |     9931 (+) |  1.000 |  0.825 | gggTAATTtgcatgtatg
 V$CART1_01             |    10119 (-) |  1.000 |  0.744 | tccccaataaAATTAgtt
 V$CART1_01             |    10123 (-) |  0.783 |  0.764 | caataaaattAGTTAaga
 V$CART1_01             |    10137 (-) |  0.924 |  0.882 | aagaaattatTATTAttg
 V$CART1_01             |    10140 (+) |  0.854 |  0.850 | aaaTTATTattattgttg
 V$CART1_01             |    10143 (+) |  0.854 |  0.755 | ttaTTATTattgttgttg
 V$CART1_01             |    10146 (+) |  0.854 |  0.759 | ttaTTATTgttgttgtcg
 V$CART1_01             |    10307 (+) |  0.783 |  0.752 | tttTAACTgtttttatat
 V$CART1_01             |    10329 (+) |  0.778 |  0.758 | attTTATAgtttttattg
 V$CART1_01             |    10347 (+) |  1.000 |  0.798 | tttTAATTcaaagtgtca
 V$CART1_01             |    10382 (-) |  0.778 |  0.787 | ttgcaatccaTATAAaaa
 V$CART1_01             |    10388 (-) |  0.839 |  0.741 | tccatataaaAATGAacg
 V$CART1_01             |    10499 (-) |  1.000 |  0.829 | atcaaaagtcAATTAtgg
 V$CART1_01             |    10907 (-) |  0.854 |  0.754 | ctactatgcaAATAAtag
 V$CART1_01             |    11150 (+) |  0.797 |  0.766 | ctcTGATGaaaatgaagc
 V$CART1_01             |    11150 (-) |  0.839 |  0.795 | ctctgatgaaAATGAagc
 V$CART1_01             |    11196 (-) |  0.924 |  0.746 | cttgattgatTATTAatt
 V$CART1_01             |    11206 (+) |  1.000 |  0.797 | tatTAATTtgtttgaact
 V$CART1_01             |    11267 (-) |  1.000 |  0.832 | aagaaaaggaAATTAagg
 V$CART1_01             |    11294 (-) |  0.854 |  0.837 | aagaaataatAATAAcga
 V$CART1_01             |    11300 (+) |  0.924 |  0.808 | taaTAATAacgactacgg
 V$CART1_01             |    11338 (+) |  0.774 |  0.856 | atgTAAATgccattatcg
 V$CART1_01             |    11338 (-) |  0.951 |  0.857 | atgtaaatgcCATTAtcg
 V$CART1_01             |    11381 (-) |  0.924 |  0.778 | tttgaaaactTATTAaat
 V$CART1_01             |    11387 (+) |  0.854 |  0.751 | aacTTATTaaattttgta
 V$CART1_01             |    11470 (+) |  0.854 |  0.742 | tttTTATTtgtttttccc
 V$CART1_01             |    11662 (-) |  0.805 |  0.812 | acacaattttCATAAcca
 V$CART1_01             |    11679 (-) |  0.854 |  0.752 | aaaaaagaccAATAAagt
 V$CART1_01             |    11688 (-) |  0.847 |  0.805 | caataaagttAATCActg
 V$CART1_01             |    11694 (+) |  0.933 |  0.778 | agtTAATCactgtcaccc
 V$TGIF_01              |       45 (+) |  1.000 |  0.965 | agaTGTCAtta
 V$TGIF_01              |      470 (-) |  1.000 |  0.932 | attTGACActt
 V$TGIF_01              |      622 (-) |  1.000 |  0.931 | acaTGACActt
 V$TGIF_01              |     9382 (+) |  1.000 |  0.972 | agcTGTCAgcc
 V$TGIF_01              |    10357 (+) |  1.000 |  0.929 | aagTGTCAgag
 V$MEIS1_01             |     1254 (-) |  1.000 |  0.996 | attcTGTCAtca
 V$MEIS1_01             |     1281 (+) |  1.000 |  0.996 | ggaTGACAggga
 V$MEIS1_01             |     6052 (+) |  1.000 |  0.998 | ctgTGACAgccc
 V$MEIS1_01             |     8101 (-) |  1.000 |  0.998 | gtccTGTCAcac
 V$MEIS1_01             |     9381 (-) |  1.000 |  0.996 | gagcTGTCAgcc
 V$MEIS1_01             |    11700 (-) |  1.000 |  0.995 | tcacTGTCAccc
 V$MEIS1AHOXA9_01       |     1026 (+) |  0.821 |  0.789 | TGGCAgttgaatca
 V$MEIS1AHOXA9_01       |     1137 (-) |  0.668 |  0.820 | tcctaaaacCGTTA
 V$MEIS1AHOXA9_01       |     1230 (+) |  0.847 |  0.800 | TGACTgctttgaca
 V$MEIS1AHOXA9_01       |     1249 (-) |  1.000 |  0.731 | gcagcattcTGTCA
 V$MEIS1AHOXA9_01       |     1783 (-) |  0.821 |  0.736 | tggagcaccTGCCA
 V$MEIS1AHOXA9_01       |     2545 (+) |  0.821 |  0.802 | TAACAggtttctgt
 V$MEIS1AHOXA9_01       |     3223 (-) |  0.847 |  0.765 | acttttaccAGTCA
 V$MEIS1AHOXA9_01       |     3445 (+) |  0.821 |  0.741 | TAACAgttaataaa
 V$MEIS1AHOXA9_01       |     3928 (-) |  0.847 |  0.732 | tacattatcAGTCA
 V$MEIS1AHOXA9_01       |     4926 (+) |  0.805 |  0.762 | TTACAgatcatgga
 V$MEIS1AHOXA9_01       |     5088 (+) |  0.847 |  0.793 | TGACTggtttgggt
 V$MEIS1AHOXA9_01       |     6428 (-) |  0.875 |  0.778 | gctttcatcGGTCA
 V$MEIS1AHOXA9_01       |     7301 (+) |  0.821 |  0.742 | TGAGAgagtaagga
 V$MEIS1AHOXA9_01       |     7679 (+) |  0.805 |  0.739 | TCACAgctgtaaag
 V$MEIS1AHOXA9_01       |     8720 (-) |  0.805 |  0.733 | ctgaagaacTGTAA
 V$MEIS1AHOXA9_01       |     9376 (-) |  1.000 |  0.781 | agggagagcTGTCA
 V$MEIS1AHOXA9_01       |     9506 (+) |  0.805 |  0.788 | TGAAAgtttcccca
 V$MEIS1AHOXA9_01       |     9760 (-) |  0.847 |  0.768 | attgaaaacAGTCA
 V$MEIS1AHOXA9_01       |    10185 (-) |  0.847 |  0.747 | gtgttcagcAGTCA
 V$MEIS1AHOXA9_01       |    10310 (+) |  0.668 |  0.742 | TAACTgtttttata
 V$MEIS1AHOXA9_01       |    10363 (-) |  0.805 |  0.745 | cagagaatcTTTCA
 V$MEIS1AHOXA9_01       |    11453 (-) |  0.652 |  0.747 | tggtgaatcAGTGA
 V$MEIS1BHOXA9_02       |      625 (+) |  1.000 |  0.859 | TGACActttttttt
 V$MEIS1BHOXA9_02       |    10351 (-) |  1.000 |  0.913 | aattcaaagTGTCA
 V$FOXJ2_01             |      210 (-) |  0.960 |  0.898 | cctggTATTTtttttttt
 V$FOXJ2_01             |      503 (-) |  0.960 |  0.917 | ttataTATTTgtcttctg
 V$FOXJ2_01             |      844 (+) |  0.960 |  0.948 | agttaaatAAATAcgatc
 V$FOXJ2_01             |      873 (+) |  1.000 |  0.894 | aaatgcacAAACAcgaaa
 V$FOXJ2_01             |     1524 (-) |  1.000 |  0.921 | agagcTGTTTttttgttc
 V$FOXJ2_01             |     1891 (-) |  0.960 |  0.964 | ttttaTATTTattttatt
 V$FOXJ2_01             |     2358 (-) |  0.960 |  0.949 | acttgTATTTattttgcc
 V$FOXJ2_01             |     2406 (+) |  1.000 |  0.934 | cttaaaaaAAACAaaaaa
 V$FOXJ2_01             |     2410 (+) |  0.917 |  0.906 | aaaaaaacAAAAAatcac
 V$FOXJ2_01             |     4000 (+) |  0.960 |  0.907 | acaacgatAAATAaatat
 V$FOXJ2_01             |     4004 (+) |  0.960 |  0.956 | cgataaatAAATAttctg
 V$FOXJ2_01             |     4217 (+) |  0.960 |  0.895 | agttaaaaAAATAaattc
 V$FOXJ2_01             |     4490 (+) |  1.000 |  0.898 | tgaacaaaAAACAaaaca
 V$FOXJ2_01             |     5432 (-) |  0.960 |  0.900 | cacttTATTTgtattgcc
 V$FOXJ2_01             |     5642 (+) |  0.917 |  0.924 | gacaaaatAAAAAgaaga
 V$FOXJ2_01             |     5714 (+) |  1.000 |  0.909 | tcccacaaAAACActaaa
 V$FOXJ2_01             |     5804 (+) |  0.960 |  0.901 | aaaaaaaaAAATAgccct
 V$FOXJ2_01             |     6586 (+) |  0.960 |  0.926 | cacaaaacAAATAaggtg
 V$FOXJ2_01             |     6821 (-) |  0.917 |  0.897 | tccctTTTTTatgtgcta
 V$FOXJ2_01             |     7045 (-) |  0.960 |  0.909 | ttgacTATTTtttttctt
 V$FOXJ2_01             |     7062 (-) |  1.000 |  0.907 | taattTGTTTttgtttgt
 V$FOXJ2_01             |     7064 (-) |  0.917 |  0.899 | atttgTTTTTgtttgtgt
 V$FOXJ2_01             |     7068 (-) |  1.000 |  0.939 | gttttTGTTTgtgtatga
 V$FOXJ2_01             |     7423 (-) |  0.960 |  0.937 | aggttTATTTgtttttat
 V$FOXJ2_01             |     7427 (-) |  1.000 |  0.914 | ttattTGTTTttatttta
 V$FOXJ2_01             |     7429 (-) |  0.917 |  0.927 | atttgTTTTTattttatg
 V$FOXJ2_01             |     7768 (+) |  1.000 |  0.897 | gtctcaaaAAACAaaaca
 V$FOXJ2_01             |     7777 (+) |  0.917 |  0.905 | aacaaaacAAAAAttatc
 V$FOXJ2_01             |     7795 (+) |  0.917 |  0.902 | ccaaagatAAAGAacaac
 V$FOXJ2_01             |     7819 (+) |  1.000 |  0.972 | tccaaaacAAACAattaa
 V$FOXJ2_01             |     7890 (-) |  0.917 |  0.931 | tttggTTTTTattttgat
 V$FOXJ2_01             |     7936 (-) |  1.000 |  0.908 | ttgtgTGTTTagttttga
 V$FOXJ2_01             |     7967 (-) |  1.000 |  0.963 | atagtTGTTTgtttttca
 V$FOXJ2_01             |     8895 (+) |  1.000 |  0.898 | cgtaccacAAACAgattc
 V$FOXJ2_01             |     9108 (+) |  0.917 |  0.896 | agcaaaacAAAAAaccgg
 V$FOXJ2_01             |     9422 (+) |  0.960 |  0.896 | tatcccatAAATAacagg
 V$FOXJ2_01             |     9531 (+) |  1.000 |  0.911 | actagaacAAACAagtcc
 V$FOXJ2_01             |    10309 (-) |  1.000 |  0.917 | ttaacTGTTTttatattt
 V$FOXJ2_01             |    10311 (-) |  0.917 |  0.905 | aactgTTTTTatattttt
 V$FOXJ2_01             |    10319 (-) |  0.917 |  0.933 | ttataTTTTTattttata
 V$FOXJ2_01             |    10333 (-) |  0.917 |  0.901 | tatagTTTTTattgtttt
 V$FOXJ2_01             |    10387 (+) |  0.917 |  0.896 | atccatatAAAAAtgaac
 V$FOXJ2_01             |    10698 (-) |  1.000 |  0.905 | acccgTGTTTatgaaaca
 V$FOXJ2_01             |    11186 (-) |  1.000 |  0.895 | tgcctTGTTTcttgattg
 V$FOXJ2_01             |    11289 (+) |  0.960 |  0.893 | gggcaaagAAATAataat
 V$FOXJ2_01             |    11465 (-) |  0.917 |  0.925 | gaaatTTTTTatttgttt
 V$FOXJ2_01             |    11469 (-) |  0.960 |  0.929 | tttttTATTTgtttttcc
 V$E2F_Q3               |     2472 (-) |  1.000 |  0.946 | gcGCGAAg
 V$E2F_Q6               |     2472 (-) |  1.000 |  0.930 | gCGCGAag
 V$E2F1_Q3              |     2472 (-) |  1.000 |  0.997 | gCGCGAag
 V$E2F1_Q3              |     8331 (-) |  0.982 |  0.911 | gCGCCAgt
 V$E2F1_Q3              |     8511 (-) |  0.943 |  0.932 | gCGGGAca
 V$E2F1_Q3              |     9122 (-) |  0.943 |  0.908 | cCGGGAaa
 V$E2F1_Q4              |     1720 (+) |  0.819 |  0.870 | tTTTCCgg
 V$E2F1_Q4              |     2472 (-) |  0.973 |  0.907 | gcGCGAAg
 V$E2F1_Q4              |     2502 (-) |  0.785 |  0.846 | ccGAAAAa
 V$E2F1_Q4              |     3718 (+) |  0.785 |  0.845 | aTTTACgg
 V$E2F1_Q4              |     5750 (-) |  0.919 |  0.845 | acGCAAAg
 V$E2F1_Q4              |     6129 (+) |  0.839 |  0.885 | tTTCTCgg
 V$E2F1_Q4              |     7089 (+) |  0.919 |  0.869 | cTTTGCgc
 V$E2F1_Q4              |     8547 (-) |  0.839 |  0.885 | ccGAGAAa
 V$E2F1_Q4              |     8614 (-) |  0.866 |  0.903 | ccGTCAAt
 V$E2F1_Q4              |     9122 (-) |  0.873 |  0.909 | ccGGGAAa
 V$E2F1_Q4              |     9217 (-) |  0.919 |  0.845 | acGCAAAg
 V$E2F1_Q4              |    10270 (+) |  0.900 |  0.928 | tTTGCCgg
 V$E2F1_Q6              |     2472 (-) |  1.000 |  0.982 | gCGCGAag
 V$E2F1_Q6              |     7089 (+) |  0.886 |  0.892 | ctTTGCGc
 V$E2F1_Q6              |     9122 (-) |  0.932 |  0.908 | cCGGGAaa
 V$E2F1_Q6              |    10270 (+) |  0.897 |  0.880 | ttTGCCGg
 V$TITF1_Q3             |       38 (-) |  0.880 |  0.823 | caaCTTCAga
 V$TITF1_Q3             |      281 (+) |  0.857 |  0.782 | atGCAAGtca
 V$TITF1_Q3             |      286 (+) |  1.000 |  0.984 | agTCAAGtgt
 V$TITF1_Q3             |      542 (-) |  0.880 |  0.809 | gcgCTTGTgt
 V$TITF1_Q3             |      627 (-) |  0.737 |  0.775 | acaCTTTTtt
 V$TITF1_Q3             |      679 (-) |  0.880 |  0.765 | gctCTTCAga
 V$TITF1_Q3             |      839 (+) |  0.880 |  0.815 | aaACAAGtta
 V$TITF1_Q3             |      937 (+) |  0.880 |  0.765 | ccACAAGtta
 V$TITF1_Q3             |     1059 (-) |  0.857 |  0.772 | caaCTTTAaa
 V$TITF1_Q3             |     1346 (-) |  0.857 |  0.810 | aggCTTGCct
 V$TITF1_Q3             |     1444 (+) |  0.880 |  0.816 | agTGAAGtca
 V$TITF1_Q3             |     1655 (-) |  0.857 |  0.795 | ctaCTTGGca
 V$TITF1_Q3             |     1864 (+) |  0.880 |  0.830 | acTGAAGaag
 V$TITF1_Q3             |     1938 (-) |  0.857 |  0.799 | agcCTTGGct
 V$TITF1_Q3             |     2028 (+) |  0.857 |  0.768 | atTAAAGgag
 V$TITF1_Q3             |     2356 (-) |  0.880 |  0.863 | aaaCTTGTat
 V$TITF1_Q3             |     2606 (+) |  0.857 |  0.766 | aaCCAAGagc
 V$TITF1_Q3             |     3202 (+) |  1.000 |  0.919 | ccTCAAGtat
 V$TITF1_Q3             |     3215 (+) |  0.857 |  0.768 | agGCAAGcac
 V$TITF1_Q3             |     3311 (+) |  0.857 |  0.817 | agTTAAGatt
 V$TITF1_Q3             |     3550 (-) |  0.857 |  0.784 | gttCTTTAgt
 V$TITF1_Q3             |     3583 (+) |  0.762 |  0.766 | atTCAACtct
 V$TITF1_Q3             |     3657 (+) |  0.857 |  0.812 | agTAAAGtaa
 V$TITF1_Q3             |     3681 (+) |  0.857 |  0.774 | tgCCAAGtgc
 V$TITF1_Q3             |     3696 (+) |  0.880 |  0.809 | acACAAGaga
 V$TITF1_Q3             |     3705 (-) |  1.000 |  0.851 | atgCTTGAtc
 V$TITF1_Q3             |     3759 (-) |  0.857 |  0.763 | attCTTAAaa
 V$TITF1_Q3             |     3866 (+) |  0.857 |  0.768 | atTTAAGgag
 V$TITF1_Q3             |     3886 (-) |  1.000 |  0.820 | ctcCTTGAcc
 V$TITF1_Q3             |     3911 (+) |  0.857 |  0.808 | aaTAAAGctt
 V$TITF1_Q3             |     4201 (+) |  1.000 |  0.818 | gtTCAAGgct
 V$TITF1_Q3             |     4206 (-) |  0.857 |  0.810 | aggCTTGCct
 V$TITF1_Q3             |     4253 (-) |  0.857 |  0.804 | ttaCTTGGtt
 V$TITF1_Q3             |     4416 (-) |  0.880 |  0.824 | aacCTTGTct
 V$TITF1_Q3             |     4693 (-) |  1.000 |  0.888 | aaaCTTGAtg
 V$TITF1_Q3             |     4707 (-) |  0.857 |  0.870 | agaCTTGGgt
 V$TITF1_Q3             |     4794 (-) |  0.857 |  0.782 | tgaCTTGCat
 V$TITF1_Q3             |     4851 (-) |  0.880 |  0.872 | agaCTTCAct
 V$TITF1_Q3             |     5171 (-) |  0.880 |  0.809 | tcaCTTGTga
 V$TITF1_Q3             |     5208 (-) |  0.880 |  0.763 | cctCTTGTgc
 V$TITF1_Q3             |     5431 (-) |  0.857 |  0.839 | ccaCTTTAtt
 V$TITF1_Q3             |     5578 (+) |  0.857 |  0.784 | tcTAAAGgat
 V$TITF1_Q3             |     5607 (+) |  0.880 |  0.802 | acACAAGaaa
 V$TITF1_Q3             |     5969 (+) |  0.857 |  0.786 | ttTTAAGtgg
 V$TITF1_Q3             |     6121 (-) |  0.880 |  0.764 | gggCTTGTtt
 V$TITF1_Q3             |     6195 (+) |  0.857 |  0.765 | atTTAAGccg
 V$TITF1_Q3             |     6326 (+) |  0.880 |  0.802 | acTGAAGcac
 V$TITF1_Q3             |     6336 (-) |  0.762 |  0.795 | acaCTGGAtt
 V$TITF1_Q3             |     6697 (+) |  0.880 |  0.800 | gcTGAAGtag
 V$TITF1_Q3             |     6894 (+) |  0.880 |  0.821 | agACAAGagg
 V$TITF1_Q3             |     6942 (+) |  0.857 |  0.835 | acCCAAGtga
 V$TITF1_Q3             |     7032 (+) |  0.880 |  0.791 | gcTGAAGagt
 V$TITF1_Q3             |     7128 (+) |  1.000 |  0.836 | gcTCAAGgag
 V$TITF1_Q3             |     7382 (-) |  0.880 |  0.802 | ttgCTTGTgt
 V$TITF1_Q3             |     7407 (+) |  0.880 |  0.802 | acTGAAGaac
 V$TITF1_Q3             |     7525 (+) |  0.880 |  0.839 | acTGAAGtta
 V$TITF1_Q3             |     7696 (-) |  0.857 |  0.777 | gaaCTTGGga
 V$TITF1_Q3             |     7980 (+) |  1.000 |  0.813 | ttTCAAGgga
 V$TITF1_Q3             |     7991 (-) |  0.880 |  0.816 | ggaCTTCAct
 V$TITF1_Q3             |     8015 (-) |  0.857 |  0.822 | aacCTTTAgt
 V$TITF1_Q3             |     8043 (-) |  1.000 |  0.852 | ggcCTTGAct
 V$TITF1_Q3             |     8182 (-) |  0.880 |  0.815 | gaaCTTGTtt
 V$TITF1_Q3             |     8349 (-) |  0.857 |  0.802 | ccaCTTGCca
 V$TITF1_Q3             |     8529 (+) |  1.000 |  0.787 | ctTCAAGaac
 V$TITF1_Q3             |     8595 (-) |  0.857 |  0.772 | catCTTTAat
 V$TITF1_Q3             |     8639 (+) |  0.857 |  0.779 | atTTAAGaag
 V$TITF1_Q3             |     8709 (+) |  1.000 |  0.812 | caTCAAGgag
 V$TITF1_Q3             |     8859 (+) |  0.857 |  0.801 | aaTTAAGact
 V$TITF1_Q3             |     8937 (+) |  0.857 |  0.784 | acTAAAGcaa
 V$TITF1_Q3             |     9035 (+) |  1.000 |  0.783 | gtTCAAGggc
 V$TITF1_Q3             |     9088 (+) |  0.880 |  0.779 | agTGAAGctc
 V$TITF1_Q3             |     9129 (-) |  0.880 |  0.840 | aacCTTCAgt
 V$TITF1_Q3             |     9193 (+) |  1.000 |  0.900 | acTCAAGaga
 V$TITF1_Q3             |     9223 (+) |  0.857 |  0.805 | agGCAAGtta
 V$TITF1_Q3             |     9295 (-) |  0.880 |  0.823 | cagCTTGTgt
 V$TITF1_Q3             |     9345 (+) |  0.880 |  0.814 | ccTGAAGtct
 V$TITF1_Q3             |     9482 (-) |  0.857 |  0.832 | ctaCTTTAtt
 V$TITF1_Q3             |     9539 (+) |  0.880 |  0.808 | aaACAAGtcc
 V$TITF1_Q3             |     9633 (+) |  1.000 |  0.769 | gtTCAAGgtc
 V$TITF1_Q3             |     9662 (-) |  0.880 |  0.768 | gacCTTGTct
 V$TITF1_Q3             |     9674 (+) |  0.761 |  0.766 | aaAGAAGtgg
 V$TITF1_Q3             |     9862 (+) |  0.857 |  0.779 | atTAAAGaag
 V$TITF1_Q3             |    10133 (+) |  0.857 |  0.768 | agTTAAGaaa
 V$TITF1_Q3             |    10249 (-) |  0.880 |  0.770 | aggCTTGTgc
 V$TITF1_Q3             |    10472 (-) |  0.857 |  0.791 | tcaCTTTAga
 V$TITF1_Q3             |    10491 (+) |  1.000 |  0.870 | taTCAAGgat
 V$TITF1_Q3             |    10505 (+) |  0.762 |  0.796 | agTCAATtat
 V$TITF1_Q3             |    10545 (+) |  0.857 |  0.840 | tcTAAAGtat
 V$TITF1_Q3             |    10932 (-) |  0.880 |  0.763 | cctCTTGTgg
 V$TITF1_Q3             |    11111 (-) |  0.880 |  0.816 | cgaCTTCAga
 V$TITF1_Q3             |    11121 (-) |  0.857 |  0.764 | tccCTTAAct
 V$TITF1_Q3             |    11160 (+) |  0.880 |  0.799 | aaTGAAGctg
 V$TITF1_Q3             |    11193 (-) |  1.000 |  0.869 | tttCTTGAtt
 V$TITF1_Q3             |    11439 (-) |  0.737 |  0.776 | ataCTTATct
 V$TITF1_Q3             |    11596 (-) |  0.762 |  0.798 | agaCTAGAgt
 V$TITF1_Q3             |    11689 (+) |  0.857 |  0.797 | aaTAAAGtta
 V$TITF1_Q3             |    11778 (-) |  1.000 |  0.895 | ataCTTGAtg
 V$TITF1_Q3             |    11945 (+) |  1.000 |  0.869 | ttTCAAGggt
 V$IPF1_Q4              |       48 (-) |  1.000 |  0.920 | tgtCATTActtg
 V$IPF1_Q4              |       61 (+) |  0.869 |  0.874 | gccaTAATTact
 V$IPF1_Q4              |      176 (-) |  1.000 |  0.915 | tggCATTActac
 V$IPF1_Q4              |      495 (-) |  1.000 |  0.861 | caaCATTAttat
 V$IPF1_Q4              |     1647 (+) |  0.869 |  0.821 | gtgcTAATCtac
 V$IPF1_Q4              |     1902 (-) |  0.891 |  0.835 | tttTATTAtttt
 V$IPF1_Q4              |     3173 (-) |  1.000 |  0.927 | gtaCATTAtatc
 V$IPF1_Q4              |     3274 (-) |  1.000 |  0.873 | tgcCATTAtgat
 V$IPF1_Q4              |     3411 (+) |  1.000 |  0.918 | aagtTAATGatt
 V$IPF1_Q4              |     3734 (-) |  0.891 |  0.870 | aatTATTAtttc
 V$IPF1_Q4              |     3906 (+) |  0.891 |  0.862 | gtatTAATAaag
 V$IPF1_Q4              |     3927 (-) |  1.000 |  0.846 | ttaCATTAtcag
 V$IPF1_Q4              |     4030 (+) |  0.891 |  0.845 | gaatTAATAttc
 V$IPF1_Q4              |     4058 (+) |  0.869 |  0.854 | gcaaTAATTaaa
 V$IPF1_Q4              |     4283 (-) |  1.000 |  0.891 | acaCATTAgacc
 V$IPF1_Q4              |     5012 (-) |  1.000 |  0.864 | accCATTAagcc
 V$IPF1_Q4              |     5099 (-) |  0.891 |  0.841 | ggtTATTAtttg
 V$IPF1_Q4              |     5412 (-) |  0.891 |  0.871 | tctTATTAaatc
 V$IPF1_Q4              |     5586 (+) |  0.891 |  0.830 | ataaTAATAaaa
 V$IPF1_Q4              |     5788 (+) |  0.869 |  0.859 | gaaaTAATTaaa
 V$IPF1_Q4              |     6785 (+) |  1.000 |  0.882 | gatcTAATGctg
 V$IPF1_Q4              |     6808 (-) |  1.000 |  0.898 | cctCATTAcctt
 V$IPF1_Q4              |     6956 (-) |  1.000 |  0.842 | gtcCATTAttct
 V$IPF1_Q4              |     7258 (-) |  1.000 |  0.910 | tctCATTAaaat
 V$IPF1_Q4              |     7904 (-) |  0.891 |  0.823 | tgaTATTAgctt
 V$IPF1_Q4              |     8151 (-) |  1.000 |  0.875 | aaaCATTAgctt
 V$IPF1_Q4              |     8685 (-) |  0.869 |  0.837 | ggtAATTAgcct
 V$IPF1_Q4              |     9733 (+) |  1.000 |  0.908 | atgaTAATGtcc
 V$IPF1_Q4              |     9993 (-) |  0.891 |  0.843 | gggTATTAggtc
 V$IPF1_Q4              |    10141 (-) |  0.891 |  0.823 | aatTATTAttat
 V$IPF1_Q4              |    10144 (-) |  0.891 |  0.830 | tatTATTAttgt
 V$IPF1_Q4              |    10521 (-) |  1.000 |  0.839 | agcCATTAtagg
 V$IPF1_Q4              |    10655 (+) |  1.000 |  0.944 | gtccTAATGtca
 V$IPF1_Q4              |    11203 (-) |  0.891 |  0.845 | gatTATTAattt
 V$IPF1_Q4              |    11274 (-) |  0.869 |  0.850 | ggaAATTAaggc
 V$IPF1_Q4              |    11296 (+) |  0.891 |  0.877 | gaaaTAATAata
 V$IPF1_Q4              |    11299 (+) |  0.891 |  0.844 | ataaTAATAacg
 V$IPF1_Q4              |    11345 (-) |  1.000 |  0.846 | tgcCATTAtcga
 V$IPF1_Q4              |    11388 (-) |  0.891 |  0.823 | actTATTAaatt
 V$IPF1_Q4              |    11511 (-) |  0.891 |  0.822 | ggaTATTAccgt
 V$IPF1_Q4              |    11693 (+) |  0.869 |  0.842 | aagtTAATCact
 V$IPF1_Q4              |    11784 (+) |  0.783 |  0.819 | gatgTAAGGaca
 V$CHX10_01             |     8684 (+) |  1.000 |  0.997 | aggTAATTagcctt
 P$C1_Q2                |      126 (+) |  0.981 |  0.951 | ctAACTGctca
 P$C1_Q2                |      400 (+) |  0.985 |  0.953 | ccAACAAggcg
 P$C1_Q2                |      456 (-) |  0.996 |  0.960 | gtttTGGTTgg
 P$C1_Q2                |      607 (+) |  0.966 |  0.948 | taAACATcctg
 P$C1_Q2                |      719 (-) |  0.996 |  0.957 | cagaTGGTTgt
 P$C1_Q2                |      737 (-) |  0.996 |  0.946 | cacgTGGTTgc
 P$C1_Q2                |      933 (+) |  0.996 |  0.943 | gaAACCAcaag
 P$C1_Q2                |      937 (-) |  0.981 |  0.948 | ccacAAGTTag
 P$C1_Q2                |     1025 (-) |  0.981 |  0.954 | ttggCAGTTga
 P$C1_Q2                |     1317 (+) |  0.981 |  0.964 | ctAACTCcctt
 P$C1_Q2                |     1366 (-) |  0.981 |  0.946 | atgcTCGTTtg
 P$C1_Q2                |     1594 (-) |  0.978 |  0.944 | cactGGGTTtg
 P$C1_Q2                |     1736 (+) |  0.981 |  0.948 | tgAACTTccta
 P$C1_Q2                |     1969 (-) |  0.978 |  0.955 | gagcAGGTTgg
 P$C1_Q2                |     1983 (+) |  0.981 |  0.952 | caAACTCacca
 P$C1_Q2                |     2391 (-) |  0.981 |  0.944 | ctgaGAGTTgc
 P$C1_Q2                |     2426 (-) |  0.978 |  0.946 | acagGGGTTgg
 P$C1_Q2                |     2481 (-) |  0.978 |  0.944 | ccctGGGTTcg
 P$C1_Q2                |     2604 (+) |  0.996 |  0.946 | taAACCAagag
 P$C1_Q2                |     3238 (+) |  0.966 |  0.956 | ccAACATtccc
 P$C1_Q2                |     3306 (-) |  1.000 |  0.964 | catgTAGTTaa
 P$C1_Q2                |     3500 (+) |  1.000 |  0.966 | ttAACTAccct
 P$C1_Q2                |     3508 (-) |  0.966 |  0.950 | cctgCTGTTag
 P$C1_Q2                |     3534 (-) |  0.978 |  0.958 | cccgAGGTTtg
 P$C1_Q2                |     3585 (+) |  0.981 |  0.944 | tcAACTCtcct
 P$C1_Q2                |     4195 (-) |  0.981 |  0.946 | ctgcAAGTTca
 P$C1_Q2                |     4257 (-) |  0.985 |  0.972 | ttggTTGTTag
 P$C1_Q2                |     4538 (+) |  0.966 |  0.946 | tcAACAGcctc
 P$C1_Q2                |     4570 (-) |  0.978 |  0.955 | gttgCGGTTag
 P$C1_Q2                |     5088 (-) |  0.996 |  0.946 | tgacTGGTTtg
 P$C1_Q2                |     5147 (-) |  0.981 |  0.948 | taggCAGTTta
 P$C1_Q2                |     5277 (+) |  0.985 |  0.969 | ccAACAAcagg
 P$C1_Q2                |     5336 (-) |  1.000 |  0.957 | ccgaTAGTTtt
 P$C1_Q2                |     5564 (+) |  0.985 |  0.950 | aaAACAAccag
 P$C1_Q2                |     5691 (-) |  1.000 |  0.946 | ccacTAGTTca
 P$C1_Q2                |     5907 (-) |  1.000 |  0.962 | agagTAGTTtg
 P$C1_Q2                |     6012 (+) |  0.981 |  0.960 | ccAACTCtcct
 P$C1_Q2                |     6024 (+) |  0.981 |  0.943 | tcAACTCtagg
 P$C1_Q2                |     6387 (+) |  0.981 |  0.946 | cgAACTGgcct
 P$C1_Q2                |     6522 (-) |  0.981 |  0.944 | cacgAAGTTca
 P$C1_Q2                |     6615 (+) |  0.981 |  0.944 | taAACTCcgtg
 P$C1_Q2                |     7034 (-) |  0.981 |  0.945 | tgaaGAGTTag
 P$C1_Q2                |     7038 (-) |  1.000 |  0.963 | gagtTAGTTga
 P$C1_Q2                |     7068 (-) |  0.985 |  0.945 | gtttTTGTTtg
 P$C1_Q2                |     7186 (+) |  0.963 |  0.955 | cgAACGGccac
 P$C1_Q2                |     7231 (-) |  0.981 |  0.961 | caggAAGTTca
 P$C1_Q2                |     7531 (-) |  0.981 |  0.953 | gttaCAGTTgg
 P$C1_Q2                |     7535 (-) |  0.996 |  0.950 | cagtTGGTTgt
 P$C1_Q2                |     7549 (+) |  0.981 |  0.945 | ccAACTGtgta
 P$C1_Q2                |     7588 (+) |  0.985 |  0.945 | caAACAAatgc
 P$C1_Q2                |     7722 (-) |  0.981 |  0.948 | tcagCAGTTtg
 P$C1_Q2                |     7826 (+) |  0.985 |  0.945 | caAACAAttaa
 P$C1_Q2                |     7928 (-) |  0.981 |  0.947 | caatTCGTTtg
 P$C1_Q2                |     7967 (-) |  0.985 |  0.949 | atagTTGTTtg
 P$C1_Q2                |     8001 (-) |  0.966 |  0.946 | gtgcCTGTTgg
 P$C1_Q2                |     8356 (+) |  0.978 |  0.946 | ccAACCCctgt
 P$C1_Q2                |     8667 (+) |  0.996 |  0.992 | caAACCAccgg
 P$C1_Q2                |     8671 (-) |  0.978 |  0.944 | ccacCGGTTag
 P$C1_Q2                |     8796 (-) |  0.981 |  0.946 | tgtaGAGTTgg
 P$C1_Q2                |     8934 (+) |  1.000 |  0.942 | taAACTAaagc
 P$C1_Q2                |     9223 (-) |  0.981 |  0.949 | aggcAAGTTag
 P$C1_Q2                |     9314 (-) |  0.963 |  0.942 | ggagGCGTTgg
 P$C1_Q2                |     9417 (+) |  1.000 |  0.951 | aaAACTAtccc
 P$C1_Q2                |     9538 (+) |  0.985 |  0.942 | caAACAAgtcc
 P$C1_Q2                |     9627 (-) |  0.981 |  0.949 | tcggGAGTTca
 P$C1_Q2                |    10025 (-) |  1.000 |  0.962 | accgTAGTTtg
 P$C1_Q2                |    10405 (-) |  0.996 |  0.989 | gaggTGGTTgg
 P$C1_Q2                |    10617 (-) |  0.981 |  0.943 | gaggGAGTTgt
 P$C1_Q2                |    10756 (-) |  0.966 |  0.951 | ccgtGTGTTtg
 P$C1_Q2                |    10963 (-) |  0.966 |  0.946 | gtgcCTGTTgg
 P$C1_Q2                |    11038 (-) |  0.985 |  0.952 | actgTTGTTgg
 P$C1_Q2                |    11125 (+) |  0.981 |  0.948 | ttAACTCgctg
 P$C1_Q2                |    11218 (+) |  0.981 |  0.950 | tgAACTGccca
 P$C1_Q2                |    11711 (+) |  0.981 |  0.967 | ccAACTGccct
 P$C1_Q2                |    11816 (-) |  0.978 |  0.955 | cccaGGGTTgg
 P$C1_Q2                |    11895 (+) |  0.996 |  0.950 | tcAACCAatag
 P$C1_Q2                |    11922 (+) |  0.963 |  0.950 | ccAACGCccat
 P$O2_Q2                |       15 (+) |  0.858 |  0.811 | aagtaCATGTgaa
 P$O2_Q2                |       37 (-) |  0.862 |  0.842 | acaACTTCagatg
 P$O2_Q2                |       74 (+) |  0.890 |  0.857 | ttgttGATGTtga
 P$O2_Q2                |      282 (-) |  0.844 |  0.823 | tgcAAGTCaagtg
 P$O2_Q2                |      350 (-) |  0.890 |  0.888 | tctACATCagatt
 P$O2_Q2                |      431 (+) |  0.969 |  0.885 | aatacCACGTtta
 P$O2_Q2                |      434 (-) |  0.906 |  0.836 | accACGTTtaatc
 P$O2_Q2                |      571 (-) |  1.000 |  0.837 | taaACGTCtacct
 P$O2_Q2                |      732 (+) |  0.969 |  0.865 | gccacCACGTggt
 P$O2_Q2                |      735 (-) |  0.969 |  0.865 | accACGTGgttgc
 P$O2_Q2                |     1077 (-) |  0.844 |  0.811 | tgtAGGTCatttt
 P$O2_Q2                |     1126 (-) |  0.969 |  0.818 | tgcACGTGtgttc
 P$O2_Q2                |     1238 (-) |  0.890 |  0.812 | ttgACATCagggc
 P$O2_Q2                |     3287 (+) |  0.862 |  0.847 | gggatGAGGTgaa
 P$O2_Q2                |     3432 (+) |  0.844 |  0.811 | taattGACTTagg
 P$O2_Q2                |     4510 (-) |  0.890 |  0.823 | acaACATCagacc
 P$O2_Q2                |     4694 (+) |  0.890 |  0.829 | aacttGATGTcct
 P$O2_Q2                |     6695 (+) |  0.862 |  0.832 | gtgctGAAGTaga
 P$O2_Q2                |     6853 (+) |  0.969 |  0.810 | gtgagCACGTcca
 P$O2_Q2                |     6883 (+) |  0.969 |  0.834 | agcacCACGTaag
 P$O2_Q2                |     6886 (-) |  0.906 |  0.856 | accACGTAagaca
 P$O2_Q2                |     7581 (-) |  0.844 |  0.819 | atcAGGTCaaaca
 P$O2_Q2                |     7881 (-) |  0.844 |  0.818 | tagAAGTCatttg
 P$O2_Q2                |     8730 (-) |  1.000 |  0.812 | gtaACGTCggggt
 P$O2_Q2                |     8789 (+) |  0.890 |  0.839 | aagaaGATGTaga
 P$O2_Q2                |     9052 (-) |  0.858 |  0.810 | tctACATGgcaag
 P$O2_Q2                |     9610 (+) |  0.862 |  0.828 | aagctGAGGTggg
 P$O2_Q2                |     9635 (-) |  0.844 |  0.841 | tcaAGGTCagctt
 P$O2_Q2                |     9801 (-) |  0.890 |  0.845 | tgtACATCacata
 P$O2_Q2                |     9815 (-) |  0.862 |  0.814 | gtaACTTCaaatt
 P$O2_Q2                |    10442 (-) |  1.000 |  0.821 | gcaACGTCtcttt
 P$O2_Q2                |    11054 (+) |  0.906 |  0.853 | ttgttAACGTtgt
 P$O2_Q2                |    11057 (-) |  0.906 |  0.812 | ttaACGTTgtgat
 P$O2_Q2                |    11110 (-) |  0.862 |  0.848 | acgACTTCagatc
 P$O2_Q2                |    11332 (+) |  0.890 |  0.836 | atgacGATGTaaa
 P$O2_Q2                |    11779 (+) |  0.890 |  0.834 | tacttGATGTaag
 V$VDR_Q3               |      415 (+) |  1.000 |  0.838 | GGGTGagcttgtcca
 V$VDR_Q3               |     1320 (-) |  0.846 |  0.876 | actcccttctCACTC
 V$VDR_Q3               |     1381 (+) |  0.846 |  0.860 | GGGCGaggtagggca
 V$VDR_Q3               |     1391 (+) |  0.843 |  0.854 | GGGCAggtgaggaga
 V$VDR_Q3               |     1488 (+) |  0.802 |  0.846 | GAGGGaggggggggg
 V$VDR_Q3               |     1490 (+) |  0.846 |  0.867 | GGGAGggggggggga
 V$VDR_Q3               |     1496 (+) |  0.956 |  0.881 | GGGGGgggagggagg
 V$VDR_Q3               |     1499 (+) |  0.956 |  0.855 | GGGGGagggagggag
 V$VDR_Q3               |     1500 (+) |  0.953 |  0.880 | GGGGAgggagggagg
 V$VDR_Q3               |     1574 (+) |  0.843 |  0.831 | GGGAAtgcatggaga
 V$VDR_Q3               |     1604 (+) |  0.956 |  0.832 | GGGGCtcagggggtc
 V$VDR_Q3               |     1605 (+) |  0.837 |  0.839 | GGGCTcagggggtct
 V$VDR_Q3               |     1613 (+) |  0.947 |  0.848 | GGGGTctcgtggaca
 V$VDR_Q3               |     4047 (+) |  0.956 |  0.877 | GGGGGaaataggcaa
 V$VDR_Q3               |     5503 (-) |  0.843 |  0.841 | gctcccaggtTTCCC
 V$VDR_Q3               |     5766 (+) |  0.997 |  0.829 | GGGTAaaaggagaga
 V$VDR_Q3               |     6024 (-) |  1.000 |  0.837 | tcaactctagGACCC
 V$VDR_Q3               |     6180 (-) |  1.000 |  0.825 | ttcccagagaCACCC
 V$VDR_Q3               |     6902 (+) |  0.843 |  0.838 | GGGCAtaagtggaga
 V$VDR_Q3               |     8194 (-) |  0.953 |  0.853 | tctgcctgttTCCCC
 V$VDR_Q3               |     8759 (-) |  0.802 |  0.835 | tgtcctcccaGCACC
 V$VDR_Q3               |     8963 (+) |  0.846 |  0.850 | GGGAGaaccaggtgt
 V$VDR_Q3               |     9572 (+) |  1.000 |  0.831 | GGGTGtggtggtata
 V$VDR_Q3               |     9585 (-) |  0.837 |  0.826 | tagccctgtaATCCC
 V$VDR_Q3               |     9629 (+) |  0.846 |  0.829 | GGGAGttcaaggtca
 V$VDR_Q3               |     9686 (+) |  0.956 |  0.826 | GGGGGgtggtggtgg
 V$VDR_Q3               |     9689 (+) |  1.000 |  0.847 | GGGTGgtggtggtgg
 V$VDR_Q3               |    11706 (-) |  0.843 |  0.858 | tcaccccaacTGCCC
 V$VDR_Q3               |    11852 (+) |  0.947 |  0.866 | GGGGTatgggggtag
 V$VDR_Q3               |    11853 (+) |  0.997 |  0.841 | GGGTAtgggggtagg
 V$VDR_Q3               |    11861 (+) |  0.997 |  0.826 | GGGTAggtccggggg
 V$SPZ1_01              |     1488 (+) |  1.000 |  0.920 | gagGGAGGggggggg
 V$SPZ1_01              |     1491 (+) |  0.998 |  0.918 | ggaGGGGGgggggag
 V$SPZ1_01              |     1494 (+) |  0.998 |  0.927 | gggGGGGGggaggga
 V$SPZ1_01              |     1495 (+) |  0.998 |  0.950 | gggGGGGGgagggag
 V$SPZ1_01              |     1499 (+) |  1.000 |  0.952 | gggGGAGGgagggag
 V$SPZ1_01              |     1503 (+) |  1.000 |  0.951 | gagGGAGGgagggag
 V$SPZ1_01              |     1507 (+) |  1.000 |  0.951 | gagGGAGGgagggag
 V$SPZ1_01              |     1511 (+) |  1.000 |  0.940 | gagGGAGGgaggtag
 V$SPZ1_01              |     1871 (+) |  1.000 |  0.921 | aagGGAGGatctgcc
 V$SPZ1_01              |     3177 (-) |  0.998 |  0.917 | attatatCCCCCctc
 V$SPZ1_01              |     3178 (-) |  0.998 |  0.940 | ttatatcCCCCCtct
 V$SPZ1_01              |     3336 (-) |  1.000 |  0.948 | ctatttcCCTCCtgt
 V$SPZ1_01              |     3776 (-) |  0.998 |  0.956 | ctccttcCCCCCttt
 V$SPZ1_01              |     4175 (+) |  1.000 |  0.920 | tcaGGAGGctgagca
 V$SPZ1_01              |     4353 (+) |  1.000 |  0.920 | gcaGGAGGatcagaa
 V$SPZ1_01              |     5421 (-) |  1.000 |  0.951 | atctttcCCTCCact
 V$SPZ1_01              |     7501 (+) |  1.000 |  0.940 | cttGGAGGgtgtcag
 V$SPZ1_01              |     8112 (-) |  0.989 |  0.922 | cactctcCCACCctg
 V$SPZ1_01              |     8482 (+) |  0.998 |  0.925 | taaGGGGGttatttt
 V$SPZ1_01              |     9614 (+) |  0.989 |  0.929 | tgaGGTGGgaggatc
 V$SPZ1_01              |     9618 (+) |  1.000 |  0.921 | gtgGGAGGatcggga
 V$SPZ1_01              |     9682 (+) |  0.998 |  0.926 | ggaGGGGGggtggtg
 V$SPZ1_01              |     9683 (+) |  0.998 |  0.967 | gagGGGGGgtggtgg
 V$SPZ1_01              |    10613 (+) |  1.000 |  0.944 | gtgGGAGGgagttgt
 V$SPZ1_01              |    10737 (+) |  0.998 |  0.960 | attGGGGGgtttcag
 V$SPZ1_01              |    10738 (+) |  0.998 |  0.915 | ttgGGGGGtttcagt
 V$SPZ1_01              |    10875 (+) |  0.989 |  0.927 | ggtGGTGGgagcact
 V$SPZ1_01              |    11712 (-) |  1.000 |  0.928 | caactgcCCTCCacc
 V$SPZ1_01              |    11842 (+) |  0.998 |  0.967 | agtGGGGGgtggggt
 V$SPZ1_01              |    11871 (+) |  1.000 |  0.944 | gggGGAGGgacttag
 V$AR_Q2                |     2810 (-) |  0.875 |  0.837 | TGAACaccgtgctct
 V$AR_Q2                |     3024 (-) |  0.939 |  0.793 | AGTACaccgacttcc
 V$AR_Q2                |     4692 (+) |  0.899 |  0.785 | gaaacttgatGTCCT
 V$AR_Q2                |     6518 (+) |  0.875 |  0.853 | agaacacgaaGTTCA
 V$AR_Q2                |     6518 (-) |  1.000 |  0.877 | AGAACacgaagttca
 V$AR_Q2                |     7805 (-) |  1.000 |  0.867 | AGAACaacgacaact
 V$AR_Q2                |     8534 (-) |  1.000 |  0.783 | AGAACacagtgggcc
 V$AR_Q2                |     8966 (-) |  1.000 |  0.784 | AGAACcaggtgtggt
 V$AR_Q2                |     9465 (+) |  1.000 |  0.883 | tgtacaggatGTTCT
 V$AR_Q2                |     9465 (-) |  0.814 |  0.873 | TGTACaggatgttct
 V$AR_Q2                |    10062 (-) |  0.875 |  0.783 | TGAACcgggtcttct
 V$AR_Q2                |    10080 (+) |  0.899 |  0.789 | agggcagccaGTGCT
 V$AR_Q2                |    10194 (+) |  0.899 |  0.809 | agtcagttctGTCCT
 V$AR_Q2                |    11223 (+) |  1.000 |  0.785 | tgcccagtttGTTCT
 V$ZIC1_01              |      105 (+) |  0.817 |  0.781 | ggGGGTGgc
 V$ZIC1_01              |      106 (+) |  1.000 |  0.905 | ggGGTGGcc
 V$ZIC1_01              |      137 (-) |  0.819 |  0.774 | gtCAATCca
 V$ZIC1_01              |      182 (-) |  0.940 |  0.860 | taCTACCcg
 V$ZIC1_01              |      200 (-) |  1.000 |  0.762 | caCCACCat
 V$ZIC1_01              |      249 (+) |  0.782 |  0.778 | tgGGCTGta
 V$ZIC1_01              |      419 (+) |  0.833 |  0.801 | gaGCTTGtc
 V$ZIC1_01              |      446 (+) |  0.940 |  0.858 | caGGTTGtc
 V$ZIC1_01              |      459 (+) |  0.940 |  0.757 | ttGGTTGgc
 V$ZIC1_01              |      460 (+) |  0.901 |  0.754 | tgGTTGGct
 V$ZIC1_01              |      576 (-) |  0.940 |  0.749 | gtCTACCtg
 V$ZIC1_01              |      687 (-) |  0.718 |  0.817 | gaCACACca
 V$ZIC1_01              |      782 (+) |  0.682 |  0.773 | cgGGTGCtc
 V$ZIC1_01              |     1008 (-) |  0.722 |  0.785 | gaCGCACct
 V$ZIC1_01              |     1184 (-) |  0.817 |  0.787 | ggCACCCcc
 V$ZIC1_01              |     1279 (+) |  0.782 |  0.750 | tgGGATGac
 V$ZIC1_01              |     1330 (-) |  0.817 |  0.791 | caCTCCCca
 V$ZIC1_01              |     1346 (+) |  0.833 |  0.771 | agGCTTGcc
 V$ZIC1_01              |     1404 (+) |  0.778 |  0.764 | gaGTGGGtc
 V$ZIC1_01              |     1516 (+) |  0.842 |  0.782 | agGGAGGta
 V$ZIC1_01              |     1610 (+) |  0.877 |  0.817 | caGGGGGtc
 V$ZIC1_01              |     1632 (-) |  0.894 |  0.787 | gtCCAGCct
 V$ZIC1_01              |     1681 (+) |  0.817 |  0.781 | tcGGGTGtc
 V$ZIC1_01              |     1696 (+) |  0.940 |  0.747 | ggGGTAGat
 V$ZIC1_01              |     1812 (+) |  1.000 |  0.874 | agGGTGGtg
 V$ZIC1_01              |     1840 (+) |  0.944 |  0.955 | ggGGTCGtc
 V$ZIC1_01              |     1943 (+) |  0.833 |  0.801 | tgGCTAGgc
 V$ZIC1_01              |     1972 (+) |  0.940 |  0.766 | caGGTTGgc
 V$ZIC1_01              |     1973 (+) |  0.901 |  0.815 | agGTTGGcc
 V$ZIC1_01              |     2429 (+) |  0.940 |  0.770 | ggGGTTGgg
 V$ZIC1_01              |     2637 (-) |  0.940 |  0.753 | ctCTACCcc
 V$ZIC1_01              |     2792 (+) |  0.894 |  0.848 | taGCTGGtc
 V$ZIC1_01              |     2921 (-) |  0.687 |  0.789 | gaCGGACcc
 V$ZIC1_01              |     3032 (-) |  0.782 |  0.749 | gaCTTCCgc
 V$ZIC1_01              |     3040 (-) |  1.000 |  0.780 | ctCCACCcg
 V$ZIC1_01              |     3050 (-) |  0.682 |  0.759 | gaCATACct
 V$ZIC1_01              |     3245 (-) |  0.894 |  0.751 | tcCCAGCcc
 V$ZIC1_01              |     3357 (-) |  0.682 |  0.794 | gaCAGACca
 V$ZIC1_01              |     3502 (-) |  0.940 |  0.830 | aaCTACCct
 V$ZIC1_01              |     3523 (-) |  1.000 |  0.796 | ggCCACCtt
 V$ZIC1_01              |     3636 (-) |  0.743 |  0.753 | taCCTACca
 V$ZIC1_01              |     4206 (+) |  0.833 |  0.771 | agGCTTGcc
 V$ZIC1_01              |     4244 (+) |  0.819 |  0.794 | ggGATTGta
 V$ZIC1_01              |     4257 (+) |  0.940 |  0.752 | ttGGTTGtt
 V$ZIC1_01              |     4341 (+) |  1.000 |  0.806 | caGGTGGtg
 V$ZIC1_01              |     4413 (-) |  0.940 |  0.752 | caCAACCtt
 V$ZIC1_01              |     4469 (-) |  0.682 |  0.794 | gaCTGACca
 V$ZIC1_01              |     4473 (-) |  0.894 |  0.784 | gaCCAGCat
 V$ZIC1_01              |     4632 (+) |  0.940 |  0.795 | tgGGTAGca
 V$ZIC1_01              |     4740 (+) |  0.880 |  0.789 | ctGATGGtc
 V$ZIC1_01              |     4828 (+) |  0.940 |  0.770 | ggGGTAGgg
 V$ZIC1_01              |     4862 (+) |  0.842 |  0.863 | agGGAGGtc
 V$ZIC1_01              |     4963 (+) |  0.782 |  0.755 | caGGAAGtc
 V$ZIC1_01              |     5060 (+) |  0.940 |  0.767 | caGGTAGtg
 V$ZIC1_01              |     5140 (-) |  0.940 |  0.769 | gtCAACCta
 V$ZIC1_01              |     5295 (+) |  0.833 |  0.798 | ggGCTAGcc
 V$ZIC1_01              |     5296 (-) |  0.833 |  0.806 | ggCTAGCca
 V$ZIC1_01              |     5688 (-) |  0.778 |  0.773 | gaCCCACta
 V$ZIC1_01              |     5857 (+) |  0.901 |  0.748 | gaGTTGGtt
 V$ZIC1_01              |     5873 (-) |  0.880 |  0.830 | gaCCATCtc
 V$ZIC1_01              |     5895 (-) |  0.771 |  0.757 | ggCCCGCcc
 V$ZIC1_01              |     5896 (-) |  0.842 |  0.797 | gcCCGCCcc
 V$ZIC1_01              |     5930 (-) |  0.817 |  0.763 | gaCTCCCtt
 V$ZIC1_01              |     6056 (-) |  0.782 |  0.823 | gaCAGCCct
 V$ZIC1_01              |     6121 (+) |  0.833 |  0.787 | ggGCTTGtt
 V$ZIC1_01              |     6385 (-) |  0.845 |  0.796 | gaCGAACtg
 V$ZIC1_01              |     6438 (-) |  0.940 |  0.852 | gtCAACCca
 V$ZIC1_01              |     6540 (-) |  0.841 |  0.776 | gaCAAACgg
 V$ZIC1_01              |     6598 (+) |  1.000 |  0.791 | aaGGTGGtg
 V$ZIC1_01              |     6717 (-) |  0.940 |  0.752 | caCAACCtt
 V$ZIC1_01              |     6753 (-) |  0.819 |  0.783 | caCTATCcc
 V$ZIC1_01              |     6986 (+) |  0.894 |  0.758 | taGCTGGtg
 V$ZIC1_01              |     7176 (+) |  0.880 |  0.819 | caGATGGtc
 V$ZIC1_01              |     7393 (+) |  1.000 |  0.817 | caGGTGGta
 V$ZIC1_01              |     7503 (+) |  0.757 |  0.752 | tgGAGGGtg
 V$ZIC1_01              |     7505 (+) |  0.817 |  0.790 | gaGGGTGtc
 V$ZIC1_01              |     7538 (+) |  0.940 |  0.758 | ttGGTTGtg
 V$ZIC1_01              |     7701 (+) |  0.842 |  0.817 | tgGGAGGta
 V$ZIC1_01              |     7813 (-) |  0.642 |  0.760 | gaCAACTcc
 V$ZIC1_01              |     8117 (-) |  1.000 |  0.793 | tcCCACCct
 V$ZIC1_01              |     8354 (-) |  0.901 |  0.761 | tgCCAACcc
 V$ZIC1_01              |     8355 (-) |  0.940 |  0.861 | gcCAACCcc
 V$ZIC1_01              |     8400 (-) |  0.833 |  0.801 | gcCAAGCca
 V$ZIC1_01              |     8405 (-) |  0.782 |  0.747 | gcCAGCCcg
 V$ZIC1_01              |     8440 (-) |  0.940 |  0.775 | tgCAACCcg
 V$ZIC1_01              |     8669 (-) |  1.000 |  0.783 | aaCCACCgg
 V$ZIC1_01              |     8737 (+) |  0.817 |  0.770 | cgGGGTGtg
 V$ZIC1_01              |     8743 (+) |  1.000 |  0.793 | gtGGTGGcc
 V$ZIC1_01              |     8760 (-) |  0.842 |  0.789 | gtCCTCCca
 V$ZIC1_01              |     8774 (+) |  0.842 |  0.812 | tgGGAGGcc
 V$ZIC1_01              |     8976 (+) |  1.000 |  0.799 | gtGGTGGta
 V$ZIC1_01              |     9014 (+) |  0.782 |  0.758 | ggGGCAGgc
 V$ZIC1_01              |     9069 (+) |  0.833 |  0.771 | agGCTAGcc
 V$ZIC1_01              |     9070 (-) |  0.833 |  0.806 | ggCTAGCca
 V$ZIC1_01              |     9189 (-) |  0.703 |  0.807 | gaCCACTca
 V$ZIC1_01              |     9338 (-) |  0.626 |  0.749 | gaGGACCcc
 V$ZIC1_01              |     9419 (-) |  0.819 |  0.778 | aaCTATCcc
 V$ZIC1_01              |     9549 (+) |  0.642 |  0.768 | tgCGTAGtc
 V$ZIC1_01              |     9576 (+) |  1.000 |  0.799 | gtGGTGGta
 V$ZIC1_01              |     9685 (+) |  0.877 |  0.821 | ggGGGGGtg
 V$ZIC1_01              |     9688 (+) |  1.000 |  0.900 | ggGGTGGtg
 V$ZIC1_01              |     9691 (+) |  1.000 |  0.788 | gtGGTGGtg
 V$ZIC1_01              |     9694 (+) |  1.000 |  0.788 | gtGGTGGtg
 V$ZIC1_01              |     9697 (+) |  1.000 |  0.788 | gtGGTGGtg
 V$ZIC1_01              |     9700 (+) |  1.000 |  0.788 | gtGGTGGtg
 V$ZIC1_01              |     9703 (+) |  1.000 |  0.788 | gtGGTGGtg
 V$ZIC1_01              |     9706 (+) |  1.000 |  0.788 | gtGGTGGtg
 V$ZIC1_01              |    10114 (-) |  0.880 |  0.747 | tgCCATCcc
 V$ZIC1_01              |    10115 (-) |  0.782 |  0.758 | gcCATCCcc
 V$ZIC1_01              |    10237 (+) |  0.901 |  0.810 | agGTTGGtg
 V$ZIC1_01              |    10240 (+) |  1.000 |  0.888 | ttGGTGGtc
 V$ZIC1_01              |    10249 (+) |  0.833 |  0.766 | agGCTTGtg
 V$ZIC1_01              |    10405 (+) |  1.000 |  0.812 | gaGGTGGtt
 V$ZIC1_01              |    10408 (+) |  0.940 |  0.748 | gtGGTTGgc
 V$ZIC1_01              |    10409 (+) |  0.901 |  0.770 | tgGTTGGca
 V$ZIC1_01              |    10480 (-) |  0.894 |  0.931 | gaCCAGCca
 V$ZIC1_01              |    10645 (-) |  0.817 |  0.748 | gaCACCCag
 V$ZIC1_01              |    10739 (+) |  0.877 |  0.824 | tgGGGGGtt
 V$ZIC1_01              |    10792 (+) |  0.782 |  0.759 | ggGGATGtg
 V$ZIC1_01              |    10873 (+) |  1.000 |  0.788 | gtGGTGGtg
 V$ZIC1_01              |    11016 (+) |  0.940 |  0.754 | agGGTAGga
 V$ZIC1_01              |    11220 (-) |  0.782 |  0.762 | aaCTGCCca
 V$ZIC1_01              |    11705 (-) |  0.817 |  0.773 | gtCACCCca
 V$ZIC1_01              |    11809 (+) |  1.000 |  0.796 | aaGGTGGcc
 V$ZIC1_01              |    11844 (+) |  0.877 |  0.830 | tgGGGGGtg
 V$ZIC1_01              |    11847 (+) |  1.000 |  0.809 | ggGGTGGgg
 V$ZIC1_01              |    11860 (+) |  0.940 |  0.765 | ggGGTAGgt
 V$ZIC1_01              |    11861 (+) |  0.743 |  0.825 | ggGTAGGtc
 V$ZIC3_01              |      106 (+) |  1.000 |  0.939 | gGGGTGgcc
 V$ZIC3_01              |      182 (-) |  0.921 |  0.867 | tacTACCCg
 V$ZIC3_01              |      414 (+) |  1.000 |  0.909 | tGGGTGagc
 V$ZIC3_01              |      534 (+) |  1.000 |  0.919 | tGGGTGatg
 V$ZIC3_01              |      782 (+) |  1.000 |  0.969 | cGGGTGctc
 V$ZIC3_01              |     1183 (-) |  1.000 |  0.913 | gggCACCCc
 V$ZIC3_01              |     1185 (-) |  0.966 |  0.877 | gcaCCCCCa
 V$ZIC3_01              |     1310 (-) |  0.887 |  0.872 | gagTCCCCt
 V$ZIC3_01              |     1318 (-) |  0.948 |  0.857 | taaCTCCCt
 V$ZIC3_01              |     1330 (-) |  0.887 |  0.851 | cacTCCCCa
 V$ZIC3_01              |     1355 (+) |  0.916 |  0.853 | tGGGTCacc
 V$ZIC3_01              |     1516 (+) |  0.948 |  0.887 | aGGGAGgta
 V$ZIC3_01              |     1612 (+) |  0.878 |  0.864 | gGGGGTctc
 V$ZIC3_01              |     1682 (+) |  1.000 |  0.852 | cGGGTGtca
 V$ZIC3_01              |     1706 (-) |  1.000 |  0.911 | aagCACCCt
 V$ZIC3_01              |     1812 (+) |  1.000 |  0.937 | aGGGTGgtg
 V$ZIC3_01              |     1829 (-) |  1.000 |  0.864 | agaCACCCa
 V$ZIC3_01              |     1840 (+) |  0.916 |  0.921 | gGGGTCgtc
 V$ZIC3_01              |     3040 (-) |  1.000 |  0.874 | ctcCACCCg
 V$ZIC3_01              |     3081 (+) |  1.000 |  0.911 | aGGGTGatt
 V$ZIC3_01              |     3181 (-) |  0.966 |  0.876 | tatCCCCCc
 V$ZIC3_01              |     3502 (-) |  0.921 |  0.871 | aacTACCCt
 V$ZIC3_01              |     3723 (+) |  1.000 |  0.862 | cGGGTGact
 V$ZIC3_01              |     4712 (+) |  0.921 |  0.853 | tGGGTAatt
 V$ZIC3_01              |     4862 (+) |  0.948 |  0.948 | aGGGAGgtc
 V$ZIC3_01              |     5008 (-) |  0.921 |  0.847 | tatTACCCa
 V$ZIC3_01              |     5097 (+) |  0.912 |  0.846 | tGGGTTatt
 V$ZIC3_01              |     5371 (+) |  0.860 |  0.848 | cGGGATttc
 V$ZIC3_01              |     5896 (-) |  0.933 |  0.869 | gccCGCCCc
 V$ZIC3_01              |     6056 (-) |  0.845 |  0.862 | gacAGCCCt
 V$ZIC3_01              |     6187 (-) |  1.000 |  0.864 | agaCACCCa
 V$ZIC3_01              |     6438 (-) |  0.912 |  0.861 | gtcAACCCa
 V$ZIC3_01              |     6528 (-) |  1.000 |  0.900 | gttCACCCt
 V$ZIC3_01              |     6630 (-) |  1.000 |  0.922 | gggCACCCa
 V$ZIC3_01              |     6729 (+) |  1.000 |  0.900 | aGGGTGagc
 V$ZIC3_01              |     6746 (-) |  0.912 |  0.897 | gaaAACCCa
 V$ZIC3_01              |     6938 (-) |  0.921 |  0.853 | cagTACCCa
 V$ZIC3_01              |     7196 (+) |  0.966 |  0.871 | cGGGGGtgc
 V$ZIC3_01              |     7198 (+) |  1.000 |  0.904 | gGGGTGcta
 V$ZIC3_01              |     7506 (+) |  1.000 |  0.849 | aGGGTGtca
 V$ZIC3_01              |     7701 (+) |  0.948 |  0.895 | tGGGAGgta
 V$ZIC3_01              |     7731 (+) |  0.849 |  0.848 | tGGGCCatc
 V$ZIC3_01              |     7954 (-) |  0.878 |  0.873 | gatACCCCa
 V$ZIC3_01              |     8098 (+) |  0.916 |  0.850 | tGGGTCctg
 V$ZIC3_01              |     8117 (-) |  1.000 |  0.865 | tccCACCCt
 V$ZIC3_01              |     8235 (-) |  1.000 |  0.850 | ccaCACCCa
 V$ZIC3_01              |     8355 (-) |  0.912 |  0.852 | gccAACCCc
 V$ZIC3_01              |     8484 (+) |  0.966 |  0.873 | aGGGGGtta
 V$ZIC3_01              |     8760 (-) |  0.948 |  0.891 | gtcCTCCCa
 V$ZIC3_01              |     8774 (+) |  0.948 |  0.905 | tGGGAGgcc
 V$ZIC3_01              |     8962 (+) |  0.948 |  0.857 | aGGGAGaac
 V$ZIC3_01              |     9338 (-) |  0.916 |  0.895 | gagGACCCc
 V$ZIC3_01              |     9376 (+) |  0.948 |  0.857 | aGGGAGagc
 V$ZIC3_01              |     9571 (+) |  1.000 |  0.850 | tGGGTGtgg
 V$ZIC3_01              |     9628 (+) |  0.948 |  0.921 | cGGGAGttc
 V$ZIC3_01              |     9685 (+) |  0.966 |  0.908 | gGGGGGgtg
 V$ZIC3_01              |     9688 (+) |  1.000 |  0.936 | gGGGTGgtg
 V$ZIC3_01              |     9930 (+) |  0.921 |  0.853 | tGGGTAatt
 V$ZIC3_01              |     9952 (-) |  1.000 |  0.901 | taaCACCCt
 V$ZIC3_01              |    10067 (+) |  0.916 |  0.895 | cGGGTCttc
 V$ZIC3_01              |    10618 (+) |  0.948 |  0.864 | aGGGAGttg
 V$ZIC3_01              |    10644 (-) |  1.000 |  0.864 | agaCACCCa
 V$ZIC3_01              |    10694 (-) |  1.000 |  0.910 | caaCACCCg
 V$ZIC3_01              |    10739 (+) |  0.966 |  0.917 | tGGGGGgtt
 V$ZIC3_01              |    10740 (+) |  0.966 |  0.878 | gGGGGGttt
 V$ZIC3_01              |    10741 (+) |  0.878 |  0.860 | gGGGGTttc
 V$ZIC3_01              |    10790 (+) |  0.966 |  0.883 | aGGGGGatg
 V$ZIC3_01              |    10880 (+) |  0.948 |  0.865 | tGGGAGcac
 V$ZIC3_01              |    11552 (+) |  0.921 |  0.904 | tGGGTAttc
 V$ZIC3_01              |    11704 (-) |  1.000 |  0.852 | tgtCACCCc
 V$ZIC3_01              |    11844 (+) |  0.966 |  0.917 | tGGGGGgtg
 V$ZIC3_01              |    11847 (+) |  1.000 |  0.870 | gGGGTGggg
 V$ZIC3_01              |    11923 (-) |  0.933 |  0.859 | caaCGCCCa
 V$NKX3A_01             |      660 (+) |  1.000 |  0.953 | atatAAGTAcac
 V$NKX3A_01             |     2569 (+) |  1.000 |  0.944 | ccgtAAGTAttt
 V$NKX3A_01             |    11437 (-) |  1.000 |  0.955 | gcaTACTTatct
 V$IRF7_01              |      897 (-) |  0.976 |  0.931 | agacttttcacTTTCTtt
 V$IRF7_01              |     3328 (-) |  1.000 |  0.905 | tcctgattctaTTTCCct
 V$IRF7_01              |     6516 (+) |  0.850 |  0.880 | aaAGAACacgaagttcac
 V$IRF7_01              |     8548 (+) |  0.976 |  0.896 | cgAGAAAatgaacaatgt
 V$IRF7_01              |    10579 (-) |  1.000 |  0.915 | ctttggttcaaTTTCCta
 V$IRF7_01              |    11154 (+) |  0.971 |  0.919 | gaTGAAAatgaagctgca
 V$IRF7_01              |    11266 (+) |  0.976 |  0.950 | caAGAAAaggaaattaag
 V$MRF2_01              |      211 (-) |  1.000 |  0.894 | ctgGTATTtttttt
 V$MRF2_01              |      425 (+) |  1.000 |  0.924 | gtccaaAATACcac
 V$MRF2_01              |      510 (-) |  0.859 |  0.844 | tttGTCTTctgatt
 V$MRF2_01              |      822 (+) |  1.000 |  0.843 | ctttttAATACtat
 V$MRF2_01              |     1848 (+) |  0.914 |  0.874 | caacacAATAGagc
 V$MRF2_01              |     1904 (-) |  0.906 |  0.852 | ttaTTATTttattt
 V$MRF2_01              |     2359 (-) |  1.000 |  0.856 | cttGTATTtatttt
 V$MRF2_01              |     2572 (-) |  1.000 |  0.855 | taaGTATTtacaac
 V$MRF2_01              |     3142 (+) |  0.931 |  0.851 | cacaacAATATatg
 V$MRF2_01              |     3798 (+) |  0.914 |  0.853 | ggacagAATAGaaa
 V$MRF2_01              |     4011 (-) |  0.931 |  0.871 | taaATATTctgctc
 V$MRF2_01              |     4063 (+) |  0.931 |  0.850 | aattaaAATATgta
 V$MRF2_01              |     4168 (-) |  1.000 |  0.879 | ctaGTATTcaggag
 V$MRF2_01              |     4304 (+) |  1.000 |  0.905 | accctcAATACtgc
 V$MRF2_01              |     5004 (-) |  1.000 |  0.860 | cttGTATTacccat
 V$MRF2_01              |     5439 (-) |  1.000 |  0.915 | tttGTATTgccata
 V$MRF2_01              |     5582 (+) |  0.906 |  0.861 | aaggatAATAAtaa
 V$MRF2_01              |     5595 (+) |  0.931 |  0.855 | aaatatAATATaac
 V$MRF2_01              |     5641 (+) |  0.906 |  0.851 | agacaaAATAAaaa
 V$MRF2_01              |     5663 (+) |  0.906 |  0.863 | gaacacAATAAgag
 V$MRF2_01              |     5737 (+) |  0.931 |  0.877 | agccatAATATaga
 V$MRF2_01              |     5777 (+) |  0.931 |  0.861 | gagaaaAATATgaa
 V$MRF2_01              |     5792 (+) |  1.000 |  0.882 | taattaAATACaaa
 V$MRF2_01              |     6583 (+) |  0.847 |  0.864 | aaacacAAAACaaa
 V$MRF2_01              |     7046 (-) |  0.914 |  0.843 | tgaCTATTtttttt
 V$MRF2_01              |     7330 (+) |  0.914 |  0.854 | tggaacAATAGaca
 V$MRF2_01              |     7376 (-) |  0.931 |  0.852 | ttgATATTgcttgt
 V$MRF2_01              |     7895 (-) |  0.906 |  0.864 | tttTTATTttgata
 V$MRF2_01              |     7903 (-) |  0.931 |  0.848 | ttgATATTagcttt
 V$MRF2_01              |     8068 (-) |  1.000 |  0.891 | ctgGTATTgcagaa
 V$MRF2_01              |     8600 (-) |  0.931 |  0.877 | ttaATATTatcatt
 V$MRF2_01              |     8698 (+) |  1.000 |  0.857 | tctgaaAATACcat
 V$MRF2_01              |     9489 (+) |  0.914 |  0.857 | atttgcAATAGaaa
 V$MRF2_01              |     9755 (-) |  0.931 |  0.864 | ttaATATTgaaaac
 V$MRF2_01              |    10143 (-) |  0.906 |  0.862 | ttaTTATTattgtt
 V$MRF2_01              |    10146 (-) |  0.906 |  0.894 | ttaTTATTgttgtt
 V$MRF2_01              |    10318 (-) |  0.931 |  0.872 | tttATATTtttatt
 V$MRF2_01              |    10338 (-) |  0.906 |  0.871 | tttTTATTgtttta
 V$MRF2_01              |    11298 (+) |  0.906 |  0.851 | aataatAATAAcga
 V$MRF2_01              |    11444 (-) |  0.914 |  0.859 | tatCTATTttggtg
 V$MRF2_01              |    11510 (-) |  0.931 |  0.846 | tggATATTaccgtt
 V$MRF2_01              |    11552 (-) |  1.000 |  0.867 | tggGTATTcaacca
 I$DRI_01               |       64 (+) |  1.000 |  0.955 | atAATTActg
 I$DRI_01               |      439 (-) |  1.000 |  0.984 | gttTAATCag
 I$DRI_01               |      586 (+) |  1.000 |  0.985 | tgAATTAaca
 I$DRI_01               |      990 (-) |  1.000 |  0.951 | taaTAATTtt
 I$DRI_01               |     1648 (-) |  1.000 |  0.947 | tgcTAATCta
 I$DRI_01               |     2025 (+) |  1.000 |  0.983 | ggGATTAaag
 I$DRI_01               |     3106 (-) |  1.000 |  0.956 | tacTAATTtc
 I$DRI_01               |     3126 (-) |  1.000 |  0.999 | tatTAATTta
 I$DRI_01               |     3429 (-) |  1.000 |  0.987 | gctTAATTga
 I$DRI_01               |     3732 (+) |  1.000 |  0.951 | aaAATTAtta
 I$DRI_01               |     3923 (+) |  1.000 |  0.948 | tgAATTAcat
 I$DRI_01               |     4029 (+) |  1.000 |  0.993 | ggAATTAata
 I$DRI_01               |     4059 (-) |  1.000 |  0.956 | caaTAATTaa
 I$DRI_01               |     4061 (+) |  1.000 |  0.984 | atAATTAaaa
 I$DRI_01               |     4446 (+) |  1.000 |  0.996 | acAATTAata
 I$DRI_01               |     5789 (-) |  1.000 |  0.956 | aaaTAATTaa
 I$DRI_01               |     5791 (+) |  1.000 |  0.984 | atAATTAaat
 I$DRI_01               |     5989 (+) |  1.000 |  0.948 | tgGATTAggg
 I$DRI_01               |     7059 (-) |  1.000 |  0.981 | tctTAATTtg
 I$DRI_01               |     7354 (-) |  1.000 |  0.981 | tgtTAATCat
 I$DRI_01               |     7401 (+) |  1.000 |  0.955 | agAATTActg
 I$DRI_01               |     7637 (+) |  1.000 |  0.951 | agAATTAttt
 I$DRI_01               |     7829 (+) |  1.000 |  0.982 | acAATTAacc
 I$DRI_01               |     8572 (+) |  1.000 |  0.989 | ttGATTAaat
 I$DRI_01               |     8857 (+) |  1.000 |  0.982 | aaAATTAaga
 I$DRI_01               |     8953 (+) |  1.000 |  0.957 | aaAATTAgta
 I$DRI_01               |     8990 (-) |  1.000 |  0.983 | cttTAATTcc
 I$DRI_01               |    10127 (+) |  1.000 |  0.957 | aaAATTAgtt
 I$DRI_01               |    10139 (+) |  1.000 |  0.951 | gaAATTAtta
 I$DRI_01               |    10347 (-) |  1.000 |  0.988 | tttTAATTca
 I$DRI_01               |    11201 (+) |  1.000 |  0.956 | ttGATTAtta
 I$DRI_01               |    11206 (-) |  1.000 |  0.994 | tatTAATTtg
 I$DRI_01               |    11275 (+) |  1.000 |  0.981 | gaAATTAagg
 I$DRI_01               |    11694 (-) |  1.000 |  0.980 | agtTAATCac
 V$FAC1_01              |       68 (-) |  1.000 |  0.907 | ttactGTTGTtgat
 V$FAC1_01              |      215 (-) |  0.904 |  0.868 | tatttTTTTTtttt
 V$FAC1_01              |      289 (-) |  0.978 |  0.871 | caagtGTTTTacag
 V$FAC1_01              |      425 (+) |  0.885 |  0.870 | gtccAAAATaccac
 V$FAC1_01              |      451 (-) |  0.978 |  0.948 | tgtctGTTTTggtt
 V$FAC1_01              |      510 (-) |  0.854 |  0.888 | tttgtCTTCTgatt
 V$FAC1_01              |      545 (-) |  0.978 |  0.891 | cttgtGTTTTaacc
 V$FAC1_01              |      834 (+) |  0.978 |  0.878 | atatAAAACaagtt
 V$FAC1_01              |     1528 (-) |  0.904 |  0.868 | ctgttTTTTTgttc
 V$FAC1_01              |     1959 (-) |  0.904 |  0.884 | ttcctTTTTTgagc
 V$FAC1_01              |     2291 (-) |  0.926 |  0.909 | tagttTTTGTgtgt
 V$FAC1_01              |     2310 (-) |  0.978 |  0.981 | tgtgtGTTTTggat
 V$FAC1_01              |     2363 (-) |  0.885 |  0.877 | tatttATTTTgcca
 V$FAC1_01              |     2407 (+) |  0.904 |  0.873 | ttaaAAAAAacaaa
 V$FAC1_01              |     2409 (+) |  0.978 |  0.922 | aaaaAAAACaaaaa
 V$FAC1_01              |     2540 (+) |  0.956 |  0.866 | gagaATAACaggtt
 V$FAC1_01              |     2552 (-) |  1.000 |  0.944 | tttctGTTGTgaaa
 V$FAC1_01              |     2577 (+) |  1.000 |  0.890 | atttACAACaaatg
 V$FAC1_01              |     3139 (+) |  1.000 |  0.931 | tcccACAACaatat
 V$FAC1_01              |     3452 (+) |  0.978 |  0.886 | taatAAAACacagg
 V$FAC1_01              |     3689 (+) |  0.934 |  0.888 | gccaAGAACacaag
 V$FAC1_01              |     3694 (+) |  0.919 |  0.880 | gaacACAAGagatg
 V$FAC1_01              |     3788 (-) |  0.854 |  0.866 | tttttCTTCTggac
 V$FAC1_01              |     3807 (+) |  0.978 |  0.880 | agaaAAAACatcgt
 V$FAC1_01              |     4100 (+) |  0.978 |  0.867 | ttctAAAACatcca
 V$FAC1_01              |     4426 (+) |  0.904 |  0.868 | aaaaAAAAAaaaaa
 V$FAC1_01              |     4427 (+) |  0.904 |  0.868 | aaaaAAAAAaaaaa
 V$FAC1_01              |     4428 (+) |  0.904 |  0.868 | aaaaAAAAAaaaaa
 V$FAC1_01              |     4481 (-) |  0.897 |  0.894 | tttttCTTTTgaac
 V$FAC1_01              |     4489 (+) |  0.926 |  0.867 | ttgaACAAAaaaca
 V$FAC1_01              |     4491 (+) |  0.904 |  0.924 | gaacAAAAAacaaa
 V$FAC1_01              |     4493 (+) |  0.978 |  0.896 | acaaAAAACaaaac
 V$FAC1_01              |     4496 (+) |  0.926 |  0.904 | aaaaACAAAacaaa
 V$FAC1_01              |     4498 (+) |  0.978 |  0.935 | aaacAAAACaaaac
 V$FAC1_01              |     4501 (+) |  0.926 |  0.869 | caaaACAAAacaac
 V$FAC1_01              |     4503 (+) |  0.978 |  0.928 | aaacAAAACaacat
 V$FAC1_01              |     4506 (+) |  1.000 |  0.887 | caaaACAACatcag
 V$FAC1_01              |     4522 (+) |  1.000 |  0.891 | caagACAACaaatg
 V$FAC1_01              |     4663 (-) |  0.978 |  0.937 | actttGTTTTgctc
 V$FAC1_01              |     5206 (-) |  0.919 |  0.874 | ggcctCTTGTgctt
 V$FAC1_01              |     5276 (+) |  1.000 |  0.901 | gccaACAACaggct
 V$FAC1_01              |     5357 (+) |  0.926 |  0.869 | tttgACAAAacaca
 V$FAC1_01              |     5359 (+) |  0.978 |  0.945 | tgacAAAACacacg
 V$FAC1_01              |     5560 (+) |  0.978 |  0.879 | ctagAAAACaacca
 V$FAC1_01              |     5600 (+) |  0.956 |  0.871 | taatATAACacaag
 V$FAC1_01              |     5605 (+) |  0.919 |  0.879 | taacACAAGaaacc
 V$FAC1_01              |     5641 (+) |  0.885 |  0.891 | agacAAAATaaaaa
 V$FAC1_01              |     5658 (+) |  0.934 |  0.889 | gaaaAGAACacaat
 V$FAC1_01              |     5663 (+) |  0.907 |  0.883 | gaacACAATaagag
 V$FAC1_01              |     5714 (+) |  0.926 |  0.872 | tcccACAAAaacac
 V$FAC1_01              |     5717 (+) |  0.978 |  0.919 | cacaAAAACactaa
 V$FAC1_01              |     5737 (+) |  0.863 |  0.870 | agccATAATataga
 V$FAC1_01              |     5799 (+) |  0.904 |  0.904 | atacAAAAAaaaaa
 V$FAC1_01              |     5801 (+) |  0.904 |  0.868 | acaaAAAAAaaaaa
 V$FAC1_01              |     5803 (+) |  0.904 |  0.868 | aaaaAAAAAaaata
 V$FAC1_01              |     5962 (-) |  0.978 |  0.890 | ccagtGTTTTtaag
 V$FAC1_01              |     6514 (+) |  0.934 |  0.896 | taaaAGAACacgaa
 V$FAC1_01              |     6578 (+) |  0.978 |  0.978 | atgcAAAACacaaa
 V$FAC1_01              |     6583 (+) |  0.926 |  0.943 | aaacACAAAacaaa
 V$FAC1_01              |     6585 (+) |  0.978 |  0.962 | acacAAAACaaata
 V$FAC1_01              |     6770 (+) |  0.926 |  0.874 | atgaACAAAacagc
 V$FAC1_01              |     6772 (+) |  0.978 |  0.908 | gaacAAAACagcag
 V$FAC1_01              |     7063 (-) |  0.978 |  0.905 | aatttGTTTTtgtt
 V$FAC1_01              |     7066 (-) |  0.926 |  0.870 | ttgttTTTGTttgt
 V$FAC1_01              |     7428 (-) |  0.978 |  0.920 | tatttGTTTTtatt
 V$FAC1_01              |     7436 (-) |  0.882 |  0.885 | tttatTTTATgtgt
 V$FAC1_01              |     7451 (-) |  0.978 |  0.936 | ggagtGTTTTgcct
 V$FAC1_01              |     7769 (+) |  0.904 |  0.912 | tctcAAAAAacaaa
 V$FAC1_01              |     7771 (+) |  0.978 |  0.883 | tcaaAAAACaaaac
 V$FAC1_01              |     7774 (+) |  0.926 |  0.904 | aaaaACAAAacaaa
 V$FAC1_01              |     7776 (+) |  0.978 |  0.961 | aaacAAAACaaaaa
 V$FAC1_01              |     7801 (+) |  0.934 |  0.873 | ataaAGAACaacga
 V$FAC1_01              |     7818 (+) |  0.978 |  0.951 | ctccAAAACaaaca
 V$FAC1_01              |     7895 (-) |  0.885 |  0.877 | tttttATTTTgata
 V$FAC1_01              |     7972 (-) |  0.978 |  0.905 | tgtttGTTTTtcaa
 V$FAC1_01              |     8530 (+) |  0.934 |  0.878 | ttcaAGAACacagt
 V$FAC1_01              |     8837 (+) |  0.978 |  0.922 | aaccAAAACagaac
 V$FAC1_01              |     9107 (+) |  0.978 |  0.960 | aagcAAAACaaaaa
 V$FAC1_01              |     9112 (+) |  0.904 |  0.892 | aaacAAAAAaccgg
 V$FAC1_01              |     9359 (-) |  0.934 |  0.875 | tcagtGTTCTctat
 V$FAC1_01              |     9428 (+) |  0.956 |  0.887 | ataaATAACaggaa
 V$FAC1_01              |     9530 (+) |  0.934 |  0.867 | gactAGAACaaaca
 V$FAC1_01              |     9760 (+) |  0.978 |  0.869 | attgAAAACagtca
 V$FAC1_01              |    10149 (-) |  1.000 |  0.921 | ttattGTTGTtgtc
 V$FAC1_01              |    10152 (-) |  1.000 |  0.908 | ttgttGTTGTcgtt
 V$FAC1_01              |    10310 (-) |  0.978 |  0.876 | taactGTTTTtata
 V$FAC1_01              |    10341 (-) |  0.978 |  0.881 | ttattGTTTTaatt
 V$FAC1_01              |    10930 (-) |  0.919 |  0.876 | cgcctCTTGTggac
 V$FAC1_01              |    10942 (-) |  1.000 |  0.903 | acggtGTTGTagct
 V$FAC1_01              |    11036 (-) |  1.000 |  0.887 | ccactGTTGTtggt
 V$FAC1_01              |    11444 (-) |  0.885 |  0.871 | tatctATTTTggtg
 V$FAC1_01              |    11474 (-) |  0.978 |  0.916 | tatttGTTTTtccc
 V$FAC1_01              |    11501 (-) |  0.926 |  0.881 | gaattTTTGTggat
 V$FAC1_01              |    11675 (+) |  0.904 |  0.868 | aaccAAAAAagacc
 V$STAT5A_01            |      924 (-) |  0.995 |  0.974 | caCTTCCacgaaacc
 V$STAT5A_01            |     1818 (+) |  0.995 |  0.930 | gtgttcagGGAAGac
 V$STAT5A_01            |    10049 (+) |  0.908 |  0.932 | gggttctaAGAACtg
 V$STAT5A_01            |    10049 (-) |  0.908 |  0.930 | ggGTTCTaagaactg
 V$STAT5B_01            |      924 (+) |  0.951 |  0.909 | caCTTCCacgaaacc
 V$STAT5B_01            |      924 (-) |  0.922 |  0.946 | cacttccaCGAAAcc
 V$STAT5B_01            |     1164 (-) |  0.968 |  0.901 | tttttcaaAGAAAgg
 V$STAT5B_01            |    10049 (+) |  0.923 |  0.907 | ggGTTCTaagaactg
 V$STAT5B_01            |    10049 (-) |  0.923 |  0.906 | gggttctaAGAACtg
 V$STAT5A_02            |      730 (-) |  0.786 |  0.724 | gagccaccacgtggTTGCTgggaa
 V$STAT5A_02            |      745 (+) |  0.998 |  0.736 | tgctgGGAATtgaactcaggacct
 V$STAT5A_02            |      912 (-) |  0.988 |  0.812 | tttcatgcgtagcaCTTCCacgaa
 V$STAT5A_02            |      927 (+) |  0.980 |  0.760 | ttccaCGAAAccacaagttaggaa
 V$STAT5A_02            |     1121 (-) |  0.991 |  0.747 | gtgtatgcacgtgtGTTCCtaaaa
 V$STAT5A_02            |     1152 (-) |  0.977 |  0.776 | tttatgtagttcttTTTCAaagaa
 V$STAT5A_02            |     1167 (+) |  0.996 |  0.786 | ttcaaAGAAAggagatgggcaccc
 V$STAT5A_02            |     1641 (-) |  0.814 |  0.732 | ttcctagtgctaatCTACTtggca
 V$STAT5A_02            |     1806 (-) |  0.974 |  0.767 | ttcatcagggtggtGTTCAgggaa
 V$STAT5A_02            |     1821 (+) |  0.988 |  0.738 | ttcagGGAAGacacccattggggt
 V$STAT5A_02            |     3078 (-) |  0.655 |  0.743 | cacagggtgattctATTTTtcgaa
 V$STAT5A_02            |     3123 (-) |  0.998 |  0.727 | ctatattaatttacATTCCcacaa
 V$STAT5A_02            |     3829 (-) |  1.000 |  0.725 | cataataaatttccATTCTcataa
 V$STAT5A_02            |     4024 (+) |  0.998 |  0.825 | ctcatGGAATtaatattccagcag
 V$STAT5A_02            |     4024 (-) |  0.998 |  0.738 | ctcatggaattaatATTCCagcag
 V$STAT5A_02            |     5021 (-) |  0.789 |  0.792 | gccacgggactgggATGCTcagga
 V$STAT5A_02            |     6766 (+) |  0.974 |  0.713 | taccaTGAACaaaacagcagatct
 V$STAT5A_02            |     7187 (-) |  0.782 |  0.727 | gaacggccacggggGTGCTatgaa
 V$STAT5A_02            |     7581 (-) |  0.789 |  0.781 | atcaggtcaaacaaATGCTctgaa
 V$STAT5A_02            |     7596 (+) |  0.974 |  0.724 | tgctcTGAACtgctgagccatctc
 V$STAT5A_02            |     7981 (+) |  0.798 |  0.747 | ttcaaGGGAAggacttcactgtgc
 V$STAT5A_02            |     8241 (-) |  0.977 |  0.862 | ccagatgaaggtgtGTTCGtggca
 V$STAT5A_02            |     8256 (+) |  0.788 |  0.731 | ttcgtGGCATtgacctgatgatgc
 V$STAT5A_02            |     9390 (-) |  0.993 |  0.729 | gcccctggaatgtgGTTCTatgtc
 V$STAT5A_02            |     9652 (+) |  0.996 |  0.794 | tacttAGAAAgaccttgtctcaaa
 V$STAT5A_02            |    10991 (+) |  0.998 |  0.717 | gccctGGAATcagattacctgctt
 V$STAT5A_02            |    11263 (+) |  0.996 |  0.722 | tgccaAGAAAaggaaattaaggca
 V$STAT5A_02            |    11378 (+) |  0.977 |  0.750 | tgcttTGAAAacttattaaatttt
 V$STAT5A_02            |    11639 (+) |  0.805 |  0.715 | ttaaaTGTATttctgtactgttaa
 V$STAT5A_02            |    11639 (-) |  0.817 |  0.718 | ttaaatgtatttctGTACTgttaa
 I$OVO_01               |     1141 (-) |  0.998 |  0.991 | aaaaCCGTTacttta
 I$OVO_01               |     9560 (-) |  0.999 |  0.963 | ctgtCGGTTtctggg
 I$OVO_01               |    11066 (-) |  0.999 |  0.969 | tgatCAGTTacaagc
 V$GATA6_01             |       82 (+) |  0.989 |  0.987 | gttGATAGgg
 V$GATA6_01             |       91 (-) |  0.989 |  0.988 | gcCTATCttc
 V$GATA6_01             |      307 (-) |  0.989 |  0.987 | agCTATCtct
 V$GATA6_01             |      566 (+) |  1.000 |  0.997 | ggaGATAAac
 V$GATA6_01             |     1649 (-) |  0.987 |  0.985 | gcTAATCtac
 V$GATA6_01             |     1992 (+) |  0.987 |  0.985 | caaGATTAtc
 V$GATA6_01             |     1995 (-) |  1.000 |  0.997 | gaTTATCtgg
 V$GATA6_01             |     2722 (+) |  1.000 |  0.999 | ataGATAAtc
 V$GATA6_01             |     2725 (-) |  0.987 |  0.985 | gaTAATCttc
 V$GATA6_01             |     2902 (-) |  1.000 |  0.993 | ttTTATCcac
 V$GATA6_01             |     3374 (-) |  0.987 |  0.984 | ccTAATCata
 V$GATA6_01             |     3930 (-) |  1.000 |  0.998 | caTTATCagt
 V$GATA6_01             |     3977 (+) |  0.989 |  0.986 | tatGATAGac
 V$GATA6_01             |     4002 (+) |  1.000 |  0.998 | aacGATAAat
 V$GATA6_01             |     4374 (-) |  1.000 |  0.997 | agTTATCtgg
 V$GATA6_01             |     4779 (+) |  1.000 |  0.992 | ctgGATAAag
 V$GATA6_01             |     4801 (-) |  0.987 |  0.985 | caTAATCtct
 V$GATA6_01             |     5236 (+) |  0.987 |  0.985 | aacGATTAca
 V$GATA6_01             |     5335 (+) |  0.989 |  0.985 | gccGATAGtt
 V$GATA6_01             |     5582 (+) |  1.000 |  0.994 | aagGATAAta
 V$GATA6_01             |     5633 (+) |  1.000 |  0.991 | tggGATAAag
 V$GATA6_01             |     5977 (+) |  1.000 |  0.997 | ggtGATAAct
 V$GATA6_01             |     6465 (+) |  1.000 |  0.997 | cctGATAAaa
 V$GATA6_01             |     7375 (+) |  0.987 |  0.985 | attGATATtg
 V$GATA6_01             |     7788 (-) |  1.000 |  0.991 | aaTTATCcca
 V$GATA6_01             |     7797 (+) |  1.000 |  0.999 | aaaGATAAag
 V$GATA6_01             |     8062 (-) |  1.000 |  0.997 | gtTTATCtgg
 V$GATA6_01             |     8604 (-) |  1.000 |  0.999 | taTTATCatt
 V$GATA6_01             |     9367 (-) |  0.989 |  0.985 | ctCTATCaca
 V$GATA6_01             |     9732 (+) |  1.000 |  0.997 | tatGATAAtg
 V$GATA6_01             |     9833 (+) |  1.000 |  0.993 | aggGATAAtt
 V$GATA6_01             |    10488 (-) |  0.987 |  0.984 | acATATCaag
 V$GATA6_01             |    11200 (+) |  0.987 |  0.985 | attGATTAtt
 V$GATA6_01             |    11348 (-) |  1.000 |  0.996 | caTTATCgaa
 V$GATA6_01             |    11369 (-) |  0.989 |  0.987 | ttCTATCtgt
 V$GATA6_01             |    11441 (-) |  1.000 |  0.999 | acTTATCtat
 V$GATA6_01             |    11569 (-) |  1.000 |  0.999 | tcTTATCatt
 V$POU3F2_02            |       19 (+) |  0.674 |  0.719 | ACATGtgaat
 V$POU3F2_02            |       78 (+) |  0.783 |  0.775 | TGATGttgat
 V$POU3F2_02            |      149 (+) |  0.674 |  0.710 | ATTTGctcat
 V$POU3F2_02            |      499 (-) |  0.674 |  0.798 | attatTATAT
 V$POU3F2_02            |      589 (-) |  0.652 |  0.820 | attaaCAGAC
 V$POU3F2_02            |     1017 (+) |  0.891 |  0.719 | ATATGtgatt
 V$POU3F2_02            |     1063 (-) |  0.783 |  0.775 | tttaaAATAA
 V$POU3F2_02            |     1559 (+) |  0.783 |  0.743 | TTCTGgaaat
 V$POU3F2_02            |     1893 (+) |  0.783 |  0.775 | TTATAtttat
 V$POU3F2_02            |     1899 (+) |  0.783 |  0.775 | TTATTttatt
 V$POU3F2_02            |     1907 (+) |  0.783 |  0.775 | TTATTttatt
 V$POU3F2_02            |     2522 (-) |  0.891 |  0.719 | aattaCATAT
 V$POU3F2_02            |     2565 (-) |  0.783 |  0.743 | atttcCGTAA
 V$POU3F2_02            |     3103 (+) |  0.652 |  0.812 | CTATActaat
 V$POU3F2_02            |     3123 (+) |  0.652 |  0.820 | CTATAttaat
 V$POU3F2_02            |     3137 (-) |  0.783 |  0.743 | attccCACAA
 V$POU3F2_02            |     3256 (+) |  1.000 |  0.743 | TTATGgtttt
 V$POU3F2_02            |     3369 (-) |  0.783 |  0.767 | aatagCCTAA
 V$POU3F2_02            |     3494 (-) |  0.783 |  0.767 | aatagCTTAA
 V$POU3F2_02            |     3627 (+) |  0.783 |  0.743 | TTATAatagt
 V$POU3F2_02            |     3843 (-) |  1.000 |  0.855 | attctCATAA
 V$POU3F2_02            |     4064 (-) |  0.674 |  0.831 | attaaAATAT
 V$POU3F2_02            |     4070 (+) |  0.891 |  0.719 | ATATGtaaaa
 V$POU3F2_02            |     4088 (+) |  0.674 |  0.719 | ATATTttact
 V$POU3F2_02            |     4121 (+) |  0.674 |  0.719 | AGATGttaaa
 V$POU3F2_02            |     4669 (+) |  0.783 |  0.767 | TTTTGctcat
 V$POU3F2_02            |     4796 (-) |  1.000 |  0.767 | acttgCATAA
 V$POU3F2_02            |     5444 (-) |  0.891 |  0.798 | attgcCATAT
 V$POU3F2_02            |     5586 (-) |  0.783 |  0.743 | ataatAATAA
 V$POU3F2_02            |     5591 (-) |  0.674 |  0.719 | aataaAATAT
 V$POU3F2_02            |     6576 (+) |  1.000 |  0.767 | TTATGcaaaa
 V$POU3F2_02            |     6609 (+) |  0.674 |  0.710 | ATTTGctaaa
 V$POU3F2_02            |     6770 (-) |  0.783 |  0.775 | atgaaCAAAA
 V$POU3F2_02            |     6831 (+) |  0.674 |  0.710 | ATGTGctatt
 V$POU3F2_02            |     7262 (-) |  0.674 |  0.831 | attaaAATAT
 V$POU3F2_02            |     7267 (-) |  0.783 |  0.743 | aatatCCTAA
 V$POU3F2_02            |     7268 (+) |  0.674 |  0.710 | ATATCctaaa
 V$POU3F2_02            |     7351 (+) |  0.674 |  0.831 | ACATGttaat
 V$POU3F2_02            |     7641 (+) |  0.783 |  0.775 | TTATTttaaa
 V$POU3F2_02            |     7898 (+) |  0.783 |  0.775 | TTATTttgat
 V$POU3F2_02            |     7901 (+) |  0.783 |  0.743 | TTTTGatatt
 V$POU3F2_02            |     8605 (-) |  0.652 |  0.787 | attatCATTC
 V$POU3F2_02            |     8697 (+) |  0.783 |  0.743 | TTCTGaaaat
 V$POU3F2_02            |     8704 (-) |  0.783 |  0.743 | aatacCATCA
 V$POU3F2_02            |     8815 (+) |  0.783 |  0.743 | TTCTGgtact
 V$POU3F2_02            |     9154 (+) |  0.891 |  0.719 | ATATGtgagt
 V$POU3F2_02            |     9731 (+) |  0.869 |  0.900 | GTATGataat
 V$POU3F2_02            |     9750 (+) |  0.674 |  0.831 | ATATAttaat
 V$POU3F2_02            |     9936 (-) |  0.674 |  0.710 | atttgCATGT
 V$POU3F2_02            |    10143 (+) |  0.783 |  0.743 | TTATTattat
 V$POU3F2_02            |    10321 (+) |  0.674 |  0.719 | ATATTtttat
 V$POU3F2_02            |    10910 (+) |  0.869 |  0.812 | CTATGcaaat
 V$POU3F2_02            |    11153 (+) |  0.783 |  0.743 | TGATGaaaat
 V$POU3F2_02            |    11299 (-) |  0.783 |  0.743 | ataatAATAA
 V$POU3F2_02            |    11658 (-) |  0.783 |  0.775 | gttaaCACAA
 V$POU3F2_02            |    11667 (-) |  1.000 |  0.855 | attttCATAA
 V$POU3F2_02            |    11673 (-) |  0.783 |  0.743 | ataacCAAAA
 V$HIF1_Q5              |     6062 (-) |  1.000 |  0.966 | cctgCACGTgct
 V$HIF1_Q5              |     6064 (+) |  1.000 |  0.962 | tgcACGTGctgc
 V$HIF1_Q5              |     6884 (-) |  1.000 |  0.940 | gcacCACGTaag
 V$HIF1_Q5              |     7484 (-) |  1.000 |  0.935 | cgcgCACGTctg
 V$AP2REP_01            |      114 (+) |  1.000 |  0.927 | CAGTGag
 V$AP2REP_01            |      126 (-) |  0.918 |  0.854 | ctAACTG
 V$AP2REP_01            |      300 (-) |  0.918 |  0.866 | caGACTG
 V$AP2REP_01            |      667 (-) |  1.000 |  0.909 | taCACTG
 V$AP2REP_01            |     1029 (+) |  0.918 |  0.897 | CAGTTga
 V$AP2REP_01            |     1267 (+) |  0.907 |  0.856 | CCGTGtg
 V$AP2REP_01            |     1377 (+) |  1.000 |  1.000 | CAGTGgg
 V$AP2REP_01            |     1418 (+) |  0.907 |  0.844 | CCGTGag
 V$AP2REP_01            |     1434 (+) |  1.000 |  0.962 | CAGTGgc
 V$AP2REP_01            |     1450 (-) |  1.000 |  0.889 | gtCACTG
 V$AP2REP_01            |     1592 (-) |  1.000 |  0.897 | agCACTG
 V$AP2REP_01            |     1750 (-) |  1.000 |  0.909 | aaCACTG
 V$AP2REP_01            |     1861 (-) |  0.918 |  0.927 | ccAACTG
 V$AP2REP_01            |     2041 (-) |  1.000 |  0.970 | acCACTG
 V$AP2REP_01            |     2309 (+) |  0.907 |  0.856 | CTGTGtg
 V$AP2REP_01            |     2373 (-) |  0.907 |  0.880 | gcCACAG
 V$AP2REP_01            |     2447 (+) |  1.000 |  0.970 | CAGTGgt
 V$AP2REP_01            |     2805 (-) |  0.932 |  0.866 | ctTACTG
 V$AP2REP_01            |     2828 (+) |  0.918 |  0.897 | CAGTTgt
 V$AP2REP_01            |     2876 (-) |  0.870 |  0.854 | tcCACCG
 V$AP2REP_01            |     2889 (-) |  0.932 |  0.866 | cgTACTG
 V$AP2REP_01            |     2916 (+) |  0.907 |  0.887 | CTGTGga
 V$AP2REP_01            |     2963 (+) |  1.000 |  0.889 | CAGTGac
 V$AP2REP_01            |     3231 (+) |  0.918 |  0.854 | CAGTCag
 V$AP2REP_01            |     3251 (-) |  0.854 |  0.870 | ccCACTT
 V$AP2REP_01            |     3362 (-) |  1.000 |  0.970 | acCACTG
 V$AP2REP_01            |     3562 (+) |  0.907 |  0.856 | CTGTGtg
 V$AP2REP_01            |     3959 (-) |  0.932 |  0.939 | ccTACTG
 V$AP2REP_01            |     3966 (-) |  1.000 |  0.897 | agCACTG
 V$AP2REP_01            |     4310 (-) |  0.932 |  0.848 | aaTACTG
 V$AP2REP_01            |     4463 (-) |  1.000 |  0.939 | caCACTG
 V$AP2REP_01            |     4467 (-) |  0.918 |  0.854 | ctGACTG
 V$AP2REP_01            |     4568 (+) |  0.918 |  0.889 | CAGTTgc
 V$AP2REP_01            |     4683 (+) |  0.907 |  0.880 | CTGTGgc
 V$AP2REP_01            |     4719 (-) |  1.000 |  0.897 | ttCACTG
 V$AP2REP_01            |     4758 (+) |  0.839 |  0.856 | CTGTAgg
 V$AP2REP_01            |     4855 (-) |  1.000 |  0.897 | ttCACTG
 V$AP2REP_01            |     5021 (-) |  0.907 |  0.880 | gcCACGG
 V$AP2REP_01            |     5048 (+) |  0.907 |  0.887 | CTGTGgt
 V$AP2REP_01            |     5087 (-) |  0.918 |  0.854 | ctGACTG
 V$AP2REP_01            |     5202 (+) |  0.907 |  0.880 | CTGTGgc
 V$AP2REP_01            |     5329 (+) |  1.000 |  0.927 | CAGTGcg
 V$AP2REP_01            |     5367 (-) |  0.907 |  0.856 | caCACGG
 V$AP2REP_01            |     5430 (-) |  0.854 |  0.840 | tcCACTT
 V$AP2REP_01            |     5628 (-) |  1.000 |  0.909 | taCACTG
 V$AP2REP_01            |     5690 (-) |  0.830 |  0.849 | ccCACTA
 V$AP2REP_01            |     5761 (+) |  0.839 |  0.856 | CTGTAgg
 V$AP2REP_01            |     5827 (-) |  1.000 |  0.889 | ggCACTG
 V$AP2REP_01            |     5963 (+) |  1.000 |  0.909 | CAGTGtt
 V$AP2REP_01            |     5973 (+) |  0.854 |  0.840 | AAGTGgt
 V$AP2REP_01            |     6074 (-) |  0.907 |  0.880 | gcCACAG
 V$AP2REP_01            |     6084 (+) |  0.907 |  0.844 | CTGTGag
 V$AP2REP_01            |     6094 (+) |  0.907 |  0.856 | CTGTGtg
 V$AP2REP_01            |     6306 (-) |  1.000 |  0.889 | ggCACTG
 V$AP2REP_01            |     6323 (-) |  0.918 |  0.854 | ctGACTG
 V$AP2REP_01            |     6335 (-) |  1.000 |  0.939 | caCACTG
 V$AP2REP_01            |     6387 (-) |  0.918 |  0.854 | cgAACTG
 V$AP2REP_01            |     6569 (-) |  0.907 |  0.880 | gcCACAG
 V$AP2REP_01            |     6621 (+) |  0.907 |  0.844 | CCGTGag
 V$AP2REP_01            |     6649 (+) |  0.918 |  0.866 | CAGTCtg
 V$AP2REP_01            |     6751 (-) |  0.830 |  0.849 | ccCACTA
 V$AP2REP_01            |     6846 (-) |  0.918 |  0.927 | ccAACTG
 V$AP2REP_01            |     6908 (+) |  0.854 |  0.840 | AAGTGga
 V$AP2REP_01            |     6950 (-) |  0.932 |  0.841 | gaTACTG
 V$AP2REP_01            |     7192 (-) |  0.907 |  0.880 | gcCACGG
 V$AP2REP_01            |     7535 (+) |  0.918 |  0.927 | CAGTTgg
 V$AP2REP_01            |     7549 (-) |  0.918 |  0.927 | ccAACTG
 V$AP2REP_01            |     7678 (-) |  0.907 |  0.844 | ctCACAG
 V$AP2REP_01            |     7726 (+) |  0.918 |  0.866 | CAGTTtg
 V$AP2REP_01            |     7837 (-) |  0.854 |  0.870 | ccCACTT
 V$AP2REP_01            |     7995 (-) |  1.000 |  0.897 | ttCACTG
 V$AP2REP_01            |     8005 (+) |  0.825 |  0.844 | CTGTTgg
 V$AP2REP_01            |     8335 (+) |  0.932 |  0.848 | CAGTAtt
 V$AP2REP_01            |     8348 (-) |  0.854 |  0.840 | acCACTT
 V$AP2REP_01            |     8519 (-) |  0.907 |  0.844 | ctCACAG
 V$AP2REP_01            |     8540 (+) |  1.000 |  1.000 | CAGTGgg
 V$AP2REP_01            |     8670 (-) |  0.870 |  0.854 | acCACCG
 V$AP2REP_01            |     8929 (+) |  0.932 |  0.848 | CAGTAta
 V$AP2REP_01            |     9181 (-) |  0.907 |  0.880 | gcCACAG
 V$AP2REP_01            |     9360 (+) |  1.000 |  0.909 | CAGTGtt
 V$AP2REP_01            |     9560 (+) |  0.825 |  0.844 | CTGTCgg
 V$AP2REP_01            |     9678 (+) |  0.854 |  0.840 | AAGTGga
 V$AP2REP_01            |     9911 (-) |  0.932 |  0.866 | ctTACTG
 V$AP2REP_01            |    10043 (+) |  0.907 |  0.856 | CCGTGtg
 V$AP2REP_01            |    10088 (+) |  1.000 |  0.897 | CAGTGct
 V$AP2REP_01            |    10193 (+) |  0.918 |  0.854 | CAGTCag
 V$AP2REP_01            |    10209 (-) |  0.907 |  0.887 | tcCACAG
 V$AP2REP_01            |    10213 (+) |  1.000 |  0.962 | CAGTGgc
 V$AP2REP_01            |    10651 (+) |  1.000 |  0.902 | CAGTGtc
 V$AP2REP_01            |    10676 (-) |  0.907 |  0.887 | tcCACAG
 V$AP2REP_01            |    10749 (+) |  1.000 |  0.897 | CAGTGat
 V$AP2REP_01            |    10756 (+) |  0.907 |  0.856 | CCGTGtg
 V$AP2REP_01            |    10779 (+) |  0.825 |  0.844 | CTGTCgg
 V$AP2REP_01            |    10821 (+) |  0.918 |  0.854 | CAGTCcg
 V$AP2REP_01            |    10884 (-) |  1.000 |  0.897 | agCACTG
 V$AP2REP_01            |    10967 (+) |  0.825 |  0.844 | CTGTTgg
 V$AP2REP_01            |    10984 (+) |  0.907 |  0.856 | CTGTGtg
 V$AP2REP_01            |    11035 (-) |  1.000 |  0.970 | acCACTG
 V$AP2REP_01            |    11095 (-) |  1.000 |  0.970 | tcCACTG
 V$AP2REP_01            |    11227 (+) |  0.918 |  0.866 | CAGTTtg
 V$AP2REP_01            |    11236 (-) |  0.918 |  0.854 | ctAACTG
 V$AP2REP_01            |    11255 (+) |  0.907 |  0.887 | CTGTGgt
 V$AP2REP_01            |    11461 (+) |  1.000 |  0.897 | CAGTGaa
 V$AP2REP_01            |    11699 (-) |  1.000 |  0.897 | atCACTG
 V$AP2REP_01            |    11711 (-) |  0.918 |  0.927 | ccAACTG
 V$AP2ALPHA_01          |      101 (+) |  0.998 |  0.998 | GCCTGgggg
 V$AP2ALPHA_01          |     1334 (-) |  0.999 |  0.999 | ccccAGGGC
 V$AP2ALPHA_01          |     1341 (-) |  0.996 |  0.986 | gcttAAGGC
 V$AP2ALPHA_01          |     3388 (+) |  0.999 |  0.990 | GCCCTgagg
 V$AP2ALPHA_01          |     3569 (+) |  0.996 |  0.992 | GCCTTtggc
 V$AP2ALPHA_01          |     6147 (+) |  0.997 |  0.993 | GCCTCtggc
 V$AP2ALPHA_01          |     6147 (-) |  0.995 |  0.994 | gcctCTGGC
 V$AP2ALPHA_01          |     7192 (+) |  0.995 |  0.996 | GCCACgggg
 V$AP2ALPHA_01          |     7226 (+) |  0.995 |  0.984 | GCCAGcagg
 V$AP2ALPHA_01          |     7461 (+) |  0.998 |  0.986 | GCCTGcagg
 V$AP2ALPHA_01          |     7627 (+) |  0.998 |  0.983 | GCCTGgcgg
 V$AP2ALPHA_01          |     9925 (+) |  0.994 |  0.990 | GCCTAtggg
 V$AP2ALPHA_01          |    11913 (-) |  1.000 |  0.989 | gcttCGGGC
 V$AP2GAMMA_01          |      101 (+) |  0.993 |  0.994 | GCCTGgggg
 V$AP2GAMMA_01          |     1334 (-) |  0.995 |  0.995 | ccccAGGGC
 V$AP2GAMMA_01          |     1341 (-) |  0.987 |  0.954 | gcttAAGGC
 V$AP2GAMMA_01          |     2480 (+) |  0.995 |  0.982 | GCCCTgggt
 V$AP2GAMMA_01          |     3388 (+) |  0.995 |  0.964 | GCCCTgagg
 V$AP2GAMMA_01          |     3533 (+) |  1.000 |  0.984 | GCCCGaggt
 V$AP2GAMMA_01          |     3569 (+) |  0.987 |  0.977 | GCCTTtggc
 V$AP2GAMMA_01          |     3569 (-) |  0.969 |  0.970 | gcctTTGGC
 V$AP2GAMMA_01          |     5021 (+) |  0.975 |  0.964 | GCCACggga
 V$AP2GAMMA_01          |     5889 (-) |  0.998 |  0.955 | gcatGGGGC
 V$AP2GAMMA_01          |     6116 (-) |  0.995 |  0.952 | ccagAGGGC
 V$AP2GAMMA_01          |     6147 (+) |  0.991 |  0.980 | GCCTCtggc
 V$AP2GAMMA_01          |     6147 (-) |  0.977 |  0.976 | gcctCTGGC
 V$AP2GAMMA_01          |     6421 (-) |  0.977 |  0.963 | tcctCTGGC
 V$AP2GAMMA_01          |     7192 (+) |  0.975 |  0.979 | GCCACgggg
 V$AP2GAMMA_01          |     7461 (+) |  0.993 |  0.958 | GCCTGcagg
 V$AP2GAMMA_01          |     7627 (+) |  0.993 |  0.955 | GCCTGgcgg
 V$AP2GAMMA_01          |     8162 (-) |  0.991 |  0.967 | tccaGAGGC
 V$AP2GAMMA_01          |     9241 (+) |  0.995 |  0.978 | GCCCTagga
 V$AP2GAMMA_01          |     9331 (+) |  0.991 |  0.967 | GCCTCtgga
 V$AP2GAMMA_01          |     9390 (+) |  0.998 |  0.973 | GCCCCtgga
 V$AP2GAMMA_01          |     9442 (+) |  0.992 |  0.977 | GCCCAaggt
 V$AP2GAMMA_01          |     9925 (+) |  0.985 |  0.977 | GCCTAtggg
 V$AP2GAMMA_01          |    10560 (+) |  0.987 |  0.971 | GCCGGcggt
 V$AP2GAMMA_01          |    11284 (-) |  0.995 |  0.952 | gcatAGGGC
 V$AP2GAMMA_01          |    11815 (+) |  0.992 |  0.979 | GCCCAgggt
 V$AP2GAMMA_01          |    11913 (-) |  1.000 |  0.964 | gcttCGGGC
 V$AP2GAMMA_01          |    11920 (+) |  0.992 |  0.950 | GCCCAacgc
 V$AP2GAMMA_01          |    11928 (-) |  0.969 |  0.964 | cccaTTGGC
 V$TBP_01               |      241 (+) |  0.934 |  0.927 | tTTAAAtc
 V$TBP_01               |      569 (+) |  1.000 |  0.891 | gATAAAcg
 V$TBP_01               |      642 (-) |  1.000 |  0.945 | caTTTATt
 V$TBP_01               |      650 (-) |  1.000 |  0.945 | caTTTATt
 V$TBP_01               |      661 (+) |  0.881 |  0.895 | tATAAGta
 V$TBP_01               |      835 (+) |  1.000 |  0.923 | tATAAAac
 V$TBP_01               |      845 (+) |  0.934 |  0.910 | gTTAAAta
 V$TBP_01               |      849 (+) |  1.000 |  0.959 | aATAAAta
 V$TBP_01               |      962 (-) |  0.932 |  0.940 | taTTTACa
 V$TBP_01               |     1150 (-) |  1.000 |  0.901 | acTTTATg
 V$TBP_01               |     1890 (-) |  1.000 |  0.935 | atTTTATa
 V$TBP_01               |     1896 (-) |  1.000 |  0.959 | taTTTATt
 V$TBP_01               |     1901 (-) |  1.000 |  0.894 | atTTTATt
 V$TBP_01               |     1909 (-) |  1.000 |  0.894 | atTTTATt
 V$TBP_01               |     2363 (-) |  1.000 |  0.959 | taTTTATt
 V$TBP_01               |     2576 (-) |  0.932 |  0.940 | taTTTACa
 V$TBP_01               |     2737 (-) |  1.000 |  0.889 | ccTTTATg
 V$TBP_01               |     2901 (-) |  1.000 |  0.905 | ttTTTATc
 V$TBP_01               |     3130 (-) |  0.932 |  0.937 | aaTTTACa
 V$TBP_01               |     3406 (+) |  1.000 |  0.923 | tATAAAag
 V$TBP_01               |     3624 (-) |  1.000 |  0.923 | cgTTTATa
 V$TBP_01               |     3717 (-) |  0.932 |  0.900 | taTTTACg
 V$TBP_01               |     3832 (+) |  1.000 |  0.957 | aATAAAtt
 V$TBP_01               |     3848 (+) |  1.000 |  0.895 | cATAAAat
 V$TBP_01               |     3917 (-) |  1.000 |  0.889 | gcTTTATg
 V$TBP_01               |     4005 (+) |  1.000 |  0.968 | gATAAAta
 V$TBP_01               |     4009 (+) |  1.000 |  0.959 | aATAAAta
 V$TBP_01               |     4226 (+) |  1.000 |  0.957 | aATAAAtt
 V$TBP_01               |     4782 (+) |  1.000 |  0.911 | gATAAAga
 V$TBP_01               |     5396 (-) |  1.000 |  0.929 | ccTTTATa
 V$TBP_01               |     5433 (-) |  1.000 |  0.900 | acTTTATt
 V$TBP_01               |     5591 (+) |  1.000 |  0.894 | aATAAAat
 V$TBP_01               |     5636 (+) |  1.000 |  0.911 | gATAAAga
 V$TBP_01               |     5647 (+) |  1.000 |  0.896 | aATAAAaa
 V$TBP_01               |     5794 (+) |  0.934 |  0.901 | aTTAAAta
 V$TBP_01               |     5952 (-) |  1.000 |  0.894 | atTTTATt
 V$TBP_01               |     6468 (+) |  1.000 |  0.903 | gATAAAat
 V$TBP_01               |     6669 (-) |  1.000 |  0.894 | atTTTATt
 V$TBP_01               |     6673 (-) |  0.917 |  0.895 | taTTTAGc
 V$TBP_01               |     6760 (-) |  1.000 |  0.929 | ccTTTATa
 V$TBP_01               |     6826 (-) |  1.000 |  0.898 | ttTTTATg
 V$TBP_01               |     6837 (-) |  0.932 |  0.899 | taTTTACt
 V$TBP_01               |     7434 (-) |  1.000 |  0.896 | ttTTTATt
 V$TBP_01               |     7439 (-) |  1.000 |  0.895 | atTTTATg
 V$TBP_01               |     7800 (+) |  1.000 |  0.911 | gATAAAga
 V$TBP_01               |     7895 (-) |  1.000 |  0.896 | ttTTTATt
 V$TBP_01               |     8061 (-) |  1.000 |  0.903 | agTTTATc
 V$TBP_01               |     8638 (-) |  0.934 |  0.903 | taTTTAAg
 V$TBP_01               |     8932 (+) |  1.000 |  0.935 | tATAAAct
 V$TBP_01               |     9427 (+) |  1.000 |  0.961 | cATAAAta
 V$TBP_01               |     9484 (-) |  1.000 |  0.900 | acTTTATt
 V$TBP_01               |     9884 (-) |  0.934 |  0.939 | aaTTTAAa
 V$TBP_01               |    10124 (+) |  1.000 |  0.894 | aATAAAat
 V$TBP_01               |    10316 (-) |  1.000 |  0.937 | ttTTTATa
 V$TBP_01               |    10324 (-) |  1.000 |  0.896 | ttTTTATt
 V$TBP_01               |    10329 (-) |  1.000 |  0.935 | atTTTATa
 V$TBP_01               |    10338 (-) |  1.000 |  0.896 | ttTTTATt
 V$TBP_01               |    10392 (+) |  1.000 |  0.937 | tATAAAaa
 V$TBP_01               |    10451 (-) |  1.000 |  0.923 | ctTTTATa
 V$TBP_01               |    10703 (-) |  1.000 |  0.898 | tgTTTATg
 V$TBP_01               |    10812 (+) |  0.917 |  0.912 | tCTAAAtc
 V$TBP_01               |    11339 (+) |  0.932 |  0.925 | tGTAAAtg
 V$TBP_01               |    11392 (+) |  0.934 |  0.899 | aTTAAAtt
 V$TBP_01               |    11407 (-) |  1.000 |  0.945 | caTTTATt
 V$TBP_01               |    11424 (-) |  0.917 |  0.895 | taTTTAGc
 V$TBP_01               |    11470 (-) |  1.000 |  0.896 | ttTTTATt
 V$TBP_01               |    11638 (+) |  0.934 |  0.927 | tTTAAAtg
 V$TBP_01               |    11689 (+) |  1.000 |  0.900 | aATAAAgt
 V$FOXO1_01             |    10701 (-) |  1.000 |  0.990 | cgTGTTTatg
 V$FOXO4_02             |       30 (-) |  1.000 |  0.903 | tgtgtgAACAActt
 V$FOXO4_02             |       71 (+) |  1.000 |  0.836 | ctgTTGTTgatgtt
 V$FOXO4_02             |      219 (+) |  0.800 |  0.773 | tttTTTTTttcctt
 V$FOXO4_02             |      220 (+) |  0.800 |  0.759 | tttTTTTTtccttt
 V$FOXO4_02             |      396 (-) |  1.000 |  0.792 | tttgccAACAAggc
 V$FOXO4_02             |      482 (-) |  0.800 |  0.749 | caagtcAACATtgc
 V$FOXO4_02             |      508 (+) |  0.800 |  0.747 | tatTTGTCttctga
 V$FOXO4_02             |      603 (-) |  0.800 |  0.748 | tttttaAACATcct
 V$FOXO4_02             |      630 (+) |  0.800 |  0.725 | cttTTTTTtaaaca
 V$FOXO4_02             |      834 (-) |  1.000 |  0.787 | atataaAACAAgtt
 V$FOXO4_02             |      843 (-) |  0.800 |  0.745 | aagttaAATAAata
 V$FOXO4_02             |      985 (-) |  0.800 |  0.738 | acagttAATAAttt
 V$FOXO4_02             |     1033 (-) |  1.000 |  0.792 | tgaatcAACAAagc
 V$FOXO4_02             |     1051 (-) |  1.000 |  0.833 | aaaatcAACAActt
 V$FOXO4_02             |     1088 (-) |  0.800 |  0.750 | ttggtcAACTAaaa
 V$FOXO4_02             |     1116 (+) |  0.800 |  0.733 | gatTTGTGtatgca
 V$FOXO4_02             |     1367 (+) |  0.800 |  0.728 | tgcTCGTTtgcagt
 V$FOXO4_02             |     1843 (-) |  0.800 |  0.752 | gtcgtcAACACaat
 V$FOXO4_02             |     2169 (+) |  0.800 |  0.745 | tccTTCTTtccttc
 V$FOXO4_02             |     2177 (+) |  0.800 |  0.758 | tccTTCTTttcttc
 V$FOXO4_02             |     2395 (+) |  0.800 |  0.789 | gagTTGCTttcctt
 V$FOXO4_02             |     2404 (-) |  0.800 |  0.724 | tccttaAAAAAaac
 V$FOXO4_02             |     2409 (-) |  1.000 |  0.821 | aaaaaaAACAAaaa
 V$FOXO4_02             |     2501 (-) |  0.800 |  0.749 | tccgaaAAAAAagg
 V$FOXO4_02             |     2511 (-) |  0.800 |  0.760 | aagggaAAAAAaat
 V$FOXO4_02             |     2512 (-) |  0.800 |  0.753 | agggaaAAAAAatt
 V$FOXO4_02             |     2600 (-) |  0.800 |  0.729 | ctattaAACCAaga
 V$FOXO4_02             |     2661 (+) |  0.800 |  0.747 | actTTGATgacact
 V$FOXO4_02             |     2747 (+) |  0.800 |  0.753 | tttTTCTTttctct
 V$FOXO4_02             |     2828 (+) |  0.800 |  0.760 | cagTTGTCtgcaaa
 V$FOXO4_02             |     2897 (+) |  0.800 |  0.726 | atcTTTTTtatcca
 V$FOXO4_02             |     3256 (+) |  0.800 |  0.756 | ttaTGGTTttcttg
 V$FOXO4_02             |     3292 (-) |  0.800 |  0.785 | gaggtgAACATctc
 V$FOXO4_02             |     3424 (+) |  0.800 |  0.762 | tggTTGCTtaattg
 V$FOXO4_02             |     3447 (-) |  0.800 |  0.754 | acagttAATAAaac
 V$FOXO4_02             |     3548 (+) |  0.800 |  0.750 | ctgTTCTTtagtag
 V$FOXO4_02             |     3691 (-) |  0.800 |  0.761 | caagaaCACAAgag
 V$FOXO4_02             |     3814 (+) |  0.800 |  0.744 | acaTCGTTttcaat
 V$FOXO4_02             |     3940 (+) |  1.000 |  0.787 | cacTTGTTcattca
 V$FOXO4_02             |     3993 (-) |  1.000 |  0.793 | tcatgaAACAAcga
 V$FOXO4_02             |     4003 (-) |  0.800 |  0.734 | acgataAATAAata
 V$FOXO4_02             |     4215 (-) |  0.800 |  0.752 | tcagttAAAAAaat
 V$FOXO4_02             |     4216 (-) |  0.800 |  0.743 | cagttaAAAAAata
 V$FOXO4_02             |     4258 (+) |  1.000 |  0.746 | tggTTGTTaggatg
 V$FOXO4_02             |     4421 (-) |  0.800 |  0.725 | tgtctaAAAAAaaa
 V$FOXO4_02             |     4486 (-) |  1.000 |  0.795 | cttttgAACAAaaa
 V$FOXO4_02             |     4493 (-) |  1.000 |  0.801 | acaaaaAACAAaac
 V$FOXO4_02             |     4498 (-) |  1.000 |  0.812 | aaacaaAACAAaac
 V$FOXO4_02             |     4503 (-) |  1.000 |  0.831 | aaacaaAACAAcat
 V$FOXO4_02             |     4522 (-) |  1.000 |  0.829 | caagacAACAAatg
 V$FOXO4_02             |     4534 (-) |  0.800 |  0.764 | tgcgtcAACAGcct
 V$FOXO4_02             |     4663 (+) |  1.000 |  0.809 | actTTGTTttgctc
 V$FOXO4_02             |     4787 (+) |  0.800 |  0.750 | agaTTGCTgacttg
 V$FOXO4_02             |     4813 (+) |  1.000 |  0.804 | catTTGTTaccagg
 V$FOXO4_02             |     5121 (-) |  0.800 |  0.757 | aaaggaAACAGatg
 V$FOXO4_02             |     5273 (-) |  1.000 |  0.817 | tgggccAACAAcag
 V$FOXO4_02             |     5560 (-) |  1.000 |  0.911 | ctagaaAACAAcca
 V$FOXO4_02             |     5610 (-) |  0.800 |  0.790 | caagaaACCAAcat
 V$FOXO4_02             |     5655 (-) |  0.800 |  0.788 | gaagaaAAGAAcac
 V$FOXO4_02             |     5660 (-) |  0.800 |  0.758 | aaagaaCACAAtaa
 V$FOXO4_02             |     5831 (-) |  1.000 |  0.773 | ctgtgaAACAAggc
 V$FOXO4_02             |     5857 (+) |  0.800 |  0.768 | gagTTGGTttccca
 V$FOXO4_02             |     5858 (+) |  0.800 |  0.745 | agtTGGTTtcccat
 V$FOXO4_02             |     5912 (+) |  1.000 |  0.874 | agtTTGTTtcccca
 V$FOXO4_02             |     5952 (+) |  0.800 |  0.745 | attTTATTtgccag
 V$FOXO4_02             |     6106 (+) |  0.800 |  0.742 | gtcCTGTTgaccag
 V$FOXO4_02             |     6122 (+) |  1.000 |  0.878 | ggcTTGTTttctcg
 V$FOXO4_02             |     6456 (+) |  0.800 |  0.725 | aacTTATTtcctga
 V$FOXO4_02             |     6534 (-) |  0.800 |  0.736 | cctggaGACAAacg
 V$FOXO4_02             |     6585 (-) |  1.000 |  0.789 | acacaaAACAAata
 V$FOXO4_02             |     6652 (-) |  0.800 |  0.734 | tctgcaAACAGatg
 V$FOXO4_02             |     6669 (+) |  0.800 |  0.747 | attTTATTtagctt
 V$FOXO4_02             |     6767 (-) |  1.000 |  0.800 | accatgAACAAaac
 V$FOXO4_02             |     6822 (+) |  0.800 |  0.745 | cccTTTTTtatgtg
 V$FOXO4_02             |     6910 (-) |  1.000 |  0.809 | gtggagAACAAgga
 V$FOXO4_02             |     7014 (+) |  0.800 |  0.753 | cggATGTTtcctgc
 V$FOXO4_02             |     7039 (+) |  0.800 |  0.752 | agtTAGTTgactat
 V$FOXO4_02             |     7050 (+) |  0.800 |  0.767 | tatTTTTTttctta
 V$FOXO4_02             |     7063 (+) |  1.000 |  0.821 | aatTTGTTtttgtt
 V$FOXO4_02             |     7069 (+) |  1.000 |  0.806 | tttTTGTTtgtgta
 V$FOXO4_02             |     7073 (+) |  0.800 |  0.740 | tgtTTGTGtatgag
 V$FOXO4_02             |     7208 (-) |  1.000 |  0.807 | gaattgAACAAaaa
 V$FOXO4_02             |     7383 (+) |  0.800 |  0.727 | tgcTTGTGtccagg
 V$FOXO4_02             |     7428 (+) |  1.000 |  0.820 | tatTTGTTtttatt
 V$FOXO4_02             |     7563 (-) |  0.800 |  0.737 | gctggaAACCAaat
 V$FOXO4_02             |     7564 (-) |  0.800 |  0.756 | ctggaaACCAAatc
 V$FOXO4_02             |     7584 (-) |  1.000 |  0.779 | aggtcaAACAAatg
 V$FOXO4_02             |     7655 (+) |  0.800 |  0.745 | cttTTGTAtgccag
 V$FOXO4_02             |     7771 (-) |  1.000 |  0.798 | tcaaaaAACAAaac
 V$FOXO4_02             |     7776 (-) |  1.000 |  0.812 | aaacaaAACAAaaa
 V$FOXO4_02             |     7798 (-) |  0.800 |  0.775 | aagataAAGAAcaa
 V$FOXO4_02             |     7801 (-) |  1.000 |  0.753 | ataaagAACAAcga
 V$FOXO4_02             |     7818 (-) |  1.000 |  0.796 | ctccaaAACAAaca
 V$FOXO4_02             |     7822 (-) |  1.000 |  0.792 | aaaacaAACAAtta
 V$FOXO4_02             |     7937 (+) |  0.800 |  0.745 | tgtGTGTTtagttt
 V$FOXO4_02             |     7968 (+) |  1.000 |  0.825 | tagTTGTTtgtttt
 V$FOXO4_02             |     7972 (+) |  1.000 |  0.804 | tgtTTGTTtttcaa
 V$FOXO4_02             |     8057 (+) |  0.800 |  0.745 | gtcTAGTTtatctg
 V$FOXO4_02             |     8146 (-) |  0.800 |  0.740 | agggaaAACATtag
 V$FOXO4_02             |     8183 (+) |  1.000 |  0.866 | aacTTGTTtgctct
 V$FOXO4_02             |     8196 (+) |  0.800 |  0.730 | tgcCTGTTtcccct
 V$FOXO4_02             |     8487 (+) |  0.800 |  0.773 | gggTTATTttctac
 V$FOXO4_02             |     8552 (-) |  1.000 |  0.805 | aaaatgAACAAtgt
 V$FOXO4_02             |     8569 (+) |  0.800 |  0.744 | tctTTGATtaaatg
 V$FOXO4_02             |     8642 (-) |  0.800 |  0.753 | taagaaGACAAttc
 V$FOXO4_02             |     8657 (+) |  0.800 |  0.740 | caaTGGTTttcaaa
 V$FOXO4_02             |     8930 (-) |  0.800 |  0.738 | agtataAACTAaag
 V$FOXO4_02             |     9107 (-) |  1.000 |  0.812 | aagcaaAACAAaaa
 V$FOXO4_02             |     9296 (+) |  0.800 |  0.728 | agcTTGTGtgccca
 V$FOXO4_02             |     9413 (-) |  0.800 |  0.741 | ctagaaAACTAtcc
 V$FOXO4_02             |     9425 (-) |  0.800 |  0.754 | cccataAATAAcag
 V$FOXO4_02             |     9484 (+) |  0.800 |  0.745 | actTTATTtgcaat
 V$FOXO4_02             |     9530 (-) |  1.000 |  0.736 | gactagAACAAaca
 V$FOXO4_02             |     9534 (-) |  1.000 |  0.778 | agaacaAACAAgtc
 V$FOXO4_02             |     9760 (-) |  0.800 |  0.743 | attgaaAACAGtca
 V$FOXO4_02             |     9786 (+) |  1.000 |  0.794 | attTTGTTcagtaa
 V$FOXO4_02             |     9875 (-) |  0.800 |  0.754 | gaggaaATCAAttt
 V$FOXO4_02             |    10131 (-) |  0.800 |  0.756 | ttagttAAGAAatt
 V$FOXO4_02             |    10149 (+) |  1.000 |  0.729 | ttaTTGTTgttgtc
 V$FOXO4_02             |    10152 (+) |  1.000 |  0.852 | ttgTTGTTgtcgtt
 V$FOXO4_02             |    10158 (+) |  0.800 |  0.789 | ttgTCGTTttcgtc
 V$FOXO4_02             |    10302 (+) |  0.800 |  0.730 | acaTTTTTtaactg
 V$FOXO4_02             |    10303 (+) |  0.800 |  0.752 | catTTTTTaactgt
 V$FOXO4_02             |    10341 (+) |  1.000 |  0.798 | ttaTTGTTttaatt
 V$FOXO4_02             |    10415 (+) |  0.800 |  0.740 | gcaTTTTTaacact
 V$FOXO4_02             |    10455 (-) |  1.000 |  0.797 | tatatcAACAAtgc
 V$FOXO4_02             |    10660 (-) |  0.800 |  0.758 | aatgtcAACAGgag
 V$FOXO4_02             |    10699 (+) |  0.800 |  0.730 | cccGTGTTtatgaa
 V$FOXO4_02             |    10911 (-) |  0.800 |  0.743 | tatgcaAATAAtag
 V$FOXO4_02             |    10933 (+) |  0.800 |  0.738 | ctcTTGTGgacggt
 V$FOXO4_02             |    11039 (+) |  1.000 |  0.729 | ctgTTGTTggttcc
 V$FOXO4_02             |    11042 (+) |  0.800 |  0.778 | ttgTTGGTtccttt
 V$FOXO4_02             |    11051 (+) |  1.000 |  0.911 | cctTTGTTaacgtt
 V$FOXO4_02             |    11100 (-) |  0.800 |  0.742 | tgtttaAAGAAcga
 V$FOXO4_02             |    11187 (+) |  1.000 |  0.774 | gccTTGTTtcttga
 V$FOXO4_02             |    11198 (+) |  0.800 |  0.724 | tgaTTGATtattaa
 V$FOXO4_02             |    11210 (+) |  1.000 |  0.779 | aatTTGTTtgaact
 V$FOXO4_02             |    11288 (-) |  0.800 |  0.739 | agggcaAAGAAata
 V$FOXO4_02             |    11466 (+) |  0.800 |  0.739 | aaaTTTTTtatttg
 V$FOXO4_02             |    11474 (+) |  1.000 |  0.798 | tatTTGTTtttccc
 V$FOXO4_02             |    11574 (+) |  0.800 |  0.738 | tcaTTGCTtatatc
 V$FOXO4_02             |    11632 (+) |  0.800 |  0.735 | cccTCGTTtaaatg
 V$FOXO4_02             |    11653 (+) |  0.800 |  0.739 | gtaCTGTTaacaca
 V$FOXO4_02             |    11655 (-) |  0.800 |  0.755 | actgttAACACaat
 V$FOXO4_02             |    11670 (-) |  0.800 |  0.740 | ttcataACCAAaaa
 V$FOXO4_02             |    11759 (-) |  0.800 |  0.747 | agagttAACAGgat
 V$FOXO3_01             |       30 (-) |  1.000 |  0.867 | tgtgtgAACAActt
 V$FOXO3_01             |       71 (+) |  1.000 |  0.835 | ctgTTGTTgatgtt
 V$FOXO3_01             |      396 (-) |  1.000 |  0.778 | tttgccAACAAggc
 V$FOXO3_01             |      603 (-) |  0.829 |  0.778 | tttttaAACATcct
 V$FOXO3_01             |      634 (-) |  0.829 |  0.776 | tttttaAACATtta
 V$FOXO3_01             |      834 (-) |  1.000 |  0.796 | atataaAACAAgtt
 V$FOXO3_01             |      843 (-) |  0.793 |  0.776 | aagttaAATAAata
 V$FOXO3_01             |     1033 (-) |  1.000 |  0.795 | tgaatcAACAAagc
 V$FOXO3_01             |     1051 (-) |  1.000 |  0.834 | aaaatcAACAActt
 V$FOXO3_01             |     2409 (-) |  1.000 |  0.836 | aaaaaaAACAAaaa
 V$FOXO3_01             |     3292 (-) |  0.829 |  0.771 | gaggtgAACATctc
 V$FOXO3_01             |     3940 (+) |  1.000 |  0.793 | cacTTGTTcattca
 V$FOXO3_01             |     3993 (-) |  1.000 |  0.786 | tcatgaAACAAcga
 V$FOXO3_01             |     4486 (-) |  1.000 |  0.784 | cttttgAACAAaaa
 V$FOXO3_01             |     4493 (-) |  1.000 |  0.790 | acaaaaAACAAaac
 V$FOXO3_01             |     4498 (-) |  1.000 |  0.824 | aaacaaAACAAaac
 V$FOXO3_01             |     4503 (-) |  1.000 |  0.830 | aaacaaAACAAcat
 V$FOXO3_01             |     4522 (-) |  1.000 |  0.796 | caagacAACAAatg
 V$FOXO3_01             |     4663 (+) |  1.000 |  0.812 | actTTGTTttgctc
 V$FOXO3_01             |     5121 (-) |  0.829 |  0.775 | aaaggaAACAGatg
 V$FOXO3_01             |     5273 (-) |  1.000 |  0.771 | tgggccAACAAcag
 V$FOXO3_01             |     5560 (-) |  1.000 |  0.867 | ctagaaAACAAcca
 V$FOXO3_01             |     5912 (+) |  1.000 |  0.854 | agtTTGTTtcccca
 V$FOXO3_01             |     6122 (+) |  1.000 |  0.847 | ggcTTGTTttctcg
 V$FOXO3_01             |     6585 (-) |  1.000 |  0.793 | acacaaAACAAata
 V$FOXO3_01             |     6669 (+) |  0.793 |  0.775 | attTTATTtagctt
 V$FOXO3_01             |     6767 (-) |  1.000 |  0.786 | accatgAACAAaac
 V$FOXO3_01             |     6910 (-) |  1.000 |  0.774 | gtggagAACAAgga
 V$FOXO3_01             |     7063 (+) |  1.000 |  0.829 | aatTTGTTtttgtt
 V$FOXO3_01             |     7069 (+) |  1.000 |  0.828 | tttTTGTTtgtgta
 V$FOXO3_01             |     7208 (-) |  1.000 |  0.812 | gaattgAACAAaaa
 V$FOXO3_01             |     7428 (+) |  1.000 |  0.838 | tatTTGTTtttatt
 V$FOXO3_01             |     7584 (-) |  1.000 |  0.775 | aggtcaAACAAatg
 V$FOXO3_01             |     7771 (-) |  1.000 |  0.792 | tcaaaaAACAAaac
 V$FOXO3_01             |     7776 (-) |  1.000 |  0.832 | aaacaaAACAAaaa
 V$FOXO3_01             |     7798 (-) |  0.793 |  0.789 | aagataAAGAAcaa
 V$FOXO3_01             |     7818 (-) |  1.000 |  0.790 | ctccaaAACAAaca
 V$FOXO3_01             |     7822 (-) |  1.000 |  0.822 | aaaacaAACAAtta
 V$FOXO3_01             |     7937 (+) |  0.837 |  0.811 | tgtGTGTTtagttt
 V$FOXO3_01             |     7968 (+) |  1.000 |  0.830 | tagTTGTTtgtttt
 V$FOXO3_01             |     7972 (+) |  1.000 |  0.809 | tgtTTGTTtttcaa
 V$FOXO3_01             |     8183 (+) |  1.000 |  0.854 | aacTTGTTtgctct
 V$FOXO3_01             |     8552 (-) |  1.000 |  0.822 | aaaatgAACAAtgt
 V$FOXO3_01             |     9107 (-) |  1.000 |  0.830 | aagcaaAACAAaaa
 V$FOXO3_01             |     9534 (-) |  1.000 |  0.784 | agaacaAACAAgtc
 V$FOXO3_01             |     9786 (+) |  1.000 |  0.797 | attTTGTTcagtaa
 V$FOXO3_01             |    10152 (+) |  1.000 |  0.822 | ttgTTGTTgtcgtt
 V$FOXO3_01             |    10341 (+) |  1.000 |  0.826 | ttaTTGTTttaatt
 V$FOXO3_01             |    10455 (-) |  1.000 |  0.829 | tatatcAACAAtgc
 V$FOXO3_01             |    10660 (-) |  0.829 |  0.789 | aatgtcAACAGgag
 V$FOXO3_01             |    10699 (+) |  0.837 |  0.785 | cccGTGTTtatgaa
 V$FOXO3_01             |    11051 (+) |  1.000 |  0.899 | cctTTGTTaacgtt
 V$FOXO3_01             |    11187 (+) |  1.000 |  0.783 | gccTTGTTtcttga
 V$FOXO3_01             |    11210 (+) |  1.000 |  0.778 | aatTTGTTtgaact
 V$FOXO3_01             |    11474 (+) |  1.000 |  0.787 | tatTTGTTtttccc
 V$FOXO3_01             |    11574 (+) |  0.793 |  0.773 | tcaTTGCTtatatc
 V$CDC5_01              |     3873 (+) |  0.926 |  0.864 | gagTTAATacaa
 V$CDC5_01              |     4121 (-) |  1.000 |  0.885 | agatGTTAAaac
 V$CDC5_01              |     9944 (-) |  0.867 |  0.873 | gtatGTTATaac
 V$LUN1_01              |      736 (-) |  1.000 |  0.711 | ccacgtggttgcTGGGA
 V$LUN1_01              |     8764 (+) |  1.000 |  0.685 | TCCCAgcacctgggagg
 V$AR_01                |     1622 (+) |  0.975 |  0.890 | tggacagcaTGTCCa
 V$AR_01                |     1622 (-) |  0.975 |  0.886 | tGGACAgcatgtcca
 V$AR_01                |     2810 (+) |  0.747 |  0.828 | tgaacaccgTGCTCt
 V$AR_01                |     2810 (-) |  1.000 |  0.835 | tGAACAccgtgctct
 V$AR_01                |     4692 (+) |  0.975 |  0.797 | gaaacttgaTGTCCt
 V$AR_01                |     6518 (+) |  0.905 |  0.869 | agaacacgaAGTTCa
 V$AR_01                |     6518 (-) |  1.000 |  0.909 | aGAACAcgaagttca
 V$AR_01                |     6856 (-) |  0.896 |  0.783 | aGCACGtccagaccg
 V$AR_01                |     8534 (+) |  0.737 |  0.807 | agaacacagTGGGCc
 V$AR_01                |     8534 (-) |  1.000 |  0.902 | aGAACAcagtgggcc
 V$AR_01                |     9465 (+) |  1.000 |  0.955 | tgtacaggaTGTTCt
 V$AR_01                |     9465 (-) |  0.977 |  0.898 | tGTACAggatgttct
 V$AR_01                |    10080 (+) |  0.885 |  0.807 | agggcagccAGTGCt
 V$AR_01                |    10645 (+) |  0.975 |  0.790 | gacacccagTGTCCt
 V$AR_01                |    11223 (+) |  1.000 |  0.854 | tgcccagttTGTTCt
 V$AR_01                |    11223 (-) |  0.737 |  0.785 | tGCCCAgtttgttct
 V$AR_01                |    11619 (-) |  0.866 |  0.791 | gGTACCagaaggacc
 V$PITX2_Q2             |     2023 (-) |  1.000 |  0.995 | ctggGATTAaa
 V$PITX2_Q2             |     4161 (+) |  1.000 |  0.905 | tgTAATCctag
 V$PITX2_Q2             |     9591 (+) |  1.000 |  0.995 | tgTAATCccag
 V$NKX22_01             |      288 (+) |  0.938 |  0.946 | tCAAGTgttt
 I$MTTFA_01             |     5582 (-) |  1.000 |  0.975 | aagGATAAtaa
 I$MTTFA_01             |    11440 (+) |  1.000 |  0.991 | tacTTATCtat
 I$MTTFA_01             |    11568 (+) |  1.000 |  0.982 | ctcTTATCatt
 V$NKX62_Q2             |       63 (-) |  1.000 |  0.970 | catAATTActgt
 V$NKX62_Q2             |      585 (-) |  1.000 |  0.946 | ttgAATTAacag
 V$NKX62_Q2             |      648 (-) |  0.980 |  0.960 | ttcATTTAttat
 V$NKX62_Q2             |      843 (+) |  0.980 |  0.948 | aagtTAAATaaa
 V$NKX62_Q2             |      847 (+) |  0.980 |  0.977 | taaaTAAATacg
 V$NKX62_Q2             |      989 (+) |  1.000 |  0.977 | ttaaTAATTttc
 V$NKX62_Q2             |     1894 (-) |  0.980 |  0.979 | tatATTTAtttt
 V$NKX62_Q2             |     2361 (-) |  0.980 |  0.979 | tgtATTTAtttt
 V$NKX62_Q2             |     2574 (-) |  0.980 |  0.942 | agtATTTAcaac
 V$NKX62_Q2             |     3105 (+) |  1.000 |  0.956 | atacTAATTtcc
 V$NKX62_Q2             |     3125 (+) |  1.000 |  0.971 | atatTAATTtac
 V$NKX62_Q2             |     3731 (-) |  1.000 |  0.979 | taaAATTAttat
 V$NKX62_Q2             |     3734 (-) |  0.932 |  0.940 | aatTATTAtttc
 V$NKX62_Q2             |     3830 (+) |  0.980 |  0.962 | ataaTAAATttc
 V$NKX62_Q2             |     4007 (+) |  0.980 |  0.977 | taaaTAAATatt
 V$NKX62_Q2             |     4028 (-) |  1.000 |  0.971 | tggAATTAatat
 V$NKX62_Q2             |     4058 (+) |  1.000 |  0.979 | gcaaTAATTaaa
 V$NKX62_Q2             |     4060 (-) |  1.000 |  0.957 | aatAATTAaaat
 V$NKX62_Q2             |     4224 (+) |  0.980 |  0.962 | aaaaTAAATtct
 V$NKX62_Q2             |     4445 (-) |  1.000 |  0.972 | cacAATTAatat
 V$NKX62_Q2             |     5414 (+) |  0.980 |  0.951 | ttatTAAATctt
 V$NKX62_Q2             |     5788 (+) |  1.000 |  0.998 | gaaaTAATTaaa
 V$NKX62_Q2             |     5790 (-) |  1.000 |  0.954 | aatAATTAaata
 V$NKX62_Q2             |     5792 (+) |  0.980 |  0.968 | taatTAAATaca
 V$NKX62_Q2             |     6835 (-) |  0.980 |  0.955 | gctATTTActgc
 V$NKX62_Q2             |     7400 (-) |  1.000 |  0.949 | tagAATTActga
 V$NKX62_Q2             |     7636 (-) |  1.000 |  0.979 | tagAATTAtttt
 V$NKX62_Q2             |     8683 (+) |  1.000 |  0.968 | aaggTAATTagc
 V$NKX62_Q2             |     8952 (-) |  1.000 |  0.953 | taaAATTAgtag
 V$NKX62_Q2             |    10126 (-) |  1.000 |  0.953 | taaAATTAgtta
 V$NKX62_Q2             |    10138 (-) |  1.000 |  0.980 | agaAATTAttat
 V$NKX62_Q2             |    10346 (+) |  1.000 |  0.940 | gtttTAATTcaa
 V$NKX62_Q2             |    11205 (+) |  1.000 |  0.969 | ttatTAATTtgt
 V$NKX62_Q2             |    11390 (+) |  0.980 |  0.951 | ttatTAAATttt
 V$BACH2_01             |    10034 (+) |  1.000 |  0.983 | tgTGAGTcacc
 V$MAZR_01              |     1492 (+) |  1.000 |  0.949 | gagggGGGGGgga
 V$MAZR_01              |     1493 (+) |  1.000 |  0.968 | aggggGGGGGgag
 V$MAZR_01              |     1494 (+) |  1.000 |  0.979 | gggggGGGGGagg
 V$MAZR_01              |     9682 (+) |  1.000 |  0.939 | ggaggGGGGGtgg
 V$BACH1_01             |    10032 (+) |  1.000 |  0.904 | tttgTGAGTcaccgt
 P$ANT_01               |      161 (+) |  0.984 |  0.875 | ctccgttCCCAAtg
 P$ANT_01               |     3439 (-) |  0.886 |  0.790 | ctTAGGTaacagtt
 P$ANT_01               |     6262 (+) |  0.894 |  0.845 | cccatctGCCGAag
 P$ANT_01               |     8648 (+) |  0.984 |  0.879 | gacaattCCCAAtg
 P$ANT_01               |    10789 (-) |  0.774 |  0.825 | caGGGGGatgtgag
 P$TEIL_01              |        5 (+) |  0.976 |  0.912 | ATGCAtgt
 P$TEIL_01              |       15 (-) |  1.000 |  0.943 | aagTACAT
 P$TEIL_01              |     1009 (+) |  0.874 |  0.904 | ACGCAcct
 P$TEIL_01              |     1125 (+) |  0.976 |  0.930 | ATGCAcgt
 P$TEIL_01              |     1155 (+) |  1.000 |  0.883 | ATGTAgtt
 P$TEIL_01              |     2045 (+) |  0.869 |  0.901 | CTGTAcct
 P$TEIL_01              |     2657 (+) |  0.976 |  0.925 | ATGCActt
 P$TEIL_01              |     3307 (+) |  1.000 |  0.883 | ATGTAgtt
 P$TEIL_01              |     4107 (-) |  0.969 |  0.907 | acaTCCAT
 P$TEIL_01              |     4453 (-) |  0.992 |  0.916 | ataTTCAT
 P$TEIL_01              |     4908 (-) |  0.976 |  0.925 | aagTGCAT
 P$TEIL_01              |     7235 (-) |  0.992 |  0.937 | aagTTCAT
 P$TEIL_01              |     7321 (+) |  1.000 |  0.948 | ATGTAcgt
 P$TEIL_01              |     8276 (+) |  0.976 |  0.922 | ATGCAgct
 P$TEIL_01              |     9169 (-) |  0.976 |  0.964 | agaTGCAT
 P$TEIL_01              |     9739 (-) |  0.969 |  0.916 | atgTCCAT
 P$TEIL_01              |     9800 (+) |  1.000 |  0.940 | ATGTAcat
 P$TEIL_01              |     9800 (-) |  1.000 |  0.940 | atgTACAT
 P$TEIL_01              |     9942 (+) |  1.000 |  0.931 | ATGTAtgt
 P$TEIL_01              |    10465 (+) |  0.976 |  0.964 | ATGCAtct
 P$TEIL_01              |    11161 (+) |  0.992 |  0.934 | ATGAAgct
 P$TEIL_01              |    11643 (+) |  1.000 |  0.925 | ATGTAttt
 P$ATHB5_01             |     4059 (+) |  0.971 |  0.964 | caaTAATTa
 P$LIM1_01              |      202 (+) |  1.000 |  0.922 | CCACCatgcctg
 P$LIM1_01              |      427 (+) |  0.796 |  0.827 | CCAAAataccac
 P$LIM1_01              |      451 (-) |  0.796 |  0.826 | tgtctgtTTTGG
 P$LIM1_01              |      454 (-) |  0.813 |  0.837 | ctgttttGGTTG
 P$LIM1_01              |      733 (+) |  1.000 |  0.895 | CCACCacgtggt
 P$LIM1_01              |      739 (-) |  0.789 |  0.819 | cgtggttGCTGG
 P$LIM1_01              |      929 (+) |  0.968 |  0.950 | CCACGaaaccac
 P$LIM1_01              |      937 (+) |  0.977 |  0.884 | CCACAagttagg
 P$LIM1_01              |      995 (-) |  0.977 |  0.820 | attttcaTGTGG
 P$LIM1_01              |     1080 (-) |  0.796 |  0.819 | aggtcatTTTGG
 P$LIM1_01              |     1314 (+) |  0.791 |  0.836 | CCCCTaactccc
 P$LIM1_01              |     1596 (-) |  0.805 |  0.821 | ctgggttTGGGG
 P$LIM1_01              |     1613 (-) |  0.968 |  0.971 | ggggtctCGTGG
 P$LIM1_01              |     1980 (+) |  0.845 |  0.846 | CCTCAaactcac
 P$LIM1_01              |     2310 (-) |  0.796 |  0.832 | tgtgtgtTTTGG
 P$LIM1_01              |     2998 (+) |  0.868 |  0.820 | CCTCCaaggtgc
 P$LIM1_01              |     3141 (+) |  0.977 |  0.939 | CCACAacaatat
 P$LIM1_01              |     3148 (-) |  0.868 |  0.843 | aatatatGGAGG
 P$LIM1_01              |     3238 (+) |  0.819 |  0.832 | CCAACattccca
 P$LIM1_01              |     3259 (-) |  0.787 |  0.841 | tggttttCTTGG
 P$LIM1_01              |     3418 (-) |  0.813 |  0.843 | tgattctGGTTG
 P$LIM1_01              |     3510 (-) |  0.831 |  0.829 | tgctgttAGAGG
 P$LIM1_01              |     3525 (+) |  1.000 |  0.847 | CCACCttggccc
 P$LIM1_01              |     3641 (-) |  1.000 |  0.893 | accacatGGTGG
 P$LIM1_01              |     4306 (+) |  0.845 |  0.836 | CCTCAatactgc
 P$LIM1_01              |     4339 (-) |  1.000 |  0.903 | tccaggtGGTGG
 P$LIM1_01              |     4342 (-) |  0.868 |  0.885 | aggtggtGGAGG
 P$LIM1_01              |     4412 (+) |  0.977 |  0.911 | CCACAaccttgt
 P$LIM1_01              |     4919 (+) |  0.977 |  0.922 | CCACAacttaca
 P$LIM1_01              |     5278 (+) |  0.790 |  0.818 | CAACAacaggct
 P$LIM1_01              |     5428 (+) |  0.868 |  0.834 | CCTCCactttat
 P$LIM1_01              |     5691 (+) |  0.963 |  0.908 | CCACTagttcat
 P$LIM1_01              |     5716 (+) |  0.977 |  0.951 | CCACAaaaacac
 P$LIM1_01              |     5967 (-) |  0.963 |  0.815 | gtttttaAGTGG
 P$LIM1_01              |     6374 (-) |  0.813 |  0.826 | gagatttGGTAG
 P$LIM1_01              |     6507 (+) |  0.977 |  0.898 | CCACAaataaaa
 P$LIM1_01              |     6593 (-) |  1.000 |  0.829 | caaataaGGTGG
 P$LIM1_01              |     6716 (+) |  0.977 |  0.904 | CCACAaccttta
 P$LIM1_01              |     6752 (+) |  0.963 |  0.915 | CCACTatccctt
 P$LIM1_01              |     6887 (+) |  0.968 |  0.838 | CCACGtaagaca
 P$LIM1_01              |     6902 (-) |  0.963 |  0.826 | gggcataAGTGG
 P$LIM1_01              |     7388 (-) |  1.000 |  0.820 | gtgtccaGGTGG
 P$LIM1_01              |     7666 (-) |  1.000 |  0.922 | caggcatGGTGG
 P$LIM1_01              |     7702 (-) |  0.831 |  0.859 | gggaggtAGAGG
 P$LIM1_01              |     7735 (+) |  0.789 |  0.817 | CCATCacaggct
 P$LIM1_01              |     7820 (+) |  0.796 |  0.827 | CCAAAacaaaca
 P$LIM1_01              |     7962 (-) |  0.776 |  0.825 | agactatAGTTG
 P$LIM1_01              |     8000 (-) |  0.819 |  0.814 | tgtgcctGTTGG
 P$LIM1_01              |     8032 (-) |  0.789 |  0.813 | agagcttGCTGG
 P$LIM1_01              |     8251 (-) |  0.968 |  0.930 | gtgtgttCGTGG
 P$LIM1_01              |     8336 (-) |  0.789 |  0.834 | agtatttGCTGG
 P$LIM1_01              |     8738 (-) |  1.000 |  0.995 | ggggtgtGGTGG
 P$LIM1_01              |     8798 (-) |  0.828 |  0.815 | tagagttGGGGG
 P$LIM1_01              |     8899 (+) |  0.977 |  0.910 | CCACAaacagat
 P$LIM1_01              |     8971 (-) |  1.000 |  0.954 | caggtgtGGTGG
 P$LIM1_01              |     9000 (-) |  0.868 |  0.842 | agcacatGGAGG
 P$LIM1_01              |     9279 (+) |  1.000 |  0.912 | CCACCaagctga
 P$LIM1_01              |     9330 (-) |  0.868 |  0.869 | agcctctGGAGG
 P$LIM1_01              |     9571 (-) |  1.000 |  0.989 | tgggtgtGGTGG
 P$LIM1_01              |     9610 (-) |  1.000 |  0.841 | aagctgaGGTGG
 P$LIM1_01              |     9675 (-) |  0.868 |  0.831 | aagaagtGGAGG
 P$LIM1_01              |     9686 (-) |  1.000 |  0.980 | ggggggtGGTGG
 P$LIM1_01              |     9689 (-) |  1.000 |  0.975 | gggtggtGGTGG
 P$LIM1_01              |     9692 (-) |  1.000 |  0.969 | tggtggtGGTGG
 P$LIM1_01              |     9695 (-) |  1.000 |  0.969 | tggtggtGGTGG
 P$LIM1_01              |     9698 (-) |  1.000 |  0.969 | tggtggtGGTGG
 P$LIM1_01              |     9701 (-) |  1.000 |  0.969 | tggtggtGGTGG
 P$LIM1_01              |    10008 (-) |  0.868 |  0.865 | tgggactGGAGG
 P$LIM1_01              |    10235 (-) |  1.000 |  0.945 | ctaggttGGTGG
 P$LIM1_01              |    10400 (-) |  1.000 |  0.835 | tgaacgaGGTGG
 P$LIM1_01              |    10618 (-) |  0.790 |  0.821 | agggagtTGTAG
 P$LIM1_01              |    10730 (-) |  0.783 |  0.818 | agcttttATTGG
 P$LIM1_01              |    10868 (-) |  1.000 |  0.914 | gcagcgtGGTGG
 P$LIM1_01              |    10871 (-) |  1.000 |  0.935 | gcgtggtGGTGG
 P$LIM1_01              |    10930 (-) |  0.977 |  0.942 | cgcctctTGTGG
 P$LIM1_01              |    10962 (-) |  0.819 |  0.814 | tgtgcctGTTGG
 P$LIM1_01              |    11173 (-) |  0.796 |  0.813 | agatcttTTTGG
 P$LIM1_01              |    11501 (-) |  0.977 |  0.928 | gaattttTGTGG
 P$LIM1_01              |    11560 (+) |  0.813 |  0.861 | CAACCaaactct
 P$LIM1_01              |    11677 (+) |  0.796 |  0.835 | CCAAAaaagacc
 P$LIM1_01              |    11709 (+) |  0.805 |  0.824 | CCCCAactgccc
 P$LIM1_01              |    11719 (+) |  0.868 |  0.835 | CCTCCaccattt
 P$LIM1_01              |    11722 (+) |  1.000 |  0.950 | CCACCattttct
 P$LIM1_01              |    11804 (-) |  1.000 |  0.826 | attggaaGGTGG
 P$LIM1_01              |    11852 (-) |  0.828 |  0.875 | ggggtatGGGGG
 V$LHX3_01              |     5791 (-) |  1.000 |  0.979 | ataATTAAat
 V$ATF3_Q6              |     1236 (+) |  0.881 |  0.887 | cttTGACAtcaggg
 V$ATF3_Q6              |     1236 (-) |  0.877 |  0.893 | ctttgaCATCAggg
 V$ATF3_Q6              |     1443 (+) |  0.861 |  0.872 | tagTGAAGtcactg
 V$ATF3_Q6              |     1443 (-) |  0.862 |  0.844 | tagtgaAGTCActg
 V$ATF3_Q6              |     2963 (-) |  0.809 |  0.862 | cagtgaCGGCAgat
 V$ATF3_Q6              |     4331 (+) |  0.881 |  0.811 | tggTGACAtccagg
 V$ATF3_Q6              |     4848 (-) |  0.861 |  0.810 | ctgagaCTTCActg
 V$ATF3_Q6              |     4861 (-) |  0.862 |  0.802 | gagggaGGTCAgca
 V$ATF3_Q6              |     4962 (-) |  0.862 |  0.803 | gcaggaAGTCAggc
 V$ATF3_Q6              |     8208 (+) |  0.862 |  0.864 | ctcTGACCtcagtt
 V$ATF3_Q6              |     8208 (-) |  0.877 |  0.884 | ctctgaCCTCAgtt
 V$ATF3_Q6              |     9344 (+) |  0.861 |  0.801 | cccTGAAGtctctt
 V$ATF3_Q6              |    11108 (-) |  0.861 |  0.806 | gaacgaCTTCAgat
 V$ATF4_Q2              |     6322 (+) |  0.933 |  0.875 | ccTGACTgaagc
 V$ATF4_Q2              |     8046 (+) |  0.933 |  0.874 | ctTGACTcgagg
 V$ATF4_Q2              |     8321 (-) |  1.000 |  0.889 | ttctgCGTCAgc
 V$ATF4_Q2              |     8610 (-) |  1.000 |  0.867 | cattcCGTCAat
 V$ATF4_Q2              |     9319 (-) |  0.888 |  0.857 | cgttgGGTCAga
 V$E2F_03               |     2468 (-) |  0.992 |  0.887 | gcaagCGCGAag
 V$E2F_03               |     7089 (+) |  0.940 |  0.891 | ctTTGCGcgcac
 V$AP1_01               |      131 (+) |  1.000 |  0.894 | tgctcAGTCAatc
 V$AP1_01               |      438 (+) |  0.948 |  0.889 | cgtttAATCAggt
 V$AP1_01               |      796 (-) |  0.871 |  0.890 | cgcTGAGCcattt
 V$AP1_01               |     1030 (+) |  0.948 |  0.925 | agttgAATCAaca
 V$AP1_01               |     1030 (-) |  0.946 |  0.923 | agtTGAATcaaca
 V$AP1_01               |     1352 (+) |  0.903 |  0.895 | gcctgGGTCAcct
 V$AP1_01               |     3433 (-) |  1.000 |  0.897 | aatTGACTtaggt
 V$AP1_01               |     3724 (-) |  1.000 |  0.925 | gggTGACTaaaat
 V$AP1_01               |     3750 (+) |  1.000 |  0.919 | tttttAGTCAttc
 V$AP1_01               |     3932 (+) |  1.000 |  0.909 | ttatcAGTCActt
 V$AP1_01               |     3944 (+) |  0.946 |  0.886 | tgttcATTCAgcc
 V$AP1_01               |     4465 (-) |  1.000 |  0.923 | cacTGACTgacca
 V$AP1_01               |     4531 (+) |  0.909 |  0.899 | aaatgCGTCAaca
 V$AP1_01               |     6292 (-) |  1.000 |  0.915 | tgaTGACTgagca
 V$AP1_01               |     6321 (-) |  1.000 |  0.922 | cccTGACTgaagc
 V$AP1_01               |     6414 (-) |  1.000 |  0.901 | gaaTGACTcctct
 V$AP1_01               |     6554 (+) |  1.000 |  0.902 | gtaagAGTCAtgg
 V$AP1_01               |     7606 (-) |  0.871 |  0.890 | tgcTGAGCcatct
 V$AP1_01               |     8321 (+) |  0.909 |  0.910 | ttctgCGTCAgcg
 V$AP1_01               |     9287 (+) |  1.000 |  0.922 | ctgagAGTCAgct
 V$AP1_01               |     9319 (+) |  0.903 |  0.904 | cgttgGGTCAgag
 V$AP1_01               |    10033 (+) |  1.000 |  0.977 | ttgtgAGTCAccg
 V$AP1_01               |    10033 (-) |  0.968 |  0.945 | ttgTGAGTcaccg
 V$AP1_01               |    10631 (-) |  1.000 |  0.899 | aagTGACTgagga
 V$AP1_01               |    11453 (+) |  0.948 |  0.940 | tggtgAATCAgtg
 V$AP1_01               |    11453 (-) |  0.946 |  0.929 | tggTGAATcagtg
 V$PPARA_02             |      191 (-) |  0.810 |  0.736 | tgcctcccacaCCACCatg
 V$PPARA_02             |     1078 (+) |  1.000 |  0.901 | gtaGGTCAttttggtcaac
 V$PPARA_02             |     1348 (-) |  0.945 |  0.761 | gcttgcctgggTCACCtga
 V$PPARA_02             |     1379 (+) |  0.768 |  0.744 | gtgGGCGAggtagggcagg
 V$PPARA_02             |     1384 (+) |  0.805 |  0.834 | cgaGGTAGggcaggtgagg
 V$PPARA_02             |     1393 (+) |  0.945 |  0.755 | gcaGGTGAggagagtgggt
 V$PPARA_02             |     1497 (+) |  0.768 |  0.716 | gggGGGGAgggagggaggg
 V$PPARA_02             |     2666 (-) |  0.950 |  0.779 | gatgacactctTAACCcgt
 V$PPARA_02             |     3257 (+) |  0.796 |  0.817 | tatGGTTTtcttggtgatg
 V$PPARA_02             |     3520 (-) |  0.823 |  0.714 | ggaggccacctTGGCCcga
 V$PPARA_02             |     3880 (-) |  1.000 |  0.745 | tacaagctcctTGACCctc
 V$PPARA_02             |     4977 (-) |  0.812 |  0.723 | cagcccctaccTGTCCgaa
 V$PPARA_02             |     5746 (-) |  0.856 |  0.733 | atagacgcaaaGGACCtgt
 V$PPARA_02             |     6022 (-) |  0.856 |  0.720 | tttcaactctaGGACCcat
 V$PPARA_02             |     6434 (+) |  1.000 |  0.772 | atcGGTCAacccagtcatg
 V$PPARA_02             |     6754 (-) |  0.786 |  0.735 | actatccctttATACCatg
 V$PPARA_02             |     6802 (-) |  0.940 |  0.791 | tcctcccctcaTTACCttc
 V$PPARA_02             |     7188 (+) |  0.823 |  0.831 | aacGGCCAcgggggtgcta
 V$PPARA_02             |     8200 (-) |  1.000 |  0.842 | tgtttcccctcTGACCtca
 V$PPARA_02             |     8299 (-) |  0.823 |  0.736 | gcatgcccctcTGCCCtgc
 V$PPARA_02             |     8673 (+) |  0.950 |  0.858 | accGGTTAggaaggtaatt
 V$PPARA_02             |     9038 (+) |  0.823 |  0.782 | caaGGGCAgcctggtctac
 V$PPARA_02             |     9067 (+) |  0.773 |  0.714 | ccaGGCTAgccagggcagc
 V$PPARA_02             |     9117 (-) |  0.796 |  0.766 | aaaaaccgggaAAACCttc
 V$PPARA_02             |     9177 (-) |  0.846 |  0.712 | gaacgccacagAGACCact
 V$PPARA_02             |     9636 (+) |  1.000 |  0.783 | caaGGTCAgcttgggctac
 V$PPARA_02             |     9687 (+) |  0.810 |  0.826 | gggGGTGGtggtggtggtg
 V$PPARA_02             |     9690 (+) |  0.810 |  0.818 | ggtGGTGGtggtggtggtg
 V$PPARA_02             |     9693 (+) |  0.810 |  0.818 | ggtGGTGGtggtggtggtg
 V$PPARA_02             |     9696 (+) |  0.810 |  0.818 | ggtGGTGGtggtggtggtg
 V$PPARA_02             |     9699 (+) |  0.810 |  0.790 | ggtGGTGGtggtggtgtaa
 V$PPARA_02             |     9968 (+) |  0.805 |  0.713 | tctGGTTCctatggggatc
 V$PPARA_02             |     9998 (+) |  0.856 |  0.791 | ttaGGTCCtctgggactgg
 V$PPARA_02             |    10242 (+) |  1.000 |  0.735 | ggtGGTCAggcttgtgcag
 V$PPARA_02             |    11313 (+) |  0.945 |  0.746 | tacGGTGAcgacgatgatg
 V$PPARA_02             |    11618 (-) |  0.856 |  0.783 | gggtaccagaaGGACCctc
 V$PPARA_02             |    11695 (-) |  0.945 |  0.732 | gttaatcactgTCACCcca
 V$PPARA_02             |    11705 (-) |  0.823 |  0.742 | gtcaccccaacTGCCCtcc
 V$PPARA_02             |    11808 (+) |  0.810 |  0.714 | gaaGGTGGcccagggttgg
 V$PPARA_02             |    11850 (+) |  0.773 |  0.824 | gtgGGGTAtgggggtaggt
 V$PPARA_02             |    11859 (+) |  0.805 |  0.727 | gggGGTAGgtccgggggag
 V$PPARG_03             |     3438 (+) |  0.800 |  0.817 | acttaggtaACAGTtaa
 V$PPARG_03             |     5453 (-) |  1.000 |  0.904 | taaCCTTTtccccacat
 V$PPARG_03             |     5762 (+) |  1.000 |  0.802 | tgtagggtaAAAGGaga
 V$PPARG_03             |     8204 (-) |  0.900 |  0.797 | tccCCTCTgacctcagt
 V$PPARG_03             |     8578 (+) |  1.000 |  0.837 | aaatggggcAAAGGcaa
 V$PPARG_03             |    11516 (-) |  0.840 |  0.825 | ttaCCGTTgtccgtagc
 V$NERF_Q2              |      570 (-) |  0.800 |  0.801 | ataaacgtctACCTGttg
 V$NERF_Q2              |      603 (-) |  1.000 |  0.770 | tttttaaacaTCCTGtcg
 V$NERF_Q2              |      735 (-) |  0.800 |  0.724 | accacgtggtTGCTGgga
 V$NERF_Q2              |      766 (+) |  0.800 |  0.785 | cctCTGGAagagtagtcg
 V$NERF_Q2              |     1189 (+) |  1.000 |  0.775 | cccCAGGAaagctggtta
 V$NERF_Q2              |     1723 (-) |  1.000 |  0.794 | tccgggctcaTCCTGaac
 V$NERF_Q2              |     1732 (-) |  0.800 |  0.780 | atcctgaactTCCTAtag
 V$NERF_Q2              |     1770 (-) |  1.000 |  0.775 | tcgcctgtccTCCTGgag
 V$NERF_Q2              |     2140 (-) |  0.800 |  0.809 | ctctctctctTCCTTcct
 V$NERF_Q2              |     2144 (-) |  0.800 |  0.814 | ctctcttcctTCCTTcct
 V$NERF_Q2              |     2148 (-) |  0.800 |  0.812 | cttccttcctTCCTCttc
 V$NERF_Q2              |     2154 (-) |  0.800 |  0.790 | tccttcctctTCCTTtcc
 V$NERF_Q2              |     2198 (-) |  0.800 |  0.799 | ctttctttctTCCTTtct
 V$NERF_Q2              |     2679 (-) |  1.000 |  0.816 | acccgttgcaTCCTGgtc
 V$NERF_Q2              |     2700 (-) |  0.800 |  0.801 | ctcttctcctTCCTCttc
 V$NERF_Q2              |     2778 (-) |  0.800 |  0.827 | gtgagattctTCCTTagc
 V$NERF_Q2              |     2797 (-) |  0.800 |  0.782 | ggtcttctctTACTGaac
 V$NERF_Q2              |     3318 (-) |  1.000 |  0.795 | attggcctttTCCTGatt
 V$NERF_Q2              |     3335 (-) |  1.000 |  0.808 | tctatttcccTCCTGttc
 V$NERF_Q2              |     4173 (+) |  1.000 |  0.773 | attCAGGAggctgagcag
 V$NERF_Q2              |     4351 (+) |  1.000 |  0.762 | aggCAGGAggatcagaag
 V$NERF_Q2              |     4585 (-) |  1.000 |  0.787 | agtctcctccTCCTGccc
 V$NERF_Q2              |     4596 (-) |  0.800 |  0.828 | cctgcccgctTGCTGgaa
 V$NERF_Q2              |     4605 (+) |  0.800 |  0.762 | ttgCTGGAaggtaaaacc
 V$NERF_Q2              |     4686 (+) |  1.000 |  0.800 | tggCAGGAaacttgatgt
 V$NERF_Q2              |     4945 (-) |  0.800 |  0.784 | aactgggactTTCTGcag
 V$NERF_Q2              |     4960 (+) |  1.000 |  0.933 | cagCAGGAagtcaggctc
 V$NERF_Q2              |     4975 (-) |  0.800 |  0.847 | ctcagcccctACCTGtcc
 V$NERF_Q2              |     5057 (+) |  0.800 |  0.814 | aagCAGGTagtgagagat
 V$NERF_Q2              |     5189 (+) |  1.000 |  0.740 | tagCAGGAtttgtctgtg
 V$NERF_Q2              |     5260 (-) |  1.000 |  0.803 | gtcacagtcaTCCTGggc
 V$NERF_Q2              |     5466 (-) |  1.000 |  0.806 | acatactattTCCTGatt
 V$NERF_Q2              |     5538 (-) |  0.800 |  0.827 | ttcactctctTTCTGtct
 V$NERF_Q2              |     5729 (+) |  0.800 |  0.753 | aaaCTGGAagccataata
 V$NERF_Q2              |     6060 (-) |  0.800 |  0.718 | gccctgcacgTGCTGcca
 V$NERF_Q2              |     6082 (-) |  1.000 |  0.772 | ctctgtgagtTCCTGtgt
 V$NERF_Q2              |     6273 (+) |  0.800 |  0.808 | aagAAGGAagcctctctg
 V$NERF_Q2              |     6454 (-) |  1.000 |  0.865 | caaacttattTCCTGata
 V$NERF_Q2              |     6476 (+) |  1.000 |  0.792 | gctCAGGAtgaggactgg
 V$NERF_Q2              |     6519 (+) |  0.800 |  0.772 | gaaCACGAagttcaccct
 V$NERF_Q2              |     6792 (-) |  0.800 |  0.789 | tgctggctctTCCTCccc
 V$NERF_Q2              |     6875 (+) |  0.800 |  0.813 | ttaTAGGAagcaccacgt
 V$NERF_Q2              |     7012 (-) |  1.000 |  0.808 | ggcggatgttTCCTGcat
 V$NERF_Q2              |     7149 (-) |  1.000 |  0.718 | gcgccgtatcTCCTGgag
 V$NERF_Q2              |     7228 (+) |  1.000 |  0.928 | cagCAGGAagttcatcgt
 V$NERF_Q2              |     7245 (+) |  1.000 |  0.789 | tctCAGGAaaaagtctca
 V$NERF_Q2              |     7364 (+) |  0.800 |  0.792 | gggCAGAAagaattgata
 V$NERF_Q2              |     7463 (+) |  1.000 |  0.735 | ctgCAGGAtttgagtgtg
 V$NERF_Q2              |     7490 (-) |  0.800 |  0.783 | cgtctgttctTCTTGgag
 V$NERF_Q2              |     7663 (+) |  0.800 |  0.723 | tgcCAGGCatggtggctc
 V$NERF_Q2              |     8028 (-) |  0.800 |  0.748 | tgtcagagctTGCTGggc
 V$NERF_Q2              |     8075 (-) |  0.800 |  0.794 | tgcagaaactTCCTAtac
 V$NERF_Q2              |     8116 (-) |  0.800 |  0.821 | ctcccaccctGCCTGgtc
 V$NERF_Q2              |     8128 (-) |  0.800 |  0.820 | ctggtctgctTTCTGctg
 V$NERF_Q2              |     8152 (-) |  0.800 |  0.791 | aacattagctTCCAGagg
 V$NERF_Q2              |     8167 (+) |  0.800 |  0.803 | aggCAGGTagcaccagaa
 V$NERF_Q2              |     8187 (-) |  0.800 |  0.759 | tgtttgctctGCCTGttt
 V$NERF_Q2              |     8441 (-) |  0.800 |  0.727 | gcaacccgcaTCCTAagc
 V$NERF_Q2              |     8676 (+) |  0.800 |  0.802 | ggtTAGGAaggtaattag
 V$NERF_Q2              |     8687 (-) |  0.800 |  0.762 | taattagcctTTCTGaaa
 V$NERF_Q2              |     8909 (+) |  1.000 |  0.758 | attCAGGAatactcggaa
 V$NERF_Q2              |     9015 (+) |  0.800 |  0.798 | gggCAGGCagatctttgt
 V$NERF_Q2              |     9305 (+) |  1.000 |  0.809 | gccCAGGAgggaggcgtt
 V$NERF_Q2              |     9372 (+) |  0.800 |  0.785 | tcaCAGGGagagctgtca
 V$NERF_Q2              |     9433 (+) |  1.000 |  0.898 | taaCAGGAagcccaaggt
 V$NERF_Q2              |     9466 (+) |  1.000 |  0.764 | gtaCAGGAtgttctagct
 V$NERF_Q2              |     9847 (+) |  0.800 |  0.777 | agtCAGGCaggcagcatt
 V$NERF_Q2              |     9851 (+) |  0.800 |  0.800 | aggCAGGCagcattaaag
 V$NERF_Q2              |     9903 (-) |  0.800 |  0.838 | aagacttactTACTGgat
 V$NERF_Q2              |    10072 (+) |  0.800 |  0.785 | cttCTGGAagggcagcca
 V$NERF_Q2              |    10255 (+) |  1.000 |  0.953 | gtgCAGGAagtgattttt
 V$NERF_Q2              |    10636 (+) |  0.800 |  0.764 | actGAGGAagacacccag
 V$NERF_Q2              |    10665 (+) |  1.000 |  0.778 | caaCAGGAggatccacag
 V$NERF_Q2              |    10842 (+) |  1.000 |  0.921 | tcgCAGGAagaagccatt
 V$NERF_Q2              |    11903 (+) |  0.800 |  0.791 | tagCACGAaggcttcggg
 V$RP58_01              |     4118 (-) |  1.000 |  0.974 | cccAGATGttaa
 V$HTF_01               |      427 (+) |  1.000 |  0.855 | ccaaaatacCACGTttaatcaggt
 V$HTF_01               |     5996 (-) |  1.000 |  0.858 | gggatggggtACGTGtccaactct
 V$HTF_01               |     6879 (+) |  1.000 |  0.901 | aggaagcacCACGTaagacaagag
 V$HTF_01               |     7479 (+) |  1.000 |  0.866 | tgctacgcgCACGTctgttcttct
 V$ARNT_02              |       13 (+) |  0.800 |  0.798 | acaagtaCATGTgaatgtgt
 V$ARNT_02              |       13 (-) |  0.800 |  0.798 | acaagtacATGTGaatgtgt
 V$ARNT_02              |      282 (+) |  0.800 |  0.811 | tgcaagtCAAGTgttttaca
 V$ARNT_02              |      282 (-) |  0.800 |  0.811 | tgcaagtcAAGTGttttaca
 V$ARNT_02              |      730 (+) |  1.000 |  0.918 | gagccacCACGTggttgctg
 V$ARNT_02              |      730 (-) |  1.000 |  0.918 | gagccaccACGTGgttgctg
 V$ARNT_02              |      993 (+) |  0.800 |  0.791 | taattttCATGTggggacgc
 V$ARNT_02              |      993 (-) |  0.800 |  0.791 | taattttcATGTGgggacgc
 V$ARNT_02              |     1121 (+) |  1.000 |  0.919 | gtgtatgCACGTgtgttcct
 V$ARNT_02              |     1121 (-) |  1.000 |  0.919 | gtgtatgcACGTGtgttcct
 V$ARNT_02              |     1353 (+) |  0.800 |  0.846 | cctgggtCACCTgatgctcg
 V$ARNT_02              |     1353 (-) |  0.800 |  0.846 | cctgggtcACCTGatgctcg
 V$ARNT_02              |     1387 (+) |  0.800 |  0.811 | ggtagggCAGGTgaggagag
 V$ARNT_02              |     1387 (-) |  0.800 |  0.811 | ggtagggcAGGTGaggagag
 V$ARNT_02              |     1611 (+) |  0.800 |  0.797 | agggggtCTCGTggacagca
 V$ARNT_02              |     1611 (-) |  0.800 |  0.797 | agggggtcTCGTGgacagca
 V$ARNT_02              |     1781 (+) |  0.800 |  0.791 | cctggagCACCTgccattca
 V$ARNT_02              |     1781 (-) |  0.800 |  0.791 | cctggagcACCTGccattca
 V$ARNT_02              |     2768 (+) |  0.800 |  0.804 | gattccgCATGTgagattct
 V$ARNT_02              |     2768 (-) |  0.800 |  0.804 | gattccgcATGTGagattct
 V$ARNT_02              |     3933 (+) |  0.800 |  0.815 | tatcagtCACTTgttcattc
 V$ARNT_02              |     3933 (-) |  0.800 |  0.815 | tatcagtcACTTGttcattc
 V$ARNT_02              |     5016 (+) |  0.800 |  0.804 | attaagcCACGGgactggga
 V$ARNT_02              |     5016 (-) |  0.800 |  0.804 | attaagccACGGGactggga
 V$ARNT_02              |     5165 (+) |  0.800 |  0.800 | ggactttCACTTgtgactgt
 V$ARNT_02              |     5165 (-) |  0.800 |  0.800 | ggactttcACTTGtgactgt
 V$ARNT_02              |     5245 (+) |  0.800 |  0.795 | atgggttCACATgtggtcac
 V$ARNT_02              |     5245 (-) |  0.800 |  0.795 | atgggttcACATGtggtcac
 V$ARNT_02              |     5362 (+) |  0.800 |  0.808 | caaaacaCACGGgatttctt
 V$ARNT_02              |     5362 (-) |  0.800 |  0.808 | caaaacacACGGGatttctt
 V$ARNT_02              |     5998 (+) |  0.800 |  0.790 | gatggggTACGTgtccaact
 V$ARNT_02              |     5998 (-) |  1.000 |  0.790 | gatggggtACGTGtccaact
 V$ARNT_02              |     6059 (+) |  1.000 |  0.926 | agccctgCACGTgctgccac
 V$ARNT_02              |     6059 (-) |  1.000 |  0.926 | agccctgcACGTGctgccac
 V$ARNT_02              |     6881 (+) |  1.000 |  0.798 | gaagcacCACGTaagacaag
 V$ARNT_02              |     6881 (-) |  0.800 |  0.798 | gaagcaccACGTAagacaag
 V$ARNT_02              |     6938 (+) |  0.800 |  0.799 | cagtaccCAAGTgatactgt
 V$ARNT_02              |     6938 (-) |  0.800 |  0.799 | cagtacccAAGTGatactgt
 V$MYCMAX_03            |      730 (+) |  1.000 |  0.994 | gagccacCACGTggttgctg
 V$MYCMAX_03            |      730 (-) |  1.000 |  0.994 | gagccaccACGTGgttgctg
 V$AFP1_Q6              |     8057 (-) |  0.905 |  0.893 | gtctagTTTAT
 V$CEBPDELTA_Q6         |      490 (+) |  1.000 |  0.967 | cATTGCaacatt
 V$CEBPDELTA_Q6         |     9872 (-) |  0.986 |  0.966 | aatgagGAAATc
 V$CEBPDELTA_Q6         |    10133 (-) |  0.986 |  0.977 | agttaaGAAATt
 V$CEBPDELTA_Q6         |    10378 (-) |  1.000 |  0.957 | aatgttGCAATc
 V$CEBPGAMMA_Q6         |       37 (+) |  0.907 |  0.802 | acaACTTCagatg
 V$CEBPGAMMA_Q6         |      238 (-) |  0.907 |  0.853 | cttttTAAATctg
 V$CEBPGAMMA_Q6         |      467 (+) |  0.845 |  0.849 | cttATTTGacact
 V$CEBPGAMMA_Q6         |      499 (+) |  0.752 |  0.784 | attATTATatatt
 V$CEBPGAMMA_Q6         |      515 (-) |  0.691 |  0.795 | cttctGATTTtaa
 V$CEBPGAMMA_Q6         |      518 (+) |  0.845 |  0.920 | ctgATTTTaaaaa
 V$CEBPGAMMA_Q6         |      522 (-) |  0.845 |  0.809 | ttttaAAAATgat
 V$CEBPGAMMA_Q6         |      585 (+) |  0.752 |  0.800 | ttgAATTAacaga
 V$CEBPGAMMA_Q6         |      648 (+) |  0.907 |  0.780 | ttcATTTAttata
 V$CEBPGAMMA_Q6         |      652 (+) |  0.752 |  0.792 | tttATTATatata
 V$CEBPGAMMA_Q6         |      908 (-) |  0.721 |  0.791 | tttctTTCATgcg
 V$CEBPGAMMA_Q6         |      984 (+) |  0.752 |  0.784 | cacAGTTAataat
 V$CEBPGAMMA_Q6         |     1058 (+) |  0.752 |  0.794 | acaACTTTaaaat
 V$CEBPGAMMA_Q6         |     1061 (-) |  0.845 |  0.875 | actttAAAATaag
 V$CEBPGAMMA_Q6         |     1098 (+) |  0.845 |  0.809 | aaaATTTGagaaa
 V$CEBPGAMMA_Q6         |     1102 (-) |  1.000 |  0.810 | tttgaGAAATcgc
 V$CEBPGAMMA_Q6         |     1235 (-) |  0.907 |  0.890 | gctttGACATcag
 V$CEBPGAMMA_Q6         |     1254 (-) |  0.814 |  0.880 | attctGTCATcat
 V$CEBPGAMMA_Q6         |     1887 (+) |  0.845 |  0.814 | cccATTTTatatt
 V$CEBPGAMMA_Q6         |     1911 (+) |  0.845 |  0.848 | tttATTTGagaca
 V$CEBPGAMMA_Q6         |     2552 (-) |  0.660 |  0.820 | tttctGTTGTgaa
 V$CEBPGAMMA_Q6         |     2557 (-) |  1.000 |  0.847 | gttgtGAAATttc
 V$CEBPGAMMA_Q6         |     3613 (-) |  0.845 |  0.836 | gttttCAAATgcg
 V$CEBPGAMMA_Q6         |     3819 (-) |  0.691 |  0.806 | gttttCAATTcat
 V$CEBPGAMMA_Q6         |     3822 (+) |  0.845 |  0.887 | ttcAATTCataat
 V$CEBPGAMMA_Q6         |     3919 (-) |  0.845 |  0.807 | tttatGAATTaca
 V$CEBPGAMMA_Q6         |     3992 (+) |  0.721 |  0.837 | ctcATGAAacaac
 V$CEBPGAMMA_Q6         |     4096 (+) |  0.691 |  0.831 | ctgATTCTaaaac
 V$CEBPGAMMA_Q6         |     4120 (+) |  0.752 |  0.786 | cagATGTTaaaac
 V$CEBPGAMMA_Q6         |     4157 (-) |  0.907 |  0.784 | catttGTAATcct
 V$CEBPGAMMA_Q6         |     4214 (+) |  0.752 |  0.881 | ctcAGTTAaaaaa
 V$CEBPGAMMA_Q6         |     4367 (-) |  0.752 |  0.783 | agtttAAAGTtat
 V$CEBPGAMMA_Q6         |     4456 (+) |  1.000 |  0.913 | ttcATTTCacact
 V$CEBPGAMMA_Q6         |     5413 (-) |  0.907 |  0.807 | cttatTAAATctt
 V$CEBPGAMMA_Q6         |     5556 (+) |  0.660 |  0.822 | ctcACTAGaaaac
 V$CEBPGAMMA_Q6         |     5637 (+) |  0.660 |  0.794 | ataAAGACaaaat
 V$CEBPGAMMA_Q6         |     5783 (-) |  1.000 |  0.903 | aatatGAAATaat
 V$CEBPGAMMA_Q6         |     5791 (+) |  0.814 |  0.791 | ataATTAAataca
 V$CEBPGAMMA_Q6         |     5795 (+) |  0.752 |  0.847 | ttaAATACaaaaa
 V$CEBPGAMMA_Q6         |     5967 (-) |  0.814 |  0.827 | gttttTAAGTggt
 V$CEBPGAMMA_Q6         |     5985 (-) |  0.691 |  0.779 | cttctGGATTagg
 V$CEBPGAMMA_Q6         |     6447 (+) |  0.752 |  0.792 | gtcATGGCaaact
 V$CEBPGAMMA_Q6         |     6549 (+) |  0.660 |  0.786 | ctgAGGTAagagt
 V$CEBPGAMMA_Q6         |     7057 (-) |  0.752 |  0.794 | tttctTAATTtgt
 V$CEBPGAMMA_Q6         |     7203 (-) |  0.845 |  0.828 | gctatGAATTgaa
 V$CEBPGAMMA_Q6         |     7404 (+) |  0.660 |  0.791 | attACTGAagaac
 V$CEBPGAMMA_Q6         |     7581 (+) |  0.752 |  0.800 | atcAGGTCaaaca
 V$CEBPGAMMA_Q6         |     7640 (+) |  0.845 |  0.895 | attATTTTaaaaa
 V$CEBPGAMMA_Q6         |     7814 (+) |  0.752 |  0.780 | acaACTCCaaaac
 V$CEBPGAMMA_Q6         |     7900 (-) |  0.845 |  0.908 | attttGATATtag
 V$CEBPGAMMA_Q6         |     7947 (-) |  0.845 |  0.798 | gttttGAGATacc
 V$CEBPGAMMA_Q6         |     8070 (+) |  0.845 |  0.812 | ggtATTGCagaaa
 V$CEBPGAMMA_Q6         |     8207 (-) |  0.752 |  0.809 | cctctGACCTcag
 V$CEBPGAMMA_Q6         |     8219 (-) |  0.752 |  0.804 | gttctGATGTtgg
 V$CEBPGAMMA_Q6         |     8636 (+) |  0.907 |  0.928 | cttATTTAagaag
 V$CEBPGAMMA_Q6         |     8852 (-) |  0.845 |  0.785 | gtttaAAAATtaa
 V$CEBPGAMMA_Q6         |     8881 (-) |  0.691 |  0.829 | attctAGAATcaa
 V$CEBPGAMMA_Q6         |     8948 (-) |  0.845 |  0.908 | tttttAAAATtag
 V$CEBPGAMMA_Q6         |     9028 (-) |  0.691 |  0.814 | tttgtGAGTTcaa
 V$CEBPGAMMA_Q6         |     9137 (-) |  0.752 |  0.860 | gttttTGAATaag
 V$CEBPGAMMA_Q6         |     9488 (-) |  0.845 |  0.814 | tatttGCAATaga
 V$CEBPGAMMA_Q6         |     9770 (+) |  0.752 |  0.782 | gtcATGCCataga
 V$CEBPGAMMA_Q6         |     9788 (-) |  0.660 |  0.799 | tttgtTCAGTaaa
 V$CEBPGAMMA_Q6         |     9815 (+) |  0.907 |  0.861 | gtaACTTCaaatt
 V$CEBPGAMMA_Q6         |     9822 (+) |  0.845 |  0.812 | caaATTTTagaag
 V$CEBPGAMMA_Q6         |     9837 (+) |  0.845 |  0.839 | ataATTTTaaagt
 V$CEBPGAMMA_Q6         |     9840 (-) |  0.752 |  0.875 | attttAAAGTcag
 V$CEBPGAMMA_Q6         |     9859 (+) |  0.814 |  0.790 | agcATTAAagaag
 V$CEBPGAMMA_Q6         |     9881 (+) |  0.691 |  0.826 | atcAATTTaaaat
 V$CEBPGAMMA_Q6         |     9882 (+) |  0.907 |  0.832 | tcaATTTAaaatt
 V$CEBPGAMMA_Q6         |    10130 (+) |  0.752 |  0.850 | attAGTTAagaaa
 V$CEBPGAMMA_Q6         |    10134 (-) |  1.000 |  0.830 | gttaaGAAATtat
 V$CEBPGAMMA_Q6         |    10305 (-) |  0.752 |  0.782 | tttttTAACTgtt
 V$CEBPGAMMA_Q6         |    10326 (+) |  0.845 |  0.837 | tttATTTTatagt
 V$CEBPGAMMA_Q6         |    10345 (-) |  0.752 |  0.803 | tgtttTAATTcaa
 V$CEBPGAMMA_Q6         |    10348 (+) |  0.845 |  0.859 | tttAATTCaaagt
 V$CEBPGAMMA_Q6         |    10388 (+) |  0.752 |  0.820 | tccATATAaaaat
 V$CEBPGAMMA_Q6         |    10450 (-) |  0.752 |  0.814 | tctttTATATcaa
 V$CEBPGAMMA_Q6         |    10471 (+) |  0.752 |  0.810 | ctcACTTTagacc
 V$CEBPGAMMA_Q6         |    10593 (+) |  0.845 |  0.875 | cctATATCaaaaa
 V$CEBPGAMMA_Q6         |    11110 (+) |  0.907 |  0.821 | acgACTTCagatc
 V$CEBPGAMMA_Q6         |    11142 (-) |  0.752 |  0.786 | gttttGTACTctg
 V$CEBPGAMMA_Q6         |    11389 (-) |  0.907 |  0.795 | cttatTAAATttt
 V$CEBPGAMMA_Q6         |    11648 (-) |  0.752 |  0.782 | tttctGTACTgtt
 V$CRX_Q4               |     2023 (-) |  1.000 |  0.977 | ctggGATTAaagg
 V$CRX_Q4               |     2723 (+) |  1.000 |  0.943 | tagaTAATCttct
 V$CRX_Q4               |     3903 (-) |  0.948 |  0.933 | caggTATTAataa
 V$CRX_Q4               |     4027 (-) |  0.955 |  0.926 | atggAATTAatat
 V$CRX_Q4               |     4159 (+) |  1.000 |  0.957 | tttgTAATCctag
 V$CRX_Q4               |     4274 (+) |  0.955 |  0.932 | taccTAAGCacac
 V$CRX_Q4               |     4799 (+) |  1.000 |  0.961 | tgcaTAATCtctg
 V$CRX_Q4               |     6611 (+) |  0.948 |  0.935 | ttgcTAAACtccg
 V$CRX_Q4               |     7399 (-) |  0.955 |  0.928 | gtagAATTActga
 V$CRX_Q4               |     8989 (+) |  0.955 |  0.940 | ccttTAATTccag
 V$CRX_Q4               |     9589 (+) |  1.000 |  0.973 | cctgTAATCccag
 V$CRX_Q4               |    10999 (-) |  1.000 |  0.943 | atcaGATTAcctg
 V$DBP_Q6               |      149 (-) |  1.000 |  0.974 | atTTGCT
 V$DBP_Q6               |     1047 (+) |  1.000 |  0.979 | AGCAAaa
 V$DBP_Q6               |     1475 (-) |  1.000 |  0.974 | atTTGCT
 V$DBP_Q6               |     2621 (-) |  0.985 |  0.987 | gtATGCT
 V$DBP_Q6               |     3208 (-) |  0.985 |  0.987 | gtATGCT
 V$DBP_Q6               |     4280 (+) |  0.985 |  0.987 | AGCACac
 V$DBP_Q6               |     4637 (+) |  1.000 |  0.979 | AGCAAaa
 V$DBP_Q6               |     4669 (-) |  1.000 |  0.979 | ttTTGCT
 V$DBP_Q6               |     4788 (-) |  1.000 |  0.968 | gaTTGCT
 V$DBP_Q6               |     5043 (-) |  1.000 |  0.968 | gaTTGCT
 V$DBP_Q6               |     5212 (-) |  0.985 |  0.966 | ttGTGCT
 V$DBP_Q6               |     6331 (+) |  0.985 |  0.987 | AGCACac
 V$DBP_Q6               |     6609 (-) |  1.000 |  0.974 | atTTGCT
 V$DBP_Q6               |     6831 (-) |  0.985 |  0.961 | atGTGCT
 V$DBP_Q6               |     7476 (-) |  0.985 |  0.987 | gtGTGCT
 V$DBP_Q6               |     8131 (-) |  0.965 |  0.969 | gtCTGCT
 V$DBP_Q6               |     8188 (-) |  1.000 |  1.000 | gtTTGCT
 V$DBP_Q6               |     8339 (-) |  1.000 |  0.974 | atTTGCT
 V$DBP_Q6               |     9000 (+) |  0.985 |  0.961 | AGCACat
 V$DBP_Q6               |     9108 (+) |  1.000 |  0.979 | AGCAAaa
 V$DBP_Q6               |    10281 (+) |  1.000 |  0.968 | AGCAAtc
 V$DBP_Q6               |    10574 (-) |  1.000 |  1.000 | gtTTGCT
 V$DBP_Q6               |    11530 (+) |  1.000 |  0.974 | AGCAAat
 V$EFC_Q6               |      206 (-) |  0.820 |  0.756 | catgcctgGTATTt
 V$EFC_Q6               |      477 (+) |  0.820 |  0.788 | aCTTACaagtcaac
 V$EFC_Q6               |     1653 (+) |  0.640 |  0.818 | aTCTACttggcaaa
 V$EFC_Q6               |     2621 (+) |  0.640 |  0.805 | gTATGCtaggcaaa
 V$EFC_Q6               |     3208 (+) |  0.640 |  0.755 | gTATGCtaggcaag
 V$EFC_Q6               |     3262 (-) |  0.820 |  0.774 | ttttcttgGTGATg
 V$EFC_Q6               |     3679 (-) |  0.730 |  0.754 | attgccaaGTGCCa
 V$EFC_Q6               |     4374 (+) |  0.719 |  0.803 | aGTTATctggctac
 V$EFC_Q6               |     4896 (+) |  0.820 |  0.790 | tGTTCCttggccaa
 V$EFC_Q6               |     5169 (-) |  0.910 |  0.788 | tttcacttGTGACt
 V$EFC_Q6               |     6940 (-) |  0.820 |  0.766 | gtacccaaGTGATa
 V$EFC_Q6               |     8063 (-) |  0.820 |  0.756 | tttatctgGTATTg
 V$EFC_Q6               |    10433 (+) |  0.640 |  0.792 | cTTCGCaatgcaac
 V$EFC_Q6               |    10434 (-) |  0.910 |  0.825 | ttcgcaatGCAACg
 V$EFC_Q6               |    10905 (+) |  0.820 |  0.892 | cGCTACtatgcaaa
 V$EFC_Q6               |    11184 (-) |  0.730 |  0.752 | gctgccttGTTTCt
 V$EFC_Q6               |    11482 (-) |  0.730 |  0.828 | tttcccttGGAATg
 I$EVE_Q6               |     1227 (+) |  0.982 |  0.921 | tgatgACTGC
 I$EVE_Q6               |     1244 (+) |  0.940 |  0.942 | tcaggGCAGC
 I$EVE_Q6               |     4182 (-) |  0.958 |  0.954 | GCTGAgcaga
 I$EVE_Q6               |     5918 (+) |  0.952 |  0.922 | tttccCCAGC
 I$EVE_Q6               |     6057 (+) |  0.994 |  0.930 | acagcCCTGC
 I$EVE_Q6               |     6548 (-) |  0.958 |  0.944 | GCTGAggtaa
 I$EVE_Q6               |     8189 (+) |  1.000 |  0.977 | tttgcTCTGC
 I$EVE_Q6               |     8308 (+) |  0.994 |  0.979 | tctgcCCTGC
 I$EVE_Q6               |     9091 (+) |  1.000 |  0.939 | gaagcTCTGC
 I$EVE_Q6               |    10882 (+) |  0.982 |  0.929 | ggagcACTGC
 I$EVE_Q6               |    11954 (+) |  0.982 |  0.970 | tcaggACTGC
 V$FOXM1_01             |      484 (-) |  1.000 |  0.882 | AGTCAacat
 V$FOXM1_01             |     1652 (-) |  0.957 |  0.908 | AATCTactt
 V$FOXM1_01             |     2586 (+) |  0.827 |  0.885 | aaatGCAGT
 V$FOXM1_01             |     2793 (+) |  0.827 |  0.879 | agctGGTCT
 V$FOXM1_01             |     2892 (-) |  0.827 |  0.909 | ACTGCatct
 V$FOXM1_01             |     3087 (-) |  0.935 |  0.942 | ATTCTattt
 V$FOXM1_01             |     3333 (-) |  0.935 |  0.942 | ATTCTattt
 V$FOXM1_01             |     3755 (-) |  1.000 |  0.909 | AGTCAttct
 V$FOXM1_01             |     3985 (-) |  0.827 |  0.909 | ACACCatct
 V$FOXM1_01             |     4890 (-) |  0.957 |  0.904 | ATTCCatgt
 V$FOXM1_01             |     5535 (+) |  0.827 |  0.909 | agatTCACT
 V$FOXM1_01             |     5852 (+) |  1.000 |  0.882 | atgtTGAGT
 V$FOXM1_01             |     6413 (+) |  1.000 |  0.909 | agaaTGACT
 V$FOXM1_01             |     7314 (+) |  0.935 |  0.893 | atatAGAAT
 V$FOXM1_01             |     9088 (-) |  0.827 |  0.879 | AGTGAagct
 V$FOXM1_01             |     9296 (+) |  0.827 |  0.879 | agctTGTGT
 V$FOXM1_01             |     9880 (-) |  0.978 |  0.964 | AATCAattt
 V$FOXM1_01             |    10386 (-) |  0.978 |  0.916 | AATCCatat
 V$FOXM1_01             |    10464 (-) |  0.805 |  0.898 | AATGCatct
 V$FOXM1_01             |    10602 (+) |  1.000 |  0.885 | aaaaGGAGT
 V$FOXM1_01             |    10681 (+) |  1.000 |  0.879 | agcaGGACT
 V$FOXM1_01             |    11107 (+) |  0.957 |  0.887 | agaaCGACT
 V$FOXM1_01             |    11238 (+) |  1.000 |  0.946 | aactGGAGT
 V$FOXM1_01             |    11368 (-) |  0.935 |  0.966 | ATTCTatct
 V$FOXM1_01             |    11662 (-) |  0.827 |  0.885 | ACACAattt
 V$FOXM1_01             |    11755 (+) |  0.978 |  0.898 | agaaAGAGT
 V$FXR_Q3               |      439 (-) |  0.871 |  0.842 | GTTTAatcaggttg
 V$FXR_Q3               |      842 (+) |  0.742 |  0.827 | caagttaaaTAAAT
 V$FXR_Q3               |     3412 (-) |  0.871 |  0.805 | AGTTAatgattctg
 V$FXR_Q3               |     3725 (-) |  0.897 |  0.795 | GGTGActaaaatta
 V$FXR_Q3               |     3882 (+) |  0.948 |  0.807 | caagctcctTGACC
 V$FXR_Q3               |     4463 (+) |  0.948 |  0.799 | cacactgacTGACC
 V$FXR_Q3               |     4714 (-) |  0.897 |  0.833 | GGTAAttcactgtg
 V$FXR_Q3               |     8615 (-) |  0.787 |  0.836 | CGTCAatcactttg
 V$FXR_Q3               |     8682 (+) |  0.713 |  0.820 | gaaggtaatTAGCC
 V$FXR_Q3               |     8685 (-) |  0.897 |  0.816 | GGTAAttagccttt
 V$FXR_Q3               |    10034 (-) |  0.735 |  0.822 | TGTGAgtcaccgtg
 V$FXR_Q3               |    11694 (-) |  0.871 |  0.804 | AGTTAatcactgtc
 V$GATA4_Q3             |      151 (-) |  0.845 |  0.841 | ttgctcaTCTCT
 V$GATA4_Q3             |      208 (-) |  0.907 |  0.918 | tgcctggTATTT
 V$GATA4_Q3             |     1040 (+) |  0.791 |  0.829 | ACAAAgcagcaa
 V$GATA4_Q3             |     1099 (+) |  0.814 |  0.842 | AAATTtgagaaa
 V$GATA4_Q3             |     1111 (-) |  0.791 |  0.854 | tcgctgaTTTGT
 V$GATA4_Q3             |     1882 (-) |  0.791 |  0.856 | tgcctccCATTT
 V$GATA4_Q3             |     2048 (-) |  0.791 |  0.842 | tacctggCTTCT
 V$GATA4_Q3             |     2052 (-) |  0.845 |  0.865 | tggcttcTCTCT
 V$GATA4_Q3             |     2184 (-) |  0.845 |  0.873 | tttcttcTCTCT
 V$GATA4_Q3             |     2271 (-) |  0.791 |  0.852 | tttctttCTTCT
 V$GATA4_Q3             |     2275 (-) |  0.907 |  0.904 | tttcttcTTTCT
 V$GATA4_Q3             |     2505 (+) |  0.814 |  0.906 | AAAAAaaaggga
 V$GATA4_Q3             |     2506 (+) |  0.814 |  0.834 | AAAAAaagggaa
 V$GATA4_Q3             |     2749 (-) |  0.845 |  0.879 | tttctttTCTCT
 V$GATA4_Q3             |     3183 (-) |  0.845 |  0.854 | tccccccTCTCT
 V$GATA4_Q3             |     3781 (-) |  0.814 |  0.838 | tccccccTTTTT
 V$GATA4_Q3             |     4150 (-) |  0.791 |  0.856 | tgcctccCATTT
 V$GATA4_Q3             |     4720 (-) |  0.814 |  0.881 | tcactgtGATTT
 V$GATA4_Q3             |     4806 (-) |  0.791 |  0.859 | tctctggCATTT
 V$GATA4_Q3             |     4930 (+) |  0.907 |  0.866 | AGATCatggaga
 V$GATA4_Q3             |     5045 (-) |  0.752 |  0.815 | ttgctgtGGTCT
 V$GATA4_Q3             |     5178 (-) |  0.814 |  0.864 | tgactgtGTTCT
 V$GATA4_Q3             |     5393 (-) |  0.907 |  0.855 | ttaccttTATAT
 V$GATA4_Q3             |     5475 (-) |  0.814 |  0.875 | ttcctgaTTTTT
 V$GATA4_Q3             |     5523 (-) |  0.769 |  0.837 | ttcctccTATCC
 V$GATA4_Q3             |     5650 (+) |  0.814 |  0.857 | AAAAAgaagaaa
 V$GATA4_Q3             |     5834 (+) |  0.715 |  0.821 | TGAAAcaaggca
 V$GATA4_Q3             |     6707 (+) |  0.845 |  0.871 | AGAGAaaagcca
 V$GATA4_Q3             |     6819 (-) |  0.814 |  0.827 | tctccctTTTTT
 V$GATA4_Q3             |     6821 (-) |  0.814 |  0.906 | tccctttTTTAT
 V$GATA4_Q3             |     7046 (-) |  0.814 |  0.841 | tgactatTTTTT
 V$GATA4_Q3             |     8377 (-) |  0.907 |  0.820 | gctctttGATCT
 V$GATA4_Q3             |     9023 (+) |  0.907 |  0.821 | AGATCtttgtga
 V$GATA4_Q3             |     9116 (+) |  0.814 |  0.828 | AAAAAaccggga
 V$GATA4_Q3             |     9117 (+) |  0.814 |  0.815 | AAAAAccgggaa
 V$GATA4_Q3             |     9430 (+) |  0.907 |  0.928 | AAATAacaggaa
 V$GATA4_Q3             |    10448 (-) |  0.907 |  0.936 | tctctttTATAT
 V$GATA4_Q3             |    11186 (-) |  0.907 |  0.918 | tgccttgTTTCT
 V$GATA4_Q3             |    11577 (-) |  0.769 |  0.818 | ttgcttaTATCC
 V$GATA4_Q3             |    11731 (-) |  0.884 |  0.817 | tctcaaaCATCT
 F$GBF_Q6               |      103 (+) |  1.000 |  0.914 | ctgGGGGTg
 F$GBF_Q6               |      971 (-) |  1.000 |  0.947 | gACCCCtaa
 F$GBF_Q6               |     1186 (-) |  1.000 |  0.914 | cACCCCcag
 F$GBF_Q6               |    11857 (+) |  1.000 |  0.914 | atgGGGGTa
 V$GCM_Q2               |     6803 (+) |  0.938 |  0.937 | cctcCCCTCatt
 V$GCM_Q2               |     8441 (+) |  1.000 |  0.952 | gcaaCCCGCatc
 V$GCM_Q2               |    11856 (-) |  0.922 |  0.941 | tatGGGGGtagg
 P$GT1_Q6               |       65 (-) |  0.888 |  0.923 | taATTAC
 P$GT1_Q6               |       82 (+) |  0.932 |  0.953 | GTTGAta
 P$GT1_Q6               |      551 (-) |  0.984 |  0.959 | ttTTAAC
 P$GT1_Q6               |      605 (-) |  0.932 |  0.924 | ttTAAAC
 P$GT1_Q6               |      636 (-) |  0.932 |  0.924 | ttTAAAC
 P$GT1_Q6               |      901 (-) |  1.000 |  0.971 | ttTTCAC
 P$GT1_Q6               |      962 (-) |  1.000 |  1.000 | taTTTAC
 P$GT1_Q6               |      988 (+) |  0.984 |  0.989 | GTTAAta
 P$GT1_Q6               |     1124 (-) |  0.922 |  0.946 | taTGCAC
 P$GT1_Q6               |     2576 (-) |  1.000 |  1.000 | taTTTAC
 P$GT1_Q6               |     2905 (-) |  0.948 |  0.964 | taTCCAC
 P$GT1_Q6               |     3450 (+) |  0.984 |  0.989 | GTTAAta
 P$GT1_Q6               |     3625 (+) |  0.932 |  0.953 | GTTTAta
 P$GT1_Q6               |     3717 (-) |  1.000 |  1.000 | taTTTAC
 P$GT1_Q6               |     3742 (-) |  0.948 |  0.935 | ttTCTAC
 P$GT1_Q6               |     3875 (+) |  0.984 |  0.989 | GTTAAta
 P$GT1_Q6               |     4125 (+) |  0.984 |  0.959 | GTTAAaa
 P$GT1_Q6               |     4218 (+) |  0.984 |  0.959 | GTTAAaa
 P$GT1_Q6               |     4368 (+) |  0.932 |  0.924 | GTTTAaa
 P$GT1_Q6               |     5697 (+) |  0.906 |  0.935 | GTTCAta
 P$GT1_Q6               |     5745 (-) |  0.928 |  0.950 | taTAGAC
 P$GT1_Q6               |     6022 (-) |  0.932 |  0.924 | ttTCAAC
 P$GT1_Q6               |     6762 (-) |  0.948 |  0.935 | ttTATAC
 P$GT1_Q6               |     6837 (-) |  1.000 |  1.000 | taTTTAC
 P$GT1_Q6               |     7346 (-) |  0.932 |  0.924 | ttTCAAC
 P$GT1_Q6               |     8494 (-) |  0.948 |  0.935 | ttTCTAC
 P$GT1_Q6               |     8686 (+) |  0.888 |  0.923 | GTAATta
 P$GT1_Q6               |     8852 (+) |  0.932 |  0.924 | GTTTAaa
 P$GT1_Q6               |     8931 (+) |  0.948 |  0.935 | GTATAaa
 P$GT1_Q6               |     8932 (-) |  0.932 |  0.953 | taTAAAC
 P$GT1_Q6               |     9712 (+) |  0.948 |  0.935 | GTGTAaa
 P$GT1_Q6               |     9741 (+) |  0.902 |  0.932 | GTCCAta
 P$GT1_Q6               |    10020 (-) |  0.928 |  0.950 | taTAGAC
 P$GT1_Q6               |    10307 (-) |  0.984 |  0.959 | ttTTAAC
 P$GT1_Q6               |    10419 (-) |  0.984 |  0.959 | ttTTAAC
 P$GT1_Q6               |    10457 (-) |  0.932 |  0.953 | taTCAAC
 P$GT1_Q6               |    10552 (-) |  0.922 |  0.946 | taTGTAC
 P$GT1_Q6               |    10626 (+) |  0.948 |  0.935 | GTAGAaa
 P$GT1_Q6               |    11093 (-) |  0.948 |  0.935 | ttTCCAC
 P$GT1_Q6               |    11101 (+) |  0.932 |  0.924 | GTTTAaa
 P$GT1_Q6               |    11509 (+) |  0.948 |  0.964 | GTGGAta
 P$GT1_Q6               |    11637 (+) |  0.932 |  0.924 | GTTTAaa
 P$GT1_Q6               |    11697 (-) |  0.888 |  0.923 | taATCAC
 V$HNF4ALPHA_Q6         |      417 (+) |  0.779 |  0.832 | gtgagCTTGTcca
 V$HNF4ALPHA_Q6         |      856 (+) |  0.869 |  0.855 | acgatCGTTGccc
 V$HNF4ALPHA_Q6         |      948 (-) |  0.869 |  0.835 | gaaCAATGatcaa
 V$HNF4ALPHA_Q6         |     1735 (+) |  0.769 |  0.840 | ctgaaCTTCCtat
 V$HNF4ALPHA_Q6         |     1952 (+) |  0.898 |  0.808 | tggaaCTTTCctt
 V$HNF4ALPHA_Q6         |     2657 (+) |  1.000 |  0.816 | atgcaCTTTGatg
 V$HNF4ALPHA_Q6         |     2923 (+) |  0.829 |  0.815 | cggacCCTTAgct
 V$HNF4ALPHA_Q6         |     3319 (+) |  0.923 |  0.807 | ttggcCTTTTcct
 V$HNF4ALPHA_Q6         |     3566 (+) |  1.000 |  0.843 | gtggcCTTTGgca
 V$HNF4ALPHA_Q6         |     3768 (-) |  0.869 |  0.840 | aggCAATGctcct
 V$HNF4ALPHA_Q6         |     4873 (-) |  1.000 |  0.881 | cagCAAAGctctg
 V$HNF4ALPHA_Q6         |     5452 (+) |  0.923 |  0.829 | ataacCTTTTccc
 V$HNF4ALPHA_Q6         |     6351 (-) |  0.898 |  0.858 | cacGAAAGctcag
 V$HNF4ALPHA_Q6         |     6469 (-) |  0.793 |  0.838 | ataAAATGctcag
 V$HNF4ALPHA_Q6         |     6521 (-) |  0.872 |  0.855 | acaCGAAGttcac
 V$HNF4ALPHA_Q6         |     7121 (-) |  0.869 |  0.884 | gtgCAATGctcaa
 V$HNF4ALPHA_Q6         |     7230 (-) |  0.769 |  0.807 | gcaGGAAGttcat
 V$HNF4ALPHA_Q6         |     7411 (+) |  0.923 |  0.884 | aagaaCTTTTaaa
 V$HNF4ALPHA_Q6         |     7694 (+) |  0.856 |  0.846 | cagaaCTTGGgag
 V$HNF4ALPHA_Q6         |     7713 (-) |  0.816 |  0.818 | gcaGAAGGatcag
 V$HNF4ALPHA_Q6         |     7868 (-) |  0.923 |  0.866 | tagAAAAGctcac
 V$HNF4ALPHA_Q6         |     7908 (+) |  0.923 |  0.805 | attagCTTTTact
 V$HNF4ALPHA_Q6         |     8040 (+) |  0.918 |  0.815 | ctgggCCTTGact
 V$HNF4ALPHA_Q6         |     8375 (+) |  1.000 |  0.808 | ctgctCTTTGatc
 V$HNF4ALPHA_Q6         |     8432 (+) |  1.000 |  0.896 | tagagCTTTGcaa
 V$HNF4ALPHA_Q6         |     9022 (+) |  1.000 |  0.861 | cagatCTTTGtga
 V$HNF4ALPHA_Q6         |     9204 (-) |  0.918 |  0.811 | cacCAAGGctcct
 V$HNF4ALPHA_Q6         |     9632 (-) |  0.766 |  0.848 | agtTCAAGgtcag
 V$HNF4ALPHA_Q6         |    10491 (-) |  0.918 |  0.855 | tatCAAGGatcaa
 V$HNF4ALPHA_Q6         |    10798 (+) |  0.918 |  0.874 | gtgagCCTTGtgc
 V$HNF4ALPHA_Q6         |    11172 (+) |  0.923 |  0.825 | gagatCTTTTtgg
 V$HNF4ALPHA_Q6         |    11375 (+) |  1.000 |  0.830 | ctgtgCTTTGaaa
 V$HNF4ALPHA_Q6         |    11945 (-) |  0.918 |  0.916 | tttCAAGGgtcag
 V$HNF6_Q6              |     3432 (-) |  1.000 |  0.945 | taATTGActtag
 V$HNF6_Q6              |     9877 (+) |  1.000 |  0.961 | ggaaaTCAATtt
 V$HNF6_Q6              |    10502 (+) |  1.000 |  0.951 | aaaagTCAATta
 V$LBP1_Q6              |     4959 (-) |  0.955 |  0.962 | gcAGCAG
 V$LBP1_Q6              |     7621 (-) |  0.970 |  0.954 | ccAGCCG
 V$LBP1_Q6              |     8278 (-) |  1.000 |  1.000 | gcAGCTG
 V$LBP1_Q6              |     8279 (+) |  1.000 |  1.000 | CAGCTgc
 V$LBP1_Q6              |     8372 (+) |  0.955 |  0.962 | CTGCTgc
 V$LBP1_Q6              |     8422 (-) |  1.000 |  1.000 | gcAGCTG
 V$LFA1_Q6              |     1605 (+) |  0.986 |  0.990 | GGGCTcag
 V$LFA1_Q6              |     5486 (-) |  0.972 |  0.962 | ttgATCCC
 V$LFA1_Q6              |     9237 (-) |  0.986 |  0.972 | cagAGCCC
 V$LFA1_Q6              |     9981 (+) |  0.972 |  0.980 | GGGATcag
 V$LFA1_Q6              |    11117 (-) |  0.972 |  0.962 | cagATCCC
 V$MAZ_Q6               |     1489 (+) |  1.000 |  0.970 | aGGGAGgg
 V$MAZ_Q6               |     1500 (+) |  1.000 |  1.000 | gGGGAGgg
 V$MAZ_Q6               |     1504 (+) |  1.000 |  0.970 | aGGGAGgg
 V$MAZ_Q6               |     1508 (+) |  1.000 |  0.970 | aGGGAGgg
 V$MAZ_Q6               |     1512 (+) |  1.000 |  0.970 | aGGGAGgg
 V$MAZ_Q6               |    11872 (+) |  1.000 |  1.000 | gGGGAGgg
 P$OCSBF1_01            |      436 (+) |  1.000 |  1.000 | CACGT
 P$OCSBF1_01            |      737 (+) |  1.000 |  1.000 | CACGT
 P$OCSBF1_01            |      738 (-) |  1.000 |  1.000 | ACGTG
 P$OCSBF1_01            |     1128 (+) |  1.000 |  1.000 | CACGT
 P$OCSBF1_01            |     1129 (-) |  1.000 |  1.000 | ACGTG
 P$OCSBF1_01            |     6006 (-) |  1.000 |  1.000 | ACGTG
 P$OCSBF1_01            |     6066 (+) |  1.000 |  1.000 | CACGT
 P$OCSBF1_01            |     6067 (-) |  1.000 |  1.000 | ACGTG
 P$OCSBF1_01            |     6858 (+) |  1.000 |  1.000 | CACGT
 P$OCSBF1_01            |     6888 (+) |  1.000 |  1.000 | CACGT
 P$OCSBF1_01            |     7488 (+) |  1.000 |  1.000 | CACGT
 V$PEA3_Q6              |      610 (+) |  1.000 |  1.000 | aCATCCt
 V$PEA3_Q6              |     1730 (+) |  1.000 |  0.934 | tCATCCt
 V$PEA3_Q6              |     1739 (+) |  1.000 |  1.000 | aCTTCCt
 V$PEA3_Q6              |     2147 (+) |  1.000 |  0.934 | tCTTCCt
 V$PEA3_Q6              |     2161 (+) |  1.000 |  0.934 | tCTTCCt
 V$PEA3_Q6              |     2205 (+) |  1.000 |  0.934 | tCTTCCt
 V$PEA3_Q6              |     2686 (+) |  1.000 |  0.934 | gCATCCt
 V$PEA3_Q6              |     2785 (+) |  1.000 |  0.934 | tCTTCCt
 V$PEA3_Q6              |     2989 (+) |  1.000 |  0.978 | aCTTCCg
 V$PEA3_Q6              |     3033 (+) |  1.000 |  0.978 | aCTTCCg
 V$PEA3_Q6              |     4266 (-) |  1.000 |  0.934 | aGGATGc
 V$PEA3_Q6              |     4964 (-) |  1.000 |  1.000 | aGGAAGt
 V$PEA3_Q6              |     5267 (+) |  1.000 |  0.934 | tCATCCt
 V$PEA3_Q6              |     6277 (-) |  1.000 |  0.934 | aGGAAGc
 V$PEA3_Q6              |     6480 (-) |  1.000 |  0.934 | aGGATGa
 V$PEA3_Q6              |     6799 (+) |  1.000 |  0.934 | tCTTCCt
 V$PEA3_Q6              |     6879 (-) |  1.000 |  0.934 | aGGAAGc
 V$PEA3_Q6              |     7014 (-) |  1.000 |  0.978 | cGGATGt
 V$PEA3_Q6              |     7232 (-) |  1.000 |  1.000 | aGGAAGt
 V$PEA3_Q6              |     8082 (+) |  1.000 |  1.000 | aCTTCCt
 V$PEA3_Q6              |     8448 (+) |  1.000 |  0.934 | gCATCCt
 V$PEA3_Q6              |     9437 (-) |  1.000 |  0.934 | aGGAAGc
 V$PEA3_Q6              |     9470 (-) |  1.000 |  1.000 | aGGATGt
 V$PEA3_Q6              |    10259 (-) |  1.000 |  1.000 | aGGAAGt
 V$PEA3_Q6              |    10640 (-) |  1.000 |  0.934 | aGGAAGa
 V$PEA3_Q6              |    10846 (-) |  1.000 |  0.934 | aGGAAGa
 V$PTF1BETA_Q6          |     8194 (-) |  1.000 |  0.930 | tctgcctgtTTCCC
 V$PTF1BETA_Q6          |     9504 (-) |  1.000 |  0.950 | tctgaaagtTTCCC
 V$PU1_Q6               |     2156 (-) |  1.000 |  1.000 | CTTCCtct
 V$PU1_Q6               |     2708 (-) |  1.000 |  1.000 | CTTCCtct
 V$PU1_Q6               |     2990 (-) |  1.000 |  0.963 | CTTCCgct
 V$PU1_Q6               |     3034 (-) |  1.000 |  0.963 | CTTCCgct
 V$PU1_Q6               |     3779 (-) |  1.000 |  0.931 | CTTCCccc
 V$PU1_Q6               |     6800 (-) |  1.000 |  0.962 | CTTCCtcc
 V$PU1_Q6               |     9435 (+) |  1.000 |  0.926 | acaGGAAG
 V$PU1_Q6               |    10207 (-) |  1.000 |  0.937 | CTTCCaca
 V$PU1_Q6               |    10638 (+) |  1.000 |  0.984 | tgaGGAAG
 P$RITA1_01             |      736 (+) |  1.000 |  0.997 | cCACGTg
 P$RITA1_01             |      737 (-) |  1.000 |  0.997 | cACGTGg
 P$RITA1_01             |     1128 (-) |  1.000 |  0.984 | cACGTGt
 P$RITA1_01             |     6887 (+) |  1.000 |  0.987 | cCACGTa
 I$SGF3_Q6              |       10 (-) |  0.950 |  0.966 | tGTACAa
 I$SGF3_Q6              |       34 (-) |  0.976 |  0.984 | tGAACAa
 I$SGF3_Q6              |      275 (+) |  0.976 |  0.984 | tTGTGCa
 I$SGF3_Q6              |      423 (+) |  0.937 |  0.957 | tTGTCCa
 I$SGF3_Q6              |      645 (+) |  1.000 |  1.000 | tTATTCa
 I$SGF3_Q6              |      876 (-) |  0.976 |  0.984 | tGCACAa
 I$SGF3_Q6              |     1123 (+) |  1.000 |  0.945 | gTATGCa
 I$SGF3_Q6              |     2904 (+) |  0.961 |  0.973 | tTATCCa
 I$SGF3_Q6              |     3581 (+) |  1.000 |  1.000 | tTATTCa
 I$SGF3_Q6              |     3943 (+) |  0.976 |  0.984 | tTGTTCa
 I$SGF3_Q6              |     4171 (+) |  1.000 |  0.945 | gTATTCa
 I$SGF3_Q6              |     4315 (-) |  1.000 |  1.000 | tGCATAa
 I$SGF3_Q6              |     4490 (-) |  0.976 |  0.984 | tGAACAa
 I$SGF3_Q6              |     4780 (-) |  0.961 |  0.973 | tGGATAa
 I$SGF3_Q6              |     4799 (-) |  1.000 |  1.000 | tGCATAa
 I$SGF3_Q6              |     6576 (+) |  1.000 |  1.000 | tTATGCa
 I$SGF3_Q6              |     6771 (-) |  0.976 |  0.984 | tGAACAa
 I$SGF3_Q6              |     7212 (-) |  0.976 |  0.984 | tGAACAa
 I$SGF3_Q6              |     8556 (-) |  0.976 |  0.984 | tGAACAa
 I$SGF3_Q6              |     9142 (-) |  1.000 |  1.000 | tGAATAa
 I$SGF3_Q6              |     9789 (+) |  0.976 |  0.984 | tTGTTCa
 I$SGF3_Q6              |    10253 (+) |  0.976 |  0.984 | tTGTGCa
 I$SGF3_Q6              |    10805 (+) |  0.976 |  0.984 | tTGTGCa
 I$SGF3_Q6              |    11555 (+) |  1.000 |  0.945 | gTATTCa
 F$STE12_Q4             |     3995 (+) |  1.000 |  1.000 | aTGAAAc
 F$STE12_Q4             |    10708 (+) |  1.000 |  1.000 | aTGAAAc
 F$STE12_Q4             |    10745 (-) |  1.000 |  0.980 | gTTTCAg
 F$STE12_Q4             |    11936 (+) |  1.000 |  0.980 | cTGAAAc
 V$SP3_Q3               |      163 (-) |  0.728 |  0.867 | cCGTTCccaatgct
 V$SP3_Q3               |     1172 (+) |  0.906 |  0.800 | agaaaggaGATGGg
 V$SP3_Q3               |     1330 (-) |  0.765 |  0.880 | cACTCCccagggct
 V$SP3_Q3               |     1487 (+) |  0.981 |  0.810 | agagggagGGGGGg
 V$SP3_Q3               |     1489 (+) |  0.981 |  0.844 | agggagggGGGGGg
 V$SP3_Q3               |     1638 (-) |  0.775 |  0.797 | cCTTTCctagtgct
 V$SP3_Q3               |     1794 (-) |  0.728 |  0.801 | cCATTCacaggatt
 V$SP3_Q3               |     2341 (-) |  0.944 |  0.825 | cCCTACgctcttct
 V$SP3_Q3               |     3246 (-) |  0.925 |  0.891 | cCCAGCccacttat
 V$SP3_Q3               |     3778 (-) |  0.812 |  0.810 | cCTTCCcccctttt
 V$SP3_Q3               |     5020 (+) |  0.690 |  0.801 | agccacggGACTGg
 V$SP3_Q3               |     5427 (-) |  1.000 |  0.836 | cCCTCCactttatt
 V$SP3_Q3               |     5462 (-) |  0.925 |  0.790 | cCCCACatactatt
 V$SP3_Q3               |     5492 (-) |  0.962 |  0.897 | cCCTTCcctctgct
 V$SP3_Q3               |     5898 (-) |  0.746 |  0.823 | cCGCCCctaagagt
 V$SP3_Q3               |     6294 (+) |  0.981 |  0.840 | atgactgaGCAGGg
 V$SP3_Q3               |     6960 (+) |  0.765 |  0.795 | attattctGGATGg
 V$SP3_Q3               |     9003 (+) |  0.981 |  0.803 | acatggagGCAGGg
 V$SP3_Q3               |     9674 (+) |  1.000 |  0.815 | aaagaagtGGAGGg
 V$SP3_Q3               |    10608 (+) |  1.000 |  0.840 | agtgtgtgGGAGGg
 V$SP3_Q3               |    10870 (+) |  0.944 |  0.862 | agcgtggtGGTGGg
 V$SP3_Q3               |    11718 (-) |  1.000 |  0.883 | cCCTCCaccatttt
 V$SP3_Q3               |    11819 (+) |  0.709 |  0.809 | agggttggGGTGAg
 V$SP3_Q3               |    11837 (+) |  0.981 |  0.875 | agcagagtGGGGGg
 V$SP3_Q3               |    11840 (+) |  0.746 |  0.808 | agagtgggGGGTGg
 V$SP3_Q3               |    11842 (+) |  0.925 |  0.839 | agtgggggGTGGGg
 I$SRYBETA_Q6           |      154 (+) |  0.905 |  0.948 | CTCATctct
 I$SRYBETA_Q6           |     5069 (-) |  0.905 |  0.948 | agagATGAG
 V$TCF4_Q5              |     1167 (-) |  1.000 |  0.975 | ttCAAAGa
 V$TCF4_Q5              |     2661 (+) |  1.000 |  0.975 | aCTTTGat
 V$TCF4_Q5              |     6741 (+) |  1.000 |  1.000 | cCTTTGaa
 V$TCF4_Q5              |    10353 (-) |  1.000 |  0.983 | ttCAAAGt
 V$TCF4_Q5              |    11379 (+) |  1.000 |  0.992 | gCTTTGaa
 V$TEF_Q6               |      633 (-) |  0.821 |  0.913 | TTTTTtaaacat
 V$TEF_Q6               |     1255 (-) |  0.836 |  0.877 | TTCTGtcatcat
 V$TEF_Q6               |     1899 (-) |  0.985 |  0.904 | TTATTttattat
 V$TEF_Q6               |     3739 (-) |  0.985 |  0.918 | TTATTtctacat
 V$TEF_Q6               |     4269 (+) |  0.836 |  0.901 | atgcttaCCTAA
 V$TEF_Q6               |     7270 (+) |  0.985 |  0.894 | atcctaaAATAA
 V$TEF_Q6               |    10454 (-) |  1.000 |  0.926 | TTATAtcaacaa
 V$TEF_Q6               |    11656 (+) |  0.877 |  0.861 | ctgttaaCACAA
 V$TEL2_Q6              |     2569 (-) |  0.800 |  0.824 | ccgTAAGTat
 V$TEL2_Q6              |     2987 (+) |  1.000 |  0.830 | ctACTTCcgc
 V$TEL2_Q6              |     4963 (-) |  1.000 |  0.937 | cagGAAGTca
 V$TEL2_Q6              |     5060 (-) |  0.800 |  0.830 | cagGTAGTga
 V$TEL2_Q6              |     5471 (+) |  0.800 |  0.877 | ctATTTCctg
 V$TEL2_Q6              |     6459 (+) |  0.800 |  0.877 | ttATTTCctg
 V$TEL2_Q6              |     7231 (-) |  1.000 |  0.925 | cagGAAGTtc
 V$TEL2_Q6              |     9908 (+) |  0.800 |  0.877 | ttACTTActg
 V$TEL2_Q6              |    10258 (-) |  1.000 |  0.953 | cagGAAGTga
 V$TEL2_Q6              |    10845 (-) |  0.800 |  0.877 | cagGAAGAag
 P$WRKY_Q2              |      130 (+) |  1.000 |  0.857 | ctgctcAGTCA
 P$WRKY_Q2              |     1075 (+) |  0.973 |  0.787 | tgtgtaGGTCA
 P$WRKY_Q2              |     1084 (+) |  0.973 |  0.787 | cattttGGTCA
 P$WRKY_Q2              |     1252 (+) |  0.919 |  0.809 | gcattcTGTCA
 P$WRKY_Q2              |     1351 (+) |  0.973 |  0.798 | tgcctgGGTCA
 P$WRKY_Q2              |     3069 (+) |  0.973 |  0.780 | tagctaGGTCA
 P$WRKY_Q2              |     3436 (-) |  1.000 |  0.794 | TGACTtaggta
 P$WRKY_Q2              |     3727 (-) |  1.000 |  0.784 | TGACTaaaatt
 P$WRKY_Q2              |     3749 (+) |  1.000 |  0.857 | atttttAGTCA
 P$WRKY_Q2              |     3931 (+) |  1.000 |  0.827 | attatcAGTCA
 P$WRKY_Q2              |     3947 (+) |  0.900 |  0.872 | tcattcAGCCA
 P$WRKY_Q2              |     4468 (-) |  1.000 |  0.827 | TGACTgaccag
 P$WRKY_Q2              |     5359 (-) |  0.919 |  0.794 | TGACAaaacac
 P$WRKY_Q2              |     6295 (-) |  1.000 |  0.857 | TGACTgagcag
 P$WRKY_Q2              |     6324 (-) |  1.000 |  0.872 | TGACTgaagca
 P$WRKY_Q2              |     6431 (+) |  0.973 |  0.868 | ttcatcGGTCA
 P$WRKY_Q2              |     8320 (+) |  0.919 |  0.787 | cttctgCGTCA
 P$WRKY_Q2              |     8609 (+) |  0.919 |  0.882 | tcattcCGTCA
 P$WRKY_Q2              |    10032 (+) |  1.000 |  0.856 | tttgtgAGTCA
 P$WRKY_Q2              |    10634 (-) |  1.000 |  0.912 | TGACTgaggaa
 P$WRKY_Q2              |    11333 (-) |  0.919 |  0.783 | TGACGatgtaa
 F$XBP1_Q2              |     8051 (-) |  1.000 |  0.984 | CTCGAgg
 F$XBP1_Q2              |     8825 (-) |  1.000 |  0.984 | CTCGAtg
 V$XPF1_Q6              |      679 (-) |  1.000 |  0.934 | gctctTCAGA
 V$XPF1_Q6              |     1357 (-) |  0.958 |  0.945 | ggtcaCCTGA
 V$XPF1_Q6              |     3349 (-) |  1.000 |  0.990 | gttcaTCAGA
 V$XPF1_Q6              |     6111 (-) |  0.958 |  0.945 | gttgaCCAGA
 V$XPF1_Q6              |     8719 (+) |  1.000 |  1.000 | TCTGAagaac
 V$XPF1_Q6              |     9162 (-) |  0.842 |  0.918 | gttccTAAGA
 V$ALPHACP1_01          |      110 (+) |  0.800 |  0.791 | tggCCAGTgag
 V$ALPHACP1_01          |     1021 (-) |  1.000 |  0.761 | gtgATTGGcag
 V$ALPHACP1_01          |     1209 (-) |  0.800 |  0.746 | cccATTGCttg
 V$ALPHACP1_01          |     1426 (+) |  0.800 |  0.795 | cacGCAATcag
 V$ALPHACP1_01          |     1832 (+) |  0.800 |  0.739 | cacCCATTggg
 V$ALPHACP1_01          |     1834 (-) |  1.000 |  0.767 | cccATTGGggt
 V$ALPHACP1_01          |     2445 (-) |  0.800 |  0.791 | ctcAGTGGtag
 V$ALPHACP1_01          |     3479 (+) |  0.800 |  0.818 | ctgCCTATgag
 V$ALPHACP1_01          |     4527 (+) |  0.800 |  0.746 | caaCAAATgcg
 V$ALPHACP1_01          |     5011 (+) |  0.800 |  0.756 | tacCCATTaag
 V$ALPHACP1_01          |     5087 (-) |  0.800 |  0.774 | ctgACTGGttt
 V$ALPHACP1_01          |     5664 (+) |  0.800 |  0.756 | aacACAATaag
 V$ALPHACP1_01          |     6590 (+) |  0.800 |  0.763 | aaaCAAATaag
 V$ALPHACP1_01          |     9256 (-) |  0.800 |  0.763 | ctcATGGGaca
 V$ALPHACP1_01          |     9911 (-) |  0.800 |  0.763 | cttACTGGatt
 V$ALPHACP1_01          |    11177 (-) |  0.800 |  0.818 | cttTTTGGctg
 V$ALPHACP1_01          |    11743 (+) |  0.800 |  0.739 | cacCAAATgac
 V$ALPHACP1_01          |    11928 (-) |  1.000 |  0.887 | cccATTGGctg
 N$UNC86_Q2             |     3829 (+) |  0.907 |  0.920 | cataaTAAAT
 N$UNC86_Q2             |     5303 (+) |  0.969 |  0.936 | catccAAAAT
 V$AP3_Q6               |     1468 (+) |  0.978 |  0.943 | tCTCAAta
 V$AP3_Q6               |     1665 (-) |  0.927 |  0.942 | aaTGGAGa
 V$AP3_Q6               |     3744 (+) |  0.949 |  0.959 | tCTACAtt
 V$AP3_Q6               |     4294 (+) |  1.000 |  0.961 | cCTAAAtt
 V$AP3_Q6               |     7059 (+) |  0.934 |  0.947 | tCTTAAtt
 V$AP3_Q6               |     8859 (-) |  0.934 |  0.947 | aaTTAAGa
 V$AP3_Q6               |     9825 (-) |  1.000 |  0.931 | atTTTAGa
 V$AP3_Q6               |    10474 (-) |  1.000 |  0.941 | acTTTAGa
 V$AP3_Q6               |    10545 (+) |  1.000 |  0.941 | tCTAAAgt
 V$AP3_Q6               |    10812 (+) |  1.000 |  0.941 | tCTAAAtc
 V$ATF1_Q6              |     1239 (-) |  0.820 |  0.886 | tGACATcaggg
 V$ATF1_Q6              |     2963 (+) |  0.902 |  0.910 | cagtgACGGCa
 V$E12_Q6               |     1392 (+) |  1.000 |  0.985 | ggCAGGTgagg
 V$E12_Q6               |     1785 (-) |  1.000 |  0.983 | gagcACCTGcc
 V$E12_Q6               |     8504 (+) |  1.000 |  0.977 | gaCAGGTgcgg
 V$ETF_Q6               |     5898 (-) |  1.000 |  0.996 | CCGCCcc
 I$EN_Q6                |     3432 (-) |  1.000 |  0.987 | TAATTga
 I$EN_Q6                |    10507 (+) |  1.000 |  0.987 | tcAATTA
 V$HEB_Q6               |     8370 (+) |  0.976 |  0.984 | gCCTGCtg
 V$ICSBP_Q6             |     5120 (+) |  1.000 |  0.886 | aaaagGAAACag
 V$ICSBP_Q6             |    11158 (+) |  0.783 |  0.874 | aaaatGAAGCtg
 P$ROM_Q2               |     9614 (-) |  1.000 |  0.948 | tgAGGTGgg
 V$SMAD3_Q6             |      893 (-) |  1.000 |  0.902 | ggaCAGACt
 V$SMAD3_Q6             |     2081 (+) |  1.000 |  1.000 | tGTCTGtct
 V$SMAD3_Q6             |     2944 (+) |  1.000 |  0.945 | aGTCTGcct
 V$SMAD3_Q6             |     3232 (-) |  0.910 |  0.922 | agtCAGCCa
 V$SMAD3_Q6             |     3356 (-) |  1.000 |  0.954 | agaCAGACc
 V$SMAD3_Q6             |     5675 (-) |  1.000 |  1.000 | agaCAGACa
 V$SMAD3_Q6             |     6237 (+) |  1.000 |  0.972 | tGTCTGgct
 V$SMAD3_Q6             |     8563 (+) |  0.847 |  0.896 | tGTCCGtct
 V$SMAD3_Q6             |     9847 (-) |  0.874 |  0.898 | agtCAGGCa
 V$SMAD3_Q6             |     9851 (-) |  0.874 |  0.898 | aggCAGGCa
 V$SMAD3_Q6             |    11182 (+) |  0.910 |  0.922 | tGGCTGcct
 P$SPF1_Q2              |      828 (-) |  1.000 |  0.949 | aatACTATat
 P$SPF1_Q2              |     5467 (-) |  1.000 |  0.949 | catACTATtt
 P$SPF1_Q2              |     7045 (-) |  1.000 |  0.945 | ttgACTATtt
 V$TEF1_Q6              |      410 (+) |  1.000 |  1.000 | GGAATg
 V$TEF1_Q6              |     1575 (+) |  1.000 |  1.000 | GGAATg
 V$TEF1_Q6              |     2848 (-) |  1.000 |  1.000 | cATTCC
 V$TEF1_Q6              |     3136 (-) |  1.000 |  1.000 | cATTCC
 V$TEF1_Q6              |     3163 (-) |  1.000 |  1.000 | cATTCC
 V$TEF1_Q6              |     3242 (-) |  1.000 |  1.000 | cATTCC
 V$TEF1_Q6              |     4889 (-) |  1.000 |  1.000 | cATTCC
 V$TEF1_Q6              |     8610 (-) |  1.000 |  1.000 | cATTCC
 V$TEF1_Q6              |     9396 (+) |  1.000 |  1.000 | GGAATg
 V$TEF1_Q6              |    11490 (+) |  1.000 |  1.000 | GGAATg
 V$TFIII_Q6             |     1316 (-) |  0.873 |  0.913 | CCTAActcc
 V$TFIII_Q6             |     1384 (+) |  0.973 |  0.965 | cgagGTAGG
 V$TFIII_Q6             |     1487 (+) |  1.000 |  1.000 | agagGGAGG
 V$TFIII_Q6             |     1498 (+) |  1.000 |  0.932 | ggggGGAGG
 V$TFIII_Q6             |     1502 (+) |  1.000 |  1.000 | ggagGGAGG
 V$TFIII_Q6             |     1506 (+) |  1.000 |  1.000 | ggagGGAGG
 V$TFIII_Q6             |     1510 (+) |  1.000 |  1.000 | ggagGGAGG
 V$TFIII_Q6             |     1514 (+) |  1.000 |  1.000 | ggagGGAGG
 V$TFIII_Q6             |     1675 (-) |  1.000 |  0.949 | CCTCCttcg
 V$TFIII_Q6             |     2155 (-) |  0.919 |  0.945 | CCTTCctct
 V$TFIII_Q6             |     2707 (-) |  0.919 |  0.945 | CCTTCctct
 V$TFIII_Q6             |     4349 (+) |  0.919 |  0.945 | ggagGCAGG
 V$TFIII_Q6             |     4860 (+) |  1.000 |  0.991 | tgagGGAGG
 V$TFIII_Q6             |     6159 (-) |  0.919 |  0.945 | CCTGCctcc
 V$TFIII_Q6             |     7023 (-) |  0.919 |  0.914 | CCTGCatca
 V$TFIII_Q6             |     8165 (+) |  0.919 |  0.945 | agagGCAGG
 V$TFIII_Q6             |     8243 (+) |  0.919 |  0.923 | agatGAAGG
 V$TFIII_Q6             |     9007 (+) |  0.919 |  0.945 | ggagGCAGG
 V$TFIII_Q6             |     9310 (+) |  1.000 |  1.000 | ggagGGAGG
 V$TFIII_Q6             |    11859 (+) |  0.973 |  0.913 | ggggGTAGG
 V$TFIII_Q6             |    11870 (+) |  1.000 |  0.915 | cgggGGAGG
 V$TFIIA_Q6             |     3513 (+) |  0.961 |  0.889 | tgttaGAGGAgg
 V$TFIIA_Q6             |     5932 (-) |  0.961 |  0.901 | ctCCCTTggaga
 I$ZEN_Q6               |       23 (-) |  1.000 |  0.960 | gtgAATGT
 I$ZEN_Q6               |      641 (+) |  1.000 |  0.928 | ACATTtat
 I$ZEN_Q6               |      649 (+) |  0.981 |  0.914 | TCATTtat
 I$ZEN_Q6               |      985 (+) |  0.888 |  0.913 | ACAGTtaa
 I$ZEN_Q6               |     3413 (-) |  0.981 |  0.971 | gttAATGA
 I$ZEN_Q6               |     3431 (-) |  0.869 |  0.899 | ttaATTGA
 I$ZEN_Q6               |     3447 (+) |  0.888 |  0.913 | ACAGTtaa
 I$ZEN_Q6               |     3655 (+) |  0.869 |  0.899 | TCAGTaaa
 I$ZEN_Q6               |     3864 (+) |  0.907 |  0.928 | CCATTtaa
 I$ZEN_Q6               |     4092 (-) |  0.869 |  0.899 | tttACTGA
 I$ZEN_Q6               |     4215 (+) |  0.869 |  0.899 | TCAGTtaa
 I$ZEN_Q6               |     4446 (+) |  0.888 |  0.913 | ACAATtaa
 I$ZEN_Q6               |     4457 (+) |  0.981 |  0.898 | TCATTtca
 I$ZEN_Q6               |     5724 (+) |  0.869 |  0.899 | ACACTaaa
 I$ZEN_Q6               |     6193 (+) |  0.907 |  0.928 | CCATTtaa
 I$ZEN_Q6               |     7260 (+) |  0.981 |  0.986 | TCATTaaa
 I$ZEN_Q6               |     7343 (+) |  1.000 |  0.912 | ACATTtca
 I$ZEN_Q6               |     7829 (+) |  0.888 |  0.913 | ACAATtaa
 I$ZEN_Q6               |     8576 (-) |  0.907 |  0.928 | ttaAATGG
 I$ZEN_Q6               |     9793 (+) |  0.869 |  0.899 | TCAGTaaa
 I$ZEN_Q6               |     9796 (-) |  1.000 |  0.986 | gtaAATGT
 I$ZEN_Q6               |     9860 (+) |  0.907 |  0.928 | GCATTaaa
 I$ZEN_Q6               |    10309 (-) |  0.888 |  0.913 | ttaACTGT
 I$ZEN_Q6               |    10340 (-) |  0.888 |  0.913 | tttATTGT
 I$ZEN_Q6               |    11340 (-) |  0.907 |  0.914 | gtaAATGC
 I$ZEN_Q6               |    11639 (-) |  1.000 |  1.000 | ttaAATGT
 V$ZTA_Q2               |    10036 (-) |  1.000 |  0.985 | TGAGTcaccgtgt
 V$MYOGENIN_Q6          |     1027 (+) |  0.973 |  0.981 | ggCAGTTg
 V$MYOGENIN_Q6          |     1392 (+) |  1.000 |  1.000 | ggCAGGTg
 V$MYOGENIN_Q6          |     1788 (-) |  1.000 |  1.000 | cACCTGcc
 V$MYOGENIN_Q6          |     2970 (+) |  0.964 |  0.974 | ggCAGATg
 V$MYOGENIN_Q6          |     6264 (-) |  0.964 |  0.974 | cATCTGcc
 V$MYOGENIN_Q6          |     8279 (-) |  1.000 |  1.000 | cAGCTGcc
 V$MYOGENIN_Q6          |     8421 (+) |  1.000 |  0.989 | agCAGCTg
 V$MYOGENIN_Q6          |     8423 (-) |  1.000 |  0.971 | cAGCTGtt
 V$MYOGENIN_Q6          |     8504 (+) |  1.000 |  0.982 | gaCAGGTg
 V$MYOGENIN_Q6          |     8969 (+) |  1.000 |  0.971 | acCAGGTg
 V$MYOGENIN_Q6          |    11712 (-) |  0.973 |  0.981 | cAACTGcc
 F$TBP_Q6               |      500 (+) |  1.000 |  0.934 | ttaTTATAt
 F$TBP_Q6               |      653 (+) |  1.000 |  0.934 | ttaTTATAt
 F$TBP_Q6               |      658 (-) |  0.903 |  0.906 | aTATATaag
 F$TBP_Q6               |      660 (-) |  1.000 |  0.963 | aTATAAgta
 F$TBP_Q6               |      834 (-) |  1.000 |  0.971 | aTATAAaac
 F$TBP_Q6               |     1890 (+) |  1.000 |  0.961 | attTTATAt
 F$TBP_Q6               |     3405 (-) |  1.000 |  0.935 | tTATAAaag
 F$TBP_Q6               |     3624 (+) |  1.000 |  0.931 | cgtTTATAa
 F$TBP_Q6               |     5396 (+) |  1.000 |  0.986 | cctTTATAt
 F$TBP_Q6               |     6760 (+) |  1.000 |  0.930 | cctTTATAc
 F$TBP_Q6               |    10316 (+) |  1.000 |  0.999 | tttTTATAt
 F$TBP_Q6               |    10329 (+) |  1.000 |  0.917 | attTTATAg
 F$TBP_Q6               |    10391 (-) |  1.000 |  0.999 | aTATAAaaa
 F$TBP_Q6               |    10451 (+) |  1.000 |  0.987 | cttTTATAt
 F$TBP_Q6               |    11578 (+) |  1.000 |  0.958 | tgcTTATAt
 V$ZF5_01               |      105 (+) |  0.844 |  0.759 | GGGGGtgg
 V$ZF5_01               |      163 (-) |  0.694 |  0.796 | ccgTTCCC
 V$ZF5_01               |      728 (+) |  0.799 |  0.781 | GTGAGcca
 V$ZF5_01               |     1379 (+) |  0.799 |  0.855 | GTGGGcga
 V$ZF5_01               |     1381 (+) |  1.000 |  0.852 | GGGCGagg
 V$ZF5_01               |     1585 (+) |  0.805 |  0.785 | GAGAGcca
 V$ZF5_01               |     1603 (-) |  0.783 |  0.770 | tggGGCTC
 V$ZF5_01               |     1605 (+) |  0.822 |  0.808 | GGGCTcag
 V$ZF5_01               |     1724 (-) |  0.783 |  0.856 | ccgGGCTC
 V$ZF5_01               |     1783 (-) |  0.777 |  0.766 | tggAGCAC
 V$ZF5_01               |     2018 (+) |  0.792 |  0.788 | GAGTGctg
 V$ZF5_01               |     2343 (-) |  0.961 |  0.762 | ctaCGCTC
 V$ZF5_01               |     2470 (+) |  0.671 |  0.770 | AAGCGcga
 V$ZF5_01               |     2472 (+) |  1.000 |  0.777 | GCGCGaag
 V$ZF5_01               |     2485 (+) |  0.653 |  0.770 | GGGTTcgg
 V$ZF5_01               |     2816 (-) |  0.811 |  0.874 | ccgTGCTC
 V$ZF5_01               |     2818 (+) |  0.777 |  0.777 | GTGCTctg
 V$ZF5_01               |     2918 (+) |  0.648 |  0.766 | GTGGAcgg
 V$ZF5_01               |     3006 (+) |  0.955 |  0.896 | GTGCGcag
 V$ZF5_01               |     3059 (+) |  0.844 |  0.759 | GCGAGtgg
 V$ZF5_01               |     3248 (-) |  0.799 |  0.792 | cagCCCAC
 V$ZF5_01               |     3384 (-) |  0.822 |  0.796 | tggGGCCC
 V$ZF5_01               |     3386 (+) |  0.822 |  0.808 | GGGCCctg
 V$ZF5_01               |     3963 (-) |  0.777 |  0.777 | ctgAGCAC
 V$ZF5_01               |     3965 (+) |  0.811 |  0.800 | GAGCActg
 V$ZF5_01               |     4019 (-) |  0.805 |  0.796 | ctgCTCTC
 V$ZF5_01               |     4597 (-) |  0.844 |  0.822 | ctgCCCGC
 V$ZF5_01               |     4601 (-) |  0.623 |  0.750 | ccgCTTGC
 V$ZF5_01               |     4731 (-) |  0.805 |  0.785 | tggCCCTC
 V$ZF5_01               |     4834 (+) |  0.694 |  0.785 | GGGAAcga
 V$ZF5_01               |     5114 (+) |  0.777 |  0.766 | GTGCTcaa
 V$ZF5_01               |     5222 (+) |  0.961 |  0.752 | GAGCGgag
 V$ZF5_01               |     5233 (+) |  0.694 |  0.785 | GGGAAcga
 V$ZF5_01               |     5329 (-) |  0.850 |  0.826 | cagTGCGC
 V$ZF5_01               |     5331 (+) |  0.955 |  0.896 | GTGCGccg
 V$ZF5_01               |     5501 (-) |  0.844 |  0.822 | ctgCTCCC
 V$ZF5_01               |     5887 (+) |  0.850 |  0.762 | GGGCAtgg
 V$ZF5_01               |     5892 (-) |  0.822 |  0.796 | tggGGCCC
 V$ZF5_01               |     5894 (+) |  0.822 |  0.769 | GGGCCcgc
 V$ZF5_01               |     6152 (-) |  0.805 |  0.785 | tggCTCTC
 V$ZF5_01               |     6222 (-) |  0.961 |  0.825 | tcaCGCTC
 V$ZF5_01               |     6303 (-) |  0.777 |  0.777 | cagGGCAC
 V$ZF5_01               |     6305 (+) |  0.850 |  0.826 | GGGCActg
 V$ZF5_01               |     6628 (-) |  0.777 |  0.766 | tggGGCAC
 V$ZF5_01               |     6693 (+) |  0.792 |  0.788 | GAGTGctg
 V$ZF5_01               |     6732 (+) |  0.799 |  0.792 | GTGAGcag
 V$ZF5_01               |     6855 (+) |  0.811 |  0.761 | GAGCAcgt
 V$ZF5_01               |     7009 (+) |  0.623 |  0.750 | GCAGGcgg
 V$ZF5_01               |     7091 (-) |  1.000 |  0.915 | ttgCGCGC
 V$ZF5_01               |     7093 (+) |  1.000 |  0.813 | GCGCGcac
 V$ZF5_01               |     7093 (-) |  0.955 |  0.857 | gcgCGCAC
 V$ZF5_01               |     7119 (+) |  0.786 |  0.772 | GTGTGcaa
 V$ZF5_01               |     7145 (+) |  0.805 |  0.758 | GAGGGcgc
 V$ZF5_01               |     7147 (+) |  1.000 |  0.926 | GGGCGccg
 V$ZF5_01               |     7199 (+) |  0.831 |  0.802 | GGGTGcta
 V$ZF5_01               |     7476 (+) |  0.786 |  0.772 | GTGTGcta
 V$ZF5_01               |     7481 (-) |  1.000 |  0.788 | ctaCGCGC
 V$ZF5_01               |     7483 (-) |  0.955 |  0.857 | acgCGCAC
 V$ZF5_01               |     7485 (+) |  0.850 |  0.787 | GCGCAcgt
 V$ZF5_01               |     7544 (+) |  0.799 |  0.781 | GTGAGcca
 V$ZF5_01               |     7675 (-) |  0.799 |  0.781 | tggCTCAC
 V$ZF5_01               |     8229 (-) |  0.844 |  0.811 | tggCTCCC
 V$ZF5_01               |     8235 (-) |  0.831 |  0.750 | ccaCACCC
 V$ZF5_01               |     8288 (-) |  0.844 |  0.811 | tggCTCCC
 V$ZF5_01               |     8509 (+) |  0.955 |  0.810 | GTGCGgga
 V$ZF5_01               |     8542 (+) |  0.799 |  0.792 | GTGGGccg
 V$ZF5_01               |     8739 (+) |  0.831 |  0.750 | GGGTGtgg
 V$ZF5_01               |     8747 (-) |  0.799 |  0.781 | tggCCCAC
 V$ZF5_01               |     8805 (+) |  0.844 |  0.811 | GGGGGcca
 V$ZF5_01               |     9201 (+) |  0.811 |  0.789 | GAGCAcca
 V$ZF5_01               |     9237 (-) |  0.822 |  0.808 | cagAGCCC
 V$ZF5_01               |     9239 (+) |  0.783 |  0.770 | GAGCCcta
 V$ZF5_01               |     9248 (+) |  0.805 |  0.796 | GAGAGctg
 V$ZF5_01               |     9303 (+) |  0.777 |  0.777 | GTGCCcag
 V$ZF5_01               |     9379 (+) |  0.805 |  0.796 | GAGAGctg
 V$ZF5_01               |     9572 (+) |  0.831 |  0.750 | GGGTGtgg
 V$ZF5_01               |     9687 (+) |  0.844 |  0.759 | GGGGGtgg
 V$ZF5_01               |    10088 (-) |  0.811 |  0.800 | cagTGCTC
 V$ZF5_01               |    10719 (-) |  0.779 |  0.779 | ctgCGTGC
 V$ZF5_01               |    10721 (+) |  0.831 |  0.813 | GCGTGctg
 V$ZF5_01               |    10764 (-) |  0.777 |  0.766 | ttgGGCAC
 V$ZF5_01               |    10766 (+) |  0.850 |  0.815 | GGGCActa
 V$ZF5_01               |    10782 (-) |  0.653 |  0.758 | tcgGACCC
 V$ZF5_01               |    10883 (+) |  0.811 |  0.800 | GAGCActg
 V$ZF5_01               |    10938 (+) |  0.648 |  0.766 | GTGGAcgg
 V$ZF5_01               |    11133 (-) |  0.792 |  0.788 | ctgCACTC
 V$ZF5_01               |    11260 (+) |  0.786 |  0.772 | GTGTGcca
 V$ZF5_01               |    11604 (+) |  0.804 |  0.796 | GTGCAcag
 V$ZF5_01               |    11715 (-) |  0.805 |  0.796 | ctgCCCTC
 V$ZF5_01               |    11846 (+) |  0.844 |  0.759 | GGGGGtgg
 V$ZF5_01               |    11916 (-) |  0.822 |  0.871 | tcgGGCCC
 V$ZF5_01               |    11918 (+) |  0.822 |  0.796 | GGGCCcaa
 V$ZF5_01               |    11923 (-) |  1.000 |  0.788 | caaCGCCC
 V$ZF5_01               |    11966 (-) |  0.783 |  0.782 | ctgAGCTC
 V$PAX8_01              |        1 (-) |  0.935 |  0.872 | gtTCATGcatgtaca
 V$PAX8_01              |       24 (+) |  0.953 |  0.880 | tgaatgtgTGTGAac
 V$PAX8_01              |      107 (+) |  0.973 |  0.839 | gggtggccAGTGAgg
 V$PAX8_01              |      132 (-) |  0.855 |  0.814 | gcTCAGTcaatccag
 V$PAX8_01              |      136 (-) |  0.862 |  0.841 | agTCAATccagacat
 V$PAX8_01              |      295 (+) |  0.855 |  0.849 | ttttacagACTGAgc
 V$PAX8_01              |      408 (+) |  0.963 |  0.884 | gcggaatgGGTGAgc
 V$PAX8_01              |      528 (+) |  0.963 |  0.939 | aaatgatgGGTGAtg
 V$PAX8_01              |      912 (-) |  0.935 |  0.872 | ttTCATGcgtagcac
 V$PAX8_01              |      981 (-) |  0.953 |  0.814 | caTCACAgttaataa
 V$PAX8_01              |     1261 (-) |  0.897 |  0.844 | caTCATCcgtgtgta
 V$PAX8_01              |     1274 (+) |  0.897 |  0.873 | tactctggGATGAca
 V$PAX8_01              |     1327 (-) |  0.973 |  0.937 | tcTCACTccccaggg
 V$PAX8_01              |     1411 (+) |  1.000 |  0.810 | tccattgcCGTGAga
 V$PAX8_01              |     1728 (-) |  0.897 |  0.887 | gcTCATCctgaactt
 V$PAX8_01              |     2011 (+) |  0.822 |  0.821 | atctcctgAGTGCtg
 V$PAX8_01              |     2292 (+) |  0.802 |  0.825 | agtttttgTGTGTgt
 V$PAX8_01              |     2294 (+) |  0.802 |  0.825 | tttttgtgTGTGTgt
 V$PAX8_01              |     2551 (+) |  0.953 |  0.810 | gtttctgtTGTGAaa
 V$PAX8_01              |     2668 (-) |  0.822 |  0.811 | tgACACTcttaaccc
 V$PAX8_01              |     2693 (-) |  0.953 |  0.874 | ggTCACActcttctc
 V$PAX8_01              |     2845 (-) |  0.908 |  0.813 | caTCATTccgtcctt
 V$PAX8_01              |     3040 (-) |  0.834 |  0.830 | ctCCACCcgggacat
 V$PAX8_01              |     3075 (+) |  0.963 |  0.880 | ggtcacagGGTGAtt
 V$PAX8_01              |     3232 (-) |  0.845 |  0.860 | agTCAGCcaacattc
 V$PAX8_01              |     3261 (+) |  0.963 |  0.827 | gttttcttGGTGAtg
 V$PAX8_01              |     3281 (+) |  0.897 |  0.829 | atgattggGATGAgg
 V$PAX8_01              |     3467 (-) |  0.935 |  0.824 | ccTCATGatttactg
 V$PAX8_01              |     3700 (+) |  0.889 |  0.844 | aagagatgCTTGAtc
 V$PAX8_01              |     3717 (+) |  0.963 |  0.942 | tatttacgGGTGAct
 V$PAX8_01              |     3755 (-) |  0.908 |  0.894 | agTCATTcttaaaag
 V$PAX8_01              |     3933 (-) |  0.855 |  0.813 | taTCAGTcacttgtt
 V$PAX8_01              |     3945 (-) |  0.908 |  0.844 | gtTCATTcagccatc
 V$PAX8_01              |     3969 (+) |  0.887 |  0.810 | actggctgTATGAta
 V$PAX8_01              |     3991 (-) |  0.935 |  0.827 | tcTCATGaaacaacg
 V$PAX8_01              |     4279 (-) |  0.802 |  0.822 | aaGCACAcattagac
 V$PAX8_01              |     4382 (+) |  0.973 |  0.836 | ggctacatAGTGAgt
 V$PAX8_01              |     4406 (-) |  0.845 |  0.833 | ggTCAGCcacaacct
 V$PAX8_01              |     4460 (-) |  0.953 |  0.853 | ttTCACActgactga
 V$PAX8_01              |     4716 (+) |  0.953 |  0.828 | taattcacTGTGAtt
 V$PAX8_01              |     4718 (-) |  0.973 |  0.814 | atTCACTgtgatttg
 V$PAX8_01              |     4833 (+) |  0.973 |  0.871 | agggaacgAGTGAtc
 V$PAX8_01              |     4933 (+) |  0.855 |  0.840 | tcatggagACTGAac
 V$PAX8_01              |     4968 (-) |  0.882 |  0.814 | agTCAGGctcagccc
 V$PAX8_01              |     4974 (-) |  0.845 |  0.826 | gcTCAGCccctacct
 V$PAX8_01              |     5101 (+) |  0.953 |  0.839 | ttattattTGTGAgt
 V$PAX8_01              |     5105 (+) |  0.822 |  0.834 | tatttgtgAGTGCtc
 V$PAX8_01              |     5168 (+) |  0.953 |  0.831 | ctttcactTGTGAct
 V$PAX8_01              |     5169 (-) |  0.973 |  0.852 | ttTCACTtgtgactg
 V$PAX8_01              |     5265 (-) |  0.897 |  0.826 | agTCATCctgggcca
 V$PAX8_01              |     5364 (-) |  0.802 |  0.818 | aaACACAcgggattt
 V$PAX8_01              |     5537 (-) |  0.973 |  0.886 | atTCACTctctttct
 V$PAX8_01              |     5555 (-) |  0.973 |  0.840 | tcTCACTagaaaaca
 V$PAX8_01              |     5697 (-) |  0.887 |  0.844 | gtTCATAcacttagg
 V$PAX8_01              |     5969 (+) |  0.963 |  0.812 | ttttaagtGGTGAta
 V$PAX8_01              |     6089 (+) |  0.824 |  0.832 | agttcctgTGTGGat
 V$PAX8_01              |     6220 (-) |  1.000 |  0.910 | tcTCACGctctgcat
 V$PAX8_01              |     6289 (+) |  0.855 |  0.861 | tgatgatgACTGAgc
 V$PAX8_01              |     6318 (+) |  0.855 |  0.820 | cttccctgACTGAag
 V$PAX8_01              |     6332 (-) |  0.802 |  0.814 | gcACACActggattt
 V$PAX8_01              |     6407 (+) |  0.908 |  0.834 | acgctcagAATGAct
 V$PAX8_01              |     6474 (+) |  0.897 |  0.832 | atgctcagGATGAgg
 V$PAX8_01              |     6528 (-) |  0.963 |  0.925 | gtTCACCctggagac
 V$PAX8_01              |     6540 (+) |  0.845 |  0.815 | gacaaacgGCTGAgg
 V$PAX8_01              |     6614 (+) |  1.000 |  0.844 | ctaaactcCGTGAgt
 V$PAX8_01              |     6630 (-) |  0.812 |  0.815 | ggGCACCcagaaggc
 V$PAX8_01              |     6646 (-) |  0.855 |  0.847 | ccTCAGTctgcaaac
 V$PAX8_01              |     6723 (+) |  0.963 |  0.943 | ctttaaagGGTGAgc
 V$PAX8_01              |     6761 (+) |  0.935 |  0.818 | ctttatacCATGAac
 V$PAX8_01              |     6983 (+) |  0.963 |  0.824 | acttagctGGTGAgg
 V$PAX8_01              |     7073 (+) |  0.887 |  0.886 | tgtttgtgTATGAgt
 V$PAX8_01              |     7439 (+) |  0.824 |  0.839 | attttatgTGTGGga
 V$PAX8_01              |     7535 (+) |  0.953 |  0.828 | cagttggtTGTGAgc
 V$PAX8_01              |     7747 (+) |  0.953 |  0.821 | ggctacatTGTGAgt
 V$PAX8_01              |     8014 (+) |  0.973 |  0.820 | taacctttAGTGAgt
 V$PAX8_01              |     8018 (+) |  0.822 |  0.831 | ctttagtgAGTGTca
 V$PAX8_01              |     8105 (-) |  0.953 |  0.855 | tgTCACAcactctcc
 V$PAX8_01              |     9022 (+) |  0.953 |  0.812 | cagatcttTGTGAgt
 V$PAX8_01              |     9166 (+) |  0.935 |  0.885 | ctaagatgCATGAac
 V$PAX8_01              |     9189 (-) |  0.845 |  0.858 | gaCCACTcaagagag
 V$PAX8_01              |     9255 (-) |  0.935 |  0.830 | gcTCATGggacaggg
 V$PAX8_01              |     9565 (+) |  0.812 |  0.823 | ggtttctgGGTGTgg
 V$PAX8_01              |     9724 (+) |  0.887 |  0.835 | tctctttgTATGAta
 V$PAX8_01              |     9769 (-) |  0.935 |  0.898 | agTCATGccatagaa
 V$PAX8_01              |     9847 (-) |  0.882 |  0.813 | agTCAGGcaggcagc
 V$PAX8_01              |     9864 (+) |  0.908 |  0.853 | taaagaagAATGAgg
 V$PAX8_01              |    10026 (+) |  0.953 |  0.844 | ccgtagttTGTGAgt
 V$PAX8_01              |    10174 (+) |  0.802 |  0.834 | tattagtgTGTGTgt
 V$PAX8_01              |    10219 (+) |  0.845 |  0.814 | catctaagAGTGGaa
 V$PAX8_01              |    10245 (-) |  0.882 |  0.811 | ggTCAGGcttgtgca
 V$PAX8_01              |    10269 (+) |  0.845 |  0.848 | ttttgccgGCTGAgc
 V$PAX8_01              |    10289 (-) |  0.882 |  0.817 | caTCAGGcttcggac
 V$PAX8_01              |    10470 (-) |  0.973 |  0.828 | tcTCACTttagacca
 V$PAX8_01              |    10624 (+) |  0.973 |  0.819 | ttgtagaaAGTGAct
 V$PAX8_01              |    10714 (+) |  0.849 |  0.820 | catctctgCGTGCtg
 V$PAX8_01              |    10831 (-) |  0.882 |  0.812 | ttTCAGGcccatcgc
 V$PAX8_01              |    10864 (+) |  0.872 |  0.842 | agatgcagCGTGGtg
 V$PAX8_01              |    11192 (+) |  0.862 |  0.868 | gtttcttgATTGAtt
 V$PAX8_01              |    11356 (+) |  0.935 |  0.848 | aacgagagCATGAtt
 V$PAX8_01              |    11584 (+) |  0.973 |  0.899 | tatccaggAGTGAga
 V$PAX8_01              |    11704 (-) |  0.963 |  0.851 | tgTCACCccaactgc
 V$PAX8_01              |    11731 (-) |  0.842 |  0.812 | tcTCAAAcatctcac
 V$PAX8_01              |    11819 (+) |  0.963 |  0.859 | agggttggGGTGAga
 V$PAX8_01              |    11841 (+) |  0.834 |  0.832 | gagtggggGGTGGgg
 V$PAX8_01              |    11887 (-) |  0.973 |  0.932 | tcTCACTctcaacca
 V$PAX8_01              |    11893 (-) |  0.852 |  0.859 | tcTCAACcaatagca
 V$CACBINDINGPROTEIN_Q6 |      105 (+) |  1.000 |  0.941 | gggGGTGGc
 V$CACBINDINGPROTEIN_Q6 |      118 (+) |  0.980 |  0.941 | gagGCTGGc
 V$CACBINDINGPROTEIN_Q6 |     1488 (+) |  0.934 |  0.955 | gagGGAGGg
 V$CACBINDINGPROTEIN_Q6 |     1499 (+) |  0.934 |  0.941 | gggGGAGGg
 V$CACBINDINGPROTEIN_Q6 |     1503 (+) |  0.934 |  0.955 | gagGGAGGg
 V$CACBINDINGPROTEIN_Q6 |     1507 (+) |  0.934 |  0.955 | gagGGAGGg
 V$CACBINDINGPROTEIN_Q6 |     1511 (+) |  0.934 |  0.955 | gagGGAGGg
 V$CACBINDINGPROTEIN_Q6 |     2429 (+) |  0.922 |  0.933 | gggGTTGGg
 V$CACBINDINGPROTEIN_Q6 |     4237 (+) |  0.980 |  0.928 | aggGCTGGg
 V$CACBINDINGPROTEIN_Q6 |     5077 (+) |  0.980 |  0.941 | gagGCTGGc
 V$CACBINDINGPROTEIN_Q6 |     9008 (+) |  0.914 |  0.941 | gagGCAGGg
 V$CACBINDINGPROTEIN_Q6 |    11846 (+) |  1.000 |  0.987 | gggGGTGGg
 V$CACBINDINGPROTEIN_Q6 |    11871 (+) |  0.934 |  0.941 | gggGGAGGg
 V$CACCCBINDINGFACTOR_Q6|     8235 (-) |  1.000 |  0.934 | ccaCACCCagatgaag
 V$CACCCBINDINGFACTOR_Q6|     9564 (+) |  1.000 |  0.912 | cggtttctGGGTGtgg
 V$COREBINDINGFACTOR_Q6 |      934 (-) |  1.000 |  1.000 | aaaCCACA
 V$COREBINDINGFACTOR_Q6 |     4439 (-) |  1.000 |  1.000 | aaaCCACA
 V$COREBINDINGFACTOR_Q6 |     5049 (+) |  1.000 |  0.983 | TGTGGtct
 V$COREBINDINGFACTOR_Q6 |     5256 (+) |  1.000 |  0.972 | TGTGGtca
 V$COREBINDINGFACTOR_Q6 |     9400 (+) |  1.000 |  0.948 | TGTGGttc
 V$COREBINDINGFACTOR_Q6 |    11256 (+) |  1.000 |  0.971 | TGTGGtgt
 I$GAGAFACTOR_Q6        |      378 (+) |  0.993 |  0.898 | ggtGAGAGatg
 I$GAGAFACTOR_Q6        |     2055 (-) |  0.993 |  0.944 | cttCTCTCtct
 I$GAGAFACTOR_Q6        |     2057 (-) |  0.993 |  0.993 | tctCTCTCtct
 I$GAGAFACTOR_Q6        |     2059 (-) |  0.993 |  0.993 | tctCTCTCtct
 I$GAGAFACTOR_Q6        |     2061 (-) |  0.993 |  0.989 | tctCTCTCtgt
 I$GAGAFACTOR_Q6        |     2085 (-) |  0.993 |  0.968 | tgtCTCTCtgt
 I$GAGAFACTOR_Q6        |     2093 (-) |  0.993 |  0.968 | tgtCTCTCtgt
 I$GAGAFACTOR_Q6        |     2101 (-) |  0.993 |  0.968 | tgtCTCTCtgt
 I$GAGAFACTOR_Q6        |     2109 (-) |  0.993 |  0.972 | tgtCTCTCtct
 I$GAGAFACTOR_Q6        |     2111 (-) |  0.993 |  0.993 | tctCTCTCtct
 I$GAGAFACTOR_Q6        |     2113 (-) |  0.993 |  0.993 | tctCTCTCtct
 I$GAGAFACTOR_Q6        |     2115 (-) |  0.993 |  0.993 | tctCTCTCtct
 I$GAGAFACTOR_Q6        |     2117 (-) |  0.993 |  0.993 | tctCTCTCtct
 I$GAGAFACTOR_Q6        |     2119 (-) |  0.993 |  0.993 | tctCTCTCtct
 I$GAGAFACTOR_Q6        |     2121 (-) |  0.993 |  0.993 | tctCTCTCtct
 I$GAGAFACTOR_Q6        |     2123 (-) |  0.993 |  0.993 | tctCTCTCtct
 I$GAGAFACTOR_Q6        |     2125 (-) |  0.993 |  0.953 | tctCTCTCttt
 I$GAGAFACTOR_Q6        |     2133 (-) |  0.993 |  0.986 | tttCTCTCtct
 I$GAGAFACTOR_Q6        |     2135 (-) |  0.993 |  0.993 | tctCTCTCtct
 I$GAGAFACTOR_Q6        |     2137 (-) |  0.993 |  0.993 | tctCTCTCtct
 I$GAGAFACTOR_Q6        |     2139 (-) |  0.993 |  0.993 | tctCTCTCtct
 I$GAGAFACTOR_Q6        |     2141 (-) |  0.993 |  0.939 | tctCTCTCttc
 I$GAGAFACTOR_Q6        |     2187 (-) |  0.993 |  0.944 | cttCTCTCtct
 I$GAGAFACTOR_Q6        |     2189 (-) |  0.993 |  0.993 | tctCTCTCtct
 I$GAGAFACTOR_Q6        |     2191 (-) |  0.993 |  0.953 | tctCTCTCttt
 I$GAGAFACTOR_Q6        |     2343 (-) |  1.000 |  0.894 | ctaCGCTCttc
 I$GAGAFACTOR_Q6        |     2991 (-) |  1.000 |  0.901 | ttcCGCTCctc
 I$GAGAFACTOR_Q6        |     3186 (-) |  0.993 |  0.910 | cccCTCTCttt
 I$GAGAFACTOR_Q6        |     5065 (+) |  0.993 |  0.913 | agtGAGAGatg
 I$GAGAFACTOR_Q6        |     5219 (+) |  1.000 |  0.912 | tctGAGCGgag
 I$GAGAFACTOR_Q6        |     5539 (-) |  0.993 |  0.953 | tcaCTCTCttt
 I$GAGAFACTOR_Q6        |     5551 (-) |  0.993 |  0.960 | tgtCTCTCact
 I$GAGAFACTOR_Q6        |     5772 (+) |  0.993 |  0.911 | aagGAGAGaaa
 I$GAGAFACTOR_Q6        |     6222 (-) |  1.000 |  0.980 | tcaCGCTCtgc
 I$GAGAFACTOR_Q6        |     6703 (+) |  0.993 |  0.924 | gtaGAGAGaaa
 I$GAGAFACTOR_Q6        |     7299 (+) |  0.993 |  0.908 | gctGAGAGagt
 I$GAGAFACTOR_Q6        |     7301 (+) |  0.993 |  0.965 | tgaGAGAGtaa
 I$GAGAFACTOR_Q6        |     9286 (+) |  0.993 |  0.941 | gctGAGAGtca
 I$GAGAFACTOR_Q6        |    11020 (+) |  0.993 |  0.898 | tagGAGAGaga
 I$GAGAFACTOR_Q6        |    11887 (-) |  0.904 |  0.902 | tctCACTCtca
 I$GAGAFACTOR_Q6        |    11889 (-) |  0.993 |  0.919 | tcaCTCTCaac
 V$HNF3ALPHA_Q6         |      215 (+) |  0.972 |  0.916 | TATTTtttttt
 V$HNF3ALPHA_Q6         |      508 (+) |  0.972 |  0.931 | TATTTgtcttc
 V$HNF3ALPHA_Q6         |      846 (-) |  0.972 |  0.931 | ttaaatAAATA
 V$HNF3ALPHA_Q6         |      875 (-) |  1.000 |  0.928 | atgcacAAACA
 V$HNF3ALPHA_Q6         |      953 (-) |  0.972 |  0.925 | atgatcAAATA
 V$HNF3ALPHA_Q6         |     1474 (+) |  0.972 |  0.956 | TATTTgctctg
 V$HNF3ALPHA_Q6         |     1533 (+) |  0.909 |  0.915 | TTTTTgttcta
 V$HNF3ALPHA_Q6         |     1896 (+) |  0.972 |  0.939 | TATTTatttta
 V$HNF3ALPHA_Q6         |     2363 (+) |  0.972 |  0.939 | TATTTattttg
 V$HNF3ALPHA_Q6         |     2408 (-) |  1.000 |  0.937 | taaaaaAAACA
 V$HNF3ALPHA_Q6         |     2412 (-) |  0.909 |  0.930 | aaaaacAAAAA
 V$HNF3ALPHA_Q6         |     3597 (+) |  1.000 |  0.922 | TGTTTgggttt
 V$HNF3ALPHA_Q6         |     3806 (-) |  1.000 |  0.922 | tagaaaAAACA
 V$HNF3ALPHA_Q6         |     4006 (-) |  0.972 |  0.931 | ataaatAAATA
 V$HNF3ALPHA_Q6         |     4219 (-) |  0.972 |  0.907 | ttaaaaAAATA
 V$HNF3ALPHA_Q6         |     4489 (-) |  0.909 |  0.906 | ttgaacAAAAA
 V$HNF3ALPHA_Q6         |     4497 (-) |  1.000 |  0.910 | aaaacaAAACA
 V$HNF3ALPHA_Q6         |     4502 (-) |  1.000 |  0.910 | aaaacaAAACA
 V$HNF3ALPHA_Q6         |     5120 (-) |  1.000 |  0.924 | aaaaggAAACA
 V$HNF3ALPHA_Q6         |     5437 (+) |  0.972 |  0.943 | TATTTgtattg
 V$HNF3ALPHA_Q6         |     5806 (-) |  0.972 |  0.916 | aaaaaaAAATA
 V$HNF3ALPHA_Q6         |     6588 (-) |  0.972 |  0.978 | caaaacAAATA
 V$HNF3ALPHA_Q6         |     6608 (+) |  0.972 |  0.932 | TATTTgctaaa
 V$HNF3ALPHA_Q6         |     6651 (-) |  1.000 |  0.905 | gtctgcAAACA
 V$HNF3ALPHA_Q6         |     7050 (+) |  0.972 |  0.912 | TATTTtttttc
 V$HNF3ALPHA_Q6         |     7073 (+) |  1.000 |  0.942 | TGTTTgtgtat
 V$HNF3ALPHA_Q6         |     7211 (-) |  0.909 |  0.906 | ttgaacAAAAA
 V$HNF3ALPHA_Q6         |     7428 (+) |  0.972 |  0.979 | TATTTgttttt
 V$HNF3ALPHA_Q6         |     7583 (-) |  1.000 |  0.910 | caggtcAAACA
 V$HNF3ALPHA_Q6         |     7775 (-) |  1.000 |  0.910 | aaaacaAAACA
 V$HNF3ALPHA_Q6         |     7779 (-) |  0.909 |  0.930 | caaaacAAAAA
 V$HNF3ALPHA_Q6         |     7821 (-) |  1.000 |  1.000 | caaaacAAACA
 V$HNF3ALPHA_Q6         |     7941 (+) |  1.000 |  0.933 | TGTTTagtttt
 V$HNF3ALPHA_Q6         |     7972 (+) |  1.000 |  1.000 | TGTTTgttttt
 V$HNF3ALPHA_Q6         |     8187 (+) |  1.000 |  0.977 | TGTTTgctctg
 V$HNF3ALPHA_Q6         |     8897 (-) |  1.000 |  0.911 | taccacAAACA
 V$HNF3ALPHA_Q6         |     9110 (-) |  0.909 |  0.930 | caaaacAAAAA
 V$HNF3ALPHA_Q6         |     9488 (+) |  0.972 |  0.905 | TATTTgcaata
 V$HNF3ALPHA_Q6         |     9533 (-) |  1.000 |  0.985 | tagaacAAACA
 V$HNF3ALPHA_Q6         |    10910 (-) |  0.972 |  0.926 | ctatgcAAATA
 V$HNF3ALPHA_Q6         |    11214 (+) |  1.000 |  0.918 | TGTTTgaactg
 V$HNF3ALPHA_Q6         |    11474 (+) |  0.972 |  0.979 | TATTTgttttt
 V$HP1SITEFACTOR_Q6     |     6954 (-) |  0.941 |  0.889 | CTGTCcattatt
 V$HP1SITEFACTOR_Q6     |     8947 (-) |  0.858 |  0.870 | CTTTTtaaaatt
 V$USF2_Q6              |      737 (+) |  1.000 |  1.000 | CACGTg
 V$USF2_Q6              |      737 (-) |  1.000 |  1.000 | cACGTG
 V$USF2_Q6              |     1128 (+) |  1.000 |  1.000 | CACGTg
 V$USF2_Q6              |     1128 (-) |  1.000 |  1.000 | cACGTG
 V$USF2_Q6              |     6066 (+) |  1.000 |  1.000 | CACGTg
 V$USF2_Q6              |     6066 (-) |  1.000 |  1.000 | cACGTG
 V$SF1_Q6               |     1937 (+) |  1.000 |  0.932 | tagCCTTG
 V$SF1_Q6               |     9636 (-) |  1.000 |  1.000 | CAAGGtca
 F$ROX1_Q6              |     3145 (-) |  1.000 |  0.972 | aACAATata
 F$ROX1_Q6              |     7333 (-) |  1.000 |  0.997 | aACAATaga
 F$ROX1_Q6              |    10340 (+) |  1.000 |  0.980 | tttATTGTt
 F$ROX1_Q6              |    10461 (-) |  1.000 |  0.983 | aACAATgca
 V$CDX2_Q5              |       60 (-) |  0.854 |  0.759 | ggccATAATtactg
 V$CDX2_Q5              |      291 (+) |  0.823 |  0.758 | agtgtTTTACagac
 V$CDX2_Q5              |      566 (-) |  1.000 |  0.863 | ggagATAAAcgtct
 V$CDX2_Q5              |      639 (+) |  1.000 |  0.776 | aaacaTTTATtcat
 V$CDX2_Q5              |      647 (+) |  1.000 |  0.812 | attcaTTTATtata
 V$CDX2_Q5              |      820 (+) |  0.798 |  0.773 | cacttTTTAAtact
 V$CDX2_Q5              |      821 (+) |  0.896 |  0.757 | actttTTAATacta
 V$CDX2_Q5              |      832 (-) |  1.000 |  0.752 | ctatATAAAacaag
 V$CDX2_Q5              |      952 (-) |  0.854 |  0.766 | aatgATCAAatatt
 V$CDX2_Q5              |     1221 (+) |  0.750 |  0.779 | agtttCTGATgact
 V$CDX2_Q5              |     1757 (-) |  0.896 |  0.754 | atctATAAGcctct
 V$CDX2_Q5              |     1887 (+) |  1.000 |  0.779 | cccatTTTATattt
 V$CDX2_Q5              |     1898 (+) |  1.000 |  0.808 | tttatTTTATtatt
 V$CDX2_Q5              |     1906 (+) |  1.000 |  0.807 | attatTTTATttga
 V$CDX2_Q5              |     2024 (-) |  0.896 |  0.772 | tgggATTAAaggag
 V$CDX2_Q5              |     2540 (-) |  0.854 |  0.753 | gagaATAACaggtt
 V$CDX2_Q5              |     2659 (+) |  0.854 |  0.807 | gcactTTGATgaca
 V$CDX2_Q5              |     2734 (+) |  1.000 |  0.769 | ctgccTTTATgcct
 V$CDX2_Q5              |     3121 (-) |  0.677 |  0.791 | ggctATATTaattt
 V$CDX2_Q5              |     3403 (-) |  1.000 |  0.894 | agttATAAAagtta
 V$CDX2_Q5              |     3409 (+) |  0.896 |  0.775 | aaaagTTAATgatt
 V$CDX2_Q5              |     3450 (-) |  1.000 |  0.799 | gttaATAAAacaca
 V$CDX2_Q5              |     3470 (+) |  0.823 |  0.762 | catgaTTTACtgcc
 V$CDX2_Q5              |     3579 (-) |  0.694 |  0.772 | agttATTCAactct
 V$CDX2_Q5              |     3621 (+) |  1.000 |  0.786 | atgcgTTTATaata
 V$CDX2_Q5              |     3733 (+) |  0.854 |  0.840 | aaattATTATttct
 V$CDX2_Q5              |     3826 (-) |  0.854 |  0.754 | attcATAATaaatt
 V$CDX2_Q5              |     3829 (-) |  1.000 |  0.764 | cataATAAAtttcc
 V$CDX2_Q5              |     3845 (-) |  1.000 |  0.777 | tctcATAAAatatc
 V$CDX2_Q5              |     3908 (-) |  1.000 |  0.808 | attaATAAAgcttt
 V$CDX2_Q5              |     3914 (+) |  1.000 |  0.803 | aaagcTTTATgaat
 V$CDX2_Q5              |     4002 (-) |  1.000 |  0.803 | aacgATAAAtaaat
 V$CDX2_Q5              |     4060 (-) |  0.896 |  0.843 | aataATTAAaatat
 V$CDX2_Q5              |     4314 (-) |  1.000 |  0.787 | ctgcATAAAactgg
 V$CDX2_Q5              |     5001 (+) |  0.798 |  0.757 | gacctTGTATtacc
 V$CDX2_Q5              |     5382 (+) |  1.000 |  0.798 | ttagtTTTATttta
 V$CDX2_Q5              |     5412 (-) |  0.896 |  0.759 | tcttATTAAatctt
 V$CDX2_Q5              |     5436 (+) |  0.798 |  0.808 | ttattTGTATtgcc
 V$CDX2_Q5              |     5446 (-) |  0.823 |  0.820 | tgccATATAacctt
 V$CDX2_Q5              |     5481 (+) |  0.854 |  0.805 | attttTTGATcccc
 V$CDX2_Q5              |     5585 (-) |  0.854 |  0.803 | gataATAATaaaat
 V$CDX2_Q5              |     5588 (-) |  1.000 |  0.808 | aataATAAAatata
 V$CDX2_Q5              |     5737 (-) |  0.854 |  0.785 | agccATAATataga
 V$CDX2_Q5              |     5943 (-) |  0.823 |  0.756 | aaaaGTAAAatttt
 V$CDX2_Q5              |     5949 (+) |  1.000 |  0.857 | aaaatTTTATttgc
 V$CDX2_Q5              |     6465 (-) |  1.000 |  0.809 | cctgATAAAatgct
 V$CDX2_Q5              |     6666 (+) |  1.000 |  0.779 | aagatTTTATttag
 V$CDX2_Q5              |     6757 (+) |  1.000 |  0.806 | atcccTTTATacca
 V$CDX2_Q5              |     6823 (+) |  1.000 |  0.784 | cctttTTTATgtgc
 V$CDX2_Q5              |     7258 (-) |  0.896 |  0.812 | tctcATTAAaatat
 V$CDX2_Q5              |     7421 (+) |  1.000 |  0.777 | aaaggTTTATttgt
 V$CDX2_Q5              |     7733 (-) |  0.708 |  0.773 | ggccATCACaggct
 V$CDX2_Q5              |     8685 (-) |  0.791 |  0.798 | ggtaATTAGccttt
 V$CDX2_Q5              |     8870 (-) |  0.798 |  0.768 | tggcATAGAatatt
 V$CDX2_Q5              |     8987 (+) |  0.896 |  0.791 | cacctTTAATtcca
 V$CDX2_Q5              |     9492 (-) |  0.798 |  0.758 | tgcaATAGAaaatc
 V$CDX2_Q5              |     9774 (-) |  0.798 |  0.821 | tgccATAGAacaat
 V$CDX2_Q5              |     9837 (+) |  0.798 |  0.801 | ataatTTTAAagtc
 V$CDX2_Q5              |     9943 (+) |  0.854 |  0.771 | tgtatGTTATaaca
 V$CDX2_Q5              |     9947 (-) |  0.854 |  0.823 | tgttATAACaccct
 V$CDX2_Q5              |    10121 (-) |  1.000 |  0.847 | cccaATAAAattag
 V$CDX2_Q5              |    10140 (+) |  0.854 |  0.817 | aaattATTATtatt
 V$CDX2_Q5              |    10143 (+) |  0.854 |  0.760 | ttattATTATtgtt
 V$CDX2_Q5              |    10313 (+) |  1.000 |  0.773 | ctgttTTTATattt
 V$CDX2_Q5              |    10321 (+) |  1.000 |  0.865 | atattTTTATttta
 V$CDX2_Q5              |    10326 (+) |  1.000 |  0.808 | tttatTTTATagtt
 V$CDX2_Q5              |    10335 (+) |  1.000 |  0.802 | tagttTTTATtgtt
 V$CDX2_Q5              |    10343 (+) |  0.798 |  0.773 | attgtTTTAAttca
 V$CDX2_Q5              |    10415 (+) |  0.798 |  0.758 | gcattTTTAAcact
 V$CDX2_Q5              |    10448 (+) |  1.000 |  0.818 | tctctTTTATatca
 V$CDX2_Q5              |    10505 (+) |  0.854 |  0.791 | agtcaATTATggct
 V$CDX2_Q5              |    10729 (+) |  1.000 |  0.764 | tagctTTTATtggg
 V$CDX2_Q5              |    10914 (-) |  0.854 |  0.766 | gcaaATAATagtct
 V$CDX2_Q5              |    11203 (-) |  0.896 |  0.785 | gattATTAAtttgt
 V$CDX2_Q5              |    11274 (-) |  0.896 |  0.761 | ggaaATTAAggcat
 V$CDX2_Q5              |    11295 (-) |  0.854 |  0.772 | agaaATAATaataa
 V$CDX2_Q5              |    11388 (-) |  0.896 |  0.808 | acttATTAAatttt
 V$CDX2_Q5              |    11467 (+) |  1.000 |  0.807 | aatttTTTATttgt
 V$CDX2_Q5              |    11565 (+) |  0.896 |  0.824 | aaactCTTATcatt
 V$CDX2_Q5              |    11665 (+) |  0.854 |  0.856 | caattTTCATaacc
 V$CDX2_Q5              |    11686 (-) |  1.000 |  0.751 | accaATAAAgttaa
 V$CDX2_Q5              |    11691 (+) |  0.896 |  0.757 | taaagTTAATcact
 F$HAC1_Q2              |     2974 (-) |  0.898 |  0.900 | gATGCGcaggca
 V$OSF2_Q6              |      936 (+) |  1.000 |  0.967 | aCCACAag
 V$OSF2_Q6              |     3563 (-) |  1.000 |  0.918 | tgTGTGGc
 V$OSF2_Q6              |     3641 (+) |  1.000 |  0.960 | aCCACAtg
 V$OSF2_Q6              |     4143 (-) |  1.000 |  0.971 | ggTGTGGt
 V$OSF2_Q6              |     4411 (+) |  1.000 |  0.907 | gCCACAac
 V$OSF2_Q6              |     4441 (+) |  1.000 |  0.991 | aCCACAca
 V$OSF2_Q6              |     4570 (-) |  0.915 |  0.907 | gtTGCGGt
 V$OSF2_Q6              |     4682 (-) |  1.000 |  0.921 | tcTGTGGc
 V$OSF2_Q6              |     5047 (-) |  1.000 |  0.973 | gcTGTGGt
 V$OSF2_Q6              |     5201 (-) |  1.000 |  0.921 | tcTGTGGc
 V$OSF2_Q6              |     5254 (-) |  1.000 |  0.960 | caTGTGGt
 V$OSF2_Q6              |     6506 (+) |  1.000 |  0.927 | gCCACAaa
 V$OSF2_Q6              |     6715 (+) |  1.000 |  0.907 | gCCACAac
 V$OSF2_Q6              |     7112 (+) |  1.000 |  0.960 | aCCACAtg
 V$OSF2_Q6              |     8740 (-) |  1.000 |  0.971 | ggTGTGGt
 V$OSF2_Q6              |     8898 (+) |  1.000 |  1.000 | aCCACAaa
 V$OSF2_Q6              |     8973 (-) |  1.000 |  0.971 | ggTGTGGt
 V$OSF2_Q6              |     9181 (+) |  1.000 |  0.921 | gCCACAga
 V$OSF2_Q6              |     9398 (-) |  1.000 |  0.953 | aaTGTGGt
 V$OSF2_Q6              |     9573 (-) |  1.000 |  0.971 | ggTGTGGt
 V$OSF2_Q6              |    10485 (+) |  1.000 |  0.921 | gCCACAta
 V$OSF2_Q6              |    10985 (-) |  1.000 |  0.918 | tgTGTGGc
 V$OSF2_Q6              |    11254 (-) |  1.000 |  0.993 | tcTGTGGt
 F$CAT8_Q6              |      407 (-) |  1.000 |  0.981 | ggcggAATGG
 F$CAT8_Q6              |      803 (+) |  1.000 |  0.976 | CCATTtctcc
 F$CAT8_Q6              |     3162 (+) |  1.000 |  0.981 | CCATTccgcc
 F$CAT8_Q6              |     4111 (+) |  1.000 |  0.959 | CCATTttccc
 F$CAT8_Q6              |     5014 (+) |  1.000 |  0.974 | CCATTaagcc
 V$SMAD4_Q6             |      116 (-) |  0.876 |  0.803 | gtgAGGCTggctaac
 V$SMAD4_Q6             |      120 (-) |  1.000 |  0.843 | ggcTGGCTaactgct
 V$SMAD4_Q6             |      138 (+) |  0.990 |  0.800 | tcaatccAGACAttt
 V$SMAD4_Q6             |      448 (-) |  0.990 |  0.795 | ggtTGTCTgttttgg
 V$SMAD4_Q6             |      679 (+) |  0.990 |  0.804 | gctcttcAGACAcac
 V$SMAD4_Q6             |      724 (+) |  1.000 |  0.797 | ggttgtgAGCCAcca
 V$SMAD4_Q6             |      890 (+) |  0.866 |  0.800 | atgggacAGACTttt
 V$SMAD4_Q6             |     1348 (-) |  0.949 |  0.801 | gctTGCCTgggtcac
 V$SMAD4_Q6             |     1581 (+) |  1.000 |  0.795 | catggagAGCCAgca
 V$SMAD4_Q6             |     1822 (+) |  0.990 |  0.826 | tcagggaAGACAccc
 V$SMAD4_Q6             |     1852 (+) |  1.000 |  0.812 | acaatagAGCCAact
 V$SMAD4_Q6             |     1999 (-) |  1.000 |  0.826 | atcTGGCTatacatc
 V$SMAD4_Q6             |     2078 (-) |  0.990 |  0.839 | ctcTGTCTgtctctc
 V$SMAD4_Q6             |     2082 (-) |  0.990 |  0.832 | gtcTGTCTctctgtc
 V$SMAD4_Q6             |     2090 (-) |  0.990 |  0.793 | ctcTGTCTctctgtc
 V$SMAD4_Q6             |     2098 (-) |  0.990 |  0.793 | ctcTGTCTctctgtc
 V$SMAD4_Q6             |     2106 (-) |  0.990 |  0.799 | ctcTGTCTctctctc
 V$SMAD4_Q6             |     2829 (-) |  0.990 |  0.833 | agtTGTCTgcaaatg
 V$SMAD4_Q6             |     2974 (+) |  0.949 |  0.868 | gatgcgcAGGCAtct
 V$SMAD4_Q6             |     3229 (+) |  1.000 |  0.846 | accagtcAGCCAaca
 V$SMAD4_Q6             |     3353 (+) |  0.825 |  0.799 | atcagacAGACCact
 V$SMAD4_Q6             |     3946 (+) |  1.000 |  0.869 | ttcattcAGCCAtcc
 V$SMAD4_Q6             |     4344 (+) |  0.949 |  0.795 | gtggtggAGGCAgga
 V$SMAD4_Q6             |     4403 (+) |  1.000 |  0.807 | acaggtcAGCCAcaa
 V$SMAD4_Q6             |     4465 (-) |  0.959 |  0.817 | cacTGACTgaccagc
 V$SMAD4_Q6             |     4985 (-) |  0.868 |  0.799 | accTGTCCgaatggc
 V$SMAD4_Q6             |     5132 (+) |  0.837 |  0.817 | atggtgcGGTCAacc
 V$SMAD4_Q6             |     5293 (+) |  1.000 |  0.869 | atgggctAGCCAtcc
 V$SMAD4_Q6             |     5672 (+) |  0.990 |  0.791 | aagagacAGACAcag
 V$SMAD4_Q6             |     6149 (-) |  1.000 |  0.801 | ctcTGGCTctcctgc
 V$SMAD4_Q6             |     6234 (-) |  0.990 |  0.825 | tgcTGTCTggctacg
 V$SMAD4_Q6             |     6623 (+) |  0.827 |  0.809 | gtgagtgGGGCAccc
 V$SMAD4_Q6             |     6792 (-) |  1.000 |  0.806 | tgcTGGCTcttcctc
 V$SMAD4_Q6             |     7540 (+) |  1.000 |  0.855 | ggttgtgAGCCAact
 V$SMAD4_Q6             |     7604 (+) |  1.000 |  0.801 | actgctgAGCCAtct
 V$SMAD4_Q6             |     7743 (-) |  1.000 |  0.809 | ggcTGGCTacattgt
 V$SMAD4_Q6             |     8226 (-) |  1.000 |  0.842 | tgtTGGCTcccacac
 V$SMAD4_Q6             |     8362 (+) |  0.876 |  0.825 | cctgtgcAGCCTgct
 V$SMAD4_Q6             |     8397 (+) |  1.000 |  0.815 | gaagccaAGCCAgcc
 V$SMAD4_Q6             |     8714 (-) |  0.866 |  0.803 | aggAGTCTgaagaac
 V$SMAD4_Q6             |     9012 (+) |  0.949 |  0.878 | caggggcAGGCAgat
 V$SMAD4_Q6             |     9038 (+) |  0.876 |  0.795 | caagggcAGCCTggt
 V$SMAD4_Q6             |     9270 (+) |  1.000 |  0.806 | cagcgacAGCCAcca
 V$SMAD4_Q6             |     9285 (+) |  0.959 |  0.793 | agctgagAGTCAgct
 V$SMAD4_Q6             |     9382 (-) |  0.851 |  0.860 | agcTGTCAgcccctg
 V$SMAD4_Q6             |     9848 (+) |  0.949 |  0.885 | gtcaggcAGGCAgca
 V$SMAD4_Q6             |    10078 (+) |  1.000 |  0.857 | gaagggcAGCCAgtg
 V$SMAD4_Q6             |    10242 (+) |  0.825 |  0.794 | ggtggtcAGGCTtgt
 V$SMAD4_Q6             |    10477 (+) |  1.000 |  0.806 | ttagaccAGCCAcat
 V$SMAD4_Q6             |    10637 (+) |  0.990 |  0.859 | ctgaggaAGACAccc
 V$SMAD4_Q6             |    11179 (-) |  1.000 |  0.797 | tttTGGCTgccttgt
 V$CIZ_01               |     3808 (+) |  1.000 |  0.998 | gAAAAAaca
 V$CIZ_01               |     5402 (-) |  1.000 |  0.999 | tatTTTTTc
 V$CIZ_01               |     7251 (+) |  1.000 |  0.999 | gAAAAAgtc
 P$ZAP1_01              |     5135 (-) |  1.000 |  0.937 | gtgcgGTCAA
 P$ZAP1_01              |     6433 (-) |  1.000 |  0.946 | catcgGTCAA
 V$E2F1DP1_01           |     2472 (-) |  0.982 |  0.947 | gCGCGAag
 V$E2F1DP1_01           |     9122 (-) |  1.000 |  0.931 | cCGGGAaa
 V$E2F1DP1RB_01         |     2472 (-) |  1.000 |  0.917 | gCGCGAag
 V$CETS168_Q6           |      610 (-) |  0.933 |  0.923 | aCATCCtg
 V$CETS168_Q6           |      769 (+) |  1.000 |  0.914 | ctGGAAGa
 V$CETS168_Q6           |      925 (-) |  1.000 |  0.851 | aCTTCCac
 V$CETS168_Q6           |     1459 (+) |  0.900 |  0.890 | ccGGACGt
 V$CETS168_Q6           |     1730 (-) |  0.933 |  0.888 | tCATCCtg
 V$CETS168_Q6           |     1739 (-) |  1.000 |  0.862 | aCTTCCta
 V$CETS168_Q6           |     1777 (-) |  0.900 |  0.861 | tCCTCCtg
 V$CETS168_Q6           |     2147 (-) |  1.000 |  0.827 | tCTTCCtt
 V$CETS168_Q6           |     2151 (-) |  1.000 |  0.827 | cCTTCCtt
 V$CETS168_Q6           |     2155 (-) |  1.000 |  0.843 | cCTTCCtc
 V$CETS168_Q6           |     2161 (-) |  1.000 |  0.827 | tCTTCCtt
 V$CETS168_Q6           |     2205 (-) |  1.000 |  0.827 | tCTTCCtt
 V$CETS168_Q6           |     2686 (-) |  0.933 |  0.947 | gCATCCtg
 V$CETS168_Q6           |     2707 (-) |  1.000 |  0.843 | cCTTCCtc
 V$CETS168_Q6           |     2785 (-) |  1.000 |  0.827 | tCTTCCtt
 V$CETS168_Q6           |     2989 (-) |  1.000 |  0.872 | aCTTCCgc
 V$CETS168_Q6           |     3033 (-) |  1.000 |  0.872 | aCTTCCgc
 V$CETS168_Q6           |     3342 (-) |  0.900 |  0.861 | cCCTCCtg
 V$CETS168_Q6           |     3518 (+) |  0.900 |  0.822 | gaGGAGGc
 V$CETS168_Q6           |     3778 (-) |  1.000 |  0.823 | cCTTCCcc
 V$CETS168_Q6           |     4176 (+) |  0.900 |  0.920 | caGGAGGc
 V$CETS168_Q6           |     4265 (+) |  0.933 |  0.832 | taGGATGc
 V$CETS168_Q6           |     4336 (-) |  0.933 |  0.896 | aCATCCag
 V$CETS168_Q6           |     4354 (+) |  0.900 |  0.861 | caGGAGGa
 V$CETS168_Q6           |     4592 (-) |  0.900 |  0.861 | tCCTCCtg
 V$CETS168_Q6           |     4603 (-) |  0.775 |  0.820 | gCTTGCtg
 V$CETS168_Q6           |     4608 (+) |  1.000 |  0.914 | ctGGAAGg
 V$CETS168_Q6           |     4689 (+) |  0.775 |  0.820 | caGGAAAc
 V$CETS168_Q6           |     4963 (+) |  1.000 |  0.976 | caGGAAGt
 V$CETS168_Q6           |     5031 (+) |  0.933 |  0.812 | tgGGATGc
 V$CETS168_Q6           |     5267 (-) |  0.933 |  0.888 | tCATCCtg
 V$CETS168_Q6           |     5347 (-) |  0.933 |  0.828 | gCATCCcc
 V$CETS168_Q6           |     5732 (+) |  1.000 |  0.973 | ctGGAAGc
 V$CETS168_Q6           |     6162 (-) |  0.900 |  0.822 | gCCTCCtc
 V$CETS168_Q6           |     6276 (+) |  1.000 |  0.885 | aaGGAAGc
 V$CETS168_Q6           |     6317 (-) |  1.000 |  0.842 | aCTTCCct
 V$CETS168_Q6           |     6479 (+) |  0.933 |  0.888 | caGGATGa
 V$CETS168_Q6           |     6799 (-) |  1.000 |  0.843 | tCTTCCtc
 V$CETS168_Q6           |     6859 (-) |  0.900 |  0.870 | aCGTCCag
 V$CETS168_Q6           |     6878 (+) |  1.000 |  0.885 | taGGAAGc
 V$CETS168_Q6           |     6966 (+) |  0.933 |  0.861 | ctGGATGg
 V$CETS168_Q6           |     7013 (+) |  0.933 |  0.818 | gcGGATGt
 V$CETS168_Q6           |     7019 (-) |  0.775 |  0.820 | gTTTCCtg
 V$CETS168_Q6           |     7231 (+) |  1.000 |  0.976 | caGGAAGt
 V$CETS168_Q6           |     8035 (-) |  0.775 |  0.820 | gCTTGCtg
 V$CETS168_Q6           |     8082 (-) |  1.000 |  0.862 | aCTTCCta
 V$CETS168_Q6           |     8135 (-) |  0.775 |  0.820 | gCTTTCtg
 V$CETS168_Q6           |     8159 (-) |  1.000 |  0.973 | gCTTCCag
 V$CETS168_Q6           |     8170 (+) |  0.775 |  0.820 | caGGTAGc
 V$CETS168_Q6           |     8394 (+) |  0.775 |  0.813 | ccTGAAGc
 V$CETS168_Q6           |     8448 (-) |  0.933 |  0.832 | gCATCCta
 V$CETS168_Q6           |     8679 (+) |  1.000 |  0.827 | taGGAAGg
 V$CETS168_Q6           |     8813 (-) |  0.775 |  0.813 | gCTTCTgg
 V$CETS168_Q6           |     9308 (+) |  0.900 |  0.861 | caGGAGGg
 V$CETS168_Q6           |     9335 (+) |  0.900 |  0.834 | ctGGAGGa
 V$CETS168_Q6           |     9436 (+) |  1.000 |  1.000 | caGGAAGc
 V$CETS168_Q6           |     9469 (+) |  0.933 |  0.923 | caGGATGt
 V$CETS168_Q6           |     9606 (+) |  1.000 |  0.865 | tgGGAAGc
 V$CETS168_Q6           |     9854 (+) |  0.775 |  0.820 | caGGCAGc
 V$CETS168_Q6           |    10013 (+) |  0.900 |  0.870 | ctGGAGGt
 V$CETS168_Q6           |    10075 (+) |  1.000 |  0.914 | ctGGAAGg
 V$CETS168_Q6           |    10206 (-) |  1.000 |  0.816 | cCTTCCac
 V$CETS168_Q6           |    10258 (+) |  1.000 |  0.976 | caGGAAGt
 V$CETS168_Q6           |    10639 (+) |  1.000 |  0.843 | gaGGAAGa
 V$CETS168_Q6           |    10668 (+) |  0.900 |  0.861 | caGGAGGa
 V$CETS168_Q6           |    10845 (+) |  1.000 |  0.941 | caGGAAGa
 V$CETS168_Q6           |    11913 (-) |  0.775 |  0.813 | gCTTCGgg
 V$POU1F1_Q6            |      643 (-) |  1.000 |  1.000 | atttATTCAt
 V$ELF1_Q6              |     2155 (-) |  1.000 |  0.963 | ccTTCCTcttcc
 V$ELF1_Q6              |     2707 (-) |  1.000 |  0.963 | ccTTCCTcttcc
 V$ELF1_Q6              |     4959 (+) |  1.000 |  0.958 | gcagcAGGAAgt
 V$ELF1_Q6              |     5473 (-) |  1.000 |  0.958 | atTTCCTgattt
 V$ELF1_Q6              |     5521 (-) |  1.000 |  0.945 | ctTTCCTcctat
 V$ELF1_Q6              |     9432 (+) |  1.000 |  0.949 | ataacAGGAAgc
 V$ELF1_Q6              |     9871 (+) |  1.000 |  0.980 | gaatgAGGAAat
 V$ELF1_Q6              |    10589 (-) |  1.000 |  0.948 | atTTCCTatatc
 V$ELF1_Q6              |    11268 (+) |  1.000 |  0.963 | agaaaAGGAAat
 V$IRF1_Q6              |      903 (+) |  1.000 |  1.000 | ttCACTT
 V$IRF1_Q6              |     1863 (-) |  0.980 |  0.986 | AACTGaa
 V$IRF1_Q6              |     5170 (+) |  1.000 |  1.000 | ttCACTT
 V$IRF1_Q6              |     7524 (-) |  0.980 |  0.986 | AACTGaa
 V$IRF1_Q6              |     9133 (+) |  0.980 |  0.986 | ttCAGTT
 V$IRF1_Q6              |    10059 (-) |  0.980 |  0.986 | AACTGaa
 V$SREBP1_Q6            |      198 (+) |  0.978 |  0.984 | CACACca
 V$SREBP1_Q6            |      689 (+) |  0.978 |  0.984 | CACACca
 V$SREBP1_Q6            |     5821 (-) |  0.989 |  0.992 | tgGCGTG
 V$SREBP1_Q6            |    10177 (-) |  0.978 |  0.905 | taGTGTG
 V$SREBP1_Q6            |    11258 (-) |  0.978 |  0.984 | tgGTGTG
 V$SREBP1_Q6            |    11707 (+) |  1.000 |  1.000 | CACCCca
 V$SREBP1_Q6            |    11824 (-) |  1.000 |  1.000 | tgGGGTG
 V$HMGIY_Q6             |      224 (-) |  1.000 |  0.931 | ttTTTCC
 V$HMGIY_Q6             |      294 (-) |  0.964 |  0.922 | gtTTTAC
 V$HMGIY_Q6             |      331 (+) |  1.000 |  1.000 | GGAAAtt
 V$HMGIY_Q6             |      899 (-) |  0.942 |  0.926 | acTTTTC
 V$HMGIY_Q6             |      994 (-) |  0.942 |  0.948 | aaTTTTC
 V$HMGIY_Q6             |     1194 (+) |  1.000 |  0.939 | GGAAAgc
 V$HMGIY_Q6             |     1551 (+) |  0.942 |  0.916 | GAAAAct
 V$HMGIY_Q6             |     1563 (+) |  1.000 |  0.960 | GGAAAtc
 V$HMGIY_Q6             |     1638 (-) |  1.000 |  0.923 | ccTTTCC
 V$HMGIY_Q6             |     1719 (-) |  1.000 |  0.939 | ctTTTCC
 V$HMGIY_Q6             |     1956 (-) |  1.000 |  0.979 | acTTTCC
 V$HMGIY_Q6             |     2165 (-) |  1.000 |  0.923 | ccTTTCC
 V$HMGIY_Q6             |     2173 (-) |  1.000 |  0.915 | tcTTTCC
 V$HMGIY_Q6             |     2368 (-) |  0.957 |  0.955 | atTTTGC
 V$HMGIY_Q6             |     2378 (-) |  0.942 |  0.916 | agTTTTC
 V$HMGIY_Q6             |     2379 (-) |  1.000 |  0.955 | gtTTTCC
 V$HMGIY_Q6             |     2400 (-) |  1.000 |  0.939 | gcTTTCC
 V$HMGIY_Q6             |     2514 (+) |  1.000 |  0.931 | GGAAAaa
 V$HMGIY_Q6             |     2564 (-) |  1.000 |  1.000 | aaTTTCC
 V$HMGIY_Q6             |     3092 (-) |  0.942 |  0.942 | atTTTTC
 V$HMGIY_Q6             |     3110 (-) |  1.000 |  1.000 | aaTTTCC
 V$HMGIY_Q6             |     3130 (-) |  0.964 |  0.967 | aaTTTAC
 V$HMGIY_Q6             |     3324 (-) |  1.000 |  0.939 | ctTTTCC
 V$HMGIY_Q6             |     3337 (-) |  1.000 |  0.936 | taTTTCC
 V$HMGIY_Q6             |     3473 (-) |  0.964 |  0.927 | gaTTTAC
 V$HMGIY_Q6             |     3612 (-) |  0.942 |  0.916 | agTTTTC
 V$HMGIY_Q6             |     3658 (+) |  0.964 |  0.946 | GTAAAgt
 V$HMGIY_Q6             |     3836 (-) |  1.000 |  1.000 | aaTTTCC
 V$HMGIY_Q6             |     4050 (+) |  1.000 |  0.936 | GGAAAta
 V$HMGIY_Q6             |     4074 (+) |  0.964 |  0.962 | GTAAAat
 V$HMGIY_Q6             |     4090 (-) |  0.964 |  0.962 | atTTTAC
 V$HMGIY_Q6             |     4113 (-) |  1.000 |  0.995 | atTTTCC
 V$HMGIY_Q6             |     4480 (-) |  0.942 |  0.942 | atTTTTC
 V$HMGIY_Q6             |     4615 (+) |  0.964 |  0.922 | GTAAAac
 V$HMGIY_Q6             |     4638 (+) |  0.957 |  0.955 | GCAAAat
 V$HMGIY_Q6             |     4668 (-) |  0.957 |  0.915 | gtTTTGC
 V$HMGIY_Q6             |     4691 (+) |  1.000 |  0.968 | GGAAAct
 V$HMGIY_Q6             |     5152 (-) |  0.964 |  0.935 | agTTTAC
 V$HMGIY_Q6             |     5342 (-) |  0.957 |  0.915 | gtTTTGC
 V$HMGIY_Q6             |     5390 (-) |  0.964 |  0.962 | atTTTAC
 V$HMGIY_Q6             |     5422 (-) |  1.000 |  0.915 | tcTTTCC
 V$HMGIY_Q6             |     5457 (-) |  1.000 |  0.939 | ctTTTCC
 V$HMGIY_Q6             |     5472 (-) |  1.000 |  0.936 | taTTTCC
 V$HMGIY_Q6             |     5510 (-) |  1.000 |  0.928 | ggTTTCC
 V$HMGIY_Q6             |     5520 (-) |  1.000 |  0.923 | ccTTTCC
 V$HMGIY_Q6             |     5779 (+) |  0.942 |  0.942 | GAAAAat
 V$HMGIY_Q6             |     5862 (-) |  1.000 |  0.928 | ggTTTCC
 V$HMGIY_Q6             |     5942 (+) |  0.942 |  0.926 | GAAAAgt
 V$HMGIY_Q6             |     5947 (+) |  0.964 |  0.962 | GTAAAat
 V$HMGIY_Q6             |     6453 (+) |  0.957 |  0.929 | GCAAAct
 V$HMGIY_Q6             |     6460 (-) |  1.000 |  0.936 | taTTTCC
 V$HMGIY_Q6             |     6580 (+) |  0.957 |  0.915 | GCAAAac
 V$HMGIY_Q6             |     6972 (+) |  1.000 |  0.923 | GGAAAgg
 V$HMGIY_Q6             |     7002 (+) |  1.000 |  0.939 | GGAAAag
 V$HMGIY_Q6             |     7250 (+) |  1.000 |  0.931 | GGAAAaa
 V$HMGIY_Q6             |     7456 (-) |  0.957 |  0.915 | gtTTTGC
 V$HMGIY_Q6             |     7566 (+) |  1.000 |  0.928 | GGAAAcc
 V$HMGIY_Q6             |     8148 (+) |  1.000 |  0.955 | GGAAAac
 V$HMGIY_Q6             |     9109 (+) |  0.957 |  0.915 | GCAAAac
 V$HMGIY_Q6             |     9125 (+) |  1.000 |  0.955 | GGAAAac
 V$HMGIY_Q6             |     9416 (+) |  0.942 |  0.916 | GAAAAct
 V$HMGIY_Q6             |     9510 (-) |  1.000 |  0.968 | agTTTCC
 V$HMGIY_Q6             |     9714 (+) |  0.964 |  0.962 | GTAAAat
 V$HMGIY_Q6             |     9877 (+) |  1.000 |  0.960 | GGAAAtc
 V$HMGIY_Q6             |     9935 (-) |  0.957 |  0.961 | aaTTTGC
 V$HMGIY_Q6             |    10588 (-) |  1.000 |  1.000 | aaTTTCC
 V$HMGIY_Q6             |    11090 (-) |  0.942 |  0.948 | aaTTTTC
 V$HMGIY_Q6             |    11091 (-) |  1.000 |  0.995 | atTTTCC
 V$HMGIY_Q6             |    11274 (+) |  1.000 |  1.000 | GGAAAtt
 V$HMGIY_Q6             |    11384 (+) |  0.942 |  0.916 | GAAAAct
 V$HMGIY_Q6             |    11480 (-) |  1.000 |  0.931 | ttTTTCC
 V$HMGIY_Q6             |    11531 (+) |  0.957 |  0.921 | GCAAAtc
 V$HMGIY_Q6             |    11666 (-) |  0.942 |  0.948 | aaTTTTC
 V$AML1_Q6              |      936 (-) |  1.000 |  1.000 | aCCACA
 V$AML1_Q6              |     3641 (-) |  1.000 |  1.000 | aCCACA
 V$AML1_Q6              |     4145 (+) |  1.000 |  1.000 | TGTGGt
 V$AML1_Q6              |     4441 (-) |  1.000 |  1.000 | aCCACA
 V$AML1_Q6              |     5049 (+) |  1.000 |  1.000 | TGTGGt
 V$AML1_Q6              |     5256 (+) |  1.000 |  1.000 | TGTGGt
 V$AML1_Q6              |     7112 (-) |  1.000 |  1.000 | aCCACA
 V$AML1_Q6              |     8742 (+) |  1.000 |  1.000 | TGTGGt
 V$AML1_Q6              |     8898 (-) |  1.000 |  1.000 | aCCACA
 V$AML1_Q6              |     8975 (+) |  1.000 |  1.000 | TGTGGt
 V$AML1_Q6              |     9400 (+) |  1.000 |  1.000 | TGTGGt
 V$AML1_Q6              |     9575 (+) |  1.000 |  1.000 | TGTGGt
 V$AML1_Q6              |    11256 (+) |  1.000 |  1.000 | TGTGGt
 V$P53_DECAMER_Q2       |      419 (-) |  1.000 |  0.936 | gagCTTGTcc
 V$P53_DECAMER_Q2       |     1346 (-) |  0.977 |  0.973 | aggCTTGCct
 V$P53_DECAMER_Q2       |     3215 (+) |  0.977 |  0.929 | agGCAAGcac
 V$P53_DECAMER_Q2       |     4206 (-) |  0.977 |  0.973 | aggCTTGCct
 V$P53_DECAMER_Q2       |     4401 (+) |  0.930 |  0.930 | agACAGGtca
 V$P53_DECAMER_Q2       |     4416 (-) |  1.000 |  0.941 | aacCTTGTct
 V$P53_DECAMER_Q2       |     6121 (-) |  1.000 |  0.916 | gggCTTGTtt
 V$P53_DECAMER_Q2       |     6894 (+) |  1.000 |  0.937 | agACAAGagg
 V$P53_DECAMER_Q2       |     8754 (-) |  1.000 |  0.911 | cacCTTGTcc
 V$P53_DECAMER_Q2       |     9223 (+) |  0.977 |  0.921 | agGCAAGtta
 V$P53_DECAMER_Q2       |     9539 (+) |  1.000 |  0.917 | aaACAAGtcc
 V$P53_DECAMER_Q2       |     9662 (-) |  1.000 |  0.950 | gacCTTGTct
 V$DR1_Q3               |      947 (+) |  0.855 |  0.818 | ggaaCAATGatca
 V$DR1_Q3               |     4896 (-) |  0.906 |  0.850 | tgttCCTTGgcca
 V$DR1_Q3               |     5453 (-) |  0.849 |  0.812 | taacCTTTTcccc
 V$DR1_Q3               |     6392 (-) |  0.904 |  0.836 | tggcCTGTGttca
 V$DR1_Q3               |     7120 (+) |  0.855 |  0.812 | tgtgCAATGctca
 V$DR1_Q3               |     8376 (-) |  1.000 |  0.838 | tgctCTTTGatct
 V$DR1_Q3               |     8556 (-) |  0.759 |  0.830 | tgaaCAATGtccg
 V$DR1_Q3               |     8582 (+) |  1.000 |  0.840 | ggggCAAAGgcaa
 V$DR1_Q3               |    10799 (-) |  0.906 |  0.841 | tgagCCTTGtgca
 V$PPAR_DR1_Q2          |     3567 (+) |  0.854 |  0.839 | tGGCCTttggcaa
 V$PPAR_DR1_Q2          |     5453 (+) |  0.824 |  0.848 | tAACCTtttcccc
 V$PPAR_DR1_Q2          |     8204 (+) |  0.739 |  0.836 | tCCCCTctgacct
 V$HNF4_DR1_Q3          |      857 (+) |  0.846 |  0.805 | cgatCGTTGccct
 V$HNF4_DR1_Q3          |      947 (-) |  0.846 |  0.836 | ggaaCAATGatca
 V$HNF4_DR1_Q3          |     3567 (+) |  1.000 |  0.876 | tggcCTTTGgcaa
 V$HNF4_DR1_Q3          |     4724 (+) |  0.777 |  0.814 | tgtgATTTGgccc
 V$HNF4_DR1_Q3          |     4896 (+) |  0.893 |  0.872 | tgttCCTTGgcca
 V$HNF4_DR1_Q3          |     6392 (+) |  0.830 |  0.805 | tggcCTGTGttca
 V$HNF4_DR1_Q3          |     7120 (-) |  0.846 |  0.825 | tgtgCAATGctca
 V$HNF4_DR1_Q3          |     8041 (+) |  0.893 |  0.830 | tgggCCTTGactc
 V$HNF4_DR1_Q3          |     8376 (+) |  1.000 |  0.866 | tgctCTTTGatct
 V$HNF4_DR1_Q3          |     8556 (+) |  0.692 |  0.817 | tgaaCAATGtccg
 V$HNF4_DR1_Q3          |     8582 (-) |  1.000 |  0.832 | ggggCAAAGgcaa
 V$HNF4_DR1_Q3          |    10497 (-) |  0.757 |  0.805 | ggatCAAAAgtca
 V$HNF4_DR1_Q3          |    10799 (+) |  0.893 |  0.864 | tgagCCTTGtgca
 V$HNF4_DR1_Q3          |    11281 (-) |  0.846 |  0.803 | aaggCATAGggca
 V$HNF4_DR1_Q3          |    11790 (-) |  0.777 |  0.824 | aggaCAAATccca
 V$HNF4_DR1_Q3          |    11919 (-) |  0.846 |  0.808 | ggccCAACGccca
 V$COUP_DR1_Q6          |     3567 (+) |  0.759 |  0.824 | tGGCCTttggcaa
 V$COUP_DR1_Q6          |    11944 (-) |  0.917 |  0.835 | atttcaaGGGTCa
 V$AML_Q6               |      932 (-) |  1.000 |  0.968 | cgaaaCCACAagtta
 V$AML_Q6               |     3637 (-) |  1.000 |  0.920 | acctaCCACAtggtg
 V$AML_Q6               |     4140 (+) |  1.000 |  0.919 | ctaggTGTGGtgcct
 V$AML_Q6               |     4437 (-) |  1.000 |  0.974 | aaaaaCCACAcaatt
 V$AML_Q6               |     4567 (+) |  0.901 |  0.902 | acagtTGCGGttaga
 V$AML_Q6               |     5044 (+) |  1.000 |  0.963 | attgcTGTGGtctaa
 V$AML_Q6               |     5131 (+) |  0.901 |  0.883 | gatggTGCGGtcaac
 V$AML_Q6               |     5251 (+) |  1.000 |  0.952 | tcacaTGTGGtcaca
 V$AML_Q6               |     6711 (-) |  1.000 |  0.885 | aaaagCCACAacctt
 V$AML_Q6               |     7108 (-) |  1.000 |  0.928 | gtgtaCCACAtgtgt
 V$AML_Q6               |     8737 (+) |  1.000 |  0.940 | cggggTGTGGtggcc
 V$AML_Q6               |     8894 (-) |  1.000 |  0.934 | acgtaCCACAaacag
 V$AML_Q6               |     8970 (+) |  1.000 |  0.922 | ccaggTGTGGtggta
 V$AML_Q6               |     9395 (+) |  1.000 |  0.933 | tggaaTGTGGttcta
 V$AML_Q6               |     9570 (+) |  1.000 |  0.930 | ctgggTGTGGtggta
 V$AML_Q6               |    10950 (+) |  0.901 |  0.883 | gtagcTGCGGtctgt
 V$AML_Q6               |    11251 (+) |  1.000 |  0.972 | aactcTGTGGtgtgc
 V$CEBP_Q3              |      150 (-) |  0.991 |  0.959 | tTTGCTcatctc
 V$CEBP_Q3              |      165 (-) |  0.989 |  0.961 | gTTCCCaatgct
 V$CEBP_Q3              |      324 (+) |  0.987 |  0.959 | ctgtgcTGGAAa
 V$CEBP_Q3              |      335 (-) |  0.989 |  0.966 | aTTCCCtcagac
 V$CEBP_Q3              |      396 (-) |  1.000 |  0.961 | tTTGCCaacaag
 V$CEBP_Q3              |      491 (-) |  0.997 |  0.980 | aTTGCAacatta
 V$CEBP_Q3              |      805 (-) |  0.982 |  0.958 | aTTTCTccagcc
 V$CEBP_Q3              |     1100 (+) |  0.982 |  0.976 | aatttgAGAAAt
 V$CEBP_Q3              |     1135 (-) |  0.980 |  0.979 | gTTCCTaaaacc
 V$CEBP_Q3              |     1465 (-) |  0.982 |  0.976 | gTTTCTcaatat
 V$CEBP_Q3              |     1556 (+) |  0.987 |  0.976 | ctcttcTGGAAa
 V$CEBP_Q3              |     1557 (+) |  0.991 |  0.959 | tcttctGGAAAt
 V$CEBP_Q3              |     1655 (+) |  1.000 |  0.967 | ctacttGGCAAa
 V$CEBP_Q3              |     2370 (-) |  1.000 |  0.981 | tTTGCCacagtt
 V$CEBP_Q3              |     2381 (-) |  0.989 |  0.959 | tTTCCCagagct
 V$CEBP_Q3              |     2402 (-) |  0.980 |  0.974 | tTTCCTtaaaaa
 V$CEBP_Q3              |     2523 (-) |  0.990 |  0.959 | aTTACAtattac
 V$CEBP_Q3              |     2555 (+) |  0.988 |  0.981 | ctgttgTGAAAt
 V$CEBP_Q3              |     2564 (+) |  0.980 |  0.970 | aatttcCGTAAg
 V$CEBP_Q3              |     2566 (-) |  0.976 |  0.972 | tTTCCGtaagta
 V$CEBP_Q3              |     2578 (-) |  0.990 |  0.971 | tTTACAacaaat
 V$CEBP_Q3              |     2623 (+) |  1.000 |  0.962 | atgctaGGCAAa
 V$CEBP_Q3              |     2714 (-) |  0.989 |  0.988 | cTTCCCaaatag
 V$CEBP_Q3              |     2805 (-) |  0.984 |  0.974 | cTTACTgaacac
 V$CEBP_Q3              |     3137 (-) |  0.989 |  0.970 | aTTCCCacaaca
 V$CEBP_Q3              |     3210 (+) |  1.000 |  0.962 | atgctaGGCAAg
 V$CEBP_Q3              |     3325 (-) |  0.991 |  0.958 | tTTTCCtgattc
 V$CEBP_Q3              |     3426 (-) |  0.991 |  0.986 | gTTGCTtaattg
 V$CEBP_Q3              |     3437 (+) |  0.993 |  0.988 | gacttaGGTAAc
 V$CEBP_Q3              |     3569 (+) |  1.000 |  0.996 | gcctttGGCAAg
 V$CEBP_Q3              |     3614 (-) |  0.988 |  0.960 | tTTTCAaatgcg
 V$CEBP_Q3              |     3644 (+) |  0.987 |  0.962 | acatggTGGAAt
 V$CEBP_Q3              |     3679 (-) |  1.000 |  0.967 | aTTGCCaagtgc
 V$CEBP_Q3              |     3741 (-) |  0.982 |  0.965 | aTTTCTacattt
 V$CEBP_Q3              |     4038 (-) |  0.987 |  0.957 | aTTCCAgcaggg
 V$CEBP_Q3              |     4051 (+) |  1.000 |  0.969 | gaaataGGCAAt
 V$CEBP_Q3              |     4067 (+) |  0.990 |  0.960 | aaaataTGTAAa
 V$CEBP_Q3              |     4115 (-) |  0.989 |  0.959 | tTTCCCagatgt
 V$CEBP_Q3              |     4155 (+) |  0.990 |  0.961 | cccattTGTAAt
 V$CEBP_Q3              |     4209 (-) |  1.000 |  0.976 | cTTGCCtcagtt
 V$CEBP_Q3              |     4272 (-) |  0.993 |  0.986 | cTTACCtaagca
 V$CEBP_Q3              |     4708 (+) |  0.993 |  0.987 | gacttgGGTAAt
 V$CEBP_Q3              |     4797 (-) |  0.997 |  0.991 | cTTGCAtaatct
 V$CEBP_Q3              |     5009 (-) |  0.993 |  0.960 | aTTACCcattaa
 V$CEBP_Q3              |     5152 (+) |  0.977 |  0.972 | agtttaCGAAAa
 V$CEBP_Q3              |     5154 (-) |  0.980 |  0.978 | tTTACGaaaagg
 V$CEBP_Q3              |     5444 (-) |  1.000 |  0.969 | aTTGCCatataa
 V$CEBP_Q3              |     5458 (-) |  0.991 |  0.967 | tTTTCCccacat
 V$CEBP_Q3              |     5473 (-) |  0.991 |  0.958 | aTTTCCtgattt
 V$CEBP_Q3              |     5781 (+) |  0.988 |  0.957 | aaaataTGAAAt
 V$CEBP_Q3              |     5917 (-) |  0.991 |  0.965 | gTTTCCccagcg
 V$CEBP_Q3              |     6179 (-) |  0.989 |  0.959 | gTTCCCagagac
 V$CEBP_Q3              |     6494 (-) |  0.997 |  0.959 | aTTGCAgatgcg
 V$CEBP_Q3              |     6547 (+) |  0.993 |  0.969 | ggctgaGGTAAg
 V$CEBP_Q3              |     6566 (-) |  1.000 |  0.981 | gTTGCCacagtt
 V$CEBP_Q3              |     6573 (+) |  0.997 |  0.992 | cagttaTGCAAa
 V$CEBP_Q3              |     6610 (-) |  0.991 |  0.991 | tTTGCTaaactc
 V$CEBP_Q3              |     7056 (-) |  0.982 |  0.978 | tTTTCTtaattt
 V$CEBP_Q3              |     7172 (-) |  0.997 |  0.958 | gTTGCAgatggt
 V$CEBP_Q3              |     7345 (-) |  0.988 |  0.969 | aTTTCAacatgt
 V$CEBP_Q3              |     7404 (-) |  0.984 |  0.974 | aTTACTgaagaa
 V$CEBP_Q3              |     7559 (+) |  0.987 |  0.960 | agatgcTGGAAa
 V$CEBP_Q3              |     7840 (+) |  1.000 |  0.968 | acttctGGCAAa
 V$CEBP_Q3              |     8006 (+) |  0.990 |  0.965 | tgttggTGTAAc
 V$CEBP_Q3              |     8073 (-) |  0.997 |  0.986 | aTTGCAgaaact
 V$CEBP_Q3              |     8141 (+) |  0.989 |  0.966 | tgctgaGGGAAa
 V$CEBP_Q3              |     8352 (-) |  1.000 |  0.962 | cTTGCCaacccc
 V$CEBP_Q3              |     8434 (+) |  0.997 |  0.965 | gagcttTGCAAc
 V$CEBP_Q3              |     8468 (+) |  1.000 |  0.964 | atctaaGGCAAa
 V$CEBP_Q3              |     8493 (-) |  0.982 |  0.962 | tTTTCTacaggg
 V$CEBP_Q3              |     8578 (+) |  1.000 |  0.977 | aaatggGGCAAa
 V$CEBP_Q3              |     8623 (+) |  0.982 |  0.974 | actttgAGAAAa
 V$CEBP_Q3              |     8652 (-) |  0.989 |  0.961 | aTTCCCaatggt
 V$CEBP_Q3              |     8694 (+) |  0.988 |  0.976 | cctttcTGAAAa
 V$CEBP_Q3              |     8695 (-) |  0.982 |  0.971 | cTTTCTgaaaat
 V$CEBP_Q3              |     8907 (+) |  0.980 |  0.972 | agattcAGGAAt
 V$CEBP_Q3              |     8995 (-) |  0.987 |  0.959 | aTTCCAgcacat
 V$CEBP_Q3              |     9100 (-) |  0.990 |  0.988 | cTTACAaaagca
 V$CEBP_Q3              |     9450 (-) |  0.993 |  0.967 | tTTACCaatctc
 V$CEBP_Q3              |     9486 (+) |  0.997 |  0.968 | tttattTGCAAt
 V$CEBP_Q3              |     9490 (-) |  0.997 |  0.965 | tTTGCAatagaa
 V$CEBP_Q3              |     9511 (-) |  0.991 |  0.966 | gTTTCCccatgt
 V$CEBP_Q3              |     9512 (-) |  0.989 |  0.957 | tTTCCCcatgtc
 V$CEBP_Q3              |     9601 (+) |  0.989 |  0.988 | gcatttGGGAAg
 V$CEBP_Q3              |     9707 (+) |  0.990 |  0.967 | tggtggTGTAAa
 V$CEBP_Q3              |     9756 (+) |  0.988 |  0.959 | taatatTGAAAa
 V$CEBP_Q3              |     9789 (+) |  0.984 |  0.975 | ttgttcAGTAAa
 V$CEBP_Q3              |     9871 (+) |  0.991 |  0.969 | gaatgaGGAAAt
 V$CEBP_Q3              |     9922 (-) |  1.000 |  0.966 | tTTGCCtatggg
 V$CEBP_Q3              |     9926 (+) |  0.993 |  0.958 | cctatgGGTAAt
 V$CEBP_Q3              |    10070 (+) |  0.987 |  0.976 | gtcttcTGGAAg
 V$CEBP_Q3              |    10132 (+) |  0.982 |  0.978 | tagttaAGAAAt
 V$CEBP_Q3              |    10371 (-) |  0.988 |  0.986 | cTTTCAaaatgt
 V$CEBP_Q3              |    10377 (+) |  0.997 |  0.980 | aaatgtTGCAAt
 V$CEBP_Q3              |    10589 (-) |  0.991 |  0.959 | aTTTCCtatatc
 V$CEBP_Q3              |    10622 (+) |  0.982 |  0.962 | agttgtAGAAAg
 V$CEBP_Q3              |    10686 (+) |  1.000 |  0.969 | gactctGGCAAc
 V$CEBP_Q3              |    10703 (+) |  0.988 |  0.981 | tgtttaTGAAAc
 V$CEBP_Q3              |    10907 (+) |  0.997 |  0.960 | ctactaTGCAAa
 V$CEBP_Q3              |    10968 (+) |  0.991 |  0.965 | tgttggAGCAAg
 V$CEBP_Q3              |    11081 (+) |  0.989 |  0.959 | tgctctGGGAAt
 V$CEBP_Q3              |    11150 (+) |  0.988 |  0.964 | ctctgaTGAAAa
 V$CEBP_Q3              |    11284 (+) |  1.000 |  0.963 | gcatagGGCAAa
 V$CEBP_Q3              |    11576 (-) |  0.991 |  0.959 | aTTGCTtatatc
 V$CEBP_Q3              |    11668 (-) |  0.988 |  0.983 | tTTTCAtaacca
 V$CEBP_Q3              |    11728 (-) |  0.982 |  0.975 | tTTTCTcaaaca
 V$CEBP_Q3              |    11780 (+) |  0.990 |  0.965 | acttgaTGTAAg
 V$ETS_Q4               |      606 (+) |  0.922 |  0.908 | ttaaacATCCTg
 V$ETS_Q4               |     1192 (-) |  1.000 |  0.911 | cAGGAAagctgg
 V$ETS_Q4               |     1726 (+) |  0.922 |  0.898 | gggctcATCCTg
 V$ETS_Q4               |     1735 (+) |  1.000 |  0.935 | ctgaacTTCCTa
 V$ETS_Q4               |     2143 (+) |  1.000 |  0.934 | tctctcTTCCTt
 V$ETS_Q4               |     2147 (+) |  1.000 |  0.924 | tcttccTTCCTt
 V$ETS_Q4               |     2151 (+) |  1.000 |  0.938 | ccttccTTCCTc
 V$ETS_Q4               |     2157 (+) |  1.000 |  0.937 | ttcctcTTCCTt
 V$ETS_Q4               |     2201 (+) |  1.000 |  0.925 | tctttcTTCCTt
 V$ETS_Q4               |     2682 (+) |  0.922 |  0.902 | cgttgcATCCTg
 V$ETS_Q4               |     2703 (+) |  1.000 |  0.941 | ttctccTTCCTc
 V$ETS_Q4               |     2781 (+) |  1.000 |  0.931 | agattcTTCCTt
 V$ETS_Q4               |     2985 (+) |  0.914 |  0.896 | atctacTTCCGc
 V$ETS_Q4               |     3321 (+) |  1.000 |  0.924 | ggccttTTCCTg
 V$ETS_Q4               |     4689 (-) |  1.000 |  0.919 | cAGGAAacttga
 V$ETS_Q4               |     4963 (-) |  1.000 |  0.977 | cAGGAAgtcagg
 V$ETS_Q4               |     5122 (-) |  1.000 |  0.899 | aAGGAAacagat
 V$ETS_Q4               |     5263 (+) |  0.922 |  0.900 | acagtcATCCTg
 V$ETS_Q4               |     5469 (+) |  1.000 |  0.938 | tactatTTCCTg
 V$ETS_Q4               |     5517 (+) |  1.000 |  0.902 | ctgcctTTCCTc
 V$ETS_Q4               |     6085 (+) |  1.000 |  0.919 | tgtgagTTCCTg
 V$ETS_Q4               |     6276 (-) |  1.000 |  0.936 | aAGGAAgcctct
 V$ETS_Q4               |     6457 (+) |  1.000 |  0.944 | acttatTTCCTg
 V$ETS_Q4               |     6479 (-) |  0.922 |  0.902 | cAGGATgaggac
 V$ETS_Q4               |     6795 (+) |  1.000 |  0.948 | tggctcTTCCTc
 V$ETS_Q4               |     6878 (-) |  1.000 |  0.927 | tAGGAAgcacca
 V$ETS_Q4               |     6919 (-) |  1.000 |  0.902 | aAGGAAttgatt
 V$ETS_Q4               |     7015 (+) |  1.000 |  0.916 | ggatgtTTCCTg
 V$ETS_Q4               |     7231 (-) |  1.000 |  0.985 | cAGGAAgttcat
 V$ETS_Q4               |     7248 (-) |  1.000 |  0.915 | cAGGAAaaagtc
 V$ETS_Q4               |     8078 (+) |  1.000 |  0.943 | agaaacTTCCTa
 V$ETS_Q4               |     8679 (-) |  1.000 |  0.926 | tAGGAAggtaat
 V$ETS_Q4               |     8912 (-) |  1.000 |  0.898 | cAGGAAtactcg
 V$ETS_Q4               |     9436 (-) |  1.000 |  0.966 | cAGGAAgcccaa
 V$ETS_Q4               |     9469 (-) |  0.922 |  0.910 | cAGGATgttcta
 V$ETS_Q4               |     9875 (-) |  1.000 |  0.921 | gAGGAAatcaat
 V$ETS_Q4               |    10258 (-) |  1.000 |  0.998 | cAGGAAgtgatt
 V$ETS_Q4               |    10585 (+) |  1.000 |  0.895 | ttcaatTTCCTa
 V$ETS_Q4               |    10639 (-) |  1.000 |  0.933 | gAGGAAgacacc
 V$ETS_Q4               |    10845 (-) |  1.000 |  0.959 | cAGGAAgaagcc
 V$ETS_Q4               |    11272 (-) |  1.000 |  0.896 | aAGGAAattaag
 V$MYB_Q3               |      127 (-) |  1.000 |  0.962 | tAACTGctcag
 V$MYB_Q3               |      158 (+) |  0.980 |  0.945 | tctctCCGTTc
 V$MYB_Q3               |      449 (+) |  0.962 |  0.956 | gttgtCTGTTt
 V$MYB_Q3               |      591 (-) |  0.962 |  0.959 | tAACAGactta
 V$MYB_Q3               |      981 (+) |  1.000 |  0.964 | catcaCAGTTa
 V$MYB_Q3               |     1024 (+) |  1.000 |  0.997 | attggCAGTTg
 V$MYB_Q3               |     1862 (-) |  1.000 |  0.970 | cAACTGaagaa
 V$MYB_Q3               |     2372 (+) |  1.000 |  0.963 | tgccaCAGTTt
 V$MYB_Q3               |     2823 (+) |  1.000 |  0.970 | ctgtcCAGTTg
 V$MYB_Q3               |     3397 (+) |  1.000 |  0.970 | atctcCAGTTa
 V$MYB_Q3               |     3443 (+) |  1.000 |  0.965 | ggtaaCAGTTa
 V$MYB_Q3               |     3606 (+) |  1.000 |  0.966 | ttctgCAGTTt
 V$MYB_Q3               |     4211 (+) |  1.000 |  0.967 | tgcctCAGTTa
 V$MYB_Q3               |     4321 (-) |  1.000 |  0.965 | aAACTGggtct
 V$MYB_Q3               |     4539 (-) |  0.962 |  0.964 | cAACAGcctct
 V$MYB_Q3               |     4563 (+) |  1.000 |  0.968 | ggacaCAGTTg
 V$MYB_Q3               |     4944 (-) |  1.000 |  0.966 | gAACTGggact
 V$MYB_Q3               |     5146 (+) |  1.000 |  0.992 | ctaggCAGTTt
 V$MYB_Q3               |     5281 (-) |  0.962 |  0.963 | cAACAGgctca
 V$MYB_Q3               |     5729 (-) |  1.000 |  0.969 | aAACTGgaagc
 V$MYB_Q3               |     6388 (-) |  1.000 |  0.993 | gAACTGgcctg
 V$MYB_Q3               |     6568 (+) |  1.000 |  0.967 | tgccaCAGTTa
 V$MYB_Q3               |     6847 (-) |  1.000 |  0.962 | cAACTGgtgag
 V$MYB_Q3               |     7187 (-) |  0.980 |  0.977 | gAACGGccacg
 V$MYB_Q3               |     7488 (+) |  0.962 |  0.957 | cacgtCTGTTc
 V$MYB_Q3               |     7523 (-) |  1.000 |  0.968 | gAACTGaagtt
 V$MYB_Q3               |     7530 (+) |  1.000 |  0.974 | agttaCAGTTg
 V$MYB_Q3               |     7550 (-) |  1.000 |  0.965 | cAACTGtgtag
 V$MYB_Q3               |     7602 (-) |  1.000 |  0.959 | gAACTGctgag
 V$MYB_Q3               |     7721 (+) |  1.000 |  0.959 | atcagCAGTTt
 V$MYB_Q3               |     8000 (+) |  0.962 |  0.963 | tgtgcCTGTTg
 V$MYB_Q3               |     8194 (+) |  0.962 |  0.958 | tctgcCTGTTt
 V$MYB_Q3               |     8212 (+) |  1.000 |  0.962 | gacctCAGTTc
 V$MYB_Q3               |     8725 (-) |  1.000 |  0.970 | gAACTGtaacg
 V$MYB_Q3               |     9130 (+) |  1.000 |  0.969 | accttCAGTTt
 V$MYB_Q3               |     9559 (+) |  0.968 |  0.964 | cctgtCGGTTt
 V$MYB_Q3               |     9765 (-) |  0.962 |  0.956 | aAACAGtcatg
 V$MYB_Q3               |    10058 (-) |  1.000 |  0.970 | gAACTGaaccg
 V$MYB_Q3               |    10192 (+) |  1.000 |  0.996 | gcagtCAGTTc
 V$MYB_Q3               |    10310 (-) |  1.000 |  0.963 | tAACTGttttt
 V$MYB_Q3               |    10962 (+) |  0.962 |  0.963 | tgtgcCTGTTg
 V$MYB_Q3               |    11065 (+) |  1.000 |  0.962 | gtgatCAGTTa
 V$MYB_Q3               |    11135 (+) |  1.000 |  0.963 | gcactCAGTTt
 V$MYB_Q3               |    11219 (-) |  1.000 |  0.993 | gAACTGcccag
 V$MYB_Q3               |    11222 (+) |  1.000 |  0.961 | ctgccCAGTTt
 V$MYB_Q3               |    11237 (-) |  1.000 |  0.970 | tAACTGgagtc
 V$MYB_Q3               |    11514 (+) |  0.980 |  0.951 | tattaCCGTTg
 V$MYB_Q3               |    11712 (-) |  1.000 |  0.996 | cAACTGccctc
 V$NFKB_Q6_01           |      326 (+) |  1.000 |  0.996 | gtgctGGAAAttccct
 V$NFY_Q6_01            |     1022 (-) |  1.000 |  0.972 | tgATTGGcagttg
 V$NFY_Q6_01            |    11893 (+) |  1.000 |  0.960 | tctcaaCCAATag
 V$NFY_Q6_01            |    11929 (-) |  1.000 |  0.974 | ccATTGGctgaaa
 V$SREBP_Q3             |       99 (-) |  0.817 |  0.768 | tcGCCTGggggt
 V$SREBP_Q3             |      130 (+) |  0.807 |  0.828 | ctgctCAGTCaa
 V$SREBP_Q3             |      134 (+) |  0.776 |  0.828 | tcagtCAATCca
 V$SREBP_Q3             |      193 (+) |  0.936 |  0.873 | cctccCACACca
 V$SREBP_Q3             |      249 (-) |  0.892 |  0.812 | tgGGCTGtaagg
 V$SREBP_Q3             |      413 (-) |  1.000 |  0.784 | atGGGTGagctt
 V$SREBP_Q3             |      459 (-) |  0.861 |  0.780 | ttGGTTGgctta
 V$SREBP_Q3             |      533 (-) |  1.000 |  0.791 | atGGGTGatgcg
 V$SREBP_Q3             |      684 (+) |  0.936 |  0.842 | tcagaCACACca
 V$SREBP_Q3             |      781 (-) |  1.000 |  0.877 | tcGGGTGctctt
 V$SREBP_Q3             |     1279 (-) |  0.861 |  0.895 | tgGGATGacagg
 V$SREBP_Q3             |     1355 (+) |  0.741 |  0.780 | tgggtCACCTga
 V$SREBP_Q3             |     1421 (+) |  0.926 |  0.803 | tgagaCACGCaa
 V$SREBP_Q3             |     1681 (-) |  1.000 |  0.872 | tcGGGTGtcagc
 V$SREBP_Q3             |     1947 (-) |  0.892 |  0.822 | taGGCTGgaact
 V$SREBP_Q3             |     2297 (-) |  0.936 |  0.821 | ttGTGTGtgtgt
 V$SREBP_Q3             |     2334 (+) |  0.741 |  0.794 | tatgtGACCCta
 V$SREBP_Q3             |     3080 (-) |  1.000 |  0.812 | caGGGTGattct
 V$SREBP_Q3             |     3230 (+) |  0.892 |  0.884 | ccagtCAGCCaa
 V$SREBP_Q3             |     3243 (+) |  0.892 |  0.843 | attccCAGCCca
 V$SREBP_Q3             |     3286 (-) |  0.861 |  0.896 | tgGGATGaggtg
 V$SREBP_Q3             |     3291 (-) |  0.741 |  0.805 | tgAGGTGaacat
 V$SREBP_Q3             |     3354 (+) |  0.828 |  0.770 | tcagaCAGACca
 V$SREBP_Q3             |     3722 (-) |  1.000 |  0.778 | acGGGTGactaa
 V$SREBP_Q3             |     3951 (+) |  0.861 |  0.802 | tcagcCATCCta
 V$SREBP_Q3             |     4257 (-) |  0.861 |  0.777 | ttGGTTGttagg
 V$SREBP_Q3             |     4265 (-) |  0.861 |  0.802 | taGGATGcttac
 V$SREBP_Q3             |     4329 (-) |  0.741 |  0.792 | tcTGGTGacatc
 V$SREBP_Q3             |     4438 (+) |  0.936 |  0.848 | aaaacCACACaa
 V$SREBP_Q3             |     4512 (+) |  0.828 |  0.881 | aacatCAGACca
 V$SREBP_Q3             |     4711 (-) |  0.741 |  0.781 | ttGGGTAattca
 V$SREBP_Q3             |     5031 (-) |  0.861 |  0.810 | tgGGATGctcag
 V$SREBP_Q3             |     5092 (-) |  0.797 |  0.770 | tgGTTTGggtta
 V$SREBP_Q3             |     5096 (-) |  0.741 |  0.790 | ttGGGTTattat
 V$SREBP_Q3             |     5137 (+) |  0.861 |  0.889 | gcggtCAACCta
 V$SREBP_Q3             |     5298 (+) |  0.861 |  0.791 | ctagcCATCCaa
 V$SREBP_Q3             |     5764 (-) |  0.741 |  0.794 | taGGGTAaaagg
 V$SREBP_Q3             |     5821 (-) |  0.926 |  0.866 | tgGCGTGgcact
 V$SREBP_Q3             |     6392 (-) |  0.817 |  0.776 | tgGCCTGtgttc
 V$SREBP_Q3             |     6435 (+) |  0.861 |  0.886 | tcggtCAACCca
 V$SREBP_Q3             |     6526 (+) |  1.000 |  0.795 | aagttCACCCtg
 V$SREBP_Q3             |     6728 (-) |  1.000 |  0.805 | aaGGGTGagcag
 V$SREBP_Q3             |     7102 (-) |  0.828 |  0.773 | taGTCTGtgtac
 V$SREBP_Q3             |     7472 (-) |  0.915 |  0.797 | ttGAGTGtgcta
 V$SREBP_Q3             |     7517 (-) |  0.817 |  0.856 | tgGCCTGaactg
 V$SREBP_Q3             |     7538 (-) |  0.861 |  0.773 | ttGGTTGtgagc
 V$SREBP_Q3             |     7583 (+) |  0.797 |  0.821 | caggtCAAACaa
 V$SREBP_Q3             |     7612 (+) |  0.656 |  0.770 | gccatCTCTCca
 V$SREBP_Q3             |     7936 (-) |  0.936 |  0.828 | ttGTGTGtttag
 V$SREBP_Q3             |     7956 (+) |  0.828 |  0.780 | tacccCAGACta
 V$SREBP_Q3             |     8009 (-) |  0.678 |  0.773 | tgGTGTAacctt
 V$SREBP_Q3             |     8129 (-) |  0.828 |  0.791 | tgGTCTGctttc
 V$SREBP_Q3             |     8397 (+) |  0.786 |  0.776 | gaagcCAAGCca
 V$SREBP_Q3             |     8444 (+) |  0.861 |  0.792 | acccgCATCCta
 V$SREBP_Q3             |     8662 (+) |  0.797 |  0.845 | gttttCAAACca
 V$SREBP_Q3             |     8961 (-) |  0.741 |  0.785 | taGGGAGaacca
 V$SREBP_Q3             |     9063 (+) |  0.817 |  0.772 | agttcCAGGCta
 V$SREBP_Q3             |     9187 (+) |  0.915 |  0.838 | gagacCACTCaa
 V$SREBP_Q3             |     9299 (-) |  0.936 |  0.821 | ttGTGTGcccag
 V$SREBP_Q3             |     9321 (-) |  0.741 |  0.787 | ttGGGTCagagc
 V$SREBP_Q3             |     9729 (-) |  0.797 |  0.828 | ttGTATGataat
 V$SREBP_Q3             |     9767 (+) |  0.786 |  0.845 | acagtCATGCca
 V$SREBP_Q3             |    10177 (-) |  0.936 |  0.842 | taGTGTGtgtgt
 V$SREBP_Q3             |    10236 (-) |  0.861 |  0.820 | taGGTTGgtggt
 V$SREBP_Q3             |    10877 (-) |  0.678 |  0.777 | tgGTGGGagcac
 V$SREBP_Q3             |    11181 (-) |  0.892 |  0.791 | ttGGCTGccttg
 V$SREBP_Q3             |    11197 (-) |  0.776 |  0.813 | ttGATTGattat
 V$SREBP_Q3             |    11213 (-) |  0.797 |  0.811 | ttGTTTGaactg
 V$SREBP_Q3             |    11258 (-) |  0.936 |  0.852 | tgGTGTGccaag
 V$SREBP_Q3             |    11313 (-) |  0.741 |  0.808 | taCGGTGacgac
 V$SREBP_Q3             |    11555 (+) |  0.861 |  0.856 | gtattCAACCaa
 V$SREBP_Q3             |    11600 (-) |  0.915 |  0.818 | taGAGTGcacag
 V$SREBP_Q3             |    11702 (+) |  1.000 |  0.988 | actgtCACCCca
 V$SREBP_Q3             |    11736 (+) |  0.678 |  0.780 | aacatCTCACca
 V$SREBP_Q3             |    11738 (+) |  0.741 |  0.783 | catctCACCAaa
 V$SREBP_Q3             |    11824 (-) |  1.000 |  0.978 | tgGGGTGagaaa
 V$SREBP_Q3             |    11891 (+) |  0.861 |  0.863 | actctCAACCaa
 V$SREBP_Q3             |    11932 (-) |  0.892 |  0.873 | ttGGCTGaaact
 V$STAT_Q6              |      556 (+) |  0.984 |  0.986 | accttTTCTAgga
 V$STAT_Q6              |     3259 (+) |  0.994 |  0.935 | tggttTTCTTggt
 V$STAT_Q6              |     3689 (-) |  0.994 |  0.937 | gccAAGAAcacaa
 V$STAT_Q6              |     4131 (-) |  1.000 |  0.937 | accCAGAAtctag
 V$STAT_Q6              |     6125 (+) |  0.981 |  0.930 | ttgttTTCTCggc
 V$STAT_Q6              |     6634 (-) |  1.000 |  0.938 | accCAGAAggcac
 V$STAT_Q6              |     7494 (+) |  0.994 |  0.992 | tgttcTTCTTgga
 V$STAT_Q6              |     8546 (-) |  0.981 |  0.933 | gccGAGAAaatga
 V$STAT_Q6              |     9563 (+) |  1.000 |  0.938 | tcggtTTCTGggt
 V$STAT_Q6              |    10053 (-) |  0.994 |  0.940 | tctAAGAActgaa
 V$STAT_Q6              |    11264 (-) |  0.994 |  0.945 | gccAAGAAaagga
 P$EMBP1_02             |      434 (-) |  1.000 |  0.951 | acCACGTtta
 P$EMBP1_02             |      735 (+) |  1.000 |  0.928 | accACGTGgt
 P$EMBP1_02             |      735 (-) |  1.000 |  0.928 | acCACGTggt
 P$EMBP1_02             |     1126 (-) |  1.000 |  0.943 | tgCACGTgtg
 P$EMBP1_02             |     6886 (-) |  1.000 |  0.926 | acCACGTaag
 V$GATA_Q6              |       84 (+) |  0.984 |  0.978 | tGATAGg
 V$GATA_Q6              |       92 (-) |  0.984 |  0.984 | cCTATCt
 V$GATA_Q6              |      308 (-) |  0.984 |  0.976 | gCTATCt
 V$GATA_Q6              |      568 (+) |  1.000 |  0.995 | aGATAAa
 V$GATA_Q6              |     1996 (-) |  1.000 |  0.990 | aTTATCt
 V$GATA_Q6              |     2724 (+) |  1.000 |  0.990 | aGATAAt
 V$GATA_Q6              |     3931 (-) |  1.000 |  0.985 | aTTATCa
 V$GATA_Q6              |     4375 (-) |  1.000 |  0.992 | gTTATCt
 V$GATA_Q6              |     5979 (+) |  1.000 |  0.987 | tGATAAc
 V$GATA_Q6              |     6467 (+) |  1.000 |  0.989 | tGATAAa
 V$GATA_Q6              |     7799 (+) |  1.000 |  0.995 | aGATAAa
 V$GATA_Q6              |     8063 (-) |  1.000 |  0.995 | tTTATCt
 V$GATA_Q6              |     8605 (-) |  1.000 |  0.985 | aTTATCa
 V$GATA_Q6              |     9734 (+) |  1.000 |  0.985 | tGATAAt
 V$GATA_Q6              |    11370 (-) |  0.984 |  0.979 | tCTATCt
 V$GATA_Q6              |    11442 (-) |  1.000 |  1.000 | cTTATCt
 V$GATA_Q6              |    11570 (-) |  1.000 |  0.994 | cTTATCa
 V$HNF1_Q6              |      986 (+) |  1.000 |  0.950 | cagTTAATaattttcatg
 V$HNF1_Q6              |     3411 (+) |  1.000 |  0.926 | aagTTAATgattctggtt
 V$HNF1_Q6              |     4054 (-) |  1.000 |  0.891 | ataggcaataATTAAaat
 V$HNF1_Q6              |     5098 (+) |  0.935 |  0.879 | gggTTATTatttgtgagt
 V$HNF1_Q6              |     5784 (-) |  1.000 |  0.883 | atatgaaataATTAAata
 V$HNF1_Q6              |     7353 (+) |  1.000 |  0.898 | atgTTAATcatgggcaga
 V$HNF1_Q6              |     7822 (-) |  1.000 |  0.927 | aaaacaaacaATTAAccc
 V$HNF1_Q6              |    11693 (+) |  1.000 |  0.869 | aagTTAATcactgtcacc
 V$HNF3_Q6              |      213 (-) |  0.977 |  0.923 | ggTATTTtttttt
 V$HNF3_Q6              |      229 (-) |  0.952 |  0.927 | ccTTTTTgtcttt
 V$HNF3_Q6              |      506 (-) |  0.977 |  0.944 | taTATTTgtcttc
 V$HNF3_Q6              |      846 (+) |  0.977 |  0.949 | ttaaatAAATAcg
 V$HNF3_Q6              |      875 (+) |  1.000 |  0.959 | atgcacAAACAcg
 V$HNF3_Q6              |      953 (+) |  0.977 |  0.918 | atgatcAAATAtt
 V$HNF3_Q6              |     1472 (-) |  0.977 |  0.943 | aaTATTTgctctg
 V$HNF3_Q6              |     1527 (-) |  1.000 |  0.936 | gcTGTTTttttgt
 V$HNF3_Q6              |     1531 (-) |  0.952 |  0.939 | ttTTTTTgttcta
 V$HNF3_Q6              |     1894 (-) |  0.977 |  0.944 | taTATTTatttta
 V$HNF3_Q6              |     2292 (-) |  0.952 |  0.916 | agTTTTTgtgtgt
 V$HNF3_Q6              |     2361 (-) |  0.977 |  0.947 | tgTATTTattttg
 V$HNF3_Q6              |     2408 (+) |  1.000 |  0.943 | taaaaaAAACAaa
 V$HNF3_Q6              |     2412 (+) |  0.952 |  0.951 | aaaaacAAAAAat
 V$HNF3_Q6              |     3595 (-) |  1.000 |  0.914 | taTGTTTgggttt
 V$HNF3_Q6              |     3806 (+) |  1.000 |  0.930 | tagaaaAAACAtc
 V$HNF3_Q6              |     4006 (+) |  0.977 |  0.958 | ataaatAAATAtt
 V$HNF3_Q6              |     4219 (+) |  0.977 |  0.934 | ttaaaaAAATAaa
 V$HNF3_Q6              |     4424 (+) |  0.952 |  0.917 | ctaaaaAAAAAaa
 V$HNF3_Q6              |     4489 (+) |  0.952 |  0.943 | ttgaacAAAAAac
 V$HNF3_Q6              |     4492 (+) |  1.000 |  0.930 | aacaaaAAACAaa
 V$HNF3_Q6              |     5103 (-) |  0.977 |  0.915 | atTATTTgtgagt
 V$HNF3_Q6              |     5120 (+) |  1.000 |  0.924 | aaaaggAAACAga
 V$HNF3_Q6              |     5400 (-) |  0.977 |  0.931 | taTATTTtttcat
 V$HNF3_Q6              |     5435 (-) |  0.977 |  0.951 | ttTATTTgtattg
 V$HNF3_Q6              |     5644 (+) |  0.952 |  0.927 | caaaatAAAAAga
 V$HNF3_Q6              |     5797 (+) |  0.952 |  0.931 | aaatacAAAAAaa
 V$HNF3_Q6              |     5806 (+) |  0.977 |  0.924 | aaaaaaAAATAgc
 V$HNF3_Q6              |     6253 (-) |  0.977 |  0.924 | tcTATTTgtccca
 V$HNF3_Q6              |     6588 (+) |  0.977 |  0.966 | caaaacAAATAag
 V$HNF3_Q6              |     6606 (-) |  0.977 |  0.930 | gcTATTTgctaaa
 V$HNF3_Q6              |     6651 (+) |  1.000 |  0.937 | gtctgcAAACAga
 V$HNF3_Q6              |     7048 (-) |  0.977 |  0.924 | acTATTTtttttc
 V$HNF3_Q6              |     7065 (-) |  1.000 |  0.920 | ttTGTTTttgttt
 V$HNF3_Q6              |     7067 (-) |  0.952 |  0.944 | tgTTTTTgtttgt
 V$HNF3_Q6              |     7071 (-) |  1.000 |  0.971 | ttTGTTTgtgtat
 V$HNF3_Q6              |     7211 (+) |  0.952 |  0.949 | ttgaacAAAAAgt
 V$HNF3_Q6              |     7426 (-) |  0.977 |  0.971 | ttTATTTgttttt
 V$HNF3_Q6              |     7430 (-) |  1.000 |  0.928 | ttTGTTTttattt
 V$HNF3_Q6              |     7432 (-) |  0.952 |  0.923 | tgTTTTTatttta
 V$HNF3_Q6              |     7770 (+) |  1.000 |  0.938 | ctcaaaAAACAaa
 V$HNF3_Q6              |     7779 (+) |  0.952 |  0.950 | caaaacAAAAAtt
 V$HNF3_Q6              |     7821 (+) |  1.000 |  0.989 | caaaacAAACAat
 V$HNF3_Q6              |     7893 (-) |  0.952 |  0.921 | ggTTTTTattttg
 V$HNF3_Q6              |     7939 (-) |  1.000 |  0.919 | tgTGTTTagtttt
 V$HNF3_Q6              |     7970 (-) |  1.000 |  0.984 | gtTGTTTgttttt
 V$HNF3_Q6              |     7974 (-) |  1.000 |  0.913 | ttTGTTTttcaag
 V$HNF3_Q6              |     8185 (-) |  1.000 |  0.957 | ctTGTTTgctctg
 V$HNF3_Q6              |     8336 (-) |  0.977 |  0.922 | agTATTTgctgga
 V$HNF3_Q6              |     8897 (+) |  1.000 |  0.940 | taccacAAACAga
 V$HNF3_Q6              |     9110 (+) |  0.952 |  0.944 | caaaacAAAAAac
 V$HNF3_Q6              |     9533 (+) |  1.000 |  0.974 | tagaacAAACAag
 V$HNF3_Q6              |     9724 (-) |  0.947 |  0.917 | tcTCTTTgtatga
 V$HNF3_Q6              |     9918 (-) |  0.952 |  0.914 | gaTTTTTgcctat
 V$HNF3_Q6              |    10312 (-) |  1.000 |  0.938 | acTGTTTttatat
 V$HNF3_Q6              |    10322 (-) |  0.952 |  0.923 | taTTTTTatttta
 V$HNF3_Q6              |    10701 (-) |  1.000 |  0.918 | cgTGTTTatgaaa
 V$HNF3_Q6              |    10910 (+) |  0.977 |  0.940 | ctatgcAAATAat
 V$HNF3_Q6              |    11189 (-) |  1.000 |  0.931 | ctTGTTTcttgat
 V$HNF3_Q6              |    11468 (-) |  0.952 |  0.921 | atTTTTTatttgt
 V$HNF3_Q6              |    11472 (-) |  0.977 |  0.971 | ttTATTTgttttt
 V$HNF3_Q6              |    11502 (-) |  0.952 |  0.915 | aaTTTTTgtggat
 V$SMAD_Q6              |      301 (+) |  0.996 |  0.974 | AGACTgagc
 V$SMAD_Q6              |      343 (+) |  1.000 |  0.984 | AGACActtc
 V$SMAD_Q6              |      595 (+) |  0.996 |  0.969 | AGACTtact
 V$SMAD_Q6              |      686 (+) |  1.000 |  0.987 | AGACAcacc
 V$SMAD_Q6              |     1423 (+) |  1.000 |  0.984 | AGACAcgca
 V$SMAD_Q6              |     1611 (-) |  0.989 |  0.990 | agggGGTCT
 V$SMAD_Q6              |     1829 (+) |  1.000 |  0.997 | AGACAccca
 V$SMAD_Q6              |     1919 (+) |  1.000 |  0.977 | AGACAgagt
 V$SMAD_Q6              |     1925 (-) |  1.000 |  0.973 | agtaTGTCT
 V$SMAD_Q6              |     2065 (-) |  1.000 |  0.974 | tctcTGTCT
 V$SMAD_Q6              |     2071 (-) |  1.000 |  0.974 | tctcTGTCT
 V$SMAD_Q6              |     2077 (-) |  1.000 |  0.974 | tctcTGTCT
 V$SMAD_Q6              |     2081 (-) |  1.000 |  0.977 | tgtcTGTCT
 V$SMAD_Q6              |     2089 (-) |  1.000 |  0.974 | tctcTGTCT
 V$SMAD_Q6              |     2097 (-) |  1.000 |  0.974 | tctcTGTCT
 V$SMAD_Q6              |     2105 (-) |  1.000 |  0.974 | tctcTGTCT
 V$SMAD_Q6              |     2302 (-) |  1.000 |  0.984 | tgtgTGTCT
 V$SMAD_Q6              |     2322 (-) |  0.996 |  0.976 | atacAGTCT
 V$SMAD_Q6              |     2940 (-) |  0.996 |  0.980 | gcgaAGTCT
 V$SMAD_Q6              |     3011 (-) |  0.985 |  0.981 | caggCGTCT
 V$SMAD_Q6              |     3356 (+) |  1.000 |  0.980 | AGACAgacc
 V$SMAD_Q6              |     3983 (+) |  1.000 |  1.000 | AGACAccat
 V$SMAD_Q6              |     4290 (+) |  0.989 |  0.974 | AGACCctaa
 V$SMAD_Q6              |     4323 (-) |  0.989 |  0.974 | actgGGTCT
 V$SMAD_Q6              |     4401 (+) |  1.000 |  0.977 | AGACAggtc
 V$SMAD_Q6              |     4772 (-) |  0.996 |  0.983 | agcgAGTCT
 V$SMAD_Q6              |     4851 (+) |  0.996 |  0.982 | AGACTtcac
 V$SMAD_Q6              |     4939 (+) |  0.996 |  0.976 | AGACTgaac
 V$SMAD_Q6              |     5228 (+) |  0.996 |  0.971 | AGACTggga
 V$SMAD_Q6              |     5547 (-) |  1.000 |  0.977 | tttcTGTCT
 V$SMAD_Q6              |     5675 (+) |  1.000 |  0.977 | AGACAgaca
 V$SMAD_Q6              |     5679 (+) |  1.000 |  0.982 | AGACAcaga
 V$SMAD_Q6              |     5687 (+) |  0.989 |  0.976 | AGACCcact
 V$SMAD_Q6              |     5748 (+) |  0.985 |  0.970 | AGACGcaaa
 V$SMAD_Q6              |     5929 (+) |  0.996 |  0.997 | AGACTccct
 V$SMAD_Q6              |     6075 (-) |  0.996 |  0.971 | ccacAGTCT
 V$SMAD_Q6              |     6133 (-) |  0.985 |  0.981 | tcggCGTCT
 V$SMAD_Q6              |     6187 (+) |  1.000 |  0.997 | AGACAccca
 V$SMAD_Q6              |     6233 (-) |  1.000 |  0.993 | atgcTGTCT
 V$SMAD_Q6              |     6646 (-) |  0.996 |  0.971 | cctcAGTCT
 V$SMAD_Q6              |     7281 (+) |  0.989 |  0.971 | AGACCcata
 V$SMAD_Q6              |     7339 (+) |  1.000 |  0.984 | AGACAcatt
 V$SMAD_Q6              |     7763 (-) |  0.989 |  0.974 | tgagGGTCT
 V$SMAD_Q6              |     8052 (-) |  0.989 |  0.970 | tcgaGGTCT
 V$SMAD_Q6              |     8713 (-) |  0.996 |  0.994 | aaggAGTCT
 V$SMAD_Q6              |     8864 (+) |  0.996 |  0.978 | AGACTctgg
 V$SMAD_Q6              |     9148 (+) |  1.000 |  0.982 | AGACAcata
 V$SMAD_Q6              |     9346 (-) |  0.996 |  0.980 | ctgaAGTCT
 V$SMAD_Q6              |     9904 (+) |  0.996 |  0.969 | AGACTtact
 V$SMAD_Q6              |    10065 (-) |  0.989 |  0.974 | accgGGTCT
 V$SMAD_Q6              |    10644 (+) |  1.000 |  0.997 | AGACAccca
 V$SMAD_Q6              |    10902 (+) |  0.985 |  0.973 | AGACGctac
 V$SMAD_Q6              |    10954 (-) |  0.989 |  0.980 | ctgcGGTCT
 V$YY1_Q6               |       61 (+) |  1.000 |  0.905 | GCCATaatt
 V$YY1_Q6               |      718 (-) |  0.902 |  0.863 | acagATGGT
 V$YY1_Q6               |      802 (+) |  1.000 |  0.942 | GCCATttct
 V$YY1_Q6               |      886 (-) |  0.889 |  0.853 | cgaaATGGG
 V$YY1_Q6               |     1662 (-) |  0.915 |  0.868 | gcaaATGGA
 V$YY1_Q6               |     1887 (+) |  0.889 |  0.895 | CCCATttta
 V$YY1_Q6               |     2456 (-) |  1.000 |  0.857 | cgctATGGC
 V$YY1_Q6               |     2614 (+) |  1.000 |  0.942 | GCCATgtgt
 V$YY1_Q6               |     2837 (-) |  1.000 |  0.939 | gcaaATGGC
 V$YY1_Q6               |     3149 (-) |  0.915 |  0.860 | atatATGGA
 V$YY1_Q6               |     3275 (+) |  1.000 |  0.912 | GCCATtatg
 V$YY1_Q6               |     3304 (+) |  0.915 |  0.867 | TCCATgtag
 V$YY1_Q6               |     3642 (-) |  0.902 |  0.864 | ccacATGGT
 V$YY1_Q6               |     3954 (+) |  1.000 |  0.899 | GCCATccta
 V$YY1_Q6               |     3987 (+) |  0.902 |  0.857 | ACCATctca
 V$YY1_Q6               |     4110 (+) |  0.915 |  0.919 | TCCATtttc
 V$YY1_Q6               |     4155 (+) |  0.889 |  0.850 | CCCATttgt
 V$YY1_Q6               |     4892 (+) |  0.915 |  0.919 | TCCATgttc
 V$YY1_Q6               |     4991 (-) |  1.000 |  0.855 | ccgaATGGC
 V$YY1_Q6               |     5128 (-) |  0.902 |  0.863 | acagATGGT
 V$YY1_Q6               |     5307 (-) |  1.000 |  0.997 | caaaATGGC
 V$YY1_Q6               |     5447 (+) |  1.000 |  0.925 | GCCATataa
 V$YY1_Q6               |     5738 (+) |  1.000 |  0.898 | GCCATaata
 V$YY1_Q6               |     5874 (+) |  0.902 |  0.860 | ACCATctcc
 V$YY1_Q6               |     6036 (+) |  0.889 |  0.856 | CCCATctgg
 V$YY1_Q6               |     6446 (-) |  1.000 |  0.857 | agtcATGGC
 V$YY1_Q6               |     6996 (-) |  0.915 |  0.871 | ggagATGGA
 V$YY1_Q6               |     7175 (-) |  0.902 |  0.860 | gcagATGGT
 V$YY1_Q6               |     7512 (-) |  1.000 |  0.939 | tcagATGGC
 V$YY1_Q6               |     7612 (+) |  1.000 |  0.945 | GCCATctct
 V$YY1_Q6               |     7734 (+) |  1.000 |  0.853 | GCCATcaca
 V$YY1_Q6               |     9001 (-) |  0.915 |  0.868 | gcacATGGA
 V$YY1_Q6               |     9053 (-) |  1.000 |  0.938 | ctacATGGC
 V$YY1_Q6               |    10107 (+) |  1.000 |  1.000 | GCCATcttg
 V$YY1_Q6               |    10115 (+) |  1.000 |  0.851 | GCCATcccc
 V$YY1_Q6               |    10388 (+) |  0.915 |  0.854 | TCCATataa
 V$YY1_Q6               |    10509 (-) |  1.000 |  0.905 | aattATGGC
 V$YY1_Q6               |    10522 (+) |  1.000 |  0.902 | GCCATtata
 V$YY1_Q6               |    10854 (+) |  1.000 |  0.902 | GCCATtgta
 V$YY1_Q6               |    11346 (+) |  1.000 |  0.904 | GCCATtatc
 V$YY1_Q6               |    11540 (-) |  0.902 |  0.857 | acatATGGT
 V$YY1_Q6               |    11724 (+) |  0.902 |  0.908 | ACCATtttc
 V$TTF1_Q6              |       10 (+) |  0.991 |  0.944 | tgtACAAGtaca
 V$TTF1_Q6              |       52 (-) |  0.993 |  0.961 | attaCTTGGgcc
 V$TTF1_Q6              |       98 (-) |  0.872 |  0.871 | ttcgCCTGGggg
 V$TTF1_Q6              |      270 (-) |  0.991 |  0.956 | ggtcCTTGTgca
 V$TTF1_Q6              |      280 (+) |  0.988 |  0.950 | catGCAAGtcaa
 V$TTF1_Q6              |      285 (+) |  1.000 |  0.978 | aagTCAAGtgtt
 V$TTF1_Q6              |      400 (+) |  0.991 |  0.946 | ccaACAAGgcgg
 V$TTF1_Q6              |      418 (-) |  0.991 |  0.934 | tgagCTTGTcca
 V$TTF1_Q6              |      478 (+) |  0.991 |  0.951 | cttACAAGtcaa
 V$TTF1_Q6              |      541 (-) |  0.991 |  0.973 | tgcgCTTGTgtt
 V$TTF1_Q6              |      838 (+) |  0.991 |  0.937 | aaaACAAGttaa
 V$TTF1_Q6              |      936 (+) |  0.991 |  0.958 | accACAAGttag
 V$TTF1_Q6              |     1212 (-) |  0.993 |  0.952 | attgCTTGGagt
 V$TTF1_Q6              |     1345 (-) |  0.988 |  0.951 | aaggCTTGCctg
 V$TTF1_Q6              |     1654 (-) |  0.993 |  0.950 | tctaCTTGGcaa
 V$TTF1_Q6              |     1937 (-) |  0.993 |  0.941 | tagcCTTGGcta
 V$TTF1_Q6              |     1988 (+) |  0.993 |  0.937 | tcaCCAAGatta
 V$TTF1_Q6              |     2011 (-) |  0.878 |  0.883 | atctCCTGAgtg
 V$TTF1_Q6              |     2325 (-) |  0.988 |  0.934 | cagtCTTGCtat
 V$TTF1_Q6              |     2355 (-) |  0.991 |  0.944 | caaaCTTGTatt
 V$TTF1_Q6              |     2465 (+) |  0.988 |  0.957 | ctaGCAAGcgcg
 V$TTF1_Q6              |     2605 (+) |  0.993 |  0.964 | aaaCCAAGagcc
 V$TTF1_Q6              |     2998 (+) |  0.993 |  0.955 | cctCCAAGgtgc
 V$TTF1_Q6              |     3201 (+) |  1.000 |  0.970 | gccTCAAGtatg
 V$TTF1_Q6              |     3214 (+) |  0.988 |  0.944 | tagGCAAGcact
 V$TTF1_Q6              |     3262 (-) |  0.993 |  0.944 | ttttCTTGGtga
 V$TTF1_Q6              |     3525 (-) |  0.993 |  0.937 | ccacCTTGGccc
 V$TTF1_Q6              |     3573 (+) |  0.988 |  0.939 | ttgGCAAGttat
 V$TTF1_Q6              |     3680 (+) |  0.993 |  0.966 | ttgCCAAGtgcc
 V$TTF1_Q6              |     3687 (+) |  0.993 |  0.950 | gtgCCAAGaaca
 V$TTF1_Q6              |     3695 (+) |  0.991 |  0.980 | aacACAAGagat
 V$TTF1_Q6              |     3704 (-) |  1.000 |  0.944 | gatgCTTGAtca
 V$TTF1_Q6              |     3878 (+) |  0.991 |  0.942 | aatACAAGctcc
 V$TTF1_Q6              |     3885 (-) |  1.000 |  0.954 | gctcCTTGAccc
 V$TTF1_Q6              |     3938 (-) |  0.991 |  0.953 | gtcaCTTGTtca
 V$TTF1_Q6              |     4194 (+) |  0.988 |  0.938 | gctGCAAGttca
 V$TTF1_Q6              |     4200 (+) |  1.000 |  0.949 | agtTCAAGgctt
 V$TTF1_Q6              |     4205 (-) |  0.988 |  0.938 | aaggCTTGCctc
 V$TTF1_Q6              |     4252 (-) |  0.993 |  0.958 | attaCTTGGttg
 V$TTF1_Q6              |     4395 (+) |  0.993 |  0.940 | gttCCAAGacag
 V$TTF1_Q6              |     4415 (-) |  0.991 |  0.937 | caacCTTGTcta
 V$TTF1_Q6              |     4518 (+) |  0.993 |  0.938 | agaCCAAGacaa
 V$TTF1_Q6              |     4600 (-) |  0.988 |  0.961 | cccgCTTGCtgg
 V$TTF1_Q6              |     4692 (-) |  1.000 |  0.951 | gaaaCTTGAtgt
 V$TTF1_Q6              |     4706 (-) |  0.993 |  0.956 | tagaCTTGGgta
 V$TTF1_Q6              |     4793 (-) |  0.988 |  0.937 | ctgaCTTGCata
 V$TTF1_Q6              |     4897 (-) |  0.993 |  0.947 | gttcCTTGGcca
 V$TTF1_Q6              |     4903 (+) |  0.993 |  0.962 | tggCCAAGtgca
 V$TTF1_Q6              |     5000 (-) |  0.991 |  0.942 | agacCTTGTatt
 V$TTF1_Q6              |     5170 (-) |  0.991 |  0.971 | ttcaCTTGTgac
 V$TTF1_Q6              |     5207 (-) |  0.991 |  0.978 | gcctCTTGTgct
 V$TTF1_Q6              |     5606 (+) |  0.991 |  0.968 | aacACAAGaaac
 V$TTF1_Q6              |     5835 (+) |  0.991 |  0.932 | gaaACAAGgcat
 V$TTF1_Q6              |     5932 (-) |  0.993 |  0.959 | ctccCTTGGaga
 V$TTF1_Q6              |     6120 (-) |  0.991 |  0.937 | agggCTTGTttt
 V$TTF1_Q6              |     6209 (+) |  0.993 |  0.945 | atgCCAAGgttt
 V$TTF1_Q6              |     6893 (+) |  0.991 |  0.968 | aagACAAGaggg
 V$TTF1_Q6              |     6914 (+) |  0.991 |  0.940 | agaACAAGgaat
 V$TTF1_Q6              |     6941 (+) |  0.993 |  0.977 | tacCCAAGtgat
 V$TTF1_Q6              |     7127 (+) |  1.000 |  0.961 | tgcTCAAGgagg
 V$TTF1_Q6              |     7292 (+) |  0.993 |  0.928 | gtaCCAAGctga
 V$TTF1_Q6              |     7381 (-) |  0.991 |  0.957 | attgCTTGTgtc
 V$TTF1_Q6              |     7497 (-) |  0.993 |  0.964 | tcttCTTGGagg
 V$TTF1_Q6              |     7695 (-) |  0.993 |  0.969 | agaaCTTGGgag
 V$TTF1_Q6              |     7979 (+) |  1.000 |  0.961 | tttTCAAGggaa
 V$TTF1_Q6              |     8032 (-) |  0.988 |  0.943 | agagCTTGCtgg
 V$TTF1_Q6              |     8042 (-) |  1.000 |  0.951 | gggcCTTGActc
 V$TTF1_Q6              |     8181 (-) |  0.991 |  0.949 | agaaCTTGTttg
 V$TTF1_Q6              |     8348 (-) |  0.988 |  0.960 | accaCTTGCcaa
 V$TTF1_Q6              |     8398 (+) |  0.993 |  0.945 | aagCCAAGccag
 V$TTF1_Q6              |     8455 (+) |  0.993 |  0.947 | aagCCAAGgtct
 V$TTF1_Q6              |     8528 (+) |  1.000 |  0.957 | gctTCAAGaaca
 V$TTF1_Q6              |     8708 (+) |  1.000 |  0.963 | ccaTCAAGgagt
 V$TTF1_Q6              |     8753 (-) |  0.991 |  0.942 | acacCTTGTcct
 V$TTF1_Q6              |     8768 (-) |  0.872 |  0.876 | agcaCCTGGgag
 V$TTF1_Q6              |     9034 (+) |  1.000 |  0.966 | agtTCAAGggca
 V$TTF1_Q6              |     9057 (+) |  0.988 |  0.945 | atgGCAAGttcc
 V$TTF1_Q6              |     9192 (+) |  1.000 |  0.994 | cacTCAAGagag
 V$TTF1_Q6              |     9203 (+) |  0.993 |  0.937 | gcaCCAAGgctc
 V$TTF1_Q6              |     9222 (+) |  0.988 |  0.943 | aagGCAAGttag
 V$TTF1_Q6              |     9279 (+) |  0.993 |  0.945 | ccaCCAAGctga
 V$TTF1_Q6              |     9294 (-) |  0.991 |  0.961 | tcagCTTGTgtg
 V$TTF1_Q6              |     9441 (+) |  0.993 |  0.954 | agcCCAAGgttt
 V$TTF1_Q6              |     9523 (+) |  0.991 |  0.950 | ccaACAAGacta
 V$TTF1_Q6              |     9538 (+) |  0.991 |  0.951 | caaACAAGtcct
 V$TTF1_Q6              |     9632 (+) |  1.000 |  0.945 | agtTCAAGgtca
 V$TTF1_Q6              |     9641 (-) |  0.993 |  0.951 | tcagCTTGGgct
 V$TTF1_Q6              |     9661 (-) |  0.991 |  0.940 | agacCTTGTctc
 V$TTF1_Q6              |    10108 (-) |  0.988 |  0.942 | ccatCTTGCcat
 V$TTF1_Q6              |    10248 (-) |  0.991 |  0.946 | caggCTTGTgca
 V$TTF1_Q6              |    10490 (+) |  1.000 |  0.951 | ataTCAAGgatc
 V$TTF1_Q6              |    10800 (-) |  0.991 |  0.949 | gagcCTTGTgca
 V$TTF1_Q6              |    10931 (-) |  0.991 |  0.978 | gcctCTTGTgga
 V$TTF1_Q6              |    10972 (+) |  0.988 |  0.933 | ggaGCAAGgagc
 V$TTF1_Q6              |    11072 (+) |  0.991 |  0.935 | gttACAAGctgc
 V$TTF1_Q6              |    11185 (-) |  0.991 |  0.929 | ctgcCTTGTttc
 V$TTF1_Q6              |    11192 (-) |  1.000 |  0.965 | gtttCTTGAttg
 V$TTF1_Q6              |    11262 (+) |  0.993 |  0.949 | gtgCCAAGaaaa
 V$TTF1_Q6              |    11483 (-) |  0.993 |  0.960 | ttccCTTGGaat
 V$TTF1_Q6              |    11777 (-) |  1.000 |  0.959 | gataCTTGAtgt
 V$TTF1_Q6              |    11944 (+) |  1.000 |  0.970 | attTCAAGggtc
 V$TTF1_Q6              |    11961 (-) |  0.878 |  0.870 | tgcaCCTGAgct
 V$OCT_Q6               |      993 (+) |  0.957 |  0.959 | taattTTCATg
 V$OCT_Q6               |     3109 (+) |  0.950 |  0.955 | taattTCCATg
 V$OCT_Q6               |     3129 (+) |  0.963 |  0.966 | taattTACATt
 V$OCT_Q6               |     3835 (+) |  0.950 |  0.948 | aaattTCCATt
 V$OCT_Q6               |     4071 (-) |  0.963 |  0.923 | tATGTAaaatg
 V$OCT_Q6               |     4451 (+) |  0.957 |  0.890 | taataTTCATt
 V$OCT_Q6               |     5341 (+) |  1.000 |  0.936 | agtttTGCATc
 V$OCT_Q6               |     5403 (+) |  0.957 |  0.906 | attttTTCATc
 V$OCT_Q6               |     6577 (-) |  1.000 |  0.960 | tATGCAaaaca
 V$OCT_Q6               |     6969 (-) |  0.950 |  0.908 | gATGGAaagga
 V$OCT_Q6               |     6999 (-) |  0.950 |  0.900 | gATGGAaaagg
 V$OCT_Q6               |     9737 (+) |  0.950 |  0.881 | taatgTCCATa
 V$OCT_Q6               |     9799 (-) |  0.963 |  0.882 | aATGTAcatca
 V$OCT_Q6               |     9934 (+) |  1.000 |  0.990 | taattTGCATg
 V$OCT_Q6               |    10911 (-) |  1.000 |  1.000 | tATGCAaataa
 V$OCT_Q6               |    11154 (-) |  0.957 |  0.955 | gATGAAaatga
 V$OCT_Q6               |    11337 (-) |  0.963 |  0.950 | gATGTAaatgc
 V$OCT_Q6               |    11411 (+) |  1.000 |  0.876 | tattcTGCATt
 V$OCT_Q6               |    11665 (+) |  0.957 |  0.958 | caattTTCATa
 V$USF_Q6_01            |      734 (+) |  1.000 |  0.907 | caccACGTGgtt
 V$USF_Q6_01            |      734 (-) |  1.000 |  0.908 | cacCACGTggtt
 V$USF_Q6_01            |     1125 (+) |  1.000 |  0.880 | atgcACGTGtgt
 V$USF_Q6_01            |     1357 (-) |  0.927 |  0.930 | ggtCACCTgatg
 V$USF_Q6_01            |     1391 (+) |  0.927 |  0.905 | gggcAGGTGagg
 V$USF_Q6_01            |     2772 (+) |  0.907 |  0.886 | ccgcATGTGaga
 V$USF_Q6_01            |     3937 (-) |  0.907 |  0.926 | agtCACTTgttc
 V$USF_Q6_01            |     6942 (+) |  0.907 |  0.884 | acccAAGTGata
 V$HIF1_Q3              |     6061 (-) |  1.000 |  0.951 | ccctgCACGTgctg
 V$HIF1_Q3              |     6063 (+) |  1.000 |  0.954 | ctgcACGTGctgcc
 V$HIF1_Q3              |     6853 (-) |  1.000 |  0.942 | gtgagCACGTccag
 V$HIF1_Q3              |     7483 (-) |  1.000 |  0.950 | acgcgCACGTctgt
 P$MYBAS1_01            |      124 (+) |  1.000 |  0.995 | ggCTAACtgct
 P$MYBAS1_01            |      789 (+) |  0.997 |  0.992 | tcTTAACcgct
 P$MYBAS1_01            |     1027 (-) |  0.997 |  0.990 | ggcaGTTGAat
 P$MYBAS1_01            |     1143 (-) |  0.999 |  0.987 | aaccGTTACtt
 P$MYBAS1_01            |     1315 (+) |  1.000 |  0.993 | ccCTAACtccc
 P$MYBAS1_01            |     2428 (-) |  1.000 |  0.992 | agggGTTGGgg
 P$MYBAS1_01            |     3442 (+) |  0.999 |  0.987 | agGTAACagtt
 P$MYBAS1_01            |     4536 (+) |  0.997 |  0.994 | cgTCAACagcc
 P$MYBAS1_01            |     5278 (+) |  0.999 |  0.988 | caACAACaggc
 P$MYBAS1_01            |     5615 (+) |  1.000 |  0.986 | aaCCAACatct
 P$MYBAS1_01            |     5979 (+) |  0.999 |  0.985 | tgATAACttct
 P$MYBAS1_01            |     6844 (+) |  1.000 |  0.986 | tgCCAACtggt
 P$MYBAS1_01            |     8003 (-) |  1.000 |  0.988 | gcctGTTGGtg
 P$MYBAS1_01            |     8354 (+) |  1.000 |  0.985 | tgCCAACccct
 P$MYBAS1_01            |     8485 (-) |  0.999 |  0.985 | ggggGTTATtt
 P$MYBAS1_01            |     8589 (+) |  0.999 |  0.986 | agGCAACatct
 P$MYBAS1_01            |     8673 (-) |  1.000 |  0.987 | accgGTTAGga
 P$MYBAS1_01            |     9316 (-) |  1.000 |  0.990 | aggcGTTGGgt
 P$MYBAS1_01            |    10619 (-) |  0.999 |  0.987 | gggaGTTGTag
 P$MYBAS1_01            |    10965 (-) |  1.000 |  0.986 | gcctGTTGGag
 P$MYBAS1_01            |    11709 (+) |  1.000 |  1.000 | ccCCAACtgcc
 P$MYBAS1_01            |    11920 (+) |  1.000 |  0.990 | gcCCAACgccc
 V$MYC_Q2               |      736 (-) |  1.000 |  1.000 | ccACGTG
 V$MYC_Q2               |      737 (+) |  1.000 |  1.000 | CACGTgg
 V$MYC_Q2               |     1127 (-) |  1.000 |  1.000 | gcACGTG
 V$MYC_Q2               |     1128 (+) |  1.000 |  0.994 | CACGTgt
 V$MYC_Q2               |     6065 (-) |  1.000 |  1.000 | gcACGTG
 V$MYC_Q2               |     6066 (+) |  1.000 |  1.000 | CACGTgc
 V$AP2_Q3               |       95 (-) |  1.000 |  0.956 | atcttcGCCTGggggt
 V$AP2_Q3               |     1209 (-) |  0.869 |  0.827 | cccattGCTTGgagtt
 V$AP2_Q3               |     1333 (+) |  0.893 |  0.847 | tccccAGGGCttaagg
 V$AP2_Q3               |     1375 (+) |  0.903 |  0.853 | tgcagTGGGCgaggta
 V$AP2_Q3               |     1411 (-) |  0.827 |  0.843 | tccattGCCGTgagac
 V$AP2_Q3               |     1452 (-) |  0.934 |  0.822 | cactgaGCCGGacgtt
 V$AP2_Q3               |     3527 (-) |  1.000 |  0.898 | accttgGCCCGaggtt
 V$AP2_Q3               |     3563 (-) |  0.893 |  0.818 | tgtgtgGCCTTtggca
 V$AP2_Q3               |     4174 (+) |  0.871 |  0.838 | ttcagGAGGCtgagca
 V$AP2_Q3               |     4186 (+) |  0.893 |  0.851 | agcagAAGGCtgcaag
 V$AP2_Q3               |     4232 (+) |  0.893 |  0.850 | ttctcAGGGCtgggga
 V$AP2_Q3               |     4599 (+) |  0.755 |  0.839 | gcccgCTTGCtggaag
 V$AP2_Q3               |     5015 (-) |  0.796 |  0.819 | cattaaGCCACgggac
 V$AP2_Q3               |     5279 (+) |  1.000 |  0.842 | aacaaCAGGCtcagat
 V$AP2_Q3               |     5883 (-) |  0.830 |  0.857 | tgctggGCATGgggcc
 V$AP2_Q3               |     6043 (-) |  0.893 |  0.874 | ggtgcaGCCCTgtgac
 V$AP2_Q3               |     6141 (-) |  0.871 |  0.824 | ttccatGCCTCtggct
 V$AP2_Q3               |     6225 (-) |  0.830 |  0.847 | cgctctGCATGctgtc
 V$AP2_Q3               |     6540 (+) |  0.827 |  0.818 | gacaaACGGCtgaggt
 V$AP2_Q3               |     6839 (-) |  0.828 |  0.821 | tttactGCCAActggt
 V$AP2_Q3               |     7455 (-) |  1.000 |  0.886 | tgttttGCCTGcagga
 V$AP2_Q3               |     7618 (-) |  0.805 |  0.841 | tctccaGCCGCctggc
 V$AP2_Q3               |     7621 (-) |  1.000 |  0.897 | ccagccGCCTGgcggt
 V$AP2_Q3               |     7624 (+) |  0.925 |  0.918 | gccgcCTGGCggtaga
 V$AP2_Q3               |     7663 (-) |  0.830 |  0.846 | tgccagGCATGgtggc
 V$AP2_Q3               |     7997 (-) |  1.000 |  0.870 | cactgtGCCTGttggt
 V$AP2_Q3               |     8029 (-) |  0.869 |  0.834 | gtcagaGCTTGctggg
 V$AP2_Q3               |     8088 (-) |  0.762 |  0.818 | tatacaGCTCTgggtc
 V$AP2_Q3               |     8364 (-) |  1.000 |  0.908 | tgtgcaGCCTGctgct
 V$AP2_Q3               |     8538 (+) |  0.903 |  0.859 | cacagTGGGCcgagaa
 V$AP2_Q3               |     9235 (-) |  0.893 |  0.833 | tccagaGCCCTaggag
 V$AP2_Q3               |     9278 (+) |  0.869 |  0.902 | gccacCAAGCtgagag
 V$AP2_Q3               |     9552 (-) |  1.000 |  0.850 | gtagtcGCCTGtcggt
 V$AP2_Q3               |     9919 (-) |  0.903 |  0.846 | atttttGCCTAtgggt
 V$AP2_Q3               |    10267 (-) |  0.934 |  0.853 | atttttGCCGGctgag
 V$AP2_Q3               |    10287 (+) |  1.000 |  0.873 | ctcatCAGGCttcgga
 V$AP2_Q3               |    10554 (-) |  0.934 |  0.864 | tgtacaGCCGGcggta
 V$AP2_Q3               |    10556 (+) |  0.934 |  0.841 | tacagCCGGCggtaca
 V$AP2_Q3               |    10865 (-) |  0.843 |  0.835 | gatgcaGCGTGgtggt
 V$AP2_Q3               |    10959 (-) |  1.000 |  0.857 | gtctgtGCCTGttgga
 V$AP2_Q3               |    11283 (+) |  0.893 |  0.867 | ggcatAGGGCaaagaa
 V$AP2_Q3               |    11809 (-) |  0.903 |  0.821 | aaggtgGCCCAgggtt
 V$AP2_Q3               |    11912 (+) |  1.000 |  0.875 | ggcttCGGGCccaacg
 V$AP2_Q3               |    11914 (-) |  0.903 |  0.831 | cttcggGCCCAacgcc
 V$AP2_Q3               |    11921 (-) |  0.903 |  0.860 | cccaacGCCCAttggc
 V$AP2_Q3               |    11927 (+) |  0.828 |  0.851 | gcccaTTGGCtgaaac
 V$CREB_Q3              |     1845 (+) |  1.000 |  0.993 | CGTCAa
 V$CREB_Q3              |     2965 (-) |  1.000 |  0.999 | gTGACG
 V$CREB_Q3              |     4536 (+) |  1.000 |  0.993 | CGTCAa
 V$CREB_Q3              |     8326 (+) |  1.000 |  0.999 | CGTCAg
 V$CREB_Q3              |     8615 (+) |  1.000 |  0.993 | CGTCAa
 V$CREB_Q3              |    11317 (-) |  1.000 |  0.999 | gTGACG
 V$CREB_Q3              |    11332 (-) |  1.000 |  1.000 | aTGACG
 V$PIT1_Q6              |     3825 (+) |  1.000 |  0.881 | aaTTCATaataaatttcc
 V$PIT1_Q6              |     3911 (-) |  1.000 |  0.883 | aataaagctttATGAAtt
 V$PIT1_Q6              |     5775 (-) |  1.000 |  0.879 | gagagaaaaatATGAAat
 V$PIT1_Q6              |    10388 (-) |  1.000 |  0.917 | tccatataaaaATGAAcg
 V$PIT1_Q6              |    11150 (-) |  1.000 |  0.874 | ctctgatgaaaATGAAgc
 V$E2F_Q2               |     4825 (+) |  0.962 |  0.964 | GGCGGg
 V$E2F_Q2               |     5332 (-) |  1.000 |  0.946 | tGCGCC
 V$E2F_Q2               |     5897 (-) |  0.962 |  0.964 | cCCGCC
 V$E2F_Q2               |     7148 (+) |  1.000 |  0.951 | GGCGCc
 V$E2F_Q2               |     7148 (-) |  1.000 |  0.951 | gGCGCC
 V$E2F_Q2               |     8330 (-) |  1.000 |  0.951 | aGCGCC
 V$E2F_Q2               |    10928 (-) |  1.000 |  0.951 | aGCGCC
 V$E2A_Q2               |     1359 (+) |  1.000 |  0.932 | tCACCTgatgctcg
 V$E2A_Q2               |     1387 (-) |  1.000 |  0.943 | ggtagggcAGGTGa
 V$E2A_Q2               |     1787 (+) |  1.000 |  0.944 | gCACCTgccattca
 V$E2A_Q2               |     2609 (-) |  0.909 |  0.917 | caagagccATGTGt
 V$E2A_Q2               |     7023 (-) |  0.942 |  0.925 | cctgcatcAGCTGa
 V$E2A_Q2               |     8278 (+) |  0.942 |  0.937 | gCAGCTgccctggc
 V$E2A_Q2               |     8499 (-) |  1.000 |  0.996 | acagggacAGGTGc
 V$E2A_Q2               |     8964 (-) |  1.000 |  0.934 | ggagaaccAGGTGt
 V$LEF1_Q2              |     1040 (+) |  1.000 |  0.928 | aCAAAG
 V$LEF1_Q2              |     1168 (+) |  1.000 |  1.000 | tCAAAG
 V$LEF1_Q2              |     1236 (-) |  1.000 |  1.000 | CTTTGa
 V$LEF1_Q2              |     2662 (-) |  1.000 |  1.000 | CTTTGa
 V$LEF1_Q2              |     4664 (-) |  1.000 |  0.928 | CTTTGt
 V$LEF1_Q2              |     5356 (-) |  1.000 |  1.000 | CTTTGa
 V$LEF1_Q2              |     6742 (-) |  1.000 |  1.000 | CTTTGa
 V$LEF1_Q2              |     8380 (-) |  1.000 |  1.000 | CTTTGa
 V$LEF1_Q2              |     8570 (-) |  1.000 |  1.000 | CTTTGa
 V$LEF1_Q2              |     8624 (-) |  1.000 |  1.000 | CTTTGa
 V$LEF1_Q2              |     8786 (+) |  1.000 |  0.928 | aCAAAG
 V$LEF1_Q2              |     9027 (-) |  1.000 |  0.928 | CTTTGt
 V$LEF1_Q2              |     9727 (-) |  1.000 |  0.928 | CTTTGt
 V$LEF1_Q2              |    10354 (+) |  1.000 |  1.000 | tCAAAG
 V$LEF1_Q2              |    11052 (-) |  1.000 |  0.928 | CTTTGt
 V$LEF1_Q2              |    11380 (-) |  1.000 |  1.000 | CTTTGa
 V$NF1_Q6_01            |     1974 (-) |  1.000 |  0.964 | ggTTGGCctcaaactca
 V$NF1_Q6_01            |     3317 (-) |  1.000 |  0.964 | gaTTGGCcttttcctga
 V$NF1_Q6_01            |     3679 (+) |  1.000 |  0.980 | attgccaagtGCCAAga
 V$NF1_Q6_01            |     7538 (+) |  1.000 |  0.992 | ttggttgtgaGCCAAct
 V$NF1_Q6_01            |    11254 (+) |  1.000 |  0.967 | tctgtggtgtGCCAAga
 V$EGR_Q6               |     1379 (+) |  0.979 |  0.910 | gtGGGCGaggt
 V$EGR_Q6               |     1492 (+) |  1.000 |  0.915 | gaGGGGGgggg
 V$EGR_Q6               |     1495 (+) |  1.000 |  0.906 | ggGGGGGggag
 V$EGR_Q6               |     8228 (-) |  0.959 |  0.922 | ttggCTCCCac
 V$EGR_Q6               |    10613 (+) |  0.959 |  0.929 | gtGGGAGggag
 V$EGR_Q6               |    10879 (+) |  0.959 |  0.906 | gtGGGAGcact
 V$EGR_Q6               |    11843 (+) |  1.000 |  0.929 | gtGGGGGgtgg
 V$PAX_Q6               |      329 (+) |  1.000 |  0.885 | CTGGAaattcc
 V$PAX_Q6               |     1561 (+) |  1.000 |  0.829 | CTGGAaatcta
 V$PAX_Q6               |     1951 (+) |  1.000 |  0.924 | CTGGAactttc
 V$PAX_Q6               |     2023 (+) |  0.900 |  0.815 | CTGGGattaaa
 V$PAX_Q6               |     4333 (-) |  1.000 |  0.852 | gtgacaTCCAG
 V$PAX_Q6               |     4391 (-) |  0.728 |  0.855 | gtgagtTCCAA
 V$PAX_Q6               |     4883 (+) |  1.000 |  0.822 | CTGGAacattc
 V$PAX_Q6               |     4947 (+) |  0.900 |  0.871 | CTGGGactttc
 V$PAX_Q6               |     6086 (-) |  0.857 |  0.924 | gtgagtTCCTG
 V$PAX_Q6               |     7161 (+) |  1.000 |  0.812 | CTGGAgctggc
 V$PAX_Q6               |     8023 (-) |  0.702 |  0.841 | gtgagtGTCAG
 V$PAX_Q6               |     8327 (-) |  0.883 |  0.809 | gtcagcGCCAG
 V$PAX_Q6               |     8817 (+) |  0.883 |  0.882 | CTGGTactctc
 V$PAX_Q6               |     8991 (-) |  1.000 |  0.868 | tttaatTCCAG
 V$PAX_Q6               |     9031 (-) |  0.760 |  0.872 | gtgagtTCAAG
 V$PAX_Q6               |     9060 (-) |  1.000 |  0.920 | gcaagtTCCAG
 V$PAX_Q6               |     9229 (-) |  1.000 |  0.892 | gttagcTCCAG
 V$PAX_Q6               |     9629 (-) |  0.760 |  0.817 | gggagtTCAAG
 V$FOX_Q2               |      847 (-) |  0.934 |  0.900 | taaatAAATAcga
 V$FOX_Q2               |     1893 (+) |  0.934 |  0.916 | ttaTATTTatttt
 V$FOX_Q2               |     2360 (+) |  0.934 |  0.912 | ttgTATTTatttt
 V$FOX_Q2               |     2409 (-) |  1.000 |  0.915 | aaaaaAAACAaaa
 V$FOX_Q2               |     2413 (-) |  0.881 |  0.915 | aaaacAAAAAatc
 V$FOX_Q2               |     4007 (-) |  0.934 |  0.953 | taaatAAATAttc
 V$FOX_Q2               |     6589 (-) |  0.934 |  0.894 | aaaacAAATAagg
 V$FOX_Q2               |     7047 (+) |  0.934 |  0.893 | gacTATTTttttt
 V$FOX_Q2               |     7425 (+) |  0.934 |  0.925 | gttTATTTgtttt
 V$FOX_Q2               |     7780 (-) |  0.881 |  0.900 | aaaacAAAAAtta
 V$FOX_Q2               |     7822 (-) |  1.000 |  0.964 | aaaacAAACAatt
 V$FOX_Q2               |     7934 (+) |  0.854 |  0.888 | gttTGTGTgttta
 V$FOX_Q2               |     7969 (+) |  1.000 |  0.928 | agtTGTTTgtttt
 V$FOX_Q2               |    11471 (+) |  0.934 |  0.918 | tttTATTTgtttt
 P$KNOX3_01             |      621 (+) |  1.000 |  0.975 | tacaTGACActt
 P$KNOX3_01             |     1280 (+) |  1.000 |  0.977 | gggaTGACAggg
 P$KNOX3_01             |     1354 (-) |  0.991 |  0.977 | ctgGGTCAcctg
 P$KNOX3_01             |     1683 (-) |  1.000 |  0.979 | gggTGTCAgctc
 P$KNOX3_01             |     2334 (+) |  0.991 |  0.977 | tatgTGACCcta
 P$KNOX3_01             |     2962 (+) |  0.997 |  0.982 | acagTGACGgca
 P$KNOX3_01             |     3072 (-) |  0.991 |  0.976 | ctaGGTCAcagg
 P$KNOX3_01             |     3934 (-) |  0.981 |  0.978 | atcAGTCActtg
 P$KNOX3_01             |     5084 (+) |  0.981 |  0.977 | gctcTGACTggt
 P$KNOX3_01             |     6051 (+) |  1.000 |  0.991 | cctgTGACAgcc
 P$KNOX3_01             |     7507 (-) |  1.000 |  0.982 | gggTGTCAgatg
 P$KNOX3_01             |     8025 (-) |  1.000 |  0.980 | gagTGTCAgagc
 P$KNOX3_01             |     8102 (-) |  1.000 |  0.993 | tccTGTCAcaca
 P$KNOX3_01             |     8323 (-) |  0.997 |  0.978 | ctgCGTCAgcgc
 P$KNOX3_01             |     9382 (-) |  1.000 |  0.990 | agcTGTCAgccc
 P$KNOX3_01             |    10357 (-) |  1.000 |  0.986 | aagTGTCAgaga
 P$KNOX3_01             |    11701 (-) |  1.000 |  0.990 | cacTGTCAcccc
 P$HAHB4_01             |     3415 (+) |  1.000 |  0.984 | tAATGAttc
 V$NRF2_Q4              |      130 (+) |  1.000 |  0.942 | ctgctcAGTCAat
 V$NRF2_Q4              |     1031 (-) |  0.905 |  0.860 | gtTGAATcaacaa
 V$NRF2_Q4              |     4466 (-) |  1.000 |  0.904 | acTGACTgaccag
 V$NRF2_Q4              |     6293 (-) |  1.000 |  0.963 | gaTGACTgagcag
 V$NRF2_Q4              |     6415 (-) |  1.000 |  0.883 | aaTGACTcctctg
 V$NRF2_Q4              |    10632 (-) |  1.000 |  0.881 | agTGACTgaggaa
 V$NRF2_Q4              |    11452 (+) |  0.873 |  0.845 | ttggtgAATCAgt
 V$CEBP_Q2_01           |      491 (+) |  1.000 |  0.955 | aTTGCAacatta
 V$CEBP_Q2_01           |      805 (+) |  0.971 |  0.926 | aTTTCTccagcc
 V$CEBP_Q2_01           |     1100 (-) |  0.971 |  0.966 | aatttgAGAAAt
 V$CEBP_Q2_01           |     1135 (+) |  0.957 |  0.948 | gTTCCTaaaacc
 V$CEBP_Q2_01           |     1465 (+) |  0.971 |  0.974 | gTTTCTcaatat
 V$CEBP_Q2_01           |     1556 (-) |  0.963 |  0.949 | ctcttcTGGAAa
 V$CEBP_Q2_01           |     2370 (+) |  0.995 |  0.943 | tTTGCCacagtt
 V$CEBP_Q2_01           |     2402 (+) |  0.957 |  0.949 | tTTCCTtaaaaa
 V$CEBP_Q2_01           |     2555 (-) |  0.977 |  0.970 | ctgttgTGAAAt
 V$CEBP_Q2_01           |     2564 (-) |  0.973 |  0.960 | aatttcCGTAAg
 V$CEBP_Q2_01           |     2566 (+) |  0.954 |  0.952 | tTTCCGtaagta
 V$CEBP_Q2_01           |     2578 (+) |  0.982 |  0.928 | tTTACAacaaat
 V$CEBP_Q2_01           |     2714 (+) |  0.958 |  0.955 | cTTCCCaaatag
 V$CEBP_Q2_01           |     2805 (+) |  0.976 |  0.965 | cTTACTgaacac
 V$CEBP_Q2_01           |     3426 (+) |  0.994 |  0.987 | gTTGCTtaattg
 V$CEBP_Q2_01           |     3437 (-) |  0.977 |  0.970 | gacttaGGTAAc
 V$CEBP_Q2_01           |     3569 (-) |  0.995 |  0.982 | gcctttGGCAAg
 V$CEBP_Q2_01           |     3644 (-) |  0.963 |  0.927 | acatggTGGAAt
 V$CEBP_Q2_01           |     3741 (+) |  0.971 |  0.931 | aTTTCTacattt
 V$CEBP_Q2_01           |     3926 (+) |  0.982 |  0.923 | aTTACAttatca
 V$CEBP_Q2_01           |     4209 (+) |  0.995 |  0.945 | cTTGCCtcagtt
 V$CEBP_Q2_01           |     4272 (+) |  0.977 |  0.970 | cTTACCtaagca
 V$CEBP_Q2_01           |     4708 (-) |  0.977 |  0.974 | gacttgGGTAAt
 V$CEBP_Q2_01           |     4797 (+) |  1.000 |  0.996 | cTTGCAtaatct
 V$CEBP_Q2_01           |     5152 (-) |  0.968 |  0.960 | agtttaCGAAAa
 V$CEBP_Q2_01           |     5154 (+) |  0.973 |  0.957 | tTTACGaaaagg
 V$CEBP_Q2_01           |     5444 (+) |  0.995 |  0.932 | aTTGCCatataa
 V$CEBP_Q2_01           |     5458 (+) |  0.972 |  0.929 | tTTTCCccacat
 V$CEBP_Q2_01           |     5917 (+) |  0.972 |  0.923 | gTTTCCccagcg
 V$CEBP_Q2_01           |     6547 (-) |  0.977 |  0.929 | ggctgaGGTAAg
 V$CEBP_Q2_01           |     6566 (+) |  0.995 |  0.943 | gTTGCCacagtt
 V$CEBP_Q2_01           |     6573 (-) |  1.000 |  0.987 | cagttaTGCAAa
 V$CEBP_Q2_01           |     6610 (+) |  0.994 |  0.984 | tTTGCTaaactc
 V$CEBP_Q2_01           |     7056 (+) |  0.971 |  0.973 | tTTTCTtaattt
 V$CEBP_Q2_01           |     7345 (+) |  0.977 |  0.934 | aTTTCAacatgt
 V$CEBP_Q2_01           |     7404 (+) |  0.976 |  0.964 | aTTACTgaagaa
 V$CEBP_Q2_01           |     8006 (-) |  0.982 |  0.932 | tgttggTGTAAc
 V$CEBP_Q2_01           |     8073 (+) |  1.000 |  0.982 | aTTGCAgaaact
 V$CEBP_Q2_01           |     8468 (-) |  0.995 |  0.926 | atctaaGGCAAa
 V$CEBP_Q2_01           |     8578 (-) |  0.995 |  0.954 | aaatggGGCAAa
 V$CEBP_Q2_01           |     8623 (-) |  0.971 |  0.963 | actttgAGAAAa
 V$CEBP_Q2_01           |     8694 (-) |  0.977 |  0.956 | cctttcTGAAAa
 V$CEBP_Q2_01           |     8695 (+) |  0.971 |  0.956 | cTTTCTgaaaat
 V$CEBP_Q2_01           |     8907 (-) |  0.957 |  0.957 | agattcAGGAAt
 V$CEBP_Q2_01           |     8936 (-) |  0.994 |  0.926 | aactaaAGCAAc
 V$CEBP_Q2_01           |     9100 (+) |  0.982 |  0.972 | cTTACAaaagca
 V$CEBP_Q2_01           |     9490 (+) |  1.000 |  0.928 | tTTGCAatagaa
 V$CEBP_Q2_01           |     9511 (+) |  0.972 |  0.933 | gTTTCCccatgt
 V$CEBP_Q2_01           |     9601 (-) |  0.958 |  0.958 | gcatttGGGAAg
 V$CEBP_Q2_01           |     9707 (-) |  0.982 |  0.937 | tggtggTGTAAa
 V$CEBP_Q2_01           |     9789 (-) |  0.976 |  0.965 | ttgttcAGTAAa
 V$CEBP_Q2_01           |     9871 (-) |  0.972 |  0.933 | gaatgaGGAAAt
 V$CEBP_Q2_01           |    10070 (-) |  0.963 |  0.953 | gtcttcTGGAAg
 V$CEBP_Q2_01           |    10132 (-) |  0.971 |  0.968 | tagttaAGAAAt
 V$CEBP_Q2_01           |    10371 (+) |  0.977 |  0.974 | cTTTCAaaatgt
 V$CEBP_Q2_01           |    10377 (-) |  1.000 |  0.955 | aaatgtTGCAAt
 V$CEBP_Q2_01           |    10686 (-) |  0.995 |  0.924 | gactctGGCAAc
 V$CEBP_Q2_01           |    10703 (-) |  0.977 |  0.966 | tgtttaTGAAAc
 V$CEBP_Q2_01           |    10968 (-) |  0.994 |  0.942 | tgttggAGCAAg
 V$CEBP_Q2_01           |    11150 (-) |  0.977 |  0.924 | ctctgaTGAAAa
 V$CEBP_Q2_01           |    11284 (-) |  0.995 |  0.934 | gcatagGGCAAa
 V$CEBP_Q2_01           |    11668 (+) |  0.977 |  0.972 | tTTTCAtaacca
 V$CEBP_Q2_01           |    11728 (+) |  0.971 |  0.964 | tTTTCTcaaaca
 V$CEBP_Q2_01           |    11780 (-) |  0.982 |  0.929 | acttgaTGTAAg
 V$MYB_Q5_01            |       68 (-) |  0.984 |  0.958 | ttaCTGTTg
 V$MYB_Q5_01            |      127 (+) |  1.000 |  0.964 | tAACTGctc
 V$MYB_Q5_01            |      160 (-) |  0.992 |  0.959 | tctCCGTTc
 V$MYB_Q5_01            |      451 (-) |  0.984 |  0.978 | tgtCTGTTt
 V$MYB_Q5_01            |      591 (+) |  0.984 |  0.982 | tAACAGact
 V$MYB_Q5_01            |      792 (+) |  0.989 |  0.953 | tAACCGctg
 V$MYB_Q5_01            |      983 (-) |  1.000 |  0.970 | tcaCAGTTa
 V$MYB_Q5_01            |     1026 (-) |  1.000 |  1.000 | tggCAGTTg
 V$MYB_Q5_01            |     1142 (-) |  0.992 |  0.956 | aaaCCGTTa
 V$MYB_Q5_01            |     1862 (+) |  1.000 |  0.974 | cAACTGaag
 V$MYB_Q5_01            |     2374 (-) |  1.000 |  0.965 | ccaCAGTTt
 V$MYB_Q5_01            |     2552 (-) |  0.984 |  0.958 | tttCTGTTg
 V$MYB_Q5_01            |     2678 (-) |  0.992 |  0.958 | aacCCGTTg
 V$MYB_Q5_01            |     2825 (-) |  1.000 |  0.974 | gtcCAGTTg
 V$MYB_Q5_01            |     2867 (+) |  0.984 |  0.954 | gAACAGaac
 V$MYB_Q5_01            |     3344 (-) |  0.984 |  0.954 | ctcCTGTTc
 V$MYB_Q5_01            |     3399 (-) |  1.000 |  0.972 | ctcCAGTTa
 V$MYB_Q5_01            |     3445 (-) |  1.000 |  0.964 | taaCAGTTa
 V$MYB_Q5_01            |     3509 (-) |  0.984 |  0.957 | ctgCTGTTa
 V$MYB_Q5_01            |     3545 (-) |  0.984 |  0.954 | gttCTGTTc
 V$MYB_Q5_01            |     3608 (-) |  1.000 |  0.968 | ctgCAGTTt
 V$MYB_Q5_01            |     4213 (-) |  1.000 |  0.969 | cctCAGTTa
 V$MYB_Q5_01            |     4321 (+) |  1.000 |  0.965 | aAACTGggt
 V$MYB_Q5_01            |     4539 (+) |  0.984 |  0.984 | cAACAGcct
 V$MYB_Q5_01            |     4565 (-) |  1.000 |  0.971 | acaCAGTTg
 V$MYB_Q5_01            |     4571 (-) |  0.989 |  0.961 | ttgCGGTTa
 V$MYB_Q5_01            |     4944 (+) |  1.000 |  0.967 | gAACTGgga
 V$MYB_Q5_01            |     5148 (-) |  1.000 |  0.994 | aggCAGTTt
 V$MYB_Q5_01            |     5281 (+) |  0.984 |  0.984 | cAACAGgct
 V$MYB_Q5_01            |     5729 (+) |  1.000 |  0.968 | aAACTGgaa
 V$MYB_Q5_01            |     6106 (-) |  0.984 |  0.958 | gtcCTGTTg
 V$MYB_Q5_01            |     6388 (+) |  1.000 |  0.995 | gAACTGgcc
 V$MYB_Q5_01            |     6570 (-) |  1.000 |  0.969 | ccaCAGTTa
 V$MYB_Q5_01            |     6847 (+) |  1.000 |  0.966 | cAACTGgtg
 V$MYB_Q5_01            |     7187 (+) |  0.992 |  0.988 | gAACGGcca
 V$MYB_Q5_01            |     7490 (-) |  0.984 |  0.980 | cgtCTGTTc
 V$MYB_Q5_01            |     7523 (+) |  1.000 |  0.969 | gAACTGaag
 V$MYB_Q5_01            |     7532 (-) |  1.000 |  0.974 | ttaCAGTTg
 V$MYB_Q5_01            |     7550 (+) |  1.000 |  0.971 | cAACTGtgt
 V$MYB_Q5_01            |     7602 (+) |  1.000 |  0.962 | gAACTGctg
 V$MYB_Q5_01            |     7723 (-) |  1.000 |  0.960 | cagCAGTTt
 V$MYB_Q5_01            |     8002 (-) |  0.984 |  0.984 | tgcCTGTTg
 V$MYB_Q5_01            |     8196 (-) |  0.984 |  0.978 | tgcCTGTTt
 V$MYB_Q5_01            |     8214 (-) |  1.000 |  0.967 | cctCAGTTc
 V$MYB_Q5_01            |     8672 (-) |  0.989 |  0.953 | cacCGGTTa
 V$MYB_Q5_01            |     8725 (+) |  1.000 |  0.969 | gAACTGtaa
 V$MYB_Q5_01            |     8847 (+) |  0.992 |  0.954 | gAACGGttt
 V$MYB_Q5_01            |     9119 (+) |  0.989 |  0.954 | aAACCGgga
 V$MYB_Q5_01            |     9132 (-) |  1.000 |  0.968 | cttCAGTTt
 V$MYB_Q5_01            |     9433 (+) |  0.984 |  0.956 | tAACAGgaa
 V$MYB_Q5_01            |     9561 (-) |  0.989 |  0.983 | tgtCGGTTt
 V$MYB_Q5_01            |     9765 (+) |  0.984 |  0.978 | aAACAGtca
 V$MYB_Q5_01            |    10058 (+) |  1.000 |  0.969 | gAACTGaac
 V$MYB_Q5_01            |    10063 (+) |  0.989 |  0.956 | gAACCGggt
 V$MYB_Q5_01            |    10194 (-) |  1.000 |  0.995 | agtCAGTTc
 V$MYB_Q5_01            |    10310 (+) |  1.000 |  0.964 | tAACTGttt
 V$MYB_Q5_01            |    10665 (+) |  0.984 |  0.958 | cAACAGgag
 V$MYB_Q5_01            |    10964 (-) |  0.984 |  0.984 | tgcCTGTTg
 V$MYB_Q5_01            |    11036 (-) |  0.984 |  0.955 | ccaCTGTTg
 V$MYB_Q5_01            |    11067 (-) |  1.000 |  0.964 | gatCAGTTa
 V$MYB_Q5_01            |    11137 (-) |  1.000 |  0.965 | actCAGTTt
 V$MYB_Q5_01            |    11219 (+) |  1.000 |  0.996 | gAACTGccc
 V$MYB_Q5_01            |    11224 (-) |  1.000 |  0.965 | gccCAGTTt
 V$MYB_Q5_01            |    11237 (+) |  1.000 |  0.972 | tAACTGgag
 V$MYB_Q5_01            |    11493 (-) |  0.989 |  0.963 | atgCGGTTg
 V$MYB_Q5_01            |    11516 (-) |  0.992 |  0.966 | ttaCCGTTg
 V$MYB_Q5_01            |    11653 (-) |  0.984 |  0.956 | gtaCTGTTa
 V$MYB_Q5_01            |    11712 (+) |  1.000 |  1.000 | cAACTGccc
 V$MYB_Q5_01            |    11764 (+) |  0.984 |  0.956 | tAACAGgat
 V$AP2_Q6_01            |      100 (-) |  1.000 |  0.991 | cGCCTGggggtgg
 V$AP2_Q6_01            |     1331 (+) |  0.869 |  0.873 | actccccAGGGCt
 V$AP2_Q6_01            |     2479 (-) |  0.869 |  0.893 | gGCCCTgggttcg
 V$AP2_Q6_01            |     3532 (-) |  0.986 |  0.963 | gGCCCGaggtttg
 V$AP2_Q6_01            |     3566 (+) |  0.863 |  0.886 | gtggcctTTGGCa
 V$AP2_Q6_01            |     3568 (-) |  0.883 |  0.903 | gGCCTTtggcaag
 V$AP2_Q6_01            |     5020 (-) |  0.884 |  0.916 | aGCCACgggactg
 V$AP2_Q6_01            |     6144 (+) |  0.980 |  0.969 | catgcctCTGGCt
 V$AP2_Q6_01            |     6146 (-) |  0.904 |  0.881 | tGCCTCtggctct
 V$AP2_Q6_01            |     6418 (+) |  0.980 |  0.961 | gactcctCTGGCt
 V$AP2_Q6_01            |     7191 (-) |  0.884 |  0.920 | gGCCACgggggtg
 V$AP2_Q6_01            |     7622 (+) |  0.980 |  0.877 | cagccgcCTGGCg
 V$AP2_Q6_01            |     7626 (-) |  1.000 |  0.881 | cGCCTGgcggtag
 V$AP2_Q6_01            |     8159 (+) |  0.904 |  0.904 | gcttccaGAGGCa
 V$AP2_Q6_01            |     9240 (-) |  0.869 |  0.898 | aGCCCTaggagag
 V$AP2_Q6_01            |     9330 (-) |  0.904 |  0.899 | aGCCTCtggagga
 V$AP2_Q6_01            |     9389 (-) |  0.890 |  0.906 | aGCCCCtggaatg
 V$AP2_Q6_01            |     9924 (-) |  0.883 |  0.880 | tGCCTAtgggtaa
 V$AP2_Q6_01            |    10559 (-) |  0.986 |  0.946 | aGCCGGcggtaca
 V$AP2_Q6_01            |    11814 (-) |  0.869 |  0.893 | gGCCCAgggttgg
 V$CREB_Q2_01           |     1237 (+) |  0.904 |  0.899 | tttgaCATCAgggc
 V$CREB_Q2_01           |     1840 (+) |  1.000 |  0.916 | ggggtCGTCAacac
 V$CREB_Q2_01           |     2962 (-) |  1.000 |  0.917 | acagTGACGgcaga
 V$CREB_Q2_01           |     4531 (+) |  1.000 |  0.922 | aaatgCGTCAacag
 V$CREB_Q2_01           |     8321 (+) |  1.000 |  0.929 | ttctgCGTCAgcgc
 V$CREB_Q2_01           |     8610 (+) |  1.000 |  0.909 | cattcCGTCAatca
 V$CREB_Q2_01           |    11314 (-) |  1.000 |  0.912 | acggTGACGacgat
 V$CREB_Q2_01           |    11329 (-) |  1.000 |  0.899 | atgaTGACGatgta
 V$CREB_Q4_01           |     1239 (-) |  0.914 |  0.920 | tgaCATCAggg
 V$CREB_Q4_01           |     1842 (-) |  1.000 |  0.915 | ggtCGTCAaca
 V$CREB_Q4_01           |     2963 (+) |  1.000 |  0.939 | cagTGACGgca
 V$CREB_Q4_01           |     4533 (-) |  1.000 |  0.923 | atgCGTCAaca
 V$CREB_Q4_01           |     8323 (-) |  1.000 |  0.941 | ctgCGTCAgcg
 V$CREB_Q4_01           |     8612 (-) |  1.000 |  0.914 | ttcCGTCAatc
 V$CREB_Q4_01           |    11315 (+) |  1.000 |  0.936 | cggTGACGacg
 V$CREB_Q4_01           |    11330 (+) |  1.000 |  0.914 | tgaTGACGatg
 V$E2F_Q6_01            |     7088 (-) |  0.949 |  0.926 | gctTTGCGcgca
 V$SRF_Q5_01            |    11538 (+) |  0.990 |  0.926 | ccacaTATGGtagat
 V$AP1_Q2_01            |     1350 (-) |  0.978 |  0.962 | ttgcctgGGTCA
 V$AP1_Q2_01            |     3436 (+) |  1.000 |  0.958 | TGACTtaggtaa
 V$AP1_Q2_01            |     3727 (+) |  1.000 |  0.961 | TGACTaaaatta
 V$AP1_Q2_01            |     3748 (-) |  1.000 |  0.956 | catttttAGTCA
 V$AP1_Q2_01            |     4529 (-) |  0.978 |  0.966 | acaaatgCGTCA
 V$AP1_Q2_01            |     6324 (+) |  1.000 |  0.954 | TGACTgaagcac
 V$AP1_Q2_01            |     8319 (-) |  0.978 |  0.960 | gcttctgCGTCA
 V$AP1_Q2_01            |     9317 (-) |  0.978 |  0.970 | ggcgttgGGTCA
 V$AP1_Q2_01            |    10031 (-) |  1.000 |  0.970 | gtttgtgAGTCA
 V$AP1_Q6_01            |      133 (-) |  1.000 |  0.964 | ctcAGTCAa
 V$AP1_Q6_01            |     1078 (-) |  0.961 |  0.945 | gtaGGTCAt
 V$AP1_Q6_01            |     1087 (-) |  0.961 |  0.938 | tttGGTCAa
 V$AP1_Q6_01            |     1255 (-) |  0.963 |  0.937 | ttcTGTCAt
 V$AP1_Q6_01            |     1354 (-) |  0.961 |  0.962 | ctgGGTCAc
 V$AP1_Q6_01            |     3072 (-) |  0.961 |  0.942 | ctaGGTCAc
 V$AP1_Q6_01            |     3435 (+) |  1.000 |  0.974 | tTGACTtag
 V$AP1_Q6_01            |     3726 (+) |  1.000 |  0.977 | gTGACTaaa
 V$AP1_Q6_01            |     3752 (-) |  1.000 |  0.980 | tttAGTCAt
 V$AP1_Q6_01            |     3934 (-) |  1.000 |  0.967 | atcAGTCAc
 V$AP1_Q6_01            |     4467 (+) |  1.000 |  0.966 | cTGACTgac
 V$AP1_Q6_01            |     4533 (-) |  0.960 |  0.957 | atgCGTCAa
 V$AP1_Q6_01            |     5358 (+) |  0.963 |  0.940 | tTGACAaaa
 V$AP1_Q6_01            |     6294 (+) |  1.000 |  0.970 | aTGACTgag
 V$AP1_Q6_01            |     6323 (+) |  1.000 |  0.966 | cTGACTgaa
 V$AP1_Q6_01            |     6416 (+) |  1.000 |  0.946 | aTGACTcct
 V$AP1_Q6_01            |     6556 (-) |  1.000 |  0.935 | aagAGTCAt
 V$AP1_Q6_01            |     8323 (-) |  0.960 |  0.960 | ctgCGTCAg
 V$AP1_Q6_01            |     9321 (-) |  0.961 |  0.961 | ttgGGTCAg
 V$AP1_Q6_01            |    10035 (+) |  0.932 |  0.935 | gTGAGTcac
 V$AP1_Q6_01            |    10035 (-) |  1.000 |  0.997 | gtgAGTCAc
 V$AP1_Q6_01            |    10633 (+) |  1.000 |  0.967 | gTGACTgag
 V$AP1_Q6_01            |    11455 (-) |  0.930 |  0.933 | gtgAATCAg
 V$AP1_Q4_01            |      134 (+) |  1.000 |  0.964 | tcAGTCAa
 V$AP1_Q4_01            |     1355 (+) |  0.957 |  0.959 | tgGGTCAc
 V$AP1_Q4_01            |     3435 (-) |  1.000 |  0.975 | tTGACTta
 V$AP1_Q4_01            |     3726 (-) |  1.000 |  0.976 | gTGACTaa
 V$AP1_Q4_01            |     3753 (+) |  1.000 |  0.979 | ttAGTCAt
 V$AP1_Q4_01            |     3935 (+) |  1.000 |  0.967 | tcAGTCAc
 V$AP1_Q4_01            |     4467 (-) |  1.000 |  0.968 | cTGACTga
 V$AP1_Q4_01            |     4534 (+) |  0.957 |  0.956 | tgCGTCAa
 V$AP1_Q4_01            |     6294 (-) |  1.000 |  0.971 | aTGACTga
 V$AP1_Q4_01            |     6323 (-) |  1.000 |  0.968 | cTGACTga
 V$AP1_Q4_01            |     8324 (+) |  0.957 |  0.959 | tgCGTCAg
 V$AP1_Q4_01            |     9322 (+) |  0.957 |  0.959 | tgGGTCAg
 V$AP1_Q4_01            |    10036 (+) |  1.000 |  0.997 | tgAGTCAc
 V$AP1_Q4_01            |    10633 (-) |  1.000 |  0.967 | gTGACTga
 V$AP4_Q6_01            |     1787 (-) |  0.924 |  0.936 | gCACCTgcc
 V$AP4_Q6_01            |     2970 (+) |  0.924 |  0.936 | ggcAGATGc
 V$AP4_Q6_01            |     7028 (+) |  1.000 |  0.962 | atcAGCTGa
 V$AP4_Q6_01            |     7029 (-) |  1.000 |  0.934 | tCAGCTgaa
 V$AP4_Q6_01            |     7680 (+) |  1.000 |  0.957 | cacAGCTGt
 V$AP4_Q6_01            |     7681 (-) |  1.000 |  0.947 | aCAGCTgta
 V$AP4_Q6_01            |     8277 (+) |  1.000 |  0.966 | tgcAGCTGc
 V$AP4_Q6_01            |     8278 (-) |  1.000 |  0.995 | gCAGCTgcc
 V$AP4_Q6_01            |     8370 (+) |  0.924 |  0.941 | gccTGCTGc
 V$AP4_Q6_01            |     8421 (+) |  1.000 |  0.973 | agcAGCTGt
 V$AP4_Q6_01            |     8422 (-) |  1.000 |  0.997 | gCAGCTgtt
 V$AP4_Q6_01            |     8504 (+) |  0.924 |  0.938 | gacAGGTGc
 V$MYOD_Q6_01           |     1354 (-) |  1.000 |  0.965 | ctgggtcACCTGatgctc
 V$MYOD_Q6_01           |     1388 (+) |  1.000 |  0.957 | gtagggCAGGTgaggaga
 V$MYOD_Q6_01           |     4335 (+) |  1.000 |  0.960 | gacatcCAGGTggtggag
 V$MYOD_Q6_01           |     8500 (+) |  1.000 |  0.985 | cagggaCAGGTgcgggac
 V$MYOD_Q6_01           |     8965 (+) |  1.000 |  0.971 | gagaacCAGGTgtggtgg
 V$OCT1_Q5_01           |      993 (+) |  0.985 |  0.983 | taaTTTTCatg
 V$OCT1_Q5_01           |     3109 (+) |  0.981 |  0.981 | taaTTTCCatg
 V$OCT1_Q5_01           |     3129 (+) |  0.986 |  0.989 | taaTTTACatt
 V$OCT1_Q5_01           |     3835 (+) |  0.981 |  0.965 | aaaTTTCCatt
 V$OCT1_Q5_01           |     4071 (-) |  0.986 |  0.909 | tatGTAAAatg
 V$OCT1_Q5_01           |     5341 (+) |  1.000 |  0.911 | agtTTTGCatc
 V$OCT1_Q5_01           |     6577 (-) |  1.000 |  0.943 | tatGCAAAaca
 V$OCT1_Q5_01           |     6969 (-) |  0.981 |  0.921 | gatGGAAAgga
 V$OCT1_Q5_01           |     9934 (+) |  1.000 |  0.992 | taaTTTGCatg
 V$OCT1_Q5_01           |    10911 (-) |  1.000 |  1.000 | tatGCAAAtaa
 V$OCT1_Q5_01           |    11154 (-) |  0.985 |  0.980 | gatGAAAAtga
 V$OCT1_Q5_01           |    11337 (-) |  0.986 |  0.959 | gatGTAAAtgc
 V$OCT1_Q5_01           |    11665 (+) |  0.985 |  0.966 | caaTTTTCata
 V$SP1_Q6_01            |     1489 (+) |  0.949 |  0.935 | agGGAGGggg
 V$SP1_Q6_01            |     1493 (+) |  0.934 |  0.924 | agGGGGGggg
 V$SP1_Q6_01            |     1494 (+) |  0.934 |  0.942 | ggGGGGGggg
 V$SP1_Q6_01            |     1495 (+) |  0.934 |  0.941 | ggGGGGGgga
 V$SP1_Q6_01            |     1496 (+) |  0.934 |  0.910 | ggGGGGGgag
 V$SP1_Q6_01            |     1500 (+) |  0.949 |  0.921 | ggGGAGGgag
 V$SP1_Q6_01            |     5895 (-) |  1.000 |  0.968 | ggcCCGCCcc
 V$SP1_Q6_01            |    10614 (+) |  0.949 |  0.904 | tgGGAGGgag
 V$SP1_Q6_01            |    11847 (+) |  0.945 |  0.951 | ggGGTGGggt
 V$SP1_Q6_01            |    11872 (+) |  0.949 |  0.930 | ggGGAGGgac
 V$SP1_Q4_01            |     1487 (+) |  0.964 |  0.952 | agagGGAGGgggg
 V$SP1_Q4_01            |     1491 (+) |  0.947 |  0.939 | ggagGGGGGgggg
 V$SP1_Q4_01            |     1492 (+) |  0.947 |  0.944 | gaggGGGGGggga
 V$SP1_Q4_01            |     1493 (+) |  0.947 |  0.952 | agggGGGGGggag
 V$SP1_Q4_01            |     1494 (+) |  0.947 |  0.919 | ggggGGGGGgagg
 V$SP1_Q4_01            |     1498 (+) |  0.964 |  0.931 | ggggGGAGGgagg
 V$SP1_Q4_01            |     5894 (-) |  1.000 |  0.958 | gggcCCGCCccta
 V$SP1_Q4_01            |    11845 (+) |  0.958 |  0.959 | ggggGGTGGggta
 V$SP1_Q4_01            |    11870 (+) |  0.964 |  0.937 | cgggGGAGGgact
 V$SP1_Q2_01            |     1488 (-) |  0.972 |  0.955 | gagGGAGGgg
 V$SP1_Q2_01            |     1492 (-) |  0.957 |  0.945 | gagGGGGGgg
 V$SP1_Q2_01            |     1493 (-) |  0.957 |  0.963 | aggGGGGGgg
 V$SP1_Q2_01            |     1494 (-) |  0.957 |  0.969 | gggGGGGGgg
 V$SP1_Q2_01            |     1495 (-) |  0.957 |  0.930 | gggGGGGGga
 V$SP1_Q2_01            |     1496 (-) |  0.957 |  0.918 | gggGGGGGag
 V$SP1_Q2_01            |     1499 (-) |  0.972 |  0.941 | gggGGAGGga
 V$SP1_Q2_01            |     1503 (-) |  0.972 |  0.917 | gagGGAGGga
 V$SP1_Q2_01            |     1507 (-) |  0.972 |  0.917 | gagGGAGGga
 V$SP1_Q2_01            |     1511 (-) |  0.972 |  0.917 | gagGGAGGga
 V$SP1_Q2_01            |     5896 (+) |  1.000 |  0.953 | gcCCGCCcct
 V$SP1_Q2_01            |    10613 (-) |  0.972 |  0.920 | gtgGGAGGga
 V$SP1_Q2_01            |    11846 (-) |  0.966 |  0.976 | gggGGTGGgg
 V$SP1_Q2_01            |    11871 (-) |  0.972 |  0.941 | gggGGAGGga
 I$ZESTE_Q2_01          |     7469 (+) |  1.000 |  0.994 | gatttGAGTGt
 I$ZESTE_Q2_01          |     9191 (-) |  1.000 |  0.990 | cCACTCaagag
 V$NFAT_Q4_01           |      329 (+) |  1.000 |  0.996 | ctGGAAAttc
 V$NFAT_Q4_01           |     1561 (+) |  1.000 |  0.982 | ctGGAAAtct
 V$NFAT_Q4_01           |     1955 (-) |  1.000 |  0.985 | aacTTTCCtt
 V$NFAT_Q4_01           |     2563 (-) |  1.000 |  0.981 | aaaTTTCCgt
 V$NFAT_Q4_01           |     3109 (-) |  1.000 |  0.991 | taaTTTCCat
 V$NFAT_Q4_01           |     3835 (-) |  1.000 |  0.997 | aaaTTTCCat
 V$NFAT_Q4_01           |     4689 (+) |  1.000 |  0.987 | caGGAAActt
 V$NFAT_Q4_01           |    10587 (-) |  1.000 |  0.982 | caaTTTCCta
 V$NFAT_Q4_01           |    11090 (-) |  1.000 |  1.000 | aatTTTCCac
 V$NFAT_Q4_01           |    11272 (+) |  1.000 |  0.980 | aaGGAAAtta
 V$E2F1_Q3_01           |     1380 (+) |  0.834 |  0.847 | tggGCGAGgtagggca
 V$E2F1_Q3_01           |     2463 (-) |  0.936 |  0.850 | gcctagcaAGCGCgaa
 V$E2F1_Q3_01           |     4823 (+) |  0.871 |  0.813 | cagGCGGGgtagggaa
 V$E2F1_Q3_01           |     5820 (+) |  0.834 |  0.808 | ctgGCGTGgcactgtg
 V$E2F1_Q3_01           |     9176 (+) |  0.830 |  0.843 | tgaACGCCacagagac
 V$E2F1_Q6_01           |     2471 (-) |  1.000 |  0.912 | aGCGCGaagg
 V$E2F1_Q6_01           |     9121 (-) |  0.870 |  0.882 | aCCGGGaaaa
 V$MEF2_Q6_01           |     3121 (+) |  0.962 |  0.936 | ggcTATATtaat
 P$TAF1_01              |      735 (+) |  1.000 |  0.992 | accACGTGgt
 P$TAF1_01              |      735 (-) |  1.000 |  0.992 | acCACGTggt
 P$CPRF3_01             |      735 (+) |  1.000 |  0.982 | acCACGTggt
 P$CPRF3_01             |      735 (-) |  1.000 |  0.982 | accACGTGgt
 P$CPRF2_01             |      735 (+) |  1.000 |  1.000 | acCACGTggt
 P$CPRF2_01             |      735 (-) |  1.000 |  1.000 | accACGTGgt
 V$CP2_02               |      102 (+) |  0.941 |  0.862 | CCTGGgggtggccag
 V$CP2_02               |      103 (-) |  0.968 |  0.869 | ctgggggtggCCAGT
 V$CP2_02               |      121 (+) |  1.000 |  0.777 | GCTGGctaactgctc
 V$CP2_02               |      133 (-) |  0.957 |  0.790 | ctcagtcaatCCAGA
 V$CP2_02               |      328 (+) |  1.000 |  0.826 | GCTGGaaattccctc
 V$CP2_02               |     1199 (+) |  1.000 |  0.873 | GCTGGttatacccat
 V$CP2_02               |     1200 (-) |  0.743 |  0.805 | ctggttatacCCATT
 V$CP2_02               |     1580 (-) |  1.000 |  0.773 | gcatggagagCCAGC
 V$CP2_02               |     1714 (+) |  0.705 |  0.767 | TCTGCcttttccggg
 V$CP2_02               |     1724 (-) |  0.759 |  0.804 | ccgggctcatCCTGA
 V$CP2_02               |     1800 (+) |  0.770 |  0.809 | ACAGGattcatcagg
 V$CP2_02               |     1950 (+) |  1.000 |  0.800 | GCTGGaactttcctt
 V$CP2_02               |     2680 (-) |  0.743 |  0.793 | cccgttgcatCCTGG
 V$CP2_02               |     2764 (+) |  0.732 |  0.790 | TCTAGattccgcatg
 V$CP2_02               |     2794 (+) |  1.000 |  0.822 | GCTGGtcttctctta
 V$CP2_02               |     2817 (-) |  0.968 |  0.874 | cgtgctctgtCCAGT
 V$CP2_02               |     3046 (-) |  0.802 |  0.780 | ccgggacataCCTGC
 V$CP2_02               |     3645 (-) |  0.700 |  0.762 | catggtggaaTCAGT
 V$CP2_02               |     3848 (-) |  0.968 |  0.787 | cataaaatatCCAGT
 V$CP2_02               |     4313 (+) |  0.715 |  0.794 | ACTGCataaaactgg
 V$CP2_02               |     4329 (+) |  0.957 |  0.867 | TCTGGtgacatccag
 V$CP2_02               |     4330 (-) |  0.941 |  0.924 | ctggtgacatCCAGG
 V$CP2_02               |     4343 (+) |  0.802 |  0.765 | GGTGGtggaggcagg
 V$CP2_02               |     4379 (+) |  0.957 |  0.783 | TCTGGctacatagtg
 V$CP2_02               |     4757 (-) |  1.000 |  0.796 | tctgtaggtcCCAGC
 V$CP2_02               |     4778 (+) |  0.957 |  0.807 | TCTGGataaagattg
 V$CP2_02               |     4882 (+) |  0.957 |  0.769 | TCTGGaacattccat
 V$CP2_02               |     4946 (+) |  0.968 |  0.829 | ACTGGgactttctgc
 V$CP2_02               |     5004 (-) |  0.743 |  0.790 | cttgtattacCCATT
 V$CP2_02               |     5029 (+) |  0.968 |  0.876 | ACTGGgatgctcagg
 V$CP2_02               |     5080 (+) |  1.000 |  0.978 | GCTGGctctgactgg
 V$CP2_02               |     5191 (+) |  0.802 |  0.761 | GCAGGatttgtctgt
 V$CP2_02               |     5549 (+) |  0.690 |  0.779 | TCTGTctctcactag
 V$CP2_02               |     5987 (+) |  0.957 |  0.804 | TCTGGattagggatg
 V$CP2_02               |     6040 (+) |  0.957 |  0.861 | TCTGGtgcagccctg
 V$CP2_02               |     6041 (-) |  0.770 |  0.766 | ctggtgcagcCCTGT
 V$CP2_02               |     6097 (+) |  0.759 |  0.807 | TGTGGatcagtcctg
 V$CP2_02               |     6123 (+) |  0.802 |  0.782 | GCTTGttttctcggc
 V$CP2_02               |     6183 (-) |  0.743 |  0.815 | ccagagacacCCATT
 V$CP2_02               |     6202 (+) |  0.716 |  0.770 | CCGGGgtatgccaag
 V$CP2_02               |     6239 (+) |  0.957 |  0.860 | TCTGGctacggcttt
 V$CP2_02               |     6424 (+) |  0.957 |  0.801 | TCTGGctttcatcgg
 V$CP2_02               |     6434 (-) |  0.968 |  0.853 | atcggtcaacCCAGT
 V$CP2_02               |     6489 (+) |  0.968 |  0.817 | ACTGGattgcagatg
 V$CP2_02               |     6626 (-) |  0.957 |  0.824 | agtggggcacCCAGA
 V$CP2_02               |     6769 (-) |  0.733 |  0.798 | catgaacaaaACAGC
 V$CP2_02               |     6793 (+) |  1.000 |  0.905 | GCTGGctcttcctcc
 V$CP2_02               |     6849 (+) |  0.968 |  0.818 | ACTGGtgagcacgtc
 V$CP2_02               |     6988 (+) |  1.000 |  0.769 | GCTGGtgaggagatg
 V$CP2_02               |     7160 (+) |  0.941 |  0.761 | CCTGGagctggcgtt
 V$CP2_02               |     7744 (+) |  1.000 |  0.810 | GCTGGctacattgtg
 V$CP2_02               |     7843 (+) |  0.957 |  0.801 | TCTGGcaaaagcgac
 V$CP2_02               |     8035 (+) |  0.802 |  0.849 | GCTTGctgggccttg
 V$CP2_02               |     8169 (-) |  0.957 |  0.820 | gcaggtagcaCCAGA
 V$CP2_02               |     8184 (+) |  0.770 |  0.789 | ACTTGtttgctctgc
 V$CP2_02               |     8324 (-) |  0.968 |  0.768 | tgcgtcagcgCCAGT
 V$CP2_02               |     8816 (+) |  0.957 |  0.770 | TCTGGtactctcgat
 V$CP2_02               |     8960 (-) |  0.941 |  0.879 | gtagggagaaCCAGG
 V$CP2_02               |     9057 (-) |  0.941 |  0.770 | atggcaagttCCAGG
 V$CP2_02               |     9226 (-) |  0.957 |  0.874 | caagttagctCCAGA
 V$CP2_02               |     9269 (-) |  0.802 |  0.799 | gcagcgacagCCACC
 V$CP2_02               |     9297 (+) |  0.802 |  0.769 | GCTTGtgtgcccagg
 V$CP2_02               |     9334 (+) |  0.957 |  0.853 | TCTGGaggacccctg
 V$CP2_02               |     9532 (-) |  0.770 |  0.842 | ctagaacaaaCAAGT
 V$CP2_02               |     9578 (+) |  0.802 |  0.764 | GGTGGtatagccctg
 V$CP2_02               |     9617 (+) |  0.802 |  0.771 | GGTGGgaggatcggg
 V$CP2_02               |     9968 (+) |  0.957 |  0.794 | TCTGGttcctatggg
 V$CP2_02               |    10247 (+) |  0.759 |  0.821 | TCAGGcttgtgcagg
 V$CP2_02               |    10689 (+) |  0.957 |  0.771 | TCTGGcaacacccgt
 V$CP2_02               |    10778 (-) |  0.941 |  0.832 | tctgtcggacCCAGG
 V$CP2_02               |    10845 (-) |  0.743 |  0.800 | caggaagaagCCATT
 V$CP2_02               |    10966 (-) |  0.743 |  0.794 | cctgttggagCAAGG
 V$CP2_02               |    11129 (-) |  0.700 |  0.772 | ctcgctgcacTCAGT
 V$CP2_02               |    11216 (-) |  0.968 |  0.785 | tttgaactgcCCAGT
 P$PCF2_01              |     1406 (-) |  1.000 |  0.997 | GTGGGtccat
 P$PCF2_01              |     5892 (+) |  0.877 |  0.905 | tggggCCCGC
 P$AGL15_01             |     1959 (+) |  0.880 |  0.890 | ttccttttTTGAGcag
 P$AGL15_01             |     1959 (-) |  0.894 |  0.881 | ttcCTTTTttgagcag
 P$AGL15_01             |     9404 (+) |  0.900 |  0.877 | gttctatgTCTAGaaa
 P$AGL15_01             |     9404 (-) |  0.827 |  0.878 | gttCTATGtctagaaa
 P$AGL15_01             |    11535 (+) |  0.946 |  0.893 | atcccacaTATGGtag
 P$AGL15_01             |    11535 (-) |  0.852 |  0.889 | atcCCACAtatggtag
 P$AG_02                |      165 (+) |  0.849 |  0.715 | GTTCCcaatgctggca
 P$AG_02                |      166 (+) |  0.972 |  0.817 | TTCCCaatgctggcat
 P$AG_02                |      166 (-) |  0.857 |  0.817 | ttcccaatgctGGCAT
 P$AG_02                |      320 (-) |  1.000 |  0.712 | agtcctgtgctGGAAA
 P$AG_02                |      554 (+) |  0.745 |  0.724 | TAACCttttctaggag
 P$AG_02                |      554 (-) |  0.718 |  0.734 | taaccttttctAGGAG
 P$AG_02                |      875 (+) |  0.678 |  0.735 | ATGCAcaaacacgaaa
 P$AG_02                |      875 (-) |  0.821 |  0.732 | atgcacaaacaCGAAA
 P$AG_02                |      908 (+) |  0.869 |  0.711 | TTTCTttcatgcgtag
 P$AG_02                |      908 (-) |  0.697 |  0.714 | tttctttcatgCGTAG
 P$AG_02                |     1135 (+) |  0.849 |  0.718 | GTTCCtaaaaccgtta
 P$AG_02                |     1135 (-) |  0.565 |  0.712 | gttcctaaaacCGTTA
 P$AG_02                |     1148 (+) |  0.869 |  0.710 | TTACTttatgtagttc
 P$AG_02                |     1166 (+) |  0.821 |  0.718 | TTTCAaagaaaggaga
 P$AG_02                |     1166 (-) |  0.724 |  0.708 | tttcaaagaaaGGAGA
 P$AG_02                |     1715 (+) |  0.871 |  0.712 | CTGCCttttccgggct
 P$AG_02                |     1715 (-) |  0.559 |  0.706 | ctgccttttccGGGCT
 P$AG_02                |     1791 (+) |  0.871 |  0.715 | CTGCCattcacaggat
 P$AG_02                |     1791 (-) |  0.704 |  0.719 | ctgccattcacAGGAT
 P$AG_02                |     1959 (+) |  0.842 |  0.780 | TTCCTtttttgagcag
 P$AG_02                |     1959 (-) |  0.740 |  0.782 | ttccttttttgAGCAG
 P$AG_02                |     2350 (+) |  0.746 |  0.708 | CTTCTcaaacttgtat
 P$AG_02                |     2350 (-) |  0.683 |  0.705 | cttctcaaactTGTAT
 P$AG_02                |     2714 (+) |  0.876 |  0.753 | CTTCCcaaatagataa
 P$AG_02                |     2714 (-) |  0.635 |  0.750 | cttcccaaataGATAA
 P$AG_02                |     2715 (+) |  0.972 |  0.717 | TTCCCaaatagataat
 P$AG_02                |     2786 (+) |  0.876 |  0.709 | CTTCCttagctggtct
 P$AG_02                |     2832 (+) |  0.593 |  0.711 | TGTCTgcaaatggcat
 P$AG_02                |     2832 (-) |  0.857 |  0.717 | tgtctgcaaatGGCAT
 P$AG_02                |     3087 (+) |  0.732 |  0.717 | ATTCTatttttcgaat
 P$AG_02                |     3087 (-) |  0.683 |  0.717 | attctatttttCGAAT
 P$AG_02                |     3639 (+) |  0.876 |  0.819 | CTACCacatggtggaa
 P$AG_02                |     3639 (-) |  0.793 |  0.822 | ctaccacatggTGGAA
 P$AG_02                |     3861 (+) |  0.849 |  0.734 | GTACCatttaaggagt
 P$AG_02                |     3861 (-) |  0.586 |  0.724 | gtaccatttaaGGAGT
 P$AG_02                |     4038 (+) |  0.863 |  0.795 | ATTCCagcagggggaa
 P$AG_02                |     4038 (-) |  0.972 |  0.798 | attccagcaggGGGAA
 P$AG_02                |     4039 (+) |  0.793 |  0.805 | TTCCAgcagggggaaa
 P$AG_02                |     4039 (-) |  1.000 |  0.804 | ttccagcagggGGAAA
 P$AG_02                |     4116 (+) |  0.972 |  0.730 | TTCCCagatgttaaaa
 P$AG_02                |     4210 (+) |  0.994 |  0.708 | TTGCCtcagttaaaaa
 P$AG_02                |     4395 (+) |  0.849 |  0.718 | GTTCCaagacaggtca
 P$AG_02                |     4395 (-) |  0.724 |  0.707 | gttccaagacaGGTCA
 P$AG_02                |     4598 (-) |  0.793 |  0.712 | tgcccgcttgcTGGAA
 P$AG_02                |     4680 (+) |  0.718 |  0.740 | GTTCTgtggcaggaaa
 P$AG_02                |     4680 (-) |  1.000 |  0.736 | gttctgtggcaGGAAA
 P$AG_02                |     4819 (+) |  1.000 |  0.788 | TTACCaggcggggtag
 P$AG_02                |     4819 (-) |  0.876 |  0.790 | ttaccaggcggGGTAG
 P$AG_02                |     4926 (+) |  0.821 |  0.716 | TTACAgatcatggaga
 P$AG_02                |     4954 (+) |  0.869 |  0.796 | TTTCTgcagcaggaag
 P$AG_02                |     4954 (-) |  0.876 |  0.792 | tttctgcagcaGGAAG
 P$AG_02                |     5010 (+) |  1.000 |  0.739 | TTACCcattaagccac
 P$AG_02                |     5349 (+) |  0.835 |  0.710 | ATCCCctctttgacaa
 P$AG_02                |     5349 (-) |  0.629 |  0.707 | atcccctctttGACAA
 P$AG_02                |     5985 (+) |  0.746 |  0.807 | CTTCTggattagggat
 P$AG_02                |     5985 (-) |  0.835 |  0.803 | cttctggattaGGGAT
 P$AG_02                |     6260 (+) |  0.821 |  0.710 | GTCCCatctgccgaag
 P$AG_02                |     6260 (-) |  0.697 |  0.714 | gtcccatctgcCGAAG
 P$AG_02                |     6267 (+) |  0.871 |  0.827 | CTGCCgaagaaggaag
 P$AG_02                |     6267 (-) |  0.876 |  0.823 | ctgccgaagaaGGAAG
 P$AG_02                |     6370 (-) |  0.876 |  0.704 | aagcgagatttGGTAG
 P$AG_02                |     6441 (+) |  0.580 |  0.710 | AACCCagtcatggcaa
 P$AG_02                |     6441 (-) |  0.994 |  0.720 | aacccagtcatGGCAA
 P$AG_02                |     7835 (+) |  0.580 |  0.754 | AACCCacttctggcaa
 P$AG_02                |     7835 (-) |  0.994 |  0.764 | aacccacttctGGCAA
 P$AG_02                |     8001 (+) |  0.843 |  0.784 | GTGCCtgttggtgtaa
 P$AG_02                |     8001 (-) |  0.821 |  0.787 | gtgcctgttggTGTAA
 P$AG_02                |     8137 (+) |  0.869 |  0.818 | TTTCTgctgagggaaa
 P$AG_02                |     8137 (-) |  1.000 |  0.817 | tttctgctgagGGAAA
 P$AG_02                |     8161 (+) |  0.793 |  0.720 | TTCCAgaggcaggtag
 P$AG_02                |     8161 (-) |  0.876 |  0.716 | ttccagaggcaGGTAG
 P$AG_02                |     8266 (+) |  0.724 |  0.721 | TGACCtgatgatgcag
 P$AG_02                |     8266 (-) |  0.691 |  0.732 | tgacctgatgaTGCAG
 P$AG_02                |     8463 (-) |  0.994 |  0.706 | gtctcatctaaGGCAA
 P$AG_02                |     9097 (+) |  0.740 |  0.731 | CTGCTtacaaaagcaa
 P$AG_02                |     9097 (-) |  0.864 |  0.731 | ctgcttacaaaAGCAA
 P$AG_02                |     9404 (+) |  0.718 |  0.753 | GTTCTatgtctagaaa
 P$AG_02                |     9404 (-) |  0.869 |  0.753 | gttctatgtctAGAAA
 P$AG_02                |     9596 (-) |  0.972 |  0.770 | tcccagcatttGGGAA
 P$AG_02                |     9819 (+) |  0.697 |  0.729 | CTTCAaattttagaag
 P$AG_02                |     9819 (-) |  0.746 |  0.729 | cttcaaattttAGAAG
 P$AG_02                |    10372 (+) |  0.821 |  0.829 | TTTCAaaatgttgcaa
 P$AG_02                |    10372 (-) |  0.815 |  0.829 | tttcaaaatgtTGCAA
 P$AG_02                |    10590 (+) |  1.000 |  0.708 | TTTCCtatatcaaaaa
 P$AG_02                |    10963 (+) |  0.843 |  0.802 | GTGCCtgttggagcaa
 P$AG_02                |    10963 (-) |  0.864 |  0.805 | gtgcctgttggAGCAA
 P$AG_02                |    11262 (+) |  0.843 |  0.767 | GTGCCaagaaaaggaa
 P$AG_02                |    11262 (-) |  0.842 |  0.767 | gtgccaagaaaAGGAA
 P$AG_02                |    11263 (-) |  1.000 |  0.756 | tgccaagaaaaGGAAA
 P$AG_02                |    11279 (-) |  0.994 |  0.740 | ttaaggcatagGGCAA
 P$AG_02                |    11516 (+) |  1.000 |  0.762 | TTACCgttgtccgtag
 P$AG_02                |    11516 (-) |  0.697 |  0.762 | ttaccgttgtcCGTAG
 P$AG_02                |    11535 (+) |  0.835 |  0.861 | ATCCCacatatggtag
 P$AG_02                |    11535 (-) |  0.876 |  0.861 | atcccacatatGGTAG
 I$GRH_01               |     2547 (+) |  1.000 |  0.976 | acaGGTTT
 I$GRH_01               |     5090 (+) |  1.000 |  1.000 | actGGTTT
 V$AR_02                |     2804 (+) |  0.800 |  0.856 | tcttactgaacaccgTGCTCtgtccag
 V$AR_02                |     6512 (-) |  1.000 |  0.944 | aataaaaGAACAcgaagttcaccctgg
 V$AR_02                |     8528 (-) |  1.000 |  0.917 | gcttcaaGAACAcagtgggccgagaaa
 V$AR_02                |     9459 (+) |  1.000 |  0.949 | ctctgctgtacaggaTGTTCtagctac
 V$AR_02                |    10056 (+) |  0.800 |  0.821 | aagaactgaaccgggTCTTCtggaagg
 V$AR_02                |    11217 (+) |  1.000 |  0.885 | ttgaactgcccagttTGTTCtaactgg
 V$PR_01                |     6512 (-) |  1.000 |  0.961 | aataaaaGAACAcgaagttcaccctgg
 V$PR_01                |     9459 (+) |  1.000 |  0.969 | ctctgctgtacaggaTGTTCtagctac
 V$GR_01                |     1522 (+) |  1.000 |  0.924 | gtagagctgttttttTGTTCtaaggga
 V$GR_01                |     1742 (-) |  1.000 |  0.922 | tcctataGAACActgatctataagcct
 V$GR_01                |     2686 (+) |  0.800 |  0.818 | gcatcctggtcacacTCTTCtccttcc
 V$GR_01                |     2804 (+) |  0.800 |  0.830 | tcttactgaacaccgTGCTCtgtccag
 V$GR_01                |     2804 (-) |  1.000 |  0.822 | tcttactGAACAccgtgctctgtccag
 V$GR_01                |     3534 (+) |  1.000 |  0.931 | cccgaggtttggttcTGTTCtttagta
 V$GR_01                |     3687 (-) |  1.000 |  0.920 | gtgccaaGAACAcaagagatgcttgat
 V$GR_01                |     5169 (+) |  1.000 |  0.926 | tttcacttgtgactgTGTTCtagcagg
 V$GR_01                |     5656 (-) |  1.000 |  0.914 | aagaaaaGAACAcaataagagacagac
 V$GR_01                |     6512 (-) |  1.000 |  0.970 | aataaaaGAACAcgaagttcaccctgg
 V$GR_01                |     6908 (-) |  1.000 |  0.915 | aagtggaGAACAaggaattgattgtat
 V$GR_01                |     7479 (+) |  1.000 |  0.912 | tgctacgcgcacgtcTGTTCttcttgg
 V$GR_01                |     7799 (-) |  1.000 |  0.951 | agataaaGAACAacgacaactccaaaa
 V$GR_01                |     8412 (+) |  1.000 |  0.933 | cggcctgtaagcagcTGTTCtagagct
 V$GR_01                |     8528 (-) |  1.000 |  0.967 | gcttcaaGAACAcagtgggccgagaaa
 V$GR_01                |     9034 (+) |  0.800 |  0.823 | agttcaagggcagccTGGTCtacatgg
 V$GR_01                |     9348 (+) |  1.000 |  0.942 | gaagtctcttctcagTGTTCtctatca
 V$GR_01                |     9426 (-) |  0.800 |  0.820 | ccataaaTAACAggaagcccaaggttt
 V$GR_01                |     9459 (+) |  1.000 |  0.984 | ctctgctgtacaggaTGTTCtagctac
 V$GR_01                |     9528 (-) |  1.000 |  0.946 | aagactaGAACAaacaagtcctgcgta
 V$GR_01                |     9774 (-) |  1.000 |  0.928 | tgccataGAACAattttgttcagtaaa
 V$GR_01                |    10056 (+) |  0.800 |  0.824 | aagaactgaaccgggTCTTCtggaagg
 V$GR_01                |    11217 (+) |  1.000 |  0.966 | ttgaactgcccagttTGTTCtaactgg
 V$AR_03                |     2804 (+) |  0.800 |  0.854 | tcttactgaacaccgTGCTCtgtccag
 V$AR_03                |     2804 (-) |  1.000 |  0.817 | tcttactGAACAccgtgctctgtccag
 V$AR_03                |     6512 (-) |  1.000 |  0.970 | aataaaaGAACAcgaagttcaccctgg
 V$AR_03                |     6908 (-) |  1.000 |  0.803 | aagtggaGAACAaggaattgattgtat
 V$AR_03                |     7799 (-) |  1.000 |  0.853 | agataaaGAACAacgacaactccaaaa
 V$AR_03                |     8412 (+) |  1.000 |  0.821 | cggcctgtaagcagcTGTTCtagagct
 V$AR_03                |     8528 (-) |  1.000 |  0.930 | gcttcaaGAACAcagtgggccgagaaa
 V$AR_03                |     9034 (+) |  0.800 |  0.804 | agttcaagggcagccTGGTCtacatgg
 V$AR_03                |     9348 (+) |  1.000 |  0.836 | gaagtctcttctcagTGTTCtctatca
 V$AR_03                |     9459 (+) |  1.000 |  0.964 | ctctgctgtacaggaTGTTCtagctac
 V$AR_03                |     9528 (-) |  1.000 |  0.843 | aagactaGAACAaacaagtcctgcgta
 V$AR_03                |    10056 (+) |  0.800 |  0.843 | aagaactgaaccgggTCTTCtggaagg
 V$AR_03                |    11217 (+) |  1.000 |  0.903 | ttgaactgcccagttTGTTCtaactgg
 V$PR_02                |     6512 (-) |  1.000 |  0.964 | aataaaaGAACAcgaagttcaccctgg
 V$PR_02                |     9459 (+) |  1.000 |  0.975 | ctctgctgtacaggaTGTTCtagctac
 P$ABI4_01              |     1183 (+) |  0.892 |  0.908 | gggcaCCCCCa
 P$ABI4_01              |     1813 (-) |  0.897 |  0.872 | gGGTGGtgttc
 P$ABI4_01              |     4144 (-) |  0.795 |  0.864 | gTGTGGtgcct
 P$ABI4_01              |     6599 (-) |  0.897 |  0.909 | aGGTGGtgcta
 P$ABI4_01              |     7196 (-) |  0.892 |  0.910 | cGGGGGtgcta
 P$ABI4_01              |     9686 (-) |  0.892 |  0.870 | gGGGGGtggtg
 P$ABI4_01              |     9689 (-) |  0.897 |  0.874 | gGGTGGtggtg
 P$ABI4_01              |    11845 (-) |  0.892 |  0.867 | gGGGGGtgggg
 V$DR4_Q2               |     2658 (+) |  0.754 |  0.793 | tgcactttgaTGACAct
 V$DR4_Q2               |     5000 (+) |  0.884 |  0.844 | agaccttgtaTTACCca
 V$DR4_Q2               |     5247 (-) |  0.853 |  0.840 | ggGTTCAcatgtggtca
 V$DR4_Q2               |     7135 (-) |  0.807 |  0.824 | gaGGCCAgaagagggcg
 V$DR4_Q2               |     9981 (-) |  0.813 |  0.794 | ggGATCAgaagagggta
 V$DR4_Q2               |    10243 (-) |  1.000 |  0.820 | gtGGTCAggcttgtgca
 V$DR3_Q4               |      294 (+) |  0.897 |  0.757 | gttttacagacTGAGCtatct
 V$DR3_Q4               |      411 (-) |  0.941 |  0.802 | gaatgGGTGAgcttgtccaaa
 V$DR3_Q4               |      434 (-) |  0.894 |  0.741 | accacGTTTAatcaggttgtc
 V$DR3_Q4               |      596 (+) |  0.894 |  0.791 | gacttacttttTAAACatcct
 V$DR3_Q4               |     1076 (-) |  1.000 |  0.788 | gtgtaGGTCAttttggtcaac
 V$DR3_Q4               |     1348 (+) |  0.941 |  0.761 | gcttgcctgggTCACCtgatg
 V$DR3_Q4               |     1377 (-) |  0.822 |  0.802 | cagtgGGCGAggtagggcagg
 V$DR3_Q4               |     1396 (-) |  0.808 |  0.762 | ggtgaGGAGAgtgggtccatt
 V$DR3_Q4               |     1602 (-) |  0.897 |  0.751 | ttgggGCTCAgggggtctcgt
 V$DR3_Q4               |     1618 (-) |  0.867 |  0.781 | ctcgtGGACAgcatgtccagc
 V$DR3_Q4               |     1620 (+) |  0.867 |  0.773 | cgtggacagcaTGTCCagcct
 V$DR3_Q4               |     1694 (-) |  0.808 |  0.782 | cagggGTAGAtgaagcaccct
 V$DR3_Q4               |     1723 (-) |  0.897 |  0.747 | tccggGCTCAtcctgaacttc
 V$DR3_Q4               |     1725 (+) |  1.000 |  0.806 | cgggctcatccTGAACttcct
 V$DR3_Q4               |     2327 (+) |  1.000 |  0.748 | gtcttgctatgTGACCctacg
 V$DR3_Q4               |     2665 (+) |  0.906 |  0.775 | tgatgacactcTTAACccgtt
 V$DR3_Q4               |     2799 (+) |  1.000 |  0.771 | tcttctcttacTGAACaccgt
 V$DR3_Q4               |     2808 (+) |  0.804 |  0.748 | actgaacaccgTGCTCtgtcc
 V$DR3_Q4               |     3070 (-) |  1.000 |  0.812 | agctaGGTCAcagggtgattc
 V$DR3_Q4               |     3307 (-) |  0.906 |  0.780 | atgtaGTTAAgattggccttt
 V$DR3_Q4               |     3520 (+) |  0.881 |  0.795 | ggaggccacctTGGCCcgagg
 V$DR3_Q4               |     3644 (-) |  0.848 |  0.803 | acatgGTGGAatcagtaaagt
 V$DR3_Q4               |     3770 (+) |  0.848 |  0.755 | gcaatgctcctTCCCCccttt
 V$DR3_Q4               |     3880 (+) |  1.000 |  0.811 | tacaagctcctTGACCctcat
 V$DR3_Q4               |     4043 (-) |  0.848 |  0.782 | agcagGGGGAaataggcaata
 V$DR3_Q4               |     4342 (-) |  0.848 |  0.778 | aggtgGTGGAggcaggaggat
 V$DR3_Q4               |     4461 (+) |  1.000 |  0.755 | ttcacactgacTGACCagcat
 V$DR3_Q4               |     5256 (+) |  0.838 |  0.752 | tgtggtcacagTCATCctggg
 V$DR3_Q4               |     5282 (-) |  0.897 |  0.806 | aacagGCTCAgatgggctagc
 V$DR3_Q4               |     5321 (-) |  1.000 |  0.796 | catcgGTTCAgtgcgccgata
 V$DR3_Q4               |     6248 (+) |  0.867 |  0.750 | ggctttctattTGTCCcatct
 V$DR3_Q4               |     6381 (+) |  0.881 |  0.779 | ggtagacgaacTGGCCtgtgt
 V$DR3_Q4               |     6395 (-) |  1.000 |  0.768 | cctgtGTTCAgaacgctcaga
 V$DR3_Q4               |     6471 (-) |  0.897 |  0.752 | aaaatGCTCAggatgaggact
 V$DR3_Q4               |     6523 (-) |  1.000 |  0.790 | acgaaGTTCAccctggagaca
 V$DR3_Q4               |     6794 (+) |  0.848 |  0.742 | ctggctcttccTCCCCtcatt
 V$DR3_Q4               |     6847 (-) |  0.941 |  0.814 | caactGGTGAgcacgtccaga
 V$DR3_Q4               |     7123 (-) |  0.897 |  0.754 | gcaatGCTCAaggaggccaga
 V$DR3_Q4               |     7220 (-) |  0.881 |  0.764 | aagtaGGCCAgcaggaagttc
 V$DR3_Q4               |     7350 (-) |  0.906 |  0.792 | aacatGTTAAtcatgggcaga
 V$DR3_Q4               |     8192 (+) |  0.813 |  0.765 | gctctgcctgtTTCCCctctg
 V$DR3_Q4               |     8200 (+) |  1.000 |  0.792 | tgtttcccctcTGACCtcagt
 V$DR3_Q4               |     8671 (-) |  0.894 |  0.784 | ccaccGGTTAggaaggtaatt
 V$DR3_Q4               |     8959 (-) |  0.808 |  0.739 | agtagGGAGAaccaggtgtgg
 V$DR3_Q4               |     9010 (-) |  0.907 |  0.779 | ggcagGGGCAggcagatcttt
 V$DR3_Q4               |     9461 (-) |  0.867 |  0.740 | ctgctGTACAggatgttctag
 V$DR3_Q4               |     9634 (-) |  1.000 |  0.758 | ttcaaGGTCAgcttgggctac
 V$DR3_Q4               |     9675 (-) |  0.848 |  0.737 | aagaaGTGGAgggggggtggt
 V$DR3_Q4               |     9988 (-) |  0.801 |  0.764 | gaagaGGGTAttaggtcctct
 V$DR3_Q4               |    10076 (-) |  0.907 |  0.787 | tggaaGGGCAgccagtgctct
 V$DR3_Q4               |    10250 (-) |  0.907 |  0.739 | ggcttGTGCAggaagtgattt
 V$DR3_Q4               |    10978 (+) |  0.881 |  0.737 | aggagcctgtgTGGCCctgga
 V$DR3_Q4               |    11046 (+) |  0.906 |  0.741 | tggttcctttgTTAACgttgt
 V$DR3_Q4               |    11055 (+) |  0.897 |  0.736 | tgttaacgttgTGATCagtta
 V$DR3_Q4               |    11123 (+) |  0.907 |  0.780 | ccttaactcgcTGCACtcagt
 V$DR3_Q4               |    11311 (-) |  0.941 |  0.752 | actacGGTGAcgacgatgatg
 V$DR3_Q4               |    11326 (-) |  0.838 |  0.743 | atgatGATGAcgatgtaaatg
 V$DR3_Q4               |    11449 (-) |  0.941 |  0.747 | attttGGTGAatcagtgaaat
 V$DR3_Q4               |    11884 (+) |  0.941 |  0.740 | agttctcactcTCAACcaata
 V$ETS_Q6               |      925 (+) |  1.000 |  0.948 | aCTTCCac
 V$ETS_Q6               |     1192 (-) |  0.954 |  0.944 | caGGAAAg
 V$ETS_Q6               |     1739 (+) |  1.000 |  0.987 | aCTTCCta
 V$ETS_Q6               |     2147 (+) |  1.000 |  0.976 | tCTTCCtt
 V$ETS_Q6               |     2151 (+) |  1.000 |  0.978 | cCTTCCtt
 V$ETS_Q6               |     2155 (+) |  1.000 |  0.988 | cCTTCCtc
 V$ETS_Q6               |     2161 (+) |  1.000 |  0.976 | tCTTCCtt
 V$ETS_Q6               |     2205 (+) |  1.000 |  0.976 | tCTTCCtt
 V$ETS_Q6               |     2707 (+) |  1.000 |  0.988 | cCTTCCtc
 V$ETS_Q6               |     2785 (+) |  1.000 |  0.976 | tCTTCCtt
 V$ETS_Q6               |     2989 (+) |  1.000 |  0.958 | aCTTCCgc
 V$ETS_Q6               |     3033 (+) |  1.000 |  0.958 | aCTTCCgc
 V$ETS_Q6               |     3325 (+) |  0.954 |  0.942 | tTTTCCtg
 V$ETS_Q6               |     3778 (+) |  1.000 |  0.939 | cCTTCCcc
 V$ETS_Q6               |     4689 (-) |  0.954 |  0.948 | caGGAAAc
 V$ETS_Q6               |     4963 (-) |  1.000 |  0.999 | caGGAAGt
 V$ETS_Q6               |     5473 (+) |  0.954 |  0.957 | aTTTCCtg
 V$ETS_Q6               |     5521 (+) |  0.954 |  0.945 | cTTTCCtc
 V$ETS_Q6               |     6089 (+) |  0.938 |  0.942 | aGTTCCtg
 V$ETS_Q6               |     6276 (-) |  1.000 |  0.981 | aaGGAAGc
 V$ETS_Q6               |     6317 (+) |  1.000 |  0.942 | aCTTCCct
 V$ETS_Q6               |     6461 (+) |  0.954 |  0.957 | aTTTCCtg
 V$ETS_Q6               |     6799 (+) |  1.000 |  0.986 | tCTTCCtc
 V$ETS_Q6               |     6878 (-) |  1.000 |  0.978 | taGGAAGc
 V$ETS_Q6               |     7019 (+) |  0.954 |  0.948 | gTTTCCtg
 V$ETS_Q6               |     7231 (-) |  1.000 |  0.999 | caGGAAGt
 V$ETS_Q6               |     7248 (-) |  0.954 |  0.942 | caGGAAAa
 V$ETS_Q6               |     8082 (+) |  1.000 |  0.987 | aCTTCCta
 V$ETS_Q6               |     8679 (-) |  1.000 |  0.975 | taGGAAGg
 V$ETS_Q6               |     9436 (-) |  1.000 |  0.990 | caGGAAGc
 V$ETS_Q6               |     9875 (-) |  0.954 |  0.958 | gaGGAAAt
 V$ETS_Q6               |    10258 (-) |  1.000 |  0.999 | caGGAAGt
 V$ETS_Q6               |    10589 (+) |  0.954 |  0.945 | aTTTCCta
 V$ETS_Q6               |    10639 (-) |  1.000 |  0.986 | gaGGAAGa
 V$ETS_Q6               |    10845 (-) |  1.000 |  0.985 | caGGAAGa
 V$ETS_Q6               |    11272 (-) |  0.954 |  0.948 | aaGGAAAt
 V$IRF_Q6_01            |      225 (-) |  0.968 |  0.972 | tTTTCCttttt
 V$IRF_Q6_01            |      901 (-) |  1.000 |  0.999 | tTTTCActttc
 V$IRF_Q6_01            |     1957 (-) |  0.968 |  0.973 | cTTTCCttttt
 V$IRF_Q6_01            |     2509 (+) |  0.968 |  0.978 | aaaagGGAAAa
 V$IRF_Q6_01            |    11269 (+) |  0.968 |  0.976 | gaaaaGGAAAt
 V$E2A_Q6               |     1360 (+) |  1.000 |  0.984 | CACCTgat
 V$E2A_Q6               |     1392 (-) |  1.000 |  1.000 | ggcAGGTG
 V$E2A_Q6               |     1788 (+) |  1.000 |  1.000 | CACCTgcc
 V$E2A_Q6               |     2970 (-) |  0.976 |  0.982 | ggcAGATG
 V$E2A_Q6               |     6264 (+) |  0.976 |  0.982 | CATCTgcc
 V$E2A_Q6               |     8279 (+) |  0.976 |  0.982 | CAGCTgcc
 V$E2A_Q6               |     8504 (-) |  1.000 |  1.000 | gacAGGTG
 V$E2A_Q6               |     8770 (+) |  1.000 |  0.980 | CACCTggg
 V$E2A_Q6               |     8969 (-) |  1.000 |  0.986 | accAGGTG
 V$SMAD_Q6_01           |      140 (+) |  1.000 |  0.974 | aatcCAGACat
 V$SMAD_Q6_01           |      296 (+) |  1.000 |  0.974 | tttaCAGACtg
 V$SMAD_Q6_01           |      338 (+) |  1.000 |  0.962 | ccctCAGACac
 V$SMAD_Q6_01           |      450 (-) |  1.000 |  0.966 | ttGTCTGtttt
 V$SMAD_Q6_01           |      590 (+) |  1.000 |  0.965 | ttaaCAGACtt
 V$SMAD_Q6_01           |      681 (+) |  1.000 |  0.980 | tcttCAGACac
 V$SMAD_Q6_01           |      892 (+) |  1.000 |  0.957 | gggaCAGACtt
 V$SMAD_Q6_01           |     1928 (-) |  0.925 |  0.915 | atGTCTAtgta
 V$SMAD_Q6_01           |     2080 (-) |  1.000 |  0.976 | ctGTCTGtctc
 V$SMAD_Q6_01           |     2305 (-) |  1.000 |  0.971 | gtGTCTGtgtg
 V$SMAD_Q6_01           |     2831 (-) |  1.000 |  0.983 | ttGTCTGcaaa
 V$SMAD_Q6_01           |     2943 (-) |  1.000 |  0.983 | aaGTCTGccta
 V$SMAD_Q6_01           |     3351 (+) |  1.000 |  0.977 | tcatCAGACag
 V$SMAD_Q6_01           |     3355 (+) |  1.000 |  0.954 | cagaCAGACca
 V$SMAD_Q6_01           |     3665 (+) |  1.000 |  0.956 | aacaCAGACtt
 V$SMAD_Q6_01           |     3978 (+) |  0.925 |  0.908 | atgaTAGACac
 V$SMAD_Q6_01           |     4326 (-) |  1.000 |  0.953 | ggGTCTGgtga
 V$SMAD_Q6_01           |     4420 (-) |  0.925 |  0.913 | ttGTCTAaaaa
 V$SMAD_Q6_01           |     4513 (+) |  1.000 |  0.933 | acatCAGACca
 V$SMAD_Q6_01           |     4775 (-) |  1.000 |  0.978 | gaGTCTGgata
 V$SMAD_Q6_01           |     4995 (+) |  1.000 |  0.953 | atggCAGACct
 V$SMAD_Q6_01           |     5198 (-) |  1.000 |  0.951 | ttGTCTGtggc
 V$SMAD_Q6_01           |     5674 (+) |  1.000 |  0.974 | gagaCAGACac
 V$SMAD_Q6_01           |     6236 (-) |  1.000 |  1.000 | ctGTCTGgcta
 V$SMAD_Q6_01           |     6649 (-) |  1.000 |  0.975 | caGTCTGcaaa
 V$SMAD_Q6_01           |     6860 (+) |  1.000 |  0.951 | cgtcCAGACcg
 V$SMAD_Q6_01           |     7102 (-) |  1.000 |  0.969 | taGTCTGtgta
 V$SMAD_Q6_01           |     7325 (-) |  1.000 |  0.936 | acGTCTGgaac
 V$SMAD_Q6_01           |     7489 (-) |  1.000 |  0.938 | acGTCTGttct
 V$SMAD_Q6_01           |     7957 (+) |  1.000 |  0.946 | acccCAGACta
 V$SMAD_Q6_01           |     8129 (-) |  1.000 |  0.943 | tgGTCTGcttt
 V$SMAD_Q6_01           |     8716 (-) |  1.000 |  0.967 | gaGTCTGaaga
 V$SMAD_Q6_01           |     9409 (-) |  0.925 |  0.916 | atGTCTAgaaa
 V$SMAD_Q6_01           |    10957 (-) |  1.000 |  0.939 | cgGTCTGtgcc
 V$RFX_Q6               |       71 (+) |  0.925 |  0.897 | ctGTTGTtg
 V$RFX_Q6               |       80 (+) |  0.938 |  0.890 | atGTTGAta
 V$RFX_Q6               |      383 (+) |  0.934 |  0.921 | gaGATGCca
 V$RFX_Q6               |      398 (-) |  0.913 |  0.888 | tgCCAACaa
 V$RFX_Q6               |      484 (-) |  0.938 |  0.920 | agTCAACat
 V$RFX_Q6               |      492 (-) |  1.000 |  0.937 | ttGCAACat
 V$RFX_Q6               |      537 (+) |  0.934 |  0.912 | gtGATGCgc
 V$RFX_Q6               |      582 (+) |  0.938 |  0.898 | ctGTTGAat
 V$RFX_Q6               |      701 (-) |  0.934 |  0.929 | ggGCATCgg
 V$RFX_Q6               |      741 (+) |  1.000 |  0.907 | tgGTTGCtg
 V$RFX_Q6               |      860 (+) |  1.000 |  0.954 | tcGTTGCcc
 V$RFX_Q6               |      978 (-) |  0.934 |  0.889 | aaGCATCac
 V$RFX_Q6               |     1029 (+) |  0.938 |  0.892 | caGTTGAat
 V$RFX_Q6               |     1090 (-) |  0.938 |  0.898 | ggTCAACta
 V$RFX_Q6               |     1363 (+) |  0.934 |  0.901 | ctGATGCtc
 V$RFX_Q6               |     1845 (-) |  0.938 |  0.928 | cgTCAACac
 V$RFX_Q6               |     1859 (-) |  0.913 |  0.912 | agCCAACtg
 V$RFX_Q6               |     2395 (+) |  1.000 |  0.943 | gaGTTGCtt
 V$RFX_Q6               |     2555 (+) |  0.925 |  0.924 | ctGTTGTga
 V$RFX_Q6               |     2681 (+) |  1.000 |  0.948 | ccGTTGCat
 V$RFX_Q6               |     2828 (+) |  0.925 |  0.923 | caGTTGTct
 V$RFX_Q6               |     2842 (-) |  0.934 |  0.920 | tgGCATCat
 V$RFX_Q6               |     2972 (+) |  0.934 |  0.920 | caGATGCgc
 V$RFX_Q6               |     2981 (-) |  0.934 |  0.897 | agGCATCta
 V$RFX_Q6               |     3141 (-) |  0.925 |  0.888 | ccACAACaa
 V$RFX_Q6               |     3236 (-) |  0.913 |  0.897 | agCCAACat
 V$RFX_Q6               |     3270 (+) |  0.934 |  0.927 | gtGATGCca
 V$RFX_Q6               |     3424 (+) |  1.000 |  0.905 | tgGTTGCtt
 V$RFX_Q6               |     4524 (-) |  0.925 |  0.895 | agACAACaa
 V$RFX_Q6               |     4536 (-) |  0.938 |  0.942 | cgTCAACag
 V$RFX_Q6               |     4568 (+) |  1.000 |  0.984 | caGTTGCgg
 V$RFX_Q6               |     4919 (-) |  0.925 |  0.896 | ccACAACtt
 V$RFX_Q6               |     5139 (-) |  0.938 |  0.895 | ggTCAACct
 V$RFX_Q6               |     5278 (-) |  0.925 |  0.897 | caACAACag
 V$RFX_Q6               |     5841 (-) |  0.934 |  0.917 | agGCATCtc
 V$RFX_Q6               |     5852 (+) |  0.938 |  0.911 | atGTTGAgt
 V$RFX_Q6               |     6109 (+) |  0.938 |  0.938 | ctGTTGAcc
 V$RFX_Q6               |     6437 (-) |  0.938 |  0.902 | ggTCAACcc
 V$RFX_Q6               |     6498 (+) |  0.934 |  0.925 | caGATGCgg
 V$RFX_Q6               |     6564 (+) |  1.000 |  0.943 | tgGTTGCca
 V$RFX_Q6               |     6844 (-) |  0.913 |  0.916 | tgCCAACtg
 V$RFX_Q6               |     7024 (-) |  0.934 |  0.896 | ctGCATCag
 V$RFX_Q6               |     7042 (+) |  0.938 |  0.900 | taGTTGAct
 V$RFX_Q6               |     7170 (+) |  1.000 |  0.936 | gcGTTGCag
 V$RFX_Q6               |     7547 (-) |  0.913 |  0.912 | agCCAACtg
 V$RFX_Q6               |     7812 (-) |  0.925 |  0.912 | cgACAACtc
 V$RFX_Q6               |     8225 (+) |  0.913 |  0.897 | atGTTGGct
 V$RFX_Q6               |     8439 (-) |  1.000 |  0.921 | ttGCAACcc
 V$RFX_Q6               |     8446 (-) |  0.934 |  0.887 | ccGCATCct
 V$RFX_Q6               |     8523 (+) |  0.934 |  0.897 | caGATGCtt
 V$RFX_Q6               |     8589 (-) |  1.000 |  0.975 | agGCAACat
 V$RFX_Q6               |     8800 (+) |  0.913 |  0.892 | gaGTTGGgg
 V$RFX_Q6               |     8941 (-) |  1.000 |  0.936 | aaGCAACtt
 V$RFX_Q6               |     9318 (+) |  0.913 |  0.890 | gcGTTGGgt
 V$RFX_Q6               |    10155 (+) |  0.925 |  0.897 | ttGTTGTcg
 V$RFX_Q6               |    10216 (-) |  0.934 |  0.901 | tgGCATCta
 V$RFX_Q6               |    10379 (+) |  1.000 |  0.937 | atGTTGCaa
 V$RFX_Q6               |    10440 (-) |  1.000 |  0.927 | atGCAACgt
 V$RFX_Q6               |    10538 (-) |  1.000 |  0.932 | gtGCAACtc
 V$RFX_Q6               |    10662 (-) |  0.938 |  0.944 | tgTCAACag
 V$RFX_Q6               |    10691 (-) |  1.000 |  0.986 | tgGCAACac
 V$RFX_Q6               |    11039 (+) |  0.925 |  0.897 | ctGTTGTtg
 V$RFX_Q6               |    11060 (+) |  0.925 |  0.898 | acGTTGTga
 V$RFX_Q6               |    11519 (+) |  0.925 |  0.921 | ccGTTGTcc
 V$RFX_Q6               |    11709 (-) |  0.913 |  0.906 | ccCCAACtg
 V$RFX_Q6               |    11920 (-) |  0.913 |  0.888 | gcCCAACgc
 V$AHRHIF_Q6            |     1423 (-) |  1.000 |  0.980 | agaCACGCa
 V$AHRHIF_Q6            |     6220 (-) |  1.000 |  0.990 | tctCACGCt
 V$AHRHIF_Q6            |     7485 (-) |  0.982 |  0.980 | gcgCACGTc
 V$AHRHIF_Q6            |    10720 (+) |  1.000 |  0.986 | tGCGTGctg
 V$EBF_Q6               |     1332 (+) |  0.976 |  0.934 | cTCCCCagggc
 V$EBF_Q6               |     5919 (+) |  0.976 |  0.923 | tTCCCCagcga
 V$LEF1TCF1_Q4          |     1036 (-) |  1.000 |  0.962 | atcaaCAAAGc
 V$LEF1TCF1_Q4          |     1164 (-) |  1.000 |  0.915 | tttttCAAAGa
 V$LEF1TCF1_Q4          |     1235 (+) |  1.000 |  0.894 | gCTTTGacatc
 V$LEF1TCF1_Q4          |     2661 (+) |  1.000 |  0.985 | aCTTTGatgac
 V$LEF1TCF1_Q4          |     4663 (+) |  1.000 |  0.933 | aCTTTGttttg
 V$LEF1TCF1_Q4          |     4871 (-) |  1.000 |  0.926 | agcagCAAAGc
 V$LEF1TCF1_Q4          |     5355 (+) |  1.000 |  0.881 | tCTTTGacaaa
 V$LEF1TCF1_Q4          |     6741 (+) |  1.000 |  0.935 | cCTTTGaaaac
 V$LEF1TCF1_Q4          |     8379 (+) |  1.000 |  0.972 | tCTTTGatctg
 V$LEF1TCF1_Q4          |     8436 (+) |  1.000 |  0.865 | gCTTTGcaacc
 V$LEF1TCF1_Q4          |     8569 (+) |  1.000 |  0.943 | tCTTTGattaa
 V$LEF1TCF1_Q4          |     8623 (+) |  1.000 |  0.888 | aCTTTGagaaa
 V$LEF1TCF1_Q4          |     8707 (-) |  0.863 |  0.869 | accatCAAGGa
 V$LEF1TCF1_Q4          |     9026 (+) |  1.000 |  0.865 | tCTTTGtgagt
 V$LEF1TCF1_Q4          |     9726 (+) |  1.000 |  0.886 | tCTTTGtatga
 V$LEF1TCF1_Q4          |    10350 (-) |  1.000 |  0.921 | taattCAAAGt
 V$LEF1TCF1_Q4          |    10578 (+) |  1.000 |  0.888 | gCTTTGgttca
 V$LEF1TCF1_Q4          |    11051 (+) |  1.000 |  0.947 | cCTTTGttaac
 V$LEF1TCF1_Q4          |    11379 (+) |  1.000 |  0.924 | gCTTTGaaaac
 V$PAX6_Q2              |      324 (+) |  1.000 |  0.862 | ctgtgcTGGAAatt
 V$PAX6_Q2              |     4393 (-) |  1.000 |  0.891 | gagTTCCAagacag
 V$PAX6_Q2              |     4942 (+) |  0.861 |  0.873 | ctgaacTGGGActt
 V$PAX6_Q2              |     9033 (-) |  0.821 |  0.870 | gagTTCAAgggcag
 V$PAX6_Q2              |     9631 (-) |  0.821 |  0.921 | gagTTCAAggtcag
 V$TBP_Q6               |      568 (-) |  1.000 |  0.971 | agATAAA
 V$TBP_Q6               |      644 (+) |  1.000 |  0.974 | TTTATtc
 V$TBP_Q6               |      652 (+) |  1.000 |  0.969 | TTTATta
 V$TBP_Q6               |      834 (-) |  1.000 |  0.997 | atATAAA
 V$TBP_Q6               |      848 (-) |  1.000 |  0.971 | aaATAAA
 V$TBP_Q6               |     1152 (+) |  1.000 |  0.969 | TTTATgt
 V$TBP_Q6               |     1892 (+) |  1.000 |  0.997 | TTTATat
 V$TBP_Q6               |     1898 (+) |  1.000 |  0.971 | TTTATtt
 V$TBP_Q6               |     1903 (+) |  1.000 |  0.969 | TTTATta
 V$TBP_Q6               |     1911 (+) |  1.000 |  0.971 | TTTATtt
 V$TBP_Q6               |     2365 (+) |  1.000 |  0.971 | TTTATtt
 V$TBP_Q6               |     2739 (+) |  1.000 |  0.972 | TTTATgc
 V$TBP_Q6               |     2903 (+) |  1.000 |  0.974 | TTTATcc
 V$TBP_Q6               |     3405 (-) |  1.000 |  0.994 | ttATAAA
 V$TBP_Q6               |     3452 (-) |  1.000 |  0.969 | taATAAA
 V$TBP_Q6               |     3626 (+) |  1.000 |  0.994 | TTTATaa
 V$TBP_Q6               |     3742 (+) |  0.923 |  0.926 | TTTCTac
 V$TBP_Q6               |     3831 (-) |  1.000 |  0.969 | taATAAA
 V$TBP_Q6               |     3847 (-) |  1.000 |  0.966 | tcATAAA
 V$TBP_Q6               |     3910 (-) |  1.000 |  0.969 | taATAAA
 V$TBP_Q6               |     3919 (+) |  1.000 |  0.966 | TTTATga
 V$TBP_Q6               |     4004 (-) |  1.000 |  0.971 | cgATAAA
 V$TBP_Q6               |     4008 (-) |  1.000 |  0.971 | aaATAAA
 V$TBP_Q6               |     4225 (-) |  1.000 |  0.971 | aaATAAA
 V$TBP_Q6               |     4316 (-) |  1.000 |  0.972 | gcATAAA
 V$TBP_Q6               |     4781 (-) |  1.000 |  0.974 | ggATAAA
 V$TBP_Q6               |     5387 (+) |  1.000 |  0.971 | TTTATtt
 V$TBP_Q6               |     5398 (+) |  1.000 |  0.997 | TTTATat
 V$TBP_Q6               |     5435 (+) |  1.000 |  0.971 | TTTATtt
 V$TBP_Q6               |     5590 (-) |  1.000 |  0.969 | taATAAA
 V$TBP_Q6               |     5635 (-) |  1.000 |  0.974 | ggATAAA
 V$TBP_Q6               |     5646 (-) |  1.000 |  0.971 | aaATAAA
 V$TBP_Q6               |     5954 (+) |  1.000 |  0.971 | TTTATtt
 V$TBP_Q6               |     6467 (-) |  1.000 |  0.969 | tgATAAA
 V$TBP_Q6               |     6511 (-) |  1.000 |  0.971 | aaATAAA
 V$TBP_Q6               |     6671 (+) |  1.000 |  0.971 | TTTATtt
 V$TBP_Q6               |     6762 (+) |  1.000 |  1.000 | TTTATac
 V$TBP_Q6               |     6828 (+) |  1.000 |  0.969 | TTTATgt
 V$TBP_Q6               |     7426 (+) |  1.000 |  0.971 | TTTATtt
 V$TBP_Q6               |     7436 (+) |  1.000 |  0.971 | TTTATtt
 V$TBP_Q6               |     7441 (+) |  1.000 |  0.969 | TTTATgt
 V$TBP_Q6               |     7799 (-) |  1.000 |  0.971 | agATAAA
 V$TBP_Q6               |     7897 (+) |  1.000 |  0.971 | TTTATtt
 V$TBP_Q6               |     8063 (+) |  1.000 |  0.971 | TTTATct
 V$TBP_Q6               |     8494 (+) |  0.923 |  0.926 | TTTCTac
 V$TBP_Q6               |     8931 (-) |  1.000 |  1.000 | gtATAAA
 V$TBP_Q6               |     9426 (-) |  1.000 |  0.969 | ccATAAA
 V$TBP_Q6               |     9486 (+) |  1.000 |  0.971 | TTTATtt
 V$TBP_Q6               |    10123 (-) |  1.000 |  0.971 | caATAAA
 V$TBP_Q6               |    10318 (+) |  1.000 |  0.997 | TTTATat
 V$TBP_Q6               |    10326 (+) |  1.000 |  0.971 | TTTATtt
 V$TBP_Q6               |    10331 (+) |  1.000 |  0.997 | TTTATag
 V$TBP_Q6               |    10340 (+) |  1.000 |  0.971 | TTTATtg
 V$TBP_Q6               |    10391 (-) |  1.000 |  0.997 | atATAAA
 V$TBP_Q6               |    10453 (+) |  1.000 |  0.997 | TTTATat
 V$TBP_Q6               |    10626 (-) |  0.923 |  0.926 | gtAGAAA
 V$TBP_Q6               |    10705 (+) |  1.000 |  0.966 | TTTATga
 V$TBP_Q6               |    10734 (+) |  1.000 |  0.971 | TTTATtg
 V$TBP_Q6               |    11409 (+) |  1.000 |  0.974 | TTTATtc
 V$TBP_Q6               |    11472 (+) |  1.000 |  0.971 | TTTATtt
 V$TBP_Q6               |    11688 (-) |  1.000 |  0.971 | caATAAA
 V$CREBATF_Q6           |     1239 (-) |  0.893 |  0.897 | tgaCATCAg
 V$CREBATF_Q6           |     1842 (-) |  1.000 |  0.937 | ggtCGTCAa
 V$CREBATF_Q6           |     2965 (+) |  1.000 |  0.954 | gTGACGgca
 V$CREBATF_Q6           |     4533 (-) |  1.000 |  0.948 | atgCGTCAa
 V$CREBATF_Q6           |     8323 (-) |  1.000 |  0.951 | ctgCGTCAg
 V$CREBATF_Q6           |     8612 (-) |  1.000 |  0.947 | ttcCGTCAa
 V$CREBATF_Q6           |    11317 (+) |  1.000 |  0.947 | gTGACGacg
 V$CREBATF_Q6           |    11332 (+) |  1.000 |  0.938 | aTGACGatg
 V$KROX_Q6              |     1494 (-) |  1.000 |  0.896 | gggggGGGGGaggg
 V$KROX_Q6              |     9682 (-) |  1.000 |  0.879 | ggaggGGGGGtggt
 V$PEBP_Q6              |      932 (+) |  1.000 |  0.921 | cgaaACCACaagtta
 V$PEBP_Q6              |     3637 (+) |  1.000 |  0.891 | acctACCACatggtg
 V$PEBP_Q6              |     4140 (-) |  1.000 |  0.886 | ctaggtGTGGTgcct
 V$PEBP_Q6              |     4437 (+) |  1.000 |  0.936 | aaaaACCACacaatt
 V$PEBP_Q6              |     4567 (-) |  0.910 |  0.891 | acagttGCGGTtaga
 V$PEBP_Q6              |     5044 (-) |  1.000 |  0.925 | attgctGTGGTctaa
 V$PEBP_Q6              |     5251 (-) |  1.000 |  0.932 | tcacatGTGGTcaca
 V$PEBP_Q6              |     7108 (+) |  1.000 |  0.911 | gtgtACCACatgtgt
 V$PEBP_Q6              |     8737 (-) |  1.000 |  0.907 | cggggtGTGGTggcc
 V$PEBP_Q6              |     8894 (+) |  1.000 |  0.918 | acgtACCACaaacag
 V$PEBP_Q6              |     8970 (-) |  1.000 |  0.885 | ccaggtGTGGTggta
 V$PEBP_Q6              |     9570 (-) |  1.000 |  0.885 | ctgggtGTGGTggta
 V$PEBP_Q6              |    11251 (-) |  1.000 |  0.963 | aactctGTGGTgtgc
 V$CHCH_01              |      185 (-) |  0.997 |  0.994 | tACCCG
 V$CHCH_01              |      782 (+) |  0.997 |  0.997 | CGGGTg
 V$CHCH_01              |     1572 (+) |  1.000 |  0.997 | CGGGGa
 V$CHCH_01              |     1682 (+) |  0.997 |  0.997 | CGGGTg
 V$CHCH_01              |     3043 (-) |  0.997 |  0.997 | cACCCG
 V$CHCH_01              |     3047 (+) |  0.998 |  0.991 | CGGGAc
 V$CHCH_01              |     3532 (-) |  0.994 |  0.987 | gGCCCG
 V$CHCH_01              |     3723 (+) |  0.997 |  0.997 | CGGGTg
 V$CHCH_01              |     4598 (-) |  0.994 |  0.991 | tGCCCG
 V$CHCH_01              |     4827 (+) |  1.000 |  0.989 | CGGGGt
 V$CHCH_01              |     5025 (+) |  0.998 |  0.991 | CGGGAc
 V$CHCH_01              |     5895 (-) |  0.994 |  0.987 | gGCCCG
 V$CHCH_01              |     6203 (+) |  1.000 |  0.989 | CGGGGt
 V$CHCH_01              |     7182 (-) |  0.998 |  0.991 | gTCCCG
 V$CHCH_01              |     7196 (+) |  1.000 |  1.000 | CGGGGg
 V$CHCH_01              |     8512 (+) |  0.998 |  0.991 | CGGGAc
 V$CHCH_01              |     8737 (+) |  1.000 |  0.989 | CGGGGt
 V$CHCH_01              |     9123 (+) |  0.998 |  0.995 | CGGGAa
 V$CHCH_01              |     9628 (+) |  0.998 |  0.998 | CGGGAg
 V$CHCH_01              |    10067 (+) |  0.997 |  0.990 | CGGGTc
 V$CHCH_01              |    10697 (-) |  0.997 |  0.997 | cACCCG
 V$CHCH_01              |    11870 (+) |  1.000 |  1.000 | CGGGGg
 V$CHCH_01              |    11917 (+) |  0.994 |  0.987 | CGGGCc
 V$TAL1_Q6              |     5127 (-) |  1.000 |  0.991 | aacaGATGGt
 V$TAL1_Q6              |     6036 (+) |  1.000 |  0.983 | cCCATCtggt
 V$TAL1_Q6              |     6845 (+) |  0.977 |  0.976 | gCCAACtggt
 V$TAL1_Q6              |     7511 (-) |  1.000 |  0.975 | gtcaGATGGc
 V$DEC_Q1               |       17 (+) |  0.987 |  0.918 | gtaCATGTgaatg
 V$DEC_Q1               |     1391 (+) |  0.973 |  0.920 | gggCAGGTgagga
 V$DEC_Q1               |     1859 (+) |  0.894 |  0.905 | agcCAACTgaaga
 V$DEC_Q1               |     2772 (+) |  0.987 |  0.917 | ccgCATGTgagat
 V$DEC_Q1               |     5168 (-) |  1.000 |  0.921 | ctttcACTTGtga
 V$DEC_Q1               |     5248 (-) |  0.987 |  0.938 | ggttcACATGtgg
 V$DEC_Q1               |     6942 (+) |  1.000 |  0.938 | accCAAGTgatac
 V$DEC_Q1               |    10887 (-) |  0.987 |  0.905 | actgcACATGcgc
 V$PBX_Q3               |      132 (-) |  1.000 |  0.919 | gctcagtCAATC
 V$PBX_Q3               |     8611 (-) |  1.000 |  0.931 | attccgtCAATC
 V$PBX_Q3               |    11199 (+) |  1.000 |  0.931 | GATTGattatta
 V$AIRE_01              |      102 (+) |  0.891 |  0.826 | cctgggggTGGCCagtgaggctggct
 V$AIRE_01              |      181 (-) |  0.891 |  0.844 | ttactacccgtgcCTCCCacaccacc
 V$AIRE_01              |      182 (-) |  0.907 |  0.858 | tactacccgtgccTCCCAcaccacca
 V$AIRE_01              |      187 (-) |  0.952 |  0.829 | cccgtgcctcccaCACCAccatgcct
 V$AIRE_01              |      190 (-) |  0.952 |  0.879 | gtgcctcccacacCACCAtgcctggt
 V$AIRE_01              |     1072 (+) |  0.931 |  0.893 | agatgtgtAGGTCattttggtcaact
 V$AIRE_01              |     1271 (+) |  0.907 |  0.855 | gtgtactcTGGGAtgacagggacctg
 V$AIRE_01              |     1272 (+) |  0.940 |  0.862 | tgtactctGGGATgacagggacctgg
 V$AIRE_01              |     1308 (-) |  0.891 |  0.845 | aagagtcccctaaCTCCCttctcact
 V$AIRE_01              |     1338 (+) |  0.906 |  0.836 | agggcttaAGGCTtgcctgggtcacc
 V$AIRE_01              |     1347 (-) |  0.925 |  0.845 | ggcttgcctgggtCACCTgatgctcg
 V$AIRE_01              |     1378 (+) |  0.960 |  0.853 | agtgggcgAGGTAgggcaggtgagga
 V$AIRE_01              |     1383 (+) |  0.891 |  0.834 | gcgaggtaGGGCAggtgaggagagtg
 V$AIRE_01              |     1482 (+) |  0.891 |  0.849 | ctggcagaGGGAGgggggggggaggg
 V$AIRE_01              |     1566 (+) |  0.927 |  0.878 | aatctacgGGGAAtgcatggagagcc
 V$AIRE_01              |     1597 (+) |  0.904 |  0.850 | tgggtttgGGGCTcagggggtctcgt
 V$AIRE_01              |     1628 (-) |  0.929 |  0.907 | gcatgtccagcctTTCCTagtgctaa
 V$AIRE_01              |     1728 (-) |  0.929 |  0.874 | gctcatcctgaacTTCCTatagaaca
 V$AIRE_01              |     1775 (-) |  0.925 |  0.856 | tgtcctcctggagCACCTgccattca
 V$AIRE_01              |     1808 (+) |  0.952 |  0.857 | catcagggTGGTGttcagggaagaca
 V$AIRE_01              |     1935 (+) |  0.933 |  0.869 | tgtagcctTGGCTaggctggaacttt
 V$AIRE_01              |     2016 (+) |  0.907 |  0.889 | ctgagtgcTGGGAttaaaggagtgta
 V$AIRE_01              |     2675 (-) |  0.942 |  0.925 | cttaacccgttgcATCCTggtcacac
 V$AIRE_01              |     3031 (-) |  0.886 |  0.857 | cgacttccgctccACCCGggacatac
 V$AIRE_01              |     3232 (-) |  0.907 |  0.865 | agtcagccaacatTCCCAgcccactt
 V$AIRE_01              |     3251 (+) |  1.000 |  0.894 | cccacttaTGGTTttcttggtgatgc
 V$AIRE_01              |     4334 (+) |  0.925 |  0.870 | tgacatccAGGTGgtggaggcaggag
 V$AIRE_01              |     4976 (-) |  0.893 |  0.858 | tcagcccctacctGTCCGaatggcag
 V$AIRE_01              |     5007 (-) |  0.933 |  0.880 | gtattacccattaAGCCAcgggactg
 V$AIRE_01              |     5024 (+) |  0.940 |  0.883 | acgggactGGGATgctcaggattgct
 V$AIRE_01              |     5277 (+) |  0.906 |  0.868 | ccaacaacAGGCTcagatgggctagc
 V$AIRE_01              |     5492 (-) |  0.907 |  0.830 | cccttccctctgcTCCCAggtttccc
 V$AIRE_01              |     5500 (-) |  0.927 |  0.844 | tctgctcccaggtTTCCCtgcctttc
 V$AIRE_01              |     5510 (-) |  0.929 |  0.868 | ggtttccctgcctTTCCTcctatcca
 V$AIRE_01              |     5748 (+) |  0.900 |  0.877 | agacgcaaAGGACctgtagggtaaaa
 V$AIRE_01              |     6177 (-) |  0.923 |  0.866 | gggttcccagagaCACCCatttaagc
 V$AIRE_01              |     6187 (-) |  0.899 |  0.855 | agacacccatttaAGCCGgggtatgc
 V$AIRE_01              |     6753 (-) |  0.987 |  0.949 | cactatccctttaTACCAtgaacaaa
 V$AIRE_01              |     6801 (-) |  0.960 |  0.901 | ttcctcccctcatTACCTtctccctt
 V$AIRE_01              |     6894 (+) |  0.891 |  0.856 | agacaagaGGGCAtaagtggagaaca
 V$AIRE_01              |     6903 (+) |  0.920 |  0.852 | ggcataagTGGAGaacaaggaattga
 V$AIRE_01              |     6959 (+) |  0.969 |  0.899 | cattattcTGGATggaaaggaacgac
 V$AIRE_01              |     7178 (-) |  0.891 |  0.830 | gatggtcccgaacGGCCAcgggggtg
 V$AIRE_01              |     7694 (+) |  0.891 |  0.857 | cagaacttGGGAGgtagaggcagaag
 V$AIRE_01              |     8112 (-) |  0.893 |  0.856 | cactctcccacccTGCCTggtctgct
 V$AIRE_01              |     8199 (-) |  0.931 |  0.866 | ctgtttcccctctGACCTcagttctg
 V$AIRE_01              |     8356 (-) |  0.906 |  0.843 | ccaacccctgtgcAGCCTgctgctct
 V$AIRE_01              |     8395 (-) |  0.904 |  0.882 | ctgaagccaagccAGCCCggcctgta
 V$AIRE_01              |     8667 (+) |  0.966 |  0.895 | caaaccacCGGTTaggaaggtaatta
 V$AIRE_01              |     8730 (+) |  0.890 |  0.842 | gtaacgtcGGGGTgtggtggcccaca
 V$AIRE_01              |     8750 (-) |  0.891 |  0.841 | cccacaccttgtcCTCCCagcacctg
 V$AIRE_01              |     8905 (+) |  0.929 |  0.876 | acagattcAGGAAtactcggaattca
 V$AIRE_01              |     8955 (+) |  0.891 |  0.840 | aattagtaGGGAGaaccaggtgtggt
 V$AIRE_01              |     8983 (-) |  0.956 |  0.900 | tacacacctttaaTTCCAgcacatgg
 V$AIRE_01              |     8998 (+) |  0.920 |  0.845 | ccagcacaTGGAGgcaggggcaggca
 V$AIRE_01              |     9041 (+) |  0.958 |  0.861 | gggcagccTGGTCtacatggcaagtt
 V$AIRE_01              |     9061 (+) |  0.906 |  0.859 | caagttccAGGCTagccagggcagca
 V$AIRE_01              |     9061 (-) |  0.933 |  0.861 | caagttccaggctAGCCAgggcagca
 V$AIRE_01              |     9116 (-) |  0.973 |  0.904 | aaaaaaccgggaaAACCTtcagtttt
 V$AIRE_01              |     9176 (-) |  0.958 |  0.881 | tgaacgccacagaGACCActcaagag
 V$AIRE_01              |     9563 (+) |  0.920 |  0.876 | tcggtttcTGGGTgtggtggtatagc
 V$AIRE_01              |     9582 (-) |  0.940 |  0.893 | gtatagccctgtaATCCCagcatttg
 V$AIRE_01              |     9583 (-) |  0.907 |  0.872 | tatagccctgtaaTCCCAgcatttgg
 V$AIRE_01              |     9599 (+) |  0.927 |  0.869 | cagcatttGGGAAgctgaggtgggag
 V$AIRE_01              |     9611 (+) |  0.907 |  0.856 | agctgaggTGGGAggatcgggagttc
 V$AIRE_01              |     9612 (+) |  0.891 |  0.828 | gctgaggtGGGAGgatcgggagttca
 V$AIRE_01              |     9621 (+) |  0.891 |  0.854 | ggaggatcGGGAGttcaaggtcagct
 V$AIRE_01              |     9630 (+) |  0.931 |  0.872 | ggagttcaAGGTCagcttgggctact
 V$AIRE_01              |     9681 (+) |  0.923 |  0.837 | tggaggggGGGTGgtggtggtggtgg
 V$AIRE_01              |     9684 (+) |  0.952 |  0.842 | agggggggTGGTGgtggtggtggtgg
 V$AIRE_01              |     9687 (+) |  0.952 |  0.845 | gggggtggTGGTGgtggtggtggtgg
 V$AIRE_01              |     9690 (+) |  0.952 |  0.853 | ggtggtggTGGTGgtggtggtggtgt
 V$AIRE_01              |     9693 (+) |  0.952 |  0.884 | ggtggtggTGGTGgtggtggtgtaaa
 V$AIRE_01              |     9962 (+) |  1.000 |  0.927 | tatgtttcTGGTTcctatggggatca
 V$AIRE_01              |     9992 (+) |  0.931 |  0.867 | agggtattAGGTCctctgggactgga
 V$AIRE_01              |    10000 (+) |  0.907 |  0.837 | aggtcctcTGGGActggaggtataga
 V$AIRE_01              |    10059 (+) |  0.886 |  0.849 | aactgaacCGGGTcttctggaagggc
 V$AIRE_01              |    10597 (+) |  0.893 |  0.855 | tatcaaaaAGGAGtgtgtgggaggga
 V$AIRE_01              |    10775 (+) |  0.893 |  0.847 | aactctgtCGGACccagggggatgtg
 V$AIRE_01              |    11265 (+) |  0.929 |  0.882 | ccaagaaaAGGAAattaaggcatagg
 V$AIRE_01              |    11617 (-) |  0.929 |  0.878 | ggggtaccagaagGACCCtcgtttaa
 V$AIRE_01              |    11703 (-) |  0.891 |  0.877 | ctgtcaccccaacTGCCCtccaccat
 V$AIRE_01              |    11802 (+) |  0.925 |  0.837 | agattggaAGGTGgcccagggttggg
 V$AIRE_01              |    11844 (+) |  0.890 |  0.833 | tggggggtGGGGTatgggggtaggtc
 V$AIRE_01              |    11853 (+) |  0.958 |  0.846 | gggtatggGGGTAggtccgggggagg
 V$AIRE_02              |      643 (+) |  1.000 |  0.639 | atTTATTcatttattatatataagt
 V$AIRE_02              |      830 (-) |  0.679 |  0.625 | tactatataaaacaagttAAATAaa
 V$AIRE_02              |     1047 (-) |  0.673 |  0.621 | agcaaaaatcaacaacttTAAAAta
 V$AIRE_02              |     2404 (-) |  0.802 |  0.622 | tccttaaaaaaaacaaaaAATCAca
 V$AIRE_02              |     3351 (-) |  0.802 |  0.639 | tcatcagacagaccactgAATAGcc
 V$AIRE_02              |     3389 (-) |  0.623 |  0.618 | ccctgaggatctccagttATAAAag
 V$AIRE_02              |     3758 (+) |  0.877 |  0.642 | caTTCTTaaaaggcaatgctccttc
 V$AIRE_02              |     4248 (+) |  0.802 |  0.674 | ttGTATTacttggttgttaggatgc
 V$AIRE_02              |     4251 (+) |  0.745 |  0.621 | taTTACTtggttgttaggatgctta
 V$AIRE_02              |     4430 (-) |  0.802 |  0.700 | aaaaaaaaaaaaccacacAATTAat
 V$AIRE_02              |     4434 (-) |  0.802 |  0.639 | aaaaaaaaccacacaattAATATtc
 V$AIRE_02              |     5001 (-) |  0.481 |  0.626 | gaccttgtattacccattAAGCCac
 V$AIRE_02              |     5314 (+) |  0.877 |  0.683 | gcTTCTTcatcggttcagtgcgccg
 V$AIRE_02              |     5966 (+) |  0.877 |  0.704 | tgTTTTTaagtggtgataacttctg
 V$AIRE_02              |     6181 (-) |  0.481 |  0.626 | tcccagagacacccatttAAGCCgg
 V$AIRE_02              |     7056 (+) |  0.877 |  0.681 | ttTTCTTaatttgtttttgtttgtg
 V$AIRE_02              |     7413 (+) |  0.481 |  0.638 | gaACTTTtaaaggtttatttgtttt
 V$AIRE_02              |     7414 (+) |  0.679 |  0.619 | aaCTTTTaaaggtttatttgttttt
 V$AIRE_02              |     7782 (-) |  0.783 |  0.639 | aacaaaaattatcccaaaGATAAag
 V$AIRE_02              |     7817 (-) |  0.472 |  0.697 | actccaaaacaaacaattAACCCac
 V$AIRE_02              |     7922 (+) |  0.585 |  0.623 | agGTATCaattcgtttgtgtgttta
 V$AIRE_02              |     8838 (-) |  0.877 |  0.651 | accaaaacagaacggtttAAAAAtt
 V$AIRE_02              |     9179 (-) |  0.679 |  0.619 | acgccacagagaccactcAAGAGag
 V$AIRE_02              |     9413 (-) |  1.000 |  0.731 | ctagaaaactatcccataAATAAca
 V$AIRE_02              |     9824 (+) |  0.673 |  0.619 | aaTTTTAgaagggataattttaaag
 V$AIRE_02              |    10119 (-) |  0.877 |  0.678 | tccccaataaaattagttAAGAAat
 V$AIRE_02              |    10304 (+) |  0.877 |  0.666 | atTTTTTaactgtttttatattttt
 V$AIRE_02              |    10325 (+) |  1.000 |  0.636 | ttTTATTttatagtttttattgttt
 V$AIRE_02              |    10326 (+) |  0.679 |  0.655 | ttTATTTtatagtttttattgtttt
 V$AIRE_02              |    10733 (+) |  1.000 |  0.651 | ttTTATTggggggtttcagtgatcc
 V$AIRE_02              |    11192 (+) |  0.877 |  0.657 | gtTTCTTgattgattattaatttgt
 V$AIRE_02              |    11203 (+) |  1.000 |  0.672 | gaTTATTaatttgtttgaactgccc
 V$AIRE_02              |    11665 (-) |  0.679 |  0.665 | caattttcataaccaaaaAAGACca
 V$AIRE_02              |    11675 (-) |  0.481 |  0.651 | aaccaaaaaagaccaataAAGTTaa
 V$DEAF1_01             |     1708 (+) |  1.000 |  0.821 | gcaccctctgccttTTCCGggctca
 V$HELIOSA_02           |      224 (-) |  1.000 |  0.998 | tttTTCCTttt
 V$HELIOSA_02           |      422 (-) |  0.881 |  0.902 | cttGTCCAaaa
 V$HELIOSA_02           |      767 (+) |  0.965 |  0.851 | ctcTGGAAgag
 V$HELIOSA_02           |      806 (-) |  0.877 |  0.885 | tttCTCCAgcc
 V$HELIOSA_02           |      943 (+) |  1.000 |  0.901 | gttAGGAAcaa
 V$HELIOSA_02           |     1133 (-) |  1.000 |  0.907 | gtgTTCCTaaa
 V$HELIOSA_02           |     1190 (+) |  1.000 |  0.858 | cccAGGAAagc
 V$HELIOSA_02           |     1559 (+) |  0.965 |  0.847 | ttcTGGAAatc
 V$HELIOSA_02           |     1638 (-) |  1.000 |  0.870 | cctTTCCTagt
 V$HELIOSA_02           |     1719 (-) |  0.942 |  0.931 | cttTTCCGggc
 V$HELIOSA_02           |     1822 (+) |  0.942 |  0.851 | tcaGGGAAgac
 V$HELIOSA_02           |     1956 (-) |  1.000 |  0.876 | actTTCCTttt
 V$HELIOSA_02           |     2146 (-) |  1.000 |  0.883 | ctcTTCCTtcc
 V$HELIOSA_02           |     2160 (-) |  1.000 |  0.885 | ctcTTCCTttc
 V$HELIOSA_02           |     2165 (-) |  1.000 |  0.872 | cctTTCCTtct
 V$HELIOSA_02           |     2173 (-) |  1.000 |  0.877 | tctTTCCTtct
 V$HELIOSA_02           |     2204 (-) |  1.000 |  0.890 | ttcTTCCTttc
 V$HELIOSA_02           |     2379 (-) |  0.942 |  0.948 | gttTTCCCaga
 V$HELIOSA_02           |     2400 (-) |  1.000 |  0.878 | gctTTCCTtaa
 V$HELIOSA_02           |     2510 (+) |  0.942 |  0.954 | aaaGGGAAaaa
 V$HELIOSA_02           |     2702 (-) |  0.912 |  0.917 | cttCTCCTtcc
 V$HELIOSA_02           |     2712 (-) |  0.942 |  0.848 | ctcTTCCCaaa
 V$HELIOSA_02           |     2784 (-) |  1.000 |  0.892 | ttcTTCCTtag
 V$HELIOSA_02           |     2903 (-) |  0.894 |  0.910 | tttATCCAcat
 V$HELIOSA_02           |     3110 (-) |  0.965 |  0.846 | aatTTCCAtgc
 V$HELIOSA_02           |     3324 (-) |  1.000 |  0.985 | cttTTCCTgat
 V$HELIOSA_02           |     3836 (-) |  0.965 |  0.847 | aatTTCCAttc
 V$HELIOSA_02           |     4036 (-) |  0.965 |  0.869 | ataTTCCAgca
 V$HELIOSA_02           |     4113 (-) |  0.942 |  0.948 | attTTCCCaga
 V$HELIOSA_02           |     4162 (-) |  0.929 |  0.851 | gtaATCCTagt
 V$HELIOSA_02           |     4687 (+) |  1.000 |  0.856 | ggcAGGAAact
 V$HELIOSA_02           |     4777 (+) |  0.894 |  0.902 | gtcTGGATaaa
 V$HELIOSA_02           |     4881 (+) |  0.965 |  0.865 | ctcTGGAAcat
 V$HELIOSA_02           |     4895 (-) |  1.000 |  0.899 | atgTTCCTtgg
 V$HELIOSA_02           |     5120 (+) |  1.000 |  0.879 | aaaAGGAAaca
 V$HELIOSA_02           |     5457 (-) |  0.942 |  0.933 | cttTTCCCcac
 V$HELIOSA_02           |     5472 (-) |  1.000 |  0.875 | tatTTCCTgat
 V$HELIOSA_02           |     5520 (-) |  1.000 |  0.862 | cctTTCCTcct
 V$HELIOSA_02           |     5580 (+) |  0.929 |  0.942 | taaAGGATaat
 V$HELIOSA_02           |     5631 (+) |  0.870 |  0.896 | actGGGATaaa
 V$HELIOSA_02           |     5935 (+) |  0.877 |  0.893 | cctTGGAGaaa
 V$HELIOSA_02           |     6138 (-) |  0.965 |  0.861 | gtcTTCCAtgc
 V$HELIOSA_02           |     6257 (-) |  0.858 |  0.880 | tttGTCCCatc
 V$HELIOSA_02           |     6460 (-) |  1.000 |  0.875 | tatTTCCTgat
 V$HELIOSA_02           |     6798 (-) |  1.000 |  0.873 | ctcTTCCTccc
 V$HELIOSA_02           |     6817 (-) |  0.853 |  0.883 | cttCTCCCttt
 V$HELIOSA_02           |     6908 (+) |  0.877 |  0.893 | aagTGGAGaac
 V$HELIOSA_02           |     6998 (+) |  0.965 |  0.965 | agaTGGAAaag
 V$HELIOSA_02           |     7018 (-) |  1.000 |  0.867 | tgtTTCCTgca
 V$HELIOSA_02           |     7246 (+) |  1.000 |  0.982 | ctcAGGAAaaa
 V$HELIOSA_02           |     7327 (+) |  0.965 |  0.868 | gtcTGGAAcaa
 V$HELIOSA_02           |     7715 (+) |  0.929 |  0.850 | agaAGGATcag
 V$HELIOSA_02           |     7789 (-) |  0.870 |  0.896 | attATCCCaaa
 V$HELIOSA_02           |     8144 (+) |  0.942 |  0.950 | tgaGGGAAaac
 V$HELIOSA_02           |     8757 (-) |  0.916 |  0.910 | cttGTCCTccc
 V$HELIOSA_02           |     8910 (+) |  1.000 |  0.900 | ttcAGGAAtac
 V$HELIOSA_02           |     8960 (+) |  0.853 |  0.879 | gtaGGGAGaac
 V$HELIOSA_02           |     9121 (+) |  0.942 |  0.941 | accGGGAAaac
 V$HELIOSA_02           |     9831 (+) |  0.870 |  0.890 | gaaGGGATaat
 V$HELIOSA_02           |     9873 (+) |  1.000 |  0.873 | atgAGGAAatc
 V$HELIOSA_02           |    10493 (+) |  0.929 |  0.856 | tcaAGGATcaa
 V$HELIOSA_02           |    10588 (-) |  1.000 |  0.878 | aatTTCCTata
 V$HELIOSA_02           |    10637 (+) |  1.000 |  0.880 | ctgAGGAAgac
 V$HELIOSA_02           |    10843 (+) |  1.000 |  0.878 | cgcAGGAAgaa
 V$HELIOSA_02           |    11091 (-) |  0.965 |  0.951 | attTTCCActg
 V$HELIOSA_02           |    11270 (+) |  1.000 |  0.881 | aaaAGGAAatt
 V$HELIOSA_02           |    11480 (-) |  0.942 |  0.946 | tttTTCCCttg
 V$HELIOSA_02           |    11521 (-) |  0.858 |  0.883 | gttGTCCGtag
 V$HELIOSA_02           |    11787 (+) |  0.916 |  0.929 | gtaAGGACaaa
 P$AGP1_01              |     6782 (+) |  1.000 |  0.993 | gcAGATCtaa
 V$SRF_Q5_02            |    11534 (-) |  0.926 |  0.901 | aatcCCACAtatggtagat
 V$HES1_Q2              |     1614 (+) |  1.000 |  0.976 | gggtcTCGTGgacag
 V$HES1_Q2              |     5207 (+) |  0.989 |  0.943 | gcctcTTGTGcttct
 V$HES1_Q2              |    10248 (+) |  0.989 |  0.947 | caggcTTGTGcagga
 V$HES1_Q2              |    10800 (+) |  0.989 |  0.958 | gagccTTGTGcatct
 V$HES1_Q2              |    10931 (+) |  0.989 |  0.955 | gcctcTTGTGgacgg
 V$HMGIY_Q3             |      210 (+) |  0.890 |  0.904 | cctggTATTTttttt
 V$HMGIY_Q3             |      211 (+) |  0.960 |  0.933 | ctggtATTTTttttt
 V$HMGIY_Q3             |      328 (-) |  1.000 |  0.879 | gctggAAATTccctc
 V$HMGIY_Q3             |      901 (+) |  0.908 |  0.883 | ttttcACTTTctttc
 V$HMGIY_Q3             |      989 (-) |  0.905 |  0.902 | ttaatAATTTtcatg
 V$HMGIY_Q3             |      990 (+) |  0.960 |  0.869 | taataATTTTcatgt
 V$HMGIY_Q3             |     1080 (+) |  0.960 |  0.883 | aggtcATTTTggtca
 V$HMGIY_Q3             |     1891 (+) |  0.890 |  0.864 | ttttaTATTTatttt
 V$HMGIY_Q3             |     1896 (+) |  0.960 |  0.917 | tatttATTTTattat
 V$HMGIY_Q3             |     1904 (+) |  0.960 |  0.887 | ttattATTTTatttg
 V$HMGIY_Q3             |     1951 (+) |  0.908 |  0.880 | ctggaACTTTccttt
 V$HMGIY_Q3             |     2358 (+) |  0.890 |  0.878 | acttgTATTTatttt
 V$HMGIY_Q3             |     2416 (-) |  0.867 |  0.882 | acaaaAAATCacagg
 V$HMGIY_Q3             |     2515 (-) |  0.960 |  0.906 | gaaaaAAAATtacat
 V$HMGIY_Q3             |     2516 (-) |  1.000 |  0.981 | aaaaaAAATTacata
 V$HMGIY_Q3             |     2558 (-) |  1.000 |  0.899 | ttgtgAAATTtccgt
 V$HMGIY_Q3             |     2559 (+) |  1.000 |  0.892 | tgtgaAATTTccgta
 V$HMGIY_Q3             |     2656 (+) |  0.908 |  0.895 | aatgcACTTTgatga
 V$HMGIY_Q3             |     3105 (-) |  0.905 |  0.870 | atactAATTTccatg
 V$HMGIY_Q3             |     3125 (-) |  0.905 |  0.879 | atattAATTTacatt
 V$HMGIY_Q3             |     3607 (+) |  0.928 |  0.863 | tctgcAGTTTtcaaa
 V$HMGIY_Q3             |     3830 (-) |  1.000 |  0.960 | ataatAAATTtccat
 V$HMGIY_Q3             |     3831 (-) |  0.905 |  0.897 | taataAATTTccatt
 V$HMGIY_Q3             |     4085 (+) |  0.960 |  0.896 | actatATTTTactga
 V$HMGIY_Q3             |     4219 (-) |  0.960 |  0.936 | ttaaaAAAATaaatt
 V$HMGIY_Q3             |     4224 (-) |  1.000 |  0.910 | aaaatAAATTctcag
 V$HMGIY_Q3             |     4432 (-) |  0.851 |  0.874 | aaaaaAAAAAccaca
 V$HMGIY_Q3             |     4475 (+) |  0.960 |  0.922 | ccagcATTTTtcttt
 V$HMGIY_Q3             |     4490 (-) |  0.851 |  0.863 | tgaacAAAAAacaaa
 V$HMGIY_Q3             |     4635 (-) |  0.960 |  0.912 | gtagcAAAATcccgg
 V$HMGIY_Q3             |     4658 (+) |  0.908 |  0.873 | ctcggACTTTgtttt
 V$HMGIY_Q3             |     4808 (+) |  0.875 |  0.875 | tctggCATTTgttac
 V$HMGIY_Q3             |     5379 (+) |  0.928 |  0.873 | cttttAGTTTtattt
 V$HMGIY_Q3             |     5385 (+) |  0.960 |  0.860 | gttttATTTTacctt
 V$HMGIY_Q3             |     5397 (+) |  0.890 |  0.874 | ctttaTATTTtttca
 V$HMGIY_Q3             |     5589 (-) |  0.960 |  0.900 | ataatAAAATataat
 V$HMGIY_Q3             |     5640 (-) |  0.960 |  0.877 | aagacAAAATaaaaa
 V$HMGIY_Q3             |     5778 (-) |  0.865 |  0.868 | agaaaAATATgaaat
 V$HMGIY_Q3             |     5806 (-) |  0.960 |  0.874 | aaaaaAAAATagccc
 V$HMGIY_Q3             |     5807 (-) |  0.890 |  0.896 | aaaaaAAATAgccct
 V$HMGIY_Q3             |     5907 (+) |  0.928 |  0.891 | agagtAGTTTgtttc
 V$HMGIY_Q3             |     5939 (-) |  0.908 |  0.875 | ggagaAAAGTaaaat
 V$HMGIY_Q3             |     5944 (-) |  0.960 |  0.864 | aaagtAAAATtttat
 V$HMGIY_Q3             |     5945 (-) |  1.000 |  0.868 | aagtaAAATTttatt
 V$HMGIY_Q3             |     5946 (+) |  1.000 |  0.910 | agtaaAATTTtattt
 V$HMGIY_Q3             |     6466 (-) |  0.960 |  0.876 | ctgatAAAATgctca
 V$HMGIY_Q3             |     6603 (+) |  0.890 |  0.885 | ggtgcTATTTgctaa
 V$HMGIY_Q3             |     6664 (+) |  0.960 |  0.874 | tgaagATTTTattta
 V$HMGIY_Q3             |     6832 (+) |  0.890 |  0.880 | tgtgcTATTTactgc
 V$HMGIY_Q3             |     7046 (+) |  0.960 |  0.862 | tgactATTTTttttc
 V$HMGIY_Q3             |     7058 (+) |  1.000 |  0.913 | ttcttAATTTgtttt
 V$HMGIY_Q3             |     7890 (+) |  0.851 |  0.865 | tttggTTTTTatttt
 V$HMGIY_Q3             |     7895 (+) |  0.960 |  0.890 | tttttATTTTgatat
 V$HMGIY_Q3             |     8547 (-) |  0.960 |  0.886 | ccgagAAAATgaaca
 V$HMGIY_Q3             |     9712 (-) |  1.000 |  0.864 | gtgtaAAATTgatct
 V$HMGIY_Q3             |     9780 (+) |  1.000 |  0.876 | agaacAATTTtgttc
 V$HMGIY_Q3             |     9885 (+) |  0.905 |  0.889 | atttaAAATTctttt
 V$HMGIY_Q3             |     9914 (+) |  0.960 |  0.885 | actggATTTTtgcct
 V$HMGIY_Q3             |     9930 (+) |  1.000 |  0.879 | tgggtAATTTgcatg
 V$HMGIY_Q3             |    10122 (-) |  0.960 |  0.886 | ccaatAAAATtagtt
 V$HMGIY_Q3             |    10123 (-) |  1.000 |  0.868 | caataAAATTagtta
 V$HMGIY_Q3             |    10135 (-) |  1.000 |  0.912 | ttaagAAATTattat
 V$HMGIY_Q3             |    10298 (+) |  0.875 |  0.870 | tcggaCATTTtttaa
 V$HMGIY_Q3             |    10318 (+) |  0.960 |  0.873 | tttatATTTTtattt
 V$HMGIY_Q3             |    10391 (-) |  0.960 |  0.904 | atataAAAATgaacg
 V$HMGIY_Q3             |    10583 (+) |  1.000 |  0.944 | ggttcAATTTcctat
 V$HMGIY_Q3             |    11085 (+) |  1.000 |  0.906 | ctgggAATTTtccac
 V$HMGIY_Q3             |    11153 (-) |  0.960 |  0.898 | tgatgAAAATgaagc
 V$HMGIY_Q3             |    11205 (+) |  1.000 |  0.918 | ttattAATTTgtttg
 V$HMGIY_Q3             |    11271 (-) |  1.000 |  0.902 | aaaggAAATTaaggc
 V$HMGIY_Q3             |    11391 (+) |  1.000 |  0.911 | tattaAATTTtgtac
 V$HMGIY_Q3             |    11444 (+) |  0.960 |  0.860 | tatctATTTTggtga
 V$HMGIY_Q3             |    11461 (+) |  0.905 |  0.875 | cagtgAAATTtttta
 V$HMGIY_Q3             |    11462 (+) |  1.000 |  0.986 | agtgaAATTTtttat
 V$HMGIY_Q3             |    11469 (+) |  0.890 |  0.867 | tttttTATTTgtttt
 V$HMGIY_Q3             |    11497 (+) |  1.000 |  0.872 | ggttgAATTTttgtg
 V$HMGIY_Q3             |    11498 (+) |  0.960 |  0.906 | gttgaATTTTtgtgg
 V$HMGIY_Q3             |    11687 (-) |  0.908 |  0.868 | ccaatAAAGTtaatc
 V$HNF1_Q6_01           |      984 (-) |  1.000 |  0.942 | cacagTTAATaattttcatgt
 V$HNF1_Q6_01           |     1043 (+) |  0.910 |  0.853 | aagcagcaaaaATCAAcaact
 V$HNF1_Q6_01           |     1887 (-) |  0.933 |  0.860 | cccatTTTATatttattttat
 V$HNF1_Q6_01           |     3409 (-) |  1.000 |  0.892 | aaaagTTAATgattctggttg
 V$HNF1_Q6_01           |     3901 (+) |  0.933 |  0.844 | cacaggtattaATAAAgcttt
 V$HNF1_Q6_01           |     4053 (+) |  1.000 |  0.902 | aataggcaataATTAAaatat
 V$HNF1_Q6_01           |     5581 (+) |  0.933 |  0.891 | aaaggataataATAAAatata
 V$HNF1_Q6_01           |     5775 (+) |  0.910 |  0.845 | gagagaaaaatATGAAataat
 V$HNF1_Q6_01           |     5783 (+) |  1.000 |  0.868 | aatatgaaataATTAAataca
 V$HNF1_Q6_01           |     7821 (+) |  1.000 |  0.919 | caaaacaaacaATTAAcccac
 V$HNF1_Q6_01           |     8849 (+) |  1.000 |  0.890 | acggtttaaaaATTAAgactc
 V$HNF1_Q6_01           |    10388 (+) |  0.910 |  0.879 | tccatataaaaATGAAcgagg
 V$HNF1_Q6_01           |    11196 (-) |  0.910 |  0.869 | cttgaTTGATtattaatttgt
 V$HNF1_Q6_01           |    11691 (-) |  1.000 |  0.865 | taaagTTAATcactgtcaccc
 V$HNF3_Q6_01           |      226 (+) |  0.946 |  0.918 | tttccTTTTTgtcttttt
 V$HNF3_Q6_01           |      503 (+) |  0.988 |  0.950 | ttataTATTTgtcttctg
 V$HNF3_Q6_01           |      840 (-) |  0.988 |  0.936 | aacaagttAAATAaatac
 V$HNF3_Q6_01           |      844 (-) |  0.988 |  0.945 | agttaaatAAATAcgatc
 V$HNF3_Q6_01           |      873 (-) |  1.000 |  0.947 | aaatgcacAAACAcgaaa
 V$HNF3_Q6_01           |      951 (-) |  0.988 |  0.946 | caatgatcAAATAtttac
 V$HNF3_Q6_01           |     1469 (+) |  0.988 |  0.978 | ctcaaTATTTgctctggc
 V$HNF3_Q6_01           |     1528 (+) |  0.946 |  0.919 | ctgttTTTTTgttctaag
 V$HNF3_Q6_01           |     1891 (+) |  0.988 |  0.963 | ttttaTATTTattttatt
 V$HNF3_Q6_01           |     2358 (+) |  0.988 |  0.953 | acttgTATTTattttgcc
 V$HNF3_Q6_01           |     2406 (-) |  1.000 |  0.929 | cttaaaaaAAACAaaaaa
 V$HNF3_Q6_01           |     2410 (-) |  0.946 |  0.941 | aaaaaaacAAAAAatcac
 V$HNF3_Q6_01           |     3592 (+) |  1.000 |  0.934 | tcctaTGTTTgggtttct
 V$HNF3_Q6_01           |     3804 (-) |  1.000 |  0.918 | aatagaaaAAACAtcgtt
 V$HNF3_Q6_01           |     4000 (-) |  0.988 |  0.926 | acaacgatAAATAaatat
 V$HNF3_Q6_01           |     4004 (-) |  0.988 |  0.950 | cgataaatAAATAttctg
 V$HNF3_Q6_01           |     4495 (-) |  1.000 |  0.921 | aaaaaacaAAACAaaaca
 V$HNF3_Q6_01           |     5118 (-) |  1.000 |  0.932 | tcaaaaggAAACAgatgg
 V$HNF3_Q6_01           |     5432 (+) |  0.988 |  0.945 | cacttTATTTgtattgcc
 V$HNF3_Q6_01           |     5642 (-) |  0.946 |  0.927 | gacaaaatAAAAAgaaga
 V$HNF3_Q6_01           |     5789 (-) |  0.988 |  0.948 | aaataattAAATAcaaaa
 V$HNF3_Q6_01           |     5951 (+) |  0.988 |  0.924 | aatttTATTTgccagtgt
 V$HNF3_Q6_01           |     6250 (+) |  0.988 |  0.926 | ctttcTATTTgtcccatc
 V$HNF3_Q6_01           |     6586 (-) |  0.988 |  0.966 | cacaaaacAAATAaggtg
 V$HNF3_Q6_01           |     6603 (+) |  0.988 |  0.942 | ggtgcTATTTgctaaact
 V$HNF3_Q6_01           |     6649 (-) |  1.000 |  0.938 | cagtctgcAAACAgatga
 V$HNF3_Q6_01           |     6668 (+) |  0.988 |  0.928 | gatttTATTTagcttttg
 V$HNF3_Q6_01           |     7045 (+) |  0.988 |  0.928 | ttgacTATTTtttttctt
 V$HNF3_Q6_01           |     7064 (+) |  0.946 |  0.922 | atttgTTTTTgtttgtgt
 V$HNF3_Q6_01           |     7068 (+) |  1.000 |  0.959 | gttttTGTTTgtgtatga
 V$HNF3_Q6_01           |     7209 (-) |  0.946 |  0.922 | aattgaacAAAAAgtagg
 V$HNF3_Q6_01           |     7423 (+) |  0.988 |  0.957 | aggttTATTTgtttttat
 V$HNF3_Q6_01           |     7427 (+) |  1.000 |  0.919 | ttattTGTTTttatttta
 V$HNF3_Q6_01           |     7429 (+) |  0.946 |  0.925 | atttgTTTTTattttatg
 V$HNF3_Q6_01           |     7581 (-) |  1.000 |  0.929 | atcaggtcAAACAaatgc
 V$HNF3_Q6_01           |     7773 (-) |  1.000 |  0.929 | aaaaaacaAAACAaaaat
 V$HNF3_Q6_01           |     7777 (-) |  0.946 |  0.935 | aacaaaacAAAAAttatc
 V$HNF3_Q6_01           |     7819 (-) |  1.000 |  0.987 | tccaaaacAAACAattaa
 V$HNF3_Q6_01           |     7890 (+) |  0.946 |  0.920 | tttggTTTTTattttgat
 V$HNF3_Q6_01           |     7936 (+) |  1.000 |  0.959 | ttgtgTGTTTagttttga
 V$HNF3_Q6_01           |     7967 (+) |  1.000 |  0.972 | atagtTGTTTgtttttca
 V$HNF3_Q6_01           |     8182 (+) |  1.000 |  0.971 | gaactTGTTTgctctgcc
 V$HNF3_Q6_01           |     8333 (+) |  0.988 |  0.931 | gccagTATTTgctggacc
 V$HNF3_Q6_01           |     8469 (-) |  0.946 |  0.920 | tctaaggcAAAAAtaagg
 V$HNF3_Q6_01           |     8895 (-) |  1.000 |  0.919 | cgtaccacAAACAgattc
 V$HNF3_Q6_01           |     9108 (-) |  0.946 |  0.925 | agcaaaacAAAAAaccgg
 V$HNF3_Q6_01           |     9483 (+) |  0.988 |  0.933 | tacttTATTTgcaataga
 V$HNF3_Q6_01           |     9531 (-) |  1.000 |  0.962 | actagaacAAACAagtcc
 V$HNF3_Q6_01           |     9915 (+) |  0.946 |  0.923 | ctggaTTTTTgcctatgg
 V$HNF3_Q6_01           |    10309 (+) |  1.000 |  0.919 | ttaacTGTTTttatattt
 V$HNF3_Q6_01           |    10319 (+) |  0.946 |  0.926 | ttataTTTTTattttata
 V$HNF3_Q6_01           |    10756 (+) |  1.000 |  0.926 | ccgtgTGTTTgggcacta
 V$HNF3_Q6_01           |    10908 (-) |  0.988 |  0.959 | tactatgcAAATAatagt
 V$HNF3_Q6_01           |    11209 (+) |  1.000 |  0.929 | taattTGTTTgaactgcc
 V$HNF3_Q6_01           |    11285 (-) |  0.946 |  0.920 | catagggcAAAGAaataa
 V$HNF3_Q6_01           |    11419 (+) |  0.988 |  0.929 | atttcTATTTagctatcc
 V$HNF3_Q6_01           |    11469 (+) |  0.988 |  0.969 | tttttTATTTgtttttcc
 V$IPF1_Q4_01           |       46 (+) |  1.000 |  0.949 | gatgtCATTActtgg
 V$IPF1_Q4_01           |       60 (-) |  0.929 |  0.908 | ggccaTAATTactgt
 V$IPF1_Q4_01           |      174 (+) |  1.000 |  0.930 | gctggCATTActacc
 V$IPF1_Q4_01           |      493 (+) |  1.000 |  0.924 | tgcaaCATTAttata
 V$IPF1_Q4_01           |     3171 (+) |  1.000 |  0.904 | ctgtaCATTAtatcc
 V$IPF1_Q4_01           |     3272 (+) |  1.000 |  0.929 | gatgcCATTAtgatt
 V$IPF1_Q4_01           |     3410 (-) |  1.000 |  0.944 | aaagtTAATGattct
 V$IPF1_Q4_01           |     4281 (+) |  1.000 |  0.924 | gcacaCATTAgaccc
 V$IPF1_Q4_01           |     5010 (+) |  1.000 |  0.924 | ttaccCATTAagcca
 V$IPF1_Q4_01           |     5097 (+) |  0.914 |  0.904 | tgggtTATTAtttgt
 V$IPF1_Q4_01           |     6806 (+) |  1.000 |  0.953 | cccctCATTAccttc
 V$IPF1_Q4_01           |     6954 (+) |  1.000 |  0.912 | ctgtcCATTAttctg
 V$IPF1_Q4_01           |     7256 (+) |  1.000 |  0.952 | agtctCATTAaaata
 V$IPF1_Q4_01           |     8149 (+) |  1.000 |  0.909 | gaaaaCATTAgcttc
 V$IPF1_Q4_01           |     9732 (-) |  1.000 |  0.930 | tatgaTAATGtccat
 V$IPF1_Q4_01           |    10519 (+) |  1.000 |  0.932 | gtagcCATTAtagga
 V$IPF1_Q4_01           |    10654 (-) |  1.000 |  0.919 | tgtccTAATGtcaac
 V$IPF1_Q4_01           |    11343 (+) |  1.000 |  0.934 | aatgcCATTAtcgaa
 V$SOX_Q6               |      398 (-) |  0.877 |  0.793 | tgccaaCAAGGcg
 V$SOX_Q6               |      945 (-) |  0.901 |  0.847 | taggaaCAATGat
 V$SOX_Q6               |     1035 (-) |  1.000 |  0.833 | aatcaaCAAAGca
 V$SOX_Q6               |     1163 (-) |  1.000 |  0.797 | ctttttCAAAGaa
 V$SOX_Q6               |     1532 (+) |  0.781 |  0.778 | ttTTTTGttctaa
 V$SOX_Q6               |     2196 (+) |  0.781 |  0.791 | ctCTTTCtttctt
 V$SOX_Q6               |     2602 (-) |  0.781 |  0.799 | attaaaCCAAGag
 V$SOX_Q6               |     2660 (+) |  1.000 |  0.793 | caCTTTGatgaca
 V$SOX_Q6               |     2897 (+) |  0.781 |  0.800 | atCTTTTttatcc
 V$SOX_Q6               |     3661 (-) |  0.781 |  0.782 | aagtaaCACAGac
 V$SOX_Q6               |     3995 (-) |  0.877 |  0.835 | atgaaaCAACGat
 V$SOX_Q6               |     4488 (-) |  0.781 |  0.777 | tttgaaCAAAAaa
 V$SOX_Q6               |     4546 (+) |  0.781 |  0.831 | ctCTTAGttttga
 V$SOX_Q6               |     4662 (+) |  1.000 |  0.853 | gaCTTTGttttgc
 V$SOX_Q6               |     5354 (+) |  1.000 |  0.829 | ctCTTTGacaaaa
 V$SOX_Q6               |     5833 (-) |  0.877 |  0.772 | gtgaaaCAAGGca
 V$SOX_Q6               |     6587 (-) |  0.781 |  0.800 | acaaaaCAAATaa
 V$SOX_Q6               |     6822 (+) |  0.781 |  0.773 | ccCTTTTttatgt
 V$SOX_Q6               |     6912 (-) |  0.877 |  0.835 | ggagaaCAAGGaa
 V$SOX_Q6               |     7210 (-) |  0.781 |  0.799 | attgaaCAAAAag
 V$SOX_Q6               |     7778 (-) |  0.781 |  0.800 | acaaaaCAAAAat
 V$SOX_Q6               |     7790 (-) |  1.000 |  0.803 | ttatccCAAAGat
 V$SOX_Q6               |     7803 (-) |  0.877 |  0.818 | aaagaaCAACGac
 V$SOX_Q6               |     7820 (-) |  0.781 |  0.800 | ccaaaaCAAACaa
 V$SOX_Q6               |     8378 (+) |  1.000 |  0.905 | ctCTTTGatctgt
 V$SOX_Q6               |     8568 (+) |  1.000 |  0.847 | gtCTTTGattaaa
 V$SOX_Q6               |     8706 (-) |  0.877 |  0.784 | taccatCAAGGag
 V$SOX_Q6               |     8781 (-) |  1.000 |  0.862 | ccgagaCAAAGaa
 V$SOX_Q6               |     9025 (+) |  1.000 |  0.868 | atCTTTGtgagtt
 V$SOX_Q6               |     9109 (-) |  0.781 |  0.800 | gcaaaaCAAAAaa
 V$SOX_Q6               |     9532 (-) |  0.781 |  0.773 | ctagaaCAAACaa
 V$SOX_Q6               |     9725 (+) |  1.000 |  0.861 | ctCTTTGtatgat
 V$SOX_Q6               |     9893 (+) |  0.781 |  0.799 | ttCTTTTttaaag
 V$SOX_Q6               |    10457 (-) |  0.901 |  0.774 | tatcaaCAATGca
 V$SOX_Q6               |    10488 (-) |  0.877 |  0.825 | acatatCAAGGat
 V$SOX_Q6               |    10577 (+) |  1.000 |  0.776 | tgCTTTGgttcaa
 V$SOX_Q6               |    10970 (-) |  0.877 |  0.787 | ttggagCAAGGag
 V$SOX_Q6               |    11050 (+) |  1.000 |  0.861 | tcCTTTGttaacg
 P$PEND_01              |     7056 (-) |  1.000 |  0.892 | ttTTCTTa
 P$PEND_01              |     8642 (+) |  1.000 |  0.920 | tAAGAAga
 P$PEND_01              |    10055 (+) |  1.000 |  0.956 | tAAGAAct
 P$PEND_01              |    10136 (+) |  1.000 |  0.972 | tAAGAAat
 V$PBX1_03              |       72 (-) |  1.000 |  0.875 | tgttgTTGATgt
 V$PBX1_03              |      135 (+) |  0.895 |  0.851 | caGTCAAtccag
 V$PBX1_03              |      256 (-) |  0.884 |  0.820 | taaggTTGAAct
 V$PBX1_03              |      532 (-) |  0.840 |  0.844 | gatggGTGATgc
 V$PBX1_03              |      954 (+) |  1.000 |  0.898 | tgATCAAatatt
 V$PBX1_03              |     1034 (+) |  1.000 |  0.871 | gaATCAAcaaag
 V$PBX1_03              |     1052 (+) |  1.000 |  0.872 | aaATCAAcaact
 V$PBX1_03              |     1911 (-) |  0.900 |  0.819 | tttatTTGAGac
 V$PBX1_03              |     1979 (+) |  0.900 |  0.839 | gcCTCAAactca
 V$PBX1_03              |     2351 (+) |  0.900 |  0.836 | ttCTCAAacttg
 V$PBX1_03              |     2659 (-) |  1.000 |  0.839 | gcactTTGATga
 V$PBX1_03              |     3351 (+) |  0.854 |  0.858 | tcATCAGacaga
 V$PBX1_03              |     3430 (-) |  0.895 |  0.837 | cttaaTTGACtt
 V$PBX1_03              |     3704 (-) |  1.000 |  0.967 | gatgcTTGATca
 V$PBX1_03              |     3710 (+) |  1.000 |  0.840 | tgATCAAtattt
 V$PBX1_03              |     3932 (+) |  0.854 |  0.877 | ttATCAGtcact
 V$PBX1_03              |     3973 (-) |  0.847 |  0.852 | gctgtATGATag
 V$PBX1_03              |     4550 (-) |  1.000 |  0.819 | tagttTTGATgc
 V$PBX1_03              |     4692 (-) |  1.000 |  0.841 | gaaacTTGATgt
 V$PBX1_03              |     4837 (-) |  0.840 |  0.817 | aacgaGTGATcc
 V$PBX1_03              |     5138 (+) |  0.895 |  0.829 | cgGTCAAcctag
 V$PBX1_03              |     5481 (-) |  1.000 |  0.876 | attttTTGATcc
 V$PBX1_03              |     6100 (+) |  0.854 |  0.818 | ggATCAGtcctg
 V$PBX1_03              |     6436 (+) |  0.895 |  0.826 | cgGTCAAcccag
 V$PBX1_03              |     6920 (-) |  1.000 |  0.861 | aggaaTTGATtg
 V$PBX1_03              |     7371 (-) |  1.000 |  0.863 | aagaaTTGATat
 V$PBX1_03              |     7584 (+) |  0.895 |  0.890 | agGTCAAacaaa
 V$PBX1_03              |     7898 (-) |  1.000 |  0.821 | ttattTTGATat
 V$PBX1_03              |     7924 (+) |  1.000 |  0.861 | gtATCAAttcgt
 V$PBX1_03              |     8377 (-) |  1.000 |  0.895 | gctctTTGATct
 V$PBX1_03              |     8567 (-) |  1.000 |  0.892 | cgtctTTGATta
 V$PBX1_03              |     8614 (+) |  0.895 |  0.914 | ccGTCAAtcact
 V$PBX1_03              |     8663 (+) |  0.884 |  0.819 | ttTTCAAaccac
 V$PBX1_03              |     8708 (+) |  1.000 |  0.892 | ccATCAAggagt
 V$PBX1_03              |     8887 (+) |  1.000 |  0.923 | gaATCAAacgta
 V$PBX1_03              |     9715 (-) |  1.000 |  0.866 | taaaaTTGATct
 V$PBX1_03              |     9728 (-) |  0.847 |  0.850 | tttgtATGATaa
 V$PBX1_03              |     9879 (+) |  1.000 |  0.865 | aaATCAAtttaa
 V$PBX1_03              |    10456 (+) |  1.000 |  0.874 | atATCAAcaatg
 V$PBX1_03              |    10490 (+) |  1.000 |  0.890 | atATCAAggatc
 V$PBX1_03              |    10497 (+) |  1.000 |  0.826 | ggATCAAaagtc
 V$PBX1_03              |    10504 (+) |  0.895 |  0.837 | aaGTCAAttatg
 V$PBX1_03              |    10596 (+) |  1.000 |  0.877 | atATCAAaaagg
 V$PBX1_03              |    11192 (-) |  1.000 |  0.870 | gtttcTTGATtg
 V$PBX1_03              |    11196 (-) |  1.000 |  0.994 | cttgaTTGATta
 V$PBX1_03              |    11212 (-) |  0.884 |  0.881 | tttgtTTGAAct
 V$PBX1_03              |    11494 (-) |  0.884 |  0.826 | tgcggTTGAAtt
 V$PBX1_03              |    11543 (-) |  0.850 |  0.852 | tatggTAGATgg
 V$PBX1_03              |    11556 (+) |  0.884 |  0.874 | taTTCAAccaaa
 V$PBX1_03              |    11730 (+) |  0.900 |  0.893 | ttCTCAAacatc
 V$PBX1_03              |    11777 (-) |  1.000 |  0.897 | gatacTTGATgt
 V$PBX1_03              |    11892 (+) |  0.900 |  0.891 | ctCTCAAccaat
 V$TBX5_01              |     4140 (+) |  1.000 |  0.971 | ctaGGTGTggtg
 V$TBX5_01              |     8247 (+) |  1.000 |  0.960 | gaaGGTGTgttc
 V$TBX5_01              |     8749 (-) |  1.000 |  0.970 | gcccACACCttg
 V$TBX5_01              |     8970 (+) |  1.000 |  0.968 | ccaGGTGTggtg
 V$TBX5_01              |     8982 (-) |  1.000 |  0.961 | gtacACACCttt
 V$TBX5_02              |     1681 (+) |  1.000 |  0.968 | tcgGGTGTca
 V$TBX5_02              |     1814 (+) |  1.000 |  0.962 | ggtGGTGTtc
 V$TBX5_02              |     2811 (-) |  1.000 |  0.964 | gaACACCgtg
 V$TBX5_02              |     4140 (+) |  1.000 |  0.969 | ctaGGTGTgg
 V$TBX5_02              |     8235 (-) |  1.000 |  0.958 | ccACACCcag
 V$TBX5_02              |     8737 (+) |  1.000 |  0.960 | cggGGTGTgg
 V$TBX5_02              |     8751 (-) |  1.000 |  0.970 | ccACACCttg
 V$TBX5_02              |     8970 (+) |  1.000 |  0.970 | ccaGGTGTgg
 V$TBX5_02              |     9570 (+) |  1.000 |  0.958 | ctgGGTGTgg
 V$TBX5_02              |     9952 (-) |  1.000 |  0.979 | taACACCctg
 V$TBX5_02              |    10694 (-) |  1.000 |  0.964 | caACACCcgt
 V$TBX5_02              |    10941 (+) |  1.000 |  0.959 | gacGGTGTtg
 V$TBX5_02              |    11256 (+) |  1.000 |  0.965 | tgtGGTGTgc
 P$ID1_01               |      224 (+) |  0.855 |  0.888 | tTTTTCctttt
 P$ID1_01               |      233 (+) |  1.000 |  0.975 | tTTGTCttttt
 P$ID1_01               |     5637 (-) |  1.000 |  0.961 | ataaaGACAAa
 P$ID1_01               |    10157 (+) |  1.000 |  0.905 | gTTGTCgtttt
 P$ID1_01               |    11787 (-) |  1.000 |  0.911 | gtaagGACAAa
 V$LEF1_Q2_01           |     1166 (+) |  1.000 |  0.979 | tttCAAAGaa
 V$LEF1_Q2_01           |     2660 (-) |  1.000 |  0.999 | caCTTTGatg
 V$LEF1_Q2_01           |     6740 (-) |  1.000 |  0.986 | ccCTTTGaaa
 V$LEF1_Q2_01           |     8378 (-) |  1.000 |  0.997 | ctCTTTGatc
 V$LEF1_Q2_01           |     8568 (-) |  1.000 |  0.988 | gtCTTTGatt
 V$LEF1_Q2_01           |     8622 (-) |  1.000 |  0.977 | caCTTTGaga
 V$LEF1_Q2_01           |    10352 (+) |  1.000 |  0.983 | attCAAAGtg
 V$LEF1_Q2_01           |    11378 (-) |  1.000 |  0.978 | tgCTTTGaaa
 V$HSF1_Q6              |     8874 (-) |  1.000 |  0.952 | atagaatattCTAGAat
 V$TFE_Q6               |       19 (+) |  1.000 |  0.987 | aCATGTga
 V$TFE_Q6               |      999 (+) |  1.000 |  0.999 | tCATGTgg
 V$TFE_Q6               |     2615 (+) |  1.000 |  0.982 | cCATGTgt
 V$TFE_Q6               |     2774 (+) |  1.000 |  0.984 | gCATGTga
 V$TFE_Q6               |     3642 (-) |  1.000 |  0.983 | ccACATGg
 V$TFE_Q6               |     5251 (-) |  1.000 |  0.987 | tcACATGt
 V$TFE_Q6               |     5253 (+) |  1.000 |  0.987 | aCATGTgg
 V$TFE_Q6               |     7113 (-) |  1.000 |  0.987 | ccACATGt
 V$TFE_Q6               |     7115 (+) |  1.000 |  0.986 | aCATGTgt
 V$TFE_Q6               |     9001 (-) |  1.000 |  0.983 | gcACATGg
 V$TFE_Q6               |    10890 (-) |  1.000 |  0.983 | gcACATGc
 F$RIM101_01            |       53 (-) |  1.000 |  0.994 | ttaCTTGG
 F$RIM101_01            |     1213 (-) |  1.000 |  0.997 | ttgCTTGG
 F$RIM101_01            |     3263 (-) |  1.000 |  1.000 | tttCTTGG
 F$RIM101_01            |     3690 (+) |  1.000 |  0.967 | CCAAGaac
 F$RIM101_01            |     4253 (-) |  1.000 |  0.994 | ttaCTTGG
 F$RIM101_01            |     4398 (+) |  1.000 |  0.950 | CCAAGaca
 F$RIM101_01            |     4521 (+) |  1.000 |  0.950 | CCAAGaca
 F$RIM101_01            |     4898 (-) |  1.000 |  0.992 | ttcCTTGG
 F$RIM101_01            |    11265 (+) |  1.000 |  1.000 | CCAAGaaa
 V$HNF4_Q6_01           |     2657 (-) |  1.000 |  0.891 | atgcaCTTTGatga
 V$HNF4_Q6_01           |     3566 (-) |  1.000 |  0.914 | gtggcCTTTGgcaa
 V$HNF4_Q6_01           |     8375 (-) |  1.000 |  0.941 | ctgctCTTTGatct
 V$HNF4_Q6_01           |     8582 (+) |  1.000 |  0.897 | ggggCAAAGgcaac
 V$EBOX_Q6_01           |      286 (-) |  0.980 |  0.973 | agtcAAGTGt
 V$EBOX_Q6_01           |      734 (-) |  1.000 |  0.972 | caccACGTGg
 V$EBOX_Q6_01           |      736 (+) |  1.000 |  0.973 | cCACGTggtt
 V$EBOX_Q6_01           |     1127 (+) |  1.000 |  0.957 | gCACGTgtgt
 V$EBOX_Q6_01           |     1359 (+) |  0.998 |  0.965 | tCACCTgatg
 V$EBOX_Q6_01           |     1391 (-) |  0.998 |  0.988 | gggcAGGTGa
 V$EBOX_Q6_01           |     1787 (+) |  0.998 |  0.984 | gCACCTgcca
 V$EBOX_Q6_01           |     2613 (-) |  0.989 |  0.977 | agccATGTGt
 V$EBOX_Q6_01           |     3642 (+) |  0.989 |  0.964 | cCACATggtg
 V$EBOX_Q6_01           |     3681 (-) |  0.980 |  0.970 | tgccAAGTGc
 V$EBOX_Q6_01           |     4338 (-) |  0.998 |  0.958 | atccAGGTGg
 V$EBOX_Q6_01           |     4904 (-) |  0.980 |  0.974 | ggccAAGTGc
 V$EBOX_Q6_01           |     6065 (+) |  1.000 |  0.964 | gCACGTgctg
 V$EBOX_Q6_01           |     7113 (+) |  0.989 |  0.957 | cCACATgtgt
 V$EBOX_Q6_01           |     7390 (-) |  0.998 |  0.960 | gtccAGGTGg
 V$EBOX_Q6_01           |     8349 (+) |  0.980 |  0.979 | cCACTTgcca
 V$EBOX_Q6_01           |     8503 (-) |  0.998 |  0.988 | ggacAGGTGc
 V$EBOX_Q6_01           |     8968 (-) |  0.998 |  0.962 | aaccAGGTGt
 V$EBOX_Q6_01           |    11962 (+) |  0.998 |  0.959 | gCACCTgagc
 V$YY1_Q6_02            |       58 (+) |  1.000 |  0.932 | tggGCCATaat
 V$YY1_Q6_02            |      530 (-) |  0.968 |  0.918 | atgATGGGtga
 V$YY1_Q6_02            |      719 (-) |  0.972 |  0.949 | cagATGGTtgt
 V$YY1_Q6_02            |      799 (+) |  1.000 |  0.957 | tgaGCCATttc
 V$YY1_Q6_02            |      887 (-) |  0.968 |  0.930 | gaaATGGGaca
 V$YY1_Q6_02            |     1178 (-) |  0.968 |  0.937 | gagATGGGcac
 V$YY1_Q6_02            |     1663 (-) |  0.983 |  0.957 | caaATGGAgat
 V$YY1_Q6_02            |     1790 (+) |  1.000 |  0.919 | cctGCCATtca
 V$YY1_Q6_02            |     1884 (+) |  0.968 |  0.967 | cctCCCATttt
 V$YY1_Q6_02            |     2611 (+) |  1.000 |  0.958 | agaGCCATgtg
 V$YY1_Q6_02            |     2838 (-) |  1.000 |  0.963 | caaATGGCatc
 V$YY1_Q6_02            |     3150 (-) |  0.983 |  0.962 | tatATGGAggt
 V$YY1_Q6_02            |     3272 (+) |  1.000 |  0.935 | gatGCCATtat
 V$YY1_Q6_02            |     3301 (+) |  0.983 |  0.955 | atcTCCATgta
 V$YY1_Q6_02            |     3380 (-) |  0.968 |  0.935 | catATGGGgcc
 V$YY1_Q6_02            |     3643 (-) |  0.972 |  0.954 | cacATGGTgga
 V$YY1_Q6_02            |     3837 (+) |  0.983 |  0.917 | attTCCATtct
 V$YY1_Q6_02            |     3860 (+) |  0.972 |  0.934 | agtACCATtta
 V$YY1_Q6_02            |     3951 (+) |  1.000 |  0.938 | tcaGCCATcct
 V$YY1_Q6_02            |     3984 (+) |  0.972 |  0.938 | gacACCATctc
 V$YY1_Q6_02            |     4107 (+) |  0.983 |  0.980 | acaTCCATttt
 V$YY1_Q6_02            |     4152 (+) |  0.968 |  0.948 | cctCCCATttg
 V$YY1_Q6_02            |     4889 (+) |  0.983 |  0.966 | catTCCATgtt
 V$YY1_Q6_02            |     4932 (-) |  0.983 |  0.928 | atcATGGAgac
 V$YY1_Q6_02            |     4992 (-) |  1.000 |  0.921 | cgaATGGCaga
 V$YY1_Q6_02            |     5129 (-) |  0.972 |  0.939 | cagATGGTgcg
 V$YY1_Q6_02            |     5242 (-) |  0.968 |  0.931 | tacATGGGttc
 V$YY1_Q6_02            |     5290 (-) |  0.968 |  0.934 | cagATGGGcta
 V$YY1_Q6_02            |     5308 (-) |  1.000 |  0.982 | aaaATGGCttc
 V$YY1_Q6_02            |     5444 (+) |  1.000 |  0.966 | attGCCATata
 V$YY1_Q6_02            |     5735 (+) |  1.000 |  0.933 | gaaGCCATaat
 V$YY1_Q6_02            |     5871 (+) |  0.972 |  0.932 | tggACCATctc
 V$YY1_Q6_02            |     6033 (+) |  0.968 |  0.931 | ggaCCCATctg
 V$YY1_Q6_02            |     6189 (+) |  0.968 |  0.945 | acaCCCATtta
 V$YY1_Q6_02            |     6259 (+) |  0.968 |  0.931 | tgtCCCATctg
 V$YY1_Q6_02            |     6447 (-) |  1.000 |  0.917 | gtcATGGCaaa
 V$YY1_Q6_02            |     6954 (+) |  0.983 |  0.926 | ctgTCCATtat
 V$YY1_Q6_02            |     6997 (-) |  0.983 |  0.950 | gagATGGAaaa
 V$YY1_Q6_02            |     7176 (-) |  0.972 |  0.935 | cagATGGTccc
 V$YY1_Q6_02            |     7359 (-) |  0.968 |  0.911 | atcATGGGcag
 V$YY1_Q6_02            |     7513 (-) |  1.000 |  0.962 | cagATGGCctg
 V$YY1_Q6_02            |     7609 (+) |  1.000 |  0.956 | tgaGCCATctc
 V$YY1_Q6_02            |     8577 (-) |  0.968 |  0.935 | taaATGGGgca
 V$YY1_Q6_02            |     9002 (-) |  0.983 |  0.964 | cacATGGAggc
 V$YY1_Q6_02            |     9054 (-) |  1.000 |  0.966 | tacATGGCaag
 V$YY1_Q6_02            |     9513 (+) |  0.968 |  0.940 | ttcCCCATgtc
 V$YY1_Q6_02            |    10104 (+) |  1.000 |  0.978 | tgaGCCATctt
 V$YY1_Q6_02            |    10385 (+) |  0.983 |  0.944 | caaTCCATata
 V$YY1_Q6_02            |    10510 (-) |  1.000 |  0.946 | attATGGCtgt
 V$YY1_Q6_02            |    10519 (+) |  1.000 |  0.940 | gtaGCCATtat
 V$YY1_Q6_02            |    10851 (+) |  1.000 |  0.924 | gaaGCCATtgt
 V$YY1_Q6_02            |    11343 (+) |  1.000 |  0.935 | aatGCCATtat
 V$YY1_Q6_02            |    11541 (-) |  0.972 |  0.950 | catATGGTaga
 V$YY1_Q6_02            |    11548 (-) |  0.968 |  0.937 | tagATGGGtat
 V$YY1_Q6_02            |    11721 (+) |  0.972 |  0.975 | tccACCATttt
 V$COUPTF_Q6            |     3562 (+) |  0.927 |  0.857 | ctgtgTGGCCtttggcaagttat
 V$COUPTF_Q6            |     6387 (+) |  0.927 |  0.846 | cgaacTGGCCtgtgttcagaacg
 V$COUPTF_Q6            |     9626 (-) |  1.000 |  0.845 | atcgggagttcaaGGTCAgcttg
 V$GLI_Q2               |    10238 (+) |  1.000 |  0.924 | ggttGGTGGtca
 V$NKX25_Q5             |    10470 (+) |  1.000 |  0.963 | tctCACTTta
 V$AP2ALPHA_02          |       98 (+) |  1.000 |  0.946 | ttCGCCTgggggtgg
 V$AP2ALPHA_02          |     1331 (-) |  0.946 |  0.921 | actccccaGGGCTta
 V$AP2ALPHA_02          |     3566 (+) |  0.979 |  0.906 | gtGGCCTttggcaag
 V$AP2ALPHA_02          |     3566 (-) |  0.911 |  0.912 | gtggccttTGGCAag
 V$AP2ALPHA_02          |     6144 (+) |  0.991 |  0.926 | caTGCCTctggctct
 V$AP2ALPHA_02          |     6144 (-) |  0.908 |  0.915 | catgcctcTGGCTct
 V$AP2ALPHA_02          |     7189 (+) |  0.898 |  0.901 | acGGCCAcgggggtg
 V$AP2ALPHA_02          |     9238 (+) |  0.946 |  0.906 | agAGCCCtaggagag
 V$AP2ALPHA_02          |     9328 (+) |  0.989 |  0.888 | agAGCCTctggagga
 V$AP2ALPHA_02          |     9922 (+) |  0.991 |  0.922 | ttTGCCTatgggtaa
 V$AP2ALPHA_03          |       98 (+) |  1.000 |  0.782 | ttCGCCTgggggtgg
 V$AP2ALPHA_03          |       98 (-) |  0.609 |  0.782 | ttcgcctgGGGGTgg
 V$AP2ALPHA_03          |     1331 (+) |  0.595 |  0.733 | acTCCCCagggctta
 V$AP2ALPHA_03          |     1331 (-) |  0.890 |  0.733 | actccccaGGGCTta
 V$AP2ALPHA_03          |     1338 (+) |  0.673 |  0.815 | agGGCTTaaggcttg
 V$AP2ALPHA_03          |     1338 (-) |  0.980 |  0.815 | agggcttaAGGCTtg
 V$AP2ALPHA_03          |     1349 (+) |  0.966 |  0.760 | ctTGCCTgggtcacc
 V$AP2ALPHA_03          |     1349 (-) |  0.595 |  0.760 | cttgcctgGGTCAcc
 V$AP2ALPHA_03          |     1373 (+) |  0.586 |  0.725 | ttTGCAGtgggcgag
 V$AP2ALPHA_03          |     1373 (-) |  0.910 |  0.725 | tttgcagtGGGCGag
 V$AP2ALPHA_03          |     1762 (+) |  0.980 |  0.747 | taAGCCTctcgcctg
 V$AP2ALPHA_03          |     1762 (-) |  0.562 |  0.747 | taagcctcTCGCCtg
 V$AP2ALPHA_03          |     2477 (+) |  0.864 |  0.729 | aaGGCCCtgggttcg
 V$AP2ALPHA_03          |     2477 (-) |  0.609 |  0.729 | aaggccctGGGTTcg
 V$AP2ALPHA_03          |     3530 (+) |  0.864 |  0.758 | ttGGCCCgaggtttg
 V$AP2ALPHA_03          |     3530 (-) |  0.699 |  0.758 | ttggcccgAGGTTtg
 V$AP2ALPHA_03          |     3566 (+) |  0.954 |  0.878 | gtGGCCTttggcaag
 V$AP2ALPHA_03          |     3566 (-) |  0.855 |  0.878 | gtggccttTGGCAag
 V$AP2ALPHA_03          |     4184 (+) |  0.599 |  0.764 | tgAGCAGaaggctgc
 V$AP2ALPHA_03          |     4184 (-) |  0.980 |  0.764 | tgagcagaAGGCTgc
 V$AP2ALPHA_03          |     5197 (+) |  0.685 |  0.741 | ttTGTCTgtggcctc
 V$AP2ALPHA_03          |     5197 (-) |  0.843 |  0.741 | tttgtctgTGGCCtc
 V$AP2ALPHA_03          |     5886 (+) |  0.673 |  0.746 | tgGGCATggggcccg
 V$AP2ALPHA_03          |     5886 (-) |  0.864 |  0.746 | tgggcatgGGGCCcg
 V$AP2ALPHA_03          |     6071 (+) |  0.855 |  0.770 | gcTGCCAcagtctct
 V$AP2ALPHA_03          |     6071 (-) |  0.699 |  0.770 | gctgccacAGTCTct
 V$AP2ALPHA_03          |     6144 (+) |  0.966 |  0.905 | caTGCCTctggctct
 V$AP2ALPHA_03          |     6144 (-) |  0.869 |  0.905 | catgcctcTGGCTct
 V$AP2ALPHA_03          |     6239 (+) |  0.685 |  0.772 | tcTGGCTacggcttt
 V$AP2ALPHA_03          |     6239 (-) |  0.881 |  0.772 | tctggctaCGGCTtt
 V$AP2ALPHA_03          |     6418 (+) |  0.719 |  0.785 | gaCTCCTctggcttt
 V$AP2ALPHA_03          |     6418 (-) |  0.869 |  0.785 | gactcctcTGGCTtt
 V$AP2ALPHA_03          |     6863 (+) |  0.609 |  0.771 | ccAGACCgaggctta
 V$AP2ALPHA_03          |     6863 (-) |  0.980 |  0.771 | ccagaccgAGGCTta
 V$AP2ALPHA_03          |     7189 (+) |  0.843 |  0.731 | acGGCCAcgggggtg
 V$AP2ALPHA_03          |     7189 (-) |  0.629 |  0.731 | acggccacGGGGGtg
 V$AP2ALPHA_03          |     8159 (+) |  0.574 |  0.751 | gcTTCCAgaggcagg
 V$AP2ALPHA_03          |     8159 (-) |  0.966 |  0.751 | gcttccagAGGCAgg
 V$AP2ALPHA_03          |     8367 (+) |  0.980 |  0.782 | gcAGCCTgctgctct
 V$AP2ALPHA_03          |     8367 (-) |  0.599 |  0.782 | gcagcctgCTGCTct
 V$AP2ALPHA_03          |     8581 (+) |  0.562 |  0.740 | tgGGGCAaaggcaac
 V$AP2ALPHA_03          |     8581 (-) |  0.966 |  0.740 | tggggcaaAGGCAac
 V$AP2ALPHA_03          |     8862 (+) |  0.699 |  0.751 | taAGACTctggcata
 V$AP2ALPHA_03          |     8862 (-) |  0.855 |  0.751 | taagactcTGGCAta
 V$AP2ALPHA_03          |     9238 (+) |  0.890 |  0.795 | agAGCCCtaggagag
 V$AP2ALPHA_03          |     9238 (-) |  0.719 |  0.795 | agagccctAGGAGag
 V$AP2ALPHA_03          |     9328 (+) |  0.980 |  0.785 | agAGCCTctggagga
 V$AP2ALPHA_03          |     9328 (-) |  0.608 |  0.785 | agagcctcTGGAGga
 V$AP2ALPHA_03          |     9439 (+) |  0.890 |  0.767 | gaAGCCCaaggttta
 V$AP2ALPHA_03          |     9439 (-) |  0.699 |  0.767 | gaagcccaAGGTTta
 V$AP2ALPHA_03          |     9922 (+) |  0.966 |  0.751 | ttTGCCTatgggtaa
 V$AP2ALPHA_03          |     9922 (-) |  0.588 |  0.751 | tttgcctaTGGGTaa
 V$AP2ALPHA_03          |    10557 (+) |  0.881 |  0.726 | acAGCCGgcggtaca
 V$AP2ALPHA_03          |    10557 (-) |  0.586 |  0.726 | acagccggCGGTAca
 V$AP2ALPHA_03          |    10683 (+) |  0.673 |  0.744 | caGGACTctggcaac
 V$AP2ALPHA_03          |    10683 (-) |  0.855 |  0.744 | caggactcTGGCAac
 V$AP2ALPHA_03          |    10799 (+) |  0.980 |  0.761 | tgAGCCTtgtgcatc
 V$AP2ALPHA_03          |    10799 (-) |  0.595 |  0.761 | tgagccttGTGCAtc
 V$AP2ALPHA_03          |    11281 (+) |  0.673 |  0.764 | aaGGCATagggcaaa
 V$AP2ALPHA_03          |    11281 (-) |  0.876 |  0.764 | aaggcataGGGCAaa
 V$AP2ALPHA_03          |    11812 (+) |  0.864 |  0.716 | gtGGCCCagggttgg
 V$AP2ALPHA_03          |    11812 (-) |  0.609 |  0.716 | gtggcccaGGGTTgg
 V$AP2ALPHA_03          |    11910 (+) |  0.673 |  0.759 | aaGGCTTcgggccca
 V$AP2ALPHA_03          |    11910 (-) |  0.864 |  0.759 | aaggcttcGGGCCca
 V$AP2ALPHA_03          |    11917 (+) |  0.864 |  0.744 | cgGGCCCaacgccca
 V$AP2ALPHA_03          |    11917 (-) |  0.673 |  0.744 | cgggcccaACGCCca
 N$TRA1_01              |      106 (+) |  0.998 |  0.902 | ggGGTGGc
 N$TRA1_01              |      192 (-) |  1.000 |  0.941 | gCCTCCca
 N$TRA1_01              |      201 (-) |  0.998 |  0.881 | aCCACCat
 N$TRA1_01              |     1489 (+) |  1.000 |  0.912 | agGGAGGg
 N$TRA1_01              |     1493 (+) |  0.985 |  0.900 | agGGGGGg
 N$TRA1_01              |     1494 (+) |  0.985 |  0.892 | ggGGGGGg
 N$TRA1_01              |     1495 (+) |  0.985 |  0.892 | ggGGGGGg
 N$TRA1_01              |     1496 (+) |  0.985 |  0.892 | ggGGGGGg
 N$TRA1_01              |     1497 (+) |  0.985 |  0.879 | ggGGGGGa
 N$TRA1_01              |     1500 (+) |  1.000 |  0.904 | ggGGAGGg
 N$TRA1_01              |     1504 (+) |  1.000 |  0.912 | agGGAGGg
 N$TRA1_01              |     1508 (+) |  1.000 |  0.912 | agGGAGGg
 N$TRA1_01              |     1512 (+) |  1.000 |  0.912 | agGGAGGg
 N$TRA1_01              |     1516 (+) |  1.000 |  0.971 | agGGAGGt
 N$TRA1_01              |     1812 (+) |  0.998 |  0.969 | agGGTGGt
 N$TRA1_01              |     1872 (+) |  1.000 |  0.899 | agGGAGGa
 N$TRA1_01              |     1883 (-) |  1.000 |  0.941 | gCCTCCca
 N$TRA1_01              |     3041 (-) |  0.998 |  0.895 | tCCACCcg
 N$TRA1_01              |     3153 (+) |  1.000 |  0.882 | atGGAGGt
 N$TRA1_01              |     3183 (-) |  0.985 |  0.887 | tCCCCCct
 N$TRA1_01              |     3637 (-) |  0.856 |  0.887 | aCCTACca
 N$TRA1_01              |     3781 (-) |  0.985 |  0.887 | tCCCCCct
 N$TRA1_01              |     4151 (-) |  1.000 |  0.941 | gCCTCCca
 N$TRA1_01              |     4862 (+) |  1.000 |  0.971 | agGGAGGt
 N$TRA1_01              |     5897 (-) |  0.981 |  0.888 | cCCGCCcc
 N$TRA1_01              |     6802 (-) |  1.000 |  0.891 | tCCTCCcc
 N$TRA1_01              |     7701 (+) |  1.000 |  1.000 | tgGGAGGt
 N$TRA1_01              |     8118 (-) |  0.998 |  0.910 | cCCACCct
 N$TRA1_01              |     8761 (-) |  1.000 |  0.928 | tCCTCCca
 N$TRA1_01              |     8774 (+) |  1.000 |  0.941 | tgGGAGGc
 N$TRA1_01              |     9312 (+) |  1.000 |  0.912 | agGGAGGc
 N$TRA1_01              |     9619 (+) |  1.000 |  0.928 | tgGGAGGa
 N$TRA1_01              |     9684 (+) |  0.985 |  0.900 | agGGGGGg
 N$TRA1_01              |     9685 (+) |  0.985 |  0.951 | ggGGGGGt
 N$TRA1_01              |     9688 (+) |  0.998 |  0.961 | ggGGTGGt
 N$TRA1_01              |    10013 (+) |  1.000 |  0.880 | ctGGAGGt
 N$TRA1_01              |    10240 (+) |  0.998 |  0.910 | ttGGTGGt
 N$TRA1_01              |    10614 (+) |  1.000 |  0.941 | tgGGAGGg
 N$TRA1_01              |    10739 (+) |  0.985 |  0.988 | tgGGGGGt
 N$TRA1_01              |    11844 (+) |  0.985 |  0.988 | tgGGGGGt
 N$TRA1_01              |    11847 (+) |  0.998 |  0.902 | ggGGTGGg
 N$TRA1_01              |    11872 (+) |  1.000 |  0.904 | ggGGAGGg
 N$TRA1_02              |     1516 (+) |  0.979 |  0.920 | aggGAGGT
 N$TRA1_02              |     1812 (+) |  1.000 |  0.936 | aggGTGGT
 N$TRA1_02              |     4441 (-) |  1.000 |  0.957 | ACCACaca
 N$TRA1_02              |     4862 (+) |  0.979 |  0.920 | aggGAGGT
 N$TRA1_02              |     7701 (+) |  0.979 |  0.984 | tggGAGGT
 N$TRA1_02              |     9190 (-) |  1.000 |  0.930 | ACCACtca
 N$TRA1_02              |     9685 (+) |  0.975 |  0.917 | gggGGGGT
 N$TRA1_02              |     9688 (+) |  1.000 |  0.936 | gggGTGGT
 N$TRA1_02              |    10240 (+) |  1.000 |  0.921 | ttgGTGGT
 N$TRA1_02              |    10739 (+) |  0.975 |  0.981 | tggGGGGT
 N$TRA1_02              |    11844 (+) |  0.975 |  0.981 | tggGGGGT
 P$ARR10_01             |      707 (-) |  1.000 |  1.000 | cgGATCT
 P$ARR10_01             |     1072 (+) |  0.979 |  0.960 | AGATGtg
 P$ARR10_01             |     1754 (-) |  1.000 |  0.934 | ctGATCT
 P$ARR10_01             |     1876 (-) |  1.000 |  0.978 | agGATCT
 P$ARR10_01             |     2781 (+) |  0.996 |  0.975 | AGATTct
 P$ARR10_01             |     2909 (-) |  0.979 |  0.960 | caCATCT
 P$ARR10_01             |     2973 (+) |  0.979 |  0.982 | AGATGcg
 P$ARR10_01             |     3098 (-) |  0.996 |  0.997 | cgAATCT
 P$ARR10_01             |     3298 (-) |  0.979 |  0.938 | aaCATCT
 P$ARR10_01             |     3394 (-) |  1.000 |  0.978 | agGATCT
 P$ARR10_01             |     3703 (+) |  0.979 |  0.960 | AGATGct
 P$ARR10_01             |     4121 (+) |  0.979 |  0.938 | AGATGtt
 P$ARR10_01             |     4135 (-) |  0.996 |  0.975 | agAATCT
 P$ARR10_01             |     5619 (-) |  0.979 |  0.938 | aaCATCT
 P$ARR10_01             |     6310 (-) |  1.000 |  0.934 | ctGATCT
 P$ARR10_01             |     6375 (+) |  0.996 |  0.975 | AGATTtg
 P$ARR10_01             |     6499 (+) |  0.979 |  0.982 | AGATGcg
 P$ARR10_01             |     6667 (+) |  0.996 |  0.953 | AGATTtt
 P$ARR10_01             |     6783 (-) |  1.000 |  0.978 | caGATCT
 P$ARR10_01             |     7153 (-) |  0.993 |  0.994 | cgTATCT
 P$ARR10_01             |     7559 (+) |  0.979 |  0.960 | AGATGct
 P$ARR10_01             |     8524 (+) |  0.979 |  0.960 | AGATGct
 P$ARR10_01             |     8593 (-) |  0.979 |  0.938 | aaCATCT
 P$ARR10_01             |     9022 (-) |  1.000 |  0.978 | caGATCT
 P$ARR10_01             |     9023 (+) |  1.000 |  0.956 | AGATCtt
 P$ARR10_01             |     9500 (-) |  0.996 |  0.953 | aaAATCT
 P$ARR10_01             |    10366 (-) |  0.996 |  0.975 | agAATCT
 P$ARR10_01             |    10712 (-) |  0.979 |  0.938 | aaCATCT
 P$ARR10_01             |    11028 (+) |  1.000 |  0.978 | AGATCct
 P$ARR10_01             |    11118 (+) |  1.000 |  0.934 | AGATCcc
 P$ARR10_01             |    11173 (+) |  1.000 |  0.956 | AGATCtt
 P$ARR10_01             |    11736 (-) |  0.979 |  0.938 | aaCATCT
 P$ARR10_01             |    11776 (+) |  0.993 |  0.972 | AGATAct
 F$MCM1_02              |      214 (-) |  0.977 |  0.741 | gTATTTtttttttttcctttttgtctt
 F$MCM1_02              |      223 (-) |  0.907 |  0.689 | tTTTTTcctttttgtctttttaaatct
 F$MCM1_02              |      474 (+) |  0.939 |  0.652 | gacacttacaagtcaacattgCAACAt
 F$MCM1_02              |     1046 (+) |  0.977 |  0.649 | cagcaaaaatcaacaactttaAAATAa
 F$MCM1_02              |     1155 (-) |  0.701 |  0.693 | aTGTAGttctttttcaaagaaaggaga
 F$MCM1_02              |     2212 (-) |  0.907 |  0.655 | tTCTTTctttctttctttctttctttc
 F$MCM1_02              |     2216 (-) |  0.907 |  0.655 | tTCTTTctttctttctttctttctttc
 F$MCM1_02              |     2220 (-) |  0.907 |  0.655 | tTCTTTctttctttctttctttctttc
 F$MCM1_02              |     2224 (-) |  0.907 |  0.655 | tTCTTTctttctttctttctttctttc
 F$MCM1_02              |     2228 (-) |  0.907 |  0.655 | tTCTTTctttctttctttctttctttc
 F$MCM1_02              |     2232 (-) |  0.907 |  0.655 | tTCTTTctttctttctttctttctttc
 F$MCM1_02              |     2236 (-) |  0.907 |  0.655 | tTCTTTctttctttctttctttctttc
 F$MCM1_02              |     2240 (-) |  0.907 |  0.655 | tTCTTTctttctttctttctttctttc
 F$MCM1_02              |     2244 (-) |  0.907 |  0.655 | tTCTTTctttctttctttctttctttc
 F$MCM1_02              |     2248 (-) |  0.907 |  0.655 | tTCTTTctttctttctttctttctttc
 F$MCM1_02              |     2252 (-) |  0.907 |  0.655 | tTCTTTctttctttctttctttctttc
 F$MCM1_02              |     2256 (-) |  0.907 |  0.655 | tTCTTTctttctttctttctttcttct
 F$MCM1_02              |     2260 (-) |  0.907 |  0.652 | tTCTTTctttctttctttcttctttct
 F$MCM1_02              |     2264 (-) |  0.907 |  0.673 | tTCTTTctttctttcttctttctcttc
 F$MCM1_02              |     2360 (-) |  0.762 |  0.674 | tTGTATttattttgccacagttttccc
 F$MCM1_02              |     2503 (+) |  0.682 |  0.671 | cgaaaaaaaagggaaaaaaaaTTACAt
 F$MCM1_02              |     2555 (-) |  0.939 |  0.693 | cTGTTGtgaaatttccgtaagtattta
 F$MCM1_02              |     3309 (-) |  0.696 |  0.655 | gTAGTTaagattggccttttcctgatt
 F$MCM1_02              |     3581 (-) |  0.885 |  0.661 | tTATTCaactctcctatgtttgggttt
 F$MCM1_02              |     3985 (+) |  0.669 |  0.650 | acaccatctcatgaaacaacgATAAAt
 F$MCM1_02              |     4038 (+) |  0.916 |  0.857 | attccagcagggggaaataggCAATAa
 F$MCM1_02              |     4415 (+) |  0.907 |  0.695 | caaccttgtctaaaaaaaaaaAAAAAa
 F$MCM1_02              |     4482 (+) |  1.000 |  0.698 | ttttcttttgaacaaaaaacaAAACAa
 F$MCM1_02              |     4490 (+) |  0.939 |  0.652 | tgaacaaaaaacaaaacaaaaCAACAt
 F$MCM1_02              |     4518 (+) |  0.939 |  0.699 | agaccaagacaacaaatgcgtCAACAg
 F$MCM1_02              |     4598 (+) |  0.719 |  0.672 | tgcccgcttgctggaaggtaaAACCAa
 F$MCM1_02              |     5382 (-) |  0.696 |  0.676 | tTAGTTttattttacctttatattttt
 F$MCM1_02              |     5414 (-) |  0.897 |  0.690 | tTATTAaatctttccctccactttatt
 F$MCM1_02              |     5442 (-) |  0.916 |  0.663 | gTATTGccatataaccttttccccaca
 F$MCM1_02              |     5625 (+) |  0.977 |  0.660 | taatacactgggataaagacaAAATAa
 F$MCM1_02              |     5631 (+) |  0.907 |  0.655 | actgggataaagacaaaataaAAAGAa
 F$MCM1_02              |     5647 (+) |  0.916 |  0.650 | aataaaaagaagaaaagaacaCAATAa
 F$MCM1_02              |     5757 (+) |  0.654 |  0.675 | ggacctgtagggtaaaaggagAGAAAa
 F$MCM1_02              |     5768 (+) |  0.977 |  0.650 | gtaaaaggagagaaaaatatgAAATAa
 F$MCM1_02              |     5776 (+) |  0.977 |  0.692 | agagaaaaatatgaaataattAAATAc
 F$MCM1_02              |     5815 (+) |  1.000 |  0.676 | tagccctggcgtggcactgtgAAACAa
 F$MCM1_02              |     6256 (-) |  0.654 |  0.672 | aTTTGTcccatctgccgaagaaggaag
 F$MCM1_02              |     6569 (+) |  1.000 |  0.696 | gccacagttatgcaaaacacaAAACAa
 F$MCM1_02              |     6607 (-) |  0.977 |  0.661 | cTATTTgctaaactccgtgagtggggc
 F$MCM1_02              |     6644 (+) |  0.816 |  0.664 | cacctcagtctgcaaacagatGAAGAt
 F$MCM1_02              |     7389 (+) |  0.816 |  0.665 | tgtccaggtggtagaattactGAAGAa
 F$MCM1_02              |     7431 (-) |  1.000 |  0.650 | tTGTTTttattttatgtgtgggagtgt
 F$MCM1_02              |     7641 (-) |  0.977 |  0.663 | tTATTTtaaaaatgcttttgtatgcca
 F$MCM1_02              |     7802 (+) |  1.000 |  0.648 | taaagaacaacgacaactccaAAACAa
 F$MCM1_02              |     7898 (-) |  0.977 |  0.663 | tTATTTtgatattagcttttacttagg
 F$MCM1_02              |     9514 (+) |  0.908 |  0.666 | tccccatgtccaacaagactaGAACAa
 F$MCM1_02              |    10315 (-) |  0.907 |  0.654 | gTTTTTatatttttattttatagtttt
 F$MCM1_02              |    10372 (+) |  0.669 |  0.691 | tttcaaaatgttgcaatccatATAAAa
 F$MCM1_02              |    10735 (-) |  0.916 |  0.665 | tTATTGgggggtttcagtgatccgtgt
 F$MCM1_02              |    11279 (+) |  0.897 |  0.734 | ttaaggcatagggcaaagaaaTAATAa
 F$MCM1_02              |    11469 (-) |  0.907 |  0.669 | tTTTTTatttgtttttcccttggaatg
 F$MCM1_02              |    11505 (-) |  0.654 |  0.718 | tTTTGTggatattaccgttgtccgtag
 P$BHLH66_01            |     6065 (+) |  1.000 |  1.000 | gCACGTgc
 P$BHLH66_01            |     6065 (-) |  1.000 |  1.000 | gcACGTGc
 P$ERF2_01              |     7148 (-) |  0.899 |  0.924 | GGCGCcg
 P$ERF2_01              |     7623 (+) |  1.000 |  0.922 | agCCGCC
 P$ERF2_01              |    10560 (-) |  0.856 |  0.892 | GCCGGcg
 V$GFI1B_01             |     4721 (-) |  1.000 |  0.910 | cactgTGATTtg
 V$GFI1B_01             |    10260 (-) |  1.000 |  0.941 | ggaagTGATTtt
 P$AGL1_01              |      165 (+) |  0.924 |  0.881 | gttcCCAATgctggcatt
 P$AGL1_01              |     6266 (+) |  0.973 |  0.904 | tctgCCGAAgaaggaagc
 P$AGL1_01              |     7834 (-) |  0.974 |  0.880 | taacccactTCTGGcaaa
 P$AGL1_01              |    11534 (+) |  0.975 |  0.941 | aatcCCACAtatggtaga
 P$AGL1_01              |    11534 (-) |  0.991 |  0.930 | aatcccacaTATGGtaga
 P$AGL1_02              |      165 (+) |  0.991 |  0.890 | gTTCCCaatgctggcatt
 P$AGL1_02              |      165 (-) |  0.967 |  0.882 | gttcccaatgctGGCATt
 P$AGL1_02              |     4037 (+) |  0.965 |  0.880 | tATTCCagcagggggaaa
 P$AGL1_02              |     4037 (-) |  0.991 |  0.874 | tattccagcaggGGGAAa
 P$AGL1_02              |     6266 (+) |  0.960 |  0.905 | tCTGCCgaagaaggaagc
 P$AGL1_02              |     6266 (-) |  0.957 |  0.868 | tctgccgaagaaGGAAGc
 P$AGL1_02              |     7834 (-) |  1.000 |  0.874 | taacccacttctGGCAAa
 P$AGL1_02              |    11534 (+) |  0.959 |  0.935 | aATCCCacatatggtaga
 P$AGL1_02              |    11534 (-) |  0.959 |  0.932 | aatcccacatatGGTAGa
 P$AGL2_01              |    11534 (+) |  0.940 |  0.942 | aatcCCACAtatggtaga
 P$AGL2_01              |    11534 (-) |  1.000 |  0.942 | aatcccacaTATGGtaga
 P$AGL2_02              |    11534 (+) |  0.956 |  0.937 | aatcCCACAtatggtaga
 P$AGL2_02              |    11534 (-) |  1.000 |  0.941 | aatcccacaTATGGtaga
 P$AG_03                |      164 (+) |  0.967 |  0.775 | cgttCCCAAtgctggcat
 P$AG_03                |      165 (+) |  0.878 |  0.858 | gttcCCAATgctggcatt
 P$AG_03                |     1134 (+) |  0.994 |  0.776 | tgttCCTAAaaccgttac
 P$AG_03                |     1551 (-) |  0.875 |  0.790 | gaaaactctTCTGGaaat
 P$AG_03                |     2381 (+) |  0.875 |  0.768 | tttcCCAGAgctgagagt
 P$AG_03                |     2713 (+) |  0.967 |  0.813 | tcttCCCAAatagataat
 P$AG_03                |     2714 (+) |  1.000 |  0.809 | cttcCCAAAtagataatc
 P$AG_03                |     2785 (+) |  0.915 |  0.786 | tcttCCTTAgctggtctt
 P$AG_03                |     3638 (+) |  0.881 |  0.771 | cctaCCACAtggtggaat
 P$AG_03                |     3860 (+) |  0.798 |  0.780 | agtaCCATTtaaggagtt
 P$AG_03                |     4394 (+) |  0.840 |  0.795 | agttCCAAGacaggtcag
 P$AG_03                |     5009 (+) |  0.845 |  0.807 | attaCCCATtaagccacg
 P$AG_03                |     5984 (-) |  0.994 |  0.825 | acttctggaTTAGGgatg
 P$AG_03                |     6266 (+) |  0.971 |  0.846 | tctgCCGAAgaaggaagc
 P$AG_03                |     6369 (-) |  1.000 |  0.784 | taagcgagaTTTGGtaga
 P$AG_03                |     7573 (-) |  0.869 |  0.788 | aaatccccaTCAGGtcaa
 P$AG_03                |     7834 (-) |  0.875 |  0.856 | taacccactTCTGGcaaa
 P$AG_03                |     8135 (-) |  0.875 |  0.770 | gctttctgcTGAGGgaaa
 P$AG_03                |     8462 (-) |  0.915 |  0.785 | ggtctcatcTAAGGcaaa
 P$AG_03                |     9595 (-) |  1.000 |  0.851 | atcccagcaTTTGGgaag
 P$AG_03                |    11442 (-) |  1.000 |  0.795 | cttatctatTTTGGtgaa
 P$AG_03                |    11534 (+) |  0.881 |  0.858 | aatcCCACAtatggtaga
 P$AG_03                |    11534 (-) |  0.920 |  0.875 | aatcccacaTATGGtaga
 P$AG_03                |    11673 (+) |  1.000 |  0.774 | ataaCCAAAaaagaccaa
 P$AG_03                |    11795 (-) |  0.878 |  0.773 | aaatcccagATTGGaagg
 P$AGL3_03              |     3590 (-) |  0.998 |  0.879 | tctcctatgTTTGGgttt
 P$AGL3_03              |    11534 (+) |  0.959 |  0.923 | aatcCCACAtatggtaga
 P$AGL3_03              |    11534 (-) |  1.000 |  0.874 | aatcccacaTATGGtaga
 P$ABZ1_01              |     6884 (-) |  1.000 |  0.973 | gcacCACGTaagac
 V$GFI1_Q6              |      242 (+) |  0.984 |  0.979 | ttaAATCTgggct
 V$GFI1_Q6              |     1428 (+) |  1.000 |  0.977 | cgcAATCAgtggc
 V$GFI1_Q6              |     2419 (+) |  1.000 |  0.991 | aaaAATCAcaggg
 V$GFI1_Q6              |     3467 (-) |  1.000 |  0.975 | cctcaTGATTtac
 V$GFI1_Q6              |     4639 (+) |  0.986 |  0.986 | caaAATCCcggca
 V$GFI1_Q6              |     4721 (-) |  1.000 |  0.987 | cactgTGATTtgg
 V$GFI1_Q6              |     7355 (+) |  1.000 |  0.976 | gttAATCAtgggc
 V$GFI1_Q6              |    10260 (-) |  1.000 |  0.988 | ggaagTGATTttt
 V$GFI1_Q6              |    11695 (+) |  1.000 |  0.975 | gttAATCActgtc
 V$CMAF_01              |      168 (+) |  1.000 |  0.823 | cccaaTGCTGgcattacta
 V$CMAF_01              |      478 (-) |  0.785 |  0.805 | cttacaagtCAACAttgca
 V$CMAF_01              |     1037 (-) |  1.000 |  0.810 | tcaacaaagCAGCAaaaat
 V$CMAF_01              |     1107 (+) |  0.816 |  0.820 | gaaatCGCTGatttgtgta
 V$CMAF_01              |     1222 (+) |  0.799 |  0.827 | gtttcTGATGactgctttg
 V$CMAF_01              |     1241 (-) |  1.000 |  0.814 | acatcagggCAGCAttctg
 V$CMAF_01              |     1582 (-) |  1.000 |  0.828 | atggagagcCAGCActggg
 V$CMAF_01              |     1617 (-) |  1.000 |  0.821 | tctcgtggaCAGCAtgtcc
 V$CMAF_01              |     1680 (-) |  0.822 |  0.826 | ttcgggtgtCAGCTcaggg
 V$CMAF_01              |     1839 (-) |  0.785 |  0.818 | tggggtcgtCAACAcaata
 V$CMAF_01              |     2660 (+) |  0.799 |  0.823 | cacttTGATGacactctta
 V$CMAF_01              |     2763 (-) |  0.867 |  0.828 | atctagattCCGCAtgtga
 V$CMAF_01              |     2826 (-) |  0.871 |  0.867 | tccagttgtCTGCAaatgg
 V$CMAF_01              |     2927 (+) |  0.822 |  0.808 | cccttAGCTGattgcgaag
 V$CMAF_01              |     3011 (-) |  0.867 |  0.833 | caggcgtctCGGCAgtaca
 V$CMAF_01              |     3226 (-) |  0.803 |  0.831 | tttaccagtCAGCCaacat
 V$CMAF_01              |     3599 (-) |  0.871 |  0.831 | tttgggtttCTGCAgtttt
 V$CMAF_01              |     4400 (-) |  0.803 |  0.822 | aagacaggtCAGCCacaac
 V$CMAF_01              |     4530 (-) |  0.785 |  0.814 | caaatgcgtCAACAgcctc
 V$CMAF_01              |     4786 (+) |  1.000 |  0.979 | aagatTGCTGacttgcata
 V$CMAF_01              |     4861 (-) |  1.000 |  0.956 | gagggaggtCAGCAgcaaa
 V$CMAF_01              |     4948 (-) |  0.871 |  0.815 | tgggactttCTGCAgcagg
 V$CMAF_01              |     5041 (+) |  1.000 |  0.807 | aggatTGCTGtggtctaag
 V$CMAF_01              |     6065 (+) |  1.000 |  0.817 | gcacgTGCTGccacagtct
 V$CMAF_01              |     6163 (-) |  0.871 |  0.837 | cctcctcttCTGCAgggtt
 V$CMAF_01              |     6220 (-) |  0.871 |  0.831 | tctcacgctCTGCAtgctg
 V$CMAF_01              |     6229 (+) |  1.000 |  0.827 | ctgcaTGCTGtctggctac
 V$CMAF_01              |     6263 (+) |  0.867 |  0.832 | ccatcTGCCGaagaaggaa
 V$CMAF_01              |     6287 (+) |  0.799 |  0.814 | tctgaTGATGactgagcag
 V$CMAF_01              |     6491 (+) |  0.871 |  0.856 | tggatTGCAGatgcggcca
 V$CMAF_01              |     6644 (-) |  0.871 |  0.884 | cacctcagtCTGCAaacag
 V$CMAF_01              |     6691 (+) |  1.000 |  0.946 | cagagTGCTGaagtagaga
 V$CMAF_01              |     6771 (-) |  1.000 |  0.807 | tgaacaaaaCAGCAgatct
 V$CMAF_01              |     6787 (+) |  1.000 |  0.834 | tctaaTGCTGgctcttcct
 V$CMAF_01              |     7021 (-) |  0.822 |  0.816 | ttcctgcatCAGCTgaaga
 V$CMAF_01              |     7169 (+) |  0.871 |  0.839 | ggcgtTGCAGatggtcccg
 V$CMAF_01              |     7219 (-) |  1.000 |  0.819 | aaagtaggcCAGCAggaag
 V$CMAF_01              |     7601 (+) |  1.000 |  0.930 | tgaacTGCTGagccatctc
 V$CMAF_01              |     7714 (-) |  1.000 |  0.940 | cagaaggatCAGCAgtttg
 V$CMAF_01              |     8070 (+) |  0.871 |  0.838 | ggtatTGCAGaaacttcct
 V$CMAF_01              |     8136 (+) |  1.000 |  0.944 | ctttcTGCTGagggaaaac
 V$CMAF_01              |     8320 (-) |  0.816 |  0.836 | cttctgcgtCAGCGccagt
 V$CMAF_01              |     9073 (-) |  1.000 |  0.823 | tagccagggCAGCAtagtg
 V$CMAF_01              |     9286 (-) |  0.822 |  0.829 | gctgagagtCAGCTtgtgt
 V$CMAF_01              |     9379 (-) |  0.803 |  0.810 | gagagctgtCAGCCcctgg
 V$CMAF_01              |     9633 (-) |  0.822 |  0.819 | gttcaaggtCAGCTtgggc
 V$CMAF_01              |     9849 (-) |  1.000 |  0.824 | tcaggcaggCAGCAttaaa
 V$CMAF_01              |    10181 (-) |  1.000 |  0.916 | gtgtgtgttCAGCAgtcag
 V$CMAF_01              |    10719 (+) |  1.000 |  0.809 | ctgcgTGCTGtagctttta
 V$CMAF_01              |    11163 (+) |  0.871 |  0.835 | gaagcTGCAGagatctttt
 V$CMAF_01              |    11325 (+) |  0.799 |  0.824 | gatgaTGATGacgatgtaa
 V$CMAF_01              |    11406 (-) |  0.871 |  0.831 | gcatttattCTGCAtttct
 V$CMAF_01              |    11426 (-) |  0.867 |  0.837 | tttagctatCCGCAtactt
 V$CMAF_01              |    11827 (-) |  1.000 |  0.807 | ggtgagaaaCAGCAgagtg
 V$HIC1_02              |      697 (-) |  1.000 |  0.951 | aagaGGGCAtcggat
 V$HIC1_02              |     1179 (-) |  1.000 |  0.956 | agatGGGCAccccca
 V$HIC1_02              |     4592 (+) |  1.000 |  0.969 | tcctccTGCCCgctt
 V$HIC1_02              |     5883 (-) |  1.000 |  0.957 | tgctGGGCAtggggc
 V$HIC1_02              |     6626 (-) |  1.000 |  0.962 | agtgGGGCAcccaga
 V$HIC1_02              |     8277 (+) |  1.000 |  0.966 | tgcagcTGCCCtggc
 V$HIC1_02              |     8304 (+) |  1.000 |  0.957 | cccctcTGCCCtgca
 V$HIC1_02              |     9011 (-) |  1.000 |  0.952 | gcagGGGCAggcaga
 V$HIC1_02              |     9037 (-) |  1.000 |  0.955 | tcaaGGGCAgcctgg
 V$HIC1_02              |    10077 (-) |  1.000 |  0.953 | ggaaGGGCAgccagt
 V$HIC1_02              |    11710 (+) |  1.000 |  0.955 | cccaacTGCCCtcca
 V$HIC1_03              |     1176 (-) |  1.000 |  0.943 | aggagatGGGCAccccca
 V$HIC1_03              |     6037 (-) |  0.975 |  0.929 | ccatctgGTGCAgccctg
 V$HIC1_03              |     6623 (-) |  1.000 |  0.954 | gtgagtgGGGCAcccaga
 V$HIC1_03              |     8358 (-) |  0.975 |  0.928 | aacccctGTGCAgcctgc
 V$HIC1_03              |     9034 (-) |  1.000 |  0.924 | agttcaaGGGCAgcctgg
 V$PLZF_02              |      231 (+) |  0.979 |  0.751 | tttttgtcttttTAAATctgggctgtaag
 V$PLZF_02              |      513 (+) |  0.978 |  0.737 | gtcttctgatttTAAAAatgatgggtgat
 V$PLZF_02              |      559 (+) |  0.976 |  0.868 | ttttctaggagaTAAACgtctacctgttg
 V$PLZF_02              |      626 (+) |  0.976 |  0.741 | gacactttttttTAAACatttattcattt
 V$PLZF_02              |      631 (-) |  0.979 |  0.742 | ttttttttaaacATTTAttcatttattat
 V$PLZF_02              |      639 (-) |  0.979 |  0.733 | aaacatttattcATTTAttatatataagt
 V$PLZF_02              |      812 (-) |  0.978 |  0.725 | cagcccgacactTTTTAatactatataaa
 V$PLZF_02              |      825 (+) |  0.978 |  0.738 | tttaatactataTAAAAcaagttaaataa
 V$PLZF_02              |      951 (-) |  0.979 |  0.766 | caatgatcaaatATTTAcaggacccctaa
 V$PLZF_02              |     1050 (-) |  1.000 |  0.734 | aaaaatcaacaaCTTTAaaataagatgtg
 V$PLZF_02              |     1053 (+) |  0.978 |  0.711 | aatcaacaacttTAAAAtaagatgtgtag
 V$PLZF_02              |     1085 (+) |  0.978 |  0.790 | attttggtcaacTAAAAtttgagaaatcg
 V$PLZF_02              |     1879 (-) |  0.978 |  0.707 | atctgcctcccaTTTTAtatttattttat
 V$PLZF_02              |     1898 (-) |  0.978 |  0.708 | tttattttattaTTTTAtttgagacagag
 V$PLZF_02              |     2427 (-) |  0.979 |  0.729 | caggggttggggATTTAgctcagtggtag
 V$PLZF_02              |     2565 (-) |  0.979 |  0.748 | atttccgtaagtATTTAcaacaaatgcag
 V$PLZF_02              |     2845 (-) |  1.000 |  0.727 | catcattccgtcCTTTAgagctgaacaga
 V$PLZF_02              |     2890 (-) |  0.978 |  0.716 | gtactgcatcttTTTTAtccacatctctg
 V$PLZF_02              |     3119 (-) |  0.979 |  0.783 | gcggctatattaATTTAcattcccacaac
 V$PLZF_02              |     3213 (-) |  0.978 |  0.720 | ctaggcaagcacTTTTAccagtcagccaa
 V$PLZF_02              |     3396 (+) |  0.978 |  0.714 | gatctccagttaTAAAAgttaatgattct
 V$PLZF_02              |     3462 (-) |  0.979 |  0.719 | cagggcctcatgATTTActgcctatgagg
 V$PLZF_02              |     3706 (-) |  0.979 |  0.774 | tgcttgatcaatATTTAcgggtgactaaa
 V$PLZF_02              |     3719 (+) |  0.978 |  0.761 | tttacgggtgacTAAAAttattatttcta
 V$PLZF_02              |     3739 (-) |  0.978 |  0.746 | ttatttctacatTTTTAgtcattcttaaa
 V$PLZF_02              |     3822 (+) |  0.979 |  0.767 | ttcaattcataaTAAATttccattctcat
 V$PLZF_02              |     3901 (+) |  1.000 |  0.717 | cacaggtattaaTAAAGctttatgaatta
 V$PLZF_02              |     3906 (-) |  1.000 |  0.764 | gtattaataaagCTTTAtgaattacatta
 V$PLZF_02              |     3995 (+) |  0.979 |  0.748 | atgaaacaacgaTAAATaaatattctgct
 V$PLZF_02              |     4054 (+) |  0.978 |  0.711 | ataggcaataatTAAAAtatgtaaaatgt
 V$PLZF_02              |     4079 (-) |  0.978 |  0.746 | atgtatactataTTTTActgattctaaaa
 V$PLZF_02              |     4091 (+) |  0.978 |  0.815 | ttttactgattcTAAAAcatccattttcc
 V$PLZF_02              |     4115 (+) |  0.978 |  0.735 | tttcccagatgtTAAAAcccagaatctag
 V$PLZF_02              |     4208 (+) |  0.978 |  0.719 | gcttgcctcagtTAAAAaaataaattctc
 V$PLZF_02              |     4284 (+) |  0.979 |  0.725 | cacattagacccTAAATttgaccctcaat
 V$PLZF_02              |     4307 (+) |  0.978 |  0.815 | ctcaatactgcaTAAAActgggtctggtg
 V$PLZF_02              |     4604 (+) |  0.978 |  0.749 | cttgctggaaggTAAAAccaatatccttt
 V$PLZF_02              |     4772 (+) |  1.000 |  0.740 | agcgagtctggaTAAAGattgctgacttg
 V$PLZF_02              |     5368 (-) |  0.978 |  0.735 | acacgggatttcTTTTAgttttattttac
 V$PLZF_02              |     5374 (-) |  0.978 |  0.789 | gatttcttttagTTTTAttttacctttat
 V$PLZF_02              |     5385 (-) |  1.000 |  0.732 | gttttattttacCTTTAtattttttcatc
 V$PLZF_02              |     5406 (+) |  0.979 |  0.768 | ttttcatcttatTAAATctttccctccac
 V$PLZF_02              |     5411 (-) |  0.756 |  0.730 | atcttattaaatCTTTCcctccactttat
 V$PLZF_02              |     5781 (-) |  0.735 |  0.716 | aaaatatgaaatAATTAaatacaaaaaaa
 V$PLZF_02              |     5936 (+) |  0.978 |  0.789 | cttggagaaaagTAAAAttttatttgcca
 V$PLZF_02              |     5941 (-) |  0.978 |  0.753 | agaaaagtaaaaTTTTAtttgccagtgtt
 V$PLZF_02              |     6662 (-) |  0.979 |  0.787 | gatgaagattttATTTAgcttttgaagag
 V$PLZF_02              |     6711 (-) |  1.000 |  0.765 | aaaagccacaacCTTTAaagggtgagcag
 V$PLZF_02              |     6714 (+) |  1.000 |  0.738 | agccacaaccttTAAAGggtgagcagccc
 V$PLZF_02              |     6749 (-) |  1.000 |  0.776 | aacccactatccCTTTAtaccatgaacaa
 V$PLZF_02              |     6815 (-) |  0.978 |  0.750 | accttctcccttTTTTAtgtgctatttac
 V$PLZF_02              |     7049 (+) |  0.735 |  0.725 | ctattttttttcTTAATttgtttttgttt
 V$PLZF_02              |     7262 (+) |  0.978 |  0.746 | attaaaatatccTAAAAtaagacccatag
 V$PLZF_02              |     7405 (-) |  0.978 |  0.714 | ttactgaagaacTTTTAaaggtttatttg
 V$PLZF_02              |     7408 (+) |  1.000 |  0.868 | ctgaagaactttTAAAGgtttatttgttt
 V$PLZF_02              |     7413 (-) |  0.976 |  0.765 | gaacttttaaagGTTTAtttgtttttatt
 V$PLZF_02              |     7521 (+) |  0.756 |  0.751 | ctgaactgaagtTACAGttggttgtgagc
 V$PLZF_02              |     7635 (+) |  0.978 |  0.796 | gtagaattatttTAAAAatgcttttgtat
 V$PLZF_02              |     7776 (-) |  0.735 |  0.742 | aaacaaaacaaaAATTAtcccaaagataa
 V$PLZF_02              |     7790 (+) |  1.000 |  0.749 | ttatcccaaagaTAAAGaacaacgacaac
 V$PLZF_02              |     7884 (-) |  0.978 |  0.726 | aagtcatttggtTTTTAttttgatattag
 V$PLZF_02              |     7902 (-) |  0.978 |  0.740 | tttgatattagcTTTTActtaggtatcaa
 V$PLZF_02              |     8927 (+) |  1.000 |  0.728 | ttcagtataaacTAAAGcaactttttaaa
 V$PLZF_02              |     8978 (-) |  1.000 |  0.748 | ggtggtacacacCTTTAattccagcacat
 V$PLZF_02              |     9437 (-) |  0.976 |  0.717 | aggaagcccaagGTTTAccaatctctgct
 V$PLZF_02              |     9473 (-) |  1.000 |  0.757 | atgttctagctaCTTTAtttgcaatagaa
 V$PLZF_02              |     9703 (+) |  0.978 |  0.765 | gtggtggtggtgTAAAAttgatctctttg
 V$PLZF_02              |     9785 (+) |  0.979 |  0.718 | aattttgttcagTAAATgtacatcacata
 V$PLZF_02              |     9814 (-) |  0.978 |  0.738 | agtaacttcaaaTTTTAgaagggataatt
 V$PLZF_02              |     9829 (-) |  0.978 |  0.712 | tagaagggataaTTTTAaagtcaggcagg
 V$PLZF_02              |     9886 (-) |  0.978 |  0.719 | tttaaaattcttTTTTAaagacttactta
 V$PLZF_02              |     9889 (+) |  1.000 |  0.743 | aaaattctttttTAAAGacttacttactg
 V$PLZF_02              |    10114 (+) |  0.978 |  0.707 | tgccatccccaaTAAAAttagttaagaaa
 V$PLZF_02              |    10295 (-) |  0.978 |  0.722 | gcttcggacattTTTTAactgtttttata
 V$PLZF_02              |    10308 (+) |  0.735 |  0.742 | tttaactgttttTATATttttattttata
 V$PLZF_02              |    10321 (+) |  0.756 |  0.742 | atatttttatttTATAGtttttattgttt
 V$PLZF_02              |    10382 (+) |  0.978 |  0.793 | ttgcaatccataTAAAAatgaacgaggtg
 V$PLZF_02              |    10463 (-) |  1.000 |  0.730 | caatgcatctcaCTTTAgaccagccacat
 V$PLZF_02              |    10535 (+) |  1.000 |  0.729 | gccgtgcaactcTAAAGtatgtacagccg
 V$PLZF_02              |    11089 (-) |  0.976 |  0.717 | gaattttccactGTTTAaagaacgacttc
 V$PLZF_02              |    11092 (+) |  1.000 |  0.733 | ttttccactgttTAAAGaacgacttcaga
 V$PLZF_02              |    11382 (+) |  0.979 |  0.785 | ttgaaaacttatTAAATtttgtacgcatt
 V$PLZF_02              |    11628 (+) |  0.979 |  0.729 | aggaccctcgttTAAATgtatttctgtac
 V$CETS1P54_03          |      606 (-) |  0.917 |  0.919 | ttaaacATCCTgtcgt
 V$CETS1P54_03          |      702 (+) |  0.988 |  0.884 | ggcatCGGATctcttt
 V$CETS1P54_03          |     1259 (-) |  0.988 |  0.905 | gtcatcATCCGtgtgt
 V$CETS1P54_03          |     1455 (+) |  0.926 |  0.923 | tgagcCGGACgtttct
 V$CETS1P54_03          |     1716 (-) |  1.000 |  0.916 | tgccttTTCCGggctc
 V$CETS1P54_03          |     1726 (-) |  0.917 |  0.880 | gggctcATCCTgaact
 V$CETS1P54_03          |     1735 (-) |  0.929 |  0.896 | ctgaacTTCCTataga
 V$CETS1P54_03          |     2151 (-) |  0.929 |  0.880 | ccttccTTCCTcttcc
 V$CETS1P54_03          |     2561 (-) |  1.000 |  0.924 | tgaaatTTCCGtaagt
 V$CETS1P54_03          |     2682 (-) |  0.917 |  0.889 | cgttgcATCCTggtca
 V$CETS1P54_03          |     2985 (-) |  1.000 |  0.968 | atctacTTCCGctcct
 V$CETS1P54_03          |     3029 (-) |  1.000 |  0.975 | accgacTTCCGctcca
 V$CETS1P54_03          |     4685 (+) |  0.929 |  0.882 | gtggcAGGAAacttga
 V$CETS1P54_03          |     4959 (+) |  0.929 |  0.928 | gcagcAGGAAgtcagg
 V$CETS1P54_03          |     5469 (-) |  0.929 |  0.890 | tactatTTCCTgattt
 V$CETS1P54_03          |     5728 (+) |  0.886 |  0.880 | taaacTGGAAgccata
 V$CETS1P54_03          |     6272 (+) |  0.929 |  0.882 | gaagaAGGAAgcctct
 V$CETS1P54_03          |     6457 (-) |  0.929 |  0.894 | acttatTTCCTgataa
 V$CETS1P54_03          |     6874 (+) |  0.929 |  0.883 | cttatAGGAAgcacca
 V$CETS1P54_03          |     7009 (+) |  0.988 |  0.950 | gcaggCGGATgtttcc
 V$CETS1P54_03          |     7227 (+) |  0.929 |  0.923 | ccagcAGGAAgttcat
 V$CETS1P54_03          |     8078 (-) |  0.929 |  0.901 | agaaacTTCCTataca
 V$CETS1P54_03          |     8917 (+) |  1.000 |  0.881 | atactCGGAAttcagt
 V$CETS1P54_03          |     9432 (+) |  0.929 |  0.912 | ataacAGGAAgcccaa
 V$CETS1P54_03          |     9465 (+) |  0.917 |  0.924 | tgtacAGGATgttcta
 V$CETS1P54_03          |    10254 (+) |  0.929 |  0.929 | tgtgcAGGAAgtgatt
 V$CETS1P54_03          |    10841 (+) |  0.929 |  0.893 | atcgcAGGAAgaagcc
 V$CETS1P54_03          |    11427 (-) |  0.988 |  0.880 | ttagctATCCGcatac
 V$CBF_01               |      789 (-) |  1.000 |  0.994 | tcttaACCGCtgagcc
 V$CBF_01               |     2766 (-) |  0.994 |  0.976 | tagatTCCGCatgtga
 V$CBF_01               |     2987 (-) |  0.994 |  0.982 | ctactTCCGCtcctcc
 V$CBF_01               |     3031 (-) |  0.994 |  0.982 | cgactTCCGCtccacc
 V$CBF_01               |     3113 (+) |  0.981 |  0.979 | ttccatGCGGCtatat
 V$CBF_01               |     4436 (-) |  0.978 |  0.975 | aaaaaACCACacaatt
 V$CBF_01               |     4567 (+) |  1.000 |  0.993 | acagttGCGGTtagat
 V$CBF_01               |     5131 (+) |  1.000 |  0.979 | gatggtGCGGTcaacc
 V$CBF_01               |     7007 (+) |  0.994 |  0.983 | aggcagGCGGAtgttt
 V$CBF_01               |     7626 (+) |  1.000 |  0.977 | cgcctgGCGGTagaat
 V$CBF_01               |     9395 (+) |  0.978 |  0.973 | tggaatGTGGTtctat
 V$CBF_01               |    10950 (+) |  1.000 |  0.978 | gtagctGCGGTctgtg
 V$CBF_01               |    11429 (-) |  0.994 |  0.986 | agctaTCCGCatactt
 V$CBF_01               |    11489 (+) |  1.000 |  0.994 | tggaatGCGGTtgaat
 V$CBF_02               |      789 (-) |  1.000 |  0.967 | tcttaACCGCtgagcc
 V$CBF_02               |      931 (-) |  0.989 |  0.982 | acgaaACCACaagtta
 V$CBF_02               |     3113 (+) |  0.965 |  0.961 | ttccatGCGGCtatat
 V$CBF_02               |     3636 (-) |  0.989 |  0.963 | tacctACCACatggtg
 V$CBF_02               |     4140 (+) |  0.989 |  0.959 | ctaggtGTGGTgcctc
 V$CBF_02               |     4436 (-) |  0.989 |  0.981 | aaaaaACCACacaatt
 V$CBF_02               |     4567 (+) |  1.000 |  0.993 | acagttGCGGTtagat
 V$CBF_02               |     5044 (+) |  0.989 |  0.977 | attgctGTGGTctaag
 V$CBF_02               |     5131 (+) |  1.000 |  0.985 | gatggtGCGGTcaacc
 V$CBF_02               |     5251 (+) |  0.989 |  0.976 | tcacatGTGGTcacag
 V$CBF_02               |     7107 (-) |  0.989 |  0.967 | tgtgtACCACatgtgt
 V$CBF_02               |     8737 (+) |  0.989 |  0.960 | cggggtGTGGTggccc
 V$CBF_02               |     8893 (-) |  0.989 |  0.963 | aacgtACCACaaacag
 V$CBF_02               |     8970 (+) |  0.989 |  0.961 | ccaggtGTGGTggtac
 V$CBF_02               |     9395 (+) |  0.989 |  0.980 | tggaatGTGGTtctat
 V$CBF_02               |     9570 (+) |  0.989 |  0.965 | ctgggtGTGGTggtat
 V$CBF_02               |    10950 (+) |  1.000 |  0.982 | gtagctGCGGTctgtg
 V$CBF_02               |    11251 (+) |  0.989 |  0.966 | aactctGTGGTgtgcc
 V$CBF_02               |    11429 (-) |  0.965 |  0.960 | agctaTCCGCatactt
 V$CBF_02               |    11489 (+) |  1.000 |  0.991 | tggaatGCGGTtgaat
 V$BRCA_01              |       38 (-) |  0.988 |  0.960 | CAACTtca
 V$BRCA_01              |       69 (+) |  1.000 |  0.964 | tacTGTTG
 V$BRCA_01              |       72 (+) |  1.000 |  0.974 | tgtTGTTG
 V$BRCA_01              |       78 (+) |  1.000 |  0.971 | tgaTGTTG
 V$BRCA_01              |      445 (+) |  0.997 |  0.963 | tcaGGTTG
 V$BRCA_01              |      458 (+) |  0.997 |  0.994 | tttGGTTG
 V$BRCA_01              |      495 (-) |  1.000 |  0.958 | CAACAtta
 V$BRCA_01              |      580 (+) |  1.000 |  0.956 | accTGTTG
 V$BRCA_01              |     1027 (+) |  0.988 |  0.956 | ggcAGTTG
 V$BRCA_01              |     1038 (-) |  1.000 |  0.976 | CAACAaag
 V$BRCA_01              |     1056 (-) |  1.000 |  0.958 | CAACAact
 V$BRCA_01              |     1093 (-) |  0.988 |  0.986 | CAACTaaa
 V$BRCA_01              |     1848 (-) |  1.000 |  0.999 | CAACAcaa
 V$BRCA_01              |     1862 (-) |  0.988 |  0.989 | CAACTgaa
 V$BRCA_01              |     2428 (+) |  0.997 |  0.957 | aggGGTTG
 V$BRCA_01              |     2553 (+) |  1.000 |  1.000 | ttcTGTTG
 V$BRCA_01              |     2582 (-) |  1.000 |  0.981 | CAACAaat
 V$BRCA_01              |     2826 (+) |  0.988 |  0.961 | tccAGTTG
 V$BRCA_01              |     3144 (-) |  1.000 |  0.961 | CAACAata
 V$BRCA_01              |     3422 (+) |  0.997 |  0.966 | tctGGTTG
 V$BRCA_01              |     4001 (-) |  0.994 |  0.956 | CAACGata
 V$BRCA_01              |     4256 (+) |  0.997 |  0.973 | cttGGTTG
 V$BRCA_01              |     4511 (-) |  1.000 |  0.971 | CAACAtca
 V$BRCA_01              |     4527 (-) |  1.000 |  0.981 | CAACAaat
 V$BRCA_01              |     4539 (-) |  1.000 |  0.967 | CAACAgcc
 V$BRCA_01              |     4922 (-) |  0.988 |  0.973 | CAACTtac
 V$BRCA_01              |     5142 (-) |  0.997 |  0.970 | CAACCtag
 V$BRCA_01              |     5278 (-) |  1.000 |  0.974 | CAACAaca
 V$BRCA_01              |     5281 (-) |  1.000 |  0.962 | CAACAggc
 V$BRCA_01              |     5855 (+) |  0.988 |  0.989 | ttgAGTTG
 V$BRCA_01              |     6107 (+) |  1.000 |  0.972 | tccTGTTG
 V$BRCA_01              |     6440 (-) |  0.997 |  0.976 | CAACCcag
 V$BRCA_01              |     7040 (+) |  0.988 |  0.976 | gttAGTTG
 V$BRCA_01              |     7168 (+) |  0.994 |  0.971 | tggCGTTG
 V$BRCA_01              |     7537 (+) |  0.997 |  0.984 | gttGGTTG
 V$BRCA_01              |     7809 (-) |  0.994 |  0.969 | CAACGaca
 V$BRCA_01              |     7815 (-) |  0.988 |  0.966 | CAACTcca
 V$BRCA_01              |     8003 (+) |  1.000 |  0.962 | gccTGTTG
 V$BRCA_01              |     8223 (+) |  1.000 |  0.971 | tgaTGTTG
 V$BRCA_01              |     8357 (-) |  0.997 |  0.957 | CAACCcct
 V$BRCA_01              |     8442 (-) |  0.997 |  0.958 | CAACCcgc
 V$BRCA_01              |     9524 (-) |  1.000 |  0.969 | CAACAaga
 V$BRCA_01              |    10150 (+) |  1.000 |  0.961 | tatTGTTG
 V$BRCA_01              |    10153 (+) |  1.000 |  0.974 | tgtTGTTG
 V$BRCA_01              |    10235 (+) |  0.997 |  0.970 | ctaGGTTG
 V$BRCA_01              |    10407 (+) |  0.997 |  0.961 | ggtGGTTG
 V$BRCA_01              |    10619 (+) |  0.988 |  0.955 | gggAGTTG
 V$BRCA_01              |    10665 (-) |  1.000 |  0.972 | CAACAgga
 V$BRCA_01              |    10694 (-) |  1.000 |  0.966 | CAACAccc
 V$BRCA_01              |    10943 (+) |  1.000 |  0.956 | cggTGTTG
 V$BRCA_01              |    10965 (+) |  1.000 |  0.962 | gccTGTTG
 V$BRCA_01              |    11040 (+) |  1.000 |  0.974 | tgtTGTTG
 V$BRCA_01              |    11494 (+) |  0.997 |  0.974 | tgcGGTTG
 V$BRCA_01              |    11517 (+) |  0.994 |  0.958 | tacCGTTG
 V$BRCA_01              |    11560 (-) |  0.997 |  0.994 | CAACCaaa
 V$BRCA_01              |    11712 (-) |  0.988 |  0.956 | CAACTgcc
 V$BRCA_01              |    11896 (-) |  0.997 |  0.978 | CAACCaat
 V$BRCA_01              |    11923 (-) |  0.994 |  0.961 | CAACGccc
 I$ABDA_Q6              |      391 (-) |  0.991 |  0.984 | attcATTTGc
 I$ABDA_Q6              |      585 (-) |  0.984 |  0.978 | ttgaATTAAc
 I$ABDA_Q6              |      639 (-) |  1.000 |  0.979 | aaacATTTAt
 I$ABDA_Q6              |      647 (-) |  1.000 |  0.981 | attcATTTAt
 I$ABDA_Q6              |      846 (+) |  1.000 |  0.990 | tTAAATaaat
 I$ABDA_Q6              |      957 (+) |  0.991 |  0.979 | tCAAATattt
 I$ABDA_Q6              |      959 (-) |  1.000 |  0.993 | aaatATTTAc
 I$ABDA_Q6              |      988 (+) |  0.984 |  0.980 | gTTAATaatt
 I$ABDA_Q6              |      991 (-) |  0.986 |  0.986 | aataATTTTc
 I$ABDA_Q6              |     1097 (-) |  0.991 |  0.983 | taaaATTTGa
 I$ABDA_Q6              |     1471 (-) |  0.991 |  0.979 | caatATTTGc
 I$ABDA_Q6              |     1563 (+) |  0.995 |  0.978 | gGAAATctac
 I$ABDA_Q6              |     1893 (-) |  1.000 |  0.982 | ttatATTTAt
 I$ABDA_Q6              |     1897 (-) |  0.986 |  0.977 | atttATTTTa
 I$ABDA_Q6              |     1905 (-) |  0.986 |  0.977 | tattATTTTa
 I$ABDA_Q6              |     1910 (-) |  0.991 |  0.982 | ttttATTTGa
 I$ABDA_Q6              |     2360 (-) |  1.000 |  0.978 | ttgtATTTAt
 I$ABDA_Q6              |     2561 (-) |  0.995 |  0.981 | tgaaATTTCc
 I$ABDA_Q6              |     2573 (-) |  1.000 |  0.989 | aagtATTTAc
 I$ABDA_Q6              |     3107 (-) |  0.995 |  0.987 | actaATTTCc
 I$ABDA_Q6              |     3127 (-) |  1.000 |  0.999 | attaATTTAc
 I$ABDA_Q6              |     3334 (-) |  0.995 |  0.986 | ttctATTTCc
 I$ABDA_Q6              |     3413 (+) |  0.984 |  0.978 | gTTAATgatt
 I$ABDA_Q6              |     3430 (-) |  0.982 |  0.976 | cttaATTGAc
 I$ABDA_Q6              |     3450 (+) |  0.984 |  0.981 | gTTAATaaaa
 I$ABDA_Q6              |     3470 (-) |  1.000 |  0.986 | catgATTTAc
 I$ABDA_Q6              |     3714 (-) |  1.000 |  0.988 | caatATTTAc
 I$ABDA_Q6              |     3731 (+) |  0.986 |  0.981 | tAAAATtatt
 I$ABDA_Q6              |     3737 (-) |  0.995 |  0.980 | tattATTTCt
 I$ABDA_Q6              |     3833 (-) |  0.995 |  0.992 | ataaATTTCc
 I$ABDA_Q6              |     3862 (-) |  1.000 |  0.982 | taccATTTAa
 I$ABDA_Q6              |     3875 (+) |  0.984 |  0.974 | gTTAATacaa
 I$ABDA_Q6              |     4006 (+) |  1.000 |  0.984 | aTAAATaaat
 I$ABDA_Q6              |     4010 (+) |  1.000 |  0.975 | aTAAATattc
 I$ABDA_Q6              |     4060 (-) |  0.984 |  0.978 | aataATTAAa
 I$ABDA_Q6              |     4109 (-) |  0.986 |  0.974 | atccATTTTc
 I$ABDA_Q6              |     4227 (+) |  1.000 |  0.975 | aTAAATtctc
 I$ABDA_Q6              |     4295 (+) |  1.000 |  0.976 | cTAAATttga
 I$ABDA_Q6              |     4295 (-) |  0.991 |  0.977 | ctaaATTTGa
 I$ABDA_Q6              |     4455 (-) |  0.995 |  0.982 | attcATTTCa
 I$ABDA_Q6              |     5102 (-) |  0.991 |  0.976 | tattATTTGt
 I$ABDA_Q6              |     5386 (-) |  0.986 |  0.977 | ttttATTTTa
 I$ABDA_Q6              |     5417 (+) |  1.000 |  0.983 | tTAAATcttt
 I$ABDA_Q6              |     5469 (-) |  0.995 |  0.986 | tactATTTCc
 I$ABDA_Q6              |     5593 (+) |  0.986 |  0.975 | tAAAATataa
 I$ABDA_Q6              |     5787 (+) |  0.995 |  0.985 | tGAAATaatt
 I$ABDA_Q6              |     5790 (-) |  0.984 |  0.978 | aataATTAAa
 I$ABDA_Q6              |     5795 (+) |  1.000 |  0.984 | tTAAATacaa
 I$ABDA_Q6              |     5948 (+) |  0.986 |  0.979 | tAAAATttta
 I$ABDA_Q6              |     5948 (-) |  0.986 |  0.979 | taaaATTTTa
 I$ABDA_Q6              |     5953 (-) |  0.991 |  0.988 | ttttATTTGc
 I$ABDA_Q6              |     6457 (-) |  0.995 |  0.983 | acttATTTCc
 I$ABDA_Q6              |     6509 (+) |  0.991 |  0.976 | aCAAATaaaa
 I$ABDA_Q6              |     6670 (-) |  1.000 |  0.983 | ttttATTTAg
 I$ABDA_Q6              |     6834 (-) |  1.000 |  0.979 | tgctATTTAc
 I$ABDA_Q6              |     7060 (-) |  0.991 |  0.974 | cttaATTTGt
 I$ABDA_Q6              |     7435 (-) |  0.986 |  0.977 | ttttATTTTa
 I$ABDA_Q6              |     7639 (-) |  0.986 |  0.977 | aattATTTTa
 I$ABDA_Q6              |     7828 (-) |  0.984 |  0.979 | aacaATTAAc
 I$ABDA_Q6              |     8335 (-) |  0.991 |  0.975 | cagtATTTGc
 I$ABDA_Q6              |     8635 (-) |  1.000 |  0.976 | gcttATTTAa
 I$ABDA_Q6              |     9485 (-) |  0.991 |  0.982 | ctttATTTGc
 I$ABDA_Q6              |     9715 (+) |  0.986 |  0.975 | tAAAATtgat
 I$ABDA_Q6              |     9796 (+) |  1.000 |  0.984 | gTAAATgtac
 I$ABDA_Q6              |     9821 (+) |  0.991 |  0.983 | tCAAATttta
 I$ABDA_Q6              |     9836 (-) |  0.986 |  0.974 | gataATTTTa
 I$ABDA_Q6              |     9877 (+) |  0.995 |  0.987 | gGAAATcaat
 I$ABDA_Q6              |     9881 (-) |  1.000 |  0.988 | atcaATTTAa
 I$ABDA_Q6              |     9888 (+) |  0.986 |  0.974 | tAAAATtctt
 I$ABDA_Q6              |    10138 (+) |  0.995 |  0.983 | aGAAATtatt
 I$ABDA_Q6              |    10325 (-) |  0.986 |  0.977 | ttttATTTTa
 I$ABDA_Q6              |    10348 (-) |  0.980 |  0.976 | tttaATTCAa
 I$ABDA_Q6              |    10506 (+) |  0.982 |  0.976 | gTCAATtatg
 I$ABDA_Q6              |    10585 (-) |  0.995 |  0.990 | ttcaATTTCc
 I$ABDA_Q6              |    10914 (+) |  0.991 |  0.988 | gCAAATaata
 I$ABDA_Q6              |    11157 (+) |  0.986 |  0.974 | gAAAATgaag
 I$ABDA_Q6              |    11207 (-) |  0.991 |  0.979 | attaATTTGt
 I$ABDA_Q6              |    11274 (+) |  0.995 |  0.989 | gGAAATtaag
 I$ABDA_Q6              |    11295 (+) |  0.995 |  0.980 | aGAAATaata
 I$ABDA_Q6              |    11340 (+) |  1.000 |  0.975 | gTAAATgcca
 I$ABDA_Q6              |    11393 (+) |  1.000 |  0.986 | tTAAATtttg
 I$ABDA_Q6              |    11421 (-) |  1.000 |  0.977 | ttctATTTAg
 I$ABDA_Q6              |    11464 (+) |  0.995 |  0.986 | tGAAATtttt
 I$ABDA_Q6              |    11471 (-) |  0.991 |  0.976 | ttttATTTGt
 I$ABDA_Q6              |    11639 (+) |  1.000 |  0.985 | tTAAATgtat
 I$ABDA_Q6              |    11663 (-) |  0.986 |  0.975 | cacaATTTTc
 I$ABDA_Q6              |    11940 (-) |  0.995 |  0.980 | aactATTTCa
 I$ANTP_Q6_01           |       64 (-) |  0.970 |  0.932 | aTAATTactgtt
 I$ANTP_Q6_01           |      843 (+) |  0.987 |  0.915 | aagttaAATAAa
 I$ANTP_Q6_01           |     1892 (-) |  0.911 |  0.942 | tTTATAtttatt
 I$ANTP_Q6_01           |     1906 (-) |  0.987 |  0.944 | aTTATTttattt
 I$ANTP_Q6_01           |     2516 (+) |  0.970 |  0.976 | aaaaaaAATTAc
 I$ANTP_Q6_01           |     2739 (-) |  1.000 |  0.963 | tTTATGcctttt
 I$ANTP_Q6_01           |     3128 (-) |  0.970 |  0.926 | tTAATTtacatt
 I$ANTP_Q6_01           |     3255 (-) |  1.000 |  0.928 | cTTATGgttttc
 I$ANTP_Q6_01           |     3999 (+) |  0.911 |  0.915 | aacaacGATAAa
 I$ANTP_Q6_01           |     5398 (-) |  0.911 |  0.938 | tTTATAtttttt
 I$ANTP_Q6_01           |     5435 (-) |  0.987 |  0.981 | tTTATTtgtatt
 I$ANTP_Q6_01           |     5582 (+) |  0.987 |  0.929 | aaggatAATAAt
 I$ANTP_Q6_01           |     5585 (+) |  0.987 |  0.918 | gataatAATAAa
 I$ANTP_Q6_01           |     6589 (+) |  0.987 |  0.976 | aaaacaAATAAg
 I$ANTP_Q6_01           |     6671 (-) |  0.987 |  0.915 | tTTATTtagctt
 I$ANTP_Q6_01           |     7061 (-) |  0.970 |  0.965 | tTAATTtgtttt
 I$ANTP_Q6_01           |     7426 (-) |  0.987 |  0.976 | tTTATTtgtttt
 I$ANTP_Q6_01           |     7782 (+) |  0.970 |  0.953 | aacaaaAATTAt
 I$ANTP_Q6_01           |     9866 (+) |  0.934 |  0.920 | aagaagAATGAg
 I$ANTP_Q6_01           |    10142 (-) |  0.987 |  0.984 | aTTATTattatt
 I$ANTP_Q6_01           |    10145 (-) |  0.987 |  0.957 | aTTATTattgtt
 I$ANTP_Q6_01           |    10148 (-) |  0.987 |  0.965 | aTTATTgttgtt
 I$ANTP_Q6_01           |    10331 (-) |  0.911 |  0.938 | tTTATAgttttt
 I$ANTP_Q6_01           |    10503 (+) |  0.970 |  0.921 | aaagtcAATTAt
 I$ANTP_Q6_01           |    11271 (+) |  0.970 |  0.925 | aaaggaAATTAa
 I$ANTP_Q6_01           |    11298 (+) |  0.987 |  0.984 | aataatAATAAc
 I$ANTP_Q6_01           |    11342 (+) |  0.982 |  0.927 | aaatgcCATTAt
 I$ANTP_Q6_01           |    11389 (-) |  0.987 |  0.920 | cTTATTaaattt
 I$ANTP_Q6_01           |    11442 (-) |  0.911 |  0.920 | cTTATCtatttt
 I$ANTP_Q6_01           |    11472 (-) |  0.987 |  0.976 | tTTATTtgtttt
 I$ANTP_Q6_01           |    11666 (+) |  1.000 |  0.933 | aattttCATAAc
 I$ANTP_Q6_01           |    11683 (+) |  0.987 |  0.963 | aagaccAATAAa
 I$BYN_Q6               |    11793 (+) |  0.891 |  0.857 | acaaaTCCCAgattg
 I$CEBP_Q6              |       25 (+) |  1.000 |  0.910 | gaatgTGTGTgaacaacttcaga
 I$CEBP_Q6              |     1115 (+) |  1.000 |  0.859 | tgattTGTGTatgcacgtgtgtt
 I$CEBP_Q6              |     1232 (+) |  0.940 |  0.864 | actgcTTTGAcatcagggcagca
 I$CEBP_Q6              |     1251 (+) |  0.885 |  0.860 | agcatTCTGTcatcatccgtgtg
 I$CEBP_Q6              |     2341 (-) |  0.940 |  0.867 | ccctacgctcttcTCAAActtgt
 I$CEBP_Q6              |     2361 (-) |  1.000 |  0.881 | tgtatttattttgCCACAgtttt
 I$CEBP_Q6              |     4270 (-) |  1.000 |  0.861 | tgcttacctaagcACACAttaga
 I$CEBP_Q6              |     4679 (+) |  1.000 |  0.887 | agttcTGTGGcaggaaacttgat
 I$CEBP_Q6              |     5251 (+) |  1.000 |  0.876 | tcacaTGTGGtcacagtcatcct
 I$CEBP_Q6              |     6062 (-) |  1.000 |  0.871 | cctgcacgtgctgCCACAgtctc
 I$CEBP_Q6              |     6440 (-) |  0.967 |  0.878 | caacccagtcatgGCAAActtat
 I$CEBP_Q6              |     6494 (-) |  1.000 |  0.903 | attgcagatgcggCCACAaataa
 I$CEBP_Q6              |     7782 (-) |  0.967 |  0.926 | aacaaaaattatcCCAAAgataa
 I$CEBP_Q6              |     7897 (+) |  0.940 |  0.880 | tttatTTTGAtattagcttttac
 I$CEBP_Q6              |     7932 (+) |  1.000 |  0.882 | tcgttTGTGTgtttagttttgag
 I$CEBP_Q6              |    11394 (+) |  0.967 |  0.904 | taaatTTTGTacgcatttattct
 I$CEBP_Q6              |    11525 (-) |  1.000 |  0.881 | tccgtagcaaatcCCACAtatgg
 I$CEBP_Q6              |    11649 (-) |  1.000 |  0.909 | ttctgtactgttaACACAatttt
 I$DEAF1_Q6             |     4988 (-) |  1.000 |  0.977 | tgtCCGAAtggc
 I$DEAF1_Q6             |     7182 (-) |  1.000 |  0.959 | gtcCCGAAcggc
 I$DEAF1_Q6             |     9558 (+) |  0.936 |  0.923 | gcctGTCGGttt
 I$KR_Q6                |      553 (+) |  0.878 |  0.904 | ttaaCCTTTtct
 I$KR_Q6                |      624 (+) |  0.930 |  0.920 | atgaCACTTttt
 I$KR_Q6                |      708 (+) |  0.930 |  0.889 | ggatCTCTTtac
 I$KR_Q6                |      816 (+) |  0.930 |  0.914 | ccgaCACTTttt
 I$KR_Q6                |      901 (+) |  0.930 |  0.878 | ttttCACTTtct
 I$KR_Q6                |     2126 (+) |  0.930 |  0.874 | ctctCTCTTtct
 I$KR_Q6                |     2192 (+) |  0.930 |  0.874 | ctctCTCTTtct
 I$KR_Q6                |     2508 (-) |  1.000 |  0.936 | aaaAAGGGaaaa
 I$KR_Q6                |     2656 (+) |  0.930 |  0.873 | aatgCACTTtga
 I$KR_Q6                |     2676 (+) |  0.816 |  0.859 | ttaaCCCGTtgc
 I$KR_Q6                |     3187 (+) |  0.930 |  0.870 | ccctCTCTTtct
 I$KR_Q6                |     3218 (+) |  0.930 |  0.897 | caagCACTTtta
 I$KR_Q6                |     3781 (+) |  1.000 |  0.930 | tcccCCCTTttt
 I$KR_Q6                |     3860 (+) |  0.866 |  0.861 | agtaCCATTtaa
 I$KR_Q6                |     4107 (+) |  0.866 |  0.854 | acatCCATTttc
 I$KR_Q6                |     5159 (-) |  1.000 |  0.930 | gaaAAGGGactt
 I$KR_Q6                |     5350 (+) |  0.930 |  0.874 | tcccCTCTTtga
 I$KR_Q6                |     5428 (+) |  0.930 |  0.868 | cctcCACTTtat
 I$KR_Q6                |     5452 (+) |  0.878 |  0.903 | ataaCCTTTtcc
 I$KR_Q6                |     5540 (+) |  0.930 |  0.872 | cactCTCTTtct
 I$KR_Q6                |     6725 (-) |  1.000 |  0.963 | ttaAAGGGtgag
 I$KR_Q6                |     6736 (+) |  1.000 |  0.946 | gcagCCCTTtga
 I$KR_Q6                |     6755 (+) |  1.000 |  0.948 | ctatCCCTTtat
 I$KR_Q6                |     6818 (+) |  1.000 |  0.934 | ttctCCCTTttt
 I$KR_Q6                |     7848 (-) |  0.917 |  0.867 | caaAAGCGacag
 I$KR_Q6                |     8374 (+) |  0.930 |  0.869 | gctgCTCTTtga
 I$KR_Q6                |     8618 (+) |  0.930 |  0.899 | caatCACTTtga
 I$KR_Q6                |     9721 (+) |  0.930 |  0.898 | tgatCTCTTtgt
 I$KR_Q6                |    10354 (-) |  0.930 |  0.915 | tcaAAGTGtcag
 I$KR_Q6                |    10445 (+) |  0.930 |  0.875 | acgtCTCTTtta
 I$KR_Q6                |    10469 (+) |  0.930 |  0.872 | atctCACTTtag
 I$KR_Q6                |    10628 (-) |  0.930 |  0.870 | agaAAGTGactg
 I$KR_Q6                |    11612 (-) |  1.000 |  0.953 | agaAAGGGgtac
 I$KR_Q6                |    11721 (+) |  0.866 |  0.870 | tccaCCATTttc
 I$KR_Q6                |    11755 (-) |  0.930 |  0.943 | agaAAGAGttaa
 I$MAD_Q6               |     3013 (-) |  0.981 |  0.982 | ggCGTCTc
 I$MAD_Q6               |     5747 (+) |  0.981 |  0.964 | tAGACGca
 I$MAD_Q6               |     6135 (-) |  0.981 |  0.958 | ggCGTCTt
 I$MAD_Q6               |     6383 (+) |  0.981 |  0.964 | tAGACGaa
 I$MAD_Q6               |     7241 (-) |  0.981 |  0.982 | atCGTCTc
 I$MAD_Q6               |     7853 (+) |  0.940 |  0.943 | gCGACAgc
 I$MAD_Q6               |     8565 (-) |  0.981 |  0.958 | tcCGTCTt
 I$MAD_Q6               |     8732 (-) |  1.000 |  0.953 | aaCGTCGg
 I$MAD_Q6               |     9272 (+) |  0.940 |  0.943 | gCGACAgc
 I$MAD_Q6               |    10444 (-) |  0.981 |  0.960 | aaCGTCTc
 I$MAD_Q6               |    10901 (+) |  0.981 |  0.982 | gAGACGct
 I$MAD_Q6               |    11320 (+) |  1.000 |  0.975 | aCGACGat
 I$PRD_Q6               |      992 (-) |  1.000 |  0.986 | atAATTT
 I$PRD_Q6               |     1108 (+) |  0.949 |  0.947 | AAATCgc
 I$PRD_Q6               |     2421 (+) |  0.949 |  0.933 | AAATCac
 I$PRD_Q6               |     2521 (+) |  1.000 |  0.979 | AAATTac
 I$PRD_Q6               |     3108 (-) |  1.000 |  0.959 | ctAATTT
 I$PRD_Q6               |     3128 (-) |  1.000 |  0.972 | ttAATTT
 I$PRD_Q6               |     3471 (-) |  0.949 |  0.939 | atGATTT
 I$PRD_Q6               |     3733 (+) |  1.000 |  0.986 | AAATTat
 I$PRD_Q6               |     4725 (-) |  0.949 |  0.933 | gtGATTT
 I$PRD_Q6               |     7061 (-) |  1.000 |  0.972 | ttAATTT
 I$PRD_Q6               |     7787 (+) |  1.000 |  0.986 | AAATTat
 I$PRD_Q6               |     8858 (+) |  1.000 |  0.972 | AAATTaa
 I$PRD_Q6               |     8954 (+) |  1.000 |  0.959 | AAATTag
 I$PRD_Q6               |     9717 (+) |  1.000 |  0.987 | AAATTga
 I$PRD_Q6               |     9783 (-) |  1.000 |  1.000 | acAATTT
 I$PRD_Q6               |     9837 (-) |  1.000 |  0.986 | atAATTT
 I$PRD_Q6               |     9882 (-) |  1.000 |  0.987 | tcAATTT
 I$PRD_Q6               |     9933 (-) |  1.000 |  0.979 | gtAATTT
 I$PRD_Q6               |    10128 (+) |  1.000 |  0.959 | AAATTag
 I$PRD_Q6               |    10140 (+) |  1.000 |  0.986 | AAATTat
 I$PRD_Q6               |    10264 (-) |  0.949 |  0.933 | gtGATTT
 I$PRD_Q6               |    10586 (-) |  1.000 |  0.987 | tcAATTT
 I$PRD_Q6               |    10815 (+) |  0.949 |  0.947 | AAATCgc
 I$PRD_Q6               |    11208 (-) |  1.000 |  0.972 | ttAATTT
 I$PRD_Q6               |    11276 (+) |  1.000 |  0.972 | AAATTaa
 I$PRD_Q6               |    11664 (-) |  1.000 |  1.000 | acAATTT
 I$TCF_Q6               |      144 (-) |  0.957 |  0.945 | cagacaTTTGCtcatc
 I$TCF_Q6               |      434 (-) |  0.937 |  0.915 | accacgTTTAAtcagg
 I$TCF_Q6               |      452 (-) |  0.964 |  0.956 | gtctgtTTTGGttggc
 I$TCF_Q6               |      646 (-) |  0.901 |  0.910 | tattcaTTTATtatat
 I$TCF_Q6               |      819 (-) |  0.937 |  0.928 | acacttTTTAAtacta
 I$TCF_Q6               |      906 (-) |  0.928 |  0.932 | actttcTTTCAtgcgt
 I$TCF_Q6               |      952 (+) |  1.000 |  0.980 | aatgaTCAAAtattta
 I$TCF_Q6               |      991 (-) |  0.928 |  0.924 | aataatTTTCAtgtgg
 I$TCF_Q6               |     1035 (+) |  0.964 |  0.959 | aatcaACAAAgcagca
 I$TCF_Q6               |     1043 (+) |  0.957 |  0.953 | aagcaGCAAAaatcaa
 I$TCF_Q6               |     1081 (-) |  0.964 |  0.962 | ggtcatTTTGGtcaac
 I$TCF_Q6               |     1470 (-) |  0.957 |  0.936 | tcaataTTTGCtctgg
 I$TCF_Q6               |     1529 (-) |  0.964 |  0.959 | tgttttTTTGTtctaa
 I$TCF_Q6               |     1885 (-) |  0.928 |  0.924 | ctcccaTTTTAtattt
 I$TCF_Q6               |     1896 (-) |  0.928 |  0.927 | tatttaTTTTAttatt
 I$TCF_Q6               |     1897 (-) |  0.901 |  0.916 | atttatTTTATtattt
 I$TCF_Q6               |     1904 (-) |  0.928 |  0.916 | ttattaTTTTAtttga
 I$TCF_Q6               |     2024 (+) |  0.937 |  0.929 | tgggaTTAAAggagtg
 I$TCF_Q6               |     2178 (-) |  0.891 |  0.910 | ccttctTTTCTtctct
 I$TCF_Q6               |     2411 (+) |  0.964 |  0.962 | aaaaaACAAAaaatca
 I$TCF_Q6               |     2579 (+) |  0.964 |  0.949 | ttacaACAAAtgcagt
 I$TCF_Q6               |     2598 (+) |  0.937 |  0.931 | gactaTTAAAccaaga
 I$TCF_Q6               |     2657 (-) |  1.000 |  0.978 | atgcacTTTGAtgaca
 I$TCF_Q6               |     2896 (-) |  0.928 |  0.932 | catcttTTTTAtccac
 I$TCF_Q6               |     3403 (+) |  0.928 |  0.933 | agttaTAAAAgttaat
 I$TCF_Q6               |     3449 (+) |  0.901 |  0.910 | agttaATAAAacacag
 I$TCF_Q6               |     3450 (+) |  0.928 |  0.920 | gttaaTAAAAcacagg
 I$TCF_Q6               |     3535 (-) |  0.964 |  0.935 | ccgaggTTTGGttctg
 I$TCF_Q6               |     3725 (+) |  0.901 |  0.911 | ggtgaCTAAAattatt
 I$TCF_Q6               |     3845 (+) |  0.928 |  0.912 | tctcaTAAAAtatcca
 I$TCF_Q6               |     3991 (+) |  0.928 |  0.910 | tctcaTGAAAcaacga
 I$TCF_Q6               |     4060 (+) |  0.937 |  0.938 | aataaTTAAAatatgt
 I$TCF_Q6               |     4488 (+) |  0.964 |  0.952 | tttgaACAAAaaacaa
 I$TCF_Q6               |     4495 (+) |  0.964 |  0.969 | aaaaaACAAAacaaaa
 I$TCF_Q6               |     4500 (+) |  0.964 |  0.969 | acaaaACAAAacaaca
 I$TCF_Q6               |     4524 (+) |  0.964 |  0.952 | agacaACAAAtgcgtc
 I$TCF_Q6               |     4548 (-) |  1.000 |  0.981 | cttagtTTTGAtgctg
 I$TCF_Q6               |     4633 (+) |  0.957 |  0.951 | gggtaGCAAAatcccg
 I$TCF_Q6               |     4659 (-) |  0.964 |  0.958 | tcggacTTTGTtttgc
 I$TCF_Q6               |     4664 (-) |  0.957 |  0.952 | ctttgtTTTGCtcata
 I$TCF_Q6               |     4809 (-) |  0.964 |  0.942 | ctggcaTTTGTtacca
 I$TCF_Q6               |     4870 (+) |  0.957 |  0.940 | cagcaGCAAAgctctg
 I$TCF_Q6               |     5380 (-) |  0.928 |  0.918 | ttttagTTTTAtttta
 I$TCF_Q6               |     5381 (-) |  0.901 |  0.915 | tttagtTTTATtttac
 I$TCF_Q6               |     5401 (-) |  0.928 |  0.924 | atatttTTTCAtctta
 I$TCF_Q6               |     5412 (+) |  0.937 |  0.920 | tcttaTTAAAtctttc
 I$TCF_Q6               |     5479 (-) |  1.000 |  0.988 | tgatttTTTGAtcccc
 I$TCF_Q6               |     5588 (+) |  0.928 |  0.925 | aataaTAAAAtataat
 I$TCF_Q6               |     5643 (+) |  0.901 |  0.914 | acaaaATAAAaagaag
 I$TCF_Q6               |     5644 (+) |  0.928 |  0.928 | caaaaTAAAAagaaga
 I$TCF_Q6               |     5652 (+) |  0.891 |  0.911 | aaagaAGAAAagaaca
 I$TCF_Q6               |     5782 (+) |  0.928 |  0.925 | aaataTGAAAtaatta
 I$TCF_Q6               |     5790 (+) |  0.937 |  0.933 | aataaTTAAAtacaaa
 I$TCF_Q6               |     5908 (-) |  0.964 |  0.945 | gagtagTTTGTttccc
 I$TCF_Q6               |     5947 (-) |  0.928 |  0.920 | gtaaaaTTTTAtttgc
 I$TCF_Q6               |     6372 (-) |  0.964 |  0.948 | gcgagaTTTGGtagac
 I$TCF_Q6               |     6424 (-) |  0.928 |  0.933 | tctggcTTTCAtcggt
 I$TCF_Q6               |     6465 (+) |  0.928 |  0.911 | cctgaTAAAAtgctca
 I$TCF_Q6               |     6509 (+) |  0.928 |  0.930 | acaaaTAAAAgaacac
 I$TCF_Q6               |     6587 (+) |  0.964 |  0.952 | acaaaACAAAtaaggt
 I$TCF_Q6               |     6604 (-) |  0.957 |  0.942 | gtgctaTTTGCtaaac
 I$TCF_Q6               |     6664 (-) |  0.928 |  0.913 | tgaagaTTTTAtttag
 I$TCF_Q6               |     6769 (+) |  0.964 |  0.949 | catgaACAAAacagca
 I$TCF_Q6               |     6782 (+) |  0.917 |  0.914 | gcagaTCTAAtgctgg
 I$TCF_Q6               |     6821 (-) |  0.928 |  0.930 | tcccttTTTTAtgtgc
 I$TCF_Q6               |     7059 (-) |  0.964 |  0.947 | tcttaaTTTGTttttg
 I$TCF_Q6               |     7065 (-) |  0.964 |  0.950 | tttgttTTTGTttgtg
 I$TCF_Q6               |     7210 (+) |  0.964 |  0.958 | attgaACAAAaagtag
 I$TCF_Q6               |     7258 (+) |  0.937 |  0.929 | tctcaTTAAAatatcc
 I$TCF_Q6               |     7424 (-) |  0.964 |  0.948 | ggtttaTTTGTtttta
 I$TCF_Q6               |     7429 (-) |  0.928 |  0.929 | atttgtTTTTAtttta
 I$TCF_Q6               |     7430 (-) |  0.901 |  0.914 | tttgttTTTATtttat
 I$TCF_Q6               |     7434 (-) |  0.928 |  0.929 | tttttaTTTTAtgtgt
 I$TCF_Q6               |     7566 (+) |  0.964 |  0.952 | ggaaaCCAAAtcccca
 I$TCF_Q6               |     7586 (+) |  0.964 |  0.948 | gtcaaACAAAtgctct
 I$TCF_Q6               |     7773 (+) |  0.964 |  0.969 | aaaaaACAAAacaaaa
 I$TCF_Q6               |     7778 (+) |  0.964 |  0.960 | acaaaACAAAaattat
 I$TCF_Q6               |     7820 (+) |  0.964 |  0.939 | ccaaaACAAAcaatta
 I$TCF_Q6               |     7884 (-) |  0.964 |  0.955 | aagtcaTTTGGttttt
 I$TCF_Q6               |     7890 (-) |  0.928 |  0.926 | tttggtTTTTAttttg
 I$TCF_Q6               |     7896 (-) |  1.000 |  0.989 | ttttatTTTGAtatta
 I$TCF_Q6               |     7968 (-) |  0.964 |  0.949 | tagttgTTTGTttttc
 I$TCF_Q6               |     8183 (-) |  0.957 |  0.942 | aacttgTTTGCtctgc
 I$TCF_Q6               |     8334 (-) |  0.957 |  0.941 | ccagtaTTTGCtggac
 I$TCF_Q6               |     8375 (-) |  1.000 |  0.989 | ctgctcTTTGAtctgt
 I$TCF_Q6               |     8464 (+) |  0.917 |  0.917 | tctcaTCTAAggcaaa
 I$TCF_Q6               |     8565 (-) |  1.000 |  0.977 | tccgtcTTTGAttaaa
 I$TCF_Q6               |     8571 (+) |  0.937 |  0.920 | tttgaTTAAAtggggc
 I$TCF_Q6               |     8593 (-) |  0.937 |  0.928 | aacatcTTTAAtatta
 I$TCF_Q6               |     8834 (+) |  0.964 |  0.951 | caaaaCCAAAacagaa
 I$TCF_Q6               |     8885 (+) |  1.000 |  0.973 | tagaaTCAAAcgtacc
 I$TCF_Q6               |     8933 (+) |  0.901 |  0.915 | ataaaCTAAAgcaact
 I$TCF_Q6               |     8985 (-) |  0.937 |  0.927 | cacaccTTTAAttcca
 I$TCF_Q6               |     9104 (+) |  0.957 |  0.952 | caaaaGCAAAacaaaa
 I$TCF_Q6               |     9109 (+) |  0.964 |  0.960 | gcaaaACAAAaaaccg
 I$TCF_Q6               |     9532 (+) |  0.964 |  0.937 | ctagaACAAAcaagtc
 I$TCF_Q6               |     9782 (-) |  0.964 |  0.958 | aacaatTTTGTtcagt
 I$TCF_Q6               |     9858 (+) |  0.937 |  0.924 | cagcaTTAAAgaagaa
 I$TCF_Q6               |    10311 (-) |  0.928 |  0.933 | aactgtTTTTAtattt
 I$TCF_Q6               |    10319 (-) |  0.928 |  0.925 | ttatatTTTTAtttta
 I$TCF_Q6               |    10320 (-) |  0.901 |  0.915 | tatattTTTATtttat
 I$TCF_Q6               |    10324 (-) |  0.928 |  0.926 | tttttaTTTTAtagtt
 I$TCF_Q6               |    10333 (-) |  0.928 |  0.934 | tatagtTTTTAttgtt
 I$TCF_Q6               |    10342 (-) |  0.937 |  0.935 | tattgtTTTAAttcaa
 I$TCF_Q6               |    10389 (+) |  0.928 |  0.924 | ccataTAAAAatgaac
 I$TCF_Q6               |    10446 (-) |  0.928 |  0.926 | cgtctcTTTTAtatca
 I$TCF_Q6               |    10495 (+) |  1.000 |  0.991 | aaggaTCAAAagtcaa
 I$TCF_Q6               |    10569 (-) |  0.957 |  0.933 | acagcgTTTGCtttgg
 I$TCF_Q6               |    10574 (-) |  0.964 |  0.954 | gtttgcTTTGGttcaa
 I$TCF_Q6               |    10594 (+) |  1.000 |  0.978 | ctataTCAAAaaggag
 I$TCF_Q6               |    10704 (+) |  0.928 |  0.915 | gtttaTGAAAcatctc
 I$TCF_Q6               |    10727 (-) |  0.928 |  0.922 | tgtagcTTTTAttggg
 I$TCF_Q6               |    10807 (+) |  0.917 |  0.918 | gtgcaTCTAAatcgca
 I$TCF_Q6               |    11047 (-) |  0.964 |  0.953 | ggttccTTTGTtaacg
 I$TCF_Q6               |    11151 (+) |  0.928 |  0.926 | tctgaTGAAAatgaag
 I$TCF_Q6               |    11206 (-) |  0.964 |  0.947 | tattaaTTTGTttgaa
 I$TCF_Q6               |    11224 (-) |  0.964 |  0.939 | gcccagTTTGTtctaa
 I$TCF_Q6               |    11388 (+) |  0.937 |  0.929 | acttaTTAAAttttgt
 I$TCF_Q6               |    11445 (-) |  0.964 |  0.959 | atctatTTTGGtgaat
 I$TCF_Q6               |    11465 (-) |  0.928 |  0.930 | gaaattTTTTAtttgt
 I$TCF_Q6               |    11470 (-) |  0.964 |  0.957 | tttttaTTTGTttttc
 I$TCF_Q6               |    11526 (+) |  0.957 |  0.932 | ccgtaGCAAAtcccac
 I$TCF_Q6               |    11558 (+) |  0.964 |  0.937 | ttcaaCCAAActctta
 I$TCF_Q6               |    11663 (-) |  0.928 |  0.927 | cacaatTTTCAtaacc
 I$TCF_Q6               |    11672 (+) |  0.964 |  0.946 | cataaCCAAAaaagac
 I$TCF_Q6               |    11740 (+) |  0.964 |  0.945 | tctcaCCAAAtgacta
 I$ABDB_Q6              |      835 (+) |  1.000 |  0.916 | tATAAAa
 I$ABDB_Q6              |      912 (-) |  0.868 |  0.896 | tTTCATg
 I$ABDB_Q6              |      997 (-) |  0.868 |  0.896 | tTTCATg
 I$ABDB_Q6              |     1891 (-) |  1.000 |  0.916 | tTTTATa
 I$ABDB_Q6              |     1902 (-) |  1.000 |  0.949 | tTTTATt
 I$ABDB_Q6              |     1910 (-) |  1.000 |  0.949 | tTTTATt
 I$ABDB_Q6              |     2902 (-) |  1.000 |  0.916 | tTTTATc
 I$ABDB_Q6              |     3406 (+) |  1.000 |  0.916 | tATAAAa
 I$ABDB_Q6              |     3453 (+) |  1.000 |  0.949 | aATAAAa
 I$ABDB_Q6              |     3848 (+) |  1.000 |  1.000 | cATAAAa
 I$ABDB_Q6              |     3994 (+) |  0.868 |  0.896 | cATGAAa
 I$ABDB_Q6              |     4317 (+) |  1.000 |  1.000 | cATAAAa
 I$ABDB_Q6              |     5386 (-) |  1.000 |  0.949 | tTTTATt
 I$ABDB_Q6              |     5591 (+) |  1.000 |  0.949 | aATAAAa
 I$ABDB_Q6              |     5647 (+) |  1.000 |  0.949 | aATAAAa
 I$ABDB_Q6              |     5953 (-) |  1.000 |  0.949 | tTTTATt
 I$ABDB_Q6              |     6468 (+) |  1.000 |  0.916 | gATAAAa
 I$ABDB_Q6              |     6512 (+) |  1.000 |  0.949 | aATAAAa
 I$ABDB_Q6              |     6670 (-) |  1.000 |  0.949 | tTTTATt
 I$ABDB_Q6              |     6827 (-) |  1.000 |  1.000 | tTTTATg
 I$ABDB_Q6              |     7435 (-) |  1.000 |  0.949 | tTTTATt
 I$ABDB_Q6              |     7440 (-) |  1.000 |  1.000 | tTTTATg
 I$ABDB_Q6              |     7896 (-) |  1.000 |  0.949 | tTTTATt
 I$ABDB_Q6              |     9427 (+) |  1.000 |  0.896 | cATAAAt
 I$ABDB_Q6              |    10124 (+) |  1.000 |  0.949 | aATAAAa
 I$ABDB_Q6              |    10317 (-) |  1.000 |  0.916 | tTTTATa
 I$ABDB_Q6              |    10325 (-) |  1.000 |  0.949 | tTTTATt
 I$ABDB_Q6              |    10330 (-) |  1.000 |  0.916 | tTTTATa
 I$ABDB_Q6              |    10339 (-) |  1.000 |  0.949 | tTTTATt
 I$ABDB_Q6              |    10392 (+) |  1.000 |  0.916 | tATAAAa
 I$ABDB_Q6              |    10452 (-) |  1.000 |  0.916 | tTTTATa
 I$ABDB_Q6              |    10733 (-) |  1.000 |  0.949 | tTTTATt
 I$ABDB_Q6              |    11471 (-) |  1.000 |  0.949 | tTTTATt
 I$BRK_Q6               |     5820 (-) |  1.000 |  0.992 | cTGGCGt
 I$BRK_Q6               |     7167 (-) |  1.000 |  0.992 | cTGGCGt
 I$BRK_Q6               |     7629 (-) |  1.000 |  0.992 | cTGGCGg
 I$BRK_Q6               |     8331 (+) |  1.000 |  1.000 | gCGCCAg
 I$CAD_Q6               |      228 (+) |  0.990 |  0.984 | tccTTTTTgt
 I$CAD_Q6               |      877 (-) |  0.990 |  0.979 | gcACAAAcac
 I$CAD_Q6               |     1048 (-) |  0.990 |  0.972 | gcAAAAAtca
 I$CAD_Q6               |     1115 (+) |  0.990 |  0.971 | tgaTTTGTgt
 I$CAD_Q6               |     1137 (-) |  0.936 |  0.936 | tcCTAAAacc
 I$CAD_Q6               |     1149 (+) |  1.000 |  0.984 | tacTTTATgt
 I$CAD_Q6               |     1220 (+) |  0.983 |  0.974 | gagTTTCTga
 I$CAD_Q6               |     1530 (+) |  0.990 |  0.981 | gttTTTTTgt
 I$CAD_Q6               |     1718 (+) |  0.962 |  0.961 | cctTTTCCgg
 I$CAD_Q6               |     1961 (+) |  0.990 |  0.987 | cctTTTTTga
 I$CAD_Q6               |     2291 (+) |  0.990 |  0.978 | tagTTTTTgt
 I$CAD_Q6               |     2293 (+) |  0.990 |  0.981 | gttTTTGTgt
 I$CAD_Q6               |     2416 (-) |  0.990 |  0.979 | acAAAAAatc
 I$CAD_Q6               |     2502 (-) |  0.969 |  0.965 | ccGAAAAaaa
 I$CAD_Q6               |     2549 (+) |  0.983 |  0.968 | aggTTTCTgt
 I$CAD_Q6               |     2563 (+) |  0.962 |  0.943 | aaaTTTCCgt
 I$CAD_Q6               |     2736 (+) |  1.000 |  0.992 | gccTTTATgc
 I$CAD_Q6               |     3091 (+) |  0.969 |  0.965 | tatTTTTCga
 I$CAD_Q6               |     3602 (+) |  0.983 |  0.972 | gggTTTCTgc
 I$CAD_Q6               |     3716 (+) |  0.979 |  0.960 | ataTTTACgg
 I$CAD_Q6               |     3761 (-) |  0.926 |  0.933 | tcTTAAAagg
 I$CAD_Q6               |     3847 (-) |  1.000 |  0.992 | tcATAAAata
 I$CAD_Q6               |     3916 (+) |  1.000 |  0.983 | agcTTTATga
 I$CAD_Q6               |     4316 (-) |  1.000 |  0.985 | gcATAAAact
 I$CAD_Q6               |     4493 (-) |  0.990 |  0.980 | acAAAAAaca
 I$CAD_Q6               |     4951 (+) |  0.983 |  0.969 | gacTTTCTgc
 I$CAD_Q6               |     5104 (+) |  0.990 |  0.976 | ttaTTTGTga
 I$CAD_Q6               |     5151 (+) |  0.979 |  0.967 | cagTTTACga
 I$CAD_Q6               |     5157 (-) |  0.969 |  0.962 | acGAAAAggg
 I$CAD_Q6               |     5480 (+) |  0.990 |  0.982 | gatTTTTTga
 I$CAD_Q6               |     5544 (+) |  0.983 |  0.968 | ctcTTTCTgt
 I$CAD_Q6               |     5716 (-) |  0.990 |  0.982 | ccACAAAaac
 I$CAD_Q6               |     5718 (-) |  0.990 |  0.978 | acAAAAAcac
 I$CAD_Q6               |     5750 (-) |  0.969 |  0.966 | acGCAAAgga
 I$CAD_Q6               |     5801 (-) |  0.990 |  0.982 | acAAAAAaaa
 I$CAD_Q6               |     6507 (-) |  0.990 |  0.974 | ccACAAAtaa
 I$CAD_Q6               |     6585 (-) |  0.990 |  0.980 | acACAAAaca
 I$CAD_Q6               |     6825 (+) |  1.000 |  0.991 | tttTTTATgt
 I$CAD_Q6               |     7066 (+) |  0.990 |  0.980 | ttgTTTTTgt
 I$CAD_Q6               |     7072 (+) |  0.990 |  0.980 | ttgTTTGTgt
 I$CAD_Q6               |     7087 (+) |  0.969 |  0.959 | tgcTTTGCgc
 I$CAD_Q6               |     7215 (-) |  0.990 |  0.976 | acAAAAAgta
 I$CAD_Q6               |     7271 (-) |  0.936 |  0.938 | tcCTAAAata
 I$CAD_Q6               |     7366 (-) |  0.983 |  0.973 | gcAGAAAgaa
 I$CAD_Q6               |     7438 (+) |  1.000 |  0.989 | tatTTTATgt
 I$CAD_Q6               |     7771 (-) |  0.990 |  0.983 | tcAAAAAaca
 I$CAD_Q6               |     7783 (-) |  0.990 |  0.971 | acAAAAAtta
 I$CAD_Q6               |     7932 (+) |  0.990 |  0.986 | tcgTTTGTgt
 I$CAD_Q6               |     8076 (-) |  0.983 |  0.969 | gcAGAAActt
 I$CAD_Q6               |     8134 (+) |  0.983 |  0.971 | tgcTTTCTgc
 I$CAD_Q6               |     8475 (-) |  0.990 |  0.974 | gcAAAAAtaa
 I$CAD_Q6               |     8693 (+) |  0.983 |  0.980 | gccTTTCTga
 I$CAD_Q6               |     8899 (-) |  0.990 |  0.976 | ccACAAAcag
 I$CAD_Q6               |     9025 (+) |  0.990 |  0.976 | atcTTTGTga
 I$CAD_Q6               |     9114 (-) |  0.990 |  0.979 | acAAAAAacc
 I$CAD_Q6               |     9135 (+) |  0.990 |  0.976 | cagTTTTTga
 I$CAD_Q6               |     9217 (-) |  0.969 |  0.965 | acGCAAAggc
 I$CAD_Q6               |     9426 (-) |  1.000 |  0.983 | ccATAAAtaa
 I$CAD_Q6               |     9564 (+) |  0.983 |  0.969 | cggTTTCTgg
 I$CAD_Q6               |     9917 (+) |  0.990 |  0.971 | ggaTTTTTgc
 I$CAD_Q6               |     9963 (+) |  0.983 |  0.971 | atgTTTCTgg
 I$CAD_Q6               |    10029 (+) |  0.990 |  0.981 | tagTTTGTga
 I$CAD_Q6               |    10161 (+) |  0.969 |  0.968 | tcgTTTTCgt
 I$CAD_Q6               |    10265 (+) |  0.990 |  0.972 | tgaTTTTTgc
 I$CAD_Q6               |    10599 (-) |  0.990 |  0.987 | tcAAAAAgga
 I$CAD_Q6               |    10702 (+) |  1.000 |  0.990 | gtgTTTATga
 I$CAD_Q6               |    11010 (+) |  0.936 |  0.931 | tgcTTTAGgg
 I$CAD_Q6               |    11175 (+) |  0.990 |  0.974 | atcTTTTTgg
 I$CAD_Q6               |    11176 (+) |  0.926 |  0.936 | tctTTTTGgc
 I$CAD_Q6               |    11501 (+) |  0.990 |  0.970 | gaaTTTTTgt
 I$CAD_Q6               |    11503 (+) |  0.990 |  0.979 | attTTTGTgg
 I$CAD_Q6               |    11645 (+) |  0.983 |  0.966 | gtaTTTCTgt
 I$CAD_Q6               |    11677 (-) |  0.990 |  0.989 | ccAAAAAaga
 I$CF1A_Q6              |      645 (-) |  1.000 |  0.939 | ttattcatttATTATa
 I$CF1A_Q6              |     1891 (-) |  0.877 |  0.882 | ttttatatttATTTTa
 I$CF1A_Q6              |     3820 (-) |  0.911 |  0.947 | ttttcaattcATAATa
 I$CF1A_Q6              |     3829 (+) |  1.000 |  0.883 | cATAATaaatttccat
 I$CF1A_Q6              |     4054 (-) |  1.000 |  0.887 | ataggcaataATTAAa
 I$CF1A_Q6              |     5406 (-) |  1.000 |  0.935 | ttttcatcttATTAAa
 I$CF1A_Q6              |     5588 (+) |  1.000 |  0.875 | aATAATaaaatataat
 I$CF1A_Q6              |     5784 (-) |  1.000 |  0.944 | atatgaaataATTAAa
 I$CF1A_Q6              |     5790 (+) |  1.000 |  0.902 | aATAATtaaatacaaa
 I$CF1A_Q6              |     7636 (+) |  0.947 |  0.945 | tAGAATtattttaaaa
 I$CF1A_Q6              |    10135 (-) |  1.000 |  0.875 | ttaagaaattATTATt
 I$CF1A_Q6              |    11064 (+) |  0.881 |  0.878 | tGTGATcagttacaag
 V$LRF_Q2               |      968 (+) |  0.981 |  0.972 | caggACCCC
 V$LRF_Q2               |     1184 (+) |  1.000 |  0.975 | ggcaCCCCC
 V$LRF_Q2               |     1612 (-) |  1.000 |  0.977 | GGGGGtctc
 V$LRF_Q2               |     1613 (-) |  0.981 |  0.972 | GGGGTctcg
 V$LRF_Q2               |     1840 (-) |  0.981 |  0.969 | GGGGTcgtc
 V$LRF_Q2               |     7197 (-) |  1.000 |  0.975 | GGGGGtgct
 V$LRF_Q2               |     8485 (-) |  1.000 |  0.969 | GGGGGttat
 V$LRF_Q2               |     8805 (-) |  1.000 |  0.987 | GGGGGccag
 V$LRF_Q2               |     9338 (+) |  0.981 |  0.977 | gaggACCCC
 V$LRF_Q2               |    10741 (-) |  1.000 |  0.972 | GGGGGtttc
 I$OVO_Q6               |       69 (-) |  1.000 |  0.928 | taCTGTTg
 I$OVO_Q6               |      127 (+) |  0.987 |  0.967 | tAACTGct
 I$OVO_Q6               |      591 (+) |  1.000 |  0.966 | tAACAGac
 I$OVO_Q6               |      792 (+) |  0.975 |  0.956 | tAACCGct
 I$OVO_Q6               |      984 (-) |  0.987 |  0.978 | caCAGTTa
 I$OVO_Q6               |     1143 (-) |  0.994 |  0.989 | aaCCGTTa
 I$OVO_Q6               |     2545 (+) |  1.000 |  0.978 | tAACAGgt
 I$OVO_Q6               |     3400 (-) |  0.987 |  0.973 | tcCAGTTa
 I$OVO_Q6               |     3445 (+) |  1.000 |  0.994 | tAACAGtt
 I$OVO_Q6               |     3446 (-) |  0.987 |  0.983 | aaCAGTTa
 I$OVO_Q6               |     3510 (-) |  1.000 |  0.984 | tgCTGTTa
 I$OVO_Q6               |     4214 (-) |  0.987 |  0.966 | ctCAGTTa
 I$OVO_Q6               |     4572 (-) |  0.975 |  0.961 | tgCGGTTa
 I$OVO_Q6               |     6571 (-) |  0.987 |  0.978 | caCAGTTa
 I$OVO_Q6               |     8673 (-) |  0.975 |  0.956 | acCGGTTa
 I$OVO_Q6               |     9433 (+) |  1.000 |  0.984 | tAACAGga
 I$OVO_Q6               |    10310 (+) |  0.987 |  0.983 | tAACTGtt
 I$OVO_Q6               |    11068 (-) |  0.987 |  0.971 | atCAGTTa
 I$OVO_Q6               |    11237 (+) |  0.987 |  0.973 | tAACTGga
 I$OVO_Q6               |    11517 (-) |  0.994 |  0.922 | taCCGTTg
 I$OVO_Q6               |    11654 (-) |  1.000 |  1.000 | taCTGTTa
 I$OVO_Q6               |    11764 (+) |  1.000 |  0.984 | tAACAGga
 I$SD_Q6                |       23 (-) |  1.000 |  0.932 | gtGAATG
 I$SD_Q6                |       51 (+) |  0.934 |  0.939 | CATTAct
 I$SD_Q6                |      156 (+) |  0.930 |  0.936 | CATCTct
 I$SD_Q6                |      179 (+) |  0.934 |  0.939 | CATTAct
 I$SD_Q6                |      331 (-) |  0.940 |  0.941 | ggAAATT
 I$SD_Q6                |      334 (+) |  0.940 |  0.941 | AATTCcc
 I$SD_Q6                |      382 (-) |  0.930 |  0.936 | agAGATG
 I$SD_Q6                |      390 (+) |  1.000 |  0.936 | CATTCat
 I$SD_Q6                |      409 (-) |  1.000 |  0.996 | cgGAATG
 I$SD_Q6                |      490 (+) |  0.926 |  0.931 | CATTGca
 I$SD_Q6                |      526 (-) |  1.000 |  0.929 | aaAAATG
 I$SD_Q6                |      642 (+) |  1.000 |  0.936 | CATTTat
 I$SD_Q6                |      650 (+) |  1.000 |  0.936 | CATTTat
 I$SD_Q6                |      749 (-) |  0.940 |  0.941 | ggGAATT
 I$SD_Q6                |      804 (+) |  1.000 |  1.000 | CATTTct
 I$SD_Q6                |      871 (-) |  1.000 |  1.000 | agAAATG
 I$SD_Q6                |      886 (-) |  1.000 |  0.996 | cgAAATG
 I$SD_Q6                |     1177 (-) |  0.930 |  0.932 | ggAGATG
 I$SD_Q6                |     1211 (+) |  0.926 |  0.932 | CATTGct
 I$SD_Q6                |     1279 (-) |  0.930 |  0.935 | tgGGATG
 I$SD_Q6                |     1574 (-) |  1.000 |  0.996 | ggGAATG
 I$SD_Q6                |     1795 (+) |  1.000 |  0.932 | CATTCac
 I$SD_Q6                |     1889 (+) |  1.000 |  0.928 | CATTTta
 I$SD_Q6                |     2010 (+) |  0.930 |  0.932 | CATCTcc
 I$SD_Q6                |     2561 (-) |  0.940 |  0.944 | tgAAATT
 I$SD_Q6                |     2564 (+) |  0.940 |  0.941 | AATTTcc
 I$SD_Q6                |     2653 (-) |  0.934 |  0.935 | cgTAATG
 I$SD_Q6                |     2848 (+) |  1.000 |  0.996 | CATTCcg
 I$SD_Q6                |     2911 (+) |  0.930 |  0.936 | CATCTct
 I$SD_Q6                |     3052 (+) |  0.923 |  0.929 | CATACct
 I$SD_Q6                |     3110 (+) |  0.940 |  0.941 | AATTTcc
 I$SD_Q6                |     3136 (+) |  1.000 |  0.996 | CATTCcc
 I$SD_Q6                |     3163 (+) |  1.000 |  0.996 | CATTCcg
 I$SD_Q6                |     3242 (+) |  1.000 |  0.996 | CATTCcc
 I$SD_Q6                |     3286 (-) |  0.930 |  0.935 | tgGGATG
 I$SD_Q6                |     3300 (+) |  0.930 |  0.932 | CATCTcc
 I$SD_Q6                |     3337 (+) |  0.932 |  0.934 | TATTTcc
 I$SD_Q6                |     3701 (-) |  0.930 |  0.936 | agAGATG
 I$SD_Q6                |     3740 (+) |  0.932 |  0.938 | TATTTct
 I$SD_Q6                |     3748 (+) |  1.000 |  0.929 | CATTTtt
 I$SD_Q6                |     3758 (+) |  1.000 |  0.929 | CATTCtt
 I$SD_Q6                |     3836 (+) |  0.940 |  0.941 | AATTTcc
 I$SD_Q6                |     3865 (+) |  1.000 |  0.935 | CATTTaa
 I$SD_Q6                |     3948 (+) |  1.000 |  0.932 | CATTCag
 I$SD_Q6                |     3989 (+) |  0.930 |  0.935 | CATCTca
 I$SD_Q6                |     4028 (-) |  0.940 |  0.944 | tgGAATT
 I$SD_Q6                |     4037 (+) |  0.932 |  0.937 | TATTCca
 I$SD_Q6                |     4050 (-) |  0.932 |  0.934 | ggAAATA
 I$SD_Q6                |     4075 (-) |  1.000 |  0.928 | taAAATG
 I$SD_Q6                |     4458 (+) |  1.000 |  0.999 | CATTTca
 I$SD_Q6                |     4479 (+) |  1.000 |  0.929 | CATTTtt
 I$SD_Q6                |     4889 (+) |  1.000 |  0.999 | CATTCca
 I$SD_Q6                |     5031 (-) |  0.930 |  0.935 | tgGGATG
 I$SD_Q6                |     5069 (-) |  0.930 |  0.936 | agAGATG
 I$SD_Q6                |     5348 (+) |  0.930 |  0.932 | CATCCcc
 I$SD_Q6                |     5472 (+) |  0.932 |  0.934 | TATTTcc
 I$SD_Q6                |     5787 (-) |  0.932 |  0.937 | tgAAATA
 I$SD_Q6                |     5844 (+) |  0.930 |  0.932 | CATCTcc
 I$SD_Q6                |     5876 (+) |  0.930 |  0.932 | CATCTcc
 I$SD_Q6                |     5995 (-) |  0.930 |  0.936 | agGGATG
 I$SD_Q6                |     6194 (+) |  1.000 |  0.935 | CATTTaa
 I$SD_Q6                |     6460 (+) |  0.932 |  0.934 | TATTTcc
 I$SD_Q6                |     6470 (-) |  1.000 |  0.928 | taAAATG
 I$SD_Q6                |     6811 (+) |  0.934 |  0.935 | CATTAcc
 I$SD_Q6                |     6920 (-) |  0.940 |  0.945 | agGAATT
 I$SD_Q6                |     6996 (-) |  0.930 |  0.932 | ggAGATG
 I$SD_Q6                |     7122 (-) |  0.926 |  0.931 | tgCAATG
 I$SD_Q6                |     7317 (-) |  1.000 |  0.928 | taGAATG
 I$SD_Q6                |     7344 (+) |  1.000 |  0.999 | CATTTca
 I$SD_Q6                |     7614 (+) |  0.930 |  0.936 | CATCTct
 I$SD_Q6                |     7648 (-) |  1.000 |  0.929 | aaAAATG
 I$SD_Q6                |     8576 (-) |  1.000 |  0.935 | ttAAATG
 I$SD_Q6                |     8610 (+) |  1.000 |  0.996 | CATTCcg
 I$SD_Q6                |     8651 (+) |  0.940 |  0.941 | AATTCcc
 I$SD_Q6                |     8913 (-) |  0.932 |  0.938 | agGAATA
 I$SD_Q6                |     8922 (-) |  0.940 |  0.941 | cgGAATT
 I$SD_Q6                |     8994 (+) |  0.940 |  0.944 | AATTCca
 I$SD_Q6                |     9395 (-) |  1.000 |  0.999 | tgGAATG
 I$SD_Q6                |     9796 (-) |  1.000 |  0.932 | gtAAATG
 I$SD_Q6                |     9869 (-) |  1.000 |  0.929 | aaGAATG
 I$SD_Q6                |    10117 (+) |  0.930 |  0.932 | CATCCcc
 I$SD_Q6                |    10138 (-) |  0.940 |  0.945 | agAAATT
 I$SD_Q6                |    10303 (+) |  1.000 |  0.929 | CATTTtt
 I$SD_Q6                |    10395 (-) |  1.000 |  0.929 | aaAAATG
 I$SD_Q6                |    10416 (+) |  1.000 |  0.929 | CATTTtt
 I$SD_Q6                |    10468 (+) |  0.930 |  0.935 | CATCTca
 I$SD_Q6                |    10489 (+) |  0.923 |  0.928 | CATATca
 I$SD_Q6                |    10588 (+) |  0.940 |  0.941 | AATTTcc
 I$SD_Q6                |    10714 (+) |  0.930 |  0.936 | CATCTct
 I$SD_Q6                |    10792 (-) |  0.930 |  0.932 | ggGGATG
 I$SD_Q6                |    10862 (-) |  0.930 |  0.936 | agAGATG
 I$SD_Q6                |    11087 (-) |  0.940 |  0.941 | ggGAATT
 I$SD_Q6                |    11274 (-) |  0.940 |  0.941 | ggAAATT
 I$SD_Q6                |    11295 (-) |  0.932 |  0.938 | agAAATA
 I$SD_Q6                |    11340 (-) |  1.000 |  0.932 | gtAAATG
 I$SD_Q6                |    11407 (+) |  1.000 |  0.936 | CATTTat
 I$SD_Q6                |    11418 (+) |  1.000 |  1.000 | CATTTct
 I$SD_Q6                |    11464 (-) |  0.940 |  0.944 | tgAAATT
 I$SD_Q6                |    11489 (-) |  1.000 |  0.999 | tgGAATG
 I$SD_Q6                |    11575 (+) |  0.926 |  0.932 | CATTGct
 I$SD_Q6                |    11639 (-) |  1.000 |  0.935 | ttAAATG
 I$SD_Q6                |    11646 (+) |  0.932 |  0.938 | TATTTct
 I$SD_Q6                |    11738 (+) |  0.930 |  0.935 | CATCTca
 I$SD_Q6                |    11943 (+) |  0.932 |  0.937 | TATTTca
 I$TWI_Q6               |      711 (-) |  0.951 |  0.886 | tctctttACAGAtg
 I$TWI_Q6               |     1130 (+) |  1.000 |  0.874 | cgTGTGTtcctaaa
 I$TWI_Q6               |     2577 (-) |  0.941 |  0.888 | atttacaACAAAtg
 I$TWI_Q6               |     4522 (-) |  0.941 |  0.879 | caagacaACAAAtg
 I$TWI_Q6               |     5121 (-) |  0.951 |  0.879 | aaaggaaACAGAtg
 I$TWI_Q6               |     5359 (-) |  1.000 |  0.917 | tgacaaaACACAcg
 I$TWI_Q6               |     6093 (+) |  1.000 |  0.885 | ccTGTGTggatcag
 I$TWI_Q6               |     6395 (+) |  1.000 |  0.900 | ccTGTGTtcagaac
 I$TWI_Q6               |     7116 (+) |  1.000 |  0.904 | caTGTGTgcaatgc
 I$TWI_Q6               |     7490 (+) |  0.951 |  0.882 | cgTCTGTtcttctt
 I$TWI_Q6               |     7584 (-) |  0.941 |  0.894 | aggtcaaACAAAtg
 I$TWI_Q6               |     8971 (+) |  0.917 |  0.894 | caGGTGTggtggta
 I$TWI_Q6               |     9145 (-) |  0.980 |  0.910 | ataagacACATAtg
 I$TWI_Q6               |     9153 (+) |  0.980 |  0.898 | caTATGTgagttcc
 I$TWI_Q6               |     9802 (-) |  0.980 |  0.879 | gtacatcACATAag
 I$TWI_Q6               |    10757 (+) |  1.000 |  0.890 | cgTGTGTttgggca
 I$TWI_Q6               |    11533 (-) |  0.980 |  0.880 | aaatcccACATAtg
 V$MOVOB_01             |      103 (+) |  1.000 |  0.959 | ctGGGGG
 V$MOVOB_01             |      194 (-) |  0.906 |  0.910 | CTCCCac
 V$MOVOB_01             |      196 (-) |  0.938 |  0.941 | CCCACac
 V$MOVOB_01             |     1001 (+) |  0.938 |  0.900 | atGTGGG
 V$MOVOB_01             |     1188 (-) |  1.000 |  0.959 | CCCCCag
 V$MOVOB_01             |     1404 (+) |  0.938 |  0.939 | gaGTGGG
 V$MOVOB_01             |     1488 (+) |  0.906 |  0.908 | gaGGGAG
 V$MOVOB_01             |     1492 (+) |  1.000 |  0.998 | gaGGGGG
 V$MOVOB_01             |     1493 (+) |  1.000 |  0.958 | agGGGGG
 V$MOVOB_01             |     1494 (+) |  1.000 |  0.998 | ggGGGGG
 V$MOVOB_01             |     1495 (+) |  1.000 |  0.998 | ggGGGGG
 V$MOVOB_01             |     1496 (+) |  1.000 |  0.998 | ggGGGGG
 V$MOVOB_01             |     1497 (+) |  1.000 |  0.998 | ggGGGGG
 V$MOVOB_01             |     1499 (+) |  0.906 |  0.908 | ggGGGAG
 V$MOVOB_01             |     1503 (+) |  0.906 |  0.908 | gaGGGAG
 V$MOVOB_01             |     1507 (+) |  0.906 |  0.908 | gaGGGAG
 V$MOVOB_01             |     1511 (+) |  0.906 |  0.908 | gaGGGAG
 V$MOVOB_01             |     1515 (+) |  0.906 |  0.908 | gaGGGAG
 V$MOVOB_01             |     1610 (+) |  1.000 |  0.957 | caGGGGG
 V$MOVOB_01             |     3140 (-) |  0.938 |  0.903 | CCCACaa
 V$MOVOB_01             |     3184 (-) |  1.000 |  0.958 | CCCCCct
 V$MOVOB_01             |     3185 (-) |  1.000 |  0.998 | CCCCCtc
 V$MOVOB_01             |     3782 (-) |  1.000 |  0.958 | CCCCCct
 V$MOVOB_01             |     3783 (-) |  1.000 |  0.957 | CCCCCtt
 V$MOVOB_01             |     4045 (+) |  1.000 |  0.957 | caGGGGG
 V$MOVOB_01             |     4861 (+) |  0.906 |  0.908 | gaGGGAG
 V$MOVOB_01             |     5463 (-) |  0.938 |  0.900 | CCCACat
 V$MOVOB_01             |     5690 (-) |  0.938 |  0.901 | CCCACta
 V$MOVOB_01             |     5715 (-) |  0.938 |  0.903 | CCCACaa
 V$MOVOB_01             |     6625 (+) |  0.938 |  0.939 | gaGTGGG
 V$MOVOB_01             |     6751 (-) |  0.938 |  0.901 | CCCACta
 V$MOVOB_01             |     7195 (+) |  1.000 |  0.960 | acGGGGG
 V$MOVOB_01             |     7446 (+) |  0.938 |  0.941 | gtGTGGG
 V$MOVOB_01             |     7448 (+) |  0.906 |  0.910 | gtGGGAG
 V$MOVOB_01             |     8116 (-) |  0.906 |  0.910 | CTCCCac
 V$MOVOB_01             |     8118 (-) |  0.938 |  0.939 | CCCACcc
 V$MOVOB_01             |     8232 (-) |  0.906 |  0.910 | CTCCCac
 V$MOVOB_01             |     8234 (-) |  0.938 |  0.941 | CCCACac
 V$MOVOB_01             |     8483 (+) |  1.000 |  0.957 | aaGGGGG
 V$MOVOB_01             |     8750 (-) |  0.938 |  0.941 | CCCACac
 V$MOVOB_01             |     8803 (+) |  1.000 |  0.962 | ttGGGGG
 V$MOVOB_01             |     9311 (+) |  0.906 |  0.908 | gaGGGAG
 V$MOVOB_01             |     9618 (+) |  0.906 |  0.910 | gtGGGAG
 V$MOVOB_01             |     9683 (+) |  1.000 |  0.998 | gaGGGGG
 V$MOVOB_01             |     9684 (+) |  1.000 |  0.958 | agGGGGG
 V$MOVOB_01             |     9685 (+) |  1.000 |  0.998 | ggGGGGG
 V$MOVOB_01             |    10045 (+) |  0.938 |  0.941 | gtGTGGG
 V$MOVOB_01             |    10611 (+) |  0.938 |  0.941 | gtGTGGG
 V$MOVOB_01             |    10613 (+) |  0.906 |  0.910 | gtGGGAG
 V$MOVOB_01             |    10617 (+) |  0.906 |  0.908 | gaGGGAG
 V$MOVOB_01             |    10738 (+) |  1.000 |  0.962 | ttGGGGG
 V$MOVOB_01             |    10739 (+) |  1.000 |  0.960 | tgGGGGG
 V$MOVOB_01             |    10789 (+) |  1.000 |  0.957 | caGGGGG
 V$MOVOB_01             |    10877 (+) |  0.938 |  0.901 | tgGTGGG
 V$MOVOB_01             |    10879 (+) |  0.906 |  0.910 | gtGGGAG
 V$MOVOB_01             |    11537 (-) |  0.938 |  0.900 | CCCACat
 V$MOVOB_01             |    11841 (+) |  0.938 |  0.939 | gaGTGGG
 V$MOVOB_01             |    11843 (+) |  1.000 |  1.000 | gtGGGGG
 V$MOVOB_01             |    11844 (+) |  1.000 |  0.960 | tgGGGGG
 V$MOVOB_01             |    11848 (+) |  0.938 |  0.939 | ggGTGGG
 V$MOVOB_01             |    11857 (+) |  1.000 |  0.959 | atGGGGG
 V$MOVOB_01             |    11869 (+) |  1.000 |  0.960 | ccGGGGG
 V$MOVOB_01             |    11871 (+) |  0.906 |  0.908 | ggGGGAG
 V$RUSH1A_02            |       11 (-) |  0.993 |  0.972 | gtACAAGtac
 V$RUSH1A_02            |      227 (+) |  0.997 |  0.994 | ttcCTTTTtg
 V$RUSH1A_02            |      271 (+) |  0.993 |  0.992 | gtcCTTGTgc
 V$RUSH1A_02            |      401 (-) |  0.993 |  0.986 | caACAAGgcg
 V$RUSH1A_02            |      555 (+) |  0.997 |  0.997 | aacCTTTTct
 V$RUSH1A_02            |      599 (+) |  0.997 |  0.974 | ttaCTTTTta
 V$RUSH1A_02            |      627 (+) |  0.997 |  0.973 | acaCTTTTtt
 V$RUSH1A_02            |      660 (-) |  1.000 |  0.978 | atATAAGtac
 V$RUSH1A_02            |      819 (+) |  0.997 |  0.972 | acaCTTTTta
 V$RUSH1A_02            |      839 (-) |  0.993 |  0.973 | aaACAAGtta
 V$RUSH1A_02            |      897 (+) |  0.997 |  0.970 | agaCTTTTca
 V$RUSH1A_02            |      937 (-) |  0.993 |  0.973 | ccACAAGtta
 V$RUSH1A_02            |     1322 (+) |  0.989 |  0.987 | tccCTTCTca
 V$RUSH1A_02            |     1716 (+) |  0.997 |  0.990 | tgcCTTTTcc
 V$RUSH1A_02            |     1867 (-) |  0.989 |  0.986 | gaAGAAGgga
 V$RUSH1A_02            |     1959 (+) |  0.997 |  0.994 | ttcCTTTTtt
 V$RUSH1A_02            |     2168 (+) |  0.989 |  0.988 | ttcCTTCTtt
 V$RUSH1A_02            |     2176 (+) |  0.989 |  0.988 | ttcCTTCTtt
 V$RUSH1A_02            |     2356 (+) |  0.993 |  0.974 | aaaCTTGTat
 V$RUSH1A_02            |     2507 (-) |  0.997 |  0.993 | aaAAAAGgga
 V$RUSH1A_02            |     2531 (+) |  0.997 |  0.975 | ttaCTTTTag
 V$RUSH1A_02            |     2743 (+) |  0.997 |  0.990 | tgcCTTTTtc
 V$RUSH1A_02            |     3149 (-) |  0.971 |  0.972 | atATATGgag
 V$RUSH1A_02            |     3221 (+) |  0.997 |  0.973 | gcaCTTTTac
 V$RUSH1A_02            |     3252 (+) |  1.000 |  0.976 | ccaCTTATgg
 V$RUSH1A_02            |     3321 (+) |  0.997 |  0.990 | ggcCTTTTcc
 V$RUSH1A_02            |     3379 (-) |  0.971 |  0.970 | tcATATGggg
 V$RUSH1A_02            |     3407 (-) |  0.997 |  0.976 | atAAAAGtta
 V$RUSH1A_02            |     3763 (-) |  0.997 |  0.991 | ttAAAAGgca
 V$RUSH1A_02            |     3784 (+) |  0.997 |  0.992 | cccCTTTTtc
 V$RUSH1A_02            |     3862 (+) |  0.967 |  0.970 | tacCATTTaa
 V$RUSH1A_02            |     3939 (+) |  0.993 |  0.969 | tcaCTTGTtc
 V$RUSH1A_02            |     4187 (-) |  0.989 |  0.984 | gcAGAAGgct
 V$RUSH1A_02            |     4362 (-) |  0.989 |  0.970 | tcAGAAGttt
 V$RUSH1A_02            |     4416 (+) |  0.993 |  0.994 | aacCTTGTct
 V$RUSH1A_02            |     4650 (+) |  0.989 |  0.990 | cacCTTCTct
 V$RUSH1A_02            |     5001 (+) |  0.993 |  0.994 | gacCTTGTat
 V$RUSH1A_02            |     5118 (-) |  0.997 |  0.995 | tcAAAAGgaa
 V$RUSH1A_02            |     5158 (-) |  0.997 |  0.993 | cgAAAAGgga
 V$RUSH1A_02            |     5171 (+) |  0.993 |  0.970 | tcaCTTGTga
 V$RUSH1A_02            |     5454 (+) |  0.997 |  0.997 | aacCTTTTcc
 V$RUSH1A_02            |     5768 (-) |  0.997 |  0.995 | gtAAAAGgag
 V$RUSH1A_02            |     5836 (-) |  0.993 |  0.987 | aaACAAGgca
 V$RUSH1A_02            |     5941 (-) |  0.997 |  0.975 | agAAAAGtaa
 V$RUSH1A_02            |     5982 (+) |  0.989 |  0.969 | taaCTTCTgg
 V$RUSH1A_02            |     6272 (-) |  0.989 |  0.987 | gaAGAAGgaa
 V$RUSH1A_02            |     6455 (+) |  1.000 |  0.979 | aaaCTTATtt
 V$RUSH1A_02            |     6594 (-) |  1.000 |  0.999 | aaATAAGgtg
 V$RUSH1A_02            |     6636 (-) |  0.989 |  0.984 | ccAGAAGgca
 V$RUSH1A_02            |     6814 (+) |  0.989 |  0.990 | tacCTTCTcc
 V$RUSH1A_02            |     6821 (+) |  0.997 |  0.993 | tccCTTTTtt
 V$RUSH1A_02            |     6904 (-) |  1.000 |  0.976 | gcATAAGtgg
 V$RUSH1A_02            |     6915 (-) |  0.993 |  0.991 | gaACAAGgaa
 V$RUSH1A_02            |     7002 (-) |  0.997 |  0.990 | ggAAAAGgca
 V$RUSH1A_02            |     7216 (-) |  0.997 |  0.974 | caAAAAGtag
 V$RUSH1A_02            |     7251 (-) |  0.997 |  0.970 | gaAAAAGtct
 V$RUSH1A_02            |     7413 (+) |  0.997 |  0.976 | gaaCTTTTaa
 V$RUSH1A_02            |     7713 (-) |  0.989 |  0.988 | gcAGAAGgat
 V$RUSH1A_02            |     8182 (+) |  0.993 |  0.973 | gaaCTTGTtt
 V$RUSH1A_02            |     8479 (-) |  1.000 |  0.996 | aaATAAGggg
 V$RUSH1A_02            |     8754 (+) |  0.993 |  0.993 | cacCTTGTcc
 V$RUSH1A_02            |     8944 (+) |  0.997 |  0.975 | caaCTTTTta
 V$RUSH1A_02            |     9662 (+) |  0.993 |  0.993 | gacCTTGTct
 V$RUSH1A_02            |     9809 (-) |  1.000 |  0.978 | acATAAGtaa
 V$RUSH1A_02            |     9828 (-) |  0.989 |  0.987 | ttAGAAGgga
 V$RUSH1A_02            |    10169 (+) |  1.000 |  0.997 | gtcCTTATta
 V$RUSH1A_02            |    10387 (+) |  0.971 |  0.972 | atcCATATaa
 V$RUSH1A_02            |    10500 (-) |  0.997 |  0.970 | tcAAAAGtca
 V$RUSH1A_02            |    10600 (-) |  0.997 |  0.994 | caAAAAGgag
 V$RUSH1A_02            |    10801 (+) |  0.993 |  0.987 | agcCTTGTgc
 V$RUSH1A_02            |    10826 (+) |  0.997 |  0.990 | cgcCTTTTca
 V$RUSH1A_02            |    11186 (+) |  0.993 |  0.987 | tgcCTTGTtt
 V$RUSH1A_02            |    11268 (-) |  0.997 |  0.995 | agAAAAGgaa
 V$RUSH1A_02            |    11386 (+) |  1.000 |  0.979 | aaaCTTATta
 V$RUSH1A_02            |    11439 (+) |  1.000 |  0.978 | ataCTTATct
 V$RUSH1A_02            |    11540 (-) |  0.971 |  0.973 | acATATGgta
 V$RUSH1A_02            |    11623 (-) |  0.989 |  0.988 | ccAGAAGgac
 V$RUSH1A_02            |    11723 (+) |  0.967 |  0.969 | cacCATTTtc
 V$HOXA7_01             |     3316 (-) |  1.000 |  1.000 | aGATTGg
 V$HOXA7_01             |     9454 (+) |  1.000 |  1.000 | cCAATCt
 V$HOXA7_01             |    11802 (-) |  1.000 |  1.000 | aGATTGg
 V$SZF11_01             |     1336 (+) |  1.000 |  0.822 | cCAGGGcttaaggct
 V$SZF11_01             |     5763 (+) |  0.878 |  0.813 | gTAGGGtaaaaggag
 V$SZF11_01             |     7504 (+) |  0.896 |  0.811 | gGAGGGtgtcagatg
 V$SZF11_01             |     8276 (-) |  1.000 |  0.823 | atgcagctgCCCTGg
 V$RBPJK_Q4             |     3138 (+) |  1.000 |  0.988 | TTCCCaca
 V$RBPJK_01             |     3137 (-) |  1.000 |  0.934 | atTCCCAcaac
 V$RBPJK_01             |     6218 (-) |  0.914 |  0.941 | ttTCTCAcgct
 V$CACD_01              |      105 (-) |  0.960 |  0.973 | GGGGGtgg
 V$CACD_01              |      197 (+) |  0.768 |  0.843 | ccaCACCA
 V$CACD_01              |      535 (-) |  1.000 |  0.844 | GGGTGatg
 V$CACD_01              |     1185 (+) |  0.960 |  0.833 | gcaCCCCC
 V$CACD_01              |     1381 (-) |  0.983 |  0.925 | GGGCGagg
 V$CACD_01              |     1490 (-) |  0.948 |  0.917 | GGGAGggg
 V$CACD_01              |     1494 (-) |  0.960 |  0.925 | GGGGGggg
 V$CACD_01              |     1495 (-) |  0.960 |  0.925 | GGGGGggg
 V$CACD_01              |     1496 (-) |  0.960 |  0.925 | GGGGGggg
 V$CACD_01              |     1499 (-) |  0.960 |  0.909 | GGGGGagg
 V$CACD_01              |     1598 (-) |  0.766 |  0.841 | GGGTTtgg
 V$CACD_01              |     1813 (-) |  1.000 |  0.860 | GGGTGgtg
 V$CACD_01              |     2431 (-) |  0.848 |  0.849 | GGTTGggg
 V$CACD_01              |     3040 (+) |  1.000 |  0.835 | ctcCACCC
 V$CACD_01              |     3288 (-) |  0.859 |  0.841 | GGATGagg
 V$CACD_01              |     4142 (-) |  0.784 |  0.853 | AGGTGtgg
 V$CACD_01              |     4239 (-) |  0.870 |  0.864 | GGCTGggg
 V$CACD_01              |     4326 (-) |  0.751 |  0.831 | GGGTCtgg
 V$CACD_01              |     4343 (-) |  0.808 |  0.870 | GGTGGtgg
 V$CACD_01              |     4412 (+) |  0.848 |  0.897 | ccaCAACC
 V$CACD_01              |     4748 (+) |  0.948 |  0.901 | cctCTCCC
 V$CACD_01              |     5821 (-) |  0.751 |  0.831 | TGGCGtgg
 V$CACD_01              |     5997 (-) |  0.859 |  0.857 | GGATGggg
 V$CACD_01              |     6481 (-) |  0.859 |  0.841 | GGATGagg
 V$CACD_01              |     6547 (-) |  0.870 |  0.848 | GGCTGagg
 V$CACD_01              |     6716 (+) |  0.848 |  0.897 | ccaCAACC
 V$CACD_01              |     7197 (-) |  0.960 |  0.833 | GGGGGtgc
 V$CACD_01              |     7450 (-) |  0.948 |  0.844 | GGGAGtgt
 V$CACD_01              |     8235 (+) |  1.000 |  1.000 | ccaCACCC
 V$CACD_01              |     8446 (+) |  0.859 |  0.851 | ccgCATCC
 V$CACD_01              |     8739 (-) |  1.000 |  1.000 | GGGTGtgg
 V$CACD_01              |     8751 (+) |  0.784 |  0.853 | ccaCACCT
 V$CACD_01              |     8972 (-) |  0.784 |  0.853 | AGGTGtgg
 V$CACD_01              |     9572 (-) |  1.000 |  1.000 | GGGTGtgg
 V$CACD_01              |     9686 (-) |  0.960 |  0.833 | GGGGGgtg
 V$CACD_01              |     9687 (-) |  0.960 |  0.973 | GGGGGtgg
 V$CACD_01              |     9689 (-) |  1.000 |  0.860 | GGGTGgtg
 V$CACD_01              |     9690 (-) |  0.808 |  0.870 | GGTGGtgg
 V$CACD_01              |     9693 (-) |  0.808 |  0.870 | GGTGGtgg
 V$CACD_01              |     9696 (-) |  0.808 |  0.870 | GGTGGtgg
 V$CACD_01              |     9699 (-) |  0.808 |  0.870 | GGTGGtgg
 V$CACD_01              |     9702 (-) |  0.808 |  0.870 | GGTGGtgg
 V$CACD_01              |     9705 (-) |  0.808 |  0.870 | GGTGGtgg
 V$CACD_01              |    10619 (-) |  0.948 |  0.873 | GGGAGttg
 V$CACD_01              |    10694 (+) |  1.000 |  0.908 | caaCACCC
 V$CACD_01              |    10875 (-) |  0.808 |  0.870 | GGTGGtgg
 V$CACD_01              |    11821 (-) |  0.848 |  0.849 | GGTTGggg
 V$CACD_01              |    11845 (-) |  0.960 |  0.833 | GGGGGgtg
 V$CACD_01              |    11846 (-) |  0.960 |  0.973 | GGGGGtgg
 V$CACD_01              |    11848 (-) |  1.000 |  0.952 | GGGTGggg
 V$CACD_01              |    11853 (-) |  0.751 |  0.831 | GGGTAtgg
 V$CACD_01              |    11859 (-) |  0.960 |  0.855 | GGGGGtag
 V$CACD_01              |    11871 (-) |  0.960 |  0.909 | GGGGGagg
 V$CACD_01              |    11923 (+) |  0.983 |  0.896 | caaCGCCC
 V$OTX_Q1               |     1648 (-) |  1.000 |  0.943 | tgcTAATC
 V$OTX_Q1               |     1995 (+) |  1.000 |  0.993 | GATTAtct
 V$OTX_Q1               |     2724 (-) |  1.000 |  0.993 | agaTAATC
 V$OTX_Q1               |     3429 (+) |  0.905 |  0.914 | GCTTAatt
 V$OTX_Q1               |     4160 (-) |  1.000 |  0.946 | ttgTAATC
 V$OTX_Q1               |     5239 (+) |  1.000 |  0.997 | GATTAcat
 V$OTX_Q1               |     5416 (-) |  0.905 |  0.912 | attAAATC
 V$OTX_Q1               |     6195 (-) |  0.905 |  0.912 | attTAAGC
 V$OTX_Q1               |     7354 (-) |  1.000 |  0.944 | tgtTAATC
 V$OTX_Q1               |     8574 (+) |  1.000 |  0.998 | GATTAaat
 V$OTX_Q1               |    11003 (+) |  1.000 |  0.993 | GATTAcct
 V$OTX_Q1               |    11203 (+) |  1.000 |  0.948 | GATTAtta
 V$OTX_Q1               |    11694 (-) |  1.000 |  0.995 | agtTAATC
 V$WT1_Q6               |     1488 (-) |  1.000 |  0.991 | gagGGAGGg
 V$WT1_Q6               |     1491 (-) |  0.998 |  0.994 | ggaGGGGGg
 V$WT1_Q6               |     1492 (-) |  0.998 |  0.990 | gagGGGGGg
 V$WT1_Q6               |     1494 (-) |  0.998 |  0.999 | gggGGGGGg
 V$WT1_Q6               |     1495 (-) |  0.998 |  0.999 | gggGGGGGg
 V$WT1_Q6               |     1499 (-) |  1.000 |  1.000 | gggGGAGGg
 V$WT1_Q6               |     1503 (-) |  1.000 |  0.991 | gagGGAGGg
 V$WT1_Q6               |     1507 (-) |  1.000 |  0.991 | gagGGAGGg
 V$WT1_Q6               |     1511 (-) |  1.000 |  0.991 | gagGGAGGg
 V$WT1_Q6               |     7448 (-) |  0.986 |  0.981 | gtgGGAGTg
 V$WT1_Q6               |     9682 (-) |  0.998 |  0.994 | ggaGGGGGg
 V$WT1_Q6               |     9683 (-) |  0.998 |  0.990 | gagGGGGGg
 V$WT1_Q6               |     9685 (-) |  0.985 |  0.987 | gggGGGGTg
 V$WT1_Q6               |    10613 (-) |  1.000 |  0.993 | gtgGGAGGg
 V$WT1_Q6               |    10875 (-) |  0.992 |  0.980 | ggtGGTGGg
 V$WT1_Q6               |    11718 (+) |  1.000 |  0.986 | cCCTCCacc
 V$WT1_Q6               |    11846 (-) |  0.992 |  0.993 | gggGGTGGg
 V$WT1_Q6               |    11871 (-) |  1.000 |  1.000 | gggGGAGGg
 V$KAISO_01             |     4685 (-) |  1.000 |  0.991 | gtgGCAGGaa
 V$KAISO_01             |     5188 (-) |  1.000 |  0.998 | ctaGCAGGat
 V$KAISO_01             |    10841 (-) |  1.000 |  0.997 | atcGCAGGaa
 V$ZNF219_01            |     1490 (-) |  1.000 |  0.989 | gggagGGGGGgg
 V$ZNF219_01            |     1494 (-) |  1.000 |  0.995 | gggggGGGGGag
 V$NANOG_01             |     1408 (+) |  1.000 |  0.983 | gggtCCATTgcc
 V$NANOG_01             |     3769 (-) |  0.937 |  0.941 | ggcAATGCtcct
 V$NANOG_01             |    11925 (+) |  1.000 |  0.941 | acgcCCATTggc
 V$OCT4_01              |     9051 (-) |  0.955 |  0.837 | gtcTACATggcaagt
 V$OCT4_01              |     9489 (-) |  0.794 |  0.886 | attTGCAAtagaaaa
 V$OCT4_01              |    10345 (+) |  0.793 |  0.833 | tgttttaATTCAaag
 V$OCT4_01              |    10805 (-) |  1.000 |  0.882 | ttgTGCATctaaatc
 V$OCT4_01              |    11413 (-) |  1.000 |  0.830 | ttcTGCATttctatt
 V$OCT4_01              |    11667 (-) |  0.933 |  0.865 | attTTCATaaccaaa
 P$BPC1_Q2              |      369 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |      907 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     1172 (+) |  1.000 |  1.000 | AGAAAg
 P$BPC1_Q2              |     2132 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2198 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2202 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2210 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2214 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2218 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2222 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2226 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2230 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2234 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2238 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2242 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2246 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2250 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2254 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2258 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2262 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2266 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2270 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2274 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     2281 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     3193 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     4953 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     5546 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     6250 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     7368 (+) |  1.000 |  1.000 | AGAAAg
 P$BPC1_Q2              |     8136 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     8695 (-) |  1.000 |  1.000 | cTTTCT
 P$BPC1_Q2              |     9657 (+) |  1.000 |  1.000 | AGAAAg
 P$BPC1_Q2              |    10628 (+) |  1.000 |  1.000 | AGAAAg
 P$BPC1_Q2              |    11612 (+) |  1.000 |  1.000 | AGAAAg
 P$BPC1_Q2              |    11755 (+) |  1.000 |  1.000 | AGAAAg
 P$SED_Q2               |     1173 (-) |  1.000 |  0.984 | gAAAGGagat
 P$SED_Q2               |     1957 (+) |  1.000 |  0.992 | ctttCCTTTt
 P$SED_Q2               |     3409 (-) |  0.985 |  0.984 | aAAAGTtaat
 P$SED_Q2               |     3765 (-) |  1.000 |  0.996 | aAAAGGcaat
 P$SED_Q2               |     5120 (-) |  1.000 |  0.997 | aAAAGGaaac
 P$SED_Q2               |     5452 (+) |  1.000 |  0.999 | ataaCCTTTt
 P$SED_Q2               |     5770 (-) |  1.000 |  0.992 | aAAAGGagag
 P$SED_Q2               |     7871 (-) |  0.985 |  0.983 | aAAAGCtcac
 P$SED_Q2               |     7908 (+) |  0.985 |  0.984 | attaGCTTTt
 P$SED_Q2               |     8013 (+) |  1.000 |  0.985 | gtaaCCTTTa
 P$SED_Q2               |     8631 (-) |  0.985 |  0.985 | aAAAGCttat
 P$SED_Q2               |    10502 (-) |  0.985 |  0.983 | aAAAGTcaat
 P$SED_Q2               |    11270 (-) |  1.000 |  0.997 | aAAAGGaaat
 P$PBF_Q2               |      229 (-) |  1.000 |  1.000 | CCTTTt
 P$PBF_Q2               |      368 (-) |  1.000 |  0.965 | CCTTTc
 P$PBF_Q2               |      557 (-) |  1.000 |  1.000 | CCTTTt
 P$PBF_Q2               |      601 (-) |  0.963 |  0.964 | ACTTTt
 P$PBF_Q2               |      629 (-) |  0.963 |  0.964 | ACTTTt
 P$PBF_Q2               |      821 (-) |  0.963 |  0.964 | ACTTTt
 P$PBF_Q2               |      899 (-) |  0.963 |  0.964 | ACTTTt
 P$PBF_Q2               |     1173 (+) |  1.000 |  0.965 | gAAAGG
 P$PBF_Q2               |     1638 (-) |  1.000 |  0.965 | CCTTTc
 P$PBF_Q2               |     1718 (-) |  1.000 |  1.000 | CCTTTt
 P$PBF_Q2               |     1961 (-) |  1.000 |  1.000 | CCTTTt
 P$PBF_Q2               |     2030 (+) |  1.000 |  0.986 | tAAAGG
 P$PBF_Q2               |     2165 (-) |  1.000 |  0.965 | CCTTTc
 P$PBF_Q2               |     2209 (-) |  1.000 |  0.965 | CCTTTc
 P$PBF_Q2               |     2509 (+) |  1.000 |  1.000 | aAAAGG
 P$PBF_Q2               |     2533 (-) |  0.963 |  0.964 | ACTTTt
 P$PBF_Q2               |     2737 (-) |  1.000 |  0.986 | CCTTTa
 P$PBF_Q2               |     2745 (-) |  1.000 |  1.000 | CCTTTt
 P$PBF_Q2               |     2856 (-) |  1.000 |  0.986 | CCTTTa
 P$PBF_Q2               |     3223 (-) |  0.963 |  0.964 | ACTTTt
 P$PBF_Q2               |     3323 (-) |  1.000 |  1.000 | CCTTTt
 P$PBF_Q2               |     3409 (+) |  0.963 |  0.964 | aAAAGT
 P$PBF_Q2               |     3765 (+) |  1.000 |  1.000 | aAAAGG
 P$PBF_Q2               |     3786 (-) |  1.000 |  1.000 | CCTTTt
 P$PBF_Q2               |     5120 (+) |  1.000 |  1.000 | aAAAGG
 P$PBF_Q2               |     5160 (+) |  1.000 |  1.000 | aAAAGG
 P$PBF_Q2               |     5396 (-) |  1.000 |  0.986 | CCTTTa
 P$PBF_Q2               |     5456 (-) |  1.000 |  1.000 | CCTTTt
 P$PBF_Q2               |     5520 (-) |  1.000 |  0.965 | CCTTTc
 P$PBF_Q2               |     5580 (+) |  1.000 |  0.986 | tAAAGG
 P$PBF_Q2               |     5770 (+) |  1.000 |  1.000 | aAAAGG
 P$PBF_Q2               |     5943 (+) |  0.963 |  0.964 | aAAAGT
 P$PBF_Q2               |     6020 (-) |  1.000 |  0.965 | CCTTTc
 P$PBF_Q2               |     6679 (-) |  0.963 |  0.964 | GCTTTt
 P$PBF_Q2               |     6711 (+) |  0.963 |  0.964 | aAAAGC
 P$PBF_Q2               |     6722 (-) |  1.000 |  0.986 | CCTTTa
 P$PBF_Q2               |     6726 (+) |  1.000 |  0.986 | tAAAGG
 P$PBF_Q2               |     6760 (-) |  1.000 |  0.986 | CCTTTa
 P$PBF_Q2               |     6823 (-) |  1.000 |  1.000 | CCTTTt
 P$PBF_Q2               |     6973 (+) |  1.000 |  0.965 | gAAAGG
 P$PBF_Q2               |     7004 (+) |  1.000 |  1.000 | aAAAGG
 P$PBF_Q2               |     7218 (+) |  0.963 |  0.964 | aAAAGT
 P$PBF_Q2               |     7253 (+) |  0.963 |  0.964 | aAAAGT
 P$PBF_Q2               |     7415 (-) |  0.963 |  0.964 | ACTTTt
 P$PBF_Q2               |     7420 (+) |  1.000 |  0.986 | tAAAGG
 P$PBF_Q2               |     7654 (-) |  0.963 |  0.964 | GCTTTt
 P$PBF_Q2               |     7849 (+) |  0.963 |  0.964 | aAAAGC
 P$PBF_Q2               |     7871 (+) |  0.963 |  0.964 | aAAAGC
 P$PBF_Q2               |     7912 (-) |  0.963 |  0.964 | GCTTTt
 P$PBF_Q2               |     8017 (-) |  1.000 |  0.986 | CCTTTa
 P$PBF_Q2               |     8631 (+) |  0.963 |  0.964 | aAAAGC
 P$PBF_Q2               |     8694 (-) |  1.000 |  0.965 | CCTTTc
 P$PBF_Q2               |     8946 (-) |  0.963 |  0.964 | ACTTTt
 P$PBF_Q2               |     8989 (-) |  1.000 |  0.986 | CCTTTa
 P$PBF_Q2               |     9105 (+) |  0.963 |  0.964 | aAAAGC
 P$PBF_Q2               |    10502 (+) |  0.963 |  0.964 | aAAAGT
 P$PBF_Q2               |    10602 (+) |  1.000 |  1.000 | aAAAGG
 P$PBF_Q2               |    10731 (-) |  0.963 |  0.964 | GCTTTt
 P$PBF_Q2               |    10828 (-) |  1.000 |  1.000 | CCTTTt
 P$PBF_Q2               |    11270 (+) |  1.000 |  1.000 | aAAAGG
 P$PBF_Q2               |    11613 (+) |  1.000 |  0.965 | gAAAGG
 V$SOX10_Q6             |      949 (-) |  0.991 |  0.986 | aACAATg
 V$SOX10_Q6             |     1039 (-) |  1.000 |  0.995 | aACAAAg
 V$SOX10_Q6             |     3999 (-) |  0.953 |  0.952 | aACAACg
 V$SOX10_Q6             |     4664 (+) |  1.000 |  0.995 | cTTTGTt
 V$SOX10_Q6             |     7752 (+) |  0.991 |  0.992 | cATTGTg
 V$SOX10_Q6             |     7807 (-) |  0.953 |  0.952 | aACAACg
 V$SOX10_Q6             |     8558 (-) |  0.991 |  0.986 | aACAATg
 V$SOX10_Q6             |     8785 (-) |  1.000 |  1.000 | gACAAAg
 V$SOX10_Q6             |     9027 (+) |  1.000 |  1.000 | cTTTGTg
 V$SOX10_Q6             |     9727 (+) |  1.000 |  0.998 | cTTTGTa
 V$SOX10_Q6             |    10461 (-) |  0.991 |  0.986 | aACAATg
 V$SOX10_Q6             |    10856 (+) |  0.991 |  0.990 | cATTGTa
 V$SOX10_Q6             |    11052 (+) |  1.000 |  0.995 | cTTTGTt
 V$SOX10_Q6             |    11061 (+) |  0.953 |  0.958 | cGTTGTg
 V$SOX10_Q6             |    11520 (+) |  0.953 |  0.958 | cGTTGTc

 Total sequences length=11973

 Total number of found sites=13438

 Frequency of sites per nucleotide=1.122359

BioPerl-1.007002/t/data/megablast_output.paracel_btk000444000766000024       764013155576321 22447 0ustar00cjfieldsstaff000000000000MEGABLAST 1.4.13-Paracel [2002-12-12]


Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), 
"A greedy algorithm for aligning DNA sequences", 
J Comput Biol 2000; 7(1-2):203-14.

Database: bwb/tmp/vISbyVPvvB 
           2 sequences; 80 total letters

Searching. done
Query= DNA sequence #1
         (40 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

reverse-complement of sequence #1                                      74   1e-19
DNA sequence #1                                                        74   1e-19

>reverse-complement of sequence #1
          Length = 40

 Score = 73.8 bits (37), Expect = 1e-19
 Identities = 37/37 (100%)
 Strand = Plus / Minus

                                               
Query: 2  ccccccccccccccccccccccccccccccccccccc 38
          |||||||||||||||||||||||||||||||||||||
Sbjct: 40 ccccccccccccccccccccccccccccccccccccc 4



 Score = 67.9 bits (34), Expect = 8e-18
 Identities = 34/34 (100%)
 Strand = Plus / Minus

                                            
Query: 1  cccccccccccccccccccccccccccccccccc 34
          ||||||||||||||||||||||||||||||||||
Sbjct: 36 cccccccccccccccccccccccccccccccccc 3


>DNA sequence #1
          Length = 40

 Score = 73.8 bits (37), Expect = 1e-19
 Identities = 37/37 (100%)
 Strand = Plus / Plus

                                               
Query: 2  ccccccccccccccccccccccccccccccccccccc 38
          |||||||||||||||||||||||||||||||||||||
Sbjct: 1  ccccccccccccccccccccccccccccccccccccc 37



 Score = 71.9 bits (36), Expect = 5e-19
 Identities = 36/36 (100%)
 Strand = Plus / Plus

                                              
Query: 1  cccccccccccccccccccccccccccccccccccc 36
          ||||||||||||||||||||||||||||||||||||
Sbjct: 3  cccccccccccccccccccccccccccccccccccc 38


Searching. done
Query= reverse-complement of sequence #1
         (40 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

reverse-complement of sequence #1                                      74   1e-19
DNA sequence #1                                                        74   1e-19

>reverse-complement of sequence #1
          Length = 40

 Score = 73.8 bits (37), Expect = 1e-19
 Identities = 37/37 (100%)
 Strand = Plus / Plus

                                               
Query: 3  ggggggggggggggggggggggggggggggggggggg 39
          |||||||||||||||||||||||||||||||||||||
Sbjct: 4  ggggggggggggggggggggggggggggggggggggg 40



 Score = 67.9 bits (34), Expect = 8e-18
 Identities = 34/34 (100%)
 Strand = Plus / Plus

                                            
Query: 7  gggggggggggggggggggggggggggggggggg 40
          ||||||||||||||||||||||||||||||||||
Sbjct: 3  gggggggggggggggggggggggggggggggggg 36


>DNA sequence #1
          Length = 40

 Score = 73.8 bits (37), Expect = 1e-19
 Identities = 37/37 (100%)
 Strand = Plus / Minus

                                               
Query: 3  ggggggggggggggggggggggggggggggggggggg 39
          |||||||||||||||||||||||||||||||||||||
Sbjct: 37 ggggggggggggggggggggggggggggggggggggg 1



 Score = 71.9 bits (36), Expect = 5e-19
 Identities = 36/36 (100%)
 Strand = Plus / Minus

                                              
Query: 5  gggggggggggggggggggggggggggggggggggg 40
          ||||||||||||||||||||||||||||||||||||
Sbjct: 38 gggggggggggggggggggggggggggggggggggg 3


  Database: bwb/tmp/vISbyVPvvB
    Posted date:  Jan 23, 2003  9:25 AM
  Number of letters in database: 80
  Number of sequences in database:  2
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 0, Extension: 0
Number of Hits to DB: 0
Number of Sequences: 2
length of database: 80
effective search space used:        0
S2: 4 ( 8.4 bits)
BioPerl-1.007002/t/data/meme.dat000444000766000024      5334613155576321 16340 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.0 (Release date: 2001/03/05 14:24:28)

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.sdsc.edu.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.sdsc.edu.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= D10Mit194.set.genbank.fasta.nref
ALPHABET= ACGT
Sequence name           Weight Length  Sequence name           Weight Length  
-------------           ------ ------  -------------           ------ ------  
20218                   1.0000   2000  10657                   1.0000   2000  
83796                   1.0000   2000  6603                    1.0000   2000  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme D10Mit194.set.genbank.fasta.nref -dna -print_fasta -nmotifs 3 -maxw 25 

model:  mod=         zoops    nmotifs=         3    evt=           inf
object function=  E-value of product of p-values
width:  minw=            8    maxw=           25    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        2    maxsites=        4    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            8000    N=               4
strands: +
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.255 C 0.236 G 0.252 T 0.257 
Background letter frequencies (from dataset with add-one prior applied):
A 0.255 C 0.236 G 0.252 T 0.257 
********************************************************************************


********************************************************************************
MOTIF  1	width =   25   sites =   4   llr = 106   E-value = 1.2e-002
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :8:88aaa:53a8:::3:a::3::3
pos.-specific     C  a3::3:::::3:::5a8a:8a5aa8
probability       G  ::8:::::3:5::::::::3:::::
matrix            T  ::33::::85::3a5::::::3:::

         bits    2.1 *              * *  * ** 
                 1.9 *    ***   * * * ** * ** 
                 1.7 *    ***   * * * ** * ** 
                 1.5 *    ***   * * * ** * ** 
Information      1.2 *********  *** ****** ***
content          1.0 ********** ********** ***
(38.1 bits)      0.8 ********** ********** ***
                 0.6 ********** **************
                 0.4 *************************
                 0.2 *************************
                 0.0 -------------------------

Multilevel           CAGAAAAATAGAATCCCCACCCCCC
consensus             CTTC   GTA T T A  G A  A
sequence                       C          T   
                                              
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                      Site         
-------------             ----- ---------            -------------------------
6603                       1311  2.59e-15 GGCGCATTGA CAGAAAAATTGAATTCCCACCCCCC AATGAGGAGG
83796                      1284  2.59e-15 GGAGGATTGA CAGAAAAATTGAATTCCCACCCCCC AACGAGGAGG
20218                       938  6.34e-12 TTTTTGGTAA CCTTAAAATAAAATCCCCACCACCA CTTTTAAAAA
10657                      1685  8.70e-12 GGCCCGCGCG CAGACAAAGACATTCCACAGCTCCC GCCCCCTCCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
6603                              2.6e-15  1310_[1]_665
83796                             2.6e-15  1283_[1]_692
20218                             6.3e-12  937_[1]_1038
10657                             8.7e-12  1684_[1]_291
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in FASTA format
--------------------------------------------------------------------------------
>6603                     pos 1311
CAGAAAAATTGAATTCCCACCCCCC
>83796                    pos 1284
CAGAAAAATTGAATTCCCACCCCCC
>20218                    pos  938
CCTTAAAATAAAATCCCCACCACCA
>10657                    pos 1685
CAGACAAAGACATTCCACAGCTCCC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 25 n= 7904 bayes= 11.6849 E= 1.2e-002 
  -865    208   -865   -865 
   156      8   -865   -865 
  -865   -865    157     -4 
   156   -865   -865     -4 
   156      8   -865   -865 
   197   -865   -865   -865 
   197   -865   -865   -865 
   197   -865   -865   -865 
  -865   -865     -1    154 
    97   -865   -865     96 
    -3      8     99   -865 
   197   -865   -865   -865 
   156   -865   -865     -4 
  -865   -865   -865    196 
  -865    108   -865     96 
  -865    208   -865   -865 
    -3    166   -865   -865 
  -865    208   -865   -865 
   197   -865   -865   -865 
  -865    166     -1   -865 
  -865    208   -865   -865 
    -3    108   -865     -4 
  -865    208   -865   -865 
  -865    208   -865   -865 
    -3    166   -865   -865 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 25 n= 7904 E= 1.2e-002 
 0.000635  0.998096  0.000629  0.000640 
 0.748765  0.249966  0.000629  0.000640 
 0.000635  0.000589  0.748759  0.250017 
 0.748765  0.000589  0.000629  0.250017 
 0.748765  0.249966  0.000629  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.000635  0.000589  0.250006  0.748770 
 0.499388  0.000589  0.000629  0.499393 
 0.250012  0.249966  0.499382  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.748765  0.000589  0.000629  0.250017 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.499343  0.000629  0.499393 
 0.000635  0.998096  0.000629  0.000640 
 0.250012  0.748719  0.000629  0.000640 
 0.000635  0.998096  0.000629  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.000635  0.748719  0.250006  0.000640 
 0.000635  0.998096  0.000629  0.000640 
 0.250012  0.499343  0.000629  0.250017 
 0.000635  0.998096  0.000629  0.000640 
 0.000635  0.998096  0.000629  0.000640 
 0.250012  0.748719  0.000629  0.000640 
--------------------------------------------------------------------------------





Time 38.44 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   25   sites =   4   llr = 101   E-value = 4.5e-001
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  ::::a::383:5:3:::a33:83:a
pos.-specific     C  a3a8:3a33:a::5::8::::383:
probability       G  ::::::::::::::::3:38a::8:
matrix            T  :8:3:8:5:8:5a3aa::5::::::

         bits    2.1 * *   *   *         *    
                 1.9 * * * *   * * ** *  *   *
                 1.7 * * * *   * * ** *  *   *
                 1.5 * * * *   * * ** *  *   *
Information      1.2 ******* *** * **** ******
content          1.0 ******* ***** **** ******
(36.6 bits)      0.8 ******* ***** **** ******
                 0.6 ******* ********** ******
                 0.4 *************************
                 0.2 *************************
                 0.0 -------------------------

Multilevel           CTCCATCTATCATCTTCATGGACGA
consensus             C T C ACA T A  G AA CAC 
sequence                    C     T    G      
                                              
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                      Site         
-------------             ----- ---------            -------------------------
6603                       1000  1.62e-15 CGGGAACATG CTCCATCTATCATCTTCATGGACGA AATCGACTCC
83796                       978  4.69e-15 CGAGAACATG CTCCATCCATCATCTTCATGGACGA GATTGACTCT
20218                      1545  1.69e-11 TAGCTTCTCT CCCCATCAATCTTATTCAGAGCCCA CCCCTCCCCC
10657                      1075  3.40e-11 AGGATCTGGT CTCTACCTCACTTTTTGAAGGAAGA AACACTTAAT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
6603                              1.6e-15  999_[2]_976
83796                             4.7e-15  977_[2]_998
20218                             1.7e-11  1544_[2]_431
10657                             3.4e-11  1074_[2]_901
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in FASTA format
--------------------------------------------------------------------------------
>6603                     pos 1000
CTCCATCTATCATCTTCATGGACGA
>83796                    pos  978
CTCCATCCATCATCTTCATGGACGA
>20218                    pos 1545
CCCCATCAATCTTATTCAGAGCCCA
>10657                    pos 1075
CTCTACCTCACTTTTTGAAGGAAGA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 25 n= 7904 bayes= 10.9476 E= 4.5e-001 
  -865    208   -865   -865 
  -865      8   -865    154 
  -865    208   -865   -865 
  -865    166   -865     -4 
   197   -865   -865   -865 
  -865      8   -865    154 
  -865    208   -865   -865 
    -3      8   -865     96 
   156      8   -865   -865 
    -3   -865   -865    154 
  -865    208   -865   -865 
    97   -865   -865     96 
  -865   -865   -865    196 
    -3    108   -865     -4 
  -865   -865   -865    196 
  -865   -865   -865    196 
  -865    166     -1   -865 
   197   -865   -865   -865 
    -3   -865     -1     96 
    -3   -865    157   -865 
  -865   -865    198   -865 
   156      8   -865   -865 
    -3    166   -865   -865 
  -865      8    157   -865 
   197   -865   -865   -865 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 25 n= 7904 E= 4.5e-001 
 0.000635  0.998096  0.000629  0.000640 
 0.000635  0.249966  0.000629  0.748770 
 0.000635  0.998096  0.000629  0.000640 
 0.000635  0.748719  0.000629  0.250017 
 0.998141  0.000589  0.000629  0.000640 
 0.000635  0.249966  0.000629  0.748770 
 0.000635  0.998096  0.000629  0.000640 
 0.250012  0.249966  0.000629  0.499393 
 0.748765  0.249966  0.000629  0.000640 
 0.250012  0.000589  0.000629  0.748770 
 0.000635  0.998096  0.000629  0.000640 
 0.499388  0.000589  0.000629  0.499393 
 0.000635  0.000589  0.000629  0.998147 
 0.250012  0.499343  0.000629  0.250017 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.748719  0.250006  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.250012  0.000589  0.250006  0.499393 
 0.250012  0.000589  0.748759  0.000640 
 0.000635  0.000589  0.998135  0.000640 
 0.748765  0.249966  0.000629  0.000640 
 0.250012  0.748719  0.000629  0.000640 
 0.000635  0.249966  0.748759  0.000640 
 0.998141  0.000589  0.000629  0.000640 
--------------------------------------------------------------------------------





Time 78.29 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   21   sites =   4   llr = 88   E-value = 4.8e-001
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :::58:::::3::::33::::
pos.-specific     C  8:833::8:8:a:8a8:a5a8
probability       G  3::::::3:::::3:::::::
matrix            T  :a33:aa:a38:a:::8:5:3

         bits    2.1            *  *  * * 
                 1.9  *   ** *  ** *  * * 
                 1.7  *   ** *  ** *  * * 
                 1.5  *   ** *  ** *  * * 
Information      1.2 *** ************** **
content          1.0 *** *****************
(31.8 bits)      0.8 *** *****************
                 0.6 *** *****************
                 0.4 *********************
                 0.2 *********************
                 0.0 ---------------------

Multilevel           CTCAATTCTCTCTCCCTCCCC
consensus            G TCC  G TA  G AA T T
sequence                T                 
                                          
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                    Site       
-------------             ----- ---------            ---------------------
10657                      1511  1.45e-13 CCCAGGCGGT CTCAATTCTCTCTCCCTCCCC TTTCCGTGAC
83796                      1801  7.40e-12 TGTATATGCA CTCTCTTCTCTCTCCCTCTCC AGGTCATGCA
6603                       1811  1.22e-10 GTAACTTAAT GTTCATTCTCTCTCCCACCCC TAGGTCATGC
20218                       606  7.57e-10 CCCAGGCCAG CTCAATTGTTACTGCATCTCT AGGATTGGAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
10657                             1.5e-13  1510_[3]_469
83796                             7.4e-12  1800_[3]_179
6603                              1.2e-10  1810_[3]_169
20218                             7.6e-10  605_[3]_1374
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in FASTA format
--------------------------------------------------------------------------------
>10657                    pos 1511
CTCAATTCTCTCTCCCTCCCC
>83796                    pos 1801
CTCTCTTCTCTCTCCCTCTCC
>6603                     pos 1811
GTTCATTCTCTCTCCCACCCC
>20218                    pos  606
CTCAATTGTTACTGCATCTCT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 21 n= 7920 bayes= 10.9506 E= 4.8e-001 
  -865    166     -1   -865 
  -865   -865   -865    196 
  -865    166   -865     -4 
    97      8   -865     -4 
   156      8   -865   -865 
  -865   -865   -865    196 
  -865   -865   -865    196 
  -865    166     -1   -865 
  -865   -865   -865    196 
  -865    166   -865     -4 
    -3   -865   -865    154 
  -865    208   -865   -865 
  -865   -865   -865    196 
  -865    166     -1   -865 
  -865    208   -865   -865 
    -3    166   -865   -865 
    -3   -865   -865    154 
  -865    208   -865   -865 
  -865    108   -865     96 
  -865    208   -865   -865 
  -865    166   -865     -4 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 21 n= 7920 E= 4.8e-001 
 0.000635  0.748719  0.250006  0.000640 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.748719  0.000629  0.250017 
 0.499388  0.249966  0.000629  0.250017 
 0.748765  0.249966  0.000629  0.000640 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.748719  0.250006  0.000640 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.748719  0.000629  0.250017 
 0.250012  0.000589  0.000629  0.748770 
 0.000635  0.998096  0.000629  0.000640 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.748719  0.250006  0.000640 
 0.000635  0.998096  0.000629  0.000640 
 0.250012  0.748719  0.000629  0.000640 
 0.250012  0.000589  0.000629  0.748770 
 0.000635  0.998096  0.000629  0.000640 
 0.000635  0.499343  0.000629  0.499393 
 0.000635  0.998096  0.000629  0.000640 
 0.000635  0.748719  0.000629  0.250017 
--------------------------------------------------------------------------------





Time 117.82 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
20218                            7.77e-19  605_[3(7.57e-10)]_311_[1(6.34e-12)]_582_[2(1.69e-11)]_431
10657                            5.46e-22  1_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_7_[1(6.00e-08)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_5_[1(1.18e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_4_[1(1.29e-07)]_332_[2(3.40e-11)]_383_[3(7.75e-07)]_7_[3(1.45e-13)]_56_[3(3.47e-05)]_76_[1(8.70e-12)]_291
83796                            1.73e-27  977_[2(4.69e-15)]_281_[1(2.59e-15)]_492_[3(7.40e-12)]_179
6603                             9.32e-27  597_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_327_[2(1.62e-15)]_286_[1(2.59e-15)]_475_[3(1.22e-10)]_169
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 3 reached.
********************************************************************************

CPU: hydra-1.lsd.ornl.gov

********************************************************************************
BioPerl-1.007002/t/data/mini-AE001405.gb000444000766000024       573613155576321 17106 0ustar00cjfieldsstaff000000000000LOCUS       AE001405               11389 bp    DNA     linear   INV 04-OCT-2002
DEFINITION  Plasmodium falciparum 3D7 chromosome 2 section 42 of 73 of the
            complete sequence.
ACCESSION   AE001405 AE001362
VERSION     AE001405.2  GI:23503395
KEYWORDS    .
SOURCE      Plasmodium falciparum 3D7
  ORGANISM  Plasmodium falciparum 3D7
            Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium.
REFERENCE   1  (bases 1 to 11389)
  AUTHORS   Gardner,M.J., Tettelin,H., Carucci,D.J., Cummings,L.M., Aravind,L.,
            Koonin,E.V., Shallom,S., Mason,T., Yu,K., Fujii,C., Pederson,J.,
            Shen,K., Jing,J., Aston,C., Lai,Z., Schwartz,D.C., Pertea,M.,
            Salzberg,S., Zhou,L., Sutton,G.G., Clayton,R., White,O.,
            Smith,H.O., Fraser,C.M., Adams,M.D., Venter,J.C. and Hoffman,S.L.
  TITLE     Chromosome 2 sequence of the human malaria parasite Plasmodium
            falciparum
  JOURNAL   Science 282 (5391), 1126-1132 (1998)
   PUBMED   9804551
REFERENCE   2  (bases 1 to 11389)
  AUTHORS   Gardner,M.J., Hall,N., Fung,E., White,O., Berriman,M., Hyman,R.W.,
            Carlton,J.M., Pain,A., Nelson,K.E., Bowman,S., Paulsen,I.T.,
            James,K., Eisen,J.A., Rutherford,K., Salzberg,S.L., Craig,A.,
            Kyes,S., Chan,M.S., Nene,V., Shallom,S.J., Suh,B., Peterson,J.,
            Angiuoli,S., Pertea,M., Allen,J., Selengut,J., Haft,D.,
            Mather,M.W., Vaidya,A.B., Martin,D.M., Fairlamb,A.H.,
            Fraunholz,M.J., Roos,D.S., Ralph,S.A., McFadden,G.I.,
            Cummings,L.M., Subramanian,G.M., Mungall,C., Venter,J.C.,
            Carucci,D.J., Hoffman,S.L., Newbold,C., Davis,R.W., Fraser,C.M. and
            Barrell,B.
  TITLE     Genome sequence of the human malaria parasite Plasmodium falciparum
  JOURNAL   Nature 419 (6906), 498-511 (2002)
   PUBMED   12368864
REFERENCE   3  (bases 1 to 11389)
  AUTHORS   Gardner,M.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-OCT-2002) The Institute for Genomic Research, 9712
            Medical Center Dr, Rockville, MD 20850, USA
COMMENT     On Oct 4, 2002 this sequence version replaced gi:3845224.
FEATURES             Location/Qualifiers
     source          1..180
                     /organism="Plasmodium falciparum 3D7"
                     /mol_type="genomic DNA"
                     /isolate="3D7"
                     /db_xref="taxon:36329"
                     /chromosome="2"
     repeat_region   complement(<1..55)
                     /rpt_type=tandem
                     /rpt_unit=(TG)10;A;(TG)7
     repeat_region   112..117
                     /rpt_type=tandem
                     /rpt_unit_seq="(TAAAA)n"
     repeat_region   complement(116..119)
                     /rpt_type=tandem
                     /rpt_unit_seq="(TA)n"
ORIGIN      
        1 tattatattt ttattaaatg caaatatgtt gatatgtaca tatatatata tatatgatca
       61 taatatattt catttttatc atttttaaag tgtttgttta tttatattta ttatttttaa
      121 tttttttatt ttatttaatt attttttttt attttttaaa tttttgtgac aagtttatat
//

BioPerl-1.007002/t/data/mini-align.aln000444000766000024        54313155576321 17372 0ustar00cjfieldsstaff000000000000CLUSTAL W (1.74) multiple sequence alignment


P84139                MNEGEHQIKLDELFEKLLRARLIFKNKDVLRRC
P814153               MNEGMHQIKLDVLFEKLLRARLIFKNKDVLRRC
BAB68554              -------------------AMLIFKDKQLLQQC
gb|443893|124775      -MRFRFQIKVPPAVEGARPALLIFKSRPELGGC
                                                                                  

BioPerl-1.007002/t/data/mixedmast.dat000555000766000024     33355213155576321 17433 0ustar00cjfieldsstaff000000000000********************************************************************************
MAST - Motif Alignment and Search Tool
********************************************************************************
	MAST version 3.5.3 (Release date: 2006-04-30 01:41:24 -0700 (Sun, 30 Apr 2006))

	For further information on how to interpret these results or to get
	a copy of the MAST software please access http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
	If you use this program in your research, please cite:

	Timothy L. Bailey and Michael Gribskov,
	"Combining evidence using p-values: application to sequence homology
	searches", Bioinformatics, 14(48-54), 1998.
********************************************************************************


********************************************************************************
DATABASE AND MOTIFS
********************************************************************************
	DATABASE /home/struckma/XXXXX/xxxxx.seq.fasta (nucleotide)
	Last updated on Tue Jul 11 18:30:00 2006
	Database contains 4390 sequences, 173499994 residues

	Scores for positive and reverse complement strands are combined.

	MOTIFS test2.fasta.meme.out (peptide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    15   SQTTICRFEALQLSF
	  2    15   LEKEVVRVWFCNRRQ
	  3    15   FKQRRIKLGFTQADV
	  4    15   KNMCKLKPLLQKWLE

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1     2     3
	----- ----- ----- -----
	   2   0.12
	   3   0.15  0.14
	   4   0.21  0.19  0.17
	No overly similar pairs (correlation > 0.60) found.

	Random model letter frequencies (from non-redundant database):
	A 0.070 C 0.024 D 0.040 E 0.052 F 0.040 G 0.074 H 0.029 I 0.041 K 0.052 
	L 0.096 M 0.017 N 0.032 P 0.065 Q 0.042 R 0.067 S 0.084 T 0.052 V 0.059 
	W 0.016 Y 0.022 
********************************************************************************


********************************************************************************
SECTION I: HIGH-SCORING SEQUENCES
********************************************************************************
SEQUENCE NAME                      DESCRIPTION           FRAME   E-VALUE  LENGTH
-------------                      -----------           -----   -------- ------
chr04q                                                       c    3.3e-26 6776397
chr02q                                                       b    9.1e-20 8059593

********************************************************************************



********************************************************************************
SECTION II: MOTIF DIAGRAMS
********************************************************************************
SEQUENCE NAME                      E-VALUE   MOTIF DIAGRAM
-------------                      --------  -------------
chr04q                              3.3e-26  170163_[-3a]_45546_[+4a]_316730_
                                             [+2c]_6917_[-1b]_46576_[+2c]_
                                             112087_[-4a]_106122_[-3a]_54413_
                                             [-3c]_2646_[-3c]_55292_[-1b]_
                                             229973_[-1a]_168811_[+1b]_320302_
                                             [+3c]_36_[+1c]_192_[+4c]_879_
                                             [+2c]_15041_[+4b]_12578_[+2a]_
                                             15085_[-2b]_34466_[-2a]_3572_
                                             [-3c]_106732_[-4a]_100884_[-1a]_
                                             150814_[+2b]_50394_[-2b]_2709_
                                             [+1b]_80737_[-2c]_9981_[+4c]_
                                             134258_[+2b]_5742_[+2b]_9723_
                                             [-1b]_120512_[-2a]_180_[+2a]_
                                             53270_[-4c]_17749_[-2a]_105178_
                                             [-1b]_47045_[-2a]_86702_[+2c]_
                                             6448_[-4a]_10586_[-2c]_30988_
                                             [-2a]_125990_[-2c]_69247_[-4a]_
                                             250534_[-2b]_143429_[-2a]_41053_
                                             [-4b]_167542_[-1c]_126920_[-2b]_
                                             79648_[-2c]_41344_[-1a]_34611_
                                             [-1a]_32643_[-2a]_69929_[+1c]_
                                             20774_[+1b]_62113_[+2c]_23189_
                                             [-4b]_9299_[-4a]_39496_[+1b]_
                                             43277_[-2a]_116690_[+4c]_6861_
                                             [+4c]_71133_[+2c]_143200_[-2a]_
                                             382714_[+1b]_15009_[+3b]_167995_
                                             [-3c]_11445_[+3c]_85905_[-2c]_
                                             116003_[+2b]_62888_[-3a]_64899_
                                             [+2a]_49005_[+2a]_56736_[+3a]_
                                             14883_[+2a]_6123_[-2a]_24729_
                                             [-2a]_75491_[-2c]_33025_[+2a]_
                                             223953_[+2a]_3536_[+2c]_57658_
                                             [+1a]_321010_[-2b]_99474_[+4b]_
                                             14568_[+4b]_14260_[-2c]_151646_
                                             [-4b]_91790_[-2a]_60756
chr02q                              9.1e-20  181586_[+1c]_84138_[-3c]_15167_
                                             [-2b]_135571_[-4c]_325471_[+4a]_
                                             12798_[-4a]_4700_[-2c]_182142_
                                             [-1c]_7912_[-1a]_80644_[-2b]_
                                             143591_[-2a]_5286_[-1a]_17554_
                                             [-4b]_104512_[+2c]_75992_[-2b]_
                                             1994_[+2a]_7759_[-2b]_11678_[+4a]_
                                             544_[+2b]_15348_[+2b]_53558_[+2a]_
                                             756_[-2a]_132170_[-3c]_6820_[+1a]_
                                             226852_[+2b]_107962_[+1c]_5949_
                                             [-2c]_138458_[-4b]_133762_[+1c]_
                                             126753_[-2c]_69234_[+1c]_33_[+1c]_
                                             72_[+1c]_150_[+1c]_33_[+1c]_72_
                                             [+1c]_267_[+1c]_33_[+1c]_15489_
                                             [-1c]_21704_[+1b]_72_[+1b]_346_
                                             [+1c]_96059_[-4b]_36498_[-2b]_
                                             335_[-4a]_[-1a]_155_[-3c]_18189_
                                             [-1c]_174870_[-2c]_38785_[+1a]_
                                             40123_[+2b]_147684_[-1b]_122397_
                                             [+2b]_45479_[+4a]_74846_[+1c]_
                                             23231_[+3b]_38245_[-4c]_152196_
                                             [-2c]_304660_[+2a]_165655_[-4b]_
                                             38440_[-4c]_21816_[+1c]_25500_
                                             [-2c]_336004_[+3a]_323232_[-4a]_
                                             7268_[+2c]_47044_[+4a]_41451_
                                             [-2a]_66303_[+2a]_30342_[+1a]_
                                             40657_[-4b]_180301_[-2c]_35205_
                                             [-2c]_59610_[-2c]_2222_[+1b]_
                                             1400_[-2a]_53171_[-2c]_175866_
                                             [-2c]_162426_[-2c]_70915_[+2a]_
                                             33010_[-1b]_139023_[+1b]_248403_
                                             [-2b]_102258_[+2b]_13294_[-4c]_
                                             85097_[+2b]_13395_[-4b]_217923_
                                             [-2b]_252830_[-2a]_40346_[-3c]_
                                             9779_[+1b]_15798_[-1b]_16835_
                                             [+1a]_31854_[-2a]_3867_[+2a]_
                                             28000_[+1b]_14934_[+2b]_18632_
                                             [+4a]_54520_[+2b]_53902_[+1c]_
                                             198948_[-2c]_10079_[+1b]_162971_
                                             [-2a]_106411_[+2b]_74994_[-4b]_
                                             11202_[-4b]_165552_[+2b]_7010_
                                             [-2a]_12481_[-2b]_23349_[+1b]_
                                             102412_[+2c]_100606_[-4a]_31326

********************************************************************************



********************************************************************************
SECTION III: ANNOTATED SEQUENCES
********************************************************************************


chr04q
  
  LENGTH = 6776397  COMBINED P-VALUE = 7.48e-30  E-VALUE =  3.3e-26
  DIAGRAM: 170163_[-3a]_45546_[+4a]_316730_[+2c]_6917_[-1b]_46576_[+2c]_112087_
           [-4a]_106122_[-3a]_54413_[-3c]_2646_[-3c]_55292_[-1b]_229973_[-1a]_
           168811_[+1b]_320302_[+3c]_36_[+1c]_192_[+4c]_879_[+2c]_15041_[+4b]_
           12578_[+2a]_15085_[-2b]_34466_[-2a]_3572_[-3c]_106732_[-4a]_100884_
           [-1a]_150814_[+2b]_50394_[-2b]_2709_[+1b]_80737_[-2c]_9981_[+4c]_
           134258_[+2b]_5742_[+2b]_9723_[-1b]_120512_[-2a]_180_[+2a]_53270_
           [-4c]_17749_[-2a]_105178_[-1b]_47045_[-2a]_86702_[+2c]_6448_[-4a]_
           10586_[-2c]_30988_[-2a]_125990_[-2c]_69247_[-4a]_250534_[-2b]_143429_
           [-2a]_41053_[-4b]_167542_[-1c]_126920_[-2b]_79648_[-2c]_41344_[-1a]_
           34611_[-1a]_32643_[-2a]_69929_[+1c]_20774_[+1b]_62113_[+2c]_23189_
           [-4b]_9299_[-4a]_39496_[+1b]_43277_[-2a]_116690_[+4c]_6861_[+4c]_
           71133_[+2c]_143200_[-2a]_382714_[+1b]_15009_[+3b]_167995_[-3c]_
           11445_[+3c]_85905_[-2c]_116003_[+2b]_62888_[-3a]_64899_[+2a]_49005_
           [+2a]_56736_[+3a]_14883_[+2a]_6123_[-2a]_24729_[-2a]_75491_[-2c]_
           33025_[+2a]_223953_[+2a]_3536_[+2c]_57658_[+1a]_321010_[-2b]_99474_
           [+4b]_14568_[+4b]_14260_[-2c]_151646_[-4b]_91790_[-2a]_60756


                                   [-3a]
                                   3.3e-07
                                   ..V..D..A..Q..T..F..G..L..K..I..R..R..Q..K..F
                                        +  +  +  +  +     +     +     +        +
                                   ..T..D..T..Q..T..V..N..L..*..I..P..R..A..Q..F
170137  CAGAAAAATCGAAGACGAGTATAAAATTGTGTCAGTCTGAGTAACATTCAGCTAAATAGGTCTAGCTTGAAA

                                                  [+4a]
                                                  5.6e-07
                                                  K..N..M..C..K..L..K..P..L..L..
                                                  +        +     +  +     +  +
                                                  N..*..L..I..T..L..K..S..I..L..
215713  TGTGTGAAAGGATATGGCCTATGGCATCAATAGGACTGAATCAACTAGCTAATCACATTAAAAAGTATTCTA

        
        
        Q..K..W..L..E..
        +        +
        N..*..T..V..H..
215785  AATTAAACAGTACACAACACTGACAAATGCAAGCGAATTTATAGAATGTGTGAGCACTGAGCAGGATGTATA

                         [+2c]
                         6.2e-07
                         L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                               +     +  +        +  +     +  +
                         V..H..K..K..V..V..K..C..W..F..S..N..R..N..N..
532513  AATCCTATTTATCGCATGTCCACAAAAAAGTTGTAAAATGTTGGTTTAGTAATAGAAACAACAAAGCTCTTT

                                                                           [-1b]
                                                                           8.7e-
                                                                           ..F..
        
                                                                           ..Y..
539425  TTTATTTTCTTTCAACTTGAGACGCTAATAGGAACACCGAGTGCTTATTGAAGAAACGTTCGAGTATGTATG

        
        07
        S..L..Q..L..A..E..F..R..C..I..T..T..Q..S
        +  +        +     +     +  +  +  +     +
        T..I..K..T..S..S..F..N..S..I..A..T..Y..S
539497  TTATTTTAGTTGATGAGAAATTACTGATTGCAGTATATGACCTACTTCACATGTTATGCACCTATTATGTCA

                                        [+2c]
                                        9.6e-07
                                        L..E..K..E..V..V..R..V..W..F..C..N..R..R
                                           +  +     +  +  +        +  +     +
                                        R..K..K..K..V..V..R..R..D..F..C..G..R..E
586081  ACACACAAAGATATACGTCATAATCGTGAGAACGTAAGAAAAAGGTAGTAAGACGCGATTTCTGTGGTCGCG

        
        
        ..Q..
        
        ..R..
586153  AACGTTTAGTTTCTATTCCATTTTGGCAGAAGTTTAGAATTGTGATCTTACTAAGTATAACGGCAATCTTGT

                                                                    [-4a]
                                                                    8.5e-07
                                                                    ..E..L..W..K
                                                                      +        +
                                                                    ..N..T..L..K
698185  AGACGGAATGTCTCAGAATGCATCTTCGCACTAGTGCATACTTTTATATATATATATAGAGTTAGTCAGTTT

        
        
        ..Q..L..L..P..K..L..K..C..M..N..K
          +  +  +        +  +  +  +     +
        ..Q..L..I..V..M..L..K..I..A..Q..K
698257  TTGTAGTATCACCATCAGCTTTATGGCTTGTTTTTATTGTATGTACATTATACATGATATTTTATTGTAATG

                                   [-3a]
                                   3.8e-07
                                   ..V..D..A..Q..T..F..G..L..K..I..R..R..Q..K..F
                                        +  +  +     +  +     +     +  +     +
                                   ..L..N..T..Q..K..V..G..*..K..G..R..R..L..K..G
804385  AATAAAATTATTAAATTACAACAAAAATAAATTTGTTTGTTTTACACCTCACTTACCTCTGCGTAACTTTCC

                                                             [-3c]
                                                             8.2e-08
                                                             ..V..D..A..Q..T..F.
                                                               +  +  +     +  +
                                                             ..V..Q..G..V..T..Y.
858817  CAACACACCTAAAAAAGTTATTTCTAGACATCTAGTGGTTTGTATAACCTATGTACCTGTCCTACAGTATAT

        
        
        .G..L..K..I..R..R..Q..K..F
         +     +     +           +
        .G..S..T..L..R..Y..L..*..F
858889  CCACTGGTAAGCCTGTATAACTAAAATAGAATGCGGAACAATTTTCATGGATGTACTTACTACATAGCTACC

                [-3c]
                3.6e-07
                ..V..D..A..Q..T..F..G..L..K..I..R..R..Q..K..F
                     +     +     +  +     +  +  +  +        +
                ..Y..N..P..Q..Q..Y..G..F..T..I..R..K..R..H..F
861553  GTAAGGGTATAGTTTGGTTGCTGATAGCCGAAAGTAATTCTTTTGCGGTGGAAGTCGTAGTTTAGAAGCAAC

                                                         [-1b]
                                                         1.1e-07
                                                         ..F..S..L..Q..L..A..E..
                                                              +  +  +  +  +  +
                                                         ..L..S..L..D..L..A..E..
916849  ATTCCCATTGGCAGGAGCCAAGTATATCGAGTGTGTCGAGTTTAGATGATAAACTAAGGTCAAGTGCTTCTG

        
        
        F..R..C..I..T..T..Q..S
              +        +     +
        A..S..S..S..N..T..R..S
916921  CTGAAGAAGAATTAGTGCGTGATGTGTTATATTCTACAAGGCAAAATATCAACATTGTCCATGAGATGTTTC

                                   [-1a]
                                   5.7e-07
                                   ..F..S..L..Q..L..A..E..F..R..C..I..T..T..Q..S
                                     +  +  +           +  +        +     +     +
                                   ..P..S..I..K..R..T..E..F..S..P..I..*..T..R..S
1146889 CTTAATGAGCTTTGAATGACCGAAACTAGGAGATATTTTGCGGGTTTCGAAACTCGGAATTCACGTGCGTGA

                                                   [+1b]
                                                   3.7e-07
                                                   S..Q..T..T..I..C..R..F..E..A.
                                                   +     +     +     +  +     +
                                                   S..F..T..S..I..V..R..F..T..N.
1315729 GAACGATTAAACTAGATAAACAACAGCTGACGTGAAATTCTGTTCTTTCACTTCGATCGTAAGATTCACTAA

        
        
        .L..Q..L..S..F..
            +     +  +
        .Y..D..A..T..F..
1315801 CTATGACGCAACTTTCTTCTTCGGTTTTGATTGGCTTGATTTCATGAAACGGAAATTACATCAAAAAATGGC

                                                                      [+3c]
                                                                      1.1e-16
                                                                      F..K..Q..R
                                                                      +  +  +  +
                                                                      F..K..Q..K
1636057 TTGATGTGGCTTTTTAGGAAGAAGCAAAGCAGTTGGAGCAGCTGGAACTTTTCGCGAAGGATTTCAAGCAGA

                                                                               [
                                                                               6
        ..R..I..K..L..G..F..T..Q..A..D..V..                                    S
          +  +  +     +  +  +  +  +  +  +                                      +
        ..R..I..K..M..G..F..T..Q..G..D..V..                                    S
1636129 AGCGAATTAAGATGGGGTTTACTCAGGGTGATGTTGGACAAGCAATGGGTTGTCTGTATGGCAATGATTTCA

        +1c]
        .3e-15
        ..Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
          +  +  +  +  +  +  +  +  +  +  +  +     +
        ..Q..T..T..I..S..R..F..E..A..L..N..L..R..F..
1636201 GTCAAACCACCATTTCAAGATTTGAAGCACTGAACTTGAGGTTTGTTTGTTCAGTTGGAGTCTTAGTTTTGT

                            [+4c]
                            1.8e-13
                            K..N..M..C..K..L..K..P..L..L..Q..K..W..L..E..
                            +  +  +  +  +  +  +  +     +  +  +  +  +
                            K..N..M..I..K..L..K..P..M..L..E..R..W..L..L..
1636417 ATTGATCATTACACAGCTTTAAAAATATGATCAAGCTGAAGCCCATGCTAGAAAGATGGTTGCTGGATGCTA

                [+2c]
                2.1e-20
                L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                +  +  +  +  +  +  +  +  +  +  +  +  +  +  +
                M..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
1637353 AATGTAAAATGGAGAAGGAGGTAGTTCGTGTTTGGTTTTGCAACCGACGGCAAAAGCAAAAGAGAATATCGC

                                                      [+4b]
                                                      6.1e-07
                                                      K..N..M..C..K..L..K..P..L.
                                                      +  +  +     +           +
                                                      N..S..A..*..K..I..I..C..L.
1652401 TATAAATGGCACATTTTAAAAGTTAACAGATTATCATAAAAAATAGAATTCTGCTTGAAAAATAATATGTTT

        
        
        .L..Q..K..W..L..E..
            +  +  +  +  +
        .T..S..K..W..V..E..
1652473 GACATCAAAGTGGGTTGAGTTTTTAGGCACACTTTTGTTTGTATTAGAGGATTAACTTAATGATATTTAAAC

                                                                             [+2
                                                                             6.2
                                                                             L..
                                                                             +
                                                                             Y..
1665001 CAATTCGCCCCGCACCCTATATATAAATATAACGCATTAACTTACGTGCATGAAATAAATTTCTTATGCTAT

        a]
        e-07
        E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
           +     +  +     +     +     +  +
        *..R..L..V..I..A..V..C..F..F..N..R..A..V..
1665073 TGAAGGCTCGTTATAGCAGTATGTTTTTTCAATCGAGCTGTGGCGGTTTTCGACAAAACTATATATACTGCA

               [-2b]
               2.7e-08
               ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                          +     +  +  +  +  +  +  +
               ..N..S..S..N..Y..F..W..V..R..V..V..E..M..F..R
1680193 AAAGAACATTCGAAGAATTATAAAACCATACCCTCACGACTTCCATAAACCGTTGTTTATTGTTTAAAACTT

                                      [-2a]
                                      1.4e-07
                                      ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E
                                                 +     +  +     +  +  +  +
                                      ..N..S..S..N..Y..F..W..I..R..V..V..E..M..F
1714681 TCACGTTCCATTTGGTAGTAAACAAAGAACATTCGAAGAATTATAAAACCATATCCTCACGACTTCCATAAA

        
        
        ..L
        
        ..R
1714753 CCGTTGTTTATTGTTTAAAACTTGATTAGGATATTTGAATATTAGGTTTCCCATCTTCCCCCACAGTACTAT

                                                       [-3c]
                                                       3.4e-07
                                                       ..V..D..A..Q..T..F..G..L.
                                                            +     +  +  +     +
                                                       ..I..D..R..Q..T..V..N..L.
1718281 GATGACCTTGAAAATGAAACCTTGACGTGACAGATTTATTCTTATTGTATGTCTCGTTGTGTAACATTAAGT

        
        
        .K..I..R..R..Q..K..F
         +  +     +
        .K..I..*..K..V..R..I
1718353 TTTATTTATTTAACCCTAATTTTAGCATTGTTGTACTCAAGGATTTTTACATTTTATTATTACTTAGTTGCG

                                                        [-4a]
                                                        4.4e-07
                                                        ..E..L..W..K..Q..L..L..P
                                                             +     +  +  +  +  +
                                                        ..R..V..R..K..S..L..V..P
1825057 AGACGTACAATGGGAAGCTTATAGAAACATTTAATTGGATGACCGTGTTCTCACACGTTTGCTTAAGACGGG

        
        
        ..K..L..K..C..M..N..K
             +     +  +     +
        ..D..L..T..V..M..R..N
1825129 ATCTAAGGTTACCATTCTATTCGAACGAAATTATTTATCAATTGAATCAGCCCTCGGAACTAAACAAACTGA

                                         [-1a]
                                         1.6e-07
                                         ..F..S..L..Q..L..A..E..F..R..C..I..T..T
                                              +  +  +        +  +     +  +     +
                                         ..S..S..L..N..Q..K..E..F..L..C..I..N..S
1926001 ACACTGCGTGTATGTCAAACAGATCTAAGTTTATGAACTCAAATTTTGTTTTTCAAATAGGCAAATATTTGA

        
        
        ..Q..S
        
        ..L..W
1926073 TAACCAAAATTTCTCTTTTTAGGGTGGCAAAGGAGAGAAAGACAAAGGAAAAAAGAAGATTGGTGGAAGAGA

                                                            [+2b]
                                                            8.8e-07
                                                            L..E..K..E..V..V..R.
                                                                        +  +  +
                                                            R..S..M..G..V..V..R.
2076841 TTGAGCACAACATAATATTAAATTATCCTGATTGTGCTTAAACCATTAATAACGGTCTATGGGAGTCGTGAG

        
        
        .V..W..F..C..N..R..R..Q..
            +  +     +
        .I..W..F..Y..N..S..L..N..
2076913 AATATGGTTTTATAATTCATTAAATGTTTTTTGTTTACTACCAAATGGGACGAAAAAATAGGATGAAAAGGT

                           [-2b]
                           6.8e-07
                           ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                      +     +     +  +  +  +           +
                           ..F..L..S..N..Y..F..*..V..R..V..V..G..M..S..L
2127313 TTAGTAGTATACAAAGAACAAACAAAGAATTATAAAACTATACCCTCACTACTCCCATAGACAGTAGTTAAT

                                             [+1b]
                                             2.9e-07
                                             S..Q..T..T..I..C..R..F..E..A..L..Q.
                                                   +     +  +     +     +  +  +
                                             F..F..T..F..I..S..C..F..T..S..L..T.
2130049 TACAGCTTCAACTTTGATCTCCGGTTGATTTTCTTCTTTTTTCACCTTTATCTCTTGTTTTACTTCTTTAAC

        
        
        .L..S..F..
         +  +
        .L..S..L..
2130121 TTTATCTTTGGTTTGTTCATTTTCCACTTTTTTGGCAGTTTCTATATCAGGTTTACTTGTTTGTTGTTCTTC

                                           [-2c]
                                           3.7e-07
                                           ..Q..R..R..N..C..F..W..V..R..V..V..E.
                                                   +  +        +     +  +
                                           ..T..L..R..N..K..K..W..N..R..V..L..V.
2210833 AGAAGAGCGCAAGAAATTGCAAGATCTCAAACTAAAGTAAGCCGATTTTTTTTCCAATTCCGTACTAGAACC

        
        
        .K..E..L
         +  +  +
        .K..K..Y
2210905 TTCTTGTAGATATAGCTATTGCTGTCGAAATATGTACAAAACTCTTATTTAAACGGTACATTTTCCAGCAGA

                                                             [+4c]
                                                             5.1e-07
                                                             K..N..M..C..K..L..K
                                                             +        +     +  +
                                                             N..D..T..I..T..L..R
2220841 ATTATGTTTCTTTCCCTTTAAACTTCTTCAATATACAGTGTACGATACGCACGAATGACACAATAACACTGC

        
        
        ..P..L..L..Q..K..W..L..E..
             +  +  +     +
        ..L..L..L..A..H..W..S..K..
2220913 GACTATTATTGGCTCACTGGTCAAAATATTTTAGAATCTAAAACTTACATACAGAAACAATACAATAGCAGC

            [+2b]
            1.7e-08
            L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                  +  +  +  +  +        +  +  +
            R..S..K..E..V..V..R..I..R..F..C..N..S..L..Y..
2355193 ACAACGGTCTAAGGAAGTCGTGAGGATACGATTTTGTAATTCTTTGTATGTTCTTTGTTTACTACCAAATGG

                                       [+2b]
                                       6.8e-07
                                       L..E..K..E..V..V..R..V..W..F..C..N..R..R.
                                       +  +     +  +        +  +  +
                                       L..K..G..E..V..L..S..V..W..F..A..R..S..I.
2360953 ACCAAAACCGCAAGCGGAATTCGCCTTCGGCTTGAAAGGGGAGGTTTTGTCGGTTTGGTTCGCAAGATCTAT

        
        
        .Q..
        
        .S..
2361025 TAGCGCGCTTTTAGGCTTTAGTTAATTCGATCAGCAGTTTTAATAAAATAAGCCCATTGCGAATTATACGCC

               [-1b]
               9.9e-07
               ..F..S..L..Q..L..A..E..F..R..C..I..T..T..Q..S
                 +  +        +  +     +     +  +  +  +
               ..H..T..Q..E..L..S..N..F..V..C..I..A..S..S..A
2370745 CAACGTCGTGTGTTTGCTCAAGGGAATTGAATACGCATATCGCAGACGAAGCTAAACAATGTCTGCCCTATA

                                            [-2a]
                                            8.7e-08
                                            ..Q..R..R..N..C..F..W..V..R..V..V..E
                                                       +     +  +  +  +  +  +
                                            ..N..S..S..N..Y..F..W..V..R..V..V..*
2491273 CTATTTTTTCGCTCCATTTGGTAGTAAACAGAGAGCATTCGAAGAATTATAAAACCATACTCTCACGACTCA

        
        
        ..K..E..L
        
        ..G..V..S
2491345 TCCCACAGACCGTTGTTAATTGTTTAAAACACAATCAGGATATTTCAACACTATGTGCTATAAAGGCGTCTC

                                                     [+2a]
                                                     8.7e-08
                                                     L..E..K..E..V..V..R..V..W..
                                                                 +  +  +  +  +
                                                     S..V..G..*..V..V..R..V..W..
2491489 ATAGTGTTGAAATATCCTGATTGTGTTTTAAACAATTAACAACGGTCTGTGGGATGAGTCGTGAGAGTATGG

        
        
        F..C..N..R..R..Q..
        +     +
        F..Y..N..S..S..N..
2491561 TTTTATAATTCTTCGAATGCTCTCTGTTTACTACCAAATGGAGCGAAAAAATAGAATAAAGGGGTGTCCGAT

                [-4c]
                3.8e-07
                ..E..L..W..K..Q..L..L..P..K..L..K..C..M..N..K
                  +        +     +  +           +     +  +
                ..E..M..K..K..*..L..I..S..V..I..K..N..M..N..*
2544841 AATTGCAATTCCATCTTCTTTTACAAAATTGACACGATTTTGTTCATGTTTTAGACATGAAAACTTTAATAT

                          [-2a]
                          9.6e-07
                          ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                           +  +  +     +  +        +  +
                          ..N..S..I..S..I..F..W..V..Y..V..V..K..D..K..L
2562625 ACAGCTATACAAAAGATGGTTGCTTATTGATATAAACCATACATAAACAACTTTGTCTTTCAAATTAAAGCG

                                                         [-1b]
                                                         4.4e-07
                                                         ..F..S..L..Q..L..A..E..
                                                              +     +  +     +
                                                         ..Y..S..T..Q..L..C..E..
2667817 ACTTCAAATGTGGGCGATTTATTGCCTGTTTAGTCTTGTGTTGGATAACATACGAAGTCTGCAAGCACTCAA

        
        
        F..R..C..I..T..T..Q..S
        +  +           +
        F..R..H..F..C..T..M..N
2667889 AGCGATGGAAACAAGTCATATTTTCATGGCAGTGGAAAATAACTGGTCTGGCTTTCGCCATAACTACGCTGA

                                                           [-2a]
                                                           2.1e-07
                                                           ..Q..R..R..N..C..F..W
                                                                      +  +  +
                                                           ..L..S..S..N..C..F..G
2714905 CACCTTTTTCTTTTAATTTCTAGTCACATTTAGAAGTAAACAGAGAACATTCAATGAAGAATTACAAAACCC

        
        
        ..V..R..V..V..E..K..E..L
             +  +  +           +
        ..I..R..V..V..G..M..P..L
2714977 TATCCTCACGACTCCCATAGGCAGTTGTTAATTGTTTAAAACACGATCAGGATATTTCGATATTATGTGTTA

                                              [+2c]
                                              9.6e-07
                                              L..E..K..E..V..V..R..V..W..F..C..N
                                                       +  +  +  +  +     +     +
                                              R..S..M..E..V..V..R..V..R..F..Y..N
2801665 TATTCAAATATCATGATCGTGTTTTAATCAATTACCAACGGTCTATGGAAGTCGTAAGGGTTCGGTTTTATA

        
        
        ..R..R..Q..
        
        ..S..L..N..
2801737 ATTCTTTGAACGTTTTTTGTTTACTAGCAAATGGGACGAGAAAATGTAACGAAAATGTGTCCCATCTTTACT

                                                           [-4a]
                                                           4.6e-07
                                                           ..E..L..W..K..Q..L..L
                                                                   +     +  +  +
                                                           ..L..S..W..L..S..L..V
2808145 GAAGATCAAATGCGAACTGCTTTGCTTTATGGTGAAATCTACAACGCTTGTTAAACTCCACAAACTTAACAC

        
        
        ..P..K..L..K..C..M..N..K
          +  +  +        +     +
        ..P..K..L..S..S..A..L..K
2808217 CGGCTTGAGCGAGCTTGCTAACTTTGGTGCCGCAGTTGTAATAGTCTCGATGTGACGGGCGCCACGGCTGCA

                                  [-2c]
                                  7.4e-07
                                  ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                             +     +  +     +  +  +
                                  ..N..L..S..N..Y..F..W..I..R..V..V..G..L..S..R
2818801 CCAATTTGTTCGTGAACAAAAAAAACATTCAAAGAATTATAAAACCATATTCTCACAACTCCCAAAGACCGT

                                   [-2a]
                                   4.3e-08
                                   ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                              +     +  +     +  +  +  +
                                   ..N..L..S..N..Y..F..W..I..R..V..V..E..M..Y..F
2849833 CATGTTATTTGGTAGTAAACAAAGAACATTCAAAGAATTATAAAACCATATCCTCACGACTTCCATATAGAA

                                                                      [-2c]
                                                                      6.0e-07
                                                                      ..Q..R..R.
        
                                                                      ..E..E..K.
2975833 TCCAGCACAACACACATGCCCAGGACAAGTTATTCACCAGAATTGCTGATAGTTACATTGCTCTCTTCTTTA

        
        
        .N..C..F..W..V..R..V..V..E..K..E..L
            +     +  +        +     +  +  +
        .T..C..M..W..V..Y..S..V..F..K..E..L
2975905 GTGCACATCCAGACATAAGAGACAAATTTTTCAAGGTAAATTTTTGGCTTGAAACTGTCAAATAAAAGTACA

                          [-4a]
                          6.1e-07
                          ..E..L..W..K..Q..L..L..P..K..L..K..C..M..N..K
                               +  +  +     +  +  +  +        +        +
                          ..V..V..W..K..R..L..I..A..R..T..S..C..C..E..N
3045169 TTCTATTCTTACACAACCTACCACCCATTTTCTTAATATAGCCCGAGTAGAACAACATTCGTTCTGTTGTTG

                                             [-2b]
                                             3.7e-07
                                             ..Q..R..R..N..C..F..W..V..R..V..V..
                                                        +     +  +     +  +
                                             ..N..S..Y..N..Y..F..W..I..R..V..L..
3295729 TTCCTTTTCTTGTCCCAATGGGTAGTAAACAAAGAGCATTCGAATAATTATAAAACCATATCCTCACGAGTC

        
        
        E..K..E..L
                 +
        G..M..Y..L
3295801 CCATATACAGTTGTTAATTGTTTATATCATGATCAGCATATTTGGATATTATGTACTAAAGGTGTCCCATCT

                       [-2a]
                       2.8e-07
                       ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                     +  +  +  +  +  +           +  +
                       ..C..G..*..C..C..F..W..V..R..V..C..Q..S..D..Y
3439225 TTGTTTTAGCCAAAAACAACCTTAACAACAAAACCATACCCTAACACACTGTGAATCATACATAATAATGCA

         [-4b]
         9.8e-07
         ..E..L..W..K..Q..L..L..P..K..L..K..C..M..N..K
              +  +     +     +  +           +  +  +  +
         ..K..L..W..L..Q..G..V..A..G..V..T..C..M..S..N
3480337 TTTTAAGCCACAGTTGACCTACTGCCCCCACTGTACACATGCTATTTATGGCGGATAGTTATTTGAGCCATT

                                                    [-1c]
                                                    5.5e-07
                                                    ..F..S..L..Q..L..A..E..F..R.
                                                      +  +        +        +
                                                    ..H..T..N..L..L..K..A..F..G.
3647881 CGCCACCGTTAGATTCCGATCTATATACCTAGGATTTGCCATAAATGTGTGTTTAGAAGTTTCGCGAAACCG

        
        
        .C..I..T..T..Q..S
         +  +  +        +
        .C..I..T..H..T..S
3647953 CAAATCGTGTGTGTAGATGCGTATCCCAATCCCCTGCTCTTTATCTCAAGATCCAGCGCTCGCTTGTCAATC

         [-2b]
         1.9e-07
         ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                    +     +  +     +  +  +  +
         ..N..L..S..N..Y..F..W..I..R..V..V..E..M..F..R
3774889 CATTTAAAGAATTATAAAACCATATCCTTACGACTTCCATAAACCGTTGTTTATTGTTTAAAACTTGATCAG

                                                                      [-2c]
                                                                      2.6e-07
                                                                      ..Q..R..R.
        
                                                                      ..N..L..S.
3854521 GGGAGAAGATGGGACACATTTTCATTCCATTTTCTTTGTACGTTTTGTTGTAAACAAAAGACATTCAAAGAA

        
        
        .N..C..F..W..V..R..V..V..E..K..E..L
         +     +        +  +  +  +  +
        .N..Y..F..Q..I..R..V..V..E..R..S..R
3854593 TTATAAAACTGTATCCTCACGACTTCCCTAGACCGTTGTTAATTGTTTAGAAACCAATCAGGAAGTTTAAAT

                                                           [-1a]
                                                           4.3e-07
                                                           ..F..S..L..Q..L..A..E
                                                                +  +     +     +
                                                           ..S..S..I..K..L..D..E
3895921 TACGGTATGGCTGACAACTTAAACAATCCATATGGAAGGCTACTGTGTTGGAGAACTTATTTTTAAGTCTTC

        
        
        ..F..R..C..I..T..T..Q..S
          +  +     +           +
        ..F..R..T..I..C..I..*..S
3895993 AAATCTTGTAATGCAGATCTACGACACCGAACTTGAGAATGCGAACGAGTTTTCAGGTTTTAACGACCTTTT

           [-1a]
           6.4e-08
           ..F..S..L..Q..L..A..E..F..R..C..I..T..T..Q..S
                +  +  +  +  +     +  +  +     +
           ..V..S..L..N..L..N..G..F..R..C..V..T..N..*..*
3930625 ACGAACCGATAAGTTCAAGTTTCCGAAACGACAAACGGTATTTTATCAACAATAGATAAACGACTAAAAACA

           [-2a]
           8.4e-07
           ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                      +  +  +              +     +  +  +
           ..I..L..A..N..C..F..N..G..S..Y..V..Q..K..E..L
3963313 ACTGATTAATGCATTGCAGAAATTTCCAGAGTATACCTGTTTCTCTAAAATGAGGACTTGTGATTGTCATAA

                                                                         [+1c]
                                                                         1.2e-08
                                                                         S..Q..T
                                                                         +     +
                                                                         S..H..S
4033225 AAACCCAAAAAGAAATGCACTTGTAGTACTGTGGGGTAAGATGGATGTCGATATAGCACATTTTATCCCATT

        
        
        ..T..I..C..R..F..E..A..L..Q..L..S..F..
                +  +  +     +     +  +  +  +
        ..S..*..S..R..F..N..N..*..Q..L..S..F..
4033297 CTTCATAATCGCGTTTTAACAATTAACAACTCTCTTTTACAATCGTGAGGTAACGGTTATATAATTCTGTAA

            [+1b]
            1.2e-08
            S..Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
            +     +        +  +  +     +     +  +  +  +
            S..H..S..S..*..S..R..F..N..N..*..Q..L..S..F..
4054105 TTTATCCCATTCTTCATAATCGCGTTTTAACAATTAACAACTCTCTTTTACAATCGTGAGGTAACGGTTATA

                                  [+2c]
                                  8.4e-07
                                  L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                                  +     +        +        +  +     +
                                  L..Y..R..S..L..V..K..I..W..F..Y..N..S..L..V..
4116241 TTATGTTTTAAACAATTAACAACGGTCTATATAGGAGTCTCGTGAAAATATGGTTTTATAATTCTTTGGTTG

            [-4b]
            1.7e-07
            ..E..L..W..K..Q..L..L..P..K..L..K..C..M..N..K
                 +        +  +  +     +  +  +  +  +     +
            ..L..L..G..L..S..L..V..L..K..L..K..I..A..T..K
4139497 TGGACAATAATCCCAGACTGAGGACTAACTTCAATTTGATTGCGGTTTTCATCTTTCTAATAAGAACAAAGA

                                                                    [-4a]
                                                                    9.3e-07
                                                                    ..E..L..W..K
                                                                      +     +  +
                                                                    ..E..R..W..A
4148785 TTTGGTTATTAGGAGAATGAAGGTATAATAAAAATAGTATTCAAAACTAAAAAAATGATATTCACGCCATGC

        
        
        ..Q..L..L..P..K..L..K..C..M..N..K
             +     +        +        +  +
        ..*..L..*..A..Q..*..K..N..I..N..K
4148857 TTATAACTATGCTTGTCATTTATTGATGTTTTTTATTTGTATTAGGTAAATGAACAAAATCCTCAAGTGTTT

         [+1b]
         8.0e-07
         S..Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
         +           +  +     +        +  +  +  +  +
         S..*..P..G..I..S..T..F..Q..*..L..D..I..S..H..
4188385 ATCCTGACCTGGAATCTCAACTTTTCAATAACTTGACATCAGCCATACAATTACTACAAGGTAAGATAATGT

                                                           [-2a]
                                                           8.0e-08
                                                           ..Q..R..R..N..C..F..W
                                                                      +  +  +  +
                                                           ..H..L..F..N..C..F..W
4231657 GGACATCATTTCATTTTATTTACTCGTCTCACTTGGTAGTAAAAAAAGAAAATGCAAAAAATTACAAAACCA

        
        
        ..V..R..V..V..E..K..E..L
             +  +  +
        ..I..R..V..V..G..T..S..R
4231729 TATCCTCACAACTCCCGTAGACCGTTGTTAATTGTTCAAATCACAATCAAGATGTTTGGAGATTATGAGCTA

          [+4c]
          3.3e-07
          K..N..M..C..K..L..K..P..L..L..Q..K..W..L..E..
          +           +     +  +  +  +  +  +     +
          N..L..L..K..K..I..K..P..I..L..Q..K..F..V..H..
4348441 AAAACCTTCTTAAAAAGATCAAACCAATCTTGCAGAAGTTTGTCCACGATGACACCAACTTACAACTACATG

                                                                            [+4c
                                                                            9.3e
                                                                            K..N
                                                                            +  +
                                                                            N..S
4355281 TAAATTTTGAACGTATATATACTGTGTTTTGTAAATTTTGAACATATTCAGTTTTTAAACATCTACAAAATT

        ]
        -07
        ..M..C..K..L..K..P..L..L..Q..K..W..L..E..
                +     +  +  +  +     +
        ..Q..N..A..I..K..P..I..L..I..K..Y..*..L..
4355353 CCCAAAATGCAATTAAACCCATACTTATAAAATATTAATTACAAGTCGCATTAATTAATTTGGCAAATACAC

                                              [+2c]
                                              1.9e-07
                                              L..E..K..E..V..V..R..V..W..F..C..N
                                                          +  +  +  +  +  +     +
                                              R..S..M..G..V..V..R..V..W..F..Y..N
4426489 AATCCAAATATTCTGATCATGTTTTAAACAATTCACAACGGTCTATGGGAGTTGTAAGGGTATGGTTTTATA

        
        
        ..R..R..Q..
        
        ..T..L..N..
4426561 ATACTTTGAATGTTCTTTGTTTACTACCAAATGGGACAAAAATAATTAAAGGGTGTCCCATCTTTCCCTACC

           [-2a]
           4.6e-07
           ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                +           +           +  +     +  +  +
           ..M..R..*..V..Y..F..F..I..S..V..V..S..R..K..L
4569769 TCCCATTCGCTAAACATAAAAGAAAATTGAAACTACGCTGCGTTTTAATAGTGTATATACGGCCATAGATAC

                  [+1b]
                  7.1e-07
                  S..Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
                  +     +        +     +  +        +  +  +
                  S..L..T..S..L..S..P..F..E..L..G..T..I..S..L..
4952521 TAGCGATCAAAGTTTGACGAGCCTCTCTCCTTTTGAACTTGGCACAATTTCTCTTACTTGTTGGTTTAATAT

                        [+3b]
                        7.8e-07
                        F..K..Q..R..R..I..K..L..G..F..T..Q..A..D..V..
                              +  +        +  +        +  +  +  +  +
                        E..R..I..R..N..C..K..L..S..K..T..Q..G..N..V..
4967569 GGAAATTGTGGTTTCTGAAAGGATAAGAAACTGCAAATTATCTAAAACTCAGGGAAACGTTTAAAATCATGT

                [-3c]
                3.8e-07
                ..V..D..A..Q..T..F..G..L..K..I..R..R..Q..K..F
                  +     +     +  +  +        +     +        +
                ..V..S..A..T..T..V..G..I..I..I..N..R..R..R..F
5135617 CAGATGGTTACAGAAGCAGTGGTAACACCAATGATAATGTTGCGCCTTCTAAACAGAGCAAAGAATCTTGTA

                                                          [+3c]
                                                          7.8e-07
                                                          F..K..Q..R..R..I..K..L
                                                          +     +     +     +  +
                                                          F..I..Q..C..R..E..S..L
5147065 ACTTAATTGCCCCCCAAAAAATAATTAATTACATTTTCCGAAATGGTTGCTTTATACAGTGTAGAGAAAGTC

        
        
        ..G..F..T..Q..A..D..V..
          +           +     +
        ..G..L..S..L..A..Y..V..
5147137 TTGGCCTAAGTTTAGCTTATGTGTCACAATTTGACATTACAATTATCATTATAATACAATTTAAATAGTTTG

                                        [-2c]
                                        5.7e-07
                                        ..Q..R..R..N..C..F..W..V..R..V..V..E..K.
                                             +     +     +     +     +        +
                                        ..F..R..I..N..Y..F..F..V..Q..V..C..Q..K.
5233033 ATTATATGATGCAAAAATTATATGATGCTTAAAAACCTAATGTTGTAGAAAAATACCTGAACACATTGTTTT

        
        
        .E..L
            +
        .R..Y
5233105 CTATAGAGTTTGTGAGTTCAGTAAGACTGAGTGCTTTTGCGCATGATTTGACTACAAATTTCACGGCTTCAA

                        [+2b]
                        4.0e-07
                        L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                        +     +  +  +  +  +        +     +
                        L..F..K..E..V..V..R..P..L..F..D..N..L..I..I..
5349097 GGAACCTGTAAGACCTTTGTTTAAGGAAGTTGTAAGACCTTTGTTTGATAACTTAATAATAGTTGTCACATG

                             [-3a]
                             4.7e-07
                             ..V..D..A..Q..T..F..G..L..K..I..R..R..Q..K..F
                                  +  +  +     +     +  +  +  +  +     +
                             ..R..N..T..Q..W..F..S..L..S..I..R..R..L..K..G
5412025 TATGCTTTGCTAAATCAACTGTCTGTTTGTTTGCCAAAACGACAAACTAATGCGGCGCAATTTACCCTGCGA

                             [+2a]
                             2.6e-07
                             L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                             +     +  +  +        +           +  +     +
                             L..Q..R..N..V..C..S..V..S..R..*..N..R..T..Q..
5476969 TTTATATCAACTTGTATTTTTTTACAAAGAAATGTGTGTTCTGTAAGTCGTTAAAACCGAACACAAAACGTG

                                               [+2a]
                                               6.8e-07
                                               L..E..K..E..V..V..R..V..W..F..C..
                                                        +  +  +  +        +  +
                                               Q..S..M..E..V..V..R..I..Q..F..C..
5526001 GACACTATCTTGATCGTTGTTTTTAAAAACAATTAGCATCAGTCTATGGAAGTTGTAAGGATACAGTTTTGC

        
        
        N..R..R..Q..
        +
        N..S..L..N..
5526073 AATTCTTTGAATGTCTTTGTTTACCACCAAATACGACGAGAAAATAGAATGAAAAGGTGTCCTATCTTTCCC

                    [+3a]
                    8.2e-07
                    F..K..Q..R..R..I..K..L..G..F..T..Q..A..D..V..
                    +  +        +     +     +  +  +     +     +
                    L..K..E..S..R..N..K..R..G..V..T..F..T..T..V..
5582809 AGGAAGTACTCGCTAAAAGAGTCGCGAAATAAACGTGGTGTCACATTTACTACCGTTGCGCGGGTGGTAAAG

                                            [+2a]
                                            4.1e-08
                                            L..E..K..E..V..V..R..V..W..F..C..N..
                                            +           +  +  +     +  +     +
                                            L..S..M..G..V..V..R..I..W..F..Y..N..
5597713 TACAAATATCCTGATCTTGTTTTAAACAGTTAACAACTGTCTATGGGAGTCGTGAGGATATGGTTTTATAAT

        
        
        R..R..Q..
        
        S..L..N..
5597785 TCTTTAAATGTTCTTTATTTACTACCAAGTGGGACAAGAAAATAGAACTAAAAGGTGTCCCATCTTCTCGCA

                    [-2a]
                    6.5e-07
                    ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                               +  +  +     +     +     +  +
                    ..Y..K..K..N..C..F..S..V..S..V..K..D..K..T..S
5603905 AGTATAATTTCTATACTTTTTATTGCAGAAAGAAACAGAAACTTTATCTTTTGTTGAAAAACTTCTGACACA

                          [-2a]
                          8.8e-07
                          ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                     +     +  +     +  +  +
                          ..I..L..S..N..Y..F..W..I..R..V..V..G..I..S..R
5628673 TTTTAGTAAACAAAGAACAATCAAAGAATTATAAAACCATATCCTCACGACTCCTATAGACCTTTGTTGATT

                                  [-2c]
                                  7.7e-07
                                  ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                          +        +  +     +  +        +  +
                                  ..P..Y..R..T..A..F..W..L..R..V..K..G..K..E..R
5704201 GTTCCAGTCTATTATGGTGTGGTGTATGGATAGCGAGTAGCGAACCAGAGTCTCACTTTCCCTTTTTCTCGC

                                                        [+2a]
                                                        2.1e-07
                                                        L..E..K..E..V..V..R..V..
                                                        +        +  +     +
                                                        Y..Q..V..N..V..K..R..I..
5737249 CGACAAGAGAATGTTCGGAACTTGTGGTTGAGGCCACTTACAAGACGATACCAAGTTAATGTGAAACGAATT

        
        
        W..F..C..N..R..R..Q..
           +     +  +     +
        R..F..R..N..R..A..Q..
5737321 CGTTTTCGAAACCGAGCACAGAACTTTACTAATGACCAAACACAGGTTAATACAGTTTAAATATTTCGTTTT

                                                              [+2a]
                                                              4.4e-07
                                                              L..E..K..E..V..V..
                                                                       +  +  +
                                                              R..F..V..E..V..V..
5961241 NNCCTTTAACAGATAGTTTTCAAATAGCCTGATCGTGTTTTAAAGAATTAACAACGGTTTGTGGAAGTCGTA

        
        
        R..V..W..F..C..N..R..R..Q..
        +     +  +     +
        R..I..W..F..H..N..S..L..D..
5961313 AGGATATGGTTTCATAATTCTTTGGATGTTCTTTGTTTACTACCAAATGGAAAGAGAAAACTAAATGAAAAG

                                           [+2c]
                                           1.9e-07
                                           L..E..K..E..V..V..R..V..W..F..C..N..R
                                                    +  +  +  +     +  +     +
                                           R..S..V..E..V..V..R..I..W..F..H..N..S
5964841 CCAAATAGCCTGATCGTGTTTTAAAGAATTAACAACGGTCTGTGGAAGTCGTAAGGATATGGTTTCATAACT

        
        
        ..R..Q..
        
        ..L..D..
5964913 CTTTGGATGTTCTTTGTTTACTTCCAAATGGAAAGAGAAAACAAAATGAAAAGGTGTCCCATCTTCCCCCAT

                                                                          [+1a]
                                                                          1.5e-0
                                                                          S..Q..
        
                                                                          H..L..
6022513 ATCCAAAATAACACTTTTGCAAATTGAAAGAACTTTTTTTTTCAAATTTAAACATTTTTAAAATTGCACCTT

        
        7
        T..T..I..C..R..F..E..A..L..Q..L..S..F..
              +  +     +     +  +  +  +  +  +
        F..*..I..C..T..F..L..S..L..N..L..S..F..
6022585 TTTTAAATTTGCACCTTTTTAAGTTTAAACCTGTCTTTTAATGCTGGCTATTTTTAGTCACCACTGTGGCCT

         [-2b]
         7.1e-07
         ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                    +     +  +     +  +  +
         ..N..L..S..N..Y..F..W..I..R..V..V..G..L..S..Q
6343633 CATTCAAAGAATTATAAAACCATATCCTTACGACTCCCAAAGACTGTTGTTAATTGTTTAAAACATGATCAG

                        [+4b]
                        1.9e-07
                        K..N..M..C..K..L..K..P..L..L..Q..K..W..L..E..
                        +  +  +  +  +                 +  +  +  +  +
                        N..N..A..C..K..Y..S..L..F..T..N..K..W..V..E..
6443137 TCGTGTTTCAACAATTAACAACGCTTGTAAATATTCTTTGTTTACTAATAAATGGGTCGAATAAAAAATTGG

                     [+4b]
                     5.9e-07
                     K..N..M..C..K..L..K..P..L..L..Q..K..W..L..E..
                     +  +  +  +  +           +  +  +        +  +
                     N..S..A..V..K..I..V..K..I..L..N..M..K..L..E..
6457753 CTCGCGACTCTGAAATAGCGCTGTTAAAATTGTTAAAATCTTGAATATGAAACTCGAGTATTATCTGTAACC

                                                                      [-2c]
                                                                      4.6e-07
                                                                      ..Q..R..R.
        
                                                                      ..C..L..V.
6472009 GAGTGGGTTAAAGATGCGACGAAGTCACATTCATTCTATTTTCTTGTCCAATTTGGTAGTAAACAAAGAACA

        
        
        .N..C..F..W..V..R..V..V..E..K..E..L
         +     +     +  +  +  +     +
        .N..F..F..Q..V..R..V..V..G..K..S..W
6472081 TTAAAAAACTGTACCCTCACGACTCCCTTAGACCATTGTTAATTGTTTAAACACAATCAGGATATTTTGGAT

                                                         [-4b]
                                                         3.8e-07
                                                         ..E..L..W..K..Q..L..L..
                                                              +     +     +  +
                                                         ..K..L..E..R..H..L..L..
6623713 GGAGCAGAATAATGCTTTGATTGTGAAAGAAATGACTTTCCAGGTCGCTTTTTAGTTCTCGGTGTAAAAGGT

        
        
        P..K..L..K..C..M..N..K
           +  +  +  +        +
        N..R..L..K..I..S..D..K
6623785 TTCTCAGTTTTATTGAATCTTTCTTCATGTCTTTCCAGATAATCCCCGTTATAAGTTACATCCATAACTTGT

                    [-2a]
                    2.2e-08
                    ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                               +     +  +     +  +  +     +
                    ..L..*..S..N..Y..F..W..I..R..V..V..K..K..S..R
6715585 TTAGTAAACGAAAAGCTAAGAATTATAAAACCATATCCTCACGACTTTCTTAGACCGTTTAATAATTGTTTA


chr02q
  
  LENGTH = 8059593  COMBINED P-VALUE = 2.06e-23  E-VALUE =  9.1e-20
  DIAGRAM: 181586_[+1c]_84138_[-3c]_15167_[-2b]_135571_[-4c]_325471_[+4a]_
           12798_[-4a]_4700_[-2c]_182142_[-1c]_7912_[-1a]_80644_[-2b]_143591_
           [-2a]_5286_[-1a]_17554_[-4b]_104512_[+2c]_75992_[-2b]_1994_[+2a]_
           7759_[-2b]_11678_[+4a]_544_[+2b]_15348_[+2b]_53558_[+2a]_756_[-2a]_
           132170_[-3c]_6820_[+1a]_226852_[+2b]_107962_[+1c]_5949_[-2c]_138458_
           [-4b]_133762_[+1c]_126753_[-2c]_69234_[+1c]_33_[+1c]_72_[+1c]_150_
           [+1c]_33_[+1c]_72_[+1c]_267_[+1c]_33_[+1c]_15489_[-1c]_21704_[+1b]_
           72_[+1b]_346_[+1c]_96059_[-4b]_36498_[-2b]_335_[-4a]_[-1a]_155_
           [-3c]_18189_[-1c]_174870_[-2c]_38785_[+1a]_40123_[+2b]_147684_[-1b]_
           122397_[+2b]_45479_[+4a]_74846_[+1c]_23231_[+3b]_38245_[-4c]_152196_
           [-2c]_304660_[+2a]_165655_[-4b]_38440_[-4c]_21816_[+1c]_25500_[-2c]_
           336004_[+3a]_323232_[-4a]_7268_[+2c]_47044_[+4a]_41451_[-2a]_66303_
           [+2a]_30342_[+1a]_40657_[-4b]_180301_[-2c]_35205_[-2c]_59610_[-2c]_
           2222_[+1b]_1400_[-2a]_53171_[-2c]_175866_[-2c]_162426_[-2c]_70915_
           [+2a]_33010_[-1b]_139023_[+1b]_248403_[-2b]_102258_[+2b]_13294_
           [-4c]_85097_[+2b]_13395_[-4b]_217923_[-2b]_252830_[-2a]_40346_[-3c]_
           9779_[+1b]_15798_[-1b]_16835_[+1a]_31854_[-2a]_3867_[+2a]_28000_
           [+1b]_14934_[+2b]_18632_[+4a]_54520_[+2b]_53902_[+1c]_198948_[-2c]_
           10079_[+1b]_162971_[-2a]_106411_[+2b]_74994_[-4b]_11202_[-4b]_165552_
           [+2b]_7010_[-2a]_12481_[-2b]_23349_[+1b]_102412_[+2c]_100606_[-4a]_
           31326


          [+1c]
          5.5e-07
          S..Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
          +              +  +     +  +  +     +  +  +
          S..S..P..S..L..S..R..N..E..S..L..R..I..T..F..
181585  CATCAAGTCCGTCATTATCGAGAAACGAATCGTTGAGAATTACCTTCTTCTCTTCTTCTCTCAAGCGAGTTT

                         [-3c]
                         1.9e-07
                         ..V..D..A..Q..T..F..G..L..K..I..R..R..Q..K..F
                           +        +  +  +  +  +     +           +  +
                         ..V..L..S..Q..T..V..G..L..L..I..N..V..F..K..L
265753  AGCCAAATAAAACACAGGACCAAACTCTGGGTAACACCTAAAAGTATGTTAACAAACTTCAAGGGGAAATTG

                                             [-2b]
                                             8.4e-07
                                             ..Q..R..R..N..C..F..W..V..R..V..V..
                                                        +     +  +        +
                                             ..Y..*..N..N..Y..F..W..Q..*..I..F..
280945  AAAAAAACATGACATATACAGTGTGTTAAGGCTGGTAATACTAGTTGTTGTAAAACCATTGCTAAATAAACT

        
        
        E..K..E..L
        +  +     +
        E..K..M..L
281017  CTTTCATTAAAACTAGAACTAAAATAATGTGACAGAAAATATACTTACTGCATTGATAATATATGATGAATA

             [-4c]
             2.3e-07
             ..E..L..W..K..Q..L..L..P..K..L..K..C..M..N..K
               +  +  +     +  +  +  +  +              +  +
             ..N..L..W..S..Q..L..V..P..K..G..I..A..E..S..N
416593  ATGGAATTTAGCCAAGATTGCAGAACAGGTTTGCCTATTGCTTCAGAATTATGATTGTTACGCCTAGATGAA

                 [+4a]
                 8.5e-07
                 K..N..M..C..K..L..K..P..L..L..Q..K..W..L..E..
                 +  +        +  +        +  +        +  +
                 N..S..F..Y..K..L..V..*..L..L..I..S..W..L..*..
742105  TGGCAAAGTAACAGTTTTTATAAATTAGTTTAGCTTCTTATATCTTGGCTATAAACTTAAAAATTCATTATA

                                            [-4a]
                                            5.3e-07
                                            ..E..L..W..K..Q..L..L..P..K..L..K..C
                                                       +     +     +  +     +  +
                                            ..I..G..Q..K..F..L..*..P..K..I..K..V
754921  TTCACTGTGAGTTAACCAAAAACTCCAGACATGCAGTATACCTTGTTTAAATAGTTACGGCTTTATTTTGAC

        
        
        ..M..N..K
          +  +  +
        ..A..N..N
754993  AGCATTGTTTTATCGTTAAACCCATATGTTTGCCAACAAATTACTTTTATTTGTTTAACTTTTTGCACTTTT

                                     [-2c]
                                     4.8e-07
                                     ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E.
                                       +        +     +           +  +  +  +
                                     ..Q..W..V..N..G..F..D..F..Y..I..V..N..K..Q.
759673  TGGGGGAAGATGGGACACTTAAACATATATTGCCAAACATTTCCAAAATCAAAATAGATGACGTTTTTTTGG

        
        
        .L
         +
        .Y
759745  TAATACCACGAAGTAGTACTACTATTCCTTTATTAATTGACAACGATTTAATAATATAAATATAATAAAACA

                                                                [-1c]
                                                                6.2e-07
                                                                ..F..S..L..Q..L.
                                                                     +  +
                                                                ..L..S..L..S..Y.
941833  TATGTTTAATATTCAAAATTGATTAGCAACAAGTTAGGGTATCTGTTTGCGATTTTGAGGCTTAAAGAATAT

        
        
        .A..E..F..R..C..I..T..T..Q..S
            +  +  +     +
        .K..E..F..R..N..I..S..K..H..T
941905  TTTTCAAATCTATTTATTGATTTGTGTGTTTGAGGGAAATATTAGTTCTCTGTTTTGAATTAAAATATATTA

                             [-1a]
                             6.2e-07
                             ..F..S..L..Q..L..A..E..F..R..C..I..T..T..Q..S
                                  +  +           +  +  +     +
                             ..L..S..L..S..Y..K..E..F..R..N..I..S..K..H..T
949825  AGGGTATCCATTTGCGATTTTGAGGCTTAAAGAATATTTTTCAAATCTATTTATTGATTTGTGTGTTTGAGG

                                                                              [-
                                                                              8.
                                                                              ..
        
                                                                              ..
1030465 GTATTGCATTGGTGCGATGTATAGTAGAGTGGGGGAATTTTCTCGACTCATTTGATAGTAAATATAAAACAT

        2b]
        0e-08
        Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                 +     +  +     +  +  +  +
        N..L..S..N..Y..F..W..I..R..V..V..E..M..S..R
1030537 TCAAAGAATTATAAAACCATATCCTCACGACTTCCATAGACCGTTGGTAAATATTTAAAACACGATCAGAGT

                                                                          [-2a]
                                                                          5.5e-0
                                                                          ..Q..R
        
                                                                          ..V..*
1174105 TTGGTGGGGGAAGATGGGACACCTTTTTATTCTATTTTCTTGTGTCATTCGGTAGTAAACAAAGAACACTCA

        
        7
        ..R..N..C..F..W..V..R..V..V..E..K..E..L
             +     +     +  +  +  +           +
        ..F..N..Y..F..R..V..R..V..V..G..A..T..L
1174177 AAAATTATAAAACCGTACCCTCACGACTCCCGCCGTTAGTAGTTGTTAAAAACAAGATCAAGATGTTTGGAC

                                                                             [-1
                                                                             2.4
                                                                             ..F
                                                                               +
                                                                             ..F
1179433 TATCAATTTATTATACAATCATATACTGTGGGTAACATGTTAAAAACCATAGCAGTAGGGCAGGACAAAAAA

        a]
        e-08
        ..S..L..Q..L..A..E..F..R..C..I..T..T..Q..S
          +  +     +  +  +  +  +     +        +
        ..T..L..I..L..N..E..F..R..K..I..N..N..Q..*
1179505 TGTTAAAATTAGATTTTCAAACCGTTTAATATTATTTTGTTAAGTTTACGTGTATTTCTAATAATAAATTCA

                                    [-4b]
                                    4.4e-07
                                    ..E..L..W..K..Q..L..L..P..K..L..K..C..M..N..
                                      +        +     +  +        +     +  +  +
                                    ..N..K..V..K..K..L..V..S..F..L..Y..C..M..N..
1197073 TGTCGCAAATCAACCGCTTCTAATTCTAATTTTTGACTTTTTTTAACACAGAAAACAAATAACACATGTTTT

        
        
        K
        +
        K
1197145 TTACATTTTTCAACCTTTAAATTTGTTTTTAGGCCCAAGTTTTTCTGTAATTTACCGAAAAACATACATTTT

                                                 [+2c]
                                                 1.4e-07
                                                 L..E..K..E..V..V..R..V..W..F..C
                                                             +  +  +  +  +  +
                                                 R..S..M..*..V..V..R..V..W..F..Y
1301617 TAATATCCAAATATCCTGATCGTGTTTTATACAGCCACCAACGGTCTATGTGAGTCGTGAGGGTGTGGTTTT

        
        
        ..N..R..R..Q..
          +
        ..N..S..S..N..
1301689 ATAATTCCTCGAATGCTCTTTGTTTACTACCAAATTGGACGAGAAAATAGAATGAAAAGATGTCCCATCTTC

                                                      [-2b]
                                                      6.2e-07
                                                      ..Q..R..R..N..C..F..W..V..
                                                        +        +     +
                                                      ..Q..L..I..N..*..F..R..L..
1377649 ATTATTCTATCGTTGAGTGGAGTTAGAGGGGACATTTATGCACATATTGAAGAATATTTTAAAATCTTAAAT

        
        
        R..V..V..E..K..E..L
           +  +     +  +  +
        D..I..V..S..R..E..L
1377721 CTATAACGCTTCGTTCGAGCATCTCTAGCTACAAAATATTTTGAATTCCTGTTAACTTTTAATGCTAAATAT

                                                                             [+2
                                                                             2.5
                                                                             L..
        
                                                                             Q..
1379665 TTTCGTACTGTAGGACACCTTTAGCACATAATATCGAAATATTCTGATCGTATTTTAAACAATTAACAGCAG

        a]
        e-07
        E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                 +  +  +  +  +  +     +
        S..M..A..V..V..R..V..W..F..Y..N..F..L..N..
1379737 TCTATGGCAGTCGTCAGGGTGTGGTTTTATAATTTTTTGAATGTTCTTTGTTTACTAATAAATAGGACGAGA

                                 [-2b]
                                 1.8e-07
                                 ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                            +     +        +  +  +  +  +
                                 ..H..L..S..N..Y..F..R..I..R..V..V..E..R..P..R
1387513 CCCAATTTGGTAGTAAACAAATAAAATGCAAAGAATTATAAAAGCGTATCCTAACGACTTCCCTAGGCCGTT

                    [+4a]
                    4.6e-07
                    K..N..M..C..K..L..K..P..L..L..Q..K..W..L..E..
                    +  +  +  +        +  +  +  +
                    N..N..A..C..C..I..K..A..I..L..G..T..F..M..I..
1399249 CGGGTAAACAATAATAACGCGTGCTGTATCAAAGCTATTCTTGGAACATTCATGATCCATCTATTTCTAAGT

                                 [+2b]
                                 8.8e-07
                                 L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                                 +  +  +  +     +           +           +
                                 L..E..K..N..L..V..F..I..S..F..K..*..N..R..*..
1399825 CTGGTAAGCATATGCAAGATTCCTCTTGGAAAAAAATCTTGTGTTTATCTCATTTAAGTGAAACCGATAATG

                  [+2b]
                  4.3e-08
                  L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                           +  +  +  +     +  +     +
                  V..S..M..E..V..V..R..I..W..F..Y..N..S..S..N..
1415233 AAATTAACAAGTGTCTATGGAAGTCGTGAGAATATGGTTTTATAATTCTTCGAATTTTCTTTGTTTACTACT

                                                     [+2a]
                                                     2.4e-07
                                                     L..E..K..E..V..V..R..V..W..
                                                     +        +  +  +  +
                                                     L..S..M..E..V..V..R..I..L..
1468801 GCACATAATTTCCAAATATCCTGATCGTCTTTTAAACAATTAAAACTGTCTATGGAAGTCGTAAGGATACTG

        
        
        F..C..N..R..R..Q..
        +     +
        F..Y..N..S..L..N..
1468873 TTTTATAATTCCTTGAATGTTCTTTGTTTACTACCAAATGCAATGAAAAAGTAGAATAAAAGGGTGTCCCAT

                                                              [-2a]
                                                              5.7e-07
                                                              ..Q..R..R..N..C..F
                                                                         +     +
                                                              ..V..S..N..N..T..F
1469593 ACTTTGCATCATGTTGAGGCTCTGGTGCTTGGAAATTAACCTCTTCCACTAACAAACGCTGTTGTTCGTAAA

        
        
        ..W..V..R..V..V..E..K..E..L
             +        +  +  +     +
        ..S..V..I..*..V..E..K..S..L
1469665 ACTAACAATTCACACTTCTTTGCTTAAGCATGGGCAGGAAATGTCAGAATGTCATTTTGAGATCGCTCTCAC

             [-3c]
             9.0e-07
             ..V..D..A..Q..T..F..G..L..K..I..R..R..Q..K..F
                     +     +     +  +  +  +  +  +     +  +
             ..C..K..A..T..T..A..G..L..K..I..R..K..N..K..L
1601857 GTAAAACATTTCGCCGTAGTGGCACCGAGTTTAATGCGCTTGTTTTTTAACCAGAGAACATGTGGTGTAAAT

                                      [+1a]
                                      7.4e-07
                                      S..Q..T..T..I..C..R..F..E..A..L..Q..L..S..
                                      +        +     +     +  +     +     +  +
                                      S..R..L..T..P..S..V..F..E..K..L..H..L..S..
1608697 TTAATCCGAATTAACAAGAATTTATAACTGTCTCGACTTACCCCGTCTGTTTTCGAAAAATTACACCTGTCA

        
        
        F..
        
        S..
1608769 AGCGAACCGCTAAATAACTCGTGTGTTTTATTATATTTTTTGACCAATAGAGTTATCAACTAATAAAGGTAT

                                                               [+2b]
                                                               9.1e-08
                                                               L..E..K..E..V..V.
                                                                     +        +
                                                               D..R..K..G..H..I.
1835569 AGGGAACGCGGAAGTTGGTGGGGCATGTTTTGCTTGGGAGGAGTTCCCATACAAAGATCGTAAAGGCCACAT

        
        
        .R..V..W..F..C..N..R..R..Q..
            +  +  +     +  +  +
        .Q..V..W..F..R..N..R..R..G..
1835641 TCAAGTGTGGTTTCGAAACAGACGCGGTGAAGGCGTCATTTTCTCCTGCGTATATCGTCAGGATTGTATGAA

                                                                      [+1c]
                                                                      5.1e-07
                                                                      S..Q..T..T
                                                                            +
                                                                      K..L..T..S
1943569 GTACGACCTGGGACCAAACCGGCCACTTCAAACCTTTAACCCTGATCATATGAGTGTAGAAAAAGCTTACGT

        
        
        ..I..C..R..F..E..A..L..Q..L..S..F..
          +  +  +     +  +  +     +  +
        ..I..C..R..S..E..A..L..W..L..T..Q..
1943641 CAATCTGCAGAAGCGAGGCTCTATGGTTAACCCAGCAGATGAACCCAAACTTGGATATGCCGCACATCCCCA

                [-2c]
                8.8e-07
                ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                           +     +  +     +  +  +
                ..N..L..S..N..Y..F..W..I..R..V..V..G..M..S..R
1949617 CAAAGAGTGTTCAAAGAATTATAAAACCATATCCTCACGACTCCCATAGACCGTTGTTAATTGTTTAAAACA

                                                               [-4b]
                                                               6.7e-07
                                                               ..E..L..W..K..Q..
                                                                    +     +
                                                               ..L..L..E..K..*..
2088073 CTGGTGGCTGACTCTGATGAAGACGGAACAATATCTTTTCGTGAATTTCTGGACATAATAGTTCTTTTTACA

        
        
        L..L..P..K..L..K..C..M..N..K
        +  +     +  +  +        +  +
        L..L..H..K..L..K..K..N..N..K
2088145 AAAGGTGCTTCAACTTTTTGTTATTTTTTTTTCCTATTTAATTATTTTTACAATTTGTGACATATTGCAATT

                      [+1c]
                      6.0e-07
                      S..Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
                      +           +  +        +     +     +  +
                      S..T..A..N..I..C..A..Q..E..V..L..*..L..S..L..
2221921 TATAATGGCGTCTTTCCACAGCGAACATATGCGCACAGGAGGTCTTATAATTAAGCTTAATTGAGCTTTTGT

                            [-2c]
                            3.4e-07
                            ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                             +  +     +  +  +  +        +
                            ..N..L..S..I..Y..F..W..I..R..I..V..E..V..S..L
2348713 TTTGGCAGTAAACAAAGGATATTCAAAGAAATATAAAACCATATTCTTATAACTTCCACTGACAGCTGTTAG

                                           [+1c]
                                           5.7e-07
                                           S..Q..T..T..I..C..R..F..E..A..L..Q..L
                                           +        +     +     +  +  +  +
                                           S..L..D..A..A..S..S..F..E..S..L..P..V
2417977 TAGATGCAGCATCCTCTTTTGGATTATTTCCAGTTTCACTAGATGCAGCATCCTCTTTTGAATCGCTTCCAG

                                                 [+1c]
                                                 5.7e-07
        ..S..F..                                 S..Q..T..T..I..C..R..F..E..A..L
          +                                      +        +     +     +  +  +  +
        ..S..L..                                 S..L..D..A..A..S..S..F..E..S..L
2418049 TTTCACTAGATGCAGCATCCTCTTTTGGATCGTTTCCAGTTTCACTAGATGCAGCATCCTCTTTTGAATCGC

        
        
        ..Q..L..S..F..
                +
        ..P..V..S..L..
2418121 TTCCAGTTTCACTAGACGCAGCATCCTCTTTTGGATTATTTCCAGTTTCACTAGATGCAGCATCCCCCTCTG

                      [+1c]
                      5.7e-07
                      S..Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
                      +        +     +     +  +  +  +        +
                      S..L..D..A..A..S..S..F..E..S..L..P..V..S..L..
2418193 AATCGTTTCCAGTTTCACTAGATGCAGCATCCTCTTTTGAATCGCTTCCAGTTTCACTAGATGCAGCATCCT

                                                                         [+1c]
                                                                         5.7e-07
                                                                         S..Q..T
                                                                         +
                                                                         S..L..D
2418337 CATCCCCCTCTGAATCGCTTCCAGTTTCACTAGATGCAGCATCCTCTTTTGGATTATTTCTAGTTTCACTAG

                                                                               [
                                                                               5
        ..T..I..C..R..F..E..A..L..Q..L..S..F..                                 S
          +     +     +  +  +  +        +                                      +
        ..A..A..S..S..F..E..S..L..P..V..S..L..                                 S
2418409 ATGCAGCATCCTCTTTTGAATCGCTTCCAGTTTCACTATACGCAGCATCCTCTTTTGGATTATTTCCAGTTT

        +1c]
        .7e-07
        ..Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
                +     +     +  +  +  +        +
        ..L..D..A..A..S..S..F..E..S..L..P..V..S..L..
2418481 CACTAGATGCAGCATCCTCTTTTGAATCGCTTCCAGTTTCACTAGATGCAGCATCCTCTTTTGGATTATTTC

                                                    [+1c]
                                                    5.7e-07
                                                    S..Q..T..T..I..C..R..F..E..A
                                                    +        +     +     +  +  +
                                                    S..L..D..A..A..S..S..F..E..S
2418553 CAGTTTCACTAGATGCAGCATCCTCTTTTGAATCGTTTCCAGTTTCACTAGATGCAGCATCCTCTTTTGAAT

        
        
        ..L..Q..L..S..F..
          +        +
        ..L..P..V..S..L..
2418625 CGCTTCCAGTTTCACTAGATGCAGCATCCTCTTTTGAATCGTTTCCAGTTTCACTAGATGCAGCATCCTCTT

                                                                            [+1c
                                                                            5.7e
                                                                            S..Q
                                                                            +
                                                                            S..L
2418841 CAGCATCCTCTTTTGAATTATTTCCAGTTTCACTAGATGCAGCATCCCCCTCTGAATCGCTTCCAGTTTCAC

        ]
        -07
        ..T..T..I..C..R..F..E..A..L..Q..L..S..F..
             +     +     +  +  +  +        +
        ..D..A..A..S..S..F..E..S..L..P..V..S..L..
2418913 TAGATGCAGCATCCTCTTTTGAATCGCTTCCAGTTTCACTAGATGCAGCATCCCCCTCTGAATCGTTTCCAG

          [+1c]
          5.7e-07
          S..Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
          +        +     +     +  +  +  +        +
          S..L..D..A..A..S..S..F..E..S..L..P..V..S..L..
2418985 TTTCACTAGATGCAGCATCCTCTTTTGAATCGCTTCCAGTTTCACTAGATGCAGCATCCTCTTTTGAATCGC

                                                                [-1c]
                                                                2.0e-07
                                                                ..F..S..L..Q..L.
                                                                  +  +  +  +
                                                                ..H..S..L..Q..M.
2434465 AGTTTTAGATGTAAAGTTGATTTTTACGATAATAGTTTTTACCACATCCATGTTAAATGGCTTAATTGCATT

        
        
        .A..E..F..R..C..I..T..T..Q..S
         +     +  +     +  +
        .S..I..F..R..F..I..T..V..T..Y
2434537 GAAATAAATCTGAAAATTGTAACTGTATATTATTAAATACAGTATTAGAAACCATATTCTGTATAATTTAGA

                                                                     [+1b]
                                                                     5.7e-07
                                                                     S..Q..T..T.
                                                                     +        +
                                                                     S..L..D..A.
2456209 TNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATTTCTAGTTTCACTAGATGC

        
        
        .I..C..R..F..E..A..L..Q..L..S..F..
            +     +  +  +  +        +
        .A..S..S..F..E..S..L..P..V..S..L..
2456281 AGCATCCTCTTTTGAATCGCTTCCAGTTTCACTAGACGCAGCATCCTCTTTTGGATTATTTCCAGTTTCACT

                                          [+1b]
                                          5.7e-07
                                          S..Q..T..T..I..C..R..F..E..A..L..Q..L.
                                          +        +     +     +  +  +  +
                                          S..L..D..A..A..S..S..F..E..S..L..P..V.
2456353 AGATGCAGCATCCCCCTCTGAATCGTTTCCAGTTTCACTAGATGCAGCATCCTCTTTTGAATCGCTTCCAGT

        
        
        .S..F..
         +
        .S..L..
2456425 TTCACTAGATGCAGCATTCTCTCTTGGATTATTTCCAGTTTCACTAGATGCAGCATTCTCTTTTGAATTATT

                                                                         [+1c]
                                                                         4.2e-08
                                                                         S..Q..T
                                                                         +
                                                                         S..L..D
2456713 ATCCTCTTTTGAATCGCTTCCAGATTTCACTAGATGCAGCATCCTCTTTTGAATCGCTTCCAGTTTCACTAG

        
        
        ..T..I..C..R..F..E..A..L..Q..L..S..F..
          +     +     +  +  +  +     +  +
        ..A..A..S..S..F..E..S..L..S..L..S..L..
2456785 ATGCAGCATCCTCTTTTGAATCGCTTTCACTTTCACTAGTTGCAGCATCCCCTTTTGAATCGTTTCCAGTTT

                                                         [-4b]
                                                         4.6e-07
                                                         ..E..L..W..K..Q..L..L..
                                                           +        +     +  +
                                                         ..D..P..I..K..I..L..I..
2552833 ATTTTTATTAAGAATTAATTTGTTTTGGATAATAAAATTAAAATTGTTAGTCTGGAATCTTAATCAATATAC

        
        
        P..K..L..K..C..M..N..K
           +  +  +        +  +
        G..K..L..K..W..F..N..K
2552905 CTTTCAACTTCCAAAAGTTTTTTTTCTAAATTCTCTTTTTCTGCAGAAATCGCCTACAATGTAAAATAATGT

                        [-2b]
                        4.7e-19
                        ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                          +  +  +  +  +  +  +  +  +  +  +  +  +  +  +
                        ..Q..R..Q..N..C..F..W..V..R..V..V..N..K..K..L
2589409 TCATTCTCTTTTGTTTCTGCCTTTGATTGCAAAACCACACACGCACGACGTTTTTCTTTAAGTCGAGCTTTT

                                            [-4a]
                                            5.3e-14
                                            ..E..L..W..K..Q..L..L..P..K..L..K..C
                                              +  +  +        +  +  +  +  +  +  +
                                            ..E..L..W..T..I..L..I..P..K..L..A..V
2589769 ATTCTCCATCTTCCTCCTGTGCTCTTCCTCCGCTTTTTCTAACCACGTGATCAAGATTGGTTTCAAGGCGAC

                 [-1a]
                 9.3e-09
        ..M..N..K..F..S..L..Q..L..A..E..F..R..C..I..T..T..Q..S
          +  +  +  +  +  +  +  +  +  +  +  +           +
        ..M..N..N..H..S..L..T..L..S..E..F..R..H..V..C..S..*..I
2589841 CATGTTGTTGTGACTGAGTGTCAAGGACTCAAACCTGTGCACACAACTTTATATTAAGCACATTATACTTCA

                                                                         [-3c]
                                                                         3.3e-17
                                                                         ..V..D.
                                                                           +  +
                                                                         ..V..D.
2589985 CTGCAAATTGTGCTTTGGCTCAGCGATCCAACACCCGGTAGCTTGAGGTTGGCAAGAGCTTGCCCAACATCA

        
        
        .A..Q..T..F..G..L..K..I..R..R..Q..K..F
            +  +  +  +  +  +  +  +  +  +  +  +
        .N..Q..T..V..G..L..K..I..R..R..Q..K..F
2590057 TTCTGCGTCACTCCAAGTTTAATGCGTCGCTGCTTGAATCTGAAACAATATTGATCCTGGGTAAGTGGCTGT

                   [-1c]
                   5.6e-08
                   ..F..S..L..Q..L..A..E..F..R..C..I..T..T..Q..S
                        +  +     +  +     +  +  +  +           +
                   ..Y..T..L..*..L..A..V..F..R..S..I..P..I..T..S
2608273 AATCAACCACAGTACGTTAACTACAAAGCCACAAACCTCGAAATCGGAATCGTTGATAAGGTCAGTGATACC

                                              [-2c]
                                              6.2e-07
                                              ..Q..R..R..N..C..F..W..V..R..V..V.
                                                   +           +     +  +  +
                                              ..R..R..K..P..T..F..R..V..R..I..P.
2783161 TCTGTCTCTTCATGCTCACTGGAAGAGTATGTCCTCACTCTCCTCTTTGGAGTAAATCTCACTCTTATAGGC

        
        
        .E..K..E..L
            +  +  +
        .M..K..K..L
2783233 ATCTTTTTTAACCGTTCTTTCTTGATTGAAGAAACATCTGTAGAACCTCCAGCAGAGACATTTAAACTGGCC

                                                                    [+1a]
                                                                    4.3e-07
                                                                    S..Q..T..T..
                                                                    +     +
                                                                    S..N..T..Y..
2821969 CGTAATATTTGATAAGCCCTGAGGTACAAATTATTGAATTAAAATCAGACCCTTTTTTTTTCAAACACATAT

        
        
        I..C..R..F..E..A..L..Q..L..S..F..
        +  +     +     +     +  +  +
        I..S..L..F..F..S..Q..N..L..S..S..
2822041 ATATCTCTGTTTTTTTCACAAAACTTAAGCTCATTTCATCAGAAAAAATCCAACTCTGCGAAATGTTTCAAC

                                                            [+2b]
                                                            5.7e-07
                                                            L..E..K..E..V..V..R.
                                                            +     +        +  +
                                                            M..*..R..F..F..I..R.
2862145 CCTAAATCGAGCTGTCTGAACGTTACAGCAACAGACACAATGTCTTAAAGGCATGTGACGTTTCTTTATACG

        
        
        .V..W..F..C..N..R..R..Q..
               +  +  +        +
        .L..S..F..C..N..N..K..Q..
2862217 GTTGTCTTTCTGCAACAACAAGCAAGTCGAGCGTGGTGCCGGTGTTAGCTGGGATGTCCTACACCAAATATG

                                             [-1b]
                                             1.5e-07
                                             ..F..S..L..Q..L..A..E..F..R..C..I..
                                               +  +  +  +        +  +  +
                                             ..F..S..L..N..Y..Y..E..F..R..*..R..
3009889 TATTCATTGCTGTATGACCTATGCACCTATGGAATTTAAAAGAAAGGTTGTAATATTCAAACCTTCATCTTG

        
        
        T..T..Q..S
           +  +
        S..T..Q..L
3009961 AGGTCTGCAACATCGGCCATAAATTCTCCAGCGACAGTCTCAAGTGCCATTGCATTTGCGAGTCCATTCATT

               [+2b]
               6.0e-07
               L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
               +           +     +     +  +     +
               M..V..Q..G..V..L..R..I..W..F..Y..N..S..L..N..
3132361 ATTAACAATGGTTCAGGGAGTTCTGAGGATTTGGTTTTATAATTCTTTGAATGTTCTCTGTTTACTATCGAA

                                   [+4a]
                                   9.3e-07
                                   K..N..M..C..K..L..K..P..L..L..Q..K..W..L..E..
                                   +     +  +        +     +  +     +     +  +
                                   K..V..M..I..N..I..K..I..L..L..M..K..I..L..N..
3177865 AATTGAAAACCTTAAGGTGTTAACATAAAGGTCATGATAAACATAAAAATCCTATTAATGAAAATATTAAAT

                                              [+1c]
                                              8.0e-07
                                              S..Q..T..T..I..C..R..F..E..A..L..Q
                                                    +  +  +  +  +  +
                                              V..L..T..T..I..C..R..F..D..D..I..*
3252745 TTATAGCAACACTATAGCAACGTTGTTATTGCTTTGTTGTGCTGACTACTATATGTCGTTTTGATGACATTT

        
        
        ..L..S..F..
          +     +
        ..L..E..F..
3252817 AATTGGAATTTTGTAAATTCTAAGAAATCGCGTAATCTGTAAAGTGTTTTGATAAATCAGTTTTGCACCCGT

                                                                  [+3b]
                                                                  6.8e-07
                                                                  F..K..Q..R..R.
                                                                  +  +  +  +
                                                                  F..K..Q..R..K.
3276001 CCTGAACGCGAAACTACAGTTTCGTATTTTGTCTGGCTTTTGAACACGTCCACGAGGTTTTAAACAACGTAA

        
        
        .I..K..L..G..F..T..Q..A..D..V..
         +  +        +     +     +
        .I..K..R..F..F..*..Q..*..D..S..
3276073 GATTAAAAGATTTTTTTAACAGTAGGATTCTGCAACTTGCAGTTAATTATCTACCGAAATTAATCGACTGTG

                                                    [-4c]
                                                    1.7e-07
                                                    ..E..L..W..K..Q..L..L..P..K.
                                                      +     +     +  +  +
                                                    ..N..*..W..T..E..L..V..I..T.
3314305 TTAAGTAAACTATATATGCCACATACACATACAACAACATATTTATTCTACCATGTTTCTAACACAATAGTT

        
        
        .L..K..C..M..N..K
         +  +     +  +
        .L..K..Y..M..N..D
3314377 AACTTATACATGTTATCAACTAACAACCTATAATATACCTTAACCTATCATATCCAGGTCAAAAAGTAGGAT

             [-2c]
             8.8e-07
             ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                     +  +  +        +  +  +     +  +
             ..W..K..R..N..C..V..L..V..R..V..F..E..K..C..H
3466585 AGCTCCCACTTACGGTTACAAACTAAAACACGAACGAATTCCTTACAGTGAGAGAGAGAGAGAGAGAGCGAT

              [+2a]
              1.4e-07
              L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                          +  +  +     +  +  +  +
              R..P..I..G..V..V..R..I..W..F..C..N..S..L..I..
3771289 TAACAACGGCCTATAGGAGTTGTAAGGATATGGTTTTGTAATTCTTTGATTTTTTGTTTACCACAAAATGGG

                                          [-4b]
                                          3.5e-07
                                          ..E..L..W..K..Q..L..L..P..K..L..K..C..
                                            +  +  +     +  +  +        +  +  +
                                          ..N..V..W..S..S..L..L..N..S..L..K..I..
3936961 TGACAACGCCGACGAGCTGCACAAAATTAAACGAATTCACCCAACTGGAAAGTAAATTACTCAGTTTAATTT

        
        
        M..N..K
              +
        E..Q..K
3937033 CTTGCTTCCGTCATTTTGAAATGAATTCTTTGTATGTGGCAGGTTACTCCTGCGATTACGGGTAGAATACTG

                                                                               [
                                                                               8
                                                                               .
        
                                                                               .
3975409 TTAATACAATATCTAGTTAACCACTTGTATGTGTTTCATTATTGTCACCTAGTTTTCTTATTTCACTCCCCC

        -4c]
        .5e-07
        .E..L..W..K..Q..L..L..P..K..L..K..C..M..N..K
            +        +  +  +  +  +  +     +
        .V..L..P..S..A..L..L..P..K..L..T..Q..S..G..S
3975481 ACCAGTGGCGAAGCCAGAAGGGGCTTTAAGGTTTGCGACCCACTTTAAAAAAAAGTTGTTGTTTTTTTGTAA

                                                    [+1c]
                                                    9.9e-07
                                                    S..Q..T..T..I..C..R..F..E..A
                                                    +        +  +  +     +     +
                                                    S..V..K..A..I..C..E..F..T..S
3997297 AATGGGCATGGTAACTAATTTGGACAATAATATAGAACAAGGGTTCTGTAAAAGCAATATGTGAATTCACCT

        
        
        ..L..Q..L..S..F..
          +  +        +
        ..L..N..R..A..F..
3997369 CATTAAATCGAGCATTCAAACGACTTCTTGACCCACCTGAAACATTCGTTCCTTTTTGTACTTCTTGCCTGT

                                     [-2c]
                                     6.8e-07
                                     ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E.
                                                +     +  +     +  +  +
                                     ..R..K..F..N..S..F..W..I..R..V..V..G..I..S.
4022857 TTTTCGTCCCATTTGATAGTAAGCAAAAAACGTTTAAAATTAGAAAACCATATCCTCACGACTCCAATAGAC

        
        
        .L
        
        .R
4022929 CGCTAATAACTGTTTACAACACGATCAGAATATTTGGATATCATGTTCCAAAGGTGTTCCGTCTCCCCCCAT

                                                              [+3a]
                                                              7.1e-07
                                                              F..K..Q..R..R..I..
                                                                    +  +
                                                              *..L..I..K..K..M..
4358881 TCAGTCATGCCAAAAAAGACGCAAAACAAACAATCACCATCAAAGTTCCATGAGTAACTTATAAAAAAGATG

        
        
        K..L..G..F..T..Q..A..D..V..
        +  +     +  +     +  +  +
        K..L..C..F..T..T..T..D..V..
4358953 AAATTGTGTTTTACAACTACTGACGTTGCCCAGTAACCCAAGGTTATATAAATGTCATTCATTTATGCAATC

                                                           [-4a]
                                                           9.8e-07
                                                           ..E..L..W..K..Q..L..L
                                                             +     +  +  +     +
                                                           ..E..K..W..K..A..R..L
4682161 CATTTGAAAAAAGTCTACTTTAAACCGCTTGTAATGTTTTCATTCTCTTTCCTCTTTCCATTTGGCCCGGAG

        
        
        ..P..K..L..K..C..M..N..K
                +     +     +  +
        ..G..F..L..T..I..L..N..N
4682233 TCCAAAAAGCGTTATTAAATTGTTTAAAACATGATCAGCAGGAAATAGCAGATTTAGGTGCTAAGGGAATAT

                            [+2c]
                            2.2e-07
                            L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                            +        +  +  +  +        +     +
                            L..N..M..E..V..V..R..I..R..F..Y..N..S..L..N..
4689505 TATCTAAATATCTTCGAATTTTAAACATGGAGGTTGTGAGGATCCGGTTTTACAACTCTTTGAATGTTCTTT

                             [+4a]
                             9.3e-07
                             K..N..M..C..K..L..K..P..L..L..Q..K..W..L..E..
                             +  +     +  +           +  +     +  +  +
                             N..S..T..V..A..M..N..Q..L..L..K..R..W..L..H..
4736593 CACTAGAAGCTTTGGTGCGTCAACTCAACTGTTGCCATGAACCAACTCTTAAAGCGATGGTTACACAGCTCA

                                                     [-2a]
                                                     3.0e-07
                                                     ..Q..R..R..N..C..F..W..V..R
                                                             +  +  +  +  +
                                                     ..S..Y..R..N..C..F..W..I..S
4778065 AAAGCTAACAGGCAAACATATCATTGCCTACATAGTTTTATAAATGGAGTAACGATTACAGAACCAGATGCT

        
        
        ..V..V..E..K..E..L
             +  +
        ..S..V..D..I..Y..H
4778137 GCTAACATCGATATAATGTAGATGTTTTTGGGTCCAAACACTTCAACGGCTCCAAATGAAATTAGATAAGCA

                 [+2a]
                 7.4e-07
                 L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                 +     +  +  +              +  +        +
                 Y..Q..K..N..V..K..N..I..K..F..C..S..K..R..K..
4844449 ATATGAAAATACCAAAAAAATGTGAAAAATATAAAATTCTGTTCTAAACGAAAATACAAAAAAATATTAAAA

                    [+1a]
                    8.0e-07
                    S..Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
                    +           +  +     +     +     +  +  +  +
                    S..L..F..S..I..S..F..F..L..A..E..N..I..S..F..
4874833 TATCTCAAAATCTCTCTCTTTAGCATTAGCTTTTTCCTTGCTGAAAATATCTCATTTTCTTTTGCAGGTTAA

                                          [-4b]
                                          4.6e-07
                                          ..E..L..W..K..Q..L..L..P..K..L..K..C..
                                            +  +  +     +  +           +  +
                                          ..D..L..W..L..E..L..A..Q..A..L..A..D..
4915513 GTGACTTCTGGTTTAAAAGTTGGGGTGACATGCGATCAAGCCAGAGCTCTAAAGCTTGTGCCAGAGCGTCTG

        
        
        M..N..K
        +  +  +
        A..N..K
4915585 CATTTTTGACTCCTGTCATTTGGCGTAAAGTAAAGACAGCGTCGAGTCATATGCAATTGCTATAATGTTGCA

                            [-2c]
                            3.4e-07
                            ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                 +     +     +  +     +  +  +
                            ..M..R..S..N..Y..F..W..I..R..I..V..R..N..I..T
5095873 TGGTAGTAAACAATAAAGAACATACGAGAATTGTAAAACCATATCCTAATGACCCTGTTAATTGTTTAAAAC

                                                                      [-2c]
                                                                      2.6e-07
                                                                      ..Q..R..R.
        
                                                                      ..L..S..S.
5131081 TAGGGTGGGGGAAGGTGGGACACATTTTCCTTCTATATTATCTCCACCCATTCGGTAGTAAACAAAGAAGAA

        
        
        .N..C..F..W..V..R..V..V..E..K..E..L
         +     +  +     +  +  +           +
        .N..Y..F..W..S..R..V..V..K..M..S..L
5131153 TTATAAAACCATGATCTCACGACTTTCATAGACAGTTGTTAATGATTTAAAACACGATCAGGATATTTAGAC

                                     [-2c]
                                     1.6e-07
                                     ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E.
                                                +  +  +  +     +  +     +
                                     ..N..L..S..N..C..F..W..I..R..V..A..E..M..S.
5190769 TCATTTGGTGAACACAGTCAAAACAGAACATTCAAAGAATTGCAAAACCATATCCTCACGGCTTCCATAGAC

        
        
        .L
        
        .R
5190841 CGTTGTACTACAATCAGGATATTTGCATATTATTTGCTAAAGGTGCTTGTTTTACCTCAACCTACTGTATAT

                                                                        [+1b]
                                                                        8.4e-07
                                                                        S..Q..T.
                                                                              +
                                                                        Y..N..T.
5193001 TGGATGTTGTGTTGACTGCTTGCATGATAACTGTGTTTGTAACCCGACACAACACTGAGCAAAATACAATAC

        
        
        .T..I..C..R..F..E..A..L..Q..L..S..F..
         +  +  +     +  +  +  +           +
        .T..I..S..L..F..E..N..L..L..K..I..F..
5193073 AACAATCTCATTATTTGAAAATCTATTAAAAATATTTTTTGTTAATTCTTTCCAAGTACACTGACTGAAAAC

                                                                             [-2
                                                                             5.5
                                                                             ..Q
        
                                                                             ..T
5194441 TTTGTGAAGTATTGCTGTAATTTTTTATCAGTCACGTTTCTGTACTAGTCAAAGTTTAGGAATAGGAATTGT

        a]
        e-07
        ..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                +     +        +  +        +     +
        ..E..P..N..T..F..I..I..R..V..T..K..K..Q..M
5194513 TTCTGGGTTTGTAAAAATAATTCTGACTGTTTTTTTTTGCATTTGATGGTGCAGCTATTATTAGGTTTGCAT

             [-2c]
             6.3e-08
             ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                              +  +  +  +  +  +  +        +
             ..N..F..Y..E..Y..F..W..V..R..V..V..E..T..T..L
5247721 AGAACATTAAAATATTCATAAAACCACACCCTTACGACTTCGGTTGTTAACTTTTTTAAACACGACTAGGCT

                            [-2c]
                            8.8e-07
                            ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                       +     +  +     +  +  +
                            ..N..L..S..N..Y..F..W..I..R..V..V..G..M..S..R
5423617 TTTTGTAGTAAACAAAGAACATTCAACGAATTATAAAACCATATTCTCACGACTCCCATAGACCGTTGTTAA

                                                                   [-2c]
                                                                   4.0e-07
                                                                   ..Q..R..R..N.
                                                                              +
                                                                   ..Y..L..S..N.
5586049 AGGGCGGGGGAAGATGGGACACCTTTTTATTCTATTCCATTTGGCCGTACACAAAGAATGTACAAAGAATTA

        
        
        .C..F..W..V..R..V..V..E..K..E..L
            +  +  +  +  +  +
        .Y..F..W..V..R..V..V..R..M..P..R
5586121 TAAAACCAAACCCTCACAACTCTCATAGGCCGTTGTCAATTGTTTAAAACATGATCAGGGTATGTGAACTTT

                                   [+2a]
                                   1.6e-08
                                   L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                                   +  +           +  +     +  +     +
                                   L..E..L..*..L..V..R..I..W..F..Y..N..S..L..N..
5657041 GTGTTTTAAACAAATAACAACAGTCTATTAGAGTTGTGACTTGTGAGGATATGGTTTTATAATTCTTTGAAT

                                          [-1b]
                                          4.1e-07
                                          ..F..S..L..Q..L..A..E..F..R..C..I..T..
                                            +  +  +  +     +  +     +  +  +
                                          ..F..S..I..D..A..N..E..T..R..C..I..S..
5690089 AAATAATCCACAAAAACAAGTTGAACTTTAGCACGAATGAAATATCCGCGTTTTCAGTTCGACATATACTAC

        
        
        T..Q..S
        
        R..P..C
5690161 GTGGACAGCGGTGACAAATACATTTTGCTAATTTGTTGCGTAAACAAAAATATCTCTATAGTAGATATCGGT

                                                                              [+
                                                                              2.
                                                                              S.
        
                                                                              I.
5829121 CCTATATATACCCTTTAATTCAATAAGTGTAGTCAATATAAAATATATAAAAACTTTGTAATTTGAACAGAT

        1b]
        9e-08
        .Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
            +  +  +  +     +     +  +  +     +  +
        .A..T..A..I..S..S..F..S..S..L..N..P..S..F..
5829193 CGCGACGGCAATTTCGTCATTTAGTTCCCTGAATCCATCGTTTCGAAAAATTAAAAATCAAAGGAAACTACC

                                                      [-2b]
                                                      4.8e-08
                                                      ..Q..R..R..N..C..F..W..V..
                                                                 +     +  +
                                                      ..K..Q..S..N..Y..F..W..I..
6077593 AAAATGTGACACCTTTTTGTTCGATTTTCTTGTCCCGTTTTTAATTTTTTTGTGAATTATAAAACCATATTC

        
        
        R..V..V..E..K..E..L
        +  +  +           +
        R..V..V..G..I..S..Y
6077665 TAACGACTCCTATGGAGTAGTATTAATTGTTTGAAACACGATTAATACATTTGAATATTATACAATAAATGT

                                             [+2b]
                                             4.8e-07
                                             L..E..K..E..V..V..R..V..W..F..C..N.
                                                +  +     +  +  +        +     +
                                             *..E..K..L..V..V..R..L..*..F..T..N.
6179905 AACAAATATATCAAACCTTTTTGCAACAACTTAATATTAAGAAAAATTAGTAGTAAGGCTTTAGTTTACCAA

        
        
        .R..R..Q..
        
        .K..N..L..
6179977 CAAAAACTTATTATTTTAAAGTTGAAATAAGATTACTTACTGTAAACAATTTAAAAAAAGGAACGAATAATT

                                                                [-4c]
                                                                2.9e-07
                                                                ..E..L..W..K..Q.
                                                                     +  +  +  +
                                                                ..L..L..W..A..E.
6193225 CAGTATATGGTTAAACTTGAACAAACATAAATGGCTCGTTGTTTGTCTTCTAGGTGTAGCAACCACGCTTCT

        
        
        .L..L..P..K..L..K..C..M..N..K
                  +  +        +  +  +
        .K..K..L..K..L..Q..F..M..N..K
6193297 TTTTTTAACTTTAATTGAAACATGTTTTTACCTGTAAGCGCTTTAACAACCGTTATTTTAGTGCTACATTCT

                              [+2b]
                              4.6e-08
                              L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                              +     +  +           +  +  +        +  +
                              L..T..R..N..F..A..T..V..W..F..T..T..Q..R..H..
6278401 AATTAATGCGCACGTATTTGCTTTGACAAGAAATTTCGCAACCGTGTGGTTCACTACCCAGCGTCACTTCCC

                                                                              [-
                                                                              2.
                                                                              ..
        
                                                                              ..
6291793 ATAATTGTTTTCCAGGCTGCTTGCAAACTTGTGAAAACTGTAGACACCAAATCTTTGACATCAATCTTCTAT

        4b]
        3e-07
        E..L..W..K..Q..L..L..P..K..L..K..C..M..N..K
              +     +  +  +        +  +  +     +
        H..Q..W..*..E..L..L..S..G..L..K..C..L..S..H
6291865 GCTGCCACTACTCAAGCAGAGATCCCAGCTTGCAAAGTGAGTGCCTTTTTCTTGAGTCACTTAATCCCCACA

                              [-2b]
                              1.3e-07
                              ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                         +        +     +  +     +  +  +  +
                              ..N..V..S..N..*..L..W..I..R..I..A..N..R..K..L
6509809 TATTCGGTAGTGGACATAGAACATTTACAGAGTTTTACAACCATATCCTTATGGCATTTCTTTTCAAATCAC

                                         [-2a]
                                         9.6e-07
                                         ..Q..R..R..N..C..F..W..V..R..V..V..E..K
                                           +  +     +  +  +                 +  +
                                         ..Q..R..F..N..C..F..F..L..*..Y..*..N..K
6762673 AACAAAAAGAAAAAAAAGAGGGAACACTAACTACTGTCTAAAGTTACAAAAAAACAACTAATATTAATTTTT

        
        
        ..E..L
          +
        ..K..F
6762745 TTTAAAAGGAAACACTTTCCGCTTGACCACACACTGAGGTAATATGATATCCCATTGTGATGGAATAAACCT

                                        [-3c]
                                        7.1e-07
                                        ..V..D..A..Q..T..F..G..L..K..I..R..R..Q.
                                          +        +  +  +     +  +        +
                                        ..V..R..*..Q..T..V..I..L..K..F..L..K..L.
6803065 AGTATTTTGATTAACCCTTAGAAGTTGTGCTTAACTCTTCACTGTGTAACAATCAATTTAAATAATTTAAGT

        
        
        .K..F
         +  +
        .K..L
6803137 TTTAGACCTCTTTGTCAATCGCTTAAATAATGCTATTTGTTTATTTATAATGTAATATATATAATATGTTAT

                                                                        [+1b]
                                                                        9.5e-07
                                                                        S..Q..T.
                                                                           +
                                                                        Y..Q..L.
6812857 GGTCAAATCCTGATAGTGATACATTATAAAGTAAGTTTCCTGTTTCTTTCATTAATATTTATGGTATCAATT

        
        
        .T..I..C..R..F..E..A..L..Q..L..S..F..
            +     +  +        +  +  +     +
        .*..I..N..R..F..D..K..L..Q..I..*..F..
6812929 ATGAATAAATCGATTTGATAAGCTTCAAATATAATTCAACTATGGCAGATAAATTTAATTATGTACTTGTGA

                                                                           [-1b]
                                                                           9.9e-
                                                                           ..F..
                                                                             +
                                                                           ..F..
6828697 CTAAGGATGCATTATTACTTTAATTTCAATTATGTCTTACTTAAAGCTATAACACGTCGTATACCCTAAAAA

        
        07
        S..L..Q..L..A..E..F..R..C..I..T..T..Q..S
              +     +     +  +  +  +     +
        F..C..N..*..A..L..F..R..C..I..Q..T..N..N
6828769 AACAATTCTACGCCAAAAATCGACATATCTGCGTGTTATTTTATCCAATGCTTATTTGTAAACAAAACTATC

                                   [+1a]
                                   2.0e-07
                                   S..Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
                                               +  +     +     +     +  +  +  +
                                   N..L..A..R..I..C..N..F..C..S..Q..Q..L..S..F..
6845617 TGCACGCATGGCCTGTAATGTAAACCAAATTTAGCTCGAATTTGTAATTTTTGTTCACAACAGCTTAGTTTT

                                      [-2a]
                                      6.2e-07
                                      ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E
                                                 +     +        +  +  +  +
                                      ..N..L..F..N..Y..F..Q..I..R..V..V..E..V..F
6877513 TCTAGTCCCATTTGGTGGTACACAAACAACATTCAAAAAATTATAAAACTGTATTCTCACGACTTCAACAAA

        
        
        ..L
          +
        ..L
6877585 CAGTTGTTAATTGTTTAAAACTTGATCACAATATTTGAATATGATGTGCTAACGGTGTCCCATCTTACCCCA

                                                              [+2a]
                                                              8.8e-07
                                                              L..E..K..E..V..V..
                                                                          +  +
                                                              R..S..M..G..V..V..
6881401 ATTAAAAAAAATTCTTGCCAAAGAGCCAAAATGCATCCTGATAACATTTACCAAAGGTCTATGGGAGTAGTA

        
        
        R..V..W..F..C..N..R..R..Q..
        +     +  +     +
        R..I..W..F..Y..N..S..L..N..
6881473 AGGATATGGTTTTATAATTCTTTAAATATTCTTTGTTTACTTCCAAATGGGAGGAGAAAATACAATGAAAAG

                           [+1b]
                           6.5e-07
                           S..Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
                           +     +  +     +  +  +        +        +
                           S..*..S..T..D..C..R..F..V..K..L..*..Y..T..V..
6909481 AACTAGATATTAGATTAGGTCATGAAGTACTGACTGTAGATTTGTGAAGCTGTGATACACGGTGAAAGTTGT

                              [+2b]
                              9.2e-07
                              L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                              +        +     +  +        +     +
                              M..A..M..E..L..V..R..I..R..F..Y..N..S..L..K..
6924457 ACATCGTTTTTTACAATTAACAATGGCTATGGAACTCGTGAGGATACGGTTTTATAATTCTTTGAAGTTTCT

                                                           [+4a]
                                                           6.1e-07
                                                           K..N..M..C..K..L..K..
                                                           +     +        +
                                                           K..L..A..S..*..L..A..
6943105 TTTTTTTAATTAGTACCCTTTTTTTACTTTTTAAAACTGTTTTATTCCTAAAAACTAGCTTCCTAGCTGGCA

        
        
        P..L..L..Q..K..W..L..E..
           +  +        +  +  +
        S..L..L..H..I..W..L..E..
6943177 TCACTGCTACATATCTGGTTGGAAACACTGTATTTTTCCTTTTTAATCTTCCTAGGAACAACATGTTTTTCA

                                                [+2b]
                                                8.0e-08
                                                L..E..K..E..V..V..R..V..W..F..C.
                                                +        +     +     +  +
                                                L..*..M..N..I..V..S..V..W..V..Y.
6997681 AACTTCTAAACCAGTGAGGAAAACAGTTGAAAGGATTAAATTATAGATGAATATTGTGTCTGTTTGGGTATA

        
        
        .N..R..R..Q..
         +  +  +
        .N..R..R..K..
6997753 TAATCGAAGAAAAGCAATGTTTTACGGTTTATTATTGTATATTTTTACAAAGAGAGCGTTTTTTACTAAGAC

                                                                   [+1c]
                                                                   2.3e-07
                                                                   S..Q..T..T..I
                                                                   +        +  +
                                                                   S..A..A..A..I
7051609 TTTTAACGTATCAACTTCAATGCAACCCCAAAGGATCGTTTATTCAATAAAACTAGTTCAGCGCGGCCGCCA

        
        
        ..C..R..F..E..A..L..Q..L..S..F..
          +     +        +  +     +
        ..C..S..F..*..K..L..Q..F..T..M..
7051681 TATGTTCGTTTTAAAAACTTCAATTTACAATGAAATGGTTTTCCCTTCATTACCACAATACCCTTGTGCCAA

                                                    [-2c]
                                                    2.2e-07
                                                    ..Q..R..R..N..C..F..W..V..R.
                                                               +     +  +  +
                                                    ..N..L..S..N..*..F..W..V..S.
7250617 TTTTTATTCTGTTTTCTCGTCCTATTTAATAGTAAACAAAGAACATTCAAAGAATTTTAAAACCATACGCTC

        
        
        .V..V..E..K..E..L
         +  +  +
        .V..V..E..M..S..R
7250689 ACGACTTCCATAGACCGTTGTTAATTGTTTAAACACGATCAGATTATTCAGATATTATGTGCCAAAAGTGTC

                        [+1b]
                        6.0e-07
                        S..Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
                                    +  +  +  +     +     +     +  +
                        D..*..A..*..I..C..R..F..T..S..T..N..D..S..H..
7260769 GGAAACTGAAACCGCAGATTAGGCTTAAATTTGTCGTTTTACTTCAACAAACGACTCGCATGGCGATAAAAA

                                [-2a]
                                6.2e-07
                                ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                           +  +  +        +  +  +  +
                                ..N..L..S..N..C..F..R..I..R..V..V..E..M..S..R
7423777 CCCATTTGGTGGTAAACACGAAACATTCAAAGAATTACAAAACCGTATCCTCACGACTTCCATAGACCGTTG

                                                                        [+2b]
                                                                        1.4e-07
                                                                        L..E..K.
                                                                        +     +
                                                                        Y..Q..K.
7530193 AAGAAGTCCTTGCCAACTCCCTCCATTGCTCAGTCTCCGGAACAAAATGAAAACGAAAATCCGATATCAAAA

        
        
        .E..V..V..R..V..W..F..C..N..R..R..Q..
               +  +     +  +        +  +
        .K..M..I..R..*..W..F..S..K..Q..R..K..
7530265 GAAGATGATCAGATGATGGTTCTCGAAACAAAGAAAGCTGTTCAGAAAAGTCCAAGGCCCAACATCAAGGCT

               [-4b]
               6.4e-07
               ..E..L..W..K..Q..L..L..P..K..L..K..C..M..N..K
                    +           +  +  +  +     +  +     +  +
               ..Y..L..T..*..K..L..V..P..K..Y..A..I..L..N..N
7605289 CACCACTGTATAGTGTTTATTTTAAGACAGGTTTGTAAGCTATTAAATTGTTTTTATTTATACTGAGTAGTT

                              [-4b]
                              6.4e-07
                              ..E..L..W..K..Q..L..L..P..K..L..K..C..M..N..K
                                   +           +  +  +  +     +  +     +  +
                              ..Y..L..T..*..K..L..V..P..K..Y..A..I..L..N..N
7616521 TGATCCTTGCACTATCACCACTGTATAGTGTTTATTTTAAGACAGGTTTGTAAGCTATTAAATTGTTTTCAT

                           [+2b]
                           8.8e-07
                           L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                                       +  +  +     +  +     +
                           R..S..M..G..V..V..R..I..W..F..Y..N..S..X..X..
7782121 TGTTTTAAACAATTAACAACGGTCTATGGGGGTCGTGAGGATATGGTTTTATAATTCTNNNNNNNNNNNNNN

                          [-2a]
                          8.1e-07
                          ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                     +     +  +     +  +  +
                          ..N..L..Y..N..Y..F..W..I..R..V..V..G..I..S..R
7789177 TGGTAGTAAACAAAGAACATTCAAATAATTATAAAACCATATCCTCACGACGCCTATAGACCGTTGTTAATT

                        [-2b]
                        8.3e-08
                        ..Q..R..R..N..C..F..W..V..R..V..V..E..K..E..L
                                   +     +  +     +  +  +  +
                        ..N..*..L..N..Y..F..W..I..R..V..V..E..M..S..Q
7801705 GTAGTAAGCAAAGAACATTTTATAAATTATAAAACCATATCCTCACGACTTCCATAGACTGTTGTTAATTAT

                  [+1b]
                  1.8e-07
                  S..Q..T..T..I..C..R..F..E..A..L..Q..L..S..F..
                  +        +  +        +  +  +     +  +  +
                  S..L..A..T..I..Y..Y..F..E..S..H..Q..L..S..A..
7825105 GGGGGATTCTTCACTAGCAACCATATATTATTTTGAATCACACCAATTGTCTGCAATATTCTAGCAAAAACA

                   [+2c]
                   8.8e-07
                   L..E..K..E..V..V..R..V..W..F..C..N..R..R..Q..
                               +  +  +     +  +     +
                   R..S..I..G..V..V..R..I..W..F..Y..N..S..L..I..
7927561 ACAATTGACAACGGTCTATAGGAGTCGTGAGGATATGGTTTTATAATTCTTTAATTGTCCTTTTTTTACTCT

              [-4a]
              8.1e-07
              ..E..L..W..K..Q..L..L..P..K..L..K..C..M..N..K
                         +  +  +           +  +     +  +  +
              ..H..K..F..K..N..L..F..L..N..L..K..S..A..N..K
8028217 CGTTTTGTGTTTAAACTTGTTTAAAAATAAATTTAATTTTGATGCATTTTTTAGTTTCTTTTTTTATATAAA

********************************************************************************


CPU: ubuntu
Time 470.725418 secs.

mast.bin test2.fasta.meme.out -nostatus -mt 1e-06 -ev 2e-02 -dna -brief -d /home/struckma/XXXXX/xxxxx.seq.fasta -text -stdout
BioPerl-1.007002/t/data/mpath.ontology.test000444000766000024      1070613155576321 20577 0ustar00cjfieldsstaff000000000000!autogenerated-by:     Pathbase version 2.0
!saved-by:             	mgruenb
!date:                 	Mon Oct 20 20:15:35 BST 2003
!version: $Revision: 1.1 $
!The Pathbase mouse pathology ontology provides a description of mutant and transgenic mouse pathology phenotypes and incorporates 425 known mouse pathologies hierarchically organised as "instances of" pathological processes.
!Questions, comments and suggestions for amendment should be sent to the Co-ordinator, Dr. Paul Schofield, Dept. of Anatomy, University of Cambridge (PS@mole.bio.cam.ac.uk).
!The ontology was developed by the Pathbase consortium (http://www.pathbase.net) funded under the European Commission's Fifth Framework programme, Contract number QLRI-CT-1999-00320.
$pathology_ontology ; MPATH:0
 %cell and tissue damage ; MPATH:1
  %cell death ; MPATH:2
   %apoptosis ; MPATH:3 ; synonym:programmed cell death
   %necrosis ; MPATH:4
    %bridging necrosis ; MPATH:5
    %caseous necrosis ; MPATH:6
    %coagulation necrosis ; MPATH:7
    %fat necrosis ; MPATH:8
    %fibrinoid necrosis ; MPATH:9
    %gangrene ; MPATH:10 ; synonym:mortification
    %hemorrhagic necrosis ; MPATH:11
    %liquefactive necrosis ; MPATH:12
    %piecemeal necrosis ; MPATH:13
  %degenerative change ; MPATH:14
   %general degenerative change ; MPATH:15
    %myxoid/myxomatous degeneration ; MPATH:16 ; synonym:mucoid degeneration ; synonym:myxomatosis
   %subcellular defect ; MPATH:17
    %cytoskeletal defect ; MPATH:18
    %endoplasmic reticulum defect ; MPATH:19
    %golgi defect ; MPATH:20
    %lysosomal defect ; MPATH:21
    %mitochondrial defect ; MPATH:22
    %peroxysomal defect ; MPATH:23
    %plasma membrane defect ; MPATH:24
    %nuclear defect ; MPATH:460
   %tissue specific degenerative process ; MPATH:25
    %alopecia ; MPATH:26
    %arthrosis ; MPATH:27 ; synonym:osteoarthritis ; synonym:degenerative joint disease ; synonym:osteoarthrosis
    %atherosclerosis ; MPATH:28 ; synonym:nodular sclerosis
    %cataract ; MPATH:29
     %cataract- capsular-epithelial ; MPATH:461
     %cataract- nuclear and cortical ; MPATH:462
     %cataract- cortical liquefactive ; MPATH:463
     %cataract- lens extrusion ; MPATH:464
    %cystic medial necrosis ; MPATH:30 ; synonym:erdheim disease ; synonym:mucoid medial degeneration ; synonym:media necrosis aortae idiopathica cystica ; synonym:media necrosis of the aorta
    %emphysema ; MPATH:31
    %glaucoma ; MPATH:32
     %glaucoma developmental ; MPATH:465
     %glaucoma- open angle ; MPATH:466
     %glaucoma- angle closure ; MPATH:467
   %dystrophy ; MPATH:554
  %intracellular and extracellular accumulation ; MPATH:33
   %amyloid deposition ; MPATH:34
   %bile deposition ; MPATH:35
   %ceroid deposition ; MPATH:37
   %glycogen deposition ; MPATH:39
   %hyalinosis ; MPATH:40 ; synonym:hyaline degeneration, eosinophilic cytoplasmic change
   %lipid deposition ; MPATH:42
   %lipofuscin deposition ; MPATH:43
   %melanin deposition ; MPATH:44
   %protein deposition ; MPATH:45
    %copper deposition ; MPATH:38  % mineralisation ; MPATH:555
    %iron deposition ; MPATH:41  % mineralisation ; MPATH:555
   %uric acid deposition ; MPATH:46
   %pseudocyst ; MPATH:468
   %mucous secretions ; MPATH:547
   %mineralisation ; MPATH:555
    %calcium deposition ; MPATH:36
    %copper deposition ; MPATH:38  % protein deposition ; MPATH:45
    %iron deposition ; MPATH:41  % protein deposition ; MPATH:45
  %intracellular and extracellular depletion ; MPATH:47
   %decalcification ; MPATH:48
   %demyelination ; MPATH:49
   %glycogen depletion ; MPATH:50
   %hypocalcification ; MPATH:51
   %lipid depletion ; MPATH:52
   %osteopenia ; MPATH:53
   %osteoporosis ; MPATH:54
 %developmental and structural abnormality ; MPATH:55
  %general developmental defect ; MPATH:56
   %agenesis ; MPATH:57 ; synonym:agenesia
   %aplasia ; MPATH:58
   %branching morphogenesis defect ; MPATH:59
   %communication defect ; MPATH:60
   %curvature defect ; MPATH:61
   %cyst ; MPATH:62
   %depletion ; MPATH:63
   %developmental dysplasia ; MPATH:64
    %developmental cystic dysplasia ; MPATH:473
   %developmental hypoplasia ; MPATH:65
   %dilatation ; MPATH:66
    %ectasia ; MPATH:474
     %lymphangiectasis ; MPATH:98  % cardiovascular developmental defect ; MPATH:89
     %ductal ectasia ; MPATH:475
     %telangiectasia ; MPATH:476
   %displacement and deformity ; MPATH:67
   %diverticulum ; MPATH:68
   %fistula ; MPATH:70
   %fusion defect ; MPATH:71
   %growth acceleration ; MPATH:72
   %growth arrest ; MPATH:73
   %hamartoma ; MPATH:74
BioPerl-1.007002/t/data/multi.blast.m8000444000766000024     10544013155576321 17440 0ustar00cjfieldsstaff000000000000gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	100.00	100.00	1057	0	0	1	1057	1	1057	0.0	2083
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|41946138|gb|AAH66030.1|	100.00	100.00	1057	0	0	1	1057	42	1098	0.0	2083
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|148664617|gb|EDK97033.1|	99.81	99.81	1057	2	0	1	1057	1	1057	0.0	2079
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|27881435|ref|NP_766553.1|;gi|26343625|dbj|BAC35469.1|	99.91	99.91	1057	0	1	1	1057	1	1056	0.0	2019
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|148664619|gb|EDK97035.1|	99.72	99.72	1057	2	1	1	1057	39	1094	0.0	2016
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|109506405|ref|XP_226078.4|;gi|109507077|ref|XP_001059195.1|	97.64	98.49	1058	24	1	1	1057	89	1146	0.0	2000
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|73984136|ref|XP_533311.2|	92.72	95.74	1057	77	0	1	1057	183	1239	0.0	1902
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|119615759|gb|EAW95353.1|	93.76	96.31	1057	66	0	1	1057	1	1057	0.0	1899
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|225579127|ref|NP_001139400.1|;gi|168278084|dbj|BAG11020.1|;gi|219520104|gb|AAI43899.1|	93.76	96.31	1057	66	0	1	1057	27	1083	0.0	1899
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|114580808|ref|XP_525910.2|	93.66	96.22	1057	66	1	1	1057	27	1082	0.0	1892
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|151556977|gb|AAI49484.1|	93.00	95.84	1057	73	1	1	1057	21	1076	0.0	1882
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|126325911|ref|XP_001366266.1|	90.26	94.42	1057	102	1	1	1057	1	1056	0.0	1875
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|19923597|ref|NP_078821.2|;gi|74717977|sp|Q9H0E3.1|SP130_HUMAN;gi|12053173|emb|CAB66767.1|;gi|29468998|gb|AAO63591.1|;gi|109658530|gb|AAI17256.1|;gi|119615756|gb|EAW95350.1|	90.73	93.09	1057	63	1	1	1057	27	1048	0.0	1816
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|117646626|emb|CAL37428.1|	90.63	93.00	1057	64	1	1	1057	27	1048	0.0	1814
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|117645280|emb|CAL38106.1|	90.63	93.00	1057	64	1	1	1057	27	1048	0.0	1814
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|194664496|ref|XP_615866.4|	90.16	92.72	1057	69	1	1	1057	27	1048	0.0	1809
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|149756507|ref|XP_001504982.1|	90.16	92.43	1057	68	2	1	1057	27	1047	0.0	1783
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|71896869|ref|NP_001026472.1|;gi|82075276|sp|Q5F3U0.1|SP130_CHICK;gi|60098727|emb|CAH65194.1|	86.04	90.28	1060	142	5	1	1057	1	1057	0.0	1731
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|38648728|gb|AAH63075.1|	100.00	100.00	879	0	0	179	1057	1	879	0.0	1707
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|119615761|gb|EAW95355.1|	93.63	96.20	816	52	0	242	1057	13	828	0.0	1502
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|119615757|gb|EAW95351.1|	93.56	96.16	808	52	0	242	1049	13	820	0.0	1485
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|224059701|ref|XP_002191302.1|	83.86	87.73	880	102	3	179	1057	1	841	0.0	1429
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|119615760|gb|EAW95354.1|	89.71	92.03	816	49	1	242	1057	13	793	0.0	1420
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|62822329|gb|AAY14878.1|	90.35	92.57	767	39	1	291	1057	1	732	0.0	1352
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|148234702|ref|NP_001088898.1|;gi|82179336|sp|Q5M7C3.1|SP13B_XENLA;gi|56789809|gb|AAH88715.1|	68.25	78.64	1077	286	22	1	1057	1	1041	0.0	1334
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|48257116|gb|AAH17453.2|	89.84	92.17	728	39	1	330	1057	1	693	0.0	1278
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|148224050|ref|NP_001086872.1|;gi|82182442|sp|Q6DDH6.1|SP13A_XENLA;gi|50415583|gb|AAH77587.1|	66.39	75.86	1077	273	22	1	1057	1	1008	0.0	1258
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|193787295|dbj|BAG52501.1|	89.18	91.68	721	42	2	337	1057	1	685	0.0	1250
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|163915021|ref|NP_001106500.1|;gi|159155111|gb|AAI54703.1|	65.09	75.21	1077	270	22	1	1057	1	991	0.0	1236
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|16550845|dbj|BAB71063.1|;gi|119615758|gb|EAW95352.1|	93.53	96.06	711	45	1	1	711	1	710	0.0	1234
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|148664618|gb|EDK97034.1|	99.37	99.37	639	4	0	294	932	1	639	0.0	1213
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|10434445|dbj|BAB14261.1|	93.80	96.57	613	38	0	445	1057	1	613	0.0	1147
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|90081034|dbj|BAE89997.1|	93.87	96.02	653	40	0	1	653	1	653	0.0	1137
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|68355898|ref|XP_691063.1|;gi|169158058|emb|CAQ14165.1|	59.76	71.14	1081	371	20	1	1056	1	1042	0.0	1095
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|149017119|gb|EDL76170.1|	97.35	98.58	565	15	0	493	1057	42	606	0.0	1085
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|237757277|ref|NP_001092247.2|	59.74	70.96	1016	360	20	63	1056	83	1071	0.0	1034
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|148744304|gb|AAI42599.1|	59.74	70.67	1016	360	20	63	1056	66	1054	0.0	1032
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|26350953|dbj|BAC39113.1|	100.00	100.00	339	0	0	1	339	1	339	1e-173	 615
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|47218881|emb|CAG05647.1|	60.20	70.32	603	192	19	1	577	2	582	2e-157	 561
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|47218881|emb|CAG05647.1|	73.58	88.62	246	65	0	811	1056	600	845	9e-114	 416
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|62630230|gb|AAX88975.1|	91.70	94.46	289	24	0	1	289	27	315	6e-129	 466
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|12848436|dbj|BAB27953.1|	100.00	100.00	193	0	0	865	1057	1	193	2e-106	 392
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|116487558|gb|AAI25872.1|	83.33	92.16	102	17	0	955	1056	231	332	1e-46	 193
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|116487558|gb|AAI25872.1|	52.03	61.49	148	55	6	63	201	84	224	4e-21	 108
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|109104782|ref|XP_001116028.1|	82.35	92.44	119	21	0	689	807	1	119	6e-37	 160
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|91082015|ref|XP_969976.1|	34.68	56.31	222	131	5	840	1056	699	911	1e-33	 150
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|157115575|ref|XP_001652616.1|;gi|108876836|gb|EAT41061.1|	37.97	63.29	158	88	4	901	1056	1185	1334	3e-30	 138
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|242008273|ref|XP_002424931.1|;gi|212508545|gb|EEB12193.1|	32.62	54.94	233	121	8	834	1057	880	1085	5e-30	 138
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|110765898|ref|XP_397260.3|	34.23	55.86	222	120	8	840	1054	620	822	1e-26	 126
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|124487940|gb|ABN12053.1|	40.52	65.36	153	87	2	903	1053	38	188	2e-26	 125
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|260807880|ref|XP_002598736.1|;gi|229284010|gb|EEN54748.1|	33.96	54.48	268	151	12	790	1039	62	321	1e-25	 123
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|195128533|ref|XP_002008717.1|;gi|193920326|gb|EDW19193.1|	33.13	60.12	163	103	4	895	1057	1123	1279	9e-24	 117
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|195379392|ref|XP_002048463.1|;gi|194155621|gb|EDW70805.1|	33.13	60.12	163	103	4	895	1057	1149	1305	9e-24	 117
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|195428094|ref|XP_002062109.1|;gi|194158194|gb|EDW73095.1|	33.74	58.28	163	102	3	895	1057	1196	1352	1e-23	 117
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|27374362|gb|AAO01102.1|	33.13	60.12	163	103	4	895	1057	1158	1314	1e-23	 116
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|195493941|ref|XP_002094629.1|;gi|194180730|gb|EDW94341.1|	30.77	56.04	182	117	4	879	1057	1045	1220	2e-23	 115
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|24663485|ref|NP_729835.1|;gi|221331131|ref|NP_729836.3|;gi|23093587|gb|AAN11859.1|;gi|220902578|gb|AAN11860.3|	30.77	55.49	182	117	4	879	1057	1082	1257	6e-23	 114
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|24663481|ref|NP_729834.1|;gi|23093586|gb|AAN11858.1|	30.77	55.49	182	117	4	879	1057	1119	1294	6e-23	 114
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|194870075|ref|XP_001972581.1|;gi|190654364|gb|EDV51607.1|	30.77	55.49	182	117	4	879	1057	1040	1215	6e-23	 114
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|21355649|ref|NP_648602.1|;gi|4972710|gb|AAD34750.1|;gi|7294536|gb|AAF49877.1|;gi|220943690|gb|ACL84388.1|	30.77	55.49	182	117	4	879	1057	1044	1219	7e-23	 114
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|195327233|ref|XP_002030326.1|;gi|194119269|gb|EDW41312.1|	30.77	55.49	182	117	4	879	1057	757	932	1e-22	 113
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|194752041|ref|XP_001958331.1|;gi|190625613|gb|EDV41137.1|	30.43	56.52	184	119	4	877	1057	1116	1293	2e-22	 112
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|195589926|ref|XP_002084700.1|;gi|194196709|gb|EDX10285.1|	31.32	55.49	182	116	4	879	1057	836	1011	5e-22	 111
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|169881247|ref|NP_848737.3|;gi|68053214|sp|Q8BR65.1|SDS3_MOUSE;gi|26337403|dbj|BAC32387.1|;gi|74151871|dbj|BAE29722.1|;gi|74223871|dbj|BAE23831.1|;gi|112180557|gb|AAH55764.2|	100.00	100.00	328	0	0	1	328	1	328	0.0	 665
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|26335815|dbj|BAC31608.1|	99.70	99.70	328	1	0	1	328	1	328	0.0	 663
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|20502870|gb|AAM22676.1|AF469109_1	99.70	99.70	328	1	0	1	328	1	328	0.0	 661
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|109496051|ref|XP_341093.3|;gi|109497459|ref|XP_001080131.1|	98.78	99.39	328	4	0	1	328	535	862	0.0	 661
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|169881250|ref|NP_001116138.1|;gi|38565990|gb|AAH62176.1|	100.00	100.00	325	0	0	1	325	1	325	0.0	 659
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|194214254|ref|XP_001914936.1|	96.95	98.17	328	10	0	1	328	79	406	7e-175	 619
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|149063516|gb|EDM13839.1|	97.75	98.39	311	4	1	21	328	21	331	1e-172	 611
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|149063515|gb|EDM13838.1|	97.73	98.38	308	4	1	21	325	21	328	1e-170	 605
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119618546|gb|EAW98140.1|	99.33	100.00	299	2	0	30	328	19	317	2e-170	 604
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|126324676|ref|XP_001362875.1|	97.66	99.33	299	7	0	30	328	29	327	2e-168	 597
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|197102743|ref|NP_001125541.1|;gi|75042006|sp|Q5RBB8.1|SDS3_PONAB;gi|55728396|emb|CAH90942.1|	99.31	100.00	291	2	0	38	328	38	328	3e-166	 590
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|75677351|ref|NP_071936.2|;gi|68053233|sp|Q9H7L9.2|SDS3_HUMAN;gi|68533937|gb|AAH98404.1|;gi|119618544|gb|EAW98138.1|;gi|208967508|dbj|BAG73768.1|	99.31	100.00	291	2	0	38	328	38	328	3e-166	 590
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|194042976|ref|XP_001924353.1|	99.31	100.00	291	2	0	38	328	115	405	7e-166	 589
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|10440434|dbj|BAB15750.1|	99.31	100.00	291	2	0	38	328	78	368	9e-166	 588
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|109098940|ref|XP_001084823.1|	99.31	100.00	291	2	0	38	328	117	407	2e-165	 588
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|114647229|ref|XP_509415.2|	99.31	100.00	291	2	0	38	328	117	407	2e-165	 587
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|149944705|ref|NP_001092361.1|;gi|172048634|sp|A6H6W9.1|SDS3_BOVIN;gi|148878005|gb|AAI46028.1|	98.63	99.66	291	4	0	38	328	38	328	2e-165	 587
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|73995289|ref|XP_543419.2|	98.36	100.00	305	5	0	21	325	21	325	1e-164	 585
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|148687874|gb|EDL19821.1|	98.98	98.98	293	1	1	38	328	38	330	1e-164	 585
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119618547|gb|EAW98141.1|	98.63	99.31	291	4	0	38	328	38	328	3e-164	 583
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|148687872|gb|EDL19819.1|	98.97	98.97	290	1	1	38	325	38	327	7e-163	 579
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|71895507|ref|NP_001026642.1|;gi|53136632|emb|CAG32645.1|	94.22	98.30	294	17	0	35	328	20	313	4e-160	 570
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|90075564|dbj|BAE87462.1|	99.29	100.00	281	2	0	48	328	12	292	3e-159	 567
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|220679403|emb|CAX14305.1|	85.32	93.27	327	37	3	3	328	2	318	4e-158	 563
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|189230170|ref|NP_001121409.1|;gi|156230905|gb|AAI52171.1|;gi|183985612|gb|AAI66109.1|	88.93	96.74	307	33	1	23	328	4	310	1e-157	 561
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|148227338|ref|NP_001087071.1|;gi|50418319|gb|AAH77985.1|	85.67	92.99	328	40	2	1	328	1	321	2e-157	 561
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|147904216|ref|NP_001086559.1|;gi|49899079|gb|AAH76807.1|	85.37	92.07	328	41	2	1	328	1	321	2e-156	 558
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|220679404|emb|CAX14306.1|	83.28	91.04	335	37	4	3	328	2	326	6e-156	 556
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|51011073|ref|NP_001003493.1|;gi|50417018|gb|AAH78355.1|	86.98	94.29	315	32	2	23	328	4	318	7e-156	 556
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|49619047|gb|AAT68108.1|	86.98	94.29	315	32	2	23	328	2	316	8e-156	 555
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|47221504|emb|CAG08166.1|	80.00	86.96	345	41	2	3	328	2	337	1e-151	 541
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|213513772|ref|NP_001133103.1|;gi|197631943|gb|ACH70695.1|	85.44	93.85	309	44	1	21	328	3	311	3e-148	 530
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119618543|gb|EAW98137.1|	79.46	82.15	297	23	4	38	328	38	302	1e-123	 449
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|148687873|gb|EDL19820.1|	99.50	100.00	200	1	0	1	200	1	200	1e-107	 395
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|149063514|gb|EDM13837.1|	98.00	99.00	200	4	0	1	200	1	200	9e-106	 389
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|85700307|gb|AAI12001.1|	99.46	100.00	184	1	0	145	328	1	184	2e-102	 379
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|62739853|gb|AAH93990.1|	99.41	100.00	169	1	0	160	328	1	169	2e-94	 352
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|10435847|dbj|BAB14685.1|	98.82	99.41	169	2	0	160	328	1	169	1e-93	 349
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119618545|gb|EAW98139.1|	99.40	100.00	167	1	0	38	204	38	204	3e-88	 331
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|20988049|gb|AAH30252.1|	99.36	100.00	157	1	0	172	328	9	165	1e-87	 329
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|66514190|ref|XP_393483.2|	54.40	74.27	307	125	6	31	327	25	326	5e-84	 317
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|260803689|ref|XP_002596722.1|;gi|229281981|gb|EEN52734.1|	55.40	75.96	287	118	4	48	327	1	284	4e-81	 307
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|91093166|ref|XP_967616.1|	52.22	73.04	293	128	5	44	327	37	326	5e-78	 297
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|156394077|ref|XP_001636653.1|;gi|156223758|gb|EDO44590.1|	50.80	70.93	313	143	5	23	327	87	396	1e-77	 296
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|242012093|ref|XP_002426775.1|;gi|212510957|gb|EEB14037.1|	51.44	73.02	278	128	3	52	325	42	316	4e-71	 274
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119570782|gb|EAW50397.1|	76.80	80.41	194	20	2	1	189	1	174	5e-71	 274
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|157126307|ref|XP_001654586.1|;gi|108882558|gb|EAT46783.1|	48.51	70.15	268	126	2	71	326	1	268	2e-66	 259
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119570783|gb|EAW50398.1|	97.32	99.11	112	3	0	217	328	1	112	2e-58	 232
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|221114061|ref|XP_002158878.1|	46.21	66.90	290	148	4	45	328	72	359	5e-58	 231
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|194762662|ref|XP_001963453.1|;gi|190629112|gb|EDV44529.1|	40.00	61.52	330	158	6	30	325	7	330	3e-56	 225
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|193695368|ref|XP_001948875.1|	39.63	59.76	328	162	7	35	328	10	335	1e-55	 223
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195345751|ref|XP_002039432.1|;gi|194134658|gb|EDW56174.1|	40.76	64.01	314	160	7	36	325	15	326	3e-55	 221
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195567747|ref|XP_002107420.1|;gi|194204827|gb|EDX18403.1|	40.63	63.81	315	160	7	36	325	15	327	3e-55	 221
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|158289583|ref|XP_559379.3|;gi|157018587|gb|EAL41125.3|	44.13	63.70	281	151	2	52	326	37	317	4e-55	 221
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|21430678|gb|AAM51017.1|	40.00	62.22	315	162	5	36	325	15	327	6e-54	 217
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|24643310|ref|NP_608325.1|;gi|7293607|gb|AAF48979.1|;gi|201065977|gb|ACH92398.1|	40.00	62.22	315	162	5	36	325	15	327	6e-54	 217
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|125983450|ref|XP_001355490.1|;gi|195174327|ref|XP_002027930.1|;gi|54643806|gb|EAL32549.1|;gi|194115619|gb|EDW37662.1|	40.25	62.58	318	160	6	36	325	14	329	7e-54	 217
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195479741|ref|XP_002101010.1|;gi|194188534|gb|EDX02118.1|	40.00	62.86	315	162	6	36	325	14	326	2e-53	 215
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|198415295|ref|XP_002130717.1|	40.92	63.37	303	164	6	29	326	5	297	6e-53	 214
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195399235|ref|XP_002058226.1|;gi|194150650|gb|EDW66334.1|	43.33	63.70	270	141	3	67	325	90	358	7e-53	 213
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195134340|ref|XP_002011595.1|;gi|193906718|gb|EDW05585.1|	39.20	58.02	324	159	5	36	325	14	333	1e-52	 213
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|194893010|ref|XP_001977789.1|;gi|190649438|gb|EDV46716.1|	39.68	62.86	315	163	6	36	325	14	326	1e-52	 213
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119570784|gb|EAW50399.1|	90.68	95.76	118	11	0	72	189	1	118	8e-52	 210
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195049670|ref|XP_001992764.1|;gi|193893605|gb|EDV92471.1|	42.12	64.84	273	143	4	67	325	76	347	2e-51	 209
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195447846|ref|XP_002071396.1|;gi|194167481|gb|EDW82382.1|	37.50	56.98	344	160	6	35	325	15	356	4e-49	 201
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|221220210|gb|ACM08766.1|	75.17	85.52	145	27	1	3	147	2	137	2e-48	 199
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|241849004|ref|XP_002415664.1|;gi|215509878|gb|EEC19331.1|	47.44	68.37	215	101	3	124	328	1	213	2e-48	 199
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|156538935|ref|XP_001599334.1|	53.23	72.14	201	85	2	77	268	1	201	3e-48	 198
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|170062834|ref|XP_001866841.1|;gi|167880606|gb|EDS43989.1|	57.32	79.62	157	67	0	72	228	1	157	9e-44	 183
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|170062834|ref|XP_001866841.1|;gi|167880606|gb|EDS43989.1|	52.63	73.68	38	18	0	249	286	314	351	7e-05	54.7
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|196011982|ref|XP_002115854.1|;gi|190581630|gb|EDV21706.1|	33.79	55.86	290	129	8	23	297	6	247	9e-31	 140
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|156382010|ref|XP_001632348.1|;gi|156219402|gb|EDO40285.1|	30.97	55.60	268	171	5	62	324	66	324	2e-29	 135
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|71834364|ref|NP_001025273.1|;gi|125841402|ref|XP_001331204.1|;gi|82225989|sp|Q4V8V1.1|BRM1L_DANRE;gi|66910490|gb|AAH97187.1|	29.52	54.98	271	168	7	62	324	67	322	4e-27	 128
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|221130385|ref|XP_002166261.1|	43.28	57.71	201	65	4	45	233	205	368	3e-26	 125
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|117558752|gb|AAI27378.1|	29.96	54.68	267	176	4	60	324	81	338	3e-25	 122
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|147899930|ref|NP_001089225.1|;gi|58047689|gb|AAH89170.1|	29.96	54.31	267	176	4	60	324	55	312	5e-25	 121
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|148225003|ref|NP_001086722.1|;gi|82182058|sp|Q6AZT4.1|BRM1L_XENLA;gi|50604230|gb|AAH77352.1|	28.52	54.44	270	171	6	62	324	67	321	3e-24	 119
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|156717652|ref|NP_001096366.1|;gi|158706424|sp|A4II71.1|BRM1L_XENTR;gi|134025571|gb|AAI35889.1|	28.52	54.07	270	171	6	62	324	67	321	4e-24	 118
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|56118992|ref|NP_001007936.1|;gi|82082601|sp|Q5ZLL9.1|BRM1L_CHICK;gi|53129285|emb|CAG31374.1|	27.82	54.89	266	177	5	62	324	67	320	5e-24	 118
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|126283557|ref|XP_001363359.1|	26.93	52.32	323	196	8	26	324	16	322	7e-24	 117
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|220673407|emb|CAX13654.1|	26.80	53.26	291	191	7	42	324	42	318	8e-24	 117
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|56181500|gb|AAV83797.1|	27.69	52.00	325	191	9	26	324	16	322	1e-23	 116
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|34147416|ref|NP_115728.2|;gi|134085685|ref|NP_001076897.1|;gi|73963078|ref|XP_537414.2|;gi|109083359|ref|XP_001088972.1|;gi|114652674|ref|XP_522994.2|;gi|194038759|ref|XP_001926291.1|;gi|194207298|ref|XP_001491348.2|;gi|158706423|sp|A4FV29.1|BRM1L_BOVIN;gi|158706476|sp|Q5PSV4.2|BRM1L_HUMAN;gi|33871270|gb|AAH06250.2|;gi|119586271|gb|EAW65867.1|;gi|133777620|gb|AAI23662.1|;gi|149051262|gb|EDM03435.1|;gi|171847223|gb|AAI62034.1|	27.69	52.00	325	191	9	26	324	16	322	2e-23	 115
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|83649717|ref|NP_001032845.1|;gi|123796926|sp|Q3U1T3.1|BRM1L_MOUSE;gi|74185761|dbj|BAE32759.1|;gi|74212941|dbj|BAE33410.1|	27.69	52.00	325	191	9	26	324	16	322	2e-23	 115
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|224051440|ref|XP_002200556.1|	27.44	54.51	266	178	5	62	324	67	320	5e-23	 114
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|148704770|gb|EDL36717.1|	27.99	54.48	268	174	6	62	324	31	284	2e-22	 112
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|194386106|dbj|BAG59617.1|	27.82	54.14	266	177	5	62	324	21	274	2e-22	 112
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|149410399|ref|XP_001511853.1|	27.07	54.51	266	179	5	62	324	42	295	2e-22	 112
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|114652676|ref|XP_001141628.1|;gi|189067874|dbj|BAG37812.1|	27.44	54.51	266	178	5	62	324	21	274	2e-22	 112
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|193788411|dbj|BAG53305.1|	27.44	54.51	266	178	5	62	324	11	264	3e-22	 112
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119887913|ref|XP_001249931.1|	27.65	52.90	293	188	7	42	324	14	292	6e-22	 111
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|148704772|gb|EDL36719.1|	26.67	48.99	345	194	10	26	324	49	380	4e-21	 108
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|221108372|ref|XP_002167338.1|	26.69	50.75	266	181	5	62	324	20	274	1e-18	 100
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|118781168|ref|XP_559429.2|;gi|116130296|gb|EAL41137.2|	37.59	61.65	133	79	2	196	326	1	131	1e-17	96.7
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|198426749|ref|XP_002125654.1|	24.85	48.18	330	214	8	8	325	89	396	2e-16	92.8
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|115761379|ref|XP_001197048.1|;gi|115948498|ref|XP_780214.2|	24.53	51.70	265	179	6	62	322	67	314	2e-15	89.7
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195397031|ref|XP_002057132.1|;gi|194146899|gb|EDW62618.1|	26.42	51.89	212	139	5	44	245	44	248	2e-09	69.7
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|240995535|ref|XP_002404611.1|;gi|215491613|gb|EEC01254.1|	27.98	58.93	168	115	3	62	226	64	228	2e-09	69.3
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|158295864|ref|XP_001688873.1|;gi|157016237|gb|EDO63879.1|	34.38	56.88	160	100	2	68	223	35	193	4e-09	68.6
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|56756539|gb|AAW26442.1|	31.65	56.83	139	93	1	52	188	14	152	9e-09	67.4
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|24641636|ref|NP_572840.1|;gi|20976862|gb|AAM27506.1|;gi|22832172|gb|AAF48213.2|;gi|220950330|gb|ACL87708.1|;gi|220959308|gb|ACL92197.1|	27.98	52.75	218	130	8	32	237	31	233	4e-08	65.5
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|3915731|sp|Q03267.2|IKZF1_MOUSE	100.00	100.00	517	0	0	1	517	1	517	0.0	1074
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|60359882|dbj|BAD90160.1|	98.65	98.84	518	3	2	1	517	25	539	0.0	1051
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|71037387|ref|NP_001020768.1|;gi|148708691|gb|EDL40638.1|;gi|148708692|gb|EDL40639.1|	98.65	98.84	518	3	2	1	517	1	515	0.0	1050
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|56205318|emb|CAI25379.1|	94.98	95.17	538	3	3	1	517	1	535	0.0	1037
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|149016952|gb|EDL76057.1|;gi|149016954|gb|EDL76059.1|;gi|149016956|gb|EDL76061.1|	96.92	98.07	519	9	5	1	517	1	514	0.0	1022
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|5174501|ref|NP_006051.1|;gi|3913926|sp|Q13422.1|IKZF1_HUMAN;gi|1289371|gb|AAC50459.1|;gi|51094649|gb|EAL23900.1|;gi|119581385|gb|EAW60981.1|;gi|208966542|dbj|BAG73285.1|	91.57	94.83	522	36	6	1	517	1	519	0.0	 970
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|149704641|ref|XP_001498147.1|	89.08	94.06	522	49	6	1	517	1	519	0.0	 954
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|1911483|gb|AAB50683.1|	89.44	93.09	521	46	7	1	517	1	516	0.0	 937
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|157426913|ref|NP_001098727.1|	87.62	93.52	509	56	5	13	517	10	515	0.0	 919
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|73981822|ref|XP_540350.2|	84.69	90.36	529	53	7	14	517	54	579	0.0	 910
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|149410208|ref|XP_001506295.1|	86.02	92.15	522	64	7	1	517	211	728	0.0	 902
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|46048783|ref|NP_990419.1|;gi|3913920|sp|O42410.1|IKZF1_CHICK;gi|2330595|emb|CAA72531.1|	82.76	91.57	522	81	7	1	517	1	518	0.0	 897
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|224045852|ref|XP_002191672.1|	82.12	90.58	520	85	6	1	516	1	516	0.0	 884
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|114613538|ref|XP_001148911.1|	92.09	95.09	468	29	6	55	517	169	633	0.0	 867
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|126336572|ref|XP_001379648.1|	88.70	94.24	469	44	7	54	517	94	558	0.0	 852
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|21322628|emb|CAC84566.1|	79.31	89.08	522	98	8	1	517	1	517	0.0	 841
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|109066562|ref|XP_001082512.1|	90.47	93.79	451	34	7	73	517	1	448	0.0	 819
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|109066560|ref|XP_001082388.1|	89.56	92.67	450	29	7	73	517	1	437	0.0	 808
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|198287|gb|AAA66193.1|	99.21	99.21	381	3	0	137	517	51	431	0.0	 790
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|17390815|gb|AAH18349.1|;gi|32880015|gb|AAP88838.1|;gi|60654753|gb|AAX31941.1|;gi|60654755|gb|AAX31942.1|;gi|60654757|gb|AAX31943.1|;gi|60654759|gb|AAX31944.1|;gi|119581382|gb|EAW60978.1|;gi|119581383|gb|EAW60979.1|	77.50	83.46	520	71	7	1	517	1	477	0.0	 786
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|148708694|gb|EDL40641.1|	97.90	98.16	381	5	1	137	517	75	452	0.0	 775
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|71037385|ref|NP_033604.2|;gi|56205317|emb|CAI25378.1|;gi|148708693|gb|EDL40640.1|;gi|148708696|gb|EDL40643.1|;gi|187952041|gb|AAI38790.1|	97.90	98.16	381	5	1	137	517	51	428	0.0	 773
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|1363188|pir||B56229	97.64	97.90	381	5	2	137	517	51	427	0.0	 766
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|157821935|ref|NP_001100707.1|;gi|149016953|gb|EDL76058.1|;gi|149016955|gb|EDL76060.1|;gi|149016957|gb|EDL76062.1|	96.34	97.64	382	10	2	137	517	50	428	0.0	 760
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|6007783|gb|AAF01038.1|	73.46	82.31	520	95	9	1	516	1	481	0.0	 748
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|62751371|ref|NP_001015698.1|;gi|58618896|gb|AAH89243.1|	72.06	82.27	519	105	8	1	516	1	482	0.0	 748
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|119581381|gb|EAW60977.1|;gi|194383264|dbj|BAG64603.1|	90.81	94.23	381	28	5	141	517	55	432	0.0	 704
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|223649474|gb|ACN11495.1|	67.42	79.85	531	146	12	1	514	1	521	0.0	 697
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|185132424|ref|NP_001118184.1|;gi|3913918|sp|O13089.1|IKZF1_ONCMY;gi|2062742|gb|AAB97474.1|	66.92	80.08	532	148	13	1	514	1	522	0.0	 693
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|9408380|gb|AAF87271.1|AF163848_1	66.04	78.30	530	137	10	1	517	1	500	0.0	 685
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|119581386|gb|EAW60982.1|	71.77	77.53	503	69	8	1	480	1	453	0.0	 676
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74218692|dbj|BAE25211.1|	87.66	87.66	381	3	2	137	517	51	387	0.0	 671
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74218692|dbj|BAE25211.1|	100.00	100.00	54	0	0	1	54	1	54	1e-22	 113
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|220678857|emb|CAX12977.1|	65.36	78.21	537	150	15	1	513	1	525	0.0	 669
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|15987101|gb|AAL11906.1|AF416370_1	65.36	78.21	537	150	15	1	513	1	525	0.0	 669
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|220678853|emb|CAX12973.1|	64.05	76.64	548	150	15	1	513	1	536	0.0	 665
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|18859581|ref|NP_571061.1|;gi|3661583|gb|AAC61763.1|;gi|190338657|gb|AAI62270.1|	64.05	76.64	548	150	15	1	513	1	536	0.0	 665
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|2062736|gb|AAB53432.1|	61.39	73.07	531	134	14	1	514	1	477	5e-172	 609
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|47208098|emb|CAF91930.1|;gi|239799504|tpe|CAQ76709.1|	69.52	80.00	420	105	9	107	513	2	411	6e-162	 576
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|47078380|gb|AAT09851.1|	84.47	84.78	322	2	2	196	517	54	327	3e-152	 543
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|47078380|gb|AAT09851.1|	100.00	100.00	53	0	0	1	53	1	53	1e-21	 110
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|2062740|gb|AAB53434.1|	68.93	81.98	383	100	8	141	514	56	428	2e-148	 531
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|9408378|gb|AAF87270.1|AF163847_1	56.63	70.88	498	189	12	38	515	32	522	3e-148	 530
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|9408384|gb|AAF87273.1|AF163850_1	56.31	69.51	515	179	19	18	514	24	510	5e-143	 513
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005423|ref|XP_862767.1|	56.34	69.82	497	188	14	38	515	31	517	5e-143	 513
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005417|ref|XP_862696.1|	55.82	70.08	498	191	14	38	515	32	520	2e-142	 511
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005441|ref|XP_862975.1|	55.69	69.46	501	190	14	38	515	31	522	5e-142	 510
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005425|ref|XP_862793.1|	55.42	69.68	498	193	14	38	515	32	520	2e-141	 507
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005433|ref|XP_862881.1|	55.94	69.42	497	183	14	38	515	32	511	4e-141	 507
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|26346747|dbj|BAC37022.1|	98.40	98.80	250	3	1	1	249	1	250	5e-141	 506
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|13785508|dbj|BAB43903.1|	67.45	79.43	384	107	9	141	514	53	428	1e-140	 505
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|13785508|dbj|BAB43903.1|	28.93	45.91	159	75	4	1	156	1	124	5e-06	58.2
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|220678856|emb|CAX12976.1|	66.92	78.46	390	100	10	141	513	56	433	1e-139	 502
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005391|ref|XP_862364.1|	55.19	69.25	491	195	11	38	515	32	510	1e-139	 501
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|15987103|gb|AAL11907.1|AF416371_1	66.92	78.46	390	100	10	141	513	56	433	2e-139	 501
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005403|ref|XP_862526.1|	55.11	68.94	499	194	14	38	515	32	521	2e-139	 501
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|109100863|ref|XP_001083355.1|;gi|114583092|ref|XP_526015.2|	54.65	68.32	505	193	14	38	515	31	526	3e-139	 501
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005409|ref|XP_862601.1|	55.18	68.53	502	192	14	38	515	32	524	4e-139	 500
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|6457258|gb|AAF09441.1|AF130863_1	54.37	68.25	504	196	13	38	515	31	526	4e-139	 500
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|119590911|gb|EAW70505.1|;gi|194376906|dbj|BAG63014.1|;gi|261859314|dbj|BAI46179.1|	54.37	68.25	504	196	13	38	515	37	532	5e-139	 499
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|119220596|ref|NP_057344.2|;gi|116242509|sp|Q9UKS7.2|IKZF2_HUMAN;gi|119590908|gb|EAW70502.1|	54.37	68.25	504	196	13	38	515	31	526	6e-139	 499
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005383|ref|XP_850763.1|;gi|74005385|ref|XP_545631.2|	54.85	68.71	505	192	15	38	515	31	526	9e-139	 499
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|31544069|ref|NP_035900.2|;gi|26339040|dbj|BAC33191.1|;gi|148667835|gb|EDL00252.1|;gi|187951119|gb|AAI38609.1|;gi|187952949|gb|AAI38607.1|	54.64	69.23	507	190	16	38	515	31	526	2e-138	 498
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005387|ref|XP_862314.1|	53.98	67.73	502	195	11	38	515	32	521	2e-138	 498
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005411|ref|XP_862621.1|	54.78	68.92	502	194	14	38	515	32	524	2e-138	 498
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005405|ref|XP_862550.1|	54.98	68.92	502	193	15	38	515	32	524	2e-138	 498
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|149710110|ref|XP_001488879.1|	54.26	68.12	505	195	14	38	515	31	526	2e-138	 498
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005407|ref|XP_862577.1|	55.53	69.22	497	186	15	38	515	32	512	2e-138	 498
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|149015992|gb|EDL75273.1|	53.86	68.15	518	201	16	26	515	34	541	2e-138	 498
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|3122188|sp|P81183.1|IKZF2_MOUSE;gi|2829277|gb|AAC00513.1|	54.64	69.03	507	190	16	38	515	31	526	3e-138	 497
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|197099024|ref|NP_001126330.1|;gi|55731120|emb|CAH92275.1|	54.37	68.45	504	196	14	38	515	31	526	5e-138	 496
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|119590915|gb|EAW70509.1|	55.44	69.82	487	183	14	55	515	17	495	1e-137	 495
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005435|ref|XP_862906.1|	55.67	69.03	494	186	14	38	515	31	507	3e-137	 494
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005439|ref|XP_862954.1|	54.58	68.33	502	190	15	38	515	32	519	5e-137	 493
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|109100871|ref|XP_001082606.1|;gi|109100873|ref|XP_001082997.1|;gi|114583102|ref|XP_001147077.1|;gi|114583104|ref|XP_001147225.1|	59.45	73.04	434	148	12	104	515	46	473	9e-137	 492
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|224086429|ref|XP_002196355.1|	62.23	76.51	413	135	10	110	516	107	504	1e-136	 492
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|119590910|gb|EAW70504.1|;gi|119590918|gb|EAW70512.1|	59.12	72.98	433	151	11	104	515	46	473	2e-136	 491
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|183986683|ref|NP_001116930.1|;gi|170284528|gb|AAI61078.1|	52.58	69.25	504	200	13	38	514	31	522	2e-136	 491
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|149464956|ref|XP_001509573.1|	63.77	75.85	414	125	14	111	516	55	451	6e-136	 489
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|109114918|ref|XP_001093342.1|	63.50	76.40	411	125	14	111	513	112	505	3e-135	 487
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|109114926|ref|XP_001092666.1|	63.50	76.40	411	125	14	111	513	78	471	5e-135	 486
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|114667633|ref|XP_001171666.1|	63.50	76.40	411	125	14	111	513	112	505	6e-135	 486
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|149724491|ref|XP_001497981.1|	63.04	75.12	414	128	13	111	516	216	612	7e-135	 486
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|114667639|ref|XP_001171590.1|	63.50	76.40	411	125	14	111	513	78	471	8e-135	 486
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|33589816|ref|NP_036613.2|;gi|212276437|sp|Q9UKT9.2|IKZF3_HUMAN;gi|21595809|gb|AAH32707.1|;gi|119581010|gb|EAW60606.1|;gi|167773741|gb|ABZ92305.1|	63.26	76.16	411	126	14	111	513	112	505	6e-134	 483
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|125991956|ref|NP_001075082.1|;gi|158512834|sp|A2VDW9.1|IKZF3_BOVIN;gi|124829200|gb|AAI33440.1|	61.99	75.30	413	134	11	111	516	112	508	7e-134	 483
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|46048912|ref|NP_989938.1|;gi|15387602|emb|CAC59948.1|	51.01	65.01	543	190	17	38	515	32	563	7e-134	 483
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|157820409|ref|NP_001100517.1|;gi|149054117|gb|EDM05934.1|	52.51	67.76	518	211	15	13	516	12	508	9e-134	 482
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|40362504|gb|AAR84584.1|	63.26	76.16	411	126	14	111	513	78	471	1e-133	 482
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|224053901|ref|XP_002189421.1|	54.55	68.97	506	190	15	38	514	32	526	4e-133	 480
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|113374152|ref|NP_035901.1|;gi|123237702|emb|CAM22013.1|;gi|123238494|emb|CAM24385.1|;gi|148684199|gb|EDL16146.1|;gi|148921966|gb|AAI46284.1|;gi|151556750|gb|AAI48735.1|	53.38	66.92	517	206	16	13	516	12	506	6e-133	 479
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|1363187|pir||A56229	98.72	98.72	235	0	1	283	517	161	392	8e-133	 479
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|1363187|pir||A56229	85.80	87.04	162	3	1	1	142	1	162	2e-71	 275
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|23396447|sp|O08900.1|IKZF3_MOUSE;gi|2150044|gb|AAB58795.1|	52.80	66.34	517	209	15	13	516	12	506	2e-132	 478
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|6469927|gb|AAF13493.1|AF129512_1	63.02	75.67	411	127	14	111	513	112	505	3e-132	 477
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|73968336|ref|XP_856504.1|	57.71	70.33	428	155	10	108	513	48	471	2e-130	 471
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|70608924|gb|AAZ04718.1|	68.79	80.64	346	95	6	141	477	50	391	2e-130	 471
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|109097217|ref|XP_001113514.1|;gi|109097219|ref|XP_001113592.1|	50.96	64.18	522	203	16	33	513	74	583	8e-130	 469
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|194212244|ref|XP_001917499.1|	51.46	64.47	515	198	15	39	513	81	583	8e-130	 469
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|168275546|dbj|BAG10493.1|	49.46	62.82	554	221	18	1	513	1	536	1e-129	 469
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|56606154|ref|NP_990151.1|;gi|5918156|emb|CAB56282.1|	54.28	68.68	479	188	12	44	516	40	493	2e-129	 468
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|73968338|ref|XP_538225.2|	50.96	63.79	522	203	16	33	513	74	583	2e-129	 468
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|122891864|ref|NP_071910.3|;gi|114644298|ref|XP_001169594.1|;gi|158564025|sp|Q9H2S9.2|IKZF4_HUMAN;gi|182887905|gb|AAI60169.1|	50.77	63.98	522	204	16	33	513	74	583	3e-129	 467
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|119617280|gb|EAW96874.1|	50.77	63.98	522	204	16	33	513	21	530	3e-129	 467
BioPerl-1.007002/t/data/multi.blast.m9000444000766000024     11002013155576321 17427 0ustar00cjfieldsstaff000000000000# blastp
# Iteration: 0
# Query:  gi|143585771|sp|Q8BIH0.2|SP130_MOUSE RecName: Full=Histone deacetylase complex subunit SAP130; AltName: Full=130 kDa Sin3-associated polypeptide; AltName: Full=Sin3-associated polypeptide p130
# RID: EESSM33W014
# Database: nr
# Fields: query id, subject ids, % identity, % positives, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 63 hits found
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	100.00	100.00	1057	0	0	1	1057	1	1057	0.0	2083
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|41946138|gb|AAH66030.1|	100.00	100.00	1057	0	0	1	1057	42	1098	0.0	2083
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|148664617|gb|EDK97033.1|	99.81	99.81	1057	2	0	1	1057	1	1057	0.0	2079
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|27881435|ref|NP_766553.1|;gi|26343625|dbj|BAC35469.1|	99.91	99.91	1057	0	1	1	1057	1	1056	0.0	2019
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|148664619|gb|EDK97035.1|	99.72	99.72	1057	2	1	1	1057	39	1094	0.0	2016
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|109506405|ref|XP_226078.4|;gi|109507077|ref|XP_001059195.1|	97.64	98.49	1058	24	1	1	1057	89	1146	0.0	2000
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|73984136|ref|XP_533311.2|	92.72	95.74	1057	77	0	1	1057	183	1239	0.0	1902
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|119615759|gb|EAW95353.1|	93.76	96.31	1057	66	0	1	1057	1	1057	0.0	1899
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|225579127|ref|NP_001139400.1|;gi|168278084|dbj|BAG11020.1|;gi|219520104|gb|AAI43899.1|	93.76	96.31	1057	66	0	1	1057	27	1083	0.0	1899
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|114580808|ref|XP_525910.2|	93.66	96.22	1057	66	1	1	1057	27	1082	0.0	1892
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|151556977|gb|AAI49484.1|	93.00	95.84	1057	73	1	1	1057	21	1076	0.0	1882
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|126325911|ref|XP_001366266.1|	90.26	94.42	1057	102	1	1	1057	1	1056	0.0	1875
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|19923597|ref|NP_078821.2|;gi|74717977|sp|Q9H0E3.1|SP130_HUMAN;gi|12053173|emb|CAB66767.1|;gi|29468998|gb|AAO63591.1|;gi|109658530|gb|AAI17256.1|;gi|119615756|gb|EAW95350.1|	90.73	93.09	1057	63	1	1	1057	27	1048	0.0	1816
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|117646626|emb|CAL37428.1|	90.63	93.00	1057	64	1	1	1057	27	1048	0.0	1814
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|117645280|emb|CAL38106.1|	90.63	93.00	1057	64	1	1	1057	27	1048	0.0	1814
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|194664496|ref|XP_615866.4|	90.16	92.72	1057	69	1	1	1057	27	1048	0.0	1809
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|149756507|ref|XP_001504982.1|	90.16	92.43	1057	68	2	1	1057	27	1047	0.0	1783
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|71896869|ref|NP_001026472.1|;gi|82075276|sp|Q5F3U0.1|SP130_CHICK;gi|60098727|emb|CAH65194.1|	86.04	90.28	1060	142	5	1	1057	1	1057	0.0	1731
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|38648728|gb|AAH63075.1|	100.00	100.00	879	0	0	179	1057	1	879	0.0	1707
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|119615761|gb|EAW95355.1|	93.63	96.20	816	52	0	242	1057	13	828	0.0	1502
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|119615757|gb|EAW95351.1|	93.56	96.16	808	52	0	242	1049	13	820	0.0	1485
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|224059701|ref|XP_002191302.1|	83.86	87.73	880	102	3	179	1057	1	841	0.0	1429
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|119615760|gb|EAW95354.1|	89.71	92.03	816	49	1	242	1057	13	793	0.0	1420
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|62822329|gb|AAY14878.1|	90.35	92.57	767	39	1	291	1057	1	732	0.0	1352
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|148234702|ref|NP_001088898.1|;gi|82179336|sp|Q5M7C3.1|SP13B_XENLA;gi|56789809|gb|AAH88715.1|	68.25	78.64	1077	286	22	1	1057	1	1041	0.0	1334
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|48257116|gb|AAH17453.2|	89.84	92.17	728	39	1	330	1057	1	693	0.0	1278
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|148224050|ref|NP_001086872.1|;gi|82182442|sp|Q6DDH6.1|SP13A_XENLA;gi|50415583|gb|AAH77587.1|	66.39	75.86	1077	273	22	1	1057	1	1008	0.0	1258
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|193787295|dbj|BAG52501.1|	89.18	91.68	721	42	2	337	1057	1	685	0.0	1250
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|163915021|ref|NP_001106500.1|;gi|159155111|gb|AAI54703.1|	65.09	75.21	1077	270	22	1	1057	1	991	0.0	1236
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|16550845|dbj|BAB71063.1|;gi|119615758|gb|EAW95352.1|	93.53	96.06	711	45	1	1	711	1	710	0.0	1234
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|148664618|gb|EDK97034.1|	99.37	99.37	639	4	0	294	932	1	639	0.0	1213
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|10434445|dbj|BAB14261.1|	93.80	96.57	613	38	0	445	1057	1	613	0.0	1147
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|90081034|dbj|BAE89997.1|	93.87	96.02	653	40	0	1	653	1	653	0.0	1137
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|68355898|ref|XP_691063.1|;gi|169158058|emb|CAQ14165.1|	59.76	71.14	1081	371	20	1	1056	1	1042	0.0	1095
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|149017119|gb|EDL76170.1|	97.35	98.58	565	15	0	493	1057	42	606	0.0	1085
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|237757277|ref|NP_001092247.2|	59.74	70.96	1016	360	20	63	1056	83	1071	0.0	1034
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|148744304|gb|AAI42599.1|	59.74	70.67	1016	360	20	63	1056	66	1054	0.0	1032
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|26350953|dbj|BAC39113.1|	100.00	100.00	339	0	0	1	339	1	339	1e-173	 615
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|47218881|emb|CAG05647.1|	60.20	70.32	603	192	19	1	577	2	582	2e-157	 561
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|47218881|emb|CAG05647.1|	73.58	88.62	246	65	0	811	1056	600	845	9e-114	 416
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|62630230|gb|AAX88975.1|	91.70	94.46	289	24	0	1	289	27	315	6e-129	 466
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|12848436|dbj|BAB27953.1|	100.00	100.00	193	0	0	865	1057	1	193	2e-106	 392
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|116487558|gb|AAI25872.1|	83.33	92.16	102	17	0	955	1056	231	332	1e-46	 193
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|116487558|gb|AAI25872.1|	52.03	61.49	148	55	6	63	201	84	224	4e-21	 108
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|109104782|ref|XP_001116028.1|	82.35	92.44	119	21	0	689	807	1	119	6e-37	 160
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|91082015|ref|XP_969976.1|	34.68	56.31	222	131	5	840	1056	699	911	1e-33	 150
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|157115575|ref|XP_001652616.1|;gi|108876836|gb|EAT41061.1|	37.97	63.29	158	88	4	901	1056	1185	1334	3e-30	 138
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|242008273|ref|XP_002424931.1|;gi|212508545|gb|EEB12193.1|	32.62	54.94	233	121	8	834	1057	880	1085	5e-30	 138
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|110765898|ref|XP_397260.3|	34.23	55.86	222	120	8	840	1054	620	822	1e-26	 126
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|124487940|gb|ABN12053.1|	40.52	65.36	153	87	2	903	1053	38	188	2e-26	 125
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|260807880|ref|XP_002598736.1|;gi|229284010|gb|EEN54748.1|	33.96	54.48	268	151	12	790	1039	62	321	1e-25	 123
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|195128533|ref|XP_002008717.1|;gi|193920326|gb|EDW19193.1|	33.13	60.12	163	103	4	895	1057	1123	1279	9e-24	 117
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|195379392|ref|XP_002048463.1|;gi|194155621|gb|EDW70805.1|	33.13	60.12	163	103	4	895	1057	1149	1305	9e-24	 117
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|195428094|ref|XP_002062109.1|;gi|194158194|gb|EDW73095.1|	33.74	58.28	163	102	3	895	1057	1196	1352	1e-23	 117
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|27374362|gb|AAO01102.1|	33.13	60.12	163	103	4	895	1057	1158	1314	1e-23	 116
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|195493941|ref|XP_002094629.1|;gi|194180730|gb|EDW94341.1|	30.77	56.04	182	117	4	879	1057	1045	1220	2e-23	 115
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|24663485|ref|NP_729835.1|;gi|221331131|ref|NP_729836.3|;gi|23093587|gb|AAN11859.1|;gi|220902578|gb|AAN11860.3|	30.77	55.49	182	117	4	879	1057	1082	1257	6e-23	 114
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|24663481|ref|NP_729834.1|;gi|23093586|gb|AAN11858.1|	30.77	55.49	182	117	4	879	1057	1119	1294	6e-23	 114
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|194870075|ref|XP_001972581.1|;gi|190654364|gb|EDV51607.1|	30.77	55.49	182	117	4	879	1057	1040	1215	6e-23	 114
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|21355649|ref|NP_648602.1|;gi|4972710|gb|AAD34750.1|;gi|7294536|gb|AAF49877.1|;gi|220943690|gb|ACL84388.1|	30.77	55.49	182	117	4	879	1057	1044	1219	7e-23	 114
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|195327233|ref|XP_002030326.1|;gi|194119269|gb|EDW41312.1|	30.77	55.49	182	117	4	879	1057	757	932	1e-22	 113
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|194752041|ref|XP_001958331.1|;gi|190625613|gb|EDV41137.1|	30.43	56.52	184	119	4	877	1057	1116	1293	2e-22	 112
gi|143585771|sp|Q8BIH0.2|SP130_MOUSE	gi|195589926|ref|XP_002084700.1|;gi|194196709|gb|EDX10285.1|	31.32	55.49	182	116	4	879	1057	836	1011	5e-22	 111
# blastp
# Iteration: 0
# Query:  gi|68053214|sp|Q8BR65.1|SDS3_MOUSE RecName: Full=Sin3 histone deacetylase corepressor complex component SDS3; AltName: Full=Suppressor of defective silencing 3 protein homolog
# RID: EESSM33W014
# Database: nr
# Fields: query id, subject ids, % identity, % positives, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 101 hits found
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|169881247|ref|NP_848737.3|;gi|68053214|sp|Q8BR65.1|SDS3_MOUSE;gi|26337403|dbj|BAC32387.1|;gi|74151871|dbj|BAE29722.1|;gi|74223871|dbj|BAE23831.1|;gi|112180557|gb|AAH55764.2|	100.00	100.00	328	0	0	1	328	1	328	0.0	 665
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|26335815|dbj|BAC31608.1|	99.70	99.70	328	1	0	1	328	1	328	0.0	 663
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|20502870|gb|AAM22676.1|AF469109_1	99.70	99.70	328	1	0	1	328	1	328	0.0	 661
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|109496051|ref|XP_341093.3|;gi|109497459|ref|XP_001080131.1|	98.78	99.39	328	4	0	1	328	535	862	0.0	 661
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|169881250|ref|NP_001116138.1|;gi|38565990|gb|AAH62176.1|	100.00	100.00	325	0	0	1	325	1	325	0.0	 659
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|194214254|ref|XP_001914936.1|	96.95	98.17	328	10	0	1	328	79	406	7e-175	 619
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|149063516|gb|EDM13839.1|	97.75	98.39	311	4	1	21	328	21	331	1e-172	 611
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|149063515|gb|EDM13838.1|	97.73	98.38	308	4	1	21	325	21	328	1e-170	 605
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119618546|gb|EAW98140.1|	99.33	100.00	299	2	0	30	328	19	317	2e-170	 604
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|126324676|ref|XP_001362875.1|	97.66	99.33	299	7	0	30	328	29	327	2e-168	 597
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|197102743|ref|NP_001125541.1|;gi|75042006|sp|Q5RBB8.1|SDS3_PONAB;gi|55728396|emb|CAH90942.1|	99.31	100.00	291	2	0	38	328	38	328	3e-166	 590
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|75677351|ref|NP_071936.2|;gi|68053233|sp|Q9H7L9.2|SDS3_HUMAN;gi|68533937|gb|AAH98404.1|;gi|119618544|gb|EAW98138.1|;gi|208967508|dbj|BAG73768.1|	99.31	100.00	291	2	0	38	328	38	328	3e-166	 590
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|194042976|ref|XP_001924353.1|	99.31	100.00	291	2	0	38	328	115	405	7e-166	 589
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|10440434|dbj|BAB15750.1|	99.31	100.00	291	2	0	38	328	78	368	9e-166	 588
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|109098940|ref|XP_001084823.1|	99.31	100.00	291	2	0	38	328	117	407	2e-165	 588
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|114647229|ref|XP_509415.2|	99.31	100.00	291	2	0	38	328	117	407	2e-165	 587
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|149944705|ref|NP_001092361.1|;gi|172048634|sp|A6H6W9.1|SDS3_BOVIN;gi|148878005|gb|AAI46028.1|	98.63	99.66	291	4	0	38	328	38	328	2e-165	 587
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|73995289|ref|XP_543419.2|	98.36	100.00	305	5	0	21	325	21	325	1e-164	 585
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|148687874|gb|EDL19821.1|	98.98	98.98	293	1	1	38	328	38	330	1e-164	 585
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119618547|gb|EAW98141.1|	98.63	99.31	291	4	0	38	328	38	328	3e-164	 583
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|148687872|gb|EDL19819.1|	98.97	98.97	290	1	1	38	325	38	327	7e-163	 579
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|71895507|ref|NP_001026642.1|;gi|53136632|emb|CAG32645.1|	94.22	98.30	294	17	0	35	328	20	313	4e-160	 570
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|90075564|dbj|BAE87462.1|	99.29	100.00	281	2	0	48	328	12	292	3e-159	 567
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|220679403|emb|CAX14305.1|	85.32	93.27	327	37	3	3	328	2	318	4e-158	 563
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|189230170|ref|NP_001121409.1|;gi|156230905|gb|AAI52171.1|;gi|183985612|gb|AAI66109.1|	88.93	96.74	307	33	1	23	328	4	310	1e-157	 561
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|148227338|ref|NP_001087071.1|;gi|50418319|gb|AAH77985.1|	85.67	92.99	328	40	2	1	328	1	321	2e-157	 561
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|147904216|ref|NP_001086559.1|;gi|49899079|gb|AAH76807.1|	85.37	92.07	328	41	2	1	328	1	321	2e-156	 558
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|220679404|emb|CAX14306.1|	83.28	91.04	335	37	4	3	328	2	326	6e-156	 556
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|51011073|ref|NP_001003493.1|;gi|50417018|gb|AAH78355.1|	86.98	94.29	315	32	2	23	328	4	318	7e-156	 556
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|49619047|gb|AAT68108.1|	86.98	94.29	315	32	2	23	328	2	316	8e-156	 555
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|47221504|emb|CAG08166.1|	80.00	86.96	345	41	2	3	328	2	337	1e-151	 541
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|213513772|ref|NP_001133103.1|;gi|197631943|gb|ACH70695.1|	85.44	93.85	309	44	1	21	328	3	311	3e-148	 530
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119618543|gb|EAW98137.1|	79.46	82.15	297	23	4	38	328	38	302	1e-123	 449
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|148687873|gb|EDL19820.1|	99.50	100.00	200	1	0	1	200	1	200	1e-107	 395
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|149063514|gb|EDM13837.1|	98.00	99.00	200	4	0	1	200	1	200	9e-106	 389
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|85700307|gb|AAI12001.1|	99.46	100.00	184	1	0	145	328	1	184	2e-102	 379
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|62739853|gb|AAH93990.1|	99.41	100.00	169	1	0	160	328	1	169	2e-94	 352
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|10435847|dbj|BAB14685.1|	98.82	99.41	169	2	0	160	328	1	169	1e-93	 349
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119618545|gb|EAW98139.1|	99.40	100.00	167	1	0	38	204	38	204	3e-88	 331
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|20988049|gb|AAH30252.1|	99.36	100.00	157	1	0	172	328	9	165	1e-87	 329
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|66514190|ref|XP_393483.2|	54.40	74.27	307	125	6	31	327	25	326	5e-84	 317
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|260803689|ref|XP_002596722.1|;gi|229281981|gb|EEN52734.1|	55.40	75.96	287	118	4	48	327	1	284	4e-81	 307
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|91093166|ref|XP_967616.1|	52.22	73.04	293	128	5	44	327	37	326	5e-78	 297
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|156394077|ref|XP_001636653.1|;gi|156223758|gb|EDO44590.1|	50.80	70.93	313	143	5	23	327	87	396	1e-77	 296
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|242012093|ref|XP_002426775.1|;gi|212510957|gb|EEB14037.1|	51.44	73.02	278	128	3	52	325	42	316	4e-71	 274
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119570782|gb|EAW50397.1|	76.80	80.41	194	20	2	1	189	1	174	5e-71	 274
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|157126307|ref|XP_001654586.1|;gi|108882558|gb|EAT46783.1|	48.51	70.15	268	126	2	71	326	1	268	2e-66	 259
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119570783|gb|EAW50398.1|	97.32	99.11	112	3	0	217	328	1	112	2e-58	 232
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|221114061|ref|XP_002158878.1|	46.21	66.90	290	148	4	45	328	72	359	5e-58	 231
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|194762662|ref|XP_001963453.1|;gi|190629112|gb|EDV44529.1|	40.00	61.52	330	158	6	30	325	7	330	3e-56	 225
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|193695368|ref|XP_001948875.1|	39.63	59.76	328	162	7	35	328	10	335	1e-55	 223
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195345751|ref|XP_002039432.1|;gi|194134658|gb|EDW56174.1|	40.76	64.01	314	160	7	36	325	15	326	3e-55	 221
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195567747|ref|XP_002107420.1|;gi|194204827|gb|EDX18403.1|	40.63	63.81	315	160	7	36	325	15	327	3e-55	 221
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|158289583|ref|XP_559379.3|;gi|157018587|gb|EAL41125.3|	44.13	63.70	281	151	2	52	326	37	317	4e-55	 221
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|21430678|gb|AAM51017.1|	40.00	62.22	315	162	5	36	325	15	327	6e-54	 217
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|24643310|ref|NP_608325.1|;gi|7293607|gb|AAF48979.1|;gi|201065977|gb|ACH92398.1|	40.00	62.22	315	162	5	36	325	15	327	6e-54	 217
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|125983450|ref|XP_001355490.1|;gi|195174327|ref|XP_002027930.1|;gi|54643806|gb|EAL32549.1|;gi|194115619|gb|EDW37662.1|	40.25	62.58	318	160	6	36	325	14	329	7e-54	 217
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195479741|ref|XP_002101010.1|;gi|194188534|gb|EDX02118.1|	40.00	62.86	315	162	6	36	325	14	326	2e-53	 215
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|198415295|ref|XP_002130717.1|	40.92	63.37	303	164	6	29	326	5	297	6e-53	 214
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195399235|ref|XP_002058226.1|;gi|194150650|gb|EDW66334.1|	43.33	63.70	270	141	3	67	325	90	358	7e-53	 213
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195134340|ref|XP_002011595.1|;gi|193906718|gb|EDW05585.1|	39.20	58.02	324	159	5	36	325	14	333	1e-52	 213
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|194893010|ref|XP_001977789.1|;gi|190649438|gb|EDV46716.1|	39.68	62.86	315	163	6	36	325	14	326	1e-52	 213
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119570784|gb|EAW50399.1|	90.68	95.76	118	11	0	72	189	1	118	8e-52	 210
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195049670|ref|XP_001992764.1|;gi|193893605|gb|EDV92471.1|	42.12	64.84	273	143	4	67	325	76	347	2e-51	 209
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195447846|ref|XP_002071396.1|;gi|194167481|gb|EDW82382.1|	37.50	56.98	344	160	6	35	325	15	356	4e-49	 201
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|221220210|gb|ACM08766.1|	75.17	85.52	145	27	1	3	147	2	137	2e-48	 199
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|241849004|ref|XP_002415664.1|;gi|215509878|gb|EEC19331.1|	47.44	68.37	215	101	3	124	328	1	213	2e-48	 199
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|156538935|ref|XP_001599334.1|	53.23	72.14	201	85	2	77	268	1	201	3e-48	 198
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|170062834|ref|XP_001866841.1|;gi|167880606|gb|EDS43989.1|	57.32	79.62	157	67	0	72	228	1	157	9e-44	 183
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|170062834|ref|XP_001866841.1|;gi|167880606|gb|EDS43989.1|	52.63	73.68	38	18	0	249	286	314	351	7e-05	54.7
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|196011982|ref|XP_002115854.1|;gi|190581630|gb|EDV21706.1|	33.79	55.86	290	129	8	23	297	6	247	9e-31	 140
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|156382010|ref|XP_001632348.1|;gi|156219402|gb|EDO40285.1|	30.97	55.60	268	171	5	62	324	66	324	2e-29	 135
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|71834364|ref|NP_001025273.1|;gi|125841402|ref|XP_001331204.1|;gi|82225989|sp|Q4V8V1.1|BRM1L_DANRE;gi|66910490|gb|AAH97187.1|	29.52	54.98	271	168	7	62	324	67	322	4e-27	 128
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|221130385|ref|XP_002166261.1|	43.28	57.71	201	65	4	45	233	205	368	3e-26	 125
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|117558752|gb|AAI27378.1|	29.96	54.68	267	176	4	60	324	81	338	3e-25	 122
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|147899930|ref|NP_001089225.1|;gi|58047689|gb|AAH89170.1|	29.96	54.31	267	176	4	60	324	55	312	5e-25	 121
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|148225003|ref|NP_001086722.1|;gi|82182058|sp|Q6AZT4.1|BRM1L_XENLA;gi|50604230|gb|AAH77352.1|	28.52	54.44	270	171	6	62	324	67	321	3e-24	 119
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|156717652|ref|NP_001096366.1|;gi|158706424|sp|A4II71.1|BRM1L_XENTR;gi|134025571|gb|AAI35889.1|	28.52	54.07	270	171	6	62	324	67	321	4e-24	 118
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|56118992|ref|NP_001007936.1|;gi|82082601|sp|Q5ZLL9.1|BRM1L_CHICK;gi|53129285|emb|CAG31374.1|	27.82	54.89	266	177	5	62	324	67	320	5e-24	 118
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|126283557|ref|XP_001363359.1|	26.93	52.32	323	196	8	26	324	16	322	7e-24	 117
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|220673407|emb|CAX13654.1|	26.80	53.26	291	191	7	42	324	42	318	8e-24	 117
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|56181500|gb|AAV83797.1|	27.69	52.00	325	191	9	26	324	16	322	1e-23	 116
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|34147416|ref|NP_115728.2|;gi|134085685|ref|NP_001076897.1|;gi|73963078|ref|XP_537414.2|;gi|109083359|ref|XP_001088972.1|;gi|114652674|ref|XP_522994.2|;gi|194038759|ref|XP_001926291.1|;gi|194207298|ref|XP_001491348.2|;gi|158706423|sp|A4FV29.1|BRM1L_BOVIN;gi|158706476|sp|Q5PSV4.2|BRM1L_HUMAN;gi|33871270|gb|AAH06250.2|;gi|119586271|gb|EAW65867.1|;gi|133777620|gb|AAI23662.1|;gi|149051262|gb|EDM03435.1|;gi|171847223|gb|AAI62034.1|	27.69	52.00	325	191	9	26	324	16	322	2e-23	 115
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|83649717|ref|NP_001032845.1|;gi|123796926|sp|Q3U1T3.1|BRM1L_MOUSE;gi|74185761|dbj|BAE32759.1|;gi|74212941|dbj|BAE33410.1|	27.69	52.00	325	191	9	26	324	16	322	2e-23	 115
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|224051440|ref|XP_002200556.1|	27.44	54.51	266	178	5	62	324	67	320	5e-23	 114
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|148704770|gb|EDL36717.1|	27.99	54.48	268	174	6	62	324	31	284	2e-22	 112
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|194386106|dbj|BAG59617.1|	27.82	54.14	266	177	5	62	324	21	274	2e-22	 112
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|149410399|ref|XP_001511853.1|	27.07	54.51	266	179	5	62	324	42	295	2e-22	 112
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|114652676|ref|XP_001141628.1|;gi|189067874|dbj|BAG37812.1|	27.44	54.51	266	178	5	62	324	21	274	2e-22	 112
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|193788411|dbj|BAG53305.1|	27.44	54.51	266	178	5	62	324	11	264	3e-22	 112
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|119887913|ref|XP_001249931.1|	27.65	52.90	293	188	7	42	324	14	292	6e-22	 111
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|148704772|gb|EDL36719.1|	26.67	48.99	345	194	10	26	324	49	380	4e-21	 108
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|221108372|ref|XP_002167338.1|	26.69	50.75	266	181	5	62	324	20	274	1e-18	 100
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|118781168|ref|XP_559429.2|;gi|116130296|gb|EAL41137.2|	37.59	61.65	133	79	2	196	326	1	131	1e-17	96.7
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|198426749|ref|XP_002125654.1|	24.85	48.18	330	214	8	8	325	89	396	2e-16	92.8
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|115761379|ref|XP_001197048.1|;gi|115948498|ref|XP_780214.2|	24.53	51.70	265	179	6	62	322	67	314	2e-15	89.7
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|195397031|ref|XP_002057132.1|;gi|194146899|gb|EDW62618.1|	26.42	51.89	212	139	5	44	245	44	248	2e-09	69.7
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|240995535|ref|XP_002404611.1|;gi|215491613|gb|EEC01254.1|	27.98	58.93	168	115	3	62	226	64	228	2e-09	69.3
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|158295864|ref|XP_001688873.1|;gi|157016237|gb|EDO63879.1|	34.38	56.88	160	100	2	68	223	35	193	4e-09	68.6
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|56756539|gb|AAW26442.1|	31.65	56.83	139	93	1	52	188	14	152	9e-09	67.4
gi|68053214|sp|Q8BR65.1|SDS3_MOUSE	gi|24641636|ref|NP_572840.1|;gi|20976862|gb|AAM27506.1|;gi|22832172|gb|AAF48213.2|;gi|220950330|gb|ACL87708.1|;gi|220959308|gb|ACL92197.1|	27.98	52.75	218	130	8	32	237	31	233	4e-08	65.5
# blastp
# Iteration: 0
# Query:  gi|3915731|sp|Q03267.2|IKZF1_MOUSE RecName: Full=DNA-binding protein Ikaros; AltName: Full=Ikaros family zinc finger protein 1; AltName: Full=Lymphoid transcription factor LyF-1
# RID: EESSM33W014
# Database: nr
# Fields: query id, subject ids, % identity, % positives, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 104 hits found
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|3915731|sp|Q03267.2|IKZF1_MOUSE	100.00	100.00	517	0	0	1	517	1	517	0.0	1074
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|60359882|dbj|BAD90160.1|	98.65	98.84	518	3	2	1	517	25	539	0.0	1051
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|71037387|ref|NP_001020768.1|;gi|148708691|gb|EDL40638.1|;gi|148708692|gb|EDL40639.1|	98.65	98.84	518	3	2	1	517	1	515	0.0	1050
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|56205318|emb|CAI25379.1|	94.98	95.17	538	3	3	1	517	1	535	0.0	1037
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|149016952|gb|EDL76057.1|;gi|149016954|gb|EDL76059.1|;gi|149016956|gb|EDL76061.1|	96.92	98.07	519	9	5	1	517	1	514	0.0	1022
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|5174501|ref|NP_006051.1|;gi|3913926|sp|Q13422.1|IKZF1_HUMAN;gi|1289371|gb|AAC50459.1|;gi|51094649|gb|EAL23900.1|;gi|119581385|gb|EAW60981.1|;gi|208966542|dbj|BAG73285.1|	91.57	94.83	522	36	6	1	517	1	519	0.0	 970
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|149704641|ref|XP_001498147.1|	89.08	94.06	522	49	6	1	517	1	519	0.0	 954
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|1911483|gb|AAB50683.1|	89.44	93.09	521	46	7	1	517	1	516	0.0	 937
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|157426913|ref|NP_001098727.1|	87.62	93.52	509	56	5	13	517	10	515	0.0	 919
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|73981822|ref|XP_540350.2|	84.69	90.36	529	53	7	14	517	54	579	0.0	 910
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|149410208|ref|XP_001506295.1|	86.02	92.15	522	64	7	1	517	211	728	0.0	 902
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|46048783|ref|NP_990419.1|;gi|3913920|sp|O42410.1|IKZF1_CHICK;gi|2330595|emb|CAA72531.1|	82.76	91.57	522	81	7	1	517	1	518	0.0	 897
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|224045852|ref|XP_002191672.1|	82.12	90.58	520	85	6	1	516	1	516	0.0	 884
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|114613538|ref|XP_001148911.1|	92.09	95.09	468	29	6	55	517	169	633	0.0	 867
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|126336572|ref|XP_001379648.1|	88.70	94.24	469	44	7	54	517	94	558	0.0	 852
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|21322628|emb|CAC84566.1|	79.31	89.08	522	98	8	1	517	1	517	0.0	 841
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|109066562|ref|XP_001082512.1|	90.47	93.79	451	34	7	73	517	1	448	0.0	 819
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|109066560|ref|XP_001082388.1|	89.56	92.67	450	29	7	73	517	1	437	0.0	 808
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|198287|gb|AAA66193.1|	99.21	99.21	381	3	0	137	517	51	431	0.0	 790
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|17390815|gb|AAH18349.1|;gi|32880015|gb|AAP88838.1|;gi|60654753|gb|AAX31941.1|;gi|60654755|gb|AAX31942.1|;gi|60654757|gb|AAX31943.1|;gi|60654759|gb|AAX31944.1|;gi|119581382|gb|EAW60978.1|;gi|119581383|gb|EAW60979.1|	77.50	83.46	520	71	7	1	517	1	477	0.0	 786
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|148708694|gb|EDL40641.1|	97.90	98.16	381	5	1	137	517	75	452	0.0	 775
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|71037385|ref|NP_033604.2|;gi|56205317|emb|CAI25378.1|;gi|148708693|gb|EDL40640.1|;gi|148708696|gb|EDL40643.1|;gi|187952041|gb|AAI38790.1|	97.90	98.16	381	5	1	137	517	51	428	0.0	 773
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|1363188|pir||B56229	97.64	97.90	381	5	2	137	517	51	427	0.0	 766
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|157821935|ref|NP_001100707.1|;gi|149016953|gb|EDL76058.1|;gi|149016955|gb|EDL76060.1|;gi|149016957|gb|EDL76062.1|	96.34	97.64	382	10	2	137	517	50	428	0.0	 760
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|6007783|gb|AAF01038.1|	73.46	82.31	520	95	9	1	516	1	481	0.0	 748
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|62751371|ref|NP_001015698.1|;gi|58618896|gb|AAH89243.1|	72.06	82.27	519	105	8	1	516	1	482	0.0	 748
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|119581381|gb|EAW60977.1|;gi|194383264|dbj|BAG64603.1|	90.81	94.23	381	28	5	141	517	55	432	0.0	 704
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|223649474|gb|ACN11495.1|	67.42	79.85	531	146	12	1	514	1	521	0.0	 697
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|185132424|ref|NP_001118184.1|;gi|3913918|sp|O13089.1|IKZF1_ONCMY;gi|2062742|gb|AAB97474.1|	66.92	80.08	532	148	13	1	514	1	522	0.0	 693
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|9408380|gb|AAF87271.1|AF163848_1	66.04	78.30	530	137	10	1	517	1	500	0.0	 685
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|119581386|gb|EAW60982.1|	71.77	77.53	503	69	8	1	480	1	453	0.0	 676
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74218692|dbj|BAE25211.1|	87.66	87.66	381	3	2	137	517	51	387	0.0	 671
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74218692|dbj|BAE25211.1|	100.00	100.00	54	0	0	1	54	1	54	1e-22	 113
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|220678857|emb|CAX12977.1|	65.36	78.21	537	150	15	1	513	1	525	0.0	 669
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|15987101|gb|AAL11906.1|AF416370_1	65.36	78.21	537	150	15	1	513	1	525	0.0	 669
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|220678853|emb|CAX12973.1|	64.05	76.64	548	150	15	1	513	1	536	0.0	 665
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|18859581|ref|NP_571061.1|;gi|3661583|gb|AAC61763.1|;gi|190338657|gb|AAI62270.1|	64.05	76.64	548	150	15	1	513	1	536	0.0	 665
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|2062736|gb|AAB53432.1|	61.39	73.07	531	134	14	1	514	1	477	5e-172	 609
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|47208098|emb|CAF91930.1|;gi|239799504|tpe|CAQ76709.1|	69.52	80.00	420	105	9	107	513	2	411	6e-162	 576
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|47078380|gb|AAT09851.1|	84.47	84.78	322	2	2	196	517	54	327	3e-152	 543
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|47078380|gb|AAT09851.1|	100.00	100.00	53	0	0	1	53	1	53	1e-21	 110
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|2062740|gb|AAB53434.1|	68.93	81.98	383	100	8	141	514	56	428	2e-148	 531
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|9408378|gb|AAF87270.1|AF163847_1	56.63	70.88	498	189	12	38	515	32	522	3e-148	 530
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|9408384|gb|AAF87273.1|AF163850_1	56.31	69.51	515	179	19	18	514	24	510	5e-143	 513
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005423|ref|XP_862767.1|	56.34	69.82	497	188	14	38	515	31	517	5e-143	 513
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005417|ref|XP_862696.1|	55.82	70.08	498	191	14	38	515	32	520	2e-142	 511
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005441|ref|XP_862975.1|	55.69	69.46	501	190	14	38	515	31	522	5e-142	 510
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005425|ref|XP_862793.1|	55.42	69.68	498	193	14	38	515	32	520	2e-141	 507
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005433|ref|XP_862881.1|	55.94	69.42	497	183	14	38	515	32	511	4e-141	 507
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|26346747|dbj|BAC37022.1|	98.40	98.80	250	3	1	1	249	1	250	5e-141	 506
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|13785508|dbj|BAB43903.1|	67.45	79.43	384	107	9	141	514	53	428	1e-140	 505
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|13785508|dbj|BAB43903.1|	28.93	45.91	159	75	4	1	156	1	124	5e-06	58.2
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|220678856|emb|CAX12976.1|	66.92	78.46	390	100	10	141	513	56	433	1e-139	 502
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005391|ref|XP_862364.1|	55.19	69.25	491	195	11	38	515	32	510	1e-139	 501
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|15987103|gb|AAL11907.1|AF416371_1	66.92	78.46	390	100	10	141	513	56	433	2e-139	 501
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005403|ref|XP_862526.1|	55.11	68.94	499	194	14	38	515	32	521	2e-139	 501
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|109100863|ref|XP_001083355.1|;gi|114583092|ref|XP_526015.2|	54.65	68.32	505	193	14	38	515	31	526	3e-139	 501
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005409|ref|XP_862601.1|	55.18	68.53	502	192	14	38	515	32	524	4e-139	 500
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|6457258|gb|AAF09441.1|AF130863_1	54.37	68.25	504	196	13	38	515	31	526	4e-139	 500
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|119590911|gb|EAW70505.1|;gi|194376906|dbj|BAG63014.1|;gi|261859314|dbj|BAI46179.1|	54.37	68.25	504	196	13	38	515	37	532	5e-139	 499
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|119220596|ref|NP_057344.2|;gi|116242509|sp|Q9UKS7.2|IKZF2_HUMAN;gi|119590908|gb|EAW70502.1|	54.37	68.25	504	196	13	38	515	31	526	6e-139	 499
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005383|ref|XP_850763.1|;gi|74005385|ref|XP_545631.2|	54.85	68.71	505	192	15	38	515	31	526	9e-139	 499
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|31544069|ref|NP_035900.2|;gi|26339040|dbj|BAC33191.1|;gi|148667835|gb|EDL00252.1|;gi|187951119|gb|AAI38609.1|;gi|187952949|gb|AAI38607.1|	54.64	69.23	507	190	16	38	515	31	526	2e-138	 498
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005387|ref|XP_862314.1|	53.98	67.73	502	195	11	38	515	32	521	2e-138	 498
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005411|ref|XP_862621.1|	54.78	68.92	502	194	14	38	515	32	524	2e-138	 498
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005405|ref|XP_862550.1|	54.98	68.92	502	193	15	38	515	32	524	2e-138	 498
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|149710110|ref|XP_001488879.1|	54.26	68.12	505	195	14	38	515	31	526	2e-138	 498
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005407|ref|XP_862577.1|	55.53	69.22	497	186	15	38	515	32	512	2e-138	 498
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|149015992|gb|EDL75273.1|	53.86	68.15	518	201	16	26	515	34	541	2e-138	 498
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|3122188|sp|P81183.1|IKZF2_MOUSE;gi|2829277|gb|AAC00513.1|	54.64	69.03	507	190	16	38	515	31	526	3e-138	 497
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|197099024|ref|NP_001126330.1|;gi|55731120|emb|CAH92275.1|	54.37	68.45	504	196	14	38	515	31	526	5e-138	 496
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|119590915|gb|EAW70509.1|	55.44	69.82	487	183	14	55	515	17	495	1e-137	 495
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005435|ref|XP_862906.1|	55.67	69.03	494	186	14	38	515	31	507	3e-137	 494
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|74005439|ref|XP_862954.1|	54.58	68.33	502	190	15	38	515	32	519	5e-137	 493
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|109100871|ref|XP_001082606.1|;gi|109100873|ref|XP_001082997.1|;gi|114583102|ref|XP_001147077.1|;gi|114583104|ref|XP_001147225.1|	59.45	73.04	434	148	12	104	515	46	473	9e-137	 492
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|224086429|ref|XP_002196355.1|	62.23	76.51	413	135	10	110	516	107	504	1e-136	 492
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|119590910|gb|EAW70504.1|;gi|119590918|gb|EAW70512.1|	59.12	72.98	433	151	11	104	515	46	473	2e-136	 491
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|183986683|ref|NP_001116930.1|;gi|170284528|gb|AAI61078.1|	52.58	69.25	504	200	13	38	514	31	522	2e-136	 491
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|149464956|ref|XP_001509573.1|	63.77	75.85	414	125	14	111	516	55	451	6e-136	 489
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|109114918|ref|XP_001093342.1|	63.50	76.40	411	125	14	111	513	112	505	3e-135	 487
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|109114926|ref|XP_001092666.1|	63.50	76.40	411	125	14	111	513	78	471	5e-135	 486
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|114667633|ref|XP_001171666.1|	63.50	76.40	411	125	14	111	513	112	505	6e-135	 486
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|149724491|ref|XP_001497981.1|	63.04	75.12	414	128	13	111	516	216	612	7e-135	 486
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|114667639|ref|XP_001171590.1|	63.50	76.40	411	125	14	111	513	78	471	8e-135	 486
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|33589816|ref|NP_036613.2|;gi|212276437|sp|Q9UKT9.2|IKZF3_HUMAN;gi|21595809|gb|AAH32707.1|;gi|119581010|gb|EAW60606.1|;gi|167773741|gb|ABZ92305.1|	63.26	76.16	411	126	14	111	513	112	505	6e-134	 483
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|125991956|ref|NP_001075082.1|;gi|158512834|sp|A2VDW9.1|IKZF3_BOVIN;gi|124829200|gb|AAI33440.1|	61.99	75.30	413	134	11	111	516	112	508	7e-134	 483
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|46048912|ref|NP_989938.1|;gi|15387602|emb|CAC59948.1|	51.01	65.01	543	190	17	38	515	32	563	7e-134	 483
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|157820409|ref|NP_001100517.1|;gi|149054117|gb|EDM05934.1|	52.51	67.76	518	211	15	13	516	12	508	9e-134	 482
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|40362504|gb|AAR84584.1|	63.26	76.16	411	126	14	111	513	78	471	1e-133	 482
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|224053901|ref|XP_002189421.1|	54.55	68.97	506	190	15	38	514	32	526	4e-133	 480
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|113374152|ref|NP_035901.1|;gi|123237702|emb|CAM22013.1|;gi|123238494|emb|CAM24385.1|;gi|148684199|gb|EDL16146.1|;gi|148921966|gb|AAI46284.1|;gi|151556750|gb|AAI48735.1|	53.38	66.92	517	206	16	13	516	12	506	6e-133	 479
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|1363187|pir||A56229	98.72	98.72	235	0	1	283	517	161	392	8e-133	 479
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|1363187|pir||A56229	85.80	87.04	162	3	1	1	142	1	162	2e-71	 275
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|23396447|sp|O08900.1|IKZF3_MOUSE;gi|2150044|gb|AAB58795.1|	52.80	66.34	517	209	15	13	516	12	506	2e-132	 478
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|6469927|gb|AAF13493.1|AF129512_1	63.02	75.67	411	127	14	111	513	112	505	3e-132	 477
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|73968336|ref|XP_856504.1|	57.71	70.33	428	155	10	108	513	48	471	2e-130	 471
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|70608924|gb|AAZ04718.1|	68.79	80.64	346	95	6	141	477	50	391	2e-130	 471
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|109097217|ref|XP_001113514.1|;gi|109097219|ref|XP_001113592.1|	50.96	64.18	522	203	16	33	513	74	583	8e-130	 469
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|194212244|ref|XP_001917499.1|	51.46	64.47	515	198	15	39	513	81	583	8e-130	 469
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|168275546|dbj|BAG10493.1|	49.46	62.82	554	221	18	1	513	1	536	1e-129	 469
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|56606154|ref|NP_990151.1|;gi|5918156|emb|CAB56282.1|	54.28	68.68	479	188	12	44	516	40	493	2e-129	 468
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|73968338|ref|XP_538225.2|	50.96	63.79	522	203	16	33	513	74	583	2e-129	 468
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|122891864|ref|NP_071910.3|;gi|114644298|ref|XP_001169594.1|;gi|158564025|sp|Q9H2S9.2|IKZF4_HUMAN;gi|182887905|gb|AAI60169.1|	50.77	63.98	522	204	16	33	513	74	583	3e-129	 467
gi|3915731|sp|Q03267.2|IKZF1_MOUSE	gi|119617280|gb|EAW96874.1|	50.77	63.98	522	204	16	33	513	21	530	3e-129	 467




BioPerl-1.007002/t/data/multi.phd000444000766000024      3562713155576321 16554 0ustar00cjfieldsstaff000000000000BEGIN_SEQUENCE ML4924F

BEGIN_COMMENT

CHROMAT_FILE: ML4924F
ABI_THUMBPRINT: 0
PHRED_VERSION: 0.980904.e
CALL_METHOD: phred
QUALITY_LEVELS: 99
TIME: Thu Jun 21 11:27:03 2001
TRACE_ARRAY_MIN_INDEX: 0
TRACE_ARRAY_MAX_INDEX: 8444
CHEM: term
DYE: big

END_COMMENT

BEGIN_DNA
t 10 3
t 16 14
g 19 26
t 19 36
t 8 47
c 6 55
t 6 74
t 6 77
t 6 95
t 9 98
c 9 105
t 15 119
c 17 128
g 17 143
a 22 148
g 22 162
g 25 173
g 25 185
t 22 197
a 22 202
c 22 213
t 25 227
t 34 239
g 34 250
a 42 260
g 35 270
g 35 282
a 38 294
t 40 303
t 40 314
c 35 323
t 34 335
a 31 344
c 31 351
c 33 364
a 34 373
c 35 381
c 33 394
a 29 404
c 35 412
a 29 424
a 29 434
c 32 443
a 34 454
a 34 463
c 35 473
a 35 484
a 42 494
a 42 506
g 42 516
c 42 526
c 35 539
t 35 551
t 37 562
a 35 571
t 35 581
c 35 592
a 35 600
t 35 612
c 31 623
c 33 635
a 24 644
g 24 655
a 24 667
a 29 677
c 26 686
c 29 698
g 29 712
c 29 719
a 29 731
a 29 740
a 29 751
t 35 763
t 35 775
a 35 782
t 35 794
a 35 803
a 35 813
a 42 824
a 42 835
a 47 846
a 47 857
g 40 869
a 35 880
g 35 891
c 35 900
c 32 913
a 32 921
a 32 932
c 32 942
a 42 953
c 42 963
c 42 976
a 37 986
c 37 996
a 30 1007
a 30 1018
a 35 1030
a 35 1041
c 35 1050
a 35 1061
a 35 1071
a 37 1083
a 32 1095
t 32 1106
g 35 1119
a 35 1128
a 37 1139
a 37 1150
a 42 1161
g 42 1174
a 37 1184
a 37 1194
a 40 1206
c 37 1215
a 37 1226
a 35 1236
a 35 1249
c 35 1259
t 37 1274
c 35 1284
t 35 1298
t 37 1310
c 37 1319
a 37 1328
a 37 1339
c 35 1349
c 32 1362
a 29 1371
g 31 1385
t 31 1400
g 29 1410
a 35 1419
t 35 1433
g 35 1445
t 35 1457
t 35 1469
c 35 1478
t 35 1492
g 35 1505
a 35 1514
g 32 1526
a 32 1538
c 35 1547
t 32 1562
t 35 1573
g 35 1586
t 32 1596
t 32 1608
g 32 1622
a 32 1630
g 32 1644
g 35 1656
a 35 1666
t 35 1679
a 35 1687
a 35 1698
c 35 1709
a 37 1721
c 37 1731
c 35 1745
t 35 1760
t 32 1773
c 32 1782
g 32 1796
t 32 1808
a 32 1817
c 30 1826
t 35 1842
t 35 1854
a 35 1862
a 35 1874
c 35 1884
t 35 1900
t 32 1913
g 35 1924
g 42 1936
a 42 1948
a 42 1958
c 42 1968
c 35 1981
a 35 1992
c 38 2002
t 38 2018
t 38 2030
c 38 2040
a 42 2052
t 40 2064
g 40 2077
g 38 2089
c 35 2098
a 35 2112
t 35 2124
c 42 2135
a 50 2147
t 56 2159
c 56 2171
c 50 2183
t 56 2196
t 56 2209
g 42 2222
g 42 2234
t 42 2246
a 38 2256
a 38 2267
c 38 2277
t 38 2293
c 38 2303
t 38 2318
a 40 2328
t 38 2339
g 38 2353
c 38 2363
t 40 2378
g 40 2390
a 40 2401
a 44 2413
t 42 2425
c 42 2435
c 42 2448
c 38 2460
a 36 2471
a 36 2483
c 32 2492
g 32 2507
c 32 2517
g 35 2532
a 35 2543
g 38 2555
t 41 2569
c 41 2579
t 41 2593
t 41 2605
g 41 2617
c 42 2627
a 41 2638
c 41 2649
c 41 2662
t 41 2676
a 41 2686
c 41 2697
g 41 2711
g 41 2723
c 41 2735
g 35 2749
a 40 2759
c 35 2769
g 32 2784
t 32 2796
g 36 2809
c 38 2818
a 35 2830
a 35 2842
c 37 2852
a 38 2865
c 35 2876
g 35 2891
g 35 2903
t 35 2915
a 37 2926
t 37 2938
c 41 2950
c 41 2962
c 41 2974
g 41 2989
g 41 3000
g 41 3012
c 41 3023
g 35 3038
t 35 3050
t 35 3063
c 32 3071
a 35 3083
a 31 3094
g 33 3107
a 32 3120
a 35 3131
c 35 3140
a 37 3153
a 29 3164
c 33 3174
a 16 3187
t 16 3198
a 9 3210
g 20 3223
a 13 3236
a 23 3247
g 23 3259
t 33 3272
c 35 3281
c 37 3294
a 35 3305
t 40 3317
t 40 3331
c 45 3341
c 40 3353
a 40 3364
t 50 3375
a 30 3388
g 30 3400
a 33 3413
t 40 3424
a 33 3434
c 37 3444
c 29 3458
c 29 3470
g 21 3485
t 25 3497
a 21 3508
g 23 3519
a 23 3532
a 50 3543
g 50 3554
g 37 3567
a 35 3579
t 35 3591
c 35 3600
g 32 3616
t 32 3627
a 32 3637
c 37 3647
t 37 3662
t 37 3675
g 40 3686
a 37 3698
t 37 3709
t 37 3722
c 37 3731
c 35 3744
a 35 3755
a 44 3766
g 44 3778
a 44 3791
t 44 3802
c 44 3813
a 56 3824
a 44 3836
t 56 3849
g 37 3861
t 35 3873
g 35 3885
c 35 3894
t 35 3910
c 35 3918
c 26 3932
t 32 3945
g 26 3958
g 26 3969
a 26 3982
t 32 3992
a 32 4003
c 35 4012
c 35 4025
g 35 4040
a 35 4051
a 35 4063
t 42 4075
c 42 4085
c 35 4097
a 42 4108
a 42 4119
a 42 4131
a 42 4143
c 35 4153
a 33 4165
g 29 4178
c 33 4189
c 29 4202
a 30 4212
g 28 4225
t 35 4236
g 33 4250
t 35 4261
c 35 4273
a 35 4283
c 35 4293
t 37 4308
g 37 4321
a 45 4332
a 44 4344
g 44 4355
t 44 4367
t 44 4378
c 44 4391
c 44 4402
t 44 4415
c 39 4427
c 39 4438
t 42 4450
c 42 4461
a 42 4472
a 42 4483
c 42 4493
a 35 4505
g 28 4517
c 27 4529
t 24 4543
c 20 4555
g 20 4567
t 22 4576
a 29 4589
c 29 4599
t 40 4613
c 40 4624
c 42 4637
t 42 4648
t 35 4662
g 35 4673
a 35 4685
c 37 4694
t 35 4708
t 35 4720
t 33 4733
c 33 4743
a 33 4752
a 35 4764
g 35 4776
c 34 4787
c 34 4801
a 33 4811
c 33 4821
t 33 4835
c 29 4847
t 28 4860
c 28 4872
a 27 4881
a 21 4894
c 21 4908
a 15 4917
a 15 4928
g 21 4939
c 21 4949
t 25 4964
g 29 4976
c 29 4984
a 29 4998
t 29 5010
t 33 5023
g 33 5034
c 25 5044
c 27 5058
t 23 5071
t 23 5083
g 11 5094
c 10 5104
c 10 5117
t 24 5130
c 24 5139
c 29 5152
t 29 5165
c 27 5177
t 29 5189
c 29 5202
a 29 5209
c 29 5220
g 32 5233
g 36 5245
t 36 5258
g 35 5269
a 45 5281
c 40 5291
g 38 5305
t 38 5317
a 28 5328
g 28 5338
c 26 5351
a 32 5363
c 32 5372
g 35 5387
c 35 5397
a 35 5410
a 42 5421
t 37 5432
c 34 5445
t 34 5456
t 42 5468
t 29 5480
t 29 5491
c 29 5505
a 35 5513
t 35 5526
t 26 5538
a 24 5548
c 17 5557
g 14 5574
t 12 5585
c 12 5598
t 25 5609
a 27 5618
a 35 5630
t 37 5643
a 38 5653
c 40 5663
c 34 5677
g 34 5690
a 34 5700
a 35 5711
a 32 5725
g 33 5735
a 32 5747
c 29 5756
c 29 5770
t 21 5782
c 21 5794
a 27 5805
c 33 5815
a 26 5827
g 16 5838
t 16 5851
g 10 5863
c 10 5873
a 10 5885
c 20 5894
c 12 5908
t 6 5921
g 6 5931
g 8 5946
c 9 5950
c 9 5970
t 11 5981
t 13 5995
g 18 6004
g 15 6017
a 15 6030
c 17 6042
a 11 6050
a 8 6064
c 11 6077
a 9 6086
c 13 6093
a 9 6106
g 19 6119
g 21 6132
t 24 6146
g 24 6156
t 18 6168
t 15 6181
t 15 6194
g 21 6205
a 25 6215
c 29 6225
c 29 6239
a 25 6248
c 25 6260
t 14 6274
g 14 6285
a 9 6298
g 9 6309
c 9 6322
t 24 6333
g 14 6345
t 11 6355
t 8 6369
a 8 6383
c 8 6391
a 15 6400
a 20 6410
a 27 6422
a 40 6433
c 40 6444
c 40 6457
t 26 6470
t 24 6481
g 12 6493
g 12 6503
a 15 6517
g 13 6528
g 10 6540
c 17 6549
a 18 6565
c 15 6574
g 12 6586
g 15 6597
g 16 6609
t 19 6621
g 23 6635
a 20 6645
g 24 6658
a 21 6670
c 21 6679
g 21 6693
a 21 6703
t 24 6712
c 16 6725
a 20 6736
c 18 6746
c 20 6763
a 16 6771
c 16 6781
t 14 6796
c 12 6808
t 10 6819
c 10 6829
a 12 6841
c 17 6850
c 17 6864
a 29 6873
a 29 6885
c 29 6893
g 19 6908
g 16 6919
a 9 6934
g 9 6941
a 9 6956
t 16 6965
g 13 6978
t 11 6990
c 9 6998
g 11 7014
a 9 7025
g 10 7037
a 9 7049
a 19 7059
c 14 7069
g 14 7081
a 10 7093
g 10 7104
c 10 7118
t 14 7129
t 14 7142
c 25 7154
t 26 7166
g 28 7176
a 32 7187
a 32 7198
c 32 7208
c 33 7222
t 33 7234
t 28 7244
g 21 7256
a 18 7268
t 12 7279
a 11 7288
t 13 7300
t 9 7314
c 9 7322
c 12 7336
t 10 7346
c 11 7359
a 10 7368
t 11 7378
t 12 7394
g 11 7402
g 11 7413
g 10 7423
c 10 7439
t 10 7454
c 10 7462
c 8 7477
a 8 7484
c 10 7497
a 9 7506
g 9 7518
c 9 7527
t 6 7544
c 6 7546
t 8 7557
t 8 7574
t 11 7590
c 9 7600
t 9 7611
c 10 7621
t 10 7632
g 14 7644
a 14 7655
c 10 7666
g 8 7678
c 8 7690
c 17 7703
a 10 7711
t 10 7719
t 9 7729
c 12 7746
t 9 7755
g 11 7770
a 7 7781
g 7 7787
g 10 7802
a 12 7813
t 9 7821
c 6 7837
t 6 7840
a 6 7852
g 6 7864
g 8 7880
g 8 7893
a 11 7903
t 12 7915
g 10 7925
c 9 7938
a 9 7947
c 8 7961
a 8 7968
c 12 7978
c 14 7991
c 20 8004
a 16 8013
c 17 8026
a 10 8036
a 10 8045
g 12 8059
g 17 8071
a 17 8084
c 24 8096
a 18 8107
t 14 8116
g 14 8128
a 11 8140
c 14 8149
c 12 8162
a 15 8174
a 15 8183
a 10 8193
a 9 8205
t 11 8214
c 9 8228
g 9 8237
a 10 8252
c 8 8259
a 6 8275
t 6 8279
c 8 8286
t 8 8305
g 7 8318
g 7 8327
g 9 8341
c 9 8349
c 7 8365
c 6 8372
a 10 8387
c 6 8400
t 6 8400
c 6 8415
g 6 8437
END_DNA

END_SEQUENCE

BEGIN_SEQUENCE ML4924R

BEGIN_COMMENT

CHROMAT_FILE: ML4924R
ABI_THUMBPRINT: 0
PHRED_VERSION: 0.980904.e
CALL_METHOD: phred
QUALITY_LEVELS: 99
TIME: Thu Jun 21 11:27:03 2001
TRACE_ARRAY_MIN_INDEX: 0
TRACE_ARRAY_MAX_INDEX: 8792
CHEM: term
DYE: big

END_COMMENT

BEGIN_DNA
a 6 1
c 6 20
t 6 17
t 8 26
t 8 35
g 12 48
g 18 58
t 16 66
c 14 83
g 11 98
c 9 104
c 6 122
t 6 128
g 9 140
c 19 147
a 20 159
g 32 167
g 34 178
t 34 190
a 39 200
c 39 208
c 39 221
g 29 233
g 40 243
t 28 255
c 21 267
c 13 277
g 4 288
n 4 297
g 4 298
a 8 314
t 8 328
t 23 339
c 29 349
c 39 359
c 40 369
g 40 381
g 40 390
g 40 401
t 46 413
c 34 425
g 33 436
a 29 447
c 29 453
c 32 466
c 33 476
a 34 485
c 34 492
g 34 505
c 34 514
g 40 527
t 40 537
c 34 548
c 34 559
g 34 572
c 34 579
t 34 592
t 34 602
t 39 613
g 40 625
c 40 633
t 40 645
c 40 656
a 40 664
t 40 673
c 40 685
t 46 697
c 51 707
c 51 718
c 56 728
t 51 738
c 51 749
t 35 760
g 35 772
a 35 783
c 35 790
t 35 803
t 35 813
t 39 824
g 40 836
c 40 844
a 40 855
t 40 865
c 56 876
c 42 887
c 51 898
t 46 909
t 46 921
a 46 931
a 46 940
t 46 951
c 46 962
c 46 974
t 46 985
c 40 995
a 40 1004
g 40 1015
a 40 1028
a 40 1037
t 40 1048
g 35 1060
g 35 1071
c 35 1080
g 35 1096
t 35 1106
c 35 1116
a 40 1125
g 40 1138
a 40 1150
g 51 1160
a 51 1172
a 51 1182
g 51 1193
a 40 1204
a 35 1214
g 35 1226
c 39 1235
t 39 1250
c 39 1259
t 39 1272
c 40 1282
g 51 1295
a 51 1305
a 51 1315
c 51 1325
c 51 1337
c 51 1348
a 51 1358
a 51 1368
t 51 1381
g 51 1393
a 51 1403
g 51 1415
g 51 1427
g 39 1440
a 39 1450
t 39 1462
a 39 1470
t 39 1483
c 35 1494
a 40 1503
a 40 1514
g 40 1528
g 40 1540
t 40 1552
t 39 1565
c 39 1574
a 39 1583
g 39 1598
a 38 1609
a 40 1619
g 39 1632
c 39 1642
t 39 1657
c 39 1666
g 39 1680
t 40 1691
t 45 1703
c 51 1713
t 51 1726
c 51 1736
a 51 1746
a 51 1757
c 51 1767
a 45 1778
t 45 1791
c 45 1802
t 45 1816
c 45 1826
c 45 1838
g 45 1852
t 51 1863
t 51 1875
g 56 1887
g 43 1899
t 43 1911
g 43 1924
a 43 1933
g 43 1946
a 43 1958
g 56 1970
t 56 1982
g 56 1994
g 56 2006
t 56 2017
g 51 2030
a 43 2041
t 43 2053
c 43 2063
g 43 2079
t 43 2089
c 43 2100
t 43 2114
c 43 2124
a 43 2135
c 43 2144
c 43 2157
c 43 2169
g 43 2184
t 43 2195
g 43 2207
c 43 2216
c 43 2229
t 43 2244
c 43 2253
c 43 2265
a 46 2277
a 56 2288
g 56 2299
g 56 2311
t 56 2324
t 56 2336
t 56 2348
t 56 2360
g 56 2373
g 51 2385
a 51 2397
a 51 2408
c 51 2418
a 43 2430
g 43 2443
c 45 2454
t 45 2469
c 45 2480
a 45 2491
g 56 2503
t 56 2516
g 56 2528
g 51 2540
t 51 2552
c 51 2564
a 51 2574
a 51 2585
a 51 2598
c 45 2608
a 45 2620
c 45 2630
c 45 2644
t 45 2658
g 51 2671
t 51 2682
c 51 2693
t 51 2707
t 45 2719
c 45 2730
t 51 2743
c 51 2753
c 51 2765
a 51 2775
a 51 2787
g 43 2798
g 43 2810
c 43 2822
g 43 2837
a 43 2847
g 43 2859
g 51 2872
t 51 2884
a 51 2894
c 43 2904
a 43 2917
c 43 2927
t 43 2943
g 43 2956
t 43 2967
g 51 2980
a 51 2992
g 45 3003
g 45 3017
t 45 3029
c 45 3039
t 45 3053
t 45 3065
t 51 3077
c 51 3088
g 51 3102
g 51 3113
t 51 3125
a 43 3136
t 43 3148
t 43 3161
a 43 3170
g 43 3183
a 43 3196
c 43 3205
g 43 3220
t 43 3231
a 45 3243
a 56 3254
t 56 3266
g 56 3279
a 56 3290
a 56 3302
a 56 3314
a 51 3325
g 51 3337
a 51 3350
t 43 3360
t 43 3373
g 43 3385
c 43 3394
g 43 3410
t 43 3421
g 43 3434
c 43 3443
t 43 3458
a 43 3468
c 43 3477
g 43 3493
t 43 3505
c 43 3515
a 43 3527
c 43 3536
c 43 3550
g 43 3565
t 43 3576
g 43 3588
a 45 3601
g 45 3611
a 45 3625
g 45 3635
g 45 3648
a 43 3660
g 43 3672
a 38 3684
c 38 3692
a 38 3705
a 43 3717
g 56 3729
g 56 3741
c 56 3752
a 56 3765
a 51 3776
t 51 3789
g 51 3801
c 51 3811
a 43 3824
g 43 3836
c 43 3846
t 43 3862
t 43 3874
c 43 3884
t 51 3897
t 51 3909
g 56 3922
a 56 3933
g 56 3944
a 56 3957
g 56 3968
t 43 3980
g 43 3992
g 43 4004
c 43 4013
t 43 4029
t 43 4041
g 43 4053
a 56 4064
a 56 4075
a 51 4087
g 51 4098
t 51 4111
c 51 4121
a 51 4132
a 51 4144
g 56 4155
g 56 4168
a 51 4181
g 51 4192
t 43 4205
a 43 4215
c 43 4225
g 43 4240
a 43 4250
g 43 4263
c 43 4274
t 45 4289
g 45 4301
t 45 4312
t 56 4324
g 56 4336
a 56 4347
g 56 4358
g 56 4371
a 56 4383
g 56 4394
g 51 4407
a 43 4419
a 43 4430
c 43 4440
t 43 4455
t 43 4467
c 43 4477
a 51 4488
g 51 4500
t 51 4513
g 51 4525
a 51 4536
c 45 4546
a 45 4558
c 45 4569
t 51 4583
g 45 4595
g 45 4607
c 45 4618
t 45 4633
g 45 4645
t 45 4656
t 56 4668
t 56 4680
t 56 4692
g 56 4704
g 56 4716
a 56 4727
t 56 4738
t 56 4751
c 56 4762
g 56 4775
g 56 4787
t 51 4798
a 51 4809
t 51 4821
c 51 4831
c 51 4844
a 51 4854
g 51 4866
g 51 4879
a 56 4892
g 51 4903
c 51 4914
a 51 4926
c 51 4936
a 51 4948
t 51 4960
t 56 4973
g 56 4985
a 56 4997
t 56 5008
c 56 5020
t 56 5033
t 56 5045
g 56 5057
g 56 5069
a 56 5080
a 40 5091
t 40 5104
c 40 5115
a 40 5124
a 40 5136
g 40 5149
t 40 5162
a 40 5172
c 40 5182
g 40 5197
a 40 5207
t 40 5220
c 51 5231
c 56 5243
t 56 5256
t 51 5268
c 51 5279
t 51 5292
a 51 5302
c 51 5312
g 51 5325
g 51 5338
g 51 5350
t 51 5362
a 45 5372
t 45 5384
c 45 5395
t 45 5409
a 45 5419
t 45 5431
g 51 5444
g 56 5456
a 56 5468
a 56 5479
t 56 5492
g 40 5503
g 39 5516
a 39 5528
c 39 5537
t 39 5552
t 39 5564
c 39 5575
t 40 5588
a 40 5597
t 40 5609
g 40 5622
t 56 5634
t 56 5646
g 51 5658
t 51 5669
t 51 5682
c 51 5692
t 51 5705
t 51 5718
g 51 5730
a 45 5741
a 40 5752
c 40 5762
g 37 5776
c 37 5785
c 40 5798
c 40 5810
g 56 5823
g 56 5834
g 51 5846
a 51 5859
t 40 5870
a 40 5880
c 40 5890
c 40 5904
g 40 5918
t 51 5929
g 51 5941
t 37 5953
t 37 5966
g 37 5978
c 37 5987
a 37 5999
c 40 6009
g 40 6023
t 34 6035
c 34 6047
g 29 6060
c 29 6068
c 29 6083
g 29 6096
t 32 6107
a 29 6118
g 25 6128
g 19 6142
t 27 6154
g 27 6167
c 32 6176
a 32 6187
a 34 6199
g 40 6212
a 34 6224
c 40 6234
t 34 6248
c 35 6258
g 35 6272
c 35 6281
g 35 6296
t 39 6307
t 40 6320
g 56 6331
g 56 6342
g 56 6355
a 51 6367
t 51 6378
t 46 6391
c 46 6401
a 42 6411
g 42 6424
c 42 6435
a 46 6447
t 40 6459
a 37 6469
g 37 6482
a 40 6494
g 29 6506
t 29 6518
t 29 6531
a 29 6539
c 29 6549
c 27 6563
a 32 6573
a 29 6585
g 29 6596
g 34 6609
a 48 6622
t 48 6633
g 48 6645
a 32 6656
t 34 6668
g 34 6681
c 34 6690
c 31 6704
a 31 6714
t 37 6726
g 46 6739
a 48 6750
a 48 6762
g 40 6774
t 40 6786
g 40 6797
g 27 6810
t 25 6821
t 21 6834
c 16 6842
c 16 6856
a 18 6865
a 19 6877
g 23 6889
t 27 6901
t 25 6915
a 29 6923
a 24 6936
g 29 6947
t 32 6960
a 29 6970
c 29 6980
g 25 6995
a 25 7004
a 21 7018
g 15 7026
g 15 7041
t 23 7053
g 27 7065
t 27 7075
t 27 7089
a 27 7098
t 25 7110
c 22 7120
c 24 7133
t 29 7147
c 32 7157
a 32 7168
a 40 7179
c 29 7189
a 29 7200
a 29 7211
g 48 7224
t 48 7237
c 40 7248
t 40 7261
c 40 7272
a 29 7282
g 29 7294
a 25 7306
a 29 7317
c 29 7327
a 40 7338
t 40 7350
c 32 7362
a 32 7372
c 32 7383
t 32 7397
g 32 7409
g 25 7422
t 25 7432
t 25 7445
g 29 7457
a 40 7467
a 36 7479
g 40 7491
a 36 7503
g 36 7514
t 37 7525
t 33 7537
t 46 7549
g 24 7561
t 24 7571
t 24 7584
t 32 7596
c 32 7606
t 40 7619
t 34 7630
t 22 7642
t 25 7654
c 25 7665
a 27 7674
t 25 7685
t 22 7698
t 29 7709
t 29 7721
g 25 7734
t 21 7744
t 21 7757
t 22 7767
t 29 7779
g 24 7791
t 24 7802
g 24 7814
g 31 7827
t 31 7838
g 28 7850
t 28 7861
t 24 7873
g 19 7884
g 19 7897
c 23 7906
t 27 7921
c 25 7931
t 22 7943
t 29 7954
t 34 7965
t 32 7976
t 32 7988
t 32 8000
a 25 8009
t 18 8020
a 18 8031
a 18 8039
t 18 8053
t 23 8066
t 32 8077
g 26 8089
c 25 8099
g 19 8112
g 15 8124
t 15 8134
t 15 8148
c 23 8157
t 23 8170
g 22 8182
g 34 8193
a 37 8205
t 40 8216
g 32 8227
a 32 8238
t 29 8250
a 22 8259
a 18 8269
g 18 8281
g 13 8294
c 22 8305
t 16 8318
t 20 8328
t 25 8341
g 29 8353
t 24 8364
t 24 8376
g 25 8388
t 19 8398
t 19 8412
g 25 8422
t 24 8433
g 21 8444
g 21 8455
t 27 8467
g 21 8479
g 20 8491
t 26 8502
a 25 8512
g 18 8524
a 15 8536
a 15 8545
t 10 8558
c 13 8566
c 13 8581
t 17 8593
c 21 8603
a 22 8613
a 25 8624
g 29 8635
t 25 8647
a 25 8657
c 25 8666
c 24 8678
c 19 8691
t 10 8703
c 10 8712
g 11 8726
a 17 8736
g 17 8747
a 12 8759
t 19 8768
a 16 8778
t 11 8787
END_DNA

END_SEQUENCE
BioPerl-1.007002/t/data/multi_1.fa000444000766000024       161713155576321 16557 0ustar00cjfieldsstaff000000000000>gi|239758|bbs|68379 glucocorticoid receptor,  GR [human, Peptide Partial, 394 aa]
MDSKESLTPGREENPSSVLAQERGDVMDFYKTLRGGATVKVSASSPSLAVASQSDSKQRRLLVDFPKGSV
>gi|239752|bbs|68871 PML-3=putative zinc finger protein [human, Peptide, 802 aa]
MPPPETPSEGRQPSPSPSPTERAPASEEEFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASGMQCPICQ
>gi|238775|bbs|65126 putative tyrosine kinase receptor=UFO [human, NIH3T3, Peptide, 894 aa]
MAWRCPRMGRVPLAWCLALCGWACMAPRGTQAEESPFVGNPGNITGARGLTGTLRCQLQVQGEPPEVHWL
>gi|239006|bbs|65162 alpha(1,3)-fucosyltransferase, ELFT [human, Peptide, 400 aa]
MGAPWGSPTAAAGGRRGWRRGRGLPWTVCVLAAAGLTCTALITYACWGQLPPLPWASPTPSRPVGVLLWW
>gi|237597|bbs|60089 putative adhesion molecule=ADMLX [human, Peptide, 679 aa]
MVPGVPGAVLTLCLWLAASSGSWRPAPARLCAAAGRVAVCRERPARSCASRCLSLQITRISAFFQHFQNN
>gi|237995|bbs|62046 NK-1 receptor [human, lung, Peptide, 407 aa]
MDNVLPVDSDLSPNISTNTSEPNQFVQPAWEIVLWAAAYTVIVVTSVVGNVVVMWIILAHKRMRTVTNYF


BioPerl-1.007002/t/data/multi_2.fa000444000766000024       161713155576321 16560 0ustar00cjfieldsstaff000000000000>gi|239758|bbs|68379 glucocorticoid receptor,  GR [human, Peptide Partial, 394 aa]
MDSKESLTPGREENPSSVLAQERGDVMDFYKTLRGGATVKVSASSPSLAVASQSDSKQRRLLVDFPKGSV
>gi|239752|bbs|68871 PML-3=putative zinc finger protein [human, Peptide, 802 aa]
MPPPETPSEGRQPSPSPSPTERAPASEEEFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASGMQCPICQ
>gi|238775|bbs|65126 putative tyrosine kinase receptor=UFO [human, NIH3T3, Peptide, 894 aa]
MAWRCPRMGRVPLAWCLALCGWACMAPRGTQAEESPFVGNPGNITGARGLTGTLRCQLQVQGEPPEVHWL
>gi|239006|bbs|65162 alpha(1,3)-fucosyltransferase, ELFT [human, Peptide, 400 aa]
MGAPWGSPTAAAGGRRGWRRGRGLPWTVCVLAAAGLTCTALITYACWGQLPPLPWASPTPSRPVGVLLWW
>gi|237597|bbs|60089 putative adhesion molecule=ADMLX [human, Peptide, 679 aa]
MVPGVPGAVLTLCLWLAASSGSWRPAPARLCAAAGRVAVCRERPARSCASRCLSLQITRISAFFQHFQNN
>gi|237995|bbs|62046 NK-1 receptor [human, lung, Peptide, 407 aa]
MDNVLPVDSDLSPNISTNTSEPNQFVQPAWEIVLWAAAYTVIVVTSVVGNVVVMWIILAHKRMRTVTNYF


BioPerl-1.007002/t/data/multi_blast.bls000444000766000024     32225613155576321 17763 0ustar00cjfieldsstaff000000000000BLASTP 2.1.3 [Apr-11-2001]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= CATH_RAT
         (333 letters)

Database: /data_2/jason/blastdb/wormpep62
           20,085 sequences; 8,813,425 total letters

Searching..................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

T03E6.7 CE16333   cathepsin-like protease (HINXTON) TR:O4573...   196  2e-50
F41E6.6 CE10254   cysteine protease and a protease inhibitor...   166  2e-41
R09F10.1 CE28755   peptidase (ST.LOUIS) TR:Q23030 protein_id...   162  3e-40
R07E3.1 CE02295   cysteine proteinase (HINXTON) TR:Q21810 pr...   126  2e-29
Y40H7A.10 CE21821   Cysteine protease (HINXTON) TR:Q9XWA4 pr...   123  1e-28

>T03E6.7 CE16333   cathepsin-like protease (HINXTON) TR:O45734
           protein_id:CAB07275.1
          Length = 337

 Score =  196 bits (498), Expect = 2e-50
 Identities = 122/318 (38%), Positives = 174/318 (54%), Gaps = 21/318 (6%)

Query: 26  NAIEKFHFTSWMKQHQKTYSSREYSHRLQVFANNWRKIQAHNQRNH-----TFKMGLNQF 80
           +AIEK+    + +   K YS  E    ++ F  N   I+ HN R+H     TF+MGLN  
Sbjct: 27  SAIEKWD--DYKEDFDKEYSESEEQTYMEAFVKNMIHIENHN-RDHRLGRKTFEMGLNHI 83

Query: 81  SDMSFAEIK----HKYLWSEPQNCSATKSNYLRGTG-PYPSSMDWRKKGNVVSPVKNQGA 135
           +D+ F++ +    ++ L+ + +      S++L       P  +DWR   ++V+ VKNQG 
Sbjct: 84  ADLPFSQYRKLNGYRRLFGDSR--IKNSSSFLAPFNVQVPDEVDWRDT-HLVTDVKNQGM 140

Query: 136 CGSCWTFSTTGALESAVAIASGKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNK 195
           CGSCW FS TGALE   A   G++++L+EQ LVDC+  + NHGC GGL  QAFEYI  N 
Sbjct: 141 CGSCWAFSATGALEGQHARKLGQLVSLSEQNLVDCSTKYGNHGCNGGLMDQAFEYIRDNH 200

Query: 196 GIMGEDSYPYIGKNGQCKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEV-T 254
           G+  E+SYPY G++ +C FN +   A  K  V+    DE  +  AVA   P+S A +   
Sbjct: 201 GVDTEESYPYKGRDMKCHFNKKTVGADDKGYVDTPEGDEEQLKIAVATQGPISIAIDAGH 260

Query: 255 EDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYG-EQNGLLYWIVKXXXXXXXXXXXYFLI 313
             F +YK GVY    C  + ++++H VL VGYG +     YWIVK           Y  I
Sbjct: 261 RSFQLYKKGVYYDEEC--SSEELDHGVLLVGYGTDPEHGDYWIVKNSWGAGWGEKGYIRI 318

Query: 314 ERGK-NMCGLAACASYPI 330
            R + N CG+A  ASYP+
Sbjct: 319 ARNRNNHCGVATKASYPL 336


>F41E6.6 CE10254   cysteine protease and a protease inhibitor (ST.LOUIS)
           TR:O16454 protein_id:AAB65956.1
          Length = 498

 Score =  166 bits (419), Expect = 2e-41
 Identities = 108/325 (33%), Positives = 155/325 (47%), Gaps = 35/325 (10%)

Query: 33  FTSWMKQHQKTYSS-REYSHRLQVFANNWRKI-QAHNQRNHTFKMGLNQFSDMSFAEIKH 90
           F  ++ +H+K Y++ RE   R +VF  N + I +       T   G  +FSDM+  E K 
Sbjct: 174 FLDFVDRHEKKYTNKREVLKRFRVFKKNAKVIRELQKNEQGTAVYGFTKFSDMTTMEFKK 233

Query: 91  ---KYLWSEP----QNCSATKSNYLRGTGPYPSSMDWRKKGNVVSPVKNQGACGSCWTFS 143
               Y W +P    +  +  K +        P S DWR+KG  V+ VKNQG CGSCW FS
Sbjct: 234 IMLPYQWEQPVYPMEQANFEKHDVTINEEDLPESFDWREKG-AVTQVKNQGNCGSCWAFS 292

Query: 144 TTGALESAVAIASGKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFE------------YI 191
           TTG +E A  IA  K+++L+EQ+LVDC  +  + GC GGLPS A++             +
Sbjct: 293 TTGNVEGAWFIAKNKLVSLSEQELVDC--DSMDQGCNGGLPSNAYKIGKFVVSDNYCFLV 350

Query: 192 LYNK---------GIMGEDSYPYIGKNGQCKFNPEKAVAFVKNVVNITLNDEAAMVEAVA 242
            Y+K         G+  ED+YPY G+   C    +    ++   V +  +DE  M + + 
Sbjct: 351 FYHKTTKEIIRMGGLEPEDAYPYDGRGETCHLVRKDIAVYINGSVELP-HDEVEMQKWLV 409

Query: 243 LYNPVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYGEQNGLLYWIVKXXXX 302
              P+S           Y+ GV         P  +NH VL VGYG+     YWIVK    
Sbjct: 410 TKGPISIGLN-ANTLQFYRHGVVHPFKIFCEPFMLNHGVLIVGYGKDGRKPYWIVKNSWG 468

Query: 303 XXXXXXXYFLIERGKNMCGLAACAS 327
                  YF + RGKN+CG+   A+
Sbjct: 469 PNWGEAGYFKLYRGKNVCGVQEMAT 493


>R09F10.1 CE28755   peptidase (ST.LOUIS) TR:Q23030 protein_id:AAC69091.2
          Length = 383

 Score =  162 bits (410), Expect = 3e-40
 Identities = 97/304 (31%), Positives = 157/304 (50%), Gaps = 19/304 (6%)

Query: 37  MKQHQKTYSSREYSHRLQVFANNWRKIQAHNQRNHTFKMGLNQFSDMSFAEIKH------ 90
           +K  +K  S  E+ +R Q+F  N  + +A  +RN    + +N+F+D +  E++       
Sbjct: 87  LKFDRKYTSVEEFEYRYQIFLRNVIEFEAEEERNLGLDLDVNEFTDWTDEELQKMVQENK 146

Query: 91  --KYLWSEPQNCSATKSNYLRGTGPYPSSMDWRKKGNVVSPVKNQGACGSCWTFSTTGAL 148
             KY +  P+     + +YL      P+S+DWR++G + +P+KNQG CGSCW F+T  ++
Sbjct: 147 YTKYDFDTPK----FEGSYLETGVIRPASIDWREQGKL-TPIKNQGQCGSCWAFATVASV 201

Query: 149 ESAVAIASGKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIG- 207
           E+  AI  GK+++L+EQ++VDC  +  N+GC GG    A +++  N G+  E  YPY   
Sbjct: 202 EAQNAIKKGKLVSLSEQEMVDC--DGRNNGCSGGYRPYAMKFVKEN-GLESEKEYPYSAL 258

Query: 208 KNGQCKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEVTEDFMMYKSGVYSS 267
           K+ QC         F+ +   +  N+E  +   V    PV+F   V +    Y+SG+++ 
Sbjct: 259 KHDQCFLKENDTRVFIDD-FRMLSNNEEDIANWVGTKGPVTFGMNVVKAMYSYRSGIFNP 317

Query: 268 NSCHKTPDKVN-HAVLAVGYGEQNGLLYWIVKXXXXXXXXXXXYFLIERGKNMCGLAACA 326
           +    T   +  HA+  +GYG +    YWIVK           YF + RG N CGLA   
Sbjct: 318 SVEDCTEKSMGAHALTIIGYGGEGESAYWIVKNSWGTSWGASGYFRLARGVNSCGLANTV 377

Query: 327 SYPI 330
             PI
Sbjct: 378 VAPI 381


>R07E3.1 CE02295   cysteine proteinase (HINXTON) TR:Q21810
           protein_id:CAA89070.1
          Length = 402

 Score =  126 bits (316), Expect = 2e-29
 Identities = 97/325 (29%), Positives = 152/325 (45%), Gaps = 31/325 (9%)

Query: 20  TAELTVNAIEKFHFTSWMKQHQKTYS-SREYSHRLQVFANNWRKIQAHNQRNH--TFKMG 76
           T E  +  I K  + ++ ++  K+Y+ S+E   RL  + N    I   N +N   + + G
Sbjct: 78  TNERGIQNIAK-EYIAYTEKFDKSYATSQESLKRLNAYYNTDENIANWNIQNEHGSAEYG 136

Query: 77  LNQFSDMSFAEIK--------HKYLWSE-------PQNCSATKSNYLRGTGPYPSSMDWR 121
            N  SD +  E +        +K L  E       P++ +A K      + P+P   DWR
Sbjct: 137 HNDMSDWTDEEFEKTLLPKSFYKRLHKEAEFIEPIPESLTAKKGE---SSSPFPDFFDWR 193

Query: 122 KKGNVVSPVKNQGACGSCWTFSTTGALESAVAIASGKMMTLAEQQLVDCAQNFNNHGCQG 181
            K NV++PVK QG CGSCW F++T  +E+A AIA G+   L+EQ L+DC  +  ++ C G
Sbjct: 194 DK-NVITPVKAQGQCGSCWAFASTATVEAAWAIAHGEKRNLSEQTLLDC--DLVDNACDG 250

Query: 182 GLPSQAFEYILYNKGIMGEDSYPYIG-KNGQCKFNPEKAVAFVKNVVNITLNDEAAMVEA 240
           G   +AF YI +  G+      PY+  +   C  N       +K       +DE +++  
Sbjct: 251 GDEDKAFRYI-HRNGLANAVDLPYVAHRQNGCAVNDHWNTTRIK-AAYFLHHDEDSIINW 308

Query: 241 VALYNPVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVN-HAVLAVGYG-EQNGLLYWIVK 298
           +  + PV+    V +    YK GV++ +      + +  HA+L  GYG  + G  YWIVK
Sbjct: 309 LVNFGPVNIGMAVIQPMRAYKGGVFTPSEYACKNEVIGLHALLITGYGTSKTGEKYWIVK 368

Query: 299 XX-XXXXXXXXXYFLIERGKNMCGL 322
                       Y    RG N CG+
Sbjct: 369 NSWGNTWGVEHGYIYFARGINACGI 393


>Y40H7A.10 CE21821   Cysteine protease (HINXTON) TR:Q9XWA4
           protein_id:CAA22062.1
          Length = 343

 Score =  123 bits (309), Expect = 1e-28
 Identities = 92/304 (30%), Positives = 145/304 (47%), Gaps = 26/304 (8%)

Query: 26  NAIEKFHFTSWMKQHQKTYSSREYSHRLQVFANNWRKIQAHNQRNH---TFKMGLNQFSD 82
           NA + F    +++++   Y   E   R  +F+ N   ++ +N+ +    T++  LN FSD
Sbjct: 49  NAFQNF-LVKYLREYPNEY---EIVKRFTIFSRNLDLVERYNKEDAGKVTYE--LNDFSD 102

Query: 83  MSFAEIKHKYLWSEPQNCSAT-KSNYLRGTGPYPSSMDWRKKG--NVVSPVKNQGACGSC 139
           ++  E K   +  +P +   + K   L      P+S+DWR     N V+ +K QG CGSC
Sbjct: 103 LTEEEWKKYLMTPKPDHSEKSLKPKTLIDKKNLPNSVDWRNVNGTNHVTGIKYQGPCGSC 162

Query: 140 WTFSTTGALESAVAIASGKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKGIMG 199
           W F+T  A+ESAV+I+ G + +L+ QQL+DC     +  C GG P +A +Y   + GI  
Sbjct: 163 WAFATAAAIESAVSISGGGLQSLSSQQLLDC--TVVSDKCGGGEPVEALKY-AQSHGITT 219

Query: 200 EDSYPYIGKNGQCKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNP-VSFAFEVTEDFM 258
             +YPY     +C+      VA + + +     DE  M + VAL  P +  A   T    
Sbjct: 220 AHNYPYYFWTTKCR-ETVPTVARISSWMKAESEDE--MAQIVALNGPMIVCANFATNKNR 276

Query: 259 MYKSGVYSSNSCHKTPDKVNHAVLAVGYGEQNGLLYWIVKXXXXXXXXXXXYFLIERGKN 318
            Y SG+     C   P    HA++ +GYG      YWI+K           Y  ++R  N
Sbjct: 277 FYHSGIAEDPDCGTEP---THALIVIGYGPD----YWILKNTYSKVWGEKGYMRVKRDVN 329

Query: 319 MCGL 322
            CG+
Sbjct: 330 WCGI 333


>Y113G7B.15 CE23295    (HINXTON) TR:Q9U2X1 protein_id:CAB54334.1
          Length = 328

 Score =  120 bits (302), Expect = 9e-28
 Identities = 94/317 (29%), Positives = 140/317 (43%), Gaps = 40/317 (12%)

Query: 40  HQKTYSS-REYSHRLQVFANNWRKIQAHNQ------RNHTFKMGLNQFSDMSFAEIKHKY 92
           H+K Y +  E   RL  FA N +KIQ  N       RN TF  G N+F+D +  E+  + 
Sbjct: 3   HKKHYRTPAEKDRRLAHFAKNHQKIQELNAKARREGRNVTF--GWNKFADKNRQELSARN 60

Query: 93  LWSEPQNCSAT---KSNYLRGTGPYPSSMDWRKKGN----------------VVSPVKNQ 133
               P+N +     K  + RG+  + +    R+ G+                VV PVK+Q
Sbjct: 61  SKIHPKNHTDLPIYKPRHPRGSRNHHNKRSKRQSGDIPDYFDLRDIYVDGSPVVGPVKDQ 120

Query: 134 GACGSCWTFSTTGALESAVAIASGKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILY 193
             CG CW F+TT   E+A  + S    +L++Q++ DCA + +  GC GG P    + +++
Sbjct: 121 EQCGCCWAFATTAITEAANTLYSKSFTSLSDQEICDCADSGDTPGCVGGDPRNGLK-MVH 179

Query: 194 NKGIMGEDSYPY----IGKNGQCKFNPEKAVAFVKNVVNITLND-----EAAMVEAVALY 244
            +G   +  YPY        G C    EK+       +N+   D     E  M      +
Sbjct: 180 LRGQSSDGDYPYEEYRANTTGNC-VGDEKSTVIQPETLNVYRFDQDYAEEDIMENLYLNH 238

Query: 245 NPVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYG-EQNGLLYWIVKXXXXX 303
            P +  F V E+F  Y SGV  S  C++      H+V  VGYG   +G+ YW+V+     
Sbjct: 239 IPTAVYFRVGENFEWYTSGVLQSEDCYQMTPAEWHSVAIVGYGTSDDGVPYWLVRNSWNS 298

Query: 304 XXXXXXYFLIERGKNMC 320
                 Y  I RG N C
Sbjct: 299 DWGLHGYVKIRRGVNWC 315


>K02E7.10 CE11640   protease (ST.LOUIS) TR:O17255 protein_id:AAB71030.1
          Length = 299

 Score =  114 bits (284), Expect = 1e-25
 Identities = 70/216 (32%), Positives = 107/216 (49%), Gaps = 8/216 (3%)

Query: 118 MDWRKKGNVVSPVKNQGACGSCWTFSTTGALESAVAIAS-GKMMTLAEQQLVDCAQNFNN 176
           +DWR+KG +V PVK+QG C + + F+   A+ES  A A+ GK+++ +EQQ++DCA NF N
Sbjct: 84  LDWREKG-IVGPVKDQGKCNASYAFAAIAAIESMYAKANNGKLLSFSEQQIIDCA-NFTN 141

Query: 177 HGCQGGLPSQAFEYILYNKGIMGEDSYPYIGKN--GQCKFNPEKAVAFVKNVVNITLNDE 234
             CQ  L +      L   G+  E  YPY+GK   G+C+++  K +      +++  N+E
Sbjct: 142 P-CQENLENVLSNRFLKENGVGTEADYPYVGKENVGKCEYDSSK-MKLRPTYIDVYPNEE 199

Query: 235 AAMVEAVALYNPVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYGEQNGLLY 294
            A    +  +    F       F  YK+G+Y+             ++  VGYG+     Y
Sbjct: 200 WARAH-ITTFGTGYFRMRSPPSFFHYKTGIYNPTKEECGNANEARSLAIVGYGKDGAEKY 258

Query: 295 WIVKXXXXXXXXXXXYFLIERGKNMCGLAACASYPI 330
           WIVK           Y  + R  N CG+A   S PI
Sbjct: 259 WIVKGSFGTSWGEHGYMKLARNVNACGMAESISIPI 294


>C32B5.7 CE08515   cathepsin-like peptidase (ST.LOUIS) TR:P91111
           protein_id:AAB37963.1
          Length = 250

 Score =  108 bits (270), Expect = 5e-24
 Identities = 69/197 (35%), Positives = 104/197 (52%), Gaps = 18/197 (9%)

Query: 106 NYLRGTGPYPSSMDWRKKGNVVSPVKNQGACGSCWTFSTTGALESAVAIASGKMMTLAEQ 165
           NY     P+   +DWR +G VV PVK+QG C + + F+   A+ES  AIA+G++++ +EQ
Sbjct: 63  NYKNAKKPF---LDWRDEG-VVGPVKDQGNCNASYAFAAISAIESMYAIANGQLLSFSEQ 118

Query: 166 QLVDCAQNFNNHGCQ-GGLPSQAFEYILYNKGIMGEDSYPYIG-KNGQCKFNPEKAVAFV 223
           Q++DC       GC     P  A  Y L  KGI     YP++G KN +C+++ +KA   +
Sbjct: 119 QIIDCL-----GGCAIESDPMMAMTY-LERKGIETYTDYPFVGKKNEKCEYDSKKAYLIL 172

Query: 224 KNVVNITLNDEAAMVEAVALYNPVSFAFEVTEDFMMYKSGVY--SSNSCHKTPDKVNHAV 281
            +  +  ++DE+  +  +    P  F       F  YKSG+Y  +   C  T +K   A+
Sbjct: 173 DDTYD--MSDESLALVFIDERGPGLFTMNTPPSFFNYKSGIYNPTEEECKSTNEK--RAL 228

Query: 282 LAVGYGEQNGLLYWIVK 298
             VGYG   G  YWIVK
Sbjct: 229 TIVGYGNDKGQNYWIVK 245


>Y51A2D.8 CE19204   Cysteine proteases (2 domains) (HINXTON) TR:Q9XXQ7
           protein_id:CAA16407.1
          Length = 386

 Score =  106 bits (265), Expect = 2e-23
 Identities = 82/330 (24%), Positives = 137/330 (40%), Gaps = 44/330 (13%)

Query: 33  FTSWMKQHQKTYSSR-EYSHRLQVFANNWRKIQAHNQRN----HTFKMGLNQFSDMSFAE 87
           F  + K++ + Y    E   R   F  ++  +   N ++    +  + G+N+FSD+S AE
Sbjct: 43  FEDFKKKYNRKYKDESENQQRFNNFVKSYNNVDKLNAKSKAAGYDTQFGINKFSDLSTAE 102

Query: 88  IKHKYLWSEPQN------------------CSATKSNYLRGTGPYPSSMDWRKKG----N 125
              +     P N                      K+ + R +  YP   D R +      
Sbjct: 103 FHGRLSNVVPSNNTGLPMLNFDKKKPDFRAADMNKTRHKRRSTRYPDYFDLRNEKINGRY 162

Query: 126 VVSPVKNQGACGSCWTFSTTGALESAVAIASGKMMTLAEQQLVDCAQNFNNHGCQGGLPS 185
           +V P+K+QG C  CW F+ T  +E+  A  SGK  +L++Q++ DC       GC+GG  +
Sbjct: 163 IVGPIKDQGQCACCWGFAVTALVETVYAAHSGKFKSLSDQEVCDCGTE-GTPGCKGGSLT 221

Query: 186 QAFEYILYNKGIMGEDSYPY----IGKNGQCKFNPEKAV----AFVKNVVNITLNDEAAM 237
              +Y+    G+ G++ YPY      +  +C+      +    AF   V+N    +E  +
Sbjct: 222 LGVQYV-KKYGLSGDEDYPYDQNRANQGRRCRLRETDRIVPARAFNFAVINPRRAEEQII 280

Query: 238 VEAVALYNPVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYG---EQNGLL- 293
                   PV+  F+V + F  YK GV   + C +      HA   VGY    +  G   
Sbjct: 281 QVLTEWKVPVAVYFKVGDQFKEYKEGVIIEDDCRRATQW--HAGAIVGYDTVEDSRGRSH 338

Query: 294 -YWIVKXXXXXXXXXXXYFLIERGKNMCGL 322
            YWI+K           Y  + RG++ C +
Sbjct: 339 DYWIIKNSWGGDWAESGYVRVVRGRDWCSI 368


>Y71H2AR.2 CE22930    (ST.LOUIS) protein_id:AAK29985.1
          Length = 345

 Score =  103 bits (257), Expect = 1e-22
 Identities = 72/235 (30%), Positives = 105/235 (44%), Gaps = 16/235 (6%)

Query: 91  KYLWSEPQNCSATKSNYLRGTGPYPSSMDWRKKGNVVSPVKNQGACGSCWTFSTTGALES 150
           ++ W  P +   T   +L          DWR+KG +V PVK+QG C +   F+ T ++ES
Sbjct: 69  RFQWETPIHMDRTTEEFL----------DWREKG-IVGPVKDQGKCNASHAFAITSSIES 117

Query: 151 AVAIAS-GKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIGK- 208
             A A+ G +++ +EQQL+DC       GC+      A  Y L   GI  E  YPY+ K 
Sbjct: 118 MYAKATNGTLLSFSEQQLIDCNDQ-GYKGCEEQFAMNAIGY-LATHGIETEADYPYVDKT 175

Query: 209 NGQCKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEVTEDFMMYKSGVYSSN 268
           N +C F+  K+   +K  V    N+    V  V  Y P  F          YK G+Y+ +
Sbjct: 176 NEKCTFDSTKSKIHLKKGVVAEGNEVLGKVY-VTNYGPAFFTMRAPPSLYDYKIGIYNPS 234

Query: 269 SCHKTPDKVNHAVLAVGYGEQNGLLYWIVKXXXXXXXXXXXYFLIERGKNMCGLA 323
               T      +++ VGYG +    YWIVK           Y  + R  N C +A
Sbjct: 235 IEECTSTHEIRSMVIVGYGIEGEQKYWIVKGSFGTSWGEQGYMKLARDVNACAMA 289


>C50F4.3 CE05468   thiol protease (HINXTON) TR:Q18740 protein_id:CAA94738.1
          Length = 374

 Score =  102 bits (254), Expect = 3e-22
 Identities = 86/319 (26%), Positives = 129/319 (39%), Gaps = 31/319 (9%)

Query: 33  FTSWMKQHQKTYSSR-EYSHRLQVFANNWRKI----QAHNQRNHTFKMGLNQFSDMSFAE 87
           F  ++ ++++ Y    E   R Q F     ++    +A  +  H  K G+N+FSD+S  E
Sbjct: 47  FEDFIVKYKRNYKDEIEKKFRFQQFVATHNRVGKMNKAAKKAGHDTKYGINKFSDLSKKE 106

Query: 88  IKHKYLWSEP--QNCSATKSNYL-----RGTGPYPSSMDWRKKG----NVVSPVKNQGAC 136
           I   Y    P   N +  K N       R     P + D R K      ++ P+K Q +C
Sbjct: 107 IHGMYSKFGPPKNNTNVPKFNLKNLRVKRQMEGLPKTFDLRNKKVGGHYIIGPIKTQDSC 166

Query: 137 GSCWTFSTTGALESAVAIASGKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKG 196
             CW F+ T   E+A+ +   K M L+EQ++ DCA   +  GC GG P    EYI    G
Sbjct: 167 ACCWGFAATAVAEAALTVHLKKAMNLSEQEVCDCAPK-HGPGCNGGDPVDGLEYI-KEMG 224

Query: 197 IMGEDSYPY-------IGKNGQCKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYN-PVS 248
           + G   YP+       +G+    K++ E     +        N E  M   + L N P+S
Sbjct: 225 LTGGKEYPFNVNRSTQLGRCESEKYDRELNPLELDYYAIDPFNAEYQMTHHLYLLNLPIS 284

Query: 249 FAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYGEQNG-----LLYWIVKXXXXX 303
            AF        Y SG+     C        H+   VGYG         + YWI +     
Sbjct: 285 VAFRTGASLSSYLSGILELADCDDEKGGHWHSGAIVGYGTTKNSAGRTVDYWIFRNSWWT 344

Query: 304 XXXXXXYFLIERGKNMCGL 322
                 Y  I RG++ C +
Sbjct: 345 DWGDDGYARIVRGEDWCSI 363


>F26E4.3 CE17714   cysteine protease (HINXTON) TR:P90850
           protein_id:CAB03007.1
          Length = 491

 Score = 87.4 bits (215), Expect = 1e-17
 Identities = 70/237 (29%), Positives = 102/237 (42%), Gaps = 33/237 (13%)

Query: 115 PSSMDWRKK-GNVVSPVKNQGACGSCWTFSTTGALESAVAIAS-GKM-MTLAEQQLVDCA 171
           P   D R K G ++ PV +QG CGS W+ STT      +AI S G++  TL+ QQL+ C 
Sbjct: 224 PEHFDARDKWGPLIHPVADQGDCGSSWSVSTTAISSDRLAIISEGRINSTLSSQQLLSCN 283

Query: 172 QNFNNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIGKNG-------------------QC 212
           Q+    GC+GG   +A+ YI    G++G+  YPY+                       +C
Sbjct: 284 QH-RQKGCEGGYLDRAWWYI-RKLGVVGDHCYPYVSGQSREPGHCLIPKRDYTNRQGLRC 341

Query: 213 KFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEVTEDFMMYKSGVY--SSNSC 270
               + + AF         + E  +   +    PV   F V EDF MY  GVY  S  + 
Sbjct: 342 PSGSQDSTAFKMTPPYKVSSREEDIQTELMTNGPVQATFVVHEDFFMYAGGVYQHSDLAA 401

Query: 271 HKTPDKV---NHAVLAVGYGEQNG----LLYWIVKXXXXXXXXXXXYFLIERGKNMC 320
            K    V    H+V  +G+G  +     + YW+             YF + RG+N C
Sbjct: 402 QKGASSVAEGYHSVRVLGWGVDHSTGKPIKYWLCANSWGTQWGEDGYFKVLRGENHC 458


>C52E4.1 CE08943  locus:cpr-1 cathepsin-like cysteine protease (HINXTON)
           TR:Q18783 protein_id:CAB01410.1
          Length = 340

 Score = 85.1 bits (209), Expect = 5e-17
 Identities = 67/269 (24%), Positives = 111/269 (40%), Gaps = 33/269 (12%)

Query: 82  DMSFAEIKHKYLWSEPQNCSATKSNYLRGTGP--YPSSMDWRKKGNVVSPVKNQGACGSC 139
           +M F  +  KY  +      AT+   +  + P  + S   W +  ++   +++Q  CGSC
Sbjct: 66  EMKFKLMDGKYAAAHSDEIRATEQEVVLASVPATFDSRTQWSECKSI-KLIRDQATCGSC 124

Query: 140 WTFSTTGALESAVAIAS--GKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKGI 197
           W F     +     I +   +   ++   L+ C  +   +GC+GG P QA  +   +KG+
Sbjct: 125 WAFGAAEMISDRTCIETKGAQQPIISPDDLLSCCGSSCGNGCEGGYPIQALRW-WDSKGV 183

Query: 198 MGEDSYPYIG-----------------KNGQCKFNPEK--AVAFVKN----VVNITLNDE 234
           +    Y   G                 K   C  + +   + A+ K+    V    +   
Sbjct: 184 VTGGDYHGAGCKPYPIAPCTSGNCPESKTPSCSMSCQSGYSTAYAKDKHFGVSAYAVPKN 243

Query: 235 AAMVEAVALYN-PVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYGEQNGLL 293
           AA ++A    N PV  AF V EDF  YKSGVY   +         HA+  +G+G ++G  
Sbjct: 244 AASIQAEIYANGPVEAAFSVYEDFYKYKSGVYKHTAGKYLG---GHAIKIIGWGTESGSP 300

Query: 294 YWIVKXXXXXXXXXXXYFLIERGKNMCGL 322
           YW+V            +F I RG + CG+
Sbjct: 301 YWLVANSWGVNWGESGFFKIYRGDDQCGI 329


>M04G12.2 CE12424   cysteine protease (HINXTON) TR:P92005
           protein_id:CAB03209.1
          Length = 467

 Score = 75.1 bits (183), Expect = 6e-14
 Identities = 68/224 (30%), Positives = 100/224 (44%), Gaps = 44/224 (19%)

Query: 101 SATKSNYLRGTGPYPSSMDWRKKG--NVVSPVKNQGA---CGSCWTFSTTGALESAVAIA 155
           S+ KSN L      P+  DWR     N  SP +NQ     CGSCW F TTGAL     +A
Sbjct: 214 SSFKSNDL------PTGWDWRNVSGVNYCSPTRNQHIPVYCGSCWVFGTTGALNDRFNVA 267

Query: 156 -SGK--MMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIGKNGQC 212
             G+  M  L+ Q+++DC    N   CQGG      E+    +G++ E    Y   NG+C
Sbjct: 268 RKGRWPMTQLSPQEIIDCNGKGN---CQGGEIGNVLEHAKI-QGLVEEGCNVYRATNGEC 323

Query: 213 KFNPEKAVA----------------FVKNVVNITLNDEAAMVEAVALYNPVSFAFEVTED 256
             NP                     +VK+   +   D+  ++  +    P++ A   T+ 
Sbjct: 324 --NPYHRCGSCWPNECFSLTNYTRYYVKDYGQVQGRDK--IMSEIKKGGPIACAIGATKK 379

Query: 257 F-MMYKSGVYSSNSCHKTPDKVNHAVLAVGYG-EQNGLLYWIVK 298
           F   Y  GVYS     K+  + NH +   G+G ++NG+ YWI +
Sbjct: 380 FEYEYVKGVYS----EKSDLESNHIISLTGWGVDENGVEYWIAR 419


>F15D4.4 CE28917   cysteine protease (HINXTON) TR:Q93512
           protein_id:CAB02487.1
          Length = 622

 Score = 75.1 bits (183), Expect = 6e-14
 Identities = 85/332 (25%), Positives = 130/332 (38%), Gaps = 51/332 (15%)

Query: 25  VNAIEKFH--------FTSWMKQHQKTYSSREYSHRLQVFANNWRKIQAHNQRNH----T 72
           ++ +EKF+        F S M       +++E   R  V++   +++  HN        +
Sbjct: 119 LSPLEKFNEAMNNDGAFKSLMDVINFNSTAKEGLKRFNVYSKVKKEVDEHNIMYELGMSS 178

Query: 73  FKMGLNQFSDMSFAEIKHKYLWSEPQNCSAT------KSNYLRGTGPYPSSMDWRKKGNV 126
           +KM  NQFS     E+    L  +    +AT       S   R T P   ++DWR     
Sbjct: 179 YKMSTNQFSVALDGEVAPLTLNLDALTPTATVIPATISSRKKRDTEP---TVDWRP---F 232

Query: 127 VSPVKNQGACGSCWTFSTTGALESAVAIASGKMMTLAEQQL------VDCAQNFNNHGCQ 180
           + P+ +Q  CG CW FS    +ES  AI      +L+ QQL      VD      N GC+
Sbjct: 233 LKPILDQSTCGGCWAFSMISMIESFFAIQGYNTSSLSVQQLLTCDTKVDSTYGLANVGCK 292

Query: 181 GGLPSQAFEYILYNKGIMGEDSYPYIGKNGQCK---FNPEKAVAFVKNVVNITLNDEAAM 237
           GG    A  Y L           P+  ++  C    F P      + +   I+ N  AA 
Sbjct: 293 GGYFQIAGSY-LEVSAARDASLIPFDLEDTSCDSSFFPPVVPTILLFDDGYISGNFTAAQ 351

Query: 238 -------VEAVALYNPVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYGEQN 290
                  +E      P++       D   Y  GVY  + C      +NHAV+ VG+ +  
Sbjct: 352 LITMEQNIEDKVRKGPIAVGMAAGPDIYKYSEGVYDGD-CGTI---INHAVVIVGFTDD- 406

Query: 291 GLLYWIVKXXXXXXXXXXXYFLIER--GKNMC 320
              YWI++           YF ++R  GK+ C
Sbjct: 407 ---YWIIRNSWGASWGEAGYFRVKRTPGKDPC 435


>Y71H2AM.3 CE26272    (ST.LOUIS) protein_id:AAK29976.1
          Length = 716

 Score = 73.9 bits (180), Expect = 1e-13
 Identities = 52/176 (29%), Positives = 77/176 (43%), Gaps = 32/176 (18%)

Query: 92  YLWSEPQNCSATKSNYLRGTGPYPSSMDWRKKGNVVSPVKNQGACGSCWTFSTTGALESA 151
           + W  P+    T   +L          DWR KG +V PVK+QG C +   F+ + ++ES 
Sbjct: 70  FQWKTPKYTIQTTEEFL----------DWRDKG-IVGPVKDQGKCNASHAFAISSSIESM 118

Query: 152 VAIA-SGKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIGKNG 210
            A A +G +++ +EQQL+DC  +    GC+      A  Y +++ GI  E  YPY GK  
Sbjct: 119 YAKATNGSLLSFSEQQLIDC-DDHGFKGCEEQPAINAVSYFIFH-GIETEADYPYAGKE- 175

Query: 211 QCKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEVTEDFMMYKSGVYS 266
                            N  L++E    E V  Y P  F          YK G+Y+
Sbjct: 176 -----------------NGKLSNETQGKELVTNYGPAFFTMRAPPSLYDYKIGIYN 214


>C32B5.13 CE08521    (ST.LOUIS) TR:P91110 protein_id:AAB37968.1
          Length = 150

 Score = 71.6 bits (174), Expect = 6e-13
 Identities = 45/143 (31%), Positives = 73/143 (50%), Gaps = 10/143 (6%)

Query: 159 MMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIGK-NGQCKFNPE 217
           +++ +EQQ++DC  NF +  CQ  + S  F   +   G++ E  YPY+GK N +CK++  
Sbjct: 10  VLSFSEQQIIDCG-NFTSP-CQENILSHEF---IKKNGVVTEADYPYVGKENEKCKYDEN 64

Query: 218 KAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEVTEDFMMYKSGVYS--SNSCHKTPD 275
           K   +  N++ +    E  +   +  + P  F  +    F  YK+G+YS     C K  D
Sbjct: 65  KIKLWPTNMLLVGNLPETLLKLFIKEHGPGYFRMKAPPSFFNYKTGIYSPTQEECGKATD 124

Query: 276 KVNHAVLAVGYGEQNGLLYWIVK 298
               ++  VGYG + G  YWIVK
Sbjct: 125 A--RSLTIVGYGIEGGQNYWIVK 145


  Database: /data_2/jason/blastdb/wormpep62
    Posted date:  Sep 3, 2001  2:17 PM
  Number of letters in database: 8,813,425
  Number of sequences in database:  20,085
  
Lambda     K      H
   0.319    0.131    0.412 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5933049
Number of Sequences: 20085
Number of extensions: 243404
Number of successful extensions: 614
Number of sequences better than 1.0e-10: 17
Number of HSP's better than  0.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 568
Number of HSP's gapped (non-prelim): 17
length of query: 333
length of database: 8,813,425
effective HSP length: 46
effective length of query: 287
effective length of database: 7,889,515
effective search space: 2264290805
effective search space used: 2264290805
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 155 (64.3 bits)
BLASTP 2.1.3 [Apr-11-2001]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= CATL_HUMAN
         (333 letters)

Database: /data_2/jason/blastdb/wormpep62
           20,085 sequences; 8,813,425 total letters

Searching..................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

T03E6.7 CE16333   cathepsin-like protease (HINXTON) TR:O4573...   334  4e-92
F41E6.6 CE10254   cysteine protease and a protease inhibitor...   194  6e-50
R09F10.1 CE28755   peptidase (ST.LOUIS) TR:Q23030 protein_id...   176  2e-44
Y40H7A.10 CE21821   Cysteine protease (HINXTON) TR:Q9XWA4 pr...   133  1e-31
R07E3.1 CE02295   cysteine proteinase (HINXTON) TR:Q21810 pr...   130  1e-30

>T03E6.7 CE16333   cathepsin-like protease (HINXTON) TR:O45734
           protein_id:CAB07275.1
          Length = 337

 Score =  334 bits (857), Expect = 4e-92
 Identities = 164/341 (48%), Positives = 228/341 (66%), Gaps = 12/341 (3%)

Query: 1   MNPTLILAAFCLGIASATLTFDHSLEA---QWTKWKAMHNRLYGMNEEGWRRAVWEKNMK 57
           MN  ++LA     +A  +      +E+   +W  +K   ++ Y  +EE      + KNM 
Sbjct: 1   MNRFILLALVAAVVAVNSAKLSRQIESAIEKWDDYKEDFDKEYSESEEQTYMEAFVKNMI 60

Query: 58  MIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQ----NRKPRKGKVFQEPLFYE 113
            IE HN+++R G+ +F M +N   D+   ++R+ +NG++    + + +    F  P   +
Sbjct: 61  HIENHNRDHRLGRKTFEMGLNHIADLPFSQYRK-LNGYRRLFGDSRIKNSSSFLAPFNVQ 119

Query: 114 APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQ 173
            P  VDWR+   VT VKNQG CGSCWAFSATGALEGQ  RK G+L+SLSEQNLVDCS   
Sbjct: 120 VPDEVDWRDTHLVTDVKNQGMCGSCWAFSATGALEGQHARKLGQLVSLSEQNLVDCSTKY 179

Query: 174 GNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPK-QE 232
           GN GCNGGLMD AF+Y++DN G+D+EESYPY+  +  C +N K   A+D G+VD P+  E
Sbjct: 180 GNHGCNGGLMDQAFEYIRDNHGVDTEESYPYKGRDMKCHFNKKTVGADDKGYVDTPEGDE 239

Query: 233 KALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDN 292
           + L  AVAT GPIS+AIDAGH SF  YK+G+Y++ +CSSE++DHGVL+VGYG   T+ ++
Sbjct: 240 EQLKIAVATQGPISIAIDAGHRSFQLYKKGVYYDEECSSEELDHGVLLVGYG---TDPEH 296

Query: 293 NKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV 333
             YW+VKNSWG  WG  GY+++A++R NHCG+A+ ASYP V
Sbjct: 297 GDYWIVKNSWGAGWGEKGYIRIARNRNNHCGVATKASYPLV 337


>F41E6.6 CE10254   cysteine protease and a protease inhibitor (ST.LOUIS)
           TR:O16454 protein_id:AAB65956.1
          Length = 498

 Score =  194 bits (493), Expect = 6e-50
 Identities = 124/330 (37%), Positives = 171/330 (51%), Gaps = 53/330 (16%)

Query: 36  HNRLYGMNEEGWRR-AVWEKNMKMI-ELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMN 93
           H + Y    E  +R  V++KN K+I EL   E     + FT     F DMT+ EF+++M 
Sbjct: 181 HEKKYTNKREVLKRFRVFKKNAKVIRELQKNEQGTAVYGFTK----FSDMTTMEFKKIML 236

Query: 94  GFQNRKP-----------RKGKVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSCWAFS 142
            +Q  +P               + +E L    P S DWREKG VT VKNQG CGSCWAFS
Sbjct: 237 PYQWEQPVYPMEQANFEKHDVTINEEDL----PESFDWREKGAVTQVKNQGNCGSCWAFS 292

Query: 143 ATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQ----YVQDN----- 193
            TG +EG  F    +L+SLSEQ LVDC     ++GCNGGL   A++     V DN     
Sbjct: 293 TTGNVEGAWFIAKNKLVSLSEQELVDCDSM--DQGCNGGLPSNAYKIGKFVVSDNYCFLV 350

Query: 194 ------------GGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVAT 241
                       GGL+ E++YPY+   E+C    K       G V++P  E  + K + T
Sbjct: 351 FYHKTTKEIIRMGGLEPEDAYPYDGRGETCHLVRKDIAVYINGSVELPHDEVEMQKWLVT 410

Query: 242 VGPISVAIDAGHESFLFYKEGIY--FEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVK 299
            GPIS+ ++A   +  FY+ G+   F+  C    ++HGVL+VGYG    +     YW+VK
Sbjct: 411 KGPISIGLNA--NTLQFYRHGVVHPFKIFCEPFMLNHGVLIVGYG----KDGRKPYWIVK 464

Query: 300 NSWGEEWGMGGYVKMAKDRRNHCGIASAAS 329
           NSWG  WG  GY K+ +  +N CG+   A+
Sbjct: 465 NSWGPNWGEAGYFKLYRG-KNVCGVQEMAT 493


>R09F10.1 CE28755   peptidase (ST.LOUIS) TR:Q23030 protein_id:AAC69091.2
          Length = 383

 Score =  176 bits (446), Expect = 2e-44
 Identities = 113/309 (36%), Positives = 171/309 (54%), Gaps = 39/309 (12%)

Query: 42  MNEEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQNRKPR 101
           + E  +R  ++ +N+  IE   +E R       + +N F D T EE ++++   Q  K  
Sbjct: 96  VEEFEYRYQIFLRNV--IEFEAEEERN--LGLDLDVNEFTDWTDEELQKMV---QENKYT 148

Query: 102 KGKVFQEPLFYEA--------PRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFR 153
           K   F  P F  +        P S+DWRE+G +TP+KNQGQCGSCWAF+   ++E Q   
Sbjct: 149 KYD-FDTPKFEGSYLETGVIRPASIDWREQGKLTPIKNQGQCGSCWAFATVASVEAQNAI 207

Query: 154 KTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKY 213
           K G+L+SLSEQ +VDC G   N GC+GG   YA ++V++N GL+SE+ YPY A     K+
Sbjct: 208 KKGKLVSLSEQEMVDCDG--RNNGCSGGYRPYAMKFVKEN-GLESEKEYPYSA----LKH 260

Query: 214 NPKYSVANDTG-FVD----IPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEP- 267
           +  +   NDT  F+D    +   E+ +   V T GP++  ++   ++   Y+ GI F P 
Sbjct: 261 DQCFLKENDTRVFIDDFRMLSNNEEDIANWVGTKGPVTFGMNV-VKAMYSYRSGI-FNPS 318

Query: 268 --DCSSEDMD-HGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGI 324
             DC+ + M  H + ++GYG E      + YW+VKNSWG  WG  GY ++A+   N CG+
Sbjct: 319 VEDCTEKSMGAHALTIIGYGGEG----ESAYWIVKNSWGTSWGASGYFRLARG-VNSCGL 373

Query: 325 ASAASYPTV 333
           A+    P +
Sbjct: 374 ANTVVAPII 382


>Y40H7A.10 CE21821   Cysteine protease (HINXTON) TR:Q9XWA4
           protein_id:CAA22062.1
          Length = 343

 Score =  133 bits (335), Expect = 1e-31
 Identities = 91/284 (32%), Positives = 146/284 (51%), Gaps = 28/284 (9%)

Query: 48  RRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQ 107
           R  ++ +N+ ++E +N+E   GK   T  +N F D+T EE+++ +      KP   +   
Sbjct: 71  RFTIFSRNLDLVERYNKE-DAGK--VTYELNDFSDLTEEEWKKYL---MTPKPDHSEKSL 124

Query: 108 EPLFY----EAPRSVDWRE---KGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLIS 160
           +P         P SVDWR      +VT +K QG CGSCWAF+   A+E  +    G L S
Sbjct: 125 KPKTLIDKKNLPNSVDWRNVNGTNHVTGIKYQGPCGSCWAFATAAAIESAVSISGGGLQS 184

Query: 161 LSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVA 220
           LS Q L+DC+    ++ C GG    A +Y Q + G+ +  +YPY      C+     +VA
Sbjct: 185 LSSQQLLDCT--VVSDKCGGGEPVEALKYAQSH-GITTAHNYPYYFWTTKCRETVP-TVA 240

Query: 221 NDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLV 280
             + ++   + E  + + VA  GP+ V  +       FY  GI  +PDC +E   H ++V
Sbjct: 241 RISSWMK-AESEDEMAQIVALNGPMIVCANFATNKNRFYHSGIAEDPDCGTEP-THALIV 298

Query: 281 VGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGI 324
           +GYG +        YW++KN++ + WG  GY+++ +D  N CGI
Sbjct: 299 IGYGPD--------YWILKNTYSKVWGEKGYMRVKRD-VNWCGI 333


>R07E3.1 CE02295   cysteine proteinase (HINXTON) TR:Q21810
           protein_id:CAA89070.1
          Length = 402

 Score =  130 bits (327), Expect = 1e-30
 Identities = 89/265 (33%), Positives = 130/265 (48%), Gaps = 27/265 (10%)

Query: 78  NAFGDMTSEEFRQVM--NGFQNRKPRKGKVFQEPLFYEA-----------PRSVDWREKG 124
           N   D T EEF + +    F  R  ++ + F EP+               P   DWR+K 
Sbjct: 138 NDMSDWTDEEFEKTLLPKSFYKRLHKEAE-FIEPIPESLTAKKGESSSPFPDFFDWRDKN 196

Query: 125 YVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMD 184
            +TPVK QGQCGSCWAF++T  +E       G   +LSEQ L+DC     +  C+GG  D
Sbjct: 197 VITPVKAQGQCGSCWAFASTATVEAAWAIAHGEKRNLSEQTLLDCD--LVDNACDGGDED 254

Query: 185 YAFQYVQDNGGLDSEESYPYEA-TEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVG 243
            AF+Y+  N GL +    PY A  +  C  N  ++         +   E +++  +   G
Sbjct: 255 KAFRYIHRN-GLANAVDLPYVAHRQNGCAVNDHWNTTRIKAAYFLHHDEDSIINWLVNFG 313

Query: 244 PISVAIDAGHESFLFYKEGIY--FEPDCSSEDMD-HGVLVVGYGFESTESDNNKYWLVKN 300
           P+++ + A  +    YK G++   E  C +E +  H +L+ GYG   T     KYW+VKN
Sbjct: 314 PVNIGM-AVIQPMRAYKGGVFTPSEYACKNEVIGLHALLITGYG---TSKTGEKYWIVKN 369

Query: 301 SWGEEWGM-GGYVKMAKDRRNHCGI 324
           SWG  WG+  GY+  A+   N CGI
Sbjct: 370 SWGNTWGVEHGYIYFARG-INACGI 393


>Y51A2D.8 CE19204   Cysteine proteases (2 domains) (HINXTON) TR:Q9XXQ7
           protein_id:CAA16407.1
          Length = 386

 Score =  123 bits (308), Expect = 2e-28
 Identities = 87/322 (27%), Positives = 145/322 (45%), Gaps = 39/322 (12%)

Query: 32  WKAMHNRLYGMNEEGWRRAV-WEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQ 90
           +K  +NR Y    E  +R   + K+   ++  N + +   +     +N F D+++ EF  
Sbjct: 46  FKKKYNRKYKDESENQQRFNNFVKSYNNVDKLNAKSKAAGYDTQFGINKFSDLSTAEFHG 105

Query: 91  VMNG-------------FQNRKP-----------RKGKVFQEPLFYEAPRSVDWREKGYV 126
            ++              F  +KP            K +  + P +++  R+     +  V
Sbjct: 106 RLSNVVPSNNTGLPMLNFDKKKPDFRAADMNKTRHKRRSTRYPDYFDL-RNEKINGRYIV 164

Query: 127 TPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYA 186
            P+K+QGQC  CW F+ T  +E      +G+  SLS+Q + DC G +G  GC GG +   
Sbjct: 165 GPIKDQGQCACCWGFAVTALVETVYAAHSGKFKSLSDQEVCDC-GTEGTPGCKGGSLTLG 223

Query: 187 FQYVQDNGGLDSEESYPYEATEES----CKYNPKYSVANDTGF---VDIPKQEKALMKAV 239
            QYV+   GL  +E YPY+    +    C+      +     F   V  P++ +  +  V
Sbjct: 224 VQYVK-KYGLSGDEDYPYDQNRANQGRRCRLRETDRIVPARAFNFAVINPRRAEEQIIQV 282

Query: 240 ATVG--PISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYG-FESTESDNNKYW 296
            T    P++V    G + F  YKEG+  E DC      H   +VGY   E +   ++ YW
Sbjct: 283 LTEWKVPVAVYFKVG-DQFKEYKEGVIIEDDCRRATQWHAGAIVGYDTVEDSRGRSHDYW 341

Query: 297 LVKNSWGEEWGMGGYVKMAKDR 318
           ++KNSWG +W   GYV++ + R
Sbjct: 342 IIKNSWGGDWAESGYVRVVRGR 363


>K02E7.10 CE11640   protease (ST.LOUIS) TR:O17255 protein_id:AAB71030.1
          Length = 299

 Score =  119 bits (298), Expect = 3e-27
 Identities = 73/219 (33%), Positives = 112/219 (50%), Gaps = 14/219 (6%)

Query: 118 VDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFR-KTGRLISLSEQNLVDCSGPQGNE 176
           +DWREKG V PVK+QG+C + +AF+A  A+E    +   G+L+S SEQ ++DC+      
Sbjct: 84  LDWREKGIVGPVKDQGKCNASYAFAAIAAIESMYAKANNGKLLSFSEQQIIDCA--NFTN 141

Query: 177 GCNGGLMDYAFQYVQDNGGLDSEESYPYEATEE--SCKYNPKYSVANDTGFVDIPKQEKA 234
            C   L +          G+ +E  YPY   E    C+Y+        T ++D+   E+ 
Sbjct: 142 PCQENLENVLSNRFLKENGVGTEADYPYVGKENVGKCEYDSSKMKLRPT-YIDVYPNEEW 200

Query: 235 LMKAVATVGPISVAIDAGHESFLFYKEGIY--FEPDCSSEDMDHGVLVVGYGFESTESDN 292
               + T G     +     SF  YK GIY   + +C + +    + +VGYG +  E   
Sbjct: 201 ARAHITTFGTGYFRM-RSPPSFFHYKTGIYNPTKEECGNANEARSLAIVGYGKDGAE--- 256

Query: 293 NKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYP 331
            KYW+VK S+G  WG  GY+K+A++  N CG+A + S P
Sbjct: 257 -KYWIVKGSFGTSWGEHGYMKLARN-VNACGMAESISIP 293


>Y71H2AR.2 CE22930    (ST.LOUIS) protein_id:AAK29985.1
          Length = 345

 Score =  119 bits (297), Expect = 3e-27
 Identities = 79/219 (36%), Positives = 115/219 (52%), Gaps = 12/219 (5%)

Query: 118 VDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKT-GRLISLSEQNLVDCSGPQGNE 176
           +DWREKG V PVK+QG+C +  AF+ T ++E    + T G L+S SEQ L+DC+  QG +
Sbjct: 86  LDWREKGIVGPVKDQGKCNASHAFAITSSIESMYAKATNGTLLSFSEQQLIDCN-DQGYK 144

Query: 177 GCNGGLMDYAFQYVQDNGGLDSEESYPY-EATEESCKYNPKYSVANDTGFVDIPKQEKAL 235
           GC       A  Y+  + G+++E  YPY + T E C ++   S  +    V     E   
Sbjct: 145 GCEEQFAMNAIGYLATH-GIETEADYPYVDKTNEKCTFDSTKSKIHLKKGVVAEGNEVLG 203

Query: 236 MKAVATVGPISVAIDAGHESFLFYKEGIYFE--PDCSSEDMDHGVLVVGYGFESTESDNN 293
              V   GP    + A   S   YK GIY     +C+S      +++VGYG E  +    
Sbjct: 204 KVYVTNYGPAFFTMRA-PPSLYDYKIGIYNPSIEECTSTHEIRSMVIVGYGIEGEQ---- 258

Query: 294 KYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPT 332
           KYW+VK S+G  WG  GY+K+A+D  N C +A+  +  T
Sbjct: 259 KYWIVKGSFGTSWGEQGYMKLARD-VNACAMATTIAVLT 296


>Y51A2D.1 CE18411   Cysteine proteases (2 domains) (HINXTON) TR:O62484
           protein_id:CAA16404.1
          Length = 382

 Score =  105 bits (262), Expect = 4e-23
 Identities = 95/353 (26%), Positives = 148/353 (41%), Gaps = 76/353 (21%)

Query: 28  QWTKWKAMHNRLYGMNEEGWRRA---VWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMT 84
           ++ ++K   +R Y    E   R    V  +N  ++ L+    + G++S   A+N F D+T
Sbjct: 43  EFVEFKKKFSRTYKSEAENQLRLQNFVKSRN-NVVRLNKNAQKAGRNS-NFAVNQFSDLT 100

Query: 85  SEEFRQVMNGF-----------QNRKPRKGKVFQEPLFYEAPRSVDWREKGY-----VTP 128
           + E  Q ++ F           +N K   GK   +    E  R+ D R +       V P
Sbjct: 101 TSELHQRLSRFPPNLTENSVFHKNFKKLLGKTRTKRQNSEFARNFDLRSQKVNGRYIVGP 160

Query: 129 VKNQGQCGSCWAFSATGALEG------------------------------QMFRKTGRL 158
           +KNQGQC  CW F+ T  LE                               +   K    
Sbjct: 161 IKNQGQCACCWGFAVTAMLETIYAVNVGRFKLMSHIPALAPNFSDFDFFFFEFLAKLNMF 220

Query: 159 ISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYS 218
           +S S+Q + DC+      GC GG + +  +Y  +N GL SE  YP      + +     +
Sbjct: 221 LSFSDQEMCDCATDGTKAGCAGGGLMWGVEYAINN-GLASEFDYPEFDQNRATRPGTCEA 279

Query: 219 VANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCS-SEDMDHG 277
           + +D                  T  P++ A  AG  +FL YK G+    DC  +  + H 
Sbjct: 280 MDDD-----------------KTFPPVNFA--AG-TAFLQYKSGVLVTEDCDLAGTVWHA 319

Query: 278 VLVVGYGFES-TESDNNKYWLVKNSWG-EEWGMGGYVKMAKDRRNHCGIASAA 328
             +VGYG E+     + ++W++KNSWG   WG GGYVK+ +  +N CGI   A
Sbjct: 320 GAIVGYGEENDLRGRSQRFWIMKNSWGVSGWGTGGYVKLIRG-KNWCGIERGA 371


>F26E4.3 CE17714   cysteine protease (HINXTON) TR:P90850
           protein_id:CAB03007.1
          Length = 491

 Score =  100 bits (250), Expect = 1e-21
 Identities = 73/245 (29%), Positives = 110/245 (44%), Gaps = 35/245 (14%)

Query: 113 EAPRSVDWREKG--YVTPVKNQGQCGSCWAFSATGALEGQM-FRKTGRLIS-LSEQNLVD 168
           E P   D R+K    + PV +QG CGS W+ S T     ++     GR+ S LS Q L+ 
Sbjct: 222 ELPEHFDARDKWGPLIHPVADQGDCGSSWSVSTTAISSDRLAIISEGRINSTLSSQQLLS 281

Query: 169 CSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPY---EATEESCKYNPKYSVANDTGF 225
           C+  +  +GC GG +D A+ Y++  G +  +  YPY   ++ E      PK    N  G 
Sbjct: 282 CNQHR-QKGCEGGYLDRAWWYIRKLGVV-GDHCYPYVSGQSREPGHCLIPKRDYTNRQGL 339

Query: 226 -----------------VDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPD 268
                              +  +E+ +   + T GP+       HE F  Y  G+Y   D
Sbjct: 340 RCPSGSQDSTAFKMTPPYKVSSREEDIQTELMTNGPVQATFVV-HEDFFMYAGGVYQHSD 398

Query: 269 CSSE-------DMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNH 321
            +++       +  H V V+G+G + +     KYWL  NSWG +WG  GY K+ +   NH
Sbjct: 399 LAAQKGASSVAEGYHSVRVLGWGVDHSTGKPIKYWLCANSWGTQWGEDGYFKVLRG-ENH 457

Query: 322 CGIAS 326
           C I S
Sbjct: 458 CEIES 462


>Y113G7B.15 CE23295    (HINXTON) TR:Q9U2X1 protein_id:CAB54334.1
          Length = 328

 Score =  100 bits (248), Expect = 2e-21
 Identities = 92/317 (29%), Positives = 130/317 (40%), Gaps = 37/317 (11%)

Query: 44  EEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMNG--------- 94
           E+  R A + KN + I+  N + R    + T   N F D   +E     +          
Sbjct: 12  EKDRRLAHFAKNHQKIQELNAKARREGRNVTFGWNKFADKNRQELSARNSKIHPKNHTDL 71

Query: 95  --FQNRKPRKGKVFQEPLFY----EAPRSVDWRE-----KGYVTPVKNQGQCGSCWAFSA 143
             ++ R PR  +            + P   D R+        V PVK+Q QCG CWAF+ 
Sbjct: 72  PIYKPRHPRGSRNHHNKRSKRQSGDIPDYFDLRDIYVDGSPVVGPVKDQEQCGCCWAFAT 131

Query: 144 TGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYP 203
           T   E      +    SLS+Q + DC+      GC GG      + V    G  S+  YP
Sbjct: 132 TAITEAANTLYSKSFTSLSDQEICDCADSGDTPGCVGGDPRNGLKMVHLR-GQSSDGDYP 190

Query: 204 YEA----TEESCKYNPKYSV-----ANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHE 254
           YE     T  +C  + K +V      N   F     +E  +        P +V    G E
Sbjct: 191 YEEYRANTTGNCVGDEKSTVIQPETLNVYRFDQDYAEEDIMENLYLNHIPTAVYFRVG-E 249

Query: 255 SFLFYKEGIYFEPDC--SSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYV 312
           +F +Y  G+    DC   +    H V +VGYG   T  D   YWLV+NSW  +WG+ GYV
Sbjct: 250 NFEWYTSGVLQSEDCYQMTPAEWHSVAIVGYG---TSDDGVPYWLVRNSWNSDWGLHGYV 306

Query: 313 KMAKDRRNHCGIASAAS 329
           K+ +   N C I S A+
Sbjct: 307 KIRRG-VNWCLIESHAA 322


>F15D4.4 CE28917   cysteine protease (HINXTON) TR:Q93512
           protein_id:CAB02487.1
          Length = 622

 Score = 97.8 bits (242), Expect = 8e-21
 Identities = 77/296 (26%), Positives = 127/296 (42%), Gaps = 39/296 (13%)

Query: 44  EEGWRRA-VWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRK 102
           +EG +R  V+ K  K ++ HN  Y  G  S+ M+ N F      E   +        P  
Sbjct: 149 KEGLKRFNVYSKVKKEVDEHNIMYELGMSSYKMSTNQFSVALDGEVAPLTLNLDALTPTA 208

Query: 103 GKV---FQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLI 159
             +          +   +VDWR   ++ P+ +Q  CG CWAFS    +E     +     
Sbjct: 209 TVIPATISSRKKRDTEPTVDWRP--FLKPILDQSTCGGCWAFSMISMIESFFAIQGYNTS 266

Query: 160 SLSEQNLVDCSGP------QGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCK- 212
           SLS Q L+ C           N GC GG    A  Y++ +   D+    P++  + SC  
Sbjct: 267 SLSVQQLLTCDTKVDSTYGLANVGCKGGYFQIAGSYLEVSAARDA-SLIPFDLEDTSCDS 325

Query: 213 ------------YNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYK 260
                       ++  Y   N T    I  ++   ++     GPI+V + AG + +  Y 
Sbjct: 326 SFFPPVVPTILLFDDGYISGNFTAAQLITMEQN--IEDKVRKGPIAVGMAAGPDIYK-YS 382

Query: 261 EGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAK 316
           EG+Y + DC +  ++H V++VG+         + YW+++NSWG  WG  GY ++ +
Sbjct: 383 EGVY-DGDCGT-IINHAVVIVGF--------TDDYWIIRNSWGASWGEAGYFRVKR 428


>C50F4.3 CE05468   thiol protease (HINXTON) TR:Q18740 protein_id:CAA94738.1
          Length = 374

 Score = 94.4 bits (233), Expect = 9e-20
 Identities = 80/292 (27%), Positives = 125/292 (42%), Gaps = 36/292 (12%)

Query: 63  NQEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQ-----------NRKPRKGKVFQEPLF 111
           N+  ++  H     +N F D++ +E   + + F            N K  + K   E L 
Sbjct: 82  NKAAKKAGHDTKYGINKFSDLSKKEIHGMYSKFGPPKNNTNVPKFNLKNLRVKRQMEGL- 140

Query: 112 YEAPRSVDWREKGY-----VTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNL 166
              P++ D R K       + P+K Q  C  CW F+AT   E  +     + ++LSEQ +
Sbjct: 141 ---PKTFDLRNKKVGGHYIIGPIKTQDSCACCWGFAATAVAEAALTVHLKKAMNLSEQEV 197

Query: 167 VDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATE-------ESCKYNPKYS- 218
            DC+ P+   GCNGG      +Y+++  GL   + YP+           ES KY+ + + 
Sbjct: 198 CDCA-PKHGPGCNGGDPVDGLEYIKEM-GLTGGKEYPFNVNRSTQLGRCESEKYDRELNP 255

Query: 219 VANDTGFVDIPKQEKALMKAVATVG-PISVAIDAGHESFLFYKEGIYFEPDCSSEDMD-- 275
           +  D   +D    E  +   +  +  PISVA   G  S   Y  GI    DC  E     
Sbjct: 256 LELDYYAIDPFNAEYQMTHHLYLLNLPISVAFRTG-ASLSSYLSGILELADCDDEKGGHW 314

Query: 276 HGVLVVGYGFESTESDNN-KYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIAS 326
           H   +VGYG     +     YW+ +NSW  +WG  GY ++ +   + C I S
Sbjct: 315 HSGAIVGYGTTKNSAGRTVDYWIFRNSWWTDWGDDGYARIVRG-EDWCSIES 365


>C32B5.7 CE08515   cathepsin-like peptidase (ST.LOUIS) TR:P91111
           protein_id:AAB37963.1
          Length = 250

 Score = 94.0 bits (232), Expect = 1e-19
 Identities = 63/191 (32%), Positives = 100/191 (51%), Gaps = 18/191 (9%)

Query: 118 VDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEG 177
           +DWR++G V PVK+QG C + +AF+A  A+E       G+L+S SEQ ++DC G    E 
Sbjct: 72  LDWRDEGVVGPVKDQGNCNASYAFAAISAIESMYAIANGQLLSFSEQQIIDCLGGCAIES 131

Query: 178 CNGGLMDYAFQYVQDNGGLDSEESYPYEATE-ESCKYNPK--YSVANDTGFVDIPKQEKA 234
                M Y      +  G+++   YP+   + E C+Y+ K  Y + +DT   D+  +  A
Sbjct: 132 DPMMAMTYL-----ERKGIETYTDYPFVGKKNEKCEYDSKKAYLILDDT--YDMSDESLA 184

Query: 235 LMKAVATVGPISVAIDAGHESFLFYKEGIY--FEPDCSSEDMDHGVLVVGYGFESTESDN 292
           L+  +   GP    ++    SF  YK GIY   E +C S +    + +VGYG +  ++  
Sbjct: 185 LV-FIDERGPGLFTMNT-PPSFFNYKSGIYNPTEEECKSTNEKRALTIVGYGNDKGQN-- 240

Query: 293 NKYWLVKNSWG 303
             YW+VK S+G
Sbjct: 241 --YWIVKGSFG 249


>M04G12.2 CE12424   cysteine protease (HINXTON) TR:P92005
           protein_id:CAB03209.1
          Length = 467

 Score = 92.0 bits (227), Expect = 4e-19
 Identities = 82/288 (28%), Positives = 133/288 (45%), Gaps = 45/288 (15%)

Query: 66  YREGKHSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRK-GKVFQE---PLFYEA------- 114
           Y E      + M++  + +SEE+ +     +    +K GKVF+    P  +E+       
Sbjct: 161 YYEPNDEALVDMSSESEESSEEWEEARPYLKCGCLKKSGKVFESKTAPREWESSSFKSND 220

Query: 115 -PRSVDWREKG---YVTPVKNQG---QCGSCWAFSATGALEGQM-FRKTGR--LISLSEQ 164
            P   DWR      Y +P +NQ     CGSCW F  TGAL  +    + GR  +  LS Q
Sbjct: 221 LPTGWDWRNVSGVNYCSPTRNQHIPVYCGSCWVFGTTGALNDRFNVARKGRWPMTQLSPQ 280

Query: 165 NLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEE---------SCKYNP 215
            ++DC+G +GN  C GG +    ++ +  G L  E    Y AT           SC  N 
Sbjct: 281 EIIDCNG-KGN--CQGGEIGNVLEHAKIQG-LVEEGCNVYRATNGECNPYHRCGSCWPNE 336

Query: 216 KYSVANDTGFV-----DIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCS 270
            +S+ N T +       +  ++K +M  +   GPI+ AI A  +    Y +G+Y E   S
Sbjct: 337 CFSLTNYTRYYVKDYGQVQGRDK-IMSEIKKGGPIACAIGATKKFEYEYVKGVYSEK--S 393

Query: 271 SEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDR 318
             + +H + + G+G    + +  +YW+ +NSWGE WG  G+ ++   +
Sbjct: 394 DLESNHIISLTGWG---VDENGVEYWIARNSWGEAWGELGWFRVVTSK 438


>C52E4.1 CE08943  locus:cpr-1 cathepsin-like cysteine protease (HINXTON)
           TR:Q18783 protein_id:CAB01410.1
          Length = 340

 Score = 88.6 bits (218), Expect = 5e-18
 Identities = 66/251 (26%), Positives = 104/251 (41%), Gaps = 37/251 (14%)

Query: 107 QEPLFYEAPRSVD----WREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKT--GRLIS 160
           QE +    P + D    W E   +  +++Q  CGSCWAF A   +  +   +T   +   
Sbjct: 89  QEVVLASVPATFDSRTQWSECKSIKLIRDQATCGSCWAFGAAEMISDRTCIETKGAQQPI 148

Query: 161 LSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESY-----PYE---------- 205
           +S  +L+ C G     GC GG    A ++    G +   + +     PY           
Sbjct: 149 ISPDDLLSCCGSSCGNGCEGGYPIQALRWWDSKGVVTGGDYHGAGCKPYPIAPCTSGNCP 208

Query: 206 -----ATEESCKYNPKYSVANDTGF----VDIPKQEKALMKAVATVGPISVAIDAGHESF 256
                +   SC+     + A D  F      +PK   ++   +   GP+  A    +E F
Sbjct: 209 ESKTPSCSMSCQSGYSTAYAKDKHFGVSAYAVPKNAASIQAEIYANGPVEAAFSV-YEDF 267

Query: 257 LFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAK 316
             YK G+Y +         H + ++G+G ES     + YWLV NSWG  WG  G+ K+ +
Sbjct: 268 YKYKSGVY-KHTAGKYLGGHAIKIIGWGTES----GSPYWLVANSWGVNWGESGFFKIYR 322

Query: 317 DRRNHCGIASA 327
              + CGI SA
Sbjct: 323 G-DDQCGIESA 332


>F32B5.8 CE09855   cysteine proteinase (ST.LOUIS) TR:O01850
           protein_id:AAB54210.1
          Length = 427

 Score = 88.2 bits (217), Expect = 6e-18
 Identities = 85/288 (29%), Positives = 130/288 (44%), Gaps = 54/288 (18%)

Query: 75  MAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLF---YEA--------PRSVDWREK 123
           +A +A+G +     R   N  +    + G+VF+   +   YE         P++ DWR+ 
Sbjct: 137 LASSAYGKVRKYSNRNRYN-LKGCYKQTGRVFEHKRYDRIYETEDFDSEDLPKTWDWRDA 195

Query: 124 G---YVTPVKNQG---QCGSCWAFSATGALEGQMFRKTGRL---ISLSEQNLVDCSGP-- 172
               Y +  +NQ     CGSCWAF AT AL  ++  K         LS Q ++DCSG   
Sbjct: 196 NGINYASADRNQHIPQYCGSCWAFGATSALADRINIKRKNAWPQAYLSVQEVIDCSGAGT 255

Query: 173 --QGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCK-YN-------------PK 216
              G E   GG+  YA ++     G+  E    Y+A +  C  YN               
Sbjct: 256 CVMGGEP--GGVYKYAHEH-----GIPHETCNNYQARDGKCDPYNRCGSCWPGECFSIKN 308

Query: 217 YSVANDTGFVDIPKQEKALMKA-VATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMD 275
           Y++   + +  +   EK  MKA +   GPI+  I A  ++F  Y  GIY E   + ED+D
Sbjct: 309 YTLYKVSEYGTVHGYEK--MKAEIYHKGPIACGI-AATKAFETYAGGIYKE--VTDEDID 363

Query: 276 HGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCG 323
           H + V G+G +       +YW+ +NSWGE WG  G+ K+   +  + G
Sbjct: 364 HIISVHGWGVD--HESGVEYWIGRNSWGEPWGEHGWFKIVTSQYKNAG 409


>F57F5.1 CE05999   cysteine protease (HINXTON) TR:Q20950
           protein_id:CAB00098.1
          Length = 400

 Score = 85.9 bits (211), Expect = 3e-17
 Identities = 72/280 (25%), Positives = 114/280 (40%), Gaps = 51/280 (18%)

Query: 89  RQVMNGFQNRKPRKGKVFQ--EPLFYEA--PRSVD----WREKGYVTPVKNQGQCGSCWA 140
           +Q+M       P + +VF+   P   +A  P S D    W     ++ +++Q  CGSCWA
Sbjct: 117 KQLMGAKMVEIPEEYRVFEMTHPEVEDAAVPDSFDSRTAWPNCPSISKIRDQSSCGSCWA 176

Query: 141 FSATGALEGQ--MFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQY--------- 189
            SA   +  +  +      ++S+S  ++  C G     GCNGG    A+++         
Sbjct: 177 VSAAETISDRICIASNAKTILSISADDINACCGMVCGNGCNGGYPIEAWRHYVKKGYVTG 236

Query: 190 --VQDNGGLD-------------------SEESYPYEATEESCKYNPKYSVANDTGF--- 225
              QD  G                         YP +  E SC+     +   D  F   
Sbjct: 237 GSYQDKTGCKPYPYPPCEHHVNGTHYKPCPSNMYPTDKCERSCQAGYALTYQQDLHFGQS 296

Query: 226 -VDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYG 284
              + K+   + K + T GP+ VA    +E F  Y  G+Y     +S    H V ++G+G
Sbjct: 297 AYAVSKKAAEIQKEIMTHGPVEVAFTV-YEDFEHYSGGVYVHTAGASLG-GHAVKMLGWG 354

Query: 285 FESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGI 324
            +    +   YWL  NSW E+WG  GY ++ +   N CGI
Sbjct: 355 VD----NGTPYWLCANSWNEDWGENGYFRIIRG-VNECGI 389


>T10H4.12 CE27590  locus:cpr-3 protease (HINXTON) TR:Q9TW93
           protein_id:CAB61024.2
          Length = 370

 Score = 77.4 bits (189), Expect = 1e-14
 Identities = 80/345 (23%), Positives = 131/345 (37%), Gaps = 76/345 (22%)

Query: 12  LGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGKH 71
           +G +   +  DH    Q T W A HN +          + +E   K++++          
Sbjct: 27  IGQSPQKVLVDHVNTVQ-TSWVAEHNEI----------SEFEMKFKVMDV---------- 65

Query: 72  SFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFYEAPRSVDWREK----GYVT 127
            F   +    D+ SE F             +G++  EPL    P + D REK      + 
Sbjct: 66  KFAEPLEKDSDVASELFV------------RGEIVPEPL----PDTFDAREKWPDCNTIK 109

Query: 128 PVKNQGQCGSCWAFSATGALEGQMFRKTG--RLISLSEQNLVDCSGPQGNEGCNGGLMDY 185
            ++NQ  CGSCWAF A   +  ++  ++   +   +S ++++ C G     GC GG    
Sbjct: 110 LIRNQATCGSCWAFGAAEVISDRVCIQSNGTQQPVISVEDILSCCGTTCGYGCKGGYSIE 169

Query: 186 AFQYVQDNGGLDSEE-----SYPY----------EATEESCK-----------YNPKYSV 219
           A ++   +G +   +       PY          E+T  SCK           Y      
Sbjct: 170 ALRFWASSGAVTGGDYGGHGCMPYSFAPCTKNCPESTTPSCKTTCQSSYKTEEYKKDKHY 229

Query: 220 ANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVL 279
                 V   K    +   +   GP+  +    +E F  YK G+Y           H V 
Sbjct: 230 GASAYKVTTTKSVTEIQTEIYHYGPVEASYKV-YEDFYHYKSGVYHYTSGKLVG-GHAVK 287

Query: 280 VVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGI 324
           ++G+G E    +   YWL+ NSWG  +G  G+ K+ +   N C I
Sbjct: 288 IIGWGVE----NGVDYWLIANSWGTSFGEKGFFKIRRG-TNECQI 327


>F36D3.9 CE15973   cysteine protease (HINXTON) TR:O45466
           protein_id:CAB04322.1
          Length = 345

 Score = 77.0 bits (188), Expect = 1e-14
 Identities = 65/245 (26%), Positives = 100/245 (40%), Gaps = 36/245 (14%)

Query: 109 PLFYEAPRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLIS--LSEQNL 166
           PL ++A     W +   +  ++ Q  CGSCWAFS    +  +    +       +S  +L
Sbjct: 102 PLNFDA--RTRWPQCKSMKLIREQSNCGSCWAFSTAEVISDRTCIASNGTQQPIISPTDL 159

Query: 167 VDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEE-------SYPYEATEE---------- 209
           + C G    EGC+GG    AFQ+    G +   +        YP                
Sbjct: 160 LTCCGMSCGEGCDGGFPYRAFQWWARRGVVTGGDYLGTGCKPYPIRPCNSDNCVNLQTPP 219

Query: 210 ---SCKYNPKYSVANDTGF-----VDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKE 261
              SC+   + +  ND  +       +P+   A+   +   GP+ VA    +E F  YK 
Sbjct: 220 CRLSCQPGYRTTYTNDKNYGSNSAYPVPRTVAAIQADIYYNGPV-VAAFIVYEDFEKYKS 278

Query: 262 GIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNH 321
           GIY      S+   H V ++G+G E        YWL  NSWG +WG  G  ++ +   + 
Sbjct: 279 GIYRHIAGRSKG-GHAVKLIGWGTER----GTPYWLAVNSWGSQWGESGTFRILRG-VDE 332

Query: 322 CGIAS 326
           CGI S
Sbjct: 333 CGIES 337


>C25B8.3 CE04078  locus:cpr-6  (ST.LOUIS) protein_id:AAK39189.1
          Length = 379

 Score = 77.0 bits (188), Expect = 1e-14
 Identities = 67/255 (26%), Positives = 106/255 (41%), Gaps = 49/255 (19%)

Query: 113 EAPRSVD----WREKGYVTPVKNQGQCGSCWAFSATGALEGQM-FRKTGRL-ISLSEQNL 166
           + P S D    W +   +  +++Q  CGSCWAF A  A+  ++     G L ++LS  +L
Sbjct: 104 DIPESFDSRDNWPKCDSIKVIRDQSSCGSCWAFGAVEAMSDRICIASHGELQVTLSADDL 163

Query: 167 VDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSE--------ESYPYEATEESCKYN---- 214
           + C    G  GCNGG    A++Y   +G +           + YP+   E   K      
Sbjct: 164 LSCCKSCGF-GCNGGDPLAAWRYWVKDGIVTGSNYTANNGCKPYPFPPCEHHSKKTHFDP 222

Query: 215 --------PKYSVANDTGFVDIPKQE---------------KALMKAVATVGPISVAIDA 251
                   PK      + + D    E               +A+ K + T GP+ +A + 
Sbjct: 223 CPHDLYPTPKCEKKCVSDYTDKTYSEDKFFGASAYGVKDDVEAIQKELMTHGPLEIAFEV 282

Query: 252 GHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGY 311
            +E FL Y  G+Y           H V ++G+G +    D   YW V NSW  +WG  G+
Sbjct: 283 -YEDFLNYDGGVYVHTG-GKLGGGHAVKLIGWGID----DGIPYWTVANSWNTDWGEDGF 336

Query: 312 VKMAKDRRNHCGIAS 326
            ++ +   + CGI S
Sbjct: 337 FRILRG-VDECGIES 350


>W07B8.4 CE14680   thiol protease (ST.LOUIS) TR:O16288 protein_id:AAB65345.1
          Length = 335

 Score = 75.9 bits (185), Expect = 3e-14
 Identities = 66/249 (26%), Positives = 99/249 (39%), Gaps = 47/249 (18%)

Query: 120 WREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLIS--LSEQNLVDCSGPQGN-- 175
           W +   V  +++Q  CGSCWA +A  A+  +    +   ++  LS ++++ C   + N  
Sbjct: 83  WPQCISVNNIRDQSHCGSCWAVAAAEAISDRTCIASNGDVNTLLSAEDILTCCTGKFNCG 142

Query: 176 EGCNGGLMDYAFQYVQDNG---GLDSEESY---PYEAT---------------------- 207
           +GC GG    A++Y   NG   G   E  Y   PY                         
Sbjct: 143 DGCEGGYPIQAWRYWVKNGLVTGGSFESQYGCKPYSIAPCGETIDGVTWPECPMKISDTP 202

Query: 208 --EESCKYNPKYSVAND------TGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFY 259
             E  C  N  Y +  D           I +  K +   +   GP+ V     +E F  Y
Sbjct: 203 KCEHHCTGNNSYPIPYDQDKHFGASAYAIGRSAKQIQTEILAHGPVEVGFIV-YEDFYLY 261

Query: 260 KEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRR 319
           K GIY       E   H V ++G+G ++       YWL  NSW   WG  GY ++ +   
Sbjct: 262 KTGIYTHV-AGGELGGHAVKMLGWGVDN----GTPYWLAANSWNTVWGEKGYFRILRG-V 315

Query: 320 NHCGIASAA 328
           + CGI SAA
Sbjct: 316 DECGIESAA 324


>Y71H2AM.3 CE26272    (ST.LOUIS) protein_id:AAK29976.1
          Length = 716

 Score = 68.6 bits (166), Expect = 5e-12
 Identities = 55/168 (32%), Positives = 81/168 (47%), Gaps = 23/168 (13%)

Query: 118 VDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKT-GRLISLSEQNLVDCSGPQGNE 176
           +DWR+KG V PVK+QG+C +  AF+ + ++E    + T G L+S SEQ L+DC    G +
Sbjct: 86  LDWRDKGIVGPVKDQGKCNASHAFAISSSIESMYAKATNGSLLSFSEQQLIDCD-DHGFK 144

Query: 177 GCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALM 236
           GC       A  Y   + G+++E  YPY   E          ++N+T       Q K L 
Sbjct: 145 GCEEQPAINAVSYFIFH-GIETEADYPYAGKENG-------KLSNET-------QGKEL- 188

Query: 237 KAVATVGPISVAIDAGHESFLFYKEGIYFE--PDCSSEDMDHGVLVVG 282
             V   GP    + A   S   YK GIY     +C+S      +++VG
Sbjct: 189 --VTNYGPAFFTMRA-PPSLYDYKIGIYNPSIEECTSTHEIRSMVIVG 233


  Database: /data_2/jason/blastdb/wormpep62
    Posted date:  Sep 3, 2001  2:17 PM
  Number of letters in database: 8,813,425
  Number of sequences in database:  20,085
  
Lambda     K      H
   0.317    0.133    0.417 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6230268
Number of Sequences: 20085
Number of extensions: 270881
Number of successful extensions: 651
Number of sequences better than 1.0e-10: 23
Number of HSP's better than  0.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 588
Number of HSP's gapped (non-prelim): 27
length of query: 333
length of database: 8,813,425
effective HSP length: 45
effective length of query: 288
effective length of database: 7,909,600
effective search space: 2277964800
effective search space used: 2277964800
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 155 (64.3 bits)
BLASTP 2.1.3 [Apr-11-2001]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= CATL_RAT
         (334 letters)

Database: /data_2/jason/blastdb/wormpep62
           20,085 sequences; 8,813,425 total letters

Searching..................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

T03E6.7 CE16333   cathepsin-like protease (HINXTON) TR:O4573...   325  2e-89
F41E6.6 CE10254   cysteine protease and a protease inhibitor...   203  1e-52
R09F10.1 CE28755   peptidase (ST.LOUIS) TR:Q23030 protein_id...   192  2e-49
R07E3.1 CE02295   cysteine proteinase (HINXTON) TR:Q21810 pr...   139  2e-33
Y40H7A.10 CE21821   Cysteine protease (HINXTON) TR:Q9XWA4 pr...   131  5e-31

>T03E6.7 CE16333   cathepsin-like protease (HINXTON) TR:O45734
           protein_id:CAB07275.1
          Length = 337

 Score =  325 bits (834), Expect = 2e-89
 Identities = 159/311 (51%), Positives = 208/311 (66%), Gaps = 9/311 (2%)

Query: 28  QWHQWKSTHRRLYGTNEEEWRRAVWEKNMRMIQLHNGEYSNGKHGFTMEMNAFGDMTNEE 87
           +W  +K    + Y  +EE+     + KNM  I+ HN ++  G+  F M +N   D+   +
Sbjct: 31  KWDDYKEDFDKEYSESEEQTYMEAFVKNMIHIENHNRDHRLGRKTFEMGLNHIADLPFSQ 90

Query: 88  FRQIVNGYRH----QKHKKGRLFQEPLMLQIPKTVDWREKGCVTPVKNQGQCGSCWAFSA 143
           +R++ NGYR      + K    F  P  +Q+P  VDWR+   VT VKNQG CGSCWAFSA
Sbjct: 91  YRKL-NGYRRLFGDSRIKNSSSFLAPFNVQVPDEVDWRDTHLVTDVKNQGMCGSCWAFSA 149

Query: 144 SGCLEGQMFLKTGKLISLSEQNLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLDSEESYP 203
           +G LEGQ   K G+L+SLSEQNLVDCS   GN GCNGGLMD AF+YI++N G+D+EESYP
Sbjct: 150 TGALEGQHARKLGQLVSLSEQNLVDCSTKYGNHGCNGGLMDQAFEYIRDNHGVDTEESYP 209

Query: 204 YEAKDGSCKYRAEYAVANDTGFVDIPQ-QEKALMKAVATVGPISVAMDASHPSLQFYSSG 262
           Y+ +D  C +  +   A+D G+VD P+  E+ L  AVAT GPIS+A+DA H S Q Y  G
Sbjct: 210 YKGRDMKCHFNKKTVGADDKGYVDTPEGDEEQLKIAVATQGPISIAIDAGHRSFQLYKKG 269

Query: 263 IYYEPNCSSKDLDHGVLVVGYGYEGTDSNKDKYWLVKNSWGKEWGMDGYIKIAKDRNNHC 322
           +YY+  CSS++LDHGVL+VGY   GTD     YW+VKNSWG  WG  GYI+IA++RNNHC
Sbjct: 270 VYYDEECSSEELDHGVLLVGY---GTDPEHGDYWIVKNSWGAGWGEKGYIRIARNRNNHC 326

Query: 323 GLATAASYPIV 333
           G+AT ASYP+V
Sbjct: 327 GVATKASYPLV 337


>F41E6.6 CE10254   cysteine protease and a protease inhibitor (ST.LOUIS)
           TR:O16454 protein_id:AAB65956.1
          Length = 498

 Score =  203 bits (516), Expect = 1e-52
 Identities = 122/331 (36%), Positives = 183/331 (54%), Gaps = 45/331 (13%)

Query: 36  HRRLYGTNEEEWRR-AVWEKNMRMI-QLHNGEYSNGKHGFTMEMNAFGDMTNEEFRQIVN 93
           H + Y    E  +R  V++KN ++I +L   E     +GFT     F DMT  EF++I+ 
Sbjct: 181 HEKKYTNKREVLKRFRVFKKNAKVIRELQKNEQGTAVYGFTK----FSDMTTMEFKKIML 236

Query: 94  GYRHQKH----KKGRLFQEPLMLQ---IPKTVDWREKGCVTPVKNQGQCGSCWAFSASGC 146
            Y+ ++     ++    +  + +    +P++ DWREKG VT VKNQG CGSCWAFS +G 
Sbjct: 237 PYQWEQPVYPMEQANFEKHDVTINEEDLPESFDWREKGAVTQVKNQGNCGSCWAFSTTGN 296

Query: 147 LEGQMFLKTGKLISLSEQNLVDCSHDQGNQGCNGGLMDFAFQ----YIKEN--------- 193
           +EG  F+   KL+SLSEQ LVDC  D  +QGCNGGL   A++     + +N         
Sbjct: 297 VEGAWFIAKNKLVSLSEQELVDC--DSMDQGCNGGLPSNAYKIGKFVVSDNYCFLVFYHK 354

Query: 194 --------GGLDSEESYPYEAKDGSCKYRAEYAVANDTGFVDIPQQEKALMKAVATVGPI 245
                   GGL+ E++YPY+ +  +C    +       G V++P  E  + K + T GPI
Sbjct: 355 TTKEIIRMGGLEPEDAYPYDGRGETCHLVRKDIAVYINGSVELPHDEVEMQKWLVTKGPI 414

Query: 246 SVAMDASHPSLQFYSSGIY--YEPNCSSKDLDHGVLVVGYGYEGTDSNKDKYWLVKNSWG 303
           S+ ++A+  +LQFY  G+   ++  C    L+HGVL+VGYG +G    +  YW+VKNSWG
Sbjct: 415 SIGLNAN--TLQFYRHGVVHPFKIFCEPFMLNHGVLIVGYGKDG----RKPYWIVKNSWG 468

Query: 304 KEWGMDGYIKIAKDRNNHCGLATAASYPIVN 334
             WG  GY K+ + + N CG+   A+  +VN
Sbjct: 469 PNWGEAGYFKLYRGK-NVCGVQEMATSALVN 498


>R09F10.1 CE28755   peptidase (ST.LOUIS) TR:Q23030 protein_id:AAC69091.2
          Length = 383

 Score =  192 bits (488), Expect = 2e-49
 Identities = 116/310 (37%), Positives = 176/310 (56%), Gaps = 29/310 (9%)

Query: 37  RRLYGTNEEEWRRAVWEKNMRMIQLHNGEYSNGKHGFTMEMNAFGDMTNEEFRQIVNGYR 96
           R+     E E+R  ++ +N+  I+    E  N   G  +++N F D T+EE +++V   +
Sbjct: 91  RKYTSVEEFEYRYQIFLRNV--IEFEAEEERN--LGLDLDVNEFTDWTDEELQKMVQENK 146

Query: 97  HQKHKKGRLFQEPLMLQI----PKTVDWREKGCVTPVKNQGQCGSCWAFSASGCLEGQMF 152
           + K+       E   L+     P ++DWRE+G +TP+KNQGQCGSCWAF+    +E Q  
Sbjct: 147 YTKYDFDTPKFEGSYLETGVIRPASIDWREQGKLTPIKNQGQCGSCWAFATVASVEAQNA 206

Query: 153 LKTGKLISLSEQNLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGSCK 212
           +K GKL+SLSEQ +VDC  D  N GC+GG   +A +++KEN GL+SE+ YPY A     K
Sbjct: 207 IKKGKLVSLSEQEMVDC--DGRNNGCSGGYRPYAMKFVKEN-GLESEKEYPYSA----LK 259

Query: 213 YRAEYAVANDTG-FVD----IPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYE- 266
           +   +   NDT  F+D    +   E+ +   V T GP++  M+    ++  Y SGI+   
Sbjct: 260 HDQCFLKENDTRVFIDDFRMLSNNEEDIANWVGTKGPVTFGMNVV-KAMYSYRSGIFNPS 318

Query: 267 -PNCSSKDLD-HGVLVVGYGYEGTDSNKDKYWLVKNSWGKEWGMDGYIKIAKDRNNHCGL 324
             +C+ K +  H + ++GYG EG    +  YW+VKNSWG  WG  GY ++A+  N+ CGL
Sbjct: 319 VEDCTEKSMGAHALTIIGYGGEG----ESAYWIVKNSWGTSWGASGYFRLARGVNS-CGL 373

Query: 325 ATAASYPIVN 334
           A     PI+N
Sbjct: 374 ANTVVAPIIN 383


>R07E3.1 CE02295   cysteine proteinase (HINXTON) TR:Q21810
           protein_id:CAA89070.1
          Length = 402

 Score =  139 bits (351), Expect = 2e-33
 Identities = 96/307 (31%), Positives = 154/307 (49%), Gaps = 36/307 (11%)

Query: 40  YGTNEEEWRRAV----WEKNMRMIQLHNGEYSNGKHGFTMEMNAFGDMTNEEFRQIV--N 93
           Y T++E  +R       ++N+    + N E+ + ++G     N   D T+EEF + +   
Sbjct: 101 YATSQESLKRLNAYYNTDENIANWNIQN-EHGSAEYGH----NDMSDWTDEEFEKTLLPK 155

Query: 94  GYRHQKHKKGRLFQEPLMLQI-----------PKTVDWREKGCVTPVKNQGQCGSCWAFS 142
            +  + HK+   F EP+   +           P   DWR+K  +TPVK QGQCGSCWAF+
Sbjct: 156 SFYKRLHKEAE-FIEPIPESLTAKKGESSSPFPDFFDWRDKNVITPVKAQGQCGSCWAFA 214

Query: 143 ASGCLEGQMFLKTGKLISLSEQNLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLDSEESY 202
           ++  +E    +  G+  +LSEQ L+DC  D  +  C+GG  D AF+YI  N GL +    
Sbjct: 215 STATVEAAWAIAHGEKRNLSEQTLLDC--DLVDNACDGGDEDKAFRYIHRN-GLANAVDL 271

Query: 203 PYEA-KDGSCKYRAEYAVANDTGFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSS 261
           PY A +   C     +          +   E +++  +   GP+++ M    P ++ Y  
Sbjct: 272 PYVAHRQNGCAVNDHWNTTRIKAAYFLHHDEDSIINWLVNFGPVNIGMAVIQP-MRAYKG 330

Query: 262 GIY--YEPNCSSKDLD-HGVLVVGYGYEGTDSNKDKYWLVKNSWGKEWGMD-GYIKIAKD 317
           G++   E  C ++ +  H +L+ GY   GT    +KYW+VKNSWG  WG++ GYI  A+ 
Sbjct: 331 GVFTPSEYACKNEVIGLHALLITGY---GTSKTGEKYWIVKNSWGNTWGVEHGYIYFARG 387

Query: 318 RNNHCGL 324
             N CG+
Sbjct: 388 -INACGI 393


>Y40H7A.10 CE21821   Cysteine protease (HINXTON) TR:Q9XWA4
           protein_id:CAA22062.1
          Length = 343

 Score =  131 bits (330), Expect = 5e-31
 Identities = 88/284 (30%), Positives = 152/284 (52%), Gaps = 24/284 (8%)

Query: 48  RRAVWEKNMRMIQLHNGEYSNGKHGFTMEMNAFGDMTNEEFRQIVNGYRHQKHKKGRLFQ 107
           R  ++ +N+ +++ +N E + GK   T E+N F D+T EE+++ +   +   H +  L  
Sbjct: 71  RFTIFSRNLDLVERYNKEDA-GK--VTYELNDFSDLTEEEWKKYLMTPKPD-HSEKSLKP 126

Query: 108 EPLM--LQIPKTVDWRE---KGCVTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLISLS 162
           + L+    +P +VDWR       VT +K QG CGSCWAF+ +  +E  + +  G L SLS
Sbjct: 127 KTLIDKKNLPNSVDWRNVNGTNHVTGIKYQGPCGSCWAFATAAAIESAVSISGGGLQSLS 186

Query: 163 EQNLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGSCKYRAEYAVAND 222
            Q L+DC+    +  C GG    A +Y + + G+ +  +YPY      C+      VA  
Sbjct: 187 SQQLLDCT--VVSDKCGGGEPVEALKYAQSH-GITTAHNYPYYFWTTKCRETVP-TVARI 242

Query: 223 TGFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCSSKDLDHGVLVVG 282
           + ++   + E  + + VA  GP+ V  + +    +FY SGI  +P+C ++   H ++V+G
Sbjct: 243 SSWMK-AESEDEMAQIVALNGPMIVCANFATNKNRFYHSGIAEDPDCGTEP-THALIVIG 300

Query: 283 YGYEGTDSNKDKYWLVKNSWGKEWGMDGYIKIAKDRNNHCGLAT 326
           YG +        YW++KN++ K WG  GY+++ +D  N CG+ T
Sbjct: 301 YGPD--------YWILKNTYSKVWGEKGYMRVKRD-VNWCGINT 335


>K02E7.10 CE11640   protease (ST.LOUIS) TR:O17255 protein_id:AAB71030.1
          Length = 299

 Score =  128 bits (321), Expect = 6e-30
 Identities = 81/222 (36%), Positives = 125/222 (55%), Gaps = 18/222 (8%)

Query: 118 VDWREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLK--TGKLISLSEQNLVDCSHDQGN 175
           +DWREKG V PVK+QG+C + +AF+A   +E  M+ K   GKL+S SEQ ++DC++    
Sbjct: 84  LDWREKGIVGPVKDQGKCNASYAFAAIAAIE-SMYAKANNGKLLSFSEQQIIDCAN--FT 140

Query: 176 QGCNGGLMD-FAFQYIKENGGLDSEESYPYEAKD--GSCKYRAEYAVANDTGFVDIPQQE 232
             C   L +  + +++KEN G+ +E  YPY  K+  G C+Y +       T ++D+   E
Sbjct: 141 NPCQENLENVLSNRFLKEN-GVGTEADYPYVGKENVGKCEYDSSKMKLRPT-YIDVYPNE 198

Query: 233 KALMKAVATVGPISVAMDASHPSLQFYSSGIY--YEPNCSSKDLDHGVLVVGYGYEGTDS 290
           +     + T G     M  S PS   Y +GIY   +  C + +    + +VGYG +G   
Sbjct: 199 EWARAHITTFGTGYFRM-RSPPSFFHYKTGIYNPTKEECGNANEARSLAIVGYGKDGA-- 255

Query: 291 NKDKYWLVKNSWGKEWGMDGYIKIAKDRNNHCGLATAASYPI 332
             +KYW+VK S+G  WG  GY+K+A++  N CG+A + S PI
Sbjct: 256 --EKYWIVKGSFGTSWGEHGYMKLARN-VNACGMAESISIPI 294


>Y71H2AR.2 CE22930    (ST.LOUIS) protein_id:AAK29985.1
          Length = 345

 Score =  120 bits (301), Expect = 1e-27
 Identities = 81/214 (37%), Positives = 114/214 (52%), Gaps = 14/214 (6%)

Query: 118 VDWREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLK--TGKLISLSEQNLVDCSHDQGN 175
           +DWREKG V PVK+QG+C +  AF+ +  +E  M+ K   G L+S SEQ L+DC +DQG 
Sbjct: 86  LDWREKGIVGPVKDQGKCNASHAFAITSSIE-SMYAKATNGTLLSFSEQQLIDC-NDQGY 143

Query: 176 QGCNGGLMDFAFQYIKENGGLDSEESYPYEAK-DGSCKYRAEYAVANDTGFVDIPQQEKA 234
           +GC       A  Y+  + G+++E  YPY  K +  C + +  +  +    V     E  
Sbjct: 144 KGCEEQFAMNAIGYLATH-GIETEADYPYVDKTNEKCTFDSTKSKIHLKKGVVAEGNEVL 202

Query: 235 LMKAVATVGPISVAMDASHPSLQFYSSGIYYE--PNCSSKDLDHGVLVVGYGYEGTDSNK 292
               V   GP    M A  PSL  Y  GIY      C+S      +++VGYG EG    +
Sbjct: 203 GKVYVTNYGPAFFTMRAP-PSLYDYKIGIYNPSIEECTSTHEIRSMVIVGYGIEG----E 257

Query: 293 DKYWLVKNSWGKEWGMDGYIKIAKDRNNHCGLAT 326
            KYW+VK S+G  WG  GY+K+A+D  N C +AT
Sbjct: 258 QKYWIVKGSFGTSWGEQGYMKLARD-VNACAMAT 290


>Y51A2D.8 CE19204   Cysteine proteases (2 domains) (HINXTON) TR:Q9XXQ7
           protein_id:CAA16407.1
          Length = 386

 Score =  108 bits (271), Expect = 4e-24
 Identities = 64/203 (31%), Positives = 99/203 (48%), Gaps = 11/203 (5%)

Query: 126 VTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLISLSEQNLVDCSHDQGNQGCNGGLMDF 185
           V P+K+QGQC  CW F+ +  +E      +GK  SLS+Q + DC   +G  GC GG +  
Sbjct: 164 VGPIKDQGQCACCWGFAVTALVETVYAAHSGKFKSLSDQEVCDCG-TEGTPGCKGGSLTL 222

Query: 186 AFQYIKENGGLDSEESYPYE---AKDG-SCKYRAEYAVANDTGF---VDIPQQEKALMKA 238
             QY+K+  GL  +E YPY+   A  G  C+ R    +     F   V  P++ +  +  
Sbjct: 223 GVQYVKKY-GLSGDEDYPYDQNRANQGRRCRLRETDRIVPARAFNFAVINPRRAEEQIIQ 281

Query: 239 VATVGPISVAMDAS-HPSLQFYSSGIYYEPNCSSKDLDHGVLVVGYG-YEGTDSNKDKYW 296
           V T   + VA+        + Y  G+  E +C      H   +VGY   E +      YW
Sbjct: 282 VLTEWKVPVAVYFKVGDQFKEYKEGVIIEDDCRRATQWHAGAIVGYDTVEDSRGRSHDYW 341

Query: 297 LVKNSWGKEWGMDGYIKIAKDRN 319
           ++KNSWG +W   GY+++ + R+
Sbjct: 342 IIKNSWGGDWAESGYVRVVRGRD 364


>Y113G7B.15 CE23295    (HINXTON) TR:Q9U2X1 protein_id:CAB54334.1
          Length = 328

 Score = 99.4 bits (246), Expect = 3e-21
 Identities = 87/321 (27%), Positives = 127/321 (39%), Gaps = 47/321 (14%)

Query: 36  HRRLYGTNEEEWRR-AVWEKNMRMIQLHNGEYSNGKHGFTMEMNAFGDMTNEEFRQIVNG 94
           H++ Y T  E+ RR A + KN + IQ  N +        T   N F D   +E     N 
Sbjct: 3   HKKHYRTPAEKDRRLAHFAKNHQKIQELNAKARREGRNVTFGWNKFADKNRQEL-SARNS 61

Query: 95  YRHQKHKKGRLFQEPLMLQ----------------IPKTVDWRE-----KGCVTPVKNQG 133
             H K+       +P   +                IP   D R+        V PVK+Q 
Sbjct: 62  KIHPKNHTDLPIYKPRHPRGSRNHHNKRSKRQSGDIPDYFDLRDIYVDGSPVVGPVKDQE 121

Query: 134 QCGSCWAFSASGCLEGQMFLKTGKLISLSEQNLVDCSHDQGNQGCNGGLMDFAFQYIKEN 193
           QCG CWAF+ +   E    L +    SLS+Q + DC+      GC GG      + +   
Sbjct: 122 QCGCCWAFATTAITEAANTLYSKSFTSLSDQEICDCADSGDTPGCVGGDPRNGLKMVHLR 181

Query: 194 GGLDSEESYPYEA----KDGSCKYRAEYAVAN---------DTGFVDIPQQEKALMKAVA 240
            G  S+  YPYE       G+C    +  V           D  + +    E   +  + 
Sbjct: 182 -GQSSDGDYPYEEYRANTTGNCVGDEKSTVIQPETLNVYRFDQDYAEEDIMENLYLNHIP 240

Query: 241 TVGPISVAMDASHPSLQFYSSGIYYEPNCSSKDLD--HGVLVVGYGYEGTDSNKDKYWLV 298
           T     V       + ++Y+SG+    +C        H V +VGY   GT  +   YWLV
Sbjct: 241 TAVYFRVG-----ENFEWYTSGVLQSEDCYQMTPAEWHSVAIVGY---GTSDDGVPYWLV 292

Query: 299 KNSWGKEWGMDGYIKIAKDRN 319
           +NSW  +WG+ GY+KI +  N
Sbjct: 293 RNSWNSDWGLHGYVKIRRGVN 313


>C50F4.3 CE05468   thiol protease (HINXTON) TR:Q18740 protein_id:CAA94738.1
          Length = 374

 Score = 98.2 bits (243), Expect = 6e-21
 Identities = 80/270 (29%), Positives = 119/270 (43%), Gaps = 27/270 (10%)

Query: 71  HGFTMEMNAFGDMTNEEFRQIVNGYRHQKHKKG-------RLFQEPLMLQIPKTVDWREK 123
           H     +N F D++ +E   + + +   K+           L  +  M  +PKT D R K
Sbjct: 90  HDTKYGINKFSDLSKKEIHGMYSKFGPPKNNTNVPKFNLKNLRVKRQMEGLPKTFDLRNK 149

Query: 124 GC-----VTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLISLSEQNLVDCSHDQGNQGC 178
                  + P+K Q  C  CW F+A+   E  + +   K ++LSEQ + DC+   G  GC
Sbjct: 150 KVGGHYIIGPIKTQDSCACCWGFAATAVAEAALTVHLKKAMNLSEQEVCDCAPKHG-PGC 208

Query: 179 NGGLMDFAFQYIKENGGLDSEESYPYEAKD----GSC---KYRAEY-AVANDTGFVDIPQ 230
           NGG      +YIKE  GL   + YP+        G C   KY  E   +  D   +D   
Sbjct: 209 NGGDPVDGLEYIKEM-GLTGGKEYPFNVNRSTQLGRCESEKYDRELNPLELDYYAIDPFN 267

Query: 231 QEKALMKAVATVG-PISVAMDASHPSLQFYSSGIYYEPNCSSKDLD--HGVLVVGYGYEG 287
            E  +   +  +  PISVA   +  SL  Y SGI    +C  +     H   +VGYG   
Sbjct: 268 AEYQMTHHLYLLNLPISVAF-RTGASLSSYLSGILELADCDDEKGGHWHSGAIVGYGTTK 326

Query: 288 TDSNKD-KYWLVKNSWGKEWGMDGYIKIAK 316
             + +   YW+ +NSW  +WG DGY +I +
Sbjct: 327 NSAGRTVDYWIFRNSWWTDWGDDGYARIVR 356


>F26E4.3 CE17714   cysteine protease (HINXTON) TR:P90850
           protein_id:CAB03007.1
          Length = 491

 Score = 97.8 bits (242), Expect = 8e-21
 Identities = 68/241 (28%), Positives = 113/241 (46%), Gaps = 35/241 (14%)

Query: 113 QIPKTVDWREKG--CVTPVKNQGQCGSCWAFSASGCLEGQM-FLKTGKLIS-LSEQNLVD 168
           ++P+  D R+K    + PV +QG CGS W+ S +     ++  +  G++ S LS Q L+ 
Sbjct: 222 ELPEHFDARDKWGPLIHPVADQGDCGSSWSVSTTAISSDRLAIISEGRINSTLSSQQLLS 281

Query: 169 CSHDQGNQGCNGGLMDFAFQYIKENGGLDSEESYPYEA----KDGSCKY----------- 213
           C+  +  +GC GG +D A+ YI++ G +  +  YPY +    + G C             
Sbjct: 282 CNQHR-QKGCEGGYLDRAWWYIRKLGVV-GDHCYPYVSGQSREPGHCLIPKRDYTNRQGL 339

Query: 214 RAEYAVANDTGFVDIP-----QQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPN 268
           R      + T F   P      +E+ +   + T GP+       H     Y+ G+Y   +
Sbjct: 340 RCPSGSQDSTAFKMTPPYKVSSREEDIQTELMTNGPVQATF-VVHEDFFMYAGGVYQHSD 398

Query: 269 CSSK-------DLDHGVLVVGYGYEGTDSNKDKYWLVKNSWGKEWGMDGYIKIAKDRNNH 321
            +++       +  H V V+G+G + +     KYWL  NSWG +WG DGY K+ +   NH
Sbjct: 399 LAAQKGASSVAEGYHSVRVLGWGVDHSTGKPIKYWLCANSWGTQWGEDGYFKVLRG-ENH 457

Query: 322 C 322
           C
Sbjct: 458 C 458


>F15D4.4 CE28917   cysteine protease (HINXTON) TR:Q93512
           protein_id:CAB02487.1
          Length = 622

 Score = 96.7 bits (239), Expect = 2e-20
 Identities = 65/219 (29%), Positives = 102/219 (45%), Gaps = 35/219 (15%)

Query: 117 TVDWREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLISLSEQNLVDC------S 170
           TVDWR    + P+ +Q  CG CWAFS    +E    ++     SLS Q L+ C      +
Sbjct: 226 TVDWRP--FLKPILDQSTCGGCWAFSMISMIESFFAIQGYNTSSLSVQQLLTCDTKVDST 283

Query: 171 HDQGNQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGSCK-------------YRAEY 217
           +   N GC GG    A  Y++ +   D+    P++ +D SC              +   Y
Sbjct: 284 YGLANVGCKGGYFQIAGSYLEVSAARDAS-LIPFDLEDTSCDSSFFPPVVPTILLFDDGY 342

Query: 218 AVANDTGFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCSSKDLDHG 277
              N T    I  ++    K     GPI+V M A+ P +  YS G+Y + +C +  ++H 
Sbjct: 343 ISGNFTAAQLITMEQNIEDKV--RKGPIAVGM-AAGPDIYKYSEGVY-DGDCGTI-INHA 397

Query: 278 VLVVGYGYEGTDSNKDKYWLVKNSWGKEWGMDGYIKIAK 316
           V++VG+         D YW+++NSWG  WG  GY ++ +
Sbjct: 398 VVIVGF--------TDDYWIIRNSWGASWGEAGYFRVKR 428


>C32B5.7 CE08515   cathepsin-like peptidase (ST.LOUIS) TR:P91111
           protein_id:AAB37963.1
          Length = 250

 Score = 90.1 bits (222), Expect = 2e-18
 Identities = 63/191 (32%), Positives = 98/191 (50%), Gaps = 18/191 (9%)

Query: 118 VDWREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLISLSEQNLVDCSHDQGNQG 177
           +DWR++G V PVK+QG C + +AF+A   +E    +  G+L+S SEQ ++DC    G   
Sbjct: 72  LDWRDEGVVGPVKDQGNCNASYAFAAISAIESMYAIANGQLLSFSEQQIIDC---LGGCA 128

Query: 178 CNGGLMDFAFQYIKENGGLDSEESYPYEA-KDGSCKY--RAEYAVANDTGFVDIPQQEKA 234
                M  A  Y+ E  G+++   YP+   K+  C+Y  +  Y + +DT   D+  +  A
Sbjct: 129 IESDPM-MAMTYL-ERKGIETYTDYPFVGKKNEKCEYDSKKAYLILDDT--YDMSDESLA 184

Query: 235 LMKAVATVGPISVAMDASHPSLQFYSSGIY--YEPNCSSKDLDHGVLVVGYGYEGTDSNK 292
           L+  +   GP    M+ + PS   Y SGIY   E  C S +    + +VGYG    +   
Sbjct: 185 LV-FIDERGPGLFTMN-TPPSFFNYKSGIYNPTEEECKSTNEKRALTIVGYG----NDKG 238

Query: 293 DKYWLVKNSWG 303
             YW+VK S+G
Sbjct: 239 QNYWIVKGSFG 249


>Y51A2D.1 CE18411   Cysteine proteases (2 domains) (HINXTON) TR:O62484
           protein_id:CAA16404.1
          Length = 382

 Score = 87.8 bits (216), Expect = 8e-18
 Identities = 87/350 (24%), Positives = 139/350 (38%), Gaps = 76/350 (21%)

Query: 31  QWKSTHRRLYGTNEEEWRRA---VWEKNMRMIQLHNGEYSNGKHGFTMEMNAFGDMTNEE 87
           ++K    R Y +  E   R    V  +N  +++L+      G++     +N F D+T  E
Sbjct: 46  EFKKKFSRTYKSEAENQLRLQNFVKSRN-NVVRLNKNAQKAGRNS-NFAVNQFSDLTTSE 103

Query: 88  FRQIV---------NGYRHQKHKK--GRLFQEPLMLQIPKTVDWREKGC-----VTPVKN 131
             Q +         N   H+  KK  G+   +    +  +  D R +       V P+KN
Sbjct: 104 LHQRLSRFPPNLTENSVFHKNFKKLLGKTRTKRQNSEFARNFDLRSQKVNGRYIVGPIKN 163

Query: 132 QGQCGSCWAFSASGCLEG------------------------------QMFLKTGKLISL 161
           QGQC  CW F+ +  LE                               +   K    +S 
Sbjct: 164 QGQCACCWGFAVTAMLETIYAVNVGRFKLMSHIPALAPNFSDFDFFFFEFLAKLNMFLSF 223

Query: 162 SEQNLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGSCKYRAEYAVAN 221
           S+Q + DC+ D    GC GG + +  +Y   N GL SE  YP   ++ + +     A+ +
Sbjct: 224 SDQEMCDCATDGTKAGCAGGGLMWGVEY-AINNGLASEFDYPEFDQNRATRPGTCEAMDD 282

Query: 222 DTGFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCS-SKDLDHGVLV 280
           D                  T  P++ A  A    LQ Y SG+    +C  +  + H   +
Sbjct: 283 D-----------------KTFPPVNFA--AGTAFLQ-YKSGVLVTEDCDLAGTVWHAGAI 322

Query: 281 VGYGYEG-TDSNKDKYWLVKNSWG-KEWGMDGYIKIAKDRNNHCGLATAA 328
           VGYG E        ++W++KNSWG   WG  GY+K+ + + N CG+   A
Sbjct: 323 VGYGEENDLRGRSQRFWIMKNSWGVSGWGTGGYVKLIRGK-NWCGIERGA 371


>C52E4.1 CE08943  locus:cpr-1 cathepsin-like cysteine protease (HINXTON)
           TR:Q18783 protein_id:CAB01410.1
          Length = 340

 Score = 87.4 bits (215), Expect = 1e-17
 Identities = 66/252 (26%), Positives = 110/252 (43%), Gaps = 39/252 (15%)

Query: 107 QEPLMLQIPKTVD----WREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLKT--GKLIS 160
           QE ++  +P T D    W E   +  +++Q  CGSCWAF A+  +  +  ++T   +   
Sbjct: 89  QEVVLASVPATFDSRTQWSECKSIKLIRDQATCGSCWAFGAAEMISDRTCIETKGAQQPI 148

Query: 161 LSEQNLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLDSEESY-----PY----------- 204
           +S  +L+ C       GC GG    A ++    G +   + +     PY           
Sbjct: 149 ISPDDLLSCCGSSCGNGCEGGYPIQALRWWDSKGVVTGGDYHGAGCKPYPIAPCTSGNCP 208

Query: 205 EAKDGSCKYRAEY----AVANDTGF----VDIPQQEKALMKAVATVGPISVAMDASHPSL 256
           E+K  SC    +     A A D  F      +P+   ++   +   GP+  A    +   
Sbjct: 209 ESKTPSCSMSCQSGYSTAYAKDKHFGVSAYAVPKNAASIQAEIYANGPVEAAFSV-YEDF 267

Query: 257 QFYSSGIYYEPNCSSKDLD-HGVLVVGYGYEGTDSNKDKYWLVKNSWGKEWGMDGYIKIA 315
             Y SG+Y   + + K L  H + ++G+G E    +   YWLV NSWG  WG  G+ KI 
Sbjct: 268 YKYKSGVY--KHTAGKYLGGHAIKIIGWGTE----SGSPYWLVANSWGVNWGESGFFKIY 321

Query: 316 KDRNNHCGLATA 327
           +  ++ CG+ +A
Sbjct: 322 RG-DDQCGIESA 332


>F32B5.8 CE09855   cysteine proteinase (ST.LOUIS) TR:O01850
           protein_id:AAB54210.1
          Length = 427

 Score = 85.9 bits (211), Expect = 3e-17
 Identities = 73/261 (27%), Positives = 123/261 (46%), Gaps = 36/261 (13%)

Query: 88  FRQIVNGYRHQKHKKGRLFQEPLMLQIPKTVDWREKGCVTPV---KNQG---QCGSCWAF 141
           ++Q    + H+++ +    ++     +PKT DWR+   +      +NQ     CGSCWAF
Sbjct: 160 YKQTGRVFEHKRYDRIYETEDFDSEDLPKTWDWRDANGINYASADRNQHIPQYCGSCWAF 219

Query: 142 SASGCLEGQMFLKTGKL---ISLSEQNLVDCSHDQGNQGC-NGGLMDFAFQYIKENGGLD 197
            A+  L  ++ +K         LS Q ++DCS   G   C  GG     ++Y  E+G + 
Sbjct: 220 GATSALADRINIKRKNAWPQAYLSVQEVIDCS---GAGTCVMGGEPGGVYKYAHEHG-IP 275

Query: 198 SEESYPYEAKDGSCK-YRA-------------EYAVANDTGFVDIPQQEKALMKA-VATV 242
            E    Y+A+DG C  Y                Y +   + +  +   EK  MKA +   
Sbjct: 276 HETCNNYQARDGKCDPYNRCGSCWPGECFSIKNYTLYKVSEYGTVHGYEK--MKAEIYHK 333

Query: 243 GPISVAMDASHPSLQFYSSGIYYEPNCSSKDLDHGVLVVGYGYEGTDSNKDKYWLVKNSW 302
           GPI+  + A+  + + Y+ GIY E   + +D+DH + V G+G +    +  +YW+ +NSW
Sbjct: 334 GPIACGIAATK-AFETYAGGIYKE--VTDEDIDHIISVHGWGVD--HESGVEYWIGRNSW 388

Query: 303 GKEWGMDGYIKIAKDRNNHCG 323
           G+ WG  G+ KI   +  + G
Sbjct: 389 GEPWGEHGWFKIVTSQYKNAG 409


>M04G12.2 CE12424   cysteine protease (HINXTON) TR:P92005
           protein_id:CAB03209.1
          Length = 467

 Score = 83.2 bits (204), Expect = 2e-16
 Identities = 62/228 (27%), Positives = 107/228 (46%), Gaps = 33/228 (14%)

Query: 114 IPKTVDWREKGCV---TPVKNQG---QCGSCWAFSASGCLEGQMFL-KTGK--LISLSEQ 164
           +P   DWR    V   +P +NQ     CGSCW F  +G L  +  + + G+  +  LS Q
Sbjct: 221 LPTGWDWRNVSGVNYCSPTRNQHIPVYCGSCWVFGTTGALNDRFNVARKGRWPMTQLSPQ 280

Query: 165 NLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLD---------SEESYPYEAKDGSCKYRA 215
            ++DC+   G   C GG +    ++ K  G ++         + E  PY  + GSC    
Sbjct: 281 EIIDCN---GKGNCQGGEIGNVLEHAKIQGLVEEGCNVYRATNGECNPYH-RCGSCWPNE 336

Query: 216 EYAVANDTGFV-----DIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCS 270
            +++ N T +       +  ++K +M  +   GPI+ A+ A+      Y  G+Y E   S
Sbjct: 337 CFSLTNYTRYYVKDYGQVQGRDK-IMSEIKKGGPIACAIGATKKFEYEYVKGVYSEK--S 393

Query: 271 SKDLDHGVLVVGYGYEGTDSNKDKYWLVKNSWGKEWGMDGYIKIAKDR 318
             + +H + + G+G    D N  +YW+ +NSWG+ WG  G+ ++   +
Sbjct: 394 DLESNHIISLTGWG---VDENGVEYWIARNSWGEAWGELGWFRVVTSK 438


>Y71H2AM.3 CE26272    (ST.LOUIS) protein_id:AAK29976.1
          Length = 716

 Score = 75.5 bits (184), Expect = 4e-14
 Identities = 60/169 (35%), Positives = 83/169 (48%), Gaps = 25/169 (14%)

Query: 118 VDWREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLK--TGKLISLSEQNLVDCSHDQGN 175
           +DWR+KG V PVK+QG+C +  AF+ S  +E  M+ K   G L+S SEQ L+DC  D G 
Sbjct: 86  LDWRDKGIVGPVKDQGKCNASHAFAISSSIE-SMYAKATNGSLLSFSEQQLIDCD-DHGF 143

Query: 176 QGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGSCKYRAEYAVANDTGFVDIPQQEKAL 235
           +GC       A  Y   + G+++E  YPY  K+          ++N+T       Q K L
Sbjct: 144 KGCEEQPAINAVSYFIFH-GIETEADYPYAGKENG-------KLSNET-------QGKEL 188

Query: 236 MKAVATVGPISVAMDASHPSLQFYSSGIYYE--PNCSSKDLDHGVLVVG 282
              V   GP    M A  PSL  Y  GIY      C+S      +++VG
Sbjct: 189 ---VTNYGPAFFTMRAP-PSLYDYKIGIYNPSIEECTSTHEIRSMVIVG 233


>T10H4.12 CE27590  locus:cpr-3 protease (HINXTON) TR:Q9TW93
           protein_id:CAB61024.2
          Length = 370

 Score = 74.7 bits (182), Expect = 7e-14
 Identities = 60/250 (24%), Positives = 102/250 (40%), Gaps = 42/250 (16%)

Query: 102 KGRLFQEPLMLQIPKTVDWREK----GCVTPVKNQGQCGSCWAFSASGCLEGQMFLKTG- 156
           +G +  EPL    P T D REK      +  ++NQ  CGSCWAF A+  +  ++ +++  
Sbjct: 84  RGEIVPEPL----PDTFDAREKWPDCNTIKLIRNQATCGSCWAFGAAEVISDRVCIQSNG 139

Query: 157 -KLISLSEQNLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLDSEE-----SYPY------ 204
            +   +S ++++ C       GC GG    A ++   +G +   +       PY      
Sbjct: 140 TQQPVISVEDILSCCGTTCGYGCKGGYSIEALRFWASSGAVTGGDYGGHGCMPYSFAPCT 199

Query: 205 ----EAKDGSCK-----------YRAEYAVANDTGFVDIPQQEKALMKAVATVGPISVAM 249
               E+   SCK           Y+ +         V   +    +   +   GP+  + 
Sbjct: 200 KNCPESTTPSCKTTCQSSYKTEEYKKDKHYGASAYKVTTTKSVTEIQTEIYHYGPVEASY 259

Query: 250 DASHPSLQFYSSGIYYEPNCSSKDLDHGVLVVGYGYEGTDSNKDKYWLVKNSWGKEWGMD 309
              +     Y SG+Y+  +       H V ++G+G E    N   YWL+ NSWG  +G  
Sbjct: 260 KV-YEDFYHYKSGVYHYTSGKLVG-GHAVKIIGWGVE----NGVDYWLIANSWGTSFGEK 313

Query: 310 GYIKIAKDRN 319
           G+ KI +  N
Sbjct: 314 GFFKIRRGTN 323


>F36D3.9 CE15973   cysteine protease (HINXTON) TR:O45466
           protein_id:CAB04322.1
          Length = 345

 Score = 71.6 bits (174), Expect = 6e-13
 Identities = 63/235 (26%), Positives = 98/235 (40%), Gaps = 40/235 (17%)

Query: 120 WREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLIS--LSEQNLVDCSHDQGNQG 177
           W +   +  ++ Q  CGSCWAFS +  +  +  + +       +S  +L+ C      +G
Sbjct: 111 WPQCKSMKLIREQSNCGSCWAFSTAEVISDRTCIASNGTQQPIISPTDLLTCCGMSCGEG 170

Query: 178 CNGGLMDFAFQYIKENGGLDSEE-------SYPYEAKDG-------------SCK--YRA 215
           C+GG    AFQ+    G +   +        YP    +              SC+  YR 
Sbjct: 171 CDGGFPYRAFQWWARRGVVTGGDYLGTGCKPYPIRPCNSDNCVNLQTPPCRLSCQPGYRT 230

Query: 216 EYAVANDTGF-----VDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCS 270
            Y   ND  +       +P+   A+   +   GP+ VA    +   + Y SGIY      
Sbjct: 231 TYT--NDKNYGSNSAYPVPRTVAAIQADIYYNGPV-VAAFIVYEDFEKYKSGIYRHIAGR 287

Query: 271 SKDLDHGVLVVGYGYE-GTDSNKDKYWLVKNSWGKEWGMDGYIKIAKDRNNHCGL 324
           SK   H V ++G+G E GT      YWL  NSWG +WG  G  +I +   + CG+
Sbjct: 288 SKG-GHAVKLIGWGTERGTP-----YWLAVNSWGSQWGESGTFRILRG-VDECGI 335


  Database: /data_2/jason/blastdb/wormpep62
    Posted date:  Sep 3, 2001  2:17 PM
  Number of letters in database: 8,813,425
  Number of sequences in database:  20,085
  
Lambda     K      H
   0.317    0.134    0.426 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6241552
Number of Sequences: 20085
Number of extensions: 276768
Number of successful extensions: 629
Number of sequences better than 1.0e-10: 20
Number of HSP's better than  0.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 578
Number of HSP's gapped (non-prelim): 20
length of query: 334
length of database: 8,813,425
effective HSP length: 44
effective length of query: 290
effective length of database: 7,929,685
effective search space: 2299608650
effective search space used: 2299608650
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 156 (64.7 bits)
BLASTP 2.1.3 [Apr-11-2001]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= PAPA_CARPA
         (345 letters)

Database: /data_2/jason/blastdb/wormpep62
           20,085 sequences; 8,813,425 total letters

Searching..................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

R09F10.1 CE28755   peptidase (ST.LOUIS) TR:Q23030 protein_id...   174  7e-44
T03E6.7 CE16333   cathepsin-like protease (HINXTON) TR:O4573...   171  5e-43
Y40H7A.10 CE21821   Cysteine protease (HINXTON) TR:Q9XWA4 pr...   160  8e-40
F41E6.6 CE10254   cysteine protease and a protease inhibitor...   156  2e-38
Y51A2D.8 CE19204   Cysteine proteases (2 domains) (HINXTON) ...   127  1e-29

>R09F10.1 CE28755   peptidase (ST.LOUIS) TR:Q23030 protein_id:AAC69091.2
          Length = 383

 Score =  174 bits (441), Expect = 7e-44
 Identities = 107/348 (30%), Positives = 173/348 (48%), Gaps = 18/348 (5%)

Query: 7   ISKLLFVAICLFVYMGLSFGDFSIVGYSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKI 66
           +++L    + L + + LSF  F  + +   +L       Q+F  ++LK ++ Y +++E  
Sbjct: 45  LTQLFSGLVLLTMLILLSFFVFQRLNHKMENLKHE----QMFNDFILKFDRKYTSVEEFE 100

Query: 67  YRFEIFKDNLKYIDETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEV 126
           YR++IF  N+   +   ++N    L +N F D +++E ++    +    Y      +E  
Sbjct: 101 YRYQIFLRNVIEFEAEEERNLGLDLDVNEFTDWTDEELQKMVQENKYTKYDFDTPKFEGS 160

Query: 127 LNDGDVNIPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQEL 186
             +  V  P  +DWR++G +TP+KNQG CGSCWAF+ V ++E    I+ G L   SEQE+
Sbjct: 161 YLETGVIRPASIDWREQGKLTPIKNQGQCGSCWAFATVASVEAQNAIKKGKLVSLSEQEM 220

Query: 187 LDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQV 246
           +DCD R+ GC+GGY   A++ V + G+     YPY  ++      ++       D  R +
Sbjct: 221 VDCDGRNNGCSGGYRPYAMKFVKENGLESEKEYPYSALKHDQCFLKENDTRVFIDDFRML 280

Query: 247 QPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIF---VGPCGNKV--DHAVAAVGYGP 301
               E    +     PV+  +    K    YR GIF   V  C  K    HA+  +GYG 
Sbjct: 281 SNNEEDIANWVGTKGPVTFGMNVV-KAMYSYRSGIFNPSVEDCTEKSMGAHALTIIGYGG 339

Query: 302 N----YILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN 345
                Y ++KNSWGT WG +GY R+ RG  +    CGL  +   P+ N
Sbjct: 340 EGESAYWIVKNSWGTSWGASGYFRLARGVNS----CGLANTVVAPIIN 383


>T03E6.7 CE16333   cathepsin-like protease (HINXTON) TR:O45734
           protein_id:CAB07275.1
          Length = 337

 Score =  171 bits (434), Expect = 5e-43
 Identities = 107/319 (33%), Positives = 163/319 (50%), Gaps = 25/319 (7%)

Query: 42  ERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKKNN----SYWLGLNVFA 97
           E  I+ ++ +    +K Y   +E+ Y  E F  N+ +I+  N+ +     ++ +GLN  A
Sbjct: 26  ESAIEKWDDYKEDFDKEYSESEEQTY-MEAFVKNMIHIENHNRDHRLGRKTFEMGLNHIA 84

Query: 98  DMSNDEFKEK--YTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKGAVTPVKNQGSC 155
           D+   ++++   Y      +      S+    N   V +P+ VDWR    VT VKNQG C
Sbjct: 85  DLPFSQYRKLNGYRRLFGDSRIKNSSSFLAPFN---VQVPDEVDWRDTHLVTDVKNQGMC 141

Query: 156 GSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRR--SYGCNGGYPWSALQLVA-QYG 212
           GSCWAFSA   +EG    + G L   SEQ L+DC  +  ++GCNGG    A + +   +G
Sbjct: 142 GSCWAFSATGALEGQHARKLGQLVSLSEQNLVDCSTKYGNHGCNGGLMDQAFEYIRDNHG 201

Query: 213 IHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQ-PVSVVLEAAG 271
           +    +YPY+G    C   +K    A   G       +E  L  ++A Q P+S+ ++A  
Sbjct: 202 VDTEESYPYKGRDMKCHFNKK-TVGADDKGYVDTPEGDEEQLKIAVATQGPISIAIDAGH 260

Query: 272 KDFQLYRGGIFVGP--CGNKVDHAVAAVGYGP-----NYILIKNSWGTGWGENGYIRIKR 324
           + FQLY+ G++        ++DH V  VGYG      +Y ++KNSWG GWGE GYIRI R
Sbjct: 261 RSFQLYKKGVYYDEECSSEELDHGVLLVGYGTDPEHGDYWIVKNSWGAGWGEKGYIRIAR 320

Query: 325 GTGNSYGVCGLYTSSFYPV 343
              N    CG+ T + YP+
Sbjct: 321 NRNNH---CGVATKASYPL 336


>Y40H7A.10 CE21821   Cysteine protease (HINXTON) TR:Q9XWA4
           protein_id:CAA22062.1
          Length = 343

 Score =  160 bits (406), Expect = 8e-40
 Identities = 100/295 (33%), Positives = 153/295 (50%), Gaps = 15/295 (5%)

Query: 48  FESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKKN-NSYWLGLNVFADMSNDEFKE 106
           F+++++K+ + Y N  E + RF IF  NL  ++  NK++       LN F+D++ +E+K 
Sbjct: 51  FQNFLVKYLREYPNEYEIVKRFTIFSRNLDLVERYNKEDAGKVTYELNDFSDLTEEEWK- 109

Query: 107 KYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKGA---VTPVKNQGSCGSCWAFSA 163
           KY  +   +++   L  + +++    N+P  VDWR       VT +K QG CGSCWAF+ 
Sbjct: 110 KYLMTPKPDHSEKSLKPKTLIDKK--NLPNSVDWRNVNGTNHVTGIKYQGPCGSCWAFAT 167

Query: 164 VVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEG 223
              IE  + I  G L   S Q+LLDC   S  C GG P  AL+    +GI   + YPY  
Sbjct: 168 AAAIESAVSISGGGLQSLSSQQLLDCTVVSDKCGGGEPVEALKYAQSHGITTAHNYPYYF 227

Query: 224 VQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFV 283
               C  RE  P  A+     + +  +E A + ++ N P+ V    A    + Y  GI  
Sbjct: 228 WTTKC--RETVPTVARISSWMKAESEDEMAQIVAL-NGPMIVCANFATNKNRFYHSGIAE 284

Query: 284 GP-CGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYT 337
            P CG +  HA+  +GYGP+Y ++KN++   WGE GY+R+KR        CG+ T
Sbjct: 285 DPDCGTEPTHALIVIGYGPDYWILKNTYSKVWGEKGYMRVKR----DVNWCGINT 335


>F41E6.6 CE10254   cysteine protease and a protease inhibitor (ST.LOUIS)
           TR:O16454 protein_id:AAB65956.1
          Length = 498

 Score =  156 bits (395), Expect = 2e-38
 Identities = 110/327 (33%), Positives = 156/327 (47%), Gaps = 51/327 (15%)

Query: 48  FESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKKNNSYWL-GLNVFADMSNDEFKE 106
           F  ++ +H K Y N  E + RF +FK N K I E  K      + G   F+DM+  EFK+
Sbjct: 174 FLDFVDRHEKKYTNKREVLKRFRVFKKNAKVIRELQKNEQGTAVYGFTKFSDMTTMEFKK 233

Query: 107 -----KYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKGAVTPVKNQGSCGSCWAF 161
                ++   +          ++  +N+ D  +PE  DWR+KGAVT VKNQG+CGSCWAF
Sbjct: 234 IMLPYQWEQPVYPMEQANFEKHDVTINEED--LPESFDWREKGAVTQVKNQGNCGSCWAF 291

Query: 162 SAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSAL---------------- 205
           S    +EG   I    L   SEQEL+DCD    GCNGG P +A                 
Sbjct: 292 STTGNVEGAWFIAKNKLVSLSEQELVDCDSMDQGCNGGLPSNAYKIGKFVVSDNYCFLVF 351

Query: 206 ------QLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGAL-LYSI 258
                 +++   G+   + YPY+G    C    K   A   +G  ++ P++E  +  + +
Sbjct: 352 YHKTTKEIIRMGGLEPEDAYPYDGRGETCHLVRK-DIAVYINGSVEL-PHDEVEMQKWLV 409

Query: 259 ANQPVSVVLEAAGKDFQLYRGG------IFVGPCGNKVDHAVAAVGYGPN----YILIKN 308
              P+S+ L A     Q YR G      IF  P    ++H V  VGYG +    Y ++KN
Sbjct: 410 TKGPISIGLNA--NTLQFYRHGVVHPFKIFCEPF--MLNHGVLIVGYGKDGRKPYWIVKN 465

Query: 309 SWGTGWGENGYIRIKRGTGNSYGVCGL 335
           SWG  WGE GY ++ RG      VCG+
Sbjct: 466 SWGPNWGEAGYFKLYRGK----NVCGV 488


>Y51A2D.8 CE19204   Cysteine proteases (2 domains) (HINXTON) TR:Q9XXQ7
           protein_id:CAA16407.1
          Length = 386

 Score =  127 bits (318), Expect = 1e-29
 Identities = 95/332 (28%), Positives = 148/332 (43%), Gaps = 44/332 (13%)

Query: 37  DLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKKNNSYW----LG 92
           D    E+L + FE +  K+N+ YK+  E   RF  F  +   +D+ N K+ +       G
Sbjct: 32  DRDHPEKLYKAFEDFKKKYNRKYKDESENQQRFNNFVKSYNNVDKLNAKSKAAGYDTQFG 91

Query: 93  LNVFADMSNDEFKEKYTGSIAGNYTTTE-LSYEEVLND---GDVN----------IPEYV 138
           +N F+D+S  EF  + +  +  N T    L++++   D    D+N           P+Y 
Sbjct: 92  INKFSDLSTAEFHGRLSNVVPSNNTGLPMLNFDKKKPDFRAADMNKTRHKRRSTRYPDYF 151

Query: 139 DWRQKGA-----VTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRR- 192
           D R +       V P+K+QG C  CW F+    +E +    +G     S+QE+ DC    
Sbjct: 152 DLRNEKINGRYIVGPIKDQGQCACCWGFAVTALVETVYAAHSGKFKSLSDQEVCDCGTEG 211

Query: 193 SYGCNGGYPWSALQLVAQYGIHYRNTYPYE----GVQRYCRSREKGPYA-AKTDGVRQVQ 247
           + GC GG     +Q V +YG+     YPY+       R CR RE      A+      + 
Sbjct: 212 TPGCKGGSLTLGVQYVKKYGLSGDEDYPYDQNRANQGRRCRLRETDRIVPARAFNFAVIN 271

Query: 248 PYNEGALLYSIANQ---PVSVVLEAAGKDFQLYRGGIFV-GPCGNKVD-HAVAAVGY--- 299
           P      +  +  +   PV+V  +  G  F+ Y+ G+ +   C      HA A VGY   
Sbjct: 272 PRRAEEQIIQVLTEWKVPVAVYFK-VGDQFKEYKEGVIIEDDCRRATQWHAGAIVGYDTV 330

Query: 300 ------GPNYILIKNSWGTGWGENGYIRIKRG 325
                   +Y +IKNSWG  W E+GY+R+ RG
Sbjct: 331 EDSRGRSHDYWIIKNSWGGDWAESGYVRVVRG 362


>R07E3.1 CE02295   cysteine proteinase (HINXTON) TR:Q21810
           protein_id:CAA89070.1
          Length = 402

 Score =  114 bits (286), Expect = 7e-26
 Identities = 90/309 (29%), Positives = 139/309 (44%), Gaps = 41/309 (13%)

Query: 54  KHNKIYKNIDEKIYRFEIFKDNLKYIDETNKKNN--SYWLGLNVFADMSNDEFKEKYTGS 111
           K +K Y    E + R   + +  + I   N +N   S   G N  +D +++EF++     
Sbjct: 96  KFDKSYATSQESLKRLNAYYNTDENIANWNIQNEHGSAEYGHNDMSDWTDEEFEKTLLPK 155

Query: 112 IAGNYTTTELSYEEVL--------NDGDVNIPEYVDWRQKGAVTPVKNQGSCGSCWAFSA 163
                   E  + E +         +     P++ DWR K  +TPVK QG CGSCWAF++
Sbjct: 156 SFYKRLHKEAEFIEPIPESLTAKKGESSSPFPDFFDWRDKNVITPVKAQGQCGSCWAFAS 215

Query: 164 VVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEG 223
             T+E    I  G     SEQ LLDCD     C+GG    A + + + G+      PY  
Sbjct: 216 TATVEAAWAIAHGEKRNLSEQTLLDCDLVDNACDGGDEDKAFRYIHRNGLANAVDLPYVA 275

Query: 224 VQR--------YCRSREKGPYAAKTDGVRQVQPYNEGALLYSIAN-QPVSVVLEAAGKDF 274
            ++        +  +R K  Y    D         E +++  + N  PV++ + A  +  
Sbjct: 276 HRQNGCAVNDHWNTTRIKAAYFLHHD---------EDSIINWLVNFGPVNIGM-AVIQPM 325

Query: 275 QLYRGGIFVG---PCGNKVD--HAVAAVGYGPN-----YILIKNSWGTGWG-ENGYIRIK 323
           + Y+GG+F      C N+V   HA+   GYG +     Y ++KNSWG  WG E+GYI   
Sbjct: 326 RAYKGGVFTPSEYACKNEVIGLHALLITGYGTSKTGEKYWIVKNSWGNTWGVEHGYIYFA 385

Query: 324 RGTGNSYGV 332
           RG  N+ G+
Sbjct: 386 RGI-NACGI 393


>C50F4.3 CE05468   thiol protease (HINXTON) TR:Q18740 protein_id:CAA94738.1
          Length = 374

 Score =  114 bits (286), Expect = 7e-26
 Identities = 97/357 (27%), Positives = 152/357 (42%), Gaps = 39/357 (10%)

Query: 6   SISKLLFVAICLFVYMGLSFG-DFSIVGYSQN-DLTSTERLIQLFESWMLKHNKIYKNID 63
           S+  L F+ I +F       G +F    +  N D  + E+L + FE +++K+ + YK+  
Sbjct: 3   SLLALFFIQIFIFTVTSFDVGANFEDSFFEINIDRNNPEKLYKEFEDFIVKYKRNYKDEI 62

Query: 64  EKIYRFEIFKDNLKYIDETNKK----NNSYWLGLNVFADMSNDEFKEKYT--GSIAGNYT 117
           EK +RF+ F      + + NK      +    G+N F+D+S  E    Y+  G    N  
Sbjct: 63  EKKFRFQQFVATHNRVGKMNKAAKKAGHDTKYGINKFSDLSKKEIHGMYSKFGPPKNNTN 122

Query: 118 TTELSYEEVLNDGDVN-IPEYVDWRQKGA-----VTPVKNQGSCGSCWAFSAVVTIEGII 171
             + + + +     +  +P+  D R K       + P+K Q SC  CW F+A    E  +
Sbjct: 123 VPKFNLKNLRVKRQMEGLPKTFDLRNKKVGGHYIIGPIKTQDSCACCWGFAATAVAEAAL 182

Query: 172 KIRTGNLNEYSEQELLDC-DRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQR---- 226
            +        SEQE+ DC  +   GCNGG P   L+ + + G+     YP+  V R    
Sbjct: 183 TVHLKKAMNLSEQEVCDCAPKHGPGCNGGDPVDGLEYIKEMGLTGGKEYPF-NVNRSTQL 241

Query: 227 -YCRS----REKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGI 281
             C S    RE  P       +       +      + N P+SV     G     Y  GI
Sbjct: 242 GRCESEKYDRELNPLELDYYAIDPFNAEYQMTHHLYLLNLPISVAFR-TGASLSSYLSGI 300

Query: 282 F-VGPCGNKVD---HAVAAVGYGP---------NYILIKNSWGTGWGENGYIRIKRG 325
             +  C ++     H+ A VGYG          +Y + +NSW T WG++GY RI RG
Sbjct: 301 LELADCDDEKGGHWHSGAIVGYGTTKNSAGRTVDYWIFRNSWWTDWGDDGYARIVRG 357


>F15D4.4 CE28917   cysteine protease (HINXTON) TR:Q93512
           protein_id:CAB02487.1
          Length = 622

 Score =  110 bits (276), Expect = 1e-24
 Identities = 84/290 (28%), Positives = 127/290 (42%), Gaps = 34/290 (11%)

Query: 64  EKIYRFEIFKDNLKYIDETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIA------GNYT 117
           E + RF ++    K +DE    N  Y LG++ +  MS ++F     G +A         T
Sbjct: 150 EGLKRFNVYSKVKKEVDE---HNIMYELGMSSYK-MSTNQFSVALDGEVAPLTLNLDALT 205

Query: 118 TTELSYEEVLNDGDVNIPE-YVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTG 176
            T       ++       E  VDWR    + P+ +Q +CG CWAFS +  IE    I+  
Sbjct: 206 PTATVIPATISSRKKRDTEPTVDWRP--FLKPILDQSTCGGCWAFSMISMIESFFAIQGY 263

Query: 177 NLNEYSEQELLDCDRR--------SYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYC 228
           N +  S Q+LL CD +        + GC GGY   A   +        +  P++     C
Sbjct: 264 NTSSLSVQQLLTCDTKVDSTYGLANVGCKGGYFQIAGSYLEVSAARDASLIPFDLEDTSC 323

Query: 229 RSREKGP-----------YAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLY 277
            S    P           Y +      Q+    +  +   +   P++V + AAG D   Y
Sbjct: 324 DSSFFPPVVPTILLFDDGYISGNFTAAQLITMEQN-IEDKVRKGPIAVGM-AAGPDIYKY 381

Query: 278 RGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTG 327
             G++ G CG  ++HAV  VG+  +Y +I+NSWG  WGE GY R+KR  G
Sbjct: 382 SEGVYDGDCGTIINHAVVIVGFTDDYWIIRNSWGASWGEAGYFRVKRTPG 431


>Y113G7B.15 CE23295    (HINXTON) TR:Q9U2X1 protein_id:CAB54334.1
          Length = 328

 Score =  103 bits (256), Expect = 2e-22
 Identities = 89/312 (28%), Positives = 132/312 (41%), Gaps = 40/312 (12%)

Query: 53  LKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKK----NNSYWLGLNVFADMSNDEFKEKY 108
           + H K Y+   EK  R   F  N + I E N K      +   G N FAD +  E   + 
Sbjct: 1   MHHKKHYRTPAEKDRRLAHFAKNHQKIQELNAKARREGRNVTFGWNKFADKNRQELSARN 60

Query: 109 TGSIAGNYTTTELSYEEVLNDGDVN------------IPEYVDWRQ-----KGAVTPVKN 151
           +     N+T   + Y+     G  N            IP+Y D R         V PVK+
Sbjct: 61  SKIHPKNHTDLPI-YKPRHPRGSRNHHNKRSKRQSGDIPDYFDLRDIYVDGSPVVGPVKD 119

Query: 152 QGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDC--DRRSYGCNGGYPWSALQLVA 209
           Q  CG CWAF+     E    + + +    S+QE+ DC     + GC GG P + L++V 
Sbjct: 120 QEQCGCCWAFATTAITEAANTLYSKSFTSLSDQEICDCADSGDTPGCVGGDPRNGLKMVH 179

Query: 210 QYGIHYRNTYPYE----GVQRYCRSREKGP--YAAKTDGVRQVQPYNEGALLYSI-ANQP 262
             G      YPYE         C   EK         +  R  Q Y E  ++ ++  N  
Sbjct: 180 LRGQSSDGDYPYEEYRANTTGNCVGDEKSTVIQPETLNVYRFDQDYAEEDIMENLYLNHI 239

Query: 263 VSVVLEAAGKDFQLYRGGIFVGPCGNKVD----HAVAAVGYGPN-----YILIKNSWGTG 313
            + V    G++F+ Y  G+       ++     H+VA VGYG +     Y L++NSW + 
Sbjct: 240 PTAVYFRVGENFEWYTSGVLQSEDCYQMTPAEWHSVAIVGYGTSDDGVPYWLVRNSWNSD 299

Query: 314 WGENGYIRIKRG 325
           WG +GY++I+RG
Sbjct: 300 WGLHGYVKIRRG 311


>Y71H2AR.2 CE22930    (ST.LOUIS) protein_id:AAK29985.1
          Length = 345

 Score = 93.6 bits (231), Expect = 2e-19
 Identities = 65/213 (30%), Positives = 106/213 (49%), Gaps = 29/213 (13%)

Query: 131 DVNIPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGI-IKIRTGNLNEYSEQELLDC 189
           D    E++DWR+KG V PVK+QG C +  AF+   +IE +  K   G L  +SEQ+L+DC
Sbjct: 79  DRTTEEFLDWREKGIVGPVKDQGKCNASHAFAITSSIESMYAKATNGTLLSFSEQQLIDC 138

Query: 190 DRRSY-GCNGGYPWSALQLVAQYGIHYRNTYPY-EGVQRYC-----RSR---EKGPYAAK 239
           + + Y GC   +  +A+  +A +GI     YPY +     C     +S+   +KG  A  
Sbjct: 139 NDQGYKGCEEQFAMNAIGYLATHGIETEADYPYVDKTNEKCTFDSTKSKIHLKKGVVAEG 198

Query: 240 TDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIF---VGPCGNKVD-HAVA 295
            + + +V   N G   +++   P              Y+ GI+   +  C +  +  ++ 
Sbjct: 199 NEVLGKVYVTNYGPAFFTMRAPP----------SLYDYKIGIYNPSIEECTSTHEIRSMV 248

Query: 296 AVGYG----PNYILIKNSWGTGWGENGYIRIKR 324
            VGYG      Y ++K S+GT WGE GY+++ R
Sbjct: 249 IVGYGIEGEQKYWIVKGSFGTSWGEQGYMKLAR 281


>K02E7.10 CE11640   protease (ST.LOUIS) TR:O17255 protein_id:AAB71030.1
          Length = 299

 Score = 93.6 bits (231), Expect = 2e-19
 Identities = 64/219 (29%), Positives = 104/219 (47%), Gaps = 15/219 (6%)

Query: 136 EYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGI-IKIRTGNLNEYSEQELLDCDRRSY 194
           +++DWR+KG V PVK+QG C + +AF+A+  IE +  K   G L  +SEQ+++DC   + 
Sbjct: 82  DFLDWREKGIVGPVKDQGKCNASYAFAAIAAIESMYAKANNGKLLSFSEQQIIDCANFTN 141

Query: 195 GCNGGYP-WSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGA 253
            C        + + + + G+     YPY G +   +                V P  E A
Sbjct: 142 PCQENLENVLSNRFLKENGVGTEADYPYVGKENVGKCEYDSSKMKLRPTYIDVYPNEEWA 201

Query: 254 LLYSIANQPVSVVLEAAGKDFQLYRGGIF---VGPCGNKVD-HAVAAVGYGPN----YIL 305
             + I           +   F  Y+ GI+      CGN  +  ++A VGYG +    Y +
Sbjct: 202 RAH-ITTFGTGYFRMRSPPSFFHYKTGIYNPTKEECGNANEARSLAIVGYGKDGAEKYWI 260

Query: 306 IKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVK 344
           +K S+GT WGE+GY+++ R    +   CG+  S   P+K
Sbjct: 261 VKGSFGTSWGEHGYMKLAR----NVNACGMAESISIPIK 295


>F57F5.1 CE05999   cysteine protease (HINXTON) TR:Q20950
           protein_id:CAB00098.1
          Length = 400

 Score = 91.3 bits (225), Expect = 8e-19
 Identities = 84/315 (26%), Positives = 127/315 (39%), Gaps = 72/315 (22%)

Query: 79  IDETNKKNNSYWLGLNVFADMSNDEFKEKYTGS----IAGNYTTTELSYEEVLNDGDVNI 134
           +D  NK   S+   L  +     D  K++  G+    I   Y   E+++ EV    D  +
Sbjct: 90  VDYVNKVQTSFKAELGSYFSSYPDTIKKQLMGAKMVEIPEEYRVFEMTHPEV---EDAAV 146

Query: 135 PEYVD----WRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTG--NLNEYSEQELLD 188
           P+  D    W    +++ +++Q SCGSCWA SA  TI   I I +    +   S  ++  
Sbjct: 147 PDSFDSRTAWPNCPSISKIRDQSSCGSCWAVSAAETISDRICIASNAKTILSISADDINA 206

Query: 189 CDRR--SYGCNGGYPWSALQLVAQ---------------------------YGIHYR--- 216
           C       GCNGGYP  A +   +                            G HY+   
Sbjct: 207 CCGMVCGNGCNGGYPIEAWRHYVKKGYVTGGSYQDKTGCKPYPYPPCEHHVNGTHYKPCP 266

Query: 217 -NTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLE------- 268
            N YP +  +R C++     Y          Q  + G   Y+++ +   +  E       
Sbjct: 267 SNMYPTDKCERSCQAGYALTYQ---------QDLHFGQSAYAVSKKAAEIQKEIMTHGPV 317

Query: 269 ----AAGKDFQLYRGGIFVGPCGNKV-DHAVAAVGYGPN----YILIKNSWGTGWGENGY 319
                  +DF+ Y GG++V   G  +  HAV  +G+G +    Y L  NSW   WGENGY
Sbjct: 318 EVAFTVYEDFEHYSGGVYVHTAGASLGGHAVKMLGWGVDNGTPYWLCANSWNEDWGENGY 377

Query: 320 IRIKRGTGNSYGVCG 334
            RI RG  N  G+ G
Sbjct: 378 FRIIRGV-NECGIEG 391


>T10H4.12 CE27590  locus:cpr-3 protease (HINXTON) TR:Q9TW93
           protein_id:CAB61024.2
          Length = 370

 Score = 85.9 bits (211), Expect = 3e-17
 Identities = 67/233 (28%), Positives = 104/233 (43%), Gaps = 42/233 (18%)

Query: 134 IPEYVDWRQK----GAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNE--YSEQELL 187
           +P+  D R+K      +  ++NQ +CGSCWAF A   I   + I++    +   S +++L
Sbjct: 92  LPDTFDAREKWPDCNTIKLIRNQATCGSCWAFGAAEVISDRVCIQSNGTQQPVISVEDIL 151

Query: 188 DCDRRS--YGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRY----------------CR 229
            C   +  YGC GGY   AL+  A  G      Y   G   Y                C+
Sbjct: 152 SCCGTTCGYGCKGGYSIEALRFWASSGAVTGGDYGGHGCMPYSFAPCTKNCPESTTPSCK 211

Query: 230 SREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVV--------LEAAGK---DFQLYR 278
           +  +  Y  KT+  ++ + Y   A   +       +         +EA+ K   DF  Y+
Sbjct: 212 TTCQSSY--KTEEYKKDKHYGASAYKVTTTKSVTEIQTEIYHYGPVEASYKVYEDFYHYK 269

Query: 279 GGIFVGPCGNKVD-HAVAAVGYGP----NYILIKNSWGTGWGENGYIRIKRGT 326
            G++    G  V  HAV  +G+G     +Y LI NSWGT +GE G+ +I+RGT
Sbjct: 270 SGVYHYTSGKLVGGHAVKIIGWGVENGVDYWLIANSWGTSFGEKGFFKIRRGT 322


>C52E4.1 CE08943  locus:cpr-1 cathepsin-like cysteine protease (HINXTON)
           TR:Q18783 protein_id:CAB01410.1
          Length = 340

 Score = 85.5 bits (210), Expect = 4e-17
 Identities = 73/252 (28%), Positives = 102/252 (39%), Gaps = 36/252 (14%)

Query: 107 KYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVT 166
           KY  + +     TE   E VL            W +  ++  +++Q +CGSCWAF A   
Sbjct: 75  KYAAAHSDEIRATE--QEVVLASVPATFDSRTQWSECKSIKLIRDQATCGSCWAFGAAEM 132

Query: 167 IEGIIKIRTGNLNE--YSEQELLDCDRRSYG--CNGGYPWSALQLVAQYGIHYRNTYPYE 222
           I     I T    +   S  +LL C   S G  C GGYP  AL+     G+     Y   
Sbjct: 133 ISDRTCIETKGAQQPIISPDDLLSCCGSSCGNGCEGGYPIQALRWWDSKGVVTGGDYHGA 192

Query: 223 GVQRY---------------------CRSREKGPYAA-KTDGVRQVQ-PYNEGALLYSI- 258
           G + Y                     C+S     YA  K  GV     P N  ++   I 
Sbjct: 193 GCKPYPIAPCTSGNCPESKTPSCSMSCQSGYSTAYAKDKHFGVSAYAVPKNAASIQAEIY 252

Query: 259 ANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVD-HAVAAVGYGPN----YILIKNSWGTG 313
           AN PV        +DF  Y+ G++    G  +  HA+  +G+G      Y L+ NSWG  
Sbjct: 253 ANGPVEAAFSVY-EDFYKYKSGVYKHTAGKYLGGHAIKIIGWGTESGSPYWLVANSWGVN 311

Query: 314 WGENGYIRIKRG 325
           WGE+G+ +I RG
Sbjct: 312 WGESGFFKIYRG 323


>F26E4.3 CE17714   cysteine protease (HINXTON) TR:P90850
           protein_id:CAB03007.1
          Length = 491

 Score = 80.5 bits (197), Expect = 1e-15
 Identities = 66/233 (28%), Positives = 98/233 (41%), Gaps = 42/233 (18%)

Query: 134 IPEYVDWRQKGA--VTPVKNQGSCGSCWAFSAV-VTIEGIIKIRTGNLNE-YSEQELLDC 189
           +PE+ D R K    + PV +QG CGS W+ S   ++ + +  I  G +N   S Q+LL C
Sbjct: 223 LPEHFDARDKWGPLIHPVADQGDCGSSWSVSTTAISSDRLAIISEGRINSTLSSQQLLSC 282

Query: 190 DR-RSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRY-------------------CR 229
           ++ R  GC GGY   A   + + G+   + YPY   Q                     C 
Sbjct: 283 NQHRQKGCEGGYLDRAWWYIRKLGVVGDHCYPYVSGQSREPGHCLIPKRDYTNRQGLRCP 342

Query: 230 SREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFV------ 283
           S  +   A K     +V    E      + N PV        +DF +Y GG++       
Sbjct: 343 SGSQDSTAFKMTPPYKVSSREEDIQTELMTNGPVQATF-VVHEDFFMYAGGVYQHSDLAA 401

Query: 284 ---GPCGNKVDHAVAAVGYGPN--------YILIKNSWGTGWGENGYIRIKRG 325
                   +  H+V  +G+G +        Y L  NSWGT WGE+GY ++ RG
Sbjct: 402 QKGASSVAEGYHSVRVLGWGVDHSTGKPIKYWLCANSWGTQWGEDGYFKVLRG 454


>W07B8.4 CE14680   thiol protease (ST.LOUIS) TR:O16288 protein_id:AAB65345.1
          Length = 335

 Score = 78.2 bits (191), Expect = 7e-15
 Identities = 71/260 (27%), Positives = 108/260 (41%), Gaps = 60/260 (23%)

Query: 133 NIPEYVD----WRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRT-GNLNE-YSEQEL 186
           +IP+  D    W Q  +V  +++Q  CGSCWA +A   I     I + G++N   S +++
Sbjct: 72  SIPDSYDVRDHWPQCISVNNIRDQSHCGSCWAVAAAEAISDRTCIASNGDVNTLLSAEDI 131

Query: 187 LDCDRRSY----GCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDG 242
           L C    +    GC GGYP  A +   + G+    ++     Q  C+     P     DG
Sbjct: 132 LTCCTGKFNCGDGCEGGYPIQAWRYWVKNGLVTGGSFE---SQYGCKPYSIAPCGETIDG 188

Query: 243 VRQVQ-----------------------PYNE----GALLYSIANQPVSVVLEAAG---- 271
           V   +                       PY++    GA  Y+I      +  E       
Sbjct: 189 VTWPECPMKISDTPKCEHHCTGNNSYPIPYDQDKHFGASAYAIGRSAKQIQTEILAHGPV 248

Query: 272 -------KDFQLYRGGIFVGPCGNKV-DHAVAAVGYGPN----YILIKNSWGTGWGENGY 319
                  +DF LY+ GI+    G ++  HAV  +G+G +    Y L  NSW T WGE GY
Sbjct: 249 EVGFIVYEDFYLYKTGIYTHVAGGELGGHAVKMLGWGVDNGTPYWLAANSWNTVWGEKGY 308

Query: 320 IRIKRGTGNSYGVCGLYTSS 339
            RI RG       CG+ +++
Sbjct: 309 FRILRGVDE----CGIESAA 324


>C32B5.7 CE08515   cathepsin-like peptidase (ST.LOUIS) TR:P91111
           protein_id:AAB37963.1
          Length = 250

 Score = 73.9 bits (180), Expect = 1e-13
 Identities = 57/189 (30%), Positives = 87/189 (45%), Gaps = 22/189 (11%)

Query: 137 YVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGC 196
           ++DWR +G V PVK+QG+C + +AF+A+  IE +  I  G L  +SEQ+++DC     GC
Sbjct: 71  FLDWRDEGVVGPVKDQGNCNASYAFAAISAIESMYAIANGQLLSFSEQQIIDC---LGGC 127

Query: 197 N-GGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPY---NEG 252
                P  A+  + + GI     YP+ G     +  EK  Y +K   +     Y   +E 
Sbjct: 128 AIESDPMMAMTYLERKGIETYTDYPFVG-----KKNEKCEYDSKKAYLILDDTYDMSDES 182

Query: 253 ALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPC-----GNKVDHAVAAVGY----GPNY 303
             L  I  +   +        F  Y+ GI+  P            A+  VGY    G NY
Sbjct: 183 LALVFIDERGPGLFTMNTPPSFFNYKSGIY-NPTEEECKSTNEKRALTIVGYGNDKGQNY 241

Query: 304 ILIKNSWGT 312
            ++K S+GT
Sbjct: 242 WIVKGSFGT 250


>Y71H2AM.3 CE26272    (ST.LOUIS) protein_id:AAK29976.1
          Length = 716

 Score = 71.2 bits (173), Expect = 9e-13
 Identities = 42/116 (36%), Positives = 60/116 (51%), Gaps = 9/116 (7%)

Query: 136 EYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGI-IKIRTGNLNEYSEQELLDCDRRSY 194
           E++DWR KG V PVK+QG C +  AF+   +IE +  K   G+L  +SEQ+L+DCD   +
Sbjct: 84  EFLDWRDKGIVGPVKDQGKCNASHAFAISSSIESMYAKATNGSLLSFSEQQLIDCDDHGF 143

Query: 195 -GCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPY 249
            GC      +A+     +GI     YPY G       +E G  + +T G   V  Y
Sbjct: 144 KGCEEQPAINAVSYFIFHGIETEADYPYAG-------KENGKLSNETQGKELVTNY 192


>F32B5.8 CE09855   cysteine proteinase (ST.LOUIS) TR:O01850
           protein_id:AAB54210.1
          Length = 427

 Score = 69.7 bits (169), Expect = 2e-12
 Identities = 58/217 (26%), Positives = 91/217 (41%), Gaps = 28/217 (12%)

Query: 133 NIPEYVDWRQKGAVTPV---KNQGS---CGSCWAFSAVVTIEGIIKIRTGNL---NEYSE 183
           ++P+  DWR    +      +NQ     CGSCWAF A   +   I I+  N       S 
Sbjct: 185 DLPKTWDWRDANGINYASADRNQHIPQYCGSCWAFGATSALADRINIKRKNAWPQAYLSV 244

Query: 184 QELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYC----RSREKGP---Y 236
           QE++DC        GG P    +   ++GI +     Y+     C    R     P   +
Sbjct: 245 QEVIDCSGAGTCVMGGEPGGVYKYAHEHGIPHETCNNYQARDGKCDPYNRCGSCWPGECF 304

Query: 237 AAKTDGVRQVQPYN-----EGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVD 291
           + K   + +V  Y      E          P++  + AA K F+ Y GGI+       +D
Sbjct: 305 SIKNYTLYKVSEYGTVHGYEKMKAEIYHKGPIACGI-AATKAFETYAGGIYKEVTDEDID 363

Query: 292 HAVAAVGYGPN------YILIKNSWGTGWGENGYIRI 322
           H ++  G+G +      Y + +NSWG  WGE+G+ +I
Sbjct: 364 HIISVHGWGVDHESGVEYWIGRNSWGEPWGEHGWFKI 400


  Database: /data_2/jason/blastdb/wormpep62
    Posted date:  Sep 3, 2001  2:17 PM
  Number of letters in database: 8,813,425
  Number of sequences in database:  20,085
  
Lambda     K      H
   0.318    0.138    0.428 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6611257
Number of Sequences: 20085
Number of extensions: 311359
Number of successful extensions: 788
Number of sequences better than 1.0e-10: 19
Number of HSP's better than  0.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 741
Number of HSP's gapped (non-prelim): 23
length of query: 345
length of database: 8,813,425
effective HSP length: 44
effective length of query: 301
effective length of database: 7,929,685
effective search space: 2386835185
effective search space used: 2386835185
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 156 (64.7 bits)
BioPerl-1.007002/t/data/multifa.seq000444000766000024       127713155576321 17052 0ustar00cjfieldsstaff000000000000>HSEARLOBE 321bp
gctcggactctatctagcagaaacctcgttcagctagtcttgcttcatggaggtttgatc
tagactgcaaacgtcggtgctaaaagaccatacttccgtatgtgcctatcgggagcagtc
gctgagaagtgcggaatgatccttcaatgaccgccgttaaagcctgggagtccgcgccac
aatcattccatatacagcaacacgcgctacgcggacctctcggtgggtgacgattctatt
gaggcgttgaagcgagaaagatattccgattcttttcgagtctatagttaaatcggactg
catcatccattttagggcata
>HSMETOO 134bp
ggccgggatggccggacctgttctgaacatcttatatccacccgaacaagttataaacaa
tttaaatctgggcggccatctataagcgtgtcttcagtatgagagtcttcggatatcacg
acccattaggaaag
>empty1 an empty seq well-formatted

>empty2 an empty seq without subsequent empty line
>MMWHISK 62bp
gctgcctctatcaagggtgaaaattgcctgcccggctgggtagacactcgcaccactccc
cg
>empty3 empty seq at the end of the file
BioPerl-1.007002/t/data/multifa.seq.qual000555000766000024       331313155576321 20007 0ustar00cjfieldsstaff000000000000>HSEARLOBE 321bp 
50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
>HSMETOO 134bp
50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
>empty1 an empty seq well-formatted

>empty2 an empty seq without subsequent empty line
>MMWHISK 62bp
50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
50 50 50 50 50 50 50 50 50 50 50 50 
>empty3 empty seq at the end of the file
BioPerl-1.007002/t/data/multiline-intrablock-comment.nex000444000766000024       111613155576321 23173 0ustar00cjfieldsstaff000000000000#NEXUS

BEGIN TAXA;
[block-level 
comment 
in 
the 
TAXA 
block]
      dimensions ntax=8;
      taxlabels A B C D E F G H;  
END;

BEGIN CHARACTERS;
[block-level comment 
in the 
CHARACTERS block]

      dimensions nchar=5;
      format datatype=protein missing=? gap=-;
      charlabels 1 2 3 4 5;
      matrix
A     --ONE
B     --ONE
C     TWO--
D     THREE
E     F-OUR
F     FIVE-
G     SIX--
H     SEVEN;
END;

BEGIN TREES;
[block-level 
comment 
                                  in the TREES block]

       tree ladder = (((((((A:1,B:1):1,C:2):1,D:3):1,E:4):1,F:5):1,G:6):1,H:7);
END;BioPerl-1.007002/t/data/multiresult_blastn+.bls000444000766000024      4545413155576321 21435 0ustar00cjfieldsstaff000000000000BLASTN 2.2.25+


Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.



Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
           14,049,258 sequences; 36,075,095,184 total letters



Query= GFAVMM201BADC0

Length=477
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

gi|194750627|ref|XM_001957596.1|  Drosophila ananassae GF23929 (D...  42.8    2.1  
gi|118568029|gb|CP000325.1|  Mycobacterium ulcerans Agy99, comple...  42.8    2.1  
gi|24395301|emb|AL928579.6|  Mouse DNA sequence from clone RP23-3...  42.8    2.1  
gi|326411376|gb|CP002568.1|  Polymorphum gilvum SL003B-26A1, comp...  41.0    7.4  
gi|317165637|gb|CP002447.1|  Mesorhizobium ciceri biovar biserrul...  41.0    7.4  
gi|312283773|gb|AC243242.1|  Panicum virgatum clone PV_ABa051-K05...  41.0    7.4  
gi|303315262|ref|XM_003067593.1|  Coccidioides posadasii C735 del...  41.0    7.4  
gi|297153409|gb|CP002047.1|  Streptomyces bingchenggensis BCW-1, ...  41.0    7.4  
gi|295434944|gb|CP002013.1|  Burkholderia sp. CCGE1002 chromosome...  41.0    7.4  
gi|283945692|gb|CP001854.1|  Conexibacter woesei DSM 14684, compl...  41.0    7.4  
gi|194346582|gb|CP001111.1|  Stenotrophomonas maltophilia R551-3,...  41.0    7.4  
gi|166857509|gb|CP000926.1|  Pseudomonas putida GB-1, complete ge...  41.0    7.4  
gi|148498119|gb|CP000699.1|  Sphingomonas wittichii RW1, complete...  41.0    7.4  


>gi|194750627|ref|XM_001957596.1| Drosophila ananassae GF23929 (Dana\GF23929), mRNA
Length=1641

 Score = 42.8 bits (46),  Expect = 2.1
 Identities = 37/45 (83%), Gaps = 1/45 (2%)
 Strand=Plus/Plus

Query  236  ACGCCGACGACAAGCGGCGAGTCCCTTGTGGACGATCTCGGCCAC  280
            |||||||||||||| ||||||||| ||  ||||  ||||  ||||
Sbjct  137  ACGCCGACGACAAG-GGCGAGTCCATTTGGGACTTTCTCACCCAC  180


>gi|118568029|gb|CP000325.1| Mycobacterium ulcerans Agy99, complete genome
Length=5631606

 Score = 42.8 bits (46),  Expect = 2.1
 Identities = 36/43 (84%), Gaps = 1/43 (2%)
 Strand=Plus/Minus

Query  69      CCATGACTGCCGGCAGAACATCGACCGGCCAG-TATGTCGGCC  110
               ||||| ||||||||||||| |||| || || | |||| |||||
Sbjct  890715  CCATGTCTGCCGGCAGAACTTCGAGCGACCCGATATGGCGGCC  890673


>gi|24395301|emb|AL928579.6| Mouse DNA sequence from clone RP23-302M15 on chromosome 4, complete 
sequence
Length=184057

 Score = 42.8 bits (46),  Expect = 2.1
 Identities = 31/35 (89%), Gaps = 1/35 (2%)
 Strand=Plus/Plus

Query  437     AGCTGCAACATGAATGTGCTCGCAGATCTTCAGGA  471
               |||||||||||| ||||||| ||||| |||| |||
Sbjct  146437  AGCTGCAACATGGATGTGCTAGCAGA-CTTCTGGA  146470


>gi|326411376|gb|CP002568.1| Polymorphum gilvum SL003B-26A1, complete genome
Length=4649365

 Score = 41.0 bits (44),  Expect = 7.4
 Identities = 33/40 (83%), Gaps = 0/40 (0%)
 Strand=Plus/Plus

Query  238      GCCGACGACAAGCGGCGAGTCCCTTGTGGACGATCTCGGC  277
                |||||||||  ||||||||||| | |||  |||| |||||
Sbjct  2023755  GCCGACGACGCGCGGCGAGTCCGTGGTGCTCGATGTCGGC  2023794


>gi|317165637|gb|CP002447.1| Mesorhizobium ciceri biovar biserrulae WSM1271, complete genome
Length=6264489

 Score = 41.0 bits (44),  Expect = 7.4
 Identities = 22/22 (100%), Gaps = 0/22 (0%)
 Strand=Plus/Plus

Query  300      TTGATGCCGAGGCGGATGCCAT  321
                ||||||||||||||||||||||
Sbjct  4510008  TTGATGCCGAGGCGGATGCCAT  4510029


>gi|312283773|gb|AC243242.1| Panicum virgatum clone PV_ABa051-K05, complete sequence
Length=161398

 Score = 41.0 bits (44),  Expect = 7.4
 Identities = 28/32 (88%), Gaps = 0/32 (0%)
 Strand=Plus/Plus

Query  271     TCTCGGCCACCTGTTTGAGTGGTATTCTTTTG  302
               ||| |||||||||||||||| ||||| || ||
Sbjct  137850  TCTTGGCCACCTGTTTGAGTTGTATTTTTCTG  137881


>gi|303315262|ref|XM_003067593.1| Coccidioides posadasii C735 delta SOWgp Sugar transporter family 
protein, mRNA
Length=1947

 Score = 41.0 bits (44),  Expect = 7.4
 Identities = 31/37 (84%), Gaps = 0/37 (0%)
 Strand=Plus/Minus

Query  289  GTGGTATTCTTTTGATGCCGAGGCGGATGCCATTGCA  325
            ||||| ||| | ||||||||||||| | ||| |||||
Sbjct  84   GTGGTCTTCATATGATGCCGAGGCGTAAGCCTTTGCA  48


>gi|297153409|gb|CP002047.1| Streptomyces bingchenggensis BCW-1, complete genome
Length=11936683

 Score = 41.0 bits (44),  Expect = 7.4
 Identities = 27/30 (90%), Gaps = 0/30 (0%)
 Strand=Plus/Plus

Query  38       GTCGGCAGCGGATCTCCGAAAACCATCAAG  67
                |||||||||||| |||||||  ||||||||
Sbjct  3073377  GTCGGCAGCGGAACTCCGAATTCCATCAAG  3073406


>gi|295434944|gb|CP002013.1| Burkholderia sp. CCGE1002 chromosome 1, complete sequence
Length=3518940

 Score = 41.0 bits (44),  Expect = 7.4
 Identities = 33/40 (83%), Gaps = 0/40 (0%)
 Strand=Plus/Minus

Query  212      ATGGGCGAATCGATCACCTTCAACACGCCGACGACAAGCG  251
                || |||||||||||| | |||||||||| | |||  ||||
Sbjct  2243828  ATCGGCGAATCGATCGCGTTCAACACGCTGGCGATGAGCG  2243789


>gi|283945692|gb|CP001854.1| Conexibacter woesei DSM 14684, complete genome
Length=6359369

 Score = 41.0 bits (44),  Expect = 7.4
 Identities = 35/43 (82%), Gaps = 3/43 (6%)
 Strand=Plus/Minus

Query  101      TATGTCGGCCATGGCTTCTACAGTCCGGACATGATCGACGGCG  143
                ||||||||||| | |||||||   ||| || || |||||||||
Sbjct  2039361  TATGTCGGCCACGACTTCTAC---CCGAACCTGGTCGACGGCG  2039322


>gi|194346582|gb|CP001111.1| Stenotrophomonas maltophilia R551-3, complete genome
Length=4573969

 Score = 41.0 bits (44),  Expect = 7.4
 Identities = 32/36 (89%), Gaps = 2/36 (5%)
 Strand=Plus/Minus

Query  102      ATGTCGGCCATGGC-TTCTACAGTCCGGACATGATC  136
                |||||||||||||| ||  |||| ||||||||||||
Sbjct  3897524  ATGTCGGCCATGGCGTTGCACAG-CCGGACATGATC  3897490


>gi|166857509|gb|CP000926.1| Pseudomonas putida GB-1, complete genome
Length=6078430

 Score = 41.0 bits (44),  Expect = 7.4
 Identities = 35/41 (86%), Gaps = 2/41 (4%)
 Strand=Plus/Minus

Query  222      CGATCACCTTCAACACG-CCGACGACAAGCGGCGAGTCCCT  261
                ||||||||||| ||||| ||||||| ||||| | |||| ||
Sbjct  5087565  CGATCACCTTCGACACGTCCGACGA-AAGCGCCAAGTCGCT  5087526


>gi|148498119|gb|CP000699.1| Sphingomonas wittichii RW1, complete genome
Length=5382261

 Score = 41.0 bits (44),  Expect = 7.4
 Identities = 32/38 (85%), Gaps = 3/38 (7%)
 Strand=Plus/Plus

Query  208      GACGATG---GGCGAATCGATCACCTTCAACACGCCGA  242
                |||||||   ||||  |||||||||||||| |||||||
Sbjct  4265124  GACGATGTGGGGCGGCTCGATCACCTTCAAGACGCCGA  4265161



Lambda     K      H
   0.634    0.408    0.912 

Gapped
Lambda     K      H
   0.625    0.410    0.780 

Effective search space used: 15727850050068


Query= GFAVMM201A1JOH

Length=57
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

gi|22416007|emb|AL772315.4|  Mouse DNA sequence from clone RP23-5...  41.0    0.42 
gi|117168385|gb|AC190175.4|  Pan troglodytes BAC clone CH251-542A...  39.2    1.5  
gi|45238691|gb|AC145377.2|  Pan troglodytes BAC clone RP43-11P19 ...  39.2    1.5  
gi|4926907|gb|AC004936.2|  Homo sapiens PAC clone RP5-959C21 from...  39.2    1.5  
gi|31414500|emb|AL831797.4|  Oryza sativa chromosome 12, . BAC OS...  39.2    1.5  
gi|158967071|gb|CP000033.3|  Lactobacillus acidophilus NCFM, comp...  37.4    5.1  


>gi|22416007|emb|AL772315.4| Mouse DNA sequence from clone RP23-54A13 on chromosome 4, complete 
sequence
Length=200266

 Score = 41.0 bits (44),  Expect = 0.42
 Identities = 28/31 (91%), Gaps = 2/31 (6%)
 Strand=Plus/Minus

Query  6      CGTTCCAGTCACGATACATACCAATAACGAC  36
              ||||||||| |  ||||||||||||||||||
Sbjct  26821  CGTTCCAGTGA--ATACATACCAATAACGAC  26793


>gi|117168385|gb|AC190175.4| Pan troglodytes BAC clone CH251-542A7 from chromosome 7, complete 
sequence
Length=214222

 Score = 39.2 bits (42),  Expect = 1.5
 Identities = 26/29 (90%), Gaps = 0/29 (0%)
 Strand=Plus/Minus

Query  19      ATACATACCAATAACGACTTCTATATGTA  47
               ||||||||||||||  | |||||||||||
Sbjct  166678  ATACATACCAATAAATATTTCTATATGTA  166650


>gi|45238691|gb|AC145377.2| Pan troglodytes BAC clone RP43-11P19 from chromosome 7, complete 
sequence
Length=194463

 Score = 39.2 bits (42),  Expect = 1.5
 Identities = 26/29 (90%), Gaps = 0/29 (0%)
 Strand=Plus/Plus

Query  19      ATACATACCAATAACGACTTCTATATGTA  47
               ||||||||||||||  | |||||||||||
Sbjct  192749  ATACATACCAATAAATATTTCTATATGTA  192777


>gi|4926907|gb|AC004936.2| Homo sapiens PAC clone RP5-959C21 from 7, complete sequence
Length=139949

 Score = 39.2 bits (42),  Expect = 1.5
 Identities = 26/29 (90%), Gaps = 0/29 (0%)
 Strand=Plus/Minus

Query  19     ATACATACCAATAACGACTTCTATATGTA  47
              ||||||||||||||  | |||||||||||
Sbjct  12654  ATACATACCAATAAATATTTCTATATGTA  12626


>gi|31414500|emb|AL831797.4| Oryza sativa chromosome 12, . BAC OSJNBa0010M16 of library OSJNBa 
from chromosome 12 of cultivar Nipponbare of ssp. japonica 
of Oryza sativa (rice), complete sequence
Length=132741

 Score = 39.2 bits (42),  Expect = 1.5
 Identities = 23/24 (96%), Gaps = 0/24 (0%)
 Strand=Plus/Plus

Query  18      GATACATACCAATAACGACTTCTA  41
               ||||||||||||||| ||||||||
Sbjct  126346  GATACATACCAATAAAGACTTCTA  126369


>gi|158967071|gb|CP000033.3| Lactobacillus acidophilus NCFM, complete genome
Length=1993560

 Score = 37.4 bits (40),  Expect = 5.1
 Identities = 20/20 (100%), Gaps = 0/20 (0%)
 Strand=Plus/Minus

Query  14      TCACGATACATACCAATAAC  33
               ||||||||||||||||||||
Sbjct  756012  TCACGATACATACCAATAAC  755993



Lambda     K      H
   0.634    0.408    0.912 

Gapped
Lambda     K      H
   0.625    0.410    0.780 

Effective search space used: 890637973200


Query= GFAVMM201D933Z

Length=119
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

gi|332189094|gb|CP002684.1|  Arabidopsis thaliana chromosome 1, c...  41.0    1.4  
gi|313747610|gb|AC237431.3|  Macaca mulatta Y Chr BAC RMAEX-106G5...  41.0    1.4  
gi|168693784|gb|AC213321.3|  MACACA MULATTA BAC clone CH250-541A1...  41.0    1.4  
gi|8778954|gb|AC007932.3|F11A17  Arabidopsis thaliana chromosome ...  41.0    1.4  
gi|256052438|ref|XM_002569731.1|  Schistosoma mansoni GTP-binding...  39.2    5.0  
gi|238867551|gb|CP001600.1|  Edwardsiella ictaluri 93-146, comple...  39.2    5.0  
gi|224465197|ref|NG_009929.1|  Homo sapiens like-glycosyltransfer...  39.2    5.0  
gi|147784643|emb|AM469007.2|  Vitis vinifera contig VV78X098884.1...  39.2    5.0  
gi|123663234|emb|AM455601.1|  Vitis vinifera, whole genome shotgu...  39.2    5.0  
gi|118344518|gb|AC192748.2|  Gallus gallus BAC clone CH261-166H21...  39.2    5.0  
gi|90309320|gb|AY607844.2|  Edwardsiella ictaluri transposase-lik...  39.2    5.0  
gi|55908997|gb|AC102414.8|  Mus musculus chromosome 15, clone RP2...  39.2    5.0  
gi|72096292|gb|AC162857.5|  Mus musculus chromosome 15, clone RP2...  39.2    5.0  
gi|22415845|emb|AL139016.8|  Human DNA sequence from clone RP4-65...  39.2    5.0  
gi|6572307|emb|Z82173.2|  Human DNA sequence from clone SC22CB-1D...  39.2    5.0  
gi|56410822|gb|AC140454.4|  Mus musculus BAC clone RP24-163I14 fr...  39.2    5.0  
gi|38707373|emb|BX255930.3|  Zebrafish DNA sequence from clone DK...  39.2    5.0  


>gi|332189094|gb|CP002684.1| Arabidopsis thaliana chromosome 1, complete sequence
Length=30427671

 Score = 41.0 bits (44),  Expect = 1.4
 Identities = 25/27 (93%), Gaps = 0/27 (0%)
 Strand=Plus/Minus

Query  70        AACAGAAACCACTACGAAAGGAAAGAA  96
                 |||||||||  ||||||||||||||||
Sbjct  17871124  AACAGAAACTTCTACGAAAGGAAAGAA  17871098


>gi|313747610|gb|AC237431.3| Macaca mulatta Y Chr BAC RMAEX-106G5 complete sequence
Length=169910

 Score = 41.0 bits (44),  Expect = 1.4
 Identities = 28/31 (91%), Gaps = 2/31 (6%)
 Strand=Plus/Minus

Query  75     AAACCACTACGAAAGGAAAGAAATGCCTCTA  105
              ||||||  ||||||||||| |||||||||||
Sbjct  60448  AAACCA--ACGAAAGGAAATAAATGCCTCTA  60420


>gi|168693784|gb|AC213321.3| MACACA MULATTA BAC clone CH250-541A11 from chromosome y, complete 
sequence
Length=156689

 Score = 41.0 bits (44),  Expect = 1.4
 Identities = 28/31 (91%), Gaps = 2/31 (6%)
 Strand=Plus/Plus

Query  75     AAACCACTACGAAAGGAAAGAAATGCCTCTA  105
              ||||||  ||||||||||| |||||||||||
Sbjct  62327  AAACCA--ACGAAAGGAAATAAATGCCTCTA  62355


>gi|8778954|gb|AC007932.3|F11A17 Arabidopsis thaliana chromosome 1 BAC F11A17 sequence, complete 
sequence
Length=102078

 Score = 41.0 bits (44),  Expect = 1.4
 Identities = 25/27 (93%), Gaps = 0/27 (0%)
 Strand=Plus/Plus

Query  70     AACAGAAACCACTACGAAAGGAAAGAA  96
              |||||||||  ||||||||||||||||
Sbjct  32940  AACAGAAACTTCTACGAAAGGAAAGAA  32966


>gi|256052438|ref|XM_002569731.1| Schistosoma mansoni GTP-binding protein era, putative (Smp_164220) 
mRNA, complete cds
Length=1341

 Score = 39.2 bits (42),  Expect = 5.0
 Identities = 21/21 (100%), Gaps = 0/21 (0%)
 Strand=Plus/Minus

Query  40   TTCTCTTTTCGTATTTGGAAC  60
            |||||||||||||||||||||
Sbjct  159  TTCTCTTTTCGTATTTGGAAC  139


>gi|238867551|gb|CP001600.1| Edwardsiella ictaluri 93-146, complete genome
Length=3812315

 Score = 39.2 bits (42),  Expect = 5.0
 Identities = 31/37 (84%), Gaps = 3/37 (8%)
 Strand=Plus/Plus

Query  58       AACAGCTGTTATA---ACAGAAACCACTACGAAAGGA  91
                |||||| ||||||   ||| ||||||||||| |||||
Sbjct  1978968  AACAGCCGTTATATCCACATAAACCACTACGCAAGGA  1979004


>gi|224465197|ref|NG_009929.1| Homo sapiens like-glycosyltransferase (LARGE), RefSeqGene on 
chromosome 22
Length=654355

 Score = 39.2 bits (42),  Expect = 5.0
 Identities = 30/36 (84%), Gaps = 0/36 (0%)
 Strand=Plus/Plus

Query  66      TTATAACAGAAACCACTACGAAAGGAAAGAAATGCC  101
               ||| |||||||||||  || |||||||| ||| |||
Sbjct  603836  TTAAAACAGAAACCAAAACCAAAGGAAAAAAAAGCC  603871


>gi|147784643|emb|AM469007.2| Vitis vinifera contig VV78X098884.11, whole genome shotgun sequence
Length=7756

 Score = 39.2 bits (42),  Expect = 5.0
 Identities = 24/26 (93%), Gaps = 0/26 (0%)
 Strand=Plus/Minus

Query  71    ACAGAAACCACTACGAAAGGAAAGAA  96
             ||| |||||||||| |||||||||||
Sbjct  6827  ACAAAAACCACTACAAAAGGAAAGAA  6802


>gi|123663234|emb|AM455601.1| Vitis vinifera, whole genome shotgun sequence, contig VV78X123660.5, 
clone ENTAV 115
Length=34741

 Score = 39.2 bits (42),  Expect = 5.0
 Identities = 24/26 (93%), Gaps = 0/26 (0%)
 Strand=Plus/Plus

Query  71     ACAGAAACCACTACGAAAGGAAAGAA  96
              ||| |||||||||| |||||||||||
Sbjct  34120  ACAAAAACCACTACAAAAGGAAAGAA  34145


>gi|118344518|gb|AC192748.2| Gallus gallus BAC clone CH261-166H21 from chromosome z, complete 
sequence
Length=226699

 Score = 39.2 bits (42),  Expect = 5.0
 Identities = 27/31 (88%), Gaps = 0/31 (0%)
 Strand=Plus/Plus

Query  58      AACAGCTGTTATAACAGAAACCACTACGAAA  88
               ||||||||| ||||||||||||  || ||||
Sbjct  178051  AACAGCTGTCATAACAGAAACCCATATGAAA  178081


>gi|90309320|gb|AY607844.2| Edwardsiella ictaluri transposase-like protein gene, complete 
cds; urease operon, complete sequence; and ammonium transporter 
(amtB) and TnpA (tnpA) genes, complete cds
Length=11426

 Score = 39.2 bits (42),  Expect = 5.0
 Identities = 31/37 (84%), Gaps = 3/37 (8%)
 Strand=Plus/Minus

Query  58    AACAGCTGTTATA---ACAGAAACCACTACGAAAGGA  91
             |||||| ||||||   ||| ||||||||||| |||||
Sbjct  8030  AACAGCCGTTATATCCACATAAACCACTACGCAAGGA  7994


>gi|55908997|gb|AC102414.8| Mus musculus chromosome 15, clone RP24-474D5, complete sequence
Length=159739

 Score = 39.2 bits (42),  Expect = 5.0
 Identities = 24/26 (93%), Gaps = 0/26 (0%)
 Strand=Plus/Plus

Query  70     AACAGAAACCACTACGAAAGGAAAGA  95
              ||||||||||||||| |||||| |||
Sbjct  71851  AACAGAAACCACTACAAAAGGAGAGA  71876


>gi|72096292|gb|AC162857.5| Mus musculus chromosome 15, clone RP23-333C11, complete sequence
Length=224913

 Score = 39.2 bits (42),  Expect = 5.0
 Identities = 24/26 (93%), Gaps = 0/26 (0%)
 Strand=Plus/Minus

Query  70    AACAGAAACCACTACGAAAGGAAAGA  95
             ||||||||||||||| |||||| |||
Sbjct  3370  AACAGAAACCACTACAAAAGGAGAGA  3345


>gi|22415845|emb|AL139016.8| Human DNA sequence from clone RP4-658C17 on chromosome 1p11.1-13.3, 
complete sequence
Length=100643

 Score = 39.2 bits (42),  Expect = 5.0
 Identities = 22/23 (96%), Gaps = 0/23 (0%)
 Strand=Plus/Plus

Query  87     AAGGAAAGAAATGCCTCTANAAG  109
              ||||||||||||||||||| |||
Sbjct  22086  AAGGAAAGAAATGCCTCTAGAAG  22108


>gi|6572307|emb|Z82173.2| Human DNA sequence from clone SC22CB-1D7 on chromosome 22 Contains 
a novel gene and part of the LARGE gene for like-glycosyltransferase, 
complete sequence
Length=37731

 Score = 39.2 bits (42),  Expect = 5.0
 Identities = 30/36 (84%), Gaps = 0/36 (0%)
 Strand=Plus/Minus

Query  66     TTATAACAGAAACCACTACGAAAGGAAAGAAATGCC  101
              ||| |||||||||||  || |||||||| ||| |||
Sbjct  15530  TTAAAACAGAAACCAAAACCAAAGGAAAAAAAAGCC  15495


>gi|56410822|gb|AC140454.4| Mus musculus BAC clone RP24-163I14 from 1, complete sequence
Length=171533

 Score = 39.2 bits (42),  Expect = 5.0
 Identities = 28/32 (88%), Gaps = 4/32 (12%)
 Strand=Plus/Plus

Query  66      TTATAACAGAAACCACTACGAAAGGAAAGAAA  97
               ||||||||||||||||    ||||||||||||
Sbjct  140248  TTATAACAGAAACCAC----AAAGGAAAGAAA  140275


>gi|38707373|emb|BX255930.3| Zebrafish DNA sequence from clone DKEY-101K6 in linkage group 
9 Contains the 3' end of the mcm3ap gene for MCM3 minichromosome 
maintenance deficient 3 (S. cerevisiae) associated protein, 
the gene for a novel protein similar to vertebrate lanosterol 
synthase (2,3-oxidosqualene-lanosterol cyclase) (LSS), 
the gene for a novel protein similar to human and mouse leishmanolysin-like 
(metallopeptidase M8 family) (LMLN), the 
gene for a novel protein similar to vertebrate oxysterol binding 
protein-like 10 (OSBPL10), the gene for a novel protein 
similar to vertebrate transforming growth factor, beta receptor 
II (70/80kDa) (TGFBR2), the snx4 gene for sorting nexin 
4, the gene for a novel protein similar to vertebrate zinc 
finger protein 148 (ZNF148) and the 5' end of the gene for a 
novel protein similar to vertebrate solute carrier family 12 
(potassium/chloride transporters), member 8 (SLC12A8), complete 
sequence
Length=185559

 Score = 39.2 bits (42),  Expect = 5.0
 Identities = 21/21 (100%), Gaps = 0/21 (0%)
 Strand=Plus/Plus

Query  62      GCTGTTATAACAGAAACCACT  82
               |||||||||||||||||||||
Sbjct  124003  GCTGTTATAACAGAAACCACT  124023



Lambda     K      H
   0.634    0.408    0.912 

Gapped
Lambda     K      H
   0.625    0.410    0.780 

Effective search space used: 3062586391620


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
    Posted date:  May 21, 2011  4:39 PM
  Number of letters in database: 36,075,095,184
  Number of sequences in database:  14,049,258



Matrix: blastn matrix 2 -3
Gap Penalties: Existence: 5, Extension: 2
BioPerl-1.007002/t/data/multiseq.bls000444000766000024      3305413155576321 17262 0ustar00cjfieldsstaff000000000000BLASTP 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= gi|10038724|dbj|BAB12759.1| DNA-binding protein hu-alpha
[Buchnera sp. APS]
         (92 letters)

Database: mycge
           1 sequences; 607 total letters

Searchingdone

 ***** No hits found ******

  Database: mycge
    Posted date:  May 8, 2001  3:12 PM
  Number of letters in database: 607
  Number of sequences in database:  1

Lambda     K      H
   0.310    0.127    0.323

Gapped
Lambda     K      H
   0.270   0.0470    0.230


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 99
Number of Sequences: 1
Number of extensions: 4
Number of successful extensions: 0
Number of sequences better than 1.0e-15: 0
Number of HSP's better than  0.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 0
length of query: 92
length of database: 607
effective HSP length: 24
effective length of query: 68
effective length of database: 583
effective search space:    39644
effective search space used:    39644
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 42 (21.8 bits)
S2: 156 (65.2 bits)
BLASTP 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= gi|10038744|dbj|BAB12779.1| DNA primase [Buchnera sp. APS]
         (577 letters)

Database: mycge
           1 sequences; 607 total letters

Searchingdone

                                                                   Score     E
Sequences producing significant alignments:                        (bits) 
Value

gi|12045104|ref|NP_072915.1| DNA primase (dnaE) [Mycoplasma gen...   125  7e-33

>gi|12045104|ref|NP_072915.1| DNA primase (dnaE) [Mycoplasma
           genitalium]
          Length = 607

 Score =  125 bits (310), Expect = 7e-33
 Identities = 118/461 (25%), Positives = 222/461 (47%), Gaps = 57/461 (12%)

Query: 10  ITELLSRTNIIELI-NTRLELKKYGKNYQTNCPFHHDKTPSFTVSNEKQFYYCFGCNAHG 68
           + ELL +  I E+I +  ++++  G +    CPFH DK PS ++S+ K  + C+ CNA G
Sbjct: 8   LDELLKQIKITEIIQHYGVKIQTKGNSLLALCPFHDDKNPSMSISSSKNIFKCWACNAAG 67

Query: 69  NAIDFLIQYEHLSFIESIEELALIHGVKIPFENTVQNSIYVKKQKLYLLMEKICKLY--- 125
           N I F+ +++ L +  ++++   I G+K+   N+   +    KQK Y  +      Y
Sbjct: 68  NGIAFIQKHDQLDWKTALKKAIEICGIKLENWNSNLLTKVDPKQKRYWEINNALITYYQT 127

Query: 126 --KKNINVTHLANKYLARRGINQNMIDFFLIGFSSLKWNEFYKKINISKEFEQELLINNI 183
             K+  N   + N  + +R +N+ +I+ F +G +    +++     + +  E+   IN
Sbjct: 128 RLKRETNPNGM-NYLVEKRKLNKTLIEQFQLGLAFHNEDKY-----LCESMERYPFINPK 181

Query: 184 I---------ATDKNGY-IYD------RFQGRIIFPIQDNHGRIIGFGGRSLNDMSP-KY 226
           I          T++ G   +D       FQ +I+ PI D +G  +GF  RS+++++  KY
Sbjct: 182 IKPSELYLFSKTNQQGLGFFDFNTKKATFQNQIMIPIHDFNGNPVGFSARSVDNINKLKY 241

Query: 227 LNSPETDIFYKRKQIYGLYQVIKKCSKPVYLLVVEGYIDVITLTQYNIDYAVSILGTSTT 286
            NS + + F K + ++  +++ K  ++   L +VEGY DV TLT    + AV+++G +
Sbjct: 242 KNSADHEFFKKGELLFNFHRLNKNLNQ---LFIVEGYFDVFTLTNSKFE-AVALMGLALN 297

Query: 287 TEHIQLL---FKNTDIIICCYDGDDAGKNAAWKTLKKALPYISDKKTLKFILL--PNQED 341
              I+ +   FK    ++   D D +G+NA +  ++K    +++   +  I+    N +D
Sbjct: 298 DVQIKAIKAHFKELQTLVLALDNDASGQNAVFSLIEK----LNNNNFIVEIVQWEHNYKD 353

Query: 342 PDTIIRKEGREKF----QKRIDNAITMSKFFFKNILKNINLSSDDDKFHLSVHALPLINT 397
            D +   +G E+      KR +    +  FF K  L    +++    F      L    T
Sbjct: 354 WDELYLNKGSEQVILQANKRQNLIEYLVSFFKKQQLDQRVITNKIIAF------LTKNQT 407

Query: 398 ISSD-TIRIYLRQILARMIGILDDNQFEKFLYEKETKNTQK 437
           I +D +  I+L + L +++   D    EK LYE   K+ +K
Sbjct: 408 ILNDHSFLIFLIKNLVKLLEYSD----EKTLYETVLKHKEK 444


  Database: mycge
    Posted date:  May 8, 2001  3:12 PM
  Number of letters in database: 607
  Number of sequences in database:  1

Lambda     K      H
   0.322    0.140    0.406

Gapped
Lambda     K      H
   0.270   0.0470    0.230


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 932
Number of Sequences: 1
Number of extensions: 63
Number of successful extensions: 4
Number of sequences better than 1.0e-15: 1
Number of HSP's better than  0.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1
Number of HSP's gapped (non-prelim): 1
length of query: 577
length of database: 607
effective HSP length: 24
effective length of query: 553
effective length of database: 583
effective search space:   322399
effective search space used:   322399
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 41 (21.9 bits)
S2: 164 (68.3 bits)
BLASTP 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= gi|10038814|dbj|BAB12849.1| integration host factor
alpha-subunit [Buchnera sp. APS]
         (102 letters)

Database: mycge
           1 sequences; 607 total letters

Searchingdone

 ***** No hits found ******

  Database: mycge
    Posted date:  May 8, 2001  3:12 PM
  Number of letters in database: 607
  Number of sequences in database:  1

Lambda     K      H
   0.321    0.138    0.372

Gapped
Lambda     K      H
   0.270   0.0470    0.230


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 101
Number of Sequences: 1
Number of extensions: 4
Number of successful extensions: 0
Number of sequences better than 1.0e-15: 0
Number of HSP's better than  0.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 0
length of query: 102
length of database: 607
effective HSP length: 21
effective length of query: 81
effective length of database: 586
effective search space:    47466
effective search space used:    47466
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 41 (21.9 bits)
S2: 157 (65.6 bits)
BLASTP 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= gi|10038947|dbj|BAB12982.1| DNA-binding protein H-ns [Buchnera
sp. APS]
         (135 letters)

Database: mycge
           1 sequences; 607 total letters

Searchingdone

 ***** No hits found ******

  Database: mycge
    Posted date:  May 8, 2001  3:12 PM
  Number of letters in database: 607
  Number of sequences in database:  1

Lambda     K      H
   0.319    0.137    0.390

Gapped
Lambda     K      H
   0.270   0.0470    0.230


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 132
Number of Sequences: 1
Number of extensions: 3
Number of successful extensions: 0
Number of sequences better than 1.0e-15: 0
Number of HSP's better than  0.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 0
length of query: 135
length of database: 607
effective HSP length: 23
effective length of query: 112
effective length of database: 584
effective search space:    65408
effective search space used:    65408
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 41 (21.7 bits)
S2: 158 (66.0 bits)
BLASTP 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= gi|10038982|dbj|BAB13017.1| integration host factor
beta-subunit [Buchnera sp. APS]
         (94 letters)

Database: mycge
           1 sequences; 607 total letters

Searchingdone

 ***** No hits found ******

  Database: mycge
    Posted date:  May 8, 2001  3:12 PM
  Number of letters in database: 607
  Number of sequences in database:  1

Lambda     K      H
   0.319    0.136    0.372

Gapped
Lambda     K      H
   0.270   0.0470    0.230


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 114
Number of Sequences: 1
Number of extensions: 6
Number of successful extensions: 0
Number of sequences better than 1.0e-15: 0
Number of HSP's better than  0.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 0
length of query: 94
length of database: 607
effective HSP length: 21
effective length of query: 73
effective length of database: 586
effective search space:    42778
effective search space used:    42778
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 41 (21.7 bits)
S2: 157 (65.6 bits)
BLASTP 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= gi|10038996|dbj|BAB13030.1| cold shock-like protein cspC
[Buchnera sp. APS]
         (69 letters)

Database: mycge
           1 sequences; 607 total letters

Searchingdone

 ***** No hits found ******

  Database: mycge
    Posted date:  May 8, 2001  3:12 PM
  Number of letters in database: 607
  Number of sequences in database:  1

Lambda     K      H
   0.316    0.136    0.399

Gapped
Lambda     K      H
   0.270   0.0470    0.230


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 100
Number of Sequences: 1
Number of extensions: 5
Number of successful extensions: 0
Number of sequences better than 1.0e-15: 0
Number of HSP's better than  0.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 0
length of query: 69
length of database: 607
effective HSP length: 20
effective length of query: 49
effective length of database: 587
effective search space:    28763
effective search space used:    28763
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 41 (21.6 bits)
S2: 155 (64.8 bits)
BLASTP 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= gi|10039073|dbj|BAB13107.1| carbon storage regulator [Buchnera
sp. APS]
         (57 letters)

Database: mycge
           1 sequences; 607 total letters

Searchingdone

 ***** No hits found ******

  Database: mycge
    Posted date:  May 8, 2001  3:12 PM
  Number of letters in database: 607
  Number of sequences in database:  1

Lambda     K      H
   0.318    0.138    0.362

Gapped
Lambda     K      H
   0.270   0.0470    0.230


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 64
Number of Sequences: 1
Number of extensions: 2
Number of successful extensions: 0
Number of sequences better than 1.0e-15: 0
Number of HSP's better than  0.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 0
length of query: 57
length of database: 607
effective HSP length: 22
effective length of query: 35
effective length of database: 585
effective search space:    20475
effective search space used:    20475
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 41 (21.7 bits)
S2: 154 (64.4 bits)
BLASTP 2.1.2 [Oct-19-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= gi|10039151|dbj|BAB13185.1| cold shock-like protein cspE
[Buchnera sp. APS]
         (69 letters)

Database: mycge
           1 sequences; 607 total letters

Searchingdone

 ***** No hits found ******

  Database: mycge
    Posted date:  May 8, 2001  3:12 PM
  Number of letters in database: 607
  Number of sequences in database:  1

Lambda     K      H
   0.313    0.132    0.375

Gapped
Lambda     K      H
   0.270   0.0470    0.230


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 80
Number of Sequences: 1
Number of extensions: 2
Number of successful extensions: 0
Number of sequences better than 1.0e-15: 0
Number of HSP's better than  0.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 0
length of query: 69
length of database: 607
effective HSP length: 21
effective length of query: 48
effective length of database: 586
effective search space:    28128
effective search space used:    28128
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 42 (21.9 bits)
S2: 155 (64.8 bits)
BioPerl-1.007002/t/data/multiseq_tags.phd000444000766000024      4602313155576321 20273 0ustar00cjfieldsstaff000000000000BEGIN_SEQUENCE BIXY17487.b12

BEGIN_COMMENT

CHROMAT_FILE: BIXY17487.b12
ABI_THUMBPRINT: 0
PHRED_VERSION: 0.990722.g
CALL_METHOD: phred
QUALITY_LEVELS: 99
TIME: Fri Jan 27 15:28:57 2006
TRACE_ARRAY_MIN_INDEX: 0
TRACE_ARRAY_MAX_INDEX: 11184
TRIM: 43 815 0.0500
CHEM: term
DYE: big

END_COMMENT

BEGIN_DNA
n 0 7
n 0 18
n 0 29
a 4 51
a 9 52
a 9 52
a 4 54
n 0 85
n 0 96
n 0 107
n 0 117
n 0 128
n 0 139
n 0 150
n 0 160
n 0 171
n 0 181
a 4 205
a 9 206
c 9 213
c 6 215
a 6 236
t 6 247
c 6 250
t 4 264
a 6 267
a 4 285
g 8 291
a 13 306
t 6 322
t 6 327
g 9 342
t 19 358
c 19 365
g 9 373
a 9 386
g 9 400
a 11 415
c 6 422
t 7 440
t 7 444
c 7 451
g 13 470
c 19 483
a 20 492
g 33 502
t 32 518
a 32 526
t 34 537
c 34 547
a 34 555
g 19 567
a 19 580
t 9 592
c 9 611
a 9 618
a 19 629
g 19 641
c 37 656
g 37 666
g 37 680
c 45 693
c 45 705
g 51 715
c 51 728
a 46 738
t 39 751
c 35 761
c 29 773
a 29 781
g 29 793
t 32 809
t 34 822
t 34 834
a 35 842
c 35 852
c 35 864
g 45 875
a 45 889
c 40 900
c 39 912
t 39 927
c 35 937
a 35 946
g 35 958
t 35 974
g 35 983
c 35 996
a 39 1007
c 39 1017
t 39 1032
t 39 1045
g 39 1054
c 40 1068
c 40 1080
g 45 1092
a 51 1105
c 45 1115
c 45 1128
g 45 1138
c 45 1152
a 40 1163
c 35 1173
c 35 1185
c 35 1197
t 35 1213
t 35 1226
g 35 1235
g 39 1249
t 39 1264
c 40 1274
a 40 1284
g 39 1296
c 35 1308
g 35 1320
t 29 1336
c 29 1345
c 29 1357
g 35 1369
c 35 1381
a 35 1393
t 35 1407
a 35 1415
c 35 1427
g 39 1439
c 51 1452
c 40 1465
g 39 1476
g 39 1490
t 39 1506
c 39 1516
c 39 1527
a 40 1537
g 39 1550
t 39 1565
t 39 1578
c 39 1587
g 40 1600
g 39 1614
c 45 1625
c 39 1637
t 39 1652
t 39 1665
g 39 1674
g 40 1688
t 40 1702
t 40 1714
t 39 1726
t 39 1738
c 39 1747
t 39 1762
c 39 1771
g 39 1784
g 40 1798
c 51 1809
g 51 1821
a 56 1834
g 56 1845
c 56 1858
g 56 1871
c 56 1882
g 51 1895
a 45 1907
t 45 1920
c 45 1930
g 45 1944
c 45 1955
c 51 1967
g 56 1980
c 56 1993
g 51 2005
a 51 2018
c 51 2030
a 51 2040
g 51 2052
c 40 2065
c 40 2078
g 40 2090
t 40 2105
g 43 2115
c 43 2128
g 51 2140
a 51 2153
c 51 2164
g 51 2175
g 51 2189
t 51 2203
c 51 2214
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n 0 10035
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g 12 10487
c 15 10498
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c 7 10535
g 7 10542
c 7 10559
g 13 10570
t 10 10582
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a 7 10671
g 6 10687
a 6 10693
a 6 10703
c 6 10722
g 7 10737
c 7 10745
g 13 10760
t 12 10774
t 7 10783
g 9 10792
a 7 10808
a 8 10814
a 8 10824
c 10 10837
c 16 10846
c 8 10858
t 8 10868
t 8 10879
g 8 10898
g 8 10909
c 11 10923
a 12 10935
a 9 10945
g 11 10955
c 11 10970
g 11 10977
c 8 10993
g 8 11003
g 8 11010
g 7 11020
c 9 11037
t 12 11054
g 9 11066
t 12 11081
c 8 11090
c 9 11099
g 10 11116
g 10 11124
t 13 11139
c 11 11148
g 9 11160
t 4 11173
END_DNA

END_SEQUENCE

WR{
template dscript 060127:153025
name: BIXY17487
lib: BIXY
}

WR{
primer dscript 060127:153025
type: univ fwd
}

BEGIN_SEQUENCE BIXY17488.b12

BEGIN_COMMENT

CHROMAT_FILE: BIXY17488.b12
ABI_THUMBPRINT: 0
PHRED_VERSION: 0.990722.g
CALL_METHOD: phred
QUALITY_LEVELS: 99
TIME: Fri Jan 27 15:28:58 2006
TRACE_ARRAY_MIN_INDEX: 0
TRACE_ARRAY_MAX_INDEX: 11295
TRIM: 41 800 0.0500
CHEM: term
DYE: big

END_COMMENT

BEGIN_DNA
n 0 6
n 0 17
n 0 28
a 4 55
a 6 58
g 6 63
c 4 74
t 4 81
n 0 96
n 0 107
n 0 119
n 0 130
n 0 141
n 0 152
n 0 163
n 0 174
n 0 185
a 4 210
a 6 215
t 6 220
a 9 234
c 9 242
g 9 249
a 9 263
t 9 273
a 4 294
g 4 301
a 8 314
g 12 320
a 12 335
t 7 346
t 6 355
g 8 370
t 11 387
c 14 392
g 8 401
a 9 415
g 9 428
a 9 442
c 12 450
a 12 466
g 28 475
c 24 490
a 34 498
g 34 508
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c 35 553
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g 35 572
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t 32 598
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g 33 7017
a 30 7030
t 33 7040
g 33 7052
g 40 7066
c 40 7077
a 40 7089
a 48 7101
g 48 7112
t 48 7125
c 40 7137
g 40 7148
c 40 7161
t 40 7173
g 34 7184
a 28 7198
a 28 7210
c 29 7221
a 29 7231
a 25 7244
c 29 7255
g 32 7266
a 32 7280
g 32 7290
c 34 7304
t 40 7315
t 40 7328
g 40 7339
a 40 7353
t 40 7363
g 40 7374
t 46 7386
g 56 7398
g 56 7411
t 56 7423
c 30 7435
g 30 7446
a 21 7459
g 29 7468
g 29 7481
g 39 7494
c 46 7506
a 44 7518
t 44 7528
g 40 7539
c 40 7552
a 48 7564
g 48 7575
t 34 7587
t 34 7599
t 29 7612
g 40 7623
a 40 7636
c 40 7646
c 40 7659
g 40 7670
c 32 7683
g 32 7693
g 32 7707
c 32 7719
t 32 7731
a 34 7743
c 29 7753
c 28 7765
t 27 7778
g 27 7789
a 23 7803
g 21 7812
c 17 7826
c 18 7837
c 29 7849
c 40 7861
t 40 7874
a 40 7886
t 44 7896
t 44 7908
t 44 7921
c 40 7933
a 40 7943
t 40 7955
c 29 7967
a 29 7977
a 29 7989
c 29 8002
a 29 8012
a 29 8024
c 29 8037
a 29 8047
a 22 8060
c 25 8071
g 24 8082
a 21 8097
a 4 8109
n 0 8120
a 4 8132
g 25 8142
c 24 8155
a 25 8167
g 25 8178
a 19 8192
a 22 8204
c 22 8215
g 27 8226
c 20 8238
c 15 8251
a 20 8263
t 20 8274
c 22 8286
c 22 8299
t 29 8311
c 24 8323
g 26 8334
a 21 8348
g 21 8358
a 16 8371
a 29 8383
c 22 8395
c 29 8405
c 29 8418
g 29 8430
t 40 8443
a 40 8455
t 40 8466
g 40 8477
t 44 8491
g 44 8502
c 40 8515
t 48 8527
g 56 8539
a 40 8552
t 40 8563
c 40 8576
t 32 8587
t 30 8599
c 19 8612
g 19 8622
a 17 8636
c 19 8648
a 12 8659
a 10 8671
g 14 8680
a 10 8696
a 10 8708
g 10 8717
a 13 8731
t 20 8741
c 24 8754
t 19 8765
c 15 8777
c 10 8789
a 10 8798
a 10 8811
c 19 8825
a 27 8836
t 40 8848
c 48 8861
c 40 8873
g 32 8885
t 27 8898
g 27 8909
a 24 8924
c 22 8934
c 20 8945
t 28 8958
g 40 8970
c 40 8984
t 40 8996
g 29 9007
c 25 9021
c 19 9033
g 24 9043
a 19 9057
t 19 9069
t 22 9081
c 31 9093
t 31 9105
c 22 9117
g 25 9129
a 18 9142
a 12 9152
c 17 9165
a 21 9176
g 13 9185
g 13 9200
t 18 9213
t 19 9225
g 29 9235
c 29 9248
c 25 9261
a 20 9271
a 20 9284
a 19 9296
g 25 9307
c 19 9320
c 25 9331
a 27 9344
g 27 9355
c 29 9368
c 21 9381
g 23 9392
t 15 9406
c 18 9419
c 15 9428
g 17 9442
c 23 9455
t 32 9467
g 32 9478
c 40 9492
t 40 9504
c 40 9516
a 40 9527
t 32 9539
c 29 9552
g 24 9562
t 20 9576
c 8 9587
g 8 9597
c 8 9612
c 8 9624
g 6 9634
a 6 9651
a 6 9664
g 6 9669
a 6 9686
c 8 9696
g 9 9706
t 11 9721
c 8 9732
g 8 9742
a 9 9758
c 13 9769
g 8 9786
g 10 9793
t 16 9807
g 10 9817
a 14 9833
a 12 9843
g 12 9855
c 9 9867
c 15 9878
c 11 9889
t 17 9904
c 8 9915
g 8 9925
c 8 9937
c 9 9949
a 14 9964
c 11 9975
g 14 9986
c 14 9999
t 16 10013
g 11 10022
g 13 10034
t 14 10049
g 19 10061
g 22 10072
t 14 10086
c 19 10098
a 15 10114
t 15 10132
a 10 10146
a 10 10156
c 17 10168
a 21 10179
t 19 10191
c 15 10207
c 10 10219
g 15 10230
c 15 10242
g 9 10251
g 9 10262
a 15 10280
c 14 10291
g 11 10304
t 21 10315
c 8 10327
g 8 10338
t 9 10351
c 14 10364
a 10 10380
a 12 10389
c 8 10398
g 8 10412
a 7 10423
a 10 10435
t 9 10453
t 7 10460
c 6 10471
a 6 10476
a 6 10490
g 10 10506
c 15 10517
t 15 10530
t 12 10543
g 17 10553
a 12 10568
t 11 10578
a 8 10594
t 7 10602
c 13 10615
a 13 10624
t 9 10642
t 9 10650
c 14 10662
a 12 10673
g 8 10692
g 7 10698
a 6 10712
c 7 10722
g 8 10735
a 8 10749
g 8 10757
c 8 10769
c 8 10779
t 11 10795
c 9 10809
a 4 10819
g 4 10827
a 4 10845
c 11 10856
t 10 10867
c 7 10881
c 7 10888
a 10 10904
g 10 10914
c 12 10929
g 13 10937
t 11 10951
a 7 10963
a 7 10970
c 10 10987
t 11 11000
g 9 11015
g 10 11023
a 13 11037
c 12 11051
t 14 11061
g 13 11072
c 10 11087
a 15 11098
a 9 11106
t 8 11118
c 9 11132
a 8 11140
a 8 11155
c 11 11167
t 10 11180
c 10 11192
a 6 11203
a 6 11210
t 6 11229
g 6 11232
g 6 11244
c 8 11264
t 8 11275
t 4 11294
END_DNA

END_SEQUENCE

WR{
template dscript 060127:153025
name: BIXY17488
lib: BIXY
}

WR{
primer dscript 060127:153025
type: univ fwd
}
BioPerl-1.007002/t/data/mutations.dat000444000766000024      3117413155576321 17433 0ustar00cjfieldsstaff000000000000ID           M20132:(362)c.+4G>A; E2K
Feature      DNA; 1
Feature        /label: point, transition
Feature        /proof: computed
Feature        /location: 4
Feature        /upflank: gaagattcagccaagctcaaggatg
Feature        /change: g>a
Feature        /dnflank: aagtgcagttagggctgggaagggt
Feature        /re_site: -BccI
Feature      RNA; 1
Feature        /label: missense
Feature        /proof: experimental
Feature        /location: 4 (M20132::366)
Feature        /upflank: gaagattcagccaagctcaaggatg
Feature        /change: g>a
Feature        /dnflank: aagtgcagttagggctgggaagggt
Feature        /re_site: -BccI
Feature        /codon_table: 1
Feature        /codon: gaa>aaa; 1
Feature        /region: coding
Feature      AA; 1
Feature        /label: substitution, conservative
Feature        /proof: computed
Feature        /location: 2
Feature        /change: E>K
//
ID           M20132:(362)c.+14T>A; L5X
Feature      DNA; 1
Feature        /label: point, transversion
Feature        /proof: computed
Feature        /location: 14
Feature        /upflank: ccaagctcaaggatggaagtgcagt
Feature        /change: t>a
Feature        /dnflank: agggctgggaagggtctaccctcgg
Feature      RNA; 1
Feature        /label: nonsense
Feature        /proof: experimental
Feature        /location: 14 (M20132::376)
Feature        /upflank: ccaagctcaaggatggaagtgcagt
Feature        /change: t>a
Feature        /dnflank: agggctgggaagggtctaccctcgg
Feature        /codon_table: 1
Feature        /codon: tta>taa; 2
Feature        /region: coding
Feature      AA; 1
Feature        /label: truncation
Feature        /proof: computed
Feature        /location: 5
Feature        /change: L>*
//
ID           M20132:(362)c.+4G>A; E2K
Feature      DNA; 1
Feature        /label: point, transition
Feature        /proof: computed
Feature        /location: 4
Feature        /upflank: gaagattcagccaagctcaaggatg
Feature        /change: g>a
Feature        /dnflank: aagtgcagttagggctgggaagggt
Feature        /re_site: -BccI
Feature      RNA; 1
Feature        /label: missense
Feature        /proof: experimental
Feature        /location: 4 (M20132::366)
Feature        /upflank: gaagattcagccaagctcaaggatg
Feature        /change: g>a
Feature        /dnflank: aagtgcagttagggctgggaagggt
Feature        /re_site: -BccI
Feature        /codon_table: 1
Feature        /codon: gaa>aaa; 1
Feature        /region: coding
Feature      AA; 1
Feature        /label: substitution, conservative
Feature        /proof: computed
Feature        /location: 2
Feature        /change: E>K
//
ID           M20132:(362)c.+100delATCCAG; I34del-2
Feature      DNA; 1
Feature        /label: deletion
Feature        /proof: computed
Feature        /location: 100..105
Feature        /upflank: tctgttccagagcgtgcgcgaagtg
Feature        /change: atccag>
Feature        /dnflank: aacccgggccccaggcacccagagg
Feature        /re_site: -BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV
Feature      RNA; 1
Feature        /label: inframe, deletion
Feature        /proof: experimental
Feature        /location: 100..105 (M20132::462..467)
Feature        /upflank: tctgttccagagcgtgcgcgaagtg
Feature        /change: atccag>
Feature        /dnflank: aacccgggccccaggcacccagagg
Feature        /re_site: -BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV
Feature        /codon_table: 1
Feature        /codon: atc>-; 1
Feature        /region: coding
Feature      AA; 1
Feature        /label: deletion
Feature        /proof: computed
Feature        /location: 34..35
Feature        /change: IQ>
//
ID           M20132:(362)c.+101delT; I34delX172
Feature      DNA; 1
Feature        /label: deletion
Feature        /proof: computed
Feature        /location: 101
Feature        /upflank: ctgttccagagcgtgcgcgaagtga
Feature        /change: t>
Feature        /dnflank: ccagaacccgggccccaggcaccca
Feature        /re_site: -BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I
Feature      RNA; 1
Feature        /label: frameshift, deletion
Feature        /proof: experimental
Feature        /location: 101 (M20132::463)
Feature        /upflank: ctgttccagagcgtgcgcgaagtga
Feature        /change: t>
Feature        /dnflank: ccagaacccgggccccaggcaccca
Feature        /re_site: -BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I
Feature        /codon_table: 1
Feature        /codon: atc>-; 2
Feature        /region: coding
Feature      AA; 1
Feature        /label: out-of-frame translation, truncation
Feature        /proof: computed
Feature        /location: 34
Feature        /change: I>TRTRAPGTQRPRAQHLPAPVCCCCSSSSSSSSSSSSSSSSSSSSKRLAP
Feature         GSSSSSRVRMVLPKPIVEAPQATWSWMRNSNLHSRSRPWSATPREVASQSLEPPWPPAR
Feature         GCRSSCQHLRTRMTQLPHPRCPCWAPLSPA*
//
ID           M20132:(362)c.+101insGGGCCC; I34ins+2
Feature      DNA; 1
Feature        /label: insertion
Feature        /proof: computed
Feature        /location: 100^101
Feature        /upflank: ctgttccagagcgtgcgcgaagtga
Feature        /change: >gggccc
Feature        /dnflank: tccagaacccgggccccaggcaccc
Feature        /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
Feature         +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV,
Feature         +SduI
Feature      RNA; 1
Feature        /label: inframe, insertion
Feature        /proof: experimental
Feature        /location: 100^101 (M20132::462^463)
Feature        /upflank: ctgttccagagcgtgcgcgaagtga
Feature        /change: >gggccc
Feature        /dnflank: tccagaacccgggccccaggcaccc
Feature        /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
Feature         +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV,
Feature         +SduI
Feature        /codon_table: 1
Feature        /codon: atc>-; 2
Feature        /region: coding
Feature      AA; 1
Feature        /label: insertion, complex
Feature        /proof: computed
Feature        /location: 34
Feature        /change: I>RAL
//
ID           M20132:(362)c.+100insG; I34ins81X
Feature      DNA; 1
Feature        /label: insertion
Feature        /proof: computed
Feature        /location: 99^100
Feature        /upflank: tctgttccagagcgtgcgcgaagtg
Feature        /change: >g
Feature        /dnflank: atccagaacccgggccccaggcacc
Feature        /re_site: +BamHI, +BinI, +NlaIV, +XhoII
Feature      RNA; 1
Feature        /label: frameshift, insertion
Feature        /proof: experimental
Feature        /location: 99^100 (M20132::461^462)
Feature        /upflank: tctgttccagagcgtgcgcgaagtg
Feature        /change: >g
Feature        /dnflank: atccagaacccgggccccaggcacc
Feature        /re_site: +BamHI, +BinI, +NlaIV, +XhoII
Feature        /codon_table: 1
Feature        /codon: atc>-; 1
Feature        /region: coding
Feature      AA; 1
Feature        /label: out-of-frame translation, truncation
Feature        /proof: computed
Feature        /location: 34
Feature        /change: I>DPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*
//
ID           M20132:(362)c.+100AT>GGGCCC; I34ins82X
Feature      DNA; 1
Feature        /label: complex
Feature        /proof: computed
Feature        /location: 100..101
Feature        /upflank: tctgttccagagcgtgcgcgaagtg
Feature        /change: at>gggccc
Feature        /dnflank: ccagaacccgggccccaggcaccca
Feature        /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
Feature         +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI
Feature      RNA; 1
Feature        /label: frameshift, complex
Feature        /proof: experimental
Feature        /location: 100..101 (M20132::462..463)
Feature        /upflank: tctgttccagagcgtgcgcgaagtg
Feature        /change: at>gggccc
Feature        /dnflank: ccagaacccgggccccaggcaccca
Feature        /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
Feature         +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI
Feature        /codon_table: 1
Feature        /codon: atc>-; 1
Feature        /region: coding
Feature      AA; 1
Feature        /label: out-of-frame translation, truncation
Feature        /proof: computed
Feature        /location: 34
Feature        /change: I>GPPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*
//
ID           M20132:(362+1)c.-1G>A
Feature      DNA; 1
Feature        /label: point, transition
Feature        /proof: computed
Feature        /location: -1
Feature        /upflank: ggtggaagattcagccaagctcaag
Feature        /change: g>a
Feature        /dnflank: atggaagtgcagttagggctgggaa
Feature        /re_site: -BccI, -FokI, +Hpy178III
Feature      RNA; 1
Feature        /label: unknown
Feature        /proof: experimental
Feature        /location: -1 (M20132::361)
Feature        /upflank: ggtggaagattcagccaagctcaag
Feature        /change: g>a
Feature        /dnflank: atggaagtgcagttagggctgggaa
Feature        /re_site: -BccI, -FokI, +Hpy178III
Feature        /region: 5'UTR
//
ID           M20132:(362)c.+2766T>C
Feature      DNA; 1
Feature        /label: point, transition
Feature        /proof: computed
Feature        /location: 2766
Feature        /upflank: tctatttccacacccagtgaagcat
Feature        /change: t>c
Feature        /dnflank: ggaaaccctatttccccaccccagc
Feature        /re_site: +Hpy188I, +SfaNI, -XcmI
Feature      RNA; 1
Feature        /label: unknown
Feature        /proof: experimental
Feature        /location: 2766 (M20132::3128)
Feature        /upflank: tctatttccacacccagtgaagcat
Feature        /change: t>c
Feature        /dnflank: ggaaaccctatttccccaccccagc
Feature        /re_site: +Hpy188I, +SfaNI, -XcmI
Feature        /region: 3'UTR
//
ID           J02933:(521)g.+12165A>G
Feature      DNA; 1
Feature        /label: point, transition
Feature        /proof: experimental
Feature        /location: 12165 (J02933::12686)
Feature        /upflank: cgcacacctgtggtgcctgccaccc
Feature        /change: a>g
Feature        /dnflank: ctgggttgcccatgattcatttttg
Feature        /re_site: +AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I,
Feature         -TspRI
Feature        /region: 3'UTR; (+1027)
Feature      RNA; 1
Feature        /label: unknown
Feature        /proof: computed
Feature        /location: 2428
Feature        /upflank: cgcacacctgtggtgcctgccaccc
Feature        /change: a>g
Feature        /dnflank: ctgggttgcccatgattcatttttg
Feature        /re_site: +AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I,
Feature         -TspRI
Feature        /region: 3'UTR; (-1)
//
ID           J02933:(521)g.+4G>T; V2F
Feature      DNA; 1
Feature        /label: point, transversion
Feature        /proof: computed
Feature        /location: 4 (J02933::525)
Feature        /upflank: gcagcactgcagagatttcatcatg
Feature        /change: g>t
Feature        /dnflank: tctcccaggccctcaggctcctctg
Feature        /re_site: -BsmAI, -Eco31I
Feature        /region: exon; 1 (+4)
Feature      RNA; 1
Feature        /label: missense
Feature        /proof: experimental
Feature        /location: 4
Feature        /upflank: gcagcactgcagagatttcatcatg
Feature        /change: g>t
Feature        /dnflank: tctcccaggccctcaggctcctctg
Feature        /re_site: -BsmAI, -Eco31I
Feature        /codon_table: 1
Feature        /codon: gtc>ttc; 1
Feature        /region: coding
Feature      AA; 1
Feature        /label: substitution, nonconservative
Feature        /proof: computed
Feature        /location: 2
Feature        /change: V>F
//
ID           J02933:(521)g.+1168G>T; D34Y
Feature      DNA; 1
Feature        /label: point, transversion
Feature        /proof: computed
Feature        /location: 1168 (J02933::1689)
Feature        /upflank: taaggcctcaggaggagaaacacgg
Feature        /change: g>t
Feature        /dnflank: acatgccgtggaagccggggcctca
Feature        /re_site: -BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I,
Feature         +Tsp4CI
Feature        /region: exon; 1 (-29)
Feature      RNA; 1
Feature        /label: missense
Feature        /proof: experimental
Feature        /location: 100
Feature        /upflank: taaggcctcaggaggagaaacacgg
Feature        /change: g>t
Feature        /dnflank: acatgccgtggaagccggggcctca
Feature        /re_site: -BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I,
Feature         +Tsp4CI
Feature        /codon_table: 1
Feature        /codon: gac>tac; 1
Feature        /region: coding
Feature      AA; 1
Feature        /label: substitution, nonconservative
Feature        /proof: computed
Feature        /location: 34
Feature        /change: D>Y
//
ID           J02933:(521+1)g.-4C>G
Feature      DNA; 1
Feature        /label: point, transversion
Feature        /proof: computed
Feature        /location: -4 (J02933::518)
Feature        /upflank: ggcaggggcagcactgcagagattt
Feature        /change: c>g
Feature        /dnflank: atcatggtctcccaggccctcaggc
Feature        /re_site: +BclI, +DpnI, +MboI
Feature        /region: 5'UTR; (-4)
Feature      RNA; 1
Feature        /label: unknown
Feature        /proof: experimental
Feature        /location: -4
Feature        /upflank: ggcaggggcagcactgcagagattt
Feature        /change: c>g
Feature        /dnflank: atcatggtctcccaggccctcaggc
Feature        /re_site: +BclI, +DpnI, +MboI
Feature        /region: 5'UTR; (+31)
//
BioPerl-1.007002/t/data/mutations.old.dat000444000766000024      3117413155576321 20210 0ustar00cjfieldsstaff000000000000ID           M20132:(362)c.+4G>A; E2K
Feature      DNA; 1
Feature        /label: point, transition
Feature        /proof: computed
Feature        /location: 4
Feature        /upflank: gaagattcagccaagctcaaggatg
Feature        /change: g>a
Feature        /dnflank: aagtgcagttagggctgggaagggt
Feature        /re_site: -BccI
Feature      RNA; 1
Feature        /label: missense
Feature        /proof: experimental
Feature        /location: 4 (M20132::366)
Feature        /upflank: gaagattcagccaagctcaaggatg
Feature        /change: g>a
Feature        /dnflank: aagtgcagttagggctgggaagggt
Feature        /re_site: -BccI
Feature        /codon_table: 1
Feature        /codon: gaa>aaa; 1
Feature        /region: coding
Feature      AA; 1
Feature        /label: substitution, conservative
Feature        /proof: computed
Feature        /location: 2
Feature        /change: E>K
//
ID           M20132:(362)c.+14T>A; L5X
Feature      DNA; 1
Feature        /label: point, transversion
Feature        /proof: computed
Feature        /location: 14
Feature        /upflank: ccaagctcaaggatggaagtgcagt
Feature        /change: t>a
Feature        /dnflank: agggctgggaagggtctaccctcgg
Feature      RNA; 1
Feature        /label: nonsense
Feature        /proof: experimental
Feature        /location: 14 (M20132::376)
Feature        /upflank: ccaagctcaaggatggaagtgcagt
Feature        /change: t>a
Feature        /dnflank: agggctgggaagggtctaccctcgg
Feature        /codon_table: 1
Feature        /codon: tta>taa; 2
Feature        /region: coding
Feature      AA; 1
Feature        /label: truncation
Feature        /proof: computed
Feature        /location: 5
Feature        /change: L>*
//
ID           M20132:(362)c.+4G>A; E2K
Feature      DNA; 1
Feature        /label: point, transition
Feature        /proof: computed
Feature        /location: 4
Feature        /upflank: gaagattcagccaagctcaaggatg
Feature        /change: g>a
Feature        /dnflank: aagtgcagttagggctgggaagggt
Feature        /re_site: -BccI
Feature      RNA; 1
Feature        /label: missense
Feature        /proof: experimental
Feature        /location: 4 (M20132::366)
Feature        /upflank: gaagattcagccaagctcaaggatg
Feature        /change: g>a
Feature        /dnflank: aagtgcagttagggctgggaagggt
Feature        /re_site: -BccI
Feature        /codon_table: 1
Feature        /codon: gaa>aaa; 1
Feature        /region: coding
Feature      AA; 1
Feature        /label: substitution, conservative
Feature        /proof: computed
Feature        /location: 2
Feature        /change: E>K
//
ID           M20132:(362)c.+100delATCCAG; I34del-2
Feature      DNA; 1
Feature        /label: deletion
Feature        /proof: computed
Feature        /location: 100..105
Feature        /upflank: tctgttccagagcgtgcgcgaagtg
Feature        /change: atccag>
Feature        /dnflank: aacccgggccccaggcacccagagg
Feature        /re_site: -BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV
Feature      RNA; 1
Feature        /label: inframe, deletion
Feature        /proof: experimental
Feature        /location: 100..105 (M20132::462..467)
Feature        /upflank: tctgttccagagcgtgcgcgaagtg
Feature        /change: atccag>
Feature        /dnflank: aacccgggccccaggcacccagagg
Feature        /re_site: -BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV
Feature        /codon_table: 1
Feature        /codon: atc>-; 1
Feature        /region: coding
Feature      AA; 1
Feature        /label: deletion
Feature        /proof: computed
Feature        /location: 34..35
Feature        /change: IQ>
//
ID           M20132:(362)c.+101delT; I34delX172
Feature      DNA; 1
Feature        /label: deletion
Feature        /proof: computed
Feature        /location: 101
Feature        /upflank: ctgttccagagcgtgcgcgaagtga
Feature        /change: t>
Feature        /dnflank: ccagaacccgggccccaggcaccca
Feature        /re_site: -BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I
Feature      RNA; 1
Feature        /label: frameshift, deletion
Feature        /proof: experimental
Feature        /location: 101 (M20132::463)
Feature        /upflank: ctgttccagagcgtgcgcgaagtga
Feature        /change: t>
Feature        /dnflank: ccagaacccgggccccaggcaccca
Feature        /re_site: -BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I
Feature        /codon_table: 1
Feature        /codon: atc>-; 2
Feature        /region: coding
Feature      AA; 1
Feature        /label: out-of-frame translation, truncation
Feature        /proof: computed
Feature        /location: 34
Feature        /change: I>TRTRAPGTQRPRAQHLPAPVCCCCSSSSSSSSSSSSSSSSSSSSKRLAP
Feature         GSSSSSRVRMVLPKPIVEAPQATWSWMRNSNLHSRSRPWSATPREVASQSLEPPWPPAR
Feature         GCRSSCQHLRTRMTQLPHPRCPCWAPLSPA*
//
ID           M20132:(362)c.+101insGGGCCC; I34ins+2
Feature      DNA; 1
Feature        /label: insertion
Feature        /proof: computed
Feature        /location: 100^101
Feature        /upflank: ctgttccagagcgtgcgcgaagtga
Feature        /change: >gggccc
Feature        /dnflank: tccagaacccgggccccaggcaccc
Feature        /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
Feature         +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV,
Feature         +SduI
Feature      RNA; 1
Feature        /label: inframe, insertion
Feature        /proof: experimental
Feature        /location: 100^101 (M20132::462^463)
Feature        /upflank: ctgttccagagcgtgcgcgaagtga
Feature        /change: >gggccc
Feature        /dnflank: tccagaacccgggccccaggcaccc
Feature        /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
Feature         +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV,
Feature         +SduI
Feature        /codon_table: 1
Feature        /codon: atc>-; 2
Feature        /region: coding
Feature      AA; 1
Feature        /label: insertion, complex
Feature        /proof: computed
Feature        /location: 34
Feature        /change: I>RAL
//
ID           M20132:(362)c.+100insG; I34ins81X
Feature      DNA; 1
Feature        /label: insertion
Feature        /proof: computed
Feature        /location: 99^100
Feature        /upflank: tctgttccagagcgtgcgcgaagtg
Feature        /change: >g
Feature        /dnflank: atccagaacccgggccccaggcacc
Feature        /re_site: +BamHI, +BinI, +NlaIV, +XhoII
Feature      RNA; 1
Feature        /label: frameshift, insertion
Feature        /proof: experimental
Feature        /location: 99^100 (M20132::461^462)
Feature        /upflank: tctgttccagagcgtgcgcgaagtg
Feature        /change: >g
Feature        /dnflank: atccagaacccgggccccaggcacc
Feature        /re_site: +BamHI, +BinI, +NlaIV, +XhoII
Feature        /codon_table: 1
Feature        /codon: atc>-; 1
Feature        /region: coding
Feature      AA; 1
Feature        /label: out-of-frame translation, truncation
Feature        /proof: computed
Feature        /location: 34
Feature        /change: I>DPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*
//
ID           M20132:(362)c.+100AT>GGGCCC; I34ins82X
Feature      DNA; 1
Feature        /label: complex
Feature        /proof: computed
Feature        /location: 100..101
Feature        /upflank: tctgttccagagcgtgcgcgaagtg
Feature        /change: at>gggccc
Feature        /dnflank: ccagaacccgggccccaggcaccca
Feature        /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
Feature         +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI
Feature      RNA; 1
Feature        /label: frameshift, complex
Feature        /proof: experimental
Feature        /location: 100..101 (M20132::462..463)
Feature        /upflank: tctgttccagagcgtgcgcgaagtg
Feature        /change: at>gggccc
Feature        /dnflank: ccagaacccgggccccaggcaccca
Feature        /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
Feature         +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI
Feature        /codon_table: 1
Feature        /codon: atc>-; 1
Feature        /region: coding
Feature      AA; 1
Feature        /label: out-of-frame translation, truncation
Feature        /proof: computed
Feature        /location: 34
Feature        /change: I>GPPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*
//
ID           M20132:(362+1)c.-1G>A
Feature      DNA; 1
Feature        /label: point, transition
Feature        /proof: computed
Feature        /location: -1
Feature        /upflank: ggtggaagattcagccaagctcaag
Feature        /change: g>a
Feature        /dnflank: atggaagtgcagttagggctgggaa
Feature        /re_site: -BccI, -FokI, +Hpy178III
Feature      RNA; 1
Feature        /label: unknown
Feature        /proof: experimental
Feature        /location: -1 (M20132::361)
Feature        /upflank: ggtggaagattcagccaagctcaag
Feature        /change: g>a
Feature        /dnflank: atggaagtgcagttagggctgggaa
Feature        /re_site: -BccI, -FokI, +Hpy178III
Feature        /region: 5'UTR
//
ID           M20132:(362)c.+2766T>C
Feature      DNA; 1
Feature        /label: point, transition
Feature        /proof: computed
Feature        /location: 2766
Feature        /upflank: tctatttccacacccagtgaagcat
Feature        /change: t>c
Feature        /dnflank: ggaaaccctatttccccaccccagc
Feature        /re_site: +Hpy188I, +SfaNI, -XcmI
Feature      RNA; 1
Feature        /label: unknown
Feature        /proof: experimental
Feature        /location: 2766 (M20132::3128)
Feature        /upflank: tctatttccacacccagtgaagcat
Feature        /change: t>c
Feature        /dnflank: ggaaaccctatttccccaccccagc
Feature        /re_site: +Hpy188I, +SfaNI, -XcmI
Feature        /region: 3'UTR
//
ID           J02933:(521)g.+12165A>G
Feature      DNA; 1
Feature        /label: point, transition
Feature        /proof: experimental
Feature        /location: 12165 (J02933::12686)
Feature        /upflank: cgcacacctgtggtgcctgccaccc
Feature        /change: a>g
Feature        /dnflank: ctgggttgcccatgattcatttttg
Feature        /re_site: +AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I,
Feature         -TspRI
Feature        /region: 3'UTR; (+1027)
Feature      RNA; 1
Feature        /label: unknown
Feature        /proof: computed
Feature        /location: 2428
Feature        /upflank: cgcacacctgtggtgcctgccaccc
Feature        /change: a>g
Feature        /dnflank: ctgggttgcccatgattcatttttg
Feature        /re_site: +AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I,
Feature         -TspRI
Feature        /region: 3'UTR; (-1)
//
ID           J02933:(521)g.+4G>T; V2F
Feature      DNA; 1
Feature        /label: point, transversion
Feature        /proof: computed
Feature        /location: 4 (J02933::525)
Feature        /upflank: gcagcactgcagagatttcatcatg
Feature        /change: g>t
Feature        /dnflank: tctcccaggccctcaggctcctctg
Feature        /re_site: -BsmAI, -Eco31I
Feature        /region: exon; 1 (+4)
Feature      RNA; 1
Feature        /label: missense
Feature        /proof: experimental
Feature        /location: 4
Feature        /upflank: gcagcactgcagagatttcatcatg
Feature        /change: g>t
Feature        /dnflank: tctcccaggccctcaggctcctctg
Feature        /re_site: -BsmAI, -Eco31I
Feature        /codon_table: 1
Feature        /codon: gtc>ttc; 1
Feature        /region: coding
Feature      AA; 1
Feature        /label: substitution, nonconservative
Feature        /proof: computed
Feature        /location: 2
Feature        /change: V>F
//
ID           J02933:(521)g.+1168G>T; D34Y
Feature      DNA; 1
Feature        /label: point, transversion
Feature        /proof: computed
Feature        /location: 1168 (J02933::1689)
Feature        /upflank: taaggcctcaggaggagaaacacgg
Feature        /change: g>t
Feature        /dnflank: acatgccgtggaagccggggcctca
Feature        /re_site: -BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I,
Feature         +Tsp4CI
Feature        /region: exon; 1 (-29)
Feature      RNA; 1
Feature        /label: missense
Feature        /proof: experimental
Feature        /location: 100
Feature        /upflank: taaggcctcaggaggagaaacacgg
Feature        /change: g>t
Feature        /dnflank: acatgccgtggaagccggggcctca
Feature        /re_site: -BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I,
Feature         +Tsp4CI
Feature        /codon_table: 1
Feature        /codon: gac>tac; 1
Feature        /region: coding
Feature      AA; 1
Feature        /label: substitution, nonconservative
Feature        /proof: computed
Feature        /location: 34
Feature        /change: D>Y
//
ID           J02933:(521+1)g.-4C>G
Feature      DNA; 1
Feature        /label: point, transversion
Feature        /proof: computed
Feature        /location: -4 (J02933::518)
Feature        /upflank: ggcaggggcagcactgcagagattt
Feature        /change: c>g
Feature        /dnflank: atcatggtctcccaggccctcaggc
Feature        /re_site: +BclI, +DpnI, +MboI
Feature        /region: 5'UTR; (-4)
Feature      RNA; 1
Feature        /label: unknown
Feature        /proof: experimental
Feature        /location: -4
Feature        /upflank: ggcaggggcagcactgcagagattt
Feature        /change: c>g
Feature        /dnflank: atcatggtctcccaggccctcaggc
Feature        /re_site: +BclI, +DpnI, +MboI
Feature        /region: 5'UTR; (+31)
//
BioPerl-1.007002/t/data/mutations.old.xml000444000766000024      4147113155576321 20241 0ustar00cjfieldsstaff000000000000

    
        
        
        computed
        gaagattcagccaagctcaaggatg
        g
        a
        aagtgcagttagggctgggaagggt
        -BccI
    
    
        
        experimental
        gaagattcagccaagctcaaggatg
        g
        a
        aagtgcagttagggctgggaagggt
        
        -BccI
        coding
    
    
        
        
        computed
        E
        K
    



    
        
        
        computed
        ccaagctcaaggatggaagtgcagt
        t
        a
        agggctgggaagggtctaccctcgg
    
    
        
        experimental
        ccaagctcaaggatggaagtgcagt
        t
        a
        agggctgggaagggtctaccctcgg
        
        coding
    
    
        
        computed
        L
        *
    



    
        
        
        computed
        gaagattcagccaagctcaaggatg
        g
        a
        aagtgcagttagggctgggaagggt
        -BccI
    
    
        
        experimental
        gaagattcagccaagctcaaggatg
        g
        a
        aagtgcagttagggctgggaagggt
        
        -BccI
        coding
    
    
        
        
        computed
        E
        K
    



    
        
        computed
        tctgttccagagcgtgcgcgaagtg
        atccag
        
        aacccgggccccaggcacccagagg
        -BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV
    
    
        
        
        experimental
        tctgttccagagcgtgcgcgaagtg
        atccag
        
        aacccgggccccaggcacccagagg
        
        -BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV
        coding
    
    
        
        computed
        IQ
        
    



    
        
        computed
        ctgttccagagcgtgcgcgaagtga
        t
        
        ccagaacccgggccccaggcaccca
        -BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I
    
    
        
        
        experimental
        ctgttccagagcgtgcgcgaagtga
        t
        
        ccagaacccgggccccaggcaccca
        
        -BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I
        coding
    
    
        
        
        computed
        I
        TRTRAPGTQRPRAQHLPAPVCCCCSSSSSSSSSSSSSSSSSSSSKRLAPGSSSSSRVRMVLPKPIVEAPQATWSWMRNSNLHSRSRPWSATPREVASQSLEPPWPPARGCRSSCQHLRTRMTQLPHPRCPCWAPLSPA*
    



    
        
        computed
        ctgttccagagcgtgcgcgaagtga
        
        gggccc
        tccagaacccgggccccaggcaccc
        +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV, +SduI
    
    
        
        
        experimental
        ctgttccagagcgtgcgcgaagtga
        
        gggccc
        tccagaacccgggccccaggcaccc
        
        +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV, +SduI
        coding
    
    
        
        
        computed
        I
        RAL
    



    
        
        computed
        tctgttccagagcgtgcgcgaagtg
        
        g
        atccagaacccgggccccaggcacc
        +BamHI, +BinI, +NlaIV, +XhoII
    
    
        
        
        experimental
        tctgttccagagcgtgcgcgaagtg
        
        g
        atccagaacccgggccccaggcacc
        
        +BamHI, +BinI, +NlaIV, +XhoII
        coding
    
    
        
        
        computed
        I
        DPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*
    



    
        
        computed
        tctgttccagagcgtgcgcgaagtg
        at
        gggccc
        ccagaacccgggccccaggcaccca
        +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI
    
    
        
        
        experimental
        tctgttccagagcgtgcgcgaagtg
        at
        gggccc
        ccagaacccgggccccaggcaccca
        
        +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI
        coding
    
    
        
        
        computed
        I
        GPPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*
    



    
        
        
        computed
        ggtggaagattcagccaagctcaag
        g
        a
        atggaagtgcagttagggctgggaa
        -BccI, -FokI, +Hpy178III
    
    
        
        experimental
        ggtggaagattcagccaagctcaag
        g
        a
        atggaagtgcagttagggctgggaa
        -BccI, -FokI, +Hpy178III
        5'UTR
    



    
        
        
        computed
        tctatttccacacccagtgaagcat
        t
        c
        ggaaaccctatttccccaccccagc
        +Hpy188I, +SfaNI, -XcmI
    
    
        
        experimental
        tctatttccacacccagtgaagcat
        t
        c
        ggaaaccctatttccccaccccagc
        +Hpy188I, +SfaNI, -XcmI
        3'UTR
    



    
        
        
        experimental
        cgcacacctgtggtgcctgccaccc
        a
        g
        ctgggttgcccatgattcatttttg
        +AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I, -TspRI
        3'UTR
    
    
        
        computed
        cgcacacctgtggtgcctgccaccc
        a
        g
        ctgggttgcccatgattcatttttg
        +AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I, -TspRI
        3'UTR
    



    
        
        
        computed
        gcagcactgcagagatttcatcatg
        g
        t
        tctcccaggccctcaggctcctctg
        -BsmAI, -Eco31I
        exon
    
    
        
        experimental
        gcagcactgcagagatttcatcatg
        g
        t
        tctcccaggccctcaggctcctctg
        
        -BsmAI, -Eco31I
        coding
    
    
        
        
        computed
        V
        F
    



    
        
        
        computed
        taaggcctcaggaggagaaacacgg
        g
        t
        acatgccgtggaagccggggcctca
        -BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I, +Tsp4CI
        exon
    
    
        
        experimental
        taaggcctcaggaggagaaacacgg
        g
        t
        acatgccgtggaagccggggcctca
        
        -BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I, +Tsp4CI
        coding
    
    
        
        
        computed
        D
        Y
    



    
        
        
        computed
        ggcaggggcagcactgcagagattt
        c
        g
        atcatggtctcccaggccctcaggc
        +BclI, +DpnI, +MboI
        5'UTR
    
    
        
        experimental
        ggcaggggcagcactgcagagattt
        c
        g
        atcatggtctcccaggccctcaggc
        +BclI, +DpnI, +MboI
        5'UTR
    

BioPerl-1.007002/t/data/mutations.xml000444000766000024      4145313155576321 17464 0ustar00cjfieldsstaff000000000000
    
        
        
        computed
        gaagattcagccaagctcaaggatg
        g
        a
        aagtgcagttagggctgggaagggt
        -BccI
    
    
        
        experimental
        gaagattcagccaagctcaaggatg
        g
        a
        aagtgcagttagggctgggaagggt
        
        -BccI
        coding
    
    
        
        
        computed
        E
        K
    


    
        
        
        computed
        ccaagctcaaggatggaagtgcagt
        t
        a
        agggctgggaagggtctaccctcgg
    
    
        
        experimental
        ccaagctcaaggatggaagtgcagt
        t
        a
        agggctgggaagggtctaccctcgg
        
        coding
    
    
        
        computed
        L
        *
    


    
        
        
        computed
        gaagattcagccaagctcaaggatg
        g
        a
        aagtgcagttagggctgggaagggt
        -BccI
    
    
        
        experimental
        gaagattcagccaagctcaaggatg
        g
        a
        aagtgcagttagggctgggaagggt
        
        -BccI
        coding
    
    
        
        
        computed
        E
        K
    


    
        
        computed
        tctgttccagagcgtgcgcgaagtg
        atccag
        
        aacccgggccccaggcacccagagg
        -BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV
    
    
        
        
        experimental
        tctgttccagagcgtgcgcgaagtg
        atccag
        
        aacccgggccccaggcacccagagg
        
        -BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV
        coding
    
    
        
        computed
        IQ
        
    


    
        
        computed
        ctgttccagagcgtgcgcgaagtga
        t
        
        ccagaacccgggccccaggcaccca
        -BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I
    
    
        
        
        experimental
        ctgttccagagcgtgcgcgaagtga
        t
        
        ccagaacccgggccccaggcaccca
        
        -BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I
        coding
    
    
        
        
        computed
        I
        TRTRAPGTQRPRAQHLPAPVCCCCSSSSSSSSSSSSSSSSSSSSKRLAPGSSSSSRVRMVLPKPIVEAPQATWSWMRNSNLHSRSRPWSATPREVASQSLEPPWPPARGCRSSCQHLRTRMTQLPHPRCPCWAPLSPA*
    


    
        
        computed
        ctgttccagagcgtgcgcgaagtga
        
        gggccc
        tccagaacccgggccccaggcaccc
        +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV, +SduI
    
    
        
        
        experimental
        ctgttccagagcgtgcgcgaagtga
        
        gggccc
        tccagaacccgggccccaggcaccc
        
        +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV, +SduI
        coding
    
    
        
        
        computed
        I
        RAL
    


    
        
        computed
        tctgttccagagcgtgcgcgaagtg
        
        g
        atccagaacccgggccccaggcacc
        +BamHI, +BinI, +NlaIV, +XhoII
    
    
        
        
        experimental
        tctgttccagagcgtgcgcgaagtg
        
        g
        atccagaacccgggccccaggcacc
        
        +BamHI, +BinI, +NlaIV, +XhoII
        coding
    
    
        
        
        computed
        I
        DPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*
    


    
        
        computed
        tctgttccagagcgtgcgcgaagtg
        at
        gggccc
        ccagaacccgggccccaggcaccca
        +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI
    
    
        
        
        experimental
        tctgttccagagcgtgcgcgaagtg
        at
        gggccc
        ccagaacccgggccccaggcaccca
        
        +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI
        coding
    
    
        
        
        computed
        I
        GPPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*
    


    
        
        
        computed
        ggtggaagattcagccaagctcaag
        g
        a
        atggaagtgcagttagggctgggaa
        -BccI, -FokI, +Hpy178III
    
    
        
        experimental
        ggtggaagattcagccaagctcaag
        g
        a
        atggaagtgcagttagggctgggaa
        -BccI, -FokI, +Hpy178III
        5'UTR
    


    
        
        
        computed
        tctatttccacacccagtgaagcat
        t
        c
        ggaaaccctatttccccaccccagc
        +Hpy188I, +SfaNI, -XcmI
    
    
        
        experimental
        tctatttccacacccagtgaagcat
        t
        c
        ggaaaccctatttccccaccccagc
        +Hpy188I, +SfaNI, -XcmI
        3'UTR
    


    
        
        
        experimental
        cgcacacctgtggtgcctgccaccc
        a
        g
        ctgggttgcccatgattcatttttg
        +AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I, -TspRI
        3'UTR
    
    
        
        computed
        cgcacacctgtggtgcctgccaccc
        a
        g
        ctgggttgcccatgattcatttttg
        +AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I, -TspRI
        3'UTR
    


    
        
        
        computed
        gcagcactgcagagatttcatcatg
        g
        t
        tctcccaggccctcaggctcctctg
        -BsmAI, -Eco31I
        exon
    
    
        
        experimental
        gcagcactgcagagatttcatcatg
        g
        t
        tctcccaggccctcaggctcctctg
        
        -BsmAI, -Eco31I
        coding
    
    
        
        
        computed
        V
        F
    


    
        
        
        computed
        taaggcctcaggaggagaaacacgg
        g
        t
        acatgccgtggaagccggggcctca
        -BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I, +Tsp4CI
        exon
    
    
        
        experimental
        taaggcctcaggaggagaaacacgg
        g
        t
        acatgccgtggaagccggggcctca
        
        -BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I, +Tsp4CI
        coding
    
    
        
        
        computed
        D
        Y
    


    
        
        
        computed
        ggcaggggcagcactgcagagattt
        c
        g
        atcatggtctcccaggccctcaggc
        +BclI, +DpnI, +MboI
        5'UTR
    
    
        
        experimental
        ggcaggggcagcactgcagagattt
        c
        g
        atcatggtctcccaggccctcaggc
        +BclI, +DpnI, +MboI
        5'UTR
    

BioPerl-1.007002/t/data/myco_sites.gff000444000766000024     13015413155576321 17576 0ustar00cjfieldsstaff000000000000L43967	TFBS	TF binding site	845	850	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	2294	2299	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	4869	4874	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	5114	5119	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	5381	5386	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	6116	6121	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	8532	8537	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	9753	9758	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	11057	11062	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	11778	11783	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	12031	12036	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	13228	13233	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	14076	14081	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	16100	16105	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	16856	16861	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	17811	17816	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	18498	18503	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	22239	22244	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	22668	22673	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	25371	25376	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	27174	27179	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	28699	28704	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	31536	31541	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	32280	32285	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	34908	34913	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	35342	35347	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	36013	36018	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	36249	36254	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	37296	37301	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	40336	40341	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	41696	41701	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	42937	42942	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	43383	43388	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	43663	43668	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	44794	44799	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	45682	45687	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	45689	45694	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	45933	45938	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	45961	45966	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	49079	49084	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	50046	50051	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	50673	50678	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	54403	54408	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	56322	56327	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	56604	56609	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	57762	57767	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	62005	62010	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	64485	64490	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	67266	67271	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	67778	67783	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	68301	68306	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	68783	68788	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	70794	70799	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	70850	70855	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	71267	71272	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	76218	76223	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	76491	76496	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	76755	76760	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	77661	77666	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	78567	78572	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	80048	80053	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	85510	85515	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	89992	89997	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	92257	92262	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	96234	96239	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	96297	96302	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	97614	97619	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	99414	99419	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	99819	99824	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	105921	105926	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	107636	107641	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	110308	110313	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	111015	111020	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	111073	111078	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	111804	111809	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	113602	113607	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	114253	114258	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	114809	114814	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	115046	115051	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	116069	116074	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	119248	119253	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	119816	119821	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	121917	121922	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	123025	123030	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	123270	123275	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	123923	123928	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	124335	124340	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	128198	128203	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	129032	129037	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	129236	129241	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	131425	131430	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	132247	132252	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	132405	132410	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	133735	133740	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	138310	138315	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	139126	139131	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	139442	139447	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	141227	141232	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	141243	141248	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	143687	143692	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	145015	145020	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	147561	147566	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	147913	147918	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	149139	149144	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	149664	149669	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	153814	153819	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	157201	157206	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	157667	157672	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	158641	158646	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	162903	162908	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	163175	163180	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	163819	163824	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	164743	164748	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	167447	167452	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	169414	169419	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	169421	169426	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	169751	169756	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	170006	170011	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	170998	171003	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	171452	171457	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	172732	172737	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	179757	179762	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	180069	180074	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	182094	182099	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	183142	183147	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	183269	183274	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	186054	186059	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	186931	186936	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	189325	189330	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	192962	192967	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	194690	194695	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	195004	195009	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	195562	195567	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	195724	195729	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	196909	196914	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	197612	197617	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	198208	198213	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	198704	198709	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	201352	201357	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	201957	201962	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	202165	202170	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	202841	202846	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	204241	204246	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	211108	211113	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	211423	211428	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	213816	213821	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	215780	215785	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	216829	216834	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	218083	218088	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	218198	218203	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	218893	218898	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	219001	219006	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	219782	219787	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	223559	223564	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	225993	225998	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	227069	227074	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	227076	227081	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	227391	227396	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	228047	228052	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	231632	231637	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	231899	231904	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	232782	232787	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	232802	232807	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	233418	233423	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	234390	234395	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	235811	235816	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	235889	235894	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	237044	237049	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	237126	237131	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	238244	238249	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	238591	238596	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	239219	239224	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	239284	239289	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	241552	241557	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	243029	243034	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	243055	243060	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	243412	243417	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	244800	244805	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	245364	245369	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	247846	247851	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	250269	250274	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	255006	255011	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	256084	256089	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	256757	256762	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	260434	260439	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	262015	262020	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	262765	262770	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	265170	265175	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	267453	267458	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	270147	270152	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	272537	272542	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	272756	272761	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	273921	273926	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	275355	275360	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	275431	275436	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	277976	277981	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	280297	280302	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	282577	282582	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	283777	283782	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	284089	284094	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	284594	284599	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	285254	285259	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	288191	288196	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	289168	289173	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	289365	289370	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	290063	290068	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	290312	290317	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	290933	290938	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	291190	291195	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	297466	297471	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	302074	302079	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	302262	302267	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	302827	302832	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	304031	304036	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	307621	307626	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	307741	307746	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	307935	307940	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	309939	309944	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	311141	311146	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	316583	316588	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	317137	317142	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	318511	318516	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	320015	320020	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	321001	321006	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	321214	321219	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	322838	322843	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	323180	323185	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	323197	323202	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	324701	324706	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	324863	324868	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	326911	326916	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	327902	327907	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	327971	327976	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	328658	328663	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	328724	328729	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	332208	332213	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	333136	333141	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	334039	334044	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	335067	335072	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	337948	337953	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	337957	337962	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	338991	338996	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	339252	339257	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	340352	340357	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	342514	342519	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	346001	346006	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	346641	346646	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	347444	347449	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	347860	347865	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	347891	347896	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	348013	348018	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	349913	349918	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	351391	351396	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	351398	351403	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	351713	351718	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	352043	352048	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	352140	352145	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	355393	355398	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	357131	357136	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	360824	360829	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	364016	364021	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	364142	364147	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	365403	365408	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	372018	372023	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	373754	373759	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	374344	374349	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	375437	375442	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	376138	376143	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	377142	377147	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	382337	382342	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	384202	384207	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	384425	384430	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	385502	385507	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	386494	386499	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	387502	387507	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	388064	388069	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	388879	388884	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	389669	389674	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	390581	390586	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	390917	390922	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	393588	393593	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	394387	394392	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	394904	394909	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	395493	395498	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	399504	399509	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	399825	399830	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	402061	402066	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	404493	404498	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	405229	405234	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	406073	406078	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	406177	406182	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	406556	406561	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	408978	408983	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	409263	409268	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	409434	409439	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	414153	414158	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	414393	414398	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	414965	414970	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	417932	417937	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	418307	418312	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	418580	418585	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	418682	418687	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	419628	419633	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	421619	421624	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	424418	424423	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	427596	427601	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	428041	428046	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	428257	428262	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	429247	429252	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	429254	429259	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	431369	431374	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	431449	431454	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	431474	431479	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	431650	431655	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	434107	434112	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	434482	434487	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	434615	434620	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	436479	436484	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	437344	437349	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	437598	437603	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	439230	439235	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	439592	439597	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	440655	440660	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	442011	442016	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	442102	442107	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	442868	442873	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	446506	446511	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	452302	452307	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	453058	453063	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	453880	453885	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	454279	454284	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	456596	456601	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	458508	458513	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	463490	463495	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	464267	464272	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	467140	467145	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	467569	467574	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	468724	468729	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	468820	468825	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	471485	471490	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	471526	471531	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	471807	471812	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	472752	472757	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	472762	472767	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	472962	472967	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	474627	474632	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	476038	476043	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	476194	476199	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	477451	477456	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	479116	479121	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	479150	479155	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	480805	480810	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	488811	488816	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	489777	489782	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	492141	492146	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	494766	494771	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	496378	496383	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	497406	497411	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	499139	499144	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	503505	503510	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	504674	504679	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	506112	506117	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	506989	506994	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	509237	509242	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	510134	510139	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	511768	511773	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	512727	512732	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	513329	513334	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	513462	513467	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	515629	515634	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	516164	516169	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	517465	517470	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	519394	519399	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	523635	523640	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	524706	524711	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	525703	525708	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	526026	526031	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	527753	527758	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	531141	531146	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	533969	533974	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	535504	535509	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	535933	535938	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	537846	537851	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	539424	539429	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	544688	544693	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	545686	545691	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	546394	546399	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	547730	547735	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	548041	548046	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	551431	551436	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	553155	553160	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	553709	553714	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	555572	555577	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	556008	556013	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	556135	556140	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	556897	556902	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	558828	558833	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	559903	559908	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	560315	560320	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	560742	560747	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	563254	563259	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	565681	565686	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	566779	566784	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	567667	567672	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	567940	567945	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	568458	568463	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	569632	569637	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	575394	575399	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	578596	578601	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	579055	579060	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	579079	579084	7.932	+	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
L43967	TFBS	TF binding site	579845	579850	7.932	-	0	TF "-35 Consensus"   ; class unknown  ; sequence TTGACA  
BioPerl-1.007002/t/data/nei_gojobori_test.aln000444000766000024       103113155576321 21063 0ustar00cjfieldsstaff000000000000>seq1 
ATGTATTCCTTCGCCGGCCCGGAGTATGACGAGGAGACAGGGAAAGTGAAGGCCCACTCACAGACTGACCGAGAGAACATCGCGCTCTACCTCATGTTTCACTACACCCGCAAGTGGGCGGCCCGTGTGGAGCAGTTGAGAGCCTACGAGGGCACGGTGGACGGGCGCTAC
>seq2
ATGTATTACTTCGCCGGCCCGGAGTATGACCGGAACACACGGAATGTGAAGGCCCACTCACAGACTGACCGAGAGAGCATCGCGCTCTACATCAGGTATCAGGACACCCGCAAGTGGACGGCCCATGAGGAGCAGTGGAGAGCCTACGAGGGCCGGGTGGAGTGGCGCTAC
>seq3 
ATGTATACCTTCGCCGGCCCGGAGTATGACCGGAACACACGGAATGTGAAGGCCCACTCACAGATTGACCGAGTGGACACCCTGCGCTACATCATGTATCAGGACACCCGCAAGTGGGCGGCCCGTGTGGAGCAGTTGAGAGCCTACGAGGGCACGGTGGAGTGGCGCTAC

BioPerl-1.007002/t/data/neighbor.dist000444000766000024        20113155576321 17323 0ustar00cjfieldsstaff000000000000    3
SINFRUP001     0.00000  0.16316  0.28603
SINFRUP002     0.16316  0.00000  0.27995
ENSP000002     0.28603  0.27995  0.00000
BioPerl-1.007002/t/data/new_blastn.txt000444000766000024      1213013155576321 17602 0ustar00cjfieldsstaff000000000000BLASTN 2.2.13 [Nov-27-2005]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman 
(1997), "Gapped BLAST and PSI-BLAST: a new generation of 
protein database search programs", Nucleic Acids Res. 25:3389-3402.

RID: 1141079027-8324-8848328247.BLASTQ4


Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
           3,742,891 sequences; 16,670,205,594 total letters
Query=  pyrR, 558 bases, FB21E40C checksum.
Length=558


                                                                   Score     E
Sequences producing significant alignments:                        (Bits)  Value

gi|41400296|gb|AE016958.1|  Mycobacterium avium subsp. paratub...   236    6e-59
gi|54013472|dbj|AP006618.1|  Nocardia farcinica IFM 10152 DNA, co   127    4e-26
gi|57546753|dbj|BA000030.2|  Streptomyces avermitilis MA-4680 gen   119    1e-23

ALIGNMENTS
>gi|41400296|gb|AE016958.1| Mycobacterium avium subsp. paratuberculosis str. k10, complete 
genome
Length=4829781

 Features in this part of subject sequence:
   PyrR

 Score =  236 bits (119),  Expect = 6e-59
 Identities = 248/291 (85%), Gaps = 0/291 (0%)
 Strand=Plus/Plus

Query  262      CCGCCGCGTCCGCTGGAGGCCACCTCCATTCCCGCGGGCGGTGTCGACGACGCGATCGTC  321
                |||||||| ||||||||||||||||| || || || |||||  ||||||||||| | || 
Sbjct  1166897  CCGCCGCGGCCGCTGGAGGCCACCTCGATCCCGGCCGGCGGCATCGACGACGCGCTGGTG  1166956

Query  322      ATCCTCGTCGACGACGTCCTGTACTCGGGCCGCTCGGTCCGCTCGGCGCTGGACGCGCTG  381
                ||||| ||||||||||| || ||||| ||||||||||| |||||||| ||||||||||||
Sbjct  1166957  ATCCTGGTCGACGACGTGCTCTACTCCGGCCGCTCGGTGCGCTCGGCACTGGACGCGCTG  1167016

Query  382      CGCGACATCGGTCGCCCCCGCATCGTGCAGCTGGCGGTGCTGGTCGACCGCGGGCACCGC  441
                |||||| | || ||||| ||  | ||||| ||||||||||||||||||||||| ||||||
Sbjct  1167017  CGCGACGTGGGCCGCCCGCGGGTGGTGCAACTGGCGGTGCTGGTCGACCGCGGTCACCGC  1167076

Query  442      GAGCTGCCCATCCGGGCCGACTACGTGGGCAAGAACGTCCCGACCTCACGCAGCGAAAGC  501
                ||||||||  | || ||||||||||| |||||||||||||| ||||| ||||| || |||
Sbjct  1167077  GAGCTGCCGCTGCGCGCCGACTACGTCGGCAAGAACGTCCCCACCTCGCGCAGTGAGAGC  1167136

Query  502      GTCCACGTGCTGCTCAGCGAACACGACGACCGCGACGGAGTGGTGATCTCG  552
                || |||||||||||   ||| ||||||| |  |||||| ||||||||||||
Sbjct  1167137  GTGCACGTGCTGCTGGCCGAGCACGACGGCGCCGACGGGGTGGTGATCTCG  1167187


>gi|54013472|dbj|AP006618.1| Nocardia farcinica IFM 10152 DNA, complete genome
Length=6021225

 Features in this part of subject sequence:
   putative pyrimidine operon regulator

 Score =  127 bits (64),  Expect = 4e-26
 Identities = 85/92 (92%), Gaps = 0/92 (0%)
 Strand=Plus/Minus

Query  406      GTGCAGCTGGCGGTGCTGGTCGACCGCGGGCACCGCGAGCTGCCCATCCGGGCCGACTAC  465
                ||||||||||| ||||||||||||||||| |||||||||||||| ||||| |||||||||
Sbjct  3837536  GTGCAGCTGGCCGTGCTGGTCGACCGCGGCCACCGCGAGCTGCCGATCCGCGCCGACTAC  3837477

Query  466      GTGGGCAAGAACGTCCCGACCTCACGCAGCGA  497
                |||||||||||||| || ||||| ||||||||
Sbjct  3837476  GTGGGCAAGAACGTGCCCACCTCCCGCAGCGA  3837445


>gi|57546753|dbj|BA000030.2| Streptomyces avermitilis MA-4680 genomic DNA, complete genome
Length=9025608

 Features in this part of subject sequence:
   putative pyrimidine operon regulatory protein

 Score =  119 bits (60),  Expect = 1e-23
 Identities = 135/160 (84%), Gaps = 0/160 (0%)
 Strand=Plus/Plus

Query  323      TCCTCGTCGACGACGTCCTGTACTCGGGCCGCTCGGTCCGCTCGGCGCTGGACGCGCTGC  382
                ||||||||||||||||||| | ||| |||||| |  ||||| | || || ||||||||| 
Sbjct  8189890  TCCTCGTCGACGACGTCCTCTTCTCCGGCCGCACCATCCGCGCCGCCCTCGACGCGCTGA  8189949

Query  383      GCGACATCGGTCGCCCCCGCATCGTGCAGCTGGCGGTGCTGGTCGACCGCGGGCACCGCG  442
                 ||||||||| ||||| |||  ||| ||||| ||||| || ||||||||||| |||||||
Sbjct  8189950  ACGACATCGGCCGCCCGCGCGCCGTACAGCTCGCGGTCCTCGTCGACCGCGGTCACCGCG  8190009

Query  443      AGCTGCCCATCCGGGCCGACTACGTGGGCAAGAACGTCCC  482
                | ||||||||||| ||||||||||| ||||||||| ||||
Sbjct  8190010  AACTGCCCATCCGCGCCGACTACGTCGGCAAGAACCTCCC  8190049



  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,environmental 
samples or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Feb 23, 2006  9:00 AM
  Number of letters in database: -509,663,586
  Number of sequences in database:  3,742,891
Lambda     K      H
    1.37    0.711     1.31 
Gapped
Lambda     K      H
    1.37    0.711     1.31 
Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 3742891
Number of Hits to DB: 2465616
Number of extensions: 117843
Number of successful extensions: 1771
Number of sequences better than 1e-23: 0
Number of HSP's better than 1e-23 without gapping: 0
Number of HSP's gapped: 1771
Number of HSP's successfully gapped: 0
Length of query: 558
Length of database: 16670205594
Length adjustment: 22
Effective length of query: 536
Effective length of database: 16670205594
Effective search space: 8935230198384
Effective search space used: 8891094027712
A: 0
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 25 (49.6 bits)
S1: 14 (28.2 bits)
S2: 60 (119.4 bits)


BioPerl-1.007002/t/data/nhmmer-3.1.out000444000766000024       677113155576321 17221 0ustar00cjfieldsstaff000000000000# nhmmer :: search a DNA model or alignment against a DNA database
# HMMER 3.1b1 (May 2013); http://hmmer.org/
# Copyright (C) 2013 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query file:                      ../HMMs/A_HA_H7_CDS_nucleotide.hmm
# target sequence database:        tmp.fa
# number of worker threads:        4
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       A_HA_H7_CDS_nucleotide  [M=1683]
Scores for complete hits:
    E-value  score  bias  Sequence  start    end  Description
    ------- ------ -----  --------  -----  -----  -----------
    3.2e-48  148.2   5.7  seq1          1    151  Description of seq1
    3.9e-15   38.6   0.4  seq2         59      1  Description of seq2


Annotation for each hit  (and alignments):
>> seq1  Description of seq1
    score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to    sq len      acc
   ------ ----- ---------   -------   -------    --------- ---------    --------- --------- ---------    ----
 !  148.2   5.7   3.2e-48       258       411 ..         1       151 []         1       151 []       151    0.98

  Alignment:
  score: 148.2 bits
  A_HA_H7_CDS_nucleotide 258 attcctagaattttcagctgatttaattattgagaggcgagaaggaagtaatgatgtctgttatcctgggaaattcgtaaatgaaga 344
                             attcctagaattttcagc+gatttaattattgagaggcgagaaggaagt   gatgtctgttatcctgggaaattcgt+aatgaaga
                    seq1   1 ATTCCTAGAATTTTCAGCCGATTTAATTATTGAGAGGCGAGAAGGAAGT---GATGTCTGTTATCCTGGGAAATTCGTGAATGAAGA 84 
                             689*******************************************777...*********************************** PP

  A_HA_H7_CDS_nucleotide 345 agctctgaggcaaattctcagggggtcaggcggaattgacaaggagacaatgggattcacatatagc 411
                             agctctgaggcaaattctcaggg+gtcaggcggaattgacaaggagacaatgggattcac+ta+agc
                    seq1  85 AGCTCTGAGGCAAATTCTCAGGGAGTCAGGCGGAATTGACAAGGAGACAATGGGATTCACCTACAGC 151
                             ****************************************************************986 PP

>> seq2  Description of seq2
    score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to    sq len      acc
   ------ ----- ---------   -------   -------    --------- ---------    --------- --------- ---------    ----
 !   38.6   0.4   3.9e-15        34        92 ..        59         1 ..        60         1 ..        60    0.97

  Alignment:
  score: 38.6 bits
  A_HA_H7_CDS_nucleotide 34 gtgatgattgcaacaaatgcagacaaaatctgccttgggcaccatgctgtgtcaaacgg 92
                            g+gat+att+c+acaaatgcagacaa atctgccttgggca+catgc+gtgtcaaacgg
                    seq2 59 GCGATCATTCCGACAAATGCAGACAAGATCTGCCTTGGGCATCATGCCGTGTCAAACGG 1 
                            6899****************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                              1  (1683 nodes)
Target sequences:                            2  (422 residues searched)
Residues passing SSV filter:               211  (0.5); expected (0.02)
Residues passing bias filter:              211  (0.5); expected (0.02)
Residues passing Vit filter:               211  (0.5); expected (0.003)
Residues passing Fwd filter:               211  (0.5); expected (3e-05)
Total number of hits:                        2  (0.498)
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.30
# Mc/sec: 2.37
//
[ok]
BioPerl-1.007002/t/data/nhx-bacteria.nhx000444000766000024       206713155576321 17761 0ustar00cjfieldsstaff000000000000(((((('C.acetobtylicm':0.040074,'C.tetani':0.033756):0.0[&&NHX:B=37],'C.
botlinm':0.034362):0.007026[&&NHX:B=64],('C.klyveri':0.044196,'C.novyi':
0.037374):0.003659[&&NHX:B=43]):0.047598[&&NHX:B=100],(('L.rminis':0.057
449,'Carnobacterim':0.029411):0.009985[&&NHX:B=82],(('L.welshimeri':4.48
E-4,('L.innoca':7.3E-5,'L.monocytogenes':0.002059):8.99E-4[&&NHX:B=39]):
0.033037[&&NHX:B=100],('B.clasii':0.032157,(((('B.amyloliqefaciens':0.0,
'B.sbtilis':0.0):0.004558[&&NHX:B=100],'B.licheniformis':0.006884):0.002
919[&&NHX:B=77],'B.pmils':0.006346):0.013484[&&NHX:B=100],('B.thringiens
is':0.0,'B.ceres':7.28E-4):0.021758[&&NHX:B=100]):0.003801[&&NHX:B=63]):
0.006339[&&NHX:B=86]):0.005397[&&NHX:B=79]):0.036009[&&NHX:B=100]):0.020
375[&&NHX:B=96],(('P.aerginosa':0.058529,(('E.coli':0.007283,'S.typhimri
m':0.004915):0.007918[&&NHX:B=89],'Y.enterocolitica':0.024069):0.059706[
&&NHX:B=100]):0.031177[&&NHX:B=100],('R.sphaeroides':0.059893,'A.tmefaci
ens':0.058672):0.038391[&&NHX:B=100]):0.023241[&&NHX:B=99]):0.0070239455
[&&NHX:B=100],'T.maritima':0.13345505):0.0[&&NHX:B=100];
BioPerl-1.007002/t/data/no-genes.genscan000555000766000024        72313155576321 17730 0ustar00cjfieldsstaff000000000000GENSCAN 1.0	Date run: 29-Nov-101	Time: 16:19:58

Sequence 5922693.fa : 780 bp : 52.82% C+G : Isochore 3 (51 - 57 C+G%)

Parameter matrix: HumanIso.smat

Predicted genes/exons:

Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------

 1.00 Prom -    305    266   40                               2.29


Predicted peptide sequence(s):

Predicted coding sequence(s):


NO PEPTIDES PREDICTED
BioPerl-1.007002/t/data/no_FH.embl000444000766000024      3404013155576321 16543 0ustar00cjfieldsstaff000000000000ID   AE000001;
FT   CDS             202..1557
FT                   /M1_GAS_orthologue="SPy0002"
FT                   /MGAS10394_orthologue="M6_Spy0001"
FT                   /MGAS315_orthologue="dnaA"
FT                   /MGAS8232_orthologue="dnaA"
FT                   /SSI_1_orthologue="SPs0001"
FT                   /cds_id="subject0"
FT                   /cds_id="subject0"
FT                   /class="1.2.1"
FT                   /colour=2
FT                   /fasta_file="fasta/SP_new.tab.seq.00001.out"
FT                   /gene="dnaA"
FT                   /gene="dnaH"
FT                   /product="chromosomal replication initiator protein"
FT                   /systematic_id="SpyM50001"
FT   misc_feature    535..1488
FT                   /colour=9
FT                   /domain="HMMPfam:PF00308;Bacterial  dnaA
FT                   protein;1.7e-156;codon 112-429"
FT                   /id="SpyM50001"
FT                   /label=HMMPfam
FT                   /note="HMMPfam hit to PF00308, Bacterial  dnaA  protein,
FT                   score 1.7e-156"
FT   misc_feature    655..678
FT                   /colour=8
FT                   /note="PS00017 ATP/GTP-binding site motif A (P-loop)."
FT   misc_feature    1429..1488
FT                   /colour=8
FT                   /note="PS01008 DnaA protein signature."
SQ   Sequence 1841271 BP; 564546 A; 354645 C; 356610 G; 565470 T; 0 other;
     ttgttgatat tctgtttttt cttttttagt tttccacata aaaaatagtt gaaaacaata        60
     gcggtgtcac cttaaaatgg cttttccaca ggttgtggag aacccaaatt aacagtgtta       120
     atttattttc cacaggttgt ggaaaactag aatagtttat ggtagaatag ttctagaatt       180
     atccacaaga aggaacctag tatgactgaa aatgaacaaa ttttttggaa cagggtcttg       240
     gaattagctc agagtcaatt aaaacaggca acttatgaat tttttgttca tgatgcccgt       300
     ctattaaagg tcgataagca tattgcaact atttacttag atcaaatgaa agaactcttt       360
     tgggaaaaaa atcttaaaga tgttattctt actgctggtt ttgaagttta taacgctcaa       420
     atttctgttg actatgtttt cgaagaagac ctaatgattg agcaaaatca gaccaaaatc       480
     aatcaaaaac ctaagcagca agccttaaat tctttgccta ctgttacttc agatttaaac       540
     tcgaaatata gttttgaaaa ctttattcaa ggagatgaaa atcgttgggc tgttgctgct       600
     tcaatagcag tagctaatac tcctggaact acctataatc ctttgtttat ttggggtggc       660
     cctgggcttg gaaaaaccca tttattaaat gctattggta attctgtact attagaaaat       720
     ccaaatgctc gaattaaata tatcacagct gaaaacttta ttaatgagtt tgttatccat       780
     attcgccttg ataccatgga tgaattgaaa gaaaaatttc gtaatttaga tttactcctt       840
     attgatgata tccaatcttt agctaaaaaa acgctctctg gaacacaaga agagttcttt       900
     aatactttta atgcacttca taataataac aaacaaattg tcctaacaag cgaccgtaca       960
     ccagatcatc tcaatgattt agaagatcga ttagttactc gttttaaatg gggattaaca      1020
     gtcaatatca cacctcctga ttttgaaaca cgagtggcta ttttgacaaa taaaattcaa      1080
     gaatataact ttatttttcc tcaagatacc attgagtatt tggctggtca atttgattct      1140
     aatgtcagag atttagaagg tgccttaaaa gatattagtc tggttgctaa tttcaaacaa      1200
     attgacacga ttactgttga cattgctgcc gaagctattc gcgccagaaa gcaagatgga      1260
     cctaaaatga cagttattcc catcgaagaa attcaagcgc aagttggaaa attttacggt      1320
     gttaccgtca aagaaattaa agctactaaa cgaacacaaa atattgtttt agcaagacaa      1380
     gtagctatgt ttttagcacg tgaaatgaca gataacagtc ttcctaaaat tggaaaagaa      1440
     tttggtggca gagaccattc aacagtactc catgcctata ataaaatcaa aaacatgatc      1500
     agccaggacg aaagccttag gatcgaaatt gaaaccataa aaaacaaaat taaataacat      1560
     gtggaaaaga atatctttta tgaaatagtt atccacaagt tgtgaacaac catttagtct      1620
     tggattctct cgtttattta gagttatcca ctatatacac aagacctact actactactt      1680
     attattatac ttattaaata aaggagttct catgattcaa ttttcaatta atcgcacatt      1740
     atttattcat gctttaaatg caactaaacg tgctattagc actaaaaatg ccattcctat      1800
     tctttcatca ataaaaattg aagtcactcc tacaggagta actttaacag ggtctaacgg      1860
     tcaaatatca attgaaaaca ctattcctgt aagtaatgaa aatgctggtt tgctaattac      1920
     ctctccagga gctattttat tagaagctag tttttttatt aatattattt caagtttgcc      1980
     agatattagt ataaatgtta aagaaattga acaacaccaa gttgttttaa ccagtggtaa      2040
     atcagagatt accttaaaag gaaaagatgt tgaccagtat cctcgtctac aagaagtatc      2100
     aacagaaaat cctttgattt taaaaacaaa attattgaag tctattattg ctgaaacagc      2160
     ttttgcagcc agtttacaag aaagtcgtcc tattttaaca ggagttcata ttgtattaag      2220
     taatcataaa gattttaaag cagtagcgac tgactctcat cgtatgagcc aacgtttaat      2280
     cactttggac aatacttcag cagattttga tgtggttatt ccaagtaaat ctttgagaga      2340
     attttcagca gtatttacag atgatattga gaccgttgag gtatttttct caccaagcca      2400
     aatcttgttc agaagtgaac acatttcttt ttatacacgc ctcttagaag gaaattatcc      2460
     cgatacagac cgtttattaa tgacagaatt tgagacggag gttgttttca atacccaatc      2520
     ccttcgccac gctatggaac gtgccttctt gatttctaat gctactcaaa atggtactgt      2580
     taagcttgag attactcaaa atcatatttc agctcatgtt aactcacctg aggttggtaa      2640
     ggtaaacgag gatttagata ttgttagtca gtctggtagt gatttaacta tcagcttcaa      2700
     tccaacttac cttattgagt ctttaaaagc tattaaaagt gaaacagtaa aaattcattt      2760
     cttatcacca gttcgaccat tcaccctaac accaggcgat gaggaagaaa gttttatcca      2820
     attaattaca ccagtacgaa caaactaagt aagaaaaagc tcccttttag gagttttttt      2880
     gttattataa atattaacga taatataagt ggagaaaagt gaatgtatca aattggatca      2940
     tttgttgaaa tgaaaaaacc tcatgcttgt gtaattaaag aaactggtaa aaaggctaat      3000
     caatggaagg tactgagagt aggagctgat attaaaattc agtgtactaa ctgtcagcat      3060
     gtgattatga tgagtcgtta tgattttgag cgaaaattaa aaaaagtact gcaaccatga      3120
     aagtcctttt aaataaataa ttctagctat atttgcaacc aatactttcc taaaaaattg      3180
     ttagtatgcc gttggaaaat tagctattct aacgttatcg aaagaagaaa ggtggctatt      3240
     gacaatgacg aaagttgtag cacagttact tagtttctcg gcaaactata tcaaaatgag      3300
     aataatacac caaactttga taatttaaat gaaggtgaaa gagtggcata atgataagca      3360
     aatctgaaat tttcttctta ttcataccgc tttttcttct attttttggt ataataatct      3420
     tgattgaaat ttgaatggag attcgctaaa tggctttaac agcaggtatt gtaggcttac      3480
     caaatgttgg taaatcaacc ttatttaacg caattacaaa agcaggagca gaagctgcta      3540
     attatccttt tgcgactatt gatcccaatg ttggtatggt agaggttcca gatgagcgtc      3600
     tgcaaaaatt gacagaattg attacaccta aaaaaacagt tccgacaacc tttgaattta      3660
     ctgatattgc aggtatcgtt aaaggtgctt ctagagggga aggtctagga aataaatttt      3720
     tagctaatat tcgtgaagtc gatgctattg ttcatgtggt acgtgctttt gatgatgaaa      3780
     atgtcatgcg tgaacaaggt cgtgaggatg ctttcgttga tcctatagca gatattgaca      3840
     ctattaatct tgaattaatc ttagctgatt tagagtcaat caataaacgt tatgcgcgtg      3900
     ttgaaaaaat ggcacgaact caaaaagata aagaatcagt agcagagttc aatgttttac      3960
     aaaagattaa acctgttttg gaagatggga aatcagctag gacaattgag tttacagaag      4020
     aggaagcaaa agttgttaaa ggtctctttt tattaacaac taaacctgtt ttatatgtag      4080
     ctaatgtcga tgaagataaa gttgctaatc cagatggtat tgattatgtc aaacaaattc      4140
     gtgactttgc agctactgaa aatgctgaag tagttgttat ctcagcgcgt gcagaagaag      4200
     aaatttcaga gcttgacgat gaggataaag aagaattttt ggaagctatc ggtcttactg      4260
     aatcaggcgt tgataaatta accagagcag cttatcatct cttaggcctt ggaacctatt      4320
     ttacagcagg tgaaaaagag gttcgtgctt ggacgtttaa gcgtggtata aaagctccac      4380
     aagctgctgg tattatccat tcagattttg aaagaggttt tattcgtgca gtaaccatgt      4440
     cttatgatga tctaatgatc tacggttcag aaaaagccgt caaagaagct ggacgcttgc      4500
     gtgaagaagg aaaagaatac gttgttcaag atggggacat catggaattc agatttaatg      4560
     tgtaattata ttaaaacaat atcagaaggt tggaagaaca ttccagccct tttggcattt      4620
     tagaaagaga aaatatggta aaaatgattg ttggtctggg aaatccaggc tctaaatatg      4680
     aaaaaacaaa gcacaatatt ggttttatgg ctattgacaa tattgtcaag aaccttgacg      4740
     ttacctttac agatgataaa aattttaaag cacagatagg aagtactttt attaatcatg      4800
     aaaaagttta ctttgtgaaa cctactactt ttatgaataa tagcggcata gcagtaaaag      4860
     cattactaac ctactataat attgacataa cagatttaat tgttatctat gatgatttag      4920
     acatggaagt cagtaaatta cgtttacgta gtaagggttc agcaggagga cataatggca      4980
     ttaagtcaat cattgcccac attggaactc aggaatttaa ccgaatcaaa gttggtattg      5040
     gacgaccttt aaaaggtatg actgttatta gccatgtgat gggccaattc aataccgaag      5100
     ataatattgc tatttcgtta actcttgaca gagttgtcaa tgctgtcaag ttttatttac      5160
     aagaaaatga ttttgaaaaa acaatgcaga aatttaatgg ataatcatgg atattttaga      5220
     attatttagt cagaataaga aagtccaatc ctggcactct ggattaacca ccttaggaag      5280
     acaactggta atggggttat cgggttcaag taaagcattg gctatagctt ccgcttattt      5340
     agatgatcaa aaaaaaatag ttgtggttac atcaactcaa aatgaggttg aaaaattagc      5400
     cagcgattta tctagtttac ttgatgaaga acttgttttc caattttttg cagacgatgt      5460
     ggctgcagcg gaatttatct ttgcgtcaat ggataaagct ctatcaagaa tagaaaccct      5520
     gcaattttta aggaatccta aatctcaggg cgttttaatt gttagtttat caagcttaag      5580
     aactttattg ccaaacccag atgtttttac aaagagtcag attcaactaa cagttggaga      5640
     agattatgat agtgatactc ttactaaaca actgatgaca attggctatc agaaggtctc      5700
     acaggtcatt agtccgggag aatttagccg tcgaggggat attttagata tctatgagat      5760
     tacacaagaa ttgccttatc gattggaatt ttttggcgat gatattgata gtattaggca      5820
     attttatcca gaaactcaaa aatcttttga acaactagaa ggtattttta ttaatccagc      5880
     aagtgatctt atttttgagg ctagtgattt tcaacgtggc attgagcaat tagaaaaggc      5940
     tctacaaaca gcacaagatg ataaaaaatc ttatttagaa gatgtattag ctgtttcaaa      6000
     aaacggtttt aaacataagg atatccgtaa atttcaatca ttattttacg aaaaagagtg      6060
     gtcattatta gattatattc ctaagggaac gccaatcttt tttgatgatt ttcaaaaact      6120
     agttgataaa aatgcaagat ttgatttaga gattgctaat ctcttgacag aagatttaca      6180
     gcaaggaaag gctctttcca atcttaacta ctttgcagat aattatcgag agcttaggca      6240
     ctataagcca gcgaccttct tttcaaattt tcataaggga cttggaaata tcaaatttga      6300
     tcagatgcat cagctaactc agtatgccat gcaggaattt tttaatcaat ttcctttgtt      6360
     gattgatgag attaaacggt atcaaaaaaa tcaaacaacg gttattgtac aggtagagtc      6420
     tcagtatgct tacgaacgac ttgaaaaatc ttttcaagat taccaatttc gccttccttt      6480
     agtgagtgct aatcaaattg tttcacgtga atcacaaatt gtaattggag ctatctccag      6540
     tggtttttat tttgctgatg aaaagttagc gttaatcaca gagcatgaaa tttatcataa      6600
     aaagatcaaa cgacgcgcta gacgatctaa tattagcaat gctgagcgtt tgaaagatta      6660
     caatgagtta gcagtaggtg attacgtggt tcataatgtc catggtatcg gtcgctttct      6720
     tggaattgaa acgattcagg ttcagggaat ccatcgagat tacgttacta ttcaatatca      6780
     aaattcagac cgtatttctc ttccaattga ccaaattggt agcttatcaa agtacgtttc      6840
     tgctgatgga aaagaaccta aaattaataa actcaatgat ggtcgttttc aaaagacaaa      6900
     gcaaaaggtc gctagacaag tagaagatat tgctgatgac cttctaaaat tatatgctga      6960
     aagaagtcag caaaaaggat tttcattttc accagatgat gacttgcagc gcgcttttga      7020
     tgatgatttt gcttttgtag aaacagaaga tcaacttagg tctataaagg aaattaaagc      7080
     tgatatggag agcatgcaac ctatggatcg tcttttagta ggcgatgtag gatttggtaa      7140
     gacagaagta gctatgaggg cagcctttaa agcggtgaat gatcacaaac aagtagctgt      7200
     cttagttcca accacagtct tggcccagca gcattatgaa aacttcaaag cacgctttga      7260
     aaattacctt gttgaggttg acgtcttaag tcgtttccgt agtaaaaaag agcaagctga      7320
     aacactagaa catgtacaaa aaggtcaaat tgacattatt atcggaaccc atcgactcct      7380
     atcaaaagat gtggtctttt ctgatttagg attaattgtg attgatgagg aacaacggtt      7440
     tggtgttaag cataaagaaa ctttaaagga attaaaaact aaggttgacg tcttaacctt      7500
     aacagctact ccgattccta gaaccttaca catgtctatg ttaggtatcc gagatttatc      7560
     ggttattgag accccaccaa ccaatcgtta tcctgttcaa acctatgttt tggaaaataa      7620
     tccaggtctc gttagagaag ctatcattcg tgaaatggat cgtggaggac aaatttttta      7680
     cgtttacaat aaagttgaca ctattgaaaa gaaagttgca gagctacaag aattagtccc      7740
     agaagcttct atcggttttg ttcatgggca aatgagtgaa attcaacttg aaaatacctt      7800
     gattgacttt ataaatggtg attatgatgt ccttgtggct acaacaatca tcgaaacagg      7860
     agttgacatt tctaatgtaa acactttgtt tattgagaat gctgatcata tgggattgtc      7920
     aactttatat caactgaggg ggcgcgtcgg aagaagtaat cgtattgcct atgcttacct      7980
     gatgtatcgt cctgataaga tcctaacaga agtctctgaa aaacgtttag aggctattaa      8040
     aggctttact gaattaggtt caggcttcaa gattgctatg cgagatttgt ctatacgagg      8100
     agcaggtaat attttaggag cttctcaaag tggctttatt gattcggtcg gttttgaaat      8160
     gtattctcag ttattggaac aggctattgc tagcaagcaa ggaaaaacga ctgttcgcca      8220
     aaaaggtaat actgaaatca atcttcagat tgatgcttat ttaccagatg attatattgc      8280
     agatgagcgc caaaaaattg acatttacaa gcgtattcga gaaattcaat caagagaaga      8340
     ttatctcaat ttgcaagatg agctgataga tcgttttgga gagtatcctg atcaagttgc      8400
     ctatttgtta gagatagctc tgctaaaaca ttatatggac aatgcctttg cggaattagt      8460
     tgaacgcaaa aataatcagg tcattgttcg atttgaagta acttctttaa gttatttctt      8520
     gactcaggat tatttcgaag ccttatctaa aacccatctt aaagctaaaa ttagtgaaca      8580
     tcaggggaaa atcgatatcg tctttgacgt tcgccatcaa aaagattata gaattttaga      8640
     agaattgatg ttatttggag aaaggcttag tgagataaaa atcagaaaaa acaattcagt      8700
     ttttaaataa taatttgaaa caacttttag actgaatagt attaatgaca atggaacgaa      8760
     ctagctcttt atacttttgt caaaaatcta agatctttgc tgcgaaatta ggatcttttc      8820
     taccatttaa aaaataaaaa tgataaaatg aagaggattg taggagaaat tatgagacta      8880
     gataaatatc taaaggtatc gcgccttatt aaacgtcgtt cagtagcaaa agaagttgcg      8940
     gataagggac gaattaaagt taatgggata cttgctaaaa gttcaacgaa tgtaaaacta      9000
     aatgatcaca ttgaaattag ttttggaaat aaattactga cagtaagagt cattgaaata      9060
     aaagatagta caaaaaaaga agatgctctt aagatgtatg agataatcag tgaaacaagg      9120
     ataacattaa atgaagaagc ctagtattgt tcaattaaat aatcattata ttaagaaaga      9180
     gaatctcaaa aaaaaatttg aagaagaaga atctcaaaaa agaaatcgtt ttatgggatg      9240
     gatccttgta agtatgatgt ttttatttat tttgccaact tataatcttg tcaaaagtta      9300
     tgttgatttt gaaaagcaaa atcaacaggt ggttaaatta aaaaaagagt ataatgaatt      9360
     gtcaaagagt acaaaaaaag aaaaacaatt agcagaacga ctaaaagatg ataattttgt      9420
     caaaaaatat gctagggcaa aatactattt atcgcgtgaa ggagaaatga tttatcctat      9480
     tccaggacta ttaccaaaat gatgatggac aatattataa aaaaaataga agcatttctt      9540
     gctttttctg ataaaaaatt agcagagctg caacaggaaa atcaaaaagt taaagaagaa      9600
     
BioPerl-1.007002/t/data/no_cds_example.gb000444000766000024      4412513155576321 20210 0ustar00cjfieldsstaff000000000000LOCUS       AAEL01000195           13065 bp    DNA     linear   INV 27-OCT-2004
DEFINITION  Cryptosporidium hominis strain TU502 chromosome 2 CHRO012040, whole
            genome shotgun sequence.
ACCESSION   AAEL01000195 AAEL01000000
VERSION     AAEL01000195.1  GI:54657549
KEYWORDS    WGS.
SOURCE      Cryptosporidium hominis
  ORGANISM  Cryptosporidium hominis
            Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida;
            Cryptosporidiidae; Cryptosporidium.
REFERENCE   1  (bases 1 to 13065)
  AUTHORS   Xu,P., Widmer,G., Wang,Y., Ozaki,L.S., Alves,J.M., Serrano,M.G.,
            Puiu,D., Manque,P., Akiyoshi,D., Mackey,A.J., Pearson,W.R.,
            Dear,P.H., Bankier,A.T., Peterson,D.L., Abrahamsen,M.S., Kapur,V.,
            Tzipori,S. and Buck,G.A.
  TITLE     The genome of Cryptosporidium hominis
  JOURNAL   Nature 431, 1107-1112 (2004)
REFERENCE   2  (bases 1 to 13065)
  AUTHORS   Xu,P., Widmer,G., Wang,Y., Ozaki,L.S., Alves,J.M., Serrano,M.G.,
            Puiu,D., Manque,P., Akiyoshi,D., Mackey,A.J., Pearson,W.R.,
            Dear,P.H., Bankier,A.T., Peterson,D.L., Abrahamsen,M.S., Kapur,V.,
            Tzipori,S. and Buck,G.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-JUN-2004) Center for the Study of Biological
            Complexity, Virginia Commonwealth University, Trani Center for Life
            Sciences, 1000 W Cary St, Richmond, VA 23298, USA
FEATURES             Location/Qualifiers
     source          1..13065
                     /organism="Cryptosporidium hominis"
                     /mol_type="genomic DNA"
                     /strain="TU502"
                     /db_xref="taxon:237895"
                     /chromosome="2"
     gene            complement(334..2082)
                     /locus_tag="Chro.rrn021"
     rRNA            complement(join(334..1392,1456..2082))
                     /locus_tag="Chro.rrn021"
                     /product="18S ribosomal RNA"
ORIGIN      
        1 attatgttgt tagagggcgc agaagcacac ancccgacgg accgcgcacg aagggccacc
       61 ccggacggcg aaccagccga cgcgcgccac agagcaaaga gaggggacca gaggggagcg
      121 gatggagaca tcccgaagac cgcaatagga gaccacactg agagagcggg ggcaatccgc
      181 atgcgcgacc tataggtaca cgacgtaaat cttatattat aaataacaaa attaaatttt
      241 ctttttgttc atgttcattt aatttttaaa tgacatatat atataatata atataatata
      301 atataatata tcaaaaactc atttctcaaa taagaatgat ccttccgcag gttcacctac
      361 ggaaaccttg ttacgacttc tccttcctct aaatgataag gtttacgaaa ctttccttac
      421 atgtattgct acaaagtatg gtccgaataa ttcaccggat cattcaatcg gtaggagcga
      481 cgggcggtgt gtacaaaggg cagggacgta atcagcgcaa gctgatgact tgcgcttact
      541 aggaattcct cgttcaagat caataattgc aatgatctat ccccatcacg atgcatattc
      601 aaaagattac ccatttcctt cgaaacagga atatatactt gatggatgca tcagtgtagc
      661 gcgcgcgcgg cccaggacat ctaagggcat cacagacctg ttattgccta aaacttccct
      721 gtattaaaca tacaaagtcc ctctaagaag acagataaaa aatataatat ttcttatgtc
      781 tatttagcag gttaaggtct cgttcgttaa cggaattaac cagacaaatc actccaccaa
      841 ctaagaacgg ccatgcacca ccacccatag aatcaagaaa gagctatcaa tctgtcaatc
      901 cttcctatgt ctggacctgg tgagttttcc cgtgttgagt caaattaagc cgcaggctcc
      961 actcctggtg gtgcccttcc gtcaattcct ttaagtttca gccttgcgac catactcccc
     1021 ccagaaccca aagactttga tttctcataa ggtgctgaag gagtaaggaa caacctccaa
     1081 tctctagttg gcatagttta tggttaagac tacgacggta tctgatcgtc ttcgatcccc
     1141 taactttcgt tcttgattaa tgaaaacatc cttggcaaat gctttcgcat tagtctgtct
     1201 ttaacaaatc taagaatttc acctctgact gttaaataca aatgccccca actgtcccta
     1261 ttaatcatta ttcttatctt agaaccaata agaaagataa aaatctttaa tattattcca
     1321 tgctggagta ttcaaggcat atgcctgctt taagcactct aattttctca aagtaaaatt
     1381 tcatatacta aaaaaaatag taatatgaat tatgttaata ttatataaat attcatcaaa
     1441 atattttata taaattatta acagaaatcc aactacgagc tttttaactg caacaacttt
     1501 aatatacgct attggagctg gaattaccgc ggctgctggc accagacttg ccctccaatt
     1561 gatacttgta aaggggttta tacttaactc attccaatta caaaaccaaa aagtcctgta
     1621 ttgttatttc ttgtcactac ctccctgtat taggattggg taatttgcgc gcctgctgcc
     1681 ttccttagat gtggtagccg tttctcaggc tccctctccg gaatcgaacc ctaattcccc
     1741 gttacccgtc attgccacgg taggccaata ccctaccgtc taaagctgat aggtcagaaa
     1801 cttgaatgat atgtcacatt aattgtgatc cgtaaagtta ttatgagtca ccaatcatat
     1861 tggttcttta tctaataaat acaacccttc cataaagtcg agttttttcg catgtattag
     1921 ctctagaatt accacggtta tccatgtaag taaagattat caagtaaact ataactgtta
     1981 taatgagcca ttcgcagttt aaccgtataa aagtttatac ttagacatgc atggcttaat
     2041 ctttgagaca agcatatgac tactggcagg atcaaccagg ttactatcat taatattaat
     2101 aatattttct ctttttattt tgtcctcatg aagtaaaaaa caaaaaaaaa aaatattatc
     2161 aacattgaat acatattttg tctatcattt ataataaaca aaagaatcat caagaaatta
     2221 ttaatgatta ttatacatac atcacataca tatatagacc atatatatat aagactgtat
     2281 aaatatcaca agaacttctc atccagttaa attaataaga aatatcattg acttaactgg
     2341 caatttaaga tagtattgaa accacattgt aaaatacccc acaaccttga atccaatagt
     2401 actaataagt actctttaaa caacagtggt tacggaatat tccaacaccg tacgctccaa
     2461 aacaccatta tatatactct caaattgact tagttatttt tacttcccaa tataaataac
     2521 atataattaa tcataataaa accaattata cactatccat tgaaagtaat caacacatca
     2581 aagaaaatat attaacaatg tagagtcata cattgatact tatcacatgt aactctttgg
     2641 aaaccataat aatacaacaa cctcttgtac ttaacattcg tgtatctgtc aatccgacaa
     2701 catgctatca aattgaccac actaaataca ccgcgcatac aatcgaaaca caatttcaat
     2761 cgtaagacgt gcgcatttac ccgcaactca tatatacatt ttaccagtac taatcaattc
     2821 acagcctttt cagatcgaaa tagactacga gttcttaata ctcaatgtca gcccattact
     2881 aacacgccaa ttcccacatc cccaggttga atactcttca ccccggaaaa aaaatttacc
     2941 gctatttttg aataaatttt ctattacaga actgtttcag agctgttcta aagaagctag
     3001 gtaatacaaa taaataaaag ctaaacttaa tatctctatt atttatttct aatagttctc
     3061 aataacgcta atttatttac atgaaaaata tctaattcta ccccttatta atttatttca
     3121 ttccagatgt aatatttcta gttgtccttc taatatgcct taatatgcta gtaatatcac
     3181 tgatgatcga cccatccgtg aagcatgcag gtacaatata gttcatgctt ttacttacat
     3241 cgctaaccga atttataatg ctaatgcatt tgttcatgct ttctgaaatt tcatttagta
     3301 tttgcattac gtcactaggt gtaagagtat cagtaaatgg ttcgaaacag tgaatggttt
     3361 cttttatcca taatattctc aattttaaat ctgaaataca gttaatttga gaaaaattac
     3421 cgctggtctt taaagactca attaaatgag gaagagtatc actcaaaatt tttgaaattc
     3481 ctaatattac tggatggcta ataggaagtg gatcatccaa ccaaacgcat gggtcaaact
     3541 tatatgcaag gctcaaaaca aaacattctc cacttgggat ttccctctta tctgactgag
     3601 atagagtaga ttgatcggca gaaattgcta tcgcaaatgc gcgatcgtaa tgtttttgtt
     3661 ttaaggcatc atcaatttgc aaagctatgt tttgggcgct cttatttgca attgagttgt
     3721 ctggtgtaag agcttttagt ggtattccat tactgatctg taattccaaa cgattaacag
     3781 ttgtttgcaa ttgagtaact gcactagtta atgtcccaaa tgaatctgct actacttgag
     3841 taaagttgtc tattggattc gagctaatgt tatcgcattg tttatttaat ttagtcactt
     3901 tttcacgaac gcttctagat tcgccaacaa gcctcgaaat gcaagtgtca atacttgtta
     3961 atttctcatt tgtacttgta aaaagttcct taacatttgt ttcaatttta gaaatttcat
     4021 tgatattgac ataattatca acagacttct cgattcctga caaatgcgac ttaatagatt
     4081 gaatatcacg ttcgatcggt tctaaatact tgctaattgc tgaggaaacc gaatcattta
     4141 actctttgga caagctgaag gtcaattttt ttaattcatc tgtaatcatt tcaaatattt
     4201 tatcatttaa accaaaatct ttgtggttgg tattgcttgt attcgtattt ttcgattgtg
     4261 gattgctcat tgactgtttt tcctccatat ttaatgtact aaaaatagat gtaagtaaat
     4321 ttgatctatc agatggtaat ttattctgag gtgtattatt gtattgaaaa tcgcttttct
     4381 cagttttatg tgatgcattt gccatcaaaa cagcataata atcatcagca atctcgtcat
     4441 tcgtgtcaat attagttttt ttctgattag acaagtttat agtaaatgtg tcactaggta
     4501 tactgatatt ttcggatgaa taatgggctt tattcgcact caaatctaaa acaggtggga
     4561 taatgattga ttcgagccct ccaaaaatat ttgaaacaaa aacttcgatg ggttgttttg
     4621 ataaattttc acttgattta gtttttccag catcaagcca ggtaacattt tttggaggtc
     4681 tgaaagcagc cgtctctaat agtctagagg ggaagaaaaa caaatcttta atgggtagct
     4741 cttcgccaac agagcaaacg attaattggt taaaaatctg tattgcgaaa tactcacccc
     4801 aatttggtcc aataatatga gcattaaatt ggttattttt attatcatcc ataatatgaa
     4861 tatttatgct ctgtaaaagt gtaatttcgc caaagttatt gtttgaatct atcggtaagt
     4921 tatatatgcg aacagtatag atatcttttt ctactgataa taatgtagct gttacattca
     4981 tgtggttaat ggtaggatct ctgattctta tattcggata tactgcagta tcaagtagta
     5041 atgaatttga atcgataatt tgccttgaca ttatcgatct atagtactct ccagggctta
     5101 aatttgagga aaaagtatca taatagccat ttgaagtaaa aagaattatt agttctccaa
     5161 taaattggca actagaaatt ttaacatcat ccgggtagtt aatcagtacg caacatgata
     5221 aattagcagc tgaatgctgg ggagcattgg acttgttgga gttagaacat tcttgtagaa
     5281 tgtggtattc atatgaagaa cgattccata gacacactga gcatttattc caagcaacaa
     5341 aacaacgatc atctaaatgg ttaaatacaa cagatttcca atgggtattt ccccttacca
     5401 aagtattaat agtgtctgat tgaatattta ctattgaaag ttccttccct ttaatataaa
     5461 caatattatt cgacaccttt gaaagcgaaa aactttccat tccaagccct gataatttac
     5521 tgctgcattt agatccattg tttagttctt cttggctatt aataccagaa tctaacatga
     5581 taactcttgg aacatcagaa aacatatgga caacatattc tctattacat tgtagtatag
     5641 aggctgcttg agatgtagaa gcattgtgag acgatggtat cttaatatct aaagatgaac
     5701 cagaaacatg gtaccactgc cttttcggta gttcaatcaa ctccatgatg attattaatc
     5761 tgcaaccaaa taaatagtaa attttttttt taccaaattg cgccataaat ttctcggaat
     5821 aattaaacta agagggaaaa atattcgttt gaaaaataaa atcttatcat tcacctaatc
     5881 atgttcagaa actaataagt agaatctggc tttcctagac tatcaagact acctttcata
     5941 taaaacattg tctctgggag gttatccatt tcaccgctga caatagcatt aaaaccttta
     6001 attgtatcaa ttaagttgac aaaaacccct ggctttccgg taaaagcttc cgacataaaa
     6061 aacggttgag taagaaactt ttggactttt cttgccctgg agacaatcaa cctttcctct
     6121 tcagaaagtg catgagaacc ttgagtagaa attttgctct gtaactgctt atacttttgt
     6181 aaaatcgaaa gaacttcaat agaaactttg tagtgctctt cgcctataat atttcgatct
     6241 aaaaccttag acctactttc caatggatca atggatggga atatcccaac ctcggacatc
     6301 tttctagaga gaactattgt agaatcgagg tgggtgaaag ctgcaacagg tgctggatca
     6361 ttaatgtcgt cagatggaat ataaagtgcc tgaatagatg ttattgaacc atttctcgtg
     6421 gttgtgattc tttcttgaag tttaccaaga tcagtagcca gagtaggttg atacccgatt
     6481 tcagttggta atagccctag aaaaagtcat taaaaaaaaa aataaaaaat aacccatcag
     6541 tcggtaattc cagctatttt ccagttgttt cagcattgaa actcagataa atatggaaag
     6601 tttgcatcat ttgggaaaat tacactaaat atttacttac ctaaaagtgc agaaacttca
     6661 ctccctgcct gagtaaatcg gtaaatatta tctacgaaaa ataatacgtc ttgcatcatt
     6721 gaatctctaa aatattctgc cattgttaga cctgtaagtg caactcgcgc tcgcgctcct
     6781 ggagtttcat tcatttgacc atataccagc gctgtcttag aacctaaaaa atcgtatatg
     6841 ggttgtctct tatgcttgct gtcaactcgt gatccaacaa tcgacttttt attgacgcca
     6901 tttgctagca tttcattata taaatcgtac ccttccctga tgcgctctcc aacccctgta
     6961 tagacagagt aaccaccata cttttttgca atattgttta ttagttccat gataagaaca
     7021 gtcttgccaa cccccgctcc accaaatagt cctattttcc caccttttat gaatggtgta
     7081 agtagatcta ttgccttaat cccagtaaca attaatgaag gctccattac ttgttccatg
     7141 tattcagggg ccgttctatg aatcggtttt ttaactttag cgtcgatctc tccacatccg
     7201 tcaattgcat tccccataac attcaccatt ctaccaagtg tggccttgcc tactggaacg
     7261 catattgggc ttccagtgtc tataactttc tctcctctag agagtccttc tgtaacatcc
     7321 attgcaattg ccctaactga attatcactt aagtgttgcg ccacttcaag tactagtttg
     7381 ttttgatgcc ctttaacttc caaagcgttt aacaattctg gtagtttacc ctcaaatttt
     7441 acatctacaa ctgaacccat gatttgtgat atatagcctt ctgagagatt tttgctagtt
     7501 ttactataag acttccatct tttgtttaag ttataatatt ctaggttgcg gatcgctttt
     7561 ttctggaaaa ataccgaaaa tagtggtaaa aattctcttc gtgtgaattt gaagcatgga
     7621 agagattgac ttaacaattt tcctcgaatc ataaacattg cctccactct ttaattaaaa
     7681 ttaaaaagta attgtgcaaa attgcattaa agccaaattc tatgcaattt aatttttgcg
     7741 tataaacaac ataacaaaaa taggaaatat attctgaaaa tcgatatcca atgtttacta
     7801 aggaactgag tgtatttaat agcaggaagg caaaatagca gaagttaaat ataaaaaaaa
     7861 tacaaaaata gagaaatttt caaagcagga ataagtagtg aacaattttg atgagtgaga
     7921 tgaaagtgtt aagagaatta taattaccat tcaaaataga atataattat cttaagtact
     7981 aaaacagatt tagagcgggt gttaaacaaa atcaaattgc tgtgggtggg gggaaatgtt
     8041 attgcaagag taattttcca aatagttgag ttaatttacg ttgtaatacc aatgtcatct
     8101 gaggaaggca ccgataattg gtctgcagag gaggctgtag agagcgtaaa gactctgagt
     8161 gttagtgagc ttcagtctag gattcgcctt ttagatggtg aaattcgact tatgaaaagc
     8221 gaaagtaatc gtcttaagca tgaattaaac cagatgaatg aaagaatcag aagtaatact
     8281 gaaaaaataa aacttaacaa acagcttcct tatctggttg ccaacattgt cgaatcactg
     8341 gatttttcag atgaacagga aaatgagggt gaagggatgg aattcgatgg agacaaaaac
     8401 gataaatgca tggtaataaa aacatcatca aggcagactg tctttctccc tgtcattggg
     8461 ttggttccag agaatgaatt aaagcctgga gatcttgttg gagtgaataa ggatagttat
     8521 ttgattcttg ataaattgcc accggagtat gactctagag ttaaggctat ggaagttgat
     8581 gaaagaccaa tggaagagta ttcagatatt ggaggattag ataagcagat ccaggaatta
     8641 gtggaggcaa tcgtccttcc gatgacccat aaagaaaggt ttgaaaaaat tggtataaaa
     8701 cccccaaagg gtgtactaat gtatggacct ccaggcacag ggaaaactct tttggcaagg
     8761 gcatgtgcag cacaaactaa agccacattt ttgaaattag caggcccgca actcgtacaa
     8821 atgtttattg gtgatggtgc aaagatggtt agagatgcat ttgaaattgc acgtgaaaaa
     8881 gctccttcaa taatatttat tgacgagctt gacgctatag gtatgaaaag gtttgatagt
     8941 gagcatagtg gggatagaga ggtacaaagg actatgcttg agttacttaa tcaattagat
     9001 ggatttagct cagacgacag agttaaagtt attgctgcaa cgaataggcc ggatactctc
     9061 gatccagccc ttttaagatc aggtaggctt gaccgtaagg tcgagttacc gcatccaaac
     9121 gaagaagcaa ggtccagaat acttcaaata catagcagaa aaatgaatgt tgatttaaat
     9181 gacgtgaatt tccaagagct atcgagatca acagatgatt ttaacggtgc tcagcttaag
     9241 gcagtttgtg tcgaagcggg gatgacagca ctcagaaggg gagcaacgat actttgccat
     9301 gaagattatg tcgaagggat tgcagcagta ctagcaaaga agaaatcccc acttagctat
     9361 ttttcataaa gcaagtgaaa tacaaaaaaa aacttaatca actaattgtt agaattctta
     9421 aatatatata tatttatacc attagcaata atctttttct ttagccgaaa tatccttatt
     9481 cttgccttcg tcaaatacct cttctccaaa atatgggtac tcttcccatt tgggatgttt
     9541 atcaatgatt aaatgtttca tctcctgctc taatacttca aaaaatacat gttcgaagtg
     9601 tttgtcgccc cattgaattg gaatgatgtt attttctctg tctagcaaca tccatgtggc
     9661 gttttgagga gcaagcccga gtaaaagctg agttcgatag gcagtacttc tagacgctcc
     9721 atttaaacag ctcttttgga agcttgaagg tgtaagttgt tcatttggac acgaatgaat
     9781 atctgatttc tggctttgcg aagatttttg ctttctctta cgcgattccc accacttact
     9841 tttaatagtt gaattatctg atgaaaattc agattcagaa tctgagattt gtgaattatc
     9901 tgataattcg caatcatcaa taaaattgtc taccgtattt gtattctgac cctttttagg
     9961 tgatttatta aaaactctag ctctgttagg tgcggaagaa gttgttgcta agtcaatatg
    10021 aatattgcct aacctgtttg atgaaattaa tgcagttgca tcaaatgcgc gatagcaatg
    10081 ttgaaggcta cgctgaatta gtagctcaat tgaagatgga atttccagat cttctctaca
    10141 aagaaaactg gcaatttgat acaagttgag atgcattgat gatgcaagcc tcaaccatct
    10201 gactgaaact ctcatgcttc ttaaacactc gcttctaatc aataactttc tttttaacct
    10261 ctctgcatcc gcatctggat ccatatactt tattactctc aattcagacc tgctaaaggg
    10321 tatcttcgaa tgtggccaat caaaccatac ccaatcaaat tgtgcaacat cgagaacatc
    10381 tggtaaacaa agcccatggt cgattggaat taacttatac ttggtttttt tgccgtcagg
    10441 agtgctcaga gggtgttcat atggtgaaat agctggactt ggattatttg aattactaat
    10501 gttgaatttg attgaataat tgggctggtt cgcgacaaca agaatattac tatcatttct
    10561 atctaaatta aagagacaaa tatccaaaat tccaatgcgg tgtacatctc taatgcagaa
    10621 tacagagggg ttgaaattac caactgtttc tgtagttgaa ataaactctt gaaatgcccc
    10681 caacttccaa tcaacggtta tttcactatt tgccttatta ttatcttttt gaaaaatatc
    10741 gccccattca agagtaatct tattccagct atcataatta aaagcctgat ggcatgcctc
    10801 aagtagtgta gtatcaggaa cgccggcaaa attatggtag tatgcatccc aaattgctgt
    10861 tgcaacctct ctgctagctc cttcacctga caatactcct gacctaaaac cttgttggcc
    10921 taatttacct tgataacccc ttggattatt tggagagaat gcctcctcat ctagtggttt
    10981 aaacattgca acaacttggc cttttgcatt gtacattcta taggtagcgc ccgttccatc
    11041 caatgtaagt ttgggatgga catttctctg cattgcaagt ttaacttcaa ctacaagttt
    11101 ctgaatttta ctcgaccatt taagtccagt acttctaatt ccaaaatctg acttgttcat
    11161 cctgagagaa tagtgcaatg ggtgtctttg tttttcaaat gtatgcataa acctgctatt
    11221 cggaatttct acgcctctat aaaatagctg aatgtcacga atgcttgtgc cttctgggag
    11281 atccagatac ttaattacta gtcttttaac catttggcaa tcatagaatg ggtatattga
    11341 caaaagtatg cgctttgtcc catccagctc gtcaatatat aagacaaatt tctggatttc
    11401 attttcacct gcacgcaaag cattatgagt tgaaaaatat acctgttgag caacagggaa
    11461 gttgttaatt tgattcattt acaataaaca tgacaacata ttattcttta ctcaattttt
    11521 atcattccat taaagtgacc cgtctaaaaa tataaccgct ctatcataat taaaaattaa
    11581 aaccaaattt cggggaaaaa aaatttatca atgcttaata atctgacatt acttccatca
    11641 attggatcta gatatgaatc cacaacctaa aattttttat taaattaatt agaatcacaa
    11701 tttattgcta tttggattgc tggtaaattt caacttacat gcaacattcc atcttctact
    11761 gccttggaaa tcattaaatt atattcttct atagttagtt catcgccatt ttttaataaa
    11821 ctcctaatct gagctttaat ttgtatgata ctaaatttag tctataacct acctttttag
    11881 ttttatttgc cataaaccaa cttataagtg agatatcgct ttgcggttgt ttccattcaa
    11941 tttcaagctt cttaagttgg ttgcaaactt gaatacaaaa atttaaataa gttttccaag
    12001 gtatcgatct tttctatatt ggaaatattg agaagataat tagtgtttat tttattatcc
    12061 ttgcaaatct actcaccttc atgcttaact attaagaaag cgtgaaaatt atagaaaaat
    12121 cagtatgtca ggtgtgggtg ggggatctac catgtaaaat aatattcagt tagcgcaaat
    12181 aaacaattaa aaaatggtaa tataataaat tatatatatt caagattaaa gaatttacta
    12241 attcgtgtaa aaattgacta tgattgtgat ttactaataa tttaaaaata gtaagctaac
    12301 agaaaaatgc atctatattc aagacatttg taaaaatgct ttgttctact tattctttgc
    12361 tagctttttt tgaaaccttt ttgttcaatt cacttaatat actgagtagt ttatctttaa
    12421 ttccaataga ctccttgtag tttttaaata aatctggatg agaatttcga gtagaaaagt
    12481 gaatgatata gtcgccgaat gtatctttgc caaaaatagg tggcccttta ccctttaata
    12541 tatatggaac cctcggatta gttttaggag gtaccttaac tcgcatgctt gtacctttaa
    12601 ttaaactagg cacaacaatt tctccgccaa aaatacatgt attaattgaa attggaatat
    12661 ctacatgaat attatccttt atccatttga gtttcgtatt tggcttaata ttcaccttaa
    12721 tgaataaatc tccataattt cctgaaacaa agttaccttc tgagctcagc tttagttgcg
    12781 ttccatcctt cgttcctctt gggattctta gtaaaacgtt cttttcttta ataatatggc
    12841 cgctaccatt acactttatg caaagcatta aatttgaata tccagtacca ctgcacttca
    12901 tgcacaatga cttgattaat aaaggaccat tttggtaaac attcaggcca gaaccaccac
    12961 aatttgaaca tttagctatt tttagtcctt taatgatgcc aacgccattg caggcatcac
    13021 atttacaact agaattagtt ttaagtgttc tgcttgtccc attaa
//
BioPerl-1.007002/t/data/no_hsps.blastp000444000766000024     10541013155576321 17611 0ustar00cjfieldsstaff000000000000BLASTP 2.0MP-WashU [16-Feb-2003] [macosx-10.2-ppc-ILP32F64 2003-02-18T10:00:41]

Copyright (C) 1996-2003 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2003) http://blast.wustl.edu

Query=  mgri:MG00189.3 hypothetical protein 6892 8867 +
        (601 letters; record 1)

Database:  /nfs1/jason_input/all_euk/metazoans;
           /nfs1/jason_input/fungi/ascopeps; /nfs1/jason_input/fungi/basido
           351,440 sequences; 145,589,111 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done

                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

mgri:MG00189.3 hypothetical protein 6892 8867 +               3098  0.        1
fgram:FG01141.1 hypothetical protein 47007 48803 -            2182  4.2e-226  1
ncra:NCU03076.1 hypothetical protein (28850 - 30771)          2148  1.7e-222  1
anid:AN1733.1 AF252630_1 delta-1-pyrroline-5-carboxylate ...  2001  6.4e-207  1
spom:SPBC24C6.04 |||putative delta-1-pyrroline-5-carboxyl...  1718  6.2e-177  1
calb:orf6.5650  orf6-2420:8022-6235:e  1788 bp, 595 aa, c...  1706  1.2e-175  1
duh99:cneo_DUH99_Contig425.Gene2 Start=40771 End=43016 St...  1659  1.1e-170  1
wih99:cneo_WIH99_107.Gene1 Start=41629 End=44150 Strand=1...  1613  8.3e-166  1
jec21:cneo_TIGRJEC21_chr11a.pseudo.Gene521 Start=371763 E...  1582  1.6e-162  1
pchr:pchr_Scaffold_43.Gene3 Start=38145 End=40814 Strand=...  1577  5.4e-162  1
fgram:FG03073.1 hypothetical protein 68551 70406 -            1576  6.9e-162  1
ccin:ccin_Contig257.Gene8 Start=55703 End=53090 Strand=-1...  1176  2.7e-161  2
agos:AAL072C location=AgChr1:complement(223170..224891)       1540  4.5e-158  1
umay:umay_Contig44.Gene2 Start=5123 End=2772 Strand=-1 Le...  1535  1.5e-157  1
scer:YHR037W PUT2 SGDID:S0001079, Chr VIII from 181968-18...  1533  2.5e-157  1
hsap:ENSP00000290597 Database:core Gene:ENSG00000159423 C...  1298  2.0e-132  1
hsap:ENSP00000328453 Database:core Gene:ENSG00000159423 C...  1298  2.0e-132  1
mmus:ENSMUSP00000043821 Database:core Gene:ENSMUSG0000002...  1295  4.2e-132  1
afum:4563_glimmerf_85                                         1279  2.1e-130  1
dmel:CG7145-PA translation from_gene[CG7145 CG7145 FBgn00...  1256  5.6e-128  1
dmel:CG7145-PD translation from_gene[CG7145 CG7145 FBgn00...  1256  5.6e-128  1
dmel:CG7145-PB translation from_gene[CG7145 CG7145 FBgn00...  1256  5.6e-128  1
rnor:ENSRNOP00000025090 Database:core Gene:ENSRNOG0000001...  1235  9.5e-126  1
agam:ENSANGP00000013138 Database:core Gene:ENSANGG0000001...  1217  7.7e-124  1
cbri:CBG07110 CBP01802 (cb25.fpc0305.en1909a/cb25.fpc0305...  1216  9.8e-124  1
cele:F56D12.1 CE29047   aldehyde dehydrogenase status:Par...  1201  3.8e-122  1
anid:AN9278.1 hypothetical protein 133790 135518 +            1194  2.1e-121  1
drer:ENSDARP00000025931 Database:core Gene:ENSDARG0000000...   614  5.1e-115  2
drer:ENSDARP00000004693 Database:core Gene:ENSDARG0000000...   617  1.8e-108  2
drer:ENSDARP00000006345 Database:core Gene:ENSDARG0000000...   614  2.3e-108  2
anid:AN6022.1 hypothetical protein 49043 51304 -               625  3.3e-107  2
dmel:CG33092-PA translation from_gene[CG33092 CG33092 FBg...   994  3.3e-100  1
dmel:CG33092-PB translation from_gene[CG33092 CG33092 FBg...   994  3.3e-100  1
dmel:CG33092-PC translation from_gene[CG33092 CG33092 FBg...   994  3.3e-100  1
dmel:CG33092-PF translation from_gene[CG33092 CG33092 FBg...   994  3.3e-100  1
drer:ENSDARP00000009693 Database:core Gene:ENSDARG0000000...   535  3.9e-100  2
dmel:CG33092-PD translation from_gene[CG33092 CG33092 FBg...   989  1.1e-99   1
dmel:CG33092-PE translation from_gene[CG33092 CG33092 FBg...   989  1.1e-99   1
dmel:CG33092-PG translation from_gene[CG33092 CG33092 FBg...   984  3.8e-99   1
dmel:CG6661-PA translation from_gene[CG6661 CG6661 FBgn00...   753  1.1e-74   1
afum:4562_glimmerf_84                                          590  2.1e-57   1
drer:ENSDARP00000025173 Database:core Gene:ENSDARG0000000...   571  2.2e-55   1
duh99:cneo_DUH99_Contig338.Gene3 Start=10629 End=8428 Str...   498  1.2e-47   1
wih99:cneo_WIH99_138.Gene135 Start=318644 End=316438 Stra...   498  1.2e-47   1
jec21:cneo_TIGRJEC21_chr8.pseudo.Gene367 Start=297286 End...   488  2.5e-45   1
pchr:pchr_Scaffold_257.Gene2 Start=4723 End=1965 Strand=-...   470  1.1e-44   1
afum:3004_glimmerf_56                                          462  7.8e-44   1
umay:umay_Contig84.Gene5 Start=5778 End=8094 Strand=1 Len...   454  5.5e-43   1
afum:9560_glimmerf_188                                         449  1.9e-42   1
hsap:ENSP00000261733 Database:core Gene:ENSG00000111275 C...   448  2.4e-42   1
mmus:ENSMUSP00000031411 Database:core Gene:ENSMUSG0000002...   444  6.3e-42   1
fgram:FG02273.1 hypothetical protein 136532 138142 +           437  3.5e-41   1
hsap:ENSP00000332256 Database:core Gene:ENSG00000184254 C...   436  4.4e-41   1
anid:AN9034.1 hypothetical protein 161667 163308 -             434  7.2e-41   1
hsap:ENSP00000297785 Database:core Gene:ENSG00000165092 C...   433  9.2e-41   1
cele:K04F1.15 CE23852   aldehyde dehydrogenase status:Pre...   431  1.5e-40   1
mgri:MG03900.3 hypothetical protein (  (AL669991) probabl...   430  1.9e-40   1
agam:ENSANGP00000020207 Database:core Gene:ENSANGG0000001...   429  2.4e-40   1
agam:ENSANGP00000011393 Database:core Gene:ENSANGG0000000...   428  3.1e-40   1
ncra:NCU00378.1 hypothetical protein (49878 - 51422)           427  4.0e-40   1
anid:AN0554.1 AF260123_1 aldehyde dehydrogenase ALDH 5455...   426  5.1e-40   1
fgram:FG02160.1 hypothetical protein 41708 43408 +             426  5.1e-40   1
ncra:NCU07053.1 hypothetical protein (11322 - 12871)           422  1.3e-39   1
hsap:ENSP00000331360 Database:core Gene:ENSG00000111275 C...   417  4.8e-39   1
mmus:ENSMUSP00000034723 Database:core Gene:ENSMUSG0000001...   417  4.8e-39   1
mmus:ENSMUSP00000015278 Database:core Gene:ENSMUSG0000001...   415  8.5e-39   1
fgram:FG00979.1 conserved hypothetical protein 134502 136...   415  8.5e-39   1
scer:YER073W ALD5 SGDID:S0000875, Chr V from 304027-305589     414  1.1e-38   1
scer:YMR169C ALD3 SGDID:S0004779, Chr XIII from 600871-59...   414  1.1e-38   1
hsap:ENSP00000249750 Database:core Gene:ENSG00000128918 C...   413  1.5e-38   1
scer:YMR170C ALD2 SGDID:S0004780, Chr XIII from 603081-60...   413  1.5e-38   1
spom:SPAC922.07c |||putative aldehyde dehydrogenase            412  1.9e-38   1
ncra:NCU03415.1 hypothetical protein (100613 - 98979)          412  1.9e-38   1
calb:orf6.5499  orf6-2412:4933-6438:e  1506 bp, 501 aa, c...   410  3.4e-38   1
fgram:FG04194.1 hypothetical protein 53878 55487 -             409  4.4e-38   1
rnor:ENSRNOP00000024000 Database:core Gene:ENSRNOG0000001...   407  7.7e-38   1
anid:AN1689.1 hypothetical protein 308010 309618 -             405  1.3e-37   1
mmus:ENSMUSP00000025656 Database:core Gene:ENSMUSG0000002...   404  1.7e-37   1
rnor:ENSRNOP00000015282 Database:core Gene:ENSRNOG0000001...   404  1.7e-37   1
dmel:CG3752-PA translation from_gene[CG3752 CG3752 FBgn00...   402  3.0e-37   1
anid:AN4126.1 hypothetical protein 112110 113903 +             402  3.0e-37   1
duh99:cneo_DUH99_Contig581.Gene1 Start=122995 End=125826 ...   413  4.0e-37   1
hsap:ENSP00000259658 Database:core Gene:ENSG00000137124 C...   399  6.6e-37   1
fgram:FG00139.1 hypothetical protein 120379 121938 +           399  6.6e-37   1
mgri:MG05008.3 hypothetical protein 911 2404 +                 399  6.6e-37   1
mmus:ENSMUSP00000041260 Database:core Gene:ENSMUSG0000003...   397  1.1e-36   1
rnor:ENSRNOP00000024027 Database:core Gene:ENSRNOG0000001...   396  1.5e-36   1
scer:YOR374W ALD4 SGDID:S0005901, Chr XV from 1039834-104...   396  1.5e-36   1
agos:AFL044W location=AgChr3:286029..287570                    394  2.5e-36   1
mmus:ENSMUSP00000020497 Database:core Gene:ENSMUSG0000002...   413  5.4e-36   1
hsap:ENSP00000328288 Database:core Gene:ENSG00000111275 C...   391  5.4e-36   1
spom:SPCC550.10 |meu8||putative betaine aldehyde dehydrog...   388  1.2e-35   1
drer:ENSDARP00000022715 Database:core Gene:ENSDARG0000000...   387  1.6e-35   1
anid:AN9198.1 hypothetical protein 77039 78964 -               387  1.6e-35   1
ccin:ccin_Contig143.Gene21 Start=155829 End=153396 Strand...   397  2.2e-35   1
umay:umay_Contig117.Gene40 Start=118398 End=115663 Strand...   395  2.9e-35   1
agam:ENSANGP00000013314 Database:core Gene:ENSANGG0000001...   384  3.4e-35   1
agos:AFL201W location=AgChr6:58424..59917                      383  4.4e-35   1
fgram:FG02220.1 hypothetical protein 57928 59634 +             383  4.4e-35   1
hsap:ENSP00000271359 Database:core Gene:ENSG00000143149 C...   382  5.8e-35   1
calb:orf6.6640  orf6-2467:32772-34271:e  1500 bp, 499 aa,...   382  5.8e-35   1
spom:SPAC9E9.09c |||putative aldehyde dehydrogenase            382  5.8e-35   1
fgram:FG02392.1 hypothetical protein 112635 114218 -           381  7.5e-35   1
scer:YPL061W ALD6 SGDID:S0005982, Chr XVI from 432583-434085   380  9.7e-35   1
mgri:MG01991.3 hypothetical protein 16355 18108 +              387  1.3e-34   1
rnor:ENSRNOP00000021799 Database:core Gene:ENSRNOG0000001...   379  1.3e-34   1
drer:ENSDARP00000015715 Database:core Gene:ENSDARG0000002...   379  1.3e-34   1
fgram:FG05831.1 hypothetical protein 397480 399069 -           379  1.3e-34   1
drer:ENSDARP00000011744 Database:core Gene:ENSDARG0000000...   377  2.1e-34   1
cbri:CBG05984 CBP15436 (cb25.fpc0143.gc246)                    397  4.1e-34   1
rnor:ENSRNOP00000005611 Database:core Gene:ENSRNOG0000000...   372  7.7e-34   1
frub:SINFRUP00000157742 Database:core Gene:SINFRUG0000014...   372  7.7e-34   1
mgri:MG09456.3 hypothetical protein 830 2335 -                 372  7.7e-34   1
fgram:FG11034.1 hypothetical protein 7087 10802 -              393  1.3e-33   1
drer:ENSDARP00000024587 Database:core Gene:ENSDARG0000000...   370  1.3e-33   1
mgri:MG00652.3 hypothetical protein 20025 21464 -              339  1.9e-33   2
umay:umay_Contig94.Gene5 Start=7986 End=9677 Strand=1 Len...   380  2.3e-33   1
hsap:ENSP00000308809 Database:core Gene:ENSG00000144908 C...   390  2.7e-33   1
anid:AN4054.1 hypothetical protein 274503 276139 +             366  3.6e-33   1
anid:AN1430.1 hypothetical protein 75595 77158 +               366  3.6e-33   1
rnor:ENSRNOP00000018010 Database:core Gene:ENSRNOG0000001...   339  6.9e-33   2
cele:F54D8.3 CE29809   Aldehyde dehydrogenase 2 status:Co...   371  7.0e-33   1
pchr:pchr_Scaffold_36.Gene34 Start=136323 End=131305 Stra...   388  7.2e-33   1
frub:SINFRUP00000146331 Database:core Gene:SINFRUG0000013...   385  8.5e-33   1
drer:ENSDARP00000023429 Database:core Gene:ENSDARG0000000...   362  1.0e-32   1
agam:ENSANGP00000021005 Database:core Gene:ENSANGG0000001...   385  1.2e-32   1
fgram:FG11542.1 hypothetical protein 85606 87343 +             361  1.3e-32   1
cbri:CBG23008 CBP05486 (cb25.fpc4426.en2389a/cb25.fpc4426...   369  1.7e-32   1
pchr:pchr_Scaffold_42.Gene29 Start=118985 End=116126 Stra...   377  2.1e-32   1
cbri:CBG15207 CBP03688 (cb25.fpc4010.en576a)                   379  2.1e-32   1
dmel:CG4685-PA translation from_gene[CG4685 CG4685 FBgn00...   368  2.2e-32   1
agam:ENSANGP00000014625 Database:core Gene:ENSANGG0000001...   359  2.2e-32   1
frub:SINFRUP00000156880 Database:core Gene:SINFRUG0000014...   358  2.8e-32   1
duh99:MATCHRContig45.Gene17 Start=28159 End=25771 Strand=...   371  3.4e-32   1
cele:F42G9.5 CE07233   betaine-aldehyde dehydrogenase sta...   376  4.9e-32   1
umay:umay_Contig192.Gene3 Start=244542 End=247243 Strand=...   375  7.1e-32   1
rnor:ENSRNOP00000011483 Database:core Gene:ENSRNOG0000000...   377  8.6e-32   1
jec21:cneo_TIGRJEC21_chr11b.pseudo.Gene216 Start=332496 E...   371  1.2e-31   1
hsap:ENSP00000265605 Database:core Gene:ENSG00000118514 C...   355  3.0e-31   1
wih99:cneo_WIH99_20.Gene3 Start=298791 End=301339 Strand=...   363  3.6e-31   1
dmel:CG31075-PA translation from_gene[CG31075 CG31075 FBg...   352  9.1e-31   1
jec21:cneo_TIGRJEC21_CH9.Gene24 Start=553523 End=556049 S...   356  2.4e-30   1
anid:AN3573.1 hypothetical protein 96168 97759 +               306  2.5e-30   2
anid:AN4847.1 hypothetical protein 21287 24043 +               363  2.5e-30   1
drer:ENSDARP00000008179 Database:core Gene:ENSDARG0000000...   340  2.8e-30   1
agos:ADR418W location=AgChr4:1453729..1455252                  352  3.9e-30   1
ncra:NCU00715.1 hypothetical protein (54297 - 55937)           351  8.4e-30   1
ncra:NCU03348.1 hypothetical protein (46178 - 44665)           345  9.3e-30   1
frub:SINFRUP00000146332 Database:core Gene:SINFRUG0000013...   356  9.6e-30   1
agam:ENSANGP00000014662 Database:core Gene:ENSANGG0000001...   343  1.4e-29   1
umay:umay_Contig115.Gene5 Start=29009 End=31339 Strand=1 ...   350  2.1e-29   1
fgram:FG05375.1 hypothetical protein 97901 99430 +             346  2.4e-29   1
ncra:NCU02056.1 hypothetical protein (21232 - 19740)           341  3.0e-29   1
cele:C54D1.4 CE06980   aldehyde dehydrogenase status:Part...   343  5.3e-29   1
wih99:cneo_WIH99_80.Gene78 Start=108689 End=105572 Strand...   346  5.8e-29   1
cele:Y69F12A.2 CE24573   aldehyde dehydrogenase status:Pa...   345  8.2e-29   1
pchr:pchr_Scaffold_68.Gene2 Start=118512 End=121055 Stran...   342  1.5e-28   1
anid:AN0740.1 hypothetical protein 38806 40367 -               335  2.4e-28   1
drer:ENSDARP00000025035 Database:core Gene:ENSDARG0000000...   322  2.6e-28   1
anid:AN3205.1 hypothetical protein 19806 21394 +               333  3.6e-28   1
frub:SINFRUP00000135525 Database:core Gene:SINFRUG0000012...   335  3.7e-28   1
anid:AN7315.1 hypothetical protein 94182 95712 -               334  5.0e-28   1
dmel:CG8665-PA translation from_gene[CG8665 CG8665 FBgn00...   343  5.8e-28   1
ncra:NCU09648.1 hypothetical protein (17442 - 19120)           331  6.8e-28   2
afum:1839_glimmerf_24                                          333  7.1e-28   1
rnor:ENSRNOP00000001816 Database:core Gene:ENSRNOG0000000...   290  7.4e-28   2
mgri:MG01230.3 hypothetical protein 11881 13666 +              335  8.0e-28   1
fgram:FG04196.1 hypothetical protein 60704 62429 +             331  1.2e-27   1
afum:3202_glimmerf_68                                          337  1.5e-27   1
umay:umay_Contig222.Gene6 Start=19170 End=17353 Strand=-1...   332  2.0e-27   1
rnor:ENSRNOP00000020015 Database:core Gene:ENSRNOG0000001...   314  2.0e-27   1
fgram:FG06752.1 hypothetical protein 57054 58751 +             328  2.6e-27   1
hsap:ENSP00000309623 Database:core Gene:ENSG00000128918 C...   277  3.2e-27   2
ccin:ccin_Contig206.Gene14 Start=13195 End=10953 Strand=-...   330  3.4e-27   1
duh99:cneo_DUH99_Contig548.Gene28 Start=81130 End=78906 S...   331  3.4e-27   1
rnor:ENSRNOP00000023774 Database:core Gene:ENSRNOG0000001...   311  4.2e-27   1
ncra:NCU00936.1 hypothetical protein (87196 - 85536)           325  6.6e-27   1
anid:AN4050.1 hypothetical protein 262048 263673 -             324  6.8e-27   1
jec21:cneo_TIGRJEC21_CH2.Gene1 Start=223094 End=225269 St...   328  6.9e-27   1
cbri:CBG09190 CBP08192 (cb25.fpc2193.fg55/cb25.fpc2193.gc...   325  7.1e-27   1
cele:F01F1.6 CE01232   Aldehyde dehydrogenase status:Conf...   322  2.0e-26   1
drer:ENSDARP00000010714 Database:core Gene:ENSDARG0000000...   328  2.5e-26   1
drer:ENSDARP00000023106 Database:core Gene:ENSDARG0000000...   328  2.6e-26   1
drer:ENSDARP00000025029 Database:core Gene:ENSDARG0000000...   328  2.6e-26   1
fgram:FG01759.1 hypothetical protein 58734 60362 +             320  2.6e-26   1
anid:AN1541.1 hypothetical protein 30562 32195 +               319  2.9e-26   1
anid:AN5435.1 hypothetical protein 161833 164046 -             318  3.7e-26   1
mgri:MG02766.3 hypothetical protein 6094 8116 -                323  4.0e-26   1
frub:SINFRUP00000163952 Database:core Gene:SINFRUG0000015...   272  4.7e-26   2
mgri:MG03263.3 hypothetical protein 3369 5047 +                317  5.2e-26   1
agam:ENSANGP00000016555 Database:core Gene:ENSANGG0000001...   319  5.6e-26   1
fgram:FG00854.1 hypothetical protein 138293 142157 -           324  6.6e-26   1
pchr:pchr_Scaffold_15.Gene44 Start=10646 End=8127 Strand=...   318  9.4e-26   1
cbri:CBG09070 CBP02216 (cb25.fpc2187.en7002a)                  316  1.0e-25   1
spom:SPAC139.05 |||putative succinate semialdehyde dehydr...   314  1.3e-25   1
mmus:ENSMUSP00000028004 Database:core Gene:ENSMUSG0000002...   312  1.8e-25   1
cbri:CBG10981 CBP02675 (cb25.fpc2397.en1670b/cb25.fpc2397...   312  2.7e-25   1
ncra:NCU07442.1 hypothetical protein (58745 - 56640)           314  3.8e-25   1
mmus:ENSMUSP00000001749 Database:core Gene:ENSMUSG0000002...   310  4.8e-25   1
afum:3310_glimmerf_183                                         307  6.6e-25   1
fgram:FG11482.1 hypothetical protein 39753 41214 -             289  1.0e-24   1
spom:SPAC1002.12c |||putative succinate-semialdehyde dehy...   306  1.2e-24   1
ccin:ccin_Contig143.Gene26 Start=93392 End=90406 Strand=-...   308  1.5e-24   1
fgram:FG02296.1 hypothetical protein 42345 43942 -             305  1.5e-24   1
agam:ENSANGP00000017723 Database:core Gene:ENSANGG0000001...   305  1.7e-24   1
drer:ENSDARP00000005458 Database:core Gene:ENSDARG0000000...   234  2.0e-24   2
anid:AN3829.1 hypothetical protein 18018 19747 +               305  2.1e-24   1
calb:orf6.6689  orf6-2469:28972-30501:e  1530 bp, 509 aa,...   303  3.1e-24   1
fgram:FG00718.1 hypothetical protein 48603 50089 -             301  3.5e-24   1
rnor:ENSRNOP00000024093 Database:core Gene:ENSRNOG0000001...   185  4.6e-24   3
calb:orf6.7782  orf6-2501:55143-53707:e  1437 bp, 478 aa,...   299  6.2e-24   1
frub:SINFRUP00000152737 Database:core Gene:SINFRUG0000014...   300  6.4e-24   1
drer:ENSDARP00000015309 Database:core Gene:ENSDARG0000001...   280  9.9e-24   1
mmus:ENSMUSP00000040591 Database:core Gene:ENSMUSG0000003...   299  1.0e-23   1
mmus:ENSMUSP00000025657 Database:core Gene:ENSMUSG0000002...   279  1.3e-23   1
hsap:ENSP00000297542 Database:core Gene:ENSG00000164904 C...   297  1.5e-23   1
frub:SINFRUP00000142953 Database:core Gene:SINFRUG0000013...   278  1.6e-23   1
ncra:NCU08669.1 hypothetical protein (11260 - 12786)           294  2.1e-23   1
fgram:FG02356.1 hypothetical protein 25485 28604 +             194  2.2e-23   2
anid:AN3591.1 hypothetical protein ( (MG01606.1) hypothet...   296  2.4e-23   1
frub:SINFRUP00000148708 Database:core Gene:SINFRUG0000014...   295  2.6e-23   1
cele:F36H1.6 CE05817   formyltetrahydrofolate dehydrogena...   298  5.3e-23   1
calb:orf6.7055  orf6-2481:60364-58520:e  1845 bp, 614 aa,...   294  6.4e-23   1
agam:ENSANGP00000022164 Database:core Gene:ENSANGG0000001...   292  6.6e-23   1
umay:umay_Contig141.Gene14 Start=5134 End=3036 Strand=-1 ...   292  7.7e-23   1
dmel:CG17896-PA translation from_gene[CG17896 EG:171D11.1...   289  1.2e-22   1
dmel:CG17896-PB translation from_gene[CG17896 EG:171D11.1...   289  1.3e-22   1
umay:umay_Contig124.Gene6 Start=37930 End=40228 Strand=1 ...   292  1.4e-22   1
hsap:ENSP00000238696 Database:core Gene:ENSG00000119711 C...   289  1.6e-22   1
cele:F45H10.1 CE?????     succinate semi-aldehyde dehydro...   287  1.7e-22   1
ncra:NCU09266.1 hypothetical protein (94540 - 96177)           288  2.1e-22   1
anid:AN4820.1 hypothetical protein 149242 150844 -             283  5.4e-22   1
wih99:cneo_WIH99_14.Gene173 Start=142339 End=139677 Stran...   285  6.0e-22   1
afum:9439_glimmerf_146                                         278  6.9e-22   1
duh99:cneo_DUH99_Contig585.Gene10 Start=82555 End=84824 S...   283  8.4e-22   1
fgram:FG03936.1 hypothetical protein 156552 158199 +           281  9.7e-22   1
rnor:ENSRNOP00000015545 Database:core Gene:ENSRNOG0000001...   281  1.1e-21   1
dmel:CG9629-PA translation from_gene[CG9629 CG9629 FBgn00...   281  1.2e-21   1
dmel:CG9629-PB translation from_gene[CG9629 CG9629 FBgn00...   281  1.2e-21   1
rnor:ENSRNOP00000021757 Database:core Gene:ENSRNOG0000001...   279  1.2e-21   1
drer:ENSDARP00000012423 Database:core Gene:ENSDARG0000000...   279  1.3e-21   1
pchr:pchr_Scaffold_2.Gene87 Start=346907 End=343843 Stran...   282  1.3e-21   1
fgram:FG08596.1 hypothetical protein 57232 59131 +             282  1.4e-21   1
afum:7129_glimmerf_213                                         279  1.5e-21   1
cbri:CBG20774 CBP11572 (cb25.fpc4206.fg128/cb25.fpc4206.g...   279  1.5e-21   1
pchr:pchr_Scaffold_70.Gene18 Start=126124 End=123573 Stra...   280  1.9e-21   1
mmus:ENSMUSP00000021664 Database:core Gene:ENSMUSG0000002...   279  2.0e-21   1
frub:SINFRUP00000144622 Database:core Gene:SINFRUG0000013...   277  2.0e-21   1
umay:umay_Contig203.Gene28 Start=130123 End=127586 Strand...   279  2.1e-21   1
mmus:ENSMUSP00000049810 Database:core Gene:ENSMUSG0000002...   278  2.3e-21   1
anid:AN0079.1 hypothetical protein 72529 76110 -               284  2.4e-21   1
fgram:FG00490.1 conserved hypothetical protein 3891 5622 -     278  3.0e-21   1
drer:ENSDARP00000027544 Database:core Gene:ENSDARG0000000...   269  6.4e-21   1
umay:umay_Contig3.Gene2 Start=12357 End=13920 Strand=1 Le...   273  8.6e-21   1
agos:AgYBR006W location=AgChr5:642837..644324                  272  9.3e-21   1
anid:AN7141.1 hypothetical protein 28075 29616 +               271  9.7e-21   1
mgri:MG05814.3 hypothetical protein 33559 35087 -              271  9.7e-21   1
umay:umay_Contig203.Gene4 Start=102418 End=104786 Strand=...   271  1.3e-20   1
mmus:ENSMUSP00000038878 Database:core Gene:ENSMUSG0000003...   251  1.4e-20   1
duh99:cneo_DUH99_Contig560.Gene45 Start=69535 End=67388 S...   271  1.5e-20   1
calb:orf6.7229  orf6-2487:29860-31335:e  1476 bp, 491 aa,...   270  1.5e-20   1
ccin:ccin_Contig199.Gene11 Start=493217 End=496163 Strand...   273  1.6e-20   1
duh99:cneo_DUH99_Contig575.Gene5 Start=73052 End=75270 St...   272  1.7e-20   1
ccin:ccin_Contig198.Gene198 Start=520002 End=516613 Stran...   272  1.7e-20   1
drer:ENSDARP00000011728 Database:core Gene:ENSDARG0000000...   274  1.9e-20   1
wih99:cneo_WIH99_48.Gene135 Start=262989 End=260742 Stran...   269  2.6e-20   1
anid:AN6636.1 hypothetical protein 188016 190076 -             271  2.6e-20   1
fgram:FG10673.1 hypothetical protein 110458 112011 +           267  3.5e-20   1
cele:F13D12.4 CE02183   methylmalonate-semialdehyde dehyd...   266  5.3e-20   1
jec21:cneo_TIGRJEC21_chr5.pseudo.Gene416 Start=965498 End...   270  6.6e-20   1
drer:ENSDARP00000024566 Database:core Gene:ENSDARG0000000...   262  1.1e-19   1
anid:AN1585.1 hypothetical protein 180201 181769 -             262  1.3e-19   1
duh99:MATCHRContig46.Gene18 Start=5071 End=7234 Strand=1 ...   263  1.4e-19   1
wih99:cneo_WIH99_20.Gene17 Start=160223 End=162565 Strand...   263  1.6e-19   1
jec21:cneo_TIGRJEC21_chr4.pseudo.Gene688 Start=1937332 En...   262  2.0e-19   1
jec21:cneo_TIGRJEC21_CH2.Gene354 Start=550124 End=547388 ...   261  2.5e-19   1
ccin:ccin_Contig308.Gene1 Start=4191 End=6444 Strand=1 Le...   259  2.7e-19   1
fgram:FG09762.1 hypothetical protein 5035 6633 +               258  2.9e-19   1
drer:ENSDARP00000020121 Database:core Gene:ENSDARG0000000...   252  2.9e-19   1
afum:8240_glimmerf_104                                         259  3.3e-19   1
pchr:pchr_Scaffold_25.Gene48 Start=210869 End=208531 Stra...   260  3.6e-19   1
fgram:FG04670.1 hypothetical protein 154840 156421 -           257  3.9e-19   1
cbri:CBG03134 CBP06431 (cb25.fpc0058.fg640/cb25.fpc0058.g...   258  4.2e-19   1
frub:SINFRUP00000132841 Database:core Gene:SINFRUG0000012...   257  4.2e-19   1
hsap:ENSP00000259696 Database:core Gene:ENSG00000112294 C...   257  5.8e-19   1
frub:SINFRUP00000155714 Database:core Gene:SINFRUG0000014...   236  5.8e-19   1
calb:orf6.4131  orf6-2316:7542-5869:e  1674 bp, 557 aa, c...   257  6.5e-19   1
afum:5674_glimmerf_172                                         234  9.5e-19   1
wih99:cneo_WIH99_77.Gene9 Start=240235 End=242652 Strand=...   252  2.3e-18   1
fgram:FG07803.1 hypothetical protein 81767 83572 +             250  2.4e-18   1
duh99:MATCHRContig45.Gene1 Start=32346 End=34255 Strand=1...   250  3.1e-18   1
wih99:cneo_WIH99_20.Gene108 Start=294712 End=292322 Stran...   250  3.6e-18   1
jec21:cneo_TIGRJEC21_chr11b.pseudo.Gene24 Start=539782 En...   251  4.1e-18   1
frub:SINFRUP00000138575 Database:core Gene:SINFRUG0000013...   228  4.2e-18   1
pchr:pchr_Scaffold_41.Gene38 Start=135527 End=133723 Stra...   246  7.7e-18   1
scer:YHR039C MSC7 SGDID:S0001081, Chr VIII from 186800-18...   247  1.2e-17   1
jec21:cneo_TIGRJEC21_CH9.Gene516 Start=549767 End=547581 ...   245  1.3e-17   1
pchr:pchr_Scaffold_4.Gene75 Start=259710 End=257130 Stran...   187  1.8e-17   2
hsap:ENSP00000325473 Database:core Gene:ENSG00000118514 C...   200  1.9e-17   2
fgram:FG01826.1 hypothetical protein 3352 4961 +               243  1.9e-17   1
scer:YBR006W UGA2 SGDID:S0000210, Chr II from 246971-248464    242  2.2e-17   1
mgri:MG01606.3 hypothetical protein ( (NCU09266.1) hypoth...   241  3.6e-17   1
agos:AAL076W location=AgChr1:213684..215597                    242  4.0e-17   1
hsap:ENSP00000314649 Database:core Gene:ENSG00000112294 C...   235  1.7e-16   1
ccin:ccin_Contig26.Gene76 Start=185685 End=182747 Strand=...   198  1.8e-16   2
drer:ENSDARP00000009551 Database:core Gene:ENSDARG0000000...   212  2.3e-16   1
wih99:cneo_WIH99_84.Gene109 Start=254919 End=252452 Stran...   234  3.0e-16   1
drer:ENSDARP00000003517 Database:core Gene:ENSDARG0000001...   228  3.0e-16   1
scer:YMR110C YMR110C SGDID:S0004716, Chr XIII from 491991...   232  3.4e-16   1
duh99:cneo_DUH99_Contig88.Gene1 Start=947 End=2 Strand=-1...   209  4.8e-16   1
afum:6343_glimmerf_397                                         222  1.2e-15   1
umay:umay_Contig126.Gene6 Start=44007 End=46488 Strand=1 ...   228  1.3e-15   1
duh99:cneo_DUH99_Contig572.Gene12 Start=60677 End=63143 S...   226  2.2e-15   1
rnor:ENSRNOP00000003182 Database:core Gene:ENSRNOG0000000...   224  2.4e-15   1
drer:ENSDARP00000016103 Database:core Gene:ENSDARG0000001...   206  2.8e-15   2
spom:SPBC21C3.15c |||putative aldehyde-dehydrogenase-like...   222  4.2e-15   1
ccin:ccin_Contig86.Gene6 Start=60023 End=62098 Strand=1 L...   217  1.4e-14   1
jec21:cneo_TIGRJEC21_chr3.pseudo.Gene44 Start=853936 End=...   216  2.2e-14   1
drer:ENSDARP00000025142 Database:core Gene:ENSDARG0000001...   198  2.4e-14   2
ccin:ccin_Contig112.Gene67 Start=228881 End=226835 Strand...   215  2.9e-14   1
jec21:cneo_TIGRJEC21_CH9.Gene40 Start=432690 End=434826 S...   215  3.8e-14   1
umay:umay_Contig154.Gene37 Start=150500 End=148105 Strand...   211  8.9e-14   1
pchr:pchr_Scaffold_1.Gene119 Start=403089 End=405051 Stra...   208  1.4e-13   1
wih99:cneo_WIH99_63.Gene197 Start=28565 End=25737 Strand=...   208  1.6e-13   1
frub:SINFRUP00000138576 Database:core Gene:SINFRUG0000013...   181  4.9e-13   1
duh99:cneo_DUH99_Contig562.Gene45 Start=26299 End=23976 S...   182  1.2e-12   2
pchr:pchr_Scaffold_1.Gene91 Start=392557 End=390664 Stran...   198  1.4e-12   1
calb:orf6.7642  orf6-2498:45415-43430:e  1986 bp, 661 aa,...   198  2.9e-12   1
calb:orf6.7610  orf6-2497:61254-62882:e  1629 bp, 542 aa,...   192  9.1e-12   1
cele:T08B1.3 CE13415   aldehyde dehydrogenase status:Conf...   190  9.5e-12   1
afum:4684_glimmerf_1                                           169  9.7e-12   1
pchr:pchr_Scaffold_201.Gene1 Start=14631 End=17178 Strand...   199  1.4e-11   2
drer:ENSDARP00000005081 Database:core Gene:ENSDARG0000000...   188  1.9e-11   1
mgri:MG00719.3 hypothetical protein 80568 82139 +              188  2.3e-11   1
hsap:ENSP00000258494 Database:core Gene:ENSG00000136010 C...   188  4.2e-11   1
frub:SINFRUP00000134540 Database:core Gene:SINFRUG0000012...   184  4.3e-11   1
drer:ENSDARP00000019543 Database:core Gene:ENSDARG0000001...   170  4.3e-10   1
rnor:ENSRNOP00000020325 Database:core Gene:ENSRNOG0000001...   160  9.9e-10   1
agam:ENSANGP00000009992 Database:core Gene:ENSANGG0000000...   167  2.0e-09   2
rnor:ENSRNOP00000017506 Database:core Gene:ENSRNOG0000001...   157  2.8e-09   1
afum:5076_glimmerf_157                                         160  3.2e-09   1
anid:AN5644.1 hypothetical protein 119417 121388 -             166  5.9e-09   1
mgri:MG07270.3 hypothetical protein 24200 27609 -              165  9.7e-09   1
mmus:ENSMUSP00000019246 Database:core Gene:ENSMUSG0000001...   163  9.9e-09   1
umay:umay_Contig248.Gene23 Start=64732 End=62912 Strand=-...   162  1.6e-08   1
ccin:ccin_Contig197.Gene16 Start=193203 End=195572 Strand...   160  2.5e-08   1
hsap:ENSP00000225740 Database:core Gene:ENSG00000108602 C...   159  2.7e-08   1
cele:T05H4.13 CE27441   aldehyde dehydrogenase status:Con...   158  4.1e-08   1
dmel:CG11140-PI translation from_gene[CG11140 Aldh-III FB...   156  6.9e-08   1
mmus:ENSMUSP00000062524 Database:core Gene:ENSMUSG0000002...   127  7.5e-08   3
dmel:CG11140-PF translation from_gene[CG11140 Aldh-III FB...   156  8.4e-08   1
dmel:CG11140-PG translation from_gene[CG11140 Aldh-III FB...   156  8.4e-08   1
dmel:CG11140-PC translation from_gene[CG11140 Aldh-III FB...   156  8.4e-08   1
dmel:CG11140-PB translation from_gene[CG11140 Aldh-III FB...   156  8.4e-08   1
dmel:CG11140-PA translation from_gene[CG11140 Aldh-III FB...   156  8.4e-08   1
dmel:CG11140-PD translation from_gene[CG11140 Aldh-III FB...   156  8.4e-08   1
cbri:CBG18932 CBP19504 (cb25.fpc4126.gc41)                     153  1.4e-07   1
drer:ENSDARP00000014385 Database:core Gene:ENSDARG0000001...   138  1.6e-07   2
mgri:MG06551.3 hypothetical protein 62216 63824 +              105  2.4e-07   2
frub:SINFRUP00000148431 Database:core Gene:SINFRUG0000013...   147  6.2e-07   1
rnor:ENSRNOP00000017655 Database:core Gene:ENSRNOG0000001...   132  1.1e-06   1
drer:ENSDARP00000013496 Database:core Gene:ENSDARG0000000...   134  1.1e-06   1
pchr:pchr_Scaffold_12.Gene51 Start=268702 End=266658 Stra...   145  1.4e-06   1
rnor:ENSRNOP00000023789 Database:core Gene:ENSRNOG0000001...   141  2.5e-06   1
mmus:ENSMUSP00000025795 Database:core Gene:ENSMUSG0000003...   139  2.6e-06   1
mmus:ENSMUSP00000050692 Database:core Gene:ENSMUSG0000001...   141  2.9e-06   1
mmus:ENSMUSP00000010169 Database:core Gene:ENSMUSG0000001...   141  2.9e-06   1
hsap:ENSP00000007633 Database:core Gene:ENSG00000006534 C...   139  3.9e-06   1
mmus:ENSMUSP00000039838 Database:core Gene:ENSMUSG0000003...   138  5.6e-06   1
hsap:ENSP00000316241 Database:core Gene:ENSG00000006534 C...   138  5.7e-06   1
rnor:ENSRNOP00000003200 Database:core Gene:ENSRNOG0000000...   138  6.6e-06   1
frub:SINFRUP00000134534 Database:core Gene:SINFRUG0000012...   134  1.3e-05   1
pchr:pchr_Scaffold_19.Gene52 Start=124215 End=122095 Stra...   135  1.4e-05   1
afum:10580_glimmerf_8                                          131  1.6e-05   1
ncra:NCU04013.1 hypothetical protein (59219 - 57534)           131  4.2e-05   1
anid:AN8985.1 hypothetical protein 22123 23804 -               131  5.4e-05   2
frub:SINFRUP00000129119 Database:core Gene:SINFRUG0000012...   129  5.5e-05   1
frub:SINFRUP00000160622 Database:core Gene:SINFRUG0000015...   116  5.7e-05   1
hsap:ENSP00000314367 Database:core Gene:ENSG00000072210 C...   128  8.2e-05   1
drer:ENSDARP00000025640 Database:core Gene:ENSDARG0000001...   120  8.5e-05   2
hsap:ENSP00000176643 Database:core Gene:ENSG00000072210 C...   128  9.3e-05   1
dmel:CG11140-PH translation from_gene[CG11140 Aldh-III FB...   125  0.00014   1
mmus:ENSMUSP00000056276 Database:core Gene:ENSMUSG0000002...   127  0.00014   3
fgram:FG09960.1 hypothetical protein 40904 42572 +             126  0.00015   1
mmus:ENSMUSP00000057475 Database:core Gene:ENSMUSG0000003...   130  0.00015   1
frub:SINFRUP00000138573 Database:core Gene:SINFRUG0000013...   102  0.00015   1
drer:ENSDARP00000027868 Database:core Gene:ENSDARG0000001...   121  0.00035   1
drer:ENSDARP00000004886 Database:core Gene:ENSDARG0000001...   122  0.00037   1
drer:ENSDARP00000002746 Database:core Gene:ENSDARG0000001...   121  0.00043   1
umay:umay_Contig153.Gene4 Start=24926 End=23503 Strand=-1...   116  0.00044   1
mmus:ENSMUSP00000056922 Database:core Gene:ENSMUSG0000003...   118  0.00047   1
mmus:ENSMUSP00000025816 Database:core Gene:ENSMUSG0000002...   118  0.00078   1
hsap:ENSP00000255084 Database:core Gene:ENSG00000132746 C...   116  0.0011    1
drer:ENSDARP00000012767 Database:core Gene:ENSDARG0000000...    93  0.0014    1
mgri:MG07890.3 hypothetical protein 2215 4003 +                111  0.0062    1
afum:9099_glimmerf_102                                         102  0.023     1
drer:ENSDARP00000008677 Database:core Gene:ENSDARG0000000...   101  0.043     1
drer:ENSDARP00000020199 Database:core Gene:ENSDARG0000000...   101  0.050     1
drer:ENSDARP00000003039 Database:core Gene:ENSDARG0000000...   101  0.052     1
drer:ENSDARP00000015570 Database:core Gene:ENSDARG0000000...   101  0.053     1
drer:ENSDARP00000021159 Database:core Gene:ENSDARG0000001...   100  0.054     1
mmus:ENSMUSP00000050448 Database:core Gene:ENSMUSG0000004...    78  0.055     1
drer:ENSDARP00000010518 Database:core Gene:ENSDARG0000001...   100  0.062     1
drer:ENSDARP00000027140 Database:core Gene:ENSDARG0000002...    98  0.086     1
drer:ENSDARP00000023944 Database:core Gene:ENSDARG0000000...    88  0.15      1
drer:ENSDARP00000017270 Database:core Gene:ENSDARG0000001...    94  0.17      1
hsap:ENSP00000318252 Database:core Gene:ENSG00000006534 C...    92  0.17      1
drer:ENSDARP00000024731 Database:core Gene:ENSDARG0000001...    92  0.42      1
hsap:ENSP00000293350 Database:core Gene:ENSG00000161618 C...    95  0.44      1
rnor:ENSRNOP00000024064 Database:core Gene:ENSRNOG0000001...    86  0.47      1
afum:3599_glimmerf_174                                          88  0.58      1
umay:umay_Contig153.Gene5 Start=23500 End=22157 Strand=-1...    82  0.93      1
agos:AGL192C location=AgChr7:complement(361641..363485)         87  0.95      1
jec21:cneo_TIGRJEC21_chr3.pseudo.Gene262 Start=1259945 En...    59  0.998     1
dmel:CG8358-PA translation from_gene[CG8358 CG8358 FBgn00...    84  0.9995    1



Parameters:
  -i /nfs1/jason_input/euk_split/eukall.597
  -d /nfs1/jason_input/all_euk/metazoans /nfs1/jason_input/fungi/ascopeps /nfs1/jason_input/fungi/basido
  W=3
  T=1000
  B=0

  ctxfactor=1.00
  E=10

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.317   0.134   0.392    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E    S W    T  X   E2     S2
   +0      0      601       601       10.  82 3 1000 22  0.21    34
                                                     36  0.22    37


Statistics:

  Database:  /nfs1/jason_input/all_euk/metazoans; /nfs1/jason_input/fungi/ascopeps; /nfs1/jason_input/fungi/basido
   Title:  /nfs1/jason_input/all_euk/metazoans; /nfs1/jason_input/fungi/ascopeps; /nfs1/jason_input/fungi/basido
   Format:  VirtualDB
   # of letters in database:  145,589,111
   # of sequences in database:  351,440
   # of database sequences satisfying E:  415
  No. of states in DFA:  281 (30 KB)
  Total size of DFA:  44 KB (2055 KB)
  Time to generate neighborhood:  0.01u 0.00s 0.01t  Elapsed: 00:00:00
  No. of threads or processors used:  2
  Search cpu time:  28.63u 0.00s 28.63t  Elapsed: 00:00:15
  Total cpu time:  28.68u 0.00s 28.68t  Elapsed: 00:00:15
  Start:  Wed Nov  5 04:46:09 2003   End:  Wed Nov  5 04:46:24 2003
BioPerl-1.007002/t/data/no_semicolon.newick000444000766000024         7113155576321 20514 0ustar00cjfieldsstaff000000000000(((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1)BioPerl-1.007002/t/data/noninterleaved.phy000444000766000024       310213155576321 20423 0ustar00cjfieldsstaff000000000000 4 297
SBP-5.05   CCTCAGATCA CTCTTTGGCA ACGACCCCTT GTCACAATAA AGATAGGGGG 
           GCAACTAAAG GAAGCTCTAT TAGATACAGG AGCAGATGAT ACAGTATTAG 
           AAGAAATGAA TTTGCCAGGA AGATGGAAAC CAAAAATGAT AGGGGGAATT 
           GGAGGGTTTA TCAAAGTAAA ACAGTATGAT CAGATACCCA TAGAGATCTG 
           TGGACATAAA GCTATAGGTA CAGTATTAGT AGGACCCACA CCTGTCAATA 
           TAATTGGAAG AAATCTGTTG ACTCAGATTG GTTGCACTTT AAATTTT

SBP-5.21_S CCTCAGATCA CTCTTTGGCA ACGACCCCTC GTCACAATAA AGGTAGGGGG 
           GCAACTAAAG GAAGCTCTAT TAGATACAGG AGCAGATGAT ACAGTATTAG 
           AAGACATGAA TTTGCCAGGA AGATGGAAAC CAAAAATGAT AGGGGGAATT 
           GGAGGGTTTA TCAAAGTAAG ACAGTATGAT CAGATACCCA TAGAGATCTG 
           TGGACATAAA GCTATAGGTA CAGTATTAGT AGGACCCACA CCTGTCAATA 
           TAATTGGAAG AAATCTGTTG ACTCAGATTG GTTGCACTTT AAATTTT

SBP-5.04_2 CCTCAGATCA CTCTTTGGCA ACGACCCCTC GTCACAATAA AGATAGGGGG 
           GCAACTAAAG GAAGCTCTAT TAGATACAGG AGCAGATGAT ACAGTATTAG 
           AAGAAATGAA TTTGCCAGGA AGATGGAAAC CAAAAATGAT AGGGGGAATT 
           GGAGGGTTTA TCAAAGTAAG ACAGTATGAT CAGATACCCA TAGAGATCTG 
           TGGACATAAA GCTATAGGTA CAGTATTAGT AGGACCCACA CCTGTCAATA 
           TAATTGGAAG AAATCTGTTG ACTCAGATTG GTTGCACTTT AAATTTT

REC_SBP0.2 CCTCAGATCA CTCTTTGGCA ACGACCCCTC GTCACAATAA AGATAGGGGG 
           GCAACTAAAG GAAGCTCTAT TAGATACAGG AGCAGATGAT ACAGTATTAG 
           AGGAAACGAA TTTGCCAGGA AGATGGAAAC CAAAAATGAT AGGGGGAATT 
           GGAGGGTTTA TCAAAGTAAG ACAGTATGAT CAGATACCCA TAGAGATCTG 
           TGGACATAAA GCTATAGGTA CAGTATTAGT AGGACCCACA CCTGTCAATA 
           TAATTGGAAG AAATCTGTTG ACTCAGATTG GTTGCACTTT AAATTTT
BioPerl-1.007002/t/data/nucmatrix.txt000444000766000024        35213155576321 17423 0ustar00cjfieldsstaff000000000000     A    C    G    T    .    N
A  100 -150  -50 -150    0  -50
C -150  100 -150  -50    0  -50
G  -50 -150  100 -150    0  -50
T -150  -50 -150  100    0  -50
.    0    0    0    0    0    0
N  -50  -50  -50  -50    0  -50

-300 -25
BioPerl-1.007002/t/data/omim_genemap_test000444000766000024      3703713155576321 20341 0ustar00cjfieldsstaff0000000000001.1|9|11|95|1pter-p36.13|CCV|P|Cataract, congenital, Volkmann type||115665|Fd|linked to Rh in Scottish family||Cataract, congenital, Volkmann type (2)| | ||
1.2|9|25|01|1pter-p36.13|ENO1, PPH, MPB1|C|Enolase-1, alpha||172430|S, F, R, REa|||Enolase deficiency (1)| | |4(Eno1)|
1.3|10|23|87|1pter-p36.13|GDH|C|Glucose dehydrogenase||138090|S, F|||| | ||
1.3|10|23|87|1pter-p36.14|gene-symbol1|C|XXX||100500|M method 1|comment1||| | |mousecorrelate1|
1.3|10|23|87|1pter-p36.15|gene-symbol2|C|XXX||100501|M method 2|comment2||| | |mousecorrelate2|
1.4|6|7|99|1pter-p36.1|CTPP, CPP, CTPA|P|Cataract, posterior polar||116600|Fd|?relation to Volkmann cataract||Cataract, posterior polar (2)| | ||
1.5|12|22|87|1pter-p36|ERPL1, HLM2|C|Endogenous retroviral pol gene-like sequence 1 (oncogene HLM2)||131190|REa, F|||| | ||
1.6|1|18|95|1pter-p33|HMGCL|P|3-hydroxy-3-methylglutaryl-Coenzyme A lyase||246450|REa, A|||HMG-CoA lyase deficiency (3)| | |4(Hmgcl)|
1.7|12|16|93|1pter-p32|AGRN|P|Agrin||103320|REa|||| | |4(Agrn)|
1.8|3|15|92|1pter-p31.2|GNB1|C|Guanine nucleotide-binding protein, beta polypeptide-1||139380|REa, A|||| | |4(Gnb1)|
1.9|8|28|98|1pter-p22.1|SAI1, MTS1, TFS1|C|Suppression of anchorage independence-1 (malignant transformation|suppression-1)|154280|S, H|||| | |4(Tfs1)|
1.10|4|24|01|1p36.33|TAS1R3, T1R3|P|Taste receptor type 1, member 3||605865|REn|||| | |4(Tas1r3)|
1.11|10|27|89|1p36.33-p36.22|CA6|C|Carbonic anhydrase VI||114780|REa, A, REc, R|||| | ||
1.12|8|9|99|1p36.3|C1orf1|P|Chromosome 1, open reading frame 1||604006|A|||| | ||
1.13|12|1|98|1p36.3|CDC2L1|C|Cell division cycle 2-like 1||176873|REa, A, Pcm, A|||| | ||
1.14|12|1|98|1p36.3|CDC2L2|P|Cell division cycle 2-like 2||116951|A|||| | ||
1.15|8|4|99|1p36.3|DFFB, CAD, DFF2|C|DNA fragmentation factor, 40kD, beta subunit||601883|A|||| | ||
1.16|11|5|99|1p36.3|EGFL3, MEGF6|P|Epidermal growth factor-like 3||604266|R|||| | ||
1.17|1|24|01|1p36.3|GABRD|C|Gamma-aminobutyric acid (GABA) A receptor, delta||137163|REa, R|||| | ||
1.18|9|12|96|1p36.3|HKR3|C|GLI-Kruppel family member HKR3||165270|REa, A|||| | ||
1.19|6|15|99|1p36.3|TNFRSF18, AITR, GITR|P|Tumor necrosis factor receptor superfamily, member 18||603905|R|||| | ||
1.20|3|30|99|1p36.3|KCNAB2, KCNA2B|P|Potassium voltage-gated channel, shaker-related subfamily, beta|member 2|601142|A|||| | ||
1.21|11|1|99|1p36.3|MMP23A, MMP21, MIFR|P|Matrix metalloproteinase 23A||603320|REc|||| | ||
1.22|11|1|99|1p36.3|MMP23B, MMP22|P|Matrix metalloproteinase 23B||603321|REc|||| | ||
1.23|10|4|93|1p36.3|MTHFR|P|Methylenetetrahydrofolate reductase||236250|A|||Homocystinuria due to MTHFR deficiency (3)| | |4(Mthfr)|
1.24|1|17|01|1p36.3|PRDM16, MEL1|P|PR domain-containing protein 16||605557|REc, Ch|||| | ||
1.25|8|9|99|1p36.3|PTPRZ2|P|Protein-tyrosine phosphatase, receptor-type, zeta-2||604008|A|||| | ||
1.26|1|20|98|1p36.3|RNU1A, RNU1|C|RNA, U1A small nuclear||180680|REa, A|?same as A12M2||| | |3(Rnu1b1)|
1.27|12|21|98|1p36.3|TNFRSF12, DR3, LARD|C|Tumor necrosis factor receptor superfamily, member 12||603366|A, Ch|||| | ||
1.28|6|20|01|1p36.3|WDR8|P|WD repeat-containing protein 8||606040|A|||| | ||
1.29|8|9|99|1p36.3|XBX1|P|Xylan 1,4-beta-xylosidase 1||604007|A|||| | ||
1.30|2|6|94|1p36.3-p34.3|HTR1D|C|5-hydroxytryptamine (serotonin) receptor-1D||182133|REa, A|||| | |4(Htr1d)|
1.31|6|10|98|1p36.3-p36.2|DFFA, DFF1|C|DNA fragmentation factor, 45kD, alpha subunit||601882|A|||| | ||
1.32|1|30|01|1p36.3-p36.2|MASP2|P|Mannan-binding lectin serine protease 2||605102|A, R|||| | ||
1.33|7|4|95|1p36.3-p36.2|NB, NBS|C|Neuroblastoma (neuroblastoma suppressor)||256700|Ch, D|?role of DAN||Neuroblastoma (2)| | ||
1.34|1|1|95|1p36.3-p36.2|PLOD, PLOD1|P|Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase)||153454|REa, A|||Ehlers-Danlos syndrome, type VI, 225400 (3)| | |4(Plod)|Hautala (1992)
1.35|9|15|96|1p36.3-p36.2|SCNN1D|P|Sodium channel, voltage-gated, type I, delta polypeptide||601328|A|||| | ||
1.36|12|18|98|1p36.3-p36.2|TNFRSF1B, TNFR2, TNFBR|C|Tumor necrosis factor receptor superfamily, member 1B||191191|REa, A, Fd|||| | |4(Tnfr1)|
1.37|12|14|98|1p36.3-p36.2|TNFRSF14, HVEM, TR2|P|Tumor necrosis factor receptor superfamily, member 14 (herpesvirus|entry mediator)|602746|A|||| | ||
1.38|11|18|96|1p36.3-p34.1|C1QA|C|Complement component-1, q subcomponent, alpha polypeptide||120550|REa, REb|||C1q deficiency, type A (3)| | ||
1.39|11|18|96|1p36.3-p34.1|C1QB|C|Complement component-1, q subcomponent, beta polypeptide||120570|REa, REb|||C1q deficiency, type B (3)| | |(C1qb)|
1.40|11|18|96|1p36.3-p34.1|C1QG|P|Complement component-1, q subcomponent, gamma polypeptide||120575|REn, REb|||C1q deficiency, type C (3)| | ||
1.41|6|18|97|1p36.2|FRAP1|P|FK506 binding protein 12-rapamycin associated protein-1||601231|R, A|||| | ||
1.42|12|11|01|1p36.2|KIF1B, CMT2A|C|Kinesin family member 1B||605995|Fd, REc, D|||Charcot-Marie-Tooth neuropathy, type 2A, 118210 (3)| | |4(Kif1b)|
1.43|6|2|94|1p36.2|NPPA, PND, ANP|C|Pronatriodilatin (atrial natriuretic peptide)||108780|REa, A, H|||| | |4(Pnd)|
1.44|5|9|95|1p36.2|NPPB, BNP|C|Natriuretic peptide precursor B||600295|H, REa, A, REn|||| | |4(Nppb)|
1.45|8|4|99|1p36.2|SLC2A5, GLUT5|C|Solute carrier family 2 (facilitated glucose transporter), member 5||138230|REa, A, REc, R|||| | ||
1.46|4|10|90|1p36.2-p36.13|PGD|C|6-phosphogluconate dehydrogenase||172200|F, S|||| | |4(Pgd)|
1.47|2|19|96|1p36.2-p36.12|PAX7|C|Paired box homeotic gene-7||167410|Psh, H, REa, A|fused with FKHR in rhabdomyosarcoma||Rhabdomyosarcoma, alveolar, 268220 (3)| | |4(Pax7)|
1.48|4|19|01|1p36.2-p36.1|DNB5|P|Deleted in neuroblastoma 5||605763|REc|||| | ||
1.49|3|24|88|1p36.2-p36.1|FGR, SRC2|P|Oncogene FGR||164940|A, REb, REa, Fd|same as SRC2||| | |4(Fgr)|
1.50|9|22|97|1p36.2-p36.1|GLC3B|P|Glaucoma 3, primary infantile, B||600975|Fd|||Glaucoma 3, primary infantile, B (2)| | ||
1.51|9|7|00|1p36.2-p36.1|RERE|P|RE repeats-encoding gene||605226|REc, Ch|||| | ||
1.52|6|19|00|1p36.2-p36.1|ZNF151|P|Zinc finger protein-151||604084|A|||| | ||
1.53|1|1|95|1p36.2-p35|CDA|C|Cytidine deaminase||123920|A, Psh|||| | ||
1.54|10|22|92|1p36.2-p34|EPB41, EL1|C|Erythrocyte surface protein band 4.1||130500|F, REb|||Elliptocytosis-1 (3)| | |4(Elp1)|
1.55|10|23|87|1p36.2-p34|RD|C|Radin blood group||111620|F|||| | ||
1.56|8|4|97|1p36.2-p34|RHCE|C|Rhesus system C and E polypeptides||111700|F, D, Fd|?order: C-E-D||| | ||
1.57|1|10|89|1p36.2-p34|RHD|C|Rhesus system D polypeptide||111680|F, D, Fd|||| | ||
1.58|10|23|87|1p36.2-p34|SC|C|Scianna blood group||111750|F|||| | ||
1.59|10|18|00|1p36.2-p34|SMP1|P|Small membrane protein 1||605348|REc|between RHD and RHCE||| | ||
1.60|1|11|95|1p36.13-p36.12|ID3|C|Inhibitor of DNA binding 3, dominant negative, helix-loop-helix|protein|600277|RE, A|||| | ||
1.61|10|24|97|1p36.13-p36.11|D1S1733E, DAN|P|Differential-screening-selected gene aberrant in neuroblastoma||600613|A|aberrant in some neuroblastomas||| | |4(D4H1S1733E)|
1.62|3|1|01|1p36.12|PLA2G2D, SPLASH|C|Phospholipase A2, group IID||605630|R|||| | |4(Pla2g2d)|
1.63|4|24|01|1p36.11-p34.3|WASF2, WAVE2, SCAR2|P|Wiskott-Aldrich syndrome protein family, member 2||605875|REc|?pseudogene on Xp11.21||| | ||
1.64|8|18|99|1p36.1-p35|C1orf4, B120|P|Brain protein 120||603024|A|||| | ||
1.65|8|28|97|1p36.1|CAPZB, CAPPB|P|Capping protein (actin filament) muscle Z-line, beta||601572|A|||| | ||
1.66|10|20|99|1p36.1|CDC42|P|Cell division cycle 42 (GTP-binding protein, 25kD)||116952|H, R, REc|||| | |4(cdc42)|
1.67|1|1|95|1p36.1|CHC1, RCC1|C|Regulator of chromosome condensation||179710|REb, A|||| | |4(Chc1)|
1.68|5|28|98|1p36.1|DDOST, OST, OST48|P|Dolichyl-diphosphooligosaccharide-protein glycosyltransferase||602202|A|||| | ||
1.69|6|16|99|1p36.1|ECE1|C|Endothelin converting enzyme 1||600423|A, R, Psh|||Hirschsprung disease, cardiac defects, and autonomic dysfunction (3)| | ||
1.70|5|5|98|1p36.1|EPHA2, ECK|P|Ephrin receptor EphA2||176946|A, REa|||| | |4(Epha2)|
1.71|4|11|97|1p36.1|EXTL1|P|Exostosin-like 1||601738|R, A|||| | ||
1.72|10|12|90|1p36.1|HMG17|C|Nonhistone chromosomal protein HMG-17||163910|REa, A|||| | ||
1.73|4|1|01|1p36.1|HSPG2, PLC, SJS, SJA, SJS1|C|Heparan sulfate proteoglycan of basement membrane (perlecan)||142461|A, REa, LD|||Schwartz-Jampel syndrome, type 1, 255800 (3); Dyssegmental dysplasia,|Silverman-Handmaker type, 224410 (3) | |4(Plc)|
1.74|3|6|01|1p36.1|NR0B2, SHP|P|Nuclear receptor subfamily 0, group B, member 2||604630|REa, A|||Obesity, mild, early-onset, 601665 (3)| | ||
1.75|8|21|91|1p36.1|PRKACB|P|Protein kinase, cAMP-dependent, catalytic, beta||176892|REa, A|||| | ||
1.76|11|3|98|1p36.1|RNU17A, RNE1|C|RNA, U17a small nucleolar||180645|REn|in IVS1 of CHC1||| | ||
1.77|11|3|98|1p36.1|RNU17B|P|RNA, U17b small nucleolar||603239|REn|||| | ||
1.78|12|15|99|1p36.1|RNU17D, U17HG|P|RNA, U17d small nucleolar||603238|REn|||| | ||
1.79|2|20|98|1p36.1|RSC1A1, RS1|P|Regulatory solute carrier protein, family 1, member 1||601966|A|||| | ||
1.80|2|15|96|1p36.1|TCEB3|P|Transcription elongation factor B (SIII), polypeptide 3 (110kD,|elongin A)|600786|A|||| | ||
1.81|9|13|89|1p36.1|TRN|P|tRNA asparagine||189880|REa, RE|||| | ||
1.82|11|5|97|1p36.1-p35|EPHB2, EPHT3, DRT, ERK|P|eph tyrosine kinase 3 (ephrin receptor EphB2)||600997|Psh, A|||| | ||
1.83|4|23|96|1p36.1-p35|MEMO1|P|Methylation modifier for class I HLA||601201|D|||| | ||
1.84|10|22|95|1p36.1-p35|MFAP2, MAGP, MAGP1|P|Microfibrillar-associated protein-2||156790|REa, A|||| | |4(Mfap2)|
1.85|2|26|95|1p36.1-p35|RAP1GA1|P|RAP1, GTPase activating protein 1||600278|A, REa|||| | ||
1.86|10|20|99|1p36.1-p35|RPL11|C|Ribosomal protein L11||604175|REa, R, A|||| | ||
1.87|11|28|01|1p36.1-p35|SDHB, SDH1, SDHIP|C|Succinate dehydrogenase complex, subunit B, iron sulfur (Ip)||185470|S, REa, A|1 of 2 polypeptides||Pheochromocytoma, extraadrenal, and cervical paraganglioma, 115310|(3) | ||
1.88|3|28|95|1p36.1-p35|SLC9A1, NHE1, APNH|C|Solute carrier family 9 (sodium/hydrogen exhanger), isoform 1|(antiporter, Na+/H+, amiloride sensitive)|107310|A, F, Fd|3cM proximal to RH||| | |4(Apnh, Nhe1)|
1.89|7|17|01|1p36.1-p35|STMN1, LAP18, SMN|P|Stathmin||151442|REa, A|||| | |4(Lap18)|
1.90|1|1|95|1p36.1-p34.3|GPR3|C|G protein-coupled receptor-3||600241|A|||| | ||
1.91|3|17|94|1p36.1-p34.3|OPRD1|P|Opioid receptor, delta-1||165195|H, A|||| | |4(Nbor, Oprd1)|
1.92|6|15|99|1p36.1-p34|ALPL, HOPS|C|Alkaline phosphatase, liver/bone/kidney||171760|S, H, Fd, F, A|||Hypophosphatasia, infantile, 241500 (3); Hypophosphatasia, childhood,|241510 (3); ?Hypophosphatasia, adult, 146300 (1) | |4(Akp2)|
1.93|1|25|99|1p36|ALDH4A1, ALDH4, P5CDH|P|Aldehyde dehydrogenase 4 family, member A1|(delta-1-pyrroline 5-carboxylate dehydrogenase)|606811|A|||Hyperprolinemia, type II, 239510 (3)| | ||
1.94|5|14|02|1p36|BMND3|P|Bone mineral density variability 3||606928|Fd|||[Bone mineral density variability 3], 601884 (2)| | ||
1.95|10|2|89|1p36|BRCD2|P|Breast cancer, ductal||211420|Ch, F, D|||Breast cancer, ductal (2)| | ||
1.96|6|19|98|1p36|CLCN6|P|Chloride channel 6||602726|REa, A|||| | ||
1.97|10|15|97|1p36|CLCNKA|C|Chloride channel, kidney, A||602024|Fd, REc|11kb from CLCNKB||| | ||
1.98|10|15|97|1p36|CLCNKB|C|Chloride channel, kidney, B||602023|Fd, REc|unequal crossingover with CLCNKA||Bartter syndrome, antenatal, 601678 (3); Bartter syndrome, 241200 (3)| | ||
1.99|1|4|93|1p36|CMM, MLM, DNS|P|Cutaneous malignant melanoma/dysplastic nevus||155600|F, Fd, D|some linkage studies negative; see 9p||Malignant melanoma, cutaneous (2)| | ||Greene (1983); Goldstein (1992)
1.100|8|15|96|1p36|DVL1|C|Dishevelled 1 (homologous to Drosophila dsh)||601365|Psh, A|||| | ||
1.101|2|01|01|1p36|CORT|C|Cortistatin||602784|H, R, REc|||| | |4(Cort)|
1.102|2|23|95|1p36|E2F2|P|E2F transcription factor 2||600426|A|||| | ||
1.103|4|18|97|1p36|EYA3|P|Eyes absent, Drosophila, homolog of, 3||601655|A, H|||| | |4(Eya3)|
1.104|9|7|00|1p36|IBD7|P|Inflammatory bowel disease-7||605225|Fd|||{Inflammatory bowel disease-7}, 266600 (2)| | ||
1.105|4|17|01|1p36|ICMT|P|Isoprenylcysteine carboxylmethyltransferase||605851|R|||| | ||
1.106|2|15|02|1p36|KRPPD|P|Kufor-Rakeb pallidopyramidal degeneration with supranuclear upgaze|paresis and dementia|606693|Fd|||Kufor-Rakeb syndrome (2)| | ||
1.107|4|2|01|1p36|LUZP1|P|Leucine zipper protein 1||601422|H, R|||| | |4(Luzp)|
1.108|3|9|00|1p36|MAD2L2, MAD2B|P|Mitotic arrest-deficient 2, S. cerevisiae, homolog-like 2||604094|R|pseudogene on 14q21-q23||| | ||
1.109|6|3|02|1p36|PARK7|P|Parkinson disease 7, autosomal recessive early-onset||606324|Fd|||Parkinson disease, 168600 (2)| | ||
1.110|4|21|99|1p36|PCBC, CAPB|P|Prostate cancer-brain cancer susceptibility||603688|Fd|||{Prostate cancer-brain cancer susceptibility} (2)| | ||
1.111|9|28|96|1p36|PRDM2, RIZ|P|PR domain-containing protein 2 (retinoblastoma protein-binding|zinc-finger protein RIZ)|601196|REc, A|||| | |4(Riz)|
1.112|11|29|99|1p36|RUNX3, CBFA3, PEBP2A3, AML2|C|Runt-related transcription factor 3||600210|A, REa|||| | |4(Aml2, Cbfa3)|
1.113|12|18|98|1p36|TNFRSF4, TXGP1L, OX40, ACT35|P|Tumor necrosis factor receptor superfamily, member 4||600315|A|||| | |4(Ox40)|
1.114|12|18|98|1p36|TNFRSF8, CD30, D1S166E|P|Tumor necrosis factor receptor superfamily, member 8|(CD30 antigen; Ki-1 antigen)|153243|A|||| | |4(Cd30)|
1.115|12|18|98|1p36|TNFRSF9, ILA, CD137|P|Tumor necrosis factor receptor superfamily, member 9|(interleukin-activated receptor; Ly63, mouse, homolog of)|602250|REa|||| | |(Cd157)|
1.116|10|15|97|1p36|TP73|P|p53-related protein||601990|D|imprinted||?Neuroblastoma (1)| | ||
1.117|9|13|89|1p36|TRE|P|tRNA glutamic acid||180640|A|||| | ||
1.118|6|12|01|1p36-p35|ARH, FHCB2, FHCB1|P|Autosomal recessive hypercholesterolemia gene||605747|Fd|||Hypercholesterolemia, familial, autosomal recessive, 603813 (3)| | ||
1.119|5|29|02|1p36-p35|GALE|C|UDP galactose-4-epimerase||606953|S, LD|||Galactose epimerase deficiency, 230350 (3)| | ||
1.120|3|12|96|1p36-p35|HTR6|P|5-hydroxytryptamine (serotonin) receptor-6||601109|REa|||| | ||
1.121|6|18|01|1p36-p35|PARK6|P|Parkinson disease 6, autosomal recessive early-onset||605909|Fd|||Parkinson disease, 168600 (2)| | ||
1.122|8|23|01|1p36-p35|SEPN1, SELN, RSMD1|C|Selenoprotein N||606210|REc, Fd|||Muscular dystrophy, rigid spine, 1, 602771 (3)| | ||
1.123|1|26|97|1p36-p34.1|SCCD|P|Schnyder crystalline corneal dystrophy||121800|Fd|||Corneal dystrophy, crystalline, Schnyder (2)| | ||
1.124|3|9|98|1p36-p34|PLA2G5|P|Phospholipase A2, group V||601192|A|||| | |4(Pla2g5)|
1.125|5|4|00|1p36-p32|PABPC4, PABP4, IPABP, APP1|P|Polyadenylate-binding protein, cytoplasmic, 4||603407|Psh, R|||| | ||
1.126|12|3|91|1p36-p22|SRM, SPS1|C|Spermidine synthase-1||182891|REa, A, Psh|?pseudogene on 3p14-q21||| | ||
1.127|8|9|01|1p35.2-p33|DSCR1L2, MCIP3|P|Down syndrome critical region gene 1-like 2 (myocyte-enriched|calcineurin-interacting protein 3)|605860|REc|||| | |4(Dscr1l2)|
1.128|2|18|96|1p35.1|GJA4, CX37|C|Gap junction protein, alpha-4, 37kD (connexin 37)||121012|REa, A, REc|||| | |(Gja4)|
1.129|12|28|01|1p35.1|GJB3, CX31, DFNA2|C|Gap junction protein, beta-3||603324|REn, REc, Psh, A|same YAC as GJA4||Erythrokeratodermia variabilis, 133200 (3); Deafness, autosomal|dominant 2, 600101 (3); Deafness, autosomal recessive (3); Deafness, autosomal dominant, with peripheral neuropathy (3)| ||
1.130|11|29|00|1p35.1|GJB4, CX30.3|P|Gap junction protein, beta-4||605425|REn, Fd|||Erythrokeratodermia variabilis with erythema gyratum repens,|133200 (3) | ||
1.131|11|29|00|1p35.1|GJB5, CX31.1|P|Gap junction protein, beta-5||604493|R, REc|||| | ||
1.132|12|2|97|1p35.1|P28|P|Inner dynein arm, clamydomonas, homolog of||602135|REa, R|||| | ||
1.133|6|10|98|1p35|BAI2|P|Brain-specific angiongenesis inhibitor-2||602683|A|||| | ||
1.134|8|21|91|1p35|EBVS1|P|Epstein-Barr virus integration site||132850|A|||| | ||
1.135|3|21|93|1p35|G1P3, IFI616|C|Interferon, alpha-inducible protein (clone IFI-6-16)||147572|A, T|||| | ||
BioPerl-1.007002/t/data/omim_genemap_test_nolinebreak000444000766000024      3703613155576321 22711 0ustar00cjfieldsstaff0000000000001.1|9|11|95|1pter-p36.13|CCV|P|Cataract, congenital, Volkmann type||115665|Fd|linked to Rh in Scottish family||Cataract, congenital, Volkmann type (2)| | ||
1.2|9|25|01|1pter-p36.13|ENO1, PPH, MPB1|C|Enolase-1, alpha||172430|S, F, R, REa|||Enolase deficiency (1)| | |4(Eno1)|
1.3|10|23|87|1pter-p36.13|GDH|C|Glucose dehydrogenase||138090|S, F|||| | ||
1.3|10|23|87|1pter-p36.14|gene-symbol1|C|XXX||100500|M method 1|comment1||| | |mousecorrelate1|
1.3|10|23|87|1pter-p36.15|gene-symbol2|C|XXX||100501|M method 2|comment2||| | |mousecorrelate2|
1.4|6|7|99|1pter-p36.1|CTPP, CPP, CTPA|P|Cataract, posterior polar||116600|Fd|?relation to Volkmann cataract||Cataract, posterior polar (2)| | ||
1.5|12|22|87|1pter-p36|ERPL1, HLM2|C|Endogenous retroviral pol gene-like sequence 1 (oncogene HLM2)||131190|REa, F|||| | ||
1.6|1|18|95|1pter-p33|HMGCL|P|3-hydroxy-3-methylglutaryl-Coenzyme A lyase||246450|REa, A|||HMG-CoA lyase deficiency (3)| | |4(Hmgcl)|
1.7|12|16|93|1pter-p32|AGRN|P|Agrin||103320|REa|||| | |4(Agrn)|
1.8|3|15|92|1pter-p31.2|GNB1|C|Guanine nucleotide-binding protein, beta polypeptide-1||139380|REa, A|||| | |4(Gnb1)|
1.9|8|28|98|1pter-p22.1|SAI1, MTS1, TFS1|C|Suppression of anchorage independence-1 (malignant transformation|suppression-1)|154280|S, H|||| | |4(Tfs1)|
1.10|4|24|01|1p36.33|TAS1R3, T1R3|P|Taste receptor type 1, member 3||605865|REn|||| | |4(Tas1r3)|
1.11|10|27|89|1p36.33-p36.22|CA6|C|Carbonic anhydrase VI||114780|REa, A, REc, R|||| | ||
1.12|8|9|99|1p36.3|C1orf1|P|Chromosome 1, open reading frame 1||604006|A|||| | ||
1.13|12|1|98|1p36.3|CDC2L1|C|Cell division cycle 2-like 1||176873|REa, A, Pcm, A|||| | ||
1.14|12|1|98|1p36.3|CDC2L2|P|Cell division cycle 2-like 2||116951|A|||| | ||
1.15|8|4|99|1p36.3|DFFB, CAD, DFF2|C|DNA fragmentation factor, 40kD, beta subunit||601883|A|||| | ||
1.16|11|5|99|1p36.3|EGFL3, MEGF6|P|Epidermal growth factor-like 3||604266|R|||| | ||
1.17|1|24|01|1p36.3|GABRD|C|Gamma-aminobutyric acid (GABA) A receptor, delta||137163|REa, R|||| | ||
1.18|9|12|96|1p36.3|HKR3|C|GLI-Kruppel family member HKR3||165270|REa, A|||| | ||
1.19|6|15|99|1p36.3|TNFRSF18, AITR, GITR|P|Tumor necrosis factor receptor superfamily, member 18||603905|R|||| | ||
1.20|3|30|99|1p36.3|KCNAB2, KCNA2B|P|Potassium voltage-gated channel, shaker-related subfamily, beta|member 2|601142|A|||| | ||
1.21|11|1|99|1p36.3|MMP23A, MMP21, MIFR|P|Matrix metalloproteinase 23A||603320|REc|||| | ||
1.22|11|1|99|1p36.3|MMP23B, MMP22|P|Matrix metalloproteinase 23B||603321|REc|||| | ||
1.23|10|4|93|1p36.3|MTHFR|P|Methylenetetrahydrofolate reductase||236250|A|||Homocystinuria due to MTHFR deficiency (3)| | |4(Mthfr)|
1.24|1|17|01|1p36.3|PRDM16, MEL1|P|PR domain-containing protein 16||605557|REc, Ch|||| | ||
1.25|8|9|99|1p36.3|PTPRZ2|P|Protein-tyrosine phosphatase, receptor-type, zeta-2||604008|A|||| | ||
1.26|1|20|98|1p36.3|RNU1A, RNU1|C|RNA, U1A small nuclear||180680|REa, A|?same as A12M2||| | |3(Rnu1b1)|
1.27|12|21|98|1p36.3|TNFRSF12, DR3, LARD|C|Tumor necrosis factor receptor superfamily, member 12||603366|A, Ch|||| | ||
1.28|6|20|01|1p36.3|WDR8|P|WD repeat-containing protein 8||606040|A|||| | ||
1.29|8|9|99|1p36.3|XBX1|P|Xylan 1,4-beta-xylosidase 1||604007|A|||| | ||
1.30|2|6|94|1p36.3-p34.3|HTR1D|C|5-hydroxytryptamine (serotonin) receptor-1D||182133|REa, A|||| | |4(Htr1d)|
1.31|6|10|98|1p36.3-p36.2|DFFA, DFF1|C|DNA fragmentation factor, 45kD, alpha subunit||601882|A|||| | ||
1.32|1|30|01|1p36.3-p36.2|MASP2|P|Mannan-binding lectin serine protease 2||605102|A, R|||| | ||
1.33|7|4|95|1p36.3-p36.2|NB, NBS|C|Neuroblastoma (neuroblastoma suppressor)||256700|Ch, D|?role of DAN||Neuroblastoma (2)| | ||
1.34|1|1|95|1p36.3-p36.2|PLOD, PLOD1|P|Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase)||153454|REa, A|||Ehlers-Danlos syndrome, type VI, 225400 (3)| | |4(Plod)|Hautala (1992)
1.35|9|15|96|1p36.3-p36.2|SCNN1D|P|Sodium channel, voltage-gated, type I, delta polypeptide||601328|A|||| | ||
1.36|12|18|98|1p36.3-p36.2|TNFRSF1B, TNFR2, TNFBR|C|Tumor necrosis factor receptor superfamily, member 1B||191191|REa, A, Fd|||| | |4(Tnfr1)|
1.37|12|14|98|1p36.3-p36.2|TNFRSF14, HVEM, TR2|P|Tumor necrosis factor receptor superfamily, member 14 (herpesvirus|entry mediator)|602746|A|||| | ||
1.38|11|18|96|1p36.3-p34.1|C1QA|C|Complement component-1, q subcomponent, alpha polypeptide||120550|REa, REb|||C1q deficiency, type A (3)| | ||
1.39|11|18|96|1p36.3-p34.1|C1QB|C|Complement component-1, q subcomponent, beta polypeptide||120570|REa, REb|||C1q deficiency, type B (3)| | |(C1qb)|
1.40|11|18|96|1p36.3-p34.1|C1QG|P|Complement component-1, q subcomponent, gamma polypeptide||120575|REn, REb|||C1q deficiency, type C (3)| | ||
1.41|6|18|97|1p36.2|FRAP1|P|FK506 binding protein 12-rapamycin associated protein-1||601231|R, A|||| | ||
1.42|12|11|01|1p36.2|KIF1B, CMT2A|C|Kinesin family member 1B||605995|Fd, REc, D|||Charcot-Marie-Tooth neuropathy, type 2A, 118210 (3)| | |4(Kif1b)|
1.43|6|2|94|1p36.2|NPPA, PND, ANP|C|Pronatriodilatin (atrial natriuretic peptide)||108780|REa, A, H|||| | |4(Pnd)|
1.44|5|9|95|1p36.2|NPPB, BNP|C|Natriuretic peptide precursor B||600295|H, REa, A, REn|||| | |4(Nppb)|
1.45|8|4|99|1p36.2|SLC2A5, GLUT5|C|Solute carrier family 2 (facilitated glucose transporter), member 5||138230|REa, A, REc, R|||| | ||
1.46|4|10|90|1p36.2-p36.13|PGD|C|6-phosphogluconate dehydrogenase||172200|F, S|||| | |4(Pgd)|
1.47|2|19|96|1p36.2-p36.12|PAX7|C|Paired box homeotic gene-7||167410|Psh, H, REa, A|fused with FKHR in rhabdomyosarcoma||Rhabdomyosarcoma, alveolar, 268220 (3)| | |4(Pax7)|
1.48|4|19|01|1p36.2-p36.1|DNB5|P|Deleted in neuroblastoma 5||605763|REc|||| | ||
1.49|3|24|88|1p36.2-p36.1|FGR, SRC2|P|Oncogene FGR||164940|A, REb, REa, Fd|same as SRC2||| | |4(Fgr)|
1.50|9|22|97|1p36.2-p36.1|GLC3B|P|Glaucoma 3, primary infantile, B||600975|Fd|||Glaucoma 3, primary infantile, B (2)| | ||
1.51|9|7|00|1p36.2-p36.1|RERE|P|RE repeats-encoding gene||605226|REc, Ch|||| | ||
1.52|6|19|00|1p36.2-p36.1|ZNF151|P|Zinc finger protein-151||604084|A|||| | ||
1.53|1|1|95|1p36.2-p35|CDA|C|Cytidine deaminase||123920|A, Psh|||| | ||
1.54|10|22|92|1p36.2-p34|EPB41, EL1|C|Erythrocyte surface protein band 4.1||130500|F, REb|||Elliptocytosis-1 (3)| | |4(Elp1)|
1.55|10|23|87|1p36.2-p34|RD|C|Radin blood group||111620|F|||| | ||
1.56|8|4|97|1p36.2-p34|RHCE|C|Rhesus system C and E polypeptides||111700|F, D, Fd|?order: C-E-D||| | ||
1.57|1|10|89|1p36.2-p34|RHD|C|Rhesus system D polypeptide||111680|F, D, Fd|||| | ||
1.58|10|23|87|1p36.2-p34|SC|C|Scianna blood group||111750|F|||| | ||
1.59|10|18|00|1p36.2-p34|SMP1|P|Small membrane protein 1||605348|REc|between RHD and RHCE||| | ||
1.60|1|11|95|1p36.13-p36.12|ID3|C|Inhibitor of DNA binding 3, dominant negative, helix-loop-helix|protein|600277|RE, A|||| | ||
1.61|10|24|97|1p36.13-p36.11|D1S1733E, DAN|P|Differential-screening-selected gene aberrant in neuroblastoma||600613|A|aberrant in some neuroblastomas||| | |4(D4H1S1733E)|
1.62|3|1|01|1p36.12|PLA2G2D, SPLASH|C|Phospholipase A2, group IID||605630|R|||| | |4(Pla2g2d)|
1.63|4|24|01|1p36.11-p34.3|WASF2, WAVE2, SCAR2|P|Wiskott-Aldrich syndrome protein family, member 2||605875|REc|?pseudogene on Xp11.21||| | ||
1.64|8|18|99|1p36.1-p35|C1orf4, B120|P|Brain protein 120||603024|A|||| | ||
1.65|8|28|97|1p36.1|CAPZB, CAPPB|P|Capping protein (actin filament) muscle Z-line, beta||601572|A|||| | ||
1.66|10|20|99|1p36.1|CDC42|P|Cell division cycle 42 (GTP-binding protein, 25kD)||116952|H, R, REc|||| | |4(cdc42)|
1.67|1|1|95|1p36.1|CHC1, RCC1|C|Regulator of chromosome condensation||179710|REb, A|||| | |4(Chc1)|
1.68|5|28|98|1p36.1|DDOST, OST, OST48|P|Dolichyl-diphosphooligosaccharide-protein glycosyltransferase||602202|A|||| | ||
1.69|6|16|99|1p36.1|ECE1|C|Endothelin converting enzyme 1||600423|A, R, Psh|||Hirschsprung disease, cardiac defects, and autonomic dysfunction (3)| | ||
1.70|5|5|98|1p36.1|EPHA2, ECK|P|Ephrin receptor EphA2||176946|A, REa|||| | |4(Epha2)|
1.71|4|11|97|1p36.1|EXTL1|P|Exostosin-like 1||601738|R, A|||| | ||
1.72|10|12|90|1p36.1|HMG17|C|Nonhistone chromosomal protein HMG-17||163910|REa, A|||| | ||
1.73|4|1|01|1p36.1|HSPG2, PLC, SJS, SJA, SJS1|C|Heparan sulfate proteoglycan of basement membrane (perlecan)||142461|A, REa, LD|||Schwartz-Jampel syndrome, type 1, 255800 (3); Dyssegmental dysplasia,|Silverman-Handmaker type, 224410 (3) | |4(Plc)|
1.74|3|6|01|1p36.1|NR0B2, SHP|P|Nuclear receptor subfamily 0, group B, member 2||604630|REa, A|||Obesity, mild, early-onset, 601665 (3)| | ||
1.75|8|21|91|1p36.1|PRKACB|P|Protein kinase, cAMP-dependent, catalytic, beta||176892|REa, A|||| | ||
1.76|11|3|98|1p36.1|RNU17A, RNE1|C|RNA, U17a small nucleolar||180645|REn|in IVS1 of CHC1||| | ||
1.77|11|3|98|1p36.1|RNU17B|P|RNA, U17b small nucleolar||603239|REn|||| | ||
1.78|12|15|99|1p36.1|RNU17D, U17HG|P|RNA, U17d small nucleolar||603238|REn|||| | ||
1.79|2|20|98|1p36.1|RSC1A1, RS1|P|Regulatory solute carrier protein, family 1, member 1||601966|A|||| | ||
1.80|2|15|96|1p36.1|TCEB3|P|Transcription elongation factor B (SIII), polypeptide 3 (110kD,|elongin A)|600786|A|||| | ||
1.81|9|13|89|1p36.1|TRN|P|tRNA asparagine||189880|REa, RE|||| | ||
1.82|11|5|97|1p36.1-p35|EPHB2, EPHT3, DRT, ERK|P|eph tyrosine kinase 3 (ephrin receptor EphB2)||600997|Psh, A|||| | ||
1.83|4|23|96|1p36.1-p35|MEMO1|P|Methylation modifier for class I HLA||601201|D|||| | ||
1.84|10|22|95|1p36.1-p35|MFAP2, MAGP, MAGP1|P|Microfibrillar-associated protein-2||156790|REa, A|||| | |4(Mfap2)|
1.85|2|26|95|1p36.1-p35|RAP1GA1|P|RAP1, GTPase activating protein 1||600278|A, REa|||| | ||
1.86|10|20|99|1p36.1-p35|RPL11|C|Ribosomal protein L11||604175|REa, R, A|||| | ||
1.87|11|28|01|1p36.1-p35|SDHB, SDH1, SDHIP|C|Succinate dehydrogenase complex, subunit B, iron sulfur (Ip)||185470|S, REa, A|1 of 2 polypeptides||Pheochromocytoma, extraadrenal, and cervical paraganglioma, 115310|(3) | ||
1.88|3|28|95|1p36.1-p35|SLC9A1, NHE1, APNH|C|Solute carrier family 9 (sodium/hydrogen exhanger), isoform 1|(antiporter, Na+/H+, amiloride sensitive)|107310|A, F, Fd|3cM proximal to RH||| | |4(Apnh, Nhe1)|
1.89|7|17|01|1p36.1-p35|STMN1, LAP18, SMN|P|Stathmin||151442|REa, A|||| | |4(Lap18)|
1.90|1|1|95|1p36.1-p34.3|GPR3|C|G protein-coupled receptor-3||600241|A|||| | ||
1.91|3|17|94|1p36.1-p34.3|OPRD1|P|Opioid receptor, delta-1||165195|H, A|||| | |4(Nbor, Oprd1)|
1.92|6|15|99|1p36.1-p34|ALPL, HOPS|C|Alkaline phosphatase, liver/bone/kidney||171760|S, H, Fd, F, A|||Hypophosphatasia, infantile, 241500 (3); Hypophosphatasia, childhood,|241510 (3); ?Hypophosphatasia, adult, 146300 (1) | |4(Akp2)|
1.93|1|25|99|1p36|ALDH4A1, ALDH4, P5CDH|P|Aldehyde dehydrogenase 4 family, member A1|(delta-1-pyrroline 5-carboxylate dehydrogenase)|606811|A|||Hyperprolinemia, type II, 239510 (3)| | ||
1.94|5|14|02|1p36|BMND3|P|Bone mineral density variability 3||606928|Fd|||[Bone mineral density variability 3], 601884 (2)| | ||
1.95|10|2|89|1p36|BRCD2|P|Breast cancer, ductal||211420|Ch, F, D|||Breast cancer, ductal (2)| | ||
1.96|6|19|98|1p36|CLCN6|P|Chloride channel 6||602726|REa, A|||| | ||
1.97|10|15|97|1p36|CLCNKA|C|Chloride channel, kidney, A||602024|Fd, REc|11kb from CLCNKB||| | ||
1.98|10|15|97|1p36|CLCNKB|C|Chloride channel, kidney, B||602023|Fd, REc|unequal crossingover with CLCNKA||Bartter syndrome, antenatal, 601678 (3); Bartter syndrome, 241200 (3)| | ||
1.99|1|4|93|1p36|CMM, MLM, DNS|P|Cutaneous malignant melanoma/dysplastic nevus||155600|F, Fd, D|some linkage studies negative; see 9p||Malignant melanoma, cutaneous (2)| | ||Greene (1983); Goldstein (1992)
1.100|8|15|96|1p36|DVL1|C|Dishevelled 1 (homologous to Drosophila dsh)||601365|Psh, A|||| | ||
1.101|2|01|01|1p36|CORT|C|Cortistatin||602784|H, R, REc|||| | |4(Cort)|
1.102|2|23|95|1p36|E2F2|P|E2F transcription factor 2||600426|A|||| | ||
1.103|4|18|97|1p36|EYA3|P|Eyes absent, Drosophila, homolog of, 3||601655|A, H|||| | |4(Eya3)|
1.104|9|7|00|1p36|IBD7|P|Inflammatory bowel disease-7||605225|Fd|||{Inflammatory bowel disease-7}, 266600 (2)| | ||
1.105|4|17|01|1p36|ICMT|P|Isoprenylcysteine carboxylmethyltransferase||605851|R|||| | ||
1.106|2|15|02|1p36|KRPPD|P|Kufor-Rakeb pallidopyramidal degeneration with supranuclear upgaze|paresis and dementia|606693|Fd|||Kufor-Rakeb syndrome (2)| | ||
1.107|4|2|01|1p36|LUZP1|P|Leucine zipper protein 1||601422|H, R|||| | |4(Luzp)|
1.108|3|9|00|1p36|MAD2L2, MAD2B|P|Mitotic arrest-deficient 2, S. cerevisiae, homolog-like 2||604094|R|pseudogene on 14q21-q23||| | ||
1.109|6|3|02|1p36|PARK7|P|Parkinson disease 7, autosomal recessive early-onset||606324|Fd|||Parkinson disease, 168600 (2)| | ||
1.110|4|21|99|1p36|PCBC, CAPB|P|Prostate cancer-brain cancer susceptibility||603688|Fd|||{Prostate cancer-brain cancer susceptibility} (2)| | ||
1.111|9|28|96|1p36|PRDM2, RIZ|P|PR domain-containing protein 2 (retinoblastoma protein-binding|zinc-finger protein RIZ)|601196|REc, A|||| | |4(Riz)|
1.112|11|29|99|1p36|RUNX3, CBFA3, PEBP2A3, AML2|C|Runt-related transcription factor 3||600210|A, REa|||| | |4(Aml2, Cbfa3)|
1.113|12|18|98|1p36|TNFRSF4, TXGP1L, OX40, ACT35|P|Tumor necrosis factor receptor superfamily, member 4||600315|A|||| | |4(Ox40)|
1.114|12|18|98|1p36|TNFRSF8, CD30, D1S166E|P|Tumor necrosis factor receptor superfamily, member 8|(CD30 antigen; Ki-1 antigen)|153243|A|||| | |4(Cd30)|
1.115|12|18|98|1p36|TNFRSF9, ILA, CD137|P|Tumor necrosis factor receptor superfamily, member 9|(interleukin-activated receptor; Ly63, mouse, homolog of)|602250|REa|||| | |(Cd157)|
1.116|10|15|97|1p36|TP73|P|p53-related protein||601990|D|imprinted||?Neuroblastoma (1)| | ||
1.117|9|13|89|1p36|TRE|P|tRNA glutamic acid||180640|A|||| | ||
1.118|6|12|01|1p36-p35|ARH, FHCB2, FHCB1|P|Autosomal recessive hypercholesterolemia gene||605747|Fd|||Hypercholesterolemia, familial, autosomal recessive, 603813 (3)| | ||
1.119|5|29|02|1p36-p35|GALE|C|UDP galactose-4-epimerase||606953|S, LD|||Galactose epimerase deficiency, 230350 (3)| | ||
1.120|3|12|96|1p36-p35|HTR6|P|5-hydroxytryptamine (serotonin) receptor-6||601109|REa|||| | ||
1.121|6|18|01|1p36-p35|PARK6|P|Parkinson disease 6, autosomal recessive early-onset||605909|Fd|||Parkinson disease, 168600 (2)| | ||
1.122|8|23|01|1p36-p35|SEPN1, SELN, RSMD1|C|Selenoprotein N||606210|REc, Fd|||Muscular dystrophy, rigid spine, 1, 602771 (3)| | ||
1.123|1|26|97|1p36-p34.1|SCCD|P|Schnyder crystalline corneal dystrophy||121800|Fd|||Corneal dystrophy, crystalline, Schnyder (2)| | ||
1.124|3|9|98|1p36-p34|PLA2G5|P|Phospholipase A2, group V||601192|A|||| | |4(Pla2g5)|
1.125|5|4|00|1p36-p32|PABPC4, PABP4, IPABP, APP1|P|Polyadenylate-binding protein, cytoplasmic, 4||603407|Psh, R|||| | ||
1.126|12|3|91|1p36-p22|SRM, SPS1|C|Spermidine synthase-1||182891|REa, A, Psh|?pseudogene on 3p14-q21||| | ||
1.127|8|9|01|1p35.2-p33|DSCR1L2, MCIP3|P|Down syndrome critical region gene 1-like 2 (myocyte-enriched|calcineurin-interacting protein 3)|605860|REc|||| | |4(Dscr1l2)|
1.128|2|18|96|1p35.1|GJA4, CX37|C|Gap junction protein, alpha-4, 37kD (connexin 37)||121012|REa, A, REc|||| | |(Gja4)|
1.129|12|28|01|1p35.1|GJB3, CX31, DFNA2|C|Gap junction protein, beta-3||603324|REn, REc, Psh, A|same YAC as GJA4||Erythrokeratodermia variabilis, 133200 (3); Deafness, autosomal|dominant 2, 600101 (3); Deafness, autosomal recessive (3); Deafness, autosomal dominant, with peripheral neuropathy (3)| ||
1.130|11|29|00|1p35.1|GJB4, CX30.3|P|Gap junction protein, beta-4||605425|REn, Fd|||Erythrokeratodermia variabilis with erythema gyratum repens,|133200 (3) | ||
1.131|11|29|00|1p35.1|GJB5, CX31.1|P|Gap junction protein, beta-5||604493|R, REc|||| | ||
1.132|12|2|97|1p35.1|P28|P|Inner dynein arm, clamydomonas, homolog of||602135|REa, R|||| | ||
1.133|6|10|98|1p35|BAI2|P|Brain-specific angiongenesis inhibitor-2||602683|A|||| | ||
1.134|8|21|91|1p35|EBVS1|P|Epstein-Barr virus integration site||132850|A|||| | ||
1.135|3|21|93|1p35|G1P3, IFI616|C|Interferon, alpha-inducible protein (clone IFI-6-16)||147572|A, T|||| | ||BioPerl-1.007002/t/data/omim_text_test000444000766000024       652613155576321 17670 0ustar00cjfieldsstaff000000000000*RECORD*
*FIELD* NO
100500
*FIELD* TI
*100500 title
;;title1;;
title2;;
title3

*FIELD* MN
Mini MIM text

*FIELD* CN
Mini MIM - cn
*FIELD* CD
Mini MIM - cd
*FIELD* ED
Mini MIM - ed

*FIELD* TX
DESCRIPTION1

*FIELD* TX
DESCRIPTION2
 
*FIELD* AV
.0001
ALCOHOL INTOLERANCE, ACUTE
ACETALDEHYDE DEHYDROGENASE 2, ALLELE 2, INCLUDED; ALDH2*2, INCLUDED XXX!
ACETALDEHYDE DEHYDROGENASE 2, ALLELE 2, INCLUDED; ALDH2*2, INCLUDED XXX!
ACETALDEHYDE DEHYDROGENASE 2, ALLELE 2, INCLUDED; ALDH2*2, INCLUDED XXX! 
ALDH2, GLU487LYS

AV1-text

.0002
MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL
ACETALDEHYDE DEHYDROGENASE 2, ALLELE 2, INCLUDED; ALDH2*2, INCLUDED XXX!
CHRNA1, VAL156MET

AV2-text

.0003
MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL
CHRNE, ARG147LEU

AV2-text a
AV2-text b

.0004
MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL
CHRNE, 1-BP DEL, 911T

Sieb et al. (2000) found that a brother and sister with congenital
myasthenic syndrome (601462) were compound heterozygotes for a deletion
of 911T and a splicing mutation (IVS4+1G-A; 100725.0007).

.0005
MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL
CHRNE, IVS4DS, G-A, +1

See 100725.0006 and Sieb et al. (2000).

.0006
MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL
CHRNE, 1-BP DEL, 1030C

AV6-text




*FIELD* SA
sa

*FIELD* RF
1. Author11, A. A.; Author12, A. A.: Title 1. Am. J. Med. Genet1. 11: 11-111, 1981.

2. Author21, A. A.; Author22, A. A.: Title 2. Am. J. Med. Genet2. 12: 22-222, 1982.

3. Author31, A. A.; Author32, A. A.: Title 3. Am. J. Med. Genet3. 13: 33-333, 1983.

4. other reference undef format

*FIELD* CS

clinical symptoms

*FIELD* CN
cn1

*FIELD* CD
cd1

*FIELD* ED
ed1

*FIELD* CN
cn2
cn3

*FIELD* ED
ed2
ed3


*FIELD* CD
cd2
cd3





*RECORD*
*FIELD* NO
100501
*FIELD* TI
#100501 second entry
;;title1;;
title2;;
title3

*FIELD* MN
Mini MIM text

*FIELD* CN
Mini MIM - cn
*FIELD* CD
Mini MIM - cd
*FIELD* ED
Mini MIM - ed

*FIELD* TX
DESCRIPTION1

*FIELD* TX
DESCRIPTION2
 
*FIELD* AV
.0001
ALCOHOL INTOLERANCE, ACUTE
ACETALDEHYDE DEHYDROGENASE 2, ALLELE 2, INCLUDED; ALDH2*2, INCLUDED XXX!
ACETALDEHYDE DEHYDROGENASE 2, ALLELE 2, INCLUDED; ALDH2*2, INCLUDED XXX!
ACETALDEHYDE DEHYDROGENASE 2, ALLELE 2, INCLUDED; ALDH2*2, INCLUDED XXX! 
ALDH2, GLU487LYS

AV1-text

.0002
MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL
ACETALDEHYDE DEHYDROGENASE 2, ALLELE 2, INCLUDED; ALDH2*2, INCLUDED XXX!
CHRNA1, VAL156MET

AV2-text

.0003
MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL
CHRNE, ARG147LEU

AV2-text a
AV2-text b

.0004
MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL
CHRNE, 1-BP DEL, 911T

Sieb et al. (2000) found that a brother and sister with congenital
myasthenic syndrome (601462) were compound heterozygotes for a deletion
of 911T and a splicing mutation (IVS4+1G-A; 100725.0007).

.0005
MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL
CHRNE, IVS4DS, G-A, +1

See 100725.0006 and Sieb et al. (2000).

.0006
MYASTHENIC SYNDROME, SLOW-CHANNEL CONGENITAL
CHRNE, 1-BP DEL, 1030C

AV6-text




*FIELD* SA
sa

*FIELD* RF
1. Author11, A. A.; Author12, A. A.: Title 1. Am. J. Med. Genet1. 11: 11-111, 1981.

2. Author21, A. A.; Author22, A. A.: Title 2. Am. J. Med. Genet2. 12: 22-222, 1982.

3. Author31, A. A.; Author32, A. A.: Title 3. Am. J. Med. Genet3. 13: 33-333, 1983.

4. other reference undef format

*FIELD* CS

clinical symptoms

*FIELD* CN
cn1

*FIELD* CD
cd1

*FIELD* ED
ed1

*FIELD* CN
cn2
cn3

*FIELD* ED
ed2
ed3


*FIELD* CD
cd2
cd3




BioPerl-1.007002/t/data/pep-266.aln000444000766000024      2044313155576321 16506 0ustar00cjfieldsstaff000000000000CLUSTAL W (1.82) multiple sequence alignment


Spar_21273             -------------MPFAQIVIGPPGSGKSTYCN------GCSQFFNAIGRHSQVVNMDPA
YOR262W                -------------MPFAQIVIGPPGSGKSTYCN------GCSQFFNAIGRHSQVVNMDPA
Smik_Contig1103.1      -------------MPFAQIVIGPPGSGKSTYCN------GCSQFFNAIGRHSQVVNMDPA
Skud_Contig1703.7      -------------MPFAQIVIGPPGSGKSTYCN------GCSQFFNAIGRHSQVVNMDPA
Sbay_Contig635.43      -------------MPFAQIVIGPPGSGKSTYCN------GCSQFFNAIGRHSQVVNMDPA
Scas_Contig692.20      -------------MPFAQIVIGPPGSGKSTYCN------GCSQFFNAIGRHGQIVNMDPA
Sklu_Contig2277.4      -------------MPFGQIVIGPPGSGKSTYCN------GCSQFFNAVGRHAQVINMDPA
AAL117C                -------------MAYGQIVIGPPGSGKSTYCN------GCSQFFNAIGRHARIVNMDPA
SPAC144.07c            -------------MPFCQVVVGPPGSGKSTYCF------GMYQLLSAIGRSSIIVNLDPA
MG06110.4              -----------------------------------------MGFLGAIGRACSVVNLDPA
NCU09745.1             ----------------------------------MTSPLPVQQFMGAIGRQCSVVNLDPA
FG05298.1              -------------MPFAQLVLGSPGCGKSTYCDGIQLTGQVHQFLGAIGRACSVVNLDPA
AN2438.1               ------------------------------------------------------------
183.m01790             MDDKELEIPVEHSTAFGQLVTGPPGAGKSTYCH------GLHQFLTAIGRPVHIINLDPA
                                                                                   

Spar_21273             NDALPYPCAVDIRDFITLEEIMQEQQLGPNGGLVYAVESLDKSIDLFILQIKSLV--EEE
YOR262W                NDALPYPCAVDIRDFITLEEIMQEQQLGPNGGLMYAVESLDNSIDLFILQIKSLV--EEE
Smik_Contig1103.1      NDALPYPCAVDIRDFITLEEIMQEQQLGPNGGLMYAVESLDKSIDLFLLQIKSLV--EEE
Skud_Contig1703.7      NDALPYPCAVDIRDFITLEEVMQEQQLGPNGGLMYAVESLDNSIDLFILQIKSLV--EEE
Sbay_Contig635.43      NDALPYPCAVDIRDFITLEEIMKEQHLGPNGGLMYAVESLDKSIDLFILQIKSLV--EEE
Scas_Contig692.20      NDALPYPCAVDIRDFVTLEEIMQEQQLGPNGGLMYAVESLDESIDLFILQIKSLV--QEE
Sklu_Contig2277.4      NDSLPYPCAVDIRDFITLEEIMTEQQLGPNGGLMYALESLDKSIDLFVLQIKSLV--QDE
AAL117C                NDSLPYQCDVDIRDFITLEEIMNEQHLGPNGGLVYAFESVEHSLSLFALQIKTLV--KDE
SPAC144.07c            NDFIKYPCAIDIRKVLDVEMIQKDYDLGPNGALIYAMEAIEYHVEWLLKELK-----KHR
MG06110.4              NDHTSYPCALDIRNLVTLEEIMGDDNLGPNGGILYAIEELEHNFEWLEDGLK-----ELG
NCU09745.1             NDHTNYPCALDIRDLVTLEEIMADDKLGPNGGILYALEELENNMEWLENGLK-----ELG
FG05298.1              NDHTNYPAALDIRSLIKLEEIMKDDKLGPNGGILYALEELEHNFEWLEEGLK-----EFS
AN2438.1               ---------------------MSEDQLGPNGGVLYALEELEENFDFLEEGLK-----ELG
183.m01790             VPNPPYPCSINITELITLESVMEEYNLGPNGAMLYCIEFLEANFDWLVERLDEVLAEEGG
                                              : .*****.::*..* ::  .. :   :.     :  

Spar_21273             KAYLVFDCPGQVELFTHHSSLFSIFKKMEKELDMRFCVVNLIDCFYMTSPSQYISILLLA
YOR262W                KAYLVFDCPGQVELFTHHSSLFNIFKKMEKELDIRFCVVNLIDCFYMTSPSQYISILLLA
Smik_Contig1103.1      KAYLVFDCPGQVELFTHHSSLFNIFKKMEKELDMRFCVINLIDCFYMTSPSQYVSILLLA
Skud_Contig1703.7      KAYLVFDCPGQVELFTHHSSLFSIFKKMEKELDMRFCVVNLIDCFYMTSPSQYVSILLLA
Sbay_Contig635.43      KAYVVFDCPGQVELFTHHSSLFSIFKKLEKELDMRFCVVNLIDCFYMTSPSQYVSILLLA
Scas_Contig692.20      KAYLVFDCPGQVELFTHHSSLFKIFKKLEKELDMRFCVVNLIDSFYITSPSQYVSILLLA
Sklu_Contig2277.4      HAYVVFDCPGQVELFTHHSSLFRIFKKLERELDMRLCVVNLIDCFYITSPSQYVSILLLA
AAL117C                NAYLVFDCPGQVELFTHHSALSKIFQQLVRDLDLRVCVVNLMDSIYITSPSQYVSVLLLA
SPAC144.07c            DSYVIFDCPGQVELFTNHNSLQKIIKTLEKELDYRPVSVQLVDAYCCTNPSAYVSALLVC
MG06110.4              DDYILFDCPGQVELYTHHNSLRNIFFKLQK-LGYRLVVVHLSDSICLTQPSLYISNLLLA
NCU09745.1             EDYVLFDCPGQVELYTHHNSLRNIFYRLQK-LGYRLVVVHLSDCFCLTQPSLYISNVLLS
FG05298.1              EDYILFDCPGQVELYTHHNSLRNIFYKLQK-IGFRLVSVHLSDSFCLTQPSLYVSNVLLS
AN2438.1               EDYIIFDCPGQVEIFTHHSSLRNIFFKIQK-MGYRLIVLHLIDSYNLTLPSMYISSLILC
183.m01790             NGYVVFDTPGQAELWTNHDSLKNVVEKLVK-MDYRLAAVHLSDAHYITDASKFISVVLLA
                       . *::** ***.*::*:*.:*  :.  : : :. *   ::* *.   * .* ::* :::.

Spar_21273             LRSMLMMDLPHINVFSKIDMLKSYGELPFRLDYYTEVQDLDYLEPYIEKEGSSVLGKKYS
YOR262W                LRSMLMMDLPHINVFSKIDMLKSYGELPFRLDYYTEVQDLDYLEPYIEKEGSSVLGKKYS
Smik_Contig1103.1      LRSMLMMDLPHINVFSKIDMLKSYGELPFRLDYYTEVQDLDYLEPYIEKEGSSVLGKKYN
Skud_Contig1703.7      LRSMLMMDLPHINVFSKIDMLKSYGELPFRLDYYTEVQELDHLEPYIEKEGSSVLGKKYS
Sbay_Contig635.43      LRSMLMMDLPHINVFSKIDKLKSYGELPFRLDYYTEVQDLDYLEPYIEKEGSGALGKRYS
Scas_Contig692.20      LRSMLMMDLPQINVFSKIDMLKSYGELPFRLDYYTEVQDLDYLQPFIEKESSSVLGRRYS
Sklu_Contig2277.4      LRSMLMMDLPHINVFSKIDLLKSYGELPFRLDYYTEVQELDYLKPHIDKEGSSVLGRKYS
AAL117C                LRSMLMMDLPHINVLSKIDMLSSYGDLPFRLDYYTEVQDLEYLQPHIEREHKGAKALRYR
SPAC144.07c            LKGMLQLDMPHVNILSKADLLCTYGTLPMKLDFFTEVQDLSYLAPLLDRDKR---LQRYS
MG06110.4              LRAMLQMDLSHVNVLTKIDKVSSYDRLAFNLDFYTEVHDLSYLLPELEAENPSLRSEKFA
NCU09745.1             LRAMLQMDLPHINVLTKIDKISSYDPLPFNLDYYTEVQDLRYLMPSLDAESPALKKGKFT
FG05298.1              LRAMIQMDMPHINILSKIDKVADYDELPFNLDYYTDVDDLTYLTPHLETESPALRSEKFG
AN2438.1               LRAMLQMDLPHLNVLTKIDNLSNYTSLPFNLDFYTEVQDLTYLLPHLEAESSRLSHEKFG
183.m01790             LRAMLQMEMPHLNVLSKIDLISTYGELPFDLSYYTEVQDLSYLLGSLDSDPR---TAKYH
                       *:.*: :::.::*:::* * :  *  *.: *.::*:*.:* :*   :: :       :: 

Spar_21273             KLTETIKELVSDFNLVSFEVLSVDDKESMINLQGVIDKANGYIFGAS---EVGG------
YOR262W                KLTETIKELVSDFNLVSFEVLSVDDKESMINLQGVIDKANGYIFGAS---EVGG------
Smik_Contig1103.1      KLTDAIKELVSDFNLVSFEVLSVDDKESMINLQGVIDKANGYIFGAS---EVGG------
Skud_Contig1703.7      KLTETIKELVSDFNLVSFEVLSVDDKESMINLQGVIDKANGYIFGAS---EVGG------
Sbay_Contig635.43      KLTETISELVSDFNLVSFEVLAVDDKESMINLQGVIDKANGYIFGAS---EVGG------
Scas_Contig692.20      KLTETISELVSDFNLVSFEVLAVDDKQSMINLQSVVDKANGYIFGAS---EVGG------
Sklu_Contig2277.4      RLTETISELVSDFNLVSFEVLCVDDKQSMINLQSIVDKANGYIFGVS---EIGG------
AAL117C                RLTEAIGEVVSDFNLVAFEVLCVDDKQSMINLQSAIDKANGYIFGAS---EVGG------
SPAC144.07c            DLNKAICELVEDFNLVSFEVVAVENKASMLRVLRKIDQAGGYAYGST---EIGG------
MG06110.4              KLNRAVANLIEDFGLVRFEVLAVENKKSMMHLLRVLDRANGYVFGGA---EGAN------
NCU09745.1             KLNEAVANMVEQFGLVSFEVLAVENKKSMMHLLRVIDRASGYVFGGA---EGTN------
FG05298.1              KLNEAIANLIESYGLVRYEVLAVENKKSMMHILRVIDRAGGYVFGSA---EGAN------
AN2438.1               ALNNAIITLIEEFGLVGFETLAVEDKKSMMNLLRAIDRASGYVFGPA---EGAN------
183.m01790             KLNKALVELIEGFSLVGFQTLAVEDKESMLNIVRLVDKMTGYIFIPSGDLEGTNAINTQA
                        *. ::  ::. :.** ::.:.*::* **:.:   :*:  ** :  :   *  .      

Spar_21273             --DTVWAEASREGA-LLANYDIQDRWIDNKEKYDKEEEEKRAALLKEQELQNKAVDVNEE
YOR262W                --DTVWAEASREGA-LIANYDIQDRWIDNKEKYDKEEEEKRTALLKEQELQNKAVDVNEE
Smik_Contig1103.1      --DTVWAEASREGA-LLTSYDIQDRWIDNKEKYDKEEEEKRVILLKEQELQNKAVDVNED
Skud_Contig1703.7      --DTVWAEASREGA-LLENYDIQDRWIDNKETYDKEEQEKRASLLKEQELQNKTVDVKEE
Sbay_Contig635.43      --DTVWAEASREGA-LLASYDIQDRWIDNKEKYDKEEQEKRAAMVKEQELQNKEVNVDEE
Scas_Contig692.20      --DTVWAEATREGA-MMVNYDIQDRWIDNKEKYDEEERKRQEEQAKEQNMQEKEVDVDNE
Sklu_Contig2277.4      --DTVWAEATRQGS-AIANYDIQERWIDNKDMYDREEQEKREQLLKEEELQNKEVDVDKG
AAL117C                --DTVWAEATRQGT-AAIEYDIQDRWIDNKDFYDKEEEARRKKLLEEHELLEKEVDVNQD
SPAC144.07c            --DAVWVNAVRQGGDPLQGISPQERWIDKKEEYDK----------YEWELEQK--STMDE
MG06110.4              --DTVWQVAMRNEGSLMGVQDIQERWIDNKEAYDEMEQREWEEQVKAQEAMAEADAAAAE
NCU09745.1             --DTVWQVAMRNESSLPDALDIQERWIDSKEEYDEMERKEEEEQEKLRAEQARAAEEAGL
FG05298.1              --DTVWSVAMRNESSMLGVQDIQERWIDQKVEYDQMEREAEEEQARIQEEQAMEMEQSQP
AN2438.1               --DSVWQVAVREGMGSMDIRDIQERWIDAKDEYDELERRQREEEIKNHQQAATYQAGNED
183.m01790             LFGSAMSSAKLTGRAGGDVRDVQERWMDNKEAWDEWEKKEWKREAEIRAQMGTGIPEGMK
                         .:.   *           . *:**:* *  :*.                         

Spar_21273             DEWENALKEWEEKQGTDFVR--------------
YOR262W                DEWENALKEWEEKQGMDFVR--------------
Smik_Contig1103.1      DEWESALKEWEEKQGMDFVR--------------
Skud_Contig1703.7      DEWENALKEWEEKQDTEFVR--------------
Sbay_Contig635.43      DEWENALNDWEEKQGTDFVR--------------
Scas_Contig692.20      DEWEKALKDWEEKQGTGYVR--------------
Sklu_Contig2277.4      DEWENALKEWEEKQGMSYVK--------------
AAL117C                DEWERAVKEWESQHSVNFVK--------------
SPAC144.07c            DENEG-----------------------------
MG06110.4              -EG-----DDDLMGGPGAR---------------
NCU09745.1             GDGSVPGVAPQFTSGSGIRVTLSLVAAFTKYSDL
FG05298.1              PPAPTGGMDPDFGDMTVPKDSGIKVVRK------
AN2438.1               DDDDN---DYEFGRRMPVPDSGVKVMRK------
183.m01790             GGED--------AESTGI----------------
                                                         
BioPerl-1.007002/t/data/pfamOutput-bug3376.out000444000766000024       312513155576321 20664 0ustar00cjfieldsstaff000000000000hmmpfam - search one or more sequences against HMM database
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:                 testInput.hmm
Sequence file:            testInput.fasta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query sequence: Test
Accession:      [none]
Description:    [none]

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
TEST                                                    184.7    2.5e-56   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
TEST       1/1       8    97 .]     1    95 []   184.7  2.5e-56

Alignments of top-scoring domains:
TEST: domain 1 of 1, from 8 to 97: score 184.7, E = 2.5e-56
                   *->svfqqqqssksttgstvtAiAiAigYRYRYRAvtWnsGsLssGvnDn
                      sv+qqqq+  +    +vtAiAiAigYRYRYRAv Wn GsLs G nDn
        Test     8    SVYQQQQGGSA----MVTAIAIAIGYRYRYRAVVWNKGSLSTGTNDN 50   

                   DnDqqsdgLYtiYYsvtvpssslpsqtviHHHaHkasstkiiikiePr<-
                   DnDq +d LYtiYYsvtv +ss+p q+v+HHHaH+asstkiiiki P   
        Test    51 DNDQAAD-LYTIYYSVTVSASSWPGQSVTHHHAHPASSTKIIIKIAPS   97   

                   *
                    
        Test     -   -    

//
BioPerl-1.007002/t/data/pfam_tests.stk000444000766000024      3525213155576321 17607 0ustar00cjfieldsstaff000000000000# STOCKHOLM 1.0
#=GF ID   14-3-3
#=GF AC   PF00244.9
#=GF DE   14-3-3 protein
#=GF AU   Finn RD
#=GF SE   Prosite
#=GF GA   25.00 25.00; 25.00 25.00;
#=GF TC   28.50 28.50; 30.20 29.80;
#=GF NC   22.70 22.70; 20.60 20.60;
#=GF TP   Domain
#=GF BM   hmmbuild -F HMM_ls SEED
#=GF BM   hmmcalibrate --seed 0 HMM_ls
#=GF BM   hmmbuild -f -F HMM_fs SEED
#=GF BM   hmmcalibrate --seed 0 HMM_fs
#=GF AM   globalfirst
#=GF RN   [1]
#=GF RM   95327195
#=GF RT   Structure of a 14-3-3 protein and implications for
#=GF RT   coordination of multiple signalling pathways. 
#=GF RA   Xiao B, Smerdon SJ, Jones DH, Dodson GG, Soneji Y, Aitken
#=GF RA   A, Gamblin SJ; 
#=GF RL   Nature 1995;376:188-191.
#=GF RN   [2]
#=GF RM   95327196
#=GF RT   Crystal structure of the zeta isoform of the 14-3-3
#=GF RT   protein. 
#=GF RA   Liu D, Bienkowska J, Petosa C, Collier RJ, Fu H, Liddington
#=GF RA   R; 
#=GF RL   Nature 1995;376:191-194.
#=GF RN   [3]
#=GF RM   96182649
#=GF RT   Interaction of 14-3-3 with signaling proteins is mediated
#=GF RT   by the recognition of phosphoserine. 
#=GF RA   Muslin AJ, Tanner JW, Allen PM, Shaw AS; 
#=GF RL   Cell 1996;84:889-897.
#=GF RN   [4]
#=GF RM   97424374
#=GF RT   The 14-3-3 protein binds its target proteins with a common
#=GF RT   site located towards the C-terminus. 
#=GF RA   Ichimura T, Ito M, Itagaki C, Takahashi M, Horigome T,
#=GF RA   Omata S, Ohno S, Isobe T 
#=GF RL   FEBS Lett 1997;413:273-276.
#=GF RN   [5]
#=GF RM   96394689
#=GF RT   Molecular evolution of the 14-3-3 protein family. 
#=GF RA   Wang W, Shakes DC 
#=GF RL   J Mol Evol 1996;43:384-398.
#=GF RN   [6]
#=GF RM   96300316
#=GF RT   Function of 14-3-3 proteins. 
#=GF RA   Jin DY, Lyu MS, Kozak CA, Jeang KT 
#=GF RL   Nature 1996;382:308-308.
#=GF RN   [7]
#=GF RM   12184815
#=GF RT   The 14-3-3s. 
#=GF RA   Ferl RJ, Manak MS, Reyes MF; 
#=GF RL   Genome Biol 2002;3:REVIEWS3010.
#=GF DR   PROSITE; PDOC00633;
#=GF DR   SMART; 14_3_3;
#=GF DR   PRINTS; PR00305;
#=GF DR   SCOP; 1a4o; fa;
#=GF DR   INTERPRO; IPR000308;
#=GF SQ   16
#=GS RAD25_SCHPO/5-240  AC P42657
#=GS RAD24_SCHPO/6-241  AC P42656
#=GS BMH1_YEAST/4-240   AC P29311
#=GS 1433E_SHEEP/4-239  AC P62262
#=GS 1433B_VICFA/7-242  AC P42654
#=GS 14334_LYCES/6-243  AC P42652
#=GS 14333_LYCES/9-246  AC P93209
#=GS 14336_ARATH/7-240  AC P48349
#=GS 14332_ENTHI/4-238  AC P42649
#=GS 14331_ENTHI/4-239  AC P42648
#=GS 1433T_HUMAN/3-236  AC P27348
#=GS 1433_XENLA/1-227   AC P29309
#=GS 1433Z_DROME/6-239  AC P29310
#=GS 14331_CAEEL/5-237  AC P41932
#=GS 1433F_RAT/3-240    AC P68511
#=GS 1433S_HUMAN/3-238  AC P31947
RAD25_SCHPO/5-240            RENSVYLAKLAEQAERYEEMVENMKKVACSND...KLSVEERNLLSVAYKNIIGARRASWRIISSIEQKEESRG.NTRQAALIKEYRKKIEDELSDICHDVLSVLEKHLIPAA..TTGESKVFYYKMKGDYYRYLAEFTVGEVCKEAADSSLEAYKAASDIAVAELPPTDPMRLGLALNFSVFYYEILDSPESACHLAKQVFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYNQ
RAD24_SCHPO/6-241            REDAVYLAKLAEQAERYEGMVENMKSVASTDQ...ELTVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKG.NTAQVELIKEYRQKIEQELDTICQDILTVLEKHLIPNA..ASAESKVFYYKMKGDYYRYLAEFAVGEKRQHSADQSLEGYKAASEIATAELAPTHPIRLGLALNFSVFYYEILNSPDRACYLAKQAFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYSA
BMH1_YEAST/4-240             REDSVYLAKLAEQAERYEEMVENMKTVASSGQ...ELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKEKSEHQVELICSYRSKIETELTKISDDILSVLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFSSGDAREKATNASLEAYKTASEIATTELPPTHPIRLGLALNFSVFYYEIQNSPDKACHLAKQAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMSESG
1433E_SHEEP/4-239            REDLVYQAKLAEQAERYDEMVESMKKVAGMDV...ELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKG.GEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAA..NTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDG
1433B_VICFA/7-242            RENFVYIAKLAEQAERYEEMVDSMKNVANLDV...ELTIEERNLLSVGYKNVIGARRASWRILSSIEQKEESKG.NDVNAKRIKEYRHKVETELSNICIDVMRVIDEHLIPSA..AAGESTVFYYKMKGDYYRYLAEFKTGNEKKEAGDQSMKAYESATTAAEAELPPTHPIRLGLALNFSVFYYEILNSPERACHLAKQAFDEAISELDTLNEESYKDSTLIMQLLRDNLTLWTSDIPEDG
14334_LYCES/6-243            REENVYLAKLAEQAERYEEMIEFMEKVAKTADV.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVNTIKEYRSKIEADLSKICDGILSLLESNLIPSA..STAESKVFHLKMKGDYHRYLAEFKTGTERKEAAENTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAISELDTLGEESYKDSTLIMQLLRDNLTLWTSDNADDV
14333_LYCES/9-246            REENVYMAKLADRAESDEEMVEFMEKVSNSLGS.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKICDGILKLLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFKTGAERKEAAESTLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDMQDDG
14336_ARATH/7-240            RDQYVYMAKLAEQAERYEEMVQFMEQLVTGATPAEELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NDEHVSLVKDYRSKVESELSSVCSGILKLLDSHLIPSA..GASESKVFYLKMKGDYHRYMAEFKSGDERKTAAEDTMLAYKAAQDIAAADMAPTHPIRLGLALNFSVFYYEILNSSDKACNMAKQAFEEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSD.....
14332_ENTHI/4-238            REDLVYLSKLAEQSERYEEMVQYMKQVAEMGT...ELSVEERNLISVAYKNVVGSRRASWRIISSLEQKEQAKG.NTQRVELIKTYRAKIEQELSQKCDDVLKIITEFLLKNS..TSIESKVFFKKMEGDYYRYYAEFTVDEKRKEVADKSLAAYQEATDTA.ASLVPTHPIRLGLALNFSVFYYQIMNDADKACQLAKEAFDEAIQKLDEVPEESYKESTLIMQLLRDNLTLWTSDMGDDE
14331_ENTHI/4-239            REDCVYTAKLAEQSERYDEMVQCMKQVAEMEA...ELSIEERNLLSVAYKNVIGAKRASWRIISSLEQKEQAKG.NDKHVEIIKGYRAKIEKELSTCCDDVLKVIQENLLPKA..STSESKVFFKKMEGDYYRYFAEFTVDEKRKEVADKSLAAYTEATEISNAELAPTHPIRLGLALNFSVFYFEIMNDADKACQLAKQAFDDAIAKLDEVPENMYKDSTLIMQLLRDNLTLWTSDACDEE
1433T_HUMAN/3-236            KTELIQKAKLAEQAERYDDMATCMKAVTEQGA...ELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDT...SDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEE
1433_XENLA/1-227             .......AKLSEQAERYDDMAASMKAVTELGA...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...NDKRQQMAREYREKVETELQDICKDVLDLLDRFLVPNA..TPPESKVFYLKMKGDYYRYLSEVASGDSKQETVASSQQAYQEAFEISKSEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKSAFDEAIRELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGEE
1433Z_DROME/6-239            KEELVQKAKLAEQSERYDDMAQAMKSVTETGV...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEA...SARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKA..SNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDE
14331_CAEEL/5-237            VEELVQRAKLAEQAERYDDMAAAMKKVTEQGQ...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...SEKKQQLAKEYRVKVEQELNDICQDVLKLLDEFLIVKA..GAAESKAFYLKMKGDYYRYLAEVAS.EDRAAVVEKSQKAYQEALDIAKDKMQPTHPIRLGLALNFSVFYYEILNTPEHACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDVGAED
1433F_RAT/3-240              REQLLQRARLAEQAERYDDMASAMKAVTELNE...PLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADG.NEKKLEKVKAYREKIEKELETVCNDVLALLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEHMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEE
1433S_HUMAN/3-238            RASLIQKAKLAEQAERYEDMAAFMKGAVEKGE...ELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEG.SEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEA..GDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEE
#=GC seq_cons                RE-hVYhAKLAEQAERY--MlpsMKpVsptss...ELSlEERNLLSVAYKNVlGARRASWRIISSIEQKEEu+G.N-c+lphIKEYRpKlEsELssICsDVLplLDcaLIPsA..ssuESKVFYhKMKGDYYRYLAEFsoG-cRKcss-sShtAYppApDIApuEhsPTHPIRLGLALNFSVFYYEILNSP-+ACpLAKQAFDEAIAELDTLsEESYKDSTLIMQLLRDNLTLWTSDhts-t
//
# STOCKHOLM 1.0
#=GF ID   2-ph_phosp
#=GF AC   PF04029.4
#=GF DE   2-phosphosulpholactate phosphatase
#=GF AU   Kerrison ND, Finn RD
#=GF SE   COG2045
#=GF GA   25.00 25.00; 25.00 25.00;
#=GF TC   43.30 43.30; 28.00 28.00;
#=GF NC   3.00 3.00; 22.60 22.00;
#=GF TP   Family
#=GF BM   hmmbuild -F HMM_ls SEED
#=GF BM   hmmcalibrate --seed 0 HMM_ls
#=GF BM   hmmbuild -f -F HMM_fs SEED
#=GF BM   hmmcalibrate --seed 0 HMM_fs
#=GF AM   globalfirst
#=GF RN   [1]
#=GF RM   21474017
#=GF RT   Identification of coenzyme M biosynthetic
#=GF RT   2-phosphosulfolactate phosphatase. A member of a new class
#=GF RT   of Mg(2+)-dependent acid phosphatases. 
#=GF RA   Graham DE, Graupner M, Xu H, White RH; 
#=GF RL   Eur J Biochem 2001;268:5176-5188.
#=GF DR   INTERPRO; IPR005238;
#=GF CC   Thought to catalyse 2-phosphosulpholactate = sulpholactate + phosphate.
#=GF CC   Probable magnesium cofactor.  Involved in the second step of coenzyme M
#=GF CC   biosynthesis.  Inhibited by vanadate in Methanococcus jannaschii.  Also
#=GF CC   known as the ComB family [1].
#=GF SQ   10
#=GS COMB_CLOAB/6-235   AC Q97E82
#=GS COMB_THEMA/1-224   AC Q9WZQ4
#=GS COMB_METTH/2-219   AC O27250
#=GS COMB_METJA/1-219   AC Q58540
#=GS COMB_DEIRA/2-232   AC Q9RUI6
#=GS COMB_SYNY3/2-241   AC P73849
#=GS COMB_THEVO/1-211   AC Q97CK6
#=GS COMB_THEAC/1-211   AC Q9HIA9
#=GS COMB_BACSU/2-223   AC O06738
#=GS COMB_STRCO/12-227  AC Q9F3E6
COMB_CLOAB/6-235             IISADDIKE.EKVKN..KTAVVIDMLRATSVITTALNNGCKRVVPVLTVEEALKKVKEY.GKDAILGGERKGLKIEGFDFSNSPMEY.TEDVV......KGKTLIMTTTNGTRAIKGSET.ARDILIGSVLNGEAVAEKIVELN.NDVVIVNAGTYGEFSIDDFICSGYIINCVMDRMKKLELT.DAATTA..QYVYKTNEDIKGFVKYAK.HYKRIMELGLKKDFEYCCKKDIVKLVPQYTN.GEIL..
COMB_THEMA/1-224             MVDVVMAPC.SPVEC..RTAVVIDVLRATSTIVTALSNGASGVIPVKTIEEALEKKK....EGVLICGERNAQKPKGFNLGNSPLEY.RKEKI......SGKTIVLTTTNGTQVIEKIRS..EEIIAASFLNLSAVVEYLKSKE..DILLVCAGTNGRFSLEDFLLAGAIV..KRLKRNDLG...DGAHAA..ERYFESVENTREEIKKHSSHAKRLISLGFENDIEFCTTEDLFKTVPALVN.GVFILK
COMB_METTH/2-219             AMRIRLSFE.RPEGS..GLCIMVDLLRASATITAALDR.FREVIPVADIEEAMEYSR....KGYLVAGERGGETLPGF.IANSPLEV.KNYR........GDVLVLTTSNGTRILESVKS...DALVGCLNNLDAVAEAARELS.DEVEVVMAGVNGRFAIEDFLCAGEIIAAIDGEMDEYA...EASVLA..VQDRSLVDDAIRRSRSAER....LGGLGFMDDVEYCIKRNITGNVPVYRD.GRIELM
COMB_METJA/1-219             MITLCNRFT..EYKC.GNVAIVVDVLRASTTITTLLSF.IDEVYITTST.....SKK....ENAIYIGERKGRKIEGFDFGNSPTEILANKDIIKERYENGEKVILTTTNGTRVLKSLDA..EHIFIGAIVNAKYVAKAVEDFE..DVSLVPCHRENNFAIDDFIGCGVIAKYLNGEFDEF.....IKAAL..ELTKHDWMSLILNSSSAEN....LKNLGYEKDVTFAILENSIDAVGIYKK...DKSK
COMB_DEIRA/2-232             RLRVDLLPD..SHYP..DVALVIDVLRATTTAVTLLEQGAAELLLTRTTEAALAVRETV..PDVLLAGERGGLTIPGFDLGNSPVEV.SGGAV......AGRRVVMTTTNGTIAAHRAAQTARHVVLAALVNAHAVARHALAVASEEIAIVCAGTDGRVGLDDVYAAGVIA.EYLLALGDFQVD.DGARIA..LTMRRGGGDPGEALRSSG.HGATLARLGLSSDVDYAAQLSTSRLIPTLVP.GDDVPA
COMB_SYNY3/2-241             EIFVYHTPELTPDQSLPDCAVVIDVLRATTTIATALKVGAEAVQVFSSLDDLMATSESWPGEKRLRAGERGGAAVAGYDLGNSPLDC.TSELM......AGKRLFLSTTNGTRALQRVKDC.PQLVTASLVNRGAAVDYLAQTQPKTVWLLGSGWEGGYSLEDTVCAGAIASLLREKGIDFTVGNDEVVAA..QSLYRQWRSDLLNLFKQASHGQRLLKLDRLEDLRYCATEDLIDILPKQVSPGVLTAA
COMB_THEVO/1-211             MIRIADGRK.EENWS..SINIIIDIFRSTTTIPVILSRGARYIVPFKDVTSALNFKRKN..KNVVLIGEKYGIKPPFFDYDNSPAQI.INADL......EGKIIAFTSTNGMYVLSRIKR..GRILFSSLVNMSATIKKVKGKD..DILVVPSNRPIGKAVEDNIFAEMLK..LALEGKNY....DREILV..NRIRETKENTVVSISTQ..............DLEICLKLDLLDCVPEYIE.GKIVND
COMB_THEAC/1-211             MIRIGDGRK.SDSWA..EINVVVDIFRSTTTIPMILFRGAKYILPFRDVRKAIEFKRRN..PGTILVGEKYGIKPPYFDYDNSPAEI.AEADL......SGKVVAFTSTNGTYVLSRIRS..GRIIFSSYVNLSATVAMIRSQR..DVLILPSNRPIGKAPEDILFANLLK..LMAEGHEV....DVSEYT..RKTEEINRNIIAGVGER..............DLEFCLRVDHTNIVPEYID.GRIVQS
COMB_BACSU/2-223             PIAIYQGHH..HSLAPADINIVIDVIRAFTVAHYAFIGGAKEILLVRTADEAFALKDTY..PDYVLTGEEKGVGISGFDLDNSPKRM.AGQNM......TDKSLIQKTTNGVTAALGALN.AKHLFVTGFSNAKTTAQHVKKLVANDCVINIVASHP.SGDDDMACAEYIK..GIIEGTNV.....VTAAE..AIERIKGSSVAEKFFDCR......QPLFDSEDIVYCTKELTGDFVMKVKQDGEVPTI
COMB_STRCO/12-227            DTRFVGIPE..VGEA.PAVAVVVDVMRAFTVAAWAFARGAEKIVLAGSLDEALALKERD..PARVAL..KDGPLTPGFDLVNSPGLL.RSADL......AGRTVVQKTTAGTVGALAVRD.ASLVLCAGFVVAEATARVLRARAPEHVTFVVTGEDG.RADEDLACARYIA..RRAAGHDA....DAAGFLGRAAESRAATELVQGVRQGVH..........PDDVALCLELDRFPFAMVAAP..EDSLM
#=GC seq_cons                hIclspshc.psstu..clAlVIDVLRATTTIssALspGAccllsspol--AlthK+p...cssllsGERtGhplsGFDluNSPhEl.sstcl......sGKsllhTTTNGTpslppl+s..pcllhuulVNtcAsActl+shs.pDVhlVsuGpsGthulEDhlsAGhIt..lttctc-h....Dsushs..pphccsscssltslppst.....lhtLsh.cDl-aChccDhhchVPphhs.Gcls.t
//
# STOCKHOLM 1.0
#=GF ID   3-alpha
#=GF AC   PF03475.3
#=GF DE   3-alpha domain
#=GF AU   Aravind L, Anantharaman V
#=GF SE   Aravind L, Anantharaman V
#=GF GA   25.00 25.00; 25.00 25.00;
#=GF TC   25.40 25.40; 25.00 25.00;
#=GF NC   24.40 24.40; 24.60 24.60;
#=GF TP   Domain
#=GF BM   hmmbuild -F HMM_ls SEED
#=GF BM   hmmcalibrate --seed 0 HMM_ls
#=GF BM   hmmbuild -f -F HMM_fs SEED
#=GF BM   hmmcalibrate --seed 0 HMM_fs
#=GF AM   globalfirst
#=GF RC   See figure 2.
#=GF RN   [1]
#=GF RM   11886751
#=GF RT   MOSC domains: ancient, predicted sulfur-carrier domains,
#=GF RT   present in diverse metal--sulfur cluster biosynthesis
#=GF RT   proteins including Molybdenum cofactor sulfurases. 
#=GF RA   Anantharaman V, Aravind L; 
#=GF RL   FEMS Microbiol Lett 2002;207:55-61.
#=GF DR   SCOP; 1o67; fa;
#=GF DR   INTERPRO; IPR005163;
#=GF DR   PDB; 1o65 A; 178; 224;
#=GF DR   PDB; 1o65 B; 178; 224;
#=GF DR   PDB; 1o65 C; 178; 224;
#=GF DR   PDB; 1o67 A; 178; 224;
#=GF DR   PDB; 1o67 B; 178; 224;
#=GF DR   PDB; 1o67 C; 178; 224;
#=GF CC   This small triple helical domain has been predicted
#=GF CC   to assume a topology similar to helix-turn-helix
#=GF CC   domains. These domains are found at the C-terminus
#=GF CC   of proteins related to Swiss:P32157.
#=GF SQ   11
#=GS Y278_HAEIN/174-219    AC P43976
#=GS Q99RT6_STAAM/171-217  AC Q99RT6
#=GS Q9PHR4_CAMJE/164-215  AC Q9PHR4
#=GS Q9RT82_DEIRA/181-226  AC Q9RT82
#=GS Q9KF70_BACHD/170-214  AC Q9KF70
#=GS Q9I1P0_PSEAE/174-219  AC Q9I1P0
#=GS Q9I607_PSEAE/169-215  AC Q9I607
#=GS O86804_STRCO/189-233  AC O86804
#=GS P95151_MYCTU/201-244  AC P95151
#=GS YIIM_ECOLI/168-214    AC P32157
#=GS O34542_BACSU/173-219  AC O34542
#=GS YIIM_ECOLI/168-214 DR PDB; 1o65 A; 178; 224;
#=GS YIIM_ECOLI/168-214 DR PDB; 1o65 B; 178; 224;
#=GS YIIM_ECOLI/168-214 DR PDB; 1o65 C; 178; 224;
#=GS YIIM_ECOLI/168-214 DR PDB; 1o67 A; 178; 224;
#=GS YIIM_ECOLI/168-214 DR PDB; 1o67 B; 178; 224;
#=GS YIIM_ECOLI/168-214 DR PDB; 1o67 C; 178; 224;
Y278_HAEIN/174-219           QITIRHLNRLLSTP.....KNEAELDSALEIEV.LAEAFKRSIRSQISKFKQ
Q99RT6_STAAM/171-217         RLSVQQLNDLYYNDRQ....NQDMLRYALNNPF.LSPTRRDKLQKMYNRTLK
Q9PHR4_CAMJE/164-215         SLSVFELNQLFYSPHQILKQNPNLLDKLEKLNSLISQNWHETIHKRLKNTYD
Q9RT82_DEIRA/181-226         APTIGELFDADFAKSH....DPAELRAWLTFP..LGKRQRKEVEKWLAKAEG
Q9KF70_BACHD/170-214         HPTVLEVNQLYYPKDI....NKEQLRRMSQLPE.LADAWKKAFSKKLANA..
Q9I1P0_PSEAE/174-219         DWSLLRLSEVLFDRRA....DAELLRQCLPLP..LTPSWRRTLERRLEKGQV
Q9I607_PSEAE/169-215         ELTVARLLQWYFGDPL....EPLGLRQMMACDA.LSQRWRKTAAKRLSSGVV
O86804_STRCO/189-233         EVTVALQFRAVTTQ.......RELLPRLLAAGGALHPEALATARKYVAEYGA
P95151_MYCTU/201-244         NVTVGLVFRARTSE.......SELLPQLLAADA.LAAELKAYARERTPSPPP
YIIM_ECOLI/168-214           DVTVQEAAAIAWHMPF....DDDQYHRLLSAAG.LSKSWTRTMQKRRLSGKI
#=GR YIIM_ECOLI/168-214 SS   SCBHHHHHHHHHTSCC....CHHHHHHHHTSTT.CCHHHHHHHHHHHHHSSC
#=GR YIIM_ECOLI/168-214 SA   6000320010013274....3372052026033.108303630350385563
O34542_BACSU/173-219         GISVQFANRINYHDAK....NLTAIERILSEAA.LSESWRASFMKKKDRLLP
#=GC SS_cons                 SCBHHHHHHHHHTSCC....CHHHHHHHHTSTT.CCHHHHHHHHHHHHHSSC
#=GC SA_cons                 6000320010013274....3372052026033.108303630350385563
#=GC seq_cons                plTVtclsclhasc......stphLcphLshss.Lupsa+cohpK+lspshs
//BioPerl-1.007002/t/data/phi.out000444000766000024      3363213155576321 16230 0ustar00cjfieldsstaff000000000000BLASTP 2.0.14 [Jun-29-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= CYS1_DICDI
         (351 letters)

Database: /home/peter/blast/data/swissprot
           88,780 sequences; 31,984,247 total letters

Searching......................................................................................................................................................
3 occurrence(s) of pattern in query
  CYS1_DICDI; PATTERN.
 pattern P-E-E-Q at position 23 of query sequence
effective database length=3.2e+07
 pattern probability=8.9e-06
lengthXprobability=2.8e+02

Number of occurrences of pattern in the database is 349
  CYS1_DICDI; PATTERN.
 pattern P-E-E-Q at position 120 of query sequence
effective database length=3.2e+07
 pattern probability=8.9e-06
lengthXprobability=2.8e+02

Number of occurrences of pattern in the database is 349
  CYS1_DICDI; PATTERN.
 pattern P-E-E-Q at position 237 of query sequence
effective database length=3.2e+07
 pattern probability=8.9e-06
lengthXprobability=2.8e+02

Number of occurrences of pattern in the database is 349
done


                                                                   Score     E
                                                                   (bits)  Value

Significant matches for pattern occurrence 1 at position 23


sp|P04988|CYS1_DICDI CYSTEINE PROTEINASE 1 PRECURSOR                  688  0.0
sp|P30957|RYNC_RABIT RYANODINE RECEPTOR, CARDIAC MUSCLE                 8  4.8
sp|Q08862|GTC_RABIT GLUTATHIONE S-TRANSFERASE YC (ALPHA II) (GST...     7  6.0
sp|O95801|TTC4_HUMAN TETRATRICOPEPTIDE REPEAT PROTEIN 4                 7  7.6
sp|P36114|YKZ8_YEAST HYPOTHETICAL 81.8 KDA PROTEIN IN YPT52-DBP7...     7  9.6


Significant matches for pattern occurrence 2 at position 120


sp|P11559|MCRA_METVO METHYL-COENZYME M REDUCTASE ALPHA SUBUNIT         13  0.13
sp|Q49605|MCRA_METKA METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT...    11  0.43
sp|P81901|FER_PYRIS FERREDOXIN (SEVEN-IRON FERREDOXIN)                 11  0.55
sp|Q58256|MCRX_METJA METHYL-COENZYME M REDUCTASE II ALPHA SUBUNI...    10  1.1
sp|P53203|YG14_YEAST HYPOTHETICAL 52.9 KD PROTEIN IN ERP6-TFG2 I...     8  3.0
sp|P55002|MGP1_MOUSE MICROFIBRIL-ASSOCIATED GLYCOPROTEIN PRECURS...     7  6.0
sp|Q06234|ASH1_XENLA ACHAETE-SCUTE HOMOLOG 1                            7  7.6
sp|P20918|PLMN_MOUSE PLASMINOGEN PRECURSOR [CONTAINS: ANGIOSTATIN]      7  7.6


Significant matches for pattern occurrence 3 at position 237


sp|P49362|GCSB_FLAPR GLYCINE DEHYDROGENASE [DECARBOXYLATING] B, ...     9  1.4
sp|P49361|GCSA_FLAPR GLYCINE DEHYDROGENASE [DECARBOXYLATING] A, ...     9  1.4
sp|O49852|GCSP_FLATR GLYCINE DEHYDROGENASE [DECARBOXYLATING], MI...     8  4.8
sp|P32767|PDR6_YEAST PLEIOTROPIC DRUG RESISTANCE REGULATORY PROT...     7  6.0
sp|O49850|GCSP_FLAAN GLYCINE DEHYDROGENASE [DECARBOXYLATING], MI...     7  9.6


Significant alignments for pattern occurrence 1 at position 23

>sp|P04988|CYS1_DICDI CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 343

 Score =  688 bits (1789), Expect = 0.0
 Identities = 343/351 (97%), Positives = 343/351 (97%), Gaps = 8/351 (2%)

Query:  1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60
pattern 23                        ****
            MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE
Sbjct:  1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60

Query:  61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPP 120
pattern 120                                                            *
            ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 
Sbjct:  61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP- 119

Query:  121 EEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 180
pattern 121 ***
               TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE
Sbjct:  120 ---TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 176

Query:  181 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQ 240
pattern 237                                                         ****
            CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG    
Sbjct:  177 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG---- 232

Query:  241 AKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVG 300
            AKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVG
Sbjct:  233 AKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVG 292

Query:  301 YSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 351
            YSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII
Sbjct:  293 YSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343


>sp|P30957|RYNC_RABIT RYANODINE RECEPTOR, CARDIAC MUSCLE
          Length = 4969

 Score =  7.8 bits (25), Expect = 4.8
 Identities = 14/39 (35%), Positives = 19/39 (47%)

Query:  23   PEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEE 61
pattern 23   ****
             PEEQ +F E + K  +K   EE     E  +   G+ EE
Sbjct:  4414 PEEQEKFQEQKTKEEEKEEKEETKSEPEKAEGEDGEKEE 4452


>sp|Q08862|GTC_RABIT GLUTATHIONE S-TRANSFERASE YC (ALPHA II) (GST CLASS-ALPHA)
          Length = 221

 Score =  7.4 bits (24), Expect = 6.0
 Identities = 19/67 (28%), Positives = 35/67 (51%), Gaps = 12/67 (17%)

Query:  21  IPPEEQ-SQFLEFQDKFNKKY---------SH-EEYLERFEIFKSNLGKIEEL-NLIAIN 68
pattern 23    ****
            +PPEEQ ++  + +DK   +Y         SH ++YL   ++ K+++  +E L N+  +N
Sbjct:  112 LPPEEQEAKLAQIKDKAKNRYFPAFEKVLKSHGQDYLVGNKLSKADILLVELLYNVEELN 171

Query:  69  HKADTKF 75
              A   F
Sbjct:  172 PGATASF 178


>sp|O95801|TTC4_HUMAN TETRATRICOPEPTIDE REPEAT PROTEIN 4
          Length = 356

 Score =  7.1 bits (23), Expect = 7.6
 Identities = 14/67 (20%), Positives = 32/67 (46%), Gaps = 5/67 (7%)

Query:  23  PEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGK---IEELNLIAINHKADTKFGVNK 79
pattern 23  ****
            PEEQ++   ++D+ N  +  ++Y +    +   L K     +LN +   ++A  ++ +  
Sbjct:  75  PEEQAK--TYKDEGNDYFKEKDYKKAVISYTEGLKKKCADPDLNAVLYTNRAAAQYYLGN 132

Query:  80  FADLSSD 86
            F    +D
Sbjct:  133 FRSALND 139


>sp|P36114|YKZ8_YEAST HYPOTHETICAL 81.8 KDA PROTEIN IN YPT52-DBP7 INTERGENIC REGION
          Length = 725

 Score =  6.8 bits (22), Expect = 9.6
 Identities = 21/99 (21%), Positives = 43/99 (43%), Gaps = 21/99 (21%)

Query:  21  IPPEEQ--SQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVN 78
pattern 23    ****
            + PEEQ     L+F ++      H    ER  +  +++G    +N      +   + G+ 
Sbjct:  213 LTPEEQKDKDLLQFAEQI-----HSMRTER--LSGAHIGNSPAIN------RLRGELGLQ 259

Query:  79  KFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINS 117
               DL  +E  ++       + +DD+ ++    DEF++S
Sbjct:  260 AMEDLPEEEITDH------KVLSDDIDLSQATIDEFVHS 292



Significant alignments for pattern occurrence 2 at position 120

>sp|P11559|MCRA_METVO METHYL-COENZYME M REDUCTASE ALPHA SUBUNIT
          Length = 555

 Score = 13.0 bits (40), Expect = 0.13
 Identities = 16/28 (57%), Positives = 18/28 (64%), Gaps = 3/28 (10%)

Query:  99  IFTDDLPVADYLDDEF---INSIPPEEQ 123
pattern 120                         ****
            IFT D  +AD LDD F   IN + PEEQ
Sbjct:  170 IFTGDDELADELDDRFVIDINKLFPEEQ 197


>sp|Q49605|MCRA_METKA METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT (MCR I ALPHA)
          Length = 553

 Score = 11.2 bits (35), Expect = 0.43
 Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 3/28 (10%)

Query:  99  IFTDDLPVADYLDDEFINSIP---PEEQ 123
pattern 120                         ****
            I T DL +AD +DD+F+  I    PEEQ
Sbjct:  168 IITGDLELADEIDDKFLIDIEKLFPEEQ 195


>sp|P81901|FER_PYRIS FERREDOXIN (SEVEN-IRON FERREDOXIN)
          Length = 101

 Score = 10.9 bits (34), Expect = 0.55
 Identities = 12/23 (52%), Positives = 16/23 (69%), Gaps = 1/23 (4%)

Query:  114 FINSIPPEEQTAF-DWRTRGAVT 135
pattern 120       ****
            F  S+ PEEQ AF +W+TR  +T
Sbjct:  78  FGKSLTPEEQRAFEEWKTRYGIT 100


>sp|Q58256|MCRX_METJA METHYL-COENZYME M REDUCTASE II ALPHA SUBUNIT (MCR II ALPHA)
          Length = 553

 Score =  9.8 bits (31), Expect = 1.1
 Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 3/28 (10%)

Query:  99  IFTDDLPVADYLDDEF---INSIPPEEQ 123
pattern 120                         ****
            IFT D  +AD +D  F   IN + PEEQ
Sbjct:  168 IFTGDDELADEIDKRFLIDINKLFPEEQ 195


>sp|P53203|YG14_YEAST HYPOTHETICAL 52.9 KD PROTEIN IN ERP6-TFG2 INTERGENIC REGION
          Length = 462

 Score =  8.5 bits (27), Expect = 3.0
 Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 9/39 (23%)

Query:  112 DEFINSIP-------PEEQT--AFDWRTRGAVTPVKNQG 141
pattern 120                ****
            DEF+N+ P       PEEQ+  A++W  +  +  + N G
Sbjct:  308 DEFLNTSPSPEVFTLPEEQSGMAWEWHDKDWMLDLTNDG 346


>sp|P55002|MGP1_MOUSE MICROFIBRIL-ASSOCIATED GLYCOPROTEIN PRECURSOR (MAGP) (MAGP-1)
          Length = 183

 Score =  7.4 bits (24), Expect = 6.0
 Identities = 11/37 (29%), Positives = 18/37 (47%)

Query:  100 FTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTP 136
pattern 120                     ****
            + D +  ADY D + ++   PEEQ     + +  V P
Sbjct:  37  YGDQIDNADYYDYQEVSPRTPEEQFQSQQQVQQEVIP 73


>sp|Q06234|ASH1_XENLA ACHAETE-SCUTE HOMOLOG 1
          Length = 199

 Score =  7.1 bits (23), Expect = 7.6
 Identities = 11/27 (40%), Positives = 15/27 (54%), Gaps = 1/27 (3%)

Query:  105 PVADYLDDE-FINSIPPEEQTAFDWRT 130
pattern 120                 ****
            PV+ Y  DE   + + PEEQ   D+ T
Sbjct:  171 PVSSYSSDEGSYDPLSPEEQELLDFTT 197


>sp|P20918|PLMN_MOUSE PLASMINOGEN PRECURSOR [CONTAINS: ANGIOSTATIN]
          Length = 812

 Score =  7.1 bits (23), Expect = 7.6
 Identities = 8/13 (61%), Positives = 11/13 (84%)

Query:  112 DEFINSIPPEEQT 124
pattern 120         ****
            D+  +S+PPEEQT
Sbjct:  359 DQSDSSVPPEEQT 371



Significant alignments for pattern occurrence 3 at position 237

>sp|P49362|GCSB_FLAPR GLYCINE DEHYDROGENASE [DECARBOXYLATING] B, MITOCHONDRIAL PRECURSOR
            (GLYCINE DECARBOXYLASE B) (GLYCINE CLEAVAGE SYSTEM
            P-PROTEIN B)
          Length = 1034

 Score =  9.5 bits (30), Expect = 1.4
 Identities = 21/79 (26%), Positives = 39/79 (48%), Gaps = 13/79 (16%)

Query:  231 NSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPN 290
pattern 237       ****
            NSA   PEEQ K++ F   P  +++    I +T P +I  D++++  +  G+ +     +
Sbjct:  80  NSAT--PEEQTKMAEFVGFPNLDSL----IDATVPKSIRLDSMKYSKFDEGLTESQMIAH 133

Query:  291 SLDHGILIVGYSAKNTIFR 309
              D        ++KN IF+
Sbjct:  134 MQD-------LASKNKIFK 145


>sp|P49361|GCSA_FLAPR GLYCINE DEHYDROGENASE [DECARBOXYLATING] A, MITOCHONDRIAL PRECURSOR
            (GLYCINE DECARBOXYLASE A) (GLYCINE CLEAVAGE SYSTEM
            P-PROTEIN A)
          Length = 1037

 Score =  9.5 bits (30), Expect = 1.4
 Identities = 21/79 (26%), Positives = 39/79 (48%), Gaps = 13/79 (16%)

Query:  231 NSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPN 290
pattern 237       ****
            NSA   PEEQ K++ F   P  +++    I +T P +I  D++++  +  G+ +     +
Sbjct:  83  NSAT--PEEQTKMAEFVGFPNLDSL----IDATVPKSIRLDSMKYSKFDEGLTESQMIAH 136

Query:  291 SLDHGILIVGYSAKNTIFR 309
              D        ++KN IF+
Sbjct:  137 MQD-------LASKNKIFK 148


>sp|O49852|GCSP_FLATR GLYCINE DEHYDROGENASE [DECARBOXYLATING], MITOCHONDRIAL PRECURSOR
            (GLYCINE DECARBOXYLASE) (GLYCINE CLEAVAGE SYSTEM
            P-PROTEIN)
          Length = 1034

 Score =  7.8 bits (25), Expect = 4.8
 Identities = 21/79 (26%), Positives = 38/79 (47%), Gaps = 13/79 (16%)

Query:  231 NSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPN 290
pattern 237       ****
            NSA   PEEQ K++ F      +++    I +T P AI  D++++  +  G+ +     +
Sbjct:  80  NSAT--PEEQTKMAEFVGFSNLDSL----IDATVPKAIRLDSMKYSKFDEGLTESQMIAH 133

Query:  291 SLDHGILIVGYSAKNTIFR 309
              D        ++KN IF+
Sbjct:  134 MQD-------LASKNKIFK 145


>sp|P32767|PDR6_YEAST PLEIOTROPIC DRUG RESISTANCE REGULATORY PROTEIN 6
          Length = 1081

 Score =  7.4 bits (24), Expect = 6.0
 Identities = 25/93 (26%), Positives = 37/93 (38%), Gaps = 17/93 (18%)

Query:  159 HFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYI-IKNGGIQTESS 217
            +F S+N+   +S   L     E M  +      E C   L P   ++I   N  I  +S+
Sbjct:  642 NFTSKNEQEKISNDKL-----EVMVIKTVSTLCETCREELTPYLMHFISFLNTVIMPDSN 696

Query:  218 YPYTAETG--------TQCNFNSANIGPEEQAK 242
pattern 237                            ****
              +   T          QC  ++   GPEEQAK
Sbjct:  697 VSHFTRTKLVRSIGYVVQCQVSN---GPEEQAK 726


>sp|O49850|GCSP_FLAAN GLYCINE DEHYDROGENASE [DECARBOXYLATING], MITOCHONDRIAL PRECURSOR
            (GLYCINE DECARBOXYLASE) (GLYCINE CLEAVAGE SYSTEM
            P-PROTEIN)
          Length = 1034

 Score =  6.8 bits (22), Expect = 9.6
 Identities = 20/79 (25%), Positives = 38/79 (47%), Gaps = 13/79 (16%)

Query:  231 NSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPN 290
pattern 237       ****
            NSA   PEEQ K++ F      +++    I +T P +I  D++++  +  G+ +     +
Sbjct:  80  NSAT--PEEQTKMAEFVGFSNLDSL----IDATVPKSIRLDSMKYSKFDEGLTESQMIAH 133

Query:  291 SLDHGILIVGYSAKNTIFR 309
              D        ++KN IF+
Sbjct:  134 MQD-------LASKNKIFK 145


  Database: /home/peter/blast/data/swissprot
    Posted date:  Oct 10, 2000 10:43 AM
  Number of letters in database: 31,984,247
  Number of sequences in database:  88,780
  
Lambda     K      H      C
   0.270   0.0470    0.230    0.500 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1047
Number of Sequences: 88780
Number of extensions: 1047
Number of successful extensions: 36
Number of sequences better than 10.0: 36
Number of HSP's better than 10.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 0
length of query: 351
length of database: 31,984,247
effective HSP length: 50
effective length of query: 301
effective length of database: 27,545,247
effective search space: 8291119347
effective search space used: 8291119347
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 41 (21.6 bits)
S2: 65 (29.7 bits)
BioPerl-1.007002/t/data/phipsi.out000444000766000024     55115113155576321 16765 0ustar00cjfieldsstaff000000000000BLASTP 2.0.14 [Jun-29-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= CYS1_DICDI
         (351 letters)

Database: /home/peter/blast/data/swissprot
           88,780 sequences; 31,984,247 total letters

Searching......................................................................................................................................................
3 occurrence(s) of pattern in query
  CYS1_DICDI; PATTERN.
 pattern P-E-E-Q at position 23 of query sequence
effective database length=3.2e+07
 pattern probability=8.9e-06
lengthXprobability=2.8e+02

Number of occurrences of pattern in the database is 349
  CYS1_DICDI; PATTERN.
 pattern P-E-E-Q at position 120 of query sequence
effective database length=3.2e+07
 pattern probability=8.9e-06
lengthXprobability=2.8e+02

Number of occurrences of pattern in the database is 349
  CYS1_DICDI; PATTERN.
 pattern P-E-E-Q at position 237 of query sequence
effective database length=3.2e+07
 pattern probability=8.9e-06
lengthXprobability=2.8e+02

Number of occurrences of pattern in the database is 349
done


Results from round 1

                                                                   Score     E
                                                                   (bits)  Value

Significant matches for pattern occurrence 1 at position 23


sp|P04988|CYS1_DICDI CYSTEINE PROTEINASE 1 PRECURSOR                  688  0.0
sp|P30957|RYNC_RABIT RYANODINE RECEPTOR, CARDIAC MUSCLE                 8  4.8
sp|Q08862|GTC_RABIT GLUTATHIONE S-TRANSFERASE YC (ALPHA II) (GST...     7  6.0
sp|O95801|TTC4_HUMAN TETRATRICOPEPTIDE REPEAT PROTEIN 4                 7  7.6
sp|P36114|YKZ8_YEAST HYPOTHETICAL 81.8 KDA PROTEIN IN YPT52-DBP7...     7  9.6


Significant matches for pattern occurrence 2 at position 120


sp|P11559|MCRA_METVO METHYL-COENZYME M REDUCTASE ALPHA SUBUNIT         13  0.13
sp|Q49605|MCRA_METKA METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT...    11  0.43
sp|P81901|FER_PYRIS FERREDOXIN (SEVEN-IRON FERREDOXIN)                 11  0.55
sp|Q58256|MCRX_METJA METHYL-COENZYME M REDUCTASE II ALPHA SUBUNI...    10  1.1
sp|P53203|YG14_YEAST HYPOTHETICAL 52.9 KD PROTEIN IN ERP6-TFG2 I...     8  3.0
sp|P55002|MGP1_MOUSE MICROFIBRIL-ASSOCIATED GLYCOPROTEIN PRECURS...     7  6.0
sp|Q06234|ASH1_XENLA ACHAETE-SCUTE HOMOLOG 1                            7  7.6
sp|P20918|PLMN_MOUSE PLASMINOGEN PRECURSOR [CONTAINS: ANGIOSTATIN]      7  7.6


Significant matches for pattern occurrence 3 at position 237


sp|P49362|GCSB_FLAPR GLYCINE DEHYDROGENASE [DECARBOXYLATING] B, ...     9  1.4
sp|P49361|GCSA_FLAPR GLYCINE DEHYDROGENASE [DECARBOXYLATING] A, ...     9  1.4
sp|O49852|GCSP_FLATR GLYCINE DEHYDROGENASE [DECARBOXYLATING], MI...     8  4.8
sp|P32767|PDR6_YEAST PLEIOTROPIC DRUG RESISTANCE REGULATORY PROT...     7  6.0
sp|O49850|GCSP_FLAAN GLYCINE DEHYDROGENASE [DECARBOXYLATING], MI...     7  9.6


Significant alignments for pattern occurrence 1 at position 23

>sp|P04988|CYS1_DICDI CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 343

 Score =  688 bits (1789), Expect = 0.0
 Identities = 343/351 (97%), Positives = 343/351 (97%), Gaps = 8/351 (2%)

Query:  1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60
pattern 23                        ****
            MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE
Sbjct:  1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60

Query:  61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPP 120
pattern 120                                                            *
            ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 
Sbjct:  61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP- 119

Query:  121 EEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 180
pattern 121 ***
               TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE
Sbjct:  120 ---TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 176

Query:  181 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQ 240
pattern 237                                                         ****
            CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG    
Sbjct:  177 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG---- 232

Query:  241 AKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVG 300
            AKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVG
Sbjct:  233 AKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVG 292

Query:  301 YSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 351
            YSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII
Sbjct:  293 YSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343


>sp|P30957|RYNC_RABIT RYANODINE RECEPTOR, CARDIAC MUSCLE
          Length = 4969

 Score =  7.8 bits (25), Expect = 4.8
 Identities = 14/39 (35%), Positives = 19/39 (47%)

Query:  23   PEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEE 61
pattern 23   ****
             PEEQ +F E + K  +K   EE     E  +   G+ EE
Sbjct:  4414 PEEQEKFQEQKTKEEEKEEKEETKSEPEKAEGEDGEKEE 4452


>sp|Q08862|GTC_RABIT GLUTATHIONE S-TRANSFERASE YC (ALPHA II) (GST CLASS-ALPHA)
          Length = 221

 Score =  7.4 bits (24), Expect = 6.0
 Identities = 19/67 (28%), Positives = 35/67 (51%), Gaps = 12/67 (17%)

Query:  21  IPPEEQ-SQFLEFQDKFNKKY---------SH-EEYLERFEIFKSNLGKIEEL-NLIAIN 68
pattern 23    ****
            +PPEEQ ++  + +DK   +Y         SH ++YL   ++ K+++  +E L N+  +N
Sbjct:  112 LPPEEQEAKLAQIKDKAKNRYFPAFEKVLKSHGQDYLVGNKLSKADILLVELLYNVEELN 171

Query:  69  HKADTKF 75
              A   F
Sbjct:  172 PGATASF 178


>sp|O95801|TTC4_HUMAN TETRATRICOPEPTIDE REPEAT PROTEIN 4
          Length = 356

 Score =  7.1 bits (23), Expect = 7.6
 Identities = 14/67 (20%), Positives = 32/67 (46%), Gaps = 5/67 (7%)

Query:  23  PEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGK---IEELNLIAINHKADTKFGVNK 79
pattern 23  ****
            PEEQ++   ++D+ N  +  ++Y +    +   L K     +LN +   ++A  ++ +  
Sbjct:  75  PEEQAK--TYKDEGNDYFKEKDYKKAVISYTEGLKKKCADPDLNAVLYTNRAAAQYYLGN 132

Query:  80  FADLSSD 86
            F    +D
Sbjct:  133 FRSALND 139


>sp|P36114|YKZ8_YEAST HYPOTHETICAL 81.8 KDA PROTEIN IN YPT52-DBP7 INTERGENIC REGION
          Length = 725

 Score =  6.8 bits (22), Expect = 9.6
 Identities = 21/99 (21%), Positives = 43/99 (43%), Gaps = 21/99 (21%)

Query:  21  IPPEEQ--SQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVN 78
pattern 23    ****
            + PEEQ     L+F ++      H    ER  +  +++G    +N      +   + G+ 
Sbjct:  213 LTPEEQKDKDLLQFAEQI-----HSMRTER--LSGAHIGNSPAIN------RLRGELGLQ 259

Query:  79  KFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINS 117
               DL  +E  ++       + +DD+ ++    DEF++S
Sbjct:  260 AMEDLPEEEITDH------KVLSDDIDLSQATIDEFVHS 292



Significant alignments for pattern occurrence 2 at position 120

>sp|P11559|MCRA_METVO METHYL-COENZYME M REDUCTASE ALPHA SUBUNIT
          Length = 555

 Score = 13.0 bits (40), Expect = 0.13
 Identities = 16/28 (57%), Positives = 18/28 (64%), Gaps = 3/28 (10%)

Query:  99  IFTDDLPVADYLDDEF---INSIPPEEQ 123
pattern 120                         ****
            IFT D  +AD LDD F   IN + PEEQ
Sbjct:  170 IFTGDDELADELDDRFVIDINKLFPEEQ 197


>sp|Q49605|MCRA_METKA METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT (MCR I ALPHA)
          Length = 553

 Score = 11.2 bits (35), Expect = 0.43
 Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 3/28 (10%)

Query:  99  IFTDDLPVADYLDDEFINSIP---PEEQ 123
pattern 120                         ****
            I T DL +AD +DD+F+  I    PEEQ
Sbjct:  168 IITGDLELADEIDDKFLIDIEKLFPEEQ 195


>sp|P81901|FER_PYRIS FERREDOXIN (SEVEN-IRON FERREDOXIN)
          Length = 101

 Score = 10.9 bits (34), Expect = 0.55
 Identities = 12/23 (52%), Positives = 16/23 (69%), Gaps = 1/23 (4%)

Query:  114 FINSIPPEEQTAF-DWRTRGAVT 135
pattern 120       ****
            F  S+ PEEQ AF +W+TR  +T
Sbjct:  78  FGKSLTPEEQRAFEEWKTRYGIT 100


>sp|Q58256|MCRX_METJA METHYL-COENZYME M REDUCTASE II ALPHA SUBUNIT (MCR II ALPHA)
          Length = 553

 Score =  9.8 bits (31), Expect = 1.1
 Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 3/28 (10%)

Query:  99  IFTDDLPVADYLDDEF---INSIPPEEQ 123
pattern 120                         ****
            IFT D  +AD +D  F   IN + PEEQ
Sbjct:  168 IFTGDDELADEIDKRFLIDINKLFPEEQ 195


>sp|P53203|YG14_YEAST HYPOTHETICAL 52.9 KD PROTEIN IN ERP6-TFG2 INTERGENIC REGION
          Length = 462

 Score =  8.5 bits (27), Expect = 3.0
 Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 9/39 (23%)

Query:  112 DEFINSIP-------PEEQT--AFDWRTRGAVTPVKNQG 141
pattern 120                ****
            DEF+N+ P       PEEQ+  A++W  +  +  + N G
Sbjct:  308 DEFLNTSPSPEVFTLPEEQSGMAWEWHDKDWMLDLTNDG 346


>sp|P55002|MGP1_MOUSE MICROFIBRIL-ASSOCIATED GLYCOPROTEIN PRECURSOR (MAGP) (MAGP-1)
          Length = 183

 Score =  7.4 bits (24), Expect = 6.0
 Identities = 11/37 (29%), Positives = 18/37 (47%)

Query:  100 FTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTP 136
pattern 120                     ****
            + D +  ADY D + ++   PEEQ     + +  V P
Sbjct:  37  YGDQIDNADYYDYQEVSPRTPEEQFQSQQQVQQEVIP 73


>sp|Q06234|ASH1_XENLA ACHAETE-SCUTE HOMOLOG 1
          Length = 199

 Score =  7.1 bits (23), Expect = 7.6
 Identities = 11/27 (40%), Positives = 15/27 (54%), Gaps = 1/27 (3%)

Query:  105 PVADYLDDE-FINSIPPEEQTAFDWRT 130
pattern 120                 ****
            PV+ Y  DE   + + PEEQ   D+ T
Sbjct:  171 PVSSYSSDEGSYDPLSPEEQELLDFTT 197


>sp|P20918|PLMN_MOUSE PLASMINOGEN PRECURSOR [CONTAINS: ANGIOSTATIN]
          Length = 812

 Score =  7.1 bits (23), Expect = 7.6
 Identities = 8/13 (61%), Positives = 11/13 (84%)

Query:  112 DEFINSIPPEEQT 124
pattern 120         ****
            D+  +S+PPEEQT
Sbjct:  359 DQSDSSVPPEEQT 371



Significant alignments for pattern occurrence 3 at position 237

>sp|P49362|GCSB_FLAPR GLYCINE DEHYDROGENASE [DECARBOXYLATING] B, MITOCHONDRIAL PRECURSOR
            (GLYCINE DECARBOXYLASE B) (GLYCINE CLEAVAGE SYSTEM
            P-PROTEIN B)
          Length = 1034

 Score =  9.5 bits (30), Expect = 1.4
 Identities = 21/79 (26%), Positives = 39/79 (48%), Gaps = 13/79 (16%)

Query:  231 NSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPN 290
pattern 237       ****
            NSA   PEEQ K++ F   P  +++    I +T P +I  D++++  +  G+ +     +
Sbjct:  80  NSAT--PEEQTKMAEFVGFPNLDSL----IDATVPKSIRLDSMKYSKFDEGLTESQMIAH 133

Query:  291 SLDHGILIVGYSAKNTIFR 309
              D        ++KN IF+
Sbjct:  134 MQD-------LASKNKIFK 145


>sp|P49361|GCSA_FLAPR GLYCINE DEHYDROGENASE [DECARBOXYLATING] A, MITOCHONDRIAL PRECURSOR
            (GLYCINE DECARBOXYLASE A) (GLYCINE CLEAVAGE SYSTEM
            P-PROTEIN A)
          Length = 1037

 Score =  9.5 bits (30), Expect = 1.4
 Identities = 21/79 (26%), Positives = 39/79 (48%), Gaps = 13/79 (16%)

Query:  231 NSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPN 290
pattern 237       ****
            NSA   PEEQ K++ F   P  +++    I +T P +I  D++++  +  G+ +     +
Sbjct:  83  NSAT--PEEQTKMAEFVGFPNLDSL----IDATVPKSIRLDSMKYSKFDEGLTESQMIAH 136

Query:  291 SLDHGILIVGYSAKNTIFR 309
              D        ++KN IF+
Sbjct:  137 MQD-------LASKNKIFK 148


>sp|O49852|GCSP_FLATR GLYCINE DEHYDROGENASE [DECARBOXYLATING], MITOCHONDRIAL PRECURSOR
            (GLYCINE DECARBOXYLASE) (GLYCINE CLEAVAGE SYSTEM
            P-PROTEIN)
          Length = 1034

 Score =  7.8 bits (25), Expect = 4.8
 Identities = 21/79 (26%), Positives = 38/79 (47%), Gaps = 13/79 (16%)

Query:  231 NSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPN 290
pattern 237       ****
            NSA   PEEQ K++ F      +++    I +T P AI  D++++  +  G+ +     +
Sbjct:  80  NSAT--PEEQTKMAEFVGFSNLDSL----IDATVPKAIRLDSMKYSKFDEGLTESQMIAH 133

Query:  291 SLDHGILIVGYSAKNTIFR 309
              D        ++KN IF+
Sbjct:  134 MQD-------LASKNKIFK 145


>sp|P32767|PDR6_YEAST PLEIOTROPIC DRUG RESISTANCE REGULATORY PROTEIN 6
          Length = 1081

 Score =  7.4 bits (24), Expect = 6.0
 Identities = 25/93 (26%), Positives = 37/93 (38%), Gaps = 17/93 (18%)

Query:  159 HFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYI-IKNGGIQTESS 217
            +F S+N+   +S   L     E M  +      E C   L P   ++I   N  I  +S+
Sbjct:  642 NFTSKNEQEKISNDKL-----EVMVIKTVSTLCETCREELTPYLMHFISFLNTVIMPDSN 696

Query:  218 YPYTAETG--------TQCNFNSANIGPEEQAK 242
pattern 237                            ****
              +   T          QC  ++   GPEEQAK
Sbjct:  697 VSHFTRTKLVRSIGYVVQCQVSN---GPEEQAK 726


>sp|O49850|GCSP_FLAAN GLYCINE DEHYDROGENASE [DECARBOXYLATING], MITOCHONDRIAL PRECURSOR
            (GLYCINE DECARBOXYLASE) (GLYCINE CLEAVAGE SYSTEM
            P-PROTEIN)
          Length = 1034

 Score =  6.8 bits (22), Expect = 9.6
 Identities = 20/79 (25%), Positives = 38/79 (47%), Gaps = 13/79 (16%)

Query:  231 NSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPN 290
pattern 237       ****
            NSA   PEEQ K++ F      +++    I +T P +I  D++++  +  G+ +     +
Sbjct:  80  NSAT--PEEQTKMAEFVGFSNLDSL----IDATVPKSIRLDSMKYSKFDEGLTESQMIAH 133

Query:  291 SLDHGILIVGYSAKNTIFR 309
              D        ++KN IF+
Sbjct:  134 MQD-------LASKNKIFK 145


Searching..................................................done


Results from round 2


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value
Sequences used in model and found again:

Sequences not found previously or not previously below threshold:

sp|P04988|CYS1_DICDI CYSTEINE PROTEINASE 1 PRECURSOR                  709  0.0
sp|P43295|A494_ARATH PROBABLE CYSTEINE PROTEINASE A494 PRECURSOR      273  4e-73
sp|P25804|CYSP_PEA CYSTEINE PROTEINASE 15A PRECURSOR (TURGOR-RES...   270  2e-72
sp|P43296|RD19_ARATH CYSTEINE PROTEINASE RD19A PRECURSOR              266  6e-71
sp|Q10716|CYS1_MAIZE CYSTEINE PROTEINASE 1 PRECURSOR                  252  6e-67
sp|P04989|CYS2_DICDI CYSTEINE PROTEINASE 2 PRECURSOR (PRESTALK C...   250  2e-66
sp|P54640|CYS5_DICDI CYSTEINE PROTEINASE 5 PRECURSOR                  238  1e-62
sp|P14658|CYSP_TRYBB CYSTEINE PROTEINASE PRECURSOR                    236  4e-62
sp|Q26534|CATL_SCHMA CATHEPSIN L PRECURSOR (SMCL1)                    233  3e-61
sp|P35591|CYS1_LEIPI CYSTEINE PROTEINASE 1 PRECURSOR (AMASTIGOTE...   233  3e-61
sp|P25775|LCPA_LEIME CYSTEINE PROTEINASE A PRECURSOR                  231  1e-60
sp|P13277|CYS1_HOMAM DIGESTIVE CYSTEINE PROTEINASE 1 PRECURSOR        221  1e-57
sp|P25779|CYSP_TRYCR CRUZIPAIN PRECURSOR (MAJOR CYSTEINE PROTEIN...   221  2e-57
sp|P41721|CATV_NPVBM VIRAL CATHEPSIN (V-CATH)                         216  5e-56
sp|P25782|CYS2_HOMAM DIGESTIVE CYSTEINE PROTEINASE 2 PRECURSOR        215  1e-55
sp|P41715|CATV_NPVCF VIRAL CATHEPSIN (V-CATH)                         214  2e-55
sp|P25784|CYS3_HOMAM DIGESTIVE CYSTEINE PROTEINASE 3 PRECURSOR        214  2e-55
sp|P07154|CATL_RAT CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTEIN...   212  7e-55
sp|P06797|CATL_MOUSE CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTE...   212  1e-54
sp|P12412|CYSP_VIGMU VIGNAIN PRECURSOR (BEAN ENDOPEPTIDASE) (CYS...   209  8e-54
sp|P25783|CATV_NPVAC VIRAL CATHEPSIN (V-CATH)                         209  8e-54
sp|P25975|CATL_BOVIN CATHEPSIN L PRECURSOR                            208  1e-53
sp|Q40143|CYS3_LYCES CYSTEINE PROTEINASE 3 PRECURSOR                  207  2e-53
sp|Q05094|CYS2_LEIPI CYSTEINE PROTEINASE 2 PRECURSOR (AMASTIGOTE...   207  3e-53
sp|P36400|LCPB_LEIME CYSTEINE PROTEINASE B PRECURSOR                  206  4e-53
sp|P07711|CATL_HUMAN CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTE...   206  4e-53
sp|Q28944|CATL_PIG CATHEPSIN L PRECURSOR                              206  5e-53
sp|P00785|ACTN_ACTCH ACTINIDAIN PRECURSOR (ACTINIDIN)                 204  3e-52
sp|P25803|CYSP_PHAVU VIGNAIN PRECURSOR (BEAN ENDOPEPTIDASE) (CYS...   203  6e-52
sp|Q10991|CATL_SHEEP CATHEPSIN L                                      201  1e-51
sp|P43156|CYSP_HEMSP THIOL PROTEASE SEN102 PRECURSOR                  201  2e-51
sp|P54639|CYS4_DICDI CYSTEINE PROTEINASE 4 PRECURSOR                  200  3e-51
sp|O60911|CATM_HUMAN CATHEPSIN L2 PRECURSOR (CATHEPSIN V)             199  7e-51
sp|O10364|CATV_NPVOP VIRAL CATHEPSIN (V-CATH)                         196  5e-50
sp|P25777|ORYB_ORYSA ORYZAIN BETA CHAIN PRECURSOR                     196  5e-50
sp|P25776|ORYA_ORYSA ORYZAIN ALPHA CHAIN PRECURSOR                    194  2e-49
sp|P43297|RD21_ARATH CYSTEINE PROTEINASE RD21A PRECURSOR              193  4e-49
sp|Q10717|CYS2_MAIZE CYSTEINE PROTEINASE 2 PRECURSOR                  193  5e-49
sp|P14080|PAP2_CARPA CHYMOPAPAIN PRECURSOR (PAPAYA PROTEINASE II...   192  1e-48
sp|P00786|CATH_RAT CATHEPSIN H PRECURSOR (CATHEPSIN B3) (CATHEPS...   192  1e-48
sp|P25251|CYS4_BRANA CYSTEINE PROTEINASE COT44 PRECURSOR              190  5e-48
sp|P09668|CATH_HUMAN CATHEPSIN H PRECURSOR                            188  2e-47
sp|P10056|PAP3_CARPA CARICAIN PRECURSOR (PAPAYA PROTEINASE OMEGA...   187  2e-47
sp|P25778|ORYC_ORYSA ORYZAIN GAMMA CHAIN PRECURSOR                    187  2e-47
sp|P15242|TES1_RAT TESTIN 1/2 PRECURSOR (CMB-22/CMB-23)               187  4e-47
sp|O46427|CATH_PIG CATHEPSIN H PRECURSOR                              186  5e-47
sp|P05167|ALEU_HORVU THIOL PROTEASE ALEURAIN PRECURSOR                185  9e-47
sp|P43235|CATK_HUMAN CATHEPSIN K PRECURSOR (CATHEPSIN O) (CATHEP...   185  1e-46
sp|P05994|PAP4_CARPA PAPAYA PROTEINASE IV PRECURSOR (PPIV) (PAPA...   184  3e-46
sp|P25250|CYS2_HORVU CYSTEINE PROTEINASE EP-B 2 PRECURSOR             183  3e-46
sp|P25249|CYS1_HORVU CYSTEINE PROTEINASE EP-B 1 PRECURSOR             183  5e-46
sp|P43236|CATK_RABIT CATHEPSIN K PRECURSOR (OC-2 PROTEIN)             183  6e-46
sp|P22895|P34_SOYBN P34 PROBABLE THIOL PROTEASE PRECURSOR             182  8e-46
sp|P49935|CATH_MOUSE CATHEPSIN H PRECURSOR (CATHEPSIN B3) (CATHE...   180  5e-45
sp|P55097|CATK_MOUSE CATHEPSIN K PRECURSOR                            178  2e-44
sp|P56202|CATW_HUMAN CATHEPSIN W PRECURSOR (LYMPHOPAIN)               177  3e-44
sp|P56203|CATW_MOUSE CATHEPSIN W PRECURSOR (LYMPHOPAIN)               176  6e-44
sp|P43234|CATO_HUMAN CATHEPSIN O PRECURSOR                            173  4e-43
sp|P00784|PAPA_CARPA PAPAIN PRECURSOR (PAPAYA PROTEINASE I) (PPI)     173  7e-43
sp|P25774|CATS_HUMAN CATHEPSIN S PRECURSOR                            171  3e-42
sp||CATL_CHICK_1 [Segment 1 of 2] CATHEPSIN L                         167  2e-41
sp|P25326|CATS_BOVIN CATHEPSIN S                                      165  1e-40
sp|P80884|ANAN_ANACO ANANAIN                                          161  2e-39
sp|Q02765|CATS_RAT CATHEPSIN S PRECURSOR                              158  1e-38
sp|P20721|CYSL_LYCES LOW-TEMPERATURE-INDUCED CYSTEINE PROTEINASE...   158  2e-38
sp|P36184|ACP1_ENTHI CYSTEINE PROTEINASE ACP1 PRECURSOR               152  1e-36
sp|Q01957|CPP1_ENTHI CYSTEINE PROTEINASE 1 PRECURSOR                  150  4e-36
sp|O17473|CATL_BRUPA CATHEPSIN L-LIKE PRECURSOR                       150  6e-36
sp|P46102|CYSP_PLAVN CYSTEINE PROTEINASE PRECURSOR                    150  6e-36
sp|Q06964|CPP3_ENTHI CYSTEINE PROTEINASE 3 PRECURSOR (CYSTEINE P...   149  9e-36
sp|Q01958|CPP2_ENTHI CYSTEINE PROTEINASE 2 PRECURSOR                  149  9e-36
sp|P36185|ACP2_ENTHI CYSTEINE PROTEINASE ACP2 PRECURSOR               145  1e-34
sp|P25781|CYSP_THEAN CYSTEINE PROTEINASE PRECURSOR                    145  1e-34
sp|P22497|CYSP_THEPA CYSTEINE PROTEINASE PRECURSOR                    143  5e-34
sp|P25805|CYSP_PLAFA THROPHOZOITE CYSTEINE PROTEINASE PRECURSOR ...   141  3e-33
sp|P14518|BROM_ANACO BROMELAIN, STEM                                  139  6e-33
sp|P16311|MMAL_DERFA MAJOR MITE FECAL ALLERGEN DER F 1 PRECURSOR...   138  1e-32
sp|P42666|CYSP_PLAVI CYSTEINE PROTEINASE PRECURSOR                    129  1e-29
sp|P08176|MMAL_DERPT MAJOR MITE FECAL ALLERGEN DER P 1 PRECURSOR...   121  3e-27
sp|P80067|CATC_RAT DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (DPP...   111  3e-24
sp|P97821|CATC_MOUSE DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (D...   109  9e-24
sp|P25773|CATL_FELCA CATHEPSIN L (PROGESTERONE-DEPENDENT PROTEIN...   108  2e-23
sp|Q26563|CATC_SCHMA CATHEPSIN C PRECURSOR                            108  3e-23
sp|P53634|CATC_HUMAN DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (D...   107  3e-23
sp|P25780|EUM1_EURMA MITE GROUP I ALLERGEN EUR M 1 (EUR M I)          100  7e-21
sp|Q23894|CYS3_DICDI CYSTEINE PROTEINASE 3 (CYSTEINE PROTEINASE II)    95  2e-19
sp|P43509|CPR5_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 5 PREC...    91  4e-18
sp|P43508|CPR4_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 4 PREC...    90  5e-18
sp|P05993|PAP5_CARPA CYSTEINE PROTEINASE (CLONE PLBPC13)               90  5e-18
sp|P07688|CATB_BOVIN CATHEPSIN B PRECURSOR                             89  2e-17
sp|P00787|CATB_RAT CATHEPSIN B PRECURSOR (CATHEPSIN B1) (RSG-2)        87  4e-17
sp|P25807|CYS1_CAEEL GUT-SPECIFIC CYSTEINE PROTEINASE PRECURSOR        87  5e-17
sp|P07858|CATB_HUMAN CATHEPSIN B PRECURSOR (CATHEPSIN B1) (APP S...    86  9e-17
sp|P43157|CYSP_SCHJA CATHEPSIN B-LIKE CYSTEINE PROTEINASE PRECUR...    85  2e-16
sp|P43233|CATB_CHICK CATHEPSIN B PRECURSOR (CATHEPSIN B1)              85  2e-16
sp|P43510|CPR6_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 6 PREC...    85  2e-16
sp|P25792|CYSP_SCHMA CATHEPSIN B-LIKE CYSTEINE PROTEINASE PRECUR...    85  3e-16
sp|P10605|CATB_MOUSE CATHEPSIN B PRECURSOR (CATHEPSIN B1)              85  3e-16
sp|P25802|CYS1_OSTOS CATHEPSIN B-LIKE CYSTEINE PROTEINASE 1 PREC...    80  9e-15
sp|P25793|CYS2_HAECO CATHEPSIN B-LIKE CYSTEINE PROTEINASE 2 PREC...    78  2e-14
sp|P19092|CYS1_HAECO CATHEPSIN B-LIKE CYSTEINE PROTEINASE 1 PREC...    78  4e-14
sp|P43507|CPR3_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 3 PREC...    73  7e-13
sp|P13823|SERA_PLAFG SERINE-REPEAT ANTIGEN PROTEIN PRECURSOR (P1...    70  6e-12
sp|P32956|CC3_CARCN CYSTEINE PROTEINASE III (CC-III)                   61  4e-09
sp|P32957|CC4_CARCN CYSTEINE PROTEINASE IV (CC-IV)                     60  9e-09
sp|Q06544|CYS3_OSTOS CATHEPSIN B-LIKE CYSTEINE PROTEINASE 3            59  1e-08
sp|P32954|CC1_CARCN CYSTEINE PROTEINASE I (CC-I)                       58  3e-08
sp|P32955|CC2_CARCN CYSTEINE PROTEINASE II (CC-II)                     56  1e-07
sp||CATL_CHICK_2 [Segment 2 of 2] CATHEPSIN L                          52  2e-06
sp|P12399|CT2A_MOUSE CTLA-2-ALPHA PROTEIN PRECURSOR                    42  0.002
sp|P05689|CATX_BOVIN CATHEPSIN                                         40  0.006
sp|P12400|CT2B_MOUSE CTLA-2-BETA PROTEIN PRECURSOR                     39  0.019
sp|P23897|HSER_RAT HEAT-STABLE ENTEROTOXIN RECEPTOR PRECURSOR (G...    36  0.16
sp|P20736|BM86_BOOMI GLYCOPROTEIN ANTIGEN BM86 PRECURSOR (PROTEC...    35  0.22
sp|P46992|YJR1_YEAST HYPOTHETICAL 43.0 KD PROTEIN IN CPS1-FPP1 I...    32  1.9
sp|P28493|PR5_ARATH PATHOGENESIS-RELATED PROTEIN 5 PRECURSOR (PR-5)    32  1.9
sp|P54634|POLN_LORDV NON-STRUCTURAL POLYPROTEIN [CONTAINS: RNA-D...    31  3.2
sp|Q02521|SPP2_YEAST SPLICEOSOME MATURATION PROTEIN SPP2               31  4.2
sp|P41901|SPR3_YEAST SPORULATION-SPECIFIC SEPTIN                       31  4.2
sp|Q01532|BLH1_YEAST CYSTEINE PROTEINASE 1 (Y3) (BLEOMYCIN HYDRO...    30  5.5
sp|P24896|NU5M_CAEEL NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 5            30  5.5
sp|P25648|SRB8_YEAST SUPPRESSOR OF RNA POLYMERASE B SRB8               30  7.2
sp|Q04723|PEPC_LACLC AMINOPEPTIDASE C                                  30  7.2
sp|Q13867|BLMH_HUMAN BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH)         30  9.4
sp|P87362|BLMH_CHICK BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH) (...    30  9.4
sp|P70645|BLMH_RAT BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH)           30  9.4

>sp|P04988|CYS1_DICDI CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 343

 Score =  709 bits (1811), Expect = 0.0
 Identities = 343/351 (97%), Positives = 343/351 (97%), Gaps = 8/351 (2%)

Query:  1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60
            MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE
Sbjct:  1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60

Query:  61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPP 120
            ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 
Sbjct:  61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP- 119

Query:  121 EEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 180
               TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE
Sbjct:  120 ---TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 176

Query:  181 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQ 240
pattern 237                                                         ****
            CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG    
Sbjct:  177 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG---- 232

Query:  241 AKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVG 300
            AKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVG
Sbjct:  233 AKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVG 292

Query:  301 YSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 351
            YSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII
Sbjct:  293 YSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343


>sp|P43295|A494_ARATH PROBABLE CYSTEINE PROTEINASE A494 PRECURSOR
          Length = 313

 Score =  273 bits (691), Expect = 4e-73
 Identities = 149/324 (45%), Positives = 194/324 (58%), Gaps = 26/324 (8%)

Query:  32  FQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKA---DTKFGVNKFADLSSDE 87
            F+ KF K Y S EE+  RF +FK+NL       L A+ H+      + GV +F+DL+  E
Sbjct:  3   FKKKFGKVYGSIEEHYYRFSVFKANL-------LRAMRHQKMDPSARHGVTQFSDLTRSE 55

Query:  88  FKNYYLNNKEAI-FTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSC 146
            F+  +L  K       D   A  L  + +    PEE   FDWR RGAVTPVKNQG CGSC
Sbjct:  56  FRRKHLGVKGGFKLPKDANQAPILPTQNL----PEE---FDWRDRGAVTPVKNQGSCGSC 108

Query:  147 WSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYI 206
            WSFSTTG +EG HF++  KLVSLSEQ LVDCDHEC + E E +CD GCNGGL  +A+ Y 
Sbjct:  109 WSFSTTGALEGAHFLATGKLVSLSEQQLVDCDHEC-DPEEEGSCDSGCNGGLMNSAFEYT 167

Query:  207 IKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPL 266
pattern 237                               ****
            +K GG+  E  YPYT   G  C  + + I     A +SNF+++  NE  +A  ++  GPL
Sbjct:  168 LKTGGLMREKDYPYTGTDGGSCKLDRSKI----VASVSNFSVVSINEDQIAANLIKNGPL 223

Query:  267 AIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAK--NTIFRKNMPYWIVKNSWGAD 324
            A+A +A   Q YIGGV         L+HG+L+VGY +   +    K  PYWI+KNSWG  
Sbjct:  224 AVAINAAYMQTYIGGVSCPYICSRRLNHGVLLVGYGSAGFSQARLKEKPYWIIKNSWGES 283

Query:  325 WGEQGYIYLRRGKNTCGVSNFVST 348
            WGE G+  + +G+N CGV + VST
Sbjct:  284 WGENGFYKICKGRNICGVDSLVST 307


>sp|P25804|CYSP_PEA CYSTEINE PROTEINASE 15A PRECURSOR (TURGOR-RESPONSIVE PROTEIN 15A)
          Length = 363

 Score =  270 bits (684), Expect = 2e-72
 Identities = 144/327 (44%), Positives = 201/327 (61%), Gaps = 20/327 (6%)

Query:  26  QSQFLEFQDKFNKKYS-HEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLS 84
            +  F  F+ KF+K Y+  EE+  RF +FKSNL K +    +  N     + G+ KF+DL+
Sbjct:  45  EHHFTSFKSKFSKSYATKEEHDYRFGVFKSNLIKAK----LHQNRDPTAEHGITKFSDLT 100

Query:  85  SDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCG 144
            + EF+  +L  K+ +    LP           +  PE+   FDWR +GAVTPVK+QG CG
Sbjct:  101 ASEFRRQFLGLKKRL---RLPAHAQKAPILPTTNLPED---FDWREKGAVTPVKDQGSCG 154

Query:  145 SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYN 204
            SCW+FSTTG +EG H+++  KLVSLSEQ LVDCDH C + E   +CD GCNGGL  NA+ 
Sbjct:  155 SCWAFSTTGALEGAHYLATGKLVSLSEQQLVDCDHVC-DPEQAGSCDSGCNGGLMNNAFE 213

Query:  205 YIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTG 264
pattern 237                                 ****
            Y++++GG+  E  Y YT   G+ C F+ + +     A +SNF+++  +E  +A  +V  G
Sbjct:  214 YLLESGGVVQEKDYAYTGRDGS-CKFDKSKV----VASVSNFSVVTLDEDQIAANLVKNG 268

Query:  265 PLAIAADAVEWQFYIGGV-FDIPCNPNSLDHGILIVGY--SAKNTIFRKNMPYWIVKNSW 321
            PLA+A +A   Q Y+ GV     C  + LDHG+L+VG+   A   I  K  PYWI+KNSW
Sbjct:  269 PLAVAINAAWMQTYMSGVSCPYVCAKSRLDHGVLLVGFGKGAYAPIRLKEKPYWIIKNSW 328

Query:  322 GADWGEQGYIYLRRGKNTCGVSNFVST 348
            G +WGEQGY  + RG+N CGV + VST
Sbjct:  329 GQNWGEQGYYKICRGRNVCGVDSMVST 355


>sp|P43296|RD19_ARATH CYSTEINE PROTEINASE RD19A PRECURSOR
          Length = 368

 Score =  266 bits (672), Expect = 6e-71
 Identities = 156/367 (42%), Positives = 206/367 (55%), Gaps = 42/367 (11%)

Query:  6   LFVLAVFTVFVSSR---------------GIPPE---EQSQFLEFQDKFNKKY-SHEEYL 46
            +FVL+ F V VSS                G  P+    +  F  F+ KF K Y S+EE+ 
Sbjct:  10  VFVLSFFIVSVSSSDVNDGDDLVIRQVVGGAEPQVLTSEDHFSLFKRKFGKVYASNEEHD 69

Query:  47  ERFEIFKSNLGKIEELNLIAINHKADTK--FGVNKFADLSSDEFKNYYLNNKEAI-FTDD 103
             RF +FK+NL +         + K D     GV +F+DL+  EF+  +L  +       D
Sbjct:  70  YRFSVFKANLRRARR------HQKLDPSATHGVTQFSDLTRSEFRKKHLGVRSGFKLPKD 123

Query:  104 LPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQ 163
               A  L  E +    PE+   FDWR  GAVTPVKNQG CGSCWSFS TG +EG +F++ 
Sbjct:  124 ANKAPILPTENL----PED---FDWRDHGAVTPVKNQGSCGSCWSFSATGALEGANFLAT 176

Query:  164 NKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAE 223
             KLVSLSEQ LVDCDHEC + E  ++CD GCNGGL  +A+ Y +K GG+  E  YPYT +
Sbjct:  177 GKLVSLSEQQLVDCDHEC-DPEEADSCDSGCNGGLMNSAFEYTLKTGGLMKEEDYPYTGK 235

Query:  224 TGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVF 283
pattern 237              ****
             G  C  + + I     A +SNF++I  +E  +A  +V  GPLA+A +A   Q YIGGV 
Sbjct:  236 DGKTCKLDKSKI----VASVSNFSVISIDEEQIAANLVKNGPLAVAINAGYMQTYIGGVS 291

Query:  284 DIPCNPNSLDHGILIVGYSAKN--TIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCG 341
                    L+HG+L+VGY A        K  PYWI+KNSWG  WGE G+  + +G+N CG
Sbjct:  292 CPYICTRRLNHGVLLVGYGAAGYAPARFKEKPYWIIKNSWGETWGENGFYKICKGRNICG 351

Query:  342 VSNFVST 348
            V + VST
Sbjct:  352 VDSMVST 358


>sp|Q10716|CYS1_MAIZE CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 371

 Score =  252 bits (638), Expect = 6e-67
 Identities = 138/332 (41%), Positives = 190/332 (56%), Gaps = 23/332 (6%)

Query:  26  QSQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLS 84
            +S FL F  +F K Y   +E+  R  +FK NL +     L+        + GV KF+DL+
Sbjct:  45  ESHFLSFVQRFGKSYKDADEHAYRLSVFKDNLRRARRHQLL----DPSAEHGVTKFSDLT 100

Query:  85  SDEFKNYYLN---NKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQG 141
              EF+  YL    ++ A+  +    A        + +P +    FDWR  GAV PVKNQG
Sbjct:  101 PAEFRRTYLGLRKSRRALLRELGESAHEAPVLPTDGLPDD----FDWRDHGAVGPVKNQG 156

Query:  142 QCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPN 201
             CGSCWSFS +G +EG H+++  KL  LSEQ  VDCDHEC   E  ++CD GCNGGL   
Sbjct:  157 SCGSCWSFSASGALEGAHYLATGKLEVLSEQQFVDCDHECDSSE-PDSCDSGCNGGLMTT 215

Query:  202 AYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIV 261
pattern 237                                    ****
            A++Y+ K GG+++E  YPYT   G +C F+ + I     A + NF+++  +E  ++  ++
Sbjct:  216 AFSYLQKAGGLESEKDYPYTGSDG-KCKFDKSKI----VASVQNFSVVSVDEAQISANLI 270

Query:  262 STGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKN--TIFRKNMPYWIVKN 319
              GPLAI  +A   Q YIGGV         LDHG+L+VGY A     I  K+ PYWI+KN
Sbjct:  271 KHGPLAIGINAAYMQTYIGGVSCPYICGRHLDHGVLLVGYGASGFAPIRLKDKPYWIIKN 330

Query:  320 SWGADWGEQGYIYLRRG---KNTCGVSNFVST 348
            SWG +WGE GY  + RG   +N CGV + VST
Sbjct:  331 SWGENWGENGYYKICRGSNVRNKCGVDSMVST 362


>sp|P04989|CYS2_DICDI CYSTEINE PROTEINASE 2 PRECURSOR (PRESTALK CATHEPSIN)
          Length = 376

 Score =  250 bits (633), Expect = 2e-66
 Identities = 147/391 (37%), Positives = 213/391 (53%), Gaps = 63/391 (16%)

Query:  1   MKVILLFVLAVFTVFVSSRGIP-------PEEQSQFLEFQDKFNKKYSHEEYLERFEIFK 53
            M++++  +L +F  F  +   P        + ++ F E+  KFN++YS  E+  R+ IFK
Sbjct:  1   MRLLVFLILLIFVNFSFANVRPNGRRFSESQYRTAFTEWTLKFNRQYSSSEFSNRYSIFK 60

Query:  54  SNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNK-EAIFTDDLPVADYLDD 112
            SN+  ++  N       + T  G+N FAD++++E++  YL  +  A   +     + L+ 
Sbjct:  61  SNMDYVDNWNS---KGDSQTVLGLNNFADITNEEYRKTYLGTRVNAHSYNGYDGREVLNV 117

Query:  113 EFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQ 172
            E + + P     + DWRT+ AVTP+K+QGQCGSCWSFSTTG+ EG H +   KLVSLSEQ
Sbjct:  118 EDLQTNPK----SIDWRTKNAVTPIKDQGQCGSCWSFSTTGSTEGAHALKTKKLVSLSEQ 173

Query:  173 NLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNS 232
            NLVDC        G E  + GC+GGL  NA++YIIKN GI TESSYPYTAETG+ C FN 
Sbjct:  174 NLVDC-------SGPEE-NFGCDGGLMNNAFDYIIKNKGIDTESSYPYTAETGSTCLFNK 225

Query:  233 ANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIP-CNP 289
pattern 237     ****
            ++IG    A I  +  I     +        GP+++A DA    +Q Y  G++  P C+P
Sbjct:  226 SDIG----ATIKGYVNITAGSEISLENGAQHGPVSVAIDASHNSFQLYTSGIYYEPKCSP 281

Query:  290 NSLDHGILIVGY--------------------------------SAKNTIFRKNMPYWIV 317
              LDHG+L+VGY                                 + +++  K   YWIV
Sbjct:  282 TELDHGVLVVGYGVQGKDDEGPVLNRKQTIVIHKNEDNKVESSDDSSDSVRPKANNYWIV 341

Query:  318 KNSWGADWGEQGYIYLRRG-KNTCGVSNFVS 347
            KNSWG  WG +GYI + +  KN CG+++  S
Sbjct:  342 KNSWGTSWGIKGYILMSKDRKNNCGIASVSS 372


>sp|P54640|CYS5_DICDI CYSTEINE PROTEINASE 5 PRECURSOR
          Length = 344

 Score =  238 bits (601), Expect = 1e-62
 Identities = 139/370 (37%), Positives = 201/370 (53%), Gaps = 45/370 (12%)

Query:  1   MKVI-LLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKI 59
            MKV+  L VL V       +    + ++ F ++     K Y+ EE+  R+ IF +N+  +
Sbjct:  1   MKVLSFLCVLLVSVATAKQQFSELQYRNAFTDWMITHQKSYTSEEFGARYNIFTANMDYV 60

Query:  60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
            ++ N    +  ++T  G+N FAD++++E++N YL  K   F     +    +    NS  
Sbjct:  61  QQWN----SKGSETVLGLNNFADITNEEYRNTYLGTK---FDASSLIGTQEEKVHTNSSA 113

Query:  120 PEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDH 179
              +    DWR+ GAVTPVKNQGQCG CWSFSTTG+ EG HF S+ +LVSLSEQNL+DC  
Sbjct:  114 ASK----DWRSEGAVTPVKNQGQCGGCWSFSTTGSTEGAHFQSKGELVSLSEQNLIDCST 169

Query:  180 ECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEE 239
pattern 237                                                          ***
            E          + GC+GGL   A+ YII N GI TESSYPY AE G +C + S N G   
Sbjct:  170 E----------NSGCDGGLMTYAFEYIINNNGIDTESSYPYKAENG-KCEYKSENSG--- 215

Query:  240 QAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIP-CNPNSLDHGI 296
pattern 240 *
             A +S++  +           V+  P+++A DA    +Q Y  G++  P C+  +LDHG+
Sbjct:  216 -ATLSSYKTVTAGSESSLESAVNVNPVSVAIDASHQSFQLYTSGIYYEPECSSENLDHGV 274

Query:  297 LIVGY--------------SAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCG 341
            L VGY              S+ N     +  YWIVKNSWG  WG +GYI + R + N CG
Sbjct:  275 LAVGYGSGSGSSSGQSSGQSSGNLSASSSNEYWIVKNSWGTSWGIEGYILMSRNRDNNCG 334

Query:  342 VSNFVSTSII 351
            +++  S  ++
Sbjct:  335 IASSASFPVV 344


>sp|P14658|CYSP_TRYBB CYSTEINE PROTEINASE PRECURSOR
          Length = 450

 Score =  236 bits (597), Expect = 4e-62
 Identities = 137/354 (38%), Positives = 193/354 (53%), Gaps = 34/354 (9%)

Query:  3   VILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEE 61
            V+L     + +V + S  +    + +F  F+ K+ K Y   +E   RF  F+ N+   E+
Sbjct:  15  VLLAMAACLASVALGSLHVEESLEMRFAAFKKKYGKVYKDAKEEAFRFRAFEENM---EQ 71

Query:  62  LNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPE 121
              + A  +   T FGV  F+D++ +EF+  Y N            A     + +N     
Sbjct:  72  AKIQAAANPYAT-FGVTPFSDMTREEFRARYRNGASYF-----AAAQKRLRKTVNVTTGR 125

Query:  122 EQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHEC 181
               A DWR +GAVTPVK QGQCGSCW+FST GN+EGQ  ++ N LVSLSEQ LV CD   
Sbjct:  126 APAAVDWREKGAVTPVKVQGQCGSCWAFSTIGNIEGQWQVAGNPLVSLSEQMLVSCD--- 182

Query:  182 MEYEGEEACDEGCNGGLQPNAYNYIIKN--GGIQTESSYPYTAETG--TQCNFNSANIGP 237
pattern 237                                                            *
                     D GCNGGL  NA+N+I+ +  G + TE+SYPY +  G   QC  N   IG 
Sbjct:  183 -------TIDSGCNGGLMDNAFNWIVNSNGGNVFTEASYPYVSGNGEQPQCQMNGHEIG- 234

Query:  238 EEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGIL 297
pattern 238 ***
               A I++   +P++E  +A Y+   GPLAIA DA  +  Y GG+    C    LDHG+L
Sbjct:  235 ---AAITDHVDLPQDEDAIAAYLAENGPLAIAVDAESFMDYNGGIL-TSCTSKQLDHGVL 290

Query:  298 IVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 351
            +VGY+  +     N PYWI+KNSW   WGE GYI + +G N C ++  VS++++
Sbjct:  291 LVGYNDNS-----NPPYWIIKNSWSNMWGEDGYIRIEKGTNQCLMNQAVSSAVV 339


>sp|Q26534|CATL_SCHMA CATHEPSIN L PRECURSOR (SMCL1)
          Length = 319

 Score =  233 bits (589), Expect = 3e-61
 Identities = 128/334 (38%), Positives = 190/334 (56%), Gaps = 30/334 (8%)

Query:  21  IPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKF 80
            +P     ++++F+ K+ K+Y   E   RF IFKSN+ K +   L  +  +    +GV  +
Sbjct:  12  LPGNVDEKYVQFKLKYRKQYHETEDEIRFNIFKSNILKAQ---LYQVFVRGSAIYGVTPY 68

Query:  81  ADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQ 140
            +DL++DEF   +L     + +        L  E +N+IP      FDWR +GAVT VKNQ
Sbjct:  69  SDLTTDEFARTHLTASWVVPSSRSNTPTSLGKE-VNNIPKN----FDWREKGAVTEVKNQ 123

Query:  141 GQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQP 200
            G CGSCW+FSTTGNVE Q F    KL+SLSEQ LVDCD            D+GCNGGL  
Sbjct:  124 GMCGSCWAFSTTGNVESQWFRKTGKLLSLSEQQLVDCD----------GLDDGCNGGLPS 173

Query:  201 NAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYI 260
pattern 237                                     ****
            NAY  IIK GG+  E +YPY A+   +C+  +  +       I++   + ++ET +A ++
Sbjct:  174 NAYESIIKMGGLMLEDNYPYDAK-NEKCHLKTDGVA----VYINSSVNLTQDETELAAWL 228

Query:  261 VSTGPLAIAADAVEWQFYIGGV---FDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIV 317
                 +++  +A+  QFY  G+   + I C+   LDH +L+VGY     +  KN P+WIV
Sbjct:  229 YHNSTISVGMNALLLQFYQHGISHPWWIFCSKYLLDHAVLLVGYG----VSEKNEPFWIV 284

Query:  318 KNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 351
            KNSWG +WGE GY  + RG  +CG++   ++++I
Sbjct:  285 KNSWGVEWGENGYFRMYRGDGSCGINTVATSAMI 318


>sp|P35591|CYS1_LEIPI CYSTEINE PROTEINASE 1 PRECURSOR (AMASTIGOTE CYSTEINE PROTEINASE A-1)
          Length = 354

 Score =  233 bits (589), Expect = 3e-61
 Identities = 144/355 (40%), Positives = 192/355 (53%), Gaps = 40/355 (11%)

Query:  5   LLFVLAVFTVFVSSRGI-------PPEEQ----SQFLEFQDKFNKKYSHE-EYLERFEIF 52
            LLF + V  +FV   G        PP +     + +  F+ +  K +  + E   RF  F
Sbjct:  7   LLFAIVVTILFVVCYGSALIAQTPPPVDNFVASAHYGSFKKRHGKAFGGDAEEGHRFNAF 66

Query:  53  KSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDD 112
            K N+     LN    +   D      KFADL+  EF   YLN           + D+ +D
Sbjct:  67  KQNMQTAYFLNTQNPHAHYDVS---GKFADLTPQEFAKLYLNPDYYA----RHLKDHKED 119

Query:  113 EFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQ 172
              ++   P    + DWR +GAVTPVKNQG CGSCW+FS  GN+EGQ   S + LVSLSEQ
Sbjct:  120 VHVDDSAPSGVMSVDWRDKGAVTPVKNQGLCGSCWAFSAIGNIEGQWAASGHSLVSLSEQ 179

Query:  173 NLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIK--NGGIQTESSYPYTAETGTQCNF 230
             LV CD+           DEGCNGGL   A N+I++  NG + TE+SYPYT+  GT+   
Sbjct:  180 MLVSCDN----------IDEGCNGGLMDQAMNWIMQSHNGSVFTEASYPYTSGGGTRPPC 229

Query:  231 NSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPN 290
pattern 237       ****
            +      E  AKI+ F  +P +E  +A ++   GP+A+A DA  WQ Y GGV  + C   
Sbjct:  230 HDEG---EVGAKITGFLSLPHDEERIAEWVEKRGPVAVAVDATTWQLYFGGVVSL-CLAW 285

Query:  291 SLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNF 345
            SL+HG+LIVG++ KN       PYWIVKNSWG+ WGE+GYI L  G N C + N+
Sbjct:  286 SLNHGVLIVGFN-KNA----KPPYWIVKNSWGSSWGEKGYIRLAMGSNQCMLKNY 335


>sp|P25775|LCPA_LEIME CYSTEINE PROTEINASE A PRECURSOR
          Length = 354

 Score =  231 bits (584), Expect = 1e-60
 Identities = 143/355 (40%), Positives = 192/355 (53%), Gaps = 40/355 (11%)

Query:  5   LLFVLAVFTVFVSSRGI-------PPEEQ----SQFLEFQDKFNKKYSHE-EYLERFEIF 52
            LLF + V  +FV   G        PP +     + +  F+ +  K +  + E   RF  F
Sbjct:  7   LLFAIVVTILFVVCYGSALIAQTPPPVDNFVASAHYGSFKKRHGKAFGGDAEEGHRFNAF 66

Query:  53  KSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDD 112
            K N+     LN    +   D      KFADL+  EF   YLN           + ++ +D
Sbjct:  67  KQNMQTAYFLNTQNPHAHYDVS---GKFADLTPQEFAKLYLNPDYYA----RHLKNHKED 119

Query:  113 EFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQ 172
              ++   P    + DWR +GAVTPVKNQG CGSCW+FS  GN+EGQ   S + LVSLSEQ
Sbjct:  120 VHVDDSAPSGVMSVDWRDKGAVTPVKNQGLCGSCWAFSAIGNIEGQWAASGHSLVSLSEQ 179

Query:  173 NLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIK--NGGIQTESSYPYTAETGTQCNF 230
             LV CD+           DEGCNGGL   A N+I++  NG + TE+SYPYT+  GT+   
Sbjct:  180 MLVSCDN----------IDEGCNGGLMDQAMNWIMQSHNGSVFTEASYPYTSGGGTRPPC 229

Query:  231 NSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPN 290
pattern 237       ****
            +      E  AKI+ F  +P +E  +A ++   GP+A+A DA  WQ Y GGV  + C   
Sbjct:  230 HDEG---EVGAKITGFLSLPHDEERIAEWVEKRGPVAVAVDATTWQLYFGGVVSL-CLAW 285

Query:  291 SLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNF 345
            SL+HG+LIVG++ KN       PYWIVKNSWG+ WGE+GYI L  G N C + N+
Sbjct:  286 SLNHGVLIVGFN-KNA----KPPYWIVKNSWGSSWGEKGYIRLAMGSNQCMLKNY 335


>sp|P13277|CYS1_HOMAM DIGESTIVE CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 322

 Score =  221 bits (558), Expect = 1e-57
 Identities = 132/349 (37%), Positives = 184/349 (51%), Gaps = 41/349 (11%)

Query:  1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKI 59
            MKV+ LF+  +     +           + EF+ KF +KY   EE   R  +F  NL  I
Sbjct:  1   MKVVALFLFGLALAAANP---------SWEEFKGKFGRKYVDLEEERYRLNVFLDNLQYI 51

Query:  60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
            EE N      +      +N+F+D+++++F       K+       P A      F ++  
Sbjct:  52  EEFNKKYERGEVTYNLAINQFSDMTNEKFNAVMKGYKKG----PRPAA-----VFTSTDA 102

Query:  120 PEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDH 179
              E T  DWRT+GAVTPVK+QGQCGSCW+FSTTG +EGQHF+   +LVSLSEQ LVDC  
Sbjct:  103 APESTEVDWRTKGAVTPVKDQGQCGSCWAFSTTGGIEGQHFLKTGRLVSLSEQQLVDC-- 160

Query:  180 ECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEE 239
pattern 237                                                          ***
                  G    ++GCNGG    A  Y+  NGG+ TESSYPY A   T C FNS  IG   
Sbjct:  161 -----AGGSYYNQGCNGGWVERAIMYVRDNGGVDTESSYPYEARDNT-CRFNSNTIG--- 211

Query:  240 QAKISNFTMIPK-NETVMAGYIVSTGPLAIAADAVEWQF---YIGGVFDIPCNPNSLDHG 295
pattern 240 *
             A  + +  I + +E+ +       GP+++A DA    F   Y G  ++  C+ + LDH 
Sbjct:  212 -ATCTGYVGIAQGSESALKTATRDIGPISVAIDASHRSFQSYYTGVYYEPSCSSSQLDHA 270

Query:  296 ILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVS 343
            +L VGY ++         +W+VKNSW   WGE GYI + R + N CG++
Sbjct:  271 VLAVGYGSEG-----GQDFWLVKNSWATSWGESGYIKMARNRNNNCGIA 314


>sp|P25779|CYSP_TRYCR CRUZIPAIN PRECURSOR (MAJOR CYSTEINE PROTEINASE) (CRUZAINE)
          Length = 467

 Score =  221 bits (557), Expect = 2e-57
 Identities = 134/358 (37%), Positives = 189/358 (52%), Gaps = 38/358 (10%)

Query:  3   VILLFVLAVFTVFV--SSRGIPPEEQ--SQFLEFQDKFNKKY-SHEEYLERFEIFKSNLG 57
            ++L  VL V    V  ++  +  EE   SQF EF+ K  + Y S  E   R  +F+ NL 
Sbjct:  8   LLLAAVLVVMACLVPAATASLHAEETLTSQFAEFKQKHGRVYESAAEEAFRLSVFRENLF 67

Query:  58  KIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINS 117
             +  L+  A  H     FGV  F+DL+ +EF++ Y N               +  E + +
Sbjct:  68  -LARLHAAANPHAT---FGVTPFSDLTREEFRSRYHNGAAHFAAAQERARVPVKVEVVGA 123

Query:  118 IPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDC 177
                   A DWR RGAVT VK+QGQCGSCW+FS  GNVE Q F++ + L +LSEQ LV C
Sbjct:  124 -----PAAVDWRARGAVTAVKDQGQCGSCWAFSAIGNVECQWFLAGHPLTNLSEQMLVSC 178

Query:  178 DHECMEYEGEEACDEGCNGGLQPNAYNYIIK--NGGIQTESSYPYTAETGTQ--CNFNSA 233
            D            D GC+GGL  NA+ +I++  NG + TE SYPY +  G    C  +  
Sbjct:  179 D----------KTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGH 228

Query:  234 NIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLD 293
pattern 237    ****
             +G    A I+    +P++E  +A ++   GP+A+A DA  W  Y GGV    C    LD
Sbjct:  229 TVG----ATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVM-TSCVSEQLD 283

Query:  294 HGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 351
            HG+L+VGY+    +     PYWI+KNSW   WGE+GYI + +G N C V    S++++
Sbjct:  284 HGVLLVGYNDSAAV-----PYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVV 336


>sp|P41721|CATV_NPVBM VIRAL CATHEPSIN (V-CATH)
          Length = 323

 Score =  216 bits (545), Expect = 5e-56
 Identities = 131/349 (37%), Positives = 181/349 (51%), Gaps = 32/349 (9%)

Query:  5   LLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELN 63
            +LF L V+ V  S+   P +  + F EF  +FNK YS E E L RF+IF+ NL +I    
Sbjct:  4   ILFYLFVYAVVKSAAYDPLKAPNYFEEFVHRFNKNYSSEVEKLRRFKIFQHNLNEI---- 59

Query:  64  LIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQ 123
             I  N     K+ +NKF+DLS DE    Y        T +      LD       P +  
Sbjct:  60  -INKNQNDSAKYEINKFSDLSKDETIAKYTGLSLPTQTQNFCKVILLDQP-----PGKGP 113

Query:  124 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 183
              FDWR    VT VKNQG CG+CW+F+T G++E Q  I  N+L++LSEQ ++DCD     
Sbjct:  114 LEFDWRRLNKVTSVKNQGMCGACWAFATLGSLESQFAIKHNELINLSEQQMIDCDF---- 169

Query:  184 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKI 243
pattern 237                                                      ****
                   D GCNGGL   A+  IIK GG+Q ES YPY A+    C  NS     + +   
Sbjct:  170 ------VDAGCNGGLLHTAFEAIIKMGGVQLESDYPYEAD-NNNCRMNSNKFLVQVK--- 219

Query:  244 SNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSA 303
              +  I   E  +   +   GP+ +A DA +   Y  G+    C  + L+H +L+VGY  
Sbjct:  220 DCYRYIIVYEEKLKDLLPLVGPIPMAIDAADIVNYKQGIIKY-CFDSGLNHAVLLVGYGV 278

Query:  304 KNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN-FVSTSII 351
            +N     N+PYW  KN+WG DWGE G+  +++  N CG+ N   ST++I
Sbjct:  279 EN-----NIPYWTFKNTWGTDWGEDGFFRVQQNINACGMRNELASTAVI 322


>sp|P25782|CYS2_HOMAM DIGESTIVE CYSTEINE PROTEINASE 2 PRECURSOR
          Length = 323

 Score =  215 bits (541), Expect = 1e-55
 Identities = 132/357 (36%), Positives = 189/357 (51%), Gaps = 40/357 (11%)

Query:  1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKI 59
            MKV +LF+  V     S           +  F+ K+ ++Y   EE   R  IF+ N   I
Sbjct:  1   MKVAVLFLCGVALAAASP---------SWEHFKGKYGRQYVDAEEDSYRRVIFEQNQKYI 51

Query:  60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
            EE N    N +      +NKF D++ +EF      N   I     PV+ +   +      
Sbjct:  52  EEFNKKYENGEVTFNLAMNKFGDMTLEEFNAVMKGN---IPRRSAPVSVFYPKKETGP-- 106

Query:  120 PEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDH 179
              + T  DWRT+GAVTPVK+QGQCGSCW+FSTTG++EGQHF+    L+SL+EQ LVDC  
Sbjct:  107 --QATEVDWRTKGAVTPVKDQGQCGSCWAFSTTGSLEGQHFLKTGSLISLAEQQLVDC-- 162

Query:  180 ECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEE 239
pattern 237                                                          ***
                        +GCNGG   +A++YI  N GI TE++YPY A  G+ C F+S ++    
Sbjct:  163 ------SRPYGPQGCNGGWMNDAFDYIKANNGIDTEAAYPYEARDGS-CRFDSNSVA--- 212

Query:  240 QAKISNFTMIPK-NETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIP-CNPNSLDHG 295
pattern 240 *
             A  S  T I   +ET +   +   GP+++  DA    +QFY  GV+  P C+P+ LDH 
Sbjct:  213 -ATCSGHTNIASGSETGLQQAVRDIGPISVTIDAAHSSFQFYSSGVYYEPSCSPSYLDHA 271

Query:  296 ILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTSII 351
            +L VGY ++         +W+VKNSW   WG+ GYI + R + N CG++   S  ++
Sbjct:  272 VLAVGYGSEG-----GQDFWLVKNSWATSWGDAGYIKMSRNRNNNCGIATVASYPLV 323


>sp|P41715|CATV_NPVCF VIRAL CATHEPSIN (V-CATH)
          Length = 324

 Score =  214 bits (540), Expect = 2e-55
 Identities = 130/351 (37%), Positives = 188/351 (53%), Gaps = 33/351 (9%)

Query:  1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKI 59
            M  I+L++L    V  ++  +  +  + F +F  KFNK YS E E L RF+IF+ NL +I
Sbjct:  1   MNKIVLYLLVYGAVQCAAYDVL-KAPNYFEDFLHKFNKSYSSESEKLRRFQIFRHNLEEI 59

Query:  60  EELNLIAINHKADT-KFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSI 118
                 I  NH   T ++ +NKFADLS DE  + Y      + T +      LD       
Sbjct:  60  -----INKNHNDSTAQYEINKFADLSKDETISKYTGLSLPLQTQNFCEVVVLDRP----- 109

Query:  119 PPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCD 178
            P +    FDWR    VT VKNQG CG+CW+F+T G++E Q  I  N+ ++LSEQ L+DCD
Sbjct:  110 PDKGPLEFDWRRLNKVTSVKNQGMCGACWAFATLGSLESQFAIKHNQFINLSEQQLIDCD 169

Query:  179 HECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPE 238
pattern 237                                                           **
                        D GC+GGL   A+  ++  GGIQ ES YPY A  G  C  N+A    +
Sbjct:  170 F----------VDAGCDGGLLHTAFEAVMNMGGIQAESDYPYEANNG-DCRANAAKFVVK 218

Query:  239 EQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILI 298
pattern 239 **
             +      T+    E  +   + S GP+ +A DA +   Y  G+    C  + L+H +L+
Sbjct:  219 VKKCYRYITVF---EEKLKDLLRSVGPIPVAIDASDIVNYKRGIMKY-CANHGLNHAVLL 274

Query:  299 VGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTS 349
            VGY+ +N      +P+WI+KN+WGADWGEQGY  +++  N CG+ N + +S
Sbjct:  275 VGYAVEN-----GVPFWILKNTWGADWGEQGYFRVQQNINACGIQNELPSS 320


>sp|P25784|CYS3_HOMAM DIGESTIVE CYSTEINE PROTEINASE 3 PRECURSOR
          Length = 321

 Score =  214 bits (539), Expect = 2e-55
 Identities = 125/326 (38%), Positives = 184/326 (56%), Gaps = 47/326 (14%)

Query:  32  FQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEF-- 88
            F+ ++ +KY   +E L R  +F+ N   IE+ N    N +   K  +N+F D++++EF  
Sbjct:  23  FKTQYGRKYGDAKEELYRQRVFQQNEQLIEDFNKKFENGEVTFKVAMNQFGDMTNEEFNA 82

Query:  89  --KNYYLNNK---EAIFTDDL-PVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQ 142
              K Y   ++   +A+FT +  P+A                   DWRT+  VTPVK+Q Q
Sbjct:  83  VMKGYKKGSRGEPKAVFTAEAGPMA----------------ADVDWRTKALVTPVKDQEQ 126

Query:  143 CGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNA 202
            CGSCW+FS TG +EGQHF+  ++LVSLSEQ LVDC          +  ++GC GG   +A
Sbjct:  127 CGSCWAFSATGALEGQHFLKNDELVSLSEQQLVDC--------STDYGNDGCGGGWMTSA 178

Query:  203 YNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVS 262
pattern 237                                   ****
            ++YI  NGGI TESSYPY AE    C F++ +IG    A  +    +   E  +   +  
Sbjct:  179 FDYIKDNGGIDTESSYPYEAE-DRSCRFDANSIG----AICTGSVEVQHTEEALQEAVSG 233

Query:  263 TGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKN 319
             GP+++A DA    +QFY  GV ++  C+P  LDHG+L VGY  ++T       YW+VKN
Sbjct:  234 VGPISVAIDASHFSFQFYSSGVYYEQNCSPTFLDHGVLAVGYGTEST-----KDYWLVKN 288

Query:  320 SWGADWGEQGYIYLRRGK-NTCGVSN 344
            SWG+ WG+ GYI + R + N CG+++
Sbjct:  289 SWGSSWGDAGYIKMSRNRDNNCGIAS 314


>sp|P07154|CATL_RAT CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTEIN) (MEP) (CYCLIC
            PROTEIN-2) (CP-2)
          Length = 334

 Score =  212 bits (535), Expect = 7e-55
 Identities = 127/359 (35%), Positives = 195/359 (53%), Gaps = 39/359 (10%)

Query:  3   VILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEEL 62
            ++LL VL + T   + +       +Q+ +++    + Y   E   R  +++ N+  I+  
Sbjct:  4   LLLLAVLCLGTALATPK-FDQTFNAQWHQWKSTHRRLYGTNEEEWRRAVWEKNMRMIQLH 62

Query:  63  NLIAINHKADTKFGVNKFADLSSDEFKN------YYLNNKEAIFTDDLPVADYLDDEFIN 116
            N    N K      +N F D++++EF+       +  + K  +F + L +          
Sbjct:  63  NGEYSNGKHGFTMEMNAFGDMTNEEFRQIVNGYRHQKHKKGRLFQEPLML---------- 112

Query:  117 SIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVD 176
             IP       DWR +G VTPVKNQGQCGSCW+FS +G +EGQ F+   KL+SLSEQNLVD
Sbjct:  113 QIPK----TVDWREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLISLSEQNLVD 168

Query:  177 CDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG 236
            C H+    +G    ++GCNGGL   A+ YI +NGG+ +E SYPY A+ G+ C + +    
Sbjct:  169 CSHD----QG----NQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGS-CKYRA---- 215

Query:  237 PEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIP-CNPNSLD 293
pattern 237 ****
                A  + F  IP+ E  +   + + GP+++A DA     QFY  G++  P C+   LD
Sbjct:  216 EYAVANDTGFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCSSKDLD 275

Query:  294 HGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT-CGVSNFVSTSII 351
            HG+L+VGY  + T   K+  YW+VKNSWG +WG  GYI + + +N  CG++   S  I+
Sbjct:  276 HGVLVVGYGYEGTDSNKD-KYWLVKNSWGKEWGMDGYIKIAKDRNNHCGLATAASYPIV 333


>sp|P06797|CATL_MOUSE CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTEIN) (MEP)
          Length = 334

 Score =  212 bits (533), Expect = 1e-54
 Identities = 126/359 (35%), Positives = 198/359 (55%), Gaps = 39/359 (10%)

Query:  3   VILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEEL 62
            ++LL VL + T   + +       +++ +++    + Y   E   R  I++ N+  I+  
Sbjct:  4   LLLLAVLCLGTALATPK-FDQTFSAEWHQWKSTHRRLYGTNEEEWRRAIWEKNMRMIQLH 62

Query:  63  NLIAINHKADTKFGVNKFADLSSDEFKN------YYLNNKEAIFTDDLPVADYLDDEFIN 116
            N    N +      +N F D++++EF+       +  + K  +F + L +          
Sbjct:  63  NGEYSNGQHGFSMEMNAFGDMTNEEFRQVVNGYRHQKHKKGRLFQEPLML---------- 112

Query:  117 SIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVD 176
             IP     + DWR +G VTPVKNQGQCGSCW+FS +G +EGQ F+   KL+SLSEQNLVD
Sbjct:  113 KIPK----SVDWREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLISLSEQNLVD 168

Query:  177 CDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG 236
            C H     +G    ++GCNGGL   A+ YI +NGG+ +E SYPY A+ G+ C + +    
Sbjct:  169 CSHA----QG----NQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGS-CKYRA---- 215

Query:  237 PEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIP-CNPNSLD 293
pattern 237 ****
                A  + F  IP+ E  +   + + GP+++A DA     QFY  G++  P C+  +LD
Sbjct:  216 EFAVANDTGFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCSSKNLD 275

Query:  294 HGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTSII 351
            HG+L+VGY  + T   KN  YW+VKNSWG++WG +GYI + + + N CG++   S  ++
Sbjct:  276 HGVLLVGYGYEGTDSNKN-KYWLVKNSWGSEWGMEGYIKIAKDRDNHCGLATAASYPVV 333


>sp|P12412|CYSP_VIGMU VIGNAIN PRECURSOR (BEAN ENDOPEPTIDASE) (CYSTEINE PROTEINASE)
            (SULFHYDRYL-ENDOPEPTIDASE) (SH-EP)
          Length = 362

 Score =  209 bits (526), Expect = 8e-54
 Identities = 127/313 (40%), Positives = 179/313 (56%), Gaps = 35/313 (11%)

Query:  47  ERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNK---EAIFTDD 103
            +RF +FK+N+  +   N +   +K      +NKFAD+++ EF++ Y  +K     +F   
Sbjct:  58  KRFNVFKANVMHVHNTNKMDKPYKLK----LNKFADMTNHEFRSTYAGSKVNHHKMFRGS 113

Query:  104 LPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQ 163
               +     E + S+P     + DWR +GAVT VK+QGQCGSCW+FST   VEG + I  
Sbjct:  114 QHGSGTFMYEKVGSVP----ASVDWRKKGAVTDVKDQGQCGSCWAFSTIVAVEGINQIKT 169

Query:  164 NKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAE 223
            NKLVSLSEQ LVDCD E          ++GCNGGL  +A+ +I + GGI TES+YPYTA+
Sbjct:  170 NKLVSLSEQELVDCDKE---------ENQGCNGGLMESAFEFIKQKGGITTESNYPYTAQ 220

Query:  224 TGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGG 281
pattern 237              ****
             GT C+ +  N   +    I     +P N+       V+  P+++A DA   ++QFY  G
Sbjct:  221 EGT-CDESKVN---DLAVSIDGHENVPVNDENALLKAVANQPVSVAIDAGGSDFQFYSEG 276

Query:  282 VFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG----K 337
            VF   CN   L+HG+ IVGY    T+   N  YWIV+NSWG +WGEQGYI ++R     +
Sbjct:  277 VFTGDCN-TDLNHGVAIVGYG--TTVDGTN--YWIVRNSWGPEWGEQGYIRMQRNISKKE 331

Query:  338 NTCGVSNFVSTSI 350
              CG++   S  I
Sbjct:  332 GLCGIAMMASYPI 344


>sp|P25783|CATV_NPVAC VIRAL CATHEPSIN (V-CATH)
          Length = 323

 Score =  209 bits (526), Expect = 8e-54
 Identities = 129/349 (36%), Positives = 179/349 (50%), Gaps = 32/349 (9%)

Query:  5   LLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELN 63
            +LF L V+ V  S+     +  + F EF  +FNK Y  E E L RF+IF+ NL +I    
Sbjct:  4   ILFYLFVYGVVNSAAYDLLKAPNYFEEFVHRFNKDYGSEVEKLRRFKIFQHNLNEI---- 59

Query:  64  LIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQ 123
             I  N     K+ +NKF+DLS DE    Y      I T +      LD       P +  
Sbjct:  60  -INKNQNDSAKYEINKFSDLSKDETIAKYTGLSLPIQTQNFCKVIVLDQP-----PGKGP 113

Query:  124 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 183
              FDWR    VT VKNQG CG+CW+F+T  ++E Q  I  N+L++LSEQ ++DCD     
Sbjct:  114 LEFDWRRLNKVTSVKNQGMCGACWAFATLASLESQFAIKHNQLINLSEQQMIDCDF---- 169

Query:  184 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKI 243
pattern 237                                                      ****
                   D GCNGGL   A+  IIK GG+Q ES YPY A+    C  NS     + +   
Sbjct:  170 ------VDAGCNGGLLHTAFEAIIKMGGVQLESDYPYEAD-NNNCRMNSNKFLVQVK--- 219

Query:  244 SNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSA 303
              +  I   E  +   +   GP+ +A DA +   Y  G+    C  + L+H +L+VGY  
Sbjct:  220 DCYRYITVYEEKLKDLLRLVGPIPMAIDAADIVNYKQGIIKY-CFNSGLNHAVLLVGYGV 278

Query:  304 KNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN-FVSTSII 351
            +N     N+PYW  KN+WG DWGE G+  +++  N CG+ N   ST++I
Sbjct:  279 EN-----NIPYWTFKNTWGTDWGEDGFFRVQQNINACGMRNELASTAVI 322


>sp|P25975|CATL_BOVIN CATHEPSIN L PRECURSOR
          Length = 334

 Score =  208 bits (525), Expect = 1e-53
 Identities = 126/351 (35%), Positives = 184/351 (51%), Gaps = 35/351 (9%)

Query:  7   FVLAVFTVFVSSRG--IPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNL 64
            F L V  + V+S    + P   + + +++    + Y   E   R  +++ N   I+  N 
Sbjct:  5   FFLTVLCLGVASAAPKLDPNLDAHWHQWKATHRRLYGMNEEEWRRAVWEKNKKIIDLHNQ 64

Query:  65  IAINHKADTKFGVNKFADLSSDEFK---NYYLNNKEAIFTDDLPVADYLDDEFINSIPPE 121
                 K   +  +N F D++++EF+   N + N K               +  +  +P  
Sbjct:  65  EYSEGKHAFRMAMNAFGDMTNEEFRQVMNGFQNQKHK-------KGKLFHEPLLVDVPK- 116

Query:  122 EQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHEC 181
               + DW  +G VTPVKNQGQCGSCW+FS TG +EGQ F    KLVSLSEQNLVDC    
Sbjct:  117 ---SVDWTKKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRA- 172

Query:  182 MEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPE-EQ 240
pattern 237                                                        ** **
               +G    ++GCNGGL  NA+ YI  NGG+ +E SYPY A     CN+      PE   
Sbjct:  173 ---QG----NQGCNGGLMDNAFQYIKDNGGLDSEESYPYLATDTNSCNYK-----PECSA 220

Query:  241 AKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGIL 297
            A  + F  IP+ E  +   + + GP+++A DA    +QFY  G+ +D  C+   LDHG+L
Sbjct:  221 ANDTGFVDIPQREKALMKAVATVGPISVAIDAGHTSFQFYKSGIYYDPDCSCKDLDHGVL 280

Query:  298 IVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT-CGVSNFVS 347
            +VGY  + T    N  +WIVKNSWG +WG  GY+ + + +N  CG++   S
Sbjct:  281 VVGYGFEGTDSNNN-KFWIVKNSWGPEWGWNGYVKMAKDQNNHCGIATAAS 330


>sp|Q40143|CYS3_LYCES CYSTEINE PROTEINASE 3 PRECURSOR
          Length = 356

 Score =  207 bits (522), Expect = 2e-53
 Identities = 129/331 (38%), Positives = 181/331 (53%), Gaps = 40/331 (12%)

Query:  29  FLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE 87
            F  F  +  K+Y S EE  +RFEIF  NL  I   N   +++K     G+N+F DL+ DE
Sbjct:  57  FARFAIRHRKRYDSVEEIKQRFEIFLDNLKMIRSHNRKGLSYK----LGINEFTDLTWDE 112

Query:  88  FKNYYLN---NKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCG 144
            F+ + L    N  A    +L +         N + PE +   DWR  G V+PVK QG+CG
Sbjct:  113 FRKHKLGASQNCSATTKGNLKLT--------NVVLPETK---DWRKDGIVSPVKAQGKCG 161

Query:  145 SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYN 204
            SCW+FSTTG +E  +  +  K +SLSEQ LVDC      +        GCNGGL   A+ 
Sbjct:  162 SCWTFSTTGALEAAYAQAFGKGISLSEQQLVDCAGAFNNF--------GCNGGLPSQAFE 213

Query:  205 YIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTG 264
pattern 237                                 ****
            YI  NGG+ TE +YPYT + G  C F+ ANIG +  + + N T+  + E   A  +V   
Sbjct:  214 YIKFNGGLDTEEAYPYTGKNGI-CKFSQANIGVKVISSV-NITLGAEYELKYAVALVR-- 269

Query:  265 PLAIAADAVE-WQFYIGGVF---DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNS 320
            P+++A + V+ ++ Y  GV+   +    P  ++H +L VGY  +N       PYW++KNS
Sbjct:  270 PVSVAFEVVKGFKQYKSGVYASTECGDTPMDVNHAVLAVGYGVEN-----GTPYWLIKNS 324

Query:  321 WGADWGEQGYIYLRRGKNTCGVSNFVSTSII 351
            WGADWGE GY  +  GKN CGV+   S  I+
Sbjct:  325 WGADWGEDGYFKMEMGKNMCGVATCASYPIV 355


>sp|Q05094|CYS2_LEIPI CYSTEINE PROTEINASE 2 PRECURSOR (AMASTIGOTE CYSTEINE PROTEINASE A-2)
          Length = 444

 Score =  207 bits (521), Expect = 3e-53
 Identities = 122/327 (37%), Positives = 177/327 (53%), Gaps = 39/327 (11%)

Query:  29  FLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKA---DTKFGVNKFADLS 84
            F EF+  + + Y    E  +R   F+ NL  + E       H+A     +FG+ KF DLS
Sbjct:  38  FEEFKRTYGRAYETLAEEQQRLANFERNLELMRE-------HQARNPHAQFGITKFFDLS 90

Query:  85  SDEFKNYYLNNKEAIFTDDLPVADYLDDEF--INSIPPEEQTAFDWRTRGAVTPVKNQGQ 142
              EF   YLN            A +       ++++P     A DWR +GAVTPVK+QG 
Sbjct:  91  EAEFAARYLNGAAYFAAAKRHAAQHYRKARADLSAVPD----AVDWREKGAVTPVKDQGA 146

Query:  143 CGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNA 202
            CGSCW+FS  GN+EGQ +++ ++LVSLSEQ LV CD            ++GC+GGL   A
Sbjct:  147 CGSCWAFSAVGNIEGQWYLAGHELVSLSEQQLVSCDD----------MNDGCDGGLMLQA 196

Query:  203 YNYIIK--NGGIQTESSYPYTAETG--TQCNFNSANIGPEEQAKISNFTMIPKNETVMAG 258
pattern 237                                       ****
            ++++++  NG + TE SYPY +  G   +C+ +S  +     A+I    +I  +E  MA 
Sbjct:  197 FDWLLQNTNGHLHTEDSYPYVSGNGYVPECSNSSEEL--VVGAQIDGHVLIGSSEKAMAA 254

Query:  259 YIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVK 318
            ++   GP+AIA DA  +  Y  GV    C    L+HG+L+VGY     +     PYW++K
Sbjct:  255 WLAKNGPIAIALDASSFMSYKSGVL-TACIGKQLNHGVLLVGYDMTGEV-----PYWVIK 308

Query:  319 NSWGADWGEQGYIYLRRGKNTCGVSNF 345
            NSWG DWGEQGY+ +  G N C +S +
Sbjct:  309 NSWGGDWGEQGYVRVVMGVNACLLSEY 335


>sp|P36400|LCPB_LEIME CYSTEINE PROTEINASE B PRECURSOR
          Length = 443

 Score =  206 bits (520), Expect = 4e-53
 Identities = 122/327 (37%), Positives = 177/327 (53%), Gaps = 40/327 (12%)

Query:  29  FLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKA---DTKFGVNKFADLS 84
            F EF+  + + Y    E  +R   F+ NL  + E       H+A     +FG+ KF DLS
Sbjct:  38  FEEFKRTYGRAYETLAEEQQRLANFERNLELMRE-------HQARNPHAQFGITKFFDLS 90

Query:  85  SDEFKNYYLNNKEAIFTDDLPVADYLDDEF--INSIPPEEQTAFDWRTRGAVTPVKNQGQ 142
              EF   YLN            A +       ++++P     A DWR +GAVTPVK+QG 
Sbjct:  91  EAEFAARYLNGAAYFAAAKRHAAQHYRKARADLSAVPD----AVDWREKGAVTPVKDQGA 146

Query:  143 CGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNA 202
            CGSCW+FS  GN+EGQ +++ ++LVSLSEQ LV CD            ++GC+GGL   A
Sbjct:  147 CGSCWAFSAVGNIEGQWYLAGHELVSLSEQQLVSCDD----------MNDGCDGGLMLQA 196

Query:  203 YNYIIK--NGGIQTESSYPYTAETG--TQCNFNSANIGPEEQAKISNFTMIPKNETVMAG 258
pattern 237                                       ****
            ++++++  NG + TE SYPY +  G   +C+ +S  +     A+I    +I  +E  MA 
Sbjct:  197 FDWLLQNTNGHLHTEDSYPYVSGNGYVPECSNSSELV---VGAQIDGHVLIGSSEKAMAA 253

Query:  259 YIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVK 318
            ++   GP+AIA DA  +  Y  GV    C    L+HG+L+VGY     +     PYW++K
Sbjct:  254 WLAKNGPIAIALDASSFMSYKSGVL-TACIGKQLNHGVLLVGYDMTGEV-----PYWVIK 307

Query:  319 NSWGADWGEQGYIYLRRGKNTCGVSNF 345
            NSWG DWGEQGY+ +  G N C +S +
Sbjct:  308 NSWGGDWGEQGYVRVVMGVNACLLSEY 334


>sp|P07711|CATL_HUMAN CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTEIN) (MEP)
          Length = 333

 Score =  206 bits (520), Expect = 4e-53
 Identities = 125/349 (35%), Positives = 187/349 (52%), Gaps = 34/349 (9%)

Query:  8   VLAVFTVFVSSRGIPPEE--QSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLI 65
            +LA F + ++S  +  +   ++Q+ +++   N+ Y   E   R  +++ N+  IE  N  
Sbjct:  6   ILAAFCLGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQE 65

Query:  66  AINHKADTKFGVNKFADLSSDEFK---NYYLNNKEAIFTDDLPVADYLDDEFINSIPPEE 122
                K      +N F D++S+EF+   N + N K                 F   +  E 
Sbjct:  66  YREGKHSFTMAMNAFGDMTSEEFRQVMNGFQNRKPR-----------KGKVFQEPLFYEA 114

Query:  123 QTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECM 182
              + DWR +G VTPVKNQGQCGSCW+FS TG +EGQ F    +L+SLSEQNLVDC     
Sbjct:  115 PRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDC----- 169

Query:  183 EYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAK 242
pattern 237                                                       ****
               G +  +EGCNGGL   A+ Y+  NGG+ +E SYPY A T   C +N         A 
Sbjct:  170 --SGPQG-NEGCNGGLMDYAFQYVQDNGGLDSEESYPYEA-TEESCKYNP----KYSVAN 221

Query:  243 ISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIV 299
             + F  IPK E  +   + + GP+++A DA    + FY  G+ F+  C+   +DHG+L+V
Sbjct:  222 DTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVV 281

Query:  300 GYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG-KNTCGVSNFVS 347
            GY  ++T    N  YW+VKNSWG +WG  GY+ + +  +N CG+++  S
Sbjct:  282 GYGFEST-ESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAAS 329


>sp|Q28944|CATL_PIG CATHEPSIN L PRECURSOR
          Length = 334

 Score =  206 bits (519), Expect = 5e-53
 Identities = 121/316 (38%), Positives = 167/316 (52%), Gaps = 33/316 (10%)

Query:  40  YSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFK---NYYLNNK 96
            Y   E   R  +++ N+  IE  N      K      +N F D++++EF+   N + N K
Sbjct:  40  YGMNEEGWRRAVWEKNMKMIELHNQEYSQGKHGFSMAMNAFGDMTNEEFRQVMNGFQNQK 99

Query:  97  EAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVE 156
                             F  S+  E   + DWR +G VT VKNQGQCGSCW+FS TG +E
Sbjct:  100 HK-----------KGKVFHESLVLEVPKSVDWREKGYVTAVKNQGQCGSCWAFSATGALE 148

Query:  157 GQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTES 216
            GQ F    KLVSLSEQNLVDC       +G    ++GCNGGL  NA+ Y+  NGG+ TE 
Sbjct:  149 GQMFRKTGKLVSLSEQNLVDCSRP----QG----NQGCNGGLMDNAFQYVKDNGGLDTEE 200

Query:  217 SYPYTAETGTQCNFNSANIGPE-EQAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--V 273
pattern 237                     ** **
            SYPY       C +      PE   A  + F  IP+ E  +   + + GP+++A DA   
Sbjct:  201 SYPYLGRETNSCTYK-----PECSAANDTGFVDIPQREKALMKAVATVGPISVAIDAGHS 255

Query:  274 EWQFYIGGV-FDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIY 332
             +QFY  G+ +D  C+   LDHG+L+VGY  + T    +  +WIVKNSWG +WG  GY+ 
Sbjct:  256 SFQFYKSGIYYDPDCSSKDLDHGVLVVGYGFEGT-DSNSSKFWIVKNSWGPEWGWNGYVK 314

Query:  333 LRRGKNT-CGVSNFVS 347
            + + +N  CG+S   S
Sbjct:  315 MAKDQNNHCGISTAAS 330


>sp|P00785|ACTN_ACTCH ACTINIDAIN PRECURSOR (ACTINIDIN)
          Length = 380

 Score =  204 bits (513), Expect = 3e-52
 Identities = 124/334 (37%), Positives = 178/334 (53%), Gaps = 41/334 (12%)

Query:  24  EEQSQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADT----KFGVN 78
            E ++ +  +  K+ K Y S  E+  RFEIFK  L  I+E       H ADT    K G+N
Sbjct:  37  EVKAMYESWLIKYGKSYNSLGEWERRFEIFKETLRFIDE-------HNADTNRSYKVGLN 89

Query:  79  KFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVK 138
            +FADL+ +EF++ YL       ++   V++  +  F   +P    +  DWR+ GAV  +K
Sbjct:  90  QFADLTDEEFRSTYLGFTSG--SNKTKVSNRYEPRFGQVLP----SYVDWRSAGAVVDIK 143

Query:  139 NQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGL 198
            +QG+CG CW+FS    VEG + I    L+SLSEQ L+DC        G      GCNGG 
Sbjct:  144 SQGECGGCWAFSAIATVEGINKIVTGVLISLSEQELIDC--------GRTQNTRGCNGGY 195

Query:  199 QPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAG 258
pattern 237                                       ****
              + + +II NGGI TE +YPYTA+ G +CN +  N   E+   I  +  +P N      
Sbjct:  196 ITDGFQFIINNGGINTEENYPYTAQDG-ECNLDLQN---EKYVTIDTYENVPYNNEWALQ 251

Query:  259 YIVSTGPLAIAADAV--EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWI 316
              V+  P+++A DA    ++ Y  G+F  PC   ++DH + IVGY  +  I      YWI
Sbjct:  252 TAVTYQPVSVALDAAGDAFKHYSSGIFTGPCG-TAIDHAVTIVGYGTEGGI-----DYWI 305

Query:  317 VKNSWGADWGEQGYIYLRR---GKNTCGVSNFVS 347
            VKNSW   WGE+GY+ + R   G  TCG++   S
Sbjct:  306 VKNSWDTTWGEEGYMRILRNVGGAGTCGIATMPS 339


>sp|P25803|CYSP_PHAVU VIGNAIN PRECURSOR (BEAN ENDOPEPTIDASE) (CYSTEINE PROTEINASE EP-C1)
          Length = 362

 Score =  203 bits (510), Expect = 6e-52
 Identities = 125/313 (39%), Positives = 177/313 (55%), Gaps = 35/313 (11%)

Query:  47  ERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNK---EAIFTDD 103
            +RF +FK+NL  +   N +   +K      +NKFAD+++ EF++ Y  +K     +F   
Sbjct:  58  KRFNVFKANLMHVHNTNKMDKPYKLK----LNKFADMTNHEFRSTYAGSKVNHPRMFRGT 113

Query:  104 LPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQ 163
                     E + S+PP    + DWR +GAVT VK+QGQCGSCW+FST   VEG + I  
Sbjct:  114 PHENGAFMYEKVVSVPP----SVDWRKKGAVTDVKDQGQCGSCWAFSTVVAVEGINQIKT 169

Query:  164 NKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAE 223
            NKLV+LSEQ LVDCD E          ++GCNGGL  +A+ +I + GGI TES+YPY A+
Sbjct:  170 NKLVALSEQELVDCDKE---------ENQGCNGGLMESAFEFIKQKGGITTESNYPYKAQ 220

Query:  224 TGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGG 281
pattern 237              ****
             GT C+ +  N   +    I     +P N+       V+  P+++A DA   ++QFY  G
Sbjct:  221 EGT-CDASKVN---DLAVSIDGHENVPANDEDALLKAVANQPVSVAIDAGGSDFQFYSEG 276

Query:  282 VFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG----K 337
            VF   C+   L+HG+ IVGY    T+   N  YWIV+NSWG +WGE GYI ++R     +
Sbjct:  277 VFTGDCS-TDLNHGVAIVGYG--TTVDGTN--YWIVRNSWGPEWGEHGYIRMQRNISKKE 331

Query:  338 NTCGVSNFVSTSI 350
              CG++   S  I
Sbjct:  332 GLCGIAMLPSYPI 344


>sp|Q10991|CATL_SHEEP CATHEPSIN L
          Length = 217

 Score =  201 bits (507), Expect = 1e-51
 Identities = 105/226 (46%), Positives = 139/226 (61%), Gaps = 23/226 (10%)

Query:  127 DWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEG 186
            DW  +G VTPVKNQGQCGSCW+FS TG +EGQ F    KLVSLSEQNLVD          
Sbjct:  6   DWTKKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGKLVSLSEQNLVD--------SS 57

Query:  187 EEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPE-EQAKISN 245
pattern 237                                                   ** **
                ++GCNGGL  NA+ YI +NGG+ +E SYPY A T T CN+      PE   AK + 
Sbjct:  58  RPQGNQGCNGGLMDNAFQYIKENGGLDSEESYPYEA-TDTSCNYK-----PEYSAAKDTG 111

Query:  246 FTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIVGYS 302
            F  IP+ E  +   + + GP+++A DA    +QFY  G+ +D  C+   LDHG+L+VGY 
Sbjct:  112 FVDIPQREKALMKAVATVGPISVAIDAGHSSFQFYKSGIYYDPDCSSKDLDHGVLVVGYG 171

Query:  303 AKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT-CGVSNFVS 347
             + T    N  +WIVKNSWG +WG +GY+ + + +N  CG++   S
Sbjct:  172 FEGT----NNKFWIVKNSWGPEWGNKGYVKMAKDQNNHCGIATAAS 213


>sp|P43156|CYSP_HEMSP THIOL PROTEASE SEN102 PRECURSOR
          Length = 360

 Score =  201 bits (506), Expect = 2e-51
 Identities = 121/307 (39%), Positives = 161/307 (52%), Gaps = 28/307 (9%)

Query:  43  EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTD 102
            +E   RF +FK N+  I E N       A  K  +NKF D+++ EF++ Y  +K      
Sbjct:  54  DEKNRRFNVFKENVKFIHEFNQ---KKDAPYKLALNKFGDMTNQEFRSKYAGSKIQHHRS 110

Query:  103 DLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFIS 162
               +          ++      + DWR +GAVT VK+QGQCGSCW+FST  +VEG + I 
Sbjct:  111 QRGIQKNTGSFMYENVGSLPAASIDWRAKGAVTGVKDQGQCGSCWAFSTIASVEGINQIK 170

Query:  163 QNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTA 222
              +LVSLSEQ LVDCD          + +EGCNGGL   A+ +I KN GI TE SYPY  
Sbjct:  171 TGELVSLSEQELVDCD---------TSYNEGCNGGLMDYAFEFIQKN-GITTEDSYPYAE 220

Query:  223 ETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIG 280
pattern 237               ****
            + GT C  N  N        I     +P N        V+  P++++ +A    +QFY  
Sbjct:  221 QDGT-CASNLLN---SPVVSIDGHQDVPANNENALMQAVANQPISVSIEASGYGFQFYSE 276

Query:  281 GVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG---- 336
            GVF   C    LDHG+ IVGY A     R    YWIVKNSWG +WGE GYI ++RG    
Sbjct:  277 GVFTGRCG-TELDHGVAIVGYGAT----RDGTKYWIVKNSWGEEWGESGYIRMQRGISDK 331

Query:  337 KNTCGVS 343
            +  CG++
Sbjct:  332 RGKCGIA 338


>sp|P54639|CYS4_DICDI CYSTEINE PROTEINASE 4 PRECURSOR
          Length = 442

 Score =  200 bits (504), Expect = 3e-51
 Identities = 117/308 (37%), Positives = 169/308 (53%), Gaps = 32/308 (10%)

Query:  4   ILLFVLAVFTVFVSSRGIPPEEQ--SQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEE 61
            +L F+  +   + S++    E Q  + F  +     + YS EE+  R++IFKSN+  + +
Sbjct:  3   VLSFLCLLLVSYASAKQQFSELQYRNAFTNWMQAHQRTYSSEEFNARYQIFKSNMDYVHQ 62

Query:  62  LNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPE 121
             N    +   +T  G+N FAD+++ E++  YL      F     +    ++E I S P  
Sbjct:  63  WN----SKGGETVLGLNVFADITNQEYRTTYLGTP---FDGSALIGT--EEEKIFSTPAP 113

Query:  122 EQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFI---SQNKLVSLSEQNLVDCD 178
                 DWR +GAVTP+KNQGQCG CWSFSTTG+ EG HFI   ++  LVSLSEQNL+DC 
Sbjct:  114 ---TVDWRAQGAVTPIKNQGQCGGCWSFSTTGSTEGAHFIASGTKKDLVSLSEQNLIDC- 169

Query:  179 HECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPE 238
pattern 237                                                           **
                    +   + GC GGL    + YII N GI TESSYPYTAE G +C F ++NIG  
Sbjct:  170 -------SKSYGNNGCEGGLMTLGFEYIINNKGIDTESSYPYTAEDGKECKFKTSNIG-- 220

Query:  239 EQAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIP-CNPNSLDHG 295
pattern 239 **
              A+I ++  +            +  P+++A DA    +Q Y  G++  P C P  LDHG
Sbjct:  221 --AQIVSYQNVTSGSEASLQSASNNAPVSVAIDASNESFQLYESGIYYEPACTPTQLDHG 278

Query:  296 ILIVGYSA 303
            +L+VGY +
Sbjct:  279 VLVVGYGS 286


 Score = 48.8 bits (114), Expect = 2e-05
 Identities = 18/35 (51%), Positives = 24/35 (68%), Gaps = 1/35 (2%)

Query: 314 YWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVS 347
           YWIVKNSWG  WG  GYI++ + + N CG++   S
Sbjct: 401 YWIVKNSWGTSWGMDGYIFMSKDRNNNCGIATMAS 435


>sp|O60911|CATM_HUMAN CATHEPSIN L2 PRECURSOR (CATHEPSIN V)
          Length = 334

 Score =  199 bits (501), Expect = 7e-51
 Identities = 127/357 (35%), Positives = 191/357 (52%), Gaps = 43/357 (12%)

Query:  5   LLFVLAVFTVFVSSRGIPPEEQS---QFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEE 61
            L  VLA F + ++S  +P  +Q+   ++ +++    + Y   E   R  +++ N+  IE 
Sbjct:  3   LSLVLAAFCLGIAS-AVPKFDQNLDTKWYQWKATHRRLYGANEEGWRRAVWEKNMKMIEL 61

Query:  62  LNLIAINHKADTKFGVNKFADLSSDEFKNY---YLNNK---EAIFTDDLPVADYLDDEFI 115
             N      K      +N F D++++EF+     + N K     +F + L    +LD    
Sbjct:  62  HNGEYSQGKHGFTMAMNAFPDMTNEEFRQMMGCFRNQKFRKGKVFREPL----FLD---- 113

Query:  116 NSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLV 175
              +P     + DWR +G VTPVKNQ QCGSCW+FS TG +EGQ F    KLVSLSEQNLV
Sbjct:  114 --LPK----SVDWRKKGYVTPVKNQKQCGSCWAFSATGALEGQMFRKTGKLVSLSEQNLV 167

Query:  176 DCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANI 235
            DC       +G    ++GCNGG    A+ Y+ +NGG+ +E SYPY A     C +   N 
Sbjct:  168 DCSRP----QG----NQGCNGGFMARAFQYVKENGGLDSEESYPYVA-VDEICKYRPEN- 217

Query:  236 GPEEQAKISNFTMI-PKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNS 291
pattern 237  ****
                 A  + FT++ P  E  +   + + GP+++A DA    +QFY  G+ F+  C+  +
Sbjct:  218 ---SVANDTGFTVVAPGKEKALMKAVATVGPISVAMDAGHSSFQFYKSGIYFEPDCSSKN 274

Query:  292 LDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT-CGVSNFVS 347
            LDHG+L+VGY  +      N  YW+VKNSWG +WG  GY+ + + KN  CG++   S
Sbjct:  275 LDHGVLVVGYGFEGA-NSNNSKYWLVKNSWGPEWGSNGYVKIAKDKNNHCGIATAAS 330


>sp|O10364|CATV_NPVOP VIRAL CATHEPSIN (V-CATH)
          Length = 324

 Score =  196 bits (494), Expect = 5e-50
 Identities = 116/322 (36%), Positives = 168/322 (52%), Gaps = 30/322 (9%)

Query:  29  FLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE 87
            F +F  KFNK YS E E L RF+IF+ NL +I   N     + +  ++ +NKF+DLS +E
Sbjct:  28  FEDFLHKFNKNYSSESEKLHRFKIFQHNLEEIINKN----QNDSTAQYEINKFSDLSKEE 83

Query:  88  FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCW 147
              + Y        T +      LD       P      FDWR    VT VKNQG CG+CW
Sbjct:  84  AISKYTGLSLPHQTQNFCEVVILDRP-----PDRGPLEFDWRQFNKVTSVKNQGVCGACW 138

Query:  148 SFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYII 207
            +F+T G++E Q  I  N+L++LSEQ  +DCD            + GC+GGL   A+   +
Sbjct:  139 AFATLGSLESQFAIKYNRLINLSEQQFIDCDR----------VNAGCDGGLLHTAFESAM 188

Query:  208 KNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLA 267
pattern 237                              ****
            + GG+Q ES YPY    G QC  N        ++      M    E  +   + + GP+ 
Sbjct:  189 EMGGVQMESDYPYETANG-QCRINPNRFVVGVRSCRRYIVMF---EEKLKDLLRAVGPIP 244

Query:  268 IAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGE 327
            +A DA +   Y  G+    C  + L+H +L+VGY+ +N     N+PYWI+KN+WG DWGE
Sbjct:  245 VAIDASDIVNYRRGIMR-QCANHGLNHAVLLVGYAVEN-----NIPYWILKNTWGTDWGE 298

Query:  328 QGYIYLRRGKNTCGVSNFVSTS 349
             GY  +++  N CG+ N + +S
Sbjct:  299 DGYFRVQQNINACGIRNELVSS 320


>sp|P25777|ORYB_ORYSA ORYZAIN BETA CHAIN PRECURSOR
          Length = 471

 Score =  196 bits (494), Expect = 5e-50
 Identities = 115/310 (37%), Positives = 166/310 (53%), Gaps = 31/310 (10%)

Query:  44  EYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDD 103
            E+  RF +F  NL  ++  N  A +     + G+N+FADL+++EF+  +L  K A     
Sbjct:  69  EHERRFLVFWDNLKFVDAHNARA-DEGGGFRLGMNRFADLTNEEFRATFLGAKVA--ERS 125

Query:  104 LPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQ 163
                +    + +  +P     + DWR +GAV PVKNQGQCGSCW+FS    VE  + +  
Sbjct:  126 RAAGERYRHDGVEELPE----SVDWREKGAVAPVKNQGQCGSCWAFSAVSTVESINQLVT 181

Query:  164 NKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAE 223
             ++++LSEQ LV+C             + GCNGGL  +A+++IIKNGGI TE  YPY A 
Sbjct:  182 GEMITLSEQELVEC--------STNGQNSGCNGGLMADAFDFIIKNGGIDTEDDYPYKAV 233

Query:  224 TGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGG 281
pattern 237              ****
             G +C+ N  N    +   I  F  +P+N+       V+  P+++A +A   E+Q Y  G
Sbjct:  234 DG-KCDINREN---AKVVSIDGFEDVPQNDEKSLQKAVAHQPVSVAIEAGGREFQLYHSG 289

Query:  282 VFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT-- 339
            VF   C   SLDHG++ VGY   N        YWIV+NSWG  WGE GY+ + R  N   
Sbjct:  290 VFSGRCG-TSLDHGVVAVGYGTDN-----GKDYWIVRNSWGPKWGESGYVRMERNINVTT 343

Query:  340 --CGVSNFVS 347
              CG++   S
Sbjct:  344 GKCGIAMMAS 353


>sp|P25776|ORYA_ORYSA ORYZAIN ALPHA CHAIN PRECURSOR
          Length = 458

 Score =  194 bits (488), Expect = 2e-49
 Identities = 124/355 (34%), Positives = 183/355 (50%), Gaps = 43/355 (12%)

Query:  3   VILLFVLAVFTVFVSSRGIPPEEQSQ--FLEFQDKFNKKYSHE-EYLERFEIFKSNLGKI 59
            ++LL  LA   + + S G   EE+++  + E++ +  K Y+   E   R+  F+ NL  I
Sbjct:  12  LLLLLSLAAADMSIVSYGERSEEEARRLYAEWKAEHGKSYNAVGEEERRYAAFRDNLRYI 71

Query:  60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLN-----NKEAIFTDDLPVADYLDDEF 114
            +E N  A       + G+N+FADL+++E+++ YL       +E   +D    AD      
Sbjct:  72  DEHNAAADAGVHSFRLGLNRFADLTNEEYRDTYLGLRNKPRRERKVSDRYLAAD------ 125

Query:  115 INSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNL 174
             N   PE   + DWRT+GAV  +K+QG CGSCW+FS    VE  + I    L+SLSEQ L
Sbjct:  126 -NEALPE---SVDWRTKGAVAEIKDQGGCGSCWAFSAIAAVEDINQIVTGDLISLSEQEL 181

Query:  175 VDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSAN 234
            VDCD          + +EGCNGGL   A+++II NGGI TE  YPY  +   +C+ N  N
Sbjct:  182 VDCD---------TSYNEGCNGGLMDYAFDFIINNGGIDTEDDYPYKGK-DERCDVNRKN 231

Query:  235 IGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNPNSL 292
pattern 237   ****
                +   I ++  +  N        V   P+++A +A    +Q Y  G+F   C   +L
Sbjct:  232 ---AKVVTIDSYEDVTPNSETSLQKAVRNQPVSVAIEAGGRAFQLYSSGIFTGKCG-TAL 287

Query:  293 DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRR----GKNTCGVS 343
            DHG+  VGY  +N        YWIV+NSWG  WGE GY+ + R        CG++
Sbjct:  288 DHGVAAVGYGTEN-----GKDYWIVRNSWGKSWGESGYVRMERNIKASSGKCGIA 337


>sp|P43297|RD21_ARATH CYSTEINE PROTEINASE RD21A PRECURSOR
          Length = 462

 Score =  193 bits (486), Expect = 4e-49
 Identities = 122/321 (38%), Positives = 168/321 (52%), Gaps = 43/321 (13%)

Query:  35  KFNKKYSHEEYLE---RFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNY 91
            K  K  S    +E   RFEIFK NL  ++E N   ++++     G+ +FADL++DE+++ 
Sbjct:  56  KHGKAQSQNSLVEKDRRFEIFKDNLRFVDEHNEKNLSYR----LGLTRFADLTNDEYRSK 111

Query:  92  YLN---NKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWS 148
            YL     K+      L     + DE   SI        DWR +GAV  VK+QG CGSCW+
Sbjct:  112 YLGAKMEKKGERRTSLRYEARVGDELPESI--------DWRKKGAVAEVKDQGGCGSCWA 163

Query:  149 FSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIK 208
            FST G VEG + I    L++LSEQ LVDCD          + +EGCNGGL   A+ +IIK
Sbjct:  164 FSTIGAVEGINQIVTGDLITLSEQELVDCD---------TSYNEGCNGGLMDYAFEFIIK 214

Query:  209 NGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAI 268
pattern 237                             ****
            NGGI T+  YPY    GT C+    N    +   I ++  +P          V+  P++I
Sbjct:  215 NGGIDTDKDYPYKGVDGT-CDQIRKN---AKVVTIDSYEDVPTYSEESLKKAVAHQPISI 270

Query:  269 AADA--VEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWG 326
            A +A    +Q Y  G+FD  C    LDHG++ VGY  +N        YWIV+NSWG  WG
Sbjct:  271 AIEAGGRAFQLYDSGIFDGSCG-TQLDHGVVAVGYGTEN-----GKDYWIVRNSWGKSWG 324

Query:  327 EQGYIYLRR----GKNTCGVS 343
            E GY+ + R        CG++
Sbjct:  325 ESGYLRMARNIASSSGKCGIA 345


>sp|Q10717|CYS2_MAIZE CYSTEINE PROTEINASE 2 PRECURSOR
          Length = 360

 Score =  193 bits (485), Expect = 5e-49
 Identities = 115/329 (34%), Positives = 172/329 (51%), Gaps = 32/329 (9%)

Query:  28  QFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSD 86
            +F  F  ++ K Y S  E  +RF IF  +L  +   N   ++++     G+N+FAD+S +
Sbjct:  58  RFARFAVRYGKSYESAAEVHKRFRIFSESLQLVRSTNRKGLSYR----LGINRFADMSWE 113

Query:  87  EFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSC 146
            EF+   L   +         A    +  + +         DWR  G V+PVKNQG CGSC
Sbjct:  114 EFRATRLGAAQNCS------ATLTGNHRMRAAAVALPETKDWREDGIVSPVKNQGHCGSC 167

Query:  147 WSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYI 206
            W+FSTTG +E  +  +  K +SLSEQ LVDC      +        GCNGGL   A+ YI
Sbjct:  168 WTFSTTGALEAAYTQATGKPISLSEQQLVDCGFAFNNF--------GCNGGLPSQAFEYI 219

Query:  207 IKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPL 266
pattern 237                               ****
              NGG+ TE SYPY    G  C F + N+G +    + N T+  ++E   A  +V   P+
Sbjct:  220 KYNGGLDTEESYPYQGVNGI-CKFKNENVGVKVLDSV-NITLGAEDELKDAVGLVR--PV 275

Query:  267 AIAADAVE-WQFYIGGVF---DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWG 322
            ++A + +  ++ Y  GV+        P  ++H +L VGY  ++      +PYW++KNSWG
Sbjct:  276 SVAFEVITGFRLYKSGVYTSDHCGTTPMDVNHAVLAVGYGVED-----GVPYWLIKNSWG 330

Query:  323 ADWGEQGYIYLRRGKNTCGVSNFVSTSII 351
            ADWG++GY  +  GKN CGV+   S  I+
Sbjct:  331 ADWGDEGYFKMEMGKNMCGVATCASYPIV 359


>sp|P14080|PAP2_CARPA CHYMOPAPAIN PRECURSOR (PAPAYA PROTEINASE II) (PPII)
          Length = 352

 Score =  192 bits (482), Expect = 1e-48
 Identities = 128/319 (40%), Positives = 169/319 (52%), Gaps = 43/319 (13%)

Query:  35  KFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKF--GVNKFADLSSDEFKNY 91
            K NK Y S +E + RFEIF+ NL  I+E N      K +  +  G+N FADLS+DEFK  
Sbjct:  54  KHNKIYESIDEKIYRFEIFRDNLMYIDETN------KKNNSYWLGLNGFADLSNDEFKKK 107

Query:  92  YLNNKEAIFTDDLPVADYLDDE-FINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFS 150
            Y+        +D    ++ D+E F          + DWR +GAVTPVKNQG CGSCW+FS
Sbjct:  108 YVG----FVAEDFTGLEHFDNEDFTYKHVTNYPQSIDWRAKGAVTPVKNQGACGSCWAFS 163

Query:  151 TTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNG 210
            T   VEG + I    L+ LSEQ LVDCD              GC GG Q  +  Y + N 
Sbjct:  164 TIATVEGINKIVTGNLLELSEQELVDCDKH----------SYGCKGGYQTTSLQY-VANN 212

Query:  211 GIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKN-ETVMAGYIVSTGPLAIA 269
pattern 237                           ****
            G+ T   YPY A+   +C    A   P  + KI+ +  +P N ET   G + +  PL++ 
Sbjct:  213 GVHTSKVYPYQAKQ-YKCR---ATDKPGPKVKITGYKRVPSNCETSFLGALANQ-PLSVL 267

Query:  270 ADA--VEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGE 327
             +A    +Q Y  GVFD PC    LDH +  VGY   +    KN  Y I+KNSWG +WGE
Sbjct:  268 VEAGGKPFQLYKSGVFDGPCG-TKLDHAVTAVGYGTSD---GKN--YIIIKNSWGPNWGE 321

Query:  328 QGYIYLRR----GKNTCGV 342
            +GY+ L+R     + TCGV
Sbjct:  322 KGYMRLKRQSGNSQGTCGV 340


>sp|P00786|CATH_RAT CATHEPSIN H PRECURSOR (CATHEPSIN B3) (CATHEPSIN BA)
          Length = 333

 Score =  192 bits (482), Expect = 1e-48
 Identities = 121/333 (36%), Positives = 173/333 (51%), Gaps = 38/333 (11%)

Query:  25  EQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLS 84
            E+  F  +  +  K YS  EY  R ++F +N  KI+  N    NH    K G+N+F+D+S
Sbjct:  29  EKFHFTSWMKQHQKTYSSREYSHRLQVFANNWRKIQAHN--QRNHTF--KMGLNQFSDMS 84

Query:  85  SDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRG-AVTPVKNQGQC 143
              E K+ YL ++                 ++    P   ++ DWR +G  V+PVKNQG C
Sbjct:  85  FAEIKHKYLWSEPQN-------CSATKSNYLRGTGPYP-SSMDWRKKGNVVSPVKNQGAC 136

Query:  144 GSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAY 203
            GSCW+FSTTG +E    I+  K+++L+EQ LVDC         +   + GC GGL   A+
Sbjct:  137 GSCWTFSTTGALESAVAIASGKMMTLAEQQLVDC--------AQNFNNHGCQGGLPSQAF 188

Query:  204 NYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQ-AKISNFTMIPKN-ETVMAGYIV 261
pattern 237                                  ****
             YI+ N GI  E SYPY  + G QC FN     PE+  A + N   I  N E  M   + 
Sbjct:  189 EYILYNKGIMGEDSYPYIGKNG-QCKFN-----PEKAVAFVKNVVNITLNDEAAMVEAVA 242

Query:  262 STGPLAIAADAVE-WQFYIGGVFDI-PCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIV 317
               P++ A +  E +  Y  GV+    C+  P+ ++H +L VGY  +N +      YWIV
Sbjct:  243 LYNPVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYGEQNGLL-----YWIV 297

Query:  318 KNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 350
            KNSWG++WG  GY  + RGKN CG++   S  I
Sbjct:  298 KNSWGSNWGNNGYFLIERGKNMCGLAACASYPI 330


>sp|P25251|CYS4_BRANA CYSTEINE PROTEINASE COT44 PRECURSOR
          Length = 328

 Score =  190 bits (477), Expect = 5e-48
 Identities = 114/304 (37%), Positives = 164/304 (53%), Gaps = 29/304 (9%)

Query:  47  ERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPV 106
            ERF IFK NL  I+  N    N  A  K G+  FA+L++DE+++ YL  +       +  
Sbjct:  27  ERFNIFKDNLRFIDLHN--ENNKNATYKLGLTIFANLTNDEYRSLYLGARTEPVRR-ITK 83

Query:  107 ADYLDDEFINSIPPEE-QTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNK 165
            A  ++ ++  ++  +E     DWR +GAV  +K+QG CGSCW+FST   VEG + I   +
Sbjct:  84  AKNVNMKYSAAVNVDEVPVTVDWRQKGAVNAIKDQGTCGSCWAFSTAAAVEGINKIVTGE 143

Query:  166 LVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETG 225
            LVSLSEQ LVDCD         ++ ++GCNGGL   A+ +I+KNGG+ TE  YPY    G
Sbjct:  144 LVSLSEQELVDCD---------KSYNQGCNGGLMDYAFQFIMKNGGLNTEKDYPYHGTNG 194

Query:  226 TQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVF 283
pattern 237            ****
             +CN    N        I  +  +P  +       VS  P+++A DA    +Q Y  G+F
Sbjct:  195 -KCNSLLKN---SRVVTIDGYEDVPSKDETALKRAVSYQPVSVAIDAGGRAFQHYQSGIF 250

Query:  284 DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG----KNT 339
               C  N +DH ++ VGY ++N      + YWIV+NSWG  WGE GYI + R        
Sbjct:  251 TGKCGTN-MDHAVVAVGYGSEN-----GVDYWIVRNSWGTRWGEDGYIRMERNVASKSGK 304

Query:  340 CGVS 343
            CG++
Sbjct:  305 CGIA 308


>sp|P09668|CATH_HUMAN CATHEPSIN H PRECURSOR
          Length = 335

 Score =  188 bits (472), Expect = 2e-47
 Identities = 123/332 (37%), Positives = 170/332 (51%), Gaps = 36/332 (10%)

Query:  25  EQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLS 84
            E+  F  +  K  K YS EEY  R + F SN  KI   N    N     K  +N+F+D+S
Sbjct:  31  EKFHFKSWMSKHRKTYSTEEYHHRLQTFASNWRKINAHN----NGNHTFKMALNQFSDMS 86

Query:  85  SDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGA-VTPVKNQGQC 143
              E K+ YL ++          ++YL        PP    + DWR +G  V+PVKNQG C
Sbjct:  87  FAEIKHKYLWSEPQ--NCSATKSNYLRGT--GPYPP----SVDWRKKGNFVSPVKNQGAC 138

Query:  144 GSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAY 203
            GSCW+FSTTG +E    I+  K++SL+EQ LVDC  +   Y        GC GGL   A+
Sbjct:  139 GSCWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNY--------GCQGGLPSQAF 190

Query:  204 NYIIKNGGIQTESSYPYTAETGTQCNFNSAN-IGPEEQAKISNFTMIPKNETVMAGYIVS 262
pattern 237                                   ****
             YI+ N GI  E +YPY  + G  C F     IG  +   ++N T+   +E  M   +  
Sbjct:  191 EYILYNKGIMGEDTYPYQGKDG-YCKFQPGKAIGFVKD--VANITIY--DEEAMVEAVAL 245

Query:  263 TGPLAIAADAV-EWQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVK 318
              P++ A +   ++  Y  G++    C+  P+ ++H +L VGY  KN I     PYWIVK
Sbjct:  246 YNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNGI-----PYWIVK 300

Query:  319 NSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 350
            NSWG  WG  GY  + RGKN CG++   S  I
Sbjct:  301 NSWGPQWGMNGYFLIERGKNMCGLAACASYPI 332


>sp|P10056|PAP3_CARPA CARICAIN PRECURSOR (PAPAYA PROTEINASE OMEGA) (PAPAYA PROTEINASE III)
            (PPIII) (PAPAYA PEPTIDASE A)
          Length = 348

 Score =  187 bits (471), Expect = 2e-47
 Identities = 121/319 (37%), Positives = 161/319 (49%), Gaps = 38/319 (11%)

Query:  37  NKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKF--GVNKFADLSSDEFKNYYL 93
            NK Y + +E L RFEIFK NL  I+E N      K +  +  G+N+FADLS+DEF   Y+
Sbjct:  56  NKFYENVDEKLYRFEIFKDNLNYIDETN------KKNNSYWLGLNEFADLSNDEFNEKYV 109

Query:  94  NNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTG 153
             +       D  +    D+EFIN          DWR +GAVTPV++QG CGSCW+FS   
Sbjct:  110 GS-----LIDATIEQSYDEEFINEDTVNLPENVDWRKKGAVTPVRHQGSCGSCWAFSAVA 164

Query:  154 NVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQ 213
             VEG + I   KLV LSEQ LVDC+              GC GG  P A  Y+ KN GI 
Sbjct:  165 TVEGINKIRTGKLVELSEQELVDCERR----------SHGCKGGYPPYALEYVAKN-GIH 213

Query:  214 TESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAV 273
pattern 237                        ****
              S YPY A+ GT C       GP    K S    +  N        ++  P+++  ++ 
Sbjct:  214 LRSKYPYKAKQGT-CRAKQVG-GP--IVKTSGVGRVQPNNEGNLLNAIAKQPVSVVVESK 269

Query:  274 --EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYI 331
               +Q Y GG+F+ PC    +DH +  VGY            Y ++KNSWG  WGE+GYI
Sbjct:  270 GRPFQLYKGGIFEGPCG-TKVDHAVTAVGYGKSG-----GKGYILIKNSWGTAWGEKGYI 323

Query:  332 YLRRGK-NTCGVSNFVSTS 349
             ++R   N+ GV     +S
Sbjct:  324 RIKRAPGNSPGVCGLYKSS 342


>sp|P25778|ORYC_ORYSA ORYZAIN GAMMA CHAIN PRECURSOR
          Length = 362

 Score =  187 bits (471), Expect = 2e-47
 Identities = 112/329 (34%), Positives = 170/329 (51%), Gaps = 33/329 (10%)

Query:  28  QFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSD 86
            +F  F  +  K+Y    E   RF IF  +L  +   N   + ++     G+N+FAD+S +
Sbjct:  61  RFARFAVRHGKRYGDAAEVQRRFRIFSESLELVRSTNRRGLPYR----LGINRFADMSWE 116

Query:  87  EFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSC 146
            EF+   L   +         A    +  +   P   +T  DWR  G V+PVK+QG CGSC
Sbjct:  117 EFQASRLGAAQNCS------ATLAGNHRMRDAPALPETK-DWREDGIVSPVKDQGHCGSC 169

Query:  147 WSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYI 206
            W FSTTG++E ++  +    VSLSEQ L DC      +        GC+GGL   A+ YI
Sbjct:  170 WPFSTTGSLEARYTQATGPPVSLSEQQLADCATRYNNF--------GCSGGLPSQAFEYI 221

Query:  207 IKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPL 266
pattern 237                               ****
              NGG+ TE +YPYT   G  C++   N G +    + N T++ ++E   A  +V   P+
Sbjct:  222 KYNGGLDTEEAYPYTGVNGI-CHYKPENAGVKVLDSV-NITLVAEDELKNAVGLVR--PV 277

Query:  267 AIAADAVE-WQFYIGGVF---DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWG 322
            ++A   +  ++ Y  GV+       +P  ++H +L VGY  +N      +PYW++KNSWG
Sbjct:  278 SVAFQVINGFRMYKSGVYTSDHCGTSPMDVNHAVLAVGYGVEN-----GVPYWLIKNSWG 332

Query:  323 ADWGEQGYIYLRRGKNTCGVSNFVSTSII 351
            ADWG+ GY  +  GKN CG++   S  I+
Sbjct:  333 ADWGDNGYFTMEMGKNMCGIATCASYPIV 361


>sp|P15242|TES1_RAT TESTIN 1/2 PRECURSOR (CMB-22/CMB-23)
          Length = 333

 Score =  187 bits (469), Expect = 4e-47
 Identities = 115/356 (32%), Positives = 184/356 (51%), Gaps = 30/356 (8%)

Query:  3   VILLFVLAVFTVFVSSRGIPPEEQS--QFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60
            +I +  LA+  + V S    P+     ++ E++ K  K Y+  E   +  +++ N   IE
Sbjct:  1   MIAVLFLAILCLEVDSTAPTPDPSLDVEWNEWRTKHGKTYNMNEERLKRAVWEKNFKMIE 60

Query:  61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLN-NKEAIFTDDLPVADYLDDEFINSIP 119
              N   +  + D    +N F DL++ EF        ++ I    +    + D +F+  +P
Sbjct:  61  LHNWEYLEGRHDFTMAMNAFGDLTNIEFVKMMTGFQRQKIKKTHI----FQDHQFLY-VP 115

Query:  120 PEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDH 179
                   DWR  G VTPVKNQG C S W+FS TG++EGQ F    +L+ LSEQNL+DC  
Sbjct:  116 KR----VDWRQLGYVTPVKNQGHCASSWAFSATGSLEGQMFRKTERLIPLSEQNLLDCMG 171

Query:  180 ECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEE 239
pattern 237                                                          ***
              + +        GC+GG    A+ Y+  NGG+ TE SYPY  + G +C +++ N     
Sbjct:  172 SNVTH--------GCSGGFMQYAFQYVKDNGGLATEESYPYRGQ-GRECRYHAEN----S 218

Query:  240 QAKISNFTMIPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIP-CNPNSLDHGI 296
pattern 240 *
             A + +F  IP +E  +   +   GP+++A DA    +QFY  G++  P C    L+H +
Sbjct:  219 AANVRDFVQIPGSEEALMKAVAKVGPISVAVDASHGSFQFYGSGIYYEPQCKRVHLNHAV 278

Query:  297 LIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG-KNTCGVSNFVSTSII 351
            L+VGY  +      N  +W+VKNSWG +WG +GY+ L +   N CG++ + +  I+
Sbjct:  279 LVVGYGFEGEESDGN-SFWLVKNSWGEEWGMKGYMKLAKDWSNHCGIATYSTYPIV 333


>sp|O46427|CATH_PIG CATHEPSIN H PRECURSOR
          Length = 335

 Score =  186 bits (468), Expect = 5e-47
 Identities = 124/343 (36%), Positives = 176/343 (51%), Gaps = 42/343 (12%)

Query:  17  SSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFG 76
            S+  +   E+  F  +  +  KKYS EEY  R ++F SN  KI   N  A NH    K G
Sbjct:  23  SNLAVSSFEKLHFKSWMVQHQKKYSLEEYHHRLQVFVSNWRKINAHN--AGNHTF--KLG 78

Query:  77  VNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGA-VT 135
            +N+F+D+S DE ++ YL ++           +YL        PP    + DWR +G  V+
Sbjct:  79  LNQFSDMSFDEIRHKYLWSEPQ--NCSATKGNYLRGT--GPYPP----SMDWRKKGNFVS 130

Query:  136 PVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCN 195
            PVKNQG CGSCW+FSTTG +E    I+  K++SL+EQ LVDC         +   + GC 
Sbjct:  131 PVKNQGSCGSCWTFSTTGALESAVAIATGKMLSLAEQQLVDC--------AQNFNNHGCQ 182

Query:  196 GGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQ----AKISNFTMIPK 251
pattern 237                                          ****
            GGL   A+ YI  N GI  E +YPY  +    C F      P++       ++N TM   
Sbjct:  183 GGLPSQAFEYIRYNKGIMGEDTYPYKGQ-DDHCKFQ-----PDKAIAFVKDVANITM--N 234

Query:  252 NETVMAGYIVSTGPLAIAADAV-EWQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTI 307
            +E  M   +    P++ A +   ++  Y  G++    C+  P+ ++H +L VGY  +N I
Sbjct:  235 DEEAMVEAVALYNPVSFAFEVTNDFLMYRKGIYSSTSCHKTPDKVNHAVLAVGYGEENGI 294

Query:  308 FRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 350
                 PYWIVKNSWG  WG  GY  + RGKN CG++   S  I
Sbjct:  295 -----PYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPI 332


>sp|P05167|ALEU_HORVU THIOL PROTEASE ALEURAIN PRECURSOR
          Length = 362

 Score =  185 bits (466), Expect = 9e-47
 Identities = 111/329 (33%), Positives = 169/329 (50%), Gaps = 33/329 (10%)

Query:  28  QFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSD 86
            +F  F  ++ K Y S  E   RF IF  +L ++   N   + ++     G+N+F+D+S +
Sbjct:  60  RFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYR----LGINRFSDMSWE 115

Query:  87  EFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSC 146
            EF+   L   +         A    +  +       +T  DWR  G V+PVKNQ  CGSC
Sbjct:  116 EFQATRLGAAQTCS------ATLAGNHLMRDAAALPETK-DWREDGIVSPVKNQAHCGSC 168

Query:  147 WSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYI 206
            W+FSTTG +E  +  +  K +SLSEQ LVDC      +        GCNGGL   A+ YI
Sbjct:  169 WTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNF--------GCNGGLPSQAFEYI 220

Query:  207 IKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPL 266
pattern 237                               ****
              NGGI TE SYPY    G  C++ + N   +    + N T+  ++E   A  +V   P+
Sbjct:  221 KYNGGIDTEESYPYKGVNGV-CHYKAENAAVQVLDSV-NITLNAEDELKNAVGLVR--PV 276

Query:  267 AIAADAVE-WQFYIGGVF---DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWG 322
            ++A   ++ ++ Y  GV+        P+ ++H +L VGY  +N      +PYW++KNSWG
Sbjct:  277 SVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVEN-----GVPYWLIKNSWG 331

Query:  323 ADWGEQGYIYLRRGKNTCGVSNFVSTSII 351
            ADWG+ GY  +  GKN C ++   S  ++
Sbjct:  332 ADWGDNGYFKMEMGKNMCAIATCASYPVV 360


>sp|P43235|CATK_HUMAN CATHEPSIN K PRECURSOR (CATHEPSIN O) (CATHEPSIN X) (CATHEPSIN O2)
          Length = 329

 Score =  185 bits (465), Expect = 1e-46
 Identities = 123/350 (35%), Positives = 185/350 (52%), Gaps = 39/350 (11%)

Query:  9   LAVFTVFVSSRGIPPEE--QSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLI 65
            L V  + V S  + PEE   + +  ++    K+Y+++ + + R  I++ NL  I   NL 
Sbjct:  4   LKVLLLPVVSFALYPEEILDTHWELWKKTHRKQYNNKVDEISRRLIWEKNLKYISIHNLE 63

Query:  66  AINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTA 125
            A       +  +N   D++S+E        K       +P++    ++ +  IP  E  A
Sbjct:  64  ASLGVHTYELAMNHLGDMTSEEVVQKMTGLK-------VPLSHSRSNDTLY-IPEWEGRA 115

Query:  126 ---FDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECM 182
                D+R +G VTPVKNQGQCGSCW+FS+ G +EGQ      KL++LS QNLVDC  E  
Sbjct:  116 PDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSE-- 173

Query:  183 EYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAK 242
pattern 237                                                       ****
                    ++GC GG   NA+ Y+ KN GI +E +YPY  +    C +N       + AK
Sbjct:  174 --------NDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQE-ESCMYNPTG----KAAK 220

Query:  243 ISNFTMIPK-NETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILI 298
               +  IP+ NE  +   +   GP+++A DA    +QFY  GV +D  CN ++L+H +L 
Sbjct:  221 CRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLA 280

Query:  299 VGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVS 347
            VGY       +K   +WI+KNSWG +WG +GYI + R K N CG++N  S
Sbjct:  281 VGYG-----IQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLAS 325


>sp|P05994|PAP4_CARPA PAPAYA PROTEINASE IV PRECURSOR (PPIV) (PAPAYA PEPTIDASE B) (GLYCYL
            ENDOPEPTIDASE)
          Length = 348

 Score =  184 bits (462), Expect = 3e-46
 Identities = 116/315 (36%), Positives = 162/315 (50%), Gaps = 37/315 (11%)

Query:  35  KFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYL 93
            K NK Y + +E L RFEIFK NL  I+E N +   +      G+N+F+DLS+DEFK  Y+
Sbjct:  54  KHNKNYKNVDEKLYRFEIFKDNLKYIDERNKMINGYW----LGLNEFSDLSNDEFKEKYV 109

Query:  94  NNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTG 153
             +    +T+        D+EF+N    +   + DWR +GAVTPVK+QG C SCW+FST  
Sbjct:  110 GSLPEDYTNQP-----YDEEFVNEDIVDLPESVDWRAKGAVTPVKHQGYCESCWAFSTVA 164

Query:  154 NVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQ 213
             VEG + I    LV LSEQ LVDCD +            GCN G Q  +  Y+ +N GI 
Sbjct:  165 TVEGINKIKTGNLVELSEQELVDCDKQ----------SYGCNRGYQSTSLQYVAQN-GIH 213

Query:  214 TESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAV 273
pattern 237                        ****
              + YPY A+  T C  N    GP  + K +    +  N        ++  P+++  ++ 
Sbjct:  214 LRAKYPYIAKQQT-CRANQVG-GP--KVKTNGVGRVQSNNEGSLLNAIAHQPVSVVVESA 269

Query:  274 --EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYI 331
              ++Q Y GG+F+  C    +DH +  VGY            Y ++KNSWG  WGE GYI
Sbjct:  270 GRDFQNYKGGIFEGSCG-TKVDHAVTAVGYGKSG-----GKGYILIKNSWGPGWGENGYI 323

Query:  332 YLRRGK----NTCGV 342
             +RR        CGV
Sbjct:  324 RIRRASGNSPGVCGV 338


>sp|P25250|CYS2_HORVU CYSTEINE PROTEINASE EP-B 2 PRECURSOR
          Length = 373

 Score =  183 bits (461), Expect = 3e-46
 Identities = 125/349 (35%), Positives = 171/349 (48%), Gaps = 40/349 (11%)

Query:  8   VLAVFTVFVSSRGIPPEEQSQFLE---------FQDKFNKKYSHEEYLERFEIFKSNLGK 58
            VLAV  V + S  IP E++    E         +Q     +  H E   RF  FKSN   
Sbjct:  17  VLAVAAVELCS-AIPMEDKDLESEEALWDLYERWQSAHRVRRHHAEKHRRFGTFKSNAHF 75

Query:  59  IEELNLIAINHKADTKFGV--NKFADLSSDEFKNYYLNNKEAIFTDDLP-VADYLDDEF- 114
            I      + N + D  + +  N+F D+   EF+  ++ +         P V  ++     
Sbjct:  76  IH-----SHNKRGDHPYRLHLNRFGDMDQAEFRATFVGDLRRDTPSKPPSVPGFMYAALN 130

Query:  115 INSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNL 174
            ++ +PP    + DWR +GAVT VK+QG+CGSCW+FST  +VEG + I    LVSLSEQ L
Sbjct:  131 VSDLPP----SVDWRQKGAVTGVKDQGKCGSCWAFSTVVSVEGINAIRTGSLVSLSEQEL 186

Query:  175 VDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSAN 234
            +DCD          A ++GC GGL  NA+ YI  NGG+ TE++YPY A  GT CN   A 
Sbjct:  187 IDCD---------TADNDGCQGGLMDNAFEYIKNNGGLITEAAYPYRAARGT-CNVARAA 236

Query:  235 IGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNPNSL 292
pattern 237   ****
                    I     +P N        V+  P+++A +A    + FY  GVF   C    L
Sbjct:  237 QNSPVVVHIDGHQDVPANSEEDLARAVANQPVSVAVEASGKAFMFYSEGVFTGECG-TEL 295

Query:  293 DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCG 341
            DHG+ +VGY     +      YW VKNSWG  WGEQGYI + +     G
Sbjct:  296 DHGVAVVGYG----VAEDGKAYWTVKNSWGPSWGEQGYIRVEKDSGASG 340


>sp|P25249|CYS1_HORVU CYSTEINE PROTEINASE EP-B 1 PRECURSOR
          Length = 371

 Score =  183 bits (460), Expect = 5e-46
 Identities = 126/353 (35%), Positives = 170/353 (47%), Gaps = 48/353 (13%)

Query:  8   VLAVFTVFVSSRGIPPEEQSQFLE---------FQDKFNKKYSHEEYLERFEIFKSNLGK 58
            VLAV  V + S  IP E++    E         +Q     +  H E   RF  FKSN   
Sbjct:  17  VLAVAAVELCS-AIPMEDKDLESEEALWDLYERWQSAHRVRRHHAEKHRRFGTFKSNAHF 75

Query:  59  IEELNLIAINHKADTKFGV--NKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEF-- 114
            I      + N + D  + +  N+F D+   EF+  ++ +       D P        F  
Sbjct:  76  IH-----SHNKRGDHPYRLHLNRFGDMDQAEFRATFVGDLRR----DTPAKPPSVPGFMY 126

Query:  115 ----INSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLS 170
                ++ +PP    + DWR +GAVT VK+QG+CGSCW+FST  +VEG + I    LVSLS
Sbjct:  127 AALNVSDLPP----SVDWRQKGAVTGVKDQGKCGSCWAFSTVVSVEGINAIRTGSLVSLS 182

Query:  171 EQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNF 230
            EQ L+DCD          A ++GC GGL  NA+ YI  NGG+ TE++YPY A  GT CN 
Sbjct:  183 EQELIDCD---------TADNDGCQGGLMDNAFEYIKNNGGLITEAAYPYRAARGT-CNV 232

Query:  231 NSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCN 288
pattern 237       ****
              A         I     +P N        V+  P+++A +A    + FY  GVF   C 
Sbjct:  233 ARAAQNSPVVVHIDGHQDVPANSEEDLARAVANQPVSVAVEASGKAFMFYSEGVFTGDCG 292

Query:  289 PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCG 341
               LDHG+ +VGY     +      YW VKNSWG  WGEQGYI + +     G
Sbjct:  293 -TELDHGVAVVGYG----VAEDGKAYWTVKNSWGPSWGEQGYIRVEKDSGASG 340


>sp|P43236|CATK_RABIT CATHEPSIN K PRECURSOR (OC-2 PROTEIN)
          Length = 329

 Score =  183 bits (459), Expect = 6e-46
 Identities = 119/348 (34%), Positives = 181/348 (51%), Gaps = 35/348 (10%)

Query:  9   LAVFTVFVSSRGIPPEE--QSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLI 65
            L V  + V S  + PEE   +Q+  ++  ++K+Y+ + + + R  I++ NL  I   NL 
Sbjct:  4   LKVLLLPVVSFALHPEEILDTQWELWKKTYSKQYNSKVDEISRRLIWEKNLKHISIHNLE 63

Query:  66  AINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDE-FINSIPPEEQT 124
            A       +  +N   D++S+E        K        P   + +D  +I         
Sbjct:  64  ASLGVHTYELAMNHLGDMTSEEVVQKMTGLKVP------PSRSHSNDTLYIPDWEGRTPD 117

Query:  125 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY 184
            + D+R +G VTPVKNQGQCGSCW+FS+ G +EGQ      KL++LS QNLVDC  E    
Sbjct:  118 SIDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSE---- 173

Query:  185 EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKIS 244
pattern 237                                                     ****
                  + GC GG   NA+ Y+ +N GI +E +YPY  +    C +N       + AK  
Sbjct:  174 ------NYGCGGGYMTNAFQYVQRNRGIDSEDAYPYVGQ-DESCMYNPTG----KAAKCR 222

Query:  245 NFTMIPK-NETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIVG 300
             +  IP+ NE  +   +   GP+++A DA    +QFY  GV +D  C+ ++++H +L VG
Sbjct:  223 GYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDENCSSDNVNHAVLAVG 282

Query:  301 YSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVS 347
            Y       +K   +WI+KNSWG  WG +GYI + R K N CG++N  S
Sbjct:  283 YG-----IQKGNKHWIIKNSWGESWGNKGYILMARNKNNACGIANLAS 325


>sp|P22895|P34_SOYBN P34 PROBABLE THIOL PROTEASE PRECURSOR
          Length = 379

 Score =  182 bits (458), Expect = 8e-46
 Identities = 110/322 (34%), Positives = 173/322 (53%), Gaps = 38/322 (11%)

Query:  40  YSHEEYLERFEIFKSNLGKIEELNLIAINHKA--DTKFGVNKFADLSSDEFKNYYLNNKE 97
            ++HEE  +R EIFK+N   I ++N    N K+    + G+NKFAD++  EF   YL   +
Sbjct:  56  HNHEEEAKRLEIFKNNSNYIRDMNA---NRKSPHSHRLGLNKFADITPQEFSKKYLQAPK 112

Query:  98  AIFTDDLPVAD--YLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNV 155
             + +  + +A+     +++    PP    ++DWR +G +T VK QG CG  W+FS TG +
Sbjct:  113 DV-SQQIKMANKKMKKEQYSCDHPP---ASWDWRKKGVITQVKYQGGCGRGWAFSATGAI 168

Query:  156 EGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTE 215
            E  H I+   LVSLSEQ LVDC  E           EG   G Q  ++ +++++GGI T+
Sbjct:  169 EAAHAIATGDLVSLSEQELVDCVEE----------SEGSYNGWQYQSFEWVLEHGGIATD 218

Query:  216 SSYPYTAETGTQCNFN----SANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAAD 271
pattern 237                          ****
              YPY A+ G +C  N       I   E   +S+ +   + E      I+   P++++ D
Sbjct:  219 DDYPYRAKEG-RCKANKIQDKVTIDGYETLIMSDESTESETEQAFLSAILEQ-PISVSID 276

Query:  272 AVEWQFYIGGVFDIP--CNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQG 329
            A ++  Y GG++D     +P  ++H +L+VGY + +      + YWI KNSWG DWGE G
Sbjct:  277 AKDFHLYTGGIYDGENCTSPYGINHFVLLVGYGSAD-----GVDYWIAKNSWGFDWGEDG 331

Query:  330 YIYLRRGK----NTCGVSNFVS 347
            YI+++R        CG++ F S
Sbjct:  332 YIWIQRNTGNLLGVCGMNYFAS 353


>sp|P49935|CATH_MOUSE CATHEPSIN H PRECURSOR (CATHEPSIN B3) (CATHEPSIN BA)
          Length = 333

 Score =  180 bits (451), Expect = 5e-45
 Identities = 115/332 (34%), Positives = 166/332 (49%), Gaps = 36/332 (10%)

Query:  25  EQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLS 84
            E+  F  +  +  K YS  EY  R ++F +N  KI+  N    NH    K  +N+F+D+S
Sbjct:  29  EKFHFKSWMKQHQKTYSSVEYNHRLQMFANNWRKIQAHN--QRNHTF--KMALNQFSDMS 84

Query:  85  SDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRG-AVTPVKNQGQC 143
              E K+ +L ++                 ++    P   ++ DWR +G  V+PVKNQG C
Sbjct:  85  FAEIKHKFLWSEPQN-------CSATKSNYLRGTGPYP-SSMDWRKKGNVVSPVKNQGAC 136

Query:  144 GSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAY 203
             SCW+FSTTG +E    I+  K++SL+EQ LVDC         +   + GC GGL   A+
Sbjct:  137 ASCWTFSTTGALESAVAIASGKMLSLAEQQLVDC--------AQAFNNHGCKGGLPSQAF 188

Query:  204 NYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKN-ETVMAGYIVS 262
pattern 237                                  ****
             YI+ N GI  E SYPY  +  + C FN      +  A + N   I  N E  M   +  
Sbjct:  189 EYILYNKGIMEEDSYPYIGK-DSSCRFNP----QKAVAFVKNVVNITLNDEAAMVEAVAL 243

Query:  263 TGPLAIAADAVE-WQFYIGGVFDIPC---NPNSLDHGILIVGYSAKNTIFRKNMPYWIVK 318
              P++ A +  E +  Y  GV+        P+ ++H +L VGY  +N +      YWIVK
Sbjct:  244 YNPVSFAFEVTEDFLMYKSGVYSSKSCHKTPDKVNHAVLAVGYGEQNGLL-----YWIVK 298

Query:  319 NSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 350
            NSWG+ WGE GY  + RGKN CG++   S  I
Sbjct:  299 NSWGSQWGENGYFLIERGKNMCGLAACASYPI 330


>sp|P55097|CATK_MOUSE CATHEPSIN K PRECURSOR
          Length = 329

 Score =  178 bits (447), Expect = 2e-44
 Identities = 117/352 (33%), Positives = 182/352 (51%), Gaps = 43/352 (12%)

Query:  9   LAVFTVFVSSRGIPPEEQ--SQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLI 65
            L V  + + S  + PEE   +Q+  ++    K+Y+ + + + R  I++ NL +I   NL 
Sbjct:  4   LKVLLLPMVSFALSPEEMLDTQWELWKKTHQKQYNSKVDEISRRLIWEKNLKQISAHNLE 63

Query:  66  AINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDD-----EFINSIPP 120
            A       +  +N   D++S+E        +        P   Y +D     E+   +P 
Sbjct:  64  ASLGVHTYELAMNHLGDMTSEEVVQKMTGLRIP------PSRSYSNDTLYTPEWEGRVPD 117

Query:  121 EEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 180
                + D+R +G VTPVKNQGQCGSCW+FS+ G +EGQ      KL++LS QNLVDC  E
Sbjct:  118 ----SIDYRKKGYVTPVKNQGQCGSCWAFSSAGALEGQLKKKTGKLLALSPQNLVDCVTE 173

Query:  181 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQ 240
pattern 237                                                         ****
                      + GC GG    A+ Y+ +NGGI +E ++PY  +    C +N+      + 
Sbjct:  174 ----------NYGCGGGYMTTAFQYVQQNGGIDSEDAFPYVGQ-DESCMYNAT----AKA 218

Query:  241 AKISNFTMIP-KNETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGI 296
            AK   +  IP  NE  +   +   GP++++ DA    +QFY  GV +D  C+ ++++H +
Sbjct:  219 AKCRGYREIPVGNEKALKRAVARVGPISVSIDASLASFQFYSRGVYYDENCDRDNVNHAV 278

Query:  297 LIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVS 347
            L+VGY       +K   +WI+KNSWG  WG +GY  L R K N CG++N  S
Sbjct:  279 LVVGYGT-----QKGSKHWIIKNSWGESWGNKGYALLARNKNNACGITNMAS 325


>sp|P56202|CATW_HUMAN CATHEPSIN W PRECURSOR (LYMPHOPAIN)
          Length = 376

 Score =  177 bits (445), Expect = 3e-44
 Identities = 112/351 (31%), Positives = 171/351 (47%), Gaps = 47/351 (13%)

Query:  22  PPEEQSQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKF 80
            P E +  F  FQ +FN+ Y S EE+  R +IF  NL + + L    +      +FGV  F
Sbjct:  35  PLELKEAFKLFQIQFNRSYLSPEEHAHRLDIFAHNLAQAQRLQEEDLG---TAEFGVTPF 91

Query:  81  ADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAF--DWR-TRGAVTPV 137
            +DL+ +EF   Y   + A     +          I S  PEE   F  DWR   GA++P+
Sbjct:  92  SDLTEEEFGQLYGYRRAAGGVPSM-------GREIRSEEPEESVPFSCDWRKVAGAISPI 144

Query:  138 KNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGG 197
            K+Q  C  CW+ +  GN+E    IS    V +S   L+DC            C +GC+GG
Sbjct:  145 KDQKNCNCCWAMAAAGNIETLWRISFWDFVDVSVHELLDCGR----------CGDGCHGG 194

Query:  198 LQPNAYNYIIKNGGIQTESSYPYTAETGT-QCNFNSANIGPEEQAKISNFTMIPKNETVM 256
pattern 237                                         ****
               +A+  ++ N G+ +E  YP+  +    +C+        ++ A I +F M+  NE  +
Sbjct:  195 FVWDAFITVLNNSGLASEKDYPFQGKVRAHRCHPKKY----QKVAWIQDFIMLQNNEHRI 250

Query:  257 AGYIVSTGPLAIAADAVEWQFYIGGVFDIP---CNPNSLDHGILIVGYSA--------KN 305
            A Y+ + GP+ +  +    Q Y  GV       C+P  +DH +L+VG+ +          
Sbjct:  251 AQYLATYGPITVTINMKPLQLYRKGVIKATPTTCDPQLVDHSVLLVGFGSVKSEEGIWAE 310

Query:  306 TIFRKNMP-------YWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTS 349
            T+  ++ P       YWI+KNSWGA WGE+GY  L RG NTCG++ F  T+
Sbjct:  311 TVSSQSQPQPPHPTPYWILKNSWGAQWGEKGYFRLHRGSNTCGITKFPLTA 361


>sp|P56203|CATW_MOUSE CATHEPSIN W PRECURSOR (LYMPHOPAIN)
          Length = 371

 Score =  176 bits (442), Expect = 6e-44
 Identities = 110/346 (31%), Positives = 166/346 (47%), Gaps = 40/346 (11%)

Query:  22  PPEEQSQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKF 80
            P E +  F  FQ +FN+ Y +  EY  R  IF  NL + + L    +      +FG   F
Sbjct:  33  PLELKEVFKLFQIRFNRSYWNPAEYTRRLSIFAHNLAQAQRLQQEDLG---TAEFGETPF 89

Query:  81  ADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWR-TRGAVTPVKN 139
            +DL+ +EF   Y   +    T ++       + +  S+P       DWR  +  ++ VKN
Sbjct:  90  SDLTEEEFGQLYGQERSPERTPNM-TKKVESNTWGESVP----RTCDWRKAKNIISSVKN 144

Query:  140 QGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQ 199
            QG C  CW+ +   N++    I   + V +S Q L+DC          E C  GCNGG  
Sbjct:  145 QGSCKCCWAMAAADNIQALWRIKHQQFVDVSVQELLDC----------ERCGNGCNGGFV 194

Query:  200 PNAYNYIIKNGGIQTESSYPYTAETGT-QCNFNSANIGPEEQAKISNFTMIPKNETVMAG 258
pattern 237                                       ****
             +AY  ++ N G+ +E  YP+  +    +C         ++ A I +FTM+  NE  +A 
Sbjct:  195 WDAYLTVLNNSGLASEKDYPFQGDRKPHRCLAKKY----KKVAWIQDFTMLSNNEQAIAH 250

Query:  259 YIVSTGPLAIAADAVEWQFYIGGVFDIP---CNPNSLDHGILIVGYSAKN------TIF- 308
            Y+   GP+ +  +    Q Y  GV       C+P  +DH +L+VG+  K       T+  
Sbjct:  251 YLAVHGPITVTINMKLLQHYQKGVIKATPSSCDPRQVDHSVLLVGFGKKKEGMQTGTVLS 310

Query:  309 -----RKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTS 349
                 R + PYWI+KNSWGA WGE+GY  L RG NTCGV+ +  T+
Sbjct:  311 HSRKRRHSSPYWILKNSWGAHWGEKGYFRLYRGNNTCGVTKYPFTA 356


>sp|P43234|CATO_HUMAN CATHEPSIN O PRECURSOR
          Length = 321

 Score =  173 bits (435), Expect = 4e-43
 Identities = 100/304 (32%), Positives = 152/304 (49%), Gaps = 30/304 (9%)

Query:  52  FKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLD 111
            F+ +L +   LN +  +  +   +G+N+F+ L  +EFK  YL +K + F           
Sbjct:  44  FRESLNRHRYLNSLFPSENSTAFYGINQFSYLFPEEFKAIYLRSKPSKFPR-------YS 96

Query:  112 DEFINSIPPEE-QTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLS 170
             E   SIP       FDWR +  VT V+NQ  CG CW+FS  G VE  + I    L  LS
Sbjct:  97  AEVHMSIPNVSLPLRFDWRDKQVVTQVRNQQMCGGCWAFSVVGAVESAYAIKGKPLEDLS 156

Query:  171 EQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIK-NGGIQTESSYPYTAETGTQCN 229
             Q ++DC +           + GCNGG   NA N++ K    +  +S YP+ A+ G  C+
Sbjct:  157 VQQVIDCSYN----------NYGCNGGSTLNALNWLNKMQVKLVKDSEYPFKAQNGL-CH 205

Query:  230 FNSANIGPEEQAKISNFTM--IPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPC 287
pattern 237        ****
            + S   G      I  ++       E  MA  +++ GPL +  DAV WQ Y+GG+    C
Sbjct:  206 YFS---GSHSGFSIKGYSAYDFSDQEDEMAKALLTFGPLVVIVDAVSWQDYLGGIIQHHC 262

Query:  288 NPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVS 347
            +    +H +LI G+         + PYWIV+NSWG+ WG  GY +++ G N CG+++ VS
Sbjct:  263 SSGEANHAVLITGFDKTG-----STPYWIVRNSWGSSWGVDGYAHVKMGSNVCGIADSVS 317

Query:  348 TSII 351
            +  +
Sbjct:  318 SIFV 321


>sp|P00784|PAPA_CARPA PAPAIN PRECURSOR (PAPAYA PROTEINASE I) (PPI)
          Length = 345

 Score =  173 bits (433), Expect = 7e-43
 Identities = 119/322 (36%), Positives = 163/322 (49%), Gaps = 43/322 (13%)

Query:  35  KFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKF--GVNKFADLSSDEFKNY 91
            K NK Y + +E + RFEIFK NL  I+E N      K +  +  G+N FAD+S+DEFK  
Sbjct:  54  KHNKIYKNIDEKIYRFEIFKDNLKYIDETN------KKNNSYWLGLNVFADMSNDEFKEK 107

Query:  92  YLNNKEAIFTD-DLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFS 150
            Y  +    +T  +L   + L+D  +N   PE     DWR +GAVTPVKNQG CGSCW+FS
Sbjct:  108 YTGSIAGNYTTTELSYEEVLNDGDVNI--PEY---VDWRQKGAVTPVKNQGSCGSCWAFS 162

Query:  151 TTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNG 210
                +EG   I    L   SEQ L+DCD              GCNGG   +A   ++   
Sbjct:  163 AVVTIEGIIKIRTGNLNEYSEQELLDCDRR----------SYGCNGGYPWSALQ-LVAQY 211

Query:  211 GIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAA 270
pattern 237                           ****
            GI   ++YPY    G Q    S   GP          + P NE  +  Y ++  P+++  
Sbjct:  212 GIHYRNTYPY---EGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALL-YSIANQPVSVVL 267

Query:  271 DAV--EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQ 328
            +A   ++Q Y GG+F  PC  N +DH +  VGY            Y ++KNSWG  WGE 
Sbjct:  268 EAAGKDFQLYRGGIFVGPCG-NKVDHAVAAVGYGPN---------YILIKNSWGTGWGEN 317

Query:  329 GYIYLRRGK-NTCGVSNFVSTS 349
            GYI ++RG  N+ GV    ++S
Sbjct:  318 GYIRIKRGTGNSYGVCGLYTSS 339


>sp|P25774|CATS_HUMAN CATHEPSIN S PRECURSOR
          Length = 331

 Score =  171 bits (428), Expect = 3e-42
 Identities = 116/351 (33%), Positives = 175/351 (49%), Gaps = 35/351 (9%)

Query:  5   LLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYS--HEEYLERFEIFKSNLGKIEEL 62
            L+ VL V +  V+     P     +  ++  + K+Y   +EE + R  I++ NL  +   
Sbjct:  4   LVCVLLVCSSAVAQLHKDPTLDHHWHLWKKTYGKQYKEKNEEAVRRL-IWEKNLKFVMLH 62

Query:  63  NLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEE 122
            NL           G+N   D++S+E  +          T  L V             P  
Sbjct:  63  NLEHSMGMHSYDLGMNHLGDMTSEEVMS---------LTSSLRVPSQWQRNITYKSNPNR 113

Query:  123 --QTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 180
                + DWR +G VT VK QG CG+CW+FS  G +E Q  +   KLV+LS QNLVDC   
Sbjct:  114 ILPDSVDWREKGCVTEVKYQGSCGACWAFSAVGALEAQLKLKTGKLVTLSAQNLVDC--- 170

Query:  181 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQ 240
pattern 237                                                         ****
                  E+  ++GCNGG    A+ YII N GI +++SYPY A    +C ++S        
Sbjct:  171 ----STEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKA-MDQKCQYDS----KYRA 221

Query:  241 AKISNFTMIP-KNETVMAGYIVSTGPLAIAADAVEWQFYI--GGVFDIPCNPNSLDHGIL 297
            A  S +T +P   E V+   + + GP+++  DA    F++   GV+  P    +++HG+L
Sbjct:  222 ATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCTQNVNHGVL 281

Query:  298 IVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVS 347
            +VGY   N        YW+VKNSWG ++GE+GYI + R K N CG+++F S
Sbjct:  282 VVGYGDLN-----GKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPS 327


>sp||CATL_CHICK_1 [Segment 1 of 2] CATHEPSIN L
          Length = 176

 Score =  167 bits (420), Expect = 2e-41
 Identities = 87/179 (48%), Positives = 115/179 (63%), Gaps = 16/179 (8%)

Query:  127 DWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEG 186
            DWR +G VTPVK+QGQCGSCW+FSTTG +EGQHF ++ KLVSLSEQNLVDC       EG
Sbjct:  6   DWREKGYVTPVKDQGQCGSCWAFSTTGALEGQHFRTKGKLVSLSEQNLVDCSRP----EG 61

Query:  187 EEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNF 246
pattern 237                                                   ****
                ++GCNGGL   A+ Y+  NGGI +E SYPYTA+    C + +        A  + F
Sbjct:  62  ----NQGCNGGLMDQAFQYVQDNGGIDSEESYPYTAKDDEDCRYKA----EYNAANDTGF 113

Query:  247 TMIPK-NETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIP-CNPNSLDHGILIVGY 301
              IP+ +E  +   + S GP+++A DA    +QFY  G++  P C+   LDHG+L+VGY
Sbjct:  114 VDIPQGHERALMKAVASVGPVSVAIDAGHSSFQFYQSGIYYEPDCSSEDLDHGVLVVGY 172


>sp|P25326|CATS_BOVIN CATHEPSIN S
          Length = 217

 Score =  165 bits (413), Expect = 1e-40
 Identities = 90/227 (39%), Positives = 129/227 (56%), Gaps = 21/227 (9%)

Query:  125 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY 184
            + DWR +G VT VK QG CGSCW+FS  G +E Q  +   KLVSLS QNLVDC       
Sbjct:  4   SMDWREKGCVTEVKYQGACGSCWAFSAVGALEAQVKLKTGKLVSLSAQNLVDC------- 56

Query:  185 EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKIS 244
pattern 237                                                     ****
               +  ++GCNGG    A+ YII N GI +E+SYPY A  G +C ++  N      A  S
Sbjct:  57  STAKYGNKGCNGGFMTEAFQYIIDNNGIDSEASYPYKAMDG-KCQYDVKN----RAATCS 111

Query:  245 NFTMIP-KNETVMAGYIVSTGPLAIAADAVEWQFYI--GGVFDIPCNPNSLDHGILIVGY 301
             +  +P  +E  +   + + GP+++  DA    F++   GV+  P    +++HG+L+VGY
Sbjct:  112 RYIELPFGSEEALKEAVANKGPVSVGIDASHSSFFLYKTGVYYDPSCTQNVNHGVLVVGY 171

Query:  302 SAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVS 347
               +        YW+VKNSWG  +G+QGYI + R   N CG++N+ S
Sbjct:  172 GNLD-----GKDYWLVKNSWGLHFGDQGYIRMARNSGNHCGIANYPS 213


>sp|P80884|ANAN_ANACO ANANAIN
          Length = 216

 Score =  161 bits (403), Expect = 2e-39
 Identities = 93/224 (41%), Positives = 123/224 (54%), Gaps = 26/224 (11%)

Query:  125 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY 184
            + DWR  GAVT VKNQG+CGSCW+F++   VE  + I +  LVSLSEQ ++DC       
Sbjct:  4   SIDWRDSGAVTSVKNQGRCGSCWAFASIATVESIYKIKRGNLVSLSEQQVLDC------- 56

Query:  185 EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKIS 244
pattern 237                                                     ****
                A   GC GG    AY++II N G+ + + YPY A  GT C  N    G    A I+
Sbjct:  57  ----AVSYGCKGGWINKAYSFIISNKGVASAAIYPYKAAKGT-CKTN----GVPNSAYIT 107

Query:  245 NFTMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSA 303
             +T + +N      Y VS  P+A A DA   +Q Y  GVF  PC    L+H I+I+GY  
Sbjct:  108 RYTYVQRNNERNMMYAVSNQPIAAALDASGNFQHYKRGVFTGPCG-TRLNHAIVIIGYGQ 166

Query:  304 KNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT----CGVS 343
             +        +WIV+NSWGA WGE GYI L R  ++    CG++
Sbjct:  167 DSA----GKKFWIVRNSWGAGWGEGGYIRLARDVSSSFGICGIA 206


>sp|Q02765|CATS_RAT CATHEPSIN S PRECURSOR
          Length = 330

 Score =  158 bits (396), Expect = 1e-38
 Identities = 89/226 (39%), Positives = 128/226 (56%), Gaps = 22/226 (9%)

Query:  127 DWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEG 186
            DWR +G VT VK QG CGSCW+FS  G +EGQ  +   KLVSLS QNLVDC  E      
Sbjct:  118 DWREKGCVTNVKYQGSCGSCWAFSAEGALEGQLKLKTGKLVSLSAQNLVDCSTE------ 171

Query:  187 EEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNF 246
pattern 237                                                   ****
            E+  ++GC GG    A+ YII +  I +E+SYPY A    +C ++  N      A  S +
Sbjct:  172 EKYGNKGCGGGFMTEAFQYII-DTSIDSEASYPYKA-MDEKCLYDPKN----RAATCSRY 225

Query:  247 TMIP-KNETVMAGYIVSTGPLAIAADAV---EWQFYIGGVFDIPCNPNSLDHGILIVGYS 302
              +P  +E  +   + + GP+++  D      +  Y  GV+D P    +++HG+L+VGY 
Sbjct:  226 IELPFGDEEALKEAVATKGPVSVGIDDASHSSFFLYQSGVYDDPSCTENMNHGVLVVGYG 285

Query:  303 AKNTIFRKNMPYWIVKNSWGADWGEQGYIYL-RRGKNTCGVSNFVS 347
              +        YW+VKNSWG  +G+QGYI + R  KN CG++++ S
Sbjct:  286 TLD-----GKDYWLVKNSWGLHFGDQGYIRMARNNKNHCGIASYCS 326


>sp|P20721|CYSL_LYCES LOW-TEMPERATURE-INDUCED CYSTEINE PROTEINASE PRECURSOR
          Length = 346

 Score =  158 bits (395), Expect = 2e-38
 Identities = 87/238 (36%), Positives = 130/238 (54%), Gaps = 25/238 (10%)

Query:  112 DEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSE 171
            D ++  +      + DWR +G +  VK+QG CGSCW+FS    +E  + I    L+SLSE
Sbjct:  8   DRYLPKVGDSLPESIDWREKGVLVGVKDQGSCGSCWAFSAVAAMESINAIVTGNLISLSE 67

Query:  172 QNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFN 231
            Q LVDCD          + +EGC+GGL   A+ ++IKNGGI TE  YPY    G  C+  
Sbjct:  68  QELVDCD---------RSYNEGCDGGLMDYAFEFVIKNGGIDTEEDYPYKERNGV-CDQY 117

Query:  232 SANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNP 289
pattern 237      ****
              N    +  KI ++  +P N        V+  P++IA +A   ++Q Y  G+F   C  
Sbjct:  118 RKN---AKVVKIDSYEDVPVNNEKALQKAVAHQPVSIALEAGGRDFQHYKSGIFTGKCG- 173

Query:  290 NSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT----CGVS 343
             ++DHG++I GY  +N      M YWIV+NSWGA+  E GY+ ++R  ++    CG++
Sbjct:  174 TAVDHGVVIAGYGTEN-----GMDYWIVRNSWGANCRENGYLRVQRNVSSSSGLCGLA 226


>sp|P36184|ACP1_ENTHI CYSTEINE PROTEINASE ACP1 PRECURSOR
          Length = 308

 Score =  152 bits (379), Expect = 1e-36
 Identities = 105/320 (32%), Positives = 151/320 (46%), Gaps = 48/320 (15%)

Query:  29  FLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE 87
            F ++    NK +++  EYL RF +F  N   +E          A+    +N FAD++ +E
Sbjct:  18  FKQWAATHNKVFANRAEYLYRFAVFLDNKKFVE----------ANANTELNVFADMTHEE 67

Query:  88  FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCW 147
            F   +L       T ++P         + + P     + DWR+   + P K+QGQCGSCW
Sbjct:  68  FIQTHLG-----MTYEVPETTSNVKAAVKAAPE----SVDWRS--IMNPAKDQGQCGSCW 116

Query:  148 SFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYII 207
            +F TT  +EG+      KL S SEQ LVDCD          A D GC GG   N+  +I 
Sbjct:  117 TFCTTAVLEGRVNKDLGKLYSFSEQQLVDCD----------ASDNGCEGGHPSNSLKFIQ 166

Query:  208 KNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLA 267
pattern 237                              ****
            +N G+  ES YPY A  GT C     N+     ++     +   +ET +   I   GP+A
Sbjct:  167 ENNGLGLESDYPYKAVAGT-CK-KVKNVATVTGSR----RVTDGSETGLQTIIAENGPVA 220

Query:  268 IAADA--VEWQFYIGGVF--DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGA 323
            +  DA    +Q Y  G    D  C    ++H +  VGY + +     N  YWI++NSWG 
Sbjct:  221 VGMDASRPSFQLYKKGTIYSDTKCRSRMMNHCVTAVGYGSNS-----NGKYWIIRNSWGT 275

Query:  324 DWGEQGYIYLRR-GKNTCGV 342
             WG+ GY  L R   N CG+
Sbjct:  276 SWGDAGYFLLARDSNNMCGI 295


>sp|Q01957|CPP1_ENTHI CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 315

 Score =  150 bits (375), Expect = 4e-36
 Identities = 103/317 (32%), Positives = 163/317 (50%), Gaps = 47/317 (14%)

Query:  37  NKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADT-KFGVN-KFADLSSDEFKNYYLN 94
            NK ++  E L R  IF  N        ++A N++ +T K  V+  FA ++++E+ +    
Sbjct:  24  NKHFTAVESLRRRAIFNMNA------RIVAENNRKETFKLSVDGPFAAMTNEEYNSLLKL 77

Query:  95  NKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGN 154
             +      ++         ++N   P+   A DWR +G VTP+++QG CGSC++F +   
Sbjct:  78  KRSGEEKGEV--------RYLNIQAPK---AVDWRKKGKVTPIRDQGNCGSCYTFGSIAA 126

Query:  155 VEGQHFISQ---NKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGG 211
            +EG+  I +   ++ + LSE+++V C  E    +G    + GCNGGL  N YNYI++N G
Sbjct:  127 LEGRLLIEKGGDSETLDLSEEHMVQCTRE----DG----NNGCNGGLGSNVYNYIMEN-G 177

Query:  212 IQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAAD 271
pattern 237                          ****
            I  ES YPYT    T           +  AKI ++  + +N  V     +S G + ++ D
Sbjct:  178 IAKESDYPYTGSDST------CRSDVKAFAKIKSYNRVARNNEVELKAAISQGLVDVSID 231

Query:  272 A--VEWQFYIGGVF-DIPCNPN--SLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWG 326
            A  V++Q Y  G + D  C  N  +L+H +  VGY   +         WIV+NSWG  WG
Sbjct:  232 ASSVQFQLYKSGAYTDTQCKNNYFALNHEVCAVGYGVVD-----GKECWIVRNSWGTGWG 286

Query:  327 EQGYIYLRRGKNTCGVS 343
            E+GYI +    NTCGV+
Sbjct:  287 EKGYINMVIEGNTCGVA 303


>sp|O17473|CATL_BRUPA CATHEPSIN L-LIKE PRECURSOR
          Length = 395

 Score =  150 bits (374), Expect = 6e-36
 Identities = 101/331 (30%), Positives = 157/331 (46%), Gaps = 29/331 (8%)

Query:  26  QSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSS 85
            ++++ ++     K Y  +E   R  IF+SN    E +N             +N  ADL+ 
Sbjct:  88  ETEWKDYVTALGKHYDQKENNFRMAIFESNELMTERINKKYEQGLVSYTTALNDLADLTD 147

Query:  86  DEF--KNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQC 143
            +EF  +N      +         +++   +    +P +     DWRT+GAVTPV+NQG+C
Sbjct:  148 EEFMVRNGLRLPNQTDLRGKRQTSEFYRYDKSERLPDQ----VDWRTKGAVTPVRNQGEC 203

Query:  144 GSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAY 203
            GSC++F+T   +E  H     +L+ LS QN+VDC             + GC+GG  P A+
Sbjct:  204 GSCYAFATAAALEAYHKQMTGRLLDLSPQNIVDCT--------RNLGNNGCSGGYMPTAF 255

Query:  204 NYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMI-PKNETVMAGYIVS 262
pattern 237                                  ****
             Y  +  GI  ES YPY   T  +C +  +     +    + F  I P +E  +   +  
Sbjct:  256 QYASRY-GIAMESRYPYVG-TEQRCRWQQSIAVVTD----NGFNEIQPGDELALKHAVAK 309

Query:  263 TGP--LAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNS 320
             GP  + I+     ++FY  GV+    N    DH +L VGY    +       YWIVKNS
Sbjct:  310 RGPVVVGISGSKRSFRFYKDGVYS-EGNCGRPDHAVLAVGYGTHPSY----GDYWIVKNS 364

Query:  321 WGADWGEQGYIYLRRGK-NTCGVSNFVSTSI 350
            WG DWG+ GY+Y+ R + N C +++  S  I
Sbjct:  365 WGTDWGKDGYVYMARNRGNMCHIASAASFPI 395


>sp|P46102|CYSP_PLAVN CYSTEINE PROTEINASE PRECURSOR
          Length = 506

 Score =  150 bits (374), Expect = 6e-36
 Identities = 116/363 (31%), Positives = 180/363 (48%), Gaps = 64/363 (17%)

Query:  27  SQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSS 85
            S+F ++  + NKKY + +E L+RFE FK    K ++ N +   +       VN+++D S 
Sbjct:  160 SKFFKYMKENNKKYENMDEQLQRFENFKIRYMKTQKHNEMVGKNGLTYVQKVNQYSDFSK 219

Query:  86  DEFKNYYLNNKEAIFTDDL------PVADYLDDEFINSIPPEEQT---AFDWRTRGAVTP 136
            +EF NY+   K      DL      P+  +L +  + S+  + +    + D+R++    P
Sbjct:  220 EEFDNYF--KKLLSVPMDLKSKYIVPLKKHLANTNLISVDNKSKDFPDSRDYRSKFNFLP 277

Query:  137 VKNQGQCGSCWSFSTTGNVEGQHFISQNKL-VSLSEQNLVDCDHECMEYEGEEACDEGCN 195
             K+QG CGSCW+F+  GN E  +  +++++ +S SEQ +VDC  E          + GC+
Sbjct:  278 PKDQGNCGSCWAFAAIGNFEYLYVHTRHEMPISFSEQQMVDCSTE----------NYGCD 327

Query:  196 GGLQPNAYNYIIKNGGIQTESSYPYTAETGTQC-NFNSANIGPEEQAKISNFTMIPKNET 254
pattern 237                                           ****
            GG    A+ Y+I NG +     YPY       C N+  + +G     ++     +  NE 
Sbjct:  328 GGNPFYAFLYMINNG-VCLGDEYPYKGHEDFFCLNYRCSLLG-----RVHFIGDVKPNEL 381

Query:  255 VMAGYIVSTGPLAIAADAVE-WQFYIGGVFDIPCNPNSLDHGILIVGYSA---------- 303
            +MA   V  GP+ IA  A E +  Y GGVFD  CNP  L+H +L+VGY            
Sbjct:  382 IMALNYV--GPVTIAVGASEDFVLYSGGVFDGECNPE-LNHSVLLVGYGQVKKSLAFEDS 438

Query:  304 -----KNTI--FRKNMP---------YWIVKNSWGADWGEQGYIYLRRGK----NTCGVS 343
                  N I  +++N+          YWIV+NSWG +WGE GYI ++R K      CGV 
Sbjct:  439 HSNVDSNLIKKYKENIKGDDDDDIIYYWIVRNSWGPNWGEGGYIRIKRNKAGDDGFCGVG 498

Query:  344 NFV 346
            + V
Sbjct:  499 SDV 501


>sp|Q06964|CPP3_ENTHI CYSTEINE PROTEINASE 3 PRECURSOR (CYSTEINE PROTEINASE ACP3)
          Length = 308

 Score =  149 bits (372), Expect = 9e-36
 Identities = 103/316 (32%), Positives = 159/316 (49%), Gaps = 45/316 (14%)

Query:  37  NKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVN-KFADLSSDEFKNYYLNN 95
            NK ++  E L R  IF  N   + E N      K   K  V+  FA ++++E++   L +
Sbjct:  17  NKHFTAVEALRRRAIFNMNARFVAEFN-----KKGSFKLSVDGPFAAMTNEEYRTL-LKS 70

Query:  96  KEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNV 155
            K  +  +           ++N   PE   + DWR +G VTP+++Q QCGSC++F +   +
Sbjct:  71  KRTVEENGKVT-------YLNIQAPE---SVDWRAQGKVTPIRDQAQCGSCYTFGSLAAL 120

Query:  156 EGQHFISQN---KLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGI 212
            EG+  I +      + LSE++LV C          +  + GCNGGL  N Y+YII+N G+
Sbjct:  121 EGRLLIEKGGNANTLDLSEEHLVQCT--------RDNGNNGCNGGLGSNVYDYIIQN-GV 171

Query:  213 QTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADA 272
pattern 237                         ****
              ES YPYT  T + C  N      +  AKI+ +  +P+N        +S G + ++ DA
Sbjct:  172 AKESDYPYTG-TDSTCKTN-----VKAFAKITGYNKVPRNNEAELKAALSQGLVDVSIDA 225

Query:  273 --VEWQFYIGGVF-DIPCNPN--SLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGE 327
               ++Q Y  G + D  C  N  +L+H +  VGY   +         WIV+NSWG  WG+
Sbjct:  226 SSAKFQLYKSGAYSDTKCKNNFFALNHEVCAVGYGVVD-----GKECWIVRNSWGTGWGD 280

Query:  328 QGYIYLRRGKNTCGVS 343
            +GYI +    NTCGV+
Sbjct:  281 KGYINMVIEGNTCGVA 296


>sp|Q01958|CPP2_ENTHI CYSTEINE PROTEINASE 2 PRECURSOR
          Length = 315

 Score =  149 bits (372), Expect = 9e-36
 Identities = 102/324 (31%), Positives = 161/324 (49%), Gaps = 45/324 (13%)

Query:  29  FLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVN-KFADLSSDE 87
            F  +  K NK ++  E L R  IF  N   ++  N I        K  V+  FA ++++E
Sbjct:  16  FNTWASKNNKHFTAIEKLRRRAIFNMNAKFVDSFNKIG-----SFKLSVDGPFAAMTNEE 70

Query:  88  FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCW 147
            ++    + +    T++     YL+ +   S+        DWR  G VTP+++Q QCGSC+
Sbjct:  71  YRTLLKSKRT---TEENGQVKYLNIQAPESV--------DWRKEGKVTPIRDQAQCGSCY 119

Query:  148 SFSTTGNVEGQHFISQN---KLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYN 204
            +F +   +EG+  I +      + LSE+++V C          +  + GCNGGL  N Y+
Sbjct:  120 TFGSLAALEGRLLIEKGGDANTLDLSEEHMVQCT--------RDNGNNGCNGGLGSNVYD 171

Query:  205 YIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTG 264
pattern 237                                 ****
            YII++ G+  ES YPYT    T C  N  +      AKI+ +T +P+N        +S G
Sbjct:  172 YIIEH-GVAKESDYPYTGSDST-CKTNVKSF-----AKITGYTKVPRNNEAELKAALSQG 224

Query:  265 PLAIAADA--VEWQFYIGGVF-DIPCNPN--SLDHGILIVGYSAKNTIFRKNMPYWIVKN 319
             + ++ DA   ++Q Y  G + D  C  N  +L+H +  VGY   +         WIV+N
Sbjct:  225 LVDVSIDASSAKFQLYKSGAYTDTKCKNNYFALNHEVCAVGYGVVD-----GKECWIVRN 279

Query:  320 SWGADWGEQGYIYLRRGKNTCGVS 343
            SWG  WG++GYI +    NTCGV+
Sbjct:  280 SWGTGWGDKGYINMVIEGNTCGVA 303


>sp|P36185|ACP2_ENTHI CYSTEINE PROTEINASE ACP2 PRECURSOR
          Length = 310

 Score =  145 bits (363), Expect = 1e-34
 Identities = 102/330 (30%), Positives = 160/330 (47%), Gaps = 40/330 (12%)

Query:  20  GIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVN- 78
            GI       F  +  K NK ++  E L R  IF  N   ++  N I        K  V+ 
Sbjct:  3   GIRIASAIDFNTWASKNNKHFTAIEKLRRRAIFNMNAKFVDSFNKIG-----SFKLSVDG 57

Query:  79  KFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVK 138
             FA ++++E++    + +    T++     YL+ +   S+        DWR  G VTP++
Sbjct:  58  PFAAMTNEEYRTLLKSKRT---TEENGQVKYLNIQAPESV--------DWRKEGKVTPLR 106

Query:  139 NQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGL 198
            +Q QCGSC++F +   +EG+  I +       + N +D   E M+   +   + GCNGGL
Sbjct:  107 DQAQCGSCYTFGSLAALEGRLLIEKG-----GDANTLDLSEEHMQCTRDNG-NNGCNGGL 160

Query:  199 QPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAG 258
pattern 237                                       ****
              N Y+YII++G +  ES YPYT    T C  N  +       KI+ +T +P+N      
Sbjct:  161 GSNVYDYIIEHG-VAKESDYPYTGSDST-CKTNVKSF-----RKITGYTKVPRNNEAELK 213

Query:  259 YIVSTGPLAIAAD--AVEWQFYIGGVF-DIPCNPN--SLDHGILIVGYSAKNTIFRKNMP 313
              +S G L ++ D  + ++Q Y  G + D  C  N  +L+H +  VGY   +        
Sbjct:  214 AALSQGLLDVSIDVSSAKFQLYKSGAYTDTKCKNNYFALNHEVCAVGYGVVD-----GKE 268

Query:  314 YWIVKNSWGADWGEQGYIYLRRGKNTCGVS 343
             WIV+NSWG  WG++GYI +    NTCGV+
Sbjct:  269 CWIVRNSWGTSWGDKGYINMVIEGNTCGVA 298


>sp|P25781|CYSP_THEAN CYSTEINE PROTEINASE PRECURSOR
          Length = 441

 Score =  145 bits (362), Expect = 1e-34
 Identities = 107/345 (31%), Positives = 165/345 (47%), Gaps = 58/345 (16%)

Query:  28  QFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGV--NKFADLS 84
            +F  F +K+ K + S ++ ++RF  F+ N   ++        HK    + +  NKF+DLS
Sbjct:  119 EFDAFVEKYKKVHRSFDQRVQRFLTFRKNYHIVK-------THKPTEPYSLDLNKFSDLS 171

Query:  85  SDEFKNYY--------------------LNNKEAIFTDDLPVADYLDDEFINSIPPEEQT 124
             +EFK  Y                    +++K  I+   L  A  +++    S+   E  
Sbjct:  172 DEEFKALYPVITPPKTYTSLSKHLEFKKMSHKNPIYISKLKKAKGIEEIKDLSLITGEN- 230

Query:  125 AFDWRTRGAVTPVKNQGQ-CGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 183
              +W    AV+P K+QG  CGSCW+FS+  +VE  + + +NK   LSEQ LV+CD   M 
Sbjct:  231 -LNWARTDAVSPTKDQGDHCGSCWAFSSIASVESLYRLYKNKSYFLSEQELVNCDKSSM- 288

Query:  184 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKI 243
pattern 237                                                      ****
                     GC GGL   A  Y I + G+  ES  PYT    + C  +  N     +  I
Sbjct:  289 ---------GCAGGLPITALEY-IHSKGVSFESEVPYTGIV-SPCKPSIKN-----KVFI 332

Query:  244 SNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSA 303
             + +++  N+ V    ++S   + IA    E + Y GG+F   C    L+H +L+VG   
Sbjct:  333 DSISILKGNDVVNKSLVISPTVVGIAV-TKELKLYSGGIFTGKCG-GELNHAVLLVGEGV 390

Query:  304 KNTIFRKNMPYWIVKNSWGADWGEQGYIYLRR---GKNTCGVSNF 345
             +      M YWI+KNSWG DWGE G++ L+R   G + CG+  F
Sbjct:  391 DH---ETGMRYWIIKNSWGEDWGENGFLRLQRTKKGLDKCGILTF 432


>sp|P22497|CYSP_THEPA CYSTEINE PROTEINASE PRECURSOR
          Length = 439

 Score =  143 bits (357), Expect = 5e-34
 Identities = 105/351 (29%), Positives = 163/351 (45%), Gaps = 72/351 (20%)

Query:  24  EEQSQFLEFQDKFNKKYS-HEEYLERFEIFKSNLGKIEELNLIAINHKADTKF--GVNKF 80
            E   +F EF  K+N++++  +E L R   F+SN  +++E        K D  +  G+N+F
Sbjct:  119 EVYREFEEFNSKYNRRHATQQERLNRLVTFRSNYLEVKE-------QKGDEPYVKGINRF 171

Query:  81  ADLSSDEF--------------------------KNYYLNNKEAIFTDDLPVADYLDDEF 114
            +DL+  EF                          K Y  N K+A+ TD+        D  
Sbjct:  172 SDLTEREFYKLFPVMKPPKATYSNGYYLLSHMANKTYLKNLKKALNTDE--------DVD 223

Query:  115 INSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNL 174
            +  +  E     DWR   +VT VK+Q  CG CW+FST G+VEG +    +K   LS Q L
Sbjct:  224 LAKLTGEN---LDWRRSSSVTSVKDQSNCGGCWAFSTVGSVEGYYMSHFDKSYELSVQEL 280

Query:  175 VDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSAN 234
            +DCD          +   GC GGL  +AY Y+ K  G+ +    P+  +   +C+   A 
Sbjct:  281 LDCD----------SFSNGCQGGLLESAYEYVRKY-GLVSAKDLPF-VDKARRCSVPKA- 327

Query:  235 IGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDH 294
pattern 237   ****
                ++  + ++ +  K + VM   + S+      + + E   Y  GVF   C   SL+H
Sbjct:  328 ----KKVSVPSYHVF-KGKEVMTRSLTSSPCSVYLSVSPELAKYKSGVFTGECG-KSLNH 381

Query:  295 GILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRR---GKNTCGV 342
             +++VG        ++   YW+V+NSWG DWGE GY+ L R   G + CGV
Sbjct:  382 AVVLVGEGYDEVTKKR---YWVVQNSWGTDWGENGYMRLERTNMGTDKCGV 429


>sp|P25805|CYSP_PLAFA THROPHOZOITE CYSTEINE PROTEINASE PRECURSOR (TCP)
          Length = 569

 Score =  141 bits (351), Expect = 3e-33
 Identities = 107/367 (29%), Positives = 169/367 (45%), Gaps = 62/367 (16%)

Query:  27  SQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSS 85
            S+F +F  + NK Y + +E + +FEIFK N   I+  N   +N  A  K  VN+F+D S 
Sbjct:  223 SKFFKFMKEHNKVYKNIDEQMRKFEIFKINYISIKNHN--KLNKNAMYKKKVNQFSDYSE 280

Query:  86  DEFKNYYLN----NKEAIFTDDLPVADYLDD-----EFINSIPPEEQTAF-------DWR 129
            +E K Y+          I     P  ++L D     EF  +    E+  F       D+R
Sbjct:  281 EELKEYFKTLLHVPNHMIEKYSKPFENHLKDNILISEFYTNGKRNEKDIFSKVPEILDYR 340

Query:  130 TRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEA 189
             +G V   K+QG CGSCW+F++ GN+E         ++S SEQ +VDC  +         
Sbjct:  341 EKGIVHEPKDQGLCGSCWAFASVGNIESVFAKKNKNILSFSEQEVVDCSKD--------- 391

Query:  190 CDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMI 249
pattern 237                                                ****
             + GC+GG    ++ Y+++N  +     Y Y A+    C     N   + +  +S+   +
Sbjct:  392 -NFGCDGGHPFYSFLYVLQN-ELCLGDEYKYKAKDDMFC----LNYRCKRKVSLSSIGAV 445

Query:  250 PKNETVMAGYIVSTGPLAIAADA-VEWQFYIGGVFDIPCNPNSLDHGILIVGY------- 301
             +N+ ++A  +   GPL++      ++  Y  GV++  C+   L+H +L+VGY       
Sbjct:  446 KENQLILA--LNEVGPLSVNVGVNNDFVAYSEGVYNGTCS-EELNHSVLLVGYGQVEKTK 502

Query:  302 -------SAKNTIFRKNMP------YWIVKNSWGADWGEQGYIYLRRGKN----TCGVSN 344
                      NT    N P      YWI+KNSW   WGE G++ L R KN     CG+  
Sbjct:  503 LNYNNKIQTYNTKENSNQPDDNIIYYWIIKNSWSKKWGENGFMRLSRNKNGDNVFCGIGE 562

Query:  345 FVSTSII 351
             V   I+
Sbjct:  563 EVFYPIL 569


>sp|P14518|BROM_ANACO BROMELAIN, STEM
          Length = 212

 Score =  139 bits (348), Expect = 6e-33
 Identities = 81/224 (36%), Positives = 113/224 (50%), Gaps = 31/224 (13%)

Query:  125 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY 184
            + DWR  GAVT VKNQ  CG+CW+F+    VE  + I +  L  LSEQ ++DC       
Sbjct:  5   SIDWRDYGAVTSVKNQNPCGACWAFAAIATVESIYKIKKGILEPLSEQQVLDC------- 57

Query:  185 EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKIS 244
pattern 237                                                     ****
                A   GC GG +  A+ +II N G+ + + YPY A  GT C  +    G    A I+
Sbjct:  58  ----AKGYGCKGGWEFRAFEFIISNKGVASGAIYPYKAAKGT-CKTD----GVPNSAYIT 108

Query:  245 NFTMIPKNETVMAGYIVSTGPLAIAADA-VEWQFYIGGVFDIPCNPNSLDHGILIVGYSA 303
             +  +P+N      Y VS  P+ +A DA   +Q+Y  GVF+ PC   SL+H +  +GY  
Sbjct:  109 GYARVPRNNESSMMYAVSKQPITVAVDANANFQYYKSGVFNGPCG-TSLNHAVTAIGYGQ 167

Query:  304 KNTIFRKNMPYWIVKNSWGADWGEQGYIYLRR----GKNTCGVS 343
             + I+ K          WGA WGE GYI + R        CG++
Sbjct:  168 DSIIYPK---------KWGAKWGEAGYIRMARDVSSSSGICGIA 202


>sp|P16311|MMAL_DERFA MAJOR MITE FECAL ALLERGEN DER F 1 PRECURSOR (DER F I)
          Length = 321

 Score =  138 bits (345), Expect = 1e-32
 Identities = 115/352 (32%), Positives = 157/352 (43%), Gaps = 52/352 (14%)

Query:  7   FVLAVFTVFVSSRGIP-PEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLI 65
            FVLA+ ++ V S     P     F EF+  FNK Y+    +E  E+ + N   +E L  +
Sbjct:  3   FVLAIASLLVLSTVYARPASIKTFEEFKKAFNKNYAT---VEEEEVARKNF--LESLKYV 57

Query:  66  AINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEF----INSIPPE 121
              N     K  +N  +DLS DEFKN YL + EA   + L     L+ E     INS+   
Sbjct:  58  EAN-----KGAINHLSDLSLDEFKNRYLMSAEAF--EQLKTQFDLNAETSACRINSVNVP 110

Query:  122 EQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHEC 181
             +   D R+   VTP++ QG CGSCW+FS     E  +   +N  + LSEQ LVDC    
Sbjct:  111 SE--LDLRSLRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNTSLDLSEQELVDC---- 164

Query:  182 MEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQA 241
pattern 237                                                        ****
                   A   GC+G   P    YI +NG ++ E SYPY A        NS + G     
Sbjct:  165 -------ASQHGCHGDTIPRGIEYIQQNGVVE-ERSYPYVAREQRCRRPNSQHYG----- 211

Query:  242 KISNFTMIPKNETVMAGYIVSTGPLAIAA-----DAVEWQFYIGGVF---DIPCNPNSLD 293
             ISN+  I   +       ++    AIA      D   +Q Y G      D    PN   
Sbjct:  212 -ISNYCQIYPPDVKQIREALTQTHTAIAVIIGIKDLRAFQHYDGRTIIQHDNGYQPNY-- 268

Query:  294 HGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNF 345
            H + IVGY +      +   YWIV+NSW   WG+ GY Y + G N   +  +
Sbjct:  269 HAVNIVGYGS-----TQGDDYWIVRNSWDTTWGDSGYGYFQAGNNLMMIEQY 315


>sp|P42666|CYSP_PLAVI CYSTEINE PROTEINASE PRECURSOR
          Length = 583

 Score =  129 bits (320), Expect = 1e-29
 Identities = 100/370 (27%), Positives = 166/370 (44%), Gaps = 84/370 (22%)

Query:  27  SQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSS 85
            S+F  F +K+ + Y    E +E+++ FK N  KI++ N          K  VN+F+D S 
Sbjct:  235 SKFFNFMNKYKRSYKDINEQMEKYKNFKMNYLKIKKHN----ETNQMYKMKVNQFSDYSK 290

Query:  86  DEFKNYYLNNKEAIFTDDLPVADYLDDEFI--------------------NSIPPEEQTA 125
             +F++Y        F   +P+ D+L  +++                     ++  +    
Sbjct:  291 KDFESY--------FRKLVPIPDHLKKKYVVPFSSMNNGKGKNVVTSSSGANLLADVPEI 342

Query:  126 FDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNK-LVSLSEQNLVDCDHECMEY 184
             D+R +G V   K+QG CGSCW+F++ GNVE  +    NK +++LSEQ +VDC       
Sbjct:  343 LDYREKGIVHEPKDQGLCGSCWAFASVGNVECMYAKEHNKTILTLSEQEVVDC------- 395

Query:  185 EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKIS 244
pattern 237                                                     ****
                  + GC+GG    ++ Y I+N GI     Y Y A     C     N   + +  +S
Sbjct:  396 ---SKLNFGCDGGHPFYSFIYAIEN-GICMGDDYKYKAMDNLFC----LNYRCKNKVTLS 447

Query:  245 NFTMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYS- 302
            +   + +NE + A  +   GP+++      ++ FY GG+F+  C    L+H +L+VGY  
Sbjct:  448 SVGGVKENELIRA--LNEVGPVSVNVGVTDDFSFYGGGIFNGTCT-EELNHSVLLVGYGQ 504

Query:  303 -AKNTIFRKN-------------------------MPYWIVKNSWGADWGEQGYIYLRRG 336
               + IF++                            YWI+KNSW   WGE G++ + R 
Sbjct:  505 VQSSKIFQEKNAYDDASGVTKKGALSYPSKADDGIQYYWIIKNSWSKFWGENGFMRISRN 564

Query:  337 KN----TCGV 342
            K      CG+
Sbjct:  565 KEGDNVFCGI 574


>sp|P08176|MMAL_DERPT MAJOR MITE FECAL ALLERGEN DER P 1 PRECURSOR (DER P I)
          Length = 320

 Score =  121 bits (300), Expect = 3e-27
 Identities = 111/345 (32%), Positives = 151/345 (43%), Gaps = 57/345 (16%)

Query:  1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60
            MK++L     +    V +R   P     F E++  FNK Y+     E  E  + N   +E
Sbjct:  1   MKIVLAIASLLALSAVYAR---PSSIKTFEEYKKAFNKSYAT---FEDEEAARKNF--LE 52

Query:  61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEF----IN 116
             +  +  N  A     +N  +DLS DEFKN +L + EA   + L     L+ E     IN
Sbjct:  53  SVKYVQSNGGA-----INHLSDLSLDEFKNRFLMSAEAF--EHLKTQFDLNAETNACSIN 105

Query:  117 SIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVD 176
               P E    D R    VTP++ QG CGSCW+FS     E  +   +N+ + L+EQ LVD
Sbjct:  106 GNAPAE---IDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLAEQELVD 162

Query:  177 CDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG 236
            C           A   GC+G   P    YI  NG +Q ES Y Y A   +    N+   G
Sbjct:  163 C-----------ASQHGCHGDTIPRGIEYIQHNGVVQ-ESYYRYVAREQSCRRPNAQRFG 210

Query:  237 PEEQAKISNFTMI-PKNETVMAGYIVSTGPLAIAA-----DAVEWQFYIGGVF---DIPC 287
pattern 237 ****
                  ISN+  I P N   +   +  T   AIA      D   ++ Y G      D   
Sbjct:  211 ------ISNYCQIYPPNVNKIREALAQTHS-AIAVIIGIKDLDAFRHYDGRTIIQRDNGY 263

Query:  288 NPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIY 332
             PN   H + IVGYS       + + YWIV+NSW  +WG+ GY Y
Sbjct:  264 QPNY--HAVNIVGYSN-----AQGVDYWIVRNSWDTNWGDNGYGY 301


>sp|P80067|CATC_RAT DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (DPPI) (CATHEPSIN C)
            (CATHEPSIN J) (DIPEPTIDYL TRANSFERASE)
          Length = 462

 Score =  111 bits (274), Expect = 3e-24
 Identities = 83/260 (31%), Positives = 128/260 (48%), Gaps = 34/260 (13%)

Query:  105 PVADYLDDEFINSIPPEEQTAFDWRT-RGA--VTPVKNQGQCGSCWSFSTTGNVEGQHFI 161
            P+ D +  + + S+P     ++DWR  RG   V+PV+NQ  CGSC+SF++ G +E +  I
Sbjct:  218 PITDEIQQQIL-SLPE----SWDWRNVRGINFVSPVRNQESCGSCYSFASIGMLEARIRI 272

Query:  162 SQNKLVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYP 219
              N   +  LS Q +V C              +GC+GG          ++ G+  E+ +P
Sbjct:  273 LTNNSQTPILSPQEVVSCSPYA----------QGCDGGFPYLIAGKYAQDFGVVEENCFP 322

Query:  220 YTAETGTQCN--FNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVE-WQ 276
pattern 237                    ****
            YTA T   C    N       E   +  F     NE +M   +V  GP+A+A +  + + 
Sbjct:  323 YTA-TDAPCKPKENCLRYYSSEYYYVGGFYG-GCNEALMKLELVKHGPMAVAFEVHDDFL 380

Query:  277 FYIGGVF-----DIPCNPNSL-DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGY 330
             Y  G++       P NP  L +H +L+VGY  K+ +    + YWIVKNSWG+ WGE GY
Sbjct:  381 HYHSGIYHHTGLSDPFNPFELTNHAVLLVGYG-KDPV--TGLDYWIVKNSWGSQWGESGY 437

Query:  331 IYLRRGKNTCGVSNFVSTSI 350
              +RRG + C + +    +I
Sbjct:  438 FRIRRGTDECAIESIAMAAI 457


>sp|P97821|CATC_MOUSE DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (DPPI) (CATHEPSIN C)
            (CATHEPSIN J) (DIPEPTIDYL TRANSFERASE)
          Length = 462

 Score =  109 bits (270), Expect = 9e-24
 Identities = 91/335 (27%), Positives = 155/335 (46%), Gaps = 42/335 (12%)

Query:  34  DKFNKKYSH-----EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEF 88
            +K N   +H     E Y ER  ++  N   ++ +N +    K+ T     ++  +S  + 
Sbjct:  147 EKVNMNAAHLGGLQERYSER--LYTHNHNFVKAINTV---QKSWTATAYKEYEKMSLRDL 201

Query:  89  KNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRT-RGA--VTPVKNQGQCGS 145
                 +++        P+ D +  + +N   PE   ++DWR  +G   V+PV+NQ  CGS
Sbjct:  202 IRRSGHSQRIPRPKPAPMTDEIQQQILNL--PE---SWDWRNVQGVNYVSPVRNQESCGS 256

Query:  146 CWSFSTTGNVEGQHFISQNKLVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAY 203
            C+SF++ G +E +  I  N   +  LS Q +V C              +GC+GG      
Sbjct:  257 CYSFASMGMLEARIRILTNNSQTPILSPQEVVSCSPYA----------QGCDGGFPYLIA 306

Query:  204 NYIIKNGGIQTESSYPYTA-ETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVS 262
pattern 237                                   ****
                ++ G+  ES +PYTA ++  +   N       +   +  F     NE +M   +V 
Sbjct:  307 GKYAQDFGVVEESCFPYTAKDSPCKPRENCLRYYSSDYYYVGGFYG-GCNEALMKLELVK 365

Query:  263 TGPLAIAADAVE-WQFYIGGVF-----DIPCNPNSL-DHGILIVGYSAKNTIFRKNMPYW 315
             GP+A+A +  + +  Y  G++       P NP  L +H +L+VGY          + YW
Sbjct:  366 HGPMAVAFEVHDDFLHYHSGIYHHTGLSDPFNPFELTNHAVLLVGYGRDPVT---GIEYW 422

Query:  316 IVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 350
            I+KNSWG++WGE GY  +RRG + C + +    +I
Sbjct:  423 IIKNSWGSNWGESGYFRIRRGTDECAIESIAVAAI 457


>sp|P25773|CATL_FELCA CATHEPSIN L (PROGESTERONE-DEPENDENT PROTEIN) (PDP)
          Length = 139

 Score =  108 bits (267), Expect = 2e-23
 Identities = 55/145 (37%), Positives = 84/145 (57%), Gaps = 9/145 (6%)

Query:  196 GGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETV 255
pattern 237                                          ****
            GGL  +A+ Y+  NGG+ +E SYPY A+ G  C +   N      A ++++  IP  E  
Sbjct:  1   GGLIDDAFQYVKDNGGLDSEESYPYHAQ-GDSCKYRPEN----SVANVTDYWDIPSKENE 55

Query:  256 MAGYIVSTGPLAIAADAV--EWQFYIGGVF-DIPCNPNSLDHGILIVGYSAKNTIFRKNM 312
            +   + + GP++ A DA    ++FY  G++ D  C+   +DHG+L+VGY A  T   +N 
Sbjct:  56  LMITLAAVGPISAAIDASLDTFRFYKEGIYYDPSCSSEDVDHGVLVVGYGADGTE-TENK 114

Query:  313 PYWIVKNSWGADWGEQGYIYLRRGK 337
             YWI+KNSWG DWG  GYI + + +
Sbjct:  115 KYWIIKNSWGTDWGMDGYIKMAKDR 139


>sp|Q26563|CATC_SCHMA CATHEPSIN C PRECURSOR
          Length = 454

 Score =  108 bits (266), Expect = 3e-23
 Identities = 75/238 (31%), Positives = 109/238 (45%), Gaps = 33/238 (13%)

Query:  126 FDWRT-----RGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQN--KLVSLSEQNLVDCD 178
            FDW +     R  VTP++NQG CGSC++  +   +E +  +  N  +   LS Q +VDC 
Sbjct:  222 FDWTSPPDGSRSPVTPIRNQGICGSCYASPSAAALEARIRLVSNFSEQPILSPQTVVDCS 281

Query:  179 HECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNF--NSANIG 236
                         EGCNGG          ++ G+  +   PYT E   +C    N     
Sbjct:  282 ----------PYSEGCNGGFPFLIAGKYGEDFGLPQKIVIPYTGEDTGKCTVSKNCTRYY 331

Query:  237 PEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVE-WQFYIGGVFDIPC-------- 287
pattern 237 ****
              + + I  +     NE +M   ++S GP  +  +  E +QFY  G++            
Sbjct:  332 TTDYSYIGGYYGAT-NEKLMQLELISNGPFPVGFEVYEDFQFYKEGIYHHTTVQTDHYNF 390

Query:  288 NPNSL-DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN 344
            NP  L +H +L+VGY           PYW VKNSWG +WGEQGY  + RG + CGV +
Sbjct:  391 NPFELTNHAVLLVGYGVDKL---SGEPYWKVKNSWGVEWGEQGYFRILRGTDECGVES 445


>sp|P53634|CATC_HUMAN DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (DPPI) (CATHEPSIN C)
            (CATHEPSIN J) (DIPEPTIDYL TRANSFERASE)
          Length = 463

 Score =  107 bits (265), Expect = 3e-23
 Identities = 75/235 (31%), Positives = 111/235 (46%), Gaps = 29/235 (12%)

Query:  124 TAFDWRTRGA---VTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVS--LSEQNLVDCD 178
            T++DWR       V+PV+NQ  CGSC+SF++ G +E +  I  N   +  LS Q +V C 
Sbjct:  233 TSWDWRNVHGINFVSPVRNQASCGSCYSFASMGMLEARIRILTNNSQTPILSPQEVVSCS 292

Query:  179 HECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSA--NIG 236
                         +GC GG          ++ G+  E+ +PYT  T + C          
Sbjct:  293 QYA----------QGCEGGFPYLIAGKYAQDFGLVEEACFPYTG-TDSPCKMKEDCFRYY 341

Query:  237 PEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVE-WQFYIGGVFDI-----PCNPN 290
pattern 237 ****
              E   +  F     NE +M   +V  GP+A+A +  + +  Y  G++       P NP 
Sbjct:  342 SSEYHYVGGFYG-GCNEALMKLELVHHGPMAVAFEVYDDFLHYKKGIYHHTGLRDPFNPF 400

Query:  291 SL-DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN 344
             L +H +L+VGY   +      M YWIVKNSWG  WGE GY  +RRG + C + +
Sbjct:  401 ELTNHAVLLVGYGTDSA---SGMDYWIVKNSWGTGWGENGYFRIRRGTDECAIES 452


>sp|P25780|EUM1_EURMA MITE GROUP I ALLERGEN EUR M 1 (EUR M I)
          Length = 211

 Score = 99.8 bits (245), Expect = 7e-21
 Identities = 73/228 (32%), Positives = 102/228 (44%), Gaps = 33/228 (14%)

Query:  117 SIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVD 176
            S+P E     D R+   VTP++ QG CGSCW+FS   + E  +   +N  + L+EQ LVD
Sbjct:  10  SLPSE----LDLRSLRTVTPIRMQGGCGSCWAFSGVASTESAYLAYRNMSLDLAEQELVD 65

Query:  177 CDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG 236
            C           A   GC+G   P    YI +NG +Q E  YPY A   +    N+   G
Sbjct:  66  C-----------ASQNGCHGDTIPRGIEYIQQNGVVQ-EHYYPYVAREQSCHRPNAQRYG 113

Query:  237 PEEQAKISNFTMIPKNETVMAGYIVSTGPLAI---AADAVEWQFYIGGVF---DIPCNPN 290
pattern 237 ****
             +   +IS     P +  +      +   +A+     D   ++ Y G      D    PN
Sbjct:  114 LKNYCQISP----PDSNKIRQALTQTHTAVAVIIGIKDLNAFRHYDGRTIMQHDNGYQPN 169

Query:  291 SLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKN 338
               H + IVGY   NT   + + YWIV+NSW   WG+ GY Y     N
Sbjct:  170 Y--HAVNIVGYG--NT---QGVDYWIVRNSWDTTWGDNGYGYFAANIN 210


>sp|Q23894|CYS3_DICDI CYSTEINE PROTEINASE 3 (CYSTEINE PROTEINASE II)
          Length = 151

 Score = 94.8 bits (232), Expect = 2e-19
 Identities = 60/158 (37%), Positives = 87/158 (54%), Gaps = 15/158 (9%)

Query: 41  SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIF 100
           +H+E++ R+E FK N+  +   N    +  + T  G+N+ ADLS++E++  YL  +  I 
Sbjct: 1   THKEFMPRYEEFKKNMDYVHNWN----SKGSKTVLGLNQHADLSNEEYRLNYLGTRAHIK 56

Query: 101 TDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHF 160
            +     +      +N    ++    DWR + AVTPVK+QGQCGSC   STTG+VEG   
Sbjct: 57  LNGYHKRNL--GLRLNRPHFKQPLNVDWREKDAVTPVKDQGQCGSC-IISTTGSVEGVTA 113

Query: 161 ISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGL 198
           I   KLVSLSEQN++               +EGCNGGL
Sbjct: 114 IKTGKLVSLSEQNILRL--------SSSFGNEGCNGGL 143


>sp|P43509|CPR5_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 5 PRECURSOR
          Length = 344

 Score = 90.9 bits (222), Expect = 4e-18
 Identities = 69/272 (25%), Positives = 111/272 (40%), Gaps = 47/272 (17%)

Query:  108 DYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLV 167
            D +  E  ++IP        W    ++  +++Q  CGSCW+F+    +  +  I+ N  V
Sbjct:  72  DIVATEVSDAIPDHFDARDQWPNCMSINNIRDQSDCGSCWAFAAAEAISDRTCIASNGAV 131

Query:  168 S--LSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSY------- 218
            +  LS ++L+ C        G  +C  GC GG    A+ + +K+G + T  SY       
Sbjct:  132 NTLLSSEDLLSC------CTGMFSCGNGCEGGYPIQAWKWWVKHG-LVTGGSYETQFGCK 184

Query:  219 PY-----------------------TAETGTQCNFNSANIGPEEQAKISNFTM--IPKNE 253
pattern 237                                          ****
            PY                       T +    C   +    P  Q K    T   + K  
Sbjct:  185 PYSIAPCGETVNGVKWPACPEDTEPTPKCVDSCTSKNNYATPYLQDKHFGSTAYAVGKKV 244

Query:  254 TVMAGYIVSTGPLAIAADAVE-WQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNM 312
              +   I++ GP+ +A    E +  Y  GV+      +   H + I+G+   N       
Sbjct:  245 EQIQTEILTNGPIEVAFTVYEDFYQYTTGVYVHTAGASLGGHAVKILGWGVDN-----GT 299

Query:  313 PYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN 344
            PYW+V NSW   WGE+GY  + RG N CG+ +
Sbjct:  300 PYWLVANSWNVAWGEKGYFRIIRGLNECGIEH 331


>sp|P43508|CPR4_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 4 PRECURSOR
          Length = 335

 Score = 90.5 bits (221), Expect = 5e-18
 Identities = 73/299 (24%), Positives = 124/299 (41%), Gaps = 50/299 (16%)

Query:  82  DLSSDEFKNYYLNNK-EAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQ 140
            D++ ++ K   +  +  A  T D+ V  +  +E  ++IP        W    ++  +++Q
Sbjct:  46  DITIEQVKKRLMRTEFVAPHTPDVEVVKHDINE--DTIPATFDARTQWPNCMSINNIRDQ 103

Query:  141 GQCGSCWSFSTTGNVEGQHFISQNKLVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGL 198
              CGSCW+F+       +  I+ N  V+  LS ++++ C   C        C  GC GG 
Sbjct:  104 SDCGSCWAFAAAEAASDRFCIASNGAVNTLLSAEDVLSC---CSN------CGYGCEGGY 154

Query:  199 QPNAYNYIIKNG---GIQTESSYPYTAETGTQCNFNSANI--------GPEEQAKISNFT 247
pattern 237                                                  ****
              NA+ Y++K+G   G   E+ +     +   C     N+        G +  A ++  T
Sbjct:  155 PINAWKYLVKSGFCTGGSYEAQFGCKPYSLAPCGETVGNVTWPSCPDDGYDTPACVNKCT 214

Query:  248 -------------------MIPKNETVMAGYIVSTGPLAIAADAVE-WQFYIGGVFDIPC 287
                                + K  + +   I++ GP+  A    E +  Y  GV+    
Sbjct:  215 NKNYNVAYTADKHFGSTAYAVGKKVSQIQAEIIAHGPVEAAFTVYEDFYQYKTGVYVHTT 274

Query:  288 NPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFV 346
                  H I I+G+   N       PYW+V NSW  +WGE GY  + RG N CG+ + V
Sbjct:  275 GQELGGHAIRILGWGTDN-----GTPYWLVANSWNVNWGENGYFRIIRGTNECGIEHAV 328


>sp|P05993|PAP5_CARPA CYSTEINE PROTEINASE (CLONE PLBPC13)
          Length = 96

 Score = 90.5 bits (221), Expect = 5e-18
 Identities = 43/87 (49%), Positives = 55/87 (62%), Gaps = 2/87 (2%)

Query: 264 GPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKN--TIFRKNMPYWIVKNSW 321
           GPLA+A +A   Q YIGGV         L+HG+L+VGY +     I  K  PYW++KNSW
Sbjct: 1   GPLAVAINAAYMQTYIGGVSCPYICSRRLNHGVLLVGYGSAGYAPIRLKEKPYWVIKNSW 60

Query: 322 GADWGEQGYIYLRRGKNTCGVSNFVST 348
           G +WGE GY  + RG+N CGV + VST
Sbjct: 61  GENWGENGYYKICRGRNICGVDSMVST 87


>sp|P07688|CATB_BOVIN CATHEPSIN B PRECURSOR
          Length = 335

 Score = 88.5 bits (216), Expect = 2e-17
 Identities = 65/259 (25%), Positives = 105/259 (40%), Gaps = 47/259 (18%)

Query:  118 IPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSL---SEQNL 174
            +P        W     +  +++QG CGSCW+F     +  +  I  N  V++   +E  L
Sbjct:  80  LPESFDAREQWPNCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHSNGRVNVEVSAEDML 139

Query:  175 VDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQ--------------------- 213
              C  EC          +GCNGG    A+N+  K G +                      
Sbjct:  140 TCCGGEC---------GDGCNGGFPSGAWNFWTKKGLVSGGLYNSHVGCRPYSIPPCEHH 190

Query:  214 -TESSYPYTAETGT-QCNFN-----SANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPL 266
pattern 237                               ****
               S  P T E  T +CN       S +   ++    S++++    + +MA  I   GP+
Sbjct:  191 VNGSRPPCTGEGDTPKCNKTCEPGYSPSYKEDKHFGCSSYSVANNEKEIMAE-IYKNGPV 249

Query:  267 AIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADW 325
              A     ++  Y  GV+          H I I+G+  +N       PYW+V NSW  DW
Sbjct:  250 EGAFSVYSDFLLYKSGVYQHVSGEIMGGHAIRILGWGVEN-----GTPYWLVGNSWNTDW 304

Query:  326 GEQGYIYLRRGKNTCGVSN 344
            G+ G+  + RG++ CG+ +
Sbjct:  305 GDNGFFKILRGQDHCGIES 323


>sp|P00787|CATB_RAT CATHEPSIN B PRECURSOR (CATHEPSIN B1) (RSG-2)
          Length = 339

 Score = 87.4 bits (213), Expect = 4e-17
 Identities = 66/265 (24%), Positives = 113/265 (41%), Gaps = 45/265 (16%)

Query:  117 SIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSL--SEQNL 174
            ++P        W     +  +++QG CGSCW+F     +  +  I  N  V++  S ++L
Sbjct:  79  NLPESFDAREQWSNCPTIAQIRDQGSCGSCWAFGAVEAMSDRICIHTNGRVNVEVSAEDL 138

Query:  175 VDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIK----NGGIQTE--------------- 215
            + C   C        C +GCNGG    A+N+  +    +GG+                  
Sbjct:  139 LTC---C-----GIQCGDGCNGGYPSGAWNFWTRKGLVSGGVYNSHIGCLPYTIPPCEHH 190

Query:  216 ---SSYPYTAETGT-QCNFN-----SANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPL 266
pattern 237                               ****
               S  P T E  T +CN       S +   ++    +++++    + +MA  I   GP+
Sbjct:  191 VNGSRPPCTGEGDTPKCNKMCEAGYSTSYKEDKHYGYTSYSVSDSEKEIMAE-IYKNGPV 249

Query:  267 AIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADW 325
              A     ++  Y  GV+          H I I+G+  +N +     PYW+V NSW  DW
Sbjct:  250 EGAFTVFSDFLTYKSGVYKHEAGDVMGGHAIRILGWGIENGV-----PYWLVANSWNVDW 304

Query:  326 GEQGYIYLRRGKNTCGVSNFVSTSI 350
            G+ G+  + RG+N CG+ + +   I
Sbjct:  305 GDNGFFKILRGENHCGIESEIVAGI 329


>sp|P25807|CYS1_CAEEL GUT-SPECIFIC CYSTEINE PROTEINASE PRECURSOR
          Length = 329

 Score = 87.0 bits (212), Expect = 5e-17
 Identities = 66/288 (22%), Positives = 117/288 (39%), Gaps = 38/288 (13%)

Query:  82  DLSSDEFKNYYLNNK-EAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQ 140
            +++ +E K   ++ K  A  +D++   +   +  + S+P    +   W    ++  +++Q
Sbjct:  50  EITEEEMKFKLMDGKYAAAHSDEIRATE--QEVVLASVPATFDSRTQWSECKSIKLIRDQ 107

Query:  141 GQCGSCWSFSTTGNVEGQHFISQNKLVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGL 198
              CGSCW+F     +  +  I         +S  +L+ C   C       +C  GC GG 
Sbjct:  108 ATCGSCWAFGAAEMISDRTCIETKGAQQPIISPDDLLSC---C-----GSSCGNGCEGGY 159

Query:  199 QPNAYNY-----IIKNGGIQTESSYPYTAETGTQ----------CNFNSANIGPEEQAKI 243
pattern 237                                                      ****
               A  +     ++  G        PY     T           C+ +  +      AK 
Sbjct:  160 PIQALRWWDSKGVVTGGDYHGAGCKPYPIAPCTSGNCPESKTPSCSMSCQSGYSTAYAKD 219

Query:  244 SNFTM----IPKNETVMAGYIVSTGPLAIAADAVE-WQFYIGGVFDIPCNPNSLDHGILI 298
             +F +    +PKN   +   I + GP+  A    E +  Y  GV+          H I I
Sbjct:  220 KHFGVSAYAVPKNAASIQAEIYANGPVEAAFSVYEDFYKYKSGVYKHTAGKYLGGHAIKI 279

Query:  299 VGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFV 346
            +G+  ++       PYW+V NSWG +WGE G+  + RG + CG+ + V
Sbjct:  280 IGWGTES-----GSPYWLVANSWGVNWGESGFFKIYRGDDQCGIESAV 322


>sp|P07858|CATB_HUMAN CATHEPSIN B PRECURSOR (CATHEPSIN B1) (APP SECRETASE)
          Length = 339

 Score = 86.2 bits (210), Expect = 9e-17
 Identities = 68/285 (23%), Positives = 110/285 (37%), Gaps = 55/285 (19%)

Query:  96  KEAIFTDDLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNV 155
            +  +FT+DL             +P        W     +  +++QG CGSCW+F     +
Sbjct:  70  QRVMFTEDL------------KLPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAI 117

Query:  156 EGQHFISQNKLVSL--SEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQ 213
              +  I  N  VS+  S ++L+ C   C        C +GCNGG    A+N+  + G + 
Sbjct:  118 SDRICIHTNAHVSVEVSAEDLLTC---C-----GSMCGDGCNGGYPAEAWNFWTRKGLVS 169

Query:  214 ----------------------TESSYPYTAETGTQ-----CNFNSANIGPEEQAKISNF 246
pattern 237                                                   ****
                                    S  P T E  T      C    +    +++    N 
Sbjct:  170 GGLYESHVGCRPYSIPPCEHHVNGSRPPCTGEGDTPKCSKICEPGYSPTYKQDKHYGYNS 229

Query:  247 TMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKN 305
              +  +E  +   I   GP+  A     ++  Y  GV+          H I I+G+  +N
Sbjct:  230 YSVSNSEKDIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVTGEMMGGHAIRILGWGVEN 289

Query:  306 TIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 350
                   PYW+V NSW  DWG+ G+  + RG++ CG+ + V   I
Sbjct:  290 -----GTPYWLVANSWNTDWGDNGFFKILRGQDHCGIESEVVAGI 329


>sp|P43157|CYSP_SCHJA CATHEPSIN B-LIKE CYSTEINE PROTEINASE PRECURSOR (ANTIGEN SJ31)
          Length = 342

 Score = 85.4 bits (208), Expect = 2e-16
 Identities = 64/271 (23%), Positives = 109/271 (39%), Gaps = 57/271 (21%)

Query:  118 IPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQ--NKLVSLSEQNLV 175
            IP +  +   W    +++ +++Q +CGSCW+F     +  +  I     +   LS  +L+
Sbjct:  90  IPSQFDSRKKWPHCKSISQIRDQSRCGSCWAFGAVEAMTDRICIQSGGGQSAELSALDLI 149

Query:  176 DCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGI---------------------QT 214
             C   C +      C +GC GG    A++Y +K G +                      T
Sbjct:  150 SC---CKD------CGDGCQGGFPGVAWDYWVKRGIVTGGSKENHTGCQPYPFPKCEHHT 200

Query:  215 ESSYP-------------YTAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIV 261
pattern 237                                    ****
            +  YP              T + G +  +       +E   + N      NE V+   I+
Sbjct:  201 KGKYPACGTKIYKTPQCKQTCQKGYKTPYEQDKHYGDESYNVQN------NEKVIQRDIM 254

Query:  262 STGPLAIAADAVE-WQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNS 320
              GP+  A D  E +  Y  G++          H I I+G+  +     K  PYW++ NS
Sbjct:  255 MYGPVEAAFDVYEDFLNYKSGIYRHVTGSIVGGHAIRIIGWGVE-----KRTPYWLIANS 309

Query:  321 WGADWGEQGYIYLRRGKNTCGVSNFVSTSII 351
            W  DWGE+G   + RG++ C + + V   +I
Sbjct:  310 WNEDWGEKGLFRMVRGRDECSIESDVVAGLI 340


>sp|P43233|CATB_CHICK CATHEPSIN B PRECURSOR (CATHEPSIN B1)
          Length = 340

 Score = 85.4 bits (208), Expect = 2e-16
 Identities = 66/265 (24%), Positives = 111/265 (40%), Gaps = 46/265 (17%)

Query:  118 IPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSL--SEQNLV 175
            +P    T   W     ++ +++QG CGSCW+F     +  +  +  N  VS+  S ++L+
Sbjct:  80  LPDTFDTRKQWPNCPTISEIRDQGSCGSCWAFGAVEAISDRICVHTNAKVSVEVSAEDLL 139

Query:  176 DCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQ---------------------- 213
             C   C    G E C  GCNGG    A+ Y  + G +                       
Sbjct:  140 SC---C----GFE-CGMGCNGGYPSGAWRYWTERGLVSGGLYDSHVGCRAYTIPPCEHHV 191

Query:  214 TESSYPYTAETGT--QCNFN-----SANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPL 266
pattern 237                               ****
              S  P T E G   +C+ +     S +   ++   I+++  +P++E  +   I   GP+
Sbjct:  192 NGSRPPCTGEGGETPRCSRHCEPGYSPSYKEDKHYGITSYG-VPRSEKEIMAEIYKNGPV 250

Query:  267 AIAADAVE-WQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADW 325
              A    E +  Y  GV+          H I I+G+  +N       PYW+  NSW  DW
Sbjct:  251 EGAFIVYEDFLMYKSGVYQHVSGEQVGGHAIRILGWGVEN-----GTPYWLAANSWNTDW 305

Query:  326 GEQGYIYLRRGKNTCGVSNFVSTSI 350
            G  G+  + RG++ CG+ + +   +
Sbjct:  306 GITGFFKILRGEDHCGIESEIVAGV 330


>sp|P43510|CPR6_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 6 PRECURSOR
          Length = 379

 Score = 85.0 bits (207), Expect = 2e-16
 Identities = 71/265 (26%), Positives = 116/265 (42%), Gaps = 53/265 (20%)

Query:  118 IPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNK--LVSLSEQNLV 175
            IP    +  +W    ++  +++Q  CGSCW+F     +  +  I+ +    V+LS  +L+
Sbjct:  105 IPESFDSRDNWPKCDSIKVIRDQSSCGSCWAFGAVEAMSDRICIASHGELQVTLSADDLL 164

Query:  176 DCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQ------CN 229
             C   C      ++C  GCNGG    A+ Y +K+G I T S+Y  TA  G +      C 
Sbjct:  165 SC---C------KSCGFGCNGGDPLAAWRYWVKDG-IVTGSNY--TANNGCKPYPFPPCE 212

Query:  230 FNSANIGPE------------EQAKISNFTMIPKNETVMAGY---------------IVS 262
pattern 237        **            **
             +S     +            E+  +S++T    +E    G                +++
Sbjct:  213 HHSKKTHFDPCPHDLYPTPKCEKKCVSDYTDKTYSEDKFFGASAYGVKDDVEAIQKELMT 272

Query:  263 TGPLAIAADAVE-WQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSW 321
             GPL IA +  E +  Y GGV+          H + ++G+   + I     PYW V NSW
Sbjct:  273 HGPLEIAFEVYEDFLNYDGGVYVHTGGKLGGGHAVKLIGWGIDDGI-----PYWTVANSW 327

Query:  322 GADWGEQGYIYLRRGKNTCGVSNFV 346
              DWGE G+  + RG + CG+ + V
Sbjct:  328 NTDWGEDGFFRILRGVDECGIESGV 352


>sp|P25792|CYSP_SCHMA CATHEPSIN B-LIKE CYSTEINE PROTEINASE PRECURSOR (ANTIGEN SM31)
          Length = 340

 Score = 84.6 bits (206), Expect = 3e-16
 Identities = 64/260 (24%), Positives = 107/260 (40%), Gaps = 45/260 (17%)

Query:  118 IPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQN--KLVSLSEQNLV 175
            IP    +   W    ++  +++Q +CGSCWSF     +  +  I     + V LS  +L+
Sbjct:  89  IPSNFDSRKKWPGCKSIATIRDQSRCGSCWSFGAVEAMSDRSCIQSGGKQNVELSAVDLL 148

Query:  176 DCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTA---ETGTQCNFNS 232
             C   C      E+C  GC GG+   A++Y +K G +   S   +T        +C  ++
Sbjct:  149 TC---C------ESCGLGCEGGILGPAWDYWVKEGIVTASSKENHTGCEPYPFPKCEHHT 199

Query:  233 ANIGPEEQAKISN---------------FTM----------IPKNETVMAGYIVSTGPLA 267
pattern 237     ****
                P   +KI N               +T           +  +E  +   I+  GP+ 
Sbjct:  200 KGKYPPCGSKIYNTPRCKQTCQRKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVE 259

Query:  268 IAADAVE-WQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWG 326
             +    E +  Y  G++          H I I+G+  +N       PYW++ NSW  DWG
Sbjct:  260 ASFTVYEDFLNYKSGIYKHITGEALGGHAIRIIGWGVEN-----KTPYWLIANSWNEDWG 314

Query:  327 EQGYIYLRRGKNTCGVSNFV 346
            E GY  + RG++ C + + V
Sbjct:  315 ENGYFRIVRGRDECSIESEV 334


>sp|P10605|CATB_MOUSE CATHEPSIN B PRECURSOR (CATHEPSIN B1)
          Length = 339

 Score = 84.6 bits (206), Expect = 3e-16
 Identities = 66/253 (26%), Positives = 108/253 (42%), Gaps = 43/253 (16%)

Query:  128 WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSL--SEQNLVDCDHECMEYE 185
            W     +  +++QG CGSCW+F     +  +  I  N  V++  S ++L+ C   C    
Sbjct:  90  WSNCPTIGQIRDQGSCGSCWAFGAVEAISDRTCIHTNGRVNVEVSAEDLLTC---C---- 142

Query:  186 GEEACDEGCNGGLQPNAYNYIIK----NGGIQTE------------------SSYPYTAE 223
                C +GCNGG    A+++  K    +GG+                     S  P T E
Sbjct:  143 -GIQCGDGCNGGYPSGAWSFWTKKGLVSGGVYNSHVGCLPYTIPPCEHHVNGSRPPCTGE 201

Query:  224 TGT-QCNFN-SANIGPE-EQAKISNFTMIPKNETV--MAGYIVSTGPLAIAADAV-EWQF 277
pattern 237                ** **
              T +CN +  A   P  ++ K   +T    + +V  +   I   GP+  A     ++  
Sbjct:  202 GDTPRCNKSCEAGYSPSYKEDKHFGYTSYSVSNSVKEIMAEIYKNGPVEGAFTVFSDFLT 261

Query:  278 YIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK 337
            Y  GV+          H I I+G+  +N +     PYW+  NSW  DWG+ G+  + RG+
Sbjct:  262 YKSGVYKHEAGDMMGGHAIRILGWGVENGV-----PYWLAANSWNLDWGDNGFFKILRGE 316

Query:  338 NTCGVSNFVSTSI 350
            N CG+ + +   I
Sbjct:  317 NHCGIESEIVAGI 329


>sp|P25802|CYS1_OSTOS CATHEPSIN B-LIKE CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 341

 Score = 79.6 bits (193), Expect = 9e-15
 Identities = 63/270 (23%), Positives = 106/270 (38%), Gaps = 46/270 (17%)

Query:  103 DLPVADYLDDEFINSIPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFIS 162
            D  V D   +E  + IP        W    ++  + +Q  CGSCW+ S+   +  +  I+
Sbjct:  76  DEEVEDEELEENNDDIPESYDPRIQWANCSSLFHIPDQANCGSCWAVSSAAAMSDRICIA 135

Query:  163 QN--KLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNY-----IIKNGGIQTE 215
                K V +S Q++V C   C        C +GC GG   +A+ +     ++  G   T+
Sbjct:  136 SKGAKQVLISAQDVVSC---CTW------CGDGCEGGWPISAFRFHADEGVVTGGDYNTK 186

Query:  216 SSY-PYTAET----GTQCNFNSANIGPEEQAKISNFTMI------PKNETVMAGYIVSTG 264
pattern 237                           ****
             S  PY        G +  +    +G  +  +     ++      P +      Y +   
Sbjct:  187 GSCRPYEIHPCGHHGNETYYGEC-VGMADTPRCKRRCLLGYPKSYPSDRYYKKAYQLKNS 245

Query:  265 PLAIAADAV-------------EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKN 311
              AI  D +             ++  Y  G++       +  H + ++G+  +     K 
Sbjct:  246 VKAIQKDIMKNGPVVATYTVYEDFAHYRSGIYKHKAGRKTGLHAVKVIGWGEE-----KG 300

Query:  312 MPYWIVKNSWGADWGEQGYIYLRRGKNTCG 341
             PYWIV NSW  DWGE G+  + RG N CG
Sbjct:  301 TPYWIVANSWHDDWGENGFFRMHRGSNDCG 330


>sp|P25793|CYS2_HAECO CATHEPSIN B-LIKE CYSTEINE PROTEINASE 2 PRECURSOR
          Length = 342

 Score = 78.4 bits (190), Expect = 2e-14
 Identities = 59/266 (22%), Positives = 110/266 (41%), Gaps = 47/266 (17%)

Query:  118 IPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQN--KLVSLSEQNLV 175
            IPP       W+       +++Q  CGSCW+ ST   +  +  I+    K V++S  +++
Sbjct:  87  IPPSYDPRDVWKNCTTFY-IRDQANCGSCWAVSTAAAISDRICIASKAEKQVNISATDIM 145

Query:  176 DCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQ------TESSYPY--------- 220
             C   C        C +GC GG    A+ Y I +G +        +   PY         
Sbjct:  146 TC---C-----RPQCGDGCEGGWPIEAWKYFIYDGVVSGGEYLTKDVCRPYPIHPCGHHG 197

Query:  221 -------------TAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLA 267
pattern 237                              ****
                         T     +C      +   ++    +  ++ ++   +   I+  GP+ 
Sbjct:  198 NDTYYGECRGTAPTPPCKRKCRPGVRKMYRIDKRYGKDAYIVKQSVKAIQSEILKNGPV- 256

Query:  268 IAADAV--EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADW 325
            +A+ AV  +++ Y  G++          H + ++G+  +N     N  +W++ NSW  DW
Sbjct:  257 VASFAVYEDFRHYKSGIYKHTAGELRGYHAVKMIGWGNEN-----NTDFWLIANSWHNDW 311

Query:  326 GEQGYIYLRRGKNTCGVSNFVSTSII 351
            GE+GY  + RG N CG+   ++  I+
Sbjct:  312 GEKGYFRIVRGSNDCGIEGTIAAGIV 337


>sp|P19092|CYS1_HAECO CATHEPSIN B-LIKE CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 342

 Score = 77.6 bits (188), Expect = 4e-14
 Identities = 59/266 (22%), Positives = 110/266 (41%), Gaps = 47/266 (17%)

Query:  118 IPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQN--KLVSLSEQNLV 175
            IPP       W+       +++Q  CGSCW+ ST   +  +  I+    K V++S  +++
Sbjct:  87  IPPSYDPRDVWKNCTTFY-IRDQANCGSCWAVSTAAAISDRICIASKAEKQVNISATDIM 145

Query:  176 DCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQ------TESSYPY--------- 220
             C   C        C +GC GG    A+ Y I +G +        +   PY         
Sbjct:  146 TC---C-----RPQCGDGCEGGWPIEAWKYFIYDGVVSGGEYLTKDVCRPYPIHPCGHHG 197

Query:  221 -------------TAETGTQCNFNSANIGPEEQAKISNFTMIPKNETVMAGYIVSTGPLA 267
pattern 237                              ****
                         T     +C      +   ++    +  ++ ++   +   I+  GP+ 
Sbjct:  198 NDTYYGECRGTAPTPPCKRKCRPGVRKMYRIDKRYGKDAYIVKQSVKAIQSEILRNGPV- 256

Query:  268 IAADAV--EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADW 325
            +A+ AV  +++ Y  G++          H + ++G+  +N     N  +W++ NSW  DW
Sbjct:  257 VASFAVYEDFRHYKSGIYKHTAGELRGYHAVKMIGWGNEN-----NTDFWLIANSWHNDW 311

Query:  326 GEQGYIYLRRGKNTCGVSNFVSTSII 351
            GE+GY  + RG N CG+   ++  I+
Sbjct:  312 GEKGYFRIIRGTNDCGIEGTIAAGIV 337


>sp|P43507|CPR3_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 3 PRECURSOR
          Length = 370

 Score = 73.3 bits (177), Expect = 7e-13
 Identities = 56/248 (22%), Positives = 98/248 (38%), Gaps = 39/248 (15%)

Query:  128 WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVS--LSEQNLVDCDHECMEYE 185
            W     +  ++NQ  CGSCW+F     +  +  I  N      +S ++++ C   C    
Sbjct:  102 WPDCNTIKLIRNQATCGSCWAFGAAEVISDRVCIQSNGTQQPVISVEDILSC---C---- 154

Query:  186 GEEACDEGCNGGLQPNAYNYIIKNGGIQ---------------------TESSYPYTAET 224
                C  GC GG    A  +   +G +                       ES+ P + +T
Sbjct:  155 -GTTCGYGCKGGYSIEALRFWASSGAVTGGDYGGHGCMPYSFAPCTKNCPESTTP-SCKT 212

Query:  225 GTQCNFNSANIGPEEQAKISNFTMIP-KNETVMAGYIVSTGPLAIAADAVE-WQFYIGGV 282
pattern 237             ****
              Q ++ +     ++    S + +   K+ T +   I   GP+  +    E +  Y  GV
Sbjct:  213 TCQSSYKTEEYKKDKHYGASAYKVTTTKSVTEIQTEIYHYGPVEASYKVYEDFYHYKSGV 272

Query:  283 FDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGV 342
            +          H + I+G+  +N +      YW++ NSWG  +GE+G+  +RRG N C +
Sbjct:  273 YHYTSGKLVGGHAVKIIGWGVENGV-----DYWLIANSWGTSFGEKGFFKIRRGTNECQI 327

Query:  343 SNFVSTSI 350
               V   I
Sbjct:  328 EGNVVAGI 335


>sp|P13823|SERA_PLAFG SERINE-REPEAT ANTIGEN PROTEIN PRECURSOR (P126) (111 KD ANTIGEN)
          Length = 989

 Score = 70.2 bits (169), Expect = 6e-12
 Identities = 63/247 (25%), Positives = 102/247 (40%), Gaps = 46/247 (18%)

Query:  137 VKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE--EACDEGC 194
            V++QG C + W F++  ++E    +   +   +S   + +C      Y+GE  + CDEG 
Sbjct:  579 VEDQGNCDTSWIFASKYHLETIRCMKGYEPTKISALYVANC------YKGEHKDRCDEGS 632

Query:  195 NGGLQPNAYNYIIKNGG-IQTESSYPYT-AETGTQC------------------NFNSAN 234
            +    P  +  II++ G +  ES+YPY   + G QC                  N N  N
Sbjct:  633 S----PMEFLQIIEDYGFLPAESNYPYNYVKVGEQCPKVEDHWMNLWDNGKILHNKNEPN 688

Query:  235 I----------GPEEQAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFD 284
pattern 237             ****
                              +  F  I K E +  G +++     I A+ V    + G    
Sbjct:  689 SLDGKGYTAYESERFHDNMDAFVKIIKTEVMNKGSVIAY----IKAENVMGYEFSGKKVQ 744

Query:  285 IPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN 344
              C  ++ DH + IVGY        +   YWIV+NSWG  WG++GY  +     T    N
Sbjct:  745 NLCGDDTADHAVNIVGYGNYVNSEGEKKSYWIVRNSWGPYWGDEGYFKVDMYGPTHCHFN 804

Query:  345 FVSTSII 351
            F+ + +I
Sbjct:  805 FIHSVVI 811


>sp|P32956|CC3_CARCN CYSTEINE PROTEINASE III (CC-III)
          Length = 43

 Score = 60.9 bits (145), Expect = 4e-09
 Identities = 24/33 (72%), Positives = 27/33 (81%)

Query: 125 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEG 157
           + DWR +GAVTPVKNQG CGSCW+FST   VEG
Sbjct: 4   SIDWRKKGAVTPVKNQGSCGSCWAFSTIATVEG 36


>sp|P32957|CC4_CARCN CYSTEINE PROTEINASE IV (CC-IV)
          Length = 43

 Score = 59.7 bits (142), Expect = 9e-09
 Identities = 24/33 (72%), Positives = 27/33 (81%)

Query: 125 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEG 157
           + DWR +GAVTPVKNQG CGSCW+FST   VEG
Sbjct: 4   SIDWRKKGAVTPVKNQGSCGSCWAFSTIVTVEG 36


>sp|Q06544|CYS3_OSTOS CATHEPSIN B-LIKE CYSTEINE PROTEINASE 3
          Length = 174

 Score = 59.3 bits (141), Expect = 1e-08
 Identities = 31/103 (30%), Positives = 49/103 (47%), Gaps = 15/103 (14%)

Query: 249 IPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIF 308
           I KN  V+AG+IV            ++  Y  G++       +  H + I+G+  +    
Sbjct: 87  IMKNGPVVAGFIVYE----------DFAHYKSGIYKHTAGRMTGGHAVKIIGWGKE---- 132

Query: 309 RKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 351
            K  PYW++ NSW  DWGE+G+  + RG N C +   V   I+
Sbjct: 133 -KGTPYWLIANSWHDDWGEKGFYRMIRGINNCRIEEMVFAGIV 174


>sp|P32954|CC1_CARCN CYSTEINE PROTEINASE I (CC-I)
          Length = 43

 Score = 57.8 bits (137), Expect = 3e-08
 Identities = 22/33 (66%), Positives = 27/33 (81%)

Query: 125 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEG 157
           + DWR +GAVTPV+NQG CGSCW+FS+   VEG
Sbjct: 4   SIDWRQKGAVTPVRNQGSCGSCWTFSSVAAVEG 36


>sp|P32955|CC2_CARCN CYSTEINE PROTEINASE II (CC-II)
          Length = 43

 Score = 56.2 bits (133), Expect = 1e-07
 Identities = 22/31 (70%), Positives = 25/31 (79%)

Query: 127 DWRTRGAVTPVKNQGQCGSCWSFSTTGNVEG 157
           DWR +GAVTPVK+Q  CGSCW+FST   VEG
Sbjct: 6   DWRQKGAVTPVKDQNPCGSCWAFSTVATVEG 36


>sp||CATL_CHICK_2 [Segment 2 of 2] CATHEPSIN L
          Length = 42

 Score = 51.9 bits (122), Expect = 2e-06
 Identities = 20/39 (51%), Positives = 28/39 (71%), Gaps = 1/39 (2%)

Query: 314 YWIVKNSWGADWGEQGYIYLRRG-KNTCGVSNFVSTSII 351
           YWIVKNSWG  WG++GYIY+ +  KN CG++   S  ++
Sbjct: 4   YWIVKNSWGEKWGDKGYIYMAKDRKNHCGIATAASYPLV 42


>sp|P12399|CT2A_MOUSE CTLA-2-ALPHA PROTEIN PRECURSOR
          Length = 136

 Score = 41.8 bits (96), Expect = 0.002
 Identities = 31/101 (30%), Positives = 50/101 (48%), Gaps = 4/101 (3%)

Query: 9   LAVFTVFVSSRGIPPEEQ--SQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIA 66
           L +  + + S   PP+    +++ E++ KF K Y+  E   R  +++ N  KIE  N   
Sbjct: 17  LLILCLGMMSAAPPPDPSLDNEWKEWKTKFAKAYNLNEERHRRLVWEENKKKIEAHNADY 76

Query: 67  INHKADTKFGVNKFADLSSDEFK-NYYLNN-KEAIFTDDLP 105
              K     G+N+F+DL+ +EFK N Y N+        DLP
Sbjct: 77  EQGKTSFYMGLNQFSDLTPEEFKTNCYGNSLNRGEMAPDLP 117


>sp|P05689|CATX_BOVIN CATHEPSIN
          Length = 73

 Score = 40.2 bits (92), Expect = 0.006
 Identities = 15/40 (37%), Positives = 24/40 (59%), Gaps = 5/40 (12%)

Query: 292 LDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYI 331
           ++H + + G+   +      M YWIV+NSWG  WGE G++
Sbjct: 9   INHIVSVAGWGVSD-----GMEYWIVRNSWGEPWGEHGWM 43


>sp|P12400|CT2B_MOUSE CTLA-2-BETA PROTEIN PRECURSOR
          Length = 141

 Score = 38.7 bits (88), Expect = 0.019
 Identities = 25/85 (29%), Positives = 45/85 (52%), Gaps = 1/85 (1%)

Query: 6   LFVLAVFTVFVSSRGIP-PEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNL 64
           +F+L +    +S+   P P   +++ E++  F K YS +E   R  +++ N  KIE  N 
Sbjct: 20  VFLLILCLGMMSAAPSPDPSLDNEWKEWKTTFAKAYSLDEERHRRLMWEENKKKIEAHNA 79

Query: 65  IAINHKADTKFGVNKFADLSSDEFK 89
                K     G+N+F+DL+ +EF+
Sbjct: 80  DYERGKTSFYMGLNQFSDLTPEEFR 104


>sp|P23897|HSER_RAT HEAT-STABLE ENTEROTOXIN RECEPTOR PRECURSOR (GC-C) (INTESTINAL
           GUANYLATE CYCLASE) (STA RECEPTOR)
          Length = 1072

 Score = 35.6 bits (80), Expect = 0.16
 Identities = 32/120 (26%), Positives = 56/120 (46%), Gaps = 19/120 (15%)

Query: 15  FVSSRGIPPEEQSQFLEFQDK----FNKKYSHEEYLERFEIFKSNL-GKIEELNLIAINH 69
           +V   G  PE+   +L   +     F++  S ++ L R E F+  L G+  + N+I +  
Sbjct: 190 YVYKNGSEPEDCFWYLNALEAGVSYFSEVLSFKDVLRRSEQFQEILMGRNRKSNVIVMCG 249

Query: 70  KADTKFGVN---KFAD----LSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEE 122
             +T + V    K AD    +  D F N+Y       F DD    +Y+D+  + ++PPE+
Sbjct: 250 TPETFYNVKGDLKVADDTVVILVDLFSNHY-------FEDDTRAPEYMDNVLVLTLPPEK 302


>sp|P20736|BM86_BOOMI GLYCOPROTEIN ANTIGEN BM86 PRECURSOR (PROTECTIVE ANTIGEN)
          Length = 650

 Score = 35.2 bits (79), Expect = 0.22
 Identities = 24/81 (29%), Positives = 36/81 (43%), Gaps = 5/81 (6%)

Query: 151 TTGNVEGQHFISQNKLVSLSEQNLVDC----DHECMEYEGEEACDEGCNGGLQPNAYNYI 206
           TT N +        KL  + + +  +C    DHEC     +++C E  NG  Q +    +
Sbjct: 533 TTCNPKEIQECQDKKLECVYKNHKAECECPDDHECYREPAKDSCSEEDNGKCQSSGQRCV 592

Query: 207 IKNG-GIQTESSYPYTAETGT 226
           I+NG  +  E S   TA T T
Sbjct: 593 IENGKAVCKEKSEATTAATTT 613


>sp|P46992|YJR1_YEAST HYPOTHETICAL 43.0 KD PROTEIN IN CPS1-FPP1 INTERGENIC REGION
          Length = 396

 Score = 32.0 bits (71), Expect = 1.9
 Identities = 39/191 (20%), Positives = 77/191 (39%), Gaps = 39/191 (20%)

Query: 77  VNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPPEE-------------- 122
           VNKF D++++E     + ++      + P+ADYL   F   +  ++              
Sbjct: 42  VNKFKDITNNESCTCEVGDRVWFSGKNAPLADYLSVHFRGPLKLKQFAFYTSPGFTVNNS 101

Query: 123 QTAFDW----------RTRGAVTPVKNQGQCGSCW-------SFSTTGNVEGQHFISQNK 165
           +++ DW          +T   VT + + G+   C        S + TG+      ++   
Sbjct: 102 RSSSDWNRLAYYESSSKTADNVTFLNHGGEASPCLGNALSYASSNGTGSASEATVLADGT 161

Query: 166 LVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETG 225
           L+S  ++ ++  +  C +   ++ C    +G   P  Y Y    GG  T   + +  E  
Sbjct: 162 LISSDQEYIIYSNVSCPKSGYDKGCGVYRSG--IPAYYGY----GG--TTKMFLFEFEMP 213

Query: 226 TQCNFNSANIG 236
           T+   NS++IG
Sbjct: 214 TETEKNSSSIG 224


>sp|P28493|PR5_ARATH PATHOGENESIS-RELATED PROTEIN 5 PRECURSOR (PR-5)
          Length = 239

 Score = 32.0 bits (71), Expect = 1.9
 Identities = 24/93 (25%), Positives = 36/93 (37%), Gaps = 7/93 (7%)

Query: 137 VKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNG 196
           ++  G  G C      G V   +    + L  + + N+V C   C  +  ++ C  G N 
Sbjct: 137 IRPSGGSGDC---KYAGCVSDLNAACPDMLKVMDQNNVVACKSACERFNTDQYCCRGAND 193

Query: 197 GLQ---PNAYNYIIKNGGIQTESSYPYTAETGT 226
             +   P  Y+ I KN       SY Y  ET T
Sbjct: 194 KPETCPPTDYSRIFKN-ACPDAYSYAYDDETST 225


>sp|P54634|POLN_LORDV NON-STRUCTURAL POLYPROTEIN [CONTAINS: RNA-DIRECTED RNA POLYMERASE ;
           THIOL PROTEASE 3C ; HELICASE (2C LIKE PROTEIN)]
          Length = 1699

 Score = 31.3 bits (69), Expect = 3.2
 Identities = 13/31 (41%), Positives = 21/31 (66%)

Query: 17  SSRGIPPEEQSQFLEFQDKFNKKYSHEEYLE 47
           SS+G+  EE  ++   +++ N KYS EEYL+
Sbjct: 893 SSKGLSDEEYDEYKRIREERNGKYSIEEYLQ 923


>sp|Q02521|SPP2_YEAST SPLICEOSOME MATURATION PROTEIN SPP2
          Length = 185

 Score = 30.9 bits (68), Expect = 4.2
 Identities = 24/99 (24%), Positives = 47/99 (47%), Gaps = 6/99 (6%)

Query: 30  LEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKF---GVNKF-ADLSS 85
           L+   K  KK   ++  ++  + K+NL   ++    +++HK  +K     ++KF  D  S
Sbjct: 6   LKLGSKTLKKNISKKTKKKNSLQKANLFDWDDAETASLSHKPQSKIKIQSIDKFDLDEES 65

Query: 86  DEFKNYYLNNKEAIFT--DDLPVADYLDDEFINSIPPEE 122
              K   +   E   T  +D P+ +Y+ ++  N +P EE
Sbjct: 66  SSKKKLVIKLSENADTKKNDAPLVEYVTEKEYNEVPVEE 104


>sp|P41901|SPR3_YEAST SPORULATION-SPECIFIC SEPTIN
          Length = 512

 Score = 30.9 bits (68), Expect = 4.2
 Identities = 17/58 (29%), Positives = 29/58 (49%), Gaps = 9/58 (15%)

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINS 117
           + +NLI +  K+D          L+ +E KN+    +E I   D+PV  +  DE +N+
Sbjct: 237 KRVNLIPVIAKSDL---------LTKEELKNFKTQVREIIRVQDIPVCFFFGDEVLNA 285


>sp|Q01532|BLH1_YEAST CYSTEINE PROTEINASE 1 (Y3) (BLEOMYCIN HYDROLASE) (BLM HYDROLASE)
          Length = 454

 Score = 30.5 bits (67), Expect = 5.5
 Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 11/66 (16%)

Query: 111 DDEFINS--IPPEEQTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVS 168
           DD  +N   +  ++   F+       TPV NQ   G CW F+ T         +Q +L  
Sbjct: 36  DDALLNKTRLQKQDNRVFNTVVSTDSTPVTNQKSSGRCWLFAAT---------NQLRLNV 86

Query: 169 LSEQNL 174
           LSE NL
Sbjct: 87  LSELNL 92


>sp|P24896|NU5M_CAEEL NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 5
          Length = 527

 Score = 30.5 bits (67), Expect = 5.5
 Identities = 21/52 (40%), Positives = 26/52 (49%), Gaps = 7/52 (13%)

Query: 44  EYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNN 95
           +YL +  I+K    K  +L L  IN K  T F       LSS  FKNYYL +
Sbjct: 466 DYLAKNSIYKMKNLKFMDLFLNNINSKGYTLF-------LSSGMFKNYYLKS 510


>sp|P25648|SRB8_YEAST SUPPRESSOR OF RNA POLYMERASE B SRB8
          Length = 1427

 Score = 30.1 bits (66), Expect = 7.2
 Identities = 22/89 (24%), Positives = 44/89 (48%), Gaps = 10/89 (11%)

Query: 21   IPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGV--- 77
            +PP + S F++     +  Y  EE  ++ E F  NLG    + ++ I H+ + K+ +   
Sbjct: 1314 LPPFQVSSFVKETKLHSGDYGEEEDADQEESFSLNLG----IGIVEIAHENEQKWLIYDK 1369

Query: 78   --NKFADLSSDEFKNYYLNNKEAIFTDDL 104
              +K+    S E   ++++N    +TDD+
Sbjct: 1370 KDHKYVCTFSME-PYHFISNYNTKYTDDM 1397


>sp|Q04723|PEPC_LACLC AMINOPEPTIDASE C
          Length = 436

 Score = 30.1 bits (66), Expect = 7.2
 Identities = 11/20 (55%), Positives = 14/20 (70%)

Query: 311 NMPYWIVKNSWGADWGEQGY 330
           N   W V+NSWG D G++GY
Sbjct: 370 NSTKWKVENSWGKDAGQKGY 389


>sp|Q13867|BLMH_HUMAN BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH)
          Length = 455

 Score = 29.7 bits (65), Expect = 9.4
 Identities = 10/17 (58%), Positives = 13/17 (75%)

Query: 315 WIVKNSWGADWGEQGYI 331
           W V+NSWG D G +GY+
Sbjct: 392 WRVENSWGEDHGHKGYL 408


>sp|P87362|BLMH_CHICK BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH) (AMINOPEPTIDASE H)
          Length = 455

 Score = 29.7 bits (65), Expect = 9.4
 Identities = 10/19 (52%), Positives = 14/19 (73%)

Query: 315 WIVKNSWGADWGEQGYIYL 333
           W V+NSWG D G +GY+ +
Sbjct: 392 WRVENSWGEDRGNKGYLIM 410


>sp|P70645|BLMH_RAT BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH)
          Length = 454

 Score = 29.7 bits (65), Expect = 9.4
 Identities = 10/17 (58%), Positives = 13/17 (75%)

Query: 315 WIVKNSWGADWGEQGYI 331
           W V+NSWG D G +GY+
Sbjct: 392 WRVENSWGEDHGHKGYL 408


  Database: /home/peter/blast/data/swissprot
    Posted date:  Oct 10, 2000 10:43 AM
  Number of letters in database: 31,984,247
  Number of sequences in database:  88,780
  
Lambda     K      H
   0.317    0.136    0.414 

Lambda     K      H
   0.270   0.0477    0.230 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23348054
Number of Sequences: 88780
Number of extensions: 1039466
Number of successful extensions: 3135
Number of sequences better than 10.0: 162
Number of HSP's better than 10.0 without gapping: 118
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 2557
Number of HSP's gapped (non-prelim): 148
length of query: 351
length of database: 31,984,247
effective HSP length: 50
effective length of query: 301
effective length of database: 27,545,247
effective search space: 8291119347
effective search space used: 8291119347
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 41 (21.6 bits)
S2: 65 (29.7 bits)
BioPerl-1.007002/t/data/phmmer.out000444000766000024      2770013155576321 16737 0ustar00cjfieldsstaff000000000000# phmmer :: search a protein sequence against a protein database
# HMMER 3.1b1 (May 2013); http://hmmer.org/
# Copyright (C) 2013 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /tmp/task-hmmsearch-TCHn9R/ZRkI2xwebU
# target sequence database:        /cath/data/v4_0_0/release_data/CathDomainSeqs.COMBS
# output directed to file:         /tmp/phmmer.out
# sequence reporting threshold:    E-value <= 0.01
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       A0R3R7  [L=762]
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    2.1e-55  191.8   3.7    2.3e-55  191.7   3.7    1.0  1  cath|4_0_0|1vs0A03/639-759          
    2.1e-55  191.8   3.7    2.3e-55  191.7   3.7    1.0  1  cath|4_0_0|1vs0B03/639-759          
    1.9e-46  162.2   0.2    2.1e-46  162.1   0.2    1.0  1  cath|4_0_0|1vs0A02/484-593          
    1.9e-46  162.2   0.2    2.1e-46  162.1   0.2    1.0  1  cath|4_0_0|1vs0B02/484-593          
    5.8e-17   64.7   1.4    7.1e-10   41.3   0.1    2.0  2  cath|4_0_0|1vs0A01/453-483_594-638  
    5.8e-17   64.7   1.4    7.1e-10   41.3   0.1    2.0  2  cath|4_0_0|1vs0B01/453-483_594-638  
    6.4e-07   31.5   0.1    8.1e-07   31.2   0.1    1.0  1  cath|4_0_0|2cfmA03/422-561          
    0.00065   21.6   0.0    0.00069   21.5   0.0    1.0  1  cath|4_0_0|1x9nA03/571-696          


Domain annotation for each sequence (and alignments):
>> cath|4_0_0|1vs0A03/639-759  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.7   3.7   7.9e-60   2.3e-55     642     761 ..       1     120 [.       1     121 [] 0.99

  Alignments for each domain:
  == domain 1  score: 191.7 bits;  conditional E-value: 7.9e-60
                      A0R3R7 642 wntqevviggwrqgeggrssgigalvlgipgpeglqfvgrvgtgftekelsklkdmlkplhtdespfnaplpkvdargvtfvr 724
                                 wntqevviggwr geggrssg+g+l+ gipgp glqf grvgtg++e+el+ lk+ l plhtdespf+ plp  da+g+t+v+
  cath|4_0_0|1vs0A03/639-759   1 WNTQEVVIGGWRAGEGGRSSGVGSLLXGIPGPGGLQFAGRVGTGLSERELANLKEXLAPLHTDESPFDVPLPARDAKGITYVK 83 
                                 *********************************************************************************** PP

                      A0R3R7 725 pelvgevrysertsdgrlrqpswrglrpdktpdevvw 761
                                 p lv+evryse t +grlrq swrglrpdk p evv 
  cath|4_0_0|1vs0A03/639-759  84 PALVAEVRYSEWTPEGRLRQSSWRGLRPDKKPSEVVR 120
                                 ***********************************96 PP

>> cath|4_0_0|1vs0B03/639-759  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.7   3.7   7.9e-60   2.3e-55     642     761 ..       1     120 [.       1     121 [] 0.99

  Alignments for each domain:
  == domain 1  score: 191.7 bits;  conditional E-value: 7.9e-60
                      A0R3R7 642 wntqevviggwrqgeggrssgigalvlgipgpeglqfvgrvgtgftekelsklkdmlkplhtdespfnaplpkvdargvtfvr 724
                                 wntqevviggwr geggrssg+g+l+ gipgp glqf grvgtg++e+el+ lk+ l plhtdespf+ plp  da+g+t+v+
  cath|4_0_0|1vs0B03/639-759   1 WNTQEVVIGGWRAGEGGRSSGVGSLLXGIPGPGGLQFAGRVGTGLSERELANLKEXLAPLHTDESPFDVPLPARDAKGITYVK 83 
                                 *********************************************************************************** PP

                      A0R3R7 725 pelvgevrysertsdgrlrqpswrglrpdktpdevvw 761
                                 p lv+evryse t +grlrq swrglrpdk p evv 
  cath|4_0_0|1vs0B03/639-759  84 PALVAEVRYSEWTPEGRLRQSSWRGLRPDKKPSEVVR 120
                                 ***********************************96 PP

>> cath|4_0_0|1vs0A02/484-593  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   0.2     7e-51   2.1e-46     487     596 ..       1     110 []       1     110 [] 0.99

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 7e-51
                      A0R3R7 487 gyrviidadhgqlqirsrtgrevtgeypqfkalaadlaehhvvldgeavaldesgvpsfgqmqnrarstrvefwafdilwldg 569
                                 gyr++++adhg +++rsr+gr+vt+eypq++ala dla+hhvvldgeav ld sgvpsf+q qnr r trvefwafd+l+ldg
  cath|4_0_0|1vs0A02/484-593   1 GYRLLVEADHGAVRLRSRSGRDVTAEYPQLRALAEDLADHHVVLDGEAVVLDSSGVPSFSQXQNRGRDTRVEFWAFDLLYLDG 83 
                                 8********************************************************************************** PP

                      A0R3R7 570 rsllrakysdrrkilealadggglivp 596
                                 r+ll  +y drrk+le la++ +l vp
  cath|4_0_0|1vs0A02/484-593  84 RALLGTRYQDRRKLLETLANATSLTVP 110
                                 *********************999998 PP

>> cath|4_0_0|1vs0B02/484-593  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   0.2     7e-51   2.1e-46     487     596 ..       1     110 []       1     110 [] 0.99

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 7e-51
                      A0R3R7 487 gyrviidadhgqlqirsrtgrevtgeypqfkalaadlaehhvvldgeavaldesgvpsfgqmqnrarstrvefwafdilwldg 569
                                 gyr++++adhg +++rsr+gr+vt+eypq++ala dla+hhvvldgeav ld sgvpsf+q qnr r trvefwafd+l+ldg
  cath|4_0_0|1vs0B02/484-593   1 GYRLLVEADHGAVRLRSRSGRDVTAEYPQLRALAEDLADHHVVLDGEAVVLDSSGVPSFSQXQNRGRDTRVEFWAFDLLYLDG 83 
                                 8********************************************************************************** PP

                      A0R3R7 570 rsllrakysdrrkilealadggglivp 596
                                 r+ll  +y drrk+le la++ +l vp
  cath|4_0_0|1vs0B02/484-593  84 RALLGTRYQDRRKLLETLANATSLTVP 110
                                 *********************999998 PP

>> cath|4_0_0|1vs0A01/453-483_594-638  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   4.2e-09   0.00012     459     487 ..       7      35 ..       4      37 .. 0.93
   2 !   41.3   0.1   2.4e-14   7.1e-10     598     640 ..      36      78 ..      34      79 .] 0.96

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.2e-09
                              A0R3R7 459 edfapmlategsvakykakqwafegkwdg 487
                                         +++ap lat g+va  ka qwafeg wd 
  cath|4_0_0|1vs0A01/453-483_594-638   7 DNLAPXLATHGTVAGLKASQWAFEGXWDE 35 
                                         578************************95 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 2.4e-14
                              A0R3R7 598 qlpgdgpeamehvrkkrfegvvakkwdstyqpgrrssswikdk 640
                                          lpgdg +a+   rk  +egv+ak+ ds yqpgrr +sw+kdk
  cath|4_0_0|1vs0A01/453-483_594-638  36 LLPGDGAQAFACSRKHGWEGVIAKRRDSRYQPGRRCASWVKDK 78 
                                         69****************************************8 PP

>> cath|4_0_0|1vs0B01/453-483_594-638  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   4.2e-09   0.00012     459     487 ..       7      35 ..       4      37 .. 0.93
   2 !   41.3   0.1   2.4e-14   7.1e-10     598     640 ..      36      78 ..      34      79 .] 0.96

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.2e-09
                              A0R3R7 459 edfapmlategsvakykakqwafegkwdg 487
                                         +++ap lat g+va  ka qwafeg wd 
  cath|4_0_0|1vs0B01/453-483_594-638   7 DNLAPXLATHGTVAGLKASQWAFEGXWDE 35 
                                         578************************95 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 2.4e-14
                              A0R3R7 598 qlpgdgpeamehvrkkrfegvvakkwdstyqpgrrssswikdk 640
                                          lpgdg +a+   rk  +egv+ak+ ds yqpgrr +sw+kdk
  cath|4_0_0|1vs0B01/453-483_594-638  36 LLPGDGAQAFACSRKHGWEGVIAKRRDSRYQPGRRCASWVKDK 78 
                                         69****************************************8 PP

>> cath|4_0_0|2cfmA03/422-561  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.1   2.7e-11   8.1e-07     646     758 ..       8     117 ..       2     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.7e-11
                      A0R3R7 646 evviggwrqgeggrssgigalvlgipgpeglqf..vgrvgtgftekelsklkdmlkplhtdespfnapl.pkvdargvtfvrp 725
                                 ++vi g + geg r+  +g+++lg   pe  +f  vg+vg+gft+ +l ++   lkpl   e      l pkv    vt+   
  cath|4_0_0|2cfmA03/422-561   8 DLVIIGAEWGEGRRAHLFGSFILGAYDPETGEFleVGKVGSGFTDDDLVEFTKXLKPLIIKEEGKRVWLqPKVV-IEVTYQ-- 87 
                                 456667789********************9888667**********************9988877776636664.446663.. PP

                      A0R3R7 726 elvgevrysertsdgrlrqpswrglrpdktpde 758
                                 e+    +y    s   lr p + +lr dk p++
  cath|4_0_0|2cfmA03/422-561  88 EIQKSPKY---RSGFALRFPRFVALRDDKGPED 117
                                 44444444...355689************9987 PP

>> cath|4_0_0|1x9nA03/571-696  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.3e-08   0.00069     494     585 ..       9     113 ..       1     124 [. 0.74

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.3e-08
                      A0R3R7 494 adhgqlqirsrtgrevtgeypqfkalaadlae...hhvvldgeavalde..sgvpsfgqmqnrars........trvefwafd 563
                                  + g+++i sr  ++ tg+yp + +    +        +ld eava d     +  f  +  r r          +v ++afd
  cath|4_0_0|1x9nA03/571-696   9 LEGGEVKIFSRNQEDNTGKYPDIISRIPKIKLpsvTSFILDTEAVAWDRekKQIQPFQVLTTRKRKevdaseiqVQVCLYAFD 91 
                                 36799*****************98776665430114679*******9962256889998888877422222211345589*** PP

                      A0R3R7 564 ilwldgrsllrakysdrrkile 585
                                 +++l+g+sl+r   s rr++l 
  cath|4_0_0|1x9nA03/571-696  92 LIYLNGESLVREPLSRRRQLLR 113
                                 ******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                              1  (762 nodes)
Target sequences:                       235858  (38973128 residues searched)
Passed MSV filter:                      6997  (0.0296662); expected 4717.2 (0.02)
Passed bias filter:                     6066  (0.0257189); expected 4717.2 (0.02)
Passed Vit filter:                       317  (0.00134403); expected 235.9 (0.001)
Passed Fwd filter:                         9  (3.81586e-05); expected 2.4 (1e-05)
Initial search space (Z):             235858  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 4.10u 0.03s 00:00:04.13 Elapsed: 00:00:00.62
# Mc/sec: 47899.23
//
[ok]
BioPerl-1.007002/t/data/phylipdist-36.out000444000766000024      3072713155576321 20071 0ustar00cjfieldsstaff000000000000   39
CBG01299    0.0000  0.0817  0.0592  0.3233  1.1054  1.8888  2.1754  1.8934
  2.1527  1.7524  3.0956  2.1666  2.5412  1.7686  2.7063  4.1339  4.2758
  2.0880  2.7562  2.5353  2.8402  2.6241  2.5270  3.2007  2.5240  2.7543
  2.8516  2.6939  3.2467  3.5679  3.6727  4.0515  4.1651  5.2267  4.8451
  4.3745  3.2268  5.0186  4.7793
CBG01300    0.0817  0.0000  0.0950  0.3111  1.1311  1.9558  2.2197  1.9320
  2.0299  1.8101  3.0581  2.2421  2.4764  1.7550  2.6971  4.5407  4.6271
  2.1786  2.8859  2.4726  2.8045  2.6099  2.4506  3.1862  2.5982  2.7305
  2.7926  2.8251  3.1864  3.5483  3.6954  4.0547  3.9877  5.3975  4.5982
  4.3584  3.0069  4.7190  4.7592
CBG01310    0.0592  0.0950  0.0000  0.3044  1.0783  1.7794  2.0800  1.7604
  2.1519  1.6822  3.0648  2.2776  2.3625  1.7116  2.5222  4.0405  4.0662
  1.8746  2.6138  2.4393  2.6637  2.3819  2.3785  2.9213  2.4552  2.5751
  2.7080  2.5817  3.0913  3.3989  3.5036  3.8942  4.1556  4.7610  4.0620
  3.9918  3.1087  4.5302  4.1661
CBG01309    0.3233  0.3111  0.3044  0.0000  1.2678  2.0095  2.2611  1.7987
  2.2973  2.5338  3.3318  2.2343  2.4923  2.0327  2.8308  4.2220  4.5559
  2.1512  3.0813  2.4151  2.6066  2.6837  2.7222  3.2280  3.2690  2.9720
  2.7759  2.9316  3.0455  4.3733  3.9787  4.8184  4.8889  4.9857  5.9673
  4.5837  4.1999  5.7211  4.7700
CBG22544    1.1054  1.1311  1.0783  1.2678  0.0000  2.3005  2.2678  2.0929
  2.6664  2.3400  3.7396  2.8023  2.5696  2.4446  2.8767  4.5479  4.1948
  2.1784  3.4408  2.5884  2.8710  2.8704  2.8186  2.9751  3.2856  3.2412
  3.3431  3.0718  3.6222  4.8202  4.4527  4.5427  4.2937  4.9768  4.6224
  4.3548  3.4335  5.1190  4.5442
CBG20585    1.8888  1.9558  1.7794  2.0095  2.3005  0.0000  1.6243  1.7037
  2.5358  2.9125  2.9857  3.8051  2.8146  2.1396  2.9517  3.6259  3.3024
  2.3407  2.5640  2.9741  2.9219  2.8086  2.7746  2.4331  2.4465  3.5125
  2.5244  3.2094  3.1828  4.5101  4.5919  4.4979  3.8859  5.1380  5.1993
  5.9836  4.3432  6.4117  4.8479
CBG23176    2.1754  2.2197  2.0800  2.2611  2.2678  1.6243  0.0000  1.3465
  2.4525  2.9269  3.1125  3.2487  2.3650  1.9584  3.1241  3.3811  3.2762
  2.1610  1.9983  2.8666  3.3917  2.4625  2.5294  2.8067  2.3930  3.3267
  2.4879  3.3610  3.3407  4.2896  4.8651  4.7867  3.7278  4.2166  5.4427
  5.7439  5.0511  5.4130  4.2919
CBG23612    1.8934  1.9320  1.7604  1.7987  2.0929  1.7037  1.3465  0.0000
  2.7833  2.7880  2.7217  3.0016  1.9889  1.8519  2.6404  3.5699  3.1966
  2.0200  2.1845  2.2500  2.5397  2.1483  2.0645  2.8851  2.3342  2.9882
  2.6273  2.9374  2.6007  4.2752  3.5955  3.2871  3.2864  4.3964  4.2783
  5.1700  4.4989  4.7197  3.4620
CBG10552    2.1527  2.0299  2.1519  2.2973  2.6664  2.5358  2.4525  2.7833
  0.0000  1.2087  3.1408  2.2870  3.5466  2.7371  4.3457  3.9308  3.6277
  2.4312  3.0315  2.6773  3.5620  3.1399  3.6217  3.0567  3.2404  3.3961
  3.1915  3.4462  3.8474  4.9926  4.9183  4.3491  4.5937  5.6950  5.0554
  7.6270  3.8392  5.2635  5.0165
CBG23530    1.7524  1.8101  1.6822  2.5338  2.3400  2.9125  2.9269  2.7880
  1.2087  0.0000  4.0816  2.7703  3.6054  2.9679  4.3304  4.8338  4.6208
  2.6064  3.3095  3.0407  4.5735  3.9027  3.4701  3.8061  3.7082  3.5302
  3.4530  4.6425  3.7924  4.9159  5.1012  4.8005  5.4006  5.4801  5.8932
  9.8750  5.1466  6.8839  6.2445
CBG01466    3.0956  3.0581  3.0648  3.3318  3.7396  2.9857  3.1125  2.7217
  3.1408  4.0816  0.0000  1.8592  2.3738  1.8216  2.3118  5.5897  4.6319
  2.8710  2.6876  4.1532  3.7306  3.1374  2.7316  3.1479  2.2777  3.9899
  2.7702  3.2043  3.3944  5.5110  4.6346  4.3744  4.1109  4.6211  4.4749
  5.8343  5.5416  5.8238  5.8422
CBG22548    2.1666  2.2421  2.2776  2.2343  2.8023  3.8051  3.2487  3.0016
  2.2870  2.7703  1.8592  0.0000  2.8299  2.4083  2.9370  3.5815  3.5466
  2.8880  3.0227  3.5764  3.0695  3.2547  3.5399  3.3406  2.9640  4.4963
  3.0453  3.7199  3.9175  8.1129  5.2160  5.6628  4.6900  6.2934  5.3828
  8.8144  5.2604  6.1903  8.6700
CBG05066    2.5412  2.4764  2.3625  2.4923  2.5696  2.8146  2.3650  1.9889
  3.5466  3.6054  2.3738  2.8299  0.0000  1.0051  1.9109  3.8239  3.8704
  2.4515  2.7870  2.7949  2.7684  2.4166  2.5454  2.5808  2.4503  3.1563
  2.8138  2.6766  3.0600  4.5917  4.2574  3.1549  3.9069  4.6103  4.4913
  4.4304  4.7055  4.9398  5.0936
CBG05832    1.7686  1.7550  1.7116  2.0327  2.4446  2.1396  1.9584  1.8519
  2.7371  2.9679  1.8216  2.4083  1.0051  0.0000  1.5844  3.1844  3.3444
  2.1097  2.3244  2.5432  2.1652  2.0448  2.0314  2.3851  1.9003  2.5341
  2.3383  2.5572  2.4384  3.7584  3.8479  2.5321  3.7703  3.7069  4.3240
  4.1994  3.9430  4.4252  3.6651
CBG09376    2.7063  2.6971  2.5222  2.8308  2.8767  2.9517  3.1241  2.6404
  4.3457  4.3304  2.3118  2.9370  1.9109  1.5844  0.0000  4.5978  4.3393
  2.5303  2.3488  3.8541  3.9204  3.0260  2.7213  2.8089  2.3821  4.2228
  2.5335  3.4108  2.7139  5.0363  4.6480  3.5726  4.1650  4.9869  5.1834
  4.9909  4.8281  5.5340  4.0523
CBG11598    4.1339  4.5407  4.0405  4.2220  4.5479  3.6259  3.3811  3.5699
  3.9308  4.8338  5.5897  3.5815  3.8239  3.1844  4.5978  0.0000  0.4235
  4.0731  4.2514  5.0939  3.5672  4.0178  4.0286  3.8919  3.8081  6.1309
  5.2024  5.0333  6.3027  4.9386  7.1985  4.2140  5.1831  6.5824  8.8471
 33.9888  5.4456 35.2800 11.7598
CBG11599    4.2758  4.6271  4.0662  4.5559  4.1948  3.3024  3.2762  3.1966
  3.6277  4.6208  4.6319  3.5466  3.8704  3.3444  4.3393  0.4235  0.0000
  3.9215  4.4659  5.1513  3.8787  3.8038  3.9034  3.7433  3.8979  5.5936
  4.5541  4.6220  6.3167  4.0992  7.2295  3.7229  4.7145  6.2658  7.1633
 18.8916  5.1039  7.1689 13.6941
CBG17648    2.0880  2.1786  1.8746  2.1512  2.1784  2.3407  2.1610  2.0200
  2.4312  2.6064  2.8710  2.8880  2.4515  2.1097  2.5303  4.0731  3.9215
  0.0000  2.8196  2.5896  2.7113  2.4208  2.4304  2.6635  2.7791  2.6486
  3.5471  2.6170  4.4278  3.8149  3.8812  3.2632  3.6267  4.5500  3.5307
  4.3285  3.5710  4.5875  4.1427
CBG24285    2.7562  2.8859  2.6138  3.0813  3.4408  2.5640  1.9983  2.1845
  3.0315  3.3095  2.6876  3.0227  2.7870  2.3244  2.3488  4.2514  4.4659
  2.8196  0.0000  2.6854  2.8606  2.5016  2.5539  2.5206  2.3332  3.3910
  2.4810  2.6546  2.9475  3.4766  3.8721  4.2607  4.1390  4.3110  3.8713
  4.8306  3.7968  4.2638  4.8254
CBG11540    2.5353  2.4726  2.4393  2.4151  2.5884  2.9741  2.8666  2.2500
  2.6773  3.0407  4.1532  3.5764  2.7949  2.5432  3.8541  5.0939  5.1513
  2.5896  2.6854  0.0000  3.7728  3.0711  2.9263  3.0104  3.1937  3.2678
  2.5709  4.1542  3.2024  4.6574  4.1274  5.1118  4.7469  4.7083  6.1301
  8.2226  5.4888  6.7308  6.5432
CBG09384    2.8402  2.8045  2.6637  2.6066  2.8710  2.9219  3.3917  2.5397
  3.5620  4.5735  3.7306  3.0695  2.7684  2.1652  3.9204  3.5672  3.8787
  2.7113  2.8606  3.7728  0.0000  2.8881  2.8447  3.0452  2.9702  3.7626
  2.9891  4.3174  3.5895  4.9629  4.7565  3.8767  4.1603  5.2401  9.4937
  4.7434  4.7223  5.4665  6.3838
CBG09498    2.6241  2.6099  2.3819  2.6837  2.8704  2.8086  2.4625  2.1483
  3.1399  3.9027  3.1374  3.2547  2.4166  2.0448  3.0260  4.0178  3.8038
  2.4208  2.5016  3.0711  2.8881  0.0000  2.3759  2.8964  2.3451  3.4168
  2.3817  3.8947  3.3078  4.1428  4.1551  3.5709  3.4280  4.6755  5.0728
  5.2081  5.4351  6.3079  4.8578
CBG19005    2.5270  2.4506  2.3785  2.7222  2.8186  2.7746  2.5294  2.0645
  3.6217  3.4701  2.7316  3.5399  2.5454  2.0314  2.7213  4.0286  3.9034
  2.4304  2.5539  2.9263  2.8447  2.3759  0.0000  2.9129  2.1658  3.9315
  2.3019  3.1963  2.8577  3.9306  3.9931  2.8974  3.3150  3.9219  5.4877
  5.5611  4.3223  4.4717  4.4160
CBG23622    3.2007  3.1862  2.9213  3.2280  2.9751  2.4331  2.8067  2.8851
  3.0567  3.8061  3.1479  3.3406  2.5808  2.3851  2.8089  3.8919  3.7433
  2.6635  2.5206  3.0104  3.0452  2.8964  2.9129  0.0000  2.2713  4.1687
  2.8117  3.8018  2.8588  4.4209  3.9024  3.2947  4.4194  4.2776  4.0199
  4.8392  4.3750  5.5841  5.4572
CBG19006    2.5240  2.5982  2.4552  3.2690  3.2856  2.4465  2.3930  2.3342
  3.2404  3.7082  2.2777  2.9640  2.4503  1.9003  2.3821  3.8081  3.8979
  2.7791  2.3332  3.1937  2.9702  2.3451  2.1658  2.2713  0.0000  3.1393
  2.4880  3.0211  2.9315  3.9284  3.5686  3.8554  3.6731  4.7036  4.0803
  4.3514  4.1644  4.2497  4.3599
CBG05117    2.7543  2.7305  2.5751  2.9720  3.2412  3.5125  3.3267  2.9882
  3.3961  3.5302  3.9899  4.4963  3.1563  2.5341  4.2228  6.1309  5.5936
  2.6486  3.3910  3.2678  3.7626  3.4168  3.9315  4.1687  3.1393  0.0000
  4.0873  4.8328  3.1335  4.9343  4.1052  3.7843  4.0682  4.2055  5.1586
  6.8573  4.2813  5.7905  4.5807
CBG06938    2.8516  2.7926  2.7080  2.7759  3.3431  2.5244  2.4879  2.6273
  3.1915  3.4530  2.7702  3.0453  2.8138  2.3383  2.5335  5.2024  4.5541
  3.5471  2.4810  2.5709  2.9891  2.3817  2.3019  2.8117  2.4880  4.0873
  0.0000  2.9802  3.2309  3.9309  4.7128  4.4982  4.4156  5.4946  4.9963
  6.0390  4.3920  5.3974  5.2162
CBG05569    2.6939  2.8251  2.5817  2.9316  3.0718  3.2094  3.3610  2.9374
  3.4462  4.6425  3.2043  3.7199  2.6766  2.5572  3.4108  5.0333  4.6220
  2.6170  2.6546  4.1542  4.3174  3.8947  3.1963  3.8018  3.0211  4.8328
  2.9802  0.0000  3.7514  4.7160  4.5549  4.3316  3.8211  5.9466  5.4133
  5.8945  5.1835  4.8958  5.1716
CBG01473    3.2467  3.1864  3.0913  3.0455  3.6222  3.1828  3.3407  2.6007
  3.8474  3.7924  3.3944  3.9175  3.0600  2.4384  2.7139  6.3027  6.3167
  4.4278  2.9475  3.2024  3.5895  3.3078  2.8577  2.8588  2.9315  3.1335
  3.2309  3.7514  0.0000  2.8729  3.6229  3.3751  3.2855  3.8873  3.2016
  4.4501  4.1784  5.5009  6.1935
CBG20565    3.5679  3.5483  3.3989  4.3733  4.8202  4.5101  4.2896  4.2752
  4.9926  4.9159  5.5110  8.1129  4.5917  3.7584  5.0363  4.9386  4.0992
  3.8149  3.4766  4.6574  4.9629  4.1428  3.9306  4.4209  3.9284  4.9343
  3.9309  4.7160  2.8729  0.0000  2.8421  2.9834  3.0900  3.1468  4.3755
  5.5408  4.0756  4.7912  4.9496
CBG08040    3.6727  3.6954  3.5036  3.9787  4.4527  4.5919  4.8651  3.5955
  4.9183  5.1012  4.6346  5.2160  4.2574  3.8479  4.6480  7.1985  7.2295
  3.8812  3.8721  4.1274  4.7565  4.1551  3.9931  3.9024  3.5686  4.1052
  4.7128  4.5549  3.6229  2.8421  0.0000  2.5113  3.0329  2.6063  3.7315
  6.1202  4.1715  4.5099  6.1951
CBG11008    4.0515  4.0547  3.8942  4.8184  4.5427  4.4979  4.7867  3.2871
  4.3491  4.8005  4.3744  5.6628  3.1549  2.5321  3.5726  4.2140  3.7229
  3.2632  4.2607  5.1118  3.8767  3.5709  2.8974  3.2947  3.8554  3.7843
  4.4982  4.3316  3.3751  2.9834  2.5113  0.0000  3.0012  3.5271  5.2530
  7.9480  3.9136  4.1362  4.1935
CBG19232    4.1651  3.9877  4.1556  4.8889  4.2937  3.8859  3.7278  3.2864
  4.5937  5.4006  4.1109  4.6900  3.9069  3.7703  4.1650  5.1831  4.7145
  3.6267  4.1390  4.7469  4.1603  3.4280  3.3150  4.4194  3.6731  4.0682
  4.4156  3.8211  3.2855  3.0900  3.0329  3.0012  0.0000  3.0649  5.7627
  7.8215  4.0200  4.3420  6.2253
CBG09297    5.2267  5.3975  4.7610  4.9857  4.9768  5.1380  4.2166  4.3964
  5.6950  5.4801  4.6211  6.2934  4.6103  3.7069  4.9869  6.5824  6.2658
  4.5500  4.3110  4.7083  5.2401  4.6755  3.9219  4.2776  4.7036  4.2055
  5.4946  5.9466  3.8873  3.1468  2.6063  3.5271  3.0649  0.0000  4.4712
  7.1902  4.4573  4.4089  5.8707
CBG17433    4.8451  4.5982  4.0620  5.9673  4.6224  5.1993  5.4427  4.2783
  5.0554  5.8932  4.4749  5.3828  4.4913  4.3240  5.1834  8.8471  7.1633
  3.5307  3.8713  6.1301  9.4937  5.0728  5.4877  4.0199  4.0803  5.1586
  4.9963  5.4133  3.2016  4.3755  3.7315  5.2530  5.7627  4.4712  0.0000
  8.9961  4.6166  4.4816  5.4284
CBG23193    4.3745  4.3584  3.9918  4.5837  4.3548  5.9836  5.7439  5.1700
  7.6270  9.8750  5.8343  8.8144  4.4304  4.1994  4.9909 33.9888 18.8916
  4.3285  4.8306  8.2226  4.7434  5.2081  5.5611  4.8392  4.3514  6.8573
  6.0390  5.8945  4.4501  5.5408  6.1202  7.9480  7.8215  7.1902  8.9961
  0.0000  7.4108  6.0423  6.4791
CBG22788    3.2268  3.0069  3.1087  4.1999  3.4335  4.3432  5.0511  4.4989
  3.8392  5.1466  5.5416  5.2604  4.7055  3.9430  4.8281  5.4456  5.1039
  3.5710  3.7968  5.4888  4.7223  5.4351  4.3223  4.3750  4.1644  4.2813
  4.3920  5.1835  4.1784  4.0756  4.1715  3.9136  4.0200  4.4573  4.6166
  7.4108  0.0000  5.3195  4.4669
CBG22521    5.0186  4.7190  4.5302  5.7211  5.1190  6.4117  5.4130  4.7197
  5.2635  6.8839  5.8238  6.1903  4.9398  4.4252  5.5340 35.2800  7.1689
  4.5875  4.2638  6.7308  5.4665  6.3079  4.4717  5.5841  4.2497  5.7905
  5.3974  4.8958  5.5009  4.7912  4.5099  4.1362  4.3420  4.4089  4.4816
  6.0423  5.3195  0.0000  5.3441
CBG00435    4.7793  4.7592  4.1661  4.7700  4.5442  4.8479  4.2919  3.4620
  5.0165  6.2445  5.8422  8.6700  5.0936  3.6651  4.0523 11.7598 13.6941
  4.1427  4.8254  6.5432  6.3838  4.8578  4.4160  5.4572  4.3599  4.5807
  5.2162  5.1716  6.1935  4.9496  6.1951  4.1935  6.2253  5.8707  5.4284
  6.4791  4.4669  5.3441  0.0000
BioPerl-1.007002/t/data/phylipdist.out000444000766000024        45513155576321 17576 0ustar00cjfieldsstaff000000000000    5
Alpha          0.00000  4.23419  3.63330  6.20865  3.45431
Beta           4.23419  0.00000  3.49289  3.36540  4.29179
Gamma          3.63330  3.49289  0.00000  3.68733  5.84929
Delta          6.20865  3.36540  3.68733  0.00000  4.43345
Epsilon        3.45431  4.29179  5.84929  4.43345  0.00000
BioPerl-1.007002/t/data/phyloxml_examples.xml000444000766000024      3567313155576321 21222 0ustar00cjfieldsstaff000000000000

   
      example from Prof. Joe Felsenstein's book "Inferring Phylogenies"
      phyloXML allows to use either a "branch_length" attribute or element to indicate branch lengths.
      
         
            
               A
            
            
               B
            
         
         
            C
         
      
   
   
      example from Prof. Joe Felsenstein's book "Inferring Phylogenies"
      phyloXML allows to use either a "branch_length" attribute or element to indicate branch lengths.
      
         
            0.06
            
               A
               0.102
            
            
               B
               0.23
            
         
         
            C
            0.4
         
      
   
   
      same example, with support of type "bootstrap"
      
         
            AB
            89
            
               A
            
            
               B
            
         
         
            C
         
      
   
   
      same example, with species and sequence
      
         
            AB
            
               A
               
                  E. coli
               
               
                  
                     alcohol dehydrogenase
                     0.99
                  
               
            
            
               B
               
                  B. subtilis
               
               
                  
                     alcohol dehydrogenase
                     0.91
                  
               
            
         
         
            C
            
               C. elegans
            
            
               
                  alcohol dehydrogenase
                  0.67
               
            
         
      
   
   
      same example, with gene duplication information and sequence relationships
      
         
            1
         
         
            
               1
            
            
               
                  Bacillus subtilis
               
               
                  adhB
                  AAB80874
                  alcohol dehydrogenase
               
            
            
               
                  Bacillus subtilis
               
               
                  gbsB
                  CAB15083
                  alcohol dehydrogenase
               
            
         
         
            
               Caenorhabditis elegans
            
            
               ADHX
               Q17335
               alcohol dehydrogenase
               
            
         
      
      
      
      
   
   
      similar example, with more detailed sequence data
      
         
            
               
                  6645
                  OCTVU
                  Octopus vulgaris
               
               
                  ADHX
                  P81431
                  Alcohol dehydrogenase class-3
                  TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD
                  
                  
               
            
            
               
                  44689
                  DICDI
                  Dictyostelium discoideum
               
               
                  RT4I1
                  Q54II4
                  Reticulon-4-interacting protein 1 homolog, mitochondrial precursor
                  MKGILLNGYGESLDLLEYKTDLPVPKPIKSQVLIKIHSTSINPLDNVMRK
                  
                  
               
            
         
         
            
               1488
               CLOAB
               Clostridium acetobutylicum
            
            
               ADHB
               Q04945
               NADH-dependent butanol dehydrogenase B
               MVDFEYSIPTRIFFGKDKINVLGRELKKYGSKVLIVYGGGSIKRNGIYDK
               
               
            
         
      
   
   
      network, node B is connected to TWO nodes: AB and C
      
         
            AB
            
               A
            
            
               B
            
         
         
            C
         
      
      
   
   
      same example, using property elements to indicate a "depth" value for marine organisms
      
         
            AB
            
               A
                1200 
            
            
               B
                2300 
            
         
         
            C
             200 
         
      
   
   
      same example, using property elements to indicate a "depth" value for marine organisms by using id refs in
         order to have property elements outside of the tree topology
      
         
            AB
            
               A
            
            
               B
            
         
         
            C
         
      
       1200 
       2300 
       200 
   
   
      monitor lizards
      a pylogeny of some monitor lizards
      
         
            8556
            Varanus
            genus
            http://www.embl-heidelberg.de/~uetz/families/Varanidae.html
         
         
            
               62046
               Varanus niloticus
               Nile monitor
               species
            
            
               Africa
            
         
         
            
               Odatria
               subgenus
            
            
               
                  169855
                  Varanus storri
                  Storr's monitor
                  species
               
               
                  Australia
               
            
            
               
                  62053
                  Varanus timorensis
                  Timor monitor
                  species
               
               
                  Asia
               
            
         
      
   
   
      A tree with phylogeographic information
      
         
            
               A
               
                  Hirschweg, Winterthur, Switzerland
                  
                     47.481277
                     8.769303
                     472
                  
               
            
            
               B
               
                  Nagoya, Aichi, Japan
                  
                     35.155904
                     136.915863
                     10
                  
               
            
            
               C
               
                  ETH Zürich
                  
                     47.376334
                     8.548108
                     452
                  
               
            
         
         
            D
            
               San Diego
               
                  32.880933
                  -117.217543
                  104
               
            
         
      
   
   
      A tree with date information
      
         
            
               A
               
                  Silurian
                  425
                  416.0
                  443.7
               
            
            
               B
               
                  Devonian
                  320
               
            
         
         
            C
            
               Ediacaran
               600
            
         
      
   
   
      Using another XML language to store an alignment
      
         
            
               A
            
            
               B
            
         
         
            C
         
      
   
   
      acgtcgcggcccgtggaagtcctctcct
      aggtcgcggcctgtggaagtcctctcct
      taaatcgc--cccgtgg-agtccc-cct
   

BioPerl-1.007002/t/data/pictogram.fa000444000766000024        34013155576321 17142 0ustar00cjfieldsstaff000000000000>seq1
AGCGTCACA
>seq2
ATCGTACTC
>seq3
GTGTAATTG
>seq3
GTGTAATTG
>seq3
GTGTAATTG
>seq3
GTGTAATTG
>seq3
GTGTAATTG
>seq3
GTGTAATTG
>seq4
CTCGTACTG
>seq4
CTCGTACTG
>seq4
CTCGTACTG
>seq4
CTCGTACTG
>seq4
CTCGTACTG
>seq4
CTCGTACTG
BioPerl-1.007002/t/data/polymorphism.dat000444000766000024       500413155576321 20123 0ustar00cjfieldsstaff000000000000ID           M20132:(362)[c.+4G|A|T;c.+31C|A]; [E2|K|X;Q11|K]
Feature      DNA; 1.1
Feature        /label: point, transition
Feature        /proof: computed
Feature        /location: 4
Feature        /upflank: gaagattcagccaagctcaaggatg
Feature        /change: g|a
Feature        /dnflank: aagtgcagttagggctgggaagggt
Feature        /re_site: -BccI
Feature      DNA; 1.2
Feature        /label: point, transversion
Feature        /proof: computed
Feature        /location: 4
Feature        /upflank: gaagattcagccaagctcaaggatg
Feature        /change: g|t
Feature        /dnflank: aagtgcagttagggctgggaagggt
Feature        /re_site: -BccI
Feature      RNA; 1.1
Feature        /label: missense
Feature        /proof: experimental
Feature        /location: 4 (M20132::366)
Feature        /upflank: gaagattcagccaagctcaaggatg
Feature        /change: g|a
Feature        /dnflank: aagtgcagttagggctgggaagggt
Feature        /re_site: -BccI
Feature        /codon_table: 1
Feature        /codon: gaa|aaa; 1
Feature        /region: coding
Feature      RNA; 1.2
Feature        /label: nonsense
Feature        /proof: experimental
Feature        /location: 4 (M20132::366)
Feature        /upflank: gaagattcagccaagctcaaggatg
Feature        /change: g|t
Feature        /dnflank: aagtgcagttagggctgggaagggt
Feature        /re_site: -BccI
Feature        /codon_table: 1
Feature        /codon: gaa|taa; 1
Feature        /region: coding
Feature      AA; 1.1
Feature        /label: substitution, conservative
Feature        /proof: computed
Feature        /location: 2
Feature        /change: E|K
Feature      AA; 1.2
Feature        /label: truncation
Feature        /proof: computed
Feature        /location: 2
Feature        /change: E|*
Feature      DNA; 2
Feature        /label: point, transversion
Feature        /proof: computed
Feature        /location: 31
Feature        /upflank: gaagattcagccaagctcaaggatg
Feature        /change: c|a
Feature        /dnflank: aagtgcagttagggctgggaagggt
Feature        /re_site: -CviRI, -SfaNI
Feature      RNA; 2
Feature        /label: missense
Feature        /proof: experimental
Feature        /location: 31 (M20132::393)
Feature        /upflank: gaagattcagccaagctcaaggatg
Feature        /change: c|a
Feature        /dnflank: aagtgcagttagggctgggaagggt
Feature        /re_site: -CviRI, -SfaNI
Feature        /codon_table: 1
Feature        /codon: caa|aaa; 1
Feature        /region: coding
Feature      AA; 2
Feature        /label: substitution, conservative
Feature        /proof: computed
Feature        /location: 11
Feature        /change: Q|K
//
BioPerl-1.007002/t/data/polymorphism.old.xml000444000766000024       667113155576321 20743 0ustar00cjfieldsstaff000000000000

    
        
        
        computed
        gaagattcagccaagctcaaggatg
        g
        a
        aagtgcagttagggctgggaagggt
        -BccI
    
    
        
        
        computed
        gaagattcagccaagctcaaggatg
        g
        t
        aagtgcagttagggctgggaagggt
        -BccI
    
    
        
        experimental
        gaagattcagccaagctcaaggatg
        g
        a
        aagtgcagttagggctgggaagggt
        
        -BccI
        coding
    
    
        
        experimental
        gaagattcagccaagctcaaggatg
        g
        t
        aagtgcagttagggctgggaagggt
        
        -BccI
        coding
    
    
        
        
        computed
        E
        K
    
    
        
        computed
        E
        *
    
    
        
        
        computed
        gaagattcagccaagctcaaggatg
        c
        a
        aagtgcagttagggctgggaagggt
        -CviRI, -SfaNI
    
    
        
        experimental
        gaagattcagccaagctcaaggatg
        c
        a
        aagtgcagttagggctgggaagggt
        
        -CviRI, -SfaNI
        coding
    
    
        
        
        computed
        Q
        K
    

BioPerl-1.007002/t/data/polymorphism.xml000444000766000024       667013155576321 20165 0ustar00cjfieldsstaff000000000000
    
        
        
        computed
        gaagattcagccaagctcaaggatg
        g
        a
        aagtgcagttagggctgggaagggt
        -BccI
    
    
        
        
        computed
        gaagattcagccaagctcaaggatg
        g
        t
        aagtgcagttagggctgggaagggt
        -BccI
    
    
        
        experimental
        gaagattcagccaagctcaaggatg
        g
        a
        aagtgcagttagggctgggaagggt
        
        -BccI
        coding
    
    
        
        experimental
        gaagattcagccaagctcaaggatg
        g
        t
        aagtgcagttagggctgggaagggt
        
        -BccI
        coding
    
    
        
        
        computed
        E
        K
    
    
        
        computed
        E
        *
    
    
        
        
        computed
        gaagattcagccaagctcaaggatg
        c
        a
        aagtgcagttagggctgggaagggt
        -CviRI, -SfaNI
    
    
        
        experimental
        gaagattcagccaagctcaaggatg
        c
        a
        aagtgcagttagggctgggaagggt
        
        -CviRI, -SfaNI
        coding
    
    
        
        
        computed
        Q
        K
    

BioPerl-1.007002/t/data/popgen_saureus.dat000444000766000024       111413155576321 20416 0ustar00cjfieldsstaff000000000000# J.Stajich unpublished results, S.aureus clinical and environmental
# isolates AFLP data 2 Markers where alleles are assigned based on unique
# banding pattern
SAMPLE,AFLP1,AFLP2
MRSA-1748-7,6,15
MRSA-1826-24,6,15
MRSA-1902-18,6,15
MRSA-1905-9,6,15
MRSA-1933-10,8,15
MRSA-1964-26,12,21
MRSA-1969-1,1,13
MRSA-1980-6,6,15
MRSA-1983-12,6,15
MSSA-1741-22,10,15
MSSA-1755-13,9,15
MSSA-1763-3,3,15
MSSA-1819-21,6,19
MSSA-1868-19,2,15
MSSA-1894-14,10,15
MSSA-1915-17,6,15
MSSA-1925-2,2,14
MSSA-1940-15,6,15
MSSA-1948-5,5,15
NC-17A-8,7,16
NC-2-16,6,18
NC-21A-25,11,15
NC-23A-4,4,14
NC-4-20,6,15
BioPerl-1.007002/t/data/popgen_saureus.multidat000444000766000024       242313155576321 21475 0ustar00cjfieldsstaff000000000000# J.Stajich unpublished results, S.aureus clinical and environmental
# isolates AFLP data 2 Markers where alleles are assigned based on unique
# banding pattern
SAMPLE,B1,B2,B3,B4,B5,B6,B7,B8,B9,B10,B11,B12,B13,B14,B15,B16,B17,B18,B19,B20
NC23A,0,0,0,0,0,0,0,1,1,1,0,0,0,1,1,1,0,0,1,0
MSSA1940,0,0,0,1,0,0,1,1,1,1,0,1,0,0,1,0,1,1,1,0
MRSA1983,0,0,0,1,0,0,1,1,1,1,0,1,0,0,1,0,1,1,1,0
NC21A,0,0,0,0,0,0,0,0,0,1,0,1,0,0,1,0,1,1,1,0
NC4,0,0,0,1,0,0,1,1,1,1,0,1,0,0,1,0,1,1,1,0
MSSA1915,0,0,0,1,0,0,1,1,1,1,0,1,0,0,1,0,1,1,1,0
NC2,0,0,0,1,0,0,1,1,1,1,0,1,0,0,1,0,0,1,0,1
NC17A,0,0,0,1,1,0,1,1,0,1,0,1,0,0,1,0,0,1,1,0
MRSA1748,0,0,0,1,0,0,1,1,1,1,0,1,0,0,1,0,1,1,1,0
MRSA1905,0,0,0,1,0,0,1,1,1,1,0,1,0,0,1,0,1,1,1,0
MSSA1925,0,0,0,1,0,0,1,1,0,1,0,1,0,1,1,1,0,0,1,0
MSSA1763,0,0,0,1,0,0,1,1,0,1,1,1,0,0,1,0,1,1,1,0
MRSA1980,0,0,0,1,0,0,1,1,1,1,0,1,0,0,1,0,1,1,1,0
MSSA1948,0,0,0,1,0,1,0,1,1,1,0,1,0,0,1,0,1,1,1,0
MSSA1741,0,0,0,1,0,0,1,1,1,1,0,0,0,0,1,0,1,1,1,0
MSSA1755,0,1,1,1,0,0,1,1,1,1,0,1,0,0,1,0,1,1,1,0
MSSA1819,0,0,0,1,0,0,1,1,1,1,0,1,0,0,1,0,1,1,0,1
MSSA1868,0,0,0,1,0,0,1,1,0,1,0,1,0,0,1,0,1,1,1,0
MSSA1894,0,0,0,1,0,0,1,1,1,1,0,0,0,0,1,0,1,1,1,0
MRSA1826,0,0,0,1,0,0,1,1,1,1,0,1,0,0,1,0,1,1,1,0
MRSA1902,0,0,0,1,0,0,1,1,1,1,0,1,0,0,1,0,1,1,1,0
MRSA1933,0,0,0,1,0,0,1,1,1,1,1,1,0,0,1,0,1,1,1,0

BioPerl-1.007002/t/data/popstats.prettybase000444000766000024        42213155576321 20627 0ustar00cjfieldsstaff00000000000001	A01	A
01	A02	A
01	A03	A
01	A04	A
01	A05	A
02	A01	A
02	A02	T
02	A03	T
02	A04	T
02	A05	T
04	A01	G
04	A02	G
04	A03	C
04	A04	C
04	A05	G
05	A01	T
05	A02	C
05	A03	T
05	A04	T
05	A05	T
11	A01	G
11	A02	G
11	A03	G
11	A04	A
11	A05	A

01	out	G
02	out	A
04	out	G
05	out	T
11	out	G



BioPerl-1.007002/t/data/pre_rel9.swiss000444000766000024      2154713155576321 17534 0ustar00cjfieldsstaff000000000000ID   GCDH_CAEEL     STANDARD;      PRT;   409 AA.
AC   Q20772;
DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   30-MAY-2006, entry version 44.
DE   Probable glutaryl-CoA dehydrogenase, mitochondrial precursor
DE   (EC 1.3.99.7) (GCD).
GN   ORFNames=F54D5.7;
OS   Caenorhabditis elegans.
OC   Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea;
OC   Rhabditidae; Peloderinae; Caenorhabditis.
OX   NCBI_TaxID=6239;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Bristol N2;
RX   MEDLINE=99069613; PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG   The C. elegans sequencing consortium;
RT   "Genome sequence of the nematode C. elegans: a platform for
RT   investigating biology.";
RL   Science 282:2012-2018(1998).
CC   -!- CATALYTIC ACTIVITY: Glutaryl-CoA + acceptor = crotonoyl-CoA +
CC       CO(2) + reduced acceptor.
CC   -!- COFACTOR: FAD (By similarity).
CC   -!- PATHWAY: Degradative pathway of L-lysine, L-hydroxylysine, and L-
CC       tryptophan metabolism.
CC   -!- INTERACTION:
CC       P39745:mpk-1; NbExp=1; IntAct=EBI-313068, EBI-321013;
CC       Q17446:pmk-1; NbExp=1; IntAct=EBI-313068, EBI-312987;
CC   -!- SUBCELLULAR LOCATION: Mitochondrion; mitochondrial matrix
CC       (Potential).
CC   -!- SIMILARITY: Belongs to the acyl-CoA dehydrogenase family.
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------
DR   EMBL; Z66513; CAA91333.1; -; Genomic_DNA.
DR   PIR; T22647; T22647.
DR   UniGene; Cel.30446; -.
DR   HSSP; Q06319; 1BUC.
DR   IntAct; Q20772; -.
DR   Ensembl; F54D5.7; Caenorhabditis elegans.
DR   WormBase; WBGene00010052; F54D5.7.
DR   WormPep; F54D5.7; CE03411.
DR   GO; GO:0005515; F:protein binding; IPI.
DR   InterPro; IPR006089; Acyl_CoA_DH.
DR   InterPro; IPR006091; Acyl_CoA_DH/ox_M.
DR   InterPro; IPR006090; Acyl_CoA_DH_1.
DR   InterPro; IPR006092; Acyl_CoA_DH_N.
DR   InterPro; IPR009075; AcylCo_DH/ox_C.
DR   InterPro; IPR009100; AcylCoA_DH/ox_NM.
DR   InterPro; IPR013764; AcylCoA_DH_1/2_C.
DR   Pfam; PF00441; Acyl-CoA_dh_1; 1.
DR   Pfam; PF02770; Acyl-CoA_dh_M; 1.
DR   Pfam; PF02771; Acyl-CoA_dh_N; 1.
DR   PROSITE; PS00072; ACYL_COA_DH_1; FALSE_NEG.
DR   PROSITE; PS00073; ACYL_COA_DH_2; 1.
KW   Complete proteome; FAD; Flavoprotein; Hypothetical protein;
KW   Mitochondrion; Oxidoreductase; Transit peptide.
FT   TRANSIT       1      ?       Mitochondrion (Potential).
FT   CHAIN         ?    409       Probable glutaryl-CoA dehydrogenase.
FT                                /FTId=PRO_0000000530.
FT   ACT_SITE    388    388       Proton acceptor (Potential).
SQ   SEQUENCE   409 AA;  44964 MW;  4D06241FB6768069 CRC64;
     MLTRGFTSIG KIASRGLSST FYQDAFQLSD QLTEDERSLM LSAREYCQER LLPRVTEAYR
     TEKFDPSLIP EMGSMGLLGA PYQGYGCAGT STVGYGLIAR EVERVDSGYR STMSVQTSLV
     IGPIYNYGSE DQKQKYIPDL ASGKKIGCFG LTEPNHGSNP GGMETKATWD ETTKTYKLNG
     SKTWISNSPV SDVMVVWARS ARHNNKIKGF ILERGMKGLT TPKIEGKLSL RASITGQIAM
     DDVPVPEENL LPNAEGLQGP FGCLNNARLG IAWGALGAAE ECFHLARQYT LDRQQFGRPL
     AQNQLMQLKM ADMLTEISLG LQGCLRVSRL KDEGKVQSEQ ISIIKRNSCG KALEVARKAR
     DMLGGNGIVD EYHIMRHMVN LETVNTYEGT HDVHALILGR AITGLNGFC
//
ID   Q41V66_FERAC   PRELIMINARY;   PRT;   607 AA.
AC   Q41V66;
DT   27-SEP-2005, integrated into UniProtKB/TrEMBL.
DT   27-SEP-2005, sequence version 1.
DT   30-MAY-2006, entry version 5.
DE   Glycoside hydrolase, family 15.
GN   ORFNames=FaciDRAFT_1685;
OS   Ferroplasma acidarmanus Fer1.
OC   Archaea; Euryarchaeota; Thermoplasmata; Thermoplasmatales;
OC   Ferroplasmaceae; Ferroplasma.
OX   NCBI_TaxID=333146;
RN   [1]
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Fer1;
RG   US DOE Joint Genome Institute (JGI-PGF);
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter C., Glavina T.,
RA   Hammon N., Israni S., Pitluck S., Richardson P.;
RT   "Sequencing of the draft genome and assembly of Ferroplasma
RT   acidarmanus fer1.";
RL   Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Fer1;
RG   US DOE Joint Genome Institute (JGI-ORNL);
RA   Larimer F., Land M.;
RT   "Annotation of the draft genome assembly of Ferroplasma acidarmanus
RT   fer1.";
RL   Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Fer1;
RG   US DOE Joint Genome Institute (JGI-PGF);
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter C., Glavina T.,
RA   Hammon N., Israni S., Pitluck S., Richardson P.;
RL   Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases.
CC   -!- CAUTION: The sequence shown here is derived from an
CC       EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is
CC       preliminary data.
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------
DR   EMBL; AABC04000001; EAM94575.1; -; Genomic_DNA.
DR   GO; GO:0004339; F:glucan 1,4-alpha-glucosidase activity; IEA.
DR   GO; GO:0016787; F:hydrolase activity; IEA.
DR   GO; GO:0005976; P:polysaccharide metabolism; IEA.
DR   InterPro; IPR008928; 6hp_glycosidase.
DR   InterPro; IPR011613; Glyco_hydro_15_rel.
DR   InterPro; IPR012343; Glyco_trans_sub.
DR   Pfam; PF00723; Glyco_hydro_15; 1.
KW   Hydrolase.
SQ   SEQUENCE   607 AA;  69495 MW;  8AC6297BA16ED500 CRC64;
     MGTYRGLYDL HDAYRSDYLK IANHGFIANN RTAALVGIDG TIDWACLPNF NSNPVFDSIL
     DARNGGYFKT SPVMESNVNQ YYEESTNILI TEFVNNNQVI LRLTDFLPTS SYSTITFPEI
     HRLIEAPYSD VEVSIDIKSH FNFGSGKTNI TRDRNGYIFS CTDDTLGIST NLKLKKGNGN
     VYSRIKVEKG SHEWIVVLSG VRQIGNVRQY ESYTRLEETR NYWSAWAGKI NYSGLYYDHV
     IRSALTLRGL FYDPTGMMVA APTTSLPEII GGERNWDYRY TWIRDTAYVV EALSLIGLND
     VATKFLYDIM SIVQKDKKVK TIYPVNGDSK LEEKKVNLSG YMDSIPVRIG NEASEQLQID
     QYGSIVNAVF RFHEAGGLVT TYLWDFLIEI LDTLKDIWKL PDSSIWEFRS EPKHYLYSKL
     ISWSAFNRAI KMGRELGYSA PYRTWHKIRE EIKNEIMEKG YNPDVKAFTQ YYGSDQMDAS
     VLRMPLTGII SAKDPRFVST LARVEAELKN PCGMFIRYHS DDGLKGHDNA FLLLSFWYVE
     DLILSGRIME AKETFENILD HSNHLMLFSE EINFNDCREM LGNFPQAITH LGVIRAAIKL
     DEALRGK
//
ID   Q41US7_FERAC   PRELIMINARY;   PRT;   270 AA.
AC   Q41US7;
DT   27-SEP-2005, integrated into UniProtKB/TrEMBL.
DT   27-SEP-2005, sequence version 1.
DT   30-MAY-2006, entry version 4.
DE   Potassium channel protein.
GN   ORFNames=FaciDRAFT_1443;
OS   Ferroplasma acidarmanus Fer1.
OC   Archaea; Euryarchaeota; Thermoplasmata; Thermoplasmatales;
OC   Ferroplasmaceae; Ferroplasma.
OX   NCBI_TaxID=333146;
RN   [1]
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Fer1;
RG   US DOE Joint Genome Institute (JGI-PGF);
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter C., Glavina T.,
RA   Hammon N., Israni S., Pitluck S., Richardson P.;
RT   "Sequencing of the draft genome and assembly of Ferroplasma
RT   acidarmanus fer1.";
RL   Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Fer1;
RG   US DOE Joint Genome Institute (JGI-ORNL);
RA   Larimer F., Land M.;
RT   "Annotation of the draft genome assembly of Ferroplasma acidarmanus
RT   fer1.";
RL   Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Fer1;
RG   US DOE Joint Genome Institute (JGI-PGF);
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter C., Glavina T.,
RA   Hammon N., Israni S., Pitluck S., Richardson P.;
RL   Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases.
CC   -!- CAUTION: The sequence shown here is derived from an
CC       EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is
CC       preliminary data.
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------
DR   EMBL; AABC04000002; EAM94333.1; -; Genomic_DNA.
DR   GO; GO:0016020; C:membrane; IEA.
DR   GO; GO:0005216; F:ion channel activity; IEA.
DR   GO; GO:0005267; F:potassium channel activity; IEA.
DR   GO; GO:0006813; P:potassium ion transport; IEA.
DR   InterPro; IPR013099; Ion_trans_2_bac.
DR   InterPro; IPR001622; K+channel_pore.
DR   InterPro; IPR003148; TrkA_N.
DR   Pfam; PF07885; Ion_trans_2; 1.
DR   Pfam; PF02254; TrkA_N; 1.
KW   Ionic channel.
SQ   SEQUENCE   270 AA;  30497 MW;  528C4EA75C41DF75 CRC64;
     MQTITTVGYG DTPVYGLAGR ANGMLIMVIG IGSLGYLMAG LTSMLIDIRL SSKLGERMAA
     EKKHIVLCNY NESTKKVLDK IKYDGIDIVI LNENEVKGDN EYTYIKGSFL RENDLIRAGI
     KKASSVIIFS RSEDKEQMAM DAESILSAMI IRKLNPEIRI IGEILNPDSR EHASSFMDDI
     IIKGDVSSML IYSSIMIPGI PEFINDLLMS NSISEEDIDK KYASNTYREF ISNMEKENRI
     VLAFRKQDKI YLRENSDKKI DVDSYIFIKN
//

BioPerl-1.007002/t/data/primedseq.fa000444000766000024        34513155576321 17153 0ustar00cjfieldsstaff000000000000>Test1
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
AAAAAAAA
BioPerl-1.007002/t/data/primer3_infile.txt000555000766000024       465313155576321 20353 0ustar00cjfieldsstaff000000000000PRIMER_SEQUENCE_ID=sN11902
PRIMER_COMMENT=3831
SEQUENCE=ACAGCAACATCGAACTCGTCGTCTTCGAAAGCCTCTTTGGCCTTCGCTGCAAGCTTCTTAGCCATGTCGATTGTGGTTTTTGGTTAGGTTGAGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGATGATGATTCGATTCAAGAAAGGGAATGAAGTAGTAGACGAGGGCCAAAGAGTATAAAGATGGATGCTATCTTTTTCTCTTCTATTGTTCTGTTATTGTTTTGTGAGGGAAGTTTTGGCGCTTCAATACAAAAAAATAAATAAAGAATAAACAAATACAGCTTAGTTAAATGGGTATAACATGGGCCGGAATATATAATCACGAATTAAGGCCCATCATTGTCTCAAAATTAAACTCGGCCTCTATAATACTTCTCCCACACCGGTAATCTTGAGATGAACACTCCTCTTTCGTGTAGTATAAAATAAGACGAAGGTCCAACGTTGAAAGATACTTACCTGGACGGGGTCTAGTCCACGCGTGGACTAAACTTGAGGACCAACGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGAGTCGTAAAGTGGAAGCAGCGATGAAGAGTAACGATAGTAGTAAGAACAGAGTGAGTTGGTTTATAGATGAAGATCCGTCTCCACGTCCTCCGAAATGCACAGTTCTTTGGAAAGAGCTTTTGCGTTTGAAGAAACAGAGGAGCTCTTCGTCGGTGAAGTCCTCTCTGTCTCCGTCGTCGTCCACGTCATCATCTAGCTCGCTTGAGGATAAGAGAGAAGGGAAGAGAGGTAAGAAAGGATTAGAGAGGACGAGATCGTC
TARGET=513,26
PRIMER_PRODUCT_SIZE_RANGE=100-500
PRIMER_FILE_FLAG=0
PRIMER_LIBERAL_BASE=1
PRIMER_NUM_RETURN=1
PRIMER_FIRST_BASE_INDEX=1
PRIMER_EXPLAIN_FLAG=1
=
PRIMER_SEQUENCE_ID=sN11926
PRIMER_COMMENT=3854
SEQUENCE=ACGCTGCTCGGAGAAGCGGCGCCGATATCAATCCGTCAGAAAATGTTTGTTTTCTTCTTCTTCTTCTTCTTCTTCTTCTCGATCTTTGTGTGTGTGTTTCTTTTAGATCTGACTTTGTAGTTTTAGGTTTGATTGGGCGATTGAATCGAGATGAGTTTTGTTCATTTAAGTTTCAGTTGCCGACACTGACGTAGAGATTTGTGTTAGGGTCCTCGTTTGTTGTGAATTTCAATTGACAAATCTGTTTTGGACATCTAACAAAGGGCTTTGTTTTTGTTTTTGTTGCATATGTAGTCAATGCTGGAACCAACAAAGCGGCTTCGAGCAGCACCTCCTTGAACACAAAGAGGCTCGATGATGATACTGAGACCTTAGCTCGTGAGTATATATAATTCATCTATTCTCTCATTCACAGCGAATTAGTATCGACTTCTATATCTCTCTGTGGTTCAAATAAACTTTAGTTGTATCTTCAAAGCTTTATATACTGTTTTTCTTTCCCGTGTTTAAGAGATTGATTAGTATATTGCTTGTTCGAAGAGTCTTTGTT
TARGET=54,23
PRIMER_PRODUCT_SIZE_RANGE=100-500
PRIMER_FILE_FLAG=0
PRIMER_LIBERAL_BASE=1
PRIMER_NUM_RETURN=1
PRIMER_FIRST_BASE_INDEX=1
PRIMER_EXPLAIN_FLAG=1
=
PRIMER_SEQUENCE_ID=sN1922
PRIMER_COMMENT=3922
SEQUENCE=ACAGCAACATCGAACTCGTCGTCTTCGAAAGCCTCTTTGGCCTTCGCTGCAAGCTTCTTAGCCATGTCGATTGTGGTTTTTGGTTAGGTTGAGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGATGATGATTCGATTCAAGAAAGGGAATGAAGTAGTAGACGAGGGCCAAAGAGTATAAAGATGGATGCGATCTTTTTCTCTTCTATTGTTCTGTTATTGTTTTGTGAGGGAAGTTTTGGCGCTTCAATACAAAAAAATAAATAAAGAATAAACAAATACAGCTTAGTTAAATGGGTATAACATGGGCCGGAATATATAATCACGGATTAAGGCCCATCATTGTCTCAAAATTAAACTCGGCCTCTATAATACTTCTCCCACACCGGTAATCTTGAGATGAACACTCCTCTTTCGTGTAGTATAAAATAAGACGAAGGTCCAACGTTGAAAGATACTTACCTGGACGGGGTC
TARGET=96,32
PRIMER_PRODUCT_SIZE_RANGE=100-500
PRIMER_FILE_FLAG=0
PRIMER_LIBERAL_BASE=1
PRIMER_NUM_RETURN=1
PRIMER_FIRST_BASE_INDEX=1
PRIMER_EXPLAIN_FLAG=1
=

BioPerl-1.007002/t/data/primer3_outfile.txt000555000766000024      1141113155576321 20562 0ustar00cjfieldsstaff000000000000PRIMER_SEQUENCE_ID=sN11902
PRIMER_COMMENT=3831
SEQUENCE=ACAGCAACATCGAACTCGTCGTCTTCGAAAGCCTCTTTGGCCTTCGCTGCAAGCTTCTTAGCCATGTCGATTGTGGTTTTTGGTTAGGTTGAGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGATGATGATTCGATTCAAGAAAGGGAATGAAGTAGTAGACGAGGGCCAAAGAGTATAAAGATGGATGCTATCTTTTTCTCTTCTATTGTTCTGTTATTGTTTTGTGAGGGAAGTTTTGGCGCTTCAATACAAAAAAATAAATAAAGAATAAACAAATACAGCTTAGTTAAATGGGTATAACATGGGCCGGAATATATAATCACGAATTAAGGCCCATCATTGTCTCAAAATTAAACTCGGCCTCTATAATACTTCTCCCACACCGGTAATCTTGAGATGAACACTCCTCTTTCGTGTAGTATAAAATAAGACGAAGGTCCAACGTTGAAAGATACTTACCTGGACGGGGTCTAGTCCACGCGTGGACTAAACTTGAGGACCAACGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGAGTCGTAAAGTGGAAGCAGCGATGAAGAGTAACGATAGTAGTAAGAACAGAGTGAGTTGGTTTATAGATGAAGATCCGTCTCCACGTCCTCCGAAATGCACAGTTCTTTGGAAAGAGCTTTTGCGTTTGAAGAAACAGAGGAGCTCTTCGTCGGTGAAGTCCTCTCTGTCTCCGTCGTCGTCCACGTCATCATCTAGCTCGCTTGAGGATAAGAGAGAAGGGAAGAGAGGTAAGAAAGGATTAGAGAGGACGAGATCGTC
TARGET=513,26
PRIMER_PRODUCT_SIZE_RANGE=100-500
PRIMER_FILE_FLAG=0
PRIMER_LIBERAL_BASE=1
PRIMER_NUM_RETURN=1
PRIMER_FIRST_BASE_INDEX=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 4849, GC content failed 207, low tm 2062, high tm 1173, long poly-x seq 11, ok 1396
PRIMER_RIGHT_EXPLAIN=considered 2415, low tm 892, high tm 844, high end compl 3, ok 676
PRIMER_PAIR_EXPLAIN=considered 2, high end compl 1, ok 1
PRIMER_PAIR_PENALTY=0.0991
PRIMER_LEFT_PENALTY=0.095506
PRIMER_RIGHT_PENALTY=0.003589
PRIMER_LEFT_SEQUENCE=CACGCGTGGACTAAACTTGA
PRIMER_RIGHT_SEQUENCE=AACGCAAAAGCTCTTTCCAA
PRIMER_LEFT=484,20
PRIMER_RIGHT=668,20
PRIMER_LEFT_TM=59.904
PRIMER_RIGHT_TM=59.996
PRIMER_LEFT_GC_PERCENT=50.000
PRIMER_RIGHT_GC_PERCENT=40.000
PRIMER_LEFT_SELF_ANY=8.00
PRIMER_RIGHT_SELF_ANY=6.00
PRIMER_LEFT_SELF_END=3.00
PRIMER_RIGHT_SELF_END=2.00
PRIMER_LEFT_END_STABILITY=7.0000
PRIMER_RIGHT_END_STABILITY=8.5000
PRIMER_PAIR_COMPL_ANY=4.00
PRIMER_PAIR_COMPL_END=2.00
PRIMER_PRODUCT_SIZE=185
=
PRIMER_SEQUENCE_ID=sN11926
PRIMER_COMMENT=3854
SEQUENCE=ACGCTGCTCGGAGAAGCGGCGCCGATATCAATCCGTCAGAAAATGTTTGTTTTCTTCTTCTTCTTCTTCTTCTTCTTCTCGATCTTTGTGTGTGTGTTTCTTTTAGATCTGACTTTGTAGTTTTAGGTTTGATTGGGCGATTGAATCGAGATGAGTTTTGTTCATTTAAGTTTCAGTTGCCGACACTGACGTAGAGATTTGTGTTAGGGTCCTCGTTTGTTGTGAATTTCAATTGACAAATCTGTTTTGGACATCTAACAAAGGGCTTTGTTTTTGTTTTTGTTGCATATGTAGTCAATGCTGGAACCAACAAAGCGGCTTCGAGCAGCACCTCCTTGAACACAAAGAGGCTCGATGATGATACTGAGACCTTAGCTCGTGAGTATATATAATTCATCTATTCTCTCATTCACAGCGAATTAGTATCGACTTCTATATCTCTCTGTGGTTCAAATAAACTTTAGTTGTATCTTCAAAGCTTTATATACTGTTTTTCTTTCCCGTGTTTAAGAGATTGATTAGTATATTGCTTGTTCGAAGAGTCTTTGTT
TARGET=54,23
PRIMER_PRODUCT_SIZE_RANGE=100-500
PRIMER_FILE_FLAG=0
PRIMER_LIBERAL_BASE=1
PRIMER_NUM_RETURN=1
PRIMER_FIRST_BASE_INDEX=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 315, low tm 52, high tm 212, ok 51
PRIMER_RIGHT_EXPLAIN=considered 4504, GC content failed 63, low tm 2423, high tm 832, ok 1186
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=1.0219
PRIMER_LEFT_PENALTY=0.973324
PRIMER_RIGHT_PENALTY=0.048588
PRIMER_LEFT_SEQUENCE=GCCGATATCAATCCGTCAGA
PRIMER_RIGHT_SEQUENCE=CTCTACGTCAGTGTCGGCAA
PRIMER_LEFT=21,20
PRIMER_RIGHT=196,20
PRIMER_LEFT_TM=60.973
PRIMER_RIGHT_TM=60.049
PRIMER_LEFT_GC_PERCENT=50.000
PRIMER_RIGHT_GC_PERCENT=55.000
PRIMER_LEFT_SELF_ANY=6.00
PRIMER_RIGHT_SELF_ANY=5.00
PRIMER_LEFT_SELF_END=3.00
PRIMER_RIGHT_SELF_END=2.00
PRIMER_LEFT_END_STABILITY=6.7000
PRIMER_RIGHT_END_STABILITY=10.0000
PRIMER_PAIR_COMPL_ANY=5.00
PRIMER_PAIR_COMPL_END=3.00
PRIMER_PRODUCT_SIZE=176
=
PRIMER_SEQUENCE_ID=sN1922
PRIMER_COMMENT=3922
SEQUENCE=ACAGCAACATCGAACTCGTCGTCTTCGAAAGCCTCTTTGGCCTTCGCTGCAAGCTTCTTAGCCATGTCGATTGTGGTTTTTGGTTAGGTTGAGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGATGATGATTCGATTCAAGAAAGGGAATGAAGTAGTAGACGAGGGCCAAAGAGTATAAAGATGGATGCGATCTTTTTCTCTTCTATTGTTCTGTTATTGTTTTGTGAGGGAAGTTTTGGCGCTTCAATACAAAAAAATAAATAAAGAATAAACAAATACAGCTTAGTTAAATGGGTATAACATGGGCCGGAATATATAATCACGGATTAAGGCCCATCATTGTCTCAAAATTAAACTCGGCCTCTATAATACTTCTCCCACACCGGTAATCTTGAGATGAACACTCCTCTTTCGTGTAGTATAAAATAAGACGAAGGTCCAACGTTGAAAGATACTTACCTGGACGGGGTC
TARGET=96,32
PRIMER_PRODUCT_SIZE_RANGE=100-500
PRIMER_FILE_FLAG=0
PRIMER_LIBERAL_BASE=1
PRIMER_NUM_RETURN=1
PRIMER_FIRST_BASE_INDEX=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_LEFT_EXPLAIN=considered 735, low tm 100, high tm 441, ok 194
PRIMER_RIGHT_EXPLAIN=considered 3232, GC content failed 191, low tm 1479, high tm 573, long poly-x seq 12, ok 977
PRIMER_PAIR_EXPLAIN=considered 3, high end compl 1, ok 2
PRIMER_PAIR_PENALTY=0.2733
PRIMER_LEFT_PENALTY=0.124828
PRIMER_RIGHT_PENALTY=0.148509
PRIMER_LEFT_SEQUENCE=CGTCTTCGAAAGCCTCTTTG
PRIMER_RIGHT_SEQUENCE=CAACGTTGGACCTTCGTCTT
PRIMER_LEFT=20,20
PRIMER_RIGHT=454,20
PRIMER_LEFT_TM=60.125
PRIMER_RIGHT_TM=60.149
PRIMER_LEFT_GC_PERCENT=50.000
PRIMER_RIGHT_GC_PERCENT=50.000
PRIMER_LEFT_SELF_ANY=6.00
PRIMER_RIGHT_SELF_ANY=8.00
PRIMER_LEFT_SELF_END=3.00
PRIMER_RIGHT_SELF_END=1.00
PRIMER_LEFT_END_STABILITY=7.3000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=4.00
PRIMER_PAIR_COMPL_END=0.00
PRIMER_PRODUCT_SIZE=435
=

BioPerl-1.007002/t/data/primer3_output.txt000444000766000024      2503113155576321 20453 0ustar00cjfieldsstaff000000000000PRIMER_SEQUENCE_ID=XXU25548
SEQUENCE=CTGACTCTTATACACAAGTAGCGTCCTGGACGGAACCTTTCCCGTTTTGCCCTGTTCTGGAAAACCGGGCTGCTCAGGGCGATATTACTGCACCCGGCGGTGCTCGCCGTTTAACGGGTGATCAGACTGCCGCTCTGCGTGATTCTCTTAGCGATAAACCTGCAAAAAATATTATTTTGCTGATTGGCGATGGGATGGGGGACTCGGAAATTACTGCCGCACGTAATTATGCCGAAGGTGCGGGCGGCTTTTTTAAAGGTATAGATGCCTTACCGCTTACCGGGCAATACACTCACTATGCGCTGAATAAAAAAACCGGCAAACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGATGCTGCCTCACTGAATTCGGTGACGGAAGCGAATCAGCAAAAACCCCTGCTTGGCCTGTTTGCTGACGGCAATATGCCAGTGCGCTGGCTAGGACCGAAAGCAACGTACCATGGCAATATCGATAAGCCCGCAGTCACCTGTACGCCAAATCCGCAACGTAATGACAGTGTACCAACCCTGGCGCAGATGACCGACAAAGCCATTGAATTGTTGAGTAAAAATGAGAAAGGCTTTTTCCTGCAAGTTGAAGGTGCGTCAATCGATAAACAGGATCATGCTGCGAATCCTTGTGGGCAAATTGGCGAGACGGTCGATCTCGATGAAGCCGTACAACGGGCGCTGGAATTCGCTAAAAAGGAGGGTAACACGCTGGTCATAGTCACCGCTGATCACGCCCACGCCAGCCAGATTGTTGCGCCGGATACCAAAGCTCCGGGCCTCACCCAGGCGCTAAATACCAAAGATGGCGCAGTGATGGTGATGAGTTACGGGAACTCCGAAGAGGATTCACAAGAACATACCGGCAGTCAGTTGCGTATTGCGGCGTATGGCCCGCATGCCGCCAATGTTGTTGGACTGACCGACCAGACCGATCTCTTCTACACCATGAAAGCCGCTCTGGGGCTGAAATAAAACCGCGCCCGGCAGTGAATTTTCGCTGCCGGGTGGTTTTTTTGCTGTTAGCAACCAGACTTAATGGCAGATCACGGGCGCATACGCTCATGGTTAAAACATGAAGAGGGATGGTGCTATGAAAATAACATTACTGGTTACCTTGCTTTTCGGTCTGGTTTTTTTAACCACCGTCGGCGCTGCCGAGAGAACTTTAACCCCACAACAACAGCGTATGACCTCCTGTAATCAGCAGGCGACGGCGCAGGCGTTGAAAGGGGATGCTCGTAAGACCTACATGAGTGATTGCCTGAAGAACAGCAAGTCTGCGCCTGGCGAAAAAAGTTTGACGCCACAGCAGCAAAAGATGCGCGAATGCAATAATCAAGCAACACAACAATCTCTGAAAGGTGATGATCGTAATAAGTTTATGAGTGCCTGCCTCAAGAAAGCCGCCTGATACCTGATAGTGCTAACGGGTGAGCTACGAAAATGGCTCACCCGAAATATCATACTTCTGCCTTTAGCTCCGTCTCTATAATTTGGGAAAATTGTTTCTGAATGTTCCCAAAAATAATGAATGATGAAAACTTTTTCAAAAAAGCGGCGGCGCACGGGGAGGAACCTCCTTTAACTCCTCAAAACGAACATCAGCGGTCCGGGCTGCGCTTCGCCCGTCGCGTCAGACTACCCCGTGCGGTTGGCCTGGCTGGCATGTTCTTACCGATTGCTTCAACGCTGGTTTCACACCCGCCGCCGGGCTGGTGGTGGCTGGTGTTGGTCGGCTGGGCGTTCGTCTGGCCGCATTTAGCCTGGCAGATAGCGAGCAGGGCCGTCGATCCGCTTAGCCGGGAAATTTACAACTTAAAAACCGATGCAGTATTAGCGGGAATGTGGGTAGGCGTAATGGGCGTAAACGTGCTGCCTTCCACCGCGATGTTGATGATTATGTGTCTGAATTTGATGGGGGCAGGCGGCCCCCGTCTGTTTGTCGCGGGTCTGGTGTTGATGGTGGTTTCCTGCCTTGTCACCCTCGAGGCCACCACATTCCGCACCGTAGGATTACTGCATCAGGAGTGGTGGATGCGCCCGGATGACCCTGCCGATGCGGATGAAAAGGAGAGTGGCAAATGGCTGGCAGCGGCCGCAACTAGCCGGTTACGCATGGGCAGCATGATGAGCAACGTGATTGCGGTCTGTGACCGCGAAGCCGATATTCATGCTTATCTGCAGGACAGGCTGGCGCATAACGAGCGCTTCGTGGTGCGCTCCAAGCACCCACGCAAGGACGTAGAGTCTGGGTTGTATCTGATCGACCATCTGAAGAACCAACCGGAGTTGGGTGGCTATCAGATCAGCATTCCGCAAAAGGGCGTGGTGGATAAACGCGGTAAACGTAAAAATCGACCAGCCCGCAAGGCGAGCTTGAGCCTGCGCAGTGGGCGCATCACGCTAAAACAGGGGAATATCACGCTCAACGCGGTGCTGGCCGAGGAGATTAACCCGCCCAAGGGTGAGACCCCGTTGAAATGGTTGTTGCTGACCGGCGAACCGGTCGAGTCGCTAGCCCAAGCCTTGCGCGTCATCGACATTTATACCCATCGCTGGCGGATCGAGGAGTTCCATAAGGCATGGAAAACCGGAGCAGGAGCCGAGAGGCAACGCATGGAGGAGCCGGATAATCTGGAGCGGATGGTCTCGATCCTCTCGTTTGTTGCGGTCAGGCTGTTACAGCTCAGAGAAAGCTTCACGCTGCCGCAAGCACTCAGGGCGCAAGGGCTGCTAAAGGAAGCGGAACACGTAGAAAGCCAGTCCGCAGAAACGGTGCTGACCCCGGATGAATGTCAGCTACTGGGCTATCTGGACAAGGGAAAACGCAAGCGCAAAGAGAAAGCAGGTAGCTTGCAGTGGGCTTACATGGCGATAGCTAGACTGGGCGGTTTTATGGACAGCAAGCGAACCGGAATTGCCAGCTGGGGCGCCCTCTGGTAAGGTTGGGAAGCCCTGCAAAGTAAACTGGATGGCTTTCTTGCCGCCAAGGATCTGATGGCGCAGGGGATCAAGATCTGATCAAGAGACAGGATGAGGATCGTTTCGCATGATTGAACAAGATGGATTGCACGCAGGTTCTCCGGCCGCTTGGGTGGAGAGGCTATTCGGCTATGACTGGGCACAACAGACAATCGGCTGCTCTGATGCCGCCGTGTTCCGGCTGTCAGCGCAGGGGCGCCCGGTTCTTTTTGTCAAGACCGACCTGTCCGGTGCCCTGAATGAACTGCAGGACGAGGCAGCGCGGCTATCGTGGCTGGCCACGACGGGCGTTCCTTGCGCAGCTGTGCTCGACGTTGTCACTGAAGCGGGAAGGGACTGGCTGCTATTGGGCGAAGTGCCGGGGCAGGATCTCCTGTCATCTCACCTTGCTCCTGCCGAGAAAGTATCCATCATGGCTGATGCAATGCGGCGGCTGCATACGCTTGATCCGGCTACCTGCCCATTCGACCACCAAGCGAAACATCGCATCGAGCGAGCACGTACTCGGATGGAAGCCGGTCTTGTCGATCAGGATGATCTGGACGAAGAGCATCAGGGGCTCGCGCCAGCCGAACTGTTCGCCAGGCTCAAGGCGCGCATGCCCGACGGCGAGGATCTCGTCGTGACCCATGGCGATGCCTGCTTGCCGAATATCATGGTGGAAAATGGCCGCTTTTCTGGATTCATCGACTGTGGCCGGCTGGGTGTGGCGGACCGCTATCAGGACATAGCGTTGGCTACCCGTGATATTGCTGAAGAGCTTGGCGGCGAATGGGCTGACCGCTTCCTCGTGCTTTACGGTATCGCCGCTCCCGATTCGCAGCGCATCGCCTTCTATCGCCTTCTTGACGAGTTCTTCTGAGCGGGACTCTGGGGTTCGAAATGACCGACCAAGCGACGCCCAACCTGCCATCACGAGATTTCGATTCCACCGCCGCCTTCTATGAAAGGTTGGGCTTCGGAATCGTTTTCCGGGACGCCGGCTGGATGATCCTCCAGCGCGGGGATCTCATGCTGGAGTTCTTCGCCCACCCCGGGCTCGATCCCCTCGCGAGTTGGTTCAGCTGCTGCCTGAGGCTGGACGACCTCGCGGAGTTCTACCGGCAGTGCAAATCCGTCGGCATCCAGGAAACCAGCAGCGGCTATCCGCGCATCCATGCCCCCGAACTGCAGGAGTGGGGAGGCACGATGGCCGCTTTGGTCGACCCGGACGGGACGCTCCTGCGCCTGATACAGAACGAATTGCTTGCAGGCATCTCATGAGTGTGTCTTCCCGTTTTCCGCCTGAGGTCACTGCGTGGATGGAGCGCTGGCGCCTGCTGCGCGACGGCGAGCTGCTCACCACCCACTCGAGCTGGATACTTCCCGTCCGCCAGGGGGACATGCCGGCGATGCTGAAGGTCGCGCGCATTCCCGATGAAGAGGCCGGTTACCGCCTGTTGACCTGGTGGGACGGGCAGGGCGCCGCCCGAGTCTTCGCCTCGGCGGCGGGCGCTCTGCTCATGGAGCGCGCGTCCGGGGCCGGGGACCTTGCACAGATAGCGTGGTCCGGCCAGGACGACGAGGCTTGCAGGATCCTCTGCGACACCGCCGCTCGTCTGCACGCGCCGCGGTCCGGACCGCCGCCCGATCTCCATCCGCTACAGGAATGGTTCCAGCCGCTTTTCCGGTTGGCCGCTGAGCACGCGGCACTTGCGCCCGCCGCCAGCGTAGCGCGCCAACTTCTGGCGGCGCCGCGCGAGGTGTGCCCGCTCCACGGCGACCTGCACCACGAGAACGTGCTCGACTTCGGCGACCGCGGCTGGCTGGCCATCGACCCGCACGGACTGCTCGGCGAGCGCACCTTCGACTATGCCAACATCTTCACGAATCCCGATCTCAGCGACCCCGGTCGCCCGCTTGCGATCCTGCCGGGCAGGCTGGAGGCTCGACTCAGCATTGTGGTCGCGACGACCGGGTTTGAGCCCGAACGGCTTCTTCGCTGGATCATTGCATGGACGGGCTTGTCGGCAGCCTGGTTCATCGGCGACGGCGACGGCGAGGGCGAGGGCGCTGCGATTGATCTGGCCGTAAACGCCATGGCACGCCGGTTGCTTGACTAGCGCGGTCACCGATCTCACCTGGTCGTCGAGCTAGGTCAGGCCGTGTCGGGCGTGATCCGCTGGAAGTCGTTGCGGGCCACACCCGCCGCCTCGAAGCCCTGCACCAGGCCGGCATCGTGGTGTGCGTGGCCGAGGGACTATGGAAGGTGCCGGACGATCTGCCCGAGCAGGGCCGCCGCTATGACGCCCAGCGTCTTGGTGGCGTGACGGTGGAGCTGAAATCGCACCTGCCCATCGAGCGGCAGGCCCGCGTGATCGGTGCCACCTGGCTTGACCAGCAGTTGATCGACGGTGGCTCGGGCTTGGGCGACCTGGGCTTTAGCAGTGAGGCCAAGTAGGCGATACAGCAGCGCGCGGACTTCCTGGCCGAACAGGGACTGGCCGAGCGGCGCGGGCAGCGCGTGATCCTCACCGGAATCTGCTCGGCAGCAGCGGGCTCGGGAACTGGCGCAGGCCGCGAAGGACATTGCCGCCGATACCGGCCTGGAGCATCGCCCCGTGGCCGACGGCCAGCGCGTTGCCGGCGTCTACCGGCGCCCCGTCATGCTCGCCAGCGGGCGAAATGGGATGCTTGATGACGCCAAGGGGTCCAGCCTCGTGCGGTGGAAGCCCATCGAACAGCGGCTTGGGGAGCAGCTCGCCGCGACGGTGCGCGGTGGCGGCGTGTCTTGGGAGATTGGACGACAGCGTGGGCCGGCCCCTGTCTCTTGATCAGATCTTGATCCCCTGCGCCATCAGATCCTTGGCGGCAAGAAAGCCATCCAGTTTACTTTGCAGGGCTTCCCAACCTTCCCAGAGGGCGCCCCAGCTGGCAATTCCGGTTCGCTTGCTGTCCATAAAACCGCCCAGTCTAGCTATCGCCATGTAAGCCCACTGCAAGCTACCTGCTTTCTCTTTGCGCTTGCGTTTTCCCTTGTCCAGATAGCCCAGTAGCTGACATTCATCCGGGGTCAGCACCGTTTCTGCGGACTGGCTTTCTACGTGTTCCGCTTCCTTTAGCAGCCCTTGCGCCCTGAGTGCTTGCGGCAGCGTGAAGCTTTCTCTGAGCTGTAACAGCCTGACCGCAACAAACGAGAGGATCGAGACCATCCGCTCCAGATTATCCGGCTCCTCCATGCGTTGCCTCTCGGCTCCTGCTCCGGTTTTCCATGCCTTATGGAACTCCTCGATCCGCCAGCGATGGGTATAAATGTCGATGACGCGCAAGGCTTGGGCTAGCGACTCGACCGGTTCGCCGGTCAGCAACAACCATTTCAACGGGGTCTCACCCTTGGGCGGGTTAATCTCCTCGGCCAGCACCGCGTTGAGCGTGATATTCCCCTGTTTTAGCGTGATGCGCCCACTGCGCAGGCTCAAGCTCGCCTTGCGGGCTGGTCGATTTTTACGTTTACCGCGTTTATCCACCACGCCCTTTTGCGGAATGCTGATCTGATAGCCACCCAACTCCGGTTGGTTCTTCAGATGGTCGATCAGATACAACCCAGACTCTACGTCCTTGCGTGGGTGCTTGGAGCGCACCACGAAGCGCTCGTTATGCGCCAGCCTGTCCTGCAGATAAGCATGAATATCGGCTTCGCGGTCACAGACCGCAATCACGTTGCTCATCATGCTGCCCATGCGTAACCGGCTAGTTGCGGCCGCTGCCAGCCATTTGCCACTCTCCTTTTCATCCGCATCGGCAGGGTCATCCGGGCGCATCCACCACTCCTGATGCAGTAATCCTACGGTGCGGAATGTGGTGGCCTCGAGCAAGAGAACGGAGTGAACCCACCATCCGCGGGATTTATCCTGAATAGAGCCCAGCTTGCCAAGCTCTTCGGCGACCTGGTGGCGATAACTCAAAGAGGTGGTGTCCTCAATGGCCAGCAGTTCGGGAAACTCCTGAGCCAACTTGACTGTTTGCATGGCGCCAGCCTTTCTGATCGCCTCGGCAGAAACGTTGGGATTGCGGTAAAATCGGTAAGCGCCTTCCTGCATGGCTTCACTACCCTCTGATGAGATGGTTATTGATTTACCAGAATATTTTGCCAATTGGGCGGCGACGTTAACCAAGCGGGCAGTACGGCGAGGATCACCCAGCGCCGCCGAAGAGAACACAGATTTAGCCCAGTCGGCCGCACGATGAAGAGCAGAAGTTATCATGAACGTTACCATGTTAGGAGGTCACATGGAAGTCAGATCCTGGAAAACGGGAAAGGTTCCGTTCAGGACGCTACTTGTGTATAAGAGTCAG
PRIMER_PAIR_PENALTY=0.0034
PRIMER_LEFT_PENALTY=0.000037
PRIMER_RIGHT_PENALTY=0.003322
PRIMER_LEFT_SEQUENCE=GACCGAAAGCAACGTACCAT
PRIMER_RIGHT_SEQUENCE=ATGACCAGCGTGTTACCCTC
PRIMER_LEFT=846,20
PRIMER_RIGHT=1131,20
PRIMER_LEFT_TM=60.000
PRIMER_RIGHT_TM=59.997
PRIMER_LEFT_GC_PERCENT=50.000
PRIMER_RIGHT_GC_PERCENT=55.000
PRIMER_LEFT_SELF_ANY=4.00
PRIMER_RIGHT_SELF_ANY=3.00
PRIMER_LEFT_SELF_END=2.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=7.8000
PRIMER_RIGHT_END_STABILITY=9.4000
PRIMER_PAIR_COMPL_ANY=4.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=286
PRIMER_PAIR_PENALTY_1=0.0180
PRIMER_LEFT_1_PENALTY=0.003322
PRIMER_RIGHT_1_PENALTY=0.014712
PRIMER_LEFT_1_SEQUENCE=GAGGGTAACACGCTGGTCAT
PRIMER_RIGHT_1_SEQUENCE=GAATCCTCTTCGGAGTTCCC
PRIMER_LEFT_1=1112,20
PRIMER_RIGHT_1=1263,20
PRIMER_LEFT_1_TM=59.997
PRIMER_RIGHT_1_TM=60.015
PRIMER_LEFT_1_GC_PERCENT=55.000
PRIMER_RIGHT_1_GC_PERCENT=55.000
PRIMER_LEFT_1_SELF_ANY=3.00
PRIMER_RIGHT_1_SELF_ANY=4.00
PRIMER_LEFT_1_SELF_END=2.00
PRIMER_RIGHT_1_SELF_END=2.00
PRIMER_LEFT_1_END_STABILITY=6.3000
PRIMER_RIGHT_1_END_STABILITY=9.7000
PRIMER_PAIR_1_COMPL_ANY=4.00
PRIMER_PAIR_1_COMPL_END=1.00
PRIMER_PRODUCT_SIZE_1=152
PRIMER_PAIR_PENALTY_2=0.0213
PRIMER_LEFT_2_PENALTY=0.000037
PRIMER_RIGHT_2_PENALTY=0.021275
PRIMER_LEFT_2_SEQUENCE=GACCGAAAGCAACGTACCAT
PRIMER_RIGHT_2_SEQUENCE=CTTTTTAGCGAATTCCAGCG
PRIMER_LEFT_2=846,20
PRIMER_RIGHT_2=1111,20
PRIMER_LEFT_2_TM=60.000
PRIMER_RIGHT_2_TM=59.979
PRIMER_LEFT_2_GC_PERCENT=50.000
PRIMER_RIGHT_2_GC_PERCENT=45.000
PRIMER_LEFT_2_SELF_ANY=4.00
PRIMER_RIGHT_2_SELF_ANY=6.00
PRIMER_LEFT_2_SELF_END=2.00
PRIMER_RIGHT_2_SELF_END=2.00
PRIMER_LEFT_2_END_STABILITY=7.8000
PRIMER_RIGHT_2_END_STABILITY=10.2000
PRIMER_PAIR_2_COMPL_ANY=4.00
PRIMER_PAIR_2_COMPL_END=0.00
PRIMER_PRODUCT_SIZE_2=266
PRIMER_PAIR_PENALTY_3=0.0354
PRIMER_LEFT_3_PENALTY=0.019325
PRIMER_RIGHT_3_PENALTY=0.016052
PRIMER_LEFT_3_SEQUENCE=AGACAATCGGCTGCTCTGAT
PRIMER_RIGHT_3_SEQUENCE=CTCGTCCTGCAGTTCATTCA
PRIMER_LEFT_3=3544,20
PRIMER_RIGHT_3=3653,20
PRIMER_LEFT_3_TM=59.981
PRIMER_RIGHT_3_TM=59.984
PRIMER_LEFT_3_GC_PERCENT=50.000
PRIMER_RIGHT_3_GC_PERCENT=50.000
PRIMER_LEFT_3_SELF_ANY=4.00
PRIMER_RIGHT_3_SELF_ANY=6.00
PRIMER_LEFT_3_SELF_END=3.00
PRIMER_RIGHT_3_SELF_END=1.00
PRIMER_LEFT_3_END_STABILITY=6.6000
PRIMER_RIGHT_3_END_STABILITY=6.9000
PRIMER_PAIR_3_COMPL_ANY=4.00
PRIMER_PAIR_3_COMPL_END=2.00
PRIMER_PRODUCT_SIZE_3=110
PRIMER_PAIR_PENALTY_4=0.0354
PRIMER_LEFT_4_PENALTY=0.019325
PRIMER_RIGHT_4_PENALTY=0.016052
PRIMER_LEFT_4_SEQUENCE=AGACAATCGGCTGCTCTGAT
PRIMER_RIGHT_4_SEQUENCE=TCGTCCTGCAGTTCATTCAG
PRIMER_LEFT_4=3544,20
PRIMER_RIGHT_4=3652,20
PRIMER_LEFT_4_TM=59.981
PRIMER_RIGHT_4_TM=59.984
PRIMER_LEFT_4_GC_PERCENT=50.000
PRIMER_RIGHT_4_GC_PERCENT=50.000
PRIMER_LEFT_4_SELF_ANY=4.00
PRIMER_RIGHT_4_SELF_ANY=6.00
PRIMER_LEFT_4_SELF_END=3.00
PRIMER_RIGHT_4_SELF_END=2.00
PRIMER_LEFT_4_END_STABILITY=6.6000
PRIMER_RIGHT_4_END_STABILITY=7.0000
PRIMER_PAIR_4_COMPL_ANY=4.00
PRIMER_PAIR_4_COMPL_END=3.00
PRIMER_PRODUCT_SIZE_4=109
=
BioPerl-1.007002/t/data/prints.out000444000766000024      6507613155576321 16776 0ustar00cjfieldsstaff000000000000Sn; BIOPERL_TEST_SEQUENCE_ID
Si; Fasta sequence
1TBS
1TBH DNAGYRASEB      2.035573e-70
1TBH TPI2FAMILY      3.830756e-70
1TBF
2TBS
2TBT FingerPrint     No.Motifs SumId    AveId    ProfScore  Ppvalue     Evalue      GraphScan               
2TBH DNAGYRASEB      10 of  11 5.3e+02  53       4363       2.5e-75     2e-70       IIII.IIIIII     
2TBH TPI2FAMILY      9  of  9  539.06   59.90    4433       4.8e-75     3.8e-70     IIIIIIIII       
2TBN BCTRLSENSOR     2  of  4  64.27    32.14    391        2.4e-06     0.19        I.i.            
2TBN TROPOMYOSIN     2  of  5  58.53    29.26    483        4.4e-05     3.5         I.i..           
2TBN MEROZOITESA     2  of  15 52.70    26.35    488        8e-05       6.4         .i...........i. 
2TBN FADG3PDH        2  of  6  72.65    36.32    400        0.00012     9.8         I....I          
2TBN PROXISOMPAGR    2  of  6  97.06    48.53    481        0.00046     37          .I..I.          
2TBN CYANASE         2  of  5  60.96    30.48    322        0.00068     54          i...I           
2TBN ALARACEMASE     2  of  9  49.23    24.61    344        0.00068     54          ..I...i..       
2TBN FMOXYGENASE     2  of  13 44.28    22.14    327        0.00073     58          i........i...   
2TBF
3TBS
3TBT MotifName       No.Mots   IdScore PfScore Pvalue    Sequence                                                Len  low  pos  high 
3TBH DNAGYRASEB      1  of  11 56.97   334     4.14e-05  YSAGQIKILEG                                             11   4    8    33   
3TBH DNAGYRASEB      2  of  11 48.33   419     1.44e-07  DFQFDILSARFRELAF                                        16   178  182  207  
3TBH DNAGYRASEB      3  of  11 48.81   352     4.94e-06  FLNKGLVLIVEDRR                                          14   193  197  222  
3TBH DNAGYRASEB      4  of  11 40.58   487     2.12e-10  GGIVSFVEHINENKHPMHKVIHF                                 23   217  227  277  
3TBH DNAGYRASEB      6  of  11 65.69   637     1.20e-11  GEDVKEGLTAVISIKIP                                       17   310  319  369  
3TBH DNAGYRASEB      7  of  11 45.33   358     7.99e-07  FFEENPNITKKILEK                                         15   359  367  417  
3TBH DNAGYRASEB      8  of  11 60.16   604     3.60e-13  KCILSAKAREAARKARDLTRR                                   21   373  381  431  
3TBH DNAGYRASEB      9  of  11 60.33   332     1.39e-06  LVSALGTGIG                                              10   459  477  911  
3TBH DNAGYRASEB      10 of  11 44.62   312     2.07e-05  PSNRVVLKVKLDD                                           13   588  594  1029 
3TBH DNAGYRASEB      11 of  11 54.51   528     4.10e-09  AEETFNILMGDEVQPRK                                       17   604  610  1045 
3TBB
3TBH TPI2FAMILY      1  of  9  56.63   501     7.92e-09  GLHKMVYEVVDNSVDE                                        16   31   37   172  
3TBH TPI2FAMILY      2  of  9  62.28   483     2.55e-08  EVKDNGRGIPVDIH                                          14   66   72   209  
3TBH TPI2FAMILY      3  of  9  73.17   547     2.56e-10  GGLHGVGVSVVNALS                                         15   109  115  252  
3TBH TPI2FAMILY      4  of  9  50.35   371     8.26e-06  CFTNNINNNLGGTH                                          14   251  274  414  
3TBH TPI2FAMILY      5  of  9  70.89   498     6.45e-10  LYLVEGDSAGGSAKQ                                         15   399  427  561  
3TBH TPI2FAMILY      6  of  9  66.21   629     3.61e-10  KIRYHKIMIMTDADIDG                                       17   461  494  928  
3TBH TPI2FAMILY      7  of  9  52.17   503     4.41e-10  HIRTLLLTFFFRYMRPVI                                      18   479  512  946  
3TBH TPI2FAMILY      8  of  9  43.15   321     1.38e-06  GYLYVAQPPLYLI                                           13   499  532  966  
3TBH TPI2FAMILY      9  of  9  64.20   580     7.91e-11  IQRYKGLGEMNPEQLWE                                       17   539  573  1008 
3TBB
3TBN BCTRLSENSOR     1  of  4  40.72   272     2.48e-05  NIIEVKDNGRGIPVD                                         15   219  69   1911 
3TBN BCTRLSENSOR     3  of  4  23.55   119     9.78e-02  GLHGVGVSVVNALSEYLEV                                     19   252  116  1946 
3TBB
3TBN TROPOMYOSIN     1  of  5  35.76   286     9.84e-04  ELAFLNKGLVLIVEDRRR                                      18   9    194  357  
3TBN TROPOMYOSIN     3  of  5  22.77   197     4.43e-02  ILEKCILSAKAREAARKARDLTRRKTVLE                           29   70   378  560  
3TBB
3TBN MEROZOITESA     2  of  15 28.21   293     1.55e-03  NGRGIPVDIHPDKKISTIEV                                    20   68   76   123  
3TBN MEROZOITESA     14 of  15 24.49   195     5.17e-02  LIKHGKNSTYAYSDKEKEELL                                   21   510  543  576  
3TBB
3TBN FADG3PDH        1  of  6  32.91   209     6.51e-03  NDAYKVSGGLHGV                                           13   4    108  75   
3TBN FADG3PDH        6  of  6  39.74   191     1.88e-02  LYLIKHGKNSTYA                                           13   347  541  454  
3TBB
3TBN PROXISOMPAGR    2  of  6  50.00   241     1.57e-02  PDATIFTTVDFQFD                                          14   30   173  60   
3TBN PROXISOMPAGR    5  of  6  47.06   240     2.93e-02  EDVKEGLTAVISIKIPQ                                       17   185  320  215  
3TBB
3TBN CYANASE         1  of  5  25.89   131     4.96e-02  KHPTGLSGEDVKEGLT                                        16   13   312  77   
3TBN CYANASE         5  of  5  35.06   191     1.37e-02  QAILPLKGKIL                                             11   131  448  297  
3TBB
3TBN ALARACEMASE     3  of  9  32.91   191     1.08e-02  AYKVSGGLHGVGV                                           13   120  110  155  
3TBN ALARACEMASE     7  of  9  16.32   153     6.29e-02  LAEISIQYSETYTENI                                        16   265  257  307  
3TBB
3TBN FMOXYGENASE     1  of  13 22.06   151     7.01e-02  RKTVLEGGGLPGKLADC                                       17   2    401  7    
3TBN FMOXYGENASE     10 of  13 22.22   176     1.04e-02  RVVLKVKLDDFVEAEETF                                      18   225  597  296  
3TBB
3TBF
4TBT --------------------------------------------------------------------------
4TBN DNAGYRASEB
4TBS MSQKETSYSAGQIKILEGLEAVRKRPGMYIGTQDETGLHKMVYEVVDNSVDEAMAGHCTEIRISILPNNIIEVK
4TBL        YDASsIqVLEG                                                        
4TBL 
4TBS DNGRGIPVDIHPDKKISTIEVVMTILHAGGKFENDAYKVSGGLHGVGVSVVNALSEYLEVEVHQKGKIYTQKYE
4TBL                                                                           
4TBL 
4TBS KGIPVSPVEIKGDSSERGTIVRFKPDATIFTTVDFQFDILSARFRELAFLNKGLVLIVEDRRRGAEGENLLRNE
4TBL                                  eFdFetLakRLRELAFFLNkGltItLtDeR           
4TBL 
4TBS FQFSGGIVSFVEHINENKHPMHKVIHFERNKDDVLAEISIQYSETYTENIFCFTNNINNNLGGTHLEGFRAALT
4TBL      GGIvsFVeYLNrnKtplhdepiY                                              
4TBL 
4TBS RTLNDFLKKDTTLSKKHPTGLSGEDVKEGLTAVISIKIPQPQFNSQTKEKLVNAEIKGIMQTLSSEGLTLFFEE
4TBL                        GeDiREGLTAiISVKvP                               fLe
4TBL 
4TBS NPNITKKILEKCILSAKAREAARKARDLTRRKTVLEGGGLPGKLADCSEKDPAFSELYLVEGDSAGGSAKQGRD
4TBL ENPqeAKkIveKKiidAArAReAARkARElTRR                                         
4TBL 
4TBS RNTQAILPLKGKILNVEKARLDKILSSEEIRILVSALGTGIGEDEFNINKIRYHKIMIMTDADIDGSHIRTLLL
4TBL                                   LITALGtGIG                              
4TBL 
4TBS TFFFRYMRPVIERGYLYVAQPPLYLIKHGKNSTYAYSDKEKEELLKNVGTEKVVIQRYKGLGEMNPEQLWETTM
4TBL                                                                           
4TBL 
4TBS DPSNRVVLKVKLDDFVEAEETFNILMGDEVQPRKQFIEINAAKVANLDL
4TBL    PevRtLlqVTleD   ADeiFstLMGDdVEPRR             
4TBL 
4TBS --------------------------------------------------------------------------
4TBT --------------------------------------------------------------------------
4TBN TPI2FAMILY
4TBS MSQKETSYSAGQIKILEGLEAVRKRPGMYIGTQDETGLHKMVYEVVDNSVDEAMAGHCTEIRISILPNNIIEVK
4TBL                                     GLHHlvdEIvDNAaDE                   sVe
4TBL 
4TBS DNGRGIPVDIHPDKKISTIEVVMTILHAGGKFENDAYKVSGGLHGVGVSVVNALSEYLEVEVHQKGKIYTQKYE
4TBL DNGRGIPVdiH                             GGLHGVGASVVNALS                   
4TBL 
4TBS KGIPVSPVEIKGDSSERGTIVRFKPDATIFTTVDFQFDILSARFRELAFLNKGLVLIVEDRRRGAEGENLLRNE
4TBL                                                                           
4TBL 
4TBS FQFSGGIVSFVEHINENKHPMHKVIHFERNKDDVLAEISIQYSETYTENIFCFTNNINNNLGGTHLEGFRAALT
4TBL                                                    SFVNnIaTteGGTH         
4TBL 
4TBS RTLNDFLKKDTTLSKKHPTGLSGEDVKEGLTAVISIKIPQPQFNSQTKEKLVNAEIKGIMQTLSSEGLTLFFEE
4TBL                                                                           
4TBL 
4TBS NPNITKKILEKCILSAKAREAARKARDLTRRKTVLEGGGLPGKLADCSEKDPAFSELYLVEGDSAGGSAKQGRD
4TBL                                                         LiLVEGDSAGGSAKs   
4TBL 
4TBS RNTQAILPLKGKILNVEKARLDKILSSEEIRILVSALGTGIGEDEFNINKIRYHKIMIMTDADIDGSHIRTLLL
4TBL                                                  kLRYgKIiIMTDADvDG HIktLLL
4TBL 
4TBS TFFFRYMRPVIERGYLYVAQPPLYLIKHGKNSTYAYSDKEKEELLKNVGTEKVVIQRYKGLGEMNPEQLWETTM
4TBL TFFyRymPpLi  GfvyiAqPPLYKv                            IQRYKGLGEMnakqLwE   
4TBL 
4TBS DPSNRVVLKVKLDDFVEAEETFNILMGDEVQPRKQFIEINAAKVANLDL
4TBL                                                  
4TBL 
4TBS --------------------------------------------------------------------------
4TBT --------------------------------------------------------------------------
4TBN BCTRLSENSOR
4TBS MSQKETSYSAGQIKILEGLEAVRKRPGMYIGTQDETGLHKMVYEVVDNSVDEAMAGHCTEIRISILPNNIIEVK
4TBL                                                                     vlieVs
4TBL 
4TBS DNGRGIPVDIHPDKKISTIEVVMTILHAGGKFENDAYKVSGGLHGVGVSVVNALSEYLEVEVHQKGKIYTQKYE
4TBL DtGiGIppe                                gGTGLGLaIVkriveahGG              
4TBL 
4TBS KGIPVSPVEIKGDSSERGTIVRFKPDATIFTTVDFQFDILSARFRELAFLNKGLVLIVEDRRRGAEGENLLRNE
4TBL                                                                           
4TBL 
4TBS FQFSGGIVSFVEHINENKHPMHKVIHFERNKDDVLAEISIQYSETYTENIFCFTNNINNNLGGTHLEGFRAALT
4TBL                                                                           
4TBL 
4TBS RTLNDFLKKDTTLSKKHPTGLSGEDVKEGLTAVISIKIPQPQFNSQTKEKLVNAEIKGIMQTLSSEGLTLFFEE
4TBL                                                                           
4TBL 
4TBS NPNITKKILEKCILSAKAREAARKARDLTRRKTVLEGGGLPGKLADCSEKDPAFSELYLVEGDSAGGSAKQGRD
4TBL                                                                           
4TBL 
4TBS RNTQAILPLKGKILNVEKARLDKILSSEEIRILVSALGTGIGEDEFNINKIRYHKIMIMTDADIDGSHIRTLLL
4TBL                                                                           
4TBL 
4TBS TFFFRYMRPVIERGYLYVAQPPLYLIKHGKNSTYAYSDKEKEELLKNVGTEKVVIQRYKGLGEMNPEQLWETTM
4TBL                                                                           
4TBL 
4TBS DPSNRVVLKVKLDDFVEAEETFNILMGDEVQPRKQFIEINAAKVANLDL
4TBL                                                  
4TBL 
4TBS --------------------------------------------------------------------------
4TBT --------------------------------------------------------------------------
4TBN TROPOMYOSIN
4TBS MSQKETSYSAGQIKILEGLEAVRKRPGMYIGTQDETGLHKMVYEVVDNSVDEAMAGHCTEIRISILPNNIIEVK
4TBL                                                                           
4TBL 
4TBS DNGRGIPVDIHPDKKISTIEVVMTILHAGGKFENDAYKVSGGLHGVGVSVVNALSEYLEVEVHQKGKIYTQKYE
4TBL                                                                           
4TBL 
4TBS KGIPVSPVEIKGDSSERGTIVRFKPDATIFTTVDFQFDILSARFRELAFLNKGLVLIVEDRRRGAEGENLLRNE
4TBL                                              EVASLNRRIQLVEEELDR           
4TBL 
4TBS FQFSGGIVSFVEHINENKHPMHKVIHFERNKDDVLAEISIQYSETYTENIFCFTNNINNNLGGTHLEGFRAALT
4TBL                                                                           
4TBL 
4TBS RTLNDFLKKDTTLSKKHPTGLSGEDVKEGLTAVISIKIPQPQFNSQTKEKLVNAEIKGIMQTLSSEGLTLFFEE
4TBL                                                                           
4TBL 
4TBS NPNITKKILEKCILSAKAREAARKARDLTRRKTVLEGGGLPGKLADCSEKDPAFSELYLVEGDSAGGSAKQGRD
4TBL        EiQLKEAKHIAEEADRKYEEVARKLVIiE                                      
4TBL 
4TBS RNTQAILPLKGKILNVEKARLDKILSSEEIRILVSALGTGIGEDEFNINKIRYHKIMIMTDADIDGSHIRTLLL
4TBL                                                                           
4TBL 
4TBS TFFFRYMRPVIERGYLYVAQPPLYLIKHGKNSTYAYSDKEKEELLKNVGTEKVVIQRYKGLGEMNPEQLWETTM
4TBL                                                                           
4TBL 
4TBS DPSNRVVLKVKLDDFVEAEETFNILMGDEVQPRKQFIEINAAKVANLDL
4TBL                                                  
4TBL 
4TBS --------------------------------------------------------------------------
4TBT --------------------------------------------------------------------------
4TBN MEROZOITESA
4TBS MSQKETSYSAGQIKILEGLEAVRKRPGMYIGTQDETGLHKMVYEVVDNSVDEAMAGHCTEIRISILPNNIIEVK
4TBL                                                                           
4TBL 
4TBS DNGRGIPVDIHPDKKISTIEVVMTILHAGGKFENDAYKVSGGLHGVGVSVVNALSEYLEVEVHQKGKIYTQKYE
4TBL  HGSGIRVDLGEDAEVaNtqY                                                     
4TBL 
4TBS KGIPVSPVEIKGDSSERGTIVRFKPDATIFTTVDFQFDILSARFRELAFLNKGLVLIVEDRRRGAEGENLLRNE
4TBL                                                                           
4TBL 
4TBS FQFSGGIVSFVEHINENKHPMHKVIHFERNKDDVLAEISIQYSETYTENIFCFTNNINNNLGGTHLEGFRAALT
4TBL                                                                           
4TBL 
4TBS RTLNDFLKKDTTLSKKHPTGLSGEDVKEGLTAVISIKIPQPQFNSQTKEKLVNAEIKGIMQTLSSEGLTLFFEE
4TBL                                                                           
4TBL 
4TBS NPNITKKILEKCILSAKAREAARKARDLTRRKTVLEGGGLPGKLADCSEKDPAFSELYLVEGDSAGGSAKQGRD
4TBL                                                                           
4TBL 
4TBS RNTQAILPLKGKILNVEKARLDKILSSEEIRILVSALGTGIGEDEFNINKIRYHKIMIMTDADIDGSHIRTLLL
4TBL                                                                           
4TBL 
4TBS TFFFRYMRPVIERGYLYVAQPPLYLIKHGKNSTYAYSDKEKEELLKNVGTEKVVIQRYKGLGEMNPEQLWETTM
4TBL                         YDKMDQAddYGKStSRkDEML                             
4TBL 
4TBS DPSNRVVLKVKLDDFVEAEETFNILMGDEVQPRKQFIEINAAKVANLDL
4TBL                                                  
4TBL 
4TBS --------------------------------------------------------------------------
4TBT --------------------------------------------------------------------------
4TBN FADG3PDH
4TBS MSQKETSYSAGQIKILEGLEAVRKRPGMYIGTQDETGLHKMVYEVVDNSVDEAMAGHCTEIRISILPNNIIEVK
4TBL                                                                           
4TBL 
4TBS DNGRGIPVDIHPDKKISTIEVVMTILHAGGKFENDAYKVSGGLHGVGVSVVNALSEYLEVEVHQKGKIYTQKYE
4TBL                                  fDVlVIGGGaTGa                            
4TBL 
4TBS KGIPVSPVEIKGDSSERGTIVRFKPDATIFTTVDFQFDILSARFRELAFLNKGLVLIVEDRRRGAEGENLLRNE
4TBL                                                                           
4TBL 
4TBS FQFSGGIVSFVEHINENKHPMHKVIHFERNKDDVLAEISIQYSETYTENIFCFTNNINNNLGGTHLEGFRAALT
4TBL                                                                           
4TBL 
4TBS RTLNDFLKKDTTLSKKHPTGLSGEDVKEGLTAVISIKIPQPQFNSQTKEKLVNAEIKGIMQTLSSEGLTLFFEE
4TBL                                                                           
4TBL 
4TBS NPNITKKILEKCILSAKAREAARKARDLTRRKTVLEGGGLPGKLADCSEKDPAFSELYLVEGDSAGGSAKQGRD
4TBL                                                                           
4TBL 
4TBS RNTQAILPLKGKILNVEKARLDKILSSEEIRILVSALGTGIGEDEFNINKIRYHKIMIMTDADIDGSHIRTLLL
4TBL                                                                           
4TBL 
4TBS TFFFRYMRPVIERGYLYVAQPPLYLIKHGKNSTYAYSDKEKEELLKNVGTEKVVIQRYKGLGEMNPEQLWETTM
4TBL                       LITIAGGKlTTYR                                       
4TBL 
4TBS DPSNRVVLKVKLDDFVEAEETFNILMGDEVQPRKQFIEINAAKVANLDL
4TBL                                                  
4TBL 
4TBS --------------------------------------------------------------------------
4TBT --------------------------------------------------------------------------
4TBN PROXISOMPAGR
4TBS MSQKETSYSAGQIKILEGLEAVRKRPGMYIGTQDETGLHKMVYEVVDNSVDEAMAGHCTEIRISILPNNIIEVK
4TBL                                                                           
4TBL 
4TBS DNGRGIPVDIHPDKKISTIEVVMTILHAGGKFENDAYKVSGGLHGVGVSVVNALSEYLEVEVHQKGKIYTQKYE
4TBL                                                                           
4TBL 
4TBS KGIPVSPVEIKGDSSERGTIVRFKPDATIFTTVDFQFDILSARFRELAFLNKGLVLIVEDRRRGAEGENLLRNE
4TBL                         FDIKPFTTVDFSSI                                    
4TBL 
4TBS FQFSGGIVSFVEHINENKHPMHKVIHFERNKDDVLAEISIQYSETYTENIFCFTNNINNNLGGTHLEGFRAALT
4TBL                                                                           
4TBL 
4TBS RTLNDFLKKDTTLSKKHPTGLSGEDVKEGLTAVISIKIPQPQFNSQTKEKLVNAEIKGIMQTLSSEGLTLFFEE
4TBL                        QAEKEKLLAEISSDIDQ                                  
4TBL 
4TBS NPNITKKILEKCILSAKAREAARKARDLTRRKTVLEGGGLPGKLADCSEKDPAFSELYLVEGDSAGGSAKQGRD
4TBL                                                                           
4TBL 
4TBS RNTQAILPLKGKILNVEKARLDKILSSEEIRILVSALGTGIGEDEFNINKIRYHKIMIMTDADIDGSHIRTLLL
4TBL                                                                           
4TBL 
4TBS TFFFRYMRPVIERGYLYVAQPPLYLIKHGKNSTYAYSDKEKEELLKNVGTEKVVIQRYKGLGEMNPEQLWETTM
4TBL                                                                           
4TBL 
4TBS DPSNRVVLKVKLDDFVEAEETFNILMGDEVQPRKQFIEINAAKVANLDL
4TBL                                                  
4TBL 
4TBS --------------------------------------------------------------------------
4TBT --------------------------------------------------------------------------
4TBN CYANASE
4TBS MSQKETSYSAGQIKILEGLEAVRKRPGMYIGTQDETGLHKMVYEVVDNSVDEAMAGHCTEIRISILPNNIIEVK
4TBL                                                                           
4TBL 
4TBS DNGRGIPVDIHPDKKISTIEVVMTILHAGGKFENDAYKVSGGLHGVGVSVVNALSEYLEVEVHQKGKIYTQKYE
4TBL                                                                           
4TBL 
4TBS KGIPVSPVEIKGDSSERGTIVRFKPDATIFTTVDFQFDILSARFRELAFLNKGLVLIVEDRRRGAEGENLLRNE
4TBL                                                                           
4TBL 
4TBS FQFSGGIVSFVEHINENKHPMHKVIHFERNKDDVLAEISIQYSETYTENIFCFTNNINNNLGGTHLEGFRAALT
4TBL                                                                           
4TBL 
4TBS RTLNDFLKKDTTLSKKHPTGLSGEDVKEGLTAVISIKIPQPQFNSQTKEKLVNAEIKGIMQTLSSEGLTLFFEE
4TBL                KaakGlTFadLadelG                                           
4TBL 
4TBS NPNITKKILEKCILSAKAREAARKARDLTRRKTVLEGGGLPGKLADCSEKDPAFSELYLVEGDSAGGSAKQGRD
4TBL                                                                           
4TBL 
4TBS RNTQAILPLKGKILNVEKARLDKILSSEEIRILVSALGTGIGEDEFNINKIRYHKIMIMTDADIDGSHIRTLLL
4TBL    RVVVTlDGKYL                                                            
4TBL 
4TBS TFFFRYMRPVIERGYLYVAQPPLYLIKHGKNSTYAYSDKEKEELLKNVGTEKVVIQRYKGLGEMNPEQLWETTM
4TBL                                                                           
4TBL 
4TBS DPSNRVVLKVKLDDFVEAEETFNILMGDEVQPRKQFIEINAAKVANLDL
4TBL                                                  
4TBL 
4TBS --------------------------------------------------------------------------
4TBT --------------------------------------------------------------------------
4TBN ALARACEMASE
4TBS MSQKETSYSAGQIKILEGLEAVRKRPGMYIGTQDETGLHKMVYEVVDNSVDEAMAGHCTEIRISILPNNIIEVK
4TBL                                                                           
4TBL 
4TBS DNGRGIPVDIHPDKKISTIEVVMTILHAGGKFENDAYKVSGGLHGVGVSVVNALSEYLEVEVHQKGKIYTQKYE
4TBL                                    hLKvDTGMnRLGv                          
4TBL 
4TBS KGIPVSPVEIKGDSSERGTIVRFKPDATIFTTVDFQFDILSARFRELAFLNKGLVLIVEDRRRGAEGENLLRNE
4TBL                                                                           
4TBL 
4TBS FQFSGGIVSFVEHINENKHPMHKVIHFERNKDDVLAEISIQYSETYTENIFCFTNNINNNLGGTHLEGFRAALT
4TBL                                   iGvVaiGYADGypRal                        
4TBL 
4TBS RTLNDFLKKDTTLSKKHPTGLSGEDVKEGLTAVISIKIPQPQFNSQTKEKLVNAEIKGIMQTLSSEGLTLFFEE
4TBL                                                                           
4TBL 
4TBS NPNITKKILEKCILSAKAREAARKARDLTRRKTVLEGGGLPGKLADCSEKDPAFSELYLVEGDSAGGSAKQGRD
4TBL                                                                           
4TBL 
4TBS RNTQAILPLKGKILNVEKARLDKILSSEEIRILVSALGTGIGEDEFNINKIRYHKIMIMTDADIDGSHIRTLLL
4TBL                                                                           
4TBL 
4TBS TFFFRYMRPVIERGYLYVAQPPLYLIKHGKNSTYAYSDKEKEELLKNVGTEKVVIQRYKGLGEMNPEQLWETTM
4TBL                                                                           
4TBL 
4TBS DPSNRVVLKVKLDDFVEAEETFNILMGDEVQPRKQFIEINAAKVANLDL
4TBL                                                  
4TBL 
4TBS --------------------------------------------------------------------------
4TBT --------------------------------------------------------------------------
4TBN FMOXYGENASE
4TBS MSQKETSYSAGQIKILEGLEAVRKRPGMYIGTQDETGLHKMVYEVVDNSVDEAMAGHCTEIRISILPNNIIEVK
4TBL                                                                           
4TBL 
4TBS DNGRGIPVDIHPDKKISTIEVVMTILHAGGKFENDAYKVSGGLHGVGVSVVNALSEYLEVEVHQKGKIYTQKYE
4TBL                                                                           
4TBL 
4TBS KGIPVSPVEIKGDSSERGTIVRFKPDATIFTTVDFQFDILSARFRELAFLNKGLVLIVEDRRRGAEGENLLRNE
4TBL                                                                           
4TBL 
4TBS FQFSGGIVSFVEHINENKHPMHKVIHFERNKDDVLAEISIQYSETYTENIFCFTNNINNNLGGTHLEGFRAALT
4TBL                                                                           
4TBL 
4TBS RTLNDFLKKDTTLSKKHPTGLSGEDVKEGLTAVISIKIPQPQFNSQTKEKLVNAEIKGIMQTLSSEGLTLFFEE
4TBL                                                                           
4TBL 
4TBS NPNITKKILEKCILSAKAREAARKARDLTRRKTVLEGGGLPGKLADCSEKDPAFSELYLVEGDSAGGSAKQGRD
4TBL                               KRVAiIGAGVSGLASIK                           
4TBL 
4TBS RNTQAILPLKGKILNVEKARLDKILSSEEIRILVSALGTGIGEDEFNINKIRYHKIMIMTDADIDGSHIRTLLL
4TBL                                                                           
4TBL 
4TBS TFFFRYMRPVIERGYLYVAQPPLYLIKHGKNSTYAYSDKEKEELLKNVGTEKVVIQRYKGLGEMNPEQLWETTM
4TBL                                                                           
4TBL 
4TBS DPSNRVVLKVKLDDFVEAEETFNILMGDEVQPRKQFIEINAAKVANLDL
4TBL     kVkiKpsVKEfTETSAIF                           
4TBL 
4TBS --------------------------------------------------------------------------
4TBT --------------------------------------------------------------------------
4TBN CD44
4TBS MSQKETSYSAGQIKILEGLEAVRKRPGMYIGTQDETGLHKMVYEVVDNSVDEAMAGHCTEIRISILPNNIIEVK
4TBL                                                            DLNITCRYAGVFHVE
4TBL 
4TBS DNGRGIPVDIHPDKKISTIEVVMTILHAGGKFENDAYKVSGGLHGVGVSVVNALSEYLEVEVHQKGKIYTQKYE
4TBL KNGRY                                                                     
4TBL 
4TBS KGIPVSPVEIKGDSSERGTIVRFKPDATIFTTVDFQFDILSARFRELAFLNKGLVLIVEDRRRGAEGENLLRNE
4TBL                                                                           
4TBL 
4TBS FQFSGGIVSFVEHINENKHPMHKVIHFERNKDDVLAEISIQYSETYTENIFCFTNNINNNLGGTHLEGFRAALT
4TBL                                                                           
4TBL 
4TBS RTLNDFLKKDTTLSKKHPTGLSGEDVKEGLTAVISIKIPQPQFNSQTKEKLVNAEIKGIMQTLSSEGLTLFFEE
4TBL                                                                           
4TBL 
4TBS NPNITKKILEKCILSAKAREAARKARDLTRRKTVLEGGGLPGKLADCSEKDPAFSELYLVEGDSAGGSAKQGRD
4TBL                                                                           
4TBL 
4TBS RNTQAILPLKGKILNVEKARLDKILSSEEIRILVSALGTGIGEDEFNINKIRYHKIMIMTDADIDGSHIRTLLL
4TBL                                                                           
4TBL 
4TBS TFFFRYMRPVIERGYLYVAQPPLYLIKHGKNSTYAYSDKEKEELLKNVGTEKVVIQRYKGLGEMNPEQLWETTM
4TBL                                                                           
4TBL 
4TBS DPSNRVVLKVKLDDFVEAEETFNILMGDEVQPRKQFIEINAAKVANLDL
4TBL             DQFMTADETRNLQNVDMKIG                 
4TBL 
4TBS --------------------------------------------------------------------------
4TBT --------------------------------------------------------------------------
4TBN JANUSKINASE3
4TBS MSQKETSYSAGQIKILEGLEAVRKRPGMYIGTQDETGLHKMVYEVVDNSVDEAMAGHCTEIRISILPNNIIEVK
4TBL                                                                           
4TBL 
4TBS DNGRGIPVDIHPDKKISTIEVVMTILHAGGKFENDAYKVSGGLHGVGVSVVNALSEYLEVEVHQKGKIYTQKYE
4TBL                                                                      aETFh
4TBL 
4TBS KGIPVSPVEIKGDSSERGTIVRFKPDATIFTTVDFQFDILSARFRELAFLNKGLVLIVEDRRRGAEGENLLRNE
4TBL VGLPGA                                                                    
4TBL 
4TBS FQFSGGIVSFVEHINENKHPMHKVIHFERNKDDVLAEISIQYSETYTENIFCFTNNINNNLGGTHLEGFRAALT
4TBL                                                                           
4TBL 
4TBS RTLNDFLKKDTTLSKKHPTGLSGEDVKEGLTAVISIKIPQPQFNSQTKEKLVNAEIKGIMQTLSSEGLTLFFEE
4TBL                                                     GLhVDGvAlnLTS         
4TBL 
4TBS NPNITKKILEKCILSAKAREAARKARDLTRRKTVLEGGGLPGKLADCSEKDPAFSELYLVEGDSAGGSAKQGRD
4TBL                                                                           
4TBL 
4TBS RNTQAILPLKGKILNVEKARLDKILSSEEIRILVSALGTGIGEDEFNINKIRYHKIMIMTDADIDGSHIRTLLL
4TBL                                                                           
4TBL 
4TBS TFFFRYMRPVIERGYLYVAQPPLYLIKHGKNSTYAYSDKEKEELLKNVGTEKVVIQRYKGLGEMNPEQLWETTM
4TBL                                                                           
4TBL 
4TBS DPSNRVVLKVKLDDFVEAEETFNILMGDEVQPRKQFIEINAAKVANLDL
4TBL                                                  
4TBL 
4TBS --------------------------------------------------------------------------
4TBT --------------------------------------------------------------------------
4TBN KUPTAKETRKA
4TBS MSQKETSYSAGQIKILEGLEAVRKRPGMYIGTQDETGLHKMVYEVVDNSVDEAMAGHCTEIRISILPNNIIEVK
4TBL                                                                           
4TBL 
4TBS DNGRGIPVDIHPDKKISTIEVVMTILHAGGKFENDAYKVSGGLHGVGVSVVNALSEYLEVEVHQKGKIYTQKYE
4TBL                                                                           
4TBL 
4TBS KGIPVSPVEIKGDSSERGTIVRFKPDATIFTTVDFQFDILSARFRELAFLNKGLVLIVEDRRRGAEGENLLRNE
4TBL                                                                           
4TBL 
4TBS FQFSGGIVSFVEHINENKHPMHKVIHFERNKDDVLAEISIQYSETYTENIFCFTNNINNNLGGTHLEGFRAALT
4TBL                                                                           
4TBL 
4TBS RTLNDFLKKDTTLSKKHPTGLSGEDVKEGLTAVISIKIPQPQFNSQTKEKLVNAEIKGIMQTLSSEGLTLFFEE
4TBL                                                                           
4TBL 
4TBS NPNITKKILEKCILSAKAREAARKARDLTRRKTVLEGGGLPGKLADCSEKDPAFSELYLVEGDSAGGSAKQGRD
4TBL                                KIIILGAGQVGgTLA                            
4TBL 
4TBS RNTQAILPLKGKILNVEKARLDKILSSEEIRILVSALGTGIGEDEFNINKIRYHKIMIMTDADIDGSHIRTLLL
4TBL                                                                           
4TBL 
4TBS TFFFRYMRPVIERGYLYVAQPPLYLIKHGKNSTYAYSDKEKEELLKNVGTEKVVIQRYKGLGEMNPEQLWETTM
4TBL                                                                        TaS
4TBL 
4TBS DPSNRVVLKVKLDDFVEAEETFNILMGDEVQPRKQFIEINAAKVANLDL
4TBL DEtNMvACQvAy                                     
4TBL 
4TBS --------------------------------------------------------------------------
BioPerl-1.007002/t/data/promoterwise.out000444000766000024       140713155576321 20162 0ustar00cjfieldsstaff0000000000001596.49	MUSSPSYN	4	18	1	4.143962167-143965267	29	43	1	group_0_0
1596.49	MUSSPSYN	19	242	1	4.143962167-143965267	45	268	1	group_0_0
1596.49	MUSSPSYN	244	365	1	4.143962167-143965267	527	648	1	group_0_0
1596.49	MUSSPSYN	367	457	1	4.143962167-143965267	967	1057	1	group_0_0
1596.49	MUSSPSYN	459	611	1	4.143962167-143965267	1772	1924	1	group_0_0
1596.49	MUSSPSYN	613	840	1	4.143962167-143965267	2252	2479	1	group_0_0
1596.49	MUSSPSYN	842	964	1	4.143962167-143965267	2566	2688	1	group_0_0
1596.49	MUSSPSYN	1146	1152	1	4.143962167-143965267	2693	2699	1	group_0_0
1596.49	MUSSPSYN	1154	1159	1	4.143962167-143965267	2700	2705	1	group_0_0
1596.49	MUSSPSYN	1161	1161	1	4.143962167-143965267	2706	2706	1	group_0_0
1596.49	MUSSPSYN	1163	1172	1	4.143962167-143965267	2707	2716	1	group_0_0
BioPerl-1.007002/t/data/protpars.phy000444000766000024      5155513155576321 17317 0ustar00cjfieldsstaff000000000000 3 5127
SINFRUP001   .......... ......DDQV VLQCTASVLK EQIKLCLSCE GFGNRLCFLE 
SINFRUP002   .......... ......DDQV VLQCTASVLK EQIKLCLSCE GFGNRLCFLE 
ENSP000003   .MGDAEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE 

             TTSNAQNVPP DLAICTFILE QSLSVRALQE MLANTVEMTE AVDLDKWSSQ 
             TTSNAQNVPP DLAICTFILE QSLSVRALQE MLANTVEMTE AVDLDKWSSQ 
             PTSNAQNVPP DLAICCFVLE QSLSVRALQE MLANT..... .VEAGVESSQ 

             GGGHRTLLYG HAILLRHNHS GMYLSCLTTS RSLTDKLAFD VGLQEDSTGE 
             GGGHRTLLYG HAILLRHNHS GMYLSCLTTS RSLTDKLAFD VGLQEDSTGE 
             GGGHRTLLYG HAILLRHAHS RMYLSCLTTS RSMTDKLAFD VGLQEDATGE 

             ACWWTIHPAS KQRSEGEKVR VGDDLILVSV SSERYLHLSY ASGDLMVDAS 
             ACWWTIHPAS KQRSEGEKVR VGDDLILVSV SSERYLHLSY ASGDLMVDAS 
             ACWWTMHPAS KQRSEGEKVR VGDDIILVSV SSERYLHLST ASGELQVDAS 

             FMQTLWNMNP ISSGCELAEG FLTGGHVLRL FHGHMDECLA IATPEEGEEK 
             FMQTLWNMNP ISSGCELAEG FLTGGHVLRL FHGHMDECLA IATPEEGEEK 
             FMQTLWNMNP ICSRCE..EG FVTGGHVLRL FHGHMDECLT ISPADS.DDQ 

             RRMAHYEGGS VCSQARSLWR LEPLRISWSG SHMKWGQSFR IRHITTGRYL 
             RRMAHYEGGS VCSQARSLWR LEPLRISWSG SHMKWGQSFR IRHITTGRYL 
             RRLVYYEGGA VCTHARSLWR LEPLRISWSG SHLRWGQPLR VRHVTTGQYL 

             CLDEEKGLLV VDPERANTKL SAFCFRASKE KVDVAQKRDV EGMGIPEIKY 
             CLDEEKGLLV VDPERANTKL SAFCFRASKE KVDVAQKRDV EGMGIPEIKY 
             ALTEDQGLVV VDASKAHTKA TSFCFRISKE KLDVAPKRDV EGMGPPEIKY 

             GESMCFVQHV STGLWLTYAS LDAKAARLGM MKRKVILHQE GHMDDALTVS 
             GESMCFVQHV STGLWLTYAS LDAKAARLGM MKRKVILHQE GHMDDALTVS 
             GESLCFVQHV ASGLWLTYAA PDPKALRLGV LKKKAMLHQE GHMDDALSLT 

             RSQTEESQAA RMIYSTVGLF RQFIKGLDTL TGKNKSPGAL S...LPLEGV 
             RSQTEESQAA RMIYSTVGLF RQFIKGLDTL TGKNKSPGAL S...LPLEGV 
             RCQQEESQAA RMIHSTNGLY NQFIKSLDSF SGKPRGSGPP AGTALPIEGV 

             ILSLQDLIFY FRPPDEELEH EEKQTKLRSL RNRQNLFQEE GMITIVLECI 
             ILSLQDLIFY FRPPDEELEH EEKQTKLRSL RNRQNLFQEE GMITIVLECI 
             ILSLQDLIIY FEPPSEDLQH EEKQSKLRSL RNRQSLFQEE GMLSMVLNCI 

             DRLNVYNTAA HFSEFAGEEA AESWKEIVNL LYELLASLIR GNRSNCALFC 
             DRLNVYNTAA HFSEFAGEEA AESWKEIVNL LYELLASLIR GNRSNCALFC 
             DRLNVYTTAA HFAEFAGEEA AESWKEIVNL LYELLASLIR GNRSNCALFS 

             DNLDWLVSKL DRLEASSGIL EVLYCVLIES PEVLNIIQEN HIKSIISLLD 
             DNLDWLVSKL DRLEASSGIL EVLYCVLIES PEVLNIIQEN HIKSIISLLD 
             TNLDWLVSKL DRLEASSGIL EVLYCVLIES PEVLNIIQEN HIKSIISLLD 

             KHGRNHKVLD VLRSLCVCNG VAVRSNQNLI TENLLPGRDL LLQTNIVNYV 
             KHGRNHKVLD VLRSLCVCNG VAVRSNQNLI TENLLPGRDL LLQTNIVNYV 
             KHGRNHKVLD VLCSLCVCNG VAVRSNQDLI TENLLPGREL LLQTNLINYV 

             TSVRPNIFLG TCEGSTQYKK WYYEVMVDHV EAFVTAQATH LRVGWAMTEG 
             TSVRPNIFLG TCEGSTQYKK WYYEVMVDHV EAFVTAQATH LRVGWAMTEG 
             TSIRPNIFVG RAEGTTQYSK WYFEVMVDEV TPFLTAQATH LRVGWALTEG 

             YSPYPGGGEG WGGNGVGDDL YSYSFDGLHL WSGTVPRQVA SPNAHTLAAD 
             YSPYPGGGEG WGGNGVGDDL YSYSFDGLHL WSGTVPRQVA SPNAHTLAAD 
             YTPYPGAGEG WGGNGVGDDL YSYGFDGLHL WTGHVARPVT SPGQHLLAPE 

             DVVSCCLDLS VPSISFRING HPVQGMFENF NVDSLFFPVI SFSAGVKARF 
             DVVSCCLDLS VPSISFRING HPVQGMFENF NVDSLFFPVI SFSAGVKARF 
             DVISCCLDLS VPSISFRING CPVQGVFESF NLDGLFFPVV SFSAGVKVRF 

             LLGGRHGDFK FMPPPGYAPC YEALLPRERM RIEPIKEYKH DFNGVRNLLG 
             LLGGRHGDFK FMPPPGYAPC YEALLPRERM RIEPIKEYKH DFNGVRNLLG 
             LLGGRHGEFK FLPPPGYAPC HEAVLPRERL HLEPIKEYRR EGPRGPHLVG 

             PTLSLTHTSF TPCPVDTVQI VLPPHLERIR EKLAENIHEL WAVTRIEQGW 
             PTLSLTHTSF TPCPVDTVQI VLPPHLERIR EKLAENIHEL WAVTRIEQGW 
             PSRCLSHTDF VPCPVDTVQI VLPPHLERIR EKLAENIHEL WALTRIEQGW 

             TYGSFRDDNK KLHPCLVDFQ SLPEPERNYN LQMSAETLKC VCAV...A.. 
             TYGSFRDDNK KLHPCLVDFQ SLPEPERNYN LQMSAETLKC VCAV...A.. 
             TYGPVRDDNK RLHPCLVDFH SLPEPERNYN LQMSGETLKT LLALGCHVGM 

             ......ETLH DCVSSR.YVM SNAYKPAPLD LSHVKLTPNQ NQLVEKLAEN 
             ......ETLH DCVSSR.YVM SNAYKPAPLD LSHVKLTPNQ NQLVEKLAEN 
             ADEKAEDNLK KTKLPKTYMM SNGYKPAPLD LSHVRLTPAQ TTLVDRLAEN 

             GHNVWARDRV RQGWTYSIVQ DILNKRNPRL VPYILLDERT KKTNRDSVNN 
             GHNVWARDRV RQGWTYSIVQ DILNKRNPRL VPYILLDERT KKTNRDSVNN 
             GHNVWARDRV GQGWSYSAVQ DIPARRNPRL VPYRLLDEAT KRSNRDSLCQ 

             AVRTLIGYGY NIEPPDQEST GHGLENTRGD KVRIFRAEKS YAVTQGKWYF 
             AVRTLIGYGY NIEPPDQEST GHGLENTRGD KVRIFRAEKS YAVTQGKWYF 
             AVRTLLGYGY NIEPPDQEPS Q.VENQSRCD RVRIFRAEKS YTVQSGRWYF 

             EFEAVTTGEM RVGWARPNVH SDTELGADEL AYVFNGNKA. ........QR 
             EFEAVTTGEM RVGWARPNVH SDTELGADEL AYVFNGNKA. ........QR 
             EFEAVTTGEM RVGWARPELR PDVELGADEL AYVFNGHRG. ........QR 

             WHIGNEPFGR QWQSGDVVGC MIDLTEMNIM FTLNGEMLIS DSGSEMAFKD 
             WHIGNEPFGR QWQSGDVVGC MIDLTEMNIM FTLNGEMLIS DSGSEMAFKD 
             WHLGSEPFGR PWQPGDVVGC MIDLTENTII FTLNGEVLMS DSGSETAFRE 

             IEIGEGFIPV CTLGLSQVGR INLGQNVSSL RYFAICGLQE GFEPFAINMK 
             IEIGEGFIPV CTLGLSQVGR INLGQNVSSL RYFAICGLQE GFEPFAINMK 
             IEIGDGFLPV CSLGPGQVGH LNLGQDVSSL RFFAICGLQE GFEPFAINMQ 

             RDTTMWFSKS LPQFVPVPAD HNHIEVSRVD GTVDSAPCLK LTHKTYGSQN 
             RDTTMWFSKS LPQFVPVPAD HNHIEVSRVD GTVDSAPCLK LTHKTYGSQN 
             RPVTTWFSKG LPQFEPVPLE HPHYEVSRVD GTVDTPPCLR LTHRTWGSQN 

             ANTDMLFLRL SMPIQFHATF KVPAGTTPLT RALTIP...E DVAVVEPDSE 
             ANTDMLFLRL SMPIQFHATF KVPAGTTPLT RALTIP...E DVAVVEPDSE 
             SLVEMLFLRL SLPVQFHQHF RCTAGATPLA PPGLQPPAED EARAAEPDPD 

             FEVLKKSASR KEQEEDKKEP SVPKEI.... ........L. .AENEKDTMS 
             FEVLKKSASR KEQEEDKKEP SVPKEI.... ........L. .AENEKDTMS 
             YENLRRSAGG WSEAENGKEG TAKEGAPGGT PQAGGEAQPA RAENEKDATT 

             EKGKKRGFFS KAKKAAMTPL A.....PPPP PTVPRLVEDV VPDD.RDDPE 
             EKGKKRGFFS KAKKAAMTPL A.....PPPP PTVPRLVEDV VPDD.RDDPE 
             EKNKKRGFLF KAKKVAMMTQ P......PAT PTLPRLPHDV VPADNRDDPE 

             IILSTTTYYY SVRIFAGQEP SGVWVGWVTP DYHQYDQTFD LSKVRSVTVT 
             IILSTTTYYY SVRIFAGQEP SGVWVGWVTP DYHQYDQTFD LSKVRSVTVT 
             IILNTTTYYY SVRVFAGQEP SCVWAGWVTP DYHQHDMSFD LSKVRVVTVT 

             VGDDKGNIYN SMKRSNCYMV WGDDLVS.NH QTRFSQEDMV IGCLVDLATG 
             VGDDKGNIYN SMKRSNCYMV WGDDLVS.NH QTRFSQEDMV IGCLVDLATG 
             MGDEQGNVHS SLKCSNCYMV WGGDFVSPGQ QGRISHTDLV IGCLVDLATG 

             LMTFTANGKE INTFYQVEPN TKLFPAVFVQ PLSQNMVQLE LGKLKNIMPI 
             LMTFTANGKE INTFYQVEPN TKLFPAVFVQ PLSQNMVQLE LGKLKNIMPI 
             LMTFTANGKE SNTFFQVEPN TKLFPAVFVL PTHQNVIQFE LGKQKNIMPL 

             SAAMFRSERN NPVPQCPPRL DVQMLTPVIW SRMPNRFLNP DVGRVSERLG 
             SAAMFRSERN NPVPQCPPRL DVQMLTPVIW SRMPNRFLNP DVGRVSERLG 
             SAAMFQSERK NPAPQCPPRL EMQMLMPVSW SRMPNHFLQV ETRRAGERLG 

             WVVECTEPLI MMALHIPEEN RCIDILELSE RQDLMKFHYH TLMLYCAVCA 
             WVVECTEPLI MMALHIPEEN RCIDILELSE RQDLMKFHYH TLMLYCAVCA 
             WAVQCQEPLT MMALHIPEEN RCMDILELSE RLDLQRFHSH TLRLYRAVCA 

             LGNNRVAHAL CSHVDESQLF YATENTYLPG PLRSGYYDLL ISIHLESAKR 
             LGNNRVAHAL CSHVDESQLF YATENTYLPG PLRSGYYDLL ISIHLESAKR 
             LGNNRVAHAL CSHVDQAQLL HALEDAHLPG PLRAGYYDLL ISIHLESACR 

             ARLGTNREFI VPMTEETLSI KLYPDAV... ...KAHSLPG VGLTTCLRPK 
             ARLGTNREFI VPMTEETLSI KLYPDAV... ...KAHSLPG VGLTTCLRPK 
             SRRSMLSEYI VPLTPETRAI TLFPPGRSTE NGHPRHGLPG VGVTTSLRPP 

             LHFS...... SINFVGTDLD LYTLSPVFPL QELKNRAISM LTEAVLDGSQ 
             LHFS...... SINFVGTDLD LYTLSPVFPL QELKNRAISM LTEAVLDGSQ 
             HHFSPPCFVA ALPAAGAAEA PARLSPAIPL EALRDKALRM LGEAVRDGGQ 

             AMRDPVGGSV EFHFVPILKL ISTLLIMGIF NDDDTKHILK MIDPNVFSGK 
             AMRDPVGGSV EFHFVPILKL ISTLLIMGIF NDDDTKHILK MIDPNVFSGK 
             HARDPVGGSV EFQFVPVLKL VSTLLVMGIF GDEDVKQILK MIEPEVFTEE 

             DDEE...... ETDKPVEGGP AEGEGDKAKG EESEEAAELE D...EGVGKV 
             DDEE...... ETDKPVEGGP AEGEGDKAKG EESEEAAELE D...EGVGKV 
             EEEE...... ..DEEEEGEE EDEEE..... .........K E...EDEEET 

             DGEKMEEEKE AEVVAVDLKD EEEGLEEGLL QMKLPESVKL QMCTLLQFFC 
             DGEKMEEEKE AEVVAVDLKD EEEGLEEGLL QMKLPESVKL QMCTLLQFFC 
             AQEKEDEEKE EEEAAE..GE KEEGLEEGLL QMKLPESVKL QMCHLLEYFC 

             DCELRHRVEA IVAYSDKFVH NIQDNQRIRY NQLMRAFTMS AAETARKTRE 
             DCELRHRVEA IVAYSDKFVH NIQDNQRIRY NQLMRAFTMS AAETARKTRE 
             DQELQHRVES LAAFAERYVD KLQANQRSRY GLLIKAFSMT AAETARRTRE 

             FRSPPQDQVL LLTNFKHSLE EEECPVPDNV RETLKEFHND LLLHCGIHIE 
             FRSPPQDQVL LLTNFKHSLE EEECPVPDNV RETLKEFHND LLLHCGIHIE 
             FRSPPQEQIN MLLQFKDGTD EEDCPLPEEI RQDLLDFHQD LLAHCGIQLD 

             EEPVEEEVDT SLRGRLLSLV DKIKSIRGKK TEEKPE.VEE ETKPSTLQEL 
             EEPVEEEVDT SLRGRLLSLV DKIKSIRGKK TEEKPE.VEE ETKPSTLQEL 
             GEEEEPEEET TLGSRLMSLL EKVRLVKKKE EKPEEERSAE ESKPRSLQEL 

             ISHTMIHWAQ ESFIQNPELV RLMFSLLHRQ YDGLGELIRA LPKAYAINAV 
             ISHTMIHWAQ ESFIQNPELV RLMFSLLHRQ YDGLGELIRA LPKAYAINAV 
             VSHMVVRWAQ EDFVQSPELV RAMFSLLHRQ YDGLGELLRA LPRAYTISPS 

             SVQDTMDLLE CLGQIRSLLI VQMGPEEERL MIQSIGNIMN NKVFYQHPNL 
             SVQDTMDLLE CLGQIRSLLI VQMGPEEERL MIQSIGNIMN NKVFYQHPNL 
             SVEDTMSLLE CLGQIRSLLI VQMGPQEENL MIQSIGNIMN NKVFYQHPNL 

             MRALGMHETV MEVMVNVLGG GGDSKEIRFP QMVTNCCRFL CYFCRISRQN 
             MRALGMHETV MEVMVNVLGG GGDSKEIRFP QMVTNCCRFL CYFCRISRQN 
             MRALGMHETV MEVMVNVLGG G.ESKEIRFP KMVTSCCRFL CYFCRISRQN 

             QRSMFDHLSY LLQNSSIGLG MRGSTPLDVA AASCIDNNEL ALALQEQDLE 
             QRSMFDHLSY LLQNSSIGLG MRGSTPLDVA AASCIDNNEL ALALQEQDLE 
             QRSMFDHLSY LLENSGIGLG MQGSTPLDVA AASVIDNNEL ALALQEQDLE 

             MVVTYLAGCG LQMCPMLLSK CYPDIGWNPC GGERYLDFLR FAVFVNGESV 
             MVVTYLAGCG LQMCPMLLSK CYPDIGWNPC GGERYLDFLR FAVFVNGESV 
             KVVSYLAGCG LQSCPMLVAK GYPDIGWNPC GGERYLDFLR FAVFVNGESV 

             EENANVVVRL LIRRPECFGP ALRGEGGNGL LAAMEEAIKI SEDPARDGPT 
             EENANVVVRL LIRRPECFGP ALRGEGGNGL LAAMEEAIKI SEDPARDGPT 
             EENANVVVRL LIRKPECFGP ALRGEGGSGL LAAIEEAIRI SEDPARDGPG 

             VKKDRRF.MF GGEEQQEENR VHLGNAIMSF YSALIDLLGR CAPEMHLIQA 
             VKKDRRF.MF GGEEQQEENR VHLGNAIMSF YSALIDLLGR CAPEMHLIQA 
             IRRDRRR.EH FGEEPPEENR VHLGHAIMSF YAALIDLLGR CAPEMHLIQA 

             GKGEALRIRA ILRSLVPIED LVGVISLPVQ IPSYGKDSQI VEPKMSASFV 
             GKGEALRIRA ILRSLVPIED LVGVISLPVQ IPSYGKDSQI VEPKMSASFV 
             GKGEALRIRA ILRSLVPLED LVGIISLPLQ IPTLGKDGAL VQPKMSASFV 

             PDHKASMVLF LDRVYGIDNQ DFLLHVLEVG FLPDMRAAAS LDTVAFSTTE 
             PDHKASMVLF LDRVYGIDNQ DFLLHVLEVG FLPDMRAAAS LDTVAFSTTE 
             PDHKASMVLF LDRVYGIENQ DFLLHVLDVG FLPDMRAAAS LDTATFSTTE 

             MALALNRYLC SAVLPLLTKC APLFAGTDHR AIMIDSMLHT IYRLSRGRAL 
             MALALNRYLC SAVLPLLTKC APLFAGTDHR AIMIDSMLHT IYRLSRGRAL 
             MALALNRYLC LAVLPLITKC APLFAGTEHR AIMVDSMLHT VYRLSRGRSL 

             TKAQRDVIEE CLMSLCKYLR PSMLQHLLRR LVFDVPILNE YAKMPLKLLT 
             TKAQRDVIEE CLMSLCKYLR PSMLQHLLRR LVFDVPILNE YAKMPLKLLT 
             TKAQRDVIED CLMSLCRYIR PSMLQHLLRR LVFDVPILNE FAKMPLKLLT 

             NHYERCWKYY CLPNGWANFG VTSEEELHLS RKLFWGIFES LAHKKFDAEL 
             NHYERCWKYY CLPNGWANFG VTSEEELHLS RKLFWGIFES LAHKKFDAEL 
             NHYERCWKYY CLPTGWANFG VTSEEELHLT RKLFWGIFDS LAHKKYDPEL 

             FKIAMPCLCA IAGAIPPDYV DASYSSHTEK KASVDAEGNF DPKPVETTNT 
             FKIAMPCLCA IAGAIPPDYV DASYSSHTEK KASVDAEGNF DPKPVETTNT 
             YRMAMPCLCA IAGALPPDYV DASYSSKAEK KATVDAEGNF DPRPVETLNV 

             IIPERLDAFI NKYAEHTHDK WAFEKIQNNW TYGEVLDEDA KTHPMLRPYK 
             IIPERLDAFI NKYAEHTHDK WAFEKIQNNW TYGEVLDEDA KTHPMLRPYK 
             IIPEKLDSFI NKFAEYTHEK WAFDKIQNNW SYGENIDEEL KTHPMLRPYK 

             TFSEKDKEIY RWPIKESIKA MLAWEWTLEK ARDGEGEVEK KAATRKISQT 
             TFSEKDKEIY RWPIKESIKA MLAWEWTLEK ARDGEGEVEK KAATRKISQT 
             TFSEKDKEIY RWPIKESLKA MIAWEWTIEK AREGEEEKTE KKKTRKISQS 

             AQATYDPSHG YSPQPIDISG MTLSRELQSM AEQLAENYHN TWGRKKKVEL 
             AQATYDPSHG YSPQPIDISG MTLSRELQSM AEQLAENYHN TWGRKKKVEL 
             AQ.TYDPREG YNPQPPDLSA VTLSRELQAM AEQLAENYHN TWGRKKKQEL 

             QSKGGGTHPL LVPYDTLTAK EKARDREKAQ DLLKFLQLNG YAVTR..GMK 
             QSKGGGTHPL LVPYDTLTAK EKARDREKAQ DLLKFLQLNG YAVTR..GMK 
             EAKGGGTHPL LVPYDTLTAK EKARDREKAQ ELLKFLQMNG YAVTRHAGLK 

             DMEQDISSIE KRFAYGFLQK LLKWMDIAQE FIAHLEAVVS SGRVEKSPHE 
             DMEQDISSIE KRFAYGFLQK LLKWMDIAQE FIAHLEAVVS SGRVEKSPHE 
             DMELDSSSIE KRFAFGFLQQ LLRWMDISQE FIAHLEAVVS SGRVEKSPHE 

             QEIKFFAKIL LPLVNQYFKN HCLYFLSTPA KVLGSGGHSS NKEKEMIASI 
             QEIKFFAKIL LPLVNQYFKN HCLYFLSTPA KVLGSGGHSS NKEKEMIASI 
             QEIKFFAKIL LPLINQYFTN HCLYFLSTPA KVLGSGGHAS NKEKEMITSL 

             FCKLAALVRH RVSLFGTDAS AVVNCLHILS RSLDARTVMK SGPEIVKAGL 
             FCKLAALVRH RVSLFGTDAS AVVNCLHILS RSLDARTVMK SGPEIVKAGL 
             FCKLAALVRH RVSLFGTDAP AVVNCLHILA RSLDARTVMK SGPEIVKAGL 

             RQFFESAADD IEKMVENLKL GKVSSRNQ.V KGVSQNINYT TIALLPVLTS 
             RQFFESAADD IEKMVENLKL GKVSSRNQ.V KGVSQNINYT TIALLPVLTS 
             RSFFESASED IEKMVENLRL GKVSQARTQV KGVGQNLTYT TVALLPVLTT 

             LFDHIAQHQF GDDVILDDLQ ISCYRIMCSI YSLGTVKTPH AEKQRPALGE 
             LFDHIAQHQF GDDVILDDLQ ISCYRIMCSI YSLGTVKTPH AEKQRPALGE 
             LFQHIAQHQF GDDVILDDVQ VSCYRTLCSI YSLGTTKNTY VEKLRPALGE 

             CLAHLAAAMP VAFLEPTLNE FNTFSVYTTK TPRERSILGL PSQVEELCPD 
             CLAHLAAAMP VAFLEPTLNE FNTFSVYTTK TPRERSILGL PSQVEELCPD 
             CLARLAAAMP VAFLEPQLNE YNACSVYTTK SPRERAILGL PNSVEEMCPD 

             IPELEVLMKD IHDLAESGAR YTEMPHVIEI TLPMLCNYLP RWWERGLEN. 
             IPELEVLMKD IHDLAESGAR YTEMPHVIEI TLPMLCNYLP RWWERGLEN. 
             IPVLERLMAD IGGLAESGAR YTEMPHVIEI TLPMLCSYLP RWWERGPEAP 

             ...FPEQEGQ ICTSVTSEQL NQLLGSIMKI VVNNLGIDEA SWMKRLAVFA 
             ...FPEQEGQ ICTSVTSEQL NQLLGSIMKI VVNNLGIDEA SWMKRLAVFA 
             PSALPAGAPP PCTAVTSDHL NSLLGNILRI IVNNLGIDEA SWMKRLAVFA 

             QPIVSRAKPE MLKSHFIPTM EKLKKRCGKV VAEEDHLRME GKTEVDSENG 
             QPIVSRAKPE MLKSHFIPTM EKLKKRCGKV VAEEDHLRME GKTEVDSENG 
             QPIVSRARPE LLQSHFIPTI GRLRKRAGKV VSEEEQLRLE AKAEAQEGEL 

             TIRDEFAVLC RDLYALYPLL IRYVDNSRAR WLTNPDPDAE ELFRMVGEVF 
             TIRDEFAVLC RDLYALYPLL IRYVDNSRAR WLTNPDPDAE ELFRMVGEVF 
             LVRDEFSVLC RDLYALYPLL IRYVDNNRAQ WLTEPNPSAE ELFRMVGEIF 

             IFWSKSHNFK REEQNFVVMN EINNMSFLTA DSKSKMSKS. ........GG 
             IFWSKSHNFK REEQNFVVMN EINNMSFLTA DSKSKMSKS. ........GG 
             IYWSKSHNFK REEQNFVVQN EINNMSFLTA DNKSKMAKVG ACPVSPQSGG 

             SEQERTKKKR RGDRYSVQTS LIVAALKKLL PIGLNMCSPA DQELINLAKI 
             SEQERTKKKR RGDRYSVQTS LIVAALKKLL PIGLNMCSPA DQELINLAKI 
             SDQERTKKKR RGDRYSVQTS LIVATLKKML PIGLNMCAPT DQDLITLAKT 

             RYSLKDTDEE VREFLHNNLH LQGKVE.DPA MRWQMSLYKE MAGKAEDAED 
             RYSLKDTDEE VREFLHNNLH LQGKVE.DPA MRWQMSLYKE MAGKAEDAED 
             RYALKDTDEE VREFLHNNLH LQGKVEGSPS LRWQMALYRG VPGREEDADD 

             PEKVVKRVQE VSAVLYHIEV TEHPFKSKKM VWHKLLSKQR RRAVVACFRM 
             PEKVVKRVQE VSAVLYHIEV TEHPFKSKKM VWHKLLSKQR RRAVVACFRM 
             PEKIVRRVQE VSAVLYYLDQ TEHPYKSKKA VWHKLLSKQR RRAVVACFRM 

             TPLYNIITHR ATNMFLDAYK RNWLETEGYS FEDKMIDDLS VSLDHIRSE. 
             TPLYNIITHR ATNMFLDAYK RNWLETEGYS FEDKMIDDLS VSLDHIRSE. 
             TPLYNLPTHR ACNMFLESYK AAWILTEDHS FEDRMIDDLS KAGEQEEEEE 

             ....KKPDPL HQLILHFSRT ALTEKMKLDV DHLYMSYADI MAKGFSVSPP 
             ....KKPDPL HQLILHFSRT ALTEKMKLDV DHLYMSYADI MAKGFSVSPP 
             EVEEKKPDPL HQLVLHFSRT ALTEKSKLDE DYLYMAYADI MAKSCHLEEG 

             CSASQ..... ........EK EMEKQRLLYQ QSRLHNRGAA EMVLQMISAC 
             CSASQ..... ........EK EMEKQRLLYQ QSRLHNRGAA EMVLQMISAC 
             GENGE...AE EEVEVSFEEK QMEKQRLLYQ QARLHTRGAA EMVLQMISAC 

             KGEPGAMVSS TLKLGISILN GGNSDVQQKM LDYLKDKKDV GFFLSIQSLM 
             KGEPGAMVSS TLKLGISILN GGNSDVQQKM LDYLKDKKDV GFFLSIQSLM 
             KGETGAMVSS TLKLGISILN GGNAEVQQKM LDYLKDKKEV GFFQSIQALM 

             QTCSVLDLNA FERQNKAEGL GMVSEEGTNE KVMADDEFTC DLFRFLQLLC 
             QTCSVLDLNA FERQNKAEGL GMVSEEGTNE KVMADDEFTC DLFRFLQLLC 
             QTCSVLDLNA FERQNKAEGL GMVNEDGTGE KVMADDEFTQ DLFRFLQLLC 

             EGHNNDFQNY LRTQTGSTTT INVIICTVDY LLRLQESISD FYWYYSGKDI 
             EGHNNDFQNY LRTQTGSTTT INVIICTVDY LLRLQESISD FYWYYSGKDI 
             EGHNNDFQNY LRTQTGNTTT INIIICTVDY LLRLQESISD FYWYYSGKDV 

             IDEPGKRNFS KAMNVAKQVF NSLTEYIQGP CTGNQQSLAH SRLWDAVVGF 
             IDEPGKRNFS KAMNVAKQVF NSLTEYIQGP CTGNQQSLAH SRLWDAVVGF 
             IEEQGKRNFS KAMSVAKQVF NSLTEYIQGP CTGNQQSLAH SRLWDAVVGF 

             LHVFAHMMMK LAQ....... ..DSSQIGLL KELLDLQKDM VVMLLSLLEG 
             LHVFAHMMMK LAQ....... ..DSSQIGLL KELLDLQKDM VVMLLSLLEG 
             LHVFAHMMMK LAQ....... ..DSSQIELL KELLDLQKDM VVMLLSLLEG 

             NVVNGTIAKQ MVDMLVESSS NVEMILKFFD MFLKLKDIVA SDAFRDYVTD 
             NVVNGTIAKQ MVDMLVESSS NVEMILKFFD MFLKLKDIVA SDAFRDYVTD 
             NVVNGMIARQ MVDMLVESSS NVEMILKFFD MFLKLKDIVG SEAFQDYVTD 

             PRGLISKKDF SKAMDSQKQY TPAEIQFLLS CSEADENEMI NFEEFADRFQ 
             PRGLISKKDF SKAMDSQKQY TPAEIQFLLS CSEADENEMI NFEEFADRFQ 
             PRGLISKKDF QKAMDSQKQF SGPEIQFLLS CSEADENEMI NCEEFANRFQ 

             EPAKDIGFNI AVLLTNLSEH VPHDTRLQNF LEQAESVLNY FRPFLGRIEI 
             EPAKDIGFNI AVLLTNLSEH VPHDTRLQNF LEQAESVLNY FRPFLGRIEI 
             EPARDIGFNV AVLLTNLSEH VPHDPRLHNF LELAESILEY FRPYLGRIEI 

             MGASRKIERI YFEISEANRN QWEMPQVRES KRQFIFDVVN EGGESEKMEM 
             MGASRKIERI YFEISEANRN QWEMPQVRES KRQFIFDVVN EGGESEKMEM 
             MGASRRIERI YFEISETNRA QWEMPQVKES KRQFIFDVVN EGGEAEKMEL 

             FVNFCEDTIF EMNIA...AH A......... .......... .......... 
             FVNFCEDTIF EMNIA...AH A......... .......... .......... 
             FVSFCEDTIF EMQIAAQISE PEGEPETDED EGAGAAEAGA EGAEEGAAGL 

             .....PESTS AFADFLKSVV NFFNMFTFRN LRRRYRRFRK MTVKEMVIGL 
             .....PESTS AFADFLKSVV NFFNMFTFRN LRRRYRRFRK MTVKEMVIGL 
             EGTAATAAAG ATARVVAAAG RALRGLSYRS LRRRVRRLRR LTAREAATAV 

             ATFVYTVVMG ILMFVYSICK GFFTLIWKVL FGGGLVESAK KMTVTDILAS 
             ATFVYTVVMG ILMFVYSICK GFFTLIWKVL FGGGLVESAK KMTVTDILAS 
             AALLWAAVTR AGAAGAGAAA GALGLLWGSL FGGGLVEGAK KVTVTELLAG 

             MPDPTQDEVH GELPPEPGSR EDQD..TEGG ADLLDPVGGE EEEEDSEERE 
             MPDPTQDEVH GELPPEPGSR EDQD..TEGG ADLLDPVGGE EEEEDSEERE 
             MPDPTSDEVH GEQPAGPGGD ADGEGASEGA GDAAEG.AGD EEEAVHEAGP 

             GGRLPGFNTP .......... GGLGDFGETT PEEPPTPEGT PLLKRKLVSR 
             GGRLPGFNTP .......... GGLGDFGETT PEEPPTPEGT PLLKRKLVSR 
             GGADGAVAVT DGGPFRPEGA GGLGDMGDTT PAEPPTPEGS PILKRKLGVD 

             HNQIGGQGEE ENAEHEEPPQ ETEKADTENG EKAKKPEAEP EVKEEEPVEE 
             HNQIGGQGEE ENAEHEEPPQ ETEKADTENG EKAKKPEAEP EVKEEEPVEE 
             GVEEE..LPP EPEPEPEPEL EPEKADAENG EKEEV....P EPTPEP.... 

             EEITVKAKAK KSKKPVEEGF ELWNELEIQR VKFMNYLSRN FYNLRYLALF 
             EEITVKAKAK KSKKPVEEGF ELWNELEIQR VKFMNYLSRN FYNLRYLALF 
             PKKQAPPSPP PKKE..EAGG EFWGELEVQR VKFLNYLSRN FYTLRFLALF 

             IAFALNFILL FYKVSDSPP. GEED.....F EGSGLFEGSG LFEGSGVQED 
             IAFALNFILL FYKVSDSPP. GEED.....F EGSGLFEGSG LFEGSGVQED 
             LAFAINFILL FYKVSDSPP. GEDD.....M EGSAAGDVSG AGSG.GSSGW 

             GSGLDDGGED DDEEGPLYYF LEESTGYMEP AMAFLSIVHT IISFLCIIGY 
             GSGLDDGGED DDEEGPLYYF LEESTGYMEP AMAFLSIVHT IISFLCIIGY 
             GLGAGEEAEG DEDENMVYYF LEESTGYMEP ALRCLSLLHT LVAFLCIIGY 

             NCLKVPLVIF KREKELARKL EFDGVYVTEQ PEDDDIKGQW DRLVLNTPSF 
             NCLKVPLVIF KREKELARKL EFDGVYVTEQ PEDDDIKGQW DRLVLNTPSF 
             NCLKVPLVIF KREKELARKL EFDGLYITEQ PEDDDVKGQW DRLVLNTPSF 

             PNNYWDKFVK RKVLDKYGDI YGRERIAELL GMDLASLDVS AMTHEKKPEP 
             PNNYWDKFVK RKVLDKYGDI YGRERIAELL GMDLASLDVS AMTHEKKPEP 
             PSNYWDKFVK RKVLDKHGDI YGRERIAELL GMDLATLEIT AHNERK.PNP 

             DTSMFSWITS IDIKYQIWKF GVVFTDNTFL YLVWYFLMSI LGHYNNFFFA 
             DTSMFSWITS IDIKYQIWKF GVVFTDNTFL YLVWYFLMSI LGHYNNFFFA 
             PPGLLTWLMS IDVKYQIWKF GVIFTDNSFL YLGWYMVMSL LGHYNNFFFA 

             AHLLDIAMGV KTLRTILSSV THNGKQLMMT VGLLAVVVYL YTVVAFNFFR 
             AHLLDIAMGV KTLRTILSSV THNGKQLMMT VGLLAVVVYL YTVVAFNFFR 
             AHLLDIAMGV KTLRTILSSV THNGKQLVMT VGLLAVVVYL YTVVAFNFFR 

             KFYNKSEDED EPDMKCDDMM TCYLFHMYVG VRAGGGIGDE IEDPAGDEYE 
             KFYNKSEDED EPDMKCDDMM TCYLFHMYVG VRAGGGIGDE IEDPAGDEYE 
             KFYNKSEDED EPDMKCDDMM TCYLFHMYVG VRAGGGIGDE IEDPAGDEYE 

             LYRVVFDITF FFFVIVILLA IIQGLIIDAF GELRDQQEQV REDMETKCFI 
             LYRVVFDITF FFFVIVILLA IIQGLIIDAF GELRDQQEQV REDMETKCFI 
             LYRVVFDITF FFFVIVILLA IIQGLIIDAF GELRDQQEQV KEDMETKCFI 

             CGIGSDYFDT TPHGFETHTL EEHNLANYMF FLMYLINKDE TEHTGQESYV 
             CGIGSDYFDT TPHGFETHTL EEHNLANYMF FLMYLINKDE TEHTGQESYV 
             CGIGSDYFDT TPHGFETHTL EEHNLANYMF FLMYLINKDE TEHTGQESYV 

             WKMYQERCWD FFPAGDCFRK QYEDQL. 
             WKMYQERCWD FFPAGDCFRK QYEDQL. 
             WKMYQERCWD FFPAGDCFRK QYEDQLS 

BioPerl-1.007002/t/data/protpars_longid.phy000444000766000024        67313155576321 20606 0ustar00cjfieldsstaff000000000000 3 100
'S I N F R U  P 0 0 1 '   .......... ......DDQV VLQCTASVLK EQIKLCLSCE GFGNRLCFLE 
  SINFRUP002         .......... ......DDQV VLQCTASVLK EQIKLCLSCE GFGNRLCFLE 
ENSP000003   .MGDAEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE 

             TTSNAQNVPP DLAICTFILE QSLSVRALQE MLANTVEMTE AVDLDKWSSQ 
             TTSNAQNVPP DLAICTFILE QSLSVRALQE MLANTVEMTE AVDLDKWSSQ 
             PTSNAQNVPP DLAICCFVLE QSLSVRALQE MLANT..... .VEAGVESSQ 
BioPerl-1.007002/t/data/pseudowise.out000444000766000024        44113155576321 17567 0ustar00cjfieldsstaff000000000000Synonymous     : 7
Nonsynonymous  : 18
Ka/Ks          : 2.57
Unlikely       : 0
Identical      : 5
Stop           : 0
Total codons   : 30
Frameshift     : 0
Intron         : 1
//
Breaking with no 5'SS on END with 625
Gene 1
Gene 163 626 
  Exon 163 213 phase -1
  Exon 585 626 phase -1
//
BioPerl-1.007002/t/data/psi_xml.dat000444000766000024      1000413155576321 17050 0ustar00cjfieldsstaff000000000000
 
   
     
       
         
         adenine specific DNA methyltransferase (dpnA) HP0050
       
       
         







Helicobacter pylori 26695






hypothetical HP0001











Helicobacter pylori 26695






GTP-binding membrane protein (lepA) HP0355











Helicobacter pylori 26695






bogus-binding membrane protein (lepA) HP0355











Helicobacter pylori 26695
















Two hybrid test






























Two hybrid test






























Two hybrid test

























BioPerl-1.007002/t/data/psiblastreport.out000444000766000024    124673413155576321 20577 0ustar00cjfieldsstaff000000000000BLASTP 2.0.14 [Jun-29-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= CYS1_DICDI
         (343 letters)

Database: /home/peter/blast/data/swissprot.pr
           88,780 sequences; 31,984,247 total letters

Searching..................................................done


Results from round 1


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

sp|P04988|CYS1_DICDI CYSTEINE PROTEINASE 1 PRECURSOR                  721  0.0
sp|P43295|A494_ARATH PROBABLE CYSTEINE PROTEINASE A494 PRECURSOR      281  1e-75
sp|P25804|CYSP_PEA CYSTEINE PROTEINASE 15A PRECURSOR (TURGOR-RES...   278  1e-74
sp|P43296|RD19_ARATH CYSTEINE PROTEINASE RD19A PRECURSOR              275  1e-73
sp|Q10716|CYS1_MAIZE CYSTEINE PROTEINASE 1 PRECURSOR                  262  7e-70
sp|P04989|CYS2_DICDI CYSTEINE PROTEINASE 2 PRECURSOR (PRESTALK C...   262  7e-70
sp|P54640|CYS5_DICDI CYSTEINE PROTEINASE 5 PRECURSOR                  249  7e-66
sp|Q26534|CATL_SCHMA CATHEPSIN L PRECURSOR (SMCL1)                    244  2e-64
sp|P14658|CYSP_TRYBB CYSTEINE PROTEINASE PRECURSOR                    243  4e-64
sp|P35591|CYS1_LEIPI CYSTEINE PROTEINASE 1 PRECURSOR (AMASTIGOTE...   236  5e-62
sp|P25775|LCPA_LEIME CYSTEINE PROTEINASE A PRECURSOR                  235  9e-62
sp|P25779|CYSP_TRYCR CRUZIPAIN PRECURSOR (MAJOR CYSTEINE PROTEIN...   232  1e-60
sp|P13277|CYS1_HOMAM DIGESTIVE CYSTEINE PROTEINASE 1 PRECURSOR        225  1e-58
sp|P25782|CYS2_HOMAM DIGESTIVE CYSTEINE PROTEINASE 2 PRECURSOR        224  2e-58
sp|P07154|CATL_RAT CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTEIN...   224  3e-58
sp|P06797|CATL_MOUSE CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTE...   223  5e-58
sp|P25784|CYS3_HOMAM DIGESTIVE CYSTEINE PROTEINASE 3 PRECURSOR        221  1e-57
sp|P41721|CATV_NPVBM VIRAL CATHEPSIN (V-CATH)                         221  2e-57
sp|P41715|CATV_NPVCF VIRAL CATHEPSIN (V-CATH)                         220  4e-57
sp|P25975|CATL_BOVIN CATHEPSIN L PRECURSOR                            218  1e-56
sp|P36400|LCPB_LEIME CYSTEINE PROTEINASE B PRECURSOR                  218  2e-56
sp|Q05094|CYS2_LEIPI CYSTEINE PROTEINASE 2 PRECURSOR (AMASTIGOTE...   218  2e-56
sp|P12412|CYSP_VIGMU VIGNAIN PRECURSOR (BEAN ENDOPEPTIDASE) (CYS...   217  3e-56
sp|P07711|CATL_HUMAN CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTE...   215  8e-56
sp|Q28944|CATL_PIG CATHEPSIN L PRECURSOR                              214  2e-55
sp|P25783|CATV_NPVAC VIRAL CATHEPSIN (V-CATH)                         213  3e-55
sp|Q40143|CYS3_LYCES CYSTEINE PROTEINASE 3 PRECURSOR                  212  7e-55
sp|O60911|CATM_HUMAN CATHEPSIN L2 PRECURSOR (CATHEPSIN V)             210  5e-54
sp|P54639|CYS4_DICDI CYSTEINE PROTEINASE 4 PRECURSOR                  209  6e-54
sp|Q10991|CATL_SHEEP CATHEPSIN L                                      209  6e-54
sp|P25803|CYSP_PHAVU VIGNAIN PRECURSOR (BEAN ENDOPEPTIDASE) (CYS...   208  2e-53
sp|P00785|ACTN_ACTCH ACTINIDAIN PRECURSOR (ACTINIDIN)                 206  4e-53
sp|P43156|CYSP_HEMSP THIOL PROTEASE SEN102 PRECURSOR                  203  6e-52
sp|P25777|ORYB_ORYSA ORYZAIN BETA CHAIN PRECURSOR                     203  6e-52
sp|Q10717|CYS2_MAIZE CYSTEINE PROTEINASE 2 PRECURSOR                  201  2e-51
sp|P00786|CATH_RAT CATHEPSIN H PRECURSOR (CATHEPSIN B3) (CATHEPS...   200  3e-51
sp|O10364|CATV_NPVOP VIRAL CATHEPSIN (V-CATH)                         199  9e-51
sp|P43297|RD21_ARATH CYSTEINE PROTEINASE RD21A PRECURSOR              198  2e-50
sp|P15242|TES1_RAT TESTIN 1/2 PRECURSOR (CMB-22/CMB-23)               198  2e-50
sp|P25776|ORYA_ORYSA ORYZAIN ALPHA CHAIN PRECURSOR                    198  2e-50
sp|P14080|PAP2_CARPA CHYMOPAPAIN PRECURSOR (PAPAYA PROTEINASE II...   194  2e-49
sp|P43235|CATK_HUMAN CATHEPSIN K PRECURSOR (CATHEPSIN O) (CATHEP...   194  2e-49
sp|P25778|ORYC_ORYSA ORYZAIN GAMMA CHAIN PRECURSOR                    194  3e-49
sp|P25251|CYS4_BRANA CYSTEINE PROTEINASE COT44 PRECURSOR              194  3e-49
sp|P09668|CATH_HUMAN CATHEPSIN H PRECURSOR                            192  1e-48
sp|O46427|CATH_PIG CATHEPSIN H PRECURSOR                              191  2e-48
sp|P05167|ALEU_HORVU THIOL PROTEASE ALEURAIN PRECURSOR                191  2e-48
sp|P43236|CATK_RABIT CATHEPSIN K PRECURSOR (OC-2 PROTEIN)             191  2e-48
sp|P10056|PAP3_CARPA CARICAIN PRECURSOR (PAPAYA PROTEINASE OMEGA...   190  3e-48
sp|P49935|CATH_MOUSE CATHEPSIN H PRECURSOR (CATHEPSIN B3) (CATHE...   189  6e-48
sp|P55097|CATK_MOUSE CATHEPSIN K PRECURSOR                            188  1e-47
sp|P56203|CATW_MOUSE CATHEPSIN W PRECURSOR (LYMPHOPAIN)               185  9e-47
sp|P25250|CYS2_HORVU CYSTEINE PROTEINASE EP-B 2 PRECURSOR             184  2e-46
sp|P25249|CYS1_HORVU CYSTEINE PROTEINASE EP-B 1 PRECURSOR             184  3e-46
sp|P05994|PAP4_CARPA PAPAYA PROTEINASE IV PRECURSOR (PPIV) (PAPA...   183  3e-46
sp|P22895|P34_SOYBN P34 PROBABLE THIOL PROTEASE PRECURSOR             183  3e-46
sp|P43234|CATO_HUMAN CATHEPSIN O PRECURSOR                            182  8e-46
sp|P56202|CATW_HUMAN CATHEPSIN W PRECURSOR (LYMPHOPAIN)               182  1e-45
sp|P25774|CATS_HUMAN CATHEPSIN S PRECURSOR                            177  3e-44
sp|P00784|PAPA_CARPA PAPAIN PRECURSOR (PAPAYA PROTEINASE I) (PPI)     176  6e-44
sp||CATL_CHICK_1 [Segment 1 of 2] CATHEPSIN L                         175  1e-43
sp|P25326|CATS_BOVIN CATHEPSIN S                                      173  5e-43
sp|P80884|ANAN_ANACO ANANAIN                                          167  3e-41
sp|Q02765|CATS_RAT CATHEPSIN S PRECURSOR                              167  4e-41
sp|P20721|CYSL_LYCES LOW-TEMPERATURE-INDUCED CYSTEINE PROTEINASE...   164  3e-40
sp|P36184|ACP1_ENTHI CYSTEINE PROTEINASE ACP1 PRECURSOR               162  7e-40
sp|O17473|CATL_BRUPA CATHEPSIN L-LIKE PRECURSOR                       159  8e-39
sp|Q01957|CPP1_ENTHI CYSTEINE PROTEINASE 1 PRECURSOR                  156  5e-38
sp|Q06964|CPP3_ENTHI CYSTEINE PROTEINASE 3 PRECURSOR (CYSTEINE P...   153  4e-37
sp|Q01958|CPP2_ENTHI CYSTEINE PROTEINASE 2 PRECURSOR                  153  5e-37
sp|P46102|CYSP_PLAVN CYSTEINE PROTEINASE PRECURSOR                    153  6e-37
sp|P36185|ACP2_ENTHI CYSTEINE PROTEINASE ACP2 PRECURSOR               150  5e-36
sp|P25781|CYSP_THEAN CYSTEINE PROTEINASE PRECURSOR                    146  5e-35
sp|P14518|BROM_ANACO BROMELAIN, STEM                                  146  6e-35
sp|P22497|CYSP_THEPA CYSTEINE PROTEINASE PRECURSOR                    145  1e-34
sp|P16311|MMAL_DERFA MAJOR MITE FECAL ALLERGEN DER F 1 PRECURSOR...   144  3e-34
sp|P25805|CYSP_PLAFA THROPHOZOITE CYSTEINE PROTEINASE PRECURSOR ...   144  3e-34
sp|P42666|CYSP_PLAVI CYSTEINE PROTEINASE PRECURSOR                    132  1e-30
sp|P08176|MMAL_DERPT MAJOR MITE FECAL ALLERGEN DER P 1 PRECURSOR...   123  7e-28
sp|P80067|CATC_RAT DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (DPP...   117  3e-26
sp|P97821|CATC_MOUSE DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (D...   116  8e-26
sp|P53634|CATC_HUMAN DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (D...   113  4e-25
sp|Q26563|CATC_SCHMA CATHEPSIN C PRECURSOR                            113  7e-25
sp|P25773|CATL_FELCA CATHEPSIN L (PROGESTERONE-DEPENDENT PROTEIN...   113  7e-25
sp|P25780|EUM1_EURMA MITE GROUP I ALLERGEN EUR M 1 (EUR M I)          105  1e-22
sp|Q23894|CYS3_DICDI CYSTEINE PROTEINASE 3 (CYSTEINE PROTEINASE II)    96  1e-19
sp|P43508|CPR4_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 4 PREC...    94  3e-19
sp|P05993|PAP5_CARPA CYSTEINE PROTEINASE (CLONE PLBPC13)               90  5e-18
sp|P25807|CYS1_CAEEL GUT-SPECIFIC CYSTEINE PROTEINASE PRECURSOR        90  5e-18
sp|P43509|CPR5_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 5 PREC...    89  1e-17
sp|P00787|CATB_RAT CATHEPSIN B PRECURSOR (CATHEPSIN B1) (RSG-2)        88  3e-17
sp|P07688|CATB_BOVIN CATHEPSIN B PRECURSOR                             87  5e-17
sp|P07858|CATB_HUMAN CATHEPSIN B PRECURSOR (CATHEPSIN B1) (APP S...    86  1e-16
sp|P43157|CYSP_SCHJA CATHEPSIN B-LIKE CYSTEINE PROTEINASE PRECUR...    85  3e-16
sp|P25792|CYSP_SCHMA CATHEPSIN B-LIKE CYSTEINE PROTEINASE PRECUR...    85  3e-16
sp|P10605|CATB_MOUSE CATHEPSIN B PRECURSOR (CATHEPSIN B1)              84  5e-16
sp|P43510|CPR6_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 6 PREC...    83  6e-16
sp|P43233|CATB_CHICK CATHEPSIN B PRECURSOR (CATHEPSIN B1)              83  6e-16
sp|P25802|CYS1_OSTOS CATHEPSIN B-LIKE CYSTEINE PROTEINASE 1 PREC...    76  1e-13
sp|P25793|CYS2_HAECO CATHEPSIN B-LIKE CYSTEINE PROTEINASE 2 PREC...    75  2e-13
sp|P19092|CYS1_HAECO CATHEPSIN B-LIKE CYSTEINE PROTEINASE 1 PREC...    75  3e-13
sp|P43507|CPR3_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 3 PREC...    73  7e-13
sp|P13823|SERA_PLAFG SERINE-REPEAT ANTIGEN PROTEIN PRECURSOR (P1...    71  4e-12
sp|P32956|CC3_CARCN CYSTEINE PROTEINASE III (CC-III)                   63  8e-10
sp|P32957|CC4_CARCN CYSTEINE PROTEINASE IV (CC-IV)                     62  2e-09
sp|Q06544|CYS3_OSTOS CATHEPSIN B-LIKE CYSTEINE PROTEINASE 3            59  1e-08
sp|P32954|CC1_CARCN CYSTEINE PROTEINASE I (CC-I)                       59  2e-08
sp|P32955|CC2_CARCN CYSTEINE PROTEINASE II (CC-II)                     58  3e-08
sp||CATL_CHICK_2 [Segment 2 of 2] CATHEPSIN L                          52  2e-06
sp|P12399|CT2A_MOUSE CTLA-2-ALPHA PROTEIN PRECURSOR                    42  0.002
sp|P21381|THPA_THADA THAUMATOPAIN                                      41  0.005
sp|P05689|CATX_BOVIN CATHEPSIN                                         40  0.006
sp|P12400|CT2B_MOUSE CTLA-2-BETA PROTEIN PRECURSOR                     39  0.018
sp|P20736|BM86_BOOMI GLYCOPROTEIN ANTIGEN BM86 PRECURSOR (PROTEC...    35  0.21
sp|Q11121|PLB1_TORDE LYSOPHOSPHOLIPASE PRECURSOR (PHOSPHOLIPASE B)     35  0.27
sp|P46992|YJR1_YEAST HYPOTHETICAL 43.0 KD PROTEIN IN CPS1-FPP1 I...    34  0.61
sp|P28493|PR5_ARATH PATHOGENESIS-RELATED PROTEIN 5 PRECURSOR (PR-5)    32  1.8
sp|P41901|SPR3_YEAST SPORULATION-SPECIFIC SEPTIN                       32  2.4
sp|P54634|POLN_LORDV NON-STRUCTURAL POLYPROTEIN [CONTAINS: RNA-D...    31  3.1
sp|P21173|DNAA_MICLU CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA    31  3.1
sp|P89263|Y022_GVXN HYPOTHETICAL ORF22 HOMOLOG                         31  5.3
sp|P24896|NU5M_CAEEL NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 5            31  5.3
sp|P25648|SRB8_YEAST SUPPRESSOR OF RNA POLYMERASE B SRB8               30  7.0
sp|Q04723|PEPC_LACLC AMINOPEPTIDASE C                                  30  7.0
sp|Q13867|BLMH_HUMAN BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH)         30  9.1
sp|P87362|BLMH_CHICK BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH) (...    30  9.1
sp|P70645|BLMH_RAT BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH)           30  9.1

>sp|P04988|CYS1_DICDI CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 343

 Score =  721 bits (1841), Expect = 0.0
 Identities = 343/343 (100%), Positives = 343/343 (100%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60
           MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE
Sbjct: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60

Query: 61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPT 120
           ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPT
Sbjct: 61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPT 120

Query: 121 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY 180
           AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY
Sbjct: 121 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY 180

Query: 181 EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTM 240
           EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTM
Sbjct: 181 EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTM 240

Query: 241 IPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIF 300
           IPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIF
Sbjct: 241 IPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIF 300

Query: 301 RKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
           RKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII
Sbjct: 301 RKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343


>sp|P43295|A494_ARATH PROBABLE CYSTEINE PROTEINASE A494 PRECURSOR
          Length = 313

 Score =  281 bits (712), Expect = 1e-75
 Identities = 147/316 (46%), Positives = 193/316 (60%), Gaps = 18/316 (5%)

Query: 32  FQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKA---DTKFGVNKFADLSSDE 87
           F+ KF K Y S EE+  RF +FK+NL       L A+ H+      + GV +F+DL+  E
Sbjct: 3   FKKKFGKVYGSIEEHYYRFSVFKANL-------LRAMRHQKMDPSARHGVTQFSDLTRSE 55

Query: 88  FKNYYLNNKEAI-FTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFS 146
           F+  +L  K       D   A  L  +   ++P  FDWR RGAVTPVKNQG CGSCWSFS
Sbjct: 56  FRRKHLGVKGGFKLPKDANQAPILPTQ---NLPEEFDWRDRGAVTPVKNQGSCGSCWSFS 112

Query: 147 TTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNG 206
           TTG +EG HF++  KLVSLSEQ LVDCDHEC + E E +CD GCNGGL  +A+ Y +K G
Sbjct: 113 TTGALEGAHFLATGKLVSLSEQQLVDCDHEC-DPEEEGSCDSGCNGGLMNSAFEYTLKTG 171

Query: 207 GIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVE 266
           G+  E  YPYT   G  C  + + I A +SNF+++  NE  +A  ++  GPLA+A +A  
Sbjct: 172 GLMREKDYPYTGTDGGSCKLDRSKIVASVSNFSVVSINEDQIAANLIKNGPLAVAINAAY 231

Query: 267 WQFYIGGVFDIPCNPNSLDHGILIVGYSAK--NTIFRKNMPYWIVKNSWGADWGEQGYIY 324
            Q YIGGV         L+HG+L+VGY +   +    K  PYWI+KNSWG  WGE G+  
Sbjct: 232 MQTYIGGVSCPYICSRRLNHGVLLVGYGSAGFSQARLKEKPYWIIKNSWGESWGENGFYK 291

Query: 325 LRRGKNTCGVSNFVST 340
           + +G+N CGV + VST
Sbjct: 292 ICKGRNICGVDSLVST 307


>sp|P25804|CYSP_PEA CYSTEINE PROTEINASE 15A PRECURSOR (TURGOR-RESPONSIVE PROTEIN 15A)
          Length = 363

 Score =  278 bits (703), Expect = 1e-74
 Identities = 144/320 (45%), Positives = 201/320 (62%), Gaps = 14/320 (4%)

Query: 26  QSQFLEFQDKFNKKYS-HEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLS 84
           +  F  F+ KF+K Y+  EE+  RF +FKSNL K +    +  N     + G+ KF+DL+
Sbjct: 45  EHHFTSFKSKFSKSYATKEEHDYRFGVFKSNLIKAK----LHQNRDPTAEHGITKFSDLT 100

Query: 85  SDEFKNYYLNNKEAIFTDDLPV-ADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCW 143
           + EF+  +L  K+ +    LP  A         ++P  FDWR +GAVTPVK+QG CGSCW
Sbjct: 101 ASEFRRQFLGLKKRL---RLPAHAQKAPILPTTNLPEDFDWREKGAVTPVKDQGSCGSCW 157

Query: 144 SFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYII 203
           +FSTTG +EG H+++  KLVSLSEQ LVDCDH C + E   +CD GCNGGL  NA+ Y++
Sbjct: 158 AFSTTGALEGAHYLATGKLVSLSEQQLVDCDHVC-DPEQAGSCDSGCNGGLMNNAFEYLL 216

Query: 204 KNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAAD 263
           ++GG+  E  Y YT   G+ C F+ + + A +SNF+++  +E  +A  +V  GPLA+A +
Sbjct: 217 ESGGVVQEKDYAYTGRDGS-CKFDKSKVVASVSNFSVVTLDEDQIAANLVKNGPLAVAIN 275

Query: 264 AVEWQFYIGGV-FDIPCNPNSLDHGILIVGY--SAKNTIFRKNMPYWIVKNSWGADWGEQ 320
           A   Q Y+ GV     C  + LDHG+L+VG+   A   I  K  PYWI+KNSWG +WGEQ
Sbjct: 276 AAWMQTYMSGVSCPYVCAKSRLDHGVLLVGFGKGAYAPIRLKEKPYWIIKNSWGQNWGEQ 335

Query: 321 GYIYLRRGKNTCGVSNFVST 340
           GY  + RG+N CGV + VST
Sbjct: 336 GYYKICRGRNVCGVDSMVST 355


>sp|P43296|RD19_ARATH CYSTEINE PROTEINASE RD19A PRECURSOR
          Length = 368

 Score =  275 bits (695), Expect = 1e-73
 Identities = 155/359 (43%), Positives = 205/359 (56%), Gaps = 34/359 (9%)

Query: 6   LFVLAVFTVFVSSR---------------GIPPE---EQSQFLEFQDKFNKKY-SHEEYL 46
           +FVL+ F V VSS                G  P+    +  F  F+ KF K Y S+EE+ 
Sbjct: 10  VFVLSFFIVSVSSSDVNDGDDLVIRQVVGGAEPQVLTSEDHFSLFKRKFGKVYASNEEHD 69

Query: 47  ERFEIFKSNLGKIEELNLIAINHKADTK--FGVNKFADLSSDEFKNYYLNNKEAI-FTDD 103
            RF +FK+NL +         + K D     GV +F+DL+  EF+  +L  +       D
Sbjct: 70  YRFSVFKANLRRARR------HQKLDPSATHGVTQFSDLTRSEFRKKHLGVRSGFKLPKD 123

Query: 104 LPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLV 163
              A  L  E   ++P  FDWR  GAVTPVKNQG CGSCWSFS TG +EG +F++  KLV
Sbjct: 124 ANKAPILPTE---NLPEDFDWRDHGAVTPVKNQGSCGSCWSFSATGALEGANFLATGKLV 180

Query: 164 SLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQ 223
           SLSEQ LVDCDHEC + E  ++CD GCNGGL  +A+ Y +K GG+  E  YPYT + G  
Sbjct: 181 SLSEQQLVDCDHEC-DPEEADSCDSGCNGGLMNSAFEYTLKTGGLMKEEDYPYTGKDGKT 239

Query: 224 CNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNS 283
           C  + + I A +SNF++I  +E  +A  +V  GPLA+A +A   Q YIGGV         
Sbjct: 240 CKLDKSKIVASVSNFSVISIDEEQIAANLVKNGPLAVAINAGYMQTYIGGVSCPYICTRR 299

Query: 284 LDHGILIVGYSAKN--TIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVST 340
           L+HG+L+VGY A        K  PYWI+KNSWG  WGE G+  + +G+N CGV + VST
Sbjct: 300 LNHGVLLVGYGAAGYAPARFKEKPYWIIKNSWGETWGENGFYKICKGRNICGVDSMVST 358


>sp|Q10716|CYS1_MAIZE CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 371

 Score =  262 bits (663), Expect = 7e-70
 Identities = 138/324 (42%), Positives = 189/324 (57%), Gaps = 15/324 (4%)

Query: 26  QSQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLS 84
           +S FL F  +F K Y   +E+  R  +FK NL +     L+        + GV KF+DL+
Sbjct: 45  ESHFLSFVQRFGKSYKDADEHAYRLSVFKDNLRRARRHQLL----DPSAEHGVTKFSDLT 100

Query: 85  SDEFKNYYLN---NKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGS 141
             EF+  YL    ++ A+  +    A        + +P  FDWR  GAV PVKNQG CGS
Sbjct: 101 PAEFRRTYLGLRKSRRALLRELGESAHEAPVLPTDGLPDDFDWRDHGAVGPVKNQGSCGS 160

Query: 142 CWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNY 201
           CWSFS +G +EG H+++  KL  LSEQ  VDCDHEC   E  ++CD GCNGGL   A++Y
Sbjct: 161 CWSFSASGALEGAHYLATGKLEVLSEQQFVDCDHECDSSE-PDSCDSGCNGGLMTTAFSY 219

Query: 202 IIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIA 261
           + K GG+++E  YPYT   G +C F+ + I A + NF+++  +E  ++  ++  GPLAI 
Sbjct: 220 LQKAGGLESEKDYPYTGSDG-KCKFDKSKIVASVQNFSVVSVDEAQISANLIKHGPLAIG 278

Query: 262 ADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKN--TIFRKNMPYWIVKNSWGADWGE 319
            +A   Q YIGGV         LDHG+L+VGY A     I  K+ PYWI+KNSWG +WGE
Sbjct: 279 INAAYMQTYIGGVSCPYICGRHLDHGVLLVGYGASGFAPIRLKDKPYWIIKNSWGENWGE 338

Query: 320 QGYIYLRRG---KNTCGVSNFVST 340
            GY  + RG   +N CGV + VST
Sbjct: 339 NGYYKICRGSNVRNKCGVDSMVST 362


>sp|P04989|CYS2_DICDI CYSTEINE PROTEINASE 2 PRECURSOR (PRESTALK CATHEPSIN)
          Length = 376

 Score =  262 bits (663), Expect = 7e-70
 Identities = 147/383 (38%), Positives = 213/383 (55%), Gaps = 55/383 (14%)

Query: 1   MKVILLFVLAVFTVFVSSRGIP-------PEEQSQFLEFQDKFNKKYSHEEYLERFEIFK 53
           M++++  +L +F  F  +   P        + ++ F E+  KFN++YS  E+  R+ IFK
Sbjct: 1   MRLLVFLILLIFVNFSFANVRPNGRRFSESQYRTAFTEWTLKFNRQYSSSEFSNRYSIFK 60

Query: 54  SNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNK-EAIFTDDLPVADYLDD 112
           SN+  ++  N       + T  G+N FAD++++E++  YL  +  A   +     + L+ 
Sbjct: 61  SNMDYVDNWNS---KGDSQTVLGLNNFADITNEEYRKTYLGTRVNAHSYNGYDGREVLNV 117

Query: 113 EFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVD 172
           E + + P + DWRT+ AVTP+K+QGQCGSCWSFSTTG+ EG H +   KLVSLSEQNLVD
Sbjct: 118 EDLQTNPKSIDWRTKNAVTPIKDQGQCGSCWSFSTTGSTEGAHALKTKKLVSLSEQNLVD 177

Query: 173 CDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG 232
           C        G E  + GC+GGL  NA++YIIKN GI TESSYPYTAETG+ C FN ++IG
Sbjct: 178 C-------SGPEE-NFGCDGGLMNNAFDYIIKNKGIDTESSYPYTAETGSTCLFNKSDIG 229

Query: 233 AKISNFTMIPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIP-CNPNSLDHGIL 289
           A I  +  I     +        GP+++A DA    +Q Y  G++  P C+P  LDHG+L
Sbjct: 230 ATIKGYVNITAGSEISLENGAQHGPVSVAIDASHNSFQLYTSGIYYEPKCSPTELDHGVL 289

Query: 290 IVGY--------------------------------SAKNTIFRKNMPYWIVKNSWGADW 317
           +VGY                                 + +++  K   YWIVKNSWG  W
Sbjct: 290 VVGYGVQGKDDEGPVLNRKQTIVIHKNEDNKVESSDDSSDSVRPKANNYWIVKNSWGTSW 349

Query: 318 GEQGYIYLRRG-KNTCGVSNFVS 339
           G +GYI + +  KN CG+++  S
Sbjct: 350 GIKGYILMSKDRKNNCGIASVSS 372


>sp|P54640|CYS5_DICDI CYSTEINE PROTEINASE 5 PRECURSOR
          Length = 344

 Score =  249 bits (629), Expect = 7e-66
 Identities = 139/362 (38%), Positives = 201/362 (55%), Gaps = 37/362 (10%)

Query: 1   MKVI-LLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKI 59
           MKV+  L VL V       +    + ++ F ++     K Y+ EE+  R+ IF +N+  +
Sbjct: 1   MKVLSFLCVLLVSVATAKQQFSELQYRNAFTDWMITHQKSYTSEEFGARYNIFTANMDYV 60

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
           ++ N    +  ++T  G+N FAD++++E++N YL  K   F     +    +    NS  
Sbjct: 61  QQWN----SKGSETVLGLNNFADITNEEYRNTYLGTK---FDASSLIGTQEEKVHTNSSA 113

Query: 120 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 179
            + DWR+ GAVTPVKNQGQCG CWSFSTTG+ EG HF S+ +LVSLSEQNL+DC  E   
Sbjct: 114 ASKDWRSEGAVTPVKNQGQCGGCWSFSTTGSTEGAHFQSKGELVSLSEQNLIDCSTE--- 170

Query: 180 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFT 239
                  + GC+GGL   A+ YII N GI TESSYPY AE G +C + S N GA +S++ 
Sbjct: 171 -------NSGCDGGLMTYAFEYIINNNGIDTESSYPYKAENG-KCEYKSENSGATLSSYK 222

Query: 240 MIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIP-CNPNSLDHGILIVGY--- 293
            +           V+  P+++A DA    +Q Y  G++  P C+  +LDHG+L VGY   
Sbjct: 223 TVTAGSESSLESAVNVNPVSVAIDASHQSFQLYTSGIYYEPECSSENLDHGVLAVGYGSG 282

Query: 294 -----------SAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTS 341
                      S+ N     +  YWIVKNSWG  WG +GYI + R + N CG+++  S  
Sbjct: 283 SGSSSGQSSGQSSGNLSASSSNEYWIVKNSWGTSWGIEGYILMSRNRDNNCGIASSASFP 342

Query: 342 II 343
           ++
Sbjct: 343 VV 344


>sp|Q26534|CATL_SCHMA CATHEPSIN L PRECURSOR (SMCL1)
          Length = 319

 Score =  244 bits (617), Expect = 2e-64
 Identities = 128/326 (39%), Positives = 190/326 (58%), Gaps = 22/326 (6%)

Query: 21  IPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKF 80
           +P     ++++F+ K+ K+Y   E   RF IFKSN+ K +   L  +  +    +GV  +
Sbjct: 12  LPGNVDEKYVQFKLKYRKQYHETEDEIRFNIFKSNILKAQ---LYQVFVRGSAIYGVTPY 68

Query: 81  ADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCG 140
           +DL++DEF   +L     + +        L  E +N+IP  FDWR +GAVT VKNQG CG
Sbjct: 69  SDLTTDEFARTHLTASWVVPSSRSNTPTSLGKE-VNNIPKNFDWREKGAVTEVKNQGMCG 127

Query: 141 SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYN 200
           SCW+FSTTGNVE Q F    KL+SLSEQ LVDCD            D+GCNGGL  NAY 
Sbjct: 128 SCWAFSTTGNVESQWFRKTGKLLSLSEQQLVDCD----------GLDDGCNGGLPSNAYE 177

Query: 201 YIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAI 260
            IIK GG+  E +YPY A+   +C+  +  +   I++   + ++ET +A ++     +++
Sbjct: 178 SIIKMGGLMLEDNYPYDAK-NEKCHLKTDGVAVYINSSVNLTQDETELAAWLYHNSTISV 236

Query: 261 AADAVEWQFYIGGV---FDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADW 317
             +A+  QFY  G+   + I C+   LDH +L+VGY     +  KN P+WIVKNSWG +W
Sbjct: 237 GMNALLLQFYQHGISHPWWIFCSKYLLDHAVLLVGYG----VSEKNEPFWIVKNSWGVEW 292

Query: 318 GEQGYIYLRRGKNTCGVSNFVSTSII 343
           GE GY  + RG  +CG++   ++++I
Sbjct: 293 GENGYFRMYRGDGSCGINTVATSAMI 318


>sp|P14658|CYSP_TRYBB CYSTEINE PROTEINASE PRECURSOR
          Length = 450

 Score =  243 bits (614), Expect = 4e-64
 Identities = 136/346 (39%), Positives = 193/346 (55%), Gaps = 26/346 (7%)

Query: 3   VILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEE 61
           V+L     + +V + S  +    + +F  F+ K+ K Y   +E   RF  F+ N+   E+
Sbjct: 15  VLLAMAACLASVALGSLHVEESLEMRFAAFKKKYGKVYKDAKEEAFRFRAFEENM---EQ 71

Query: 62  LNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTA 121
             + A  +   T FGV  F+D++ +EF+  Y N           +   ++       P A
Sbjct: 72  AKIQAAANPYAT-FGVTPFSDMTREEFRARYRNGASYFAAAQKRLRKTVNVT-TGRAPAA 129

Query: 122 FDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYE 181
            DWR +GAVTPVK QGQCGSCW+FST GN+EGQ  ++ N LVSLSEQ LV CD       
Sbjct: 130 VDWREKGAVTPVKVQGQCGSCWAFSTIGNIEGQWQVAGNPLVSLSEQMLVSCD------- 182

Query: 182 GEEACDEGCNGGLQPNAYNYIIKN--GGIQTESSYPYTAETG--TQCNFNSANIGAKISN 237
                D GCNGGL  NA+N+I+ +  G + TE+SYPY +  G   QC  N   IGA I++
Sbjct: 183 ---TIDSGCNGGLMDNAFNWIVNSNGGNVFTEASYPYVSGNGEQPQCQMNGHEIGAAITD 239

Query: 238 FTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKN 297
              +P++E  +A Y+   GPLAIA DA  +  Y GG+    C    LDHG+L+VGY+  +
Sbjct: 240 HVDLPQDEDAIAAYLAENGPLAIAVDAESFMDYNGGIL-TSCTSKQLDHGVLLVGYNDNS 298

Query: 298 TIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
                N PYWI+KNSW   WGE GYI + +G N C ++  VS++++
Sbjct: 299 -----NPPYWIIKNSWSNMWGEDGYIRIEKGTNQCLMNQAVSSAVV 339


>sp|P35591|CYS1_LEIPI CYSTEINE PROTEINASE 1 PRECURSOR (AMASTIGOTE CYSTEINE PROTEINASE
           A-1)
          Length = 354

 Score =  236 bits (596), Expect = 5e-62
 Identities = 146/350 (41%), Positives = 196/350 (55%), Gaps = 38/350 (10%)

Query: 5   LLFVLAVFTVFVSSRGI-------PPEEQ----SQFLEFQDKFNKKYSHE-EYLERFEIF 52
           LLF + V  +FV   G        PP +     + +  F+ +  K +  + E   RF  F
Sbjct: 7   LLFAIVVTILFVVCYGSALIAQTPPPVDNFVASAHYGSFKKRHGKAFGGDAEEGHRFNAF 66

Query: 53  KSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLN-NKEAIFTDDLPVADYLD 111
           K N+     LN    +   D      KFADL+  EF   YLN +  A    D     ++D
Sbjct: 67  KQNMQTAYFLNTQNPHAHYDVS---GKFADLTPQEFAKLYLNPDYYARHLKDHKEDVHVD 123

Query: 112 DEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLV 171
           D   + + +  DWR +GAVTPVKNQG CGSCW+FS  GN+EGQ   S + LVSLSEQ LV
Sbjct: 124 DSAPSGVMSV-DWRDKGAVTPVKNQGLCGSCWAFSAIGNIEGQWAASGHSLVSLSEQMLV 182

Query: 172 DCDHECMEYEGEEACDEGCNGGLQPNAYNYIIK--NGGIQTESSYPYTAETGTQ--CNFN 227
            CD+           DEGCNGGL   A N+I++  NG + TE+SYPYT+  GT+  C+ +
Sbjct: 183 SCDN----------IDEGCNGGLMDQAMNWIMQSHNGSVFTEASYPYTSGGGTRPPCH-D 231

Query: 228 SANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHG 287
              +GAKI+ F  +P +E  +A ++   GP+A+A DA  WQ Y GGV  + C   SL+HG
Sbjct: 232 EGEVGAKITGFLSLPHDEERIAEWVEKRGPVAVAVDATTWQLYFGGVVSL-CLAWSLNHG 290

Query: 288 ILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNF 337
           +LIVG++ KN       PYWIVKNSWG+ WGE+GYI L  G N C + N+
Sbjct: 291 VLIVGFN-KNA----KPPYWIVKNSWGSSWGEKGYIRLAMGSNQCMLKNY 335


>sp|P25775|LCPA_LEIME CYSTEINE PROTEINASE A PRECURSOR
          Length = 354

 Score =  235 bits (594), Expect = 9e-62
 Identities = 146/359 (40%), Positives = 195/359 (53%), Gaps = 56/359 (15%)

Query: 5   LLFVLAVFTVFVSSRGI-------PPEEQ----SQFLEFQDKFNKKYSHE-EYLERFEIF 52
           LLF + V  +FV   G        PP +     + +  F+ +  K +  + E   RF  F
Sbjct: 7   LLFAIVVTILFVVCYGSALIAQTPPPVDNFVASAHYGSFKKRHGKAFGGDAEEGHRFNAF 66

Query: 53  KSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLN----------NKEAIFTD 102
           K N+     LN    +   D      KFADL+  EF   YLN          +KE +  D
Sbjct: 67  KQNMQTAYFLNTQNPHAHYDVS---GKFADLTPQEFAKLYLNPDYYARHLKNHKEDVHVD 123

Query: 103 DLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKL 162
           D   +  +          + DWR +GAVTPVKNQG CGSCW+FS  GN+EGQ   S + L
Sbjct: 124 DSAPSGVM----------SVDWRDKGAVTPVKNQGLCGSCWAFSAIGNIEGQWAASGHSL 173

Query: 163 VSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIK--NGGIQTESSYPYTAET 220
           VSLSEQ LV CD+           DEGCNGGL   A N+I++  NG + TE+SYPYT+  
Sbjct: 174 VSLSEQMLVSCDN----------IDEGCNGGLMDQAMNWIMQSHNGSVFTEASYPYTSGG 223

Query: 221 GTQ--CNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIP 278
           GT+  C+ +   +GAKI+ F  +P +E  +A ++   GP+A+A DA  WQ Y GGV  + 
Sbjct: 224 GTRPPCH-DEGEVGAKITGFLSLPHDEERIAEWVEKRGPVAVAVDATTWQLYFGGVVSL- 281

Query: 279 CNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNF 337
           C   SL+HG+LIVG++ KN       PYWIVKNSWG+ WGE+GYI L  G N C + N+
Sbjct: 282 CLAWSLNHGVLIVGFN-KNA----KPPYWIVKNSWGSSWGEKGYIRLAMGSNQCMLKNY 335


>sp|P25779|CYSP_TRYCR CRUZIPAIN PRECURSOR (MAJOR CYSTEINE PROTEINASE) (CRUZAINE)
          Length = 467

 Score =  232 bits (585), Expect = 1e-60
 Identities = 137/350 (39%), Positives = 191/350 (54%), Gaps = 30/350 (8%)

Query: 3   VILLFVLAVFTVFV--SSRGIPPEEQ--SQFLEFQDKFNKKY-SHEEYLERFEIFKSNLG 57
           ++L  VL V    V  ++  +  EE   SQF EF+ K  + Y S  E   R  +F+ NL 
Sbjct: 8   LLLAAVLVVMACLVPAATASLHAEETLTSQFAEFKQKHGRVYESAAEEAFRLSVFRENLF 67

Query: 58  KIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINS 117
            +  L+  A  H     FGV  F+DL+ +EF++ Y +N  A F      A       +  
Sbjct: 68  -LARLHAAANPHAT---FGVTPFSDLTREEFRSRY-HNGAAHFAAAQERARVPVKVEVVG 122

Query: 118 IPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHEC 177
            P A DWR RGAVT VK+QGQCGSCW+FS  GNVE Q F++ + L +LSEQ LV CD   
Sbjct: 123 APAAVDWRARGAVTAVKDQGQCGSCWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCD--- 179

Query: 178 MEYEGEEACDEGCNGGLQPNAYNYIIK--NGGIQTESSYPYTAETGTQ--CNFNSANIGA 233
                    D GC+GGL  NA+ +I++  NG + TE SYPY +  G    C  +   +GA
Sbjct: 180 -------KTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGA 232

Query: 234 KISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGY 293
            I+    +P++E  +A ++   GP+A+A DA  W  Y GGV    C    LDHG+L+VGY
Sbjct: 233 TITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVM-TSCVSEQLDHGVLLVGY 291

Query: 294 SAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
           +    +     PYWI+KNSW   WGE+GYI + +G N C V    S++++
Sbjct: 292 NDSAAV-----PYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVV 336


>sp|P13277|CYS1_HOMAM DIGESTIVE CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 322

 Score =  225 bits (567), Expect = 1e-58
 Identities = 130/341 (38%), Positives = 182/341 (53%), Gaps = 33/341 (9%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKI 59
           MKV+ LF+  +     +           + EF+ KF +KY   EE   R  +F  NL  I
Sbjct: 1   MKVVALFLFGLALAAANP---------SWEEFKGKFGRKYVDLEEERYRLNVFLDNLQYI 51

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
           EE N      +      +N+F+D+++++F       K+       P A +   +      
Sbjct: 52  EEFNKKYERGEVTYNLAINQFSDMTNEKFNAVMKGYKKG----PRPAAVFTSTDAAPE-S 106

Query: 120 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 179
           T  DWRT+GAVTPVK+QGQCGSCW+FSTTG +EGQHF+   +LVSLSEQ LVDC      
Sbjct: 107 TEVDWRTKGAVTPVKDQGQCGSCWAFSTTGGIEGQHFLKTGRLVSLSEQQLVDC------ 160

Query: 180 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFT 239
             G    ++GCNGG    A  Y+  NGG+ TESSYPY A   T C FNS  IGA  + + 
Sbjct: 161 -AGGSYYNQGCNGGWVERAIMYVRDNGGVDTESSYPYEARDNT-CRFNSNTIGATCTGYV 218

Query: 240 MIPK-NETVMAGYIVSTGPLAIAADAVEWQF---YIGGVFDIPCNPNSLDHGILIVGYSA 295
            I + +E+ +       GP+++A DA    F   Y G  ++  C+ + LDH +L VGY +
Sbjct: 219 GIAQGSESALKTATRDIGPISVAIDASHRSFQSYYTGVYYEPSCSSSQLDHAVLAVGYGS 278

Query: 296 KNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVS 335
           +         +W+VKNSW   WGE GYI + R + N CG++
Sbjct: 279 EG-----GQDFWLVKNSWATSWGESGYIKMARNRNNNCGIA 314


>sp|P25782|CYS2_HOMAM DIGESTIVE CYSTEINE PROTEINASE 2 PRECURSOR
          Length = 323

 Score =  224 bits (566), Expect = 2e-58
 Identities = 132/349 (37%), Positives = 188/349 (53%), Gaps = 32/349 (9%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKI 59
           MKV +LF+  V     S           +  F+ K+ ++Y   EE   R  IF+ N   I
Sbjct: 1   MKVAVLFLCGVALAAASP---------SWEHFKGKYGRQYVDAEEDSYRRVIFEQNQKYI 51

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
           EE N    N +      +NKF D++ +EF      N   I     PV+ +   +      
Sbjct: 52  EEFNKKYENGEVTFNLAMNKFGDMTLEEFNAVMKGN---IPRRSAPVSVFYPKKETGPQA 108

Query: 120 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 179
           T  DWRT+GAVTPVK+QGQCGSCW+FSTTG++EGQHF+    L+SL+EQ LVDC      
Sbjct: 109 TEVDWRTKGAVTPVKDQGQCGSCWAFSTTGSLEGQHFLKTGSLISLAEQQLVDC------ 162

Query: 180 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFT 239
                   +GCNGG   +A++YI  N GI TE++YPY A  G+ C F+S ++ A  S  T
Sbjct: 163 --SRPYGPQGCNGGWMNDAFDYIKANNGIDTEAAYPYEARDGS-CRFDSNSVAATCSGHT 219

Query: 240 MIPK-NETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIP-CNPNSLDHGILIVGYSA 295
            I   +ET +   +   GP+++  DA    +QFY  GV+  P C+P+ LDH +L VGY +
Sbjct: 220 NIASGSETGLQQAVRDIGPISVTIDAAHSSFQFYSSGVYYEPSCSPSYLDHAVLAVGYGS 279

Query: 296 KNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTSII 343
           +         +W+VKNSW   WG+ GYI + R + N CG++   S  ++
Sbjct: 280 EG-----GQDFWLVKNSWATSWGDAGYIKMSRNRNNNCGIATVASYPLV 323


>sp|P07154|CATL_RAT CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTEIN) (MEP) (CYCLIC
           PROTEIN-2) (CP-2)
          Length = 334

 Score =  224 bits (564), Expect = 3e-58
 Identities = 127/351 (36%), Positives = 195/351 (55%), Gaps = 31/351 (8%)

Query: 3   VILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEEL 62
           ++LL VL + T   + +       +Q+ +++    + Y   E   R  +++ N+  I+  
Sbjct: 4   LLLLAVLCLGTALATPK-FDQTFNAQWHQWKSTHRRLYGTNEEEWRRAVWEKNMRMIQLH 62

Query: 63  NLIAINHKADTKFGVNKFADLSSDEFKN------YYLNNKEAIFTDDLPVADYLDDEFIN 116
           N    N K      +N F D++++EF+       +  + K  +F + L +          
Sbjct: 63  NGEYSNGKHGFTMEMNAFGDMTNEEFRQIVNGYRHQKHKKGRLFQEPLML---------- 112

Query: 117 SIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 176
            IP   DWR +G VTPVKNQGQCGSCW+FS +G +EGQ F+   KL+SLSEQNLVDC H+
Sbjct: 113 QIPKTVDWREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLISLSEQNLVDCSHD 172

Query: 177 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKIS 236
               +G    ++GCNGGL   A+ YI +NGG+ +E SYPY A+ G+ C + +    A  +
Sbjct: 173 ----QG----NQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGS-CKYRAEYAVANDT 223

Query: 237 NFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIP-CNPNSLDHGILIVGY 293
            F  IP+ E  +   + + GP+++A DA     QFY  G++  P C+   LDHG+L+VGY
Sbjct: 224 GFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCSSKDLDHGVLVVGY 283

Query: 294 SAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT-CGVSNFVSTSII 343
             + T   K+  YW+VKNSWG +WG  GYI + + +N  CG++   S  I+
Sbjct: 284 GYEGTDSNKD-KYWLVKNSWGKEWGMDGYIKIAKDRNNHCGLATAASYPIV 333


>sp|P06797|CATL_MOUSE CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTEIN) (MEP)
          Length = 334

 Score =  223 bits (562), Expect = 5e-58
 Identities = 126/351 (35%), Positives = 198/351 (55%), Gaps = 31/351 (8%)

Query: 3   VILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEEL 62
           ++LL VL + T   + +       +++ +++    + Y   E   R  I++ N+  I+  
Sbjct: 4   LLLLAVLCLGTALATPK-FDQTFSAEWHQWKSTHRRLYGTNEEEWRRAIWEKNMRMIQLH 62

Query: 63  NLIAINHKADTKFGVNKFADLSSDEFKN------YYLNNKEAIFTDDLPVADYLDDEFIN 116
           N    N +      +N F D++++EF+       +  + K  +F + L +          
Sbjct: 63  NGEYSNGQHGFSMEMNAFGDMTNEEFRQVVNGYRHQKHKKGRLFQEPLML---------- 112

Query: 117 SIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 176
            IP + DWR +G VTPVKNQGQCGSCW+FS +G +EGQ F+   KL+SLSEQNLVDC H 
Sbjct: 113 KIPKSVDWREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLISLSEQNLVDCSHA 172

Query: 177 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKIS 236
               +G    ++GCNGGL   A+ YI +NGG+ +E SYPY A+ G+ C + +    A  +
Sbjct: 173 ----QG----NQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGS-CKYRAEFAVANDT 223

Query: 237 NFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIP-CNPNSLDHGILIVGY 293
            F  IP+ E  +   + + GP+++A DA     QFY  G++  P C+  +LDHG+L+VGY
Sbjct: 224 GFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCSSKNLDHGVLLVGY 283

Query: 294 SAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTSII 343
             + T   KN  YW+VKNSWG++WG +GYI + + + N CG++   S  ++
Sbjct: 284 GYEGTDSNKN-KYWLVKNSWGSEWGMEGYIKIAKDRDNHCGLATAASYPVV 333


>sp|P25784|CYS3_HOMAM DIGESTIVE CYSTEINE PROTEINASE 3 PRECURSOR
          Length = 321

 Score =  221 bits (558), Expect = 1e-57
 Identities = 123/317 (38%), Positives = 182/317 (56%), Gaps = 37/317 (11%)

Query: 32  FQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEF-- 88
           F+ ++ +KY   +E L R  +F+ N   IE+ N    N +   K  +N+F D++++EF  
Sbjct: 23  FKTQYGRKYGDAKEELYRQRVFQQNEQLIEDFNKKFENGEVTFKVAMNQFGDMTNEEFNA 82

Query: 89  --KNYYLNNK---EAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCW 143
             K Y   ++   +A+FT +              +    DWRT+  VTPVK+Q QCGSCW
Sbjct: 83  VMKGYKKGSRGEPKAVFTAEA-----------GPMAADVDWRTKALVTPVKDQEQCGSCW 131

Query: 144 SFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYII 203
           +FS TG +EGQHF+  ++LVSLSEQ LVDC          +  ++GC GG   +A++YI 
Sbjct: 132 AFSATGALEGQHFLKNDELVSLSEQQLVDC--------STDYGNDGCGGGWMTSAFDYIK 183

Query: 204 KNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAAD 263
            NGGI TESSYPY AE    C F++ +IGA  +    +   E  +   +   GP+++A D
Sbjct: 184 DNGGIDTESSYPYEAE-DRSCRFDANSIGAICTGSVEVQHTEEALQEAVSGVGPISVAID 242

Query: 264 A--VEWQFYIGGV-FDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQ 320
           A    +QFY  GV ++  C+P  LDHG+L VGY  ++T       YW+VKNSWG+ WG+ 
Sbjct: 243 ASHFSFQFYSSGVYYEQNCSPTFLDHGVLAVGYGTEST-----KDYWLVKNSWGSSWGDA 297

Query: 321 GYIYLRRGK-NTCGVSN 336
           GYI + R + N CG+++
Sbjct: 298 GYIKMSRNRDNNCGIAS 314


>sp|P41721|CATV_NPVBM VIRAL CATHEPSIN (V-CATH)
          Length = 323

 Score =  221 bits (557), Expect = 2e-57
 Identities = 131/342 (38%), Positives = 181/342 (52%), Gaps = 26/342 (7%)

Query: 5   LLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELN 63
           +LF L V+ V  S+   P +  + F EF  +FNK YS E E L RF+IF+ NL +I    
Sbjct: 4   ILFYLFVYAVVKSAAYDPLKAPNYFEEFVHRFNKNYSSEVEKLRRFKIFQHNLNEI---- 59

Query: 64  LIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFD 123
            I  N     K+ +NKF+DLS DE    Y        T +      LD       P  FD
Sbjct: 60  -INKNQNDSAKYEINKFSDLSKDETIAKYTGLSLPTQTQNFCKVILLDQP-PGKGPLEFD 117

Query: 124 WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE 183
           WR    VT VKNQG CG+CW+F+T G++E Q  I  N+L++LSEQ ++DCD         
Sbjct: 118 WRRLNKVTSVKNQGMCGACWAFATLGSLESQFAIKHNELINLSEQQMIDCDF-------- 169

Query: 184 EACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISN-FTMIP 242
              D GCNGGL   A+  IIK GG+Q ES YPY A+    C  NS     ++ + +  I 
Sbjct: 170 --VDAGCNGGLLHTAFEAIIKMGGVQLESDYPYEAD-NNNCRMNSNKFLVQVKDCYRYII 226

Query: 243 KNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRK 302
             E  +   +   GP+ +A DA +   Y  G+    C  + L+H +L+VGY  +N     
Sbjct: 227 VYEEKLKDLLPLVGPIPMAIDAADIVNYKQGIIKY-CFDSGLNHAVLLVGYGVEN----- 280

Query: 303 NMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN-FVSTSII 343
           N+PYW  KN+WG DWGE G+  +++  N CG+ N   ST++I
Sbjct: 281 NIPYWTFKNTWGTDWGEDGFFRVQQNINACGMRNELASTAVI 322


>sp|P41715|CATV_NPVCF VIRAL CATHEPSIN (V-CATH)
          Length = 324

 Score =  220 bits (554), Expect = 4e-57
 Identities = 131/344 (38%), Positives = 188/344 (54%), Gaps = 27/344 (7%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKI 59
           M  I+L++L    V  ++  +  +  + F +F  KFNK YS E E L RF+IF+ NL +I
Sbjct: 1   MNKIVLYLLVYGAVQCAAYDVL-KAPNYFEDFLHKFNKSYSSESEKLRRFQIFRHNLEEI 59

Query: 60  EELNLIAINHKADT-KFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSI 118
                I  NH   T ++ +NKFADLS DE  + Y      + T +      LD    +  
Sbjct: 60  -----INKNHNDSTAQYEINKFADLSKDETISKYTGLSLPLQTQNFCEVVVLDRP-PDKG 113

Query: 119 PTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECM 178
           P  FDWR    VT VKNQG CG+CW+F+T G++E Q  I  N+ ++LSEQ L+DCD    
Sbjct: 114 PLEFDWRRLNKVTSVKNQGMCGACWAFATLGSLESQFAIKHNQFINLSEQQLIDCDF--- 170

Query: 179 EYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISN- 237
                   D GC+GGL   A+  ++  GGIQ ES YPY A  G  C  N+A    K+   
Sbjct: 171 -------VDAGCDGGLLHTAFEAVMNMGGIQAESDYPYEANNG-DCRANAAKFVVKVKKC 222

Query: 238 FTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKN 297
           +  I   E  +   + S GP+ +A DA +   Y  G+    C  + L+H +L+VGY+ +N
Sbjct: 223 YRYITVFEEKLKDLLRSVGPIPVAIDASDIVNYKRGIMKY-CANHGLNHAVLLVGYAVEN 281

Query: 298 TIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTS 341
                 +P+WI+KN+WGADWGEQGY  +++  N CG+ N + +S
Sbjct: 282 -----GVPFWILKNTWGADWGEQGYFRVQQNINACGIQNELPSS 320


>sp|P25975|CATL_BOVIN CATHEPSIN L PRECURSOR
          Length = 334

 Score =  218 bits (550), Expect = 1e-56
 Identities = 124/342 (36%), Positives = 182/342 (52%), Gaps = 25/342 (7%)

Query: 7   FVLAVFTVFVSSRG--IPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNL 64
           F L V  + V+S    + P   + + +++    + Y   E   R  +++ N   I+  N 
Sbjct: 5   FFLTVLCLGVASAAPKLDPNLDAHWHQWKATHRRLYGMNEEEWRRAVWEKNKKIIDLHNQ 64

Query: 65  IAINHKADTKFGVNKFADLSSDEFK---NYYLNNKEAIFTDDLPVADYLDDEFINSIPTA 121
                K   +  +N F D++++EF+   N + N K               +  +  +P +
Sbjct: 65  EYSEGKHAFRMAMNAFGDMTNEEFRQVMNGFQNQKHK-------KGKLFHEPLLVDVPKS 117

Query: 122 FDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYE 181
            DW  +G VTPVKNQGQCGSCW+FS TG +EGQ F    KLVSLSEQNLVDC       +
Sbjct: 118 VDWTKKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRA----Q 173

Query: 182 GEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMI 241
           G    ++GCNGGL  NA+ YI  NGG+ +E SYPY A     CN+      A  + F  I
Sbjct: 174 G----NQGCNGGLMDNAFQYIKDNGGLDSEESYPYLATDTNSCNYKPECSAANDTGFVDI 229

Query: 242 PKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIVGYSAKNT 298
           P+ E  +   + + GP+++A DA    +QFY  G+ +D  C+   LDHG+L+VGY  + T
Sbjct: 230 PQREKALMKAVATVGPISVAIDAGHTSFQFYKSGIYYDPDCSCKDLDHGVLVVGYGFEGT 289

Query: 299 IFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT-CGVSNFVS 339
               N  +WIVKNSWG +WG  GY+ + + +N  CG++   S
Sbjct: 290 DSNNN-KFWIVKNSWGPEWGWNGYVKMAKDQNNHCGIATAAS 330


>sp|P36400|LCPB_LEIME CYSTEINE PROTEINASE B PRECURSOR
          Length = 443

 Score =  218 bits (549), Expect = 2e-56
 Identities = 123/320 (38%), Positives = 177/320 (54%), Gaps = 34/320 (10%)

Query: 29  FLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKA---DTKFGVNKFADLS 84
           F EF+  + + Y    E  +R   F+ NL  + E       H+A     +FG+ KF DLS
Sbjct: 38  FEEFKRTYGRAYETLAEEQQRLANFERNLELMRE-------HQARNPHAQFGITKFFDLS 90

Query: 85  SDEFKNYYLNNKEAIFTDDLPVADYLDDEF--INSIPTAFDWRTRGAVTPVKNQGQCGSC 142
             EF   YLN            A +       ++++P A DWR +GAVTPVK+QG CGSC
Sbjct: 91  EAEFAARYLNGAAYFAAAKRHAAQHYRKARADLSAVPDAVDWREKGAVTPVKDQGACGSC 150

Query: 143 WSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYI 202
           W+FS  GN+EGQ +++ ++LVSLSEQ LV CD            ++GC+GGL   A++++
Sbjct: 151 WAFSAVGNIEGQWYLAGHELVSLSEQQLVSCDD----------MNDGCDGGLMLQAFDWL 200

Query: 203 IK--NGGIQTESSYPYTAETG--TQC-NFNSANIGAKISNFTMIPKNETVMAGYIVSTGP 257
           ++  NG + TE SYPY +  G   +C N +   +GA+I    +I  +E  MA ++   GP
Sbjct: 201 LQNTNGHLHTEDSYPYVSGNGYVPECSNSSELVVGAQIDGHVLIGSSEKAMAAWLAKNGP 260

Query: 258 LAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADW 317
           +AIA DA  +  Y  GV    C    L+HG+L+VGY     +     PYW++KNSWG DW
Sbjct: 261 IAIALDASSFMSYKSGVL-TACIGKQLNHGVLLVGYDMTGEV-----PYWVIKNSWGGDW 314

Query: 318 GEQGYIYLRRGKNTCGVSNF 337
           GEQGY+ +  G N C +S +
Sbjct: 315 GEQGYVRVVMGVNACLLSEY 334


>sp|Q05094|CYS2_LEIPI CYSTEINE PROTEINASE 2 PRECURSOR (AMASTIGOTE CYSTEINE PROTEINASE
           A-2)
          Length = 444

 Score =  218 bits (549), Expect = 2e-56
 Identities = 123/321 (38%), Positives = 178/321 (55%), Gaps = 35/321 (10%)

Query: 29  FLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKA---DTKFGVNKFADLS 84
           F EF+  + + Y    E  +R   F+ NL  + E       H+A     +FG+ KF DLS
Sbjct: 38  FEEFKRTYGRAYETLAEEQQRLANFERNLELMRE-------HQARNPHAQFGITKFFDLS 90

Query: 85  SDEFKNYYLNNKEAIFTDDLPVADYLDDEF--INSIPTAFDWRTRGAVTPVKNQGQCGSC 142
             EF   YLN            A +       ++++P A DWR +GAVTPVK+QG CGSC
Sbjct: 91  EAEFAARYLNGAAYFAAAKRHAAQHYRKARADLSAVPDAVDWREKGAVTPVKDQGACGSC 150

Query: 143 WSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYI 202
           W+FS  GN+EGQ +++ ++LVSLSEQ LV CD            ++GC+GGL   A++++
Sbjct: 151 WAFSAVGNIEGQWYLAGHELVSLSEQQLVSCDD----------MNDGCDGGLMLQAFDWL 200

Query: 203 IK--NGGIQTESSYPYTAETG--TQCNFNSAN--IGAKISNFTMIPKNETVMAGYIVSTG 256
           ++  NG + TE SYPY +  G   +C+ +S    +GA+I    +I  +E  MA ++   G
Sbjct: 201 LQNTNGHLHTEDSYPYVSGNGYVPECSNSSEELVVGAQIDGHVLIGSSEKAMAAWLAKNG 260

Query: 257 PLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGAD 316
           P+AIA DA  +  Y  GV    C    L+HG+L+VGY     +     PYW++KNSWG D
Sbjct: 261 PIAIALDASSFMSYKSGVL-TACIGKQLNHGVLLVGYDMTGEV-----PYWVIKNSWGGD 314

Query: 317 WGEQGYIYLRRGKNTCGVSNF 337
           WGEQGY+ +  G N C +S +
Sbjct: 315 WGEQGYVRVVMGVNACLLSEY 335


>sp|P12412|CYSP_VIGMU VIGNAIN PRECURSOR (BEAN ENDOPEPTIDASE) (CYSTEINE PROTEINASE)
           (SULFHYDRYL-ENDOPEPTIDASE) (SH-EP)
          Length = 362

 Score =  217 bits (547), Expect = 3e-56
 Identities = 127/306 (41%), Positives = 179/306 (57%), Gaps = 29/306 (9%)

Query: 47  ERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNK---EAIFTDD 103
           +RF +FK+N+  +   N +   +K      +NKFAD+++ EF++ Y  +K     +F   
Sbjct: 58  KRFNVFKANVMHVHNTNKMDKPYKLK----LNKFADMTNHEFRSTYAGSKVNHHKMFRGS 113

Query: 104 LPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLV 163
              +     E + S+P + DWR +GAVT VK+QGQCGSCW+FST   VEG + I  NKLV
Sbjct: 114 QHGSGTFMYEKVGSVPASVDWRKKGAVTDVKDQGQCGSCWAFSTIVAVEGINQIKTNKLV 173

Query: 164 SLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQ 223
           SLSEQ LVDCD E          ++GCNGGL  +A+ +I + GGI TES+YPYTA+ GT 
Sbjct: 174 SLSEQELVDCDKE---------ENQGCNGGLMESAFEFIKQKGGITTESNYPYTAQEGT- 223

Query: 224 CNFNSAN-IGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCN 280
           C+ +  N +   I     +P N+       V+  P+++A DA   ++QFY  GVF   CN
Sbjct: 224 CDESKVNDLAVSIDGHENVPVNDENALLKAVANQPVSVAIDAGGSDFQFYSEGVFTGDCN 283

Query: 281 PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG----KNTCGVSN 336
              L+HG+ IVGY    T+   N  YWIV+NSWG +WGEQGYI ++R     +  CG++ 
Sbjct: 284 -TDLNHGVAIVGYG--TTVDGTN--YWIVRNSWGPEWGEQGYIRMQRNISKKEGLCGIAM 338

Query: 337 FVSTSI 342
             S  I
Sbjct: 339 MASYPI 344


>sp|P07711|CATL_HUMAN CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTEIN) (MEP)
          Length = 333

 Score =  215 bits (543), Expect = 8e-56
 Identities = 124/341 (36%), Positives = 186/341 (54%), Gaps = 26/341 (7%)

Query: 8   VLAVFTVFVSSRGIPPEE--QSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLI 65
           +LA F + ++S  +  +   ++Q+ +++   N+ Y   E   R  +++ N+  IE  N  
Sbjct: 6   ILAAFCLGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQE 65

Query: 66  AINHKADTKFGVNKFADLSSDEFK---NYYLNNKEAIFTDDLPVADYLDDEFINSIPTAF 122
               K      +N F D++S+EF+   N + N K               +      P + 
Sbjct: 66  YREGKHSFTMAMNAFGDMTSEEFRQVMNGFQNRKPR-------KGKVFQEPLFYEAPRSV 118

Query: 123 DWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEG 182
           DWR +G VTPVKNQGQCGSCW+FS TG +EGQ F    +L+SLSEQNLVDC        G
Sbjct: 119 DWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDC-------SG 171

Query: 183 EEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP 242
            +  +EGCNGGL   A+ Y+  NGG+ +E SYPY A T   C +N     A  + F  IP
Sbjct: 172 PQG-NEGCNGGLMDYAFQYVQDNGGLDSEESYPYEA-TEESCKYNPKYSVANDTGFVDIP 229

Query: 243 KNETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIVGYSAKNTI 299
           K E  +   + + GP+++A DA    + FY  G+ F+  C+   +DHG+L+VGY  ++T 
Sbjct: 230 KQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFEST- 288

Query: 300 FRKNMPYWIVKNSWGADWGEQGYIYLRRG-KNTCGVSNFVS 339
              N  YW+VKNSWG +WG  GY+ + +  +N CG+++  S
Sbjct: 289 ESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAAS 329


>sp|Q28944|CATL_PIG CATHEPSIN L PRECURSOR
          Length = 334

 Score =  214 bits (540), Expect = 2e-55
 Identities = 117/307 (38%), Positives = 165/307 (53%), Gaps = 23/307 (7%)

Query: 40  YSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFK---NYYLNNK 96
           Y   E   R  +++ N+  IE  N      K      +N F D++++EF+   N + N K
Sbjct: 40  YGMNEEGWRRAVWEKNMKMIELHNQEYSQGKHGFSMAMNAFGDMTNEEFRQVMNGFQNQK 99

Query: 97  EAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHF 156
                          +  +  +P + DWR +G VT VKNQGQCGSCW+FS TG +EGQ F
Sbjct: 100 HK-------KGKVFHESLVLEVPKSVDWREKGYVTAVKNQGQCGSCWAFSATGALEGQMF 152

Query: 157 ISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPY 216
               KLVSLSEQNLVDC       +G    ++GCNGGL  NA+ Y+  NGG+ TE SYPY
Sbjct: 153 RKTGKLVSLSEQNLVDCSRP----QG----NQGCNGGLMDNAFQYVKDNGGLDTEESYPY 204

Query: 217 TAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGV 274
                  C +      A  + F  IP+ E  +   + + GP+++A DA    +QFY  G+
Sbjct: 205 LGRETNSCTYKPECSAANDTGFVDIPQREKALMKAVATVGPISVAIDAGHSSFQFYKSGI 264

Query: 275 -FDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT-C 332
            +D  C+   LDHG+L+VGY  + T    +  +WIVKNSWG +WG  GY+ + + +N  C
Sbjct: 265 YYDPDCSSKDLDHGVLVVGYGFEGT-DSNSSKFWIVKNSWGPEWGWNGYVKMAKDQNNHC 323

Query: 333 GVSNFVS 339
           G+S   S
Sbjct: 324 GISTAAS 330


>sp|P25783|CATV_NPVAC VIRAL CATHEPSIN (V-CATH)
          Length = 323

 Score =  213 bits (538), Expect = 3e-55
 Identities = 129/342 (37%), Positives = 179/342 (51%), Gaps = 26/342 (7%)

Query: 5   LLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELN 63
           +LF L V+ V  S+     +  + F EF  +FNK Y  E E L RF+IF+ NL +I    
Sbjct: 4   ILFYLFVYGVVNSAAYDLLKAPNYFEEFVHRFNKDYGSEVEKLRRFKIFQHNLNEI---- 59

Query: 64  LIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFD 123
            I  N     K+ +NKF+DLS DE    Y      I T +      LD       P  FD
Sbjct: 60  -INKNQNDSAKYEINKFSDLSKDETIAKYTGLSLPIQTQNFCKVIVLDQP-PGKGPLEFD 117

Query: 124 WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE 183
           WR    VT VKNQG CG+CW+F+T  ++E Q  I  N+L++LSEQ ++DCD         
Sbjct: 118 WRRLNKVTSVKNQGMCGACWAFATLASLESQFAIKHNQLINLSEQQMIDCDF-------- 169

Query: 184 EACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISN-FTMIP 242
              D GCNGGL   A+  IIK GG+Q ES YPY A+    C  NS     ++ + +  I 
Sbjct: 170 --VDAGCNGGLLHTAFEAIIKMGGVQLESDYPYEAD-NNNCRMNSNKFLVQVKDCYRYIT 226

Query: 243 KNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRK 302
             E  +   +   GP+ +A DA +   Y  G+    C  + L+H +L+VGY  +N     
Sbjct: 227 VYEEKLKDLLRLVGPIPMAIDAADIVNYKQGIIKY-CFNSGLNHAVLLVGYGVEN----- 280

Query: 303 NMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN-FVSTSII 343
           N+PYW  KN+WG DWGE G+  +++  N CG+ N   ST++I
Sbjct: 281 NIPYWTFKNTWGTDWGEDGFFRVQQNINACGMRNELASTAVI 322


>sp|Q40143|CYS3_LYCES CYSTEINE PROTEINASE 3 PRECURSOR
          Length = 356

 Score =  212 bits (535), Expect = 7e-55
 Identities = 126/324 (38%), Positives = 176/324 (53%), Gaps = 34/324 (10%)

Query: 29  FLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE 87
           F  F  +  K+Y S EE  +RFEIF  NL  I   N   +++K     G+N+F DL+ DE
Sbjct: 57  FARFAIRHRKRYDSVEEIKQRFEIFLDNLKMIRSHNRKGLSYK----LGINEFTDLTWDE 112

Query: 88  FKNYYLN---NKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWS 144
           F+ + L    N  A    +L + + +       +P   DWR  G V+PVK QG+CGSCW+
Sbjct: 113 FRKHKLGASQNCSATTKGNLKLTNVV-------LPETKDWRKDGIVSPVKAQGKCGSCWT 165

Query: 145 FSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIK 204
           FSTTG +E  +  +  K +SLSEQ LVDC      +        GCNGGL   A+ YI  
Sbjct: 166 FSTTGALEAAYAQAFGKGISLSEQQLVDCAGAFNNF--------GCNGGLPSQAFEYIKF 217

Query: 205 NGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVS-TGPLAIAAD 263
           NGG+ TE +YPYT + G  C F+ ANIG K+ +   I         Y V+   P+++A +
Sbjct: 218 NGGLDTEEAYPYTGKNGI-CKFSQANIGVKVISSVNITLGAEYELKYAVALVRPVSVAFE 276

Query: 264 AVE-WQFYIGGVF---DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGE 319
            V+ ++ Y  GV+   +    P  ++H +L VGY  +N       PYW++KNSWGADWGE
Sbjct: 277 VVKGFKQYKSGVYASTECGDTPMDVNHAVLAVGYGVEN-----GTPYWLIKNSWGADWGE 331

Query: 320 QGYIYLRRGKNTCGVSNFVSTSII 343
            GY  +  GKN CGV+   S  I+
Sbjct: 332 DGYFKMEMGKNMCGVATCASYPIV 355


>sp|O60911|CATM_HUMAN CATHEPSIN L2 PRECURSOR (CATHEPSIN V)
          Length = 334

 Score =  210 bits (528), Expect = 5e-54
 Identities = 127/349 (36%), Positives = 191/349 (54%), Gaps = 35/349 (10%)

Query: 5   LLFVLAVFTVFVSSRGIPPEEQS---QFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEE 61
           L  VLA F + ++S  +P  +Q+   ++ +++    + Y   E   R  +++ N+  IE 
Sbjct: 3   LSLVLAAFCLGIAS-AVPKFDQNLDTKWYQWKATHRRLYGANEEGWRRAVWEKNMKMIEL 61

Query: 62  LNLIAINHKADTKFGVNKFADLSSDEFKNY---YLNNK---EAIFTDDLPVADYLDDEFI 115
            N      K      +N F D++++EF+     + N K     +F + L    +LD    
Sbjct: 62  HNGEYSQGKHGFTMAMNAFPDMTNEEFRQMMGCFRNQKFRKGKVFREPL----FLD---- 113

Query: 116 NSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDH 175
             +P + DWR +G VTPVKNQ QCGSCW+FS TG +EGQ F    KLVSLSEQNLVDC  
Sbjct: 114 --LPKSVDWRKKGYVTPVKNQKQCGSCWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSR 171

Query: 176 ECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKI 235
                +G    ++GCNGG    A+ Y+ +NGG+ +E SYPY A     C +   N  A  
Sbjct: 172 P----QG----NQGCNGGFMARAFQYVKENGGLDSEESYPYVA-VDEICKYRPENSVAND 222

Query: 236 SNFTMI-PKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIV 291
           + FT++ P  E  +   + + GP+++A DA    +QFY  G+ F+  C+  +LDHG+L+V
Sbjct: 223 TGFTVVAPGKEKALMKAVATVGPISVAMDAGHSSFQFYKSGIYFEPDCSSKNLDHGVLVV 282

Query: 292 GYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT-CGVSNFVS 339
           GY  +      N  YW+VKNSWG +WG  GY+ + + KN  CG++   S
Sbjct: 283 GYGFEGA-NSNNSKYWLVKNSWGPEWGSNGYVKIAKDKNNHCGIATAAS 330


>sp|P54639|CYS4_DICDI CYSTEINE PROTEINASE 4 PRECURSOR
          Length = 442

 Score =  209 bits (527), Expect = 6e-54
 Identities = 116/300 (38%), Positives = 167/300 (55%), Gaps = 24/300 (8%)

Query: 4   ILLFVLAVFTVFVSSRGIPPEEQ--SQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEE 61
           +L F+  +   + S++    E Q  + F  +     + YS EE+  R++IFKSN+  + +
Sbjct: 3   VLSFLCLLLVSYASAKQQFSELQYRNAFTNWMQAHQRTYSSEEFNARYQIFKSNMDYVHQ 62

Query: 62  LNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTA 121
            N    +   +T  G+N FAD+++ E++  YL      F     +    +  F    PT 
Sbjct: 63  WN----SKGGETVLGLNVFADITNQEYRTTYLGTP---FDGSALIGTEEEKIFSTPAPTV 115

Query: 122 FDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFIS---QNKLVSLSEQNLVDCDHECM 178
            DWR +GAVTP+KNQGQCG CWSFSTTG+ EG HFI+   +  LVSLSEQNL+DC     
Sbjct: 116 -DWRAQGAVTPIKNQGQCGGCWSFSTTGSTEGAHFIASGTKKDLVSLSEQNLIDCS---- 170

Query: 179 EYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNF 238
               +   + GC GGL    + YII N GI TESSYPYTAE G +C F ++NIGA+I ++
Sbjct: 171 ----KSYGNNGCEGGLMTLGFEYIINNKGIDTESSYPYTAEDGKECKFKTSNIGAQIVSY 226

Query: 239 TMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIP-CNPNSLDHGILIVGYSA 295
             +            +  P+++A DA    +Q Y  G++  P C P  LDHG+L+VGY +
Sbjct: 227 QNVTSGSEASLQSASNNAPVSVAIDASNESFQLYESGIYYEPACTPTQLDHGVLVVGYGS 286


 Score = 48.8 bits (114), Expect = 2e-05
 Identities = 18/35 (51%), Positives = 24/35 (68%), Gaps = 1/35 (2%)

Query: 306 YWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVS 339
           YWIVKNSWG  WG  GYI++ + + N CG++   S
Sbjct: 401 YWIVKNSWGTSWGMDGYIFMSKDRNNNCGIATMAS 435


>sp|Q10991|CATL_SHEEP CATHEPSIN L
          Length = 217

 Score =  209 bits (527), Expect = 6e-54
 Identities = 104/226 (46%), Positives = 140/226 (61%), Gaps = 17/226 (7%)

Query: 118 IPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHEC 177
           +P + DW  +G VTPVKNQGQCGSCW+FS TG +EGQ F    KLVSLSEQNLVD     
Sbjct: 1   VPKSVDWTKKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGKLVSLSEQNLVD----- 55

Query: 178 MEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISN 237
                    ++GCNGGL  NA+ YI +NGG+ +E SYPY A T T CN+      AK + 
Sbjct: 56  ---SSRPQGNQGCNGGLMDNAFQYIKENGGLDSEESYPYEA-TDTSCNYKPEYSAAKDTG 111

Query: 238 FTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIVGYS 294
           F  IP+ E  +   + + GP+++A DA    +QFY  G+ +D  C+   LDHG+L+VGY 
Sbjct: 112 FVDIPQREKALMKAVATVGPISVAIDAGHSSFQFYKSGIYYDPDCSSKDLDHGVLVVGYG 171

Query: 295 AKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT-CGVSNFVS 339
            + T    N  +WIVKNSWG +WG +GY+ + + +N  CG++   S
Sbjct: 172 FEGT----NNKFWIVKNSWGPEWGNKGYVKMAKDQNNHCGIATAAS 213


>sp|P25803|CYSP_PHAVU VIGNAIN PRECURSOR (BEAN ENDOPEPTIDASE) (CYSTEINE PROTEINASE EP-C1)
          Length = 362

 Score =  208 bits (523), Expect = 2e-53
 Identities = 124/306 (40%), Positives = 176/306 (56%), Gaps = 29/306 (9%)

Query: 47  ERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNK---EAIFTDD 103
           +RF +FK+NL  +   N +   +K      +NKFAD+++ EF++ Y  +K     +F   
Sbjct: 58  KRFNVFKANLMHVHNTNKMDKPYKLK----LNKFADMTNHEFRSTYAGSKVNHPRMFRGT 113

Query: 104 LPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLV 163
                    E + S+P + DWR +GAVT VK+QGQCGSCW+FST   VEG + I  NKLV
Sbjct: 114 PHENGAFMYEKVVSVPPSVDWRKKGAVTDVKDQGQCGSCWAFSTVVAVEGINQIKTNKLV 173

Query: 164 SLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQ 223
           +LSEQ LVDCD E          ++GCNGGL  +A+ +I + GGI TES+YPY A+ GT 
Sbjct: 174 ALSEQELVDCDKE---------ENQGCNGGLMESAFEFIKQKGGITTESNYPYKAQEGT- 223

Query: 224 CNFNSAN-IGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCN 280
           C+ +  N +   I     +P N+       V+  P+++A DA   ++QFY  GVF   C+
Sbjct: 224 CDASKVNDLAVSIDGHENVPANDEDALLKAVANQPVSVAIDAGGSDFQFYSEGVFTGDCS 283

Query: 281 PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG----KNTCGVSN 336
              L+HG+ IVGY    T+   N  YWIV+NSWG +WGE GYI ++R     +  CG++ 
Sbjct: 284 -TDLNHGVAIVGYG--TTVDGTN--YWIVRNSWGPEWGEHGYIRMQRNISKKEGLCGIAM 338

Query: 337 FVSTSI 342
             S  I
Sbjct: 339 LPSYPI 344


>sp|P00785|ACTN_ACTCH ACTINIDAIN PRECURSOR (ACTINIDIN)
          Length = 380

 Score =  206 bits (520), Expect = 4e-53
 Identities = 123/327 (37%), Positives = 176/327 (53%), Gaps = 35/327 (10%)

Query: 24  EEQSQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADT----KFGVN 78
           E ++ +  +  K+ K Y S  E+  RFEIFK  L  I+E       H ADT    K G+N
Sbjct: 37  EVKAMYESWLIKYGKSYNSLGEWERRFEIFKETLRFIDE-------HNADTNRSYKVGLN 89

Query: 79  KFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQ 138
           +FADL+ +EF++ YL       ++   V++  +  F   +P+  DWR+ GAV  +K+QG+
Sbjct: 90  QFADLTDEEFRSTYLGFTSG--SNKTKVSNRYEPRFGQVLPSYVDWRSAGAVVDIKSQGE 147

Query: 139 CGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNA 198
           CG CW+FS    VEG + I    L+SLSEQ L+DC        G      GCNGG   + 
Sbjct: 148 CGGCWAFSAIATVEGINKIVTGVLISLSEQELIDC--------GRTQNTRGCNGGYITDG 199

Query: 199 YNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG-AKISNFTMIPKNETVMAGYIVSTGP 257
           + +II NGGI TE +YPYTA+ G +CN +  N     I  +  +P N        V+  P
Sbjct: 200 FQFIINNGGINTEENYPYTAQDG-ECNLDLQNEKYVTIDTYENVPYNNEWALQTAVTYQP 258

Query: 258 LAIAADAV--EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGA 315
           +++A DA    ++ Y  G+F  PC   ++DH + IVGY  +  I      YWIVKNSW  
Sbjct: 259 VSVALDAAGDAFKHYSSGIFTGPCG-TAIDHAVTIVGYGTEGGI-----DYWIVKNSWDT 312

Query: 316 DWGEQGYIYLRR---GKNTCGVSNFVS 339
            WGE+GY+ + R   G  TCG++   S
Sbjct: 313 TWGEEGYMRILRNVGGAGTCGIATMPS 339


>sp|P43156|CYSP_HEMSP THIOL PROTEASE SEN102 PRECURSOR
          Length = 360

 Score =  203 bits (510), Expect = 6e-52
 Identities = 125/304 (41%), Positives = 164/304 (53%), Gaps = 30/304 (9%)

Query: 43  EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTD 102
           +E   RF +FK N+  I E N       A  K  +NKF D+++ EF++ Y  +K      
Sbjct: 54  DEKNRRFNVFKENVKFIHEFNQ---KKDAPYKLALNKFGDMTNQEFRSKYAGSKIQHHRS 110

Query: 103 DLPVADYLDD---EFINSIPTA-FDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFIS 158
              +         E + S+P A  DWR +GAVT VK+QGQCGSCW+FST  +VEG + I 
Sbjct: 111 QRGIQKNTGSFMYENVGSLPAASIDWRAKGAVTGVKDQGQCGSCWAFSTIASVEGINQIK 170

Query: 159 QNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTA 218
             +LVSLSEQ LVDCD          + +EGCNGGL   A+ +I KN GI TE SYPY  
Sbjct: 171 TGELVSLSEQELVDCD---------TSYNEGCNGGLMDYAFEFIQKN-GITTEDSYPYAE 220

Query: 219 ETGTQCNFNSANIG-AKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVF 275
           + GT C  N  N     I     +P N        V+  P++++ +A    +QFY  GVF
Sbjct: 221 QDGT-CASNLLNSPVVSIDGHQDVPANNENALMQAVANQPISVSIEASGYGFQFYSEGVF 279

Query: 276 DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG----KNT 331
              C    LDHG+ IVGY A     R    YWIVKNSWG +WGE GYI ++RG    +  
Sbjct: 280 TGRCG-TELDHGVAIVGYGAT----RDGTKYWIVKNSWGEEWGESGYIRMQRGISDKRGK 334

Query: 332 CGVS 335
           CG++
Sbjct: 335 CGIA 338


>sp|P25777|ORYB_ORYSA ORYZAIN BETA CHAIN PRECURSOR
          Length = 471

 Score =  203 bits (510), Expect = 6e-52
 Identities = 115/303 (37%), Positives = 165/303 (53%), Gaps = 25/303 (8%)

Query: 44  EYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDD 103
           E+  RF +F  NL  ++  N  A +     + G+N+FADL+++EF+  +L  K A     
Sbjct: 69  EHERRFLVFWDNLKFVDAHNARA-DEGGGFRLGMNRFADLTNEEFRATFLGAKVA--ERS 125

Query: 104 LPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLV 163
               +    + +  +P + DWR +GAV PVKNQGQCGSCW+FS    VE  + +   +++
Sbjct: 126 RAAGERYRHDGVEELPESVDWREKGAVAPVKNQGQCGSCWAFSAVSTVESINQLVTGEMI 185

Query: 164 SLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQ 223
           +LSEQ LV+C             + GCNGGL  +A+++IIKNGGI TE  YPY A  G +
Sbjct: 186 TLSEQELVEC--------STNGQNSGCNGGLMADAFDFIIKNGGIDTEDDYPYKAVDG-K 236

Query: 224 CNFNSANIG-AKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCN 280
           C+ N  N     I  F  +P+N+       V+  P+++A +A   E+Q Y  GVF   C 
Sbjct: 237 CDINRENAKVVSIDGFEDVPQNDEKSLQKAVAHQPVSVAIEAGGREFQLYHSGVFSGRCG 296

Query: 281 PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT----CGVSN 336
             SLDHG++ VGY   N        YWIV+NSWG  WGE GY+ + R  N     CG++ 
Sbjct: 297 -TSLDHGVVAVGYGTDN-----GKDYWIVRNSWGPKWGESGYVRMERNINVTTGKCGIAM 350

Query: 337 FVS 339
             S
Sbjct: 351 MAS 353


>sp|Q10717|CYS2_MAIZE CYSTEINE PROTEINASE 2 PRECURSOR
          Length = 360

 Score =  201 bits (505), Expect = 2e-51
 Identities = 119/327 (36%), Positives = 175/327 (53%), Gaps = 36/327 (11%)

Query: 28  QFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSD 86
           +F  F  ++ K Y S  E  +RF IF  +L  +   N   ++++     G+N+FAD+S +
Sbjct: 58  RFARFAVRYGKSYESAAEVHKRFRIFSESLQLVRSTNRKGLSYR----LGINRFADMSWE 113

Query: 87  EFKNYYLN---NKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCW 143
           EF+   L    N  A  T      ++       ++P   DWR  G V+PVKNQG CGSCW
Sbjct: 114 EFRATRLGAAQNCSATLT-----GNHRMRAAAVALPETKDWREDGIVSPVKNQGHCGSCW 168

Query: 144 SFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYII 203
           +FSTTG +E  +  +  K +SLSEQ LVDC      +        GCNGGL   A+ YI 
Sbjct: 169 TFSTTGALEAAYTQATGKPISLSEQQLVDCGFAFNNF--------GCNGGLPSQAFEYIK 220

Query: 204 KNGGIQTESSYPYTAETGTQCNFNSANIGAKI---SNFTMIPKNETVMAGYIVSTGPLAI 260
            NGG+ TE SYPY    G  C F + N+G K+    N T+  ++E   A  +V   P+++
Sbjct: 221 YNGGLDTEESYPYQGVNGI-CKFKNENVGVKVLDSVNITLGAEDELKDAVGLVR--PVSV 277

Query: 261 AADAVE-WQFYIGGVF---DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGAD 316
           A + +  ++ Y  GV+        P  ++H +L VGY  ++      +PYW++KNSWGAD
Sbjct: 278 AFEVITGFRLYKSGVYTSDHCGTTPMDVNHAVLAVGYGVED-----GVPYWLIKNSWGAD 332

Query: 317 WGEQGYIYLRRGKNTCGVSNFVSTSII 343
           WG++GY  +  GKN CGV+   S  I+
Sbjct: 333 WGDEGYFKMEMGKNMCGVATCASYPIV 359


>sp|P00786|CATH_RAT CATHEPSIN H PRECURSOR (CATHEPSIN B3) (CATHEPSIN BA)
          Length = 333

 Score =  200 bits (504), Expect = 3e-51
 Identities = 121/324 (37%), Positives = 172/324 (52%), Gaps = 28/324 (8%)

Query: 25  EQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLS 84
           E+  F  +  +  K YS  EY  R ++F +N  KI+  N    NH    K G+N+F+D+S
Sbjct: 29  EKFHFTSWMKQHQKTYSSREYSHRLQVFANNWRKIQAHN--QRNHTF--KMGLNQFSDMS 84

Query: 85  SDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG-AVTPVKNQGQCGSCW 143
             E K+ YL ++          ++YL        P++ DWR +G  V+PVKNQG CGSCW
Sbjct: 85  FAEIKHKYLWSEPQ--NCSATKSNYLRGT--GPYPSSMDWRKKGNVVSPVKNQGACGSCW 140

Query: 144 SFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYII 203
           +FSTTG +E    I+  K+++L+EQ LVDC         +   + GC GGL   A+ YI+
Sbjct: 141 TFSTTGALESAVAIASGKMMTLAEQQLVDC--------AQNFNNHGCQGGLPSQAFEYIL 192

Query: 204 KNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN-ETVMAGYIVSTGPLAIAA 262
            N GI  E SYPY  + G QC FN     A + N   I  N E  M   +    P++ A 
Sbjct: 193 YNKGIMGEDSYPYIGKNG-QCKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAF 251

Query: 263 DAVE-WQFYIGGVFDI-PCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWG 318
           +  E +  Y  GV+    C+  P+ ++H +L VGY  +N +      YWIVKNSWG++WG
Sbjct: 252 EVTEDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYGEQNGLL-----YWIVKNSWGSNWG 306

Query: 319 EQGYIYLRRGKNTCGVSNFVSTSI 342
             GY  + RGKN CG++   S  I
Sbjct: 307 NNGYFLIERGKNMCGLAACASYPI 330


>sp|O10364|CATV_NPVOP VIRAL CATHEPSIN (V-CATH)
          Length = 324

 Score =  199 bits (500), Expect = 9e-51
 Identities = 118/316 (37%), Positives = 170/316 (53%), Gaps = 26/316 (8%)

Query: 29  FLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE 87
           F +F  KFNK YS E E L RF+IF+ NL +I   N     + +  ++ +NKF+DLS +E
Sbjct: 28  FEDFLHKFNKNYSSESEKLHRFKIFQHNLEEIINKN----QNDSTAQYEINKFSDLSKEE 83

Query: 88  FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFST 147
             + Y        T +      LD       P  FDWR    VT VKNQG CG+CW+F+T
Sbjct: 84  AISKYTGLSLPHQTQNFCEVVILDRPPDRG-PLEFDWRQFNKVTSVKNQGVCGACWAFAT 142

Query: 148 TGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGG 207
            G++E Q  I  N+L++LSEQ  +DCD            + GC+GGL   A+   ++ GG
Sbjct: 143 LGSLESQFAIKYNRLINLSEQQFIDCDR----------VNAGCDGGLLHTAFESAMEMGG 192

Query: 208 IQTESSYPYTAETGTQCNFNSAN--IGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAV 265
           +Q ES YPY    G QC  N     +G + S    I   E  +   + + GP+ +A DA 
Sbjct: 193 VQMESDYPYETANG-QCRINPNRFVVGVR-SCRRYIVMFEEKLKDLLRAVGPIPVAIDAS 250

Query: 266 EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYL 325
           +   Y  G+    C  + L+H +L+VGY+ +N     N+PYWI+KN+WG DWGE GY  +
Sbjct: 251 DIVNYRRGIMR-QCANHGLNHAVLLVGYAVEN-----NIPYWILKNTWGTDWGEDGYFRV 304

Query: 326 RRGKNTCGVSNFVSTS 341
           ++  N CG+ N + +S
Sbjct: 305 QQNINACGIRNELVSS 320


>sp|P43297|RD21_ARATH CYSTEINE PROTEINASE RD21A PRECURSOR
          Length = 462

 Score =  198 bits (498), Expect = 2e-50
 Identities = 119/313 (38%), Positives = 165/313 (52%), Gaps = 35/313 (11%)

Query: 35  KFNKKYSHEEYLE---RFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNY 91
           K  K  S    +E   RFEIFK NL  ++E N   ++++     G+ +FADL++DE+++ 
Sbjct: 56  KHGKAQSQNSLVEKDRRFEIFKDNLRFVDEHNEKNLSYR----LGLTRFADLTNDEYRSK 111

Query: 92  YLN---NKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTT 148
           YL     K+      L     + DE    +P + DWR +GAV  VK+QG CGSCW+FST 
Sbjct: 112 YLGAKMEKKGERRTSLRYEARVGDE----LPESIDWRKKGAVAEVKDQGGCGSCWAFSTI 167

Query: 149 GNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGI 208
           G VEG + I    L++LSEQ LVDCD          + +EGCNGGL   A+ +IIKNGGI
Sbjct: 168 GAVEGINQIVTGDLITLSEQELVDCD---------TSYNEGCNGGLMDYAFEFIIKNGGI 218

Query: 209 QTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VE 266
            T+  YPY    GT            I ++  +P          V+  P++IA +A    
Sbjct: 219 DTDKDYPYKGVDGTCDQIRKNAKVVTIDSYEDVPTYSEESLKKAVAHQPISIAIEAGGRA 278

Query: 267 WQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLR 326
           +Q Y  G+FD  C    LDHG++ VGY  +N        YWIV+NSWG  WGE GY+ + 
Sbjct: 279 FQLYDSGIFDGSCG-TQLDHGVVAVGYGTEN-----GKDYWIVRNSWGKSWGESGYLRMA 332

Query: 327 R----GKNTCGVS 335
           R        CG++
Sbjct: 333 RNIASSSGKCGIA 345


>sp|P15242|TES1_RAT TESTIN 1/2 PRECURSOR (CMB-22/CMB-23)
          Length = 333

 Score =  198 bits (497), Expect = 2e-50
 Identities = 115/348 (33%), Positives = 184/348 (52%), Gaps = 22/348 (6%)

Query: 3   VILLFVLAVFTVFVSSRGIPPEEQS--QFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60
           +I +  LA+  + V S    P+     ++ E++ K  K Y+  E   +  +++ N   IE
Sbjct: 1   MIAVLFLAILCLEVDSTAPTPDPSLDVEWNEWRTKHGKTYNMNEERLKRAVWEKNFKMIE 60

Query: 61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLN-NKEAIFTDDLPVADYLDDEFINSIP 119
             N   +  + D    +N F DL++ EF        ++ I    +    + D +F+  +P
Sbjct: 61  LHNWEYLEGRHDFTMAMNAFGDLTNIEFVKMMTGFQRQKIKKTHI----FQDHQFLY-VP 115

Query: 120 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 179
              DWR  G VTPVKNQG C S W+FS TG++EGQ F    +L+ LSEQNL+DC    + 
Sbjct: 116 KRVDWRQLGYVTPVKNQGHCASSWAFSATGSLEGQMFRKTERLIPLSEQNLLDCMGSNVT 175

Query: 180 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFT 239
           +        GC+GG    A+ Y+  NGG+ TE SYPY  + G +C +++ N  A + +F 
Sbjct: 176 H--------GCSGGFMQYAFQYVKDNGGLATEESYPYRGQ-GRECRYHAENSAANVRDFV 226

Query: 240 MIPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIP-CNPNSLDHGILIVGYSAK 296
            IP +E  +   +   GP+++A DA    +QFY  G++  P C    L+H +L+VGY  +
Sbjct: 227 QIPGSEEALMKAVAKVGPISVAVDASHGSFQFYGSGIYYEPQCKRVHLNHAVLVVGYGFE 286

Query: 297 NTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG-KNTCGVSNFVSTSII 343
                 N  +W+VKNSWG +WG +GY+ L +   N CG++ + +  I+
Sbjct: 287 GEESDGN-SFWLVKNSWGEEWGMKGYMKLAKDWSNHCGIATYSTYPIV 333


>sp|P25776|ORYA_ORYSA ORYZAIN ALPHA CHAIN PRECURSOR
          Length = 458

 Score =  198 bits (497), Expect = 2e-50
 Identities = 122/348 (35%), Positives = 182/348 (52%), Gaps = 37/348 (10%)

Query: 3   VILLFVLAVFTVFVSSRGIPPEEQSQ--FLEFQDKFNKKYSHE-EYLERFEIFKSNLGKI 59
           ++LL  LA   + + S G   EE+++  + E++ +  K Y+   E   R+  F+ NL  I
Sbjct: 12  LLLLLSLAAADMSIVSYGERSEEEARRLYAEWKAEHGKSYNAVGEEERRYAAFRDNLRYI 71

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLN-----NKEAIFTDDLPVADYLDDEF 114
           +E N  A       + G+N+FADL+++E+++ YL       +E   +D    AD      
Sbjct: 72  DEHNAAADAGVHSFRLGLNRFADLTNEEYRDTYLGLRNKPRRERKVSDRYLAADN----- 126

Query: 115 INSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCD 174
             ++P + DWRT+GAV  +K+QG CGSCW+FS    VE  + I    L+SLSEQ LVDCD
Sbjct: 127 -EALPESVDWRTKGAVAEIKDQGGCGSCWAFSAIAAVEDINQIVTGDLISLSEQELVDCD 185

Query: 175 HECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG-A 233
                     + +EGCNGGL   A+++II NGGI TE  YPY  +   +C+ N  N    
Sbjct: 186 ---------TSYNEGCNGGLMDYAFDFIINNGGIDTEDDYPYKGK-DERCDVNRKNAKVV 235

Query: 234 KISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNPNSLDHGILIV 291
            I ++  +  N        V   P+++A +A    +Q Y  G+F   C   +LDHG+  V
Sbjct: 236 TIDSYEDVTPNSETSLQKAVRNQPVSVAIEAGGRAFQLYSSGIFTGKCG-TALDHGVAAV 294

Query: 292 GYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRR----GKNTCGVS 335
           GY  +N        YWIV+NSWG  WGE GY+ + R        CG++
Sbjct: 295 GYGTEN-----GKDYWIVRNSWGKSWGESGYVRMERNIKASSGKCGIA 337


>sp|P14080|PAP2_CARPA CHYMOPAPAIN PRECURSOR (PAPAYA PROTEINASE II) (PPII)
          Length = 352

 Score =  194 bits (488), Expect = 2e-49
 Identities = 125/315 (39%), Positives = 167/315 (52%), Gaps = 43/315 (13%)

Query: 35  KFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKF--GVNKFADLSSDEFKNY 91
           K NK Y S +E + RFEIF+ NL  I+E N      K +  +  G+N FADLS+DEFK  
Sbjct: 54  KHNKIYESIDEKIYRFEIFRDNLMYIDETN------KKNNSYWLGLNGFADLSNDEFKKK 107

Query: 92  YLNNKEAIFTDDLPVADYLDDE-----FINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFS 146
           Y+        +D    ++ D+E      + + P + DWR +GAVTPVKNQG CGSCW+FS
Sbjct: 108 YVG----FVAEDFTGLEHFDNEDFTYKHVTNYPQSIDWRAKGAVTPVKNQGACGSCWAFS 163

Query: 147 TTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNG 206
           T   VEG + I    L+ LSEQ LVDCD              GC GG Q  +  Y + N 
Sbjct: 164 TIATVEGINKIVTGNLLELSEQELVDCDKH----------SYGCKGGYQTTSLQY-VANN 212

Query: 207 GIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN-ETVMAGYIVSTGPLAIAADA- 264
           G+ T   YPY A+       +      KI+ +  +P N ET   G + +  PL++  +A 
Sbjct: 213 GVHTSKVYPYQAKQYKCRATDKPGPKVKITGYKRVPSNCETSFLGALANQ-PLSVLVEAG 271

Query: 265 -VEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYI 323
              +Q Y  GVFD PC    LDH +  VGY   +    KN  Y I+KNSWG +WGE+GY+
Sbjct: 272 GKPFQLYKSGVFDGPCG-TKLDHAVTAVGYGTSD---GKN--YIIIKNSWGPNWGEKGYM 325

Query: 324 YLRR----GKNTCGV 334
            L+R     + TCGV
Sbjct: 326 RLKRQSGNSQGTCGV 340


>sp|P43235|CATK_HUMAN CATHEPSIN K PRECURSOR (CATHEPSIN O) (CATHEPSIN X) (CATHEPSIN O2)
          Length = 329

 Score =  194 bits (488), Expect = 2e-49
 Identities = 121/339 (35%), Positives = 180/339 (52%), Gaps = 25/339 (7%)

Query: 9   LAVFTVFVSSRGIPPEE--QSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLI 65
           L V  + V S  + PEE   + +  ++    K+Y+++ + + R  I++ NL  I   NL 
Sbjct: 4   LKVLLLPVVSFALYPEEILDTHWELWKKTHRKQYNNKVDEISRRLIWEKNLKYISIHNLE 63

Query: 66  AINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWR 125
           A       +  +N   D++S+E        K  +         Y+  E+    P + D+R
Sbjct: 64  ASLGVHTYELAMNHLGDMTSEEVVQKMTGLKVPLSHSRSNDTLYIP-EWEGRAPDSVDYR 122

Query: 126 TRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEA 185
            +G VTPVKNQGQCGSCW+FS+ G +EGQ      KL++LS QNLVDC  E         
Sbjct: 123 KKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSE--------- 173

Query: 186 CDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPK-N 244
            ++GC GG   NA+ Y+ KN GI +E +YPY  +    C +N     AK   +  IP+ N
Sbjct: 174 -NDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQE-ESCMYNPTGKAAKCRGYREIPEGN 231

Query: 245 ETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIVGYSAKNTIFR 301
           E  +   +   GP+++A DA    +QFY  GV +D  CN ++L+H +L VGY       +
Sbjct: 232 EKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYG-----IQ 286

Query: 302 KNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVS 339
           K   +WI+KNSWG +WG +GYI + R K N CG++N  S
Sbjct: 287 KGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLAS 325


>sp|P25778|ORYC_ORYSA ORYZAIN GAMMA CHAIN PRECURSOR
          Length = 362

 Score =  194 bits (487), Expect = 3e-49
 Identities = 114/327 (34%), Positives = 171/327 (51%), Gaps = 37/327 (11%)

Query: 28  QFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSD 86
           +F  F  +  K+Y    E   RF IF  +L  +   N   + ++     G+N+FAD+S +
Sbjct: 61  RFARFAVRHGKRYGDAAEVQRRFRIFSESLELVRSTNRRGLPYR----LGINRFADMSWE 116

Query: 87  EFKNYYLN---NKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCW 143
           EF+   L    N  A    +  + D        ++P   DWR  G V+PVK+QG CGSCW
Sbjct: 117 EFQASRLGAAQNCSATLAGNHRMRD------APALPETKDWREDGIVSPVKDQGHCGSCW 170

Query: 144 SFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYII 203
            FSTTG++E ++  +    VSLSEQ L DC      +        GC+GGL   A+ YI 
Sbjct: 171 PFSTTGSLEARYTQATGPPVSLSEQQLADCATRYNNF--------GCSGGLPSQAFEYIK 222

Query: 204 KNGGIQTESSYPYTAETGTQCNFNSANIGAKI---SNFTMIPKNETVMAGYIVSTGPLAI 260
            NGG+ TE +YPYT   G  C++   N G K+    N T++ ++E   A  +V   P+++
Sbjct: 223 YNGGLDTEEAYPYTGVNGI-CHYKPENAGVKVLDSVNITLVAEDELKNAVGLVR--PVSV 279

Query: 261 AADAVE-WQFYIGGVF---DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGAD 316
           A   +  ++ Y  GV+       +P  ++H +L VGY  +N      +PYW++KNSWGAD
Sbjct: 280 AFQVINGFRMYKSGVYTSDHCGTSPMDVNHAVLAVGYGVEN-----GVPYWLIKNSWGAD 334

Query: 317 WGEQGYIYLRRGKNTCGVSNFVSTSII 343
           WG+ GY  +  GKN CG++   S  I+
Sbjct: 335 WGDNGYFTMEMGKNMCGIATCASYPIV 361


>sp|P25251|CYS4_BRANA CYSTEINE PROTEINASE COT44 PRECURSOR
          Length = 328

 Score =  194 bits (487), Expect = 3e-49
 Identities = 115/300 (38%), Positives = 160/300 (53%), Gaps = 29/300 (9%)

Query: 47  ERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNK----EAIFTD 102
           ERF IFK NL  I+  N    N  A  K G+  FA+L++DE+++ YL  +      I   
Sbjct: 27  ERFNIFKDNLRFIDLHN--ENNKNATYKLGLTIFANLTNDEYRSLYLGARTEPVRRITKA 84

Query: 103 DLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKL 162
                 Y     ++ +P   DWR +GAV  +K+QG CGSCW+FST   VEG + I   +L
Sbjct: 85  KNVNMKYSAAVNVDEVPVTVDWRQKGAVNAIKDQGTCGSCWAFSTAAAVEGINKIVTGEL 144

Query: 163 VSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGT 222
           VSLSEQ LVDCD         ++ ++GCNGGL   A+ +I+KNGG+ TE  YPY    G 
Sbjct: 145 VSLSEQELVDCD---------KSYNQGCNGGLMDYAFQFIMKNGGLNTEKDYPYHGTNG- 194

Query: 223 QCNFNSANIG-AKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPC 279
           +CN    N     I  +  +P  +       VS  P+++A DA    +Q Y  G+F   C
Sbjct: 195 KCNSLLKNSRVVTIDGYEDVPSKDETALKRAVSYQPVSVAIDAGGRAFQHYQSGIFTGKC 254

Query: 280 NPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG----KNTCGVS 335
             N +DH ++ VGY ++N      + YWIV+NSWG  WGE GYI + R        CG++
Sbjct: 255 GTN-MDHAVVAVGYGSEN-----GVDYWIVRNSWGTRWGEDGYIRMERNVASKSGKCGIA 308


>sp|P09668|CATH_HUMAN CATHEPSIN H PRECURSOR
          Length = 335

 Score =  192 bits (482), Expect = 1e-48
 Identities = 122/326 (37%), Positives = 168/326 (51%), Gaps = 32/326 (9%)

Query: 25  EQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLS 84
           E+  F  +  K  K YS EEY  R + F SN  KI   N    N     K  +N+F+D+S
Sbjct: 31  EKFHFKSWMSKHRKTYSTEEYHHRLQTFASNWRKINAHN----NGNHTFKMALNQFSDMS 86

Query: 85  SDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGA-VTPVKNQGQCGSCW 143
             E K+ YL ++          ++YL        P + DWR +G  V+PVKNQG CGSCW
Sbjct: 87  FAEIKHKYLWSEPQ--NCSATKSNYLRGT--GPYPPSVDWRKKGNFVSPVKNQGACGSCW 142

Query: 144 SFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYII 203
           +FSTTG +E    I+  K++SL+EQ LVDC  +   Y        GC GGL   A+ YI+
Sbjct: 143 TFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNY--------GCQGGLPSQAFEYIL 194

Query: 204 KNGGIQTESSYPYTAETGTQCNFNSAN-IG--AKISNFTMIPKNETVMAGYIVSTGPLAI 260
            N GI  E +YPY  + G  C F     IG    ++N T+   +E  M   +    P++ 
Sbjct: 195 YNKGIMGEDTYPYQGKDG-YCKFQPGKAIGFVKDVANITIY--DEEAMVEAVALYNPVSF 251

Query: 261 AADAV-EWQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGAD 316
           A +   ++  Y  G++    C+  P+ ++H +L VGY  KN I     PYWIVKNSWG  
Sbjct: 252 AFEVTQDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNGI-----PYWIVKNSWGPQ 306

Query: 317 WGEQGYIYLRRGKNTCGVSNFVSTSI 342
           WG  GY  + RGKN CG++   S  I
Sbjct: 307 WGMNGYFLIERGKNMCGLAACASYPI 332


>sp|O46427|CATH_PIG CATHEPSIN H PRECURSOR
          Length = 335

 Score =  191 bits (481), Expect = 2e-48
 Identities = 122/332 (36%), Positives = 171/332 (50%), Gaps = 28/332 (8%)

Query: 17  SSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFG 76
           S+  +   E+  F  +  +  KKYS EEY  R ++F SN  KI   N  A NH    K G
Sbjct: 23  SNLAVSSFEKLHFKSWMVQHQKKYSLEEYHHRLQVFVSNWRKINAHN--AGNHTF--KLG 78

Query: 77  VNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGA-VTPVKN 135
           +N+F+D+S DE ++ YL ++           +YL        P + DWR +G  V+PVKN
Sbjct: 79  LNQFSDMSFDEIRHKYLWSEPQ--NCSATKGNYLRGT--GPYPPSMDWRKKGNFVSPVKN 134

Query: 136 QGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQ 195
           QG CGSCW+FSTTG +E    I+  K++SL+EQ LVDC         +   + GC GGL 
Sbjct: 135 QGSCGSCWTFSTTGALESAVAIATGKMLSLAEQQLVDC--------AQNFNNHGCQGGLP 186

Query: 196 PNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN-ETVMAGYIVS 254
             A+ YI  N GI  E +YPY  +    C F      A + +   I  N E  M   +  
Sbjct: 187 SQAFEYIRYNKGIMGEDTYPYKGQ-DDHCKFQPDKAIAFVKDVANITMNDEEAMVEAVAL 245

Query: 255 TGPLAIAADAV-EWQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVK 310
             P++ A +   ++  Y  G++    C+  P+ ++H +L VGY  +N I     PYWIVK
Sbjct: 246 YNPVSFAFEVTNDFLMYRKGIYSSTSCHKTPDKVNHAVLAVGYGEENGI-----PYWIVK 300

Query: 311 NSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 342
           NSWG  WG  GY  + RGKN CG++   S  I
Sbjct: 301 NSWGPQWGMNGYFLIERGKNMCGLAACASYPI 332


>sp|P05167|ALEU_HORVU THIOL PROTEASE ALEURAIN PRECURSOR
          Length = 362

 Score =  191 bits (481), Expect = 2e-48
 Identities = 111/322 (34%), Positives = 167/322 (51%), Gaps = 27/322 (8%)

Query: 28  QFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSD 86
           +F  F  ++ K Y S  E   RF IF  +L ++   N   + ++     G+N+F+D+S +
Sbjct: 60  RFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYR----LGINRFSDMSWE 115

Query: 87  EFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFS 146
           EF+   L    A  T    +A         ++P   DWR  G V+PVKNQ  CGSCW+FS
Sbjct: 116 EFQATRLG---AAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFS 172

Query: 147 TTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNG 206
           TTG +E  +  +  K +SLSEQ LVDC      +        GCNGGL   A+ YI  NG
Sbjct: 173 TTGALEAAYTQATGKNISLSEQQLVDCAGGFNNF--------GCNGGLPSQAFEYIKYNG 224

Query: 207 GIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN-ETVMAGYIVSTGPLAIAADAV 265
           GI TE SYPY    G  C++ + N   ++ +   I  N E  +   +    P+++A   +
Sbjct: 225 GIDTEESYPYKGVNGV-CHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVI 283

Query: 266 E-WQFYIGGVF---DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQG 321
           + ++ Y  GV+        P+ ++H +L VGY  +N      +PYW++KNSWGADWG+ G
Sbjct: 284 DGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVEN-----GVPYWLIKNSWGADWGDNG 338

Query: 322 YIYLRRGKNTCGVSNFVSTSII 343
           Y  +  GKN C ++   S  ++
Sbjct: 339 YFKMEMGKNMCAIATCASYPVV 360


>sp|P43236|CATK_RABIT CATHEPSIN K PRECURSOR (OC-2 PROTEIN)
          Length = 329

 Score =  191 bits (480), Expect = 2e-48
 Identities = 119/339 (35%), Positives = 179/339 (52%), Gaps = 25/339 (7%)

Query: 9   LAVFTVFVSSRGIPPEE--QSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLI 65
           L V  + V S  + PEE   +Q+  ++  ++K+Y+ + + + R  I++ NL  I   NL 
Sbjct: 4   LKVLLLPVVSFALHPEEILDTQWELWKKTYSKQYNSKVDEISRRLIWEKNLKHISIHNLE 63

Query: 66  AINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWR 125
           A       +  +N   D++S+E        K            Y+ D +    P + D+R
Sbjct: 64  ASLGVHTYELAMNHLGDMTSEEVVQKMTGLKVPPSRSHSNDTLYIPD-WEGRTPDSIDYR 122

Query: 126 TRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEA 185
            +G VTPVKNQGQCGSCW+FS+ G +EGQ      KL++LS QNLVDC  E         
Sbjct: 123 KKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSE--------- 173

Query: 186 CDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPK-N 244
            + GC GG   NA+ Y+ +N GI +E +YPY  +    C +N     AK   +  IP+ N
Sbjct: 174 -NYGCGGGYMTNAFQYVQRNRGIDSEDAYPYVGQ-DESCMYNPTGKAAKCRGYREIPEGN 231

Query: 245 ETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIVGYSAKNTIFR 301
           E  +   +   GP+++A DA    +QFY  GV +D  C+ ++++H +L VGY       +
Sbjct: 232 EKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDENCSSDNVNHAVLAVGYG-----IQ 286

Query: 302 KNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVS 339
           K   +WI+KNSWG  WG +GYI + R K N CG++N  S
Sbjct: 287 KGNKHWIIKNSWGESWGNKGYILMARNKNNACGIANLAS 325


>sp|P10056|PAP3_CARPA CARICAIN PRECURSOR (PAPAYA PROTEINASE OMEGA) (PAPAYA PROTEINASE
           III) (PPIII) (PAPAYA PEPTIDASE A)
          Length = 348

 Score =  190 bits (479), Expect = 3e-48
 Identities = 122/319 (38%), Positives = 166/319 (51%), Gaps = 46/319 (14%)

Query: 37  NKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKF--GVNKFADLSSDEFKNYYL 93
           NK Y + +E L RFEIFK NL  I+E N      K +  +  G+N+FADLS+DEF   Y+
Sbjct: 56  NKFYENVDEKLYRFEIFKDNLNYIDETN------KKNNSYWLGLNEFADLSNDEFNEKYV 109

Query: 94  NNKEAIFTDDLPVADYLDDEFIN----SIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTG 149
            +       D  +    D+EFIN    ++P   DWR +GAVTPV++QG CGSCW+FS   
Sbjct: 110 GS-----LIDATIEQSYDEEFINEDTVNLPENVDWRKKGAVTPVRHQGSCGSCWAFSAVA 164

Query: 150 NVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQ 209
            VEG + I   KLV LSEQ LVDC+              GC GG  P A  Y+ KN GI 
Sbjct: 165 TVEGINKIRTGKLVELSEQELVDCERR----------SHGCKGGYPPYALEYVAKN-GIH 213

Query: 210 TESSYPYTAETGTQCNFNSANIGAKISNFTMI----PKNETVMAGYIVSTGPLAIAADAV 265
             S YPY A+ GT     +  +G  I   + +    P NE  +   I    P+++  ++ 
Sbjct: 214 LRSKYPYKAKQGT---CRAKQVGGPIVKTSGVGRVQPNNEGNLLNAIAKQ-PVSVVVESK 269

Query: 266 --EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYI 323
              +Q Y GG+F+ PC    +DH +  VGY            Y ++KNSWG  WGE+GYI
Sbjct: 270 GRPFQLYKGGIFEGPCG-TKVDHAVTAVGYGKSG-----GKGYILIKNSWGTAWGEKGYI 323

Query: 324 YLRRGK-NTCGVSNFVSTS 341
            ++R   N+ GV     +S
Sbjct: 324 RIKRAPGNSPGVCGLYKSS 342


>sp|P49935|CATH_MOUSE CATHEPSIN H PRECURSOR (CATHEPSIN B3) (CATHEPSIN BA)
          Length = 333

 Score =  189 bits (476), Expect = 6e-48
 Identities = 117/324 (36%), Positives = 167/324 (51%), Gaps = 28/324 (8%)

Query: 25  EQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLS 84
           E+  F  +  +  K YS  EY  R ++F +N  KI+  N    NH    K  +N+F+D+S
Sbjct: 29  EKFHFKSWMKQHQKTYSSVEYNHRLQMFANNWRKIQAHN--QRNHTF--KMALNQFSDMS 84

Query: 85  SDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG-AVTPVKNQGQCGSCW 143
             E K+ +L ++          ++YL        P++ DWR +G  V+PVKNQG C SCW
Sbjct: 85  FAEIKHKFLWSEPQ--NCSATKSNYLRGT--GPYPSSMDWRKKGNVVSPVKNQGACASCW 140

Query: 144 SFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYII 203
           +FSTTG +E    I+  K++SL+EQ LVDC         +   + GC GGL   A+ YI+
Sbjct: 141 TFSTTGALESAVAIASGKMLSLAEQQLVDC--------AQAFNNHGCKGGLPSQAFEYIL 192

Query: 204 KNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN-ETVMAGYIVSTGPLAIAA 262
            N GI  E SYPY  +  + C FN     A + N   I  N E  M   +    P++ A 
Sbjct: 193 YNKGIMEEDSYPYIGK-DSSCRFNPQKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAF 251

Query: 263 DAVE-WQFYIGGVFDIPC---NPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWG 318
           +  E +  Y  GV+        P+ ++H +L VGY  +N +      YWIVKNSWG+ WG
Sbjct: 252 EVTEDFLMYKSGVYSSKSCHKTPDKVNHAVLAVGYGEQNGLL-----YWIVKNSWGSQWG 306

Query: 319 EQGYIYLRRGKNTCGVSNFVSTSI 342
           E GY  + RGKN CG++   S  I
Sbjct: 307 ENGYFLIERGKNMCGLAACASYPI 330


>sp|P55097|CATK_MOUSE CATHEPSIN K PRECURSOR
          Length = 329

 Score =  188 bits (473), Expect = 1e-47
 Identities = 117/344 (34%), Positives = 181/344 (52%), Gaps = 35/344 (10%)

Query: 9   LAVFTVFVSSRGIPPEEQ--SQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLI 65
           L V  + + S  + PEE   +Q+  ++    K+Y+ + + + R  I++ NL +I   NL 
Sbjct: 4   LKVLLLPMVSFALSPEEMLDTQWELWKKTHQKQYNSKVDEISRRLIWEKNLKQISAHNLE 63

Query: 66  AINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDD-----EFINSIPT 120
           A       +  +N   D++S+E        +        P   Y +D     E+   +P 
Sbjct: 64  ASLGVHTYELAMNHLGDMTSEEVVQKMTGLRIP------PSRSYSNDTLYTPEWEGRVPD 117

Query: 121 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY 180
           + D+R +G VTPVKNQGQCGSCW+FS+ G +EGQ      KL++LS QNLVDC  E    
Sbjct: 118 SIDYRKKGYVTPVKNQGQCGSCWAFSSAGALEGQLKKKTGKLLALSPQNLVDCVTE---- 173

Query: 181 EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTM 240
                 + GC GG    A+ Y+ +NGGI +E ++PY  +    C +N+    AK   +  
Sbjct: 174 ------NYGCGGGYMTTAFQYVQQNGGIDSEDAFPYVGQ-DESCMYNATAKAAKCRGYRE 226

Query: 241 IP-KNETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIVGYSAK 296
           IP  NE  +   +   GP++++ DA    +QFY  GV +D  C+ ++++H +L+VGY   
Sbjct: 227 IPVGNEKALKRAVARVGPISVSIDASLASFQFYSRGVYYDENCDRDNVNHAVLVVGYGT- 285

Query: 297 NTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVS 339
               +K   +WI+KNSWG  WG +GY  L R K N CG++N  S
Sbjct: 286 ----QKGSKHWIIKNSWGESWGNKGYALLARNKNNACGITNMAS 325


>sp|P56203|CATW_MOUSE CATHEPSIN W PRECURSOR (LYMPHOPAIN)
          Length = 371

 Score =  185 bits (466), Expect = 9e-47
 Identities = 110/338 (32%), Positives = 164/338 (47%), Gaps = 32/338 (9%)

Query: 22  PPEEQSQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKF 80
           P E +  F  FQ +FN+ Y +  EY  R  IF  NL + + L    +      +FG   F
Sbjct: 33  PLELKEVFKLFQIRFNRSYWNPAEYTRRLSIFAHNLAQAQRLQQEDLG---TAEFGETPF 89

Query: 81  ADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWR-TRGAVTPVKNQGQC 139
           +DL+ +EF   Y   +    T ++       + +  S+P   DWR  +  ++ VKNQG C
Sbjct: 90  SDLTEEEFGQLYGQERSPERTPNM-TKKVESNTWGESVPRTCDWRKAKNIISSVKNQGSC 148

Query: 140 GSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAY 199
             CW+ +   N++    I   + V +S Q L+DC          E C  GCNGG   +AY
Sbjct: 149 KCCWAMAAADNIQALWRIKHQQFVDVSVQELLDC----------ERCGNGCNGGFVWDAY 198

Query: 200 NYIIKNGGIQTESSYPYTAETGT-QCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPL 258
             ++ N G+ +E  YP+  +    +C        A I +FTM+  NE  +A Y+   GP+
Sbjct: 199 LTVLNNSGLASEKDYPFQGDRKPHRCLAKKYKKVAWIQDFTMLSNNEQAIAHYLAVHGPI 258

Query: 259 AIAADAVEWQFYIGGVFDIP---CNPNSLDHGILIVGYSAKN------TIF------RKN 303
            +  +    Q Y  GV       C+P  +DH +L+VG+  K       T+       R +
Sbjct: 259 TVTINMKLLQHYQKGVIKATPSSCDPRQVDHSVLLVGFGKKKEGMQTGTVLSHSRKRRHS 318

Query: 304 MPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTS 341
            PYWI+KNSWGA WGE+GY  L RG NTCGV+ +  T+
Sbjct: 319 SPYWILKNSWGAHWGEKGYFRLYRGNNTCGVTKYPFTA 356


>sp|P25250|CYS2_HORVU CYSTEINE PROTEINASE EP-B 2 PRECURSOR
          Length = 373

 Score =  184 bits (463), Expect = 2e-46
 Identities = 123/345 (35%), Positives = 172/345 (49%), Gaps = 40/345 (11%)

Query: 8   VLAVFTVFVSSRGIPPEEQSQFLE---------FQDKFNKKYSHEEYLERFEIFKSNLGK 58
           VLAV  V + S  IP E++    E         +Q     +  H E   RF  FKSN   
Sbjct: 17  VLAVAAVELCS-AIPMEDKDLESEEALWDLYERWQSAHRVRRHHAEKHRRFGTFKSNAHF 75

Query: 59  IEELNLIAINHKADTKFGV--NKFADLSSDEFKNYYLNNKEAIFTDDLP-VADYLDDEF- 114
           I      + N + D  + +  N+F D+   EF+  ++ +         P V  ++     
Sbjct: 76  IH-----SHNKRGDHPYRLHLNRFGDMDQAEFRATFVGDLRRDTPSKPPSVPGFMYAALN 130

Query: 115 INSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCD 174
           ++ +P + DWR +GAVT VK+QG+CGSCW+FST  +VEG + I    LVSLSEQ L+DCD
Sbjct: 131 VSDLPPSVDWRQKGAVTGVKDQGKCGSCWAFSTVVSVEGINAIRTGSLVSLSEQELIDCD 190

Query: 175 HECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNF----NSAN 230
                     A ++GC GGL  NA+ YI  NGG+ TE++YPY A  GT CN      ++ 
Sbjct: 191 ---------TADNDGCQGGLMDNAFEYIKNNGGLITEAAYPYRAARGT-CNVARAAQNSP 240

Query: 231 IGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNPNSLDHGI 288
           +   I     +P N        V+  P+++A +A    + FY  GVF   C    LDHG+
Sbjct: 241 VVVHIDGHQDVPANSEEDLARAVANQPVSVAVEASGKAFMFYSEGVFTGECG-TELDHGV 299

Query: 289 LIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCG 333
            +VGY     +      YW VKNSWG  WGEQGYI + +     G
Sbjct: 300 AVVGYG----VAEDGKAYWTVKNSWGPSWGEQGYIRVEKDSGASG 340


>sp|P25249|CYS1_HORVU CYSTEINE PROTEINASE EP-B 1 PRECURSOR
          Length = 371

 Score =  184 bits (462), Expect = 3e-46
 Identities = 124/349 (35%), Positives = 171/349 (48%), Gaps = 48/349 (13%)

Query: 8   VLAVFTVFVSSRGIPPEEQSQFLE---------FQDKFNKKYSHEEYLERFEIFKSNLGK 58
           VLAV  V + S  IP E++    E         +Q     +  H E   RF  FKSN   
Sbjct: 17  VLAVAAVELCS-AIPMEDKDLESEEALWDLYERWQSAHRVRRHHAEKHRRFGTFKSNAHF 75

Query: 59  IEELNLIAINHKADTKFGV--NKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEF-- 114
           I      + N + D  + +  N+F D+   EF+  ++ +       D P        F  
Sbjct: 76  IH-----SHNKRGDHPYRLHLNRFGDMDQAEFRATFVGDLRR----DTPAKPPSVPGFMY 126

Query: 115 ----INSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNL 170
               ++ +P + DWR +GAVT VK+QG+CGSCW+FST  +VEG + I    LVSLSEQ L
Sbjct: 127 AALNVSDLPPSVDWRQKGAVTGVKDQGKCGSCWAFSTVVSVEGINAIRTGSLVSLSEQEL 186

Query: 171 VDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNF---- 226
           +DCD          A ++GC GGL  NA+ YI  NGG+ TE++YPY A  GT CN     
Sbjct: 187 IDCD---------TADNDGCQGGLMDNAFEYIKNNGGLITEAAYPYRAARGT-CNVARAA 236

Query: 227 NSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNPNSL 284
            ++ +   I     +P N        V+  P+++A +A    + FY  GVF   C    L
Sbjct: 237 QNSPVVVHIDGHQDVPANSEEDLARAVANQPVSVAVEASGKAFMFYSEGVFTGDCG-TEL 295

Query: 285 DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCG 333
           DHG+ +VGY     +      YW VKNSWG  WGEQGYI + +     G
Sbjct: 296 DHGVAVVGYG----VAEDGKAYWTVKNSWGPSWGEQGYIRVEKDSGASG 340


>sp|P05994|PAP4_CARPA PAPAYA PROTEINASE IV PRECURSOR (PPIV) (PAPAYA PEPTIDASE B) (GLYCYL
           ENDOPEPTIDASE)
          Length = 348

 Score =  183 bits (461), Expect = 3e-46
 Identities = 112/309 (36%), Positives = 164/309 (52%), Gaps = 33/309 (10%)

Query: 35  KFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYL 93
           K NK Y + +E L RFEIFK NL  I+E N +   +      G+N+F+DLS+DEFK  Y+
Sbjct: 54  KHNKNYKNVDEKLYRFEIFKDNLKYIDERNKMINGYW----LGLNEFSDLSNDEFKEKYV 109

Query: 94  NNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEG 153
            +    +T+     ++++++ ++ +P + DWR +GAVTPVK+QG C SCW+FST   VEG
Sbjct: 110 GSLPEDYTNQPYDEEFVNEDIVD-LPESVDWRAKGAVTPVKHQGYCESCWAFSTVATVEG 168

Query: 154 QHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESS 213
            + I    LV LSEQ LVDCD +            GCN G Q  +  Y+ +N GI   + 
Sbjct: 169 INKIKTGNLVELSEQELVDCDKQ----------SYGCNRGYQSTSLQYVAQN-GIHLRAK 217

Query: 214 YPYTAETGTQCNFNSANIGAKI--SNFTMIPKNETVMAGYIVSTGPLAIAADAV--EWQF 269
           YPY A+  T C  N    G K+  +    +  N        ++  P+++  ++   ++Q 
Sbjct: 218 YPYIAKQQT-CRANQVG-GPKVKTNGVGRVQSNNEGSLLNAIAHQPVSVVVESAGRDFQN 275

Query: 270 YIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK 329
           Y GG+F+  C    +DH +  VGY            Y ++KNSWG  WGE GYI +RR  
Sbjct: 276 YKGGIFEGSCG-TKVDHAVTAVGYGKSG-----GKGYILIKNSWGPGWGENGYIRIRRAS 329

Query: 330 ----NTCGV 334
                 CGV
Sbjct: 330 GNSPGVCGV 338


>sp|P22895|P34_SOYBN P34 PROBABLE THIOL PROTEASE PRECURSOR
          Length = 379

 Score =  183 bits (461), Expect = 3e-46
 Identities = 108/318 (33%), Positives = 171/318 (52%), Gaps = 38/318 (11%)

Query: 40  YSHEEYLERFEIFKSNLGKIEELNLIAINHKA--DTKFGVNKFADLSSDEFKNYYLNNKE 97
           ++HEE  +R EIFK+N   I ++N    N K+    + G+NKFAD++  EF   YL   +
Sbjct: 56  HNHEEEAKRLEIFKNNSNYIRDMNA---NRKSPHSHRLGLNKFADITPQEFSKKYLQAPK 112

Query: 98  AIFTDDLPVADYL---DDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQ 154
            + +  + +A+     +    +  P ++DWR +G +T VK QG CG  W+FS TG +E  
Sbjct: 113 DV-SQQIKMANKKMKKEQYSCDHPPASWDWRKKGVITQVKYQGGCGRGWAFSATGAIEAA 171

Query: 155 HFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSY 214
           H I+   LVSLSEQ LVDC  E           EG   G Q  ++ +++++GGI T+  Y
Sbjct: 172 HAIATGDLVSLSEQELVDCVEE----------SEGSYNGWQYQSFEWVLEHGGIATDDDY 221

Query: 215 PYTAETGTQCNFNSANIGAKISNF-TMIPKNETVMAG------YIVSTGPLAIAADAVEW 267
           PY A+ G +C  N       I  + T+I  +E+  +         +   P++++ DA ++
Sbjct: 222 PYRAKEG-RCKANKIQDKVTIDGYETLIMSDESTESETEQAFLSAILEQPISVSIDAKDF 280

Query: 268 QFYIGGVFDIP--CNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYL 325
             Y GG++D     +P  ++H +L+VGY + +      + YWI KNSWG DWGE GYI++
Sbjct: 281 HLYTGGIYDGENCTSPYGINHFVLLVGYGSAD-----GVDYWIAKNSWGFDWGEDGYIWI 335

Query: 326 RRGK----NTCGVSNFVS 339
           +R        CG++ F S
Sbjct: 336 QRNTGNLLGVCGMNYFAS 353


>sp|P43234|CATO_HUMAN CATHEPSIN O PRECURSOR
          Length = 321

 Score =  182 bits (458), Expect = 8e-46
 Identities = 98/299 (32%), Positives = 155/299 (51%), Gaps = 28/299 (9%)

Query: 52  FKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLD 111
           F+ +L +   LN +  +  +   +G+N+F+ L  +EFK  YL +K + F        Y  
Sbjct: 44  FRESLNRHRYLNSLFPSENSTAFYGINQFSYLFPEEFKAIYLRSKPSKFPR------YSA 97

Query: 112 DEFIN----SIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSE 167
           +  ++    S+P  FDWR +  VT V+NQ  CG CW+FS  G VE  + I    L  LS 
Sbjct: 98  EVHMSIPNVSLPLRFDWRDKQVVTQVRNQQMCGGCWAFSVVGAVESAYAIKGKPLEDLSV 157

Query: 168 QNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIK-NGGIQTESSYPYTAETGTQCNF 226
           Q ++DC +           + GCNGG   NA N++ K    +  +S YP+ A+ G    F
Sbjct: 158 QQVIDCSYN----------NYGCNGGSTLNALNWLNKMQVKLVKDSEYPFKAQNGLCHYF 207

Query: 227 NSANIGAKISNFTM--IPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSL 284
           + ++ G  I  ++       E  MA  +++ GPL +  DAV WQ Y+GG+    C+    
Sbjct: 208 SGSHSGFSIKGYSAYDFSDQEDEMAKALLTFGPLVVIVDAVSWQDYLGGIIQHHCSSGEA 267

Query: 285 DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
           +H +LI G+         + PYWIV+NSWG+ WG  GY +++ G N CG+++ VS+  +
Sbjct: 268 NHAVLITGFDKTG-----STPYWIVRNSWGSSWGVDGYAHVKMGSNVCGIADSVSSIFV 321


>sp|P56202|CATW_HUMAN CATHEPSIN W PRECURSOR (LYMPHOPAIN)
          Length = 376

 Score =  182 bits (457), Expect = 1e-45
 Identities = 109/341 (31%), Positives = 170/341 (48%), Gaps = 35/341 (10%)

Query: 22  PPEEQSQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKF 80
           P E +  F  FQ +FN+ Y S EE+  R +IF  NL + + L    +      +FGV  F
Sbjct: 35  PLELKEAFKLFQIQFNRSYLSPEEHAHRLDIFAHNLAQAQRLQEEDLG---TAEFGVTPF 91

Query: 81  ADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWR-TRGAVTPVKNQGQC 139
           +DL+ +EF   Y   + A     +   +   +E   S+P + DWR   GA++P+K+Q  C
Sbjct: 92  SDLTEEEFGQLYGYRRAAGGVPSMG-REIRSEEPEESVPFSCDWRKVAGAISPIKDQKNC 150

Query: 140 GSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAY 199
             CW+ +  GN+E    IS    V +S   L+DC            C +GC+GG   +A+
Sbjct: 151 NCCWAMAAAGNIETLWRISFWDFVDVSVHELLDCGR----------CGDGCHGGFVWDAF 200

Query: 200 NYIIKNGGIQTESSYPYTAETGT-QCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPL 258
             ++ N G+ +E  YP+  +    +C+       A I +F M+  NE  +A Y+ + GP+
Sbjct: 201 ITVLNNSGLASEKDYPFQGKVRAHRCHPKKYQKVAWIQDFIMLQNNEHRIAQYLATYGPI 260

Query: 259 AIAADAVEWQFYIGGVFDIP---CNPNSLDHGILIVGYSA--------KNTIFRKNMP-- 305
            +  +    Q Y  GV       C+P  +DH +L+VG+ +          T+  ++ P  
Sbjct: 261 TVTINMKPLQLYRKGVIKATPTTCDPQLVDHSVLLVGFGSVKSEEGIWAETVSSQSQPQP 320

Query: 306 -----YWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTS 341
                YWI+KNSWGA WGE+GY  L RG NTCG++ F  T+
Sbjct: 321 PHPTPYWILKNSWGAQWGEKGYFRLHRGSNTCGITKFPLTA 361


>sp|P25774|CATS_HUMAN CATHEPSIN S PRECURSOR
          Length = 331

 Score =  177 bits (444), Expect = 3e-44
 Identities = 116/347 (33%), Positives = 176/347 (50%), Gaps = 35/347 (10%)

Query: 5   LLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYS--HEEYLERFEIFKSNLGKIEEL 62
           L+ VL V +  V+     P     +  ++  + K+Y   +EE + R  I++ NL  +   
Sbjct: 4   LVCVLLVCSSAVAQLHKDPTLDHHWHLWKKTYGKQYKEKNEEAVRRL-IWEKNLKFVMLH 62

Query: 63  NLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINS----- 117
           NL           G+N   D++S+E  +          T  L V                
Sbjct: 63  NLEHSMGMHSYDLGMNHLGDMTSEEVMS---------LTSSLRVPSQWQRNITYKSNPNR 113

Query: 118 -IPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 176
            +P + DWR +G VT VK QG CG+CW+FS  G +E Q  +   KLV+LS QNLVDC   
Sbjct: 114 ILPDSVDWREKGCVTEVKYQGSCGACWAFSAVGALEAQLKLKTGKLVTLSAQNLVDC--- 170

Query: 177 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKIS 236
                 E+  ++GCNGG    A+ YII N GI +++SYPY A    +C ++S    A  S
Sbjct: 171 ----STEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKA-MDQKCQYDSKYRAATCS 225

Query: 237 NFTMIP-KNETVMAGYIVSTGPLAIAADAVEWQFYI--GGVFDIPCNPNSLDHGILIVGY 293
            +T +P   E V+   + + GP+++  DA    F++   GV+  P    +++HG+L+VGY
Sbjct: 226 KYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCTQNVNHGVLVVGY 285

Query: 294 SAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVS 339
              N        YW+VKNSWG ++GE+GYI + R K N CG+++F S
Sbjct: 286 GDLN-----GKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPS 327


>sp|P00784|PAPA_CARPA PAPAIN PRECURSOR (PAPAYA PROTEINASE I) (PPI)
          Length = 345

 Score =  176 bits (442), Expect = 6e-44
 Identities = 116/315 (36%), Positives = 161/315 (50%), Gaps = 37/315 (11%)

Query: 35  KFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKF--GVNKFADLSSDEFKNY 91
           K NK Y + +E + RFEIFK NL  I+E N      K +  +  G+N FAD+S+DEFK  
Sbjct: 54  KHNKIYKNIDEKIYRFEIFKDNLKYIDETN------KKNNSYWLGLNVFADMSNDEFKEK 107

Query: 92  YLNNKEAIFTD-DLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGN 150
           Y  +    +T  +L   + L+D  +N IP   DWR +GAVTPVKNQG CGSCW+FS    
Sbjct: 108 YTGSIAGNYTTTELSYEEVLNDGDVN-IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVT 166

Query: 151 VEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQT 210
           +EG   I    L   SEQ L+DCD              GCNGG   +A   ++   GI  
Sbjct: 167 IEGIIKIRTGNLNEYSEQELLDCDRR----------SYGCNGGYPWSALQ-LVAQYGIHY 215

Query: 211 ESSYPYTAETGTQCNFNSANIGAKISNFTMI-PKNETVMAGYIVSTGPLAIAADAV--EW 267
            ++YPY        +       AK      + P NE  +  Y ++  P+++  +A   ++
Sbjct: 216 RNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALL-YSIANQPVSVVLEAAGKDF 274

Query: 268 QFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRR 327
           Q Y GG+F  PC  N +DH +  VGY            Y ++KNSWG  WGE GYI ++R
Sbjct: 275 QLYRGGIFVGPCG-NKVDHAVAAVGYGPN---------YILIKNSWGTGWGENGYIRIKR 324

Query: 328 GK-NTCGVSNFVSTS 341
           G  N+ GV    ++S
Sbjct: 325 GTGNSYGVCGLYTSS 339


>sp||CATL_CHICK_1 [Segment 1 of 2] CATHEPSIN L
          Length = 176

 Score =  175 bits (439), Expect = 1e-43
 Identities = 88/179 (49%), Positives = 117/179 (65%), Gaps = 12/179 (6%)

Query: 119 PTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECM 178
           P + DWR +G VTPVK+QGQCGSCW+FSTTG +EGQHF ++ KLVSLSEQNLVDC     
Sbjct: 2   PRSVDWREKGYVTPVKDQGQCGSCWAFSTTGALEGQHFRTKGKLVSLSEQNLVDCSRP-- 59

Query: 179 EYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNF 238
             EG    ++GCNGGL   A+ Y+  NGGI +E SYPYTA+    C + +    A  + F
Sbjct: 60  --EG----NQGCNGGLMDQAFQYVQDNGGIDSEESYPYTAKDDEDCRYKAEYNAANDTGF 113

Query: 239 TMIPK-NETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIP-CNPNSLDHGILIVGY 293
             IP+ +E  +   + S GP+++A DA    +QFY  G++  P C+   LDHG+L+VGY
Sbjct: 114 VDIPQGHERALMKAVASVGPVSVAIDAGHSSFQFYQSGIYYEPDCSSEDLDHGVLVVGY 172


>sp|P25326|CATS_BOVIN CATHEPSIN S
          Length = 217

 Score =  173 bits (434), Expect = 5e-43
 Identities = 91/226 (40%), Positives = 131/226 (57%), Gaps = 17/226 (7%)

Query: 118 IPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHEC 177
           +P + DWR +G VT VK QG CGSCW+FS  G +E Q  +   KLVSLS QNLVDC    
Sbjct: 1   LPDSMDWREKGCVTEVKYQGACGSCWAFSAVGALEAQVKLKTGKLVSLSAQNLVDC---- 56

Query: 178 MEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISN 237
                 +  ++GCNGG    A+ YII N GI +E+SYPY A  G +C ++  N  A  S 
Sbjct: 57  ---STAKYGNKGCNGGFMTEAFQYIIDNNGIDSEASYPYKAMDG-KCQYDVKNRAATCSR 112

Query: 238 FTMIP-KNETVMAGYIVSTGPLAIAADAVEWQFYI--GGVFDIPCNPNSLDHGILIVGYS 294
           +  +P  +E  +   + + GP+++  DA    F++   GV+  P    +++HG+L+VGY 
Sbjct: 113 YIELPFGSEEALKEAVANKGPVSVGIDASHSSFFLYKTGVYYDPSCTQNVNHGVLVVGYG 172

Query: 295 AKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVS 339
             +        YW+VKNSWG  +G+QGYI + R   N CG++N+ S
Sbjct: 173 NLD-----GKDYWLVKNSWGLHFGDQGYIRMARNSGNHCGIANYPS 213


>sp|P80884|ANAN_ANACO ANANAIN
          Length = 216

 Score =  167 bits (419), Expect = 3e-41
 Identities = 93/223 (41%), Positives = 124/223 (54%), Gaps = 22/223 (9%)

Query: 118 IPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHEC 177
           +P + DWR  GAVT VKNQG+CGSCW+F++   VE  + I +  LVSLSEQ ++DC    
Sbjct: 1   VPQSIDWRDSGAVTSVKNQGRCGSCWAFASIATVESIYKIKRGNLVSLSEQQVLDC---- 56

Query: 178 MEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISN 237
                  A   GC GG    AY++II N G+ + + YPY A  GT C  N     A I+ 
Sbjct: 57  -------AVSYGCKGGWINKAYSFIISNKGVASAAIYPYKAAKGT-CKTNGVPNSAYITR 108

Query: 238 FTMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAK 296
           +T + +N      Y VS  P+A A DA   +Q Y  GVF  PC    L+H I+I+GY   
Sbjct: 109 YTYVQRNNERNMMYAVSNQPIAAALDASGNFQHYKRGVFTGPCG-TRLNHAIVIIGYGQD 167

Query: 297 NTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT----CGVS 335
           +        +WIV+NSWGA WGE GYI L R  ++    CG++
Sbjct: 168 SA----GKKFWIVRNSWGAGWGEGGYIRLARDVSSSFGICGIA 206


>sp|Q02765|CATS_RAT CATHEPSIN S PRECURSOR
          Length = 330

 Score =  167 bits (418), Expect = 4e-41
 Identities = 90/228 (39%), Positives = 132/228 (57%), Gaps = 18/228 (7%)

Query: 117 SIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 176
           ++P + DWR +G VT VK QG CGSCW+FS  G +EGQ  +   KLVSLS QNLVDC  E
Sbjct: 112 TLPDSVDWREKGCVTNVKYQGSCGSCWAFSAEGALEGQLKLKTGKLVSLSAQNLVDCSTE 171

Query: 177 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKIS 236
                 E+  ++GC GG    A+ YII +  I +E+SYPY A    +C ++  N  A  S
Sbjct: 172 ------EKYGNKGCGGGFMTEAFQYII-DTSIDSEASYPYKA-MDEKCLYDPKNRAATCS 223

Query: 237 NFTMIP-KNETVMAGYIVSTGPLAIAADAV---EWQFYIGGVFDIPCNPNSLDHGILIVG 292
            +  +P  +E  +   + + GP+++  D      +  Y  GV+D P    +++HG+L+VG
Sbjct: 224 RYIELPFGDEEALKEAVATKGPVSVGIDDASHSSFFLYQSGVYDDPSCTENMNHGVLVVG 283

Query: 293 YSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYL-RRGKNTCGVSNFVS 339
           Y   +        YW+VKNSWG  +G+QGYI + R  KN CG++++ S
Sbjct: 284 YGTLD-----GKDYWLVKNSWGLHFGDQGYIRMARNNKNHCGIASYCS 326


>sp|P20721|CYSL_LYCES LOW-TEMPERATURE-INDUCED CYSTEINE PROTEINASE PRECURSOR
          Length = 346

 Score =  164 bits (410), Expect = 3e-40
 Identities = 86/226 (38%), Positives = 127/226 (56%), Gaps = 21/226 (9%)

Query: 116 NSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDH 175
           +S+P + DWR +G +  VK+QG CGSCW+FS    +E  + I    L+SLSEQ LVDCD 
Sbjct: 16  DSLPESIDWREKGVLVGVKDQGSCGSCWAFSAVAAMESINAIVTGNLISLSEQELVDCD- 74

Query: 176 ECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKI 235
                    + +EGC+GGL   A+ ++IKNGGI TE  YPY    G    +       KI
Sbjct: 75  --------RSYNEGCDGGLMDYAFEFVIKNGGIDTEEDYPYKERNGVCDQYRKNAKVVKI 126

Query: 236 SNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNPNSLDHGILIVGY 293
            ++  +P N        V+  P++IA +A   ++Q Y  G+F   C   ++DHG++I GY
Sbjct: 127 DSYEDVPVNNEKALQKAVAHQPVSIALEAGGRDFQHYKSGIFTGKCG-TAVDHGVVIAGY 185

Query: 294 SAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNT----CGVS 335
             +N      M YWIV+NSWGA+  E GY+ ++R  ++    CG++
Sbjct: 186 GTEN-----GMDYWIVRNSWGANCRENGYLRVQRNVSSSSGLCGLA 226


>sp|P36184|ACP1_ENTHI CYSTEINE PROTEINASE ACP1 PRECURSOR
          Length = 308

 Score =  162 bits (407), Expect = 7e-40
 Identities = 105/312 (33%), Positives = 150/312 (47%), Gaps = 40/312 (12%)

Query: 29  FLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE 87
           F ++    NK +++  EYL RF +F  N   +E          A+    +N FAD++ +E
Sbjct: 18  FKQWAATHNKVFANRAEYLYRFAVFLDNKKFVE----------ANANTELNVFADMTHEE 67

Query: 88  FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFST 147
           F   +L       T ++P         + + P + DWR+   + P K+QGQCGSCW+F T
Sbjct: 68  FIQTHLG-----MTYEVPETTSNVKAAVKAAPESVDWRS--IMNPAKDQGQCGSCWTFCT 120

Query: 148 TGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGG 207
           T  +EG+      KL S SEQ LVDCD          A D GC GG   N+  +I +N G
Sbjct: 121 TAVLEGRVNKDLGKLYSFSEQQLVDCD----------ASDNGCEGGHPSNSLKFIQENNG 170

Query: 208 IQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--V 265
           +  ES YPY A  GT C     N+     +  +   +ET +   I   GP+A+  DA   
Sbjct: 171 LGLESDYPYKAVAGT-CK-KVKNVATVTGSRRVTDGSETGLQTIIAENGPVAVGMDASRP 228

Query: 266 EWQFYIGGVF--DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYI 323
            +Q Y  G    D  C    ++H +  VGY + +     N  YWI++NSWG  WG+ GY 
Sbjct: 229 SFQLYKKGTIYSDTKCRSRMMNHCVTAVGYGSNS-----NGKYWIIRNSWGTSWGDAGYF 283

Query: 324 YLRR-GKNTCGV 334
            L R   N CG+
Sbjct: 284 LLARDSNNMCGI 295


>sp|O17473|CATL_BRUPA CATHEPSIN L-LIKE PRECURSOR
          Length = 395

 Score =  159 bits (398), Expect = 8e-39
 Identities = 101/323 (31%), Positives = 155/323 (47%), Gaps = 21/323 (6%)

Query: 26  QSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSS 85
           ++++ ++     K Y  +E   R  IF+SN    E +N             +N  ADL+ 
Sbjct: 88  ETEWKDYVTALGKHYDQKENNFRMAIFESNELMTERINKKYEQGLVSYTTALNDLADLTD 147

Query: 86  DEF--KNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCW 143
           +EF  +N      +         +++   +    +P   DWRT+GAVTPV+NQG+CGSC+
Sbjct: 148 EEFMVRNGLRLPNQTDLRGKRQTSEFYRYDKSERLPDQVDWRTKGAVTPVRNQGECGSCY 207

Query: 144 SFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYII 203
           +F+T   +E  H     +L+ LS QN+VDC             + GC+GG  P A+ Y  
Sbjct: 208 AFATAAALEAYHKQMTGRLLDLSPQNIVDCT--------RNLGNNGCSGGYMPTAFQYAS 259

Query: 204 KNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMI-PKNETVMAGYIVSTGP--LAI 260
           +  GI  ES YPY   T  +C +  +      + F  I P +E  +   +   GP  + I
Sbjct: 260 RY-GIAMESRYPYVG-TEQRCRWQQSIAVVTDNGFNEIQPGDELALKHAVAKRGPVVVGI 317

Query: 261 AADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQ 320
           +     ++FY  GV+    N    DH +L VGY    +       YWIVKNSWG DWG+ 
Sbjct: 318 SGSKRSFRFYKDGVYS-EGNCGRPDHAVLAVGYGTHPSY----GDYWIVKNSWGTDWGKD 372

Query: 321 GYIYLRRGK-NTCGVSNFVSTSI 342
           GY+Y+ R + N C +++  S  I
Sbjct: 373 GYVYMARNRGNMCHIASAASFPI 395


>sp|Q01957|CPP1_ENTHI CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 315

 Score =  156 bits (391), Expect = 5e-38
 Identities = 108/309 (34%), Positives = 166/309 (52%), Gaps = 39/309 (12%)

Query: 37  NKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADT-KFGVN-KFADLSSDEFKNYYLN 94
           NK ++  E L R  IF  N        ++A N++ +T K  V+  FA ++++E+ N  L 
Sbjct: 24  NKHFTAVESLRRRAIFNMNA------RIVAENNRKETFKLSVDGPFAAMTNEEY-NSLLK 76

Query: 95  NKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQ 154
            K +   ++     YL+ +     P A DWR +G VTP+++QG CGSC++F +   +EG+
Sbjct: 77  LKRS--GEEKGEVRYLNIQ----APKAVDWRKKGKVTPIRDQGNCGSCYTFGSIAALEGR 130

Query: 155 HFISQ---NKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTE 211
             I +   ++ + LSE+++V C  E    +G    + GCNGGL  N YNYI++N GI  E
Sbjct: 131 LLIEKGGDSETLDLSEEHMVQCTRE----DG----NNGCNGGLGSNVYNYIMEN-GIAKE 181

Query: 212 SSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQF 269
           S YPYT    T C  +     AKI ++  + +N  V     +S G + ++ DA  V++Q 
Sbjct: 182 SDYPYTGSDST-CR-SDVKAFAKIKSYNRVARNNEVELKAAISQGLVDVSIDASSVQFQL 239

Query: 270 YIGGVF-DIPCNPN--SLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLR 326
           Y  G + D  C  N  +L+H +  VGY   +         WIV+NSWG  WGE+GYI + 
Sbjct: 240 YKSGAYTDTQCKNNYFALNHEVCAVGYGVVD-----GKECWIVRNSWGTGWGEKGYINMV 294

Query: 327 RGKNTCGVS 335
              NTCGV+
Sbjct: 295 IEGNTCGVA 303


>sp|Q06964|CPP3_ENTHI CYSTEINE PROTEINASE 3 PRECURSOR (CYSTEINE PROTEINASE ACP3)
          Length = 308

 Score =  153 bits (384), Expect = 4e-37
 Identities = 103/308 (33%), Positives = 159/308 (51%), Gaps = 37/308 (12%)

Query: 37  NKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVN-KFADLSSDEFKNYYLNN 95
           NK ++  E L R  IF  N   + E N      K   K  V+  FA ++++E++   L +
Sbjct: 17  NKHFTAVEALRRRAIFNMNARFVAEFN-----KKGSFKLSVDGPFAAMTNEEYRTL-LKS 70

Query: 96  KEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQH 155
           K  +  ++     YL+ +     P + DWR +G VTP+++Q QCGSC++F +   +EG+ 
Sbjct: 71  KRTV--EENGKVTYLNIQ----APESVDWRAQGKVTPIRDQAQCGSCYTFGSLAALEGRL 124

Query: 156 FISQN---KLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTES 212
            I +      + LSE++LV C          +  + GCNGGL  N Y+YII+N G+  ES
Sbjct: 125 LIEKGGNANTLDLSEEHLVQCT--------RDNGNNGCNGGLGSNVYDYIIQN-GVAKES 175

Query: 213 SYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFY 270
            YPYT  T + C  N     AKI+ +  +P+N        +S G + ++ DA   ++Q Y
Sbjct: 176 DYPYTG-TDSTCKTN-VKAFAKITGYNKVPRNNEAELKAALSQGLVDVSIDASSAKFQLY 233

Query: 271 IGGVF-DIPCNPN--SLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRR 327
             G + D  C  N  +L+H +  VGY   +         WIV+NSWG  WG++GYI +  
Sbjct: 234 KSGAYSDTKCKNNFFALNHEVCAVGYGVVD-----GKECWIVRNSWGTGWGDKGYINMVI 288

Query: 328 GKNTCGVS 335
             NTCGV+
Sbjct: 289 EGNTCGVA 296


>sp|Q01958|CPP2_ENTHI CYSTEINE PROTEINASE 2 PRECURSOR
          Length = 315

 Score =  153 bits (383), Expect = 5e-37
 Identities = 102/316 (32%), Positives = 161/316 (50%), Gaps = 37/316 (11%)

Query: 29  FLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVN-KFADLSSDE 87
           F  +  K NK ++  E L R  IF  N   ++  N I        K  V+  FA ++++E
Sbjct: 16  FNTWASKNNKHFTAIEKLRRRAIFNMNAKFVDSFNKIG-----SFKLSVDGPFAAMTNEE 70

Query: 88  FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFST 147
           ++    + +    T++     YL+ +     P + DWR  G VTP+++Q QCGSC++F +
Sbjct: 71  YRTLLKSKRT---TEENGQVKYLNIQ----APESVDWRKEGKVTPIRDQAQCGSCYTFGS 123

Query: 148 TGNVEGQHFISQN---KLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIK 204
              +EG+  I +      + LSE+++V C          +  + GCNGGL  N Y+YII+
Sbjct: 124 LAALEGRLLIEKGGDANTLDLSEEHMVQCT--------RDNGNNGCNGGLGSNVYDYIIE 175

Query: 205 NGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA 264
           + G+  ES YPYT    T C  N  +  AKI+ +T +P+N        +S G + ++ DA
Sbjct: 176 H-GVAKESDYPYTGSDST-CKTNVKSF-AKITGYTKVPRNNEAELKAALSQGLVDVSIDA 232

Query: 265 --VEWQFYIGGVF-DIPCNPN--SLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGE 319
              ++Q Y  G + D  C  N  +L+H +  VGY   +         WIV+NSWG  WG+
Sbjct: 233 SSAKFQLYKSGAYTDTKCKNNYFALNHEVCAVGYGVVD-----GKECWIVRNSWGTGWGD 287

Query: 320 QGYIYLRRGKNTCGVS 335
           +GYI +    NTCGV+
Sbjct: 288 KGYINMVIEGNTCGVA 303


>sp|P46102|CYSP_PLAVN CYSTEINE PROTEINASE PRECURSOR
          Length = 506

 Score =  153 bits (382), Expect = 6e-37
 Identities = 115/358 (32%), Positives = 176/358 (49%), Gaps = 62/358 (17%)

Query: 27  SQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSS 85
           S+F ++  + NKKY + +E L+RFE FK    K ++ N +   +       VN+++D S 
Sbjct: 160 SKFFKYMKENNKKYENMDEQLQRFENFKIRYMKTQKHNEMVGKNGLTYVQKVNQYSDFSK 219

Query: 86  DEFKNYYLNNKEAIFTDDL------PVADYLDDEFINSI-------PTAFDWRTRGAVTP 132
           +EF NY+   K      DL      P+  +L +  + S+       P + D+R++    P
Sbjct: 220 EEFDNYF--KKLLSVPMDLKSKYIVPLKKHLANTNLISVDNKSKDFPDSRDYRSKFNFLP 277

Query: 133 VKNQGQCGSCWSFSTTGNVEGQHFISQNKL-VSLSEQNLVDCDHECMEYEGEEACDEGCN 191
            K+QG CGSCW+F+  GN E  +  +++++ +S SEQ +VDC  E          + GC+
Sbjct: 278 PKDQGNCGSCWAFAAIGNFEYLYVHTRHEMPISFSEQQMVDCSTE----------NYGCD 327

Query: 192 GGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGY 251
           GG    A+ Y+I NG +     YPY       C     ++  ++     +  NE +MA  
Sbjct: 328 GGNPFYAFLYMINNG-VCLGDEYPYKGHEDFFCLNYRCSLLGRVHFIGDVKPNELIMALN 386

Query: 252 IVSTGPLAIAADAVE-WQFYIGGVFDIPCNPNSLDHGILIVGYSA--------------- 295
            V  GP+ IA  A E +  Y GGVFD  CNP  L+H +L+VGY                 
Sbjct: 387 YV--GPVTIAVGASEDFVLYSGGVFDGECNPE-LNHSVLLVGYGQVKKSLAFEDSHSNVD 443

Query: 296 KNTI--FRKNMP---------YWIVKNSWGADWGEQGYIYLRRGK----NTCGVSNFV 338
            N I  +++N+          YWIV+NSWG +WGE GYI ++R K      CGV + V
Sbjct: 444 SNLIKKYKENIKGDDDDDIIYYWIVRNSWGPNWGEGGYIRIKRNKAGDDGFCGVGSDV 501


>sp|P36185|ACP2_ENTHI CYSTEINE PROTEINASE ACP2 PRECURSOR
          Length = 310

 Score =  150 bits (374), Expect = 5e-36
 Identities = 102/322 (31%), Positives = 160/322 (49%), Gaps = 32/322 (9%)

Query: 20  GIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVN- 78
           GI       F  +  K NK ++  E L R  IF  N   ++  N I        K  V+ 
Sbjct: 3   GIRIASAIDFNTWASKNNKHFTAIEKLRRRAIFNMNAKFVDSFNKIG-----SFKLSVDG 57

Query: 79  KFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQ 138
            FA ++++E++    + +    T++     YL+ +     P + DWR  G VTP+++Q Q
Sbjct: 58  PFAAMTNEEYRTLLKSKRT---TEENGQVKYLNIQ----APESVDWRKEGKVTPLRDQAQ 110

Query: 139 CGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNA 198
           CGSC++F +   +EG+  I +       + N +D   E M+   +   + GCNGGL  N 
Sbjct: 111 CGSCYTFGSLAALEGRLLIEKG-----GDANTLDLSEEHMQCTRDNG-NNGCNGGLGSNV 164

Query: 199 YNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPL 258
           Y+YII++ G+  ES YPYT    T C  N  +   KI+ +T +P+N        +S G L
Sbjct: 165 YDYIIEH-GVAKESDYPYTGSDST-CKTNVKSF-RKITGYTKVPRNNEAELKAALSQGLL 221

Query: 259 AIAAD--AVEWQFYIGGVF-DIPCNPN--SLDHGILIVGYSAKNTIFRKNMPYWIVKNSW 313
            ++ D  + ++Q Y  G + D  C  N  +L+H +  VGY   +         WIV+NSW
Sbjct: 222 DVSIDVSSAKFQLYKSGAYTDTKCKNNYFALNHEVCAVGYGVVD-----GKECWIVRNSW 276

Query: 314 GADWGEQGYIYLRRGKNTCGVS 335
           G  WG++GYI +    NTCGV+
Sbjct: 277 GTSWGDKGYINMVIEGNTCGVA 298


>sp|P25781|CYSP_THEAN CYSTEINE PROTEINASE PRECURSOR
          Length = 441

 Score =  146 bits (366), Expect = 5e-35
 Identities = 107/339 (31%), Positives = 164/339 (47%), Gaps = 54/339 (15%)

Query: 28  QFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGV--NKFADLS 84
           +F  F +K+ K + S ++ ++RF  F+ N   ++        HK    + +  NKF+DLS
Sbjct: 119 EFDAFVEKYKKVHRSFDQRVQRFLTFRKNYHIVK-------THKPTEPYSLDLNKFSDLS 171

Query: 85  SDEFKNYY--------------------LNNKEAIFTDDLPVADYLDDEFINSIPTA--F 122
            +EFK  Y                    +++K  I+   L  A  +++    S+ T    
Sbjct: 172 DEEFKALYPVITPPKTYTSLSKHLEFKKMSHKNPIYISKLKKAKGIEEIKDLSLITGENL 231

Query: 123 DWRTRGAVTPVKNQGQ-CGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYE 181
           +W    AV+P K+QG  CGSCW+FS+  +VE  + + +NK   LSEQ LV+CD   M   
Sbjct: 232 NWARTDAVSPTKDQGDHCGSCWAFSSIASVESLYRLYKNKSYFLSEQELVNCDKSSM--- 288

Query: 182 GEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMI 241
                  GC GGL   A  Y I + G+  ES  PYT    + C  +  N    I + +++
Sbjct: 289 -------GCAGGLPITALEY-IHSKGVSFESEVPYTGIV-SPCKPSIKN-KVFIDSISIL 338

Query: 242 PKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFR 301
             N+ V    ++S   + IA    E + Y GG+F   C    L+H +L+VG    +    
Sbjct: 339 KGNDVVNKSLVISPTVVGIAV-TKELKLYSGGIFTGKCG-GELNHAVLLVGEGVDH---E 393

Query: 302 KNMPYWIVKNSWGADWGEQGYIYLRR---GKNTCGVSNF 337
             M YWI+KNSWG DWGE G++ L+R   G + CG+  F
Sbjct: 394 TGMRYWIIKNSWGEDWGENGFLRLQRTKKGLDKCGILTF 432


>sp|P14518|BROM_ANACO BROMELAIN, STEM
          Length = 212

 Score =  146 bits (365), Expect = 6e-35
 Identities = 81/224 (36%), Positives = 115/224 (51%), Gaps = 27/224 (12%)

Query: 117 SIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 176
           ++P + DWR  GAVT VKNQ  CG+CW+F+    VE  + I +  L  LSEQ ++DC   
Sbjct: 1   AVPQSIDWRDYGAVTSVKNQNPCGACWAFAAIATVESIYKIKKGILEPLSEQQVLDC--- 57

Query: 177 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKIS 236
                   A   GC GG +  A+ +II N G+ + + YPY A  GT C  +     A I+
Sbjct: 58  --------AKGYGCKGGWEFRAFEFIISNKGVASGAIYPYKAAKGT-CKTDGVPNSAYIT 108

Query: 237 NFTMIPKNETVMAGYIVSTGPLAIAADA-VEWQFYIGGVFDIPCNPNSLDHGILIVGYSA 295
            +  +P+N      Y VS  P+ +A DA   +Q+Y  GVF+ PC   SL+H +  +GY  
Sbjct: 109 GYARVPRNNESSMMYAVSKQPITVAVDANANFQYYKSGVFNGPCG-TSLNHAVTAIGYGQ 167

Query: 296 KNTIFRKNMPYWIVKNSWGADWGEQGYIYLRR----GKNTCGVS 335
            + I+ K          WGA WGE GYI + R        CG++
Sbjct: 168 DSIIYPK---------KWGAKWGEAGYIRMARDVSSSSGICGIA 202


>sp|P22497|CYSP_THEPA CYSTEINE PROTEINASE PRECURSOR
          Length = 439

 Score =  145 bits (363), Expect = 1e-34
 Identities = 104/343 (30%), Positives = 159/343 (46%), Gaps = 64/343 (18%)

Query: 24  EEQSQFLEFQDKFNKKYS-HEEYLERFEIFKSNLGKIEELNLIAINHKADTKF--GVNKF 80
           E   +F EF  K+N++++  +E L R   F+SN  +++E        K D  +  G+N+F
Sbjct: 119 EVYREFEEFNSKYNRRHATQQERLNRLVTFRSNYLEVKE-------QKGDEPYVKGINRF 171

Query: 81  ADLSSDEF--------------------------KNYYLNNKEAIFTDDLPVADYLDDEF 114
           +DL+  EF                          K Y  N K+A+ TD+       D + 
Sbjct: 172 SDLTEREFYKLFPVMKPPKATYSNGYYLLSHMANKTYLKNLKKALNTDE-------DVDL 224

Query: 115 INSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCD 174
                   DWR   +VT VK+Q  CG CW+FST G+VEG +    +K   LS Q L+DCD
Sbjct: 225 AKLTGENLDWRRSSSVTSVKDQSNCGGCWAFSTVGSVEGYYMSHFDKSYELSVQELLDCD 284

Query: 175 HECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAK 234
                     +   GC GGL  +AY Y+ K  G+ +    P+  +   +C+   A     
Sbjct: 285 ----------SFSNGCQGGLLESAYEYVRKY-GLVSAKDLPF-VDKARRCSVPKAK-KVS 331

Query: 235 ISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYS 294
           + ++ +  K + VM   + S+      + + E   Y  GVF   C   SL+H +++VG  
Sbjct: 332 VPSYHVF-KGKEVMTRSLTSSPCSVYLSVSPELAKYKSGVFTGECG-KSLNHAVVLVGEG 389

Query: 295 AKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRR---GKNTCGV 334
                 ++   YW+V+NSWG DWGE GY+ L R   G + CGV
Sbjct: 390 YDEVTKKR---YWVVQNSWGTDWGENGYMRLERTNMGTDKCGV 429


>sp|P16311|MMAL_DERFA MAJOR MITE FECAL ALLERGEN DER F 1 PRECURSOR (DER F I)
          Length = 321

 Score =  144 bits (359), Expect = 3e-34
 Identities = 116/346 (33%), Positives = 158/346 (45%), Gaps = 48/346 (13%)

Query: 7   FVLAVFTVFVSSRGIP-PEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLI 65
           FVLA+ ++ V S     P     F EF+  FNK Y+    +E  E+ + N   +E L  +
Sbjct: 3   FVLAIASLLVLSTVYARPASIKTFEEFKKAFNKNYAT---VEEEEVARKNF--LESLKYV 57

Query: 66  AINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEF----INSI--P 119
             N     K  +N  +DLS DEFKN YL + EA   + L     L+ E     INS+  P
Sbjct: 58  EAN-----KGAINHLSDLSLDEFKNRYLMSAEAF--EQLKTQFDLNAETSACRINSVNVP 110

Query: 120 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 179
           +  D R+   VTP++ QG CGSCW+FS     E  +   +N  + LSEQ LVDC      
Sbjct: 111 SELDLRSLRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNTSLDLSEQELVDC------ 164

Query: 180 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFT 239
                A   GC+G   P    YI +NG ++ E SYPY A        NS + G  ISN+ 
Sbjct: 165 -----ASQHGCHGDTIPRGIEYIQQNGVVE-ERSYPYVAREQRCRRPNSQHYG--ISNYC 216

Query: 240 MIPKNETVMAGYIVSTGPLAIAA-----DAVEWQFYIGGVF---DIPCNPNSLDHGILIV 291
            I   +       ++    AIA      D   +Q Y G      D    PN   H + IV
Sbjct: 217 QIYPPDVKQIREALTQTHTAIAVIIGIKDLRAFQHYDGRTIIQHDNGYQPNY--HAVNIV 274

Query: 292 GYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNF 337
           GY +      +   YWIV+NSW   WG+ GY Y + G N   +  +
Sbjct: 275 GYGS-----TQGDDYWIVRNSWDTTWGDSGYGYFQAGNNLMMIEQY 315


>sp|P25805|CYSP_PLAFA THROPHOZOITE CYSTEINE PROTEINASE PRECURSOR (TCP)
          Length = 569

 Score =  144 bits (359), Expect = 3e-34
 Identities = 102/363 (28%), Positives = 167/363 (45%), Gaps = 62/363 (17%)

Query: 27  SQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSS 85
           S+F +F  + NK Y + +E + +FEIFK N   I+  N   +N  A  K  VN+F+D S 
Sbjct: 223 SKFFKFMKEHNKVYKNIDEQMRKFEIFKINYISIKNHN--KLNKNAMYKKKVNQFSDYSE 280

Query: 86  DEFKNY--------------YLNNKEAIFTDDLPVADYL------DDEFINSIPTAFDWR 125
           +E K Y              Y    E    D++ ++++       + +  + +P   D+R
Sbjct: 281 EELKEYFKTLLHVPNHMIEKYSKPFENHLKDNILISEFYTNGKRNEKDIFSKVPEILDYR 340

Query: 126 TRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEA 185
            +G V   K+QG CGSCW+F++ GN+E         ++S SEQ +VDC  +         
Sbjct: 341 EKGIVHEPKDQGLCGSCWAFASVGNIESVFAKKNKNILSFSEQEVVDCSKD--------- 391

Query: 186 CDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNE 245
            + GC+GG    ++ Y+++N  +     Y Y A+    C          +S+   + +N+
Sbjct: 392 -NFGCDGGHPFYSFLYVLQN-ELCLGDEYKYKAKDDMFCLNYRCKRKVSLSSIGAVKENQ 449

Query: 246 TVMAGYIVSTGPLAIAADA-VEWQFYIGGVFDIPCNPNSLDHGILIVGY----------- 293
            ++A  +   GPL++      ++  Y  GV++  C+   L+H +L+VGY           
Sbjct: 450 LILA--LNEVGPLSVNVGVNNDFVAYSEGVYNGTCS-EELNHSVLLVGYGQVEKTKLNYN 506

Query: 294 ---SAKNTIFRKNMP------YWIVKNSWGADWGEQGYIYLRRGKN----TCGVSNFVST 340
                 NT    N P      YWI+KNSW   WGE G++ L R KN     CG+   V  
Sbjct: 507 NKIQTYNTKENSNQPDDNIIYYWIIKNSWSKKWGENGFMRLSRNKNGDNVFCGIGEEVFY 566

Query: 341 SII 343
            I+
Sbjct: 567 PIL 569


>sp|P42666|CYSP_PLAVI CYSTEINE PROTEINASE PRECURSOR
          Length = 583

 Score =  132 bits (329), Expect = 1e-30
 Identities = 102/367 (27%), Positives = 165/367 (44%), Gaps = 86/367 (23%)

Query: 27  SQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSS 85
           S+F  F +K+ + Y    E +E+++ FK N  KI++ N          K  VN+F+D S 
Sbjct: 235 SKFFNFMNKYKRSYKDINEQMEKYKNFKMNYLKIKKHN----ETNQMYKMKVNQFSDYSK 290

Query: 86  DEFKNYYLNNKEAIFTDDLPVADYLDDEFI------------------------NSIPTA 121
            +F++Y        F   +P+ D+L  +++                          +P  
Sbjct: 291 KDFESY--------FRKLVPIPDHLKKKYVVPFSSMNNGKGKNVVTSSSGANLLADVPEI 342

Query: 122 FDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNK-LVSLSEQNLVDCDHECMEY 180
            D+R +G V   K+QG CGSCW+F++ GNVE  +    NK +++LSEQ +VDC       
Sbjct: 343 LDYREKGIVHEPKDQGLCGSCWAFASVGNVECMYAKEHNKTILTLSEQEVVDC------- 395

Query: 181 EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQC-NFNSANIGAKISNFT 239
                 + GC+GG    ++ Y I+N GI     Y Y A     C N+   N    +S+  
Sbjct: 396 ---SKLNFGCDGGHPFYSFIYAIEN-GICMGDDYKYKAMDNLFCLNYRCKN-KVTLSSVG 450

Query: 240 MIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYS--AK 296
            + +NE + A  +   GP+++      ++ FY GG+F+  C    L+H +L+VGY     
Sbjct: 451 GVKENELIRA--LNEVGPVSVNVGVTDDFSFYGGGIFNGTCT-EELNHSVLLVGYGQVQS 507

Query: 297 NTIFRKN-------------------------MPYWIVKNSWGADWGEQGYIYLRRGKN- 330
           + IF++                            YWI+KNSW   WGE G++ + R K  
Sbjct: 508 SKIFQEKNAYDDASGVTKKGALSYPSKADDGIQYYWIIKNSWSKFWGENGFMRISRNKEG 567

Query: 331 ---TCGV 334
               CG+
Sbjct: 568 DNVFCGI 574


>sp|P08176|MMAL_DERPT MAJOR MITE FECAL ALLERGEN DER P 1 PRECURSOR (DER P I)
          Length = 320

 Score =  123 bits (305), Expect = 7e-28
 Identities = 110/338 (32%), Positives = 151/338 (44%), Gaps = 51/338 (15%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60
           MK++L     +    V +R   P     F E++  FNK Y+     E  E  + N   +E
Sbjct: 1   MKIVLAIASLLALSAVYAR---PSSIKTFEEYKKAFNKSYAT---FEDEEAARKNF--LE 52

Query: 61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEF----IN 116
            +  +  N  A     +N  +DLS DEFKN +L + EA   + L     L+ E     IN
Sbjct: 53  SVKYVQSNGGA-----INHLSDLSLDEFKNRFLMSAEAF--EHLKTQFDLNAETNACSIN 105

Query: 117 -SIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDH 175
            + P   D R    VTP++ QG CGSCW+FS     E  +   +N+ + L+EQ LVDC  
Sbjct: 106 GNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLAEQELVDC-- 163

Query: 176 ECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKI 235
                    A   GC+G   P    YI  NG +Q ES Y Y A   +    N+   G  I
Sbjct: 164 ---------ASQHGCHGDTIPRGIEYIQHNGVVQ-ESYYRYVAREQSCRRPNAQRFG--I 211

Query: 236 SNFTMI-PKNETVMAGYIVSTGPLAIAA-----DAVEWQFYIGGVF---DIPCNPNSLDH 286
           SN+  I P N   +   +  T   AIA      D   ++ Y G      D    PN   H
Sbjct: 212 SNYCQIYPPNVNKIREALAQTHS-AIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNY--H 268

Query: 287 GILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIY 324
            + IVGYS       + + YWIV+NSW  +WG+ GY Y
Sbjct: 269 AVNIVGYSN-----AQGVDYWIVRNSWDTNWGDNGYGY 301


>sp|P80067|CATC_RAT DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (DPPI) (CATHEPSIN C)
           (CATHEPSIN J) (DIPEPTIDYL TRANSFERASE)
          Length = 462

 Score =  117 bits (291), Expect = 3e-26
 Identities = 81/255 (31%), Positives = 128/255 (49%), Gaps = 32/255 (12%)

Query: 105 PVADYLDDEFINSIPTAFDWRT-RGA--VTPVKNQGQCGSCWSFSTTGNVEGQHFISQNK 161
           P+ D +  + + S+P ++DWR  RG   V+PV+NQ  CGSC+SF++ G +E +  I  N 
Sbjct: 218 PITDEIQQQIL-SLPESWDWRNVRGINFVSPVRNQESCGSCYSFASIGMLEARIRILTNN 276

Query: 162 LVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAE 219
             +  LS Q +V C              +GC+GG          ++ G+  E+ +PYTA 
Sbjct: 277 SQTPILSPQEVVSCSPYA----------QGCDGGFPYLIAGKYAQDFGVVEENCFPYTA- 325

Query: 220 TGTQCNFNSANIGAKISNFTMIPK-----NETVMAGYIVSTGPLAIAADAVE-WQFYIGG 273
           T   C      +    S +  +       NE +M   +V  GP+A+A +  + +  Y  G
Sbjct: 326 TDAPCKPKENCLRYYSSEYYYVGGFYGGCNEALMKLELVKHGPMAVAFEVHDDFLHYHSG 385

Query: 274 VF-----DIPCNPNSL-DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRR 327
           ++       P NP  L +H +L+VGY  K+ +    + YWIVKNSWG+ WGE GY  +RR
Sbjct: 386 IYHHTGLSDPFNPFELTNHAVLLVGYG-KDPV--TGLDYWIVKNSWGSQWGESGYFRIRR 442

Query: 328 GKNTCGVSNFVSTSI 342
           G + C + +    +I
Sbjct: 443 GTDECAIESIAMAAI 457


>sp|P97821|CATC_MOUSE DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (DPPI) (CATHEPSIN C)
           (CATHEPSIN J) (DIPEPTIDYL TRANSFERASE)
          Length = 462

 Score =  116 bits (287), Expect = 8e-26
 Identities = 90/331 (27%), Positives = 156/331 (46%), Gaps = 42/331 (12%)

Query: 34  DKFNKKYSH-----EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEF 88
           +K N   +H     E Y ER  ++  N   ++ +N +    K+ T     ++  +S  + 
Sbjct: 147 EKVNMNAAHLGGLQERYSER--LYTHNHNFVKAINTV---QKSWTATAYKEYEKMSLRDL 201

Query: 89  KNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRT-RGA--VTPVKNQGQCGSCWSF 145
                +++        P+ D +  + +N +P ++DWR  +G   V+PV+NQ  CGSC+SF
Sbjct: 202 IRRSGHSQRIPRPKPAPMTDEIQQQILN-LPESWDWRNVQGVNYVSPVRNQESCGSCYSF 260

Query: 146 STTGNVEGQHFISQNKLVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYII 203
           ++ G +E +  I  N   +  LS Q +V C              +GC+GG          
Sbjct: 261 ASMGMLEARIRILTNNSQTPILSPQEVVSCSPYA----------QGCDGGFPYLIAGKYA 310

Query: 204 KNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPK-----NETVMAGYIVSTGPL 258
           ++ G+  ES +PYTA+  + C      +    S++  +       NE +M   +V  GP+
Sbjct: 311 QDFGVVEESCFPYTAKD-SPCKPRENCLRYYSSDYYYVGGFYGGCNEALMKLELVKHGPM 369

Query: 259 AIAADAVE-WQFYIGGVF-----DIPCNPNSL-DHGILIVGYSAKNTIFRKNMPYWIVKN 311
           A+A +  + +  Y  G++       P NP  L +H +L+VGY          + YWI+KN
Sbjct: 370 AVAFEVHDDFLHYHSGIYHHTGLSDPFNPFELTNHAVLLVGYGRDPVT---GIEYWIIKN 426

Query: 312 SWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 342
           SWG++WGE GY  +RRG + C + +    +I
Sbjct: 427 SWGSNWGESGYFRIRRGTDECAIESIAVAAI 457


>sp|P53634|CATC_HUMAN DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (DPPI) (CATHEPSIN C)
           (CATHEPSIN J) (DIPEPTIDYL TRANSFERASE)
          Length = 463

 Score =  113 bits (281), Expect = 4e-25
 Identities = 75/236 (31%), Positives = 113/236 (47%), Gaps = 31/236 (13%)

Query: 118 IPTAFDWRTRGA---VTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVS--LSEQNLVD 172
           +PT++DWR       V+PV+NQ  CGSC+SF++ G +E +  I  N   +  LS Q +V 
Sbjct: 231 LPTSWDWRNVHGINFVSPVRNQASCGSCYSFASMGMLEARIRILTNNSQTPILSPQEVVS 290

Query: 173 CDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG 232
           C              +GC GG          ++ G+  E+ +PYT  T + C        
Sbjct: 291 CSQYA----------QGCEGGFPYLIAGKYAQDFGLVEEACFPYTG-TDSPCKMKEDCFR 339

Query: 233 AKISNFTMIPK-----NETVMAGYIVSTGPLAIAADAVE-WQFYIGGVFDI-----PCNP 281
              S +  +       NE +M   +V  GP+A+A +  + +  Y  G++       P NP
Sbjct: 340 YYSSEYHYVGGFYGGCNEALMKLELVHHGPMAVAFEVYDDFLHYKKGIYHHTGLRDPFNP 399

Query: 282 NSL-DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN 336
             L +H +L+VGY   +      M YWIVKNSWG  WGE GY  +RRG + C + +
Sbjct: 400 FELTNHAVLLVGYGTDSA---SGMDYWIVKNSWGTGWGENGYFRIRRGTDECAIES 452


>sp|Q26563|CATC_SCHMA CATHEPSIN C PRECURSOR
          Length = 454

 Score =  113 bits (279), Expect = 7e-25
 Identities = 75/242 (30%), Positives = 113/242 (45%), Gaps = 35/242 (14%)

Query: 117 SIPTAFDWRT-----RGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQN--KLVSLSEQN 169
           ++P  FDW +     R  VTP++NQG CGSC++  +   +E +  +  N  +   LS Q 
Sbjct: 217 NLPLEFDWTSPPDGSRSPVTPIRNQGICGSCYASPSAAALEARIRLVSNFSEQPILSPQT 276

Query: 170 LVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSA 229
           +VDC              EGCNGG          ++ G+  +   PYT E   +C  +  
Sbjct: 277 VVDCS----------PYSEGCNGGFPFLIAGKYGEDFGLPQKIVIPYTGEDTGKCTVSKN 326

Query: 230 NIGAKISNFTMI-----PKNETVMAGYIVSTGPLAIAADAVE-WQFYIGGVFDIPC---- 279
                 ++++ I       NE +M   ++S GP  +  +  E +QFY  G++        
Sbjct: 327 CTRYYTTDYSYIGGYYGATNEKLMQLELISNGPFPVGFEVYEDFQFYKEGIYHHTTVQTD 386

Query: 280 ----NPNSL-DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGV 334
               NP  L +H +L+VGY           PYW VKNSWG +WGEQGY  + RG + CGV
Sbjct: 387 HYNFNPFELTNHAVLLVGYGVDKL---SGEPYWKVKNSWGVEWGEQGYFRILRGTDECGV 443

Query: 335 SN 336
            +
Sbjct: 444 ES 445


>sp|P25773|CATL_FELCA CATHEPSIN L (PROGESTERONE-DEPENDENT PROTEIN) (PDP)
          Length = 139

 Score =  113 bits (279), Expect = 7e-25
 Identities = 55/141 (39%), Positives = 84/141 (59%), Gaps = 5/141 (3%)

Query: 192 GGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGY 251
           GGL  +A+ Y+  NGG+ +E SYPY A+ G  C +   N  A ++++  IP  E  +   
Sbjct: 1   GGLIDDAFQYVKDNGGLDSEESYPYHAQ-GDSCKYRPENSVANVTDYWDIPSKENELMIT 59

Query: 252 IVSTGPLAIAADAV--EWQFYIGGVF-DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWI 308
           + + GP++ A DA    ++FY  G++ D  C+   +DHG+L+VGY A  T   +N  YWI
Sbjct: 60  LAAVGPISAAIDASLDTFRFYKEGIYYDPSCSSEDVDHGVLVVGYGADGTE-TENKKYWI 118

Query: 309 VKNSWGADWGEQGYIYLRRGK 329
           +KNSWG DWG  GYI + + +
Sbjct: 119 IKNSWGTDWGMDGYIKMAKDR 139


>sp|P25780|EUM1_EURMA MITE GROUP I ALLERGEN EUR M 1 (EUR M I)
          Length = 211

 Score =  105 bits (260), Expect = 1e-22
 Identities = 73/222 (32%), Positives = 102/222 (45%), Gaps = 29/222 (13%)

Query: 117 SIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 176
           S+P+  D R+   VTP++ QG CGSCW+FS   + E  +   +N  + L+EQ LVDC   
Sbjct: 10  SLPSELDLRSLRTVTPIRMQGGCGSCWAFSGVASTESAYLAYRNMSLDLAEQELVDC--- 66

Query: 177 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKIS 236
                   A   GC+G   P    YI +NG +Q E  YPY A   +    N+   G K  
Sbjct: 67  --------ASQNGCHGDTIPRGIEYIQQNGVVQ-EHYYPYVAREQSCHRPNAQRYGLK-- 115

Query: 237 NFTMIPKNETVMAGYIVSTGPLAIAA-----DAVEWQFYIGGVF---DIPCNPNSLDHGI 288
           N+  I   ++      ++    A+A      D   ++ Y G      D    PN   H +
Sbjct: 116 NYCQISPPDSNKIRQALTQTHTAVAVIIGIKDLNAFRHYDGRTIMQHDNGYQPNY--HAV 173

Query: 289 LIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKN 330
            IVGY   NT   + + YWIV+NSW   WG+ GY Y     N
Sbjct: 174 NIVGYG--NT---QGVDYWIVRNSWDTTWGDNGYGYFAANIN 210


>sp|Q23894|CYS3_DICDI CYSTEINE PROTEINASE 3 (CYSTEINE PROTEINASE II)
          Length = 151

 Score = 95.6 bits (234), Expect = 1e-19
 Identities = 61/157 (38%), Positives = 86/157 (53%), Gaps = 17/157 (10%)

Query: 41  SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIF 100
           +H+E++ R+E FK N+  +   N    +  + T  G+N+ ADLS++E++  YL  +  I 
Sbjct: 1   THKEFMPRYEEFKKNMDYVHNWN----SKGSKTVLGLNQHADLSNEEYRLNYLGTRAHIK 56

Query: 101 TDDLPVADY---LDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFI 157
            +     +    L+       P   DWR + AVTPVK+QGQCGSC   STTG+VEG   I
Sbjct: 57  LNGYHKRNLGLRLNRPHFKQ-PLNVDWREKDAVTPVKDQGQCGSC-IISTTGSVEGVTAI 114

Query: 158 SQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGL 194
              KLVSLSEQN++               +EGCNGGL
Sbjct: 115 KTGKLVSLSEQNILRL--------SSSFGNEGCNGGL 143


>sp|P43508|CPR4_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 4 PRECURSOR
          Length = 335

 Score = 94.4 bits (231), Expect = 3e-19
 Identities = 82/300 (27%), Positives = 129/300 (42%), Gaps = 60/300 (20%)

Query: 82  DLSSDEFKNYYLNNK-EAIFTDDLPVADYLDDEFINSIPTAFDWRTRG----AVTPVKNQ 136
           D++ ++ K   +  +  A  T D+ V  +  +E  ++IP  FD RT+     ++  +++Q
Sbjct: 46  DITIEQVKKRLMRTEFVAPHTPDVEVVKHDINE--DTIPATFDARTQWPNCMSINNIRDQ 103

Query: 137 GQCGSCWSFSTTGNVEGQHFISQNKLVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGL 194
             CGSCW+F+       +  I+ N  V+  LS ++++ C   C        C  GC GG 
Sbjct: 104 SDCGSCWAFAAAEAASDRFCIASNGAVNTLLSAEDVLSC---CSN------CGYGCEGGY 154

Query: 195 QPNAYNYIIKNGGIQTESSY-------PYT-AETG------------------------- 221
             NA+ Y++K+G   T  SY       PY+ A  G                         
Sbjct: 155 PINAWKYLVKSG-FCTGGSYEAQFGCKPYSLAPCGETVGNVTWPSCPDDGYDTPACVNKC 213

Query: 222 TQCNFNSANIGAKISNFTM--IPKNETVMAGYIVSTGPLAIAADAVE-WQFYIGGVFDIP 278
           T  N+N A    K    T   + K  + +   I++ GP+  A    E +  Y  GV+   
Sbjct: 214 TNKNYNVAYTADKHFGSTAYAVGKKVSQIQAEIIAHGPVEAAFTVYEDFYQYKTGVYVHT 273

Query: 279 CNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFV 338
                  H I I+G+   N       PYW+V NSW  +WGE GY  + RG N CG+ + V
Sbjct: 274 TGQELGGHAIRILGWGTDN-----GTPYWLVANSWNVNWGENGYFRIIRGTNECGIEHAV 328


>sp|P05993|PAP5_CARPA CYSTEINE PROTEINASE (CLONE PLBPC13)
          Length = 96

 Score = 90.5 bits (221), Expect = 5e-18
 Identities = 43/87 (49%), Positives = 55/87 (62%), Gaps = 2/87 (2%)

Query: 256 GPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKN--TIFRKNMPYWIVKNSW 313
           GPLA+A +A   Q YIGGV         L+HG+L+VGY +     I  K  PYW++KNSW
Sbjct: 1   GPLAVAINAAYMQTYIGGVSCPYICSRRLNHGVLLVGYGSAGYAPIRLKEKPYWVIKNSW 60

Query: 314 GADWGEQGYIYLRRGKNTCGVSNFVST 340
           G +WGE GY  + RG+N CGV + VST
Sbjct: 61  GENWGENGYYKICRGRNICGVDSMVST 87


>sp|P25807|CYS1_CAEEL GUT-SPECIFIC CYSTEINE PROTEINASE PRECURSOR
          Length = 329

 Score = 90.5 bits (221), Expect = 5e-18
 Identities = 69/288 (23%), Positives = 118/288 (40%), Gaps = 46/288 (15%)

Query: 82  DLSSDEFKNYYLNNK-EAIFTDDLPVADYLDDEFINSIPTAFDWRTRGA----VTPVKNQ 136
           +++ +E K   ++ K  A  +D++   +   +  + S+P  FD RT+ +    +  +++Q
Sbjct: 50  EITEEEMKFKLMDGKYAAAHSDEIRATE--QEVVLASVPATFDSRTQWSECKSIKLIRDQ 107

Query: 137 GQCGSCWSFSTTGNVEGQHFISQNKLVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGL 194
             CGSCW+F     +  +  I         +S  +L+ C   C       +C  GC GG 
Sbjct: 108 ATCGSCWAFGAAEMISDRTCIETKGAQQPIISPDDLLSC---C-----GSSCGNGCEGGY 159

Query: 195 QPNAYNY-----IIKNGGIQTESSYPY--------------TAETGTQCNFNSANIGAKI 235
              A  +     ++  G        PY              T      C    +   AK 
Sbjct: 160 PIQALRWWDSKGVVTGGDYHGAGCKPYPIAPCTSGNCPESKTPSCSMSCQSGYSTAYAKD 219

Query: 236 SNFTM----IPKNETVMAGYIVSTGPLAIAADAVE-WQFYIGGVFDIPCNPNSLDHGILI 290
            +F +    +PKN   +   I + GP+  A    E +  Y  GV+          H I I
Sbjct: 220 KHFGVSAYAVPKNAASIQAEIYANGPVEAAFSVYEDFYKYKSGVYKHTAGKYLGGHAIKI 279

Query: 291 VGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFV 338
           +G+  ++       PYW+V NSWG +WGE G+  + RG + CG+ + V
Sbjct: 280 IGWGTES-----GSPYWLVANSWGVNWGESGFFKIYRGDDQCGIESAV 322


>sp|P43509|CPR5_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 5 PRECURSOR
          Length = 344

 Score = 89.3 bits (218), Expect = 1e-17
 Identities = 69/272 (25%), Positives = 113/272 (41%), Gaps = 55/272 (20%)

Query: 108 DYLDDEFINSIPTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLV 163
           D +  E  ++IP  FD    W    ++  +++Q  CGSCW+F+    +  +  I+ N  V
Sbjct: 72  DIVATEVSDAIPDHFDARDQWPNCMSINNIRDQSDCGSCWAFAAAEAISDRTCIASNGAV 131

Query: 164 S--LSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSY------- 214
           +  LS ++L+ C        G  +C  GC GG    A+ + +K+G + T  SY       
Sbjct: 132 NTLLSSEDLLSC------CTGMFSCGNGCEGGYPIQAWKWWVKHG-LVTGGSYETQFGCK 184

Query: 215 -------------------PYTAETGTQC--------NFNSANIGAKISNFTM--IPKNE 245
                              P   E   +C        N+ +  +  K    T   + K  
Sbjct: 185 PYSIAPCGETVNGVKWPACPEDTEPTPKCVDSCTSKNNYATPYLQDKHFGSTAYAVGKKV 244

Query: 246 TVMAGYIVSTGPLAIAADAVE-WQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNM 304
             +   I++ GP+ +A    E +  Y  GV+      +   H + I+G+   N       
Sbjct: 245 EQIQTEILTNGPIEVAFTVYEDFYQYTTGVYVHTAGASLGGHAVKILGWGVDN-----GT 299

Query: 305 PYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN 336
           PYW+V NSW   WGE+GY  + RG N CG+ +
Sbjct: 300 PYWLVANSWNVAWGEKGYFRIIRGLNECGIEH 331


>sp|P00787|CATB_RAT CATHEPSIN B PRECURSOR (CATHEPSIN B1) (RSG-2)
          Length = 339

 Score = 87.8 bits (214), Expect = 3e-17
 Identities = 68/264 (25%), Positives = 114/264 (42%), Gaps = 51/264 (19%)

Query: 117 SIPTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSL--SEQNL 170
           ++P +FD    W     +  +++QG CGSCW+F     +  +  I  N  V++  S ++L
Sbjct: 79  NLPESFDAREQWSNCPTIAQIRDQGSCGSCWAFGAVEAMSDRICIHTNGRVNVEVSAEDL 138

Query: 171 VDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIK----NGGIQTE--------------- 211
           + C   C        C +GCNGG    A+N+  +    +GG+                  
Sbjct: 139 LTC---C-----GIQCGDGCNGGYPSGAWNFWTRKGLVSGGVYNSHIGCLPYTIPPCEHH 190

Query: 212 ---SSYPYTAETGT-QCN------FNSANIGAKISNFTM--IPKNETVMAGYIVSTGPLA 259
              S  P T E  T +CN      ++++    K   +T   +  +E  +   I   GP+ 
Sbjct: 191 VNGSRPPCTGEGDTPKCNKMCEAGYSTSYKEDKHYGYTSYSVSDSEKEIMAEIYKNGPVE 250

Query: 260 IAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWG 318
            A     ++  Y  GV+          H I I+G+  +N +     PYW+V NSW  DWG
Sbjct: 251 GAFTVFSDFLTYKSGVYKHEAGDVMGGHAIRILGWGIENGV-----PYWLVANSWNVDWG 305

Query: 319 EQGYIYLRRGKNTCGVSNFVSTSI 342
           + G+  + RG+N CG+ + +   I
Sbjct: 306 DNGFFKILRGENHCGIESEIVAGI 329


>sp|P07688|CATB_BOVIN CATHEPSIN B PRECURSOR
          Length = 335

 Score = 87.0 bits (212), Expect = 5e-17
 Identities = 67/259 (25%), Positives = 103/259 (38%), Gaps = 55/259 (21%)

Query: 118 IPTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSL---SEQNL 170
           +P +FD    W     +  +++QG CGSCW+F     +  +  I  N  V++   +E  L
Sbjct: 80  LPESFDAREQWPNCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHSNGRVNVEVSAEDML 139

Query: 171 VDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQ--------------------- 209
             C  EC          +GCNGG    A+N+  K G +                      
Sbjct: 140 TCCGGEC---------GDGCNGGFPSGAWNFWTKKGLVSGGLYNSHVGCRPYSIPPCEHH 190

Query: 210 -TESSYPYTAETGT-QCNFNSANIGAKIS---------NFTMIPKNETVMAGYIVSTGPL 258
              S  P T E  T +CN  +   G   S         +   +  NE  +   I   GP+
Sbjct: 191 VNGSRPPCTGEGDTPKCN-KTCEPGYSPSYKEDKHFGCSSYSVANNEKEIMAEIYKNGPV 249

Query: 259 AIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADW 317
             A     ++  Y  GV+          H I I+G+  +N       PYW+V NSW  DW
Sbjct: 250 EGAFSVYSDFLLYKSGVYQHVSGEIMGGHAIRILGWGVEN-----GTPYWLVGNSWNTDW 304

Query: 318 GEQGYIYLRRGKNTCGVSN 336
           G+ G+  + RG++ CG+ +
Sbjct: 305 GDNGFFKILRGQDHCGIES 323


>sp|P07858|CATB_HUMAN CATHEPSIN B PRECURSOR (CATHEPSIN B1) (APP SECRETASE)
          Length = 339

 Score = 85.8 bits (209), Expect = 1e-16
 Identities = 70/285 (24%), Positives = 110/285 (38%), Gaps = 63/285 (22%)

Query: 96  KEAIFTDDLPVADYLDDEFINSIPTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNV 151
           +  +FT+DL             +P +FD    W     +  +++QG CGSCW+F     +
Sbjct: 70  QRVMFTEDL------------KLPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAI 117

Query: 152 EGQHFISQNKLVSL--SEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQ 209
             +  I  N  VS+  S ++L+ C   C        C +GCNGG    A+N+  + G + 
Sbjct: 118 SDRICIHTNAHVSVEVSAEDLLTC---C-----GSMCGDGCNGGYPAEAWNFWTRKGLVS 169

Query: 210 ----------------------TESSYPYTAETGTQCNFNSANIGAKIS---------NF 238
                                   S  P T E  T         G   +         N 
Sbjct: 170 GGLYESHVGCRPYSIPPCEHHVNGSRPPCTGEGDTPKCSKICEPGYSPTYKQDKHYGYNS 229

Query: 239 TMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKN 297
             +  +E  +   I   GP+  A     ++  Y  GV+          H I I+G+  +N
Sbjct: 230 YSVSNSEKDIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVTGEMMGGHAIRILGWGVEN 289

Query: 298 TIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 342
                  PYW+V NSW  DWG+ G+  + RG++ CG+ + V   I
Sbjct: 290 -----GTPYWLVANSWNTDWGDNGFFKILRGQDHCGIESEVVAGI 329


>sp|P43157|CYSP_SCHJA CATHEPSIN B-LIKE CYSTEINE PROTEINASE PRECURSOR (ANTIGEN SJ31)
          Length = 342

 Score = 84.7 bits (206), Expect = 3e-16
 Identities = 66/268 (24%), Positives = 111/268 (40%), Gaps = 59/268 (22%)

Query: 118 IPTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQN--KLVSLSEQNLV 171
           IP+ FD    W    +++ +++Q +CGSCW+F     +  +  I     +   LS  +L+
Sbjct: 90  IPSQFDSRKKWPHCKSISQIRDQSRCGSCWAFGAVEAMTDRICIQSGGGQSAELSALDLI 149

Query: 172 DCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGI---------------------QT 210
            C   C +      C +GC GG    A++Y +K G +                      T
Sbjct: 150 SC---CKD------CGDGCQGGFPGVAWDYWVKRGIVTGGSKENHTGCQPYPFPKCEHHT 200

Query: 211 ESSYP-------------YTAETGTQCNFNS-ANIGAKISNFTMIPKNETVMAGYIVSTG 256
           +  YP              T + G +  +    + G +  N   +  NE V+   I+  G
Sbjct: 201 KGKYPACGTKIYKTPQCKQTCQKGYKTPYEQDKHYGDESYN---VQNNEKVIQRDIMMYG 257

Query: 257 PLAIAADAVE-WQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGA 315
           P+  A D  E +  Y  G++          H I I+G+  +     K  PYW++ NSW  
Sbjct: 258 PVEAAFDVYEDFLNYKSGIYRHVTGSIVGGHAIRIIGWGVE-----KRTPYWLIANSWNE 312

Query: 316 DWGEQGYIYLRRGKNTCGVSNFVSTSII 343
           DWGE+G   + RG++ C + + V   +I
Sbjct: 313 DWGEKGLFRMVRGRDECSIESDVVAGLI 340


>sp|P25792|CYSP_SCHMA CATHEPSIN B-LIKE CYSTEINE PROTEINASE PRECURSOR (ANTIGEN SM31)
          Length = 340

 Score = 84.7 bits (206), Expect = 3e-16
 Identities = 66/260 (25%), Positives = 109/260 (41%), Gaps = 53/260 (20%)

Query: 118 IPTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQN--KLVSLSEQNLV 171
           IP+ FD    W    ++  +++Q +CGSCWSF     +  +  I     + V LS  +L+
Sbjct: 89  IPSNFDSRKKWPGCKSIATIRDQSRCGSCWSFGAVEAMSDRSCIQSGGKQNVELSAVDLL 148

Query: 172 DCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTA---ETGTQCNFNS 228
            C   C      E+C  GC GG+   A++Y +K G +   S   +T        +C  ++
Sbjct: 149 TC---C------ESCGLGCEGGILGPAWDYWVKEGIVTASSKENHTGCEPYPFPKCEHHT 199

Query: 229 AN----IGAKISN---------------FTM----------IPKNETVMAGYIVSTGPLA 259
                  G+KI N               +T           +  +E  +   I+  GP+ 
Sbjct: 200 KGKYPPCGSKIYNTPRCKQTCQRKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVE 259

Query: 260 IAADAVE-WQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWG 318
            +    E +  Y  G++          H I I+G+  +N       PYW++ NSW  DWG
Sbjct: 260 ASFTVYEDFLNYKSGIYKHITGEALGGHAIRIIGWGVEN-----KTPYWLIANSWNEDWG 314

Query: 319 EQGYIYLRRGKNTCGVSNFV 338
           E GY  + RG++ C + + V
Sbjct: 315 ENGYFRIVRGRDECSIESEV 334


>sp|P10605|CATB_MOUSE CATHEPSIN B PRECURSOR (CATHEPSIN B1)
          Length = 339

 Score = 83.9 bits (204), Expect = 5e-16
 Identities = 69/265 (26%), Positives = 111/265 (41%), Gaps = 55/265 (20%)

Query: 118 IPTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSL--SEQNLV 171
           +P  FD    W     +  +++QG CGSCW+F     +  +  I  N  V++  S ++L+
Sbjct: 80  LPETFDAREQWSNCPTIGQIRDQGSCGSCWAFGAVEAISDRTCIHTNGRVNVEVSAEDLL 139

Query: 172 DCDHECMEYEGEEACDEGCNGGLQPNAYNYIIK----NGGIQTE---------------- 211
            C   C        C +GCNGG    A+++  K    +GG+                   
Sbjct: 140 TC---C-----GIQCGDGCNGGYPSGAWSFWTKKGLVSGGVYNSHVGCLPYTIPPCEHHV 191

Query: 212 --SSYPYTAETGT-QCNFNSANIGAKIS----------NFTMIPKNETVMAGYIVSTGPL 258
             S  P T E  T +CN  S   G   S          ++++    + +MA  I   GP+
Sbjct: 192 NGSRPPCTGEGDTPRCN-KSCEAGYSPSYKEDKHFGYTSYSVSNSVKEIMAE-IYKNGPV 249

Query: 259 AIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADW 317
             A     ++  Y  GV+          H I I+G+  +N +     PYW+  NSW  DW
Sbjct: 250 EGAFTVFSDFLTYKSGVYKHEAGDMMGGHAIRILGWGVENGV-----PYWLAANSWNLDW 304

Query: 318 GEQGYIYLRRGKNTCGVSNFVSTSI 342
           G+ G+  + RG+N CG+ + +   I
Sbjct: 305 GDNGFFKILRGENHCGIESEIVAGI 329


>sp|P43510|CPR6_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 6 PRECURSOR
          Length = 379

 Score = 83.5 bits (203), Expect = 6e-16
 Identities = 72/265 (27%), Positives = 114/265 (42%), Gaps = 61/265 (23%)

Query: 118 IPTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNK--LVSLSEQNLV 171
           IP +FD    W    ++  +++Q  CGSCW+F     +  +  I+ +    V+LS  +L+
Sbjct: 105 IPESFDSRDNWPKCDSIKVIRDQSSCGSCWAFGAVEAMSDRICIASHGELQVTLSADDLL 164

Query: 172 DCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQ------CN 225
            C   C      ++C  GCNGG    A+ Y +K+G I T S+Y  TA  G +      C 
Sbjct: 165 SC---C------KSCGFGCNGGDPLAAWRYWVKDG-IVTGSNY--TANNGCKPYPFPPCE 212

Query: 226 FNSANIGAK----------------ISNFTMIPKNETVMAGY---------------IVS 254
            +S                      +S++T    +E    G                +++
Sbjct: 213 HHSKKTHFDPCPHDLYPTPKCEKKCVSDYTDKTYSEDKFFGASAYGVKDDVEAIQKELMT 272

Query: 255 TGPLAIAADAVE-WQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSW 313
            GPL IA +  E +  Y GGV+          H + ++G+   + I     PYW V NSW
Sbjct: 273 HGPLEIAFEVYEDFLNYDGGVYVHTGGKLGGGHAVKLIGWGIDDGI-----PYWTVANSW 327

Query: 314 GADWGEQGYIYLRRGKNTCGVSNFV 338
             DWGE G+  + RG + CG+ + V
Sbjct: 328 NTDWGEDGFFRILRGVDECGIESGV 352


>sp|P43233|CATB_CHICK CATHEPSIN B PRECURSOR (CATHEPSIN B1)
          Length = 340

 Score = 83.5 bits (203), Expect = 6e-16
 Identities = 69/278 (24%), Positives = 112/278 (39%), Gaps = 56/278 (20%)

Query: 100 FTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQ 159
           F +D+ + D  D        T   W     ++ +++QG CGSCW+F     +  +  +  
Sbjct: 74  FAEDMDLPDTFD--------TRKQWPNCPTISEIRDQGSCGSCWAFGAVEAISDRICVHT 125

Query: 160 NKLVSL--SEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQ-------- 209
           N  VS+  S ++L+ C   C    G E C  GCNGG    A+ Y  + G +         
Sbjct: 126 NAKVSVEVSAEDLLSC---C----GFE-CGMGCNGGYPSGAWRYWTERGLVSGGLYDSHV 177

Query: 210 --------------TESSYPYTAETGT--QCN------FNSANIGAKISNFTM--IPKNE 245
                           S  P T E G   +C+      ++ +    K    T   +P++E
Sbjct: 178 GCRAYTIPPCEHHVNGSRPPCTGEGGETPRCSRHCEPGYSPSYKEDKHYGITSYGVPRSE 237

Query: 246 TVMAGYIVSTGPLAIAADAVE-WQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNM 304
             +   I   GP+  A    E +  Y  GV+          H I I+G+  +N       
Sbjct: 238 KEIMAEIYKNGPVEGAFIVYEDFLMYKSGVYQHVSGEQVGGHAIRILGWGVEN-----GT 292

Query: 305 PYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 342
           PYW+  NSW  DWG  G+  + RG++ CG+ + +   +
Sbjct: 293 PYWLAANSWNTDWGITGFFKILRGEDHCGIESEIVAGV 330


>sp|P25802|CYS1_OSTOS CATHEPSIN B-LIKE CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 341

 Score = 76.1 bits (184), Expect = 1e-13
 Identities = 65/270 (24%), Positives = 104/270 (38%), Gaps = 54/270 (20%)

Query: 103 DLPVADYLDDEFINSIPTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFIS 158
           D  V D   +E  + IP ++D    W    ++  + +Q  CGSCW+ S+   +  +  I+
Sbjct: 76  DEEVEDEELEENNDDIPESYDPRIQWANCSSLFHIPDQANCGSCWAVSSAAAMSDRICIA 135

Query: 159 QN--KLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNY-----IIKNGGIQTE 211
               K V +S Q++V C   C        C +GC GG   +A+ +     ++  G   T+
Sbjct: 136 SKGAKQVLISAQDVVSC---CTW------CGDGCEGGWPISAFRFHADEGVVTGGDYNTK 186

Query: 212 SSY-PYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGY------------------- 251
            S  PY        + N    G  +            + GY                   
Sbjct: 187 GSCRPYEIHPCGH-HGNETYYGECVGMADTPRCKRRCLLGYPKSYPSDRYYKKAYQLKNS 245

Query: 252 -------IVSTGPLAIAADAVE-WQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKN 303
                  I+  GP+       E +  Y  G++       +  H + ++G+  +     K 
Sbjct: 246 VKAIQKDIMKNGPVVATYTVYEDFAHYRSGIYKHKAGRKTGLHAVKVIGWGEE-----KG 300

Query: 304 MPYWIVKNSWGADWGEQGYIYLRRGKNTCG 333
            PYWIV NSW  DWGE G+  + RG N CG
Sbjct: 301 TPYWIVANSWHDDWGENGFFRMHRGSNDCG 330


>sp|P25793|CYS2_HAECO CATHEPSIN B-LIKE CYSTEINE PROTEINASE 2 PRECURSOR
          Length = 342

 Score = 75.3 bits (182), Expect = 2e-13
 Identities = 55/247 (22%), Positives = 102/247 (41%), Gaps = 50/247 (20%)

Query: 133 VKNQGQCGSCWSFSTTGNVEGQHFISQN--KLVSLSEQNLVDCDHECMEYEGEEACDEGC 190
           +++Q  CGSCW+ ST   +  +  I+    K V++S  +++ C   C        C +GC
Sbjct: 105 IRDQANCGSCWAVSTAAAISDRICIASKAEKQVNISATDIMTC---C-----RPQCGDGC 156

Query: 191 NGGLQPNAYNYIIKNGGIQ------TESSYPYTAET----GTQCNFNSANIGAKI----- 235
            GG    A+ Y I +G +        +   PY        G    +      A       
Sbjct: 157 EGGWPIEAWKYFIYDGVVSGGEYLTKDVCRPYPIHPCGHHGNDTYYGECRGTAPTPPCKR 216

Query: 236 -----------------SNFTMIPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFD 276
                             +  ++ ++   +   I+  GP+ +A+ AV  +++ Y  G++ 
Sbjct: 217 KCRPGVRKMYRIDKRYGKDAYIVKQSVKAIQSEILKNGPV-VASFAVYEDFRHYKSGIYK 275

Query: 277 IPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN 336
                    H + ++G+  +N     N  +W++ NSW  DWGE+GY  + RG N CG+  
Sbjct: 276 HTAGELRGYHAVKMIGWGNEN-----NTDFWLIANSWHNDWGEKGYFRIVRGSNDCGIEG 330

Query: 337 FVSTSII 343
            ++  I+
Sbjct: 331 TIAAGIV 337


>sp|P19092|CYS1_HAECO CATHEPSIN B-LIKE CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 342

 Score = 74.5 bits (180), Expect = 3e-13
 Identities = 55/247 (22%), Positives = 102/247 (41%), Gaps = 50/247 (20%)

Query: 133 VKNQGQCGSCWSFSTTGNVEGQHFISQN--KLVSLSEQNLVDCDHECMEYEGEEACDEGC 190
           +++Q  CGSCW+ ST   +  +  I+    K V++S  +++ C   C        C +GC
Sbjct: 105 IRDQANCGSCWAVSTAAAISDRICIASKAEKQVNISATDIMTC---C-----RPQCGDGC 156

Query: 191 NGGLQPNAYNYIIKNGGIQ------TESSYPYTAET----GTQCNFNSANIGAKI----- 235
            GG    A+ Y I +G +        +   PY        G    +      A       
Sbjct: 157 EGGWPIEAWKYFIYDGVVSGGEYLTKDVCRPYPIHPCGHHGNDTYYGECRGTAPTPPCKR 216

Query: 236 -----------------SNFTMIPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFD 276
                             +  ++ ++   +   I+  GP+ +A+ AV  +++ Y  G++ 
Sbjct: 217 KCRPGVRKMYRIDKRYGKDAYIVKQSVKAIQSEILRNGPV-VASFAVYEDFRHYKSGIYK 275

Query: 277 IPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN 336
                    H + ++G+  +N     N  +W++ NSW  DWGE+GY  + RG N CG+  
Sbjct: 276 HTAGELRGYHAVKMIGWGNEN-----NTDFWLIANSWHNDWGEKGYFRIIRGTNDCGIEG 330

Query: 337 FVSTSII 343
            ++  I+
Sbjct: 331 TIAAGIV 337


>sp|P43507|CPR3_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 3 PRECURSOR
          Length = 370

 Score = 73.4 bits (177), Expect = 7e-13
 Identities = 61/259 (23%), Positives = 101/259 (38%), Gaps = 49/259 (18%)

Query: 118 IPTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVS--LSEQNLV 171
           +P  FD    W     +  ++NQ  CGSCW+F     +  +  I  N      +S ++++
Sbjct: 92  LPDTFDAREKWPDCNTIKLIRNQATCGSCWAFGAAEVISDRVCIQSNGTQQPVISVEDIL 151

Query: 172 DCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQ---------------------T 210
            C   C        C  GC GG    A  +   +G +                       
Sbjct: 152 SC---C-----GTTCGYGCKGGYSIEALRFWASSGAVTGGDYGGHGCMPYSFAPCTKNCP 203

Query: 211 ESSYPYTAETGTQCNFNSA------NIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA 264
           ES+ P + +T  Q ++ +       + GA     T   K+ T +   I   GP+  +   
Sbjct: 204 ESTTP-SCKTTCQSSYKTEEYKKDKHYGASAYKVTTT-KSVTEIQTEIYHYGPVEASYKV 261

Query: 265 VE-WQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYI 323
            E +  Y  GV+          H + I+G+  +N +      YW++ NSWG  +GE+G+ 
Sbjct: 262 YEDFYHYKSGVYHYTSGKLVGGHAVKIIGWGVENGV-----DYWLIANSWGTSFGEKGFF 316

Query: 324 YLRRGKNTCGVSNFVSTSI 342
            +RRG N C +   V   I
Sbjct: 317 KIRRGTNECQIEGNVVAGI 335


>sp|P13823|SERA_PLAFG SERINE-REPEAT ANTIGEN PROTEIN PRECURSOR (P126) (111 KD ANTIGEN)
          Length = 989

 Score = 70.6 bits (170), Expect = 4e-12
 Identities = 61/247 (24%), Positives = 101/247 (40%), Gaps = 50/247 (20%)

Query: 133 VKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE--EACDEGC 190
           V++QG C + W F++  ++E    +   +   +S   + +C      Y+GE  + CDEG 
Sbjct: 579 VEDQGNCDTSWIFASKYHLETIRCMKGYEPTKISALYVANC------YKGEHKDRCDEGS 632

Query: 191 NGGLQPNAYNYIIKNGG-IQTESSYPYT-AETGTQCN----------------------- 225
           +    P  +  II++ G +  ES+YPY   + G QC                        
Sbjct: 633 S----PMEFLQIIEDYGFLPAESNYPYNYVKVGEQCPKVEDHWMNLWDNGKILHNKNEPN 688

Query: 226 ---------FNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFD 276
                    + S      +  F  I K E +  G +++     I A+ V    + G    
Sbjct: 689 SLDGKGYTAYESERFHDNMDAFVKIIKTEVMNKGSVIAY----IKAENVMGYEFSGKKVQ 744

Query: 277 IPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN 336
             C  ++ DH + IVGY        +   YWIV+NSWG  WG++GY  +     T    N
Sbjct: 745 NLCGDDTADHAVNIVGYGNYVNSEGEKKSYWIVRNSWGPYWGDEGYFKVDMYGPTHCHFN 804

Query: 337 FVSTSII 343
           F+ + +I
Sbjct: 805 FIHSVVI 811


>sp|P32956|CC3_CARCN CYSTEINE PROTEINASE III (CC-III)
          Length = 43

 Score = 63.2 bits (151), Expect = 8e-10
 Identities = 25/35 (71%), Positives = 28/35 (79%)

Query: 119 PTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEG 153
           P + DWR +GAVTPVKNQG CGSCW+FST   VEG
Sbjct: 2   PESIDWRKKGAVTPVKNQGSCGSCWAFSTIATVEG 36


>sp|P32957|CC4_CARCN CYSTEINE PROTEINASE IV (CC-IV)
          Length = 43

 Score = 62.1 bits (148), Expect = 2e-09
 Identities = 25/35 (71%), Positives = 28/35 (79%)

Query: 119 PTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEG 153
           P + DWR +GAVTPVKNQG CGSCW+FST   VEG
Sbjct: 2   PESIDWRKKGAVTPVKNQGSCGSCWAFSTIVTVEG 36


>sp|Q06544|CYS3_OSTOS CATHEPSIN B-LIKE CYSTEINE PROTEINASE 3
          Length = 174

 Score = 59.3 bits (141), Expect = 1e-08
 Identities = 31/103 (30%), Positives = 49/103 (47%), Gaps = 15/103 (14%)

Query: 241 IPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIF 300
           I KN  V+AG+IV            ++  Y  G++       +  H + I+G+  +    
Sbjct: 87  IMKNGPVVAGFIVYE----------DFAHYKSGIYKHTAGRMTGGHAVKIIGWGKE---- 132

Query: 301 RKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
            K  PYW++ NSW  DWGE+G+  + RG N C +   V   I+
Sbjct: 133 -KGTPYWLIANSWHDDWGEKGFYRMIRGINNCRIEEMVFAGIV 174


>sp|P32954|CC1_CARCN CYSTEINE PROTEINASE I (CC-I)
          Length = 43

 Score = 58.6 bits (139), Expect = 2e-08
 Identities = 23/36 (63%), Positives = 28/36 (76%)

Query: 118 IPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEG 153
           I  + DWR +GAVTPV+NQG CGSCW+FS+   VEG
Sbjct: 1   IVASIDWRQKGAVTPVRNQGSCGSCWTFSSVAAVEG 36


>sp|P32955|CC2_CARCN CYSTEINE PROTEINASE II (CC-II)
          Length = 43

 Score = 58.2 bits (138), Expect = 3e-08
 Identities = 23/35 (65%), Positives = 27/35 (76%)

Query: 119 PTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEG 153
           P + DWR +GAVTPVK+Q  CGSCW+FST   VEG
Sbjct: 2   PGSVDWRQKGAVTPVKDQNPCGSCWAFSTVATVEG 36


>sp||CATL_CHICK_2 [Segment 2 of 2] CATHEPSIN L
          Length = 42

 Score = 51.9 bits (122), Expect = 2e-06
 Identities = 20/39 (51%), Positives = 28/39 (71%), Gaps = 1/39 (2%)

Query: 306 YWIVKNSWGADWGEQGYIYLRRG-KNTCGVSNFVSTSII 343
           YWIVKNSWG  WG++GYIY+ +  KN CG++   S  ++
Sbjct: 4   YWIVKNSWGEKWGDKGYIYMAKDRKNHCGIATAASYPLV 42


>sp|P12399|CT2A_MOUSE CTLA-2-ALPHA PROTEIN PRECURSOR
          Length = 136

 Score = 41.8 bits (96), Expect = 0.002
 Identities = 31/101 (30%), Positives = 50/101 (48%), Gaps = 4/101 (3%)

Query: 9   LAVFTVFVSSRGIPPEEQ--SQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIA 66
           L +  + + S   PP+    +++ E++ KF K Y+  E   R  +++ N  KIE  N   
Sbjct: 17  LLILCLGMMSAAPPPDPSLDNEWKEWKTKFAKAYNLNEERHRRLVWEENKKKIEAHNADY 76

Query: 67  INHKADTKFGVNKFADLSSDEFK-NYYLNN-KEAIFTDDLP 105
              K     G+N+F+DL+ +EFK N Y N+        DLP
Sbjct: 77  EQGKTSFYMGLNQFSDLTPEEFKTNCYGNSLNRGEMAPDLP 117


>sp|P21381|THPA_THADA THAUMATOPAIN
          Length = 35

 Score = 40.6 bits (93), Expect = 0.005
 Identities = 16/31 (51%), Positives = 22/31 (70%)

Query: 117 SIPTAFDWRTRGAVTPVKNQGQCGSCWSFST 147
           ++P + DW  +GAV  VKNQ  CGSC +FS+
Sbjct: 1   NLPNSVDWWKKGAVAAVKNQRXCGSCXAFSS 31


>sp|P05689|CATX_BOVIN CATHEPSIN
          Length = 73

 Score = 40.2 bits (92), Expect = 0.006
 Identities = 15/40 (37%), Positives = 24/40 (59%), Gaps = 5/40 (12%)

Query: 284 LDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYI 323
           ++H + + G+   +      M YWIV+NSWG  WGE G++
Sbjct: 9   INHIVSVAGWGVSD-----GMEYWIVRNSWGEPWGEHGWM 43


>sp|P12400|CT2B_MOUSE CTLA-2-BETA PROTEIN PRECURSOR
          Length = 141

 Score = 38.7 bits (88), Expect = 0.018
 Identities = 25/85 (29%), Positives = 45/85 (52%), Gaps = 1/85 (1%)

Query: 6   LFVLAVFTVFVSSRGIP-PEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNL 64
           +F+L +    +S+   P P   +++ E++  F K YS +E   R  +++ N  KIE  N 
Sbjct: 20  VFLLILCLGMMSAAPSPDPSLDNEWKEWKTTFAKAYSLDEERHRRLMWEENKKKIEAHNA 79

Query: 65  IAINHKADTKFGVNKFADLSSDEFK 89
                K     G+N+F+DL+ +EF+
Sbjct: 80  DYERGKTSFYMGLNQFSDLTPEEFR 104


>sp|P20736|BM86_BOOMI GLYCOPROTEIN ANTIGEN BM86 PRECURSOR (PROTECTIVE ANTIGEN)
          Length = 650

 Score = 35.2 bits (79), Expect = 0.21
 Identities = 24/81 (29%), Positives = 36/81 (43%), Gaps = 5/81 (6%)

Query: 147 TTGNVEGQHFISQNKLVSLSEQNLVDC----DHECMEYEGEEACDEGCNGGLQPNAYNYI 202
           TT N +        KL  + + +  +C    DHEC     +++C E  NG  Q +    +
Sbjct: 533 TTCNPKEIQECQDKKLECVYKNHKAECECPDDHECYREPAKDSCSEEDNGKCQSSGQRCV 592

Query: 203 IKNG-GIQTESSYPYTAETGT 222
           I+NG  +  E S   TA T T
Sbjct: 593 IENGKAVCKEKSEATTAATTT 613


>sp|Q11121|PLB1_TORDE LYSOPHOSPHOLIPASE PRECURSOR (PHOSPHOLIPASE B)
          Length = 649

 Score = 34.8 bits (78), Expect = 0.27
 Identities = 31/144 (21%), Positives = 56/144 (38%), Gaps = 13/144 (9%)

Query: 109 YLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQ 168
           Y DDE +  I   F+  TRG +T   +   C +C              + + K  SL+  
Sbjct: 519 YTDDERLKMIKNGFEAATRGNLTDDSSFMGCVAC-------------AVMRRKQQSLNAT 565

Query: 169 NLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNS 228
              +C      Y      D+    GL  + ++    +      ++  Y++ + T    N 
Sbjct: 566 LPEECSTCFTNYCWNGTIDDTPVSGLDNSDFDPTAASSAYSAYNTESYSSSSATGSKKNG 625

Query: 229 ANIGAKISNFTMIPKNETVMAGYI 252
           A + A  ++FT I    T +AG++
Sbjct: 626 AGLPATPTSFTSILTLLTAIAGFL 649


>sp|P46992|YJR1_YEAST HYPOTHETICAL 43.0 KD PROTEIN IN CPS1-FPP1 INTERGENIC REGION
          Length = 396

 Score = 33.6 bits (75), Expect = 0.61
 Identities = 40/191 (20%), Positives = 76/191 (38%), Gaps = 43/191 (22%)

Query: 77  VNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEF------------------INSI 118
           VNKF D++++E     + ++      + P+ADYL   F                  +N+ 
Sbjct: 42  VNKFKDITNNESCTCEVGDRVWFSGKNAPLADYLSVHFRGPLKLKQFAFYTSPGFTVNNS 101

Query: 119 PTAFDW----------RTRGAVTPVKNQGQCGSCW-------SFSTTGNVEGQHFISQNK 161
            ++ DW          +T   VT + + G+   C        S + TG+      ++   
Sbjct: 102 RSSSDWNRLAYYESSSKTADNVTFLNHGGEASPCLGNALSYASSNGTGSASEATVLADGT 161

Query: 162 LVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETG 221
           L+S  ++ ++  +  C +   ++ C    +G   P  Y Y    GG  T   + +  E  
Sbjct: 162 LISSDQEYIIYSNVSCPKSGYDKGCGVYRSG--IPAYYGY----GG--TTKMFLFEFEMP 213

Query: 222 TQCNFNSANIG 232
           T+   NS++IG
Sbjct: 214 TETEKNSSSIG 224


>sp|P28493|PR5_ARATH PATHOGENESIS-RELATED PROTEIN 5 PRECURSOR (PR-5)
          Length = 239

 Score = 32.1 bits (71), Expect = 1.8
 Identities = 24/93 (25%), Positives = 36/93 (37%), Gaps = 7/93 (7%)

Query: 133 VKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNG 192
           ++  G  G C      G V   +    + L  + + N+V C   C  +  ++ C  G N 
Sbjct: 137 IRPSGGSGDC---KYAGCVSDLNAACPDMLKVMDQNNVVACKSACERFNTDQYCCRGAND 193

Query: 193 GLQ---PNAYNYIIKNGGIQTESSYPYTAETGT 222
             +   P  Y+ I KN       SY Y  ET T
Sbjct: 194 KPETCPPTDYSRIFKN-ACPDAYSYAYDDETST 225


>sp|P41901|SPR3_YEAST SPORULATION-SPECIFIC SEPTIN
          Length = 512

 Score = 31.7 bits (70), Expect = 2.4
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 9/63 (14%)

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
           + +NLI +  K+D          L+ +E KN+    +E I   D+PV  +  DE +N+  
Sbjct: 237 KRVNLIPVIAKSDL---------LTKEELKNFKTQVREIIRVQDIPVCFFFGDEVLNATQ 287

Query: 120 TAF 122
             F
Sbjct: 288 DIF 290


>sp|P54634|POLN_LORDV NON-STRUCTURAL POLYPROTEIN [CONTAINS: RNA-DIRECTED RNA POLYMERASE ;
           THIOL PROTEASE 3C ; HELICASE (2C LIKE PROTEIN)]
          Length = 1699

 Score = 31.3 bits (69), Expect = 3.1
 Identities = 13/31 (41%), Positives = 21/31 (66%)

Query: 17  SSRGIPPEEQSQFLEFQDKFNKKYSHEEYLE 47
           SS+G+  EE  ++   +++ N KYS EEYL+
Sbjct: 893 SSKGLSDEEYDEYKRIREERNGKYSIEEYLQ 923


>sp|P21173|DNAA_MICLU CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
          Length = 515

 Score = 31.3 bits (69), Expect = 3.1
 Identities = 25/104 (24%), Positives = 46/104 (44%), Gaps = 13/104 (12%)

Query: 31  EFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKN 90
           EF + F     H+E     +++++    ++ L +  I   AD +  V +F       F  
Sbjct: 247 EFTNDFINSIRHDEGASFKQVYRN----VDILLIDDIQFLADKEATVEEFFHT----FNT 298

Query: 91  YYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVK 134
            Y NNK+ + T DLP        F + + + F+W   G +T ++
Sbjct: 299 LYNNNKQVVITSDLPPKQL--SGFEDRLRSRFEW---GLITDIQ 337


>sp|P89263|Y022_GVXN HYPOTHETICAL ORF22 HOMOLOG
          Length = 166

 Score = 30.5 bits (67), Expect = 5.3
 Identities = 27/107 (25%), Positives = 43/107 (39%), Gaps = 9/107 (8%)

Query: 144 SFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYII 203
           SF T     G H  SQ   V +S Q+LV        Y+    CD+          Y+ ++
Sbjct: 66  SFDTLEGPGGGHCFSQP--VRVSRQDLVT-------YDCASLCDDVRAAYFYVGPYDRLV 116

Query: 204 KNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAG 250
            +G    E  Y  T      CN  ++ +   I+++T I ++    AG
Sbjct: 117 VDGNELQEGGYCTTNSVPRNCNRETSILLHSINHWTCIAEDPRYYAG 163


>sp|P24896|NU5M_CAEEL NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 5
          Length = 527

 Score = 30.5 bits (67), Expect = 5.3
 Identities = 21/52 (40%), Positives = 26/52 (49%), Gaps = 7/52 (13%)

Query: 44  EYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNN 95
           +YL +  I+K    K  +L L  IN K  T F       LSS  FKNYYL +
Sbjct: 466 DYLAKNSIYKMKNLKFMDLFLNNINSKGYTLF-------LSSGMFKNYYLKS 510


>sp|P25648|SRB8_YEAST SUPPRESSOR OF RNA POLYMERASE B SRB8
          Length = 1427

 Score = 30.1 bits (66), Expect = 7.0
 Identities = 22/89 (24%), Positives = 44/89 (48%), Gaps = 10/89 (11%)

Query: 21   IPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGV--- 77
            +PP + S F++     +  Y  EE  ++ E F  NLG    + ++ I H+ + K+ +   
Sbjct: 1314 LPPFQVSSFVKETKLHSGDYGEEEDADQEESFSLNLG----IGIVEIAHENEQKWLIYDK 1369

Query: 78   --NKFADLSSDEFKNYYLNNKEAIFTDDL 104
              +K+    S E   ++++N    +TDD+
Sbjct: 1370 KDHKYVCTFSME-PYHFISNYNTKYTDDM 1397


>sp|Q04723|PEPC_LACLC AMINOPEPTIDASE C
          Length = 436

 Score = 30.1 bits (66), Expect = 7.0
 Identities = 11/20 (55%), Positives = 14/20 (70%)

Query: 303 NMPYWIVKNSWGADWGEQGY 322
           N   W V+NSWG D G++GY
Sbjct: 370 NSTKWKVENSWGKDAGQKGY 389


>sp|Q13867|BLMH_HUMAN BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH)
          Length = 455

 Score = 29.7 bits (65), Expect = 9.1
 Identities = 10/17 (58%), Positives = 13/17 (75%)

Query: 307 WIVKNSWGADWGEQGYI 323
           W V+NSWG D G +GY+
Sbjct: 392 WRVENSWGEDHGHKGYL 408


>sp|P87362|BLMH_CHICK BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH) (AMINOPEPTIDASE H)
          Length = 455

 Score = 29.7 bits (65), Expect = 9.1
 Identities = 10/19 (52%), Positives = 14/19 (73%)

Query: 307 WIVKNSWGADWGEQGYIYL 325
           W V+NSWG D G +GY+ +
Sbjct: 392 WRVENSWGEDRGNKGYLIM 410


>sp|P70645|BLMH_RAT BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH)
          Length = 454

 Score = 29.7 bits (65), Expect = 9.1
 Identities = 10/17 (58%), Positives = 13/17 (75%)

Query: 307 WIVKNSWGADWGEQGYI 323
           W V+NSWG D G +GY+
Sbjct: 392 WRVENSWGEDHGHKGYL 408


Searching..................................................done


Results from round 2


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value
Sequences used in model and found again:

sp|P04988|CYS1_DICDI CYSTEINE PROTEINASE 1 PRECURSOR                  527  e-149
sp|P25975|CATL_BOVIN CATHEPSIN L PRECURSOR                            440  e-123
sp|P07154|CATL_RAT CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTEIN...   431  e-121
sp|P06797|CATL_MOUSE CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTE...   431  e-120
sp|Q28944|CATL_PIG CATHEPSIN L PRECURSOR                              430  e-120
sp|P07711|CATL_HUMAN CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTE...   421  e-118
sp|O60911|CATM_HUMAN CATHEPSIN L2 PRECURSOR (CATHEPSIN V)             417  e-116
sp|P43296|RD19_ARATH CYSTEINE PROTEINASE RD19A PRECURSOR              412  e-115
sp|P25776|ORYA_ORYSA ORYZAIN ALPHA CHAIN PRECURSOR                    407  e-113
sp|P25782|CYS2_HOMAM DIGESTIVE CYSTEINE PROTEINASE 2 PRECURSOR        403  e-112
sp|P43295|A494_ARATH PROBABLE CYSTEINE PROTEINASE A494 PRECURSOR      402  e-112
sp|P43235|CATK_HUMAN CATHEPSIN K PRECURSOR (CATHEPSIN O) (CATHEP...   401  e-111
sp|P25804|CYSP_PEA CYSTEINE PROTEINASE 15A PRECURSOR (TURGOR-RES...   399  e-111
sp|P04989|CYS2_DICDI CYSTEINE PROTEINASE 2 PRECURSOR (PRESTALK C...   398  e-111
sp|P43236|CATK_RABIT CATHEPSIN K PRECURSOR (OC-2 PROTEIN)             395  e-110
sp|P54640|CYS5_DICDI CYSTEINE PROTEINASE 5 PRECURSOR                  394  e-109
sp|P13277|CYS1_HOMAM DIGESTIVE CYSTEINE PROTEINASE 1 PRECURSOR        393  e-109
sp|P25784|CYS3_HOMAM DIGESTIVE CYSTEINE PROTEINASE 3 PRECURSOR        392  e-109
sp|P25774|CATS_HUMAN CATHEPSIN S PRECURSOR                            392  e-109
sp|P15242|TES1_RAT TESTIN 1/2 PRECURSOR (CMB-22/CMB-23)               391  e-109
sp|Q10716|CYS1_MAIZE CYSTEINE PROTEINASE 1 PRECURSOR                  391  e-108
sp|P12412|CYSP_VIGMU VIGNAIN PRECURSOR (BEAN ENDOPEPTIDASE) (CYS...   389  e-108
sp|P43297|RD21_ARATH CYSTEINE PROTEINASE RD21A PRECURSOR              387  e-107
sp|P55097|CATK_MOUSE CATHEPSIN K PRECURSOR                            384  e-106
sp|P09668|CATH_HUMAN CATHEPSIN H PRECURSOR                            383  e-106
sp|O46427|CATH_PIG CATHEPSIN H PRECURSOR                              382  e-106
sp|P25803|CYSP_PHAVU VIGNAIN PRECURSOR (BEAN ENDOPEPTIDASE) (CYS...   380  e-105
sp|P00786|CATH_RAT CATHEPSIN H PRECURSOR (CATHEPSIN B3) (CATHEPS...   377  e-104
sp|P25251|CYS4_BRANA CYSTEINE PROTEINASE COT44 PRECURSOR              376  e-104
sp|P05167|ALEU_HORVU THIOL PROTEASE ALEURAIN PRECURSOR                375  e-104
sp|Q10717|CYS2_MAIZE CYSTEINE PROTEINASE 2 PRECURSOR                  374  e-103
sp|P25777|ORYB_ORYSA ORYZAIN BETA CHAIN PRECURSOR                     374  e-103
sp|Q40143|CYS3_LYCES CYSTEINE PROTEINASE 3 PRECURSOR                  373  e-103
sp|P43156|CYSP_HEMSP THIOL PROTEASE SEN102 PRECURSOR                  373  e-103
sp|P49935|CATH_MOUSE CATHEPSIN H PRECURSOR (CATHEPSIN B3) (CATHE...   372  e-103
sp|P25778|ORYC_ORYSA ORYZAIN GAMMA CHAIN PRECURSOR                    370  e-102
sp|P00785|ACTN_ACTCH ACTINIDAIN PRECURSOR (ACTINIDIN)                 368  e-102
sp|P41721|CATV_NPVBM VIRAL CATHEPSIN (V-CATH)                         367  e-101
sp|Q02765|CATS_RAT CATHEPSIN S PRECURSOR                              365  e-100
sp|P14658|CYSP_TRYBB CYSTEINE PROTEINASE PRECURSOR                    365  e-100
sp|P25783|CATV_NPVAC VIRAL CATHEPSIN (V-CATH)                         363  e-100
sp|P41715|CATV_NPVCF VIRAL CATHEPSIN (V-CATH)                         363  e-100
sp|P25250|CYS2_HORVU CYSTEINE PROTEINASE EP-B 2 PRECURSOR             361  e-100
sp|P25249|CYS1_HORVU CYSTEINE PROTEINASE EP-B 1 PRECURSOR             361  1e-99
sp|Q26534|CATL_SCHMA CATHEPSIN L PRECURSOR (SMCL1)                    361  2e-99
sp|P25779|CYSP_TRYCR CRUZIPAIN PRECURSOR (MAJOR CYSTEINE PROTEIN...   356  4e-98
sp|O10364|CATV_NPVOP VIRAL CATHEPSIN (V-CATH)                         351  2e-96
sp|P36400|LCPB_LEIME CYSTEINE PROTEINASE B PRECURSOR                  348  1e-95
sp|P25775|LCPA_LEIME CYSTEINE PROTEINASE A PRECURSOR                  348  1e-95
sp|Q05094|CYS2_LEIPI CYSTEINE PROTEINASE 2 PRECURSOR (AMASTIGOTE...   347  2e-95
sp|P35591|CYS1_LEIPI CYSTEINE PROTEINASE 1 PRECURSOR (AMASTIGOTE...   347  3e-95
sp|P05994|PAP4_CARPA PAPAYA PROTEINASE IV PRECURSOR (PPIV) (PAPA...   346  3e-95
sp|P10056|PAP3_CARPA CARICAIN PRECURSOR (PAPAYA PROTEINASE OMEGA...   341  1e-93
sp|P14080|PAP2_CARPA CHYMOPAPAIN PRECURSOR (PAPAYA PROTEINASE II...   339  6e-93
sp|P00784|PAPA_CARPA PAPAIN PRECURSOR (PAPAYA PROTEINASE I) (PPI)     334  1e-91
sp|P22895|P34_SOYBN P34 PROBABLE THIOL PROTEASE PRECURSOR             331  1e-90
sp|O17473|CATL_BRUPA CATHEPSIN L-LIKE PRECURSOR                       327  2e-89
sp|Q10991|CATL_SHEEP CATHEPSIN L                                      325  1e-88
sp|P54639|CYS4_DICDI CYSTEINE PROTEINASE 4 PRECURSOR                  323  4e-88
sp|P56203|CATW_MOUSE CATHEPSIN W PRECURSOR (LYMPHOPAIN)               319  4e-87
sp|P56202|CATW_HUMAN CATHEPSIN W PRECURSOR (LYMPHOPAIN)               318  9e-87
sp|Q01958|CPP2_ENTHI CYSTEINE PROTEINASE 2 PRECURSOR                  318  9e-87
sp|P36185|ACP2_ENTHI CYSTEINE PROTEINASE ACP2 PRECURSOR               315  8e-86
sp|Q06964|CPP3_ENTHI CYSTEINE PROTEINASE 3 PRECURSOR (CYSTEINE P...   312  9e-85
sp|P36184|ACP1_ENTHI CYSTEINE PROTEINASE ACP1 PRECURSOR               309  5e-84
sp|P25326|CATS_BOVIN CATHEPSIN S                                      307  2e-83
sp|Q01957|CPP1_ENTHI CYSTEINE PROTEINASE 1 PRECURSOR                  301  1e-81
sp|P25805|CYSP_PLAFA THROPHOZOITE CYSTEINE PROTEINASE PRECURSOR ...   299  5e-81
sp|P20721|CYSL_LYCES LOW-TEMPERATURE-INDUCED CYSTEINE PROTEINASE...   298  9e-81
sp|P43234|CATO_HUMAN CATHEPSIN O PRECURSOR                            296  5e-80
sp|P46102|CYSP_PLAVN CYSTEINE PROTEINASE PRECURSOR                    291  1e-78
sp|P42666|CYSP_PLAVI CYSTEINE PROTEINASE PRECURSOR                    278  1e-74
sp|P16311|MMAL_DERFA MAJOR MITE FECAL ALLERGEN DER F 1 PRECURSOR...   272  8e-73
sp|P80884|ANAN_ANACO ANANAIN                                          271  1e-72
sp||CATL_CHICK_1 [Segment 1 of 2] CATHEPSIN L                         264  1e-70
sp|P97821|CATC_MOUSE DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (D...   262  9e-70
sp|P25781|CYSP_THEAN CYSTEINE PROTEINASE PRECURSOR                    259  6e-69
sp|P08176|MMAL_DERPT MAJOR MITE FECAL ALLERGEN DER P 1 PRECURSOR...   255  1e-67
sp|P14518|BROM_ANACO BROMELAIN, STEM                                  253  4e-67
sp|P53634|CATC_HUMAN DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (D...   251  2e-66
sp|P80067|CATC_RAT DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (DPP...   250  4e-66
sp|P22497|CYSP_THEPA CYSTEINE PROTEINASE PRECURSOR                    243  5e-64
sp|P07858|CATB_HUMAN CATHEPSIN B PRECURSOR (CATHEPSIN B1) (APP S...   238  1e-62
sp|P00787|CATB_RAT CATHEPSIN B PRECURSOR (CATHEPSIN B1) (RSG-2)       236  4e-62
sp|P10605|CATB_MOUSE CATHEPSIN B PRECURSOR (CATHEPSIN B1)             233  4e-61
sp|P43509|CPR5_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 5 PREC...   232  8e-61
sp|P07688|CATB_BOVIN CATHEPSIN B PRECURSOR                            232  8e-61
sp|P43233|CATB_CHICK CATHEPSIN B PRECURSOR (CATHEPSIN B1)             232  1e-60
sp|Q26563|CATC_SCHMA CATHEPSIN C PRECURSOR                            231  1e-60
sp|P25807|CYS1_CAEEL GUT-SPECIFIC CYSTEINE PROTEINASE PRECURSOR       231  1e-60
sp|P43508|CPR4_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 4 PREC...   231  2e-60
sp|P43510|CPR6_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 6 PREC...   225  8e-59
sp|P43157|CYSP_SCHJA CATHEPSIN B-LIKE CYSTEINE PROTEINASE PRECUR...   222  1e-57
sp|P25792|CYSP_SCHMA CATHEPSIN B-LIKE CYSTEINE PROTEINASE PRECUR...   216  5e-56
sp|P25802|CYS1_OSTOS CATHEPSIN B-LIKE CYSTEINE PROTEINASE 1 PREC...   213  4e-55
sp|P25793|CYS2_HAECO CATHEPSIN B-LIKE CYSTEINE PROTEINASE 2 PREC...   212  1e-54
sp|P19092|CYS1_HAECO CATHEPSIN B-LIKE CYSTEINE PROTEINASE 1 PREC...   208  2e-53
sp|P43507|CPR3_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 3 PREC...   204  3e-52
sp|P25780|EUM1_EURMA MITE GROUP I ALLERGEN EUR M 1 (EUR M I)          201  1e-51
sp|P25773|CATL_FELCA CATHEPSIN L (PROGESTERONE-DEPENDENT PROTEIN...   185  2e-46
sp|Q23894|CYS3_DICDI CYSTEINE PROTEINASE 3 (CYSTEINE PROTEINASE II)   158  2e-38
sp|P13823|SERA_PLAFG SERINE-REPEAT ANTIGEN PROTEIN PRECURSOR (P1...   157  3e-38
sp|Q06544|CYS3_OSTOS CATHEPSIN B-LIKE CYSTEINE PROTEINASE 3           139  6e-33
sp|P05993|PAP5_CARPA CYSTEINE PROTEINASE (CLONE PLBPC13)              131  2e-30
sp|P32957|CC4_CARCN CYSTEINE PROTEINASE IV (CC-IV)                     85  3e-16
sp|P32956|CC3_CARCN CYSTEINE PROTEINASE III (CC-III)                   84  4e-16
sp|P32955|CC2_CARCN CYSTEINE PROTEINASE II (CC-II)                     81  2e-15
sp||CATL_CHICK_2 [Segment 2 of 2] CATHEPSIN L                          77  5e-14
sp|P32954|CC1_CARCN CYSTEINE PROTEINASE I (CC-I)                       76  1e-13

Sequences not found previously or not previously below threshold:

sp|P12399|CT2A_MOUSE CTLA-2-ALPHA PROTEIN PRECURSOR                    98  2e-20
sp|P12400|CT2B_MOUSE CTLA-2-BETA PROTEIN PRECURSOR                     96  1e-19
sp|P05689|CATX_BOVIN CATHEPSIN                                         60  9e-09
sp|P94869|PEPG_LACDL AMINOPEPTIDASE G                                  46  1e-04
sp|P94870|PEPE_LACHE AMINOPEPTIDASE E                                  43  0.001
sp|P94868|PEPW_LACDL AMINOPEPTIDASE W                                  42  0.002
sp|Q10744|PEPC_LACHE AMINOPEPTIDASE C                                  41  0.003
sp|Q04723|PEPC_LACLC AMINOPEPTIDASE C                                  40  0.009
sp|Q48543|PEPC_LACDL AMINOPEPTIDASE C                                  38  0.025
sp|P21381|THPA_THADA THAUMATOPAIN                                      38  0.025
sp|Q56115|PEPC_STRTR AMINOPEPTIDASE C                                  36  0.13
sp|P09983|HLY1_ECOLI HEMOLYSIN, CHROMOSOMAL                            36  0.17
sp|P33403|CYSP_TRIFO CYSTEINE PROTEINASE                               35  0.28
sp|P08715|HLYA_ECOLI HEMOLYSIN, PLASMID                                35  0.28
sp|P87362|BLMH_CHICK BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH) (...    34  0.37
sp|P54704|PSPB_DICDI PRESPORE PROTEIN B PRECURSOR                      34  0.37
sp|Q13867|BLMH_HUMAN BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH)         34  0.49
sp|P70645|BLMH_RAT BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH)           34  0.49
sp|P80532|CAT3_FASHE PUTATIVE CATHEPSIN L3 (NEWLY EXCYSTED JUVEN...    34  0.49
sp|P16462|LKTA_ACTAC LEUKOTOXIN                                        34  0.49
sp|P13438|TSP_MOUSE TROPHOBLAST-SPECIFIC PROTEIN PRECURSOR             32  1.4
sp|Q00951|HLYA_ACTSU HEMOLYSIN (CYTOLYSIN II) (CLY-IIA) (HLY-IIA...    32  1.4
sp|P15377|RT2A_ACTPL RTX-II TOXIN DETERMINANT A (APX-IIA) (HEMOL...    32  1.4
sp|P52181|TGLC_PAGMA PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE...    32  1.9
sp|P35681|TCTP_ORYSA TRANSLATIONALLY CONTROLLED TUMOR PROTEIN HO...    32  1.9
sp|Q01532|BLH1_YEAST CYSTEINE PROTEINASE 1 (Y3) (BLEOMYCIN HYDRO...    32  2.5
sp|P16312|MMAL_DERMI MAJOR MITE FECAL ALLERGEN DER M 1 (DER M I)       31  3.2
sp|O03992|TCTP_FRAAN TRANSLATIONALLY CONTROLLED TUMOR PROTEIN HO...    31  4.2
sp|Q04489|YMJ6_YEAST HYPOTHETICAL 59.5 KD PROTEIN IN VPS9-RAD10 ...    31  4.2
sp|Q03164|HRX_HUMAN ZINC FINGER PROTEIN HRX (ALL-1) (TRITHORAX-L...    31  4.2
sp||CATB_COTJA_1 [Segment 1 of 2] CATHEPSIN B (CATHEPSIN B1)           30  5.6
sp|Q62703|RCN2_RAT RETICULOCALBIN 2 PRECURSOR (CALCIUM-BINDING P...    30  5.6
sp|P48651|PSS1_HUMAN PHOSPHATIDYLSERINE SYNTHASE I (SERINE-EXCHA...    30  5.6
sp|P33404|CYSP_TRIVA CYSTEINE PROTEINASE                               30  5.6
sp|Q00576|PSS1_CRILO PHOSPHATIDYLSERINE SYNTHASE I (SERINE-EXCHA...    30  5.6
sp|Q9ZRX0|TCTP_PSEMZ TRANSLATIONALLY CONTROLLED TUMOR PROTEIN HO...    30  7.3
sp|Q94480|V136_DICDI VEG136 PROTEIN                                    30  7.3
sp|P55131|RT32_ACTPL RTX-III TOXIN DETERMINANT A FROM SEROTYPE 8...    30  7.3
sp|P55130|RT31_ACTPL RTX-III TOXIN DETERMINANT A FROM SEROTYPE 2...    30  7.3
sp|P40101|YE16_YEAST HYPOTHETICAL 35.9 KD PROTEIN IN ISC10 3'REGION    30  7.3
sp|P13388|XMRK_XIPMA MELANOMA RECEPTOR PROTEIN-TYROSINE KINASE P...    30  7.3
sp|Q9ZL75|MOAA_HELPJ MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN A        30  9.5
sp|P55129|RT12_ACTPL RTX-I TOXIN DETERMINANT A FROM SEROTYPES 5/...    30  9.5
sp|P55128|RT11_ACTPL RTX-I TOXIN DETERMINANT A FROM SEROTYPES 1/...    30  9.5
sp|P35669|GSHB_SCHPO GLUTATHIONE SYNTHETASE LARGE CHAIN (GLUTATH...    30  9.5
sp|P11140|ABRA_ABRPR ABRIN-A PRECURSOR (RRNA N-GLYCOSIDASE)            30  9.5
sp|Q00690|LEM2_MOUSE E-SELECTIN PRECURSOR (ENDOTHELIAL LEUKOCYTE...    30  9.5
sp|P06620|ICEN_PSESY ICE NUCLEATION PROTEIN                            30  9.5

>sp|P04988|CYS1_DICDI CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 343

 Score =  527 bits (1343), Expect = e-149
 Identities = 343/343 (100%), Positives = 343/343 (100%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60
           MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE
Sbjct: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60

Query: 61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPT 120
           ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPT
Sbjct: 61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPT 120

Query: 121 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY 180
           AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY
Sbjct: 121 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY 180

Query: 181 EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTM 240
           EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTM
Sbjct: 181 EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTM 240

Query: 241 IPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIF 300
           IPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIF
Sbjct: 241 IPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIF 300

Query: 301 RKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
           RKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII
Sbjct: 301 RKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343


>sp|P25975|CATL_BOVIN CATHEPSIN L PRECURSOR
          Length = 334

 Score =  440 bits (1119), Expect = e-123
 Identities = 120/343 (34%), Positives = 176/343 (50%), Gaps = 19/343 (5%)

Query: 7   FVLAVFTVFVSSRG--IPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNL 64
           F L V  + V+S    + P   + + +++    + Y   E   R  +++ N   I+  N 
Sbjct: 5   FFLTVLCLGVASAAPKLDPNLDAHWHQWKATHRRLYGMNEEEWRRAVWEKNKKIIDLHNQ 64

Query: 65  IAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDW 124
                K   +  +N F D++++EF+                      +  +  +P + DW
Sbjct: 65  EYSEGKHAFRMAMNAFGDMTNEEFRQVMNG----FQNQKHKKGKLFHEPLLVDVPKSVDW 120

Query: 125 RTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEE 184
             +G VTPVKNQGQCGSCW+FS TG +EGQ F    KLVSLSEQNLVDC           
Sbjct: 121 TKKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRA-------- 172

Query: 185 ACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN 244
             ++GCNGGL  NA+ YI  NGG+ +E SYPY A     CN+      A  + F  IP+ 
Sbjct: 173 QGNQGCNGGLMDNAFQYIKDNGGLDSEESYPYLATDTNSCNYKPECSAANDTGFVDIPQR 232

Query: 245 ETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIVGYSAKNTIFR 301
           E  +   + + GP+++A DA    +QFY  G+ +D  C+   LDHG+L+VGY  + T   
Sbjct: 233 EKALMKAVATVGPISVAIDAGHTSFQFYKSGIYYDPDCSCKDLDHGVLVVGYGFEGTDSN 292

Query: 302 KNMPYWIVKNSWGADWGEQGYIYLRRG-KNTCGVSNFVSTSII 343
            N  +WIVKNSWG +WG  GY+ + +   N CG++   S   +
Sbjct: 293 NNK-FWIVKNSWGPEWGWNGYVKMAKDQNNHCGIATAASYPTV 334


>sp|P07154|CATL_RAT CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTEIN) (MEP) (CYCLIC
           PROTEIN-2) (CP-2)
          Length = 334

 Score =  431 bits (1097), Expect = e-121
 Identities = 123/345 (35%), Positives = 187/345 (53%), Gaps = 19/345 (5%)

Query: 3   VILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEEL 62
           ++LL VL + T   + +       +Q+ +++    + Y   E   R  +++ N+  I+  
Sbjct: 4   LLLLAVLCLGTALATPKF-DQTFNAQWHQWKSTHRRLYGTNEEEWRRAVWEKNMRMIQLH 62

Query: 63  NLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAF 122
           N    N K      +N F D++++EF+      +               +  +  IP   
Sbjct: 63  NGEYSNGKHGFTMEMNAFGDMTNEEFRQIVNGYRHQKH----KKGRLFQEPLMLQIPKTV 118

Query: 123 DWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEG 182
           DWR +G VTPVKNQGQCGSCW+FS +G +EGQ F+   KL+SLSEQNLVDC H       
Sbjct: 119 DWREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLISLSEQNLVDCSH------- 171

Query: 183 EEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP 242
            +  ++GCNGGL   A+ YI +NGG+ +E SYPY A+ G  C + +    A  + F  IP
Sbjct: 172 -DQGNQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDG-SCKYRAEYAVANDTGFVDIP 229

Query: 243 KNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIP-CNPNSLDHGILIVGYSAKNTI 299
           + E  +   + + GP+++A DA     QFY  G++  P C+   LDHG+L+VGY  + T 
Sbjct: 230 QQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCSSKDLDHGVLVVGYGYEGTD 289

Query: 300 FRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTSII 343
             K+  YW+VKNSWG +WG  GYI + + + N CG++   S  I+
Sbjct: 290 SNKDK-YWLVKNSWGKEWGMDGYIKIAKDRNNHCGLATAASYPIV 333


>sp|P06797|CATL_MOUSE CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTEIN) (MEP)
          Length = 334

 Score =  431 bits (1096), Expect = e-120
 Identities = 120/347 (34%), Positives = 189/347 (53%), Gaps = 18/347 (5%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60
           M ++LL  +      +++        +++ +++    + Y   E   R  I++ N+  I+
Sbjct: 1   MNLLLLLAVLCLGTALATPKFDQTFSAEWHQWKSTHRRLYGTNEEEWRRAIWEKNMRMIQ 60

Query: 61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPT 120
             N    N +      +N F D++++EF+      +               +  +  IP 
Sbjct: 61  LHNGEYSNGQHGFSMEMNAFGDMTNEEFRQVVNGYRHQKH----KKGRLFQEPLMLKIPK 116

Query: 121 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY 180
           + DWR +G VTPVKNQGQCGSCW+FS +G +EGQ F+   KL+SLSEQNLVDC H     
Sbjct: 117 SVDWREKGCVTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLISLSEQNLVDCSHA---- 172

Query: 181 EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTM 240
                 ++GCNGGL   A+ YI +NGG+ +E SYPY A+ G  C + +    A  + F  
Sbjct: 173 ----QGNQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDG-SCKYRAEFAVANDTGFVD 227

Query: 241 IPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIP-CNPNSLDHGILIVGYSAKN 297
           IP+ E  +   + + GP+++A DA     QFY  G++  P C+  +LDHG+L+VGY  + 
Sbjct: 228 IPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCSSKNLDHGVLLVGYGYEG 287

Query: 298 TIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTSII 343
           T   KN  YW+VKNSWG++WG +GYI + + + N CG++   S  ++
Sbjct: 288 TDSNKNK-YWLVKNSWGSEWGMEGYIKIAKDRDNHCGLATAASYPVV 333


>sp|Q28944|CATL_PIG CATHEPSIN L PRECURSOR
          Length = 334

 Score =  430 bits (1094), Expect = e-120
 Identities = 115/343 (33%), Positives = 171/343 (49%), Gaps = 19/343 (5%)

Query: 7   FVLAVFTVFVSSRG--IPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNL 64
             L    + ++S    +     + + +++    + Y   E   R  +++ N+  IE  N 
Sbjct: 5   LFLTALCLGIASAAPKLDQNLDADWYKWKATHGRLYGMNEEGWRRAVWEKNMKMIELHNQ 64

Query: 65  IAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDW 124
                K      +N F D++++EF+                      +  +  +P + DW
Sbjct: 65  EYSQGKHGFSMAMNAFGDMTNEEFRQVMNG----FQNQKHKKGKVFHESLVLEVPKSVDW 120

Query: 125 RTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEE 184
           R +G VT VKNQGQCGSCW+FS TG +EGQ F    KLVSLSEQNLVDC           
Sbjct: 121 REKGYVTAVKNQGQCGSCWAFSATGALEGQMFRKTGKLVSLSEQNLVDCS--------RP 172

Query: 185 ACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN 244
             ++GCNGGL  NA+ Y+  NGG+ TE SYPY       C +      A  + F  IP+ 
Sbjct: 173 QGNQGCNGGLMDNAFQYVKDNGGLDTEESYPYLGRETNSCTYKPECSAANDTGFVDIPQR 232

Query: 245 ETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIVGYSAKNTIFR 301
           E  +   + + GP+++A DA    +QFY  G+ +D  C+   LDHG+L+VGY  + T   
Sbjct: 233 EKALMKAVATVGPISVAIDAGHSSFQFYKSGIYYDPDCSSKDLDHGVLVVGYGFEGTDSN 292

Query: 302 KNMPYWIVKNSWGADWGEQGYIYLRRG-KNTCGVSNFVSTSII 343
            +  +WIVKNSWG +WG  GY+ + +   N CG+S   S   +
Sbjct: 293 SSK-FWIVKNSWGPEWGWNGYVKMAKDQNNHCGISTAASYPTV 334


>sp|P07711|CATL_HUMAN CATHEPSIN L PRECURSOR (MAJOR EXCRETED PROTEIN) (MEP)
          Length = 333

 Score =  421 bits (1072), Expect = e-118
 Identities = 118/343 (34%), Positives = 180/343 (52%), Gaps = 20/343 (5%)

Query: 7   FVLAVFTVFVSSRGIPPE--EQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNL 64
            +LA F + ++S  +  +   ++Q+ +++   N+ Y   E   R  +++ N+  IE  N 
Sbjct: 5   LILAAFCLGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQ 64

Query: 65  IAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDW 124
                K      +N F D++S+EF+                      +      P + DW
Sbjct: 65  EYREGKHSFTMAMNAFGDMTSEEFRQVMNG----FQNRKPRKGKVFQEPLFYEAPRSVDW 120

Query: 125 RTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEE 184
           R +G VTPVKNQGQCGSCW+FS TG +EGQ F    +L+SLSEQNLVDC           
Sbjct: 121 REKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCS--------GP 172

Query: 185 ACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN 244
             +EGCNGGL   A+ Y+  NGG+ +E SYPY A     C +N     A  + F  IPK 
Sbjct: 173 QGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATE-ESCKYNPKYSVANDTGFVDIPKQ 231

Query: 245 ETVMAGYIVSTGPLAIAADA--VEWQFYIGGVF-DIPCNPNSLDHGILIVGYSAKNTIFR 301
           E  +   + + GP+++A DA    + FY  G++ +  C+   +DHG+L+VGY  ++T   
Sbjct: 232 EKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESD 291

Query: 302 KNMPYWIVKNSWGADWGEQGYIYLRRG-KNTCGVSNFVSTSII 343
            N  YW+VKNSWG +WG  GY+ + +  +N CG+++  S   +
Sbjct: 292 NNK-YWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV 333


>sp|O60911|CATM_HUMAN CATHEPSIN L2 PRECURSOR (CATHEPSIN V)
          Length = 334

 Score =  417 bits (1061), Expect = e-116
 Identities = 118/346 (34%), Positives = 179/346 (51%), Gaps = 21/346 (6%)

Query: 5   LLFVLAVFTVFVSSRGI--PPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEEL 62
           L  VLA F + ++S          +++ +++    + Y   E   R  +++ N+  IE  
Sbjct: 3   LSLVLAAFCLGIASAVPKFDQNLDTKWYQWKATHRRLYGANEEGWRRAVWEKNMKMIELH 62

Query: 63  NLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAF 122
           N      K      +N F D++++EF+      +   F           +     +P + 
Sbjct: 63  NGEYSQGKHGFTMAMNAFPDMTNEEFRQMMGCFRNQKFR----KGKVFREPLFLDLPKSV 118

Query: 123 DWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEG 182
           DWR +G VTPVKNQ QCGSCW+FS TG +EGQ F    KLVSLSEQNLVDC         
Sbjct: 119 DWRKKGYVTPVKNQKQCGSCWAFSATGALEGQMFRKTGKLVSLSEQNLVDCS-------- 170

Query: 183 EEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMI- 241
               ++GCNGG    A+ Y+ +NGG+ +E SYPY A     C +   N  A  + FT++ 
Sbjct: 171 RPQGNQGCNGGFMARAFQYVKENGGLDSEESYPYVAVD-EICKYRPENSVANDTGFTVVA 229

Query: 242 PKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVF-DIPCNPNSLDHGILIVGYSAKNT 298
           P  E  +   + + GP+++A DA    +QFY  G++ +  C+  +LDHG+L+VGY  +  
Sbjct: 230 PGKEKALMKAVATVGPISVAMDAGHSSFQFYKSGIYFEPDCSSKNLDHGVLVVGYGFE-G 288

Query: 299 IFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTSII 343
               N  YW+VKNSWG +WG  GY+ + + K N CG++   S   +
Sbjct: 289 ANSNNSKYWLVKNSWGPEWGSNGYVKIAKDKNNHCGIATAASYPNV 334


>sp|P43296|RD19_ARATH CYSTEINE PROTEINASE RD19A PRECURSOR
          Length = 368

 Score =  412 bits (1048), Expect = e-115
 Identities = 148/356 (41%), Positives = 199/356 (55%), Gaps = 28/356 (7%)

Query: 6   LFVLAVFTVFVSSRGIP------------------PEEQSQFLEFQDKFNKKY-SHEEYL 46
           +FVL+ F V VSS  +                      +  F  F+ KF K Y S+EE+ 
Sbjct: 10  VFVLSFFIVSVSSSDVNDGDDLVIRQVVGGAEPQVLTSEDHFSLFKRKFGKVYASNEEHD 69

Query: 47  ERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPV 106
            RF +FK+NL +      +          GV +F+DL+  EF+  +L  +          
Sbjct: 70  YRFSVFKANLRRARRHQKLDP----SATHGVTQFSDLTRSEFRKKHLGVRSGFKLP--KD 123

Query: 107 ADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLS 166
           A+        ++P  FDWR  GAVTPVKNQG CGSCWSFS TG +EG +F++  KLVSLS
Sbjct: 124 ANKAPILPTENLPEDFDWRDHGAVTPVKNQGSCGSCWSFSATGALEGANFLATGKLVSLS 183

Query: 167 EQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNF 226
           EQ LVDCDHEC + E  ++CD GCNGGL  +A+ Y +K GG+  E  YPYT + G  C  
Sbjct: 184 EQQLVDCDHEC-DPEEADSCDSGCNGGLMNSAFEYTLKTGGLMKEEDYPYTGKDGKTCKL 242

Query: 227 NSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDH 286
           + + I A +SNF++I  +E  +A  +V  GPLA+A +A   Q YIGGV         L+H
Sbjct: 243 DKSKIVASVSNFSVISIDEEQIAANLVKNGPLAVAINAGYMQTYIGGVSCPYICTRRLNH 302

Query: 287 GILIVGYSAKN--TIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVST 340
           G+L+VGY A        K  PYWI+KNSWG  WGE G+  + +G+N CGV + VST
Sbjct: 303 GVLLVGYGAAGYAPARFKEKPYWIIKNSWGETWGENGFYKICKGRNICGVDSMVST 358


>sp|P25776|ORYA_ORYSA ORYZAIN ALPHA CHAIN PRECURSOR
          Length = 458

 Score =  407 bits (1036), Expect = e-113
 Identities = 121/350 (34%), Positives = 183/350 (51%), Gaps = 27/350 (7%)

Query: 3   VILLFVLAVFTVFVSSRGIPPEEQSQ--FLEFQDKFNKKYSHE-EYLERFEIFKSNLGKI 59
           ++LL  LA   + + S G   EE+++  + E++ +  K Y+   E   R+  F+ NL  I
Sbjct: 12  LLLLLSLAAADMSIVSYGERSEEEARRLYAEWKAEHGKSYNAVGEEERRYAAFRDNLRYI 71

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
           +E N  A       + G+N+FADL+++E+++ YL  +     +   V+D        ++P
Sbjct: 72  DEHNAAADAGVHSFRLGLNRFADLTNEEYRDTYLGLRNKPRRER-KVSDRYLAADNEALP 130

Query: 120 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 179
            + DWRT+GAV  +K+QG CGSCW+FS    VE  + I    L+SLSEQ LVDCD     
Sbjct: 131 ESVDWRTKGAVAEIKDQGGCGSCWAFSAIAAVEDINQIVTGDLISLSEQELVDCD----- 185

Query: 180 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANI-GAKISNF 238
                + +EGCNGGL   A+++II NGGI TE  YPY  +   +C+ N  N     I ++
Sbjct: 186 ----TSYNEGCNGGLMDYAFDFIINNGGIDTEDDYPYKGKD-ERCDVNRKNAKVVTIDSY 240

Query: 239 TMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNPNSLDHGILIVGYSAK 296
             +  N        V   P+++A +A    +Q Y  G+F   C   +LDHG+  VGY  +
Sbjct: 241 EDVTPNSETSLQKAVRNQPVSVAIEAGGRAFQLYSSGIFTGKCG-TALDHGVAAVGYGTE 299

Query: 297 NTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG----KNTCGVSNFVSTSI 342
           N        YWIV+NSWG  WGE GY+ + R        CG++   S  +
Sbjct: 300 N-----GKDYWIVRNSWGKSWGESGYVRMERNIKASSGKCGIAVEPSYPL 344


>sp|P25782|CYS2_HOMAM DIGESTIVE CYSTEINE PROTEINASE 2 PRECURSOR
          Length = 323

 Score =  403 bits (1024), Expect = e-112
 Identities = 132/349 (37%), Positives = 187/349 (52%), Gaps = 32/349 (9%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKI 59
           MKV +LF+  V     S           +  F+ K+ ++Y   EE   R  IF+ N   I
Sbjct: 1   MKVAVLFLCGVALAAASPS---------WEHFKGKYGRQYVDAEEDSYRRVIFEQNQKYI 51

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
           EE N    N +      +NKF D++ +EF      N   I     PV+ +   +      
Sbjct: 52  EEFNKKYENGEVTFNLAMNKFGDMTLEEFNAVMKGN---IPRRSAPVSVFYPKKETGPQA 108

Query: 120 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 179
           T  DWRT+GAVTPVK+QGQCGSCW+FSTTG++EGQHF+    L+SL+EQ LVDC      
Sbjct: 109 TEVDWRTKGAVTPVKDQGQCGSCWAFSTTGSLEGQHFLKTGSLISLAEQQLVDCS----- 163

Query: 180 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFT 239
                   +GCNGG   +A++YI  N GI TE++YPY A  G  C F+S ++ A  S  T
Sbjct: 164 ---RPYGPQGCNGGWMNDAFDYIKANNGIDTEAAYPYEARDG-SCRFDSNSVAATCSGHT 219

Query: 240 MI-PKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIP-CNPNSLDHGILIVGYSA 295
            I   +ET +   +   GP+++  DA    +QFY  GV+  P C+P+ LDH +L VGY +
Sbjct: 220 NIASGSETGLQQAVRDIGPISVTIDAAHSSFQFYSSGVYYEPSCSPSYLDHAVLAVGYGS 279

Query: 296 KNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTSII 343
           +         +W+VKNSW   WG+ GYI + R + N CG++   S  ++
Sbjct: 280 EG-----GQDFWLVKNSWATSWGDAGYIKMSRNRNNNCGIATVASYPLV 323


>sp|P43295|A494_ARATH PROBABLE CYSTEINE PROTEINASE A494 PRECURSOR
          Length = 313

 Score =  402 bits (1021), Expect = e-112
 Identities = 141/312 (45%), Positives = 187/312 (59%), Gaps = 10/312 (3%)

Query: 32  FQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKN 90
           F+ KF K Y   EE+  RF +FK+NL +      +  + +     GV +F+DL+  EF+ 
Sbjct: 3   FKKKFGKVYGSIEEHYYRFSVFKANLLRAMRHQKMDPSARH----GVTQFSDLTRSEFRR 58

Query: 91  YYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGN 150
            +L  K          A+        ++P  FDWR RGAVTPVKNQG CGSCWSFSTTG 
Sbjct: 59  KHLGVKGGFKLP--KDANQAPILPTQNLPEEFDWRDRGAVTPVKNQGSCGSCWSFSTTGA 116

Query: 151 VEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQT 210
           +EG HF++  KLVSLSEQ LVDCDHEC + E E +CD GCNGGL  +A+ Y +K GG+  
Sbjct: 117 LEGAHFLATGKLVSLSEQQLVDCDHEC-DPEEEGSCDSGCNGGLMNSAFEYTLKTGGLMR 175

Query: 211 ESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFY 270
           E  YPYT   G  C  + + I A +SNF+++  NE  +A  ++  GPLA+A +A   Q Y
Sbjct: 176 EKDYPYTGTDGGSCKLDRSKIVASVSNFSVVSINEDQIAANLIKNGPLAVAINAAYMQTY 235

Query: 271 IGGVFDIPCNPNSLDHGILIVGYSAKN--TIFRKNMPYWIVKNSWGADWGEQGYIYLRRG 328
           IGGV         L+HG+L+VGY +        K  PYWI+KNSWG  WGE G+  + +G
Sbjct: 236 IGGVSCPYICSRRLNHGVLLVGYGSAGFSQARLKEKPYWIIKNSWGESWGENGFYKICKG 295

Query: 329 KNTCGVSNFVST 340
           +N CGV + VST
Sbjct: 296 RNICGVDSLVST 307


>sp|P43235|CATK_HUMAN CATHEPSIN K PRECURSOR (CATHEPSIN O) (CATHEPSIN X) (CATHEPSIN O2)
          Length = 329

 Score =  401 bits (1020), Expect = e-111
 Identities = 121/341 (35%), Positives = 179/341 (52%), Gaps = 25/341 (7%)

Query: 9   LAVFTVFVSSRGIPPEE--QSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLI 65
           L V  + V S  + PEE   + +  ++    K+Y+++ + + R  I++ NL  I   NL 
Sbjct: 4   LKVLLLPVVSFALYPEEILDTHWELWKKTHRKQYNNKVDEISRRLIWEKNLKYISIHNLE 63

Query: 66  AINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWR 125
           A       +  +N   D++S+E        K  +         Y+  E+    P + D+R
Sbjct: 64  ASLGVHTYELAMNHLGDMTSEEVVQKMTGLKVPLSHSRSNDTLYIP-EWEGRAPDSVDYR 122

Query: 126 TRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEA 185
            +G VTPVKNQGQCGSCW+FS+ G +EGQ      KL++LS QNLVDC  E         
Sbjct: 123 KKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSE--------- 173

Query: 186 CDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP-KN 244
            ++GC GG   NA+ Y+ KN GI +E +YPY  +    C +N     AK   +  IP  N
Sbjct: 174 -NDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQE-ESCMYNPTGKAAKCRGYREIPEGN 231

Query: 245 ETVMAGYIVSTGPLAIAADAV--EWQFYIGGV-FDIPCNPNSLDHGILIVGYSAKNTIFR 301
           E  +   +   GP+++A DA    +QFY  GV +D  CN ++L+H +L VGY       +
Sbjct: 232 EKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYG-----IQ 286

Query: 302 KNMPYWIVKNSWGADWGEQGYIYLRRGKNT-CGVSNFVSTS 341
           K   +WI+KNSWG +WG +GYI + R KN  CG++N  S  
Sbjct: 287 KGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFP 327


>sp|P25804|CYSP_PEA CYSTEINE PROTEINASE 15A PRECURSOR (TURGOR-RESPONSIVE PROTEIN 15A)
          Length = 363

 Score =  399 bits (1015), Expect = e-111
 Identities = 141/322 (43%), Positives = 196/322 (60%), Gaps = 12/322 (3%)

Query: 23  PEEQSQFLEFQDKFNKKYSHEEYL-ERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFA 81
              +  F  F+ KF+K Y+ +E    RF +FKSNL K +       N     + G+ KF+
Sbjct: 42  LNAEHHFTSFKSKFSKSYATKEEHDYRFGVFKSNLIKAKLHQ----NRDPTAEHGITKFS 97

Query: 82  DLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGS 141
           DL++ EF+  +L  K+ +       A         ++P  FDWR +GAVTPVK+QG CGS
Sbjct: 98  DLTASEFRRQFLGLKKRLRLPAH--AQKAPILPTTNLPEDFDWREKGAVTPVKDQGSCGS 155

Query: 142 CWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNY 201
           CW+FSTTG +EG H+++  KLVSLSEQ LVDCDH C + E   +CD GCNGGL  NA+ Y
Sbjct: 156 CWAFSTTGALEGAHYLATGKLVSLSEQQLVDCDHVC-DPEQAGSCDSGCNGGLMNNAFEY 214

Query: 202 IIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIA 261
           ++++GG+  E  Y YT   G  C F+ + + A +SNF+++  +E  +A  +V  GPLA+A
Sbjct: 215 LLESGGVVQEKDYAYTGRDG-SCKFDKSKVVASVSNFSVVTLDEDQIAANLVKNGPLAVA 273

Query: 262 ADAVEWQFYIGGVFD-IPCNPNSLDHGILIVGY--SAKNTIFRKNMPYWIVKNSWGADWG 318
            +A   Q Y+ GV     C  + LDHG+L+VG+   A   I  K  PYWI+KNSWG +WG
Sbjct: 274 INAAWMQTYMSGVSCPYVCAKSRLDHGVLLVGFGKGAYAPIRLKEKPYWIIKNSWGQNWG 333

Query: 319 EQGYIYLRRGKNTCGVSNFVST 340
           EQGY  + RG+N CGV + VST
Sbjct: 334 EQGYYKICRGRNVCGVDSMVST 355


>sp|P04989|CYS2_DICDI CYSTEINE PROTEINASE 2 PRECURSOR (PRESTALK CATHEPSIN)
          Length = 376

 Score =  398 bits (1012), Expect = e-111
 Identities = 145/386 (37%), Positives = 211/386 (54%), Gaps = 55/386 (14%)

Query: 1   MKVILLFVLAVFTVFVSSRGIP-------PEEQSQFLEFQDKFNKKYSHEEYLERFEIFK 53
           M++++  +L +F  F  +   P        + ++ F E+  KFN++YS  E+  R+ IFK
Sbjct: 1   MRLLVFLILLIFVNFSFANVRPNGRRFSESQYRTAFTEWTLKFNRQYSSSEFSNRYSIFK 60

Query: 54  SNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKE-AIFTDDLPVADYLDD 112
           SN+  ++  N       + T  G+N FAD++++E++  YL  +  A   +     + L+ 
Sbjct: 61  SNMDYVDNWNSK---GDSQTVLGLNNFADITNEEYRKTYLGTRVNAHSYNGYDGREVLNV 117

Query: 113 EFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVD 172
           E + + P + DWRT+ AVTP+K+QGQCGSCWSFSTTG+ EG H +   KLVSLSEQNLVD
Sbjct: 118 EDLQTNPKSIDWRTKNAVTPIKDQGQCGSCWSFSTTGSTEGAHALKTKKLVSLSEQNLVD 177

Query: 173 CDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG 232
           C      +        GC+GGL  NA++YIIKN GI TESSYPYTAETG+ C FN ++IG
Sbjct: 178 CSGPEENF--------GCDGGLMNNAFDYIIKNKGIDTESSYPYTAETGSTCLFNKSDIG 229

Query: 233 AKISNFTMIPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIP-CNPNSLDHGIL 289
           A I  +  I     +        GP+++A DA    +Q Y  G++  P C+P  LDHG+L
Sbjct: 230 ATIKGYVNITAGSEISLENGAQHGPVSVAIDASHNSFQLYTSGIYYEPKCSPTELDHGVL 289

Query: 290 IVGYSA--------------------------------KNTIFRKNMPYWIVKNSWGADW 317
           +VGY                                   +++  K   YWIVKNSWG  W
Sbjct: 290 VVGYGVQGKDDEGPVLNRKQTIVIHKNEDNKVESSDDSSDSVRPKANNYWIVKNSWGTSW 349

Query: 318 GEQGYIYLRRG-KNTCGVSNFVSTSI 342
           G +GYI + +  KN CG+++  S  +
Sbjct: 350 GIKGYILMSKDRKNNCGIASVSSYPL 375


>sp|P43236|CATK_RABIT CATHEPSIN K PRECURSOR (OC-2 PROTEIN)
          Length = 329

 Score =  395 bits (1005), Expect = e-110
 Identities = 118/341 (34%), Positives = 178/341 (51%), Gaps = 25/341 (7%)

Query: 9   LAVFTVFVSSRGIPPEE--QSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLI 65
           L V  + V S  + PEE   +Q+  ++  ++K+Y+ + + + R  I++ NL  I   NL 
Sbjct: 4   LKVLLLPVVSFALHPEEILDTQWELWKKTYSKQYNSKVDEISRRLIWEKNLKHISIHNLE 63

Query: 66  AINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWR 125
           A       +  +N   D++S+E        K            Y+  ++    P + D+R
Sbjct: 64  ASLGVHTYELAMNHLGDMTSEEVVQKMTGLKVPPSRSHSNDTLYIP-DWEGRTPDSIDYR 122

Query: 126 TRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEA 185
            +G VTPVKNQGQCGSCW+FS+ G +EGQ      KL++LS QNLVDC  E         
Sbjct: 123 KKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSE--------- 173

Query: 186 CDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP-KN 244
            + GC GG   NA+ Y+ +N GI +E +YPY  +    C +N     AK   +  IP  N
Sbjct: 174 -NYGCGGGYMTNAFQYVQRNRGIDSEDAYPYVGQD-ESCMYNPTGKAAKCRGYREIPEGN 231

Query: 245 ETVMAGYIVSTGPLAIAADAV--EWQFYIGGV-FDIPCNPNSLDHGILIVGYSAKNTIFR 301
           E  +   +   GP+++A DA    +QFY  GV +D  C+ ++++H +L VGY       +
Sbjct: 232 EKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDENCSSDNVNHAVLAVGYG-----IQ 286

Query: 302 KNMPYWIVKNSWGADWGEQGYIYLRRGKNT-CGVSNFVSTS 341
           K   +WI+KNSWG  WG +GYI + R KN  CG++N  S  
Sbjct: 287 KGNKHWIIKNSWGESWGNKGYILMARNKNNACGIANLASFP 327


>sp|P54640|CYS5_DICDI CYSTEINE PROTEINASE 5 PRECURSOR
          Length = 344

 Score =  394 bits (1001), Expect = e-109
 Identities = 138/362 (38%), Positives = 200/362 (55%), Gaps = 37/362 (10%)

Query: 1   MKVI-LLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKI 59
           MKV+  L VL V       +    + ++ F ++     K Y+ EE+  R+ IF +N+  +
Sbjct: 1   MKVLSFLCVLLVSVATAKQQFSELQYRNAFTDWMITHQKSYTSEEFGARYNIFTANMDYV 60

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
           ++ N    +  ++T  G+N FAD++++E++N YL  K   F     +    +    NS  
Sbjct: 61  QQWN----SKGSETVLGLNNFADITNEEYRNTYLGTK---FDASSLIGTQEEKVHTNSSA 113

Query: 120 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 179
            + DWR+ GAVTPVKNQGQCG CWSFSTTG+ EG HF S+ +LVSLSEQNL+DC  E   
Sbjct: 114 ASKDWRSEGAVTPVKNQGQCGGCWSFSTTGSTEGAHFQSKGELVSLSEQNLIDCSTE--- 170

Query: 180 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFT 239
                  + GC+GGL   A+ YII N GI TESSYPY AE G +C + S N GA +S++ 
Sbjct: 171 -------NSGCDGGLMTYAFEYIINNNGIDTESSYPYKAENG-KCEYKSENSGATLSSYK 222

Query: 240 MIPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIP-CNPNSLDHGILIVGYS-- 294
            +           V+  P+++A DA    +Q Y  G++  P C+  +LDHG+L VGY   
Sbjct: 223 TVTAGSESSLESAVNVNPVSVAIDASHQSFQLYTSGIYYEPECSSENLDHGVLAVGYGSG 282

Query: 295 ------------AKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTS 341
                       + N     +  YWIVKNSWG  WG +GYI + R + N CG+++  S  
Sbjct: 283 SGSSSGQSSGQSSGNLSASSSNEYWIVKNSWGTSWGIEGYILMSRNRDNNCGIASSASFP 342

Query: 342 II 343
           ++
Sbjct: 343 VV 344


>sp|P13277|CYS1_HOMAM DIGESTIVE CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 322

 Score =  393 bits (998), Expect = e-109
 Identities = 130/351 (37%), Positives = 186/351 (52%), Gaps = 37/351 (10%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKI 59
           MKV+ LF+  +     +           + EF+ KF +KY   EE   R  +F  NL  I
Sbjct: 1   MKVVALFLFGLALAAANPS---------WEEFKGKFGRKYVDLEEERYRLNVFLDNLQYI 51

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
           EE N      +      +N+F+D+++++F       K+      +  +        ++ P
Sbjct: 52  EEFNKKYERGEVTYNLAINQFSDMTNEKFNAVMKGYKKGPRPAAVFTS-------TDAAP 104

Query: 120 TA--FDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHEC 177
            +   DWRT+GAVTPVK+QGQCGSCW+FSTTG +EGQHF+   +LVSLSEQ LVDC    
Sbjct: 105 ESTEVDWRTKGAVTPVKDQGQCGSCWAFSTTGGIEGQHFLKTGRLVSLSEQQLVDC---- 160

Query: 178 MEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISN 237
               G    ++GCNGG    A  Y+  NGG+ TESSYPY A   T C FNS  IGA  + 
Sbjct: 161 ---AGGSYYNQGCNGGWVERAIMYVRDNGGVDTESSYPYEARDNT-CRFNSNTIGATCTG 216

Query: 238 FTMIPK-NETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIP-CNPNSLDHGILIVGY 293
           +  I + +E+ +       GP+++A DA    +Q Y  GV+  P C+ + LDH +L VGY
Sbjct: 217 YVGIAQGSESALKTATRDIGPISVAIDASHRSFQSYYTGVYYEPSCSSSQLDHAVLAVGY 276

Query: 294 SAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTSII 343
            ++         +W+VKNSW   WGE GYI + R + N CG++       +
Sbjct: 277 GSEG-----GQDFWLVKNSWATSWGESGYIKMARNRNNNCGIATDACYPTV 322


>sp|P25784|CYS3_HOMAM DIGESTIVE CYSTEINE PROTEINASE 3 PRECURSOR
          Length = 321

 Score =  392 bits (997), Expect = e-109
 Identities = 126/348 (36%), Positives = 185/348 (52%), Gaps = 32/348 (9%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKI 59
           MKV  LF+  +     S           +  F+ ++ +KY   +E L R  +F+ N   I
Sbjct: 1   MKVAALFLCGLALATASPS---------WDHFKTQYGRKYGDAKEELYRQRVFQQNEQLI 51

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
           E+ N    N +   K  +N+F D++++EF       K+            +       + 
Sbjct: 52  EDFNKKFENGEVTFKVAMNQFGDMTNEEFNAVMKGYKKG----SRGEPKAVFTAEAGPMA 107

Query: 120 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 179
              DWRT+  VTPVK+Q QCGSCW+FS TG +EGQHF+  ++LVSLSEQ LVDC      
Sbjct: 108 ADVDWRTKALVTPVKDQEQCGSCWAFSATGALEGQHFLKNDELVSLSEQQLVDCST---- 163

Query: 180 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFT 239
               +  ++GC GG   +A++YI  NGGI TESSYPY AE    C F++ +IGA  +   
Sbjct: 164 ----DYGNDGCGGGWMTSAFDYIKDNGGIDTESSYPYEAED-RSCRFDANSIGAICTGSV 218

Query: 240 MIPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDI-PCNPNSLDHGILIVGYSAK 296
            +   E  +   +   GP+++A DA    +QFY  GV+    C+P  LDHG+L VGY  +
Sbjct: 219 EVQHTEEALQEAVSGVGPISVAIDASHFSFQFYSSGVYYEQNCSPTFLDHGVLAVGYGTE 278

Query: 297 NTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTSII 343
           +T       YW+VKNSWG+ WG+ GYI + R + N CG+++  S   +
Sbjct: 279 ST-----KDYWLVKNSWGSSWGDAGYIKMSRNRDNNCGIASEPSYPTV 321


>sp|P25774|CATS_HUMAN CATHEPSIN S PRECURSOR
          Length = 331

 Score =  392 bits (996), Expect = e-109
 Identities = 112/342 (32%), Positives = 172/342 (49%), Gaps = 21/342 (6%)

Query: 5   LLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELN 63
           L+ VL V +  V+     P     +  ++  + K+Y    E   R  I++ NL  +   N
Sbjct: 4   LVCVLLVCSSAVAQLHKDPTLDHHWHLWKKTYGKQYKEKNEEAVRRLIWEKNLKFVMLHN 63

Query: 64  LIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFD 123
           L           G+N   D++S+E  +   + +               +     +P + D
Sbjct: 64  LEHSMGMHSYDLGMNHLGDMTSEEVMSLTSSLRVPSQWQRNITYKSNPNRI---LPDSVD 120

Query: 124 WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE 183
           WR +G VT VK QG CG+CW+FS  G +E Q  +   KLV+LS QNLVDC  E       
Sbjct: 121 WREKGCVTEVKYQGSCGACWAFSAVGALEAQLKLKTGKLVTLSAQNLVDCSTE------- 173

Query: 184 EACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP- 242
           +  ++GCNGG    A+ YII N GI +++SYPY A    +C ++S    A  S +T +P 
Sbjct: 174 KYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKAMD-QKCQYDSKYRAATCSKYTELPY 232

Query: 243 KNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIF 300
             E V+   + + GP+++  DA    +  Y  GV+  P    +++HG+L+VGY   N   
Sbjct: 233 GREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCTQNVNHGVLVVGYGDLN--- 289

Query: 301 RKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTS 341
                YW+VKNSWG ++GE+GYI + R K N CG+++F S  
Sbjct: 290 --GKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYP 329


>sp|P15242|TES1_RAT TESTIN 1/2 PRECURSOR (CMB-22/CMB-23)
          Length = 333

 Score =  391 bits (995), Expect = e-109
 Identities = 112/347 (32%), Positives = 175/347 (50%), Gaps = 20/347 (5%)

Query: 3   VILLFVLAVFTVFVSSRGI--PPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60
           +I +  LA+  + V S      P    ++ E++ K  K Y+  E   +  +++ N   IE
Sbjct: 1   MIAVLFLAILCLEVDSTAPTPDPSLDVEWNEWRTKHGKTYNMNEERLKRAVWEKNFKMIE 60

Query: 61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPT 120
             N   +  + D    +N F DL++ EF               +       D     +P 
Sbjct: 61  LHNWEYLEGRHDFTMAMNAFGDLTNIEFVKMMTG----FQRQKIKKTHIFQDHQFLYVPK 116

Query: 121 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY 180
             DWR  G VTPVKNQG C S W+FS TG++EGQ F    +L+ LSEQNL+DC    + +
Sbjct: 117 RVDWRQLGYVTPVKNQGHCASSWAFSATGSLEGQMFRKTERLIPLSEQNLLDCMGSNVTH 176

Query: 181 EGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTM 240
                   GC+GG    A+ Y+  NGG+ TE SYPY  + G +C +++ N  A + +F  
Sbjct: 177 --------GCSGGFMQYAFQYVKDNGGLATEESYPYRGQ-GRECRYHAENSAANVRDFVQ 227

Query: 241 IPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIP-CNPNSLDHGILIVGYSAKN 297
           IP +E  +   +   GP+++A DA    +QFY  G++  P C    L+H +L+VGY  + 
Sbjct: 228 IPGSEEALMKAVAKVGPISVAVDASHGSFQFYGSGIYYEPQCKRVHLNHAVLVVGYGFE- 286

Query: 298 TIFRKNMPYWIVKNSWGADWGEQGYIYLRRG-KNTCGVSNFVSTSII 343
                   +W+VKNSWG +WG +GY+ L +   N CG++ + +  I+
Sbjct: 287 GEESDGNSFWLVKNSWGEEWGMKGYMKLAKDWSNHCGIATYSTYPIV 333


>sp|Q10716|CYS1_MAIZE CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 371

 Score =  391 bits (993), Expect = e-108
 Identities = 141/368 (38%), Positives = 201/368 (54%), Gaps = 34/368 (9%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEE-------------------QSQFLEFQDKFNKKYS 41
           M   +L +L++ +    +  +  E+                   +S FL F  +F K Y 
Sbjct: 1   MAHRVLLLLSLASAAAVAAAVDAEDPLIRQVVPGGDDNDLELNAESHFLSFVQRFGKSYK 60

Query: 42  H-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLN---NKE 97
             +E+  R  +FK NL +     L+        + GV KF+DL+  EF+  YL    ++ 
Sbjct: 61  DADEHAYRLSVFKDNLRRARRHQLLDP----SAEHGVTKFSDLTPAEFRRTYLGLRKSRR 116

Query: 98  AIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFI 157
           A+  +    A        + +P  FDWR  GAV PVKNQG CGSCWSFS +G +EG H++
Sbjct: 117 ALLRELGESAHEAPVLPTDGLPDDFDWRDHGAVGPVKNQGSCGSCWSFSASGALEGAHYL 176

Query: 158 SQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYT 217
           +  KL  LSEQ  VDCDHEC +    ++CD GCNGGL   A++Y+ K GG+++E  YPYT
Sbjct: 177 ATGKLEVLSEQQFVDCDHEC-DSSEPDSCDSGCNGGLMTTAFSYLQKAGGLESEKDYPYT 235

Query: 218 AETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDI 277
              G +C F+ + I A + NF+++  +E  ++  ++  GPLAI  +A   Q YIGGV   
Sbjct: 236 GSDG-KCKFDKSKIVASVQNFSVVSVDEAQISANLIKHGPLAIGINAAYMQTYIGGVSCP 294

Query: 278 PCNPNSLDHGILIVGYSAKN--TIFRKNMPYWIVKNSWGADWGEQGYIYLRRG---KNTC 332
                 LDHG+L+VGY A     I  K+ PYWI+KNSWG +WGE GY  + RG   +N C
Sbjct: 295 YICGRHLDHGVLLVGYGASGFAPIRLKDKPYWIIKNSWGENWGENGYYKICRGSNVRNKC 354

Query: 333 GVSNFVST 340
           GV + VST
Sbjct: 355 GVDSMVST 362


>sp|P12412|CYSP_VIGMU VIGNAIN PRECURSOR (BEAN ENDOPEPTIDASE) (CYSTEINE PROTEINASE)
           (SULFHYDRYL-ENDOPEPTIDASE) (SH-EP)
          Length = 362

 Score =  389 bits (989), Expect = e-108
 Identities = 131/360 (36%), Positives = 187/360 (51%), Gaps = 36/360 (10%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQ---------FLEFQDKFNKKYSHEEYLERFEI 51
           MK +L  VL++  V   +      E+           +  ++       S  E  +RF +
Sbjct: 3   MKKLLWVVLSLSLVLGVANSFDFHEKDLESEESLWDLYERWRSHHTVSRSLGEKHKRFNV 62

Query: 52  FKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAI---FTDDLPVAD 108
           FK+N+  +   N +        K  +NKFAD+++ EF++ Y  +K      F      + 
Sbjct: 63  FKANVMHVHNTNKMDKP----YKLKLNKFADMTNHEFRSTYAGSKVNHHKMFRGSQHGSG 118

Query: 109 YLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQ 168
               E + S+P + DWR +GAVT VK+QGQCGSCW+FST   VEG + I  NKLVSLSEQ
Sbjct: 119 TFMYEKVGSVPASVDWRKKGAVTDVKDQGQCGSCWAFSTIVAVEGINQIKTNKLVSLSEQ 178

Query: 169 NLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNS 228
            LVDCD E          ++GCNGGL  +A+ +I + GGI TES+YPYTA+ GT      
Sbjct: 179 ELVDCDKE---------ENQGCNGGLMESAFEFIKQKGGITTESNYPYTAQEGTCDESKV 229

Query: 229 ANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNPNSLDH 286
            ++   I     +P N+       V+  P+++A DA   ++QFY  GVF   C    L+H
Sbjct: 230 NDLAVSIDGHENVPVNDENALLKAVANQPVSVAIDAGGSDFQFYSEGVFTGDC-NTDLNH 288

Query: 287 GILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG----KNTCGVSNFVSTSI 342
           G+ IVGY            YWIV+NSWG +WGEQGYI ++R     +  CG++   S  I
Sbjct: 289 GVAIVGYGTTV----DGTNYWIVRNSWGPEWGEQGYIRMQRNISKKEGLCGIAMMASYPI 344


>sp|P43297|RD21_ARATH CYSTEINE PROTEINASE RD21A PRECURSOR
          Length = 462

 Score =  387 bits (984), Expect = e-107
 Identities = 120/330 (36%), Positives = 167/330 (50%), Gaps = 29/330 (8%)

Query: 22  PPEEQSQFLEFQDKFNKKYSHE---EYLERFEIFKSNLGKIEELNLIAINHKADTKFGVN 78
             E  S +  +  K  K  S     E   RFEIFK NL  ++E N   +      + G+ 
Sbjct: 43  EAEVMSIYEAWLVKHGKAQSQNSLVEKDRRFEIFKDNLRFVDEHNEKNL----SYRLGLT 98

Query: 79  KFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQ 138
           +FADL++DE+++ YL  K      +   +   +    + +P + DWR +GAV  VK+QG 
Sbjct: 99  RFADLTNDEYRSKYLGAKME-KKGERRTSLRYEARVGDELPESIDWRKKGAVAEVKDQGG 157

Query: 139 CGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNA 198
           CGSCW+FST G VEG + I    L++LSEQ LVDCD          + +EGCNGGL   A
Sbjct: 158 CGSCWAFSTIGAVEGINQIVTGDLITLSEQELVDCD---------TSYNEGCNGGLMDYA 208

Query: 199 YNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPL 258
           + +IIKNGGI T+  YPY    GT            I ++  +P          V+  P+
Sbjct: 209 FEFIIKNGGIDTDKDYPYKGVDGTCDQIRKNAKVVTIDSYEDVPTYSEESLKKAVAHQPI 268

Query: 259 AIAADA--VEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGAD 316
           +IA +A    +Q Y  G+FD  C    LDHG++ VGY  +N        YWIV+NSWG  
Sbjct: 269 SIAIEAGGRAFQLYDSGIFDGSCG-TQLDHGVVAVGYGTEN-----GKDYWIVRNSWGKS 322

Query: 317 WGEQGYIYLRRG----KNTCGVSNFVSTSI 342
           WGE GY+ + R        CG++   S  I
Sbjct: 323 WGESGYLRMARNIASSSGKCGIAIEPSYPI 352


>sp|P55097|CATK_MOUSE CATHEPSIN K PRECURSOR
          Length = 329

 Score =  384 bits (976), Expect = e-106
 Identities = 115/341 (33%), Positives = 178/341 (51%), Gaps = 25/341 (7%)

Query: 9   LAVFTVFVSSRGIPPEE--QSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLI 65
           L V  + + S  + PEE   +Q+  ++    K+Y+ + + + R  I++ NL +I   NL 
Sbjct: 4   LKVLLLPMVSFALSPEEMLDTQWELWKKTHQKQYNSKVDEISRRLIWEKNLKQISAHNLE 63

Query: 66  AINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWR 125
           A       +  +N   D++S+E        +            Y   E+   +P + D+R
Sbjct: 64  ASLGVHTYELAMNHLGDMTSEEVVQKMTGLRIPPSRSYSNDTLYTP-EWEGRVPDSIDYR 122

Query: 126 TRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEA 185
            +G VTPVKNQGQCGSCW+FS+ G +EGQ      KL++LS QNLVDC  E         
Sbjct: 123 KKGYVTPVKNQGQCGSCWAFSSAGALEGQLKKKTGKLLALSPQNLVDCVTE--------- 173

Query: 186 CDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP-KN 244
            + GC GG    A+ Y+ +NGGI +E ++PY  +    C +N+    AK   +  IP  N
Sbjct: 174 -NYGCGGGYMTTAFQYVQQNGGIDSEDAFPYVGQD-ESCMYNATAKAAKCRGYREIPVGN 231

Query: 245 ETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIVGYSAKNTIFR 301
           E  +   +   GP++++ DA    +QFY  GV +D  C+ ++++H +L+VGY       +
Sbjct: 232 EKALKRAVARVGPISVSIDASLASFQFYSRGVYYDENCDRDNVNHAVLVVGYGT-----Q 286

Query: 302 KNMPYWIVKNSWGADWGEQGYIYLRRGKNT-CGVSNFVSTS 341
           K   +WI+KNSWG  WG +GY  L R KN  CG++N  S  
Sbjct: 287 KGSKHWIIKNSWGESWGNKGYALLARNKNNACGITNMASFP 327


>sp|P09668|CATH_HUMAN CATHEPSIN H PRECURSOR
          Length = 335

 Score =  383 bits (974), Expect = e-106
 Identities = 119/341 (34%), Positives = 167/341 (48%), Gaps = 28/341 (8%)

Query: 8   VLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAI 67
           +L V     +   +   E+  F  +  K  K YS EEY  R + F SN  KI   N    
Sbjct: 14  LLGVPVCGAAELSVNSLEKFHFKSWMSKHRKTYSTEEYHHRLQTFASNWRKINAHN---- 69

Query: 68  NHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTR 127
           N     K  +N+F+D+S  E K+ YL ++          ++YL        P + DWR +
Sbjct: 70  NGNHTFKMALNQFSDMSFAEIKHKYLWSEPQ--NCSATKSNYLRGT--GPYPPSVDWRKK 125

Query: 128 GA-VTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEAC 186
           G  V+PVKNQG CGSCW+FSTTG +E    I+  K++SL+EQ LVDC  +   Y      
Sbjct: 126 GNFVSPVKNQGACGSCWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNY------ 179

Query: 187 DEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP-KNE 245
             GC GGL   A+ YI+ N GI  E +YPY  + G  C F        + +   I   +E
Sbjct: 180 --GCQGGLPSQAFEYILYNKGIMGEDTYPYQGKDGY-CKFQPGKAIGFVKDVANITIYDE 236

Query: 246 TVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCN---PNSLDHGILIVGYSAKNTIFR 301
             M   +    P++ A +   ++  Y  G++        P+ ++H +L VGY  KN    
Sbjct: 237 EAMVEAVALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKN---- 292

Query: 302 KNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 342
             +PYWIVKNSWG  WG  GY  + RGKN CG++   S  I
Sbjct: 293 -GIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPI 332


>sp|O46427|CATH_PIG CATHEPSIN H PRECURSOR
          Length = 335

 Score =  382 bits (971), Expect = e-106
 Identities = 117/336 (34%), Positives = 165/336 (48%), Gaps = 28/336 (8%)

Query: 13  TVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKAD 72
               S+  +   E+  F  +  +  KKYS EEY  R ++F SN  KI   N         
Sbjct: 19  ACGASNLAVSSFEKLHFKSWMVQHQKKYSLEEYHHRLQVFVSNWRKINAHNA----GNHT 74

Query: 73  TKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGA-VT 131
            K G+N+F+D+S DE ++ YL ++           +YL        P + DWR +G  V+
Sbjct: 75  FKLGLNQFSDMSFDEIRHKYLWSEPQ--NCSATKGNYLRGT--GPYPPSMDWRKKGNFVS 130

Query: 132 PVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCN 191
           PVKNQG CGSCW+FSTTG +E    I+  K++SL+EQ LVDC             + GC 
Sbjct: 131 PVKNQGSCGSCWTFSTTGALESAVAIATGKMLSLAEQQLVDCAQNFN--------NHGCQ 182

Query: 192 GGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN-ETVMAG 250
           GGL   A+ YI  N GI  E +YPY  +    C F      A + +   I  N E  M  
Sbjct: 183 GGLPSQAFEYIRYNKGIMGEDTYPYKGQDD-HCKFQPDKAIAFVKDVANITMNDEEAMVE 241

Query: 251 YIVSTGPLAIAADA-VEWQFYIGGVFDIPCN---PNSLDHGILIVGYSAKNTIFRKNMPY 306
            +    P++ A +   ++  Y  G++        P+ ++H +L VGY  +N      +PY
Sbjct: 242 AVALYNPVSFAFEVTNDFLMYRKGIYSSTSCHKTPDKVNHAVLAVGYGEEN-----GIPY 296

Query: 307 WIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 342
           WIVKNSWG  WG  GY  + RGKN CG++   S  I
Sbjct: 297 WIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPI 332


>sp|P25803|CYSP_PHAVU VIGNAIN PRECURSOR (BEAN ENDOPEPTIDASE) (CYSTEINE PROTEINASE EP-C1)
          Length = 362

 Score =  380 bits (966), Expect = e-105
 Identities = 128/354 (36%), Positives = 182/354 (51%), Gaps = 32/354 (9%)

Query: 3   VILLFVLAVFTVFVSSRGIP--PEEQSQF---LEFQDKFNKKYSHEEYLERFEIFKSNLG 57
           V+L F L +               E+S +     ++       S  E  +RF +FK+NL 
Sbjct: 9   VVLSFSLVLGVANSFDFHDKDLASEESLWDLYERWRSHHTVSRSLGEKHKRFNVFKANLM 68

Query: 58  KIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNK---EAIFTDDLPVADYLDDEF 114
            +   N +        K  +NKFAD+++ EF++ Y  +K     +F            E 
Sbjct: 69  HVHNTNKMDKP----YKLKLNKFADMTNHEFRSTYAGSKVNHPRMFRGTPHENGAFMYEK 124

Query: 115 INSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCD 174
           + S+P + DWR +GAVT VK+QGQCGSCW+FST   VEG + I  NKLV+LSEQ LVDCD
Sbjct: 125 VVSVPPSVDWRKKGAVTDVKDQGQCGSCWAFSTVVAVEGINQIKTNKLVALSEQELVDCD 184

Query: 175 HECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAK 234
            E          ++GCNGGL  +A+ +I + GGI TES+YPY A+ GT       ++   
Sbjct: 185 KE---------ENQGCNGGLMESAFEFIKQKGGITTESNYPYKAQEGTCDASKVNDLAVS 235

Query: 235 ISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNPNSLDHGILIVG 292
           I     +P N+       V+  P+++A DA   ++QFY  GVF   C    L+HG+ IVG
Sbjct: 236 IDGHENVPANDEDALLKAVANQPVSVAIDAGGSDFQFYSEGVFTGDC-STDLNHGVAIVG 294

Query: 293 YSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG----KNTCGVSNFVSTSI 342
           Y            YWIV+NSWG +WGE GYI ++R     +  CG++   S  I
Sbjct: 295 YGTTV----DGTNYWIVRNSWGPEWGEHGYIRMQRNISKKEGLCGIAMLPSYPI 344


>sp|P00786|CATH_RAT CATHEPSIN H PRECURSOR (CATHEPSIN B3) (CATHEPSIN BA)
          Length = 333

 Score =  377 bits (958), Expect = e-104
 Identities = 117/324 (36%), Positives = 167/324 (51%), Gaps = 28/324 (8%)

Query: 25  EQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLS 84
           E+  F  +  +  K YS  EY  R ++F +N  KI+  N          K G+N+F+D+S
Sbjct: 29  EKFHFTSWMKQHQKTYSSREYSHRLQVFANNWRKIQAHNQRN----HTFKMGLNQFSDMS 84

Query: 85  SDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAV-TPVKNQGQCGSCW 143
             E K+ YL ++          ++YL        P++ DWR +G V +PVKNQG CGSCW
Sbjct: 85  FAEIKHKYLWSEPQ--NCSATKSNYLRGT--GPYPSSMDWRKKGNVVSPVKNQGACGSCW 140

Query: 144 SFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYII 203
           +FSTTG +E    I+  K+++L+EQ LVDC             + GC GGL   A+ YI+
Sbjct: 141 TFSTTGALESAVAIASGKMMTLAEQQLVDCAQNFN--------NHGCQGGLPSQAFEYIL 192

Query: 204 KNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN-ETVMAGYIVSTGPLAIAA 262
            N GI  E SYPY  + G QC FN     A + N   I  N E  M   +    P++ A 
Sbjct: 193 YNKGIMGEDSYPYIGKNG-QCKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAF 251

Query: 263 DAV-EWQFYIGGVFDIPCN---PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWG 318
           +   ++  Y  GV+        P+ ++H +L VGY  +N +      YWIVKNSWG++WG
Sbjct: 252 EVTEDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYGEQNGLL-----YWIVKNSWGSNWG 306

Query: 319 EQGYIYLRRGKNTCGVSNFVSTSI 342
             GY  + RGKN CG++   S  I
Sbjct: 307 NNGYFLIERGKNMCGLAACASYPI 330


>sp|P25251|CYS4_BRANA CYSTEINE PROTEINASE COT44 PRECURSOR
          Length = 328

 Score =  376 bits (955), Expect = e-104
 Identities = 115/329 (34%), Positives = 167/329 (49%), Gaps = 32/329 (9%)

Query: 29  FLEFQDKFNKKYSH-----EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADL 83
           +L +  +  K  S+      +  ERF IFK NL  I+  N    N  A  K G+  FA+L
Sbjct: 4   YLRWSLEHGKSNSNSNGIINQQDERFNIFKDNLRFIDLHNE--NNKNATYKLGLTIFANL 61

Query: 84  SSDEFKNYYLNNK----EAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQC 139
           ++DE+++ YL  +      I         Y     ++ +P   DWR +GAV  +K+QG C
Sbjct: 62  TNDEYRSLYLGARTEPVRRITKAKNVNMKYSAAVNVDEVPVTVDWRQKGAVNAIKDQGTC 121

Query: 140 GSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAY 199
           GSCW+FST   VEG + I   +LVSLSEQ LVDCD          + ++GCNGGL   A+
Sbjct: 122 GSCWAFSTAAAVEGINKIVTGELVSLSEQELVDCDK---------SYNQGCNGGLMDYAF 172

Query: 200 NYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLA 259
            +I+KNGG+ TE  YPY    G   +    +    I  +  +P  +       VS  P++
Sbjct: 173 QFIMKNGGLNTEKDYPYHGTNGKCNSLLKNSRVVTIDGYEDVPSKDETALKRAVSYQPVS 232

Query: 260 IAADA--VEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADW 317
           +A DA    +Q Y  G+F   C   ++DH ++ VGY ++N +      YWIV+NSWG  W
Sbjct: 233 VAIDAGGRAFQHYQSGIFTGKCG-TNMDHAVVAVGYGSENGV-----DYWIVRNSWGTRW 286

Query: 318 GEQGYIYLRRG----KNTCGVSNFVSTSI 342
           GE GYI + R        CG++   S  +
Sbjct: 287 GEDGYIRMERNVASKSGKCGIAIEASYPV 315


>sp|P05167|ALEU_HORVU THIOL PROTEASE ALEURAIN PRECURSOR
          Length = 362

 Score =  375 bits (954), Expect = e-104
 Identities = 119/374 (31%), Positives = 179/374 (47%), Gaps = 54/374 (14%)

Query: 3   VILLFVLAVFTVFVSSRGIPPEEQ---------------------------SQFLEFQDK 35
           ++ L VLA   V V+S     +                              +F  F  +
Sbjct: 8   LLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVR 67

Query: 36  FNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLN 94
           + K Y S  E   RF IF  +L ++   N   + ++     G+N+F+D+S +EF+   L 
Sbjct: 68  YGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYR----LGINRFSDMSWEEFQATRLG 123

Query: 95  NKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQ 154
              A  T    +A         ++P   DWR  G V+PVKNQ  CGSCW+FSTTG +E  
Sbjct: 124 ---AAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAA 180

Query: 155 HFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSY 214
           +  +  K +SLSEQ LVDC      +        GCNGGL   A+ YI  NGGI TE SY
Sbjct: 181 YTQATGKNISLSEQQLVDCAGGFNNF--------GCNGGLPSQAFEYIKYNGGIDTEESY 232

Query: 215 PYTAETGTQCNFNSANIGAKISNFTMIPKN-ETVMAGYIVSTGPLAIAADAVE-WQFYIG 272
           PY    G  C++ + N   ++ +   I  N E  +   +    P+++A   ++ ++ Y  
Sbjct: 233 PYKGVNGV-CHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKS 291

Query: 273 GVFD-IPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK 329
           GV+    C   P+ ++H +L VGY  +N +     PYW++KNSWGADWG+ GY  +  GK
Sbjct: 292 GVYTSDHCGTTPDDVNHAVLAVGYGVENGV-----PYWLIKNSWGADWGDNGYFKMEMGK 346

Query: 330 NTCGVSNFVSTSII 343
           N C ++   S  ++
Sbjct: 347 NMCAIATCASYPVV 360


>sp|Q10717|CYS2_MAIZE CYSTEINE PROTEINASE 2 PRECURSOR
          Length = 360

 Score =  374 bits (951), Expect = e-103
 Identities = 114/322 (35%), Positives = 168/322 (51%), Gaps = 26/322 (8%)

Query: 28  QFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSD 86
           +F  F  ++ K Y S  E  +RF IF  +L  +   N   +      + G+N+FAD+S +
Sbjct: 58  RFARFAVRYGKSYESAAEVHKRFRIFSESLQLVRSTNRKGL----SYRLGINRFADMSWE 113

Query: 87  EFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFS 146
           EF+   L   +          ++       ++P   DWR  G V+PVKNQG CGSCW+FS
Sbjct: 114 EFRATRLGAAQNCSAT--LTGNHRMRAAAVALPETKDWREDGIVSPVKNQGHCGSCWTFS 171

Query: 147 TTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNG 206
           TTG +E  +  +  K +SLSEQ LVDC      +        GCNGGL   A+ YI  NG
Sbjct: 172 TTGALEAAYTQATGKPISLSEQQLVDCGFAFNNF--------GCNGGLPSQAFEYIKYNG 223

Query: 207 GIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN-ETVMAGYIVSTGPLAIAADAV 265
           G+ TE SYPY    G  C F + N+G K+ +   I    E  +   +    P+++A + +
Sbjct: 224 GLDTEESYPYQGVNGI-CKFKNENVGVKVLDSVNITLGAEDELKDAVGLVRPVSVAFEVI 282

Query: 266 E-WQFYIGGVFD-IPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQG 321
             ++ Y  GV+    C   P  ++H +L VGY  ++ +     PYW++KNSWGADWG++G
Sbjct: 283 TGFRLYKSGVYTSDHCGTTPMDVNHAVLAVGYGVEDGV-----PYWLIKNSWGADWGDEG 337

Query: 322 YIYLRRGKNTCGVSNFVSTSII 343
           Y  +  GKN CGV+   S  I+
Sbjct: 338 YFKMEMGKNMCGVATCASYPIV 359


>sp|P25777|ORYB_ORYSA ORYZAIN BETA CHAIN PRECURSOR
          Length = 471

 Score =  374 bits (951), Expect = e-103
 Identities = 112/304 (36%), Positives = 159/304 (51%), Gaps = 23/304 (7%)

Query: 44  EYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDD 103
           E+  RF +F  NL  ++  N  A       + G+N+FADL+++EF+  +L  K A     
Sbjct: 69  EHERRFLVFWDNLKFVDAHNARADEGGG-FRLGMNRFADLTNEEFRATFLGAKVAER--S 125

Query: 104 LPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLV 163
               +    + +  +P + DWR +GAV PVKNQGQCGSCW+FS    VE  + +   +++
Sbjct: 126 RAAGERYRHDGVEELPESVDWREKGAVAPVKNQGQCGSCWAFSAVSTVESINQLVTGEMI 185

Query: 164 SLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQ 223
           +LSEQ LV+C             + GCNGGL  +A+++IIKNGGI TE  YPY A  G  
Sbjct: 186 TLSEQELVECST--------NGQNSGCNGGLMADAFDFIIKNGGIDTEDDYPYKAVDGKC 237

Query: 224 CNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNP 281
                      I  F  +P+N+       V+  P+++A +A   E+Q Y  GVF   C  
Sbjct: 238 DINRENAKVVSIDGFEDVPQNDEKSLQKAVAHQPVSVAIEAGGREFQLYHSGVFSGRCG- 296

Query: 282 NSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKN----TCGVSNF 337
            SLDHG++ VGY   N        YWIV+NSWG  WGE GY+ + R  N     CG++  
Sbjct: 297 TSLDHGVVAVGYGTDN-----GKDYWIVRNSWGPKWGESGYVRMERNINVTTGKCGIAMM 351

Query: 338 VSTS 341
            S  
Sbjct: 352 ASYP 355


>sp|Q40143|CYS3_LYCES CYSTEINE PROTEINASE 3 PRECURSOR
          Length = 356

 Score =  373 bits (948), Expect = e-103
 Identities = 123/321 (38%), Positives = 169/321 (52%), Gaps = 28/321 (8%)

Query: 29  FLEFQDKFNKKYSHEEYL-ERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE 87
           F  F  +  K+Y   E + +RFEIF  NL  I   N   +      K G+N+F DL+ DE
Sbjct: 57  FARFAIRHRKRYDSVEEIKQRFEIFLDNLKMIRSHNRKGL----SYKLGINEFTDLTWDE 112

Query: 88  FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFST 147
           F+ + L    A           L    +  +P   DWR  G V+PVK QG+CGSCW+FST
Sbjct: 113 FRKHKLG---ASQNCSATTKGNLKLTNVV-LPETKDWRKDGIVSPVKAQGKCGSCWTFST 168

Query: 148 TGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGG 207
           TG +E  +  +  K +SLSEQ LVDC      +        GCNGGL   A+ YI  NGG
Sbjct: 169 TGALEAAYAQAFGKGISLSEQQLVDCAGAFNNF--------GCNGGLPSQAFEYIKFNGG 220

Query: 208 IQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN-ETVMAGYIVSTGPLAIAADAVE 266
           + TE +YPYT + G  C F+ ANIG K+ +   I    E  +   +    P+++A + V+
Sbjct: 221 LDTEEAYPYTGKNGI-CKFSQANIGVKVISSVNITLGAEYELKYAVALVRPVSVAFEVVK 279

Query: 267 -WQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGY 322
            ++ Y  GV+    C   P  ++H +L VGY  +N       PYW++KNSWGADWGE GY
Sbjct: 280 GFKQYKSGVYASTECGDTPMDVNHAVLAVGYGVEN-----GTPYWLIKNSWGADWGEDGY 334

Query: 323 IYLRRGKNTCGVSNFVSTSII 343
             +  GKN CGV+   S  I+
Sbjct: 335 FKMEMGKNMCGVATCASYPIV 355


>sp|P43156|CYSP_HEMSP THIOL PROTEASE SEN102 PRECURSOR
          Length = 360

 Score =  373 bits (947), Expect = e-103
 Identities = 127/352 (36%), Positives = 181/352 (51%), Gaps = 30/352 (8%)

Query: 3   VILLFVLAVFTVFVSSRGIPPEEQ--SQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60
           V L F+    ++  + + +  E+   + + +++         +E   RF +FK N+  I 
Sbjct: 12  VALSFLSIAQSIPFTEKDLASEDSLWNLYEKWRTHHTVARDLDEKNRRFNVFKENVKFIH 71

Query: 61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADY---LDDEFINS 117
           E N       A  K  +NKF D+++ EF++ Y  +K         +         E + S
Sbjct: 72  EFNQK---KDAPYKLALNKFGDMTNQEFRSKYAGSKIQHHRSQRGIQKNTGSFMYENVGS 128

Query: 118 IPT-AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 176
           +P  + DWR +GAVT VK+QGQCGSCW+FST  +VEG + I   +LVSLSEQ LVDCD  
Sbjct: 129 LPAASIDWRAKGAVTGVKDQGQCGSCWAFSTIASVEGINQIKTGELVSLSEQELVDCD-- 186

Query: 177 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKIS 236
                   + +EGCNGGL   A+ +I KN GI TE SYPY  + GT  +    +    I 
Sbjct: 187 -------TSYNEGCNGGLMDYAFEFIQKN-GITTEDSYPYAEQDGTCASNLLNSPVVSID 238

Query: 237 NFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNPNSLDHGILIVGYS 294
               +P N        V+  P++++ +A    +QFY  GVF   C    LDHG+ IVGY 
Sbjct: 239 GHQDVPANNENALMQAVANQPISVSIEASGYGFQFYSEGVFTGRCG-TELDHGVAIVGYG 297

Query: 295 AKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG----KNTCGVSNFVSTSI 342
           A     R    YWIVKNSWG +WGE GYI ++RG    +  CG++   S  I
Sbjct: 298 AT----RDGTKYWIVKNSWGEEWGESGYIRMQRGISDKRGKCGIAMEASYPI 345


>sp|P49935|CATH_MOUSE CATHEPSIN H PRECURSOR (CATHEPSIN B3) (CATHEPSIN BA)
          Length = 333

 Score =  372 bits (944), Expect = e-103
 Identities = 114/324 (35%), Positives = 164/324 (50%), Gaps = 28/324 (8%)

Query: 25  EQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLS 84
           E+  F  +  +  K YS  EY  R ++F +N  KI+  N          K  +N+F+D+S
Sbjct: 29  EKFHFKSWMKQHQKTYSSVEYNHRLQMFANNWRKIQAHNQRN----HTFKMALNQFSDMS 84

Query: 85  SDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAV-TPVKNQGQCGSCW 143
             E K+ +L ++          ++YL        P++ DWR +G V +PVKNQG C SCW
Sbjct: 85  FAEIKHKFLWSEPQ--NCSATKSNYLRGT--GPYPSSMDWRKKGNVVSPVKNQGACASCW 140

Query: 144 SFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYII 203
           +FSTTG +E    I+  K++SL+EQ LVDC             + GC GGL   A+ YI+
Sbjct: 141 TFSTTGALESAVAIASGKMLSLAEQQLVDCAQAFN--------NHGCKGGLPSQAFEYIL 192

Query: 204 KNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKN-ETVMAGYIVSTGPLAIAA 262
            N GI  E SYPY  +  + C FN     A + N   I  N E  M   +    P++ A 
Sbjct: 193 YNKGIMEEDSYPYIGKD-SSCRFNPQKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAF 251

Query: 263 DAV-EWQFYIGGVFDIPCN---PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWG 318
           +   ++  Y  GV+        P+ ++H +L VGY  +N +      YWIVKNSWG+ WG
Sbjct: 252 EVTEDFLMYKSGVYSSKSCHKTPDKVNHAVLAVGYGEQNGLL-----YWIVKNSWGSQWG 306

Query: 319 EQGYIYLRRGKNTCGVSNFVSTSI 342
           E GY  + RGKN CG++   S  I
Sbjct: 307 ENGYFLIERGKNMCGLAACASYPI 330


>sp|P25778|ORYC_ORYSA ORYZAIN GAMMA CHAIN PRECURSOR
          Length = 362

 Score =  370 bits (940), Expect = e-102
 Identities = 110/322 (34%), Positives = 164/322 (50%), Gaps = 27/322 (8%)

Query: 28  QFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSD 86
           +F  F  +  K+Y    E   RF IF  +L  +   N   + ++     G+N+FAD+S +
Sbjct: 61  RFARFAVRHGKRYGDAAEVQRRFRIFSESLELVRSTNRRGLPYR----LGINRFADMSWE 116

Query: 87  EFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFS 146
           EF+   L    A       +A         ++P   DWR  G V+PVK+QG CGSCW FS
Sbjct: 117 EFQASRLG---AAQNCSATLAGNHRMRDAPALPETKDWREDGIVSPVKDQGHCGSCWPFS 173

Query: 147 TTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNG 206
           TTG++E ++  +    VSLSEQ L DC      +        GC+GGL   A+ YI  NG
Sbjct: 174 TTGSLEARYTQATGPPVSLSEQQLADCATRYNNF--------GCSGGLPSQAFEYIKYNG 225

Query: 207 GIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP-KNETVMAGYIVSTGPLAIAADAV 265
           G+ TE +YPYT   G  C++   N G K+ +   I    E  +   +    P+++A   +
Sbjct: 226 GLDTEEAYPYTGVNGI-CHYKPENAGVKVLDSVNITLVAEDELKNAVGLVRPVSVAFQVI 284

Query: 266 E-WQFYIGGVF---DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQG 321
             ++ Y  GV+       +P  ++H +L VGY  +N +     PYW++KNSWGADWG+ G
Sbjct: 285 NGFRMYKSGVYTSDHCGTSPMDVNHAVLAVGYGVENGV-----PYWLIKNSWGADWGDNG 339

Query: 322 YIYLRRGKNTCGVSNFVSTSII 343
           Y  +  GKN CG++   S  I+
Sbjct: 340 YFTMEMGKNMCGIATCASYPIV 361


>sp|P00785|ACTN_ACTCH ACTINIDAIN PRECURSOR (ACTINIDIN)
          Length = 380

 Score =  368 bits (936), Expect = e-102
 Identities = 116/352 (32%), Positives = 180/352 (50%), Gaps = 29/352 (8%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPP----EEQSQFLEFQDKFNKKYSH-EEYLERFEIFKSN 55
           M ++    L + ++  +++ +      E ++ +  +  K+ K Y+   E+  RFEIFK  
Sbjct: 10  MSLLFFSTLLILSLAFNAKNLTQRTNDEVKAMYESWLIKYGKSYNSLGEWERRFEIFKET 69

Query: 56  LGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFI 115
           L  I+E N    +     K G+N+FADL+ +EF++ YL       ++   V++  +  F 
Sbjct: 70  LRFIDEHNA---DTNRSYKVGLNQFADLTDEEFRSTYLGFTSG--SNKTKVSNRYEPRFG 124

Query: 116 NSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDH 175
             +P+  DWR+ GAV  +K+QG+CG CW+FS    VEG + I    L+SLSEQ L+DC  
Sbjct: 125 QVLPSYVDWRSAGAVVDIKSQGECGGCWAFSAIATVEGINKIVTGVLISLSEQELIDC-- 182

Query: 176 ECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKI 235
                 G      GCNGG   + + +II NGGI TE +YPYTA+ G             I
Sbjct: 183 ------GRTQNTRGCNGGYITDGFQFIINNGGINTEENYPYTAQDGECNLDLQNEKYVTI 236

Query: 236 SNFTMIPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIPCNPNSLDHGILIVGY 293
             +  +P N        V+  P+++A DA    ++ Y  G+F  PC   ++DH + IVGY
Sbjct: 237 DTYENVPYNNEWALQTAVTYQPVSVALDAAGDAFKHYSSGIFTGPCG-TAIDHAVTIVGY 295

Query: 294 SAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK---NTCGVSNFVSTSI 342
             +       + YWIVKNSW   WGE+GY+ + R      TCG++   S  +
Sbjct: 296 GTEG-----GIDYWIVKNSWDTTWGEEGYMRILRNVGGAGTCGIATMPSYPV 342


>sp|P41721|CATV_NPVBM VIRAL CATHEPSIN (V-CATH)
          Length = 323

 Score =  367 bits (932), Expect = e-101
 Identities = 131/342 (38%), Positives = 180/342 (52%), Gaps = 26/342 (7%)

Query: 5   LLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELN 63
           +LF L V+ V  S+   P +  + F EF  +FNK YS E E L RF+IF+ NL +I    
Sbjct: 4   ILFYLFVYAVVKSAAYDPLKAPNYFEEFVHRFNKNYSSEVEKLRRFKIFQHNLNEI---- 59

Query: 64  LIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFD 123
            I  N     K+ +NKF+DLS DE    Y        T +      LD       P  FD
Sbjct: 60  -INKNQNDSAKYEINKFSDLSKDETIAKYTGLSLPTQTQNFCKVILLDQPPGKG-PLEFD 117

Query: 124 WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE 183
           WR    VT VKNQG CG+CW+F+T G++E Q  I  N+L++LSEQ ++DCD         
Sbjct: 118 WRRLNKVTSVKNQGMCGACWAFATLGSLESQFAIKHNELINLSEQQMIDCD--------- 168

Query: 184 EACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISN-FTMIP 242
              D GCNGGL   A+  IIK GG+Q ES YPY A     C  NS     ++ + +  I 
Sbjct: 169 -FVDAGCNGGLLHTAFEAIIKMGGVQLESDYPYEA-DNNNCRMNSNKFLVQVKDCYRYII 226

Query: 243 KNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRK 302
             E  +   +   GP+ +A DA +   Y  G+    C  + L+H +L+VGY  +N     
Sbjct: 227 VYEEKLKDLLPLVGPIPMAIDAADIVNYKQGIIKY-CFDSGLNHAVLLVGYGVEN----- 280

Query: 303 NMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN-FVSTSII 343
           N+PYW  KN+WG DWGE G+  +++  N CG+ N   ST++I
Sbjct: 281 NIPYWTFKNTWGTDWGEDGFFRVQQNINACGMRNELASTAVI 322


>sp|Q02765|CATS_RAT CATHEPSIN S PRECURSOR
          Length = 330

 Score =  365 bits (926), Expect = e-100
 Identities = 104/330 (31%), Positives = 161/330 (48%), Gaps = 22/330 (6%)

Query: 18  SRGIPPEEQSQFLEFQD-KFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFG 76
           +    P     +  ++  +  +     E   R  I++ NL  I   NL           G
Sbjct: 15  ATAERPTLDHHWDLWKKTRMRRNTDQNEEDVRRLIWEKNLKFIMLHNLEHSMGMHSYSVG 74

Query: 77  VNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQ 136
           +N   D++ +E   Y  + +     +         ++    +P + DWR +G VT VK Q
Sbjct: 75  MNHMGDMTPEEVIGYMGSLRIPRPWNRSGTLKSSSNQT---LPDSVDWREKGCVTNVKYQ 131

Query: 137 GQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQP 196
           G CGSCW+FS  G +EGQ  +   KLVSLS QNLVDC  E      E+  ++GC GG   
Sbjct: 132 GSCGSCWAFSAEGALEGQLKLKTGKLVSLSAQNLVDCSTE------EKYGNKGCGGGFMT 185

Query: 197 NAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP-KNETVMAGYIVST 255
            A+ YII +  I +E+SYPY A    +C ++  N  A  S +  +P  +E  +   + + 
Sbjct: 186 EAFQYII-DTSIDSEASYPYKAMD-EKCLYDPKNRAATCSRYIELPFGDEEALKEAVATK 243

Query: 256 GPLAIAADA---VEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNS 312
           GP+++  D      +  Y  GV+D P    +++HG+L+VGY            YW+VKNS
Sbjct: 244 GPVSVGIDDASHSSFFLYQSGVYDDPSCTENMNHGVLVVGYGT-----LDGKDYWLVKNS 298

Query: 313 WGADWGEQGYIYLRR-GKNTCGVSNFVSTS 341
           WG  +G+QGYI + R  KN CG++++ S  
Sbjct: 299 WGLHFGDQGYIRMARNNKNHCGIASYCSYP 328


>sp|P14658|CYSP_TRYBB CYSTEINE PROTEINASE PRECURSOR
          Length = 450

 Score =  365 bits (926), Expect = e-100
 Identities = 136/346 (39%), Positives = 190/346 (54%), Gaps = 26/346 (7%)

Query: 3   VILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEE 61
           V+L     + +V + S  +    + +F  F+ K+ K Y   +E   RF  F+ N+ + + 
Sbjct: 15  VLLAMAACLASVALGSLHVEESLEMRFAAFKKKYGKVYKDAKEEAFRFRAFEENMEQAK- 73

Query: 62  LNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTA 121
              I         FGV  F+D++ +EF+  Y N           +   ++       P A
Sbjct: 74  ---IQAAANPYATFGVTPFSDMTREEFRARYRNGASYFAAAQKRLRKTVNVT-TGRAPAA 129

Query: 122 FDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYE 181
            DWR +GAVTPVK QGQCGSCW+FST GN+EGQ  ++ N LVSLSEQ LV CD       
Sbjct: 130 VDWREKGAVTPVKVQGQCGSCWAFSTIGNIEGQWQVAGNPLVSLSEQMLVSCDT------ 183

Query: 182 GEEACDEGCNGGLQPNAYNYIIK-NGG-IQTESSYPYTAETGT--QCNFNSANIGAKISN 237
                D GCNGGL  NA+N+I+  NGG + TE+SYPY +  G   QC  N   IGA I++
Sbjct: 184 ----IDSGCNGGLMDNAFNWIVNSNGGNVFTEASYPYVSGNGEQPQCQMNGHEIGAAITD 239

Query: 238 FTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKN 297
              +P++E  +A Y+   GPLAIA DA  +  Y GG+    C    LDHG+L+VGY+   
Sbjct: 240 HVDLPQDEDAIAAYLAENGPLAIAVDAESFMDYNGGIL-TSCTSKQLDHGVLLVGYN--- 295

Query: 298 TIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
                N PYWI+KNSW   WGE GYI + +G N C ++  VS++++
Sbjct: 296 --DNSNPPYWIIKNSWSNMWGEDGYIRIEKGTNQCLMNQAVSSAVV 339


>sp|P25783|CATV_NPVAC VIRAL CATHEPSIN (V-CATH)
          Length = 323

 Score =  363 bits (923), Expect = e-100
 Identities = 129/342 (37%), Positives = 178/342 (51%), Gaps = 26/342 (7%)

Query: 5   LLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELN 63
           +LF L V+ V  S+     +  + F EF  +FNK Y  E E L RF+IF+ NL +I    
Sbjct: 4   ILFYLFVYGVVNSAAYDLLKAPNYFEEFVHRFNKDYGSEVEKLRRFKIFQHNLNEI---- 59

Query: 64  LIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFD 123
            I  N     K+ +NKF+DLS DE    Y      I T +      LD       P  FD
Sbjct: 60  -INKNQNDSAKYEINKFSDLSKDETIAKYTGLSLPIQTQNFCKVIVLDQPPGKG-PLEFD 117

Query: 124 WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE 183
           WR    VT VKNQG CG+CW+F+T  ++E Q  I  N+L++LSEQ ++DCD         
Sbjct: 118 WRRLNKVTSVKNQGMCGACWAFATLASLESQFAIKHNQLINLSEQQMIDCD--------- 168

Query: 184 EACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISN-FTMIP 242
              D GCNGGL   A+  IIK GG+Q ES YPY A     C  NS     ++ + +  I 
Sbjct: 169 -FVDAGCNGGLLHTAFEAIIKMGGVQLESDYPYEA-DNNNCRMNSNKFLVQVKDCYRYIT 226

Query: 243 KNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRK 302
             E  +   +   GP+ +A DA +   Y  G+    C  + L+H +L+VGY  +N     
Sbjct: 227 VYEEKLKDLLRLVGPIPMAIDAADIVNYKQGIIKY-CFNSGLNHAVLLVGYGVEN----- 280

Query: 303 NMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN-FVSTSII 343
           N+PYW  KN+WG DWGE G+  +++  N CG+ N   ST++I
Sbjct: 281 NIPYWTFKNTWGTDWGEDGFFRVQQNINACGMRNELASTAVI 322


>sp|P41715|CATV_NPVCF VIRAL CATHEPSIN (V-CATH)
          Length = 324

 Score =  363 bits (922), Expect = e-100
 Identities = 128/343 (37%), Positives = 187/343 (54%), Gaps = 25/343 (7%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKI 59
           M  I+L++L    V  ++  +  +  + F +F  KFNK YS E E L RF+IF+ NL +I
Sbjct: 1   MNKIVLYLLVYGAVQCAAYDV-LKAPNYFEDFLHKFNKSYSSESEKLRRFQIFRHNLEEI 59

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
              N    ++ +  ++ +NKFADLS DE  + Y      + T +      LD       P
Sbjct: 60  INKN----HNDSTAQYEINKFADLSKDETISKYTGLSLPLQTQNFCEVVVLDRPPDKG-P 114

Query: 120 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 179
             FDWR    VT VKNQG CG+CW+F+T G++E Q  I  N+ ++LSEQ L+DCD     
Sbjct: 115 LEFDWRRLNKVTSVKNQGMCGACWAFATLGSLESQFAIKHNQFINLSEQQLIDCD----- 169

Query: 180 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISN-F 238
                  D GC+GGL   A+  ++  GGIQ ES YPY A  G  C  N+A    K+   +
Sbjct: 170 -----FVDAGCDGGLLHTAFEAVMNMGGIQAESDYPYEANNG-DCRANAAKFVVKVKKCY 223

Query: 239 TMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNT 298
             I   E  +   + S GP+ +A DA +   Y  G+    C  + L+H +L+VGY+ +N 
Sbjct: 224 RYITVFEEKLKDLLRSVGPIPVAIDASDIVNYKRGIMKY-CANHGLNHAVLLVGYAVENG 282

Query: 299 IFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTS 341
           +     P+WI+KN+WGADWGEQGY  +++  N CG+ N + +S
Sbjct: 283 V-----PFWILKNTWGADWGEQGYFRVQQNINACGIQNELPSS 320


>sp|P25250|CYS2_HORVU CYSTEINE PROTEINASE EP-B 2 PRECURSOR
          Length = 373

 Score =  361 bits (918), Expect = e-100
 Identities = 121/358 (33%), Positives = 170/358 (46%), Gaps = 38/358 (10%)

Query: 5   LLFVLAVFTVFVSSRGIPPEEQSQ---------FLEFQDKFNKKYSHEEYLERFEIFKSN 55
           +  VLAV  V + S  IP E++           +  +Q     +  H E   RF  FKSN
Sbjct: 14  VAAVLAVAAVELCS-AIPMEDKDLESEEALWDLYERWQSAHRVRRHHAEKHRRFGTFKSN 72

Query: 56  LGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFI 115
              I   N          +  +N+F D+   EF+  ++ +         P         +
Sbjct: 73  AHFIHSHNKR---GDHPYRLHLNRFGDMDQAEFRATFVGDLRRDTPSKPPSVPGFMYAAL 129

Query: 116 N--SIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDC 173
           N   +P + DWR +GAVT VK+QG+CGSCW+FST  +VEG + I    LVSLSEQ L+DC
Sbjct: 130 NVSDLPPSVDWRQKGAVTGVKDQGKCGSCWAFSTVVSVEGINAIRTGSLVSLSEQELIDC 189

Query: 174 DHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQ---CNFNSAN 230
           D          A ++GC GGL  NA+ YI  NGG+ TE++YPY A  GT        ++ 
Sbjct: 190 D---------TADNDGCQGGLMDNAFEYIKNNGGLITEAAYPYRAARGTCNVARAAQNSP 240

Query: 231 IGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIPCNPNSLDHGI 288
           +   I     +P N        V+  P+++A +A    + FY  GVF   C    LDHG+
Sbjct: 241 VVVHIDGHQDVPANSEEDLARAVANQPVSVAVEASGKAFMFYSEGVFTGECG-TELDHGV 299

Query: 289 LIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK----NTCGVSNFVSTSI 342
            +VGY     +      YW VKNSWG  WGEQGYI + +        CG++   S  +
Sbjct: 300 AVVGYG----VAEDGKAYWTVKNSWGPSWGEQGYIRVEKDSGASGGLCGIAMEASYPV 353


>sp|P25249|CYS1_HORVU CYSTEINE PROTEINASE EP-B 1 PRECURSOR
          Length = 371

 Score =  361 bits (917), Expect = 1e-99
 Identities = 121/358 (33%), Positives = 170/358 (46%), Gaps = 38/358 (10%)

Query: 5   LLFVLAVFTVFVSSRGIPPEEQSQ---------FLEFQDKFNKKYSHEEYLERFEIFKSN 55
           +  VLAV  V + S  IP E++           +  +Q     +  H E   RF  FKSN
Sbjct: 14  VAAVLAVAAVELCS-AIPMEDKDLESEEALWDLYERWQSAHRVRRHHAEKHRRFGTFKSN 72

Query: 56  LGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFI 115
              I   N          +  +N+F D+   EF+  ++ +         P         +
Sbjct: 73  AHFIHSHNKR---GDHPYRLHLNRFGDMDQAEFRATFVGDLRRDTPAKPPSVPGFMYAAL 129

Query: 116 N--SIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDC 173
           N   +P + DWR +GAVT VK+QG+CGSCW+FST  +VEG + I    LVSLSEQ L+DC
Sbjct: 130 NVSDLPPSVDWRQKGAVTGVKDQGKCGSCWAFSTVVSVEGINAIRTGSLVSLSEQELIDC 189

Query: 174 DHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQ---CNFNSAN 230
           D          A ++GC GGL  NA+ YI  NGG+ TE++YPY A  GT        ++ 
Sbjct: 190 D---------TADNDGCQGGLMDNAFEYIKNNGGLITEAAYPYRAARGTCNVARAAQNSP 240

Query: 231 IGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIPCNPNSLDHGI 288
           +   I     +P N        V+  P+++A +A    + FY  GVF   C    LDHG+
Sbjct: 241 VVVHIDGHQDVPANSEEDLARAVANQPVSVAVEASGKAFMFYSEGVFTGDCG-TELDHGV 299

Query: 289 LIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK----NTCGVSNFVSTSI 342
            +VGY     +      YW VKNSWG  WGEQGYI + +        CG++   S  +
Sbjct: 300 AVVGYG----VAEDGKAYWTVKNSWGPSWGEQGYIRVEKDSGASGGLCGIAMEASYPV 353


>sp|Q26534|CATL_SCHMA CATHEPSIN L PRECURSOR (SMCL1)
          Length = 319

 Score =  361 bits (916), Expect = 2e-99
 Identities = 128/326 (39%), Positives = 190/326 (58%), Gaps = 22/326 (6%)

Query: 21  IPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKF 80
           +P     ++++F+ K+ K+Y   E   RF IFKSN+ K +   L  +  +    +GV  +
Sbjct: 12  LPGNVDEKYVQFKLKYRKQYHETEDEIRFNIFKSNILKAQ---LYQVFVRGSAIYGVTPY 68

Query: 81  ADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCG 140
           +DL++DEF   +L     + +        L  E +N+IP  FDWR +GAVT VKNQG CG
Sbjct: 69  SDLTTDEFARTHLTASWVVPSSRSNTPTSLGKE-VNNIPKNFDWREKGAVTEVKNQGMCG 127

Query: 141 SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYN 200
           SCW+FSTTGNVE Q F    KL+SLSEQ LVDCD            D+GCNGGL  NAY 
Sbjct: 128 SCWAFSTTGNVESQWFRKTGKLLSLSEQQLVDCDG----------LDDGCNGGLPSNAYE 177

Query: 201 YIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAI 260
            IIK GG+  E +YPY A+   +C+  +  +   I++   + ++ET +A ++     +++
Sbjct: 178 SIIKMGGLMLEDNYPYDAKN-EKCHLKTDGVAVYINSSVNLTQDETELAAWLYHNSTISV 236

Query: 261 AADAVEWQFYIGGV---FDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADW 317
             +A+  QFY  G+   + I C+   LDH +L+VGY     +  KN P+WIVKNSWG +W
Sbjct: 237 GMNALLLQFYQHGISHPWWIFCSKYLLDHAVLLVGYG----VSEKNEPFWIVKNSWGVEW 292

Query: 318 GEQGYIYLRRGKNTCGVSNFVSTSII 343
           GE GY  + RG  +CG++   ++++I
Sbjct: 293 GENGYFRMYRGDGSCGINTVATSAMI 318


>sp|P25779|CYSP_TRYCR CRUZIPAIN PRECURSOR (MAJOR CYSTEINE PROTEINASE) (CRUZAINE)
          Length = 467

 Score =  356 bits (904), Expect = 4e-98
 Identities = 133/350 (38%), Positives = 184/350 (52%), Gaps = 30/350 (8%)

Query: 3   VILLFVLAVFTVFV----SSRGIPPEEQSQFLEFQDKFNKKY-SHEEYLERFEIFKSNLG 57
           ++L  VL V    V    +S        SQF EF+ K  + Y S  E   R  +F+ NL 
Sbjct: 8   LLLAAVLVVMACLVPAATASLHAEETLTSQFAEFKQKHGRVYESAAEEAFRLSVFRENLF 67

Query: 58  KIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINS 117
                     +      FGV  F+DL+ +EF++ Y +N  A F      A       +  
Sbjct: 68  LARLHAAANPH----ATFGVTPFSDLTREEFRSRY-HNGAAHFAAAQERARVPVKVEVVG 122

Query: 118 IPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHEC 177
            P A DWR RGAVT VK+QGQCGSCW+FS  GNVE Q F++ + L +LSEQ LV CD   
Sbjct: 123 APAAVDWRARGAVTAVKDQGQCGSCWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCDK-- 180

Query: 178 MEYEGEEACDEGCNGGLQPNAYNYIIK--NGGIQTESSYPYTAETG--TQCNFNSANIGA 233
                    D GC+GGL  NA+ +I++  NG + TE SYPY +  G    C  +   +GA
Sbjct: 181 --------TDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGA 232

Query: 234 KISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGY 293
            I+    +P++E  +A ++   GP+A+A DA  W  Y GGV    C    LDHG+L+VGY
Sbjct: 233 TITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVM-TSCVSEQLDHGVLLVGY 291

Query: 294 SAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
           +    +     PYWI+KNSW   WGE+GYI + +G N C V    S++++
Sbjct: 292 NDSAAV-----PYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVV 336


>sp|O10364|CATV_NPVOP VIRAL CATHEPSIN (V-CATH)
          Length = 324

 Score =  351 bits (890), Expect = 2e-96
 Identities = 122/343 (35%), Positives = 181/343 (52%), Gaps = 25/343 (7%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKI 59
           M  I+L +L    V  ++  +  +  + F +F  KFNK YS E E L RF+IF+ NL +I
Sbjct: 1   MNKIMLCLLVCGVVHAATYDL-LKAPNYFEDFLHKFNKNYSSESEKLHRFKIFQHNLEEI 59

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
              N     + +  ++ +NKF+DLS +E  + Y        T +      LD    +  P
Sbjct: 60  INKNQ----NDSTAQYEINKFSDLSKEEAISKYTGLSLPHQTQNFCEVVILDRPP-DRGP 114

Query: 120 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 179
             FDWR    VT VKNQG CG+CW+F+T G++E Q  I  N+L++LSEQ  +DCD     
Sbjct: 115 LEFDWRQFNKVTSVKNQGVCGACWAFATLGSLESQFAIKYNRLINLSEQQFIDCDR---- 170

Query: 180 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKI-SNF 238
                  + GC+GGL   A+   ++ GG+Q ES YPY    G QC  N       + S  
Sbjct: 171 ------VNAGCDGGLLHTAFESAMEMGGVQMESDYPYETANG-QCRINPNRFVVGVRSCR 223

Query: 239 TMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNT 298
             I   E  +   + + GP+ +A DA +   Y  G+    C  + L+H +L+VGY+ +N 
Sbjct: 224 RYIVMFEEKLKDLLRAVGPIPVAIDASDIVNYRRGIMR-QCANHGLNHAVLLVGYAVEN- 281

Query: 299 IFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTS 341
               N+PYWI+KN+WG DWGE GY  +++  N CG+ N + +S
Sbjct: 282 ----NIPYWILKNTWGTDWGEDGYFRVQQNINACGIRNELVSS 320


>sp|P36400|LCPB_LEIME CYSTEINE PROTEINASE B PRECURSOR
          Length = 443

 Score =  348 bits (883), Expect = 1e-95
 Identities = 123/348 (35%), Positives = 184/348 (52%), Gaps = 28/348 (8%)

Query: 4   ILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEEL 62
           ++  VLA       +  +     + F EF+  + + Y    E  +R   F+ NL  + E 
Sbjct: 13  VVCVVLAAACAPARAIHVGTPAAALFEEFKRTYGRAYETLAEEQQRLANFERNLELMREH 72

Query: 63  NLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDE--FINSIPT 120
                +     +FG+ KF DLS  EF   YLN            A +       ++++P 
Sbjct: 73  QARNPH----AQFGITKFFDLSEAEFAARYLNGAAYFAAAKRHAAQHYRKARADLSAVPD 128

Query: 121 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY 180
           A DWR +GAVTPVK+QG CGSCW+FS  GN+EGQ +++ ++LVSLSEQ LV CD      
Sbjct: 129 AVDWREKGAVTPVKDQGACGSCWAFSAVGNIEGQWYLAGHELVSLSEQQLVSCDD----- 183

Query: 181 EGEEACDEGCNGGLQPNAYNYIIK--NGGIQTESSYPYTAETG---TQCNFNSANIGAKI 235
                 ++GC+GGL   A++++++  NG + TE SYPY +  G      N +   +GA+I
Sbjct: 184 -----MNDGCDGGLMLQAFDWLLQNTNGHLHTEDSYPYVSGNGYVPECSNSSELVVGAQI 238

Query: 236 SNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSA 295
               +I  +E  MA ++   GP+AIA DA  +  Y  GV    C    L+HG+L+VGY  
Sbjct: 239 DGHVLIGSSEKAMAAWLAKNGPIAIALDASSFMSYKSGVL-TACIGKQLNHGVLLVGYDM 297

Query: 296 KNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
              +     PYW++KNSWG DWGEQGY+ +  G N C +S +  ++ +
Sbjct: 298 TGEV-----PYWVIKNSWGGDWGEQGYVRVVMGVNACLLSEYPVSAHV 340


>sp|P25775|LCPA_LEIME CYSTEINE PROTEINASE A PRECURSOR
          Length = 354

 Score =  348 bits (883), Expect = 1e-95
 Identities = 143/355 (40%), Positives = 190/355 (53%), Gaps = 36/355 (10%)

Query: 5   LLFVLAVFTVFVSSRGI-------PPEEQ----SQFLEFQDKFNKKYSHE-EYLERFEIF 52
           LLF + V  +FV   G        PP +     + +  F+ +  K +  + E   RF  F
Sbjct: 7   LLFAIVVTILFVVCYGSALIAQTPPPVDNFVASAHYGSFKKRHGKAFGGDAEEGHRFNAF 66

Query: 53  KSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDD 112
           K N+     LN    +   D      KFADL+  EF   YLN             D   D
Sbjct: 67  KQNMQTAYFLNTQNPHAHYDVS---GKFADLTPQEFAKLYLNPDYYARHLKNHKEDVHVD 123

Query: 113 EFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVD 172
           +   S   + DWR +GAVTPVKNQG CGSCW+FS  GN+EGQ   S + LVSLSEQ LV 
Sbjct: 124 DSAPSGVMSVDWRDKGAVTPVKNQGLCGSCWAFSAIGNIEGQWAASGHSLVSLSEQMLVS 183

Query: 173 CDHECMEYEGEEACDEGCNGGLQPNAYNYIIK--NGGIQTESSYPYTAETGTQ--CNFNS 228
           CD            DEGCNGGL   A N+I++  NG + TE+SYPYT+  GT+  C+ + 
Sbjct: 184 CD----------NIDEGCNGGLMDQAMNWIMQSHNGSVFTEASYPYTSGGGTRPPCH-DE 232

Query: 229 ANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGI 288
             +GAKI+ F  +P +E  +A ++   GP+A+A DA  WQ Y GGV    C   SL+HG+
Sbjct: 233 GEVGAKITGFLSLPHDEERIAEWVEKRGPVAVAVDATTWQLYFGGVVS-LCLAWSLNHGV 291

Query: 289 LIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
           LIVG++          PYWIVKNSWG+ WGE+GYI L  G N C + N+  ++ +
Sbjct: 292 LIVGFN-----KNAKPPYWIVKNSWGSSWGEKGYIRLAMGSNQCMLKNYPVSATV 341


>sp|Q05094|CYS2_LEIPI CYSTEINE PROTEINASE 2 PRECURSOR (AMASTIGOTE CYSTEINE PROTEINASE
           A-2)
          Length = 444

 Score =  347 bits (882), Expect = 2e-95
 Identities = 124/349 (35%), Positives = 187/349 (53%), Gaps = 29/349 (8%)

Query: 4   ILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEEL 62
           ++  VLA       +  +     + F EF+  + + Y    E  +R   F+ NL  + E 
Sbjct: 13  VVCVVLAAACAPARAIHVGTPAAALFEEFKRTYGRAYETLAEEQQRLANFERNLELMREH 72

Query: 63  NLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDE--FINSIPT 120
                +     +FG+ KF DLS  EF   YLN            A +       ++++P 
Sbjct: 73  QARNPH----AQFGITKFFDLSEAEFAARYLNGAAYFAAAKRHAAQHYRKARADLSAVPD 128

Query: 121 AFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEY 180
           A DWR +GAVTPVK+QG CGSCW+FS  GN+EGQ +++ ++LVSLSEQ LV CD      
Sbjct: 129 AVDWREKGAVTPVKDQGACGSCWAFSAVGNIEGQWYLAGHELVSLSEQQLVSCDD----- 183

Query: 181 EGEEACDEGCNGGLQPNAYNYIIK--NGGIQTESSYPYTAETG--TQCNFNSAN--IGAK 234
                 ++GC+GGL   A++++++  NG + TE SYPY +  G   +C+ +S    +GA+
Sbjct: 184 -----MNDGCDGGLMLQAFDWLLQNTNGHLHTEDSYPYVSGNGYVPECSNSSEELVVGAQ 238

Query: 235 ISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYS 294
           I    +I  +E  MA ++   GP+AIA DA  +  Y  GV    C    L+HG+L+VGY 
Sbjct: 239 IDGHVLIGSSEKAMAAWLAKNGPIAIALDASSFMSYKSGVL-TACIGKQLNHGVLLVGYD 297

Query: 295 AKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
               +     PYW++KNSWG DWGEQGY+ +  G N C +S +  ++ +
Sbjct: 298 MTGEV-----PYWVIKNSWGGDWGEQGYVRVVMGVNACLLSEYPVSAHV 341


>sp|P35591|CYS1_LEIPI CYSTEINE PROTEINASE 1 PRECURSOR (AMASTIGOTE CYSTEINE PROTEINASE
           A-1)
          Length = 354

 Score =  347 bits (880), Expect = 3e-95
 Identities = 143/355 (40%), Positives = 190/355 (53%), Gaps = 36/355 (10%)

Query: 5   LLFVLAVFTVFVSSRGI-------PPEEQ----SQFLEFQDKFNKKYSHE-EYLERFEIF 52
           LLF + V  +FV   G        PP +     + +  F+ +  K +  + E   RF  F
Sbjct: 7   LLFAIVVTILFVVCYGSALIAQTPPPVDNFVASAHYGSFKKRHGKAFGGDAEEGHRFNAF 66

Query: 53  KSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDD 112
           K N+     LN    +   D      KFADL+  EF   YLN             D   D
Sbjct: 67  KQNMQTAYFLNTQNPHAHYDVS---GKFADLTPQEFAKLYLNPDYYARHLKDHKEDVHVD 123

Query: 113 EFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVD 172
           +   S   + DWR +GAVTPVKNQG CGSCW+FS  GN+EGQ   S + LVSLSEQ LV 
Sbjct: 124 DSAPSGVMSVDWRDKGAVTPVKNQGLCGSCWAFSAIGNIEGQWAASGHSLVSLSEQMLVS 183

Query: 173 CDHECMEYEGEEACDEGCNGGLQPNAYNYIIK--NGGIQTESSYPYTAETGTQ--CNFNS 228
           CD            DEGCNGGL   A N+I++  NG + TE+SYPYT+  GT+  C+ + 
Sbjct: 184 CD----------NIDEGCNGGLMDQAMNWIMQSHNGSVFTEASYPYTSGGGTRPPCH-DE 232

Query: 229 ANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGI 288
             +GAKI+ F  +P +E  +A ++   GP+A+A DA  WQ Y GGV    C   SL+HG+
Sbjct: 233 GEVGAKITGFLSLPHDEERIAEWVEKRGPVAVAVDATTWQLYFGGVVS-LCLAWSLNHGV 291

Query: 289 LIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
           LIVG++          PYWIVKNSWG+ WGE+GYI L  G N C + N+  ++ +
Sbjct: 292 LIVGFN-----KNAKPPYWIVKNSWGSSWGEKGYIRLAMGSNQCMLKNYPVSATV 341


>sp|P05994|PAP4_CARPA PAPAYA PROTEINASE IV PRECURSOR (PPIV) (PAPAYA PEPTIDASE B) (GLYCYL
           ENDOPEPTIDASE)
          Length = 348

 Score =  346 bits (879), Expect = 3e-95
 Identities = 111/321 (34%), Positives = 163/321 (50%), Gaps = 29/321 (9%)

Query: 29  FLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE 87
           F  +  K NK Y + +E L RFEIFK NL  I+E N +   +      G+N+F+DLS+DE
Sbjct: 48  FNSWMLKHNKNYKNVDEKLYRFEIFKDNLKYIDERNKMINGYW----LGLNEFSDLSNDE 103

Query: 88  FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFST 147
           FK  Y+ +    +T+     ++++++ ++ +P + DWR +GAVTPVK+QG C SCW+FST
Sbjct: 104 FKEKYVGSLPEDYTNQPYDEEFVNEDIVD-LPESVDWRAKGAVTPVKHQGYCESCWAFST 162

Query: 148 TGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGG 207
              VEG + I    LV LSEQ LVDCD +            GCN G Q  +  Y+ +N G
Sbjct: 163 VATVEGINKIKTGNLVELSEQELVDCDKQ----------SYGCNRGYQSTSLQYVAQN-G 211

Query: 208 IQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAV-- 265
           I   + YPY A+  T           K +    +  N        ++  P+++  ++   
Sbjct: 212 IHLRAKYPYIAKQQTCRANQVGGPKVKTNGVGRVQSNNEGSLLNAIAHQPVSVVVESAGR 271

Query: 266 EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYL 325
           ++Q Y GG+F+  C    +DH +  VGY            Y ++KNSWG  WGE GYI +
Sbjct: 272 DFQNYKGGIFEGSCG-TKVDHAVTAVGYGKSG-----GKGYILIKNSWGPGWGENGYIRI 325

Query: 326 RRGKNT----CGVSNFVSTSI 342
           RR        CGV       I
Sbjct: 326 RRASGNSPGVCGVYRSSYYPI 346


>sp|P10056|PAP3_CARPA CARICAIN PRECURSOR (PAPAYA PROTEINASE OMEGA) (PAPAYA PROTEINASE
           III) (PPIII) (PAPAYA PEPTIDASE A)
          Length = 348

 Score =  341 bits (865), Expect = 1e-93
 Identities = 114/317 (35%), Positives = 162/317 (50%), Gaps = 26/317 (8%)

Query: 29  FLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE 87
           F  +    NK Y + +E L RFEIFK NL  I+E N    ++      G+N+FADLS+DE
Sbjct: 48  FNSWMLNHNKFYENVDEKLYRFEIFKDNLNYIDETNKKNNSYW----LGLNEFADLSNDE 103

Query: 88  FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFST 147
           F   Y+ +      +     ++++++ +N +P   DWR +GAVTPV++QG CGSCW+FS 
Sbjct: 104 FNEKYVGSLIDATIEQSYDEEFINEDTVN-LPENVDWRKKGAVTPVRHQGSCGSCWAFSA 162

Query: 148 TGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGG 207
              VEG + I   KLV LSEQ LVDC+              GC GG  P A  Y+ KN G
Sbjct: 163 VATVEGINKIRTGKLVELSEQELVDCERR----------SHGCKGGYPPYALEYVAKN-G 211

Query: 208 IQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--V 265
           I   S YPY A+ GT           K S    +  N        ++  P+++  ++   
Sbjct: 212 IHLRSKYPYKAKQGTCRAKQVGGPIVKTSGVGRVQPNNEGNLLNAIAKQPVSVVVESKGR 271

Query: 266 EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYL 325
            +Q Y GG+F+ PC    +DH +  VGY            Y ++KNSWG  WGE+GYI +
Sbjct: 272 PFQLYKGGIFEGPCG-TKVDHAVTAVGYGKSG-----GKGYILIKNSWGTAWGEKGYIRI 325

Query: 326 RRG-KNTCGVSNFVSTS 341
           +R   N+ GV     +S
Sbjct: 326 KRAPGNSPGVCGLYKSS 342


>sp|P14080|PAP2_CARPA CHYMOPAPAIN PRECURSOR (PAPAYA PROTEINASE II) (PPII)
          Length = 352

 Score =  339 bits (860), Expect = 6e-93
 Identities = 119/321 (37%), Positives = 160/321 (49%), Gaps = 29/321 (9%)

Query: 29  FLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE 87
           F  +  K NK Y S +E + RFEIF+ NL  I+E N    ++      G+N FADLS+DE
Sbjct: 48  FDSWMLKHNKIYESIDEKIYRFEIFRDNLMYIDETNKKNNSYW----LGLNGFADLSNDE 103

Query: 88  FKNYYLNNKEAIFTDDLP-VADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFS 146
           FK  Y+      FT       +    + + + P + DWR +GAVTPVKNQG CGSCW+FS
Sbjct: 104 FKKKYVGFVAEDFTGLEHFDNEDFTYKHVTNYPQSIDWRAKGAVTPVKNQGACGSCWAFS 163

Query: 147 TTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNG 206
           T   VEG + I    L+ LSEQ LVDCD              GC GG Q  +  Y+  N 
Sbjct: 164 TIATVEGINKIVTGNLLELSEQELVDCDKH----------SYGCKGGYQTTSLQYVANN- 212

Query: 207 GIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA-- 264
           G+ T   YPY A+       +      KI+ +  +P N        ++  PL++  +A  
Sbjct: 213 GVHTSKVYPYQAKQYKCRATDKPGPKVKITGYKRVPSNCETSFLGALANQPLSVLVEAGG 272

Query: 265 VEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIY 324
             +Q Y  GVFD PC    LDH +  VGY   +        Y I+KNSWG +WGE+GY+ 
Sbjct: 273 KPFQLYKSGVFDGPCG-TKLDHAVTAVGYGTSD-----GKNYIIIKNSWGPNWGEKGYMR 326

Query: 325 LRR----GKNTCGVSNFVSTS 341
           L+R     + TCGV       
Sbjct: 327 LKRQSGNSQGTCGVYKSSYYP 347


>sp|P00784|PAPA_CARPA PAPAIN PRECURSOR (PAPAYA PROTEINASE I) (PPI)
          Length = 345

 Score =  334 bits (848), Expect = 1e-91
 Identities = 107/321 (33%), Positives = 152/321 (47%), Gaps = 32/321 (9%)

Query: 29  FLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE 87
           F  +  K NK Y + +E + RFEIFK NL  I+E N    ++      G+N FAD+S+DE
Sbjct: 48  FESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKKNNSYW----LGLNVFADMSNDE 103

Query: 88  FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFST 147
           FK  Y  +    +T      + + ++   +IP   DWR +GAVTPVKNQG CGSCW+FS 
Sbjct: 104 FKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKGAVTPVKNQGSCGSCWAFSA 163

Query: 148 TGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGG 207
              +EG   I    L   SEQ L+DCD              GCNGG   +A   + +  G
Sbjct: 164 VVTIEGIIKIRTGNLNEYSEQELLDCDRR----------SYGCNGGYPWSALQLVAQ-YG 212

Query: 208 IQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAV-- 265
           I   ++YPY        +       AK      +         Y ++  P+++  +A   
Sbjct: 213 IHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGK 272

Query: 266 EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYL 325
           ++Q Y GG+F  PC  N +DH +  VGY            Y ++KNSWG  WGE GYI +
Sbjct: 273 DFQLYRGGIFVGPCG-NKVDHAVAAVGYG---------PNYILIKNSWGTGWGENGYIRI 322

Query: 326 RRGKNT----CGVSNFVSTSI 342
           +RG       CG+       +
Sbjct: 323 KRGTGNSYGVCGLYTSSFYPV 343


>sp|P22895|P34_SOYBN P34 PROBABLE THIOL PROTEASE PRECURSOR
          Length = 379

 Score =  331 bits (840), Expect = 1e-90
 Identities = 109/334 (32%), Positives = 169/334 (49%), Gaps = 33/334 (9%)

Query: 24  EEQSQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFAD 82
           +  S F  ++ +  + Y +HEE  +R EIFK+N   I ++N          + G+NKFAD
Sbjct: 39  QVSSLFQLWKSEHGRVYHNHEEEAKRLEIFKNNSNYIRDMNA-NRKSPHSHRLGLNKFAD 97

Query: 83  LSSDEFKNYYLNNKEAIFTDDLPVADYLDDE--FINSIPTAFDWRTRGAVTPVKNQGQCG 140
           ++  EF   YL   + +          +  E    +  P ++DWR +G +T VK QG CG
Sbjct: 98  ITPQEFSKKYLQAPKDVSQQIKMANKKMKKEQYSCDHPPASWDWRKKGVITQVKYQGGCG 157

Query: 141 SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYN 200
             W+FS TG +E  H I+   LVSLSEQ LVDC  E           EG   G Q  ++ 
Sbjct: 158 RGWAFSATGAIEAAHAIATGDLVSLSEQELVDCVEE----------SEGSYNGWQYQSFE 207

Query: 201 YIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNF-TMIPKNE------TVMAGYIV 253
           +++++GGI T+  YPY A+ G +C  N       I  + T+I  +E             +
Sbjct: 208 WVLEHGGIATDDDYPYRAKEG-RCKANKIQDKVTIDGYETLIMSDESTESETEQAFLSAI 266

Query: 254 STGPLAIAADAVEWQFYIGGVFDIP--CNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKN 311
              P++++ DA ++  Y GG++D     +P  ++H +L+VGY + + +      YWI KN
Sbjct: 267 LEQPISVSIDAKDFHLYTGGIYDGENCTSPYGINHFVLLVGYGSADGV-----DYWIAKN 321

Query: 312 SWGADWGEQGYIYLRRGKNT----CGVSNFVSTS 341
           SWG DWGE GYI+++R        CG++ F S  
Sbjct: 322 SWGFDWGEDGYIWIQRNTGNLLGVCGMNYFASYP 355


>sp|O17473|CATL_BRUPA CATHEPSIN L-LIKE PRECURSOR
          Length = 395

 Score =  327 bits (829), Expect = 2e-89
 Identities = 99/325 (30%), Positives = 153/325 (46%), Gaps = 23/325 (7%)

Query: 25  EQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLS 84
            ++++ ++     K Y  +E   R  IF+SN    E +N             +N  ADL+
Sbjct: 87  LETEWKDYVTALGKHYDQKENNFRMAIFESNELMTERINKKYEQGLVSYTTALNDLADLT 146

Query: 85  SDEF--KNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSC 142
            +EF  +N      +         +++   +    +P   DWRT+GAVTPV+NQG+CGSC
Sbjct: 147 DEEFMVRNGLRLPNQTDLRGKRQTSEFYRYDKSERLPDQVDWRTKGAVTPVRNQGECGSC 206

Query: 143 WSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYI 202
           ++F+T   +E  H     +L+ LS QN+VDC             + GC+GG  P A+ Y 
Sbjct: 207 YAFATAAALEAYHKQMTGRLLDLSPQNIVDC--------TRNLGNNGCSGGYMPTAFQY- 257

Query: 203 IKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMI-PKNETVMAGYIVSTGPLAIA 261
               GI  ES YPY      +C +  +      + F  I P +E  +   +   GP+ + 
Sbjct: 258 ASRYGIAMESRYPYVGTE-QRCRWQQSIAVVTDNGFNEIQPGDELALKHAVAKRGPVVVG 316

Query: 262 A--DAVEWQFYIGGVF-DIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWG 318
                  ++FY  GV+ +  C     DH +L VGY    +       YWIVKNSWG DWG
Sbjct: 317 ISGSKRSFRFYKDGVYSEGNCG--RPDHAVLAVGYGTHPSY----GDYWIVKNSWGTDWG 370

Query: 319 EQGYIYLRRGK-NTCGVSNFVSTSI 342
           + GY+Y+ R + N C +++  S  I
Sbjct: 371 KDGYVYMARNRGNMCHIASAASFPI 395


>sp|Q10991|CATL_SHEEP CATHEPSIN L
          Length = 217

 Score =  325 bits (824), Expect = 1e-88
 Identities = 104/230 (45%), Positives = 140/230 (60%), Gaps = 17/230 (7%)

Query: 118 IPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHEC 177
           +P + DW  +G VTPVKNQGQCGSCW+FS TG +EGQ F    KLVSLSEQNLVD     
Sbjct: 1   VPKSVDWTKKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGKLVSLSEQNLVD----- 55

Query: 178 MEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISN 237
                    ++GCNGGL  NA+ YI +NGG+ +E SYPY A T T CN+      AK + 
Sbjct: 56  ---SSRPQGNQGCNGGLMDNAFQYIKENGGLDSEESYPYEA-TDTSCNYKPEYSAAKDTG 111

Query: 238 FTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGV-FDIPCNPNSLDHGILIVGYS 294
           F  IP+ E  +   + + GP+++A DA    +QFY  G+ +D  C+   LDHG+L+VGY 
Sbjct: 112 FVDIPQREKALMKAVATVGPISVAIDAGHSSFQFYKSGIYYDPDCSSKDLDHGVLVVGYG 171

Query: 295 AKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG-KNTCGVSNFVSTSII 343
            + T    N  +WIVKNSWG +WG +GY+ + +   N CG++   S   +
Sbjct: 172 FEGT----NNKFWIVKNSWGPEWGNKGYVKMAKDQNNHCGIATAASYPTV 217


>sp|P54639|CYS4_DICDI CYSTEINE PROTEINASE 4 PRECURSOR
          Length = 442

 Score =  323 bits (819), Expect = 4e-88
 Identities = 115/308 (37%), Positives = 166/308 (53%), Gaps = 23/308 (7%)

Query: 1   MKVI-LLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKI 59
           M+V+  L +L V       +    + ++ F  +     + YS EE+  R++IFKSN+  +
Sbjct: 1   MRVLSFLCLLLVSYASAKQQFSELQYRNAFTNWMQAHQRTYSSEEFNARYQIFKSNMDYV 60

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
            + N    +   +T  G+N FAD+++ E++  YL      F     +    +  F    P
Sbjct: 61  HQWN----SKGGETVLGLNVFADITNQEYRTTYLGTP---FDGSALIGTEEEKIFSTPAP 113

Query: 120 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQN---KLVSLSEQNLVDCDHE 176
              DWR +GAVTP+KNQGQCG CWSFSTTG+ EG HFI+      LVSLSEQNL+DC   
Sbjct: 114 -TVDWRAQGAVTPIKNQGQCGGCWSFSTTGSTEGAHFIASGTKKDLVSLSEQNLIDCSK- 171

Query: 177 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKIS 236
                     + GC GGL    + YII N GI TESSYPYTAE G +C F ++NIGA+I 
Sbjct: 172 -------SYGNNGCEGGLMTLGFEYIINNKGIDTESSYPYTAEDGKECKFKTSNIGAQIV 224

Query: 237 NFTMIPKNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVFDIP-CNPNSLDHGILIVGY 293
           ++  +            +  P+++A DA    +Q Y  G++  P C P  LDHG+L+VGY
Sbjct: 225 SYQNVTSGSEASLQSASNNAPVSVAIDASNESFQLYESGIYYEPACTPTQLDHGVLVVGY 284

Query: 294 SAKNTIFR 301
            + ++   
Sbjct: 285 GSGSSSSS 292


 Score = 70.2 bits (169), Expect = 6e-12
 Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 297 NTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTS 341
             +   +  YWIVKNSWG  WG  GYI++ + + N CG++   S  
Sbjct: 392 GAVEASSGNYWIVKNSWGTSWGMDGYIFMSKDRNNNCGIATMASFP 437


>sp|P56203|CATW_MOUSE CATHEPSIN W PRECURSOR (LYMPHOPAIN)
          Length = 371

 Score =  319 bits (810), Expect = 4e-87
 Identities = 108/340 (31%), Positives = 162/340 (46%), Gaps = 32/340 (9%)

Query: 22  PPEEQSQFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKF 80
           P E +  F  FQ +FN+ Y +  EY  R  IF  NL + + L    +      +FG   F
Sbjct: 33  PLELKEVFKLFQIRFNRSYWNPAEYTRRLSIFAHNLAQAQRLQQEDL---GTAEFGETPF 89

Query: 81  ADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRT-RGAVTPVKNQGQC 139
           +DL+ +EF   Y   +    T ++       + +  S+P   DWR  +  ++ VKNQG C
Sbjct: 90  SDLTEEEFGQLYGQERSPERTPNMTK-KVESNTWGESVPRTCDWRKAKNIISSVKNQGSC 148

Query: 140 GSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAY 199
             CW+ +   N++    I   + V +S Q L+DC          E C  GCNGG   +AY
Sbjct: 149 KCCWAMAAADNIQALWRIKHQQFVDVSVQELLDC----------ERCGNGCNGGFVWDAY 198

Query: 200 NYIIKNGGIQTESSYPYTAETGT-QCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPL 258
             ++ N G+ +E  YP+  +    +C        A I +FTM+  NE  +A Y+   GP+
Sbjct: 199 LTVLNNSGLASEKDYPFQGDRKPHRCLAKKYKKVAWIQDFTMLSNNEQAIAHYLAVHGPI 258

Query: 259 AIAADAVEWQFYIGGVFDIP---CNPNSLDHGILIVGYSAKNTIFRKNM----------- 304
            +  +    Q Y  GV       C+P  +DH +L+VG+  K    +              
Sbjct: 259 TVTINMKLLQHYQKGVIKATPSSCDPRQVDHSVLLVGFGKKKEGMQTGTVLSHSRKRRHS 318

Query: 305 -PYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
            PYWI+KNSWGA WGE+GY  L RG NTCGV+ +  T+ +
Sbjct: 319 SPYWILKNSWGAHWGEKGYFRLYRGNNTCGVTKYPFTAQV 358


>sp|P56202|CATW_HUMAN CATHEPSIN W PRECURSOR (LYMPHOPAIN)
          Length = 376

 Score =  318 bits (807), Expect = 9e-87
 Identities = 114/368 (30%), Positives = 177/368 (47%), Gaps = 44/368 (11%)

Query: 6   LFVLAVFTVFVSSRGI---------PPEEQSQFLEFQDKFNKKY-SHEEYLERFEIFKSN 55
           L  L V  +    RG          P E +  F  FQ +FN+ Y S EE+  R +IF  N
Sbjct: 10  LLALLVAGLAQGIRGPLRAQDLGPQPLELKEAFKLFQIQFNRSYLSPEEHAHRLDIFAHN 69

Query: 56  LGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFI 115
           L + + L    +      +FGV  F+DL+ +EF   Y   + A     +   +   +E  
Sbjct: 70  LAQAQRLQEEDL---GTAEFGVTPFSDLTEEEFGQLYGYRRAAGGVPSMG-REIRSEEPE 125

Query: 116 NSIPTAFDWRT-RGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCD 174
            S+P + DWR   GA++P+K+Q  C  CW+ +  GN+E    IS    V +S   L+DC 
Sbjct: 126 ESVPFSCDWRKVAGAISPIKDQKNCNCCWAMAAAGNIETLWRISFWDFVDVSVHELLDCG 185

Query: 175 HECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGT-QCNFNSANIGA 233
                      C +GC+GG   +A+  ++ N G+ +E  YP+  +    +C+       A
Sbjct: 186 R----------CGDGCHGGFVWDAFITVLNNSGLASEKDYPFQGKVRAHRCHPKKYQKVA 235

Query: 234 KISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFD---IPCNPNSLDHGILI 290
            I +F M+  NE  +A Y+ + GP+ +  +    Q Y  GV       C+P  +DH +L+
Sbjct: 236 WIQDFIMLQNNEHRIAQYLATYGPITVTINMKPLQLYRKGVIKATPTTCDPQLVDHSVLL 295

Query: 291 VGYSA--------KNTIFRKN-------MPYWIVKNSWGADWGEQGYIYLRRGKNTCGVS 335
           VG+ +          T+  ++        PYWI+KNSWGA WGE+GY  L RG NTCG++
Sbjct: 296 VGFGSVKSEEGIWAETVSSQSQPQPPHPTPYWILKNSWGAQWGEKGYFRLHRGSNTCGIT 355

Query: 336 NFVSTSII 343
            F  T+ +
Sbjct: 356 KFPLTARV 363


>sp|Q01958|CPP2_ENTHI CYSTEINE PROTEINASE 2 PRECURSOR
          Length = 315

 Score =  318 bits (807), Expect = 9e-87
 Identities = 102/330 (30%), Positives = 160/330 (47%), Gaps = 37/330 (11%)

Query: 21  IPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVN-K 79
           +       F  +  K NK ++  E L R  IF  N   ++  N I        K  V+  
Sbjct: 8   LAIASAIDFNTWASKNNKHFTAIEKLRRRAIFNMNAKFVDSFNKIG-----SFKLSVDGP 62

Query: 80  FADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQC 139
           FA ++++E++    + +    T++     YL+ +     P + DWR  G VTP+++Q QC
Sbjct: 63  FAAMTNEEYRTLLKSKRT---TEENGQVKYLNIQA----PESVDWRKEGKVTPIRDQAQC 115

Query: 140 GSCWSFSTTGNVEGQHFISQN---KLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQP 196
           GSC++F +   +EG+  I +      + LSE+++V C          +  + GCNGGL  
Sbjct: 116 GSCYTFGSLAALEGRLLIEKGGDANTLDLSEEHMVQC--------TRDNGNNGCNGGLGS 167

Query: 197 NAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTG 256
           N Y+YII++ G+  ES YPYT    T C  N  +  AKI+ +T +P+N        +S G
Sbjct: 168 NVYDYIIEH-GVAKESDYPYTGSDST-CKTNVKSF-AKITGYTKVPRNNEAELKAALSQG 224

Query: 257 PLAIAADAVE--WQFYIGGVF-DIPCNPNS--LDHGILIVGYSAKNTIFRKNMPYWIVKN 311
            + ++ DA    +Q Y  G + D  C  N   L+H +  VGY   +         WIV+N
Sbjct: 225 LVDVSIDASSAKFQLYKSGAYTDTKCKNNYFALNHEVCAVGYGVVD-----GKECWIVRN 279

Query: 312 SWGADWGEQGYIYLRRGKNTCGVSNFVSTS 341
           SWG  WG++GYI +    NTCGV+      
Sbjct: 280 SWGTGWGDKGYINMVIEGNTCGVATDPLYP 309


>sp|P36185|ACP2_ENTHI CYSTEINE PROTEINASE ACP2 PRECURSOR
          Length = 310

 Score =  315 bits (799), Expect = 8e-86
 Identities = 102/330 (30%), Positives = 158/330 (46%), Gaps = 32/330 (9%)

Query: 18  SRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGV 77
           + GI       F  +  K NK ++  E L R  IF  N   ++  N I        K  V
Sbjct: 1   AAGIRIASAIDFNTWASKNNKHFTAIEKLRRRAIFNMNAKFVDSFNKIG-----SFKLSV 55

Query: 78  N-KFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQ 136
           +  FA ++++E++    + +    T++     YL+ +     P + DWR  G VTP+++Q
Sbjct: 56  DGPFAAMTNEEYRTLLKSKRT---TEENGQVKYLNIQA----PESVDWRKEGKVTPLRDQ 108

Query: 137 GQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQP 196
            QCGSC++F +   +EG+  I +       + N +D   E M+    +  + GCNGGL  
Sbjct: 109 AQCGSCYTFGSLAALEGRLLIEKG-----GDANTLDLSEEHMQCT-RDNGNNGCNGGLGS 162

Query: 197 NAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTG 256
           N Y+YII++ G+  ES YPYT    T C  N  +   KI+ +T +P+N        +S G
Sbjct: 163 NVYDYIIEH-GVAKESDYPYTGSDST-CKTNVKSFR-KITGYTKVPRNNEAELKAALSQG 219

Query: 257 PLAIAADAVE--WQFYIGGVF-DIPCNPNS--LDHGILIVGYSAKNTIFRKNMPYWIVKN 311
            L ++ D     +Q Y  G + D  C  N   L+H +  VGY   +         WIV+N
Sbjct: 220 LLDVSIDVSSAKFQLYKSGAYTDTKCKNNYFALNHEVCAVGYGVVD-----GKECWIVRN 274

Query: 312 SWGADWGEQGYIYLRRGKNTCGVSNFVSTS 341
           SWG  WG++GYI +    NTCGV+      
Sbjct: 275 SWGTSWGDKGYINMVIEGNTCGVATDPLYP 304


>sp|Q06964|CPP3_ENTHI CYSTEINE PROTEINASE 3 PRECURSOR (CYSTEINE PROTEINASE ACP3)
          Length = 308

 Score =  312 bits (790), Expect = 9e-85
 Identities = 102/322 (31%), Positives = 157/322 (48%), Gaps = 37/322 (11%)

Query: 29  FLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVN-KFADLSSDE 87
           F  +    NK ++  E L R  IF  N   + E N      K   K  V+  FA ++++E
Sbjct: 9   FNTWAANNNKHFTAVEALRRRAIFNMNARFVAEFNK-----KGSFKLSVDGPFAAMTNEE 63

Query: 88  FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFST 147
           ++    + +     ++     YL+ +     P + DWR +G VTP+++Q QCGSC++F +
Sbjct: 64  YRTLLKSKRTV---EENGKVTYLNIQA----PESVDWRAQGKVTPIRDQAQCGSCYTFGS 116

Query: 148 TGNVEGQHFISQN---KLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIK 204
              +EG+  I +      + LSE++LV C          +  + GCNGGL  N Y+YII+
Sbjct: 117 LAALEGRLLIEKGGNANTLDLSEEHLVQC--------TRDNGNNGCNGGLGSNVYDYIIQ 168

Query: 205 NGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA 264
           N G+  ES YPYT    T C  N     AKI+ +  +P+N        +S G + ++ DA
Sbjct: 169 N-GVAKESDYPYTGTDST-CKTN-VKAFAKITGYNKVPRNNEAELKAALSQGLVDVSIDA 225

Query: 265 VE--WQFYIGGVF-DIPCNPN--SLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGE 319
               +Q Y  G + D  C  N  +L+H +  VGY   +         WIV+NSWG  WG+
Sbjct: 226 SSAKFQLYKSGAYSDTKCKNNFFALNHEVCAVGYGVVD-----GKECWIVRNSWGTGWGD 280

Query: 320 QGYIYLRRGKNTCGVSNFVSTS 341
           +GYI +    NTCGV+      
Sbjct: 281 KGYINMVIEGNTCGVATDPLYP 302


>sp|P36184|ACP1_ENTHI CYSTEINE PROTEINASE ACP1 PRECURSOR
          Length = 308

 Score =  309 bits (784), Expect = 5e-84
 Identities = 109/348 (31%), Positives = 156/348 (44%), Gaps = 53/348 (15%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKI 59
           M  ++LFV       V+           F ++    NK +++  EYL RF +F  N   +
Sbjct: 1   MFALILFVSLACANEVA-----------FKQWAATHNKVFANRAEYLYRFAVFLDNKKFV 49

Query: 60  EELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIP 119
           E          A+    +N FAD++ +EF   +L       T ++P         + + P
Sbjct: 50  E----------ANANTELNVFADMTHEEFIQTHLG-----MTYEVPETTSNVKAAVKAAP 94

Query: 120 TAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECME 179
            + DWR+   + P K+QGQCGSCW+F TT  +EG+      KL S SEQ LVDCD     
Sbjct: 95  ESVDWRS--IMNPAKDQGQCGSCWTFCTTAVLEGRVNKDLGKLYSFSEQQLVDCD----- 147

Query: 180 YEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFT 239
                A D GC GG   N+  +I +N G+  ES YPY A  GT          A ++   
Sbjct: 148 -----ASDNGCEGGHPSNSLKFIQENNGLGLESDYPYKAVAGTC---KKVKNVATVTGSR 199

Query: 240 MIP-KNETVMAGYIVSTGPLAIAADAV--EWQFYIGGVF--DIPCNPNSLDHGILIVGYS 294
            +   +ET +   I   GP+A+  DA    +Q Y  G    D  C    ++H +  VGY 
Sbjct: 200 RVTDGSETGLQTIIAENGPVAVGMDASRPSFQLYKKGTIYSDTKCRSRMMNHCVTAVGYG 259

Query: 295 AKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTS 341
                   N  YWI++NSWG  WG+ GY  L R   N CG+    +  
Sbjct: 260 -----SNSNGKYWIIRNSWGTSWGDAGYFLLARDSNNMCGIGRDSNYP 302


>sp|P25326|CATS_BOVIN CATHEPSIN S
          Length = 217

 Score =  307 bits (778), Expect = 2e-83
 Identities = 91/228 (39%), Positives = 129/228 (55%), Gaps = 17/228 (7%)

Query: 118 IPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHEC 177
           +P + DWR +G VT VK QG CGSCW+FS  G +E Q  +   KLVSLS QNLVDC    
Sbjct: 1   LPDSMDWREKGCVTEVKYQGACGSCWAFSAVGALEAQVKLKTGKLVSLSAQNLVDCST-- 58

Query: 178 MEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISN 237
                 +  ++GCNGG    A+ YII N GI +E+SYPY A  G +C ++  N  A  S 
Sbjct: 59  -----AKYGNKGCNGGFMTEAFQYIIDNNGIDSEASYPYKAMDG-KCQYDVKNRAATCSR 112

Query: 238 FTMIP-KNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNPNSLDHGILIVGYS 294
           +  +P  +E  +   + + GP+++  DA    +  Y  GV+  P    +++HG+L+VGY 
Sbjct: 113 YIELPFGSEEALKEAVANKGPVSVGIDASHSSFFLYKTGVYYDPSCTQNVNHGVLVVGYG 172

Query: 295 AKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK-NTCGVSNFVSTS 341
                      YW+VKNSWG  +G+QGYI + R   N CG++N+ S  
Sbjct: 173 N-----LDGKDYWLVKNSWGLHFGDQGYIRMARNSGNHCGIANYPSYP 215


>sp|Q01957|CPP1_ENTHI CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 315

 Score =  301 bits (763), Expect = 1e-81
 Identities = 103/322 (31%), Positives = 155/322 (47%), Gaps = 37/322 (11%)

Query: 29  FLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVN-KFADLSSDE 87
           F  +    NK ++  E L R  IF  N   + E N          K  V+  FA ++++E
Sbjct: 16  FNTWVANNNKHFTAVESLRRRAIFNMNARIVAENNRKE-----TFKLSVDGPFAAMTNEE 70

Query: 88  FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFST 147
           + +     +     ++     YL+ +     P A DWR +G VTP+++QG CGSC++F +
Sbjct: 71  YNSLLKLKRSG---EEKGEVRYLNIQA----PKAVDWRKKGKVTPIRDQGNCGSCYTFGS 123

Query: 148 TGNVEGQHFISQN---KLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIK 204
              +EG+  I +    + + LSE+++V C  E          + GCNGGL  N YNYI++
Sbjct: 124 IAALEGRLLIEKGGDSETLDLSEEHMVQCTRE--------DGNNGCNGGLGSNVYNYIME 175

Query: 205 NGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA 264
           N GI  ES YPYT    T C  +     AKI ++  + +N  V     +S G + ++ DA
Sbjct: 176 N-GIAKESDYPYTGSDST-CRSD-VKAFAKIKSYNRVARNNEVELKAAISQGLVDVSIDA 232

Query: 265 VE--WQFYIGGVF-DIPCNPNS--LDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGE 319
               +Q Y  G + D  C  N   L+H +  VGY   +         WIV+NSWG  WGE
Sbjct: 233 SSVQFQLYKSGAYTDTQCKNNYFALNHEVCAVGYGVVD-----GKECWIVRNSWGTGWGE 287

Query: 320 QGYIYLRRGKNTCGVSNFVSTS 341
           +GYI +    NTCGV+      
Sbjct: 288 KGYINMVIEGNTCGVATDPLYP 309


>sp|P25805|CYSP_PLAFA THROPHOZOITE CYSTEINE PROTEINASE PRECURSOR (TCP)
          Length = 569

 Score =  299 bits (758), Expect = 5e-81
 Identities = 100/363 (27%), Positives = 161/363 (43%), Gaps = 62/363 (17%)

Query: 27  SQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSS 85
           S+F +F  + NK Y + +E + +FEIFK N   I+  N   +N  A  K  VN+F+D S 
Sbjct: 223 SKFFKFMKEHNKVYKNIDEQMRKFEIFKINYISIKNHNK--LNKNAMYKKKVNQFSDYSE 280

Query: 86  DEFKN--------------YYLNNKEAIFTDDLPVADYL------DDEFINSIPTAFDWR 125
           +E K                Y    E    D++ ++++       + +  + +P   D+R
Sbjct: 281 EELKEYFKTLLHVPNHMIEKYSKPFENHLKDNILISEFYTNGKRNEKDIFSKVPEILDYR 340

Query: 126 TRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEA 185
            +G V   K+QG CGSCW+F++ GN+E         ++S SEQ +VDC  +         
Sbjct: 341 EKGIVHEPKDQGLCGSCWAFASVGNIESVFAKKNKNILSFSEQEVVDCSKD--------- 391

Query: 186 CDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNE 245
            + GC+GG    ++ Y+++N  +     Y Y A+    C          +S+   +   E
Sbjct: 392 -NFGCDGGHPFYSFLYVLQN-ELCLGDEYKYKAKDDMFCLNYRCKRKVSLSSIGAV--KE 447

Query: 246 TVMAGYIVSTGPLAIAADA-VEWQFYIGGVFDIPCNPNSLDHGILIVGYS---------- 294
             +   +   GPL++      ++  Y  GV++  C    L+H +L+VGY           
Sbjct: 448 NQLILALNEVGPLSVNVGVNNDFVAYSEGVYNGTC-SEELNHSVLLVGYGQVEKTKLNYN 506

Query: 295 ----AKNTIFRKNMP------YWIVKNSWGADWGEQGYIYLRRGKN----TCGVSNFVST 340
                 NT    N P      YWI+KNSW   WGE G++ L R KN     CG+   V  
Sbjct: 507 NKIQTYNTKENSNQPDDNIIYYWIIKNSWSKKWGENGFMRLSRNKNGDNVFCGIGEEVFY 566

Query: 341 SII 343
            I+
Sbjct: 567 PIL 569


>sp|P20721|CYSL_LYCES LOW-TEMPERATURE-INDUCED CYSTEINE PROTEINASE PRECURSOR
          Length = 346

 Score =  298 bits (756), Expect = 9e-81
 Identities = 88/243 (36%), Positives = 130/243 (53%), Gaps = 21/243 (8%)

Query: 106 VADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSL 165
            +D    +  +S+P + DWR +G +  VK+QG CGSCW+FS    +E  + I    L+SL
Sbjct: 6   KSDRYLPKVGDSLPESIDWREKGVLVGVKDQGSCGSCWAFSAVAAMESINAIVTGNLISL 65

Query: 166 SEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCN 225
           SEQ LVDCD          + +EGC+GGL   A+ ++IKNGGI TE  YPY    G    
Sbjct: 66  SEQELVDCDR---------SYNEGCDGGLMDYAFEFVIKNGGIDTEEDYPYKERNGVCDQ 116

Query: 226 FNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIPCNPNS 283
           +       KI ++  +P N        V+  P++IA +A   ++Q Y  G+F   C   +
Sbjct: 117 YRKNAKVVKIDSYEDVPVNNEKALQKAVAHQPVSIALEAGGRDFQHYKSGIFTGKCG-TA 175

Query: 284 LDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG----KNTCGVSNFVS 339
           +DHG++I GY  +N      M YWIV+NSWGA+  E GY+ ++R        CG++   S
Sbjct: 176 VDHGVVIAGYGTEN-----GMDYWIVRNSWGANCRENGYLRVQRNVSSSSGLCGLAIEPS 230

Query: 340 TSI 342
             +
Sbjct: 231 YPV 233


>sp|P43234|CATO_HUMAN CATHEPSIN O PRECURSOR
          Length = 321

 Score =  296 bits (750), Expect = 5e-80
 Identities = 98/297 (32%), Positives = 151/297 (49%), Gaps = 20/297 (6%)

Query: 50  EIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADY 109
             F+ +L +   LN +  +  +   +G+N+F+ L  +EFK  YL +K + F      A+ 
Sbjct: 42  AAFRESLNRHRYLNSLFPSENSTAFYGINQFSYLFPEEFKAIYLRSKPSKFPR--YSAEV 99

Query: 110 LDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQN 169
                  S+P  FDWR +  VT V+NQ  CG CW+FS  G VE  + I    L  LS Q 
Sbjct: 100 HMSIPNVSLPLRFDWRDKQVVTQVRNQQMCGGCWAFSVVGAVESAYAIKGKPLEDLSVQQ 159

Query: 170 LVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGG-IQTESSYPYTAETGTQCNFNS 228
           ++DC             + GCNGG   NA N++ K    +  +S YP+ A+ G    F+ 
Sbjct: 160 VIDCS----------YNNYGCNGGSTLNALNWLNKMQVKLVKDSEYPFKAQNGLCHYFSG 209

Query: 229 ANIGAKISNF--TMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDH 286
           ++ G  I  +        E  MA  +++ GPL +  DAV WQ Y+GG+    C+    +H
Sbjct: 210 SHSGFSIKGYSAYDFSDQEDEMAKALLTFGPLVVIVDAVSWQDYLGGIIQHHCSSGEANH 269

Query: 287 GILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
            +LI G+         + PYWIV+NSWG+ WG  GY +++ G N CG+++ VS+  +
Sbjct: 270 AVLITGFDKTG-----STPYWIVRNSWGSSWGVDGYAHVKMGSNVCGIADSVSSIFV 321


>sp|P46102|CYSP_PLAVN CYSTEINE PROTEINASE PRECURSOR
          Length = 506

 Score =  291 bits (738), Expect = 1e-78
 Identities = 108/360 (30%), Positives = 167/360 (46%), Gaps = 58/360 (16%)

Query: 27  SQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSS 85
           S+F ++  + NKKY + +E L+RFE FK    K ++ N +   +       VN+++D S 
Sbjct: 160 SKFFKYMKENNKKYENMDEQLQRFENFKIRYMKTQKHNEMVGKNGLTYVQKVNQYSDFSK 219

Query: 86  DEFKNYYLNNKEAIFTDDL----PVADYLDDEFINSI-------PTAFDWRTRGAVTPVK 134
           +EF NY+                P+  +L +  + S+       P + D+R++    P K
Sbjct: 220 EEFDNYFKKLLSVPMDLKSKYIVPLKKHLANTNLISVDNKSKDFPDSRDYRSKFNFLPPK 279

Query: 135 NQGQCGSCWSFSTTGNVEGQHFISQNKL-VSLSEQNLVDCDHECMEYEGEEACDEGCNGG 193
           +QG CGSCW+F+  GN E  +  +++++ +S SEQ +VDC  E          + GC+GG
Sbjct: 280 DQGNCGSCWAFAAIGNFEYLYVHTRHEMPISFSEQQMVDCSTE----------NYGCDGG 329

Query: 194 LQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIV 253
               A+ Y+I N G+     YPY       C     ++  ++     +  NE +M   + 
Sbjct: 330 NPFYAFLYMINN-GVCLGDEYPYKGHEDFFCLNYRCSLLGRVHFIGDVKPNELIM--ALN 386

Query: 254 STGPLAIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFR----------- 301
             GP+ IA  A  ++  Y GGVFD  CNP  L+H +L+VGY                   
Sbjct: 387 YVGPVTIAVGASEDFVLYSGGVFDGECNP-ELNHSVLLVGYGQVKKSLAFEDSHSNVDSN 445

Query: 302 ---------KNMP------YWIVKNSWGADWGEQGYIYLRRGK----NTCGVSNFVSTSI 342
                    K         YWIV+NSWG +WGE GYI ++R K      CGV + V   I
Sbjct: 446 LIKKYKENIKGDDDDDIIYYWIVRNSWGPNWGEGGYIRIKRNKAGDDGFCGVGSDVFFPI 505


>sp|P42666|CYSP_PLAVI CYSTEINE PROTEINASE PRECURSOR
          Length = 583

 Score =  278 bits (704), Expect = 1e-74
 Identities = 100/383 (26%), Positives = 164/383 (42%), Gaps = 68/383 (17%)

Query: 11  VFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSH-EEYLERFEIFKSNLGKIEELNLIAINH 69
           V    +    +  +  S+F  F +K+ + Y    E +E+++ FK N  KI++ N      
Sbjct: 219 VSVAQIEGLFVNLKYASKFFNFMNKYKRSYKDINEQMEKYKNFKMNYLKIKKHNETNQM- 277

Query: 70  KADTKFGVNKFADLSSDEFKNYY---------LNNKEAIFTDDLPVADYLDDEFINS--- 117
               K  VN+F+D S  +F++Y+         L  K  +    +      +    +S   
Sbjct: 278 ---YKMKVNQFSDYSKKDFESYFRKLVPIPDHLKKKYVVPFSSMNNGKGKNVVTSSSGAN 334

Query: 118 ----IPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLV-SLSEQNLVD 172
               +P   D+R +G V   K+QG CGSCW+F++ GNVE  +    NK + +LSEQ +VD
Sbjct: 335 LLADVPEILDYREKGIVHEPKDQGLCGSCWAFASVGNVECMYAKEHNKTILTLSEQEVVD 394

Query: 173 CDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIG 232
           C             + GC+GG    ++ Y I+N GI     Y Y A     C        
Sbjct: 395 CSK----------LNFGCDGGHPFYSFIYAIEN-GICMGDDYKYKAMDNLFCLNYRCKNK 443

Query: 233 AKISNFTMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIV 291
             +S+   + +NE  +   +   GP+++      ++ FY GG+F+  C    L+H +L+V
Sbjct: 444 VTLSSVGGVKENE--LIRALNEVGPVSVNVGVTDDFSFYGGGIFNGTC-TEELNHSVLLV 500

Query: 292 GYS---------------AKNTIFRKN------------MPYWIVKNSWGADWGEQGYIY 324
           GY                  + + +K               YWI+KNSW   WGE G++ 
Sbjct: 501 GYGQVQSSKIFQEKNAYDDASGVTKKGALSYPSKADDGIQYYWIIKNSWSKFWGENGFMR 560

Query: 325 LRRGKN----TCGVSNFVSTSII 343
           + R K      CG+   V   I+
Sbjct: 561 ISRNKEGDNVFCGIGVEVFYPIL 583


>sp|P16311|MMAL_DERFA MAJOR MITE FECAL ALLERGEN DER F 1 PRECURSOR (DER F I)
          Length = 321

 Score =  272 bits (688), Expect = 8e-73
 Identities = 110/350 (31%), Positives = 150/350 (42%), Gaps = 46/350 (13%)

Query: 7   FVLAVFTVFVSSRGIP-PEEQSQFLEFQDKFNKKYSHEEYLE-RFEIFKSNLGKIEELNL 64
           FVLA+ ++ V S     P     F EF+  FNK Y+  E  E   + F  +L  +E    
Sbjct: 3   FVLAIASLLVLSTVYARPASIKTFEEFKKAFNKNYATVEEEEVARKNFLESLKYVEA--- 59

Query: 65  IAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFIN------SI 118
                    K  +N  +DLS DEFKN YL + EA   + L     L+ E         ++
Sbjct: 60  --------NKGAINHLSDLSLDEFKNRYLMSAEAF--EQLKTQFDLNAETSACRINSVNV 109

Query: 119 PTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECM 178
           P+  D R+   VTP++ QG CGSCW+FS     E  +   +N  + LSEQ LVDC     
Sbjct: 110 PSELDLRSLRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNTSLDLSEQELVDC----- 164

Query: 179 EYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNF 238
                 A   GC+G   P    YI +N G+  E SYPY A        NS + G  ISN+
Sbjct: 165 ------ASQHGCHGDTIPRGIEYIQQN-GVVEERSYPYVAREQRCRRPNSQHYG--ISNY 215

Query: 239 TMIPKNETVMAGYIVSTGPLAIAA-----DAVEWQFYIGG-VFDIPCNPNSLDHGILIVG 292
             I   +       ++    AIA      D   +Q Y G  +           H + IVG
Sbjct: 216 CQIYPPDVKQIREALTQTHTAIAVIIGIKDLRAFQHYDGRTIIQHDNGYQPNYHAVNIVG 275

Query: 293 YSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 342
           Y        +   YWIV+NSW   WG+ GY Y + G N   +  +    I
Sbjct: 276 YG-----STQGDDYWIVRNSWDTTWGDSGYGYFQAGNNLMMIEQYPYVVI 320


>sp|P80884|ANAN_ANACO ANANAIN
          Length = 216

 Score =  271 bits (687), Expect = 1e-72
 Identities = 93/229 (40%), Positives = 122/229 (52%), Gaps = 22/229 (9%)

Query: 118 IPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHEC 177
           +P + DWR  GAVT VKNQG+CGSCW+F++   VE  + I +  LVSLSEQ ++DC    
Sbjct: 1   VPQSIDWRDSGAVTSVKNQGRCGSCWAFASIATVESIYKIKRGNLVSLSEQQVLDC---- 56

Query: 178 MEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISN 237
                  A   GC GG    AY++II N G+ + + YPY A  GT C  N     A I+ 
Sbjct: 57  -------AVSYGCKGGWINKAYSFIISNKGVASAAIYPYKAAKGT-CKTNGVPNSAYITR 108

Query: 238 FTMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAK 296
           +T + +N      Y VS  P+A A DA   +Q Y  GVF  PC    L+H I+I+GY   
Sbjct: 109 YTYVQRNNERNMMYAVSNQPIAAALDASGNFQHYKRGVFTGPCG-TRLNHAIVIIGYGQD 167

Query: 297 NTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK----NTCGVSNFVSTS 341
           +        +WIV+NSWGA WGE GYI L R        CG++      
Sbjct: 168 SA----GKKFWIVRNSWGAGWGEGGYIRLARDVSSSFGICGIAMDPLYP 212


>sp||CATL_CHICK_1 [Segment 1 of 2] CATHEPSIN L
          Length = 176

 Score =  264 bits (669), Expect = 1e-70
 Identities = 86/183 (46%), Positives = 115/183 (61%), Gaps = 12/183 (6%)

Query: 119 PTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECM 178
           P + DWR +G VTPVK+QGQCGSCW+FSTTG +EGQHF ++ KLVSLSEQNLVDC     
Sbjct: 2   PRSVDWREKGYVTPVKDQGQCGSCWAFSTTGALEGQHFRTKGKLVSLSEQNLVDCS---- 57

Query: 179 EYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNF 238
                   ++GCNGGL   A+ Y+  NGGI +E SYPYTA+    C + +    A  + F
Sbjct: 58  ----RPEGNQGCNGGLMDQAFQYVQDNGGIDSEESYPYTAKDDEDCRYKAEYNAANDTGF 113

Query: 239 TMIPKN-ETVMAGYIVSTGPLAIAADA--VEWQFYIGGVFDIP-CNPNSLDHGILIVGYS 294
             IP+  E  +   + S GP+++A DA    +QFY  G++  P C+   LDHG+L+VGY 
Sbjct: 114 VDIPQGHERALMKAVASVGPVSVAIDAGHSSFQFYQSGIYYEPDCSSEDLDHGVLVVGYG 173

Query: 295 AKN 297
            + 
Sbjct: 174 FEG 176


>sp|P97821|CATC_MOUSE DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (DPPI) (CATHEPSIN C)
           (CATHEPSIN J) (DIPEPTIDYL TRANSFERASE)
          Length = 462

 Score =  262 bits (662), Expect = 9e-70
 Identities = 86/317 (27%), Positives = 148/317 (46%), Gaps = 37/317 (11%)

Query: 43  EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTD 102
           E Y ER   +  N   ++ +N +    K+ T     ++  +S  +      +++      
Sbjct: 161 ERYSERL--YTHNHNFVKAINTVQ---KSWTATAYKEYEKMSLRDLIRRSGHSQRIPRPK 215

Query: 103 DLPVADYLDDEFINSIPTAFDWRTR---GAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQ 159
             P+ D +  + +N +P ++DWR       V+PV+NQ  CGSC+SF++ G +E +  I  
Sbjct: 216 PAPMTDEIQQQILN-LPESWDWRNVQGVNYVSPVRNQESCGSCYSFASMGMLEARIRILT 274

Query: 160 NKLVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYT 217
           N   +  LS Q +V C              +GC+GG          ++ G+  ES +PYT
Sbjct: 275 NNSQTPILSPQEVVSCSPYA----------QGCDGGFPYLIAGKYAQDFGVVEESCFPYT 324

Query: 218 AETGTQCNFNSANIGAKISNFTMIPK-----NETVMAGYIVSTGPLAIAADAVE-WQFYI 271
           A+  + C      +    S++  +       NE +M   +V  GP+A+A +  + +  Y 
Sbjct: 325 AKD-SPCKPRENCLRYYSSDYYYVGGFYGGCNEALMKLELVKHGPMAVAFEVHDDFLHYH 383

Query: 272 GGVFDI-----PCNPNSL-DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYL 325
            G++       P NP  L +H +L+VGY          + YWI+KNSWG++WGE GY  +
Sbjct: 384 SGIYHHTGLSDPFNPFELTNHAVLLVGYGRDPVT---GIEYWIIKNSWGSNWGESGYFRI 440

Query: 326 RRGKNTCGVSNFVSTSI 342
           RRG + C + +    +I
Sbjct: 441 RRGTDECAIESIAVAAI 457


>sp|P25781|CYSP_THEAN CYSTEINE PROTEINASE PRECURSOR
          Length = 441

 Score =  259 bits (655), Expect = 6e-69
 Identities = 105/343 (30%), Positives = 162/343 (46%), Gaps = 50/343 (14%)

Query: 28  QFLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSD 86
           +F  F +K+ K + S ++ ++RF  F+ N   ++                +NKF+DLS +
Sbjct: 119 EFDAFVEKYKKVHRSFDQRVQRFLTFRKNYHIVKTHKPTEP-----YSLDLNKFSDLSDE 173

Query: 87  EFKNYY--------------------LNNKEAIFTDDLPVADYLDDEFINSIP--TAFDW 124
           EFK  Y                    +++K  I+   L  A  +++    S+      +W
Sbjct: 174 EFKALYPVITPPKTYTSLSKHLEFKKMSHKNPIYISKLKKAKGIEEIKDLSLITGENLNW 233

Query: 125 RTRGAVTPVKNQG-QCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE 183
               AV+P K+QG  CGSCW+FS+  +VE  + + +NK   LSEQ LV+CD   M     
Sbjct: 234 ARTDAVSPTKDQGDHCGSCWAFSSIASVESLYRLYKNKSYFLSEQELVNCDKSSM----- 288

Query: 184 EACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPK 243
                GC GGL   A  YI  + G+  ES  PYT    + C  +  N    I + +++  
Sbjct: 289 -----GCAGGLPITALEYI-HSKGVSFESEVPYTGIV-SPCKPSIKN-KVFIDSISILKG 340

Query: 244 NETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKN 303
           N+ V    ++S   + IA    E + Y GG+F   C    L+H +L+VG    +      
Sbjct: 341 NDVVNKSLVISPTVVGIAVT-KELKLYSGGIFTGKCG-GELNHAVLLVGEGVDH---ETG 395

Query: 304 MPYWIVKNSWGADWGEQGYIYLRR---GKNTCGVSNFVSTSII 343
           M YWI+KNSWG DWGE G++ L+R   G + CG+  F    I+
Sbjct: 396 MRYWIIKNSWGEDWGENGFLRLQRTKKGLDKCGILTFGLNPIL 438


>sp|P08176|MMAL_DERPT MAJOR MITE FECAL ALLERGEN DER P 1 PRECURSOR (DER P I)
          Length = 320

 Score =  255 bits (644), Expect = 1e-67
 Identities = 105/356 (29%), Positives = 153/356 (42%), Gaps = 49/356 (13%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60
           MK++L     +    V +R   P     F E++  FNK Y+  E     E  + N   +E
Sbjct: 1   MKIVLAIASLLALSAVYAR---PSSIKTFEEYKKAFNKSYATFEDE---EAARKN--FLE 52

Query: 61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFI----- 115
            +  +  N        +N  +DLS DEFKN +L + EA   + L     L+ E       
Sbjct: 53  SVKYVQSNGG-----AINHLSDLSLDEFKNRFLMSAEAF--EHLKTQFDLNAETNACSIN 105

Query: 116 NSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDH 175
            + P   D R    VTP++ QG CGSCW+FS     E  +   +N+ + L+EQ LVDC  
Sbjct: 106 GNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLAEQELVDC-- 163

Query: 176 ECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKI 235
                    A   GC+G   P    YI  NG +Q ES Y Y A   +    N+   G  I
Sbjct: 164 ---------ASQHGCHGDTIPRGIEYIQHNGVVQ-ESYYRYVAREQSCRRPNAQRFG--I 211

Query: 236 SNFTMI-PKNETVMAGYIV-STGPLAIAA---DAVEWQFYIGGVF---DIPCNPNSLDHG 287
           SN+  I P N   +   +  +   +A+     D   ++ Y G      D    PN   H 
Sbjct: 212 SNYCQIYPPNVNKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNY--HA 269

Query: 288 ILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
           + IVGYS       + + YWIV+NSW  +WG+ GY Y     +   +  +    I+
Sbjct: 270 VNIVGYSN-----AQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVVIL 320


>sp|P14518|BROM_ANACO BROMELAIN, STEM
          Length = 212

 Score =  253 bits (640), Expect = 4e-67
 Identities = 80/230 (34%), Positives = 114/230 (48%), Gaps = 27/230 (11%)

Query: 117 SIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 176
           ++P + DWR  GAVT VKNQ  CG+CW+F+    VE  + I +  L  LSEQ ++DC   
Sbjct: 1   AVPQSIDWRDYGAVTSVKNQNPCGACWAFAAIATVESIYKIKKGILEPLSEQQVLDCAK- 59

Query: 177 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKIS 236
                       GC GG +  A+ +II N G+ + + YPY A  GT C  +     A I+
Sbjct: 60  ----------GYGCKGGWEFRAFEFIISNKGVASGAIYPYKAAKGT-CKTDGVPNSAYIT 108

Query: 237 NFTMIPKNETVMAGYIVSTGPLAIAADA-VEWQFYIGGVFDIPCNPNSLDHGILIVGYSA 295
            +  +P+N      Y VS  P+ +A DA   +Q+Y  GVF+ PC   SL+H +  +GY  
Sbjct: 109 GYARVPRNNESSMMYAVSKQPITVAVDANANFQYYKSGVFNGPCG-TSLNHAVTAIGYGQ 167

Query: 296 KNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG----KNTCGVSNFVSTS 341
            + I+ K          WGA WGE GYI + R        CG++      
Sbjct: 168 DSIIYPK---------KWGAKWGEAGYIRMARDVSSSSGICGIAIDPLYP 208


>sp|P53634|CATC_HUMAN DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (DPPI) (CATHEPSIN C)
           (CATHEPSIN J) (DIPEPTIDYL TRANSFERASE)
          Length = 463

 Score =  251 bits (634), Expect = 2e-66
 Identities = 86/318 (27%), Positives = 137/318 (43%), Gaps = 36/318 (11%)

Query: 41  SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIF 100
           S E+Y  R   +K +   ++ +N I  +  A T      +  L+  +       +   I 
Sbjct: 159 SQEKYSNRL--YKYDHNFVKAINAIQKSWTATTYME---YETLTLGDMIRRSGGHSRKIP 213

Query: 101 TDDLPVADYLDDEFINSIPTAFDWRTRGA---VTPVKNQGQCGSCWSFSTTGNVEGQHFI 157
                       + I  +PT++DWR       V+PV+NQ  CGSC+SF++ G +E +  I
Sbjct: 214 RPKPAPLTAEIQQKILHLPTSWDWRNVHGINFVSPVRNQASCGSCYSFASMGMLEARIRI 273

Query: 158 SQNKLVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYP 215
             N   +  LS Q +V C              +GC GG          ++ G+  E+ +P
Sbjct: 274 LTNNSQTPILSPQEVVSCSQYA----------QGCEGGFPYLIAGKYAQDFGLVEEACFP 323

Query: 216 YTAETGTQCNFNSANIGAKISNFTMIPK-----NETVMAGYIVSTGPLAIAADAVE-WQF 269
           YT    + C           S +  +       NE +M   +V  GP+A+A +  + +  
Sbjct: 324 YTGTD-SPCKMKEDCFRYYSSEYHYVGGFYGGCNEALMKLELVHHGPMAVAFEVYDDFLH 382

Query: 270 YIGGVFDI-----PCNPNSL-DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYI 323
           Y  G++       P NP  L +H +L+VGY   +      M YWIVKNSWG  WGE GY 
Sbjct: 383 YKKGIYHHTGLRDPFNPFELTNHAVLLVGYGTDSAS---GMDYWIVKNSWGTGWGENGYF 439

Query: 324 YLRRGKNTCGVSNFVSTS 341
            +RRG + C + +    +
Sbjct: 440 RIRRGTDECAIESIAVAA 457


>sp|P80067|CATC_RAT DIPEPTIDYL-PEPTIDASE I PRECURSOR (DPP-I) (DPPI) (CATHEPSIN C)
           (CATHEPSIN J) (DIPEPTIDYL TRANSFERASE)
          Length = 462

 Score =  250 bits (631), Expect = 4e-66
 Identities = 86/317 (27%), Positives = 145/317 (45%), Gaps = 37/317 (11%)

Query: 43  EEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTD 102
           E+Y ER   +  +   ++ +N +  +  A T     ++  LS  +      ++   +   
Sbjct: 161 EKYSERL--YSHHHNFVKAINSVQKSWTATT---YRRYEKLSIRDLIRRSGHSGRILRPK 215

Query: 103 DLPVADYLDDEFINSIPTAFDWRTRGA---VTPVKNQGQCGSCWSFSTTGNVEGQHFISQ 159
             P+ D +  + + S+P ++DWR       V+PV+NQ  CGSC+SF++ G +E +  I  
Sbjct: 216 PAPITDEIQQQIL-SLPESWDWRNVRGINFVSPVRNQESCGSCYSFASIGMLEARIRILT 274

Query: 160 NKLVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYT 217
           N   +  LS Q +V C              +GC+GG          ++ G+  E+ +PYT
Sbjct: 275 NNSQTPILSPQEVVSCSPYA----------QGCDGGFPYLIAGKYAQDFGVVEENCFPYT 324

Query: 218 AETGTQCNFNSANIGAKISNFTMIPK-----NETVMAGYIVSTGPLAIAADAVE-WQFYI 271
           A     C      +    S +  +       NE +M   +V  GP+A+A +  + +  Y 
Sbjct: 325 ATDAP-CKPKENCLRYYSSEYYYVGGFYGGCNEALMKLELVKHGPMAVAFEVHDDFLHYH 383

Query: 272 GGVFDI-----PCNPNSL-DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYL 325
            G++       P NP  L +H +L+VGY          + YWIVKNSWG+ WGE GY  +
Sbjct: 384 SGIYHHTGLSDPFNPFELTNHAVLLVGYGKDPVT---GLDYWIVKNSWGSQWGESGYFRI 440

Query: 326 RRGKNTCGVSNFVSTSI 342
           RRG + C + +    +I
Sbjct: 441 RRGTDECAIESIAMAAI 457


>sp|P22497|CYSP_THEPA CYSTEINE PROTEINASE PRECURSOR
          Length = 439

 Score =  243 bits (613), Expect = 5e-64
 Identities = 98/342 (28%), Positives = 155/342 (44%), Gaps = 48/342 (14%)

Query: 24  EEQSQFLEFQDKFNKKYSHE-EYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFAD 82
           E   +F EF  K+N++++ + E L R   F+SN  +++E              G+N+F+D
Sbjct: 119 EVYREFEEFNSKYNRRHATQQERLNRLVTFRSNYLEVKE-----QKGDEPYVKGINRFSD 173

Query: 83  LSSDEFKN---------------YYLNNKEAIFTDDLPVADYLDDEFINSIP----TAFD 123
           L+  EF                 YYL +  A  T    +   L+ +    +        D
Sbjct: 174 LTEREFYKLFPVMKPPKATYSNGYYLLSHMANKTYLKNLKKALNTDEDVDLAKLTGENLD 233

Query: 124 WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE 183
           WR   +VT VK+Q  CG CW+FST G+VEG +    +K   LS Q L+DCD         
Sbjct: 234 WRRSSSVTSVKDQSNCGGCWAFSTVGSVEGYYMSHFDKSYELSVQELLDCD--------- 284

Query: 184 EACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPK 243
            +   GC GGL  +AY Y+ K  G+ +    P+  +   +C+   A     + ++ +   
Sbjct: 285 -SFSNGCQGGLLESAYEYVRK-YGLVSAKDLPFV-DKARRCSVPKAK-KVSVPSYHVFKG 340

Query: 244 NETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRK 302
            E  +    +++ P ++      E   Y  GVF   C   SL+H +++VG          
Sbjct: 341 KE--VMTRSLTSSPCSVYLSVSPELAKYKSGVFTGECG-KSLNHAVVLVGEGYDEV---T 394

Query: 303 NMPYWIVKNSWGADWGEQGYIYLRR---GKNTCGVSNFVSTS 341
              YW+V+NSWG DWGE GY+ L R   G + CGV +   ++
Sbjct: 395 KKRYWVVQNSWGTDWGENGYMRLERTNMGTDKCGVLDTSMSA 436


>sp|P07858|CATB_HUMAN CATHEPSIN B PRECURSOR (CATHEPSIN B1) (APP SECRETASE)
          Length = 339

 Score =  238 bits (602), Expect = 1e-62
 Identities = 71/299 (23%), Positives = 114/299 (37%), Gaps = 58/299 (19%)

Query: 82  DLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFD----WRTRGAVTPVKNQG 137
           D+S       YL      F         +       +P +FD    W     +  +++QG
Sbjct: 51  DMS-------YLKRLCGTFLGGPKPPQRVMFTEDLKLPASFDAREQWPQCPTIKEIRDQG 103

Query: 138 QCGSCWSFSTTGNVEGQHFISQNKLVSL--SEQNLVDCDHECMEYEGEEACDEGCNGGLQ 195
            CGSCW+F     +  +  I  N  VS+  S ++L+ C   C        C +GCNGG  
Sbjct: 104 SCGSCWAFGAVEAISDRICIHTNAHVSVEVSAEDLLTC---C-----GSMCGDGCNGGYP 155

Query: 196 PNAYNYIIKNGGIQ----------------------TESSYPYTAETGT-QCN------F 226
             A+N+  + G +                         S  P T E  T +C+      +
Sbjct: 156 AEAWNFWTRKGLVSGGLYESHVGCRPYSIPPCEHHVNGSRPPCTGEGDTPKCSKICEPGY 215

Query: 227 NSANIGAKISNF--TMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNS 283
           +      K   +    +  +E  +   I   GP+  A     ++  Y  GV+        
Sbjct: 216 SPTYKQDKHYGYNSYSVSNSEKDIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVTGEMM 275

Query: 284 LDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 342
             H I I+G+  +N       PYW+V NSW  DWG+ G+  + RG++ CG+ + V   I
Sbjct: 276 GGHAIRILGWGVEN-----GTPYWLVANSWNTDWGDNGFFKILRGQDHCGIESEVVAGI 329


>sp|P00787|CATB_RAT CATHEPSIN B PRECURSOR (CATHEPSIN B1) (RSG-2)
          Length = 339

 Score =  236 bits (597), Expect = 4e-62
 Identities = 69/289 (23%), Positives = 117/289 (39%), Gaps = 51/289 (17%)

Query: 92  YLNNKEAIFTDDLPVADYLDDEFINSIPTAFD----WRTRGAVTPVKNQGQCGSCWSFST 147
           YL            + + +      ++P +FD    W     +  +++QG CGSCW+F  
Sbjct: 54  YLKKLCGTVLGGPNLPERVGFSEDINLPESFDAREQWSNCPTIAQIRDQGSCGSCWAFGA 113

Query: 148 TGNVEGQHFISQNKLVSL--SEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKN 205
              +  +  I  N  V++  S ++L+ C   C        C +GCNGG    A+N+  + 
Sbjct: 114 VEAMSDRICIHTNGRVNVEVSAEDLLTC---C-----GIQCGDGCNGGYPSGAWNFWTRK 165

Query: 206 GGIQ----------------------TESSYPYTAETGT-QCN------FNSANIGAKIS 236
           G +                         S  P T E  T +CN      ++++    K  
Sbjct: 166 GLVSGGVYNSHIGCLPYTIPPCEHHVNGSRPPCTGEGDTPKCNKMCEAGYSTSYKEDKHY 225

Query: 237 NFTM--IPKNETVMAGYIVSTGPLAIAADA-VEWQFYIGGVFDIPCNPNSLDHGILIVGY 293
            +T   +  +E  +   I   GP+  A     ++  Y  GV+          H I I+G+
Sbjct: 226 GYTSYSVSDSEKEIMAEIYKNGPVEGAFTVFSDFLTYKSGVYKHEAGDVMGGHAIRILGW 285

Query: 294 SAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 342
             +N +     PYW+V NSW  DWG+ G+  + RG+N CG+ + +   I
Sbjct: 286 GIENGV-----PYWLVANSWNVDWGDNGFFKILRGENHCGIESEIVAGI 329


>sp|P10605|CATB_MOUSE CATHEPSIN B PRECURSOR (CATHEPSIN B1)
          Length = 339

 Score =  233 bits (588), Expect = 4e-61
 Identities = 67/289 (23%), Positives = 111/289 (38%), Gaps = 51/289 (17%)

Query: 92  YLNNKEAIFTDDLPVADYLDDEFINSIPTAFD----WRTRGAVTPVKNQGQCGSCWSFST 147
           YL            +   +       +P  FD    W     +  +++QG CGSCW+F  
Sbjct: 54  YLKKLCGTVLGGPKLPGRVAFGEDIDLPETFDAREQWSNCPTIGQIRDQGSCGSCWAFGA 113

Query: 148 TGNVEGQHFISQNKLVSL--SEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKN 205
              +  +  I  N  V++  S ++L+ C   C        C +GCNGG    A+++  K 
Sbjct: 114 VEAISDRTCIHTNGRVNVEVSAEDLLTC---C-----GIQCGDGCNGGYPSGAWSFWTKK 165

Query: 206 GGIQ----------------------TESSYPYTAETGT-QCN------FNSANIGAKIS 236
           G +                         S  P T E  T +CN      ++ +    K  
Sbjct: 166 GLVSGGVYNSHVGCLPYTIPPCEHHVNGSRPPCTGEGDTPRCNKSCEAGYSPSYKEDKHF 225

Query: 237 NFTM--IPKNETVMAGYIVSTGPLAIAADA-VEWQFYIGGVFDIPCNPNSLDHGILIVGY 293
            +T   +  +   +   I   GP+  A     ++  Y  GV+          H I I+G+
Sbjct: 226 GYTSYSVSNSVKEIMAEIYKNGPVEGAFTVFSDFLTYKSGVYKHEAGDMMGGHAIRILGW 285

Query: 294 SAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 342
             +N +     PYW+  NSW  DWG+ G+  + RG+N CG+ + +   I
Sbjct: 286 GVENGV-----PYWLAANSWNLDWGDNGFFKILRGENHCGIESEIVAGI 329


>sp|P43509|CPR5_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 5 PRECURSOR
          Length = 344

 Score =  232 bits (586), Expect = 8e-61
 Identities = 68/280 (24%), Positives = 114/280 (40%), Gaps = 53/280 (18%)

Query: 105 PVADYLDDEFINSIPTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQN 160
              D +  E  ++IP  FD    W    ++  +++Q  CGSCW+F+    +  +  I+ N
Sbjct: 69  KDEDIVATEVSDAIPDHFDARDQWPNCMSINNIRDQSDCGSCWAFAAAEAISDRTCIASN 128

Query: 161 KLVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTES------ 212
             V+  LS ++L+ C        G  +C  GC GG    A+ + +K+G +   S      
Sbjct: 129 GAVNTLLSSEDLLSC------CTGMFSCGNGCEGGYPIQAWKWWVKHGLVTGGSYETQFG 182

Query: 213 SYPYTA-------------------ETGTQC--------NFNSANIGAKISNFTM--IPK 243
             PY+                    E   +C        N+ +  +  K    T   + K
Sbjct: 183 CKPYSIAPCGETVNGVKWPACPEDTEPTPKCVDSCTSKNNYATPYLQDKHFGSTAYAVGK 242

Query: 244 NETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRK 302
               +   I++ GP+ +A     ++  Y  GV+      +   H + I+G+   N     
Sbjct: 243 KVEQIQTEILTNGPIEVAFTVYEDFYQYTTGVYVHTAGASLGGHAVKILGWGVDN----- 297

Query: 303 NMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSI 342
             PYW+V NSW   WGE+GY  + RG N CG+ +     I
Sbjct: 298 GTPYWLVANSWNVAWGEKGYFRIIRGLNECGIEHSAVAGI 337


>sp|P07688|CATB_BOVIN CATHEPSIN B PRECURSOR
          Length = 335

 Score =  232 bits (586), Expect = 8e-61
 Identities = 66/263 (25%), Positives = 108/263 (40%), Gaps = 51/263 (19%)

Query: 118 IPTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSL--SEQNLV 171
           +P +FD    W     +  +++QG CGSCW+F     +  +  I  N  V++  S ++++
Sbjct: 80  LPESFDAREQWPNCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHSNGRVNVEVSAEDML 139

Query: 172 DCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQ---------------------- 209
            C        GE  C +GCNGG    A+N+  K G +                       
Sbjct: 140 TC------CGGE--CGDGCNGGFPSGAWNFWTKKGLVSGGLYNSHVGCRPYSIPPCEHHV 191

Query: 210 TESSYPYTAETGT-QCN------FNSANIGAKISN--FTMIPKNETVMAGYIVSTGPLAI 260
             S  P T E  T +CN      ++ +    K        +  NE  +   I   GP+  
Sbjct: 192 NGSRPPCTGEGDTPKCNKTCEPGYSPSYKEDKHFGCSSYSVANNEKEIMAEIYKNGPVEG 251

Query: 261 AADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGE 319
           A     ++  Y  GV+          H I I+G+  +N       PYW+V NSW  DWG+
Sbjct: 252 AFSVYSDFLLYKSGVYQHVSGEIMGGHAIRILGWGVEN-----GTPYWLVGNSWNTDWGD 306

Query: 320 QGYIYLRRGKNTCGVSNFVSTSI 342
            G+  + RG++ CG+ + +   +
Sbjct: 307 NGFFKILRGQDHCGIESEIVAGM 329


>sp|P43233|CATB_CHICK CATHEPSIN B PRECURSOR (CATHEPSIN B1)
          Length = 340

 Score =  232 bits (585), Expect = 1e-60
 Identities = 72/323 (22%), Positives = 122/323 (37%), Gaps = 62/323 (19%)

Query: 59  IEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSI 118
           +  +N +    +A   F      D+S       Y+      F       + +D      +
Sbjct: 31  VNHINKLNTTGRAGHNF---HNTDMS-------YVKKLCGTFLGGPKAPERVDFAEDMDL 80

Query: 119 PTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVS--LSEQNLVD 172
           P  FD    W     ++ +++QG CGSCW+F     +  +  +  N  VS  +S ++L+ 
Sbjct: 81  PDTFDTRKQWPNCPTISEIRDQGSCGSCWAFGAVEAISDRICVHTNAKVSVEVSAEDLLS 140

Query: 173 CDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGI----------------------QT 210
           C   C        C  GCNGG    A+ Y  + G +                        
Sbjct: 141 C---C-----GFECGMGCNGGYPSGAWRYWTERGLVSGGLYDSHVGCRAYTIPPCEHHVN 192

Query: 211 ESSYPYTAETGT--QCN------FNSANIGAKISNFTM--IPKNETVMAGYIVSTGPLAI 260
            S  P T E G   +C+      ++ +    K    T   +P++E  +   I   GP+  
Sbjct: 193 GSRPPCTGEGGETPRCSRHCEPGYSPSYKEDKHYGITSYGVPRSEKEIMAEIYKNGPVEG 252

Query: 261 AADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGE 319
           A     ++  Y  GV+          H I I+G+  +N       PYW+  NSW  DWG 
Sbjct: 253 AFIVYEDFLMYKSGVYQHVSGEQVGGHAIRILGWGVEN-----GTPYWLAANSWNTDWGI 307

Query: 320 QGYIYLRRGKNTCGVSNFVSTSI 342
            G+  + RG++ CG+ + +   +
Sbjct: 308 TGFFKILRGEDHCGIESEIVAGV 330


>sp|Q26563|CATC_SCHMA CATHEPSIN C PRECURSOR
          Length = 454

 Score =  231 bits (584), Expect = 1e-60
 Identities = 80/281 (28%), Positives = 124/281 (43%), Gaps = 38/281 (13%)

Query: 81  ADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFI---NSIPTAFDWRT-----RGAVTP 132
           +  + DE +N     K  +    +        E I    ++P  FDW +     R  VTP
Sbjct: 178 SKYTIDELRNRAGGVKSMVTRPSVLNRKTPSKELISLTGNLPLEFDWTSPPDGSRSPVTP 237

Query: 133 VKNQGQCGSCWSFSTTGNVEGQHFISQN--KLVSLSEQNLVDCDHECMEYEGEEACDEGC 190
           ++NQG CGSC++  +   +E +  +  N  +   LS Q +VDC              EGC
Sbjct: 238 IRNQGICGSCYASPSAAALEARIRLVSNFSEQPILSPQTVVDCSPY----------SEGC 287

Query: 191 NGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPK-----NE 245
           NGG          ++ G+  +   PYT E   +C  +        ++++ I       NE
Sbjct: 288 NGGFPFLIAGKYGEDFGLPQKIVIPYTGEDTGKCTVSKNCTRYYTTDYSYIGGYYGATNE 347

Query: 246 TVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPC--------NPNSL-DHGILIVGYSA 295
            +M   ++S GP  +  +   ++QFY  G++            NP  L +H +L+VGY  
Sbjct: 348 KLMQLELISNGPFPVGFEVYEDFQFYKEGIYHHTTVQTDHYNFNPFELTNHAVLLVGYGV 407

Query: 296 KNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSN 336
                    PYW VKNSWG +WGEQGY  + RG + CGV +
Sbjct: 408 DKLS---GEPYWKVKNSWGVEWGEQGYFRILRGTDECGVES 445


>sp|P25807|CYS1_CAEEL GUT-SPECIFIC CYSTEINE PROTEINASE PRECURSOR
          Length = 329

 Score =  231 bits (584), Expect = 1e-60
 Identities = 69/290 (23%), Positives = 114/290 (38%), Gaps = 46/290 (15%)

Query: 83  LSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFD----WRTRGAVTPVKNQGQ 138
           ++ +E K   ++ K A    D  +     +  + S+P  FD    W    ++  +++Q  
Sbjct: 51  ITEEEMKFKLMDGKYAAAHSD-EIRATEQEVVLASVPATFDSRTQWSECKSIKLIRDQAT 109

Query: 139 CGSCWSFSTTGNVEGQHFISQNKLVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGLQP 196
           CGSCW+F     +  +  I         +S  +L+ C   C       +C  GC GG   
Sbjct: 110 CGSCWAFGAAEMISDRTCIETKGAQQPIISPDDLLSC---C-----GSSCGNGCEGGYPI 161

Query: 197 NAYNYIIKNGGIQTESSY------PYTAETGTQ--------------CNFNSANIGAKIS 236
            A  +   + G+ T   Y      PY     T               C    +   AK  
Sbjct: 162 QALRWW-DSKGVVTGGDYHGAGCKPYPIAPCTSGNCPESKTPSCSMSCQSGYSTAYAKDK 220

Query: 237 NFTM----IPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIV 291
           +F +    +PKN   +   I + GP+  A     ++  Y  GV+          H I I+
Sbjct: 221 HFGVSAYAVPKNAASIQAEIYANGPVEAAFSVYEDFYKYKSGVYKHTAGKYLGGHAIKII 280

Query: 292 GYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTS 341
           G+  ++       PYW+V NSWG +WGE G+  + RG + CG+ + V   
Sbjct: 281 GWGTES-----GSPYWLVANSWGVNWGESGFFKIYRGDDQCGIESAVVAG 325


>sp|P43508|CPR4_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 4 PRECURSOR
          Length = 335

 Score =  231 bits (583), Expect = 2e-60
 Identities = 78/304 (25%), Positives = 126/304 (40%), Gaps = 60/304 (19%)

Query: 82  DLSSDEFKNYYLNNK-EAIFTDDLPVADYLDDEFINSIPTAFD----WRTRGAVTPVKNQ 136
           D++ ++ K   +  +  A  T D+ V  +  +E  ++IP  FD    W    ++  +++Q
Sbjct: 46  DITIEQVKKRLMRTEFVAPHTPDVEVVKHDINE--DTIPATFDARTQWPNCMSINNIRDQ 103

Query: 137 GQCGSCWSFSTTGNVEGQHFISQNKLVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGL 194
             CGSCW+F+       +  I+ N  V+  LS ++++ C   C        C  GC GG 
Sbjct: 104 SDCGSCWAFAAAEAASDRFCIASNGAVNTLLSAEDVLSC---CSN------CGYGCEGGY 154

Query: 195 QPNAYNYIIKNGGIQTESSY-------PYT-------------------AETGTQC---- 224
             NA+ Y++K+G   T  SY       PY+                         C    
Sbjct: 155 PINAWKYLVKSG-FCTGGSYEAQFGCKPYSLAPCGETVGNVTWPSCPDDGYDTPACVNKC 213

Query: 225 ---NFNSANIGAKISNFTM--IPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIP 278
              N+N A    K    T   + K  + +   I++ GP+  A     ++  Y  GV+   
Sbjct: 214 TNKNYNVAYTADKHFGSTAYAVGKKVSQIQAEIIAHGPVEAAFTVYEDFYQYKTGVYVHT 273

Query: 279 CNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFV 338
                  H I I+G+   N       PYW+V NSW  +WGE GY  + RG N CG+ + V
Sbjct: 274 TGQELGGHAIRILGWGTDN-----GTPYWLVANSWNVNWGENGYFRIIRGTNECGIEHAV 328

Query: 339 STSI 342
              +
Sbjct: 329 VGGV 332


>sp|P43510|CPR6_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 6 PRECURSOR
          Length = 379

 Score =  225 bits (569), Expect = 8e-59
 Identities = 83/388 (21%), Positives = 143/388 (36%), Gaps = 78/388 (20%)

Query: 1   MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIE 60
           MK +L     V   + +                DK+  +    E  E        L   +
Sbjct: 1   MKTLLFLSCIVVAAYCAC-------NDNLESVLDKYRNREIDSEAAE--------LDGDD 45

Query: 61  ELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSI-- 118
            ++ +  N    T     +F+ +  +  K  +           +    +L       +  
Sbjct: 46  LIDYVNENQNLWTAKKQRRFSSVYGENDKAKWGLMGVNHVRLSVKGKQHLSKTKDLDLDI 105

Query: 119 PTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNK--LVSLSEQNLVD 172
           P +FD    W    ++  +++Q  CGSCW+F     +  +  I+ +    V+LS  +L+ 
Sbjct: 106 PESFDSRDNWPKCDSIKVIRDQSSCGSCWAFGAVEAMSDRICIASHGELQVTLSADDLLS 165

Query: 173 CDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQ------CNF 226
           C           +C  GCNGG    A+ Y +K+G I T S+Y  TA  G +      C  
Sbjct: 166 CCK---------SCGFGCNGGDPLAAWRYWVKDG-IVTGSNY--TANNGCKPYPFPPCEH 213

Query: 227 NSANIGA----------------KISNFTMIPKNE---------------TVMAGYIVST 255
           +S                      +S++T    +E                 +   +++ 
Sbjct: 214 HSKKTHFDPCPHDLYPTPKCEKKCVSDYTDKTYSEDKFFGASAYGVKDDVEAIQKELMTH 273

Query: 256 GPLAIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWG 314
           GPL IA +   ++  Y GGV+          H + ++G+   + I     PYW V NSW 
Sbjct: 274 GPLEIAFEVYEDFLNYDGGVYVHTGGKLGGGHAVKLIGWGIDDGI-----PYWTVANSWN 328

Query: 315 ADWGEQGYIYLRRGKNTCGVSNFVSTSI 342
            DWGE G+  + RG + CG+ + V   I
Sbjct: 329 TDWGEDGFFRILRGVDECGIESGVVGGI 356


>sp|P43157|CYSP_SCHJA CATHEPSIN B-LIKE CYSTEINE PROTEINASE PRECURSOR (ANTIGEN SJ31)
          Length = 342

 Score =  222 bits (559), Expect = 1e-57
 Identities = 69/299 (23%), Positives = 114/299 (38%), Gaps = 53/299 (17%)

Query: 84  SSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFD----WRTRGAVTPVKNQGQC 139
           S D+ +      KE               +    IP+ FD    W    +++ +++Q +C
Sbjct: 56  SLDDARILMGARKEDAEMKRNRRPTVDHHDLNVEIPSQFDSRKKWPHCKSISQIRDQSRC 115

Query: 140 GSCWSFSTTGNVEGQHFISQNKLVS--LSEQNLVDCDHECMEYEGEEACDEGCNGGLQPN 197
           GSCW+F     +  +  I      S  LS  +L+ C   C +      C +GC GG    
Sbjct: 116 GSCWAFGAVEAMTDRICIQSGGGQSAELSALDLISC---CKD------CGDGCQGGFPGV 166

Query: 198 AYNYIIKNGGIQTESS--------YPY----------------TAETGTQCN------FN 227
           A++Y +K G +   S         YP+                      QC       + 
Sbjct: 167 AWDYWVKRGIVTGGSKENHTGCQPYPFPKCEHHTKGKYPACGTKIYKTPQCKQTCQKGYK 226

Query: 228 SANIGAKISN--FTMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNSL 284
           +     K        +  NE V+   I+  GP+  A D   ++  Y  G++         
Sbjct: 227 TPYEQDKHYGDESYNVQNNEKVIQRDIMMYGPVEAAFDVYEDFLNYKSGIYRHVTGSIVG 286

Query: 285 DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
            H I I+G+  +     K  PYW++ NSW  DWGE+G   + RG++ C + + V   +I
Sbjct: 287 GHAIRIIGWGVE-----KRTPYWLIANSWNEDWGEKGLFRMVRGRDECSIESDVVAGLI 340


>sp|P25792|CYSP_SCHMA CATHEPSIN B-LIKE CYSTEINE PROTEINASE PRECURSOR (ANTIGEN SM31)
          Length = 340

 Score =  216 bits (545), Expect = 5e-56
 Identities = 67/303 (22%), Positives = 117/303 (38%), Gaps = 55/303 (18%)

Query: 78  NKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFD----WRTRGAVTPV 133
           N+F  L     +      +  +     P  D+  +++   IP+ FD    W    ++  +
Sbjct: 51  NRFHSLDDARIQMGARREEPDLRRKRRPTVDH--NDWNVEIPSNFDSRKKWPGCKSIATI 108

Query: 134 KNQGQCGSCWSFSTTGNVEGQHFISQN--KLVSLSEQNLVDCDHECMEYEGEEACDEGCN 191
           ++Q +CGSCWSF     +  +  I     + V LS  +L+ C   C      E+C  GC 
Sbjct: 109 RDQSRCGSCWSFGAVEAMSDRSCIQSGGKQNVELSAVDLLTC---C------ESCGLGCE 159

Query: 192 GGLQPNAYNYIIKNGGIQTESS--------YPY----------------------TAETG 221
           GG+   A++Y +K G +   S         YP+                        +  
Sbjct: 160 GGILGPAWDYWVKEGIVTASSKENHTGCEPYPFPKCEHHTKGKYPPCGSKIYNTPRCKQT 219

Query: 222 TQCNFNSANIGAKISN--FTMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIP 278
            Q  + +     K        +  +E  +   I+  GP+  +     ++  Y  G++   
Sbjct: 220 CQRKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVEASFTVYEDFLNYKSGIYKHI 279

Query: 279 CNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFV 338
                  H I I+G+  +N       PYW++ NSW  DWGE GY  + RG++ C + + V
Sbjct: 280 TGEALGGHAIRIIGWGVEN-----KTPYWLIANSWNEDWGENGYFRIVRGRDECSIESEV 334

Query: 339 STS 341
              
Sbjct: 335 IAG 337


>sp|P25802|CYS1_OSTOS CATHEPSIN B-LIKE CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 341

 Score =  213 bits (537), Expect = 4e-55
 Identities = 64/297 (21%), Positives = 110/297 (36%), Gaps = 56/297 (18%)

Query: 88  FKNYYLNNKEAIFTD--DLPVADYLDDEFINSIPTAFD----WRTRGAVTPVKNQGQCGS 141
           FK   ++ K     +  D  V D   +E  + IP ++D    W    ++  + +Q  CGS
Sbjct: 59  FKQRLMDLKYIDQNNIPDEEVEDEELEENNDDIPESYDPRIQWANCSSLFHIPDQANCGS 118

Query: 142 CWSFSTTGNVEGQHFISQN--KLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAY 199
           CW+ S+   +  +  I+    K V +S Q++V C   C        C +GC GG   +A+
Sbjct: 119 CWAVSSAAAMSDRICIASKGAKQVLISAQDVVSC---CTW------CGDGCEGGWPISAF 169

Query: 200 NYIIKNGGIQ------TESSYPYTAETGTQCNFNSANIGAKI------------------ 235
            +    G +         S  PY        + N    G  +                  
Sbjct: 170 RFHADEGVVTGGDYNTKGSCRPYEIHPCGH-HGNETYYGECVGMADTPRCKRRCLLGYPK 228

Query: 236 --------SNFTMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNSLDH 286
                        +  +   +   I+  GP+        ++  Y  G++       +  H
Sbjct: 229 SYPSDRYYKKAYQLKNSVKAIQKDIMKNGPVVATYTVYEDFAHYRSGIYKHKAGRKTGLH 288

Query: 287 GILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
            + ++G+  +     K  PYWIV NSW  DWGE G+  + RG N CG    ++   +
Sbjct: 289 AVKVIGWGEE-----KGTPYWIVANSWHDDWGENGFFRMHRGSNDCGFEERMAAGSV 340


>sp|P25793|CYS2_HAECO CATHEPSIN B-LIKE CYSTEINE PROTEINASE 2 PRECURSOR
          Length = 342

 Score =  212 bits (534), Expect = 1e-54
 Identities = 64/302 (21%), Positives = 119/302 (39%), Gaps = 56/302 (18%)

Query: 81  ADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFD----WRTRGAVTPVKNQ 136
           +D + D F+   ++ K      +L V +  D E    IP ++D    W+       +++Q
Sbjct: 53  SDPTPD-FEQKIMSIKYKHQKLNLMVKEDPDPEVD--IPPSYDPRDVWKNCTTFY-IRDQ 108

Query: 137 GQCGSCWSFSTTGNVEGQHFISQN--KLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGL 194
             CGSCW+ ST   +  +  I+    K V++S  +++ C   C        C +GC GG 
Sbjct: 109 ANCGSCWAVSTAAAISDRICIASKAEKQVNISATDIMTC---C-----RPQCGDGCEGGW 160

Query: 195 QPNAYNYIIKNGGIQTES------SYPYTAET----GTQCNFNSANIGAKI--------- 235
              A+ Y I +G +            PY        G    +      A           
Sbjct: 161 PIEAWKYFIYDGVVSGGEYLTKDVCRPYPIHPCGHHGNDTYYGECRGTAPTPPCKRKCRP 220

Query: 236 -------------SNFTMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNP 281
                         +  ++ ++   +   I+  GP+  +     +++ Y  G++      
Sbjct: 221 GVRKMYRIDKRYGKDAYIVKQSVKAIQSEILKNGPVVASFAVYEDFRHYKSGIYKHTAGE 280

Query: 282 NSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTS 341
               H + ++G+  +N     N  +W++ NSW  DWGE+GY  + RG N CG+   ++  
Sbjct: 281 LRGYHAVKMIGWGNEN-----NTDFWLIANSWHNDWGEKGYFRIVRGSNDCGIEGTIAAG 335

Query: 342 II 343
           I+
Sbjct: 336 IV 337


>sp|P19092|CYS1_HAECO CATHEPSIN B-LIKE CYSTEINE PROTEINASE 1 PRECURSOR
          Length = 342

 Score =  208 bits (523), Expect = 2e-53
 Identities = 62/295 (21%), Positives = 115/295 (38%), Gaps = 55/295 (18%)

Query: 88  FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFD----WRTRGAVTPVKNQGQCGSCW 143
           F+   ++ K      +L V +  D E    IP ++D    W+       +++Q  CGSCW
Sbjct: 59  FEQKIMDIKYKHQKLNLMVKEDPDPEVD--IPPSYDPRDVWKNCTTFY-IRDQANCGSCW 115

Query: 144 SFSTTGNVEGQHFISQN--KLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNY 201
           + ST   +  +  I+    K V++S  +++ C   C        C +GC GG    A+ Y
Sbjct: 116 AVSTAAAISDRICIASKAEKQVNISATDIMTC---C-----RPQCGDGCEGGWPIEAWKY 167

Query: 202 IIKNGGIQTES------SYPYTAET----GTQCNFNSANIGAKI---------------- 235
            I +G +            PY        G    +      A                  
Sbjct: 168 FIYDGVVSGGEYLTKDVCRPYPIHPCGHHGNDTYYGECRGTAPTPPCKRKCRPGVRKMYR 227

Query: 236 ------SNFTMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGGVFDIPCNPNSLDHGI 288
                  +  ++ ++   +   I+  GP+  +     +++ Y  G++          H +
Sbjct: 228 IDKRYGKDAYIVKQSVKAIQSEILRNGPVVASFAVYEDFRHYKSGIYKHTAGELRGYHAV 287

Query: 289 LIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 343
            ++G+  +N     N  +W++ NSW  DWGE+GY  + RG N CG+   ++  I+
Sbjct: 288 KMIGWGNEN-----NTDFWLIANSWHNDWGEKGYFRIIRGTNDCGIEGTIAAGIV 337


>sp|P43507|CPR3_CAEEL CATHEPSIN B-LIKE CYSTEINE PROTEINASE 3 PRECURSOR
          Length = 370

 Score =  204 bits (513), Expect = 3e-52
 Identities = 61/265 (23%), Positives = 99/265 (37%), Gaps = 49/265 (18%)

Query: 112 DEFINSIPTAFD----WRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVS--L 165
           +     +P  FD    W     +  ++NQ  CGSCW+F     +  +  I  N      +
Sbjct: 86  EIVPEPLPDTFDAREKWPDCNTIKLIRNQATCGSCWAFGAAEVISDRVCIQSNGTQQPVI 145

Query: 166 SEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSY------PYTAE 219
           S ++++ C   C        C  GC GG    A  +   +G + T   Y      PY+  
Sbjct: 146 SVEDILSC---C-----GTTCGYGCKGGYSIEALRFWASSGAV-TGGDYGGHGCMPYSFA 196

Query: 220 TGTQ---------CNF------------NSANIGAKISNFTMIPKNETVMAGYIVSTGPL 258
             T+         C                 + GA     T   K+ T +   I   GP+
Sbjct: 197 PCTKNCPESTTPSCKTTCQSSYKTEEYKKDKHYGASAYKVTT-TKSVTEIQTEIYHYGPV 255

Query: 259 AIAADAV-EWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADW 317
             +     ++  Y  GV+          H + I+G+  +N +      YW++ NSWG  +
Sbjct: 256 EASYKVYEDFYHYKSGVYHYTSGKLVGGHAVKIIGWGVENGV-----DYWLIANSWGTSF 310

Query: 318 GEQGYIYLRRGKNTCGVSNFVSTSI 342
           GE+G+  +RRG N C +   V   I
Sbjct: 311 GEKGFFKIRRGTNECQIEGNVVAGI 335


>sp|P25780|EUM1_EURMA MITE GROUP I ALLERGEN EUR M 1 (EUR M I)
          Length = 211

 Score =  201 bits (507), Expect = 1e-51
 Identities = 69/220 (31%), Positives = 99/220 (44%), Gaps = 25/220 (11%)

Query: 117 SIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHE 176
           S+P+  D R+   VTP++ QG CGSCW+FS   + E  +   +N  + L+EQ LVDC   
Sbjct: 10  SLPSELDLRSLRTVTPIRMQGGCGSCWAFSGVASTESAYLAYRNMSLDLAEQELVDC--- 66

Query: 177 CMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKIS 236
                   A   GC+G   P    YI +NG +Q E  YPY A   +    N+   G K  
Sbjct: 67  --------ASQNGCHGDTIPRGIEYIQQNGVVQ-EHYYPYVAREQSCHRPNAQRYGLK-- 115

Query: 237 NFTMIPKNETVMAGYIVSTGPLAIAA-----DAVEWQFYIGGVFDIPCNPNSLD-HGILI 290
           N+  I   ++      ++    A+A      D   ++ Y G       N    + H + I
Sbjct: 116 NYCQISPPDSNKIRQALTQTHTAVAVIIGIKDLNAFRHYDGRTIMQHDNGYQPNYHAVNI 175

Query: 291 VGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKN 330
           VGY        + + YWIV+NSW   WG+ GY Y     N
Sbjct: 176 VGYGN-----TQGVDYWIVRNSWDTTWGDNGYGYFAANIN 210


>sp|P25773|CATL_FELCA CATHEPSIN L (PROGESTERONE-DEPENDENT PROTEIN) (PDP)
          Length = 139

 Score =  185 bits (464), Expect = 2e-46
 Identities = 55/141 (39%), Positives = 84/141 (59%), Gaps = 5/141 (3%)

Query: 192 GGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGY 251
           GGL  +A+ Y+  NGG+ +E SYPY A+ G  C +   N  A ++++  IP  E  +   
Sbjct: 1   GGLIDDAFQYVKDNGGLDSEESYPYHAQ-GDSCKYRPENSVANVTDYWDIPSKENELMIT 59

Query: 252 IVSTGPLAIAADAV--EWQFYIGGVFDIP-CNPNSLDHGILIVGYSAKNTIFRKNMPYWI 308
           + + GP++ A DA    ++FY  G++  P C+   +DHG+L+VGY A  T   +N  YWI
Sbjct: 60  LAAVGPISAAIDASLDTFRFYKEGIYYDPSCSSEDVDHGVLVVGYGADGT-ETENKKYWI 118

Query: 309 VKNSWGADWGEQGYIYLRRGK 329
           +KNSWG DWG  GYI + + +
Sbjct: 119 IKNSWGTDWGMDGYIKMAKDR 139


>sp|Q23894|CYS3_DICDI CYSTEINE PROTEINASE 3 (CYSTEINE PROTEINASE II)
          Length = 151

 Score =  158 bits (395), Expect = 2e-38
 Identities = 61/158 (38%), Positives = 86/158 (53%), Gaps = 17/158 (10%)

Query: 41  SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIF 100
           +H+E++ R+E FK N+  +   N    +  + T  G+N+ ADLS++E++  YL  +  I 
Sbjct: 1   THKEFMPRYEEFKKNMDYVHNWN----SKGSKTVLGLNQHADLSNEEYRLNYLGTRAHIK 56

Query: 101 TDDLPVAD---YLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFI 157
            +     +    L+       P   DWR + AVTPVK+QGQCGSC   STTG+VEG   I
Sbjct: 57  LNGYHKRNLGLRLNRPHFKQ-PLNVDWREKDAVTPVKDQGQCGSC-IISTTGSVEGVTAI 114

Query: 158 SQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQ 195
              KLVSLSEQN++               +EGCNGGL 
Sbjct: 115 KTGKLVSLSEQNILRLSSSF--------GNEGCNGGLM 144


>sp|P13823|SERA_PLAFG SERINE-REPEAT ANTIGEN PROTEIN PRECURSOR (P126) (111 KD ANTIGEN)
          Length = 989

 Score =  157 bits (393), Expect = 3e-38
 Identities = 60/255 (23%), Positives = 101/255 (39%), Gaps = 46/255 (18%)

Query: 123 DWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEG 182
           D     +   V++QG C + W F++  ++E    +   +   +S   + +C      Y+G
Sbjct: 569 DENNCISNLQVEDQGNCDTSWIFASKYHLETIRCMKGYEPTKISALYVANC------YKG 622

Query: 183 EEACDEGCNGGLQPNAYNYIIKNGG-IQTESSYPYT-AETGTQCN--------------- 225
           E    + C+ G  P  +  II++ G +  ES+YPY   + G QC                
Sbjct: 623 EHK--DRCDEGSSPMEFLQIIEDYGFLPAESNYPYNYVKVGEQCPKVEDHWMNLWDNGKI 680

Query: 226 -----------------FNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQ 268
                            + S      +  F  I K E +  G +++     I A+ V   
Sbjct: 681 LHNKNEPNSLDGKGYTAYESERFHDNMDAFVKIIKTEVMNKGSVIAY----IKAENVMGY 736

Query: 269 FYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG 328
            + G      C  ++ DH + IVGY        +   YWIV+NSWG  WG++GY  +   
Sbjct: 737 EFSGKKVQNLCGDDTADHAVNIVGYGNYVNSEGEKKSYWIVRNSWGPYWGDEGYFKVDMY 796

Query: 329 KNTCGVSNFVSTSII 343
             T    NF+ + +I
Sbjct: 797 GPTHCHFNFIHSVVI 811


>sp|Q06544|CYS3_OSTOS CATHEPSIN B-LIKE CYSTEINE PROTEINASE 3
          Length = 174

 Score =  139 bits (348), Expect = 6e-33
 Identities = 31/130 (23%), Positives = 53/130 (39%), Gaps = 8/130 (6%)

Query: 217 TAETGTQCNFNSANIGAKISN--FTMIPKNETVMAGYIVSTGPLAIAADAV-EWQFYIGG 273
             +   Q  +  A    K        +P N   +   I+  GP+        ++  Y  G
Sbjct: 50  KCQKTCQRGYLKAYKEDKHFGKSAYRLPNNVKAIQRDIMKNGPVVAGFIVYEDFAHYKSG 109

Query: 274 VFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCG 333
           ++       +  H + I+G+  +     K  PYW++ NSW  DWGE+G+  + RG N C 
Sbjct: 110 IYKHTAGRMTGGHAVKIIGWGKE-----KGTPYWLIANSWHDDWGEKGFYRMIRGINNCR 164

Query: 334 VSNFVSTSII 343
           +   V   I+
Sbjct: 165 IEEMVFAGIV 174


>sp|P05993|PAP5_CARPA CYSTEINE PROTEINASE (CLONE PLBPC13)
          Length = 96

 Score =  131 bits (327), Expect = 2e-30
 Identities = 43/87 (49%), Positives = 55/87 (62%), Gaps = 2/87 (2%)

Query: 256 GPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKN--TIFRKNMPYWIVKNSW 313
           GPLA+A +A   Q YIGGV         L+HG+L+VGY +     I  K  PYW++KNSW
Sbjct: 1   GPLAVAINAAYMQTYIGGVSCPYICSRRLNHGVLLVGYGSAGYAPIRLKEKPYWVIKNSW 60

Query: 314 GADWGEQGYIYLRRGKNTCGVSNFVST 340
           G +WGE GY  + RG+N CGV + VST
Sbjct: 61  GENWGENGYYKICRGRNICGVDSMVST 87


>sp|P12399|CT2A_MOUSE CTLA-2-ALPHA PROTEIN PRECURSOR
          Length = 136

 Score = 98.2 bits (241), Expect = 2e-20
 Identities = 32/131 (24%), Positives = 53/131 (40%), Gaps = 14/131 (10%)

Query: 8   VLAVFTVFVSSRGIPPE--EQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLI 65
            L +  + + S   PP+    +++ E++ KF K Y+  E   R  +++ N  KIE  N  
Sbjct: 16  FLLILCLGMMSAAPPPDPSLDNEWKEWKTKFAKAYNLNEERHRRLVWEENKKKIEAHNAD 75

Query: 66  AINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWR 125
               K     G+N+F+DL+ +EFK     N                 E    +P   D  
Sbjct: 76  YEQGKTSFYMGLNQFSDLTPEEFKTNCYGNSL------------NRGEMAPDLPEYEDLG 123

Query: 126 TRGAVTPVKNQ 136
               +TP + Q
Sbjct: 124 KNSYLTPGRAQ 134


>sp|P12400|CT2B_MOUSE CTLA-2-BETA PROTEIN PRECURSOR
          Length = 141

 Score = 95.9 bits (235), Expect = 1e-19
 Identities = 29/133 (21%), Positives = 54/133 (39%), Gaps = 13/133 (9%)

Query: 4   ILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELN 63
           + L +L +  +  +     P   +++ E++  F K YS +E   R  +++ N  KIE  N
Sbjct: 20  VFLLILCLGMMSAAPS-PDPSLDNEWKEWKTTFAKAYSLDEERHRRLMWEENKKKIEAHN 78

Query: 64  LIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFD 123
                 K     G+N+F+DL+ +EF+             +   +     E    +P   D
Sbjct: 79  ADYERGKTSFYMGLNQFSDLTPEEFR------------TNCCGSSMCRGEMAPDLPEYED 126

Query: 124 WRTRGAVTPVKNQ 136
                 +TP + Q
Sbjct: 127 LGKNSYLTPGRAQ 139


>sp|P32957|CC4_CARCN CYSTEINE PROTEINASE IV (CC-IV)
          Length = 43

 Score = 84.6 bits (206), Expect = 3e-16
 Identities = 26/42 (61%), Positives = 30/42 (70%)

Query: 119 PTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQN 160
           P + DWR +GAVTPVKNQG CGSCW+FST   VEG + I   
Sbjct: 2   PESIDWRKKGAVTPVKNQGSCGSCWAFSTIVTVEGINKIRTG 43


>sp|P32956|CC3_CARCN CYSTEINE PROTEINASE III (CC-III)
          Length = 43

 Score = 84.2 bits (205), Expect = 4e-16
 Identities = 26/42 (61%), Positives = 30/42 (70%)

Query: 119 PTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQN 160
           P + DWR +GAVTPVKNQG CGSCW+FST   VEG + I   
Sbjct: 2   PESIDWRKKGAVTPVKNQGSCGSCWAFSTIATVEGINKIVHG 43


>sp|P32955|CC2_CARCN CYSTEINE PROTEINASE II (CC-II)
          Length = 43

 Score = 81.5 bits (198), Expect = 2e-15
 Identities = 24/42 (57%), Positives = 29/42 (68%)

Query: 119 PTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQN 160
           P + DWR +GAVTPVK+Q  CGSCW+FST   VEG + I   
Sbjct: 2   PGSVDWRQKGAVTPVKDQNPCGSCWAFSTVATVEGINKIVTG 43


>sp||CATL_CHICK_2 [Segment 2 of 2] CATHEPSIN L
          Length = 42

 Score = 77.2 bits (187), Expect = 5e-14
 Identities = 20/42 (47%), Positives = 28/42 (66%), Gaps = 1/42 (2%)

Query: 303 NMPYWIVKNSWGADWGEQGYIYLRRG-KNTCGVSNFVSTSII 343
              YWIVKNSWG  WG++GYIY+ +  KN CG++   S  ++
Sbjct: 1   GKKYWIVKNSWGEKWGDKGYIYMAKDRKNHCGIATAASYPLV 42


>sp|P32954|CC1_CARCN CYSTEINE PROTEINASE I (CC-I)
          Length = 43

 Score = 76.0 bits (184), Expect = 1e-13
 Identities = 24/40 (60%), Positives = 29/40 (72%)

Query: 118 IPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFI 157
           I  + DWR +GAVTPV+NQG CGSCW+FS+   VEG   I
Sbjct: 1   IVASIDWRQKGAVTPVRNQGSCGSCWTFSSVAAVEGIIKI 40


>sp|P05689|CATX_BOVIN CATHEPSIN
          Length = 73

 Score = 59.7 bits (142), Expect = 9e-09
 Identities = 15/41 (36%), Positives = 24/41 (57%), Gaps = 5/41 (12%)

Query: 285 DHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYL 325
           +H + + G+   +      M YWIV+NSWG  WGE G++ +
Sbjct: 10  NHIVSVAGWGVSD-----GMEYWIVRNSWGEPWGEHGWMRI 45


>sp|P94869|PEPG_LACDL AMINOPEPTIDASE G
          Length = 437

 Score = 46.0 bits (107), Expect = 1e-04
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 4/49 (8%)

Query: 280 NPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG 328
               + H + +VG        R+    W V+NSWG   GE+G+  +   
Sbjct: 355 GAGEVSHAMTLVGVDEDKGDIRQ----WKVENSWGDKSGEKGFFVMSHN 399


>sp|P94870|PEPE_LACHE AMINOPEPTIDASE E
          Length = 438

 Score = 42.9 bits (99), Expect = 0.001
 Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 4/48 (8%)

Query: 278 PCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYL 325
                 + H + +VG    N   R+    W V+NSWG   G +GY  +
Sbjct: 354 KTGVGEVSHAMTLVGVDEDNGEVRQ----WKVENSWGDKSGAKGYYVM 397


>sp|P94868|PEPW_LACDL AMINOPEPTIDASE W
          Length = 437

 Score = 42.1 bits (97), Expect = 0.002
 Identities = 14/43 (32%), Positives = 20/43 (45%), Gaps = 4/43 (9%)

Query: 286 HGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRG 328
           H + +VG        R+    W V+NSWG   GE+GY  +   
Sbjct: 361 HDMALVGVDVDGGQVRQ----WKVENSWGDKSGEKGYFTMSAD 399


>sp|Q10744|PEPC_LACHE AMINOPEPTIDASE C
          Length = 449

 Score = 41.4 bits (95), Expect = 0.003
 Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 4/46 (8%)

Query: 280 NPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYL 325
             + +DH ++I G    +    K    W ++NSWG   G +GY  +
Sbjct: 358 GESMMDHAMVITGVDIVDGKPTK----WKIENSWGEKPGFKGYFVM 399


>sp|Q04723|PEPC_LACLC AMINOPEPTIDASE C
          Length = 436

 Score = 39.8 bits (91), Expect = 0.009
 Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 9/68 (13%)

Query: 262 ADAVEWQ------FYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGA 315
            D+ +++      F       +    + + H +++ G    +     N   W V+NSWG 
Sbjct: 326 MDSYDFKSSLDIEFTQSKAGRLDYGESLMTHAMVLAG---VDLDADGNSTKWKVENSWGK 382

Query: 316 DWGEQGYI 323
           D G++GY 
Sbjct: 383 DAGQKGYF 390


 Score = 31.6 bits (70), Expect = 2.5
 Identities = 15/77 (19%), Positives = 28/77 (35%), Gaps = 10/77 (12%)

Query: 77  VNKFADLSS---DEFKN--YYLNNKEAIFTDDLPVADYLDDEFINSIPT-AFDWRTRGAV 130
           +   +D +    + F         + A+  + L  +  +      ++P  + D       
Sbjct: 1   MTVTSDFTQKLYENFAENTKLRAVENAVTKNGLLSSLEVRGSHAANLPEFSLDLTKD--- 57

Query: 131 TPVKNQGQCGSCWSFST 147
            PV NQ Q G CW F+ 
Sbjct: 58  -PVTNQKQSGRCWMFAA 73


>sp|Q48543|PEPC_LACDL AMINOPEPTIDASE C
          Length = 449

 Score = 38.2 bits (87), Expect = 0.025
 Identities = 12/46 (26%), Positives = 23/46 (49%), Gaps = 4/46 (8%)

Query: 280 NPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYL 325
             + ++H ++I    A + +  K    W ++NSWG   G +GY  +
Sbjct: 358 GESMMNHAMVIT---AVDLVDDKPTK-WKIENSWGDKSGFKGYFVM 399


>sp|P21381|THPA_THADA THAUMATOPAIN
          Length = 35

 Score = 38.2 bits (87), Expect = 0.025
 Identities = 14/27 (51%), Positives = 19/27 (69%), Gaps = 2/27 (7%)

Query: 117 SIPTAFDWRTRGAVTPVKNQGQ-CGSC 142
           ++P + DW  +GAV  VKNQ + CGSC
Sbjct: 1   NLPNSVDWWKKGAVAAVKNQ-RXCGSC 26


>sp|Q56115|PEPC_STRTR AMINOPEPTIDASE C
          Length = 445

 Score = 35.9 bits (81), Expect = 0.13
 Identities = 11/46 (23%), Positives = 21/46 (44%), Gaps = 5/46 (10%)

Query: 279 CNPNSLDHGILIVGYSAKNTIFRKNMPY-WIVKNSWGADWGEQGYI 323
            + + + H +++ G            P  W ++NSWG   G++GY 
Sbjct: 356 YSESLMTHAMVLTGVDLD----ADGKPIKWKIENSWGDKVGQKGYF 397


>sp|P09983|HLY1_ECOLI HEMOLYSIN, CHROMOSOMAL
          Length = 1023

 Score = 35.5 bits (80), Expect = 0.17
 Identities = 21/119 (17%), Positives = 35/119 (28%), Gaps = 20/119 (16%)

Query: 31  EFQDKFNKKYSHEEYLERFEIF-KSNLGKIEELNLIAI-------NHKADTKF-----GV 77
           E++ K  K Y    Y  R   F + N   + + N             +          GV
Sbjct: 430 EWEKKHGKNYFENGYDARHAAFLEDNFKILSQYNKEYSVERSVLITQQHWDTLIGELAGV 489

Query: 78  NKFAD--LSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVK 134
            +  D  LS   + +YY   K           D    +  + +    D     + T +K
Sbjct: 490 TRNGDKTLSGKSYIDYYEEGKR-----LEKKPDEFQKQVFDPLKGNIDLSDSKSSTLLK 543


>sp|P33403|CYSP_TRIFO CYSTEINE PROTEINASE
          Length = 23

 Score = 34.7 bits (78), Expect = 0.28
 Identities = 8/19 (42%), Positives = 12/19 (63%)

Query: 120 TAFDWRTRGAVTPVKNQGQ 138
            + DWR +G V  +K+Q Q
Sbjct: 2   DSLDWREKGVVNSIKDQAQ 20


>sp|P08715|HLYA_ECOLI HEMOLYSIN, PLASMID
          Length = 1024

 Score = 34.7 bits (78), Expect = 0.28
 Identities = 9/38 (23%), Positives = 14/38 (36%), Gaps = 1/38 (2%)

Query: 31  EFQDKFNKKYSHEEYLERFEIF-KSNLGKIEELNLIAI 67
           E++ K  K Y    Y  R   F + N   + + N    
Sbjct: 431 EWEKKHGKNYFENGYDARHAAFLEDNFKILSQYNKEYS 468


>sp|P87362|BLMH_CHICK BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH) (AMINOPEPTIDASE H)
          Length = 455

 Score = 34.3 bits (77), Expect = 0.37
 Identities = 10/19 (52%), Positives = 14/19 (73%)

Query: 307 WIVKNSWGADWGEQGYIYL 325
           W V+NSWG D G +GY+ +
Sbjct: 392 WRVENSWGEDRGNKGYLIM 410


>sp|P54704|PSPB_DICDI PRESPORE PROTEIN B PRECURSOR
          Length = 379

 Score = 34.3 bits (77), Expect = 0.37
 Identities = 24/109 (22%), Positives = 41/109 (37%), Gaps = 15/109 (13%)

Query: 210 TESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQF 269
           T   YP T   G    +N   +  K  +  ++PK E   + Y+   GP     D   W++
Sbjct: 78  TGKIYP-TVNMGDCHRYNVDLVFKKDKSGNVMPKKELRESAYVP-HGP----IDPATWKY 131

Query: 270 YI--GGVFDI-PCNPNSL------DHGILIVGYSAKNTIFRKNMPYWIV 309
           Y    G +    C+P ++          L +GY A        +  W++
Sbjct: 132 YTFVQGKWTGFGCDPQNVVFSGAEGGMPLQLGYGANGKNGDNGISVWLI 180


>sp|Q13867|BLMH_HUMAN BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH)
          Length = 455

 Score = 34.0 bits (76), Expect = 0.49
 Identities = 10/19 (52%), Positives = 14/19 (73%)

Query: 307 WIVKNSWGADWGEQGYIYL 325
           W V+NSWG D G +GY+ +
Sbjct: 392 WRVENSWGEDHGHKGYLCM 410


>sp|P70645|BLMH_RAT BLEOMYCIN HYDROLASE (BLM HYDROLASE) (BMH)
          Length = 454

 Score = 34.0 bits (76), Expect = 0.49
 Identities = 10/19 (52%), Positives = 14/19 (73%)

Query: 307 WIVKNSWGADWGEQGYIYL 325
           W V+NSWG D G +GY+ +
Sbjct: 392 WRVENSWGEDHGHKGYLCM 410


>sp|P80532|CAT3_FASHE PUTATIVE CATHEPSIN L3 (NEWLY EXCYSTED JUVENILE PROTEIN 8)
          Length = 19

 Score = 34.0 bits (76), Expect = 0.49
 Identities = 9/18 (50%), Positives = 12/18 (66%)

Query: 118 IPTAFDWRTRGAVTPVKN 135
           +P + DWR  G VT VK+
Sbjct: 2   VPASIDWREYGYVTEVKD 19


>sp|P16462|LKTA_ACTAC LEUKOTOXIN
          Length = 1050

 Score = 34.0 bits (76), Expect = 0.49
 Identities = 11/68 (16%), Positives = 25/68 (36%), Gaps = 2/68 (2%)

Query: 12  FTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKA 71
            +    S  I  +   +   +++K+ K YS   Y  R   F      ++  N +   +K 
Sbjct: 410 ASKQAVSEHIANQLADKIKAWENKYGKNYSENGYDARHSAFLE--DSLKLFNELREKYKT 467

Query: 72  DTKFGVNK 79
           +    + +
Sbjct: 468 ENILSITQ 475


>sp|P13438|TSP_MOUSE TROPHOBLAST-SPECIFIC PROTEIN PRECURSOR
          Length = 124

 Score = 32.4 bits (72), Expect = 1.4
 Identities = 19/129 (14%), Positives = 41/129 (31%), Gaps = 12/129 (9%)

Query: 8   VLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAI 67
            L +  + V+S  I PE Q      + K       +E L +  ++   +   +  +    
Sbjct: 6   FLVILCLGVASAVIVPEAQLDAELQEQK------DKEVLIK-AVWSKFMKTNKLHSSEND 58

Query: 68  NHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTR 127
                +   ++    L+ +E           +F ++         + +   P   D+   
Sbjct: 59  QETEGSNIEMSASGQLTDEELMKIMTTVLHPMFEEEENKP-----QPVVDDPEFEDYTES 113

Query: 128 GAVTPVKNQ 136
           G    V NQ
Sbjct: 114 GDGFFVPNQ 122


>sp|Q00951|HLYA_ACTSU HEMOLYSIN (CYTOLYSIN II) (CLY-IIA) (HLY-IIA) (CYTC) (APPA)
          Length = 956

 Score = 32.4 bits (72), Expect = 1.4
 Identities = 10/36 (27%), Positives = 16/36 (43%), Gaps = 1/36 (2%)

Query: 31  EFQDKFNKKYSHEEYLER-FEIFKSNLGKIEELNLI 65
           E++ K NK Y  + Y  R     + N+  +  LN  
Sbjct: 427 EWEKKHNKNYFEQGYDSRHLADLQDNMKFLINLNKE 462


>sp|P15377|RT2A_ACTPL RTX-II TOXIN DETERMINANT A (APX-IIA) (HEMOLYSIN IIA) (HLY-IIA)
           (CYTOLYSIN IIA) (CLY-IIA)
          Length = 956

 Score = 32.4 bits (72), Expect = 1.4
 Identities = 10/36 (27%), Positives = 16/36 (43%), Gaps = 1/36 (2%)

Query: 31  EFQDKFNKKYSHEEYLER-FEIFKSNLGKIEELNLI 65
           E++ K NK Y  + Y  R     + N+  +  LN  
Sbjct: 427 EWEKKHNKNYFEQGYDSRHLADLQDNMKFLINLNKE 462


>sp|P52181|TGLC_PAGMA PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE (TISSUE
           TRANSGLUTAMINASE) (TGASE C) (TGC)
          Length = 695

 Score = 32.0 bits (71), Expect = 1.9
 Identities = 12/48 (25%), Positives = 17/48 (35%), Gaps = 5/48 (10%)

Query: 102 DDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTG 149
           ++          +  S+P    W   G V PVK     G CW F+   
Sbjct: 237 EEPYTDGVAPYRWTGSVPILQQWSKAG-VRPVKY----GQCWVFAAVA 279


>sp|P35681|TCTP_ORYSA TRANSLATIONALLY CONTROLLED TUMOR PROTEIN HOMOLOG (TCTP)
          Length = 168

 Score = 32.0 bits (71), Expect = 1.9
 Identities = 12/34 (35%), Positives = 19/34 (55%)

Query: 22  PPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSN 55
           PP ++ QF+ F  ++ K  S +   E+ E FK N
Sbjct: 80  PPFDKKQFVTFMKRYIKNLSAKLDAEKQEEFKKN 113


>sp|Q01532|BLH1_YEAST CYSTEINE PROTEINASE 1 (Y3) (BLEOMYCIN HYDROLASE) (BLM HYDROLASE)
          Length = 454

 Score = 31.6 bits (70), Expect = 2.5
 Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 9/40 (22%)

Query: 131 TPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNL 170
           TPV NQ   G CW F+ T  +         +L  LSE NL
Sbjct: 62  TPVTNQKSSGRCWLFAATNQL---------RLNVLSELNL 92


>sp|P16312|MMAL_DERMI MAJOR MITE FECAL ALLERGEN DER M 1 (DER M I)
          Length = 30

 Score = 31.2 bits (69), Expect = 3.2
 Identities = 8/24 (33%), Positives = 14/24 (58%)

Query: 114 FINSIPTAFDWRTRGAVTPVKNQG 137
              ++P+  D R+   VTP++ QG
Sbjct: 7   NSGNVPSELDLRSLRTVTPIRMQG 30


>sp|O03992|TCTP_FRAAN TRANSLATIONALLY CONTROLLED TUMOR PROTEIN HOMOLOG (TCTP)
          Length = 170

 Score = 30.8 bits (68), Expect = 4.2
 Identities = 16/62 (25%), Positives = 30/62 (47%), Gaps = 13/62 (20%)

Query: 22  PPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFA 81
           PP ++ QF+ +  ++ K  + +   E+ E FK N+             +  TKF ++K +
Sbjct: 82  PPFDKKQFVTWVKRYIKLLTPKLEGEQQETFKKNI-------------EGATKFLLSKLS 128

Query: 82  DL 83
           DL
Sbjct: 129 DL 130


>sp|Q04489|YMJ6_YEAST HYPOTHETICAL 59.5 KD PROTEIN IN VPS9-RAD10 INTERGENIC REGION
          Length = 525

 Score = 30.8 bits (68), Expect = 4.2
 Identities = 26/122 (21%), Positives = 43/122 (34%), Gaps = 20/122 (16%)

Query: 174 DHECMEYEGEEACDEGCNGGLQPNAYNYIIKN-----GGIQ----TESSYPYTAET--GT 222
           D   +++ GE    E   G         +++N     G I      E  Y YT      +
Sbjct: 87  DRYFLQFNGELYNKEISQGDNDSLYIASMLQNLKEGMGVIDVIKSLEGEYAYTIYDVNSS 146

Query: 223 QCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPN 282
           +  F    IG +  ++++ P NE  +A         ++   A  +Q  IGGV        
Sbjct: 147 KLYFGRDPIGRRSLSYSVTPDNELYVA---------SVTGSAGSFQDCIGGVIYEYDTRT 197

Query: 283 SL 284
            L
Sbjct: 198 KL 199


>sp|Q03164|HRX_HUMAN ZINC FINGER PROTEIN HRX (ALL-1) (TRITHORAX-LIKE PROTEIN)
          Length = 3969

 Score = 30.8 bits (68), Expect = 4.2
 Identities = 17/81 (20%), Positives = 38/81 (45%), Gaps = 7/81 (8%)

Query: 126  TRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDC-DHECMEYEGEE 184
               +V+ VK QGQ  S  +     ++E    +  +     S++NL+D  + E ++ + + 
Sbjct: 2782 NCHSVSRVKTQGQ-DSLEA--QLSSLESSRRVHTSTP---SDKNLLDTYNTELLKSDSDN 2835

Query: 185  ACDEGCNGGLQPNAYNYIIKN 205
               + C   L  +  ++++KN
Sbjct: 2836 NNSDDCGNILPSDIMDFVLKN 2856


>sp||CATB_COTJA_1 [Segment 1 of 2] CATHEPSIN B (CATHEPSIN B1)
          Length = 25

 Score = 30.4 bits (67), Expect = 5.6
 Identities = 6/25 (24%), Positives = 12/25 (48%), Gaps = 4/25 (16%)

Query: 118 IPTAFD----WRTRGAVTPVKNQGQ 138
           +P  FD    W     ++ +++QG 
Sbjct: 1   LPDTFDSRKQWPNCPTISEIRDQGS 25


>sp|Q62703|RCN2_RAT RETICULOCALBIN 2 PRECURSOR (CALCIUM-BINDING PROTEIN ERC-55)
           (TAIPOXIN-ASSOCIATED CALCIUM-BINDING PROTEIN-49)
           (TCBP-49)
          Length = 318

 Score = 30.4 bits (67), Expect = 5.6
 Identities = 17/109 (15%), Positives = 40/109 (36%), Gaps = 4/109 (3%)

Query: 26  QSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIA-INHKADTKFGVNKFADLS 84
           +++  ++     K Y+ +E  ++F  +  N       +      +     F  N   D +
Sbjct: 84  ENELSQWIQMSFKHYAMQEAKQQFVEYDKNSDGTVTWDEYNVQMYDRVIDFDENTALDDT 143

Query: 85  SDE-FKNYYLNNKEAIFTDDLPVADYLDDEFINSI--PTAFDWRTRGAV 130
            +E F+  +L +K+     +      L+ E   +   P   D+ T   +
Sbjct: 144 EEESFRQLHLKDKKRFEKANQDSGPGLNLEEFIAFEHPEEVDYMTEFVI 192


>sp|P48651|PSS1_HUMAN PHOSPHATIDYLSERINE SYNTHASE I (SERINE-EXCHANGE ENZYME I) (KIAA0024)
          Length = 473

 Score = 30.4 bits (67), Expect = 5.6
 Identities = 6/20 (30%), Positives = 8/20 (40%)

Query: 142 CWSFSTTGNVEGQHFISQNK 161
           CW F   G +E    I   +
Sbjct: 354 CWVFGVIGFLEAIVCIKFGQ 373


>sp|P33404|CYSP_TRIVA CYSTEINE PROTEINASE
          Length = 22

 Score = 30.4 bits (67), Expect = 5.6
 Identities = 10/17 (58%), Positives = 13/17 (75%), Gaps = 1/17 (5%)

Query: 123 DWRTRGAVTPV-KNQGQ 138
           DWR +GAV  + K+QGQ
Sbjct: 6   DWRKKGAVNVIXKDQGQ 22


>sp|Q00576|PSS1_CRILO PHOSPHATIDYLSERINE SYNTHASE I (SERINE-EXCHANGE ENZYME I)
          Length = 471

 Score = 30.4 bits (67), Expect = 5.6
 Identities = 6/20 (30%), Positives = 8/20 (40%)

Query: 142 CWSFSTTGNVEGQHFISQNK 161
           CW F   G +E    I   +
Sbjct: 354 CWVFGVIGFLEAIVCIKFGQ 373


>sp|Q9ZRX0|TCTP_PSEMZ TRANSLATIONALLY CONTROLLED TUMOR PROTEIN HOMOLOG (TCTP)
          Length = 167

 Score = 30.1 bits (66), Expect = 7.3
 Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 13/62 (20%)

Query: 22  PPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFA 81
           PP ++ QFL F  ++ K  + +   ER   FK N+             +   K  V+K +
Sbjct: 79  PPFDKKQFLGFIKRYIKNLATKLSEERQAEFKKNV-------------EGAAKMLVSKLS 125

Query: 82  DL 83
           DL
Sbjct: 126 DL 127


>sp|Q94480|V136_DICDI VEG136 PROTEIN
          Length = 357

 Score = 30.1 bits (66), Expect = 7.3
 Identities = 21/95 (22%), Positives = 34/95 (35%), Gaps = 3/95 (3%)

Query: 70  KADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGA 129
                +G++ F  LS DE    Y ++       +     Y     I S    ++W     
Sbjct: 79  NKKYDYGLDLFL-LSIDEGITGYRDDSLETVKRNQEQ--YPIPSQILSYKELYNWTMDDI 135

Query: 130 VTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVS 164
           V  +  +G C SC  F       G   +  NK+V+
Sbjct: 136 VKEIGLKGNCTSCGVFRRQALDRGAVMLKANKIVT 170


>sp|P55131|RT32_ACTPL RTX-III TOXIN DETERMINANT A FROM SEROTYPE 8 (APX-IIIA) (CYTOLYSIN
           IIIA) (CLY-IIIA)
          Length = 1052

 Score = 30.1 bits (66), Expect = 7.3
 Identities = 9/53 (16%), Positives = 21/53 (38%), Gaps = 1/53 (1%)

Query: 20  GIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIF-KSNLGKIEELNLIAINHKA 71
            +  +  ++  E++ K+ K Y    Y  R + F + +   +   N      +A
Sbjct: 427 HVASKIGNKIDEWEKKYGKNYFENGYDARHKAFLEDSFSLLSSFNKQYETERA 479


>sp|P55130|RT31_ACTPL RTX-III TOXIN DETERMINANT A FROM SEROTYPE 2 (APX-IIIA) (CYTOLYSIN
           IIIA) (CLY-IIIA)
          Length = 1049

 Score = 30.1 bits (66), Expect = 7.3
 Identities = 9/53 (16%), Positives = 21/53 (38%), Gaps = 1/53 (1%)

Query: 20  GIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIF-KSNLGKIEELNLIAINHKA 71
            +  +  ++  E++ K+ K Y    Y  R + F + +   +   N      +A
Sbjct: 427 HVASKIGNKIDEWEKKYGKNYFENGYDARHKAFLEDSFSLLSSFNKQYETERA 479


>sp|P40101|YE16_YEAST HYPOTHETICAL 35.9 KD PROTEIN IN ISC10 3'REGION
          Length = 306

 Score = 30.1 bits (66), Expect = 7.3
 Identities = 13/48 (27%), Positives = 16/48 (33%), Gaps = 1/48 (2%)

Query: 199 YNY-IIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNE 245
           Y Y I+KNG    ES Y    E      F       K+   +     E
Sbjct: 103 YQYEILKNGDFPEESDYEVKGECDGFTLFKVLFCTVKVKKTSYYRNKE 150


>sp|P13388|XMRK_XIPMA MELANOMA RECEPTOR PROTEIN-TYROSINE KINASE PRECURSOR
          Length = 1166

 Score = 30.1 bits (66), Expect = 7.3
 Identities = 16/54 (29%), Positives = 23/54 (41%), Gaps = 11/54 (20%)

Query: 140 GSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGG 193
           GSCW+          H     KL+  +EQ    C+  C   +  + C+E C GG
Sbjct: 202 GSCWAPGPG------HCQKFTKLL-CAEQ----CNRRCRGPKPIDCCNEHCAGG 244


>sp|Q9ZL75|MOAA_HELPJ MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN A
          Length = 321

 Score = 29.7 bits (65), Expect = 9.5
 Identities = 23/162 (14%), Positives = 51/162 (31%), Gaps = 9/162 (5%)

Query: 41  SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIF 100
           + +E LE  E  K+   +I  +  +   H      G+ +   L     K   +  ++   
Sbjct: 165 NDDEILELLEYAKNRSIQIRYIEFMENTHAKSLVKGLKEKEILDLIAQKYKIMGMEKPKQ 224

Query: 101 TDDLPVADYLDDEFINSIPTAFDW-RTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQ 159
                       +F    P + D+ ++   +    +   C   +        E       
Sbjct: 225 GSSKIYTLENGYQFGIIAPHSDDFCQSCNRIRLASDGKICPCLYYQDAIDAKEAIINKDT 284

Query: 160 NKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNY 201
             +  L +Q++++   + M  +         NGG    A+ Y
Sbjct: 285 KMMKRLLKQSIINKPEKNMWNDK--------NGGTPTRAFYY 318


>sp|P55129|RT12_ACTPL RTX-I TOXIN DETERMINANT A FROM SEROTYPES 5/10 (APX-IA) (HEMOLYSIN
           IA) (HLY-IA) (CYTOLYSIN IA) (CLY-IA)
          Length = 1023

 Score = 29.7 bits (65), Expect = 9.5
 Identities = 8/42 (19%), Positives = 15/42 (35%), Gaps = 1/42 (2%)

Query: 27  SQFLEFQDKFNKKYSHEEYLERFEIF-KSNLGKIEELNLIAI 67
           ++  E++ K  K Y    Y  R   F +     + + N    
Sbjct: 423 NKIDEWEKKHGKNYFENGYDARHSAFLEDTFELLSQYNKEYS 464


>sp|P55128|RT11_ACTPL RTX-I TOXIN DETERMINANT A FROM SEROTYPES 1/9 (APX-IA) (HEMOLYSIN
           IA) (HLY-IA) (CYTOLYSIN IA) (CLY-IA)
          Length = 1023

 Score = 29.7 bits (65), Expect = 9.5
 Identities = 8/42 (19%), Positives = 15/42 (35%), Gaps = 1/42 (2%)

Query: 27  SQFLEFQDKFNKKYSHEEYLERFEIF-KSNLGKIEELNLIAI 67
           ++  E++ K  K Y    Y  R   F +     + + N    
Sbjct: 423 NKIDEWEKKHGKNYFENGYDARHSAFLEDTFELLSQYNKEYS 464


>sp|P35669|GSHB_SCHPO GLUTATHIONE SYNTHETASE LARGE CHAIN (GLUTATHIONE SYNTHASE LARGE
           CHAIN) (GSH SYNTHETASE LARGE CHAIN) (GSH-S)
           (PHYTOCHELATIN SYNTHETASE)
          Length = 498

 Score = 29.7 bits (65), Expect = 9.5
 Identities = 16/67 (23%), Positives = 26/67 (37%), Gaps = 6/67 (8%)

Query: 33  QDKFNKKYSHEEYLERFE------IFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSD 86
           Q  +NK Y+       F       I K +    +  NL   + +A      N+F  LS  
Sbjct: 66  QKAYNKLYAKIANDYEFLRLHLQSITKYDEFMNKLWNLYQKHREAVAHLKENQFQPLSLG 125

Query: 87  EFKNYYL 93
            F++ Y+
Sbjct: 126 VFRSDYM 132


>sp|P11140|ABRA_ABRPR ABRIN-A PRECURSOR (RRNA N-GLYCOSIDASE)
          Length = 528

 Score = 29.7 bits (65), Expect = 9.5
 Identities = 12/59 (20%), Positives = 22/59 (36%), Gaps = 2/59 (3%)

Query: 152 EGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQT 210
           E Q  +  +  +  S QN  +C       +G      GC+ G     + +   +G I +
Sbjct: 436 EQQWALYTDGSIR-SVQNTNNCLTSKDHKQGSTILLMGCSNGWASQRWVF-KNDGSIYS 492


>sp|Q00690|LEM2_MOUSE E-SELECTIN PRECURSOR (ENDOTHELIAL LEUKOCYTE ADHESION MOLECULE 1)
           (ELAM-1) (LEUKOCYTE-ENDOTHELIAL CELL ADHESION MOLECULE
           2) (LECAM2) (CD62E)
          Length = 612

 Score = 29.7 bits (65), Expect = 9.5
 Identities = 7/30 (23%), Positives = 13/30 (43%)

Query: 171 VDCDHECMEYEGEEACDEGCNGGLQPNAYN 200
           ++C H    +    +C  GC  G  P++  
Sbjct: 191 LNCSHPFGPFSYNSSCSFGCKRGYLPSSME 220


>sp|P06620|ICEN_PSESY ICE NUCLEATION PROTEIN
          Length = 1200

 Score = 29.7 bits (65), Expect = 9.5
 Identities = 9/33 (27%), Positives = 13/33 (39%), Gaps = 3/33 (9%)

Query: 277 IPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIV 309
              N  + +H  LI GY +  T        W+V
Sbjct: 194 YGSNETAGNHSDLIAGYGSTGTA---GSDSWLV 223


  Database: /home/peter/blast/data/swissprot.pr
    Posted date:  Oct 10, 2000 10:43 AM
  Number of letters in database: 31,984,247
  Number of sequences in database:  88,780
  
Lambda     K      H
   0.318    0.140    0.482 

Lambda     K      H
   0.270   0.0491    0.230 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 48087047
Number of Sequences: 88780
Number of extensions: 2165712
Number of successful extensions: 7103
Number of sequences better than 10.0: 284
Number of HSP's better than 10.0 without gapping: 253
Number of HSP's successfully gapped in prelim test: 31
Number of HSP's that attempted gapping in prelim test: 5661
Number of HSP's gapped (non-prelim): 339
length of query: 343
length of database: 31,984,247
effective HSP length: 49
effective length of query: 294
effective length of database: 27,634,027
effective search space: 8124403938
effective search space used: 8124403938
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 41 (21.6 bits)
S2: 65 (29.7 bits)
BioPerl-1.007002/t/data/purine_v081.infernal000444000766000024      2332613155576321 20516 0ustar00cjfieldsstaff000000000000CM 1: Purine
CM statistics calculated with simulation of 100 samples of length 238
Random seed: 1186083728
No partition points
Using CM E cutoff of 200.00

>gi|633168|emb|X83878.1|

  Plus strand results:

 Query = 1 - 102, Target = 168 - 267
 Score = 79.36, E = 1.945e-07, P = 1.945e-07, GC =  46

           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           + A A++A AA A  AA:AC+C:UAUAAU::CG:G AUAUGGC:CG::AGUUUCUACC:G
       168 UUACAAUAUAAUAGGAACACUCAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGG 227     

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
            CA CCGUAAA UG C:GACUA:G+GU:A  A+U  A+    
       228 GCA-CCGUAAA-UGUCCGACUAUGGGUGAGCAAUGGAACCGC 267     


  Minus strand results:

 Query = 1 - 102, Target = 270 - 171
 Score = 2.25, E = 6.802, P = 0.9989, GC =  48

           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
             +    +   A    +:AC C:UA  +::: ::   UA GG :: :::GU    AC: G
       270 CGUGCGGUUCCAUUGCUCACCCAUA-GUCGGACAU-UUACGG-UGCCCGGUAGAAACUUG 214     

           <<<<_______>>>>>>>,,.))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGAC.UAcGaGuaAauauuaaauauuu 102     
           ::::CC UA  ::::C :   UA:G GU: +  U+++AUAUU 
       213 CGUGCCAUAUCCACGCGAUUaUAUGAGUGUUCCUAUUAUAUUG 171     


>gi|2239287|gb|U51115.1|BSU51115

  Plus strand results:

 Query = 1 - 102, Target = 11655 - 11756
 Score = 81.29, E = 1.259e-07, P = 1.259e-07, GC =  38

           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           A AAAU AAA+AA A+   : CGUAUAAU::CG:GAAUAUGGC:CG::AGU UCUACCA:
     11655 AGAAAUCAAAUAAGAUGAAUUCGUAUAAUCGCGGGAAUAUGGCUCGCAAGUCUCUACCAA 11714   

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
           GC ACCGUAAAU GC:UGACUACG :   AU+U +++  UUU
     11715 GCUACCGUAAAUGGCUUGACUACGUAAACAUUUCUUUCGUUU 11756   


 Query = 1 - 102, Target = 15589 - 15691
 Score = 78.40, E = 2.415e-07, P = 2.415e-07, GC =  42

           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
            A+ A+A+ AAAA A   :CUC:UAUAAU: :GGGAAUAUGGCCC: :AGUUUCUACC:G
     15589 CAUGAAAUCAAAACACGACCUCAUAUAAUCUUGGGAAUAUGGCCCAUAAGUUUCUACCCG 15648   

           <<<<_______>>>>>>>,,)))).))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcG.aGuaAauauuaaauauuu 102     
           GCAACCGUAAAUUGCC:GACUA:G AG: AA + ++  +++++
     15649 GCAACCGUAAAUUGCCGGACUAUGcAGGGAAGUGAUCGAUAAA 15691   


 Query = 1 - 102, Target = 13198 - 13294
 Score = 5.41, E = 3.338, P = 0.9645, GC =  34

           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           +A+ +U + AAAA AA : :U:::A AA:C::::G A  UGGC::::G: UUU U  :: 
     13198 UAUCUUCUUAAAAUAAGGAAUGAAAAAACCAGCUGCAC-UGGCAGCUGGUUUUUUUUGU- 13255   

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
              : C  AA :U+++::  U:::A: : AUAU+   U +U 
     13256 ---UGCAAAAGAUAAAACCAUUUCAUACGAUAUACCGUCAUG 13294   


  Minus strand results:

 Query = 1 - 102, Target = 11759 - 11658
 Score = 9.64, E = 1.287, P = 0.7239, GC =  38

           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           A  AA+  AAA AAA+   : CGUA  +::::: :  UA GG: :::::GU    AC: G
     11759 AUCAAACGAAAGAAAUGUUUACGUA-GUCAAGCCAUUUACGGUAGCUUGGUAGAGACUUG 11701   

           <<<<_______>>>>>>>,,.))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGAC.UAcGaGuaAauauuaaauauuu 102     
           :: :CC UA  : ::C :   UACG :   AU UUA++U +UU
     11700 CGAGCCAUAUUCCCGCGAUUaUACGAAUUCAUCUUAUUUGAUU 11658   


 Query = 1 - 102, Target = 15695 - 15594
 Score = 7.88, E = 1.911, P = 0.8521, GC =  43

           :::::::::::::::::((((((((,,.,<<<<<<<_______>>>>>>>,,,,,,,,<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUA.aucucgggAAUAUGGcccgagaGUuUCUACCa 59      
            A ++U+A   A  A ++ C :: AUA +:C:::::  UA GG:::::G:GU    AC::
     15695 CAGUUUUAUCGAUCACUUCCCUGCAUAgUCCGGCAAUUUACGGUUGCCGGGUAGAAACUU 15636   

           <<<<<_______>>>>>>>,,))))))))::::::::::::::
        60 GgcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
           +::::CC UA  :::: ::A U :: G + +  U++++U +UU
     15635 AUGGGCCAUAUUCCCA-AGAUUAUAUGAGGUCGUGUUUUGAUU 15594   


 Query = 1 - 102, Target = 13846 - 13740
 Score = 6.35, E = 2.7, P = 0.9328, GC =  45

           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,.....
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCU..... 55      
            A  A+A+A A AA AA:A  :::A A :C ::::A  A G :::: G:  UUCU     
     13846 CAGCAAAUACACAAGAACAACUAAAAACCCGUCAUAGAAAGCAUGAUGGCGUUCUccgaa 13787   

           ,,<<<<<<<_______>>>>>>>,,))))))))::::::::::::::
        56 ACCaGgcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
           ACC::GC :CCG    : GC::G CU:::  U:AA+  +A++   ++
     13786 ACCGAGCGGCCGAUUCCAGCUUGCCUUUAACUGAAACCAAUUCCCAA 13740   


 Query = 1 - 102, Target = 825 - 748
 Score = 2.84, E = 5.952, P = 0.9974, GC =  30

           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           +AAAA+ AA AAAA  A: ::C:U:U A           UG  C+ A A   UCUAC   
       825 UAAAAACAACAAAAGGAGCUGCUUUUUA-----------UGCUCACACACGAUCUAC--- 780     

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
                 G AAA      +AC:A:G:: :A ++UU  AU+U+U
       779 ----AUGAAAA------AACAAAGCAUUACAUUUCCAUUUAU 748     


 Query = 1 - 102, Target = 8105 - 8018
 Score = 1.70, E = 7.686, P = 0.9995, GC =  36

           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
            A+A   A +A    AA   U:::AU A         UAUGGC ++A+ GU UC A    
      8105 GAUACGGAUUACGGCAAAAGUGGCAUCA---------UAUGGCGUAAAGGUAUCAAG--- 8058    

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
             A  CGUAA  U+C   ACU:::A   AA+A +AAA+ +++
      8057 --AAUCGUAAUAUACGCUACUGUCAUCAAAAAGAAAAACAAA 8018    


 Query = 1 - 102, Target = 4125 - 4023
 Score = 1.38, E = 8.261, P = 0.9997, GC =  25

           :::::::::::::::::((((((((,,,<<<<<<<_______.>>>.>>>>,,,,,,,,<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGG.ccc.gagaGUuUCUACC 58      
            AAA +AAA A  A AA: :U:::AUAA :+:G:: AU U   ::C :+:  UUUC AC 
      4125 CAAACAAAACACUACAAAUUUGAAAUAAGCUGGUAUAUUUUCuUACaCGAAUUUUCGAC- 4067    

           <<<<<<_______>>>...>>>>,,))))))))::::::::::::::
        59 aGgcaaCCGUAAAuug...cCuGACUAcGaGuaAauauuaaauauuu 102     
              :AAC GUA AUU:   + +GA U:::A: :A+ AU+A+AU+ + 
      4066 ---AAACUGUAUAUUUaugAUAGAGUUUCAAUUAUCAUAAUAUUCAG 4023    


 Query = 1 - 102, Target = 14215 - 14125
 Score = 0.90, E = 9.203, P = 0.9999, GC =  45

           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           AA    AA  AA  A    :+ :UAUA+U: :+++ A A GG   : :AGU         
     14215 AAGCGGAAUCAACGACGCCGUAAUAUAUUCAGAAAUAAACGG---CCAAGUCA------- 14166   

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
            C::CCGUAAA::GC+   CUA: +:   ++ U+ AA+++ +
     14165 -CUGCCGUAAACAGCAGCGCUAUCGCAACUACUGCAAAUACA 14125   


 Query = 1 - 102, Target = 13350 - 13253
 Score = 0.79, E = 9.449, P = 0.9999, GC =  37

           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           +AA  UA   AA A + :A +C:U:    C:::  AA       :::G G   C  C:A 
     13350 UAAGGUACCGAACAGUCAAGUCAUU---UCCAUUUAAGUAAAGCAUGGCGGCACAUCUAC 13294   

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
           : :AC GUA AU: : U:A :A:G+ U: AU UU++  A+ +
     13293 AUGACGGUAUAUCGUAUGA-AAUGGUUUUAUCUUUUGCAACA 13253   


>gi|633168|emb|X83878.1|

  Plus strand results:

 Query = 1 - 102, Target = 168 - 267
 Score = 79.36, E = 1.945e-07, P = 1.945e-07, GC =  46

           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           + A A++A AA A  AA:AC+C:UAUAAU::CG:G AUAUGGC:CG::AGUUUCUACC:G
       168 UUACAAUAUAAUAGGAACACUCAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGG 227     

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
            CA CCGUAAA UG C:GACUA:G+GU:A  A+U  A+    
       228 GCA-CCGUAAA-UGUCCGACUAUGGGUGAGCAAUGGAACCGC 267     


  Minus strand results:

 Query = 1 - 102, Target = 270 - 171
 Score = 2.25, E = 6.802, P = 0.9989, GC =  48

           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
             +    +   A    +:AC C:UA  +::: ::   UA GG :: :::GU    AC: G
       270 CGUGCGGUUCCAUUGCUCACCCAUA-GUCGGACAU-UUACGG-UGCCCGGUAGAAACUUG 214     

           <<<<_______>>>>>>>,,.))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGAC.UAcGaGuaAauauuaaauauuu 102     
           ::::CC UA  ::::C :   UA:G GU: +  U+++AUAUU 
       213 CGUGCCAUAUCCACGCGAUUaUAUGAGUGUUCCUAUUAUAUUG 171     


//
Fin
BioPerl-1.007002/t/data/puzzle.tre000444000766000024        51313155576321 16714 0ustar00cjfieldsstaff000000000000[ lh=-2673.059726 ](anid:0.11568,(histo7:0.00692,hcap_NA:0.00698,histo6:0.00352)100:0.06375,
((cpos:0.00001,cimm:0.00001)100:0.04597,uree:0.03765)100:0.05282);
[ lh=-2674.559163 ](anid:0.09945,((histo7:0.00607,hcap_NA:0.00607,histo6:0.00607)100
:0.07755,((cpos:0.00001,cimm:0.00001)100:0.03918,uree:0.03919)100:0.04443
):0.01583);
BioPerl-1.007002/t/data/qrna-relloc.out000444000766000024       562113155576321 17644 0ustar00cjfieldsstaff000000000000#---------------------------------------------------------------------------------
#      qrna 1.2b (Tue Dec 18 15:04:38 CST 2001) using squid 1.5m (Sept 1997)
#---------------------------------------------------------------------------------
#      PAM model =  BLOSUM62 scaled by 1.000
#---------------------------------------------------------------------------------
#      RNA model =  /mix_tied_linux.cfg
#---------------------------------------------------------------------------------
#      seq file  =  tst.out
#                   #seqs: 2 (max_len = 290)
#---------------------------------------------------------------------------------
#      window version: window = 150   slide = 50 -- length range = [0,9999999]
#---------------------------------------------------------------------------------
# 1  [+ strand] 
>Contig1/24732-25017 (290)
>chr5.pseudo/527251-527533 (290)

length of whole alignment after removing common gaps: 290 

length alignment: 150 (id=62.67)
posX: 0-149 [0-149](150) -- (0.19 0.25 0.31 0.25) 
posY: 0-149 [0-145](146) -- (0.14 0.31 0.25 0.31) 
 34.327235 39.943369 26.661628
 28.676235 4.323732 17.984592
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = COD 
OTH  ends = 0 149
COD  ends = 0 149
RNA  ends = 76 91
              OTH =       33.356             COD =       38.943             RNA =       25.665 
   logoddspostOTH =        0.000  logoddspostCOD =        5.588  logoddspostRNA =       -7.691 

length alignment: 150 (id=64.00)
posX: 50-199 [50-198](149) -- (0.19 0.26 0.29 0.26) 
posY: 50-199 [47-195](149) -- (0.17 0.29 0.24 0.30) 
 39.662831 22.857014 31.781677
 35.882277 13.531348 24.975088
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 50 199
COD  ends = 51 197
RNA  ends = 76 91
              OTH =       38.764             COD =       21.859             RNA =       30.795 
   logoddspostOTH =        0.000  logoddspostCOD =      -16.905  logoddspostRNA =       -7.970 

length alignment: 150 (id=61.33)
posX: 100-249 [100-246](147) -- (0.24 0.24 0.28 0.23) 
posY: 100-249 [97-243](147) -- (0.22 0.26 0.28 0.24) 
 29.980841 -9.710794 19.504746
 29.998914 -25.369993 19.522819
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 249 100
COD  ends = 100 240
RNA  ends = 250 250
              OTH =       29.990             COD =      -10.711             RNA =       19.514 
   logoddspostOTH =        0.000  logoddspostCOD =      -40.701  logoddspostRNA =      -10.476 

length alignment: 140 (id=62.86)
posX: 150-289 [150-285](136) -- (0.22 0.25 0.27 0.26) 
posY: 150-289 [146-282](137) -- (0.27 0.23 0.26 0.24) 
 27.136986 -17.070736 17.286579
 28.477528 -24.525347 18.465446
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 289 150
COD  ends = 154 288
RNA  ends = 190 290
              OTH =       27.958             COD =      -18.063             RNA =       17.993 
   logoddspostOTH =        0.000  logoddspostCOD =      -46.020  logoddspostRNA =       -9.964 

BioPerl-1.007002/t/data/qualfile.qual000555000766000024      3655613155576321 17420 0ustar00cjfieldsstaff000000000000>Run_SRC3700_2001-03-02_53+54.fasta.screen.Contig1 
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39 39 40 46 46 46 46 51 51 51 51 51 51 45 45 45 51 38 38 39 39 39 39 45 45 45 45 40 40 40 38 38 38 38 38 38 40 40 43 43 43 43 43 43 43 45 45 51 45 45 
45 51 51 51 56 56 51 51 43 43 43 43 43 43 43 35 35 35 35 35 35 43 36 36 43 43 43 36 43 43 43 43 43 43 45 45 45 51 51 51 45 45 45 45 45 45 45 43 43 43 
43 43 43 56 56 56 56 56 56 56 56 56 51 51 51 51 51 51 56 56 56 56 56 56 56 56 56 56 56 56 51 51 45 45 45 45 45 45 43 40 43 43 43 43 43 43 43 43 45 45 
51 51 51 51 45 45 45 51 51 51 51 51 51 51 51 51 43 43 43 43 43 45 56 56 51 45 45 45 43 43 43 43 43 43 43 51 51 51 51 51 51 51 51 56 56 56 51 51 51 51 
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51 51 51 51 51 56 56 51 51 51 51 51 51 51 51 51 56 56 56 56 56 56 56 56 45 45 40 40 40 40 40 40 40 40 40 45 56 40 40 40 40 40 40 39 39 40 40 40 40 51 
51 56 56 56 56 56 51 40 35 35 35 35 35 35 45 51 56 56 51 45 45 45 45 40 40 40 40 40 40 51 51 51 56 56 51 51 51 45 45 45 45 45 45 51 51 40 40 40 40 40 
40 56 56 56 56 56 56 56 56 56 56 56 56 56 56 51 51 51 51 51 51 51 51 51 56 56 51 51 51 45 32 32 29 29 
>Run_SRC3700_2001-03-02_53+54.fasta.screen.Contig2 
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47 47 47 37 37 35 35 35 35 35 35 35 35 35 35 35 35 35 35 42 32 29 29 23 23 23 37 33 35 35 26 26 26 26 29 32 32 32 32 32 35 39 35 42 35 35 35 35 35 35 
56 56 42 35 28 21 20 20 28 35 40 40 37 35 35 35 35 35 35 40 40 35 35 35 35 32 32 32 32 32 35 35 40 41 40 35 35 32 29 35 35 35 32 32 35 43 43 36 56 42 
46 44 50 50 44 44 44 44 44 44 44 44 50 50 42 42 42 42 42 42 42 42 41 42 38 38 38 38 38 40 45 46 43 42 41 41 40 38 38 40 35 35 38 40 35 35 32 33 33 38 
42 42 42 40 43 43 36 36 35 35 32 36 38 42 42 42 41 40 38 35 35 32 32 32 36 36 40 41 41 44 37 37 27 27 27 45 45 45 45 43 43 42 41 41 41 42 38 40 41 41 
41 32 38 38 38 38 43 42 42 42 35 35 35 40 40 41 41 41 41 41 41 42 46 42 38 36 36 32 32 36 36 38 38 40 38 38 50 42 42 42 42 42 42 42 46 46 35 32 33 35 
37 40 43 45 46 42 42 42 44 42 41 45 45 45 45 41 42 42 46 35 32 32 35 35 43 43 56 56 44 42 42 46 42 42 42 50 42 42 40 45 40 40 37 42 42 46 44 50 44 50 
50 50 42 42 40 40 40 45 40 40 29 29 33 46 42 43 42 56 56 44 56 44 40 35 35 35 35 35 37 42 40 40 42 42 44 48 42 40 36 39 35 39 42 44 47 47 42 40 40 40 
40 40 42 56 56 56 37 37 37 35 35 37 42 42 42 37 42 46 40 40 40 42 56 42 44 44 42 37 37 37 37 37 26 28 28 35 35 37 42 42 47 56 42 42 34 34 30 40 33 42 
42 42 42 35 40 40 33 33 26 26 21 29 29 34 29 30 40 40 34 29 25 34 40 40 29 32 27 27 21 15 16 24 29 32 32 32 34 29 31 31 31 31 31 32 35 37 37 40 46 40 
32 32 25 24 24 23 19 20 29 31 27 32 29 29 28 27 30 29 29 31 33 35 35 35 41 39 45 45 52 52 52 52 66 66 52 50 61 61 50 50 47 47 47 47 50 56 50 50 50 50 
50 50 50 36 32 24 29 40 37 34 34 34 40 40 40 40 40 40 40 37 33 33 32 39 29 29 29 28 26 36 24 16 16 22 22 37 40 40 40 37 29 29 29 40 27 24 22 29 29 25 
25 32 25 25 24 28 28 30 32 32 29 21 26 25 25 25 25 15 18 18 18 29 29 29 26 26 26 42 29 29 29 29 32 42 50 35 29 32 35 32 33 29 29 29 29 27 40 29 22 18 
23 25 34 33 32 25 19 19 21 15 10 15 25 31 31 25 21 15 16 19 25 23 29 25 19 19 24 19 22 22 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 
>Run_SRC3700_2001-03-02_53+54.fasta.screen.Contig3 
34 34 49 55 55 66 75 79 80 84 77 77 77 84 84 77 77 72 66 66 55 55 55 54 54 39 39 39 39 51 66 66 61 61 61 61 66 56 56 66 66 84 84 89 77 89 84 86 90 90 
90 90 90 90 90 90 90 71 71 40 35 35 35 35 50 55 50 68 68 56 56 56 84 84 86 78 73 73 66 66 73 81 81 75 75 70 57 57 52 47 47 44 50 56 56 53 53 59 56 61 
66 72 68 70 79 77 78 79 63 63 60 53 50 50 50 50 50 50 35 35 35 35 35 43 40 40 40 35 35 35 52 52 79 82 82 73 64 54 52 50 67 67 78 80 82 82 87 90 90 86 
78 75 71 71 62 66 56 56 60 76 81 84 84 75 75 71 80 75 79 71 71 71 72 77 80 71 71 71 76 71 71 71 71 71 71 56 56 51 51 51 66 66 66 71 79 75 73 74 74 75 
80 74 70 67 62 59 66 70 72 78 88 88 83 86 80 80 81 75 73 70 62 60 60 73 73 76 72 86 80 90 90 88 82 87 81 82 82 84 76 76 70 72 72 82 86 90 85 75 63 61 
59 58 57 61 48 48 45 60 60 70 85 85 72 87 90 90 90 90 85 85 90 90 71 65 71 56 56 51 43 43 43 43 43 45 51 56 56 50 50 50 43 43 35 43 43 43 43 43 43 45 
56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 
56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 
56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 50 48 22 22 21 27 27 33 28 24 19 13 13 13 16 16 21 24 18 18 17 13 12 25 25 25 26 13 13 10 
16 13 23 23 14 14 14 15 19 16 16 12 14 14 12 13 10 10 13 16 12 10 11 10 12 25 21 25 22 29 24 29 29 30 36 33 25 25 15 15 16 27 25 25 15 16 19 12 12 17 
25 18 17 17 22 22 16 16 15 12 12 11 13 15 12 11 12 12 11 13 21 27 27 18 15 14 12 11 10 8 8 16 24 24 13 11 12 25 25 31 29 32 36 41 35 32 29 28 28 18 
18 31 27 14 12 12 11 12 17 15 22 32 30 30 18 15 15 9 10 10 10 13 13 15 15 18 16 15 18 14 18 12 12 15 16 21 11 13 11 21 10 16 18 24 15 14 10 9 13 15 
21 21 11 11 11 19 19 18 17 21 12 12 21 16 11 10 10 15 14 27 15 21 13 13 10 10 14 14 15 19 21 16 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
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>Run_SRC3700_2001-03-02_53+54.fasta.screen.Contig4 
35 29 29 29 29 29 30 40 40 45 51 56 51 51 46 46 40 40 40 37 37 37 46 46 37 35 35 23 24 18 22 30 36 42 42 42 42 46 35 35 35 35 35 35 45 51 42 51 40 40 
40 46 46 46 56 46 46 40 40 40 35 35 35 39 39 39 51 51 51 51 51 51 39 39 35 35 35 35 45 40 51 35 35 35 35 35 35 35 35 35 35 35 35 35 38 38 38 38 40 40 
40 51 51 51 40 40 45 45 45 45 51 51 51 51 51 51 51 51 51 43 43 42 42 46 46 56 56 56 51 51 51 51 51 51 56 56 66 61 61 61 61 61 61 66 61 61 65 90 90 65 
66 66 66 61 61 61 61 61 61 61 61 61 90 90 61 66 66 66 61 53 53 53 53 68 70 81 75 90 90 90 90 90 84 83 84 80 78 79 80 66 66 51 55 54 55 55 70 70 90 87 
89 89 90 90 90 90 90 90 90 90 86 90 90 90 90 90 90 90 90 90 90 81 81 66 66 66 66 66 81 81 81 81 71 76 76 76 76 76 66 66 66 61 61 61 61 61 61 66 66 61 
61 70 70 70 70 66 81 90 90 90 84 77 77 85 90 77 74 74 70 75 79 85 90 90 90 90 88 88 88 90 90 90 90 90 90 90 86 90 90 90 90 90 90 90 90 89 83 83 81 82 
82 82 82 82 87 88 85 87 87 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 87 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 
90 90 90 87 87 89 90 90 87 88 88 86 85 82 84 90 90 90 90 90 89 89 89 89 89 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 87 87 90 
90 90 90 90 90 90 90 90 90 90 90 90 90 81 87 87 90 87 87 90 90 90 90 90 90 90 90 90 90 90 90 82 83 90 90 90 90 90 90 90 90 90 90 90 90 90 85 87 87 90 
90 90 90 90 90 90 90 90 90 87 87 90 87 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 89 89 90 90 89 90 90 87 90 85 87 90 90 
90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 85 89 82 82 82 86 90 85 87 90 89 75 75 78 78 84 82 80 80 77 77 83 87 87 87 89 90 90 90 90 90 90 90 90 90 
90 90 90 81 81 74 84 84 80 84 74 80 80 85 82 90 90 90 87 87 87 87 89 89 88 85 73 69 67 67 71 71 76 84 90 90 90 88 85 90 86 90 77 85 85 90 90 90 90 90 
90 90 82 82 80 80 80 82 85 85 90 90 90 90 90 90 81 79 79 79 73 83 79 84 84 82 72 70 68 59 50 50 50 44 39 44 39 44 50 50 50 54 58 58 50 50 54 54 43 43 
34 38 34 47 47 47 50 45 52 52 48 52 56 52 52 52 52 52 52 43 51 51 51 56 56 56 56 48 48 40 40 40 48 40 40 29 
>Run_SRC3700_2001-03-02_53+54.fasta.screen.Contig5 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 46 40 37 37 40 40 39 39 39 39 39 39 39 40 
40 51 46 46 46 46 46 51 56 51 51 51 51 40 40 40 35 35 35 40 39 39 39 39 39 39 39 39 39 39 39 39 40 51 51 51 56 56 51 40 40 40 39 39 39 40 40 40 40 40 
51 56 56 56 46 46 39 39 39 39 40 45 46 46 40 40 40 40 51 51 39 43 43 43 43 43 45 45 45 45 45 51 43 43 43 43 43 43 43 43 43 45 45 45 45 45 51 56 43 43 
43 43 43 43 43 43 43 43 43 43 43 43 45 45 43 43 43 45 45 43 43 43 43 43 43 56 56 51 45 43 43 43 43 43 43 45 45 45 45 51 51 51 56 56 56 56 51 43 43 43 
43 43 43 45 45 45 43 43 51 45 45 43 43 43 43 43 43 51 43 43 43 43 43 43 43 43 43 43 45 45 45 45 45 45 51 51 51 56 56 56 56 51 51 51 51 51 51 51 51 45 
43 36 36 36 36 36 43 45 45 45 43 43 43 43 43 36 36 36 36 36 36 43 43 43 43 43 43 43 56 56 56 51 51 56 56 56 51 43 43 43 43 43 45 51 43 43 43 43 43 43 
43 43 43 43 45 45 51 45 43 43 43 43 43 45 56 56 56 56 56 56 56 56 56 56 56 51 51 51 56 51 51 51 51 51 51 51 56 56 56 56 56 56 56 56 51 51 51 45 45 45 
45 45 51 45 45 45 45 45 51 56 56 56 56 56 56 56 56 56 56 56 56 51 76 76 80 90 90 90 90 90 90 90 76 74 76 78 82 76 74 76 76 74 74 79 84 83 81 76 76 82 
82 87 90 85 90 85 89 90 90 90 90 90 88 82 82 83 83 85 90 90 90 90 90 90 90 85 81 81 81 87 84 90 88 88 88 90 90 90 89 90 90 85 90 90 90 90 90 82 81 82 
90 89 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 82 82 78 82 74 81 87 90 87 90 90 88 85 82 90 90 90 90 90 90 90 90 90 90 90 80 78 82 87 90 90 90 
90 90 90 90 90 90 90 90 90 90 90 90 90 84 80 74 77 79 81 80 83 87 90 90 90 90 90 90 90 90 90 76 76 81 61 61 53 53 53 68 70 77 90 81 81 76 87 87 90 90 
90 90 90 83 79 80 80 90 90 90 88 85 87 80 87 81 76 76 81 81 90 90 90 90 90 90 86 86 86 90 85 90 90 85 85 82 78 73 67 72 75 67 61 68 55 55 55 32 39 34 
16 15 4 
>Run_SRC3700_2001-03-02_53+54.fasta.screen.Contig6 
56 56 56 56 56 56 56 56 56 56 56 56 56 51 51 61 61 61 61 66 61 61 61 61 61 61 61 61 61 61 61 61 61 55 55 55 61 61 61 66 66 66 66 66 66 61 61 61 61 61 
61 85 86 85 61 61 61 55 61 61 61 76 70 79 79 78 84 70 68 68 68 68 68 76 76 85 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 
90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 85 81 81 81 81 81 90 
90 90 88 88 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 88 87 87 90 90 88 88 90 90 88 88 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 
90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 
90 90 90 90 90 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 
90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 
90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 81 81 81 88 
86 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 86 86 88 86 86 86 86 86 86 88 88 88 90 90 90 90 90 90 90 90 88 90 90 90 90 90 90 90 90 
90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 82 82 82 82 78 80 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 
90 90 90 90 90 90 90 90 90 90 90 90 88 90 90 87 80 80 80 80 80 83 90 90 90 90 90 90 90 89 83 83 83 78 78 78 78 86 86 86 90 90 90 90 88 88 80 80 80 80 
80 80 90 90 90 80 80 80 88 88 88 90 90 90 85 85 85 85 83 83 90 83 83 83 83 83 88 85 82 85 85 85 85 83 86 86 86 86 86 90 90 85 90 90 90 90 90 90 90 89 
86 79 72 68 69 77 90 74 77 67 70 68 67 69 69 71 79 79 79 79 79 80 80 83 83 86 86 90 90 80 74 74 69 69 70 87 85 85 80 84 80 72 67 67 65 62 62 72 80 80 
85 79 83 83 85 90 90 62 62 58 54 57 60 80 70 64 75 75 64 64 64 64 57 59 65 71 71 65 72 70 83 70 72 72 57 52 59 59 58 57 57 62 78 66 71 71 73 74 74 66 
66 61 61 61 55 54 54 35 35 35 
>Run_SRC3700_2001-03-02_53+54.fasta.screen.Contig7 
0 0 27 28 48 48 48 48 48 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 47 56 56 56 56 56 56 56 47 47 47 48 48 48 48 56 56 56 56 56 56 56 56 
48 48 56 56 56 56 56 56 56 56 56 56 56 56 56 48 48 35 35 45 45 47 49 55 55 55 55 50 61 61 61 56 56 56 56 61 61 66 66 66 66 66 66 61 61 61 61 61 61 66 
66 66 66 66 66 55 50 50 65 65 66 70 81 81 81 85 90 90 81 81 81 90 87 88 84 86 86 90 90 90 90 90 90 90 85 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 
90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 
90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 88 88 88 87 87 90 90 90 90 
90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 88 88 90 89 89 90 90 90 90 90 90 90 90 90 90 90 
90 90 90 90 90 90 90 90 90 90 90 90 90 89 89 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 84 84 82 82 84 
90 90 90 90 90 90 90 90 90 90 90 90 89 89 89 89 88 88 90 90 90 89 89 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 
90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 89 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 
90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 84 89 89 90 
90 90 90 90 77 77 75 75 86 90 90 90 90 90 90 90 90 90 90 90 90 81 81 76 88 83 76 70 77 73 63 66 66 75 76 82 66 72 69 73 61 67 52 52 52 39 39 40 40 40 
55 66 55 68 75 79 86 86 90 90 81 81 54 50 50 50 55 50 52 35 35 35 
>Run_SRC3700_2001-03-02_53+54.fasta.screen.Contig8 
56 56 56 56 51 61 61 61 53 53 53 53 53 53 61 61 61 61 61 61 55 55 55 55 55 53 53 53 53 53 53 61 66 66 61 61 66 66 66 61 61 66 66 66 66 66 66 66 53 53 
53 53 53 53 55 55 55 55 55 55 55 55 55 61 61 55 53 53 53 53 53 61 61 55 55 53 53 53 53 53 53 53 53 53 56 53 61 61 61 61 61 66 66 66 66 66 66 66 66 66 
66 61 53 53 53 53 53 53 53 61 61 61 61 66 66 61 53 53 53 53 53 53 66 66 61 53 53 46 46 49 49 49 53 56 61 61 55 53 53 53 53 53 53 53 53 53 61 61 66 53 
53 53 53 53 53 53 53 53 55 66 66 66 66 66 66 66 66 55 55 53 53 53 53 53 53 53 55 55 61 61 53 53 53 53 53 53 53 53 53 53 53 53 55 55 55 61 61 61 61 61 
61 61 61 61 66 55 53 53 53 53 53 53 53 53 53 53 55 66 66 61 56 53 53 53 54 61 66 66 66 66 66 66 66 66 66 66 66 66 66 66 53 53 53 53 53 50 55 55 55 55 
55 55 55 55 50 61 61 55 55 55 61 55 55 66 66 66 66 66 55 55 61 55 55 55 61 61 66 66 66 66 66 61 55 50 50 50 50 50 55 61 55 55 61 61 61 55 56 61 61 61 
61 61 61 61 61 61 66 56 53 56 55 50 50 50 50 50 50 50 50 55 55 55 45 45 45 45 45 45 61 66 66 66 61 55 55 55 55 55 55 50 50 50 47 47 50 61 61 66 66 66 
61 55 55 55 50 50 50 55 55 55 66 66 61 50 50 50 50 50 50 50 47 47 47 50 58 56 54 54 43 43 42 35 35 35 58 58 58 46 44 44 39 41 44 50 66 66 66 50 50 47 
47 50 56 61 61 55 55 55 50 50 50 50 50 50 61 50 50 50 50 50 58 54 54 58 56 50 50 50 50 49 49 42 42 42 35 35 32 35 40 42 50 46 49 46 50 50 44 44 44 42 
42 43 46 46 50 56 56 56 56 54 54 50 50 58 58 44 44 39 50 50 50 54 54 58 58 58 56 56 50 50 39 44 44 42 37 37 39 35 39 44 50 50 58 49 49 39 39 39 44 44 
50 50 58 34 28 15 15 15 29 32 35 34 32 30 35 33 30 30 42 58 58 58 58 50 43 43 39 42 39 39 37 29 25 23 25 25 29 29 34 40 40 33 32 25 25 25 27 32 32 29 
29 29 34 40 40 29 29 29 29 29 29 26 25 25 35 31 27 25 24 25 40 29 25 24 25 25 22 24 27 23 19 9 9 9 17 20 24 24 25 25 22 24 34 34 37 34 34 48 34 
BioPerl-1.007002/t/data/quoted-strings1.nex000444000766000024        72513155576321 20441 0ustar00cjfieldsstaff000000000000#NEXUS

BEGIN TAXA;
      dimensions ntax=8;
      taxlabels A B "OTU C" D E F G H;
END;

BEGIN CHARACTERS;
      dimensions nchar=5;
      format datatype=protein missing=? gap=-;
      charlabels One Two "Char 3" Four Five;
      matrix
A     --ONE
B     --ONE
"OTU C"     TWO--
D     THREE
E     F-OUR
F     FIVE-
G     SIX--
H     SEVEN;
END;

BEGIN TREES;
       tree "the ladder tree" =
       (((((((A:1,B:1):1,"OTU C":2):1,D:3):1,E:4):1,F:5):1,G:6):1,H:7);
END;BioPerl-1.007002/t/data/quoted-strings2.nex000444000766000024        72513155576321 20442 0ustar00cjfieldsstaff000000000000#NEXUS

BEGIN TAXA;
      dimensions ntax=8;
      taxlabels A B 'OTU C' D E F G H;
END;

BEGIN CHARACTERS;
      dimensions nchar=5;
      format datatype=protein missing=? gap=-;
      charlabels One Two 'Char 3' Four Five;
      matrix
A     --ONE
B     --ONE
'OTU C'     TWO--
D     THREE
E     F-OUR
F     FIVE-
G     SIX--
H     SEVEN;
END;

BEGIN TREES;
       tree 'the ladder tree' =
       (((((((A:1,B:1):1,'OTU C':2):1,D:3):1,E:4):1,F:5):1,G:6):1,H:7);
END;BioPerl-1.007002/t/data/radical-whitespace.nex000444000766000024       151113155576321 21133 0ustar00cjfieldsstaff000000000000#NEXUS

BEGIN TAXA;
      dimensions ntax=7;
      taxlabels A 

B 
C 
             D      E     F      G;  
END;

BEGIN CHARACTERS;
      dimensions nchar=5;
      format datatype=protein missing=? gap=-;
      charlabels 1

 2

 3

 4

5

;
      matrix
A     -      -O      N E      
B             -   -  ON          E
C TWO        --               
D             TH               RE              E
E   F                         -OU R
F     F           I             V      E-
G            S             I         X-             -                 ;
END
;

BEGIN TREES;
       tree radical_whitespace = (
(
 (
  (
   (
    (A:1,
         B:1):1,
                C:2):1,
                       D:3):1,
                              E:4):1,
                                     F:5):1,
                                            G:6)
;
END;BioPerl-1.007002/t/data/radical-whitespace_02.nex000444000766000024       153713155576321 21444 0ustar00cjfieldsstaff000000000000#NEXUS

BEGIN TAXA;
      dimensions ntax=7;
      taxlabels A 

B 
C 
             D      E     F      G;  
END;

BEGIN CHARACTERS;
      dimensions nchar=5;
      format datatype=protein missing=? gap=-;
      charlabels 1

 2

 3

 4

5

;
      matrix
A     -      -O      N E      
B             -   -  ON          E
C TWO        --               
D             TH               RE              E
E   F                         -OU R
F     F           I             V      E-
G            S             I         X-             -
                 ;   
                 
END
;

BEGIN TREES;
       tree radical_whitespace = (
(
 (
  (
   (
    (A:1,
         B:1):1,
                C:2):1,
                       D:3):1,
                              E:4):1,
                                     F:5):1,
                                            G:6)
;
END;BioPerl-1.007002/t/data/rebase.itype2000444000766000024       173613155576321 17276 0ustar00cjfieldsstaff000000000000 
REBASE version 307                                              itype2.307
 
    =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
    REBASE, The Restriction Enzyme Database   http://rebase.neb.com
    Copyright (c)  Dr. Richard J. Roberts, 2003.   All rights reserved.
    =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
 
Rich Roberts                                                    Jun 29 2003
 
AaaI	XmaIII	C^GGCCG			1204
AagI	ClaI	AT^CGAT			1157
AaqI	ApaLI	GTGCAC			973
AarI		CACCTGC(4/8)		F	362,701
AasI	DrdI	GACNNNN^NNGTC		F	536
AatI	StuI	AGG^CCT		O	1046,1189
AatII		GACGT^C		AFGIKMNOR	1189
AbeI	BbvCI	CCTCAGC(-5/-2)			1296
AbrI	XhoI	C^TCGAG			1068
AccI		GT^MKAC	5(6)	AEGJKMNORSU	528,684,1413
AccII	FnuDII	CG^CG		AJK	561,1413
AccIII	BspMII	T^CCGGA		EGJKR	562,822
AciI		CCGC(-3/-1)	?(5),-2(5)	N	926
Bsp24I		(8/13)GACNNNNNNTGG(12/7)			261
AloI		(7/12)GAACNNNNNNTCC(12/7)	3(6),-3(6)	F	154,1050
TaqII		GACCGA(11/9),CACCCA(11/9)		X	67,822,1030
BioPerl-1.007002/t/data/rebase.withrefm000444000766000024      2424513155576321 17727 0ustar00cjfieldsstaff000000000000 
REBASE version 304                                              withrefm.304
 
    =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
    REBASE, The Restriction Enzyme Database   http://rebase.neb.com
    Copyright (c)  Dr. Richard J. Roberts, 2003.   All rights reserved.
    =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
 
Rich Roberts                                                    Mar 24 2003
 

   Restriction enzyme name.
 Other enzymes with this specificity.
 
                These are written from 5' to 3', only one strand being given.
                If the point of cleavage has been determined, the precise site
                is marked with ^.  For enzymes such as HgaI, MboII etc., which
                cleave away from their recognition sequence the cleavage sites
                are indicated in parentheses.  

                For example HgaI GACGC (5/10) indicates cleavage as follows:
                                5' GACGCNNNNN^      3'
                                3' CTGCGNNNNNNNNNN^ 5'

                In all cases the recognition sequences are oriented so that
                the cleavage sites lie on their 3' side.

                REBASE Recognition sequences representations use the standard 
                abbreviations (Eur. J. Biochem. 150: 1-5, 1985) to represent 
                ambiguity.
                                R = G or A
                                Y = C or T
                                M = A or C
                                K = G or T
                                S = G or C
                                W = A or T
                                B = not A (C or G or T)
                                D = not C (A or G or T)
                                H = not G (A or C or T)
                                V = not T (A or C or G)
                                N = A or C or G or T



                ENZYMES WITH UNUSUAL CLEAVAGE PROPERTIES:  

                Enzymes that cut on both sides of their recognition sequences,
                such as BcgI, Bsp24I, CjeI and CjePI, have 4 cleavage sites
                each instead of 2.

                Bsp24I
                          5'      ^NNNNNNNNGACNNNNNNTGGNNNNNNNNNNNN^   3'
                          3' ^NNNNNNNNNNNNNCTGNNNNNNACCNNNNNNN^        5'


                This will be described in some REBASE reports as:

                             Bsp24I (8/13)GACNNNNNNTGG(12/7)


                The site of methylation by the cognate methylase when known
                is indicated X(Y) or X,X2(Y,Y2), where X is the base within
                the recognition sequence that is modified.  A negative number
                indicates the complementary strand, numbered from the 5' base 
                of that strand, and Y is the specific type of methylation 
                involved:
                               (6) = N6-methyladenosine 
                               (5) = 5-methylcytosine 
                               (4) = N4-methylcytosine

                If the methylation information is different for the 3' strand,
                X2 and Y2 are given as well.

 Organism from which this enzyme had been isolated.
        Either an individual or a National Culture Collection.

                Each commercial source of restriction enzymes and/or methylases
                listed in REBASE is assigned a single character abbreviation 
                code.  For example:

                K        Takara (1/98)
                M        Boehringer Mannheim (10/97)
                N        New England Biolabs (4/98)
 
                The date in parentheses indicates the most recent update of 
                that organization's listings in REBASE.

only the primary references for the isolation and/or purification
of the restriction enzyme or methylase, the determination of the recognition
sequence and cleavage site or the methylation specificity are given.


REBASE codes for commercial sources of enzymes

                A        Amersham Pharmacia Biotech (1/03)
                C        Minotech Biotechnology (6/01)
                E        Stratagene (1/03)
                F        Fermentas AB (1/03)
                G        Qbiogene (1/03)
                H        American Allied Biochemical, Inc. (10/98)
                I        SibEnzyme Ltd. (1/03)
                J        Nippon Gene Co., Ltd. (6/00)
                K        Takara Shuzo Co. Ltd. (1/03)
                M        Roche Applied Science (1/03)
                N        New England Biolabs (1/03)
                O        Toyobo Biochemicals (11/98)
                P        Megabase Research Products (5/99)
                Q        CHIMERx (1/03)
                R        Promega Corporation (1/03)
                S        Sigma Chemical Corporation (1/03)
                U        Bangalore Genei (1/03)
                V        MRC-Holland (1/03)
                X        EURx Ltd. (1/03)

<1>AaaI
<2>XmaIII,BseX3I,BsoDI,BstZI,EagI,EclXI,Eco52I,SenPT16I,TauII,Tsp504I
<3>C^GGCCG
<4>
<5>Acetobacter aceti ss aceti
<6>M. Fukaya
<7>
<8>Tagami, H., Tayama, K., Tohyama, T., Fukaya, M., Okumura, H., Kawamura, Y., Horinouchi, S., Beppu, T., (1988) FEMS Microbiol. Lett., vol. 56, pp. 161-166.

<1>AacI
<2>BamHI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I
<3>GGATCC
<4>
<5>Acetobacter aceti sub. liquefaciens
<6>IFO 12388
<7>
<8>Seurinck, J., van Montagu, M., Unpublished observations.

<1>AaeI
<2>BamHI,AacI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I
<3>GGATCC
<4>
<5>Acetobacter aceti sub. liquefaciens
<6>M. Van Montagu
<7>
<8>Seurinck, J., van Montagu, M., Unpublished observations.

<1>AagI
<2>ClaI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Achromobacter agile
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Maneliene, Z.P., Butkus, V.V., Fitzner, A.B., Khoroshutina, E.B., Kalugin, A.A., Janulaitis, A., (1990) Bioorg. Khim., vol. 16, pp. 1040-1044.

<1>AamI
<2>
<3>?
<4>
<5>Azospirillum amazonense
<6>G. Schwabe
<7>
<8>Schwabe, G., Posseckert, G., Klingmuller, W., (1985) Gene, vol. 39, pp. 113-116.

<1>AaqI
<2>ApaLI,Alw44I,AmeI,Bsp146I,DaqI,Pfl23I,Pfr12I,PliI,ScoNI,SnoI,Uba1203I,Uba1387I,VneI
<3>GTGCAC
<4>
<5>Alcaligenes aquamarinus 559
<6>V.E. Repin
<7>
<8>Repin, V.E., Unpublished observations.

<1>AarI
<2>
<3>CACCTGC(4/8)
<4>
<5>Arthrobacter aurescens SS2-322
<6>A. Janulaitis
<7>F
<8>Grigaite, R., Maneliene, Z., Janulaitis, A., (2002) Nucleic Acids Res., vol. 30.
Maneliene, Z., Zakareviciene, L., Unpublished observations.

<1>AasI
<2>DrdI,DseDI
<3>GACNNNN^NNGTC
<4>
<5>Arthrobacter aurescens RFL3
<6>V. Butkus
<7>F
<8>Kazlauskiene, R., Vaitkevicius, D., Maneliene, Z., Trinkunaite, L., Kiuduliene, L., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>AatI
<2>StuI,Asp78I,AspMI,ChyI,Eco147I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGG^CCT
<4>
<5>Acetobacter aceti
<6>IFO 3281
<7>O
<8>Sato, H., Yamada, Y., (1990) J. Gen. Appl. Microbiol., vol. 36, pp. 273-277.
Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Nucleic Acids Res., vol. 10, pp. 5747-5752.

<1>TaqII
<2>
<3>GACCGA(11/9),CACCCA(11/9)
<4>
<5>Thermus aquaticus YTI
<6>J.I. Harris
<7>X
<8>Barker, D., Hoff, M., Oliphant, A., White, R., (1984) Nucleic Acids Res., vol. 12, pp. 5567-5581.
Myers, P.A., Roberts, R.J., Unpublished observations.
Rutkowska, S.M., Jaworowska, I., Skowron, P.M., Unpublished observations.

<1>M.PhiBssHII
<2>MluI,ApeI,Bbi24I,BstZ9I,Uba6I
<3>ACGCGT,CCGCGG,RGCGCY,RCCGGY,GCGCGC
<4>2(5), 2(5), 3(5), 2(5), 2(5)
<5>Bacillus stearothermophilus H3
<6>ATCC 49820
<7>
<8>Schumann, J., Walter, J., Willert, J., Wild, C., Koch, D., Trautner, T.A., (1996) J. Mol. Biol., vol. 257, pp. 949-959.
Schumann, J., Willert, J., Wild, C., Waler, J., Trautner, T.A., (1995) Gene, vol. 157, pp. 103-104.

<1>AloI
<2>
<3>(7/12)GAACNNNNNNTCC(12/7)
<4>3(6),-3(6)
<5>Acinetobacter lwoffi Ks 4-8
<6>V. Butkus
<7>F
<8>Cesnaviciene, E.E., Petrusyte, M.M., Kazlauskiene, R.R., Maneliene, Z., Timinskas, A., Lubys, A., Janulaitis, A., (2001) J. Mol. Biol., vol. 314, pp. 205-216.
Savelskiene, A., Petrusyte, M., Padegimiene, E., Vonseviciene, E., Kiuduliene, E., Butkus, V., Janulaitis, A., Unpublished observations.
BioPerl-1.007002/t/data/reference_ace.ace000444000766000024      3533313155576321 20137 0ustar00cjfieldsstaff000000000000AS 1 8

CO Contig1 1475 8 156 U
agccccgggccgtggggttccttgagcactcccaaagttccaacccagga
tgtccccgacgcttaaaccttccaagtctgaaacgggaaatttgatttgc
gggctaggataaacgccggggagaaaggcagaactgccttttacccccca
aggatatcccttgggaagggcccctttgcactcagctgctccctaattat
ggcgatcctccctctatctttgtccccctgtctttcaggatccctctcAA
CAACAgaccaCTCccattaaaGAAATCtccttctgatctgcgggatcACA
TAAAACAGTGCCattcAAaAcgtcccttcCcccAATGTCtaagtgTggtg
gagcCcttcctgcCCggctctgtgcacccacggtgcctgcatgaccccgg
atGCAGTGTGCACCAGctCCCATCATTCAAgagCATGACTGTGTTGCCAA
CCAGCcacCAGGCACTGGGGAGGGAGCtgaGGGAGCAcaaAAGGGATGAG
CCACCCTCTGTcCcagAAGTGGAGGGCATGGGGCTTGGCTGGGCTTAGAG
CTAACATACACAGGATGCTGAAAAAGAACAACACAAggtGTGTGGAGCAA
AGGAAAGGGAAATCAGCTTGAAGCTGATGTTAGTGTGCTTGGGCTGAGTA
CAGCCATGCTCTCAGTTGAGGCACGGTTGGCTCCCCATGGGCAAGATCCC
TCCTGGCCCATCTCTCCTCTTATTCTCTATCCCTTCCCCAGGTCCCTGCC
TTAGAGGTTTCACCAGAGCACAGCTCCTGCCTGTGGCCAAAACAGTATTT
GGCCACTCACCGACCCAGTGTCAGC*ATCCAGATGGGTTCCACATCTCAC
AACCCT*GAGCAGCAGAGAAGGGTTTGAAAGGCCAGGGGAG*AATGAAGA
CGAAGGAGG*TGTTGGCAACAACACAGA*G*AGTCAGCAGCCAGAACGCC
AGGTATCCACACACATAAGACATTCTAAATTTTTACTCAACAGAAATTGT
CTATGTCTGTGTCTGGGCACCATGGCAACACCTTATCTCTACAAAAATTA
GCGGAATGTAGTGGTGCCTGTGTGTAGTCCCAGCTATTCAAGAGGCTGAA
GTGGGAGGATTGCTTGAGCCATGGAAGTCAAGGCTGTAGTGAGCCATGAT
TGTGTCAATGCACTCCAGACAGAGCAAGACCCTGCTCCCACCACACACCT
CaaacgaaAAAAAAaaagggcaaagatatgaactgaaatggaatatag*a
gcagcaaaaggaacagaaaattgtctatgcctggttctctagtcatgtgc
agaacagacagtatcccggccctattgagttcttggggcagttaggcttg
tgcacccttgcttctatgccacagttagggcattcgggattcccatcctt
ttccccggggttgctttttgtttgcgattaccttttcggaacaatggggg
gaaattattttccaagttgggtttg

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 22
 23 26 24 25 25 17 17 13 14 19 21 22 22 17 17 11 8 7 10 13 18 23 28 28 31 31 32 18 18 10 10 10 12 15 8 6 6 8 8 10 15 9 11 12 15 14 15 20 20 28
 30 31 24 24 22 24 25 28 23 27 24 27 18 15 15 16 21 23 18 20 13 8 7 7 12 10 9 10 10 21 12 14 14 28 27 32 24 23 20 19 15 17 15 17 19 20 13 13 13 14
 14 10 10 10 23 10 10 10 10 10 11 11 18 25 24 10 10 10 10 10 14 10 11 11 11 13 12 12 10 12 10 10 10 10 10 10 14 10 12 10 10 10 10 10 10 10 14 13 15 15
 17 19 24 32 37 37 37 37 32 30 30 30 28 23 23 25 15 15 20 27 32 23 22 22 27 32 34 34 21 21 12 12 12 24 32 41 45 45 37 45 45 45 45 45 37 37 37 41 41 37
 37 37 41 32 32 14 14 19 32 28 37 37 41 41 45 45 37 37 37 30 30 32 32 37 37 32 28 16 16 17 32 32 37 45 37 25 25 9 9 9 25 25 37 37 37 37 37 45 40 37
 37 37 45 45 37 37 37 37 38 25 25 12 25 10 10 15 32 47 52 62 62 55 43 43 34 43 43 58 58 78 77 72 72 70 70 70 74 77 69 68 55 55 55 57 61 65 70 73 68 61
 64 58 56 56 64 65 67 70 70 75 79 70 70 70 70 70 70 67 71 71 71 84 63 63 62 62 62 59 59 61 61 64 64 49 42 32 10 6 18 32 35 46 47 48 47 47 47 55 55 55
 55 49 46 47 47 55 55 55 54 47 47 47 48 48 54 54 54 48 48 55 47 47 47 55 49 48 48 48 55 47 48 48 47 47 47 46 48 48 48 50 44 43 44 44 49 49 73 75 82 78
 74 66 66 58 54 60 68 68 61 63 47 57 45 74 85 78 70 65 62 61 61 55 73 65 59 61 75 77 80 86 81 81 83 85 85 85 90 84 78 78 73 75 78 77 86 75 76 83 79 84
 87 78 72 75 72 72 76 79 82 88 90 89 89 89 89 89 90 90 90 85 85 79 83 83 90 90 90 90 90 90 90 90 90 90 90 90 90 89 89 89 90 90 90 90 90 90 90 90 90 90
 90 90 90 81 66 66 62 62 62 73 89 90 90 86 86 86 86 88 88 90 90 90 90 90 90 90 88 71 68 61 61 66 66 70 65 64 70 70 76 90 90 90 90 90 90 85 90 90 90 87
 87 79 79 79 79 89 74 65 71 72 79 73 73 70 75 79 76 81 81 83 80 87 89 90 82 82 90 88 88 88 88 89 86 77 77 80 79 79 79 90 90 90 90 79 79 61 58 53 76 63
 57 65 76 76 76 80 89 89 89 90 90 90 90 88 88 88 88 88 88 90 90 90 90 90 90 90 90 90 90 88 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90 83 79 58 43
 45 68 70 61 75 76 73 68 84 88 90 90 90 90 90 89 72 54 62 62 53 55 55 80 83 80 80 83 85 83 87 83 83 83 85 85 86 86 84 81 83 82 77 78 76 76 77 77 80 88
 88 87 90 90 90 90 85 84 82 71 75 62 62 37 68 75 77 74 70 71 70 72 72 80 80 80 84 83 82 66 70 55 55 55 37 55 55 55 55 55 55 55 55 54 55 55 55 48 47 47
 47 47 47 47 47 47 47 47 55 50 50 50 47 47 47 47 44 44 55 48 51 51 54 54 54 54 54 55 54 54 55 55 55 55 55 55 55 55 55 55 55 55 55 51 51 51 54 51 61 61
 61 61 61 61 44 42 34 34 37 37 37 44 47 47 47 61 61 61 61 61 61 61 47 49 48 47 55 54 55 55 55 55 55 44 44 44 44 46 43 43 44 44 44 51 44 47 44 34 44 44
 44 44 39 39 43 42 50 42 42 38 37 38 41 50 52 55 47 47 39 44 44 46 41 42 40 43 40 41 42 38 37 42 55 50 44 44 46 48 55 55 55 37 34 34 33 42 47 42 42 42
 42 55 46 46 46 48 47 48 46 43 41 39 42 39 44 44 44 48 48 38 36 36 38 38 38 44 44 44 44 44 44 42 42 36 41 40 36 36 30 33 32 29 28 28 23 12 16 10 8 8
 13 14 23 20 21 28 28 31 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF K26-217c U 498
AF K26-526t U 510
AF K26-961c U 577
AF K26-394c U 797
AF K26-291s U 828
AF K26-822c U 883
AF K26-572c C 1
AF K26-766c C 408
BS 1 515 K26-572c
BS 516 516 K26-217c
BS 517 521 K26-572c
BS 522 529 K26-217c
BS 530 538 K26-572c
BS 539 569 K26-217c
BS 570 571 K26-526t
BS 572 573 K26-217c
BS 574 579 K26-526t
BS 580 584 K26-217c
BS 585 591 K26-526t
BS 592 592 K26-217c
BS 593 601 K26-526t
BS 602 604 K26-217c
BS 605 606 K26-526t
BS 607 607 K26-217c
BS 608 621 K26-526t
BS 622 628 K26-217c
BS 629 629 K26-526t
BS 630 630 K26-217c
BS 631 633 K26-526t
BS 634 634 K26-217c
BS 635 635 K26-526t
BS 636 639 K26-217c
BS 640 646 K26-526t
BS 647 648 K26-217c
BS 649 649 K26-526t
BS 650 650 K26-217c
BS 651 654 K26-766c
BS 655 655 K26-961c
BS 656 656 K26-217c
BS 657 669 K26-961c
BS 670 675 K26-217c
BS 676 676 K26-961c
BS 677 688 K26-217c
BS 689 693 K26-526t
BS 694 696 K26-217c
BS 697 698 K26-526t
BS 699 700 K26-961c
BS 701 706 K26-217c
BS 707 707 K26-961c
BS 708 708 K26-217c
BS 709 709 K26-961c
BS 710 710 K26-526t
BS 711 775 K26-961c
BS 776 776 K26-766c
BS 777 777 K26-961c
BS 778 834 K26-766c
BS 835 837 K26-961c
BS 838 840 K26-394c
BS 841 882 K26-766c
BS 883 884 K26-394c
BS 885 898 K26-766c
BS 899 899 K26-961c
BS 900 900 K26-766c
BS 901 901 K26-961c
BS 902 934 K26-766c
BS 935 935 K26-394c
BS 936 936 K26-766c
BS 937 937 K26-394c
BS 938 940 K26-766c
BS 941 944 K26-394c
BS 945 945 K26-291s
BS 946 948 K26-822c
BS 949 949 K26-766c
BS 950 951 K26-822c
BS 952 954 K26-766c
BS 955 955 K26-822c
BS 956 957 K26-394c
BS 958 962 K26-822c
BS 963 963 K26-394c
BS 964 970 K26-822c
BS 971 971 K26-394c
BS 972 972 K26-822c
BS 973 973 K26-394c
BS 974 976 K26-822c
BS 977 979 K26-394c
BS 980 986 K26-291s
BS 987 987 K26-394c
BS 988 1004 K26-822c
BS 1005 1009 K26-394c
BS 1010 1012 K26-291s
BS 1013 1014 K26-394c
BS 1015 1021 K26-822c
BS 1022 1022 K26-394c
BS 1023 1026 K26-822c
BS 1027 1028 K26-291s
BS 1029 1036 K26-822c
BS 1037 1052 K26-291s
BS 1053 1053 K26-822c
BS 1054 1060 K26-291s
BS 1061 1061 K26-822c
BS 1062 1062 K26-291s
BS 1063 1065 K26-394c
BS 1066 1068 K26-822c
BS 1069 1079 K26-291s
BS 1080 1081 K26-822c
BS 1082 1082 K26-291s
BS 1083 1084 K26-822c
BS 1085 1089 K26-291s
BS 1090 1094 K26-822c
BS 1095 1096 K26-394c
BS 1097 1099 K26-822c
BS 1100 1100 K26-291s
BS 1101 1104 K26-822c
BS 1105 1105 K26-394c
BS 1106 1110 K26-822c
BS 1111 1115 K26-291s
BS 1116 1122 K26-822c
BS 1123 1124 K26-291s
BS 1125 1135 K26-822c
BS 1136 1136 K26-394c
BS 1137 1139 K26-822c
BS 1140 1140 K26-291s
BS 1141 1150 K26-822c
BS 1151 1155 K26-291s
BS 1156 1161 K26-822c
BS 1162 1164 K26-291s
BS 1165 1167 K26-822c
BS 1168 1173 K26-291s
BS 1174 1175 K26-822c
BS 1176 1189 K26-291s
BS 1190 1196 K26-822c
BS 1197 1199 K26-291s
BS 1200 1221 K26-822c
BS 1222 1225 K26-291s
BS 1226 1227 K26-822c
BS 1228 1228 K26-394c
BS 1229 1231 K26-291s
BS 1232 1233 K26-822c
BS 1234 1235 K26-291s
BS 1236 1236 K26-394c
BS 1237 1239 K26-291s
BS 1240 1242 K26-822c
BS 1243 1244 K26-291s
BS 1245 1247 K26-394c
BS 1248 1255 K26-822c
BS 1256 1256 K26-291s
BS 1257 1257 K26-394c
BS 1258 1258 K26-291s
BS 1259 1259 K26-822c
BS 1260 1260 K26-394c
BS 1261 1265 K26-291s
BS 1266 1266 K26-822c
BS 1267 1268 K26-394c
BS 1269 1269 K26-822c
BS 1270 1275 K26-291s
BS 1276 1280 K26-822c
BS 1281 1281 K26-394c
BS 1282 1290 K26-822c
BS 1291 1292 K26-291s
BS 1293 1294 K26-822c
BS 1295 1297 K26-291s
BS 1298 1301 K26-822c
BS 1302 1302 K26-291s
BS 1303 1475 K26-822c

RD K26-217c 563 0 0
tcccCgtgagatcatcctgaAGTGGAGGGCATGGGGCTTGGCTGGGCTTA
GAGCTAACATACACAGGATGCTGAAAAAGAACAACACAAgntGTGTGGAG
CAAAGGAAAGGGAAATCAGCTTGAAGCTGATGTTAGTGTGCTTGGGCTGA
GTACAGCCATGctntCAGTTGAGGCACGGTTGGCTCCCCATGGGCAAGAT
CCCTCCTGGCCCATCTCTCCTCTTATTCTCTATCCCTTCCCCAGGTCCCT
GCCTTAGAGGTTTCACCAGAGCACAGCTCCTGcctgtggccaAAACAGTA
TTTGGCCACTCACcGAcccagTGTCAGC*atccaGatggGtTccacatct
cacaaccct*gggcagcagagaaggggtttaaaggccagggggg*tatta
agccgaaggagg*ttttggaaacaccaaggg*g*ggtcagaccccaacgc
cagtttccccaaaaaggggcattcaaatttttttctcagagattttcttt
ccttttttgggccccgggaaccttttttaaaaaatgggggattgggcccc
cttggcccccctc

QA 19 349 19 424
DS CHROMAT_FILE: K26-217c PHD_FILE: K26-217c.phd.1 TIME: Thu Sep 12 15:42:38 1996
RD K26-526t 687 0 0
ccgtcctgagtggAGggcatggggcttggctggGCTTAGAGCTAACATAC
ACAGGATGCTGAAAAAGAACAACACAAggtGTGTGGAGCAAAGGAAAGGG
AAATCAGCTTGAAGCTGATGTTAGTGTGCTTGGGCTGAGTACagcnatgc
tntgaGTTGAggaacgGTTGGCTCCCCATGGGCAAGATCCCTCCTGGCCC
ATCTCTCCTCTTATTCTCTATCCCTTCCCCAGGTCCCTGCCTTAGAGGTT
TCACcAgAGCACAgCTCctgcctgtggccaAAACAGTATTTGGccACTCA
CCGAcCCAGTGTcagt*atccAGATGGGttccACATCtcacagcccT*Ga
gcAgcagngaaGGGTttgaaagggcAgggggggaatgaaGacggaggagg
gtgttggcaaccacacaga*ggagtcaggaggcaggacggcaggtatccA
Cacacattaggcattttaaatttttacttaacaggaattgtctatggctg
ggtttgggaac*atgggaacacctattcttt*caaaa*ttggggggat*t
agtggtgc*tgt*tatagtcccgttattaaGggttaagtggggtttcttt
gccaggaggtaaggtttggggccctatttttaattacttggaaggaagcc
ttttcccagataaggaaaaaggaggtTTtttgtttta

QA 12 353 9 572
DS CHROMAT_FILE: K26-526t PHD_FILE: K26-526t.phd.1 TIME: Thu Sep 12 15:42:33 1996
RD K26-961c 517 0 0
aatattaccggcgcggggttCcgTCGGAAAGGGAAATCAGCTTGAAGCTG
ATGTTAGTGTGCTTGgGCTGAGTacaGCCATGCTCTCAGTTGAGGCACGG
TTGGCTCCCCATGGGCAAGATCCCTCCTGGCCCATCTCTCCTCTTATTCT
CTATCCCTTCCCCAGGTCCCTGCCTTAGAGGTTTCACCAGAGCACAGCTC
CTGccTGTGGCCAAAACAGTATTTGGccactgaccGACCCagtGTCAGC*
ATCCAGATGGGTTCCACATCTCacaaccCT*GAGCAGCAGAGAAGGGTTT
GAaagGcCAGGGGAG*AATGAAGACgaaggaGG*TGTTgGcaacaacaca
gA*G*AGTCAGCAGccAgaacgccaggtatccacACACATaaggCATtct
aaatttttaCtcaACaggaattgtctATgtctgtgTCtgggcaccagggc
a*cacctTATCTCTAcaaaaat*agcgggatttagtggtgcttgtgtg**
g*cccagctattcaggg

QA 20 415 26 514
DS CHROMAT_FILE: K26-961c PHD_FILE: K26-961c.phd.1 TIME: Thu Sep 12 15:42:37 1996
RD K26-394c 628 0 0
ctgcgtatcgtcacc*accCAGTGTCagctatcCAGATGGGTTCCACATC
TcacaacCCT*GAGCAGCAGAGAAGGGTTTGAAAGGCCAGGGGAG*AATG
AAGACga*gGAGG*tgTTGGCAACAacacagA*G*AGTCAGCAGCCAGAA
CGCCAGGTATCCACACACATAAGACATTCTAAATTTTTACTCAACAGAAA
TTGTCTATGTCTGTGTCTGGgcaCCATGGCAACACCTTATCTCTACAAAA
ATTAGCGGAATGTAGTGGTGCCTGtgtGTAGTCCCAGCTATTCaaGAGGC
TGAAGTGGGAGGATTGCTTGagccaTggaagtcaagGCTGTAGTGagCCa
TGattgtgtCaATGCACtcnagAcagagcaaGACCctgctcccaccacac
aacttaanaggaaaaaaaaaaaggaaaagaaatgaaatgaaatgggatat
ag*aa*aggaaaagga*cagaaa*ttgtctatgcctggt*ctctagtaat
gtcagtcagccagtttccagccttttggtcttgggcattctgctgtcaca
atctcttggaacgttgggcagggaatcccatttttcccccgtttTttttt
gtggcaattaccttttggaaccctgggt

QA 18 368 11 502
DS CHROMAT_FILE: K26-394c PHD_FILE: K26-394c.phd.1 TIME: Thu Sep 12 15:42:32 1996
RD K26-291s 556 0 0
gaggatcgcttTCCacatctcaCAaccctcgagCAgCagagAAgggTTTG
AAAGGCCAGGGGAG*AATGAAGACGa*ggAGG*TGTTGGCAACAacacag
a*G*AGTCAGCAGCCAGAACGCCAggtaTCCAcacacataAgccatTCTA
AATTTTTACTCAAcagAAATTGTCTAtgTCTGTGTCTGggcacCATGGCA
ACACCTTATCTCTACAAAAATTAGCGGAATGTAGTggtGCCTGTGTGTAG
TCCCAGCTATTCAAgaggctGAAGTgcgaggatTGCTTgagCCATGGAAG
TcaaggctgtAGTGAgccatgatTGTGTCAATGCACTCCAGACAGAGCAA
GACCCTGCTCCCAccaCACAcctcaaaaggtattgattaaaGGAaAagaa
atgaaAtgaaatgagataaaggaaaaggaaaaagaacaggatattgTCtA
Tgcctgat*ctctagt*atgtgcagacagaagtttccagccactgagttc
ttgccccagctaactttttacaaatccccctggggaaggtttggcccagg
cagatg

QA 11 373 11 476
DS CHROMAT_FILE: K26-291s PHD_FILE: K26-291s.phd.1 TIME: Thu Sep 12 15:42:31 1996
RD K26-822c 593 0 0
ggggatccg*tcatgagacga*ggAGG*TGTTGGCAACa*ca*agaag*A
GTCAGCAGCCAGAACGCCAGGTATCCACACACATAAGACATTCTAAATTT
TTACTCAACAGAAATTGTCTATGTCTGtgtCTGGGCACCATGGCAACACC
TTATCTCTACAAAAATTAGCGGAATGTAGTggTGCCTGtgtGTAGTCCCA
GCTATTCAAGAGGCTGAAGTGGGAGGATTGCTTGAGCCATGGAAGTCAAG
GCTGTAGTGAGCCATGATTGtgtCAATGCACTCCAGAcAgAGCaAgacCC
tgCTCccACCACACacctCaaacgaaAAAAAAaaagggcaaagatatgaa
ctgaaatggaatatag*agcagcaaaaggaacagaaaattgtcTATGcct
ggttctctagtcatgtgcagaacagacagtatcccggccctattgagttc
ttggggcagttaggcttgtgcacccttgcttctatgccacagttagggca
ttcgggattcccatccttttccccggggttgctttttgtttgcgattacc
ttttcggaacaatggggggaaattattttccaagttgggtttg

QA 25 333 16 593
DS CHROMAT_FILE: K26-822c PHD_FILE: K26-822c.phd.1 TIME: Thu Sep 12 15:42:36 1996
RD K26-572c 594 0 0
agccccgggccgtggggttccttgagcactcccaaagttccaacccagga
tgtccccgacgcttaaaCcttccaagtctgaaacgggaaAtttgatttgc
gggctaggataaacgccggggagaaaggcagaactgccttttaccCCcca
aggatatcccttgggaagggcccctttgcactcagctgctccctaattat
ggcgatcctccctctatctttgtccccctgtctttcaggatccctctcAA
CAACAgaccaCTCccattaaaGAAATCtccttctgatctgcgggatcACA
TAAAACAGTGCCattcAAaAcgtcccttcCcccAATGTCtaagtgTggtg
gagcCcttcctgcCCggctctgtgcacccacggtgcctgcatgaccccgg
atGCAGTGTGCACCAGctCCCATCATTCAAgagCATGACTGTGTTGCCAA
CCAGCcacCAGGCACTGGGGAGGGAGCtgaGGGAGCAcaaAAGGGATGAG
CCACCCTCTGTcCcagAAGTGGAgcgcATGGGGCTTGGCTgggcTTAGAG
CtaacaTACACAGGATGCTGAAaaagaaCAACACaatagtaaca

QA 249 584 1 586
DS CHROMAT_FILE: K26-572c PHD_FILE: K26-572c.phd.1 TIME: Thu Sep 12 15:42:34 1996
RD K26-766c 603 0 0
gaataattggaatcacggcaaaaatttggggacaaatattatttccaaaa
ttcccccagcaatcacacaggccctcaagcccatcaactcggtcattcac
cgattttcctaaatcaagggtattagcttg*ctgggcttacacctaacat
acacagcatgctcaatgagaAcaatacgagctgtgtggagcacaggaagg
ggaAAtcagcctgaagctgctgttagtgtgcttgg*ctgAGTACAGCcaT
GCTctCAGTTgaggcAcggTTGGCTCCCCATGGgCAAGATCCCTCCTggC
CCATCTCTCCTCTTaTTCTCTATCCCTTCCCCAGGTCCCTGCCTTAGagg
tttCACCAGAGCACAGCTCCTGCCTGTGGCCAAAACAGTATTTGGCCACT
CACCGACCCAGTGTCAGC*ATCCAGATGGGTTCCACATCTCACAACCCT*
GAGCAGCAGAGAAGGGTTTGAAAGGCCAGGGGAG*AATGAAGACGAAGGA
GG*TGTTGGCAACAACACAGA*G*AGTCAGCAGCCAGAACGCCAGGTATC
CACACACATAagaCATtctaAATTTTTACTCAAacgatcCccggaaccac
acg

QA 240 584 126 583
DS CHROMAT_FILE: K26-766c PHD_FILE: K26-766c.phd.1 TIME: Thu Sep 12 15:42:35 1996

WA{
phrap_params phrap 990621:161947
/usr/local/genome/bin/phrap standard.fasta.screen -new_ace -view 
phrap version 0.990319
}

CT{
Contig1 repeat consed 976 986 971218:180623
}

CT{
Contig1 oligo consed 963 987 971218:180623
standard.1 acataagacattctaaatttttact 50 U
seq from clone
}

CT{
Contig1 comment consed 996 1007 971218:180623
This is line 1 of a comment
There may be any number of lines
}
BioPerl-1.007002/t/data/regulation_test.obo000444000766000024      1663413155576321 20633 0ustar00cjfieldsstaff000000000000format-version: 1.2
date: 29:01:2008 12:06
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_goa "GOA and proteome slim"
subsetdef: goslim_pir "PIR GO slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
subsetdef: gosubset_prok "Prokaryotic GO subset"
default-namespace: gene_ontology

[Term]
id: GO:0003674
name: molecular_function
namespace: molecular_function
def: "Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions." [GOC:go_curators]
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
subset: goslim_candida
subset: goslim_generic
subset: goslim_goa
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
synonym: "molecular function unknown" NARROW []

[Term]
id: GO:0003824
name: catalytic activity
namespace: molecular_function
def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_goa
subset: goslim_pir
subset: goslim_plant
subset: gosubset_prok
synonym: "enzyme activity" RELATED []
is_a: GO:0003674 ! molecular_function

[Term]
id: GO:0008150
name: biological_process
namespace: biological_process
def: "Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete]
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
subset: goslim_candida
subset: goslim_generic
subset: goslim_goa
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
synonym: "biological process unknown" NARROW []
synonym: "physiological process" EXACT []

[Term]
id: GO:0016740
name: transferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732]
subset: goslim_candida
subset: goslim_generic
subset: goslim_goa
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
xref: EC:2
is_a: GO:0003824 ! catalytic activity

[Term]
id: GO:0043085
name: positive regulation of catalytic activity
namespace: biological_process
def: "Any process that activates or increases the activity of an enzyme." [GOC:jl, GOC:tb]
subset: gosubset_prok
synonym: "activation of enzyme activity" NARROW []
synonym: "positive regulation of enzyme activity" EXACT []
synonym: "stimulation of enzyme activity" NARROW []
synonym: "up regulation of enzyme activity" EXACT []
synonym: "up-regulation of enzyme activity" EXACT []
synonym: "upregulation of enzyme activity" EXACT []
is_a: GO:0050790 ! regulation of catalytic activity
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0003824 ! catalytic activity
relationship: positively_regulates GO:0003824 ! catalytic activity

[Term]
id: GO:0050790
name: regulation of catalytic activity
namespace: biological_process
def: "Any process that modulates the activity of an enzyme." [GOC:ai]
subset: gosubset_prok
synonym: "regulation of enzyme activity" EXACT []
is_a: GO:0065009 ! regulation of a molecular function
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0003824 ! catalytic activity
relationship: regulates GO:0003824 ! catalytic activity

[Term]
id: GO:0051338
name: regulation of transferase activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [EC:2.-.-.-, GOC:ai]
subset: gosubset_prok
synonym: "transferase regulator" EXACT []
is_a: GO:0050790 ! regulation of catalytic activity
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0016740 ! transferase activity
relationship: regulates GO:0016740 ! transferase activity

[Term]
id: GO:0051347
name: positive regulation of transferase activity
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor." [GOC:ai]
subset: gosubset_prok
synonym: "activation of transferase activity" NARROW []
synonym: "stimulation of transferase activity" NARROW []
synonym: "transferase activator" EXACT []
synonym: "up regulation of transferase activity" EXACT []
synonym: "up-regulation of transferase activity" EXACT []
synonym: "upregulation of transferase activity" EXACT []
is_a: GO:0043085 ! positive regulation of catalytic activity
is_a: GO:0051338 ! regulation of transferase activity
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0016740 ! transferase activity
relationship: positively_regulates GO:0016740 ! transferase activity

[Term]
id: GO:0065007
name: biological regulation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of any biological process, quality or function." [GOC:isa_complete]
subset: goslim_pir
subset: gosubset_prok
synonym: "regulation" BROAD []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0065009
name: regulation of a molecular function
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of molecular functions. Molecular functions are elemental biological activities occurring at the molecular level, such as catalysis or binding." [GOC:isa_complete]
subset: gosubset_prok
is_a: GO:0065007 ! biological regulation

[Typedef]
id: positively_regulates
name: positively_regulates
namespace: gene_ontology
is_a: regulates ! regulates

[Typedef]
id: regulates
name: regulates
namespace: gene_ontology

BioPerl-1.007002/t/data/rel9.swiss000444000766000024      2161413155576321 16661 0ustar00cjfieldsstaff000000000000ID   GCDH_CAEEL              Reviewed;         409 AA.
AC   Q20772;
DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   31-OCT-2006, entry version 47.
DE   Probable glutaryl-CoA dehydrogenase, mitochondrial precursor
DE   (EC 1.3.99.7) (GCD).
GN   ORFNames=F54D5.7;
OS   Caenorhabditis elegans.
OC   Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea;
OC   Rhabditidae; Peloderinae; Caenorhabditis.
OX   NCBI_TaxID=6239;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Bristol N2;
RX   MEDLINE=99069613; PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG   The C. elegans sequencing consortium;
RT   "Genome sequence of the nematode C. elegans: a platform for
RT   investigating biology.";
RL   Science 282:2012-2018(1998).
CC   -!- CATALYTIC ACTIVITY: Glutaryl-CoA + acceptor = crotonoyl-CoA +
CC       CO(2) + reduced acceptor.
CC   -!- COFACTOR: FAD (By similarity).
CC   -!- PATHWAY: Degradative pathway of L-lysine, L-hydroxylysine, and L-
CC       tryptophan metabolism.
CC   -!- INTERACTION:
CC       P39745:mpk-1; NbExp=1; IntAct=EBI-313068, EBI-321013;
CC       Q17446:pmk-1; NbExp=1; IntAct=EBI-313068, EBI-312987;
CC   -!- SUBCELLULAR LOCATION: Mitochondrion; mitochondrial matrix
CC       (Potential).
CC   -!- SIMILARITY: Belongs to the acyl-CoA dehydrogenase family.
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------
DR   EMBL; Z66513; CAA91333.1; -; Genomic_DNA.
DR   PIR; T22647; T22647.
DR   UniGene; Cel.30446; -.
DR   HSSP; Q06319; 1BUC.
DR   IntAct; Q20772; -.
DR   Ensembl; F54D5.7; Caenorhabditis elegans.
DR   KEGG; cel:F54D5.7; -.
DR   WormBase; WBGene00010052; F54D5.7.
DR   WormPep; F54D5.7; CE03411.
DR   GO; GO:0005515; F:protein binding; IPI:IntAct.
DR   InterPro; IPR006089; Acyl_CoA_DH.
DR   InterPro; IPR006091; Acyl_CoA_DH/ox_M.
DR   InterPro; IPR006090; Acyl_CoA_DH_1.
DR   InterPro; IPR006092; Acyl_CoA_DH_N.
DR   InterPro; IPR009075; AcylCo_DH/ox_C.
DR   InterPro; IPR013786; AcylCoA_DH/ox_N.
DR   InterPro; IPR009100; AcylCoA_DH/ox_NM.
DR   InterPro; IPR013764; AcylCoA_DH_1/2_C.
DR   Pfam; PF00441; Acyl-CoA_dh_1; 1.
DR   Pfam; PF02770; Acyl-CoA_dh_M; 1.
DR   Pfam; PF02771; Acyl-CoA_dh_N; 1.
DR   PROSITE; PS00072; ACYL_COA_DH_1; FALSE_NEG.
DR   PROSITE; PS00073; ACYL_COA_DH_2; 1.
KW   Complete proteome; FAD; Flavoprotein; Hypothetical protein;
KW   Mitochondrion; Oxidoreductase; Transit peptide.
FT   TRANSIT       1      ?       Mitochondrion (Potential).
FT   CHAIN         ?    409       Probable glutaryl-CoA dehydrogenase.
FT                                /FTId=PRO_0000000530.
FT   ACT_SITE    388    388       Proton acceptor (Potential).
SQ   SEQUENCE   409 AA;  44964 MW;  4D06241FB6768069 CRC64;
     MLTRGFTSIG KIASRGLSST FYQDAFQLSD QLTEDERSLM LSAREYCQER LLPRVTEAYR
     TEKFDPSLIP EMGSMGLLGA PYQGYGCAGT STVGYGLIAR EVERVDSGYR STMSVQTSLV
     IGPIYNYGSE DQKQKYIPDL ASGKKIGCFG LTEPNHGSNP GGMETKATWD ETTKTYKLNG
     SKTWISNSPV SDVMVVWARS ARHNNKIKGF ILERGMKGLT TPKIEGKLSL RASITGQIAM
     DDVPVPEENL LPNAEGLQGP FGCLNNARLG IAWGALGAAE ECFHLARQYT LDRQQFGRPL
     AQNQLMQLKM ADMLTEISLG LQGCLRVSRL KDEGKVQSEQ ISIIKRNSCG KALEVARKAR
     DMLGGNGIVD EYHIMRHMVN LETVNTYEGT HDVHALILGR AITGLNGFC
//
ID   Q41V66_FERAC            Unreviewed;       607 AA.
AC   Q41V66;
DT   27-SEP-2005, integrated into UniProtKB/TrEMBL.
DT   27-SEP-2005, sequence version 1.
DT   31-OCT-2006, entry version 6.
DE   Glycoside hydrolase, family 15.
GN   ORFNames=FaciDRAFT_1685;
OS   Ferroplasma acidarmanus Fer1.
OC   Archaea; Euryarchaeota; Thermoplasmata; Thermoplasmatales;
OC   Ferroplasmaceae; Ferroplasma.
OX   NCBI_TaxID=333146;
RN   [1]
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Fer1;
RG   US DOE Joint Genome Institute (JGI-PGF);
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter C., Glavina T.,
RA   Hammon N., Israni S., Pitluck S., Richardson P.;
RT   "Sequencing of the draft genome and assembly of Ferroplasma
RT   acidarmanus fer1.";
RL   Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Fer1;
RG   US DOE Joint Genome Institute (JGI-ORNL);
RA   Larimer F., Land M.;
RT   "Annotation of the draft genome assembly of Ferroplasma acidarmanus
RT   fer1.";
RL   Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Fer1;
RG   US DOE Joint Genome Institute (JGI-PGF);
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter C., Glavina T.,
RA   Hammon N., Israni S., Pitluck S., Richardson P.;
RL   Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases.
CC   -!- CAUTION: The sequence shown here is derived from an
CC       EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is
CC       preliminary data.
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------
DR   EMBL; AABC04000001; EAM94575.1; -; Genomic_DNA.
DR   GO; GO:0004339; F:glucan 1,4-alpha-glucosidase activity; IEA:InterPro.
DR   GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR   GO; GO:0005976; P:polysaccharide metabolism; IEA:InterPro.
DR   InterPro; IPR008928; 6hp_glycosidase.
DR   InterPro; IPR011613; Glyco_hydro_15_rel.
DR   InterPro; IPR012343; Glyco_trans_sub.
DR   Pfam; PF00723; Glyco_hydro_15; 1.
KW   Hydrolase.
SQ   SEQUENCE   607 AA;  69495 MW;  8AC6297BA16ED500 CRC64;
     MGTYRGLYDL HDAYRSDYLK IANHGFIANN RTAALVGIDG TIDWACLPNF NSNPVFDSIL
     DARNGGYFKT SPVMESNVNQ YYEESTNILI TEFVNNNQVI LRLTDFLPTS SYSTITFPEI
     HRLIEAPYSD VEVSIDIKSH FNFGSGKTNI TRDRNGYIFS CTDDTLGIST NLKLKKGNGN
     VYSRIKVEKG SHEWIVVLSG VRQIGNVRQY ESYTRLEETR NYWSAWAGKI NYSGLYYDHV
     IRSALTLRGL FYDPTGMMVA APTTSLPEII GGERNWDYRY TWIRDTAYVV EALSLIGLND
     VATKFLYDIM SIVQKDKKVK TIYPVNGDSK LEEKKVNLSG YMDSIPVRIG NEASEQLQID
     QYGSIVNAVF RFHEAGGLVT TYLWDFLIEI LDTLKDIWKL PDSSIWEFRS EPKHYLYSKL
     ISWSAFNRAI KMGRELGYSA PYRTWHKIRE EIKNEIMEKG YNPDVKAFTQ YYGSDQMDAS
     VLRMPLTGII SAKDPRFVST LARVEAELKN PCGMFIRYHS DDGLKGHDNA FLLLSFWYVE
     DLILSGRIME AKETFENILD HSNHLMLFSE EINFNDCREM LGNFPQAITH LGVIRAAIKL
     DEALRGK
//
ID   Q41US7_FERAC            Unreviewed;       270 AA.
AC   Q41US7;
DT   27-SEP-2005, integrated into UniProtKB/TrEMBL.
DT   27-SEP-2005, sequence version 1.
DT   31-OCT-2006, entry version 6.
DE   Potassium channel protein.
GN   ORFNames=FaciDRAFT_1443;
OS   Ferroplasma acidarmanus Fer1.
OC   Archaea; Euryarchaeota; Thermoplasmata; Thermoplasmatales;
OC   Ferroplasmaceae; Ferroplasma.
OX   NCBI_TaxID=333146;
RN   [1]
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Fer1;
RG   US DOE Joint Genome Institute (JGI-PGF);
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter C., Glavina T.,
RA   Hammon N., Israni S., Pitluck S., Richardson P.;
RT   "Sequencing of the draft genome and assembly of Ferroplasma
RT   acidarmanus fer1.";
RL   Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Fer1;
RG   US DOE Joint Genome Institute (JGI-ORNL);
RA   Larimer F., Land M.;
RT   "Annotation of the draft genome assembly of Ferroplasma acidarmanus
RT   fer1.";
RL   Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=Fer1;
RG   US DOE Joint Genome Institute (JGI-PGF);
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter C., Glavina T.,
RA   Hammon N., Israni S., Pitluck S., Richardson P.;
RL   Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases.
CC   -!- CAUTION: The sequence shown here is derived from an
CC       EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is
CC       preliminary data.
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------
DR   EMBL; AABC04000002; EAM94333.1; -; Genomic_DNA.
DR   GO; GO:0005216; F:ion channel activity; IEA:UniProtKB-KW.
DR   GO; GO:0006813; P:potassium ion transport; IEA:InterPro.
DR   InterPro; IPR013099; Ion_trans_2.
DR   InterPro; IPR003148; TrkA_N.
DR   Pfam; PF07885; Ion_trans_2; 1.
DR   Pfam; PF02254; TrkA_N; 1.
DR   PROSITE; PS51201; RCK_N; 1.
KW   Ionic channel.
SQ   SEQUENCE   270 AA;  30497 MW;  528C4EA75C41DF75 CRC64;
     MQTITTVGYG DTPVYGLAGR ANGMLIMVIG IGSLGYLMAG LTSMLIDIRL SSKLGERMAA
     EKKHIVLCNY NESTKKVLDK IKYDGIDIVI LNENEVKGDN EYTYIKGSFL RENDLIRAGI
     KKASSVIIFS RSEDKEQMAM DAESILSAMI IRKLNPEIRI IGEILNPDSR EHASSFMDDI
     IIKGDVSSML IYSSIMIPGI PEFINDLLMS NSISEEDIDK KYASNTYREF ISNMEKENRI
     VLAFRKQDKI YLRENSDKKI DVDSYIFIKN
//
BioPerl-1.007002/t/data/repeatmasker.fa.out000444000766000024       354613155576321 20501 0ustar00cjfieldsstaff000000000000   SW  perc perc perc  query        position in query    matching  repeat        position in  repeat
score  div. del. ins.  sequence     begin  end (left)   repeat    class/family  begin  end (left)  ID

  504   0.0  5.6  0.0  contig11600   1337 1407  (994) +  (TTAGGG)n Simple_repeat     2   76    (0)   1  
  890   5.3  5.9  0.0  contig11600   1712 2225  (176) +  (TTAGGG)n Simple_repeat     1  544    (0)   5  
   685  17.0  1.4 10.9  SL2.30ch10     31794    32004 (64801061) +  LTR_PGSC0003DMS000000301_448   LTR              11852 12044  (2451)    40      
   651  21.0  3.3  3.3  SL2.30ch10     38677    38858 (64794207) C  LTR_PGSC0003DMS000000301_448   LTR             (2465) 12030   11849    45      
   285  17.8  5.4  2.1  SL2.30ch10     38849    38940 (64794125) C  LTR_PGSC0003DMS000000301_448   LTR             (3720) 10775   10681    45   *  
   604  20.8  1.0 13.1  SL2.30ch10     38972    39176 (64793889) C  LTR_PGSC0003DMS000000301_448   LTR             (3715) 10780   10598    45      
   342  24.0  4.2  5.3  SL2.30ch10     46512    46599 (64786466) C  LTR_PGSC0003DMS000000301_448   LTR             (9298) 12245    6277    50      
   342  24.0  4.2  5.3  SL2.30ch10     46726    46745 (64786320) C  LTR_PGSC0003DMS000000301_448   LTR            (15267)  6276    4973    50      
   450  19.0  1.0  3.7  SL2.30ch10     52652    52763 (64780302) C  LTR_PGSC0003DMS000000301_448   LTR             (6884) 13693    5865    55      
   548  13.2 12.2  2.5  SL2.30ch10    183688   183835 (64649230) C  LTR_PGSC0003DMS000000301_448   LTR             (2484) 12011   11850   181      
   563  17.2  0.0  0.0  SL2.30ch10    205612   205698 (64627367) C  LTR_PGSC0003DMS000000301_448   LTR             (7392)  7103    7017   195      
   334  18.2  0.0  3.9  SL2.30ch10    221149   221228 (64611837) C  LTR_PGSC0003DMS000000301_448   LTR            (11595)  2900    2824   205      
BioPerl-1.007002/t/data/revcomp_mrna.gb000444000766000024     26443313155576321 17746 0ustar00cjfieldsstaff000000000000LOCUS       AP000868   181589 bp  DNA   HTG   
DEFINITION  Reannotated sequence via Ensembl
ACCESSION   AP000868
VERSION     NO_SV_NUMBER
SOURCE      Human.
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Vertebrata; Mammalia; Eutheria;
            Primates; Catarrhini; Hominidae; Homo.
COMMENT     This sequence was reannotated via the Ensembl system. Please visit
            the Ensembl web site, http://www.ensembl.org/ for more
            information.
COMMENT     The /gene indicates a unique id for a gene, /cds a unique id for a
            translation and a /exon a unique id for an exon. These ids are
            maintained wherever possible between versions. For more
            information on how to interpret the feature table, please visit
            http://www.ensembl.org/Docs/embl.html.
COMMENT     All the exons and transcripts in Ensembl are confirmed by
            similarity to either protein or cDNA sequences.
COMMENT     This entry represents a slice of genome sequence. The ID and
            accession give the location of the slice. The underlying clone
            information, where available, is detailed in the misc features of
            the feature table.
FEATURES             Location/Qualifiers
     source          1..181589
                     /organism="Homo sapiens"
     CDS             join(complement(23956..24166),complement(23467..23555),
                     complement(22474..22603),complement(21817..21936),
                     complement(20341..21332))
                     /gene="ENSG00000166261"
                     /cds="ENSP00000299336"
                     /transcript="ENST00000299336"
                     /note="transcript split due to inability to predict a
                     single translateable transcript"
                     /db_xref="RefSeq:NM_003455"
                     /db_xref="MIM:603430"
                     /db_xref="LocusLink:7753"
                     /db_xref="HUGO:12994"
                     /db_xref="SWISSPROT:O95125"
                     /db_xref="EMBL:AF027219"
                     /db_xref="protein_id:AAC79941"
                     /db_xref="EMBL:AF027218"
                     /db_xref="protein_id:AAC79940"
                     /db_xref="EMBL:AJ276177"
                     /db_xref="protein_id:CAC21447"
                     /db_xref="EMBL:AJ276178"
                     /db_xref="EMBL:AJ276179"
                     /db_xref="EMBL:AJ276180"
                     /db_xref="EMBL:AJ276181"
                     /db_xref="EMBL:AJ276182"
                     /db_xref="GO:GO:0006355"
                     /db_xref="GO:GO:0005634"
                     /db_xref="GO:GO:0003700"
                     /db_xref="GO:GO:0006629"
                     /db_xref="GO:GO:0003704"
                     /db_xref="GO:GO:0000122"
                     /translation="VTVHVHGQEVLSEETVHLGVEPESPNELQDPVQSSTPEQSPEET
                     TQSPDLGAPAEQRPHQEEELQTLQESEVPVPEDPDLPAERSSGDSEMVALLTALSQGL
                     VTFKDVAVCFSQDQWSDLDPTQKEFYGEYVLEEDCGIVVSLSFPIPRPDEISQVREEE
                     PWVPDIQEPQETQEPEILSFTYTGDRSKDEEECLEQEDLSLEDIHRPVLGEPEIHQTP
                     DWEIVFEDNPGRLNERRFGTNISQVNSFVNLRETTPVHPLLGRHHDCSVCGKSFTCNS
                     HLVRHLRTHTGEKPYKCMECGKSYTRSSHLARHQKVHKMNAPYKYPLNRKNLEETSPV
                     TQAERTPSVEKPYRCDDCGKHFRWTSDLVRHQRTHTGEKPFFCTICGKSFSQKSVLTT
                     HQRIHLGGKPYLCGECGEDFSEHRRYLAHRKTHAAEELYLCSECGRCFTHSAAFAKHL
                     RGHASVRPCRCNECGKSFSRRDHLVRHQRTHTGEKPFTCPTCGKSFSRGYHLIRHQRT
                     HSEKTS"
     CDS             join(complement(24828..25229))
                     /gene="ENSG00000166261"
                     /cds="ENSP00000299336"
                     /transcript="ENST00000299336"
                     /note="transcript split due to inability to predict a
                     single translateable transcript"
                     /db_xref="RefSeq:NM_003455"
                     /db_xref="MIM:603430"
                     /db_xref="LocusLink:7753"
                     /db_xref="HUGO:12994"
                     /db_xref="SWISSPROT:O95125"
                     /db_xref="EMBL:AF027219"
                     /db_xref="protein_id:AAC79941"
                     /db_xref="EMBL:AF027218"
                     /db_xref="protein_id:AAC79940"
                     /db_xref="EMBL:AJ276177"
                     /db_xref="protein_id:CAC21447"
                     /db_xref="EMBL:AJ276178"
                     /db_xref="EMBL:AJ276179"
                     /db_xref="EMBL:AJ276180"
                     /db_xref="EMBL:AJ276181"
                     /db_xref="EMBL:AJ276182"
                     /db_xref="GO:GO:0006355"
                     /db_xref="GO:GO:0005634"
                     /db_xref="GO:GO:0003700"
                     /db_xref="GO:GO:0006629"
                     /db_xref="GO:GO:0003704"
                     /db_xref="GO:GO:0000122"
                     /translation="MATAVEPEDQDLWEEEGILMVKLEDDFTCRPESVLQRDDPVLET
                     SHQNFRRFRYQEAASPREALIRLRELCHQWLRPERRTKEQILELLVLEQFLTVLPGEL
                     QSWVRGQRPESGEEAVTLVEGLQKQPRRPRRW"
     CDS             join(complement(47951..48856))
                     /gene="ENSG00000150410"
                     /cds="ENSP00000307279"
                     /transcript="ENST00000307086"
                     /translation="RNGTVITEFILLGFPVIQGLQTPLFIAIFLTYILTLAGNGLIIA
                     TVWAEPRLQIPMYFFLCNLSFLEIWYTTTVIPKLLGTFVVARTVICMSCCLLQAFFHF
                     FVGTTEFLILTIMSFDRYLTICNPLHHPTIMTSKLCLQLALSSWVVGFTIVFCQTMLL
                     IQLPFCGNNVISHFYCDVGPSLKAACIDTSILELLGVIATILVIPGSLLFNMISYIYI
                     LSAILRIPSATGHQKTFSTCASHLTVVSLLYGAVLFMYLRPTAHSSFKINKVVSVLNT
                     ILTPLLNPFIYTIRNKEVKGALRKAM"
     exon            complement(18268..21332)
                     /exon_id="ENSE00001101518"
                     /start_phase=1
                     /end_phase=0
     exon            complement(21817..21936)
                     /exon_id="ENSE00001101510"
                     /start_phase=1
                     /end_phase=1
     exon            complement(22474..22603)
                     /exon_id="ENSE00001101512"
                     /start_phase=0
                     /end_phase=1
     exon            complement(23467..23555)
                     /exon_id="ENSE00001101515"
                     /start_phase=1
                     /end_phase=0
     exon            complement(23956..24166)
                     /exon_id="ENSE00001101523"
                     /start_phase=0
                     /end_phase=1
     exon            complement(24828..25239)
                     /exon_id="ENSE00001101520"
                     /start_phase=0
                     /end_phase=1
     exon            complement(47951..48436)
                     /exon_id="ENSE00001101532"
                     /start_phase=0
                     /end_phase=0
     exon            complement(47951..48856)
                     /exon_id="ENSE00001134026"
                     /start_phase=0
                     /end_phase=0
     repeat_region   125..225
                     /note="MIR3: matches 106 to 202 of consensus"
     repeat_region   125..225
                     /note="MIR3: matches 106 to 202 of consensus"
     repeat_region   388..595
                     /note="MIR: matches 28 to 247 of consensus"
     repeat_region   388..595
                     /note="MIR: matches 28 to 247 of consensus"
     repeat_region   complement(637..860)
                     /note="L1ME3: matches 5922 to 6147 of consensus"
     repeat_region   complement(637..860)
                     /note="L1ME3: matches 5922 to 6147 of consensus"
     repeat_region   complement(1015..1295)
                     /note="AluSx: matches 1 to 287 of consensus"
     repeat_region   complement(1015..1295)
                     /note="AluSx: matches 1 to 287 of consensus"
     repeat_region   complement(1296..1913)
                     /note="L1ME3: matches 5326 to 5931 of consensus"
     repeat_region   complement(1296..1913)
                     /note="L1ME3: matches 5326 to 5931 of consensus"
     repeat_region   complement(2610..2670)
                     /note="L2: matches 3251 to 3313 of consensus"
     repeat_region   complement(2610..2670)
                     /note="L2: matches 3251 to 3313 of consensus"
     repeat_region   complement(2996..3298)
                     /note="AluJb: matches 1 to 300 of consensus"
     repeat_region   complement(2996..3298)
                     /note="AluJb: matches 1 to 300 of consensus"
     repeat_region   complement(3516..3635)
                     /note="AluJb: matches 176 to 299 of consensus"
     repeat_region   complement(3516..3635)
                     /note="AluJb: matches 176 to 299 of consensus"
     repeat_region   complement(3655..3703)
                     /note="AluSg/x: matches 172 to 220 of consensus"
     repeat_region   complement(3655..3703)
                     /note="AluSp/q: matches 172 to 220 of consensus"
     repeat_region   complement(3687..3735)
                     /note="AluSp/q: matches 172 to 220 of consensus"
     repeat_region   complement(3687..3735)
                     /note="AluSg/x: matches 172 to 220 of consensus"
     repeat_region   complement(3719..3767)
                     /note="AluSp/q: matches 172 to 220 of consensus"
     repeat_region   complement(3719..3767)
                     /note="AluSg/x: matches 172 to 220 of consensus"
     repeat_region   complement(3751..3799)
                     /note="AluSg/x: matches 172 to 220 of consensus"
     repeat_region   complement(3751..3799)
                     /note="AluSp/q: matches 172 to 220 of consensus"
     repeat_region   complement(3783..3831)
                     /note="AluSp/q: matches 172 to 220 of consensus"
     repeat_region   complement(3783..3831)
                     /note="AluSg/x: matches 172 to 220 of consensus"
     repeat_region   complement(3848..4069)
                     /note="AluJb: matches 1 to 219 of consensus"
     repeat_region   complement(3848..4069)
                     /note="AluJb: matches 1 to 219 of consensus"
     repeat_region   complement(4155..4454)
                     /note="AluSc: matches 1 to 301 of consensus"
     repeat_region   complement(4155..4454)
                     /note="AluSc: matches 1 to 301 of consensus"
     repeat_region   complement(4799..5101)
                     /note="L2: matches 2430 to 2745 of consensus"
     repeat_region   complement(4799..5101)
                     /note="L2: matches 2430 to 2745 of consensus"
     repeat_region   5244..5548
                     /note="AluJb: matches 1 to 304 of consensus"
     repeat_region   5244..5548
                     /note="AluJb: matches 1 to 304 of consensus"
     repeat_region   complement(5947..6101)
                     /note="MIR: matches 12 to 155 of consensus"
     repeat_region   complement(5947..6101)
                     /note="MIR: matches 12 to 155 of consensus"
     repeat_region   complement(6344..6647)
                     /note="AluSx: matches 1 to 309 of consensus"
     repeat_region   complement(6344..6647)
                     /note="AluSx: matches 1 to 309 of consensus"
     repeat_region   complement(6822..8048)
                     /note="L1PA7: matches 4924 to 6148 of consensus"
     repeat_region   complement(6822..8048)
                     /note="L1PA7: matches 4924 to 6148 of consensus"
     repeat_region   8054..8991
                     /note="L2: matches 2302 to 3312 of consensus"
     repeat_region   8054..8991
                     /note="L2: matches 2302 to 3312 of consensus"
     repeat_region   10131..10182
                     /note="L2: matches 3209 to 3260 of consensus"
     repeat_region   10131..10182
                     /note="L2: matches 3209 to 3260 of consensus"
     repeat_region   complement(10288..10590)
                     /note="AluSx: matches 1 to 303 of consensus"
     repeat_region   complement(10288..10590)
                     /note="AluSx: matches 1 to 303 of consensus"
     repeat_region   11254..11313
                     /note="L2: matches 3254 to 3313 of consensus"
     repeat_region   11254..11313
                     /note="L2: matches 3254 to 3313 of consensus"
     repeat_region   11615..11747
                     /note="MLT1H: matches 23 to 158 of consensus"
     repeat_region   11615..11747
                     /note="MLT1H: matches 23 to 158 of consensus"
     repeat_region   complement(12076..12357)
                     /note="AluSq: matches 21 to 301 of consensus"
     repeat_region   complement(12076..12357)
                     /note="AluSq: matches 21 to 301 of consensus"
     repeat_region   12517..12571
                     /note="MIR: matches 91 to 145 of consensus"
     repeat_region   12517..12571
                     /note="MIR: matches 91 to 145 of consensus"
     repeat_region   complement(12952..14120)
                     /note="Tigger3b: matches 2 to 1231 of consensus"
     repeat_region   complement(12952..14120)
                     /note="Tigger3b: matches 2 to 1231 of consensus"
     repeat_region   complement(14154..14506)
                     /note="L1MEc: matches 1919 to 2247 of consensus"
     repeat_region   complement(14154..14506)
                     /note="L1MEc: matches 1919 to 2247 of consensus"
     repeat_region   complement(14872..15052)
                     /note="L1MEc: matches 2319 to 2525 of consensus"
     repeat_region   complement(14872..15052)
                     /note="L1M4: matches 2250 to 2456 of consensus"
     repeat_region   15053..15352
                     /note="AluSg: matches 1 to 299 of consensus"
     repeat_region   15053..15352
                     /note="AluSg: matches 1 to 299 of consensus"
     repeat_region   complement(15353..15431)
                     /note="L1MEc: matches 2247 to 2319 of consensus"
     repeat_region   complement(15353..15431)
                     /note="L1M4: matches 2178 to 2250 of consensus"
     repeat_region   16944..17245
                     /note="AluY: matches 1 to 301 of consensus"
     repeat_region   16944..17245
                     /note="AluY: matches 1 to 301 of consensus"
     repeat_region   complement(21440..21588)
                     /note="MIR: matches 53 to 228 of consensus"
     repeat_region   25556..25701
                     /note="L2: matches 2484 to 2642 of consensus"
     repeat_region   complement(25702..25806)
                     /note="MER5A: matches 86 to 187 of consensus"
     repeat_region   25724..25866
                     /note="MER5B: matches 22 to 176 of consensus"
     repeat_region   25889..26077
                     /note="MIR: matches 16 to 198 of consensus"
     repeat_region   26460..26737
                     /note="L2: matches 2564 to 2856 of consensus"
     repeat_region   27188..27280
                     /note="L2: matches 2503 to 2596 of consensus"
     repeat_region   complement(27731..27883)
                     /note="L1MEc: matches 679 to 837 of consensus"
     repeat_region   complement(27909..28078)
                     /note="AluJo: matches 124 to 293 of consensus"
     repeat_region   28615..29091
                     /note="L2: matches 2735 to 3265 of consensus"
     repeat_region   31003..31232
                     /note="MIR: matches 10 to 259 of consensus"
     repeat_region   32097..32219
                     /note="MIR3: matches 36 to 158 of consensus"
     repeat_region   complement(32367..32650)
                     /note="AluJb: matches 1 to 286 of consensus"
     repeat_region   33309..33436
                     /note="L2: matches 3134 to 3264 of consensus"
     repeat_region   complement(33681..33786)
                     /note="L2: matches 3199 to 3308 of consensus"
     repeat_region   34120..34290
                     /note="MER5A: matches 2 to 187 of consensus"
     repeat_region   complement(36857..37015)
                     /note="MER4A: matches 261 to 466 of consensus"
     repeat_region   complement(37016..37108)
                     /note="MER4A: matches 1 to 98 of consensus"
     repeat_region   complement(37111..37459)
                     /note="MLT2B2: matches 101 to 477 of consensus"
     repeat_region   complement(37465..37675)
                     /note="AluSg/x: matches 90 to 306 of consensus"
     repeat_region   complement(37676..37767)
                     /note="MLT2B2: matches 1 to 95 of consensus"
     repeat_region   complement(37908..38394)
                     /note="MER31A: matches 1 to 485 of consensus"
     repeat_region   complement(38413..38707)
                     /note="AluSc: matches 1 to 294 of consensus"
     repeat_region   complement(38905..39443)
                     /note="L1MC4a: matches 5297 to 5736 of consensus"
     repeat_region   complement(39957..40059)
                     /note="L2: matches 3167 to 3270 of consensus"
     repeat_region   complement(40271..40366)
                     /note="L2: matches 2957 to 3058 of consensus"
     repeat_region   complement(40367..40884)
                     /note="MER4C: matches 2 to 465 of consensus"
     repeat_region   complement(40885..41109)
                     /note="L2: matches 2784 to 2957 of consensus"
     repeat_region   41110..41435
                     /note="AluJb: matches 1 to 309 of consensus"
     repeat_region   complement(41436..41656)
                     /note="L2: matches 2550 to 2784 of consensus"
     repeat_region   complement(42552..43939)
                     /note="L1PA15: matches 4780 to 6165 of consensus"
     repeat_region   complement(45781..46404)
                     /note="MER4B: matches 1 to 779 of consensus"
     repeat_region   46607..47082
                     /note="LOR1a: matches 1 to 497 of consensus"
     misc            1..19151
                     /note="Component DNA fragment"
                     /note="accession=AP002765.3"
                     /note="start=159020"
                     /note="end=178170"
                     /note="orientation=1"
     variation       complement(2261..2261)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:552820"
                     /db_xref="HGBASE:SNP000375829"
     variation       6896..6896
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:475710"
                     /db_xref="HGBASE:SNP000368989"
     variation       8597..8597
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:552467"
                     /db_xref="HGBASE:SNP001202646"
     variation       9185..9185
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:557862"
                     /db_xref="HGBASE:SNP000376288"
     variation       9242..9242
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:558021"
                     /db_xref="HGBASE:SNP000843781"
     variation       complement(9593..9593)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:655756"
                     /db_xref="HGBASE:SNP000458091"
     variation       10744..10744
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:503766"
                     /db_xref="HGBASE:SNP000076194"
     variation       complement(11324..11324)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:627134"
                     /db_xref="HGBASE:SNP000501198"
     variation       complement(11580..11580)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:625888"
                     /db_xref="HGBASE:SNP000410419"
     variation       complement(12055..12055)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:623707"
     variation       complement(12298..12298)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1791700"
                     /db_xref="HGBASE:SNP000404217"
                     /db_xref="TSC-CSHL:TSC0947239"
     variation       15872..15872
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:2276410"
     prediction      join(complement(15914..16090))
     variation       16640..16640
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:2282646"
                     /db_xref="HGBASE:SNP001239633"
     variation       17550..17550
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:2126708"
                     /db_xref="HGBASE:SNP001310527"
                     /db_xref="TSC-CSHL:TSC1134267"
     misc            19152..181589
                     /note="Component DNA fragment"
                     /note="accession=AP000868.4"
                     /note="start=19153"
                     /note="end=181590"
                     /note="orientation=1"
     variation       19560..19560
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:2126709"
                     /db_xref="HGBASE:SNP001310528"
                     /db_xref="TSC-CSHL:TSC1134268"
     variation       complement(19688..19688)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:10904"
                     /db_xref="HGBASE:SNP000017373"
     variation       complement(22574..22574)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:2282644"
                     /db_xref="HGBASE:SNP001241241"
     variation       complement(23148..23148)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:663471"
                     /db_xref="HGBASE:SNP000668983"
     variation       complement(23159..23159)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1720331"
                     /db_xref="HGBASE:SNP000606798"
     variation       complement(23419..23419)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:671898"
                     /db_xref="HGBASE:SNP000519992"
     variation       complement(24698..24698)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:2282643"
                     /db_xref="HGBASE:SNP001357715"
     prediction      join(complement(24827..25228),complement(23955..24249),
                     complement(23394..23554),complement(22473..22662),
                     complement(21816..21935),complement(20460..21331))
     variation       complement(25549..25549)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:2282642"
                     /db_xref="HGBASE:SNP001241241"
     variation       complement(25566..25566)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:2282641"
                     /db_xref="HGBASE:SNP001241241"
     variation       complement(26578..26578)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1880058"
                     /db_xref="HGBASE:SNP000858034"
                     /db_xref="TSC-CSHL:TSC0891347"
     variation       complement(28686..28686)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1791715"
                     /db_xref="HGBASE:SNP000423743"
     variation       complement(29269..29269)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:682246"
     variation       complement(32214..32214)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1940185"
                     /db_xref="HGBASE:SNP000860124"
                     /db_xref="TSC-CSHL:TSC1009511"
     variation       complement(33267..33267)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1557429"
                     /db_xref="HGBASE:SNP000400840"
                     /db_xref="TSC-CSHL:TSC0444634"
     variation       complement(33395..33395)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1557428"
                     /db_xref="HGBASE:SNP000400839"
                     /db_xref="TSC-CSHL:TSC0444633"
     variation       complement(33396..33396)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1557427"
                     /db_xref="HGBASE:SNP000400838"
                     /db_xref="TSC-CSHL:TSC0444632"
     variation       complement(33424..33424)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1557426"
                     /db_xref="HGBASE:SNP000400837"
                     /db_xref="TSC-CSHL:TSC0444631"
     variation       complement(33565..33565)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1557425"
                     /db_xref="HGBASE:SNP000400836"
                     /db_xref="TSC-CSHL:TSC0444630"
     variation       34696..34696
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1939924"
                     /db_xref="HGBASE:SNP000859985"
                     /db_xref="TSC-CSHL:TSC1009047"
     variation       34809..34809
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1939925"
                     /db_xref="HGBASE:SNP000859986"
                     /db_xref="TSC-CSHL:TSC1009048"
     variation       complement(34928..34928)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1893061"
                     /db_xref="HGBASE:SNP000858271"
                     /db_xref="TSC-CSHL:TSC0919478"
     variation       35738..35738
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:2091068"
                     /db_xref="HGBASE:SNP001309950"
                     /db_xref="TSC-CSHL:TSC1312336"
     variation       35970..35970
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:2272142"
                     /db_xref="HGBASE:SNP001314474"
     variation       37832..37832
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1940191"
                     /db_xref="HGBASE:SNP000860129"
                     /db_xref="TSC-CSHL:TSC1009519"
     variation       complement(40576..40576)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:629647"
                     /db_xref="HGBASE:SNP000763754"
     variation       complement(40807..40807)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:628708"
                     /db_xref="HGBASE:SNP000111700"
     variation       complement(40856..40856)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:634148"
                     /db_xref="HGBASE:SNP000528519"
     variation       complement(40872..40872)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:607154"
                     /db_xref="HGBASE:SNP000380635"
     variation       complement(42902..42902)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1148082"
     variation       complement(42996..42996)
                     /replace=""
                     /evidence="not_experimental"
                     /db_xref="dbSNP:1291089"
                     /db_xref="HGBASE:SNP000157115"
BASE COUNT    52693 a  34921 c  36093 g  57882 t
ORIGIN      
        1 gaattcagtt gctggctctg ccacttactt ctgagtggcc tcaaattttg taacctctct
       61 ggttaaaatc agctgttttc caattgacct tagccctggc ctttgctaac attaaatgag
      121 tgttgtcacc actctaagct ttaattcctt cacatagaaa atgaagagat tggatagacc
      181 agacaattgc cacatcccct tccaaatcca ggattctata gttctagtag gaagcaagga
      241 aacaaaacat ttcagtttat tgtttggtat aaatgaatca tcttcttctt tgaagtcctt
      301 gttaatcaac tttcccataa gccagaattc atcactccca ctgggccttg tgaaaatggg
      361 aaaacatctg aataatggac tattgctggg gctttggaac cacactgacc tgtcttcttc
      421 ctcggccgta tgcatatgat ggacacctgg acacggtact tagcacccta aacatcagct
      481 tcccagtttg taaactggag ttagtaactg agcatccctc acagagttat tgtaatgact
      541 aagtgagata atttatatgt agataaaatg ccttgcctct aaaaaatatt cagtgatgtt
      601 aagctattgc tttcttttta tttacttgtt tgttgaaata atttatatgt ggtgaagtgt
      661 ccaaattgta tacacctcaa tagatcttta catctgtata tacctctgtg acaaccccta
      721 gaacaagata cagaacattt ctagcacaac agaaggctca cttctactcc ctttcagtaa
      781 atatccaact cccaccaaag taaccaatat tctgaccttt atcaccatag attagttttt
      841 cctgttctca aacttcatct atgtatgtat gtatgtatgt gtgtatctat ctatctatct
      901 ctatcatcta tatctatctc tatcatctat atctatctat catctatacc tatcatctat
      961 atctatcata tctatctatc tatctatcta tctatctatc tatctatcta tctaattttt
     1021 gaaacagagt ctcagtcacc caggctggag tgcagtggta cgaccttggc tcactgcaac
     1081 caccacctcc caagttcaag tgattctcat gcctcagcct cctgagtagc tgggaccata
     1141 ggcctgtgcc accataccca gctcattttt gtatttttag tagacagggt tttgccacgt
     1201 tggccaggct ggtcttgaac tcctgatgtt aagtgatccg cccaccttgg cctcccaaag
     1261 tgctggcatt tcaggtgtga gccaccacac ctggccactt cacatgaata taatcataca
     1321 ttatgtgatc tttagagtct ggcttctctc aatcaatatt atatttttag tgagattcat
     1381 tcatgttgct gcaagtagca ataacatttt ggtcttcatt gctgtataac attccactta
     1441 ttgcatacca caatttattt atatactgta ctatttatgg acatttgagt tgcttccttt
     1501 ttttgctgtt aaaaaaataa ttttctatga gctacttacc catgtctttg gtttatgtaa
     1561 gcactcattt ccgttgatat acacccagca gtgaaattgc tagggcatag agtatttgta
     1621 aggttaactt tagtagatcc taccaagcag ttcttggtag tacaagcagt gcaagtgctt
     1681 gtaacagttt acattcctcc cagcagtgtg aaaggtttcc agttgctcag ctgcttcacc
     1741 atcactgggt tttctgaatt cttttcattt agtcattcta gtggcaatag ggtagtatct
     1801 cattgagctt tcaatttgca tgttcctgat gactaaaaat gttgattact ttttcctgcg
     1861 ctttttgtcc atttcgatat cctcacttgt gaagtgccta ttcaggtccc ttgcacctca
     1921 aaaatgttag ctattatttt gtatcatact aattgtgctt ttaagttatc cgtatatcta
     1981 tctactctcc aaatagatga taagcccttt gatatgcaag gtctgtgcgt cactcattta
     2041 cgaattctta gtgcctaacg taagactcat gttatacatt cgttgaatac attgtcaaac
     2101 gtctaggact cagcagatca tggcaaaatg tcgccatctg gtgtctgcag ggaatgagat
     2161 gtggaggatg caaagccagc tggctggata attcattgtt ttccatgtga gctttctctt
     2221 atgtacgatt taaaaaatat gtatatattg caaattgcct ctgcatactt gattttaaaa
     2281 atattttcta tatgtacttt catttttaaa aactcaattt aaagtgcaaa cttgtggaac
     2341 agaaaaagtt ccacaatgac taaattcttt actaaacaat tactaaacaa ttcactaaac
     2401 taaattcttt agtaattgtt tacattttca agagttgggt gctgtattca tagatgaaac
     2461 aataagtact tactatattc tagtcctgaa gtttattcaa gagatataag gtgctcatag
     2521 gctagtaagg aagaaacaaa aaaatcagcc tggagtatta taataaatgc cttaaaatag
     2581 gtgtttgttc gttcattcgt tcactcactc attcatcatt caacatatat tattgagcat
     2641 ttattctgta ccaggcattg tcacaggtac tataaaccca aacgtgtgtg tcctaaagtg
     2701 tgactgctct aagaaaacct atagtaaaaa tatatatata atttttcaag gatttggaac
     2761 tttggtatat tttcctttga gtataagctg ctgtagacgg taggccatgt gagaccccag
     2821 cttctattag ggttacacat agaacaagat ggccctagtt gaaaatactt ttccataaag
     2881 tgtactgagg tggggaggag gtggcgaact tcactgctct tctcaactct ttcttccctc
     2941 tactcactgc tcctcaatcc accaccaaga caaatggtaa caatggattg atcaggttta
     3001 tttgtttgtt ttttgagacg gggtcttgct ctgtcaccca ggctggagtg cagtggtgtg
     3061 atcacaactt actgcagcct caaccccagg ctcaagcaat cctcctacct cagcttcctc
     3121 agtagctagg actacaggca tgtgccacca tgcccagcta attaaaacaa cattattttg
     3181 tagatatggg gtccccacca tgttgcctag actggcctgg aactcctgag ctcaagcgat
     3241 cctcccaccg cagcctctca aagtgcttgg attataggtg tgagccaccg tgcctggctt
     3301 gatcaggttt agaaacattg tagtgcccat gggtaaagtc tctgtccagg ttacaggcta
     3361 gagctcacat gggcgtgacc tcccagtcac tgtcacactg ttggaggaca taggctgggg
     3421 tggcaatacg cttctgataa aggccagtag taggtgtctt aggctggcaa tattttaagc
     3481 actgggagat atgatactgc acctttcctc ttatactttt tttttttttt tttgagacag
     3541 ggtctctacc acccatgctg gggtgcagtg acactatcat agctcgttgc agcctcagcc
     3601 tcccaggttc aggcaatcct cctacctcag cctcccagat tcaggcaatc ctcctacctc
     3661 agcctcccag gttcaggcaa tcctcctacc tcagcctccc aggttcaggc aatcctccta
     3721 cctcagcctc ccaggttcag gcaatcctcc tacctcagcc tcccaggttc aggcaatcct
     3781 cctacctcag cctcccaggt tcaggcaatc ctcctacctc agcctcccag gttcaggcaa
     3841 tcctcctacc tcagcctccc aggttcaggc aatcctccta cctcagcctc ctcagtagct
     3901 ggagccacag ctgtgtgcca ccacatccag ctaatttgaa aaattatttt gtagagacgg
     3961 gggtcccatt atgttgtcca ggctggtctg gaactcctgg gctcaaacga tcctcccgcc
     4021 ttggcctccc aaagtgctgg gattacttgg gtgagccact gcgcctggcc tcctctgatg
     4081 cttcttgtga gcagatgtat tcttgaattt cttcacagca gttcacaaaa agtgtctatg
     4141 acctcatcac ccaagttttt tttttttttt tttttttgag atggtcttgc tctggcacca
     4201 ggccagagtg cagtggtgcc atctgggctc actgcaacct ccgcctccct ggttcaagtg
     4261 attttcctgc ctcagcctcc caagtagctg ggattaacag gcacgtgcca acacgcccaa
     4321 ctaatttttg tatttttagt aaagatgggg tttcaccatg ttggccagga tggtctcgat
     4381 ctcctgacct tgtgatccgc cagcctcggc ctcccaaagt gctgggatta caggcgtgag
     4441 ccaccgcacc aagccatcac ccgactttta cacattctcc tagacttctt ctgacattac
     4501 aatgcaacaa acatttattt atttcctaat ataaaccaaa aattctgcta gatgttggca
     4561 aaaaacaatg aaagacagtg tttgccttcc aagagaaaag gtaacagatg attaacatat
     4621 gtaaagggct atgacagaag tatatgaagg aaatatgaga gcttgcttct tggatgaagt
     4681 cttaagaata aaaaggaatt atccagcaag agtgggtaag agtgggggat ggacaatagg
     4741 agctgcatga gcaaagggca tgcatgcaga gctgtttgca ttccatcttc aacatgctgg
     4801 gaagctttta acctgagaag tagcagatac aaataaatat tttaaaaatt tattggcaac
     4861 catatgaagg atgaattatg gcatggtacc attggaagca ataattctgt tagcatgcca
     4921 tggtaataat tcacatggtg tagcctcagt caatgcactg aaagtgaggg aggagagatg
     4981 agagaggggc acagatgcag ttcgttaagg ttagtttaga attagtatca ctgatagata
     5041 tgaagagcaa gggaaaaaga aaaatctggg acaaatcata ggtttctgat ttaggtcaat
     5101 ggtggccagt cactttcagg aagaagaaca gatgctgggg tactggcttt agtgagggca
     5161 ctaatccctt ccccctgccc attccaactt atattcactt ctagaaagga tgaatgggat
     5221 tttggtgtaa taagaagaca ggttggccag gcgtggtggc tcatgcctgt aattccagca
     5281 ctttgggagg ccaaggcagg cagatcattt gagcccatga gtttgagacc agcctgggca
     5341 acatgatgaa accctgtctc tacaaataat acaaaaaatt agctaagtgt ggtggcacat
     5401 gcctgtagtc ccagctattc aggaggttaa ggtgggagga tggcttgaac ccaggacatg
     5461 gaggttgcag tgagccgtga tcataccgct gcactccagc ccagatgacg gaacgagact
     5521 ccatctcaag taaaacaaca acaacaaaag gtcaagaaat tgagcatggt gttgtgtttt
     5581 tcagcacctc aggcattctg atcactttta cttacttgtt tagattgctc atgtcagagt
     5641 gccgcaagtt gtatacattg cctcacagct taattgccta tgaggagttt gggtccaaaa
     5701 acctcactgg ttagcagtaa aaagctttca aaaatttata attccagaca tttccctatt
     5761 tccaccgttt tgcagagtta gagtccctgt ggactgagcg agcttccagc actgggagtc
     5821 gacctctagt ggtaattctt taaactgcaa gtcctgactt tggtgatttg gcttattttg
     5881 ccagaaccag ggcagctgag ttcaggtttt ggttacaatt aataaaaaat gttggcttct
     5941 aagagatcta ttaatatctc agttttactt atgagaggcc ttagagatat gaagtaagat
     6001 gaactcacat gcccaaggtc atacagctag taagtgatga aggtaggatt caaatcctgg
     6061 tccgtaggtt tattaatcca gagcctgtgc tcttaaccac tacctgttct gcctctgttg
     6121 ttacttgaat catctcttta ggcaaagttg accaatcttt ttctttcttt ctttctttcc
     6181 ttccttcttt ctttctttct ttctttcttt ctttctttct ttctttcttt ctttccttct
     6241 ttctttcttt ctttttcctt ccttccttcc ttctctttct ttctctttct ttccttcttt
     6301 ctttcttttt ctttcttctt tctctttctt tctttcttcc ttcctttttt tgtttctttt
     6361 tttttttttt caagttctca ctctgtcacc gaggctgaag tgccactgtg gcctgatctt
     6421 ggctcaccgc aacctcctcc caggttcaag aaatccttgc atctcagcct catcagtagc
     6481 ttggactaca ggcatgtgac accacacctg tctaattttt gtatttttgg tagagacagg
     6541 gttttgccat cttggccagg ctggtcttga actcctgagc tcaagcaatc cacctgtttc
     6601 agcctcccaa agtgttggga ttacagacat ggggcactgt gcctggcctt gaccatccct
     6661 tttatatgct ctctaatata tctactgtag cacatctcat acattagaga ccagtctttc
     6721 ccaccagttc atgaattccc tggaagcaga gctcttagta agtacacaat gaatgtttaa
     6781 tgaatgggca gatattataa tcctactctc agactctttt aattttttta ttagacttta
     6841 agttctggga tacatgtgca gaaagtgcag gtttgttaca taggtataca cgtgccatag
     6901 tggtttgctg cacccatcaa cctgtcatct gcattaggta tttctcctaa tgccctccct
     6961 ccacttgccc ccgaccccct gacaggcccc agggtctgat cttcccctcc ctgtgcccat
     7021 gtgatctcac tgttcaactc ccacttatga gtgagaatat gcagtgtttg gttttctgtc
     7081 cctgttagtt tgctgagaat gatagttaca agcttcatcc atgtccctgc aaaggacatg
     7141 aactcatcct tttttatggc tgcatagtat tccatggtgt atatgtgcca cactttcttt
     7201 atccagtcta tcattaatgg gcatttgggt tggttacgag tccttgctat cgtgaatagt
     7261 gctgcaataa acatacatgt gcatgtctct ttatagcaga atgatttata atgctttggg
     7321 tatataccca gtaatgggat ggctgggtca aatggtattt ctggttttag attcttgagg
     7381 aatcgccgcc ctgtcttcca caatggttga actagtttac acttgcacta acagtgtaaa
     7441 agtgttccta tttctccaca tcctctccag catctgtttt ttcctgactt tttaatgatc
     7501 gccattccaa ctggtgtgag atggtatctc attgtggttt tgacttgcat ttctctaatg
     7561 accagtgatg atgagctgtt tttcatatgt ttgttgacca cataaaatgt cttcttttga
     7621 caagtgtctg ttcatatcca tcgcccactt tttgatgggg ttgttttttt cttgtaaatg
     7681 tgcttatgtt ccttgtagat tctggatatt agccctttgt cagatggata gattgcaaaa
     7741 attttctccc attctgtagg ttgtctgttc actctgatga tagtttcttt tgctgtgcag
     7801 aagctcttta gtttaattag atcccatttg tcaattttgg cttttgttgc cattgctttt
     7861 ggtgttttag tcatgaagtc tttgcccatg cctatgtcct gaatggtaat gcctaggttt
     7921 tcttctaggg tttttatggt gttaggtctt atgtttaagt ctttaatcca acttgactta
     7981 atttttgtac aaggtgcaag gaaggggtcc agtttcagtt ttctcgcaga ctcttatagc
     8041 tagctattta cataacatct ccactagaat gtcaaataga catctcaaac atcccatgtc
     8101 caaactacac tcccgatgat gctaaagaga tgtattccac ctactatctt tccatcttaa
     8161 tcaatggcgt ccacctttgc ccatttactc agtccaaaat catacaattc tctttaactc
     8221 atcttcccca ccccccaaca aatctcacat ttactagcaa atcttgttaa ttctatttta
     8281 attatatgat ttgaactcta ccttttctca tcatttccac tgctctgctc cttatccaga
     8341 ctgtgcatgt gtttcgcttg gattactgtg ttagcctgcc aagtggtgtc ttagtggtct
     8401 cttcctgaac tgccaagaat ctattctcag ctatcagcat atttatagtt gtgagatgat
     8461 atgtgagttc tttgaacaat accctctagt ggctccccat cttaatcaga atcaaagaca
     8521 caattgttcc aagcccatgt atctggctcc tcattgcccc tctaagagca tctcctattg
     8581 ctctcccctc tctctccggg ttctaggctc accaagcaca cttctgtctc agggacttta
     8641 cactagctat tcactctctg gaatgctttt tcatgaatag ctgtttaaat tgctcctcca
     8701 actctttcac atctttgttt aaatgtcacc ttcccagtga agccttcctg gattatcccc
     8761 tcacccatcc gtggaacttc ctctccactt tccttgatta atttttcttc ttggcagttt
     8821 tttttccttt taatatgtga tataatttaa ataatgcttt attttgttga ctgtctttcc
     8881 tcaccatact ataagctcca tgagtgtggg gatatttgtc tcttttgttt actgctactt
     8941 ccctaacacc tccaacaata ggtgtttatt acatactttc tggatgcatg aaagaaaaac
     9001 gaagaaactc atccctcagt acaggaactg tatgttctga atgattgcat taggtgtgct
     9061 ctatacattt ttgcctctct taacagtcta caattccttg actctggggc cttctagttg
     9121 gtatgccccc tattaaacta caggcagatt tttattaaga aaattcactg cagtaagtat
     9181 ttatatagag caataattat ttgtaacttt ttgttggtca gtttagcaac aaagcttcct
     9241 atgcttagca attacgtgca atcattttcc ctgttcatgt aacagtcttc tcatatgaga
     9301 ataatggatg gagcagtatt tttatttaga ttgaactttc gctgtactct ttatgatagt
     9361 tctgatcaca gaaaatgatt actcctccac catgtcctct caaaaaataa aaaagttgac
     9421 tagttgaaac tcccaaccca ctcttcaaaa acaagaaaca caaaacaaaa acctaccagg
     9481 aaataaacat gaatatctaa ggggatgtga gggtgttgtc agttcacttt attaatcagc
     9541 ttaacacaat ccagcctaac aaaataaatt agagcttaag tcaaagccac aaggggttaa
     9601 agtggttgta ggaggtttga gaagggccat tgagccagat gttgtgtcta gtcaatctca
     9661 agcttgctgc acagttaaag ccgaccattc taccttccct aataacactt tagttgaacc
     9721 ctcaaatcct cccagaagtc ctccctagtt attattaacc aaccccttct ctcaattcct
     9781 aagtccaact cttctcttcc tgagcccatt tctttattcc acatccctca ttttcagatg
     9841 atgaccacag catttaccac aggagaaaaa aagagaaacc atcagtcaca gattgcctta
     9901 attttccttc cttccccctt ctatgagctg aacacatttt gtgttcacct gaacatcttt
     9961 ttcttttgtc ccagaatgaa atatttttca atgctaatcc cttcacctgt gcttttgatc
    10021 gtatcctctt aaagatttcc ttcctcaatt atctcctctg cctttttcag tgtttcagtc
    10081 tccccttgtt ccttctcctc agcttatata atttggcaat atgtataaat acacctccta
    10141 gcacagtgtc cggaaaatag caggtgctca ataaatgtta gtttgactcc cctaaagctt
    10201 caagtgtccc ttagcctgag aaaaaccatc cattcttgac actgcatttc cccaaactgc
    10261 cctgccacac tccttttcct tcccaagctt tttttttttt tttttttttg agacacagtc
    10321 tcgctctgtc acccaggctg gagtgcaatg gtgtgatctc ggctcactgc aaactctgcc
    10381 tcccaagttc aagcgattct cctgcctcag cctctccagt agctgggatt acaggtgtgc
    10441 accaccaggc ccggctaatt tttgtacttt tagtagagac ggggcttcac catattttcc
    10501 aggctggtct caacctcctg acctcaggtg atccgcccac ctcggcacct gaaagtgctg
    10561 ggatatcagg tgtgagccac cacgcctggc ccttcccaag attcttacaa aagcattctc
    10621 tatgcccaat ttctctactt ttacttgctc atttaagttt tgtctcactt tatataattg
    10681 aattatttaa tcaaatactc tctttcaggt ttttatttaa cttggccgtt ttacggcatt
    10741 tgataacact aaccagttcc tcctttccat tttgttaaaa aaaattcttg gacttttttc
    10801 aacatttctc tctgattccc ctttactctc tgttgttctt caatgttctt tggtgggtac
    10861 cgctctgcct ccgtcaatgg ttccttaaat gtttttctgt ccctagcaat tttcttttca
    10921 atctattcaa cttccttctt taaaatgttc ccttccacac ccattctctg aactgtcacc
    10981 tatactgcat attgctccca aatctgtatc ttctttccag attttttctc acaacagagc
    11041 tacttctact tactggatat tctagcattg ccttacattc tatataacca aaactgagct
    11101 caatatcttt cttttatgca tttttctttt tcctatgttt ccaaattgaa taataatgtc
    11161 acttgtcacc cagatcccca cagccctctg tgcatgttgt gatttattca tctttgcatc
    11221 ctccacctca tcccctagct tctcgttcat tcaagcccat tatagttccc agtacacaga
    11281 agacactcaa aagctatttg ttgaatgagt gcataaatga aacgctttca gaggaataaa
    11341 tctataagca atcaagggtg ctcttgattt ttccataaag ttacatagga cattgtaatc
    11401 acccagttga tcattgctaa gaaagtgctt gatcctattc tctattatca gcttgcagga
    11461 gaaaggagaa acaaacatgt tttatgtttc ttgtatagac aggatgacta atcttagaag
    11521 acttataaaa acgagcatct tccgagtcaa cctgaatgta aaatgctgaa agaatgaact
    11581 gtgaatcctg cttggggact ggtagagtga atttttgact cccattcttg acccctccta
    11641 atactcaaac cctttgccat ataattcatc agtccctccc actaagggaa ttggtgaaaa
    11701 ttctcacgct ttgactttgg gctctgccac gttgctttta ctaatggatg ttagtggact
    11761 ggaggcatga ggcttgacat gcacttggtg gttgggtttt ctttctttac cttttgatca
    11821 ccatgagagt aacatatgtg gctcacctca ctaagcccag gaggagaatg ggagatgtgt
    11881 agagcacaac taccccagct gacccacaga ccatcaggga gaagcaaagc cacccagtcc
    11941 aacccagcca agatcagttt ctgaaactct agctaatctg caaactgcat acgtccaata
    12001 aatgcttatt attgtaaacc accaacattc tgtgttattg tgtagcagta tttgaataat
    12061 acaaatacca acaggcttct tttttttttt ttttgagacg gagtttcgct cttgttgccc
    12121 aggctggagt gcagtggcgc gatctcagct cactgcaacc tccacccccg gggttcaagc
    12181 gattctccgg caggagaatc ctgagtagct gggattacag acatgcacca ccacactcag
    12241 ctaatttttt gtatttttag tagagatggg gtttcatcat gttggccagg ctagtcttga
    12301 actcctgacc tcaggtaatc cacctgcctc ggcctcccaa agtgcaggga ttacaggcac
    12361 cggccccatc agccttcttt tactcccttt cttctgactc tggcattctg cctcccttct
    12421 cctcagttct cttctcaaca gtctgctaat gtgaatacaa ttggctttag ggtcaaaaag
    12481 ttgtgacttt gaactcattc tgtgaatgac tgggaggctt gaatatgtta cttttctcct
    12541 ttgagccttg gtttcttaat ctgtgaagta agaaaaagat acctgtgatg actcaataag
    12601 ctacattaag caaccagcat gcaataatca gcctacactc cagaactgag tgtaactgac
    12661 cagaagggat cacaaactga gcaaaagcag cggttccttg ttcgttctgc actctcccca
    12721 tacaaaattc cattcctttc ccccagattt gttcttcttc ttaggctcag gcagttttac
    12781 catagtgtgt tctctctgcc tccagcactg tggtaaagat gatgtttctt attcctttaa
    12841 tgcctcttgg ctacatccat tctccaggga caattcattt taaggagtgc cttttatgtt
    12901 tggccttctt gtgtgtattc tttgaggtat gtctcgtgtg tgtgtgccta cacagtcatg
    12961 catcgcttaa caatgggata tgttatgaga agtgtgtcat tagatgattt cgtcattgtg
    13021 tgatcataga gtgtatgtac acaaacacag atgctatagc ctacttcaca cctaggctat
    13081 atggtatagc ctattgctcc tacgctacaa acctctatag cattttactg tactgaatac
    13141 agcaggtgat tgtaacacac tggtaagtat ttgtctatct aagcatatct aaacatagaa
    13201 aaggtacagt aaaaatacaa tgtgaaagat aaaaaatggt ccacctgtat agggcactta
    13261 ccatgaatgg agcttgcagg actggaagtt gctccaggtg agtcagtgag tgactggtga
    13321 gtgaatgtga aggtctagga cattactgta cacaactgta gacttcatca acactgtata
    13381 cttaggctac acgaaatttt tacaaatttt ttctttcttc aataataaat taacctaagc
    13441 atggtgtaac ttttttgctt tataaacttt tagctttttt aactttttga ctcttttata
    13501 ctaacactta gctaaaacac aaacacactg tacagctgta ccaaaatatt ttttttcctt
    13561 attctttaag cttttttcaa ttttttcaat ttttattgtt ttacttttta aacttctttg
    13621 ttttaaacca agacacaaac atagcttagc ctcggcctac tcagggtcag gatcatcagt
    13681 atcactgtct tccacctcta cattttgtcc cactggaaca tctttcaggg gcaataaccc
    13741 cagtggagct gtcatcttct ataataacaa tgccttcttc tggaatcctt cctgaaggat
    13801 cttcctgagg ctgtcttcta gttaactgtt ttatttctta aataagtaag agtacactct
    13861 aaaataataa tgaaaatata agtacataag cccatgacag tcatttctta tcaagtatta
    13921 tatactgtac ataattatat gtgctagaat tttccatgac tagcagcaca gtaggtttcc
    13981 agcagcatca tcatgaacat gagtaatgca ttgctatgac atcagtaggc tgtaggaatt
    14041 tttcagctcc attacaatcc tacaggacca ctgttgtata tgtggtttgt cactgatgaa
    14101 aacgttgtgt gccacatgac tctatttgtg tgcatataaa atgttaactt gatctttaat
    14161 tgaagtattt aatctattta catttaatgt tactatttat atatttgagt tttagttacc
    14221 attttactat ttgttatcta tttgactcac ttgttttata ttcctttttc tcttagcttc
    14281 atttgcataa ttttttagta cattattttc cctctattaa ctcgtcagtt atacatttgc
    14341 ttactattgt tttggtggtt actctagaaa tcataacata tattttttat tattactgtc
    14401 taaaaaacaa aatagccctt ttccactttt tcaataatgc cagaaccttc aaatgtttta
    14461 actccatcca ctctcttcat cttatgtgtt attgctgaca tatatctcat aagacatatt
    14521 tactttatac aatcattatt gatttatact tatcaacata tttaccattt ccatagctta
    14581 ttacttagtg tatttctata tttccatttc atcatcaata ttgccagaag tttttgtagt
    14641 cttttcaaag aaccagctta cttactttgt taaacatatt atatatattt tatcattact
    14701 ttctccaatt atctcctttc tatattcttt taatttattg tataaatatt tatccttttt
    14761 ttatctgctt gatctatcaa aaactaggag aggtgcattt aaattgctca ctgaagtgat
    14821 gaatttatca atttttcctg taattctact gatttttatt acaaagccag aagcatatag
    14881 aaatttagac atgttatata ttcctggtag attaaacttt taattatgta gaggccttct
    14941 cataatgctc tggcttaaaa cattttttat tcaatattaa aataattcct ttagctttct
    15001 ttgtacagta ttttcctggt atatcctcac tttttaaaaa ttttccctat cctggccggg
    15061 cccggtggct catgcctgta atcccagcac tttgggaggc cgaggtgagt ggatcacgag
    15121 gtcaggagtt caagaccaac ctgaccaata tagtgaaacc cagtctctac taaaaaaaaa
    15181 aaaaattagc cgggcatggt ggcaggcacc tgtaatccca cctacttggg aggctggggc
    15241 aggagaatta cctgaaccca ggaggtggag gttgcagtga gccaacatga tgccattgca
    15301 ctccagcctg ggcgactgag tgagattcca tctcaaaaaa aaaaaaaaaa aaatcactat
    15361 ttttgtatat ctgttgtata tactttgtta taatttactt ttttttttac ccattctgac
    15421 aatctctatc ttaaatggta gttactattt attctatttt attcatatat ttgggctgtg
    15481 ttcttcgtag ttctattttt tcatcttttt atgctttttt tggcctttct ttagacaacc
    15541 taagtcccac ttttgaaaaa aattaattcc tattttccct ccactattta gaaaattact
    15601 ctctccattc ttatgagtat ctttgatact acagtgcaca cttaatttaa caatgttgag
    15661 gttaaccaat atcttacagc ttttgtcctg aacagttcat gaatgttaaa acacttaatt
    15721 cagatcaccc tatcccaact tacatactac ttctattctc tattttagta atttattaaa
    15781 actgtagttg tattttagtg gagggccttt cagaatatca tgctaggggc actgaaggag
    15841 gcaaggatct tctcccttta tttgctgacc cagtcttctg ctttttgctg gtttcttgac
    15901 tcagggttta ctcctcattg tttggatgga ttattcaact gccccacagc tcttttgccg
    15961 tggaactgct tctctgtaga cctgttgcca agattccgca aatgaaccca agcaccaagc
    16021 aattgctgta ggcctcttcc tgaaatcttc tcgttagtag ttccttggac ttgtctagga
    16081 gagatgtaca actaaaaaag aaaccacaaa cagaagagca gagaagtcgt cttacgggaa
    16141 accctgagaa tctgcagttt tgattatatt cctgtgaaat ggcctttttg cagcgttgtt
    16201 atattctgca gagaacgcta ctaagattta ttctctactt aaatggagaa ggtttggcta
    16261 ttttcctgca tggcgtttta gatggttgaa tcttcttgct tctggaagtc tttacagctt
    16321 ctggaagtct ttacataacc ctacaatgct ctcaacctcc tctgaagagt ccctatcttt
    16381 atgaattgcc aaataaacta gtttgtgctg actgattcct tttttagaat ttgaattgca
    16441 ttcctccttc tacctgaaac ctcggtgtac acacgtgcat gcgtgcactc acacacacta
    16501 aagagaatag aaattgcaca ttaagaggta tctttgtgct ggtctgacaa tcactttgtt
    16561 cctttttgtt attaaagata aaaaaggtgg tgtctaaaga aagctgggct cctccttgct
    16621 tgatcctcag gacttccgca aggatgaatt aagttattcc acttattcca aggagatgtg
    16681 cttacatttg aaacattgta tcagttactt tgccacaata aaggttagta atcacgtggg
    16741 ttggccatcc actttgtggc tctttcagtc tttccctctc ccataaacta gattagtggg
    16801 ttagtcagcc aacatcacta gaaatataag gagatggaaa taattgtagg tatatttctc
    16861 tcagctattg tggctggact atttaggtca gctgagggaa gacgctagag gtaaaacaaa
    16921 ctatttttaa aaatactggt gtggggccag gtgcggtggc tcacgcttgc aatcccagca
    16981 ctttgggagg ccaaggcagg cggatcacaa ggtcaggaga tcgagaccat cctggctaac
    17041 atggtgaaac cccgtctcta ccaaaattac agaaaatcag ccgggcgtgg tggtgggtgc
    17101 ctgtagtccc agcttcctgg ggaggctgag gcaggagaat ggcgtgaacc cgggaggcgg
    17161 agcttgcagt gagccgagat cacgccactg cactccagcc tgggcgacag agcgagactc
    17221 catctcaaaa caaacaaaca aacaaatact ggtgtggaag ggtaccaaat tattaacctg
    17281 ctcaacatgt catcagttac tatttctcag ttcagctttc attctagaaa actactatgg
    17341 agccgttaac tctcatttgg attactgtcc tttcagccag tctggtgaat caaaattttt
    17401 tatttattaa atatcccatt tttcgcctgt ggcagggtgg tggtccagag gccttgactg
    17461 aaggggactg gaacaacttg tctgtgccat ctctgggctt ttctcctcta ctactctact
    17521 gctcagtgca aacaatgtat cttctattag atccattact tcagttgtgc tttgaagggg
    17581 gcaacaggtt tcttagtggg ttttgatttt agtaccttga tgttaatctg atttatgaaa
    17641 ttctccatgg agttcatctg agtttaccgg attctgctcc ggaatatgag gcctaagtcc
    17701 cagataataa aaatgtattt tggcttgatc tcttgggcat ttatttctcc tcggactttg
    17761 tggtgaagag gttaaatatt ccttggttat tcctaaatta tctggtcaaa catccttata
    17821 ttatcatttt taatgtgtca tacctcttta gcacatttcc aaccacctgc cacttctgtt
    17881 aattaagtag cgtattaact tcctccaaat aatatcttta aaatcccacc gttttctccc
    17941 tcagaaactt agtatggtat tcaaggatgc tagaattcta ctgctcacaa gatactagag
    18001 gggacccctc cgaatacaca ccctgtgctc caacctccct gctcacgctc agctgcacta
    18061 cttctttcct gccgctgcac actgtggttg tgtttgttca gatttgggag acaacatgtc
    18121 cctcccagaa cctcagaaaa ttcagtaatt tacaaaaggg accagagatt tagtgtcagc
    18181 atatgaaact ctgcagggag atcagtaatt aaggactatt tgatgttcca acaaaccggc
    18241 ccagcctcac aagctttccc tcatgtagaa ctctgacaga ttttcattta ttggaataat
    18301 gcaaataaga aaattaaaaa gtcaatttgt tgtcactgcc agtattttac caacctttat
    18361 aaatggttaa gtctgagcta ggagaaacta tcttttgtgg cagacatttc acccaggaca
    18421 agctgtgctt aggcttagat acttggttta gaaatgcctg cttattagga cagtatcttc
    18481 tgcaaactcc aggcttggat cttatctcag agtgcatatg tttcaccgga ctctgctaat
    18541 catcccaacc cttcctttcc tcaaggaaaa atactctgta ctcccagatc tatttgagta
    18601 tgaaccaccc tcagaagtat caggacactg aagccctgga aaaggaatgg gtaagatggg
    18661 aagtcccaga aaccagggaa cttggctgca agtgttacct ttatttattt catatatgta
    18721 tatttccaga aggacaacgg ttgactggta ttaagaccaa accagtccat cagaatatca
    18781 tcgaccaaaa tgagaatttc cctgttgggc cattagggtt ggagtcttat taaccctccc
    18841 ctattcctcg ggcccataat gcattatgag atagaggaga agaaaccagg cacagaagac
    18901 tctccctgtc atgctttaac cccataccct gtgctccact tatggaggac gtctccccag
    18961 ttcttgccac tcccacaatc agagaaggtg aggttcataa ttattcagcc tcatctccaa
    19021 ggaaccttta actggcaaca gagattgttg ggccatcatg agatgctact ttctagctct
    19081 atgaacataa aatcacgtaa gaaaaagcaa acaacacaaa tacatgaaag ccatttactc
    19141 ctggtgaatt cctcagggtc ccaggttcaa cactttccgt gatgtcagag tactcagtca
    19201 gggatgatgg ggacagggtg tcagaacagt cttgatggtc ttgccagcaa cagctttttc
    19261 ttattttcca taatttggtc ttagtcgttc tccagttgtc ttcatgtaaa taaagtggcc
    19321 catggcaatc atgattctgt aattgttata gtgcctttgt aagttgacag tttccaaatc
    19381 cccttactca tacgacccct gtgaaggggg gtgtgaaggg gttggtgggc ttgtgcatat
    19441 gagggaatgt gaacgatttc attatgaccg aattatgctt tactcaataa gcactcaaac
    19501 actaccatct cacttgtagt agaagtgcta gggatgcaac caagagactg gttgaataac
    19561 gggaaggtta aatgcatgag tattttaata gaaaaaaata ttaaaaacaa aaccaaaact
    19621 cgtatggaaa gaggcttctg actaggccct cctttctagc agtgtttggc acctgataac
    19681 aatttgacgc tgggggaggg agcagcttga caaggtccac atgaagcagc cttgagattt
    19741 ttcgcccact tccatttctc ctcagcatca aaggaaagtg catggtaaga agtgaatcag
    19801 acagcgaggg atctatgcag ttatcctgtg aatgtgtggc aaagccatca ggacgcaaac
    19861 ctcctgtctt gagtccagag ctgtgtgctt taagatttga ccccagtaaa gacagaatcc
    19921 ttcaggctcg tcccttccca aacctaaggg gctgtccttg gccactttca acttgaagct
    19981 gttgagcagt ctttaggata tgtaacagcc tattttttgg acgatatagg aaccacgacc
    20041 tcttaagtct cttagttctc ctactttata cccatgaggt agaggcaggt gcactccagt
    20101 gaaggagaag cctcaattca ggttgtactt tggatgaaac atcccctcaa ggcgtagagg
    20161 aaggctgaga ggttctgccc aggctcgtgt ttagttgcag gaagaggtaa tgtcagatct
    20221 gagcaggtca gggagactcc ctcgaaaagg tcttcccagg ctgacaagag ggcttttcct
    20281 cttcctcacc tcccttaggt gagggctgaa agcagatctc ctcacatggg gacctagcta
    20341 ggaggtcttt tctgagtggg tcctctgatg cctaattaag tgatatcctc tgctgaagct
    20401 ttttccacag gtagggcacg tgaatggttt ctccccagtg tgtgttctct gatgcctgac
    20461 gaggtggtcc ctgcgactga agctcttccc acattcgttg catcggcagg gcctcactga
    20521 ggcgtgtcct ctcaagtgct tggcgaacgc tgcgctgtgg gtgaagcagc gcccgcactc
    20581 gctgcagagg tagagttcct cagcagcgtg cgtcttccgg tgcgccaggt accgcctgtg
    20641 ttcactgaag tcctcaccac actctccaca caagtagggt ttgcctccca ggtggattct
    20701 ttggtgtgtt gttaacacag atttctggct gaagcttttg ccacaaatag tacaaaagaa
    20761 gggtttttct ccagtatgtg tcctctgatg tctgacaagg tctgaagtcc agcggaagtg
    20821 ctttccgcaa tcatcacatc tatagggttt ctccactgat ggagttctct cagcctgtgt
    20881 cacaggggag gtctcttcca aattcttccg gtttagggga tatttgtaag gcgcgttcat
    20941 cttgtgaacc ttttggtgcc tggcaagatg tgagcttcgt gtgtaacttt ttccacattc
    21001 catacattta tagggtttct ctcctgtgtg agtcctcagg tgtctaacaa ggtgggagtt
    21061 acaagtgaag ctctttccac acacagaaca gtcatgatgc ctccctaaca gggggtggac
    21121 gggtgtagtt tcccgaaggt tcacaaaact attcacttga gaaatattag taccaaatct
    21181 tctttcatta agtctacctg gattgtcctc aaagactatt tcccaatctg gagtctggtg
    21241 aatttctggt tctcccaaaa caggcctgtg tatatcctcc aaactcagat cttcctgctc
    21301 cagacactct tcctcatctt tactcctatc tcctgtagaa agggtgagag gaaaaagggg
    21361 gtcactgtag cggcaacaat gccttctaca caatggggag atttttacaa agggttttga
    21421 gatggcaaga ctaaatagaa tgcctgtcct gtgccaagca ctttctcata ttgttatgct
    21481 atcaacaaac cttggtatgc acaaatataa tcttcatttt acaaatgcag agattgagaa
    21541 tcgagggttt aagggaattg tacagtaaat ggtatagctg caattccaaa agttaacatt
    21601 tttctttcac ccttttgtat tacattgcta tcagacaaat gatgggagga gaaaagagga
    21661 gggcaatgac agaagaaatg gctgtcagag ggagaaagca gtactggctg acatgttaga
    21721 agaactgatg agagcggggc cctacagaga gagagaagca ctgcctagag gaactgctgg
    21781 ctcagggtgg gtaacaccgt ttttgtcatt cctcacctgt gtaggtaaaa ctcaggattt
    21841 ctggctcttg agtctcctga ggctcttgga tatctgggac ccaaggctct tcctctctaa
    21901 cctgggagat ctcatcaggt ctggggattg gaaatgctgc tcaagagagg gaaaatagga
    21961 tatcacgatt ggctcaacaa ttccctgtgt taagagcggt ccttttctat ttggtaggtt
    22021 gtggggcaaa tacatagcta gctcaggtga tgaaatcttt catctcttta gtttgtgtac
    22081 ttttaaccaa ggactgcgta tctcttgcct ttcttgtggt tttcacctgc aacttaataa
    22141 ttataccatt gtacacctta tcctcttttc ccatattcaa gaaagattat ctccaactct
    22201 tactgtttta aaactcatgt gcttacttca aatatttctg cactaaagct gtcatattac
    22261 aagtttgttt tcctattaga ggtttccatt tccatccatt tatcttttac ttgaaaggac
    22321 accatatttt tcacctaatc cctcaatttt attggtgggg aaggcataag agaagttcac
    22381 tgcatacaat ctaaggtcta agatccccca aaatttccag caggaaaaag atctctgggc
    22441 ttagaacact ctagaatact tgaaattcct tacacagaga gacaacaatt ccacagtctt
    22501 cttccaagac atattctcca tagaactctt tctgtgttgg gtccagatca ctccactggt
    22561 cctgggaaaa gcatacggcc acatccttga acgttaccag tccctgaaac cacataagga
    22621 tttcatcaaa acgtgatgct acgggtagcc tcgtattttg tccctgttga aggtcataca
    22681 ataggtggac tcctctagga gatgaaagga gcttgagtgg cgggctgctt aaactcattc
    22741 tcgggggagc catgtgtccc ctgtggcact ggccctgccc cctccaactc caccactttt
    22801 cctgaggacc agcttatgtt cttcttcttt aaggtattgt ttaaaattta ggaaaggtct
    22861 taaaaatcat cattcagctc cctacttgac actttaacgc tatatacatt tctgcaaaat
    22921 tcatcttttc tagtacactt tccctaaaga ctctaatcac tttcaatagt ttctatactc
    22981 tatagccaaa acaagacttt tttcctcagt tagattacaa tctaaaacca tacatgaatt
    23041 ctatttcttt ttctccagcc acatggctta gtttcagagc tttgatcatg gtgaatactt
    23101 cctaaatgtc tcagcagtac agtctgtcat acttacaaat gactatcaaa tttattcctt
    23161 taaaaaaaaa aaaaactaaa aaaccctcat ttgacaactt cgcagttgta ctggagtgtt
    23221 acaaaataat cccattttgt tagttcttct agtcaatggc aaataaactg gtgttggtgc
    23281 ctgtggatcc aatataaggt atgataattt atctcattat ctcctcccct tccaggtacc
    23341 tgcagaactg tgagcttaaa actggcaaga gtgtaaatgt gcatcctgct tcacctgttt
    23401 agtatggctt atgcccagtg gttcttcaaa caaattctct gtggtacaga ggtaactagg
    23461 gcacacctgt gacagagcag taagaagagc aaccatctct gagtctccag agctcctctc
    23521 tgcaggaagg tctgggtcct cgggcactgg gacctctatg aagaaaagaa ggcaaagatc
    23581 agtaatatgc agcatgcccc aataatgggc aaaaatctgg gcatccccca ccatctttgg
    23641 taggaaggtg gccctatcct ttctattatg ggaaccaaga aactggccta agggtagctc
    23701 ccatatccca atcccatcac ctatgagact atcagaatgc caagagaaca agcaacaatc
    23761 tgctgtctaa gcttggccct gtttatgggg gactctagct ggcggtactg tctcctcttg
    23821 acatcctgga ttctgtgatg tctttccata cagtctatct acccagcttc cttggtatag
    23881 gagaaatgtc cgagaaatgt ccccctcctt gcctgccttc tgccacaatc ccccctttct
    23941 gctgatgctt cccaccgctc tcctgcaggg tctggagctc ctcttcctgg tgtggacgct
    24001 gctctgccgg tgcccccaga tctgggctct gtgtggtttc ctcaggagac tgctcggggg
    24061 tcgagctttg cacaggatcc tgcagctcat taggtgactc aggctccact cctaaatgca
    24121 ccgtctcctc tgacaggact tcctggccgt gaacatggac agtcacctgg gaataattcc
    24181 aacttccagt caccatggag tcaggaggaa gttcttggtt gtcacgggag cttattttag
    24241 gagaagatgc ctagagaaaa cactcccaga gggacccaga caaggagggg aaactccagt
    24301 ttcaatggag caggcaagga ggagctgaag gttatcctcc ccaggacaag gcaggggatg
    24361 cgcaggcctg cactgctctc tcaccacccc cagcctgggc ccctgtcacc caaggttcct
    24421 tcccatctcc acctgtccca cctgcagctc tccttgctgc ctgcttccct agctgaccag
    24481 ccaggaaggg ggatctgtga ctggggatct atgagaacct tcgaggaagt cacaaaattc
    24541 tcctctccag gaacccacgg ctcaacattc aaagaaggga aaaccaaagc catgaccctt
    24601 tggtggctga gacccctcag atggtcccta tacaggtgtt ccaatatcca gaaagtcaca
    24661 ttcatacaca cacatccccc taatccatgg ggctcatggt atatgagcaa cccaagggca
    24721 gagcccacta ataatttatg gggatcctgc aagctctccc cgcaaatcca gccttccagc
    24781 aaatagtccc cctccacatc acacagatca ggactccccc tcctcaccca ccgccttggt
    24841 ctcctgggtt gtttctgcaa accctccacc agcgtcactg cctcctcgcc actttctggc
    24901 cgttggcccc gcacccagct ctgtagttct ccaggtagga cggtaagaaa ttgttccagc
    24961 acaagcagct ctaggatctg ctcctttgtc cgcctctctg gtctcagcca ctggtgacaa
    25021 agttctcgga gtctgatgag agcttctcta gggcttgctg cctcctggta gcggaagcgt
    25081 cggaagttct ggtgggaggt ttccagcacc gggtcatccc tctgtaagac agactctggc
    25141 cgacaggtga aatcatcttc cagtttcacc atcagaattc cctcttcttc ccaaagatcc
    25201 tggtcctctg gttccacggc tgtagccatt tcttggcttt ggggtggtct cacaccatct
    25261 agagctcaca ctgtcattag ccccccgcct cagcctggac acagcgagga ttttcttcca
    25321 agggccctgg atagagaagt aaagacaaac aagagtataa gcatgaaact atacacaagg
    25381 acaacagcct gagttcaatc ataatcctct acacaaactt cttcaaatgg ttaaatcctc
    25441 ttttccccaa ccaccatagc cataaatcaa cagatccagt tgggagagga taatttacaa
    25501 ctaaaggtat ggtcctctac tccctttcct aggcaaggtt catactctgc aagaaaatac
    25561 tgcatttcca cttcacaaat actgccaatt cccccgctta agtctccaaa ccggttccct
    25621 tctcttcctt cctacagact gctttagttt gagccttcat catctcctgc ctggactact
    25681 gctctaactt cctaagatcc ctgcagtact caactataag caaagtacaa cagaattacc
    25741 tgtggagatt ttgcaaaaca tagtatcaca catcattttt cagacactct gattcagtca
    25801 attcaggtaa ctgtatgttt agagatgcta cttgcagttc gaatgtgtat ccatggttga
    25861 gaaacaccaa ccatgaggga gatgtgtaag gttatgagcg aaagttctgg agtcaagctg
    25921 cctgggtttg aatcctggct ctgtcgctta ctaggtattt ccagagtggg accataggca
    25981 agttctcatt ctcctaatgc cagtttctct gtctatagaa gggagataat aatggttttt
    26041 atctaatagg cttactgtaa ggattaaatg tattactaaa gcctatgagc attaaatgta
    26101 ttactatctt tgcttagaag agtgatggca ccagctatta tctttctaaa ttatagttcc
    26161 aactatatta ctcagtattt taaaacaaaa cctttttcat gttagtaaaa tcagttccaa
    26221 aatcctggga atgacacgaa gctctttaca atcagccccc aatctatttt tcaagcttca
    26281 gatcctacct tttccctgta tcacctggtt ataaaaaatg cattgctgat ctccctacaa
    26341 cagggtgtct tttcagtctt ccatgtcttt ttgaaggttg ttccttctgc acaggctact
    26401 ctccaccctt ctcctttcca cgctacatgg tgtgttctct ttctttttaa cgggtcttgt
    26461 ctttattccc acaatttaca gcttaggtcc ctctcacttc tcatctggat gactgcaact
    26521 gcctccaaat gtgagctatc tgcctccaga tttgtcacct tcacgtaccc actatgatca
    26581 gaacgagctc tcttggcaaa cgtgctcatg tccctttcct atctaagatc cttccatcac
    26641 tccccgctgt cttgttaagt gaaatacaaa cttcaaacat tctacattag gttgacgttc
    26701 atcttgttat tctcttcgcc ctcctctcca atcctttcag acacacacgc acacacgtgt
    26761 gtacatgcaa agcacacaag agtcccgtgt tctttagctt ttgaatatgc tgtttcttct
    26821 gattctttat ccttggttag gttaaacttt aaatttttca agacataagc tcaagcttca
    26881 tgtcttctga gatgttttct ttgatcccat ttcccctact ctcagacata gttagaaatc
    26941 acctaagtcc tcccgtagtg acctgggcac ctctctatcc cagtattggt catattacat
    27001 agccatcgct catctttcct gtgaaactct ttgaggtcag agactatttt ccatcaatct
    27061 ccaataccta taataaagtg cacaataaat gcatttaaaa tgaataaaac tctactccaa
    27121 agcttcttcc tatggtaaca ggaagaacca ttgtttcctc cattatgctt ttactatctc
    27181 ttgattattc accatatcct gttaattcca acttccaaaa aatgtctttc gaatccatcc
    27241 atctcttcat ctctactgcc atttcccggt tgagccatta tgacccacta gaaggtattc
    27301 ataggaactt taaaaaaaat tacaatatcc tctgctccta aacggcactg gcacgtaaca
    27361 ggcacggata cattggagag atgacttagt tcaacctcca tgactggttt tcttggtcct
    27421 gtccccctcc agaccagtgt ccacaagcag cttaagggct ccatcatttc tcaacctttt
    27481 tgtgctatac tacagttgcc tcacatccac attcaaggtt atcgatccac tcttaatagc
    27541 tgtgtctcat ctattgttgc ccatcaaatg agtttacagt caatgatcac attatcttca
    27601 ttctttctca aaacgcttct aattcatgct cttatgacat ttttttcatt accctcagtc
    27661 acttgcaaca tactttcaca gtctatcttg gatagctccc taattcctag atcttcatgt
    27721 gtaatttttc ctctgctatc tctacctcat ggtgatttat ttttttctca agtggcttgt
    27781 aattttttta ttttatgtcc atctttttac tttgggagtc ctgagagccc tggatttaaa
    27841 tgtgagcccc ttgaatgtaa tttcatttgt ttcttcctaa gtgctaatgg tttcaatgat
    27901 cttggacagt ttgctttttt aagactctcc ctctgttgcc caggctggag tgcagtagta
    27961 caatcatagc tcactacagc ctggatctcc tggcctcaag tgattttcca accttggcct
    28021 cccaaagcac tgttaccaga ggctgagcca ccatgcctgg ccaaatcagt ttttatgtta
    28081 atttctcagg gtgttcctga ataatgcttt tgtgtattat ttagatcgat gccttcaagt
    28141 aatgtttggc ctacccaagg ttctggagaa cccacttcct tgcacttttc ctgggtcagt
    28201 aggacgattt tcaaaggtcc aggtttgcag gctgcttaat tctgtaactt tcacacagcg
    28261 tcagcttccc aagtcctatc tccctgttgg agtaccagta ttaaaagctc aatccctaga
    28321 aaccttattt tggtttggaa tctcactgcg ccatggtaaa gtcagcttat acttattttt
    28381 ctagtggtta tttctttttc cttctggaac ctatgcgctt tcctttagct tttgagagag
    28441 agagacagag agagagagag agacagacac acagggagag acagacacac agggagagac
    28501 agcatgggct gtcctgttcc tgacaggaac aggatttaat aatgggcagg aggcccatcc
    28561 acattagctc cacctgcaat actccaagta ggtgagtggt gaacttccta acatacaaaa
    28621 tctgccaatg gcttcccagt gaccttaggt taaaatttaa acttcttaaa atgtgataca
    28681 caaagacctt caaaagctgg tccctgctac ctctccttcc ttccatgact gccactccca
    28741 ttgaaagcca ctgcaagaat tactgttctt tcttttctat accctccctg ggctttcctg
    28801 atgctgttca ccttgtctga agtacccttc tccactcttc atgtggttaa ctctatccat
    28861 ctttcagagc tcagtttttc caagatgcct tccctggtcc tcccagatga tgcttccaca
    28921 ggaacttgta tctcccccta tcacagcatg cacatgtgtc tattttttgt gtcatcaaaa
    28981 ctgttcatct tctgttgaac tcactggact gtaaagctct gagggcaggg atatgctgtg
    29041 cccagctcga tgcctggcac acaccaggca ctcacttcac atttgatgaa tgcagagaat
    29101 gcttagtaag gttttaaaag tctgtttcca gaaggataga taccatgtta tattaaccca
    29161 tattcatcca taagtctagc aaactgtgtg ctggataaag gcatacatag ggaaaaaaac
    29221 atttattgtt tggattgtga gtaaaacaga attctcttag tggttcccaa gatgatggaa
    29281 ccacaactca tcacaaggaa tcttcaggtt gcaccgggaa taatccaaat gcaagtcaca
    29341 caacacttgg catttgaaaa aaaaaaaatc attttccatt gaggatttaa atcaatttta
    29401 ataagcgcaa aatcagacat caaataaatg gaactacaat actaattatt tatccagaca
    29461 aagctttcca aaccccaccc caactcctac ccctggaaga cagaattaat acatagggtc
    29521 ttttggctta ataaaaggac ttctagtatc ttaaaagttt gagaaccgac gtccagtgaa
    29581 gtagacttgg aatcctcatt gttttcacgc agcactaggt acaagagatt ccacagtatg
    29641 gatcctacaa cgtatgcatt gacagaagag ttcctgctct ctcaaagggc tttgctctcc
    29701 aaagaaaaaa gaacatgtaa cagtgccaca ccaaacttgc catttaaaaa tgcccttcag
    29761 aaatcacaag ctgagatttc tggtgcttgt tttgcattta ctttggcagc ctaggaagat
    29821 gaaggaaaac agatcagcaa tagaaggaat gaaggaagga gtctttgtgg ggtaagagat
    29881 gggaaatgaa taggaggtac agcagtgctg tgcacagcac caaactgggt atccaaagac
    29941 atatgccccg gccccagatc cccaagaaac tggagcttcc ctgagggttt cgtgaagtaa
    30001 cgtacccaag agcccttgta aaggataaag ccctctgcag ataaccagtc tcctaactca
    30061 gtgattatct gagatatgag agctttatga actaaaatgt gttgtgcaaa tgtcaagatt
    30121 taatattaga ggcagaaaac agatgttgtg tttttattct ataattaatg ggatgtgcta
    30181 tgccataagt ataccttgca atttgttgcc tttgctattc taataccttt cttcaatgtc
    30241 tgtccttgga agagttccag agtaagacaa aaactataga gagaatacaa tagagagaat
    30301 atgaaaccag gccaggatta agtaagagac ttggttccag aagacactaa aacagtatct
    30361 gcaaagatac aacctagtgt cttgagtgtt cctaggatgc ataggattgg agaggagcta
    30421 tcaaggtaag acctctgtac aatcctcagg ccagctgtct ctgcccctta tctgaaggtg
    30481 tcacgtggca gtgaagaccc aagctcaatt ctcttacaag aacagaaaac cacaggcaat
    30541 gaaacaatat ctagttctct accttaaaac gctactagct agggtgatct ttctggaccc
    30601 taaatgacaa agtctgtagt catataccat caacctaaag gagagacagt gatctgccta
    30661 tgtactggca aataatcttc agaagaaaat agtgattaga actgaaatta ttatatttag
    30721 cagatattta tatcccttcc agtccccatt cttattttat accttaatgc aggcctatag
    30781 tttggtaatt ttaatacaac tacttgctgg ggctaaccag ggcctgtcaa cagctcctct
    30841 cagtgttcta gaatagaaat tggctaataa aaactgttaa ccgctctttt ccaatgctgc
    30901 tgctgttctt taaaacgaaa gattagccca gtacaatcct tctaatggac atattctttt
    30961 attcttgatt gtcctatata caagcgctta cctaagcttt ccacataatg gttagtggcc
    31021 ttggcacgct gggtttgaat ccctgacctc gaatccctga cctcgcttat tagccttgta
    31081 acacaatttc cctaagcctc agtcttatcc tcaaaaatgt ggctaatact acttatctca
    31141 tgtggttgtt ttaaggagta aatgaaataa cctatagaaa cccttcagta tagagtctgg
    31201 catagggtag gtgctcaata tattttattc attttccttc aagctatttg aaatcgtttt
    31261 gggaagaagg caagatttaa atgataaaca agcaaacagt tctctattgc atcataatta
    31321 caaaaaaaca gatggcataa ggaaaatctt ggtcggtcta ttgttatatc aaagaaacca
    31381 tgctaaacca aaaaaaaaat ccttgctttg gaggcactta tgaagtagga ttaaatgaaa
    31441 gtgttggaat acagatgaga aggaacctta gacacaggtt ctcccaccga agaccatatc
    31501 agcaatgctt ctaattacca atatatcaaa gtcctctcca ctccctgtaa ctggcaggag
    31561 acaatctgag gcaaactcag tgtaccaaga agtcctgtga aaacttaacc tagacagcac
    31621 aatgaatgaa agggaatgaa ttccctggct tttggccttc taacacgtga ccagtatgct
    31681 tcaaaacatg tttaaaactg tttctgtaaa atatttttgc cacctaagtt tcccccccgc
    31741 cccttcataa aagtgatatt tgagtagtga ggggagaaat ggctcaaaat ttgttacaag
    31801 aggttccaaa gaaagacaat aaggtataga gaaagggaag acaggaagaa agagaaagag
    31861 gtcaagtatg tagtggatag tacagggaag tcacaagtat cttctgtctg gaaatgctgc
    31921 agattttgtg gttagcctca agatattagg tgggaataaa catgtcattg agagtaaatg
    31981 taaacacaaa aatgaaaaat aaaaattgta acaattcact ttattctaaa ctgtttttga
    32041 tggttatata tggcaggcct aggaggcaat gttagacagt agatagttgc cttcggcgga
    32101 gggtgacctg tgttctgtcc actgctctac attgtaaaga ggtgtcatct tggacaagtc
    32161 acggcagctc atgttgagtc ttgggatgat tctttatcta aaggtagaga actgaaccag
    32221 ctttttgatg gtgatgagga ggggttttga gaggaacaag gatatacagc atctctattg
    32281 aatatttggg ccataatgta acagcctagg atgctgagat ttactcaaga gctgaggacg
    32341 gctaggggcc aaacacagat ttttaagttt tgagataggg tttactctgt tgctaagact
    32401 ggagtgcagt ggcaagatca caactcactg caatctctgc ctcccaggtt caggccatcc
    32461 tcccacccca gcctcctaag tatctgggac tacagcacat gccaccatgc ccagctaatg
    32521 tttaaatttt ttatagagaa ggggtcttgc catgttgccc aggctggtct caaatacctg
    32581 ggctcaagtg atctgccagc tttggcctcc caaagtgtta ggattacagg tgtgagccac
    32641 tgcacccagc ctcaaataca gatttttaag aggccagatt tatacacctg gccatcatgg
    32701 tcatgttggt taacctccat catgaagcta ggctttttaa ccttcaggaa aactacccca
    32761 gagcagttaa tggcctaaat aaaggaggtc aagctatatg tctcagttta aaacagaaca
    32821 tgacaaatta acctgaagca ggaaaaggag gggacatcaa acctgacacc catcctgata
    32881 agagtaactg ctctcatttg acagccagag ttaaactaga tgtatgcaat ctctacaaca
    32941 aacatagtca atgccaatca gatagtcaga ggaaccatca tttaatggga aataacgcaa
    33001 taacatatat aacagagctg accggaggtg ttgctataga taattcataa cagcagtaaa
    33061 ttcaaaagtc atttactatg tttttagctt tgtcattaac acagcctgtg tggatactcc
    33121 ctgtttcacg tctagatgac ttcctcctgg ctttgctcaa gggtccttta gcatttgagg
    33181 agatgataag ggatgggatc cccgcctgtt gaaccagagg aatctgagga gtaccaggtt
    33241 tccactgaag actaaatcat gatccagaga aggaatctca gaagtcattc ttgtcgtggg
    33301 catggcttaa cgtctgtctc cccactgtgg gccctgccct cgagagcaag ggtctcctta
    33361 ttcattttta tattcccagt gcctaccact ttgtggagcc cttagtagaa aaggtattca
    33421 ataaacgcac attgagttta agctttctat ttctcctccc ccaactagta tatattacag
    33481 aagcactgaa aattcagaaa tcagccagtg tcagggctcc tgggtaataa accattcaca
    33541 gggatagctg taggaatttg gcataagcat ttattccaat ctcttggggg taatcaagtg
    33601 gcataatcat gccctgcttt actgtgtagc ataaggccag tagagaaaaa catcaagagg
    33661 ggaggaggac aagggatgga gttcaataca caaatatcta ctgagcgtca attacgtgtc
    33721 ccacactatt caaggtgctg ggcaaagaaa gataaaaaaa gcagaagctc tgaccttgag
    33781 gaacttaaca ggtagttaag aaattgcaga attttagcaa tactaggaat tcacagcaaa
    33841 agcccagaat acaggtgtaa tattttgatc aaaacgtgaa gcccctatca agagaattaa
    33901 gaaaatcaag gggaagaact tatcaatatt tcacctcaaa tttggcatat agcattcagt
    33961 tgttttaagt acgctttctt aattttgcga acaaaatatt cagacctaag tgattatcta
    34021 taaaagatca gattactagt ttccaacaca gaagtactca aacaaaggta ttctgaacct
    34081 caacctactg caatacatat atcacatttg gccaaaaggt agttgttctc aaagtgaaga
    34141 acccagatct gcagcatcag tacctgagcc ttgttagaag tacaaattct caagccccag
    34201 cacagaccta ttaccagaaa ctctaggggt gggccccagc aatatgcgtt taactagccc
    34261 ttcaggtgct tatagtaagt ttgagaacca ccacctagca aatgaagtaa atctgaagtt
    34321 catgcagaaa gccattgctg gccaaactaa agggtttgct ggtgagagaa cagcaaaaac
    34381 aaggggtata gaactgtttc acattttaaa tctgtgccaa atttactggg aaaaaaaaat
    34441 gtaaacctgt aacttacctc atctgtacaa tttgcaatgg ctgagtccct cacattgtgg
    34501 taaaccttgt tgtacccttg gaatgattgt ctactgcaat atagtatata cacagagtac
    34561 aaaaagggta tagctggagg agaaagggtg aaagattatg aatcccaggc gtttggtcct
    34621 aggaggaaaa attcctgtcc tctctccaac cctgcccacc ctcttatgct agatagtaac
    34681 agcagaaagt tatcccagac tgctccgcgt tcacacgctt cccaccaaca aacctcctcc
    34741 caaggctatc ccacaacctt tctgaagtag cttcctggat caagccccac ggggcagctt
    34801 ggaagagaag ctgggaggga tgaggggctc cactagcatt ccttgtggct tctgagtgta
    34861 gctgccctgg gtgtcacctg cagagcgtgg atagagaaaa agcaacagtt ctaagcccag
    34921 cctctaattg agagcctggg atctagcgct gctccccagg accaaggttg ttcaagaaag
    34981 gctgggtcta agagtctccc tctggggagg tcagtacaga ttccaaggca gacagggtta
    35041 tcaaagcgcc tagaagatga gaacattcat tgttcagaaa aacaaaaatt agactgacac
    35101 ctttctgaag gaacacagcc tatccatggc acaaaaacaa atttttaatc aagacactca
    35161 agaagtaggt atactcctgc taaaagtaac gcaggtgctg agaagaggtg ccaaaactgg
    35221 ctgttaggag tgggaggaga ggaaagttgc aagtggagac agcagctact ggcttgaggg
    35281 gacctcaggg tctgtcacag tggcagctga aaagcctctg gccaaatgga cgccaaggac
    35341 tactatcatc acaggtgaca agatcacggg tgagtgtatc tgggtgtgtg ctggggggct
    35401 gaggggggct tggtggtgta aggagatggg gctagccggg gcaaggagcc cgcggagatg
    35461 atcttaagca atctgagagg aggggtaaga aaaagctgcg gaaaataaag gggcctagac
    35521 cactcctccc tcggttccgg ggggacagtt ggcgcggaag cgttaggagg tacgaggtac
    35581 ggactaacta catttctgca ggccccagga gggggcggag ggcggtggct ggaaaggaaa
    35641 ggaagccggg agcgccatcc gtgtccccgg agatactggc tccggccacc aggaaacaca
    35701 gagaccacaa cgtctcggca ccctcagtac accgccgcca ccccttcccc aggacacggc
    35761 gatttcccca gactctgggg ggcggggtct ccggtccctc cccctcctcc ccgccctgcc
    35821 cggctctgcc cgatctggtc cggcccggtc cagcccggcc cggcccagcc cagcccactc
    35881 aggactcacg gctccgacag ctccggcggc tcctcccctg ccccggcttc tctcccaccc
    35941 actcccgacc gaaacagcgc cgccggatcc gagccgcgcg gggcctagcg ggtcggaaca
    36001 cgtggggcct ttgcgcccgg aaccggaagc gatcgctcgc cccgccttct cgccgagtag
    36061 gagcctttct aggctgtggg aggtttgatc ctctctatgc gccctccgcg ggttgcggct
    36121 cagtgctccc caaggaccca gtgcgaagaa gcctcggacc ccacagctgc cgtccgcgac
    36181 ccctaactcc actctgcagc gaataaatta acatcttggg cctttcattt acaggcatac
    36241 cttctgcaag ggttttcttt ttcttttctt ttttcttttc tgtttttgat cttttgtgtg
    36301 tttgttttca tttggatacc tctacgtgtt tttcttgatt tttttttctt tgcattgtcc
    36361 gctgcaacat ggtagaaaag ggcagcgtta ggtttgaata ctggctcttg cagtcaccat
    36421 cagcagcagg gcctcggccg aatctctcca tctttgaacc ctattgtgca tcatataaaa
    36481 cgggcataat aataccgtta ctctgaggac taaatgatac attgcacatg aactgaatgg
    36541 aacatcagaa gctcagaaag aaaatagtta tggtatcact gttctttctt ttcctttgag
    36601 tgttgcttcg tatttcttta ctttcaggct gtcttccctg atctcatttg ttcatttttg
    36661 tccgttcggt gacctttctg cccatacttg acattttcct ttgctctctg tcccttttac
    36721 cctgtaagtc accactctcc acgtgccatg tgccacttcc ttttcatggg acacattgct
    36781 gggatctgtt tactgggttt gaaccaaagg attagttact tttggtggag tggcagtgta
    36841 ttagcgaaac agaactaata ggtgtgaacc cagaaggcag gacaactcaa agcggggagg
    36901 gggcttccag gtcataggta gataagacac aaatggttgc attgagttgc tgattagcct
    36961 ctccggaagg aggcaatcag atatgcattt atctcagtga gcagagaggt gactttgaat
    37021 agaaggggag gcaggtttgc cctaagcagt tcccagcatg aattttccct ttagtgattt
    37081 tgggggcccc aaatcacttt cctttcacac ggggtatgta taaacatata aaaggagatt
    37141 tattataagg agttggctta cataattatg gacgttgaga agtcccacca tctgcttact
    37201 gcaagctgga gaaataagga ggttggtggt ataattcagt ctaaagctga aggcctgaga
    37261 actggaaagg gattgaggtg ctggtgtctg aaggccagag agcaggagga gatgatgtcc
    37321 cagctcaaga agagagaggt gaatttactt ttcctctgcc tttttatact atttgggccc
    37381 tcaatggatt ggatggtgcc tacgcatagt ggtgagagtg attttcttta ctcagtctac
    37441 tgattcaaat gctaatctct ctctcttttt tttttttttt tttttttttg gacagagtct
    37501 tgctctgtcg cccagcgatc tcggcttact gcaatgtctg cctcctgggt tcaagcaatt
    37561 ctcctgcctc agcctcccga atagctggga ttacaggcat gtgccaccat gcccagctat
    37621 tttttttttg tgtgtgtgta tttttagtag agagggggtt tcaccatatt ggccagaaac
    37681 accctcacag acacaccgac taataatgtt ttctgttgtc tgggcatccc ttagctagtc
    37741 aagttgacac ataaaattac ccaatacaaa gagaaatata catttcatga aagcctactg
    37801 tgtaccaaat atttttctct gtaaatctca ttgaatattt taaaatattg gtattaagtg
    37861 cataaataat acataaacat cttcttctaa acatttaatg cattacagtg ttaaaggaaa
    37921 aattattcag tgatacttgt tagagcatgg taagggagac cttattcagg accaggaaag
    37981 gtaaagaaac cactgcaatg aagtcttgct gtagggatga gagattgggc tgaactctga
    38041 atacagaatg ggcaagtggg aatttatagt caaggaactt tttttggagt ttgggacgtc
    38101 gatggattga aaattactaa ggggaaacat caggcttaag gcggattctg gctaagtcaa
    38161 cctaatagga ttcttgctga agacaggcca ggttgatcag acatcacctg gggcgtgatg
    38221 gaggatgagg acactgacca ggtattaagg atggtcagat atcaaggatg ggggcgttcc
    38281 tgccaaagga cttagagttc tttgctaaca gtagatttta caaggaagta cgccgatagc
    38341 cctaggagaa gtttcagaag cctgacaagt ttggcgaaga aaagagattt tgtcaatgga
    38401 taaagctaat gacttttttt ttttttttgg gacggagtct cactctgcca ccaggctgga
    38461 gtgcagtggc accatcccgg ctcactgcaa cctcgacctc ccgggttaaa gcgattctcc
    38521 tgcctcagcc tcccgagtag ctgagactac aggcatgcac caccatgccc agctaatttt
    38581 tgtattttta gtagagatgg ggtttcacca tgttggctag gatggtctca atctcttgac
    38641 ctcccgatcc accagcctca gcctcccaca agtgctggga ttacaggcat gagccaccat
    38701 gcctggccgc taatgacatt tttaccaacc ctggcttcct cctctctctc cagaagttag
    38761 ctgttcttat gaccctaatg tatttatctt ccagatattt ttattttcat gtgctgtgta
    38821 catatgtatc cacagaaagt acatagtatt attttctgtg tacttgtgtg tatacctgtg
    38881 tgttcatgtt gaattcttcc atttgttttc tcttagcagt gggccttgga gatctgttga
    38941 tagcggtaaa taaaaatctc ccttattcct tctgctttct gcataacatt ccatagtctg
    39001 aatagcaatt tgcctgttga aaacataagt ttttataatt gttgggatta caaacaatgc
    39061 tataatgatc accctctttg tgcgtacatg caatggtact ctgagacgga tactgagaaa
    39121 gagtattgct gggtcaaagg ttgcacactt ttaatgaata ctgccaagtt ttcctcccaa
    39181 atgaatgcac ctgtttacac ccttaacaac agtatacaag attttttccc tgtatccatg
    39241 cccttacctc atgttgccgg aattgtaaat ctcagccagt ttaatgggca aaaataatat
    39301 ctaattgttt tactttgcct tcccatcgtt aatggtgaga ctgaactttc tttcatacat
    39361 ttgttggtaa tttgtagttt tcctgtgagt tttattttta tattggactt tttgtttttt
    39421 taaattggtt gttagatgtt ctttatgtat cctagatcct aatgatttta cgtatatatt
    39481 gcaagagata tattaatttt atgtgtcttg actaagttca tgaaagcctg ctgtgtataa
    39541 gatgtttttc tctataaatc tcattgaata tttttaaata ttaatattaa attaatgttt
    39601 tccttaactt tctagattat tgtctaactt tgtagtatta aagtttcaaa tctgatacac
    39661 tctttccccc gcttcaaatt aggtgtttta tttaagaata tcttttctgc accaaagtca
    39721 taaaggcttc tcctgtatgt tcttctacta ctttttgctt ttccttttta tggttagatt
    39781 tggaatttat ttttgtgaat gatataaatt ggggattcta atctaatatc agtggtaatc
    39841 aatttctact tggaaaacat ggagtatgag atatttacat aatagaggat atatttacat
    39901 acaaaagata tattccatat gtgatgtgat cagaattctg tcagcgcagt tagctggtcc
    39961 ttcatttgtc aatgattttt tgagtgactg ctcttacaag acactgtggt aggtatatgg
    40021 aacagaatgg agaataagaa agacgtaata tctgttctcg atctaacttt caactggtgt
    40081 gtgtgtgtat gatatgaagg agttggggaa gaagaaaaca gtttaaataa cttacgcaat
    40141 tcactaactg tggttattta attatgatta attaaattaa ttataattat tgtaagttct
    40201 ccagagaaat acagagtgct acaagaactt gttactggag gtcctaatcc tggtggtggt
    40261 gctgttagag aggtagttag ggaaagcttt cttgaatagt gacatttgaa ctgagtctgt
    40321 ggaatgcctg ggcaggatga gcctgggggt gaggttggga gatggggtat aaaccaaaaa
    40381 gtgtctgaga cagacctcaa ttgatttaga ggtttatttt gccaaggttg aggatgcacc
    40441 gtggaaaagt agacacaagt tgcagtagga tctgtggcct gtgctttttc caaagaggac
    40501 ttcaatattt aaagcagaaa gagcaggcag gagaggaagg aggaaagaag aaaaagggga
    40561 gggtaggcac ctagcaagaa gtcccattct tgtgaagctc tgaccagtgc tcagcaatcc
    40621 acattttaca tctgaaaaga aagtagtggg gacaaagtca attatgcata gatctgcatt
    40681 ttctatgagg taaagtaaat gtgaagtaaa gtaaatatgc ctagaaacaa aaggaatttc
    40741 agaaacacat gtgtttagaa acaaaaagta tgtgtttaga aacaaaaaaa aaaggaaggc
    40801 agtttttgcg tgatttagct cccaagcata gcttttccct ttggcatagt gagtttgggg
    40861 tcccaagatt ttgttttcct tttactgagg tgagtaaaaa agaatacttg aagtaatggg
    40921 aaatagtgta taccacagct ctgaaatggg aaggagcctt ggtgtactgg agaaactgag
    40981 aagaggctgg tgtggctgcg gtctgacagc aatagaggaa tttgtgaggc ctgatattgt
    41041 ggacagagat cagacctaat agactaatgg tcttataggc caaattaact gctgaaatta
    41101 atgagaagct ggtcaggtat ggtggctcac acctataatc ccagctcttt gggaggttga
    41161 ggtgggtgga acccttgagc ttaggagttc gagaccagcc taggaaacat ggtaaaaccc
    41221 tgtctctaca aaaaaaatgc acacacacac tcacactcac ttagctaggt gtggtggcat
    41281 gcatctgtca tcccagctac tcaggaggct gaggtgggag gatcacttga accccagagg
    41341 tagaggttgc agtgagccga gatcgtgcca ctgcactcca gcctgggcaa cagagtgaga
    41401 tgctgtctcc aaaaaataaa taaataaata aataaataaa taaataaata aataaaatta
    41461 ataaaattaa tgggaagcca ttggagattt tttattaatt aagcaacatg attagatatg
    41521 cacctttata agatctttct ggtcaccgag gagaatggag gggaccatga gtggatgagg
    41581 agagataact taggaagcta ttactgtaga tcaggtactt ggactaaagc aataatagta
    41641 gatatggagg gcattgggtt atttctttaa aactatttga tgcagagcaa agaactaatt
    41701 gttagaaaaa tggttattgt tacaaaaatt gttaggaaaa taggatagag agaggttatt
    41761 ttccaaaagt tgaagaaatg gcagggataa ttagtaatag tgaagtgagc tcagctgaaa
    41821 gtgtgcatag gagttccact ctcctagtta ttcaatccaa gtctggctga acaccaagta
    41881 tagaaagtga atcgttctgg aagagctatt tgtacatgac atttttataa ttagagtcat
    41941 ttagacttgc aagaagaatt tgtaattcta agtgacctgg tggtgagcca cttggtcagg
    42001 cactagatta gatacctgga taagtatata attatctgca ttcaaatgtg tctatattat
    42061 actttatatt ttctcatatt tgatttttac actctgatcc ccaagttagc tggtcatttg
    42121 tgaataccat ggagtcataa ggtcctgata aaaacagagg tggctttaga gatatacctt
    42181 aaggaagaca gcaggagatc tagtctgaga cacgttgaga aaaatggtct gtagctggat
    42241 aagcttggaa aagaccatat actctatcct ccttttggaa atttataatg catgtgaaga
    42301 tccctagaaa tgaaaaacaa agtcgagttt attacttgac atgtaaggga gagctatatc
    42361 attcaatgtg atgggagtga gtctttctga gttaaaagag gaaagatgaa atctaggata
    42421 agaactggaa gttttgcttc aataaggcag gatcttgaag actatcactg attggttaag
    42481 tagaggattg taaagtaaag tattattttg gaatgacaat tgctctggtt ttcaataatt
    42541 atgggacagg tctttttttt cttccaactt ttattttggg tcgagggagt acacgtgcag
    42601 gtttgttata ggggtaaatt gcttgtcagt gaggtttgat gcacaaatga tcccatcacc
    42661 caggtagtga gcacagtacc cagtaggtag ttttttgatc ctcactcttc tccctccctc
    42721 caccctcaag taggccccag tgtctgttgt ctccatggtg tccgtgtgta ctcaatgttt
    42781 agctcccact tataagtgag aacatgtggt atcttgtttt ctgttcctgc gttaatttgc
    42841 ttacaataat ggcttccagc tccatccatt ttgctgcaga agacatgatg tcattctttt
    42901 ttgtggctgc atagtattcc atggtatata tgtaccacat tttctttatc cagtccacca
    42961 ttgaggggta tttaggttga ttccatgtct ttgctattgt ggaatagtgc tgcaatgaac
    43021 atatgtgtgc atgtgtcttt atggtagaag gatttatatt cttttgggtt taaacccagt
    43081 aatgggattg ctgggtcaaa tagcaattct gttttacatt caagaaatct ccaaattgct
    43141 ttccacagta gctgaactaa tttacattcc caccagcagt gtatattcat tcccctttct
    43201 ctgcaacctt gccggcatct gttatttctc ttttactttt taataatagc cattctgact
    43261 ggtatgagat ggtatcccgt tgtagttttg atttgtattt ctttaatgat tagtgatgtt
    43321 gggcattttt ttccttgtat ttgttggcca catgtatgtc ttcttttgag aagtgtctgt
    43381 tcatgtcctt tgcccatttt ttaatggaat tgtttgtttt ttgcttgttg aattgtttaa
    43441 gttccttata gattctggat attagacttt cgtcaggtgc ataattttca aatgttttct
    43501 cccattctgt aggttgtctg tgtaccctgt tgatagtttc ttttgctgtg cagaagctcc
    43561 ttagtttaat taggtcccac ttgtcaattt ttgtttttgc tgcagttgcc tttggagtct
    43621 tcatcatgaa atctttgcca ggtcctatgt ccagaatgct atttcctatg ttttcttcta
    43681 gggtgtttta tagttttagg ttttatattt aaatctttac tccatcttga gctgattttt
    43741 gtatatagtg aaagggaggg atccagtttc aatcttctgc atatggctag ccaattgtcc
    43801 cagcatcatt tattgaatag ggagtccttt ccccattgct tgtttttgtc aactttgttg
    43861 aagatcagat ggttgcaggt gtgtggcttt atttctgggt tttctaacct gttccattgg
    43921 tctctgtgtc tgtttctgta tgggcacaag tcttaatgaa ttccaagata ggatgaataa
    43981 agctatgctg ggttcaaggt catataggag gtactttcat acacatatgc ttgagatttg
    44041 gaaatttttt tttctaattt agtgttatgg attcttagaa gttcaatagt gaaggaacct
    44101 acttaatctt ttctaactct gcattccccc cacccagttt gaattctgag tcctgtttat
    44161 gaatatcctg tggcatcatg aaaacactgc tatactgaag tgtgtgtatt ttcaaaaaca
    44221 aattaactct aaagttcatt gttaaagatt tgtttcaggt ctatccaggt gctcaacttt
    44281 gtcattaaag ttattgatac tagaaaaata atatccaggg atctgggtag gttgttcgtg
    44341 atattgtttg aatggatctt tgtgtaattc cttactcttc tggagaaaag tagaatagga
    44401 aagacatttt ggctttagag acctgagaaa cagtagggta caatgtgagg tctcaagttc
    44461 tgtcttgtct ctgtggccac ggctcctttt ctttaaaaca gcactctacc ttctctggac
    44521 actggaggct gcccacaatc tccttcatgt ctttgcctcc cctgtaggtg aaggaaagtc
    44581 agattttagg catggttccc tgaaagtctt cttgtaattc atatcattct tgatgttcag
    44641 gaggcttcac cgttggatag acttctgtaa ttctaggatt tccaactccg agaactaata
    44701 cccctgcaga ctaataccca cacacacaca aatgcacaca cacacacaca caaacacaca
    44761 cgttttttcc cggtagaatc agtaccagga acatagcgtg gtacatgata tcaatatatc
    44821 agtaagacat aaacatgcat gaataaatgt tgtctatttg aagtttcatg aattgaagcc
    44881 tggtggtatt ctcatacctg ttcttccccc cttcctcctt ttcttggatc tgccaaaatg
    44941 tttttatcct accctctgtc tgccattaga catgaaaccc ttaaggtcat aggctaggcc
    45001 cagagaaact aatatttatg agatttgaag gcaaattttt aaaaactttt ttaaaataat
    45061 aatataaccc agatgttcca acacctctag atttaggtta ccttgagtac ttgcccaagc
    45121 ccctgcaaat gtgaagtgct tcctaaaatt tctgcgtatt ctgtggccat ctctgtgaga
    45181 ttctctatgg gctgtttcta atccaaatta tgtcattcca gacatgaaac gttattcctc
    45241 cttgactcac acacaacgca cacatatatg aatgcatgtg acatgcatgt tctgttcata
    45301 catgcatttg gtaatataga agactttact gaaggtttga gggggagaca gattaacatt
    45361 gtagaaatgt gacttcaaac tgagcattag gcatccccat tcttaaactg ctttctaggt
    45421 gccctgacgc tggggaattt ccactgactt cttcccacag actcctctgc tttgctccat
    45481 tttggggttc cttttttctt cctttctctg tcattttctt ttttgagaaa tattaactat
    45541 tacctttttt tcctcattca gggcactcta aaccattctt tgatgacaga gctcatgata
    45601 atattgatgt ccttaggttc tctctcttcc tttatctcca aatgatctat ttctcctgca
    45661 cagctccaag acagttccct ctctaagaga aaatcaggta cagcagttga gataataata
    45721 tttttgcctc attacatttt gttttgaatt ttcaattcaa tattaaaagg aatgtgtgca
    45781 gtgttgatga aaggagtcaa actctgcaaa atattggaag agatttattc tgagcccaat
    45841 atgagtgacc atggcctgtg gcacagccct caggagatcc tgagaacatg tgcctaaggt
    45901 ggttggggca cagcttggat ttatacactt tagagagaca tgagacatca gtcagataca
    45961 tttaaggtat acattggttc tgtccagaaa ggcaggacaa cttgaagtgg ggagtggggg
    46021 gcttccaggt tataggtaga tttaaaaatg ttctgattgg caattggttg aaagagttac
    46081 tatcaataga aaggaatgtc tgggttatga taaggggttg tggagaccaa agttttatca
    46141 tgcaaatgaa gcttccaggt agtaagcttc agagagaata gattgtacat ttgtaaatgt
    46201 ttcttatcac acttcaggtc tgtgttgatg ttaaatgctg gttggctttt cctgaattcc
    46261 aaaagggagg agggcataat gaggtgtgtc tgaccccttc ttcccgtcat gacccaaacc
    46321 agtctttcag gttaactttg gagtgccctg gccaagagga ggagtccatt cagatggttg
    46381 agaggccctt agaatttggt ttacagcagt aatttttttt tttagtcata gttttaatgg
    46441 tcttttaatg ctagtttttc tttactgttg ggaagagaca tatctaatac tcattatcac
    46501 aaactgaatc acctgcatca tcattcccta aaaagatatc ttgcctgaag acaagggtca
    46561 gatcagtagg tttgtagcct actttgaggg actttgcaca ctaaccctga aaccagccca
    46621 attgttccac acaaaagata tttatggatt tttaaatgaa cacagaaatt gacactctgt
    46681 cttaaaacct gaaacttaca tttgtcttaa ctgagttcct tcctcaggaa actgaccctc
    46741 aggcaagaga ctgaaaccca ctagatcacc aatccggaca acaagatgcc aggcccctca
    46801 ttcatcatga tggcttcctt acccctccct aattcctatt ttctcacctt accagctctt
    46861 cttccttacc cctctctaac tcctattctc cctcccttcc actatatata aacctcccaa
    46921 atttagttgg ttggggagat ggatttgaga ctctacctcc catttttctt ggctgcagca
    46981 ttcagttaaa gccttcttcc ctggcaatgc tcagtgactc agtgattgat gttctgtgca
    47041 gcaaacacca ggacctgact gaaccctggg ggttttggtg acaatcctac atgtgagccc
    47101 tgaacttcat gtaaccttgg ggctgcattt tccagtagga aagtgtttct agatatattg
    47161 gctctgagac ttttcctagc ttcctaggta catggtctac ttatattgga gcccagaaac
    47221 tgctgtaatc catgaactgc aaatggaaat tttttacaag atgttctcaa gttttggtat
    47281 tatctgagga tgaacacctc taagtttatc taaaaatttg tattatttca agatggaagt
    47341 ccccttattg agatattatc aaacaaaaag ctgattcatt tcaaatattt tggaaggacc
    47401 attagaatta ttagaagtct gtagcgtgct tctctcatga taaagatgat aggaactaag
    47461 aaaatgagat gtggaatgtt ttatgttttt gacaagaaga tgaggcaaag agggtggtca
    47521 taaaaaaaaa gatggtggtc ataaataaag agggagacag gattccttat acatttttaa
    47581 agttgttgac atttgtctct gaccttagtg gtttctactt tcagtttgca gttgacaagt
    47641 ccagagttct acttcatgca tctgaggata tactgggact tccttgttga agaattacat
    47701 tgtttcttct caagaaaaac tcctagttca tttacatgta acaagttctc atgggagacc
    47761 ttaaccatca tggtttgctt ttgcatcttt atcttactat agcattgaat cagaacttct
    47821 gggatttggg gggagcctgt tttaccaaac ttctccaaaa tcctctctca actttcattg
    47881 tttttatctg cattaagctc actttgatgt gttgcatgtt ttactttgca tgaccagtct
    47941 ttgggcaagt cattgccttt cttaaggctc ccttcacctc cttgtttcta atagtataaa
    48001 taaagggatt cagaaggggg gtgaggatag tatttagcac agacaccacc ttattaatct
    48061 taaaggagga gtgtgctgtg ggtcttaggt acatgaacag aacagccccg tagagcaggg
    48121 agacaactgt caggtgcgag gcacaggtag agaaagtctt ttggtggcca gtggctgaag
    48181 gaattcgtag gattgcggac agaatgtaga tataagaaat catattaaag agaagtgacc
    48241 ctgggatcac aaggatggtt gctatgacgc ccaggagttc caaaatgctg gtgtctatgc
    48301 aggcggcttt caaactgggc ccaacatcac agtagaaatg actgataaca ttattgccac
    48361 agaatggcaa ctggatgagc agcatcgtct gacaaaagac aatggtgaag cccaccaccc
    48421 aggagctcag ggccagctgc aggcagagtt tgctggtcat gatggtgggg tggtgaaggg
    48481 gattgcagat ggtgaggtag cggtcaaaag acatgatagt gaggatcaag aactcggtgg
    48541 tgcccacgaa gaagtggaag aaggcctgca gcaggcagca ggacatgcag attactgttc
    48601 ttgccactac aaaggttcct agcagtttgg ggatgactgt ggtggtgtac cagatttcta
    48661 agaaagacaa gttacaaagg aagaagtaca ttggaatttg tagcctgggc tcagcccaca
    48721 cagtggcaat aataagccca ttgcctgcaa gggttaatat gtaggtgaga aagattgcaa
    48781 taaagagagg tgtttgtagg ccttggataa caggaaagcc tagcaggatg aattctgtga
    48841 ttactgtgcc atttctcatg tcccttgata ccctagaaag acaagcaaga aagctcctta
    48901 gaatcttaga gcacagttga ttatagttgg gacaaaaaat aaggaggatt ctgactatgt
    48961 aaggtccttc gggacctgac tctatttcag gtcctccctc acccacatac aaatacgcac
    49021 tggccacccc ttctttactg atgatttggc tggttctttt gtcagcaaaa ccagcttcta
    49081 atggactttg aatgtattaa aaacacttga tgaatgcaaa gtgttttttc acccttatac
    49141 aactatgaga ataatcatgt gaaatgtggt tgcttcttgt caattattca tataactatt
    49201 ttcaatgcat agtgtgtata ccaacttatg tacgtaaacg tggctgtgag ttcataagaa
    49261 attaatccct attctcagag tctgaaaaag aagttactga ttacattaca gatacgttta
    49321 aggaagccat tattgtgtgt gggtgtgagt gtgtgtctta aaataacccc aaatcattgc
    49381 tattatatta gtggtgagat aaagttagat aacagaagag gtgtttttct gaagaatcca
    49441 cttccacatt ctagttcaga ctcctttgct aaaggtatca aaaataacat ttaaaactaa
    49501 atgaataaaa ctgtttagga agtagagaaa tattcaactc aaattcaaaa tttcagaaca
    49561 agctgagtca aagcctgtta tatggaagca cctaataaat gtacatggga taaagatctg
    49621 cagacactaa tctacaaaag tgaaaggtta gcaaatgcta aggataacaa aatgggaact
    49681 ctgaaaagta catttttgtc aaaatttttt ttgtgactaa atgtcttttt ataccaagta
    49741 aagtatttct atttgtatat gcaaattcat gggctgagaa catcctttct gttctaccaa
    49801 aattcagtag aaaatagtaa aactacttcc tttcttattg aggctattct tccatgtggg
    49861 tttcctttga aatgggtgag acaaattact gtgaaatgaa tttcacattt ttcaaagtac
    49921 ataagaagct tagcatgaaa gaggcaactt acaggtcatt gataggttgt ttcattcttc
    49981 cctcatgtga gataactgta attctctgag ggcttgctta gggaagaaaa acacttccat
//
BioPerl-1.007002/t/data/rfam_tests.stk000444000766000024      5400613155576321 17607 0ustar00cjfieldsstaff000000000000# STOCKHOLM 1.0

#=GF AC   RF00006
#=GF ID   Vault
#=GF DE   Vault RNA
#=GF AU   Bateman A
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD; Bateman A
#=GF GA   25.00
#=GF TC   41.33
#=GF NC   23.46
#=GF TP   Gene;
#=GF BM   cmbuild CM SEED
#=GF BM   cmsearch --local -W 150 CM SEQDB
#=GF DR   URL; http://vaults.arc.ucla.edu/sci/sci_home.htm;
#=GF CC   This family of RNAs are found as part of the enigmatic vault
#=GF CC   ribonucleoprotein complex. The complex consists of a major
#=GF CC   vault protein (MVP), two minor vault proteins (VPARP and TEP1),
#=GF CC   and several small untranslated RNA molecules. It has been
#=GF CC   suggested that the vault complex is involved in drug
#=GF CC   resistance.
#=GF CC   We have identified a putative novel vault RNA on chromosome 5
#=GF CC   EMBL:AC005219.
#=GF SQ   11

Z11765.1/1-89                        GGUCAGCAACAGCUC.AGCGGUUACUUCUCGA.....CACGGAAUUGUAA
AF210457.1/105-240                   GGCCAGCUUUAGCUC.AGCGGUUAC..UUCGACAGUGGUUCAGUUCAU.U
AY007237.1/1-136                     GGCCAGCUUUAGCUG.AGCGGUUAC..UUUGACAGUGUUUCAGUUCAU.U
Z11771.1/1-137                       GGCCAGCUUUAGCUC.AGCGGUUAC..UUCGACGUGCUCCAGUUUGAGCA
AC116353.2/181870-181951             GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGCGUGU.............C
AF058927.1/1-92                      GGYCAGCUUYAGCUC.AGCGGUUAC..UUCGACAGUUCUUUAAUUG...A
AC005219.1/49915-50008               GGUCGGAGUUAGCUCAAGCGGUUAC..CUCCUCAUGCC...........G
AF058926.1/1-82                      GGYCAGCWWYAGCUC.AGCGGUUAC..UUCGAGUAC.............A
AC116353.2/174637-174718             GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGAGUAC.............A
AC116353.2/166987-167078             GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGACAGUUCUUUAAUUG...A
Z97054.1/58392-58486                 GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGACAAUGCUUUCCAUGGUUA
#=GC SS_cons                         .<<<<<.....<<<<..<<<<.......<<<<..................

Z11765.1/1-89                        UUCUG........................AAAACCUUUC...........
AF210457.1/105-240                   ACCAGCUAUUCGUAGCAGGUUCGAACAACACAACCAACCACUUACCUAAC
AY007237.1/1-136                     ACCAGCUAUUCGUAGCAGGUUCAAAUAACACAACCAACCACUUGCCUAAC
Z11771.1/1-137                       GGCUAUGUAACGUGGUCGGUUCGAGCAACACAACCAGCCGCUUGCCUAUC
AC116353.2/181870-181951             AUCAA........................ACCACCUCUC...........
AF058927.1/1-92                      AACAA........................GCAACCUGUC...........
AC005219.1/49915-50008               GACUU........................UCUAUCUGUCCAUCUCUGU..
AF058926.1/1-82                      UUGUA........................ACCACCUCUC...........
AC116353.2/174637-174718             UUGUA........................ACCACCUCUC...........
AC116353.2/166987-167078             AACAA........................GCAACCUGUC...........
Z97054.1/58392-58486                 GGAAA........................CCAACCUCUC...........
#=GC SS_cons                         ................................<<<...............

Z11765.1/1-89                        ..........GGGGUUCGAAACCCGCGGGCGCCACCUGAC
AF210457.1/105-240                   CCGUGAGUGUUUGGUUCGAGACCCGCGGGCGCUCCCUGGC
AY007237.1/1-136                     CCAUGAGUGUUUGGUUCGAGACCGGCGGGCGCUCCCUGGC
Z11771.1/1-137                       UGGUGAGUGGUUGGUUCGAGACCCGCGGGCGCUCUCUGGC
AC116353.2/181870-181951             .......UGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGC
AF058927.1/1-92                      .......UGGGUGGUUCGARACCCGCGGCCGCUMYCUGGC
AC005219.1/49915-50008               .......GCUGGGGUUCGAGACCCGCGGGUGCUUACUGAC
AF058926.1/1-82                      .......UGGGUGGUUCGARACCCGCGGSCGCYMYCUGRC
AC116353.2/174637-174718             .......UGGGUGGUUCGAGACCCGCGGGUGCUUUCCAGC
AC116353.2/166987-167078             .......UGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGU
Z97054.1/58392-58486                 .......UGGGUGGUUUGAGACCCGUGGGCCCUCUCCAGU
#=GC SS_cons                         ............>>>>>>>...>>>>>>>>.....>>>>>
//
# STOCKHOLM 1.0

#=GF AC   RF00007
#=GF ID   U12
#=GF DE   U12 minor spliceosomal RNA
#=GF AU   Griffiths-Jones SR, Mifsud W
#=GF SE   Shukla GC and Padgett RA, PMID:10199569
#=GF SS   Published; PMID:10199569
#=GF GA   10.00
#=GF TC   11.43
#=GF NC   undefined
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild CM SEED
#=GF BM   cmsearch -W 160 CM SEQDB
#=GF RN   [1]
#=GF RM   10199569
#=GF RT   Conservation of functional features of U6atac and U12 snRNAs between
#=GF RT   vertebrates and higher plants.
#=GF RA   Shukla GC, Padgett RA;
#=GF RL   RNA 1999;5:525-538.
#=GF RN   [2]
#=GF RM   9149533
#=GF RT   Pre-mRNA splicing: the discovery of a new spliceosome doubles the
#=GF RT   challenge.
#=GF RA   Tarn WY, Steitz JA;
#=GF RL   Trends Biochem Sci 1997;22:132-137.
#=GF RN   [3]
#=GF RM   11864616
#=GF RT   The divergent U12-type spliceosome is required for pre-mRNA splicing
#=GF RT   and is essential for development in Drosophila.
#=GF RA   Otake LR, Scamborova P, Hashimoto C, Steitz JA;
#=GF RL   Mol Cell 2002;9:439-446.
#=GF CC   The U12 small nuclear (snRNA), together with U4atac/U6atac, U5,
#=GF CC   and U11 snRNAs and associated proteins, forms a spliceosome that
#=GF CC   cleaves a divergent class of low-abundance pre-mRNA introns. 
#=GF CC   Although the U12 sequence is very divergent from that of U2
#=GF CC   (Rfam:RF00004), the two are functionally analogous [2].
#=GF SQ   7

L43844.1/2-149                      .UGCCUUAAACUUAUGAGUAAGGAAAAUAACAACU......CGGGGUGAC
L43843.1/2-150                      .UGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC
L43846.1/332-460                    .UGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC
L43845.1/357-512                    AUGUCUUAAACUUAUGAGUAAGGAAAAUAACGAUUGUUAUUCGGGGUGAU
J04119.1/2-130                      .UGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC
Z93241.11/76641-76790               AUGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC
AL513366.11/57716-57871             AUGUCUUAAACUUAUGAGUAAGGAAAAUAACGAUUGUUAUUCGGGGUGAU
#=GC SS_cons                        ...<<<<<..........>>>>>........<<<<......<<<<.....

L43844.1/2-149                      GCCCGAGUCCUCACUACUGAUGUGAGAGGAAUUUUUGUGCGGGUACAGGU
L43843.1/2-150                      GCCCGAGUCCUCACUGCUUAUGUGAGAAGAAUUUUUGAGCGGGUAUAGGU
L43846.1/332-460                    GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCGGGUAAAGGU
L43845.1/357-512                    GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCUGGUAAAGGU
J04119.1/2-130                      GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCGGGUAAAGGU
Z93241.11/76641-76790               GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCGGGUAAAGGU
AL513366.11/57716-57871             GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCUGGUAAAGGU
#=GC SS_cons                        .>>>>>>>><<<<<.......>>>>>...........<<<<<<<...<<<

L43844.1/2-149                      CGUCCCC.GGGUGACCCGCUUACUUCGCGGGAUGCCCAGGUGCAAUGAUC
L43843.1/2-150                      UGCAAUCUGAGCGACCCGCCUACUUUGCGGGAUGCCUGGGUGACGCGAUC
L43846.1/332-460                    CGCCCUCAAGGUGACCCGCCUACUUUGCGGGAUGCC..............
L43845.1/357-512                    CGCCCCUAAGGUGACCAGCCUACUUUGCGGGAUGCCUAGGAGUCGCGAUC
J04119.1/2-130                      CGCCCUCAAGGUGACCCGCCUACUUUGCGGGAUGCC..............
Z93241.11/76641-76790               CGCCCUCAAGGUGACCCGCCUACUUUGCGGGAUGCCUGGGAGUUGCGAUC
AL513366.11/57716-57871             CGCCCCUAAGGUGACCAGCCUACUUUGCGGGAUGCCUAGGAGUCGCGAUC
#=GC SS_cons                        <<<<.....>>>>>>>.>>>>>>>..<<<<<<<<<.........>>>>>>

L43844.1/2-149                      UGCCCG
L43843.1/2-150                      UGCCCG
L43846.1/332-460                    ......
L43845.1/357-512                    UGCCUG
J04119.1/2-130                      ......
Z93241.11/76641-76790               UGCCCG
AL513366.11/57716-57871             UGCCUG
#=GC SS_cons                        >>>...
//
# STOCKHOLM 1.0

#=GF AC   RF00008
#=GF ID   Hammerhead_3
#=GF DE   Hammerhead ribozyme (type III)
#=GF AU   Bateman A
#=GF SE   Bateman A
#=GF SS   Published; PMID:7969422
#=GF GA   29.00
#=GF TC   29.53
#=GF NC   28.96
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild CM SEED
#=GF BM   cmsearch -W 130 CM SEQDB
#=GF RN   [1]
#=GF RM   7969422
#=GF RT   Three-dimensional structure of a hammerhead ribozyme.
#=GF RA   Pley HW, Flaherty KM, McKay DB;
#=GF RL   Nature 1994;372:68-74.
#=GF RN   [2]
#=GF RM   9506521
#=GF RT   The structural basis of hammerhead ribozyme self-cleavage.
#=GF RA   Murray JB, Terwey DP, Maloney L, Karpeisky A, Usman N, Beigelman L,
#=GF RA   Scott WG;
#=GF RL   Cell 1998;92:665-673.
#=GF RN   [3]
#=GF RM   10899150
#=GF RT   Distribution of hammerhead and hammerhead-like RNA motifs through the
#=GF RT   GenBank.
#=GF RA   Ferbeyre G, Bourdeau V, Pageau M, Miramontes P, Cedergren R;
#=GF RL   Genome Res 2000;10:1011-1019.
#=GF CC   The hammerhead ribozyme is one of the smallest catalytic
#=GF CC   RNAs. These RNAs have an endonuclease function, and most
#=GF CC   often are autocatalytic. Structurally it is composed of
#=GF CC   three base paired helices, separated by short linkers of
#=GF CC   conserved sequence. These helices are called I, II and III.
#=GF CC   We have classified hammerhead ribozymes into three types
#=GF CC   based on which helix the 5' and 3' ends of the sequence
#=GF CC   join. This family are the type III hammerheads.
#=GF CC   The conserved uridine-turn links helix I 
#=GF CC   to helix II and usually has the sequence CUGA.  Helix II and
#=GF CC   III are linked by a sequence CGAAA.  The cleavage reaction 
#=GF CC   occurs between helix III and I, and is usually a C.
#=GF CC   Hammerhead ribozymes are found in plant viroids and other
#=GF CC   small replicating sattelite RNA species.  Hammerhead
#=GF CC   ribozymes have been found in animals as well as plants.
#=GF CC   This family includes a couple of false matches currently
#=GF CC   these are EMBL:AC078923 and EMBL:BC050488. These animal
#=GF CC   sequences are not expected to be hammerhead ribozymes.
#=GF SQ   84

AJ295015.1/58-1                ACAGAGUC.UGACAAA......CCGUCACUGAAGACGUUCAACUU.....
AJ295018.1/58-1                ACAGGGUC.UGACAAA......CCGUCACUGAAGACGUUCAACUU.....
AJ536620.1/206-152             CCACCGUC.GGAAAGUG.UGCGCUUUCCCUGAUGAGCCCAA.........
AJ536615.1/1-44                .........GGGUGGUG.UGUACCAUCCCUGAUGAGUCCAA.........
AJ536612.1/206-152             UCACCGUC.GGAAAGUG.UGCGCUUUCCCUGAUGAGCCCGA.........
AJ536617.1/1-40                .........GGGUGGUGUGUA.CCACCCCUGAUGAGUCCGA.........
AJ536614.1/206-152             UCACCGUC.GGAAAGUG.UGCGCUUUCCCUGAUGAGCCCAA.........
AJ536620.1/1-40                .........GGGUGGUGUGUG.CCACCCCUGAUGAGUCCGA.........
AJ536619.1/206-152             CCACCGUC.GGAAAGUG.UGUACUUUCCCUGAUGAGUCCGA.........
AJ550911.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGUUGCUGA.......
AF170503.1/280-333             GAAAGGUC.UGUGCUU......AGCACACUGACGAGUUCCUGA.......
AF170504.1/284-337             GAUAAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ550912.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGUUGCUGA.......
AJ247113.1/134-53              .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGC
AJ241833.1/282-334             AAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ241841.1/57-3                CAAAAGUU.UGGGCUAA.....AGCCCACUGAUGAGCCGCUGA.......
AJ241839.1/282-334             GAUGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ550901.1/282-334             GAAGAGUC..GCGCUA......AGCGCACUGAUGAGUCUUUGA.......
AJ005298.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
AJ241819.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
AJ005320.1/281-333             GAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ005310.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA.......
AF339740.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGCCGUUGA.......
AJ241828.1/56-3                CAUAAGUC.UGGGUUA......AGCCCACUGAUGAGCCGUUGA.......
AJ550906.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGUCGCUGC.......
AJ550903.1/281-333             GAAGAGUC..GUGCUU......AGCACACUGAUGAGUCUCUGA.......
AJ241831.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
AJ241840.1/56-3                CAGAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA.......
AJ005303.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
AJ005312.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA.......
AJ550906.1/282-334             GAAGAGUC..GUGCUU......AGCACACUGAUGAGUCUCUGA.......
AJ550907.1/56-3                CAUAAGUC.UGGGCUU......AGCCUACUGAUGAGUCGCUGC.......
AF170503.1/55-3                CAUAAGUC.UGGGCUU......AG.CCACUGACGAGUCGCUGG.......
Y14700.1/133-53                .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGAUGAGGCUGUGGAGAGAGC
AJ005321.1/281-333             GAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ241845.1/282-335             GAUGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ005322.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGACGAGCCGUUGA.......
M83545.1/56-3                  CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGUCGCUGA.......
AJ005305.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGACGAGCCGCUGG.......
AJ550908.1/281-334             GAAGAGUC.UGCGCUU......AGCGCACUCAUGAGUCUCUGA.......
AJ550909.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGUUGCUGC.......
AJ241843.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGCCACUGA.......
AF170523.1/55-3                CAAAAGUC.UGGGCUU......AG.CCACUGAUGAGCCGUUGA.......
AF170509.1/56-3                CAUAAGUC.UAGGCUU......AGCCCACUGAUGAGCCGUUGA.......
AJ241847.1/281-334             GAAGAGUC.UGUGCUA......AGCACACUGAUGAGUUUCUGA.......
AJ241823.1/282-335             AAAGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUAA.......
AJ247122.1/132-52              .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGC
AJ005300.1/282-335             UAAGAGUC.UGUGGUA......AGCACACUGAUGAGUCUCUGA.......
AJ005302.1/281-334             AAAGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ005318.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
AF339739.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGGCGUUGA.......
AJ241838.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCUGCUGA.......
AJ247121.1/133-53              .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGC
AJ550911.1/282-335             GAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA.......
AJ550898.1/282-335             GAAGAGUC.UGCGCUA......AGCGCACUGAUGAGUCUUUGA.......
AF170516.1/283-335             GAAGAGUC..GUGCUU......AGCACACUGAUGAGUCUCUGA.......
AJ005319.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
AJ550899.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCUUUGC.......
AF170519.1/55-3                CAUAAGUC.UGGGCUU......AG.CCACUGAUGAGCCGUUGA.......
AJ247116.1/133-53              .UCCAGUC.GAGACCUGAAGUGGGUUUACUGAUGAGGCUGUGGAGAGAGC
AJ550907.1/281-333             AAAGAGUC..GCGCUU......AGCGCACUGAUGAGUCUCUGA.......
AJ241850.1/282-334             UAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
AF170499.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA.......
AF170520.1/282-335             GAUAAGUC.UGUGCUU......AGCACACUGAUGAGUCUCUGA.......
AJ005299.1/282-335             UAAGAGUC.UGUGCUA......AGCACACUGAUGAAUCUCUGA.......
AJ005312.1/282-335             GAUGAGUC.UGUGCUA......AGCACACUGAUGAGUCUAUGA.......
AJ550909.1/282-333             GAAGAGUC..GCGCUU......AGCGCACUGAUGAGUCUCUGA.......
AJ005322.1/281-334             GAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA.......
AJ005294.1/282-334             UAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ247123.1/132-52              .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGAUGAGGCUGUGGAGAGAGC
AJ550900.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCUUUGC.......
AJ241830.1/282-334             AAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ241831.1/281-334             GAAGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA.......
M83545.1/282-335               GAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA.......
AJ550910.1/282-336             GAAGAGUCCUGCGCUU......AGCGCACUGACGAGUCUCUGA.......
AJ005314.1/281-334             AAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA.......
Y12833.1/339-285               CCGCUAUA.UGGGGAUGUGUG.UCCCUACUGACGAGUUCAA.........
M63666.1/246-192               CCGGUGUC.UCAAGGUGCGUA.CCUUGACUGAUGAGUCCGA.........
J02439.1/42-95                 UGUCCGUA..GUGGAUGUGUA.UCCACUCUGAUGAGUCCGA.........
J02386.1/42-95                 UGUCCGUA..GUGGAUGUGUA.UCCACUCUGAUGAGUCCAA.........
M33000.1/55-110                ACGCUGUC.UGUACUUGUAUC.AGUACACUGACGAGUCCCU.........
M33001.1/56-111                ACGCUGUC.UGUACUUAUAUC.AGUACACUGACGAGUCCCU.........
D00685.1/1-46                  .........GCCAGACGU.GGACCCGGCCUGAUGAGUCCGAAA.......
M17439.1/1-48                  .........ACCGGAUGUGCUUUCCGGUCUGAUGAGUCCGU.........
#=GC SS_cons                   .<<<<<<..<<<<<.........>>>>>.......<<<<...........

AJ295015.1/58-1                ...............GCGUUGAACAGAAACUCUGC
AJ295018.1/58-1                ...............GCGUUGAACAGAAACUCUGC
AJ536620.1/206-152             ...................AAGGGCGAAACGGUAC
AJ536615.1/1-44                ...................AAGGACGAAAUGG...
AJ536612.1/206-152             ...................AAGGGCGAAACGGUAC
AJ536617.1/1-40                ...................AAGGACGAA.......
AJ536614.1/206-152             ...................AAGGGCGAAACGGUAC
AJ536620.1/1-40                ...................AAGGACGAA.......
AJ536619.1/206-152             ...................AAGGACGAAACGGUAC
AJ550911.1/56-3                .................AACGCAACGAAACUUUUG
AF170503.1/280-333             .................AAUGGAACGAAACCUUUU
AF170504.1/284-337             .................AAUGAGACGAAACUUAUC
AJ550912.1/56-3                .................GAUGCGACGAAACUUUUG
AJ247113.1/134-53              AAAUUGCUUUACUCCCGCACAAGCCGAAACUGGA.
AJ241833.1/282-334             .................AAUGAGACGAAACUCUUU
AJ241841.1/57-3                .................AAUGCGGCGAAACUUUUG
AJ241839.1/282-334             .................AAUGAGACGAAACUCAUA
AJ550901.1/282-334             .................GAUAAGACGAAACUCUUC
AJ005298.1/56-3                .................GAUACGGCGAAACUUUUG
AJ241819.1/56-3                .................AAUACGGCGAAACUUUUG
AJ005320.1/281-333             .................AAUGAGACGAAACUCUUU
AJ005310.1/56-3                .................AAUGCGGCGAAACUUUUG
AF339740.1/56-3                .................GAUACGGCGGAACUUAUG
AJ241828.1/56-3                .................GAUACGGCGAAACUUAUG
AJ550906.1/56-3                .................GAUGCGACGAAACUUAUG
AJ550903.1/281-333             .................AAUGAGACGAAACUCUUU
AJ241831.1/56-3                .................GAUACGGCGAAACUUCUG
AJ241840.1/56-3                .................AAUGCGGCGAAACUUUUG
AJ005303.1/56-3                .................GAUACGGCGAAACUUUUG
AJ005312.1/56-3                .................AAUGCGGCUAAACUUUUG
AJ550906.1/282-334             .................GAUGAGACGAAACUCUUC
AJ550907.1/56-3                .................GAUGCGACGAAACUUAUG
AF170503.1/55-3                .................GAUACGGCGAAACUUAUG
Y14700.1/133-53                GAAAGCUUUACUCCCA.CACAAGCCGAAACUGGA.
AJ005321.1/281-333             .................AAUGAGACGAAACUCUUG
AJ241845.1/282-335             .................AAUGAGACGAAACUCAUG
AJ005322.1/56-3                .................GAUACGGCGAAACUUAUG
M83545.1/56-3                  .................AAUGCGACGAAACUUAUG
AJ005305.1/56-3                .................GAUACGGCGAAACUUUUG
AJ550908.1/281-334             .................GAUGAGACGAAACUCUUC
AJ550909.1/56-3                .................GAUGCAACGAAACUUAUG
AJ241843.1/56-3                .................AAUGCGGCGAAACUUUUG
AF170523.1/55-3                .................GAUACGGCGAAACUUUUG
AF170509.1/56-3                .................GAUACGGCGAAACUUAUG
AJ241847.1/281-334             .................AAUGAGACGAAACUCUUG
AJ241823.1/282-335             .................AAUGAGACGAAACUCUUU
AJ247122.1/132-52              UAUUGCUUUACUCCCG.CACAAGCCGAAACUGGA.
AJ005300.1/282-335             .................AAUGAGACGAAACUCUUG
AJ005302.1/281-334             .................AUUGAGACGAAACUCUUG
AJ005318.1/56-3                .................GAUACGGUGAAACUUAUG
AF339739.1/56-3                .................GAUACGGCGAAACUUAUG
AJ241838.1/56-3                .................AAUGCGGCAAAACUUUUG
AJ247121.1/133-53              UUUCGCUUUACUCCCG.CACAAGCCGAAACUGGA.
AJ550911.1/282-335             .................AAUGAGACGAAACUCUUC
AJ550898.1/282-335             .................AAUAAGACGAAACUCUUC
AF170516.1/283-335             .................AAUGAGACGAAACUCUUC
AJ005319.1/56-3                .................GAUACGGCGAAACUUAUG
AJ550899.1/56-3                .................GAUAAGGCGAAACUUAUG
AF170519.1/55-3                .................GAUACGGCGAAACUUAUG
AJ247116.1/133-53              GAAAGCUUUACUCCCA.CACAAGCCGAAACUGGA.
AJ550907.1/281-333             .................GAUGAGACGAAACUCUUC
AJ241850.1/282-334             .................AAAGAGACGAAACUCUUU
AF170499.1/56-3                .................AAUGCGGCGAAACUUUUG
AF170520.1/282-335             .................AAUGAGACGAAACUUAUC
AJ005299.1/282-335             .................AAUGAGACGAAACUCUUG
AJ005312.1/282-335             .................AAUGAGACGAAACUCAUA
AJ550909.1/282-333             ..................AUGAGACGAAACUCUUC
AJ005322.1/281-334             .................AAUGAGACGAAACUCUUU
AJ005294.1/282-334             .................AAUGAGACGAAACUCUUG
AJ247123.1/132-52              GAAAGCUUUACUCCCG.CACAAGCCGAAACUGGA.
AJ550900.1/56-3                .................GACAAGGCGAAACUUAUG
AJ241830.1/282-334             .................AAUGAGACGAAACUCUUG
AJ241831.1/281-334             .................AAUGAGACGAAACUCUUA
M83545.1/282-335               .................GAUGAGACGAAACUCUUC
AJ550910.1/282-336             .................GAUGAGACGAAACUCUUC
AJ005314.1/281-334             .................AAUGAGACGAAACUCUUU
Y12833.1/339-285               ...................AAGAACGAAAUAGUUA
M63666.1/246-192               ...................AAGGACGAAACACCAG
J02439.1/42-95                 ...................AAGGACGAAACGGAUG
J02386.1/42-95                 ...................AAGGACGAAACGGAUG
M33000.1/55-110                ..................AAAGGACGAAACAGCGC
M33001.1/56-111                ..................AAAGGACGAAACAGCGC
D00685.1/1-46                  .....................GGACGAAACAGUA.
M17439.1/1-48                  ...................GAGGACGAAACAGGAC
#=GC SS_cons                   .....................>>>>...>>>>>>.
//BioPerl-1.007002/t/data/ribosome-slippage.gb000444000766000024      6104713155576321 20653 0ustar00cjfieldsstaff000000000000LOCUS       NT_004487               8362 bp    DNA     linear   CON 10-JUN-2009
DEFINITION  Homo sapiens chromosome 1 genomic contig, GRCh37 reference primary
            assembly.
ACCESSION   NT_004487 REGION: 3224086..3232447 GPS_000125225
VERSION     NT_004487.19  GI:224514980
DBLINK      Project:168
KEYWORDS    .
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 8362)
  AUTHORS   Gregory,S.G., Barlow,K.F., McLay,K.E., Kaul,R., Swarbreck,D.,
            Dunham,A., Scott,C.E., Howe,K.L., Woodfine,K., Spencer,C.C.,
            Jones,M.C., Gillson,C., Searle,S., Zhou,Y., Kokocinski,F.,
            McDonald,L., Evans,R., Phillips,K., Atkinson,A., Cooper,R.,
            Jones,C., Hall,R.E., Andrews,T.D., Lloyd,C., Ainscough,R.,
            Almeida,J.P., Ambrose,K.D., Anderson,F., Andrew,R.W., Ashwell,R.I.,
            Aubin,K., Babbage,A.K., Bagguley,C.L., Bailey,J., Beasley,H.,
            Bethel,G., Bird,C.P., Bray-Allen,S., Brown,J.Y., Brown,A.J.,
            Buckley,D., Burton,J., Bye,J., Carder,C., Chapman,J.C., Clark,S.Y.,
            Clarke,G., Clee,C., Cobley,V., Collier,R.E., Corby,N.,
            Coville,G.J., Davies,J., Deadman,R., Dunn,M., Earthrowl,M.,
            Ellington,A.G., Errington,H., Frankish,A., Frankland,J., French,L.,
            Garner,P., Garnett,J., Gay,L., Ghori,M.R., Gibson,R., Gilby,L.M.,
            Gillett,W., Glithero,R.J., Grafham,D.V., Griffiths,C.,
            Griffiths-Jones,S., Grocock,R., Hammond,S., Harrison,E.S., Hart,E.,
            Haugen,E., Heath,P.D., Holmes,S., Holt,K., Howden,P.J., Hunt,A.R.,
            Hunt,S.E., Hunter,G., Isherwood,J., James,R., Johnson,C.,
            Johnson,D., Joy,A., Kay,M., Kershaw,J.K., Kibukawa,M.,
            Kimberley,A.M., King,A., Knights,A.J., Lad,H., Laird,G., Lawlor,S.,
            Leongamornlert,D.A., Lloyd,D.M., Loveland,J., Lovell,J., Lush,M.J.,
            Lyne,R., Martin,S., Mashreghi-Mohammadi,M., Matthews,L.,
            Matthews,N.S., McLaren,S., Milne,S., Mistry,S., Moore,M.J.,
            Nickerson,T., O'Dell,C.N., Oliver,K., Palmeiri,A., Palmer,S.A.,
            Parker,A., Patel,D., Pearce,A.V., Peck,A.I., Pelan,S., Phelps,K.,
            Phillimore,B.J., Plumb,R., Rajan,J., Raymond,C., Rouse,G.,
            Saenphimmachak,C., Sehra,H.K., Sheridan,E., Shownkeen,R., Sims,S.,
            Skuce,C.D., Smith,M., Steward,C., Subramanian,S., Sycamore,N.,
            Tracey,A., Tromans,A., Van Helmond,Z., Wall,M., Wallis,J.M.,
            White,S., Whitehead,S.L., Wilkinson,J.E., Willey,D.L., Williams,H.,
            Wilming,L., Wray,P.W., Wu,Z., Coulson,A., Vaudin,M., Sulston,J.E.,
            Durbin,R., Hubbard,T., Wooster,R., Dunham,I., Carter,N.P.,
            McVean,G., Ross,M.T., Harrow,J., Olson,M.V., Beck,S., Rogers,J.,
            Bentley,D.R., Banerjee,R., Bryant,S.P., Burford,D.C., Burrill,W.D.,
            Clegg,S.M., Dhami,P., Dovey,O., Faulkner,L.M., Gribble,S.M.,
            Langford,C.F., Pandian,R.D., Porter,K.M. and Prigmore,E.
  TITLE     The DNA sequence and biological annotation of human chromosome 1
  JOURNAL   Nature 441 (7091), 315-321 (2006)
   PUBMED   16710414
  REMARK    Erratum:[Nature. 2006 Oct 26;443(7114):1013. Banerjee, R [added];
            Bryant, SP [added]; Burford, DC [added]; Burrill, WDH [added];
            Clegg, SM [added]; Dhami, P [added]; Dovey, O [added]; Faulkner, LM
            [added]; Gribble, SM [added]; Langford, CF [added]; Pandian, RD
            [added]; Porter, KM [added]; Prigmore, E [added]]
REFERENCE   2  (sites)
  AUTHORS   Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A and Enright
            AJ.
  TITLE     miRBase: microRNA sequences, targets and gene nomenclature
  JOURNAL   Nucleic Acids Res. 34 (DATABASE ISSUE), D140-D144 (2006)
   PUBMED   16381832
REFERENCE   3  (bases 1 to 8362)
  CONSRTM   International Human Genome Sequencing Consortium
  TITLE     Finishing the euchromatic sequence of the human genome
  JOURNAL   Nature 431 (7011), 931-945 (2004)
   PUBMED   15496913
REFERENCE   4  (sites)
  AUTHORS   Griffiths-Jones S.
  TITLE     The microRNA Registry
  JOURNAL   Nucleic Acids Res. 32 (DATABASE ISSUE), D109-D111 (2004)
   PUBMED   14681370
REFERENCE   5  (bases 1 to 8362)
  AUTHORS   Lander,E.S., Linton,L.M., Birren,B., Nusbaum,C., Zody,M.C.,
            Baldwin,J., Devon,K., Dewar,K., Doyle,M., FitzHugh,W., Funke,R.,
            Gage,D., Harris,K., Heaford,A., Howland,J., Kann,L., Lehoczky,J.,
            LeVine,R., McEwan,P., McKernan,K., Meldrim,J., Mesirov,J.P.,
            Miranda,C., Morris,W., Naylor,J., Raymond,C., Rosetti,M.,
            Santos,R., Sheridan,A., Sougnez,C., Stange-Thomann,N.,
            Stojanovic,N., Subramanian,A., Wyman,D., Rogers,J., Sulston,J.,
            Ainscough,R., Beck,S., Bentley,D., Burton,J., Clee,C., Carter,N.,
            Coulson,A., Deadman,R., Deloukas,P., Dunham,A., Dunham,I.,
            Durbin,R., French,L., Grafham,D., Gregory,S., Hubbard,T.,
            Humphray,S., Hunt,A., Jones,M., Lloyd,C., McMurray,A., Matthews,L.,
            Mercer,S., Milne,S., Mullikin,J.C., Mungall,A., Plumb,R., Ross,M.,
            Shownkeen,R., Sims,S., Waterston,R.H., Wilson,R.K., Hillier,L.W.,
            McPherson,J.D., Marra,M.A., Mardis,E.R., Fulton,L.A.,
            Chinwalla,A.T., Pepin,K.H., Gish,W.R., Chissoe,S.L., Wendl,M.C.,
            Delehaunty,K.D., Miner,T.L., Delehaunty,A., Kramer,J.B., Cook,L.L.,
            Fulton,R.S., Johnson,D.L., Minx,P.J., Clifton,S.W., Hawkins,T.,
            Branscomb,E., Predki,P., Richardson,P., Wenning,S., Slezak,T.,
            Doggett,N., Cheng,J.F., Olsen,A., Lucas,S., Elkin,C.,
            Uberbacher,E., Frazier,M., Gibbs,R.A., Muzny,D.M., Scherer,S.E.,
            Bouck,J.B., Sodergren,E.J., Worley,K.C., Rives,C.M., Gorrell,J.H.,
            Metzker,M.L., Naylor,S.L., Kucherlapati,R.S., Nelson,D.L.,
            Weinstock,G.M., Sakaki,Y., Fujiyama,A., Hattori,M., Yada,T.,
            Toyoda,A., Itoh,T., Kawagoe,C., Watanabe,H., Totoki,Y., Taylor,T.,
            Weissenbach,J., Heilig,R., Saurin,W., Artiguenave,F., Brottier,P.,
            Bruls,T., Pelletier,E., Robert,C., Wincker,P., Smith,D.R.,
            Doucette-Stamm,L., Rubenfield,M., Weinstock,K., Lee,H.M.,
            Dubois,J., Rosenthal,A., Platzer,M., Nyakatura,G., Taudien,S.,
            Rump,A., Yang,H., Yu,J., Wang,J., Huang,G., Gu,J., Hood,L.,
            Rowen,L., Madan,A., Qin,S., Davis,R.W., Federspiel,N.A.,
            Abola,A.P., Proctor,M.J., Myers,R.M., Schmutz,J., Dickson,M.,
            Grimwood,J., Cox,D.R., Olson,M.V., Kaul,R., Raymond,C., Shimizu,N.,
            Kawasaki,K., Minoshima,S., Evans,G.A., Athanasiou,M., Schultz,R.,
            Roe,B.A., Chen,F., Pan,H., Ramser,J., Lehrach,H., Reinhardt,R.,
            McCombie,W.R., de la Bastide,M., Dedhia,N., Blocker,H.,
            Hornischer,K., Nordsiek,G., Agarwala,R., Aravind,L., Bailey,J.A.,
            Bateman,A., Batzoglou,S., Birney,E., Bork,P., Brown,D.G.,
            Burge,C.B., Cerutti,L., Chen,H.C., Church,D., Clamp,M.,
            Copley,R.R., Doerks,T., Eddy,S.R., Eichler,E.E., Furey,T.S.,
            Galagan,J., Gilbert,J.G., Harmon,C., Hayashizaki,Y., Haussler,D.,
            Hermjakob,H., Hokamp,K., Jang,W., Johnson,L.S., Jones,T.A.,
            Kasif,S., Kaspryzk,A., Kennedy,S., Kent,W.J., Kitts,P.,
            Koonin,E.V., Korf,I., Kulp,D., Lancet,D., Lowe,T.M., McLysaght,A.,
            Mikkelsen,T., Moran,J.V., Mulder,N., Pollara,V.J., Ponting,C.P.,
            Schuler,G., Schultz,J., Slater,G., Smit,A.F., Stupka,E.,
            Szustakowski,J., Thierry-Mieg,D., Thierry-Mieg,J., Wagner,L.,
            Wallis,J., Wheeler,R., Williams,A., Wolf,Y.I., Wolfe,K.H.,
            Yang,S.P., Yeh,R.F., Collins,F., Guyer,M.S., Peterson,J.,
            Felsenfeld,A., Wetterstrand,K.A., Patrinos,A., Morgan,M.J., de
            Jong,P., Catanese,J.J., Osoegawa,K., Shizuya,H., Choi,S. and
            Chen,Y.J.
  CONSRTM   International Human Genome Sequencing Consortium
  TITLE     Initial sequencing and analysis of the human genome
  JOURNAL   Nature 409 (6822), 860-921 (2001)
   PUBMED   11237011
  REMARK    Erratum:[Nature 2001 Aug 2;412(6846):565]
REFERENCE   6  (sites)
  AUTHORS   Lowe,T.M. and Eddy,S.R.
  TITLE     tRNAscan-SE: a program for improved detection of transfer RNA genes
            in genomic sequence
  JOURNAL   Nucleic Acids Res. 25 (5), 955-964 (1997)
   PUBMED   9023104
  REMARK    This is the methods paper for tRNAscan-SE.
COMMENT     REFSEQ INFORMATION: Features on this sequence have been produced
            for build 37 version 1 of the NCBI's genome annotation [see
            documentation].   The reference sequence is identical to
            GL000016.1.
            On or before Jun 10, 2009 this sequence version replaced
            gi:37547157, gi:88943456, gi:37549741, gi:88943682.
            The DNA sequence is composed of genomic sequence, primarily
            finished clones that were sequenced as part of the Human Genome
            Project. PCR products and WGS shotgun sequence have been added
            where necessary to fill gaps or correct errors. All such additions
            are manually curated by GRC staff. For more information see:
            http://genomereference.org.
FEATURES             Location/Qualifiers
     source          1..8362
                     /organism="Homo sapiens"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
     gene            complement(<1..597)
                     /gene="MRPL9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:65005"
                     /db_xref="HGNC:14277"
                     /db_xref="MIM:611824"
     mRNA            complement(join(23..179,360..597))
                     /gene="MRPL9"
                     /product="mitochondrial ribosomal protein L9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_031420.2"
                     /db_xref="GI:22035596"
                     /db_xref="GeneID:65005"
                     /db_xref="HGNC:14277"
                     /db_xref="MIM:611824"
     CDS             complement(join(23..179,360..512))
                     /gene="MRPL9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /codon_start=1
                     /product="mitochondrial ribosomal protein L9"
                     /protein_id="NP_113608.1"
                     /db_xref="GI:13899231"
                     /db_xref="CCDS:CCDS1003.1"
                     /db_xref="GeneID:65005"
                     /db_xref="HGNC:14277"
                     /db_xref="MIM:611824"
     gene            2..>8362
                     /gene="OAZ3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:51686"
                     /db_xref="HGNC:8097"
                     /db_xref="MIM:605138"
     mRNA            join(2..200,4196..4332,5091..5266,7205..7290,8110..>8362)
                     /gene="OAZ3"
                     /product="ornithine decarboxylase antizyme 3, transcript
                     variant 2"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_001134939.1"
                     /db_xref="GI:201023342"
                     /db_xref="GeneID:51686"
                     /db_xref="HGNC:8097"
                     /db_xref="MIM:605138"
     CDS             join(169..200,4196..4256,4258..4332,5091..5266,7205..7290,
                     8110..8252)
                     /gene="OAZ3"
                     /ribosomal_slippage
                     /note="protein translation dependent on +1 ribosomal
                     frameshift;isoform 2 is encoded by transcript variant 2;
                     Derived by automated computational analysis using gene
                     prediction method: BestRefseq."
                     /codon_start=1
                     /product="ornithine decarboxylase antizyme 3 isoform 2"
                     /protein_id="NP_001128411.1"
                     /db_xref="GI:201023343"
                     /db_xref="GeneID:51686"
                     /db_xref="HGNC:8097"
                     /db_xref="MIM:605138"
     mRNA            join(3688..3921,4196..4332,5091..5266,7205..7290,
                     8110..>8362)
                     /gene="OAZ3"
                     /product="ornithine decarboxylase antizyme 3, transcript
                     variant 1"
                     /exception="mismatches in transcription"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_016178.2"
                     /db_xref="GI:161377479"
                     /db_xref="GeneID:51686"
                     /db_xref="HGNC:8097"
                     /db_xref="MIM:605138"
     CDS             join(3755..3921,4196..4256,4258..4332,5091..5266,
                     7205..7290,8110..8252)
                     /gene="OAZ3"
                     /ribosomal_slippage
                     /note="non-AUG (CUG) translation initiation codon;isoform
                     1 is encoded by transcript variant 1; Derived by automated
                     computational analysis using gene prediction method:
                     BestRefseq."
                     /codon_start=1
                     /transl_except=(pos:3755..3757,aa:Met)
                     /product="ornithine decarboxylase antizyme 3 isoform 1"
                     /protein_id="NP_057262.2"
                     /db_xref="GI:190886510"
                     /db_xref="GeneID:51686"
                     /db_xref="HGNC:8097"
                     /db_xref="MIM:605138"
ORIGIN      
        1 agcgcctcgg cccgggcctt actctccacc gactgcgtca ggatgagctc caggttttct
       61 ttgggccgat gcttcgtgtc ctccaccagc ttatagacgc gatgtcgccg gtgcaggcgc
      121 ggcttccggc cctccccggc cagcggtacc ttccaccagc gctccacgat gaccgtgccc
      181 tggcggccag gaaagcgacg gtaagctagt ctccacaagg aacaccctct ccctccacca
      241 cggccgccag cccctcaagg aaagcccgcc acccccacat cggccccctc caggtcccag
      301 tgcgcctcca gaaacaatac tcgagcgtat ctacccccta ccccagactc agccctcacc
      361 cgattttgag aaaggctgaa gttgcaggcc aggtcagggg cgttcccttc atgtcgcggc
      421 cgcagtagct cctggacgcc tccccgaagc agccgtccag cgcccgcccg cagcagagct
      481 ctgcccgggg ccgtgacaac gggcgccgcc atgttcacag gcacagaatg agacctgagg
      541 gaggaccccg gcgtcggcgg caggaaaggc ccccgccagt gctgcctgcg gcgcgccggt
      601 acggctgagc gaaagtatgg ggagcgggcc ggggaacaga tggcaccgcg gcttgcctat
      661 ttttgctttt tggcagaggt gacggacgcc tagaattact gactgataat ggaatgagtg
      721 ttaggtggac tgacgccgga aaagacgctc ttcctcttga aagtgtgggc tttgctgtag
      781 ctccagttgc tgggctaact tttaattcta acgttctgtg atgactggat actgaccgga
      841 gaatgaatga tgctctcact tttccttact tcaaatctac ctaaaagtgg taaaggatgg
      901 gatcccttgg aaaactctgc cagctccagg aggagcctga cccttaatca ttatactgca
      961 gtatttaagc taataaagga gaattctaaa tcacaagcta tgtaaaccgt agaaaaaaaa
     1021 gcaactatgg taaggccgcg acagttccct ctggggaggg tctcagtact ggacagaaga
     1081 ccataaaaac tggatgaaag aaggtccatt tggcagagat tatggaaaga ctggccctta
     1141 aacatactga ccagtcctcc ttcctcctaa atacactact tggcctcctg gacaccggtc
     1201 ttcttcagtc tcgtttgctg atttctcctt ttctccccgc ttcttagaat gccctcggga
     1261 ctccgttttt gaacctttac tcttctcagt atacactcac tgttgatctc atccagtctc
     1321 gtggcttaca ataccattta taagccaatg actcccaaat ttctagttcc atcctagaca
     1381 tctcccaaac tcgtctcaaa tattcaactg tttattcgtc attttcctct tacgtatcca
     1441 aaggacacct caaagttaac tgtcccaaac taatttattt attcccccct cgcccccaaa
     1501 actgccccat ctgcagcctt tttcctctca gttgacagaa actccattct ttccattcta
     1561 actcttttct ctcatactcc atcaggaaat cctgtgggtt ctacctttaa attacagata
     1621 gtccctgact tggatttaca atttttgagt ttgtgatggt gtgaaagtga tgtgcactca
     1681 gtaggacatc aataagttac atgaaatatt caacacttta ttataaaata ggctttgtgt
     1741 tagatgattt tacccaactg tcggataagt tgtctgagca tgtttaagat aggctaggct
     1801 aagctatggt gtttggtagg tgtattatat gcattttcaa cttatgatac tttcaacata
     1861 cgatgggttt atcaggacat aaccctattt taagtcaagg agcacttgta tttccagaat
     1921 ccagccactt gtcaccacct ccaatgctct accttggaat aagacactac tttctcctgg
     1981 attactgcaa tagtccccta aaagatatcc cttaattctc tacagtttat aattctatgt
     2041 agcttattta tagcagccag aatgatcttt ttaaagcata agtcagatca tgtcattctt
     2101 ccacccaaaa ctttgtaatg acttcctcct ttactcaagg taaaagaaaa aggccatcag
     2161 atggtctaca aggccataca tactctgacc ccattagctc ctctctaatt tacactgctc
     2221 cacccacagt ggcctccttg tttcttgaaa acaccaggca cgtttcctgc tcagggcttt
     2281 tgcactggct gcttttgcgt tggatgctct tatcctcaga tgctggcttg gttaacaacc
     2341 tcacatcctc caagtgttta attaaatgtc agtttttttc agtgagagat caccctattt
     2401 cttactgtaa ccctgaccca tccccttcac attccttatc ttcctttatc ttgctctatt
     2461 ccccccaccc catagcagtt accttctaac atactaaaca atttactatg tttattttct
     2521 aggtttgtcc tctcactttt agaagatacg ttccataggg cagggatttg ttttgttcac
     2581 tgatgtatca tctcaagcac ctagaatagt gcctggctaa tagtagaccc tcaataaata
     2641 tttgttgaat ggataaatat gcagaggtct caaagtggca gtcccagaac caaattttgc
     2701 ttacaatgtt gtttttttat caacaatttt ttagtagttg attttttttt ttttttgagt
     2761 tggagtctcg ctatgttgcc caggctggag tgcagtggca cgatctcagc tcactgcaag
     2821 ctccgcctcc tgggttcacg ccattctcct gcctcagcct cccgtgtagc tgggaataca
     2881 ggcgcctgcc accacgcccg gctaattttt tgtattttta gtacagacag agtttcatcg
     2941 tgttagccag gatggtctcg atctcctgac ctcgtgatcc gcccgcctcg gcctcccaaa
     3001 gcgctgggat tacagacgtg agccaccgtg cccggcccag tagtcgatat tttttaaaat
     3061 tggtgagatt tactacaaaa ctgtctttcc agtttctgtt caaaaatcat acgatacagc
     3121 accatcaagt ctgcattctt gcatggaact ggatggaatt gagttgtgtg gacttccttt
     3181 agataacgtg tgagctttcc tattttgcta cagccctacc ctgccactcc actaatttcc
     3241 ataagctgtc taggcccctg aaggggccta gacaattagt ttgcaattcc taccctacaa
     3301 ggatcctggg ttattaaggg tagggatgat aataaaaata ctcaactggt atgaactggg
     3361 aaccaactaa tcaggtcacc actggatcag agccttggaa gagtcagata ccaactcttt
     3421 acttgctgga ttttggggga aggggagtgt ccacagagga gcagggtggg tgggcacaag
     3481 tgctcaggca gggcttttgg ccaaccagta cagaagtctt caagttctat tttttaatca
     3541 ttcatacagc cataacatgc atactagtcg aatatgagcc ttggataagg gattagggta
     3601 gataagcagc agagtggagt cctgaggtga cataagggct gaccccttat ccatgtcata
     3661 gtgcccactg ggtcacaatg ccaccaggtt gcctaaacct ctgccaccca cctgtgaact
     3721 tcactttgcc acagggaggc actgaactga aaaactgcct tgtaagaggt gtcgcccctc
     3781 tgtctactcc ctttcttata tcaagagggg aaaaacacgt aactacctct acccgatctg
     3841 gtcaccatac gcctattacc tttactgtta caagtaccgg atcactctcc gggagaagat
     3901 gctgcctcgt tgttataaaa ggtacttgtt ttcatctcta tttgtagttg tttatataaa
     3961 atgtaaggaa aaagtaaaag aatttgaaag aatttcccaa atggcaagaa ataacaacag
     4021 aatagggggt ggaaagctgg catggaactt tagaattttt ccatctggtt gggcccagga
     4081 acatagaaac aggctggaca acagaaaata cagaagatca tgccagagcc tggtactgtg
     4141 tatcttccca cctcagattc caagataaac taatttgggt ctctttccca accagcatca
     4201 cttataagga agaggaggac ttgacactcc agccccgttc ctgcctccag tgctcctgag
     4261 tccctagtag gcctccagga gggcaaaagc accgagcagg gtaaccacga ccagcttaaa
     4321 gaactgtatt cggtaagtgg actgtgagct agtgctgtga cagggcaacc cttttcttgc
     4381 ataccttgca gaggagggac attagcaagt tggaagatga attacagagg tagatggaat
     4441 cttggaacgc atgtgtaaaa gctacttgct atatagacaa gcattctggc ccacagactg
     4501 taaaatcaag gtcatacaga tggtagtgaa aatcaggatt gggaaaagag ggagtgggga
     4561 caaaggtaaa acaaactctg taggacttct gggacataaa gctgtttatg ccaagatcct
     4621 gcttaaagat gctaagcagg atctggaatc cagaacttgc ccacatatca tattgcaata
     4681 acaagcctgg ttgtaaccat ggcattttaa atagaagaat ttagagaaaa cccatataat
     4741 gaaaaaagtg gaaattatta gtgagaaagg aagcacatta taaagctttg tttaaatcct
     4801 aagctctctg atgtaaacat ttctaagttc ctaaatggtt attgtactcc tgggttgaag
     4861 tcaacaggca gtaatactgc ctcagctgga ttgtttgata taaaggagaa ctccacaata
     4921 ggcataggct attagttcct gggactaagg gatattattg catctttaag atcttggctc
     4981 caattctccc aggctctccc catcaatgcc caccttgctt caacggacac acccccatct
     5041 gcctgaggtc tgatttgaag actagaggag catttttact ccttttccag gctgggaact
     5101 tgacggtgct ggctactgac cccctgctcc accaggaccc agtacagtta gactttcact
     5161 tccgccttac ctcccagacc tctgcccatt ggcacggcct tctctgtgac cgtcgactct
     5221 tcttggatat cccatatcag gccttggatc aaggcaaccg ggaaaggtga ctgagcctgg
     5281 atgggagaat ggggagggaa taggtagggg atttcaccct tctatcatgt catagtacat
     5341 aaggctaatt ctggagctag atataagcaa tccattcacc tggcatgcag acaagcctgt
     5401 gagctgagcc aggatctggg gttcaaggga taagagtcca tgggaagctg gactcagatc
     5461 cagaaatagt tgaataacgg gaagtacttt ctagctgttc atctcagtag tcctttctcc
     5521 ccagacccct tctgtggctt acatccagtg atgtgcaatc tcttggcttc caagaaaaat
     5581 ctaccaaaac tagtttagca actttcattt cctggcttgg gtgggtggag ggcagaaaac
     5641 gaccaataat atttttactg ctccaagtag gtgtctttct ggattctgag ttggccaaat
     5701 ttttttttcc cagtatttat tgatcattct tgggtgtttc tcacagaggg ggatttggca
     5761 gggtcatagg acaatagtgg agggaaggtc agcagataaa caagtgaaca agggtctctg
     5821 gttttcctag gcagaggacc ctgcggcctt ccgcagtgtt tgtgtccctg ggtacttgag
     5881 attagggagt ggtgatgact cttaacgagc atgctgcctt caagcatctg tttaacaaag
     5941 cacatcttgc accgccctta atccatttaa ccctgagtgg acacagcacg tttcagagag
     6001 catggggttg ggggtaaggt tatagattaa cagcatccca aggcagaaga atttttctta
     6061 gtacagaaca aaatggagtc tcctatgtct acttctttct acacagacac agcaacaatc
     6121 tgatttctct atcttttccc cacatttccc ccttttctat tcgacaaaac cgccatcgtc
     6181 atcatggccc attctcaatg agctcttggg tacacctccc agacggtgtg gcggccgggc
     6241 agaggggctc acttcccaaa aggggcggcc gggcagacgc accccccacc tcccggaggg
     6301 ggcggtggcc gggtggggac tgccccccac ctccctccca gacggggcgg ctgaccgggc
     6361 gggggctgcc ccccacctcc cggacggggc agctgccggg cggagacgcc cctcacttcc
     6421 cagacgaggc ggctgccggg cggaggggct cctcacttct cagacagggc ggacgggcag
     6481 agatgctcct cacctcccag atggggtcgc ggctgggcag agacactcct cagttcccag
     6541 acagggtcgt ggccgggtag aggcgctccc cacatcccag acgatgggcg gctgggcgga
     6601 gacgctcctc acttcctaga cgggatgacg gccgggcaga ggcgctcctc acatcccaga
     6661 cgatgggcgg ccaggcagag acgctcctca cttcccagac ggggtggtgg ccgggcagag
     6721 gctgcaatct cggcactttg ggaggccaag gcaggcggct gggaggtgga ggttgtagcg
     6781 agccgagatc acgccactgc actccagcct gggcaacact gagcactgag tgaacgaggc
     6841 tccgtctgca atcccggcac ctcaggaggc cgaggctggc agatcactcg tggttaggag
     6901 ctggagacca gcccggccaa cacagcgaaa ccccgtctcc accaaaatac gaaaaccagt
     6961 caggcatggc ggcacgcgcc tgcaatccca ggcactcagc aggctgaggc aggagaatca
     7021 ggcagggagg ttgcagtgag ccgagatggc agcagtacag tccagcttcg gctttcacaa
     7081 ctttggtggc atcagaggga gaccgtggag agagagggag agggagacca tggggagacg
     7141 gagacggaga gggagaggga gagggagcgg ccaaacattt taactgtttt tctgtggctc
     7201 ctagtttgac tgcaaccctg gagtacgtgg aagagaagac aaatgtggac tctgtgtttg
     7261 tgaacttcca gaatgatcgg aacgacagag gtggggatct gctgttcttc cttgcttttc
     7321 gcgctgaggc agctggataa ctccttttcc tttataggag accctcttcc cctgtcttta
     7381 aaaatgcacc ctcaggcatt tcagggattc ttttcttccc acctaccacg aaggtgggaa
     7441 gttgtaactt gttccatcaa gttacaactg gactctgagg aagcccctgc aggtggtgtt
     7501 aggggccaga ctgaaggagc actggtgaaa ttacacagaa tccattcaag ggatgtggcc
     7561 agcaggacaa aatggatctc aaacatatgg agcacctaca atgtgaaagg gtcagacata
     7621 aggccaaggg aacggggaca tatttaaccg gatgcctgga gcatatgtta cagaaactat
     7681 agcctcttgc ctcaaggagc tcaaactctg ttggatataa gggatggtga ataaccattc
     7741 ataagtgata gatactattt cagagcttac tatgtcatca ttgtattagt atataggtag
     7801 acctcactaa tctctagtgt taagcacttc atgaacatct catttcatct taaattctgt
     7861 gaggaggaag gttctatgat ttataaatgg aaaattctat agatggaaac tgaagttctg
     7921 caggactaac tcacagaaca agtgttaaaa ccagagttag agcctaggtc tgttggacta
     7981 aagcacatcc tatatgcctg cactacactg cttcccaggg ccactcccta gtggaagaaa
     8041 tcaaatctgg gggcatacat gtattgagtt ttaaagcatg ttctaatcat ttgttctatc
     8101 ctttcacagg tgccctgctg cgggccttca gctacatggg ctttgaggtg gtcagaccag
     8161 atcaccctgc cctccctccc ttggacaatg tcatctttat ggtgtatccc cttgaaaggg
     8221 atgttggcca cctgcccagt gagcctcctt gaacatgctt attccaacgc tttgaggggc
     8281 tggaagcctt gacacatgga atcaggggcc cgggatgtga ttcaggacac tttccatcct
     8341 aggaataaag ggtagtgcaa tc
//

BioPerl-1.007002/t/data/roa1.dat000444000766000024      5471013155576321 16253 0ustar00cjfieldsstaff000000000000ID   HSHNCPA1   standard; RNA; HUM; 1198 BP.
XX
AC   X79536;
XX
SV   X79536.1
XX
DT   03-JUN-1994 (Rel. 39, Created)
DT   03-JUN-1994 (Rel. 39, Last updated, Version 1)
XX
DE   H.sapiens mRNA for hnRNPcore protein A1
XX
KW   core protein.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; Eutheria;
OC   Primates; Catarrhini; Hominidae; Homo.
XX
RN   [2]
RP   1-1198
RA   Leffers H.;
RT   ;
RL   Submitted (01-JUN-1994) to the EMBL/GenBank/DDBJ databases.
RL   H. Leffers, Inst. of Medical Research Biochemistry & Danish Centre for
RL   Human Genome Research, Ole Worms Alle 170, Aarhus Univ., 8000 Aarhus C,
RL   DENMARK
XX
RN   [3]
RA   Knudsen S.M., Leffers H.;
RT   "Cloning and sequencing of a splice variant of human hnRNP core protein
RT   A1";
RL   Unpublished.
XX
DR   SWISS-PROT; P09651; ROA1_HUMAN.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1198
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
FT                   /tissue_type="lung"
FT                   /cell_type="fibroblast"
FT                   /cell_line="MRC5"
FT                   /clone_lib="lambda ZapII"
FT                   /clone="HDP1"
FT   CDS             27..989
FT                   /db_xref="SWISS-PROT:P09651"
FT                   /product="hnRNPcore protein A1"
FT                   /protein_id="CAA56072.1"
FT                   /translation="MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV
FT                   MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV
FT                   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV
FT                   IQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNF
FT                   SGRGGFGGSRGGGGYGGSGDGYNGFGNDGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNF
FT                   GGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF"
FT   misc_feature    995
FT                   /note="alternative splice site"
FT   polyA_signal    1180..1185
XX
SQ   Sequence 1198 BP; 334 A; 216 C; 336 G; 312 T; 0 other;
     ttaaagtctc tcttcaccct gccgtcatgt ctaagtcaga gtctcctaaa gagcccgaac        60
     agctgaggaa gctcttcatt ggagggttga gctttgaaac aactgatgag agcctgagga       120
     gccattttga gcaatgggga acgctcacgg actgtgtggt aatgagagat ccaaacacca       180
     agcgctctag gggctttggg tttgtcacat atgccactgt ggaggaggtg gatgcagcta       240
     tgaatgcaag gccacacaag gtggatggaa gagttgtgga accaaagaga gctgtctcca       300
     gagaagattc tcaaagacca ggtgcccact taactgtgaa aaagatattt gttggtggca       360
     ttaaagaaga cactgaagaa catcacctaa gagattattt tgaacagtat ggaaaaattg       420
     aagtgattga aatcatgact gaccgaggca gtggcaagaa aaggggcttt gcctttgtaa       480
     cctttgacga ccatgactcc gtggataaga ttgtcattca gaaataccat actgtgaatg       540
     gccacaactg tgaagttaga aaagccctgt caaagcaaga gatggctagt gcttcatcca       600
     gccaaagagg tcgaagtggt tctggaaact ttggtggtgg tcgtggaggt ggtttcggtg       660
     ggaatgacaa cttcggtcgt ggaggaaact tcagtggtcg tggtggcttt ggtggcagcc       720
     gtggtggtgg tggatatggt ggcagtgggg atggctataa tggatttggc aatgatggaa       780
     gcaattttgg aggtggtgga agctacaatg attttgggaa ttacaacaat cagtcttcaa       840
     attttggacc catgaaggga ggaaattttg gaggcagaag ctctggcccc tatggcggtg       900
     gaggccaata ctttgcaaaa ccacgaaacc aaggtggcta tggcggttcc agcagcagca       960
     gtagctatgg cagtggcaga agattttaat tagggaggag tctgctacta gtcttatcag      1020
     ctcttaaaaa cagaaactca tctgtccaag ttcgtggcag aaaggaacgt ccttgtgaag      1080
     acctttatct gagccactgt acttcgttat cacgccatgc agtttacatg agctgttctg      1140
     cagctcgaaa ttccattttg tgaatgggtt ttttttttta ataaactgta tttaactt        1198
//
ID   HSHNRNPA   standard; DNA; HUM; 5368 BP.
XX
AC   X12671;
XX
SV   X12671.1
XX
DT   23-NOV-1989 (Rel. 21, Created)
DT   24-APR-1993 (Rel. 35, Last updated, Version 3)
XX
DE   Human gene for heterogeneous nuclear ribonucleoprotein (hnRNP) core
DE   protein A1
XX
KW   hnRNP A1 proten; ribonucleoprotein; RNA binding protein.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; Eutheria;
OC   Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-5368
RA   Riva S.;
RT   ;
RL   Submitted (23-AUG-1988) to the EMBL/GenBank/DDBJ databases.
RL   Riva S., Consiglio Nazionale Delle Ricerche, Istituto Di Genetica
RL   Biochimica Ed Evoluzionistica CNR, Via Abbiategrasso 2D7, 27100 Pavia,
RL   Italy.
XX
RN   [2]
RP   1-5368
RA   Biamonti G., Buvoli M., Bassi M.T., Morandi C., Cobianchi F., Riva S.;
RT   "Isolation of an active gene encoding human hnRNP protein A1";
RL   J. Mol. Biol. 207:491-503(1988).
XX
DR   SWISS-PROT; P09651; ROA1_HUMAN.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..5368
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
FT                   /clone="pES5"
FT                   /tissue_type="liver"
FT                   /clone_lib="lambdaCh4A."
FT   mRNA            join(695..813,1377..1493,1789..1935,2084..2294,2388..2480,
FT                   2567..2659,2794..2868,3806..3961,4252..4311,4543..5240)
FT   CDS             join(799..813,1377..1493,1789..1935,2084..2294,2388..2480,
FT                   2567..2659,2794..2868,3806..3961,4252..4307)
FT                   /db_xref="SWISS-PROT:P09651"
FT                   /product="hnrnp a1 protein"
FT                   /protein_id="CAA31191.1"
FT                   /translation="MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV
FT                   MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV
FT                   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV
FT                   IQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNF
FT                   SGRGGFGGSRGGGGYGGSGDGYNGFGNDGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNF
FT                   GGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF"
FT   exon            695..813
FT                   /number=1
FT   misc_feature    695..695
FT                   /note="mRNA initiation site"
FT   misc_feature    715..715
FT                   /note="mRNA initiation site"
FT   misc_feature    735..735
FT                   /note="mRNA initiation site"
FT   intron          814..1376
FT                   /number=1
FT   exon            1377..1493
FT                   /number=2
FT   intron          1494..1788
FT                   /number=2
FT   exon            1789..1935
FT                   /number=3
FT   intron          1936..2083
FT                   /number=3
FT   exon            2084..2294
FT                   /number=4
FT   intron          2295..2387
FT                   /number=4
FT   exon            2388..2480
FT                   /number=5
FT   intron          2481..2566
FT                   /number=5
FT   exon            2567..2659
FT                   /number=6
FT   intron          2660..2793
FT                   /number=6
FT   exon            2794..2868
FT                   /number=7
FT   intron          2869..3805
FT                   /number=7
FT   exon            3806..3961
FT                   /number=8
FT   intron          3962..4251
FT                   /number=8
FT   exon            4252..4311
FT                   /number=9
FT   intron          4312..4542
FT                   /number=9
FT   exon            4543..5240
FT                   /number=10
XX
SQ   Sequence 5368 BP; 1476 A; 1052 C; 1270 G; 1570 T; 0 other;
     gggattgaga gtgatcactc acgctaacgt ctgccctgtt cctgtatggt gaggccgcac        60
     cacaagccac caccgccgcc gccttctgcg caacgccaac cgcccgccaa aacggatcct       120
     tccctgcgcc tgcgcaacca atcttgggac cggacctttt ttctccgccc actacgcatg       180
     cgcaaagcta ggacaaactc ccgccaacac gcaggcgccg taggttcact gcctactcct       240
     gcccgccatt tcacgtgttc tcagaggcag gtggaacttc ttaatgcgcc tgcgcaaaac       300
     tcgccatttt actacacgtg cggtcaacaa gagttcattg caaaaaaatt gttacctcct       360
     agctgcttgt ctaatacata gtgttaatca tgctttgcca agcgacttga ctgtaatatt       420
     tgcgcgtgga agattaaaaa gatgttaaac acccaaggta gattcaaatg tgaatgattg       480
     gtcggttggc caatcagact ggttaacaat aacattactc gggaaccaat ggactccaag       540
     gggtggagac ggcgtagaac gaccgaagga atgacgttac acagcaatgt ggcaccacag       600
     gccaatagca gggggaagcg atttcaagta tccaatcaga gctgttctag ggcggagtct       660
     accaatgccg aaagcgagga ggcggggtaa aaaagagagg gcgaaggtag gctggcagat       720
     acgttcgtca gcttgctcct ttctgcccgt ggacgccgcc gaagaagcat cgttaaagtc       780
     tctcttcacc ctgccgtcat gtctaagtca gaggtgagtt aggcgcgctt tcccacttga       840
     attttttcct ctccctttcc tgaatcggta agatgctgct gggtttcgtt ccttgcacca       900
     gcccattcta cagttccttc ggtcgctgcc acggcctacc cctcccaaag ttcaagtcgc       960
     cattttgtcc tcttgatcgc catgaggccg ctctccgcca accatgtgtt atcatgcggg      1020
     actcgttact cgtagcaaaa ttcttaggca cacaggatct ttgtcttttt ttaaaccttg      1080
     ccttggtgag cgagttttct aaagagcgat tagtcccatt gtggagatgc acccctaccg      1140
     cccaagcctt tgttgcgcgt gcgtcggaag gcgactaggg acgcatgcgc ttgcgatttc      1200
     ctagcactcc caactccagc atacggcctc ccttgatagg cagaagcacg tgtcttgttg      1260
     cgacctgaac gaacaataag tgctaggtac acagttggtg tctagttttt cttttcctcg      1320
     atggaaattg tttcgtgttg tagcccattt aacacttccc cctcccccca ctctagtctc      1380
     ctaaagagcc cgaacagctg aggaagctct tcattggagg gttgagcttt gaaacaactg      1440
     atgagagcct gaggagccat tttgagcaat ggggaacgct cacggactgt gtggtaagat      1500
     ttggaaggga caaagcagta aaacagccga tttccttggc ttatcttggt gcagtcttct      1560
     ccgaatgctt atgaaagtag ttaatagcat tatagttaga gctttgttgg caaaggaacg      1620
     tcctgctttg attttaaaag ctaacctctt aaatctaagg gtagtgggaa actggacgaa      1680
     ctttttataa aaggctggtg taaagtttcc tattgcccta ttcaaagtta aaataacaaa      1740
     agcttttgcg gtcagacttt gtgttacata aattaacact gttctcaggt aatgagagat      1800
     ccaaacacca agcgctctag gggctttggg tttgtcacat atgccactgt ggaggaggtg      1860
     gatgcagcta tgaatgcaag gccacacaag gtggatggaa gagttgtgga accaaagaga      1920
     gctgtctcca gagaagtgag tgggtttttt ttcttcttct tcttaaactt acttggatat      1980
     gtgctgctat gaacttaaga ttcgggagtt ttctaaactt accaaaattt tttattcgag      2040
     tataggcttt gctaatctaa acctatggtt tttctcctat taggattctc aaagaccagg      2100
     tgcccactta actgtgaaaa agatatttgt tggtggcatt aaagaagaca ctgaagaaca      2160
     tcacctaaga gattattttg aacagtatgg aaaaattgaa gtgattgaaa tcatgactga      2220
     ccgaggcagt ggcaagaaaa ggggctttgc ctttgtaacc tttgacgacc atgactccgt      2280
     ggataagatt gtcagtaagt atcagatagt ggcatttagt aagggttcca caatctgtat      2340
     ggcattctaa accctgatac catgttgtat ctatgttttt tttttagttc agaaatacca      2400
     tactgtgaat ggccacaact gtgaagttag aaaagccctg tcaaagcaag agatggctag      2460
     tgcttcatcc agccaaagag gtatgcttgt tgcttaatta aaccttaaag gtaactttga      2520
     gttactccag tatgaatgat ttaatgctta aacttcatgt cttaaggtcg aagtggttct      2580
     ggaaactttg gtggtggtcg tggaggtggt ttcggtggga atgacaactt cggtcgtgga      2640
     ggaaacttca gtggtcgtgg tatgtatggt ttatctacat gtagttctga cttctcacca      2700
     tctttgctat gaagatttta cagtacggga actgcattca gaatgtcact ttaagtccaa      2760
     gtcatactta aaacttgaaa ctttttctta caggtggctt tggtggcagc cgtggtggtg      2820
     gtggatatgg tggcagtggg gatggctata atggatttgg caatgatggt aagtttttta      2880
     ggaataagta gagaaaaatt cctggcaacc tggatcttta gaataggtta gtagagacta      2940
     aaattctggt gcatgtcaaa ctcaactttg cccataacac gcatgctgtg agcaggcctt      3000
     cagccgttac acttgcacaa gttttcattg tcaaatactt ttgtcttatt gagaagaatt      3060
     gtattcttgt aggtggttat ggaggaggcg gccctggtta ctctggagga agcagaggct      3120
     atggaagtgg tggacagggt tatggaaacc agggcagtgg ctatggcggg agtggcagct      3180
     atgacagcta taacaacgga ggcggaggcg gctttggcgg tggtagtggt aggtatccag      3240
     tgatccaagt acttggtgtg acagctagat tagcctttta gagcttgggt tctggtgctg      3300
     ttgaagcatt gtgtggtaca ctgcatggta tattaaaaac aaatgggctt gctatgctac      3360
     ctcctcctag ctttaagctg gggccgcctc actcccaaat agtagagata agtggatagt      3420
     gttgtctttg agttagatta gtatcataga aggatttagt attttaactc ctttgggacc      3480
     ttaggcgctt agttgatgta tccaagatac ttctgcttgc tgtggccctg gatccgtgaa      3540
     ggccttcaag gctgaagggt atgcttgtgc cactctgaaa atctctttat tttatgtcat      3600
     ggtgagttag gccagttttc tttgtattac tggattattc aactgaatgc ctttcccaga      3660
     gaatgaaatg caaagattgg agtcaccata gtttgggaga aaggaaggct gataactcaa      3720
     ccttatttta ttctgactgc taaacagaat tggaaactaa catcatcctc aggtaacaga      3780
     taaaggccct ctttcccatt cataggaagc aattttggag gtggtggaag ctacaatgat      3840
     tttgggaatt acaacaatca gtcttcaaat tttggaccca tgaagggagg aaattttgga      3900
     ggcagaagct ctggccccta tggcggtgga ggccaatact ttgcaaaacc acgaaaccaa      3960
     ggtatggtat ctatgtaatt ttggataatg tcaaaagagt gtctgtagct actgctggga      4020
     agaaagccct ttaactgcta tgtctgggca gcaaaacgtt tatagtttag aaccttcaga      4080
     aagtgataat ttgatcacaa attagaaaaa tcatgggacc tctttaccac ctcccttgta      4140
     gtagggccat ttttaaatgg ccagacactt gaatttaact tttattatcc caaatatgaa      4200
     aacattactg ttggcacttt gaaactttaa aagaaaaatt gtacttttca ggtggctatg      4260
     gcggttccag cagcagcagt agctatggca gtggcagaag attttaatta ggtaagtaag      4320
     cacctttttg tgtgttgaca taatttttta aattgctgat gaacccaata accctaatgt      4380
     agctgagcag tgcaacatag ttaacattat aattgcagta attgtggata taaagttaat      4440
     attcagatca gcaaaatttg tgggaaacaa acttgatatt ggattgtagc cttgagtctt      4500
     aatatgttta gattaacaac tctattccat attgttcaac aggaaacaaa gcttagcagg      4560
     agaggagagc cagagaagtg acagggaagc tacaggttac aacagatttg tgaactcagc      4620
     caagcacagt ggtggcaggg cctagctgct acaaagaaga catgttttag acaaatactc      4680
     atgtgtatgg gcaaaaaact cgaggactgt atttgtgact aattgtataa caggttattt      4740
     tagtttctgt tctgtggaaa gtgtaaagca ttccaacaaa gggttttaat gtagattttt      4800
     ttttttgcac cccatgctgt tgattgctaa atgtaacagt ctgatcgtga cgctgaataa      4860
     atgtcttttt tttaatgtgc tgtgtaaagt tagtctactc ttaagccatc ttggtaaatt      4920
     tccccaacag tgtgaagtta gaattccttc agggtgatgc caggttctat ttggaattta      4980
     tatacaacct gcttgggtgg agaagccatt gtcttcggaa accttggtgt agttgaactg      5040
     atagttactg ttgtgacctg aagttcacca ttaaaaggga ttacccaagc aaaatcatgg      5100
     aatggttata aaagtgattg ttggcacatc ctatgcaata tatctaaatt gaataatggt      5160
     accagataaa attatagatg ggaatgaagc ttgtgtatcc attatcatgt gtaatcaata      5220
     aacgatttaa ttctcttgaa tgaaatgaca actgtatgga tttgggactg gcagagattt      5280
     ggactttccc tacccactcc ccctgataat aatgttgaat gcttctatca caattcaagt      5340
     tcaaagctct gctagggaat agaaacta                                         5368
//
ID   HSRNPA1    standard; RNA; HUM; 1747 BP.
XX
AC   X06747;
XX
SV   X06747.1
XX
DT   08-JUN-1988 (Rel. 16, Created)
DT   12-SEP-1993 (Rel. 36, Last updated, Version 2)
XX
DE   Human hnRNP core protein A1
XX
KW   hnRNP A1 protein; ribonucleoprotein.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; Eutheria;
OC   Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-1747
RA   Riva S.;
RT   ;
RL   Submitted (26-JAN-1988) to the EMBL/GenBank/DDBJ databases.
RL   Riva S., Istituto Di Genetica Biochimica, Ed Evoluzionistica - CNR, Via
RL   Abbiategrasso 207, 27100 Pavia, Italy.
XX
RN   [2]
RP   1-1747
RX   MEDLINE; 88233978.
RA   Buvoli M., Biamonti G., Ghetti A., Riva S., Bassi M.T., Horandi C.;
RT   "cDNA cloning of human hnRNP protein A1 reveals the existence of multiple
RT   mRNA isoforms.";
RL   Nucleic Acids Res. 16:3751-3770(1988).
XX
DR   SWISS-PROT; P09651; ROA1_HUMAN.
XX
CC   pRP15 sequence encodes the protein A1 type alpha isoform,
CC   pRP12 (truncated at the 5' end, respectively) the beta isoform
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1747
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
FT                   /tissue_type="fibroblast"
FT                   /clone_lib="lambdagt11"
FT                   /clone="pRP15"
FT   CDS             86..1048
FT                   /db_xref="SWISS-PROT:P09651"
FT                   /note="protein A1-alpha (AA 1-320)"
FT                   /protein_id="CAA29922.1"
FT                   /translation="MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV
FT                   MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV
FT                   KKIFVGGIKEDTEEHHLRDYFEQFGKIEVIEIMTDRGSGKKKGFAFVTFDDHDSVDKIV
FT                   IQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNF
FT                   SGRGGFGGSRGGGGYGGSGDGYNGFGNDGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNF
FT                   GGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF"
FT   misc_feature    209..209
FT                   /note="5' end of clone pRP12"
FT   variation       467..469
FT                   /note="uau (Tyr) is uuu (Phe) in pRP12 (protein A1-beta)"
FT   variation       521..523
FT                   /note="agg (Arg) is aag (Lys) in pRP12 (protein A1-beta)"
FT   misc_feature    1365..1370
FT                   /note="polyA signal"
FT   misc_feature    1726..1731
FT                   /note="polyA signal"
FT   polyA_site      1747..1747
FT                   /note="polyA site"
XX
SQ   Sequence 1747 BP; 512 A; 300 C; 466 G; 469 T; 0 other;
     cgaaaggtta caaaggcaaa gccccttttc tgcccgtgga cgccgccgaa gaagcatcgt        60
     taaagtctct cttcaccctg ccgtcatgtc taagtcagag tctcctaaag agcccgaaca       120
     gctgaggaag ctcttcattg gagggttgag ctttgaaaca actgatgaga gcctgaggag       180
     ccattttgag caatggggaa cgctcacgga ctgtgtggta atgagagatc caaacaccaa       240
     gcgctctagg ggctttgggt ttgtcacata tgccactgtg gaggaggtgg atgcagctat       300
     gaatgcaagg ccacacaagg tggatggaag agttgtggaa ccaaagagag ctgtctccag       360
     agaagattct caaagaccag gtgcccactt aactgtgaaa aagatatttg ttggtggcat       420
     taaagaagac actgaagaac atcacctaag agattatttt gaacagtttg gaaaaattga       480
     agtgattgaa atcatgactg accgaggcag tggcaagaaa aagggctttg cctttgtaac       540
     ctttgacgac catgactccg tggataagat tgtcattcag aaataccata ctgtgaatgg       600
     ccacaactgt gaagttagaa aagccctgtc aaagcaagag atggctagtg cttcatccag       660
     ccaaagaggt cgaagtggtt ctggaaactt tggtggtggt cgtggaggtg gtttcggtgg       720
     gaatgacaac ttcggtcgtg gaggaaactt cagtggtcgt ggtggctttg gtggcagccg       780
     tggtggtggt ggatatggtg gcagtgggga tggctataat ggatttggca atgatggaag       840
     caattttgga ggtggtggaa gctacaatga ttttgggaat tacaacaatc agtcttcaaa       900
     ttttggaccc atgaagggag gaaattttgg aggcagaagc tctggcccct atggcggtgg       960
     aggccaatac tttgcaaaac cacgaaacca aggtggctat ggcggttcca gcagcagcag      1020
     tagctatggc agtggcagaa gattttaatt aggaaacaaa gcttagcagg agaggagagc      1080
     cagagaagtg acagggaagc tacaggttac aacagatttg tgaactcagc caagcacagt      1140
     ggtggcaggg cctagctgct acaaagaaga catgttttag acaaatactc atgtgtatgg      1200
     gcaaaaaact cgaggactgt atttgtgact aattgtataa caggttattt tagtttctgt      1260
     tctgtggaaa gtgtaaagca ttccaacaaa gggttttaat gtagattttt tttttgcacc      1320
     ccatgctgtt gattgctaaa tgtaacagtc tgatcgtgac gctgaataaa tgtctttttt      1380
     ttaatgtgct gtgtaaagtt agtctactct taagccatct tggtaaattt ccccaacagt      1440
     gtgaagttag aattccttca gggtgatgcc aggttctatt tggaatttat atacaacctg      1500
     cttgggtgga gaagccattg tcttcggaaa ccttggtgta gttgaactga tagttactgt      1560
     tgtgacctga agttcaccat taaaagggat tacccaagca aaatcatgga atggttataa      1620
     aagtgattgt tggcacatcc tatgcaatat atctaaattg aataatggta ccagataaaa      1680
     ttatagatgg gaatgaagct tgtgtatcca ttatcatgtg taatcaataa acgatttaat      1740
     tctcttg                                                                1747
//
ID   HSUPIR1    standard; RNA; HUM; 924 BP.
XX
AC   X04347;
XX
SV   X04347.1
XX
DT   18-NOV-1986 (Rel. 10, Created)
DT   12-JUL-1995 (Rel. 44, Last updated, Version 3)
XX
DE   Human liver mRNA fragment DNA binding protein UPI homologue
DE   (C-terminus)
XX
KW   DNA binding protein.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; Eutheria;
OC   Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-924
RX   MEDLINE; 87053868.
RA   Riva S., Morandi C., Tsoulfas P., Pandolfo M., Biamonti G., Merrill B.,
RA   Williams K.R., Multhaup G., Beyreuther K., Werr H., Heinrich B.,
RA   Schaefer K.P.;
RT   "Mammalian single-stranded DNA binding protein UP I is derived from the
RT   hnRNP cor protein A1";
RL   EMBO J. 5:2267-2273(1986).
XX
DR   SWISS-PROT; P09651; ROA1_HUMAN.
XX
CC   Pos. 1-216 is homologous to UPI (aa 126-195); pos. 184-273 is
CC   homologous to V8 protease peptide AI/II (aa 185-214)
XX
CC   Data kindly reviewed (08-NOV-1986) by K. Beyreuther
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..924
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
FT   CDS             <1..591
FT                   /codon_start=1
FT                   /db_xref="SWISS-PROT:P09651"
FT                   /note="ORF protein; C-terminal (aa 125-319; 196aa)"
FT                   /protein_id="CAA27874.1"
FT                   /translation="FEQYGKIEVIEIMTDPGSGKKRGFAFVTFDDHDSVDKIVIQKYHT
FT                   VNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGF
FT                   GGSRGGGGYGGSGDGYNGFGNDGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSG
FT                   PYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF"
FT   misc_feature    208..210
FT                   /note="dimethylated arginin"
FT   polyA_signal    908..913
FT                   /note="pot. polyA signal"
FT   polyA_site      924..924
FT                   /note="polyA site"
XX
SQ   Sequence 924 BP; 262 A; 148 C; 266 G; 248 T; 0 other;
     tttgaacagt atggaaaaat tgaagtgatt gaaatcatga ctgacccagg cagtggcaag        60
     aaaaggggct ttgcctttgt aacctttgac gaccatgact ccgtggataa gattgtcatt       120
     cagaaatacc atactgtgaa tggccacaac tgtgaagtta gaaaagccct gtcaaagcaa       180
     gagatggcta gtgcttcatc cagccaaaga ggtcgaagtg gttctggaaa ctttggtggt       240
     ggtcgtggag gtggtttcgg tgggaatgac aacttcggtc gtggaggaaa cttcagtggt       300
     cgtggtggct ttggtggcag ccgtggtggt ggtggatatg gtggcagtgg ggatggctat       360
     aatggatttg gcaatgatgg aagcaatttt ggaggtggtg gaagctacaa tgattttggg       420
     aattacaaca atcagtcttc aaattttgga cccatgaagg gaggaaattt tggaggcaga       480
     agctctggcc cctatggcgg tggaggccaa tactttgcaa aaccacgaaa ccaaggtggc       540
     tatggcggtt ccagcagcag cagtagctat ggcagtggca gaagatttta attaggaaac       600
     aagcttggca ggagaggaga gccagagaag tgacagggaa gctacaggtt acaacagatt       660
     tgtgaactca gccaagcaca gtggtggcag ggcctagctg ctacaaagaa gacatgtttt       720
     agacaaatac tcatgtgtat gggcaaaaaa ctcgaggact gtatttgtga ctaattgtat       780
     aacaggttat tttagtttct gttctgtgga aagtgaaagc attccaacaa agggttttaa       840
     tgtagatttt ttttttttgc accccatgct gttgattgct aaatgtaaca gtctgatcgt       900
     gacgctgaat aaatgtcttt tttt                                              924
//
BioPerl-1.007002/t/data/roa1.gbxml000444000766000024      2157413155576321 16616 0ustar00cjfieldsstaff000000000000




  
    
      
        
          
            
              dbEST
              
                
                  1888424
                
              
            
          
        
        
          
            
              AI129902
              1
            
          
        
        
          3598416
        
      
      
        
          
            
              
                3
                2
              
            
          
          
            qc41b07.x1 Soares_pregnant_uterus_NbHPU Homo sapiens cDNA clone IMAGE:1712149 3' similar to SW:ROA1_SCHAM P21522 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1, A2/B1 HOMOLOG. ;contains MSR1.b2 MSR1 repetitive element ;.
          
          
            
              
                
                  
                    1998
                    9
                    10
                  
                
              
            
          
          
            
              
                
                  
                    1998
                    10
                    27
                  
                
              
            
          
          
            Contact: Robert Strausberg, Ph.D.~Email: cgapbs-r@mail.nih.gov~This clone is available royalty-free through LLNL ; contact the IMAGE Consortium (info@image.llnl.gov) for further information. ~Trace considered overall poor quality~Insert Length: 525   Std Error: 0.00~Seq primer: -40m13 fwd. ET from Amersham~High quality sequence stop: 1
          
          
            
              
                
                  
                    Homo sapiens
                    human
                    
                      
                        taxon
                        
                          
                            9606
                          
                        
                      
                    
                    
                      
                        
                          
                            
                              Homo
                              sapiens
                            
                          
                        
                        
                          
                            255
                            Organ: uterus; Vector: pT7T3D-PacI; Site_1: Not I; Site_2: Eco RI; 1st strand cDNA was primed with a Not I - oligo(dT) primer [5' AACTGGAAGAATTCGCGGCCGCCTTTTTTTTTTTTTTTTTT 3'], double-stranded cDNA was ligated to Eco RI adaptors (Pharmacia), digested with Not I and cloned into the Not I and Eco RI sites of the modified pT7T3 vector. Library went through one round of normalization.  Library constructed by M. Fatima Bonaldo.
                          
                        
                        Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
                        1
                        2
                        PRI
                      
                    
                  
                
                
                  
                    3
                    IMAGE:1712149
                  
                  
                    11
                    Soares_pregnant_uterus_NbHPU
                  
                  
                    7
                    female
                  
                  
                    12
                    adult
                  
                  
                    16
                    DH10B
                  
                
              
            
          
          
            
              
                
                  
                    
                      
                        
                          Unpublished
                          
                            
                              
                                
                                  
                                    
                                      
                                        
                                          
                                            NCI-CGAP http://www.ncbi.nlm.nih.gov/ncicgap
                                          
                                        
                                      
                                    
                                  
                                
                              
                            
                          
                          
                            
                              
                                
                                  1997
                                
                              
                            
                          
                          National Cancer Institute, Cancer Genome Anatomy Project (CGAP), Tumor Gene Index
                        
                      
                    
                  
                
              
            
          
        
      
      
        
          
          
          37
          
          
            
              
                CTCCGCGCCAACTCCCCCCACCCCCCCCCCACACCCC
              
            
          
        
      
    
  



BioPerl-1.007002/t/data/roa1.genbank000444000766000024      1034213155576321 17101 0ustar00cjfieldsstaff000000000000LOCUS       AI129902       37 bp    mRNA            EST       27-OCT-1998
DEFINITION  qc41b07.x1 Soares_pregnant_uterus_NbHPU Homo sapiens cDNA clone
            IMAGE:1712149 3' similar to SW:ROA1_SCHAM P21522 HETEROGENEOUS
            NUCLEAR RIBONUCLEOPROTEIN A1, A2/B1 HOMOLOG. ;contains MSR1.b2 MSR1
            repetitive element ;, mRNA sequence.
ACCESSION   AI129902
NID         g3598416
VERSION     AI129902.1  GI:3598416
KEYWORDS    EST.
SOURCE      human.
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
            Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 37)
  AUTHORS   NCI-CGAP http://www.ncbi.nlm.nih.gov/ncicgap.
  TITLE     National Cancer Institute, Cancer Genome Anatomy Project (CGAP),
            Tumor Gene Index
  JOURNAL   Unpublished (1997)
COMMENT     On May 8, 1995 this sequence version replaced gi:800643

            Contact: Robert Strausberg, Ph.D.
            Tel: (301) 496-1550
            Email: Robert_Strausberg@nih.gov
            This clone is available royalty-free through LLNL ; contact the
            IMAGE Consortium (info@image.llnl.gov) for further information. 
            Trace considered overall poor quality
            Insert Length: 525   Std Error: 0.00
            Seq primer: -40m13 fwd. ET from Amersham
            High quality sequence stop: 1.
FEATURES             Location/Qualifiers
     source          1..37
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /clone="IMAGE:1712149"
                     /clone_lib="Soares_pregnant_uterus_NbHPU"
                     /sex="female"
                     /dev_stage="adult"
                     /lab_host="DH10B"
                     /note="Organ: uterus; Vector: pT7T3-Pac; Site_1: Not I;
                     Site_2: Eco RI; 1st strand cDNA was primed with a Not I -
                     oligo(dT) primer [5'
                     AACTGGAAGAATTCGCGGCCGCCTTTTTTTTTTTTTTTTTT 3'],
                     double-stranded cDNA was ligated to Eco RI adaptors
                     (Pharmacia), digested with Not I and cloned into the Not I
                     and Eco RI sites of the modified pT7T3 vector. Library
                     went through one round of normalization.  Library
                     constructed by M. Fatima Bonaldo."
BASE COUNT        5 a     28 c      2 g      2 t
ORIGIN      
        1 ctccgcgcca actcccccca cccccccccc acacccc
//
LOCUS       BAB68554                 141 aa            linear   VRT 11-APR-2002
DEFINITION  alpha D-globin [Aldabrachelys elephantina].
ACCESSION   BAB68554
PID         g15824047
VERSION     BAB68554.1  GI:15824047
DBSOURCE    accession AB072353.1
KEYWORDS    .
SOURCE      Aldabra giant tortoise.
  ORGANISM  Aldabrachelys elephantina
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Testudines; Cryptodira; Testudinoidea; Testudinidae; Aldabrachelys.
REFERENCE   1
  AUTHORS   Shishikura,F.
  TITLE     The primary structure of hemoglobin D from the Aldabra giant
            tortoise, Geochelone gigantea
  JOURNAL   Zoolog. Sci. 19, 197-206 (2002)
REFERENCE   2  (residues 1 to 141)
  AUTHORS   Shishikura,F.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-SEP-2001) Fumio Shishikura, Nihon University School
            of Medicine, Biology; Oyaguchi-kamimachi, 30-1, Itabashi-ku, Tokyo
            173-8610, Japan (E-mail:fshishi@med.nihon-u.ac.jp,
            Tel:81-3-3972-8111(ex.2291), Fax:81-3-3972-0027)
FEATURES             Location/Qualifiers
     source          1..141
                     /organism="Aldabrachelys elephantina"
                     /db_xref="taxon:167804"
                     /note="synonym:Dipsochelys dussumieri~synonym:Geochelone
                     gigantea"
     Protein         1..141
                     /product="alpha D-globin"
     CDS             1..141
                     /coded_by="join(AB072353.1:1..92,AB072353.1:307..511,
                     AB072353.1:739..>864)"
                     /note="hemoglobin D"
ORIGIN      
        1 mlteddkqli qhvwekvleh qedfgaeale rmfivypstk tyfphfdlhh dseqirhhgk
       61 kvvgalgdav khidnlsatl selsnlhayn lrvdpvnfkl lshcfqvvlg ahlgreytpq
      121 vqvaydkfla avsavlaeky r
//
BioPerl-1.007002/t/data/roa1.swiss000444000766000024      3041713155576321 16651 0ustar00cjfieldsstaff000000000000ID   ROA1_HUMAN     STANDARD;      PRT;   371 AA.
AC   P09651;
DT   01-MAR-1989 (Rel. 10, Created)
DT   01-AUG-1990 (Rel. 15, Last sequence update)
DT   01-NOV-1997 (Rel. 35, Last annotation update)
DE   HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1 (HELIX-DESTABILIZING
DE   PROTEIN) (SINGLE-STRAND BINDING PROTEIN) (HNRNP CORE PROTEIN A1).
GN   HNRPA1.
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN   [1]
RP   SEQUENCE OF 1-250 AND 303-371 FROM N.A.
RC   TISSUE=LIVER;
RX   MEDLINE; 89342435.
RA   BIAMONTI G., BUVOLI M., BASSI M.T., MORANDI C., COBIANCHI F., RIVA S.;
RT   "Isolation of an active gene encoding human hnRNP protein A1.
RT   Evidence for alternative splicing.";
RL   J. Mol. Biol. 207:491-503(1989).
RN   [2]
RP   SEQUENCE OF 1-250 AND 303-371 FROM N.A.
RC   TISSUE=FIBROBLAST;
RX   MEDLINE; 88233978.
RA   BUVOLI M., BIAMONTI G., GHETTI A., RIVA S., BASSI M.T., HORANDI C.;
RT   "cDNA cloning of human hnRNP protein A1 reveals the existence of
RT   multiple mRNA isoforms.";
RL   Nucleic Acids Res. 16:3751-3770(1988).
RN   [3]
RP   SEQUENCE OF 1-250 AND 303-371 FROM N.A.
RC   TISSUE=LUNG;
RA   KNUDSEN S.M., LEFFERS H.;
RL   Submitted (JUN-1994) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   SEQUENCE OF 124-250 AND 303-371 FROM N.A.
RC   TISSUE=LIVER;
RX   MEDLINE; 87053868.
RA   RIVA S., MORANDI C., TSOULFAS P., PANDOLFO M., BIAMONTI G.,
RA   MERRILL B., WILLIAMS K.R., MULTHAUP G., BEYREUTHER K., WERR H.,
RA   HEINRICH B., SCHAEFER K.P.;
RT   "Mammalian single-stranded DNA binding protein UP I is derived from
RT   the hnRNP core protein A1.";
RL   EMBO J. 5:2267-2273(1986).
RN   [5]
RP   SEQUENCE OF 251-302 FROM N.A.
RX   MEDLINE; 90214633.
RA   BUVOLI M., COBIANCHI F., BESTAGNO M.G., MANGIAROTTI A., BASSI M.T.,
RA   BIAMONTI G., RIVA S.;
RT   "Alternative splicing in the human gene for the core protein A1
RT   generates another hnRNP protein.";
RL   EMBO J. 9:1229-1235(1990).
RN   [6]
RP   NUCLEAR LOCALIZATION DOMAIN.
RX   MEDLINE; 95247808.
RA   SIOMI H., DREYFUSS G.;
RT   "A nuclear localization domain in the hnRNP A1 protein.";
RL   J. Cell Biol. 129:551-560(1995).
RN   [7]
RP   NUCLEAR LOCALIZATION DOMAIN, AND NUCLEAR EXPORT.
RX   MEDLINE; 96067639.
RA   MICHAEL W.M., CHOI M., DREYFUSS G.;
RT   "A nuclear export signal in hnRNP A1: a signal-mediated, temperature-
RT   dependent nuclear protein export pathway.";
RL   Cell 83:415-422(1995).
RN   [8]
RP   NUCLEAR LOCALIZATION DOMAIN.
RX   MEDLINE; 95286702.
RA   WEIGHARDT F., BIAMONTI G., RIVA S.;
RT   "Nucleo-cytoplasmic distribution of human hnRNP proteins: a search
RT   for the targeting domains in hnRNP A1.";
RL   J. Cell Sci. 108:545-555(1995).
RN   [9]
RP   3D-STRUCTURE MODELING OF 106-189.
RX   MEDLINE; 91099515.
RA   GHETTI A., BOLOGNESI M., COBIANCHI F., MORANDI C.;
RT   "Modeling by homology of RNA binding domain in A1 hnRNP protein.";
RL   FEBS Lett. 277:272-276(1990).
RN   [10]
RP   X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 8-180.
RX   MEDLINE; 97307256.
RA   SHAMOO Y., KRUEGER U., RICE L.M., WILLIAMS K.R., STEITZ T.A.;
RT   "Crystal structure of the two RNA binding domains of human hnRNP A1
RT   at 1.75-A resolution.";
RL   Nat. Struct. Biol. 4:215-222(1997).
RN   [11]
RP   X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 6-181.
RX   MEDLINE; 97277240.
RA   XU R.M., JOKHAN L., CHENG X., MAYEDA A., KRAINER A.R.;
RT   "Crystal structure of human UP1, the domain of hnRNP A1 that contains
RT   two RNA-recognition motifs.";
RL   Structure 5:559-570(1997).
CC   -!- FUNCTION: INVOLVED IN THE PACKAGING OF PRE-MRNA INTO HNRNP
CC       PARTICLES, TRANSPORT OF POLY-A MRNA FROM THE NUCLEUS TO THE
CC       CYTOPLASM AND MAY MODULATE SPLICE SITE SELECTION.
CC   -!- SUBCELLULAR LOCATION: NUCLEAR. SHUTTLES CONTINUOUSLY BETWEEN THE
CC       NUCLEUS AND THE CYTOPLASM ALONG WITH MRNA. COMPONENT OF
CC       RIBONUCLEOSOMES.
CC   -!- ALTERNATIVE PRODUCTS: A1-A (SHOWN HERE) AND A1-B ARE OBTAINED BY
CC       ALTERNATIVE SPLICING OF THE SAME GENE. A1-A IS TWENTY TIMES MORE
CC       ABUNDANT THEN A1-B.
CC   -!- SIMILARITY: BELONGS TO THE A/B GROUP OF HNRNP, WHICH ARE BASIC AND
CC       GLY-RICH PROTEINS.
CC   -!- SIMILARITY: CONTAINS 2 RNA RECOGNITION MOTIFS (RNP).
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; X12671; CAA31191.1; -.
DR   EMBL; X06747; CAA29922.1; ALT_SEQ.
DR   EMBL; X04347; CAA27874.1; -.
DR   EMBL; X79536; CAA56072.1; -.
DR   PIR; S04617; S04617.
DR   PIR; A24894; A24894.
DR   PIR; S02061; S02061.
DR   PDB; 1HA1; 15-MAY-97.
DR   PDB; 1UP1; 17-SEP-97.
DR   AARHUS/GHENT-2DPAGE; 207; NEPHGE.
DR   AARHUS/GHENT-2DPAGE; 2114; NEPHGE.
DR   AARHUS/GHENT-2DPAGE; 3612; NEPHGE.
DR   MIM; 164017; -.
DR   PFAM; PF00076; rrm; 2.
DR   PROSITE; PS00030; RNP_1; 2.
PE   1: Evidence at protein level;
KW   Nuclear protein; RNA-binding; Repeat; Ribonucleoprotein;
KW   Methylation; Alternative splicing; 3D-structure.
FT   INIT_MET      0      0
FT   DOMAIN        3     93       GLOBULAR A DOMAIN.
FT   DOMAIN       94    184       GLOBULAR B DOMAIN.
FT   DOMAIN      194    371       GLY-RICH.
FT   DOMAIN       15     20       RNA-BINDING (RNP2) (BY SIMILARITY).
FT   DOMAIN       54     61       RNA-BINDING (RNP1).
FT   DOMAIN      106    111       RNA-BINDING (RNP2) (BY SIMILARITY).
FT   DOMAIN      145    152       RNA-BINDING (RNP1).
FT   DOMAIN      217    239       RNA-BINDING RGG-BOX.
FT   DOMAIN      319    356       NUCLEAR TARGETING SEQUENCE (M9).
FT   MOD_RES     193    193       METHYLATION (BY SIMILARITY).
FT   VARSPLIC    251    302       MISSING (IN FORM A1-A).
FT   MUTAGEN     325    325       G->A: NO NUCLEAR IMPORT NOR EXPORT.
FT   MUTAGEN     326    326       P->A: NO NUCLEAR IMPORT NOR EXPORT.
FT   MUTAGEN     333    334       GG->LL: NORMAL NUCLEAR IMPORT AND EXPORT.
FT   CONFLICT    139    139       R -> P (IN REF. 4).
SQ   SEQUENCE   371 AA;  38715 MW;  ECBA15FB CRC32;
     SKSESPKEPE QLRKLFIGGL SFETTDESLR SHFEQWGTLT DCVVMRDPNT KRSRGFGFVT
     YATVEEVDAA MNARPHKVDG RVVEPKRAVS REDSQRPGAH LTVKKIFVGG IKEDTEEHHL
     RDYFEQYGKI EVIEIMTDRG SGKKRGFAFV TFDDHDSVDK IVIQKYHTVN GHNCEVRKAL
     SKQEMASASS SQRGRSGSGN FGGGRGGGFG GNDNFGRGGN FSGRGGFGGS RGGGGYGGSG
     DGYNGFGNDG GYGGGGPGYS GGSRGYGSGG QGYGNQGSGY GGSGSYDSYN NGGGRGFGGG
     SGSNFGGGGS YNDFGNYNNQ SSNFGPMKGG NFGGRSSGPY GGGGQYFAKP RNQGGYGGSS
     SSSSYGSGRR F
//
ID   A2S3_RAT       STANDARD;      PRT;   913 AA.
AC   Q8R2H7; Q8R2H6; Q8R4G3;
DT   28-FEB-2003 (Rel. 41, Created)
DT   15-MAR-2004 (Rel. 43, Last sequence update)
DT   15-MAR-2004 (Rel. 43, Last annotation update)
DE   Amyotrophic lateral sclerosis 2 chromosomal region candidate gene
DE   protein 3 homolog (GABA-A receptor interacting factor-1) (GRIF-1) (O-
DE   GlcNAc transferase-interacting protein of 98 kDa).
GN   ALS2CR3 OR GRIF1 OR OIP98.
OS   Rattus norvegicus (Rat).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus.
OX   NCBI_TaxID=10116;
RN   [1]
RP   SEQUENCE FROM N.A. (ISOFORMS 1 AND 2), SUBCELLULAR LOCATION, AND
RP   INTERACTION WITH GABA-A RECEPTOR.
RC   TISSUE=Brain;
RX   MEDLINE=22162448; PubMed=12034717;
RA   Beck M., Brickley K., Wilkinson H.L., Sharma S., Smith M.,
RA   Chazot P.L., Pollard S., Stephenson F.A.;
RT   "Identification, molecular cloning, and characterization of a novel
RT   GABAA receptor-associated protein, GRIF-1.";
RL   J. Biol. Chem. 277:30079-30090(2002).
RN   [2]
RP   REVISIONS TO 579 AND 595-596, AND VARIANTS VAL-609 AND PRO-820.
RA   Stephenson F.A.;
RL   Submitted (FEB-2003) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   SEQUENCE FROM N.A. (ISOFORM 3), INTERACTION WITH O-GLCNAC TRANSFERASE,
RP   AND O-GLYCOSYLATION.
RC   STRAIN=Sprague-Dawley; TISSUE=Brain;
RX   MEDLINE=22464403; PubMed=12435728;
RA   Iyer S.P.N., Akimoto Y., Hart G.W.;
RT   "Identification and cloning of a novel family of coiled-coil domain
RT   proteins that interact with O-GlcNAc transferase.";
RL   J. Biol. Chem. 278:5399-5409(2003).
CC   -!- SUBUNIT: Interacts with GABA-A receptor and O-GlcNac transferase.
CC   -!- SUBCELLULAR LOCATION: Cytoplasmic.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=3;
CC       Name=1; Synonyms=GRIF-1a;
CC         IsoId=Q8R2H7-1; Sequence=Displayed;
CC       Name=2; Synonyms=GRIF-1b;
CC         IsoId=Q8R2H7-2; Sequence=VSP_003786, VSP_003787;
CC       Name=3;
CC         IsoId=Q8R2H7-3; Sequence=VSP_003788;
CC   -!- PTM: O-glycosylated.
CC   -!- SIMILARITY: TO HUMAN OIP106.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; AJ288898; CAC81785.2; -.
DR   EMBL; AJ288898; CAC81786.2; -.
DR   EMBL; AF474163; AAL84588.1; -.
DR   GO; GO:0005737; C:cytoplasm; IEP.
DR   GO; GO:0005634; C:nucleus; IDA.
DR   GO; GO:0005886; C:plasma membrane; IEP.
DR   GO; GO:0005478; F:intracellular transporter activity; NAS.
DR   GO; GO:0005515; F:protein binding; IPI.
DR   GO; GO:0005102; F:receptor binding; IPI.
DR   GO; GO:0006836; P:neurotransmitter transport; NAS.
DR   GO; GO:0006493; P:O-linked glycosylation; IDA.
DR   GO; GO:0006605; P:protein targeting; IDA.
DR   GO; GO:0006357; P:regulation of transcription from Pol II pro...; IDA.
DR   InterPro; IPR006933; HAP1_N.
DR   Pfam; PF04849; HAP1_N; 1.
KW   Coiled coil; Alternative splicing; Polymorphism.
FT   DOMAIN      134    355       COILED COIL (POTENTIAL).
FT   DOMAIN      502    519       COILED COIL (POTENTIAL).
FT   VARSPLIC    653    672       VATSNPGKCLSFTNSTFTFT -> ALVSHHCPVEAVRAVHP
FT                                TRL (in isoform 2).
FT                                /FTId=VSP_003786.
FT   VARSPLIC    673    913       Missing (in isoform 2).
FT                                /FTId=VSP_003787.
FT   VARSPLIC    620    687       VQQPLQLEQKPAPPPPVTGIFLPPMTSAGGPVSVATSNPGK
FT                                CLSFTNSTFTFTTCRILHPSDITQVTP -> GSAASSTGAE
FT                                ACTTPASNGYLPAAHDLSRGTSL (in isoform 3).
FT                                /FTId=VSP_003788.
FT   VARIANT     609    609       E -> V.
FT   VARIANT     820    820       S -> P.
SQ   SEQUENCE   913 AA;  101638 MW;  D0E135DBEC30C28C CRC64;
     MSLSQNAIFK SQTGEENLMS SNHRDSESIT DVCSNEDLPE VELVNLLEEQ LPQYKLRVDS
     LFLYENQDWS QSSHQQQDAS ETLSPVLAEE TFRYMILGTD RVEQMTKTYN DIDMVTHLLA
     ERDRDLELAA RIGQALLKRN HVLSEQNESL EEQLGQAFDQ VNQLQHELSK KEELLRIVSI
     ASEESETDSS CSTPLRFNES FSLSQGLLQL DMMHEKLKEL EEENMALRSK ACHIKTETFT
     YEEKEQKLIN DCVNELRETN AQMSRMTEEL SGKSDELLRY QEEISSLLSQ IVDLQHKLKE
     HVIEKEELRL HLQASKDAQR QLTMELHELQ DRNMECLGML HESQEEIKEL RNKAGPSAHL
     CFSQAYGVFA GESLAAEIEG TMRKKLSLDE ESVFKQKAQQ KRVFDTVKVA NDTRGRSVTF
     PVLLPIPGSN RSSVIMTAKP FESGVQQTED KTLPNQGSST EVPGNSHPRD PPGLPEDSDL
     ATALHRLSLR RQNYLSEKQF FAEEWERKLQ ILAEQEEEVS SCEALTENLA SFCTDQSETT
     ELGSAGCLRG FMPEKLQIVK PLEGSQTLHH WQQLAQPNLG TILDPRPGVI TKGFTQMPKD
     AVYHISDLEE DEEVGITFQV QQPLQLEQKP APPPPVTGIF LPPMTSAGGP VSVATSNPGK
     CLSFTNSTFT FTTCRILHPS DITQVTPSSG FPSLSCGSSA GSASNTAVNS PAASYRLSIG
     ESITNRRDST ITFSSTRSLA KLLQERGISA KVYHSPASEN PLLQLRPKAL ATPSTPPNSP
     SQSPCSSPVP FEPRVHVSEN FLASRPAETF LQEMYGLRPS RAPPDVGQLK MNLVDRLKRL
     GIARVVKTPV PRENGKSREA EMGLQKPDSA VYLNSGGSLL GGLRRNQSLP VMMGSFGAPV
     CTTSPKMGIL KED
//
BioPerl-1.007002/t/data/roa1_v2.dat000444000766000024      1070713155576321 16660 0ustar00cjfieldsstaff000000000000ID   X79536; SV 1; linear; mRNA; STD; HUM; 1198 BP.
XX
AC   X79536;
XX
DT   03-JUN-1994 (Rel. 39, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 2)
XX
DE   H.sapiens mRNA for hnRNPcore protein A1
XX
KW   core protein.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [2]
RP   1-1198
RA   Leffers H.;
RT   ;
RL   Submitted (01-JUN-1994) to the EMBL/GenBank/DDBJ databases.
RL   H. Leffers, Inst. of Medical Research Biochemistry & Danish Centre for
RL   Human Genome Research, Ole Worms Alle 170, Aarhus Univ., 8000 Aarhus C,
RL   DENMARK
XX
RN   [3]
RA   Knudsen S.M., Leffers H.;
RT   "Cloning and sequencing of a splice variant of human hnRNP core protein
RT   A1";
RL   Unpublished.
XX
DR   H-InvDB; HIT000323756.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1198
FT                   /organism="Homo sapiens"
FT                   /mol_type="mRNA"
FT                   /clone_lib="lambda ZapII"
FT                   /clone="HDP1"
FT                   /cell_line="MRC5"
FT                   /cell_type="fibroblast"
FT                   /tissue_type="lung"
FT                   /db_xref="taxon:9606"
FT   CDS             27..989
FT                   /product="hnRNPcore protein A1"
FT                   /db_xref="GDB:127388"
FT                   /db_xref="GOA:P09651"
FT                   /db_xref="HGNC:5031"
FT                   /db_xref="InterPro:IPR000504"
FT                   /db_xref="InterPro:IPR012677"
FT                   /db_xref="PDB:1HA1"
FT                   /db_xref="PDB:1L3K"
FT                   /db_xref="PDB:1PGZ"
FT                   /db_xref="PDB:1PO6"
FT                   /db_xref="PDB:1U1K"
FT                   /db_xref="PDB:1U1L"
FT                   /db_xref="PDB:1U1M"
FT                   /db_xref="PDB:1U1N"
FT                   /db_xref="PDB:1U1O"
FT                   /db_xref="PDB:1U1P"
FT                   /db_xref="PDB:1U1Q"
FT                   /db_xref="PDB:1U1R"
FT                   /db_xref="PDB:1UP1"
FT                   /db_xref="PDB:2UP1"
FT                   /db_xref="UniProtKB/Swiss-Prot:P09651"
FT                   /protein_id="CAA56072.1"
FT                   /translation="MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV
FT                   MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV
FT                   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV
FT                   IQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNF
FT                   SGRGGFGGSRGGGGYGGSGDGYNGFGNDGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNF
FT                   GGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF"
FT   misc_feature    995
FT                   /note="alternative splice site"
FT   polyA_signal    1180..1185
XX
SQ   Sequence 1198 BP; 334 A; 216 C; 336 G; 312 T; 0 other;
     ttaaagtctc tcttcaccct gccgtcatgt ctaagtcaga gtctcctaaa gagcccgaac        60
     agctgaggaa gctcttcatt ggagggttga gctttgaaac aactgatgag agcctgagga       120
     gccattttga gcaatgggga acgctcacgg actgtgtggt aatgagagat ccaaacacca       180
     agcgctctag gggctttggg tttgtcacat atgccactgt ggaggaggtg gatgcagcta       240
     tgaatgcaag gccacacaag gtggatggaa gagttgtgga accaaagaga gctgtctcca       300
     gagaagattc tcaaagacca ggtgcccact taactgtgaa aaagatattt gttggtggca       360
     ttaaagaaga cactgaagaa catcacctaa gagattattt tgaacagtat ggaaaaattg       420
     aagtgattga aatcatgact gaccgaggca gtggcaagaa aaggggcttt gcctttgtaa       480
     cctttgacga ccatgactcc gtggataaga ttgtcattca gaaataccat actgtgaatg       540
     gccacaactg tgaagttaga aaagccctgt caaagcaaga gatggctagt gcttcatcca       600
     gccaaagagg tcgaagtggt tctggaaact ttggtggtgg tcgtggaggt ggtttcggtg       660
     ggaatgacaa cttcggtcgt ggaggaaact tcagtggtcg tggtggcttt ggtggcagcc       720
     gtggtggtgg tggatatggt ggcagtgggg atggctataa tggatttggc aatgatggaa       780
     gcaattttgg aggtggtgga agctacaatg attttgggaa ttacaacaat cagtcttcaa       840
     attttggacc catgaaggga ggaaattttg gaggcagaag ctctggcccc tatggcggtg       900
     gaggccaata ctttgcaaaa ccacgaaacc aaggtggcta tggcggttcc agcagcagca       960
     gtagctatgg cagtggcaga agattttaat tagggaggag tctgctacta gtcttatcag      1020
     ctcttaaaaa cagaaactca tctgtccaag ttcgtggcag aaaggaacgt ccttgtgaag      1080
     acctttatct gagccactgt acttcgttat cacgccatgc agtttacatg agctgttctg      1140
     cagctcgaaa ttccattttg tgaatgggtt ttttttttta ataaactgta tttaactt        1198
//BioPerl-1.007002/t/data/rpsblast.bls000444000766000024      1305313155576321 17246 0ustar00cjfieldsstaff000000000000RPS-BLAST 2.2.18 [Mar-02-2008]

Database: CDD.v.2.12 
           24,291 sequences; 6,026,850 total letters

Searching..................................................done

Query= orf10
         (129 letters)

 ***** No hits found ******


Query= orf20
         (765 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gnl|CDD|82074 PRK07003, PRK07003, DNA polymerase III subunits ga...    41   0.001

>gnl|CDD|82074 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau.
          Length = 825

 Score = 41.0 bits (95), Expect = 0.001
 Identities = 51/212 (24%), Positives = 65/212 (30%)

Query: 101 GTGTTTCAGAAGATATAATAAAAAAAATAGAAAAAAAAAATTGGAAACTAATAGCAATTT 160
           G       GA+   A      A  AA    AAAA AA  A    AA    ATA      +
Sbjct: 384 GARAAAAVGASAVPAVTGATGATGAALAPKAAAARAATRAEAPPAAPARPATAERGDDAS 443

Query: 161 TATTAACTCATAATCATATTGATCATGTAGGAGGAGTAGAAGAAATTATAAGAAGATATC 220
                    A A   A +      A   A     +G A +A       +A  AA  +A  
Sbjct: 444 DGDAPVPAKANARASADSRCDERDAQPPADSGSASGAASSAPPDTAFESAPRAAAPSAAT 503

Query: 221 CAAACGTAACTGTTTTTGGTCCTGAAGAAACAAAAACAAGAAATGTAAATAAAATTGTAA 280
            AA     A    +          AA  +     AA A  + ATG AAA       G   
Sbjct: 504 PAAVPDARAPAAASAEDAVEAAAPAAPESRPPTPAAGAPVSRATGAAAALDVLRNAGMRV 563

Query: 281 AACAAGGAGATGTAATAAAATTGTTAAAAAGT 312
           ++    GA        A+       A  +  T
Sbjct: 564 SSGRGAGAARPAAGPAASPTKPAPRAQVSVPT 595


Query= orf30
         (225 letters)

 ***** No hits found ******


Query= orf40
         (858 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gnl|CDD|33678 COG3889, COG3889, Predicted solute binding protein...    47   2e-05

>gnl|CDD|33678 COG3889, COG3889, Predicted solute binding protein [General
           function prediction only].
          Length = 872

 Score = 47.3 bits (112), Expect = 2e-05
 Identities = 33/147 (22%), Positives = 48/147 (32%), Gaps = 3/147 (2%)

Query: 505 TTGGGTGTTTTTATTTTAATTTTATTTTATAGTGTAAAGATGAAGGGATTAATTGGTTTT 564
              G   T   +     A        TT                G   TT+ T       
Sbjct: 721 VKIGQALTVYGSLEVFPAGENWGFIPTTK--RVKVRIMDPASGTGTSITTSGTFTAEVPQ 778

Query: 565 TGTAAAGAACTTACTTTACAACCTTTTAATCATCCTGTATTTTTTATTTTTAATTTTTTA 624
           + T        +A + T+     TT+   T     T T T++ +   TT+   T+T+TT 
Sbjct: 779 SPTKTETTLSYSAYSNTSILIE-TTSVVITKTVTQTQTTTSSPSPTQTTSPTQTSTSTTT 837

Query: 625 TTAGAATTAGTTTCTTTATTATCAAAA 651
           TT+ + TT G   C         AA A
Sbjct: 838 TTSPSQTTTGGGICGPIVIIVGLAALA 864



 Score = 45.4 bits (107), Expect = 5e-05
 Identities = 30/134 (22%), Positives = 44/134 (32%), Gaps = 5/134 (3%)

Query: 522 AATTTTATTTTATAGTGTAAAGATGAAGGGATTAATTGGTTTTTGTAAAGAACTTACTTT 581
            A T   +     AG        T          A+  GT+ TT         T     +
Sbjct: 725 QALTVYGSLEVFPAGENWGFIPTTKRVKVRIMDPASGTGTSITTSGTF-----TAEVPQS 779

Query: 582 ACAACCTTTTAATCATCCTGTATTTTTTATTTTTAATTTTTTATTAGAATTAGTTTCTTT 641
                 T + +A   T      T+   T T T T  TT++ + T   + T   T+T TTT
Sbjct: 780 PTKTETTLSYSAYSNTSILIETTSVVITKTVTQTQTTTSSPSPTQTTSPTQTSTSTTTTT 839

Query: 642 ATTATCAAAACCAA 655
           + + T      C  
Sbjct: 840 SPSQTTTGGGICGP 853



 Score = 45.0 bits (106), Expect = 8e-05
 Identities = 28/132 (21%), Positives = 41/132 (31%)

Query: 105 AGATTTATGTAATTTTAAGTTTGTTGAACCAGGAAAAATTGTTTCTCATTTTTGGGTTTT 164
            G   T  G+              T           A+ TGT+  T  T T     + T 
Sbjct: 723 IGQALTVYGSLEVFPAGENWGFIPTTKRVKVRIMDPASGTGTSITTSGTFTAEVPQSPTK 782

Query: 165 AAATATTGATTCAATCATATTTTCTCTTGTATTAGGATGTTTTTTTTTGAGCATCTTTTA 224
              T +  A +  +     T+   T T     T   +   T TT+ T  +   T TT+ +
Sbjct: 783 TETTLSYSAYSNTSILIETTSVVITKTVTQTQTTTSSPSPTQTTSPTQTSTSTTTTTSPS 842

Query: 225 CACAGTGGCAAA 236
               G G C   
Sbjct: 843 QTTTGGGICGPI 854



 Score = 42.3 bits (99), Expect = 4e-04
 Identities = 26/96 (27%), Positives = 39/96 (40%)

Query: 368 TTGTTTGGGTTTTTTTAATGAATCTTATGGATTTAATTCCAATTGATTTTTTTCCATTTA 427
            +GT T   T+ T T     + T T  T   +  + T+    TT    T T T   TTT+
Sbjct: 759 ASGTGTSITTSGTFTAEVPQSPTKTETTLSYSAYSNTSILIETTSVVITKTVTQTQTTTS 818

Query: 428 TTTCTGAGAGGTTTTTTCATTTTCCAGCAATGCGTA 463
           + + T   +   T+T+T  TT+          CG  
Sbjct: 819 SPSPTQTTSPTQTSTSTTTTTSPSQTTTGGGICGPI 854


Query= orf50
         (189 letters)

 ***** No hits found ******


Query= orf60
         (387 letters)

 ***** No hits found ******


Query= orf70
         (600 letters)

 ***** No hits found ******


Query= orf80
         (270 letters)

 ***** No hits found ******


Query= orf90
         (987 letters)

 ***** No hits found ******


Query= orf100
         (624 letters)

 ***** No hits found ******


Query= orf110
         (435 letters)

 ***** No hits found ******


  Database: CDD.v.2.12
    Posted date:  Aug 13, 2008 12:02 PM
  Number of letters in database: 6,026,850
  Number of sequences in database:  24,291
  
Lambda     K      H
   0.320    0.134    0.503 

Gapped
Lambda     K      H
   0.267   0.0579    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24291
Number of Hits to DB: 98,336,059
Number of extensions: 7540086
Number of successful extensions: 79485
Number of sequences better than 1.0e-03: 11
Number of HSP's gapped: 59896
Number of HSP's successfully gapped: 1457
Length of database: 6,026,850
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 86 (37.2 bits)
BioPerl-1.007002/t/data/rpsblast_no_hits.bls000444000766000024       260313155576321 20750 0ustar00cjfieldsstaff000000000000RPS-BLAST 2.2.18 [Mar-02-2008]

Database: CDD.v.2.13 
           24,083 sequences; 5,982,884 total letters

Searching..................................................done

Query= lcl|YP_134044.1|Plus1 F 4437 4742 NC_006391 hypothetical
protein {Haloarcula marismortui ATCC 43049}
         (101 letters)

 ***** No hits found ******


Query= lcl|YP_134045.1|Plus1 F 4742 5065 NC_006391 transcription
regulator {Haloarcula marismortui ATCC 43049}
         (107 letters)

 ***** No hits found ******


Query= lcl|YP_134046.1|Plus1 F 5275 5808 NC_006391 hypothetical
protein {Haloarcula marismortui ATCC 43049}
         (177 letters)

 ***** No hits found ******


  Database: CDD.v.2.13
    Posted date:  Nov 8, 2007  6:30 PM
  Number of letters in database: 5,982,884
  Number of sequences in database:  24,083
  
Lambda     K      H
   0.308    0.126    0.352 

Gapped
Lambda     K      H
   0.267   0.0606    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24083
Number of Hits to DB: 200,397,591
Number of extensions: 14170162
Number of successful extensions: 17150
Number of sequences better than 1.0e-005: 6
Number of HSP's gapped: 17124
Number of HSP's successfully gapped: 29
Length of database: 5,982,884
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 6.7 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (20.8 bits)
S2: 102 (43.3 bits)
BioPerl-1.007002/t/data/sample_dataset.tigr000444000766000024     20770713155576321 20622 0ustar00cjfieldsstaff000000000000sequence	TTCCTTGGCCGCTCTGGTCAGCCCTCGCGATATCCGTATCTCTCCCCGCAGCCAGTCTACATCCCmCCATTCTACCGCGATGAGTTCGCTGGTCCGCAGCCCGGTCCACATGGCGAACTGCAACAGGTTCCGGTACTGGCCATCGGTGCCGGCCAGArTCAGTCGCTGCTCTTCCGGCGAGAACGGATCArTCTCGTCCTCGGTCyTCGGCTTCTCCCTGACCGAGTACGTCCAGCCCGCCAGCGGGTTGATCTCGAyCAGTTCGTCATGCACGGCATCATCTAGCGCCGACCGTAGGCAGCTCTGTACGTTCGACAGGCGCTTGTTCGAGGCGTCCATGCTCGCCATAGCCTCCTTGATCATCTTGCGACTGAGCAGCACCAGGGGATGATCGCCCAGCyTCGGCACCAGTACCCCGTCGATGATCTTCCGATAGCCATCGATGGTGCTTGCCTTCAGGACCTTCTCTTTCTTCTCCCGCCAGCTTGCGAGGTATTTCGACAACGGTACTTGCCCGGTCTGGTATCCAAGCCGATTGGCTCGCTTGGACTTGGGGAAGGTGGCCAGATAGTCGAACGTGCCGTTGTAGATCGTCAGTTCGATAGCGGCCTTGTGCTGCTCGACGCGTTTCAGGTTAGCGGGGCTGGGCTCAAGTGGGATGCGTTCGCGGCACTGCTCACCATCGAACATGAAGCTGATTTCAATACTACTTTTCGACGCCGCTCTGAcGCCGCTGCGCTTTCCACCCATTCCGCATACCCATCCACACTTATTAGAGGTTTGTTGTCCGGCGCATGCCTCCATACGAGCCCCTTGGGCCATGTGCCGTCAGCGATCTTGGCTCTGATCGCGGCCTCAGTGTAGCCACTTTCGATGGCGAACTGGCTGATCGTCTTGTATTTGACCATCTCAACCCTCCTTGCTCATGGCTTCACGGAATGCAGCGGTGTATTCCTCGACGATCTTTTCAAGTGGgTCGCTGCCGGCCGGATCGCAAAGCCGGTCGATATATTTGATTGCCATTCGGCCAAGAGCTGCATCCTTGCGCAGAGCCTCGGCTTCAGCCATGArGCAGGCGTCGCACGGcTCAGACTTGCTCGCCGCCCCATCCCTGAACCCGTCCCGCGAAGCATTGGCCATGTCTACGGCGGTGTAGAGCGGAGTAGGGCCGCCGCGCAGGTGTTCGATCATCTTGGCCTGCTGAGCGACTGTGGCTTCCAGGGCGATAATTTTGTAGTCCTGCTCG
lsequence	TTCCTTGGCCGCTCTGGTCAGCCCTCGCGATATCCGTATCTCTCCCCGCAGCCAGTCTACATCCCmCCATTCTACCGCGATGAGTTCGCTGGTCCGCAGCCCGGTCCACATGGCGAACTGCAACAGGTTCCGGTACTGGCCATCGGTGCCGGCCAGArTCAGTCGCTGCTCTTCCGGCGAGAACGGATCArTCTCGTCCTCGGTCyTCGGCTTCTCCCTGACCGAGTACGTCCAGCCCGCCAGCGGGTTGATCTCGAyCAGTTCGTCATGCACGGCATCATCTAGCGCCGACCGTAGGCAGCTCTGTACGTTCGACAGGCGCTTGTTCGAGGCGTCCATGCTCGCCATAGCCTCCTTGATCATCTTGCGACTGAGCAGCACCAGGGGATGATCGCCCAGCyTCGGCACCAGTACCCCGTCGATGATCTTCCGATAGCCATCGATGGTGCTTGCCTTCAGGACCTTCTCTTTCTTCTCCCGCCAGCTTGCGAGGTATTTCGACAACGGTACTTGCCCGGTCTGGTATCCAAGCCGATTGGCTCGCTTGGACTTGGGGAAGGTGGCCAGATAGTCGAACGTGCCGTTGTAGATCGTCAGTTCGATAGCGGCCTTGTGCTGCTCGACGCGTTTCAGGTTAGCGGGGCTGGGCTCAAGTGGGATGCGTTCGCGGCACTGCTCACCATCGAACATGAAGCTGATTTCAATACTACTTTTCGACGCCGCTCTGA-cGCCGCTGCGCTTTCCACCCATTCCGCATACCCATCCACACTTATTAGAGGTTTGTTGTCCGGCGCATGCCTCCATACGAGCCCCTTGGGCCATGTGCCGTCAGCGATCTTGGCTCTGATCGCGGCCTCAGTGTAGCCACTTTCGATGGCGAACTGGCTGATCGTCTTGTATTTGACCATCTCAACCCTCCTTGCTCATGGCTTCACGGAATGCAGCGGTGTATTCCTCGACGATCTTTTCAAGTGGgTCGCTGCCGGCCGGATCGCAAAGCCGGTCGATATATTTGATTGCCATTCGGCCAAGAGCTGCATCCTTGCGCAGAGCCTCGGCTTCAGCCATGArGCAGGCGTCGCACGGcTCAGACTTGCTCGCCGCCCCATCCCTGAACCCGTCCCGCGAAGCATTGGCCATGTCTACGGCGGTGTAGAGCGGAGTAGGGCCGCCGCGCAGGTGTTCGATCATCTTGGCCTGCTGAGCGACTGTGGCTTCCAGGGCGATAATTTTGTAGTCCTGCTCG
quality	0x0B0B0B0B0B0B0B0B0B0404040404040404040404040404040E04040404040404040404040404040402020202020202020202020202020202020202020202020202160202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020404040404040404040404040404040404040416040404040404040404040404040404040404040404040404040404040404040416040404040404040404040404040416040404040404040404040404040404040402020202020202020202020202020202020202020202020202020202020202020202160202020202020202020202020202020202020909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090202020D02020D02020202020202020202020202020202020202020202020202020202020202020201010101010101010101010101010102020216020202020202020202020202020202020202020202020202020202020202020202020202090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303080303030303110303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303080303030303030303030303030303030303030303030303030303030303030303030303030803030303030303030303030303030303030303030303030303030303030303030303030303030303030313030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303050505050505050505050505050505050505050C0505050505050505050505160505050505050505050505050505050E050505050505050505050505050505050505050E050505050505050505050505050505050B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	2
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	2.13
perc_N	0.80
seq#	6
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_013_C07.x01.phd.1
asm_lend	1
asm_rend	276
seq_lend	1
seq_rend	276
best	0
comment	
db	sdsu
offset	0
lsequence	TTCCTTGGCCGCTCTGGTCAGCCCTCGCGATATCCGTATCTCTCCCCGCAGCCAGTCTACATCCCCCCATTCTACCGCGATGAGTTCGCTGGTCCGCAGCCCGGTCCACATGGCGAACTGCAACAGGTTCCGGTACTGGCCATCGGTGCCGGCCAGAATCAGTCGCTGCTCTTCCGGCGAGAACGGATCAATCTCGTCCTCGGTCTTCGGCTTCTCCCTGACCGAGTACGTCCAGCCCGCCAGCGGGTTGATCTCGACCAGTTCGTCATGCACGGC

seq_name	SDSU_RFPERU_013_G10.x01.phd.1
asm_lend	10
asm_rend	437
seq_lend	428
seq_rend	1
best	0
comment	
db	sdsu
offset	9
lsequence	CGCTCTGGTCAGCCCCCGCGATATCCGTATCTCTCCCCGCAGCCAGTCTACATCCCACCATTCTACCGCGATGAGTTCGCTGGTCCGCAGCCCGGTCCACATGGCGAACTGCAACAGGTTCCGGTACTGGCCATCGGTGCCGGCCAGAGTCAGTCGCTGCTCTTCCGGCGAGAACGGATCAGTCTCGTCCTCGGTCCTCGGCTTCTCCCTGACCGAGTACGTCCAGCCCGCCAGCGGGTTGATCTCGATCAGTTCGTCATGCACGGCATCATCTAGCGCCGACCGTAGGCAGCTCTGTACGTTCGACAGGCGCTTGTTCGAGGCGTCCATGCTCGCCATAGCCTCCTTGATCATCTTGCGACTGAGCAGCACCAGGGGATGATCGCCCAGCTTCGGCACCAGTACCCCGTCGATGATCTTCCGATAGC

seq_name	SDSU1_RFPERU_001_A09.x01.phd.1
asm_lend	343
asm_rend	839
seq_lend	2
seq_rend	496
best	0
comment	
db	sdsu
offset	342
lsequence	CGC-ATCGCCTCCTTGATCATCTTGCGACTGAGCAGCACCAGGGGATGATCGCCCAGCCTCGGCACCAGTACCCCGTCGATGATCTTCCGATAGCCATCGATGGTGCTTGCCTTCAGGACCTTCTCTTTCTTCTCCCGCCAGCTTGCGAGGTATTTCGACAACGGTACTTGCCCGGTCTGGTATCCAAGCCGATTGGCTCGCTTGGACTTGGGGAAGGTGGCCAGATAGTCGAACGTGCCGTTGTAGATCGTCAGTTCGATAGCGGCCTTGTGCTGCTCGACGCGTTTCAGGTTAGCGGGGCTGGGCTCAAGTGGGATGCGTTCGCGGCACTGCTCACCATCGAACATGAAGCTGATTTCAATACTACTTTTCGACGCCG-TCTGA-CGCCGCTGCGCTTTCCACCCATTCCGCATACCCATCCACACTTATTAGAGGTTTGTTGTCCGGCGCATGCCTCCATACGAGCCCCTTGGGCCATGTGCCGTCAGCGATCTT

seq_name	SDSU1_RFPERU_001_B04.x01.phd.1
asm_lend	498
asm_rend	1123
seq_lend	1
seq_rend	623
best	0
comment	
db	sdsu
offset	497
lsequence	TCGACAACGGTACTTGCCCGGTCTGGTATCCAAGCCGATTGGCTCGCTTGGACTTGGGGAAGGTGGCCAGATAGTCGAACGTGCCGTTGTAGATCGTCAGTTCGATAGCGGCCTTGTGCTGCTCGACGCGTTTCAGGTTAGCGGGGCTGGGCTCAAGTGGGATGCGTTCGCGGCACTGCTCACCATCGAACATGAAGCTGATTTCAATACTACTTTTCGACGCCGCTCTGA-CGCCGCTGCGCTTTCCACCCATTCCGCATACCCATCCACACTTATTAGAGGTTTGTTGTCCGGCGCATGCCTCCATACGAGCCCCTTGGGCCATGTGCCGTCAGCGATCTTGGCTCTGATCGCGGCCTCAGTGTAGCCACTTTCGATGGCGAACTGGCTGATCGTCTCGTATTTGACCATCTCAACCCTCCTTGCTCATGGCTTCACGGAATGCAGCGGTGTATTCCTCGACGATCTTTTCAAGTGGGTCGCTGCCGGCCGGATCGCAAAGCCGGTCGATATATTTGATTGCCATTCGGCCAAGAGCTGCATCCTTGCGCAGAGCCTCGG-TTCAGCCATGAGGCAGGCGTCGCACGG-TCAGACTTGCTCGCCGCCC-ATCCCTGAACCCGTCC

seq_name	SDSU_RFPERU_015_G04.x01.phd.1
asm_lend	668
asm_rend	1082
seq_lend	1
seq_rend	416
best	0
comment	
db	sdsu
offset	667
lsequence	CGGCACTGCTCACCATCGAACATGAAGCTGATTTCAATACTACTTTTCGACGCCGCTCTGAACGCCGCTGCGCTTTCCACCCATTCCGCATACCCATCCACACTTATTAGAGGTTTGTTGTCCGGCGCATGCCTCCATACGAGCCCCTTGGGCCATGTGCCGTCAGCGATCTTGGCTCTGATCGCGGCCTCAGTGTAGCCACTTTCGATGGCGAACTGGCTGATCGTCTTGTATTTGACCATCTCAACCCTCCTTGCTCATGGCTTAACGGAATGCAGCGGTGTATTCCTCGACGATCTTTTCAAGTGGGTCGCTGCCGGCCGGATCGCAAAGCCGGTCGATATATTTGATTGCCATTCGGCCAAGAGCTGCATCCTTGCGCAGAGCCTCGGCTTCAGCCATGAAGCAGGCGTCGC

seq_name	SDSU_RFPERU_014_H06.x01.phd.1
asm_lend	833
asm_rend	1246
seq_lend	1
seq_rend	413
best	0
comment	
db	sdsu
offset	833
lsequence	CGATCTTGGCTCTGATCGCGGCCTCAGTGTAGCCACTTTCGATGGCGAACTGGCTGATCGTCTTGTATTTGACCATCTCAACCCTCCTTGCTCATGGCTTCACGGAATGCAGCGGTGTATTCCTCGACGATCTTTTCAAGTGG-TCGCTGCCGGCCGGATCGCAAAGCCGGTCGATATATTTGATTGCCATTCGGCCAAGAGCTGCATCCTTGCGCAGAGCCTCGGCTTCAGCCATGAAGCAGGCGTCGCACGGCTCAGACTTGCTCGCCGCCCCATCCCTGAACCCGTCCCGCGAAGCATTGGCCATGTCTACGGCGGTGTAGAGCGGAGTAGGGCCGCCGCGCAGGTGTTCGATCATCTTGGCCTGCTGAGCGACTGTGGCTTCCAGGGCGATAATTTTGTAGTCCTGCTCG
|
sequence	TAGGATTGGATTATTTGGAAAGGGTTTTTGCGCGCTTCTTCGACCACGCAATCACGTCAAGCACCGCGCTTTTGCTGAACACGCTGCGCTGCTTGTAGTAGTCGATCGAGTCCCGGGCTACGCTGAAGCAAATGCCCTCTGGATACTTCAGCTTGCGCAGTTCGTCGTGAACGTTTTTTCGATGAACTCAAACGGAGTCATATCGCCACCCATTCGTTTTTGCCGTTGTAGAAGCCTCGCCAyTCCCCGAGCCTGAACACCAAGGTCCCAGGGtGCAGAGCCATGCGCGAGAGATTGGCCAGCCATCGAGCCGGAAGCTTTTCTTGATCGCGCTCAGACGGCGCTTGCGGATTCGCGTTCGTGACAGATCGATCCGCCGGATTCGGATTAGAGCCATGTTGAATTCCAGyCAGGCGCCGCCCTCCGGGTTCCGGATGCAGCAGGTTGGATGGGGTTACTGCTTCGGCGCTTTCGGGAAGAACGCAGGGCGTGGGCCGCCGCGCTTCGATTTTGGATAGTCGATTTCGAACTTGGTGAGGATGCGAGTGAAGGCTGTAAAAGAGATTCCGGCCTTTTCCATAGCCTGGTTTCGCGTCAAGCCAAGCTCCTTGAACGCCTTGATGCGTGCTGCGTCTTGCGCATCTTTTGCTTCATCGACAGTGGCCGGTTTCAGATTCTTGCGCGCATAATAGGATGCTGACTGAAAACTGAATCCTCCTTCTTTGGCCAGAGAA
lsequence	TAGGATTGGATTATTTGGAAAGGGTTTTTGCGCGCTTCTTCGACCACGCAATCACGTCAAGCACCGCGCTTTTGCTGAACACGCTGCGCTGCTTGTAGTAGTCGATCGAGTCCCGGGCTACGCTGAAGCAAATGCCCTCTGGATACTTCAGCTTGCGCAGTTCGTCGTGAACGTTTTTTCGATGAACTCAAACGGAGTCATATCGCCACCCATTCGTTTTTGCCGTTGTAGAAGCCTCGCCAyTCCCCGAGCCTGAACACCAAGGTCCCAGGG-tGCAGAGCCATGCGCGAGAGATTGGCCAGCCATCGAGCCGGAAGCTTTTCTTGATCGCGCTCAGACGGCGCTTGCGGATTCGCGTTCGTGACAGATCGATCCGCCGGATTCGGATTAGAGCCATGTTGAATTCCAGyCAGGCGCCGCCCTCCGGGTTCCGGATGCAGCAGGTTGGATGGGGTTACTGCTTCGGCGCTTTCGGGAAGAACGCAGGGCGTGGGCCGCCGCGCTTCGATTTTGGATAGTCGATTTCGAACTTGGTGAGGATGCGAGTGAAGGCTGTAAAAGAGATTCCGGCCTTTTCCATAGCCTGGTTTCGCGTCAAGCCAAGCTCCTTGAACGCCTTGATGCGTGCTGCGTCTTGCGCATCTTTTGCTTCATCGACAGTGGCCGGTTTCAGATTCTTGCGCGCATAATAGGATGCTGACTGAAAACTGAATCCTCCTTCTTTGGCCAGAGAA
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090903030D030303030303030303030303030303030303030303030303030303030303030303030303030303030303160303030303030303030303030303030303030303030303030303030303030D0303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030316030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030305050505050505050505050505050505050505050505050505050B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	17
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.43
perc_N	0.41
seq#	2
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU1_RFPERU_001_E04.x01.phd.1
asm_lend	1
asm_rend	510
seq_lend	1
seq_rend	511
best	0
comment	
db	sdsu
offset	0
lsequence	TAGGATTGGATTATTTGGAAAGGGTTTTTGCGCGCTTCTTCGACCACGCAATCACGTCAAGCACCGCGCTTTTGCTGAACACGCTGCGCTGCTTGTAGTAGTCGATCGAGTCCCGGGCTACGCTGAAGCAAATGCCCTCTGGATACTTCAGCTTGCGCAGTTCGTCGTGAACGTTTTTTCGATGAACTCAAACGGAGTCATATCGCCACCCATTCGTTTTTGCCGTTGTAGAAGCCTCGCCATTCCCCGAGCCTGAACACCAAGGTCCCAGGGGTGCAGAGCCATGCGCGAGAGATTGGCCAGCCATCGAGCCGGAAGCTTTTCTTGATCGCGCTCAGACGGCGCTTGCGGATTCGCGTTCGTGACAGATCGATCCGCCGGATTCGGATTAGAGCCATGTTGAATTCCAGTCAGGCGCCGCCCTCCGGGTTCCGGATGCAGCAGGTTGGATGGGGTTACTGCTTCGGCGCTTTCGGGAAGAACGCAGGGCGTGGGCCGCCGCGCTTCGATT

seq_name	SDSU_RFPERU_006_E05.x01.phd.1
asm_lend	198
asm_rend	734
seq_lend	3
seq_rend	538
best	0
comment	
db	sdsu
offset	197
lsequence	TC-TATCGCCACCCATTCGTTTTTGCCGTTGTAGAAGCCTCGCCACTCCCCGAGCCTGAACACCAAGGTCCCAGGG-TGCAGAGCCATGCGCGAGAGATTGGCCAGCCATCGAGCCGGAAGCTTTTCTTGATCGCGCTCAGACGGCGCTTGCGGATTCGCGTTCGTGACAGATCGATCCGCCGGATTCGGATTAGAGCCATGTTGAATTCCAGCCAGGCGCCGCCCTCCGGGTTCCGGATGCAGCAGGTTGGATGGGGTTACTGCTTCGGCGCTTTCGGGAAGAACGCAGGGCGTGGGCCGCCGCGCTTCGATTTTGGATAGTCGATTTCGAACTTGGTGAGGATGCGAGTGAAGGCTGTAAAAGAGATTCCGGCCTTTTCCATAGCCTGGTTTCGCGTCAAGCCAAGCTCCTTGAACGCCTTGATGCGTGCTGCGTCTTGCGCATCTTTTGCTTCATCGACAGTGGCCGGTTTCAGATTCTTGCGCGCATAATAGGATGCTGACTGAAAACTGAATCCTCCTTCTTTGGCCAGAGAA
|
sequence	TTTCCGTTATCGCTCGTAGCAGTGAGCCGATCGTGAAATCGACAAGGCCGGCGGCCCGACCCTGGATCGCTGTTACTTGATCTCGTACGAGAGTGGTGAAGTCTTTGACGTTGAGAGATGCCATATCAGCGATTTACCTCGAACGAAAGCGTCACCGGCTCACCAAGCGGCGAATCGGTGTAGCTGATATTGACGGAGATGGTGTCGTTGGAAGGAGTGACAGAAATCACTGGCGCTGGCTTCTTTGCCACGCAGTCCTCAAGCAGGATCTGTCCCCTGATGTTCGCGATGATTTCCGGAACGTTTGCCAGGGCGCCGACATATCGGCCAAGCCCAGCCCCATATTCAGGGTGGAAAAGATAATCACCAGGGTTGGTGATAgCCTGCGTAGAATTCGTTGCTTGCCTCTTTcGATACCCTCGACCGGCGACAAGCTCCCGGCCGGGGACAGGGAAAGATCATCTCCAGGGTAGTGAGTTAGGTCTTTCATGGCACAGGCACCGAAGAATCCCGCCACCAGTAGTGACGCCGCTGGTGCGGTGGGTTTTGAGACTGATCGTGTCGGCTTTGACGTCGCCGCCGGTGACGACTACGCCAGTGCTATCTGTAACGGTCAGCGTGTGATCCATCGTTACGGGGCCGCCAGTAAAATGGTGCGCCGGCGCGTCGTAGTTGATTGCCACCCCCrAATGAAGCGATACGGTGCCGTCCGTGTTGAACTTGAGCAGCGCGCCAGATTTGTGAACCATCCrGATCTCGCCAGAAGGAACCGGCGTAGCCAGATTCACGCTGTTGGTGTGCCGCGCAGTGACCCTTCCACTATTGGGATCGAAGGAATCGAATTCGACGGTTACCTCATCCCCGACCTGTGGACCGATCTGCACGCCCCAGCCATTCCCAACACCTGGGCAATCCAGCTTCAACCAGTTGGTTTCTCATCCTTCCGGCTGGATTGCGACCTTCACAACGCCGTTAACTGGGTCGTAGCTGGTGATCGTTCCAGAGCTGCGACCCAGTTGCATCGGTAGTTTGGGTTTGGTGATACGCGTTCGTCAGTTGTTGAATGCTCACGGCTGCACCATTGAGTTTGGATTGTGGTTTTTTGCCGTCAGGCTCATCGGTGTAGCCGGATTCGAAGCTCAGCGACCGGCGCACAGAGTCGACGTAATAAAGTTGGTCGAATCCAGAGCCAGTCCCCTCGACGCGAACAATGGTGTTCGGCATCAGCGAGTTGTCGCCCGGAAGCGATCCAGACATGCGCATTTCATGATCGGTGATTTGTTTGTGGATCTTCTGCGCCAGTTGTTGCGCCGCGTACTGGTCCAAGCCGGTGCGCTTGATCTCGTAGATCTGCCGCTTTGCAGTTGCCTGCCCGGGCGCAATACCCTTAGCTGAACT
lsequence	TTTCCGTTATCGCTCGTAGCAGTGAGCCGATCGTGAAATCGACAAGGCCGGCGGCCCGACCCTGGATCGCTGTTACTTGATCTCGTACGAGAGTGGTGAAGTCTTTGACGTTGAGAGATGCCATATCAGCGATTTACCTCGAACGAAAGCGTCACCGGCTCACCAAGCGGCGAATCGGTGTAGCTGATATTGACGGAGATGGTGTCGTTGGAAGGAGTGACAGAAATCACTGGCGCTGGCTTCTTTGCCACGCAGTCCTCAAGCAGGATCTGTCCCCTGATGTTCGCGATGATTTCCGGAACGTTTGCCAGGGCGCCGACATATCGGCCAAGCCCAGCCCCATATTCAGGGTGGAAAAGATAATCACCAGGGTTGGTGATA-gCCTGCGTAGAATTCGTTGCTTGCCTCTTT-cGATACCCTCGACCGGCGACAA-GCTCCCGGCCGGGGACAGGGAAAGATCATCTCCAGGGTAGTGAGTTAGGTCTTTCATGGCACAGGCACCGAAGAATCCCGCCACCAGTAGTGACGCCGCTGGTGCGGTGGGTTTTGAGACTGATCGTGTCGGCTTTGACGTCGCCGCCGGTGACGACTACGCCAGTGCTATCTGTAACGGTCAGCGTGTGATCCATCGTTACGGGGCCGCCAGTAAAATGGTGCGCCGGCGCGTCGTAGTTGATTGCCACCCCCrAATGAAGCGATACGGTGCCGTCCGTGTTGAACTTGAGCAGCGCGCCAGATTTGTGAACCATCCrGATCTCGCCAGAAGGAACCGGCGTAGCCAGATTCACGCTGTTGGTGTGCCGCGCAGTGACCCTTCCACTATTGGGATCGAAGGAATCGAATTCGACGGTTACCTCATCCCCGACCTGTGGACCGATCTGCACGCCCCAGCCATTCCCAACACCTGGGCAATCCAGCTTCAACCAGTTGGTTTCTCATCCTTCCGGCTGGATTGCGACCTTCACAACGCCGTTAACTGGGTCGTAGCTGGTGATCGTTCCAGAGCTGCGACCCAGTTGCATCGGTAGTTTGGGTTTGGTGATACGCGTTCGTCAGTTGTTGAATGCTCACGGCTGCACCATTGAGTTTGGATTGTGGTTTTTTGCCGTCAGGCTCATCGGTGTAGCCGGATTCGAAGCTCAGCGACCGGCGCACAGAGTCGACGTAATAAAGTTGGTCGAATCCAGAGCCAGTCCCCTCGACGCGAACAATGGTGTTCGGCATCAGCGAGTTGTCGCCCGGAAGCGATCCAGACATGCGCATTTCATGATCGGTGATTTGTTTGTGGATCTTCTGCGCCAGTTGTTGCGCCGCGTACTGGTCCAAGCCGGTGCGCTTGATCTCGTAGATCTGCCGCTTTGCAGTTGCCTGCCCGGGCGCAATACCCTTAGCTGAACT
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B050505050505050505050505050505050505050505050505050505050505050505050505050505050303030303030303030D0303030303030303030303030303030303030303030303030303030303030D030303030303030303030303030303030303030303030D03090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090903030303030303030303030303030303030303030303030303050505050505050505050505050505030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303031603030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030316030303030303030303030303030303030303030303030D0303090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B04040404040404040404040E04040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040E0404040404040E0404040404040404040404040404040B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	36
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.32
perc_N	0.29
seq#	4
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_002_C12.x01.phd.1
asm_lend	1
asm_rend	434
seq_lend	1
seq_rend	437
best	0
comment	
db	sdsu
offset	0
lsequence	TTTCCGTTATCGCTCGTAGCAGTGAGCCGATCGTGAAATCGACAAGGCCGGCGGCCCGACCCTGGATCGCTGTTACTTGATCTCGTACGAGAGTGGTGAAGTCTTTGACGTTGAGAGATGCCATATCAGCGATTTACCTCGAACGAAAGCGTCACCGGCTCACCAAGCGGCGAATCGGTGTAGCTGATATTGACGGAGATGGTGTCGTTGGAAGGAGTGACAGAAATCACTGGCGCTGGCTTCTTTGCCACGCAGTCCTCAAGCAGGATCTGTCCCCTGATGTTCGCGATGATTTCCGGAACGTTTGCCAGGGCGCCGACATATCGGCCAAGCCCAGCCCCATATTCAGGGTGGAAAAGATAATCACCAGGGTTGGTGATAAGCCTGCGTAGAATTCGTTGCTTGCCTCTTTTCGATACCCTCGACCGGCGACAAAG

seq_name	SDSU1_RFPERU_001_B03.x01.phd.1
asm_lend	333
asm_rend	777
seq_lend	1
seq_rend	445
best	0
comment	
db	sdsu
offset	332
lsequence	CCCAGCCCCATATTCAGGGTGGAAAAGATAATCACCAGGGTTGGTGATA-GCCTGCGTAGAATTCGTTGCTTGCCTCTTT-CGATACCCTCGACCGGCGACAA-GCTCCCGGCCGGGGACAGGGAAAGATCATCTCCAGGGTAGTGAGTTAGGTCTTTCATGGCACAGGCACCGAAGAATCCCGCCACCAGTAGTGACGCCGCTGGTGCGGTGGGTTTTGAGACTGATCGTGTCGGCTTTGACGTCGCCGCCGGTGACGACTACGCCAGTGCTATCTGTAACGGTCAGCGTGTGATCCATCGTTACGGGGCCGCCAGTAAAATGGTGCGCCGGCGCGTCGTAGTTGATTGCCACCCCCGAATGAAGCGATACGGTGCCGTCCGTGTTGAACTTGAGCAGCGCGCCAGATTTGTGAACCATCCGGATCTCGCCAGAAGGAACCGGCATA

seq_name	SDSU_RFPERU_007_F06.x01.phd.1
asm_lend	530
asm_rend	1029
seq_lend	1
seq_rend	498
best	0
comment	
db	sdsu
offset	532
lsequence	CGCTGGTGCGGTGGGTTTTGAGACTGATCGTGTCGGCTTTGACGTCGCCGCCGGTGACGACTACGCCAGTGCTATCTGTAACGGTCAGCGTGTGATCCATCGTTACGGGGCCGCCAGTAAAATGGTGCGCCGGCGCGTCGTAGTTGATTGCCACCCCCAAATGAAGCGATACGGTGCCGTCCGTGTTGAACTTGAGCAGCGCGCCAGATTTGTGAACCATCCAGATCTCGCCAGAAGGAACCGGCGTAGCCAGATTCACGCTGTTGGTGTGCCGCGCAGTGACCCTTCCACTATTGGGATCGAAGGAATCGAATTCGACGGTTACCTCATCCCCGACCTGTGGACCGATCTGCACGCCCCAGCCATTCCCAACACCTGGGCAATCCAGCTTCAACCAGTTGGTTTCTCATCCTTCCGGCTGGATTGCGACCTTCACAACGCCGTTAACTGGGTCGTAGCTGGTGATCGTTCCAGAGC-GCGACC-AGTTGCATCGGTAGT

seq_name	SDSU_RFPERU_013_B05.x01.phd.1
asm_lend	927
asm_rend	1398
seq_lend	472
seq_rend	1
best	0
comment	
db	sdsu
offset	929
lsequence	GTTGGTTTCTCTTCCTTCCGGCTGGATTGCGACCTTCACAACGCCGTTAACTGGGTCGTAGCTGGTGATCGTTCCAGAGCTGCGACCCAGTTGCATCGGTAGTTTGGGTTTGGTGATACGCGTTCGTCAGTTGTTGAATGCTCACGGCTGCACCATTGAGTTTGGATTGTGGTTTTTTGCCGTCAGGCTCATCGGTGTAGCCGGATTCGAAGCTCAGCGACCGGCGCACAGAGTCGACGTAATAAAGTTGGTCGAATCCAGAGCCAGTCCCCTCGACGCGAACAATGGTGTTCGGCATCAGCGAGTTGTCGCCCGGAAGCGATCCAGACATGCGCATTTCATGATCGGTGATTTGTTTGTGGATCTTCTGCGCCAGTTGTTGCGCCGCGTACTGGTCCAAGCCGGTGCGCTTGATCTCGTAGATCTGCCGCTTTGCAGTTGCCTGCCCGGGCGCAATACCCTTAGCTGAACT
|
sequence	CGATGCTGTACGGCTGTTGCGACAGATTGCGCTGGGTCGATACCGCGTTGGTGATCGGCTTGTTCAGCGGGCTCTGGTTCGGCGACAGCGCGGCGATCTTGGCGGCTGCGAAGGTTGCCGGCGCAATCATGCGCTGCTGACCGTTGACCTGGTCCTGCCAGTACACCCAGTCGCCCACCATGACCTTCAGCGCGTAGCTGTCACAGCCGGCTGTGGTCAGCGCAGTGGCGACGGTGGTGTAGGAGGCGCCAGCAACACCTTGGGTGATCATGTAGCAGCCTTCTGACAGGCCGTAGGTCAGCATGGTCGGCCACTGGGTACCAGTCAGTCGGGTCAACCGAGATTCGCAsCTGAGCGCCACTGCCGCGCAGAGCGTACATGCCCTTGCGGGTCGCGCCGGTAACACCATCCACGCCGATCAGAACTGCGTCGGTGATGGTGGTGTTACCCGAGGTGCCAGTGGTGAAGGCGACGGTCTGGGTGCTGGCCACAGGCGCCAGAGTGGTCGCGCCAACGGTGGCGATGACCAGTTGCGATGGGCCACGGATACCTGACTGCCCGTTGTTCACGGCGCTGACGATGTTCTGCCACAGCGCCAGGCCAGAGCCGGTGATGTTGTCGAACACTTCGGGCGCAACGCCAGGGAGCGAGACGGTCAGCTTCCAGCTCGAAGCAGCGGAGCCAGTAGCCAGGGCGGCGCTGAGCGAGTTGCCGAGCGTGCCGGTGTAGAACGCGGTCAGCGTGGCGCCGGTGGCGGCGGCAGTGTCCTTCAGCGCACTGGTCGCGGCGGTGTCGGTGCCGTCAGTGACGCGCACGGCGCGGATGTTCGAGGCGCCGCCCTGGATTGATACCGCCAGCGCGGTGCACAGGTCGTACTTGCGCACGGTCyGAGTGCCGAACTTCTGCGATGCGTCACCTGGCGAGCCGATAaGCGTGGCGCTGTTCACCGGCCCCCAGTCAGCAATGCCGACGATGCCGAGAATGTCAGTCGGGACGCCATTGATGTAGCGGGTCTTGGGCGCCACTATTTGTATGTACAAATCTGGCGCAGATAAAGCCGCCGTATTCAAATAACCAGCAGGATAGATAGGCATCACGCCTCCAGAATGAAAAAGGCCACCGATTAGGTGGCCTTTGTTGTGTTCGGCTGGCTGTTAGAGCAGCAGCCCGTTTTCCCGCGCAAACGCGAATGGGTCCTTGTCATGCTTCCTGCAATTGCAGGTAGGACAAAGAATTTGCAGGTTGGATTTGTCGTTCGATCCGCCCTTTGCAAGCGGGAACACGTGGTCAACGTGATACCCATCCCTTATGGATATAGTGCACATGGCGCATTTCCAGCGCTGAGCAGCCAGCAAAAATTTTATGTCGTCGCCGGTGTGTGAGCCGACAGCATTTTTCTTGCGAGCCTTGTATGTCCGCGAGAGTGAACGAACTTGCTCCTTGTTGGCTGTCTTCCAGAGCTTTTGAGTAAGCGCACAGAGATCCTTGTTTCTTGATCTCCACTCTCTGGTTGCGGAAAT
lsequence	CGATGCTGTACGGCTGTTGCGACAGATTGCGCTGGGTCGATACCGCGTTGGTGATCGGCTTGTTCAGCGGGCTCTGGTTCGGCGACAGCGCGGCGATCTTGGCGGCTGCGAAGGTTGCCGGCGCAATCATGCGCTGCTGACCGTTGACCTGGTCCTGCCAGTACACCCAGTCGCCCACCATGACCTTCAGCGCGTAGCTGTCACAGCCGGCTGTGGTCAGCGCAGTGGCGACGGTGGTGTAGGAGGCGCCAGCAACACCTTGGGTGATCATGTAGCAGCCTTCTGACAGGCCGTAGGTCAGCATGGTCGGCCACTGGGTACCAGTCAGTCGGGTCAACCGAGATTCG-CAsCTGAGCGCCACTGCCGCGCAGAGCGTACATGCCCTTGCGGGTCGCGCCGGTAACACCATCCACGCCGATCAGAACTGCGTCGGTGATGGTGGTGTTACCCGAGGTGCCAGTGGTGAAGGCGACGGTCTGGGTGCTGGCCACAGGCGCCAGAGTGGTCGCGCCAACGGTGGCGATGACCAGTTGCGATGGGCCACGGATACCTGACTGCCCGTTGTTCACGGCGCTGACGATGTTCTGCCACAGCGCCAGGCCAGAGCCGGTGATGTTGTCGAACACTTCGGGCGCAACGCCAGGGAGCGAGACGGTCAGCTTCCAGCTCGAAGCAGCGGAGCCAGTAGCCAGGGCGGCGCTGAGCGAGTTGCCGAGCGTGCCGGTGTAGAACGCGGTCAGCGTGGCGCCGGTGGCGGCGGCAGTGTCCTTCAGCGCACTGGTCGCGGCGGTGTCGGTGCCGTCAGTGACGCGCACGGCGCGGATGTTCGAGGCGCCGCCCTGGATTGATACCGCCAGCGCGGTGCACAGGTCGTACTTGCGCACGGTCyGAGTGCCGAACTTCTGCGATGCGTCACCTGGCGAGCCGATAaGCGTGGCGCTGTTCACCGGCCCCCAGTCAGCAATGCCGACGATGCCGAGAATGTCAGTCGGGACGCCATTGATGTAGCGGGTCTTGGGCGCCACTATTTGTATGTACAAATCTGGCGCAGATAAAGCCGCCGTATTCAAATAACCAGCAGGATAGATAGGCATCACGCCTCCAGAATGAAAAAGGCCACCGATTAGGTGGCCTTTGTTGTGTTCGGCTGGCTGTTAGAGCAGCAGCCCGTTTTCCCGCGCAAACGCGAATGGGTCCTTGTCATGCTTCCTGCAATTGCAGGTAGGACAAAGAATTTGCAGGTTGGATTTGTCGTTCGATCCGCCCTTTGCAAGCGGGAACACGTGGTCAACGTGATACCCATCCCTTATGGATATAGTGCACATGGCGCATTTCCAGCGCTGAGCAGCCAGCAAAAATTTTATGTCGTCGCCGGTGTGTGAGCCGACAGCATTTTTCTTGCGAGCCTTGTATGTCCGCGAGAGTGAACGAACTTGCTCCTTGTTGGCTGTCTTCCAGAGCTTTTGAGTAAGCGCACAGAGATCCTTGTTTCTTGATCTCCACTCTCTGGTTGCGGAAAT
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0505050505050505050E0505160505050505050505050505050505050505050505050505050505050303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0404040404040404041604040404040404040404040404040404040404040404040404040404040404040404040404040404040E0404040404040404040B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	93
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.11
perc_N	0.20
seq#	3
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_010_C09.x01.phd.1
asm_lend	1
asm_rend	442
seq_lend	1
seq_rend	442
best	0
comment	
db	sdsu
offset	0
lsequence	CGATGCTGTACGGCTGTTGCGACAGATTGCGCTGGGTCGATACCGCGTTGGTGATCGGCTTGTTCAGCGGGCTCTGGTTCGGCGACAGCGCGGCGATCTTGGCGGCTGCGAAGGTTGCCGGCGCAATCATGCGCTGCTGACCGTTGACCTGGTCCTGCCAGTACACCCAGTCGCCCACCATGACCTTCAGCGCGTAGCTGTCACAGCCGGCTGTGGTCAGCGCAGTGGCGACGGTGGTGTAGGAGGCGCCAGCAACACCTTGGGTGATCATGTAGCAGCCTTCTGACAGGCCGTAGGTCAGCATGGTCGGCCACTGGGTACCAGTCAGTCGGGTCAACCGAGATTCG-CAGCTGAGCGCCACTGCCGCGCAGAGCGTACATGCCCTTGCGGGTCGCGCCGGTAACACCATCCACGCCGATCAGAACTGCGTCGGTGATGGTGG

seq_name	SDSU_RFPERU_002_H12.x01.phd.1
asm_lend	339
asm_rend	940
seq_lend	1
seq_rend	602
best	0
comment	
db	sdsu
offset	338
lsequence	CGAGATTCGCCACCTGAGCGCCACTGCCGCGCAGAGCGTACATGCCCTTGCGGGTCGCGCCGGTAACACCATCCACGCCGATCAGAACTGCGTCGGTGATGGTGGTGTTACCCGAGGTGCCAGTGGTGAAGGCGACGGTCTGGGTGCTGGCCACAGGCGCCAGAGTGGTCGCGCCAACGGTGGCGATGACCAGTTGCGATGGGCCACGGATACCTGACTGCCCGTTGTTCACGGCGCTGACGATGTTCTGCCACAGCGCCAGGCCAGAGCCGGTGATGTTGTCGAACACTTCGGGCGCAACGCCAGGGAGCGAGACGGTCAGCTTCCAGCTCGAAGCAGCGGAGCCAGTAGCCAGGGCGGCGCTGAGCGAGTTGCCGAGCGTGCCGGTGTAGAACGCGGTCAGCGTGGCGCCGGTGGCGGCGGCAGTGTCCTTCAGCGCACTGGTCGCGGCGGTGTCGGTGCCGTCAGTGACGCGCACGGCGCGGATGTTCGAGGCGCCGCCCTGGATTGATACCGCCAGCGCGGTGCACAGGTCGTACTTGCGCACGGTCCGAGTGCCGAACTTCTGCGATGCGTCACCTGGCGAGCCGATA-GCGTGGCGC

seq_name	SDSU_RFPERU_009_E07.x01.phd.1
asm_lend	880
asm_rend	1520
seq_lend	641
seq_rend	1
best	0
comment	
db	sdsu
offset	880
lsequence	CGCACGGTCTGAGTGCCGAACTTCTGCGATGCGTCACCTGGCGAGCCGATAAGCGTGGCGCTGTTCACCGGCCCCCAGTCAGCAATGCCGACGATGCCGAGAATGTCAGTCGGGACGCCATTGATGTAGCGGGTCTTGGGCGCCACTATTTGTATGTACAAATCTGGCGCAGATAAAGCCGCCGTATTCAAATAACCAGCAGGATAGATAGGCATCACGCCTCCAGAATGAAAAAGGCCACCGATTAGGTGGCCTTTGTTGTGTTCGGCTGGCTGTTAGAGCAGCAGCCCGTTTTCCCGCGCAAACGCGAATGGGTCCTTGTCATGCTTCCTGCAATTGCAGGTAGGACAAAGAATTTGCAGGTTGGATTTGTCGTTCGATCCGCCCTTTGCAAGCGGGAACACGTGGTCAACGTGATACCCATCCCTTATGGATATAGTGCACATGGCGCATTTCCAGCGCTGAGCAGCCAGCAAAAATTTTATGTCGTCGCCGGTGTGTGAGCCGACAGCATTTTTCTTGCGAGCCTTGTATGTCCGCGAGAGTGAACGAACTTGCTCCTTGTTGGCTGTCTTCCAGAGCTTTTGAGTAAGCGCACAGAGATCCTTGTTTCTTGATCTCCACTCTCTGGTTGCGGAAAT
|
sequence	CCGTTCAAGCAGGAGATCAGCGCCTGCCATCTGCAACAGAGCATGGGGCGTCAAACCTCTGCGGCGTAGATCCTATATTCACAGGGGAGCCAAAAGCATTTGACCAACTGAGGGGAAGTGCCTCGGTGCCAAATTCAGAGCCTCGCCATCGTGCGGGGCTTTTTTGTTTCCTTCTTCCACTGCTCCCCAGCAGTTTGGCCGCCAACTGACGGCCTTTTTTATTCCTGGAGTCACGCCATGGCCGAACCCGCGAGCACCACTGCCGCCGGTGTCCTGCTCGCGAAGTACGGCATCATCATCGCTGGCTTCGCTGGAGCAATCCTTTCGCTGACCTTCCTTCAnGGGCCTGACCCGCAAGCAGGCCATTTGGGCATTCTTCACCGGGTTCGGCTCTGCGATCTTCTGCACGCCGCTGGCGATCAGCTTCTTCAAGCTGGAGCCTGGTGGCGAAACTCAATACGGCGTCGCATTCCTGATCGGCCTGCTGGCCATGAACATCATTCCCCTGTTGAAGAaAGCAATGCCGGGAGTGTTTGGCGTCTCGGGAGGTGCaGTAATGCAAACCATCCTGCAAGTCCTTGACGCTTTCCTGTGTGtgCTGGTGGTGCTAGCCGCTGCTGAGTACCT
lsequence	CCGTTCAAGCAGGAGATCAGCGCCTGCCATCTGCAACAGAGCATGGGGCGTCAAACCTCTGCGGCGTAGATCCTATATTCACAGGGGAGCCAAAAGCATTTGACCAACTGAGGGGAAGTGCCTCGGTGCCAAATTCAGAGCCTCGCCATCGTGCGGGGCTTTTTTGTTTCCTTCTTCCACTGCTCCCCAGCAGTTTGGCCGCCAACTGACGGCCTTTTTTATTCCTGGAGTCACGCCATGGCCGAACCCGCGAGCACCACTGCCGCCGGTGTCCTGCTCGCGAAGTACGGCATCATCATCGCTGGCTTCGCTGGAGCAATCCTTTCGCTGACCTTCCTTCAnGGGCCTGACCCGCAAGCAGGCCATTTGGGCATTCTTCACCGGGTTCGGCTCTGCGATCTTCTGCACGCCGCTGGCGATCAGCTTCTTCAAGCTGGAGCCTGGTGGCGAAACTCAATACGGCGTCGCATTCCTGATCGGCCTGCTGGCCATGAACATCATTCCCCTGTTGAAGA-aAGCAATGCCGGGAGTGTTTGGCGTCTCGGGAGGTGCaGTAATGCAAACCATCCTGCAAGTCCTTGACGCTTTCCTGTGTGtgCTGGTGGTGCTAGCCGCTGCTGAGTACCT
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B150B0B0B0B0B0B0B0B0B0B0B0B0B0B0B090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B04040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040404040E040404040404040404040404040402020202020202020202020202020202020202020202020D020202020202040404040404040404040404040404040404040404040404040404040404040404040404040E0E0404040B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	106
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.23
perc_N	0.80
seq#	2
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_006_E04.x01.phd.1
asm_lend	1
asm_rend	627
seq_lend	1
seq_rend	626
best	0
comment	
db	sdsu
offset	0
lsequence	CCGTTCAAGCAGGAGATCAGCGCCTGCCATCTGCAACAGAGCATGGGGCGTCAAACCTCTGCGGCGTAGATCCTATATTCACAGGGGAGCCAAAAGCATTTGACCAACTGAGGGGAAGTGCCTCGGTGCCAAATTCAGAGCCTCGCCATCGTGCGGGGCTTTTTTGTTTCCTTCTTCCACTGCTCCCCAGCAGTTTGGCCGCCAACTGACGGCCTTTTTTATTCCTGGAGTCACGCCATGGCCGAACCCGCGAGCACCACTGCCGCCGGTGTCCTGCTCGCGAAGTACGGCATCATCATCGCTGGCTTCGCTGGAGCAATCCTTTCGCTGACCTTCCTTCANGGGCCTGACCCGCAAGCAGGCCATTTGGGCATTCTTCACCGGGTTCGGCTCTGCGATCTTCTGCACGCCGCTGGCGATCAGCTTCTTCAAGCTGGAGCCTGGTGGCGAAACTCAATACGGCGTCGCATTCCTGATCGGCCTGCTGGCCATGAACATCATTCCCCTGTTGAAGA-AAGCAATGCCGGGAGTGTTTGGCGTCTCGGGAGGTGC-GTAATGCAAACCATCCTGCAAGTCCTTGACGCTTTCCTGTGTGTGCTGGTGGTGCTAGCCGCTGCTGAGTACCT

seq_name	SDSU_RFPERU_010_B05.x01.phd.1
asm_lend	460
asm_rend	601
seq_lend	141
seq_rend	1
best	0
comment	
db	sdsu
offset	459
lsequence	CGGCGTCGCATTCCTGATCGGCCTGCTGGCCATGAACATCATTCCCCTGTTGAAGAGAAGCAATGCCGGGAGTGTTTGGCGTCTCGGGAGGTGCAGTAATGCAAACCATCCTGCAAGTCCTTGACGCTTTCCTGTGTG--CTG
|
sequence	TCGGCTTTCGGCGCAACCACCGCCACCAGCCAGCTGGCTACCACTGACCTGCTGACCCTCGGCACCATCGAGGACGCGGTTGCTGCCCTGCGCAACAACACCGGCATGCAGGACGAGATGTTCAACCTGTACCTCGACAACGTGTCGATGCGCCAGCTGTTCGCCGACGGCGACTTCAAGCTGATGTACCAAGGCCAATACGGCTCGCCTGAAGCGCGTCAGGGCAAAGTGTTCCAGCTGATGGGTGTGAACTTCATCCCTACCACTGAAGCGCTGACCCAAGTCAAGGGTTCGCTGGCCACTCCGGTGCGCCGTCCAATCCTGTGCGCTCCTGGTGCACTGGTGGAAGGTGACTTCGCCGGCATCAAGCAGAAAGCCCATGAAA
lsequence	TCGGCTTTCGGCGCAACCACCGCCACCAGCCAGCTGGCTACCACTGACCTGCTGACCCTCGGCACCATCGAGGACGCGGTTGCTGCCCTGCGCAACAACACCGGCATGCAGGACGAGATGTTCAACCTGTACCTCGACAACGTGTCGATGCGCCAGCTGTTCGCCGACGGCGACTTCAAGCTGATGTACCAAGGCCAATACGGCTCGCCTGAAGCGCGTCAGGGCAAAGTGTTCCAGCTGATGGGTGTGAACTTCATCCCTACCACTGAAGCGCTGACCCAAGTCAAGGGTTCGCTGGCCACTCCGGTGCGCCGTCCAATCCTGTGCGCTCCTGGTGCACTGGTGGAAGGTGACTTCGCCGGCATCAAGCAGAAAGCCCATGAAA
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B09090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	123
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.00
perc_N	0.00
seq#	1
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	11/12/09 18:25:38
comment	
frameshift	

seq_name	asdf
asm_lend	1
asm_rend	385
seq_lend	1
seq_rend	385
best	0
comment	
db	
offset	0
lsequence	TCGGCTTTCGGCGCAACCACCGCCACCAGCCAGCTGGCTACCACTGACCTGCTGACCCTCGGCACCATCGAGGACGCGGTTGCTGCCCTGCGCAACAACACCGGCATGCAGGACGAGATGTTCAACCTGTACCTCGACAACGTGTCGATGCGCCAGCTGTTCGCCGACGGCGACTTCAAGCTGATGTACCAAGGCCAATACGGCTCGCCTGAAGCGCGTCAGGGCAAAGTGTTCCAGCTGATGGGTGTGAACTTCATCCCTACCACTGAAGCGCTGACCCAAGTCAAGGGTTCGCTGGCCACTCCGGTGCGCCGTCCAATCCTGTGCGCTCCTGGTGCACTGGTGGAAGGTGACTTCGCCGGCATCAAGCAGAAAGCCCATGAAA
|
sequence	AGCGCCGATACACATGCTCAAACCGCGCATCGAAGTCTTCGATCAAGACGCTGAAGTAGTAGCCGTCCATGTTGAAGTTGAGCGGCTGACCGGCGTCACGCAGCGTCTCCAGCTCCGTGACGCGGTCACCAGCTGTCGCGCCAGTGATCCAGCCAGACCACTGGATGTTCTTGTAATCCAGACCGAGAACATCGACAACACGCTTGCCGCCTACCAGTTTGTGCACCACGAGCTTCTGTTTGGCGCCGATCGATACTGACTCTGGGACTTCCAGGCCGGTGAACTCGACATCTCCAACGATCAACCGCGTGGCAAACGGATCCCCGCCCGGAGCGAAGTTGTCCAGGAAGCTCGTAAAGCTCATCGTTTATCCCCTTGGATAGGCTGCGCTCGGGGTTCCTGGCATCAGCATGCTGCGGTTCGGATCGAAGCCCTGCGTCCCTGTCCGTGGCTTCGCGGCTTCCTTCGCCATCCGCTGGATTACCACGTCGCTGACTTGTTTGCCGTCGATGTACAGGTTGATGTTCTGTTGGCCATCGGCGCcAGACTTGCCCGGGACCGGAGCCACCAGCGGAGACCATGCTGGCTTTTTCTCCCCGCTTCCACGGAAATCATCGGCGAATGTAGGTTTTTGAGATCTGCATCGATGCTGGAAGAATCAGGTTTGCGCCAGCGATCAGCGTGTTGAAGATCGTCTGCCAGCCGGTCAAGAAGACCAGAGCAAATGACTTGAATGCGCCGCCGATATCGCCCTGAAAGAGTTTTACAAACCCGGTCTTCATGTCGTTCCACATGAGCTTCAATGCTCCGCTGATCTCCTTCCAGTTGTTCCATAGTAGGAAGGCCGCCGCCGCGATCGCCAGATCACTAGGCCAATTGGATTCATGAGGAGTGCACGGCCAAGATTGACCACAGTCATCACAAGATAAGTTCCCATACGCGCTATCCATGGGATCAGCGGTG
lsequence	AGCGCCGATACACATGCTCAAACCGCGCATCGAAGTCTTCGATCAAGACGCTGAAGTAGTAGCCGTCCATGTTGAAGTTGAGCGGCTGACCGGCGTCACGCAGCGTCTCCAGCTCCGTGACGCGGTCACCAGCTGTCGCGCCAGTGATCCAGCCAGACCACTGGATGTTCTTGTAATCCAGACCGAGAACATCGACAACACGCTTGCCGCCTACCAGTTTGTGCACCACGAGCTTCTGTTTGGCGCCGATCGATACTGACTCTGGGACTTCCAGGCCGGTGAACTCGACATCTCCAACGATCAACCGCGTGGCAAACGGATCCCCGCCCGGAGCGAAGTTGTCCAGGAAGCTCGTAAAGCTCATCGTTTATCCCCTTGGATAGGCTGCGCTCGGGGTTCCTGGCATCAGCATGCTGCGGTTCGGATCGAAGCCCTGCGTCCCTGTCCGTGGCTTCGCGGCTTCCTTCGCCATCCGCTGGATTACCACGTCGCTGACTTGTTTGCCGTCGATGTACAGGTTGATGTTCTGTTGGCCATCGGCGCcAGACTTGCCCGGGACCGGAGCCACCAGCGGAGACCATGCTGGCTTTTTCTCCCCGCTTCCACGGAAATCATCGGCGAATGTAGGTTTTTGAGATCTGCATCGATGCTGGAAGAATCAGGTTTGCGCCAGCGATCAGCGTGTTGAAGATCGTCTGCCAGCCGGTCAAGAAGACCAGAGCAAATGACTTGAATGCGCCGCCGATATCGCCCTGAAAGAGTTTTACAAACCCGGTCTTCATGTCGTTCCACATGAGCTTCAATGCTCCGCTGATCTCCTTCCAGTTGTTCCATAGTAGGAAGGCCGCCGCCGCGATCGCCAGATCACTAGGCCAATTGGATTCATGAGGAGTGCACGGCCAAGATTGACCACAGTCATCACAAGATAAGTTCCCATACGCGCTATCCATGGGATCAGCGGTG
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B09090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B05050505050E0505050505050505050505050505050505050505050505050505050505050505050505030303030303030303030909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	144
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.05
perc_N	0.10
seq#	2
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_013_H05.x01.phd.1
asm_lend	1
asm_rend	589
seq_lend	1
seq_rend	589
best	0
comment	
db	sdsu
offset	0
lsequence	AGCGCCGATACACATGCTCAAACCGCGCATCGAAGTCTTCGATCAAGACGCTGAAGTAGTAGCCGTCCATGTTGAAGTTGAGCGGCTGACCGGCGTCACGCAGCGTCTCCAGCTCCGTGACGCGGTCACCAGCTGTCGCGCCAGTGATCCAGCCAGACCACTGGATGTTCTTGTAATCCAGACCGAGAACATCGACAACACGCTTGCCGCCTACCAGTTTGTGCACCACGAGCTTCTGTTTGGCGCCGATCGATACTGACTCTGGGACTTCCAGGCCGGTGAACTCGACATCTCCAACGATCAACCGCGTGGCAAACGGATCCCCGCCCGGAGCGAAGTTGTCCAGGAAGCTCGTAAAGCTCATCGTTTATCCCCTTGGATAGGCTGCGCTCGGGGTTCCTGGCATCAGCATGCTGCGGTTCGGATCGAAGCCCTGCGTCCCTGTCCGTGGCTTCGCGGCTTCCTTCGCCATCCGCTGGATTACCACGTCGCTGACTTGTTTGCCGTCGATGTACAGGTTGATGTTCTGTTGGCCATCGGCGCCAGACTTGCCCGGGACCGGAGCCACCAGCGGAGACCATGCTGGCTT

seq_name	SDSU_RFPERU_005_F02.x01.phd.1
asm_lend	539
asm_rend	963
seq_lend	1
seq_rend	424
best	0
comment	
db	sdsu
offset	538
lsequence	GGCGC-AGACTTGCCCGGGACCGGAGCCACCAGCGGAGACCATGCTGGCTTTTTCTCCCCGCTTCCACGGAAATCATCGGCGAATGTAGGTTTTTGAGATCTGCATCGATGCTGGAAGAATCAGGTTTGCGCCAGCGATCAGCGTGTTGAAGATCGTCTGCCAGCCGGTCAAGAAGACCAGAGCAAATGACTTGAATGCGCCGCCGATATCGCCCTGAAAGAGTTTTACAAACCCGGTCTTCATGTCGTTCCACATGAGCTTCAATGCTCCGCTGATCTCCTTCCAGTTGTTCCATAGTAGGAAGGCCGCCGCCGCGATCGCCAGATCACTAGGCCAATTGGATTCATGAGGAGTGCACGGCCAAGATTGACCACAGTCATCACAAGATAAGTTCCCATACGCGCTATCCATGGGATCAGCGGTG
|
sequence	TACGTTTCTGAATGCCGACTCGATACCCCTCAGGCCGGAGCGCGGCGGTCTTTTCGATATTGGCGATGACACGTTCAACGCCGCgAAGATCGGGTCTACTTGGCGCCCGTCCTTGAGCAGTTGATCGGCGTGGTTCCAGCCTTCACGTTCTTCAATGCGAGACATAGGGATGCTCCGAGTCAGTAGTTGGCGTACTGGGCGATCTCGTTCTGGCTGAGCTTGrGCTGCCGCACTTTCTGCCCATCGAGATGTTTGCGCAGCGCTTTCATGAAGAGGCAGATCAGCCTTGAGTTCGGCATACGCTTGACGCCGATCTTGTTGTCCGTGAGCTGATTCCTCAGTAATGArGCCAGCTCAAGAGTTGGCATCGGCTCACACATCGCGGCGAAGAACTCAGCGGTCATGAGGCGATTTTCTTTTGAGAAGTGGGCGAATACAGCGGCGCTTTGAGCTGCCGGGACAAGCTTGCGAAGGTGTGGTTTGAATCCATACAGAAGCCCTTCGTGAAGCAGTTTCTCGTTACTTCCACACGTCGCGATTACTTGGTCGTTGCGAATAGCGCTGCCGCGCTTGGCATTGTCGATCTTCCTTGCCTCCATAAGCGCAAGCAGTCGAGCGGCGCTTGCCATGTTCCCGACGTTTTTCAACTCTGGATTGGCGACCCCCAGCA
lsequence	TACGTTTCTGAATGCCGACTCGATACCCCTCAGGCCGGAGCGCGGCGGTCTTTTCGATATTGGCGATGACACGTTCAACGCCGC-gAAGATCGGGTCTACTTGGCGCCCGTCCTTGAGCAGTTGATCGGCGTGGTTCCAGCCTTCACGTTCT-TCAATGCGAGACATAGGGATGCTCCGAGTCAGTAGTTGGCGTACTGGGCGATCTCGTTCTGGCTGAGCTTGrGCTGCCGCACTTTCTGCCCATCGAGATGTTTGCGCAGCGCTTTCATGAAGAGGCAGATCAGCCTTGAGTTCGGCATACGCTTGACGCCGATCTTGTTGTCCGTGAGCTGATTCCTCAGTAATGArGCCAGCTCAAGAGTTGGCATCGGCTCACACATCGCGGCGAAGAACTCAGCGGTCATGAGGCGATTTTCTTTTGAGAAGTGGGCGAATACAGCGGCGCTTTGAGCTGCCGGGACAAGCTTGCGAAGGTGTGGTTTGAATCCATACAGAAGCCCTTCGTGAAGCAGTTTCTCGTTACTTCCACACGTCGCGATTACTTGGTCGTTGCGAATAGCGCTGCCGCGCTTGGCATTGTCGATCTTCCTTGCCTCCATAAGCGCAAGCAGTCGAGCGGCGCTTGCCATGTTCCCGACGTTTTTCAACTCTGGATTGGCGACCCCCAGCA
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0505050505030303030303030303030303030303030303030303030303030303030303030303030303030303030303030314030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030803030303030303030303030303030303030303030303030303030303030303030303030303030303030303030308030303030303030303030303030303030303030303030303031603030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303160303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	148
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.96
perc_N	0.45
seq#	3
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_003_G09.x01.phd.1
asm_lend	1
asm_rend	513
seq_lend	1
seq_rend	514
best	0
comment	
db	sdsu
offset	0
lsequence	TACGTTTCTGAATGCCGACTCGATACCCCTCAGGCCGGAGCGCGGCGGTCTTTTCGATATTGGCGATGACACGTTCAACGCCGCCGAAGATCGGGTCTACTTGGCGCCCGTCCTTGAGCAGTTGATCGGCGTGGTTCCAGCCTTCACGTTCT-TCAATGCGAGACATAGGGATGCTCCGAGTCAGTAGTTGGCGTACTGGGCGATCTCGTTCTGGCTGAGCTTGAGCTGCCGCACTTTCTGCCCATCGAGATGTTTGCGCAGCGCTTTCATGAAGAGGCAGATCAGCCTTGAGTTCGGCATACGCTTGACGCCGATCTTGTTGTCCGTGAGCTGATTCCTCAGTAATGAGGCCAGCTCAAGAGTTGGCATCGGCTCACACATCGCGGCGAAGAACTCAGCGGTCATGAGGCGATTTTCTTTTGAGAAGTGGGCGAATACAGCGGCGCTTTGAGCTGCCGGGACAAGCTTGCGAAGGTGTGGTTTGAATCCATACAGAAGCCCTTCGTGAAGCAGT

seq_name	SDSU_RFPERU_002_A01.x01.phd.1
asm_lend	36
asm_rend	252
seq_lend	1
seq_rend	218
best	0
comment	
db	sdsu
offset	35
lsequence	CGGAGCGCGGCGGTCTTTTCGATATTGGCGATGACACGTTCAACGCCGC-GAAGATCGGGTCTACTTGGCGCCCGTCCTTGAGCAGTTGATCGGCGTGGTTCCAGCCTTCACGTTCTATCAATGCGAGACATAGGGATGCTCCGAGTCAGTAGTTGGCGTACTAGGCGATCTCGTTCTGGCTGAGCTTGAGCTGCCGCACTTTCTGCCCATCGAGATGT

seq_name	SDSU_RFPERU_002_D08.x01.phd.1
asm_lend	85
asm_rend	670
seq_lend	1
seq_rend	586
best	0
comment	
db	sdsu
offset	85
lsequence	GAAGATCGGGTCTACTTGGCGCCCGTCCTTGAGCAGTTGATCGGCGTGGTTCCAGCCTTCACGTTCT-TCAATGCGAGACATAGGGATGCTCCGAGTCAGTAGTTGGCGTACTGGGCGATCTCGTTCTGGCTGAGCTTGGGCTGCCGCACTTTCTGCCCATCGAGATGTTTGCGCAGCGCTTTCATGAAGAGGCAGATCAGCCTTGAGTTCGGCATACGCTTGACGCCGATCTTGTTGTCCGTGAGCTGATTCCTCAGTAATGAAGCCAGCTCAAGAGTTGGCATCGGCTCACACATCGCGGCGAAGAACTCAGCGGTCATGAGGCGATTTTCTTTTGAGAAGTGGGCGAATACAGCGGCGCTTTGAGCTGCCGGGACAAGCTTGCGAAGGTGTGGTTTGAATCCATACAGAAGCCCTTCGTGAAGCAGTTTCTCGTTACTTCCACACGTCGCGATTACTTGGTCGTTGCGAATAGCGCTGCCGCGCTTGGCATTGTCGATCTTCCTTGCCTCCATAAGCGCAAGCAGTCGAGCGGCGCTTGCCATGTTCCCGACGTTTTTCAACTCTGGATTGGCGACCCCCAGCA
|
sequence	CGCTACCTGCTGAAGATGATATTCAACGTCGCAATTGGCGAAGAAGACGATGACGGCAACGGCGCGTCAGGCGATGACTTCCGTAACGCAATAATTGCTGACCTGATCACAAAGGTCGCAGCAGCACCAGATAAGGCAGCGCTGCAAGAGGCTTGGCAATCGGGTCTCAAAGTACTCCACGCCGCCAGGGATTCCGCCGGCGCCGACGAGCTTCGCAACGCAGTAAACAAGCGGAAATCTGAACTGGAGGTCTAGACATGATCCTCATCGAATGCGAACAAGGGAGCCCGGCATGGCATCAAGCACGCGCCGGCTGCATAACTGCCAGCATGTTCGGCGTTGCGCGCACCAAGGTTGGCGGACTGGACGAAAAGCAGCAGATGTTCGTCGCTGCGGTACAGGCCGGCATGACAGAAAAAGAAGCCATGGCTGAGGCTGGCTACAAGTCTGCGCCGAAGGCCGAGTCGGTTAGGCTGGCACTCGCTGGCAAACCCGTTGGCCAGCCTTCGGATGCCGCTCTGAACTACGCCTTCACCGTGGCGGTCGAGCGCATCAGTGGCGAGTCGCTTGATGGTGGCTTCGAGACGTGGCAAATGAAGCGCGGTCATGAGCTTGAGCCAATGGCCCGGATGGAACATGAGCTGAAGTCCGGGCTCATGGTTCAGCGTGCCGGCTTTGTTACCACCGATGATGGGGCGTTCGGCGCGAGCGCTGACGGCCTGATCGGTGAG
lsequence	CGCTACCTGCTGAAGATGATATTCAACGTCGCAATTGGCGAAGAAGACGATGACGGCAACGGCGCGTCAGGCGATGACTTCCGTAACGCAATAATTGCTGACCTGATCACAAAGGTCGCAGCAGCACCAGATAAGGCAGCGCTGCAAGAGGCTTGGCAATCGGGTCTCAAAGTACTCCACGCCGCCAGGGATTCCGCCGGCGCCGACGAGCTTCGCAACGCAGTAAACAAGCGGAAATCTGAACTGGAGGTCTAGACATGATCCTCATCGAATGCGAACAAGGGAGCCCGGCATGGCATCAAGCACGCGCCGGCTGCATAACTGCCAGCATGTTCGGCGTTGCGCGCACCAAGGTTGGCGGACTGGACGAAAAGCAGCAGATGTTCGTCGCTGCGGTACAGGCCGGCATGACAGAAAAAGAAGCCATGGCTGAGGCTGGCTACAAGTCTGCGCCGAAGGCCGAGTCGGTTAGGCTGGCACTCGCTGGCAAACCCGTTGGCCAGCCTTCGGATGCCGCTCTGAACTACGCCTTCACCGTGGCGGTCGAGCGCATCAGTGGCGAGTCGCTTGATGGTGGCTTCGAGACGTGGCAAATGAAGCGCGGTCATGAGCTTGAGCCAATGGCCCGGATGGAACATGAGCTGAAGTCCGGGCTCATGGTTCAGCGTGCCGGCTTTGTTACCACCGATGATGGGGCGTTCGGCGCGAGCGCTGACGGCCTGATCGGTGAG
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030505050B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	185
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.44
perc_N	0.00
seq#	2
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_006_H08.x01.phd.1
asm_lend	1
asm_rend	484
seq_lend	1
seq_rend	484
best	0
comment	
db	sdsu
offset	0
lsequence	CGCTACCTGCTGAAGATGATATTCAACGTCGCAATTGGCGAAGAAGACGATGACGGCAACGGCGCGTCAGGCGATGACTTCCGTAACGCAATAATTGCTGACCTGATCACAAAGGTCGCAGCAGCACCAGATAAGGCAGCGCTGCAAGAGGCTTGGCAATCGGGTCTCAAAGTACTCCACGCCGCCAGGGATTCCGCCGGCGCCGACGAGCTTCGCAACGCAGTAAACAAGCGGAAATCTGAACTGGAGGTCTAGACATGATCCTCATCGAATGCGAACAAGGGAGCCCGGCATGGCATCAAGCACGCGCCGGCTGCATAACTGCCAGCATGTTCGGCGTTGCGCGCACCAAGGTTGGCGGACTGGACGAAAAGCAGCAGATGTTCGTCGCTGCGGTACAGGCCGGCATGACAGAAAAAGAAGCCATGGCTGAGGCTGGCTACAAGTCTGCGCCGAAGGCCGAGTCGGTTAGGCTGGCACTCGC

seq_name	SDSU_RFPERU_008_B02.x01.phd.1
asm_lend	167
asm_rend	731
seq_lend	1
seq_rend	565
best	0
comment	
db	sdsu
offset	166
lsequence	TCAAAGTACTCCACGCCGCCAGGGATTCCGCCGGCGCCGACGAGCTTCGCAACGCAGTAAACAAGCGGAAATCTGAACTGGAGGTCTAGACATGATCCTCATCGAATGCGAACAAGGGAGCCCGGCATGGCATCAAGCACGCGCCGGCTGCATAACTGCCAGCATGTTCGGCGTTGCGCGCACCAAGGTTGGCGGACTGGACGAAAAGCAGCAGATGTTCGTCGCTGCGGTACAGGCCGGCATGACAGAAAAAGAAGCCATGGCTGAGGCTGGCTACAAGTCTGCGCCGAAGGCCGAGTCGGTTAGGCTGGCACTCGCTGGCAAACCCGTTGGCCAGCCTTCGGATGCCGCTCTGAACTACGCCTTCACCGTGGCGGTCGAGCGCATCAGTGGCGAGTCGCTTGATGGTGGCTTCGAGACGTGGCAAATGAAGCGCGGTCATGAGCTTGAGCCAATGGCCCGGATGGAACATGAGCTGAAGTCCGGGCTCATGGTTCAGCGTGCCGGCTTTGTTACCACCGATGATGGGGCGTTCGGCGCGAGCGCTGACGGCCTGATCGGTGAG
|
sequence	GTGGTCGCCGGATACTTGCTTGTCGAGTGCGCTCATGCTGCTTCCCCTTTCGCTGATTCAAGATGTGTGACGCATGCGGCCTTGCGGCCTTTTCGTTCTCGCCGGAGTAGAGAATTTTCGAGGCAGGCGCTGGTGTGCGGGCGATGAAAGCGTTGGTCGACTGCATCCGGTACCGGCTGACCAGGTAGCCTTCCGCGGATGCGAGGCAGTTGGTGCTGATGCCTTTCCAGTTCATGGCCGAATCCCCCGCCGAGCTCTATCCTTGCGCCACAAATAGCGGCAGAGTTCGAGCAGGCCGCCCCCGAGTACCAACAGAAATCCGAAGTAGAAGTGGACGAGATTCATGCTGCTGCTCTCCTGAGTTCACGGGTCTTGGCGCGGTATTCGGCGGTGATGGCCTTGAGGTCTTCGATGGTGTAGCGCTTGGGTTCGTGGGGGCCTTCCAGCCACTCGACAAGATCGGTGCCGATGCGCTTCACCAGTTCGATGCGGTATTCAACGATTGCCCCGGACTTCCCCATGTyGCAGTTGCGATTGCACTGCAGATGGACGTTCAGCGGCTCGAAACGCAACTCTGGGCACGACTTGACGGTGCGGTAGTGGCCGGCTGCGTACTGGACGTTCGCGGTCGTCCCGCATGAGATGCATGGCTTGCCGGCGTCTCTGGCGCGGATCCAGGCGTTGAACGCTATCTGGCAGTCACGCATGTACCGGCCCTTCGTCTTAACGCGCTCCTTGGCCGCTCTCAGCTCATTGCGGCTACATCGGCAAGGGCTTTGCGAGCCTTGTCGGCGTTCTCAGGACTTGATCGCCAGTCCGCAGGCAGGACTGCAGACCTTCTGACCGAGGCGCTGAGGGTCGAATGAGGCCATGCACTCTGGGTTGGCGCAGATCTTGGGTTTGCGGGGTTTGGACGGAAGAGTCATTCCTCGGCCCCTCCGCACGCTTGCGAGATATGCATTCCGCGCCCGCTCGTTGCGCGCCTTTTGCCGGCGCTGGTTGACCGGCCCCATCAAGC
lsequence	GTGGTCGCCGGATACTTGCTTGTCGAGTGCGCTCATGCTGCTTCCCCTTTCGCTGATTCAAGATGTGTGACGCATGCGGCCTTGCGGCCTTTTCGTTCTCGCCGGAGTAGAGAATTTTCGAGGCAGGCGCTGGTGTGCGGGCGATGAAAGCGTTGGTCGACTGCATCCGGTACCGGCTGACCAGGTAGCCTTCCGCGGATGCGAGGCAGTTGGTGCTGATGCCTTTCCAGTTCATGGCCGAATCCCCCGCCGAGCTCTATCCTTGCGCCACAAATAGCGGCAGAGTTCGAGCAGGCCGCCCCCGAGTACCAACAGAAATCCGAAGTAGAAGTGGACGAGATTCATGCTGCTGCTCTCCTGAGTTCACGGGTCTTGGCGCGGTATTCGGCGGTGATGGCCTTGAGGTCTTCGATGGTGTAGCGCTTGGGTTCGTGGGGGCCTTCCAGCCACTCGACAAGATCGGTGCCGATGCGCTTCACCAGTTCGATGCGGTATTCAACGATTGCCCCGGACTTCCCCATGTyGCAGTTGCGATTGCACTGCAGATGGACGTTCAGCGGCTCGAAACGCAACTCTGGGCACGACTTGACGGTGCGGTAGTGGCCGGCTGCGTACTGGACGTTCGCGGTCGTCCCGCATGAGATGCATGGCTTGCCGGCGTCTCTGGCGCGGATCCAGGCGTTGAACGCTATCTGGCAGTCACGCATGTACCGGCCCTTCGTCTTAACGCGCTCCTTGGCCGCTCTCAGCTCATTGCGGCTACATCGGCAAGGGCTTTGCGAGCCTTGTCGGCGTTCTCAGGACTTGATCGCCAGTCCGCAGGCAGGACTGCAGACCTTCTGACCGAGGCGCTGAGGGTCGAATGAGGCCATGCACTCTGGGTTGGCGCAGATCTTGGGTTTGCGGGGTTTGGACGGAAGAGTCATTCCTCGGCCCCTCCGCACGCTTGCGAGATATGCATTCCGCGCCCGCTCGTTGCGCGCCTTTTGCCGGCGCTGGTTGACCGGCCCCATCAAGC
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B09090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0505050505050505050505050505050505050505050505050505050505050505050505050505050503030303030303030303030303030303030303030303030303030303030303030303030303030305050505050505050505050505050505050505050503030303030303030303030303030303030303030316030303030303030303030303030303030303030303030303030303030303030303030303090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	210
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.18
perc_N	0.10
seq#	3
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_002_B07.x01.phd.1
asm_lend	1
asm_rend	486
seq_lend	1
seq_rend	486
best	0
comment	
db	sdsu
offset	0
lsequence	GTGGTCGCCGGATACTTGCTTGTCGAGTGCGCTCATGCTGCTTCCCCTTTCGCTGATTCAAGATGTGTGACGCATGCGGCCTTGCGGCCTTTTCGTTCTCGCCGGAGTAGAGAATTTTCGAGGCAGGCGCTGGTGTGCGGGCGATGAAAGCGTTGGTCGACTGCATCCGGTACCGGCTGACCAGGTAGCCTTCCGCGGATGCGAGGCAGTTGGTGCTGATGCCTTTCCAGTTCATGGCCGAATCCCCCGCCGAGCTCTATCCTTGCGCCACAAATAGCGGCAGAGTTCGAGCAGGCCGCCCCCGAGTACCAACAGAAATCCGAAGTAGAAGTGGACGAGATTCATGCTGCTGCTCTCCTGAGTTCACGGGTCTTGGCGCGGTATTCGGCGGTGATGGCCTTGAGGTCTTCGATGGTGTAGCGCTTGGGTTCGTGGGGGCCTTCCAGCCACTCGACAAGATCGGTGCCGATGCGCTTCACCAGTTCG

seq_name	SDSU_RFPERU_015_C06.x01.phd.1
asm_lend	403
asm_rend	560
seq_lend	1
seq_rend	158
best	0
comment	
db	sdsu
offset	402
lsequence	AGGTCTTCGATGGTGTAGCGCTTGGGTTCGTGGGGGCCTTCCAGCCACTCGACAAGATCGGTGCCGATGCGCTTCACCAGTTCGATGCGGTATTCAACGATTGCCCCGGACTTCCCCATGTTGCAGTTGCGATTGCACTGCAGATGGACGTTCAGCGG

seq_name	SDSU_RFPERU_015_E04.x01.phd.1
asm_lend	463
asm_rend	1018
seq_lend	1
seq_rend	556
best	0
comment	
db	sdsu
offset	462
lsequence	GTGCCGATGCGCTTCACCAGTTCGATGCGGTATTCAACGATTGCCCCGGACTTCCCCATGTCGCAGTTGCGATTGCACTGCAGATGGACGTTCAGCGGCTCGAAACGCAACTCTGGGCACGACTTGACGGTGCGGTAGTGGCCGGCTGCGTACTGGACGTTCGCGGTCGTCCCGCATGAGATGCATGGCTTGCCGGCGTCTCTGGCGCGGATCCAGGCGTTGAACGCTATCTGGCAGTCACGCATGTACCGGCCCTTCGTCTTAACGCGCTCCTTGGCCGCTCTCAGCTCATTGCGGCTACATCGGCAAGGGCTTTGCGAGCCTTGTCGGCGTTCTCAGGACTTGATCGCCAGTCCGCAGGCAGGACTGCAGACCTTCTGACCGAGGCGCTGAGGGTCGAATGAGGCCATGCACTCTGGGTTGGCGCAGATCTTGGGTTTGCGGGGTTTGGACGGAAGAGTCATTCCTCGGCCCCTCCGCACGCTTGCGAGATATGCATTCCGCGCCCGCTCGTTGCGCGCCTTTTGCCGGCGCTGGTTGACCGGCCCCATCAAGC
|
sequence	AGCCTGCTGGCGGGATGCTCTACTTGTACTTCACGGACAATCTCGGGACCGGCGGTGGCGGGAATGAsCCGTATCTTTCGGGAGCGTTGGCCAGGGCGAGCGCCAATGACCTTCAGTGGTCGGCCTCGCCATCCGCAGGATCGGTTGTGsCGGGGCCTAATGGCGTGCTGAGCGCTGCCTCCAAGGTCACTGTTAATCCCGTCAACTTTCAGATCGATACATCATCTATCACCGCCGGCGTCACTGAGGAGGTAGTCTACCGGATAGACTTTGGCTCGACTCAGATCGGTGACCTCTTCATCGAGGCATATGGTTCGTGCGACACGCGTGGCGTCATCCTCGACAACAATAAGGTGGTCAATCTGGCCATGGGCGGCCACAGCATAGGCGGCTGGCTTGGTCTTGAGGCCTCATATTCAAGCGAGACGGCCGATCACGTCGCACAAATCCTGAATCACGTCCCTGTTCAGCCATCGCACGTCATTACCCA
lsequence	AGCCTGCTGGCGGGATGCTCTACTTGTACTTCACGGACAATCTCGGGACCGGCGGTGGCGGGAATGAsCCGTATCTTTCGGGAGCGTTGGCCAGGGCGAGCGCCAATGACCTTCAGTGGTCGGCCTCGCCATCCGCAGGATCGGTTGTGsCGGGGCCTAATGGCGTGCTGAGCGCTGCCTCCAAGGTCACTGTTAATCCCGTCAACTTTCAGATCGATACATCATCTATCACCGCCGGCGTCACTGAGGAGGTAGTCTACCGGATAGACTTTGGCTCGACTCAGATCGGTGACCTCTTCATCGAGGCATATGGTTCGTGCGACACGCGTGGCGTCATCCTCGACAACAATAAGGTGGTCAATCTGGCCATGGGCGGCCACAGCATAGGCGGCTGGCTTGGTCTTGAGGCCTCATATTCAAGCGAGACGGCCGATCACGTCGCACAAATCCTGAATCACGTCCCTGTTCAGCCATCGCACGTCATTACCCA
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0505050505050505050505050505050303030303030303030303030303030303030303030303030303031603030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030316030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030305050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	453
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.66
perc_N	0.41
seq#	2
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_015_H03.x01.phd.1
asm_lend	1
asm_rend	346
seq_lend	1
seq_rend	346
best	0
comment	
db	sdsu
offset	0
lsequence	AGCCTGCTGGCGGGATGCTCTACTTGTACTTCACGGACAATCTCGGGACCGGCGGTGGCGGGAATGACCCGTATCTTTCGGGAGCGTTGGCCAGGGCGAGCGCCAATGACCTTCAGTGGTCGGCCTCGCCATCCGCAGGATCGGTTGTGCCGGGGCCTAATGGCGTGCTGAGCGCTGCCTCCAAGGTCACTGTTAATCCCGTCAACTTTCAGATCGATACATCATCTATCACCGCCGGCGTCACTGAGGAGGTAGTCTACCGGATAGACTTTGGCTCGACTCAGATCGGTGACCTCTTCATCGAGGCATATGGTTCGTGCGACACGCGTGGCGTCATCCTCGACAA

seq_name	SDSU_RFPERU_007_E09.x01.phd.1
asm_lend	26
asm_rend	490
seq_lend	1
seq_rend	465
best	0
comment	
db	sdsu
offset	25
lsequence	GTACTTCACGGACAATCTCGGGACCGGCGGTGGCGGGAATGAGCCGTATCTTTCGGGAGCGTTGGCCAGGGCGAGCGCCAATGACCTTCAGTGGTCGGCCTCGCCATCCGCAGGATCGGTTGTGGCGGGGCCTAATGGCGTGCTGAGCGCTGCCTCCAAGGTCACTGTTAATCCCGTCAACTTTCAGATCGATACATCATCTATCACCGCCGGCGTCACTGAGGAGGTAGTCTACCGGATAGACTTTGGCTCGACTCAGATCGGTGACCTCTTCATCGAGGCATATGGTTCGTGCGACACGCGTGGCGTCATCCTCGACAACAATAAGGTGGTCAATCTGGCCATGGGCGGCCACAGCATAGGCGGCTGGCTTGGTCTTGAGGCCTCATATTCAAGCGAGACGGCCGATCACGTCGCACAAATCCTGAATCACGTCCCTGTTCAGCCATCGCACGTCATTACCCA
|
sequence	GAACCGGGGCGTCAGGTGCGCCACGCCGTTAAGCGCCGTGCCGTCAGCACGGTCACGTTGCTGGAGAACGTCAGGTGCCCGAGATGCCCATTGGCGAGGTGGAGACGTTCGAGCCGTCCACTGCCACACCGGTCAGGGTGTAGACGTTGGAACCAACCAGCACGCCGGCCGTGTTGGTGCCGGATACAGCCACCATCTGGCCGTTCACCAGAACGGTCTGGAAGCCACGCACGTCGTCGACCGAAATGGTmGCAGCAGGTGCGCCCAGAGTGGTACGAACACGGGTGTTGCCGCCCAGATAGGCGTTGAACAGCGCGTTACGAGCCAGACGATCGAGGGTCTGACGAGCCTGGATGCCGTTGGTCTTCGCGTTCTTGAGGAACTGGTTCGCGATACCGACCTGGCTGGTCACGACGTTGAGGTCGATGGTGTCAGCGTACATGTTGATGCCGAGCGTGTACTGCTCGACGGTGAACGCTGACGGGGTCAGcCGTTGTCCAGGTTGGTGTTACCCGACGGGGTCAGCGGAGTGTGCTGGCGCCTTCA
lsequence	GAACCGGGGCGTCAGGTGCGCCACGCCGTTAAGCGCCGTGCCGTCAGCACGGTCACGTTGCTGGAGAACGTCAGGTGCCCGAGATGCCCATTGGCGAGGTGGAGACGTTCGAGCCGTCCACTGCCACACCGGTCAGGGTGTAGACGTTGGAACCAACCAGCACGCCGGCCGTGTTGGTGCCGGATACAGCCACCATCTGGCCGTTCACCAGAACGGTCTGGAAGCCACGCACGTC-GTCGACCGAAATGGTmGCAGCAGGTGCGCCCAGAGTGGTACGAACACGGGTGTTGCCGCCCAGATAGGCGTTGAACAGCGCGTTACGAGCCAGACGATCGAGGGTCTGACGAGCCTGGATGCCGTTGGTCTTCGCGTTCTTGAGGAACTGGTTCGCGATACCGACCTGGCTGGTCACGACGTTGAGGTCGATGGTGTCAGCGTACATGTTGATGCCGAGCGTGTACTGCTCGACGGTGAACGCTGACGGGGTCAG-cCGTTGTCCAGGTTGGTGTTACCCGACGGGGTCAGCGGAGTGTGCTGGCGCCTTCA
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090903030303030303030303030303030303030303030303030303030303030303030303030303030303030803030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303080303030303030303030303030303031603030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030305050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050E05050505050505050505050505050505050505050B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	500
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	2.21
perc_N	0.37
seq#	3
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_004_H12.x01.phd.1
asm_lend	1
asm_rend	369
seq_lend	1
seq_rend	370
best	0
comment	
db	sdsu
offset	0
lsequence	GAACCGGGGCGTCAGGTGCGCCACGCCGTTAAGCGCCGTGCCGTCAGCACGGTCACGTTGCTGGAGAACGTCAGGTGCCCGAGATGCCCATTGGCGAGGTGGAGACGTTCGAGCCGTCCACTGCCACACCGGTCAGGGTGTAGACGTTGGAACCAACCAGCACGCCGGCCGTGTTGGTGCCGGATACAGCCACCATCTGGCCGTTCACCAGAACGGTCTGGAAGCCACGCACGTCAGTCGACCGAAATGGTCGCAGCAGGTGCGCCCAGAGTGGTACGAACACGGGTGTTGCCGCCCAGATAGGCGTTGAACAGCGCGTTACGAGCCAGACGATCGAGGGTCTGACGAGCCTGGATGCCGTTGGTCTTCG

seq_name	SDSU_RFPERU_010_D10.x01.phd.1
asm_lend	97
asm_rend	546
seq_lend	2
seq_rend	451
best	0
comment	
db	sdsu
offset	96
lsequence	AGGTGGAGACGTTCGAGCCGTCCACTGCCACACCGGTCAGGGTGTAGACGTTGGAACCAACCAGCACGCCGGCCGTGTTGGTGCCGGATACAGCCACCATCTGGCCGTTCACCAGAACGGTCTGGAAGCCACGCACGTC-GTCGACCGAAATGGTAGCAGCAGGTGCGCCCAGAGTGGTACGAACACGGGTGTTGCCGCCCAGATAGGCGTTGAACAGCGCGTTACGAGCCAGACGATCGAGGGTCTGACGAGCCTGGATGCCGTTGGTCTTCGCGTTCTTGAGGAACTGGTTCGCGATACCGACCTGGCTGGTCACGACGTTGAGGTCGATGGTGTCAGCGTACATGTTGATGCCGAGCGTGTACTGCTCGACGGTGAACGCTGACGGGGTCAG-CCGTTGTCCAGGTTGGTGTTACCCGACGGGGTCAGCGGAGTGTGCTGGCGCCTTCA

seq_name	SDSU_RFPERU_006_D03.x01.phd.1
asm_lend	125
asm_rend	510
seq_lend	2
seq_rend	387
best	0
comment	
db	sdsu
offset	124
lsequence	CACACCGGTCAGG-TGTAGACGTTGGAACCAACCAGCACGCCGGCCGTGTTGGTGCCGGATACAGCCACCATCTGGCCGTTCACCAGAACGGTCTGGAAGCCACGCACGTC-GTCGACCGAAATGGTCGCAGCAGGTGCGCCCAGAGTGGTACGAACACGGGTGTTGCCGCCCAGATAGGCGTTGAACAGCGCGTTACGAGCCAGACGATCGAGGGTCTGACGAGCCTGGATGCCGTTGGTCTTCGCGTTCTTGAGGAACTGGTTCGCGATACCGACCTGGCTGGTCACGACGTTGAGGTCGATGGTGTCAGCGTACATGTTGATGCCGAGCGTGTACTGCTCGACGGTGAACGCTGACGGGGTCAGGCCGTTGTCCAGGTTGGTGTT
|
sequence	CTTGCTGTAGGAACGCCTGCACACCGCGGTTGCCGCTCATGACCGCGTCCTTCTCGTTGTCGTCGGAGAGCGATCGCCGAAGTCCAGGTTCGTCTCGCCAGGAATGCCTACCTGCGTATCCTCCGCGCCCGGCTCCTGGTCGACGTCCGGCTGGTTGACGAAGCCGGCGTTCGGGCCCTGCATGGGGTTCGACGTGTAGAGGGGATAGCCGCCTGCGCCGGCTTGGAACTGCGAGCCTTTCGCGGGCTTCTTCTCGCCCGATGCGCCAATGCTCGCGTCCGTGATGGGGCTCTGGCCCTGATTCTGAAAGATGCTGTTGAACGCCTGCAGCTGCTCCTGCTGCTGGCTGGTCGCCTCCCACTCCGCCATCGAGCGGAGGTACGCGTCCATCATGGGGTTGCCGCCCTCGATGCCCGTCTTCAGATTGCGGTCGACATCGCCGCGAGGCTGCTGCCAGTCTTGATATGTTCGTCGCCGTGTTCGCCCCA
lsequence	CTTGCTGTAGGAACGCCTGCACACCGCGGTTGCCGCTCATGACCGCGTCCTTCTCGTTGTCGTCGGAGAGCGATCGCCGAAGTCCAGGTTCGTCTCGCCAGGAATGCCTACCTGCGTATCCTCCGCGCCCGGCTCCTGGTCGACGTCCGGCTGGTTGACGAAGCCGGCGTTCGGGCCCTGCATGGGGTTCGACGTGTAGAGGGGATAGCCGCCTGCGCCGGCTTGGAACTGCGAGCCTTTCGCGGGCTTCTTCTCGCCCGATGCGCCAATGCTCGCGTCCGTGATGGGGCTCTGGCCCTGATTCTGAAAGATGCTGTTGAACGCCTGCAGCTGCTCCTGCTGCTGGCTGGTCGCCTCCCACTCCGCCATCGAGCGGAGGTACGCGTCCATCATGGGGTTGCCGCCCTCGATGCCCGTCTTCAGATTGCGGTCGACATCGCCGCGAGGCTGCTGCCAGTCTTGATATGTTCGTCGCCGTGTTCGCCCCA
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B09090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B050505050505050505050505050505050505050505050505050505050505050505050505050505050303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303050505050505050505050505050505050505050505050505050505050505050505050505050505050505050505050B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	613
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.35
perc_N	0.00
seq#	2
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_013_C08.x01.phd.1
asm_lend	1
asm_rend	408
seq_lend	1
seq_rend	408
best	0
comment	
db	sdsu
offset	0
lsequence	CTTGCTGTAGGAACGCCTGCACACCGCGGTTGCCGCTCATGACCGCGTCCTTCTCGTTGTCGTCGGAGAGCGATCGCCGAAGTCCAGGTTCGTCTCGCCAGGAATGCCTACCTGCGTATCCTCCGCGCCCGGCTCCTGGTCGACGTCCGGCTGGTTGACGAAGCCGGCGTTCGGGCCCTGCATGGGGTTCGACGTGTAGAGGGGATAGCCGCCTGCGCCGGCTTGGAACTGCGAGCCTTTCGCGGGCTTCTTCTCGCCCGATGCGCCAATGCTCGCGTCCGTGATGGGGCTCTGGCCCTGATTCTGAAAGATGCTGTTGAACGCCTGCAGCTGCTCCTGCTGCTGGCTGGTCGCCTCCCACTCCGCCATCGAGCGGAGGTACGCGTCCATCATGGGGTTGCCGCCCTC

seq_name	SDSU_RFPERU_015_A05.x01.phd.1
asm_lend	237
asm_rend	488
seq_lend	1
seq_rend	252
best	0
comment	
db	sdsu
offset	236
lsequence	CTTTCGCGGGCTTCTTCTCGCCCGATGCGCCAATGCTCGCGTCCGTGATGGGGCTCTGGCCCTGATTCTGAAAGATGCTGTTGAACGCCTGCAGCTGCTCCTGCTGCTGGCTGGTCGCCTCCCACTCCGCCATCGAGCGGAGGTACGCGTCCATCATGGGGTTGCCGCCCTCGATGCCCGTCTTCAGATTGCGGTCGACATCGCCGCGAGGCTGCTGCCAGTCTTGATATGTTCGTCGCCGTGTTCGCCCCA
|
sequence	TCGGCTTTCGGCGCAACCACCGCCACCAGCCAGCTGGCTACCACTGACCTGCTGACCCTCGGCACCATCGAGGACGCGGTTGCTGCCCTGCGCAACAACACCGGCATGCAGGACGAGATGTTCAACCTGTACCTCGACAACGTGTCGATGCGCCAGCTGTTCGCCGACGGCGACTTCAAGCTGATGTACCAAGGCCAATACGGCTCGCCTGAAGCGCGTCAGGGCAAAGTGTTCCAGCTGAyGGGTGTGAACTTCATCCCTACCACTGAAGCGCTGACCCAAGTCAAGGGTTCGCTGGCCACTCCGGTGCGCCGTCCAATCCTGTGCGCTyCTGGTGCACTGGTGGAAGGTGACTTCGCCGGCATCATGCAGAAAGCCCATGAAACCTGGGGCATCAACTCGGAAGTGCAGTTTGTGGACGACGTTGCCCAAGTCGTGCGCGCGCCGCTCGACCGCCTGCAACAGATCGTTGCCCAGTCGTGGTTCTGGATCGGCC
lsequence	TCGGCTTTCGGCGCAACCACCGCCACCAGCCAGCTGGCTACCACTGACCTGCTGACCCTCGGCACCATCGAGGACGCGGTTGCTGCCCTGCGCAACAACACCGGCATGCAGGACGAGATGTTCAACCTGTACCTCGACAACGTGTCGATGCGCCAGCTGTTCGCCGACGGCGACTTCAAGCTGATGTACCAAGGCCAATACGGCTCGCCTGAAGCGCGTCAGGGCAAAGTGTTCCAGCTGAyGGGTGTGAACTTCATCCCTACCACTGAAGCGCTGACCCAAGTCAAGGGTTCGCTGGCCACTCCGGTGCGCCGTCCAATCCTGTGCGCTyCTGGTGCACTGGTGGAAGGTGACTTCGCCGGCATCATGCAGAAAGCCCATGAAACCTGGGGCATCAACTCGGAAGTGCAGTTTGTGGACGACGTTGCCCAAGTCGTGCGCGCGCCGCTCGACCGCCTGCAACAGATCGTTGCCCAGTCGTGGTTCTGGATCGGCC
quality	0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B09090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B05050505050505050505050505050505051605050505050505050505050505050505050505050505030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303160303030303030303030303030303030303030303030303030303030303050505050505050E05050505050505050505050505050505050B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id	668
seq_id	
com_name	
type	
method	asmg
ed_status	
redundancy	1.32
perc_N	0.40
seq#	2
full_cds	
cds_start	
cds_end	
ed_pn	GRA
ed_date	08/25/07 22:59:00
comment	
frameshift	

seq_name	SDSU_RFPERU_012_H02.x01.phd.1
asm_lend	1
asm_rend	385
seq_lend	1
seq_rend	385
best	0
comment	
db	sdsu
offset	0
lsequence	TCGGCTTTCGGCGCAACCACCGCCACCAGCCAGCTGGCTACCACTGACCTGCTGACCCTCGGCACCATCGAGGACGCGGTTGCTGCCCTGCGCAACAACACCGGCATGCAGGACGAGATGTTCAACCTGTACCTCGACAACGTGTCGATGCGCCAGCTGTTCGCCGACGGCGACTTCAAGCTGATGTACCAAGGCCAATACGGCTCGCCTGAAGCGCGTCAGGGCAAAGTGTTCCAGCTGATGGGTGTGAACTTCATCCCTACCACTGAAGCGCTGACCCAAGTCAAGGGTTCGCTGGCCACTCCGGTGCGCCGTCCAATCCTGTGCGCTCCTGGTGCACTGGTGGAAGGTGACTTCGCCGGCATCAAGCAGAAAGCCCATGAAA

seq_name	SDSU_RFPERU_010_B06.x01.phd.1
asm_lend	225
asm_rend	496
seq_lend	1
seq_rend	272
best	0
comment	
db	sdsu
offset	224
lsequence	CAAAGTGTTCCAGCTGACGGGTGTGAACTTCATCCCTACCACTGAAGCGCTGACCCAAGTCAAGGGTTCGCTGGCCACTCCGGTGCGCCGTCCAATCCTGTGCGCTTCTGGTGCACTGGTGGAAGGTGACTTCGCCGGCATCATGCAGAAAGCCCATGAAACCTGGGGCATCAACTCGGAAGTGCAGTTTGTGGACGACGTTGCCCAAGTCGTGCGCGCGCCGCTCGACCGCCTGCAACAGATCGTTGCCCAGTCGTGGTTCTGGATCGGCC
BioPerl-1.007002/t/data/sbay_c127.fas000444000766000024       136113155576321 17056 0ustar00cjfieldsstaff000000000000>sbay:sbay_c127 
AGACGGCCCGAGCAAGTGGCTACTCAAGAAGTAATACATTTAAAAGGCAG
TATTATTCCGAGCAAGTGGCTACTCAAGAAGTAATACATTCGGAAAACGT
TATAAAGTTATCTAAAAATCTACATACAACGTTGCTTACTTTTGACAAAC
TCGATGATCGTTTAACAAATGTCACTCAAGTTGTTTCGCCCTTGGGTGAT
AAATTAGAAACAGCTATCAAGAAAAAGCAAAACTATATTCAAAGTGTGGA
ATTAATTCGTAGGTTCAATGACTTCTATTCCATGGGTAAATCAGATATTG
TTGAACAATTAAGATTGTCTAAAAACTGGAAATTTAACTTAAAGTCTGTG
ATACTAATGAAAAATCTACTAATATTATCATCTAAATTAGAGACAAATTC
AATACCAAAGACAATTAATACAAAATTGATTATTGAAAAATATTCTGAGA
TGATGGAAAATAAACTGTTAGAAAATTTCAATTCTGCCTATAGAGAGAAT
AATTTCACCAAGTTGAATGAAATCGCAATCATCCTCAATAATTTTAATGG
TGGTGTTAATGTCATTCAAAGTTTCATCAATCAGCACGACTATTTCATTG
ACACAAAGCAAATCGACTTAGAGAATGAATTTGAAAATGTTTTCATAAAG
AACGTGAAATTTAAGGAAAGACTGGTTGATTTCGAGAGTCACAGTGTTAT
TGTTGAAGCATCCATGCAAAA
BioPerl-1.007002/t/data/sbay_c545-yeast.BLASTZ.PSL000444000766000024      2705313155576321 21116 0ustar00cjfieldsstaff000000000000916	617	0	0	13	69	10	86	+	I	230203	139870	141472	sbay_c545	28791	12394	14013	24	45,10,9,6,334,104,93,6,6,12,18,119,6,32,376,23,33,133,14,69,12,7,31,35,	139870,139920,139930,139939,139947,140293,140400,140493,140501,140507,140525,140544,140663,140681,140713,141089,141115,141154,141287,141304,141373,141385,141393,141437,	12394,12439,12451,12462,12468,12802,12906,13006,13012,13020,13032,13050,13170,13176,13231,13613,13636,13669,13832,13846,13927,13940,13947,13978,
171	119	0	0	2	8	2	5	+	I	230203	174624	174922	sbay_c545	28791	27293	27588	5	125,24,26,5,110,	174624,174749,174776,174807,174812,	27293,27421,27445,27471,27478,
102	56	0	0	1	1	2	9	-	I	230203	123813	123972	sbay_c545	28791	27301	27468	4	116,4,19,19,	106231,106347,106351,106371,	27301,27421,27430,27449,
65	21	0	0	0	0	1	4	+	II	813140	68257	68343	sbay_c545	28791	10029	10119	2	7,79,	68257,68264,	10029,10040,
922	582	0	0	15	73	14	100	+	II	813140	84860	86437	sbay_c545	28791	12373	13977	30	55,31,320,13,107,47,11,33,11,11,4,77,12,67,29,135,232,36,8,16,7,10,89,18,7,56,13,12,7,30,	84860,84915,84956,85286,85301,85411,85458,85472,85508,85521,85532,85538,85615,85631,85698,85727,85865,86097,86145,86165,86181,86191,86201,86290,86311,86318,86374,86387,86399,86407,	12373,12435,12466,12786,12799,12906,12956,12967,13000,13011,13029,13033,13114,13126,13202,13234,13369,13622,13658,13666,13683,13690,13702,13804,13822,13846,13908,13927,13940,13947,
79	32	0	0	1	1	1	2	-	II	813140	166297	166409	sbay_c545	28791	10038	10151	3	86,14,11,	646731,646817,646832,	10038,10126,10140,
423	272	0	0	0	0	2	9	-	III	315339	189542	190237	sbay_c545	28791	5293	5997	3	131,508,56,	125102,125233,125741,	5293,5427,5941,
443	195	0	0	5	35	1	2	+	IV	1531929	366737	367410	sbay_c545	28791	902	1542	7	341,4,22,42,11,21,197,	366737,367090,367102,367124,367169,367185,367213,	902,1243,1247,1271,1313,1324,1345,
82	31	0	0	0	0	2	13	+	IV	1531929	778726	778839	sbay_c545	28791	10019	10145	3	11,14,88,	778726,778737,778751,	10019,10031,10057,
89	37	0	0	2	4	0	0	-	IV	1531929	1290928	1291058	sbay_c545	28791	10031	10157	3	84,13,29,	240871,240958,240972,	10031,10115,10128,
918	588	0	0	18	108	16	114	-	IV	1531929	44092	45706	sbay_c545	28791	12351	13971	35	23,7,13,43,30,135,10,191,52,15,17,11,48,9,53,6,20,146,15,157,8,158,5,9,17,20,13,14,125,31,40,5,18,16,26,	1486223,1486247,1486259,1486284,1486333,1486363,1486498,1486510,1486716,1486768,1486786,1486804,1486817,1486865,1486877,1486932,1486941,1486961,1487107,1487122,1487279,1487297,1487455,1487460,1487469,1487486,1487515,1487538,1487571,1487696,1487727,1487767,1487772,1487792,1487811,	12351,12374,12381,12394,12437,12470,12607,12617,12808,12863,12878,12895,12906,12957,12966,13019,13025,13050,13205,13223,13384,13392,13555,13577,13592,13616,13636,13649,13663,13801,13846,13898,13911,13929,13945,
81	44	0	0	1	1	0	0	-	V	576869	142910	143036	sbay_c545	28791	10033	10158	2	94,31,	433833,433928,	10033,10127,
991	629	0	0	8	55	13	87	-	V	576869	94727	96402	sbay_c545	28791	12267	13974	22	34,42,37,84,5,371,9,198,12,108,22,21,123,16,221,27,11,145,13,65,9,47,	480467,480514,480570,480607,480698,480703,481074,481086,481285,481308,481416,481438,481464,481587,481603,481825,481852,481863,482008,482021,482086,482095,	12267,12301,12343,12394,12478,12490,12864,12873,13071,13083,13200,13230,13251,13376,13393,13614,13645,13659,13813,13841,13909,13927,
66	15	0	0	1	2	1	8	-	VI	270148	186205	186288	sbay_c545	28791	10030	10119	3	15,7,59,	83860,83877,83884,	10030,10045,10060,
1688	962	0	0	10	43	15	175	-	VII	1090936	628575	631268	sbay_c545	28791	6807	9632	26	219,20,125,11,15,104,51,21,212,16,24,6,13,84,47,10,336,8,959,24,11,22,20,6,22,264,	459668,459887,459908,460036,460059,460080,460187,460240,460261,460473,460489,460513,460519,460532,460625,460672,460686,461024,461033,461992,462016,462027,462049,462069,462075,462097,	6807,7027,7047,7172,7183,7198,7302,7353,7388,7602,7636,7663,7677,7692,7776,7827,7837,8173,8181,9154,9227,9241,9290,9322,9331,9368,
298	102	0	0	3	10	0	0	-	VII	1090936	619156	619566	sbay_c545	28791	18118	18518	4	193,8,81,118,	471370,471564,471573,471662,	18118,18311,18319,18400,
285	103	0	0	1	1	1	3	-	VII	1090936	618080	618469	sbay_c545	28791	24049	24440	3	188,172,28,	472467,472656,472828,	24049,24237,24412,
104	62	0	0	2	10	1	7	+	VIII	562639	270904	271080	sbay_c545	28791	27336	27509	4	99,9,28,30,	270904,271005,271022,271050,	27336,27435,27444,27479,
207	136	0	0	2	19	6	28	-	VIII	562639	316825	317187	sbay_c545	28791	27172	27543	9	20,11,30,20,7,13,155,4,83,	245452,245472,245487,245532,245552,245559,245572,245727,245731,	27172,27193,27204,27234,27257,27268,27298,27454,27460,
84	23	0	0	0	0	2	20	-	IX	439885	105317	105424	sbay_c545	28791	10030	10157	3	15,62,30,	334461,334476,334538,	10030,10054,10127,
462	268	0	0	4	35	8	25	+	X	745440	67814	68579	sbay_c545	28791	5244	5999	13	23,13,27,95,20,11,9,7,391,16,53,16,49,	67814,67837,67855,67891,67986,68006,68017,68026,68051,68445,68461,68514,68530,	5244,5268,5281,5308,5406,5431,5448,5458,5465,5856,5875,5933,5950,
1108	665	0	0	5	21	15	78	+	X	745440	519403	521197	sbay_c545	28791	12123	13974	21	14,6,39,69,174,6,623,18,11,11,81,47,140,13,225,19,143,18,60,9,47,	519403,519423,519429,519468,519537,519713,519719,520344,520362,520374,520395,520476,520523,520663,520676,520901,520920,521063,521081,521141,521150,	12123,12137,12149,12197,12269,12443,12451,13074,13093,13104,13115,13199,13255,13397,13411,13639,13661,13814,13846,13909,13927,
55	19	0	0	0	0	0	0	-	X	745440	469796	469870	sbay_c545	28791	10060	10134	1	74,	275570,	10060,
909	581	0	0	9	54	15	90	-	X	745440	381175	382719	sbay_c545	28791	12394	13974	25	50,5,348,67,21,13,166,20,99,18,156,12,11,167,28,12,15,6,4,125,31,44,25,6,41,	362721,362773,362779,363133,363200,363229,363242,363408,363431,363530,363548,363704,363718,363733,363923,363951,363968,363983,363989,363993,364118,364149,364193,364218,364224,	12394,12444,12449,12797,12868,12889,12903,13072,13092,13200,13221,13383,13395,13406,13573,13619,13631,13647,13656,13663,13801,13846,13893,13920,13933,
387	246	0	0	6	34	4	34	-	X	745440	250596	251263	sbay_c545	28791	26968	27635	11	95,23,19,3,6,75,15,43,16,321,17,	494177,494284,494310,494329,494336,494342,494419,494435,494478,494506,494827,	26968,27063,27086,27106,27109,27118,27193,27208,27269,27285,27618,
69	33	0	0	0	0	0	0	-	X	745440	250471	250573	sbay_c545	28791	27802	27904	1	102,	494867,	27802,
81	43	0	0	0	0	0	0	-	XI	666445	183812	183936	sbay_c545	28791	27301	27425	1	124,	482509,	27301,
899	599	0	0	11	55	11	85	+	XII	1078172	95925	97478	sbay_c545	28791	12394	13977	23	45,10,9,6,334,104,93,6,6,12,18,119,6,32,376,23,33,119,16,12,57,11,51,	95925,95975,95985,95994,96002,96348,96455,96548,96556,96562,96580,96599,96718,96736,96768,97144,97170,97209,97328,97344,97359,97416,97427,	12394,12439,12451,12462,12468,12802,12906,13006,13012,13020,13032,13050,13170,13176,13231,13613,13636,13669,13801,13834,13846,13909,13926,
14247	3493	0	0	57	258	76	314	-	XII	1078172	855634	873632	sbay_c545	28791	0	18054	134	45,9,762,6,16,9,12,14,9,426,253,98,327,24,68,18,43,57,190,32,275,796,729,668,22,72,9,31,20,39,18,1089,21,96,33,8,47,19,16,46,26,16,16,12,49,18,9,39,18,1398,1698,206,26,16,449,306,107,16,45,22,14,25,36,18,21,12,41,9,31,8,18,457,82,25,30,10,23,6,7,12,41,9,14,1994,38,30,26,9,18,13,28,1842,25,14,16,13,69,41,271,28,38,10,27,12,51,225,33,14,12,163,33,37,66,6,25,10,19,13,23,19,78,28,10,94,35,53,20,15,15,23,20,14,15,96,	204540,204594,204604,205366,205372,205388,205398,205410,205424,205434,205860,206113,206211,206539,206563,206633,206652,206696,206754,206944,206976,207251,208050,208851,209519,209541,209626,209650,209681,209701,209740,209764,210854,210876,210984,211017,211025,211072,211091,211109,211155,211181,211199,211220,211233,211286,211304,211313,211352,211370,212771,214478,214684,214710,214726,215175,215481,215588,215606,215651,215673,215687,215713,215753,215771,215792,215813,215854,215864,215895,215903,215921,216384,216470,216495,216525,216535,216563,216570,216578,216590,216631,216643,216658,218653,218691,218721,218747,218761,218780,218796,218824,220666,220691,220709,220728,220741,220810,220853,221124,221152,221191,221201,221228,221240,221294,221522,221555,221570,221593,221756,221789,221827,221893,221899,221924,221935,221956,221969,221993,222013,222094,222122,222132,222226,222261,222314,222336,222354,222369,222392,222412,222427,222442,	0,45,54,817,824,841,850,866,881,890,1319,1590,1703,2030,2055,2123,2141,2184,2241,2449,2484,2765,3561,4290,4959,4982,5054,5063,5095,5116,5159,5177,6266,6287,6383,6417,6426,6482,6502,6518,6567,6596,6612,6628,6640,6689,6709,6719,6760,6782,8180,9878,10090,10119,10144,10599,10915,11023,11039,11085,11108,11123,11148,11184,11207,11231,11243,11286,11295,11339,11354,11374,11831,11913,11939,11971,11982,12005,12011,12018,12031,12073,12082,12096,14090,14129,14177,14204,14213,14231,14244,14283,16126,16152,16166,16182,16197,16268,16309,16587,16616,16654,16671,16702,16715,16766,16991,17025,17039,17051,17217,17251,17288,17362,17373,17400,17410,17429,17443,17466,17485,17563,17599,17625,17720,17756,17810,17830,17845,17866,17903,17924,17938,17958,
3388	970	0	0	21	71	33	128	-	XII	1078172	850217	854646	sbay_c545	28791	24305	28791	55	91,8,19,78,38,351,19,8,93,52,38,22,26,17,13,25,261,55,19,21,55,25,13,34,7,19,15,29,668,9,10,11,6,68,20,53,7,13,22,11,16,28,14,49,20,29,26,11,8,746,24,12,938,56,32,	223526,223625,223633,223652,223741,223780,224131,224150,224158,224251,224312,224350,224372,224398,224416,224430,224456,224717,224772,224793,224815,224870,224895,224908,224942,224950,224969,224984,225013,225683,225694,225704,225716,225731,225799,225819,225872,225879,225892,225914,225926,225942,225971,225988,226041,226061,226090,226125,226136,226146,226892,226916,226928,227866,227923,	24305,24396,24406,24443,24521,24559,24912,24939,24949,25044,25096,25135,25161,25188,25205,25218,25243,25505,25562,25581,25602,25660,25686,25700,25737,25744,25764,25780,25812,26480,26489,26500,26511,26517,26587,26611,26665,26673,26689,26712,26723,26740,26768,26782,26831,26852,26884,26910,26926,26934,27707,27735,27764,28703,28759,
66	23	0	0	0	0	0	0	+	XIII	924430	86939	87028	sbay_c545	28791	10030	10119	1	89,	86939,	10030,
920	583	0	0	18	111	16	117	-	XIV	784328	252084	253698	sbay_c545	28791	12351	13971	35	29,14,43,30,135,8,105,15,71,52,15,17,11,48,9,53,6,20,146,15,157,8,158,5,9,17,20,13,14,125,31,50,11,17,26,	530630,530665,530691,530740,530770,530905,530915,531022,531037,531123,531175,531193,531211,531224,531272,531284,531339,531348,531368,531514,531529,531686,531704,531862,531867,531876,531893,531922,531945,531978,532103,532134,532187,532198,532218,	12351,12380,12394,12437,12470,12607,12615,12720,12737,12808,12863,12878,12895,12906,12957,12966,13019,13025,13050,13205,13223,13384,13392,13555,13577,13592,13616,13636,13649,13663,13801,13846,13896,13928,13945,
162	102	0	0	1	1	2	10	-	XIV	784328	70957	71222	sbay_c545	28791	27120	27394	4	38,12,103,111,	713106,713145,713157,713260,	27120,27158,27171,27283,
1536	428	0	0	5	29	5	19	+	XV	1091283	459446	461439	sbay_c545	28791	18756	20739	11	12,7,1816,9,13,18,34,21,12,13,9,	459446,459458,459465,461298,461307,461320,461340,461375,461396,461411,461430,	18756,18773,18782,20598,20611,20625,20643,20677,20705,20717,20730,
1608	513	0	0	6	48	6	36	+	XV	1091283	698738	700907	sbay_c545	28791	21813	23970	13	25,13,1791,6,30,49,11,5,25,16,16,45,89,	698738,698763,698779,700570,700576,700607,700656,700667,700679,700713,700742,700773,700818,	21813,21842,21855,23660,23669,23699,23757,23770,23775,23800,23816,23832,23881,
59	27	0	0	0	0	0	0	-	XV	1091283	110777	110863	sbay_c545	28791	10033	10119	1	86,	980420,	10033,
147	87	0	0	1	1	1	10	-	XV	1091283	105814	106049	sbay_c545	28791	27147	27391	3	115,14,105,	985234,985350,985364,	27147,27262,27286,
62	30	0	0	0	0	0	0	+	XVI	948061	156852	156944	sbay_c545	28791	27301	27393	1	92,	156852,	27301,
65	26	0	0	1	1	0	0	-	XVI	948061	897071	897163	sbay_c545	28791	10043	10134	2	78,13,	50898,50977,	10043,10121,
BioPerl-1.007002/t/data/seg.out000444000766000024        30613155576321 16156 0ustar00cjfieldsstaff000000000000>LBL_0012(32-46) complexity=2.47 (12/2.20/2.50)
gdggwtfegwggppe

>LBL_0012(66-80) complexity=2.31 (12/2.20/2.50)
kfssrasakavakks

>LBL_0012(123-138) complexity=2.31 (12/2.20/2.50)
svivsqsqgvvkgvgv

BioPerl-1.007002/t/data/semicolon.newick000444000766000024         7213155576321 20021 0ustar00cjfieldsstaff000000000000(((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1);BioPerl-1.007002/t/data/seqdatabase.ini000555000766000024        45413155576321 17634 0ustar00cjfieldsstaff000000000000VERSION=1.00

[testflat]
protocol=flat
location=t/tmp
dbname=testflat

[testbdb]
protocol=flat
location=t/tmp
dbname=testbdb

[embl]
protocol=biofetch
location=http://www.ebi.ac.uk/cgi-bin/dbfetch
dbname=embl

[swissprot]
protocol=biofetch
location=http://www.ebi.ac.uk/cgi-bin/dbfetch
dbname=swall

BioPerl-1.007002/t/data/seqfile-no-desc.pir000444000766000024        55313155576321 20345 0ustar00cjfieldsstaff000000000000>P1;CCHU

MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
>P1;CCCZ

GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
>P1;CCST

GDVEK.GKKIF.VQKCAQCHTVEKGGKH.KTGPNLNGL.IGRKTGQAEGF.SYTEANKN.KGITWG.EETLM.EY.LENPKKY.IPGTKM.IF.AGIKKKAERADL.IAY.LKDATSK*
BioPerl-1.007002/t/data/seqfile.pir000444000766000024       213213155576321 17032 0ustar00cjfieldsstaff000000000000>P1;CCHU
cytochrome c [validated] - human
MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
>P1;CCCZ
cytochrome c - chimpanzee (tentative sequence)
GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
>P1;CCST
cytochrome c - snapping turtle (tentative sequence)
GDVEK.GKKIF.VQKCAQCHTVEKGGKH.KTGPNLNGL.IGRKTGQAEGF.SYTEANKN.KGITWG.EETLM.EY.LENPKKY.IPGTKM.IF.AGIKKKAERADL.IAY.LKDATSK*
>P1;CCFG
cytochrome c - bullfrog (tentative sequence)
GDVEKGKKIF(V,Q.K.C.A.Q.C.H.T.C,E.K.G.G.K.H)KVGPNLYGLIGRKTGQAAGFSYTDANKNKGITW(G.E,D,T.L.M.E.Y)LENPKKYIPGTKMIFAGI(K.K.K.G.E.R.Q)DLIAY(L.K.S,A,C,S,K)*
>P1;CCND
cytochrome c - love-in-a-mist (tentative sequence)
AS.F.BZAPAGBSAS(G.E.K)I.F.KTKCAZCHTVBZGAGH.KZGP(N.L)H.G.L.F.GRQSGT.VAG.Y.SY.SAANKN.KAVN.W.EEKT.L.Y.DYLLNPKK.Y.IP(G.T.K.M)VFPGL.KKPZZRABL.LA.Y.LKESTA*
>F1;C44264
ALL-1/AF-4 clone 25 mutant fusion protein - human (fragment)
/EKPPPVNKQENAGTLNIFSTLSNGNSSKQKIPADGVHRIRVDFKTYSNEVHCVEEILKEMTHSWPPPLTAIHTPSTAEPSKFPFPTKDSQHVSSVTQNQKQYDTSSKTHSNSQQGTSSMLEDDLQLSDSEDSDS/*
BioPerl-1.007002/t/data/seqs.fas000444000766000024       161713155576321 16343 0ustar00cjfieldsstaff000000000000>gi|239758|bbs|68379 glucocorticoid receptor,  GR [human, Peptide Partial, 394 aa]
MDSKESLTPGREENPSSVLAQERGDVMDFYKTLRGGATVKVSASSPSLAVASQSDSKQRRLLVDFPKGSV
>gi|239752|bbs|68871 PML-3=putative zinc finger protein [human, Peptide, 802 aa]
MPPPETPSEGRQPSPSPSPTERAPASEEEFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASGMQCPICQ
>gi|238775|bbs|65126 putative tyrosine kinase receptor=UFO [human, NIH3T3, Peptide, 894 aa]
MAWRCPRMGRVPLAWCLALCGWACMAPRGTQAEESPFVGNPGNITGARGLTGTLRCQLQVQGEPPEVHWL
>gi|239006|bbs|65162 alpha(1,3)-fucosyltransferase, ELFT [human, Peptide, 400 aa]
MGAPWGSPTAAAGGRRGWRRGRGLPWTVCVLAAAGLTCTALITYACWGQLPPLPWASPTPSRPVGVLLWW
>gi|237597|bbs|60089 putative adhesion molecule=ADMLX [human, Peptide, 679 aa]
MVPGVPGAVLTLCLWLAASSGSWRPAPARLCAAAGRVAVCRERPARSCASRCLSLQITRISAFFQHFQNN
>gi|237995|bbs|62046 NK-1 receptor [human, lung, Peptide, 407 aa]
MDNVLPVDSDLSPNISTNTSEPNQFVQPAWEIVLWAAAYTVIVVTSVVGNVVVMWIILAHKRMRTVTNYF


BioPerl-1.007002/t/data/sequencefamily.dat000444000766000024     11176413155576321 20446 0ustar00cjfieldsstaff000000000000ID   MA32_HUMAN     STANDARD;      PRT;   282 AA.
AC   Q07021;
DT   01-FEB-1995 (Rel. 31, Created)
DT   01-FEB-1995 (Rel. 31, Last sequence update)
DT   01-OCT-2000 (Rel. 40, Last annotation update)
DE   COMPLEMENT COMPONENT 1, Q SUBCOMPONENT BINDING PROTEIN, MITOCHONDRIAL
DE   PRECURSOR (GLYCOPROTEIN GC1QBP) (GC1Q-R PROTEIN) (HYALURONAN-BINDING
DE   PROTEIN 1) (PRE-MRNA SPLICING FACTOR SF2, P32 SUBUNIT) (P33).
GN   GC1QBP OR HABP1 OR SF2P32 OR C1QBP.
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   SEQUENCE FROM N.A., AND SEQUENCE OF 74; 76-93 AND 208-216.
RC   TISSUE=FIBROBLAST;
RX   MEDLINE=94085792; PubMed=8262387;
RA   Honore B., Madsen P., Rasmussen H.H., Vandekerckhove J., Celis J.E.,
RA   Leffers H.;
RT   "Cloning and expression of a cDNA covering the complete coding region
RT   of the P32 subunit of human pre-mRNA splicing factor SF2.";
RL   Gene 134:283-287(1993).
RN   [2]
RP   SEQUENCE OF 5-282 FROM N.A., AND SEQUENCE OF 74-114.
RX   MEDLINE=91309150; PubMed=1830244;
RA   Krainer A.R., Mayeda A., Kozak D., Binns G.;
RT   "Functional expression of cloned human splicing factor SF2: homology
RT   to RNA-binding proteins, U1 70K, and Drosophila splicing regulators.";
RL   Cell 66:383-394(1991).
RN   [3]
RP   SEQUENCE FROM N.A., AND PARTIAL SEQUENCE.
RX   MEDLINE=94253723; PubMed=8195709;
RA   Ghebrehiwet B., Lim B.L., Peerschke E.I., Willis A.C., Reid K.B.;
RT   "Isolation, cDNA cloning, and overexpression of a 33-kD cell surface
RT   glycoprotein that binds to the globular 'heads' of C1q.";
RL   J. Exp. Med. 179:1809-1821(1994).
RN   [4]
RP   X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS).
RX   MEDLINE=99199225; PubMed=10097078;
RA   Jiang J., Zhang Y., Krainer A.R., Xu R.-M.;
RT   "Crystal structure of human p32, a doughnut-shaped acidic
RT   mitochondrial matrix protein.";
RL   Proc. Natl. Acad. Sci. U.S.A. 96:3572-3577(1999).
CC   -!- FUNCTION: NOT KNOWN. BINDS TO THE GLOBULAR "HEADS" OF C1Q THUS
CC       INHIBITING C1 ACTIVATION.
CC   -!- SUBCELLULAR LOCATION: MITOCHONDRIAL MATRIX.
CC   -!- SIMILARITY: BELONGS TO THE MAM33 FAMILY.
CC   -!- CAUTION: WAS ORIGINALLY (REF.1 AND REF.2) THOUGHT TO BE A PRE-MRNA
CC       SPLICING FACTOR THAT PLAYS A ROLE IN PREVENTING EXON SKIPPING,
CC       ENSURING THE ACCURACY OF SPLICING AND REGULATING ALTERNATIVE
CC       SPLICING.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; L04636; AAA16315.1; -.
DR   EMBL; M69039; AAA73055.1; -.
DR   EMBL; X75913; CAA53512.1; -.
DR   PIR; JT0762; JT0762.
DR   PIR; S44104; S44104.
DR   PDB; 1P32; 06-APR-99.
DR   MIM; 601269; -.
KW   Mitochondrion; Transit peptide; 3D-structure.
FT   TRANSIT       1     73       MITOCHONDRION.
FT   CHAIN        74    282       COMPLEMENT COMPONENT 1, Q SUBCOMPONENT
FT                                BINDING PROTEIN.
SQ   SEQUENCE   282 AA;  31362 MW;  2F747FA73BB1314B CRC64;
     MLPLLRCVPR VLGSSVAGLR AAAPASPFRQ LLQPAPRLCT RPFGLLSVRA GSERRPGLLR
     PRGPCACGCG CGSLHTDGDK AFVDFLSDEI KEERKIQKHK TLPKMSGGWE LELNGTEAKL
     VRKVAGEKIT VTFNINNSIP PTFDGEEEPS QGQKVEEQEP ELTSTPNFVV EVIKNDDGKK
     ALVLDCHYPE DEVGQEDEAE SDIFSIREVS FQSTGESEWK DTNYTLNTDS LDWALYDHLM
     DFLADRGVDN TFADELVELS TALEHQEYIT FLEDLKSFVK SQ
//
ID   ACON_CAEEL     STANDARD;      PRT;   788 AA.
AC   P34455;
DT   01-FEB-1994 (Rel. 28, Created)
DT   01-FEB-1994 (Rel. 28, Last sequence update)
DT   15-JUL-1999 (Rel. 38, Last annotation update)
DE   Probable aconitate hydratase, mitochondrial precursor (EC 4.2.1.3)
DE   (Citrate hydro-lyase) (Aconitase).
GN   F54H12.1.
OS   Caenorhabditis elegans.
OC   Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea;
OC   Rhabditidae; Peloderinae; Caenorhabditis.
OX   NCBI_TaxID=6239;
RN   [1]
RP   SEQUENCE FROM N.A.
RC   STRAIN=BRISTOL N2;
RX   MEDLINE=94150718; PubMed=7906398;
RA   Wilson R., Ainscough R., Anderson K., Baynes C., Berks M.,
RA   Bonfield J., Burton J., Connell M., Copsey T., Cooper J., Coulson A.,
RA   Craxton M., Dear S., Du Z., Durbin R., Favello A., Fraser A.,
RA   Fulton L., Gardner A., Green P., Hawkins T., Hillier L., Jier M.,
RA   Johnston L., Jones M., Kershaw J., Kirsten J., Laisster N.,
RA   Latreille P., Lightning J., Lloyd C., Mortimore B., O'Callaghan M.,
RA   Parsons J., Percy C., Rifken L., Roopra A., Saunders D., Shownkeen R.,
RA   Sims M., Smaldon N., Smith A., Smith M., Sonnhammer E., Staden R.,
RA   Sulston J., Thierry-Mieg J., Thomas K., Vaudin M., Vaughan K.,
RA   Waterson R., Watson A., Weinstock L., Wilkinson-Sproat J.,
RA   Wohldman P.;
RT   "2.2 Mb of contiguous nucleotide sequence from chromosome III of C.
RT   elegans.";
RL   Nature 368:32-38(1994).
CC   -!- CATALYTIC ACTIVITY: Citrate = cis-aconitate + H(2)O.
CC   -!- COFACTOR: ACONITASE HAS AN ACTIVE (4FE-4S) AND AN INACTIVE (3FE-
CC       4S) FORMS. THE ACTIVE (4FE-4S) CLUSTER IS PART OF THE CATALYTIC
CC       SITE THAT INTERCONVERTS CITRATE, CIS-ACONITASE, AND ISOCITRATE (BY
CC       SIMILARITY).
CC   -!- PATHWAY: TRICARBOXYLIC ACID CYCLE.
CC   -!- SUBUNIT: MONOMER (BY SIMILARITY).
CC   -!- SUBCELLULAR LOCATION: Mitochondrial (By similarity).
CC   -!- SIMILARITY: BELONGS TO THE ACONITASE/IPM ISOMERASE FAMILY.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; L25599; AAA28050.1; -.
DR   PIR; S44831; S44831.
DR   HSSP; P20004; 1AMJ.
DR   WormPep; F54H12.1; CE00516.
DR   InterPro; IPR001030; Aconitase.
DR   InterPro; IPR000573; Aconitase_C.
DR   Pfam; PF00330; aconitase; 1.
DR   Pfam; PF00694; Aconitase_C; 1.
DR   PRINTS; PR00415; ACONITASE.
DR   ProDom; PD000511; Aconitase; 1.
DR   PROSITE; PS00450; ACONITASE_1; 1.
DR   PROSITE; PS01244; ACONITASE_2; 1.
KW   Hypothetical protein; Lyase; Tricarboxylic acid cycle; Iron-sulfur;
KW   Mitochondrion; Transit peptide; 4Fe-4S.
FT   TRANSIT       1      ?       MITOCHONDRION (POTENTIAL).
FT   CHAIN         ?    788       PROBABLE ACONITATE HYDRATASE.
FT   METAL       393    393       IRON-SULFUR (4FE-4S) (BY SIMILARITY).
FT   METAL       456    456       IRON-SULFUR (4FE-4S) (BY SIMILARITY).
FT   METAL       459    459       IRON-SULFUR (4FE-4S) (BY SIMILARITY).
SQ   SEQUENCE   788 AA;  85712 MW;  8861E6FC198B70D9 CRC64;
     MRYHFLFGSL RNHLFSFRGV IYCREKLFNC SKLSFRPSKV AISKFEPKSY LPYEKLSQTV
     KIVKDRLKRP LTLSEKILYG HLDQPKTQDI ERGVSYLRLR PDRVAMQDAT AQMAMLQFIS
     SGLPKTAVPS TIHCDHLIEA QKGGAQDLAR AKDLNKEVFN FLATAGSKYG VGFWKPGSGI
     IHQIILENYA FPGLLLIGTD SHTPNGGGLG GLCIGVGGAD AVDVMADIPW ELKCPKVIGI
     KLTGKLNGWT SAKDVILKVA DILTVKGGTG AIVEYFGPGV DSISATGMGT ICNMGAEIGA
     TTSVFPYNES MYKYLEATGR KEIAEEARKY KDLLTADDGA NYDQIIEINL DTLTPHVNGP
     FTPDLASSID KLGENAKKNG WPLDVKVSLI GSCTNSSYED MTRAASIAKQ ALDKGLKAKT
     IFTITPGSEQ VRATIERDGL SKIFADFGGM VLANACGPCI GQWDRQDVKK GEKNTIVTSY
     NRNFTGRNDA NPATHGFVTS PDITTAMAIS GRLDFNPLTD ELTAADGSKF KLQAPTGLDL
     PPKGYDPGED TFQAPSGSGQ VDVSPSSDRL QLLSPFDKWD GKDLEDMKIL IKVTGKCTTD
     HISAAGPWLK YRGHLDNISN NLFLTAINAD NGEMNKVKNQ VTGEYGAVPA TARKYKADGV
     RWVAIGDENY GEGSSREHAA LEPRHLGGRA IIVKSFARIH ETNLKKQGML PLTFANPADY
     DKIDPSDNVS IVGLSSFAPG KPLTAIFKKT NGSKVEVTLN HTFNEQQIEW FKAGSALNRM
     KEVFAKSK
//
ID   143E_HUMAN     STANDARD;      PRT;   255 AA.
AC   P42655; P29360; Q63631;
DT   01-NOV-1995 (Rel. 32, Created)
DT   01-NOV-1995 (Rel. 32, Last sequence update)
DT   15-JUL-1999 (Rel. 38, Last annotation update)
DE   14-3-3 protein epsilon (Mitochondrial import stimulation factor L
DE   subunit) (Protein kinase C inhibitor protein-1) (KCIP-1) (14-3-3E).
GN   YWHAE.
OS   Homo sapiens (Human),
OS   Mus musculus (Mouse),
OS   Rattus norvegicus (Rat),
OS   Bos taurus (Bovine), and
OS   Ovis aries (Sheep).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606, 10090, 10116, 9913, 9940;
RN   [1]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human;
RX   MEDLINE=95372385; PubMed=7644510;
RA   Conklin D.S., Galaktionov K., Beach D.;
RT   "14-3-3 proteins associate with cdc25 phosphatases.";
RL   Proc. Natl. Acad. Sci. U.S.A. 92:7892-7896(1995).
RN   [2]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human; TISSUE=Heart;
RA   Luk S.C.W., Lee C.Y., Waye M.M.Y.;
RL   Submitted (JUN-1995) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human;
RX   MEDLINE=96300316; PubMed=8684458;
RA   Jin D.-Y., Lyu M.S., Kozak C.A., Jeang K.-T.;
RT   "Function of 14-3-3 proteins.";
RL   Nature 382:308-308(1996).
RN   [4]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human; TISSUE=Liver;
RX   MEDLINE=97011338; PubMed=8858348;
RA   Chong S.S., Tanigami A., Roschke A.V., Ledbetter D.H.;
RT   "14-3-3 epsilon has no homology to LIS1 and lies telomeric to it on
RT   chromosome 17p13.3 outside the Miller-Dieker syndrome chromosome
RT   region.";
RL   Genome Res. 6:735-741(1996).
RN   [5]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human;
RA   Tanigami A., Chong S.S., Ledbetter D.H.;
RT   "14-3-3 epsilon genomic sequence.";
RL   Submitted (AUG-1998) to the EMBL/GenBank/DDBJ databases.
RN   [6]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human; TISSUE=Placenta;
RA   Strausberg R.;
RL   Submitted (DEC-2000) to the EMBL/GenBank/DDBJ databases.
RN   [7]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Rat, and Sheep; TISSUE=Pineal gland;
RX   MEDLINE=94296566; PubMed=8024705;
RA   Roseboom P.H., Weller J.L., Babila T., Aitken A., Sellers L.A.,
RA   Moffet J.R., Namboodiri M.A., Klein D.C.;
RT   "Cloning and characterization of the epsilon and zeta isoforms of the
RT   14-3-3 proteins.";
RL   DNA Cell Biol. 13:629-640(1994).
RN   [8]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Rat; TISSUE=Liver;
RX   MEDLINE=95122474; PubMed=7822263;
RA   Alam R., Hachiya N., Sakaguchi M., Shun-Ichiro K., Iwanaga S.,
RA   Kitajima M., Mihara K., Omura T.;
RT   "cDNA cloning and characterization of mitochondrial import
RT   stimulation factor (MSF) purified from rat liver cytosol.";
RL   J. Biochem. 116:416-425(1994).
RN   [9]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Rat; TISSUE=Brain;
RX   MEDLINE=96280718; PubMed=8694795;
RA   Gao L., Gu X.B., Yu D.S., Yu R.K., Zeng G.;
RT   "Association of a 14-3-3 protein with CMP-NeuAc:GM1 alpha 2,3-
RT   sialyltransferase.";
RL   Biochem. Biophys. Res. Commun. 224:103-107(1996).
RN   [10]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Mouse; STRAIN=SWISS; TISSUE=Kidney;
RX   MEDLINE=95269876; PubMed=7750640;
RA   McConnell J.E., Armstrong J.F., Bard J.B.;
RT   "The mouse 14-3-3 epsilon isoform, a kinase regulator whose
RT   expression pattern is modulated in mesenchyme and neuronal
RT   differentiation.";
RL   Dev. Biol. 169:218-228(1995).
RN   [11]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Mouse; STRAIN=129/SV;
RA   Takihara Y., Irie K., Nomura M., Motaleb M., Matsumoto K.,
RA   Shimada K.;
RL   Submitted (SEP-1996) to the EMBL/GenBank/DDBJ databases.
RN   [12]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Bovine;
RA   Jones J.M., Niikura T., Pinke R.M., Guo W., Molday L., Leykam J.,
RA   McConnell D.G.;
RT   "Expression of 14-3-3 proteins in bovine retinal photoreceptors.";
RL   Submitted (JAN-1998) to the EMBL/GenBank/DDBJ databases.
RN   [13]
RP   SEQUENCE OF 1-152; 165-184 AND 216-255.
RC   SPECIES=Sheep; TISSUE=Brain;
RX   MEDLINE=92283271; PubMed=1317796;
RA   Toker A., Sellers L.A., Amess B., Patel Y., Harris A., Aitken A.;
RT   "Multiple isoforms of a protein kinase C inhibitor (KCIP-1/14-3-3)
RT   from sheep brain. Amino acid sequence of phosphorylated forms.";
RL   Eur. J. Biochem. 206:453-461(1992).
RN   [14]
RP   SEQUENCE OF 1-23 AND 125-140.
RC   SPECIES=Sheep; TISSUE=Brain;
RX   MEDLINE=90345949; PubMed=2143472;
RA   Toker A., Ellis C.A., Sellers L.A., Aitken A.;
RT   "Protein kinase C inhibitor proteins. Purification from sheep brain
RT   and sequence similarity to lipocortins and 14-3-3 protein.";
RL   Eur. J. Biochem. 191:421-429(1990).
CC   -!- FUNCTION: ACTIVATES TYROSINE AND TRYPTOPHAN HYDROXYLASES IN THE
CC       PRESENCE OF CA(2+)/CALMODULIN-DEPENDENT PROTEIN KINASE II, AND
CC       STRONGLY ACTIVATES PROTEIN KINASE C. IS PROBABLY A MULTIFUNCTIONAL
CC       REGULATOR OF THE CELL SIGNALING PROCESSES MEDIATED BY BOTH
CC       KINASES.
CC   -!- SUBUNIT: HOMODIMER.
CC   -!- SUBCELLULAR LOCATION: CYTOPLASMIC.
CC   -!- TISSUE SPECIFICITY: 14-3-3 PROTEINS ARE LOCALIZED IN NEURONS, AND
CC       ARE AXONALLY TRANSPORTED TO THE NERVE TERMINALS. THEY MAY BE ALSO
CC       PRESENT, AT LOWER LEVELS, IN VARIOUS OTHER EUKARYOTIC TISSUES.
CC   -!- SIMILARITY: BELONGS TO THE 14-3-3 FAMILY.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; U28936; AAA75301.1; -.
DR   EMBL; U20972; AAC50175.1; -.
DR   EMBL; U43399; AAC50625.1; -.
DR   EMBL; U43430; AAD00026.1; -.
DR   EMBL; U54778; AAC50710.1; -.
DR   EMBL; AB017103; BAA32538.1; -.
DR   EMBL; AB017098; BAA32538.1; JOINED.
DR   EMBL; AB017099; BAA32538.1; JOINED.
DR   EMBL; AB017100; BAA32538.1; JOINED.
DR   EMBL; AB017101; BAA32538.1; JOINED.
DR   EMBL; AB017102; BAA32538.1; JOINED.
DR   EMBL; BC000179; AAH00179.1; -.
DR   EMBL; BC001440; AAH01440.1; -.
DR   EMBL; M84416; AAC37659.1; -.
DR   EMBL; D30739; BAA06401.1; -.
DR   EMBL; Z19599; CAA79659.1; -.
DR   EMBL; U53882; AAC52676.1; -.
DR   EMBL; L07914; AAC37321.1; -.
DR   EMBL; D87663; BAA13424.1; -.
DR   EMBL; AF043735; AAC61927.1; -.
DR   PIR; S10806; S10806.
DR   PIR; S10807; S10807.
DR   HSSP; P29312; 1A38.
DR   MIM; 605066; -.
DR   MGD; MGI:894689; Ywhae.
DR   InterPro; IPR000308; 14-3-3.
DR   Pfam; PF00244; 14-3-3; 1.
DR   PRINTS; PR00305; 1433ZETA.
DR   ProDom; PD000600; 14-3-3; 1.
DR   SMART; SM00101; 14_3_3; 1.
DR   PROSITE; PS00796; 1433_1; 1.
DR   PROSITE; PS00797; 1433_2; 1.
KW   Brain; Neurone; Acetylation; Multigene family.
FT   MOD_RES       1      1       ACETYLATION.
FT   CONFLICT     73     73       K -> T (IN REF. 9).
FT   CONFLICT    120    120       F -> S (IN REF. 9).
FT   CONFLICT    123    123       K -> Y (IN REF. 9).
FT   CONFLICT    129    129       H -> Y (IN REF. 14).
SQ   SEQUENCE   255 AA;  29174 MW;  07817CCBD1F75B26 CRC64;
     MDDREDLVYQ AKLAEQAERY DEMVESMKKV AGMDVELTVE ERNLLSVAYK NVIGARRASW
     RIISSIEQKE ENKGGEDKLK MIREYRQMVE TELKLICCDI LDVLDKHLIP AANTGESKVF
     YYKMKGDYHR YLAEFATGND RKEAAENSLV AYKAASDIAM TELPPTHPIR LGLALNFSVF
     YYEILNSPDR ACRLAKAAFD DAIAELDTLS EESYKDSTLI MQLLRDNLTL WTSDMQGDGE
     EQNKEALQDV EDENQ
//
ID   143B_BOVIN     STANDARD;      PRT;   245 AA.
AC   P29358;
DT   01-DEC-1992 (Rel. 24, Created)
DT   01-FEB-1996 (Rel. 33, Last sequence update)
DT   16-OCT-2001 (Rel. 40, Last annotation update)
DE   14-3-3 protein beta/alpha (Protein kinase C inhibitor protein-1)
DE   (KCIP-1).
GN   YWHAB.
OS   Bos taurus (Bovine), and
OS   Ovis aries (Sheep).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea;
OC   Bovidae; Bovinae; Bos.
OX   NCBI_TaxID=9913, 9940;
RN   [1]
RP   SEQUENCE.
RC   SPECIES=Bovine;
RX   MEDLINE=91108808; PubMed=1671102;
RA   Isobe T., Ichimura T., Sunaya T., Okuyama T., Takahashi N., Kuwano R.,
RA   Takahashi Y.;
RT   "Distinct forms of the protein kinase-dependent activator of tyrosine
RT   and tryptophan hydroxylases.";
RL   J. Mol. Biol. 217:125-132(1991).
RN   [2]
RP   SEQUENCE OF 2-145 FROM N.A.
RC   SPECIES=Bovine; TISSUE=Retina;
RA   Jones J.M., Niikura T., Pinke R.M., Guo W., Molday L., Leykam J.,
RA   McConnell D.G.;
RT   "Expression of 14-3-3 proteins in bovine retinal photoreceptors.";
RL   Submitted (JAN-1998) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   SEQUENCE OF 2-83; 121-186 AND 199-241.
RC   SPECIES=Sheep; TISSUE=Brain;
RX   MEDLINE=92283271; PubMed=1317796;
RA   Toker A., Sellers L.A., Amess B., Patel Y., Harris A., Aitken A.;
RT   "Multiple isoforms of a protein kinase C inhibitor (KCIP-1/14-3-3)
RT   from sheep brain. Amino acid sequence of phosphorylated forms.";
RL   Eur. J. Biochem. 206:453-461(1992).
RN   [4]
RP   SEQUENCE OF 2-23.
RC   SPECIES=Sheep; TISSUE=Brain;
RX   MEDLINE=90345949; PubMed=2143472;
RA   Toker A., Ellis C.A., Sellers L.A., Aitken A.;
RT   "Protein kinase C inhibitor proteins. Purification from sheep brain
RT   and sequence similarity to lipocortins and 14-3-3 protein.";
RL   Eur. J. Biochem. 191:421-429(1990).
RN   [5]
RP   PHOSPHORYLATION.
RC   SPECIES=Sheep;
RX   MEDLINE=95197587; PubMed=7890696;
RA   Aitken A., Howell S., Jones D., Madrazo J., Patel Y.;
RT   "14-3-3 alpha and delta are the phosphorylated forms of
RT   raf-activating 14-3-3 beta and zeta. In vivo stoichiometric
RT   phosphorylation in brain at a Ser-Pro-Glu-Lys motif.";
RL   J. Biol. Chem. 270:5706-5709(1995).
RN   [6]
RP   POST-TRANSLATIONAL MODIFICATIONS.
RC   SPECIES=Sheep;
RA   Aitken A., Patel Y., Martin H., Jones D., Robinson K., Madrazo J.,
RA   Howell S.;
RT   "Electrospray mass spectroscopy analysis with online trapping of
RT   posttranslationally modified mammalian and avian brain 14-3-3
RT   isoforms.";
RL   J. Protein Chem. 13:463-465(1994).
CC   -!- FUNCTION: ACTIVATES TYROSINE AND TRYPTOPHAN HYDROXYLASES IN THE
CC       PRESENCE OF CA(2+)/CALMODULIN-DEPENDENT PROTEIN KINASE II, AND
CC       STRONGLY ACTIVATES PROTEIN KINASE C. IS PROBABLY A MULTIFUNCTIONAL
CC       REGULATOR OF THE CELL SIGNALING PROCESSES MEDIATED BY BOTH
CC       KINASES.
CC   -!- SUBUNIT: HOMODIMER.
CC   -!- SUBCELLULAR LOCATION: CYTOPLASMIC.
CC   -!- ALTERNATIVE PRODUCTS: TWO FORMS ARE PRODUCED BY ALTERNATIVE
CC       INITIATION.
CC   -!- TISSUE SPECIFICITY: 14-3-3 PROTEINS ARE LOCALIZED IN NEURONS, AND
CC       ARE AXONALLY TRANSPORTED TO THE NERVE TERMINALS. THEY MAY BE ALSO
CC       PRESENT, AT LOWER LEVELS, IN VARIOUS OTHER EUKARYOTIC TISSUES.
CC   -!- PTM: ISOFORM ALPHA DIFFERS FROM ISOFORM BETA IN BEING
CC       PHOSPHORYLATED.
CC   -!- SIMILARITY: BELONGS TO THE 14-3-3 FAMILY.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; AF043736; AAC02090.1; -.
DR   PIR; S13467; S13467.
DR   PIR; S10804; S10804.
DR   PIR; S23179; S23179.
DR   HSSP; P29312; 1A38.
DR   InterPro; IPR000308; 14-3-3.
DR   Pfam; PF00244; 14-3-3; 1.
DR   PRINTS; PR00305; 1433ZETA.
DR   ProDom; PD000600; 14-3-3; 1.
DR   SMART; SM00101; 14_3_3; 1.
DR   PROSITE; PS00796; 1433_1; 1.
DR   PROSITE; PS00797; 1433_2; 1.
KW   Brain; Neurone; Phosphorylation; Acetylation; Multigene family;
KW   Alternative initiation.
FT   INIT_MET      0      0
FT   CHAIN         1    245       14-3-3 PROTEIN BETA/ALPHA, LONG ISOFORM.
FT   CHAIN         2    245       14-3-3 PROTEIN BETA/ALPHA, SHORT ISOFORM.
FT   INIT_MET      2      2       FOR SHORT ISOFORM.
FT   MOD_RES       1      1       ACETYLATION.
FT   MOD_RES       2      2       ACETYLATION (IN SHORT ISOFORM).
FT   MOD_RES     185    185       PHOSPHORYLATION.
SQ   SEQUENCE   245 AA;  27950 MW;  AA91C2314D99549F CRC64;
     TMDKSELVQK AKLAEQAERY DDMAAAMKAV TEQGHELSNE ERNLLSVAYK NVVGARRSSW
     RVISSIEQKT ERNEKKQQMG KEYREKIEAE LQDICNDVLQ LLDKYLIPNA TQPESKVFYL
     KMKGDYFRYL SEVASGDNKQ TTVSNSQQAY QEAFEISKKE MQPTHPIRLG LALNFSVFYY
     EILNSPEKAC SLAKTAFDEA IAELDTLNEE SYKDSTLIMQ LLRDNLTLWT SENQGDEGDA
     GEGEN
//
ID   CALM_HUMAN     STANDARD;      PRT;   148 AA.
AC   P02593; P99014; P70667; Q61379; Q61380;
DT   21-JUL-1986 (Rel. 01, Created)
DT   21-JUL-1986 (Rel. 01, Last sequence update)
DT   16-OCT-2001 (Rel. 40, Last annotation update)
DE   Calmodulin.
GN   (CALM1 OR CAM1 OR CALM OR CAM) AND (CALM2 OR CAM2 OR CAMB) AND
GN   (CALM3 OR CAM3 OR CAMC).
OS   Homo sapiens (Human),
OS   Mus musculus (Mouse),
OS   Rattus norvegicus (Rat),
OS   Oryctolagus cuniculus (Rabbit),
OS   Bos taurus (Bovine),
OS   Gallus gallus (Chicken),
OS   Anas platyrhynchos (Domestic duck),
OS   Xenopus laevis (African clawed frog),
OS   Arbacia punctulata (Punctuate sea urchin),
OS   Oncorhynchus sp. (Salmon), and
OS   Oryzias latipes (Medaka fish).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606, 10090, 10116, 9986, 9913, 9031, 8839, 8355, 7641,
OX   8025, 8090;
RN   [1]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human;
RX   MEDLINE=89034207; PubMed=3182832;
RA   Fischer R., Koller M., Flura M., Mathews S., Strehler-Page M.A.,
RA   Krebs J., Penniston J.T., Carafoli E., Strehler E.E.;
RT   "Multiple divergent mRNAs code for a single human calmodulin.";
RL   J. Biol. Chem. 263:17055-17062(1988).
RN   [2]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human;
RX   MEDLINE=88059053; PubMed=2445749;
RA   Sengupta B., Friedberg F., Detera-Wadleigh S.D.;
RT   "Molecular analysis of human and rat calmodulin complementary DNA
RT   clones. Evidence for additional active genes in these species.";
RL   J. Biol. Chem. 262:16663-16670(1987).
RN   [3]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human;
RX   MEDLINE=85022688; PubMed=6385987;
RA   Wawrzynczak E.J., Perham R.N.;
RT   "Isolation and nucleotide sequence of a cDNA encoding human
RT   calmodulin.";
RL   Biochem. Int. 9:177-185(1984).
RN   [4]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human; TISSUE=Blood;
RX   MEDLINE=95010144; PubMed=7925473;
RA   Rhyner J.A., Ottiger M., Wicki R., Greenwood T.M., Strehler E.E.;
RT   "Structure of the human CALM1 calmodulin gene and identification of
RT   two CALM1-related pseudogenes CALM1P1 and CALM1P2.";
RL   Eur. J. Biochem. 225:71-82(1994).
RN   [5]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human; TISSUE=Lymphoma;
RA   Kato S.;
RL   Submitted (FEB-1995) to the EMBL/GenBank/DDBJ databases.
RN   [6]
RP   SEQUENCE.
RC   SPECIES=Human; TISSUE=Brain;
RX   MEDLINE=82231946; PubMed=7093203;
RA   Sasagawa T., Ericsson L.H., Walsh K.A., Schreiber W.E., Fischer E.H.,
RA   Titani K.;
RT   "Complete amino acid sequence of human brain calmodulin.";
RL   Biochemistry 21:2565-2569(1982).
RN   [7]
RP   SEQUENCE.
RC   SPECIES=Rabbit; TISSUE=Skeletal muscle;
RX   MEDLINE=81138220; PubMed=7202416;
RA   Grand R.J.A., Shenolikar S., Cohen P.;
RT   "The amino acid sequence of the delta subunit (calmodulin) of rabbit
RT   skeletal muscle phosphorylase kinase.";
RL   Eur. J. Biochem. 113:359-367(1981).
RN   [8]
RP   SEQUENCE.
RC   SPECIES=Bovine; TISSUE=Brain;
RA   Kasai H., Kato Y., Isobe T., Kawasaki H., Okuyama T.;
RT   "Determination of the complete amino acid sequence of calmodulin
RT   (phenylalanine-rich acidic protein II) from bovine brain.";
RL   Biomed. Res. 1:248-264(1980).
RN   [9]
RP   SEQUENCE.
RC   SPECIES=Bovine; TISSUE=Brain;
RX   MEDLINE=80094551; PubMed=7356670;
RA   Watterson D.M., Sharief F., Vanaman T.C.;
RT   "The complete amino acid sequence of the Ca2+-dependent modulator
RT   protein (calmodulin) of bovine brain.";
RL   J. Biol. Chem. 255:962-975(1980).
RN   [10]
RP   SEQUENCE.
RC   SPECIES=Bovine; TISSUE=Uterus;
RA   Grand R.J.A., Perry S.V.;
RT   "The amino acid sequence of the troponin C-like protein (modulator
RT   protein) from bovine uterus.";
RL   FEBS Lett. 92:137-142(1978).
RN   [11]
RP   SEQUENCE OF 38-60.
RC   SPECIES=Bovine;
RX   MEDLINE=89064822; PubMed=3058479;
RA   Pribilla I., Krueger H., Buchner K., Otto H., Schiebler W.,
RA   Tripier D., Hucho F.;
RT   "Heat-resistant inhibitors of protein kinase C from bovine brain.";
RL   Eur. J. Biochem. 177:657-664(1988).
RN   [12]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Mouse;
RX   MEDLINE=88257100; PubMed=3384819;
RA   Bender P.K., Dedman J.R., Emerson C.P.;
RT   "The abundance of calmodulin mRNAs is regulated in phosphorylase
RT   kinase-deficient skeletal muscle.";
RL   J. Biol. Chem. 263:9733-9737(1988).
RN   [13]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Mouse;
RX   MEDLINE=90006775; PubMed=2551780;
RA   Danchin A., Sezer O., Glaser P., Chalon P., Caput D.;
RT   "Cloning and expression of mouse-brain calmodulin as an activator of
RT   Bordetella pertussis adenylate cyclase in Escherichia coli.";
RL   Gene 80:145-149(1989).
RN   [14]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Mouse; STRAIN=BALB/C; TISSUE=Brain;
RA   Kato K.;
RT   "A collection of cDNA clones with specific expression patterns in
RT   mouse brain.";
RL   Eur. J. Neurosci. 2:704-711(1991).
RN   [15]
RP   SEQUENCE.
RC   SPECIES=Rat; TISSUE=Testis;
RX   MEDLINE=78066877; PubMed=201628;
RA   Dedman J.R., Jackson R.L., Schreiber W.E., Means A.R.;
RT   "Sequence homology of the Ca2+-dependent regulator of cyclic
RT   nucleotide phosphodiesterase from rat testis with other Ca2+-binding
RT   proteins.";
RL   J. Biol. Chem. 253:343-346(1978).
RN   [16]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Rat; TISSUE=Brain;
RX   MEDLINE=87246077; PubMed=2885164;
RA   Sherbany A.A., Parent A.S., Brosius J.;
RT   "Rat calmodulin cDNA.";
RL   DNA 6:267-272(1987).
RN   [17]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Rat; TISSUE=Brain;
RX   MEDLINE=87226204; PubMed=3035194;
RA   Nojima H., Hirofumi S.;
RT   "Structure of a gene for rat calmodulin.";
RL   J. Mol. Biol. 193:439-445(1987).
RN   [18]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Rat;
RX   MEDLINE=87257889; PubMed=3037336;
RA   Nojima H., Kishi K., Sokabe H.;
RT   "Multiple calmodulin mRNA species are derived from two distinct
RT   genes.";
RL   Mol. Cell. Biol. 7:1873-1880(1987).
RN   [19]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Rat; STRAIN=SHR;
RX   MEDLINE=89362474; PubMed=2527998;
RA   Nojima H.;
RT   "Structural organization of multiple rat calmodulin genes.";
RL   J. Mol. Biol. 208:269-282(1989).
RN   [20]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Chicken;
RX   MEDLINE=84008199; PubMed=6137485;
RA   Putkey J.A., Ts'Ui K.F., Tanaka T., Lagace L., Stein J.P., Lai E.C.,
RA   Means A.R.;
RT   "Chicken calmodulin genes. A species comparison of cDNA sequences and
RT   isolation of a genomic clone.";
RL   J. Biol. Chem. 258:11864-11870(1983).
RN   [21]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Chicken;
RX   MEDLINE=85104969; PubMed=2981850;
RA   Simmen R.C.M., Tanaka T., Ts'Ui K.F., Putkey J.A., Scott M.J.,
RA   Lai E.C., Means A.R.;
RT   "The structural organization of the chicken calmodulin gene.";
RL   J. Biol. Chem. 260:907-912(1985).
RN   [22]
RP   ERRATUM.
RC   SPECIES=Chicken;
RA   Simmen R.C.M., Tanaka T., Ts'Ui K.F., Putkey J.A., Scott M.J.,
RA   Lai E.C., Means A.R.;
RL   J. Biol. Chem. 262:4928-4929(1987).
RN   [23]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Chicken;
RA   Iida Y.;
RT   "cDNA sequences and molecular evolution of calmodulin genes of
RT   chicken and eel.";
RL   Bull. Chem. Soc. Jpn. 57:2667-2668(1984).
RN   [24]
RP   SEQUENCE FROM N.A.
RC   SPECIES=A.platyrhynchos;
RX   MEDLINE=93287810; PubMed=8389959;
RA   Kimura N., Kurosawa N., Kondo K., Tsukada Y.;
RT   "Molecular cloning of the kainate-binding protein and calmodulin
RT   genes which are induced by an imprinting stimulus in ducklings.";
RL   Brain Res. Mol. Brain Res. 17:351-355(1993).
RN   [25]
RP   SEQUENCE FROM N.A.
RC   SPECIES=X.laevis;
RX   MEDLINE=84191128; PubMed=6325880;
RA   Chien Y.-H., Dawid I.B.;
RT   "Isolation and characterization of calmodulin genes from Xenopus
RT   laevis.";
RL   Mol. Cell. Biol. 4:507-513(1984).
RN   [26]
RP   SEQUENCE OF 1-141 FROM N.A.
RC   SPECIES=A.punctulata;
RX   MEDLINE=88172463; PubMed=3351921;
RA   Hardy D.O., Bender P.K., Kretsinger R.H.;
RT   "Two calmodulin genes are expressed in Arbacia punctulata. An ancient
RT   gene duplication is indicated.";
RL   J. Mol. Biol. 199:223-227(1988).
RN   [27]
RP   SEQUENCE.
RC   SPECIES=Salmon;
RA   Yazawa M., Toda H., Yagi Y.;
RT   "Amino acid sequence of salmon calmodulin.";
RL   Seikagaku 57:1037-1037(1985).
RN   [28]
RP   SEQUENCE FROM N.A.
RC   SPECIES=O.latipes;
RX   MEDLINE=93012998; PubMed=1398109;
RA   Matsuo K., Sato K., Ikeshima H., Shimoda K., Takano T.;
RT   "Four synonymous genes encode calmodulin in the teleost fish, medaka
RT   (Oryzias latipes): conservation of the multigene one-protein
RT   principle.";
RL   Gene 119:279-281(1992).
RN   [29]
RP   SEQUENCE OF 1-27, AND UBIQUITYLATION OF LYS-21.
RC   SPECIES=Bovine;
RX   MEDLINE=98380241; PubMed=9716384;
RA   Laub M., Steppuhn J.A., Blueggel M., Immler D., Meyer H.E.,
RA   Jennissen H.P.;
RT   "Modulation of calmodulin function by ubiquitin-calmodulin ligase and
RT   identification of the responsible ubiquitylation site in vertebrate
RT   calmodulin.";
RL   Eur. J. Biochem. 255:422-431(1998).
RN   [30]
RP   X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
RC   SPECIES=Rat;
RX   MEDLINE=85188323; PubMed=3990807;
RA   Babu Y.S., Sack J.S., Greenhough T.J., Bugg C.E., Means A.R.,
RA   Cook W.J.;
RT   "Three-dimensional structure of calmodulin.";
RL   Nature 315:37-40(1985).
RN   [31]
RP   X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
RC   SPECIES=Rat;
RX   MEDLINE=89110997; PubMed=3145979;
RA   Babu Y.S., Bugg C.E., Cook W.J.;
RT   "Structure of calmodulin refined at 2.2-A resolution.";
RL   J. Mol. Biol. 204:191-204(1988).
RN   [32]
RP   X-RAY CRYSTALLOGRAPHY (2 ANGSTROMS).
RC   SPECIES=Bovine;
RX   MEDLINE=98104088; PubMed=9438860;
RA   Wall M.E., Clarage J.B., Phillips G.N.;
RT   "Motions of calmodulin characterized using both Bragg and diffuse
RT   X-ray scattering.";
RL   Structure 5:1599-1612(1997).
RN   [33]
RP   STRUCTURE BY NMR OF 76-148.
RX   MEDLINE=94085641; PubMed=8262263;
RA   Finn B.E., Drakenberg T., Forsen S.;
RT   "The structure of apo-calmodulin. A 1H NMR examination of the
RT   carboxy-terminal domain.";
RL   FEBS Lett. 336:368-374(1993).
RN   [34]
RP   STRUCTURE BY NMR OF 76-148.
RX   MEDLINE=96018615; PubMed=7552749;
RA   Finn B.E., Evenas J., Drakenberg T., Waltho J.P., Thulin E.,
RA   Forsen S.;
RT   "Calcium-induced structural changes and domain autonomy in
RT   calmodulin.";
RL   Nat. Struct. Biol. 2:777-783(1995).
RN   [35]
RP   STRUCTURE BY NMR.
RX   MEDLINE=96018613; PubMed=7552747;
RA   Zhang M., Tanaka T., Ikura M.;
RT   "Calcium-induced conformational transition revealed by the solution
RT   structure of apo calmodulin.";
RL   Nat. Struct. Biol. 2:758-767(1995).
RN   [36]
RP   STRUCTURE BY NMR.
RX   MEDLINE=96018614; PubMed=7552748;
RA   Kuboniwa H., Tjandra N., Grzesiek S., Ren H., Klee C.B., Bax A.;
RT   "Solution structure of calcium-free calmodulin.";
RL   Nat. Struct. Biol. 2:768-776(1995).
RN   [37]
RP   STRUCTURE BY NMR.
RX   MEDLINE=98179557; PubMed=9514729;
RA   Osawa M., Swindells M.B., Tanikawa J., Tanaka T., Mase T., Furuya T.,
RA   Ikura M.;
RT   "Solution structure of calmodulin-W-7 complex: the basis of diversity
RT   in molecular recognition.";
RL   J. Mol. Biol. 276:165-176(1998).
RN   [38]
RP   STRUCTURE BY NMR.
RX   MEDLINE=99425120; PubMed=10493800;
RA   Elshorst B., Hennig M., Foersterling H., Diener A., Maurer M.,
RA   Schulte P., Schwalbe H., Griesinger C., Krebs J., Schmid H.,
RA   Vorherr T., Carafoli E.;
RT   "NMR solution structure of a complex of calmodulin with a binding
RT   peptide of the Ca(2+) pump.";
RL   Biochemistry 38:12320-12332(1999).
CC   -!- FUNCTION: CALMODULIN MEDIATES THE CONTROL OF A LARGE NUMBER OF
CC       ENZYMES BY CA(++). AMONG THE ENZYMES TO BE STIMULATED BY THE
CC       CALMODULIN-CA(++) COMPLEX ARE A NUMBER OF PROTEIN KINASES AND
CC       PHOSPHATASES.
CC   -!- PTM: UBIQUITYLATION STRONGLY DECREASES THE ACTIVITY.
CC   -!- MISCELLANEOUS: THIS PROTEIN HAS FOUR FUNCTIONAL CALCIUM-BINDING
CC       SITES.
CC   -!- SIMILARITY: TO OTHER EF-HAND CALCIUM BINDING PROTEINS.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
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DR   EMBL; L00101; AAA48653.1; -.
DR   EMBL; L00096; AAA48653.1; JOINED.
DR   EMBL; L00097; AAA48653.1; JOINED.
DR   EMBL; L00098; AAA48653.1; JOINED.
DR   EMBL; L00099; AAA48653.1; JOINED.
DR   EMBL; L00100; AAA48653.1; JOINED.
DR   EMBL; M16659; AAA40864.1; -.
DR   EMBL; M27319; AAA35635.1; -.
DR   EMBL; U12022; AAB60644.1; -.
DR   EMBL; U11886; AAB60644.1; JOINED.
DR   EMBL; D45887; BAA08302.1; -.
DR   EMBL; X13817; CAA32050.1; -.
DR   EMBL; J04046; AAA51918.1; -.
DR   EMBL; M19311; AAA35641.1; -.
DR   EMBL; M19312; AAA40862.1; -.
DR   EMBL; M17069; AAA40863.1; -.
DR   EMBL; X13933; CAA32120.1; -.
DR   EMBL; X13931; CAA32119.1; -.
DR   EMBL; X13932; CAA32119.1; JOINED.
DR   EMBL; X05117; CAA32119.1; JOINED.
DR   EMBL; X13833; CAA32062.1; -.
DR   EMBL; X13834; CAA32062.1; JOINED.
DR   EMBL; X13835; CAA32062.1; JOINED.
DR   EMBL; X14265; CAA32478.1; -.
DR   EMBL; D83350; BAA11896.1; -.
DR   EMBL; M36167; AAA48650.1; -.
DR   EMBL; K01944; AAA49668.1; -.
DR   EMBL; K01945; AAA49669.1; -.
DR   EMBL; D10363; BAA01195.1; -.
DR   EMBL; M19380; AAA66181.1; -.
DR   EMBL; M19381; AAA66182.1; -.
DR   EMBL; L31642; AAA65934.1; -.
DR   EMBL; M27844; AAA37365.1; -.
DR   EMBL; X61432; CAA43674.1; -.
DR   PIR; S13159; MCHU.
DR   PIR; JK0013; MCON.
DR   PIR; A90719; MCBO.
DR   PIR; A91104; MCRB.
DR   PIR; S03206; MCRT.
DR   PIR; A92394; MCCH.
DR   PIR; S02690; S02690.
DR   PIR; A60781; A60781.
DR   PIR; JC1305; JC1305.
DR   PDB; 2CLN; 15-OCT-94.
DR   PDB; 3CLN; 09-JAN-89.
DR   PDB; 1TRC; 15-OCT-91.
DR   PDB; 1AK8; 17-SEP-97.
DR   PDB; 1CDL; 31-AUG-94.
DR   PDB; 1CDM; 31-AUG-94.
DR   PDB; 1CFC; 07-DEC-95.
DR   PDB; 1CFD; 07-DEC-95.
DR   PDB; 1CLL; 31-OCT-93.
DR   PDB; 1CM1; 04-MAR-98.
DR   PDB; 1CM4; 04-MAR-98.
DR   PDB; 1CMF; 07-DEC-95.
DR   PDB; 1CMG; 07-DEC-95.
DR   PDB; 1CTR; 20-DEC-94.
DR   PDB; 1DEG; 31-MAY-94.
DR   PDB; 1DMO; 01-AUG-96.
DR   PDB; 1LIN; 08-MAR-96.
DR   PDB; 1AJI; 17-SEP-97.
DR   PDB; 1A29; 16-SEP-98.
DR   PDB; 1MUX; 25-NOV-98.
DR   PDB; 1CFF; 24-SEP-91.
DR   SWISS-2DPAGE; P99014; MOUSE.
DR   Aarhus/Ghent-2DPAGE; 9048; IEF.
DR   MIM; 114180; -.
DR   MIM; 114182; -.
DR   MIM; 114183; -.
DR   MGD; MGI:88251; Calm.
DR   MGD; MGI:103250; Calm2.
DR   MGD; MGI:103249; Calm3.
DR   InterPro; IPR002048; EF-hand.
DR   Pfam; PF00036; efhand; 4.
DR   SMART; SM00054; EFh; 4.
DR   PROSITE; PS00018; EF_HAND; 4.
KW   Calcium-binding; Duplication; Methylation; Acetylation;
KW   3D-structure.
FT   INIT_MET      0      0
FT   MOD_RES       1      1       ACETYLATION.
FT   MOD_RES     115    115       METHYLATION (TRI-) (IN CHICKEN).
FT   CA_BIND      20     31       EF-HAND 1.
FT   CA_BIND      56     67       EF-HAND 2.
FT   CA_BIND      93    104       EF-HAND 3.
FT   CA_BIND     129    140       EF-HAND 4.
FT   BINDING      21     21       UBIQUITIN (MULTI-).
FT   CONFLICT     25     25       G -> N (IN REF. 12; AAA66182).
FT   HELIX         5     19
FT   TURN         21     22
FT   STRAND       26     27
FT   HELIX        29     37
FT   TURN         38     40
FT   HELIX        45     55
FT   TURN         57     58
FT   STRAND       63     64
FT   HELIX        65     92
FT   TURN         94     95
FT   STRAND      100    100
FT   HELIX       102    111
FT   TURN        112    113
FT   HELIX       118    128
FT   STRAND      136    136
FT   HELIX       138    146
SQ   SEQUENCE   148 AA;  16706 MW;  464B8A287475A1CA CRC64;
     ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN
     GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE
     VDEMIREADI DGDGQVNYEE FVQMMTAK
//
BioPerl-1.007002/t/data/seqxml.xml000444000766000024       225213155576321 16724 0ustar00cjfieldsstaff000000000000

    
        
        dystroglycan 1
        AAGGC----UGAUGUC.....ACAU
        
        
        
    
    
        
        example description.
        AAGGCGAAA----AA*AAAAAGT.....CACJOXA
    
    
        
        another example description
        AAGGCGTTAAA----AAAAAAAGT.....CACTA
    
    
        NNNNACTG--AAATGTGCCCGGG
    

BioPerl-1.007002/t/data/short.blx000444000766000024      3630613155576321 16566 0ustar00cjfieldsstaff000000000000BLASTX 2.0.13 [May-26-2000]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= 18.ctg12393
         (6959 letters)

Database: h_nrNov10_2000
           57,234 sequences; 18,303,128 total letters

Searching..................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gi|728837|sp|P39194|ALU7_HUMAN ALU SUBFAMILY SQ SEQUENCE CONTAM...   161  8e-39
gi|728836|sp|P39193|ALU6_HUMAN ALU SUBFAMILY SP SEQUENCE CONTAM...   156  3e-37

>gi|728837|sp|P39194|ALU7_HUMAN ALU SUBFAMILY SQ SEQUENCE
            CONTAMINATION WARNING ENTRY
          Length = 593

 Score =  161 bits (404), Expect = 8e-39
 Identities = 73/97 (75%), Positives = 76/97 (78%)
 Frame = -1

Query: 2996 FFLRQSFTLVTQAGVQWHDLSSLQPLPPRFKGFSSLSLPISWDYRRLPPCLANFCIFHKD 2817
            FFLR+SF LV QAGVQW DL SLQP PP FK FS LSLP SWDYRR PP  ANFCIF +D
Sbjct: 299  FFLRRSFALVAQAGVQWRDLGSLQPPPPGFKRFSCLSLPSSWDYRRPPPRPANFCIFSRD 358

Query: 2816 GVLPCWPGWS*TPDLR*YAHFGIPKCWDYRREPPCPA 2706
            GV PCWPGWS TPDLR     G+PKCWDYRREPP PA
Sbjct: 359  GVSPCWPGWSRTPDLRXSTRLGLPKCWDYRREPPRPA 395


 Score =  156 bits (391), Expect = 3e-37
 Identities = 76/97 (78%), Positives = 83/97 (85%)
 Frame = +3

Query: 2706 GRARWLTPVIPALWDAKVGISSEVRSSRPAWPTWQNSVFMKNTKISQAWWQAPVIPANWE 2885
            GRARWLTPVIPALW+A+ G S EVRSSRPAWPTW N V  KNTKIS+AWW+APVIPA  E
Sbjct: 1    GRARWLTPVIPALWEAEAGGSPEVRSSRPAWPTWXNPVSTKNTKISRAWWRAPVIPATRE 60

Query: 2886 AEAGESLESRRQRLQ*AEIVPLHSSLGDKSKTLSQKK 2996
            AEAGESLE  R+RLQ AEI PLHSSLG+KS+T SQKK
Sbjct: 61   AEAGESLEPGRRRLQXAEIAPLHSSLGNKSETPSQKK 97


 Score =  140 bits (349), Expect = 2e-32
 Identities = 74/101 (73%), Positives = 79/101 (77%)
 Frame = -2

Query: 2995 FF*DRVLLLSPRLECNGTISAHCNLCLLDSRDSPASASQLAGITGACHHAWLIFVFFIKT 2816
            FF D V LL PRLEC+G ISAHCNL L  S DSPASAS++AGITGA HHA LIFVF ++T
Sbjct: 399  FFXDGVSLLLPRLECSGAISAHCNLRLPGSSDSPASASRVAGITGARHHARLIFVFLVET 458

Query: 2815 EFCHVGQAGLELLTSDDMPTLASQSAGITGVSHRARPGIMF 2693
             F HVGQAGLELLTS D P  ASQSAGITGVSHRAR    F
Sbjct: 459  GFHHVGQAGLELLTSGDPPASASQSAGITGVSHRARXXXFF 499


 Score =  134 bits (334), Expect = 1e-30
 Identities = 67/89 (75%), Positives = 71/89 (79%)
 Frame = +1

Query: 2707 AGHGGSRL*SQHFGMPKWAYHLRSGVQDQPGQHGKTPSL*KIQKLARHGGRRL*SQLIGR 2886
            AG GGSRL SQHFG P+   HLRSGV+DQPGQHG+TPSL KIQKLA  GG RL SQL+GR
Sbjct: 101  AGRGGSRLXSQHFGRPRRVDHLRSGVRDQPGQHGETPSLLKIQKLAGRGGGRLXSQLLGR 160

Query: 2887 LRLENPLNLGGRGCSELRSCHCTPAWVTR 2973
            LR EN LN GG GCSE RS HCTPAW TR
Sbjct: 161  LRQENRLNPGGGGCSEPRSRHCTPAWATR 189


 Score =  129 bits (321), Expect = 4e-29
 Identities = 72/101 (71%), Positives = 75/101 (73%)
 Frame = +2

Query: 2693 KHYTWPGTVAHACNPSTLGCQSGHII*GQEFKTSLANMAKLRLYEKYKN*PGMVAGACNP 2872
            K    PG VAHACNPSTLG + G I  GQEF+TSLANM K RLY KYKN PG+VAGACNP
Sbjct: 195  KKXXXPGAVAHACNPSTLGGRGGWITXGQEFETSLANMVKPRLYXKYKNXPGVVAGACNP 254

Query: 2873 S*LGG*GWRIP*I*EAEVAVS*DRAIALQPG*QE*NSVSKK 2995
            S  GG G RI    EAEVAVS DRA ALQPG QE NSVSKK
Sbjct: 255  SYSGGXGRRIAXTREAEVAVSRDRATALQPGQQERNSVSKK 295


 Score =  119 bits (295), Expect = 5e-26
 Identities = 74/101 (73%), Positives = 79/101 (77%), Gaps = 54/101 (53%)
 Frame = +1

Query: 5179 FFLRWSFALSPRLECSGAISAHCNLRLPGSSNSPASASRVAGTTGVRHHTRLIFVFFVKT 5358
            FF      L PRLECSGAISAHCNLRLPGSS+SPASASRVAG TG RHH RLIFVF V+T
Sbjct: 399  FFXDGVSLLLPRLECSGAISAHCNLRLPGSSDSPASASRVAGITGARHHARLIFVFLVET 458

Query: 5359 GFHHVGQ------------------AGLN------------------------------- 5391
            GFHHVGQ                  AG+                                
Sbjct: 459  GFHHVGQAGLELLTSGDPPASASQSAGITGVSHRARXXXFFETEFRSCCPGWSAVARSRL 518

Query: 5392 -----SRPQVIHLSQPPKVLGLQV*ATVPGYFMDF 5481
                 SR Q I L QPP+ LGLQ  AT PG F+ F
Sbjct: 519  TATSASRVQAILLPQPPEXLGLQAPATTPGXFLYF 553


 Score =  113 bits (281), Expect = 2e-24
 Identities = 65/94 (69%), Positives = 73/94 (77%), Gaps = 55/94 (58%)
 Frame = +3

Query: 5205 VTQAGMQWCNLSSLQPPPPRFKQFSCLSLPSSWDYRCAPPHQANFCIFCKDRFSPRWPGW 5384
            V QAG+QW +L SLQPPPP FK+FSCLSLPSSWDYR  PP  ANFCIF +D  SP WPGW
Sbjct: 308  VAQAGVQWRDLGSLQPPPPGFKRFSCLSLPSSWDYRRPPPRPANFCIFSRDGVSPCWPGW 367

Query: 5385 S-----------------------------------------ELQTSG------------ 5405
            S                                          L+ SG            
Sbjct: 368  SRTPDLRXSTRLGLPKCWDYRREPPRPAXXXFFXDGVSLLLPRLECSGAISAHCNLRLPG 427

Query: 5406 --DSPVSASQSAGITGVSHRARLLHGFLI 5486
              DSP SAS+ AGITG  H ARL+  FL+
Sbjct: 428  SSDSPASASRVAGITGARHHARLIFVFLV 456


 Score =  111 bits (276), Expect(2) = 1e-32
 Identities = 51/63 (80%), Positives = 55/63 (86%)
 Frame = -1

Query: 5387 RPAWPTW*KPVFTKNTKISLVWWRTPVVPATREAEAGELLEPGRRRLQ*AEIAPLHSSLG 5208
            RPAWPTW  PV TKNTKIS  WWR PV+PATREAEAGE LEPGRRRLQ AEIAPLHSSLG
Sbjct: 28   RPAWPTWXNPVSTKNTKISRAWWRAPVIPATREAEAGESLEPGRRRLQXAEIAPLHSSLG 87

Query: 5207 DRA 5199
            +++
Sbjct: 88   NKS 90


 Score = 89.7 bits (219), Expect(2) = 6e-24
 Identities = 45/61 (73%), Positives = 45/61 (73%)
 Frame = -2

Query: 5386 DQPGQRGENLSLQKIQKLAWCGGAHL*SQLLGRLRQENCLNLGGGGCSELRLHHCIPAWV 5207
            DQPGQ GE  SL KIQKLA  GG  L SQLLGRLRQEN LN GGGGCSE R  HC PAW 
Sbjct: 128  DQPGQHGETPSLLKIQKLAGRGGGRLXSQLLGRLRQENRLNPGGGGCSEPRSRHCTPAWA 187

Query: 5206 T 5204
            T
Sbjct: 188  T 188


 Score = 87.8 bits (214), Expect = 1e-16
 Identities = 53/89 (59%), Positives = 56/89 (62%)
 Frame = -3

Query: 2973 SCHPGWSAMARSQLTATSASXXXXXXXXXXXXXXXXXXXATMPG*FLYFS*RRSFAMLAR 2794
            SC PGWSA+ARS+LTATSAS                   AT PG FLYF  RR F MLAR
Sbjct: 505  SCCPGWSAVARSRLTATSASRVQAILLPQPPEXLGLQAPATTPGXFLYFXXRRGFTMLAR 564

Query: 2793 LVLNS*PQMICPLWHPKVLGLQA*ATVPG 2707
            LV NS PQ+I P   PKVLGLQA AT PG
Sbjct: 565  LVSNSXPQVIHPPRPPKVLGLQAXATAPG 593


 Score = 83.1 bits (202), Expect = 4e-15
 Identities = 45/62 (72%), Positives = 48/62 (76%)
 Frame = -3

Query: 5388 QTSLANVVKTCLYKKYKN*PGVVAHTCSPSYSGG*GRRIA*TWEAEVAVS*DCTTAFQPG 5209
            +TSLAN+VK  LY KYKN PGVVA  C+PSYSGG GRRIA T EAEVAVS D  TA QPG
Sbjct: 226  ETSLANMVKPRLYXKYKNXPGVVAGACNPSYSGGXGRRIAXTREAEVAVSRDRATALQPG 285

Query: 5208 *Q 5203
             Q
Sbjct: 286  QQ 287


 Score = 62.8 bits (150), Expect = 5e-09
 Identities = 36/61 (59%), Positives = 41/61 (67%)
 Frame = +2

Query: 5204 CHPGWNAVVQSQLTATSASQVQAIXXXXXXXXXXXXVCATTPG*FLYFL*RQVFTTLARL 5383
            C PGW+AV +S+LTATSAS+VQAI              ATTPG FLYF  R+ FT LARL
Sbjct: 506  CCPGWSAVARSRLTATSASRVQAILLPQPPEXLGLQAPATTPGXFLYFXXRRGFTMLARL 565

Query: 5384 V 5386
            V
Sbjct: 566  V 566


 Score = 50.4 bits (118), Expect(2) = 1e-32
 Identities = 23/26 (88%), Positives = 23/26 (88%)
 Frame = -2

Query: 5464 RARWLTPVIPALWEAETGESPEVWSS 5387
            RARWLTPVIPALWEAE G SPEV SS
Sbjct: 2    RARWLTPVIPALWEAEAGGSPEVRSS 27


 Score = 47.6 bits (111), Expect = 2e-04
 Identities = 23/38 (60%), Positives = 24/38 (62%)
 Frame = +2

Query: 5390 TPDLR*FTCLSLPKCWDYRCEPPCPATSWIFDYRLCLL 5503
            TPDLR  T L LPKCWDYR EPP PA    F   + LL
Sbjct: 370  TPDLRXSTRLGLPKCWDYRREPPRPAXXXFFXDGVSLL 407


 Score = 43.4 bits (100), Expect(2) = 6e-24
 Identities = 20/27 (74%), Positives = 23/27 (85%)
 Frame = -3

Query: 5466 AGHGGSHL*SQHFGRLRQVNHLRSGVQ 5386
            AG GGS L SQHFGR R+V+HLRSGV+
Sbjct: 101  AGRGGSRLXSQHFGRPRRVDHLRSGVR 127


>gi|728836|sp|P39193|ALU6_HUMAN ALU SUBFAMILY SP SEQUENCE
            CONTAMINATION WARNING ENTRY
          Length = 593

 Score =  156 bits (390), Expect = 3e-37
 Identities = 71/97 (73%), Positives = 74/97 (76%)
 Frame = -1

Query: 2996 FFLRQSFTLVTQAGVQWHDLSSLQPLPPRFKGFSSLSLPISWDYRRLPPCLANFCIFHKD 2817
            FFLR+SF LV QAGVQW DL S QP PP FK FS LSLP SWDYR  PP  ANFCIF +D
Sbjct: 299  FFLRRSFALVAQAGVQWRDLGSPQPPPPGFKRFSCLSLPSSWDYRHAPPRPANFCIFSRD 358

Query: 2816 GVLPCWPGWS*TPDLR*YAHFGIPKCWDYRREPPCPA 2706
            GV PCW GWS TPDLR  A  G+PKCWDYRREPP PA
Sbjct: 359  GVSPCWSGWSRTPDLRXSARLGLPKCWDYRREPPRPA 395


 Score =  146 bits (364), Expect = 4e-34
 Identities = 72/97 (74%), Positives = 81/97 (83%)
 Frame = +3

Query: 2706 GRARWLTPVIPALWDAKVGISSEVRSSRPAWPTWQNSVFMKNTKISQAWWQAPVIPANWE 2885
            GRARWLTPVIPALW+A+ G S EV SSRPA PTW+N V  KNTKIS+AWW+ PVIPA  E
Sbjct: 1    GRARWLTPVIPALWEAEAGGSPEVGSSRPAXPTWRNPVSTKNTKISRAWWRMPVIPATRE 60

Query: 2886 AEAGESLESRRQRLQ*AEIVPLHSSLGDKSKTLSQKK 2996
            AEAGESLE  R+RL+ AEI PLHSSLG+KS+T SQKK
Sbjct: 61   AEAGESLEPGRRRLRXAEIAPLHSSLGNKSETPSQKK 97


 Score =  133 bits (332), Expect = 2e-30
 Identities = 72/101 (71%), Positives = 76/101 (74%)
 Frame = -2

Query: 2995 FF*DRVLLLSPRLECNGTISAHCNLCLLDSRDSPASASQLAGITGACHHAWLIFVFFIKT 2816
            FF D V LL PRLECNG ISAH NL L  S DSPASAS++AGITG  HHA LIFVF ++T
Sbjct: 399  FFXDGVSLLLPRLECNGAISAHRNLRLPGSSDSPASASRVAGITGMRHHARLIFVFLVET 458

Query: 2815 EFCHVGQAGLELLTSDDMPTLASQSAGITGVSHRARPGIMF 2693
             F HVGQAGLEL TS D P  ASQSAGITGVSHRAR    F
Sbjct: 459  GFLHVGQAGLELPTSGDPPASASQSAGITGVSHRARXXXFF 499


 Score =  129 bits (320), Expect = 5e-29
 Identities = 65/89 (73%), Positives = 69/89 (77%)
 Frame = +1

Query: 2707 AGHGGSRL*SQHFGMPKWAYHLRSGVQDQPGQHGKTPSL*KIQKLARHGGRRL*SQLIGR 2886
            AG GGSRL SQHFG P+ A HLRSGV+DQP QHG+TPSL KIQKLA  GG  L SQL+GR
Sbjct: 101  AGRGGSRLXSQHFGRPRRADHLRSGVRDQPDQHGETPSLLKIQKLAGRGGACLXSQLLGR 160

Query: 2887 LRLENPLNLGGRGCSELRSCHCTPAWVTR 2973
            LR EN LN GG GC E RS HCTPAW TR
Sbjct: 161  LRQENRLNPGGGGCGEPRSRHCTPAWATR 189


 Score =  125 bits (311), Expect = 6e-28
 Identities = 70/101 (69%), Positives = 74/101 (72%)
 Frame = +2

Query: 2693 KHYTWPGTVAHACNPSTLGCQSGHII*GQEFKTSLANMAKLRLYEKYKN*PGMVAGACNP 2872
            K    PG VAHACNPSTLG + G I  G+EF+TSL NM K RLY KYKN PG+VA ACNP
Sbjct: 195  KKXXXPGAVAHACNPSTLGGRGGRITXGREFETSLTNMEKPRLYXKYKNXPGVVAHACNP 254

Query: 2873 S*LGG*GWRIP*I*EAEVAVS*DRAIALQPG*QE*NSVSKK 2995
            S  GG G RI    EAEVAVS DRAIALQPG QE NSVSKK
Sbjct: 255  SYSGGXGRRIAXTREAEVAVSRDRAIALQPGQQERNSVSKK 295


 Score =  109 bits (270), Expect = 4e-23
 Identities = 71/101 (70%), Positives = 78/101 (76%), Gaps = 54/101 (53%)
 Frame = +1

Query: 5179 FFLRWSFALSPRLECSGAISAHCNLRLPGSSNSPASASRVAGTTGVRHHTRLIFVFFVKT 5358
            FF      L PRLEC+GAISAH NLRLPGSS+SPASASRVAG TG+RHH RLIFVF V+T
Sbjct: 399  FFXDGVSLLLPRLECNGAISAHRNLRLPGSSDSPASASRVAGITGMRHHARLIFVFLVET 458

Query: 5359 GFHHVGQ------------------AGLN------------------------------- 5391
            GF HVGQ                  AG+                                
Sbjct: 459  GFLHVGQAGLELPTSGDPPASASQSAGITGVSHRARXXXFFETEFRSCCPGWSAMARSRL 518

Query: 5392 -----SRPQVIHLSQPPKVLGLQV*ATVPGYFMDF 5481
                 SR Q I L QPP+ LGLQ  AT PG F+ F
Sbjct: 519  TATSASRVQAILLPQPPEXLGLQACATTPGXFLYF 553


 Score =  105 bits (260), Expect = 6e-22
 Identities = 62/94 (65%), Positives = 71/94 (74%), Gaps = 55/94 (58%)
 Frame = +3

Query: 5205 VTQAGMQWCNLSSLQPPPPRFKQFSCLSLPSSWDYRCAPPHQANFCIFCKDRFSPRWPGW 5384
            V QAG+QW +L S QPPPP FK+FSCLSLPSSWDYR APP  ANFCIF +D  SP W GW
Sbjct: 308  VAQAGVQWRDLGSPQPPPPGFKRFSCLSLPSSWDYRHAPPRPANFCIFSRDGVSPCWSGW 367

Query: 5385 S-----------------------------------------------------ELQTSG 5405
            S                                                      L+  G
Sbjct: 368  SRTPDLRXSARLGLPKCWDYRREPPRPAXXXFFXDGVSLLLPRLECNGAISAHRNLRLPG 427

Query: 5406 DS--PVSASQSAGITGVSHRARLLHGFLI 5486
             S  P SAS+ AGITG+ H ARL+  FL+
Sbjct: 428  SSDSPASASRVAGITGMRHHARLIFVFLV 456


 Score =  104 bits (258), Expect(2) = 1e-30
 Identities = 49/63 (77%), Positives = 54/63 (84%)
 Frame = -1

Query: 5387 RPAWPTW*KPVFTKNTKISLVWWRTPVVPATREAEAGELLEPGRRRLQ*AEIAPLHSSLG 5208
            RPA PTW  PV TKNTKIS  WWR PV+PATREAEAGE LEPGRRRL+ AEIAPLHSSLG
Sbjct: 28   RPAXPTWRNPVSTKNTKISRAWWRMPVIPATREAEAGESLEPGRRRLRXAEIAPLHSSLG 87

Query: 5207 DRA 5199
            +++
Sbjct: 88   NKS 90


 Score = 88.2 bits (215), Expect = 1e-16
 Identities = 53/89 (59%), Positives = 56/89 (62%)
 Frame = -3

Query: 2973 SCHPGWSAMARSQLTATSASXXXXXXXXXXXXXXXXXXXATMPG*FLYFS*RRSFAMLAR 2794
            SC PGWSAMARS+LTATSAS                   AT PG FLYF  RR F+ML R
Sbjct: 505  SCCPGWSAMARSRLTATSASRVQAILLPQPPEXLGLQACATTPGXFLYFXXRRGFSMLVR 564

Query: 2793 LVLNS*PQMICPLWHPKVLGLQA*ATVPG 2707
            LV NS PQ+I P   PKVLGLQA AT PG
Sbjct: 565  LVSNSRPQVIRPPRPPKVLGLQAXATAPG 593


 Score = 85.8 bits (209), Expect(2) = 2e-22
 Identities = 44/61 (72%), Positives = 44/61 (72%)
 Frame = -2

Query: 5386 DQPGQRGENLSLQKIQKLAWCGGAHL*SQLLGRLRQENCLNLGGGGCSELRLHHCIPAWV 5207
            DQP Q GE  SL KIQKLA  GGA L SQLLGRLRQEN LN GGGGC E R  HC PAW 
Sbjct: 128  DQPDQHGETPSLLKIQKLAGRGGACLXSQLLGRLRQENRLNPGGGGCGEPRSRHCTPAWA 187

Query: 5206 T 5204
            T
Sbjct: 188  T 188


 Score = 80.8 bits (196), Expect = 2e-14
 Identities = 43/62 (69%), Positives = 46/62 (73%)
 Frame = -3

Query: 5388 QTSLANVVKTCLYKKYKN*PGVVAHTCSPSYSGG*GRRIA*TWEAEVAVS*DCTTAFQPG 5209
            +TSL N+ K  LY KYKN PGVVAH C+PSYSGG GRRIA T EAEVAVS D   A QPG
Sbjct: 226  ETSLTNMEKPRLYXKYKNXPGVVAHACNPSYSGGXGRRIAXTREAEVAVSRDRAIALQPG 285

Query: 5208 *Q 5203
             Q
Sbjct: 286  QQ 287


 Score = 63.2 bits (151), Expect = 4e-09
 Identities = 34/61 (55%), Positives = 41/61 (66%)
 Frame = +2

Query: 5204 CHPGWNAVVQSQLTATSASQVQAIXXXXXXXXXXXXVCATTPG*FLYFL*RQVFTTLARL 5383
            C PGW+A+ +S+LTATSAS+VQAI             CATTPG FLYF  R+ F+ L RL
Sbjct: 506  CCPGWSAMARSRLTATSASRVQAILLPQPPEXLGLQACATTPGXFLYFXXRRGFSMLVRL 565

Query: 5384 V 5386
            V
Sbjct: 566  V 566


 Score = 50.8 bits (119), Expect(2) = 1e-30
 Identities = 23/26 (88%), Positives = 23/26 (88%)
 Frame = -2

Query: 5464 RARWLTPVIPALWEAETGESPEVWSS 5387
            RARWLTPVIPALWEAE G SPEV SS
Sbjct: 2    RARWLTPVIPALWEAEAGGSPEVGSS 27


 Score = 45.7 bits (106), Expect = 7e-04
 Identities = 22/38 (57%), Positives = 23/38 (59%)
 Frame = +2

Query: 5390 TPDLR*FTCLSLPKCWDYRCEPPCPATSWIFDYRLCLL 5503
            TPDLR    L LPKCWDYR EPP PA    F   + LL
Sbjct: 370  TPDLRXSARLGLPKCWDYRREPPRPAXXXFFXDGVSLL 407


 Score = 41.8 bits (96), Expect(2) = 2e-22
 Identities = 19/27 (70%), Positives = 22/27 (81%)
 Frame = -3

Query: 5466 AGHGGSHL*SQHFGRLRQVNHLRSGVQ 5386
            AG GGS L SQHFGR R+ +HLRSGV+
Sbjct: 101  AGRGGSRLXSQHFGRPRRADHLRSGVR 127


  Database: h_nrNov10_2000
    Posted date:  Nov 10, 2000  9:40 AM
  Number of letters in database: 18,303,128
  Number of sequences in database:  57,234
  
Lambda     K      H
   0.318    0.135    0.401 

Gapped
Lambda     K      H
   0.270   0.0470    0.230 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 262249022
Number of Sequences: 57234
Number of extensions: 6465920
Number of successful extensions: 16162
Number of sequences better than 1.0e-03: 302
Number of HSP's better than  0.0 without gapping: 147
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 14866
Number of HSP's gapped (non-prelim): 1104
length of query: 2319
length of database: 18,303,128
effective HSP length: 55
effective length of query: 2264
effective length of database: 15,155,258
effective search space: 34311504112
effective search space used: 34311504112
frameshift window, decay const: 50,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 41 (21.7 bits)
S2: 105 (45.3 bits)
BioPerl-1.007002/t/data/signalp.hmm.short000444000766000024        72213155576321 20147 0ustar00cjfieldsstaff000000000000# SignalP-HMM euk predictions
# name      !  Cmax  pos ?  Sprob ?
BC1G_00001.1  Q  0.000   0 N  0.000 N  
BC1G_00002.1  Q  0.000  22 N  0.000 N  
BC1G_00003.1  S  0.973  22 Y  0.999 Y  
BC1G_00004.1  Q  0.001  19 N  0.003 N  
BC1G_00005.1  Q  0.007  22 N  0.008 N  
BC1G_00006.1  Q  0.000  23 N  0.000 N  
BC1G_00007.1  Q  0.228  22 N  0.240 N  
BC1G_00008.1  Q  0.061  22 N  0.222 N  
BC1G_00009.1  Q  0.000  20 N  0.000 N  
BC1G_00010.1  Q  0.000   0 N  0.000 N  
BioPerl-1.007002/t/data/signalp.hmm.summary000444000766000024       634613155576321 20535 0ustar00cjfieldsstaff000000000000*********************** SignalP 3.0 predictions ***********************
Using hidden Markov models (HMM) trained on eukaryotes

----------------------------------------------------------------------
>BC1G_00001.1 predicted protein (translation)

SignalP-HMM result:
>BC1G_00001.1
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Signal anchor probability: 0.000
Max cleavage site probability: 0.000 between pos. -1 and  0

----------------------------------------------------------------------
>BC1G_00002.1 predicted protein (translation)

SignalP-HMM result:
>BC1G_00002.1
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Signal anchor probability: 0.000
Max cleavage site probability: 0.000 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00003.1 hypothetical protein (translation)

SignalP-HMM result:
>BC1G_00003.1
Prediction: Signal peptide
Signal peptide probability: 0.999
Signal anchor probability: 0.000
Max cleavage site probability: 0.973 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00004.1 hypothetical protein (translation)

SignalP-HMM result:
>BC1G_00004.1
Prediction: Non-secretory protein
Signal peptide probability: 0.003
Signal anchor probability: 0.000
Max cleavage site probability: 0.001 between pos. 18 and 19

----------------------------------------------------------------------
>BC1G_00005.1 predicted protein (translation)

SignalP-HMM result:
>BC1G_00005.1
Prediction: Non-secretory protein
Signal peptide probability: 0.008
Signal anchor probability: 0.000
Max cleavage site probability: 0.007 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00006.1 hypothetical protein (translation)

SignalP-HMM result:
>BC1G_00006.1
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Signal anchor probability: 0.000
Max cleavage site probability: 0.000 between pos. 22 and 23

----------------------------------------------------------------------
>BC1G_00007.1 predicted protein (translation)

SignalP-HMM result:
>BC1G_00007.1
Prediction: Non-secretory protein
Signal peptide probability: 0.240
Signal anchor probability: 0.000
Max cleavage site probability: 0.228 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00008.1 Homologue of M.grisea pathogenicity protein (translation)

SignalP-HMM result:
>BC1G_00008.1
Prediction: Non-secretory protein
Signal peptide probability: 0.222
Signal anchor probability: 0.067
Max cleavage site probability: 0.061 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00009.1 hypothetical protein (translation)

SignalP-HMM result:
>BC1G_00009.1
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Signal anchor probability: 0.000
Max cleavage site probability: 0.000 between pos. 19 and 20

----------------------------------------------------------------------
>BC1G_00010.1 hypothetical protein (translation)

SignalP-HMM result:
>BC1G_00010.1
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Signal anchor probability: 0.000
Max cleavage site probability: 0.000 between pos. -1 and  0

BioPerl-1.007002/t/data/signalp.negative.out000444000766000024      1477013155576321 20710 0ustar00cjfieldsstaff000000000000SignalP 3.0 Server - prediction results
Technical University of Denmark

Using neural networks (NN) and hidden Markov models (HMM) trained on Gram-negative bacteria

>my_fasta_id



SignalP-NN result:


>my_fasta_id  length = 70

# pos  aa    C       S       Y
    1   M   0.006   0.019   0.006
    2   K   0.006   0.016   0.006
    3   G   0.006   0.019   0.005
    4   N   0.006   0.012   0.005
    5   K   0.006   0.011   0.003
    6   E   0.007   0.014   0.000
    7   V   0.006   0.012   0.000
    8   L   0.007   0.012   0.000
    9   E   0.006   0.001   0.000
   10   I   0.007   0.015   0.000
   11   L   0.006   0.007   0.000
   12   G   0.006   0.011   0.000
   13   E   0.007   0.010   0.000
   14   V   0.006   0.002   0.000
   15   L   0.006   0.005   0.000
   16   S   0.007   0.058   0.000
   17   A   0.023   0.023   0.000
   18   E   0.024   0.019   0.000
   19   L   0.008   0.038   0.000
   20   T   0.009   0.036   0.000
   21   A   0.011   0.038   0.000
   22   I   0.060   0.049   0.000
   23   N   0.009   0.120   0.000
   24   Q   0.028   0.058   0.000
   25   Y   0.007   0.056   0.000
   26   F   0.009   0.070   0.000
   27   I   0.012   0.040   0.008
   28   H   0.011   0.055   0.010
   29   A   0.008   0.048   0.011
   30   K   0.354   0.033   0.086
   31   M   0.006   0.039   0.012
   32   N   0.016   0.051   0.022
   33   K   0.020   0.030   0.025
   34   N   0.008   0.060   0.017
   35   W   0.007   0.031   0.017
   36   G   0.007   0.021   0.017
   37   F   0.009   0.017   0.019
   38   K   0.007   0.026   0.017
   39   K   0.007   0.030   0.017
   40   L   0.006   0.033   0.015
   41   A   0.007   0.002   0.017
   42   D   0.008   0.001   0.017
   43   F   0.006   0.001   0.014
   44   M   0.006   0.001   0.014
   45   K   0.006   0.001   0.013
   46   R   0.006   0.000   0.012
   47   E   0.006   0.000   0.011
   48   S   0.006   0.000   0.011
   49   I   0.006   0.000   0.010
   50   D   0.007   0.000   0.010
   51   E   0.007   0.000   0.009
   52   M   0.006   0.000   0.007
   53   K   0.006   0.000   0.007
   54   H   0.006   0.000   0.006
   55   A   0.007   0.000   0.005
   56   D   0.010   0.000   0.005
   57   E   0.006   0.000   0.002
   58   V   0.007   0.000   0.001
   59   I   0.007   0.000   0.001
   60   D   0.006   0.000   0.001
   61   R   0.006   0.000   0.001
   62   I   0.006   0.000   0.000
   63   L   0.006   0.000   0.000
   64   Y   0.006   0.000   0.000
   65   L   0.006   0.000   0.000
   66   D   0.006   0.000   0.000
   67   G   0.006   0.000   0.000
   68   V   0.006   0.000   0.000
   69   P   0.006   0.000   0.000
   70   D   0.006   0.000   0.000


>my_fasta_id  length = 70
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    30       0.354   0.52   NO
  max. Y    30       0.086   0.33   NO
  max. S    23       0.120   0.92   NO
  mean S     1-29    0.030   0.49   NO
       D     1-29    0.058   0.44   NO



SignalP-HMM result:


>my_fasta_id
# pos  aa    C       S      n-reg   h-reg   c-reg
    1   M   0.000   0.000   0.000   0.000   0.000
    2   K   0.000   0.000   0.000   0.000   0.000
    3   G   0.000   0.000   0.000   0.000   0.000
    4   N   0.000   0.000   0.000   0.000   0.000
    5   K   0.000   0.000   0.000   0.000   0.000
    6   E   0.000   0.000   0.000   0.000   0.000
    7   V   0.000   0.000   0.000   0.000   0.000
    8   L   0.000   0.000   0.000   0.000   0.000
    9   E   0.000   0.000   0.000   0.000   0.000
   10   I   0.000   0.000   0.000   0.000   0.000
   11   L   0.000   0.000   0.000   0.000   0.000
   12   G   0.000   0.000   0.000   0.000   0.000
   13   E   0.000   0.000   0.000   0.000   0.000
   14   V   0.000   0.000   0.000   0.000   0.000
   15   L   0.000   0.000   0.000   0.000   0.000
   16   S   0.000   0.000   0.000   0.000   0.000
   17   A   0.000   0.000   0.000   0.000   0.000
   18   E   0.000   0.000   0.000   0.000   0.000
   19   L   0.000   0.000   0.000   0.000   0.000
   20   T   0.000   0.000   0.000   0.000   0.000
   21   A   0.000   0.000   0.000   0.000   0.000
   22   I   0.000   0.000   0.000   0.000   0.000
   23   N   0.000   0.000   0.000   0.000   0.000
   24   Q   0.000   0.000   0.000   0.000   0.000
   25   Y   0.000   0.000   0.000   0.000   0.000
   26   F   0.000   0.000   0.000   0.000   0.000
   27   I   0.000   0.000   0.000   0.000   0.000
   28   H   0.000   0.000   0.000   0.000   0.000
   29   A   0.000   0.000   0.000   0.000   0.000
   30   K   0.000   0.000   0.000   0.000   0.000
   31   M   0.000   0.000   0.000   0.000   0.000
   32   N   0.000   0.000   0.000   0.000   0.000
   33   K   0.000   0.000   0.000   0.000   0.000
   34   N   0.000   0.000   0.000   0.000   0.000
   35   W   0.000   0.000   0.000   0.000   0.000
   36   G   0.000   0.000   0.000   0.000   0.000
   37   F   0.000   0.000   0.000   0.000   0.000
   38   K   0.000   0.000   0.000   0.000   0.000
   39   K   0.000   0.000   0.000   0.000   0.000
   40   L   0.000   0.000   0.000   0.000   0.000
   41   A   0.000   0.000   0.000   0.000   0.000
   42   D   0.000   0.000   0.000   0.000   0.000
   43   F   0.000   0.000   0.000   0.000   0.000
   44   M   0.000   0.000   0.000   0.000   0.000
   45   K   0.000   0.000   0.000   0.000   0.000
   46   R   0.000   0.000   0.000   0.000   0.000
   47   E   0.000   0.000   0.000   0.000   0.000
   48   S   0.000   0.000   0.000   0.000   0.000
   49   I   0.000   0.000   0.000   0.000   0.000
   50   D   0.000   0.000   0.000   0.000   0.000
   51   E   0.000   0.000   0.000   0.000   0.000
   52   M   0.000   0.000   0.000   0.000   0.000
   53   K   0.000   0.000   0.000   0.000   0.000
   54   H   0.000   0.000   0.000   0.000   0.000
   55   A   0.000   0.000   0.000   0.000   0.000
   56   D   0.000   0.000   0.000   0.000   0.000
   57   E   0.000   0.000   0.000   0.000   0.000
   58   V   0.000   0.000   0.000   0.000   0.000
   59   I   0.000   0.000   0.000   0.000   0.000
   60   D   0.000   0.000   0.000   0.000   0.000
   61   R   0.000   0.000   0.000   0.000   0.000
   62   I   0.000   0.000   0.000   0.000   0.000
   63   L   0.000   0.000   0.000   0.000   0.000
   64   Y   0.000   0.000   0.000   0.000   0.000
   65   L   0.000   0.000   0.000   0.000   0.000
   66   D   0.000   0.000   0.000   0.000   0.000
   67   G   0.000   0.000   0.000   0.000   0.000
   68   V   0.000   0.000   0.000   0.000   0.000
   69   P   0.000   0.000   0.000   0.000   0.000
   70   D   0.000   0.000   0.000   0.000   0.000


>my_fasta_id
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Max cleavage site probability: 0.000 between pos. -1 and  0

BioPerl-1.007002/t/data/signalp.nn.short000444000766000024       163313155576321 20023 0ustar00cjfieldsstaff000000000000# SignalP-NN euk predictions                                   
# name                Cmax  pos ?  Ymax  pos ?  Smax  pos ?  Smean ?  D     ? 
BC1G_00001.1          0.074  23 N  0.014  33 N  0.067   2 N  0.023 N  0.018 N
BC1G_00002.1          0.079  26 N  0.059  22 N  0.406   1 N  0.100 N  0.079 N
BC1G_00003.1          0.934  22 Y  0.866  22 Y  0.991  13 Y  0.938 Y  0.902 Y
BC1G_00004.1          0.078  30 N  0.101  17 N  0.425   1 N  0.221 N  0.161 N
BC1G_00005.1          0.085  18 N  0.078  18 N  0.683   3 N  0.188 N  0.133 N
BC1G_00006.1          0.244  27 N  0.035  27 N  0.161   2 N  0.053 N  0.044 N
BC1G_00007.1          0.257  22 N  0.176  22 N  0.620   2 N  0.258 N  0.217 N
BC1G_00008.1          0.576  83 Y  0.383  83 Y  0.952  45 Y  0.489 Y  0.436 Y
BC1G_00009.1          0.425  28 Y  0.153  28 N  0.448   4 N  0.140 N  0.147 N
BC1G_00010.1          0.380 421 Y  0.057  15 N  0.362   4 N  0.146 N  0.102 N
BioPerl-1.007002/t/data/signalp.nn.summary000444000766000024      1063713155576321 20405 0ustar00cjfieldsstaff000000000000*********************** SignalP 3.0 predictions ***********************
Using neural networks (NN) trained on eukaryotes

----------------------------------------------------------------------
>BC1G_00001.1 predicted protein (translation)

SignalP-NN result:
>BC1G_00001.1          length = 173
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    23       0.074   0.32   NO
  max. Y    33       0.014   0.33   NO
  max. S     2       0.067   0.87   NO
  mean S     1-32    0.023   0.48   NO
       D     1-32    0.018   0.43   NO


----------------------------------------------------------------------
>BC1G_00002.1 predicted protein (translation)

SignalP-NN result:
>BC1G_00002.1          length = 120
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    26       0.079   0.32   NO
  max. Y    22       0.059   0.33   NO
  max. S     1       0.406   0.87   NO
  mean S     1-21    0.100   0.48   NO
       D     1-21    0.079   0.43   NO


----------------------------------------------------------------------
>BC1G_00003.1 hypothetical protein (translation)

SignalP-NN result:
>BC1G_00003.1          length = 323
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    22       0.934   0.32   YES
  max. Y    22       0.866   0.33   YES
  max. S    13       0.991   0.87   YES
  mean S     1-21    0.938   0.48   YES
       D     1-21    0.902   0.43   YES
# Most likely cleavage site between pos. 21 and 22: VQG-AP


----------------------------------------------------------------------
>BC1G_00004.1 hypothetical protein (translation)

SignalP-NN result:
>BC1G_00004.1          length = 361
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    30       0.078   0.32   NO
  max. Y    17       0.101   0.33   NO
  max. S     1       0.425   0.87   NO
  mean S     1-16    0.221   0.48   NO
       D     1-16    0.161   0.43   NO


----------------------------------------------------------------------
>BC1G_00005.1 predicted protein (translation)

SignalP-NN result:
>BC1G_00005.1          length = 244
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    18       0.085   0.32   NO
  max. Y    18       0.078   0.33   NO
  max. S     3       0.683   0.87   NO
  mean S     1-17    0.188   0.48   NO
       D     1-17    0.133   0.43   NO


----------------------------------------------------------------------
>BC1G_00006.1 hypothetical protein (translation)

SignalP-NN result:
>BC1G_00006.1          length = 35
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    27       0.244   0.32   NO
  max. Y    27       0.035   0.33   NO
  max. S     2       0.161   0.87   NO
  mean S     1-26    0.053   0.48   NO
       D     1-26    0.044   0.43   NO


----------------------------------------------------------------------
>BC1G_00007.1 predicted protein (translation)

SignalP-NN result:
>BC1G_00007.1          length = 73
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    22       0.257   0.32   NO
  max. Y    22       0.176   0.33   NO
  max. S     2       0.620   0.87   NO
  mean S     1-21    0.258   0.48   NO
       D     1-21    0.217   0.43   NO


----------------------------------------------------------------------
>BC1G_00008.1 Homologue of M.grisea pathogenicity protein (translation)

SignalP-NN result:
>BC1G_00008.1          length = 349
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    83       0.576   0.32   YES
  max. Y    83       0.383   0.33   YES
  max. S    45       0.952   0.87   YES
  mean S     1-82    0.489   0.48   YES
       D     1-82    0.436   0.43   YES
# Most likely cleavage site between pos. 82 and 83: TQG-AR


----------------------------------------------------------------------
>BC1G_00009.1 hypothetical protein (translation)

SignalP-NN result:
>BC1G_00009.1          length = 514
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    28       0.425   0.32   YES
  max. Y    28       0.153   0.33   NO
  max. S     4       0.448   0.87   NO
  mean S     1-27    0.140   0.48   NO
       D     1-27    0.147   0.43   NO


----------------------------------------------------------------------
>BC1G_00010.1 hypothetical protein (translation)

SignalP-NN result:
>BC1G_00010.1          length = 440
# Measure  Position  Value  Cutoff  signal peptide?
  max. C   421       0.380   0.32   YES
  max. Y    15       0.057   0.33   NO
  max. S     4       0.362   0.87   NO
  mean S     1-14    0.146   0.48   NO
       D     1-14    0.102   0.43   NO


BioPerl-1.007002/t/data/signalp.positive.out000444000766000024      1510413155576321 20740 0ustar00cjfieldsstaff000000000000     SignalP 3.0 Server - prediction results
        Technical University of Denmark





Using neural networks (NN) and hidden Markov models (HMM) trained on Gram-negative bacteria



>my_fasta_id



SignalP-NN result:


>my_fasta_id  length = 70

# pos  aa    C       S       Y
    1   M   0.006   0.512   0.022
    2   R   0.006   0.473   0.022
    3   I   0.006   0.324   0.020
    4   T   0.006   0.454   0.013
    5   I   0.006   0.588   0.005
    6   L   0.006   0.223   0.000
    7   A   0.006   0.339   0.000
    8   S   0.012   0.504   0.000
    9   V   0.006   0.642   0.000
   10   V   0.008   0.384   0.008
   11   I   0.007   0.212   0.012
   12   P   0.007   0.160   0.009
   13   C   0.007   0.263   0.000
   14   L   0.009   0.648   0.000
   15   G   0.006   0.594   0.016
   16   F   0.011   0.538   0.031
   17   S   0.007   0.598   0.028
   18   A   0.016   0.678   0.050
   19   S   0.026   0.717   0.075
   20   C   0.008   0.748   0.047
   21   M   0.010   0.755   0.059
   22   A   0.064   0.902   0.161
   23   A   0.916   0.225   0.678
   24   E   0.467   0.046   0.487
   25   D   0.016   0.042   0.089
   26   V   0.011   0.043   0.071
   27   M   0.007   0.048   0.053
   28   I   0.009   0.042   0.061
   29   V   0.009   0.041   0.062
   30   S   0.007   0.033   0.052
   31   A   0.007   0.026   0.052
   32   S   0.028   0.022   0.097
   33   G   0.007   0.014   0.046
   34   Y   0.043   0.010   0.107
   35   E   0.008   0.018   0.042
   36   K   0.011   0.031   0.046
   37   K   0.009   0.008   0.036
   38   L   0.009   0.015   0.029
   39   T   0.006   0.017   0.015
   40   N   0.006   0.012   0.013
   41   A   0.006   0.013   0.013
   42   A   0.008   0.004   0.014
   43   A   0.007   0.001   0.013
   44   S   0.007   0.000   0.012
   45   V   0.006   0.001   0.010
   46   S   0.006   0.000   0.009
   47   V   0.006   0.000   0.008
   48   I   0.006   0.000   0.008
   49   N   0.008   0.000   0.008
   50   Q   0.009   0.000   0.009
   51   E   0.007   0.000   0.007
   52   E   0.006   0.000   0.006
   53   L   0.006   0.000   0.005
   54   Q   0.007   0.000   0.005
   55   S   0.006   0.000   0.004
   56   S   0.007   0.000   0.003
   57   Q   0.006   0.000   0.003
   58   Y   0.006   0.000   0.001
   59   H   0.007   0.000   0.001
   60   D   0.007   0.000   0.001
   61   L   0.007   0.000   0.001
   62   A   0.007   0.000   0.001
   63   E   0.008   0.000   0.001
   64   A   0.006   0.000   0.001
   65   L   0.008   0.000   0.001
   66   R   0.006   0.000   0.001
   67   S   0.006   0.000   0.001
   68   V   0.006   0.000   0.001
   69   E   0.006   0.000   0.001
   70   G   0.007   0.000   0.001


>my_fasta_id  length = 70
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    23       0.916   0.52   YES
  max. Y    23       0.678   0.33   YES
  max. S    22       0.902   0.92   NO
  mean S     1-22    0.512   0.49   YES
       D     1-22    0.595   0.44   YES
# Most likely cleavage site between pos. 22 and 23: CMA-AE



SignalP-HMM result:


>my_fasta_id
# pos  aa    C       S      n-reg   h-reg   c-reg
    1   M   0.000   1.000   1.000   0.000   0.000
    2   R   0.000   1.000   1.000   0.000   0.000
    3   I   0.000   1.000   1.000   0.000   0.000
    4   T   0.000   1.000   0.910   0.090   0.000
    5   I   0.000   1.000   0.572   0.428   0.000
    6   L   0.000   1.000   0.224   0.776   0.000
    7   A   0.000   1.000   0.011   0.989   0.000
    8   S   0.000   1.000   0.001   0.999   0.000
    9   V   0.000   1.000   0.000   1.000   0.000
   10   V   0.000   1.000   0.000   1.000   0.000
   11   I   0.000   1.000   0.000   1.000   0.000
   12   P   0.000   1.000   0.000   0.999   0.001
   13   C   0.000   1.000   0.000   0.997   0.003
   14   L   0.000   1.000   0.000   0.977   0.023
   15   G   0.000   1.000   0.000   0.849   0.151
   16   F   0.000   1.000   0.000   0.224   0.776
   17   S   0.000   1.000   0.000   0.000   1.000
   18   A   0.000   1.000   0.000   0.000   1.000
   19   S   0.000   1.000   0.000   0.000   1.000
   20   C   0.000   1.000   0.000   0.000   1.000
   21   M   0.000   1.000   0.000   0.000   1.000
   22   A   0.000   1.000   0.000   0.000   1.000
   23   A   1.000   0.000   0.000   0.000   0.000
   24   E   0.000   0.000   0.000   0.000   0.000
   25   D   0.000   0.000   0.000   0.000   0.000
   26   V   0.000   0.000   0.000   0.000   0.000
   27   M   0.000   0.000   0.000   0.000   0.000
   28   I   0.000   0.000   0.000   0.000   0.000
   29   V   0.000   0.000   0.000   0.000   0.000
   30   S   0.000   0.000   0.000   0.000   0.000
   31   A   0.000   0.000   0.000   0.000   0.000
   32   S   0.000   0.000   0.000   0.000   0.000
   33   G   0.000   0.000   0.000   0.000   0.000
   34   Y   0.000   0.000   0.000   0.000   0.000
   35   E   0.000   0.000   0.000   0.000   0.000
   36   K   0.000   0.000   0.000   0.000   0.000
   37   K   0.000   0.000   0.000   0.000   0.000
   38   L   0.000   0.000   0.000   0.000   0.000
   39   T   0.000   0.000   0.000   0.000   0.000
   40   N   0.000   0.000   0.000   0.000   0.000
   41   A   0.000   0.000   0.000   0.000   0.000
   42   A   0.000   0.000   0.000   0.000   0.000
   43   A   0.000   0.000   0.000   0.000   0.000
   44   S   0.000   0.000   0.000   0.000   0.000
   45   V   0.000   0.000   0.000   0.000   0.000
   46   S   0.000   0.000   0.000   0.000   0.000
   47   V   0.000   0.000   0.000   0.000   0.000
   48   I   0.000   0.000   0.000   0.000   0.000
   49   N   0.000   0.000   0.000   0.000   0.000
   50   Q   0.000   0.000   0.000   0.000   0.000
   51   E   0.000   0.000   0.000   0.000   0.000
   52   E   0.000   0.000   0.000   0.000   0.000
   53   L   0.000   0.000   0.000   0.000   0.000
   54   Q   0.000   0.000   0.000   0.000   0.000
   55   S   0.000   0.000   0.000   0.000   0.000
   56   S   0.000   0.000   0.000   0.000   0.000
   57   Q   0.000   0.000   0.000   0.000   0.000
   58   Y   0.000   0.000   0.000   0.000   0.000
   59   H   0.000   0.000   0.000   0.000   0.000
   60   D   0.000   0.000   0.000   0.000   0.000
   61   L   0.000   0.000   0.000   0.000   0.000
   62   A   0.000   0.000   0.000   0.000   0.000
   63   E   0.000   0.000   0.000   0.000   0.000
   64   A   0.000   0.000   0.000   0.000   0.000
   65   L   0.000   0.000   0.000   0.000   0.000
   66   R   0.000   0.000   0.000   0.000   0.000
   67   S   0.000   0.000   0.000   0.000   0.000
   68   V   0.000   0.000   0.000   0.000   0.000
   69   E   0.000   0.000   0.000   0.000   0.000
   70   G   0.000   0.000   0.000   0.000   0.000


>my_fasta_id
Prediction: Signal peptide
Signal peptide probability: 1.000
Max cleavage site probability: 1.000 between pos. 22 and 23


BioPerl-1.007002/t/data/signalp.short000444000766000024       257513155576321 17417 0ustar00cjfieldsstaff000000000000# SignalP-NN euk predictions                                   	                # SignalP-HMM euk predictions
# name                Cmax  pos ?  Ymax  pos ?  Smax  pos ?  Smean ?  D     ? 	# name      !  Cmax  pos ?  Sprob ?
BC1G_00001.1          0.074  23 N  0.014  33 N  0.067   2 N  0.023 N  0.018 N	BC1G_00001.1  Q  0.000   0 N  0.000 N  
BC1G_00002.1          0.079  26 N  0.059  22 N  0.406   1 N  0.100 N  0.079 N	BC1G_00002.1  Q  0.000  22 N  0.000 N  
BC1G_00003.1          0.934  22 Y  0.866  22 Y  0.991  13 Y  0.938 Y  0.902 Y	BC1G_00003.1  S  0.973  22 Y  0.999 Y  
BC1G_00004.1          0.078  30 N  0.101  17 N  0.425   1 N  0.221 N  0.161 N	BC1G_00004.1  Q  0.001  19 N  0.003 N  
BC1G_00005.1          0.085  18 N  0.078  18 N  0.683   3 N  0.188 N  0.133 N	BC1G_00005.1  Q  0.007  22 N  0.008 N  
BC1G_00006.1          0.244  27 N  0.035  27 N  0.161   2 N  0.053 N  0.044 N	BC1G_00006.1  Q  0.000  23 N  0.000 N  
BC1G_00007.1          0.257  22 N  0.176  22 N  0.620   2 N  0.258 N  0.217 N	BC1G_00007.1  Q  0.228  22 N  0.240 N  
BC1G_00008.1          0.576  83 Y  0.383  83 Y  0.952  45 Y  0.489 Y  0.436 Y	BC1G_00008.1  Q  0.061  22 N  0.222 N  
BC1G_00009.1          0.425  28 Y  0.153  28 N  0.448   4 N  0.140 N  0.147 N	BC1G_00009.1  Q  0.000  20 N  0.000 N  
BC1G_00010.1          0.380 421 Y  0.057  15 N  0.362   4 N  0.146 N  0.102 N	BC1G_00010.1  Q  0.000   0 N  0.000 N  
BioPerl-1.007002/t/data/signalp.summary000444000766000024      1452613155576321 17774 0ustar00cjfieldsstaff000000000000*********************** SignalP 3.0 predictions ***********************
Using neural networks (NN) and hidden Markov models (HMM) trained on eukaryotes

----------------------------------------------------------------------
>BC1G_00001.1 predicted protein (translation)

SignalP-NN result:
>BC1G_00001.1          length = 173
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    23       0.074   0.32   NO
  max. Y    33       0.014   0.33   NO	
  max. S     2       0.067   0.87   NO
  mean S     1-32    0.023   0.48   NO
       D     1-32    0.018   0.43   NO

SignalP-HMM result:
>BC1G_00001.1
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Signal anchor probability: 0.000
Max cleavage site probability: 0.000 between pos. -1 and  0

----------------------------------------------------------------------
>BC1G_00002.1 predicted protein (translation)

SignalP-NN result:
>BC1G_00002.1          length = 120
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    26       0.079   0.32   NO
  max. Y    22       0.059   0.33   NO
  max. S     1       0.406   0.87   NO
  mean S     1-21    0.100   0.48   NO
       D     1-21    0.079   0.43   NO

SignalP-HMM result:
>BC1G_00002.1
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Signal anchor probability: 0.000
Max cleavage site probability: 0.000 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00003.1 hypothetical protein (translation)

SignalP-NN result:
>BC1G_00003.1          length = 323
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    22       0.934   0.32   YES
  max. Y    22       0.866   0.33   YES
  max. S    13       0.991   0.87   YES
  mean S     1-21    0.938   0.48   YES
       D     1-21    0.902   0.43   YES
# Most likely cleavage site between pos. 21 and 22: VQG-AP

SignalP-HMM result:
>BC1G_00003.1
Prediction: Signal peptide
Signal peptide probability: 0.999
Signal anchor probability: 0.000
Max cleavage site probability: 0.973 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00004.1 hypothetical protein (translation)

SignalP-NN result:
>BC1G_00004.1          length = 361
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    30       0.078   0.32   NO
  max. Y    17       0.101   0.33   NO
  max. S     1       0.425   0.87   NO
  mean S     1-16    0.221   0.48   NO
       D     1-16    0.161   0.43   NO

SignalP-HMM result:
>BC1G_00004.1
Prediction: Non-secretory protein
Signal peptide probability: 0.003
Signal anchor probability: 0.000
Max cleavage site probability: 0.001 between pos. 18 and 19

----------------------------------------------------------------------
>BC1G_00005.1 predicted protein (translation)

SignalP-NN result:
>BC1G_00005.1          length = 244
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    18       0.085   0.32   NO
  max. Y    18       0.078   0.33   NO
  max. S     3       0.683   0.87   NO
  mean S     1-17    0.188   0.48   NO
       D     1-17    0.133   0.43   NO

SignalP-HMM result:
>BC1G_00005.1
Prediction: Non-secretory protein
Signal peptide probability: 0.008
Signal anchor probability: 0.000
Max cleavage site probability: 0.007 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00006.1 hypothetical protein (translation)

SignalP-NN result:
>BC1G_00006.1          length = 35
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    27       0.244   0.32   NO
  max. Y    27       0.035   0.33   NO
  max. S     2       0.161   0.87   NO
  mean S     1-26    0.053   0.48   NO
       D     1-26    0.044   0.43   NO

SignalP-HMM result:
>BC1G_00006.1
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Signal anchor probability: 0.000
Max cleavage site probability: 0.000 between pos. 22 and 23

----------------------------------------------------------------------
>BC1G_00007.1 predicted protein (translation)

SignalP-NN result:
>BC1G_00007.1          length = 73
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    22       0.257   0.32   NO
  max. Y    22       0.176   0.33   NO
  max. S     2       0.620   0.87   NO
  mean S     1-21    0.258   0.48   NO
       D     1-21    0.217   0.43   NO

SignalP-HMM result:
>BC1G_00007.1
Prediction: Non-secretory protein
Signal peptide probability: 0.240
Signal anchor probability: 0.000
Max cleavage site probability: 0.228 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00008.1 Homologue of M.grisea pathogenicity protein (translation)

SignalP-NN result:
>BC1G_00008.1          length = 349
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    83       0.576   0.32   YES
  max. Y    83       0.383   0.33   YES
  max. S    45       0.952   0.87   YES
  mean S     1-82    0.489   0.48   YES
       D     1-82    0.436   0.43   YES
# Most likely cleavage site between pos. 82 and 83: TQG-AR

SignalP-HMM result:
>BC1G_00008.1
Prediction: Non-secretory protein
Signal peptide probability: 0.222
Signal anchor probability: 0.067
Max cleavage site probability: 0.061 between pos. 21 and 22

----------------------------------------------------------------------
>BC1G_00009.1 hypothetical protein (translation)

SignalP-NN result:
>BC1G_00009.1          length = 514
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    28       0.425   0.32   YES
  max. Y    28       0.153   0.33   NO
  max. S     4       0.448   0.87   NO
  mean S     1-27    0.140   0.48   NO
       D     1-27    0.147   0.43   NO

SignalP-HMM result:
>BC1G_00009.1
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Signal anchor probability: 0.000
Max cleavage site probability: 0.000 between pos. 19 and 20

----------------------------------------------------------------------
>BC1G_00010.1 hypothetical protein (translation)

SignalP-NN result:
>BC1G_00010.1          length = 440
# Measure  Position  Value  Cutoff  signal peptide?
  max. C   421       0.380   0.32   YES
  max. Y    15       0.057   0.33   NO
  max. S     4       0.362   0.87   NO
  mean S     1-14    0.146   0.48   NO
       D     1-14    0.102   0.43   NO

SignalP-HMM result:
>BC1G_00010.1
Prediction: Non-secretory protein
Signal peptide probability: 0.000
Signal anchor probability: 0.000
Max cleavage site probability: 0.000 between pos. -1 and  0

BioPerl-1.007002/t/data/sim4.for.for000444000766000024        55213155576321 17023 0ustar00cjfieldsstaff000000000000
seq1 = human.genomic, 5368 bp
seq2 = est.for (>hs_est), 479 bp

695-813  (1-119)   100% ->
1377-1500  (120-243)   99% ->
1797-1935  (244-382)   100% ->
2084-2180  (383-479)   100%

seq1 = human.genomic, 5368 bp
seq2 = est.for (>hs_est), 479 bp

695-813  (1-119)   100% ->
1377-1500  (120-243)   99% ->
1797-1935  (244-382)   100% ->
2084-2180  (383-479)   100%
BioPerl-1.007002/t/data/sim4.for.rev000444000766000024        30613155576321 17026 0ustar00cjfieldsstaff000000000000
seq1 = human.genomic, 5368 bp
seq2 = hn_est.rev (>REVCOMP), 479 bp

(complement)
695-813  (1-119)   100% ->
1377-1500  (120-243)   99% ->
1797-1935  (244-382)   100% ->
2084-2180  (383-479)   100%
BioPerl-1.007002/t/data/sim4.rev000444000766000024        64713155576321 16251 0ustar00cjfieldsstaff000000000000
seq1 = /nfs/disk21/birney/prog/wise2/example/human.rev, 5368 bp
seq2 = temp.cdna (>HSHNCPA1), 1198 bp

(complement)
486-503  (10-27)   83% ==
1048-1117  (194-265)   93% <-
1408-1563  (266-421)   100% <-
2501-2575  (422-496)   100% <-
2710-2802  (497-589)   100% <-
2889-2981  (590-682)   100% <-
3075-3285  (683-893)   100% <-
3434-3580  (894-1040)   100% <-
3876-3992  (1041-1157)   100% <-
4556-4596  (1158-1198)   100%
BioPerl-1.007002/t/data/singlescore.gbk000444000766000024       556013155576321 17700 0ustar00cjfieldsstaff000000000000LOCUS       test0001                1500 bp    dna     linear   UNK 
DEFINITION  [organism=Test test] [strain=test0001] [gcode=11] [date=8-24-2011]
ACCESSION   test0001
KEYWORDS    .
FEATURES             Location/Qualifiers
     fasta_record    1..1200
                     /name="contig00002"
                     /note="untiled"
     CDS             16..1215
                     /locus_tag="test0001_10"
                     /inference="similar to AA sequence:BLASTX:2.2.18"
                     /score="463"
                     /product="tRNA uridine 5-carboxymethylaminomethyl
                     modification enzyme MnmG n=70 Tax=Proteobacteria
                     RepID=MNMG_ALTMD"
                     /note="score=463"
                     /note="similar to tRNA uridine 5-carboxymethylaminomethyl
                     modification enzyme GidA PRK05192"
     gene            16..1215
                     /locus_tag="test0001_10"
                     /inference="ab initio prediction:glimmer3:3.0.2"
ORIGIN      
        1 ctaacacaaa gtaatatgag tttttattct agatcagttg tattatcaac aggtaccttt
       61 ctaggtggaa aaatacacat aggtttagaa agttattctg ctggaagaaa aggagaaaaa
      121 gcatctatag atttagctct tcgtttaaga gatttgcctt ttcgtgtgga tagattaaaa
      181 actggaacac cacctcgaat tgatattaat acaattaatt ttgaaaattt atttgtccag
      241 catggtgatg ttcctactcc tgttttttct tttatggggg atatttctaa tcatcctctt
      301 caaataccgt gttttcttac acacactaat gaaaaaacgc atgaaataat acgtaaaaat
      361 ttacataaga gtcctctata tacaggtatt attaaaggtg tgggacctcg atattgtcct
      421 tctattgaag ataaaattgt acgtttccct gataggaaat cacatcaaat ttttttagag
      481 ccagaaggat taactagtat tgaaatatat ccaaatggta tctcaactag tttaccctta
      541 gatgttcaaa aagaaatagt aagttctgta aaaggtttag aaaagtctaa aattattact
      601 cctggttatg ctgtagaata tgattttttt gatcctaagg atttaaatct tactttagag
      661 agtaaatgga ttaaaggtct ttttttagct ggtcaaatta atggtactac tggttatgaa
      721 gaagctgcgt ctcaaggact tttagcaggt ttaaatgcag ctttaagtgc aaaagattgc
      781 aaacaatggt ttcctagacg tgatcaagct tatttaggtg ttcttattga tgatttaact
      841 actcaaggtg cgaatgaacc ttatcgaatg tttacttcaa gatctgaata tcggttaact
      901 ttaagagaag ataatgctga tttacgttta actgaaatag cttataaatt gggattagta
      961 gataatccaa gatggattcg ttataatgaa aaagtactaa atatcagtaa tgaaaaaaat
     1021 cgtttaaaaa aaataaaaat atatcctaaa tcctctgata gtactatttt aaatcagtta
     1081 tttaatattg ttttaactaa agaaattaat attttaaatt tattaaaacg tccagaaatt
     1141 acatatgaaa atttaaagta tttaaaaaat tttaaagtag gtatttctga tttagaagca
     1201 nnnttaatta attaannngg tgagtttact tctagtgatt tattaaaacg tattttttct
     1261 accttttgca taggaaaata agaatataat ttttgcccgg aggcggaatt gaaccaccga
     1321 cacggggatt ttcagtcccc tgctctaccg actgagctat ccgggcaatt tttacattaa
     1381 atcatcaaag ataaaacttt gtcaatcttt ttttgtagaa gttaatttga aattttgatt
     1441 taactaatat cttttctatt ttgaaaatat aaaataaaaa taaaaaaata attttttccc
//
BioPerl-1.007002/t/data/singlet_w_CT.ace000444000766000024      1135113155576321 17744 0ustar00cjfieldsstaff000000000000AS 1 1

CO Contig14 934 1 1 U
gaggcgggggcggacggtcttaccccgggtgaatatcatacagccctaaa
cccagacaatattgctgatgccaaaaatgcATGCTGGCAGGAGCCTGATA
TAGCTGTCTCCCGAGAGGCTCAGCCAGAGCCTGATAAATACAGAGGCAAA
TGCTAGCAGCCAATCATTGAATTGAGAATGGGGTCCCCATTGGAGGAATT
AGAGAAAGGATTGAAGGAGCTGAAGAGGCTTGCAACCCCATAAGAACAAC
AATACCAAGTAACCAGAGCTCCCAGGGACTAAACCACCATCTAAAGAGTA
CACATGGAGTGACCCATGGCTCCAGTTGCATATGTTGCAGAGGATGGCCT
TGTTGGGCACCAATGGGATGAGAAGCTCTTGGTTCTGCCAAGGCTGGACC
ACCCAGTGCAGGGGAATGTCAGGGTGGGGAGGCAGGAAAGGTTGGGTGGT
TGGGGGGGCGACACCCTCATAGAAGATAGGGGAGGGGGAGTGGGATAGGG
GACTTATGGACAGGAAAGGGGATAACATTTGAAATGTAAATAAAAAATAT
CCGAAAGGGGGTGGTGGTGGCCAGGACTGTAGCGATCAACTTTGCCAAAT
TCCTTGTACTCCTGATATCTTGCTGCATGGTGAAGAGTTTCCCGTATTCA
TTACACTTCATAGgttTTTGTCTGGTATCAGCTTTCTCATGttGCTTTTA
AAACATCTTTCTTCATTGAACATAAATTGAGATCCACAGACCtAattCtc
aACCAACTAGCATTTACCAACTCCTGggtgcttttcttcacaaagagaaa
cctcaaccaatagggcctttggatggaaaatttctggatggactgggtgt
aactgcctttatgggcgacagcctgggggttctgaaccattgttccaaaa
aaaccgcctctagggacccatcgtgtgagaaaac

BQ
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 48 68 68 68 68 68 68 68 68 57 57 57 57 57 57 59 57 57 57 50
 50 50 50 51 57 57 57 57 57 57 68 57 57 50 50 50 50 50 57 50 50 50 50 50 47 47 47 50 52 54 57 57 68 68 68 68 57 50 50 50 50 50 57 57 57 68 68 68 68 68
 68 57 57 57 57 57 57 57 57 57 57 57 57 57 57 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 62 62 62
 62 62 62 62 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 62 62 62 62 62 62 62 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 62 62
 62 68 68 62 62 62 62 62 62 62 68 44 44 43 39 39 43 43 52 62 62 68 68 68 68 68 68 62 62 62 62 62 62 62 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68
 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 62 68 62 62 62 62 62 68 68 68 68 68 68 68 68 68 62 62 62 62 62 62 62 62 62 68 68 62 68 62
 62 62 62 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 62 62 62 62 62 62 62 62 62 62 62 62 62 62
 62 62 62 62 62 62 62 62 62 62 62 62 62 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68
 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 68 62 62 62 62 62 62 62 68 68 68 68 68 68 68 68 68 68 68 68 62 62 62 62 62 62 62
 68 68 68 68 68 68 68 68 62 62 62 62 62 62 62 68 68 68 68 68 62 62 62 62 62 62 62 62 62 62 68 62 62 68 68 68 68 68 62 62 62 62 62 62 62 68 68 68 68 68
 68 68 68 68 68 68 68 68 62 62 62 62 62 62 62 62 62 62 62 62 62 62 52 52 62 62 62 62 62 62 62 62 62 62 62 62 62 62 62 62 57 59 57 57 57 57 68 57 57 59
 68 68 68 59 59 57 57 57 59 59 59 57 57 57 57 57 57 59 59 59 57 57 57 57 57 57 68 57 57 57 57 57 57 44 57 37 43 37 59 59 68 59 59 57 57 57 50 50 50 50
 50 50 68 57 57 57 57 57 59 59 57 36 36 15 15 15 32 26 43 27 27 27 43 36 28 28 28 38 44 57 57 46 46 46 57 57 57 57 42 32 24 17 17 30 34 43 44 57 57 48
 48 32 48 26 23 28 44 44 57 57 59 59 59 41 41 20 20 27 44 44 41 35 35 41 41 57 57 57 57 57 57 43 32 32 32 32 43 48 48 39 40 35 19 21 13 13 12 23 12 12
 12 27 26 33 33 33 37 37 37 41 37 30 27 24 29 22 30 34 37 32 37 30 28 28 28 28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

AF rt21f229.x.scf U 1
BS 1 934 rt21f229.x.scf

RD rt21f229.x.scf 934 0 0
gaggcgggggcggacggtcttaccccgggtgaatatcatacagccctaaa
cccagacaatattgctgatgccaaaaatgcATGCTGGCAGGAGCCTGATA
TAGCTGTCTCCCGAGAGGCTCAGCCAGAGCCTGATAAATACAGAGGCAAA
TGCTAGCAGCCAATCATTGAATTGAGAATGGGGTCCCCATTGGAGGAATT
AGAGAAAGGATTGAAGGAGCTGAAGAGGCTTGCAACCCCATAAGAACAAC
AATACCAAGTAACCAGAGCTCCCAGGGACTAAACCACCATCTAAAGAGTA
CACATGGAGTGACCCATGGCTCCAGTTGCATATGTTGCAGAGGATGGCCT
TGTTGGGCACCAATGGGATGAGAAGCTCTTGGTTCTGCCAAGGCTGGACC
ACCCAGTGCAGGGGAATGTCAGGGTGGGGAGGCAGGAAAGGTTGGGTGGT
TGGGGGGGCGACACCCTCATAGAAGATAGGGGAGGGGGAGTGGGATAGGG
GACTTATGGACAGGAAAGGGGATAACATTTGAAATGTAAATAAAAAATAT
CCGAAAGGGGGTGGTGGTGGCCAGGACTGTAGCGATCAACTTTGCCAAAT
TCCTTGTACTCCTGATATCTTGCTGCATGGTGAAGAGTTTCCCGTATTCA
TTACACTTCATAGgttTTTGTCTGGTATCAGCTTTCTCATGttGCTTTTA
AAACATCTTTCTTCATTGAACATAAATTGAGATCCACAGACCtAattCtc
aACCAACTAGCATTTACCAACTCCTGggtgcttttcttcacaaagagaaa
cctcaaccaatagggcctttggatggaaaatttctggatggactgggtgt
aactgcctttatgggcgacagcctgggggttctgaaccattgttccaaaa
aaaccgcctctagggacccatcgtgtgagaaaac

QA 81 776 1 934
DS CHROMAT_FILE: rt21f229.x.scf PHD_FILE: rt21f229.x.scf.phd.1 CHEM: term DYE: big TIME: Wed Feb 11 15:31:12 2009 TEMPLATE: rt21f229 DIRECTION: fwd

CT{
Contig14 repeat tagRepeats.perl 38 422 090211:153155 NoTrans
Lx#LINE/L1
}
BioPerl-1.007002/t/data/so.obo000444000766000024     65633413155576321 16073 0ustar00cjfieldsstaff000000000000format-version: 1.2
date: 13:02:2006 15:53
saved-by: kareneilbeck
auto-generated-by: OBO-Edit 1.000-beta15
subsetdef: SOFA "SO feature annotation"
default-namespace: sequence
remark: autogenerated-by\:   DAG-Edit version 1.417\nsaved-by\:       eilbeck\ndate\:         Tue May 11 15\:18\:44 PDT 2004\nversion\: $Revision\: 1.45 $

[Term]
id: SO:0000000
name: Sequence_Ontology
subset: SOFA

[Term]
id: SO:0000001
name: region
def: "Continuous sequence." [SO:ke]
subset: SOFA
synonym: "sequence" RELATED []
is_a: SO:0000110 ! located_sequence_feature

[Term]
id: SO:0000002
name: sequence_secondary_structure
def: "A folded sequence." [SO:ke]
is_a: SO:0000001 ! region

[Term]
id: SO:0000003
name: G_quartet
def: "G-quartets are unusual nucelic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.library.csi.cuny.edu/ ~ davis/molbiol/lecture_notes/post-transcriptional_processes/RNACapping.pdf]
synonym: "G-quartet" RELATED []
is_a: SO:0000002 ! sequence_secondary_structure

[Term]
id: SO:0000004
name: interior_coding_exon
is_a: SO:0000195 ! coding_exon

[Term]
id: SO:0000005
name: satellite_DNA
def: "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000006
name: PCR_product
def: "A region amplified by a PCR reaction." [SO:ke]
subset: SOFA
synonym: "amplicon" RELATED []
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000007
name: read_pair
def: "A pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]
subset: SOFA
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000149 ! contig

[Term]
id: SO:0000008
name: gene_sensu_your_favorite_organism
is_a: SO:0000009 ! gene_class

[Term]
id: SO:0000009
name: gene_class
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000010
name: protein_coding_gene
is_a: SO:0000009 ! gene_class

[Term]
id: SO:0000011
name: non_protein_coding_gene
is_a: SO:0000009 ! gene_class

[Term]
id: SO:0000012
name: scRNA_primary_transcript
def: "The primary transcript of any one of several small cytoplasmic RNA moleculespresent in the cytoplasm and sometimes nucleus of a eukaryote." [http:www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]
synonym: "small_cytoplasmic_RNA" RELATED []
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000013
name: scRNA
def: "Any one of several small cytoplasmic RNA moleculespresent in the cytoplasm and sometimes nucleus of a eukaryote." [http:www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]
subset: SOFA
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000014
name: INR_motif
def: "A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739]
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0000015
name: DPE_motif
def: "A sequence element characteristic of some RNA polymerase II promoters; always found with the INR_motif. Positioned from +28 to +32 with respect to the TSS (+1). Consensus sequence (A|G)G(A|T)(C|T)(G|A|C). Required for TFIID binding to TATA-less promoters." [PMID:12651739]
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0000016
name: BRE_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739]
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0000017
name: PSE_motif
def: "A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0000018
name: linkage_group
def: "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046]
is_a: SO:0000001 ! region

[Term]
id: SO:0000019
name: RNA_hairpin_loop
is_a: SO:0000715 ! RNA_motif

[Term]
id: SO:0000020
name: RNA_internal_loop
is_a: SO:0000715 ! RNA_motif

[Term]
id: SO:0000021
name: asymmetric_RNA_internal_loop
is_a: SO:0000020 ! RNA_internal_loop

[Term]
id: SO:0000022
name: A_minor_RNA_motif
is_a: SO:0000021 ! asymmetric_RNA_internal_loop

[Term]
id: SO:0000023
name: K_turn_RNA_motif
is_a: SO:0000021 ! asymmetric_RNA_internal_loop

[Term]
id: SO:0000024
name: Sarcin_like_RNA_motif
is_a: SO:0000021 ! asymmetric_RNA_internal_loop

[Term]
id: SO:0000025
name: symmetric_RNA_internal_loop
is_a: SO:0000020 ! RNA_internal_loop

[Term]
id: SO:0000026
name: RNA_junction_loop
is_a: SO:0000715 ! RNA_motif

[Term]
id: SO:0000027
name: RNA_hook_turn
is_a: SO:0000026 ! RNA_junction_loop

[Term]
id: SO:0000028
name: base_pair
is_a: SO:0000002 ! sequence_secondary_structure

[Term]
id: SO:0000029
name: WC_base_pair
def: "The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293]
synonym: "Watson_Crick_based_pair" RELATED []
is_a: SO:0000028 ! base_pair

[Term]
id: SO:0000030
name: sugar_edge_base_pair
def: "A type of non-canonical base-pairing." [PMID:12177293]
is_a: SO:0000028 ! base_pair

[Term]
id: SO:0000031
name: aptamer
def: "DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:http://aptamer.icmb.utexas.edu]
is_a: SO:0000351 ! synthetic_sequence
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000032
name: DNA_aptamer
def: "DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu]
is_a: SO:0000031 ! aptamer

[Term]
id: SO:0000033
name: RNA_aptamer
def: "RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu]
is_a: SO:0000031 ! aptamer

[Term]
id: SO:0000034
name: morpholino
def: "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http:www.gene-tools.com/Morpholinos/morpholinos.HTML]
is_a: SO:0000351 ! synthetic_sequence
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000035
name: riboswitch
def: "Riboswitches are mRNAs that can act as direct sensors of small molecules to control their own expression. A riboswitch contains a cis element within mRNA, that can act as a direct sensor of metabolites without a protein intermediate." [PMID:2820954]
is_a: SO:0000234 ! mRNA

[Term]
id: SO:0000036
name: matrix_attachment_site
def: "A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]
synonym: "MAR" RELATED []
synonym: "SMAR" RELATED []
synonym: "scaffold_attachment_site" RELATED []
is_a: SO:0000626 ! chromosomal_regulatory_element

[Term]
id: SO:0000037
name: locus_control_region
def: "A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000038
name: match_set
def: "A collection of match parts" [SO:ke]
subset: SOFA
is_a: SO:0000343 ! match

[Term]
id: SO:0000039
name: match_part
def: "A part of a match, for example an hsp from blast isa match_part." [SO:ke]
subset: SOFA
is_a: SO:0000343 ! match
relationship: part_of SO:0000038 ! match_set

[Term]
id: SO:0000040
name: genomic_clone
def: "A clone of a DNA region of a genome." [SO:ma]
is_a: SO:0000151 ! clone

[Term]
id: SO:0000041
name: variation_operation
def: "An operation that can be applied to a sequence, that results in a chnage." [SO:ke]
is_a: SO:0000000 ! Sequence_Ontology

[Term]
id: SO:0000042
name: pseudogene_attribute
def: "An attribute of a pseudogene (SO:0000336)." [SO:ma]
is_a: SO:0000009 ! gene_class

[Term]
id: SO:0000043
name: processed_pseudogene
synonym: "pseudogene_by_reverse_transcription" RELATED []
is_a: SO:0000042 ! pseudogene_attribute

[Term]
id: SO:0000044
name: pseudogene_by_unequal_crossing_over
is_a: SO:0000042 ! pseudogene_attribute

[Term]
id: SO:0000045
name: delete
def: "To remove a subsection of sequence." [SO:ke]
is_a: SO:0000041 ! variation_operation

[Term]
id: SO:0000046
name: insert
def: "To insert a subsection of sequence." [SO:ke]
is_a: SO:0000041 ! variation_operation

[Term]
id: SO:0000047
name: invert
def: "To invert a subsection of sequence." [SO:ke]
is_a: SO:0000041 ! variation_operation

[Term]
id: SO:0000048
name: substitute
def: "To substitute a subsection of sequence for another." [SO:ke]
is_a: SO:0000041 ! variation_operation

[Term]
id: SO:0000049
name: translocate
def: "To translocate a subsection of sequence." [SO:ke]
is_a: SO:0000041 ! variation_operation

[Term]
id: SO:0000050
name: gene_part
def: "A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It is also allows us to associate all the parts of genes with a gene." [SO:ke]
subset: SOFA
is_obsolete: true

[Term]
id: SO:0000051
name: probe
def: "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000052
name: assortment_derived_deficiency
synonym: "assortment-derived_deficiency" RELATED []
is_obsolete: true

[Term]
id: SO:0000053
name: mutation_affecting_regulatory_region
is_a: SO:1000132 ! consequences_of_mutation

[Term]
id: SO:0000054
name: aneuploid
is_a: SO:1000182 ! chromosome_number_variation

[Term]
id: SO:0000055
name: hyperploid
is_a: SO:0000054 ! aneuploid

[Term]
id: SO:0000056
name: hypoploid
is_a: SO:0000054 ! aneuploid

[Term]
id: SO:0000057
name: operator
def: "A regulatory element of an operon to which activators or repressors bind hereby effecting translation of genes in that operon." [SO:ma]
subset: SOFA
is_a: SO:0000752 ! gene_group_regulatory_region

[Term]
id: SO:0000058
name: assortment_derived_aneuploid
synonym: "assortment-derived_aneuploid" RELATED []
is_obsolete: true

[Term]
id: SO:0000059
name: nuclease_binding_site
is_a: SO:0000410 ! protein_binding_site

[Term]
id: SO:0000060
name: compound_chromosome_arm
is_a: SO:1000042 ! compound_chromosome

[Term]
id: SO:0000061
name: restriction_enzyme_binding_site
is_a: SO:0000059 ! nuclease_binding_site

[Term]
id: SO:0000062
name: deficient_intrachromosomal_transposition
is_a: SO:1000041 ! intrachromosomal_transposition

[Term]
id: SO:0000063
name: deficient_interchromosomal_transposition
is_a: SO:1000155 ! interchromosomal_transposition

[Term]
id: SO:0000064
name: gene_by_transcript_attribute
comment: This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004.
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000065
name: free_chromosome_arm
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:0000066
name: gene_by_polyadenylation_attribute
is_a: SO:0000064 ! gene_by_transcript_attribute

[Term]
id: SO:0000067
name: gene_to_gene_feature
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000068
name: overlapping_gene
is_a: SO:0000067 ! gene_to_gene_feature

[Term]
id: SO:0000069
name: gene_included_within_intron
is_a: SO:0000068 ! overlapping_gene

[Term]
id: SO:0000070
name: gene_included_within_intron_antiparallel
is_a: SO:0000069 ! gene_included_within_intron

[Term]
id: SO:0000071
name: gene_included_within_intron_parallel
is_a: SO:0000069 ! gene_included_within_intron

[Term]
id: SO:0000072
name: end_overlapping_gene
is_a: SO:0000068 ! overlapping_gene

[Term]
id: SO:0000073
name: end_overlapping_gene_five_primethree_prime_overlap
is_a: SO:0000072 ! end_overlapping_gene

[Term]
id: SO:0000074
name: end_overlapping_gene_five_primefive_prime_overlap
is_a: SO:0000072 ! end_overlapping_gene

[Term]
id: SO:0000075
name: end_overlapping_gene_three_primethree_prime_overlap
is_a: SO:0000072 ! end_overlapping_gene

[Term]
id: SO:0000076
name: end_overlapping_gene_three_primefive_prime_overlap
is_a: SO:0000072 ! end_overlapping_gene

[Term]
id: SO:0000077
name: antisense_gene
is_a: SO:0000068 ! overlapping_gene

[Term]
id: SO:0000078
name: polycistronic_transcript
is_a: SO:0000115 ! transcript_feature

[Term]
id: SO:0000079
name: dicistronic_transcript
is_a: SO:0000078 ! polycistronic_transcript

[Term]
id: SO:0000080
name: member_of_operon
is_a: SO:0000081 ! member_gene_array

[Term]
id: SO:0000081
name: member_gene_array
is_a: SO:0000067 ! gene_to_gene_feature

[Term]
id: SO:0000082
name: processed_transcript_attribute
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000083
name: macronuclear_sequence_feature
is_a: SO:0000735 ! sequence_location

[Term]
id: SO:0000084
name: micronuclear_sequence_feature
is_a: SO:0000735 ! sequence_location

[Term]
id: SO:0000085
name: gene_by_genome_location
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000086
name: gene_by_organelle_of_genome
is_a: SO:0000085 ! gene_by_genome_location

[Term]
id: SO:0000087
name: nuclear_gene
is_a: SO:0000086 ! gene_by_organelle_of_genome

[Term]
id: SO:0000088
name: mt_gene
synonym: "mitochondrial_gene" RELATED []
is_a: SO:0000086 ! gene_by_organelle_of_genome

[Term]
id: SO:0000089
name: kinetoplast_gene
is_a: SO:0000088 ! mt_gene

[Term]
id: SO:0000090
name: plastid_gene
is_a: SO:0000086 ! gene_by_organelle_of_genome

[Term]
id: SO:0000091
name: apicoplast_gene
is_a: SO:0000090 ! plastid_gene

[Term]
id: SO:0000092
name: ct_gene
synonym: "chloroplast_gene" RELATED []
is_a: SO:0000090 ! plastid_gene

[Term]
id: SO:0000093
name: chromoplast_gene
is_a: SO:0000090 ! plastid_gene

[Term]
id: SO:0000094
name: cyanelle_gene
is_a: SO:0000090 ! plastid_gene

[Term]
id: SO:0000095
name: leucoplast_gene
is_a: SO:0000090 ! plastid_gene

[Term]
id: SO:0000096
name: proplastid_gene
is_a: SO:0000090 ! plastid_gene

[Term]
id: SO:0000097
name: nucleomorph_gene
is_a: SO:0000086 ! gene_by_organelle_of_genome

[Term]
id: SO:0000098
name: plasmid_gene
is_a: SO:0000085 ! gene_by_genome_location

[Term]
id: SO:0000099
name: proviral_gene
is_a: SO:0000085 ! gene_by_genome_location

[Term]
id: SO:0000100
name: endogenous_retroviral_gene
is_a: SO:0000099 ! proviral_gene

[Term]
id: SO:0000101
name: transposable_element
def: "A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/ ~ smaloy/Glossary/T.html]
subset: SOFA
is_a: SO:0000187 ! repeat_family
is_a: SO:1000028 ! intrachromosomal_mutation

[Term]
id: SO:0000102
name: expressed_sequence_match
def: "A match to an EST or cDNA sequence." [SO:ke]
subset: SOFA
is_a: SO:0000347 ! nucleotide_match

[Term]
id: SO:0000103
name: clone_insert_end
def: "The end of the clone insert." [SO:ke]
subset: SOFA
is_a: SO:0000699 ! junction
relationship: part_of SO:0000753 ! clone_insert

[Term]
id: SO:0000104
name: polypeptide
def: "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversable denaturation." [SO:ma]
subset: SOFA
relationship: derives_from SO:0000316 ! CDS

[Term]
id: SO:0000105
name: chromosome_arm
def: "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.exactsciences.com/cic/glossary/_index.htm]
relationship: part_of SO:0000340 ! chromosome

[Term]
id: SO:0000106
name: non_capped_primary_transcript
is_a: SO:0000146 ! primary_transcript_by_cap_class

[Term]
id: SO:0000107
name: sequencing_primer
is_a: SO:0000112 ! primer

[Term]
id: SO:0000108
name: mRNA_with_frameshift
is_a: SO:0000082 ! processed_transcript_attribute

[Term]
id: SO:0000109
name: sequence_variant
def: "A region of sequence where variation has been observed." [SO:ke]
subset: SOFA
synonym: "mutation" RELATED []
is_a: SO:0000110 ! located_sequence_feature

[Term]
id: SO:0000110
name: located_sequence_feature
def: "A biological feature that can be attributed to a region of biological sequence." [SO:ke]
subset: SOFA
is_a: SO:0000000 ! Sequence_Ontology

[Term]
id: SO:0000111
name: transposable_element_gene
def: "A gene encoded within a transposable element. For example gag, int, env and pol are the transpable element genes of the TY element in yeast." [SO:ke]
is_a: SO:0000009 ! gene_class

[Term]
id: SO:0000112
name: primer
def: "A short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase." [http://www.ornl.gov/TechResources/Human_Genome/publicat/primer2001/glossary.html]
subset: SOFA
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000113
name: integrated_virus
def: "A viral sequence which has integrated into the host genome." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000114
name: methylated_C
def: "A methylated deoxy-cytosine." [SO:ke]
subset: SOFA
is_a: SO:0000306 ! methylated_base_feature

[Term]
id: SO:0000115
name: transcript_feature
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000116
name: edited_transcript
def: "A gene whose transcript is edited." [http://www.rna.ucla.edu/]
is_a: SO:0000115 ! transcript_feature

[Term]
id: SO:0000117
name: transcript_with_readthrough_stop_codon
is_obsolete: true

[Term]
id: SO:0000118
name: transcript_with_translational_frameshift
is_a: SO:1001261 ! recoded_mRNA

[Term]
id: SO:0000119
name: gene_by_class_of_regulation
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000120
name: protein_coding_primary_transcript
def: "A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]
comment: May contain introns
subset: SOFA
synonym: "pre-mRNA" RELATED []
is_a: SO:0000185 ! primary_transcript

[Term]
id: SO:0000121
name: forward_primer
def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
is_a: SO:0000112 ! primer

[Term]
id: SO:0000122
name: RNA_sequence_secondary_structure
def: "A folded RNA sequence." [SO:ke]
is_a: SO:0000002 ! sequence_secondary_structure

[Term]
id: SO:0000123
name: transcriptionally_regulated
def: "." [SO:ma]
comment: by\:
is_a: SO:0000119 ! gene_by_class_of_regulation

[Term]
id: SO:0000124
name: transcriptionally_constitutive
is_a: SO:0000123 ! transcriptionally_regulated

[Term]
id: SO:0000125
name: transcriptionally_induced
is_a: SO:0000123 ! transcriptionally_regulated

[Term]
id: SO:0000126
name: transcriptionally_repressed
is_a: SO:0000123 ! transcriptionally_regulated

[Term]
id: SO:0000127
name: silenced_gene
is_a: SO:0000126 ! transcriptionally_repressed

[Term]
id: SO:0000128
name: gene_silenced_by_DNA_modification
is_a: SO:0000127 ! silenced_gene

[Term]
id: SO:0000129
name: gene_silenced_by_DNA_methylation
is_a: SO:0000128 ! gene_silenced_by_DNA_modification

[Term]
id: SO:0000130
name: post_translationally_regulated
synonym: "post-translationally_regulated" RELATED []
is_a: SO:0000119 ! gene_by_class_of_regulation

[Term]
id: SO:0000131
name: translationally_regulated
is_a: SO:0000119 ! gene_by_class_of_regulation

[Term]
id: SO:0000132
name: reverse_primer
def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
is_a: SO:0000112 ! primer

[Term]
id: SO:0000133
name: gene_by_epigenetic_modification
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000134
name: imprinted
is_a: SO:0000119 ! gene_by_class_of_regulation
is_a: SO:0000133 ! gene_by_epigenetic_modification

[Term]
id: SO:0000135
name: maternally_imprinted
is_a: SO:0000134 ! imprinted

[Term]
id: SO:0000136
name: paternally_imprinted
is_a: SO:0000134 ! imprinted

[Term]
id: SO:0000137
name: allelically_excluded
is_a: SO:0000133 ! gene_by_epigenetic_modification

[Term]
id: SO:0000138
name: gene_rearranged_at_DNA_level
is_a: SO:0000133 ! gene_by_epigenetic_modification

[Term]
id: SO:0000139
name: ribosome_entry_site
def: "Region in mRNA where ribosome assembles." [SO:ke]
comment: gene\:
subset: SOFA
relationship: part_of SO:0000203 ! UTR

[Term]
id: SO:0000140
name: attenuator
def: "A sequence segment located between the promoter and a structural gene that causes partial termination of transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
is_a: SO:0000752 ! gene_group_regulatory_region
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000141
name: terminator
def: "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
is_a: SO:0000752 ! gene_group_regulatory_region
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000142
name: DNA_sequence_secondary_structure
def: "A folded DNA sequence." [SO:ke]
is_a: SO:0000002 ! sequence_secondary_structure

[Term]
id: SO:0000143
name: assembly_component
def: "A region of sequence which may be used to manufacture a longer assembled, sequence." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000144
name: primary_transcript_attribute
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000145
name: recoded_codon
is_a: SO:0000360 ! codon

[Term]
id: SO:0000146
name: primary_transcript_by_cap_class
is_a: SO:0000144 ! primary_transcript_attribute

[Term]
id: SO:0000147
name: exon
def: "A region of the genome that codes for portion of spliced messenger RNA (SO:0000234); may contain 5'-untranslated region (SO:0000204), all open reading frames (SO:0000236) and 3'-untranslated region (SO:0000205)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
relationship: part_of SO:0000673 ! transcript

[Term]
id: SO:0000148
name: supercontig
def: "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]
subset: SOFA
synonym: "scaffold" RELATED []
is_a: SO:0000353 ! assembly
relationship: part_of SO:0000719 ! ultracontig

[Term]
id: SO:0000149
name: contig
def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unvailable bases." [SO:ls]
subset: SOFA
is_a: SO:0000143 ! assembly_component
is_a: SO:0000353 ! assembly
relationship: part_of SO:0000148 ! supercontig

[Term]
id: SO:0000150
name: read
def: "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]
subset: SOFA
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000149 ! contig

[Term]
id: SO:0000151
name: clone
def: "A piece of DNA that has been inserted in a vector so that it can be propagated in E. coli or some other organism." [http://www.geospiza.com/community/support/glossary/]
subset: SOFA
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000152
name: YAC
def: "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]
is_a: SO:0000440 ! vector
relationship: part_of SO:0000760 ! YAC_clone

[Term]
id: SO:0000153
name: BAC
def: "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]
is_a: SO:0000440 ! vector
relationship: part_of SO:0000764 ! BAC_clone

[Term]
id: SO:0000154
name: PAC
def: "P1 Artificial Chromosome. These vectors can hold large inserts, typically 80-200 kb, and propagate in E. coli as a single copy episome." [https://www.ncbi.nlm.nih.gov/genome/guide/mouse/glossary.htm]
synonym: "P1" RELATED []
is_a: SO:0000440 ! vector
relationship: part_of SO:0000762 ! PAC_clone

[Term]
id: SO:0000155
name: plasmid
def: "A self-replicating circular DNA molecule that is distinct from a chromosome in the organism." [SO:ma]
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000156
name: cosmid
def: "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as aplasmids or packaged as a phage,since they retain the lambda cos sites." [SO:ma]
comment: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1)\:9-20.
is_a: SO:0000440 ! vector
relationship: part_of SO:0000765 ! cosmid_clone

[Term]
id: SO:0000157
name: phagemid
def: "A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \"helper\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]
is_a: SO:0000440 ! vector
relationship: part_of SO:0000761 ! phagemid_clone

[Term]
id: SO:0000158
name: fosmid
def: "A cloning vector that utilises the E. coli F factor." [SO:ma]
comment: Birren BW et al. A human chromosome 22 fosmid resource\: mapping and analysis of 96 clones. Genomics 1996;
is_a: SO:0000440 ! vector
relationship: part_of SO:0000763 ! fosmid_clone

[Term]
id: SO:0000159
name: deletion
def: "The sequence that is deleted." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region
is_a: SO:0000109 ! sequence_variant
relationship: sequence_of SO:0000045 ! delete

[Term]
id: SO:0000160
name: lambda_clone
def: "A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]
is_a: SO:0000151 ! clone

[Term]
id: SO:0000161
name: methylated_A
def: "A methylated adenine." [SO:ke]
subset: SOFA
is_a: SO:0000250 ! modified_RNA_base_feature
is_a: SO:0000306 ! methylated_base_feature

[Term]
id: SO:0000162
name: splice_site
def: "The position where intron is excised." [SO:ke]
subset: SOFA
is_a: SO:0000699 ! junction
relationship: part_of SO:0000185 ! primary_transcript

[Term]
id: SO:0000163
name: splice_donor_site
def: "The junction between the 3 prime end of an exon and the following intron." [http://www.ucl.ac.uk/ ~ ucbhjow/b241/glossary.html]
subset: SOFA
synonym: "donor" RELATED []
synonym: "donor_splice_site" RELATED []
is_a: SO:0000162 ! splice_site

[Term]
id: SO:0000164
name: splice_acceptor_site
def: "The junction between the 3 prime end of an intron and the following exon." [http://www.ucl.ac.uk/ ~ ucbhjow/b241/glossary.html]
subset: SOFA
synonym: "acceptor" RELATED []
synonym: "acceptor_splice_site" RELATED []
is_a: SO:0000162 ! splice_site

[Term]
id: SO:0000165
name: enhancer
def: "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000166
name: enhancer_by_bound_factor
is_a: SO:0000402 ! enhancer_attribute

[Term]
id: SO:0000167
name: promoter
def: "The region on a DNA molecule involved in RNA polymerase binding to initiate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000168
name: restriction_enzyme_cut_site
def: "A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA." [SO:ma]
is_obsolete: true

[Term]
id: SO:0000169
name: RNApol_I_promoter
def: "A DNA sequence sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]
synonym: "RNA_polymerase_A_promoter" RELATED []
is_a: SO:0000167 ! promoter

[Term]
id: SO:0000170
name: RNApol_II_promoter
def: "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]
synonym: "RNA_polymerase_B_promoter" RELATED []
is_a: SO:0000167 ! promoter

[Term]
id: SO:0000171
name: RNApol_III_promoter
def: "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]
synonym: "RNA_polymerase_C_promoter" RELATED []
is_a: SO:0000167 ! promoter

[Term]
id: SO:0000172
name: CAAT_signal
def: "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0000173
name: GC_rich_region
def: "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
synonym: "GC-rich_region" RELATED []
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0000174
name: TATA_box
def: "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
relationship: part_of SO:0000170 ! RNApol_II_promoter
relationship: part_of SO:0000171 ! RNApol_III_promoter

[Term]
id: SO:0000175
name: minus_10_signal
def: "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
synonym: "-10_signal" RELATED []
synonym: "Pribnow_box" RELATED []
relationship: part_of SO:0000613 ! bacterial_RNApol_promoter

[Term]
id: SO:0000176
name: minus_35_signal
def: "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
synonym: "-35_signal" RELATED []
relationship: part_of SO:0000613 ! bacterial_RNApol_promoter

[Term]
id: SO:0000177
name: cross_genome_match
def: "A nucleotide match against a sequence from another organism." [SO:ma]
subset: SOFA
is_a: SO:0000347 ! nucleotide_match

[Term]
id: SO:0000178
name: operon
def: "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]
subset: SOFA
is_a: SO:0005855 ! gene_group

[Term]
id: SO:0000179
name: clone_insert_start
def: "The start of the clone insert." [SO:ke]
subset: SOFA
is_a: SO:0000699 ! junction
relationship: part_of SO:0000753 ! clone_insert

[Term]
id: SO:0000180
name: retrotransposon
def: "A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.genpromag.com/scripts/glossary.asp?LETTER=R]
is_a: SO:0000101 ! transposable_element

[Term]
id: SO:0000181
name: translated_nucleotide_match
def: "A match against a translated sequence." [SO:ke]
subset: SOFA
is_a: SO:0000347 ! nucleotide_match

[Term]
id: SO:0000182
name: DNA_transposon
def: "A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]
is_a: SO:0000101 ! transposable_element

[Term]
id: SO:0000183
name: non_transcribed_region
def: "A region of the gene which is not transcribed." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region
relationship: part_of SO:0000704 ! gene

[Term]
id: SO:0000184
name: U2_intron
def: "A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]
comment: May have either GT-AG or AT-AG 5' and 3' boundaries.
is_a: SO:0000662 ! spliceosomal_intron

[Term]
id: SO:0000185
name: primary_transcript
def: "The primary (initial, unprocessed) transcript; includes five_prime_clip (SO:0000555), five_prime_untranslated_region (SO:0000204), open reading frames (SO:0000236), introns (SO:0000188) and three_prime_ untranslated_region (three_prime_UTR), and three_prime_clip (SO:0000557)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
synonym: "precursor_RNA" RELATED []
is_a: SO:0000673 ! transcript

[Term]
id: SO:0000186
name: LTR_retrotransposon
def: "A retrotransposon flanked by long terminal repeat sequences." [SO:ke]
is_a: SO:0000180 ! retrotransposon

[Term]
id: SO:0000187
name: repeat_family
def: "A group of characterized repeat sequences." [SO:ke]
subset: SOFA
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000188
name: intron
def: "A segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
relationship: part_of SO:0000185 ! primary_transcript

[Term]
id: SO:0000189
name: non_LTR_retrotransposon
def: "A retrotransposon without long terminal repeat sequences." [SO:ke]
is_a: SO:0000180 ! retrotransposon

[Term]
id: SO:0000190
name: five_prime_intron
is_a: SO:0000188 ! intron

[Term]
id: SO:0000191
name: interior_intron
is_a: SO:0000188 ! intron

[Term]
id: SO:0000192
name: three_prime_intron
is_a: SO:0000188 ! intron

[Term]
id: SO:0000193
name: RFLP_fragment
def: "A polymorphism detectable by the size differences in DNA fragments generated by a restriction enzyme." [PMID:6247908]
subset: SOFA
synonym: "restriction_fragment_length_polymorphism" RELATED []
is_a: SO:0000412 ! restriction_fragment

[Term]
id: SO:0000194
name: LINE_element
def: "A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http:www.ucl.ac.uk/~ucbhjow/b241/glossary.html]
synonym: "Long interspersed element" RELATED []
synonym: "Long interspersed nuclear element" RELATED []
is_a: SO:0000189 ! non_LTR_retrotransposon

[Term]
id: SO:0000195
name: coding_exon
def: "An exon whereby at least one base is part of a codon, including the stop_codon." [SO:ke]
is_a: SO:0000147 ! exon

[Term]
id: SO:0000196
name: five_prime_exon_coding_region
def: "The sequence of the 5' exon that encodes for protein." [SO:ke]
is_a: SO:0000195 ! coding_exon
relationship: part_of SO:0000200 ! five_prime_coding_exon

[Term]
id: SO:0000197
name: three_prime_exon_coding_region
def: "The sequence of the 3' exon that encodes for protein." [SO:ke]
is_a: SO:0000195 ! coding_exon
relationship: part_of SO:0000202 ! three_prime_coding_exon

[Term]
id: SO:0000198
name: noncoding_exon
def: "An exon that does not contain any codons." [SO:ke]
synonym: "noncoding_exon" RELATED []
is_a: SO:0000147 ! exon

[Term]
id: SO:0000199
name: translocation
def: "A region of nucleotide sequence that has translocated to a new position." [SO:ke]
relationship: sequence_of SO:0000049 ! translocate

[Term]
id: SO:0000200
name: five_prime_coding_exon
def: "The 5' most coding exon." [SO:ke]
is_a: SO:0000147 ! exon

[Term]
id: SO:0000201
name: interior_exon
is_a: SO:0000147 ! exon

[Term]
id: SO:0000202
name: three_prime_coding_exon
def: "The exon that is most 3-prime on a given transcript." [SO:ma]
is_a: SO:0000147 ! exon

[Term]
id: SO:0000203
name: UTR
def: "Messenger RNA sequences that are untranslated and lie five prime and three prime to sequences which are translated." [SO:ke]
subset: SOFA
synonym: "untranslated_region" RELATED []
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:0000204
name: five_prime_UTR
def: "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
synonym: "five_prime_untranslated_region" RELATED []
is_a: SO:0000203 ! UTR

[Term]
id: SO:0000205
name: three_prime_UTR
def: "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
synonym: "three_prime_untranslated_region" RELATED []
is_a: SO:0000203 ! UTR

[Term]
id: SO:0000206
name: SINE_element
def: "A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]
synonym: "Short interspersed element" RELATED []
synonym: "Short interspersed nuclear element" RELATED []
is_a: SO:0000189 ! non_LTR_retrotransposon

[Term]
id: SO:0000207
name: simple_sequence_length_polymorphism
is_a: SO:0000248 ! sequence_length_variation

[Term]
id: SO:0000208
name: terminal_inverted_repeat_element
def: "A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http:www.genetics.org/cgi/reprint/156/4/1983.pdf]
is_a: SO:0000182 ! DNA_transposon

[Term]
id: SO:0000209
name: rRNA_primary_transcript
def: "A primary transcript encoding a ribosomal RNA." [SO:ke]
synonym: "ribosomal_RNA_primary_transcript" RELATED []
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000210
name: tRNA_primary_transcript
def: "A primary transcript encoding a transfer RNA (SO:0000253.)" [SO:ke]
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000211
name: alanine_tRNA_primary_transcript
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000212
name: arginine_tRNA_primary_transcript
def: "A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000213
name: asparagine_tRNA_primary_transcript
def: "A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000214
name: aspartic_acid_tRNA_primary_transcript
def: "A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000215
name: cysteine_tRNA_primary_transcript
def: "A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000216
name: glutamic_acid_tRNA_primary_transcript
def: "A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000217
name: glutamine_tRNA_primary_transcript
def: "A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000218
name: glycine_tRNA_primary_transcript
def: "A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000219
name: histidine_tRNA_primary_transcript
def: "A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000220
name: isoleucine_tRNA_primary_transcript
def: "A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000221
name: leucine_tRNA_primary_transcript
def: "A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000222
name: lysine_tRNA_primary_transcript
def: "A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000223
name: methionine_tRNA_primary_transcript
def: "A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000224
name: phenylalanine_tRNA_primary_transcript
def: "A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000225
name: proline_tRNA_primary_transcript
def: "A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000226
name: serine_tRNA_primary_transcript
def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000227
name: threonine_tRNA_primary_transcript
def: "A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000228
name: tryptophan_tRNA_primary_transcript
def: "A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000229
name: tyrosine_tRNA_primary_transcript
def: "A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000230
name: valine_tRNA_primary_transcript
def: "A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000231
name: snRNA_primary_transcript
def: "A primary transcript encoding a small nuclear mRNA (SO:0000274)." [SO:ke]
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000232
name: snoRNA_primary_transcript
def: "A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000233
name: processed_transcript
def: "A transcript which has undergone processing to remove parts such as introns and transcribed_spacer_regions." [SO:ke]
comment: A processed transcript cannot contain introns.
subset: SOFA
is_a: SO:0000673 ! transcript
relationship: derives_from SO:0000185 ! primary_transcript

[Term]
id: SO:0000234
name: mRNA
def: "Messenger RNA is the intermediate molecule between DNA and protein. It  includes UTR and coding sequences. It does not contain introns." [SO:ma]
comment: mRNA does not contain introns as it is a processd_transcript.nThe equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns.
subset: SOFA
synonym: "messenger_RNA" RELATED []
is_a: SO:0000233 ! processed_transcript

[Term]
id: SO:0000235
name: TF_binding_site
def: "A region of a molecule that binds to a transcription factor." [SO:ke]
subset: SOFA
synonym: "transcription_factor_binding_site" RELATED []
is_a: SO:0000410 ! protein_binding_site
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000236
name: ORF
def: "The inframe interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER" [SO:ma, SO:rb]
comment: The definition was modified by Rama. This terms now basically is the same as a CDS. This must be revised.
subset: SOFA
synonym: "open_reading_frame" RELATED []
is_a: SO:0000717 ! reading_frame

[Term]
id: SO:0000237
name: transcript_attribute
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000238
name: foldback_element
def: "A transposable element with extensive secondary structure, characterised by large modular imperfect long inverted repeats" [http:www.genetics.org/cgi/reprint/156/4/1983.pdf]
synonym: "LVR element" RELATED []
synonym: "long inverted repeat element" RELATED []
is_a: SO:0000182 ! DNA_transposon

[Term]
id: SO:0000239
name: flanking_region
def: "The DNA sequences extending on either side of a specific locus." [http://biotech.icmb.utexas.edu/search/dict-search.mhtml]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000240
name: chromosome_variation
is_a: SO:0000000 ! Sequence_Ontology

[Term]
id: SO:0000241
name: internal_UTR
is_a: SO:0000203 ! UTR

[Term]
id: SO:0000242
name: untranslated_region_polyicistronic_mRNA
def: "The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]
is_a: SO:0000203 ! UTR

[Term]
id: SO:0000243
name: internal_ribosome_entry_site
def: "Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]
synonym: "IRES" RELATED []
is_a: SO:0000139 ! ribosome_entry_site

[Term]
id: SO:0000244
name: four_cutter_restriction_site
synonym: "4-cutter_restriction_site" RELATED []
synonym: "four-cutter_restriction_sit" RELATED []
is_obsolete: true

[Term]
id: SO:0000245
name: mRNA_by_polyadenylation_status
is_a: SO:0000082 ! processed_transcript_attribute

[Term]
id: SO:0000246
name: mRNA_polyadenylated
is_a: SO:0000245 ! mRNA_by_polyadenylation_status

[Term]
id: SO:0000247
name: mRNA_not_polyadenylated
is_a: SO:0000245 ! mRNA_by_polyadenylation_status

[Term]
id: SO:0000248
name: sequence_length_variation
is_a: SO:1000002 ! substitution

[Term]
id: SO:0000249
name: six_cutter_restriction_site
synonym: "6-cutter_restriction_site" RELATED []
synonym: "six-cutter_restriction_site" RELATED []
is_obsolete: true

[Term]
id: SO:0000250
name: modified_RNA_base_feature
def: "A post_transcriptionally modified base." [SO:ke]
relationship: part_of SO:0000673 ! transcript

[Term]
id: SO:0000251
name: eight_cutter_restriction_site
synonym: "8-cutter_restriction_site" RELATED []
synonym: "eight-cutter_restriction_site" RELATED []
is_obsolete: true

[Term]
id: SO:0000252
name: rRNA
def: "RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types, ISBN:0198506732]
subset: SOFA
synonym: "ribsomal_RNA" RELATED []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000253
name: tRNA
def: "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. tRNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). tRNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]
subset: SOFA
synonym: "transfer_RNA" RELATED []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000254
name: alanyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000255
name: rRNA_small_subunit_primary_transcript
def: "A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]
is_a: SO:0000209 ! rRNA_primary_transcript

[Term]
id: SO:0000256
name: asparaginyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000257
name: aspartyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000258
name: cysteinyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000259
name: glutaminyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000260
name: glutamyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000261
name: glycyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000262
name: histidyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000263
name: isoleucyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000264
name: leucyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000265
name: lysyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000266
name: methionyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000267
name: phenylalanyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000268
name: prolyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000269
name: seryl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000270
name: threonyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000271
name: tryptophanyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000272
name: tyrosyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000273
name: valyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000274
name: snRNA
def: "Small non-coding RNA in the nucleoplasm. A small nuclear RNA molecule involved in pre-mRNA splicing and processing" [ems:WB, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types, PMID:11733745]
subset: SOFA
synonym: "small_nuclear_RNA" RELATED []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000275
name: snoRNA
def: "Small nucleolar RNAs (snoRNAs) are involved in the processing and modification of rRNA in the nucleolus. There are two main classes of snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA is a member of the box C/D class. Indeed, the box C/D element is a subset of the six short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C, C', and D. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]
subset: SOFA
synonym: "small_nucleolar_RNA" RELATED []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000276
name: miRNA
def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. miRNAs are produced from precursor molecules (SO:0000647) that can form local hairpin strcutures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpinprecursor molecule. miRNAs may trigger the cleavage of their target molecules oract as translational repressors." [PMID:12592000]
subset: SOFA
synonym: "micro_RNA" RELATED []
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000277
name: transcript_by_bound_factor
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000278
name: transcript_by_bound_nucleic_acid
is_a: SO:0000277 ! transcript_by_bound_factor

[Term]
id: SO:0000279
name: transcript_by_bound_protein
is_a: SO:0000277 ! transcript_by_bound_factor

[Term]
id: SO:0000280
name: engineered_gene
is_a: SO:0000009 ! gene_class

[Term]
id: SO:0000281
name: engineered_foreign_gene
is_a: SO:0000280 ! engineered_gene
is_a: SO:0000285 ! foreign_gene

[Term]
id: SO:0000282
name: mRNA_with_minus_1_frameshift
is_a: SO:0000108 ! mRNA_with_frameshift

[Term]
id: SO:0000283
name: engineered_foreign_transposable_element_gene
is_a: SO:0000111 ! transposable_element_gene
is_a: SO:0000280 ! engineered_gene

[Term]
id: SO:0000284
name: type_I_enzyme_restriction_site
def: "The recognition site is bipartate and interupted." [http://www.promega.com]
is_obsolete: true

[Term]
id: SO:0000285
name: foreign_gene
is_a: SO:0000452 ! transgene

[Term]
id: SO:0000286
name: long_terminal_repeat
def: "A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
synonym: "LTR" RELATED []
synonym: "direct_terminal _repeat" RELATED []
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000186 ! LTR_retrotransposon

[Term]
id: SO:0000287
name: fusion_gene
is_a: SO:0000009 ! gene_class

[Term]
id: SO:0000288
name: engineered_fusion_gene
is_a: SO:0000280 ! engineered_gene
is_a: SO:0000287 ! fusion_gene

[Term]
id: SO:0000289
name: microsatellite
def: "A very short unit sequence of DNA (2 to 4 bp) that is repeated multiple times in tandem." [http://www.informatics.jax.org/silver/glossary.shtml]
subset: SOFA
is_a: SO:0000705 ! tandem_repeat

[Term]
id: SO:0000290
name: dinucleotide_repeat_microsatellite_feature
is_a: SO:0000289 ! microsatellite

[Term]
id: SO:0000291
name: trinucleotide_repeat_microsatellite_feature
is_a: SO:0000289 ! microsatellite

[Term]
id: SO:0000292
name: repetitive_element
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000293
name: engineered_foreign_repetitive_element
is_a: SO:0000280 ! engineered_gene
is_a: SO:0000292 ! repetitive_element

[Term]
id: SO:0000294
name: inverted_repeat
def: "The sequence is complementarily repeated on the opposite strand. Example: GCTGA-----TCAGC." [SO:ke]
subset: SOFA
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000295
name: U12_intron
def: "A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]
comment: May have either GT-AC or AT-AC 5' and 3' boundaries.
is_a: SO:0000662 ! spliceosomal_intron

[Term]
id: SO:0000296
name: origin_of_replication
def: "The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000297
name: D_loop
def: "Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
is_a: SO:0000296 ! origin_of_replication

[Term]
id: SO:0000298
name: recombination_feature
is_a: SO:0000001 ! region

[Term]
id: SO:0000299
name: specific_recombination_site
is_a: SO:0000669 ! sequence_rearrangement_feature

[Term]
id: SO:0000300
name: recombination_feature_of_rearranged_gene
is_a: SO:0000299 ! specific_recombination_site

[Term]
id: SO:0000301
name: recombination_feature_of_vertebrate_immune_system_gene
is_a: SO:0000300 ! recombination_feature_of_rearranged_gene

[Term]
id: SO:0000302
name: J_gene_recombination_feature
def: "Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#J-RS]
synonym: "J-RS" RELATED []
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene

[Term]
id: SO:0000303
name: clip
def: "Part of the primary transcript that is clipped off during processing." [SO:ke]
subset: SOFA
relationship: part_of SO:0000185 ! primary_transcript

[Term]
id: SO:0000304
name: type_II_enzyme_restriction_site
def: "The recognition site is either palindromic, partially palindromic or an interupted palidrome. Cleavage occurs within the recognition site." [http://www.promega.com]
is_obsolete: true

[Term]
id: SO:0000305
name: modified_base_site
def: "A modified nucleotide, i.e. a nucleotide other than A, T, C. G or (in RNA) U." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
comment: modified base\:
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000306
name: methylated_base_feature
def: "A nucleotide modified by methylation." [SO:ke]
subset: SOFA
is_a: SO:0000305 ! modified_base_site

[Term]
id: SO:0000307
name: CpG_island
def: "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd]
subset: SOFA
synonym: "CG_island" RELATED []
is_a: SO:0000001 ! region

[Term]
id: SO:0000308
name: sequence_feature_locating_method
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000309
name: computed_feature
is_a: SO:0000308 ! sequence_feature_locating_method

[Term]
id: SO:0000310
name: predicted_ab_initio_computation
is_a: SO:0000309 ! computed_feature

[Term]
id: SO:0000311
name: computed_feature_by_similarity
def: "." [SO:ma]
comment: similar to\:
is_a: SO:0000309 ! computed_feature

[Term]
id: SO:0000312
name: experimentally_determined_feature
is_a: SO:0000308 ! sequence_feature_locating_method

[Term]
id: SO:0000313
name: stem_loop
def: "A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
is_a: SO:0000002 ! sequence_secondary_structure

[Term]
id: SO:0000314
name: direct_repeat
def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke]
subset: SOFA
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000315
name: transcription_start_site
def: "The site where transcription begins." [SO:ke]
subset: SOFA
synonym: "TSS" RELATED []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000185 ! primary_transcript

[Term]
id: SO:0000316
name: CDS
def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]
subset: SOFA
synonym: "coding_sequence" RELATED []
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:0000317
name: cDNA_clone
def: "Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]
is_a: SO:0000151 ! clone

[Term]
id: SO:0000318
name: start_codon
def: "First codon to be translated by a ribosome." [SO:ke]
synonym: "initiation codon" RELATED []
is_a: SO:0000360 ! codon

[Term]
id: SO:0000319
name: stop_codon
def: "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]
is_a: SO:0000360 ! codon

[Term]
id: SO:0000320
name: intronic_splice_enhancer
def: "Sequences within the intron that modulate splice site selection for some introns." [SO:ke]
is_a: SO:0000344 ! splice_enhancer
relationship: part_of SO:0000662 ! spliceosomal_intron

[Term]
id: SO:0000321
name: mRNA_with_plus_1_frameshift
is_a: SO:0000108 ! mRNA_with_frameshift

[Term]
id: SO:0000322
name: nuclease_hypersensitive_site
is_a: SO:0000684 ! nuclease_sensitive_site

[Term]
id: SO:0000323
name: coding_start
def: "The first base to be translated into protein." [SO:ke]
synonym: "translation_start" RELATED []
relationship: part_of SO:0000316 ! CDS

[Term]
id: SO:0000324
name: tag
def: "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]
subset: SOFA
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000325
name: rRNA_large_subunit_primary_transcript
def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]
is_a: SO:0000209 ! rRNA_primary_transcript

[Term]
id: SO:0000326
name: SAGE_tag
def: "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [https://www.ncbi.nlm.nih.gov/pubmed/7570003]
subset: SOFA
is_a: SO:0000324 ! tag

[Term]
id: SO:0000327
name: coding_end
def: "The last base to be translated into protein. It does not include the stop codon." [SO:ke]
synonym: "translation_end" RELATED []
relationship: part_of SO:0000316 ! CDS

[Term]
id: SO:0000328
name: microarray_oligo
synonym: "microarray_oligonucleotide" RELATED []
is_a: SO:0000051 ! probe
is_a: SO:0000324 ! tag
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000329
name: mRNA_with_plus_2_frameshift
is_a: SO:0000108 ! mRNA_with_frameshift

[Term]
id: SO:0000330
name: conserved_region
def: "Region of sequence similarity by descent from a common ancestor." [SO:ke]
is_a: SO:0000001 ! region

[Term]
id: SO:0000331
name: STS
def: "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com]
subset: SOFA
synonym: "sequence_tag_site" RELATED []
is_a: SO:0000324 ! tag

[Term]
id: SO:0000332
name: coding_conserved_region
def: "Coding region of sequence similarity by descent from a common ancestor." [SO:ke]
is_a: SO:0000330 ! conserved_region

[Term]
id: SO:0000333
name: exon_junction
def: "The boundary between two exons in a processed transcript." [SO:ke]
subset: SOFA
is_a: SO:0000699 ! junction
relationship: part_of SO:0000233 ! processed_transcript

[Term]
id: SO:0000334
name: nc_conserved_region
def: "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke]
synonym: "noncoding_conserved_region" RELATED []
is_a: SO:0000330 ! conserved_region

[Term]
id: SO:0000335
name: mRNA_with_minus_2_frameshift
is_a: SO:0000108 ! mRNA_with_frameshift

[Term]
id: SO:0000336
name: pseudogene
def: "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." [http://www.ucl.ac.uk/ ~ ucbhjow/b241/glossary.html]
subset: SOFA
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000704 ! gene

[Term]
id: SO:0000337
name: RNAi_reagent
def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]
subset: SOFA
is_a: SO:0000695 ! reagent
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000338
name: MITE
def: "A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITES do not encode proteins." [http:www.pnas.org/cgi/content/full/97/18/10083]
is_a: SO:0000208 ! terminal_inverted_repeat_element

[Term]
id: SO:0000339
name: recombination_hotspot
def: "A region in a genome whioch promotes recombination." [SO:rd]
is_a: SO:0000298 ! recombination_feature

[Term]
id: SO:0000340
name: chromosome
def: "Structural unit composed of long DNA molecule." [http://biotech.icmb.utexas.edu/search/dict-search.mhtml]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000341
name: chromosome_band
def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]
synonym: "cytological_band" RELATED []
relationship: part_of SO:0000340 ! chromosome

[Term]
id: SO:0000342
name: site_specific_recombination_target_region
is_a: SO:0000299 ! specific_recombination_site

[Term]
id: SO:0000343
name: match
def: "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000344
name: splice_enhancer
def: "Region of a transcript that regulates splicing." [SO:ke]
subset: SOFA
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000345
name: EST
def: "Expressed Sequence Tag: The sequence of a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [http://genomics.phrma.org/lexicon/e.html]
subset: SOFA
synonym: "expressed_sequence_tag" RELATED []
is_a: SO:0000695 ! reagent
relationship: derives_from SO:0000234 ! mRNA

[Term]
id: SO:0000346
name: Cre_recombination_target_region
synonym: "lox_site" RELATED []
is_a: SO:0000342 ! site_specific_recombination_target_region

[Term]
id: SO:0000347
name: nucleotide_match
def: "A match against a nucleotide sequence." [SO:ke]
subset: SOFA
is_a: SO:0000343 ! match

[Term]
id: SO:0000348
name: nucleic_acid
is_a: SO:0000443 ! polymer_type

[Term]
id: SO:0000349
name: protein_match
def: "A match against a protein sequence." [SO:ke]
subset: SOFA
is_a: SO:0000343 ! match

[Term]
id: SO:0000350
name: FLP_recombination_target_region
synonym: "FRT_site" RELATED []
is_a: SO:0000342 ! site_specific_recombination_target_region

[Term]
id: SO:0000351
name: synthetic_sequence
def: "A sequence of nucleotides or amino acids that has been designed by an experimentor and which may, or may not, correspond with any natural sequence." [SO:ma]
is_a: SO:0000443 ! polymer_type

[Term]
id: SO:0000352
name: DNA
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0000353
name: assembly
def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000354
name: group_1_intron_homing_endonuclease_target_region
is_a: SO:0000684 ! nuclease_sensitive_site

[Term]
id: SO:0000355
name: haplotype_block
def: "A region of the genome which in which markers are co-inherited as the result of the lack of historic recombination between them due to their close proximity." [SO:ma]
is_a: SO:0000298 ! recombination_feature

[Term]
id: SO:0000356
name: RNA
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0000357
name: sequence_by_flanking_target_attribute
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000358
name: protein
def: "One or more polypeptides which may, or may not, be covalently bonded, and which assume a native secondary and tertiary structure." [SO:ma]
comment: This definition no longer matches the meaning of the concept! Term should probably be proteinacious or something... KEn
is_a: SO:0000443 ! polymer_type

[Term]
id: SO:0000359
name: floxed_sequence
is_a: SO:0000357 ! sequence_by_flanking_target_attribute
is_a: SO:0000452 ! transgene

[Term]
id: SO:0000360
name: codon
def: "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together signify a unique amino acid or the termination of translation." [http://genomics.phrma.org/lexicon/c.html]
subset: SOFA
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:0000361
name: FRT_flanked_sequence
is_a: SO:0000357 ! sequence_by_flanking_target_attribute

[Term]
id: SO:0000362
name: chimeric_cDNA_clone
def: "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma]
is_a: SO:0000317 ! cDNA_clone

[Term]
id: SO:0000363
name: floxed_gene
is_a: SO:0000359 ! floxed_sequence

[Term]
id: SO:0000364
name: transposable_element_flanking_region
def: "The region of sequence surrounding a transposible element." [SO:ke]
is_a: SO:0000239 ! flanking_region

[Term]
id: SO:0000365
name: integron
def: "DNA elements capable of mobilizing individual gene cassettes into bacterial chromosomes by site- specific recombination." [http://www.genomicglossaries.com/content/DNA.asp]
is_a: SO:0000669 ! sequence_rearrangement_feature

[Term]
id: SO:0000366
name: insertion_site
def: "The junction where an insertion occurred." [SO:ke]
subset: SOFA
is_a: SO:0000109 ! sequence_variant
is_a: SO:0000699 ! junction
relationship: position_of SO:0000046 ! insert

[Term]
id: SO:0000367
name: attI_site
relationship: part_of SO:0000365 ! integron

[Term]
id: SO:0000368
name: transposable_element_insertion_site
def: "The junction in a genome where a transposable_element has inserted." [SO:ke]
subset: SOFA
is_a: SO:0000366 ! insertion_site

[Term]
id: SO:0000369
name: integrase_coding_region
relationship: part_of SO:0000365 ! integron

[Term]
id: SO:0000370
name: small_regulatory_ncRNA
def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]
subset: SOFA
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000371
name: conjugative_transposon
def: "A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/ ~ smaloy/Glossary/C.html]
is_a: SO:0000182 ! DNA_transposon

[Term]
id: SO:0000372
name: enzymatic_RNA
def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]
subset: SOFA
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000373
name: recombinationally_inverted
is_a: SO:0000456 ! recombinationally_rearranged_gene

[Term]
id: SO:0000374
name: ribozyme
def: "An RNA with catalytic activity." [SO:ma]
subset: SOFA
is_a: SO:0000372 ! enzymatic_RNA

[Term]
id: SO:0000375
name: rRNA_5.8S
def: "5.8S ribosomal RNA (5.8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5.8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]
subset: SOFA
synonym: "5.8S_rRNA" RELATED []
is_a: SO:0000252 ! rRNA

[Term]
id: SO:0000376
name: RNA_6S
def: "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]
synonym: "6S_RNA" RELATED []
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000377
name: CsrB_RsmB_RNA
def: "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]
synonym: "CsrB-RsmB_RNA" RELATED []
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000378
name: DsrA_RNA
def: "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000379
name: GcvB_RNA
def: "A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]
is_a: SO:0000378 ! DsrA_RNA

[Term]
id: SO:0000380
name: hammerhead_ribozyme
def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [http:rnaworld.bio.ukans.edu/class/RNA/RNA00/RNA_World_3.html]
subset: SOFA
is_a: SO:0000374 ! ribozyme

[Term]
id: SO:0000381
name: group_IIA_intron
is_a: SO:0000603 ! group_II_intron

[Term]
id: SO:0000382
name: group_IIB_intron
is_a: SO:0000603 ! group_II_intron

[Term]
id: SO:0000383
name: MicF_RNA
def: "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]
is_a: SO:0000644 ! antisense_RNA

[Term]
id: SO:0000384
name: OxyS_RNA
def: "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000385
name: RNase_MRP_RNA
def: "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]
subset: SOFA
is_a: SO:0000372 ! enzymatic_RNA

[Term]
id: SO:0000386
name: RNase_P_RNA
def: "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterised activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]
subset: SOFA
is_a: SO:0000374 ! ribozyme

[Term]
id: SO:0000387
name: RprA_RNA
def: "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000388
name: RRE_RNA
def: "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000389
name: spot_42_RNA
def: "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000390
name: telomerase_RNA
def: "The RNA component of telomerase, a reverse transcriptase that synthesises telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]
subset: SOFA
is_a: SO:0000372 ! enzymatic_RNA

[Term]
id: SO:0000391
name: U1_snRNA
def: "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]
subset: SOFA
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000392
name: U2_snRNA
def: "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]
subset: SOFA
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000393
name: U4_snRNA
def: "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]
subset: SOFA
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000394
name: U4atac_snRNA
def: "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]
subset: SOFA
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000395
name: U5_snRNA
def: "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]
subset: SOFA
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000396
name: U6_snRNA
def: "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]
subset: SOFA
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000397
name: U6atac_snRNA
def: "U6atac_snRNA -An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [https://www.ncbi.nlm.nih.gov/pubmed/12409455]
subset: SOFA
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000398
name: U11_snRNA
def: "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]
subset: SOFA
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000399
name: U12_snRNA
def: "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]
subset: SOFA
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000400
name: sequence_attribute
is_a: SO:0000000 ! Sequence_Ontology

[Term]
id: SO:0000401
name: gene_attribute
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000402
name: enhancer_attribute
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000403
name: U14_snRNA
def: "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016]
subset: SOFA
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000404
name: vault_RNA
def: "A family of RNAs are found as part of the enigmatic vault ribonuceoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]
subset: SOFA
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000405
name: Y_RNA
def: "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]
subset: SOFA
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000406
name: twintron
def: "An intron within an intron." [PMID:1899376]
is_a: SO:0000188 ! intron

[Term]
id: SO:0000407
name: rRNA_18S
def: "18S_rRNA -A large polynucleotide which functions as a part of the small subunit of the ribosome" [SO:ke]
subset: SOFA
synonym: "16S_rRNA" RELATED []
is_a: SO:0000252 ! rRNA

[Term]
id: SO:0000408
name: site
def: "The interbase position where something (eg an aberration) occurred." [SO:ke]
is_obsolete: true

[Term]
id: SO:0000409
name: binding_site
def: "A region on the surface of a molecule that may interact with another molecule." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000410
name: protein_binding_site
def: "A region of a molecule that binds to a protein." [SO:ke]
is_a: SO:0000409 ! binding_site

[Term]
id: SO:0000411
name: rescue_fragment
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000412
name: restriction_fragment
def: "Any of the individual polynucleotide sequences produced by digestion of DNA with a restriction endonuclease." [http://www.agron.missouri.edu/cgi-bin/sybgw_mdb/mdb3/Term/119]
subset: SOFA
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000413
name: sequence_difference
def: "A region where the sequences differs from that of a specified sequence." [SO:ke]
subset: SOFA
is_a: SO:0000700 ! remark

[Term]
id: SO:0000414
name: genomically_contaminated_cDNA_clone
is_a: SO:0000317 ! cDNA_clone

[Term]
id: SO:0000415
name: genomic_polyA_primed_cDNA_clone
is_a: SO:0000317 ! cDNA_clone

[Term]
id: SO:0000416
name: partially_unprocessed_cDNA_clone
is_a: SO:0000317 ! cDNA_clone

[Term]
id: SO:0000417
name: polypeptide_domain
def: "A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains." [http:www.molbiol.bbsrc.ac.uk/new_protein/domains.html]
relationship: part_of SO:0000104 ! polypeptide

[Term]
id: SO:0000418
name: signal_peptide
def: "The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence." [http:www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "signal peptide coding sequence" RELATED []
relationship: part_of SO:0000104 ! polypeptide

[Term]
id: SO:0000419
name: mature_peptide
def: "The coding sequence for the mature or final peptide or protein product following post-translational modification." [http:www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
relationship: part_of SO:0000104 ! polypeptide

[Term]
id: SO:0000420
name: five_prime_terminal_inverted_repeat
is_a: SO:0000481 ! terminal_inverted_repeat

[Term]
id: SO:0000421
name: three_prime_terminal_inverted_repeat
is_a: SO:0000481 ! terminal_inverted_repeat

[Term]
id: SO:0000422
name: U5_LTR_region
relationship: part_of SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0000423
name: R_LTR_region
relationship: part_of SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0000424
name: U3_LTR_region
relationship: part_of SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0000425
name: five_prime_LTR
is_a: SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0000426
name: three_prime_LTR
is_a: SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0000427
name: R_five_prime_LTR_region
is_a: SO:0000423 ! R_LTR_region
relationship: part_of SO:0000425 ! five_prime_LTR

[Term]
id: SO:0000428
name: U5_five_prime_LTR_region
is_a: SO:0000422 ! U5_LTR_region
relationship: part_of SO:0000425 ! five_prime_LTR

[Term]
id: SO:0000429
name: U3_five_prime_LTR_region
is_a: SO:0000424 ! U3_LTR_region
relationship: part_of SO:0000425 ! five_prime_LTR

[Term]
id: SO:0000430
name: R_three_prime_LTR_region
relationship: part_of SO:0000426 ! three_prime_LTR

[Term]
id: SO:0000431
name: U3_three_prime_LTR_region
relationship: part_of SO:0000426 ! three_prime_LTR

[Term]
id: SO:0000432
name: U5_three_prime_LTR_region
relationship: part_of SO:0000426 ! three_prime_LTR

[Term]
id: SO:0000433
name: non_LTR_retrotransposon_polymeric_tract
def: "A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000189 ! non_LTR_retrotransposon

[Term]
id: SO:0000434
name: transposable_element_target_site_duplication
def: "A sequence of DNA that is duplicated when a transposable element inserts; usually found at each end the insertion." [http:www.koko.gov.my/CocoaBioTech/Glossaryt.html]
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000435
name: RR_tract
def: "A polypurine tract within an LTR_retrotransposon." [SO:ke]
synonym: "LTR_retrotransposon_poly_purine_tract" RELATED []
is_a: SO:0000186 ! LTR_retrotransposon

[Term]
id: SO:0000436
name: ARS
def: "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]
subset: SOFA
synonym: "autonomously_replicating_sequence" RELATED []
is_a: SO:0000001 ! region

[Term]
id: SO:0000437
name: assortment_derived_duplication
is_obsolete: true

[Term]
id: SO:0000438
name: gene_not_polyadenylated
is_a: SO:0000066 ! gene_by_polyadenylation_attribute

[Term]
id: SO:0000439
name: inverted_ring_chromosome
is_a: SO:1000030 ! chromosomal_inversion
is_a: SO:1000045 ! ring_chromosome

[Term]
id: SO:0000440
name: vector
def: "A DNA molecule that can be used to transfer DNA molecules between organisms." [SO:ma]
is_a: SO:0000695 ! reagent
relationship: part_of SO:0000151 ! clone

[Term]
id: SO:0000441
name: ss_oligo
def: "A single stranded oligonucleotide." [SO:ke]
synonym: "single stranded oligonucleotide.new synonym" RELATED []
synonym: "ss_oligonucleotide" RELATED []
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000442
name: ds_oligo
def: "A double stranded oligonucleotide." [SO:ke]
synonym: "double stranded oligonucleotide" RELATED []
synonym: "ds_oligonucleotide" RELATED []
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000443
name: polymer_type
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000444
name: three_prime_noncoding_exon
def: "Non-coding exon in the 3' UTR." [SO:ke]
is_a: SO:0000198 ! noncoding_exon

[Term]
id: SO:0000445
name: five_prime_noncoding_exon
def: "Non-coding exon in the 5' UTR." [SO:ke]
synonym: "five_prime_noncoding_exon" RELATED []
is_a: SO:0000198 ! noncoding_exon

[Term]
id: SO:0000446
name: UTR_intron
def: "Intron located in the untranslated region." [SO:ke]
is_a: SO:0000188 ! intron

[Term]
id: SO:0000447
name: five_prime_UTR_intron
def: "An intron located in the 5' UTR." [SO:ke]
is_a: SO:0000446 ! UTR_intron

[Term]
id: SO:0000448
name: three_prime_UTR_intron
def: "An intron located in the 3' UTR." [SO:ke]
is_a: SO:0000446 ! UTR_intron

[Term]
id: SO:0000449
name: random_sequence
def: "A sequence of nucleotides or amino acids which, by design, has a \"random\" order of components, given a predetermined input frequencyof these components." [SO:ma]
is_a: SO:0000351 ! synthetic_sequence

[Term]
id: SO:0000450
name: interband
def: "A light region between two darkly staining bands in a polytene chromosome." [SO:ma]
is_a: SO:0000341 ! chromosome_band

[Term]
id: SO:0000451
name: gene_polyadenylated
is_a: SO:0000066 ! gene_by_polyadenylation_attribute

[Term]
id: SO:0000452
name: transgene
is_a: SO:0000009 ! gene_class

[Term]
id: SO:0000453
name: transposition
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:0000454
name: rasiRNA
def: "A small, 17-28-nt, small interfering RNA derived from transcripts ofrepetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]
subset: SOFA
synonym: "repeat associated small interfering RNA" RELATED []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000455
name: gene_with_mRNA_with_frameshift
is_a: SO:0000064 ! gene_by_transcript_attribute

[Term]
id: SO:0000456
name: recombinationally_rearranged_gene
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000457
name: interchromosomal_duplication
is_a: SO:1000037 ! chromosomal_duplication

[Term]
id: SO:0000458
name: D_gene
def: "Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-GENE]
synonym: "D-GENE" RELATED []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene
relationship: part_of SO:0000504 ! D_DJ_C_cluster
relationship: part_of SO:0000505 ! D_DJ_cluster
relationship: part_of SO:0000506 ! D_DJ_J_C_cluster
relationship: part_of SO:0000508 ! D_DJ_J_cluster
relationship: part_of SO:0000509 ! D_J_C_cluster
relationship: part_of SO:0000527 ! V_D_DJ_C_cluster
relationship: part_of SO:0000528 ! V_D_DJ_cluster
relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster
relationship: part_of SO:0000530 ! V_D_DJ_J_cluster
relationship: part_of SO:0000531 ! V_D_J_C_cluster
relationship: part_of SO:0000532 ! V_D_J_cluster
relationship: part_of SO:0000559 ! D_cluster
relationship: part_of SO:0000560 ! D_J_cluster

[Term]
id: SO:0000459
name: gene_with_trans_spliced_transcript
is_a: SO:0000064 ! gene_by_transcript_attribute

[Term]
id: SO:0000460
name: vertebrate_immunoglobulin_T_cell_receptor_gene
synonym: "vertebrate_immunoglobulin/T-cell_receptor_gene" RELATED []
is_a: SO:0000456 ! recombinationally_rearranged_gene

[Term]
id: SO:0000461
name: inversion_derived_bipartite_deficiency
def: "A chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]
is_a: SO:1000029 ! chromosomal_deletion

[Term]
id: SO:0000462
name: pseudogenic_region
def: "A non-functional descendent of a functional entitity." [SO:cjm]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000463
name: gene_with_alternately_spliced_transcript
is_a: SO:0000064 ! gene_by_transcript_attribute

[Term]
id: SO:0000464
name: decayed_exon
def: "A non-functional descendent of an exon." [SO:ke]
subset: SOFA
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000147 ! exon

[Term]
id: SO:0000465
name: inversion_derived_deficiency_plus_duplication
def: "A chromosome generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000038 ! intrachromosomal_duplication

[Term]
id: SO:0000466
name: V_gene
def: "Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-GENE]
synonym: "V_GENE" RELATED []
synonym: "variable_gene" RELATED []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene
relationship: part_of SO:0000518 ! V_DJ_cluster
relationship: part_of SO:0000519 ! V_DJ_J_cluster
relationship: part_of SO:0000520 ! V_VDJ_C_cluster
relationship: part_of SO:0000521 ! V_VDJ_cluster
relationship: part_of SO:0000522 ! V_VDJ_J_cluster
relationship: part_of SO:0000523 ! V_VJ_C_cluster
relationship: part_of SO:0000524 ! V_VJ_cluster
relationship: part_of SO:0000525 ! V_VJ_J_cluster
relationship: part_of SO:0000526 ! V_cluster
relationship: part_of SO:0000527 ! V_D_DJ_C_cluster
relationship: part_of SO:0000528 ! V_D_DJ_cluster
relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster
relationship: part_of SO:0000530 ! V_D_DJ_J_cluster
relationship: part_of SO:0000531 ! V_D_J_C_cluster
relationship: part_of SO:0000532 ! V_D_J_cluster
relationship: part_of SO:0000534 ! V_J_cluster
relationship: part_of SO:0000535 ! V_J_C_cluster
relationship: part_of SO:0000542 ! V_DJ_C_cluster
relationship: part_of SO:0000564 ! V_DJ_J_C_cluster
relationship: part_of SO:0000565 ! V_VDJ_J_C_cluster
relationship: part_of SO:0000566 ! V_VJ_J_C_cluster

[Term]
id: SO:0000467
name: post_translationally_regulated_by_protein_stability
synonym: "post-translationally_regulated_by_protein_stability" RELATED []
is_a: SO:0000130 ! post_translationally_regulated

[Term]
id: SO:0000468
name: golden_path_fragment
def: "One of the pieces of sequence that make up a golden path." [SO:rd]
subset: SOFA
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000688 ! golden_path

[Term]
id: SO:0000469
name: post_translationally_regulated_by_protein_modification
synonym: "post-translationally_regulated_by_protein_modification" RELATED []
is_a: SO:0000130 ! post_translationally_regulated

[Term]
id: SO:0000470
name: J_gene
def: "Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#J-GENE]
synonym: "J-GENE" RELATED []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene
relationship: part_of SO:0000485 ! DJ_J_cluster
relationship: part_of SO:0000487 ! VDJ_J_C_cluster
relationship: part_of SO:0000488 ! VDJ_J_cluster
relationship: part_of SO:0000490 ! VJ_J_C_cluster
relationship: part_of SO:0000491 ! VJ_J_cluster
relationship: part_of SO:0000506 ! D_DJ_J_C_cluster
relationship: part_of SO:0000508 ! D_DJ_J_cluster
relationship: part_of SO:0000509 ! D_J_C_cluster
relationship: part_of SO:0000511 ! J_C_cluster
relationship: part_of SO:0000513 ! J_cluster
relationship: part_of SO:0000519 ! V_DJ_J_cluster
relationship: part_of SO:0000522 ! V_VDJ_J_cluster
relationship: part_of SO:0000525 ! V_VJ_J_cluster
relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster
relationship: part_of SO:0000530 ! V_D_DJ_J_cluster
relationship: part_of SO:0000531 ! V_D_J_C_cluster
relationship: part_of SO:0000532 ! V_D_J_cluster
relationship: part_of SO:0000534 ! V_J_cluster
relationship: part_of SO:0000535 ! V_J_C_cluster
relationship: part_of SO:0000540 ! DJ_J_C_cluster
relationship: part_of SO:0000560 ! D_J_cluster
relationship: part_of SO:0000564 ! V_DJ_J_C_cluster
relationship: part_of SO:0000565 ! V_VDJ_J_C_cluster
relationship: part_of SO:0000566 ! V_VJ_J_C_cluster

[Term]
id: SO:0000471
name: autoregulated
is_a: SO:0000123 ! transcriptionally_regulated

[Term]
id: SO:0000472
name: tiling_path
def: "A set of regions which overlap with minimal polymorphism to form a linear sequence." [CJM:SO]
subset: SOFA
is_a: SO:0000353 ! assembly

[Term]
id: SO:0000473
name: negatively_autoregulated
is_a: SO:0000126 ! transcriptionally_repressed
is_a: SO:0000471 ! autoregulated

[Term]
id: SO:0000474
name: tiling_path_fragment
def: "A piece of sequence that makes up a tiling_path.SO:0000472." [SO:ke]
subset: SOFA
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000472 ! tiling_path

[Term]
id: SO:0000475
name: positively_autoregulated
is_a: SO:0000125 ! transcriptionally_induced
is_a: SO:0000471 ! autoregulated

[Term]
id: SO:0000476
name: contig_read
def: "A DNA sequencer read which is part of a contig." [SO:ke]
is_a: SO:0000150 ! read

[Term]
id: SO:0000477
name: polycistronic_gene
is_a: SO:0000081 ! member_gene_array

[Term]
id: SO:0000478
name: C_gene
def: "Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#C-GENE]
synonym: "C_GENE" RELATED []
synonym: "constant_gene" RELATED []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene
relationship: part_of SO:0000487 ! VDJ_J_C_cluster
relationship: part_of SO:0000489 ! VJ_C_cluster
relationship: part_of SO:0000490 ! VJ_J_C_cluster
relationship: part_of SO:0000504 ! D_DJ_C_cluster
relationship: part_of SO:0000506 ! D_DJ_J_C_cluster
relationship: part_of SO:0000509 ! D_J_C_cluster
relationship: part_of SO:0000511 ! J_C_cluster
relationship: part_of SO:0000520 ! V_VDJ_C_cluster
relationship: part_of SO:0000523 ! V_VJ_C_cluster
relationship: part_of SO:0000527 ! V_D_DJ_C_cluster
relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster
relationship: part_of SO:0000531 ! V_D_J_C_cluster
relationship: part_of SO:0000535 ! V_J_C_cluster
relationship: part_of SO:0000539 ! DJ_C_cluster
relationship: part_of SO:0000540 ! DJ_J_C_cluster
relationship: part_of SO:0000541 ! VDJ_C_cluster
relationship: part_of SO:0000542 ! V_DJ_C_cluster
relationship: part_of SO:0000558 ! C_cluster
relationship: part_of SO:0000564 ! V_DJ_J_C_cluster
relationship: part_of SO:0000565 ! V_VDJ_J_C_cluster
relationship: part_of SO:0000566 ! V_VJ_J_C_cluster

[Term]
id: SO:0000479
name: trans_spliced_transcript
synonym: "trans-spliced_transcript" RELATED []
is_a: SO:0000082 ! processed_transcript_attribute

[Term]
id: SO:0000480
name: tiling_path_clone
def: "A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly.A minimal_tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly attempting to minimize the overlap between adjacent clones. (LS)" [SO:ke]
is_a: SO:0000151 ! clone
is_a: SO:0000474 ! tiling_path_fragment

[Term]
id: SO:0000481
name: terminal_inverted_repeat
def: "An inverted repeat (SO:0000294) occuring at the termini of a DNA transposon." [SO:ke]
synonym: "TIR" RELATED []
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000208 ! terminal_inverted_repeat_element

[Term]
id: SO:0000482
name: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
synonym: "vertebrate_immunoglobulin/T-cell_receptor_gene-cluster" RELATED []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene

[Term]
id: SO:0000483
name: nc_primary_transcript
def: "A primary transcript that is never translated into a protein." [SO:ke]
subset: SOFA
synonym: "noncoding_primary_transcript" RELATED []
is_a: SO:0000185 ! primary_transcript

[Term]
id: SO:0000484
name: three_prime_exon_noncoding_region
def: "The sequence of the 3' exon that is not coding." [SO:ke]
synonym: "three_prime_exon_noncoding_region" RELATED []
relationship: part_of SO:0000202 ! three_prime_coding_exon

[Term]
id: SO:0000485
name: DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(DJ)-J-CLUSTER]
synonym: "(DJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000486
name: five_prime_exon_noncoding_region
def: "The sequence of the 5' exon preceeding the start codon." [SO:ke]
synonym: "five_prime_exon_noncoding_region" RELATED []
relationship: part_of SO:0000200 ! five_prime_coding_exon

[Term]
id: SO:0000487
name: VDJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(VDJ)-J-C-CLUSTER]
synonym: "(VDJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000488
name: VDJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(VDJ)-J-CLUSTER]
synonym: "(VDJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000489
name: VJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(VJ)-C-CLUSTER]
synonym: "(VJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000490
name: VJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(VJ)-J-C-CLUSTER]
synonym: "(VJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000491
name: VJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(VJ)-J-CLUSTER]
synonym: "(VJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000492
name: D_gene_recombination_feature
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene

[Term]
id: SO:0000493
name: three_prime_D_heptamer
def: "7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#3'D-HEPTAMER]
synonym: "3'D-HEPTAMER" RELATED []
is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence

[Term]
id: SO:0000494
name: three_prime_D_nonamer
def: "A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#3'D-NONAMER]
synonym: "3'D-NOMAMER" RELATED []
is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence

[Term]
id: SO:0000495
name: three_prime_D_spacer
def: "A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#3'D-SPACER]
synonym: "3'D-SPACER" RELATED []
is_a: SO:0000563 ! spacer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence

[Term]
id: SO:0000496
name: five_prime_D_heptamer
def: "7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#5'D-HEPTAMER]
synonym: "5'D-HEPTAMER" RELATED []
is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence

[Term]
id: SO:0000497
name: five_prime_D_nonamer
def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#5'D-NONAMER]
synonym: "5'D-NONAMER" RELATED []
is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence

[Term]
id: SO:0000498
name: five_prime_D_spacer
def: "12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#5'D-SPACER]
synonym: "5'-SPACER" RELATED []
synonym: "five_prime_D-spacer" RELATED []
is_a: SO:0000563 ! spacer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence

[Term]
id: SO:0000499
name: virtual_sequence
def: "A continous piece of sequence similar to the 'virtual contig' concept of ensembl." [SO:ke]
subset: SOFA
is_a: SO:0000353 ! assembly

[Term]
id: SO:0000500
name: Hoogsteen_base_pair
def: "A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293]
is_a: SO:0000028 ! base_pair

[Term]
id: SO:0000501
name: reverse_Hoogsteen_base_pair
def: "A type of non-canonical base-pairing." [SO:ke]
is_a: SO:0000028 ! base_pair

[Term]
id: SO:0000502
name: transcribed_region
def: "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes." [SO:ke]
comment: This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being.
subset: SOFA
is_obsolete: true

[Term]
id: SO:0000503
name: alternately_spliced_gene_encodeing_one_transcript
is_obsolete: true

[Term]
id: SO:0000504
name: D_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-(DJ)-C-CLUSTER]
synonym: "D-(DJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000505
name: D_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-(DJ)-CLUSTER]
synonym: "D-(DJ)-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000506
name: D_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-(DJ)-J-C-CLUSTER]
synonym: "D-(DJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000507
name: pseudogenic_exon
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000147 ! exon
relationship: part_of SO:0000516 ! pseudogenic_transcript

[Term]
id: SO:0000508
name: D_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-(DJ)-J-CLUSTER]
synonym: "D-(DJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000509
name: D_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-J-C-CLUSTER]
synonym: "D-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000510
name: VD_gene
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-GENE]
synonym: "V_D_GENE" RELATED []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene

[Term]
id: SO:0000511
name: J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#J-C-CLUSTER]
synonym: "J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000512
name: inversion_derived_deficiency_plus_aneuploid
def: "A chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]
is_a: SO:1000029 ! chromosomal_deletion

[Term]
id: SO:0000513
name: J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#J-CLUSTER]
synonym: "J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000514
name: J_nonamer
def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#J-NONAMER]
synonym: "J-NONAMER" RELATED []
is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000302 ! J_gene_recombination_feature

[Term]
id: SO:0000515
name: J_heptamer
def: "7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#J-HEPTAMER]
synonym: "J-HEPTAMER" RELATED []
is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000302 ! J_gene_recombination_feature

[Term]
id: SO:0000516
name: pseudogenic_transcript
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000673 ! transcript
relationship: part_of SO:0000336 ! pseudogene

[Term]
id: SO:0000517
name: J_spacer
def: "12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#J-SPACER]
synonym: "J-SPACER" RELATED []
is_a: SO:0000563 ! spacer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000302 ! J_gene_recombination_feature

[Term]
id: SO:0000518
name: V_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(DJ)-CLUSTER]
synonym: "V-(DJ)-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000519
name: V_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(DJ)-J-CLUSTER]
synonym: "V-(DJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000520
name: V_VDJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VDJ)-C-CLUSTER]
synonym: "V-(VDJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000521
name: V_VDJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VDJ)-CLUSTER]
synonym: "V-(VDJ)-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000522
name: V_VDJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VDJ)-J-CLUSTER]
synonym: "V-(VDJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000523
name: V_VJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VJ)-C-CLUSTER]
synonym: "V-(VJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000524
name: V_VJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VJ)-CLUSTER]
synonym: "V-(VJ)-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000525
name: V_VJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VJ)-J-CLUSTER]
synonym: "V-(VJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000526
name: V_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-CLUSTER]
synonym: "V-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000527
name: V_D_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-(DJ)-C-CLUSTER]
synonym: "V-D-(DJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000528
name: V_D_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-(DJ)-CLUSTER]
synonym: "V-D-(DJ)-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000529
name: V_D_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-(DJ)-J-C-CLUSTER]
synonym: "V-D-(DJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000530
name: V_D_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-(DJ)-J-CLUSTER]
synonym: "V-D-(DJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000531
name: V_D_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-J-C-CLUSTER]
synonym: "V-D-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000532
name: V_D_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-J-CLUSTER]
synonym: "V-D-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000533
name: V_heptamer
def: "7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-HEPTAMER]
synonym: "V-HEPTAMER" RELATED []
is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000538 ! V_gene_recombination_feature

[Term]
id: SO:0000534
name: V_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-J-CLUSTER]
synonym: "V-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000535
name: V_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-J-C-CLUSTER]
synonym: "V-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000536
name: V_nonamer
def: "9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-NONAMER]
synonym: "V-NONAMER" RELATED []
is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000538 ! V_gene_recombination_feature

[Term]
id: SO:0000537
name: V_spacer
def: "12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-SPACER]
synonym: "V-SPACER" RELATED []
is_a: SO:0000563 ! spacer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000538 ! V_gene_recombination_feature

[Term]
id: SO:0000538
name: V_gene_recombination_feature
def: "Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-RS]
synonym: "V-RS" RELATED []
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene

[Term]
id: SO:0000539
name: DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(DJ)-C-CLUSTER]
synonym: "(DJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000540
name: DJ_J_C_cluster
def: "Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(DJ)-J-C-CLUSTER]
synonym: "(DJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000541
name: VDJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(VDJ)-C-CLUSTER]
synonym: "(VDJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000542
name: V_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(DJ)-C-CLUSTER]
synonym: "V-(DJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000543
name: alternately_spliced_gene_encoding_greater_than_one_transcript
is_obsolete: true

[Term]
id: SO:0000544
name: helitron
def: "A rolling circle transposon. Autonomous Helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]
is_a: SO:0000101 ! transposable_element

[Term]
id: SO:0000545
name: recoding_pseudoknot
def: "The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]
is_a: SO:0000591 ! pseudoknot
relationship: part_of SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:0000546
name: designed_sequence
is_a: SO:0000351 ! synthetic_sequence

[Term]
id: SO:0000547
name: inversion_derived_bipartite_duplication
def: "A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]
is_a: SO:1000038 ! intrachromosomal_duplication

[Term]
id: SO:0000548
name: gene_with_edited_transcript
is_a: SO:0000064 ! gene_by_transcript_attribute

[Term]
id: SO:0000549
name: inversion_derived_duplication_plus_aneuploid
def: "A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]
is_a: SO:1000038 ! intrachromosomal_duplication

[Term]
id: SO:0000550
name: aneuploid_chromosome
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:0000551
name: polyA_signal_sequence
def: "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000552
name: Shine_Dalgarno_sequence
def: "Region in 5' UTR where ribosome assembles on mRNA." [SO:ke]
synonym: "RBS" RELATED []
synonym: "Shine-Dalgarno_sequence" RELATED []
synonym: "five_prime_ribosome_binding_site" RELATED []
is_a: SO:0000139 ! ribosome_entry_site

[Term]
id: SO:0000553
name: polyA_site
def: "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
is_a: SO:0000699 ! junction
relationship: part_of SO:0000233 ! processed_transcript

[Term]
id: SO:0000554
name: assortment_derived_deficiency_plus_duplication
is_obsolete: true

[Term]
id: SO:0000555
name: five_prime_clip
def: "5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
synonym: "five_prime_-clip" RELATED []
is_a: SO:0000303 ! clip

[Term]
id: SO:0000556
name: five_prime_D_recombination_signal_sequence
def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#5'D-RS]
synonym: "5'RS" RELATED []
synonym: "five_prime_D-recombination_signal_sequence" RELATED []
is_a: SO:0000492 ! D_gene_recombination_feature

[Term]
id: SO:0000557
name: three_prime_clip
def: "3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
synonym: "3'-clip" RELATED []
is_a: SO:0000303 ! clip

[Term]
id: SO:0000558
name: C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#C-CLUSTER]
synonym: "C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000559
name: D_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-CLUSTER]
synonym: "D-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000560
name: D_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-J-CLUSTER]
synonym: "D-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000561
name: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
def: " 7 nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin/T-cell receptor gene" [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#HEPTAMER]
synonym: "HEPTAMER" RELATED []
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene

[Term]
id: SO:0000562
name: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene

[Term]
id: SO:0000563
name: spacer_of_recombination_feature_of_vertebrate_immune_system_gene
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene

[Term]
id: SO:0000564
name: V_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(DJ)-J-C-CLUSTER]
synonym: "V-(DJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000565
name: V_VDJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VDJ)-J-C-CLUSTER]
synonym: "V-(VDJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000566
name: V_VJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VJ)-J-C-CLUSTER]
synonym: "V-(VJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000567
name: inversion_derived_aneuploid_chromosome
def: "A chromosome may be generated by recombination between two inverversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]
is_a: SO:0000550 ! aneuploid_chromosome

[Term]
id: SO:0000568
name: bidirectional_promotor
is_a: SO:0000167 ! promoter

[Term]
id: SO:0000569
name: retrotransposed_protein_coding_gene
alt_id: SO:0100042
synonym: "captured_pseudogene" RELATED []
is_a: SO:0000010 ! protein_coding_gene
is_a: SO:0000042 ! pseudogene_attribute

[Term]
id: SO:0000570
name: three_prime_D_recombination_signal_sequence
def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#3'D-RS]
synonym: "3'D-RS" RELATED []
synonym: "three_prime_D-recombination_signal_sequence" RELATED []
is_a: SO:0000492 ! D_gene_recombination_feature

[Term]
id: SO:0000571
name: miRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000572
name: DJ_gene
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-J-GENE]
synonym: "D_J_GENE" RELATED []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene
relationship: part_of SO:0000485 ! DJ_J_cluster
relationship: part_of SO:0000504 ! D_DJ_C_cluster
relationship: part_of SO:0000505 ! D_DJ_cluster
relationship: part_of SO:0000506 ! D_DJ_J_C_cluster
relationship: part_of SO:0000508 ! D_DJ_J_cluster
relationship: part_of SO:0000518 ! V_DJ_cluster
relationship: part_of SO:0000519 ! V_DJ_J_cluster
relationship: part_of SO:0000527 ! V_D_DJ_C_cluster
relationship: part_of SO:0000528 ! V_D_DJ_cluster
relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster
relationship: part_of SO:0000530 ! V_D_DJ_J_cluster
relationship: part_of SO:0000539 ! DJ_C_cluster
relationship: part_of SO:0000540 ! DJ_J_C_cluster
relationship: part_of SO:0000542 ! V_DJ_C_cluster
relationship: part_of SO:0000564 ! V_DJ_J_C_cluster

[Term]
id: SO:0000573
name: rRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000574
name: DJ_gene
def: " Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)" [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-J-GENE]
synonym: "V-D-J-GENE" RELATED []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene
relationship: part_of SO:0000487 ! VDJ_J_C_cluster
relationship: part_of SO:0000488 ! VDJ_J_cluster
relationship: part_of SO:0000520 ! V_VDJ_C_cluster
relationship: part_of SO:0000521 ! V_VDJ_cluster
relationship: part_of SO:0000522 ! V_VDJ_J_cluster
relationship: part_of SO:0000541 ! VDJ_C_cluster
relationship: part_of SO:0000565 ! V_VDJ_J_C_cluster

[Term]
id: SO:0000575
name: scRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000576
name: VJ_gene
def: " Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)" [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-J-GENE]
synonym: "V-J-GENE" RELATED []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene
relationship: part_of SO:0000489 ! VJ_C_cluster
relationship: part_of SO:0000490 ! VJ_J_C_cluster
relationship: part_of SO:0000491 ! VJ_J_cluster
relationship: part_of SO:0000523 ! V_VJ_C_cluster
relationship: part_of SO:0000524 ! V_VJ_cluster
relationship: part_of SO:0000525 ! V_VJ_J_cluster
relationship: part_of SO:0000566 ! V_VJ_J_C_cluster

[Term]
id: SO:0000577
name: centromere
def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]
subset: SOFA
is_a: SO:0000628 ! chromosomal_structural_element

[Term]
id: SO:0000578
name: snoRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000579
name: edited_transcript_feature
def: "A locatable feature on a transcript that is edited." [SO:ma]
relationship: part_of SO:0000673 ! transcript

[Term]
id: SO:0000580
name: methylation_guide_snoRNA_primary_transcript
def: "A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]
is_a: SO:0000232 ! snoRNA_primary_transcript

[Term]
id: SO:0000581
name: cap
def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]
subset: SOFA
relationship: adjacent_to SO:0000234 ! mRNA

[Term]
id: SO:0000582
name: rRNA_cleavage_snoRNA_primary_transcript
def: "A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]
is_a: SO:0000232 ! snoRNA_primary_transcript

[Term]
id: SO:0000583
name: pre_edited_region
def: "The region of a transcript that will be edited." [http://www.rna.ucla.edu]
synonym: "pre-edited_region" RELATED []
is_a: SO:0000579 ! edited_transcript_feature

[Term]
id: SO:0000584
name: tmRNA
def: "tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. tmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]
synonym: "10Sa_RNA" RELATED []
synonym: "ssrA" RELATED []
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000585
name: C_D_box_snoRNA_gene
is_a: SO:0000578 ! snoRNA_gene

[Term]
id: SO:0000586
name: tmRNA_primary_transcript
def: "A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]
synonym: "10Sa_RNA_primary_transcript" RELATED []
synonym: "ssrA_RNA_primary_transcript" RELATED []
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000587
name: group_I_intron
def: "Group I catalytic introns are large self-splicing ribozymes. They catalyse their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]
subset: SOFA
is_a: SO:0000188 ! intron

[Term]
id: SO:0000588
name: autocatalytically_spliced_intron
def: "A self spliced intron." [SO:ke]
subset: SOFA
is_a: SO:0000188 ! intron
is_a: SO:0000374 ! ribozyme

[Term]
id: SO:0000589
name: SRP_RNA_primary_transcript
def: "A primary transcript encoding a signal recognition particle RNA." [SO:ke]
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000590
name: SRP_RNA
def: "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]
subset: SOFA
synonym: "7S RNA" RELATED []
synonym: "signal_recognition_particle_RNA" RELATED []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000591
name: pseudoknot
def: "A stem-loop RNA structure where nucleotides in the loop participate in complementary interactions with a region of RNA downstream of the stem-loop." [https://www.ncbi.nlm.nih.gov/pubmed/12519954]
is_a: SO:0000002 ! sequence_secondary_structure

[Term]
id: SO:0000592
name: H_pseudoknot
def: "A pseudoknot which contains two stems and at least two loops." [https://www.ncbi.nlm.nih.gov/pubmed/10334330]
synonym: "H-pseudoknot" RELATED []
is_a: SO:0000591 ! pseudoknot

[Term]
id: SO:0000593
name: C_D_box_snoRNA
def: "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]
synonym: "C/D_box_snoRNA" RELATED []
is_a: SO:0000275 ! snoRNA

[Term]
id: SO:0000594
name: H_ACA_box_snoRNA
def: "Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]
synonym: "H/ACA_box_snoRNA" RELATED []
is_a: SO:0000275 ! snoRNA

[Term]
id: SO:0000595
name: C_D_box_snoRNA_primary_transcript
def: "A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]
is_a: SO:0000232 ! snoRNA_primary_transcript

[Term]
id: SO:0000596
name: H_ACA_box_snoRNA_primary_transcript
def: "A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]
is_a: SO:0000232 ! snoRNA_primary_transcript

[Term]
id: SO:0000597
name: transcript_edited_by_U_insertion/deletion
def: "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa." [http://www.rna.ucla.edu/index.html]
is_a: SO:0000116 ! edited_transcript

[Term]
id: SO:0000598
name: transcript_edited_by_C_insertion_and_dinucleotide_insertion
def: "The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs." [http://nsm1.utdallas.edu/bio/miller/physarum/overview.htm]
synonym: "transcript_edited_by_C-insertion_and_dinucleotide_insertion" RELATED []
is_a: SO:0000116 ! edited_transcript

[Term]
id: SO:0000599
name: transcript_edited_by_C_to_U_substitution
is_a: SO:0000116 ! edited_transcript

[Term]
id: SO:0000600
name: transcript_edited_by_A_to_I_substitution
is_a: SO:0000116 ! edited_transcript

[Term]
id: SO:0000601
name: transcript_edited_by_G_addition
is_a: SO:0000116 ! edited_transcript

[Term]
id: SO:0000602
name: guide_RNA
def: "A short 3'-uridylated RNA that can form a perfect duplex (except for the oligoU tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]
subset: SOFA
synonym: "gRNA" RELATED []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000603
name: group_II_intron
def: "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]
subset: SOFA
is_a: SO:0000188 ! intron

[Term]
id: SO:0000604
name: editing_block
def: "Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://www.rna.ucla/]
is_a: SO:0000579 ! edited_transcript_feature

[Term]
id: SO:0000605
name: intergenic_region
def: "The region between two known genes." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000606
name: editing_domain
def: "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://www.rna.ucla/]
is_a: SO:0000579 ! edited_transcript_feature

[Term]
id: SO:0000607
name: unedited_region
def: "The region of an edited transcript that will not be edited." [http://www.rna.ucla.edu/]
is_a: SO:0000579 ! edited_transcript_feature

[Term]
id: SO:0000608
name: H_ACA_box_snoRNA_gene
is_a: SO:0000578 ! snoRNA_gene

[Term]
id: SO:0000609
name: oligo_U_tail
def: "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/]
relationship: adjacent_to SO:0000602 ! guide_RNA

[Term]
id: SO:0000610
name: polyA_sequence
def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke]
subset: SOFA
relationship: adjacent_to SO:0000234 ! mRNA

[Term]
id: SO:0000611
name: branch_site
def: "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]
subset: SOFA
synonym: "branch_point" RELATED []
relationship: part_of SO:0000662 ! spliceosomal_intron

[Term]
id: SO:0000612
name: polypyrimidine_tract
def: "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]
subset: SOFA
relationship: part_of SO:0000662 ! spliceosomal_intron

[Term]
id: SO:0000613
name: bacterial_RNApol_promoter
def: "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]
is_a: SO:0000167 ! promoter
is_a: SO:0000752 ! gene_group_regulatory_region

[Term]
id: SO:0000614
name: bacterial_terminator
def: "A terminator signal for bacterial transcription." [SO:ke]
is_a: SO:0000141 ! terminator

[Term]
id: SO:0000615
name: terminator_of_type_2_RNApol_III_promoter
def: "A terminator signal for RNA polymerase III transcription." [SO:ke]
is_a: SO:0000141 ! terminator

[Term]
id: SO:0000616
name: transcription_end_site
def: "The site where transcription ends." [SO:ke]
subset: SOFA
is_a: SO:0000699 ! junction
relationship: part_of SO:0000185 ! primary_transcript

[Term]
id: SO:0000617
name: RNApol_III_promoter_type_1
is_a: SO:0000171 ! RNApol_III_promoter

[Term]
id: SO:0000618
name: RNApol_III_promoter_type_2
synonym: "tRNA_promoter" RELATED []
is_a: SO:0000171 ! RNApol_III_promoter

[Term]
id: SO:0000619
name: A_box
relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2

[Term]
id: SO:0000620
name: B_box
relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2

[Term]
id: SO:0000621
name: RNApol_III_promoter_type_3
is_a: SO:0000171 ! RNApol_III_promoter

[Term]
id: SO:0000622
name: C_box
relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1

[Term]
id: SO:0000623
name: snRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000624
name: telomere
def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenence of the end," [SO:ma]
subset: SOFA
is_a: SO:0000628 ! chromosomal_structural_element

[Term]
id: SO:0000625
name: silencer
def: "Combination of short DNA sequence elements which suppress the transcription of an adjacent gene or genes." [http://www.brunel.ac.uk/depts/bio/project/old_hmg/gloss3.htm#s]
subset: SOFA
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000626
name: chromosomal_regulatory_element
relationship: part_of SO:0000340 ! chromosome

[Term]
id: SO:0000627
name: insulator
subset: SOFA
synonym: "insulator_element" RELATED []
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000628
name: chromosomal_structural_element
subset: SOFA
relationship: part_of SO:0000340 ! chromosome

[Term]
id: SO:0000629
name: five_prime_open_reading_frame
relationship: part_of SO:0000204 ! five_prime_UTR

[Term]
id: SO:0000630
name: upstream_AUG_codon
relationship: part_of SO:0000203 ! UTR

[Term]
id: SO:0000631
name: polycistronic_primary_transcript
def: "A primary transcript encoding for more than one protein product." [SO:ke]
is_a: SO:0000078 ! polycistronic_transcript

[Term]
id: SO:0000632
name: monocistronic_primary_transcript
def: "A primary transcript encoding for more than one protein product." [SO:ke]
is_a: SO:0000665 ! monocistronic_transcript

[Term]
id: SO:0000633
name: monocistronic_mRNA
def: "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]
synonym: "monocistronic_processed_transcript" RELATED []
is_a: SO:0000665 ! monocistronic_transcript

[Term]
id: SO:0000634
name: polycistronic_mRNA
def: "An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]
synonym: "polycistronic_processed_transcript" RELATED []
is_a: SO:0000078 ! polycistronic_transcript

[Term]
id: SO:0000635
name: mini_exon_donor_RNA
def: "The 3' site of a mini-exon which is trans-spliced on to the 5'end of a mature mRNA." [SO:ke]
synonym: "mini-exon_donor_RNA" RELATED []
is_a: SO:0000185 ! primary_transcript

[Term]
id: SO:0000636
name: spliced_leader_RNA
synonym: "mini-exon" RELATED []
relationship: part_of SO:0000635 ! mini_exon_donor_RNA

[Term]
id: SO:0000637
name: engineered_plasmid
synonym: "engineered_plasmid_gene" RELATED []
is_a: SO:0000098 ! plasmid_gene
is_a: SO:0000280 ! engineered_gene

[Term]
id: SO:0000638
name: transcribed_spacer_region
def: "Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]
relationship: part_of SO:0000209 ! rRNA_primary_transcript

[Term]
id: SO:0000639
name: internal_transcribed_spacer_region
def: "Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]
is_a: SO:0000638 ! transcribed_spacer_region

[Term]
id: SO:0000640
name: external_transcribed_spacer_region
def: "Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]
is_a: SO:0000638 ! transcribed_spacer_region

[Term]
id: SO:0000641
name: tetranucleotide_repeat_microsatellite_feature
is_a: SO:0000289 ! microsatellite

[Term]
id: SO:0000642
name: SRP_RNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000643
name: minisatellite
def: "A repetitive sequence spanning 500 to 20,000 base pairs (a repeat unit is 5 - 30 base pairs)." [http://www.rerf.or.jp/eigo/glossary/minisate.htm]
subset: SOFA
is_a: SO:0000705 ! tandem_repeat

[Term]
id: SO:0000644
name: antisense_RNA
def: "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]
subset: SOFA
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000645
name: antisense_primary_transcript
def: "The reverse complement of the primary transcript." [SO:ke]
subset: SOFA
is_a: SO:0000185 ! primary_transcript

[Term]
id: SO:0000646
name: siRNA
def: "Small RNA molecule that is the product of a longerexogenous or endogenous dsRNA, which is either a bimolecular duplexe or very longhairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulatefrom both strands of the dsRNA. sRNAs trigger the cleavage of their target molecules." [PMID:12592000]
subset: SOFA
synonym: "small_interfering_RNA" RELATED []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000647
name: miRNA_primary_transcript
def: "A primary transcript encoding a micro RNA." [SO:ke]
synonym: "micro_RNA_primary_transcript" RELATED []
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000648
name: stRNA_primary_transcript
def: "A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke]
synonym: "small_temporal_RNA_primary_transcript" RELATED []
is_a: SO:0000647 ! miRNA_primary_transcript

[Term]
id: SO:0000649
name: stRNA
def: "Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512]
subset: SOFA
synonym: "small_temporal_RNA" RELATED []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000650
name: small_subunit_rRNA
is_a: SO:0000252 ! rRNA

[Term]
id: SO:0000651
name: large_subunit_rRNA
is_a: SO:0000252 ! rRNA

[Term]
id: SO:0000652
name: rRNA_5S
def: "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilises 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]
subset: SOFA
is_a: SO:0000252 ! rRNA

[Term]
id: SO:0000653
name: rRNA_28S
def: "A component of the large ribosomal subunit." [SO:ke]
subset: SOFA
synonym: "23S_rRNA" RELATED []
synonym: "28S_rRNA" RELATED []
is_a: SO:0000252 ! rRNA

[Term]
id: SO:0000654
name: maxi_circle_gene
synonym: "maxi-circle" RELATED []
is_a: SO:0000088 ! mt_gene

[Term]
id: SO:0000655
name: ncRNA
def: "An mRNA sequence that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]
comment: ncRNA is a processed_transcript so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.
subset: SOFA
synonym: "noncoding_RNA" RELATED []
is_a: SO:0000233 ! processed_transcript

[Term]
id: SO:0000656
name: stRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000657
name: repeat_region
def: "A region of sequence containing one or more repeat units." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000658
name: dispersed_repeat
def: "A repeat that is located at dispersed sites in the genome." [SO:ke]
subset: SOFA
synonym: "interspersed_repeat" RELATED []
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000659
name: tmRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000660
name: DNA_invertase_target_sequence
is_a: SO:0000342 ! site_specific_recombination_target_region

[Term]
id: SO:0000661
name: intron_attribute
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000662
name: spliceosomal_intron
def: "An intron which is spliced by the spliceosome." [SO:ke]
subset: SOFA
is_a: SO:0000188 ! intron

[Term]
id: SO:0000663
name: tRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000664
name: introgressed_chromosome_region
relationship: part_of SO:0000340 ! chromosome

[Term]
id: SO:0000665
name: monocistronic_transcript
is_a: SO:0000115 ! transcript_feature

[Term]
id: SO:0000666
name: mobile_intron
is_a: SO:0000661 ! intron_attribute

[Term]
id: SO:0000667
name: insertion
def: "A region of sequence identified as having been inserted." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region
is_a: SO:0000109 ! sequence_variant
relationship: sequence_of SO:0000046 ! insert

[Term]
id: SO:0000668
name: EST_match
def: "A match against an EST sequence." [SO:ke]
subset: SOFA
is_a: SO:0000102 ! expressed_sequence_match

[Term]
id: SO:0000669
name: sequence_rearrangement_feature
is_a: SO:0000298 ! recombination_feature

[Term]
id: SO:0000670
name: chromosome_breakage_sequence
def: "A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma]
is_a: SO:0000669 ! sequence_rearrangement_feature

[Term]
id: SO:0000671
name: internal_eliminated_sequence
def: "A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma]
is_a: SO:0000669 ! sequence_rearrangement_feature

[Term]
id: SO:0000672
name: macronucleus_destined_segment
def: "A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma]
is_a: SO:0000669 ! sequence_rearrangement_feature

[Term]
id: SO:0000673
name: transcript
def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]
subset: SOFA
relationship: member_of SO:0000704 ! gene

[Term]
id: SO:0000674
name: non_canonical_splice_site
def: "A splice site where the donor and acceptor sites differ from the canonical form." [SO:ke]
synonym: "non-canonical_splice_site" RELATED []
is_a: SO:0000162 ! splice_site

[Term]
id: SO:0000675
name: canonical_splice_site
def: "The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively." [SO:ke]
is_a: SO:0000162 ! splice_site

[Term]
id: SO:0000676
name: canonical_three_prime_splice_site
def: "The canonical 3' splice site has the sequence \"AG\"." [SO:ke]
is_a: SO:0000164 ! splice_acceptor_site
is_a: SO:0000675 ! canonical_splice_site

[Term]
id: SO:0000677
name: canonical_five_prime_splice_site
def: "The canonical 5' splice site has the sequence \"GT\"." [SO:ke]
is_a: SO:0000163 ! splice_donor_site
is_a: SO:0000675 ! canonical_splice_site

[Term]
id: SO:0000678
name: non_canonical_three_prime_splice_site
def: "A 3' splice site that does not have the sequence \"AG\"." [SO:ke]
synonym: "non-canonical_three_prime_splice_site" RELATED []
is_a: SO:0000164 ! splice_acceptor_site
is_a: SO:0000674 ! non_canonical_splice_site

[Term]
id: SO:0000679
name: non_canonical_five_prime_splice_site
def: "A 5' splice site which does not have the sequence \"GT\"." [SO:ke]
synonym: "non-canonical-five_prime_splice_site" RELATED []
is_a: SO:0000163 ! splice_donor_site
is_a: SO:0000674 ! non_canonical_splice_site

[Term]
id: SO:0000680
name: non_canonical_start_codon
def: "A start codon that is not the usual AUG sequence." [SO:ke]
synonym: "non-canonical_start_codon" RELATED []
synonym: "non_ATG_start_codon" RELATED []
is_a: SO:0000318 ! start_codon

[Term]
id: SO:0000681
name: aberrant_processed_transcript
def: "A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons." [SO:ke]
is_a: SO:0000233 ! processed_transcript

[Term]
id: SO:0000682
name: splicing_feature
is_obsolete: true

[Term]
id: SO:0000683
name: exonic_splice_enhancer
def: "Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [https://www.ncbi.nlm.nih.gov/pubmed/12403462]
is_a: SO:0000344 ! splice_enhancer

[Term]
id: SO:0000684
name: nuclease_sensitive_site
def: "A region of nucleotide sequence targeting by a nuclease enzyme." [SO:ma]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000685
name: DNAaseI_hypersensitive_site
is_a: SO:0000322 ! nuclease_hypersensitive_site

[Term]
id: SO:0000686
name: translocation_element
def: "For some translocations, particularly but not exclusively, reciprocal translocations, the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements." [SO:ma]
relationship: part_of SO:1000044 ! chromosomal_translocation

[Term]
id: SO:0000687
name: deletion_junction
def: "The space between two bases in a sequence which marks the position where a deletion has occured." [SO:ke]
subset: SOFA
is_a: SO:0000109 ! sequence_variant
is_a: SO:0000699 ! junction
relationship: position_of SO:0000045 ! delete

[Term]
id: SO:0000688
name: golden_path
def: "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls]
subset: SOFA
is_a: SO:0000353 ! assembly

[Term]
id: SO:0000689
name: cDNA_match
def: "A match against cDNA sequence." [SO:ke]
subset: SOFA
is_a: SO:0000102 ! expressed_sequence_match

[Term]
id: SO:0000690
name: gene_with_polycistronic_transcript
is_a: SO:0000064 ! gene_by_transcript_attribute

[Term]
id: SO:0000691
name: translocation_site
def: "The space between two bases in a sequence which marks the position where a translocation has occurred." [SO:ke]
relationship: position_of SO:0000049 ! translocate

[Term]
id: SO:0000692
name: gene_with_dicistronic_transcript
is_a: SO:0000690 ! gene_with_polycistronic_transcript

[Term]
id: SO:0000693
name: gene_with_recoded_mRNA
is_a: SO:0000064 ! gene_by_transcript_attribute

[Term]
id: SO:0000694
name: SNP
def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives (alleles) exist in normal individuals in some population(s), wherein the least frequent allele has an abundance of 1% or greater." [http://www.cgr.ki.se/cgb/groups/brookes/Articles/essence_of_snps_article.pdf]
subset: SOFA
synonym: "single_nucleotide_polymorphism" RELATED []
is_a: SO:1000008 ! point_mutation

[Term]
id: SO:0000695
name: reagent
def: "A sequence used in experiment." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000696
name: oligo
def: "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]
subset: SOFA
synonym: "oligonucleotide" RELATED []
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000697
name: gene_with_stop_codon_read_through
is_a: SO:0000693 ! gene_with_recoded_mRNA

[Term]
id: SO:0000698
name: gene_with_stop_codon_redefined_as_pyrrolysine
is_a: SO:0000697 ! gene_with_stop_codon_read_through

[Term]
id: SO:0000699
name: junction
def: "A junction refers to an interbase location of zero in a sequence." [SO:ke]
subset: SOFA
synonym: "boundary" RELATED []
is_a: SO:0000110 ! located_sequence_feature

[Term]
id: SO:0000700
name: remark
def: "A comment about the sequence." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000701
name: possible_base_call_error
def: "A region of sequence where the validity of the base calling is questionable." [SO:ke]
subset: SOFA
is_a: SO:0000413 ! sequence_difference

[Term]
id: SO:0000702
name: possible_assembly_error
def: "A region of sequence where there may have been an error in the assembly." [SO:ke]
subset: SOFA
is_a: SO:0000413 ! sequence_difference

[Term]
id: SO:0000703
name: experimental_result_region
def: "A region of sequence implicated in an experimental result." [SO:ke]
subset: SOFA
is_a: SO:0000700 ! remark

[Term]
id: SO:0000704
name: gene
def: "A locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions" [SO:rd]
subset: SOFA
is_a: SO:0000001 ! region
relationship: member_of SO:0005855 ! gene_group

[Term]
id: SO:0000705
name: tandem_repeat
def: "Two or more adjacent copies of a DNA sequence." [http://www.sci.sdsu.edu/ ~ smaloy/Glossary/T.html]
subset: SOFA
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000005 ! satellite_DNA

[Term]
id: SO:0000706
name: trans_splice_acceptor_site
def: "The process that produces mature transcripts by combining exons of independent pre-mRNA molecules. The acceptor site lies on the 3' of these molecules." [SO:ke]
subset: SOFA
is_a: SO:0000164 ! splice_acceptor_site

[Term]
id: SO:0000707
name: trans_splice_donor_site
def: "The site at which trans-splicing occurs." [SO:ke]
synonym: "trans-splice_donor_site" RELATED []
is_a: SO:0000163 ! splice_donor_site

[Term]
id: SO:0000708
name: SL1_acceptor_site
is_a: SO:0000706 ! trans_splice_acceptor_site

[Term]
id: SO:0000709
name: SL2_acceptor_site
is_a: SO:0000706 ! trans_splice_acceptor_site

[Term]
id: SO:0000710
name: gene_with_stop_codon_redefined_as_selenocysteine
is_a: SO:0000697 ! gene_with_stop_codon_read_through

[Term]
id: SO:0000711
name: gene_with_mRNA_recoded_by_translational_bypass
is_a: SO:0000693 ! gene_with_recoded_mRNA

[Term]
id: SO:0000712
name: gene_with_transcript_with_translational_frameshift
is_a: SO:0000693 ! gene_with_recoded_mRNA

[Term]
id: SO:0000713
name: DNA_motif
is_a: SO:0000714 ! nucleotide_motif

[Term]
id: SO:0000714
name: nucleotide_motif
def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000715
name: RNA_motif
is_a: SO:0000714 ! nucleotide_motif

[Term]
id: SO:0000716
name: dicistronic_mRNA
synonym: "dicistronic_processed_transcript" RELATED []
is_a: SO:0000079 ! dicistronic_transcript

[Term]
id: SO:0000717
name: reading_frame
def: "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It does not contain the start or stop codon." [SO:rb]
comment: This term was added after a request by SGD.nAgust 2004. Modified after SO meeting in Cambridge to not include start or stop.
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000718
name: blocked_reading_frame
def: "A reading_frame that is interupted by one or more stop codons; usually identified through intergenomic sequence comparisons." [SO:rb]
comment: Term requested by Rama from SGD
is_a: SO:0000717 ! reading_frame

[Term]
id: SO:0000719
name: ultracontig
def: "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]
subset: SOFA
is_a: SO:0000353 ! assembly

[Term]
id: SO:0000720
name: foreign_transposable_element
comment: requested by Michael on 19 Nov 2004
is_a: SO:0000101 ! transposable_element

[Term]
id: SO:0000721
name: gene_with_dicistronic_primary_transcript
comment: Requested by Michael, 19 nov 2004
is_a: SO:0000692 ! gene_with_dicistronic_transcript

[Term]
id: SO:0000722
name: gene_with_dicistronic_mRNA
comment: Requested by MA nov 19 2004
synonym: "gene_with_dicistronic_processed_transcript" RELATED []
is_a: SO:0000692 ! gene_with_dicistronic_transcript

[Term]
id: SO:0000723
name: iDNA
def: "Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma]
synonym: "intervening DNA" RELATED []
is_a: SO:0000298 ! recombination_feature

[Term]
id: SO:0000724
name: origin_of_transfer
def: "A region of a DNA molecule whre transfer is initiated during the process of conjugation or mobilization." [http:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
synonym: "oriT" RELATED []
is_a: SO:0000001 ! region

[Term]
id: SO:0000725
name: transit_peptide
def: "The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein: this domain is involved in post translational import of the protein into the organelle." [http:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
comment: Added to bring SO inline with the embl ddbj genbank feature table.
subset: SOFA
relationship: part_of SO:0000104 ! polypeptide

[Term]
id: SO:0000726
name: repeat_unit
def: "A single repeat element." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
comment: Added to comply with the feature table.
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000727
name: TF_module
def: "A regulatory_region where more than 1 TF_binding_site together are regulatorily active" [SO:SG]
comment: Requested by Stepen Grossmann Dec 2004.
synonym: "CRM" RELATED []
synonym: "cis_regulatory_module" RELATED []
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000728
name: intein
relationship: part_of SO:0000104 ! polypeptide

[Term]
id: SO:0000729
name: intein_containing_protein_coding_gene
is_a: SO:0000010 ! protein_coding_gene

[Term]
id: SO:0000730
name: gap
def: "A gap in the sequence of known length. The unkown bases are filled in with N's." [SO:ke]
subset: SOFA
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000353 ! assembly

[Term]
id: SO:0000731
name: fragment
comment: added because of request by MO people.
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000732
name: predicted
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000733
name: feature_attribute
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000734
name: exemplar_mRNA
def: "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http:mged.sourceforge.net/ontologies/MGEDontology.php#exemplar_mRNA]
comment: Added for the MO people.
is_a: SO:0000082 ! processed_transcript_attribute

[Term]
id: SO:0000735
name: sequence_location
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000736
name: organelle_location
is_a: SO:0000735 ! sequence_location

[Term]
id: SO:0000737
name: mitochondrial_sequence
is_a: SO:0000736 ! organelle_location

[Term]
id: SO:0000738
name: nuclear_sequence
is_a: SO:0000736 ! organelle_location

[Term]
id: SO:0000739
name: nucleomorphic_sequence
is_a: SO:0000736 ! organelle_location

[Term]
id: SO:0000740
name: plastid_sequence
is_a: SO:0000736 ! organelle_location

[Term]
id: SO:0000741
name: kinetoplast_sequence
is_a: SO:0000737 ! mitochondrial_sequence

[Term]
id: SO:0000742
name: maxicircle_sequence
is_a: SO:0000737 ! mitochondrial_sequence

[Term]
id: SO:0000743
name: apicoplast_sequence
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000744
name: chromoplast_sequence
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000745
name: chloroplast_sequence
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000746
name: cyanelle_sequence
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000747
name: leucoplast_sequence
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000748
name: proplastid_sequence
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000749
name: plasmid_sequence
is_a: SO:0000735 ! sequence_location

[Term]
id: SO:0000750
name: amplification_origin
def: "An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma]
is_a: SO:0000296 ! origin_of_replication

[Term]
id: SO:0000751
name: proviral_sequence
is_a: SO:0000735 ! sequence_location

[Term]
id: SO:0000752
name: gene_group_regulatory_region
is_a: SO:0005836 ! regulatory_region
relationship: member_of SO:0005855 ! gene_group

[Term]
id: SO:0000753
name: clone_insert
relationship: part_of SO:0000151 ! clone

[Term]
id: SO:0000754
name: lambda_vector
is_a: SO:0000440 ! vector
relationship: part_of SO:0000160 ! lambda_clone

[Term]
id: SO:0000755
name: plasmid_vector
is_a: SO:0000440 ! vector
relationship: part_of SO:0000759 ! plasmid_clone

[Term]
id: SO:0000756
name: cDNA
def: "DNA synthesized by reverse transcriptase using RNA as a template" [SO:ma]
is_a: SO:0000695 ! reagent
relationship: part_of SO:0000317 ! cDNA_clone

[Term]
id: SO:0000757
name: single_stranded_cDNA
is_a: SO:0000756 ! cDNA

[Term]
id: SO:0000758
name: double_stranded_cDNA
is_a: SO:0000756 ! cDNA

[Term]
id: SO:0000759
name: plasmid_clone
is_a: SO:0000151 ! clone

[Term]
id: SO:0000760
name: YAC_clone
is_a: SO:0000151 ! clone

[Term]
id: SO:0000761
name: phagemid_clone
is_a: SO:0000151 ! clone

[Term]
id: SO:0000762
name: PAC_clone
synonym: "P1_clone" RELATED []
is_a: SO:0000151 ! clone

[Term]
id: SO:0000763
name: fosmid_clone
is_a: SO:0000151 ! clone

[Term]
id: SO:0000764
name: BAC_clone
is_a: SO:0000151 ! clone

[Term]
id: SO:0000765
name: cosmid_clone
is_a: SO:0000151 ! clone

[Term]
id: SO:0000766
name: pyrrolysyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000767
name: clone_insert_start
is_obsolete: true

[Term]
id: SO:0000768
name: episome
def: "A plasmid that may integrate with a chromosome. " [SO:ma]
is_a: SO:0000155 ! plasmid

[Term]
id: SO:0000769
name: tmRNA_coding_piece
def: "The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [Indiana:kw]
comment: Added in response to comment from Kelly Williams from Indiana.nhttp://nar.oxfordjournals.org/cgi/content/full/32/15/4531n10 Nov, 2005
relationship: part_of SO:0000584 ! tmRNA

[Term]
id: SO:0000770
name: tmRNA_acceptor_piece
def: "The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [Indiana:kw]
comment: Added in response to Kelly Williams from Indiananhttp://nar.oxfordjournals.org/cgi/content/full/32/15/4531n10 nov 2005
relationship: part_of SO:0000584 ! tmRNA

[Term]
id: SO:0000771
name: QTL
def: "Quantitative Trait Locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http:rgd.cbi.pku.edu.cn/tu/qtls/]
comment: Added in respose to request by Simon Twigger November 14th 2005
is_a: SO:0000001 ! region

[Term]
id: SO:0000772
name: genomic_island
comment: Genomic islands are transmissible elements characterized by large size (>10kb).
is_a: SO:0000001 ! region

[Term]
id: SO:0000773
name: pathogenic_island
def: "Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke]
comment: Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038/nrmicro884 nGENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMSnUlrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker
is_a: SO:0000772 ! genomic_island

[Term]
id: SO:0000774
name: metabolic_island
def: "A transmissible_element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]
comment: genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands
is_a: SO:0000772 ! genomic_island

[Term]
id: SO:0000775
name: adaptive_island
comment: The iron-uptake ability of many pathogens are conveyed by adaptive islands.nNature Reviews Microbiology 2, 414-424 (2004); doi:10.1038/nrmicro884 nGENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMSnUlrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker
is_a: SO:0000772 ! genomic_island

[Term]
id: SO:0000776
name: symbiosis_island
def: "A transmissible_element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]
comment: Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands.nnEvolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA genenJohn T. Sullivan and Clive W. RonsonnPNAS 1998 Apr 28 95 (9) 5145-5149n
is_a: SO:0000772 ! genomic_island

[Term]
id: SO:0000777
name: pseudogenic_rRNA
comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase.
subset: SOFA
is_a: SO:0000462 ! pseudogenic_region

[Term]
id: SO:0000778
name: pseudogenic_tRNA
comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase.
subset: SOFA
is_a: SO:0000462 ! pseudogenic_region

[Term]
id: SO:0001044
name: nuclear_mt_pseudogene
synonym: "NUMT" RELATED []
synonym: "nuclear_mitochondrial_pseudogene" RELATED []
is_a: SO:0000042 ! pseudogene_attribute

[Term]
id: SO:0005836
name: regulatory_region
def: "A DNA sequence that controls the expression of a gene." [http://www.genpromag.com/scripts/glossary.asp?LETTER=R]
subset: SOFA
is_a: SO:0000001 ! region
relationship: member_of SO:0000704 ! gene

[Term]
id: SO:0005837
name: snRNA_4.5S_primary_transcript
def: "A primary transcript encoding a 4.5S snRNA." [SO:ke]
synonym: "4.5S_snRNA_primary_transcript" RELATED []
is_a: SO:0000231 ! snRNA_primary_transcript

[Term]
id: SO:0005839
name: snRNA_4.5S
synonym: "4.5S_snRNA" RELATED []
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0005841
name: methylation_guide_snoRNA
is_a: SO:0000275 ! snoRNA

[Term]
id: SO:0005843
name: rRNA_cleavage_snoRNA
is_a: SO:0000275 ! snoRNA

[Term]
id: SO:0005845
name: single_exon
is_a: SO:0000147 ! exon

[Term]
id: SO:0005847
name: member_of_gene_cassette_array
is_a: SO:0005848 ! member_of_gene_cassette

[Term]
id: SO:0005848
name: member_of_gene_cassette
is_a: SO:0000081 ! member_gene_array

[Term]
id: SO:0005849
name: member_of_gene_subarray
is_a: SO:0000081 ! member_gene_array

[Term]
id: SO:0005850
name: primer_binding_site
def: "Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http:www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
relationship: part_of SO:0000186 ! LTR_retrotransposon

[Term]
id: SO:0005851
name: gene_array
def: "An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma]
comment: This would include\, for example\, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays.
is_a: SO:0005855 ! gene_group

[Term]
id: SO:0005852
name: gene_subarray
def: "A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma]
comment: This would include\, for example\, a cluster of genes encoding different histones.
is_a: SO:0005851 ! gene_array

[Term]
id: SO:0005853
name: gene_cassette
def: "A non-functional gene that, when captured by recombination forms a functional gene." [SO:ma]
comment: This would include\, for example\, the mating type gene cassettes of S. cerevisiae.
is_a: SO:0005855 ! gene_group

[Term]
id: SO:0005854
name: gene_cassette_array
def: "An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma]
comment: This would include\, for example\, the arrays of non-functional VSG genes of Trypanosomes.
is_a: SO:0005853 ! gene_cassette

[Term]
id: SO:0005855
name: gene_group
def: "A collection of related genes." [SO:ma]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0005856
name: selenocysteine_tRNA_primary_transcript
def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0005857
name: selenocysteinyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0005858
name: syntenic_region
def: "A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://tbase.jax.org/docs/glossary.html]
is_a: SO:0000330 ! conserved_region

[Term]
id: SO:1000002
name: substitution
def: "Any change in genomic DNA caused by a single event." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: SOFA
is_a: SO:0000001 ! region
is_a: SO:0000109 ! sequence_variant
relationship: sequence_of SO:0000048 ! substitute

[Term]
id: SO:1000004
name: partially_characterised_change_in_DNA_sequence
def: "The nature of the mutation event is only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000007 ! uncharacterised_change_in_nucleotide_sequence

[Term]
id: SO:1000005
name: complex_substitution
def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: SOFA
is_a: SO:1000002 ! substitution

[Term]
id: SO:1000007
name: uncharacterised_change_in_nucleotide_sequence
def: "The nature of the mutation event is either uncharacterised or only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000002 ! substitution

[Term]
id: SO:1000008
name: point_mutation
def: "A mutation event where a single DNA nucleotide changes into another nucleotide." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: SOFA
is_a: SO:1000002 ! substitution

[Term]
id: SO:1000009
name: transition
def: "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000008 ! point_mutation

[Term]
id: SO:1000010
name: pyrimidine_transition
def: "A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]
is_a: SO:1000009 ! transition

[Term]
id: SO:1000011
name: C_to_T_transition
def: "A transition of a cytidine to a thymine." [SO:ke]
is_a: SO:1000010 ! pyrimidine_transition

[Term]
id: SO:1000012
name: C_to_T_transition_at_pCpG_site
def: "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000011 ! C_to_T_transition

[Term]
id: SO:1000013
name: T_to_C_transition
is_a: SO:1000010 ! pyrimidine_transition

[Term]
id: SO:1000014
name: purine_transition
def: "A substitution of a purine, A or G, for another purine." [SO:ke]
is_a: SO:1000009 ! transition

[Term]
id: SO:1000015
name: A_to_G_transition
def: "A transition of an adenine to a guanine." [SO:ke]
is_a: SO:1000014 ! purine_transition

[Term]
id: SO:1000016
name: G_to_A_transition
def: "A transition of a guanine to an adenine." [SO:ke]
is_a: SO:1000014 ! purine_transition

[Term]
id: SO:1000017
name: transversion
def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000008 ! point_mutation

[Term]
id: SO:1000018
name: pyrimidine_to_purine_transversion
def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]
is_a: SO:1000017 ! transversion

[Term]
id: SO:1000019
name: C_to_A_transversion
def: "A transversion from cytidine to adenine." [SO:ke]
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000020
name: C_to_G_transversion
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000021
name: T_to_A_transversion
def: "A transversion from T to A." [SO:ke]
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000022
name: T_to_G_transversion
def: "A transversion from T to G." [SO:ke]
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000023
name: purine_to_pyrimidine_transversion
def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]
is_a: SO:1000017 ! transversion

[Term]
id: SO:1000024
name: A_to_C_transversion
def: "A transversion from adenine to cytidine." [SO:ke]
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000025
name: A_to_T_transversion
def: "A transversion from adenine to thymine." [SO:ke]
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000026
name: G_to_C_transversion
def: "A transversion from guanine to cytidine." [SO:ke]
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000027
name: G_to_T_transversion
def: "A transversion from guanine to thymine." [SO:ke]
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000028
name: intrachromosomal_mutation
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000029
name: chromosomal_deletion
synonym: "(Drosophila)Df" RELATED []
synonym: "(bacteria)&Dgr;" RELATED []
synonym: "(fungi)D" RELATED []
is_a: SO:0000550 ! aneuploid_chromosome
is_a: SO:1000028 ! intrachromosomal_mutation

[Term]
id: SO:1000030
name: chromosomal_inversion
synonym: "(Drosophila)In" RELATED []
synonym: "(bacteria)IN" RELATED []
synonym: "(fungi)In" RELATED []
is_a: SO:1000028 ! intrachromosomal_mutation

[Term]
id: SO:1000031
name: interchromosomal_mutation
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000032
name: indel
def: "A hybrid term (insertion/deletion) to describe sequence length change when the direction of the change is unspecified." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:0000109 ! sequence_variant

[Term]
id: SO:1000033
name: nucleotide_deletion
def: "One or more continuous nucleotides are excised from the sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000032 ! indel

[Term]
id: SO:1000034
name: nucleotide_insertion
def: "One or more nucleotides are added between two adjacent nucleotides in the sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000032 ! indel

[Term]
id: SO:1000035
name: nucleotide_duplication
def: "One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000034 ! nucleotide_insertion

[Term]
id: SO:1000036
name: inversion
def: "A continuous nucleotide sequence is inverted in the same position." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: SOFA
is_a: SO:0000001 ! region
is_a: SO:0000109 ! sequence_variant
relationship: sequence_of SO:0000047 ! invert

[Term]
id: SO:1000037
name: chromosomal_duplication
synonym: "(Drosophila)Dp" RELATED []
synonym: "(fungi)Dp" RELATED []
is_a: SO:0000550 ! aneuploid_chromosome
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000038
name: intrachromosomal_duplication
is_a: SO:1000028 ! intrachromosomal_mutation
is_a: SO:1000037 ! chromosomal_duplication

[Term]
id: SO:1000039
name: direct_tandem_duplication
is_a: SO:1000173 ! tandem_duplication

[Term]
id: SO:1000040
name: inverted_tandem_duplication
is_a: SO:1000173 ! tandem_duplication

[Term]
id: SO:1000041
name: intrachromosomal_transposition
synonym: "(Drosophila)Tp" RELATED []
is_a: SO:0000453 ! transposition
is_a: SO:1000038 ! intrachromosomal_duplication

[Term]
id: SO:1000042
name: compound_chromosome
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000043
name: Robertsonian_fusion
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000044
name: chromosomal_translocation
synonym: "(Drosophila)T" RELATED []
synonym: "(fungi)T" RELATED []
is_a: SO:1000031 ! interchromosomal_mutation

[Term]
id: SO:1000045
name: ring_chromosome
synonym: "(Drosophila)R" RELATED []
synonym: "(fungi)C" RELATED []
is_a: SO:1000028 ! intrachromosomal_mutation

[Term]
id: SO:1000046
name: pericentric_inversion
is_a: SO:1000030 ! chromosomal_inversion

[Term]
id: SO:1000047
name: paracentric_inversion
is_a: SO:1000030 ! chromosomal_inversion

[Term]
id: SO:1000048
name: reciprocal_chromosomal_translocation
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000049
name: mutation_affecting_transcript
def: "Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000132 ! consequences_of_mutation

[Term]
id: SO:1000050
name: no_change_in_transcript
def: "No effect on the state of the RNA." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000052
name: complex_change_in_transcript
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000054
name: mutation_affecting_coding_sequence
def: "Any of the amino acid coding triplets of a gene are affected by the DNA mutation." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000079 ! mutation_affecting_transcript_sequence

[Term]
id: SO:1000055
name: initiator_codon_change_in_transcript
def: "The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000056 ! amino_acid_coding_codon_change_in_transcript

[Term]
id: SO:1000056
name: amino_acid_coding_codon_change_in_transcript
def: "The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000054 ! mutation_affecting_coding_sequence

[Term]
id: SO:1000057
name: synonymous_codon_change_in_transcript
def: "The changed codon has the same translation product as the original codon." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000056 ! amino_acid_coding_codon_change_in_transcript

[Term]
id: SO:1000058
name: non_synonymous_codon_change_in_transcript
def: "A DNA point mutation that causes a substitution of an amino acid by an other." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "non-synonymous_codon_change_in_transcript" RELATED []
is_a: SO:1000056 ! amino_acid_coding_codon_change_in_transcript

[Term]
id: SO:1000059
name: missense_codon_change_in_transcript
def: "The nucleotide change in the codon leads to a new codon coding for a new amino acid." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000058 ! non_synonymous_codon_change_in_transcript

[Term]
id: SO:1000060
name: conservative_missense_codon_change_in_transcript
def: "The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: The exact rules need to be stated\, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
is_a: SO:1000059 ! missense_codon_change_in_transcript

[Term]
id: SO:1000061
name: nonconservative_missense_codon_change_in_transcript
def: "The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: The exact rules need to be stated\, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
is_a: SO:1000059 ! missense_codon_change_in_transcript

[Term]
id: SO:1000062
name: nonsense_codon_change_in_transcript
def: "The nucleotide change in the codon triplet creates a terminator codon." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000056 ! amino_acid_coding_codon_change_in_transcript

[Term]
id: SO:1000063
name: terminator_codon_change_in_transcript
is_a: SO:1000054 ! mutation_affecting_coding_sequence

[Term]
id: SO:1000064
name: mutation_affecting_reading_frame
def: "An umbrella term for terms describing an effect of a mutation on the frame of translation." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000054 ! mutation_affecting_coding_sequence

[Term]
id: SO:1000065
name: frameshift_mutation
def: "." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000064 ! mutation_affecting_reading_frame

[Term]
id: SO:1000066
name: plus_1_frameshift_mutation
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000067
name: minus_1_frameshift_mutation
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000068
name: plus_2_frameshift_mutation
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000069
name: minus_2_frameshift_mutation
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000070
name: mutation_affecting_transcript_processing
def: "Mutation affects the way in which the primary transcriptional product is processed to form the mature transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000079 ! mutation_affecting_transcript_sequence

[Term]
id: SO:1000071
name: mutation_affecting_splicing
def: "Mutation affects the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000132 ! consequences_of_mutation

[Term]
id: SO:1000072
name: splice_donor_mutation
is_a: SO:1000071 ! mutation_affecting_splicing
is_a: SO:1000074 ! cryptic_splice_activator_mutation

[Term]
id: SO:1000073
name: splice_acceptor_mutation
is_a: SO:1000071 ! mutation_affecting_splicing

[Term]
id: SO:1000074
name: cryptic_splice_activator_mutation
def: "Mutation creates a new (functional) splice site." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000071 ! mutation_affecting_splicing

[Term]
id: SO:1000075
name: mutation_affecting_editing
def: "Mutation affects the editing of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000070 ! mutation_affecting_transcript_processing

[Term]
id: SO:1000076
name: mutation_affecting_transcription
def: "Mutation affects the process of transcription, its initiation, progression or termination." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000078
name: mutation_decreasing_rate_of_transcription
is_a: SO:1000081 ! mutation_affecting_rate_of_transcription

[Term]
id: SO:1000079
name: mutation_affecting_transcript_sequence
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000080
name: mutation_increasing_rate_of_transcription
is_a: SO:1000081 ! mutation_affecting_rate_of_transcription

[Term]
id: SO:1000081
name: mutation_affecting_rate_of_transcription
is_a: SO:1000076 ! mutation_affecting_transcription

[Term]
id: SO:1000082
name: mutation_affecting_transcript_stability
def: "Mutation affects the stability of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000079 ! mutation_affecting_transcript_sequence

[Term]
id: SO:1000083
name: mutation_increasing_transcript_stability
def: "Mutation increases the stability (half-life) of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000082 ! mutation_affecting_transcript_stability

[Term]
id: SO:1000084
name: mutation_decreasing_transcript_stability
def: "Mutation decreases the stability (half-life) of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000082 ! mutation_affecting_transcript_stability

[Term]
id: SO:1000085
name: mutation_affecting_level_of_transcript
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000086
name: mutation_decreasing_level_of_transcript
is_a: SO:1000085 ! mutation_affecting_level_of_transcript

[Term]
id: SO:1000087
name: mutation_increasing_level_of_transcript
is_a: SO:1000085 ! mutation_affecting_level_of_transcript

[Term]
id: SO:1000088
name: mutation_affecting_translational_product
def: "Mutation causes a change in primary translation product of a transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000132 ! consequences_of_mutation

[Term]
id: SO:1000089
name: no_change_of_translational_product
def: "The change at RNA level does not lead to any change in polypeptide." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000090
name: uncharacterised_change_of_translational_product
def: "The nature of the mutation event is either uncharacterised or only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000091
name: partially_characterised_change_of_translational_product
def: "The nature of the mutation event is only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000090 ! uncharacterised_change_of_translational_product

[Term]
id: SO:1000092
name: complex_change_of_translational_product
def: "Any mutation effect that is known at nucleotide level but can not be explained by using other key terms." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000093
name: amino_acid_substitution
def: "The replacement of a single amino acid by an other." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000094
name: conservative_amino_acid_substitution
is_a: SO:1000093 ! amino_acid_substitution

[Term]
id: SO:1000095
name: nonconservative_amino_acid_substitution
is_a: SO:1000093 ! amino_acid_substitution

[Term]
id: SO:1000096
name: amino_acid_insertion
def: "The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000097
name: amino_acid_deletion
def: "The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000098
name: polypeptide_truncation
def: "The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062)." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000099
name: polypeptide_elongation
def: "The extension of the translational product at either (or both) the N-terminus and/or the C-terminus." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000100
name: polypeptide_N_terminal_elongation
def: "." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "polypeptide_N-terminal_elongation" RELATED []
is_a: SO:1000099 ! polypeptide_elongation

[Term]
id: SO:1000101
name: polypeptide_C_terminal_elongation
def: "." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "polypeptide_C-terminal_elongation" RELATED []
is_a: SO:1000099 ! polypeptide_elongation

[Term]
id: SO:1000102
name: mutation_affecting_level_of_translational_product
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000103
name: mutation_decreasing_level_of_translation_product
is_a: SO:1000102 ! mutation_affecting_level_of_translational_product

[Term]
id: SO:1000104
name: mutation_increasing_level_of_translation_product
is_a: SO:1000102 ! mutation_affecting_level_of_translational_product

[Term]
id: SO:1000105
name: mutation_affecting_polypeptide_amino_acid_sequence
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000106
name: inframe_polypeptide_N_terminal_elongation
synonym: "inframe_polypeptide_N-terminal_elongation" RELATED []
is_a: SO:1000100 ! polypeptide_N_terminal_elongation

[Term]
id: SO:1000107
name: out_of_frame_polypeptide_N_terminal_elongation
synonym: "out_of_frame_polypeptide_N-terminal_elongation" RELATED []
is_a: SO:1000100 ! polypeptide_N_terminal_elongation

[Term]
id: SO:1000108
name: inframe_polypeptide_C_terminal_elongation
synonym: "inframe_polypeptide_C-terminal_elongation" RELATED []
is_a: SO:1000101 ! polypeptide_C_terminal_elongation

[Term]
id: SO:1000109
name: out_of_frame_polypeptide_C_terminal_elongation
synonym: "out_of_frame_polypeptide_C-terminal_elongation" RELATED []
is_a: SO:1000101 ! polypeptide_C_terminal_elongation

[Term]
id: SO:1000110
name: frame_restoring_mutation
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000111
name: mutation_affecting_3D_structure_of_polypeptide
synonym: "mutation_affecting_3D-structure_of_polypeptide" RELATED []
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000112
name: no_3D_structural_change
is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide

[Term]
id: SO:1000113
name: uncharacterised_3D_structural_change
is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide

[Term]
id: SO:1000114
name: partially_characterised_3D_structural_change
is_a: SO:1000113 ! uncharacterised_3D_structural_change

[Term]
id: SO:1000115
name: complex_3D_structural_change
is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide

[Term]
id: SO:1000116
name: conformational_change
is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide

[Term]
id: SO:1000117
name: mutation_affecting_polypeptide_function
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000118
name: loss_of_function_of_polypeptide
synonym: "loss-of-function_of_polypeptide" RELATED []
is_a: SO:1000117 ! mutation_affecting_polypeptide_function

[Term]
id: SO:1000119
name: inactive_ligand_binding_site
is_a: SO:1000118 ! loss_of_function_of_polypeptide

[Term]
id: SO:1000120
name: inactive_catalytic_site
is_a: SO:1000119 ! inactive_ligand_binding_site

[Term]
id: SO:1000121
name: polypeptide_localization_affected
is_a: SO:1000117 ! mutation_affecting_polypeptide_function

[Term]
id: SO:1000122
name: polypeptide_post_translational_processing_affected
synonym: "polypeptide_post-translational_processing_affected" RELATED []
is_a: SO:1000117 ! mutation_affecting_polypeptide_function
is_a: SO:1000118 ! loss_of_function_of_polypeptide

[Term]
id: SO:1000123
name: polypeptide_post_translational_processing_affected
synonym: "polypeptide_post-translational_processing_affected" RELATED []
is_obsolete: true

[Term]
id: SO:1000124
name: partial_loss_of_function_of_polypeptide
synonym: "partial_loss-of-function_of_polypeptide" RELATED []
is_a: SO:1000118 ! loss_of_function_of_polypeptide

[Term]
id: SO:1000125
name: gain_of_function_of_polypeptide
synonym: "gain-of-function_of_polypeptide" RELATED []
is_a: SO:1000117 ! mutation_affecting_polypeptide_function

[Term]
id: SO:1000126
name: mutation_affecting_transcript_secondary_structure
is_a: SO:1000079 ! mutation_affecting_transcript_sequence

[Term]
id: SO:1000127
name: compensatory_transcript_secondary_structure_mutation
is_a: SO:1000126 ! mutation_affecting_transcript_secondary_structure

[Term]
id: SO:1000132
name: consequences_of_mutation
is_a: SO:0000000 ! Sequence_Ontology

[Term]
id: SO:1000134
name: polypeptide_fusion
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000136
name: autosynaptic_chromosome
synonym: "(Drosophila)A" RELATED []
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000138
name: homo_compound_chromosome
synonym: "homo-compound_chromosome" RELATED []
is_a: SO:1000042 ! compound_chromosome

[Term]
id: SO:1000140
name: hetero_compound_chromosome
synonym: "hetero-compound_chromosome" RELATED []
is_a: SO:1000042 ! compound_chromosome

[Term]
id: SO:1000141
name: chromosome_fission
is_a: SO:1000028 ! intrachromosomal_mutation

[Term]
id: SO:1000142
name: dexstrosynaptic_chromosome
is_a: SO:1000136 ! autosynaptic_chromosome

[Term]
id: SO:1000143
name: laevosynaptic_chromosome
is_a: SO:1000136 ! autosynaptic_chromosome

[Term]
id: SO:1000144
name: free_duplication
is_a: SO:1000037 ! chromosomal_duplication

[Term]
id: SO:1000145
name: free_ring_duplication
synonym: "(Drosophila)R" RELATED []
is_a: SO:1000045 ! ring_chromosome
is_a: SO:1000144 ! free_duplication

[Term]
id: SO:1000146
name: complex_chromosomal_mutation
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000147
name: deficient_translocation
def: "A translocation in which one of the four broken ends loses a segment before re-joining." [fb:reference_manual]
synonym: "(Drosophila)Df" RELATED []
synonym: "(Drosophila)DfT" RELATED []
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000148
name: inversion_cum_translocation
def: "The first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [fb:reference_manual]
synonym: "(Drosophila)InT" RELATED []
synonym: "(Drosophila)T" RELATED []
synonym: "inversion-cum-translocation" RELATED []
is_a: SO:1000030 ! chromosomal_inversion
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000149
name: bipartite_duplication
def: "The (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [fb:reference_manual]
synonym: "(Drosophila)bDp" RELATED []
is_a: SO:1000031 ! interchromosomal_mutation

[Term]
id: SO:1000150
name: cyclic_translocation
def: "Three breaks in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [fb:reference_manual]
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000151
name: bipartite_inversion
def: "Three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [fb:reference_manual]
synonym: "(Drosophila)bIn" RELATED []
is_a: SO:1000030 ! chromosomal_inversion

[Term]
id: SO:1000152
name: uninverted_insertional_duplication
def: "A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [fb:reference_manual]
synonym: "(Drosophila)eDp" RELATED []
is_a: SO:1000154 ! insertional_duplication

[Term]
id: SO:1000153
name: inverted_insertional_duplication
def: "A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [fb:reference_manual]
synonym: "(Drosophila)iDp" RELATED []
is_a: SO:1000154 ! insertional_duplication

[Term]
id: SO:1000154
name: insertional_duplication
synonym: "(Drosophila)Dpp" RELATED []
is_a: SO:1000037 ! chromosomal_duplication

[Term]
id: SO:1000155
name: interchromosomal_transposition
synonym: "(Drosophila)Tp" RELATED []
is_a: SO:0000453 ! transposition
is_a: SO:1000031 ! interchromosomal_mutation

[Term]
id: SO:1000156
name: inverted_interchromosomal_transposition
synonym: "(Drosophila)iTp" RELATED []
is_a: SO:1000155 ! interchromosomal_transposition

[Term]
id: SO:1000157
name: uninverted_interchromosomal_transposition
synonym: "(Drosophila)eTp" RELATED []
is_a: SO:1000155 ! interchromosomal_transposition

[Term]
id: SO:1000158
name: inverted_intrachromosomal_transposition
def: "The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [fb:reference_manual]
synonym: "(Drosophila)iTp" RELATED []
is_a: SO:1000030 ! chromosomal_inversion
is_a: SO:1000041 ! intrachromosomal_transposition

[Term]
id: SO:1000159
name: uninverted_intrachromosomal_transposition
def: "The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [fb:reference_manual]
synonym: "(Drosophila)eTp" RELATED []
is_a: SO:1000041 ! intrachromosomal_transposition

[Term]
id: SO:1000160
name: unoriented_insertional_duplication
def: "A copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [fb:reference_manual]
synonym: "(Drosophila)uDp" RELATED []
is_a: SO:1000154 ! insertional_duplication

[Term]
id: SO:1000161
name: unorientated_interchromosomal_transposition
synonym: "(Drosophila)uTp" RELATED []
is_a: SO:1000155 ! interchromosomal_transposition

[Term]
id: SO:1000162
name: unorientated_intrachromosomal_transposition
def: "The segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [fb:reference_manual]
synonym: "(Drosophila)uTp" RELATED []
is_a: SO:1000041 ! intrachromosomal_transposition

[Term]
id: SO:1000170
name: uncharacterised_chromosomal_mutation
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000171
name: deficient_inversion
def: "Three breaks in the same chromosome; one central region lost, the other inverted." [fb:reference_manual]
synonym: "(Drosophila)Df" RELATED []
synonym: "(Drosophila)DfIn" RELATED []
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000030 ! chromosomal_inversion

[Term]
id: SO:1000173
name: tandem_duplication
is_a: SO:1000038 ! intrachromosomal_duplication

[Term]
id: SO:1000175
name: partially_characterised_chromosomal_mutation
is_a: SO:1000170 ! uncharacterised_chromosomal_mutation

[Term]
id: SO:1000177
name: uncharacterised_change_in_transcript
def: "The nature of the mutation event is either uncharacterised or only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000179
name: partially_characterised_change_in_transcript
def: "The nature of the mutation event is only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000177 ! uncharacterised_change_in_transcript

[Term]
id: SO:1000180
name: mutation_affecting_gene_structure
is_a: SO:1000132 ! consequences_of_mutation

[Term]
id: SO:1000181
name: gene_fusion
is_a: SO:1000180 ! mutation_affecting_gene_structure

[Term]
id: SO:1000182
name: chromosome_number_variation
is_a: SO:0000240 ! chromosome_variation

[Term]
id: SO:1000183
name: chromosome_structure_variation
is_a: SO:0000240 ! chromosome_variation

[Term]
id: SO:1000184
name: mutation_causes_exon_loss
is_a: SO:1000071 ! mutation_affecting_splicing

[Term]
id: SO:1000185
name: mutation_causes_intron_gain
def: "Mutation causes an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072)." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000071 ! mutation_affecting_splicing

[Term]
id: SO:1000186
name: cryptic_splice_donor_activation
is_a: SO:1000074 ! cryptic_splice_activator_mutation

[Term]
id: SO:1001186
name: cryptic_splice_acceptor_activation
is_a: SO:1000074 ! cryptic_splice_activator_mutation

[Term]
id: SO:1001187
name: alternatively_spliced_transcript
is_a: SO:0000115 ! transcript_feature

[Term]
id: SO:1001188
name: alternatively_spliced_transcript_encoding_1_polypeptide
is_a: SO:1001187 ! alternatively_spliced_transcript

[Term]
id: SO:1001189
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide
is_a: SO:1001187 ! alternatively_spliced_transcript

[Term]
id: SO:1001190
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_same_start_codon_different_stop_codon
is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide
is_a: SO:1001194 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_overlapping

[Term]
id: SO:1001191
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_same_stop_codon
is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide
is_a: SO:1001194 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_overlapping

[Term]
id: SO:1001192
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon
is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide

[Term]
id: SO:1001193
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_overlapping
is_a: SO:1001192 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon
is_a: SO:1001194 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_overlapping

[Term]
id: SO:1001194
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_overlapping
is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide

[Term]
id: SO:1001195
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_not_overlapping
is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide

[Term]
id: SO:1001196
name: cryptogene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:1001197
name: dicistronic_primary_transcript
is_a: SO:0000079 ! dicistronic_transcript

[Term]
id: SO:1001217
name: member_of_regulon
is_a: SO:0000081 ! member_gene_array

[Term]
id: SO:1001244
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping
synonym: "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping" RELATED []
is_a: SO:1001192 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon
is_a: SO:1001195 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_not_overlapping

[Term]
id: SO:1001246
name: CDS_independently_known
is_a: SO:1001255 ! status_of_coding_sequence

[Term]
id: SO:1001247
name: orphan_CDS
def: "A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [MA:SO]
is_a: SO:1001254 ! CDS_predicted

[Term]
id: SO:1001249
name: CDS_supported_by_domain_match_data
is_a: SO:1001254 ! CDS_predicted

[Term]
id: SO:1001251
name: CDS_supported_by_sequence_similarity_data
is_a: SO:1001254 ! CDS_predicted

[Term]
id: SO:1001254
name: CDS_predicted
is_a: SO:1001255 ! status_of_coding_sequence

[Term]
id: SO:1001255
name: status_of_coding_sequence
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:1001259
name: CDS_supported_by_EST_or_cDNA_data
is_a: SO:1001254 ! CDS_predicted

[Term]
id: SO:1001260
name: internal_Shine_Dalgarno_sequence
def: "A Shine Delgarno sequence that is upstream of a non-5' CDS in a polycistronic mRNA." [SO:ke]
is_a: SO:0000243 ! internal_ribosome_entry_site
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001261
name: recoded_mRNA
def: "A gene coding an mRNA which is recoded before translation, usually by special cis-acting signals." [https://www.ncbi.nlm.nih.gov/pubmed/8811194]
is_a: SO:0000115 ! transcript_feature

[Term]
id: SO:1001262
name: minus_1_translational_frameshift
is_a: SO:0000118 ! transcript_with_translational_frameshift

[Term]
id: SO:1001263
name: plus_1_translational_frameshift
is_a: SO:0000118 ! transcript_with_translational_frameshift

[Term]
id: SO:1001264
name: mRNA_recoded_by_translational_bypass
def: "A gene whose mRNA is translated by ribosomes that suspend translation at a particular codon and resume translation at a particular non-overlapping downstream codon." [https://www.ncbi.nlm.nih.gov/pubmed/8811194]
is_a: SO:1001261 ! recoded_mRNA

[Term]
id: SO:1001265
name: mRNA_recoded_by_codon_redefinition
def: "A gene whose mRNA is recoded by an alteration of codon meaning." [SO:ma]
is_a: SO:1001261 ! recoded_mRNA

[Term]
id: SO:1001266
name: stop_codon_redefinition_as_selenocysteine
is_a: SO:1001267 ! stop_codon_readthrough

[Term]
id: SO:1001267
name: stop_codon_readthrough
is_a: SO:1001265 ! mRNA_recoded_by_codon_redefinition

[Term]
id: SO:1001268
name: recoding_stimulatory_region
def: "A site in an mRNA sequence that stimulates the recoding of the same mRNA." [https://www.ncbi.nlm.nih.gov/pubmed/12519954]
synonym: "recoding_stimulatory_signal" RELATED []
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:1001269
name: four_bp_start_codon
def: "A non-canonical start codon with 4 pase pairs." [SO:ke]
synonym: "4bp_start_codon" RELATED []
is_a: SO:0000680 ! non_canonical_start_codon

[Term]
id: SO:1001270
name: stop_codon_redefinition_as_pyrrolysine
is_a: SO:1001267 ! stop_codon_readthrough

[Term]
id: SO:1001271
name: archeal_intron
def: "Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism." [SO:ma]
is_a: SO:0000661 ! intron_attribute

[Term]
id: SO:1001272
name: tRNA_intron
is_a: SO:0000661 ! intron_attribute

[Term]
id: SO:1001273
name: CTG_start_codon
def: "A non-canonical start codon of sequence CTG." [SO:ke]
is_a: SO:0000680 ! non_canonical_start_codon

[Term]
id: SO:1001274
name: SECIS_element
def: "The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001275
name: retron
def: "Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma]
is_a: SO:0000009 ! gene_class

[Term]
id: SO:1001277
name: three_prime_recoding_site
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001279
name: three_prime_stem_loop_structure
def: "The stem-loop secondary structural element downstream of the redefined region." [SO:ke]
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001280
name: five_prime_recoding_site
def: "The recoding signal found 5' of the redefined codon." [SO:ke]
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001281
name: flanking_three_prime_quadruplet_recoding_signal
def: "Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [SO:ke]
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001282
name: UAG_stop_codon_signal
is_a: SO:1001288 ! stop_codon_signal

[Term]
id: SO:1001283
name: UAA_stop_codon_signal
is_a: SO:1001288 ! stop_codon_signal

[Term]
id: SO:1001284
name: regulon
def: "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732]
subset: SOFA
is_a: SO:0005855 ! gene_group

[Term]
id: SO:1001285
name: UGA_stop_codon_signal
is_a: SO:1001288 ! stop_codon_signal

[Term]
id: SO:1001286
name: three_prime_repeat_recoding_signal
def: "It is a downstream sequence important for recoding that contains repetitive elements." [SO:ke]
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001287
name: distant_three_prime_recoding_signal
def: "A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [https://www.ncbi.nlm.nih.gov/pubmed/8709208]
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001288
name: stop_codon_signal
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:2000061
name: databank_entry
def: "The sequence referred to by an entry in a databank such as Genbank or SwissProt." [SO:ke]
subset: SOFA
synonym: "accession" RELATED []
is_a: SO:0000695 ! reagent

[Typedef]
id: adjacent_to
name: adjacent_to
def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence." [SO:ke]
subset: SOFA
domain: SO:0000110 ! located_sequence_feature
range: SO:0000110 ! located_sequence_feature
is_symmetric: true

[Typedef]
id: associated_with
name: associated_with
comment: This relationship is vague and up for discussion.
is_symmetric: true

[Typedef]
id: derives_from
name: derives_from
subset: SOFA
is_transitive: true

[Typedef]
id: genome_of
name: genome_of

[Typedef]
id: has_genome_location
name: has_genome_location
domain: SO:0000085 ! gene_by_genome_location
range: SO:0000704 ! gene
is_obsolete: true

[Typedef]
id: homologous_to
name: homologous_to
is_symmetric: true
is_a: similar_to ! similar_to

[Typedef]
id: member_of
name: member_of
comment: A subtype of part_of.ninverse is collection_of.nWinston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
subset: SOFA
is_a: part_of ! part_of

[Typedef]
id: non_functional_homolog_of
name: non_functional_homolog_of
def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke]
is_a: homologous_to ! homologous_to

[Typedef]
id: orthologous_to
name: orthologous_to
is_symmetric: true
is_a: homologous_to ! homologous_to

[Typedef]
id: paralogous_to
name: paralogous_to
is_symmetric: true
is_a: homologous_to ! homologous_to

[Typedef]
id: part_of
name: part_of
subset: SOFA
is_transitive: true

[Typedef]
id: position_of
name: position_of

[Typedef]
id: regulated_by
name: regulated_by
is_obsolete: true

[Typedef]
id: sequence_of
name: sequence_of

[Typedef]
id: similar_to
name: similar_to
is_symmetric: true

BioPerl-1.007002/t/data/sofa.ontology000444000766000024       761213155576321 17422 0ustar00cjfieldsstaff000000000000!autogenerated-by:     DAG-Edit version 1.316
!saved-by:             suzi
!date:                 Wed Feb 19 16:38:05 SGT 2003
!version: $Revision: 1.1 $
!type: % ISA Is a
!type: < PARTOF Part of
!Sequence_ontology_Lite_Version
!This is only for comment; not for implementation
!Comments to: song-devel@sourceforge.net
$Sequence_Feature_Ontology ; SO:0000000
 %sofa ; GO:0000001
  %feature ; SO:20000000
   %chromosome ; GO:0000005
    CEESC12R
gcacgagtccatctccatatgccaccacaacantggtcctgtcgaaccaa
caaccagcttggctcaatgacaaaatgcttcgcgcgccanaatgccaaca
aatcccgtgccaccagagccaccggcgcgatatgcagatcataccgctgg
aagacgatctcgatcgagccgtgcatccgatgggagaggaactctgaatg
gcggactccatcaccggactagcggaagtcaacggtcggatagtccacct
cacacagatgtgagctatgttcagcttcactcatccgatggaactggtag
tagtaaggaaagaantngggagcggagaacaccaccgaataaa



>CEESC13F
cttgcttgaaaaatttatataaatatttaagagaagaaaaataaataatc
gcatctaatgacgtctgtccttgtatccctggtttccattgactggtgca
ctttcctgtctttgaggacatggacaatattcggcatcagttcctggctc
tccctcctctcctggtgctccagcagaaccgttctctccattatctccct
tgtctccacgtggtccacgctctcctggtgctcctggaataccttgagct
ccctcgtgccgaattcctgcagcccgggggatccactagttctagagcgg
ccgccaccgcggtgggagctccagcttttgttncctttagtgagggttaa
tttcgagcttggcgtaatcatggtcatagctgtttcctg


>CEESC13R
gcacgagggagctcaaggtattccaggagcaccaggagagcgtggaccac
gtggagacaagggagataatggagagaacggttctgctggagcaccagga
gaggagggagagccaggaactgatgccgaatattgtccatgtcctcaaag
acaggaaagtgcaccagtcaatggaaaccagggatacaagaacagacgtc
attagatgcgattatttatttttcttctcttaaatatttatataaatttt
tcaagcaag

>CEESC14F
aaaaaatgcgaagntccaacagttccatgctatcgttatctggatatttc
aaatggattattccttggaggccgtcctggaacttcgaagcaaatcgaga
aggccttctctggatgtatttctgatttgtcagtggataaagaagatgtc
gattttncaacgatcaaagaaatgcacaaagttggacaagttcatgaagg
atgcaagcatcgtaaagatttttnctcaacttcggatggacaatgctcgg
ctacctcgaagtgtgtcaatcgttggggaggcagaatttgtagctgtccg
caatcggttcattcgactggtgaatgtgttggagcacttggaactcaaga
tttacgtgggcattctctatttgaagaggaatcatttgtttttgtaccag
ccaagccaagtatctgtaccgtttgaagtttcatttgaattccggacatc
tcgagctgatatgcaagt
>CEESC14R
gcacgagtttttttttttcactgaaatcgatcttccatcaaccaaaacat
tccgaatgcatccttcaaaacgtgatggatgtccagttccaggtgcaatt
ccaaagtataagctctctagattcatatcagaaatggaagctttagcttc
tgcactgtagattccatttatactagttgcaactgaatctgcttcaaact
tgatgacaacattcatccaatgctttgatgttacttcaggagctggcaac
tcaacttcagaatctccaatgttatatttcaaagttccattcatcaactt
ccaagttgtaatgaacacttctttgg
>CEESC15F
cnctttgtaataaataatttattatgccncgaaaataattnccnccaaaa
tcaatctttcagcgggtgggtgtaatcattgggaacngggaagtcactag
gaaataaggaaatagngaaatacaataaataaaataataataataatagg
cgactatgattagttagaaaacacagctctgggaattgtttggaagtgtt
gagagaaattnttgattttttacaaatggggaatatgattgaccgttgga
ataagtnaaaatattantaaaaatagcgctgantgaaaacttaataagtg
acagtgaaaaggatttgaaaagntaattaanccaactacg
>CEESC15R
gcacgagggcggacaacctcaaggcgctacaccgggacaacccgatcaga
actttgactacatgttcaagctcctgataatcggaaattcatcagttgga
aaaacatcattcctcttccgttactgtgatgattcattcacttctgcctt
cgtctctactgtcggaatcgatttcaaagtgaaaactgtgttccgtggag
acaaacgagtcaaacttcaaatctgggataccgccggacaggagaggtac
cgtaccatcaccaccgcctactatcgtggagcaatgggatttcattctga
tgtatgacatcacttaatgaagggtcttttaatagtgttc
>CEESC15RB
ggcggacaacctcaaggcgctacaccgggacaacccgatcagaactttga
ctacatgttcaagctcctgataatcggaaattcatcagttggaaaaacat
cattcctcttccgttactgtgatgattcattcacttctgccttcgtctct
actgtcggaatcgatttcaaagtgaaaactgtgttccgtggagacaaacg
agtcaaacttcaaatctggggataccgccggacaggagaggtaccgtacc
atcaccaccggcttactattcgtggagcaatggggattcatttctgatgt
attgacatcactaattgaaggagtctttttaatagtgttccagggttggt
gcactcaaatcaagncatactca
>CEESC16F
cccattttacaaatttatccagaggaatggattttcaattaaaatcttga
aaaaaactaaaaagtagagaaaattggaaactttggtgggtttaaacgtt
aaaagagattaaatttaaaaaaaaagggagatcgantcgaataatttggg
tggatgggatcattgtacaatataaatagaaaaaaaggaagagttcaatt
gggatagaaaaaaaaagtgaatttttttttttgataaggtagntagtgtg
ggtggtggcggga
>CEESC17F
tttcctgaaaccgtcagtcttacttctcgacgaaccgaccaatcatttgg
atttggaagcttgtgtgtggcttgaggaggaactcgctcagtataaaaga
acctngttggtggtttctcactctcaagatttcatgaacggagtttgcac
caacatcattcatttgttccaaaagcaattggnttactatggaggaaact
acgaccagtttgtgaagacacgtcttgaattgctcgaaaatcaacaaaaa
cgntacaactgggaacagtctcaactncaacacatgaaagattacgtcgc
gaggttcggtcacggttctgccaaactcgctcgtcaagctcaatncaaag
tgaaaa
>CEESC17RB
gaaaattcacacaaaacactacacatttagtgatgtgacaacaacaaagg
agggtaattggaaaaaaagggtagaaacaggaaccggaccaacaattgga
ggaaaaccgacaaaaattgggtcaaagagagtaaaagatgaatgaaaaca
agagaaaatataatcaaaatcacaggaaaatgnaattgaaatatcctana
ttgaanatggggggnaaggtgaataatgngagaaaaatctcgggaaatca
gttcgattctaatattagaattggcagattttcgatgttttcggggggaa
atagg
>CEESC18F
aagatcaatgatatggaatggtggaatcgattccttgattccgatcctcc
aatcaatactaaggaagtgaagccagagaactcgaaattgagcgacttgg
atggagagacacgtgccatggtcgaaaagatgatgcatgaactgttgcag
catatcatgcttttccttctcatcagacgttgcggcacgagctcgtgcna
aattcctgcagcccgggggatccactagttctagagcggccgccaccgcg
gtggagctccagcttttgttccctttagtgagggttaatttcgagcttgg
cgtaatcatgggtcatagctgtttcctgtgtgaaattgttatccgctcac
aattccacacaacatacgagccggaagcataaagtgtaaagcctgggggt
gcctaatgaagtgagctaactcacattaattgcggttgcg
>CEESC18R
ctcgtgccnaacgtctgatgagaagaaaaagcatgatatgctgcaacagt
tcatgcatcatcttttcgaccatggcacgtgtctctccatccaagtcgct
caatttcgagttctctggcttcacttccttagtattgattggaggatcgg
aatcaaggaatcgattccaccattccatatcattgatcttctcgaggggg
ggcccggtacccaattcgccctatagtgagtcgtattacaattcactggc
cgtcgttttacaacgtcgtgactgggaaaaccctggggttacccaacttt
aatcgccttgcagcacatccccctttcg
>CEESC19F
gctctcgactccatcattccaccacaacgcccaactgaccgaccactccg
tctcccactccaggatgtgtacaagatcggaggaatcggaactgttccag
tcggacgngttnagaccggaatcatcaagccaggaatggtcgttaccttc
gntccacaaaacgtcaccactgaagtcaagtccgttgagatgcatcacga
ntctnttccagaggccgtcccaggagacaacgttggattcaacgtcaaga
acgtctccgtcaaggatattcgtcgtggatccgtctgctccgactccaag
caagacccantcaaggaggcttcgnaccttccacgnccaggtcatcatca
tgaaccatccagggcagatctccaacggantacactccantt
>CEESC19R
tggatccccngggctgcaggnaaaaatcaacaagataaactcaacaatga
agatttacttcttctttggtgcagccttttgggcggacttggtgaccttt
ccagaggatccatcagacttctcaacggacttgataactccgacagcgac
ggtttgtctcatgtcacgaacggcgaaacgtccgagtngagcgtagtcgg
tgaaggattcaacacaaagtggcttggttgggatgagctcgacgattcca
gcatctncagacttgnggaactttgggaagtcctcaaccttgttaccggt
acgacggtcaaccttctacttaagctcgttgaacttt
>CEESC20F
aacaacaaaattgattttaattgaaggagaggtagagaatgaaaacttgt
gaattgaaaagaatagaaacaaaaaaattaaacagttatttagggcttat
ggcgaggggtaacgaatgagaaaagccctttaactgtgagataaagtaaa
aagaagaatgaaaaatagaaacaaaaaatatttaacagttatttagggct
gaggctaaagaatgaaaatccattaactgtgagagaaattgaatggaaga
atagaaaaaaaacaagttcaacagttattggttggcccaaaatcaacctc
gatgagcgcttttcggatggcttctgtgcgcacttcgagaaccttctcgt
tttcgacgttttcgagagcctctttctacg
>CEESC21F
gaagttgaggccaacgttccaaatgttatcaatgagcagctgagccggag
tattccgaagacatgcagtttgatcagtgatctttgtctgattgcagccg
acaagatcggctagtgctgttgatttttgttttgctcgtttcggagaatc
cattgaccacttgttgtcgagggatcctgattggagaattccgttttgga
ataatcccttcgacgccggtgcaattaagtgagctacaatcgaagctgct
ccagccgattctccaaccaacgatatcctcgccggatttcctccaaacga
gaaaatatgatcccttatccaataaagtgcgagttgttgatcaagcattc
ccatatttccaggnacatcttcatgatctagg
>CEESC21R
tcgtnccgaattcggcagagntncntatgtgaatatttgggctccggcgg
atgcttacaatcttactgtacttgtatggctgtttggtggtggcttctgg
tatggntccccatnactgttactttacgncggaaaagaactagcaacacg
tggaaatgtgatagtagtgaacatcaactatcgagttggaccatttggat
acctgtttctagatcatgaagatgttcctggaaatatgggaatgcttgat
caacaactcgcactttattggataagggatcatattt
>CEESC22F
aatcacaatgattttatagtcgaaaagaaataaaaaaacgcattatgctg
agggcttcgacatacaaagtggaaagggttgggggaaatacatggaaatt
nccttttttttttcggaaaaacaaatttttgttagtatttacaattacat
tttgttaccagtcagacaagttttttgagggaaaaaaatccaataaaaat
gagcatttttcagaaggacgtataatgtacacgaaggtggtngtgtnaaa
aggagacaacaaaagggaaaaattgcgggttaaaaatggccgggaaaacc
>CEESC23F
tttttttgttagagtattttatatatttattattattacagcttacagaa
ctttgatttgttttacagaaaaaaggtgcaaccgnttagacaaattcaat
ggattatcattatttgaaactttttgcagttccttattttcaaaaaaatc
ttggtttttggtttgatcagggtgagaaaggatttcgggggtcgaaagct
agaaaattatcaattttttgtgattttcgattgtg
>CEESC24F
gtcttattaaaagctttattatgaatgtggctcaaataatgagcatgatt
cagagaaaaaatggtttaaaatgtcaatttngtaatgagaaaatgggggt
catcggcagtaatagggtacaacaacaaaagtgattgcattaaacctcaa
cttcaaaccaaagttacacagngnacctagttatacatgcctagattact
accggantagtattgancaaatacaagagaagttaccaatgaagatttgg
gtgagantgggaagcataatgcagtcggctagagaagttgg
>CEESC25F
taaaccaatatgatttattattaaaattttaaaagaacaaaaacatgctt
tagaattccaaaaatgattttaaacaagtgaatgaaagtatcacaaatac
gaaaagagaacccgaagaagagaaaagaagaaattataaaaaaaatattt
tagagctccgacttttgaaggntcgaataccgtttatcagatggcttaag
ctctttgaacactgatggaggtggtgttgtgtcaattggacgagtagatg
gagcttgagcttcatgatcatcagtgattccacgtgcagcttttgccttg
gcgagctcgatcattcgttggatcaaggttctcgtggaagtccttgtgaa
gctttccagagtgaagatccataacaaactctctaagtttacctgggata
ttca
>CEESC26F
ctactcggcgaccagctccaccaagggaaacctcttcttctacctcaacg
cgttgatcatctccatcgccccgctctacctnttctacggagttcaccag
atggagatccaagactcgcttgtcgtgtggggactctntgccgtcggcac
tgcctacctcctgtccctggcctgcaaaaaccagaagtgccttctcaagc
atcaaatcgtgatgaagcgcggntcagctgtggaacgcgagatcagcgga
caatatgctgctgacaagaaaatgactgttaaggagaaggaggagcgcgc
gcttttccgcaaaaacgaggtcgncgacancgaatncacctacttgtcgg
tcttctacacaaantcgctctacttgaccat
>CEESC27F
tcgaaagtttctccagaatttcgatcaattcacagtcgattagactattc
actgaagactatgtcattctctcaggattacggagcaatcagtgaagaag
gaccaatagaagtaggatcaggaattttgaaggtggagtcaattgaatat
atttttgaatacgatgagaacatggntcaagtgaaaatcaaatgtttgtt
ggccccggaacttgtgagattctcgaatgataagtcaataatcagaagat
attttcattattacctggccgcttcacaacgaattgttcagcatgtcaaa
ctcagggaaagtgacagtccatttcgaaaccttcaaagcctaaaanttcc
atccatttcttgggactctaaacggagctagaggatatcctcaatttcat
caattt
>CEESC28F
gttgaaaaacatttcattgaaagatcgatttttggtaaagcagatcagtc
aaatttgaatgcagtgaaatgatgatctgtggggctggagagagcgattt
agtggcaacaattgaaacgnggtaacagggtgaaactttggtttgtgtca
aaaaattaattagttaaagcaaaaaaatgtggaaatgtcgggggaacaat
aaacatgttaacangantaaaaaaccgtggatttatggaatggctcttct
aacaatgttgttgcggaagaattcttgcattctgtgaaagtttccatcaa
cattgccaactatggctcgaatattcgcctgcactgggataataattgat
tcc
>CEESC29F
caagaagacaatttgttttgattggaaatggacgaatgatgaaaggaaat
aaacatcttttaaaactctacaagtatgggttttcttgaatatttctgga
actaatgaatacatatttncagacaccttcaatcggaaaaagtcatcttc
ggaccgtcaattctcgaaaccttcaacgatcttgaggaagctgctctacc
aagatcggataaattttgatttttggttgagcttaggtttttagatgata
gtattcagtttctaacggatattcacttcatgtaactattattgatntca
tattttnatgttt
>CEESC30F
agaaaatcaacaacaatttcatttgaatgaggaagagagtaacataacca
acaatgatgaataaaaaacaaagaaatgaacaatttttggggaggggcgc
ggggaaacgaacaataatggaaatagaagaaaagagcaaagcctacgtgc
agaatagagtgaaagcgggaaatatttctcttctgcgtctctttctgttt
gtgtgtgatttagaattccatactatccgtctttcggccttcgaccacaa
ctgaagtgataacatgtccgtcttcggtttccttggattcgagctcacgg
cgaatttcaggcgagatgagatagtgtccatggaatctgatcagctcata
aatagctgccttctgctcggcattcaaatccgttcttgtatcgctggcac
ag
>CEESC32F
gacggggaatggggagcaaaacaaagaacaatttgatatactataaacca
ggggactgggaaattgaaagcagagaaagttgggatcacagattatttta
tcagtttaatggtacttgcaaacagatggcactgtgcatccgtgcttctt
gatgatttcttgagcagcataagatccacaggtgactgaagcttcgactc
cctttcctttctctcgtgccgaattcctgcagcccgggggatccactagt
tctagagcggccgccaccgcggtggagctccagcttttgttccctttagt
gagggttaatttcgagcttggcgtaatcatggtcatagctgtttcctgtg
tgaaattgttatccgctcacaattncacacaacatacgagccggaagcat
aaagtgtaaagcctgggggtgcctaatgagtgag
>CEESC33F
aataaataaaattattttattaaagtattctcaaagtcaaaatggcaaat
aaagcttganccaaaattttgttcactattattattacaacttccttgct
aatttaatgtctccgccggttcttgaatagaactgatttggagcattata
tttttnagttccattggaagatgttgagaagtaggcagtgacatctggaa
tgacttgaggagtttgagaagcttttggcattgatacacccattcgacgg
ccacggtattcacagcttttnccgaaatatggacgttcacagcggcaggc
aaagttatagatagctggatttgttttcggtcgtggtaaa
>CEESC33R
tcggtctaccacaacaagactaccaataactactggtagtacacaaactg
gtgaaccgtttcggactatggcaatcaactgaaatggggtgaagtttggt
aggaaaacgaaaaaaagaagagaaagaagaagattgcactgccaacataa
gatggtcattgtgtggtaccatcaactactgctagtacttctgatattta
taggagctgccaaaggagctcagtacataggttcgggagcctcccaaccc
aaccgaacggatgttgtgtggatggttccctcttggacatgtaaaaatga
ntattcaattgatgtagaaaagtatgggattctgcaaaattgaggtncag
ca
>CEESC34F
ccgtagttntttttttttttttttanttttatgattttattttaacgtga
ataaacatcacaaaagtgagcttactcaaggggtggggtntggggcggct
aaaccaaccactaacaagtaacaaaaagaagggtgacagtaagananaaa
aacaggngatnggtatgcttagcaactnggggaacgtgctaagagcactt
ggcaatgaacttattgcttctgagcggaaacgngaaccgatgcagcttcg
tcgaccttcgagcggaacaattcactatcttgaagcatcatgatcaactc
ggaattt
>CEESC35R
ggagacaagggacgtgagcgtgacaacatcaaggaggatcagaccctcta
ctacaccgtccagctcgtcgatctgttccgcgctgtgccaggagagaagt
ggaccaccgatgagggaatcgttattgagcagacacacaagattgatgag
gataagtgcaagaagtcgaagagtggagacaccattcaccaacagtacgt
gcttcatcttnaggacggaactttcgtcgattcgtctttttntcgcaacg
ntccattcatcttcaagtttgaataattaatgaagtcattcaagggaatn
ggacattncccattgactggaattgttgcga
>CEESC36F
aagattttaataaaactttattgaaatttgctcaatatcagangtaaata
aatcagtatcaggataaatngtgaacagttatatttgcttctgtaaacag
ttgggatttgaattcagatgtaaatttacataactnctcgttgctgaact
tnatactccaaaatccatgtatccnctttatgactgangacaatanccgn
gaagttgtttatatgaatggncagttg
>CEESC37F
agtttgaatgtttttatttttttactttaaaaaaaaatttaatttcaaaa
ataaaaaaaaacagtttgtggcaaggaaaagggggaaaaattttntgagt
gggcgtggggaacaacttgagttttttgaaagagtcattttggcgggaaa
agcggaaattnttgcgaaatatctacccgttactcgcgtggctttttgta
gnctaaaactttagtagaggaggagaaagaaaaanctggggaaaaaaatt
tgggtcacagnaaaaaaatgcaattgattagcaancgcaagaaggtgggt
agagcgtgtgaaa


>CEESC39F
agaattttagtgttttattgaattgttgaatacaaatcaataaaaaaata
acatatgancggttattatgactttctttcatatatatatcccatatatg
ggtttaccaaaatgtgcacgaaatgaatacaaataaattatttaatcagt
gtccatcttcgcctcgaaacggcttcccaacccggtttcacttccagcga
ctcctctattcacactatccagaacagagttccagtcgacgccgaatcga
tcggttctttcttggattcgaagcacaacttggagagcatcagtggcgac
agtcttcttctgttgagcacacagctcgtcggcctgctccaaaatgttgt
caatcagcttcccagcggccactgg


>CEESC40R
cagagttacaaataaaagcgggcaacaatgtcagaaaaatcattgcaatc
gaaaatnctttctactgtatttttncttgcaactctaattgcatttnctt
ctgccgatggatatacctgtnccggaaatacgctgataaatccatttntn
aatctttcggagccctactactatccagggncatggcgagaaaacatgga
accagctgantatgctccagntcaaaagtgtaactggaagatca

>CEESC41F
aagaagaggatatatttatccaaactgcaacaacaaaaaacacaacaata
taacttgaaaaataaaatacgctcataaaaaaacaattttaaaaattaaa
aattattccttgtgctcggncaattgaaatcctgccttcgtcgagttcac
tgatccntttgctttctggcgagggccccaattcttccctttattgcatt
ggnaccgtacaaggntctctttcttggnctgttcgatggctccngggtga
agagtgaagttgactgtgttggtgatgggttntcccagaatgtgatatcc
ngctgattctttggccagacg
BioPerl-1.007002/t/data/spaces.nex000444000766000024        72513155576321 16646 0ustar00cjfieldsstaff000000000000#NEXUS
BEGIN TREES;

   TRANSLATE
   1   'Allium drummondii',
   2   'Allium cernuum',
   3    A.cyaneum     
   ;
   TREE onion = [&R] ((1,2),3);
END;

#NEXUS
BEGIN TREES;

   TRANSLATE
   1   'Allium drummondii, USA',
   2   'Allium drummondii, Russia',
   3    A.cyaneum
   ;
   TREE onion = [&R] ((1,2),3);
END;

#NEXUS
BEGIN TREES;

   TRANSLATE 1   'Allium drummondii, Russia', 2   'Allium drummondii, USA', 3    A.cyaneum ;
   TREE onion = [&R] ((1,2),3);
END;

BioPerl-1.007002/t/data/sparsealn.needle000444000766000024       311613155576321 20037 0ustar00cjfieldsstaff000000000000########################################
# Program:  needle
# Rundate:  Wed Mar 13 14:01:53 2002
# Report_file: out.water
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: KV1K_HUMAN
# 2: IF1Y_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 238
# Identity:       5/238 ( 2.1%)
# Similarity:     9/238 ( 3.8%)
# Gaps:         225/238 (94.5%)
# Score: 18.0
# 
#
#=======================================

KV1K_HUMAN         1 DIQMTQSPSTLSVSVGDRVTITCEASQTVLSYLNWYQQKPGKAPKLLIYA     50
                                                                       
IF1Y_HUMAN         1                                                         0

KV1K_HUMAN        51 ASSLETGVPSRFSGQGSGTBFTFTISSVZPZBFATYYCQZYLDLPRTFGQ    100
                                                                 |:..|:
IF1Y_HUMAN         1                                             PKNKGK      6

KV1K_HUMAN       101 GTKVDLKR                                              108
                     |.| :.:|                                          
IF1Y_HUMAN         7 GGK-NRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEALCFDGVK     55

KV1K_HUMAN       109                                                       108
                                                                       
IF1Y_HUMAN        56 RLCHIRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEARSLKAY    105

KV1K_HUMAN       109                                           108
                                                           
IF1Y_HUMAN       106 GGLPEHAKINETDTFGPGDDDEIQFDDIGDDDEDIDDI    143
BioPerl-1.007002/t/data/spidey.noalignment000444000766000024        23213155576321 20377 0ustar00cjfieldsstaff000000000000--SPIDEY version 1.40--
Genomic: lcl|chr1 No definition line found, 187448317 bp
mRNA: lcl|tmpseq_0 No definition line found, 663 bp
No alignment found.

BioPerl-1.007002/t/data/spidey.test1000444000766000024      1405313155576321 17172 0ustar00cjfieldsstaff000000000000--SPIDEY version 1.40--
Genomic: lcl|chr2 No definition line found, 145732769 bp
mRNA: lcl|tmpseq_0 No definition line found, 1110 bp
Strand: minus
Number of exons: 6
Exon 1(-): 36375691-36375798 (gen)  1-108 (mRNA)  id 97.2% mismatches 3 gaps 0  splice site (d  a): 1  0
Exon 2(-): 36369345-36369492 (gen)  109-256 (mRNA)  id 100.0% mismatches 0 gaps 0  splice site (d  a): 0  1
Exon 3(-): 36367232-36367437 (gen)  257-462 (mRNA)  id 100.0% mismatches 0 gaps 0  splice site (d  a): 1  1
Exon 4(-): 36364083-36364229 (gen)  463-609 (mRNA)  id 100.0% mismatches 0 gaps 0  splice site (d  a): 1  1
Exon 5(-): 36358231-36358489 (gen)  610-868 (mRNA)  id 100.0% mismatches 0 gaps 0  splice site (d  a): 1  1
Exon 6(-): 36356457-36356698 (gen)  869-1110 (mRNA)  id 100.0% mismatches 0 gaps 0  splice site (d  a): 0  1
Number of splice sites: 4
mRNA coverage: 100%
overall percent identity: 99.7%
Missing mRNA ends: neither 

Genomic: lcl|chr2 No definition line found
mRNA: lcl|tmpseq_0 No definition line found
Exon 1: 36375798-36375691 (gen)  1-108 (mRNA)


CCTCTTTTTCTTTGCAGGGTATATACCCAGTTACTTAGACAAGGATGAGCTATGTGTAGT
           |  ||||||||||||||||||||||||||||||||||||||||||||||
          ATGTCAGGGTATATACCCAGTTACTTAGACAAGGATGAGCTATGTGTAGT
           M  S  G  Y  I  P  S  Y  L  D  K  D  E  L  C  V  V 


ATGTGGGGACAAAGCCACCGGATATCATTATCGCTGCATCACTTGTGAAGGTTGCAAGGT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ATGTGGGGACAAAGCCACCGGATATCATTATCGCTGCATCACTTGTGAAGGTTGCAAG
  C  G  D  K  A  T  G  Y  H  Y  R  C  I  T  C  E  G  C  K 


AAATGGCA

Exon 2: 36369492-36369345 (gen)  109-256 (mRNA)


TTGCACTTAGGGATTTTTCAGAAGAACCATTCAGAAAAACCTCCATCCAACCTATTCCTG
          ||||||||||||||||||||||||||||||||||||||||||||||||||
          GGATTTTTCAGAAGAACCATTCAGAAAAACCTCCATCCAACCTATTCCTG
           G  F  F  R  R  T  I  Q  K  N  L  H  P  T  Y  S  C 


TAAATATGAAGGAAAATGTGTGATAGACAAAGTAACAAGAAATCAGTGCCAGGAATGTCG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TAAATATGAAGGAAAATGTGTGATAGACAAAGTAACAAGAAATCAGTGCCAGGAATGTCG
  K  Y  E  G  K  C  V  I  D  K  V  T  R  N  Q  C  Q  E  C  R 


CTTCAAAAAATGTATCTTTGTTGGCATGGCAACAGATTGTGAGTATAT
||||||||||||||||||||||||||||||||||||||
CTTCAAAAAATGTATCTTTGTTGGCATGGCAACAGATT
  F  K  K  C  I  F  V  G  M  A  T  D 


Exon 3: 36367437-36367232 (gen)  257-462 (mRNA)


TCCCTGCTAGTGGTGTTGGATGACAGCAAGAGGCTGGCAAAGAGGAAGCTGATAGAAGAA
          ||||||||||||||||||||||||||||||||||||||||||||||||||
          TGGTGTTGGATGACAGCAAGAGGCTGGCAAAGAGGAAGCTGATAGAAGAA
          L  V  L  D  D  S  K  R  L  A  K  R  K  L  I  E  E 


AATCGAGAGAAGAGGCGTCGGGAAGAGCTGCAGAAAACGATTGGTCACAAACCAGAACCA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AATCGAGAGAAGAGGCGTCGGGAAGAGCTGCAGAAAACGATTGGTCACAAACCAGAACCA
 N  R  E  K  R  R  R  E  E  L  Q  K  T  I  G  H  K  P  E  P 


ACAGATGAGGAATGGGAGCTGATCAAAATTGTCACTGAAGCACATGTGGCCACCAATGCA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ACAGATGAGGAATGGGAGCTGATCAAAATTGTCACTGAAGCACATGTGGCCACCAATGCA
 T  D  E  E  W  E  L  I  K  I  V  T  E  A  H  V  A  T  N  A 


CAAGGAAGCCACTGGAAGCAGAAAAGGAAATTTCTGGTAGGGACTA
||||||||||||||||||||||||||||||||||||
CAAGGAAGCCACTGGAAGCAGAAAAGGAAATTTCTG
 Q  G  S  H  W  K  Q  K  R  K  F  L 


Exon 4: 36364229-36364083 (gen)  463-609 (mRNA)


ATATCCTTAGCCAGAAGACATTGGGCAAGCACCAATAGTTAATGCCCCAGAAGGGGGGAA
          ||||||||||||||||||||||||||||||||||||||||||||||||||
          CCAGAAGACATTGGGCAAGCACCAATAGTTAATGCCCCAGAAGGGGGGAA
           P  E  D  I  G  Q  A  P  I  V  N  A  P  E  G  G  K 


AGTGGATTTAGAAGCCTTCAGCCAGTTTACAAAAATTATCACACCAGCGATTACAAGAGT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AGTGGATTTAGAAGCCTTCAGCCAGTTTACAAAAATTATCACACCAGCGATTACAAGAGT
  V  D  L  E  A  F  S  Q  F  T  K  I  I  T  P  A  I  T  R  V 


GGTGGATTTTGCCAAAAAGTTGCCTATGTTTTGTGAGGTAAGACAAA
|||||||||||||||||||||||||||||||||||||
GGTGGATTTTGCCAAAAAGTTGCCTATGTTTTGTGAG
  V  D  F  A  K  K  L  P  M  F  C  E 


Exon 5: 36358489-36358231 (gen)  610-868 (mRNA)


ATTTCTGCAGCTGCCATGTGAAGACCAGATCATCCTTCTGAAAGGCTGCTGTATGGAGAT
          ||||||||||||||||||||||||||||||||||||||||||||||||||
          CTGCCATGTGAAGACCAGATCATCCTTCTGAAAGGCTGCTGTATGGAGAT
           L  P  C  E  D  Q  I  I  L  L  K  G  C  C  M  E  I 


AATGTCCCTCCGAGCAGCAGTTCGCTATGACCCCGAGAGTGAGACTTTAACGCTAAATGG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AATGTCCCTCCGAGCAGCAGTTCGCTATGACCCCGAGAGTGAGACTTTAACGCTAAATGG
  M  S  L  R  A  A  V  R  Y  D  P  E  S  E  T  L  T  L  N  G 


GGAGATGGCGGTGACAAGGGGCCAGCTGAAAAATGGGGGTCTTGGCGTAGTTTCTGATGC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GGAGATGGCGGTGACAAGGGGCCAGCTGAAAAATGGGGGTCTTGGCGTAGTTTCTGATGC
  E  M  A  V  T  R  G  Q  L  K  N  G  G  L  G  V  V  S  D  A 


CATTTTTGACCTGGGCATGTCTCTTTCTTCATTTAACCTGGATGACACCGAGGTTGCCCT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATTTTTGACCTGGGCATGTCTCTTTCTTCATTTAACCTGGATGACACCGAGGTTGCCCT
  I  F  D  L  G  M  S  L  S  S  F  N  L  D  D  T  E  V  A  L 


TCTCCAGGCTGTCCTGCTCATGTCATCAGGTGAGAACAG
|||||||||||||||||||||||||||||
TCTCCAGGCTGTCCTGCTCATGTCATCAG
  L  Q  A  V  L  L  M  S  S 


Exon 6: 36356698-36356457 (gen)  869-1110 (mRNA)


GTATCTGCAGATCGCCCAGGCCTTGTTTGCGTCGAGAGAATAGAAAAGTGTCAAGAGGGT
          ||||||||||||||||||||||||||||||||||||||||||||||||||
          ATCGCCCAGGCCTTGTTTGCGTCGAGAGAATAGAAAAGTGTCAAGAGGGT
          D  R  P  G  L  V  C  V  E  R  I  E  K  C  Q  E  G 


TTCCTCCTGGCATTTGAACACTACATTAATTACAGAAAACACCATGTTGCACATTTTTGG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TTCCTCCTGGCATTTGAACACTACATTAATTACAGAAAACACCATGTTGCACATTTTTGG
 F  L  L  A  F  E  H  Y  I  N  Y  R  K  H  H  V  A  H  F  W 


CCAAAACTGCTGATGAAAGTGACAGATCTGCGAATGATTGGAGCCTGCCATGCCAGCCGC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CCAAAACTGCTGATGAAAGTGACAGATCTGCGAATGATTGGAGCCTGCCATGCCAGCCGC
 P  K  L  L  M  K  V  T  D  L  R  M  I  G  A  C  H  A  S  R 


TTCCTGCACATGAAGGTGGAGTGCCCCACAGAACTCTTCCCTCCATTGTTCCTGGAGGTG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TTCCTGCACATGAAGGTGGAGTGCCCCACAGAACTCTTCCCTCCATTGTTCCTGGAGGTG
 F  L  H  M  K  V  E  C  P  T  E  L  F  P  P  L  F  L  E  V 


TTTGAGGATTAGAGAGACTGGA
||||||||||||
TTTGAGGATTAG
 F  E  D  * 


BioPerl-1.007002/t/data/sprintf.rnamotif000444000766000024     12641613155576321 20170 0ustar00cjfieldsstaff000000000000#RM scored
#RM descr h5 ss h3
#RM dfile sprintf.descr
>gi|173609|gb|M28984|ACARRDX A.castellani 5S ribosomal RNA
gi|173609|gb|M28984|ACARRDX -12.500,6,gcga 0      81   16 gggtgg gcga ccaccc
>gi|1236163|gb|L41047|ANNRRO Actinoplanes sp. ribosomal RNA (rRNA)
gi|1236163|gb|L41047|ANNRRO -15.400,6,gaaa 0     110   16 ccccgg gaaa ccgggg
>gi|1236163|gb|L41047|ANNRRO Actinoplanes sp. ribosomal RNA (rRNA)
gi|1236163|gb|L41047|ANNRRO -12.100,5,gaaa 0     111   14 cccgg gaaa ccggg
>gi|173741|gb|M83548|AQF16SRRN Aquifex pyrophilus 16S ribosomal RNA (16S rRNA)
gi|173741|gb|M83548|AQF16SRRN -15.400,6,gaaa 0     154   16 ccccgg gaaa ccgggg
>gi|173741|gb|M83548|AQF16SRRN Aquifex pyrophilus 16S ribosomal RNA (16S rRNA)
gi|173741|gb|M83548|AQF16SRRN -12.100,5,gaaa 0     155   14 cccgg gaaa ccggg
>gi|173741|gb|M83548|AQF16SRRN Aquifex pyrophilus 16S ribosomal RNA (16S rRNA)
gi|173741|gb|M83548|AQF16SRRN -14.900,7,gaaa 0    1028   18 actccgc gaaa gcggagt
>gi|173741|gb|M83548|AQF16SRRN Aquifex pyrophilus 16S ribosomal RNA (16S rRNA)
gi|173741|gb|M83548|AQF16SRRN -13.200,6,gaaa 0    1029   16 ctccgc gaaa gcggag
>gi|173748|gb|M64487|ARFRRLSA A.fulgicus large subunit ribosomal RNA
gi|173748|gb|M64487|ARFRRLSA -12.700,7,ttac 0     137   18 cgctccc ttac gggagcg
>gi|173748|gb|M64487|ARFRRLSA A.fulgicus large subunit ribosomal RNA
gi|173748|gb|M64487|ARFRRLSA -15.500,7,gtaa 1     154   18 cgctccc gtaa gggagcg
>gi|173748|gb|M64487|ARFRRLSA A.fulgicus large subunit ribosomal RNA
gi|173748|gb|M64487|ARFRRLSA -13.100,6,gtaa 1     153   16 gctccc gtaa gggagc
>gi|470692|gb|M82686|ARIRRE05 Aristolochia gigantea 18S ribosomal RNA (18S rRNA), ca. bp 1203 to 1414 in mature rRNA
gi|470692|gb|M82686|ARIRRE05 -12.200,7,gtca 1     174   18 gtggagg gtca cctccac
>gi|470705|gb|M82700|ARURRE05 Arundinaria gigantea 18S ribosomal RNA (18S rRNA), ca. bp 1204 to 1414 in mature rRNA
gi|470705|gb|M82700|ARURRE05 -12.000,7,catc 0     156   18 gcggagg catc cctccgc
>gi|470705|gb|M82700|ARURRE05 Arundinaria gigantea 18S ribosomal RNA (18S rRNA), ca. bp 1204 to 1414 in mature rRNA
gi|470705|gb|M82700|ARURRE05 -12.700,7,gatg 1     173   18 gcggagg gatg cctccgc
>gi|470750|gb|M82449|AVORRE05 Persea borbonia 18S ribosomal RNA (18S rRNA), ca. bp 1205 to 1414 in mature rRNA
gi|470750|gb|M82449|AVORRE05 -12.200,7,gata 1     172   18 gtggagg gata cctccac
>gi|439580|gb|L15530|AZORR16SA Azoarcus sp. (strain BH72) 16S ribosomal RNA (16S rRNA)
gi|439580|gb|L15530|AZORR16SA -12.500,5,ttcg 0      76   14 ggggc ttcg gcccc
>gi|173823|gb|M79434|BAIRRDG02 Bacterial sp. (TH3) 16S rRNA sequence
gi|173823|gb|M79434|BAIRRDG02 -13.100,6,gaaa 0      52   16 caccgg gaaa ccggtg
>gi|603438|gb|L26511|BEDERRNAA Berndtia purpurea 18S ribosomal RNA (18S rRNA)
gi|603438|gb|L26511|BEDERRNAA -13.100,6,gaaa 1     816   16 caggcg gaaa cgcctg
>gi|304227|gb|L19406|BODRR24SA Bodo caudatus 24S ribosomal RNA large subunit
gi|304227|gb|L19406|BODRR24SA -15.400,6,gaaa 0     512   16 cccggg gaaa cccggg
>gi|304227|gb|L19406|BODRR24SA Bodo caudatus 24S ribosomal RNA large subunit
gi|304227|gb|L19406|BODRR24SA -12.100,5,gaaa 0     513   14 ccggg gaaa cccgg
>gi|173977|gb|M97571|BRARREA Branchiostoma floridae 18S ribosomal RNA (18S rRNA), 5' end
gi|173977|gb|M97571|BRARREA -12.200,6,ttcg 0     225   16 ccgggg ttcg ccccgg
>gi|470792|gb|M82728|BRERRE05 Brasenia schreberi 18S ribosomal RNA (18S rRNA), ca. bp 1238 to 1414 in mature rRNA
gi|470792|gb|M82728|BRERRE05 -12.200,7,ggta 1     139   18 gtggagg ggta cctccac
>gi|289579|gb|L14636|CCYRRDB Capnocytophaga sputigena 16S ribosomal RNA
gi|289579|gb|L14636|CCYRRDB -12.400,7,ttcg 0      74   18 ggttacc ttcg ggtaacc
>gi|174069|gb|M34116|CFXRRDA C.aurantiacus 16S ribosomal RNA
gi|174069|gb|M34116|CFXRRDA -13.200,6,gaaa 0     141   16 cccgtc gaaa gacggg
>gi|174076|gb|M62791|CHBRRDAA C.vibrioforme 16S ribosomal RNA
gi|174076|gb|M62791|CHBRRDAA -12.200,6,gaaa 0     148   16 ccccga gaaa tcgggg
>gi|174079|gb|M31769|CHBSSRNA C.limicola ribosomal RNA small subunit
gi|174079|gb|M31769|CHBSSRNA -12.200,6,gaaa 0     146   16 ccccga gaaa tcgggg
>gi|174102|gb|K03164|CHKUR5B Chicken U5B small nuclear RNA, complete
gi|174102|gb|K03164|CHKUR5B -16.200,7,ttcg 0      97   18 gctccgc ttcg gcggagc
>gi|174102|gb|K03164|CHKUR5B Chicken U5B small nuclear RNA, complete
gi|174102|gb|K03164|CHKUR5B -12.800,6,ttcg 0      98   16 ctccgc ttcg gcggag
>gi|174102|gb|K03164|CHKUR5B Chicken U5B small nuclear RNA, complete
gi|174102|gb|K03164|CHKUR5B -12.400,7,cgaa 1     114   18 gctccgc cgaa gcggagc
>gi|174103|gb|K00474|CHKURU4A Chicken U4a small nuclear RNA (snRNA)
gi|174103|gb|K00474|CHKURU4A -12.000,7,tacg 0     128   18 cagtctc tacg gagactg
>gi|174104|gb|K00475|CHKURU4B Chicken U4b small nuclear RNA (snRNA)
gi|174104|gb|K00475|CHKURU4B -12.000,7,tacg 0     128   18 cagtctc tacg gagactg
>gi|174144|gb|M59092|CLORR16SR Clostridium kluyveri 16S ribosomal RNA
gi|174144|gb|M59092|CLORR16SR -13.700,7,atcg 0     809   18 ggggggt atcg acccccc
>gi|174144|gb|M59092|CLORR16SR Clostridium kluyveri 16S ribosomal RNA
gi|174144|gb|M59092|CLORR16SR -13.100,7,cgat 1     826   18 ggggggt cgat acccccc
>gi|174209|gb|M20058|CRSRREA3 Chiton (C.stelleri) 18S rRNA, segment 3 of 3
gi|174209|gb|M20058|CRSRREA3 -12.900,5,ggaa 0     118   14 ggccc ggaa gggcc
>gi|174273|gb|M59057|DEOSSRNA Dermatophilus congolensis small subunit ribosomal RNA sequence
gi|174273|gb|M59057|DEOSSRNA -12.100,5,gaaa 0     151   14 ccccg gaaa cgggg
>gi|470912|gb|M82693|DRIRRE05 Drimys aromatica 18S ribosomal RNA (18S rRNA), ca. bp 1203 to 1414 in mature rRNA
gi|470912|gb|M82693|DRIRRE05 -15.200,7,gtga 1     174   18 gtggagg gtga cctccac
>gi|470912|gb|M82693|DRIRRE05 Drimys aromatica 18S ribosomal RNA (18S rRNA), ca. bp 1203 to 1414 in mature rRNA
gi|470912|gb|M82693|DRIRRE05 -12.500,6,gtga 1     173   16 tggagg gtga cctcca
>gi|174363|gb|K01260|ECOPRM1 Escherichia coli 10sb (M1) RNA; the RNA component of RNase P
gi|174363|gb|K01260|ECOPRM1 -12.000,5,gcaa 0     152   14 cccgc gcaa gcggg
>gi|174493|gb|M59388|ELERR18S E.cuneatus 18S ribosomal RNA
gi|174493|gb|M59388|ELERR18S -13.300,6,gaaa 0     728   16 gtcgcc gaaa ggcgac
>gi|174566|gb|M62683|FIBRR16SB Fibrobacter succinogenes succinogenes (strain A3C) 16S ribosomal RNA
gi|174566|gb|M62683|FIBRR16SB -12.900,6,gttc 0     814   16 ccgggg gttc ccccgg
>gi|174566|gb|M62683|FIBRR16SB Fibrobacter succinogenes succinogenes (strain A3C) 16S ribosomal RNA
gi|174566|gb|M62683|FIBRR16SB -12.900,6,gaac 1     829   16 ccgggg gaac ccccgg
>gi|174567|gb|M62684|FIBRR16SC Fibrobacter succinogenes succinogenes (strain B1) 16S ribosomal RNA
gi|174567|gb|M62684|FIBRR16SC -12.900,6,gttc 0     810   16 ccgggg gttc ccccgg
>gi|174567|gb|M62684|FIBRR16SC Fibrobacter succinogenes succinogenes (strain B1) 16S ribosomal RNA
gi|174567|gb|M62684|FIBRR16SC -12.900,6,gaac 1     825   16 ccgggg gaac ccccgg
>gi|174568|gb|M62685|FIBRR16SD Fibrobacter succinogenes succinogenes (strain BL2) 16S ribosomal RNA
gi|174568|gb|M62685|FIBRR16SD -12.900,6,gttc 0     810   16 ccgggg gttc ccccgg
>gi|174568|gb|M62685|FIBRR16SD Fibrobacter succinogenes succinogenes (strain BL2) 16S ribosomal RNA
gi|174568|gb|M62685|FIBRR16SD -12.900,6,gaac 1     825   16 ccgggg gaac ccccgg
>gi|174570|gb|M62687|FIBRR16SF Fibrobacter intestinalis (strain DR7) 16S ribosomal RNA
gi|174570|gb|M62687|FIBRR16SF -13.900,6,gcga 0     816   16 cccggg gcga cccggg
>gi|174572|gb|M62689|FIBRR16SH Fibrobacter succinogenes (strain HM2) 16S ribosomal RNA
gi|174572|gb|M62689|FIBRR16SH -12.200,6,ttcg 0     809   16 ccgggg ttcg ccccgg
>gi|174573|gb|M62690|FIBRR16SI Fibrobacter intestinalis (strain JG1) 16S ribosomal RNA
gi|174573|gb|M62690|FIBRR16SI -13.900,6,gcga 0     816   16 cccggg gcga cccggg
>gi|174574|gb|M62691|FIBRR16SJ Fibrobacter intestinalis (strain LH1) 16S ribosomal RNA
gi|174574|gb|M62691|FIBRR16SJ -13.900,6,gcga 0     816   16 cccggg gcga cccggg
>gi|174576|gb|M62693|FIBRR16SL Fibrobacter succinogenes (strain MC1) 16S ribosomal RNA
gi|174576|gb|M62693|FIBRR16SL -12.100,6,acat 0     168   16 ccccgg acat ccgggg
>gi|174576|gb|M62693|FIBRR16SL Fibrobacter succinogenes (strain MC1) 16S ribosomal RNA
gi|174576|gb|M62693|FIBRR16SL -12.200,6,ttcg 0     808   16 ccgggg ttcg ccccgg
>gi|174576|gb|M62693|FIBRR16SL Fibrobacter succinogenes (strain MC1) 16S ribosomal RNA
gi|174576|gb|M62693|FIBRR16SL -12.100,6,atgt 1     183   16 ccccgg atgt ccgggg
>gi|174579|gb|M62696|FIBRR16SO Fibrobacter succinogenes (strain S85) 16S ribosomal RNA
gi|174579|gb|M62696|FIBRR16SO -12.900,6,gttc 0     811   16 ccgggg gttc ccccgg
>gi|174579|gb|M62696|FIBRR16SO Fibrobacter succinogenes (strain S85) 16S ribosomal RNA
gi|174579|gb|M62696|FIBRR16SO -12.900,6,gaac 1     826   16 ccgggg gaac ccccgg
>gi|174591|gb|M59231|FLXRR16S Flexistipes sinusarabici small subunit rRNA
gi|174591|gb|M59231|FLXRR16S -13.600,6,ttcg 0      76   16 cctccc ttcg gggagg
>gi|174592|gb|L11306|FRARRDX Frankia sp. 16S ribosomal RNA
gi|174592|gb|L11306|FRARRDX -12.100,5,gaaa 0     143   14 cccgg gaaa ccggg
>gi|174596|gb|M97575|FSARREE Petromyzon marinus 18S ribosomal RNA (18S rRNA), 5' end
gi|174596|gb|M97575|FSARREE -12.500,6,gcga 0    1714   16 gggcag gcga ctgccc
>gi|174670|gb|M91611|GAORRITSA Gastrosuillus laricinus ribosomal RNA internal transcribed spacer
gi|174670|gb|M91611|GAORRITSA -13.100,6,gcga 0      89   16 cgcggg gcga cccgcg
>gi|174671|gb|M91612|GAORRITSB Gastrosuillus luricinus ribosomal RNA internal transcribed spacer
gi|174671|gb|M91612|GAORRITSB -13.100,6,gcga 0     105   16 cgcggg gcga cccgcg
>gi|695346|gb|L36199|HBMRRDM Heliobacillus mobilis 16S ribosomal RNA (16S rRNA)
gi|695346|gb|L36199|HBMRRDM -13.800,6,gaaa 0     152   16 cagccc gaaa gggctg
>gi|174809|gb|M37643|HECRR16SB Helicobacter felis 16S rRNA
gi|174809|gb|M37643|HECRR16SB -12.700,7,gaaa 0     962   18 tccccta gaaa tagggga
>gi|174838|gb|L04675|HLO16SRRNA Heliothrix oregonensis 16S ribosomal RNA (16S rRNA), partial rRNA
gi|174838|gb|L04675|HLO16SRRNA -12.800,5,gaaa 1      38   14 ccccc gaaa ggggg
>gi|174913|gb|M23820|HUMRRAUA Human U5-A ribosomal RNA
gi|174913|gb|M23820|HUMRRAUA -12.500,7,cttg 0     101   18 gccttgc cttg gcaaggc
>gi|174913|gb|M23820|HUMRRAUA Human U5-A ribosomal RNA
gi|174913|gb|M23820|HUMRRAUA -12.500,7,caag 1     118   18 gccttgc caag gcaaggc
>gi|174944|gb|K00472|HUMURU4B Human U4b small nuclear RNA (snRNA)
gi|174944|gb|K00472|HUMURU4B -12.000,7,tacg 0     128   18 cagtctc tacg gagactg
>gi|174959|gb|M32851|HYM28SRRNA Hymenochirus curtipes 28S ribosomal RNA, complete
gi|174959|gb|M32851|HYM28SRRNA -13.300,7,cgcg 0     335   18 agccgcg cgcg cgcggct
>gi|174959|gb|M32851|HYM28SRRNA Hymenochirus curtipes 28S ribosomal RNA, complete
gi|174959|gb|M32851|HYM28SRRNA -13.300,7,cgcg 1     352   18 agccgcg cgcg cgcggct
>gi|175002|gb|M97573|LARRREC Lampetra aepyptera 18S ribosomal RNA (18S rRNA), 5' end
gi|175002|gb|M97573|LARRREC -12.500,6,gcga 0    1714   16 gggcag gcga ctgccc
>gi|471872|gb|M82532|LAURRE05 Lactuca sativa 18S ribosomal RNA (18S rRNA), ca. bp 1205 to 1414 in mature rRNA
gi|471872|gb|M82532|LAURRE05 -12.200,7,gata 1     172   18 gtggagg gata cctccac
>gi|175039|gb|M23727|LBARRNAV L.vitulinus 16S ribosomal RNA small subunit
gi|175039|gb|M23727|LBARRNAV -13.400,6,gaga 0    1000   16 gggacg gaga cgtccc
>gi|175044|gb|M23729|LBARRNAZ L.catenaforme 16S ribosomal RNA small subunit
gi|175044|gb|M23729|LBARRNAZ -15.700,7,gaga 0    1000   18 tcgcgcg gaga cgcgcga
>gi|175044|gb|M23729|LBARRNAZ L.catenaforme 16S ribosomal RNA small subunit
gi|175044|gb|M23729|LBARRNAZ -13.800,6,gaga 0    1001   16 cgcgcg gaga cgcgcg
>gi|471885|gb|M82539|LIQRRE05 Liquidambar styraciflua 18S ribosomal RNA (18S rRNA), ca. bp 1205 to 1414 in mature rRNA
gi|471885|gb|M82539|LIQRRE05 -12.200,7,gtca 1     172   18 gtggagg gtca cctccac
>gi|175140|gb|M58822|LISRR16ST Listeria monocytogenes 16S ribosomal RNA
gi|175140|gb|M58822|LISRR16ST -13.300,6,gaaa 0     153   16 ctccgg gaaa ccggag
>gi|951043|gb|L33974|LTTRRD Leptothrix discophora (strain SP-6) 16S ribosomal RNA (16S rRNA)
gi|951043|gb|L33974|LTTRRD -12.000,5,gaaa 0     135   14 ccggc gaaa gccgg
>gi|504534|gb|L33979|LTTRRDB Leptothrix cholodnii (strain LMG 7171) 16S ribosomal RNA (16S rRNA)
gi|504534|gb|L33979|LTTRRDB -12.000,5,gaaa 0     135   14 ccggc gaaa gccgg
>gi|504535|gb|L33981|LTTRRDC Leptothrix sp. (strain NC-1) 16S ribosomal RNA (16S rRNA)
gi|504535|gb|L33981|LTTRRDC -12.000,5,gaaa 0     135   14 ccggc gaaa gccgg
>gi|308922|gb|L10943|MABRRI Marine Eubacterial sp. (aggregate agg27) PCR generated ribosomal RNA fragment
gi|308922|gb|L10943|MABRRI -12.100,7,acat 0      81   18 gggagag acat ctctccc
>gi|308922|gb|L10943|MABRRI Marine Eubacterial sp. (aggregate agg27) PCR generated ribosomal RNA fragment
gi|308922|gb|L10943|MABRRI -12.100,7,atgt 1      98   18 gggagag atgt ctctccc
>gi|175375|gb|M95654|MTBRRDB Methylobacterium sp. 16S ribosomal RNA
gi|175375|gb|M95654|MTBRRDB -12.600,7,cttg 0     776   18 tggcctg cttg caggcca
>gi|175375|gb|M95654|MTBRRDB Methylobacterium sp. 16S ribosomal RNA
gi|175375|gb|M95654|MTBRRDB -12.600,7,caag 1     793   18 tggcctg caag caggcca
>gi|175376|gb|M95655|MTBRRDC Methylobacterium sp. 16S ribosomal RNA
gi|175376|gb|M95655|MTBRRDC -12.600,7,cttg 0     776   18 tggcctg cttg caggcca
>gi|175376|gb|M95655|MTBRRDC Methylobacterium sp. 16S ribosomal RNA
gi|175376|gb|M95655|MTBRRDC -12.600,7,caag 1     793   18 tggcctg caag caggcca
>gi|175408|gb|M14414|MUSRRMA Mouse 5.4S ribosomal small nuclear RNA
gi|175408|gb|M14414|MUSRRMA -14.000,6,gaaa 1      44   16 ccctcc gaaa ggaggg
>gi|175433|gb|M10328|MUSUR57S Mouse 5.7S U4 small nuclear RNA type a
gi|175433|gb|M10328|MUSUR57S -12.000,7,tacg 0     128   18 cagtctc tacg gagactg
>gi|175434|gb|M18004|MUSUR57T Mouse 5.7S U4 small nuclear RNA type b
gi|175434|gb|M18004|MUSUR57T -12.000,7,tacg 0     128   18 cagtctc tacg gagactg
>gi|175446|gb|M59126|MVORR16SY Methanococcus jannaschii 16S ribosomal RNA
gi|175446|gb|M59126|MVORR16SY -13.700,6,ttcg 0      65   16 gctccc ttcg gggagc
>gi|175555|gb|L06168|NGORR16SB Neisseria flavescens 16S ribosomal RNA
gi|175555|gb|L06168|NGORR16SB -13.300,6,gaga 0    1005   16 cctccg gaga cggagg
>gi|294001|gb|L16523|NYSRR23S Nyssa sativa 26S ribosomal RNA
gi|294001|gb|L16523|NYSRR23S -15.200,7,gaaa 0      88   18 gccagag gaaa ctctggc
>gi|175717|gb|M59064|PSERR16SB Pseudomonas diminuta 16S ribosomal RNA
gi|175717|gb|M59064|PSERR16SB -13.200,6,gaga 0     950   16 gccacg gaga cgtggc
>gi|472129|gb|M82490|PTNRRE04 Platanus occidentalis 18S ribosomal RNA (18S rRNA), ca. bp 1207 to 1414 in mature rRNA
gi|472129|gb|M82490|PTNRRE04 -12.200,7,gtca 1     170   18 gtggagg gtca cctccac
>gi|294428|gb|L16474|PVORR16SJ Prevotella oris (ATCC 33573) 16S ribosomal RNA
gi|294428|gb|L16474|PVORR16SJ -12.100,7,cttg 0      78   18 ggggaag cttg cttcccc
>gi|294428|gb|L16474|PVORR16SJ Prevotella oris (ATCC 33573) 16S ribosomal RNA
gi|294428|gb|L16474|PVORR16SJ -12.100,7,caag 1      95   18 ggggaag caag cttcccc
>gi|408945|gb|L19921|PYWRRDX Pyrococcus abyssi 16S ribosomal RNA
gi|408945|gb|L19921|PYWRRDX -13.400,7,ttct 0      48   18 gcgtccc ttct gggacgc
>gi|408945|gb|L19921|PYWRRDX Pyrococcus abyssi 16S ribosomal RNA
gi|408945|gb|L19921|PYWRRDX -12.900,6,gtac 0     603   16 ccgggg gtac ccccgg
>gi|408945|gb|L19921|PYWRRDX Pyrococcus abyssi 16S ribosomal RNA
gi|408945|gb|L19921|PYWRRDX -14.100,7,gctc 0    1066   18 ccctccc gctc gggaggg
>gi|408945|gb|L19921|PYWRRDX Pyrococcus abyssi 16S ribosomal RNA
gi|408945|gb|L19921|PYWRRDX -14.100,7,gagc 1    1083   18 ccctccc gagc gggaggg
>gi|408945|gb|L19921|PYWRRDX Pyrococcus abyssi 16S ribosomal RNA
gi|408945|gb|L19921|PYWRRDX -12.900,6,gtac 1     618   16 ccgggg gtac ccccgg
>gi|408945|gb|L19921|PYWRRDX Pyrococcus abyssi 16S ribosomal RNA
gi|408945|gb|L19921|PYWRRDX -12.900,7,agaa 1      65   18 gcgtccc agaa gggacgc
>gi|472171|gb|M82511|RACRRE05 Ranunculus acris 18S ribosomal RNA (18S rRNA), ca. bp 1203 to 1414 in mature rRNA
gi|472171|gb|M82511|RACRRE05 -12.200,7,ggta 1     174   18 gtggagg ggta cctccac
>gi|175815|gb|M11057|RATUR8 Rat U8 small nuclear RNA from Novikoff hepatoma cells
gi|175815|gb|M11057|RATUR8 -14.000,6,gaaa 1      43   16 ccctcc gaaa ggaggg
>gi|175816|gb|K00477|RATURU4A Rat U4a small nuclear RNA (snRNA)
gi|175816|gb|K00477|RATURU4A -12.000,7,tacg 0     128   18 cagtctc tacg gagactg
>gi|175817|gb|K00478|RATURU4B Rat U4b small nuclear RNA (snRNA)
gi|175817|gb|K00478|RATURU4B -12.000,7,tacg 0     128   18 cagtctc tacg gagactg
>gi|175851|gb|M91613|RHSRRITSA Rhizopogon subcaerulescens ribosomal RNA internal transcribed spacer
gi|175851|gb|M91613|RHSRRITSA -12.800,7,tcgc 0      40   18 gcctcgc tcgc gcgaggc
>gi|175851|gb|M91613|RHSRRITSA Rhizopogon subcaerulescens ribosomal RNA internal transcribed spacer
gi|175851|gb|M91613|RHSRRITSA -16.100,7,gcga 1      57   18 gcctcgc gcga gcgaggc
>gi|175851|gb|M91613|RHSRRITSA Rhizopogon subcaerulescens ribosomal RNA internal transcribed spacer
gi|175851|gb|M91613|RHSRRITSA -12.700,6,gcga 1      56   16 cctcgc gcga gcgagg
>gi|294741|gb|L15196|ROLRR18S Roridula gorgonias 18S ribosomal RNA
gi|294741|gb|L15196|ROLRR18S -12.200,7,gtca 1     628   18 gtggagg gtca cctccac
>gi|175876|gb|M59069|RSPRR16SD Rhodospirillum salinarum 16S ribosomal RNA
gi|175876|gb|M59069|RSPRR16SD -16.700,7,gaga 0     953   18 gcctcgg gaga ccgaggc
>gi|175876|gb|M59069|RSPRR16SD Rhodospirillum salinarum 16S ribosomal RNA
gi|175876|gb|M59069|RSPRR16SD -13.300,6,gaga 0     954   16 cctcgg gaga ccgagg
>gi|175876|gb|M59069|RSPRR16SD Rhodospirillum salinarum 16S ribosomal RNA
gi|175876|gb|M59069|RSPRR16SD -12.300,7,tctc 1     970   18 gcctcgg tctc ccgaggc
>gi|457377|gb|L25709|SGBRRNA Solemya reidi gill symbiont ribosomal RNA
gi|457377|gb|L25709|SGBRRNA -13.900,6,gaaa 0     140   16 cctggg gaaa cccagg
>gi|175944|gb|M32848|SIL28SRRNA Silurana tropicalis 28S ribosomal RNA, complete
gi|175944|gb|M32848|SIL28SRRNA -13.000,6,gcgc 0     341   16 gccggg gcgc cccggc
>gi|175944|gb|M32848|SIL28SRRNA Silurana tropicalis 28S ribosomal RNA, complete
gi|175944|gb|M32848|SIL28SRRNA -13.000,6,gcgc 1     356   16 gccggg gcgc cccggc
>gi|175988|gb|M88722|SPARR16SB Spirochaeta halophila 16S ribosomal RNA
gi|175988|gb|M88722|SPARR16SB -12.800,6,ttcg 0       2   16 cgtccc ttcg gggacg
>gi|176013|gb|M62707|SPNRR18SA Sphaeromonas communis (strain FG) 18S ribosomal RNA
gi|176013|gb|M62707|SPNRR18SA -12.700,7,gcaa 0     183   18 aacctgg gcaa ccaggtt
>gi|176061|gb|M91614|SUIRRITSA Suillus grevillei ribosomal RNA internal transcribed spacer
gi|176061|gb|M91614|SUIRRITSA -13.100,6,gcga 0     105   16 cgcggg gcga cccgcg
>gi|176062|gb|M91615|SUIRRITSB Suillus grevillei ribosomal RNA internal transcribed spacer
gi|176062|gb|M91615|SUIRRITSB -13.100,6,gcga 0     105   16 cgcggg gcga cccgcg
>gi|176197|gb|M67497|THCLRRNA T.celer 23S ribosomal RNA gene sequence
gi|176197|gb|M67497|THCLRRNA -16.600,7,gaaa 0     263   18 ctccggg gaaa cccggag
>gi|176197|gb|M67497|THCLRRNA T.celer 23S ribosomal RNA gene sequence
gi|176197|gb|M67497|THCLRRNA -14.000,6,gaaa 0     264   16 tccggg gaaa cccgga
>gi|176197|gb|M67497|THCLRRNA T.celer 23S ribosomal RNA gene sequence
gi|176197|gb|M67497|THCLRRNA -12.100,5,gaaa 0     265   14 ccggg gaaa cccgg
>gi|176197|gb|M67497|THCLRRNA T.celer 23S ribosomal RNA gene sequence
gi|176197|gb|M67497|THCLRRNA -13.100,6,gaaa 0    1004   16 ggggga gaaa tccccc
>gi|176197|gb|M67497|THCLRRNA T.celer 23S ribosomal RNA gene sequence
gi|176197|gb|M67497|THCLRRNA -12.200,7,tttc 1     280   18 ctccggg tttc cccggag
>gi|176199|gb|M21529|THCRRD T.celer 16S ribosomal RNA
gi|176199|gb|M21529|THCRRD -12.900,7,ggaa 0    1455   18 ccgtagg ggaa cctacgg
>gi|176219|gb|M67498|TMORRNAA Thermotoga maritima large subunit ribosomal RNA, complete
gi|176219|gb|M67498|TMORRNAA -12.000,5,gaaa 0     152   14 ccgcc gaaa ggcgg
>gi|176219|gb|M67498|TMORRNAA Thermotoga maritima large subunit ribosomal RNA, complete
gi|176219|gb|M67498|TMORRNAA -13.700,6,ttcg 0    1615   16 ggtccc ttcg gggacc
>gi|176254|gb|M57738|TRPRRDSB Treponema succinifaciens 16S rRNA
gi|176254|gb|M57738|TRPRRDSB -16.400,7,gaga 0    1036   18 ccgcctg gaga caggcgg
>gi|176254|gb|M57738|TRPRRDSB Treponema succinifaciens 16S rRNA
gi|176254|gb|M57738|TRPRRDSB -13.100,6,gaga 0    1037   16 cgcctg gaga caggcg
>gi|176254|gb|M57738|TRPRRDSB Treponema succinifaciens 16S rRNA
gi|176254|gb|M57738|TRPRRDSB -12.000,7,tctc 1    1053   18 ccgcctg tctc caggcgg
>gi|176257|gb|M59294|TRPSSRNAA Treponema sp. small subunit ribosomal RNA
gi|176257|gb|M59294|TRPSSRNAA -12.800,7,gaga 0    1026   18 tcgcatg gaga catgcga
>gi|1220551|gb|L27800|TRRBRDNAA Trichoderma reesei 5.8S ribosomal DNA (5.8S rDNA)
gi|1220551|gb|L27800|TRRBRDNAA -12.500,7,tatt 0     118   18 ccgccag tatt ctggcgg
>gi|1220551|gb|L27800|TRRBRDNAA Trichoderma reesei 5.8S ribosomal DNA (5.8S rDNA)
gi|1220551|gb|L27800|TRRBRDNAA -12.100,7,aata 1     135   18 ccgccag aata ctggcgg
>gi|603469|gb|L26520|TRWERRNAA Trypetesa lampas 18S ribosomal RNA (18S rRNA)
gi|603469|gb|L26520|TRWERRNAA -13.100,6,gaaa 1     818   16 caggcg gaaa cgcctg
>gi|176260|gb|M35966|TTERRDA T.tenax 16S rRNA
gi|176260|gb|M35966|TTERRDA -13.900,7,ggcg 0      63   18 cgcccgg ggcg ccgggcg
>gi|176260|gb|M35966|TTERRDA T.tenax 16S rRNA
gi|176260|gb|M35966|TTERRDA -13.200,7,cgcc 1      80   18 cgcccgg cgcc ccgggcg
>gi|603470|gb|L26521|ULOERRNAA Ulophysema oeresundense 18S ribosomal RNA (18S rRNA)
gi|603470|gb|L26521|ULOERRNAA -12.500,7,tcac 0     225   18 cgtgccc tcac gggcacg
>gi|603470|gb|L26521|ULOERRNAA Ulophysema oeresundense 18S ribosomal RNA (18S rRNA)
gi|603470|gb|L26521|ULOERRNAA -14.400,7,tgaa 0    1785   18 ccgcagg tgaa cctgcgg
>gi|603470|gb|L26521|ULOERRNAA Ulophysema oeresundense 18S ribosomal RNA (18S rRNA)
gi|603470|gb|L26521|ULOERRNAA -12.900,7,ttca 1    1802   18 ccgcagg ttca cctgcgg
>gi|603470|gb|L26521|ULOERRNAA Ulophysema oeresundense 18S ribosomal RNA (18S rRNA)
gi|603470|gb|L26521|ULOERRNAA -16.300,7,gtga 1     242   18 cgtgccc gtga gggcacg
>gi|603470|gb|L26521|ULOERRNAA Ulophysema oeresundense 18S ribosomal RNA (18S rRNA)
gi|603470|gb|L26521|ULOERRNAA -13.900,6,gtga 1     241   16 gtgccc gtga gggcac
>gi|475134|gb|M82432|ZAMRREA02 Zamia ottonis 18S ribosomal RNA (18S rRNA), ca. bp 234 to 287 in mature rRNA
gi|475134|gb|M82432|ZAMRREA02 -12.200,7,gata 1     172   18 gtggagg gata cctccac
#RM scored
#RM descr h5 ss h3
#RM dfile sprintf.descr
>gi|173609|gb|M28984|ACARRDX A.castellani 5S ribosomal RNA
gi|173609|gb|M28984|ACARRDX -12.500,6,gcga 0      81   16 gggtgg gcga ccaccc
>gi|1236163|gb|L41047|ANNRRO Actinoplanes sp. ribosomal RNA (rRNA)
gi|1236163|gb|L41047|ANNRRO -15.400,6,gaaa 0     110   16 ccccgg gaaa ccgggg
>gi|1236163|gb|L41047|ANNRRO Actinoplanes sp. ribosomal RNA (rRNA)
gi|1236163|gb|L41047|ANNRRO -12.100,5,gaaa 0     111   14 cccgg gaaa ccggg
>gi|173741|gb|M83548|AQF16SRRN Aquifex pyrophilus 16S ribosomal RNA (16S rRNA)
gi|173741|gb|M83548|AQF16SRRN -15.400,6,gaaa 0     154   16 ccccgg gaaa ccgggg
>gi|173741|gb|M83548|AQF16SRRN Aquifex pyrophilus 16S ribosomal RNA (16S rRNA)
gi|173741|gb|M83548|AQF16SRRN -12.100,5,gaaa 0     155   14 cccgg gaaa ccggg
>gi|173741|gb|M83548|AQF16SRRN Aquifex pyrophilus 16S ribosomal RNA (16S rRNA)
gi|173741|gb|M83548|AQF16SRRN -14.900,7,gaaa 0    1028   18 actccgc gaaa gcggagt
>gi|173741|gb|M83548|AQF16SRRN Aquifex pyrophilus 16S ribosomal RNA (16S rRNA)
gi|173741|gb|M83548|AQF16SRRN -13.200,6,gaaa 0    1029   16 ctccgc gaaa gcggag
>gi|173748|gb|M64487|ARFRRLSA A.fulgicus large subunit ribosomal RNA
gi|173748|gb|M64487|ARFRRLSA -12.700,7,ttac 0     137   18 cgctccc ttac gggagcg
>gi|173748|gb|M64487|ARFRRLSA A.fulgicus large subunit ribosomal RNA
gi|173748|gb|M64487|ARFRRLSA -15.500,7,gtaa 1     154   18 cgctccc gtaa gggagcg
>gi|173748|gb|M64487|ARFRRLSA A.fulgicus large subunit ribosomal RNA
gi|173748|gb|M64487|ARFRRLSA -13.100,6,gtaa 1     153   16 gctccc gtaa gggagc
>gi|470692|gb|M82686|ARIRRE05 Aristolochia gigantea 18S ribosomal RNA (18S rRNA), ca. bp 1203 to 1414 in mature rRNA
gi|470692|gb|M82686|ARIRRE05 -12.200,7,gtca 1     174   18 gtggagg gtca cctccac
>gi|470705|gb|M82700|ARURRE05 Arundinaria gigantea 18S ribosomal RNA (18S rRNA), ca. bp 1204 to 1414 in mature rRNA
gi|470705|gb|M82700|ARURRE05 -12.000,7,catc 0     156   18 gcggagg catc cctccgc
>gi|470705|gb|M82700|ARURRE05 Arundinaria gigantea 18S ribosomal RNA (18S rRNA), ca. bp 1204 to 1414 in mature rRNA
gi|470705|gb|M82700|ARURRE05 -12.700,7,gatg 1     173   18 gcggagg gatg cctccgc
>gi|470750|gb|M82449|AVORRE05 Persea borbonia 18S ribosomal RNA (18S rRNA), ca. bp 1205 to 1414 in mature rRNA
gi|470750|gb|M82449|AVORRE05 -12.200,7,gata 1     172   18 gtggagg gata cctccac
>gi|439580|gb|L15530|AZORR16SA Azoarcus sp. (strain BH72) 16S ribosomal RNA (16S rRNA)
gi|439580|gb|L15530|AZORR16SA -12.500,5,ttcg 0      76   14 ggggc ttcg gcccc
>gi|173823|gb|M79434|BAIRRDG02 Bacterial sp. (TH3) 16S rRNA sequence
gi|173823|gb|M79434|BAIRRDG02 -13.100,6,gaaa 0      52   16 caccgg gaaa ccggtg
>gi|603438|gb|L26511|BEDERRNAA Berndtia purpurea 18S ribosomal RNA (18S rRNA)
gi|603438|gb|L26511|BEDERRNAA -13.100,6,gaaa 1     816   16 caggcg gaaa cgcctg
>gi|304227|gb|L19406|BODRR24SA Bodo caudatus 24S ribosomal RNA large subunit
gi|304227|gb|L19406|BODRR24SA -15.400,6,gaaa 0     512   16 cccggg gaaa cccggg
>gi|304227|gb|L19406|BODRR24SA Bodo caudatus 24S ribosomal RNA large subunit
gi|304227|gb|L19406|BODRR24SA -12.100,5,gaaa 0     513   14 ccggg gaaa cccgg
>gi|173977|gb|M97571|BRARREA Branchiostoma floridae 18S ribosomal RNA (18S rRNA), 5' end
gi|173977|gb|M97571|BRARREA -12.200,6,ttcg 0     225   16 ccgggg ttcg ccccgg
>gi|470792|gb|M82728|BRERRE05 Brasenia schreberi 18S ribosomal RNA (18S rRNA), ca. bp 1238 to 1414 in mature rRNA
gi|470792|gb|M82728|BRERRE05 -12.200,7,ggta 1     139   18 gtggagg ggta cctccac
>gi|289579|gb|L14636|CCYRRDB Capnocytophaga sputigena 16S ribosomal RNA
gi|289579|gb|L14636|CCYRRDB -12.400,7,ttcg 0      74   18 ggttacc ttcg ggtaacc
>gi|174069|gb|M34116|CFXRRDA C.aurantiacus 16S ribosomal RNA
gi|174069|gb|M34116|CFXRRDA -13.200,6,gaaa 0     141   16 cccgtc gaaa gacggg
>gi|174076|gb|M62791|CHBRRDAA C.vibrioforme 16S ribosomal RNA
gi|174076|gb|M62791|CHBRRDAA -12.200,6,gaaa 0     148   16 ccccga gaaa tcgggg
>gi|174079|gb|M31769|CHBSSRNA C.limicola ribosomal RNA small subunit
gi|174079|gb|M31769|CHBSSRNA -12.200,6,gaaa 0     146   16 ccccga gaaa tcgggg
>gi|174102|gb|K03164|CHKUR5B Chicken U5B small nuclear RNA, complete
gi|174102|gb|K03164|CHKUR5B -16.200,7,ttcg 0      97   18 gctccgc ttcg gcggagc
>gi|174102|gb|K03164|CHKUR5B Chicken U5B small nuclear RNA, complete
gi|174102|gb|K03164|CHKUR5B -12.800,6,ttcg 0      98   16 ctccgc ttcg gcggag
>gi|174102|gb|K03164|CHKUR5B Chicken U5B small nuclear RNA, complete
gi|174102|gb|K03164|CHKUR5B -12.400,7,cgaa 1     114   18 gctccgc cgaa gcggagc
>gi|174103|gb|K00474|CHKURU4A Chicken U4a small nuclear RNA (snRNA)
gi|174103|gb|K00474|CHKURU4A -12.000,7,tacg 0     128   18 cagtctc tacg gagactg
>gi|174104|gb|K00475|CHKURU4B Chicken U4b small nuclear RNA (snRNA)
gi|174104|gb|K00475|CHKURU4B -12.000,7,tacg 0     128   18 cagtctc tacg gagactg
>gi|174144|gb|M59092|CLORR16SR Clostridium kluyveri 16S ribosomal RNA
gi|174144|gb|M59092|CLORR16SR -13.700,7,atcg 0     809   18 ggggggt atcg acccccc
>gi|174144|gb|M59092|CLORR16SR Clostridium kluyveri 16S ribosomal RNA
gi|174144|gb|M59092|CLORR16SR -13.100,7,cgat 1     826   18 ggggggt cgat acccccc
>gi|174209|gb|M20058|CRSRREA3 Chiton (C.stelleri) 18S rRNA, segment 3 of 3
gi|174209|gb|M20058|CRSRREA3 -12.900,5,ggaa 0     118   14 ggccc ggaa gggcc
>gi|174273|gb|M59057|DEOSSRNA Dermatophilus congolensis small subunit ribosomal RNA sequence
gi|174273|gb|M59057|DEOSSRNA -12.100,5,gaaa 0     151   14 ccccg gaaa cgggg
>gi|470912|gb|M82693|DRIRRE05 Drimys aromatica 18S ribosomal RNA (18S rRNA), ca. bp 1203 to 1414 in mature rRNA
gi|470912|gb|M82693|DRIRRE05 -15.200,7,gtga 1     174   18 gtggagg gtga cctccac
>gi|470912|gb|M82693|DRIRRE05 Drimys aromatica 18S ribosomal RNA (18S rRNA), ca. bp 1203 to 1414 in mature rRNA
gi|470912|gb|M82693|DRIRRE05 -12.500,6,gtga 1     173   16 tggagg gtga cctcca
>gi|174363|gb|K01260|ECOPRM1 Escherichia coli 10sb (M1) RNA; the RNA component of RNase P
gi|174363|gb|K01260|ECOPRM1 -12.000,5,gcaa 0     152   14 cccgc gcaa gcggg
>gi|174493|gb|M59388|ELERR18S E.cuneatus 18S ribosomal RNA
gi|174493|gb|M59388|ELERR18S -13.300,6,gaaa 0     728   16 gtcgcc gaaa ggcgac
>gi|174566|gb|M62683|FIBRR16SB Fibrobacter succinogenes succinogenes (strain A3C) 16S ribosomal RNA
gi|174566|gb|M62683|FIBRR16SB -12.900,6,gttc 0     814   16 ccgggg gttc ccccgg
>gi|174566|gb|M62683|FIBRR16SB Fibrobacter succinogenes succinogenes (strain A3C) 16S ribosomal RNA
gi|174566|gb|M62683|FIBRR16SB -12.900,6,gaac 1     829   16 ccgggg gaac ccccgg
>gi|174567|gb|M62684|FIBRR16SC Fibrobacter succinogenes succinogenes (strain B1) 16S ribosomal RNA
gi|174567|gb|M62684|FIBRR16SC -12.900,6,gttc 0     810   16 ccgggg gttc ccccgg
>gi|174567|gb|M62684|FIBRR16SC Fibrobacter succinogenes succinogenes (strain B1) 16S ribosomal RNA
gi|174567|gb|M62684|FIBRR16SC -12.900,6,gaac 1     825   16 ccgggg gaac ccccgg
>gi|174568|gb|M62685|FIBRR16SD Fibrobacter succinogenes succinogenes (strain BL2) 16S ribosomal RNA
gi|174568|gb|M62685|FIBRR16SD -12.900,6,gttc 0     810   16 ccgggg gttc ccccgg
>gi|174568|gb|M62685|FIBRR16SD Fibrobacter succinogenes succinogenes (strain BL2) 16S ribosomal RNA
gi|174568|gb|M62685|FIBRR16SD -12.900,6,gaac 1     825   16 ccgggg gaac ccccgg
>gi|174570|gb|M62687|FIBRR16SF Fibrobacter intestinalis (strain DR7) 16S ribosomal RNA
gi|174570|gb|M62687|FIBRR16SF -13.900,6,gcga 0     816   16 cccggg gcga cccggg
>gi|174572|gb|M62689|FIBRR16SH Fibrobacter succinogenes (strain HM2) 16S ribosomal RNA
gi|174572|gb|M62689|FIBRR16SH -12.200,6,ttcg 0     809   16 ccgggg ttcg ccccgg
>gi|174573|gb|M62690|FIBRR16SI Fibrobacter intestinalis (strain JG1) 16S ribosomal RNA
gi|174573|gb|M62690|FIBRR16SI -13.900,6,gcga 0     816   16 cccggg gcga cccggg
>gi|174574|gb|M62691|FIBRR16SJ Fibrobacter intestinalis (strain LH1) 16S ribosomal RNA
gi|174574|gb|M62691|FIBRR16SJ -13.900,6,gcga 0     816   16 cccggg gcga cccggg
>gi|174576|gb|M62693|FIBRR16SL Fibrobacter succinogenes (strain MC1) 16S ribosomal RNA
gi|174576|gb|M62693|FIBRR16SL -12.100,6,acat 0     168   16 ccccgg acat ccgggg
>gi|174576|gb|M62693|FIBRR16SL Fibrobacter succinogenes (strain MC1) 16S ribosomal RNA
gi|174576|gb|M62693|FIBRR16SL -12.200,6,ttcg 0     808   16 ccgggg ttcg ccccgg
>gi|174576|gb|M62693|FIBRR16SL Fibrobacter succinogenes (strain MC1) 16S ribosomal RNA
gi|174576|gb|M62693|FIBRR16SL -12.100,6,atgt 1     183   16 ccccgg atgt ccgggg
>gi|174579|gb|M62696|FIBRR16SO Fibrobacter succinogenes (strain S85) 16S ribosomal RNA
gi|174579|gb|M62696|FIBRR16SO -12.900,6,gttc 0     811   16 ccgggg gttc ccccgg
>gi|174579|gb|M62696|FIBRR16SO Fibrobacter succinogenes (strain S85) 16S ribosomal RNA
gi|174579|gb|M62696|FIBRR16SO -12.900,6,gaac 1     826   16 ccgggg gaac ccccgg
>gi|174591|gb|M59231|FLXRR16S Flexistipes sinusarabici small subunit rRNA
gi|174591|gb|M59231|FLXRR16S -13.600,6,ttcg 0      76   16 cctccc ttcg gggagg
>gi|174592|gb|L11306|FRARRDX Frankia sp. 16S ribosomal RNA
gi|174592|gb|L11306|FRARRDX -12.100,5,gaaa 0     143   14 cccgg gaaa ccggg
>gi|174596|gb|M97575|FSARREE Petromyzon marinus 18S ribosomal RNA (18S rRNA), 5' end
gi|174596|gb|M97575|FSARREE -12.500,6,gcga 0    1714   16 gggcag gcga ctgccc
>gi|174670|gb|M91611|GAORRITSA Gastrosuillus laricinus ribosomal RNA internal transcribed spacer
gi|174670|gb|M91611|GAORRITSA -13.100,6,gcga 0      89   16 cgcggg gcga cccgcg
>gi|174671|gb|M91612|GAORRITSB Gastrosuillus luricinus ribosomal RNA internal transcribed spacer
gi|174671|gb|M91612|GAORRITSB -13.100,6,gcga 0     105   16 cgcggg gcga cccgcg
>gi|695346|gb|L36199|HBMRRDM Heliobacillus mobilis 16S ribosomal RNA (16S rRNA)
gi|695346|gb|L36199|HBMRRDM -13.800,6,gaaa 0     152   16 cagccc gaaa gggctg
>gi|174809|gb|M37643|HECRR16SB Helicobacter felis 16S rRNA
gi|174809|gb|M37643|HECRR16SB -12.700,7,gaaa 0     962   18 tccccta gaaa tagggga
>gi|174838|gb|L04675|HLO16SRRNA Heliothrix oregonensis 16S ribosomal RNA (16S rRNA), partial rRNA
gi|174838|gb|L04675|HLO16SRRNA -12.800,5,gaaa 1      38   14 ccccc gaaa ggggg
>gi|174913|gb|M23820|HUMRRAUA Human U5-A ribosomal RNA
gi|174913|gb|M23820|HUMRRAUA -12.500,7,cttg 0     101   18 gccttgc cttg gcaaggc
>gi|174913|gb|M23820|HUMRRAUA Human U5-A ribosomal RNA
gi|174913|gb|M23820|HUMRRAUA -12.500,7,caag 1     118   18 gccttgc caag gcaaggc
>gi|174944|gb|K00472|HUMURU4B Human U4b small nuclear RNA (snRNA)
gi|174944|gb|K00472|HUMURU4B -12.000,7,tacg 0     128   18 cagtctc tacg gagactg
>gi|174959|gb|M32851|HYM28SRRNA Hymenochirus curtipes 28S ribosomal RNA, complete
gi|174959|gb|M32851|HYM28SRRNA -13.300,7,cgcg 0     335   18 agccgcg cgcg cgcggct
>gi|174959|gb|M32851|HYM28SRRNA Hymenochirus curtipes 28S ribosomal RNA, complete
gi|174959|gb|M32851|HYM28SRRNA -13.300,7,cgcg 1     352   18 agccgcg cgcg cgcggct
>gi|175002|gb|M97573|LARRREC Lampetra aepyptera 18S ribosomal RNA (18S rRNA), 5' end
gi|175002|gb|M97573|LARRREC -12.500,6,gcga 0    1714   16 gggcag gcga ctgccc
>gi|471872|gb|M82532|LAURRE05 Lactuca sativa 18S ribosomal RNA (18S rRNA), ca. bp 1205 to 1414 in mature rRNA
gi|471872|gb|M82532|LAURRE05 -12.200,7,gata 1     172   18 gtggagg gata cctccac
>gi|175039|gb|M23727|LBARRNAV L.vitulinus 16S ribosomal RNA small subunit
gi|175039|gb|M23727|LBARRNAV -13.400,6,gaga 0    1000   16 gggacg gaga cgtccc
>gi|175044|gb|M23729|LBARRNAZ L.catenaforme 16S ribosomal RNA small subunit
gi|175044|gb|M23729|LBARRNAZ -15.700,7,gaga 0    1000   18 tcgcgcg gaga cgcgcga
>gi|175044|gb|M23729|LBARRNAZ L.catenaforme 16S ribosomal RNA small subunit
gi|175044|gb|M23729|LBARRNAZ -13.800,6,gaga 0    1001   16 cgcgcg gaga cgcgcg
>gi|471885|gb|M82539|LIQRRE05 Liquidambar styraciflua 18S ribosomal RNA (18S rRNA), ca. bp 1205 to 1414 in mature rRNA
gi|471885|gb|M82539|LIQRRE05 -12.200,7,gtca 1     172   18 gtggagg gtca cctccac
>gi|175140|gb|M58822|LISRR16ST Listeria monocytogenes 16S ribosomal RNA
gi|175140|gb|M58822|LISRR16ST -13.300,6,gaaa 0     153   16 ctccgg gaaa ccggag
>gi|951043|gb|L33974|LTTRRD Leptothrix discophora (strain SP-6) 16S ribosomal RNA (16S rRNA)
gi|951043|gb|L33974|LTTRRD -12.000,5,gaaa 0     135   14 ccggc gaaa gccgg
>gi|504534|gb|L33979|LTTRRDB Leptothrix cholodnii (strain LMG 7171) 16S ribosomal RNA (16S rRNA)
gi|504534|gb|L33979|LTTRRDB -12.000,5,gaaa 0     135   14 ccggc gaaa gccgg
>gi|504535|gb|L33981|LTTRRDC Leptothrix sp. (strain NC-1) 16S ribosomal RNA (16S rRNA)
gi|504535|gb|L33981|LTTRRDC -12.000,5,gaaa 0     135   14 ccggc gaaa gccgg
>gi|308922|gb|L10943|MABRRI Marine Eubacterial sp. (aggregate agg27) PCR generated ribosomal RNA fragment
gi|308922|gb|L10943|MABRRI -12.100,7,acat 0      81   18 gggagag acat ctctccc
>gi|308922|gb|L10943|MABRRI Marine Eubacterial sp. (aggregate agg27) PCR generated ribosomal RNA fragment
gi|308922|gb|L10943|MABRRI -12.100,7,atgt 1      98   18 gggagag atgt ctctccc
>gi|175375|gb|M95654|MTBRRDB Methylobacterium sp. 16S ribosomal RNA
gi|175375|gb|M95654|MTBRRDB -12.600,7,cttg 0     776   18 tggcctg cttg caggcca
>gi|175375|gb|M95654|MTBRRDB Methylobacterium sp. 16S ribosomal RNA
gi|175375|gb|M95654|MTBRRDB -12.600,7,caag 1     793   18 tggcctg caag caggcca
>gi|175376|gb|M95655|MTBRRDC Methylobacterium sp. 16S ribosomal RNA
gi|175376|gb|M95655|MTBRRDC -12.600,7,cttg 0     776   18 tggcctg cttg caggcca
>gi|175376|gb|M95655|MTBRRDC Methylobacterium sp. 16S ribosomal RNA
gi|175376|gb|M95655|MTBRRDC -12.600,7,caag 1     793   18 tggcctg caag caggcca
>gi|175408|gb|M14414|MUSRRMA Mouse 5.4S ribosomal small nuclear RNA
gi|175408|gb|M14414|MUSRRMA -14.000,6,gaaa 1      44   16 ccctcc gaaa ggaggg
>gi|175433|gb|M10328|MUSUR57S Mouse 5.7S U4 small nuclear RNA type a
gi|175433|gb|M10328|MUSUR57S -12.000,7,tacg 0     128   18 cagtctc tacg gagactg
>gi|175434|gb|M18004|MUSUR57T Mouse 5.7S U4 small nuclear RNA type b
gi|175434|gb|M18004|MUSUR57T -12.000,7,tacg 0     128   18 cagtctc tacg gagactg
>gi|175446|gb|M59126|MVORR16SY Methanococcus jannaschii 16S ribosomal RNA
gi|175446|gb|M59126|MVORR16SY -13.700,6,ttcg 0      65   16 gctccc ttcg gggagc
>gi|175555|gb|L06168|NGORR16SB Neisseria flavescens 16S ribosomal RNA
gi|175555|gb|L06168|NGORR16SB -13.300,6,gaga 0    1005   16 cctccg gaga cggagg
>gi|294001|gb|L16523|NYSRR23S Nyssa sativa 26S ribosomal RNA
gi|294001|gb|L16523|NYSRR23S -15.200,7,gaaa 0      88   18 gccagag gaaa ctctggc
>gi|175717|gb|M59064|PSERR16SB Pseudomonas diminuta 16S ribosomal RNA
gi|175717|gb|M59064|PSERR16SB -13.200,6,gaga 0     950   16 gccacg gaga cgtggc
>gi|472129|gb|M82490|PTNRRE04 Platanus occidentalis 18S ribosomal RNA (18S rRNA), ca. bp 1207 to 1414 in mature rRNA
gi|472129|gb|M82490|PTNRRE04 -12.200,7,gtca 1     170   18 gtggagg gtca cctccac
>gi|294428|gb|L16474|PVORR16SJ Prevotella oris (ATCC 33573) 16S ribosomal RNA
gi|294428|gb|L16474|PVORR16SJ -12.100,7,cttg 0      78   18 ggggaag cttg cttcccc
>gi|294428|gb|L16474|PVORR16SJ Prevotella oris (ATCC 33573) 16S ribosomal RNA
gi|294428|gb|L16474|PVORR16SJ -12.100,7,caag 1      95   18 ggggaag caag cttcccc
>gi|408945|gb|L19921|PYWRRDX Pyrococcus abyssi 16S ribosomal RNA
gi|408945|gb|L19921|PYWRRDX -13.400,7,ttct 0      48   18 gcgtccc ttct gggacgc
>gi|408945|gb|L19921|PYWRRDX Pyrococcus abyssi 16S ribosomal RNA
gi|408945|gb|L19921|PYWRRDX -12.900,6,gtac 0     603   16 ccgggg gtac ccccgg
>gi|408945|gb|L19921|PYWRRDX Pyrococcus abyssi 16S ribosomal RNA
gi|408945|gb|L19921|PYWRRDX -14.100,7,gctc 0    1066   18 ccctccc gctc gggaggg
>gi|408945|gb|L19921|PYWRRDX Pyrococcus abyssi 16S ribosomal RNA
gi|408945|gb|L19921|PYWRRDX -14.100,7,gagc 1    1083   18 ccctccc gagc gggaggg
>gi|408945|gb|L19921|PYWRRDX Pyrococcus abyssi 16S ribosomal RNA
gi|408945|gb|L19921|PYWRRDX -12.900,6,gtac 1     618   16 ccgggg gtac ccccgg
>gi|408945|gb|L19921|PYWRRDX Pyrococcus abyssi 16S ribosomal RNA
gi|408945|gb|L19921|PYWRRDX -12.900,7,agaa 1      65   18 gcgtccc agaa gggacgc
>gi|472171|gb|M82511|RACRRE05 Ranunculus acris 18S ribosomal RNA (18S rRNA), ca. bp 1203 to 1414 in mature rRNA
gi|472171|gb|M82511|RACRRE05 -12.200,7,ggta 1     174   18 gtggagg ggta cctccac
>gi|175815|gb|M11057|RATUR8 Rat U8 small nuclear RNA from Novikoff hepatoma cells
gi|175815|gb|M11057|RATUR8 -14.000,6,gaaa 1      43   16 ccctcc gaaa ggaggg
>gi|175816|gb|K00477|RATURU4A Rat U4a small nuclear RNA (snRNA)
gi|175816|gb|K00477|RATURU4A -12.000,7,tacg 0     128   18 cagtctc tacg gagactg
>gi|175817|gb|K00478|RATURU4B Rat U4b small nuclear RNA (snRNA)
gi|175817|gb|K00478|RATURU4B -12.000,7,tacg 0     128   18 cagtctc tacg gagactg
>gi|175851|gb|M91613|RHSRRITSA Rhizopogon subcaerulescens ribosomal RNA internal transcribed spacer
gi|175851|gb|M91613|RHSRRITSA -12.800,7,tcgc 0      40   18 gcctcgc tcgc gcgaggc
>gi|175851|gb|M91613|RHSRRITSA Rhizopogon subcaerulescens ribosomal RNA internal transcribed spacer
gi|175851|gb|M91613|RHSRRITSA -16.100,7,gcga 1      57   18 gcctcgc gcga gcgaggc
>gi|175851|gb|M91613|RHSRRITSA Rhizopogon subcaerulescens ribosomal RNA internal transcribed spacer
gi|175851|gb|M91613|RHSRRITSA -12.700,6,gcga 1      56   16 cctcgc gcga gcgagg
>gi|294741|gb|L15196|ROLRR18S Roridula gorgonias 18S ribosomal RNA
gi|294741|gb|L15196|ROLRR18S -12.200,7,gtca 1     628   18 gtggagg gtca cctccac
>gi|175876|gb|M59069|RSPRR16SD Rhodospirillum salinarum 16S ribosomal RNA
gi|175876|gb|M59069|RSPRR16SD -16.700,7,gaga 0     953   18 gcctcgg gaga ccgaggc
>gi|175876|gb|M59069|RSPRR16SD Rhodospirillum salinarum 16S ribosomal RNA
gi|175876|gb|M59069|RSPRR16SD -13.300,6,gaga 0     954   16 cctcgg gaga ccgagg
>gi|175876|gb|M59069|RSPRR16SD Rhodospirillum salinarum 16S ribosomal RNA
gi|175876|gb|M59069|RSPRR16SD -12.300,7,tctc 1     970   18 gcctcgg tctc ccgaggc
>gi|457377|gb|L25709|SGBRRNA Solemya reidi gill symbiont ribosomal RNA
gi|457377|gb|L25709|SGBRRNA -13.900,6,gaaa 0     140   16 cctggg gaaa cccagg
>gi|175944|gb|M32848|SIL28SRRNA Silurana tropicalis 28S ribosomal RNA, complete
gi|175944|gb|M32848|SIL28SRRNA -13.000,6,gcgc 0     341   16 gccggg gcgc cccggc
>gi|175944|gb|M32848|SIL28SRRNA Silurana tropicalis 28S ribosomal RNA, complete
gi|175944|gb|M32848|SIL28SRRNA -13.000,6,gcgc 1     356   16 gccggg gcgc cccggc
>gi|175988|gb|M88722|SPARR16SB Spirochaeta halophila 16S ribosomal RNA
gi|175988|gb|M88722|SPARR16SB -12.800,6,ttcg 0       2   16 cgtccc ttcg gggacg
>gi|176013|gb|M62707|SPNRR18SA Sphaeromonas communis (strain FG) 18S ribosomal RNA
gi|176013|gb|M62707|SPNRR18SA -12.700,7,gcaa 0     183   18 aacctgg gcaa ccaggtt
>gi|176061|gb|M91614|SUIRRITSA Suillus grevillei ribosomal RNA internal transcribed spacer
gi|176061|gb|M91614|SUIRRITSA -13.100,6,gcga 0     105   16 cgcggg gcga cccgcg
>gi|176062|gb|M91615|SUIRRITSB Suillus grevillei ribosomal RNA internal transcribed spacer
gi|176062|gb|M91615|SUIRRITSB -13.100,6,gcga 0     105   16 cgcggg gcga cccgcg
>gi|176197|gb|M67497|THCLRRNA T.celer 23S ribosomal RNA gene sequence
gi|176197|gb|M67497|THCLRRNA -16.600,7,gaaa 0     263   18 ctccggg gaaa cccggag
>gi|176197|gb|M67497|THCLRRNA T.celer 23S ribosomal RNA gene sequence
gi|176197|gb|M67497|THCLRRNA -14.000,6,gaaa 0     264   16 tccggg gaaa cccgga
>gi|176197|gb|M67497|THCLRRNA T.celer 23S ribosomal RNA gene sequence
gi|176197|gb|M67497|THCLRRNA -12.100,5,gaaa 0     265   14 ccggg gaaa cccgg
>gi|176197|gb|M67497|THCLRRNA T.celer 23S ribosomal RNA gene sequence
gi|176197|gb|M67497|THCLRRNA -13.100,6,gaaa 0    1004   16 ggggga gaaa tccccc
>gi|176197|gb|M67497|THCLRRNA T.celer 23S ribosomal RNA gene sequence
gi|176197|gb|M67497|THCLRRNA -12.200,7,tttc 1     280   18 ctccggg tttc cccggag
>gi|176199|gb|M21529|THCRRD T.celer 16S ribosomal RNA
gi|176199|gb|M21529|THCRRD -12.900,7,ggaa 0    1455   18 ccgtagg ggaa cctacgg
>gi|176219|gb|M67498|TMORRNAA Thermotoga maritima large subunit ribosomal RNA, complete
gi|176219|gb|M67498|TMORRNAA -12.000,5,gaaa 0     152   14 ccgcc gaaa ggcgg
>gi|176219|gb|M67498|TMORRNAA Thermotoga maritima large subunit ribosomal RNA, complete
gi|176219|gb|M67498|TMORRNAA -13.700,6,ttcg 0    1615   16 ggtccc ttcg gggacc
>gi|176254|gb|M57738|TRPRRDSB Treponema succinifaciens 16S rRNA
gi|176254|gb|M57738|TRPRRDSB -16.400,7,gaga 0    1036   18 ccgcctg gaga caggcgg
>gi|176254|gb|M57738|TRPRRDSB Treponema succinifaciens 16S rRNA
gi|176254|gb|M57738|TRPRRDSB -13.100,6,gaga 0    1037   16 cgcctg gaga caggcg
>gi|176254|gb|M57738|TRPRRDSB Treponema succinifaciens 16S rRNA
gi|176254|gb|M57738|TRPRRDSB -12.000,7,tctc 1    1053   18 ccgcctg tctc caggcgg
>gi|176257|gb|M59294|TRPSSRNAA Treponema sp. small subunit ribosomal RNA
gi|176257|gb|M59294|TRPSSRNAA -12.800,7,gaga 0    1026   18 tcgcatg gaga catgcga
>gi|1220551|gb|L27800|TRRBRDNAA Trichoderma reesei 5.8S ribosomal DNA (5.8S rDNA)
gi|1220551|gb|L27800|TRRBRDNAA -12.500,7,tatt 0     118   18 ccgccag tatt ctggcgg
>gi|1220551|gb|L27800|TRRBRDNAA Trichoderma reesei 5.8S ribosomal DNA (5.8S rDNA)
gi|1220551|gb|L27800|TRRBRDNAA -12.100,7,aata 1     135   18 ccgccag aata ctggcgg
>gi|603469|gb|L26520|TRWERRNAA Trypetesa lampas 18S ribosomal RNA (18S rRNA)
gi|603469|gb|L26520|TRWERRNAA -13.100,6,gaaa 1     818   16 caggcg gaaa cgcctg
>gi|176260|gb|M35966|TTERRDA T.tenax 16S rRNA
gi|176260|gb|M35966|TTERRDA -13.900,7,ggcg 0      63   18 cgcccgg ggcg ccgggcg
>gi|176260|gb|M35966|TTERRDA T.tenax 16S rRNA
gi|176260|gb|M35966|TTERRDA -13.200,7,cgcc 1      80   18 cgcccgg cgcc ccgggcg
>gi|603470|gb|L26521|ULOERRNAA Ulophysema oeresundense 18S ribosomal RNA (18S rRNA)
gi|603470|gb|L26521|ULOERRNAA -12.500,7,tcac 0     225   18 cgtgccc tcac gggcacg
>gi|603470|gb|L26521|ULOERRNAA Ulophysema oeresundense 18S ribosomal RNA (18S rRNA)
gi|603470|gb|L26521|ULOERRNAA -14.400,7,tgaa 0    1785   18 ccgcagg tgaa cctgcgg
>gi|603470|gb|L26521|ULOERRNAA Ulophysema oeresundense 18S ribosomal RNA (18S rRNA)
gi|603470|gb|L26521|ULOERRNAA -12.900,7,ttca 1    1802   18 ccgcagg ttca cctgcgg
>gi|603470|gb|L26521|ULOERRNAA Ulophysema oeresundense 18S ribosomal RNA (18S rRNA)
gi|603470|gb|L26521|ULOERRNAA -16.300,7,gtga 1     242   18 cgtgccc gtga gggcacg
>gi|603470|gb|L26521|ULOERRNAA Ulophysema oeresundense 18S ribosomal RNA (18S rRNA)
gi|603470|gb|L26521|ULOERRNAA -13.900,6,gtga 1     241   16 gtgccc gtga gggcac
>gi|475134|gb|M82432|ZAMRREA02 Zamia ottonis 18S ribosomal RNA (18S rRNA), ca. bp 234 to 287 in mature rRNA
gi|475134|gb|M82432|ZAMRREA02 -12.200,7,gata 1     172   18 gtggagg gata cctccac
BioPerl-1.007002/t/data/ssp160.embl.1000444000766000024      2144613155576321 16753 0ustar00cjfieldsstaff000000000000ID   AF036895   standard; DNA; INV; 3693 BP.
XX
AC   AF036895;
XX
SV   AF036895.1
XX
DT   22-DEC-1997 (Rel. 54, Created)
DT   03-MAR-2000 (Rel. 62, Last updated, Version 6)
XX
DE   Chironomus thummi special lobe-specific silk protein ssp160 gene, complete
DE   cds.
XX
KW   .
XX
OS   Chironomus thummi
OC   Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera;
OC   Endopterygota; Diptera; Nematocera; Chironomoidea; Chironomidae;
OC   Chironominae; Chironomus.
XX
RN   [1]
RP   1-3644
RX   MEDLINE; 96199249.
RX   PUBMED; 8621663.
RA   Hoffman R.T., Schmidt E.R., Case S.T.;
RT   "A cell-specific glycosylated silk protein from Chironomus thummi salivary
RT   glands. Cloning, chromosomal localization, and characterization of cDNA";
RL   J. Biol. Chem. 271(16):9809-9815(1996).
XX
RN   [2]
RP   1-3693
RX   MEDLINE; 99077856.
RX   PUBMED; 9858763.
RA   Berezikov E., Blinov A.G., Scherbik S., Cox C.K., Case S.T.;
RT   "Structure and polymorphism of the Chironomus thummi gene encoding special
RT   lobe-specific silk protein, ssp160";
RL   Gene 223(1-2):347-354(1998).
XX
RN   [3]
RP   1-3693
RA   Berezikov E., Blinov A.G., Scherbik S.S., Cox C.C., Case S.T.;
RT   ;
RL   Submitted (05-DEC-1997) to the EMBL/GenBank/DDBJ databases.
RL   Biochemistry, University of Mississippi Medical Center, 2500 North State
RL   Street, Jackson, MS 39216-4505, USA
XX
CC   On Mar 4, 1998 this sequence version replaced gi:2707296.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..3693
FT                   /chromosome="IV"
FT                   /db_xref="taxon:7154"
FT                   /organism="Chironomus thummi"
FT                   /strain="German"
FT                   /map="A2b"
FT                   /dev_stage="larval"
FT                   /cell_type="lobe-specific secretory"
FT                   /tissue_type="salivary gland"
FT   CAAT_signal     84..87
FT                   /gene="ssp160"
FT   TATA_signal     169..172
FT                   /gene="ssp160"
FT   mRNA            join(198..288,604..759,825..2408,2874..3129,3188..3241,
FT                   3299..3569)
FT                   /gene="ssp160"
FT                   /product="special lobe-specific silk protein ssp160"
FT   5'UTR           198..234
FT                   /gene="ssp160"
FT   CDS             join(235..288,604..759,825..2408,2874..3129,3188..3241,
FT                   3299..3441)
FT                   /codon_start=1
FT                   /db_xref="UniProt/TrEMBL:O44416"
FT                   /note="160 kDa secretory protein"
FT                   /gene="ssp160"
FT                   /product="special lobe-specific silk protein ssp160"
FT                   /protein_id="AAD11516.1"
FT                   /translation="MNIKVILVCALVAIFFAQVAEGGPIANFVGFIISLLFSLFEVMLS
FT                   VVFDVKSFTSLSNATANATMPGFASSVGGGRFTVIMKGTFNLIAMISANIQAIQSGSGS
FT                   ASSNSSSSANSTTSSNSTTSSNSTTSSNSTTSSNSTSSGLTTGASVVSLIDTCAWVYQD
FT                   SSVGIAYLMVSILALFYGQSVSAPPYADLGIPALPANTSGAGVPQSVQIKAAITYINVT
FT                   INFITLTGQQFEDLQGPVTTDCGCPNTTSVAPLVAEWEAIMAALEAFASGSASSNSTSN
FT                   STSTSNSTTTSNSTTTTNSTTSTNSTSSSNSTTIAGSIDIAANLTVALQNLQALLMQEA
FT                   TCAPCLAANAKKSGVREFGPCKAAGSSCARSGQRKVKRKARLEKMRAKSRRAVGNRKGS
FT                   MKKRVRSRAKKFGKAAKSGVRRYRKNIKFVYIPPVMASLNAYAALMASLSDSISYQSES
FT                   ALNSTDSACNSTSNSTDEAVINATTAVTDMFVNFTAMVINNTVAHPNCTQYADMALSMV
FT                   SQINEQIIACGSQSDSAQSSIYANVTISIVAMAQEYNNFASMSDKCTRSFANSWLWMYI
FT                   KWVFYRMGMTSGVPNFLACQTKAQSSLTAFLASFNATVSATISAASANNSEVQSSEAAC
FT                   IESSLAEAAVILEMFEAAYQNCTDPGSVTVPAETTTTTSTTTTTTTTTTTAAPTTTTTK
FT                   AANAPFTYPLCTLIMSTTCSLGGAGCTYPLISSAGCCPSGKTLNTGLGGRGCCK"
FT   3'UTR           3442..3569
FT                   /gene="ssp160"
FT   polyA_signal    order(3520..3523,3532..3537,3539..3544)
FT                   /gene="ssp160"
XX
SQ   Sequence 3693 BP; 1171 A; 768 C; 633 G; 1121 T; 0 other;
     aagctttcaa ctctcattta aacctaaata agcacatcat atccacaatt catcagccaa        60
     taaaaattca ctttatttta atccaatcaa agaaagtttc acgatgtcaa aaacattcgt       120
     ggatgtcccg tcaagtggaa ggagaaacga aaattcacga aatttcacaa taaaaagtga       180
     gtaagttgtg tggtccatgt catatcgatc taatttatcg aatagtgata aaatatgaat       240
     attaaagtga tcttagtgtg cgccttggtt gcgatcttct ttgcacaggt aagttggtaa       300
     cttgggttgg gatcttcttt aaatttgact agctttgtac aagatatgag ttgtatagtc       360
     tgtagttgta gtgtcatggg ttgtatactg tcttgtaggc taggttttgc ggctcttgca       420
     caaatatatc ttaaaaagat cttaaaagtc aacgagagtg ttcaataacg tgatcaataa       480
     caagcccatg atacgtctca gctccttaaa tccaccaaat atgactcata tacagacaca       540
     accctaatct taaagtacta agcaatttta atcacaattt taaattttcc acatcttatc       600
     caggttgcag aaggcggacc aatcgccaat tttgtaggct tcatcatctc cctcttgttc       660
     tccttgtttg aagtcatgct gtcagttgtg ttcgatgtca agtcgttcac aagcttgtca       720
     aatgccacag caaatgcaac gatgcctggt tttgcatctg tgagtatttt tagctatagc       780
     ttgacctgca aaatccttga taaatatgtt gattccattt ctagagcgtt ggtggtggtc       840
     gcttcacagt catcatgaaa ggaacattca atttgattgc catgatatcg gcaaatattc       900
     aagccattca gtcaggatca ggatcagcat cgtctaattc ctcatcaagt gctaattcta       960
     caacatcctc aaactcaaca acaagctcaa actcaacgac atcctcgaac tcaacaacaa      1020
     gctcaaactc tacatccagt ggattaacaa ccggtgctag cgttgtaagc ttgattgata      1080
     cctgtgcttg ggtctatcag gacagttcag ttggaattgc ctacttgatg gtctcaattt      1140
     tggcactttt ctatggacaa tctgtctcag caccgccata tgctgatctt ggtataccag      1200
     ctctaccagc aaatacctct ggtgctggag ttccacaatc tgtacaaatt aaagcagcaa      1260
     ttacttacat caatgttact attaacttta ttaccttaac tggtcaacaa tttgaagatt      1320
     tacaaggtcc agttaccaca gattgtggat gtccaaatac aactagtgtt gcgccacttg      1380
     ttgctgaatg ggaagccata atggctgctc ttgaagcttt cgctagtgga tcagcatcat      1440
     ctaattctac atctaattca acatcaacaa gtaactcaac aacgacaagc aactcaacaa      1500
     ctacgacaaa ttcaacaact tcaactaatt caacatcctc gtcaaattcg acaacaattg      1560
     ctggatctat tgacattgct gctaatctta cagttgccct ccagaacctc caagccttgc      1620
     tcatgcaaga agctacttgt gctccatgcc tagctgcaaa tgccaaaaag agtggtgttc      1680
     gtgaatttgg accatgtaaa gctgctggct catcatgtgc tagatcagga caaagaaaag      1740
     tcaagcgtaa ggcacgattg gagaagatgc gtgccaagtc ccgtcgtgca gtcggtaaca      1800
     gaaaaggatc aatgaagaag cgcgtccgta gtcgtgcaaa gaaattcgga aaggctgcaa      1860
     agtcaggagt tagacgatac cgcaagaaca tcaagtttgt ctacattcca ccagtcatgg      1920
     cttcacttaa tgcatatgca gcattgatgg catctttaag tgacagcatc tcatatcaat      1980
     ctgaatcggc tttgaactca acagactctg catgtaactc aacatcaaac agcacagatg      2040
     aggctgtaat taatgcaaca accgctgtta ctgatatgtt tgtcaacttt actgctatgg      2100
     tcatcaataa tactgttgca catccaaatt gtactcaata tgctgacatg gctctttcaa      2160
     tggtctctca aatcaacgag caaatcattg catgcggaag tcagtctgat tctgctcagt      2220
     catcaatcta tgcaaatgtt acaatcagta ttgttgcaat ggctcaagaa tacaataact      2280
     ttgcatctat gtctgataag tgtaccagat catttgccaa tagttggttg tggatgtaca      2340
     ttaagtgggt cttctatcga atgggaatga cttctggagt tcctaacttc ctcgcttgtc      2400
     aaactaaggt ttgtgattta cttaacaaat acttgaaact aaacgtatcc cttagaactg      2460
     aacttatcat tagaaattga acttatcctt taaaaactga acttatcccg agaaaagaaa      2520
     tgtatcctta gaaacgaaat cggttttaaa aactgagctt attcttcagg aactaaactc      2580
     atccttagaa actgaccata tccttaaaaa ctgaacgtat tcttagaagc taactcatta      2640
     ttcagaaact gaacttgacc ttagaaactg aacatattct tcggactaaa ctcatcctaa      2700
     gaaactgacc gtatccttaa aaactgaact tagaagctga actcattatt cagaaactga      2760
     agttcaccct tagaaactga acttattctt caggaactaa acttatcctt tgaaactgaa      2820
     cttatcctta aaaactgatt ttactgagtc cttctttaat ccttcattaa taggctcaaa      2880
     gcagtcttac agcattcttg gcatcattta atgccacagt cagtgccacg atttcagcag      2940
     caagtgcaaa taattctgaa gttcaaagct ctgaagcagc ttgtattgaa agtagtcttg      3000
     cggaagcagc cgttatttta gaaatgtttg aggcagcata tcaaaactgt acagatccag      3060
     gatccgtaac agttccagca gagactacaa caacgaccag tacaaccacc actacaacta      3120
     ccacaacaag taggttaaaa ttggaaaagt ttagaatttt gtgtgcaatt tttttaattt      3180
     tttacagcaa ccgcagcacc aacaacaacc acaactaagg ctgctaatgc accattcaca      3240
     tgtaagatat gaaatcaaat tgtgactttt tctaagaaat tgtttccttt ttttctagat      3300
     ccattgtgta ctttgatcat gtcaacaaca tgctcactgg gtggagcagg atgtacatat      3360
     ccacttatct catctgctgg ctgctgtcca tctggcaaaa cattaaacac tggtctcggt      3420
     ggacgtggtt gttgcaaata aaatctacag cgacagttaa attgaagcaa ttattttttc      3480
     ctatttcttg atgtagaaca ttttttgtac ttaattttga taaaatgtgg cattaaacat      3540
     ataatctgaa atgtggacga gaaactttat tttaaactat ttatttattt tttaatcttt      3600
     tcagaaactc aatttatccc ataggaactg aacttatcct taataaactg gtcttatctt      3660
     aagcaacaaa acgttttctt ttcaactgaa ttc                                   3693
//
BioPerl-1.007002/t/data/sv40_small.xml000444000766000024      4642013155576321 17424 0ustar00cjfieldsstaff000000000000
     
       
         
           European Bioinformatics Institute
         
         
           
             
           
         
         
           
         
         
           Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
           http://www.ebi.ac.uk
         
       
       
         
           
             eyckerman-2001-1
             Design and application of a cytokine-receptor-based interaction trap.
           
           
             
               
             
           
           
             
             
             
             
           
           
             
               human-293t
               Homo sapiens 293 cells transformed with SV40 large T antigen
             
             
               
                 293t
                 293 cells expressing SV40 large T antigen.
               
               
                 
                 
               
             
           
           
             
               mappit
               mammalian protein protein interaction trap
             
             
               
               
             
           
           
             
               predetermined
               predetermined participant
             
             
               
               
               
             
           
           
             MAPPIT bait construct - a chimeric cytokine receptor composed of the extracellular region of homodimeric EpoR, fused to the transmembrane and cytosolic domains of the leptin receptor wherein all the tyrosine residues are mutated to phenylalanines. A bait, consisting of a region of the bait protein is C-terminally fused to this signaling-deficient receptor. The interaction is detected via activation of STAT3 and a subsequent reporter gene activation.
             2b, 2c, 5
             jan.tavernier@ugent.be
             Eyckerman S., Verhee A., der Heyden JV., Lemmens I., Ostade XV., Vandekerckhove J., Tavernier J.
           
         
       
       
         
           
             tala_sv40
             Large T antigen
           
           
             
             
             
             
             
           
           
             
               sv40
               Simian virus 40
             
           
           MDKVLNREESLQLMDLLGLERSAWGNIPLMRKAYLKKCKEFHPDKGGDEEKMKKMNTLYKKMEDGVKYAHQPDFGGFWDATEIPTYGTDEWEQWWNAFNEENLFCSEEMPSSDDEATADSQHSTPPKKKRKVEDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAINNYAQKLCTFSFLICKGVNKEYLMYSALTRDPFSVIEESLPGGLKEHDFNPEEAEETKQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEFSVPKTLQARFVKQIDFRAKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLDWLRNSDDDDEDSQENADKNEDGGEKNMEDSGHETGIDSQSQGSFQAPQSSQSVHDHNQPYHICRGFTCFKKPPTPPPEPET
         
         
           
             p53_mouse
             Cellular tumor antigen p53
           
           
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
           
           
             
               mouse
               Mus musculus
             
           
           MTAMEESQSDISLELPLSQETFSGLWKLLPPEDILPSPHCMDDLLLPQDVEEFFEGPSEALRVSGAPAAQDPVTETPGPVAPAPATPWPLSSFVPSQKTYQGNYGFHLGFLQSGTAKSVMCTYSPPLNKLFCQLAKTCPVQLWVSATPPAGSRVRAMAIYKKSQHMTEVVRRCPHHERCSDGDGLAPPQHLIRVEGNLYPEYLEDRQTFRHSVVVPYEPPEAGSEYTTIHYKYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENFRKKEVLCPELPPGSAKRALPTCTSASPPQKKKPLDGEYFTLKIRGRKRFEMFRELNEALELKDAHATEESGDSRAHSSYLKTKKGQSTSRHKKTMVKKVGPDSD
         
         
           
             epor_human
             Erythropoietin receptor precursor
           
           
             
             
             
             
             
             
             
             
             
             
             
           
           
             
               human
               Homo sapiens
             
           
           MDHLGASLWPQVGSLCLLLAGAAWAPPPNLPDPKFESKAALLAARGPEELLCFTERLEDLVCFWEEAASAGVGPGNYSFSYQLEDEPWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLDAPVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGNGAGSVQRVEILEGRTECVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSDLDPLILTLSLILVVILVLLTVLALLSHRRALKQKIWPGIPSPESEFEGLFTTHKGNFQLWLYQNDGCLWWSPCTPFTEDPPASLEVLSERCWGTMQAVEPGTDDEGPLLEPVGSEHAQDTYLVLDKWLLPRNPPSEDLPGPGGSVDIVAMDEGSEASSCSSALASKPSPEGASAASFEYTILDPSSQLLRPWTLCPELPPTPPHLKYLYLVVSDSGISTDYSSGDSQGAQGGLSDGPYSNPYENSLIPAAEPLPPSYVACS
         
         
           
             cish_mouse
             Cytokine-inducible SH2-containing protein
           
           
             
             
             
             
             
             
             
           
           
             
               mouse
               Mus musculus
             
           
           MVLCVQGSCPLLAVEQIGRRPLWAQSLELPGPAMQPLPTGAFPEEVTEETPVQAENEPKVLDPEGDLLCIAKTFSYLRESGWYWGSITASEARQHLQKMPEGTFLVRDSTHPSYLFTLSVKTTRGPTNVRIEYADSSFRLDSNCLSRPRILAFPDVVSLVQHYVASCAADTRSDSPDPAPTPALPMSKQDAPSDSVLPIPVATAVHLKLVQPFVRRSSARSLQHLCRLVINRLVADVDCLPLPRRMADYLRQYPFQL
         
         
           
             socs2_human
             Suppressor of cytokine signaling 2
           
           
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
             
           
           
             
               human
               Homo sapiens
             
           
           MTLRCLEPSGNGGEGTRSQWGTAGSAEEPSPQAARLAKALRELGQTGWYWGSMTVNEAKEKLKEAPEGTFLIRDSSHSDYLLTISVKTSAGPTNLRIEYQDGKFRLDSIICVKSKLKQFDSVVHLIDYYVQMCKDKRTGPEAPRNGTVHLYLTKPLYTSAPSLQHLCRLTINKCTGAIWGLPLPTRLKDYLEEYKFQV
         
       
       
         
           
             sv40-tp53-1
             Interactions between SV40 large T antigen and murine p53 demonstrated by MAPPIT
           
           
             
           
           
             
               
               prey
             
             
               
               bait
             
           
           
             
               physical interaction
               physical interaction
             
             
               
               
             
           
           
             
           
           
             1.0
           
         
         
           
             epor-cish-4
             Interaction between human EpoR and Murine CIS-1 demonstrated by MAPPIT
           
           
             
           
           
             
               
               bait
             
             
               
               prey
             
           
           
             
               physical interaction
               physical interaction
             
             
               
               
             
           
           
             
           
           
             1.0
           
         
         
           
             epor-socs2-3
             Interaction between human EpoR and SOCS2 demonstrated by MAPPIT
           
           
             
           
           
             
               
               prey
             
             
               
               bait
             
           
           
             
               physical interaction
               physical interaction
             
             
               
               
             
           
           
             
           
           
             SOCS2 described as fragment but no detail given
             Erythropoietin
             Phosphorylation of SOCS2 - dependent on treatment of cells with erythropoietin
             1.0
           
         
       
     
   
BioPerl-1.007002/t/data/swiss.dat000444000766000024     11176413155576321 16604 0ustar00cjfieldsstaff000000000000ID   MA32_HUMAN     STANDARD;      PRT;   282 AA.
AC   Q07021;
DT   01-FEB-1995 (Rel. 31, Created)
DT   01-FEB-1995 (Rel. 31, Last sequence update)
DT   01-OCT-2000 (Rel. 40, Last annotation update)
DE   COMPLEMENT COMPONENT 1, Q SUBCOMPONENT BINDING PROTEIN, MITOCHONDRIAL
DE   PRECURSOR (GLYCOPROTEIN GC1QBP) (GC1Q-R PROTEIN) (HYALURONAN-BINDING
DE   PROTEIN 1) (PRE-MRNA SPLICING FACTOR SF2, P32 SUBUNIT) (P33).
GN   GC1QBP OR HABP1 OR SF2P32 OR C1QBP.
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   SEQUENCE FROM N.A., AND SEQUENCE OF 74; 76-93 AND 208-216.
RC   TISSUE=FIBROBLAST;
RX   MEDLINE=94085792; PubMed=8262387;
RA   Honore B., Madsen P., Rasmussen H.H., Vandekerckhove J., Celis J.E.,
RA   Leffers H.;
RT   "Cloning and expression of a cDNA covering the complete coding region
RT   of the P32 subunit of human pre-mRNA splicing factor SF2.";
RL   Gene 134:283-287(1993).
RN   [2]
RP   SEQUENCE OF 5-282 FROM N.A., AND SEQUENCE OF 74-114.
RX   MEDLINE=91309150; PubMed=1830244;
RA   Krainer A.R., Mayeda A., Kozak D., Binns G.;
RT   "Functional expression of cloned human splicing factor SF2: homology
RT   to RNA-binding proteins, U1 70K, and Drosophila splicing regulators.";
RL   Cell 66:383-394(1991).
RN   [3]
RP   SEQUENCE FROM N.A., AND PARTIAL SEQUENCE.
RX   MEDLINE=94253723; PubMed=8195709;
RA   Ghebrehiwet B., Lim B.L., Peerschke E.I., Willis A.C., Reid K.B.;
RT   "Isolation, cDNA cloning, and overexpression of a 33-kD cell surface
RT   glycoprotein that binds to the globular 'heads' of C1q.";
RL   J. Exp. Med. 179:1809-1821(1994).
RN   [4]
RP   X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS).
RX   MEDLINE=99199225; PubMed=10097078;
RA   Jiang J., Zhang Y., Krainer A.R., Xu R.-M.;
RT   "Crystal structure of human p32, a doughnut-shaped acidic
RT   mitochondrial matrix protein.";
RL   Proc. Natl. Acad. Sci. U.S.A. 96:3572-3577(1999).
CC   -!- FUNCTION: NOT KNOWN. BINDS TO THE GLOBULAR "HEADS" OF C1Q THUS
CC       INHIBITING C1 ACTIVATION.
CC   -!- SUBCELLULAR LOCATION: MITOCHONDRIAL MATRIX.
CC   -!- SIMILARITY: BELONGS TO THE MAM33 FAMILY.
CC   -!- CAUTION: WAS ORIGINALLY (REF.1 AND REF.2) THOUGHT TO BE A PRE-MRNA
CC       SPLICING FACTOR THAT PLAYS A ROLE IN PREVENTING EXON SKIPPING,
CC       ENSURING THE ACCURACY OF SPLICING AND REGULATING ALTERNATIVE
CC       SPLICING.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; L04636; AAA16315.1; -.
DR   EMBL; M69039; AAA73055.1; -.
DR   EMBL; X75913; CAA53512.1; -.
DR   PIR; JT0762; JT0762.
DR   PIR; S44104; S44104.
DR   PDB; 1P32; 06-APR-99.
DR   MIM; 601269; -.
KW   Mitochondrion; Transit peptide; 3D-structure.
FT   TRANSIT       1     73       MITOCHONDRION.
FT   CHAIN        74    282       COMPLEMENT COMPONENT 1, Q SUBCOMPONENT
FT                                BINDING PROTEIN.
SQ   SEQUENCE   282 AA;  31362 MW;  2F747FA73BB1314B CRC64;
     MLPLLRCVPR VLGSSVAGLR AAAPASPFRQ LLQPAPRLCT RPFGLLSVRA GSERRPGLLR
     PRGPCACGCG CGSLHTDGDK AFVDFLSDEI KEERKIQKHK TLPKMSGGWE LELNGTEAKL
     VRKVAGEKIT VTFNINNSIP PTFDGEEEPS QGQKVEEQEP ELTSTPNFVV EVIKNDDGKK
     ALVLDCHYPE DEVGQEDEAE SDIFSIREVS FQSTGESEWK DTNYTLNTDS LDWALYDHLM
     DFLADRGVDN TFADELVELS TALEHQEYIT FLEDLKSFVK SQ
//
ID   ACON_CAEEL     STANDARD;      PRT;   788 AA.
AC   P34455;
DT   01-FEB-1994 (Rel. 28, Created)
DT   01-FEB-1994 (Rel. 28, Last sequence update)
DT   15-JUL-1999 (Rel. 38, Last annotation update)
DE   Probable aconitate hydratase, mitochondrial precursor (EC 4.2.1.3)
DE   (Citrate hydro-lyase) (Aconitase).
GN   F54H12.1.
OS   Caenorhabditis elegans.
OC   Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea;
OC   Rhabditidae; Peloderinae; Caenorhabditis.
OX   NCBI_TaxID=6239;
RN   [1]
RP   SEQUENCE FROM N.A.
RC   STRAIN=BRISTOL N2;
RX   MEDLINE=94150718; PubMed=7906398;
RA   Wilson R., Ainscough R., Anderson K., Baynes C., Berks M.,
RA   Bonfield J., Burton J., Connell M., Copsey T., Cooper J., Coulson A.,
RA   Craxton M., Dear S., Du Z., Durbin R., Favello A., Fraser A.,
RA   Fulton L., Gardner A., Green P., Hawkins T., Hillier L., Jier M.,
RA   Johnston L., Jones M., Kershaw J., Kirsten J., Laisster N.,
RA   Latreille P., Lightning J., Lloyd C., Mortimore B., O'Callaghan M.,
RA   Parsons J., Percy C., Rifken L., Roopra A., Saunders D., Shownkeen R.,
RA   Sims M., Smaldon N., Smith A., Smith M., Sonnhammer E., Staden R.,
RA   Sulston J., Thierry-Mieg J., Thomas K., Vaudin M., Vaughan K.,
RA   Waterson R., Watson A., Weinstock L., Wilkinson-Sproat J.,
RA   Wohldman P.;
RT   "2.2 Mb of contiguous nucleotide sequence from chromosome III of C.
RT   elegans.";
RL   Nature 368:32-38(1994).
CC   -!- CATALYTIC ACTIVITY: Citrate = cis-aconitate + H(2)O.
CC   -!- COFACTOR: ACONITASE HAS AN ACTIVE (4FE-4S) AND AN INACTIVE (3FE-
CC       4S) FORMS. THE ACTIVE (4FE-4S) CLUSTER IS PART OF THE CATALYTIC
CC       SITE THAT INTERCONVERTS CITRATE, CIS-ACONITASE, AND ISOCITRATE (BY
CC       SIMILARITY).
CC   -!- PATHWAY: TRICARBOXYLIC ACID CYCLE.
CC   -!- SUBUNIT: MONOMER (BY SIMILARITY).
CC   -!- SUBCELLULAR LOCATION: Mitochondrial (By similarity).
CC   -!- SIMILARITY: BELONGS TO THE ACONITASE/IPM ISOMERASE FAMILY.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; L25599; AAA28050.1; -.
DR   PIR; S44831; S44831.
DR   HSSP; P20004; 1AMJ.
DR   WormPep; F54H12.1; CE00516.
DR   InterPro; IPR001030; Aconitase.
DR   InterPro; IPR000573; Aconitase_C.
DR   Pfam; PF00330; aconitase; 1.
DR   Pfam; PF00694; Aconitase_C; 1.
DR   PRINTS; PR00415; ACONITASE.
DR   ProDom; PD000511; Aconitase; 1.
DR   PROSITE; PS00450; ACONITASE_1; 1.
DR   PROSITE; PS01244; ACONITASE_2; 1.
KW   Hypothetical protein; Lyase; Tricarboxylic acid cycle; Iron-sulfur;
KW   Mitochondrion; Transit peptide; 4Fe-4S.
FT   TRANSIT       1      ?       MITOCHONDRION (POTENTIAL).
FT   CHAIN         ?    788       PROBABLE ACONITATE HYDRATASE.
FT   METAL       393    393       IRON-SULFUR (4FE-4S) (BY SIMILARITY).
FT   METAL       456    456       IRON-SULFUR (4FE-4S) (BY SIMILARITY).
FT   METAL       459    459       IRON-SULFUR (4FE-4S) (BY SIMILARITY).
SQ   SEQUENCE   788 AA;  85712 MW;  8861E6FC198B70D9 CRC64;
     MRYHFLFGSL RNHLFSFRGV IYCREKLFNC SKLSFRPSKV AISKFEPKSY LPYEKLSQTV
     KIVKDRLKRP LTLSEKILYG HLDQPKTQDI ERGVSYLRLR PDRVAMQDAT AQMAMLQFIS
     SGLPKTAVPS TIHCDHLIEA QKGGAQDLAR AKDLNKEVFN FLATAGSKYG VGFWKPGSGI
     IHQIILENYA FPGLLLIGTD SHTPNGGGLG GLCIGVGGAD AVDVMADIPW ELKCPKVIGI
     KLTGKLNGWT SAKDVILKVA DILTVKGGTG AIVEYFGPGV DSISATGMGT ICNMGAEIGA
     TTSVFPYNES MYKYLEATGR KEIAEEARKY KDLLTADDGA NYDQIIEINL DTLTPHVNGP
     FTPDLASSID KLGENAKKNG WPLDVKVSLI GSCTNSSYED MTRAASIAKQ ALDKGLKAKT
     IFTITPGSEQ VRATIERDGL SKIFADFGGM VLANACGPCI GQWDRQDVKK GEKNTIVTSY
     NRNFTGRNDA NPATHGFVTS PDITTAMAIS GRLDFNPLTD ELTAADGSKF KLQAPTGLDL
     PPKGYDPGED TFQAPSGSGQ VDVSPSSDRL QLLSPFDKWD GKDLEDMKIL IKVTGKCTTD
     HISAAGPWLK YRGHLDNISN NLFLTAINAD NGEMNKVKNQ VTGEYGAVPA TARKYKADGV
     RWVAIGDENY GEGSSREHAA LEPRHLGGRA IIVKSFARIH ETNLKKQGML PLTFANPADY
     DKIDPSDNVS IVGLSSFAPG KPLTAIFKKT NGSKVEVTLN HTFNEQQIEW FKAGSALNRM
     KEVFAKSK
//
ID   143E_HUMAN     STANDARD;      PRT;   255 AA.
AC   P42655; P29360; Q63631;
DT   01-NOV-1995 (Rel. 32, Created)
DT   01-NOV-1995 (Rel. 32, Last sequence update)
DT   15-JUL-1999 (Rel. 38, Last annotation update)
DE   14-3-3 protein epsilon (Mitochondrial import stimulation factor L
DE   subunit) (Protein kinase C inhibitor protein-1) (KCIP-1) (14-3-3E).
GN   YWHAE.
OS   Homo sapiens (Human),
OS   Mus musculus (Mouse),
OS   Rattus norvegicus (Rat),
OS   Bos taurus (Bovine), and
OS   Ovis aries (Sheep).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606, 10090, 10116, 9913, 9940;
RN   [1]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human;
RX   MEDLINE=95372385; PubMed=7644510;
RA   Conklin D.S., Galaktionov K., Beach D.;
RT   "14-3-3 proteins associate with cdc25 phosphatases.";
RL   Proc. Natl. Acad. Sci. U.S.A. 92:7892-7896(1995).
RN   [2]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human; TISSUE=Heart;
RA   Luk S.C.W., Lee C.Y., Waye M.M.Y.;
RL   Submitted (JUN-1995) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human;
RX   MEDLINE=96300316; PubMed=8684458;
RA   Jin D.-Y., Lyu M.S., Kozak C.A., Jeang K.-T.;
RT   "Function of 14-3-3 proteins.";
RL   Nature 382:308-308(1996).
RN   [4]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human; TISSUE=Liver;
RX   MEDLINE=97011338; PubMed=8858348;
RA   Chong S.S., Tanigami A., Roschke A.V., Ledbetter D.H.;
RT   "14-3-3 epsilon has no homology to LIS1 and lies telomeric to it on
RT   chromosome 17p13.3 outside the Miller-Dieker syndrome chromosome
RT   region.";
RL   Genome Res. 6:735-741(1996).
RN   [5]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human;
RA   Tanigami A., Chong S.S., Ledbetter D.H.;
RT   "14-3-3 epsilon genomic sequence.";
RL   Submitted (AUG-1998) to the EMBL/GenBank/DDBJ databases.
RN   [6]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human; TISSUE=Placenta;
RA   Strausberg R.;
RL   Submitted (DEC-2000) to the EMBL/GenBank/DDBJ databases.
RN   [7]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Rat, and Sheep; TISSUE=Pineal gland;
RX   MEDLINE=94296566; PubMed=8024705;
RA   Roseboom P.H., Weller J.L., Babila T., Aitken A., Sellers L.A.,
RA   Moffet J.R., Namboodiri M.A., Klein D.C.;
RT   "Cloning and characterization of the epsilon and zeta isoforms of the
RT   14-3-3 proteins.";
RL   DNA Cell Biol. 13:629-640(1994).
RN   [8]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Rat; TISSUE=Liver;
RX   MEDLINE=95122474; PubMed=7822263;
RA   Alam R., Hachiya N., Sakaguchi M., Shun-Ichiro K., Iwanaga S.,
RA   Kitajima M., Mihara K., Omura T.;
RT   "cDNA cloning and characterization of mitochondrial import
RT   stimulation factor (MSF) purified from rat liver cytosol.";
RL   J. Biochem. 116:416-425(1994).
RN   [9]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Rat; TISSUE=Brain;
RX   MEDLINE=96280718; PubMed=8694795;
RA   Gao L., Gu X.B., Yu D.S., Yu R.K., Zeng G.;
RT   "Association of a 14-3-3 protein with CMP-NeuAc:GM1 alpha 2,3-
RT   sialyltransferase.";
RL   Biochem. Biophys. Res. Commun. 224:103-107(1996).
RN   [10]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Mouse; STRAIN=SWISS; TISSUE=Kidney;
RX   MEDLINE=95269876; PubMed=7750640;
RA   McConnell J.E., Armstrong J.F., Bard J.B.;
RT   "The mouse 14-3-3 epsilon isoform, a kinase regulator whose
RT   expression pattern is modulated in mesenchyme and neuronal
RT   differentiation.";
RL   Dev. Biol. 169:218-228(1995).
RN   [11]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Mouse; STRAIN=129/SV;
RA   Takihara Y., Irie K., Nomura M., Motaleb M., Matsumoto K.,
RA   Shimada K.;
RL   Submitted (SEP-1996) to the EMBL/GenBank/DDBJ databases.
RN   [12]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Bovine;
RA   Jones J.M., Niikura T., Pinke R.M., Guo W., Molday L., Leykam J.,
RA   McConnell D.G.;
RT   "Expression of 14-3-3 proteins in bovine retinal photoreceptors.";
RL   Submitted (JAN-1998) to the EMBL/GenBank/DDBJ databases.
RN   [13]
RP   SEQUENCE OF 1-152; 165-184 AND 216-255.
RC   SPECIES=Sheep; TISSUE=Brain;
RX   MEDLINE=92283271; PubMed=1317796;
RA   Toker A., Sellers L.A., Amess B., Patel Y., Harris A., Aitken A.;
RT   "Multiple isoforms of a protein kinase C inhibitor (KCIP-1/14-3-3)
RT   from sheep brain. Amino acid sequence of phosphorylated forms.";
RL   Eur. J. Biochem. 206:453-461(1992).
RN   [14]
RP   SEQUENCE OF 1-23 AND 125-140.
RC   SPECIES=Sheep; TISSUE=Brain;
RX   MEDLINE=90345949; PubMed=2143472;
RA   Toker A., Ellis C.A., Sellers L.A., Aitken A.;
RT   "Protein kinase C inhibitor proteins. Purification from sheep brain
RT   and sequence similarity to lipocortins and 14-3-3 protein.";
RL   Eur. J. Biochem. 191:421-429(1990).
CC   -!- FUNCTION: ACTIVATES TYROSINE AND TRYPTOPHAN HYDROXYLASES IN THE
CC       PRESENCE OF CA(2+)/CALMODULIN-DEPENDENT PROTEIN KINASE II, AND
CC       STRONGLY ACTIVATES PROTEIN KINASE C. IS PROBABLY A MULTIFUNCTIONAL
CC       REGULATOR OF THE CELL SIGNALING PROCESSES MEDIATED BY BOTH
CC       KINASES.
CC   -!- SUBUNIT: HOMODIMER.
CC   -!- SUBCELLULAR LOCATION: CYTOPLASMIC.
CC   -!- TISSUE SPECIFICITY: 14-3-3 PROTEINS ARE LOCALIZED IN NEURONS, AND
CC       ARE AXONALLY TRANSPORTED TO THE NERVE TERMINALS. THEY MAY BE ALSO
CC       PRESENT, AT LOWER LEVELS, IN VARIOUS OTHER EUKARYOTIC TISSUES.
CC   -!- SIMILARITY: BELONGS TO THE 14-3-3 FAMILY.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; U28936; AAA75301.1; -.
DR   EMBL; U20972; AAC50175.1; -.
DR   EMBL; U43399; AAC50625.1; -.
DR   EMBL; U43430; AAD00026.1; -.
DR   EMBL; U54778; AAC50710.1; -.
DR   EMBL; AB017103; BAA32538.1; -.
DR   EMBL; AB017098; BAA32538.1; JOINED.
DR   EMBL; AB017099; BAA32538.1; JOINED.
DR   EMBL; AB017100; BAA32538.1; JOINED.
DR   EMBL; AB017101; BAA32538.1; JOINED.
DR   EMBL; AB017102; BAA32538.1; JOINED.
DR   EMBL; BC000179; AAH00179.1; -.
DR   EMBL; BC001440; AAH01440.1; -.
DR   EMBL; M84416; AAC37659.1; -.
DR   EMBL; D30739; BAA06401.1; -.
DR   EMBL; Z19599; CAA79659.1; -.
DR   EMBL; U53882; AAC52676.1; -.
DR   EMBL; L07914; AAC37321.1; -.
DR   EMBL; D87663; BAA13424.1; -.
DR   EMBL; AF043735; AAC61927.1; -.
DR   PIR; S10806; S10806.
DR   PIR; S10807; S10807.
DR   HSSP; P29312; 1A38.
DR   MIM; 605066; -.
DR   MGD; MGI:894689; Ywhae.
DR   InterPro; IPR000308; 14-3-3.
DR   Pfam; PF00244; 14-3-3; 1.
DR   PRINTS; PR00305; 1433ZETA.
DR   ProDom; PD000600; 14-3-3; 1.
DR   SMART; SM00101; 14_3_3; 1.
DR   PROSITE; PS00796; 1433_1; 1.
DR   PROSITE; PS00797; 1433_2; 1.
KW   Brain; Neurone; Acetylation; Multigene family.
FT   MOD_RES       1      1       ACETYLATION.
FT   CONFLICT     73     73       K -> T (IN REF. 9).
FT   CONFLICT    120    120       F -> S (IN REF. 9).
FT   CONFLICT    123    123       K -> Y (IN REF. 9).
FT   CONFLICT    129    129       H -> Y (IN REF. 14).
SQ   SEQUENCE   255 AA;  29174 MW;  07817CCBD1F75B26 CRC64;
     MDDREDLVYQ AKLAEQAERY DEMVESMKKV AGMDVELTVE ERNLLSVAYK NVIGARRASW
     RIISSIEQKE ENKGGEDKLK MIREYRQMVE TELKLICCDI LDVLDKHLIP AANTGESKVF
     YYKMKGDYHR YLAEFATGND RKEAAENSLV AYKAASDIAM TELPPTHPIR LGLALNFSVF
     YYEILNSPDR ACRLAKAAFD DAIAELDTLS EESYKDSTLI MQLLRDNLTL WTSDMQGDGE
     EQNKEALQDV EDENQ
//
ID   143B_BOVIN     STANDARD;      PRT;   245 AA.
AC   P29358;
DT   01-DEC-1992 (Rel. 24, Created)
DT   01-FEB-1996 (Rel. 33, Last sequence update)
DT   16-OCT-2001 (Rel. 40, Last annotation update)
DE   14-3-3 protein beta/alpha (Protein kinase C inhibitor protein-1)
DE   (KCIP-1).
GN   YWHAB.
OS   Bos taurus (Bovine), and
OS   Ovis aries (Sheep).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea;
OC   Bovidae; Bovinae; Bos.
OX   NCBI_TaxID=9913, 9940;
RN   [1]
RP   SEQUENCE.
RC   SPECIES=Bovine;
RX   MEDLINE=91108808; PubMed=1671102;
RA   Isobe T., Ichimura T., Sunaya T., Okuyama T., Takahashi N., Kuwano R.,
RA   Takahashi Y.;
RT   "Distinct forms of the protein kinase-dependent activator of tyrosine
RT   and tryptophan hydroxylases.";
RL   J. Mol. Biol. 217:125-132(1991).
RN   [2]
RP   SEQUENCE OF 2-145 FROM N.A.
RC   SPECIES=Bovine; TISSUE=Retina;
RA   Jones J.M., Niikura T., Pinke R.M., Guo W., Molday L., Leykam J.,
RA   McConnell D.G.;
RT   "Expression of 14-3-3 proteins in bovine retinal photoreceptors.";
RL   Submitted (JAN-1998) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   SEQUENCE OF 2-83; 121-186 AND 199-241.
RC   SPECIES=Sheep; TISSUE=Brain;
RX   MEDLINE=92283271; PubMed=1317796;
RA   Toker A., Sellers L.A., Amess B., Patel Y., Harris A., Aitken A.;
RT   "Multiple isoforms of a protein kinase C inhibitor (KCIP-1/14-3-3)
RT   from sheep brain. Amino acid sequence of phosphorylated forms.";
RL   Eur. J. Biochem. 206:453-461(1992).
RN   [4]
RP   SEQUENCE OF 2-23.
RC   SPECIES=Sheep; TISSUE=Brain;
RX   MEDLINE=90345949; PubMed=2143472;
RA   Toker A., Ellis C.A., Sellers L.A., Aitken A.;
RT   "Protein kinase C inhibitor proteins. Purification from sheep brain
RT   and sequence similarity to lipocortins and 14-3-3 protein.";
RL   Eur. J. Biochem. 191:421-429(1990).
RN   [5]
RP   PHOSPHORYLATION.
RC   SPECIES=Sheep;
RX   MEDLINE=95197587; PubMed=7890696;
RA   Aitken A., Howell S., Jones D., Madrazo J., Patel Y.;
RT   "14-3-3 alpha and delta are the phosphorylated forms of
RT   raf-activating 14-3-3 beta and zeta. In vivo stoichiometric
RT   phosphorylation in brain at a Ser-Pro-Glu-Lys motif.";
RL   J. Biol. Chem. 270:5706-5709(1995).
RN   [6]
RP   POST-TRANSLATIONAL MODIFICATIONS.
RC   SPECIES=Sheep;
RA   Aitken A., Patel Y., Martin H., Jones D., Robinson K., Madrazo J.,
RA   Howell S.;
RT   "Electrospray mass spectroscopy analysis with online trapping of
RT   posttranslationally modified mammalian and avian brain 14-3-3
RT   isoforms.";
RL   J. Protein Chem. 13:463-465(1994).
CC   -!- FUNCTION: ACTIVATES TYROSINE AND TRYPTOPHAN HYDROXYLASES IN THE
CC       PRESENCE OF CA(2+)/CALMODULIN-DEPENDENT PROTEIN KINASE II, AND
CC       STRONGLY ACTIVATES PROTEIN KINASE C. IS PROBABLY A MULTIFUNCTIONAL
CC       REGULATOR OF THE CELL SIGNALING PROCESSES MEDIATED BY BOTH
CC       KINASES.
CC   -!- SUBUNIT: HOMODIMER.
CC   -!- SUBCELLULAR LOCATION: CYTOPLASMIC.
CC   -!- ALTERNATIVE PRODUCTS: TWO FORMS ARE PRODUCED BY ALTERNATIVE
CC       INITIATION.
CC   -!- TISSUE SPECIFICITY: 14-3-3 PROTEINS ARE LOCALIZED IN NEURONS, AND
CC       ARE AXONALLY TRANSPORTED TO THE NERVE TERMINALS. THEY MAY BE ALSO
CC       PRESENT, AT LOWER LEVELS, IN VARIOUS OTHER EUKARYOTIC TISSUES.
CC   -!- PTM: ISOFORM ALPHA DIFFERS FROM ISOFORM BETA IN BEING
CC       PHOSPHORYLATED.
CC   -!- SIMILARITY: BELONGS TO THE 14-3-3 FAMILY.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; AF043736; AAC02090.1; -.
DR   PIR; S13467; S13467.
DR   PIR; S10804; S10804.
DR   PIR; S23179; S23179.
DR   HSSP; P29312; 1A38.
DR   InterPro; IPR000308; 14-3-3.
DR   Pfam; PF00244; 14-3-3; 1.
DR   PRINTS; PR00305; 1433ZETA.
DR   ProDom; PD000600; 14-3-3; 1.
DR   SMART; SM00101; 14_3_3; 1.
DR   PROSITE; PS00796; 1433_1; 1.
DR   PROSITE; PS00797; 1433_2; 1.
KW   Brain; Neurone; Phosphorylation; Acetylation; Multigene family;
KW   Alternative initiation.
FT   INIT_MET      0      0
FT   CHAIN         1    245       14-3-3 PROTEIN BETA/ALPHA, LONG ISOFORM.
FT   CHAIN         2    245       14-3-3 PROTEIN BETA/ALPHA, SHORT ISOFORM.
FT   INIT_MET      2      2       FOR SHORT ISOFORM.
FT   MOD_RES       1      1       ACETYLATION.
FT   MOD_RES       2      2       ACETYLATION (IN SHORT ISOFORM).
FT   MOD_RES     185    185       PHOSPHORYLATION.
SQ   SEQUENCE   245 AA;  27950 MW;  AA91C2314D99549F CRC64;
     TMDKSELVQK AKLAEQAERY DDMAAAMKAV TEQGHELSNE ERNLLSVAYK NVVGARRSSW
     RVISSIEQKT ERNEKKQQMG KEYREKIEAE LQDICNDVLQ LLDKYLIPNA TQPESKVFYL
     KMKGDYFRYL SEVASGDNKQ TTVSNSQQAY QEAFEISKKE MQPTHPIRLG LALNFSVFYY
     EILNSPEKAC SLAKTAFDEA IAELDTLNEE SYKDSTLIMQ LLRDNLTLWT SENQGDEGDA
     GEGEN
//
ID   CALM_HUMAN     STANDARD;      PRT;   148 AA.
AC   P02593; P99014; P70667; Q61379; Q61380;
DT   21-JUL-1986 (Rel. 01, Created)
DT   21-JUL-1986 (Rel. 01, Last sequence update)
DT   16-OCT-2001 (Rel. 40, Last annotation update)
DE   Calmodulin.
GN   (CALM1 OR CAM1 OR CALM OR CAM) AND (CALM2 OR CAM2 OR CAMB) AND
GN   (CALM3 OR CAM3 OR CAMC).
OS   Homo sapiens (Human),
OS   Mus musculus (Mouse),
OS   Rattus norvegicus (Rat),
OS   Oryctolagus cuniculus (Rabbit),
OS   Bos taurus (Bovine),
OS   Gallus gallus (Chicken),
OS   Anas platyrhynchos (Domestic duck),
OS   Xenopus laevis (African clawed frog),
OS   Arbacia punctulata (Punctuate sea urchin),
OS   Oncorhynchus sp. (Salmon), and
OS   Oryzias latipes (Medaka fish).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606, 10090, 10116, 9986, 9913, 9031, 8839, 8355, 7641,
OX   8025, 8090;
RN   [1]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human;
RX   MEDLINE=89034207; PubMed=3182832;
RA   Fischer R., Koller M., Flura M., Mathews S., Strehler-Page M.A.,
RA   Krebs J., Penniston J.T., Carafoli E., Strehler E.E.;
RT   "Multiple divergent mRNAs code for a single human calmodulin.";
RL   J. Biol. Chem. 263:17055-17062(1988).
RN   [2]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human;
RX   MEDLINE=88059053; PubMed=2445749;
RA   Sengupta B., Friedberg F., Detera-Wadleigh S.D.;
RT   "Molecular analysis of human and rat calmodulin complementary DNA
RT   clones. Evidence for additional active genes in these species.";
RL   J. Biol. Chem. 262:16663-16670(1987).
RN   [3]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human;
RX   MEDLINE=85022688; PubMed=6385987;
RA   Wawrzynczak E.J., Perham R.N.;
RT   "Isolation and nucleotide sequence of a cDNA encoding human
RT   calmodulin.";
RL   Biochem. Int. 9:177-185(1984).
RN   [4]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human; TISSUE=Blood;
RX   MEDLINE=95010144; PubMed=7925473;
RA   Rhyner J.A., Ottiger M., Wicki R., Greenwood T.M., Strehler E.E.;
RT   "Structure of the human CALM1 calmodulin gene and identification of
RT   two CALM1-related pseudogenes CALM1P1 and CALM1P2.";
RL   Eur. J. Biochem. 225:71-82(1994).
RN   [5]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Human; TISSUE=Lymphoma;
RA   Kato S.;
RL   Submitted (FEB-1995) to the EMBL/GenBank/DDBJ databases.
RN   [6]
RP   SEQUENCE.
RC   SPECIES=Human; TISSUE=Brain;
RX   MEDLINE=82231946; PubMed=7093203;
RA   Sasagawa T., Ericsson L.H., Walsh K.A., Schreiber W.E., Fischer E.H.,
RA   Titani K.;
RT   "Complete amino acid sequence of human brain calmodulin.";
RL   Biochemistry 21:2565-2569(1982).
RN   [7]
RP   SEQUENCE.
RC   SPECIES=Rabbit; TISSUE=Skeletal muscle;
RX   MEDLINE=81138220; PubMed=7202416;
RA   Grand R.J.A., Shenolikar S., Cohen P.;
RT   "The amino acid sequence of the delta subunit (calmodulin) of rabbit
RT   skeletal muscle phosphorylase kinase.";
RL   Eur. J. Biochem. 113:359-367(1981).
RN   [8]
RP   SEQUENCE.
RC   SPECIES=Bovine; TISSUE=Brain;
RA   Kasai H., Kato Y., Isobe T., Kawasaki H., Okuyama T.;
RT   "Determination of the complete amino acid sequence of calmodulin
RT   (phenylalanine-rich acidic protein II) from bovine brain.";
RL   Biomed. Res. 1:248-264(1980).
RN   [9]
RP   SEQUENCE.
RC   SPECIES=Bovine; TISSUE=Brain;
RX   MEDLINE=80094551; PubMed=7356670;
RA   Watterson D.M., Sharief F., Vanaman T.C.;
RT   "The complete amino acid sequence of the Ca2+-dependent modulator
RT   protein (calmodulin) of bovine brain.";
RL   J. Biol. Chem. 255:962-975(1980).
RN   [10]
RP   SEQUENCE.
RC   SPECIES=Bovine; TISSUE=Uterus;
RA   Grand R.J.A., Perry S.V.;
RT   "The amino acid sequence of the troponin C-like protein (modulator
RT   protein) from bovine uterus.";
RL   FEBS Lett. 92:137-142(1978).
RN   [11]
RP   SEQUENCE OF 38-60.
RC   SPECIES=Bovine;
RX   MEDLINE=89064822; PubMed=3058479;
RA   Pribilla I., Krueger H., Buchner K., Otto H., Schiebler W.,
RA   Tripier D., Hucho F.;
RT   "Heat-resistant inhibitors of protein kinase C from bovine brain.";
RL   Eur. J. Biochem. 177:657-664(1988).
RN   [12]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Mouse;
RX   MEDLINE=88257100; PubMed=3384819;
RA   Bender P.K., Dedman J.R., Emerson C.P.;
RT   "The abundance of calmodulin mRNAs is regulated in phosphorylase
RT   kinase-deficient skeletal muscle.";
RL   J. Biol. Chem. 263:9733-9737(1988).
RN   [13]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Mouse;
RX   MEDLINE=90006775; PubMed=2551780;
RA   Danchin A., Sezer O., Glaser P., Chalon P., Caput D.;
RT   "Cloning and expression of mouse-brain calmodulin as an activator of
RT   Bordetella pertussis adenylate cyclase in Escherichia coli.";
RL   Gene 80:145-149(1989).
RN   [14]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Mouse; STRAIN=BALB/C; TISSUE=Brain;
RA   Kato K.;
RT   "A collection of cDNA clones with specific expression patterns in
RT   mouse brain.";
RL   Eur. J. Neurosci. 2:704-711(1991).
RN   [15]
RP   SEQUENCE.
RC   SPECIES=Rat; TISSUE=Testis;
RX   MEDLINE=78066877; PubMed=201628;
RA   Dedman J.R., Jackson R.L., Schreiber W.E., Means A.R.;
RT   "Sequence homology of the Ca2+-dependent regulator of cyclic
RT   nucleotide phosphodiesterase from rat testis with other Ca2+-binding
RT   proteins.";
RL   J. Biol. Chem. 253:343-346(1978).
RN   [16]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Rat; TISSUE=Brain;
RX   MEDLINE=87246077; PubMed=2885164;
RA   Sherbany A.A., Parent A.S., Brosius J.;
RT   "Rat calmodulin cDNA.";
RL   DNA 6:267-272(1987).
RN   [17]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Rat; TISSUE=Brain;
RX   MEDLINE=87226204; PubMed=3035194;
RA   Nojima H., Hirofumi S.;
RT   "Structure of a gene for rat calmodulin.";
RL   J. Mol. Biol. 193:439-445(1987).
RN   [18]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Rat;
RX   MEDLINE=87257889; PubMed=3037336;
RA   Nojima H., Kishi K., Sokabe H.;
RT   "Multiple calmodulin mRNA species are derived from two distinct
RT   genes.";
RL   Mol. Cell. Biol. 7:1873-1880(1987).
RN   [19]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Rat; STRAIN=SHR;
RX   MEDLINE=89362474; PubMed=2527998;
RA   Nojima H.;
RT   "Structural organization of multiple rat calmodulin genes.";
RL   J. Mol. Biol. 208:269-282(1989).
RN   [20]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Chicken;
RX   MEDLINE=84008199; PubMed=6137485;
RA   Putkey J.A., Ts'Ui K.F., Tanaka T., Lagace L., Stein J.P., Lai E.C.,
RA   Means A.R.;
RT   "Chicken calmodulin genes. A species comparison of cDNA sequences and
RT   isolation of a genomic clone.";
RL   J. Biol. Chem. 258:11864-11870(1983).
RN   [21]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Chicken;
RX   MEDLINE=85104969; PubMed=2981850;
RA   Simmen R.C.M., Tanaka T., Ts'Ui K.F., Putkey J.A., Scott M.J.,
RA   Lai E.C., Means A.R.;
RT   "The structural organization of the chicken calmodulin gene.";
RL   J. Biol. Chem. 260:907-912(1985).
RN   [22]
RP   ERRATUM.
RC   SPECIES=Chicken;
RA   Simmen R.C.M., Tanaka T., Ts'Ui K.F., Putkey J.A., Scott M.J.,
RA   Lai E.C., Means A.R.;
RL   J. Biol. Chem. 262:4928-4929(1987).
RN   [23]
RP   SEQUENCE FROM N.A.
RC   SPECIES=Chicken;
RA   Iida Y.;
RT   "cDNA sequences and molecular evolution of calmodulin genes of
RT   chicken and eel.";
RL   Bull. Chem. Soc. Jpn. 57:2667-2668(1984).
RN   [24]
RP   SEQUENCE FROM N.A.
RC   SPECIES=A.platyrhynchos;
RX   MEDLINE=93287810; PubMed=8389959;
RA   Kimura N., Kurosawa N., Kondo K., Tsukada Y.;
RT   "Molecular cloning of the kainate-binding protein and calmodulin
RT   genes which are induced by an imprinting stimulus in ducklings.";
RL   Brain Res. Mol. Brain Res. 17:351-355(1993).
RN   [25]
RP   SEQUENCE FROM N.A.
RC   SPECIES=X.laevis;
RX   MEDLINE=84191128; PubMed=6325880;
RA   Chien Y.-H., Dawid I.B.;
RT   "Isolation and characterization of calmodulin genes from Xenopus
RT   laevis.";
RL   Mol. Cell. Biol. 4:507-513(1984).
RN   [26]
RP   SEQUENCE OF 1-141 FROM N.A.
RC   SPECIES=A.punctulata;
RX   MEDLINE=88172463; PubMed=3351921;
RA   Hardy D.O., Bender P.K., Kretsinger R.H.;
RT   "Two calmodulin genes are expressed in Arbacia punctulata. An ancient
RT   gene duplication is indicated.";
RL   J. Mol. Biol. 199:223-227(1988).
RN   [27]
RP   SEQUENCE.
RC   SPECIES=Salmon;
RA   Yazawa M., Toda H., Yagi Y.;
RT   "Amino acid sequence of salmon calmodulin.";
RL   Seikagaku 57:1037-1037(1985).
RN   [28]
RP   SEQUENCE FROM N.A.
RC   SPECIES=O.latipes;
RX   MEDLINE=93012998; PubMed=1398109;
RA   Matsuo K., Sato K., Ikeshima H., Shimoda K., Takano T.;
RT   "Four synonymous genes encode calmodulin in the teleost fish, medaka
RT   (Oryzias latipes): conservation of the multigene one-protein
RT   principle.";
RL   Gene 119:279-281(1992).
RN   [29]
RP   SEQUENCE OF 1-27, AND UBIQUITYLATION OF LYS-21.
RC   SPECIES=Bovine;
RX   MEDLINE=98380241; PubMed=9716384;
RA   Laub M., Steppuhn J.A., Blueggel M., Immler D., Meyer H.E.,
RA   Jennissen H.P.;
RT   "Modulation of calmodulin function by ubiquitin-calmodulin ligase and
RT   identification of the responsible ubiquitylation site in vertebrate
RT   calmodulin.";
RL   Eur. J. Biochem. 255:422-431(1998).
RN   [30]
RP   X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
RC   SPECIES=Rat;
RX   MEDLINE=85188323; PubMed=3990807;
RA   Babu Y.S., Sack J.S., Greenhough T.J., Bugg C.E., Means A.R.,
RA   Cook W.J.;
RT   "Three-dimensional structure of calmodulin.";
RL   Nature 315:37-40(1985).
RN   [31]
RP   X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
RC   SPECIES=Rat;
RX   MEDLINE=89110997; PubMed=3145979;
RA   Babu Y.S., Bugg C.E., Cook W.J.;
RT   "Structure of calmodulin refined at 2.2-A resolution.";
RL   J. Mol. Biol. 204:191-204(1988).
RN   [32]
RP   X-RAY CRYSTALLOGRAPHY (2 ANGSTROMS).
RC   SPECIES=Bovine;
RX   MEDLINE=98104088; PubMed=9438860;
RA   Wall M.E., Clarage J.B., Phillips G.N.;
RT   "Motions of calmodulin characterized using both Bragg and diffuse
RT   X-ray scattering.";
RL   Structure 5:1599-1612(1997).
RN   [33]
RP   STRUCTURE BY NMR OF 76-148.
RX   MEDLINE=94085641; PubMed=8262263;
RA   Finn B.E., Drakenberg T., Forsen S.;
RT   "The structure of apo-calmodulin. A 1H NMR examination of the
RT   carboxy-terminal domain.";
RL   FEBS Lett. 336:368-374(1993).
RN   [34]
RP   STRUCTURE BY NMR OF 76-148.
RX   MEDLINE=96018615; PubMed=7552749;
RA   Finn B.E., Evenas J., Drakenberg T., Waltho J.P., Thulin E.,
RA   Forsen S.;
RT   "Calcium-induced structural changes and domain autonomy in
RT   calmodulin.";
RL   Nat. Struct. Biol. 2:777-783(1995).
RN   [35]
RP   STRUCTURE BY NMR.
RX   MEDLINE=96018613; PubMed=7552747;
RA   Zhang M., Tanaka T., Ikura M.;
RT   "Calcium-induced conformational transition revealed by the solution
RT   structure of apo calmodulin.";
RL   Nat. Struct. Biol. 2:758-767(1995).
RN   [36]
RP   STRUCTURE BY NMR.
RX   MEDLINE=96018614; PubMed=7552748;
RA   Kuboniwa H., Tjandra N., Grzesiek S., Ren H., Klee C.B., Bax A.;
RT   "Solution structure of calcium-free calmodulin.";
RL   Nat. Struct. Biol. 2:768-776(1995).
RN   [37]
RP   STRUCTURE BY NMR.
RX   MEDLINE=98179557; PubMed=9514729;
RA   Osawa M., Swindells M.B., Tanikawa J., Tanaka T., Mase T., Furuya T.,
RA   Ikura M.;
RT   "Solution structure of calmodulin-W-7 complex: the basis of diversity
RT   in molecular recognition.";
RL   J. Mol. Biol. 276:165-176(1998).
RN   [38]
RP   STRUCTURE BY NMR.
RX   MEDLINE=99425120; PubMed=10493800;
RA   Elshorst B., Hennig M., Foersterling H., Diener A., Maurer M.,
RA   Schulte P., Schwalbe H., Griesinger C., Krebs J., Schmid H.,
RA   Vorherr T., Carafoli E.;
RT   "NMR solution structure of a complex of calmodulin with a binding
RT   peptide of the Ca(2+) pump.";
RL   Biochemistry 38:12320-12332(1999).
CC   -!- FUNCTION: CALMODULIN MEDIATES THE CONTROL OF A LARGE NUMBER OF
CC       ENZYMES BY CA(++). AMONG THE ENZYMES TO BE STIMULATED BY THE
CC       CALMODULIN-CA(++) COMPLEX ARE A NUMBER OF PROTEIN KINASES AND
CC       PHOSPHATASES.
CC   -!- PTM: UBIQUITYLATION STRONGLY DECREASES THE ACTIVITY.
CC   -!- MISCELLANEOUS: THIS PROTEIN HAS FOUR FUNCTIONAL CALCIUM-BINDING
CC       SITES.
CC   -!- SIMILARITY: TO OTHER EF-HAND CALCIUM BINDING PROTEINS.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; L00101; AAA48653.1; -.
DR   EMBL; L00096; AAA48653.1; JOINED.
DR   EMBL; L00097; AAA48653.1; JOINED.
DR   EMBL; L00098; AAA48653.1; JOINED.
DR   EMBL; L00099; AAA48653.1; JOINED.
DR   EMBL; L00100; AAA48653.1; JOINED.
DR   EMBL; M16659; AAA40864.1; -.
DR   EMBL; M27319; AAA35635.1; -.
DR   EMBL; U12022; AAB60644.1; -.
DR   EMBL; U11886; AAB60644.1; JOINED.
DR   EMBL; D45887; BAA08302.1; -.
DR   EMBL; X13817; CAA32050.1; -.
DR   EMBL; J04046; AAA51918.1; -.
DR   EMBL; M19311; AAA35641.1; -.
DR   EMBL; M19312; AAA40862.1; -.
DR   EMBL; M17069; AAA40863.1; -.
DR   EMBL; X13933; CAA32120.1; -.
DR   EMBL; X13931; CAA32119.1; -.
DR   EMBL; X13932; CAA32119.1; JOINED.
DR   EMBL; X05117; CAA32119.1; JOINED.
DR   EMBL; X13833; CAA32062.1; -.
DR   EMBL; X13834; CAA32062.1; JOINED.
DR   EMBL; X13835; CAA32062.1; JOINED.
DR   EMBL; X14265; CAA32478.1; -.
DR   EMBL; D83350; BAA11896.1; -.
DR   EMBL; M36167; AAA48650.1; -.
DR   EMBL; K01944; AAA49668.1; -.
DR   EMBL; K01945; AAA49669.1; -.
DR   EMBL; D10363; BAA01195.1; -.
DR   EMBL; M19380; AAA66181.1; -.
DR   EMBL; M19381; AAA66182.1; -.
DR   EMBL; L31642; AAA65934.1; -.
DR   EMBL; M27844; AAA37365.1; -.
DR   EMBL; X61432; CAA43674.1; -.
DR   PIR; S13159; MCHU.
DR   PIR; JK0013; MCON.
DR   PIR; A90719; MCBO.
DR   PIR; A91104; MCRB.
DR   PIR; S03206; MCRT.
DR   PIR; A92394; MCCH.
DR   PIR; S02690; S02690.
DR   PIR; A60781; A60781.
DR   PIR; JC1305; JC1305.
DR   PDB; 2CLN; 15-OCT-94.
DR   PDB; 3CLN; 09-JAN-89.
DR   PDB; 1TRC; 15-OCT-91.
DR   PDB; 1AK8; 17-SEP-97.
DR   PDB; 1CDL; 31-AUG-94.
DR   PDB; 1CDM; 31-AUG-94.
DR   PDB; 1CFC; 07-DEC-95.
DR   PDB; 1CFD; 07-DEC-95.
DR   PDB; 1CLL; 31-OCT-93.
DR   PDB; 1CM1; 04-MAR-98.
DR   PDB; 1CM4; 04-MAR-98.
DR   PDB; 1CMF; 07-DEC-95.
DR   PDB; 1CMG; 07-DEC-95.
DR   PDB; 1CTR; 20-DEC-94.
DR   PDB; 1DEG; 31-MAY-94.
DR   PDB; 1DMO; 01-AUG-96.
DR   PDB; 1LIN; 08-MAR-96.
DR   PDB; 1AJI; 17-SEP-97.
DR   PDB; 1A29; 16-SEP-98.
DR   PDB; 1MUX; 25-NOV-98.
DR   PDB; 1CFF; 24-SEP-91.
DR   SWISS-2DPAGE; P99014; MOUSE.
DR   Aarhus/Ghent-2DPAGE; 9048; IEF.
DR   MIM; 114180; -.
DR   MIM; 114182; -.
DR   MIM; 114183; -.
DR   MGD; MGI:88251; Calm.
DR   MGD; MGI:103250; Calm2.
DR   MGD; MGI:103249; Calm3.
DR   InterPro; IPR002048; EF-hand.
DR   Pfam; PF00036; efhand; 4.
DR   SMART; SM00054; EFh; 4.
DR   PROSITE; PS00018; EF_HAND; 4.
KW   Calcium-binding; Duplication; Methylation; Acetylation;
KW   3D-structure.
FT   INIT_MET      0      0
FT   MOD_RES       1      1       ACETYLATION.
FT   MOD_RES     115    115       METHYLATION (TRI-) (IN CHICKEN).
FT   CA_BIND      20     31       EF-HAND 1.
FT   CA_BIND      56     67       EF-HAND 2.
FT   CA_BIND      93    104       EF-HAND 3.
FT   CA_BIND     129    140       EF-HAND 4.
FT   BINDING      21     21       UBIQUITIN (MULTI-).
FT   CONFLICT     25     25       G -> N (IN REF. 12; AAA66182).
FT   HELIX         5     19
FT   TURN         21     22
FT   STRAND       26     27
FT   HELIX        29     37
FT   TURN         38     40
FT   HELIX        45     55
FT   TURN         57     58
FT   STRAND       63     64
FT   HELIX        65     92
FT   TURN         94     95
FT   STRAND      100    100
FT   HELIX       102    111
FT   TURN        112    113
FT   HELIX       118    128
FT   STRAND      136    136
FT   HELIX       138    146
SQ   SEQUENCE   148 AA;  16706 MW;  464B8A287475A1CA CRC64;
     ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN
     GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE
     VDEMIREADI DGDGQVNYEE FVQMMTAK
//
BioPerl-1.007002/t/data/swisspfam.data000444000766000024       213713155576321 17542 0ustar00cjfieldsstaff000000000000>ROA1_MOUSE       |==============================================| P49312 319 a.a.
Pfam-B_14464     1                          --------------------- (3) PD14464
178-319
rrm              2   ----------   ----------                      (1058) PF00076  RNA recognition motif. (aka RRM, RBD, or RNP domain)  15-85 106-176
>ROA1_RAT         |==============================================| P04256 319 a.a.
Pfam-B_14464     1                          --------------------- (3) PD14464
178-319
rrm              2   ----------   ----------                      (1058) PF00076  RNA recognition motif. (aka RRM, RBD, or RNP domain)  15-85 106-176
>ROA1_SCHAM       |=================================================| P21522 342 a.a.
rrm              2   ----------   ----------                         (1058) PF00076  RNA recognition motif. (aka RRM, RBD, or RNP domain)  19-89 110-180
>ROA1_XENLA       |==============================================| P17130 365 a.a.
rrm              2  ---------   ---------                         (1058) PF00076  RNA recognition motif. (aka RRM, RBD, or RNP domain)  16-86 107-177         
BioPerl-1.007002/t/data/tab1part.mif000444000766000024      1527613155576321 17136 0ustar00cjfieldsstaff000000000000DIP:4305E	DIP:3048N			PIR:B64526	GI:2313123	DIP:3047N		SWP:O24853	PIR:A64520	GI:2313078
DIP:4307E	DIP:3050N			PIR:H64618	GI:2313921	DIP:3047N		SWP:O24853	PIR:A64520	GI:2313078
DIP:4308E	DIP:3051N			PIR:B64520	GI:2313079	DIP:3051N			PIR:B64520	GI:2313079
DIP:4309E	DIP:3052N		SWP:P56036	PIR:H64669	GI:2314362	DIP:3051N			PIR:B64520	GI:2313079
DIP:4310E	DIP:3053N			PIR:A64696	GI:2314583	DIP:3051N			PIR:B64520	GI:2313079
DIP:4311E	DIP:3054N			PIR:C64701	GI:2314631	DIP:3051N			PIR:B64520	GI:2313079
DIP:4312E	DIP:3055N		SWP:P55993	PIR:H64530	GI:2313167	DIP:3056N		SWP:P56155	PIR:E64520	GI:2313082
DIP:4313E	DIP:3057N		SWP:P55991	PIR:D64534	GI:2313198	DIP:3056N		SWP:P56155	PIR:E64520	GI:2313082
DIP:4314E	DIP:3058N		SWP:P56112	PIR:G64541	GI:2313264	DIP:3056N		SWP:P56155	PIR:E64520	GI:2313082
DIP:4315E	DIP:3059N			PIR:F64554	GI:2313368	DIP:3056N		SWP:P56155	PIR:E64520	GI:2313082
DIP:4316E	DIP:3060N			PIR:E64559	GI:2313410	DIP:3056N		SWP:P56155	PIR:E64520	GI:2313082
DIP:4317E	DIP:3061N			PIR:G64592	GI:2313700	DIP:3056N		SWP:P56155	PIR:E64520	GI:2313082
DIP:4318E	DIP:3062N		SWP:O25336	PIR:G64596	GI:2313737	DIP:3056N		SWP:P56155	PIR:E64520	GI:2313082
DIP:4319E	DIP:3063N			PIR:H64599	GI:2313761	DIP:3056N		SWP:P56155	PIR:E64520	GI:2313082
DIP:4320E	DIP:3064N		SWP:P56143	PIR:B64609	GI:2313838	DIP:3056N		SWP:P56155	PIR:E64520	GI:2313082
DIP:4321E	DIP:3065N			PIR:A64642	GI:2314119	DIP:3056N		SWP:P56155	PIR:E64520	GI:2313082
DIP:4322E	DIP:3066N			PIR:B64679	GI:2314439	DIP:3056N		SWP:P56155	PIR:E64520	GI:2313082
DIP:4323E	DIP:3067N			PIR:F64688	GI:2314520	DIP:3056N		SWP:P56155	PIR:E64520	GI:2313082
DIP:4324E	DIP:3053N			PIR:A64696	GI:2314583	DIP:3056N		SWP:P56155	PIR:E64520	GI:2313082
DIP:4325E	DIP:3068N			PIR:C64696	GI:2314584	DIP:3056N		SWP:P56155	PIR:E64520	GI:2313082
DIP:4326E	DIP:3070N			PIR:E64595	GI:2313728	DIP:3069N		SWP:P42383	PIR:S36237	GI:2313084
DIP:4327E	DIP:3071N			PIR:B64648	GI:2314168	DIP:3069N		SWP:P42383	PIR:S36237	GI:2313084
DIP:4328E	DIP:3072N			PIR:D64660	GI:2314290	DIP:3069N		SWP:P42383	PIR:S36237	GI:2313084
DIP:4329E	DIP:3073N			PIR:H64671	GI:2314377	DIP:3069N		SWP:P42383	PIR:S36237	GI:2313084
DIP:4330E	DIP:3074N		SWP:P48225	PIR:C71986	GI:2313085	DIP:3074N		SWP:P48225	PIR:C71986	GI:2313085
DIP:4331E	DIP:3053N			PIR:A64696	GI:2314583	DIP:3074N		SWP:P48225	PIR:C71986	GI:2313085
DIP:4332E	DIP:3075N			PIR:H64521	GI:2313097	DIP:3075N			PIR:H64521	GI:2313097
DIP:4333E	DIP:3076N			PIR:F64524	GI:2313125	DIP:3075N			PIR:H64521	GI:2313097
DIP:4334E	DIP:3077N			PIR:D64548	GI:2313317	DIP:3075N			PIR:H64521	GI:2313097
DIP:4335E	DIP:3078N			PIR:G64574	GI:2313548	DIP:3075N			PIR:H64521	GI:2313097
DIP:4336E	DIP:3079N			PIR:G64605	GI:2313813	DIP:3075N			PIR:H64521	GI:2313097
DIP:4337E	DIP:3080N			PIR:A64607	GI:2313821	DIP:3075N			PIR:H64521	GI:2313097
DIP:4338E	DIP:3081N			PIR:G64614	GI:2313885	DIP:3075N			PIR:H64521	GI:2313097
DIP:4339E	DIP:3082N		SWP:Q59465	PIR:G64618	GI:2313920	DIP:3075N			PIR:H64521	GI:2313097
DIP:4340E	DIP:3083N			PIR:A64641	GI:2314107	DIP:3075N			PIR:H64521	GI:2313097
DIP:4341E	DIP:3084N			PIR:A64647	GI:2314162	DIP:3075N			PIR:H64521	GI:2313097
DIP:4342E	DIP:3085N			PIR:G64667	GI:2314343	DIP:3075N			PIR:H64521	GI:2313097
DIP:4343E	DIP:3086N			PIR:C64678	GI:2314432	DIP:3075N			PIR:H64521	GI:2313097
DIP:4344E	DIP:3087N			PIR:B64701	GI:2314626	DIP:3075N			PIR:H64521	GI:2313097
DIP:4345E	DIP:3088N			PIR:B64706	GI:2314662	DIP:3075N			PIR:H64521	GI:2313097
DIP:4346E	DIP:3090N			PIR:F64546	GI:2313304	DIP:3089N			PIR:D64523	GI:2313105
DIP:4347E	DIP:3091N			PIR:B64564	GI:2313455	DIP:3089N			PIR:D64523	GI:2313105
DIP:4348E	DIP:3092N			PIR:G64585	GI:2313642	DIP:3089N			PIR:D64523	GI:2313105
DIP:4349E	DIP:3093N		SWP:P55980	PIR:C64588	GI:2313664	DIP:3089N			PIR:D64523	GI:2313105
DIP:4350E	DIP:3094N			PIR:G64595	GI:2313726	DIP:3089N			PIR:D64523	GI:2313105
DIP:4351E	DIP:3082N		SWP:Q59465	PIR:G64618	GI:2313920	DIP:3089N			PIR:D64523	GI:2313105
DIP:4352E	DIP:3083N			PIR:A64641	GI:2314107	DIP:3089N			PIR:D64523	GI:2313105
DIP:4353E	DIP:3095N		SWP:O06758	PIR:A64650	GI:2314189	DIP:3089N			PIR:D64523	GI:2313105
DIP:4354E	DIP:3096N		SWP:P55989	PIR:H64653	GI:2314221	DIP:3089N			PIR:D64523	GI:2313105
DIP:4355E	DIP:3097N			PIR:F64672	GI:2314381	DIP:3089N			PIR:D64523	GI:2313105
DIP:4356E	DIP:3087N			PIR:B64701	GI:2314626	DIP:3089N			PIR:D64523	GI:2313105
DIP:4357E	DIP:3098N		SWP:P56105	PIR:F64703	GI:2314647	DIP:3089N			PIR:D64523	GI:2313105
DIP:4358E	DIP:3099N			PIR:G64707	GI:2314677	DIP:3089N			PIR:D64523	GI:2313105
DIP:4359E	DIP:3100N		SWP:O26074	PIR:F64713	GI:2314730	DIP:3089N			PIR:D64523	GI:2313105
DIP:4360E	DIP:3102N		SWP:P56061	PIR:F64520	GI:2313083	DIP:3101N			PIR:G64523	GI:2313114
DIP:4361E	DIP:3103N			PIR:B64528	GI:2313138	DIP:3101N			PIR:G64523	GI:2313114
DIP:4362E	DIP:3104N		SWP:O08314	PIR:A64555	GI:2313378	DIP:3101N			PIR:G64523	GI:2313114
DIP:4363E	DIP:3095N		SWP:O06758	PIR:A64650	GI:2314189	DIP:3101N			PIR:G64523	GI:2313114
DIP:4364E	DIP:3105N			PIR:A64709	GI:2314693	DIP:3101N			PIR:G64523	GI:2313114
DIP:4365E	DIP:3106N		SWP:O26087	PIR:G64715	GI:2314750	DIP:3101N			PIR:G64523	GI:2313114
DIP:4366E	DIP:3107N		SWP:P56066	PIR:H64523	GI:2313107	DIP:3107N		SWP:P56066	PIR:H64523	GI:2313107
DIP:4367E	DIP:3108N			PIR:C64524	GI:2313110	DIP:3108N			PIR:C64524	GI:2313110
DIP:4368E	DIP:3110N			PIR:A64522	GI:2313091	DIP:3109N			PIR:B64525	GI:2313117
DIP:4369E	DIP:3111N			PIR:C64526	GI:2313124	DIP:3109N			PIR:B64525	GI:2313117
DIP:4370E	DIP:3112N			PIR:F64526	GI:2313132	DIP:3109N			PIR:B64525	GI:2313117
DIP:4384E	DIP:3112N			PIR:F64526	GI:2313132	DIP:3111N			PIR:C64526	GI:2313124
DIP:4371E	DIP:3059N			PIR:F64554	GI:2313368	DIP:3109N			PIR:B64525	GI:2313117
DIP:4372E	DIP:3113N			PIR:E64567	GI:2313486	DIP:3109N			PIR:B64525	GI:2313117
DIP:4373E	DIP:3114N			PIR:C64572	GI:2313522	DIP:3109N			PIR:B64525	GI:2313117
DIP:4374E	DIP:3115N		SWP:O25424	PIR:C64610	GI:2313847	DIP:3109N			PIR:B64525	GI:2313117
DIP:4375E	DIP:3116N		SWP:P56082	PIR:E64661	GI:2314284	DIP:3109N			PIR:B64525	GI:2313117
DIP:4376E	DIP:3117N		SWP:P56032	PIR:F64684	GI:2314480	DIP:3109N			PIR:B64525	GI:2313117
DIP:4377E	DIP:3118N			PIR:H64693	GI:2314561	DIP:3109N			PIR:B64525	GI:2313117
DIP:4378E	DIP:3119N			PIR:E64525	GI:2313120	DIP:3119N			PIR:E64525	GI:2313120
DIP:4379E	DIP:3053N			PIR:A64696	GI:2314583	DIP:3119N			PIR:E64525	GI:2313120
DIP:4380E	DIP:3120N			PIR:G64525	GI:2313121	DIP:3120N			PIR:G64525	GI:2313121
DIP:4381E	DIP:3121N			PIR:H64525	GI:2313122	DIP:3120N			PIR:G64525	GI:2313121
DIP:4382E	DIP:3122N			PIR:G64606	GI:2313818	DIP:3120N			PIR:G64525	GI:2313121
DIP:4383E	DIP:3103N			PIR:B64528	GI:2313138	DIP:3123N			PIR:E64527	GI:2313147
DIP:4389E	DIP:3103N			PIR:B64528	GI:2313138	DIP:3123N			PIR:E64527	GI:2313147
DIP:4390E	DIP:3103N			PIR:B64528	GI:2313138	DIP:3123N			PIR:E64527	GI:2313147
DIP:4391E	DIP:3122N			PIR:G64606	GI:2313818	DIP:3120N			PIR:G64525	GI:2313121
BioPerl-1.007002/t/data/tab2part.mif000444000766000024        35213155576321 17064 0ustar00cjfieldsstaff000000000000DIP:5000E	DIP:3122N			PIR:G64606	GI:2313818	DIP:3054N			PIR:G64525	GI:2313121
DIP:5001E	DIP:3122N			PIR:G64606	GI:2313818	DIP:3054N			PIR:G64525	GI:2313121
DIP:5002E	DIP:3122N			PIR:G64606	GI:2313818	DIP:3054N			PIR:G64525	GI:2313121
BioPerl-1.007002/t/data/tab3part.mif000444000766000024       316013155576321 17105 0ustar00cjfieldsstaff000000000000DIP:4369E	DIP:3111N			PIR:C64526	GI:2313124	DIP:3109N			PIR:B64525	GI:2313117
DIP:4370E	DIP:3112N			PIR:F64526	GI:2313132	DIP:3109N			PIR:B64525	GI:2313117
DIP:4384E	DIP:3112N			PIR:F64526	GI:2313132	DIP:3111N			PIR:C64526	GI:2313124
DIP:4371E	DIP:3059N			PIR:F64554	GI:2313368	DIP:3109N			PIR:B64525	GI:2313117
DIP:4372E	DIP:3113N			PIR:E64567	GI:2313486	DIP:3109N			PIR:B64525	GI:2313117
DIP:4373E	DIP:3114N			PIR:C64572	GI:2313522	DIP:3109N			PIR:B64525	GI:2313117
DIP:4374E	DIP:3115N		SWP:O25424	PIR:C64610	GI:2313847	DIP:3109N			PIR:B64525	GI:2313117
DIP:4375E	DIP:3116N		SWP:P56082	PIR:E64661	GI:2314284	DIP:3109N			PIR:B64525	GI:2313117
DIP:4376E	DIP:3117N		SWP:P56032	PIR:F64684	GI:2314480	DIP:3109N			PIR:B64525	GI:2313117
DIP:4377E	DIP:3118N			PIR:H64693	GI:2314561	DIP:3109N			PIR:B64525	GI:2313117
DIP:4378E	DIP:3119N			PIR:E64525	GI:2313120	DIP:3119N			PIR:E64525	GI:2313120
DIP:4379E	DIP:3053N			PIR:A64696	GI:2314583	DIP:3119N			PIR:E64525	GI:2313120
DIP:4380E	DIP:3120N			PIR:G64525	GI:2313121	DIP:3120N			PIR:G64525	GI:2313121
DIP:4381E	DIP:3121N			PIR:H64525	GI:2313122	DIP:3120N			PIR:G64525	GI:2313121
DIP:4382E	DIP:3122N			PIR:G64606	GI:2313818	DIP:3120N			PIR:G64525	GI:2313121
DIP:4383E	DIP:3103N			PIR:B64528	GI:2313138	DIP:3123N			PIR:E64527	GI:2313147
DIP:4389E	DIP:3103N			PIR:B64528	GI:2313138	DIP:3123N			PIR:E64527	GI:2313147
DIP:4390E	DIP:3103N			PIR:B64528	GI:2313138	DIP:3123N			PIR:E64527	GI:2313147
DIP:4391E	DIP:3122N			PIR:G64606	GI:2313818	DIP:3120N			PIR:G64525	GI:2313121
DIP:5000E	DIP:3122N			PIR:G64606	GI:2313818	DIP:1111N			PIR:G5	GI:4
DIP:5001E	DIP:3122N			PIR:G64606	GI:2313818	DIP:2222N			PIR:G6	GI:2
BioPerl-1.007002/t/data/tandem_repeats_finder.dat000444000766000024       116513155576321 21707 0ustar00cjfieldsstaff000000000000Tandem Repeats Finder Program writen by:



Gary Benson

Department of Biomathematical Sciences

Mount Sinai School of Medicine

Version 4.00





Sequence: DDB0169550 |Masked Chromosomal Sequence| on chromosome: M







Parameters: 2 7 7 80 10 50 12





13936 13960 12 2.1 12 100 0 50 16 8 52 24 1.70 GGCGTAATGGGT GGCGTAATGGGTGGCGTAATGGGTG

16937 16965 9 3.2 9 100 0 58 44 0 10 44 1.38 TATATAGTA TATATAGTATATATAGTATATATAGTATA







Sequence: DDB0215018 |Masked Chromosomal Sequence| on chromosome: 2F







Parameters: 2 7 7 80 10 50 12





1649 1679 1 31.0 1 100 0 62 0 0 0 100 0.00 T TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT





BioPerl-1.007002/t/data/tandem_repeats_finder.noresults000444000766000024        31013155576321 23144 0ustar00cjfieldsstaff000000000000Tandem Repeats Finder Program writen by:



Gary Benson

Department of Biomathematical Sciences

Mount Sinai School of Medicine

Version 4.00





Sequence: Test







Parameters: 2 7 7 80 10 50 10

BioPerl-1.007002/t/data/tandem_repeats_finder_no_desc.dat000444000766000024       110613155576321 23374 0ustar00cjfieldsstaff000000000000Tandem Repeats Finder Program writen by:



Gary Benson

Department of Biomathematical Sciences

Mount Sinai School of Medicine

Version 4.00





Sequence: DDB0169550







Parameters: 2 7 7 80 10 50 12





13936 13960 12 2.1 12 100 0 50 16 8 52 24 1.70 GGCGTAATGGGT GGCGTAATGGGTGGCGTAATGGGTG

16937 16965 9 3.2 9 100 0 58 44 0 10 44 1.38 TATATAGTA TATATAGTATATATAGTATATATAGTATA







Sequence: DDB0215018 |Masked Chromosomal Sequence| on chromosome: 2F







Parameters: 2 7 7 80 10 50 12





1649 1679 1 31.0 1 100 0 62 0 0 0 100 0.00 T TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT





BioPerl-1.007002/t/data/targetp.out000444000766000024       361513155576321 17074 0ustar00cjfieldsstaff000000000000### targetp v1.1 prediction results ##################################
Number of query sequences:  500
Cleavage site predictions included.
Using NON-PLANT networks.

Name                  Len            mTP     SP  other  Loc  RC  TPlen
----------------------------------------------------------------------
BC1G_00001.1          173          0.393  0.024  0.683   _    4      -
BC1G_00002.1          120          0.619  0.040  0.458   M    5     97
BC1G_00003.1          323          0.094  0.895  0.027   S    1     21
BC1G_00004.1          361          0.402  0.072  0.479   _    5      -
BC1G_00005.1          244          0.526  0.035  0.548   _    5      -
BC1G_00006.1           35          0.234  0.036  0.819   _    3      -
BC1G_00007.1           73          0.292  0.127  0.431   _    5      -
BC1G_00008.1          349          0.088  0.958  0.078   S    1     82
BC1G_00009.1          514          0.183  0.102  0.735   _    3      -
BC1G_00010.1          440          0.114  0.088  0.865   _    2      -
----------------------------------------------------------------------
cutoff                             0.000  0.000  0.000

### targetp v1.1 prediction results ##################################
Number of query sequences:  500
Cleavage site predictions included.
Using NON-PLANT networks.

Name                  Len            mTP     SP  other  Loc  RC  TPlen
----------------------------------------------------------------------
BC1G_04501.1          215          0.185  0.038  0.843   _    2      -
BC1G_04502.1          395          0.118  0.164  0.825   _    2      -
BC1G_04503.1          199          0.515  0.062  0.436   M    5     20
BC1G_04504.1          220          0.440  0.030  0.707   _    4      -
BC1G_04505.1           67          0.382  0.049  0.610   _    4      -
----------------------------------------------------------------------
cutoff                             0.000  0.000  0.000BioPerl-1.007002/t/data/tblastn.out000444000766000024       544113155576321 17074 0ustar00cjfieldsstaff000000000000TBLASTN 2.2.10 [Oct-19-2004]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= HAHU | 1114 |  Hemoglobin alpha chain - Human, chimpanzee, and
pygmy chimpanzee
         (141 letters)

Database: testnt.fa 
           2 sequences; 13,260 total letters

Searching..done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|10040111|emb|AL390796.6|AL390796 Homo sapiens chromosome 1 cl...    18   2.3  
test6                                                                  16   6.7  

>gi|10040111|emb|AL390796.6|AL390796 Homo sapiens chromosome 1 clone
            RP11-562F3, *** SEQUENCING IN PROGRESS ***, 16 unordered
            pieces /len=164198
          Length = 8160

 Score = 17.7 bits (34), Expect = 2.3
 Identities = 8/23 (34%), Positives = 11/23 (47%)
 Frame = +1

Query: 56   KGHGKKVADALTNAVAHVDDMPN 78
            KGH KK+     N  ++  D  N
Sbjct: 7603 KGHLKKITSFFFNHTSNYRDEYN 7671



 Score = 17.3 bits (33), Expect = 3.0
 Identities = 9/28 (32%), Positives = 13/28 (46%)
 Frame = +1

Query: 31   RMFLSFPTTKTYFPHFDLSHGSAQVKGH 58
            RM+  F    TY+ +F L      V G+
Sbjct: 7069 RMYFCFLKVLTYYFNFFLFFNIFYVLGY 7152


>test6
          Length = 5100

 Score = 16.2 bits (30), Expect = 6.7
 Identities = 6/9 (66%), Positives = 7/9 (77%)
 Frame = +3

Query: 72   HVDDMPNAL 80
            H+D M NAL
Sbjct: 3822 HMDYMSNAL 3848



 Score = 15.8 bits (29), Expect = 8.8
 Identities = 5/7 (71%), Positives = 6/7 (85%)
 Frame = -2

Query: 93   VDPVNFK 99
            +DP NFK
Sbjct: 1814 IDP*NFK 1794


  Database: testnt.fa
    Posted date:  Feb 5, 2005  6:26 PM
  Number of letters in database: 13,260
  Number of sequences in database:  2
  
Lambda     K      H
   0.319    0.130    0.385 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1998
Number of Sequences: 2
Number of extensions: 23
Number of successful extensions: 4
Number of sequences better than 10.0: 2
Number of HSP's better than 10.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 4
length of query: 141
length of database: 4420
effective HSP length: 39
effective length of query: 102
effective length of database: 4342
effective search space:   442884
effective search space used:   442884
frameshift window, decay const: 40,  0.1
T: 13
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 29 (16.3 bits)
S2: 29 (15.8 bits)
BioPerl-1.007002/t/data/test 2.txt000444000766000024       107513155576321 16535 0ustar00cjfieldsstaff000000000000>Test
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTBioPerl-1.007002/t/data/test-1.tab000444000766000024         3413155576321 16432 0ustar00cjfieldsstaff000000000000N	D	S
n1	d1	aaaa
n2	d2	tttt
BioPerl-1.007002/t/data/test-1.tab.gb000444000766000024        56213155576321 17047 0ustar00cjfieldsstaff000000000000LOCUS       n1                         4 bp    dna     linear   UNK 
DEFINITION  d1
ACCESSION   n1
KEYWORDS    .
FEATURES             Location/Qualifiers
ORIGIN      
        1 aaaa
//
LOCUS       n2                         4 bp    dna     linear   UNK 
DEFINITION  d2
ACCESSION   n2
KEYWORDS    .
FEATURES             Location/Qualifiers
ORIGIN      
        1 tttt
//
BioPerl-1.007002/t/data/test-3.0-1.meme000444000766000024      5334613155576321 17203 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.0 (Release date: 2001/03/05 14:24:28)

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.sdsc.edu.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.sdsc.edu.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= D10Mit194.set.genbank.fasta.nref
ALPHABET= ACGT
Sequence name           Weight Length  Sequence name           Weight Length  
-------------           ------ ------  -------------           ------ ------  
20218                   1.0000   2000  10657                   1.0000   2000  
83796                   1.0000   2000  6603                    1.0000   2000  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme D10Mit194.set.genbank.fasta.nref -dna -print_fasta -nmotifs 3 -maxw 25 

model:  mod=         zoops    nmotifs=         3    evt=           inf
object function=  E-value of product of p-values
width:  minw=            8    maxw=           25    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        2    maxsites=        4    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            8000    N=               4
strands: +
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.255 C 0.236 G 0.252 T 0.257 
Background letter frequencies (from dataset with add-one prior applied):
A 0.255 C 0.236 G 0.252 T 0.257 
********************************************************************************


********************************************************************************
MOTIF  1	width =   25   sites =   4   llr = 106   E-value = 1.2e-002
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :8:88aaa:53a8:::3:a::3::3
pos.-specific     C  a3::3:::::3:::5a8a:8a5aa8
probability       G  ::8:::::3:5::::::::3:::::
matrix            T  ::33::::85::3a5::::::3:::

         bits    2.1 *              * *  * ** 
                 1.9 *    ***   * * * ** * ** 
                 1.7 *    ***   * * * ** * ** 
                 1.5 *    ***   * * * ** * ** 
Information      1.2 *********  *** ****** ***
content          1.0 ********** ********** ***
(38.1 bits)      0.8 ********** ********** ***
                 0.6 ********** **************
                 0.4 *************************
                 0.2 *************************
                 0.0 -------------------------

Multilevel           CAGAAAAATAGAATCCCCACCCCCC
consensus             CTTC   GTA T T A  G A  A
sequence                       C          T   
                                              
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                      Site         
-------------             ----- ---------            -------------------------
6603                       1311  2.59e-15 GGCGCATTGA CAGAAAAATTGAATTCCCACCCCCC AATGAGGAGG
83796                      1284  2.59e-15 GGAGGATTGA CAGAAAAATTGAATTCCCACCCCCC AACGAGGAGG
20218                       938  6.34e-12 TTTTTGGTAA CCTTAAAATAAAATCCCCACCACCA CTTTTAAAAA
10657                      1685  8.70e-12 GGCCCGCGCG CAGACAAAGACATTCCACAGCTCCC GCCCCCTCCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
6603                              2.6e-15  1310_[1]_665
83796                             2.6e-15  1283_[1]_692
20218                             6.3e-12  937_[1]_1038
10657                             8.7e-12  1684_[1]_291
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in FASTA format
--------------------------------------------------------------------------------
>6603                     pos 1311
CAGAAAAATTGAATTCCCACCCCCC
>83796                    pos 1284
CAGAAAAATTGAATTCCCACCCCCC
>20218                    pos  938
CCTTAAAATAAAATCCCCACCACCA
>10657                    pos 1685
CAGACAAAGACATTCCACAGCTCCC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 25 n= 7904 bayes= 11.6849 E= 1.2e-002 
  -865    208   -865   -865 
   156      8   -865   -865 
  -865   -865    157     -4 
   156   -865   -865     -4 
   156      8   -865   -865 
   197   -865   -865   -865 
   197   -865   -865   -865 
   197   -865   -865   -865 
  -865   -865     -1    154 
    97   -865   -865     96 
    -3      8     99   -865 
   197   -865   -865   -865 
   156   -865   -865     -4 
  -865   -865   -865    196 
  -865    108   -865     96 
  -865    208   -865   -865 
    -3    166   -865   -865 
  -865    208   -865   -865 
   197   -865   -865   -865 
  -865    166     -1   -865 
  -865    208   -865   -865 
    -3    108   -865     -4 
  -865    208   -865   -865 
  -865    208   -865   -865 
    -3    166   -865   -865 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 25 n= 7904 E= 1.2e-002 
 0.000635  0.998096  0.000629  0.000640 
 0.748765  0.249966  0.000629  0.000640 
 0.000635  0.000589  0.748759  0.250017 
 0.748765  0.000589  0.000629  0.250017 
 0.748765  0.249966  0.000629  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.000635  0.000589  0.250006  0.748770 
 0.499388  0.000589  0.000629  0.499393 
 0.250012  0.249966  0.499382  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.748765  0.000589  0.000629  0.250017 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.499343  0.000629  0.499393 
 0.000635  0.998096  0.000629  0.000640 
 0.250012  0.748719  0.000629  0.000640 
 0.000635  0.998096  0.000629  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.000635  0.748719  0.250006  0.000640 
 0.000635  0.998096  0.000629  0.000640 
 0.250012  0.499343  0.000629  0.250017 
 0.000635  0.998096  0.000629  0.000640 
 0.000635  0.998096  0.000629  0.000640 
 0.250012  0.748719  0.000629  0.000640 
--------------------------------------------------------------------------------





Time 38.44 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   25   sites =   4   llr = 101   E-value = 4.5e-001
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  ::::a::383:5:3:::a33:83:a
pos.-specific     C  a3a8:3a33:a::5::8::::383:
probability       G  ::::::::::::::::3:38a::8:
matrix            T  :8:3:8:5:8:5a3aa::5::::::

         bits    2.1 * *   *   *         *    
                 1.9 * * * *   * * ** *  *   *
                 1.7 * * * *   * * ** *  *   *
                 1.5 * * * *   * * ** *  *   *
Information      1.2 ******* *** * **** ******
content          1.0 ******* ***** **** ******
(36.6 bits)      0.8 ******* ***** **** ******
                 0.6 ******* ********** ******
                 0.4 *************************
                 0.2 *************************
                 0.0 -------------------------

Multilevel           CTCCATCTATCATCTTCATGGACGA
consensus             C T C ACA T A  G AA CAC 
sequence                    C     T    G      
                                              
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                      Site         
-------------             ----- ---------            -------------------------
6603                       1000  1.62e-15 CGGGAACATG CTCCATCTATCATCTTCATGGACGA AATCGACTCC
83796                       978  4.69e-15 CGAGAACATG CTCCATCCATCATCTTCATGGACGA GATTGACTCT
20218                      1545  1.69e-11 TAGCTTCTCT CCCCATCAATCTTATTCAGAGCCCA CCCCTCCCCC
10657                      1075  3.40e-11 AGGATCTGGT CTCTACCTCACTTTTTGAAGGAAGA AACACTTAAT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
6603                              1.6e-15  999_[2]_976
83796                             4.7e-15  977_[2]_998
20218                             1.7e-11  1544_[2]_431
10657                             3.4e-11  1074_[2]_901
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in FASTA format
--------------------------------------------------------------------------------
>6603                     pos 1000
CTCCATCTATCATCTTCATGGACGA
>83796                    pos  978
CTCCATCCATCATCTTCATGGACGA
>20218                    pos 1545
CCCCATCAATCTTATTCAGAGCCCA
>10657                    pos 1075
CTCTACCTCACTTTTTGAAGGAAGA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 25 n= 7904 bayes= 10.9476 E= 4.5e-001 
  -865    208   -865   -865 
  -865      8   -865    154 
  -865    208   -865   -865 
  -865    166   -865     -4 
   197   -865   -865   -865 
  -865      8   -865    154 
  -865    208   -865   -865 
    -3      8   -865     96 
   156      8   -865   -865 
    -3   -865   -865    154 
  -865    208   -865   -865 
    97   -865   -865     96 
  -865   -865   -865    196 
    -3    108   -865     -4 
  -865   -865   -865    196 
  -865   -865   -865    196 
  -865    166     -1   -865 
   197   -865   -865   -865 
    -3   -865     -1     96 
    -3   -865    157   -865 
  -865   -865    198   -865 
   156      8   -865   -865 
    -3    166   -865   -865 
  -865      8    157   -865 
   197   -865   -865   -865 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 25 n= 7904 E= 4.5e-001 
 0.000635  0.998096  0.000629  0.000640 
 0.000635  0.249966  0.000629  0.748770 
 0.000635  0.998096  0.000629  0.000640 
 0.000635  0.748719  0.000629  0.250017 
 0.998141  0.000589  0.000629  0.000640 
 0.000635  0.249966  0.000629  0.748770 
 0.000635  0.998096  0.000629  0.000640 
 0.250012  0.249966  0.000629  0.499393 
 0.748765  0.249966  0.000629  0.000640 
 0.250012  0.000589  0.000629  0.748770 
 0.000635  0.998096  0.000629  0.000640 
 0.499388  0.000589  0.000629  0.499393 
 0.000635  0.000589  0.000629  0.998147 
 0.250012  0.499343  0.000629  0.250017 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.748719  0.250006  0.000640 
 0.998141  0.000589  0.000629  0.000640 
 0.250012  0.000589  0.250006  0.499393 
 0.250012  0.000589  0.748759  0.000640 
 0.000635  0.000589  0.998135  0.000640 
 0.748765  0.249966  0.000629  0.000640 
 0.250012  0.748719  0.000629  0.000640 
 0.000635  0.249966  0.748759  0.000640 
 0.998141  0.000589  0.000629  0.000640 
--------------------------------------------------------------------------------





Time 78.29 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   21   sites =   4   llr = 88   E-value = 4.8e-001
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :::58:::::3::::33::::
pos.-specific     C  8:833::8:8:a:8a8:a5a8
probability       G  3::::::3:::::3:::::::
matrix            T  :a33:aa:a38:a:::8:5:3

         bits    2.1            *  *  * * 
                 1.9  *   ** *  ** *  * * 
                 1.7  *   ** *  ** *  * * 
                 1.5  *   ** *  ** *  * * 
Information      1.2 *** ************** **
content          1.0 *** *****************
(31.8 bits)      0.8 *** *****************
                 0.6 *** *****************
                 0.4 *********************
                 0.2 *********************
                 0.0 ---------------------

Multilevel           CTCAATTCTCTCTCCCTCCCC
consensus            G TCC  G TA  G AA T T
sequence                T                 
                                          
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                    Site       
-------------             ----- ---------            ---------------------
10657                      1511  1.45e-13 CCCAGGCGGT CTCAATTCTCTCTCCCTCCCC TTTCCGTGAC
83796                      1801  7.40e-12 TGTATATGCA CTCTCTTCTCTCTCCCTCTCC AGGTCATGCA
6603                       1811  1.22e-10 GTAACTTAAT GTTCATTCTCTCTCCCACCCC TAGGTCATGC
20218                       606  7.57e-10 CCCAGGCCAG CTCAATTGTTACTGCATCTCT AGGATTGGAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
10657                             1.5e-13  1510_[3]_469
83796                             7.4e-12  1800_[3]_179
6603                              1.2e-10  1810_[3]_169
20218                             7.6e-10  605_[3]_1374
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in FASTA format
--------------------------------------------------------------------------------
>10657                    pos 1511
CTCAATTCTCTCTCCCTCCCC
>83796                    pos 1801
CTCTCTTCTCTCTCCCTCTCC
>6603                     pos 1811
GTTCATTCTCTCTCCCACCCC
>20218                    pos  606
CTCAATTGTTACTGCATCTCT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 21 n= 7920 bayes= 10.9506 E= 4.8e-001 
  -865    166     -1   -865 
  -865   -865   -865    196 
  -865    166   -865     -4 
    97      8   -865     -4 
   156      8   -865   -865 
  -865   -865   -865    196 
  -865   -865   -865    196 
  -865    166     -1   -865 
  -865   -865   -865    196 
  -865    166   -865     -4 
    -3   -865   -865    154 
  -865    208   -865   -865 
  -865   -865   -865    196 
  -865    166     -1   -865 
  -865    208   -865   -865 
    -3    166   -865   -865 
    -3   -865   -865    154 
  -865    208   -865   -865 
  -865    108   -865     96 
  -865    208   -865   -865 
  -865    166   -865     -4 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 21 n= 7920 E= 4.8e-001 
 0.000635  0.748719  0.250006  0.000640 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.748719  0.000629  0.250017 
 0.499388  0.249966  0.000629  0.250017 
 0.748765  0.249966  0.000629  0.000640 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.748719  0.250006  0.000640 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.748719  0.000629  0.250017 
 0.250012  0.000589  0.000629  0.748770 
 0.000635  0.998096  0.000629  0.000640 
 0.000635  0.000589  0.000629  0.998147 
 0.000635  0.748719  0.250006  0.000640 
 0.000635  0.998096  0.000629  0.000640 
 0.250012  0.748719  0.000629  0.000640 
 0.250012  0.000589  0.000629  0.748770 
 0.000635  0.998096  0.000629  0.000640 
 0.000635  0.499343  0.000629  0.499393 
 0.000635  0.998096  0.000629  0.000640 
 0.000635  0.748719  0.000629  0.250017 
--------------------------------------------------------------------------------





Time 117.82 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
20218                            7.77e-19  605_[3(7.57e-10)]_311_[1(6.34e-12)]_582_[2(1.69e-11)]_431
10657                            5.46e-22  1_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_7_[1(6.00e-08)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_5_[1(1.18e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_4_[1(1.29e-07)]_332_[2(3.40e-11)]_383_[3(7.75e-07)]_7_[3(1.45e-13)]_56_[3(3.47e-05)]_76_[1(8.70e-12)]_291
83796                            1.73e-27  977_[2(4.69e-15)]_281_[1(2.59e-15)]_492_[3(7.40e-12)]_179
6603                             9.32e-27  597_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_327_[2(1.62e-15)]_286_[1(2.59e-15)]_475_[3(1.22e-10)]_169
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 3 reached.
********************************************************************************

CPU: hydra-1.lsd.ornl.gov

********************************************************************************
BioPerl-1.007002/t/data/test-3.0-2.meme000444000766000024      4600613155576321 17177 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.0 (Release date: 2002/04/02 00:11:59)

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.sdsc.edu.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.sdsc.edu.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= test.fasta
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
68723                    1.0000   2000  16939                    1.0000   2001  
20754                    1.0000   2001  6707                     1.0000   2000  
20755                    1.0000   2000  6700                     1.0000   2002  
20760                    1.0000   2000  20761                    1.0000   2000  
20762                    1.0000   2000  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme test.fasta -dna -nostatus -nmotifs 2 -minsites 8 -maxw 20 -revcomp 

model:  mod=         zoops    nmotifs=         2    evt=           inf
object function=  E-value of product of p-values
width:  minw=            8    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        8    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=           18004    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.295 C 0.205 G 0.205 T 0.295 
Background letter frequencies (from dataset with add-one prior applied):
A 0.295 C 0.205 G 0.205 T 0.295 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   8   llr = 147   E-value = 1.3e-002
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  ::a1::931:6:348:1::1
pos.-specific     C  aa:::8:11841:331:139
probability       G  :::9::::63::84::3:8:
matrix            T  ::::a3161::9:::969::

         bits    2.3 **                  
                 2.1 **                  
                 1.8 *** *               
                 1.6 *****              *
Information      1.4 ******   * **  * ***
content          1.1 *******  * ** ** ***
(26.5 bits)      0.9 *******  **** ** ***
                 0.7 ******* ***** ******
                 0.5 ********************
                 0.2 ********************
                 0.0 --------------------

Multilevel           CCAGTCATGCATGAATTTGC
consensus                 T A GC AGC G C 
sequence                          C      
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
20761                        +   1879  6.50e-13 TCTGATTAAG CCAGTCATGCATGGATTTGC ATTTTGGTTG
20760                        +   1875  6.50e-13 CCCAGTCACG CCAGTCATGCATGGATTTGC ATTTTGATTG
6700                         +   1100  2.27e-10 CCTGCTCATG CCAGTCATGGATAAATTTGC ATCTGGCTTA
20755                        +   1478  5.08e-10 CCCTGTCAGG CCAGTTATGGATGAATGTGC ACTTAANNNN
6707                         +   1431  6.11e-09 TCACACAGAT CCAGTCAATCCTGCCTGTCC ATCTCAATGA
20762                        +   1878  1.89e-08 CCTGGTTAGG CCAGTTAAACACAGATTTGC ATTTTGGTTA
16939                        -    914  2.01e-08 ACTTTTCCTT CCAATCATGCCTGCCCTTGA ACCCTATTGG
20754                        +   1175  6.73e-08 GCTCACCTTG CCAGTCTCCCCTGAATACCC TACATGCCCT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
20761                             6.5e-13  1878_[+1]_102
20760                             6.5e-13  1874_[+1]_106
6700                              2.3e-10  1099_[+1]_883
20755                             5.1e-10  1477_[+1]_503
6707                              6.1e-09  1430_[+1]_550
20762                             1.9e-08  1877_[+1]_103
16939                               2e-08  913_[-1]_1068
20754                             6.7e-08  1174_[+1]_807
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=8
20761                    ( 1879) CCAGTCATGCATGGATTTGC  1 
20760                    ( 1875) CCAGTCATGCATGGATTTGC  1 
6700                     ( 1100) CCAGTCATGGATAAATTTGC  1 
20755                    ( 1478) CCAGTTATGGATGAATGTGC  1 
6707                     ( 1431) CCAGTCAATCCTGCCTGTCC  1 
20762                    ( 1878) CCAGTTAAACACAGATTTGC  1 
16939                    (  914) CCAATCATGCCTGCCCTTGA  1 
20754                    ( 1175) CCAGTCTCCCCTGAATACCC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 17833 bayes= 11.1216 E= 1.3e-002 
  -965    229   -965   -965 
  -965    229   -965   -965 
   176   -965   -965   -965 
  -124   -965    210   -965 
  -965   -965   -965    176 
  -965    187   -965    -24 
   157   -965   -965   -124 
   -24    -71   -965    108 
  -124    -71    161   -124 
  -965    187     29   -965 
   108     87   -965   -965 
  -965    -71   -965    157 
   -24   -965    187   -965 
    34     29     87   -965 
   134     29   -965   -965 
  -965    -71   -965    157 
  -124   -965     29    108 
  -965    -71   -965    157 
  -965     29    187   -965 
  -124    210   -965   -965 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 n= 17833 E= 1.3e-002 
 0.000369  0.999007  0.000255  0.000369 
 0.000369  0.999007  0.000255  0.000369 
 0.999120  0.000255  0.000255  0.000369 
 0.125213  0.000255  0.874163  0.000369 
 0.000369  0.000255  0.000255  0.999120 
 0.000369  0.749319  0.000255  0.250057 
 0.874276  0.000255  0.000255  0.125213 
 0.250057  0.125099  0.000255  0.624589 
 0.125213  0.125099  0.624475  0.125213 
 0.000369  0.749319  0.249943  0.000369 
 0.624589  0.374787  0.000255  0.000369 
 0.000369  0.125099  0.000255  0.874276 
 0.250057  0.000255  0.749319  0.000369 
 0.374901  0.249943  0.374787  0.000369 
 0.749432  0.249943  0.000255  0.000369 
 0.000369  0.125099  0.000255  0.874276 
 0.125213  0.000255  0.249943  0.624589 
 0.000369  0.125099  0.000255  0.874276 
 0.000369  0.249943  0.749319  0.000369 
 0.125213  0.874163  0.000255  0.000369 
--------------------------------------------------------------------------------





Time 75.70 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   15   sites =   8   llr = 117   E-value = 1.2e+003
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  :1a39:::::18:::
pos.-specific     C  ::::1:::8a:::::
probability       G  96:3::1:::::4::
matrix            T  13:5:a9a3:936aa

         bits    2.3          *     
                 2.1          *     
                 1.8   *  * * *   **
                 1.6 * *  * * *   **
Information      1.4 * * ******   **
content          1.1 * * *******  **
(21.0 bits)      0.9 * * ***********
                 0.7 *** ***********
                 0.5 ***************
                 0.2 ***************
                 0.0 ---------------

Multilevel           GGATATTTCCTATTT
consensus             T A    T  TG  
sequence                G           
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
20762                        +   1845  2.62e-09 TCCAGGAACA GGATATTTCCTATTT TTGAGAGTCC
6700                         +   1068  2.62e-09 TTTCAGAACA GGATATTTCCTATTT TGAGTATCCT
20755                        +   1445  2.84e-08 GCCAAGGGTG GGATATTTTCTATTT TGTAGAGTCC
20754                        -    664  5.62e-08 TTTCTTAGAA GGAAATTTCCTTGTT CTCTTTCTAT
20761                        +    670  1.06e-07 GAAGAAAAAG GAAGATTTCCTAGTT AACAATTCAA
68723                        -   1925  5.26e-07 TTGCTTTCTT TGAGATGTCCTAGTT CACTCCTAAA
20760                        -    651  5.56e-07 TTTAAACTTG GTAAATTTTCTTTTT CTTCACATTT
16939                        -   1616  6.78e-07 TAGTTCAGTT GTATCTTTCCAATTT TGATGTTTGG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
20762                             2.6e-09  1844_[+2]_141
6700                              2.6e-09  1067_[+2]_920
20755                             2.8e-08  1444_[+2]_541
20754                             5.6e-08  663_[-2]_1323
20761                             1.1e-07  669_[+2]_1316
68723                             5.3e-07  1924_[-2]_61
20760                             5.6e-07  650_[-2]_1335
16939                             6.8e-07  1615_[-2]_371
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=15 seqs=8
20762                    ( 1845) GGATATTTCCTATTT  1 
6700                     ( 1068) GGATATTTCCTATTT  1 
20755                    ( 1445) GGATATTTTCTATTT  1 
20754                    (  664) GGAAATTTCCTTGTT  1 
20761                    (  670) GAAGATTTCCTAGTT  1 
68723                    ( 1925) TGAGATGTCCTAGTT  1 
20760                    (  651) GTAAATTTTCTTTTT  1 
16939                    ( 1616) GTATCTTTCCAATTT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 17878 bayes= 11.1253 E= 1.2e+003 
  -965   -965    210   -124 
  -124   -965    161    -24 
   176   -965   -965   -965 
   -24   -965     29     76 
   157    -71   -965   -965 
  -965   -965   -965    176 
  -965   -965    -71    157 
  -965   -965   -965    176 
  -965    187   -965    -24 
  -965    229   -965   -965 
  -124   -965   -965    157 
   134   -965   -965    -24 
  -965   -965     87    108 
  -965   -965   -965    176 
  -965   -965   -965    176 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 n= 17878 E= 1.2e+003 
 0.000369  0.000255  0.874163  0.125213 
 0.125213  0.000255  0.624475  0.250057 
 0.999120  0.000255  0.000255  0.000369 
 0.250057  0.000255  0.249943  0.499745 
 0.874276  0.125099  0.000255  0.000369 
 0.000369  0.000255  0.000255  0.999120 
 0.000369  0.000255  0.125099  0.874276 
 0.000369  0.000255  0.000255  0.999120 
 0.000369  0.749319  0.000255  0.250057 
 0.000369  0.999007  0.000255  0.000369 
 0.125213  0.000255  0.000255  0.874276 
 0.749432  0.000255  0.000255  0.250057 
 0.000369  0.000255  0.374787  0.624589 
 0.000369  0.000255  0.000255  0.999120 
 0.000369  0.000255  0.000255  0.999120 
--------------------------------------------------------------------------------





Time 152.20 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
68723                            2.83e-04  473_[-1(8.43e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_35_[-1(3.15e-06)]_[+1(1.38e-05)]_9_[-1(7.89e-05)]_63_[-1(2.97e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_26_[+2(4.37e-06)]_46_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_6_[-1(7.97e-06)]_24_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_1_[-2(5.92e-05)]_279_[-1(8.43e-06)]_[+1(1.38e-05)]_[+2(5.60e-05)]_157_[-2(5.26e-07)]_61
16939                            3.50e-06  913_[-1(2.01e-08)]_682_[-2(6.78e-07)]_205_[+1(5.80e-05)]_146
20754                            1.05e-06  39_[-2(1.78e-05)]_4_[+1(4.78e-06)]_564_[-2(7.42e-05)]_6_[-2(5.62e-08)]_146_[+2(3.98e-05)]_335_[+1(6.73e-08)]_93_[+1(5.54e-05)]_694
6707                             2.26e-05  173_[+1(4.46e-05)]_655_[-2(5.60e-05)]_3_[+1(3.06e-06)]_12_[+1(4.78e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.93e-05)]_181_[-1(3.26e-05)]_251_[+1(6.11e-09)]_329_[+1(6.34e-05)]_201
20755                            5.26e-09  160_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_3_[+1(6.41e-06)]_219_[-1(4.80e-05)]_962_[+2(2.84e-08)]_18_[+1(5.08e-10)]_6_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_14_[+1(7.97e-06)]_83
6700                             2.48e-10  48_[+1(7.97e-06)]_267_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_129_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_3_[+1(4.41e-06)]_280_[+2(2.62e-09)]_17_[+1(2.27e-10)]_101_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+2(7.29e-05)]_[+1(6.41e-06)]_604_[-1(8.43e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_3
20760                            1.53e-10  259_[-1(6.20e-05)]_339_[-2(3.17e-05)]_17_[-2(5.56e-07)]_436_[-2(4.06e-05)]_7_[+1(2.95e-07)]_6_[-1(1.12e-05)]_705_[+1(6.50e-13)]_106
20761                            3.10e-11  397_[-2(1.10e-06)]_257_[+2(1.06e-07)]_382_[-2(5.60e-05)]_[+2(7.29e-05)]_[-1(3.24e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_722_[+1(6.50e-13)]_102
20762                            1.72e-08  134_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_92_[+2(9.22e-05)]_517_[+1(7.97e-06)]_7_[-1(4.78e-06)]_439_[+2(2.62e-09)]_18_[+1(1.89e-08)]_103
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 2 reached.
********************************************************************************

CPU: crick

********************************************************************************
BioPerl-1.007002/t/data/test-4.9.meme000444000766000024     51524513155576321 17100 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 4.9.0 (Release date: Wed Oct  3 11:07:26 EST 2012)

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= multibasic-uniq.fa
ALPHABET= ACDEFGHIKLMNPQRSTVWY
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
A/chicken/Bangladesh/830 1.0000     21  A/chicken/Egypt/39825/20 1.0000     21  
A/ck/Indonesia/072/10    1.0000     21  A/duck/Bangladesh/5749/1 1.0000     21  
A/mallard/Crimea/245/200 1.0000     21  A/environment/Bangladesh 1.0000     21  
A/chicken/Egypt/111945V/ 1.0000     21  A/avian/New_York/Sg00372 1.0000     21  
A/chicken/Egypt/1117AF/2 1.0000     21  A/wild_bird_feces/Cheons 1.0000     21  
A/chicken/India/241272/2 1.0000     21  A/duck/Jiangxi/80/2005   1.0000     21  
A/chicken/Inhu/BPPVRII/2 1.0000     21  A/duck/Guangxi/668/2004  1.0000     21  
A/whooper_swan/Hokkaido/ 1.0000     21  A/duck/Vietnam/1/2010    1.0000     21  
A/avian/New_York/Sg00387 1.0000     21  A/chicken/Cambodia/LC/20 1.0000     21  
A/mallard/Maryland/786/2 1.0000     21  A/chicken/Egypt/128s/201 1.0000     21  
A/guinea_fowl/Yangon/834 1.0000     21  A/chicken/WestJava/SmiAc 1.0000     21  
A/Indonesia/625/2006     1.0000     21  A/Egypt/N07460/2012      1.0000     21  
A/duck/Victoria/26/1981| 1.0000     21  A/duck/Viet_Nam/TG2401/2 1.0000     21  
A/chicken/Egypt/398252/2 1.0000     21  A/environment/Maryland/1 1.0000     21  
A/duck/New_Zealand/41/19 1.0000     21  A/heron/Cambodia/TM068/2 1.0000     21  
A/chicken/Egypt/10117/20 1.0000     21  A/VietNam/HN31413/2008   1.0000     21  
A/chicken/Egypt/398214/2 1.0000     21  A/chicken/Egypt/39823/20 1.0000     21  
A/chicken/Belgium/150VB/ 1.0000     21  A/goose/Fujian/bb/2003   1.0000     21  
A/Vietnam/UT30259/2004   1.0000     21  A/duck/Yunnan/47/2006    1.0000     21  
A/chicken/Egypt/10259SF/ 1.0000     21  A/bird/Turkey/Unye_ist06 1.0000     21  
A/chicken/Bangladesh/11r 1.0000     21  A/chicken/Vietnam/NCVD19 1.0000     21  
A/swan/England/AV3142149 1.0000     21  A/chicken/Ibaraki/17/200 1.0000     21  
A/chicken/Nepal/354/2010 1.0000     21  A/duck/Vietnam/NCVD366/2 1.0000     21  
A/duck/Korea/GJ54/2004|G 1.0000     21  A/muscovy_duck/Vietnam/L 1.0000     21  
A/duck/Egypt/1130AG/2011 1.0000     21  A/ck/Indonesia/091/10    1.0000     21  
A/duck/Vietnam/9/2010    1.0000     21  A/duck/Hokkaido/Vac3/200 1.0000     21  
A/Thailand/WRAIR1720H/20 1.0000     21  A/chicken/Cambodia/022LC 1.0000     21  
A/spurwinged_goose/Niger 1.0000     21  A/pigeon/Egypt/SHAH5803/ 1.0000     21  
A/whooper_swan/Mongolia/ 1.0000     21  A/chicken/Shan/2626/2007 1.0000     21  
A/chicken/Italy/367/97|A 1.0000     21  A/turkey/Italy/1325/2005 1.0000     21  
A/chicken/Egypt/1158SF/2 1.0000     21  A/chicken/Egypt/398220/2 1.0000     21  
A/condor/Guangdong/139/2 1.0000     21  A/chicken/Shandong/A1/20 1.0000     21  
A/chicken/Egypt/11764s/2 1.0000     21  A/swine/NorthSumatra/UT6 1.0000     21  
A/o.bill_stork/Thailand/ 1.0000     21  A/chicken/Texas/2983132/ 1.0000     21  
A/chicken/Bangladesh/11V 1.0000     21  A/chicken/Ibaraki/15/200 1.0000     21  
A/chicken/Shandong/A10/2 1.0000     21  A/duck/Vietnam/OIE1287/2 1.0000     21  
A/duck/Vietnam/NCVD1161/ 1.0000     21  A/duck/Ireland/113/1983| 1.0000     21  
A/chicken/EastKalimantan 1.0000     21  A/duck/Vietnam/3/2010    1.0000     21  
A/Muscovy_duck/Ca_Mau/11 1.0000     21  A/chicken/Turkey/Misinli 1.0000     21  
A/chicken/Italy/9097/199 1.0000     21  A/mallard/Washington/456 1.0000     21  
A/duck/Iran/11VIR53161/2 1.0000     21  A/Muscovy_Duck/Vietnam/1 1.0000     21  
A/duck/Hunan/149/2005    1.0000     21  A/Egypt/4822NAMRU3/2009  1.0000     21  
A/duck/Vietnam/NCVD1463/ 1.0000     21  A/poultry/Egypt/398256/2 1.0000     21  
A/turkey/Italy/1980|GQ24 1.0000     21  A/goose/Bangladesh/11VIR 1.0000     21  
A/mallard/Washington/454 1.0000     21  A/chicken/Cambodia/013LC 1.0000     21  
A/chicken/Banten/PdglKas 1.0000     21  A/chicken/Vietnam/NCVD03 1.0000     21  
A/wigeon/Ohio/379/1988|C 1.0000     21  A/chicken/Magelang/BBVW6 1.0000     21  
A/chicken/Lampung/BPPVRI 1.0000     21  A/chick/Pennsylvania/1/1 1.0000     21  
A/chicken/Liaoning/A1/20 1.0000     21  A/wild_bird_feces/Cheons 1.0000     21  
A/chicken/Sikkim/151466/ 1.0000     21  A/environment/ChangSha/2 1.0000     21  
A/chicken/CentralJava/UT 1.0000     21  A/Vietnam/HN36250/2010   1.0000     21  
A/chicken/Guiyang/821/20 1.0000     21  A/owstons_civet/VietNam/ 1.0000     21  
A/chicken/Bangladesh/11r 1.0000     21  A/environment/New_York/1 1.0000     21  
A/domestic_goose/Hong_Ko 1.0000     21  A/Hubei/1/2010           1.0000     21  
A/Hunan/1/2009           1.0000     21  A/chicken/Egypt/1123AL/2 1.0000     21  
A/wood_duck/MD/04623/200 1.0000     21  A/chicken/Shanxi/2/2006  1.0000     21  
A/quail/Egypt/1171SG/201 1.0000     21  A/duck/France/080036/200 1.0000     21  
A/chicken/Yangon/182/201 1.0000     21  A/chicken/Scotland/59|X0 1.0000     21  
A/chicken/Sharkia/CAI41/ 1.0000     21  A/mallard/Sweden/21/2002 1.0000     21  
A/environment/Bangladesh 1.0000     21  A/chicken/Hebei/A8/2009  1.0000     21  
A/chicken/Egypt/11VIR445 1.0000     21  A/duck/Guangxi/13/2004   1.0000     21  
A/duck/France/090043/200 1.0000     21  A/chicken/Denpasar/BBVD1 1.0000     21  
A/Egypt/N6774/2011       1.0000     21  A/parrot/CA/6032/04|DQ25 1.0000     21  
A/Cambodia/VN05103/2005  1.0000     21  A_GenBank/heron/Cambodia 1.0000     21  
A/chicken/Bangladesh/11r 1.0000     21  A/chicken/Tabanan/BBVD14 1.0000     21  
A/great_cormorant/Tibet/ 1.0000     21  A/Egypt/321NAMRU3/2007   1.0000     21  
A/chicken/Egypt/10512AG/ 1.0000     21  AHAH5_[11734;11734]      1.0000     21  
A/Egypt/9174NAMRU3/2009  1.0000     21  A/Indonesia/NIHRD12379/2 1.0000     21  
A/chicken/Korea/ES/03    1.0000     21  A/avian/New_York/Sg00377 1.0000     21  
A/chicken/Vietnam/NCVD09 1.0000     21  A/Chicken/TurkeyMus/09rs 1.0000     21  
A/duck/Hong_Kong/312/197 1.0000     21  A/Vietnam/UT3030/2003    1.0000     21  
A/crow/Bangladesh/11rs19 1.0000     21  A/duck/Primorie/2633/200 1.0000     21  
A/Indonesia/UT3006/2005  1.0000     21  A/duck/Qalubia/CAI11/201 1.0000     21  
A/green_winged_teal/Dela 1.0000     21  A/chicken/Anhui/T5/2006  1.0000     21  
A/chicken/Puebla/8623607 1.0000     21  A/duck/Guangxi/951/2005  1.0000     21  
A/chicken/Egypt/1219s/20 1.0000     21  A/chicken/WestJava/SmiSu 1.0000     21  
A/chicken/Cambodia/TLC2/ 1.0000     21  A/duck/France/05056a/200 1.0000     21  
A/Shandong/1/2009        1.0000     21  A/chicken/Vietnam/NCVD40 1.0000     21  
A/chicken/Queretaro/7653 1.0000     21  A/environment/Bangladesh 1.0000     21  
A/barn_swallow/Hong_Kong 1.0000     21  A/duck/Primorie/2621/200 1.0000     21  
A/chicken/BacLieuVietnam 1.0000     21  A_DISC/Cambodia/V0401301 1.0000     21  
A/bar_headed_goose/Mongo 1.0000     21  A/chicken/Egypt/113Q/201 1.0000     21  
A/quail/Thanatpin/2283/2 1.0000     21  A/chicken/Egypt/125s/201 1.0000     21  
A/duck/Hong_Kong/698/197 1.0000     21  A/chicken/Egypt/209573/2 1.0000     21  
A/chicken/Indonesia/SmiW 1.0000     21  A/turkey/Egypt/091QNLQP/ 1.0000     21  
A/duck/Egypt/1053/2010   1.0000     21  A/Egypt/2786NAMRU3/2006  1.0000     21  
A/mallard/Netherlands/3/ 1.0000     21  A/chicken/Bangladesh/11r 1.0000     21  
A/chicken/Liaoning/23/20 1.0000     21  A/unknown/NY/98996/01|AY 1.0000     21  
A/tern/South_Africa/1961 1.0000     21  A/chicken/Nepal/T1P/12   1.0000     21  
A/marabou_stork/Cambodia 1.0000     21  A/chicken/Cambodia/67F1/ 1.0000     21  
A/gadwall/California/442 1.0000     21  A/chicken/TanseMyanmar/S 1.0000     21  
A/duck/Cao_Bang/43/2007  1.0000     21  A/chicken/Miyazaki/T10/2 1.0000     21  
A/whitefaced_whistling_d 1.0000     21  A/muscovy_duck/Vietnam/N 1.0000     21  
A/Canada_goose/Alaska//4 1.0000     21  A/chicken/Bangladesh/967 1.0000     21  
A/chicken/Egypt/11VIR445 1.0000     21  A/Hong_Kong/7032/2012    1.0000     21  
A/chicken/Vietnam/945/20 1.0000     21  A/ostrich/South_Africa/A 1.0000     21  
A/wild_bird/Wisconsin/43 1.0000     21  A/spurwinged_goose/Niger 1.0000     21  
A/duck/Vietnam/NCVD1026/ 1.0000     21  A/tern/South_Africa/1959 1.0000     21  
A/muscovy_duck/Jakarta/S 1.0000     21  A/goose/Germany/R3160/09 1.0000     21  
A/turkey/Ontario/7732/19 1.0000     21  A/chicken/Egypt/1090/201 1.0000     21  
A/mallard/Netherlands/2/ 1.0000     21  A/chicken/Vietnam/NCVD18 1.0000     21  
A/chicken/Texas/1672804/ 1.0000     21  A/duck/Italy/775/2004|CY 1.0000     21  
A/chicken/Bangladesh/FD( 1.0000     21  A/chicken/Vietnam/NCVD40 1.0000     21  
A/swan/Hokkaido/67/1996| 1.0000     21  A/chicken/Bangladesh/152 1.0000     21  
A/chicken/Bangladesh/11r 1.0000     21  A/chicken/Indonesia/Suka 1.0000     21  
A/gull/Pennsylvania/4175 1.0000     21  A/turkey/England/N28/73| 1.0000     21  
A/chicken/Badung/BBVD302 1.0000     21  A/chicken/Bangladesh/11r 1.0000     21  
A/chicken/Yichang/lung1/ 1.0000     21  A/avian/Missouri/4655937 1.0000     21  
A/turkey/TX/14082/1982_H 1.0000     21  A/Cambodia/W0526301/2012 1.0000     21  
A/chicken/Vietnam/NCVD11 1.0000     21  A/duck/Egypt/SHZA6605/20 1.0000     21  
A/chicken/Shandong/A5/20 1.0000     21  A/chicken/VA/40018/1984_ 1.0000     21  
A/common_magpie/HongKong 1.0000     21  A/shearwater/Australia/7 1.0000     21  
A/Chicken/TurkeyEdirne/0 1.0000     21  A/goose/Guiyang/337/2006 1.0000     21  
A/chicken/Egypt/11VIR445 1.0000     21  A/environment/Thailand/I 1.0000     21  
A/wild_bird_feces/Byeong 1.0000     21  A/duck/Vietnam/NCVD422/2 1.0000     21  
A/chicken/Bhutan/4/10    1.0000     21  A/turkey/MN/40550/1987_H 1.0000     21  
A/chicken/Egypt/1085/201 1.0000     21  A/duck/France/06436/2006 1.0000     21  
A/HongKong/6841/2010     1.0000     21  A/chicken/WestBengal/239 1.0000     21  
A/duck/Bac_Lieu/1213/200 1.0000     21  A/cinnamon_teal/Californ 1.0000     21  
A/Muscovy_duck/France/07 1.0000     21  A/chicken/Vietnam/4/2010 1.0000     21  
A/chicken/Vietnam/NCVD01 1.0000     21  A/chicken/Puebla/1458665 1.0000     21  
A/Northern_shoveler/Utah 1.0000     21  A/tundra_swan/Alaska//48 1.0000     21  
A/chicken/Sheny/0606/200 1.0000     21  A/turkey/England/N28/73| 1.0000     21  
A/duck/Iran/VIR53161/201 1.0000     21  A/chicken/Yangon/1023/20 1.0000     21  
A/chicken/Vietnam/5/2010 1.0000     21  A/chicken/Hebei/326/2005 1.0000     21  
A/chicken/Bangladesh/150 1.0000     21  A/wild_bird/Minnesota/46 1.0000     21  
A/chicken/India/81766/20 1.0000     21  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme multibasic-uniq.fa -mod zoops -nmotifs 10 

model:  mod=         zoops    nmotifs=        10    evt=           inf
object function=  E-value of product of p-values
width:  minw=            8    maxw=           21    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        2    maxsites=      253    wnsites=       0.8
theta:  prob=            1    spmap=         pam    spfuzz=        120
global: substring=     yes    branching=      no    wbranch=        no
em:     prior=       megap    b=           26565    maxiter=        50
        distance=    1e-05
data:   n=            5313    N=             253

sample: seed=            0    seqfrac=         1
Dirichlet mixture priors file: prior30.plib
Letter frequencies in dataset:
A 0.481 C 0.062 D 0.001 E 0.000 F 0.000 G 0.333 H 0.000 I 0.000 K 0.000 
L 0.000 M 0.000 N 0.000 P 0.000 Q 0.000 R 0.001 S 0.000 T 0.122 V 0.000 
W 0.000 Y 0.000 
Background letter frequencies (from dataset with add-one prior applied):
A 0.479 C 0.062 D 0.001 E 0.000 F 0.000 G 0.332 H 0.000 I 0.000 K 0.001 
L 0.000 M 0.000 N 0.001 P 0.000 Q 0.000 R 0.001 S 0.000 T 0.122 V 0.000 
W 0.000 Y 0.000 
********************************************************************************


********************************************************************************
MOTIF  1	width =   21   sites =  47   llr = 971   E-value = 5.0e-239
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  928298a29a:a::4::8:::
pos.-specific     C  :::::::8::::::49:1:::
probability       D  :::::::::::::::::::::
matrix            E  :::::::::::::::::::::
                  F  :::::::::::::::::::::
                  G  :82811::1:a:aa:::1:::
                  H  :::::::::::::::::::::
                  I  :::::::::::::::::::::
                  K  :::::::::::::::::::::
                  L  :::::::::::::::::::::
                  M  :::::::::::::::::::::
                  N  :::::::::::::::::::::
                  P  :::::::::::::::::::::
                  Q  :::::::::::::::::::::
                  R  :::::::::::::::::::::
                  S  :::::::::::::::::::::
                  T  ::::::::::::::21a:9a9
                  V  :::::::::::::::::::::
                  W  :::::::::::::::::::::
                  Y  :::::::::::::::::::::

         bits   12.4                      
                11.1                      
                 9.9                      
                 8.7                      
Relative         7.4                      
Entropy          6.2                      
(29.8 bits)      5.0                      
                 3.7                *     
                 2.5        *       ** ***
                 1.2 ** ** ** ******** ***
                 0.0 ---------------------

Multilevel           AGAGAAACAAGAGGACTATTT
consensus               A   A      C      
sequence                                  
                                          
                                          
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                    Site       
-------------             ----- ---------            ---------------------
AHAH5_[11734;11734]           1  3.05e-19          . CNAAKWGAARGAGADRDNRKR           
A/environment/New_York/1      1  7.24e-13          . AGAGAAACAAGAGGCCTATTT           
A/Northern_shoveler/Utah      1  1.11e-12          . AGAGAAACAAGAGGCCTCTTT           
A/gadwall/California/442      1  2.10e-12          . AGGGAAACAAGAGGCCTATTT           
A/wigeon/Ohio/379/1988|C      1  2.82e-12          . AGAGAAACAAGAGGCCTGTTT           
A/wild_bird/Minnesota/46      1  4.20e-12          . AGAGAAACAAGAGGTCTATTT           
A/green_winged_teal/Dela      1  5.44e-12          . AGAAAAACAAGAGGCCTATTT           
A/wood_duck/MD/04623/200      1  9.89e-12          . AGAGAAACAAGAGGACTATTT           
A/mallard/Washington/454      1  9.89e-12          . AAAGAAACAAGAGGCCTATTT           
A/tundra_swan/Alaska//48      1  1.29e-11          . AGAGGAACAAGAGGCCTATTT           
A/duck/Victoria/26/1981|      1  1.29e-11          . AGGGAGACAAGAGGCCTATTT           
A/cinnamon_teal/Californ      1  1.49e-11          . AAAGAAACAAGAGGCCTCTTT           
A/turkey/TX/14082/1982_H      1  1.88e-11          . AGAGAAACAAGAGGTCTGTTT           
A/avian/Missouri/4655937      1  1.88e-11          . AGAGAAACAAGAGGCTTATTT           
A/unknown/NY/98996/01|AY      1  1.88e-11          . GGAGAAACAAGAGGCCTATTT           
A/duck/Hong_Kong/698/197      1  2.08e-11          . AGAGAGACAAGAGGTCTATTT           
A/mallard/Sweden/21/2002      1  2.67e-11          . CGAGAAACAAGAGGACTATTT           
A/environment/Maryland/1      1  3.01e-11          . AGAGAAACAAGAGGCCCATTT           
A/chicken/Texas/1672804/      1  3.63e-11          . AGAGAAAAAAGAGGCCTATTT           
A/goose/Germany/R3160/09      1  4.14e-11          . AGAGAGACAAGAGGACTATTT           
A/mallard/Netherlands/2/      1  5.83e-11          . AGAAAAACAAGAGGACTATTT           
A/chicken/Ibaraki/17/200      1  5.83e-11          . AGGGAAACAAGAGGCTTATTT           
A/shearwater/Australia/7      1  6.48e-11          . AGGGAGACAAGAGGTCTATTT           
A/mallard/Crimea/245/200      1  6.48e-11          . AGAGAAACAAGAGGGCTATTT           
A/duck/France/080036/200      1  8.17e-11          . AAAGAAACAAGAGGACTATTT           
A/duck/Italy/775/2004|CY      1  9.22e-11          . AGAGATACAAGAGGACTATTT           
A/duck/Hokkaido/Vac3/200      1  1.27e-10          . AGAGAAACAAGAGGACTATTC           
A/parrot/CA/6032/04|DQ25      1  1.65e-10          . AAAGAAACAAGAGGCTTATTT           
A/chicken/Ibaraki/15/200      1  1.65e-10          . AGAGAAACAAGAGGATTATTT           
A/swan/Hokkaido/67/1996|      1  2.49e-10          . AGAGAAACAAGAGGACTACTT           
A/duck/France/090043/200      1  2.89e-10          . AGAGAGACGAGAGGACTATTT           
A/spurwinged_goose/Niger      1  2.89e-10          . AGAGAAAAAAGAGGACTATTT           
A/duck/France/05056a/200      1  4.65e-10          . AAAGAAACAAGAGGGCTATTT           
A/chicken/Texas/2983132/      1  5.19e-10          . AGGAAAAAAAGAGGCCTATTT           
A/duck/New_Zealand/41/19      1  6.33e-10          . AGAGACACAAGGGGCCTGTTT           
A/chicken/Belgium/150VB/      1  7.84e-10          . AAGGAGACAAGAGGACTATTT           
A/duck/France/06436/2006      1  8.65e-10          . AAAGAAACAAGAGGACTATTC           
A/Muscovy_duck/France/07      1  1.05e-09          . AAAGAAGCAAGAGGACTATTT           
A/gull/Pennsylvania/4175      1  1.05e-09          . AGAGAAACAAAAGGTCTGTTT           
A/chicken/Scotland/59|X0      1  5.46e-09          . AGGAAGAAAAGAGGTCTATTT           
A/swan/England/AV3142149      1  5.93e-09          . AGAAAAAAGAGAGGACTATTT           
A/duck/Hunan/149/2005         1  8.40e-09          . AGAAGAAAAAGAGGACTATTT           
A/bar_headed_goose/Mongo      1  2.05e-08          . AGAAGAAAAAGAGGACTGTTT           
A/chick/Pennsylvania/1/1      1  2.05e-08          . AGGAAAAAGAGAGGTCTGTTT           
A/whooper_swan/Mongolia/      1  5.15e-08          . ATTGAAACTAGAGGATTATTT           
A/chicken/VA/40018/1984_      1  8.00e-08          . AAGAAAAAGAGAGGTCTGTTT           
A/mallard/Maryland/786/2      1  3.02e-04          . GGAGCAATAGCAGGATTCATA           
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
AHAH5_[11734;11734]               3.1e-19  [1]
A/environment/New_York/1          7.2e-13  [1]
A/Northern_shoveler/Utah          1.1e-12  [1]
A/gadwall/California/442          2.1e-12  [1]
A/wigeon/Ohio/379/1988|C          2.8e-12  [1]
A/wild_bird/Minnesota/46          4.2e-12  [1]
A/green_winged_teal/Dela          5.4e-12  [1]
A/wood_duck/MD/04623/200          9.9e-12  [1]
A/mallard/Washington/454          9.9e-12  [1]
A/tundra_swan/Alaska//48          1.3e-11  [1]
A/duck/Victoria/26/1981|          1.3e-11  [1]
A/cinnamon_teal/Californ          1.5e-11  [1]
A/turkey/TX/14082/1982_H          1.9e-11  [1]
A/avian/Missouri/4655937          1.9e-11  [1]
A/unknown/NY/98996/01|AY          1.9e-11  [1]
A/duck/Hong_Kong/698/197          2.1e-11  [1]
A/mallard/Sweden/21/2002          2.7e-11  [1]
A/environment/Maryland/1            3e-11  [1]
A/chicken/Texas/1672804/          3.6e-11  [1]
A/goose/Germany/R3160/09          4.1e-11  [1]
A/mallard/Netherlands/2/          5.8e-11  [1]
A/chicken/Ibaraki/17/200          5.8e-11  [1]
A/shearwater/Australia/7          6.5e-11  [1]
A/mallard/Crimea/245/200          6.5e-11  [1]
A/duck/France/080036/200          8.2e-11  [1]
A/duck/Italy/775/2004|CY          9.2e-11  [1]
A/duck/Hokkaido/Vac3/200          1.3e-10  [1]
A/parrot/CA/6032/04|DQ25          1.7e-10  [1]
A/chicken/Ibaraki/15/200          1.7e-10  [1]
A/swan/Hokkaido/67/1996|          2.5e-10  [1]
A/duck/France/090043/200          2.9e-10  [1]
A/spurwinged_goose/Niger          2.9e-10  [1]
A/duck/France/05056a/200          4.7e-10  [1]
A/chicken/Texas/2983132/          5.2e-10  [1]
A/duck/New_Zealand/41/19          6.3e-10  [1]
A/chicken/Belgium/150VB/          7.8e-10  [1]
A/duck/France/06436/2006          8.6e-10  [1]
A/Muscovy_duck/France/07            1e-09  [1]
A/gull/Pennsylvania/4175            1e-09  [1]
A/chicken/Scotland/59|X0          5.5e-09  [1]
A/swan/England/AV3142149          5.9e-09  [1]
A/duck/Hunan/149/2005             8.4e-09  [1]
A/bar_headed_goose/Mongo            2e-08  [1]
A/chick/Pennsylvania/1/1            2e-08  [1]
A/whooper_swan/Mongolia/          5.1e-08  [1]
A/chicken/VA/40018/1984_            8e-08  [1]
A/mallard/Maryland/786/2           0.0003  [1]
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=21 seqs=47
AHAH5_[11734;11734]      (    1) CNAAKWGAARGAGADRDNRKR  1 
A/environment/New_York/1 (    1) AGAGAAACAAGAGGCCTATTT  1 
A/Northern_shoveler/Utah (    1) AGAGAAACAAGAGGCCTCTTT  1 
A/gadwall/California/442 (    1) AGGGAAACAAGAGGCCTATTT  1 
A/wigeon/Ohio/379/1988|C (    1) AGAGAAACAAGAGGCCTGTTT  1 
A/wild_bird/Minnesota/46 (    1) AGAGAAACAAGAGGTCTATTT  1 
A/green_winged_teal/Dela (    1) AGAAAAACAAGAGGCCTATTT  1 
A/wood_duck/MD/04623/200 (    1) AGAGAAACAAGAGGACTATTT  1 
A/mallard/Washington/454 (    1) AAAGAAACAAGAGGCCTATTT  1 
A/tundra_swan/Alaska//48 (    1) AGAGGAACAAGAGGCCTATTT  1 
A/duck/Victoria/26/1981| (    1) AGGGAGACAAGAGGCCTATTT  1 
A/cinnamon_teal/Californ (    1) AAAGAAACAAGAGGCCTCTTT  1 
A/turkey/TX/14082/1982_H (    1) AGAGAAACAAGAGGTCTGTTT  1 
A/avian/Missouri/4655937 (    1) AGAGAAACAAGAGGCTTATTT  1 
A/unknown/NY/98996/01|AY (    1) GGAGAAACAAGAGGCCTATTT  1 
A/duck/Hong_Kong/698/197 (    1) AGAGAGACAAGAGGTCTATTT  1 
A/mallard/Sweden/21/2002 (    1) CGAGAAACAAGAGGACTATTT  1 
A/environment/Maryland/1 (    1) AGAGAAACAAGAGGCCCATTT  1 
A/chicken/Texas/1672804/ (    1) AGAGAAAAAAGAGGCCTATTT  1 
A/goose/Germany/R3160/09 (    1) AGAGAGACAAGAGGACTATTT  1 
A/mallard/Netherlands/2/ (    1) AGAAAAACAAGAGGACTATTT  1 
A/chicken/Ibaraki/17/200 (    1) AGGGAAACAAGAGGCTTATTT  1 
A/shearwater/Australia/7 (    1) AGGGAGACAAGAGGTCTATTT  1 
A/mallard/Crimea/245/200 (    1) AGAGAAACAAGAGGGCTATTT  1 
A/duck/France/080036/200 (    1) AAAGAAACAAGAGGACTATTT  1 
A/duck/Italy/775/2004|CY (    1) AGAGATACAAGAGGACTATTT  1 
A/duck/Hokkaido/Vac3/200 (    1) AGAGAAACAAGAGGACTATTC  1 
A/parrot/CA/6032/04|DQ25 (    1) AAAGAAACAAGAGGCTTATTT  1 
A/chicken/Ibaraki/15/200 (    1) AGAGAAACAAGAGGATTATTT  1 
A/swan/Hokkaido/67/1996| (    1) AGAGAAACAAGAGGACTACTT  1 
A/duck/France/090043/200 (    1) AGAGAGACGAGAGGACTATTT  1 
A/spurwinged_goose/Niger (    1) AGAGAAAAAAGAGGACTATTT  1 
A/duck/France/05056a/200 (    1) AAAGAAACAAGAGGGCTATTT  1 
A/chicken/Texas/2983132/ (    1) AGGAAAAAAAGAGGCCTATTT  1 
A/duck/New_Zealand/41/19 (    1) AGAGACACAAGGGGCCTGTTT  1 
A/chicken/Belgium/150VB/ (    1) AAGGAGACAAGAGGACTATTT  1 
A/duck/France/06436/2006 (    1) AAAGAAACAAGAGGACTATTC  1 
A/Muscovy_duck/France/07 (    1) AAAGAAGCAAGAGGACTATTT  1 
A/gull/Pennsylvania/4175 (    1) AGAGAAACAAAAGGTCTGTTT  1 
A/chicken/Scotland/59|X0 (    1) AGGAAGAAAAGAGGTCTATTT  1 
A/swan/England/AV3142149 (    1) AGAAAAAAGAGAGGACTATTT  1 
A/duck/Hunan/149/2005    (    1) AGAAGAAAAAGAGGACTATTT  1 
A/bar_headed_goose/Mongo (    1) AGAAGAAAAAGAGGACTGTTT  1 
A/chick/Pennsylvania/1/1 (    1) AGGAAAAAGAGAGGTCTGTTT  1 
A/whooper_swan/Mongolia/ (    1) ATTGAAACTAGAGGATTATTT  1 
A/chicken/VA/40018/1984_ (    1) AAGAAAAAGAGAGGTCTGTTT  1 
A/mallard/Maryland/786/2 (    1) GGAGCAATAGCAGGATTCATA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 20 w= 21 n= 253 bayes= 3.90811 E= 5.0e-239 
    90    -56    -60    174    142   -291     71    203     -4    259    154     54    235    175    -78    517   -525    377   -128    -25 
  -167   -590    204    358    201    124    239    247    205    279    197    509    293    282     96    508   -273    342      7    107 
    69   -571   -100    118     89    -81     33    138    -66    196     96     34    230    146   -121    493   -238    319   -177    -72 
  -121   -641    -19    153     68    123     59    106     -9    161     58     61    191    129    -94    427   -609    255   -157    -60 
    83   -161     94    349    310   -252    214    386    505    442    329    162    273    302     74    629   -443    554     32    133 
    68   -158     64    317    279   -135    185    354    146    410    298    139    264    276     44    606   -243    522    559    103 
    98   -625   -131     77     52   -292      2     93   -101    157     47    -17    181     98   -159    434   -598    268   -202   -104 
  -115    359   -108    110     85   -668     28    137    -74    191     90     29    229    142   -126    489   -238    315   -182    -76 
    87   -557    -81    145    114   -196     51    169    -36    226    123     44    232    159   -101    504   -238    347   -154    -50 
    96   -547    -53    178    143   -381     73    204      8    262    154     52    223    173    421    508   -536    377   -125    -23 
  -438   -209    245    398    231    148    276    278    248    305    226    301    312    313    137    513   -552    353     47    144 
   101   -633   -136     70     46   -385     -3     85   -108    150     39    -23    176     92   -165    427   -605    260   -206   -109 
  -965   -907   -110     29    -56    159    -32    -75   -117     17   -143    -80     40    -20   -205    127   -901    -11   -235   -158 
  -440   -623    223    375    209    151    254    254    225    283    202    277    289    290    115    487   -578    328     25    122 
   -26    251    481    124     87   -290     39    134    -62    192     93     49    232    149   -120    493     46    315   -180    -72 
  -681    378   -119     89     66   -770     18    119    -55    163     45    -27    152     93    418    377     -1    226   -201    -78 
  -679   -162    475    225    185   -776    161    323    128    289    245    216    224    268     11    592    292    386    -74     30 
    65      1    -57    166    131   -119     67    189    -14    246    142    523    236    172    -86    513   -526    365   -139    -34 
  -422   -164     71    261    227   -711    195    367    169    334    292    251    273    311    415    642    287    437    -36     66 
  -891   -794   -111     53     23   -922     11    119    524    117     38     15     80     88   -142    375    299    178   -207   -111 
  -420    -68     64    254    221   -707    188    359    160    327    284    243    270    304    416    635    284    431    -43     60 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 20 w= 21 nsites= 47 E= 5.0e-239 
 0.914894  0.042553  0.000000  0.000000  0.000000  0.042553  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.191489  0.000000  0.000000  0.000000  0.000000  0.765957  0.000000  0.000000  0.000000  0.000000  0.000000  0.021277  0.000000  0.000000  0.000000  0.000000  0.021277  0.000000  0.000000  0.000000 
 0.787234  0.000000  0.000000  0.000000  0.000000  0.191489  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.021277  0.000000  0.000000  0.000000 
 0.212766  0.000000  0.000000  0.000000  0.000000  0.787234  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.893617  0.021277  0.000000  0.000000  0.000000  0.063830  0.000000  0.000000  0.021277  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.787234  0.021277  0.000000  0.000000  0.000000  0.148936  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.021277  0.000000  0.021277  0.000000 
 0.957447  0.000000  0.000000  0.000000  0.000000  0.042553  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.212766  0.765957  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.021277  0.000000  0.000000  0.000000 
 0.893617  0.000000  0.000000  0.000000  0.000000  0.085106  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.021277  0.000000  0.000000  0.000000 
 0.957447  0.000000  0.000000  0.000000  0.000000  0.021277  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.021277  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.021277  0.021277  0.000000  0.000000  0.000000  0.957447  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.978723  0.000000  0.000000  0.000000  0.000000  0.021277  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.021277  0.000000  0.000000  0.000000  0.000000  0.978723  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.404255  0.361702  0.021277  0.000000  0.000000  0.042553  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.170213  0.000000  0.000000  0.000000 
 0.000000  0.851064  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.021277  0.000000  0.127660  0.000000  0.000000  0.000000 
 0.000000  0.021277  0.021277  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.957447  0.000000  0.000000  0.000000 
 0.765957  0.063830  0.000000  0.000000  0.000000  0.148936  0.000000  0.000000  0.000000  0.000000  0.000000  0.021277  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.021277  0.021277  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.021277  0.000000  0.936170  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.021277  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.978723  0.000000  0.000000  0.000000 
 0.021277  0.042553  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.021277  0.000000  0.914894  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
AGA[GA]AAA[CA]AAGAGG[AC]CTATTT
--------------------------------------------------------------------------------




Time 54.91 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   21   sites =  93   llr = 1061   E-value = 4.5e-207
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  8:9:a28189:aa19a89a75
pos.-specific     C  ::::::::1::::::::::::
probability       D  :::::::::::::::::::::
matrix            E  :::::::::::::::::::::
                  F  :::::::::::::::::::::
                  G  291a:82911a::91:21:35
                  H  :::::::::::::::::::::
                  I  :::::::::::::::::::::
                  K  :::::::::::::::::::::
                  L  :::::::::::::::::::::
                  M  :::::::::::::::::::::
                  N  :::::::::::::::::::::
                  P  :::::::::::::::::::::
                  Q  :::::::::::::::::::::
                  R  :::::::::::::::::::::
                  S  :::::::::::::::::::::
                  T  :1:::::::::::::::::::
                  V  :::::::::::::::::::::
                  W  :::::::::::::::::::::
                  Y  :::::::::::::::::::::

         bits   12.4                      
                11.1                      
                 9.9                      
                 8.7                      
Relative         7.4                      
Entropy          6.2                      
(16.5 bits)      5.0                      
                 3.7                      
                 2.5                      
                 1.2  * *** * *******  *  
                 0.0 ---------------------

Multilevel           AGAGAGAGAAGAAGAAAAAAG
consensus            G    AG            GA
sequence                                  
                                          
                                          
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                    Site       
-------------             ----- ---------            ---------------------
A/great_cormorant/Tibet/      1  3.08e-09          . GGARAGAGAAGAAGAAAAAAG           
A/chicken/Shan/2626/2007      1  1.84e-08          . AGAGAGAGAAGAAGAAAAAAG           
A/duck/Vietnam/OIE1287/2      1  3.14e-08          . AGAGAGAGAAGAAGAAAAAGG           
A/muscovy_duck/Jakarta/S      1  5.58e-08          . AGAGAGAGCAGAAGAAAAAAG           
A/Vietnam/UT3030/2003         1  5.58e-08          . AGAGAGAGAAGAAGAAAAAAA           
A/chicken/Magelang/BBVW6      1  7.67e-08          . AGAGAGAGCAGAAGAAAAAGG           
A/chicken/Vietnam/NCVD19      1  7.67e-08          . AGAGAGAGAAGAAGAAAAAGA           
A/duck/Bac_Lieu/1213/200      1  9.16e-08          . AGAGAGGGAAGAAGAAAAAAG           
A/chicken/Sharkia/CAI41/      1  1.04e-07          . GGAGAGAGAAGAAGAAAAAAG           
A/chicken/Tabanan/BBVD14      1  2.08e-07          . AGAGAGAGAAGAAGAAAGAAG           
A/duck/Jiangxi/80/2005        1  2.08e-07          . AGAGAAAGAAGAAGAAAAAAG           
A/chicken/Badung/BBVD302      1  2.17e-07          . ATAGAGAGAAGAAGAAAAAAG           
A/chicken/Banten/PdglKas      1  2.53e-07          . AGAGAGAGGAGAAGAAAAAAG           
A/o.bill_stork/Thailand/      1  2.53e-07          . AGAGAGAGAAGACGAAAAAAG           
A/chicken/Bangladesh/150      1  3.10e-07          . GGAGAGAGAAGAAGAAAAAGA           
A/chicken/Yangon/182/201      1  3.10e-07          . AGAGAGAGAAGAAGAAGAAAA           
A/chicken/Shandong/A1/20      1  3.10e-07          . AGAGAAAGAAGAAGAAAAAGG           
A/duck/Qalubia/CAI11/201      1  3.89e-07          . GGAGAGGGAAGAAGAAAAAAG           
A/Indonesia/UT3006/2005       1  3.89e-07          . AGAGAAAGCAGAAGAAAAAAG           
A/goose/Fujian/bb/2003        1  3.89e-07          . AGAGAGAGAAGAAGGAAAAAG           
A/environment/Thailand/I      1  4.76e-07          . AGAGAGAGAGGAAGAAAAAAG           
A/chicken/EastKalimantan      1  4.76e-07          . AGAGAGAGTAGAAGAAAAAAG           
A/swine/NorthSumatra/UT6      1  4.76e-07          . AGGGAGAGAAGAAGAAAAAAG           
A/duck/Cao_Bang/43/2007       1  5.46e-07          . AGAGAAAGAAGAAGAAAAAGA           
A/muscovy_duck/Vietnam/N      1  6.23e-07          . AGAGAAGGAAGAAGAAAAAAG           
A/Indonesia/NIHRD12379/2      1  6.23e-07          . AGAGAGAGCAGAAGGAAAAAG           
A/Egypt/321NAMRU3/2007        1  6.23e-07          . GGAGAGAGAAGAAGAAGAAAG           
A/chicken/India/81766/20      1  7.12e-07          . GGAGAGAGAAGAAGAAAGAAG           
A/chicken/Bangladesh/967      1  7.12e-07          . GGAGAAAGAAGAAGAAAAAAG           
A/chicken/Nepal/T1P/12        1  7.12e-07          . AGAGAGAGGAGAAGAAAAAGA           
A/Thailand/WRAIR1720H/20      1  7.12e-07          . AGAGAGAAAAGAAGAAAAAAG           
A/goose/Guiyang/337/2006      1  7.95e-07          . AGAGAGAGAAGGAGAAAAAAG           
A/Muscovy_duck/Ca_Mau/11      1  7.95e-07          . AGAGAGGGGAGAAGAAAAAAG           
A/owstons_civet/VietNam/      1  8.77e-07          . AGAGAGAGAAGAAGGAAAAGA           
A/chicken/Bangladesh/152      1  1.20e-06          . AGGGAGAGAAGAAGAAAAAGA           
A/chicken/Liaoning/23/20      1  1.20e-06          . GGAGAGAGAAGAAGGAAAAAG           
A/condor/Guangdong/139/2      1  1.20e-06          . AGAGGGAGAAGAAGAAAAAAG           
A/muscovy_duck/Vietnam/L      1  1.20e-06          . ATAGAGAGAAGAAGAAGAAAG           
A/chicken/Hebei/326/2005      1  1.32e-06          . AGAGAGGGAGGAAGAAAAAAG           
A/chicken/Inhu/BPPVRII/2      1  1.32e-06          . AGGGAGGGAAGAAGAAAAAAG           
A/chicken/WestBengal/239      1  1.45e-06          . GGAGAGAGGAGAAGAAAAAAA           
A/bird/Turkey/Unye_ist06      1  1.45e-06          . GGGGAGAGAAGAAGAAAAAAG           
A/chicken/Sheny/0606/200      1  1.67e-06          . AGAGAGGGAAGAAGGAAAAAA           
A/chicken/Miyazaki/T10/2      1  1.67e-06          . AGAGAGAAAAGAAGAAAAAGA           
A/duck/Guangxi/668/2004       1  1.67e-06          . AGAGAGATAAGAAGAAAAAAG           
A/Cambodia/W0526301/2012      1  1.92e-06          . AGAGAGGAAAGAAGAAAAAAG           
A/chicken/Egypt/11VIR445      1  1.92e-06          . GGAGAGGGAAGAAGAAAGAAG           
A/chicken/Egypt/113Q/201      1  1.92e-06          . GGAGAAGGAAGAAGAAAAAAG           
A/Hubei/1/2010                1  1.92e-06          . AGAGAGAGAAGGAGAAAAAGA           
A/duck/Vietnam/NCVD1463/      1  1.92e-06          . ATAGAGAGAAGAAGAAGAAAA           
A/chicken/Shandong/A10/2      1  1.92e-06          . AGAGGGAGAAGAAGAAAAAAA           
A/chicken/Cambodia/67F1/      1  2.10e-06          . AGAGAGGGAAGGAGAAAAAAG           
A/chicken/Liaoning/A1/20      1  2.10e-06          . AGAGAGGGAGGAAGAAAAAAA           
A/chicken/Egypt/1158SF/2      1  2.10e-06          . GGAGAGAAAAGAAGAAAAAAG           
A/Shandong/1/2009             1  2.34e-06          . AGAGAAAGAAGAAGAAGAAGA           
A/chicken/Egypt/1085/201      1  2.60e-06          . GGAGAGGGAAGAAGAAGAAAA           
A/chicken/Hebei/A8/2009       1  2.60e-06          . AGAGGGAGAAGAAGAAAAAGA           
A/chicken/CentralJava/UT      1  2.60e-06          . AGAGAGAGAAGAAAAAAAAGA           
A_DISC/Cambodia/V0401301      1  2.91e-06          . AGAGTGGGAAGAAGAAAAAAG           
A/chicken/Lampung/BPPVRI      1  2.91e-06          . AGAGAAAGCAGAAGGAAAAAG           
A/chicken/Vietnam/NCVD40      1  3.27e-06          . AGAGAAAGGAGAAGAAAAAGA           
A/duck/Vietnam/NCVD366/2      1  3.27e-06          . AGAGATGGAAGAAGAAAAAAG           
A/duck/Yunnan/47/2006         1  3.27e-06          . AGAAAGAGAAGAAGAAAAAAG           
A/chicken/Denpasar/BBVD1      1  3.61e-06          . AGAGAGAGAAGAAGAGAAAAG           
A/Hunan/1/2009                1  3.93e-06          . AGAGAAAGAAGAAGGAAAAGA           
A/chicken/Vietnam/NCVD09      1  4.40e-06          . ATAGAGGGAAGAAGAAGAAAA           
A/duck/Guangxi/951/2005       1  5.43e-06          . AGTGAAAGAAGAAGAAAAAGA           
A/environment/Bangladesh      1  5.95e-06          . AGGGAGAGGAGAAGAAAAAGA           
A/environment/ChangSha/2      1  5.95e-06          . AGAGAGAGAAGAGGAAAAAGA           
A/chicken/India/241272/2      1  5.95e-06          . GGAGAGAGGAGAAGAAAGAAA           
A/quail/Thanatpin/2283/2      1  6.62e-06          . AGAGAAAAAAGAAGAAAAAGA           
A/chicken/Sikkim/151466/      1  6.62e-06          . GGTGAGAGAAGAAGAAAGAAG           
A/chicken/Bangladesh/830      1  6.62e-06          . GGAGAGAGAAGAAAAAAAAGA           
A/chicken/Shandong/A5/20      1  7.33e-06          . AGAGAGGGAGGAAGAAGAAAA           
A/domestic_goose/Hong_Ko      1  8.76e-06          . ATAGAGAGGAGAAGAAGAAAA           
A/chicken/Egypt/10512AG/      1  9.60e-06          . GAAGAGGGAAGAAGAAAAAAG           
A/duck/Guangxi/13/2004        1  9.60e-06          . AGAGAAAGAAGAAAAAAAAGA           
A/Vietnam/UT30259/2004        1  9.60e-06          . AGAGAGAGAAGAAAAAAGAGA           
A/spurwinged_goose/Niger      1  1.16e-05          . AGAGAAAAAAGAAGAAAGAAG           
A/chicken/Vietnam/NCVD18      1  1.27e-05          . AAAGAAAGAAGAAGAAAAAGA           
A/duck/Vietnam/NCVD1026/      1  1.27e-05          . ATAGAGAGAGGAAGAAGAAAA           
A/chicken/WestJava/SmiAc      1  1.27e-05          . AGAGAGAGCAGACGTAAAAAA           
A/Vietnam/HN36250/2010        1  1.51e-05          . AGAGAAAAAAGAAGAAGAAAA           
A/chicken/Vietnam/NCVD40      1  1.66e-05          . AGAGAAAGGAGAAGGAAAAGA           
A/duck/Vietnam/NCVD422/2      1  1.96e-05          . AGGGAAAGGAGAAGAAAAAGA           
A/barn_swallow/Hong_Kong      1  2.31e-05          . ATAGAAAGAAGAAGAAGGAAA           
A/ck/Indonesia/072/10         1  2.31e-05          . AAGGAGGGAAGAAGAAAAAAG           
A/chicken/Yangon/1023/20      1  2.51e-05          . AGAGAGAAAGGAAGAAGAAAA           
A/chicken/Vietnam/NCVD01      1  2.94e-05          . AGAGAGGGAGGAAGAAGGAGA           
A/Egypt/4822NAMRU3/2009       1  4.03e-05          . GGAAAGAGTAGAAGAAAAAAG           
A/chicken/Korea/ES/03         1  5.89e-05          . AGAGAGAAAAGAAAAAAGAGA           
A/duck/Viet_Nam/TG2401/2      1  6.33e-05          . AGAGAGAGAAGGAAAAAGAGA           
A/whitefaced_whistling_d      1  1.11e-04          . AAAGAAAAAAGAAGAAAGAAG           
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
A/great_cormorant/Tibet/          3.1e-09  [2]
A/chicken/Shan/2626/2007          1.8e-08  [2]
A/duck/Vietnam/OIE1287/2          3.1e-08  [2]
A/muscovy_duck/Jakarta/S          5.6e-08  [2]
A/Vietnam/UT3030/2003             5.6e-08  [2]
A/chicken/Magelang/BBVW6          7.7e-08  [2]
A/chicken/Vietnam/NCVD19          7.7e-08  [2]
A/duck/Bac_Lieu/1213/200          9.2e-08  [2]
A/chicken/Sharkia/CAI41/            1e-07  [2]
A/chicken/Tabanan/BBVD14          2.1e-07  [2]
A/duck/Jiangxi/80/2005            2.1e-07  [2]
A/chicken/Badung/BBVD302          2.2e-07  [2]
A/chicken/Banten/PdglKas          2.5e-07  [2]
A/o.bill_stork/Thailand/          2.5e-07  [2]
A/chicken/Bangladesh/150          3.1e-07  [2]
A/chicken/Yangon/182/201          3.1e-07  [2]
A/chicken/Shandong/A1/20          3.1e-07  [2]
A/duck/Qalubia/CAI11/201          3.9e-07  [2]
A/Indonesia/UT3006/2005           3.9e-07  [2]
A/goose/Fujian/bb/2003            3.9e-07  [2]
A/environment/Thailand/I          4.8e-07  [2]
A/chicken/EastKalimantan          4.8e-07  [2]
A/swine/NorthSumatra/UT6          4.8e-07  [2]
A/duck/Cao_Bang/43/2007           5.5e-07  [2]
A/muscovy_duck/Vietnam/N          6.2e-07  [2]
A/Indonesia/NIHRD12379/2          6.2e-07  [2]
A/Egypt/321NAMRU3/2007            6.2e-07  [2]
A/chicken/India/81766/20          7.1e-07  [2]
A/chicken/Bangladesh/967          7.1e-07  [2]
A/chicken/Nepal/T1P/12            7.1e-07  [2]
A/Thailand/WRAIR1720H/20          7.1e-07  [2]
A/goose/Guiyang/337/2006          7.9e-07  [2]
A/Muscovy_duck/Ca_Mau/11          7.9e-07  [2]
A/owstons_civet/VietNam/          8.8e-07  [2]
A/chicken/Bangladesh/152          1.2e-06  [2]
A/chicken/Liaoning/23/20          1.2e-06  [2]
A/condor/Guangdong/139/2          1.2e-06  [2]
A/muscovy_duck/Vietnam/L          1.2e-06  [2]
A/chicken/Hebei/326/2005          1.3e-06  [2]
A/chicken/Inhu/BPPVRII/2          1.3e-06  [2]
A/chicken/WestBengal/239          1.5e-06  [2]
A/bird/Turkey/Unye_ist06          1.5e-06  [2]
A/chicken/Sheny/0606/200          1.7e-06  [2]
A/chicken/Miyazaki/T10/2          1.7e-06  [2]
A/duck/Guangxi/668/2004           1.7e-06  [2]
A/Cambodia/W0526301/2012          1.9e-06  [2]
A/chicken/Egypt/11VIR445          1.9e-06  [2]
A/chicken/Egypt/113Q/201          1.9e-06  [2]
A/Hubei/1/2010                    1.9e-06  [2]
A/duck/Vietnam/NCVD1463/          1.9e-06  [2]
A/chicken/Shandong/A10/2          1.9e-06  [2]
A/chicken/Cambodia/67F1/          2.1e-06  [2]
A/chicken/Liaoning/A1/20          2.1e-06  [2]
A/chicken/Egypt/1158SF/2          2.1e-06  [2]
A/Shandong/1/2009                 2.3e-06  [2]
A/chicken/Egypt/1085/201          2.6e-06  [2]
A/chicken/Hebei/A8/2009           2.6e-06  [2]
A/chicken/CentralJava/UT          2.6e-06  [2]
A_DISC/Cambodia/V0401301          2.9e-06  [2]
A/chicken/Lampung/BPPVRI          2.9e-06  [2]
A/chicken/Vietnam/NCVD40          3.3e-06  [2]
A/duck/Vietnam/NCVD366/2          3.3e-06  [2]
A/duck/Yunnan/47/2006             3.3e-06  [2]
A/chicken/Denpasar/BBVD1          3.6e-06  [2]
A/Hunan/1/2009                    3.9e-06  [2]
A/chicken/Vietnam/NCVD09          4.4e-06  [2]
A/duck/Guangxi/951/2005           5.4e-06  [2]
A/environment/Bangladesh            6e-06  [2]
A/environment/ChangSha/2            6e-06  [2]
A/chicken/India/241272/2            6e-06  [2]
A/quail/Thanatpin/2283/2          6.6e-06  [2]
A/chicken/Sikkim/151466/          6.6e-06  [2]
A/chicken/Bangladesh/830          6.6e-06  [2]
A/chicken/Shandong/A5/20          7.3e-06  [2]
A/domestic_goose/Hong_Ko          8.8e-06  [2]
A/chicken/Egypt/10512AG/          9.6e-06  [2]
A/duck/Guangxi/13/2004            9.6e-06  [2]
A/Vietnam/UT30259/2004            9.6e-06  [2]
A/spurwinged_goose/Niger          1.2e-05  [2]
A/chicken/Vietnam/NCVD18          1.3e-05  [2]
A/duck/Vietnam/NCVD1026/          1.3e-05  [2]
A/chicken/WestJava/SmiAc          1.3e-05  [2]
A/Vietnam/HN36250/2010            1.5e-05  [2]
A/chicken/Vietnam/NCVD40          1.7e-05  [2]
A/duck/Vietnam/NCVD422/2            2e-05  [2]
A/barn_swallow/Hong_Kong          2.3e-05  [2]
A/ck/Indonesia/072/10             2.3e-05  [2]
A/chicken/Yangon/1023/20          2.5e-05  [2]
A/chicken/Vietnam/NCVD01          2.9e-05  [2]
A/Egypt/4822NAMRU3/2009             4e-05  [2]
A/chicken/Korea/ES/03             5.9e-05  [2]
A/duck/Viet_Nam/TG2401/2          6.3e-05  [2]
A/whitefaced_whistling_d          0.00011  [2]
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=21 seqs=93
A/great_cormorant/Tibet/ (    1) GGARAGAGAAGAAGAAAAAAG  1 
A/chicken/Shan/2626/2007 (    1) AGAGAGAGAAGAAGAAAAAAG  1 
A/duck/Vietnam/OIE1287/2 (    1) AGAGAGAGAAGAAGAAAAAGG  1 
A/muscovy_duck/Jakarta/S (    1) AGAGAGAGCAGAAGAAAAAAG  1 
A/Vietnam/UT3030/2003    (    1) AGAGAGAGAAGAAGAAAAAAA  1 
A/chicken/Magelang/BBVW6 (    1) AGAGAGAGCAGAAGAAAAAGG  1 
A/chicken/Vietnam/NCVD19 (    1) AGAGAGAGAAGAAGAAAAAGA  1 
A/duck/Bac_Lieu/1213/200 (    1) AGAGAGGGAAGAAGAAAAAAG  1 
A/chicken/Sharkia/CAI41/ (    1) GGAGAGAGAAGAAGAAAAAAG  1 
A/chicken/Tabanan/BBVD14 (    1) AGAGAGAGAAGAAGAAAGAAG  1 
A/duck/Jiangxi/80/2005   (    1) AGAGAAAGAAGAAGAAAAAAG  1 
A/chicken/Badung/BBVD302 (    1) ATAGAGAGAAGAAGAAAAAAG  1 
A/chicken/Banten/PdglKas (    1) AGAGAGAGGAGAAGAAAAAAG  1 
A/o.bill_stork/Thailand/ (    1) AGAGAGAGAAGACGAAAAAAG  1 
A/chicken/Bangladesh/150 (    1) GGAGAGAGAAGAAGAAAAAGA  1 
A/chicken/Yangon/182/201 (    1) AGAGAGAGAAGAAGAAGAAAA  1 
A/chicken/Shandong/A1/20 (    1) AGAGAAAGAAGAAGAAAAAGG  1 
A/duck/Qalubia/CAI11/201 (    1) GGAGAGGGAAGAAGAAAAAAG  1 
A/Indonesia/UT3006/2005  (    1) AGAGAAAGCAGAAGAAAAAAG  1 
A/goose/Fujian/bb/2003   (    1) AGAGAGAGAAGAAGGAAAAAG  1 
A/environment/Thailand/I (    1) AGAGAGAGAGGAAGAAAAAAG  1 
A/chicken/EastKalimantan (    1) AGAGAGAGTAGAAGAAAAAAG  1 
A/swine/NorthSumatra/UT6 (    1) AGGGAGAGAAGAAGAAAAAAG  1 
A/duck/Cao_Bang/43/2007  (    1) AGAGAAAGAAGAAGAAAAAGA  1 
A/muscovy_duck/Vietnam/N (    1) AGAGAAGGAAGAAGAAAAAAG  1 
A/Indonesia/NIHRD12379/2 (    1) AGAGAGAGCAGAAGGAAAAAG  1 
A/Egypt/321NAMRU3/2007   (    1) GGAGAGAGAAGAAGAAGAAAG  1 
A/chicken/India/81766/20 (    1) GGAGAGAGAAGAAGAAAGAAG  1 
A/chicken/Bangladesh/967 (    1) GGAGAAAGAAGAAGAAAAAAG  1 
A/chicken/Nepal/T1P/12   (    1) AGAGAGAGGAGAAGAAAAAGA  1 
A/Thailand/WRAIR1720H/20 (    1) AGAGAGAAAAGAAGAAAAAAG  1 
A/goose/Guiyang/337/2006 (    1) AGAGAGAGAAGGAGAAAAAAG  1 
A/Muscovy_duck/Ca_Mau/11 (    1) AGAGAGGGGAGAAGAAAAAAG  1 
A/owstons_civet/VietNam/ (    1) AGAGAGAGAAGAAGGAAAAGA  1 
A/chicken/Bangladesh/152 (    1) AGGGAGAGAAGAAGAAAAAGA  1 
A/chicken/Liaoning/23/20 (    1) GGAGAGAGAAGAAGGAAAAAG  1 
A/condor/Guangdong/139/2 (    1) AGAGGGAGAAGAAGAAAAAAG  1 
A/muscovy_duck/Vietnam/L (    1) ATAGAGAGAAGAAGAAGAAAG  1 
A/chicken/Hebei/326/2005 (    1) AGAGAGGGAGGAAGAAAAAAG  1 
A/chicken/Inhu/BPPVRII/2 (    1) AGGGAGGGAAGAAGAAAAAAG  1 
A/chicken/WestBengal/239 (    1) GGAGAGAGGAGAAGAAAAAAA  1 
A/bird/Turkey/Unye_ist06 (    1) GGGGAGAGAAGAAGAAAAAAG  1 
A/chicken/Sheny/0606/200 (    1) AGAGAGGGAAGAAGGAAAAAA  1 
A/chicken/Miyazaki/T10/2 (    1) AGAGAGAAAAGAAGAAAAAGA  1 
A/duck/Guangxi/668/2004  (    1) AGAGAGATAAGAAGAAAAAAG  1 
A/Cambodia/W0526301/2012 (    1) AGAGAGGAAAGAAGAAAAAAG  1 
A/chicken/Egypt/11VIR445 (    1) GGAGAGGGAAGAAGAAAGAAG  1 
A/chicken/Egypt/113Q/201 (    1) GGAGAAGGAAGAAGAAAAAAG  1 
A/Hubei/1/2010           (    1) AGAGAGAGAAGGAGAAAAAGA  1 
A/duck/Vietnam/NCVD1463/ (    1) ATAGAGAGAAGAAGAAGAAAA  1 
A/chicken/Shandong/A10/2 (    1) AGAGGGAGAAGAAGAAAAAAA  1 
A/chicken/Cambodia/67F1/ (    1) AGAGAGGGAAGGAGAAAAAAG  1 
A/chicken/Liaoning/A1/20 (    1) AGAGAGGGAGGAAGAAAAAAA  1 
A/chicken/Egypt/1158SF/2 (    1) GGAGAGAAAAGAAGAAAAAAG  1 
A/Shandong/1/2009        (    1) AGAGAAAGAAGAAGAAGAAGA  1 
A/chicken/Egypt/1085/201 (    1) GGAGAGGGAAGAAGAAGAAAA  1 
A/chicken/Hebei/A8/2009  (    1) AGAGGGAGAAGAAGAAAAAGA  1 
A/chicken/CentralJava/UT (    1) AGAGAGAGAAGAAAAAAAAGA  1 
A_DISC/Cambodia/V0401301 (    1) AGAGTGGGAAGAAGAAAAAAG  1 
A/chicken/Lampung/BPPVRI (    1) AGAGAAAGCAGAAGGAAAAAG  1 
A/chicken/Vietnam/NCVD40 (    1) AGAGAAAGGAGAAGAAAAAGA  1 
A/duck/Vietnam/NCVD366/2 (    1) AGAGATGGAAGAAGAAAAAAG  1 
A/duck/Yunnan/47/2006    (    1) AGAAAGAGAAGAAGAAAAAAG  1 
A/chicken/Denpasar/BBVD1 (    1) AGAGAGAGAAGAAGAGAAAAG  1 
A/Hunan/1/2009           (    1) AGAGAAAGAAGAAGGAAAAGA  1 
A/chicken/Vietnam/NCVD09 (    1) ATAGAGGGAAGAAGAAGAAAA  1 
A/duck/Guangxi/951/2005  (    1) AGTGAAAGAAGAAGAAAAAGA  1 
A/environment/Bangladesh (    1) AGGGAGAGGAGAAGAAAAAGA  1 
A/environment/ChangSha/2 (    1) AGAGAGAGAAGAGGAAAAAGA  1 
A/chicken/India/241272/2 (    1) GGAGAGAGGAGAAGAAAGAAA  1 
A/quail/Thanatpin/2283/2 (    1) AGAGAAAAAAGAAGAAAAAGA  1 
A/chicken/Sikkim/151466/ (    1) GGTGAGAGAAGAAGAAAGAAG  1 
A/chicken/Bangladesh/830 (    1) GGAGAGAGAAGAAAAAAAAGA  1 
A/chicken/Shandong/A5/20 (    1) AGAGAGGGAGGAAGAAGAAAA  1 
A/domestic_goose/Hong_Ko (    1) ATAGAGAGGAGAAGAAGAAAA  1 
A/chicken/Egypt/10512AG/ (    1) GAAGAGGGAAGAAGAAAAAAG  1 
A/duck/Guangxi/13/2004   (    1) AGAGAAAGAAGAAAAAAAAGA  1 
A/Vietnam/UT30259/2004   (    1) AGAGAGAGAAGAAAAAAGAGA  1 
A/spurwinged_goose/Niger (    1) AGAGAAAAAAGAAGAAAGAAG  1 
A/chicken/Vietnam/NCVD18 (    1) AAAGAAAGAAGAAGAAAAAGA  1 
A/duck/Vietnam/NCVD1026/ (    1) ATAGAGAGAGGAAGAAGAAAA  1 
A/chicken/WestJava/SmiAc (    1) AGAGAGAGCAGACGTAAAAAA  1 
A/Vietnam/HN36250/2010   (    1) AGAGAAAAAAGAAGAAGAAAA  1 
A/chicken/Vietnam/NCVD40 (    1) AGAGAAAGGAGAAGGAAAAGA  1 
A/duck/Vietnam/NCVD422/2 (    1) AGGGAAAGGAGAAGAAAAAGA  1 
A/barn_swallow/Hong_Kong (    1) ATAGAAAGAAGAAGAAGGAAA  1 
A/ck/Indonesia/072/10    (    1) AAGGAGGGAAGAAGAAAAAAG  1 
A/chicken/Yangon/1023/20 (    1) AGAGAGAAAGGAAGAAGAAAA  1 
A/chicken/Vietnam/NCVD01 (    1) AGAGAGGGAGGAAGAAGGAGA  1 
A/Egypt/4822NAMRU3/2009  (    1) GGAAAGAGTAGAAGAAAAAAG  1 
A/chicken/Korea/ES/03    (    1) AGAGAGAAAAGAAAAAAGAGA  1 
A/duck/Viet_Nam/TG2401/2 (    1) AGAGAGAGAAGGAAAAAGAGA  1 
A/whitefaced_whistling_d (    1) AAAGAAAAAAGAAGAAAGAAG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 20 w= 21 n= 253 bayes= -2.7879 E= 4.5e-207 
    72   -749   -249    -50    -72    -70   -114    -39   -227     29    -84   -137     67    -22   -279    310   -719    136   -318   -223 
  -344   -673     49    210     76    140     95    123     55    161     75    116    181    151    -46    411    -81    242   -130    -31 
    90   -670   -203     16    -12   -213    -67     36   -169     94     -6    -67    132     46   -221    393   -243    218   -277   -173 
  -444   -670    187    339    169    151    216    216    189    242    164    241    247    252    316    445   -623    286    -13     84 
    98   -671   -204     15    -12   -331    -68     36   -169     94     -6    -68    131     45   -222    392   -334    217   -277   -173 
  -108   -673   -166     37     -7    119    -51     40   -141     96     -2    -46    134     53   -203    392   -335    216   -264   -160 
    70   -749   -249    -50    -72    -63   -114    -39   -227     29    -84   -137     67    -22   -279    310   -719    136   -318   -223 
  -223   -672     58    219     82    140    103    129     64    166     80    124    185    157    -38    413   -345    245   -123    -24 
    74      5   -200     21     -6   -163    -64     43   -164    100      0    -63    136     50   -216    398   -243    224   -273   -168 
    94   -754   -252    -54    -75   -213   -117    -43   -231     25    -89   -142     63    -26   -282    305   -724    131   -320   -226 
 -1220  -1064   -309   -185   -204    159   -192   -270   -327   -131   -355   -312   -101   -197   -390   -105  -1086   -214   -381   -314 
    99   -759   -254    -57    -78   -293   -119    -48   -233     22    -93   -146     60    -30   -285    300   -729    126   -322   -228 
   100   -150   -207     12    -15   -476    -70     33   -172     91    -10    -72    128     42   -224    388   -643    213   -279   -175 
  -294   -754     33    188     41    148     74     81     36    119     29     90    133    115    -69    337   -716    174   -150    -55 
    90   -671   -204     15    -12   -194    -68     35   -170     93     -7    -67    132     45   -222    393   -334    217   -278   -173 
   104   -775   -262    -69    -89   -485   -127    -62   -244     10   -109   -160     48    -43   -296    283   -746    109   -329   -237 
    82   -750   -250    -51    -72   -114   -115    -40   -228     28    -85   -138     67    -23   -280    309   -720    135   -318   -224 
    85   -751   -250    -51    -73   -136   -115    -41   -228     27    -86   -139     66    -23   -280    309   -721    134   -319   -224 
   106   -975   -324   -187   -188  -1037   -192   -227   -336   -107   -299   -307    -74   -175   -389     40   -969   -109   -380   -309 
    52   -750   -249    -50    -72    -10   -115    -40   -228     28    -85   -138     67    -22   -279    310   -719    135   -318   -223 
    -6   -756   -252    -55    -77     69   -118    -45   -232     23    -91   -143     62    -28   -284    303   -726    129   -321   -227 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 20 w= 21 nsites= 93 E= 4.5e-207 
 0.795699  0.000000  0.000000  0.000000  0.000000  0.204301  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.043011  0.000000  0.000000  0.000000  0.000000  0.881720  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.075269  0.000000  0.000000  0.000000 
 0.903226  0.000000  0.000000  0.000000  0.000000  0.075269  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.021505  0.000000  0.000000  0.000000 
 0.021505  0.000000  0.000000  0.000000  0.000000  0.967742  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.010753  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.956989  0.000000  0.000000  0.000000  0.000000  0.032258  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.010753  0.000000  0.000000  0.000000 
 0.225806  0.000000  0.000000  0.000000  0.000000  0.763441  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.010753  0.000000  0.000000  0.000000 
 0.784946  0.000000  0.000000  0.000000  0.000000  0.215054  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.107527  0.000000  0.000000  0.000000  0.000000  0.881720  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.010753  0.000000  0.000000  0.000000 
 0.806452  0.064516  0.000000  0.000000  0.000000  0.107527  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.021505  0.000000  0.000000  0.000000 
 0.924731  0.000000  0.000000  0.000000  0.000000  0.075269  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.956989  0.000000  0.000000  0.000000  0.000000  0.043011  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.967742  0.021505  0.000000  0.000000  0.000000  0.010753  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.064516  0.000000  0.000000  0.000000  0.000000  0.935484  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.903226  0.000000  0.000000  0.000000  0.000000  0.086022  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.010753  0.000000  0.000000  0.000000 
 0.989247  0.000000  0.000000  0.000000  0.000000  0.010753  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.849462  0.000000  0.000000  0.000000  0.000000  0.150538  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.870968  0.000000  0.000000  0.000000  0.000000  0.129032  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.688172  0.000000  0.000000  0.000000  0.000000  0.311828  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.462366  0.000000  0.000000  0.000000  0.000000  0.537634  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[AG]GAGA[GA][AG]GAAGAAGAAAAA[AG][GA]
--------------------------------------------------------------------------------




Time 56.02 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   15   sites =  25   llr = 475   E-value = 2.5e-074
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  ::9:3::24::17:a
pos.-specific     C  8:::::3:::9::1:
probability       D  :::::::::::::::
matrix            E  :::::::::::::::
                  F  :::::::::::::::
                  G  ::1::3786a:::::
                  H  :::::::::::::::
                  I  :::::::::::::::
                  K  :::::::::::::::
                  L  :::::::::::::::
                  M  :::::::::::::::
                  N  :::::::::::::::
                  P  :::::::::::::::
                  Q  :::::::::::::::
                  R  :::::::::::::::
                  S  :::::::::::::::
                  T  2a:a77::::1939:
                  V  :::::::::::::::
                  W  :::::::::::::::
                  Y  :::::::::::::::

         bits   12.4                
                11.1                
                 9.9                
                 8.7                
Relative         7.4                
Entropy          6.2                
(27.4 bits)      5.0                
                 3.7 *         *    
                 2.5 ** *      ** * 
                 1.2 ******** ******
                 0.0 ---------------

Multilevel           CTATTTGGGGCTATA
consensus                AGCAA   T  
sequence                            
                                    
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                 Site    
-------------             ----- ---------            ---------------
A/chicken/Bangladesh/FD(      1  4.15e-11          . CTATTTGGGGCTATA GCAGGT    
A/tern/South_Africa/1959      4  4.15e-11        GGT CTATTTGGGGCTATA GCA       
A/mallard/Netherlands/3/      4  4.15e-11        GGA CTATTTGGGGCTATA GCA       
A/duck/Primorie/2633/200      1  4.15e-11          . CTATTTGGGGCTATA GCAGGC    
A/wild_bird_feces/Cheons      7  4.15e-11     AGAGGA CTATTTGGGGCTATA           
A/chicken/Bangladesh/11r      1  8.33e-11          . CTATTTGGAGCTATA GCAGGT    
A/turkey/Egypt/091QNLQP/      1  8.33e-11          . CTATTTGGAGCTATA GCAGGG    
A/duck/Hong_Kong/312/197      1  8.33e-11          . CTATTTGGAGCTATA GCAGGC    
A/chicken/Bangladesh/11r      4  8.33e-11        GGA CTATTTGGAGCTATA GCA       
A/chicken/Turkey/Misinli      7  8.33e-11     AGAGGA CTATTTGGAGCTATA           
A/wild_bird_feces/Byeong      4  6.63e-10        GGA CTATTTGGGGCCATA GCA       
A/ostrich/South_Africa/A      4  7.90e-10        GGA TTATTTGGGGCTATA GCA       
A/whooper_swan/Hokkaido/      7  8.51e-10     AGAGGA CTGTTTGGAGCTATA           
A/chicken/Cambodia/TLC2/      4  1.22e-09        GGA TTATTTGGAGCTATA GCA       
A/chicken/Cambodia/013LC      7  1.22e-09     AGGGGA TTATTTGGAGCTATA           
A/avian/New_York/Sg00387      4  3.23e-09        GGC CTATTTGGAGCAATA GCA       
A/avian/New_York/Sg00372      1  3.23e-09          . CTATTTGGAGCAATA GCAGGA    
A/chicken/Egypt/1219s/20      5  4.76e-09       GGAG CTATAGCAGGCTTTA TA        
A/chicken/Egypt/128s/201      2  4.76e-09          G CTATAGCAGGCTTTA TAGAG     
A/chicken/Bangladesh/11r      1  7.12e-09          . TTGTTTGGAGCTATA GCAGGG    
A/duck/Primorie/2621/200      2  1.97e-08          G CTATAGCAGGCTTCA TAGAA     
A/turkey/England/N28/73|      2  2.10e-08          G CTATAGCGGGTTTTA TAGAA     
A/chicken/Egypt/125s/201      5  5.87e-08       GGAG CTATAGCAGGTTTTA TA        
A/chicken/Egypt/398252/2      2  5.87e-08          G CTATAGCAGGTTTTA TAGAG     
A/chicken/Italy/9097/199      2  1.05e-07          G CCATAGCAGGCTTCA TAGAG     
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
A/chicken/Bangladesh/FD(          4.2e-11  [3]_6
A/tern/South_Africa/1959          4.2e-11  3_[3]_3
A/mallard/Netherlands/3/          4.2e-11  3_[3]_3
A/duck/Primorie/2633/200          4.2e-11  [3]_6
A/wild_bird_feces/Cheons          4.2e-11  6_[3]
A/chicken/Bangladesh/11r          8.3e-11  [3]_6
A/turkey/Egypt/091QNLQP/          8.3e-11  [3]_6
A/duck/Hong_Kong/312/197          8.3e-11  [3]_6
A/chicken/Bangladesh/11r          8.3e-11  3_[3]_3
A/chicken/Turkey/Misinli          8.3e-11  6_[3]
A/wild_bird_feces/Byeong          6.6e-10  3_[3]_3
A/ostrich/South_Africa/A          7.9e-10  3_[3]_3
A/whooper_swan/Hokkaido/          8.5e-10  6_[3]
A/chicken/Cambodia/TLC2/          1.2e-09  3_[3]_3
A/chicken/Cambodia/013LC          1.2e-09  6_[3]
A/avian/New_York/Sg00387          3.2e-09  3_[3]_3
A/avian/New_York/Sg00372          3.2e-09  [3]_6
A/chicken/Egypt/1219s/20          4.8e-09  4_[3]_2
A/chicken/Egypt/128s/201          4.8e-09  1_[3]_5
A/chicken/Bangladesh/11r          7.1e-09  [3]_6
A/duck/Primorie/2621/200            2e-08  1_[3]_5
A/turkey/England/N28/73|          2.1e-08  1_[3]_5
A/chicken/Egypt/125s/201          5.9e-08  4_[3]_2
A/chicken/Egypt/398252/2          5.9e-08  1_[3]_5
A/chicken/Italy/9097/199          1.1e-07  1_[3]_5
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=15 seqs=25
A/chicken/Bangladesh/FD( (    1) CTATTTGGGGCTATA  1 
A/tern/South_Africa/1959 (    4) CTATTTGGGGCTATA  1 
A/mallard/Netherlands/3/ (    4) CTATTTGGGGCTATA  1 
A/duck/Primorie/2633/200 (    1) CTATTTGGGGCTATA  1 
A/wild_bird_feces/Cheons (    7) CTATTTGGGGCTATA  1 
A/chicken/Bangladesh/11r (    1) CTATTTGGAGCTATA  1 
A/turkey/Egypt/091QNLQP/ (    1) CTATTTGGAGCTATA  1 
A/duck/Hong_Kong/312/197 (    1) CTATTTGGAGCTATA  1 
A/chicken/Bangladesh/11r (    4) CTATTTGGAGCTATA  1 
A/chicken/Turkey/Misinli (    7) CTATTTGGAGCTATA  1 
A/wild_bird_feces/Byeong (    4) CTATTTGGGGCCATA  1 
A/ostrich/South_Africa/A (    4) TTATTTGGGGCTATA  1 
A/whooper_swan/Hokkaido/ (    7) CTGTTTGGAGCTATA  1 
A/chicken/Cambodia/TLC2/ (    4) TTATTTGGAGCTATA  1 
A/chicken/Cambodia/013LC (    7) TTATTTGGAGCTATA  1 
A/avian/New_York/Sg00387 (    4) CTATTTGGAGCAATA  1 
A/avian/New_York/Sg00372 (    1) CTATTTGGAGCAATA  1 
A/chicken/Egypt/1219s/20 (    5) CTATAGCAGGCTTTA  1 
A/chicken/Egypt/128s/201 (    2) CTATAGCAGGCTTTA  1 
A/chicken/Bangladesh/11r (    1) TTGTTTGGAGCTATA  1 
A/duck/Primorie/2621/200 (    2) CTATAGCAGGCTTCA  1 
A/turkey/England/N28/73| (    2) CTATAGCGGGTTTTA  1 
A/chicken/Egypt/125s/201 (    5) CTATAGCAGGTTTTA  1 
A/chicken/Egypt/398252/2 (    2) CTATAGCAGGTTTTA  1 
A/chicken/Italy/9097/199 (    2) CCATAGCAGGCTTCA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 20 w= 15 n= 1771 bayes= 7.27007 E= 2.5e-074 
  -645    376    -59    141    129   -726     76    206    -39    233    103     17    205    135    -98    412     25    289   -134    -19 
  -618    -75     62    244    220   -712    186    351    146    325    268    227    269    290     36    614    291    420    -37     67 
    89   -475     23    253    219   -208    148    280     77    338    228    123    294    244     -3    579   -466    451    -48     53 
  -910   -801   -108     32     30   -879     20     64    -91    115    -28    -45    112     53   -168    292    302    126   -174    -92 
   -78   -504     -6    202    174   -601    124    246     37    281    186    132    303    232    -31    573    250    397    -90     16 
  -650   -639    -37    120     81    -27     66    112    -41    174     50     50    201    131   -117    429    253    254   -150    -52 
  -712    215    -72     83     52    111     39     51    -76    136    -11    -16    167     82   -143    352   -673    189   -161    -72 
  -116   -537    135    300    189    118    194    232    141    278    184    208    304    257     47    538   -502    367    -28     71 
   -14   -524    -28    175    145     71     99    186     -6    247    142     93    286    200    -62    539   -492    363   -112    -10 
  -729   -729    104    252    116    157    152    135    103    189     78    150    202    178      0    355   -699    203    -65     23 
  -649    389     31    275    239   -749    174    337     71    349    240     92    235    218     11    399   -104    337    -71     60 
  -252    -76     84    282    251   -605    211    372    167    358    300    255    333    326     66    662    276    468    -14     90 
    55   -499    -21    194    166   -592    111    222     12    274    169    109    305    221    -44    564    115    394    -98      8 
  -618     25     44    227    204   -710    169    331    124    309    246    204    260    271     17    594    286    403    -52     53 
   104   -669    -98     78     66   -755     33     86    -85    164     19    -39    169     86   -147    374   -655    233   -159    -72 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 20 w= 15 nsites= 25 E= 2.5e-074 
 0.000000  0.840000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.160000  0.000000  0.000000  0.000000 
 0.000000  0.040000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.960000  0.000000  0.000000  0.000000 
 0.920000  0.000000  0.000000  0.000000  0.000000  0.080000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 0.280000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.720000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.280000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.720000  0.000000  0.000000  0.000000 
 0.000000  0.280000  0.000000  0.000000  0.000000  0.720000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.240000  0.000000  0.000000  0.000000  0.000000  0.760000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.440000  0.000000  0.000000  0.000000  0.000000  0.560000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.880000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.120000  0.000000  0.000000  0.000000 
 0.080000  0.040000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.880000  0.000000  0.000000  0.000000 
 0.720000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.280000  0.000000  0.000000  0.000000 
 0.000000  0.080000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.920000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
CTAT[TA][TG][GC][GA][GA]GCT[AT]TA
--------------------------------------------------------------------------------




Time 56.86 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   15   sites =  18   llr = 248   E-value = 1.6e-011
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  a:7:76:36::7:::
pos.-specific     C  ::::::::1::::::
probability       D  :::::::::::::::
matrix            E  :::::::::::::::
                  F  :::::::::::::::
                  G  ::3a:4a71aa::aa
                  H  :::::::::::::::
                  I  :::::::::::::::
                  K  :::::::::::::::
                  L  :::::::::::::::
                  M  :::::::::::::::
                  N  :::::::::::::::
                  P  :::::::::::::::
                  Q  :::::::::::::::
                  R  :::::::::::::::
                  S  :::::::::::::::
                  T  :a::3:::3::3a::
                  V  :::::::::::::::
                  W  :::::::::::::::
                  Y  :::::::::::::::

         bits   12.4                
                11.1                
                 9.9                
                 8.7                
Relative         7.4                
Entropy          6.2                
(19.9 bits)      5.0                
                 3.7                
                 2.5  *          *  
                 1.2 ** ** *  ******
                 0.0 ---------------

Multilevel           ATAGAAGGAGGATGG
consensus              G TG AT  T   
sequence                            
                                    
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                 Site    
-------------             ----- ---------            ---------------
A/VietNam/HN31413/2008        1  1.21e-07          . ATAGAGGGTGGATGG CAGGGA    
A/Muscovy_Duck/Vietnam/1      1  2.36e-07          . ATAGAGGGCGGATGG CAGGGA    
A/chicken/Vietnam/NCVD11      4  3.75e-07        TTT ATAGAAGGAGGATGG CAG       
A/environment/Bangladesh      1  3.75e-07          . ATAGAAGGAGGATGG CAGGGA    
A/chicken/Queretaro/7653      4  3.75e-07        TTC ATAGAAGGAGGATGG CAA       
A_GenBank/heron/Cambodia      7  3.75e-07     GGGTTT ATAGAAGGAGGATGG           
A/heron/Cambodia/TM068/2      1  3.75e-07          . ATAGAAGGAGGATGG CAGGGG    
A/Hong_Kong/7032/2012         4  4.39e-07        TTT ATAGAGGGAGGATGG CAG       
A/duck/Vietnam/NCVD1161/      4  4.39e-07        TTT ATAGAGGGAGGATGG CAA       
A/pigeon/Egypt/SHAH5803/      1  4.39e-07          . ATAGAGGGAGGATGG CAGGGA    
A/environment/Bangladesh      1  4.39e-07          . ATAGAGGGAGGATGG CAGGGG    
A/chicken/Egypt/39825/20      7  4.39e-07     GGTTTT ATAGAGGGAGGATGG           
A/chicken/TanseMyanmar/S      4  6.25e-07        GGA ATGGTAGATGGTTGG TAT       
A/Egypt/2786NAMRU3/2006       7  6.25e-07     CAGGGA ATGGTAGATGGTTGG           
A/chicken/BacLieuVietnam      4  6.25e-07        GGG ATGGTAGATGGTTGG TAT       
A/poultry/Egypt/398256/2      1  6.25e-07          . ATGGTAGATGGTTGG TATGGG    
A/chicken/Nepal/354/2010      4  7.69e-07        GGA ATGGTAGACGGTTGG TAT       
A/Indonesia/625/2006          4  1.47e-06        TTT ATAGAAGGGGGATGG CAG       
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
A/VietNam/HN31413/2008            1.2e-07  [4]_6
A/Muscovy_Duck/Vietnam/1          2.4e-07  [4]_6
A/chicken/Vietnam/NCVD11          3.7e-07  3_[4]_3
A/environment/Bangladesh          3.7e-07  [4]_6
A/chicken/Queretaro/7653          3.7e-07  3_[4]_3
A_GenBank/heron/Cambodia          3.7e-07  6_[4]
A/heron/Cambodia/TM068/2          3.7e-07  [4]_6
A/Hong_Kong/7032/2012             4.4e-07  3_[4]_3
A/duck/Vietnam/NCVD1161/          4.4e-07  3_[4]_3
A/pigeon/Egypt/SHAH5803/          4.4e-07  [4]_6
A/environment/Bangladesh          4.4e-07  [4]_6
A/chicken/Egypt/39825/20          4.4e-07  6_[4]
A/chicken/TanseMyanmar/S          6.2e-07  3_[4]_3
A/Egypt/2786NAMRU3/2006           6.2e-07  6_[4]
A/chicken/BacLieuVietnam          6.2e-07  3_[4]_3
A/poultry/Egypt/398256/2          6.2e-07  [4]_6
A/chicken/Nepal/354/2010          7.7e-07  3_[4]_3
A/Indonesia/625/2006              1.5e-06  3_[4]_3
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=15 seqs=18
A/VietNam/HN31413/2008   (    1) ATAGAGGGTGGATGG  1 
A/Muscovy_Duck/Vietnam/1 (    1) ATAGAGGGCGGATGG  1 
A/chicken/Vietnam/NCVD11 (    4) ATAGAAGGAGGATGG  1 
A/environment/Bangladesh (    1) ATAGAAGGAGGATGG  1 
A/chicken/Queretaro/7653 (    4) ATAGAAGGAGGATGG  1 
A_GenBank/heron/Cambodia (    7) ATAGAAGGAGGATGG  1 
A/heron/Cambodia/TM068/2 (    1) ATAGAAGGAGGATGG  1 
A/Hong_Kong/7032/2012    (    4) ATAGAGGGAGGATGG  1 
A/duck/Vietnam/NCVD1161/ (    4) ATAGAGGGAGGATGG  1 
A/pigeon/Egypt/SHAH5803/ (    1) ATAGAGGGAGGATGG  1 
A/environment/Bangladesh (    1) ATAGAGGGAGGATGG  1 
A/chicken/Egypt/39825/20 (    7) ATAGAGGGAGGATGG  1 
A/chicken/TanseMyanmar/S (    4) ATGGTAGATGGTTGG  1 
A/Egypt/2786NAMRU3/2006  (    7) ATGGTAGATGGTTGG  1 
A/chicken/BacLieuVietnam (    4) ATGGTAGATGGTTGG  1 
A/poultry/Egypt/398256/2 (    1) ATGGTAGATGGTTGG  1 
A/chicken/Nepal/354/2010 (    4) ATGGTAGACGGTTGG  1 
A/Indonesia/625/2006     (    4) ATAGAAGGGGGATGG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 20 w= 15 n= 1771 bayes= 5.89847 E= 1.6e-011 
   103   -568    -19    181    160   -667    110    204     14    270    138     48    237    174    -60    477   -563    356    -81     13 
  -802   -703    -25    128    119   -810    101    195     17    211    105     77    185    158    -75    435    301    255   -102    -11 
    54   -459     35    247    214    -33    160    263     66    322    216    154    340    263      3    602   -431    439    -48     55 
  -637   -650    192    341    193    154    233    222    192    266    167    242    277    262     86    446   -613    291     11    103 
    53   -448     35    253    222   -543    165    284     72    332    227    162    353    273     11    615    111    451    -45     62 
    31   -468     26    232    199     16    151    244     50    304    199    149    339    256     -8    595   -436    421    -61     44 
  -637   -650    192    341    193    154    233    222    192    266    167    242    277    262     86    446   -613    291     11    103 
  -101   -489    172    339    231    111    233    275    178    321    227    247    348    299     85    585   -454    414     10    110 
    18     75     47    272    242   -250    179    299     91    354    251    174    364    289     27    633    108    474    -27     78 
  -637   -650    192    341    193    154    233    222    192    266    167    242    277    262     86    446   -613    291     11    103 
  -637   -650    192    341    193    154    233    222    192    266    167    242    277    262     86    446   -613    291     11    103 
    53   -448     35    253    222   -543    165    284     72    332    227    162    353    273     11    615    111    451    -45     62 
  -802   -703    -25    128    119   -810    101    195     17    211    105     77    185    158    -75    435    301    255   -102    -11 
  -637   -650    192    341    193    154    233    222    192    266    167    242    277    262     86    446   -613    291     11    103 
  -637   -650    192    341    193    154    233    222    192    266    167    242    277    262     86    446   -613    291     11    103 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 20 w= 15 nsites= 18 E= 1.6e-011 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 0.722222  0.000000  0.000000  0.000000  0.000000  0.277778  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.722222  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.277778  0.000000  0.000000  0.000000 
 0.611111  0.000000  0.000000  0.000000  0.000000  0.388889  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.277778  0.000000  0.000000  0.000000  0.000000  0.722222  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.555556  0.111111  0.000000  0.000000  0.000000  0.055556  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.277778  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.722222  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.277778  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
AT[AG]G[AT][AG]G[GA][AT]GG[AT]TGG
--------------------------------------------------------------------------------




Time 57.67 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   14   sites =  12   llr = 196   E-value = 8.3e-010
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  :7a1a::81:61::
pos.-specific     C  a2::::713::::3
probability       D  ::::::::::::1:
matrix            E  ::::::::::::::
                  F  ::::::::::::::
                  G  :::2:a3:773:::
                  H  ::::::::::::::
                  I  ::::::::::::::
                  K  ::::::::::::::
                  L  ::::::::::::::
                  M  ::::::::::::::
                  N  ::::::::::::::
                  P  ::::::::::::::
                  Q  ::::::::::::::
                  R  ::::::::::::::
                  S  ::::::::::::::
                  T  :2:8::11:32997
                  V  ::::::::::::::
                  W  ::::::::::::::
                  Y  :::::::::1::::

         bits   12.4               
                11.1               
                 9.9               
                 8.7               
Relative         7.4               
Entropy          6.2               
(23.6 bits)      5.0               
                 3.7 *           * 
                 2.5 *     *    ***
                 1.2 ********** ***
                 0.0 --------------

Multilevel           CAATAGCAGGATTT
consensus                  G CTG  C
sequence                           
                                   
                                   
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                 Site   
-------------             ----- ---------            --------------
A/Chicken/TurkeyEdirne/0      2  1.90e-09          G CCATAGCAGGTTTT ATAGAG    
A/Canada_goose/Alaska//4      5  4.78e-09       GGAG CAATAGCAGGATTT ATA       
A/mallard/Washington/456      8  4.78e-09    TTTGGAG CAATAGCAGGATTT           
A/wild_bird/Wisconsin/43      2  5.66e-09          G CAATAGCAGGATTC ATAGAA    
A/avian/New_York/Sg00377      8  5.66e-09    TTTGGAG CAATAGCAGGATTC           
A/chicken/Egypt/398220/2      8  5.66e-09    TTTGGAG CTATAGCAGGTTTT           
A/chicken/Bangladesh/11r      8  1.10e-08    TTTGGAG CTATAGCAGGGTTT           
A/chicken/Puebla/1458665      5  1.20e-08       GGAG CAATAGCCGGATTC ATA       
A/duck/Bangladesh/5749/1      3  4.54e-08         CA CCATAGTAAYGADC AGGGG     
A/wild_bird_feces/Cheons      5  5.98e-07       GAAA CAAGAGGACTATTT GGG       
A/turkey/MN/40550/1987_H      5  9.56e-07       GAAA CAAGAGGACTGTTT GGA       
A/duck/Korea/GJ54/2004|G      5  2.69e-06       GAAA CAAAAGGTCTATTT GGG       
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
A/Chicken/TurkeyEdirne/0          1.9e-09  1_[5]_6
A/Canada_goose/Alaska//4          4.8e-09  4_[5]_3
A/mallard/Washington/456          4.8e-09  7_[5]
A/wild_bird/Wisconsin/43          5.7e-09  1_[5]_6
A/avian/New_York/Sg00377          5.7e-09  7_[5]
A/chicken/Egypt/398220/2          5.7e-09  7_[5]
A/chicken/Bangladesh/11r          1.1e-08  7_[5]
A/chicken/Puebla/1458665          1.2e-08  4_[5]_3
A/duck/Bangladesh/5749/1          4.5e-08  2_[5]_5
A/wild_bird_feces/Cheons            6e-07  4_[5]_3
A/turkey/MN/40550/1987_H          9.6e-07  4_[5]_3
A/duck/Korea/GJ54/2004|G          2.7e-06  4_[5]_3
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=14 seqs=12
A/Chicken/TurkeyEdirne/0 (    2) CCATAGCAGGTTTT  1 
A/Canada_goose/Alaska//4 (    5) CAATAGCAGGATTT  1 
A/mallard/Washington/456 (    8) CAATAGCAGGATTT  1 
A/wild_bird/Wisconsin/43 (    2) CAATAGCAGGATTC  1 
A/avian/New_York/Sg00377 (    8) CAATAGCAGGATTC  1 
A/chicken/Egypt/398220/2 (    8) CTATAGCAGGTTTT  1 
A/chicken/Bangladesh/11r (    8) CTATAGCAGGGTTT  1 
A/chicken/Puebla/1458665 (    5) CAATAGCCGGATTC  1 
A/duck/Bangladesh/5749/1 (    3) CCATAGTAAYGADC  1 
A/wild_bird_feces/Cheons (    5) CAAGAGGACTATTT  1 
A/turkey/MN/40550/1987_H (    5) CAAGAGGACTGTTT  1 
A/duck/Korea/GJ54/2004|G (    5) CAAAAGGTCTATTT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 20 w= 14 n= 2024 bayes= 8.98014 E= 8.3e-010 
  -651    396     86    340    298   -767    231    401    130    410    306    140    263    270     70    389   -504    373    -26    110 
    43    106    151    393    360   -455    278    435    220    486    375    250    410    376    132    711     14    598     85    189 
    98   -441     91    317    287   -554    215    351    148    408    285    160    320    290     58    604   -449    507     27    127 
  -228   -392    163    357    309   -117    274    404    213    417    341    307    417    383    120    714    249    528     42    152 
    98   -441     91    317    287   -554    215    351    148    408    285    160    320    290     58    604   -449    507     27    127 
  -557   -578    269    419    263    151    306    299    269    336    245    321    344    337    161    525   -538    368     81    175 
  -393    330    123    315    276    -52    231    336    137    384    277    241    407    332     68    665    -55    496      6    122 
    67    -43    230    487    448   -413    349    526    317    581    468    294    398    436    210    762   -126    692    169    270 
  -244    156    218    390    290    101    284    341    228    385    292    300    411    358    137    657   -381    485     61    164 
  -469   -485    325    472    396    112    371    373    318    414    311    390    397    404    201    615     21    458    143    701 
    23   -372    130    350    307    -57    248    367    170    422    317    244    415    353     94    689     31    539     36    144 
  -264   -405    206    397    360   -558    326    499    295    469    418    378    412    440    183    768    274    571     95    201 
  -553   -454    632    449    357   -627    355    498    321    461    418    418    387    454    193    762    276    552     96    211 
  -473    221    124    312    300   -568    248    427    192    414    323    271    368    347     93    670    238    511     31    151 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 20 w= 14 nsites= 12 E= 8.3e-010 
 0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.666667  0.166667  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.166667  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.083333  0.000000  0.000000  0.000000  0.000000  0.166667  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.750000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.666667  0.000000  0.000000  0.000000  0.250000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.083333  0.000000  0.000000  0.000000 
 0.833333  0.083333  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.083333  0.000000  0.000000  0.000000 
 0.083333  0.250000  0.000000  0.000000  0.000000  0.666667  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.666667  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.250000  0.000000  0.000000  0.083333 
 0.583333  0.000000  0.000000  0.000000  0.000000  0.250000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.166667  0.000000  0.000000  0.000000 
 0.083333  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.916667  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.083333  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.916667  0.000000  0.000000  0.000000 
 0.000000  0.333333  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.666667  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
CAATAG[CG]A[GC][GT][AG]TT[TC]
--------------------------------------------------------------------------------




Time 58.49 secs.

********************************************************************************


********************************************************************************
MOTIF  6	width =   21   sites =   4   llr = 106   E-value = 2.1e-004
********************************************************************************
--------------------------------------------------------------------------------
	Motif 6 Description
--------------------------------------------------------------------------------
Simplified        A  ::a::::::a:a:a:::8::a
pos.-specific     C  :a:::3:::::::::::3:::
probability       D  :::::::::::::::::::::
matrix            E  :::::::::::::::::::::
                  F  :::::::::::::::::::::
                  G  a::aa3::::::a:aaa:aa:
                  H  :::::::::::::::::::::
                  I  :::::::::::::::::::::
                  K  :::::::::::::::::::::
                  L  :::::::::::::::::::::
                  M  :::::::::::::::::::::
                  N  :::::::::::::::::::::
                  P  :::::::::::::::::::::
                  Q  :::::::::::::::::::::
                  R  :::::::::::::::::::::
                  S  :::::::::::::::::::::
                  T  :::::5aaa:a::::::::::
                  V  :::::::::::::::::::::
                  W  :::::::::::::::::::::
                  Y  :::::::::::::::::::::

         bits   12.4                      
                11.1                      
                 9.9                      
                 8.7                      
Relative         7.4                      
Entropy          6.2                      
(38.2 bits)      5.0                      
                 3.7  *                   
                 2.5  *    *** *          
                 1.2 *********************
                 0.0 ---------------------

Multilevel           GCAGGTTTTATAGAGGGAGGA
consensus                 C           C   
sequence                  G               
                                          
                                          
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 6 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                    Site       
-------------             ----- ---------            ---------------------
A/chicken/Indonesia/SmiW      1  5.44e-12          . GCAGGTTTTATAGAGGGAGGA           
A/chicken/Egypt/10117/20      1  6.47e-12          . GCAGGTTTTATAGAGGGCGGA           
A/turkey/Italy/1980|GQ24      1  7.65e-12          . GCAGGCTTTATAGAGGGAGGA           
A/chicken/Egypt/398214/2      1  2.63e-11          . GCAGGGTTTATAGAGGGAGGA           
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 6 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
A/chicken/Indonesia/SmiW          5.4e-12  [6]
A/chicken/Egypt/10117/20          6.5e-12  [6]
A/turkey/Italy/1980|GQ24          7.6e-12  [6]
A/chicken/Egypt/398214/2          2.6e-11  [6]
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 6 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 6 width=21 seqs=4
A/chicken/Indonesia/SmiW (    1) GCAGGTTTTATAGAGGGAGGA  1 
A/chicken/Egypt/10117/20 (    1) GCAGGTTTTATAGAGGGCGGA  1 
A/turkey/Italy/1980|GQ24 (    1) GCAGGCTTTATAGAGGGAGGA  1 
A/chicken/Egypt/398214/2 (    1) GCAGGGTTTATAGAGGGAGGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 6 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 20 w= 21 n= 253 bayes= 5.96 E= 2.1e-004 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
  -639    396     94    349    308   -756    240    412    140    420    315    150    272    279     79    401   -494    386    -17    121 
    73   -256    279    533    480   -384    392    565    359    613    494    341    456    479    249    787   -278    716    202    312 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
  -292    122    347    562    501    -98    460    615    424    631    526    464    546    559    300    849    176    692    212    358 
  -458   -371    302    494    448   -550    414    590    392    561    497    458    466    520    270    831    272    643    180    300 
  -458   -371    302    494    448   -550    414    590    392    561    497    458    466    520    270    831    272    643    180    300 
  -458   -371    302    494    448   -550    414    590    392    561    497    458    466    520    270    831    272    643    180    300 
    73   -256    279    533    480   -384    392    565    359    613    494    341    456    479    249    787   -278    716    202    312 
  -458   -371    302    494    448   -550    414    590    392    561    497    458    466    520    270    831    272    643    180    300 
    73   -256    279    533    480   -384    392    565    359    613    494    341    456    479    249    787   -278    716    202    312 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
    73   -256    279    533    480   -384    392    565    359    613    494    341    456    479    249    787   -278    716    202    312 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
    55     34    281    536    499   -365    403    587    369    634    518    351    466    491    261    809   -257    740    218    326 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
    73   -256    279    533    480   -384    392    565    359    613    494    341    456    479    249    787   -278    716    202    312 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 6 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 20 w= 21 nsites= 4 E= 2.1e-004 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.250000  0.000000  0.000000  0.000000  0.250000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.500000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.750000  0.250000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 6 regular expression
--------------------------------------------------------------------------------
GCAGG[TCG]TTTATAGAGGG[AC]GGA
--------------------------------------------------------------------------------




Time 59.26 secs.

********************************************************************************


********************************************************************************
MOTIF  7	width =   17   sites =   4   llr = 97   E-value = 6.2e-002
********************************************************************************
--------------------------------------------------------------------------------
	Motif 7 Description
--------------------------------------------------------------------------------
Simplified        A  :a::8::5:::::a:::
pos.-specific     C  :::::8:::::::::a:
probability       D  :::::::::::::::::
matrix            E  :::::::::::::::::
                  F  :::::::::::::::::
                  G  a:aa:::5:::aa:a::
                  H  :::::::::::::::::
                  I  :::::::::::::::::
                  K  :::::::::::::::::
                  L  :::::::::::::::::
                  M  :::::::::::::::::
                  N  :::::::::::::::::
                  P  :::::::::::::::::
                  Q  :::::::::::::::::
                  R  :::::::::::::::::
                  S  :::::::::::::::::
                  T  ::::33a:aaa:::::a
                  V  :::::::::::::::::
                  W  :::::::::::::::::
                  Y  :::::::::::::::::

         bits   12.4                  
                11.1                  
                 9.9                  
                 8.7                  
Relative         7.4                  
Entropy          6.2                  
(34.9 bits)      5.0                  
                 3.7                * 
                 2.5      ** ***    **
                 1.2 ******* *********
                 0.0 -----------------

Multilevel           GAGGACTGTTTGGAGCT
consensus                TT A         
sequence                              
                                      
                                      
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 7 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                  Site     
-------------             ----- ---------            -----------------
A/common_magpie/HongKong      5  1.62e-11       AAAA GAGGACTGTTTGGAGCT           
A/Chicken/TurkeyMus/09rs      5  3.22e-11       AAGA GAGGACTATTTGGAGCT           
A/ck/Indonesia/091/10         5  4.14e-11       AAGA GAGGTCTATTTGGAGCT           
A/chicken/Bangladesh/11r      5  6.12e-10       AAAA GAGGATTGTTTGGAGCT           
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 7 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
A/common_magpie/HongKong          1.6e-11  4_[7]
A/Chicken/TurkeyMus/09rs          3.2e-11  4_[7]
A/ck/Indonesia/091/10             4.1e-11  4_[7]
A/chicken/Bangladesh/11r          6.1e-10  4_[7]
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 7 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 7 width=17 seqs=4
A/common_magpie/HongKong (    5) GAGGACTGTTTGGAGCT  1 
A/Chicken/TurkeyMus/09rs (    5) GAGGACTATTTGGAGCT  1 
A/ck/Indonesia/091/10    (    5) GAGGTCTATTTGGAGCT  1 
A/chicken/Bangladesh/11r (    5) GAGGATTGTTTGGAGCT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 7 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 20 w= 17 n= 1265 bayes= 8.30035 E= 6.2e-002 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
    73   -256    279    533    480   -384    392    565    359    613    494    341    456    479    249    787   -278    716    202    312 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
    48   -241    309    566    497   -365    422    588    396    632    516    380    496    519    279    809    -13    731    215    332 
  -593    393    110    361    324   -706    253    435    162    441    333    175    296    301     93    459   -298    429      0    142 
  -458   -371    302    494    448   -550    414    590    392    561    497    458    466    520    270    831    272    643    180    300 
   -44   -306    340    542    425     57    409    492    371    539    433    413    506    491    259    761   -280    630    175    291 
  -458   -371    302    494    448   -550    414    590    392    561    497    458    466    520    270    831    272    643    180    300 
  -458   -371    302    494    448   -550    414    590    392    561    497    458    466    520    270    831    272    643    180    300 
  -458   -371    302    494    448   -550    414    590    392    561    497    458    466    520    270    831    272    643    180    300 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
    73   -256    279    533    480   -384    392    565    359    613    494    341    456    479    249    787   -278    716    202    312 
  -462   -489    361    513    350    143    394    392    362    423    337    415    428    429    251    619   -444    462    164    263 
  -639    396     94    349    308   -756    240    412    140    420    315    150    272    279     79    401   -494    386    -17    121 
  -458   -371    302    494    448   -550    414    590    392    561    497    458    466    520    270    831    272    643    180    300 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 7 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 20 w= 17 nsites= 4 E= 6.2e-002 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.750000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.250000  0.000000  0.000000  0.000000 
 0.000000  0.750000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.250000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 0.500000  0.000000  0.000000  0.000000  0.000000  0.500000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 7 regular expression
--------------------------------------------------------------------------------
GAGG[AT][CT]T[GA]TTTGGAGCT
--------------------------------------------------------------------------------




Time 59.96 secs.

********************************************************************************


********************************************************************************
MOTIF  8	width =   11   sites =   5   llr = 88   E-value = 1.2e+000
********************************************************************************
--------------------------------------------------------------------------------
	Motif 8 Description
--------------------------------------------------------------------------------
Simplified        A  ::::2:a::::
pos.-specific     C  :8:::::a:a:
probability       D  :::::::::::
matrix            E  :::::::::::
                  F  :::::::::::
                  G  a:aa8:::a::
                  H  :::::::::::
                  I  :::::::::::
                  K  :::::::::::
                  L  :::::::::::
                  M  :::::::::::
                  N  :::::::::::
                  P  :::::::::::
                  Q  :::::::::::
                  R  :::::::::::
                  S  :::::::::::
                  T  :2:::a::::a
                  V  :::::::::::
                  W  :::::::::::
                  Y  :::::::::::

         bits   12.4            
                11.1            
                 9.9            
                 8.7            
Relative         7.4            
Entropy          6.2            
(25.4 bits)      5.0            
                 3.7  *     * * 
                 2.5  *   * * **
                 1.2 ***********
                 0.0 -----------

Multilevel           GCGGGTACGCT
consensus             T  A      
sequence                        
                                
                                
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 8 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value               Site  
-------------             ----- ---------            -----------
A/chicken/Vietnam/5/2010      5  8.62e-09       GGAA GCGGGTACGCT GCAGAC    
A/chicken/Vietnam/4/2010      2  8.62e-09          A GCGGGTACGCT GCAGACAAA 
A/duck/Vietnam/1/2010        11  8.62e-09 GAGCAGGGAA GCGGGTACGCT           
A/duck/Vietnam/3/2010         8  3.40e-08    CAGGGAA GCGGATACGCT GCA       
A/chicken/Egypt/11VIR445     11  1.63e-07 GAGCAGGGGA GTGGGTACGCT           
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 8 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
A/chicken/Vietnam/5/2010          8.6e-09  4_[8]_6
A/chicken/Vietnam/4/2010          8.6e-09  1_[8]_9
A/duck/Vietnam/1/2010             8.6e-09  10_[8]
A/duck/Vietnam/3/2010             3.4e-08  7_[8]_3
A/chicken/Egypt/11VIR445          1.6e-07  10_[8]
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 8 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 8 width=11 seqs=5
A/chicken/Vietnam/5/2010 (    5) GCGGGTACGCT  1 
A/chicken/Vietnam/4/2010 (    2) GCGGGTACGCT  1 
A/duck/Vietnam/1/2010    (   11) GCGGGTACGCT  1 
A/duck/Vietnam/3/2010    (    8) GCGGATACGCT  1 
A/chicken/Egypt/11VIR445 (   11) GTGGGTACGCT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 8 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 20 w= 11 n= 2783 bayes= 9.36986 E= 1.2e+000 
  -474   -500    350    502    339    144    383    380    351    412    326    404    418    417    241    608   -456    451    154    252 
  -614    394     99    353    313   -730    244    420    147    427    321    160    282    287     84    430   -344    405    -12    127 
  -474   -500    350    502    339    144    383    380    351    412    326    404    418    417    241    608   -456    451    154    252 
  -474   -500    350    502    339    144    383    380    351    412    326    404    418    417    241    608   -456    451    154    252 
  -292   -458    365    520    356    134    397    404    368    433    351    422    440    438    257    646   -413    486    166    265 
  -486   -396    271    458    420   -574    386    560    360    530    468    430    440    490    240    803    278    613    156    272 
    78   -274    255    506    459   -402    370    541    333    590    472    318    437    455    226    768   -297    695    183    290 
  -641    396     93    347    307   -758    238    410    138    418    314    148    270    277     77    399   -496    383    -19    119 
  -474   -500    350    502    339    144    383    380    351    412    326    404    418    417    241    608   -456    451    154    252 
  -641    396     93    347    307   -758    238    410    138    418    314    148    270    277     77    399   -496    383    -19    119 
  -486   -396    271    458    420   -574    386    560    360    530    468    430    440    490    240    803    278    613    156    272 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 8 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 20 w= 11 nsites= 5 E= 1.2e+000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.800000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.200000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.200000  0.000000  0.000000  0.000000  0.000000  0.800000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 8 regular expression
--------------------------------------------------------------------------------
G[CT]GG[GA]TACGCT
--------------------------------------------------------------------------------




Time 60.70 secs.

********************************************************************************


********************************************************************************
MOTIF  9	width =   21   sites =  11   llr = 162   E-value = 8.0e-003
********************************************************************************
--------------------------------------------------------------------------------
	Motif 9 Description
--------------------------------------------------------------------------------
Simplified        A  :91a47a:aa:9aa9a92a:a
pos.-specific     C  :::::1:::::::::::::::
probability       D  :::::::::::::::::::::
matrix            E  :::::::::::::::::::::
                  F  :::::::::::::::::::::
                  G  a19:62:a::a1::1:18:a:
                  H  :::::::::::::::::::::
                  I  :::::::::::::::::::::
                  K  :::::::::::::::::::::
                  L  :::::::::::::::::::::
                  M  :::::::::::::::::::::
                  N  :::::::::::::::::::::
                  P  :::::::::::::::::::::
                  Q  :::::::::::::::::::::
                  R  :::::::::::::::::::::
                  S  :::::::::::::::::::::
                  T  :::::::::::::::::::::
                  V  :::::::::::::::::::::
                  W  :::::::::::::::::::::
                  Y  :::::::::::::::::::::

         bits   12.4                      
                11.1                      
                 9.9                      
                 8.7                      
Relative         7.4                      
Entropy          6.2                      
(21.3 bits)      5.0                      
                 3.7                      
                 2.5                      
                 1.2 ****  ***************
                 0.0 ---------------------

Multilevel           GAGAGAAGAAGAAAAAAGAGA
consensus                A                
sequence                                  
                                          
                                          
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 9 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                    Site       
-------------             ----- ---------            ---------------------
A/Egypt/9174NAMRU3/2009       1  3.52e-08          . GAGAGAAGAAGAAAAAAGAGA           
A/chicken/WestJava/SmiSu      1  4.74e-08          . GAGAGCAGAAGAAAAAAGAGA           
A/Egypt/N07460/2012           1  9.07e-08          . GAGAAAAGAAGAAAAAAGAGA           
A/chicken/Egypt/1123AL/2      1  1.20e-07          . GAGAGGAGAAGAAAAAAGAGA           
A/duck/Egypt/1130AG/2011      1  2.11e-07          . GAGAGAAGAAGGAAAAAGAGA           
A/chicken/Egypt/10259SF/      1  2.11e-07          . GAGAGAAGAAGAAAAAGGAGA           
A/chicken/Egypt/1117AF/2      1  3.30e-07          . GAGAGAAGAAGAAAAAAAAGA           
A/Egypt/N6774/2011            1  5.02e-07          . GGGAAAAGAAGAAAAAAGAGA           
A/chicken/Egypt/1090/201      1  6.98e-07          . GAGAGGAGAAGAAAGAAGAGA           
A/chicken/Egypt/111945V/      1  8.06e-07          . GAGAAAAGAAGAAAAAAAAGA           
A/quail/Egypt/1171SG/201      1  1.34e-06          . GAAAAAAGAAGAAAAAAGAGA           
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 9 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
A/Egypt/9174NAMRU3/2009           3.5e-08  [9]
A/chicken/WestJava/SmiSu          4.7e-08  [9]
A/Egypt/N07460/2012               9.1e-08  [9]
A/chicken/Egypt/1123AL/2          1.2e-07  [9]
A/duck/Egypt/1130AG/2011          2.1e-07  [9]
A/chicken/Egypt/10259SF/          2.1e-07  [9]
A/chicken/Egypt/1117AF/2          3.3e-07  [9]
A/Egypt/N6774/2011                  5e-07  [9]
A/chicken/Egypt/1090/201            7e-07  [9]
A/chicken/Egypt/111945V/          8.1e-07  [9]
A/quail/Egypt/1171SG/201          1.3e-06  [9]
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 9 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 9 width=21 seqs=11
A/Egypt/9174NAMRU3/2009  (    1) GAGAGAAGAAGAAAAAAGAGA  1 
A/chicken/WestJava/SmiSu (    1) GAGAGCAGAAGAAAAAAGAGA  1 
A/Egypt/N07460/2012      (    1) GAGAAAAGAAGAAAAAAGAGA  1 
A/chicken/Egypt/1123AL/2 (    1) GAGAGGAGAAGAAAAAAGAGA  1 
A/duck/Egypt/1130AG/2011 (    1) GAGAGAAGAAGGAAAAAGAGA  1 
A/chicken/Egypt/10259SF/ (    1) GAGAGAAGAAGAAAAAGGAGA  1 
A/chicken/Egypt/1117AF/2 (    1) GAGAGAAGAAGAAAAAAAAGA  1 
A/Egypt/N6774/2011       (    1) GGGAAAAGAAGAAAAAAGAGA  1 
A/chicken/Egypt/1090/201 (    1) GAGAGGAGAAGAAAGAAGAGA  1 
A/chicken/Egypt/111945V/ (    1) GAGAAAAGAAGAAAAAAAAGA  1 
A/quail/Egypt/1171SG/201 (    1) GAAAAAAGAAGAAAAAAGAGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 9 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 20 w= 21 n= 253 bayes= -2.07973 E= 8.0e-003 
  -545   -567    281    432    275    150    317    311    282    347    257    333    355    349    173    537   -526    381     92    187 
    76   -302    209    459    418   -229    327    493    288    549    436    281    401    416    185    742   -324    660    142    244 
  -341   -504    342    495    327    140    372    373    344    401    322    397    407    409    233    607   -458    447    143    240 
    96   -416    114    344    312   -532    236    379    174    435    313    182    337    313     82    628   -427    535     49    150 
   -65   -418    205    379    284     93    275    331    213    380    282    289    408    352    124    653   -382    481     51    155 
    56    -16    216    469    430   -157    336    506    298    561    449    288    409    426    195    754   -314    673    153    254 
    96   -416    114    344    312   -532    236    379    174    435    313    182    337    313     82    628   -427    535     49    150 
  -545   -567    281    432    275    150    317    311    282    347    257    333    355    349    173    537   -526    381     92    187 
    96   -416    114    344    312   -532    236    379    174    435    313    182    337    313     82    628   -427    535     49    150 
    96   -416    114    344    312   -532    236    379    174    435    313    182    337    313     82    628   -427    535     49    150 
  -545   -567    281    432    275    150    317    311    282    347    257    333    355    349    173    537   -526    381     92    187 
    76   -302    209    459    418   -229    327    493    288    549    436    281    401    416    185    742   -324    660    142    244 
    96   -416    114    344    312   -532    236    379    174    435    313    182    337    313     82    628   -427    535     49    150 
    96   -416    114    344    312   -532    236    379    174    435    313    182    337    313     82    628   -427    535     49    150 
    76   -302    209    459    418   -229    327    493    288    549    436    281    401    416    185    742   -324    660    142    244 
    96   -416    114    344    312   -532    236    379    174    435    313    182    337    313     82    628   -427    535     49    150 
    76   -302    209    459    418   -229    327    493    288    549    436    281    401    416    185    742   -324    660    142    244 
  -247   -487    327    482    321    134    361    367    330    397    316    385    407    401    221    615   -444    453    131    230 
    96   -416    114    344    312   -532    236    379    174    435    313    182    337    313     82    628   -427    535     49    150 
  -545   -567    281    432    275    150    317    311    282    347    257    333    355    349    173    537   -526    381     92    187 
    96   -416    114    344    312   -532    236    379    174    435    313    182    337    313     82    628   -427    535     49    150 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 9 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 20 w= 21 nsites= 11 E= 8.0e-003 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.909091  0.000000  0.000000  0.000000  0.000000  0.090909  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.090909  0.000000  0.000000  0.000000  0.000000  0.909091  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.363636  0.000000  0.000000  0.000000  0.000000  0.636364  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.727273  0.090909  0.000000  0.000000  0.000000  0.181818  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.909091  0.000000  0.000000  0.000000  0.000000  0.090909  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.909091  0.000000  0.000000  0.000000  0.000000  0.090909  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.909091  0.000000  0.000000  0.000000  0.000000  0.090909  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.181818  0.000000  0.000000  0.000000  0.000000  0.818182  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 9 regular expression
--------------------------------------------------------------------------------
GAGA[GA]AAGAAGAAAAAAGAGA
--------------------------------------------------------------------------------




Time 61.66 secs.

********************************************************************************


********************************************************************************
MOTIF 10	width =   15   sites =   3   llr = 65   E-value = 5.1e+001
********************************************************************************
--------------------------------------------------------------------------------
	Motif 10 Description
--------------------------------------------------------------------------------
Simplified        A  :::::::a:::7:a:
pos.-specific     C  ::::::::::::::a
probability       D  :::::::::::::::
matrix            E  :::::::::::::::
                  F  :::::::::::::::
                  G  aa::aa:::aa3:::
                  H  :::::::::::::::
                  I  :::::::::::::::
                  K  :::::::::::::::
                  L  :::::::::::::::
                  M  :::::::::::::::
                  N  :::::::::::::::
                  P  :::::::::::::::
                  Q  :::::::::::::::
                  R  :::::::::::::::
                  S  :::::::::::::::
                  T  ::aa::a:a:::a::
                  V  :::::::::::::::
                  W  :::::::::::::::
                  Y  :::::::::::::::

         bits   12.4                
                11.1                
                 9.9                
                 8.7                
Relative         7.4                
Entropy          6.2                
(31.2 bits)      5.0                
                 3.7               *
                 2.5   **  * *   * *
                 1.2 *********** ***
                 0.0 ---------------

Multilevel           GGTTGGTATGGATAC
consensus                       G   
sequence                            
                                    
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 10 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                 Site    
-------------             ----- ---------            ---------------
A/chicken/Anhui/T5/2006       1  6.50e-10          . GGTTGGTATGGATAC CATCAT    
A/chicken/Guiyang/821/20      7  6.50e-10     GTAGAT GGTTGGTATGGATAC           
A/chicken/Bangladesh/11V      7  1.21e-09     GTAGAT GGTTGGTATGGGTAC           
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 10 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
A/chicken/Anhui/T5/2006           6.5e-10  [10]_6
A/chicken/Guiyang/821/20          6.5e-10  6_[10]
A/chicken/Bangladesh/11V          1.2e-09  6_[10]
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 10 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 10 width=15 seqs=3
A/chicken/Anhui/T5/2006  (    1) GGTTGGTATGGATAC  1 
A/chicken/Guiyang/821/20 (    7) GGTTGGTATGGATAC  1 
A/chicken/Bangladesh/11V (    7) GGTTGGTATGGGTAC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 10 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 20 w= 15 n= 1771 bayes= 8.86125 E= 5.1e+001 
  -450   -477    373    526    362    141    405    405    375    437    349    427    440    442    263    632   -430    476    174    275 
  -450   -477    373    526    362    141    405    405    375    437    349    427    440    442    263    632   -430    476    174    275 
  -429   -346    336    539    479   -521    446    622    430    598    526    486    497    553    303    861    262    674    206    334 
  -429   -346    336    539    479   -521    446    622    430    598    526    486    497    553    303    861    262    674    206    334 
  -450   -477    373    526    362    141    405    405    375    437    349    427    440    442    263    632   -430    476    174    275 
  -450   -477    373    526    362    141    405    405    375    437    349    427    440    442    263    632   -430    476    174    275 
  -429   -346    336    539    479   -521    446    622    430    598    526    486    497    553    303    861    262    674    206    334 
    67   -239    308    567    502   -366    417    591    390    637    517    367    485    508    275    804   -258    737    221    337 
  -429   -346    336    539    479   -521    446    622    430    598    526    486    497    553    303    861    262    674    206    334 
  -450   -477    373    526    362    141    405    405    375    437    349    427    440    442    263    632   -430    476    174    275 
  -450   -477    373    526    362    141    405    405    375    437    349    427    440    442    263    632   -430    476    174    275 
    31   -240    343    583    496    -86    438    574    411    626    512    409    518    531    291    812   -243    725    221    340 
  -429   -346    336    539    479   -521    446    622    430    598    526    486    497    553    303    861    262    674    206    334 
    67   -239    308    567    502   -366    417    591    390    637    517    367    485    508    275    804   -258    737    221    337 
  -636    396     96    351    311   -752    242    415    143    423    318    152    274    281     81    405   -492    391    -15    125 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 10 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 20 w= 15 nsites= 3 E= 5.1e+001 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.666667  0.000000  0.000000  0.000000  0.000000  0.333333  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 10 regular expression
--------------------------------------------------------------------------------
GGTTGGTATGG[AG]TAC
--------------------------------------------------------------------------------




Time 62.43 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
A/chicken/Bangladesh/830         1.22e-03  [2(6.62e-06)]
A/chicken/Egypt/39825/20         4.13e-03  6_[4(4.39e-07)]
A/ck/Indonesia/072/10            3.16e-02  [2(2.31e-05)]
A/duck/Bangladesh/5749/1         2.68e-07  2_[5(4.54e-08)]_5
A/mallard/Crimea/245/200         3.86e-09  [1(6.48e-11)]
A/environment/Bangladesh         1.25e-03  [4(4.39e-07)]_6
A/chicken/Egypt/111945V/         1.66e-03  [9(8.06e-07)]
A/avian/New_York/Sg00372         7.47e-04  [3(3.23e-09)]_6
A/chicken/Egypt/1117AF/2         1.30e-03  [9(3.30e-07)]
A/wild_bird_feces/Cheons         1.32e-02  4_[5(5.98e-07)]_3
A/chicken/India/241272/2         8.88e-03  [2(5.95e-06)]
A/duck/Jiangxi/80/2005           2.00e-03  [2(2.08e-07)]
A/chicken/Inhu/BPPVRII/2         5.07e-03  [2(1.32e-06)]
A/duck/Guangxi/668/2004          3.93e-03  [2(1.67e-06)]
A/whooper_swan/Hokkaido/         5.48e-13  1_[7(1.62e-11)]_3
A/duck/Vietnam/1/2010            8.68e-04  10_[8(8.62e-09)]
A/avian/New_York/Sg00387         1.90e-04  3_[3(3.23e-09)]_3
A/chicken/Cambodia/LC/20         3.04e-01  21
A/mallard/Maryland/786/2         2.27e-09  4_[5(5.66e-09)]_3
A/chicken/Egypt/128s/201         4.88e-08  1_[3(4.76e-09)]_5
A/guinea_fowl/Yangon/834         2.87e-02  21
A/chicken/WestJava/SmiAc         1.07e-02  [2(1.27e-05)]
A/Indonesia/625/2006             1.65e-02  3_[4(1.47e-06)]_3
A/Egypt/N07460/2012              5.29e-04  [9(9.07e-08)]
A/duck/Victoria/26/1981|         1.14e-09  [1(1.29e-11)]
A/duck/Viet_Nam/TG2401/2         9.09e-03  [2(6.33e-05)]
A/chicken/Egypt/398252/2         1.21e-08  1_[5(5.66e-09)]_6
A/environment/Maryland/1         2.37e-08  [1(3.01e-11)]
A/duck/New_Zealand/41/19         3.43e-08  [1(6.33e-10)]
A/heron/Cambodia/TM068/2         3.39e-03  [4(3.75e-07)]_6
A/chicken/Egypt/10117/20         6.56e-08  [6(6.47e-12)]
A/VietNam/HN31413/2008           3.48e-04  [4(1.21e-07)]_6
A/chicken/Egypt/398214/2         4.80e-07  [6(2.63e-11)]
A/chicken/Egypt/39823/20         6.21e-02  21
A/chicken/Belgium/150VB/         1.66e-08  [1(7.84e-10)]
A/goose/Fujian/bb/2003           3.18e-03  [2(3.89e-07)]
A/Vietnam/UT30259/2004           2.87e-03  [2(9.60e-06)]
A/duck/Yunnan/47/2006            1.19e-02  [2(3.27e-06)]
A/chicken/Egypt/10259SF/         1.55e-03  [9(2.11e-07)]
A/bird/Turkey/Unye_ist06         4.33e-03  [2(1.45e-06)]
A/chicken/Bangladesh/11r         4.43e-08  4_[7(6.12e-10)]
A/chicken/Vietnam/NCVD19         2.96e-04  [2(7.67e-08)]
A/swan/England/AV3142149         8.58e-06  [1(5.93e-09)]
A/chicken/Ibaraki/17/200         3.23e-08  [1(5.83e-11)]
A/chicken/Nepal/354/2010         7.04e-03  3_[4(7.69e-07)]_3
A/duck/Vietnam/NCVD366/2         1.04e-02  [2(3.27e-06)]
A/duck/Korea/GJ54/2004|G         8.70e-02  4_[5(2.69e-06)]_3
A/muscovy_duck/Vietnam/L         5.49e-03  [2(1.20e-06)]
A/duck/Egypt/1130AG/2011         1.67e-03  [9(2.11e-07)]
A/ck/Indonesia/091/10            6.76e-08  4_[7(4.14e-11)]
A/duck/Vietnam/9/2010            8.80e-01  21
A/duck/Hokkaido/Vac3/200         6.46e-09  [1(1.27e-10)]
A/Thailand/WRAIR1720H/20         7.09e-03  [2(7.12e-07)]
A/chicken/Cambodia/022LC         5.25e-01  21
A/spurwinged_goose/Niger         1.87e-07  [1(2.89e-10)]
A/pigeon/Egypt/SHAH5803/         7.97e-04  [4(4.39e-07)]_6
A/whooper_swan/Mongolia/         1.74e-06  [1(5.15e-08)]
A/chicken/Shan/2626/2007         7.31e-04  [2(1.84e-08)]
A/chicken/Italy/367/97|A         5.38e-01  21
A/turkey/Italy/1325/2005         6.19e-01  21
A/chicken/Egypt/1158SF/2         1.23e-02  [2(2.10e-06)]
A/chicken/Egypt/398220/2         2.97e-05  7_[5(5.66e-09)]
A/condor/Guangdong/139/2         9.86e-03  [2(1.20e-06)]
A/chicken/Shandong/A1/20         1.24e-03  [2(3.10e-07)]
A/chicken/Egypt/11764s/2         2.76e-01  21
A/swine/NorthSumatra/UT6         3.58e-03  [2(4.76e-07)]
A/o.bill_stork/Thailand/         2.66e-03  [2(2.53e-07)]
A/chicken/Texas/2983132/         1.39e-06  [1(5.19e-10)]
A/chicken/Bangladesh/11V         1.24e-05  6_[10(1.21e-09)]
A/chicken/Ibaraki/15/200         2.90e-08  [1(1.65e-10)]
A/chicken/Shandong/A10/2         5.58e-03  [2(1.92e-06)]
A/duck/Vietnam/OIE1287/2         4.98e-04  [2(3.14e-08)]
A/duck/Vietnam/NCVD1161/         1.05e-02  3_[4(4.39e-07)]_3
A/duck/Ireland/113/1983|         7.45e-01  21
A/chicken/EastKalimantan         5.24e-03  [2(4.76e-07)]
A/duck/Vietnam/3/2010            2.10e-03  7_[8(3.40e-08)]_3
A/Muscovy_duck/Ca_Mau/11         1.21e-02  [2(7.95e-07)]
A/chicken/Turkey/Misinli         9.81e-14  1_[7(3.22e-11)]_3
A/chicken/Italy/9097/199         6.24e-07  1_[5(3.92e-08)]_6
A/mallard/Washington/456         7.87e-06  7_[5(4.78e-09)]
A/duck/Iran/11VIR53161/2         6.67e-01  21
A/Muscovy_Duck/Vietnam/1         1.77e-04  [4(2.36e-07)]_6
A/duck/Hunan/149/2005            3.48e-06  [1(8.40e-09)]
A/Egypt/4822NAMRU3/2009          2.66e-02  [2(4.03e-05)]
A/duck/Vietnam/NCVD1463/         3.24e-03  [2(1.92e-06)]
A/poultry/Egypt/398256/2         1.80e-03  [4(6.25e-07)]_6
A/turkey/Italy/1980|GQ24         2.83e-08  [6(7.65e-12)]
A/goose/Bangladesh/11VIR         2.97e-01  21
A/mallard/Washington/454         3.11e-09  [1(9.89e-12)]
A/chicken/Cambodia/013LC         3.57e-11  6_[3(1.22e-09)]
A/chicken/Banten/PdglKas         5.91e-03  [2(2.53e-07)]
A/chicken/Vietnam/NCVD03         3.60e-01  21
A/wigeon/Ohio/379/1988|C         1.02e-09  [1(2.82e-12)]
A/chicken/Magelang/BBVW6         1.62e-03  [2(7.67e-08)]
A/chicken/Lampung/BPPVRI         1.43e-02  [2(2.91e-06)]
A/chick/Pennsylvania/1/1         6.69e-05  [1(2.05e-08)]
A/chicken/Liaoning/A1/20         3.40e-03  [2(2.10e-06)]
A/wild_bird_feces/Cheons         1.67e-13  6_[3(4.15e-11)]
A/chicken/Sikkim/151466/         9.38e-03  [2(6.62e-06)]
A/environment/ChangSha/2         1.87e-03  [2(5.95e-06)]
A/chicken/CentralJava/UT         2.46e-03  [2(2.60e-06)]
A/Vietnam/HN36250/2010           1.88e-02  [2(1.51e-05)]
A/chicken/Guiyang/821/20         1.39e-06  6_[10(6.50e-10)]
A/owstons_civet/VietNam/         9.57e-04  [2(8.77e-07)]
A/chicken/Bangladesh/11r         3.28e-06  3_[3(8.33e-11)]_3
A/environment/New_York/1         3.29e-10  [1(7.24e-13)]
A/domestic_goose/Hong_Ko         1.50e-02  [2(8.76e-06)]
A/Hubei/1/2010                   3.24e-03  [2(1.92e-06)]
A/Hunan/1/2009                   1.76e-03  [2(3.93e-06)]
A/chicken/Egypt/1123AL/2         8.11e-04  [9(1.20e-07)]
A/wood_duck/MD/04623/200         8.07e-10  [1(9.89e-12)]
A/chicken/Shanxi/2/2006          2.04e-02  21
A/quail/Egypt/1171SG/201         1.40e-03  [9(1.34e-06)]
A/duck/France/080036/200         7.54e-09  [1(8.17e-11)]
A/chicken/Yangon/182/201         2.37e-03  [2(3.10e-07)]
A/chicken/Scotland/59|X0         5.00e-06  [1(5.46e-09)]
A/chicken/Sharkia/CAI41/         1.52e-03  [2(1.04e-07)]
A/mallard/Sweden/21/2002         2.50e-09  [1(2.67e-11)]
A/environment/Bangladesh         7.64e-03  [2(5.95e-06)]
A/chicken/Hebei/A8/2009          2.47e-03  [2(2.60e-06)]
A/chicken/Egypt/11VIR445         1.66e-03  10_[8(1.63e-07)]
A/duck/Guangxi/13/2004           3.67e-03  [2(9.60e-06)]
A/duck/France/090043/200         4.42e-08  [1(2.89e-10)]
A/chicken/Denpasar/BBVD1         2.21e-02  [2(3.61e-06)]
A/Egypt/N6774/2011               6.32e-04  [9(5.02e-07)]
A/parrot/CA/6032/04|DQ25         7.46e-08  [1(1.65e-10)]
A/Cambodia/VN05103/2005          1.41e-01  21
A_GenBank/heron/Cambodia         2.73e-03  6_[4(3.75e-07)]
A/chicken/Bangladesh/11r         6.14e-05  7_[5(1.10e-08)]
A/chicken/Tabanan/BBVD14         1.77e-03  [2(2.08e-07)]
A/great_cormorant/Tibet/         5.06e-05  [2(3.08e-09)]
A/Egypt/321NAMRU3/2007           5.79e-03  [2(6.23e-07)]
A/chicken/Egypt/10512AG/         3.04e-02  [2(9.60e-06)]
AHAH5_[11734;11734]              4.21e-37  [1(3.05e-19)]
A/Egypt/9174NAMRU3/2009          5.33e-04  [9(3.52e-08)]
A/Indonesia/NIHRD12379/2         4.50e-03  [2(6.23e-07)]
A/chicken/Korea/ES/03            1.77e-02  [2(5.89e-05)]
A/avian/New_York/Sg00377         1.75e-05  7_[5(5.66e-09)]
A/chicken/Vietnam/NCVD09         2.29e-03  [2(4.40e-06)]
A/Chicken/TurkeyMus/09rs         5.71e-08  4_[7(3.22e-11)]
A/duck/Hong_Kong/312/197         6.18e-05  [3(8.33e-11)]_6
A/Vietnam/UT3030/2003            6.22e-04  [2(5.58e-08)]
A/crow/Bangladesh/11rs19         6.76e-02  21
A/duck/Primorie/2633/200         3.16e-05  [3(4.15e-11)]_6
A/Indonesia/UT3006/2005          7.23e-03  [2(3.89e-07)]
A/duck/Qalubia/CAI11/201         5.33e-03  [2(3.89e-07)]
A/green_winged_teal/Dela         2.40e-09  [1(5.44e-12)]
A/chicken/Anhui/T5/2006          2.35e-05  [10(6.50e-10)]_6
A/chicken/Puebla/8623607         9.01e-01  21
A/duck/Guangxi/951/2005          4.60e-03  [2(5.43e-06)]
A/chicken/Egypt/1219s/20         4.44e-11  4_[3(4.76e-09)]_2
A/chicken/WestJava/SmiSu         1.15e-03  [9(4.74e-08)]
A/chicken/Cambodia/TLC2/         1.63e-05  3_[3(1.22e-09)]_3
A/duck/France/05056a/200         1.22e-08  [1(4.65e-10)]
A/Shandong/1/2009                2.38e-03  [2(2.34e-06)]
A/chicken/Vietnam/NCVD40         5.75e-03  [2(3.27e-06)]
A/chicken/Queretaro/7653         1.33e-02  3_[4(3.75e-07)]_3
A/environment/Bangladesh         2.15e-03  [4(3.75e-07)]_6
A/barn_swallow/Hong_Kong         1.05e-02  [2(2.31e-05)]
A/duck/Primorie/2621/200         9.31e-08  1_[3(1.97e-08)]_5
A/chicken/BacLieuVietnam         2.11e-03  3_[4(6.25e-07)]_3
A_DISC/Cambodia/V0401301         8.39e-03  [2(2.91e-06)]
A/bar_headed_goose/Mongo         9.64e-06  [1(2.05e-08)]
A/chicken/Egypt/113Q/201         1.22e-02  [2(1.92e-06)]
A/quail/Thanatpin/2283/2         4.14e-03  [2(6.62e-06)]
A/chicken/Egypt/125s/201         1.53e-11  4_[5(5.66e-09)]_3
A/duck/Hong_Kong/698/197         5.60e-09  [1(2.08e-11)]
A/chicken/Egypt/209573/2         8.03e-01  21
A/chicken/Indonesia/SmiW         3.08e-08  [6(5.44e-12)]
A/turkey/Egypt/091QNLQP/         7.34e-05  [3(8.33e-11)]_6
A/duck/Egypt/1053/2010           2.54e-02  21
A/Egypt/2786NAMRU3/2006          8.02e-04  6_[4(6.25e-07)]
A/mallard/Netherlands/3/         1.90e-06  3_[3(4.15e-11)]_3
A/chicken/Bangladesh/11r         3.27e-05  [3(8.33e-11)]_6
A/chicken/Liaoning/23/20         4.61e-03  [2(1.20e-06)]
A/unknown/NY/98996/01|AY         2.75e-09  [1(1.88e-11)]
A/tern/South_Africa/1961         5.03e-01  21
A/chicken/Nepal/T1P/12           2.79e-03  [2(7.12e-07)]
A/marabou_stork/Cambodia         2.36e-01  21
A/chicken/Cambodia/67F1/         1.19e-02  [2(2.10e-06)]
A/gadwall/California/442         6.07e-10  [1(2.10e-12)]
A/chicken/TanseMyanmar/S         5.35e-03  3_[4(6.25e-07)]_3
A/duck/Cao_Bang/43/2007          5.78e-04  [2(5.46e-07)]
A/chicken/Miyazaki/T10/2         2.84e-03  [2(1.67e-06)]
A/whitefaced_whistling_d         7.41e-02  21
A/muscovy_duck/Vietnam/N         5.05e-03  [2(6.23e-07)]
A/Canada_goose/Alaska//4         2.31e-09  4_[5(4.78e-09)]_3
A/chicken/Bangladesh/967         2.96e-03  [2(7.12e-07)]
A/chicken/Egypt/11VIR445         6.80e-03  [2(1.92e-06)]
A/Hong_Kong/7032/2012            1.26e-02  3_[4(4.39e-07)]_3
A/chicken/Vietnam/945/20         5.75e-01  21
A/ostrich/South_Africa/A         1.76e-05  3_[3(7.90e-10)]_3
A/wild_bird/Wisconsin/43         1.40e-06  1_[5(5.66e-09)]_6
A/spurwinged_goose/Niger         2.31e-02  [2(1.16e-05)]
A/duck/Vietnam/NCVD1026/         4.60e-03  [2(1.27e-05)]
A/tern/South_Africa/1959         1.00e-06  3_[3(4.15e-11)]_3
A/muscovy_duck/Jakarta/S         2.32e-03  [2(5.58e-08)]
A/goose/Germany/R3160/09         2.01e-09  [1(4.14e-11)]
A/turkey/Ontario/7732/19         7.44e-01  21
A/chicken/Egypt/1090/201         1.64e-03  [9(6.98e-07)]
A/mallard/Netherlands/2/         5.96e-09  [1(5.83e-11)]
A/chicken/Vietnam/NCVD18         3.46e-03  [2(1.27e-05)]
A/chicken/Texas/1672804/         1.67e-07  [1(3.63e-11)]
A/duck/Italy/775/2004|CY         1.24e-09  [1(9.22e-11)]
A/chicken/Bangladesh/FD(         2.17e-05  [3(4.15e-11)]_6
A/chicken/Vietnam/NCVD40         1.17e-02  [2(1.66e-05)]
A/swan/Hokkaido/67/1996|         1.62e-07  [1(2.49e-10)]
A/chicken/Bangladesh/152         9.67e-04  [2(1.20e-06)]
A/chicken/Bangladesh/11r         1.76e-01  21
A/chicken/Indonesia/Suka         2.79e-01  21
A/gull/Pennsylvania/4175         3.23e-07  [1(1.05e-09)]
A/turkey/England/N28/73|         2.35e-08  1_[3(2.10e-08)]_5
A/chicken/Badung/BBVD302         1.81e-03  [2(2.17e-07)]
A/chicken/Bangladesh/11r         2.34e-03  [3(7.12e-09)]_6
A/chicken/Yichang/lung1/         8.73e-01  21
A/avian/Missouri/4655937         9.68e-09  [1(1.88e-11)]
A/turkey/TX/14082/1982_H         4.49e-09  [1(1.88e-11)]
A/Cambodia/W0526301/2012         1.11e-02  [2(1.92e-06)]
A/chicken/Vietnam/NCVD11         1.10e-02  3_[4(3.75e-07)]_3
A/duck/Egypt/SHZA6605/20         6.64e-02  21
A/chicken/Shandong/A5/20         8.69e-03  [2(7.33e-06)]
A/chicken/VA/40018/1984_         1.38e-04  [1(8.00e-08)]
A/common_magpie/HongKong         3.92e-09  4_[7(1.62e-11)]
A/shearwater/Australia/7         5.83e-09  [1(6.48e-11)]
A/Chicken/TurkeyEdirne/0         2.06e-08  1_[5(1.90e-09)]_6
A/goose/Guiyang/337/2006         7.92e-03  [2(7.95e-07)]
A/chicken/Egypt/11VIR445         4.91e-01  21
A/environment/Thailand/I         3.12e-03  [2(4.76e-07)]
A/wild_bird_feces/Byeong         9.09e-06  3_[3(6.63e-10)]_3
A/duck/Vietnam/NCVD422/2         1.28e-02  [2(1.96e-05)]
A/chicken/Bhutan/4/10            9.80e-01  21
A/turkey/MN/40550/1987_H         5.51e-03  4_[5(9.56e-07)]_3
A/chicken/Egypt/1085/201         7.60e-03  [2(2.60e-06)]
A/duck/France/06436/2006         4.96e-08  [1(8.65e-10)]
A/HongKong/6841/2010             4.72e-01  21
A/chicken/WestBengal/239         6.43e-03  [2(1.45e-06)]
A/duck/Bac_Lieu/1213/200         1.71e-03  [2(9.16e-08)]
A/cinnamon_teal/Californ         2.44e-09  [1(1.49e-11)]
A/Muscovy_duck/France/07         1.85e-08  [1(1.05e-09)]
A/chicken/Vietnam/4/2010         6.85e-04  1_[8(8.62e-09)]_9
A/chicken/Vietnam/NCVD01         1.05e-02  [2(2.94e-05)]
A/chicken/Puebla/1458665         1.71e-08  4_[5(1.20e-08)]_3
A/Northern_shoveler/Utah         3.16e-10  [1(1.11e-12)]
A/tundra_swan/Alaska//48         1.72e-09  [1(1.29e-11)]
A/chicken/Sheny/0606/200         2.19e-03  [2(1.67e-06)]
A/turkey/England/N28/73|         7.65e-01  21
A/duck/Iran/VIR53161/201         9.31e-01  21
A/chicken/Yangon/1023/20         3.00e-02  [2(2.51e-05)]
A/chicken/Vietnam/5/2010         5.43e-04  4_[8(8.62e-09)]_6
A/chicken/Hebei/326/2005         4.20e-03  [2(1.32e-06)]
A/chicken/Bangladesh/150         3.10e-04  [2(3.10e-07)]
A/wild_bird/Minnesota/46         2.06e-09  [1(4.20e-12)]
A/chicken/India/81766/20         2.22e-03  [2(7.12e-07)]
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 10 reached.
********************************************************************************

CPU: bioteam52

********************************************************************************
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DT3100POP6{BDv3}v1.mob65{RBioPerl-1.007002/t/data/test.ace000444000766000024       216513155576321 16325 0ustar00cjfieldsstaff000000000000
Protein : "roa1_drome"
Peptide "roa1_drome"

Peptide : "roa1_drome"
MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVV
VMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVK
KLFVGALKDDHDEQSIRDYFQHFGNIVDNIVIDKETGKKRGFAFVEFDDYDPVDKVVLQK
QHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGN
NWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGND
FGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY


Sequence : "Name\; 4\% strewn with \\ various \/ escaped characters"
DNA "Name\; 4\% strewn with \\ various \/ escaped characters"

DNA : "Name\; 4\% strewn with \\ various \/ escaped characters"
gctcggactctatctagcagaaacctcgttcagctagtcttgcttcatggaggtttgatc
tagactgcaaacgtcggtgctaaaagaccatacttccgtatgtgcctatcgggagcagtc
gctgagaagtgcggaatgatccttcaatgaccgccgttaaagcctgggagtccgcgccac
aatcattccatatacagcaacacgcgctacgcggacctctcggtgggtgacgattctatt
gaggcgttgaagcgagaaagatattccgattcttttcgagtctatagttaaatcggactg
catcatccattttagggcata


Sequence : "Last"
DNA "Last"

DNA : "Last"
ggccgggatggccggacctgttctgaacatcttatatccacccgaacaagttataaacaa
tttaaatctgggcggccatctataagcgtgtcttcagtatgagagtcttcggatatcacg
acccattaggaaag

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cÓ‹Y’y–¾Ó³ô›6ëì,²f}êåf³ÆgµÖ:DZ˘4Ì@/4™¥/PÛ²ù¢|¢U}½gÙ‰éÕ›K fÐù‡Ás¶‹;˜Šq0=ö§âÒ§Ž*p9ôR•Ûf‹ ƒÆgqrýz‡ö©¹ÓI®¤ÖwêÑ}œzt?Nˆ(ÑÐ"ô´¦õÌÁk
„V¯•O¼RjËND –š»WÑÞ¡¯Ø€+5Úä²ÑSzQíÃ/7“ôMh ¨”ètt˜ÜþkÉ¡@“ÂNv§†¿[bÍh®E’ù_´(\Ÿÿ ¾­Ý'}’Ìÿ¾ö2ä(ŽL`Á)З%]¤WÖIí’”‰Uñö–ÿJó-L|V‹Ãx?}{‹ROy¡;›Ë^
qý^kzæðÎʈÑÏ£Ö v­·LCŠÎ•må†~ƒ¨kë¾Åu›åë#¯4óõ‘ûœyp(TÊøÅŽ“p|¹O_—6±¼ÒÌ×e'b¾FænHC¦o³p´ÛŒ¥§¯þŽäëÿ[ïÌa.‹ÿBCBioPerl-1.007002/t/data/test.bowtie000444000766000024      7516313155576321 17116 0ustar00cjfieldsstaff000000000000SRR000311.7434	+	NC_009749_frag	25327	TTTATCTTTTATTTTATAAA	+T,17:C>A
SRR000311.12215	+	NC_009749_frag	25480	TTTATAGTTAATCCGAGAGT	(;>9<;;8?5=;8?;:<<:<	0	
SRR000311.4729	+	NC_009749_frag	25482	TATAGTTAATCCGAGAGTAT	:<;<<:@:@;9@;<<<<<<<	0	
SRR000311.6501	+	NC_009749_frag	25484	TAGTTAATCCGAGAGTATTTT	<<<:?:@;:@<<<<<<<+7AC	0	
SRR000311.3051	+	NC_009749_frag	25488	TAATCCGAGAGTATTTTGTT	<:@78?;<<<<<<+7@B<:@	0	
SRR000311.8800	+	NC_009749_frag	25492	CCGAGAGTATTTTGTTAAAC	A;;	0	
SRR000311.1489	+	NC_009749_frag	25494	GAGAGTATTTTGTTAAACAC	<<<<<<<'4?A<;@/?B<<:	0	
SRR000311.2290	+	NC_009749_frag	25496	GAGTATTTTGTTAAACACAT	;<<;<(5?A<:@,=@:<<<;	0	
SRR000311.3595	+	NC_009749_frag	25496	GAGTATTTTGTTAAACACAT	<<<<:)6@B<:?/?B<:<<<	0	
SRR000311.7859	+	NC_009749_frag	25496	GAGTATTTTGTTAAACACAT	<9<<<)6@B<:?/?B<<<<<	0	
SRR000311.11501	+	NC_009749_frag	25499	TATTTTGTTAAACACATAAGA	9<&4?A:7?0?B<<<<<:@;<	0	
SRR000311.2804	+	NC_009749_frag	25500	ATTTTGTTAAACACATAAGA	;(5?A;:@,=@;<<<;:@<<	0	
SRR000311.9663	+	NC_009749_frag	25506	TTAAACACATAAGAGATAGC	8?/?A<<:;<:@<<<<<<<9	0	
SRR000311.1482	+	NC_009749_frag	25510	ACACATAAGAGATAGCATCAC	;;8<<::@<<;<<<<:<<<<:	0	
SRR000311.5790	+	NC_009749_frag	25519	AGATAGCATCACAAAATTTTT	9<<<<;<<:<<;&4?A%/8@B	0	
SRR000311.9596	+	NC_009749_frag	25521	ATAGCATCACAAAATTTTTC	<<9;<<;<<<)6@B".7@B:	0	
SRR000311.5703	+	NC_009749_frag	25527	TCACAAAATTTTTCAAAACT	<<<<*7@B&08@B<*6@B<<	0	
SRR000311.8720	+	NC_009749_frag	25527	TCACAAAATTTTTCAAAACT	9<;<)6@B$/8@B<,7AB<<	0	
SRR000311.5910	+	NC_009749_frag	25531	AAAATTTTTCAAAACTATTAT	*6@B$.8@B<'4?A:<<;@:<	0	
SRR000311.4760	+	NC_009749_frag	25534	ATTTTTCAAAACTATTATTC	<$/8@B:&4?A<<<:@26>:	0	
SRR000311.5997	+	NC_009749_frag	25535	TTTTTCAAAACTATTATTCA	#.8@B<&4?A<<;;@<:@<;	0	
SRR000311.11806	+	NC_009749_frag	25535	TTTTTCAAAACTATTATTCA	#.8@B;)6@B<<;:@<7><<	0	
SRR000311.1089	+	NC_009749_frag	25547	ATTATTCACTTTTCTAAATA	;:@<6=<<<#2>@<<0?B<;	0	
SRR000311.3514	+	NC_009749_frag	25552	TCACTTTTCTAAATATTTTT	9<<;&4?A<;.?A;;$/8@B	0	
SRR000311.14042	+	NC_009749_frag	25552	TCACTTTTCTAAATATTTTT	7<;<&4?A<:.>A<<$.8@B	0	
SRR000311.474	+	NC_009749_frag	25554	ACTTTTCTAAATATTTTTTT	:<$3>@;<.>A<<"',17>@	0	
SRR000311.3257	-	NC_009749_frag	16500	TTAAAAAATATTTAGAAAA	:@&+18?@<<.>A<<*6@B	0	17:A>T
SRR000311.719	+	NC_009749_frag	25557	TTTCTAAATATTTTTTTAAA	->@7<.>A2<"',17>@0?B	0	
SRR000311.2294	+	NC_009749_frag	25557	TTTCTAAATATTTTTTTAAA	&:=99/?A<<#(,17=@1?A	0	
SRR000311.13309	-	NC_009749_frag	16493	CTAACTTTAAAAAAATAATTT	;<>:;@=,@>71,(#;6+?<*	0	0:A>T,3:T>A
SRR000311.3061	+	NC_009749_frag	25563	AATATTTTTTTAAAGTTAGC	4<:;"&+18>@.>A<9?<<:	0	
SRR000311.4080	+	NC_009749_frag	25565	TATTTTTTTAAAGTTAGCCC	<<#(,17>@1?B<9@;<,7A	0	
SRR000311.5915	+	NC_009749_frag	25566	ATTTTTTTAAAGTTAGCCCA	<$(,17=?/?A<;@;A/?A:@'4?A	0	
SRR000311.8047	+	NC_009749_frag	25576	AGTTAGCCCAAACCT	;<:@7<.>A1?A9=2	0	
SRR000311.11642	+	NC_009749_frag	25578	TTAGCCCAAACCTTTTCAATA	:@;<0?B->@9@%3>@<9@;;	0	
SRR000311.7772	+	NC_009749_frag	25580	AGCCCAAACCTTTTCAATAG	<<;9	0	
SRR000311.4646	+	NC_009749_frag	25585	AAACCTTTTCAATAGGATTT	':=8?$3>@<8?<<;@<,=@	0	
SRR000311.6220	+	NC_009749_frag	25588	CCTTTTCAATAGGATTTAAA	:@,7AC<:@969@@<:@<;;@<0?B1?A<	0	
SRR000311.5233	+	NC_009749_frag	25592	TTCAATAGGATTTAAATCTG	6><;@<;:?<0?B1?B;;<7	0	
SRR000311.11655	+	NC_009749_frag	25593	TCAATAGGATTTAAATCTGG	:;:@::;@<1?B1?B<<;/?	0	
SRR000311.10244	+	NC_009749_frag	25594	CAATAGGATTTAAATCTGGA	@:@<;:>A;<<<<;<<	0	
SRR000311.1771	+	NC_009749_frag	25628	ATATAATATTTGTACATCAAA	;<<;8?;<.>A:<<<<9;.>A	0	
SRR000311.10135	+	NC_009749_frag	25631	TAATATTTGTACATCAAATTT	<:@<<->A<<;<<8<1?A0?B	0	
SRR000311.3069	+	NC_009749_frag	25632	AATATTTGTACATCAAATTT	:@;<.>A<<;<<;;1>A1?A	0	
SRR000311.13083	+	NC_009749_frag	25634	TATTTGTACATCAAATTTAT	;<1?B:<<;:<<0?B1>@;:	0	
SRR000311.1024	+	NC_009749_frag	25640	TACATCAAATTTATTGGCTA	<<;:<A<:@9@<<<	0	
SRR000311.8688	+	NC_009749_frag	25643	ATCAAATTTATTGGCTATTT	;:<0?B1?A<:@7?<;<0?B	0	
SRR000311.12579	+	NC_009749_frag	25643	ATCAAATTTATTGGCTATTT	<:;0?B->A<;@:@<<<0?B	0	
SRR000311.4287	+	NC_009749_frag	25644	TCAAATTTATTGGCTATTTCA	;<0?B0?B;:@8?<<<)G
SRR000311.12208	+	NC_009749_frag	25651	TATTGGCTATTTCAATCAGC	<:9@8?<<<)<8<;<:>	0	
SRR000311.9136	+	NC_009749_frag	25654	TGGCTATTTCAATCAGCTTAG	<:@;:<0?B<9@:<<:<:@;;	0	
SRR000311.13080	+	NC_009749_frag	25655	GGCTATTTCAATCAGCTTAG	8?7<;*A<:@<<:<<;@:<<	0	
SRR000311.5357	+	NC_009749_frag	25662	TCAATCAGCTTAGAGGATTT	;<;@<<<;;;@<<<:@;0?B	0	
SRR000311.1008	+	NC_009749_frag	25668	AGCTTAGAGGATTTATGGAA	<<<;@<<<:@<1?B<<9@9@	0	
SRR000311.2248	+	NC_009749_frag	25668	AGCTTAGAGGATTTATGGAA	;:::@<<9:@;/?B;<:@:@	0	
SRR000311.13551	+	NC_009749_frag	25668	AGCTTAGAGGATTTATGGAA	<<<:?<<<:@<0?B<<8?;@	0	
SRR000311.1981	+	NC_009749_frag	25670	CTTAGAGGATTTATGGAAA	<;@;<97><1?B;<6=.>A	0	
SRR000311.2018	+	NC_009749_frag	25671	TTAGAGGATTTATGGAAACTA	:?<:<;@<1?B<<9@.>A<<;	0	
SRR000311.5466	+	NC_009749_frag	25678	ATTTATGGAAACTAGCATTA	<1?B<<:@.?A<<<<<<;@<	0	
SRR000311.13570	+	NC_009749_frag	25678	ATTTATGGAAACTAGCATTA	<1?A<<:@/?B<9<<<<;@;	0	
SRR000311.152	+	NC_009749_frag	25682	ATGGAAACTAGCATTATCCA	;<8?.>A<<;<<<:?<9:@<	0	
SRR000311.5003	+	NC_009749_frag	25682	ATGGAAACTAGCATTATCCA	<<:@/?A<<:<<<:?<::@<	0	
SRR000311.7464	+	NC_009749_frag	25682	ATGGAAACTAGCATTATCCA	<<8?.?A<;9;<<:><<:@<	0	
SRR000311.10958	+	NC_009749_frag	25682	ATGGAAACTAGCATTATCCA	<<:@/?A<;<<<<:@<<;@<	0	
SRR000311.11360	+	NC_009749_frag	25683	TGGAAACTAGCATTATCCAT	::@0?B<<<<<;:@<<;@<:	0	
SRR000311.11997	+	NC_009749_frag	25685	GAAACTAGCATTATCCATTAC	<.>A;<<<<<:?<:;@<:@<;	0	
SRR000311.13016	+	NC_009749_frag	25686	AAACTAGCATTATCCATTAC	0?B:<<<<<;@<<:?<;@<;	0	
SRR000311.299	+	NC_009749_frag	25689	CTAGCATTATCCATTACTAT	@9;<;;;@<;8?<9?;999<	0	
SRR000311.9600	+	NC_009749_frag	25695	TTATCCATTACTATAGTAGTT	;@;<:@<:@<;:;;<<<<<:@	0	
SRR000311.5783	+	NC_009749_frag	25698	TCCATTACTATAGTAGTTTTA	6:@;:@<<<<<;<<<:*7@B<	0	
SRR000311.11542	+	NC_009749_frag	25701	ATTACTATAGTAGTTTTAGG	<:@<<<<<;<<<<*6@B<;@	0	
SRR000311.5120	+	NC_009749_frag	25704	ACTATAGTAGTTTTAGGTTTT	<<;:<<<;<;*6@B<:@)5@B	0	
SRR000311.3190	+	NC_009749_frag	25705	CTATAGTAGTTTTAGGTTTT	@8:<;<<<;+7@B;:?)6@B	0	
SRR000311.2991	+	NC_009749_frag	25711	TAGTTTTAGGTTTTAATGAT	;<<&4?A<:@%3>A:@<:<<	0	
SRR000311.4972	+	NC_009749_frag	25716	TTAGGTTTTAATGATGGGCAT	:><;@,7AC:@;<<;/?A<;<	0	
SRR000311.3703	+	NC_009749_frag	25723	TTAATGATGGGCATAAGTGT	9@:@<;<<->A;<<:@<9<<	0	
SRR000311.10952	+	NC_009749_frag	25727	TGATGGGCATAAGTGTTCCT	<;;;+A;;<:@<<<7>:@::	0	
SRR000311.12712	+	NC_009749_frag	25729	ATGGGCATAAGTGTTCCTCA	:<);>9:;9@<;;5=:@8<<	0	
SRR000311.13706	+	NC_009749_frag	25729	ATGGGCATAAGTGTTCCTCA	;<1>@<<;9>7:5:@9><89	0	
SRR000311.5176	+	NC_009749_frag	25734	CATAAGTGTTCCTCAAACC	;<<:@;<<7>9@9<.>A:@	0	
SRR000311.1418	+	NC_009749_frag	25736	TAAGTGTTCCTCAAACCATTG	;9@<<<6=:@5<->A:@;:@:	0	
SRR000311.2268	+	NC_009749_frag	25737	AAGTGTTCCTCAAACCATTGA	9@<<<:@:@<<0?B:@<;@<8	0	
SRR000311.10735	+	NC_009749_frag	25737	AAGTGTTCCTCAAACCATTG	7><<;7?:@5<->@:@3:@;	0	
SRR000311.465	+	NC_009749_frag	25738	AGTGTTCCTCAAACCATTGA	:;<<:@:@;<.>A:@<:@<<	0	
SRR000311.4374	+	NC_009749_frag	25738	AGTGTTCCTCAAACCATTGA	::<::@:@:<0?B;@<:@9;	0	
SRR000311.13253	+	NC_009749_frag	25750	ACCATTGATTAAAAATTTCA	<9@;;@<;:@%/8@B->A<<	0	
SRR000311.239	-	NC_009749_frag	16298	CCAATACTGAAATTTTAAT	@:@9<<<<<=9%B@7-@:<	0	0:A>T,2:T>A
SRR000311.650	+	NC_009749_frag	25760	AAAAATTTCAGTATTGGTAT	%/8@B+=@9:<<<9@;@<<;	0	
SRR000311.1603	+	NC_009749_frag	25760	AAAAATTTCAGTATTGGTATA	$.8@B&:=;<<;<6>8?<:<:	0	
SRR000311.11164	+	NC_009749_frag	25763	AATTTCAGTATTGGTATATCC	:@*;	0	
SRR000311.11037	+	NC_009749_frag	25767	TCAGTATTGGTATATCCGCTG	<<:<;<;@9@<<<;8:@;<<:	0	
SRR000311.6548	+	NC_009749_frag	25771	TATTGGTATATCCGCTGTACT	:<;@8?9<9<99@<<5<<;<;	0	
SRR000311.11941	+	NC_009749_frag	25771	TATTGGTATATCCGCTGTACT	7::@7?89<<<8?<<;;2<;;	0	
SRR000311.1417	+	NC_009749_frag	25772	ATTGGTATATCCGCTGTACTC	;:@:@;:<<9:@<<;<;<;::	0	
SRR000311.5412	+	NC_009749_frag	25772	ATTGGTATATCCGCTGTACTC	<8?9@;<<98:@<<<<<<<9:	0	
SRR000311.11397	+	NC_009749_frag	25778	ATATCCGCTGTACTCTAATG	<<;<:@;;<<<<<::::?89	0	
SRR000311.8834	+	NC_009749_frag	25779	TATCCGCTGTACTCTAATGGA	<:;:@:<<<<<<;<<:@<:@<	0	
SRR000311.8424	+	NC_009749_frag	25780	ATCCGCTGTACTCTAATGGA	<<:@<;;<<<<<;<9@::@<	0	
SRR000311.7718	+	NC_009749_frag	25782	CCGCTGTACTCTAATGGAGC	:@<<<<;:<9;89@<9@:<;	0	
SRR000311.7395	+	NC_009749_frag	25792	CTAATGGAGCTATAATCTTTT	<;;@;9@<;:<;:9@<<(5@B	0	
SRR000311.5937	+	NC_009749_frag	25799	AGCTATAATCTTTTTATCTGC	<;:<:<:@<<%/8@B<<<;;:	0	
SRR000311.6683	+	NC_009749_frag	25799	AGCTATAATCTTTTTATCTG	<;:<<77><9#.8@B<:<<;	0	
SRR000311.13878	+	NC_009749_frag	25809	TTTTTATCTGCATAATTAT	&08@B;;<5<<8<:@;@9;	0	
SRR000311.4189	+	NC_009749_frag	25811	TTTATCTGCATAATTATATC	0?B<<;<<<7<:@;@<9;28	0	
SRR000311.3141	+	NC_009749_frag	25812	TTATCTGCATAATTATATCC	:@<<<7<<<::@:@<<;;:@	0	
SRR000311.10165	+	NC_009749_frag	25814	ATCTGCATAATTATATCCAG	<<<4;<:9:?:@<;<9;@<:	0	
SRR000311.9547	+	NC_009749_frag	25820	ATAATTATATCCAGCAACAA	;9:@:@;<;::@<<<:@<;@	0	
SRR000311.6019	+	NC_009749_frag	25824	TTATATCCAGCAACAATACT	9@<<<:9@<;<:@<:@;<<<	0	
SRR000311.6122	+	NC_009749_frag	25829	TCCAGCAACAATACTTCTTCT	89@;<<9@<9@<<:9@<:@;<	0	
SRR000311.13559	+	NC_009749_frag	25829	TCCAGCAACAATACTTCTTC	;:@<<<:@<7><;<9@;8?;	0	
SRR000311.1342	+	NC_009749_frag	25836	ACAATACTTCTTCTTTGTGTT	<;:@<<<:@;7>;+=@;<<8?	0	
SRR000311.10113	+	NC_009749_frag	25842	CTTCTTCTTTGTGTTTGATAT	@:?;9@<0?B;7;0?B<<9<<	0	
SRR000311.818	+	NC_009749_frag	25843	TTCTTCTTTGTGTTTGATAT	9?<9?;0?B<<<*A<3<.>A8;;<:	0	
SRR000311.4799	+	NC_009749_frag	25846	TTCTTTGTGTTTGATATGCT	;@<1>@;751>@674<:7;<	0	
SRR000311.12654	+	NC_009749_frag	25849	TTTGTGTTTGATATGCTAAA	0?B<;A<<<<;<<<+7AB:	0	
SRR000311.7142	+	NC_009749_frag	25851	TGTGTTTGATATGCTAAAAC	7<;@:@9>88;69:>::9><5<	0	
SRR000311.4335	+	NC_009749_frag	25892	AATTAGTGACCATCCTCTTAG	4<7>:;9<<3<886><7:@9:	0	
SRR000311.5292	+	NC_009749_frag	25895	TAGTGACCATCCTCTTAGGAT	;<<<<<:@<<;@<<8?;:@:<	0	
SRR000311.8707	+	NC_009749_frag	25898	TGACCATCCTCTTAGGATAG	;:<:@;<9@<<9@;:@<<<<	0	
SRR000311.13773	+	NC_009749_frag	25898	TGACCATCCTCTTAGGATA	<<<:@9<8?:79@<:@;9<	0	
SRR000311.4014	+	NC_009749_frag	25900	ACCATCCTCTTAGGATAGAAA	<8?<;5=;<7>99?<<;<.>A	0	
SRR000311.6762	+	NC_009749_frag	25902	CATCCTCTTAGGATAGAAAGC	@99:@<<:@;:@;<<<1?B<:	0	
SRR000311.4748	+	NC_009749_frag	25906	CTCTTAGGATAGAAAGCTTA	<<<:?<:@<<<;->@<<:?<	0	
SRR000311.5338	+	NC_009749_frag	25920	AGCTTATTGTCACACCCCAT	;<<:@;:@<:<;:<)6@B<<	0	
SRR000311.11729	+	NC_009749_frag	25922	CTTATTGTCACACCCCATCTC	::?<:@<<;;<<&4?A;<<<<	0	
SRR000311.7487	+	NC_009749_frag	25927	TGTCACACCCCATCTCATCT	;;<<;<<)6@B<<<;<;:<<	0	
SRR000311.554	+	NC_009749_frag	25929	TCACACCCCATCTCATCTAT	<<<<:'5?A;8<6<<<;;<<	0	
SRR000311.1364	+	NC_009749_frag	25929	TCACACCCCATCTCATCTATA	9<<;<%3>@;<<8<;:<<:;<	0	
SRR000311.2022	+	NC_009749_frag	25929	TCACACCCCATCTCATCTATA	<<<<<%3>@;<;;:<<<<;:<	0	
SRR000311.8083	+	NC_009749_frag	25929	TCACACCCCATCTCATCTATA	;;<<<'4?A;<;:<<<<<<;;	0	
SRR000311.5184	+	NC_009749_frag	25936	CCATCTCATCTATATAAAAT	=@<;<;<;;<;<<<:,7AB<	0	
SRR000311.7178	+	NC_009749_frag	25941	TCATCTATATAAAATAACAA	;;<<<;<<7<+7AB;:@<:>	0	
SRR000311.1709	+	NC_009749_frag	25943	ATCTATATAAAATAACAAGT	;<;<<<<<(5?A<:@<;@<:	0	
SRR000311.1674	+	NC_009749_frag	25945	CTATATAAAATAACAAGTTTT	<<;<<<%3>@;9@:6=<'5?A	0	
SRR000311.616	+	NC_009749_frag	25949	ATAAAATAACAAGTTTTGAG	<<)6@B<9=:;@<(5?A<<9	0	
SRR000311.14032	+	NC_009749_frag	25950	TAAAATAACAAGTTTTGAGC	:%3>@<:@8:@<$2>@6;<7	0	
SRR000311.2143	+	NC_009749_frag	25952	AAATAACAAGTTTTGAGCTATTTCTTTTAGTTTTTCTATATACTCCAACCTTTCATGTTCTTTTCTTTGC	*<-7@B<;:<<<1>@<	0	
SRR000311.3307	+	NC_009749_frag	25958	CAAGTTTTGAGCTATTTCTT	?:?5-7@B:978942>@78<	0	
SRR000311.1610	+	NC_009749_frag	25962	TTTTGAGCTATTTCTTTTAG	'5?A<<<<;G,1:G>A
SRR000311.4402	+	NC_009749_frag	25991	ATACTCCAACCTTTCATGTT	;;<<7:@;@9@*@<;	0	
SRR000311.8850	+	NC_009749_frag	26005	CATGTTCTTTTCTTTGCTTA	>:<<;@;)6@B<0?B;<;@<	0	
SRR000311.535	+	NC_009749_frag	26008	GTTCTTTTCTTTGCTTATAT	<6><%3>@<.>A:<9@<<<<	0	
SRR000311.537	+	NC_009749_frag	26009	TTCTTTTCTTTGCTTATATT	7>;*6@B<.>A<<:@:<<:@	0	
SRR000311.8092	+	NC_009749_frag	26015	TCTTTGCTTATATTTTGGAG	:<->A9;:@::<(5?A8?:<	0	
SRR000311.11185	+	NC_009749_frag	26015	TCTTTGCTTATATTTTGGAGT	<<.?A:;;@<<<(5@B:@<<<	0	
SRR000311.2763	+	NC_009749_frag	26019	TGCTTATATTTTGGAGTCTTTTTTTAAAA	<;<:@;6;'5?A7><:2<"',17>@)6@B	0	
SRR000311.6409	+	NC_009749_frag	26021	CTTATATTTTGGAGTCT	<;@<<:(5?A6><;:;;	0	
SRR000311.9209	+	NC_009749_frag	26021	CTTATATTTTGGAGTCTTTTT	?9@<<;*6@B:@<;8;$/8@B	0	
SRR000311.5875	+	NC_009749_frag	26030	TGGAGTCTTTTTTTAAAACT	;8?<97<#(,17>@)6@B<2	0	
SRR000311.12593	+	NC_009749_frag	26032	GAGTCTTTTTTTAAAACTAA	<;<<<#',17>@,7AC<<:?	0	
SRR000311.4659	-	NC_009749_frag	16014	TACTTGGTTTTAGTTTTAAT	<<<:@;@*6@B<:,7AB:?<	0	0:A>T
SRR000311.1569	+	NC_009749_frag	26042	TTAAAACTAAAACCAAGTAT	9?#2>@<<$2>@8?9@<<<;	0	
SRR000311.6394	+	NC_009749_frag	26050	AAAACCAAGTATATTAAGACA	+7@B7?9@;<;<<9@:@<:<<	0	
SRR000311.4513	+	NC_009749_frag	26054	CCAAGTATATTAAGACAATCATAAAATGTACTTCTTGGAATATCAGGGGCTAATGCTTCTTTTA	8?:?<<<;<:@:@<<<7?8;<9&4?A<;<<79@<9@7>:@<;;<;'4?A<<9?;<<9@<+7AB<	0	
SRR000311.11802	+	NC_009749_frag	26054	CCAAGTATATTAAGACAATC	:@:@<<<<99@:@<<<:@;<	0	
SRR000311.13208	+	NC_009749_frag	26058	GTATATTAAGACAATCATAA	<<9<<:@8?<;<9?<<99:?	0	
SRR000311.6938	+	NC_009749_frag	26059	TATATTAAGACAATCATAAAA	<<<<:?:@<<<:@:<;9+7AC	0	
SRR000311.8899	+	NC_009749_frag	26059	TATATTAAGACAATCATAAAA	;9;;7>:@<<<:@;;<:*6@B	0	
SRR000311.2546	+	NC_009749_frag	26068	ACAATCATAAAATGTACTTCT	<<9@8<<:'4?A9;;<;7?<:	0	
SRR000311.12728	+	NC_009749_frag	26068	ACAATCATAAAATGTACTTCT	<;7>:<<8'5?A:;<<;:@<<	0	
SRR000311.6266	+	NC_009749_frag	26070	AATCATAAAATGTACTTCTT	9@5;<;*7@B<<:<;:@<;@	0	
SRR000311.11141	+	NC_009749_frag	26070	AATCATAAAATGTACTTCTT	6>9;;;#2>@:<<<<1:<9@	0	
SRR000311.6057	+	NC_009749_frag	26071	ATCATAAAATGTACTTCTTG	<:;<<$3>@<<;;<6=;:@:	0	
SRR000311.8264	+	NC_009749_frag	26072	TCATAAAATGTACTTCTTGGA	;:<;)6@B<<<;;9@<7>:@<	0	
SRR000311.1041	+	NC_009749_frag	26075	TAAAATGTACTTCTTGGAAT	<(5@B<<<<<:@<;@;@;@;	0	
SRR000311.6355	+	NC_009749_frag	26075	TAAAATGTACTTCTTGGAAT	<%3>A<<<<<8?<:@:@:@;	0	
SRR000311.1263	+	NC_009749_frag	26085	TTCTTGGAATATCAGGGGCT	7><:@;@9@<;;<<,7AB<<	0	
SRR000311.6044	+	NC_009749_frag	26091	GAATATCAGGGGCTAATGCT	;:@<<:;<+7@B<<:@<;<<	0	
SRR000311.6155	+	NC_009749_frag	26094	TATCAGGGGCTAATGCTTCT	;<<<;)6@B<<;@<;<:@<:	0	
SRR000311.11949	+	NC_009749_frag	26103	CTAATGCTTCTTTTATA	<<8?<;<9@<(5?A;<;	0	
SRR000311.2650	+	NC_009749_frag	26109	CTTCTTTTATATCTAATGT	@:@9+7AB;;79948<<3<	0	
SRR000311.6858	+	NC_009749_frag	26109	CTTCTTTTATATCTAATGTAC	@:?9(5?A<<<;<<:@:;<9:	0	
SRR000311.8838	+	NC_009749_frag	26113	TTTTATATCTAATGTACTTG	+7AB;<<<<<:@;<<<;;@:	0	
SRR000311.3000	+	NC_009749_frag	26114	TTTATATCTAATGTACTTGC	,=@<;<:<<:@<<<<<5=;9	0	
SRR000311.4566	+	NC_009749_frag	26114	TTTATATCTAATGTACTTGC	(;>;<<;8<6><;<<;0:;;	0	
SRR000311.7509	+	NC_009749_frag	26115	TTATATCTAATGTACTTGCAT	:@:<;;<<:@;<<<<8?<<<;	0	
SRR000311.10452	+	NC_009749_frag	26119	ATCTAATGTACTTGCATCTGG	<7;<:@<<<<<7>;<<;<<:@	0	
SRR000311.7465	+	NC_009749_frag	26120	TCTAATGTACTTGCATCTGGA	6;<:@<<<<<6><<9<9<;@<	0	
SRR000311.11034	+	NC_009749_frag	26120	TCTAATGTACTTGCATCTGG	;<;:@<<<<<6>;<<<<<0?	0	
SRR000311.6842	+	NC_009749_frag	26129	CTTGCATCTGGATGATCTATC	@9@<<5;<<8<;;7;;;29;:	0	
SRR000311.10509	+	NC_009749_frag	26129	CTTGCATCTGGATGATCTAT	?:@:<9;;;8<;<7:;799<	0	
SRR000311.13324	+	NC_009749_frag	26130	TTGCATCTGGATGATCTATCA	7><<<;;<;@<:<<<<;<;<;	0	
SRR000311.6702	+	NC_009749_frag	26132	GCATCTGGATGATCTATCAA	<;<;;<;@<<<<<<<;<<:@	0	
SRR000311.5344	+	NC_009749_frag	26137	TGGATGATCTATCAAATACT	<:@:;<:<<<<7<0?B<;<;	0	
SRR000311.11496	+	NC_009749_frag	26137	TGGATGATCTATCAAATACT	<:@9<<<;<;:<<0?B<8<<	0	
SRR000311.11560	+	NC_009749_frag	26137	TGGATGATCTATCAAATACT	<:@;<;;<<<<;<0?B<<<;	0	
SRR000311.12575	+	NC_009749_frag	26137	TGGATGATCTATCAAATACT	;7>;<<<;<<<;;.?A<<<<	0	
SRR000311.11959	+	NC_009749_frag	26143	ATCTATCAAATACTGTTCA	<;<<<8<<6=<9?9<9@;9,7AB<<9	0	
SRR000311.11982	+	NC_009749_frag	26155	CTGTTCAATCAATGTTTTAT	<9;6=<5=<;:@<:,7AB;<	0	
SRR000311.12932	+	NC_009749_frag	26156	TGTTCAATCAATGTTTTATC	<<9@<9@;<8?<<*6@B<<;	0	
SRR000311.2966	+	NC_009749_frag	26161	AATCAATGTTTTATCGGTAA	8?9<6>:<*6@B<<;8?;;@	0	
SRR000311.14148	+	NC_009749_frag	26161	AATCAATGTTTTATCGGTAA	/87:0:;<&4?A:;<:>;0:	0	
SRR000311.7581	+	NC_009749_frag	26163	TCAATGTTTTATCGGTAAAG	;<:@;;)5@B;<<9?@::	0	
SRR000311.3052	-	NC_009749_frag	15890	CGCTTTACCGATAAAACATT	;<9(;>:7><<<'5?A;:9?	0	19:A>C
SRR000311.5199	+	NC_009749_frag	26165	AATGTTTTATCGGTAAAGCT	:@<<*6@B7<;9@<1?B<<<	0	
SRR000311.8464	+	NC_009749_frag	26166	ATGTTTTATCGGTAAAGCTAG	<9<%3>@;<<8?;->A<<:;<	0	
SRR000311.7682	+	NC_009749_frag	26170	TTTATCGGTAAAGCTAGCGAC	1?A<;<:@A<;;<<<<<<<<7	0	
SRR000311.3887	+	NC_009749_frag	26174	TCGGTAAAGCTAGCGACTCT	<;;@:/?B;:<<<<<;<<;;	0	
SRR000311.7412	+	NC_009749_frag	26174	TCGGTAAAGCTAGCGACTCT	<:5=A<<;;<<<;<<<:<:	0	
SRR000311.14026	+	NC_009749_frag	26189	ACTCTGCCACAACCAACTCC	<<<;;<:@<<7>7>9@<;7>	0	
SRR000311.1554	+	NC_009749_frag	26191	TCTGCCACAACCAACTCCTT	<<;;:@<<:@9@;@<<:@;@	0	
SRR000311.5839	+	NC_009749_frag	26205	CTCCTTGCCTTGAACTATAA	@9:@:@<:@8?<9@<;<;:@	0	
SRR000311.8963	+	NC_009749_frag	26214	TTGAACTATAATCTCCGGTT	:@;9@<<<:;@;<<:@:@9@	0	
SRR000311.9994	+	NC_009749_frag	26214	TTGAACTATAATCTCCGGTT	:@::@:;<::@<<88?:@:@	0	
SRR000311.8615	+	NC_009749_frag	26216	GAACTATAATCTCCGGTTCTT	<9@9<:<:@<<:;@;@:@<9@	0	
SRR000311.12643	+	NC_009749_frag	26221	ATAATCTCCGGTTCTTTTATA	<88?:<;7>8?8?<$2>@<<<	0	
SRR000311.12307	+	NC_009749_frag	26223	AATCTCCGGTTCTTTTATAA	9@<<;8?:@:@;*6@B<;8?	0	
SRR000311.2442	+	NC_009749_frag	26226	CTCCGGTTCTTTTATAAAGC	>:7?8?6=;#2>@<:/?A<8	0	
SRR000311.13316	+	NC_009749_frag	26229	CGGTTCTTTTATAAAGCTCT	<;@:@<*6@B<;->A:9;<;	0	
SRR000311.5157	+	NC_009749_frag	26232	TTCTTTTATAAAGCTCTATC	.8<'4?A<40?B:7;<<<<:	0	
SRR000311.4080	+	NC_009749_frag	26241	AAAGCTCTATCCATGAAACAA	0?B<;<;<<9:@<<;/?B<:@	0	
SRR000311.4603	+	NC_009749_frag	26242	AAGCTCTATCCATGAAACAA	:?<<;:<;;9@<<<:<;	0	
SRR000311.1076	+	NC_009749_frag	26253	ATGAAACAACTGTACGCTTA	<<:.?A<:@;<<;<<;<9=9	0	
SRR000311.9764	+	NC_009749_frag	26253	ATGAAACAACTGTACGCTTAT	<<<0?B<:@;<<<<<:<:@;<	0	
SRR000311.3207	+	NC_009749_frag	26260	AACTGTACGCTTATCTATGTT	9@;;<<<<<<:@<:<;<<;:@	0	
SRR000311.10389	+	NC_009749_frag	26267	CGCTTATCTATGTTAAAAAA	<:<;@<<<<<<;8?$*18?A	0	
SRR000311.11190	-	NC_009749_frag	15788	GTTTTTAACATAGATAAGC	;(08?A:@<;<::<<;@<:	0	18:T>G
SRR000311.12309	+	NC_009749_frag	26269	CTTATCTATGTTAAAAAAC	;:@<;;;<<::@$*18?A<	0	
SRR000311.94	+	NC_009749_frag	26274	CTATGTTAAAAAACTTACTC	<<<<<:@"(08?A<9@<<;;	0	
SRR000311.6158	+	NC_009749_frag	26276	ATGTTAAAAAACTTACTCAGC	;<<;@$*18?A<:@<<8<<<<	0	
SRR000311.7025	+	NC_009749_frag	26280	TAAAAAACTTACTCAGCTCG	8$*18?A<;@;;<<<<<9<:	0	
SRR000311.1822	+	NC_009749_frag	26281	AAAAAACTTACTCAGCTCGA	"(08?A97?;<<;;;<<<<<	0	
SRR000311.9198	+	NC_009749_frag	26281	AAAAAACTTACTCAGCTCGA	")18?A;8?;<;<;<<<;<<	0	
SRR000311.8667	+	NC_009749_frag	26283	AAAACTTACTCAGCTCGAAC	$2>@;7>;85:;<<5;<:@;	0	
SRR000311.1608	+	NC_009749_frag	26284	AAACTTACTCAGCTCGAACT	1?B<:?<<9<<<<9<;:@;:	0	
SRR000311.5941	+	NC_009749_frag	26293	CAGCTCGAACTCCGTCATACC	<<:<;<<;@:;:@;6;<9<:@	0	
SRR000311.12711	+	NC_009749_frag	26293	CAGCTCGAACTCCGTCATACC	<<<<;<<;@<<:@<;<<<<;@	0	
SRR000311.6542	+	NC_009749_frag	26307	TCATACCTTCTTCATATTTA	7<:;;8?:@;7?:<<C
SRR000311.1382	-	NC_009749_frag	15733	AGACATCGTAATTAATAAAT	9<<<;<<<<9?:?9@:.>A;	0	13:T>C
SRR000311.13556	-	NC_009749_frag	15731	AGAGACATCGTAATTAATAAA	<<<;<<<9<;;:@:@;@<1?A	0	12:T>C
SRR000311.4740	-	NC_009749_frag	15731	AGAGACATCGTAATTAATAA	;<<;<;<<<<<:@7?:@<;@	0	11:T>C
SRR000311.12340	-	NC_009749_frag	15731	AGAGACATCGTAATTAATAA	<<<;<<<8<<<9@:@;@<;@	0	11:T>C
SRR000311.12836	-	NC_009749_frag	15726	ATTTTAGAGACATCGTAATTA	<&4?A:;<<<<<;<<<:@:@<	0	7:T>C
SRR000311.5705	+	NC_009749_frag	26336	ATGTCTCTAAAATCTTGGCT	<;<<<;<;)6@B<<;@9@<<	0	
SRR000311.6491	+	NC_009749_frag	26344	AAAATCTTGGCTATATGATGG	*6@B<<;@9@9<<:;;<;;1?	0	
SRR000311.11101	-	NC_009749_frag	15710	CCATCATATAGTCAAGATTTT	>A;;<;<<;<<<<:@<<+7@B	0	9:C>T
SRR000311.5	+	NC_009749_frag	26346	AATCTTGGCTATATGATGGC	:@<<:@8?:<<<;<<<;9@<	0	
SRR000311.11283	+	NC_009749_frag	26347	ATCTTGGCTATATGATGGCAT	<<;:@7?;<<<<<<<9:@<;<	0	
SRR000311.13731	+	NC_009749_frag	26347	ATCTTGGCTATATGATGGC	<<;;@8?<<;<;;<<<:@<	0	
SRR000311.6293	+	NC_009749_frag	26348	TCTTGGCTATATGATGGCATT	<<;@:@<<;<;<<<;:@<<:@	0	
SRR000311.9434	+	NC_009749_frag	26348	TCTTGGCTATATGATGGCAT	<88?9@<<<<<;;<<:@<<;	0	
SRR000311.10732	+	NC_009749_frag	26356	ATATGATGGCATTTTTATTAG	<9<<<<<8?;;(08@A<9><;	0	
SRR000311.12422	+	NC_009749_frag	26358	ATGATGGCATTTTTATTAGA	;<;<<:@:<&08@B<:@<<<	0	
SRR000311.6231	+	NC_009749_frag	26361	ATGGCATTTTTATTAGACATT	<<:@<9'08@B<:@<<<;<:@	0	
SRR000311.8152	+	NC_009749_frag	26365	CATTTTTATTAGACATTA	<<(08@A8:@<;<<<;@<	0	
SRR000311.8362	+	NC_009749_frag	26366	ATTTTTATTAGACATTATAA	:$/8@B<:@<<;<::@<9:@	0	
SRR000311.2648	+	NC_009749_frag	26371	TATTAGACATTATAACAT	<<:@<;<;<;@<;:@<<;	0	
SRR000311.1502	+	NC_009749_frag	26372	ATTAGACATTATAACATTTCT	;:@<;<<<:@<;:@<<,=@<<	0	
SRR000311.7739	+	NC_009749_frag	26379	ATTATAACATTTCTACAAAT	<;@<<8?<;*A<	0	
SRR000311.9097	+	NC_009749_frag	26380	TTATAACATTTCTACAAATAT	:@<<8?<:&:=;<;<,=@<;5	0	
SRR000311.13984	+	NC_009749_frag	26380	TTATAACATTTCTACAAATAT	:?<<:@<:.>A<<::.>A<;;	0	
SRR000311.4842	+	NC_009749_frag	26384	AACATTTCTACAAATATCTT	9@<<0?B<;<<.?A<:<<:@	0	
SRR000311.2	+	NC_009749_frag	26389	TTCTACAAATATCTTTCGGAT	:@<:<;->@;9<<)A;<<:->@<9@<<	0	
SRR000311.9268	+	NC_009749_frag	26393	ACAAATATCTTTCGGATTAAC	<<->@<;<;+A:<<<*A<:?<:@:@<<;<	0	
SRR000311.9009	+	NC_009749_frag	26397	ATATCTTTCGGATTAACTATA	<<;<<.>A<:@;;@9@<:<;:	0	
SRR000311.3654	+	NC_009749_frag	26398	TATCTTTCGGATTAACTATAT	<;9<6><:@:@6<;<<<	0	
SRR000311.8754	+	NC_009749_frag	26404	TCGGATTAACTATATCAATA	;<@:8@:@9<:9;:<:?7<;	0	16:T>A,19:G>A
SRR000311.7218	+	NC_009749_frag	26472	ATAAAATAAAGTAGTATTAA	<;:@<<7A?5(@:<@:<9	0	2:G>C,6:A>G
SRR000311.13203	+	NC_009749_frag	26704	CTCCTGGTTATTGCCTTATTTC	@;9@<;@:@;9@<:@:@A,10:C>T
SRR000311.3137	+	NC_009749_frag	26797	AAGATTCTTGAATTTGCTTT	9@<;9@<:@<9@/?B;<0?B	0	
SRR000311.10646	+	NC_009749_frag	26958	TGATCTATCTTACTATAACAC	;<;:<<;<<:@<<;<3:@<;:	0	
SRR000311.1371	+	NC_009749_frag	26972	ATAACACCGCTTTCCATTAAA	<<@;<;?8<<@>-?7;<3B?0	0	
SRR000311.12215	+	NC_009749_frag	27020	AAAATCATTTTCTATTAAC	'5?A:;8)6@B<:<;@9?:	0	
SRR000311.5233	+	NC_009749_frag	27066	AGTCCAGGGTAATCTTTTTG	<;97>:;3%<<<	0	
SRR000311.14100	+	NC_009749_frag	27112	GAAAATCATTTATGCCTTTTG	;B@5(<7;A>-<<<@:A?4&;	0	
SRR000311.9214	+	NC_009749_frag	27153	TTTTCATGCTTAGATAATAAT	@>3%<<<<<@;;;9:@:<@:<	0	
SRR000311.11164	+	NC_009749_frag	27156	TCATGCTTAGATAATAATAG	;<;<<;:@<<<;9@<9?<<7	0	
SRR000311.3401	+	NC_009749_frag	27166	ATAATAATAGAGATTTTGAA	<<9@<8?<<;<<<,7AB<:?	0	
SRR000311.4541	+	NC_009749_frag	27216	TGAGCATAGATAACTTCAGC	<:<;<<<;;:<7><9?<;<:	0	
SRR000311.3690	+	NC_009749_frag	27422	GGGAGTTTGATTCTTAGTTTGTTGGAAAACATTATTAACATAAGTCCACAAAGAA	A7+;3$<;@::@:@:;<;@:<<@9<6	0	
SRR000311.5854	+	NC_009749_frag	27430	GATTCTTAGTTTGTTGGAAA	;;@;<@::;A>.<@:?8@>1	0	
SRR000311.669	+	NC_009749_frag	27486	TTATTTCCTCCCCTTAGTAA	@:-@;<@>3%>6;<<>7	0	
SRR000311.9508	+	NC_009749_frag	27526	CTGCTTTAGTGATTGTTTTTT	?9:;0?B<<<<;8?:"(18?A	0	
SRR000311.7719	+	NC_009749_frag	27535	TGATTGTTTTTTTATATTGT	;:<;@:#',17>@;<<:@<<	0	
SRR000311.8365	+	NC_009749_frag	27578	TTCTAGTTCTCGGGACTTTTC	@:<;<<@:<<9@=,:;A?4&<	0	
SRR000311.12733	+	NC_009749_frag	27651	ATATAATCTTTTAATAGAGC	<<9<9@<<'4?A:@<<<<<:	0	
SRR000311.2423	+	NC_009749_frag	27764	AAAATCTTTTAAAAATCTTT	$2>@<;&4?A$/8@B<<.>A	0	10:C>A,16:T>C
SRR000311.8146	+	NC_009749_frag	27812	AGGTCAATACATGATACCAA	<9?9<:@<<<<<<;<<;@;@	0	16:T>C
SRR000311.155	+	NC_009749_frag	27900	TTTAGCTATAATAGATATATC	->A<;<:<<9@<;<<<<<<;:	0	
SRR000311.465	+	NC_009749_frag	28122	TCTAGTGAGACGTTTTATTTA	<;;<<<;<:<<<)6@B;.>A<	0	
SRR000311.5514	+	NC_009749_frag	28190	TGTTTATTTTTGAATTGATTT	<<0?B<&08@B<;@8?<<->A	0	
SRR000311.12733	+	NC_009749_frag	28332	TTAGGGTACCTTCCATAAAC	;@<*A;494<<;;;<;;	0	
SRR000311.11639	+	NC_009749_frag	28400	ATGATCCATTTAAGATTAGT	<<<:<@:;B?0@;<<@:9;<	0	
SRR000311.14100	+	NC_009749_frag	28516	TTTACGCGTGTCACCAAAT	A>.<<<<:<<;<;>6@>27	0	18:A>T
SRR000311.9214	+	NC_009749_frag	28538	GTATTAGGTAAGTTATAATAA	;7<@:9;;@;;<4	0	
SRR000311.2501	+	NC_009749_frag	28555	ATCATTTTTTATGCAATATT	;<;C,13:A>C
SRR000311.4948	+	NC_009749_frag	28595	GCTCCTCTAAAGACTGCCAT	6<;7><<<.>A<79;<:@;<	0	
SRR000311.3137	+	NC_009749_frag	28650	AAAGGCTAAAGTGTCGTAGTT	.>A6>;<,=@<<<<<<;<<:@	0	
SRR000311.6269	+	NC_009749_frag	28759	ATCATAAAAAGCTGTAGCAA	<8<<<&08@B<<:<<<<<:?	0	
SRR000311.14107	+	NC_009749_frag	28801	TACTAAAAACTCTTTAAAAT	<<9<$/8@B<<;1?A-7@B;	0	
SRR000311.4506	+	NC_009749_frag	28941	ATAGCCTATTATAGTAATTA	;:<<@:<<@93<<;@<9;;<:<$3>@<;:@.>A<:@<<:7<%+18?A8'08@B	0	
SRR000311.12122	+	NC_009749_frag	29090	ATATTTTATATGTACCTAAT	<<<%3>A<<<;<<<9?<:@<	0	
SRR000311.155	+	NC_009749_frag	29254	ATAATTAATAAGAATGATACA	<::@:@:@<9?;9@;<;<<<<	0	
SRR000311.8322	+	NC_009749_frag	29296	TAGTAATATTTAAATCTAAA	<<<<@:<;A>.A?/;<;@=,	0	
SRR000311.13203	+	NC_009749_frag	29307	AAATCTAAACCAGCAAAGGTT	->A9<A:->A;<<<<::@<;	0	5:A>G,10:T>C
SRR000311.4541	+	NC_009749_frag	29350	TTGAGATTGAGACTCTCGAT	:@<<<;:@;<<<<;;;<<<<	0	
SRR000311.12936	+	NC_009749_frag	29402	TCAATTACTTGTAGAGTCAG	;<@:@:<<@:;;<<;<<;;?	0	
SRR000311.12966	+	NC_009749_frag	29593	GAGAGTATTTTAGCTTTAAT	<<<;:<:A>3%<9.@:<	0	
SRR000311.3245	+	NC_009749_frag	29789	TAAAACTAATAAGTGTCGTT	:<@:;<<;;7<<:?79<;<<7<@:;	0	
SRR000311.13839	+	NC_009749_frag	29960	ATCAGATAACCAGCGAGTAG	<:<<<<<:@:@<;<<<<<<<	0	13:A>C
SRR000311.9739	+	NC_009749_frag	30004	CTATAGATGATGAAGGCAGT	<<<<<<<<<:;C
SRR000311.4292	+	NC_009749_frag	30072	TGGGTACATATCTCAGATCCT	<:@;.;;9<::@;	0	
SRR000311.3853	+	NC_009749_frag	30397	CTGATAAGCGTTTATCTAAA	:<<7<@9<<<@>-:<<;B?0	0	
SRR000311.1457	+	NC_009749_frag	30415	AAGGTGCAGTTGAGCTTGAT	:@:@<;:<<:@<:<<8?<;<	0	
SRR000311.10537	+	NC_009749_frag	30466	ATATAAATGGTAAATTAACT	<<<;+=@;3;<.>A9@4<;:	0	3:A>T,9:T>G
SRR000311.4948	+	NC_009749_frag	30525	ACAATGCTAATGGCTGGTGT	;<8?<<<<:@<5=7<:@<<<	0	
SRR000311.10594	+	NC_009749_frag	30531	CTAATGGCTGGTGTTGCAG	<<:@;8?9<9?9<:?<::;	0	
SRR000311.5294	+	NC_009749_frag	30539	TGGTGTTGCAGTAGGACAGT	<;@<<9@<;<<<<;@<<:<;	0	
SRR000311.13700	+	NC_009749_frag	31025	AAAACTTTCTGTCAGCGGTAA	%3>@;/?B;<<;;<<<;@;7?	0	
SRR000311.13886	+	NC_009749_frag	31036	TCAGCGGTAAGTATGATTT	<<<;<8?99@<<;<<<0?B	0	
BioPerl-1.007002/t/data/test.cns.fastq000444000766000024      1516613155576321 17522 0ustar00cjfieldsstaff000000000000@gi|65306796|gb|AY948116.1|
nnnnnnnnnnaacaccaaaaaaggAAAAATTTAAAAatgcaaaaaccaatATCCcgaagt
gcATAGCTTAGAAGAAAGCCTTGCAATaCttaaaaaaatataaaGATGATGTAAATAAGG
AaagaTTATGAAGGTATAAAATCTGTTATAAGTAATCATGCGATAGAGAGTATTTACATG
AATGAATTAGATATTATCGCTATGATAAAACAAAGTGCTTTAAAGTTAAGTGCtgaTGAA
ATCATTGCTGAATATAAGGAAAAGGGATTTgTAGAATAtgtcaaAAGTTGCCACCGCTCA
TTGCAATCCtaaAaaacaaccTGCATTAAACCACAATGATAGAACCAACGATAATGCTAA
GACAATCACTAAAGAACTTACGCATTTAAATGAATACtcttgcactagcgatgaagtgcg
TAAGAACATAGAAAGGCTTTATAAAAAAGCTTAtgaaaaTTTTTATAAATATTGTGAAAA
TAAGAATGGTTTAgctaaaaGtggAAagCCTAAAGGACTTCAAAATTTTACTAAAAAAGA
AAAATGTTATCACGAgtttatatacGAAATCGGCGAAAATACTACAATGGAGCAATGCCA
AGAGCTTACGCAAAAAATCGCAGAGCTTacaggaTTTACACCTTTACAAGTTGTAATCCA
TAGAGATGAAGTAAGTGAGaaTGctaaaggggaaaaacaaaccCATtatCACGCCCACGC
GGTATTTTTTACACTCGataacaatnncttacaacttgctagACGTGAAGCAAGTTTGAA
TAAAGCCAATCTTAGCAAAATACAAACCCTAACCGCACAAAGTTTAAAAATGGAGCGTGG
AGCTAATcgctACGAGAATAACGAAAAGCAACCTCAATACATACAAGATTATAAAACATA
CGCTCAAtttWaagaacaagaaaaagcattacttcaaagaataCAAGAACAAGAGCATAA
ATTAACGCaaatggccctannnntgaaaaaaAAAGAAAAAGAGATACAAGACAAGGCTAA
AGAGTTAAAATCGAAAGAAAAcgaattacaagcgaaaatagagcaacatcnnnnncatat
acaaAATTTAGAACTAGGACacGAAAGAGCTTtaaaggaacttacacaagagtTTGAAAA
GCGTTTAAGCCTATGGAAAAACATTTTAACCTTTGGAAAATACAACGCCAAAGTAagaGA
AGACtatcagttaacaaagaatgnnnttttaattagcacagATGAAAGCAGgagagAAGC
TAACAAagaGCTTGAATATTTAAAATTTGAATATCATAAAGTCAAAGATGAACGAGATAA
TTTAAAAACTTTGTTTGAGGCACACAAAACAAAAAATGTTAAATTAGAAACTCGACTAAA
AGAAATAGGCAaatggtgtgannnnnntttaagcgtGGAGCAGTTAAAAGAAATATTTCC
ATTAAaagccgAAAGAATAgaaaAAGAGCTTAAATATCAAAGAGCTTTTGAAAATTCTTT
TGAACAAGCAAAaagAAACGATAgagggTTTGGGTTTAGCAGATAGTTTTCTTTTTTGGT
GCttTAGCAAATCgcacctgttAAGGTGCtatgatttgcgaaaaGGGggTGCGGGGGCTG
TCTGAGtgCgtagcacggaAGACGGACAAAGCCCACCGCCCTAGAAAAAAAATTACTCAA
CTTTTTTTGTTTTTTCTCTCGCGCGCGTACGCGTACGCGATTTTTTTTATTTTTTATATA
TTTTTCTTATTTTTagggggctttctaagcCCtatatgATGGGGGCTAGCGAAATATTAA
AACGACAaAATTctactattaaaacgacaaaattctactattaaaacgacaaaattctac
tattaaaacgacAAAATTCTACTATTAAGGGGAGAAAATtctactattaaaacgacaaaa
tatttgacaaatattgttttaatatactacaataaaaAATCCGCCTTGAGTTTTCACTCT
TGGCGGAAaTTTAtcaaTCAAGGctaactatgaaacgacatannnngcgtttTGTGAGAT
TATACCTAAAATTTAGGTTTTTTAAGCTTAaagttgaagtatttnnnnnncaaaaccgca
ggggCAGAGAAGCCCCTTGCCTTGATTGTCTTACTTTGGATATGCAAATGAGCGAAATAG
TTAAATATAATAATGATTTTAATCTTTTACCTATGCCTGAACTTAAAGCCATACAAATGG
ATatgTTTATGGCTATTATCTCACTAACCAAAGACAAAAAAGAAAATACGCCATttttaa
aaaagttttttaaccctgatagaagaaaaataatTATTCCGCAAAAGAAGTTTATTGAAT
TATGTcggttaaaCgatagtaaaatggACTATAAAGAAATTTTCTTTGCCATTGATGATT
GCttgaaAAAACTTTGCAATTTTCTTATTTCATACCAAAAAGATGAAAGAACGATTTATA
attttgtttgTTTTGAAGAAGCAAATATTATTGCTGATGAagtgcatataactttacaaa
gtcgtntttacgatatgataaTAAATAAAAAATTTGGTTTCACAGCctttgaattagccg
AATTTGcAGAACTTAGCGGTAAATATACAAAAACTTTATaCAGACTTTTAAAGCAATTTA
GAACCACAGGCAAAGCTTATTTTGAGTGGGAAGAATTTTGCaggattatgaaaatacctg
annnnnnnnnnnaaatagatatagaccaAAGAATTTTAAAACCTGCTATCAAAGAACTTT
CTAAAGaacgctATCTTTTTGACCAAATCAGAGTGCCTTTTAAAAATCTTGCTTATGAAA
AAGAAAAAACcgcagggcnnnnncgtggcggtaAAGTTTCAGGTATTAGCTTTACTTTTa
AACCTGAAAATATCCAAATGCAAAAGCTAGAAAATGAAAGTCAAAAAATAATGAGCGATG
AGCAAaaaTATTTAAAGATTTTAAAcaatatGAAACTTAATCaagttagatttGATtata
atgacaagctttGGCAATttaaCGATTttgATTTTGATGAATTTAAAATTATTGCAATAG
AGCTTGTAAGAGATGAATACGAGAATTTAAACTTTGGAAATCATATGCACTTTAATGCta
aAAATCAagagcaGTTTTTTAAAATGATTGAAACCTTTAGAAAaggtattaggtaaaaat
ttgctataattaTatctttaaaggatacaagctatcCgCCACTTGTGCCAAGTGTCGAGC
TTGTAAGGGGTGCAACcccttaaccccactaataaaaatcaactAAAATCAATAAATGAT
TTttttgatttttnnn
+
!!!!!!!!!!?BBBBBBBBBBBBBEEEEEHHHHHHEBBBBBBBBBBBBB?EEEEBBBBBB
BBEEHHHHHKKKKKKEEEEEEEEEEEEBEBBBBB??BBBBBBBBEHHHHHHHHEEEEEEE
EBBBBEEEEEEEEEEEEHHHHHHKKKKKKNKKQTQNNNNNNQNNNQQTQQTTTTQQQKHH
HHHHHHHKNQNNKKKHHHKKNNNQQQQQTTTQNKHHHHHHHHHEEEHHEEEEEBBBEEEK
NNNNQWWWWWTQQTTTTWWWWTTTNKKKKHBEEEEEEEBBBBBBHHHHNNNNNNNNKKKK
KKKKKKKHHBBBE??????BBEEEHHKKKKKKKKKKKHKKKKKKHKKKKHHHHHHHKKKK
KKKHHHHKKKHEHHHHEEEHHEEHHHHHHHHHEEEEEBBBBBBB??????????????BB
EEEEEEEEKKKKKHHHHKKKKKKHHEHHHHHHHBBBBBBEEEEEEEHHKKKHHHHHKKKK
KNNNKKKHHHHEEBBBBBBBEBBBEEBBEHHKKKNNNNNNNNNNNKNNNNQQQNKKHHHE
EEEEEEHHKKKHHHEBBBBBBBBBBEEEHHHEHHHKKKKKKKKKKKKKKKHHHEHHHEHH
EEEHHHHHHHHHHHHHHHNKKKKEEEEEBBBBBBEEKKKKKKKHHHHNNTWZZZ]]]]`]
]WWWWZZZWWWWQQKHEEEBBEEBBBBBBB????????????BEEEBBBEEHKKKKKKNN
QQQQQQQNKKKKKKHHEBBBBBB??!!BBBBBBBBBBBBBBBEHHKNNNNNNKNNNNNNN
QQQQQQQNKNKKKKKKKHEEEEHHHHHHHKKKKNKKHHHHHHKKKKKHKKHKKKHHHHEE
EEEEEEEBBBBEHEHHHHHHHHHHHKKKKKKNNQQQNKKHHEEEEEEKNNKKKKKKHHEE
EEEEEEHHHK-KEBBBBBBBBBBBBBBBBBBBBB?????BBBBEEEHHHHHHHHKKHHHH
HHHHEEEEBBB????????!!!!??BBBBBBHHKKKKKKKNQQQQQQQQQNNQQQQNNKK
NNNNNNKKKKKKKHHHHEEEEBBBBBBBBB????????????????????!!!!!BBBBB
BBBBEEEHHHHHHHHHHHHHBBEEHHHHHEEEBBBBBBBBBBBBBBB??BBBBEEENNNN
NNNNNNNQQTTTWWQQQQNNNEEHHHHHHKNNKKHHHEEHHHHHHHHHEEHHHHEBBBEE
EEEEBBBBBBBBBBB????????!!!BBBBBBBBBBBBBBBEEEEEEEEEE????BEEEE
EEEEEEBBBEHHKKKKKKKKHKQQQTTWWZZZZZZWWTWWWZZ]``]WWWTTQQNNNNNQ
QQQNNQNNKHHEEEEEEEEEHHHHHHHHHHEEEEEEHHHHKKKKKHKKKEEEEEEHKKKK
KHHHHEEEEEEBBBBBBBBB?!!!!!!?BBBBBBBBEEEHKKKKKKKKKKKKHEHHHHHH
HEEEEBBBBBBEEEEEEEEBBBBEEEEEEEHHKKKKHHKKKNNNNNNQNNQQQQNKKHKK
KKKHHHEEEEEEBBBEEEEEEEEBBBBBEEEEEHHKKNNNHHKKKKKKNNNNNKKKKKHH
EEBBEHHEEEEEEBBBBBBBBBEEEEEEEB???????????BBBEEEBBEEEEEEEEEEE
EEEEEEBBEBBBBB??BBBEEEEEHHHHHHHHHHHHKNNNNKKKHKKKKHKKKKKKKKHH
HEHHHKKKNNNNNNNNNNNNNNNQQQTNNNKNNNQNNNNNKKKKKKQQNQQNNNNNKKHE
HHHHHHHKKKKEEEBBBBBBBBBBB???BBEEBBBBBBEEEEHHHHHHHHKKKHHEEHHH
HHHEEEEBEEHKKKK///////,,/////111111/,,,,,,,,,,///+++++((((%(
(((((((((EHEEHKKKNNNNNNNKKKKKKNNNNKHHHEBBB??????????BBB?????
??????????????BBB???????????BBBBBBBBBHNKKKKNNNNNQQQQQNNNNNQQ
QQKEEEEEBEEEEBBBBEEEEEEBBBBBBBBBBB????????!!!!??????EEEEHHHH
HHHHHKKKKKNKKKKKKEEHHEEEEEEEEEBBBBB?????????!!!!!!??????BBBB
BBBBEHKKKKNNNQQNNNNNNKKKKKKQTQNKKKNKKKHHHHHKKKNNNNNNHEEEHHHE
EEEEEEHKHHHEEEEEHHHHHHHHHHHHKKKHEEEEHNNNNKKKKKHHHHHHHEHHHHHH
HHBBBEEEEEEHHHHNNNNKKNNNNNNQQWTWWWWWTTTTNNNNNNKKKKKKHHBB????
?????????????BBB????????????????BBEHHHHHKKKKKKKKKNNNNNNQQNNK
HHHEEBBBBBBBBEBBBBBB????BBBEEEEHHKKKNQNQQQQQQQQQQNNNKKKKHKHH
HEBB???HHHHHHHHHHHHHHHEEEEEEEHHKEEEHHHHHKKKKKKKKKKKKKKKKHEEE
BBBBB???BBEEHKKQQQQNNNNNNNNNQQQQQNNKKHEEBBBBBBBBBBBBB???????
?????!????????????BBBEHHHHHHHHHEEEEEEEEEEHHEEEB?????????BBBB
EEEEEEBEHKKKKKQQQQQQQNNNNKKKKKKKHEEHHHHBEHNNNNNQQQQQQQQQQQTQ
NNQQTQQKKKKKHHKKNNNNNNNKKKKHHEHEEEEEHHHEEBBBBBBBBBBBBBB?????
?!!!!!!!!!!!???????????????BEEEEEHHHHHHHHNQQQQQQQQQQQNNNNNKK
KKHHHHB????BEHHHHEEEEEEEEHHHKKKKNQQQNKHHHHHNNQQQTTQQQQQQQNKK
KKKKKKKKEEBBB?????!!!!!???BBBBBBBEHHHHHHHHHHKKKKHHHEEEEEEHEB
EEEEEHHHKKKKKKKKKKKKKKHNNKKKKKKKNKKNNNNQWWWWWWWWQQQQQQQNNNNK
KKKKHBBBEEEEEEEEEHHHHHEEEBBBBBBEHEEEEEEEEEBBBBBBBBBBBEEEB???
??BBBBBBBBBBEEEEEEBBBBEEEEEBBBEEHHHHHEEEEHHHKKKKKKKKKKKHHEEE
EEHKKKHKKHKKKKKKNTTTWWWWWWWTQQQQQTTQQNNNNKHHHEEEEEEEEEEHHEBB
BEEEEEEBBBBBBEEEEEHHEEEHHHHHHHHHHHHHHHEEEEEBBBBBBBB?????????
????????????EBBBBBBBBBBBBBBBBBBBBBBBEBEEEEEEEEEEEHHKKKNNNNNN
NKHEEEEEEHHHHHEEBBB??????BBBBBBBBB???BBBBBBBEEEEHHEEEEEEEEEE
EEBBBBBBB????!!!
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SPAC= 12.74
PRIM=1523
MACH=377-96 
DYEP=DT {BD Set Any-Primer}
NAME=IIABP1D4373
LANE=50
GELN=Gel File
PROC=
RTRK=
CONV=phred version=0.990722.h
COMM=

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			ýãçýãBioPerl-1.007002/t/data/test.embl000444000766000024      3241013155576321 16530 0ustar00cjfieldsstaff000000000000ID   SC10H5 standard; DNA; PRO; 4870 BP.
XX
AC   AL031232;
XX
DE   Streptomyces coelicolor cosmid 10H5.
XX
KW   integral membrane protein.
XX
OS   Streptomyces coelicolor
OC   Eubacteria; Firmicutes; Actinomycetes; Streptomycetes;
OC   Streptomycetaceae; Streptomyces.
XX
RN   [1]
RP   1-4870
RA   Oliver K., Harris D.;
RT   ;
RL   Unpublished.
XX
RN   [2]
RP   1-4870
RA   Parkhill J., Barrell B.G., Rajandream M.A.;
RT   ;
RL   Submitted (10-AUG-1998) to the EMBL/GenBank/DDBJ databases.
RL   Streptomyces coelicolor sequencing project,
RL   Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA
RL   E-mail: barrell@sanger.ac.uk
RL   Cosmids supplied by Prof. David A. Hopwood, [3]
RL   John Innes Centre, Norwich Research Park, Colney,
RL   Norwich, Norfolk NR4 7UH, UK.
XX
RN   [3]
RP   1-4870
RA   Redenbach M., Kieser H.M., Denapaite D., Eichner A.,
RA   Cullum J., Kinashi H., Hopwood D.A.;
RT   "A set of ordered cosmids and a detailed genetic and physical
RT   map for the 8 Mb Streptomyces coelicolor A3(2) chromosome.";
RL   Mol. Microbiol. 21(1):77-96(1996).
XX
CC   Notes:
CC
CC   Streptomyces coelicolor sequencing at The Sanger Centre is funded 
CC   by the BBSRC.
CC
CC   Details of S. coelicolor sequencing at the Sanger Centre 
CC   are available on the World Wide Web. 
CC   (URL; http://www.sanger.ac.uk/Projects/S_coelicolor/)
CC
CC   CDS are numbered using the following system eg SC7B7.01c. 
CC   SC (S. coelicolor), 7B7 (cosmid name), .01 (first CDS), 
CC   c (complementary strand).
CC
CC   The more significant matches with motifs in the PROSITE
CC   database are also included but some of these may be fortuitous.
CC
CC   The length in codons is given for each CDS.
CC
CC   Usually the highest scoring match found by fasta -o is given for
CC   CDS which show significant similarity to other CDS in the database.
CC   The position of possible ribosome binding site sequences are
CC   given where these have been used to deduce the initiation codon.
CC   
CC   Gene prediction is based on positional base preference in codons 
CC   using a specially developed Hidden Markov Model (Krogh et al., 
CC   Nucleic Acids Research, 22(22):4768-4778(1994)) and the FramePlot 
CC   program of Bibb et al., Gene 30:157-66(1984) as implemented at 
CC   http://www.nih.go.jp/~jun/cgi-bin/frameplot.pl. CAUTION:  We may  
CC   not have predicted the correct initiation codon.  Where possible 
CC   we choose an initiation codon (atg, gtg, ttg or (att)) which is 
CC   preceded by an upstream ribosome binding site sequence (optimally 
CC   5-13bp before the initiation codon).  If this cannot be identified
CC   we choose the most upstream initiation codon.
CC     
CC   IMPORTANT: This sequence MAY NOT be the entire insert of
CC   the sequenced clone.  It may be shorter because we only
CC   sequence overlapping sections once, or longer, because we
CC   arrange for a small overlap between neighbouring submissions.
CC
CC   Cosmid 10H5 lies to the right of 3A7 on the AseI-B genomic restriction 
CC   fragment.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..4870
FT                   /organism="Streptomyces coelicolor"
FT                   /strain="A3(2)"
FT                   /clone="cosmid 10H5"
FT   CDS             complement(<1..327)
FT                   /note="SC10H5.01c, unknown, partial CDS, len >109 aa;
FT                   possible integral membrane protein"
FT                   /gene="SC10H5.01c"
FT                   /product="hypothetical protein SC10H5.01c"
FT   CDS             complement(350..805)
FT                   /note="SC10H5.02c, probable integral membrane protein, len:
FT                   151 aa; similar to S. coelicolor hypothetical protein
FT                   TR:O54194 (EMBL:AL021411) SC7H1.35 (155 aa), fasta scores;
FT                   opt: 431 z-score: 749.8 E(): 0, 53.5% identity in 114 aa
FT                   overlap."
FT                   /product="putative integral membrane protein"
FT                   /gene="SC10H5.02c"
FT   RBS             complement(812..815)
FT                   /note="possible RBS upstream of SC10H5.02c"
FT   CDS             complement(837..1301)
FT                   /note="SC10H5.03c, probable integral membrane protein, len:
FT                   154 aa"
FT                   /product="putative integral membrane protein"
FT                   /gene="SC10H5.03c"
FT   RBS             complement(1308..1312)
FT                   /note="possible RBS upstream of SC10H5.03c"
FT   CDS             complement(1427..1735)
FT                   /note="SC10H5.04c, unknown, len: 103 aa; possible membrane"
FT                   /gene="SC10H5.04c"
FT                   /product="hypothetical protein SC10H5.04c"
FT   RBS             complement(1738..1741)
FT                   /note="possible RBS upstream of SC10H5.05c"
FT   misc_feature    1800^1801
FT                   /note="Zero-length feature added to test Bioperl parsing"
FT   CDS             1933..2022
FT                   /note="SC10H5.05, questionable ORF, len: 29 aa"
FT                   /gene="SC10H5.05"
FT                   /product="hypothetical protein SC10H5.05"
FT   CDS             2019..2642
FT                   /note="SC10H5.06, probable membrane protein, len: 207 aa;
FT                   similar to S. coelicolor TR:O54192 SC7H1.33c (191 aa),
FT                   fasta scores; opt: 312 z-score: 355.2 E(): 1.6e-12, 36.8%
FT                   identity in 182 aa overlap"
FT                   /product="putative membrane protein"
FT                   /gene="SC10H5.06"
FT   RBS             2627..2631
FT                   /note="possible RBS upstream of SC10H5.07"
FT   CDS             2639..4048
FT                   /note="SC10H5.07, unknown, len: 469 aa"
FT                   /gene="SC10H5.07"
FT                   /product="hypothetical protein SC10H5.07"
FT   CDS             complement(4100..4297)
FT                   /note="SC10H5.08c, unknown, len: 65 aa"
FT                   /gene="SC10H5.08c"
FT                   /product="hypothetical protein SC10H5.08c"
FT   RBS             complement(4314..4319)
FT                   /note="possible RBS upstream of SC10H5.08c"
FT   CDS             complement(4439..>4870)
FT                   /note="SC10H5.09c, probable integral membrane protein,
FT                   partial CDS len: >143 aa; some similarity in C-terminus to
FT                   S. coelicolor hypothetical protein TR:O54106
FT                   (EMBL:AL021529) SC10A5.15 (114 aa), fasta scores; opt: 145
FT                   z-score: 233.8 E(): 9.2e-06, 33.3% identity in 81 aa
FT                   overlap. Overlaps and extends SC3A7.01c"
FT                   /product="putative integral membrane protein"
FT                   /gene="SC10H5.09c"
FT   misc_feature    4769..4870
FT                   /note="overlap with cosmid 3A7 from 1 to 102"
XX
SQ   Sequence 4870 BP; 769 A; 1717 C; 1693 G; 691 T; 0 other;
     gatcagtaga cccagcgaca gcagggcggg gcccagcagg ccggccgtgg cgtagagcgc        60
     gaggacggcg accggcgtgg ccaccgacag gatggctgcg gcgacgcgga cgacaccgga       120
     gtgtgccagg gcccaccaca cgccgatggc cgcgagcgcg agtcccgcgc tgccgaacag       180
     ggcccacagc acactgcgca gaccggcggc cacgagtggc gccaggacgg tgcccagcag       240
     gagcagcagg gtgacgtggg cgcgcgctgc actgtggccg ccccgtccgc ccgacgcgcg       300
     cggctcgtca tctcgcggtc ccaccaccgg tcggccccat tactcgtcct caaccctgtg       360
     gcgactgacg ttccccggac aggtcgtacc gattgccgcc acgccccacc acgcacaggg       420
     cccagacgac gaagcctgac atggtgatca tgacgacgga ccacaccggg tagtacggca       480
     gcgagaggaa gttggcgatg atcaccagcc cggcgatggc gaccccggtg acacgtgccc       540
     acatcgccgt tttgagcagc ccggcgctga cgaccatggc gagcgcgccg agcgcgagat       600
     ggatccaccc ccacccggtg agatcgaact ggaaaacgta gttgggcgtg gtgacgaaga       660
     cgtcgtcctc ggcgatggcc atgatgcccc ggaagaggct gagcagcccg gcgaggaaga       720
     gcatcaccgc cgcgaaggcg gtaaggcccg tcgcccattc ctgcctcgcg gtgtgtgccg       780
     ggtggtgggt atgtgacgtg gtcatctcgg acctcgtttc gtggaatgcg gatgcttcag       840
     cgagcggagg cgccggtgcc cgccgcgccc gtgtgccctg ccgggccgtg accggacagg       900
     accaattcct tcgccttgcg gaactcctcg tccgtgatgg caccccggtc tcggatctcg       960
     gagagccggg ccagctcgtc gacgctgctg gacccgccgc ccacggtctt cctgatgtag      1020
     gcgtcgaact cctcctgctg agcccgtgcc cgcgttgtct cccggctgcc catgttcttg      1080
     ccgcgagcga tcacgtagac gaaaacgccc aggaagggca ggaggatgca gaacaccaac      1140
     cagccggcct tcgcccagcc actcagtccg tcgtcccgga agatgtcggt gacgacgcgg      1200
     aagagcagga cgaaccacat gatccacagg aagatcatca gcatcgtcca gaaggcaccc      1260
     agcagtgggt agtcgtacgc caggtaggtc tgtgcactca tgtccgtcct ccgtcctccg      1320
     gggcgcggcc cggcggccct cgttccgtac tgacatcagg gtggtcacgg gtcccaccgg      1380
     tcggcatcac ccggcacggg tgagtggggc gccgaggccg tcgtggtcag gcccgggaca      1440
     ccggtgtgac cctggtggaa ggacgcgtcc cgtggggcac gcaccgccgg ccgagggcga      1500
     ccaccgcctc ggtcagtccg agcaggccca gccacaggcc gagaagtcgg gtcagggcac      1560
     gggccgactc ggcgggcagc gcgaggacga cgattccggc gacgtcgacg gccagcgggt      1620
     tgcgcaggcc cagcactccg gccggggcgc ccggcaccag cgtggcgagg gccgatgcca      1680
     tgagccaggt ccaggaaccc ccaagcctgg cgaggacgtg cgccggatcg ctcaatgctc      1740
     cggtgaccgc cccgcccgac ccgtctccct tgtcggcagg ttccgccgca tcacgcggaa      1800
     cggagatggc tcccctgtgg atcgggcggc cgctgcgggg ccgcccggtt ggtcggtcgg      1860
     tgagcgccgg actccccctt cagctcttcc agggtcgggg tcgacaccga ggtcctggat      1920
     cacccgtcag gggtgatccg ggcatgccgt cgtggcggtg aggtgggata cgggaacgat      1980
     cggcccacgg gggaccggac gagacgaaga gacgtgagat gagcgatacg aactcgggcg      2040
     gcgggcgcca ggccgcttcc ggaccggccc cacgtggccg actccctttc cgccggcgcg      2100
     tggccctggt cgctgtcgca cgtcccctga tcgtcacggt cggtctcgtc accgcctact      2160
     acctgcttcc cctggacgag agactcagcg ccggcaccct ggtgtcgctg gtgtgcggac      2220
     tgctcgcagt ccttctggtg ttctgctggg aggtgcgggc catcacgcgc tccccgcatc      2280
     cgcgtctgag agcgatcgag ggcctggccg ccacgctggt gctgttcctg gtcctcttcg      2340
     ccggctccta ctacctgctg ggtcgctccg cgcccggctc cttcagcgag ccgctgaaca      2400
     ggacggacgc gctgtacttc actctgacca cgttcgccac cgtcggcttc ggggacatca      2460
     ccgcacgctc cgagaccggg cggatcctca cgatggcgca gatgacggga gggctactgc      2520
     tcgtcggagt cgccgcccgg gtgctggcga gcgcagtgca ggcggggctg caccgacagg      2580
     gccggggacc ggcggcatcg ccacgctccg gtgctgcgga ggagccggag gccggaccat      2640
     gaccgtaccc ggtggcttca ccgcctccct gccgccggcc gagcgagccg cgtacggcag      2700
     gaaggcccgt aaaagggcct cacgttcgtg ccacggctgg tacgagccgg ggcagcggcg      2760
     gcctgacccc gtcgacctgc tggagcgcca gtccggcgag cgtgtcccgg cactcgtgcc      2820
     catccgctac ggtcgcatgc tggagtcgcc gttccgcttc taccgcggtg cggcagcgat      2880
     catggcggcg gacctggcac ccctgcccag cagcggactc caggtgcaat tgtgcgggga      2940
     cgcgcacccg ttgaacttcc ggctcctggc ctcaccggag cgccggctgg tcttcgacat      3000
     caacgacttc gacgagacgc tgcccggccc cttcgagtgg gacgtcaaac ggctggcggc      3060
     cggattcgtg atcgcggccc ggtcgaacgg cttctcgtcc aaggaacaga accgcaccgt      3120
     tcgggcctgt gtgcgggcct accgggagcg catgagggag ttcgccgtca tgccgaccct      3180
     ggacatctgg tacgcccagg acgacgccga ccacgtacgg caactgctgg ctacggaggc      3240
     cagaggagaa gctgagcagc ggctcaggga cgcggctgcg aaggcccgca cacgcaccca      3300
     catgagggcg ttcgcgaagc tcacccgcgt cacggccgag ggccggcgca tcacccccga      3360
     cccgccgctg atcaccccac tcggcgatct gctcaccgac ccggccgaag ccggccggga      3420
     ggaggaactg cggtccgtcg tgaacggcta cgcacggtcc ctgccgcccg agcgccggca      3480
     cctgctgcgt cactaccggc ttgtggacat ggcgcgcaag gtggtcggcg tcggcagtgt      3540
     cggcacccgc tgctgggtac tgcttctgct cggcagggac gacgacgatc ctctgctgct      3600
     ccaggccaag gaagcctcgg aatcggtgct ggcggcccac acgggcggcg aacgctacga      3660
     ccatcagggc cgcagggtcg tggccggcca gcgtctgatc cagaccaccg gtgacatctt      3720
     tctcggctgg gcgcgcgtca ccggcttcga cggaaaggcc cgggacttct acgtgcgtca      3780
     actgtgggac tggaagggcg tcgcgcggcc ggaaaccatg gggcccgacc tgctctccct      3840
     cttcgcccgg ctgtgcggtg cctgcctggc gagggcccac gcccgttccg gtgaccccgt      3900
     cgcgctcgcc gcgtacctgg gcggcagcga ccgcttcgac ggcgcgctca ccgagttcgc      3960
     ccagtcctac gccgatcaga atgaacgcga ccacgaagct ctgctggcgg cctgccgctc      4020
     cggcagggtc acggccgccc gtttgtgagg ccgacccggg aacggccggc gggctggcac      4080
     acaccgccgc cggtcggcgt cattccggaa gctgccgcat ctccaggacg cgcaggccca      4140
     gcgactggca gcgggtgagc aacccgtaca gatgggcctc gtcgatcacc gtgccgaaca      4200
     gcacggtctg gccggacatg acgacgtgct ccagctccgg gaacgcgttg gccagcgtcc      4260
     gtgacaggtg tccctcgacg cggatctcgt agcgcacgag cggtcctttc accgtaggag      4320
     ctcgggacac cgcccggggc tccgggtcgg acggtgctct tggtgacgag cctgcgcctc      4380
     gtcgccctcc ggtgccctca cccagcacag gtgactccaa ccgcagtgtc agtgcctttc      4440
     agtgcgtcac tgtgatcttg acgacgacga tcaccaggcc gagcagtacg ttgaccgtcg      4500
     cggtgacggc caccagtcgt cgcgaggcgc ccgcgcggtg cgccgcggcg acggaccagc      4560
     ccacctgacc ggcgacggcg acggacagcg ccagccacag ggtgcccggg acgtccagcc      4620
     ccagtacggg gctgacggcg atggccgcgg ccggaggcac ggcggccttg acgatcggcc      4680
     actcctcgcg gcacacacgc agaatcaccc gccggtccgg agtgtgccgc gcgagacgcg      4740
     ctccgaacag ttcggcgtgg acgtgagcga tccagaacac caagctggtg agcaacagca      4800
     gaagaaccag ttcggcgcgg gggaacgagc ccagggtgcc ggcgccgatc acgacggagg      4860
     ctgcgagcat                                                             4870
//
BioPerl-1.007002/t/data/test.embl2sq000444000766000024      3241713155576321 17165 0ustar00cjfieldsstaff000000000000ID   SC10H5 standard; DNA; PRO; 4870 BP.
XX
AC   AL031232;
XX
DE   Streptomyces coelicolor cosmid 10H5.
XX
KW   integral membrane protein.
XX
OS   Streptomyces coelicolor
OC   Eubacteria; Firmicutes; Actinomycetes; Streptomycetes;
OC   Streptomycetaceae; Streptomyces.
XX
RN   [1]
RP   1-4870
RA   Oliver K., Harris D.;
RT   ;
RL   Unpublished.
XX
RN   [2]
RP   1-4870
RA   Parkhill J., Barrell B.G., Rajandream M.A.;
RT   ;
RL   Submitted (10-AUG-1998) to the EMBL/GenBank/DDBJ databases.
RL   Streptomyces coelicolor sequencing project,
RL   Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA
RL   E-mail: barrell@sanger.ac.uk
RL   Cosmids supplied by Prof. David A. Hopwood, [3]
RL   John Innes Centre, Norwich Research Park, Colney,
RL   Norwich, Norfolk NR4 7UH, UK.
XX
RN   [3]
RP   1-4870
RA   Redenbach M., Kieser H.M., Denapaite D., Eichner A.,
RA   Cullum J., Kinashi H., Hopwood D.A.;
RT   "A set of ordered cosmids and a detailed genetic and physical
RT   map for the 8 Mb Streptomyces coelicolor A3(2) chromosome.";
RL   Mol. Microbiol. 21(1):77-96(1996).
XX
CC   Notes:
CC
CC   Streptomyces coelicolor sequencing at The Sanger Centre is funded 
CC   by the BBSRC.
CC
CC   Details of S. coelicolor sequencing at the Sanger Centre 
CC   are available on the World Wide Web. 
CC   (URL; http://www.sanger.ac.uk/Projects/S_coelicolor/)
CC
CC   CDS are numbered using the following system eg SC7B7.01c. 
CC   SC (S. coelicolor), 7B7 (cosmid name), .01 (first CDS), 
CC   c (complementary strand).
CC
CC   The more significant matches with motifs in the PROSITE
CC   database are also included but some of these may be fortuitous.
CC
CC   The length in codons is given for each CDS.
CC
CC   Usually the highest scoring match found by fasta -o is given for
CC   CDS which show significant similarity to other CDS in the database.
CC   The position of possible ribosome binding site sequences are
CC   given where these have been used to deduce the initiation codon.
CC   
CC   Gene prediction is based on positional base preference in codons 
CC   using a specially developed Hidden Markov Model (Krogh et al., 
CC   Nucleic Acids Research, 22(22):4768-4778(1994)) and the FramePlot 
CC   program of Bibb et al., Gene 30:157-66(1984) as implemented at 
CC   http://www.nih.go.jp/~jun/cgi-bin/frameplot.pl. CAUTION:  We may  
CC   not have predicted the correct initiation codon.  Where possible 
CC   we choose an initiation codon (atg, gtg, ttg or (att)) which is 
CC   preceded by an upstream ribosome binding site sequence (optimally 
CC   5-13bp before the initiation codon).  If this cannot be identified
CC   we choose the most upstream initiation codon.
CC     
CC   IMPORTANT: This sequence MAY NOT be the entire insert of
CC   the sequenced clone.  It may be shorter because we only
CC   sequence overlapping sections once, or longer, because we
CC   arrange for a small overlap between neighbouring submissions.
CC
CC   Cosmid 10H5 lies to the right of 3A7 on the AseI-B genomic restriction 
CC   fragment.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..4870
FT                   /organism="Streptomyces coelicolor"
FT                   /strain="A3(2)"
FT                   /clone="cosmid 10H5"
FT   CDS             complement(<1..327)
FT                   /note="SC10H5.01c, unknown, partial CDS, len >109 aa;
FT                   possible integral membrane protein"
FT                   /gene="SC10H5.01c"
FT                   /product="hypothetical protein SC10H5.01c"
FT   CDS             complement(350..805)
FT                   /note="SC10H5.02c, probable integral membrane protein, len:
FT                   151 aa; similar to S. coelicolor hypothetical protein
FT                   TR:O54194 (EMBL:AL021411) SC7H1.35 (155 aa), fasta scores;
FT                   opt: 431 z-score: 749.8 E(): 0, 53.5% identity in 114 aa
FT                   overlap."
FT                   /product="putative integral membrane protein"
FT                   /gene="SC10H5.02c"
FT   RBS             complement(812..815)
FT                   /note="possible RBS upstream of SC10H5.02c"
FT   CDS             complement(837..1301)
FT                   /note="SC10H5.03c, probable integral membrane protein, len:
FT                   154 aa"
FT                   /product="putative integral membrane protein"
FT                   /gene="SC10H5.03c"
FT   RBS             complement(1308..1312)
FT                   /note="possible RBS upstream of SC10H5.03c"
FT   CDS             complement(1427..1735)
FT                   /note="SC10H5.04c, unknown, len: 103 aa; possible membrane"
FT                   /gene="SC10H5.04c"
FT                   /product="hypothetical protein SC10H5.04c"
FT   RBS             complement(1738..1741)
FT                   /note="possible RBS upstream of SC10H5.05c"
FT   misc_feature    1800^1801
FT                   /note="Zero-length feature added to test Bioperl parsing"
FT   CDS             1933..2022
FT                   /note="SC10H5.05, questionable ORF, len: 29 aa"
FT                   /gene="SC10H5.05"
FT                   /product="hypothetical protein SC10H5.05"
FT   CDS             2019..2642
FT                   /note="SC10H5.06, probable membrane protein, len: 207 aa;
FT                   similar to S. coelicolor TR:O54192 SC7H1.33c (191 aa),
FT                   fasta scores; opt: 312 z-score: 355.2 E(): 1.6e-12, 36.8%
FT                   identity in 182 aa overlap"
FT                   /product="putative membrane protein"
FT                   /gene="SC10H5.06"
FT   RBS             2627..2631
FT                   /note="possible RBS upstream of SC10H5.07"
FT   CDS             2639..4048
FT                   /note="SC10H5.07, unknown, len: 469 aa"
FT                   /gene="SC10H5.07"
FT                   /product="hypothetical protein SC10H5.07"
FT   CDS             complement(4100..4297)
FT                   /note="SC10H5.08c, unknown, len: 65 aa"
FT                   /gene="SC10H5.08c"
FT                   /product="hypothetical protein SC10H5.08c"
FT   RBS             complement(4314..4319)
FT                   /note="possible RBS upstream of SC10H5.08c"
FT   CDS             complement(4439..>4870)
FT                   /note="SC10H5.09c, probable integral membrane protein,
FT                   partial CDS len: >143 aa; some similarity in C-terminus to
FT                   S. coelicolor hypothetical protein TR:O54106
FT                   (EMBL:AL021529) SC10A5.15 (114 aa), fasta scores; opt: 145
FT                   z-score: 233.8 E(): 9.2e-06, 33.3% identity in 81 aa
FT                   overlap. Overlaps and extends SC3A7.01c"
FT                   /product="putative integral membrane protein"
FT                   /gene="SC10H5.09c"
FT   misc_feature    4769..4870
FT                   /note="overlap with cosmid 3A7 from 1 to 102"
XX
SQ   Sequence 4870 BP; 769 A; 1717 C; 1693 G; 691 T; 0 
SQ   other;
     gatcagtaga cccagcgaca gcagggcggg gcccagcagg ccggccgtgg cgtagagcgc        60
     gaggacggcg accggcgtgg ccaccgacag gatggctgcg gcgacgcgga cgacaccgga       120
     gtgtgccagg gcccaccaca cgccgatggc cgcgagcgcg agtcccgcgc tgccgaacag       180
     ggcccacagc acactgcgca gaccggcggc cacgagtggc gccaggacgg tgcccagcag       240
     gagcagcagg gtgacgtggg cgcgcgctgc actgtggccg ccccgtccgc ccgacgcgcg       300
     cggctcgtca tctcgcggtc ccaccaccgg tcggccccat tactcgtcct caaccctgtg       360
     gcgactgacg ttccccggac aggtcgtacc gattgccgcc acgccccacc acgcacaggg       420
     cccagacgac gaagcctgac atggtgatca tgacgacgga ccacaccggg tagtacggca       480
     gcgagaggaa gttggcgatg atcaccagcc cggcgatggc gaccccggtg acacgtgccc       540
     acatcgccgt tttgagcagc ccggcgctga cgaccatggc gagcgcgccg agcgcgagat       600
     ggatccaccc ccacccggtg agatcgaact ggaaaacgta gttgggcgtg gtgacgaaga       660
     cgtcgtcctc ggcgatggcc atgatgcccc ggaagaggct gagcagcccg gcgaggaaga       720
     gcatcaccgc cgcgaaggcg gtaaggcccg tcgcccattc ctgcctcgcg gtgtgtgccg       780
     ggtggtgggt atgtgacgtg gtcatctcgg acctcgtttc gtggaatgcg gatgcttcag       840
     cgagcggagg cgccggtgcc cgccgcgccc gtgtgccctg ccgggccgtg accggacagg       900
     accaattcct tcgccttgcg gaactcctcg tccgtgatgg caccccggtc tcggatctcg       960
     gagagccggg ccagctcgtc gacgctgctg gacccgccgc ccacggtctt cctgatgtag      1020
     gcgtcgaact cctcctgctg agcccgtgcc cgcgttgtct cccggctgcc catgttcttg      1080
     ccgcgagcga tcacgtagac gaaaacgccc aggaagggca ggaggatgca gaacaccaac      1140
     cagccggcct tcgcccagcc actcagtccg tcgtcccgga agatgtcggt gacgacgcgg      1200
     aagagcagga cgaaccacat gatccacagg aagatcatca gcatcgtcca gaaggcaccc      1260
     agcagtgggt agtcgtacgc caggtaggtc tgtgcactca tgtccgtcct ccgtcctccg      1320
     gggcgcggcc cggcggccct cgttccgtac tgacatcagg gtggtcacgg gtcccaccgg      1380
     tcggcatcac ccggcacggg tgagtggggc gccgaggccg tcgtggtcag gcccgggaca      1440
     ccggtgtgac cctggtggaa ggacgcgtcc cgtggggcac gcaccgccgg ccgagggcga      1500
     ccaccgcctc ggtcagtccg agcaggccca gccacaggcc gagaagtcgg gtcagggcac      1560
     gggccgactc ggcgggcagc gcgaggacga cgattccggc gacgtcgacg gccagcgggt      1620
     tgcgcaggcc cagcactccg gccggggcgc ccggcaccag cgtggcgagg gccgatgcca      1680
     tgagccaggt ccaggaaccc ccaagcctgg cgaggacgtg cgccggatcg ctcaatgctc      1740
     cggtgaccgc cccgcccgac ccgtctccct tgtcggcagg ttccgccgca tcacgcggaa      1800
     cggagatggc tcccctgtgg atcgggcggc cgctgcgggg ccgcccggtt ggtcggtcgg      1860
     tgagcgccgg actccccctt cagctcttcc agggtcgggg tcgacaccga ggtcctggat      1920
     cacccgtcag gggtgatccg ggcatgccgt cgtggcggtg aggtgggata cgggaacgat      1980
     cggcccacgg gggaccggac gagacgaaga gacgtgagat gagcgatacg aactcgggcg      2040
     gcgggcgcca ggccgcttcc ggaccggccc cacgtggccg actccctttc cgccggcgcg      2100
     tggccctggt cgctgtcgca cgtcccctga tcgtcacggt cggtctcgtc accgcctact      2160
     acctgcttcc cctggacgag agactcagcg ccggcaccct ggtgtcgctg gtgtgcggac      2220
     tgctcgcagt ccttctggtg ttctgctggg aggtgcgggc catcacgcgc tccccgcatc      2280
     cgcgtctgag agcgatcgag ggcctggccg ccacgctggt gctgttcctg gtcctcttcg      2340
     ccggctccta ctacctgctg ggtcgctccg cgcccggctc cttcagcgag ccgctgaaca      2400
     ggacggacgc gctgtacttc actctgacca cgttcgccac cgtcggcttc ggggacatca      2460
     ccgcacgctc cgagaccggg cggatcctca cgatggcgca gatgacggga gggctactgc      2520
     tcgtcggagt cgccgcccgg gtgctggcga gcgcagtgca ggcggggctg caccgacagg      2580
     gccggggacc ggcggcatcg ccacgctccg gtgctgcgga ggagccggag gccggaccat      2640
     gaccgtaccc ggtggcttca ccgcctccct gccgccggcc gagcgagccg cgtacggcag      2700
     gaaggcccgt aaaagggcct cacgttcgtg ccacggctgg tacgagccgg ggcagcggcg      2760
     gcctgacccc gtcgacctgc tggagcgcca gtccggcgag cgtgtcccgg cactcgtgcc      2820
     catccgctac ggtcgcatgc tggagtcgcc gttccgcttc taccgcggtg cggcagcgat      2880
     catggcggcg gacctggcac ccctgcccag cagcggactc caggtgcaat tgtgcgggga      2940
     cgcgcacccg ttgaacttcc ggctcctggc ctcaccggag cgccggctgg tcttcgacat      3000
     caacgacttc gacgagacgc tgcccggccc cttcgagtgg gacgtcaaac ggctggcggc      3060
     cggattcgtg atcgcggccc ggtcgaacgg cttctcgtcc aaggaacaga accgcaccgt      3120
     tcgggcctgt gtgcgggcct accgggagcg catgagggag ttcgccgtca tgccgaccct      3180
     ggacatctgg tacgcccagg acgacgccga ccacgtacgg caactgctgg ctacggaggc      3240
     cagaggagaa gctgagcagc ggctcaggga cgcggctgcg aaggcccgca cacgcaccca      3300
     catgagggcg ttcgcgaagc tcacccgcgt cacggccgag ggccggcgca tcacccccga      3360
     cccgccgctg atcaccccac tcggcgatct gctcaccgac ccggccgaag ccggccggga      3420
     ggaggaactg cggtccgtcg tgaacggcta cgcacggtcc ctgccgcccg agcgccggca      3480
     cctgctgcgt cactaccggc ttgtggacat ggcgcgcaag gtggtcggcg tcggcagtgt      3540
     cggcacccgc tgctgggtac tgcttctgct cggcagggac gacgacgatc ctctgctgct      3600
     ccaggccaag gaagcctcgg aatcggtgct ggcggcccac acgggcggcg aacgctacga      3660
     ccatcagggc cgcagggtcg tggccggcca gcgtctgatc cagaccaccg gtgacatctt      3720
     tctcggctgg gcgcgcgtca ccggcttcga cggaaaggcc cgggacttct acgtgcgtca      3780
     actgtgggac tggaagggcg tcgcgcggcc ggaaaccatg gggcccgacc tgctctccct      3840
     cttcgcccgg ctgtgcggtg cctgcctggc gagggcccac gcccgttccg gtgaccccgt      3900
     cgcgctcgcc gcgtacctgg gcggcagcga ccgcttcgac ggcgcgctca ccgagttcgc      3960
     ccagtcctac gccgatcaga atgaacgcga ccacgaagct ctgctggcgg cctgccgctc      4020
     cggcagggtc acggccgccc gtttgtgagg ccgacccggg aacggccggc gggctggcac      4080
     acaccgccgc cggtcggcgt cattccggaa gctgccgcat ctccaggacg cgcaggccca      4140
     gcgactggca gcgggtgagc aacccgtaca gatgggcctc gtcgatcacc gtgccgaaca      4200
     gcacggtctg gccggacatg acgacgtgct ccagctccgg gaacgcgttg gccagcgtcc      4260
     gtgacaggtg tccctcgacg cggatctcgt agcgcacgag cggtcctttc accgtaggag      4320
     ctcgggacac cgcccggggc tccgggtcgg acggtgctct tggtgacgag cctgcgcctc      4380
     gtcgccctcc ggtgccctca cccagcacag gtgactccaa ccgcagtgtc agtgcctttc      4440
     agtgcgtcac tgtgatcttg acgacgacga tcaccaggcc gagcagtacg ttgaccgtcg      4500
     cggtgacggc caccagtcgt cgcgaggcgc ccgcgcggtg cgccgcggcg acggaccagc      4560
     ccacctgacc ggcgacggcg acggacagcg ccagccacag ggtgcccggg acgtccagcc      4620
     ccagtacggg gctgacggcg atggccgcgg ccggaggcac ggcggccttg acgatcggcc      4680
     actcctcgcg gcacacacgc agaatcaccc gccggtccgg agtgtgccgc gcgagacgcg      4740
     ctccgaacag ttcggcgtgg acgtgagcga tccagaacac caagctggtg agcaacagca      4800
     gaagaaccag ttcggcgcgg gggaacgagc ccagggtgcc ggcgccgatc acgacggagg      4860
     ctgcgagcat                                                             4870
//

BioPerl-1.007002/t/data/test.exp000444000766000024      1075013155576321 16410 0ustar00cjfieldsstaff000000000000ID   (stdin)
EN   (stdin)
LN   (stdin)
LT   SCF
QR   1107
AV   7 7 7 7 7 6 6 6 6 4 4 4 6 6 6 6 12 21 24 29 29 19 16 7 7 8 13 
AV        13 22 22 25 29 29 34 32 35 35 35 35 40 40 51 51 51 45 45 
AV        45 56 40 40 40 40 40 40 46 46 56 42 42 56 45 40 40 40 40 
AV        40 42 42 35 33 33 35 35 35 46 56 56 40 40 40 40 34 33 33 
AV        24 24 12 14 9 11 16 31 31 48 48 48 48 40 20 19 8 6 6 6 
AV        8 21 25 30 32 32 33 37 40 40 56 56 56 56 42 33 27 15 15 
AV        15 33 33 42 56 48 44 42 33 33 20 22 13 13 13 22 22 42 44 
AV        42 42 42 42 42 42 42 38 38 45 45 45 40 37 37 36 40 35 37 
AV        38 40 40 42 40 45 38 40 42 37 40 40 40 40 45 56 46 42 42 
AV        42 43 56 56 43 51 45 40 40 40 40 40 44 44 56 39 40 35 36 
AV        36 40 42 42 42 50 50 44 47 44 56 56 44 44 42 42 40 40 40 
AV        37 37 40 40 40 45 37 40 35 35 35 35 40 40 40 40 44 44 36 
AV        36 19 25 14 33 33 35 35 35 40 36 38 37 37 37 42 42 42 42 
AV        35 35 35 42 37 42 36 36 36 35 35 35 42 42 42 42 42 42 42 
AV        56 42 42 42 42 42 37 37 42 42 42 42 42 42 34 34 34 42 31 
AV        32 28 28 28 31 29 33 29 25 17 24 21 17 9 8 10 13 12 17 
AV        10 9 9 9 10 8 11 11 11 8 9 9 9 8 7 10 8 8 6 6 8 8 12 10 
AV        9 9 9 9 9 9 9 9 9 9 11 10 9 9 9 13 9 11 9 9 7 7 10 8 8 
AV        8 9 9 9 9 9 9 9 9 9 9 9 9 7 8 9 9 9 7 7 7 7 7 7 9 9 8 10 
AV        8 8 8 11 10 11 10 11 9 8 6 8 8 8 8 8 9 11 20 20 16 13 6 
AV        6 8 8 9 10 10 10 11 13 10 9 9 11 11 15 21 17 13 9 9 10 
AV        9 9 8 8 8 9 9 9 6 6 8 8 9 13 9 9 9 9 9 9 9 9 9 9 9 9 11 
AV        8 8 6 6 6 6 13 10 10 8 8 6 6 8 9 10 10 10 9 9 9 10 10 8 
AV        8 6 6 6 6 11 9 8 12 9 9 9 12 10 9 9 9 8 8 6 6 6 8 9 9 9 
AV        9 9 9 9 8 4 4 8 8 9 11 16 11 9 8 8 8 8 6 6 8 8 8 9 11 11 
AV        11 10 6 6 6 6 6 6 6 6 6 8 6 7 9 9 9 9 9 11 10 14 10 13 
AV        9 9 8 8 8 8 8 9 9 11 11 11 8 7 13 10 12 9 8 8 11 11 8 6 
AV        8 6 6 9 6 6 9 13 10 8 8 6 6 8 9 7 7 12 12 6 6 8 8 9 6 8 
AV        8 8 6 6 8 13 11 6 6 6 6 6 6 7 7 6 6 6 6 6 6 6 9 9 8 10 
AV        6 6 6 6 6 9 6 6 8 6 6 8 8 10 4 4 4 8 9 9 12 12 10 9 8 8 
AV        6 6 8 6 6 6 6 8 8 4 4 4 6 6 6 6 6 9 7 8 9 8 8 8 10 10 10 
AV        8 6 6 8 8 8 9 9 6 6 12 6 6 8 9 9 7 7 9 9 9 9 7 7 9 9 9 
AV        10 8 7 9 9 7 7 7 7 9 7 6 6 6 6 8 8 7 7 9 9 9 13 8 8 6 6 
AV        9 6 7 7 8 9 8 8 6 6 6 6 8 6 6 6 6 6 8 6 7 6 6 6 7 7 7 9 
AV        9 10 9 11 11 14 13 13 9 9 9 6 6 8 8 8 8 9 14 10 9 9 7 10 
AV        9 11 8 8 8 8 10 10 10 9 9 8 8 6 7 7 9 6 6 9 10 11 11 7 
AV        7 11 10 10 11 9 11 8 8 11 9 9 7 6 6 6 14 8 8 13 11 11 11 
AV        9 9 9 8 11 6 6 8 8 9 9 8 8 8 8 8 6 9 19 21 15 13 11 9 13 
AV        9 10 16 16 9 9 9 9 10 9 9 9 6 6 8 8 6 6 10 8 10 9 9 6 6 
AV        8 8 8 8 8 6 6 8 8 6 6 8 8 8 8 6 6 8 6 6 8 8 8 8 9 12 12 
AV        12 8 8 9 21 19 15 12 9 9 9 9 9 12 16 11 11 11 12 12 9 7 
AV        9 9 10 9 8 8 11 13 12 9 9 9 9 10 9 8 8 6 6 9 8 9 9 11 10 
AV        10 11 10 8 7 8 8 6 6 6 8 9 9 11 11 16 9 9 10 9 9 9 9 9 
AV        9 9 8 8 6 6 8 8 8 6 6 8 8 9 9 9 9 9 9 9 9 10 9 10 10 11 
AV        14 21 20 18 14 11 9 6 6 6 7 6 6 8 8 9 9 10 10 10 10 9 9 
AV        9 11 11 9 10 6 6 8 8 9 9 6 6 6 6 8 8 9 9 9 9 9 7 7 9 9 
AV        9 9 9 9 9 12 9 9 9 9 9 9 10 12 9 10 10 11 11 11 12 10 7 
AV        7 9 7 7 9 13 9 9 9 6 6 6 8 8 8 6 6 
SQ   
     GATGATTCCG GCTTCGGACG ACTCTAGAGG ATCCCCATTT TTATAGTTTT TATCTTGTAA
     TAGATGTTTA GATTTTTCGT TGTAATTATT TTCTTTATTG TTGAAATTAG TATCTCTGGG
     TAATTTATCA TATTCTCTGG AAAATGATTT ACTATCACTA GATACTTCAT AAGATTTATA
     ATCTTTATTA TGAAAATCAT CTCTATTTTT CAAATTATTA TTATATCTAT CAAAGTTTCT
     GTCTTCATTA TATCTATTAG CATATCTATC TTTATCTTTA TCCCTATCAC TATATCTATC
     ATATGGTTCA TCTTGTTCAA CCGATCAGAC TCGATTCGCC ATCGCCTCTA ACGGATGGCC
     GCTCCCCCTC TCATACCTCG CTCCCCTCGA CATCCCCCGT CTCGCCACCC TATCCGCCCC
     CTTCATCACC CCCCCTTATC CACACCCTCA CCCCCCGCAT CGCGCACCCA CGACCACCCG
     AAGAACCGCC CTTACTCCCA AGTACGCCCC GACCTCCATC ACCCTATGCG GTACCACTCC
     CACCACACCC AGTCCTACTT TCGCCCGCAC ATCGGCCCCG CTTCAGACAG CTCCCAACTA
     CGCAACCCAC GCTTGTTCTT GTTCACACTC GAATACTCGA ATCTCTCATT ACTCCGCGGA
     CTCCGCCGCA CCTGTGCACC ATTAACTGTG TAGCGCCTGA ACCGGCACCT CTGATTACCA
     CTTCCTCCAC CAGCACAGTC CTATTACCGC ATGTCGCTCT GCTAAGACAG TGCAAGACTC
     TGCGGTCGCT CTGACCCGCA TCCGCCAGGG CACCTCTCAC CCTCGCTGGC CACCCCGCCC
     CCCTCTCCCT GCCCCTTCAT TCCCCCAAAC CGCTTTCAAC GGGACACACC CCTCCGCGGC
     GGACCACAAC TCGCCGTCGG CCACCACTCA CACCTTCCCT CCTCCTTCCC CCACATCACG
     CCAACCCCGT GGGACGGCTC TCCCGCGGCT ACGACGCGCA ACCCCCCCTC GCCGCTTCCC
     CCCCAACTTC CCACGGGCTC CCCTCCGCCC CTTACCCGCG AGGAGCTTCA CCCGCGAACC
     ACCTCCCCCC TTTCCCAACA GCACCG
//
BioPerl-1.007002/t/data/test.fasta000444000766000024       144413155576321 16672 0ustar00cjfieldsstaff000000000000>roa1_drome Rea guano receptor type III >> 0.1
MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVV
VMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVK
KLFVGALKDDHDEQSIRDYFQHFGNIVDNIVIDKETGKKRGFAFVEFDDYDPVDKVVLQK
QHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGN
NWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGND
FGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY
>roa2_drome Rea guano ligand
MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVV
VMKDPTSTSTSTSTSTSTSTSTMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVK
KLFVGALKDDHDEQSIRDYFQHLLLLLLLDLLLLDLLLLDLLLFVEFDDYDPVDKVVLQK
QHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGN
NWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGND
FGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY
BioPerl-1.007002/t/data/test.fastq000444000766000024       524213155576321 16712 0ustar00cjfieldsstaff000000000000@FC12044_91407_8_200_406_24
GTTAGCTCCCACCTTAAGATGTTTA
+FC12044_91407_8_200_406_24
SXXTXXXXXXXXXTTSUXSSXKTMQ
@FC12044_91407_8_200_720_610
CTCTGTGGCACCCCATCCCTCACTT
+FC12044_91407_8_200_720_610
OXXXXXXXXXXXXXXXXXTSXQTXU
@FC12044_91407_8_200_345_133
GATTTTTTAACAATAAACGTACATA
+FC12044_91407_8_200_345_133
OQTOOSFORTFFFIIOFFFFFFFFF
@FC12044_91407_8_200_106_131
GTTGCCCAGGCTCGTCTTGAACTCC
+FC12044_91407_8_200_106_131
XXXXXXXXXXXXXXSXXXXISTXQS
@FC12044_91407_8_200_916_471
TGATTGAAGGTAGGGTAGCATACTG
+FC12044_91407_8_200_916_471
XXXXXXXXXXXXXXXUXXUSXXTXW
@FC12044_91407_8_200_57_85
GCTCCAATAGCGCAGAGGAAACCTG
+FC12044_91407_8_200_57_85
XFXMXSXXSXXXOSQROOSROFQIQ
@FC12044_91407_8_200_10_437
GCTGCTTGGGAGGCTGAGGCAGGAG
+FC12044_91407_8_200_10_437
USXSXXXXXXUXXXSXQXXUQXXKS
@FC12044_91407_8_200_154_436
AGACCTTTGGATACAATGAACGACT
+FC12044_91407_8_200_154_436
MKKMQTSRXMSQTOMRFOOIFFFFF
@FC12044_91407_8_200_336_64
AGGGAATTTTAGAGGAGGGCTGCCG
+FC12044_91407_8_200_336_64
STQMOSXSXSQXQXXKXXXKFXFFK
@FC12044_91407_8_200_620_233
TCTCCATGTTGGTCAGGCTGGTCTC
+FC12044_91407_8_200_620_233
XXXXXXXXXXXXXXXXXXXXXSXSW
@FC12044_91407_8_200_902_349
TGAACGTCGAGACGCAAGGCCCGCC
+FC12044_91407_8_200_902_349
XMXSSXMXXSXQSXTSQXFKSKTOF
@FC12044_91407_8_200_40_618
CTGTCCCCACGGCGGGGGGGCCTGG
+FC12044_91407_8_200_40_618
TXXXXSXXXXXXXXXXXXXRKFOXS
@FC12044_91407_8_200_83_511
GATGTACTCTTACACCCAGACTTTG
+FC12044_91407_8_200_83_511
SOXXXXXUXXXXXXQKQKKROOQSU
@FC12044_91407_8_200_76_246
TCAAGGGTGGATCTTGGCTCCCAGT
+FC12044_91407_8_200_76_246
XTXTUXXXXXRXXXTXXSUXSRFXQ
@FC12044_91407_8_200_303_427
TTGCGACAGAGTTTTGCTCTTGTCC
+FC12044_91407_8_200_303_427
XXQROXXXXIXFQXXXOIQSSXUFF
@FC12044_91407_8_200_31_299
TCTGCTCCAGCTCCAAGACGCCGCC
+FC12044_91407_8_200_31_299
XRXTSXXXRXXSXQQOXQTSQSXKQ
@FC12044_91407_8_200_553_135
TACGGAGCCGCGGGCGGGAAAGGCG
+FC12044_91407_8_200_553_135
XSQQXXXXXXXXXXSXXMFFQXTKU
@FC12044_91407_8_200_139_74
CCTCCCAGGTTCAAGCGATTATCCT
+FC12044_91407_8_200_139_74
RMXUSXTXXQXXQUXXXSQISISSO
@FC12044_91407_8_200_108_33
GTCATGGCGGCCCGCGCGGGGAGCG
+FC12044_91407_8_200_108_33
OOOSSXXSXXOMKMOFMKFOKFFFF
@FC12044_91407_8_200_980_965
ACAGTGGGTTCTTAAAGAAGAGTCG
+FC12044_91407_8_200_980_965
TOSSRXXXSSMSXMOMXIRXOXFFS
@FC12044_91407_8_200_981_857
AACGAGGGGCGCGACTTGACCTTGG
+FC12044_91407_8_200_981_857
RXMSSXXXXSXQXQXFSXQFQKMXS
@FC12044_91407_8_200_8_865
TTTCCCACCCCAGGAAGCCTTGGAC
+FC12044_91407_8_200_8_865
XXXFKOROMKOORMIMRIIKKORFF
@FC12044_91407_8_200_292_484
TCAGCCTCCGTGCCCAGCCCACTCC
+FC12044_91407_8_200_292_484
XQXOSXXXXXUXXXXIXXXXQTOXF
@FC12044_91407_8_200_675_16
CTCGGGAGGCTGAGGCAGGGGGGTT
+FC12044_91407_8_200_675_16
OXTXXXSXXQXXOXXKMXXMXOKQF
@FC12044_91407_8_200_285_136
CCAAATCTTGAATTGTAGCTCCCCT
+FC12044_91407_8_200_285_136
OSXOQXXXXXSXXUXXTXXXXTRMS
BioPerl-1.007002/t/data/test.game000444000766000024     13032413155576321 16545 0ustar00cjfieldsstaff000000000000






  
    Caenorhabditis elegans
    L16622
    taxon:6239
    
      GTGAACAGAAAAAAACGTTGAAAGGGAGGAAGAAGTCGTCACACAGATTCTAAAGTGACT
      TTGAGAGACGAAAATGTGTTCGTTAATCTTCTAGAGAAAACGAGAAAAAAAAACTGATGC
      AGTAAAAACTAAAAGAAGAAACTAATTCCTTTGCTCTTCGTAATGAGATTGTTTGGGTGG
      GCTTCGCTGTTTCAGAATTCAGTGGAACTCTTGAAATTTAAGGAAATGAAACTACTGTAG
      TGTGCATATTCATTTAATTTAGATTTAAAACAAATCTGGACAATATGCTTTCTTATCAGA
      ATATTCACTAGCAACTGTTATAAAAATAAAATTAGTACAATTTTTTATTTATTTTCAATT
      GAAAGTTCCGAATAAGGGATTGAATTCTAGGATTCTTCAAACTCAGATATAGTGAAGAAA
      TGACATTGTCAAGTTGATAGATTGATTGGTAAGCTTGATGCCATTGTAATTTGAGACTAG
      CTCCTAAAATTAATAAATTTCATATTAAATCAGAAAACAGAAAGTTGTCAAATCTAGAAG
      CATACTCATCGAATAGACAAGATTTGTTATTATTCTAAAATTTAAAAACTTGTGACTATG
      ATTAAAGAAGAAAAAGTCACAAGGTAGTCAAGTCTCATGGGTGTTCAGTTTTTGTTCCTA
      GAAACGGAATCAATGAAACACTCTTGGCTCACTACTTCCAACCGGTAGATTTAAATTATA
      CCGATTCCCCGGTGTGTCCGCGCCTCCAACTCCGGAAACCGTCTCTAAAAATGGAGTTAG
      GGTACATGAACATTCTACAGAGCGTTCATTAGACATTCTGCATATCTTTGAACTTTTTTT
      TCCTTTTTTAATACTTATTAAACGGAAGAGTAAAGTTTCTAAAGTATCAATAAAACCTAA
      CCAATTTAGAACATAAAACTTCAAGAGAGACCTAAAAATGTAAAATGTGCATTCTTAACC
      AATTACTTTCCATATTTTCTGTTTTTTCTATCCAATTTTGCTTCTTTCGGAAATGGCAAA
      AAAGACGTCGTTCTGTCTGGCAATGTTGAGCTCTATCAATCAGGCTGCCGTTTGGATCAG
      AAAAAGGGGAAAATTGAAGGATGAAAAGAATGGGTACTTCTTGAACTTTTTTCATCAATT
      CTTCTTTCTAACTTCATTCGTGCATTTTTCTGTTTTGGCTCTCCAGTGGCTTCTGCCGTT
      TCGTCAGGAAAATCTCATTAGATGAGCTATTGTCGTGAACTTTTTTCTGCCGGTTTTAAA
      TTTCTTTAGGGGCACGTGTATTAGATAAATATGGGTGGGAAGGAAAAAAAAACAAACACG
      AAAAAAATGAAAATGAGACAAGCGAGATGGAAGATTTTGGAAGAACTTTGATAGTTCAAA
      GAAAACAAGTAAAACAATAAACTATGTAAACGCAATTAATAAAATTTCGTAGTACAAAAA
      ACCTTGAGTTAAAATCCAGGTAAAGTCGAACGTCAGGGATTCTTTTTAAAATAAATTCCG
      CAAAATTTTTTTGGAGATATAAAACAAAAACTCGATAAATAGAGGAAAAAACTAACTGGC
      TAACATAATAAGATACTAAAGTTTGTCTTTAATCATACATACAATCAAACCTGTCTGCCT
      ACCTTTCAATCTGTATTTTACCATGTTTACAATTATTGGTAATAGGCACACCTGTAGGCA
      CAAGGCAGGTAAGCATGTCATACACGGGAAAATTGGAATTTTAAGCAACTGCATACTGCA
      ATATAATTCATTTACCCAATTTGAATATTAGAAGCTCAAAAATGTTTTGAAGTAAAAAAG
      CTTTTAGACTTTAGATTTAAAAAAATATATGTCCATTCAAATATTCCGTCAATATTCCGA
      AAACTTAAAAAATTAAATTAAATAATCAGAAGTTCTAATACCCTTTTCGATTCCCATGAC
      ACTGAATTACAATGAAAAATTTTACGTTTTCAAAAAAATGAGCGCAACATTTTTAGCATG
      TAGACCAAAAAATGAAGTCGGGGGAAATTGAAAATTGTCAGTCAACAACAAATAAGCATT
      TCTAATAAATATTTATGCATTGGGCTTTTGAAAACCTGCATAACACTAACATTTCACGGT
      TTGATTCATGACGATTTCCTTTTGCTTAAAATTTTAATTTTTTCATGAAAAGCTCATCAA
      TTGTAAAACAGAATGAATTTTCAAAAGACGTTTTTGAATATAAAAAATGAGTTTTCATTT
      TTCAACGAAAATTTACGTTGCTCAGTGACGTTTTATTACAGAAGAGGGTAAGAAGCAGTG
      ATGCCTTTTTTTTTGCAAAGTTATGGATGTGCATTTTGACTTTTTCTCAAATTTTCGAAG
      TGTATTCAATTTTTTAAATAGGAAAAAGTTATGACTTAATACCGGGACAATTTTTCCTCC
      TATCTGCAGAACTTTCTCATAGTTCTGAAACTCGGTGTGATTTCCGACAGAGTTATAAAT
      TCACCATGAACTTTTGCAAAATTTGATTAGATTAGAAAACTTGCACCAAAAAGACAAACT
      TATCCAACATTTGAAGATATTAATTTCATACAAAAAATTTCCTACAGTGAAGGCTTAACT
      CGGTTTGCAGCTAAATCAAATTTTCATTTATGGATCTTATTTTATCATCGTTGTAATAAA
      ATTAAACATTTTTCATAAGCTTTCAATTTTCCAAAAAAAATGAACATTAATTAAAAATCC
      AACAGAAAAAAAAACTTGAATCACTATTTGCAATGTGAAAATGGGGGGAAATCCAGTACA
      CATTTTACATTTATAGACAAAGTATTTTTTCTACGCTGAAAACATTCTGAAGAGTCTCTC
      GAAAGTTGGTTTGAGAACTAGACATACTTCGCAATAATCTGATAACATTTTCTGGTAGAT
      GTACTGCTAGAACACTATTTTTTGAAAATAAAATTTCTTATTTTTCTGAAAACGTTTTGT
      AAAATGAAAAATAAATTCTCTAAAAAATCCATAATTACATAAATGATAAATGGTAAACTA
      TGCACTTGAAAAGTGGCATTCTTCTGACTTGAAATTGTCTAGACAGTTTGAACAATTCCC
      AAGTCTGATGATTCTAAAAATAAAAAACAAATTTTGAAAGTATCAAAAATGTTTGAACAA
      AAAAAGGTTCTAGCTAAAGTTCCAAGGAACTTGATTTTGCGAAAAATCTTCTCCAACTCT
      CTGGTGACACCCTTCGATTATCTCTCCAACTCACAAGTTTTTCAGTCAACTCGCCGTTTA
      TTTCCGAAAAAAATAGAAAGAGTGGAAGAGATGAACGAAAATCTATTCGATAGTGTTCTC
      TTGTTTTCATTTAAAATTCTCTTTCAGATGTTTGAATTTTTCCAGTTGTTTTCAAGAAGC
      TCGGCAAACTTATCTCGCATTCATTTAAAGTTTGAATTTATGTTCTTACTTGATTAGACT
      GGAAAAGAAAAAGAAAAACACATGTTTAATTGAAACTTCAATAACTTGTTCTAGCTTCTG
      TGACCTTTCCAATCAGAACAATTATCACGAATGATTACTTGTGCTTACTCAATTTCATGT
      ACTTTTGCTTAGAATTGATGTAAATGTGTTCAGAACCATAGAAAAATTCCGAAGTTTTCG
      AAATGCAGTTACCGTCCACTTCCATTTCAGAATTTCATGCTTCATATTATCAGCATTTGA
      AGGCCTACTCCCATTATCCAGTCTGATGTGTAACCCACACTATGTGACGAATATTCTGAT
      GAAATTTAGTAAGCACAAGTTATCATTTTTAACAGTTATTTTTATCGTGACTGTCACAAA
      CTCCAATTTTCTTTTCGAACAATACCGACCTGGTGCATTTTTCTTGAAAGATATTAATCT
      CTATATTGCAATACAATATTGTAAGATAGTTCAAAGTCTTAGAATTGGTCTACATAACTC
      CGTAATTGGAATTAAAGTAAAGGCACCGGACTACCTACCGACCACTCATTGTCAGCATTT
      GGCACTAGCTTCTTGCCAAAGTTGGCCAAACGTTTATAGTTTTCTGCAATTTTTTGTTAC
      TTTTTAGTTGAGTGGTATAGTTGTTGGCAGTAGGTGCGCTTGTCGACACGAGGCAGGTAT
      TTCTGTGCCTACAGGCCTTCTACTTCAGACATGATTTCTGCAACAATTTAGATGACTAAA
      ATCTGATGAAATTGGGAAATCGCCAGACATCATTTTCTAGAAACATTTTGATCGCAATGA
      TCTTGGCAGAAAGTCTATTTCATTATCATCTCATCTTTAAAAGAACATAATTTTTAAGAA
      AAATCTATTGGCAAACTGTGTTTCTACTTTACTTCACAGGAAGAGCAACGTTTGTGTGTG
      TCTGTATTTTGTGCCAATATGTGGTTTGTAGCACAGCTATGCTACAAAGTTCAAATTCGT
      TTTGAAGGGGGAGAGAGGAACCCCGTGATTTCTGTGTTGTCTTATTCTCATCATTAAACT
      CTGAACATTCAGCAATTTTGATCCATAATACTCAAACTTCTAGTTTCATCATCCTCATCT
      TTTCTGGTGCCCCATTATCCTCTGATTCTAAAATATAGTTTTCCACCGTGAACTTCTCAA
      TTTTTTCCAAATTCTTTAGCGTACTTTACTTCTGAAAAACTGTGCAATCTCATTTTCAGA
      ATCTCCACTCAATTTTCATTCATTCAGTATGCAAACTATAAATTCGAGGTAATTTAAGGA
      TCAAAAAGTCCTTGGGAAGGTCAATAACCAATGACATGCCGCGAAGAAAAACGCAGGCAA
      TCCTTGAAAAGAGACGATACGCAGACTATTAAACAGAGATGTTTGTCATCATTTCTGTCT
      TCTCGTTCTTCTCTATTTCACTCTCCTCCATAAAAAGACTATTTATACCAAACTATTCTT
      CACTTTGAGCATCACTTTCTGAAGACTAGACTTAATTTTTGCCTTCTTTAAAAATCTGAA
      GTATTGAAGATTTTATTTCATTTAAATTTGATTTAGAACTCTTGTCTTTTACTATTCCAT
      CAAAATATAAATTAAATTTTCAGACTTATTCGCCGATTCATTTCTCAAAGAAACATGACA
      GTGCTTGCTGGAGTAAACAGTAAAATCGTCAAAAATGGTAAGGCTTCATTTCCAATTTTA
      GTTCAAGAATTCCCAAAAAAAGATAAAAAATTAATCACAGAGTAATATAATAATTGTATG
      TCCATATTGCATATGCAATACTATTTTTCTCAATCAATAACTTCAAGTGCAACTCTGATA
      GGGTTGCAATTCTTTTTCAGGGAAAATATGGTATTTAATTTGCTCAAATTGTAAAGAAGT
      GTTCCACTTTATCAAAAAATAGTTGGATATGATTAAAGTTCAAGTTTAATATTATTTATT
      AGAAAATCCTATCTTAGTTTTGCGGAAATTTAATATTATTTTTTCAGGTGACCCAGCGCC
      AGCTCCTCCGGCTGCTGGAACCATTCGTATCTACAACATGCGATTCTGCCCGTGGCTCAA
      CGTGCTCTAATCTATGCATCTGTTAAAAATATACCGAGCGATGTTATCAATGTTCACTTG
      CAAGAAAAACCCGACTGGTACTTCTCAAAACATTACAAAGGACAAGTTCCGACATTGGAG
      CACGACGAAGGAAAGAAGCATGTTATTGAATCAGCTGTGATTCCAGAATATTTGGATGAT
      ATCTATCCAGAGACTCGTATTCTTCCAACTGATCCTTACGAGAAGGTTCAGCAAAAGTTA
      TTGTTGGATAGAATCAGTGGACAAGTGTCACCTGCATTCTACGGAGTCGTTCAAGCTGTC
      AAAAATCCAGATCTCCGCGAAGAAAAATTTGCGGATATCAAGAAGGCGTATGATAATGCT
      GAGCAGTTATTGACTGGAGATTTCTATTCAGGTATTTTTTAAGAATTAAGATTGAGAATG
      CGAAACTTATAAAGAACAGAAACTAAGTTGTAGTTTTAGTCTTGTGTATTTTAAAATTAT
      TTGAATTAATTTCAGGAACCTCAAAACCTGGATTTGTTGACTATCTTCTCTACCCGAACA
      TTCAACGCGCTTACTGGGCAGCACACATAGTTCCAGATTTCCCATTGGAAGCTGAATCGT
      TCCCAGGACCAAACTATCCAAGACTATCCAAATGGTACAAGGCTCTGGAATCGATTCCAG
      AAGTTGCCGCTGCCAGTCAGCCAACAGAGAATGGGGTTGGATTCTTCAAGGATTACCTCG
      GTGGATCTCCAAACTATGACTATGGATTGTAAACATTTGTTATTATATTTTTAAACTTTG
      TGTTGTGGATGTGAATATGTGGAATTTAATAAAACATTTCTCGATATAATAATGATTTTG
      TTGAATTAGAAAAATTAGAAAAGTGGACGATTCTAAAAACAAAAGTTACAACGAAAATCA
      TCGAAGGAAAAAACAACTGAATTCCAAAATAGTTTTCAGAGGTGATCACAAAATGTTCTC
      AAACGATATATATTCTACCATCAATAATTTTATTGGCACTATATCACAGTCCATAATTCC
      TGTGCTTTAATTATACTTTTCAGTATAGAACAATATGCTATATTATCAAGTTATGCGTCC
      AATAAACACAATTTATTTTTCAGACTGAATTTAAGCCATATTGAGAATAGCGAAATAAAA
      ACGTAGAGGAAATTTGTGATCGCCATTCACAATTAATTCTTAGATCGCAATGATAACAAA
      CTTCGATTCAAAAGTCATCATGCAAATTCACCGTTCTCGTGTGTGTGTGTTTTTGGAGGA
      AATAACACAATTTTGTGACTGATTTTTTTACAACATGTGGTTTGTAGCATAGTTCAAAGT
      CATTCTAGAGGGGGCTCAGAGGGAGTTCTTTCGCTATGTCATCGTTTGTTTTTGCACACC
      AAGAAAAATGAAAATAAATGCTCTAGGATGTCATGGATCGTTTCCATTCTTAATAAGTAG
      AAGCTAGGATTTCCTATACAAAAATAAGTAATCTTCGTTTCTACGTCTATCAACTTAAAT
      TTTTGTATACAATCCACTTTGGTAATATTCAAGGCCTTCCTGTAAAATGTTTTATGATCA
      ATCCGTTACACCAAGAAAACAAGTGCAATTTGTCATCATGTAGGCTTCCGCCTGTGTTTA
      CTTCCTTCCCCCAGCACAACACTGACTATTTATACCAAATTAATAATGCAGCATTCCTCA
      TGTGATAACTCGTTTGACTTTTATATCTTTCTACGTGCATCTTTCAAGCTCGAAAATTAA
      TTTTAAAAATTTACATTGCAGAACAATTGCGGAACGAAGAAGCATGTCAGTCCTATCAGG
      ATTAAACACTAAAGTTGTCAAAAATGGTACGTTATTGAGATTGTTTTTGTCTGACAACTG
      AATTACCAAGATTCTTTCAGGTGATCCAGCTCCAGCTCCACCAGCTTCAGGAACCATTCG
      TATCTACAATATGCGATATTGCCCATGGGCTCAACGTGCTCTAATCTTTGCGTCTCTCAA
      AAAGATCCCGACCGAAGTAATCAACATCCATTTGGATCAAAAACCAGATTGGTTTTTCAC
      GAAACATTACAAAGGACAAGTTCCAGCACTAGAGCACGACGAGGGAAAGAAAATTGTGAT
      TGAGTCAGCTGTGATTCCAGAATATTTGGATGATATCTATCCAGAACCTCGTATTATTCC
      AACTGACCATTACGAGAAAGTTCAGCAAAAGTTATTGTTGGATAGAATCAGTGGACAACT
      TTCTTCTGCATTCTACGGTGTTGTTCAAGCGGCCAAAATTTCTGATCTTCTCAAGGAAAA
      ACTAGTTGAACTTGCAAAAGCATATGATACAGCAGAGGAACTCTTGACTGGAGATTTTTA
      TTCAGGCACGAAATATTTTAATATTGAAACTAATCAGTTTAATTAAAATTAATTTAATAT
      TTAAATCTTCAGGAACATCAAAACCAGGATTTGTCGATTATCTCATATATCCGAACATTC
      AACGTGCTTTCTGGACTTCCCATATCATCAAGGATTTCCCATTAAAAGTAGAATCGTTCC
      CAGGACCAAACTATCCGAAACTATCTAAATGGTATAAAAGATTGGATTCAATTCCAGAAG
      TTATTGCTACCAGCCAACCAACTGAAACAGCAGTTGAGTTCTTCAAAAGCTGGATTATTG
      GAGCACCAAACTTTGACTATGGATTGTAAATATCTTCTCTTCGTTACAAATTGCATATGA
      GTATTTGAATGTAAATAAACTTTTTGGAGAGATTGAAGCAGACTTTTTTGTTTATCCAGA
      AAGTAAGACAAAGAGGGAGATGCTATTAGTGACAGATGATGGTTGAGAATAAGAGAAAAA
      GGATGAAAACGACGAGATCTGATTGTTGTCTCTCGTCCAGTCACTTTCCATTTCATTTTT
      ATAGAAATACTTCGGCGACGCGGATGCGTGTCTGCTTCTTGCAAACTATTCTTCCTCTTA
      TAAAGTTGGCTTTGAGGATTTATTTTTTTTTGAAAATTGTTTTCTTTTAACTGACACCGG
      AGTTTTATTTCTATAGGTTTTTATGAAAAGTTTTATCATGAAGTGAACTTGTCACCTCTG
      TTCGGTTTCTTGTGTTTTTGATATTAAGTCTAACTGTCCCTTTTTATGAAATGTAATTTT
      TTTAATTTTGTATAAGCTTCATACAGTACGGACGTTTTGAACATTTGATGAGTCAGAGTT
      AAAGAGAAAACTGATAATTTTTTTTCCATCTTTCTCCTCACTTGTGAATAAACTAAACGC
      ATTTCTGTGGACGTTCCAAGTGTAATATGAGAGTTGTTTTCATTTGGAAATGCGGGAATA
      TATTGAATCTTCCATTAGATGTTCAGGAATATATAAATACGTTGTCTGCTCTGAAAATTC
      ACACGGAAAATCTAAAAATTGTCAAATTATAGATTTCATTCTCAAATGACTATATAACAT
      TTTATTTTTGCAATTTCTTTTCAATTAGGAAACATTTCAAAAAGCTACGTTGTTTTTCAC
      ATTCAAAATGATTACTGTCGGTGCGTTCATTTTCCGAGTTTTTCCAATTTCACGCTTGCT
      CTTCTTCGTAAAAAACTCGTAATTTAGAAATTGTGTCTAGATCAAAAAAAAAATTTTCTG
      AGCAATCCTGAATCAGGCATGCTCTCTAAACAACTCTCAGATATCTGAGATATGGGAAGC
      AAATTTTGAGACCTTACTAGTTATAAAAATCATTAAAAATCAACGCCGACAGTTTCTCAC
      AGAAACTTAAACCGAAAAATCCCAACGAAGACTTCAGCTCTTTTTTCTTTGAAATTTGAG
      ACAAAGGCCCGTTCTATTGTCTTTCCGACTCACATCGTTCATTAATAAATCGTTCTTTCT
      TCTACTTCATTCATCAATTTCCTCTTGACCAGAGAGAGTCCCTACTCTTGAAGCTCCTCT
      TCTTTACTCTTTTCTTACTTACGCACAAAAAGTCTCTCTATCACTGCGTCTCTCTATCCA
      TCTCTTCTACATGTCACTTGTCGTCTCTGCGCCTCTATAACACGTAACAATCTCTACCTT
      CAAGTTCTCTAGTCACCTGTCTTCGTCTATACCTTTTGCCACGAAAATTACTACGTAGAA
      GCTGTCCTATTGTAAAGATGAAACAGTTTGAAGAGAAATTGGATGATTGTGATCTATTGG
      TCTCAGAATTTGATGGATTTCTTTTCCATGTTTTCAATTTTAACGTCTATATTCTTACCT
      AGGTACTCATAATTTTAACTTTGTTTATATTTTTATAAACTTATAAGTTACAATTTTTAA
      ATCAGTTAACAACTTCCTATAATCAAATTGTATTCTATTTTTTTTGGCACAAACACATAT
      AAATGTCCAAATATTTGCGCACGAGTCACCCCTCTCCACTCATTTGCCGCCCAATTTTGA
      CGTTTTCTTCCTTGCACATTTTGACAGCATTTCTAATTTCAGGAAATTCTTCATATATCA
      ATTGGTCAGTCACAATTATCCTCCTCATTCTTGGACTTTACGCCTGTCATCGATTTTTGA
      ACATGAAGAAGTTGACTCGAGATGCACAGGAACCACTTTTACGTGAGTTTTTAAAGATTT
      TTTTTTTGAAAATTGATGTCTTGCATTTTATTTAGCTCACTGGATAGTAGAAAAAATATT
      TTTTTTATCTATTTGAAAATCAAATGTGTTAAAAAAATATTTTTGGAGAAAAATAACTGA
      AAGCTCCTTTCTGAATTATTGTTTTATTATTAAACATTTGTTTTCTTCTAACTTTATGTT
      TTTTAATGTTTTTTTTTTACTTTTTAAATCCTGAATTATTTTGTGAAAATTCAAACAGTT
      TCATTTTTAAAATTTCAAACCCTGATAAAAAGTTCAATATTTTTCACTGAACTTTAATTT
      TTTTAAAAGTTTATGAAAATTTCCTATGAAATTAAGTTCAGAAGTTTTTTAGCTCATATC
      CGCCCCTCCACAAGGAATAAAATTCGAAAATATATTTATGGAACTATTTTTATTTTATCA
      ATTTTTCTCCTTTATCGATCACTGAACAGTCCAGACACATCAAAACACGGAATTGGCAGA
      AATGGAGATGTAAGTTTTGAGATTTATTGCAACAAATAATTTACAAAATAATTTCAGTTT
      ATTGAATATGAGCCAAAAGCAGGACCCACGATAAAAGAGCCTGTAGAGAATATAGTTAAA
      TTGGACGTTTATATGGAAGCACAGTGTCCGGATACATCTAGGTGAGCAGTTAGTAATTAA
      ATTAATTTAATATTTGATTTATTTTAAGATTTTTCCGTCAACAACTTAAAAAAGCGTGGG
      ATATTCTAGGAAGGCTAAATCGAATCGAATTGAATGTAATTCCATTTGGAAAAGCGAGGT
      GTACAGAGAAAGGAAACGATTTCGAGTGAGTTTTTTTTGTTAATTGATTTTAAATCTGAT
      CATAAAATATTGCAGATGTCAATGTCAGCATGGTCCGACAGAATGTCAGATTAATCAATT
      AATGAATTGTGTCATTGATCGATTTGGGTTTCCACATAGATATTTGCCAGGTGTTTTGTG
      TATGCAGGGAAAATATTCATTAGATGAGGCAATGAAATGTGTTACTGAGAATTATCCATC
      TGAATATGAAAGGTATGTATTTTGTGCCGTAAATGCATAGTTAGACCAACGAATACTTTT
      TAAAATCATACGAAATATATTTTCATATATTATCACTGAATATAATAGTTAATGAAAGAG
      TAATGCTCATTTTTCAGTTCAACTTTATTTTTCAAAGAATATTGAATTTTAGAATGCGTG
      AATGTGCATCAGGAACTCGAGGTCGCCGCCTTCTTGCTCTTTCCGGACAGAAAACTGCAT
      CACTAACTCCAGCAATTGACTTCATTCCCTGGATTGTTATTAATGGTTCACGTAACTCGG
      ATGCTCTTTATGATCTAACACAGAATGTCTGTGAAGCAATGCAACCAATGCCATCTGCAT
      GCAAAGATTACTTACGTTCATTACAATAATCACATCTTTTACGGGTTGACTTTTCGTCTT
      ATAGTTTTTTTTAAAATACAATTGGTGTCTATCTATGAGTGCCTTTCACAACTCGGCGGG
      TCCTAAAATTGTTTATTATATTTATTTAAATTTTTGTTGTAGTTTGTGTTAGTGTGACTA
      ACTTATTGTGTTAATTTTCTTAAAAAGAACGTTTTTTATTAAAATAAAAAGTTGCAAATT
      GTAAAAGTTTGTGTTTATCACATTATGATATTTTGGGCAATTGTGAGGATCTATTAAAAA
      TTTATAAATCTCTTTGACAGTGTGTGGGAAAAATAAGTTATTTTTAGCTTCTGATATTTT
      CTAGGATTAACAGAAAAAACAGCAAATTTCAGGTATACCCGCTTGCCAGTTCGTGATCAA
      CTCCAGTGTTTTCCAAAAAAACAAATCTACCCTTCCCCAGCTTCAGATGTTACAAACTCG
      ATAAAATTTGTTTCAGAAACATCTCTTCAGTGTGACCACAAACTAGTCTTTCGCTTCCTT
      TTAACAACAAAAAATGGAAAAAGAAGGAGGGATTTACAAGAGGCTACGACGATACGAATG
      AATGAAAACGATTTGATGCAATCAGCTGCTGCTTCTGCATTTGCCATTCAATTTGTCACC
      TTTCTGCCAAATTTACACGATCTGTTTTGAGTGTGGACTTTTTGAAAGTTTAAACCACTT
      TTCGTCAATTTTTAAATGATGTTTTTACTTCAGTTTTTATTATTTTGTTTTGCAAAAAAT
      ATTTCAGTATGCCTGCATTTTTTAAATATTTAAAGTTTGATTTTTTTTAACATCCAAGTA
      GAAATGATAGCTCACCTACTCCAACTAAATTTTGACCAACAACTGTCACTTCTATATTTG
      AAGACATAATTAACATAAATCTTGAATTTTTGAAGTAATTTTAATGTCTGAACATCTTGT
      TTTGAATCTTGTTTTTTTGCCGAAAAATTTGAAGAAAAAAGAAACTGAAATATTGCAAAC
      ATCGCCAGAATGCAGACGGTAGGGTTGAATAAGATAGAGGGCATTGAACCCTTTCTAATT
      TTCTGTTTTGCAAATTATTTTACAGTAGGTCTGAACTTCACAGTTTCATGGTACGCCCAA
      TTTTTAACTTCTTTTTTGAATTCAAATTTTCTAAACTACATTATCGATTTCCATGAAAAC
      AGTTGCATTAACTTCCTCTGACCATTCCAAGAATTTCTGGCTTACCAACCGACATCACTC
      TTGCCCCCTCGTCATTAAGCCGTAATTGATAGCGACAAAAAAAAAGAAAAGCCGGCTATT
      TTAATCGAATCTTCTTCATTTGAGAATGGAGGGTGCTACTTGAATGGGTGACAATTGACT
      CGTGAAATTCTTCTTTATCTTTTCTCCTTATTTTTCTCAGAATTTCTTCATCATCCACTT
      TTTTGGAGTTTCAAATGTTAATTGCAATCTGTCTCATTTTGGTAGTCATTTGGAAAACAC
      GGGGGAGGCGATAACAGGAAGCTTAAGGGATAGACATACACTTGCAATTGTCGAAAAAGC
      GATATCTTTAACGATTATTACGATTCTTTCAGTGTGACGTAATCCTAATCAGTTTATTTT
      TATTTTTTCTGAAAGCTTCTTTTACGAATTGCGCAATTAATAGTGTCAGTAGAAAAGGCA
      TAATTTTTGAAGAATATGCCAAAATATGTAAACCCTCTCCGTTAATAGCAGTAGCTAGTG
      ATCTAGACTATATGCAATACACACTAGTTGTCCAATTGAAACAGGTATCCACAATATTCA
      CGATTTTTGAAGTGTGATGTATTAGATAATCCTATCATTTTTTCCTCATCGGCCAGTACT
      TTTTTTGTTGTTATTTTTGCAATATCCTCCGCTTTTTATTGTTTTCCTATTCACACCTGT
      ATTTGATTCTGGTTTCCCAAAAAGAACAGGCATAGTTTTTGCGTTGGGAACTGGTTTTAT
      TTCAGCATATCTTCTCATTTCTCAACCAGAATTAGAAACATTTTTAGAACAATCACATTT
      ATAGCCTAAATTTTTACTAAAAATATCTGAAAAACATGATATACACTTTGTAGAATTTTT
      GAAAATAATATCCGCCTATCCATGATTTAACCTTATTATTCGAAATCTGTGAGATTCCTC
      AAAGTAGAAACATAAAATTTCAGGCACAACACAAAAGTCGGAACTCAATTAAAATCGAAT
      ACCCTGTTTGAGATGGCGTTTCTGGCTCGTAAAACGTCTTCTCTCCTACCAGCCACCACA
      TCCTCTACAGTCAAGCATATGATCTACGATGAACCACATTTTGCAATGCAGAACAGTTTG
      GCAAAACTTATCAAAGAGAAAATAAACCCAAATGTTGCACAATGGGAAAAGAGTGGAAGA
      TATCCAGCACATTTTGTGTTCAAAATGCTTGGACAACTTGGAGTATTTGCGGTGAATAAG
      CCTGTAGGTGAGGATACTTATTTTAAAGAAAAAATTTTGGAAGTTGAAAATTATTGAAGA
      CTATGGTGGGACTGGTCGAGATTTTGCAATGTCAATAGCAATAGCTGAACAAATTGGAGC
      AGTTGATTGTGGATCGATTCCAATGTCAGTCATGGTTCAAAGTGACATGAGTACTCCTGC
      TCTTGCACAATTTGGTGAGTTCTATAAAACTTATACTGTAACTTAATTGATATATCAGGC
      TCCGATTCACTCCGCAATCGCTTTCTTCGTCCTTCAATCAATGGTGATCTAGTTAGTTCA
      ATTGCAGTCTCCGAACCACATGCAGGATCAGATGTATCCGCAATTCGCACACATGCCCGT
      CGGTACGGCAGCGACTTGATAATAAATGGCTCAAAAATGTGGATAACAAATGGAGATCAG
      GCAGATTGGGCATGTGTTCTAGTAAATACTTCAAATGCGAAAAATTTGCACAAAAATAAG
      TCGCTGGTGTGTATTCCACTGGACTCAATTGGTGTACATCGATCAACTCCGTTGGATAAA
      TTAGGAATGAGAAGCTCCGATACAGTTCAACTATTTTTTGAAGATGTTAGGGTGAGTTTC
      TTAAAATGATCTACGGCCCCTTTAACCAATTTTAATAAATAATTCAATGTTCATTTCAAT
      CGAATCATTTTTCAGGTTCCCTCGTCATACATAATAGGCGAAGAAGGACGTGGATTTGCA
      TATCAAATGAATCAATTCAATGATGAGCGCCTTGTAACAGTTGCTGTTGGGCTTCTCCCA
      CTTCAAAAATGTATAAATGAGACGATTGAGTATGCAAGAGAACGATTAATATTTGGAAAG
      ACACTTCTCGATCAGCAATATGTTCAATTTCGGTTAGCCGAGTTGGAGGCTGAACTGGAG
      GCAACCCGTTCTTTGCTCTATCGAACAGTGCTGGCACGTTGCCAAGGCGAGGATGTGAGC
      ATGTTGACTGCGATGGCGAAATTGAAAATTGGAAGACTGGCAAGAAAAGTTACTGATCAG
      TGTCTACAGGTGAGGCGTTTTTGTTCTAAAATATACAAAAAATTCTCAAAATATGTATAT
      AAATCACTTGTAATATTCTCCATATTAGACTTGAATATTCCTTGCTCTTCTTTGTCAGAT
      TATATCTCGGTTGTATTTGTTTTTATGAAAACAAAATTGCCAACTAACAAAATTTGTGCA
      AAATAATTTGCTTTATTTTGGATGTTGAACTTTTTTTGATGAAATTAAGACAACCGAGAT
      ATAAACAGTCAAAGTATAGCAATGCAAGGATAATTCGGTATATGTTTTTGTGATCCCTCC
      AGTGGCAGTTTTTCATAACTTGATGGTTTTTTTATAGAAATGAATTGGAATAACGCTAAA
      GCTTCATTATTAATATTCTCTTAATTTCAGATCTGGGGAGGTGCTGGATATCTGAATGAC
      AATGGAATATCGAGAGCCTTCAGAGATTTCCGTATATTTTCGATTGGCGCTGGTTGCGAT
      GAAGTTATGATGCAGATTATTCATAAAACACAGTCCAAAAGGCAACAGAAAAGAATTTGA
      GAACATTTTTAAATGTTATATTTGTAAATACGAAAATAAAATGCAATTGTACTGAAAACG
      ATAAAAATAAAACAGCGAAAAAGTCATATTGTATAGAATTTGGCACGTATATCTACAACC
      AGTTTCTAGTGACCCAGGTATCTTGAAGTAAGTATTCAATGAATCAATTCAAGTTATTAT
      ATTTATATTTGTCCGCATCGGAAGGAAAGCGCAAAGAAGTTTCTCTCTCCGCCTCATCAA
      ATTTTTTGTGTTTGCATTTCAAAAATGACTGCAATGAAACGCGAATTACTGCGAGTAAGT
      AAAGTTAGTTTTGATAGAAACTACTGTATGAGAAAACCGGTTGAAAAGTAAAGATGAGCA
      GCAGTATTTCATGGAAAAAAGAGGGAGACAACAAGAGACGGAGTATATAAGGTGTCATGG
      ATGCTCCGAGAGTGTTTACTTCTTTGTTTCAATTTTCACACTTTTCATTCTTTTCATTCT
      TTTTGTTTTTCACAATTATTTAGCAGATCGGTAACTTTTTGCTTTGATAATTTCATAGAT
      ACTTTCGAATCGAAATTAATTTTCAAATTAGCCTACAGTAATTTTGCTCTCATCTCTGAG
      TTCTAGATCATGTTTCAATTTACCGAAAGTGTTTACACAAGTTACCAAGAAAACAAAAAA
      TTCAAGTTTCCGAAAATTATCAAATGTTTATCAAAAAGGTCCTATGATGTTTAAAACAAT
      TTTTCAAACTTCCAGAAAAATTTTAACTTACTGTTTCTTGAGCGTTTACAGTAACTCCGG
      TGTTTCCAGTAGGCATAGCTTACCTTGAAAGCAGGCAGGCGAAAATTTCTCTAGACCAAC
      CAGAATAACTTACTTTATTGCTAAGTTGAATCAAACAATTTTGTAAAAAAAACGAATTTT
      GGAATCATGATCCCTATTCAAGCTTCTAGTTGCTGGTCAGCTAGGTTTTGGGTTTTTTTT
      TGGAAAAATATTCAAAAAACATTTATATAATAGTTAGAATTAACATTTTTTGATAAAACC
      TCGACATTTTTGTTTTGTCTGAAAAAATAGGAAAATCTTACGTTTTTCGAAAAAACCCGT
      GCTCGTGAAAAGTATGTCCTCTGAGAGAAGTAATGTTTCATCTGACCAGTTGCAACTTTC
      TGTGTGCACATTCTTTTGATAAAATGGTATCACAGATCTATTCTAAAAGCCAACATCTAA
      ATTCTTTGCTCTATCTTTATCAGTTGATACGGATCTTCTCATCTCATTCGCCCACAATCT
      TCCCATACTAATTCATCAAACCCACTTGTAAATATACGCGCGGTTGATCAAAATTTGTGT
      GTGTTATGGCACATTGTGCAAATAGTTTTACCACACTTACATACTTCAACTCAAACCTTT
      GAGGAGTTTGACAGAGAGATGGAAAGATAGTCTGCAAACGGCAGATTTTTGAAGTTTCAC
      CGCTGTCCATCTAATTTTAGGTATTTTTCGGAATCTTTTGCAGGACGTTATCATCTATCT
      TTCCCGTTATCAATTAGTCATAATTATCCAATTAGTGGCAGTTGTTAGAAGAAATAGGTA
      ATATGCATAATAGTGTCATTTGCCATTGGCCACCTCCACCAAACTTTCGATTATGCCGTT
      TTCCGTTTTCTGTGTGTTTCTTCGTCCTTCCTCATCATTTCTCATTCGCTTTTTTTTCTT
      CCCATCTTTTCCAACATGTCGCACTAAGAGTGACCAAAAAACCTTTCAAATTTTGCGTGT
      TCTTTCGGTCTTTCCGGAAGGGACAAAAATCAAAACGACACTGGAATTATGAACTCATCC
      ATTTTCCACTTTAAAAGTTGAAAAAAGTAAACAGCGGGGTTATTGTGGTTTGATCTCTTT
      TAAAAATCAGTTAAATATAGGAGTCAAGACCTCAATGAGCACTCTTCAAGATATGGTTCT
      ACTAGACTCAACTTGAAGATTTTCAAGAGTTCTGGAGACTTTTTCAAGGCTACTGCTTTC
      AAGCTTCAGAATTTTAAACATTTTGGAAATAATCTTAAACTGGAGTTCAATAGCCAATTG
      AGCAATTTGTTATAACGTTTTTTTCTTAATTTTTTAAATTAGAATCAGTGTAAATTTATA
      AGTTTCAAAATTAGTTTTGCACTTATCTTTGGGCGTTACTGAATTTTTTACGTGGTGAAC
      CTTGAGAAAAAATTCTAAGGCTTCTAATTGAGAAAACTAATTTAAATTCCGCTCCCAGGA
      GTTACCAATTTTAATACGTTTCCAAAAAATTAAATATTCTTCGAATCTCATTTTTAAAGT
      TTCCATTTGGCACAAACCACAATAATTTAAGTAAGACGTTTGATCTATGCCGTAGTTTGT
      GTACTTCAACGTTTATCCTTAAGTACCTAGGCCCGTGTTTTTACAGCTCTGCTCTTTATC
      GGTACATACTGTTCTCTGTCTTTATTGATAGAAATTTTGAAAAATGCAACAATATGGTAT
      CTATCAGGTCGTCCCATAAGTTTTTGTACTTTTTTAAAACTTTTTGAACAAGTTCTAAAC
      TGACAGAACAAAATCGAATCTTTTATAAATGCGCATGTATAGTATGTACTACTTGTCAAA
      ATTTTTATGCGTTATTTCAATATCCTCCTGATAACAATCACGGAAACCAGAGCCACAAAT
      AGCGACATACCCAAATAATGGGAGGTGTTTTCCTTCGTCCTGCTATTCACAGGGAATTTA
      TCAATGAACATGAAAACATAGTATTAGTAAAGATAATGATTCAAAATACATGTTCAGTAT
      GGTTAAAATTATCATTAGCACTTATTAGCCGTTTTGGACGTGGACTATTTGGCTCATGTT
      TATCAAGCACTGAGTGAACATCTTCATGGAATAATTTCTCACTAAAAGTGATGGGATTAT
      TTTGATTGTTGTTTCTAATTTTATATAACAATACTTGCATAGTACAAATACAAACTTCGT
      TTTACTTGCTGATTTCTCAATCATAAATTAGAAGCCCAACACTATAAATGTCGGGTATCA
      CATGAGGTTGGCCATGTAGATTGTTTGAACGAAGAGGCCACCAGTAAAGTTTGTTAATTT
      ATTTATGATACATATATCCACTTCTAAATAACACTAGACTTAATTATCTATCTTTCATTC
      CGAGGACTAAATGGACCAATATATGCTTCAATCACTCCTATAGGCAATTGTTAAAAGTAC
      AAAATAGTGTGGTTACAATGTTCTCAATTATAACATCTCCCCATGACTGAAAAAATTAAA
      TTTTTTTAAAATTTTGACTGCACATGATGTGCACTTATCGTAAACATACACGATGCACCC
      GTTCCATTCCCAGCGGCTTCACAGGAATCAAAAACTCGGGCGCCATATTTAATTGGCCTC
      AACAATTGTGTTTAGCTACAGTAGTTTTTCCGGAATAGTTATACTAAATTTAAAATTATT
      TAAAACAAGAGTGTGGAAGCATCTACTTGACAGTATATATTAACCATTACTTTAAGCTCT
      GGGTGGTGTAGAACAAACTCCAGAAGGAATGGTGTAAAAAGCTGATTCTATAGTTACTCG
      TTTTTCTAAACAACCGCGGGGGCCTGGGATGCCAGAGTTATGTTGCAATAAGGTGACAAG
      TTGGTGACATGCTACCACTAATATAAAATCTTAGAATTGTCCGAAAAAGTTTTGGGAATA
      ATTCGAAAAAAAGTACAAAAACTTATGGGACGACCTGATAGGATATATGTTAAAAACTAT
      TTTTGAAAAAATATTTTATTTTGAACAATGAAATAAGGTTCCTGCCTCAAGGTTTCTTTT
      TGACGCGAACTCCGATGACATTTTAATTATCAAACGGTCTAAGTGAAAATTTATTGGACA
      ACTCTTTAGTTGAAGTGCACTTTAGGAGCAGGCATACATGAAGGCGTGAGGCAGGCGTAG
      GTCGCTTACGAGGCAGACAATTTTTAAAAAAATCACCATCCTTTTGTACTAATAAACACT
      CTCTAAAAGTTTGCAATGTTGTCTCCCAACACGAAAAGTTCAATCAACTTCTGCACTCAA
      TTTTTTTGCAAGATGACCCATTTGATTCAAGGGGGTTACCAGTAGACTTACCTGCAAAAA
      AACAGTATTCGTGCATAAATCCATCAAAATGAAGTGTGCGTCTTCTTCTTAGTTTCCGTC
      TCCCGTTGTTTCTTAATGTATACAGAAGATGTACGGGGCAGCAGCAGCAGAAAAAAGATT
      TGCGTACACCAAACACATCAAAACGATATGCGTGAAATGAGCGAATCGTCCGCATTCTCC
      CCTTTTTTCTTTCAATTTTCAAGGAGAGAGAAAACTCTGTGAGACAGTGAAGAAGTGGGG
      TTTTGACTGGAAAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAACTGATTCTTA
      TCTGAGTTCCGACGACGATTCCACCGTTTTTTGGTCTGGTCTTCTTTCCTCCGCTTCTTC
      TTCTTCTACTTCTCTTTTCACGTCTTTCTCATATTTGGTTGTTTTTCAAGTTTTGAACTC
      TTTCTACTACATACTTTTCACATGTACCTTTAAAAAACTCATAATTCATTTTCCAATGTG
      TTGAAAACTACTGTAACTGCTTAAAAGTCAGAAACAGTAACGAAACTATTTTCATGATAA
      AATCAAAAATTGTTTCGATTCGAAAATGTTTTTATATACTCGACATGTGTGTACATGTGT
      AAACCAGTCGTTTCAAAAATTTTACAAAAAAATGTAAAGAAACTGTTCAGTGATCAGTAT
      GCTCCAGCTTCTTAGTTTCTTAGTTTCTAGGACTTCACACACTGCCTGCCTTCAAACTAC
      CGCCTATTAACATTTATTCCGGTCGCTCTTTTGTATTTATTGAGGAAATCAACTACTGTA
      GTTTTTTAAAAATTAATTTATTGATTTGGCAATTTTTCTTTTTTTTTCAAGATTCAAAAA
      TAAGAAATTGTATTTTACTCACCATTATTCAAAAAACTTGATGAAATGTTTAAATTTTAT
      GGTAAATGATCAAAACTAATTTTTTGAAAAATCGACGCCTTCTCTTTTGTTTCTGAATAT
      AGGCACTCCTAGCCGTGCAGGCAGGCATTTCTGTGCCTACACGAAAGCCCTAGAATACAT
      ACTTTCAAAATGTTCACTGTTTGTTCTTTTTCCCTGAACATAGAACATCCGGAAATTGCT
      TACATTGGAATTTCATTCAAGTACATTTGTAAAACTTACAAACACTTGAGAAAACAAAAC
      AAATCTGAAAACGTGTTGTCTGAATGCATTGGGGAGACAAGTTGGGTTCTTCCTTCCATT
      TACCTTGTTGTTGTTTTTTTTTCTGTTCAAAAATTTATTCGTTCTCTGGGTCAAATTGTT
      CAATTATAGTTGTTGTTTGCATTCGGTTGTTCCATTTTTCACAGTTTTCTCTCTTGCAAA
      AATTTTATAAAAGACTACAAGTAAATATAAAACCATGAACTCACATTTGGCACGGGCTAG
      AATTCTGACTTCTGCCCTTCATTTTCTGTTGAAAATTGTCAAATTCTTTTCAAGGTCTTT
      TATTTATTTTGTTCCTCGTGGAACATAACATTTTTGATATCTTTCAATATCAAACTTTAG
      TCTACTCATAAACTGTATGTACCTACCTACAGTAACCTCTCAGAAACATTATGATCCTAA
      GTATTTCTGATATTTGCTCCGAGGTAAAAGTAGATCCTACTTAATTTATAAATTAAGTGC
      GTCAGTATCTATGTTGATTTAGTTTTTGTGATCTTCCAACTAATCGTATCTATCAGAACA
      TCAGTAGCAAAAATCTAAAATCATGAGAGAGCATTTTCTAAAAAACACATAATTTTCAGA
      AGGCTTCATGGCGAAGGCGCATGCCGAATTTTTGCTTTTTGACTCGACATTATACAATTT
      TCCTTTAAAAAAATTAAGTTTTATTATGATATTTGGTGATTTAAAAATTATAAGATTAAT
      TTTTAATCATTGCTCTACGGGCCGCACTACGCCTTTAAGCCTCAGTTCCAATATAATCAG
      TTTGAATATTTAGTCACCGTTTTGACATTTACAGCTTAATCCAATTACTTTCAACTCAAT
      TTATCAAACTGTCAAAATGCCCACCTAATTGTTCTTTGCCAGACTTTTGAAACCAAAAGC
      CACACCCTCAATAGGTCATCTAAAAGTAGCTGTGGTCTCTCCAATGACCTCTATTGTAAA
      TTGGGCGGCAATTCTTCTTCATCATCAATTTCAGATGCATCACAAGCATCAAAAGCATCA
      TATATGAAGAACAGTAGAAAGAGGAAACTCATACTTTTCTAACCATTTTTTCTGATATAG
      ACACTGGCATAGACCAATTCAAAAGTGTTGTAATATTGTACCGGCTACTCTCTTCTTTGT
      GTTCTGCATTTTTCTGTCATTTTTCTTGAAGAAAAAGGCTTCTGACCTCTCCTCCAATGT
      CACCTTTTTAGTGTTTCACAATAGGATTATTCCCATGCTTTTCACACAGTCTCTGAATTT
      TTTGTTGTTCGAACCAAAAAAAAAAGAGAGTGTTTAGCTTTCTGTTTAGTTGGTTTTCGA
      CTTTTTTATTGACTTTTTTATTAATATTTTCGTCATCTCATCAATCATACATAATTAAGC
      GGACAAGGCATTAGGACCGGTGGGTGAGATGTGTTGTTGCGTTAGACGAATTCTAGATTA
      CGTGATTTTAGTCGAGATTGTGTCGTCTGTGAATATCGAAATAGCGATTTAATTAGTCAT
      GGGAAAAGTTGTCGTGGTAGAGATTCAAGTGACCTTTCTTTGCCGTTTTTATGGCTTAAT
      CTATAAAAGGCTTAAAGGCTTGTAGTCTTCTAACCGGACGATCTATTACATAATATAATG
      AAGGGGATATTTAACTAATTTTTTTAAAATTAAAATCCATAAGACTAGCTGAAATTTACC
      TTAGGAATGCTATAGAAATATCAAATTTCGTCAGTGTTCTATTTTTTCTGATCACCAAAA
      ATTATCAGTCGACAAAAAAAGTATATTCCATTTTTTATGCATCTACTGTGCCATGGGCAA
      TGGATTTAATTTATATTCTTGGTGAGCCCTCCCATGTAGGCTCAAAACTGCCAAAAATGT
      GCAGCAGACAGAAGCTCAGAGAGGCAGGCAGGTATGAAACAGACAAATATACCTAGATAC
      GTGCCTGCCTACGTTTTCAAAATGCATCGATTTTGTCTTGGAAAAGCTGCTAAAATCTTA
      CAGCTCCTGTGCCCTTCACATGCGCTGGAGTTCAACTCAAAATGGCAAAAATGTGTGGTA
      GGCTAATTTTTTGCCCGCCTACGTTGTTGCATTGAGACAACTTCTGAACGGATTTCGTGA
      ACAAATTTTCTTTCCAGATTAATTTTTTAAAACTTTGCTCCCAAAATTGCATCATTATCG
      GTAAAGTTCGGGTATCCCCTCTTCATCTCTTAGACTTACTGTGTAACAATTTGCATAAAT
      ATACACTGGTCTCTCTCAATCTTCTTTCATTTGATCACTTATACTTTTACACTTGGCACG
      CACACATAGGCGAACCGCCAGGCTTCTCCTTTGCCCTTCTGGCGGCCAACCCCCCCCCCC
      CCCCCCCCTCCCCCCGTTTTTTAAGTTTTCTTGTCATCTTGAAATGGTCGAAAAAATTAG
      TGTTGTATTCTTGCACTGACGATGATGATGATGAAGTGGAAGAAAGAACCTGTTCTCTCG
      GCCCACAAAAAATTCCAGAGGTGTTGGTCAATTTGACCTTCTAGACCATCACATTCCAGC
      GCGGCTTCATAAAGAAATCGTCTCGAGAAAATTGAATTCAAGAATAGAAAAAATTATATT
      TCAAATGAACTCGATTTTTGAATGCTGAATTCTTCTTCCTCACAATGACAGTCTCATTGA
      ATTATAACTCAATTTTTAGAATTTTTGATTCCGAGTGAACCACATTTCAGAAAGGAAAAA
      AGTTTTGATGATGTGTGTTCAATGTATAGGTTACTGCCACACCACACTACCAATCAACCG
      GTTCTAAAAAGACAAGCTTCTCTGGAATTCAGTTTCAGAACACTGGGGCGGGGCTTCAGG
      TTATGTTGGGAGTGGGAACCAAGAAGACACACGACTTCTTATTACTTTTTTAGTTTTACA
      AAAATTTCATTTTCTTTGAAACTGTTTTACTCAACTCAAAAAAACGAGGCCAGGAGAGAG
      TTCAATATTTATCGACTTTTATAAATTTTATATAATTTCACCATAAGTTTTATACTATTT
      TATGCAAGTACATAGAGTGTGCTCTTGGTAAAGCGTCTAATTTTTCCGAAAGTTCACTCT
      CTTTAATATTTTGGAATTTTATTTGTTTTAAAAGTTCGTTTTGAGGATAAACCTTGAAGA
      TTGGAAAACGGTAATCTTTGCAGCGATTTTTATAACTGGAAACATGCTATCAGTAACTTA
      ATTTTATTTGTTCTATAAAGTTAAAAAAACGTGAGTATAAAAATTTCAAAAAAATCCAAA
      AAACAGACTCCGCCCAAATCTTGGCTTCTTTAAATTTTTGTATAAAATGTTCGTGTGCTT
      ATAATTCAACATTTTGACTAAAATGGAATACTGTAAGAAAATACCCCCGAACTTGATATC
      AACCCATTATAAACTCTTGTGATTTTATAATTTACAAAAAATGATAGTTGACAATTATTT
      GAAAATTATGGAACCAATGTCCTAATCTACAGCCACATACAGTTATTCTTACAATTATAT
      CAAAAAATCATATTCCCGTTCCGTTTTCCCTCTTTCAAAAGTCGTTCATATCTGCTTATG
      GCACCTGTTGCGCCACCCCACGCCACCCAGATACAAGATTCTGAAAAAAAAACGAGTGAG
      AGTAAATGTAAGACGAAGAGATTTAGAGAAAGTGTCAAAATCCCACTGGTTTTTTATTCG
      ACATCCCCCTTTTTCTCACTCACTCGTTCGTCTCGCCATCGCCGTCGCAAAAAGTATCAT
      AAAGTTGCCCTCACTGAGAGAACGACTTGCCTTCCGCTGAGGATAGATGGTTCCCGCGCG
      GAAGGAGAAGGAATCCCCTCTCTTTCTCCGACACTTTCACCGCTTCTCATATGATGCCAT
      TCTCGGGAAATACATTCGTAATTGGATCATCTGGGACTGGCAAAAATGAGAAAGAGAAGG
      GGGAACGTTTTCTTTTCAACTGGAAAATAGTTACTGACCTTGAGCCAACTGGAAGCAGAA
      AATGTTTAATTAAGGGGAAGAAACTAAATAAGGAAAATTAGTGTAACTACATTTACTTTT
      ATGGTAGGAGATCACTTTGTAACTTACTAAGTTGATTTTGCTAAAAATAAAACTGATGGC
      AGACCATTATCATTAAGTTTTGTAAAGCATCAATTTGAACAGCAAAGTTGAAGCATAAGC
      CTATGCGGAAGCTTGAATCTAAGTCTATGCCTAAGCCTAAGACTAAGCCTACGCATAATT
      GTAAGCACCTTTTTTTCACATTTTGGAACATTTGGAAATTTACCAAAAACTTCAATCGAA
      ATCTTTGAAAACTCAAAGAAGTTGTGTTCTATTATGTTATTCGATCATTTTGGACTAATT
      TAAATATATTCAGACAAAACCCCTCAGTGACTTTTGAATAGGTCCAAACATTTTTTAATT
      TTACAGAAACGAATCCATCAATATTTTGTTATTTTGCTTTCATAGCCGAGGGCACAAGTG
      TCTTTAGATGAGATGACATCCTCAATTCTAGACACGGATTCTAGACATGGGCTGTTGCAA
      TTAGCATAGTTCTTGGTACTTTACGCATGTCACATTGAAAACTAAAGTGAGAATAGTTTC
      CCGTTCCAATTAATACGTCGCGCCCTCTGTTTCTCCCAAAACGATACCAATGGCATCACG
      ATTGAAAGCGGCAAAATATAGAGAGATTGAGAGAGAAACGGTTTCTATATACAGTGTAAA
      TTTGCCCCCTGTTGCCATCATCATCACATAGACATACACACTCCATAATAGCTAAGGTTA
      GCTTCCTGTCGCCCCCATCTCGGCAATAAAAATCGCTTTGATTTCAATCTCATTTGTTTT
      TTAACCACCAGTTTGCTTATTTTTACTTTATAAATTGAGTTCTCTTGTTTCCAAATTTTT
      TTGCAAATTACATACGTTGAGGACATTTAGTCATAATAACCATTCTTTGAATTTTTTAAA
      AGTTTAGTGGCTAAAAGTCTTTCGTGCTTTTTTTCTAGACATTTTTGAAAAACAGCAACA
      ACTTTCGAAAGTTTAATCAAATACTTTTAAATTGTAAAATGCCTATTTGTTTATGTATTT
      CTGTTATGAACAATAGAGTTCCAGTTTGTGTATCTATGATCTTTGATGACTACTAAACAG
      ACTTTGTTTTGATAGTTCCCGGTTTTTAGCAGTTTCAATTTGAGAAAGAGTCTAGGTATT
      TCCTTATCACATTTGATAAAGTAGCTAATGGTGGCCGTGAACTGTGATTACTCAATGATG
      ATGTCGAGGATTTTAGGGATTTGAACGGTTTTTCCAAATTTTAGTTAATTCAGTTTTTAT
      AGCTGAGCTAACTATTATAACTTAGCACTAATTCCATTTATTTTGACTCTCCAATTGTCA
      TCTGGCACAGTTAAGTATTTCTTAAAGTTTTCGGTTTCTACATTGCCTATAATTTGCTCA
      ATTTTTGACCATGCCGATATTTGATACTTTTCACCTTACTTATGTAAAAAGTCAACTACC
      TTTTTTTGCCGCATGGCTTTATTAGGCAAATAGCAAAAGTCCCCCTGAATCTTTTTGAAA
      ACTCTTATTTTTAGTCCCTTGAACATTTAATTGAACTGCAAAATTGATGCTCGTTAATCT
      ACATATATCCAGTAAATAGGCCGTAGGCAGGCAGGTGCAATATTTGATTATTTGTACCCA
      TCTAACATGCTGGTCTGCTTCTGCAGCCACTAGATCTAGTTTTCATTGTTCAGCAAAAAA
      TCCTAGGCAAGATTTACTAAAGTTGTTGCCCTTCCTGACCTAAATTACATGAATTTCGTT
      ACTCTAAAATCTTTCAACGACTTTTGTAACGCATTAATCTGTTTTTTTTCACTTCCTTGA
      TTATCTAATAGTTCTTCTTTTTCATCTTCAACATCCTTTTTCCCCTTTACTCTTTCCCTA
      CATCTTACCATCTCATCAACAATCTTTCATAAATCTCTCTTTTAACTTTCGATTCTTTCA
      GTATTCGGATTCATCTCAACATGCGTGTCACCCTTCATTACTTCCTTTTTATTACCATTT
      CTGTTTAGTAGTTGAACATTTGTACATGTGTGTTCTTCCTGTCTACAGTTTTGAATGGGG
      GCTCGAAACCTTTGATGATTCACGGTATTTTTTCTCTTGTTCTCAAGTTTTAGAAATATA
      GAATAACACCACATATTTCTGATAAGATCATTATATATAGTTATGATGTATGCTCTAACC
      AAATAAACCTTATCACTATGTTGTTTTTCCAAGTTTTCGGAAACCACAGCGTTCACTTCT
      ATTTCCTCCAGCTGTATCATCAACCGTTACCGCAATGAACATTGCGCAACACTCATTTTC
      CATCGGTTTCCTAGTTCTTCTTCATCTTCTGTCTCTCTTATATTTTATAGAAACATTGAA
      AGAGACTAGGAGATATAGAGAGAAAAAGAGACAATTGGCATTCGTTGAAAGAGAGAAGGC
      CTGTTGCGCAGAACCCTCTCTCTTGCATCCCTGCTTTTCCATCAGCTTCTAGCATCAGTA
      ATCGATCCGATTAGGTTAAGCTCATTTTAAGGATCATCTCACTCTTAGTCTTTAAATTTC
      ATTGAATACTGTAGATAGAACTCTAGACTTTGAACTGACGCTTTTCTCCAGGCTTTTAGG
      ATTTTGGGCAGAGCCGATAGTCATGGTTTGTGACAACTGCCGGTATAAATTTCACGTTTT
      TTCTGAAGAAAAAAAGCGTCCAGAATACCTCTGAGATTCAAATATCTCACATTAAATTTA
      AAAAAAAACTATTTAAAAATTTTCGCGGCGTTCGACAACTTCGGCAATTGCCGGTGTCCG
      AAAATATTTGCCTACGGCAACTAGGTTGCTGGTAGCCAAAAACATTTGGCGCAGTTCGGT
      TGCAAGATTTTTAGAAGACAAATTGATATTTTGAGGAAAAAATACGACTCCTAAGGTAAT
      TAAAAAATTATAGGCTCCAAAAATTTTGGATTGAAAAAAAGAATTAGAAAAATGTAATCA
      CACTTCGAGCAAAATTTGAAAATTACAATTTCGAAATCCGATAGATTTCCACTATAAACG
      ATTTCTAATACTTGTCTGATTTTTTTGAACCCAACCAGAACAAAAAACTTGAACCAGAAC
      AAACCAGAACAAAAAAAAACAAAAGACCTAAAACCCACAGCAAAGGGCAAAAACTACAAA
      AGGCGGAAACCATTTTTTCTAGACATTTTTCTTTATAGGACGTCAAAAAATGTAAGAAAA
      GACATAGGGTAGAGTGAGAGAATAAGAAATGGATGCAAAAACCGCAAAAACTGTTTATAT
      CTGACTATCGCTCACCCAAAATGCAATGTATCTGTCGTCTCTTCGTCTCTTTCTCTTTCA
      TTTTCCCTCTCTCTCTCTCTCTTCCTTGATAATATCTTGTGAAGATAAATGAATGAATTG
      GATGAGACGTTTGCTTTTTGGGTTCCCCTATTTCCTGAAAATCAGGAGGTTATTGGGTTA
      CTGGATAACTTCCTTGTGTCCTTTTTGTCGGTGTCCTAGAATACTGTAGACATTTTCAAG
      GTTATGATGTACCCATCTTTTTTCCCCATTTTGCATGTTTTACCTCTCCCTTTCATCTTT
      ACTATCTTGAGGGTCAATCTGAACACTCTTTTTTTATTTTGGTTTGATGTCGTGTACTAT
      TACCGCTTTCATCTTTCTTGCATGTGTAAGACTTTCAGTTAGCCTATAAACTAGAAACGG
      CAGCCGACACGTCCCAGGTTGTTATAGAACCCGTGATTTGTCGGCTGCTCATCCCTTTGT
      AGTTTGCATTTCGAGTAATTAATTAAAAATAAATGAACTTTTGCTAGCGATGTTTCCAAA
      TTTGTTTTTTTTATTTGTTTCAAAAATTTGCCCTGTCTACCAAAAAAGTTTTAAAAGCTC
      CGATGACTTTAGTTTGGAATTTTTCTAATTCAAATTCCAAGGCTATCCATACCTTTTTTT
      ACTAAAATTCCCATGTTTTTTTGGGTGTTTTTACCCGAGAGACAAAACGGCGACAAATTT
      CTCGAATTCCCCGCTCCTCTCCTAATGAGTTATGTGGTCGTTTGGAAAAAGGAAAACCGT
      TTGGCCAGCAGTGGCCACTGCTAAAAATGAAAAAAGACGATGATGGGTGATGATC
    
  
  
    
      1
      28735
    
  
  
    source
    source
    
      chromosome
      III
    
    
      clone
      C02D5
    
    
      db_xref
      taxon:6239
    
    
      mol_type
      genomic DNA
    
    
      organism
      Caenorhabditis elegans
    
    
      strain
      Bristol N2
    
    
      source
      source
      
        chromosome
        III
      
      
        clone
        C02D5
      
      
        db_xref
        taxon:6239
      
      
        mol_type
        genomic DNA
      
      
        organism
        Caenorhabditis elegans
      
      
        strain
        Bristol N2
      
      
        source
        source
        
          
            1
            28735
          
        
      
    
  
  
    C02D5.3
    gene
    
      gene
      C02D5.3
    
    
      C02D5.3
    
    
      C02D5.3
      transcript
      
        db_xref
        GI:32453032
      
      
        db_xref
        WormBase:C02D5.3
      
      
        gene
        C02D5.3
      
      
        note
        
          contains similarity to Pfam domain PF02798 
          (Glutathione S-transferase, N-terminal 
          domain)
        
      
      
        product
        Hypothetical protein C02D5.3
      
      
        protein_id
        AAO12454.2
      
      
        standard_name
        C02D5.3
      
      
        C02D5.3
        start_codon
        
          
            5035
            5037
          
        
      
      
        C02D5.3:1
        exon
        
          
            5035
            5077
          
        
      
      
        C02D5.3:2
        exon
        
          
            5411
            5851
          
        
      
      
        C02D5.3:3
        exon
        
          
            5956
            6208
          
        
      
      
        C02D5.3:4
        exon
        
          
            7984
            8008
          
        
      
    
  
  
    
      translation from_gene[C02D5.3] cds_boundaries:(L16622:5035..8008)
      transcript_info:[C02D5.3]
    
    
      MTVLAGVNSKIVKNGCWNHSYLQHAILPVAQRALIYASVKNIPSDVINVHLQEKPDWYFS
      KHYKGQVPTLEHDEGKKHVIESAVIPEYLDDIYPETRILPTDPYEKVQQKLLLDRISGQV
      SPAFYGVVQAVKNPDLREEKFADIKKAYDNAEQLLTGDFYSGTSKPGFVDYLLYPNIQRA
      YWAAHIVPDFPLEAESFPGPNYPRLSKWYKALESIPEVAAASQPTENGVGFFKDYLGGSP
      NYDYGLTKLSETI
    
  
  
    C02D5.2
    gene
    
      gene
      C02D5.2
    
    
      C02D5.2
    
    
      C02D5.2
      transcript
      
        db_xref
        GI:289605
      
      
        db_xref
        WormBase:C02D5.2
      
      
        gene
        C02D5.2
      
      
        note
        
          contains similarity to Pfam domain PF03227 
          (Gamma interferon inducible lysosomal 
          thiol reductase (GILT)); coded for 
          by the following C. elegans cDNAs: 
          CEESG21F, CEESG21R, CEESG21 
        
      
      
        product
        Hypothetical protein C02D5.2
      
      
        protein_id
        AAA27914.1
      
      
        standard_name
        C02D5.2
      
      
        C02D5.2
        start_codon
        
          
            9783
            9785
          
        
      
      
        C02D5.2:1
        exon
        
          
            9783
            10002
          
        
      
      
        C02D5.2:2
        exon
        
          
            10373
            10509
          
        
      
      
        C02D5.2:3
        exon
        
          
            10558
            10661
          
        
      
      
        C02D5.2:4
        exon
        
          
            10709
            10825
          
        
      
      
        C02D5.2:5
        exon
        
          
            10876
            11052
          
        
      
      
        C02D5.2:6
        exon
        
          
            11213
            11429
          
        
      
    
  
  
    
      translation from_gene[C02D5.2] cds_boundaries:(L16622:9783..11429)
      transcript_info:[C02D5.2]
    
    
      MSKYLRTSHPSPLICRPILTFSSLHILTAFLISGNSSYINWSVTIILLILGLYACHRFLN
      MKKLTRDAQEPLLPHIRPSTRNKIRKYIYGTIFILSIFLLYRSLNSPDTSKHGIGRNGDF
      IEYEPKAGPTIKEPVENIVKLDVYMEAQCPDTSRFFRQQLKKAWDILGRLNRIELNVIPF
      GKARCTEKGNDFECQCQHGPTECQINQLMNCVIDRFGFPHRYLPGVLCMQGKYSLDEAMK
      CVTENYPSEYERMRECASGTRGRRLLALSGQKTASLTPAIDFIPWIVINGSRNSDALYDL
      TQNVCEAMQPMPSACKDYLRSLQ
    
  
  
    C02D5.1
    gene
    
      gene
      C02D5.1
    
    
      C02D5.1
    
    
      C02D5.1
      transcript
      
        db_xref
        GI:15145275
      
      
        db_xref
        WormBase:C02D5.1
      
      
        gene
        C02D5.1
      
      
        note
        
          contains similarity to Pfam domains PF02770 
          (Acyl-CoA dehydrogenase, middle domain), 
          PF02771 (Acyl-CoA dehydrogenase, N-terminal 
          domain), PF00441 (Acyl-CoA dehydrogenases); 
          coded for by the following C. elegans 
          cDNAs: yk122b9.5 
        
      
      
        product
        Hypothetical protein C02D5.1
      
      
        protein_id
        AAA27913.2
      
      
        standard_name
        C02D5.1
      
      
        C02D5.1
        start_codon
        
          
            13633
            13635
          
        
      
      
        C02D5.1:1
        exon
        
          
            13633
            13867
          
        
      
      
        C02D5.1:2
        exon
        
          
            13920
            14054
          
        
      
      
        C02D5.1:3
        exon
        
          
            14099
            14451
          
        
      
      
        C02D5.1:4
        exon
        
          
            14536
            14889
          
        
      
      
        C02D5.1:5
        exon
        
          
            15271
            15420
          
        
      
    
  
  
    
      translation from_gene[C02D5.1] cds_boundaries:(L16622:13633..15420)
      transcript_info:[C02D5.1]
    
    
      MAFLARKTSSLLPATTSSTVKHMIYDEPHFAMQNSLAKLIKEKINPNVAQWEKSGRYPAH
      FVFKMLGQLGVFAVNKPVDYGGTGRDFAMSIAIAEQIGAVDCGSIPMSVMVQSDMSTPAL
      AQFGSDSLRNRFLRPSINGDLVSSIAVSEPHAGSDVSAIRTHARRYGSDLIINGSKMWIT
      NGDQADWACVLVNTSNAKNLHKNKSLVCIPLDSIGVHRSTPLDKLGMRSSDTVQLFFEDV
      RVPSSYIIGEEGRGFAYQMNQFNDERLVTVAVGLLPLQKCINETIEYARERLIFGKTLLD
      QQYVQFRLAELEAELEATRSLLYRTVLARCQGEDVSMLTAMAKLKIGRLARKVTDQCLQI
      WGGAGYLNDNGISRAFRDFRIFSIGAGCDEVMMQIIHKTQSKRQQKRI
    
  

BioPerl-1.007002/t/data/test.gcg000444000766000024       112113155576321 16324 0ustar00cjfieldsstaff000000000000Rea guano receptor type III >> 0.1
roa1_drome  Length: 358  Thu Apr 17 12:09:52 2003  Type: P  Check: 8903  ..

       1  MVNSNQNQNG NSNGHDDDFP QDSITEPEHM RKLFIGGLDY RTTDENLKAH

      51  EKWGNIVDVV VMKDPRTKRS RGFGFITYSH SSMIDEAQKS RPHKIDGRVE

     101  PKRAVPRQDI DSPNAGATVK KLFVGALKDD HDEQSIRDYF QHFGNIVDNI

     151  VIDKETGKKR GFAFVEFDDY DPVDKVVLQK QHQLNGKMVD VKKALPKNDQ

     201  QGGGGGRGGP GGRAGGNRGN MGGGNYGNQN GGGNWNNGGN NWGNNRGNDN

     251  WGNNSFGGGG GGGGGYGGGN NSWGNNNPWD NGNGGGNFGG GGNNWNGGND

     301  FGGYQQNYGG GPQRGGGNFN NNRMQPYQGG GGFKAGGGNQ GNYGNNQGFN

     351  NGGNNRRY
BioPerl-1.007002/t/data/test.gcgblast000444000766000024       733113155576321 17363 0ustar00cjfieldsstaff000000000000!!SEQUENCE_LIST 1.0
BLASTP 2.2.1 [Apr-13-2001]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= /v0/people/staji002/test.gcg
         (146 letters)

Database: pir
           274,514 sequences; 93,460,074 total letters

Searching. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .done

                                                         Score    E
 Sequences producing significant alignments:             (bits)  Value ..

PIR2:S44629  Begin: 342 End: 470 
!F22B7.10 protein - Caenorhabditis elegans                   57  2e-08
PIR2:T21398  Begin: 40 End: 108 
!hypothetical protein F26D2.1 - Caenorhabditis elegans       33  0.40
PIR1:WMBELM  Begin: 307 End: 385 
!membrane protein LMP-2A - human herpesvirus 4               32  0.53
\\End of List

>PIR2:S44629 F22B7.10 protein - Caenorhabditis elegans
          Length = 628

 Score = 57.0 bits (136), Expect = 2e-08
 Identities = 38/135 (28%), Positives = 69/135 (50%), Gaps = 8/135 (5%)

Query: 3   CAAEFDFMEKETPLRYTKTXXXXXXXXXXXXXXRKIISDMWGVLAKQQTHVRKHQFDHGE 62
           C+AEFDF++  T  +   T                 + +   +L +    +     ++GE
Sbjct: 342 CSAEFDFIQYSTIEKLCGTLLIPLALISLVTFVFNFVKNT-NLLWRNSEEIG----ENGE 396

Query: 63  LVYHALQLLAYTALGILIMRLKLFLTPYMCVMASLICSRQLFGW--LFCKVHPGAIVFVI 120
           ++Y+ +QL   T +  LIMRLKLF+TP++C++A+L  + +L G   +   +   A+V VI
Sbjct: 397 ILYNVVQLCCSTVMAFLIMRLKLFMTPHLCIVAALFANSKLLGGDRISKTIRVSALVGVI 456

Query: 121 LAAMSIQGSANLQTQ 135
            A +  +G  N++ Q
Sbjct: 457 -AILFYRGIPNIRQQ 470


>PIR2:T21398 hypothetical protein F26D2.1 - Caenorhabditis elegans
          Length = 346

 Score = 32.7 bits (73), Expect = 0.40
 Identities = 20/71 (28%), Positives = 41/71 (57%), Gaps = 11/71 (15%)

Query: 66  HALQLLAYTALGILIMRLKLFLTPYMCV---------MASLICSRQLFGWLFCKVHPGAI 116
           + + ++A+ +LGI+   L++F+ PY+ V         +++ I ++ L  WLF  +  G +
Sbjct: 40  YRIMIVAFASLGIIYSGLEVFIKPYLHVYNNCILYFSLSTWISAKPLLPWLFA-IWSG-M 97

Query: 117 VFVILAAMSIQ 127
             V++A +SIQ
Sbjct: 98  YLVVIAFISIQ 108


>PIR1:WMBELM membrane protein LMP-2A - human herpesvirus 4
          Length = 497

 Score = 32.3 bits (72), Expect = 0.53
 Identities = 26/79 (32%), Positives = 38/79 (47%), Gaps = 4/79 (5%)

Query: 67  ALQLLAYTALGILIMRLKLFLTPYMCVMASLICSR----QLFGWLFCKVHPGAIVFVILA 122
           AL LLA   LG L +     L     ++  LICS      L   L  ++   A+  ++LA
Sbjct: 307 ALALLASLILGTLNLTTMFLLMLLWTLVVLLICSSCSSCPLSKILLARLFLYALALLLLA 366

Query: 123 AMSIQGSANLQTQWKSTAS 141
           +  I G + LQT +KS +S
Sbjct: 367 SALIAGGSILQTNFKSLSS 385


  Database: pir
    Posted date:  Jan 3, 2002  1:13 PM
  Number of letters in database: 93,460,074
  Number of sequences in database:  274,514
  
Lambda     K      H
   0.329    0.137    0.426 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,034,208
Number of Sequences: 274514
Number of extensions: 620007
Number of successful extensions: 1381
Number of sequences better than  1.0: 3
Number of HSP's better than  1.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1379
Number of HSP's gapped (non-prelim): 3
length of query: 146
length of database: 93,460,074
effective HSP length: 102
effective length of query: 44
effective length of database: 65,459,646
effective search space: 2880224424
effective search space used: 2880224424
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 70 (31.6 bits)
BioPerl-1.007002/t/data/test.gcgfasta000444000766000024      2571413155576321 17401 0ustar00cjfieldsstaff000000000000!!SEQUENCE_LIST 1.0


(Peptide) FASTA of: test.gcg  from: 1 to: 146  August 25, 2003 13:25

 REFORMAT of: b124_sp.pep  check: -1  from: 1  to: 146  January 28, 1999 16:22
 (No documentation)

 TO: PIR:*  Sequences:    283,308  Symbols:    96,168,669  Word Size: 2

 Databases searched:
   NBRF, Release 76.0, Released on 31Mar2003, Formatted on 7Apr2003

 Scoring matrix: GenRunData:blosum50.cmp
 Variable pamfactor used
 Gap creation penalty: 12  Gap extension penalty: 2



Histogram Key:
 Each histogram symbol represents 474 search set sequences
 Each inset symbol represents 4 search set sequences
 z-scores computed from opt scores

z-score obs    exp
        (=)    (*)

< 20    789      0:==
  22      0      0:
  24      4      0:=
  26      8      6:*
  28      9     64:*
  30    101    390:*
  32    407   1509:=  *
  34   2185   4092:=====   *
  36   7555   8404:================ *
  38  16600  13889:=============================*======
  40  25000  19373:========================================*============
  42  27813  23681:=================================================*=========
  44  28394  26123:=======================================================*====
  46  26152  26607:========================================================*
  48  23191  25473:=================================================    *
  50  20419  23244:============================================     *
  52  18108  20435:=======================================    *
  54  15701  17455:==================================  *
  56  13874  14581:==============================*
  58  11026  11970:======================== *
  60   9392   9697:====================*
  62   7678   7774:================*
  64   6295   6183:=============*
  66   4986   4887:==========*
  68   3909   3844:========*
  70   3131   3012:======*
  72   2497   2354:====*=
  74   1858   1835:===*
  76   1469   1428:===*
  78   1160   1110:==*
  80    845    862:=*
  82    665    659:=*
  84    515    522:=*
  86    376    404:*
  88    261    313:*
  90    225    242:*
  92    157    187:*         :=======================================*
  94    132    145:*         :=================================   *
  96     93    112:*         :========================   *
  98     63     87:*         :================     *
 100     73     67:*         :================*==
 102     44     52:*         :=========== *
 104     32     40:*         :======== *
 106     27     31:*         :=======*
 108     18     24:*         :=====*
 110     18     19:*         :====*
 112     11     14:*         :===*
 114     11     11:*         :==*
 116     10      9:*         :==*
 118      8      7:*         :=*
>120     13      5:*         :=*==

Joining threshold: 36, opt. threshold: 24, opt. width:  16, reg.-scaled


The best scores are:                    init1 initn   opt    z-sc E(283250)..

PIR2:S44629    Begin: 342  End: 470
! F22B7.10 protein - Caenorhabditis e...  108   143   241   304.1  1.1e-09
PIR1:WMBELM    Begin: 307  End: 385
! membrane protein LMP-2A - human her...   59    91    99   130.6     5.1
PIR2:AG0762    Begin: 63  End: 144
! probable membrane protein STY2265 [...   65    65    96   128.9     6.4
PIR2:B83179    Begin: 9  End: 86
! hypothetical protein PA3730 [import...   40    40    92   127.0     8.2
\\End of List


test.gcg
PIR2:S44629

P1;S44629 - F22B7.10 protein - Caenorhabditis elegans
C;Species: Caenorhabditis elegans
C;Date: 20-Feb-1995 #sequence_revision 20-Feb-1995 #text_change 04-Mar-2000
C;Accession: S44629
R;Anderson, K.
submitted to the EMBL Data Library, March 1993 . . . 


SCORES   Init1: 108   Initn: 143   Opt: 241   z-score: 304.1 E(): 1.1e-09
>>PIR2:S44629                                             (628 aa)
 initn: 143 init1: 108 opt: 241 Z-score: 304.1 expect(): 1.1e-09
Smith-Waterman score: 241;    32.6% identity in 135 aa overlap
 (3-135:342-470)

                                                 10        20        30  
test.gcg                                 VXCAAEFDFMEKETPLRYTKTLLLPVVLVVFV
                                           |:|||||::  |  :   |||:|::|: :|
S44629       GLGIEDDAHIFDILRSKFTSFANFHTRLYTCSAEFDFIQYSTIEKLCGTLLIPLALISLV
                   320       330       340       350       360       370 

                   40        50        60        70        80        90  
test.gcg     AIVRKIISDMWGVLAKQQTHVRKHQFDHGELVYHALQLLAYTALGILIMRLKLFLTPYMC
             ::| :::::  ::| ::: ::     ::||::|:::||   |::::||||||||:||::|
S44629       TFVFNFVKNT-NLLWRNSEEIG----ENGEILYNVVQLCCSTVMAFLIMRLKLFMTPHLC
                   380        390           400       410       420      

                  100         110       120       130       140          
test.gcg     VMASLICSRQLFG--WLFCKVHPGAIVFVILAAMSIQGSANLQTQWKSTASLALET    
             ::|:|: : :|:|   :   :: :|:| || | :  :|  |:: |               
S44629       IVAALFANSKLLGGDRISKTIRVSALVGVI-AILFYRGIPNIRQQLNVKGEYSNPDQEML
              430       440       450        460       470       480     

S44629       FDWIQHNTKQDAVFAGTMPVMANVKLTTLRPIVNHPHYEHVGIRERTLKVYSMFSKKPIA
               490       500       510       520       530       540     


test.gcg
PIR1:WMBELM

P1;WMBELM - membrane protein LMP-2A - human herpesvirus 4
N;Contains: membrane protein LMP-2B
C;Species: human herpesvirus 4, Epstein-Barr virus
A;Note: host Homo sapiens (man)
C;Date: 31-Dec-1989 #sequence_revision 31-Dec-1989 #text_change 16-Jul-1999
C;Accession: A30178; B30178; S00392 . . . 


SCORES   Init1: 59    Initn: 91    Opt: 99    z-score: 130.6 E(): 5.1   
>>PIR1:WMBELM                                             (497 aa)
 initn:  91 init1:  59 opt:  99 Z-score: 130.6 expect():  5.1
Smith-Waterman score: 99;    32.9% identity in 79 aa overlap
 (67-141:307-385)

               40        50        60        70        80        90      
test.gcg     KIISDMWGVLAKQQTHVRKHQFDHGELVYHALQLLAYTALGILIMRLKLFLTPYMCVMAS
                                           || |||   || | :   ::|     ::: 
WMBELM       MTLLLLAFVLWLSSPGGLGTLGAALLTLAAALALLASLILGTLNLTTMFLLMLLWTLVVL
              280       290       300       310       320       330      

              100           110       120       130       140            
test.gcg     LICSR----QLFGWLFCKVHPGAIVFVILAAMSIQGSANLQTQWKSTASLALET      
             ||||      |   |: ::   |:::::||:  | |:: |||::|| :|           
WMBELM       LICSSCSSCPLSKILLARLFLYALALLLLASALIAGGSILQTNFKSLSSTEFIPNLFCML
              340       350       360       370       380       390      

WMBELM       LLIVAGILFILAILTEWGSGNRTYGPVFMCLGGLLTMVAGAVWLTVMSNTLLSAWILTAG
              400       410       420       430       440       450      


test.gcg
PIR2:AG0762

P1;AG0762 - probable membrane protein STY2265 [imported] - Salmonella enterica 
 subsp. enterica serovar Typhi (strain CT18)
C;Species: Salmonella enterica subsp. enterica serovar Typhi
A;Note: this species has also been called Salmonella typhi
C;Date: 09-Nov-2001 #sequence_revision 09-Nov-2001 #text_change 18-Nov-2002
C;Accession: AG0762
R;Parkhill, J.; Dougan, G.; James, K.D.; Thomson, N.R.; Pickard, D.; Wain, J.; 
 Churcher, C.; Mungall, K.L.; Bentley, S.D.; Holden, M.T.G.; Sebaihia, M.; 
 Baker, S.; Basham, D.; Brooks, K.; Chillingworth, T.; Connerton, P.; Cronin, 
 A.; Davis, P.; Davies, R.M.; Dowd, L.; White, N.; Farrar, J.; Feltwell, T.; 
 Hamlin, N.; Haque, A.; Hien, T.T.; Holroyd, S.; Jagels, K.; Krogh, A.; Larsen, 
 T.S.; Leather, S.; Moule, S.; O'Gaora, P


SCORES   Init1: 65    Initn: 65    Opt: 96    z-score: 128.9 E(): 6.4   
>>PIR2:AG0762                                             (352 aa)
 initn:  65 init1:  65 opt:  96 Z-score: 128.9 expect():  6.4
Smith-Waterman score: 96;    27.6% identity in 87 aa overlap
 (61-137:63-144)

                     40        50        60        70            80      
test.gcg     FVAIVRKIISDMWGVLAKQQTHVRKHQFDHGELVYHALQLLAYT----ALGILIMRLKLF
                                           |::| :|:: :: |    |||:: :||:||
AG0762       TFLLVRLFSIPEGTWPLITLVVIMGPISFWGNVVPRAFERIGGTILGAALGLVALRLELF
                   40        50        60        70        80        90  

               90          100       110         120       130        140
test.gcg     LTPYM---CVMASLICSRQLFGWLFCKVHP--GAIVFVILAAMSIQGSANLQTQ-WKSTA
               | |   |::| ::|     |||    :|  : :: : ||::    :::::|  |::  
AG0762       SLPLMLVWCAIAMFLC-----GWLALGKKPYQALLIGITLAVVVGAPAGDMNTALWRGGD
                  100            110       120       130       140       

                                                                         
test.gcg     SLALET                                                      
                                                                         
AG0762       VILGALLAMLFTGIWPQRAFLHWRIQLAHCVTAYNRVYQAALSPNLLERPRLDKYLQRLL
             150       160       170       180       190       200       


test.gcg
PIR2:B83179

P1;B83179 - hypothetical protein PA3730 [imported] - Pseudomonas aeruginosa 
 (strain PAO1)
C;Species: Pseudomonas aeruginosa
C;Date: 15-Sep-2000 #sequence_revision 15-Sep-2000 #text_change 31-Dec-2000
C;Accession: B83179
R;Stover, C.K.; Pham, X.Q.; Erwin, A.L.; Mizoguchi, S.D.; Warrener, P.; Hickey, 
 M.J.; Brinkman, F.S.L.; Hufnagle, W.O.; Kowalik, D.J.; Lagrou, M.; Garber, 
 R.L.; Goltry, L.; Tolentino, E.; Westbrook-Wadman, S.; Yuan, Y.; Brody, L.L.; 
 Coulter, S.N.; Folger, K.R.; Kas, A.; Larbig, K.; Lim, R.M.; Smith, K.A.; 
 Spencer, D.H.; Wong, G.K.S.; Wu, Z.; Paulsen, I.T.; Reizer, J.; Saier, M.H.; 
 Hancock, R.E.W.; Lory, S.; Olson, M.V.
Nature 406, 959-964, 2000 . . . 


SCORES   Init1: 40    Initn: 40    Opt: 92    z-score: 127.0 E(): 8.2   
>>PIR2:B83179                                             (213 aa)
 initn:  40 init1:  40 opt:  92 Z-score: 127.0 expect():  8.2
Smith-Waterman score: 92;    28.4% identity in 88 aa overlap
 (22-109:9-86)

                     10        20        30        40        50        60
test.gcg     VXCAAEFDFMEKETPLRYTKTLLLPVVLVVFVAIVRKIISDMWGVLAKQQTHVRKHQFDH
                                  | :|:||  |: |:  |   :||::|  ::::   ::| 
B83179                    MEGFLQTALSFPTVLFSFLLILAII---YWGIVALGMVEIDVLDLDA
                                  10        20           30        40    

                     70        80        90       100       110       120
test.gcg     GELVYHALQLLAYTALGILIMRLKLFLTPYMCVMASLICSRQLFGWLFCKVHPGAIVFVI
               :|  | |     :|: |: :|||  :|   |:: |    ::|:|::|           
B83179       ESVVDGAGQA---EGLAALLAKLKLNGVPVTLVLTLL----SFFAWFLCYFVQLWLLSAL
                 50           60        70            80        90       

                    130       140                                        
test.gcg     LAAMSIQGSANLQTQWKSTASLALET                                  
                                                                         
B83179       PLGWLRYPLGAVVAVGALFLAAPLAATLCRPLRPLFRKLESTSSKSVLGQVAVVRSGRVT
             100       110       120       130       140       150       



! Distributed over 1 thread.
!      Start time: Mon Aug 25 13:23:54 2003
! Completion time: Mon Aug 25 13:25:12 2003

! CPU time used:
!        Database scan:  0:01:34.1
! Post-scan processing:  0:00:00.6
!       Total CPU time:  0:01:34.7
! Output File: test.fasta
BioPerl-1.007002/t/data/test.genbank000444000766000024      3714313155576321 17226 0ustar00cjfieldsstaff000000000000LOCUS       DDU63596      310 bp    DNA             INV       14-MAY-1999
DEFINITION  Dictyostelium discoideum Tdd-4 transposable element flanking
            sequence, clone p427/428 right end.
ACCESSION   U63596
NID         g2393749
KEYWORDS    .
SOURCE      Dictyostelium discoideum.
  ORGANISM  Dictyostelium discoideum
            Eukaryota; Dictyosteliida; Dictyostelium.
REFERENCE   1  (bases 1 to 310)
  AUTHORS   Wells,D.J.
  TITLE     Tdd-4, a DNA transposon of Dictyostelium that encodes proteins
            similar to LTR retroelement integrases
  JOURNAL   Nucleic Acids Res. 27 (11), 2408-2415 (1999)
REFERENCE   2  (bases 1 to 310)
  AUTHORS   Wells,D.J. and Welker,D.L.
  TITLE     Dictyostelium discoideum Tdd-4 transposable element, right end
            flanking sequence from clone p427/428
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 310)
  AUTHORS   Wells,D.J. and Welker,D.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JUL-1996) Biology, Utah State Univ., Logan, UT
            84322-5305, USA
FEATURES             Location/Qualifiers
     source          1..310
                     /organism="Dictyostelium discoideum"
                     /strain="AX4"
                     /db_xref="taxon:44689"
                     /clone="p427/428"
     misc_feature    5.12
                     /note="Fuzzy location"
     misc_feature    join(J00194:(100..202),1..245,256..258)
                     /note="Location partly in another entry"
BASE COUNT      118 a     46 c     67 g     79 t
ORIGIN      
        1 gtgacagttg gctgtcagac atacaatgat tgtttagaag aggagaagat tgatccggag
       61 taccgtgata gtattttaaa aactatgaaa gcgggaatac ttaatggtaa actagttaga
      121 ttatgtgacg tgccaagggg tgtagatgta gaaattgaaa caactggtct aaccgattca
      181 gaaggagaaa gtgaatcaaa agaagaagag tgatgatgaa tagccaccat tactgcatac
      241 tgtagccctt acccttgtcg caccattagc cattaataaa aataaaaaat tatataaaaa
      301 ttacacccat 
//
LOCUS       DDU63595       83 bp    DNA             INV       14-MAY-1999
DEFINITION  Dictyostelium discoideum Tdd-4 transposable element flanking
            sequence, clone p427/428 left end.
ACCESSION   U63595
NID         g2393748
KEYWORDS    .
SOURCE      Dictyostelium discoideum.
  ORGANISM  Dictyostelium discoideum
            Eukaryota; Dictyosteliida; Dictyostelium.
REFERENCE   1  (bases 1 to 83)
  AUTHORS   Wells,D.J.
  TITLE     Tdd-4, a DNA transposon of Dictyostelium that encodes proteins
            similar to LTR retroelement integrases
  JOURNAL   Nucleic Acids Res. 27 (11), 2408-2415 (1999)
REFERENCE   2  (bases 1 to 83)
  AUTHORS   Wells,D.J. and Welker,D.L.
  TITLE     Dictyostelium discoideum Tdd-4 transposable element, left end
            flanking sequence from clone p427/428
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 83)
  AUTHORS   Wells,D.J. and Welker,D.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JUL-1996) Biology, Utah State Univ., Logan, UT
            84322-5305, USA
FEATURES             Location/Qualifiers
     source          1..83
                     /organism="Dictyostelium discoideum"
                     /strain="AX4"
                     /db_xref="taxon:44689"
                     /clone="p427/428"
BASE COUNT       31 a     16 c     12 g     24 t
ORIGIN      
        1 ttcgaaggat atctcaaggc agttaataat tactatgatg attgtaaaat attccaaagt
       61 ttcccagacc caccaataat gac
//
LOCUS       HUMBDNF       918 bp    DNA             PRI       31-OCT-1994
DEFINITION  Human brain-derived neurotrophic factor (BDNF) gene, complete cds.
ACCESSION   M37762
VERSION     M37762.1  GI:179402
KEYWORDS    neurotrophic factor.
SOURCE      Human DNA.
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
            Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 918)
  AUTHORS   Jones,K.R. and Reichardt,L.F.
  TITLE     Molecular cloning of a human gene that is a member of the nerve
            growth factor family
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 87 (20), 8060-8064 (1990)
  MEDLINE   91045937
COMMENT     Draft entry and computer-readable sequence for [Proc. Natl. Acad.
            Sci. U.S.A. (1990) In press] kindly submitted
            by K.R.Jones, 13-AUG-1990.
FEATURES             Location/Qualifiers
     source          1..918
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /dev_stage="adult"
     sig_peptide     76..123
                     /gene="NTF3"
                     /note="G00-125-917; putative"
                     /product="brain-derived neurotrophic factor"
     CDS             76..819
                     /gene="BDNF"
                     /note="putative"
                     /codon_start=1
                     /db_xref="GDB:G00-125-916"
                     /product="brain-derived neurotrophic factor"
                     /protein_id="AAA51820.1"
                     /db_xref="GI:179403"
                     /translation="MTILFLTMVISYFGCMKAAPMKEANIRGQGGLAYPGVRTHGTLE
                     SVNGPKAGSRGLTSLADTFEHVIEELLDEDQKVRPNEENNKDADLYTSRVMLSSQVPL
                     EPPLLFLLEEYKNYLDAANMSMRVRRHSDPARRGELSVCDSISEWVTAADKKTAVDMS
                     GGTVTVLEKVPVSKGQLKQYFYETKCNPMGYTKEGCRGIDKRHWNSQCRTTQSYVRAL
                     TMDSKKRIGWRFIRIDTSCVCTLTIKRGR"
     gene            76..816
                     /gene="NTF3"
                     /map="12p13"
     gene            76..819
                     /gene="BDNF"
                     /map="11p13"
     mat_peptide     124..816
                     /gene="NTF3"
                     /note="G00-125-917; putative"
                     /product="brain-derived neurotrophic factor"
BASE COUNT      269 a    192 c    237 g    220 t
ORIGIN
        1 ggtgaaagaa agccctaacc agttttctgt cttgtttctg ctttctccct acagttccac
       61 caggtgagaa gagtgatgac catccttttc cttactatgg ttatttcata ctttggttgc
      121 atgaaggctg cccccatgaa agaagcaaac atccgaggac aaggtggctt ggcctaccca
      181 ggtgtgcgga cccatgggac tctggagagc gtgaatgggc ccaaggcagg ttcaagaggc
      241 ttgacatcat tggctgacac tttcgaacac gtgatagaag agctgttgga tgaggaccag
      301 aaagttcggc ccaatgaaga aaacaataag gacgcagact tgtacacgtc cagggtgatg
      361 ctcagtagtc aagtgccttt ggagcctcct cttctctttc tgctggagga atacaaaaat
      421 tacctagatg ctgcaaacat gtccatgagg gtccggcgcc actctgaccc tgcccgccga
      481 ggggagctga gcgtgtgtga cagtattagt gagtgggtaa cggcggcaga caaaaagact
      541 gcagtggaca tgtcgggcgg gacggtcaca gtccttgaaa aggtccctgt atcaaaaggc
      601 caactgaagc aatacttcta cgagaccaag tgcaatccca tgggttacac aaaagaaggc
      661 tgcaggggca tagacaaaag gcattggaac tcccagtgcc gaactaccca gtcgtacgtg
      721 cgggccctta ccatggatag caaaaagaga attggctggc gattcataag gatagacact
      781 tcttgtgtat gtacattgac cattaaaagg ggaagatagt ggatttatgt tgtatagatt
      841 agattatatt gagacaaaaa ttatctattt gtatatatac ataacagggt aaattattca
      901 gttaagaaaa aaataatt
//
LOCUS       NT_010368  161485 bp    DNA             CON       16-NOV-2000
DEFINITION  Homo sapiens chromosome 15 working draft sequence segment, complete
            sequence.
ACCESSION   NT_010368
VERSION     NT_010368.1  GI:11433101
KEYWORDS    HTG.
SOURCE      human.
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 161485)
  AUTHORS   International Human Genome Project collaborators.
  TITLE     Toward the complete sequence of the human genome
  JOURNAL   Unpublished
COMMENT     GENOME ANNOTATION REFSEQ:  NCBI contigs are derived from assembled
            genomic sequence data. They may include both draft and finished
            sequence.
            COMPLETENESS: not full length.
FEATURES             Location/Qualifiers
     source          1..310
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /chromosome="15"
     source          order(1..100,251..300,300..310)
                     /note="Doctored from Accession AC011224 
	             sequenced by Whitehead Institute
                     for Biomedical Research"
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /clone="RP11-10K20"
     variation       244
                     /replace="T"
                     /replace="A"
                     /db_xref="dbSNP:140670"
ORIGIN      
        1 gtgacagttg gctgtcagac atacaatgat tgtttagaag aggagaagat tgatccggag
       61 taccgtgata gtattttaaa aactatgaaa gcgggaatac ttaatggtaa actagttaga
      121 ttatgtgacg tgccaagggg tgtagatgta gaaattgaaa caactggtct aaccgattca
      181 gaaggagaaa gtgaatcaaa agaagaagag tgatgatgaa tagccaccat tactgcatac
      241 tgtagccctt acccttgtcg caccattagc cattaataaa aataaaaaat tatataaaaa
      301 ttacacccat 
//
LOCUS       HUMBETGLOA              3002 bp    DNA     linear   PRI 26-AUG-1994
DEFINITION  Human haplotype C4 beta-globin gene, complete cds.
ACCESSION   L26462
VERSION     L26462.1  GI:432453
KEYWORDS    beta-globin.
SOURCE      Homo sapiens DNA.
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3002)
  AUTHORS   Fullerton,S.M., Harding,R.M., Boyce,A.J. and Clegg,J.B.
  TITLE     Molecular and population genetic analysis of allelic sequence
            diversity at the human beta-globin locus
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 91 (5), 1805-1809 (1994)
  MEDLINE   94173918
   PUBMED   7907422
FEATURES             Location/Qualifiers
     source          1..3002
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /haplotype="C4"
                     /note="sequence found in a Melanesian population"
     variation       111
                     /replace="t"
     variation       263
                     /note="Rsa I polymorphism"
                     /replace="t"
     variation       273
                     /replace="c"
     variation       286..287
                     /note="2 bp insertion of AT"
                     /replace=""
     variation       288
                     /replace="t"
     variation       295..296
                     /note="1 bp deletion of C or 2 bp deletion of CT"
                     /replace=""
     variation       347
                     /replace="c"
     variation       476
                     /replace="t"
     variation       500
                     /replace="c"
     CDS             join(866..957,1088..1310,2161..2289)
                     /codon_start=1
                     /product="beta-globin"
                     /protein_id="AAA21100.1"
                     /db_xref="GI:532506"
                     /translation="MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFE
                     SFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPE
                     NFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH"
     exon            <866..957
                     /number=1
     variation       874
                     /replace="c"
     intron          958..1087
                     /number=1
     exon            1088..1310
                     /number=2
     intron          1311..2160
                     /number=2
     variation       1326
                     /note="Ava II polymorphism"
                     /replace="g"
     variation       1384
                     /replace="g"
     variation       1391
                     /replace="t"
     variation       1976
                     /replace="t"
     exon            2161..>2289
                     /number=3
     variation       2522
                     /replace="c"
     variation       2602
                     /replace="a"
     variation       2604
                     /replace="c"
     variation       2760
                     /note="Hinf I polymorphism"
                     /replace="t"
     variation       2913
                     /replace="g"
BASE COUNT      810 a    601 c    599 g    992 t
ORIGIN      
        1 acctcctatt tgacaccact gattacccca ttgatagtca cactttgggt tgtaagtgac
       61 tttttattta tttgtatttt tgactgcatt aagaggtctc tagtttttta cctcttgttt
      121 cccaaaacct aataagtaac taatgcacag agcacattga tttgtattta ttctattttt
      181 agacataatt tattagcatg catgagcaaa ttaagaaaaa caacaacaaa tgaatgcata
      241 tatatgtata tgtatgtgtg tacatataca catatatata tatatatatt ttttcttttc
      301 ttaccagaag gttttaatcc aaataaggag aagatatgct tagaactgag gtagagtttt
      361 catccattct gtcctgtaag tattttgcat attctggaga cgcaggaaga gatccatcta
      421 catatcccaa agctgaatta tggtagacaa aactcttcca cttttagtgc atcaacttct
      481 tatttgtgta ataagaaaat tgggaaaacg atcttcaata tgcttaccaa gctgtgattc
      541 caaatattac gtaaatacac ttgcaaagga ggatgttttt agtagcaatt tgtactgatg
      601 gtatggggcc aagagatata tcttagaggg agggctgagg gtttgaagtc caactcctaa
      661 gccagtgcca gaagagccaa ggacaggtac ggctgtcatc acttagacct caccctgtgg
      721 agccacaccc tagggttggc caatctactc ccaggagcag ggagggcagg agccagggct
      781 gggcataaaa gtcagggcag agccatctat tgcttacatt tgcttctgac acaactgtgt
      841 tcactagcaa cctcaaacag acaccatggt gcatctgact cctgaggaga agtctgccgt
      901 tactgccctg tggggcaagg tgaacgtgga tgaagttggt ggtgaggccc tgggcaggtt
      961 ggtatcaagg ttacaagaca ggtttaagga gaccaataga aactgggcat gtggagacag
     1021 agaagactct tgggtttctg ataggcactg actctctctg cctattggtc tattttccca
     1081 cccttaggct gctggtggtc tacccttgga cccagaggtt ctttgagtcc tttggggatc
     1141 tgtccactcc tgatgctgtt atgggcaacc ctaaggtgaa ggctcatggc aagaaagtgc
     1201 tcggtgcctt tagtgatggc ctggctcacc tggacaacct caagggcacc tttgccacac
     1261 tgagtgagct gcactgtgac aagctgcacg tggatcctga gaacttcagg gtgagtctat
     1321 gggacccttg atgttttctt tccccttctt ttctatggtt aagttcatgt cataggaagg
     1381 ggataagtaa cagggtacag tttagaatgg gaaacagacg aatgattgca tcagtgtgga
     1441 agtctcagga tcgttttagt ttcttttatt tgctgttcat aacaattgtt ttcttttgtt
     1501 taattcttgc tttctttttt tttcttctcc gcaattttta ctattatact taatgcctta
     1561 acattgtgta taacaaaagg aaatatctct gagatacatt aagtaactta aaaaaaaact
     1621 ttacacagtc tgcctagtac attactattt ggaatatatg tgtgcttatt tgcatattca
     1681 taatctccct actttatttt cttttatttt taattgatac ataatcatta tacatattta
     1741 tgggttaaag tgtaatgttt taatatgtgt acacatattg accaaatcag ggtaattttg
     1801 catttgtaat tttaaaaaat gctttcttct tttaatatac ttttttgttt atcttatttc
     1861 taatactttc cctaatctct ttctttcagg gcaataatga tacaatgtat catgcctctt
     1921 tgcaccattc taaagaataa cagtgataat ttctgggtta aggcaatagc aatatctctg
     1981 catataaata tttctgcata taaattgtaa ctgatgtaag aggtttcata ttgctaatag
     2041 cagctacaat ccagctacca ttctgctttt attttatggt tgggataagg ctggattatt
     2101 ctgagtccaa gctaggccct tttgctaatc atgttcatac ctcttatctt cctcccacag
     2161 ctcctgggca acgtgctggt ctgtgtgctg gcccatcact ttggcaaaga attcacccca
     2221 ccagtgcagg ctgcctatca gaaagtggtg gctggtgtgg ctaatgccct ggcccacaag
     2281 tatcactaag ctcgctttct tgctgtccaa tttctattaa aggttccttt gttccctaag
     2341 tccaactact aaactggggg atattatgaa gggccttgag catctggatt ctgcctaata
     2401 aaaaacattt attttcattg caatgatgta tttaaattat ttctgaatat tttactaaaa
     2461 agggaatgtg ggaggtcagt gcatttaaaa cataaagaaa tgaagagcta gttcaaacct
     2521 tgggaaaata cactatatct taaactccat gaaagaaggt gaggctgcaa acagctaatg
     2581 cacattggca acagccctga tgcatatgcc ttattcatcc ctcagaaaag gattcaagta
     2641 gaggcttgat ttggaggtta aagttttgct atgctgtatt ttacattact tattgtttta
     2701 gctgtcctca tgaatgtctt ttcactaccc atttgcttat cctgcatctc tcagccttga
     2761 ctccactcag ttctcttgct tagagatacc acctttcccc tgaagtgttc cttccatgtt
     2821 ttacggcgag atggtttctc ctcgcctggc cactcagcct tagttgtctc tgttgtctta
     2881 tagaggtcta cttgaagaag gaaaaacagg ggtcatggtt tgactgtcct gtgagccctt
     2941 cttccctgcc tcccccactc acagtgaccc ggaatctgca gtgctagtct cccggaacta
     3001 tc
//
BioPerl-1.007002/t/data/test.genbank.noseq000444000766000024      2347413155576321 20354 0ustar00cjfieldsstaff000000000000LOCUS       DDU63596      310 bp    DNA             INV       14-MAY-1999
DEFINITION  Dictyostelium discoideum Tdd-4 transposable element flanking
            sequence, clone p427/428 right end.
ACCESSION   U63596
NID         g2393749
KEYWORDS    .
SOURCE      Dictyostelium discoideum.
  ORGANISM  Dictyostelium discoideum
            Eukaryota; Dictyosteliida; Dictyostelium.
REFERENCE   1  (bases 1 to 310)
  AUTHORS   Wells,D.J.
  TITLE     Tdd-4, a DNA transposon of Dictyostelium that encodes proteins
            similar to LTR retroelement integrases
  JOURNAL   Nucleic Acids Res. 27 (11), 2408-2415 (1999)
REFERENCE   2  (bases 1 to 310)
  AUTHORS   Wells,D.J. and Welker,D.L.
  TITLE     Dictyostelium discoideum Tdd-4 transposable element, right end
            flanking sequence from clone p427/428
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 310)
  AUTHORS   Wells,D.J. and Welker,D.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JUL-1996) Biology, Utah State Univ., Logan, UT
            84322-5305, USA
FEATURES             Location/Qualifiers
     source          1..310
                     /organism="Dictyostelium discoideum"
                     /strain="AX4"
                     /db_xref="taxon:44689"
                     /clone="p427/428"
     misc_feature    5.12
                     /note="Fuzzy location"
     misc_feature    join(J00194:(100..202),1..245,256..258)
                     /note="Location partly in another entry"
BASE COUNT      118 a     46 c     67 g     79 t
//
LOCUS       DDU63595       83 bp    DNA             INV       14-MAY-1999
DEFINITION  Dictyostelium discoideum Tdd-4 transposable element flanking
            sequence, clone p427/428 left end.
ACCESSION   U63595
NID         g2393748
KEYWORDS    .
SOURCE      Dictyostelium discoideum.
  ORGANISM  Dictyostelium discoideum
            Eukaryota; Dictyosteliida; Dictyostelium.
REFERENCE   1  (bases 1 to 83)
  AUTHORS   Wells,D.J.
  TITLE     Tdd-4, a DNA transposon of Dictyostelium that encodes proteins
            similar to LTR retroelement integrases
  JOURNAL   Nucleic Acids Res. 27 (11), 2408-2415 (1999)
REFERENCE   2  (bases 1 to 83)
  AUTHORS   Wells,D.J. and Welker,D.L.
  TITLE     Dictyostelium discoideum Tdd-4 transposable element, left end
            flanking sequence from clone p427/428
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 83)
  AUTHORS   Wells,D.J. and Welker,D.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JUL-1996) Biology, Utah State Univ., Logan, UT
            84322-5305, USA
FEATURES             Location/Qualifiers
     source          1..83
                     /organism="Dictyostelium discoideum"
                     /strain="AX4"
                     /db_xref="taxon:44689"
                     /clone="p427/428"
BASE COUNT       31 a     16 c     12 g     24 t
//
LOCUS       HUMBDNF       918 bp    DNA             PRI       31-OCT-1994
DEFINITION  Human brain-derived neurotrophic factor (BDNF) gene, complete cds.
ACCESSION   M37762
VERSION     M37762.1  GI:179402
KEYWORDS    neurotrophic factor.
SOURCE      Human DNA.
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
            Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 918)
  AUTHORS   Jones,K.R. and Reichardt,L.F.
  TITLE     Molecular cloning of a human gene that is a member of the nerve
            growth factor family
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 87 (20), 8060-8064 (1990)
  MEDLINE   91045937
COMMENT     Draft entry and computer-readable sequence for [Proc. Natl. Acad.
            Sci. U.S.A. (1990) In press] kindly submitted
            by K.R.Jones, 13-AUG-1990.
FEATURES             Location/Qualifiers
     source          1..918
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /dev_stage="adult"
     sig_peptide     76..123
                     /gene="NTF3"
                     /note="G00-125-917; putative"
                     /product="brain-derived neurotrophic factor"
     CDS             76..819
                     /gene="BDNF"
                     /note="putative"
                     /codon_start=1
                     /db_xref="GDB:G00-125-916"
                     /product="brain-derived neurotrophic factor"
                     /protein_id="AAA51820.1"
                     /db_xref="GI:179403"
                     /translation="MTILFLTMVISYFGCMKAAPMKEANIRGQGGLAYPGVRTHGTLE
                     SVNGPKAGSRGLTSLADTFEHVIEELLDEDQKVRPNEENNKDADLYTSRVMLSSQVPL
                     EPPLLFLLEEYKNYLDAANMSMRVRRHSDPARRGELSVCDSISEWVTAADKKTAVDMS
                     GGTVTVLEKVPVSKGQLKQYFYETKCNPMGYTKEGCRGIDKRHWNSQCRTTQSYVRAL
                     TMDSKKRIGWRFIRIDTSCVCTLTIKRGR"
     gene            76..816
                     /gene="NTF3"
                     /map="12p13"
     gene            76..819
                     /gene="BDNF"
                     /map="11p13"
     mat_peptide     124..816
                     /gene="NTF3"
                     /note="G00-125-917; putative"
                     /product="brain-derived neurotrophic factor"
BASE COUNT      269 a    192 c    237 g    220 t
//
LOCUS       NT_010368  161485 bp    DNA             CON       16-NOV-2000
DEFINITION  Homo sapiens chromosome 15 working draft sequence segment, complete
            sequence.
ACCESSION   NT_010368
VERSION     NT_010368.1  GI:11433101
KEYWORDS    HTG.
SOURCE      human.
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 161485)
  AUTHORS   International Human Genome Project collaborators.
  TITLE     Toward the complete sequence of the human genome
  JOURNAL   Unpublished
COMMENT     GENOME ANNOTATION REFSEQ:  NCBI contigs are derived from assembled
            genomic sequence data. They may include both draft and finished
            sequence.
            COMPLETENESS: not full length.
FEATURES             Location/Qualifiers
     source          1..310
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /chromosome="15"
     source          order(1..100,251..300,300..310)
                     /note="Doctored from Accession AC011224 
	             sequenced by Whitehead Institute
                     for Biomedical Research"
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /clone="RP11-10K20"
     variation       244
                     /replace="T"
                     /replace="A"
                     /db_xref="dbSNP:140670"
CONTIG      AC011224.27:1..116977
//
LOCUS       HUMBETGLOA              3002 bp    DNA     linear   PRI 26-AUG-1994
DEFINITION  Human haplotype C4 beta-globin gene, complete cds.
ACCESSION   L26462
VERSION     L26462.1  GI:432453
KEYWORDS    beta-globin.
SOURCE      Homo sapiens DNA.
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3002)
  AUTHORS   Fullerton,S.M., Harding,R.M., Boyce,A.J. and Clegg,J.B.
  TITLE     Molecular and population genetic analysis of allelic sequence
            diversity at the human beta-globin locus
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 91 (5), 1805-1809 (1994)
  MEDLINE   94173918
   PUBMED   7907422
FEATURES             Location/Qualifiers
     source          1..3002
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /haplotype="C4"
                     /note="sequence found in a Melanesian population"
     variation       111
                     /replace="t"
     variation       263
                     /note="Rsa I polymorphism"
                     /replace="t"
     variation       273
                     /replace="c"
     variation       286..287
                     /note="2 bp insertion of AT"
                     /replace=""
     variation       288
                     /replace="t"
     variation       295..296
                     /note="1 bp deletion of C or 2 bp deletion of CT"
                     /replace=""
     variation       347
                     /replace="c"
     variation       476
                     /replace="t"
     variation       500
                     /replace="c"
     CDS             join(866..957,1088..1310,2161..2289)
                     /codon_start=1
                     /product="beta-globin"
                     /protein_id="AAA21100.1"
                     /db_xref="GI:532506"
                     /translation="MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFE
                     SFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPE
                     NFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH"
     exon            <866..957
                     /number=1
     variation       874
                     /replace="c"
     intron          958..1087
                     /number=1
     exon            1088..1310
                     /number=2
     intron          1311..2160
                     /number=2
     variation       1326
                     /note="Ava II polymorphism"
                     /replace="g"
     variation       1384
                     /replace="g"
     variation       1391
                     /replace="t"
     variation       1976
                     /replace="t"
     exon            2161..>2289
                     /number=3
     variation       2522
                     /replace="c"
     variation       2602
                     /replace="a"
     variation       2604
                     /replace="c"
     variation       2760
                     /note="Hinf I polymorphism"
                     /replace="t"
     variation       2913
                     /replace="g"
BASE COUNT      810 a    601 c    599 g    992 t
BioPerl-1.007002/t/data/test.infernal000444000766000024      2021613155576321 17410 0ustar00cjfieldsstaff000000000000
CPU time (band calc): 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00
sequence: gi|2239287|gb|U51115.1|BSU51115
hit 0   :  15589  15691    78.40 bits
hit 1   :  15589  15691    78.40 bits
           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
            A+ A+A+ AAAA A   :CUC:UAUAAU: :GGGAAUAUGGCCC: :AGUUUCUACC:G
     15589 CAUGAAAUCAAAACACGACCUCAUAUAAUCUUGGGAAUAUGGCCCAUAAGUUUCUACCCG 15648   

           <<<<_______>>>>>>>,,)))).))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcG.aGuaAauauuaaauauuu 102     
           GCAACCGUAAAUUGCC:GACUA:G AG: AA + ++  +++++
     15649 GCAACCGUAAAUUGCCGGACUAUGcAGGGAAGUGAUCGAUAAA 15691   

hit 2   :  13198  13294     5.41 bits
hit 3   :  13198  13294     5.41 bits
           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           +A+ +U + AAAA AA : :U:::A AA:C::::G A  UGGC::::G: UUU U  :: 
     13198 UAUCUUCUUAAAAUAAGGAAUGAAAAAACCAGCUGCAC-UGGCAGCUGGUUUUUUUUGU- 13255   

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
              : C  AA :U+++::  U:::A: : AUAU+   U +U 
     13256 ---UGCAAAAGAUAAAACCAUUUCAUACGAUAUACCGUCAUG 13294   

hit 4   :  11655  11756    81.29 bits
hit 5   :  11655  11756    81.29 bits
           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           A AAAU AAA+AA A+   : CGUAUAAU::CG:GAAUAUGGC:CG::AGU UCUACCA:
     11655 AGAAAUCAAAUAAGAUGAAUUCGUAUAAUCGCGGGAAUAUGGCUCGCAAGUCUCUACCAA 11714   

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
           GC ACCGUAAAU GC:UGACUACG :   AU+U +++  UUU
     11715 GCUACCGUAAAUGGCUUGACUACGUAAACAUUUCUUUCGUUU 11756   

hit 0   :    825    748     2.84 bits
hit 1   :    825    748     2.84 bits
           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           +AAAA+ AA AAAA  A: ::C:U:U A           UG  C+ A A   UCUAC   
     15073 UAAAAACAACAAAAGGAGCUGCUUUUUA-----------UGCUCACACACGAUCUAC--- 15118   

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
                 G AAA      +AC:A:G:: :A ++UU  AU+U+U
     15119 ----AUGAAAA------AACAAAGCAUUACAUUUCCAUUUAU 15150   

hit 2   :   4125   4023     1.38 bits
hit 3   :   4125   4023     1.38 bits
           :::::::::::::::::((((((((,,,<<<<<<<_______.>>>.>>>>,,,,,,,,<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGG.ccc.gagaGUuUCUACC 58      
            AAA +AAA A  A AA: :U:::AUAA :+:G:: AU U   ::C :+:  UUUC AC 
     11773 CAAACAAAACACUACAAAUUUGAAAUAAGCUGGUAUAUUUUCuUACaCGAAUUUUCGAC- 11831   

           <<<<<<_______>>>...>>>>,,))))))))::::::::::::::
        59 aGgcaaCCGUAAAuug...cCuGACUAcGaGuaAauauuaaauauuu 102     
              :AAC GUA AUU:   + +GA U:::A: :A+ AU+A+AU+ + 
     11832 ---AAACUGUAUAUUUaugAUAGAGUUUCAAUUAUCAUAAUAUUCAG 11875   

hit 4   :   8105   8018     1.70 bits
hit 5   :   8105   8018     1.70 bits
           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
            A+A   A +A    AA   U:::AU A         UAUGGC ++A+ GU UC A    
      7793 GAUACGGAUUACGGCAAAAGUGGCAUCA---------UAUGGCGUAAAGGUAUCAAG--- 7840    

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
             A  CGUAA  U+C   ACU:::A   AA+A +AAA+ +++
      7841 --AAUCGUAAUAUACGCUACUGUCAUCAAAAAGAAAAACAAA 7880    

hit 6   :  11759  11658     9.64 bits
hit 7   :  11759  11658     9.64 bits
           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           A  AA+  AAA AAA+   : CGUA  +::::: :  UA GG: :::::GU    AC: G
      4139 AUCAAACGAAAGAAAUGUUUACGUA-GUCAAGCCAUUUACGGUAGCUUGGUAGAGACUUG 4197    

           <<<<_______>>>>>>>,,.))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGAC.UAcGaGuaAauauuaaauauuu 102     
           :: :CC UA  : ::C :   UACG :   AU UUA++U +UU
      4198 CGAGCCAUAUUCCCGCGAUUaUACGAAUUCAUCUUAUUUGAUU 4240    

hit 8   :  13350  13253     0.79 bits
hit 9   :  13350  13253     0.79 bits
           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           +AA  UA   AA A + :A +C:U:    C:::  AA       :::G G   C  C:A 
      2548 UAAGGUACCGAACAGUCAAGUCAUU---UCCAUUUAAGUAAAGCAUGGCGGCACAUCUAC 2604    

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
           : :AC GUA AU: : U:A :A:G+ U: AU UU++  A+ +
      2605 AUGACGGUAUAUCGUAUGA-AAUGGUUUUAUCUUUUGCAACA 2645    

hit 10  :  13846  13740     6.35 bits
hit 11  :  13846  13740     6.35 bits
           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,.....
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCU..... 55      
            A  A+A+A A AA AA:A  :::A A :C ::::A  A G :::: G:  UUCU     
      2052 CAGCAAAUACACAAGAACAACUAAAAACCCGUCAUAGAAAGCAUGAUGGCGUUCUccgaa 2111    

           ,,<<<<<<<_______>>>>>>>,,))))))))::::::::::::::
        56 ACCaGgcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
           ACC::GC :CCG    : GC::G CU:::  U:AA+  +A++   ++
      2112 ACCGAGCGGCCGAUUCCAGCUUGCCUUUAACUGAAACCAAUUCCCAA 2158    

hit 12  :  14215  14125     0.90 bits
hit 13  :  14215  14125     0.90 bits
           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           AA    AA  AA  A    :+ :UAUA+U: :+++ A A GG   : :AGU         
      1683 AAGCGGAAUCAACGACGCCGUAAUAUAUUCAGAAAUAAACGG---CCAAGUCA------- 1732    

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
            C::CCGUAAA::GC+   CUA: +:   ++ U+ AA+++ +
      1733 -CUGCCGUAAACAGCAGCGCUAUCGCAACUACUGCAAAUACA 1773    

hit 14  :  15695  15594     7.88 bits
hit 15  :  15695  15594     7.88 bits
           :::::::::::::::::((((((((,,.,<<<<<<<_______>>>>>>>,,,,,,,,<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUA.aucucgggAAUAUGGcccgagaGUuUCUACCa 59      
            A ++U+A   A  A ++ C :: AUA +:C:::::  UA GG:::::G:GU    AC::
       203 CAGUUUUAUCGAUCACUUCCCUGCAUAgUCCGGCAAUUUACGGUUGCCGGGUAGAAACUU 262     

           <<<<<_______>>>>>>>,,))))))))::::::::::::::
        60 GgcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
           +::::CC UA  :::: ::A U :: G + +  U++++U +UU
       263 AUGGGCCAUAUUCCCA-AGAUUAUAUGAGGUCGUGUUUUGAUU 304     

sequence: gi|633168|emb|X83878.1|
hit 0   :    168    267    79.36 bits
hit 1   :    168    267    79.36 bits
           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
           + A A++A AA A  AA:AC+C:UAUAAU::CG:G AUAUGGC:CG::AGUUUCUACC:G
       168 UUACAAUAUAAUAGGAACACUCAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGG 227     

           <<<<_______>>>>>>>,,))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102     
            CA CCGUAAA UG C:GACUA:G+GU:A  A+U  A+    
       228 GCA-CCGUAAA-UGUCCGACUAUGGGUGAGCAAUGGAACCGC 267     

hit 0   :    270    171     2.25 bits
hit 1   :    270    171     2.25 bits
           :::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
         1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60      
             +    +   A    +:AC C:UA  +::: ::   UA GG :: :::GU    AC: G
      2144 CGUGCGGUUCCAUUGCUCACCCAUA-GUCGGACAU-UUACGG-UGCCCGGUAGAAACUUG 2200    

           <<<<_______>>>>>>>,,.))))))))::::::::::::::
        61 gcaaCCGUAAAuugcCuGAC.UAcGaGuaAauauuaaauauuu 102     
           ::::CC UA  ::::C :   UA:G GU: +  U+++AUAUU 
      2201 CGUGCCAUAUCCACGCGAUUaUAUGAGUGUUCCUAUUAUAUUG 2243    


CPU time (search)   : 56.03u 0.38s 00:00:56.41 Elapsed: 00:00:58
CYK memory          :       0.66 MB

BioPerl-1.007002/t/data/test.interpro000444000766000024      2600313155576321 17454 0ustar00cjfieldsstaff000000000000


   
	
	  
	    
	  
	
	
	  
	    
	  
	
	
	  
	    
	    
	 
	  
	    
	  
	  
	    
	  
	
	
	  
	    
	    
	    
	    
	    
	  
	  
	    
	    
	    
	    
	 
	  
	    
	    
	    
	  
	
	  
	    
	    
	  
   
   
	
	  
	    
	    
	  
	  
	    
	  
	  
	    
	    
	    
	    
	  
	
	
	  
	    
	    
	    
	    
	    
	  
	  
	    
	  
	  
	    
	    
	    
	    
	    
	    
	    
	  
	
	
	  
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	 
	  
	    
	    
	  
	
	
	  
	    
	    
	    
	  
	  
	    
	  
	  
	    
	    
	    
	    
	    
	    
	  
	
	
	  
	    
	    
	  
	  
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	  
	
	
	  
	    
	    
	  
	  
	    
	    
	  
	  
	    
	    
	    
	    
	  
	
	
	  
	    
	    
	    
	  
	  
	    
	    
	    
	  
	  
	    
	    
	    
	    
	  
	
	
	  
	    
	    
	    
	  
	  
	    
	    
	    
	    
	    
	    
	    
	    
	    
	 
	  
	    
	  
	
	  
	    
	    
	  
	  
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	  
   

BioPerl-1.007002/t/data/test.interpro-go.xml000444000766000024      1510713155576321 20661 0ustar00cjfieldsstaff000000000000

	
    
		
		
			
			
				
				
				
				
				
				
			
		
	
    


   
	
	  
	    
	  
	  
	    Molecular Function
	    DNA binding
	  
	  
	    
	  
	
	
	  
	    
	 
	  
	    Molecular Function
	    protein binding
	  
	  
	    Molecular Function
	    zinc ion binding
	  
	  
	    
	    
	    
	  
	  
	    
	    
	    
	  
	
	
	  
	    
	  
	  
	    
	    
	    
	 
	  
	    
	  
	
	
	  
	    
	    
	    
	  
	  
	    
	 
	  
	    
	  
	  
	    Molecular Function
	    zinc ion binding
	  
	  
	    
	    
	    
	  
	
	
	  
	    
	    
	    
	    
	    
	    
	  
	  
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	    
	  
	
   


    
BioPerl-1.007002/t/data/test.lasergene000444000766000024       157013155576321 17541 0ustar00cjfieldsstaff000000000000Created: Jueves, 08 de Junio de 2006 01:56 p.m.

This is a test sequence created with EditSeq (Lasergene's DNAStar)

^^
ATCGATCGATCG
TCGATCGATCGA
CGATCGATCGTT
^^
>gi|105633134|gb|DW246643.1|DW246643 JC3_E04 Forward JC Glycine max cDNA 5', mRNA sequence
^^
ATACACCTCTTTCTCATTGAACATTGGAATCTGGACAAGCACGACGGGGTAATTAGAGTTGCCGAGTTCCTCGTCGTCTTGGAGTGGCTCGAACTTGTAGCGCTGGTGTGGCTTCTTCCAGAAGAGCTTGACGAGGATGATGACAATGCCCATGTAGACCCTCTCCATGAAGAGCATGAGCGCCATGGCGAGGCTAATGC
^^
Sample protein sequence in Lasergene format
ALEU_HORVU


^^
MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGK
SYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRD
AAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNG
GLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAF
QVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCA
IATCASYPVVAA
BioPerl-1.007002/t/data/test.locuslink000444000766000024      1763413155576321 17627 0ustar00cjfieldsstaff000000000000>>26
LOCUSID: 26
LOCUS_CONFIRMED: yes
LOCUS_TYPE: gene with protein product, function known or inferred
ORGANISM: Homo sapiens
STATUS: REVIEWED
NM: NM_001091|4501850|na
NP: NP_001082|4501851
CDD: Copper amine oxidase|pfam01179|1775|na|6.883370e+02
PRODUCT: amiloride binding protein 1 precursor
ASSEMBLY: X78212
CONTIG: NT_007914.10|22047859|na|11083771|11092582|+|7|reference
EVID: supported by alignment with mRNA
XM: XM_032220|14745402|na
XP: XP_032220|14745403|na
ACCNUM: X78212|463242|na|na|na
TYPE: g
PROT: CAA55046|463243
ACCNUM: BC014093|15559450|na|na|na
TYPE: m
PROT: AAH14093|15559451
ACCNUM: M55602|387655|na|na|na
TYPE: m
PROT: AAA58358|177960
ACCNUM: U11862|533535|na|na|na
TYPE: m
PROT: AAC50270|533536
ACCNUM: U11863|533537|na|na|na
TYPE: m
PROT: AAB60381|533538
OFFICIAL_SYMBOL: ABP1
OFFICIAL_GENE_NAME: amiloride binding protein 1 (amine oxidase (copper-containing))
ALIAS_SYMBOL: DAO
ALIAS_SYMBOL: AOC1
PREFERRED_PRODUCT: amiloride binding protein 1 precursor
SUMMARY: Summary: This gene encodes a membrane glycoprotein that binds amiloride, a diuretic that acts by closing epithelial sodium ion channels. Experimental evidence indicates, however, that the formation of an amiloride sensitive, sodium channel requires complex formation with additional proteins. Although an association was proposed between this gene and cystic fibrosis, a disorder involving sodium and water imbalance in the lungs, genetic evidence showed that it was not involved in producing that disorder.
CHR: 7
STS: RH71199|7|8014|na|seq_map|epcr
STS: ABP1|7|32801|ABP1|seq_map|epcr
COMP: 10090|Abp1|6|6  cM|76507|7|ABP1|ncbi_mgd
COMP: 10090|1600012D06Rik|6|6  cM|76507|7|ABP1|ucsc_mgd
ALIAS_PROT: diamine oxidase
ALIAS_PROT: Amiloride-binding protein-1
UNIGENE: Hs.75741
BUTTON: unigene.gif
LINK: https://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=75741
OMIM: 104610
ECNUM: 1.4.3.6
MAP: 7q34-q36|RefSeq|C|
MAPLINK: default_human_gene|ABP1
BUTTON: snp.gif
LINK: https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?locusId=26
BUTTON: homol.gif
LINK: https://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=26[loc]&TAXID=9606
BUTTON: gdb.gif
LINK: http://gdbwww.gdb.org/gdb-bin/genera/accno?GDB:127105
BUTTON: ensembl.gif
LINK: http://www.ensembl.org/Homo_sapiens/contigview?geneid=NM_001091
BUTTON: ucsc.gif
LINK: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg12&position=NM_001091
DB_DESCR: GeneCards
DB_LINK: http://bioinformatics.weizmann.ac.il/cards-bin/carddisp?ABP1
DB_DESCR: KEGG pathway: Tyrosine metabolism
DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00350
DB_DESCR: KEGG pathway: Histidine metabolism
DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00340
DB_DESCR: KEGG pathway: Tryptophan metabolism
DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00380
DB_DESCR: KEGG pathway: beta-Alanine metabolism
DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00410
DB_DESCR: KEGG pathway: Alkaloid biosynthesis II
DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00960
DB_DESCR: KEGG pathway: Phenylalanine metabolism
DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00360
DB_DESCR: KEGG pathway: Arginine and proline metabolism
DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00330
DB_DESCR: KEGG pathway: Glycine, serine and threonine metabolism
DB_LINK: http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=hsa&mapno=00260
PMID: 11603849,8595053,8182053,8144586,2217167,1356107
GRIF: 11603849|could be detected at the feto-maternal interface of human
SUMFUNC: Diamine oxidase (D-amino-acid oxidase histaminase, amiloride-binding protein); deaminates putrescine and histamine|Proteome
GO: biological process|metabolism|NR|GO:0008152|Proteome|na
GO: cellular component|peroxisome|NR|GO:0005777|Proteome|na
GO: molecular function|amine oxidase|E|GO:0008131|Proteome|8144586
GO: molecular function|drug binding|NR|GO:0008144|Proteome|na
EXTANNOT: cellular role|Other metabolism|E|Proteome|1356107
EXTANNOT: biochemical function|Oxidoreductase|E|Proteome|1356107
EXTANNOT: biochemical function|Small molecule-binding protein|E|Proteome|8182053
>>27
LOCUSID: 27
LOCUS_CONFIRMED: yes
LOCUS_TYPE: gene with protein product, function known or inferred
ORGANISM: Homo sapiens
STATUS: REVIEWED
NM: NM_005158|6382059|na
NP: NP_005149|6382060
PRODUCT: v-abl Abelson murine leukemia viral oncogene homolog 2 isoform a
TRANSVAR: Transcript Variant:  Transcript variant a includes the alternate exon IA, but not exon IB and encodes a distinct N-terminus.
ASSEMBLY: M35296
NM: NM_007314|6382061|na
NP: NP_009298|6382062
CDD: SH3 domain|pfam00018|180|na|7.394420e+01
CDD: Src homology 2 domains|SH2|229|na|9.281890e+01
CDD: Src homology 3 domains|SH3|128|na|5.391380e+01
CDD: Src homology domain 2|pfam00017|212|na|8.627050e+01
CDD: Tyrosine kinase, catalytic domain|TyrKc|869|na|3.393470e+02
CDD: Eukaryotic protein kinase domain|pfam00069|510|na|2.010600e+02
CDD: Serine/Threonine protein kinases, catalytic domain|S_TKc|417|na|1.652360e+02
PRODUCT: v-abl Abelson murine leukemia viral oncogene homolog 2 isoform b
TRANSVAR: Transcript Variant:  Transcript variant a includes the alternate exon IB, but not exon IA and encodes a distinct N-terminus.
ASSEMBLY: M35296
CONTIG: NT_004487.12|22045208|na|4192865|4314849|-|1|reference
EVID: supported by alignment with mRNA
XM: NM_005158|6382059|na
XP: NP_005149|6382060|na
EVID: supported by alignment with both mRNA and ESTs (5)
XM: NM_007314|6382061|na
XP: NP_009298|6382062|na
ACCNUM: M35296|178992|na|na|na
TYPE: m
PROT: AAA35553|178993
OFFICIAL_SYMBOL: ABL2
OFFICIAL_GENE_NAME: v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)
ALIAS_SYMBOL: ARG
ALIAS_SYMBOL: ABLL
PREFERRED_PRODUCT: v-abl Abelson murine leukemia viral oncogene homolog 2 isoform a
PREFERRED_PRODUCT: v-abl Abelson murine leukemia viral oncogene homolog 2 isoform b
SUMMARY: Summary:  ABL2 is a cytoplasmic tyrosine kinase which is closely related to but distinct from ABL1.  The similarity of the proteins includes the tyrosine kinase domains and extends amino-terminal to include the SH2 and SH3 domains.  ABL2 is expressed in both normal and tumor cells.  The ABL2 gene product is expressed as two variants bearing different amino termini, both approximately 12-kb in length.
CHR: 1
STS: RH69130|1|3401|na|seq_map|epcr
STS: RH66836|1|44261|na|seq_map|epcr
COMP: 10090|Abl2|1|1 82.10 cM|11352|1|ABL2|ncbi_mgd
COMP: 10090|Abl2|1|1 82.10 cM|11352|1|ABL2|ucsc_mgd
ALIAS_PROT: arg
ALIAS_PROT: Abelson murine leukemia viral (v-abl) oncogene homolog 2 (arg,
UNIGENE: Hs.121521
BUTTON: unigene.gif
LINK: https://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=121521
OMIM: 164690
ECNUM: 2.7.1.112
MAP: 1q24-q25|    HUGO|C|
MAPLINK: default_human_gene|ABL2
PHENOTYPE: Leukemia, acute myeloid, with eosinophilia
PHENOTYPE_ID: 164690
BUTTON: snp.gif
LINK: https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?locusId=27
BUTTON: homol.gif
LINK: https://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=27[loc]&TAXID=9606
BUTTON: gdb.gif
LINK: http://gdbwww.gdb.org/gdb-bin/genera/accno?GDB:119641
BUTTON: ensembl.gif
LINK: http://www.ensembl.org/Homo_sapiens/contigview?geneid=NM_007314
BUTTON: ucsc.gif
LINK: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg12&position=NM_007314
DB_DESCR: GeneCards
DB_LINK: http://bioinformatics.weizmann.ac.il/cards-bin/carddisp?ABL2
PMID: 3787260,2198571
SUMFUNC: Cytoplasmic tyrosine kinase of the Abelson subfamily; contains SH2 and SH3 domains and has similarity to ABL1|Proteome
GO: cellular component|cytoplasm|NR|GO:0005737|Proteome|na
GO: molecular function|protein kinase|P|GO:0004672|Proteome|2198571
GO: biological process|signal transduction|P|GO:0007165|Proteome|2198571
GO: biological process|protein modification|P|GO:0006464|Proteome|2198571
EXTANNOT: biochemical function|Transferase|P|Proteome|2198571
EXTANNOT: subcellular localization|Cytoplasmic|NR|Proteome|2198571
BioPerl-1.007002/t/data/test.maq000444000766000024     21614613155576321 16421 0ustar00cjfieldsstaff0000000000005306796|gb|AY948116.1|_11_186_3c7/2	gi|65306796|gb|AY948116.1|	11	+	0	0	78	78	78	0	0	1	0	25	AACACCAAAAAAGGAAAAATTTAAA	YYYYYYYYYWYYYYYYWYYWWWYSU
5306796|gb|AY948116.1|_12_155_3a1/1	gi|65306796|gb|AY948116.1|	12	+	0	0	78	78	78	0	0	1	0	25	ACACCAAAAAAGGAAAAATTTAAAA	YYYYYYYYYYYYYYYYYWWUWWYWW
5306796|gb|AY948116.1|_25_177_300/1	gi|65306796|gb|AY948116.1|	25	+	0	0	78	78	78	0	0	1	0	25	AAAAATTTAAAAATGCAAAAACCAA	YYYYYYYYYYYYYYWWYYWUWWWQQ
5306796|gb|AY948116.1|_30_178_303/1	gi|65306796|gb|AY948116.1|	30	+	0	0	78	78	78	0	0	1	0	25	TTTAAAAATGCAAAAACCAATATCC	YYYYYYYYYYWYYYYWYWWUWWWQQ
5306796|gb|AY948116.1|_51_174_336/2	gi|65306796|gb|AY948116.1|	51	+	0	0	78	78	78	0	0	1	0	25	ATCCCGAAGTGCATAGCTTAGAAGA	YYYYYYYYYWYYYYYYWYYWWWYSU
5306796|gb|AY948116.1|_51_250_35c/2	gi|65306796|gb|AY948116.1|	51	+	0	0	78	78	78	0	0	1	0	25	ATCCCGAAGTGCATAGCTTAGAAGA	YYYYYYYYYYYYYYYWYYYWWWWQQ
5306796|gb|AY948116.1|_63_212_3a9/1	gi|65306796|gb|AY948116.1|	63	+	0	0	78	78	78	0	0	1	0	25	ATAGCTTAGAAGAAAGCCTTGCAAT	YYYYYYYYYWYYYYYYYWWWYYYWY
5306796|gb|AY948116.1|_65_228_371/2	gi|65306796|gb|AY948116.1|	65	+	0	0	78	78	78	0	0	1	0	25	AGCTTAGAAGAAAGCCTTGCAATAC	YYYYYYYYYYWYYYYYYYYSYYYSU
5306796|gb|AY948116.1|_70_223_3bc/2	gi|65306796|gb|AY948116.1|	70	+	0	0	78	78	78	0	0	1	0	25	AGAAGAAAGCCTTGCAATACTTAAA	YYYYYYYYYYYYYYYYWYYWYWYWW
5306796|gb|AY948116.1|_89_264_37d/2	gi|65306796|gb|AY948116.1|	89	+	0	0	78	78	78	0	0	1	0	25	CTTAAAAAAATATAAAGATGATGTA	YYYYYYYYYYYYYWYYYYYWYYYSU
5306796|gb|AY948116.1|_97_282_392/1	gi|65306796|gb|AY948116.1|	97	+	0	0	78	78	78	0	0	1	0	25	AATATAAAGATGATGTAAATAAGGA	YYYYYYYYYYYYYYYYYYWWWWWQQ
306796|gb|AY948116.1|_105_251_3c0/1	gi|65306796|gb|AY948116.1|	105	+	0	0	78	78	78	0	0	1	0	25	GATGATGTAAATAAGGAAAGATTAT	YYYYYYYYYYYYYYYYYYYWYWYWY
306796|gb|AY948116.1|_106_264_3dc/1	gi|65306796|gb|AY948116.1|	106	+	0	0	78	78	78	0	0	1	0	25	ATGATGTAAATAAGGAAAGATTATG	YYYYYYYYYYYYYYYYWYYSYYYSU
306796|gb|AY948116.1|_126_265_375/1	gi|65306796|gb|AY948116.1|	126	+	0	0	78	78	78	0	0	1	0	25	TTATGAAGGTATAAAATCTGTTATA	YYYYYYYYYYYYYYYYWYWWWYYWW
306796|gb|AY948116.1|_130_278_2f0/2	gi|65306796|gb|AY948116.1|	130	+	0	0	78	78	78	0	0	1	0	25	GAAGGTATAAAATCTGTTATAAGTA	YYYYYYYYYYYYYYYYYYWYWWWQQ
5306796|gb|AY948116.1|_12_155_3a1/2	gi|65306796|gb|AY948116.1|	131	-	0	0	78	78	78	0	0	1	0	25	AAGGTATAAAATCTGTTATAAGTAA	USYYYSYYWYYYYYWYYYYYYYYYY
306796|gb|AY948116.1|_138_344_384/2	gi|65306796|gb|AY948116.1|	138	+	0	0	78	78	78	0	0	1	0	25	AAAATCTGTTATAAGTAATCATGCG	YYYYYYYYYYWYYYWWYYWYWYYWY
306796|gb|AY948116.1|_144_349_3d1/2	gi|65306796|gb|AY948116.1|	144	+	0	0	78	78	78	0	0	1	0	25	TGTTATAAGTAATCATGCGATAGAG	YYYYYYYYYYYYYYWWYYYWWWYSY
5306796|gb|AY948116.1|_51_174_336/1	gi|65306796|gb|AY948116.1|	150	-	0	0	78	78	78	0	0	1	0	25	AAGTAATCATGCGATAGAGAGTATT	WWYYYWWWYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_153_296_301/2	gi|65306796|gb|AY948116.1|	153	+	0	0	78	78	78	0	0	1	0	25	TAATCATGCGATAGAGAGTATTTAC	YYYYYYYYYYYYYYYYWYWUWWWQQ
5306796|gb|AY948116.1|_25_177_300/2	gi|65306796|gb|AY948116.1|	153	-	0	0	78	78	78	0	0	1	0	25	TAATCATGCGATAGAGAGTATTTAC	WWYYWWWWYWWYYYYWYYYYYYYYY
5306796|gb|AY948116.1|_30_178_303/2	gi|65306796|gb|AY948116.1|	154	-	0	0	78	78	78	0	0	1	0	25	AATCATGCGATAGAGAGTATTTACA	YWYWWYWYYWYYYYWYYYYYYYYYY
5306796|gb|AY948116.1|_11_186_3c7/1	gi|65306796|gb|AY948116.1|	162	-	0	0	78	78	78	0	0	1	0	25	GATAGAGAGTATTTACATGAATGAA	QQWWYSYYYWYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_166_309_31b/1	gi|65306796|gb|AY948116.1|	166	+	0	0	78	78	78	0	0	1	0	25	GAGAGTATTTACATGAATGAATTAG	YYYYYYYYYYYYYYYWYYWWYYYSU
306796|gb|AY948116.1|_168_313_3e7/1	gi|65306796|gb|AY948116.1|	168	+	0	0	78	78	78	0	0	1	0	25	GAGTATTTACATGAATGAATTAGAT	YYYYYYYYYYYYYYYYWYYWWWYSU
306796|gb|AY948116.1|_171_337_34f/2	gi|65306796|gb|AY948116.1|	171	+	0	0	78	78	78	0	0	1	0	25	TATTTACATGAATGAATTAGATATT	YYYYYYYYYYYYYWYYYYYSYYYSU
306796|gb|AY948116.1|_187_351_3b7/2	gi|65306796|gb|AY948116.1|	187	+	0	0	78	78	78	0	0	1	0	25	TTAGATATTATCGCTATGATAAAAC	YYYYYYYYYYYYYYWWYYWWYYYWW
5306796|gb|AY948116.1|_63_212_3a9/2	gi|65306796|gb|AY948116.1|	188	-	0	0	78	78	78	0	0	1	0	25	TAGATATTATCGCTATGATAAAACA	USYWYSYYYWYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_189_392_3b3/1	gi|65306796|gb|AY948116.1|	189	+	0	0	78	78	78	0	0	1	0	25	AGATATTATCGCTATGATAAAACAA	YYYYYYYYYYWYYYWWYYYWYYYWY
306796|gb|AY948116.1|_190_371_3bf/1	gi|65306796|gb|AY948116.1|	190	+	0	0	78	78	78	0	0	1	0	25	GATATTATCGCTATGATAAAACAAA	YYYYYYYYYYYYYYWWYWWWWWYWY
5306796|gb|AY948116.1|_70_223_3bc/1	gi|65306796|gb|AY948116.1|	199	-	0	0	78	78	78	0	0	1	0	25	GCTATGATAAAACAAAGTGCTTTAA	WWYWYSYYYWYWYYYYYYYYYYYYY
306796|gb|AY948116.1|_201_363_2ff/1	gi|65306796|gb|AY948116.1|	201	+	0	0	78	78	78	0	0	1	0	25	TATGATAAAACAAAGTGCTTTAAAG	YYYYYYYYYYWYYYYYYYYWYWWQQ
5306796|gb|AY948116.1|_65_228_371/1	gi|65306796|gb|AY948116.1|	204	-	0	0	78	78	78	0	0	1	0	25	GATAAAACAAAGTGCTTTAAAGTTA	USYYWUWWYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_209_376_3c6/2	gi|65306796|gb|AY948116.1|	209	+	0	0	78	78	78	0	0	1	0	25	AACAAAGTGCTTTAAAGTTAAGTGC	YYYYYYYYYYYYYWYYWYYWYYYSY
5306796|gb|AY948116.1|_51_250_35c/1	gi|65306796|gb|AY948116.1|	226	-	0	0	78	78	78	0	0	1	0	25	TTAAGTGCTGATGAAATCATTGCTG	WWYYWUWYYWWYYYYWYYYYYYYYY
306796|gb|AY948116.1|_105_251_3c0/2	gi|65306796|gb|AY948116.1|	227	-	0	0	78	78	78	0	0	1	0	25	TAAGTGCTGATGAAATCATTGCTGA	YSYWYWYYYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_237_404_398/2	gi|65306796|gb|AY948116.1|	237	+	0	0	78	78	78	0	0	1	0	25	TGAAATCATTGCTGAATATAAGGAA	YYYYYYYYYWYYYYYWYYYWWYYSY
306796|gb|AY948116.1|_106_264_3dc/2	gi|65306796|gb|AY948116.1|	240	-	0	0	78	78	78	0	0	1	0	25	AATCATTGCTGAATATAAGGAAAAG	WWYYYSYYYWWYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_89_264_37d/1	gi|65306796|gb|AY948116.1|	240	-	0	0	78	78	78	0	0	1	0	25	AATCATTGCTGAATATAAGGAAAAG	USYWWYWYWYYYYYYWYYYYYYYYY
306796|gb|AY948116.1|_126_265_375/2	gi|65306796|gb|AY948116.1|	241	-	0	0	78	78	78	0	0	1	0	25	ATCATTGCTGAATATAAGGAAAAGG	QQWWWUWYYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_245_443_313/2	gi|65306796|gb|AY948116.1|	245	+	0	0	78	78	78	0	0	1	0	25	TTGCTGAATATAAGGAAAAGGGATT	YYYYYYYYYYWYYYYWYYWWWWYWW
306796|gb|AY948116.1|_246_408_335/2	gi|65306796|gb|AY948116.1|	246	+	0	0	78	78	78	0	0	1	0	25	TGCTGAATATAAGGAAAAGGGATTT	YYYYYYYYYWYYYWYWYYWUWWYWW
306796|gb|AY948116.1|_246_433_356/1	gi|65306796|gb|AY948116.1|	246	+	0	0	78	78	78	0	0	1	0	25	TGCTGAATATAAGGAAAAGGGATTT	YYYYYYYYYYYYYYYWYYWYWWWQQ
306796|gb|AY948116.1|_130_278_2f0/1	gi|65306796|gb|AY948116.1|	254	-	0	0	78	78	78	0	0	1	0	25	ATAAGGAAAAGGGATTTGTAGAATA	USYYWYWYYYYYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_97_282_392/2	gi|65306796|gb|AY948116.1|	258	-	0	0	78	78	78	0	0	1	0	25	GGAAAAGGGATTTGTAGAATATGTC	YWYYYWWYYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_153_296_301/1	gi|65306796|gb|AY948116.1|	272	-	0	0	78	78	78	0	0	1	0	25	TAGAATATGTCAAAAGTTGCCACCG	YWYYYWWWYWWYYYYYYYYYYYYYY
306796|gb|AY948116.1|_283_462_30e/2	gi|65306796|gb|AY948116.1|	283	+	0	0	78	78	78	0	0	1	0	25	AAAAGTTGCCACCGCTCATTGCAAT	YYYYYYYYYYYYYYYYYYYWYWYWY
306796|gb|AY948116.1|_285_453_39c/1	gi|65306796|gb|AY948116.1|	285	+	0	0	78	78	78	0	0	1	0	25	AAGTTGCCACCGCTCATTGCAATCC	YYYYYYYYYYWYYYYYWYWWYWYWW
306796|gb|AY948116.1|_166_309_31b/2	gi|65306796|gb|AY948116.1|	285	-	0	0	78	78	78	0	0	1	0	25	AAGTTGCCACCGCTCATTGCAATCC	YSYYYSYYYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_289_501_3e3/2	gi|65306796|gb|AY948116.1|	289	+	0	0	78	78	78	0	0	1	0	25	TGCCACCGCTCATTGCAATCCTAAA	YYYYYYYYYYWYYWYWYWWWWYYSY
306796|gb|AY948116.1|_168_313_3e7/2	gi|65306796|gb|AY948116.1|	289	-	0	0	78	78	78	0	0	1	0	25	TGCCACCGCTCATTGCAATCCTAAA	WWYWYSYYYWWYYYYYYYYYYYYYY
306796|gb|AY948116.1|_171_337_34f/1	gi|65306796|gb|AY948116.1|	313	-	0	0	78	78	78	0	0	1	0	25	AAAACAACCTGCATTAAACCACAAT	USYWWYWYYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_138_344_384/1	gi|65306796|gb|AY948116.1|	320	-	0	0	78	78	78	0	0	1	0	25	CCTGCATTAAACCACAATGATAGAA	YWYWWWYYYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_322_487_363/1	gi|65306796|gb|AY948116.1|	322	+	0	0	78	78	78	0	0	1	0	25	TGCATTAAACCACAATGATAGAACC	YYYYYYYYYYYYYWYYYYWUWWYSY
306796|gb|AY948116.1|_144_349_3d1/1	gi|65306796|gb|AY948116.1|	325	-	0	0	78	78	78	0	0	1	0	25	ATTAAACCACAATGATAGAACCAAC	WWYWWUWYWYYWYYYYYYYYYYYYY
306796|gb|AY948116.1|_187_351_3b7/1	gi|65306796|gb|AY948116.1|	327	-	0	0	78	78	78	0	0	1	0	25	TAAACCACAATGATAGAACCAACGA	YSYYWWYYWYYYYYYWYYYYYYYYY
306796|gb|AY948116.1|_201_363_2ff/2	gi|65306796|gb|AY948116.1|	339	-	0	0	78	78	78	0	0	1	0	25	ATAGAACCAACGATAATGCTAAGAC	USYYYWYYWYYWYYYYYYYYYYYYY
306796|gb|AY948116.1|_346_491_347/1	gi|65306796|gb|AY948116.1|	346	+	0	0	78	78	78	0	0	1	0	25	CAACGATAATGCTAAGACAATCACT	YYYYYYYYYYWYYYWWYWWWWWWQQ
306796|gb|AY948116.1|_190_371_3bf/2	gi|65306796|gb|AY948116.1|	347	-	0	0	78	78	78	0	0	1	0	25	AACGATAATGCTAAGACAATCACTA	YWYWYSYYYWYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_209_376_3c6/1	gi|65306796|gb|AY948116.1|	352	-	0	0	78	78	78	0	0	1	0	25	TAATGCTAAGACAATCACTAAAGAA	QQWWWWWWYWWYYYWYYYYYYYYYY
306796|gb|AY948116.1|_357_551_308/1	gi|65306796|gb|AY948116.1|	357	+	0	0	78	78	78	0	0	1	0	25	CTAAGACAATCACTAAAGAACTTAC	YYYYYYYYYYYYYYWWYYWYWWWQQ
306796|gb|AY948116.1|_189_392_3b3/2	gi|65306796|gb|AY948116.1|	368	-	0	0	78	78	78	0	0	1	0	25	ACTAAAGAACTTACGCATTTAAATG	YSYYYWWWYWWYYYYYYYYYYYYYY
306796|gb|AY948116.1|_373_533_3a6/2	gi|65306796|gb|AY948116.1|	373	+	0	0	78	78	78	0	0	1	0	25	AGAACTTACGCATTTAAATGAATAC	YYYYYYYYYYWYYYYYWYWUWWWQQ
306796|gb|AY948116.1|_237_404_398/1	gi|65306796|gb|AY948116.1|	380	-	0	0	78	78	78	0	0	1	0	25	ACGCATTTAAATGAATACTCTTGCA	USYYYSYYYWWYYYYYYYYYYYYYY
306796|gb|AY948116.1|_246_408_335/1	gi|65306796|gb|AY948116.1|	384	-	0	0	78	78	78	0	0	1	0	25	ATTTAAATGAATACTCTTGCACTAG	USYYWWYYYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_246_433_356/2	gi|65306796|gb|AY948116.1|	409	-	0	0	78	78	78	0	0	1	0	25	CGATGAAGTGCGTAAGAACATAGAA	WWYYWYWYYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_245_443_313/1	gi|65306796|gb|AY948116.1|	419	-	0	0	78	78	78	0	0	1	0	25	CGTAAGAACATAGAAAGGCTTTATA	QQWWWUWWYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_421_628_34b/2	gi|65306796|gb|AY948116.1|	421	+	0	0	78	78	78	0	0	1	0	25	TAAGAACATAGAAAGGCTTTATAAA	YYYYYYYYYYWYYYYYYWWWYWWQQ
306796|gb|AY948116.1|_429_590_3e4/1	gi|65306796|gb|AY948116.1|	429	+	0	0	78	78	78	0	0	1	0	25	TAGAAAGGCTTTATAAAAAAGCTTA	YYYYYYYYYYWYYYWWYYYWWWYWY
306796|gb|AY948116.1|_285_453_39c/2	gi|65306796|gb|AY948116.1|	429	-	0	0	78	78	78	0	0	1	0	25	TAGAAAGGCTTTATAAAAAAGCTTA	USYWYWYYYWWYYYYYYYYYYYYYY
306796|gb|AY948116.1|_283_462_30e/1	gi|65306796|gb|AY948116.1|	438	-	0	0	78	78	78	0	0	1	0	25	TTTATAAAAAAGCTTATGAAAATTT	YWYWYSYYYWYYYYWYYYYYYYYYY
306796|gb|AY948116.1|_447_643_321/1	gi|65306796|gb|AY948116.1|	447	+	0	0	78	78	78	0	0	1	0	25	AAGCTTATGAAAATTTTTATAAATA	YYYYYYYYYYYYYWYYYYYSYYYWW
306796|gb|AY948116.1|_460_623_329/2	gi|65306796|gb|AY948116.1|	460	+	0	0	78	78	78	0	0	1	0	25	TTTTTATAAATATTGTGAAAATAAG	YYYYYYYYYYYYYYYYYYWYWWYWW
306796|gb|AY948116.1|_322_487_363/2	gi|65306796|gb|AY948116.1|	463	-	0	0	78	78	78	0	0	1	0	25	TTATAAATATTGTGAAAATAAGAAT	USYWWUWYYYYYYYYWYYYYYYYYY
306796|gb|AY948116.1|_346_491_347/2	gi|65306796|gb|AY948116.1|	467	-	0	0	78	78	78	0	0	1	0	25	AAATATTGTGAAAATAAGAATGGTT	YSYYYWYYWYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_469_600_3ab/1	gi|65306796|gb|AY948116.1|	469	+	0	0	78	78	78	0	0	1	0	25	ATATTGTGAAAATAAGAATGGTTTA	YYYYYYYYYYWYYYYWYWWUWWWQQ
306796|gb|AY948116.1|_289_501_3e3/1	gi|65306796|gb|AY948116.1|	477	-	0	0	78	78	78	0	0	1	0	25	AAAATAAGAATGGTTTAGCTAAAAG	WWYYWYWWYYYWYYYWYYYYYYYYY
306796|gb|AY948116.1|_482_661_306/1	gi|65306796|gb|AY948116.1|	482	+	0	0	78	78	78	0	0	1	0	25	AAGAATGGTTTAGCTAAAAGTGGAA	YYYYYYYYYYWYYYYYWYYSYYYSU
306796|gb|AY948116.1|_501_675_362/1	gi|65306796|gb|AY948116.1|	501	+	0	0	78	78	78	0	0	1	0	25	GTGGAAAGCCTAAAGGACTTCAAAA	YYYYYYYYYYYYYYYYWYWWYYYWY
306796|gb|AY948116.1|_505_676_386/1	gi|65306796|gb|AY948116.1|	505	+	0	0	78	78	78	0	0	1	0	25	AAAGCCTAAAGGACTTCAAAATTTT	YYYYYYYYYYYYYYWWYYYWYWWQQ
306796|gb|AY948116.1|_373_533_3a6/1	gi|65306796|gb|AY948116.1|	509	-	0	0	78	78	78	0	0	1	0	25	CCTAAAGGACTTCAAAATTTTACTA	WWYYWWWYYWYWYYYWYYYYYYYYY
306796|gb|AY948116.1|_510_683_2fa/1	gi|65306796|gb|AY948116.1|	510	+	0	0	78	78	78	0	0	1	0	25	CTAAAGGACTTCAAAATTTTACTAA	YYYYYYYYYYYYYWYYWYWYWWWQQ
306796|gb|AY948116.1|_512_674_3cf/1	gi|65306796|gb|AY948116.1|	512	+	0	0	78	78	78	0	0	1	0	25	AAAGGACTTCAAAATTTTACTAAAA	YYYYYYYYYYYYYYYYWYYSYYYWW
306796|gb|AY948116.1|_515_672_2f2/2	gi|65306796|gb|AY948116.1|	515	+	0	0	78	78	78	0	0	1	0	25	GGACTTCAAAATTTTACTAAAAAAG	YYYYYYYYYYYYYYWWYWWYWWYSU
306796|gb|AY948116.1|_357_551_308/2	gi|65306796|gb|AY948116.1|	527	-	0	0	78	78	78	0	0	1	0	25	TTTACTAAAAAAGAAAAATGTTATC	WWYWWWYYYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_530_745_302/1	gi|65306796|gb|AY948116.1|	530	+	0	0	78	78	78	0	0	1	0	25	ACTAAAAAAGAAAAATGTTATCACG	YYYYYYYYYYYYYYYYYYWUWWYWW
306796|gb|AY948116.1|_531_727_30f/2	gi|65306796|gb|AY948116.1|	531	+	0	0	78	78	78	0	0	1	0	25	CTAAAAAAGAAAAATGTTATCACGA	YYYYYYYYYYYYYYYWYYWWWYYWW
306796|gb|AY948116.1|_547_706_31d/1	gi|65306796|gb|AY948116.1|	547	+	0	0	78	78	78	0	0	1	0	25	TTATCACGAGTTTATATACGAAATC	YYYYYYYYYYYYYWYYWYWWYYYSY
306796|gb|AY948116.1|_549_659_341/1	gi|65306796|gb|AY948116.1|	549	+	0	0	78	78	78	0	0	1	0	25	ATCACGAGTTTATATACGAAATCGG	YYYYYYYYYYYYYYYYYWWUWWWQQ
306796|gb|AY948116.1|_429_590_3e4/2	gi|65306796|gb|AY948116.1|	566	-	0	0	78	78	78	0	0	1	0	25	GAAATCGGCGAAAATACTACAATGG	YWYYWWWYYWYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_569_772_33a/1	gi|65306796|gb|AY948116.1|	569	+	0	0	78	78	78	0	0	1	0	25	ATCGGCGAAAATACTACAATGGAGC	YYYYYYYYYYYYYYYWYYWYWWYSU
306796|gb|AY948116.1|_573_734_3ac/2	gi|65306796|gb|AY948116.1|	573	+	0	0	78	78	78	0	0	1	0	25	GCGAAAATACTACAATGGAGCAATG	YYYYYYYYYYYYYYWWYWWWWWWQQ
306796|gb|AY948116.1|_574_743_36f/1	gi|65306796|gb|AY948116.1|	574	+	0	0	78	78	78	0	0	1	0	25	CGAAAATACTACAATGGAGCAATGC	YYYYYYYYYYYYYYWWYWWWYWYWY
306796|gb|AY948116.1|_469_600_3ab/2	gi|65306796|gb|AY948116.1|	576	-	0	0	78	78	78	0	0	1	0	25	AAAATACTACAATGGAGCAATGCCA	QQWWWUWWYWYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_595_772_3d9/2	gi|65306796|gb|AY948116.1|	595	+	0	0	78	78	78	0	0	1	0	25	ATGCCAAGAGCTTACGCAAAAAATC	YYYYYYYYYWYYYWYYWYYSYWWQQ
306796|gb|AY948116.1|_599_805_2fb/1	gi|65306796|gb|AY948116.1|	599	+	0	0	78	78	78	0	0	1	0	25	CAAGAGCTTACGCAAAAAATCGCAG	YYYYYYYYYYYYYWYYWYYSYYYSU
306796|gb|AY948116.1|_460_623_329/1	gi|65306796|gb|AY948116.1|	599	-	0	0	78	78	78	0	0	1	0	25	CAAGAGCTTACGCAAAAAATCGCAG	QQWWWYWYYYYWYYYWYYYYYYYYY
306796|gb|AY948116.1|_421_628_34b/1	gi|65306796|gb|AY948116.1|	604	-	0	0	78	78	78	0	0	1	0	25	GCTTACGCAAAAAATCGCAGAGCTT	WWYYYWWYYYYWYYYYYYYYYYYYY
306796|gb|AY948116.1|_619_814_369/2	gi|65306796|gb|AY948116.1|	619	+	0	0	78	78	78	0	0	1	0	25	CGCAGAGCTTACAGGATTTACACCT	YYYYYYYYYYWYYYYYYYWWYWWQQ
306796|gb|AY948116.1|_447_643_321/2	gi|65306796|gb|AY948116.1|	619	-	0	0	78	78	78	0	0	1	0	25	CGCAGAGCTTACAGGATTTACACCT	WWYYWWWWYWYYYYWYYYYYYYYYY
306796|gb|AY948116.1|_549_659_341/2	gi|65306796|gb|AY948116.1|	635	-	0	0	78	78	78	0	0	1	0	25	TTTACACCTTTACAAGTTGTAATCC	QQWWWYWWYWYYYYYWYYYYYYYYY
306796|gb|AY948116.1|_637_797_33f/1	gi|65306796|gb|AY948116.1|	637	+	0	0	78	78	78	0	0	1	0	25	TACACCTTTACAAGTTGTAATCCAT	YYYYYYYYYYYYYWYYYYYWWWYSU
306796|gb|AY948116.1|_482_661_306/2	gi|65306796|gb|AY948116.1|	637	-	0	0	78	78	78	0	0	1	0	25	TACACCTTTACAAGTTGTAATCCAT	WWYWYSYYYWYWYYYYYYYYYYYYY
306796|gb|AY948116.1|_644_798_31c/2	gi|65306796|gb|AY948116.1|	644	+	0	0	78	78	78	0	0	1	0	25	TTACAAGTTGTAATCCATAGAGATG	YYYYYYYYYYYYYYYYWYYWWYYSY
306796|gb|AY948116.1|_648_834_388/2	gi|65306796|gb|AY948116.1|	648	+	0	0	78	78	78	0	0	1	0	25	AAGTTGTAATCCATAGAGATGAAGT	YYYYYYYYYYYYYWYYYWWUWWYSY
306796|gb|AY948116.1|_515_672_2f2/1	gi|65306796|gb|AY948116.1|	648	-	0	0	78	78	78	0	0	1	0	25	AAGTTGTAATCCATAGAGATGAAGT	WWYYYWYYWYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_650_853_351/1	gi|65306796|gb|AY948116.1|	650	+	0	0	78	78	78	0	0	1	0	25	GTTGTAATCCATAGAGATGAAGTAA	YYYYYYYYYWYYYWYWYWWYWWYSY
306796|gb|AY948116.1|_512_674_3cf/2	gi|65306796|gb|AY948116.1|	650	-	0	0	78	78	78	0	0	1	0	25	GTTGTAATCCATAGAGATGAAGTAA	YSYWYSYYWYYWYYYYYYYYYYYYY
306796|gb|AY948116.1|_501_675_362/2	gi|65306796|gb|AY948116.1|	651	-	0	0	78	78	78	0	0	1	0	25	TTGTAATCCATAGAGATGAAGTAAG	QQWWWWWWYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_505_676_386/2	gi|65306796|gb|AY948116.1|	652	-	0	0	78	78	78	0	0	1	0	25	TGTAATCCATAGAGATGAAGTAAGT	WWYYWWYYYWWYYYYYYYYYYYYYY
306796|gb|AY948116.1|_655_827_36d/1	gi|65306796|gb|AY948116.1|	655	+	0	0	78	78	78	0	0	1	0	25	AATCCATAGAGATGAAGTAAGTGAG	YYYYYYYYYYYYYWYYYYWUWYYWW
306796|gb|AY948116.1|_510_683_2fa/2	gi|65306796|gb|AY948116.1|	659	-	0	0	78	78	78	0	0	1	0	25	CATAGAGATGAAGTAAGTGAGAATG	WWYYWUWYYWYWYYYWYYYYYYYYY
306796|gb|AY948116.1|_666_856_36e/2	gi|65306796|gb|AY948116.1|	666	+	0	0	78	78	78	0	0	1	0	25	ATGAAGTAAGTGAGAATGCTAAAGG	YYYYYYYYYWYYYYWWYYYSYWWQQ
306796|gb|AY948116.1|_547_706_31d/2	gi|65306796|gb|AY948116.1|	682	-	0	0	78	78	78	0	0	1	0	25	TGCTAAAGGGGAAAAACAAACCCAT	USYWWWYYWYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_531_727_30f/1	gi|65306796|gb|AY948116.1|	703	-	0	0	78	78	78	0	0	1	0	25	CCATTATCACGCCCACGCGGTATTT	USYYYSYYYYYYYYWYYYYYYYYYY
306796|gb|AY948116.1|_704_876_2f7/2	gi|65306796|gb|AY948116.1|	704	+	0	0	78	78	78	0	0	1	0	25	CATTATCACGCCCACGCGGTATTTT	YYYYYYYYYYWYYWYYYYYWWYYWW
306796|gb|AY948116.1|_573_734_3ac/1	gi|65306796|gb|AY948116.1|	710	-	0	0	78	78	78	0	0	1	0	25	CACGCCCACGCGGTATTTTTTACAC	QQWWWYWWYYYWYYYYYYYYYYYYY
306796|gb|AY948116.1|_712_881_2fc/1	gi|65306796|gb|AY948116.1|	712	+	0	0	78	78	78	0	0	1	0	25	CGCCCACGCGGTATTTTTTACACTC	YYYYYYYYYYYYYYYYYYYWYYYWY
306796|gb|AY948116.1|_713_838_317/2	gi|65306796|gb|AY948116.1|	713	+	0	0	78	78	78	0	0	1	0	25	GCCCACGCGGTATTTTTTACACTCG	YYYYYYYYYWYYYYWWYYWUWWYSY
306796|gb|AY948116.1|_574_743_36f/2	gi|65306796|gb|AY948116.1|	719	-	0	0	78	78	78	0	0	1	0	25	GCGGTATTTTTTACACTCGATAACA	QQWWWWYYYWYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_530_745_302/2	gi|65306796|gb|AY948116.1|	721	-	0	0	78	78	78	0	0	1	0	25	GGTATTTTTTACACTCGATAACAAT	YSYWWYWWYWYYYYYWYYYYYYYYY
306796|gb|AY948116.1|_569_772_33a/2	gi|65306796|gb|AY948116.1|	748	-	0	0	78	78	78	0	0	1	0	25	CTTACAACTTGCTAGACGTGAAGCA	YWYWWYWWYWYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_595_772_3d9/1	gi|65306796|gb|AY948116.1|	748	-	0	0	78	78	78	0	0	1	0	25	CTTACAACTTGCTAGACGTGAAGCA	QQWWWWYYYYYYYYWYYYYYYYYYY
306796|gb|AY948116.1|_763_912_39d/1	gi|65306796|gb|AY948116.1|	763	+	0	0	78	78	78	0	0	1	0	25	ACGTGAAGCAAGTTTGAATAAAGCC	YYYYYYYYYYYYYYYYWYYWWWWQQ
306796|gb|AY948116.1|_764_890_3ae/1	gi|65306796|gb|AY948116.1|	764	+	0	0	78	78	78	0	0	1	0	25	CGTGAAGCAAGTTTGAATAAAGCCA	YYYYYYYYYWYYYYYWYWWUWWYSU
306796|gb|AY948116.1|_766_934_318/2	gi|65306796|gb|AY948116.1|	766	+	0	0	78	78	78	0	0	1	0	25	TGAAGCAAGTTTGAATAAAGCCAAT	YYYYYYYYYYYYYYWWYWWWYYYSU
306796|gb|AY948116.1|_767_956_37e/2	gi|65306796|gb|AY948116.1|	767	+	0	0	78	78	78	0	0	1	0	25	GAAGCAAGTTTGAATAAAGCCAATC	YYYYYYYYYWYYYYYYYYWYWWYSU
306796|gb|AY948116.1|_637_797_33f/2	gi|65306796|gb|AY948116.1|	773	-	0	0	78	78	78	0	0	1	0	25	AGTTTGAATAAAGCCAATCTTAGCA	QQWWWWYYWYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_644_798_31c/1	gi|65306796|gb|AY948116.1|	774	-	0	0	78	78	78	0	0	1	0	25	GTTTGAATAAAGCCAATCTTAGCAA	YSYWWYWYYWWYYYYWYYYYYYYYY
306796|gb|AY948116.1|_599_805_2fb/2	gi|65306796|gb|AY948116.1|	781	-	0	0	78	78	78	0	0	1	0	25	TAAAGCCAATCTTAGCAAAATACAA	WWYWYWYYWYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_619_814_369/1	gi|65306796|gb|AY948116.1|	790	-	0	0	78	78	78	0	0	1	0	25	TCTTAGCAAAATACAAACCCTAACC	WWYWYSYYYYYWYYYYYYYYYYYYY
306796|gb|AY948116.1|_792_968_355/1	gi|65306796|gb|AY948116.1|	792	+	0	0	78	78	78	0	0	1	0	25	TTAGCAAAATACAAACCCTAACCGC	YYYYYYYYYYYYYYYYYYWYWWWQQ
306796|gb|AY948116.1|_655_827_36d/2	gi|65306796|gb|AY948116.1|	803	-	0	0	78	78	78	0	0	1	0	25	CAAACCCTAACCGCACAAAGTTTAA	YWYYYWWYWYYYYYWYYYYYYYYYY
306796|gb|AY948116.1|_806_964_322/2	gi|65306796|gb|AY948116.1|	806	+	0	0	78	78	78	0	0	1	0	25	ACCCTAACCGCACAAAGTTTAAAAA	YYYYYYYYYWYYYYYYYYWWWYYWY
306796|gb|AY948116.1|_648_834_388/1	gi|65306796|gb|AY948116.1|	810	-	0	0	78	78	78	0	0	1	0	25	TAACCGCACAAAGTTTAAAAATGGA	YWYYWUWYYYYWYYYWYYYYYYYYY
306796|gb|AY948116.1|_713_838_317/1	gi|65306796|gb|AY948116.1|	814	-	0	0	78	78	78	0	0	1	0	25	CGCACAAAGTTTAAAAATGGAGCGT	WWYYYSYYWYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_823_1016_35b/2	gi|65306796|gb|AY948116.1|	823	+	0	0	78	78	78	0	0	1	0	25	TTTAAAAATGGAGCGTGGAGCTAAT	YYYYYYYYYYYYYYYWYYYSYYYWW
306796|gb|AY948116.1|_650_853_351/2	gi|65306796|gb|AY948116.1|	829	-	0	0	78	78	78	0	0	1	0	25	AATGGAGCGTGGAGCTAATCGCTAC	WWYWYSYYYWYWYYYYYYYYYYYYY
306796|gb|AY948116.1|_666_856_36e/1	gi|65306796|gb|AY948116.1|	832	-	0	0	78	78	78	0	0	1	0	25	GGAGCGTGGAGCTAATCGCTACGAG	YWYYYSYYYWWYYYYYYYYYYYYYY
306796|gb|AY948116.1|_704_876_2f7/1	gi|65306796|gb|AY948116.1|	852	-	0	0	78	78	78	0	0	1	0	25	ACGAGAATAACGAAAAGCAACCTCA	YWYWWUWWYWYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_853_1033_307/1	gi|65306796|gb|AY948116.1|	853	+	0	0	78	78	78	0	0	1	0	25	CGAGAATAACGAAAAGCAACCTCAA	YYYYYYYYYYYYYYYYYYYSYYYWW
06796|gb|AY948116.1|_855_1026_370/2	gi|65306796|gb|AY948116.1|	855	+	0	0	78	78	78	0	0	1	0	25	AGAATAACGAAAAGCAACCTCAATA	YYYYYYYYYWYYYWYYYYYWYWWQQ
306796|gb|AY948116.1|_712_881_2fc/2	gi|65306796|gb|AY948116.1|	857	-	0	0	78	78	78	0	0	1	0	25	AATAACGAAAAGCAACCTCAATACA	YWYWYWWWYYYYYYYWYYYYYYYYY
306796|gb|AY948116.1|_764_890_3ae/2	gi|65306796|gb|AY948116.1|	866	-	0	0	78	78	78	0	0	1	0	25	AAGCAACCTCAATACATACAAGATT	WWYWWUWYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_872_1016_332/1	gi|65306796|gb|AY948116.1|	872	+	0	0	78	78	78	0	0	1	0	25	CCTCAATACATACAAGATTATAAAA	YYYYYYYYYYYYYWYYWYYWWWYSU
06796|gb|AY948116.1|_874_1037_3ba/1	gi|65306796|gb|AY948116.1|	874	+	0	0	78	78	78	0	0	1	0	25	TCAATACATACAAGATTATAAAACA	YYYYYYYYYYYYYYYWYYYSYWWQQ
06796|gb|AY948116.1|_888_1045_3a7/1	gi|65306796|gb|AY948116.1|	888	+	0	0	78	78	78	0	0	1	0	25	ATTATAAAACATACGCTCAATTTAA	YYYYYYYYYYYYYYWWYYWWWWYWY
306796|gb|AY948116.1|_763_912_39d/2	gi|65306796|gb|AY948116.1|	888	-	0	0	78	78	78	0	0	1	0	25	ATTATAAAACATACGCTCAATTTAA	YSYYYSYYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_889_1041_3c5/2	gi|65306796|gb|AY948116.1|	889	+	0	0	78	78	78	0	0	1	0	25	TTATAAAACATACGCTCAATTTAAA	YYYYYYYYYYWYYYYWYYWWWWYSY
06796|gb|AY948116.1|_907_1070_2f1/2	gi|65306796|gb|AY948116.1|	907	+	0	0	78	78	78	0	0	1	0	25	ATTTAAAGAACAAGAAAAAGCATTA	YYYYYYYYYYYYYYYYWYYWYWYSY
306796|gb|AY948116.1|_766_934_318/1	gi|65306796|gb|AY948116.1|	910	-	0	0	58	58	58	1	30	0	1	25	TTAAGAACAAGAAAAAGCATTACTT	YWYYWUWYYWWYYYYYYYYYYYYYY
306796|gb|AY948116.1|_767_956_37e/1	gi|65306796|gb|AY948116.1|	932	-	0	0	78	78	78	0	0	1	0	25	CTTCAAAGAATACAAGAACAAGAGC	YWYYYSYYWYYWYYYYYYYYYYYYY
306796|gb|AY948116.1|_806_964_322/1	gi|65306796|gb|AY948116.1|	940	-	0	0	78	78	78	0	0	1	0	25	AATACAAGAACAAGAGCATAAATTA	YSYYYWYYYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_792_968_355/2	gi|65306796|gb|AY948116.1|	944	-	0	0	78	78	78	0	0	1	0	25	CAAGAACAAGAGCATAAATTAACGC	YWYWWWYYYYYWYYYYYYYYYYYYY
06796|gb|AY948116.1|_947_1100_32c/2	gi|65306796|gb|AY948116.1|	947	+	0	0	78	78	78	0	0	1	0	25	GAACAAGAGCATAAATTAACGCAAA	YYYYYYYYYWYYYYWWYWWYWWYWY
06796|gb|AY948116.1|_955_1100_399/2	gi|65306796|gb|AY948116.1|	955	+	0	0	78	78	78	0	0	1	0	25	GCATAAATTAACGCAAATGGCCCTA	YYYYYYYYYYYYYWYYYWWUWWYSY
06796|gb|AY948116.1|_984_1172_366/1	gi|65306796|gb|AY948116.1|	984	+	0	0	78	78	78	0	0	1	0	25	TGAAAAAAAAAGAAAAAGAGATACA	YYYYYYYYYYYYYYWWYWWUWWYWW
06796|gb|AY948116.1|_986_1188_3b5/1	gi|65306796|gb|AY948116.1|	986	+	0	0	78	78	78	0	0	1	0	25	AAAAAAAAAGAAAAAGAGATACAAG	YYYYYYYYYWYYYYWWYYWYWYYWW
06796|gb|AY948116.1|_823_1016_35b/1	gi|65306796|gb|AY948116.1|	992	-	0	0	78	78	78	0	0	1	0	25	AAAGAAAAAGAGATACAAGACAAGG	USYYYSYYWYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_872_1016_332/2	gi|65306796|gb|AY948116.1|	992	-	0	0	78	78	78	0	0	1	0	25	AAAGAAAAAGAGATACAAGACAAGG	QQWWWYWYYWWYYYYYYYYYYYYYY
06796|gb|AY948116.1|_994_1161_339/1	gi|65306796|gb|AY948116.1|	994	+	0	0	78	78	78	0	0	1	0	25	AGAAAAAGAGATACAAGACAAGGCT	YYYYYYYYYYYYYWYYYYWWYWYWW
6796|gb|AY948116.1|_1001_1161_357/1	gi|65306796|gb|AY948116.1|	1001	+	0	0	78	78	78	0	0	1	0	25	GAGATACAAGACAAGGCTAAAGAGT	YYYYYYYYYYYYYYYYWYWYWYYSY
06796|gb|AY948116.1|_855_1026_370/1	gi|65306796|gb|AY948116.1|	1002	-	0	0	78	78	78	0	0	1	0	25	AGATACAAGACAAGGCTAAAGAGTT	YSYYWUWYYWYYYYYWYYYYYYYYY
06796|gb|AY948116.1|_853_1033_307/2	gi|65306796|gb|AY948116.1|	1009	-	0	0	78	78	78	0	0	1	0	25	AGACAAGGCTAAAGAGTTAAAATCG	YSYWWUWYYWWYYYYYYYYYYYYYY
06796|gb|AY948116.1|_874_1037_3ba/2	gi|65306796|gb|AY948116.1|	1013	-	0	0	78	78	78	0	0	1	0	25	AAGGCTAAAGAGTTAAAATCGAAAG	QQWWYSYYYWYWYYYWYYYYYYYYY
06796|gb|AY948116.1|_889_1041_3c5/1	gi|65306796|gb|AY948116.1|	1017	-	0	0	78	78	78	0	0	1	0	25	CTAAAGAGTTAAAATCGAAAGAAAA	USYWWUWYWYYYYYYWYYYYYYYYY
06796|gb|AY948116.1|_888_1045_3a7/2	gi|65306796|gb|AY948116.1|	1021	-	0	0	78	78	78	0	0	1	0	25	AGAGTTAAAATCGAAAGAAAACGAA	WWYYYSYYYYYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_1026_1195_396/2	gi|65306796|gb|AY948116.1|	1026	+	0	0	78	78	78	0	0	1	0	25	TAAAATCGAAAGAAAACGAATTACA	YYYYYYYYYYYYYYYWYYYSYYYWY
06796|gb|AY948116.1|_907_1070_2f1/1	gi|65306796|gb|AY948116.1|	1046	-	0	0	78	78	78	0	0	1	0	25	TTACAAGCGAAAATAGAGCAACATC	QQWWWUWYYWWYYYYYYYYYYYYYY
06796|gb|AY948116.1|_947_1100_32c/1	gi|65306796|gb|AY948116.1|	1076	-	0	0	78	78	78	0	0	1	0	25	CATATACAAAATTTAGAACTAGGAC	QQWWYWWYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_955_1100_399/1	gi|65306796|gb|AY948116.1|	1076	-	0	0	78	78	78	0	0	1	0	25	CATATACAAAATTTAGAACTAGGAC	YSYWWWYYYYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_1085_1251_376/2	gi|65306796|gb|AY948116.1|	1085	+	0	0	78	78	78	0	0	1	0	25	AATTTAGAACTAGGACACGAAAGAG	YYYYYYYYYYYYYYYYYWWUWYYSY
6796|gb|AY948116.1|_1088_1295_3cd/1	gi|65306796|gb|AY948116.1|	1088	+	0	0	78	78	78	0	0	1	0	25	TTAGAACTAGGACACGAAAGAGCTT	YYYYYYYYYYYYYYWWYYWWYWWQQ
6796|gb|AY948116.1|_1103_1280_342/1	gi|65306796|gb|AY948116.1|	1103	+	0	0	78	78	78	0	0	1	0	25	GAAAGAGCTTTAAAGGAACTTACAC	YYYYYYYYYYWYYYWWYYYWWWWQQ
6796|gb|AY948116.1|_1105_1307_360/1	gi|65306796|gb|AY948116.1|	1105	+	0	0	78	78	78	0	0	1	0	25	AAGAGCTTTAAAGGAACTTACACAA	YYYYYYYYYYYYYYWWYYYSYWYWW
6796|gb|AY948116.1|_1130_1297_2f8/2	gi|65306796|gb|AY948116.1|	1130	+	0	0	78	78	78	0	0	1	0	25	GAGTTTGAAAAGCGTTTAAGCCTAT	YYYYYYYYYYWYYYYYYYYSYWYWW
6796|gb|AY948116.1|_1130_1312_30a/2	gi|65306796|gb|AY948116.1|	1130	+	0	0	78	78	78	0	0	1	0	25	GAGTTTGAAAAGCGTTTAAGCCTAT	YYYYYYYYYWYYYYYYYYWUWYYSY
6796|gb|AY948116.1|_1134_1328_312/2	gi|65306796|gb|AY948116.1|	1134	+	0	0	78	78	78	0	0	1	0	25	TTGAAAAGCGTTTAAGCCTATGGAA	YYYYYYYYYWYYYYYYYYYWWWYWY
6796|gb|AY948116.1|_1137_1307_39a/2	gi|65306796|gb|AY948116.1|	1137	+	0	0	78	78	78	0	0	1	0	25	AAAAGCGTTTAAGCCTATGGAAAAA	YYYYYYYYYYYYYWYYYYYWYYYSY
06796|gb|AY948116.1|_994_1161_339/2	gi|65306796|gb|AY948116.1|	1137	-	0	0	78	78	78	0	0	1	0	25	AAAAGCGTTTAAGCCTATGGAAAAA	QQWWYSYYYYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_1001_1161_357/2	gi|65306796|gb|AY948116.1|	1137	-	0	0	78	78	78	0	0	1	0	25	AAAAGCGTTTAAGCCTATGGAAAAA	USYYYSYYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_984_1172_366/2	gi|65306796|gb|AY948116.1|	1148	-	0	0	78	78	78	0	0	1	0	25	AGCCTATGGAAAAACATTTTAACCT	YSYWWUWYYWYWYYYWYYYYYYYYY
6796|gb|AY948116.1|_1150_1326_361/2	gi|65306796|gb|AY948116.1|	1150	+	0	0	78	78	78	0	0	1	0	25	CCTATGGAAAAACATTTTAACCTTT	YYYYYYYYYWYYYWYYYYYSYYYSY
6796|gb|AY948116.1|_1153_1281_3b2/1	gi|65306796|gb|AY948116.1|	1153	+	0	0	78	78	78	0	0	1	0	25	ATGGAAAAACATTTTAACCTTTGGA	YYYYYYYYYWYYYYYYYYYSYWWQQ
06796|gb|AY948116.1|_986_1188_3b5/2	gi|65306796|gb|AY948116.1|	1164	-	0	0	78	78	78	0	0	1	0	25	TTTTAACCTTTGGAAAATACAACGC	YSYWWYWYWYYWYYWYYYYYYYYYY
6796|gb|AY948116.1|_1170_1344_390/1	gi|65306796|gb|AY948116.1|	1170	+	0	0	78	78	78	0	0	1	0	25	CCTTTGGAAAATACAACGCCAAAGT	YYYYYYYYYYYYYYWWYYWUWWWQQ
6796|gb|AY948116.1|_1026_1195_396/1	gi|65306796|gb|AY948116.1|	1171	-	0	0	78	78	78	0	0	1	0	25	CTTTGGAAAATACAACGCCAAAGTA	QQWWWYWWYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1180_1385_378/2	gi|65306796|gb|AY948116.1|	1180	+	0	0	78	78	78	0	0	1	0	25	ATACAACGCCAAAGTAAGAGAAGAC	YYYYYYYYYWYYYYWWYYWYWYYWW
6796|gb|AY948116.1|_1191_1323_338/1	gi|65306796|gb|AY948116.1|	1191	+	0	0	78	78	78	0	0	1	0	25	AAGTAAGAGAAGACTATCAGTTAAC	YYYYYYYYYYYYYYYYYWWUWYYSU
6796|gb|AY948116.1|_1199_1369_32d/1	gi|65306796|gb|AY948116.1|	1199	+	0	0	78	78	78	0	0	1	0	25	GAAGACTATCAGTTAACAAAGAATG	YYYYYYYYYWYYYYWWYWWWYYYSY
6796|gb|AY948116.1|_1227_1400_38f/2	gi|65306796|gb|AY948116.1|	1227	+	0	0	78	78	78	0	0	1	0	25	TTTTAATTAGCACAGATGAAAGCAG	YYYYYYYYYYYYYYYWYWWYWYYSU
6796|gb|AY948116.1|_1085_1251_376/1	gi|65306796|gb|AY948116.1|	1227	-	0	0	78	78	78	0	0	1	0	25	TTTTAATTAGCACAGATGAAAGCAG	QQWWWYWWYYYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_1242_1401_314/2	gi|65306796|gb|AY948116.1|	1242	+	0	0	78	78	78	0	0	1	0	25	ATGAAAGCAGGAGAGAAGCTAACAA	YYYYYYYYYYYYYWYWYYYSYYYSU
6796|gb|AY948116.1|_1103_1280_342/2	gi|65306796|gb|AY948116.1|	1256	-	0	0	78	78	78	0	0	1	0	25	GAAGCTAACAAAGAGCTTGAATATT	YWYYYWYYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1153_1281_3b2/2	gi|65306796|gb|AY948116.1|	1257	-	0	0	78	78	78	0	0	1	0	25	AAGCTAACAAAGAGCTTGAATATTT	YWYWWUWYYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1270_1432_3d0/1	gi|65306796|gb|AY948116.1|	1270	+	0	0	78	78	78	0	0	1	0	25	GCTTGAATATTTAAAATTTGAATAT	YYYYYYYYYWYYYYWWYWWWYYYWW
6796|gb|AY948116.1|_1088_1295_3cd/2	gi|65306796|gb|AY948116.1|	1271	-	0	0	78	78	78	0	0	1	0	25	CTTGAATATTTAAAATTTGAATATC	QQWWYWYYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1130_1297_2f8/1	gi|65306796|gb|AY948116.1|	1273	-	0	0	78	78	78	0	0	1	0	25	TGAATATTTAAAATTTGAATATCAT	QQWWWUWYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1282_1433_324/1	gi|65306796|gb|AY948116.1|	1282	+	0	0	78	78	78	0	0	1	0	25	AAAATTTGAATATCATAAAGTCAAA	YYYYYYYYYYYYYYYYYYYWWYYWY
6796|gb|AY948116.1|_1282_1445_330/1	gi|65306796|gb|AY948116.1|	1282	+	0	0	78	78	78	0	0	1	0	25	AAAATTTGAATATCATAAAGTCAAA	YYYYYYYYYYYYYYYYYYWUWWYSU
6796|gb|AY948116.1|_1137_1307_39a/1	gi|65306796|gb|AY948116.1|	1283	-	0	0	78	78	78	0	0	1	0	25	AAATTTGAATATCATAAAGTCAAAG	WWYYYWWYYYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_1105_1307_360/2	gi|65306796|gb|AY948116.1|	1283	-	0	0	78	78	78	0	0	1	0	25	AAATTTGAATATCATAAAGTCAAAG	YWYWWYWWYYYWYYWYYYYYYYYYY
6796|gb|AY948116.1|_1286_1469_326/1	gi|65306796|gb|AY948116.1|	1286	+	0	0	78	78	78	0	0	1	0	25	TTTGAATATCATAAAGTCAAAGATG	YYYYYYYYYYYYYYWWYYWWWYYWW
6796|gb|AY948116.1|_1130_1312_30a/1	gi|65306796|gb|AY948116.1|	1288	-	0	0	78	78	78	0	0	1	0	25	TGAATATCATAAAGTCAAAGATGAA	QQWWYSYYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1290_1441_30d/2	gi|65306796|gb|AY948116.1|	1290	+	0	0	78	78	78	0	0	1	0	25	AATATCATAAAGTCAAAGATGAACG	YYYYYYYYYYWYYYYYYYYWYYYWW
6796|gb|AY948116.1|_1295_1444_32a/1	gi|65306796|gb|AY948116.1|	1295	+	0	0	78	78	78	0	0	1	0	25	CATAAAGTCAAAGATGAACGAGATA	YYYYYYYYYYYYYYYWYWWUWWYSY
6796|gb|AY948116.1|_1191_1323_338/2	gi|65306796|gb|AY948116.1|	1299	-	0	0	78	78	78	0	0	1	0	25	AAGTCAAAGATGAACGAGATAATTT	YWYYYWYYYYYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_1150_1326_361/1	gi|65306796|gb|AY948116.1|	1302	-	0	0	78	78	78	0	0	1	0	25	TCAAAGATGAACGAGATAATTTAAA	USYWWUWYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1134_1328_312/1	gi|65306796|gb|AY948116.1|	1304	-	0	0	78	78	78	0	0	1	0	25	AAAGATGAACGAGATAATTTAAAAA	YWYWWYWYYYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_1305_1488_34a/2	gi|65306796|gb|AY948116.1|	1305	+	0	0	78	78	78	0	0	1	0	25	AAGATGAACGAGATAATTTAAAAAC	YYYYYYYYYYYYYYYWYYYSYWWQQ
6796|gb|AY948116.1|_1307_1497_315/1	gi|65306796|gb|AY948116.1|	1307	+	0	0	78	78	78	0	0	1	0	25	GATGAACGAGATAATTTAAAAACTT	YYYYYYYYYYYYYYYWYYYWWWYSY
6796|gb|AY948116.1|_1320_1503_3e6/1	gi|65306796|gb|AY948116.1|	1320	+	0	0	78	78	78	0	0	1	0	25	ATTTAAAAACTTTGTTTGAGGCACA	YYYYYYYYYYYYYWYWYYYSYWWQQ
6796|gb|AY948116.1|_1170_1344_390/2	gi|65306796|gb|AY948116.1|	1320	-	0	0	78	78	78	0	0	1	0	25	ATTTAAAAACTTTGTTTGAGGCACA	YSYYYSYYWYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_1326_1459_3c3/1	gi|65306796|gb|AY948116.1|	1326	+	0	0	78	78	78	0	0	1	0	25	AAACTTTGTTTGAGGCACACAAAAC	YYYYYYYYYWYYYYYWYYYSYYYWY
6796|gb|AY948116.1|_1341_1515_35f/2	gi|65306796|gb|AY948116.1|	1341	+	0	0	78	78	78	0	0	1	0	25	CACACAAAACAAAAAATGTTAAATT	YYYYYYYYYYYYYYYYWYWWYYYWW
6796|gb|AY948116.1|_1345_1512_36a/2	gi|65306796|gb|AY948116.1|	1345	+	0	0	78	78	78	0	0	1	0	25	CAAAACAAAAAATGTTAAATTAGAA	YYYYYYYYYYWYYWYWYYYSYYYSY
6796|gb|AY948116.1|_1199_1369_32d/2	gi|65306796|gb|AY948116.1|	1345	-	0	0	78	78	78	0	0	1	0	25	CAAAACAAAAAATGTTAAATTAGAA	QQWWWUWYYYYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_1357_1495_38e/2	gi|65306796|gb|AY948116.1|	1357	+	0	0	78	78	78	0	0	1	0	25	TGTTAAATTAGAAACTCGACTAAAA	YYYYYYYYYYYYYYYYYYWWWYYWW
6796|gb|AY948116.1|_1180_1385_378/1	gi|65306796|gb|AY948116.1|	1361	-	0	0	78	78	78	0	0	1	0	25	AAATTAGAAACTCGACTAAAAGAAA	USYYWYWYYYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_1367_1540_372/1	gi|65306796|gb|AY948116.1|	1367	+	0	0	78	78	78	0	0	1	0	25	GAAACTCGACTAAAAGAAATAGGCA	YYYYYYYYYYYYYYWWYYWWWYYSU
6796|gb|AY948116.1|_1227_1400_38f/1	gi|65306796|gb|AY948116.1|	1376	-	0	0	78	78	78	0	0	1	0	25	CTAAAAGAAATAGGCAAATGGTGTG	YWYYWUWYYYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_1242_1401_314/1	gi|65306796|gb|AY948116.1|	1377	-	0	0	78	78	78	0	0	1	0	25	TAAAAGAAATAGGCAAATGGTGTGA	YSYWYSYYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1270_1432_3d0/2	gi|65306796|gb|AY948116.1|	1408	-	0	0	78	78	78	0	0	1	0	25	TTTAAGCGTGGAGCAGTTAAAAGAA	USYYYSYYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1282_1433_324/2	gi|65306796|gb|AY948116.1|	1409	-	0	0	78	78	78	0	0	1	0	25	TTAAGCGTGGAGCAGTTAAAAGAAA	YWYWWYWWYWYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_1290_1441_30d/1	gi|65306796|gb|AY948116.1|	1417	-	0	0	78	78	78	0	0	1	0	25	GGAGCAGTTAAAAGAAATATTTCCA	YWYWYSYYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1295_1444_32a/2	gi|65306796|gb|AY948116.1|	1420	-	0	0	78	78	78	0	0	1	0	25	GCAGTTAAAAGAAATATTTCCATTA	YSYWYWYYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1282_1445_330/2	gi|65306796|gb|AY948116.1|	1421	-	0	0	78	78	78	0	0	1	0	25	CAGTTAAAAGAAATATTTCCATTAA	YSYYYWWWYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1326_1459_3c3/2	gi|65306796|gb|AY948116.1|	1435	-	0	0	78	78	78	0	0	1	0	25	ATTTCCATTAAAAGCCGAAAGAATA	WWYWYWWWYWYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_1286_1469_326/2	gi|65306796|gb|AY948116.1|	1445	-	0	0	78	78	78	0	0	1	0	25	AAAGCCGAAAGAATAGAAAAAGAGC	USYWWYWYYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1452_1653_340/1	gi|65306796|gb|AY948116.1|	1452	+	0	0	78	78	78	0	0	1	0	25	AAAGAATAGAAAAAGAGCTTAAATA	YYYYYYYYYWYYYYYWYWWWYWYWW
6796|gb|AY948116.1|_1305_1488_34a/1	gi|65306796|gb|AY948116.1|	1464	-	0	0	78	78	78	0	0	1	0	25	AAGAGCTTAAATATCAAAGAGCTTT	YWYYYWYYYWWYYYYWYYYYYYYYY
6796|gb|AY948116.1|_1470_1629_327/1	gi|65306796|gb|AY948116.1|	1470	+	0	0	78	78	78	0	0	1	0	25	TTAAATATCAAAGAGCTTTTGAAAA	YYYYYYYYYYYYYYYYYYYSYYYWY
6796|gb|AY948116.1|_1357_1495_38e/1	gi|65306796|gb|AY948116.1|	1471	-	0	0	78	78	78	0	0	1	0	25	TAAATATCAAAGAGCTTTTGAAAAT	YSYYYWYYYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1307_1497_315/2	gi|65306796|gb|AY948116.1|	1473	-	0	0	78	78	78	0	0	1	0	25	AATATCAAAGAGCTTTTGAAAATTC	QQWWYSYYYYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_1320_1503_3e6/2	gi|65306796|gb|AY948116.1|	1479	-	0	0	78	78	78	0	0	1	0	25	AAAGAGCTTTTGAAAATTCTTTTGA	YWYWWYWYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1482_1607_344/1	gi|65306796|gb|AY948116.1|	1482	+	0	0	78	78	78	0	0	1	0	25	GAGCTTTTGAAAATTCTTTTGAACA	YYYYYYYYYYYYYYYYWYWWWWWQQ
6796|gb|AY948116.1|_1345_1512_36a/1	gi|65306796|gb|AY948116.1|	1488	-	0	0	78	78	78	0	0	1	0	25	TTGAAAATTCTTTTGAACAAGCAAA	QQWWWUWYWYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_1341_1515_35f/1	gi|65306796|gb|AY948116.1|	1491	-	0	0	78	78	78	0	0	1	0	25	AAAATTCTTTTGAACAAGCAAAAAG	YWYWWWWYYWYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_1499_1669_3ad/2	gi|65306796|gb|AY948116.1|	1499	+	0	0	78	78	78	0	0	1	0	25	TTTGAACAAGCAAAAAGAAACGATA	YYYYYYYYYYYYYYWWYYWYWWYWY
6796|gb|AY948116.1|_1516_1690_3e1/1	gi|65306796|gb|AY948116.1|	1516	+	0	0	78	78	78	0	0	1	0	25	AAACGATAGAGGGTTTGGGTTTAGC	YYYYYYYYYYYYYYWWYYWYWWYSY
6796|gb|AY948116.1|_1367_1540_372/2	gi|65306796|gb|AY948116.1|	1516	-	0	0	78	78	78	0	0	1	0	25	AAACGATAGAGGGTTTGGGTTTAGC	WWYWWWYYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1529_1707_3a5/1	gi|65306796|gb|AY948116.1|	1529	+	0	0	78	78	78	0	0	1	0	25	TTTGGGTTTAGCAGATAGTTTTCTT	YYYYYYYYYYYYYYYWYYYSYYYWY
6796|gb|AY948116.1|_1534_1695_3bb/1	gi|65306796|gb|AY948116.1|	1534	+	0	0	78	78	78	0	0	1	0	25	GTTTAGCAGATAGTTTTCTTTTTTG	YYYYYYYYYYWYYWYYWYWUWWYWW
6796|gb|AY948116.1|_1536_1707_38d/2	gi|65306796|gb|AY948116.1|	1536	+	0	0	78	78	78	0	0	1	0	25	TTAGCAGATAGTTTTCTTTTTTGGT	YYYYYYYYYYYYYYYYYYWUWWWQQ
6796|gb|AY948116.1|_1538_1681_37c/2	gi|65306796|gb|AY948116.1|	1538	+	0	0	78	78	78	0	0	1	0	25	AGCAGATAGTTTTCTTTTTTGGTGC	YYYYYYYYYYYYYYYYYYYWYWWQQ
6796|gb|AY948116.1|_1543_1682_397/2	gi|65306796|gb|AY948116.1|	1543	+	0	0	78	78	78	0	0	1	0	25	ATAGTTTTCTTTTTTGGTGCTTTAG	YYYYYYYYYYYYYYYWYYYWYYYSU
6796|gb|AY948116.1|_1549_1715_31e/1	gi|65306796|gb|AY948116.1|	1549	+	0	0	78	78	78	0	0	1	0	25	TTCTTTTTTGGTGCTTTAGCAAATC	YYYYYYYYYYWYYWYYYYWUWYYSU
6796|gb|AY948116.1|_1565_1738_33b/1	gi|65306796|gb|AY948116.1|	1565	+	0	0	78	78	78	0	0	1	0	25	TAGCAAATCGCACCTGTTAAGGTGC	YYYYYYYYYYYYYYYWYYWWWYYWY
6796|gb|AY948116.1|_1566_1728_3d4/2	gi|65306796|gb|AY948116.1|	1566	+	0	0	78	78	78	0	0	1	0	25	AGCAAATCGCACCTGTTAAGGTGCT	YYYYYYYYYYYYYYWWYYYSYYYWY
6796|gb|AY948116.1|_1482_1607_344/2	gi|65306796|gb|AY948116.1|	1583	-	0	0	78	78	78	0	0	1	0	25	AAGGTGCTATGATTTGCGAAAAGGG	USYWWYWWYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1602_1772_34c/1	gi|65306796|gb|AY948116.1|	1602	+	0	0	78	78	78	0	0	1	0	25	AAAGGGGGTGCGGGGGCTGTCTGAG	YYYYYYYYYYYYYYYYWYWWYWYSU
6796|gb|AY948116.1|_1470_1629_327/2	gi|65306796|gb|AY948116.1|	1605	-	0	0	78	78	78	0	0	1	0	25	GGGGGTGCGGGGGCTGTCTGAGTGC	YSYYYSYYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1610_1765_358/1	gi|65306796|gb|AY948116.1|	1610	+	0	0	78	78	78	0	0	1	0	25	TGCGGGGGCTGTCTGAGTGCGTAGC	YYYYYYYYYYYYYYYYYYWUWYYWY
6796|gb|AY948116.1|_1452_1653_340/2	gi|65306796|gb|AY948116.1|	1629	-	0	0	78	78	78	0	0	1	0	25	CGTAGCACGGAAGACGGACAAAGCC	QQWWYSYYYWYWYYYWYYYYYYYYY
6796|gb|AY948116.1|_1637_1858_348/1	gi|65306796|gb|AY948116.1|	1637	+	0	0	78	78	78	0	0	1	0	25	GGAAGACGGACAAAGCCCACCGCCC	YYYYYYYYYYYYYYYWYYYSYYYSU
6796|gb|AY948116.1|_1640_1793_31a/1	gi|65306796|gb|AY948116.1|	1640	+	0	0	78	78	78	0	0	1	0	25	AGACGGACAAAGCCCACCGCCCTAG	YYYYYYYYYYYYYYYYYYYWWWYSU
6796|gb|AY948116.1|_1499_1669_3ad/1	gi|65306796|gb|AY948116.1|	1645	-	0	0	78	78	78	0	0	1	0	25	GACAAAGCCCACCGCCCTAGAAAAA	WWYYWYWWYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1654_1822_385/1	gi|65306796|gb|AY948116.1|	1654	+	0	0	78	78	78	0	0	1	0	25	CACCGCCCTAGAAAAAAAATTACTC	YYYYYYYYYYYYYYYWYYYSYWYWY
6796|gb|AY948116.1|_1538_1681_37c/1	gi|65306796|gb|AY948116.1|	1657	-	0	0	78	78	78	0	0	1	0	25	CGCCCTAGAAAAAAAATTACTCAAC	YSYWWYWWYYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_1543_1682_397/1	gi|65306796|gb|AY948116.1|	1658	-	0	0	78	78	78	0	0	1	0	25	GCCCTAGAAAAAAAATTACTCAACT	WWYYWWYYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1516_1690_3e1/2	gi|65306796|gb|AY948116.1|	1666	-	0	0	78	78	78	0	0	1	0	25	AAAAAAATTACTCAACTTTTTTTGT	USYWWWWYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1534_1695_3bb/2	gi|65306796|gb|AY948116.1|	1671	-	0	0	78	78	78	0	0	1	0	25	AATTACTCAACTTTTTTTGTTTTTT	WWYYWYWYYWYWYYYWYYYYYYYYY
6796|gb|AY948116.1|_1529_1707_3a5/2	gi|65306796|gb|AY948116.1|	1683	-	0	0	78	78	78	0	0	1	0	25	TTTTTTGTTTTTTCTCTCGCGCGCG	QQWWYWYYYWYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_1536_1707_38d/1	gi|65306796|gb|AY948116.1|	1683	-	0	0	78	78	78	0	0	1	0	25	TTTTTTGTTTTTTCTCTCGCGCGCG	USYWYSYYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1686_1871_32f/2	gi|65306796|gb|AY948116.1|	1686	+	0	0	78	78	78	0	0	1	0	25	TTTGTTTTTTCTCTCGCGCGCGTAC	YYYYYYYYYYYYYYYWYYWUWWWQQ
6796|gb|AY948116.1|_1689_1815_34e/2	gi|65306796|gb|AY948116.1|	1689	+	0	0	78	78	78	0	0	1	0	25	GTTTTTTCTCTCGCGCGCGTACGCG	YYYYYYYYYWYYYWYYWYYSYWYSY
6796|gb|AY948116.1|_1549_1715_31e/2	gi|65306796|gb|AY948116.1|	1691	-	0	0	78	78	78	0	0	1	0	25	TTTTTCTCTCGCGCGCGTACGCGTA	YWYYYWWYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1696_1877_2f6/2	gi|65306796|gb|AY948116.1|	1696	+	0	0	78	78	78	0	0	1	0	25	CTCTCGCGCGCGTACGCGTACGCGA	YYYYYYYYYYWYYYYYWYYWWWWQQ
6796|gb|AY948116.1|_1566_1728_3d4/1	gi|65306796|gb|AY948116.1|	1704	-	0	0	78	78	78	0	0	1	0	25	CGCGTACGCGTACGCGATTTTTTTT	YSYYYWWYYYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_1707_1898_3c8/1	gi|65306796|gb|AY948116.1|	1707	+	0	0	78	78	78	0	0	1	0	25	GTACGCGTACGCGATTTTTTTTATT	YYYYYYYYYYWYYYYWYYYSYYYWY
6796|gb|AY948116.1|_1712_1876_2fe/1	gi|65306796|gb|AY948116.1|	1712	+	0	0	78	78	78	0	0	1	0	25	CGTACGCGATTTTTTTTATTTTTTA	YYYYYYYYYYYYYYWWYYWYWWYSU
6796|gb|AY948116.1|_1565_1738_33b/2	gi|65306796|gb|AY948116.1|	1714	-	0	0	78	78	78	0	0	1	0	25	TACGCGATTTTTTTTATTTTTTATA	QQWWWWWWYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1715_1880_395/1	gi|65306796|gb|AY948116.1|	1715	+	0	0	78	78	78	0	0	1	0	25	ACGCGATTTTTTTTATTTTTTATAT	YYYYYYYYYYYYYYWWYYWYWWYWW
6796|gb|AY948116.1|_1727_1884_309/1	gi|65306796|gb|AY948116.1|	1727	+	0	0	78	78	78	0	0	1	0	25	TTATTTTTTATATATTTTTCTTATT	YYYYYYYYYYYYYYYYYWWWYYYWW
6796|gb|AY948116.1|_1727_1899_33d/1	gi|65306796|gb|AY948116.1|	1727	+	0	0	78	78	78	0	0	1	0	25	TTATTTTTTATATATTTTTCTTATT	YYYYYYYYYYYYYYWWYYYWYYYWY
6796|gb|AY948116.1|_1730_1902_3e5/2	gi|65306796|gb|AY948116.1|	1730	+	0	0	78	78	78	0	0	1	0	25	TTTTTTATATATTTTTCTTATTTTT	YYYYYYYYYWYYYYYWYYWUWYYSU
6796|gb|AY948116.1|_1610_1765_358/2	gi|65306796|gb|AY948116.1|	1741	-	0	0	78	78	78	0	0	1	0	25	TTTTTCTTATTTTTAGGGGGCTTTC	YWYWWUWYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1602_1772_34c/2	gi|65306796|gb|AY948116.1|	1748	-	0	0	78	78	78	0	0	1	0	25	TATTTTTAGGGGGCTTTCTAAGCCC	YWYWYSYYYYYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_1640_1793_31a/2	gi|65306796|gb|AY948116.1|	1769	-	0	0	78	78	78	0	0	1	0	25	GCCCTATATGATGGGGGCTAGCGAA	USYWYWYYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1771_1959_367/2	gi|65306796|gb|AY948116.1|	1771	+	0	0	78	78	78	0	0	1	0	25	CCTATATGATGGGGGCTAGCGAAAT	YYYYYYYYYYWYYWYYYWWUWWWQQ
6796|gb|AY948116.1|_1779_1937_354/2	gi|65306796|gb|AY948116.1|	1779	+	0	0	78	78	78	0	0	1	0	25	ATGGGGGCTAGCGAAATATTAAAAC	YYYYYYYYYYYYYYWWYYYWYYYWW
6796|gb|AY948116.1|_1783_1973_3d5/2	gi|65306796|gb|AY948116.1|	1783	+	0	0	78	78	78	0	0	1	0	25	GGGCTAGCGAAATATTAAAACGACA	YYYYYYYYYYYYYWYWYYWWWWYSU
6796|gb|AY948116.1|_1689_1815_34e/1	gi|65306796|gb|AY948116.1|	1791	-	0	0	78	78	78	0	0	1	0	25	GAAATATTAAAACGACAAAATTCTA	QQWWWYWWYYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_1654_1822_385/2	gi|65306796|gb|AY948116.1|	1798	-	0	0	0	0	0	0	0	4	0	25	TAAAACGACAAAATTCTACTATTAA	QQWWWYWYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1696_1877_2f6/1	gi|65306796|gb|AY948116.1|	1809	-	0	0	0	0	0	0	0	4	0	25	AATTCTACTATTAAAACGACAAAAT	YWYYWWWWYWYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_1855_2061_33e/2	gi|65306796|gb|AY948116.1|	1811	+	0	0	0	0	0	0	0	3	0	25	TTCTACTATTAAAACGACAAAATTC	YYYYYYYYYYWYYYYYYYWWYYYWW
6796|gb|AY948116.1|_1637_1858_348/2	gi|65306796|gb|AY948116.1|	1812	-	0	0	0	0	0	0	0	3	0	25	TCTACTATTAAAACGACAAAATTCT	YSYWWYWYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1825_1982_35e/2	gi|65306796|gb|AY948116.1|	1825	+	0	0	0	0	0	0	0	3	0	25	CGACAAAATTCTACTATTAAAACGA	YYYYYYYYYWYYYYYWYWWUWYYSY
6796|gb|AY948116.1|_1712_1876_2fe/2	gi|65306796|gb|AY948116.1|	1830	-	0	0	0	0	0	0	0	4	0	25	AAATTCTACTATTAAAACGACAAAA	YWYYYWWYYWYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_1715_1880_395/2	gi|65306796|gb|AY948116.1|	1834	-	0	0	0	0	0	0	0	3	0	25	TCTACTATTAAAACGACAAAATTCT	YSYWYWWWYWYWYYYWYYYYYYYYY
6796|gb|AY948116.1|_1686_1871_32f/1	gi|65306796|gb|AY948116.1|	1847	-	0	0	0	0	0	0	0	3	0	25	CGACAAAATTCTACTATTAAAACGA	YWYWYWWWYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1727_1884_309/2	gi|65306796|gb|AY948116.1|	1860	-	0	0	0	0	0	0	0	3	1	25	CTATTAAAACGACAAAATTCTACTA	USYWWWYYYYYWYYWYYYYYYYYYY
6796|gb|AY948116.1|_1870_2057_2f5/1	gi|65306796|gb|AY948116.1|	1870	+	0	0	78	78	78	0	0	1	0	25	GACAAAATTCTACTATTAAGGGGAG	YYYYYYYYYWYYYYWWYYWWYWYSY
6796|gb|AY948116.1|_1871_2057_3e0/2	gi|65306796|gb|AY948116.1|	1871	+	0	0	78	78	78	0	0	1	0	25	ACAAAATTCTACTATTAAGGGGAGA	YYYYYYYYYYWYYWYYYWWUWYYWY
6796|gb|AY948116.1|_1707_1898_3c8/2	gi|65306796|gb|AY948116.1|	1874	-	0	0	78	78	78	0	0	1	0	25	AAATTCTACTATTAAGGGGAGAAAA	USYYYSYYYYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_1727_1899_33d/2	gi|65306796|gb|AY948116.1|	1875	-	0	0	78	78	78	0	0	1	0	25	AATTCTACTATTAAGGGGAGAAAAT	QQWWYSYYYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1730_1902_3e5/1	gi|65306796|gb|AY948116.1|	1878	-	0	0	78	78	78	0	0	1	0	25	TCTACTATTAAGGGGAGAAAATTCT	YWYWWWWYYYYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_1891_2070_36c/1	gi|65306796|gb|AY948116.1|	1891	+	0	0	52	52	52	0	0	1	0	25	GGAGAAAATTCTACTATTAAAACGA	YYYYYYYYYWYYYYYYYYYSYYYWW
6796|gb|AY948116.1|_1779_1937_354/1	gi|65306796|gb|AY948116.1|	1913	-	0	0	78	78	78	0	0	1	0	25	CGACAAAATATTTGACAAATATTGT	WWYWWUWWYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1771_1959_367/1	gi|65306796|gb|AY948116.1|	1935	-	0	0	58	58	58	1	30	0	1	25	TGTTTTAATATACTACAATAAAAAA	YSYWWUWYWYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_1783_1973_3d5/1	gi|65306796|gb|AY948116.1|	1949	-	0	0	78	78	78	0	0	1	0	25	ACAATAAAAAATCCGCCTTGAGTTT	YSYWWYWYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1958_2138_394/2	gi|65306796|gb|AY948116.1|	1958	+	0	0	78	78	78	0	0	1	0	25	AATCCGCCTTGAGTTTTCACTCTTG	YYYYYYYYYYYYYYWWYWWWYWWQQ
6796|gb|AY948116.1|_1825_1982_35e/1	gi|65306796|gb|AY948116.1|	1958	-	0	0	78	78	78	0	0	1	0	25	AATCCGCCTTGAGTTTTCACTCTTG	QQWWYSYYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1959_2129_343/1	gi|65306796|gb|AY948116.1|	1959	+	0	0	78	78	78	0	0	1	0	25	ATCCGCCTTGAGTTTTCACTCTTGG	YYYYYYYYYWYYYYYWYYWYWWWQQ
6796|gb|AY948116.1|_1959_2131_333/2	gi|65306796|gb|AY948116.1|	1959	+	0	0	78	78	78	0	0	1	0	25	ATCCGCCTTGAGTTTTCACTCTTGG	YYYYYYYYYYYYYWYYYYYWWWWQQ
6796|gb|AY948116.1|_1964_2153_3bd/2	gi|65306796|gb|AY948116.1|	1964	+	0	0	78	78	78	0	0	1	0	25	CCTTGAGTTTTCACTCTTGGCGGAA	YYYYYYYYYYYYYYYYYYYWYWYWY
6796|gb|AY948116.1|_1969_2159_304/2	gi|65306796|gb|AY948116.1|	1969	+	0	0	78	78	78	0	0	1	0	25	AGTTTTCACTCTTGGCGGAAATTTA	YYYYYYYYYYYYYYYYYWWYWWYWY
6796|gb|AY948116.1|_1979_2135_311/1	gi|65306796|gb|AY948116.1|	1979	+	0	0	78	78	78	0	0	1	0	25	CTTGGCGGAAATTTATCAATCAAGG	YYYYYYYYYYYYYYYWYYYWWWYWY
6796|gb|AY948116.1|_1990_2181_36b/1	gi|65306796|gb|AY948116.1|	1990	+	0	0	78	78	78	0	0	1	0	25	TTTATCAATCAAGGCTAACTATGAA	YYYYYYYYYWYYYYYWYWWYWYYSU
6796|gb|AY948116.1|_1998_2152_3cb/2	gi|65306796|gb|AY948116.1|	1998	+	0	0	78	78	78	0	0	1	0	25	TCAAGGCTAACTATGAAACGACATA	YYYYYYYYYWYYYWYYWYWUWWYWW
6796|gb|AY948116.1|_2027_2191_365/1	gi|65306796|gb|AY948116.1|	2027	+	0	0	78	78	78	0	0	1	0	25	GCGTTTTGTGAGATTATACCTAAAA	YYYYYYYYYYYYYWYYYYWWYYYWW
6796|gb|AY948116.1|_1871_2057_3e0/1	gi|65306796|gb|AY948116.1|	2033	-	0	0	78	78	78	0	0	1	0	25	TGTGAGATTATACCTAAAATTTAGG	YWYWWYWYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1870_2057_2f5/2	gi|65306796|gb|AY948116.1|	2033	-	0	0	78	78	78	0	0	1	0	25	TGTGAGATTATACCTAAAATTTAGG	WWYWWWWWYWWYYYWYYYYYYYYYY
6796|gb|AY948116.1|_1855_2061_33e/1	gi|65306796|gb|AY948116.1|	2037	-	0	0	78	78	78	0	0	1	0	25	AGATTATACCTAAAATTTAGGTTTT	YWYWWUWYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1891_2070_36c/2	gi|65306796|gb|AY948116.1|	2046	-	0	0	78	78	78	0	0	1	0	25	CTAAAATTTAGGTTTTTTAAGCTTA	YWYYWUWYYWYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_2051_2222_3b9/2	gi|65306796|gb|AY948116.1|	2051	+	0	0	78	78	78	0	0	1	0	25	ATTTAGGTTTTTTAAGCTTAAAGTT	YYYYYYYYYWYYYYWWYWWUWWWQQ
6796|gb|AY948116.1|_2060_2222_3d7/2	gi|65306796|gb|AY948116.1|	2060	+	0	0	78	78	78	0	0	1	0	25	TTTTAAGCTTAAAGTTGAAGTATTT	YYYYYYYYYYYYYYYYWYYSYYYWW
6796|gb|AY948116.1|_2091_2276_325/2	gi|65306796|gb|AY948116.1|	2091	+	0	0	78	78	78	0	0	1	0	25	CAAAACCGCAGGGGCAGAGAAGCCC	YYYYYYYYYYYYYWYWYWWUWYYWW
6796|gb|AY948116.1|_2097_2260_328/1	gi|65306796|gb|AY948116.1|	2097	+	0	0	78	78	78	0	0	1	0	25	CGCAGGGGCAGAGAAGCCCCTTGCC	YYYYYYYYYYYYYYYYWYYWWWYSY
6796|gb|AY948116.1|_1959_2129_343/2	gi|65306796|gb|AY948116.1|	2105	-	0	0	78	78	78	0	0	1	0	25	CAGAGAAGCCCCTTGCCTTGATTGT	USYYYWYYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2106_2266_374/1	gi|65306796|gb|AY948116.1|	2106	+	0	0	78	78	78	0	0	1	0	25	AGAGAAGCCCCTTGCCTTGATTGTC	YYYYYYYYYYYYYWYWYYWWYYYWW
6796|gb|AY948116.1|_1959_2131_333/1	gi|65306796|gb|AY948116.1|	2107	-	0	0	78	78	78	0	0	1	0	25	GAGAAGCCCCTTGCCTTGATTGTCT	WWYWWYWWYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1979_2135_311/2	gi|65306796|gb|AY948116.1|	2111	-	0	0	78	78	78	0	0	1	0	25	AGCCCCTTGCCTTGATTGTCTTACT	QQWWYSYYYWWYYYYWYYYYYYYYY
6796|gb|AY948116.1|_1958_2138_394/1	gi|65306796|gb|AY948116.1|	2114	-	0	0	78	78	78	0	0	1	0	25	CCCTTGCCTTGATTGTCTTACTTTG	YWYYYSYYYYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_2128_2272_3b6/1	gi|65306796|gb|AY948116.1|	2128	+	0	0	78	78	78	0	0	1	0	25	GTCTTACTTTGGATATGCAAATGAG	YYYYYYYYYYWYYYWWYWWYWYYWY
6796|gb|AY948116.1|_1998_2152_3cb/1	gi|65306796|gb|AY948116.1|	2128	-	0	0	78	78	78	0	0	1	0	25	GTCTTACTTTGGATATGCAAATGAG	QQWWWWWYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_1964_2153_3bd/1	gi|65306796|gb|AY948116.1|	2129	-	0	0	78	78	78	0	0	1	0	25	TCTTACTTTGGATATGCAAATGAGC	YSYWWWYYYYYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_1969_2159_304/1	gi|65306796|gb|AY948116.1|	2135	-	0	0	78	78	78	0	0	1	0	25	TTTGGATATGCAAATGAGCGAAATA	YSYWWUWWYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2144_2274_3c1/1	gi|65306796|gb|AY948116.1|	2144	+	0	0	78	78	78	0	0	1	0	25	GCAAATGAGCGAAATAGTTAAATAT	YYYYYYYYYYYYYYYYWYYSYYYWW
6796|gb|AY948116.1|_2147_2271_3c9/2	gi|65306796|gb|AY948116.1|	2147	+	0	0	78	78	78	0	0	1	0	25	AATGAGCGAAATAGTTAAATATAAT	YYYYYYYYYYYYYYYYWYWYWYYWW
6796|gb|AY948116.1|_1990_2181_36b/2	gi|65306796|gb|AY948116.1|	2157	-	0	0	78	78	78	0	0	1	0	25	ATAGTTAAATATAATAATGATTTTA	QQWWWUWWYWWYYYWYYYYYYYYYY
6796|gb|AY948116.1|_2027_2191_365/2	gi|65306796|gb|AY948116.1|	2167	-	0	0	78	78	78	0	0	1	0	25	ATAATAATGATTTTAATCTTTTACC	YWYYYWYYWYYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_2168_2378_334/2	gi|65306796|gb|AY948116.1|	2168	+	0	0	78	78	78	0	0	1	0	25	TAATAATGATTTTAATCTTTTACCT	YYYYYYYYYWYYYYYYWYYWYWWQQ
6796|gb|AY948116.1|_2177_2354_3d6/1	gi|65306796|gb|AY948116.1|	2177	+	0	0	78	78	78	0	0	1	0	25	TTTTAATCTTTTACCTATGCCTGAA	YYYYYYYYYYYYYWYYYYWWYYYSY
6796|gb|AY948116.1|_2182_2343_345/2	gi|65306796|gb|AY948116.1|	2182	+	0	0	78	78	78	0	0	1	0	25	ATCTTTTACCTATGCCTGAACTTAA	YYYYYYYYYYYYYYYYYYWUWWYWW
6796|gb|AY948116.1|_2189_2360_352/1	gi|65306796|gb|AY948116.1|	2189	+	0	0	78	78	78	0	0	1	0	25	ACCTATGCCTGAACTTAAAGCCATA	YYYYYYYYYYYYYYYYYWWWYYYSU
6796|gb|AY948116.1|_2197_2345_38b/1	gi|65306796|gb|AY948116.1|	2197	+	0	0	78	78	78	0	0	1	0	25	CTGAACTTAAAGCCATACAAATGGA	YYYYYYYYYYYYYYYYYYWWWYYWW
6796|gb|AY948116.1|_2051_2222_3b9/1	gi|65306796|gb|AY948116.1|	2198	-	0	0	78	78	78	0	0	1	0	25	TGAACTTAAAGCCATACAAATGGAT	QQWWWYWWYYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_2060_2222_3d7/1	gi|65306796|gb|AY948116.1|	2198	-	0	0	78	78	78	0	0	1	0	25	TGAACTTAAAGCCATACAAATGGAT	YSYWWUWYYYYWYYWYYYYYYYYYY
6796|gb|AY948116.1|_2215_2402_346/1	gi|65306796|gb|AY948116.1|	2215	+	0	0	78	78	78	0	0	1	0	25	AAATGGATATGTTTATGGCTATTAT	YYYYYYYYYYYYYYYYWYYSYWWQQ
6796|gb|AY948116.1|_2222_2389_3ca/2	gi|65306796|gb|AY948116.1|	2222	+	0	0	78	78	78	0	0	1	0	25	TATGTTTATGGCTATTATCTCACTA	YYYYYYYYYYYYYWYYWYWWYYYWW
6796|gb|AY948116.1|_2226_2396_2fd/1	gi|65306796|gb|AY948116.1|	2226	+	0	0	78	78	78	0	0	1	0	25	TTTATGGCTATTATCTCACTAACCA	YYYYYYYYYWYYYYWWYYYSYYYWW
6796|gb|AY948116.1|_2232_2404_337/1	gi|65306796|gb|AY948116.1|	2232	+	0	0	78	78	78	0	0	1	0	25	GCTATTATCTCACTAACCAAAGACA	YYYYYYYYYYYYYYWWYYWYWWYWY
6796|gb|AY948116.1|_2236_2392_3a2/1	gi|65306796|gb|AY948116.1|	2236	+	0	0	78	78	78	0	0	1	0	25	TTATCTCACTAACCAAAGACAAAAA	YYYYYYYYYYYYYYYWYYWWWYYWY
6796|gb|AY948116.1|_2097_2260_328/2	gi|65306796|gb|AY948116.1|	2236	-	0	0	78	78	78	0	0	1	0	25	TTATCTCACTAACCAAAGACAAAAA	QQWWYWYYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2106_2266_374/2	gi|65306796|gb|AY948116.1|	2242	-	0	0	78	78	78	0	0	1	0	25	CACTAACCAAAGACAAAAAAGAAAA	USYWYWWYWYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_2147_2271_3c9/1	gi|65306796|gb|AY948116.1|	2247	-	0	0	78	78	78	0	0	1	0	25	ACCAAAGACAAAAAAGAAAATACGC	WWYWWUWWYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2128_2272_3b6/2	gi|65306796|gb|AY948116.1|	2248	-	0	0	78	78	78	0	0	1	0	25	CCAAAGACAAAAAAGAAAATACGCC	WWYWWWWYYWYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_2250_2401_2f9/1	gi|65306796|gb|AY948116.1|	2250	+	0	0	78	78	78	0	0	1	0	25	AAAGACAAAAAAGAAAATACGCCAT	YYYYYYYYYWYYYYYYYYYWWWYSY
6796|gb|AY948116.1|_2144_2274_3c1/2	gi|65306796|gb|AY948116.1|	2250	-	0	0	78	78	78	0	0	1	0	25	AAAGACAAAAAAGAAAATACGCCAT	YWYWWWYYYYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_2091_2276_325/1	gi|65306796|gb|AY948116.1|	2252	-	0	0	78	78	78	0	0	1	0	25	AGACAAAAAAGAAAATACGCCATTT	QQWWWUWWYWYWYYYWYYYYYYYYY
6796|gb|AY948116.1|_2272_2422_391/2	gi|65306796|gb|AY948116.1|	2272	+	0	0	78	78	78	0	0	1	0	25	CATTTTTAAAAAAGTTTTTTAACCC	YYYYYYYYYYYYYYWWYYYWWWWQQ
6796|gb|AY948116.1|_2294_2456_38c/1	gi|65306796|gb|AY948116.1|	2294	+	0	0	58	58	58	1	30	0	1	25	CCCTGATAGAAGAAAAATAATTATT	YYYYYYYYYYYYYYWWYYWYWYYWY
6796|gb|AY948116.1|_2313_2497_393/1	gi|65306796|gb|AY948116.1|	2313	+	0	0	78	78	78	0	0	1	0	25	ATTATTCCGCAAAAGAAGTTTATTG	YYYYYYYYYYYYYWYWYWWUWYYWW
6796|gb|AY948116.1|_2315_2525_387/1	gi|65306796|gb|AY948116.1|	2315	+	0	0	78	78	78	0	0	1	0	25	TATTCCGCAAAAGAAGTTTATTGAA	YYYYYYYYYYWYYYWWYYYSYWWQQ
6796|gb|AY948116.1|_2316_2465_331/2	gi|65306796|gb|AY948116.1|	2316	+	0	0	78	78	78	0	0	1	0	25	ATTCCGCAAAAGAAGTTTATTGAAT	YYYYYYYYYYWYYYWWYYYWWWYSY
6796|gb|AY948116.1|_2182_2343_345/1	gi|65306796|gb|AY948116.1|	2319	-	0	0	78	78	78	0	0	1	0	25	CCGCAAAAGAAGTTTATTGAATTAT	QQWWWYWYWYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_2197_2345_38b/2	gi|65306796|gb|AY948116.1|	2321	-	0	0	78	78	78	0	0	1	0	25	GCAAAAGAAGTTTATTGAATTATGT	QQWWWWWWYYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_2177_2354_3d6/2	gi|65306796|gb|AY948116.1|	2330	-	0	0	78	78	78	0	0	1	0	25	GTTTATTGAATTATGTCGGTTAAAC	YSYWWWWYYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2189_2360_352/2	gi|65306796|gb|AY948116.1|	2336	-	0	0	78	78	78	0	0	1	0	25	TGAATTATGTCGGTTAAACGATAGT	YSYWWYWYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2168_2378_334/1	gi|65306796|gb|AY948116.1|	2354	-	0	0	78	78	78	0	0	1	0	25	CGATAGTAAAATGGACTATAAAGAA	WWYWYWWYYYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_2222_2389_3ca/1	gi|65306796|gb|AY948116.1|	2365	-	0	0	78	78	78	0	0	1	0	25	TGGACTATAAAGAAATTTTCTTTGC	YWYWYSYYYYYWYYWYYYYYYYYYY
6796|gb|AY948116.1|_2236_2392_3a2/2	gi|65306796|gb|AY948116.1|	2368	-	0	0	78	78	78	0	0	1	0	25	ACTATAAAGAAATTTTCTTTGCCAT	YWYYWWYYYYYWYYWYYYYYYYYYY
6796|gb|AY948116.1|_2226_2396_2fd/2	gi|65306796|gb|AY948116.1|	2372	-	0	0	78	78	78	0	0	1	0	25	TAAAGAAATTTTCTTTGCCATTGAT	QQWWYWWWYYYWYYYWYYYYYYYYY
6796|gb|AY948116.1|_2374_2566_34d/1	gi|65306796|gb|AY948116.1|	2374	+	0	0	78	78	78	0	0	1	0	25	AAGAAATTTTCTTTGCCATTGATGA	YYYYYYYYYYYYYYWWYYWYWWWQQ
6796|gb|AY948116.1|_2250_2401_2f9/2	gi|65306796|gb|AY948116.1|	2377	-	0	0	78	78	78	0	0	1	0	25	AAATTTTCTTTGCCATTGATGATTG	QQWWYSYYYWWYYYYWYYYYYYYYY
6796|gb|AY948116.1|_2215_2402_346/2	gi|65306796|gb|AY948116.1|	2378	-	0	0	78	78	78	0	0	1	0	25	AATTTTCTTTGCCATTGATGATTGC	WWYYWUWYWYYWYYYWYYYYYYYYY
6796|gb|AY948116.1|_2232_2404_337/2	gi|65306796|gb|AY948116.1|	2380	-	0	0	78	78	78	0	0	1	0	25	TTTTCTTTGCCATTGATGATTGCTT	QQWWYWWYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2272_2422_391/1	gi|65306796|gb|AY948116.1|	2398	-	0	0	78	78	78	0	0	1	0	25	ATTGCTTGAAAAAACTTTGCAATTT	QQWWWYWYYYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_2408_2551_2ee/1	gi|65306796|gb|AY948116.1|	2408	+	0	0	78	78	78	0	0	1	0	25	AAAACTTTGCAATTTTCTTATTTCA	YYYYYYYYYYYYYYYWYYYWYWYWY
6796|gb|AY948116.1|_2408_2567_377/1	gi|65306796|gb|AY948116.1|	2408	+	0	0	78	78	78	0	0	1	0	25	AAAACTTTGCAATTTTCTTATTTCA	YYYYYYYYYWYYYYYYYYYWYWYSY
6796|gb|AY948116.1|_2408_2601_305/2	gi|65306796|gb|AY948116.1|	2408	+	0	0	78	78	78	0	0	1	0	25	AAAACTTTGCAATTTTCTTATTTCA	YYYYYYYYYYYYYYYWYWWUWYYWW
6796|gb|AY948116.1|_2430_2639_3aa/2	gi|65306796|gb|AY948116.1|	2430	+	0	0	78	78	78	0	0	1	0	25	TCATACCAAAAAGATGAAAGAACGA	YYYYYYYYYWYYYYWWYYYWWWYSU
6796|gb|AY948116.1|_2294_2456_38c/2	gi|65306796|gb|AY948116.1|	2432	-	0	0	78	78	78	0	0	1	0	25	ATACCAAAAAGATGAAAGAACGATT	YWYYYSYYWYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_2433_2619_3dd/2	gi|65306796|gb|AY948116.1|	2433	+	0	0	78	78	78	0	0	1	0	25	TACCAAAAAGATGAAAGAACGATTT	YYYYYYYYYYYYYYYYYYWUWWWQQ
6796|gb|AY948116.1|_2436_2612_3df/2	gi|65306796|gb|AY948116.1|	2436	+	0	0	78	78	78	0	0	1	0	25	CAAAAAGATGAAAGAACGATTTATA	YYYYYYYYYYWYYYYYWYWYWYYWW
6796|gb|AY948116.1|_2316_2465_331/1	gi|65306796|gb|AY948116.1|	2441	-	0	0	78	78	78	0	0	1	0	25	AGATGAAAGAACGATTTATAATTTT	WWYWWUWWYYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_2455_2614_3da/2	gi|65306796|gb|AY948116.1|	2455	+	0	0	78	78	78	0	0	1	0	25	TTTATAATTTTGTTTGTTTTGAAGA	YYYYYYYYYYWYYYYYYYYSYYYWW
6796|gb|AY948116.1|_2469_2619_3c2/2	gi|65306796|gb|AY948116.1|	2469	+	0	0	78	78	78	0	0	1	0	25	TGTTTTGAAGAAGCAAATATTATTG	YYYYYYYYYYYYYYYYYYYSYWYWW
6796|gb|AY948116.1|_2471_2647_359/1	gi|65306796|gb|AY948116.1|	2471	+	0	0	78	78	78	0	0	1	0	25	TTTTGAAGAAGCAAATATTATTGCT	YYYYYYYYYYYYYYYWYYWWYWYSU
6796|gb|AY948116.1|_2313_2497_393/2	gi|65306796|gb|AY948116.1|	2473	-	0	0	78	78	78	0	0	1	0	25	TTGAAGAAGCAAATATTATTGCTGA	USYWYSYYYWWYYYYWYYYYYYYYY
6796|gb|AY948116.1|_2474_2663_319/2	gi|65306796|gb|AY948116.1|	2474	+	0	0	78	78	78	0	0	1	0	25	TGAAGAAGCAAATATTATTGCTGAT	YYYYYYYYYYYYYWYWYWWWYWYSU
6796|gb|AY948116.1|_2476_2645_3a3/2	gi|65306796|gb|AY948116.1|	2476	+	0	0	78	78	78	0	0	1	0	25	AAGAAGCAAATATTATTGCTGATGA	YYYYYYYYYYYYYYYYYYWYWWYSY
6796|gb|AY948116.1|_2476_2640_39f/1	gi|65306796|gb|AY948116.1|	2476	+	0	0	78	78	78	0	0	1	0	25	AAGAAGCAAATATTATTGCTGATGA	YYYYYYYYYYYYYWYWYYYSYYYSY
6796|gb|AY948116.1|_2489_2646_320/1	gi|65306796|gb|AY948116.1|	2489	+	0	0	78	78	78	0	0	1	0	25	TATTGCTGATGAAGTGCATATAACT	YYYYYYYYYYYYYYYYYWWWWWYWW
6796|gb|AY948116.1|_2315_2525_387/2	gi|65306796|gb|AY948116.1|	2501	-	0	0	78	78	78	0	0	1	0	25	AGTGCATATAACTTTACAAAGTCGT	USYWYSYYYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2408_2551_2ee/2	gi|65306796|gb|AY948116.1|	2527	-	0	0	78	78	78	0	0	1	0	25	TTTACGATATGATAATAAATAAAAA	USYYWYWYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2539_2695_3ce/2	gi|65306796|gb|AY948116.1|	2539	+	0	0	78	78	78	0	0	1	0	25	TAATAAATAAAAAATTTGGTTTCAC	YYYYYYYYYWYYYYYYWYYWYWWQQ
6796|gb|AY948116.1|_2374_2566_34d/2	gi|65306796|gb|AY948116.1|	2542	-	0	0	78	78	78	0	0	1	0	25	TAAATAAAAAATTTGGTTTCACAGC	USYYYSYYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2408_2567_377/2	gi|65306796|gb|AY948116.1|	2543	-	0	0	78	78	78	0	0	1	0	25	AAATAAAAAATTTGGTTTCACAGCC	USYYYWYYYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2562_2758_3e2/1	gi|65306796|gb|AY948116.1|	2562	+	0	0	78	78	78	0	0	1	0	25	ACAGCCTTTGAATTAGCCGAATTTG	YYYYYYYYYYYYYWYYYYWYWWYWY
6796|gb|AY948116.1|_2408_2601_305/1	gi|65306796|gb|AY948116.1|	2577	-	0	0	78	78	78	0	0	1	0	25	GCCGAATTTGCAGAACTTAGCGGTA	USYYYWWWYWYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_2581_2766_32e/2	gi|65306796|gb|AY948116.1|	2581	+	0	0	78	78	78	0	0	1	0	25	AATTTGCAGAACTTAGCGGTAAATA	YYYYYYYYYYYYYYWWYYYWWYYWY
6796|gb|AY948116.1|_2436_2612_3df/1	gi|65306796|gb|AY948116.1|	2588	-	0	0	78	78	78	0	0	1	0	25	AGAACTTAGCGGTAAATATACAAAA	WWYYWYWWYYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_2589_2767_3c4/2	gi|65306796|gb|AY948116.1|	2589	+	0	0	78	78	78	0	0	1	0	25	GAACTTAGCGGTAAATATACAAAAA	YYYYYYYYYYYYYWYWYWWUWWYWW
6796|gb|AY948116.1|_2455_2614_3da/1	gi|65306796|gb|AY948116.1|	2590	-	0	0	78	78	78	0	0	1	0	25	AACTTAGCGGTAAATATACAAAAAC	YWYWWUWYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2469_2619_3c2/1	gi|65306796|gb|AY948116.1|	2595	-	0	0	78	78	78	0	0	1	0	25	AGCGGTAAATATACAAAAACTTTAT	USYYWYWWYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2433_2619_3dd/1	gi|65306796|gb|AY948116.1|	2595	-	0	0	78	78	78	0	0	1	0	25	AGCGGTAAATATACAAAAACTTTAT	USYWWUWYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2430_2639_3aa/1	gi|65306796|gb|AY948116.1|	2615	-	0	0	78	78	78	0	0	1	0	25	TTTATACAGACTTTTAAAGCAATTT	QQWWWUWYYWYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_2476_2640_39f/2	gi|65306796|gb|AY948116.1|	2616	-	0	0	78	78	78	0	0	1	0	25	TTATACAGACTTTTAAAGCAATTTA	USYYWYWYYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2476_2645_3a3/1	gi|65306796|gb|AY948116.1|	2621	-	0	0	78	78	78	0	0	1	0	25	CAGACTTTTAAAGCAATTTAGAACC	USYYWUWWYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2489_2646_320/2	gi|65306796|gb|AY948116.1|	2622	-	0	0	78	78	78	0	0	1	0	25	AGACTTTTAAAGCAATTTAGAACCA	YWYWYSYYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2623_2797_3cc/1	gi|65306796|gb|AY948116.1|	2623	+	0	0	78	78	78	0	0	1	0	25	GACTTTTAAAGCAATTTAGAACCAC	YYYYYYYYYWYYYWYYYWWUWWWQQ
6796|gb|AY948116.1|_2471_2647_359/2	gi|65306796|gb|AY948116.1|	2623	-	0	0	78	78	78	0	0	1	0	25	GACTTTTAAAGCAATTTAGAACCAC	YWYWWWYYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2628_2813_364/2	gi|65306796|gb|AY948116.1|	2628	+	0	0	78	78	78	0	0	1	0	25	TTAAAGCAATTTAGAACCACAGGCA	YYYYYYYYYYYYYWYYYYYSYYYWY
6796|gb|AY948116.1|_2474_2663_319/1	gi|65306796|gb|AY948116.1|	2639	-	0	0	78	78	78	0	0	1	0	25	TAGAACCACAGGCAAAGCTTATTTT	WWYYWYWYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2643_2777_30b/2	gi|65306796|gb|AY948116.1|	2643	+	0	0	78	78	78	0	0	1	0	25	ACCACAGGCAAAGCTTATTTTGAGT	YYYYYYYYYYYYYYYYWYWYWWWQQ
6796|gb|AY948116.1|_2645_2817_3d3/2	gi|65306796|gb|AY948116.1|	2645	+	0	0	78	78	78	0	0	1	0	25	CACAGGCAAAGCTTATTTTGAGTGG	YYYYYYYYYWYYYYYYWYYSYYYWW
6796|gb|AY948116.1|_2647_2833_389/1	gi|65306796|gb|AY948116.1|	2647	+	0	0	78	78	78	0	0	1	0	25	CAGGCAAAGCTTATTTTGAGTGGGA	YYYYYYYYYYYYYYYWYYWWYWWQQ
6796|gb|AY948116.1|_2655_2828_379/1	gi|65306796|gb|AY948116.1|	2655	+	0	0	78	78	78	0	0	1	0	25	GCTTATTTTGAGTGGGAAGAATTTT	YYYYYYYYYYWYYYYYYYYWYYYWW
6796|gb|AY948116.1|_2657_2838_3d8/1	gi|65306796|gb|AY948116.1|	2657	+	0	0	78	78	78	0	0	1	0	25	TTATTTTGAGTGGGAAGAATTTTGC	YYYYYYYYYWYYYYYYYYYWWYYWW
6796|gb|AY948116.1|_2539_2695_3ce/1	gi|65306796|gb|AY948116.1|	2671	-	0	0	78	78	78	0	0	1	0	25	AAGAATTTTGCAGGATTATGAAAAT	WWYYWYWYYWYWYYYWYYYYYYYYY
6796|gb|AY948116.1|_2677_2830_350/2	gi|65306796|gb|AY948116.1|	2677	+	0	0	78	78	78	0	0	1	0	25	TTTGCAGGATTATGAAAATACCTGA	YYYYYYYYYYYYYYYYYYWUWYYWY
6796|gb|AY948116.1|_2713_2871_3b4/1	gi|65306796|gb|AY948116.1|	2713	+	0	0	78	78	78	0	0	1	0	25	AAATAGATATAGACCAAAGAATTTT	YYYYYYYYYYYYYWYYWYYWYWWQQ
6796|gb|AY948116.1|_2728_2889_349/1	gi|65306796|gb|AY948116.1|	2728	+	0	0	78	78	78	0	0	1	0	25	AAAGAATTTTAAAACCTGCTATCAA	YYYYYYYYYYWYYYYYWYWYWWWQQ
6796|gb|AY948116.1|_2729_2913_316/2	gi|65306796|gb|AY948116.1|	2729	+	0	0	78	78	78	0	0	1	0	25	AAGAATTTTAAAACCTGCTATCAAA	YYYYYYYYYYYYYYYYWYWUWYYSY
6796|gb|AY948116.1|_2562_2758_3e2/2	gi|65306796|gb|AY948116.1|	2734	-	0	0	78	78	78	0	0	1	0	25	TTTTAAAACCTGCTATCAAAGAACT	YSYWWUWYWYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_2738_2910_32b/1	gi|65306796|gb|AY948116.1|	2738	+	0	0	78	78	78	0	0	1	0	25	AAAACCTGCTATCAAAGAACTTTCT	YYYYYYYYYYYYYYYYYYYSYYYSU
6796|gb|AY948116.1|_2742_2905_3a0/2	gi|65306796|gb|AY948116.1|	2742	+	0	0	78	78	78	0	0	1	0	25	CCTGCTATCAAAGAACTTTCTAAAG	YYYYYYYYYYWYYYWWYYYWWWWQQ
6796|gb|AY948116.1|_2581_2766_32e/1	gi|65306796|gb|AY948116.1|	2742	-	0	0	78	78	78	0	0	1	0	25	CCTGCTATCAAAGAACTTTCTAAAG	QQWWYWYYWYYWYYWYYYYYYYYYY
6796|gb|AY948116.1|_2589_2767_3c4/1	gi|65306796|gb|AY948116.1|	2743	-	0	0	78	78	78	0	0	1	0	25	CTGCTATCAAAGAACTTTCTAAAGA	USYYWYWYYYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_2643_2777_30b/1	gi|65306796|gb|AY948116.1|	2753	-	0	0	58	58	58	1	30	0	1	25	AGAACTTTCTAAAGAACGCTATCTT	USYWWWWYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2772_2945_2f4/2	gi|65306796|gb|AY948116.1|	2772	+	0	0	61	61	61	1	30	0	1	25	tATCTTTTTGACCAAATCAGAGTGC	+YYYYYYYYWYYYYWWYYYSYWYWW
6796|gb|AY948116.1|_2623_2797_3cc/2	gi|65306796|gb|AY948116.1|	2773	-	0	0	78	78	78	0	0	1	0	25	ATCTTTTTGACCAAATCAGAGTGCC	YWYWYWWYYWWYYYWYYYYYYYYYY
6796|gb|AY948116.1|_2774_2935_3d2/2	gi|65306796|gb|AY948116.1|	2774	+	0	0	78	78	78	0	0	1	0	25	TCTTTTTGACCAAATCAGAGTGCCT	YYYYYYYYYYYYYWYYYYYSYWYWW
6796|gb|AY948116.1|_2786_2937_2ef/1	gi|65306796|gb|AY948116.1|	2786	+	0	0	78	78	78	0	0	1	0	25	AATCAGAGTGCCTTTTAAAAATCTT	YYYYYYYYYYWYYYWWYYWUWWYWY
6796|gb|AY948116.1|_2628_2813_364/1	gi|65306796|gb|AY948116.1|	2789	-	0	0	78	78	78	0	0	1	0	25	CAGAGTGCCTTTTAAAAATCTTGCT	USYWWUWYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2645_2817_3d3/1	gi|65306796|gb|AY948116.1|	2793	-	0	0	78	78	78	0	0	1	0	25	GTGCCTTTTAAAAATCTTGCTTATG	YWYWYWYYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2794_2944_382/2	gi|65306796|gb|AY948116.1|	2794	+	0	0	78	78	78	0	0	1	0	25	TGCCTTTTAAAAATCTTGCTTATGA	YYYYYYYYYYYYYYWWYYWYWWYWY
6796|gb|AY948116.1|_2804_2945_37a/2	gi|65306796|gb|AY948116.1|	2804	+	0	0	78	78	78	0	0	1	0	25	AAATCTTGCTTATGAAAAAGAAAAA	YYYYYYYYYYYYYYYYYWWUWWYWW
6796|gb|AY948116.1|_2655_2828_379/2	gi|65306796|gb|AY948116.1|	2804	-	0	0	78	78	78	0	0	1	0	25	AAATCTTGCTTATGAAAAAGAAAAA	YSYWWWYYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2677_2830_350/1	gi|65306796|gb|AY948116.1|	2806	-	0	0	78	78	78	0	0	1	0	25	ATCTTGCTTATGAAAAAGAAAAAAC	USYWWWYYYYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_2647_2833_389/2	gi|65306796|gb|AY948116.1|	2809	-	0	0	78	78	78	0	0	1	0	25	TTGCTTATGAAAAAGAAAAAACCGC	QQWWWYWYYWYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_2657_2838_3d8/2	gi|65306796|gb|AY948116.1|	2814	-	0	0	78	78	78	0	0	1	0	25	TATGAAAAAGAAAAAACCGCAGGGC	YWYWYSYYYYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_2844_3037_39b/2	gi|65306796|gb|AY948116.1|	2844	+	0	0	78	78	78	0	0	1	0	25	CGTGGCGGTAAAGTTTCAGGTATTA	YYYYYYYYYYYYYYWWYYYWWWYWY
6796|gb|AY948116.1|_2713_2871_3b4/2	gi|65306796|gb|AY948116.1|	2847	-	0	0	78	78	78	0	0	1	0	25	GGCGGTAAAGTTTCAGGTATTAGCT	YWYWWUWWYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2854_2996_310/2	gi|65306796|gb|AY948116.1|	2854	+	0	0	78	78	78	0	0	1	0	25	AAGTTTCAGGTATTAGCTTTACTTT	YYYYYYYYYYWYYYYWYYYSYWYWY
6796|gb|AY948116.1|_2855_3027_383/1	gi|65306796|gb|AY948116.1|	2855	+	0	0	78	78	78	0	0	1	0	25	AGTTTCAGGTATTAGCTTTACTTTT	YYYYYYYYYWYYYYYYWYWYWWWQQ
6796|gb|AY948116.1|_2728_2889_349/2	gi|65306796|gb|AY948116.1|	2865	-	0	0	78	78	78	0	0	1	0	25	ATTAGCTTTACTTTTAAACCTGAAA	WWYYWWYYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2878_3018_323/2	gi|65306796|gb|AY948116.1|	2878	+	0	0	78	78	78	0	0	1	0	25	TTAAACCTGAAAATATCCAAATGCA	YYYYYYYYYWYYYYWWYYWUWYYSU
6796|gb|AY948116.1|_2742_2905_3a0/1	gi|65306796|gb|AY948116.1|	2881	-	0	0	78	78	78	0	0	1	0	25	AACCTGAAAATATCCAAATGCAAAA	YSYYYSYYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2738_2910_32b/2	gi|65306796|gb|AY948116.1|	2886	-	0	0	78	78	78	0	0	1	0	25	GAAAATATCCAAATGCAAAAGCTAG	QQWWWYWYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2729_2913_316/1	gi|65306796|gb|AY948116.1|	2889	-	0	0	78	78	78	0	0	1	0	25	AATATCCAAATGCAAAAGCTAGAAA	WWYYYSYYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2890_3057_39e/1	gi|65306796|gb|AY948116.1|	2890	+	0	0	78	78	78	0	0	1	0	25	ATATCCAAATGCAAAAGCTAGAAAA	YYYYYYYYYYYYYYYYYWWWWWYSY
6796|gb|AY948116.1|_2904_3092_3af/2	gi|65306796|gb|AY948116.1|	2904	+	0	0	78	78	78	0	0	1	0	25	AAGCTAGAAAATGAAAGTCAAAAAA	YYYYYYYYYYYYYYYWYYYWYYYWY
6796|gb|AY948116.1|_2904_3069_3b0/2	gi|65306796|gb|AY948116.1|	2904	+	0	0	78	78	78	0	0	1	0	25	AAGCTAGAAAATGAAAGTCAAAAAA	YYYYYYYYYYYYYYYYYYYSYWWQQ
6796|gb|AY948116.1|_2774_2935_3d2/1	gi|65306796|gb|AY948116.1|	2911	-	0	0	78	78	78	0	0	1	0	25	AAAATGAAAGTCAAAAAATAATGAG	WWYYWUWYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2786_2937_2ef/2	gi|65306796|gb|AY948116.1|	2913	-	0	0	78	78	78	0	0	1	0	25	AATGAAAGTCAAAAAATAATGAGCG	YSYYWYWYWYYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_2915_3095_35d/2	gi|65306796|gb|AY948116.1|	2915	+	0	0	78	78	78	0	0	1	0	25	TGAAAGTCAAAAAATAATGAGCGAT	YYYYYYYYYWYYYYYWYYYWYWWQQ
6796|gb|AY948116.1|_2916_3066_381/1	gi|65306796|gb|AY948116.1|	2916	+	0	0	78	78	78	0	0	1	0	25	GAAAGTCAAAAAATAATGAGCGATG	YYYYYYYYYYYYYYYYYYWUWWWQQ
6796|gb|AY948116.1|_2794_2944_382/1	gi|65306796|gb|AY948116.1|	2920	-	0	0	78	78	78	0	0	1	0	25	GTCAAAAAATAATGAGCGATGAGCA	QQWWYWWYYWYWYYYWYYYYYYYYY
6796|gb|AY948116.1|_2772_2945_2f4/1	gi|65306796|gb|AY948116.1|	2921	-	0	0	78	78	78	0	0	1	0	25	TCAAAAAATAATGAGCGATGAGCAA	USYYYSYYYYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_2804_2945_37a/1	gi|65306796|gb|AY948116.1|	2921	-	0	0	78	78	78	0	0	1	0	25	TCAAAAAATAATGAGCGATGAGCAA	YWYYWYWYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2938_3097_3b8/2	gi|65306796|gb|AY948116.1|	2938	+	0	0	78	78	78	0	0	1	0	25	ATGAGCAAAAATATTTAAAGATTTT	YYYYYYYYYYYYYYYYWYYWWWWQQ
6796|gb|AY948116.1|_2941_3140_3be/2	gi|65306796|gb|AY948116.1|	2941	+	0	0	78	78	78	0	0	1	0	25	AGCAAAAATATTTAAAGATTTTAAA	YYYYYYYYYYYYYYWWYYYWYYYWY
6796|gb|AY948116.1|_2949_3105_3db/1	gi|65306796|gb|AY948116.1|	2949	+	0	0	78	78	78	0	0	1	0	25	TATTTAAAGATTTTAAACAATATGA	YYYYYYYYYYYYYYWWYYWYWWYSU
6796|gb|AY948116.1|_2958_3102_380/1	gi|65306796|gb|AY948116.1|	2958	+	0	0	78	78	78	0	0	1	0	25	ATTTTAAACAATATGAAACTTAATC	YYYYYYYYYWYYYYYWYYYWYWWQQ
6796|gb|AY948116.1|_2854_2996_310/1	gi|65306796|gb|AY948116.1|	2972	-	0	0	78	78	78	0	0	1	0	25	GAAACTTAATCAAGTTAGATTTGAT	WWYYYSYYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2973_3146_353/1	gi|65306796|gb|AY948116.1|	2973	+	0	0	78	78	78	0	0	1	0	25	AAACTTAATCAAGTTAGATTTGATT	YYYYYYYYYYYYYYYWYYWUWWYWY
6796|gb|AY948116.1|_2878_3018_323/1	gi|65306796|gb|AY948116.1|	2994	-	0	0	78	78	78	0	0	1	0	25	GATTATAATGACAAGCTTTGGCAAT	QQWWWYWWYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2855_3027_383/2	gi|65306796|gb|AY948116.1|	3003	-	0	0	78	78	78	0	0	1	0	25	GACAAGCTTTGGCAATTTAACGATT	YSYWWYWYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2844_3037_39b/1	gi|65306796|gb|AY948116.1|	3013	-	0	0	78	78	78	0	0	1	0	25	GGCAATTTAACGATTTTGATTTTGA	YSYWWYWYWYYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_3023_3193_3a8/1	gi|65306796|gb|AY948116.1|	3023	+	0	0	78	78	78	0	0	1	0	25	CGATTTTGATTTTGATGAATTTAAA	YYYYYYYYYWYYYYYWYYWWYWYSY
6796|gb|AY948116.1|_3031_3217_2f3/2	gi|65306796|gb|AY948116.1|	3031	+	0	0	78	78	78	0	0	1	0	25	ATTTTGATGAATTTAAAATTATTGC	YYYYYYYYYWYYYYWWYWWWWYYWW
6796|gb|AY948116.1|_2890_3057_39e/2	gi|65306796|gb|AY948116.1|	3033	-	0	0	78	78	78	0	0	1	0	25	TTTGATGAATTTAAAATTATTGCAA	YWYWWYWYWYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_2916_3066_381/2	gi|65306796|gb|AY948116.1|	3042	-	0	0	78	78	78	0	0	1	0	25	TTTAAAATTATTGCAATAGAGCTTG	QQWWWYWYWYYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_2904_3069_3b0/1	gi|65306796|gb|AY948116.1|	3045	-	0	0	78	78	78	0	0	1	0	25	AAAATTATTGCAATAGAGCTTGTAA	WWYYYSYYYWYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_3048_3217_35a/1	gi|65306796|gb|AY948116.1|	3048	+	0	0	78	78	78	0	0	1	0	25	ATTATTGCAATAGAGCTTGTAAGAG	YYYYYYYYYYWYYYWWYYYWYYYSU
6796|gb|AY948116.1|_3063_3243_373/1	gi|65306796|gb|AY948116.1|	3063	+	0	0	78	78	78	0	0	1	0	25	CTTGTAAGAGATGAATACGAGAATT	YYYYYYYYYYYYYYYWYYYSYYYWW
6796|gb|AY948116.1|_3064_3254_3a4/1	gi|65306796|gb|AY948116.1|	3064	+	0	0	78	78	78	0	0	1	0	25	TTGTAAGAGATGAATACGAGAATTT	YYYYYYYYYYWYYWYYYYWUWWYWW
6796|gb|AY948116.1|_2904_3092_3af/1	gi|65306796|gb|AY948116.1|	3068	-	0	0	78	78	78	0	0	1	0	25	AAGAGATGAATACGAGAATTTAAAC	USYYWUWYYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2915_3095_35d/1	gi|65306796|gb|AY948116.1|	3071	-	0	0	78	78	78	0	0	1	0	25	AGATGAATACGAGAATTTAAACTTT	WWYWWUWYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_2938_3097_3b8/1	gi|65306796|gb|AY948116.1|	3073	-	0	0	78	78	78	0	0	1	0	25	ATGAATACGAGAATTTAAACTTTGG	QQWWYSYYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_3077_3242_33c/2	gi|65306796|gb|AY948116.1|	3077	+	0	0	78	78	78	0	0	1	0	25	ATACGAGAATTTAAACTTTGGAAAT	YYYYYYYYYYYYYYWWYWWUWWYSY
6796|gb|AY948116.1|_3078_3241_37f/2	gi|65306796|gb|AY948116.1|	3078	+	0	0	78	78	78	0	0	1	0	25	TACGAGAATTTAAACTTTGGAAATC	YYYYYYYYYYYYYYYWYYWYWWWQQ
6796|gb|AY948116.1|_2958_3102_380/2	gi|65306796|gb|AY948116.1|	3078	-	0	0	78	78	78	0	0	1	0	25	TACGAGAATTTAAACTTTGGAAATC	YSYWWYWYYYYWYYWYYYYYYYYYY
6796|gb|AY948116.1|_2949_3105_3db/2	gi|65306796|gb|AY948116.1|	3081	-	0	0	78	78	78	0	0	1	0	25	GAGAATTTAAACTTTGGAAATCATA	YWYWYSYYYYYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_3093_3256_30c/1	gi|65306796|gb|AY948116.1|	3093	+	0	0	78	78	78	0	0	1	0	25	TTTGGAAATCATATGCACTTTAATG	YYYYYYYYYYWYYYYWYYYSYYYSU
6796|gb|AY948116.1|_3094_3274_368/1	gi|65306796|gb|AY948116.1|	3094	+	0	0	78	78	78	0	0	1	0	25	TTGGAAATCATATGCACTTTAATGC	YYYYYYYYYWYYYYYWYYYSYYYSU
6796|gb|AY948116.1|_3103_3259_31f/2	gi|65306796|gb|AY948116.1|	3103	+	0	0	78	78	78	0	0	1	0	25	ATATGCACTTTAATGCTAAAAATCA	YYYYYYYYYYYYYYWWYYWUWYYWW
6796|gb|AY948116.1|_2941_3140_3be/1	gi|65306796|gb|AY948116.1|	3116	-	0	0	78	78	78	0	0	1	0	25	TGCTAAAAATCAAGAGCAGTTTTTT	USYYYWWYYWYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_2973_3146_353/2	gi|65306796|gb|AY948116.1|	3122	-	0	0	78	78	78	0	0	1	0	25	AAATCAAGAGCAGTTTTTTAAAATG	YSYWWYWYYYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_3134_3309_3de/1	gi|65306796|gb|AY948116.1|	3134	+	0	0	78	78	78	0	0	1	0	25	GTTTTTTAAAATGATTGAAACCTTT	YYYYYYYYYYYYYYWWYYYWYYYWY
6796|gb|AY948116.1|_3139_3290_3b1/1	gi|65306796|gb|AY948116.1|	3139	+	0	0	78	78	78	0	0	1	0	25	TTAAAATGATTGAAACCTTTAGAAA	YYYYYYYYYWYYYYYWYWWUWWYWW
6796|gb|AY948116.1|_3144_3302_38a/1	gi|65306796|gb|AY948116.1|	3144	+	0	0	78	78	78	0	0	1	0	25	ATGATTGAAACCTTTAGAAAAGGTA	YYYYYYYYYYYYYYYYWYYWWWWQQ
6796|gb|AY948116.1|_3147_3313_37b/2	gi|65306796|gb|AY948116.1|	3147	+	0	0	78	78	78	0	0	1	0	25	ATTGAAACCTTTAGAAAAGGTATTA	YYYYYYYYYYYYYYYYYYWUWWYSY
6796|gb|AY948116.1|_3023_3193_3a8/2	gi|65306796|gb|AY948116.1|	3169	-	0	0	78	78	78	0	0	1	0	25	TTAGGTAAAAATTTGCTATAATTAT	QQWWWYWYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_3048_3217_35a/2	gi|65306796|gb|AY948116.1|	3193	-	0	0	78	78	78	0	0	1	0	25	TATCTTTAAAGGATACAAGCTATCC	YSYYWYWYYWYYYYYWYYYYYYYYY
6796|gb|AY948116.1|_3031_3217_2f3/1	gi|65306796|gb|AY948116.1|	3193	-	0	0	78	78	78	0	0	1	0	25	TATCTTTAAAGGATACAAGCTATCC	YWYYWWYYYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_3078_3241_37f/1	gi|65306796|gb|AY948116.1|	3217	-	0	0	78	78	78	0	0	1	0	25	CGCCACTTGTGCCAAGTGTCGAGCT	QQWWWWWYYYYWYYYWYYYYYYYYY
6796|gb|AY948116.1|_3077_3242_33c/1	gi|65306796|gb|AY948116.1|	3218	-	0	0	78	78	78	0	0	1	0	25	GCCACTTGTGCCAAGTGTCGAGCTT	QQWWWUWYWYYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_3063_3243_373/2	gi|65306796|gb|AY948116.1|	3219	-	0	0	78	78	78	0	0	1	0	25	CCACTTGTGCCAAGTGTCGAGCTTG	YSYWWUWYYWYWYYYYYYYYYYYYY
6796|gb|AY948116.1|_3064_3254_3a4/2	gi|65306796|gb|AY948116.1|	3230	-	0	0	78	78	78	0	0	1	0	25	AAGTGTCGAGCTTGTAAGGGGTGCA	WWYYWYWWYWWYYYYWYYYYYYYYY
6796|gb|AY948116.1|_3093_3256_30c/2	gi|65306796|gb|AY948116.1|	3232	-	0	0	78	78	78	0	0	1	0	25	GTGTCGAGCTTGTAAGGGGTGCAAC	USYWYWYYYWYWYYYWYYYYYYYYY
6796|gb|AY948116.1|_3103_3259_31f/1	gi|65306796|gb|AY948116.1|	3235	-	0	0	78	78	78	0	0	1	0	25	TCGAGCTTGTAAGGGGTGCAACCCC	QQWWYWWYYWYYYYYYYYYYYYYYY
6796|gb|AY948116.1|_3094_3274_368/2	gi|65306796|gb|AY948116.1|	3250	-	0	0	78	78	78	0	0	1	0	25	GTGCAACCCCTTAACCCCACTAATA	YWYWYSYYYWWYYYYWYYYYYYYYY
6796|gb|AY948116.1|_3139_3290_3b1/2	gi|65306796|gb|AY948116.1|	3266	-	0	0	78	78	78	0	0	1	0	25	CCACTAATAAAAATCAACTAAAATC	WWYYYSYYYYYWYYYWYYYYYYYYY
6796|gb|AY948116.1|_3144_3302_38a/2	gi|65306796|gb|AY948116.1|	3278	-	0	0	78	78	78	0	0	1	0	25	ATCAACTAAAATCAATAAATGATTT	QQWWWWYYYYYYYYWYYYYYYYYYY
6796|gb|AY948116.1|_3134_3309_3de/2	gi|65306796|gb|AY948116.1|	3285	-	0	0	78	78	78	0	0	1	0	25	AAAATCAATAAATGATTTTTTTGAT	WWYYYSYYYWWYYYYYYYYYYYYYY
6796|gb|AY948116.1|_3147_3313_37b/1	gi|65306796|gb|AY948116.1|	3289	-	0	0	78	78	78	0	0	1	0	25	TCAATAAATGATTTTTTTGATTTTT	YSYWWYWWYWYYYYYYYYYYYYYYY
BioPerl-1.007002/t/data/test.metafasta000444000766000024        33113155576321 17513 0ustar00cjfieldsstaff000000000000>test
ABCDEFHIJKLMNOPQRSTUVWXYZ
&charge
NBNAANCNJCNNNONNCNNUNNXNZ
&chemical
LBSAARCLJCLSMOIMCHHULRXRZ
&functional
HBPAAHCHJCHHPOHPCPPUHHXPZ
&hydrophobic
I & OIOIJOIIOOIOOOOUIIXOZ
&structural
ABAEEIEIJEIIEOAEEAAUIAXAZ
BioPerl-1.007002/t/data/test.nh000444000766000024        15313155576321 16155 0ustar00cjfieldsstaff000000000000(((hADH2:0.1,hADH1:0.11):0.05,nADHY:0.1,iADHX:0.12):0.1,(yADH4:0.09,yADH3:0.13,yADH2:0.12,yADH1:0.11):0.1);BioPerl-1.007002/t/data/test.nhx000444000766000024        63013155576321 16345 0ustar00cjfieldsstaff000000000000(((ADH2[&&NHX:S=human:E=1.1.1.1]:0.1,ADH1:0.11[&&NHX:S=human:E=1.1.1.1]):0.05[&&NHX:S=Primates:E=1.1.1.1:D=Y:B=100],ADHY:0.1[&&NHX:S=nematode:E=1.1.1.1],ADHX:0.12[&&NHX:S=insect:E=1.1.1.1]):0.1[&&NHX:S=Metazoa:E=1.1.1.1:D=N],(ADH4:0.09[&&NHX:S=yeast:E=1.1.1.1],ADH3:0.13[&&NHX:S=yeast:E=1.1.1.1],ADH2:0.12[&&NHX:S=yeast:E=1.1.1.1],ADH1:0.11[&&NHX:S=yeast:E=1.1.1.1]):0.1[&&NHX:S=Fungi])[&&NHX:E=1.1.1.1:D=N];BioPerl-1.007002/t/data/test.phd000555000766000024      1717313155576321 16400 0ustar00cjfieldsstaff000000000000BEGIN_SEQUENCE ML4924R

BEGIN_COMMENT

CHROMAT_FILE: ML4924R
ABI_THUMBPRINT: 0
PHRED_VERSION: 0.980904.e
CALL_METHOD: phred
QUALITY_LEVELS: 99
TIME: Thu Jun 21 11:27:03 2001
TRACE_ARRAY_MIN_INDEX: 0
TRACE_ARRAY_MAX_INDEX: 8792
CHEM: term
DYE: big

END_COMMENT

BEGIN_DNA
a 6 1
c 6 20
t 6 17
t 8 26
t 8 35
g 12 48
g 18 58
t 16 66
c 14 83
g 11 98
c 9 104
c 6 122
t 6 128
g 9 140
c 19 147
a 20 159
g 32 167
g 34 178
t 34 190
a 39 200
c 39 208
c 39 221
g 29 233
g 40 243
t 28 255
c 21 267
c 13 277
g 4 288
n 4 297
g 4 298
a 8 314
t 8 328
t 23 339
c 29 349
c 39 359
c 40 369
g 40 381
g 40 390
g 40 401
t 46 413
c 34 425
g 33 436
a 29 447
c 29 453
c 32 466
c 33 476
a 34 485
c 34 492
g 34 505
c 34 514
g 40 527
t 40 537
c 34 548
c 34 559
g 34 572
c 34 579
t 34 592
t 34 602
t 39 613
g 40 625
c 40 633
t 40 645
c 40 656
a 40 664
t 40 673
c 40 685
t 46 697
c 51 707
c 51 718
c 56 728
t 51 738
c 51 749
t 35 760
g 35 772
a 35 783
c 35 790
t 35 803
t 35 813
t 39 824
g 40 836
c 40 844
a 40 855
t 40 865
c 56 876
c 42 887
c 51 898
t 46 909
t 46 921
a 46 931
a 46 940
t 46 951
c 46 962
c 46 974
t 46 985
c 40 995
a 40 1004
g 40 1015
a 40 1028
a 40 1037
t 40 1048
g 35 1060
g 35 1071
c 35 1080
g 35 1096
t 35 1106
c 35 1116
a 40 1125
g 40 1138
a 40 1150
g 51 1160
a 51 1172
a 51 1182
g 51 1193
a 40 1204
a 35 1214
g 35 1226
c 39 1235
t 39 1250
c 39 1259
t 39 1272
c 40 1282
g 51 1295
a 51 1305
a 51 1315
c 51 1325
c 51 1337
c 51 1348
a 51 1358
a 51 1368
t 51 1381
g 51 1393
a 51 1403
g 51 1415
g 51 1427
g 39 1440
a 39 1450
t 39 1462
a 39 1470
t 39 1483
c 35 1494
a 40 1503
a 40 1514
g 40 1528
g 40 1540
t 40 1552
t 39 1565
c 39 1574
a 39 1583
g 39 1598
a 38 1609
a 40 1619
g 39 1632
c 39 1642
t 39 1657
c 39 1666
g 39 1680
t 40 1691
t 45 1703
c 51 1713
t 51 1726
c 51 1736
a 51 1746
a 51 1757
c 51 1767
a 45 1778
t 45 1791
c 45 1802
t 45 1816
c 45 1826
c 45 1838
g 45 1852
t 51 1863
t 51 1875
g 56 1887
g 43 1899
t 43 1911
g 43 1924
a 43 1933
g 43 1946
a 43 1958
g 56 1970
t 56 1982
g 56 1994
g 56 2006
t 56 2017
g 51 2030
a 43 2041
t 43 2053
c 43 2063
g 43 2079
t 43 2089
c 43 2100
t 43 2114
c 43 2124
a 43 2135
c 43 2144
c 43 2157
c 43 2169
g 43 2184
t 43 2195
g 43 2207
c 43 2216
c 43 2229
t 43 2244
c 43 2253
c 43 2265
a 46 2277
a 56 2288
g 56 2299
g 56 2311
t 56 2324
t 56 2336
t 56 2348
t 56 2360
g 56 2373
g 51 2385
a 51 2397
a 51 2408
c 51 2418
a 43 2430
g 43 2443
c 45 2454
t 45 2469
c 45 2480
a 45 2491
g 56 2503
t 56 2516
g 56 2528
g 51 2540
t 51 2552
c 51 2564
a 51 2574
a 51 2585
a 51 2598
c 45 2608
a 45 2620
c 45 2630
c 45 2644
t 45 2658
g 51 2671
t 51 2682
c 51 2693
t 51 2707
t 45 2719
c 45 2730
t 51 2743
c 51 2753
c 51 2765
a 51 2775
a 51 2787
g 43 2798
g 43 2810
c 43 2822
g 43 2837
a 43 2847
g 43 2859
g 51 2872
t 51 2884
a 51 2894
c 43 2904
a 43 2917
c 43 2927
t 43 2943
g 43 2956
t 43 2967
g 51 2980
a 51 2992
g 45 3003
g 45 3017
t 45 3029
c 45 3039
t 45 3053
t 45 3065
t 51 3077
c 51 3088
g 51 3102
g 51 3113
t 51 3125
a 43 3136
t 43 3148
t 43 3161
a 43 3170
g 43 3183
a 43 3196
c 43 3205
g 43 3220
t 43 3231
a 45 3243
a 56 3254
t 56 3266
g 56 3279
a 56 3290
a 56 3302
a 56 3314
a 51 3325
g 51 3337
a 51 3350
t 43 3360
t 43 3373
g 43 3385
c 43 3394
g 43 3410
t 43 3421
g 43 3434
c 43 3443
t 43 3458
a 43 3468
c 43 3477
g 43 3493
t 43 3505
c 43 3515
a 43 3527
c 43 3536
c 43 3550
g 43 3565
t 43 3576
g 43 3588
a 45 3601
g 45 3611
a 45 3625
g 45 3635
g 45 3648
a 43 3660
g 43 3672
a 38 3684
c 38 3692
a 38 3705
a 43 3717
g 56 3729
g 56 3741
c 56 3752
a 56 3765
a 51 3776
t 51 3789
g 51 3801
c 51 3811
a 43 3824
g 43 3836
c 43 3846
t 43 3862
t 43 3874
c 43 3884
t 51 3897
t 51 3909
g 56 3922
a 56 3933
g 56 3944
a 56 3957
g 56 3968
t 43 3980
g 43 3992
g 43 4004
c 43 4013
t 43 4029
t 43 4041
g 43 4053
a 56 4064
a 56 4075
a 51 4087
g 51 4098
t 51 4111
c 51 4121
a 51 4132
a 51 4144
g 56 4155
g 56 4168
a 51 4181
g 51 4192
t 43 4205
a 43 4215
c 43 4225
g 43 4240
a 43 4250
g 43 4263
c 43 4274
t 45 4289
g 45 4301
t 45 4312
t 56 4324
g 56 4336
a 56 4347
g 56 4358
g 56 4371
a 56 4383
g 56 4394
g 51 4407
a 43 4419
a 43 4430
c 43 4440
t 43 4455
t 43 4467
c 43 4477
a 51 4488
g 51 4500
t 51 4513
g 51 4525
a 51 4536
c 45 4546
a 45 4558
c 45 4569
t 51 4583
g 45 4595
g 45 4607
c 45 4618
t 45 4633
g 45 4645
t 45 4656
t 56 4668
t 56 4680
t 56 4692
g 56 4704
g 56 4716
a 56 4727
t 56 4738
t 56 4751
c 56 4762
g 56 4775
g 56 4787
t 51 4798
a 51 4809
t 51 4821
c 51 4831
c 51 4844
a 51 4854
g 51 4866
g 51 4879
a 56 4892
g 51 4903
c 51 4914
a 51 4926
c 51 4936
a 51 4948
t 51 4960
t 56 4973
g 56 4985
a 56 4997
t 56 5008
c 56 5020
t 56 5033
t 56 5045
g 56 5057
g 56 5069
a 56 5080
a 40 5091
t 40 5104
c 40 5115
a 40 5124
a 40 5136
g 40 5149
t 40 5162
a 40 5172
c 40 5182
g 40 5197
a 40 5207
t 40 5220
c 51 5231
c 56 5243
t 56 5256
t 51 5268
c 51 5279
t 51 5292
a 51 5302
c 51 5312
g 51 5325
g 51 5338
g 51 5350
t 51 5362
a 45 5372
t 45 5384
c 45 5395
t 45 5409
a 45 5419
t 45 5431
g 51 5444
g 56 5456
a 56 5468
a 56 5479
t 56 5492
g 40 5503
g 39 5516
a 39 5528
c 39 5537
t 39 5552
t 39 5564
c 39 5575
t 40 5588
a 40 5597
t 40 5609
g 40 5622
t 56 5634
t 56 5646
g 51 5658
t 51 5669
t 51 5682
c 51 5692
t 51 5705
t 51 5718
g 51 5730
a 45 5741
a 40 5752
c 40 5762
g 37 5776
c 37 5785
c 40 5798
c 40 5810
g 56 5823
g 56 5834
g 51 5846
a 51 5859
t 40 5870
a 40 5880
c 40 5890
c 40 5904
g 40 5918
t 51 5929
g 51 5941
t 37 5953
t 37 5966
g 37 5978
c 37 5987
a 37 5999
c 40 6009
g 40 6023
t 34 6035
c 34 6047
g 29 6060
c 29 6068
c 29 6083
g 29 6096
t 32 6107
a 29 6118
g 25 6128
g 19 6142
t 27 6154
g 27 6167
c 32 6176
a 32 6187
a 34 6199
g 40 6212
a 34 6224
c 40 6234
t 34 6248
c 35 6258
g 35 6272
c 35 6281
g 35 6296
t 39 6307
t 40 6320
g 56 6331
g 56 6342
g 56 6355
a 51 6367
t 51 6378
t 46 6391
c 46 6401
a 42 6411
g 42 6424
c 42 6435
a 46 6447
t 40 6459
a 37 6469
g 37 6482
a 40 6494
g 29 6506
t 29 6518
t 29 6531
a 29 6539
c 29 6549
c 27 6563
a 32 6573
a 29 6585
g 29 6596
g 34 6609
a 48 6622
t 48 6633
g 48 6645
a 32 6656
t 34 6668
g 34 6681
c 34 6690
c 31 6704
a 31 6714
t 37 6726
g 46 6739
a 48 6750
a 48 6762
g 40 6774
t 40 6786
g 40 6797
g 27 6810
t 25 6821
t 21 6834
c 16 6842
c 16 6856
a 18 6865
a 19 6877
g 23 6889
t 27 6901
t 25 6915
a 29 6923
a 24 6936
g 29 6947
t 32 6960
a 29 6970
c 29 6980
g 25 6995
a 25 7004
a 21 7018
g 15 7026
g 15 7041
t 23 7053
g 27 7065
t 27 7075
t 27 7089
a 27 7098
t 25 7110
c 22 7120
c 24 7133
t 29 7147
c 32 7157
a 32 7168
a 40 7179
c 29 7189
a 29 7200
a 29 7211
g 48 7224
t 48 7237
c 40 7248
t 40 7261
c 40 7272
a 29 7282
g 29 7294
a 25 7306
a 29 7317
c 29 7327
a 40 7338
t 40 7350
c 32 7362
a 32 7372
c 32 7383
t 32 7397
g 32 7409
g 25 7422
t 25 7432
t 25 7445
g 29 7457
a 40 7467
a 36 7479
g 40 7491
a 36 7503
g 36 7514
t 37 7525
t 33 7537
t 46 7549
g 24 7561
t 24 7571
t 24 7584
t 32 7596
c 32 7606
t 40 7619
t 34 7630
t 22 7642
t 25 7654
c 25 7665
a 27 7674
t 25 7685
t 22 7698
t 29 7709
t 29 7721
g 25 7734
t 21 7744
t 21 7757
t 22 7767
t 29 7779
g 24 7791
t 24 7802
g 24 7814
g 31 7827
t 31 7838
g 28 7850
t 28 7861
t 24 7873
g 19 7884
g 19 7897
c 23 7906
t 27 7921
c 25 7931
t 22 7943
t 29 7954
t 34 7965
t 32 7976
t 32 7988
t 32 8000
a 25 8009
t 18 8020
a 18 8031
a 18 8039
t 18 8053
t 23 8066
t 32 8077
g 26 8089
c 25 8099
g 19 8112
g 15 8124
t 15 8134
t 15 8148
c 23 8157
t 23 8170
g 22 8182
g 34 8193
a 37 8205
t 40 8216
g 32 8227
a 32 8238
t 29 8250
a 22 8259
a 18 8269
g 18 8281
g 13 8294
c 22 8305
t 16 8318
t 20 8328
t 25 8341
g 29 8353
t 24 8364
t 24 8376
g 25 8388
t 19 8398
t 19 8412
g 25 8422
t 24 8433
g 21 8444
g 21 8455
t 27 8467
g 21 8479
g 20 8491
t 26 8502
a 25 8512
g 18 8524
a 15 8536
a 15 8545
t 10 8558
c 13 8566
c 13 8581
t 17 8593
c 21 8603
a 22 8613
a 25 8624
g 29 8635
t 25 8647
a 25 8657
c 25 8666
c 24 8678
c 19 8691
t 10 8703
c 10 8712
g 11 8726
a 17 8736
g 17 8747
a 12 8759
t 19 8768
a 16 8778
t 11 8787
END_DNA

END_SEQUENCE
BioPerl-1.007002/t/data/test.pir000444000766000024       144213155576321 16364 0ustar00cjfieldsstaff000000000000>P1;roa1_drome
Rea guano receptor type III >> 0.1
MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVVVMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDNIVIDKETGKKRGFAFVEFDDYDPVDKVVLQKQHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY*
>P1;roa2_drome
Rea guano ligand
MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVVVMKDPTSTSTSTSTSTSTSTSTMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVKKLFVGALKDDHDEQSIRDYFQHLLLLLLLDLLLLDLLLLDLLLFVEFDDYDPVDKVVLQKQHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY*
BioPerl-1.007002/t/data/test.pln000444000766000024       214513155576321 16364 0ustar00cjfieldsstaff000000000000GATGATTCCGGCTTCGGACGACTCTAGAGGATCCCCATTTTTATAGTTTTTATCTTGTAA
TAGATGTTTAGATTTTTCGTTGTAATTATTTTCTTTATTGTTGAAATTAGTATCTCTGGG
TAATTTATCATATTCTCTGGAAAATGATTTACTATCACTAGATACTTCATAAGATTTATA
ATCTTTATTATGAAAATCATCTCTATTTTTCAAATTATTATTATATCTATCAAAGTTTCT
GTCTTCATTATATCTATTAGCATATCTATCTTTATCTTTATCCCTATCACTATATCTATC
ATATGGTTCATCTTGTTCAACCGATCAGACTCGATTCGCCATCGCCTCTAACGGATGGCC
GCTCCCCCTCTCATACCTCGCTCCCCTCGACATCCCCCGTCTCGCCACCCTATCCGCCCC
CTTCATCACCCCCCCTTATCCACACCCTCACCCCCCGCATCGCGCACCCACGACCACCCG
AAGAACCGCCCTTACTCCCAAGTACGCCCCGACCTCCATCACCCTATGCGGTACCACTCC
CACCACACCCAGTCCTACTTTCGCCCGCACATCGGCCCCGCTTCAGACAGCTCCCAACTA
CGCAACCCACGCTTGTTCTTGTTCACACTCGAATACTCGAATCTCTCATTACTCCGCGGA
CTCCGCCGCACCTGTGCACCATTAACTGTGTAGCGCCTGAACCGGCACCTCTGATTACCA
CTTCCTCCACCAGCACAGTCCTATTACCGCATGTCGCTCTGCTAAGACAGTGCAAGACTC
TGCGGTCGCTCTGACCCGCATCCGCCAGGGCACCTCTCACCCTCGCTGGCCACCCCGCCC
CCCTCTCCCTGCCCCTTCATTCCCCCAAACCGCTTTCAACGGGACACACCCCTCCGCGGC
GGACCACAACTCGCCGTCGGCCACCACTCACACCTTCCCTCCTCCTTCCCCCACATCACG
CCAACCCCGTGGGACGGCTCTCCCGCGGCTACGACGCGCAACCCCCCCTCGCCGCTTCCC
CCCCAACTTCCCACGGGCTCCCCTCCGCCCCTTACCCGCGAGGAGCTTCACCCGCGAACC
ACCTCCCCCCTTTCCCAACAGCACCG
BioPerl-1.007002/t/data/test.raw000444000766000024       100613155576321 16357 0ustar00cjfieldsstaff000000000000MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVVVMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDNIVIDKETGKKRGFAFVEFDDYDPVDKVVLQKQHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY
MNKQRGTYSEVSLAQDPKRQQRKLKGNKISISGTKQEIFQVELNLQNASSDHQGNDKTYHCKGLLPPPEKLTAEVLGIICIVLMATVLKTIVLIPCIGVLEQNNFSLNRRMQKARHCGHCPEEWITYSNSCYYIGKERRTWEERVCWPVLRRTLICFL
BioPerl-1.007002/t/data/test.ref.fas000444000766000024     10112313155576321 17153 0ustar00cjfieldsstaff000000000000>NC_009749_frag
ATTATCTTCTAATACTTGGTTAAATATGTATGTGGCAAAGCTAGGATCTTCTTTACATAA
AGTTGGATCTATCCAGATAGTAACATAATCATAGTCAAAGTTATTTGCAAATTCCAATGA
TATATTTATTGATGTATCACTTTGTTTTATGGTTGTGATATCTCTAATAGGGAGTATTAT
ATTTTCTGACTTTGTCGTATATGTTAGAGTTTTACCTGTTCTCTTGTCTTCTATGAAAAA
ATATTCCTGAGGTGGAATATAGTAACCATTGTGTCCTTTATCATTTATTTCTAATAAGCA
TGATTTAGGAACGAAATAATAAAGGTTACTATAATACTTGAATAAAAGAGCATTACTATA
ATCAAAAATTCTCTTATCAAAATCATCTCTTATATCATTACTTAGTTTGTCAAAAGTTTT
TTTTAGGATGCTAGCATCACTCGTACTTAAATCTTTTCTTTTTTCATCCATGATAATGAC
CTTCTAAGATGTTTTTACATTTATTTGTCCACTACTAATAAAATCAACTATACCACCCGG
AGCAAACATACACATTGCTTTACTATTTATTGTAGTTATAGGAGCATTTTCCAGTAGCGT
AGTAGGGTTCGTGGGGATAAAAGCAGATAAGTTTGGTATACATACCCAAGGAAAGCTAAA
TGGGTTCATTGTAGGGTTTGCTGGATTTGTACATCCAGCAAAAGGTAAAATGTTAGCTCC
TAGTTTAGAATCGGTAATATTTGAAGCTGGTAAGTTGTTCGTTAGTGTTTTTATTCTTGT
ACTAAGATAAATTCCTGATCCAAGACTATATGAGCATTTAATTTGTGCTCCCATTGATGT
GGTTAATATTGACGCATTGCTTGATAAGTGTAGTTTTGATTGAGCTAATAAAATTTTTAT
ATTGTTTAAATCCGCCACTAGATCAGATACTGAGCTACTAATACTTTCATCATTGGTCGT
TATTTCTTTCAAGCGTTTTAAGGAGTCATTTATAATATTTAACATTTAAATTTTCCAATA
AGCTTCTTGCTTGCTTTTTATACTATCAATGATCGGATTATTTGTAATCTCTTTAAGCAC
CAAAAAAAAAACTATTTGAAATTGGCGGTAGATTATATACTCCTATCAAAGTTGGATTCA
TATAGTAAGATTTACTTAAAAGAACCATCGTTAGCTCTTTAGCTGTTTCAGCGGCATTCT
TATGTTTGGCATTACAAATATTTTTGTTCAGTTTTACTAAAGATTTGTGTATGTTAATAT
CTTTATGGTCATTTGAGGTTAAGGTTCTGATTTCTTTATAGGTAGAAAAACTTTTGCTAT
TTACAAAAACACTAAGCTTATATATATCGTTTGATTCTATACTATTTTTATCATCAATAA
TTTTTTGTTCCATATTCTTTAATAATTGGTAGTTTTGATTTAGTAAAGGATATATCCTGA
TAATATTTAGAATATTCTTTTCTAGCTTTTCTTGATTAAACTGTGATTTTTTTGATACTT
CTAAAGTTACTTGATTAAAATATTTTTCAAACTCTAAGAAAGGATAAATAAGCTTTAAAT
TATTATTTACTAATTGAATATTTATTATTGTTGCTATGTCTAGCAGTATTTGGAAGTATT
TATTAGCTAACTTTGTTAATAAGTTTGCTGGAGATTTTTCTATAATATCTTCTATCAAAC
TATTGTGATTATTTAAAAAAAGGTTTTTGTAGAGTTGATTTTTTATATGGATTTTTTTAT
ATAGTGTTTCTTCATCAAACATTATATTTGAAATATTTTTTAAACTGAAAATAAGTTGTT
CTAGTGATTCTGACTTGAAAATGTCTATTTGTGATTTTTTTTGAAAAAAAATATCCTGTA
AAGGGAAATCATCAAAATACTGAGATATAGCAAATATCTGTAAATCTATAAAAGCAATAG
TTTTTTTTAAGTTTTCTGAGGGCTTAGCTTGTAGTGACGTCAGCGAAACTATTGATAGGT
TAGTATCTGTTTTTTCATTTATAAGACTTAATTTATATGTATCTTTATTTATAGAATATA
AAGCTCTTAAAAGAATAATATCGCTAGCTAAAAGACGATCTGTTTTATATAAACCATTTC
TAATTAAATAAGCTAATTTCAATAAGCTTAAAATAGGATTTTTTCTAAAGGGAATAAAAC
TAACTATATTTTTATGATCTTTTATAAATATTTTGAGCGTATCGAAATATGATTTATACT
CATCTATAGCCTCAATGGAATTGGGATTTTGTATAGTTTTTACATATAATTTTACAAGAC
TATCATCATAAGCGCTGATACTATGGTTGTTTATATAGTCTAAAAATATAGATTCTAGTT
TATCGATCTGCTTAGTTTTTATAAGTTCTATTCTATTCGATATATCTTTCTCTATTACTA
GTTTATACTTTTCTAAAAGAACCTTTAAATTCTTCATAAGGCTAGTAAAATAGTTAATAT
CAGTACAATCTAAGAGGTTATCTAATTTTTTTAATATTAAATCATTAAATTTAATTGCAG
AGTCAGATAAAATTAGATTCGTTGAGTATCTTACATCTTCAATAACATAGGTCAGATTAT
AGATGTCAGCTTTTCTATAATCTTTTATATTTATAAATTTGATTACGTTAGTGATGCACT
CATTAAGCTTACTTATTTTATAAGATTGCTCTTGTTTATAATATAAATGGATATTGCTAA
ATAAATTCTCAAACCATTTATCAATATTATTATTCATATTATTATCCAACCATTGTTGCT
GTAGAACCTTTTATACTTGCTGTTACACTTCCTTTAATATTTACATCTAACCCTTCAGCA
TTAAGGTTTACATCTGCTTTGATACTATTATTTAGACTTTTTATATCTATGTTCTGTGAT
GCTTGAATATTTATATTAGCAGAGCTTTTTATATTAATAGTTGCAGACTCTAGCGAAATA
TTTGAATCATCAAGTATAATTAAAGAATTACCTATTTTTATGACAATTTTATCTTCACTA
AGCATAATGCTTGATTTCTTAGTAGCTAACAAAATTTCTTTTTCAGTTATTGATATTTTT
GAGTCTTTGACATTTTCAATTATTTGTTTATCAGCGCTTGACTCTATCGATTCAGTTGCA
TTATGAGTGATTTTTCCAGAGGACTCTAGTTTCGTAGTGCAGCCTTTTGAATCATCTTTG
ATATCTATGAGCAAGCCTTGCTCTTCTAAGTTGAAAATATGGTCTGCTTTTGACATAAGA
ATATCCCCTTAATCTTTTTCTATGCTACTATCATTTTTTATAGTAAATTTATTTACAGAA
TCTGAACTTATTATGTATTTCCAGTTTTCAGTTTTTTTATTTTCAGGAAGTATAAAATAC
AAGGCATAATCCTTGATATCTTTATCTAATGGAAATTCATTCTTTCCTGTTTTAAGATTT
AATACTTTTACATTATCATCATATATTCTTTGAGAAATAGATTGATAGTTATCTGAGTAG
AAAATATTTTTATCAGGTTTAGATTCTAGAACTATTTTTGTCTTAGGAATATTGTTGTTG
ATATACAAACCATCACTAATACAACTGCTAAGCCCTATGATTGTGGATAATACTAAACAA
AGATTTTTCAATAATTTATTGTACATTGACTTCTCCTTGTTTTTGCCATCCTAATACTTG
TAAGAATTTTGATTCTATTTTGAAGCTTAAAGGATATTTTTTACCTTTGTGCTTGATTAT
CCAGGTACAAATATTGTTTTGATCACAATTTGCGTCTTTAATTGCTTTTAATATAGACCA
TTTTCCTTGATAGCTTATTTGCTCATTACTACCATCCTCAAATTTTATGGTAATAGTTGT
TGACTCAAGTGAATTCCAGTTGTACAAAACTTCAATACTATCTGAATATTTTATGTTTAA
TGAGTTTACATAGTTTTGCTTATCGAGGATTATGCTAAAAAATGTATAATCATTATCTTT
GTTTGGTATAGGAGTTATATCAAATTTTATAGCTTTTGGATTTATTTTATCATCCCATAG
TAGCTTATTTAAAAGATATACCTTATTGAATTTATTTAGATAGTCTATTTCCTCAGGTTT
TGAAAAATCTTTACTTTCCCATCTATCATCAGTTTTATTATAAAAAAGTAGTGGAGATAG
TTGCTCTATAAATCCAGAGTATATATAACCATTGTTATCAAAGTCTTTGGTTATAGCTTC
ATTTGTTGCAGCCGAGTTACTATCCTTATTAAAAGGGAATTGATTATTTATGTATTCGTA
CTCAATATTGACAGTATTATCAAGTTTAGTTATAGCATCTTGTATGGCGATAGTTTTTAT
AGTATTAATGGCAATATCTAGATGTTTCTTCAACAGTTTATATAAGTTATTATTACCTTG
ATGATTATTTATCTTAGAAAGTTCAGAGTAAACTTTTTGTAGTGGTTCATATCCTTGTTT
GATATTTTTATATGTACTTGAATAGCCTTGTTCTATTATTAGATTATTTAACTGTTTAAA
TATGTTTTTATAGTCGGCATAACTCTTAGACTCAAGATATTTATCGTTTTCTTTAAAGTA
GTTATCTATAGGCGCCCACAATGACTTATCATTTTGATCATTAGTATTATTTTGTTTGTT
TAATTTAGTTATTTCTCCATAAAAATGTTGAAGCTTATTTATCTTTTTAGATGAATTGGT
TTCGGATTCATTAGTTATTAGGTCTGTATTAGTGCTATAAAACTCTATTAGGCTATTAAA
GGAAGAATCCTTTGATGACATTGCTAGCAAATATAATTTAAGAGCACCCTTGTTAGATAT
ATTTTTGTTAAATTCAGAGTCATTATTAAGGCTATCAATCATCTTATTATAGGATCCTAT
ATATTTCTCAATGTAGTTATTTATAGAGCTTTTATAGATAGCAATCATAAAGTCGGGTTC
TATATTGAAGTTATTCTTTAGATTATTGACGAGTCTATTAAACTTTTTATTTGTAGGATC
TATATTATCTTTAATATATTCTTTTGAGTATATTGGAGAGATAAGTATTCTTTTACTATA
GAAATTAGGAGCAAACTCCATATATAGGTTTTTACTTACTGGACTTATTAGTGGGAGCTC
ATTTTTATTATAAGTAGGGTTGACAACACTATTTATAACGTAATTTATAAGCGATACTGT
TATCGAGCTAGTTTGTTTTTTACCATCATCTGCGACATCTTTAGCATTTTTTTCTAATGA
TTTTACTAAATAATAGATATGGTCTAGCATATCACTGAAGCTTTCAAATTTTCTTTTATT
TTCCTCTTGATTAAGTATCAAAGAAACGCTCTTTGTAATAGAGTTAATATATGATGAGTT
ACATAGCTTTTTAGAGGATGTGTCAAATTGCTCTTGATACATCTTGAAGATATTATTTAC
TTCTATTGGTATTATGTAGTTATCGTTTAAATCTAAAATTGCATTATCTGTAGCACATTT
ATATAGGTATTGTATATAAATATTATTTATGACCTTCGCTCTTTTAGTATTTGAAATCCC
TAAGTATTCAGCATTAAATCCTTTAGTACTTAAGTAACTTTTGGAGTCTTTACCTACAAC
TATTAAACGATTTGTATAAAGTTTATTTGCTCTGTTGATGGCTGACTTAATCATTTCAGT
TCTTATACTTGGGGTCGTATACTTGACCACGATATCTAGCTGCTTTTCAGATAGGTTGGT
GATACTGCTTATTATTTTAAGTATTCTATTCGTATGTTGGTTAATAATTTTGTTATCCAA
ATACTCAAAAAATATTAAAAATGATGTAATCATTGATAAGTCATATGTATCATTATATTT
TGGTAAGATTACATTCTTTAGGAGAGTATCAGCATATTGTTTGTATATGAAATGATATTT
TATCGATTTCGGATATAGGATATCTAGAAGTATAGCCTCATCAATTTTTTTTCTAGTTTC
TTCTATTATTTTATTAGAGTCGCTTTCATGTAGTTGATTAAGTTCTTGTATAGAGAATTT
TTTTTTAATATTAATTTCTTGAAAAATATTAACGATAAATATAAAACTAAATAACAAAGA
TATTAAGTTTATGATAATACTTTTTGGAAAGCTGCTAAAAAATATTGTATCTTTCTTTGC
TATGATATTATCTGGTGTGTTTAGCCCAAAATTAAAGAATGTTTCTTTATTTATAGATTT
TAATTGAGGGTGGATGTTTTTTAGCAACTTTCTTATTTGATTTAATATCTTAACATTATT
GTATTTATTATTAACATCATCTTTAGAGCTAAGAATTTTTGATAATATTTCCTCTTCAGC
TTTATGATTTGTATCCGCATCAGAAGTTAATTTAAATATTGATTTTTTATCAATTGCATT
ATTATAGCTTCTAGTATGCTCAGATAAGGTGTAAAAAGATATTATGAAGTTTTTTAATCT
TAATTTTAATAGTTCTTTATAGATTTCACTAATTTTGATATTTTCATGATAGTAATCATC
GGATATATCGAAGCAAAAGTTAAGCTTATAAAATTGTAGATTTAGTTTCTTTTTTAACTT
ATATAGGTACGAAAATTCATTATTTGCAAATACGAGAGATGTATTGTTTTTATCAATAGC
TATTAAAGGGAGTTCATTATTATCAATGATTTGAGCTTGAGGTTTTATCTTTGTTATATA
ATCTTTAGCTGCCAGATAGTCCCCATAGAAAATATACAATTCACTTAAGTTGTTTTTTAC
TTTATTCTTTTTGATCAATGATTTCGCATTTTTTATGGTCTTTGAGGCAGATTTTTTGTT
AGGATTTCTTGATGTTTTAAGCCATTTTTTAATCATAAAAATACCAAGTACTGATAAAAC
AATTATTGCTATAGTTAGTGAAATTATTAATATTTGATGATTTTTAATAAAATTCATACT
TTTAATTTCCTTTTGATTTATATCTTAGAAAAATACCTTTTTTATCATTTATCAAAAAAG
AATTCTCACAATCTTCATTTACTTGAGTTAGTGAGAATGTCTCGCTATCACTTGTTTGGG
TATATGCCATTTCACAGTTTTCTTTAGATCCAAGAAGTTGTCGTTGTAGTAGTTGCTGCT
GAGCTTTCTTTGTTGATATGGCAGAGTTTGAAATTAACTCAATAATTTCACCTTTAGTAA
AAGACTGCATTTCAATTAAGATAATATCGTCATTTCTCAATGGTATAAATTGATTATTAG
CAGAATTTATGTTTACTTTTAGAGGTAAGTATATGATTGGCTTATCTGATGATTTATCAG
ATAACATTTCCTTGGCAATTTCTATTGCGTATAAGATATCAGCCTTACTATTTAGTATAG
CTGAAGTACCTTTTTCACCATTTTCTTGAAATTCTGCGATTGAGCTTTCTTCTGGCTTAT
AATTTTTAAAGAATTTATAAGCTTTTTTGGAGTCATTATTAACATTTTCTCCAATCGTTA
CTCTACCATTAATATAAAAGTTACTAAAACTTTTGTACTTAGGATATTCAGGAGTTAGAT
TACTATAATTCTTAATTTTATAAGTTATTAAGTTGTCATGTGTCAGACTAGGGTATTTAG
TAAAAGCAATTTTTTCATATACGTCTGATTCAGAATCACTTTTATAGTGAAAATTATGTA
AGTTTTCATATAGTTGTTTAGAGCAGTATTTACTTCTTTTAAATAATAGCTTTCTTTGAC
TTATATATAAGCTTTTTATATCTGTTGCGCCTAAAAGATAGTTTTGATCATTGTCTAGTT
TAGAAAGAGTAATTTCAGTATCTAAGAAGGGCAGAGTATTTCTTGATGTCAGTAATATCT
CAAATCCTGTAGTAATAATTTCTTGTATATCATCATTATTGCTTTGTATATACTCTACAG
ATTGTAAGTTATCCTTGAGTATGGATGAGAATGGCTTTATTAGGGTATCTGAAATCTTTC
GATCTTCCTTTTTTTGAGTGGTTAAAGTCACATCAGGACATATATTTTTTTCTTTAACAT
AAAAGTTTGATTTATTTGAGATTAGAATTTGTTTTTTGAAGCAGCTTATATCATAAGGAG
ATAGTTTGTCTTTTAAATCTTCATCTGAATTTACGATATTCCTTTGTAAGTCATTATCTA
CTTGATCTACAACATGATAGCTTACTTTGCCACTCTTCTTATCACAGAAATATTTTAAAT
AGCATTTATTTTGCTCAAGTTGTTGAATAAAAAAATCATAAAAATTTCGATTAACTGTAG
AAATAAATGCTTGTGGTATACGTATTTTTAGGTTATTACTTTTGTTGGTATCTAAAGAAA
CTAAATTATCAAAGAAAAAATTCTCTTTAAAGATATCATCTAAGCTTTTATTTAAAGCTA
TATAAGATGGTTTGTGCTTAGTCCAAAGTGCTTTTAGTGGGTCATGGAATTGTATTTTAA
TTTTTTTTACTCCTGAAGAAACATTTTTGGTATAAGAATATATGCTGTATTCAAAGTTCT
CATGAATATCTATACTGTTTGAATTAAAGCCAATGGCCATAAAACGGGTTGTTCTCTTAT
GATGATCTTTTTTAGATTCTTTTTTGTAAAAATTGAAGCTATCATTAATTTGAATATCAA
ATAATATGGGTTGATTTGGGCTTAATAGGAAGTTAAAGTCTTTGTGATTATTGATATATG
CTAAATCAAAAGTTAACCAGCCATTTATGCCGTAGATATTTTCACATACTTCTAATTTTT
CAATATGAGGATTTTTAAGTGTAAGAGAGTTATGCTTAAAATATTGCTTATTTCTAGTTG
ATACAAAACTTATATCCTCAAGTTCAAAATTTTTATTAATAGGCTTTATATTTATAGTAA
TTTCTTGTTTTTGCAGTACATTATTATACCCAATATATCGTGAAAGGCTGCTTTTAAGCT
TATTTAACTGTTTTATAATTGTTTTGTTGAGATCACTTGATCTTTGTATCGCACTATCTA
TACTAGTTAGTAAGACATCAATTTTTCTTATGTAATCATGAGGGAGCTCAAGAATTAAAC
TTGATGAGCATGAGTTTTGTAATTCTTTAATTGCGATTTTTAAGCTTTGAGAGTCTTTAT
AGTTTGTCGAAAAATATAAGATAAATTCATCTATGTTATTTTTTAATCTACATATTACGC
AATATCTTTTATATTTTTCGTAATCAAGCTTAGATATCAAGCCTTTTCTATAAAGTATCT
TTGTATTTTTTAGTTGAGTATTAATAAGATTAATGTTTAATAGTTTGTAATTAATAATAT
AGCTATTAATTTCACAAGCAAACTTGGCAGAAGAAGAGGTTGTGTCGCCATTTATAACTT
CAGAAGTTAACTGACTAATTATGTCTTGTATATTTAAATCAGTTATATCTTTTACTGCTA
TCATTGTCTACTTAATTAGAACATAACTAAAGTCATTTTACATAAGCACTTATCTATTGA
CTATATGTTTACAGCTAATTGGTCTGACGATAAAGTTATAAAAAGTGTATTGATATGGTT
ATTTTAGTATTGATTTTGCTGTTGGATATATGGGAAGTATAAAAAAGATAAAAAAGTTTG
CAAAAAAGATGAAAAAAATTAAAAAAAGGTGTTGCATTTTGTGAGGAGGATGCGTATTAT
ATGTCTTCACCGGCTGACGGGTGATGTTAGCGGTTAGGAGCTAAGGTTTCTAGGATATTT
AAGAGATATATTATATACAAACACTTTGTTAAAGAATTTGAGTAATCAGTAGTTAGAGTC
AGAATTTGAGAATTAAACTGAAGAGTTTGATCCTGGCTCAGATTGAACGCTGGTGGCATG
CTTAACACATGCAAGTCGAACGGTAACAGGTCTTAGGATGCTGACGAGTGGCGGACGGGT
GAGTAACGCGTAGGAATCTGCCCATTTGAGGGGGATACCAGTTGGAAACGACTGTTAATA
CCGCATAATATCTGTGGATTAAAGGTGGCTTTCGGGCTGTCGCAGATGGATGAGCCTGCG
TTGGATTAGCTAGTTGGTGGGGTAAGGGCCCACCAAGGCTACGATCCATAGCTGATTTGA
GAGGATGATCAGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGT
GGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCAATGCCATGTGTGTGAAGAAGGC
CCTAGGGTTGTAAAGCACTTTAGTTGGGGAGGAAAGCCTCAAGGTTAATAGCCTTGGGGG
AGGACGTTACCCAAAGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGG
GGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGGGTCTGTAGGTGGTTTGTTAAGT
CAGATGTGAAAGCCCAGGGCTCAACCTTGGAACTGCATTTGATACTGGCAAACTAGAGTA
CGGTAGAGGAATGGGGAATTTCTGGTGTAGCGGTGAAATGCGTAGAGATCAGAAGGAACA
CCAATGGCGAAGGCAACATTCTGGACCGATACTGACACTGAGGGACGAAAGCGTGGGGAT
CAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGAGTACTAGCTGTTGGAG
TCGGTGTAAAGGCTCTAGTGGCGCAGCTAACGCGATAAGTACTCCGCCTGGGGACTACGG
CCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGT
TTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCTGCGAACTTTCTAGAG
ATAGATTGGTGCCTTCGGGAACGCAGTGACAGGTGCTGCACGGCTGTCGTCAGCTCGTGT
TGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTATTGATAGTTACCATCATT
AAGTTGGGTACTCTATTAAGACTGCCGCTGACAAGGCGGAGGAAGGTGGGGACGACGTCA
AGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGGTATTACAGAGGGC
TGCGAAGGTGCGAGCTGGAGCGAAACTCAAAAAGGTACTCTTAGTCCGGATTGCAGTCTG
CAACTCGACTGCATGAAGTCGGAATCGCTAGTAATCGCAGGTCAGAATACTGCGGTGAAT
ACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCTCCAGAAGT
AGATAGCTTAACGAATGGGCGTTTACCACGGAGTGATTCATGACTGGGGTGAAGTCGTAA
CAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCTTAACGGAAATGCGAAAGAAT
AAGAATAAGCTTTAATTACTGTTCAAGTGATTTAGCATAGTGTTTGTAGGTAATGTATTT
TAGTGTGAATAGAATACGGGTCTGTAGCTCAGTTGGTTAGAGCGCACCCCTGATAAGGGT
GAGGTCGGTAGTTCAAGTCTACTCAGACCCACCATTTTAGGTTTAGTTGGGGCCATAGCT
CAGCTGGGAGAGCACCTGCTTTGCACGCAGGGGGTCAGCGGTTCGATCCCGCTTGGCTCC
ACCAATATTTTATTTACATGAAGATAGAGATATTTAACAATTTAGTATAGAAATAGACTT
AAGAAAATAAGTGCAAGCGGTGGATGCCTTGGCATTCAGAGGCGATGAAGGACGTGATAA
TCTGCGATAAGCTTCGGTTAGCTGGTAAATGAGCTATGACCCGGAGATTTCCGAATGGGG
GAACCCACCTGACACAAGTTGGGTACTCACTCGATATAGAGTGTAGAGCGAACGAGGGGA
ACTGAAACATCTAAGTACCCTTAGGAAGAGAAATCAATTGAGATTCCCGTAGTAGTGGCG
AGCGAAGTGGGAAGAGCCTGGTATGATTTAGCTGTAATTATAGTAGAACAAGTTGGGAAG
CTTGACGATAGAGGGTGATAGTCCCGTATACGAAATAATCACAGTGGAACTAAGCATACG
AACAAGTAGGACGGGGCACGTGGAACCTTGTCTGAATATGGGGGGACCATCCTCCAAGGC
TAAATACTCCTGAATGACCGATAGTGAACTAGTACCGTGAGGGAAAGGTGAAAAGAACCC
TTATAAAGGGAGTGAAATAGAATCTGAAACCGCTTGCATACAAGCAGTAGGAGCATGATT
TAGTCATGTGACTGCGTACCTTTTGTATAATGGGTCAGCGAGTTATTTTTAGTGGCGAGG
ATAACTGAATAAGGGATCCGTAGCGAAAGCGAGTTTTAATAGGGCGACTAGTCGCTAGGA
GTAGACCCGAAACCGGCGCGATCTATCCATGGCCAGGTTGAAGATTAGGTAGTACTAATT
GGAGGACCGAACCCAATACTGTTGCAAAAGTATGGGATGAGCTGTGGATCGGAGTGAAAG
GCTAATCAAGCACGGAGATAGCTGGTTCTCCCCGAAAACTATTTAGGTAGTGCCTCGTGT
ATAACTCATTGGGGTAAAGCACTGTTTCGACAATGGGGGTTTTACGACCTTACTGACTCG
ATGCAAACTCAGAATACGATGAAGTTCGATCACGGGAGACACACTGCGGGTGCTAAGGTC
CGCAGTGGAAAGGGAAACAGCCCAGACCGCCAACTAAGGTCCCAAAGTCATAGCTAAGTG
GGAAACGAAGTGGGAAGGCCCAGACAGCCAGGAGGTTGGCTTAGAAGCAGCCACCCTTTA
AAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCACGTAAGATTTAACGGGGCTAAG
CTATGCACTGAAGTTGCGGAATATATTTAGTATATTGGTAGGGGAGCGTTCTGTAAGCCG
ATGAAGGTGAATTGAGAAGTTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAA
CGTAAAATAAGTGAGATTCTTATTGGCCGAAAACCCAAGGGTTCCTACGCAATGTTAATC
AACGTAGGGTAAGCCGGCCCCTAAGGCGTAGCTGAAGAGTGAAGTCGATGGGAAACAGGT
TAATATTCCTGTGCTGCTTATATGAACGAAGGAGGGACGGAGAAGGTTAGGTAGGCCTGG
CGAATGGTTGTCCAGGTGAAAGTATGTAGGTAGGAATGCTAGGCAAATCCGGTGTTCTGT
TGATCTGAGATACGAGACGAAGTTAAACTTGTTTGACGAAGCTATTGATACCATGCTTCC
AGGAAAAGCTTCTAAGTATATTGTATAAGTGACCGTACTGTAAACCGACACTGGTGGGTA
GGTAGAGAATACTAAGGCTATGAGATAACTCTGGTGAAGGAACTAGGCAAAATGACACCG
TAACTTTGGAAGAAGGTGTGCCCTTGATGGTGATGAGACTTGCTCTTTGAGCTGTTGGGG
GTTGCAGATACCAGGTGGCTGCGACTGTTTATCAAAAACACAGCACTCTGCGAAATCGTA
AGATGAAGTATAGGGTGTGACGCCTGCCCGGTGCTGGAAGGTTAATTGAAGGGGTTAGCG
CAAGCGAAGCTCTGGATCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCCTAAG
GTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGATGGCCACA
CTGTCTCCACCAGAGACTCAGTGAAATTGAAATCGCTGTGAAGATGCAGTGTACCCGCGG
TTAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTTGCACTGGACTTTGAATATTTAT
GTGTAGGATAGGTGGGAGACCATGAAGCAGCTACGCCAGTAGTTGTGGAGTCGTCCTTGA
AATACCACCCTTGAATATTTGAAGTTCTAACTCAGGAGAGATTCGAGGACAGTGTATGGT
GGGTAGTTTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGTACGAAGGTGCACT
CGGTACGGTCGGAAATCGTGCCAAGAGTATAAAGGCAAAAGTGCGCTTGACTGCGAGAGT
GACGGCTCGAGCAGGTACGAAAGTAGGTCTTAGTGATCCGGTGGTCCCGAATGGAAGGGT
CATCGCTCAACGGATAAAAGGTACTCCGGGGATAACAGGCTAATTCCTCCCAAGAGTTCA
TATCGACGGAGGAGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGG
TCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTCAGAACGTCGT
GAGACAGTTCGGTCCCTATCTGCCGTGGGCGTTAGAGATTTGAGAAGAGTTGCTCCTAGT
ACGAGAGGACCGGAGTGAACGAACCACTGGCGTTCCGGTTGTTTCGCCAGAAGCATTGCC
GGGTAGCTACGTTTGGACGGGATAAACGCTGAAAGCATCTAAGCGTGAAGCCTCCTTCAA
GATTAGATCTCTCTGATGAAAATCAGTAAGGAACGTTGGAGACTACGACGTTGATAGGCT
GGGTGTGGAAGTACAGCAATGTATGAAGCTTACCAGTACTAATGATCCGAGAGACTTAAG
TCTATTTCTATGCTGAATTGTTAAATATCTTTATAACCCAAAACACAGTTTTGGCGATGA
TAGCTTGTAGGAACCACCTGATCCCATTCCGAACTCAGAAGTGAAACTACAAAACGCCGA
TGATAGTCTGGCATTGCCCAGGTGAAAGTAGGTAATTGCCATCTTTTTCCATTCAAACTC
TTACATAATAAGCTAATATAGGGCTACTTTCCATTAAAACATTTTAATATCTTATATAAA
ATTATAATAACTCGTTGTTAATCTTAAAGTCACTTAATAATGGTTTTATTAAATAGTGTA
TTTATCTAAACCTTGTTCGATTATCTCTCAAATTGAATATCTATCTTATTTTAGAATAAT
CTATAAAAATCTAAATTTATATATCAAAATAATAAATTTTATTGTATAAAGGAAATATAA
ATTAGTTTGTATTCTTCTTTACTGCAAAAAAATAAACAACAAGGAATAGATATAATGAAG
ATATTATGTATTTTATATGATGATCCTAAAACTGGAATGCCAAAAGATTATCCATTAGCT
CAAATACCAAAATTAAGCAATTATCCTGACGGCTCATCCTTGCCTACTCCTCAAGCAATA
GATTTTAGACCGGGTGAATTGCTTGGTTGTGTTTCTGGTGAGCTGGGTCTGCGTAGTTTT
TAGAAGAACTAGGACATGAACTTGTAGTTACATCGGATAAGGATGGTGATGGTTGTAAAG
CAGAGCAAGAGTTGATTGATGCTGATATCGTTATATCTCAACCATTTTGGCCATTTTATT
TAACAAAAGAAAGAATACAAAAAGCTAAAAAACTTAAGCTAGCAATTATAGCTAGTATTG
GTTTTGATCATGTTGATTTAGATGCAGCTAAAGAGCATAAGATTGATGTTGTTGAAGTAA
CGTATTCTAACTCAATTTCAGTATCTGAGCATATTGTTATGATGATTTTATCTATAGTTA
GAGATTATTTGACCCAACATGAAATAGCTAAGTCAGGTGGTTGGAATATTGCAGATGCAG
TAAAAAGATCTTATGATCTTGAGGGTATGAACGTTGGGACAGTTGCAGCAGGTAGAATAG
GACTTTCTGTATTAAGAAAATTAAAACCGTTTAATACAAAACTTCATTATTTTGATAAAT
ATAGATTACCAAAGAATGTAGAGCAAGAGCTCAATTTAACTTATAGTTAATCCGAAAGAT
ATTTGTAGAAAAAGATATTTGTAGAAATGTTATAATGTCTAATAAAAATGCCATCATATA
GCCAAGATTTTAGAGACATTGTAATTAATAAATATGAAGAAGGTATGACGGAGTTCGAGC
TGAGTAAGTTTTTTAACATAGATAAGCGTACAGTTGTTTCATGGATAGAGCTTTATAAAA
GAACCGGAGATTATAGTTCAAGGCAAGGAGTTGGTTGTGGCAGAGTCGCTAGCTTTACCG
ATAAAACATTGATTGAACAGTATTTGATAGATCATCCAGATGCAAGTACATTAGATATAA
AAGAAGCATTAGCCCCTGATATTCCAAGAAGTACATTTTATGATTGTCTTAATATACTTG
GTTTTAGTTTTAAAAAAAGACTCCAAAATATAAGCAAAGAAAAGAACATGAAAGGTTGGA
GTATATAGAAAAACTAAAAGAAATAGCTCAAAACTTGTTATTTTATATAGATGAGATGGG
GTGTGACAATAAGCTTTCTATCCTAAGAGGATGGTCACTAATTGGTGAGCCTAGTTATGG
CGAGGTTTTAGCATATCAAACACAAAGAAGAAGTATTGTTGCTGGATATAATTATGCAGA
TAAAAAGATTATAGCTCCATTAGAGTACAGCGGATATACCAATACTGAAATTTTTAATCA
ATGGTTTGAGGAACACTTATGCCCATCATTAAAACCTAAAACTACTATAGTAATGGATAA
TGCTAGTTTCCATAAATCCTCTAAGCTGATTGAAATAGCCAATAAATTTGATGTACAAAT
ATTATATCTACCTCCGTACTCTCCAGATTTAAATCCTATTGAAAAGGTTTGGGCTAACTT
TAAAAAAATATTTAGAAAAGTGAATAATAGTTTTGAAAAATTTTGTGATGCTATCTCTTA
TGTGTTTAACAAAATACTCTCGGATTAACTATATATACTCTTGAATGCCTTTTAATAATG
CTGAAAGAGCAGAGTTTTCGCCACGGTCTGTAATTCTATAGTCTGTATTGCCAAAGAATC
TTCCCTTAAGCTCGACATAAGTTTCACCATTAGATTTACCATAATCTATAGCTGATACAT
GAATCGGAGATTTAATCTGTTTATAAGCCTGTATTAGCTCTTCATCTGTGATACCTTTTC
TACGCTCATGATAAATATCTTTTATTTGCTGAGCTATAGCAGCCTTTTCTTTGTCATCAC
AAATATAACCATTTTCTTAGATAATTTTCTTAGCATGGTTACCACCTGATAATGGACCAA
AAATAAAGCTAATTTCATTACCGACAGATTCTGGATGGAATGGCTGATATGCAATAGGAT
TTTTTAGTATGGCATTTGTATGTCCACCAGAAGTATGCCTTGCTGAGTTTAGACCAGTAA
TAGGGTGATGTGGCTGTCTTGATAACATTCTTTTGCCGATAAAATCAGAAATAGTTTTAA
AATGTGCAATATTAACATCATTGTAGTAATGATAGTCTTTTTGCTTACCAAAAAGATTTA
TAAACATCACACATTGCTCTAAAGGGGCATTACCGGCTCTCTCACCAAATCCATTGATAC
AGCCCTCTACTTGTCGTGCTGGACCATCAAAAACAGCATTCATAGAGTTTTCTAAAGCTA
ATCCCAAATCATTATGACAATGTGCTGACCAGATTATATTTCTATCAGGGAATTCTTTTT
TGATGATTTCAGCATGTTTAGCCATATTTTTGACAAAATAATTATCATTTTCACGCTCGC
ATGCTCCGCCAATAGTGTCAGGACAGTTAATAACTTTAACCCCAGCAGCTACAGCAGCTC
TAAAAATATTAGTAACATAATCAAAAGTATCGCCTAGCCTTGAATATCCTTCGGCACTAA
ACTCAACCTCAAAGCCCTCATCACTAGCTAGTTTAACTAATTCATAAACATTTTTAATAT
TCTGCTCATTATCATTTTTACTACCTAGACTTGCTTGAGCTAAATTTGGATCTACTGGTA
AATACATATGCACTCTAGCTTTACCTATTGCTAATGATGGGCGTAAGGCATCCATAGTTA
TTTCAACTTGGTTTTTTCTTAACTGACATAGTCCTAATCATATTAGAGTTTCTCTCAGCC
ATCCTCTTTGAGATAGTATTTACTATTTCAAAGTCTGTATTACTAGCAGAAGGAAAACCA
GCTTCTAATACATCAATATTTAGTTTATCAGCGAGGTCCGCGTATGCAATATTGTCTTCA
AAAGACATGCCTGCTCCTGGAGATTGTTGACCATCTCTAAGAGTCGTATCAAAAATATAA
ATTTTTTGCTTATCCATACTAGGCTCCTTATATGTATGTTAGAGCTTCTTTATAAACCTG
TCCTTGCTTTAATTTTTCAAAGACTTCTTTTATTTGGTTTGTTATTGTGTAGTCAGAACG
TTTTAACTTATTATCATCAATACTAGCTACCGGAGTGATTTCAGCAGCTGTGCCACAGAA
AAATACTTCATCAGCATTTATTAGTTCATCAACTTTAAATAAGCGTTCTGTAACTTTATA
TTCTAGGTCCTTAGCAATCTGGATTATAAGTCTTCGAGTAATACCATCTAGTATCGTGCC
TAGAGGAGTCGTTATAACTTCATTATCTTTTACAAAAAAGACATTCATTGCAGCACCTTC
AGCTACAAATCCATAAGCATCAAGAAGTAGAGATTCATGATAATGAGTACCAAGAGTTTC
CCTGGAGGCTAATATACTATTGACATAATGACCGCCAATTTTTGCATCACATACAGTTGA
GCGCGGATGAATTCTAATATATTTACTGACTTTGATATCTACTTTATCTGCAGCCATATA
TTTACCCATATCTATACAATAAATAGTAATATCAACAGGATGATCTTTCGCAGGTAAAAC
ATTGACTCCTCCTTCAGCAAAATATGCTAAAGGCCTTATATAGCATGATTTTTTACCGCT
AGCTTTGACAGTATCTAATACAGCTTGGCATAGCTCATCAAGAGTATATTTGCATGTCAT
ACCTAAGACATTCATTGAGTACATAAATCTTTGCATATGTTCTCTTAGTTTTAGTACTCC
AATTCCATTAGGCGTATCGTATGCTCTTATACCCTCAAATACAGATGAACCATAGTGTAA
AGAGTGAGTATTGATACCAACTTTTGCATCTTGATAGGAGATAATTTCTCCATTTTTCCA
AATTTTATCTATCATAATTGACCCCAGTGTTTTGTAATTGAATTTAAGTATTTTTTATAT
GAGACTGTCTTTATGTTATAGACAGAGGAGTTTTGTGCTGAGGGAGAGGAGTGCTTGAGA
AGAGTTACTTTGAGATTTGATTTTTTGATTAAACATAGCAATAGCTGAATCACCACTACT
ACTAAATGTTTCGACAGTGGAGAAATTATCTTCTCGATGTCTTCGTATCTGTATACGTGA
ACCTACTTTTTTATGCATTTTCCCTTATCTTTTTGTTTATATAATATTTTGACTAAAATA
TCATTATTTAAAATAGATATAGTTATTGTAGCTATATAATATTTTAGTGTAAACCTAGAT
TATAGCGTATTAATGATTTTTTTAAAATCAAGAGATTAAACAATAGAAATGATTATTATC
TCCGGTCTGCATATATTTTAGCTTGAGCAGCCGCTAATCTTGCGATAGGAACTCTAAAAG
GAGAGCAAGATACATAGTCAAGATCCAAATCATGACAGAAACCAACAGAATACGGTTCGC
CACCATGCTCGCCACATATACCCATCTTAGCATTAGGATTAACAGCCTTGACGCCTTCTT
TGGCTATTTGCATTAGTTTACCAACACCTTTAATATCTAGCCTAGCAAATGGATCAAAGC
TTAGTATGCCTTTTTCAAGATAGTCTTTAATAAACTTATTAGCATCATCTCTACTGAAAC
CAAAAGTCATCTGAGTCAAATCATTTGTACCAAATGAGAAAAATTCACTACCAGCAGCTG
CAAGCATACCAGCGCCGATAGCACCACGTGGAGTTTCAAGCATTACCCCAACTTTGTAAT
CAATATCAATTTTTTCACGCTTTAGGATAGTGTCTGCAACTTCTCTGACAATACCACTTA
AGAGTTTAAACTCACCAAGAGTACTAACTAGAGGAATCATAAGCTCTGGCTTAACTTCTA
TACCCATACGTTTACTTGATATCGCTGCATAGATGATAGCTTTAGTTTGCATCTCAATGA
TTTCAGGATACGTTACAGCAAGTCTACAGCCGCGATGACCCATCATAGGGTTTACTTCGC
TAAGTGCTTCAATACGTGCTTCTAGTTCACTATAGCTAATATTAAACTCACGAGCTAGAT
CATCAATCTCATCCACCTCGTGAGGTAAAAACTCATGTAAAGGCGGATCGATAAATCTAA
TCGTTACAGCTAGATTATCCATCGCTTCAAAAAGCTCTTCAAAATCTTGTTGCTGTACAG
GAAGTAGTTTATCTAAAGCTCTTTGTCTTTCTTTTTTATCTTTAGCTAGGATCATCTGTC
TAACATAAGAGATACGATCTTCCTCAAAGAACATATGCTCAGTACGACATAAACCAATAC
CTTCCGCGCCAAATGCTCTTGCAATTGAGGCATCTTTATAAGTATCGGCATTACATCTAA
CACGAAGTTTACGTACACTATCGACGAACTTCATAAAGTCTTCAAAATCTTTAGTAACTT
CAGGATCTACAGTTTTAATAATACCTCTATAGACAGTACCTTTGGTACCATCAAGAGATA
AATAATCACCTTCTGTAAATACTTGGCCCTTCTCAAATGTGATAGTTTTCTTTTCTTCAT
CAATTCTTGCTGATTCTAAACCAGACACACAACATTTACCCATACCACGAGCAACAACAG
CAGCATGAGATGTCATACCACCACGTAGAGTTAAGATACCATTACAAGCATTCATCCCCG
CGATATCTTCAGGAGAGGTTTCAATCCTAACAAGAATAGTTTTTTCTTCACCACGTGCTT
TTGCTGCAAGTAGTGATTCAACATCAAAGTATATTCTACCACTAGCAGCGCCTGGAGACG
CACCTAGAGCTGAACCAAGAGGGCGTTTAGAAGCTAGAGCTTTCTCATCAAATTTAGGAT
GTAGTAGTTGCTCTAATAAATGAGGCTCTACCATCATTACAGCTTCTTCATTTGTGATTA
AGTCTTCTTTAGCCATATCAACTGCTATTTTCAAAGCTGCTTTTGCAGTTCTTTTACCAT
TTCTTGTTTGTAGCATGAAAAGCTTACCATCTTCGATAGTAAACTCCATATCTTGCATGT
CTTTGTAAACTTTTTCTAAGTTTTTAGCAATCTTCACAAAGTCATTAAATACTTCTGGCA
TTTTATCTTTTAAAGTTGAGATATGCGCTGGGGTTCTGATACCAGCTACAACATCTTCTC
CCTGCGCATTAATTAGATATTCACCAAAAAGCTCATTTTCACCAGTCGATGGGTTTCTAG
TAAATGCTACTCCTGTCCCAGAATTATTACCAGAGTTACCATAGACCATTTCTTGGACAT
TAACAGCTGTACCCCAGTTATTTGAAATATTATTTATCTCTCTATAGATGATTGCTCTCT
CGGCATTCCATGATTTAAAAACGGCTTCTACAGCAGCCAGAAGTTGCTCAATTGGATCAG
TAGGGAAGTCCTTACCGACTAAATCTTTATAAATTTTCTTATATTCTGTAACTATATCTT
TATAATCTTGAGCTGGTAAATCACAATCATTTTTTACCTTTCTTTTAGCTTTTTTATCTT
CTAAAACTTTATCAAAAGGTTTCTTCTCACAATCCATAACAACATCTGCAAACATCATTA
TGAATCTTCTATAGCTATCATAAACAAATTGCTCATTGTTTGTCTTTGCTACCATAGCTT
GAGCAACAGTATCATTTAGTCCTAAATTAAGGACAGTATCCATCATCCCAGGCATAGAAA
CTCTTGCACCAGAGCGTACTGATACTAGTAGAGGATTATTGCCACCACCAAAAGTTTTAC
CAGTTCTTTTCTCTAAATCTTTGATATGAGCAAATATTTGTTCTTTAACTTCATTACTTA
ACTTTTGGCGATCATCATAATACTTAAGACATGCTTCTGTAGTTACGGTAAATCCATCTG
GCACAGGTAGACCACTATTTAGCATTTCACTAAGATTTGCACCTTTTCCACCTAGTAAAT
CACGCATAGACTTATTACCTTCGCTAAAGGCATAGACAAACTTCGACATAAAAACTCCTC
TCAAGTTTTTTTATAAATTAATTTGAAAACAGTACACTCTCAAGCGTACTTGAGTCTTAT
CCTATCACATTTTGATAGATATATTAAAGAGTTTTATTTTATTATTTCTATATAAAATAG
ATTGAGAATAATGCTTAAATATAAAAGCTTTCTTCGTTTGTTAGTGTTGGAGCTATATTT
TAAAGAGGTCTTTCTTTTGATTTTATAAAATAATTTATAGAATTAGTATTTAAATATGTT
TTATTTTTATAATTTTCCATATTGGTTAAATATTTATTGAGTGAATAGTATTCAGTTATA
TTTACTGCTTTTTTAGGCTTGCTAAAAGATTATCAGCTTTAGATTCGATAATATTATTGA
TCTGTGACTGGGATAAGCTAAAAGTTTTATCAGAGTTAAATTCTATAGAATCATCATTTT
CAGGAAATATAGCAGTTAATACACCCTTATCATTCTTATATAATTATCGCCTGATTCGCT
TTTATTACGACATTTCCAATAGCTAAGGTGGCAATATTATTTTTATTAGGTTTATCAATT
ATAGATCCATAGCTTGATAAAGAGTACAGACTGAAGATCATTAATAAGAATAGTATTCTC
ATTTTAAAATACCTCAAATTAATTATTGTAATACGTTATTGTACCAATCGCATAAATAAA
TCTTATAATTTTTACGCCAAATATTTCCAACTATTCATAATCTGTGAGAGTAGAATTAGT
AGCTTTAAAACTAATAAAAGTTGAAAGCCAACATAATCTTAATTTTTGTAAGTTTTAAGA
AGGCATATTTAAAGCTGTATATTCAAATTAGAATTTTAAGAGCATTTTTTACTACTACAA
CTAGAGCAGCCAGTAAGATTTGCCACGAAATTTATTTTTGTTGATAAATATTTCATCAAA
AAAACTATCCCGATGATGTATGCCATAGCTAGAGCAATACAAATGATAGAACTACTAGGG
TGCTCAGCAATATTGAGTAATTGGTAAATAACAACAGCAGCTACATAAGCGATAGAAACA
CTCCAAAGAACTGACAAAATTGCCCAGCCTCGTGTTGATTCTCTTACCATTGCTCCAACC
ACAGAAATACAAGGTATATATAATAAAACAAAGAGTAGATAAGCAAAAGCTGCTGATAGT
GAACCGAATTTTGTTACCATATTACCCATAGCCCCATTATCCATATTAGCATCAGCTTTG
CTGGCTTCTATTGGATTCATAAGAGTTGCTAGATCTATACCTTTGATATTATCAATAGTT
GTATTCCAAGATTCTTTGACACTATCTATTAGACTAAACTTATCAGGAATGACATTATCT
TCACCTTGAGTATAAATTGTATTTAATGTTCCGACTACAACCTCTTTAGCAAGTGTACCG
GTTATTAGACCGACAGTTGCTGGCCAGTTATCATCATTTATGCCCATAGGATTTAGTATT
GGTGTAATTTTTTTACCGGCATATTCAAGTGCTGTGGTTTTATTACCAATATATATACTA
TTTAGACTACCAACAATTATAGCTACAGGAACAATAACTTTACCAGCTCTAATTAAGAAA
GACTTGAGTCTATTCCAGCTATAGATCATAACTGTTTTAAATGATGGCGTATGATAGTTT
GGAATATCTAAAATAAATGGAGCAGTATCACCCTTTAAAAAAGTGAACTTAATGATATAA
CCCGTAATTATAGCTCCAAATATACCAGCTAAATATAGCAAGAATATTACAGTAGCACCA
TTATGAGGAAAAAATGCACTAGCAAATACTGAAAATATCGCAAGTCTTGCACCACAAGAC
ATAAATGGTGACATCATCAAAGTCATCAGACGATCTTTGCGTGTTTCTAAAGTTCTAGCA
GCCATAATTGAAGCGACATTGCAACCAAAGCCAACAATTAACGGTACAAAAGCTTTGCCG
GATAAACCAATAGATTGCATAAATCTATCCATAACAAAAGCAGCTCGAGACATATAGCCA
GAGTCTTCGAGTATTGATAAAAATATAAATAAAAAACCAATCTGAGGAATAAATCCTAGT
ACAGTATTGATACCTGTACCTAAACCATTTGCGAGAATACCTGTGACAGCTGTCGGTAGA
CCAAGCATATTTGAGTAATATGCCAAACCATCAACAAAAATAGCATGAGATAAATCATCA
AACATTGGTTGTATTGCGCCACCTAGTGTAATTGAAAATAAAAACATCAAGTACATCATC
AATAAAAATATCGGCACACCTAAATATTTATTCATGCAAAGTGCATCGAGTGCTTTGGTA
AAGTTAAAGCGAGAGACTTTTTTATTTTCAGTAATGCTAGCTACAATTTCAGCGACAGCA
TTATATCTGACTTTAGCAATATCAATGTCAGTGTTTGATTGTAAAAGAGACTTTAAGCTA
TCTAGTTGACTAGCTGTGATTTCTTGTGAGAGTTGTAGCTCTCTACCATCAATTAGCTCA
ATAGCAAGCCACAGACTACCAATATCATCATTTTTCTGTGTGGTTATTTGTTGTGCTAAC
TCAGTGACTATCCTTGGATAGTAACTTTTTAAGTCAAAACTAGAAATTTTTTGATGATCT
ACTAGAGTTTCTTTTAACTCTTTAATACCAATACCTTTTGCTGCAACGACTGGTAATACT
TTACAACCTAATGTTTTCTCTAATCTGTCATAGTGAATAATGAGTCCTTTTTTATTGGCA
ACATCAATCATATTAACCACTAATATGACTGGTAGCCCAAGCTCAATAAGTTGCATAGTT
AGATAAAGACTTCTATTCAAATTAGAAGCATCTACAACATTAATAATAGCATTAGGTTTC
TCTTTAACTACAAAAGAATAGGCTATTTGTTCATCAATAGAATTTGCATCTGATACTGAT
AGTGAATAAATTCCTGGTATATCAACAACTTCAATTTTTTTATCTTTTGAGTTAAAAAAA
CCAGTTTTTTTATCAACTGTAACTCCAGACCAGTTACCAACTTTTTGGTTAAGTCCTGTT
AAAGCATTAAAGATTGTTGTTTTACCGCAGTTTGGATTGCCAACTAGAGCATATTTCATA
ATCAGTTTTCAGGAGTTTATAGTATAGATTCTCTAAAGAAAGTAGGGATATTATATCAAA
ATGATTATTAATTGGTAGATGTAATAATGATAATTATTATCAATGAATTAGCTGTGCTAT
GGGTATTATGATGATTATAAATCATATCACATTGAGCATAGGCTTTTATTATTCCTGAGG
ATATCATTGCTTTAACACCTTTTTGATATTGTGGCAAAGTTGCTGTTATTACTGAGCAAT
CATCTGAAAAAGAGTTTTCAGCCTTACATACCTTGATTTGAGTTCCTGTAAATGAAATAT
AGAGCTTTTGGCTATTTTTAAAGAATTTATCATTATTGCGATAATAGGTTAATGTAGCGG
TTGTAGTTTTATCTTTTATTGTATCAAAACTAAATGCTTGGATATCATTATTCCAATCAT
TGATAAATGTTTGATACTTACCACTATCAATCACACATTGAATATATTCACCATATCTTG
GATTGGCTTTTATGTCAGCTATTTGTTGTTCTTGGTGTTGTTTATAGTTAATCCGAGAGT
ATTTTGTTAAACACATAAGAGATAGCATCACAAAATTTTTCAAAACTATTATTCACTTTT
CTAAATATTTTTTTAAAGTTAGCCCAAACCTTTTCAATAGGATTTAAATCTGGAGAGTAC
GGAGGTAGATATAATATTTGTACATCAAATTTATTGGCTATTTCAATCAGCTTAGAGGAT
TTATGGAAACTAGCATTATCCATTACTATAGTAGTTTTAGGTTTTAATGATGGGCATAAG
TGTTCCTCAAACCATTGATTAAAAATTTCAGTATTGGTATATCCGCTGTACTCTAATGGA
GCTATAATCTTTTTATCTGCATAATTATATCCAGCAACAATACTTCTTCTTTGTGTTTGA
TATGCTAAAACCTCGCCATAGCTAGGCTCACCAATTAGTGACCATCCTCTTAGGATAGAA
AGCTTATTGTCACACCCCATCTCATCTATATAAAATAACAAGTTTTGAGCTATTTCTTTT
AGTTTTTCTATATACTCCAACCTTTCATGTTCTTTTCTTTGCTTATATTTTGGAGTCTTT
TTTTAAAACTAAAACCAAGTATATTAAGACAATCATAAAATGTACTTCTTGGAATATCAG
GGGCTAATGCTTCTTTTATATCTAATGTACTTGCATCTGGATGATCTATCAAATACTGTT
CAATCAATGTTTTATCGGTAAAGCTAGCGACTCTGCCACAACCAACTCCTTGCCTTGAAC
TATAATCTCCGGTTCTTTTATAAAGCTCTATCCATGAAACAACTGTACGCTTATCTATGT
TAAAAAACTTACTCAGCTCGAACTCCGTCATACCTTCTTCATATTTATTAATTACAATGT
CTCTAAAATCTTGGCTATATGATGGCATTTTTATTAGACATTATAACATTTCTACAAATA
TCTTTCGGATTAACTATATCTATGAGTAACCTAGTATTAGTTTAGAGAATGTCAGCATTT
AGTAGGTAGAAAATAAAATAAAGTAGTATTAAGATTAATTCAACAAATTACACAAATGAG
AAAATCTTAATTTGAAAAAGAATAATAACTCATTGGATTTACCTAAGTATTTATAGTTAT
ACTGAATAAGGGGAGCGATTTTAGTCATTAAAACTCCTTCAAGATCTGAAAAAATCTACT
AATTTCAGCAGGTCTAGTTTTAAGAATAAAATCATTTATTGTATATTCAAGTTCTTTTTG
ATTACTCCTGGTTATTGCCTTATTTCGAAATTGACTCATCATCATATGTGAAGTAACTGT
TGACGGTCTTCCAAGACGTATTTTATGACCTAATTCTAAGATTCTTGAATTTGCTTTAAC
AGGACTAAAACGCATTGATTCTAAAAGAAGAAATAAACTAGACATAGATTTTTTTTAAAT
AATTCTTGAAAATTGTGCGAGACCTCTGTCATAAATTTCCCATATTTTAAAGCATCCCAA
AAACTCACAATATAGTCGTGATCTATCTTACTATAACACCGCTTTCCATTAAATAGTCCT
GTACCAAAATTACAGATATGAAAATCATTTTCTATTAACACACAAACATAAAATAAAATT
TGTATTAGTCCAGGGTAATCTTTTTGATCCCCACTAAGTGATTTATATTCTTGAAAATCA
TTTATGCCTTTTGAAGCAATACCAATAATTTTGTTTTCATGCTTAGATAATAATAGAGAT
TTTGAAGCGCGATTTCCAATAAAATAATTCCAAATTTGAGCATAGATAACTTCAGCAATT
GCATTTTCAACTTCATTATTATTAAGAGATTTAACAAAATAGTTTACTTTTTCATTCTTT
TTATCTTTATAGCGAGTCACTACATGTGCAGATGCAGTAGAATTTCCTATTTTGGAAATA
TTTTGAACAGGTAAGAAAACATCAAAAATAGGATTATTTATAATAGATAAATTGTTTTCT
ATGGGAGTTTGATTCTTAGTTTGTTGGAAAACATTATTAACATAAGTCCACAAAGAACTT
GGATGCTTATTTCCTCCCCTTAGTAATGAAGCATCAACTTTTATTTCTGCTTTAGTGATT
GTTTTTTTATATTGTAATTTAAGGTTTTAAAGAACCTCTTCTAGTTCTCGGGACTTTTCT
AAATAATGTTTGATTAATTGATTCATTATGGTTAAGTTAGGGCAATGTAAGATATAATCT
TTTAATAGAGCGGCTCTTCGAATGCCGGTATCCCTATGCCGGTGATGTATACTTAAAAAG
TGGCTCTTATATGGATGATTGATATATATTTCTATTGACTGTAGAAAATCTTTTCAAAAT
TTTTCATAGACTAGCATACAGTTAAGACTTTGAGGTCAATACATGATATCAATAAATAAT
TTTCTCTACAAGCTAGTGTTATAGCGACTTATAATTATAAACCTTATATCAACACTTTGA
TTTAGCTATAATAGATATATCAAGGTAATTTAGCGCATCTTATACAAGAAGAATTTTGCT
TAAGAAACTTCATCTATAGACTAGATTTTCAACAAATTATATATTTTTCTTCGGTTATTA
GGTTCTATGAATAAAAAATATTTTAGTTAAATAAGTAAATCAACTCTAAAGCTGTAGAGA
AAAATCTTATCAAATCCAGAAAACATTCTTATAAAATTAAGCTCTAGTGAGACGTTTTAT
TTAAACCAAAATAATTCTTCATAACAAGTAAAGAAATCAGTTCTTCTCTTTGTTTATTTT
TGAATTGATTTACATATTCGTTTGCATTTTTAATTATTTTAAGAGCTTTTTCGGGGTGAT
TGTTATAATAGTCTATTTTCTCTTGAAGATCAGAATAATCATCTTTTAATAATACATAGT
GATGATTTGGTATTAGGGTACCTTCCATAAACCACGTTTCATATTTTGGTTTATTCATAA
AACAAAGGGAATTTGAGTTCATGATCCATTTAAGATTAGTAGCAACATCGTAGCCCTCTA
TACTAACGATATATTTATATTTAAGCTGGTCTTGTATGCTCAGAAAGCCTTTGTTATATG
GTTGACCAATTGATTCTTTACGCGTGTCACCAAAATTTGTATTAGGTAAGTTATAATAAT
TTTTTATGAAATATTGTCGAGTGGGTTGATGACAAGCTCCTCTAAAGACTGCCATATTAA
GTTTATCTTCAAATTTTTGATTGTCTTCAAAAAGGCTAAAGTGTCGTAGTTTATCAAGCT
TTAGAATAATAGAGTTTTGATTATCATCAGCTATTGGTCTACTTTTTACAAAAGTTGGTT
GTTGGGGTATTTTAGTAAGATCATAAAAAGCTGTAGCAAAACTATCGGTTTTATTAAAGT
ATACTAAAAACTCTTTAAAATCATAAAAGTATGAGGAATTAATAGATTTTCTGACAAGAC
TATGGTCAATAATGTCAAATACTGGAGTGTTTCTTTTAAAATTTTTCCAATTAGAGCTAT
TTTGTAGCATAAATGGTTTAGATAGCCTATTATAGTAATTAACTCTATACTCGATATATT
CTTTGTCAAATTTTGTGATGCTTTTCAGTTTATGTTCCAAACTTAGCTCAAAAAACTTTT
TAGGTATAATAGTTCTGCTAATATTTTTTATGTAATACTTTAACTTTTTCATATTTTATA
TGTACCTAATATTTAAAAAATAAAGACATTCTTATTTTAGCATGATGATTAAGCTTAGTG
TATTATAGGAACTTGATAATACTATTTTATAGATAGCAAGTCATAGAACTTAAGACTAAA
CTTTTACTTCATCTAGCAATTGAGTAGAATATCTATAATTAATAAGAATGATACAGAAAA
ATGCAAAAAAATTCTCTAGTAATATTTAAATCTAAACCAGCAAAGGTTATTAATCTCTTA
GATAAAAAAATTGAGATTGAGACTCTCGATGGTAAAAATATTAAGTTACCCGCAAAGAGT
GTTCAATTACTTGTAGAGTCAGAAAAGTATTTTGAACTTGAAAGTTTAAAAGAGCTAGAA
ATAGCTGAACTTGAAATGACTTGGGAATTATTACAAGAGCAACAACAAACATCTGTTGAA
GAACTATGTGAGTTACTTTTTGAATCTATAGGGGTAAATCAGGCTTATACCGTGTGGCTT
TTAGTTTCAGAAGGAGAGTATTTTAGCTTTAATGATGATTTTAGTATCAATATTCATTCA
CAAGAGCAAAAAAATGCAATAGTTAGAGACAAACAAGAGAAACTTAAAAAAGAGCAAGAA
CTTAATGATTTCATAGAGCGTTTAAACAATAAAACTTTTAATGAAGATGATAGGAAATTT
CTTAAGGAAATAGAAGCTCTAGCAACACTTAAAACTAATAAGTGTCGTTTTTTTAAGTAC
TTAAACATGGAGGAGTCTGAGAATAGTGCGTATAAATTGCTTTTGGATATTGGCTATTGT
GATGAGTTTTTTAACCCTTATTTATACAGGTATGGTGCTGAGTTAGAACATAATTCTGCA
GAGTTTAACTACAATTCTAAATCAGATAACCAGAGAGTAGATCTGACACATTTAAAGGCT
TATGCTATAGATGATGAAGGTAGTAATGATCCTGATGATGCAATTAGTTGGGATAGCCAA
AAAAATAAAATGTGGGTACATATCTCAGATCCTTCTTCTAGTATTAGTTTTGGTGATGAG
GTTGATCTTCAAGCTAGAGCACGAGGCTCAAATTTATATGTGCCGGAACAGATAGTCATG
ATGTTACCTCCTCAAGCAACAGCAAAATTAGGCTTAGGCTTACAGGAGGTATCTCCTGCA
GTATCTGTAGGATTTAGGATTGATGAGCAAGGTGATATCCATGATATTGAAATATGCTTT
AGTAATATAAAAGTTACACGATATTCTTATGAATTTGTTGAAGAAAATATGCATACTTTA
GAGCTTGGCGATATAGTAAGTTATGCAAAATATTTCACTGATAAGCGTTTATCTAAAGGT
GCAGTTGAGCTTGATTTCCCAGAGATAAAGATATCATTAGATGCTAATAAAAATGTTAAA
TTAACTGATTTACCACGTTTAAACTCAAGGACACTTGTACGAGATACAATGCTAATGGCT
GGTGTTGCAGTAGGACAGTTTTGTATTAAAAATAATATTAGTGTATCCTTTTCTACACAG
CCTGAACATGATCTTGGACAAGATGGTTTAGAGAATATCGATTCAATAGCTGATATGTTT
GCAACACGCAAAAAACTCCAAAGAGGCAGATATTCTACACAACCTAGTATGCATGCAGGG
ATGGGATTAGAAGCCTATGTACAAGTGACTAGTCCATTGAGAAGATACCTTGATTTGATT
GTACACTATCAGTTACGTAATTTTCTGCAGCATAAAGAGATGATAAGTGCTCAAGAGATT
GATAACATAATTGCTCAAGTTGATATTCCTATAAAATCAAATAGACAAACTGAGCGTTTC
TCAAATTCACACTGGAAGTTGGTTTACCTAATCCAAAATCCTGACCTGGAATTTCAAGCG
ACAGTTATTGAGAAATTAGAAAAAAGTAGATTAATGGTTTCTATTGCAGCTTTAGCGATG
ACTAAAAAACTTTCTGTCAGCGGTAAGTATGATTTAAATGATCAAATAAAGTTACAAAAC
ACCTCAGTAAACCTTGTTACACAAGAGGCTTTCTTTAGAGTTATTGAATAAAATTAACCA
TATTCTAACAATAAATTAACAGTTTTATCCACAGGGCGTGAAAAATATTTATAAACAATA
TATTTCTCGATATCTAGATGCTCAAAGTATTGTAAATAAAGGCTTTTATAGTGGTGATCA
ATCTCTAATAAACTAATAAACTAACACTTTTCACAAAAATCTCATATAGATATAAACAAA
CTTATCCACAATAGATGTTGATAATATTTTTCATGGCTTGAATTACTTAGAGTACAATGC
TTTCGGAGGTGTTTAAATTTTTAGATATTAATAAATTTCTTAAACTAATGTATCATTCTA
CCTAATATTAGTAGATTTAGAAATTTTATGAATTACGAACTTATGGAGCCAGCAAAGCAG
GCTAAGTTTTGTGTTATATGGCTGCATGGCCTTGGTGCTGATGGACATGATTTTGTAGAT
ATTGTTAACTATTTTGATGTTTCATTGGATGAAATCAGATTTATTTTTCCTCATGCTGAT
ATTATACCTGTGACTATAAACATGGGGATGCAGATGCGTGCTTGGTATGATATCAAGTCA
CTTGATGCAAATAGCCTAAATAGAGTAGTTGATGTTGAAGGTATAAATAGTTCAATAGCA
AAAGTTAATAAATTAATAGATAGTCAAGTCAATCAAGGTATTGCTAGTGAAAATATTATC
TTAGCGGGTTTTTCACAAGGTGGTGTAATTGCTACCTATACGGCTATTACATCTCAAATG
AAGCTTGGTGGTATTATGGCTTTATCTACATATTTGCCAGCATGGGATAATTTTAAAGGT
AAAATTACATCTATAAATAAAGGATTACCTATACTAGTTTGCCATGGTACGGATGATCAG
GTATTACCTGAAGTTCTTGGTCATGATTTATCAGATAAACTAAAAGTTAGCGGTTTTGCT
AATGAATATAAACACTACGTAGGTATGCAGCATTCTGTATGTATGGAAGAAATAAAAGAT
ATCTCAAACTTTATTGCAAAGACATTTAAAATATGAAACAAATAACTATAGCTAGTCGAG
AAAGTAAACTAGCATTATGGCAGACAAATTTTGTCAAAAATCGTATCCAATCAGAGCTAA
ACATTCCTTGTGAAATAAGTACTATGAAAACACAGGGAGATATTATTTTGGATCAACCAC
TAAACAAAATTGGTGGTAAAGCACTATTTATGAAAGAGCTAGAAGTAGCAATGCTTAGTA
ATAAGGCTGATATTGCTGTACATTCTCTTAAAGATGTTCCTTACCAATTACCGCAAGGTT
TTTGTTTAGCAGGTTTTATGCCAAGAGAAGATCCTCGAGATGCTTTTGTATCAAATAAAT
ATAATTCTATTGATGATTTACCTAAAGGAGCTGTTGTTGGAACATCTAGTCTACGGCGAA
AAGCGCAGCTTTTGCACTATAGAGATGATCTTGAGATTAGAGATTTAAGAGGCAATATTC
AAACTAGACTGTCTAAGCTTGATAATGGTGATTATGATGCGATTATTTTAGCTAGTGCTG
GACTTATTCGCTTAGAGTTAGTTGAGAGAATAACTCAGTTTATCCCTGTAGAAATATCTT
TACCAGCGGTAGGTCAAGGTATAGTAGTTATAGAGGCATTAGAGAGAGATAATGACCTTT
TAGAAAAAATACAAAAATTAAATTGTAGAGAAAGTTCTCG
BioPerl-1.007002/t/data/test.swiss000444000766000024       543513155576321 16750 0ustar00cjfieldsstaff000000000000ID   GCDH_CAEEL     STANDARD;      PRT;   409 AA.
AC   Q20772;
DT   01-NOV-1997 (Rel. 35, Created)
DT   01-NOV-1997 (Rel. 35, Last sequence update)
DT   16-OCT-2001 (Rel. 40, Last annotation update)
DE   PROBABLE GLUTARYL-COA DEHYDROGENASE, MITOCHONDRIAL PRECURSOR
DE   (EC 1.3.99.7) (GCD).
GN   F54D5.7.
OS   Caenorhabditis elegans.
OC   Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea;
OC   Rhabditidae; Peloderinae; Caenorhabditis.
OX   NCBI_TaxID=6239;
RN   [1]
RP   SEQUENCE FROM N.A.
RC   STRAIN=BRISTOL N2;
RA   Coles L.;
RL   Submitted (OCT-1995) to the EMBL/GenBank/DDBJ databases.
CC   -!- CATALYTIC ACTIVITY: GLUTARYL-COA + ACCEPTOR = CROTONOYL-COA +
CC       CO(2) + REDUCED ACCEPTOR.
CC   -!- COFACTOR: FAD (BY SIMILARITY).
CC   -!- PATHWAY: DEGRADATIVE PATHWAY OF L-LYSINE, L-HYDROXYLYSINE,
CC       AND L-TRYPTOPHAN METABOLISM.
CC   -!- SUBCELLULAR LOCATION: MITOCHONDRIAL MATRIX (POTENTIAL).
CC   -!- SIMILARITY: BELONGS TO THE ACYL-COA DEHYDROGENASES FAMILY.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; Z66513; CAA91333.1; -.
DR   HSSP; Q06319; 1BUC.
DR   WormPep; F54D5.7; CE03411.
DR   InterPro; IPR001552; Acyl-CoA_dh.
DR   Pfam; PF00441; Acyl-CoA_dh; 1.
DR   Pfam; PF02770; Acyl-CoA_dh_M; 1.
DR   Pfam; PF02771; Acyl-CoA_dh_N; 1.
DR   PROSITE; PS00072; ACYL_COA_DH_1; FALSE_NEG.
DR   PROSITE; PS00073; ACYL_COA_DH_2; 1.
KW   Hypothetical protein; Oxidoreductase; Flavoprotein; FAD;
KW   Mitochondrion; Transit peptide.
FT   TRANSIT       1      ?       MITOCHONDRION (POTENTIAL).
FT   CHAIN         ?    409       PROBABLE GLUTARYL-COA DEHYDROGENASE.
FT   ACT_SITE    388    388       BASE (POTENTIAL).
SQ   SEQUENCE   409 AA;  44964 MW;  4D06241FB6768069 CRC64;
     MLTRGFTSIG KIASRGLSST FYQDAFQLSD QLTEDERSLM LSAREYCQER LLPRVTEAYR
     TEKFDPSLIP EMGSMGLLGA PYQGYGCAGT STVGYGLIAR EVERVDSGYR STMSVQTSLV
     IGPIYNYGSE DQKQKYIPDL ASGKKIGCFG LTEPNHGSNP GGMETKATWD ETTKTYKLNG
     SKTWISNSPV SDVMVVWARS ARHNNKIKGF ILERGMKGLT TPKIEGKLSL RASITGQIAM
     DDVPVPEENL LPNAEGLQGP FGCLNNARLG IAWGALGAAE ECFHLARQYT LDRQQFGRPL
     AQNQLMQLKM ADMLTEISLG LQGCLRVSRL KDEGKVQSEQ ISIIKRNSCG KALEVARKAR
     DMLGGNGIVD EYHIMRHMVN LETVNTYEGT HDVHALILGR AITGLNGFC
//
BioPerl-1.007002/t/data/test.tab000444000766000024       134413155576321 16341 0ustar00cjfieldsstaff000000000000roa1_drome	MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVVVMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDNIVIDKETGKKRGFAFVEFDDYDPVDKVVLQKQHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY
roa2_drome	MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVVVMKDPTSTSTSTSTSTSTSTSTMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVKKLFVGALKDDHDEQSIRDYFQHLLLLLLLDLLLLDLLLLDLLLFVEFDDYDPVDKVVLQKQHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY
BioPerl-1.007002/t/data/test.tigrxml000444000766000024       623213155576321 17262 0ustar00cjfieldsstaff000000000000
        
    
                chr9
                Cryptococcus neoformans
                
                
        
    
        
                
                        MSAHSGSCIPSTSCPSSTVSINGTCVTCPLDCATCSTASTCSTCPSDRPILKNGRCIAYCATDTYYDTSTGTCQACDWTCKNCVGEGSAMCSSCSDGYMLKDGVCVDALCGDAGFANGFGMCFSSFVHKSQKRYLGLLALVGVAIIAGIASWWYVRRERRKTRQATKEFGKRLDERNVNDRLSALRLEKVFGFNRVTFGRGGDRSARTTQEDGGKKNKLRELLLPSKRRSGNEEMEMKKSNFAPDKERDCYDSWRTSNFGKDNWVAPPPYVPSQGVPTPVDVKHTFNKRDSLDSIPTPSHQTFAPSSSTSSFTITRPATPPRKLQNPYLGSTIIHSMSTPSPPPHSRSLMPPPRPGMGRRESGNSFSSGSLWTPMTGMTSITKITADKERDVRRYSGRQDRQMDVERRPTDYDLL*
                        
                        
                        
                                
                        
                
        
        
                
                        MPRFYENKYPEVDQLVMVQVQSIEDMGAYVKLLEYDNIEGMILLSELSRRRIRSVQKLIRVGRNEVVVVMRVDPDKGYIDLSKRRVSAEEVVKCEEQYEKGKAVDSIITQVAKKRGVTPESLYEKIAWPLHRQYGHAYEAFKLSISEPEAVFGSLELDEETLADLRSGIARRLTPKPVKVRADIEVKCFSYAGIDAIKRALTAGEAVSTPDVPIKVRLVAPPLYVMSTTSTDKNAAIELMEKAVEVIGETVRKDKGDITIKMKPKVVSETEDAELKALMEQFEAANMDQAGDDESSEEDE*
                        
                                
                        
                        
                                
                        
                        
                                
                        
                        
                                
                        
                        
                                
                        
                        
                                
                        
                
        
    
BioPerl-1.007002/t/data/test.tseq000444000766000024      1433413155576321 16572 0ustar00cjfieldsstaff000000000000



  
  11321596
  ref|NM_002253.1|
  9606
  Homo sapiens
  Homo sapiens kinase insert domain receptor (a type III receptor tyrosine kinase) (KDR), mRNA
  5830
  ACTGAGTCCCGGGACCCCGGGAGAGCGGTCAGTGTGTGGTCGCTGCGTTTCCTCTGCCTGCGCCGGGCATCACTTGCGCGCCGCAGAAAGTCCGTCTGGCAGCCTGGATATCCTCTCCTACCGGCACCCGCAGACGCCCCTGCAGCCGCCGGTCGGCGCCCGGGCTCCCTAGCCCTGTGCGCTCAACTGTCCTGCGCTGCGGGGTGCCGCGAGTTCCACCTCCGCGCCTCCTTCTCTAGACAGGCGCTGGGAGAAAGAACCGGCTCCCGAGTTCTGGGCATTTCGCCCGGCTCGAGGTGCAGGATGCAGAGCAAGGTGCTGCTGGCCGTCGCCCTGTGGCTCTGCGTGGAGACCCGGGCCGCCTCTGTGGGTTTGCCTAGTGTTTCTCTTGATCTGCCCAGGCTCAGCATACAAAAAGACATACTTACAATTAAGGCTAATACAACTCTTCAAATTACTTGCAGGGGACAGAGGGACTTGGACTGGCTTTGGCCCAATAATCAGAGTGGCAGTGAGCAAAGGGTGGAGGTGACTGAGTGCAGCGATGGCCTCTTCTGTAAGACACTCACAATTCCAAAAGTGATCGGAAATGACACTGGAGCCTACAAGTGCTTCTACCGGGAAACTGACTTGGCCTCGGTCATTTATGTCTATGTTCAAGATTACAGATCTCCATTTATTGCTTCTGTTAGTGACCAACATGGAGTCGTGTACATTACTGAGAACAAAAACAAAACTGTGGTGATTCCATGTCTCGGGTCCATTTCAAATCTCAACGTGTCACTTTGTGCAAGATACCCAGAAAAGAGATTTGTTCCTGATGGTAACAGAATTTCCTGGGACAGCAAGAAGGGCTTTACTATTCCCAGCTACATGATCAGCTATGCTGGCATGGTCTTCTGTGAAGCAAAAATTAATGATGAAAGTTACCAGTCTATTATGTACATAGTTGTCGTTGTAGGGTATAGGATTTATGATGTGGTTCTGAGTCCGTCTCATGGAATTGAACTATCTGTTGGAGAAAAGCTTGTCTTAAATTGTACAGCAAGAACTGAACTAAATGTGGGGATTGACTTCAACTGGGAATACCCTTCTTCGAAGCATCAGCATAAGAAACTTGTAAACCGAGACCTAAAAACCCAGTCTGGGAGTGAGATGAAGAAATTTTTGAGCACCTTAACTATAGATGGTGTAACCCGGAGTGACCAAGGATTGTACACCTGTGCAGCATCCAGTGGGCTGATGACCAAGAAGAACAGCACATTTGTCAGGGTCCATGAAAAACCTTTTGTTGCTTTTGGAAGTGGCATGGAATCTCTGGTGGAAGCCACGGTGGGGGAGCGTGTCAGAATCCCTGCGAAGTACCTTGGTTACCCACCCCCAGAAATAAAATGGTATAAAAATGGAATACCCCTTGAGTCCAATCACACAATTAAAGCGGGGCATGTACTGACGATTATGGAAGTGAGTGAAAGAGACACAGGAAATTACACTGTCATCCTTACCAATCCCATTTCAAAGGAGAAGCAGAGCCATGTGGTCTCTCTGGTTGTGTATGTCCCACCCCAGATTGGTGAGAAATCTCTAATCTCTCCTGTGGATTCCTACCAGTACGGCACCACTCAAACGCTGACATGTACGGTCTATGCCATTCCTCCCCCGCATCACATCCACTGGTATTGGCAGTTGGAGGAAGAGTGCGCCAACGAGCCCAGCCAAGCTGTCTCAGTGACAAACCCATACCCTTGTGAAGAATGGAGAAGTGTGGAGGACTTCCAGGGAGGAAATAAAATTGAAGTTAATAAAAATCAATTTGCTCTAATTGAAGGAAAAAACAAAACTGTAAGTACCCTTGTTATCCAAGCGGCAAATGTGTCAGCTTTGTACAAATGTGAAGCGGTCAACAAAGTCGGGAGAGGAGAGAGGGTGATCTCCTTCCACGTGACCAGGGGTCCTGAAATTACTTTGCAACCTGACATGCAGCCCACTGAGCAGGAGAGCGTGTCTTTGTGGTGCACTGCAGACAGATCTACGTTTGAGAACCTCACATGGTACAAGCTTGGCCCACAGCCTCTGCCAATCCATGTGGGAGAGTTGCCCACACCTGTTTGCAAGAACTTGGATACTCTTTGGAAATTGAATGCCACCATGTTCTCTAATAGCACAAATGACATTTTGATCATGGAGCTTAAGAATGCATCCTTGCAGGACCAAGGAGACTATGTCTGCCTTGCTCAAGACAGGAAGACCAAGAAAAGACATTGCGTGGTCAGGCAGCTCACAGTCCTAGAGCGTGTGGCACCCACGATCACAGGAAACCTGGAGAATCAGACGACAAGTATTGGGGAAAGCATCGAAGTCTCATGCACGGCATCTGGGAATCCCCCTCCACAGATCATGTGGTTTAAAGATAATGAGACCCTTGTAGAAGACTCAGGCATTGTATTGAAGGATGGGAACCGGAACCTCACTATCCGCAGAGTGAGGAAGGAGGACGAAGGCCTCTACACCTGCCAGGCATGCAGTGTTCTTGGCTGTGCAAAAGTGGAGGCATTTTTCATAATAGAAGGTGCCCAGGAAAAGACGAACTTGGAAATCATTATTCTAGTAGGCACGGCGGTGATTGCCATGTTCTTCTGGCTACTTCTTGTCATCATCCTACGGACCGTTAAGCGGGCCAATGGAGGGGAACTGAAGACAGGCTACTTGTCCATCGTCATGGATCCAGATGAACTCCCATTGGATGAACATTGTGAACGACTGCCTTATGATGCCAGCAAATGGGAATTCCCCAGAGACCGGCTGAAGCTAGGTAAGCCTCTTGGCCGTGGTGCCTTTGGCCAAGTGATTGAAGCAGATGCCTTTGGAATTGACAAGACAGCAACTTGCAGGACAGTAGCAGTCAAAATGTTGAAAGAAGGAGCAACACACAGTGAGCATCGAGCTCTCATGTCTGAACTCAAGATCCTCATTCATATTGGTCACCATCTCAATGTGGTCAACCTTCTAGGTGCCTGTACCAAGCCAGGAGGGCCACTCATGGTGATTGTGGAATTCTGCAAATTTGGAAACCTGTCCACTTACCTGAGGAGCAAGAGAAATGAATTTGTCCCCTACAAGACCAAAGGGGCACGATTCCGTCAAGGGAAAGACTACGTTGGAGCAATCCCTGTGGATCTGAAACGGCGCTTGGACAGCATCACCAGTAGCCAGAGCTCAGCCAGCTCTGGATTTGTGGAGGAGAAGTCCCTCAGTGATGTAGAAGAAGAGGAAGCTCCTGAAGATCTGTATAAGGACTTCCTGACCTTGGAGCATCTCATCTGTTACAGCTTCCAAGTGGCTAAGGGCATGGAGTTCTTGGCATCGCGAAAGTGTATCCACAGGGACCTGGCGGCACGAAATATCCTCTTATCGGAGAAGAACGTGGTTAAAATCTGTGACTTTGGCTTGGCCCGGGATATTTATAAAGATCCAGATTATGTCAGAAAAGGAGATGCTCGCCTCCCTTTGAAATGGATGGCCCCAGAAACAATTTTTGACAGAGTGTACACAATCCAGAGTGACGTCTGGTCTTTTGGTGTTTTGCTGTGGGAAATATTTTCCTTAGGTGCTTCTCCATATCCTGGGGTAAAGATTGATGAAGAATTTTGTAGGCGATTGAAAGAAGGAACTAGAATGAGGGCCCCTGATTATACTACACCAGAAATGTACCAGACCATGCTGGACTGCTGGCACGGGGAGCCCAGTCAGAGACCCACGTTTTCAGAGTTGGTGGAACATTTGGGAAATCTCTTGCAAGCTAATGCTCAGCAGGATGGCAAAGACTACATTGTTCTTCCGATATCAGAGACTTTGAGCATGGAAGAGGATTCTGGACTCTCTCTGCCTACCTCACCTGTTTCCTGTATGGAGGAGGAGGAAGTATGTGACCCCAAATTCCATTATGACAACACAGCAGGAATCAGTCAGTATCTGCAGAACAGTAAGCGAAAGAGCCGGCCTGTGAGTGTAAAAACATTTGAAGATATCCCGTTAGAAGAACCAGAAGTAAAAGTAATCCCAGATGACAACCAGACGGACAGTGGTATGGTTCTTGCCTCAGAAGAGCTGAAAACTTTGGAAGACAGAACCAAATTATCTCCATCTTTTGGTGGAATGGTGCCCAGCAAAAGCAGGGAGTCTGTGGCATCTGAAGGCTCAAACCAGACAAGCGGCTACCAGTCCGGATATCACTCCGATGACACAGACACCACCGTGTACTCCAGTGAGGAAGCAGAACTTTTAAAGCTGATAGAGATTGGAGTGCAAACCGGTAGCACAGCCCAGATTCTCCAGCCTGACTCGGGGACCACACTGAGCTCTCCTCCTGTTTAAAAGGAAGCATCCACACCCCAACTCCCGGACATCACATGAGAGGTCTGCTCAGATTTTGAAGTGTTGTTCTTTCCACCAGCAGGAAGTAGCCGCATTTGATTTTCATTTCGACAACAGAAAAAGGACCTCGGACTGCAGGGAGCCAGTCTTCTAGGCATATCCTGGAAGAGGCTTGTGACCCAAGAATGTGTCTGTGTCTTCTCCCAGTGTTGACCTGATCCTCTTTTTTCATTCATTTAAAAAGCATTATCATGCCCCTGCTGCGGGTCTCACCATGGGTTTAGAACAAAGAGCTTCAAGCAATGGCCCCATCCTCAAAGAAGTAGCAGTACCTGGGGAGCTGACACTTCTGTAAAACTAGAAGATAAACCAGGCAACGTAAGTGTTCGAGGTGTTGAAGATGGGAAGGATTTGCAGGGCTGAGTCTATCCAAGAGGCTTTGTTTAGGACGTGGGTCCCAAGCCAAGCCTTAAGTGTGGAATTCGGATTGATAGAAAGGAAGACTAACGTTACCTTGCTTTGGAGAGTACTGGAGCCTGCAAATGCATTGTGTTTGCTCTGGTGGAGGTGGGCATGGGGTCTGTTCTGAAATGTAAAGGGTTCAGACGGGGTTTCTGGTTTTAGAAGGTTGCGTGTTCTTCGAGTTGGGCTAAAGTAGAGTTCGTTGTGCTGTTTCTGACTCCTAATGAGAGTTCCTTCCAGACCGTTAGCTGTCTCCTTGCCAAGCCCCAGGAAGAAAATGATGCAGCTCTGGCTCCTTGTCTCCCAGGCTGATCCTTTATTCAGAATACCACAAAGAAAGGACATTCAGCTCAAGGCTCCCTGCCGTGTTGAAGAGTTCTGACTGCACAAACCAGCTTCTGGTTTCTTCTGGAATGAATACCCTCATATCTGTCCTGATGTGATATGTCTGAGACTGAATGCGGGAGGTTCAATGTGAAGCTGTGTGTGGTGTCAAAGTTTCAGGAAGGATTTTACCCTTTTGTTCTTCCCCCTGTCCCCAACCCACTCTCACCCCGCAACCCATCAGTATTTTAGTTATTTGGCCTCTACTCCAGTAAACCTGATTGGGTTTGTTCACTCTCTGAATGATTATTAGCCAGACTTCAAAATTATTTTATAGCCCAAATTATAACATCTATTGTATTATTTAGACTTTTAACATATAGAGCTATTTCTACTGATTTTTGCCCTTGTTCTGTCCTTTTTTTCAAAAAAGAAAATGTGTTTTTTGTTTGGTACCATAGTGTGAAATGCTGGGAACAATGACTATAAGACATGCTATGGCACATATATTTATAGTCTGTTTATGTAGAAACAAATGTAATATATTAAAGCCTTATATATAATGAACTTTGTACTATTCACATTTTGTATCAGTATTATGTAGCATAACAAAGGTCATAATGCTTTCAGCAATTGATGTCATTTTATTAAAGAACATTGAAAAACTTGA




BioPerl-1.007002/t/data/test.tsv000444000766000024      7304013155576321 16431 0ustar00cjfieldsstaff000000000000Name	Accession	Group	Family	Subfamily	Pseudogene?	cDNA	Protein	Kinase Domain	Novelty
A6	SK001	Atypical	A6		N	CCGCCGGCCGGGGCCGCTGGCTGCACTCAGCGCCGGAGCCGGGAGCTAGCGGCCGCCGCCATGTCCCACCAGACCGGCATCCAAGCAAGTGAAGATGTTAAAGAGATCTTTGCCAGAGCCAGAAATGGAAAGTACAGACTTCTGAAAATATCTATTGAAAATGAGCAACTTGTGATTGGATCATATAGTCAGCCTTCAGATTCCTGGGATAAGGATTATGATTCCTTTGTTTTACCCCTGTTGGAGGACAAACAACCATGCTATATATTATTCAGGTTAGATTCTCAGAATGCCCAGGGATATGAATGGATATTCATTGCATGGTCTCCAGATCATTCTCATGTTCGTCAAAAAATGTTGTATGCAGCAACAAGAGCAACTCTGAAGAAGGAATTTGGAGGTGGCCACATTAAAGATGAAGTATTTGGAACAGTAAAGGAAGATGTATCATTACATGGATATAAAAAATACTTGCTGTCACAATCTTCCCCTGCCCCACTGACTGCAGCTGAGGAAGAACTACGACAGATTAAAATCAATGAGGTACAGACTGACGTGGGTGTGGACACTAAGCATCAAACACTACAAGGAGTAGCATTTCCCATTTCTCGAGAAGCCTTTCAGGCTTTGGAAAAATTGAATAATAGACAGCTCAACTATGTGCAGTTGGAAATAGATATAAAAAATGAAATTATAATTTTGGCCAACACAACAAATACAGAACTGAAAGATTTGCCAAAGAGGATTCCCAAGGATTCAGCTCGTTACCATTTCTTTCTGTATAAACATTCCCATGAAGGAGACTATTTAGAGTCCATAGTTTTTATTTATTCAATGCCTGGATACACATGCAGTATAAGAGAGCGGATGCTGTATTCTAGCTGCAAGAGCCGTCTGCTAGAAATTGTAGAAAGACAACTACAAATGGATGTAATTAGAAAGATCGAGATAGACAATGGGGATGAGTTGACTGCAGACTTCCTTTATGAAGAAGTACATCCCAAGCAGCATGCACACAAGCAAAGTTTTGCAAAACCAAAAGGTCCTGCAGGAAAAAGAGGAATTCGAAGACTAATTAGGGGCCCAGCGGAAACTGAAGCTACTACTGATTAAAGTCATCACATTAAACATTGTAATACTAGTTTTTTAAAAGTCCAGCTTTTAGTACAGGAGAACTGAAATCATTCCATGTTGATATAAAGTAGGGAAAAAAATTGTACTTTTTGGAAAATAGCACTTTTCACTTCTGTGTGTTTTTAAAATTAATGTTATAGAAGACTCATGATTTCTATTTTTGAGTTAAAGCTAGAAAAGGGTTCAACATAATGTTTAATTTTGTCACACTGTTTTCATAGCGTTGATTCCACACTTCAAATACTTCTTAAAATTTTATACAGTTGGGCCAGTTCTAGAAAGTCTGATGTCTCAAAGGGTAAACTTACTACTTTCTTGTGGGACAGAAAGACCTTAAAATATTCATATTACTTAATGAATATGTTAAGGACCAGGCTAGAGTATTTTCTAAGCTGGAAACTTAGTGTGCCTTGGAAAAGGCCGCAAGTTGCTTACTCCGAGTAGCTGTGCTAGCTCTGTCAGACTGTAGGATCATGTCTGCAACTTTTAGAAATAGTGCTTTATATTGCAGCAGTCTTTTATATTTGACTTTTTTTTAATAGCATTAAAATTGCAGATCAGCTCACTCTGAAACTTTAAGGGTACCAGATATTTTCTATACTGCAGGATTTCTGATGACATTGAAAGACTTTAAACAGCCTTAGTAAATTATCTTTCTAATGCTCTGTGAGGCCAAACATTTATGTTCAGATTGAAATTTAAATTAATATCATTCAAAAGGAAACAAAAAATGTTGAGTTTTAAAAATCAGGATTGACTTTTTTCTCCAAAACCATACATTTATGGGCAAATTGTGTTCTTTATCACTTCCGAGCAAATACTCAGATTTAAAATTACTTTAAAGTCCTGGTACTTAACAGGCTAACGTAGATAAACACCTTAATAATCTCAGTTAATACTGTATTTCAAAACACATTTAACTGTTTTCTAATGCTTTGCATTATCAGTTACAACCTAGAGAGATTTTGAGCCTCATATTTCTTTGATACTTGAAATAGAGGGAGCTAGAACACTTAATGTTTAATCTGTTAAACCTGCTGCAAGAGCCATAACTTTGAGGCATTTTCTAAATGAACTGTGGGGATCCAGGATTTGTAATTTCTTGATCTAAACTTTATGCTGCATAAATCACTTATCGGAAATGCACATTTCATAGTGTGAAGCACTCATTTCTAAACCTTATTATCTAAGGTAATATATGCACCTTTCAGAAATTTGTGTTCGAGTAAGTAAAGCATATTAGAATAATTGTGGGTTGACAGATTTTTAAAATAGAATTTAGAGTATTTGGGGTTTTGTTTGTTTACAAATAATCAGACTATAATATTTAAACATGCAAAATAACTGACAATAATGTTGCACTTGTTTACTAAAGATATAAGTTGTTCCATGGGTGTACACGTAGACAGACACACATACACCCAAATTATTGCATTAAGAATCCTGGAGCAGACCATAGCTGAAGCTGTTATTTTCAGTCAGGAAGACTACCTGTCATGAAGGTATAAAATAATTTAGAAGTGAATGTTTTTCTGTACCATCTATGTGCAATTATACTCTAAATTCCACTACACTACATTAAAGTAAATGGACATTCCAGAATATAGATGTGATTATAGTCTTAAACTAATTATTATTAAACCAATGATTGCTGAAAATCAGTGATGCATTTGTTATAGAGTATAACTCATCGTTTACAGTATGTTTTAGTTGGCAGTATCATACCTAGATGGTGAATAACATATTCCCAGTAAATTTATATAGCAGTGAAGAATTACATGCCTTCTGGTGGACATTTTATAAGTGCATTTTATATCACAATAAAAATTTTTTCTCTTTAAAAAAAAAAAACAAGAAAAAAAAAAAA	MSHQTGIQASEDVKEIFARARNGKYRLLKISIENEQLVIGSYSQPSDSWDKDYDSFVLPLLEDKQPCYILFRLDSQNAQGYEWIFIAWSPDHSHVRQKMLYAATRATLKKEFGGGHIKDEVFGTVKEDVSLHGYKKYLLSQSSPAPLTAAEEELRQIKINEVQTDVGVDTKHQTLQGVAFPISREAFQALEKLNNRQLNYVQLEIDIKNEIIILANTTNTELKDLPKRIPKDSARYHFFLYKHSHEGDYLESIVFIYSMPGYTCSIRERMLYSSCKSRLLEIVERQLQMDVIRKIEIDNGDELTADFLYEEVHPKQHAHKQSFAKPKGPAGKRGIRRLIRGPAETEATTD	 	Known - Literature
A6r	SK512	Atypical	A6		N	GACAGCCTCCGCCACATCCTCCACCTCTCTTGGTCCAGCGAGCGTTGCCGGGCCAGGGTCAAGCGGAGGGCTCCGACGGCGCGGACGGAGCGAAGCGCCGAGCCATGGCGCACCAAACGGGCATCCACGCCACGGAAGAGCTGAAGGAATTCTTTGCCAAGGCACGGGCTGGCTCTGTGCGGCTCATCAAGGTTGTGATTGAGGACGAGCAGCTCGTGCTGGGTGCCTCGCAGGAGCCAGTAGGCCGCTGGGATCAGGACTATGACAGGGCCGTGCTGCCACTGCTGGACGCCCAGCAGCCCTGCTACCTGCTCTACCGCCTCGACTCACAGAATGCTCAGGGCTTCGAATGGCTCTTCCTCGCCTGGTCGCCTGATAACTCCCCCGTGCGGCTGAAGATGCTGTACGCGGCCACGCGGGCCACAGTGAAAAAGGAGTTTGGAGGTGGCCACATCAAGGATGAGCTCTTCGGGACTGTGAAGGATGACCTCTCTTTTGCTGGGTACCAGAAACACCTGTCGTCCTGTGCGGCACCTGCCCCGCTGACCTCGGCTGAGAGAGAGCTCCAGCAGATCCGCATTAACGAGGTGAAGACAGAGATCAGTGTGGAAAGCAAGCACCAGACCCTGCAGGGCCTCGCCTTCCCCCTGCAGCCTGAGGCCCAGCGGGCACTCCAGCAGCTCAAGCAGAAAATGGTCAACTACATCCAGATGAAGCTGGACCTAGAGCGGGAAACCATTGAGCTGGTGCACACAGAGCCCACGGATGTGGCCCAGCTGCCCTCCCGGGTGCCCCGAGATGCTGCCCGCTACCACTTCTTCCTCTACAAGCACACCCATGAGGGCGACCCCCTTGAGTCTGTAGTGTTCATCTACTCCATGCCGGGGTACAAGTGCAGCATCAAGGAGCGAATGCTCTACTCCAGCTGCAAGAGCCGCCTCCTCGACTCCGTGGAGCAGGACTTCCATCTGGAGATCGCCAAGAAAATTGAGATTGGCGATGGGGCAGAGCTGACGGCAGAGTTCCTCTACGACGAGGTGCACCCCAAGCAACACGCCTTCAAGCAGGCCTTCGCCAAGCCCAAGGGCCCAGGGGGCAAGCGGGGCCATAAGCGCCTCATCCGCGGCCCGGGTGAAAATGGGGATGACAGCTAGGAGGCTGGAGCAGGGCCGGCCACGTGTGGACTGTGGGGCTGCCCACCTTCCGCTCCCTGCCACCATCCTCCTTCCTGGGCTCCAGGAAAGTGTTTCTGGGAGGTCAGGAGGGCTGGCAGCTGAACGCACTTGCAGCGTCCGAGGGCCACCGGGCTGGCATTTTGTGACCCTTCCCTGTTGCTGTCCCTGCATCTCGTCTGTGTGCCCAGGGTGTCCGGGGACCCTGCCTGGCTGGCTTAAGGGGGCTGGGTCAGGGGCCTGGCATGAACCTGGCCTCCCGGGGAGCTGAGACTAGGGTCCCAGCACAGCCCAGAAACCTTTGGCCACAAGAAGTGGGGTCAGTCAGGGCTGGGGCAGGGGTCACTGCAGTTTGGGATGGTTGAATGCTGTATTTTCTAAAGAATAAAATATTTTTAAATC	MAHQTGIHATEELKEFFAKARAGSVRLIKVVIEDEQLVLGASQEPVGRWDQDYDRAVLPLLDAQQPCYLLYRLDSQNAQGFEWLFLAWSPDNSPVRLKMLYAATRATVKKEFGGGHIKDELFGTVKDDLSFAGYQKHLSSCAAPAPLTSAERELQQIRINEVKTEISVESKHQTLQGLAFPLQPEAQRALQQLKQKMVNYIQMKLDLERETIELVHTEPTDVAQLPSRVPRDAARYHFFLYKHTHEGDPLESVVFIYSMPGYKCSIKERMLYSSCKSRLLDSVEQDFHLEIAKKIEIGDGAELTAEFLYDEVHPKQHAFKQAFAKPKGPGGKRGHKRLIRGPGENGDDS	 	Known - Literature
A6ps1	SK752	Atypical	A6		Y	CCGCCGGCCGGGGCCGCTGGCTGCACTCAGCGCCGGAGCCGGGAGCTAGCGGCCGCCGCCATGTCCCACCAGACCGGCATCCAAGCAAGTGAAGATGTTAAAGAGATCTTTGCCAGAGCCAGAAATGGAAAGTACAGACTTCTGAAAATATCTATTGAAAATGAGCAACTTGTGATTGGATCATATAGTCAGCCTTCAGATTCCTGGGATAAGGATTATGATTCCTTTGTTTTACCCCTGTTGGAGGACAAACAACCATGCTATATATTATTCAGGTTAGATTCTCAGAATGCCCAGGGATATGAATGGATATTCATTGCATGGTCTCCAGATCATTCTCATGTTCGTCAAAAAATGTTGTATGCAGCAACAAGAGCAACTCTGAAGAAGGAATTTGGAGGTGGCCACATTAAAGATGAAATATTTGGAACAGTAAAGGAAGATGTATCATTACATGGATATAAAAAATACTTGCTGTCACAATCTTCCCCTGCCCCACTGACTGCAGCTGAGGAAGAATTACGACAGATTAAAATCAATGAGGTACAGACTGACGTGGGTGTGGACACTAAGCATCAAACACTACAAGGAGTAGCATTTCCCATTTCTCGAGAAGCCTTTCAGGCTTTGGAAAAATTGAATAACAGACAGCTCAACTATGTGCAGTTGGAAATAGATATAAAAAATGAAATTATAATTTTGGCCAACACAACAAATACAGAACTGAAAGATTTGCCAAAGAGGATTCCCAAGGATTCAGCTCGTTACCATTTCTTTCTGTATAAACATTCCCATGAAGGAGACTATTTAGAGTCCATAGTTNTTATTTATTCAATGCCTGGATACACATGCAGTATAAGAGAGCGGATGCTGTATTCTAGCTGCAAGAGCCCTCTGCTAGAAATTGTAGAAAGACAACTACAAATGGATGTAATTAGAAAGATCGAGATAGACAATGGGGATGAGTTGACTGCAGACTTCCTTTATGAAGAAGTACATCCCAAGCAGCAGGCACACAAGCAAAGTTTTGCAAAACCAAAAGGTCCTGCAGGAAAAAGAGGAATTCGAAGACTAATTAGGGGCCCAGCGGAAACTGAAGCTACTACTGATTAAAGTCGTCACATTAAACATTGCAATACTAGTTTTTTAAAAGTCCAGCTTTTAGTACAGGAGAACTGAAATCATTCCATGTTGATATAAAGTAGGGAAAAACATTGTACTTTTTGGAAAATAGCACTTTTCACTTCTGTGTGTTTTTAAAATTAATGTTATAGAAGACTCATGATTTCTATTTTTGAGTTAAAGCTAGAAAAGGGTTCAACATAATGTTTAATTTTGTCACACTGTTTTCATAGTGTTGATTCCACACTTCAAATACTTCTTAAAATTTTATACAGTTGGGCCAGCTCTAGAAAGTCTGATGTCTCAAAGGGTAAACTTACTACTTTCTTGTGGGACAGAAGGACCTTAAAATATTCATATTACTTAATGAATATGTTAAGGACCAGGCTAGAGTATTTTCTAAGCTGGAAACTTAGTGTGCCTCGGAAAAGGCCGCAAGTTGCTTACTCCGAGTAGCTGTGCTAGCTCTGTCAGACTGTAGGATCATGTCTGCAACTTTTAGAAATAGTGCTTTATATTGCAGCAGTCTTTTATATTTGACTTTTTTTTTAATAGCATTAAAATTGCAGATCAGCTCACTCTGAAACTTTAAGGGTACCAGATATTTTCTATACTGCAGGATTTCTAATGACATTGAAAGACTTTTAAACAGCCTTAGTAAATTATCTTTCTAATGCTCTGTGAGGCCAAACATTTATGTTCAGATTGAAATTTAAATTAATATCATTCAAAAGGAAACAAAAAATGTTGAGTTTTAAAAATCAGGATTGACTTTTTTCTCCAAAACCATACATTTATAGGCAAATTGTGTTCTTTATCACTTCTGAGCAAATACTCAGATTTAAAATTACTTTAAAGTCCTGGTACTTAACAGGCTAACGTAGATAAACACCTTAATAATCTCAGTTAATACTGTATTTCAAAACACATTTAACTGTTTTCTAATGCTTTGCATTATCAGTTACAACCTAGAGAGATTTTGAGCCTCATATTTCTTTGATACTTGAAATAGAGGGAGCTAGAACACTTAATGTTTAATCTGTTAAACCTGCTGCAAGAGCCATAACTTTGAGGCATTTTCTAAATGAACTGTGGGGATCCAGGATTTGTAATTTCTTGATCTAAACTTTATGCTGCATAAATCACTTATCGGAAATGCACATTTCATAGTGTGAAGCACTCATTTCTAAACCTTATTATCTAAGGTAATATATGCACCTTTCAGAAATTTGTGTTCGAGTAAGTAAAGCATATTAGAATAATTATGGGTTGACAGATTTTTAAAATAGAATTTAGAGTATTTGTGTGGGGTTTTGTTTGTTTACAAATAATCAGACTATAATATTTAAACATGCAAAATAACTGAGAATAATGTTGCACTTGTTTACTAAAGATATAAGTTGTTCCATGGGTGTACACGTAGACAGACACACATACACCCAAATTATTGCATTAAGAATCCTGGAGCAGACCATAGCTGAAGCTGTTATTTTCAGTCAGGAAGACTACCTGTCATGAAGGTATACAATAATTTAGAAGTGAATGTTTTTCTGTACCATCTATGTGCAATTATACTCTAAATTCCACTACACTACATTAAAGTAAATGGACATTCCAGAATATAGATGTGATTATAGTCTTAAACTAATTATTAAACCAATGATTGCTGAAAATCAGTGATGCATTTGTTATAGAGTATAACTCATCGTTTACAGTATGTTTTAGTTGGCAGTATCATACCTAGATGGTGAATAACATATTCCCAGTAAATTTATATAGCAGTGAAGAATTACATGCCTTCTGGTGGACATTTTATAAGTGCATTTTATATCACAATAAAATTTTTTCTCTTTAA 	MSHQTGIQASEDVKEIFARARNGKYRLLKISIENEQLVIGSYSQPSDSWDKDYDSFVLPLLEDKQPCYILFRLDSQNAQGYEWIFIAWSPDHSHVRQKMLYAATRATLKKEFGGGHIKDEIFGTVKEDVSLHGYKKYLLSQSSPAPLTAAEEELRQIKINEVQTDVGVDTKHQTLQGVAFPISREAFQALEKLNNRQLNYVQLEIDIKNEIIILANTTNTELKDLPKRIPKDSARYHFFLYKHSHEGDYLESIVXIYSMPGYTCSIRERMLYSSCKSPLLEIVERQLQMDVIRKIEIDNGDELTADFLYEEVHPKQQAHKQSFAKPKGPAGKRGIRRLIRGPAETEATTD*	 	Pseudogene
A6ps2	SK766	Atypical	A6		Y	TCCCACCAGACCTGCATCCAAGCAAGTGAAGATGTTAAAGAGATCNNNGCCAGAGCCAGAAATGGAAAGTACAGACCTCTGAAAATATCTATTGAAAATGGGCAACTTATGATTGGATCATATNNNCAGCCTTCAGATTCCTGGGATAACGATTATGATTCCTTTGTTTTACCCCTGTTGGAGGACAAACAACTGTGCTATATATTATTCAGGTTAGATTCTCAGAATGCCCAGGGATATGAATGGATATTCATTGCATGGTTTCCAGATCATTCTCATGTCCGTCAAAAAAGGTTATATGCAGCAACAAGAGCAACTCTGGAAAAGGAATCTGGAGGTGGCCACGTTAAAGATGAAGTATTTGGAACAGTAAAGGAAGATGTATCATTACATGGATATAAAAAATGTTTGCTCTCACAATCTTCCCCTGCCCCACTGACTGCAGCTGAGGAAGAATTANNNGACATTAAAATCAATGAGGTACAGACTGACGTGGGTGTGGACGCTAAGCATCAAACACTACAAGGAGTAGCATTTCCTATTTCTCGAGAAGCTTTTCAGGCTTTGGAAAAAATAAATAACNNNCTGAACTATGTGCAGTTGGAAATAAACATAAAAAATGAAATTATAATTTTGGCCAACACAACAAATACAGAACTAAAAGATTTGCCAAAGAGGATTCCCAAGGATTCAGCTCGTTACCATTTCTTTCTGTATAAACATTCCCATGAAGGAGACTATTTAGAGTCCATAGTTTTTATCTATTCAATGCCCAGATACACATGCAGTATAAGAGAACGGATGCTGTATTCTAGCTGCAAGAGCCCTCTGCTAGAAATTGTAGAAAGACAACTANNNGTTGTAATGGATGTAATTAGAAAGATTGAGATAGACAATGAGGATTAGTTGACTTCAGACTTCCTTTGTGAAGAAGAAGTACATCCCAAGCAGCATGCAGGAAAAAGAAGAATTCGAAGACTAATTAGGGGCCCAGCGGAAAATGAAGCTACTACTGAT	SHQTCIQASEDVKEIXARARNGKYRPLKISIENGQLMIGSYXQPSDSWDNDYDSFVLPLLEDKQLCYILFRLDSQNAQGYEWIFIAWFPDHSHVRQKRLYAATRATLEKESGGGHVKDEVFGTVKEDVSLHGYKKCLLSQSSPAPLTAAEEELXDIKINEVQTDVGVDAKHQTLQGVAFPISREAFQALEKINNXLNYVQLEINIKNEIIILANTTNTELKDLPKRIPKDSARYHFFLYKHSHEGDYLESIVFIYSMPRYTCSIRERMLYSSCKSPLLEIVERQLXVVMDVIRKIEIDNED*LTSDFLCEEEVHPKQHAGKRRIRRLIRGPAENEATTD	 	Pseudogene
CaMK2d	SK703	CAMK	CAMK2		N	ATGGCTTCGACCACCACCTGCACCAGGTTCACGGACGAGTATCAGCTTTTCGAGGAGCTTGGAAAGGGGGCATTCTCAGTGGTGAGAAGATGTATGAAAATTCCTACTGGACAAGGATATGCTGCCAAAATTATCAACACCAAAAAGCTTTCTGCTAGGGATCATCAGAAACTAGAAAGAGAAGCTAGAATCTGCCGTCTTTTGAAGCACCCTAATATTGTGCGACTTCATGATAGCATATCAGAAGAGGGCTTTCACTACTTGGTGTTTGATTTAGTTACTGGAGGTGAACTGTTTGAAGACATAGTGGCAAGAGAATACTACAGTGAAGCTGATGCCAGTCATTGTATACAGCAGATTCTAGAAAGTGTTAATCATTGTCACCTAAATGGCATAGTTCACAGGGACCTGAAGCCTGAGAATTTGCTTTTAGCTAGCAAATCCAAGGGAGCAGCTGTGAAATTGGCAGACTTTGGCTTAGCCATAGAAGTTCAAGGGGACCAGCAGGCGTGGTTTGGTTTTGCTGGCACACCTGGATATCTTTCTCCAGAAGTTTTACGTAAAGATCCTTATGGAAAGCCAGTGGATATGTGGGCATGTGGTGTCATTCTCTATATTCTACTTGTGGGGTATCCACCCTTCTGGGATGAAGACCAACACAGACTCTATCAGCAGATCAAGGCTGGAGCTTATGATTTTCCATCACCAGAATGGGACACGGTGACTCCTGAAGCCAAAGACCTCATCAATAAAATGCTTACTATCAACCCTGCCAAACGCATCACAGCCTCAGAGGCACTGAAGCACCCATGGATCTGTCAACGTTCTACTGTTGCTTCCATGATGCACAGACAGGAGACTGTAGACTGCTTGAAGAAATTTAATGCTAGAAGAAAACTAAAGGGTGCCATCTTGACAACTATGCTGGCTACAAGGAATTTCTCAGCAGCCAAGAGTTTGTTGAAGAAACCAGATGGAGTAAAGGAGTCAACTGAGAGTTCAAATACAACAATTGAGGATGAAGATGTGAAAGCACGAAAGCAAGAGATTATCAAAGTCACTGAACAACTGATCGAAGCTATCAACAATGGGGACTTTGAAGCCTACACAAAAATCTGTGACCCAGGCCTTACTGCTTTTGAACCTGAAGCTTTGGGTAATTTAGTGGAAGGGATGGATTTTCACCGATTCTACTTTGAAAATGCTTTGTCCAAAAGCAATAAACCAATCCACACTATTATTCTAAACCCTCATGTACATCTGGTAGGGGATGATGCCGCCTGCATAGCATATATTAGGCTCACACAGTACATGGATGGCAGTGGAATGCCAAAGACAATGCAGTCAGAAGAGACTCGTGTGTGGCACCGCCGGGATGGAAAGTGGCAGAATGTTCATTTTCATCGCTCGGGGTCACCAACAGTACCCATCAAGCCACCCTGTATTCCAAATGGGAAAGAAAACTTCTCAGGAGGCACCTCTTTGTGGCAAAACATCTGA	MASTTTCTRFTDEYQLFEELGKGAFSVVRRCMKIPTGQGYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGFHYLVFDLVTGGELFEDIVAREYYSEADASHCIQQILESVNHCHLNGIVHRDLKPENLLLASKSKGAAVKLADFGLAIEVQGDQQAWFGFAGTPGYLSPEVLRKDPYGKPVDMWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPAKRITASEALKHPWICQRSTVASMMHRQETVDCLKKFNARRKLKGAILTTMLATRNFSAAKSLLKKPDGVKESTESSNTTIEDEDVKARKQEIIKVTEQLIEAINNGDFEAYTKICDPGLTAFEPEALGNLVEGMDFHRFYFENALSKSNKPIHTIILNPHVHLVGDDAACIAYIRLTQYMDGSGMPKTMQSEETRVWHRRDGKWQNVHFHRSGSPTVPIKPPCIPNGKENFSGGTSLWQNI	YQLFEELGKGAFSVVRRCMKIPTGQGYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGFHYLVFDLVTGGELFEDIVAREYYSEADASHCIQQILESVNHCHLNGIVHRDLKPENLLLASKSKGAAVKLADFGLAIEVQGDQQAWFGFAGTPGYLSPEVLRKDPYGKPVDMWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPAKRITASEALKHPWI	Known - Refseq
CaMKK2	SK482	Other	CAMKK	Meta	N	GAGCCGAGCCGAGCTGGGGGCGCAGACGCGGAGGCGGCGGCGGCGCGGAGCCCAGGTGGCTCCGTGCCGGATGGGAGTGCCCCAGTGTGCTGGATGAAGCTGGCGCATGCACCATGTCATCATGTGTCTCTAGCCAGCCCAGCAGCAACCGGGCCGCCCCCCAGGATGAGCTGGGGGGCAGGGGCAGCAGCAGCAGCGAAAGCCAGAAGCCCTGTGAGGCCCTGCGGGGCCTCTCATCCTTGAGCATCCACCTGGGCATGGAGTCCTTCATTGTGGTCACCGAGTGTGAGCCGGGCTGTGCTGTGGACCTCGGCTTGGCGCGGGACCGGCCCCTGGAGGCCGATGGCCAAGAGGTCCCCCTTGACACCTCCGGGTCCCAGGCCCGGCCCCACCTCTCCGGTCGCAAGCTGTCTCTGCAAGAGCGGTCCCAGGGTGGGCTGGCAGCCGGTGGCAGCCTGGACATGAACGGACGCTGCATCTGCCCGTCCCTGCCCTACTCACCCGTCAGCTCCCCGCAGTCCTCGCCTCGGCTGCCCCGGCGGCCGACAGTGGAGTCTCACCACGTCTCCATCACGGGTATGCAGGACTGTGTGCAGCTGAATCAGTATACCCTGAAGGATGAAATTGGAAAGGGCTCCTATGGTGTCGTCAAGTTGGCCTACAATGAAAATGACAATACCTACTATGCAATGAAGGTGCTGTCCAAAAAGAAGCTGATCCGGCAGGCCGCTTTTCCACGTCGCCCTCCACCCCGAGGCACCCGGCCAGCTCCTGGAGGCTGCATCCAGCCCAGGGGCCCCATTGAGCAGGTGTACCAGGAAATTGCCATCCTCAAGAAGCTGGACCACCCCAATGTGGTGAAGCTGGTGGAGGTCCTGGATGACCCCAATGAGGACCATCTGTACATGGTGTTCGAACTGGTCAACCAAGGGCCCGTGATGGAAGTGCCCACCCTCAAACCACTCTCTGAAGACCAGGCCCGTTTCTACTTCCAGGATCTGATCAAAGGCATCGAGTACTTACACTACCAGAAGATCATCCACCGTGACATCAAACCTTCCAACCTCCTGGTCGGAGAAGATGGGCACATCAAGATCGCTGACTTTGGTGTGAGCAATGAATTCAAGGGCAGTGACGCGCTCCTCTCCAACTACGTGGGCACGCCCGCCTTCATGGCTCCCGAGTCGCTCTCTGAGACCCGCAAGATCTTCTCTGGGAAGGCCAAGGATGTTTGGGCCATGGGTGTGACACTATACTGCTTTGTCTTTGGCCAGTGCCCATTCATGGACGAGCGGATCATGTGTTTACACAGTAAGATCAAGAGTCAGGCCCTGGAATTTCCAGACCAGCCCGACATAGCTGAGGACTTGAAGGACCTGATCACCCGTATGCTGGACAAGAACCCCGAGTCGAGGATCGTGGTGCCGGAAATCAAGCTGCACCCCTGGGTCACGAGGCATGGGGCGGAGCCGTTGCCGTCGGAGGATGAGAACTGCACGCTGGTCGAAGTGACTGAAGAGGAGGTCGAGAACTCAGTCAAACACATTCCCAGCTTGGCAACCGTGATCCTGGTGAAGACCATGATACGTAAACGCTCCTTTGGGAACCCATTCGAGGGCAGCCGGCGGGAGGAACGCTCACTGTCAGCGCCTGGAAACTTGCTCACCAAAAAACCAACCAGGGAATGTGAGTCCCTGTCTGAGCTCAAGGAAGCAAGGCAGCGAAGACAACCTCCAGGGCACCGACCCGCCCCCCGTGGGGGAGGAGGAAGTGCTCTTGTGAGAGGCAGTCCCTGCGTGGAAAGTTGCTGGGCCCCCGCCCCCGGCTCCCCCGCACGCATGCATCCACTGCGGCCGGAGGAGGCCATGGAGCCCGAGTAGCTGCCTGGATCGCTCGACCTCGCATGCGCGCCGCGTCGCCTCTGGGGGGCTGCTGCACCGCGTTTCCATAGCAGCATGTCCTACGGAAACCCAGCACGTGTGTTTCCATAGCAGCATGTCTGCAACCCAGACGCGGTGTGTAGAGCCTCGATCGTCATCTCTGGTTATTTGTTTTTTCCTTTGTTGTTTTAAAGGGACAAAAAAAAAAAAGGACTGACTCCATAGCTCGACCGTGGCCGCTGGCTGGCTGGACAGGCGGGTGTGAGGAGTTGCAGACCCAAACCCACGTGCATTTTGGGACAATTGCTTTTTAAAACGTTTTTATGCCAAAAATCCTTCATTGTGATTTTCAGAACCACGTCAGATATACCAAGTGACTGTGTGTGGGGTTTGACAACTGTGGAAAGGCGAGCAGAAAACTCCGGCGGTCTGAGGCCATGGAGGTGGTTGCTGCATTTGAGAGGGAGTAGGGGGCTAGATGTGGCTCCTAGTGCAAACCGGAAACCATGGCACCTTCCAGAGCCGTGGTCTCAAGGAGTCAGAGCAGGGAGCTTTGATGCAACTTATTTGTAAGAAGGATTTTTAAATTTTTTATGGGTAGAATTGTAGTCAGGAAAACAGAAAGGGCTTGAAATTTAATAAGTGCTGCTGGAGGGGATTTTCCAAGCCTGGAAGGGTATTCAGCAGCTGTGGTGGGGAAAGATTTCTCCTGAAAGACTGAACGTGTTTCTTCATGACAGCTGCTCAAAGCAGGTTTCTGAGATAGCTGACCGAGCTCTGGTAAATCTCTTTGTCAAATTACGAAAACTTCAGGGCGAAATCCTATGCTTCCATGTACATTACATGGCTTAAGTTAAACAAAAACATTTTTCAAGTCTCTAACTAGAGTGAA	MSSCVSSQPSSNRAAPQDELGGRGSSSSESQKPCEALRGLSSLSIHLGMESFIVVTECEPGCAVDLGLARDRPLEADGQEVPLDTSGSQARPHLSGRKLSLQERSQGGLAAGGSLDMNGRCICPSLPYSPVSSPQSSPRLPRRPTVESHHVSITGMQDCVQLNQYTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAAFPRRPPPRGTRPAPGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNYVGTPAFMAPESLSETRKIFSGKAKDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWVTRHGAEPLPSEDENCTLVEVTEEEVENSVKHIPSLATVILVKTMIRKRSFGNPFEGSRREERSLSAPGNLLTKKPTRECESLSELKEARQRRQPPGHRPAPRGGGGSALVRGSPCVESCWAPAPGSPARMHPLRPEEAMEPE	YTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAAFPRRPPPRGTRPAPGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNYVGTPAFMAPESLSETRKIFSGKAKDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWV	Known - Refseq
AMPKa1	SK032	CAMK	CAMKL	AMPK	N	GCAGACTCAGTTCCTGGAGAAAGATGGCGACAGCCGAGAAGCAGAAACACGACGGGCGGGTGAAGATCGGCCACTACATTCTGGGTGACACGCTGGGGGTCGGCACCTTCGGCAAAGTGAAGGTTGGCAAACATGAATTGACTGGGCATAAAGTAGCTGTGAAGATACTCAATCGACAGAAGATTCGGAGCCTTGATGTGGTAGGAAAAATCCGCAGAGAAATTCAGAACCTCAAGCTTTTCAGGCATCCTCATATAATTAAACTGTACCAGGTCATCAGTACACCATCTGATATTTTCATGGTGATGGAATATGTCTCAGGAGGAGAGCTATTTGATTATATCTGTAAGAATGGAAGGCTGGATGAAAAAGAAAGTCGGCGTCTGTTCCAACAGATCCTTTCTGGTGTGGATTATTGTCACAGGCATATGGTGGTCCATAGAGATTTGAAACCTGAAAATGTCCTGCTTGATGCACACATGAATGCAAAGATAGCTGATTTTGGTCTTTCAAACATGATGTCAGATGGTGAATTTTTAAGAACAAGTTGTGGCTCACCCAACTATGCTGCACCAGAAGTAATTTCAGGAAGATTGTATGCAGGCCCAGAGGTAGATATATGGAGCAGTGGGGTTATTCTCTATGCTTTATTATGTGGAACCCTTCCATTTGATGATGACCATGTGCCAACTCTTTTTAAGAAGATATGTGATGGGATCTTCTATACCCCTCAATATTTAAATCCTTCTGTGATTAGCCTTTTGAAACATATGCTGCAGGTGGATCCCATGAAGAGGGCCTCAATCAAAGATATCAGGGAACATGAATGGTTTAAACAGGACCTTCCAAAATATCTCTTTCCTGAGGATCCATCATATAGTTCAACCATGATTGATGATGAAGCCTTAAAAGAAGTATGTGAAAAGTTTGAGTGCTCAGAAGAGGAAGTTCTCAGCTGTCTTTACAACAGAAATCACCAGGATCCTTTGGCAGTTGCCTACCATCTCATAATAGATAACAGGAGAATAATGAATGAAGCCAAAGATTTCTATTTGGCGACAAGCCCACCTGATTCTTTTCTTGATGATCATCACCTGACTCGGCCCCATCCTGAAAGAGTACCATTCTTGGTTGCTGAAACACCAAGGGCACGCCATACCCTTGATGAATTAAATCCACAGAAATCCAAACACCAAGGTGTAAGGAAAGCAAAATGGCATTTAGGAATTAGAAGTCAAAGTCGACCAAATGATATTATGGCAGAAGTATGTAGAGCAATCAAACAATTGGATTATGAATGGAAGGTTGTAAACCCATATTATTTGCGTGTACGAAGGAAGAATCCTGTGACAAGCACTTACTCCAAAATGAGTCTACAGTTATACCAAGTGGATAGTAGAACTTATCTACTGGATTTCCGTAGTATTGATGATGAAATTACAGAAGCCAAATCAGGGACTGCTACTCCACAGAGATCGGGATCAGTTAGCAACTATCGATCTTGCCAAAGGAGTGATTCAGATGCTGAGGCTCAAGGAAAATCCTCAGAAGTTTCTCTTACCTCATCTGTGACCTCACTTGACTCTTCTCCTGTTGACCTAACTCCAAGACCTGGAAGTCACACAATAGAATTTTTTGAGATGTGTGCAAATCTAATTAAAATTCTTGCACAATAAACAGAAAACTTTGCTTATTTCTTTTGCAGCAATAAGCATGCATAATAAGTCACAGCCAAATGCTTCCATTTGTAATCAAGTTATACATAATTATAACCGAGGGCTGGCGTTTTGGAATCGAATTTCGACAGGGATTGGAACATGATTTATAGTTAAAAGCCTAATATCGAGAAATGAATTAAGATCA	MATAEKQKHDGRVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKNGRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRASIKDIREHEWFKQDLPKYLFPEDPSYSSTMIDDEALKEVCEKFECSEEEVLSCLYNRNHQDPLAVAYHLIIDNRRIMNEAKDFYLATSPPDSFLDDHHLTRPHPERVPFLVAETPRARHTLDELNPQKSKHQGVRKAKWHLGIRSQSRPNDIMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTYSKMSLQLYQVDSRTYLLDFRSIDDEITEAKSGTATPQRSGSVSNYRSCQRSDSDAEAQGKSSEVSLTSSVTSLDSSPVDLTPRPGSHTIEFFEMCANLIKILAQ	YILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKNGRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRASIKDIREHEWF	Known - Refseq
AMPKa2	SK033	CAMK	CAMKL	AMPK	N	GGTAGCGGCGGCGGCGGCGGCTAGCGGAGCGGCAGGCGGTGGAGCGAGGCCGCGCGCGCCGAAGATGGCTGAGAAGCAGAAGCACGACGGGCGGGTGAAGATCGGACACTACGTGCTGGGCGACACGCTGGGCGTCGGCACCTTCGGCAAAGTGAAGATTGGAGAACATCAATTAACAGGCCATAAAGTGGCAGTTAAAATCTTAAATAGACAGAAGATTCGCAGTTTAGATGTTGTTGGAAAAATAAAACGAGAAATTCAAAATCTAAAACTCTTTCGTCATCCTCATATTATCAAACTATACCAGGTGATCAGCACTCCAACAGATTTTTTTATGGTAATGGAATATGTGTCTGGAGGTGAATTATTTGACTACATCTGTAAGCATGGACGGGTTGAAGAGATGGAAGCCAGGCGGCTCTTTCAGCAGATTCTGTCTGCTGTGGATTACTGTCATAGGCATATGGTTGTTCATCGAGACCTGAAACCAGAGAATGTCCTGTTGGATGCACACATGAATGCCAAGATAGCCGATTTCGGATTATCTAATATGATGTCAGATGGTGAATTTCTGAGAACTAGTTGCGGATCTCCAAATTATACAGCACCTGAAGTCATCTCAGGCAGATTGTATGCAGGTCCTGAAGTTGATATCTGGAGCTGTGGTGTTATCTTGTATGCTCTTCTTTGTGGCACCCTCCCATTTGATGATGAGCATGTACCTACGTTATTTAAGAAGATCCGAGGGGGTGTCTTTTATATCCCAGAATATCTCAATCGTTCTGTCGCCACTCTCCTGATGCATATGCTGCAGGTTGACCCACTGAAACGAGCAACTATCAAAGACATAAGAGAGCATGAATGGTTTAAACAAGGTTTGCCCAGTTACTTATTTCCTGAAGACCCTTCCTATGATGCTAACGTCATTGATGATGAGGCTGTGAAAGAAGTGTGTGAAAAATTTGAATGTACAGAATCAGAAGTAATGAACAGTTTATATAGTGGTGACCCTCAAGACCAGCTTGCAGTGGCTTATCATCTTATCATTGACAATCGGAGAATAATGAACCAAGCCAGTGAGTTCTACCTCGCCTCTAGTCCTCCATCTGGTTCTTTTATGGATGATAGTGCCATGCATATTCCCCCAGGCCTGAAACCTCATCCAGAAAGGATGCCACCTCTTATAGCAGACAGCCCCAAAGCAAGATGTCCATTGGATGCACTGAATACGACTAAGCCCAAATCTTTAGCTGTGAAAAAAGCCAAGTGGCGTCAAGGAATCCGAAGTCAGAGCAAACCGTATGACATTATGGCTGAAGTTTACCGAGCTATGAAGCAGCTGGATTTTGAATGGAAGGTAGTGAATGCATACCATCTTCGTGTAAGAAGAAAAAATCCAGTGACTGGCAATTACGTGAAAATGAGCTTACAACTTTACCTGGTTGATAACAGGAGCTATCTTTTGGACTTTAAAAGCATTGATGATGAAGTAGTGGAGCAGAGATCTGGTTCCTCAACACCTCAGCGTTCCTGTTCTGCTGCTGGCTTACACAGACCAAGATCAAGTTTTGATTCCACAACTGCAGAGAGCCATTCACTTTCTGGCTCTCTCACTGGCTCTTTGACCGGAAGCACATTGTCTTCAGTTTCACCTCGCCTGGGCAGTCACACCATGGATTTTTTTGAAATGTGTGCCAGTCTGATTACTACTTTAGCCCGTTGATCTGTCTCTAGTTTCTTTCTGTTATTGCACTATGAAAATCAGTTATATTCTTTAAATTTTTATCTTACTTTTGGATAATATCCACTGCAATACTAATTGAGAAACATGAATTATTTCCAGGGGCACACAATGCTATTGAAATTACTGAAAACAAAATATCTGACATCTTATTTACTTGTAGAAATCTGTAATTCTATTGTGCCTATGATAAATTCACATAGGCAATATCTTTAATAGGTTAATATCAATGAAGATTTTTAATTACAATAATGAGTTCACTACAGACGATTAACACACCACACTGGCGAACCATCTCAATGTAAGGGTGGTTTGGCAACACCTCCTTGCTTTGCTGTTTGGTGTAGTAAATCTAGTTTACTTCCTAAATTTCAGTAGGCTTTATGCTGTGTTTATCGCCCAATTTATTTTAACAAAAGAAGATTAAAAAGTAAAGAACCACGAGTAAGATATTATTTAAATGTTGAAATCTTAAAACCTGCCTCCAAGATTTCAGAAGCCAAGTTTTTCTAACAGTATTTGTACAAATACTGCCTAGTGTATTCAACAGAAGACTGTGGTCATGTAACAGGTAACCACAATTTTCAGGTTTCTTAAAAACAGCTGTAACTAACTCAGGA	MAEKQKHDGRVKIGHYVLGDTLGVGTFGKVKIGEHQLTGHKVAVKILNRQKIRSLDVVGKIKREIQNLKLFRHPHIIKLYQVISTPTDFFMVMEYVSGGELFDYICKHGRVEEMEARRLFQQILSAVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYTAPEVISGRLYAGPEVDIWSCGVILYALLCGTLPFDDEHVPTLFKKIRGGVFYIPEYLNRSVATLLMHMLQVDPLKRATIKDIREHEWFKQGLPSYLFPEDPSYDANVIDDEAVKEVCEKFECTESEVMNSLYSGDPQDQLAVAYHLIIDNRRIMNQASEFYLASSPPSGSFMDDSAMHIPPGLKPHPERMPPLIADSPKARCPLDALNTTKPKSLAVKKAKWRQGIRSQSKPYDIMAEVYRAMKQLDFEWKVVNAYHLRVRRKNPVTGNYVKMSLQLYLVDNRSYLLDFKSIDDEVVEQRSGSSTPQRSCSAAGLHRPRSSFDSTTAESHSLSGSLTGSLTGSTLSSVSPRLGSHTMDFFEMCASLITTLAR	YVLGDTLGVGTFGKVKIGEHQLTGHKVAVKILNRQKIRSLDVVGKIKREIQNLKLFRHPHIIKLYQVISTPTDFFMVMEYVSGGELFDYICKHGRVEEMEARRLFQQILSAVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYTAPEVISGRLYAGPEVDIWSCGVILYALLCGTLPFDDEHVPTLFKKIRGGVFYIPEYLNRSVATLLMHMLQVDPLKRATIKDIREHEWF	Known - Refseq
MARK3	SK096	CAMK	CAMKL	MARK	N	GACGGCCCGGGCCAGGCCCGGGATCTAGAACGGCCGTAGGGGGAAGGGAGCCGCCCTCCCCACGGCGCCTTTTCGGAACTGCCGTGGACTCGAGGACGCTGGTCGCCGGCCTCCTAGGGCTGTGCTGTTTTGTTTTGACCCTCGCATTGTGCAGAATTAAAGTGCAGTAAAATGTCCACTAGGACCCCATTGCCAACGGTGAATGAACGAGACACTGAAAACCACACGTCACATGGAGATGGGCGTCAAGAAGTTACCTCTCGTACCAGCCGCTCAGGAGCTCGGTGTAGAAACTCTATAGCCTCCTGTGCAGATGAACAACCTCACATCGGAAACTACAGACTGTTGAAAACAATCGGCAAGGGGAATTTTGCAAAAGTAAAATTGGCAAGACATATCCTTACAGGCAGAGAGGTTGCAATAAAAATAATTGACAAAACTCAGTTGAATCCAACAAGTCTACAAAAGCTCTTCAGAGAAGTAAGAATAATGAAGATTTTAAATCATCCCAATATAGTGAAGTTATTCGAAGTCATTGAAACTCAAAAAACACTCTACCTAATCATGGAATATGCAAGTGGAGGTAAAGTATTTGACTATTTGGTTGCACATGGCAGGATGAAGGAAAAAGAAGCAAGATCTAAATTTAGACAGATTGTGTCTGCAGTTCAATACTGCCATCAGAAACGGATCGTACATCGAGACCTCAAGGCTGAAAATCTATTGTTAGATGCCGATATGAACATTAAAATAGCAGATTTCGGTTTTAGCAATGAATTTACTGTTGGCGGTAAACTCGACACGTTTTGTGGCAGTCCTCCATACGCAGCACCTGAGCTCTTCCAGGGCAAGAAATATGACGGGCCAGAAGTGGATGTGTGGAGTCTGGGGGTCATTTTATACACACTAGTCAGTGGCTCACTTCCCTTTGATGGGCAAAACCTAAAGGAACTGAGAGAGAGAGTATTAAGAGGGAAATACAGAATTCCCTTCTACATGTCTACAGACTGTGAAAACCTTCTCAAACGTTTCCTGGTGCTAAATCCAATTAAACGCGGCACTCTAGAGCAAATCATGAAGGACAGGTGGATCAATGCAGGGCATGAAGAAGATGAACTCAAACCATTTGTTGAACCAGAGCTAGACATCTCAGACCAAAAAAGAATAGATATTATGGTGGGAATGGGATATTCACAAGAAGAAATTCAAGAATCTCTTAGTAAGATGAAATACGATGAAATCACAGCTACATATTTGTTATTGGGGAGAAAATCTTCAGAGGTTAGGCCGAGCAGTGATCTCAACAACAGTACTGGCCAGTCTCCTCACCACAAAGTGCAGAGAAGTGTTTCTTCAAGCCAAAAGCAAAGACGCTACAGTGACCATGCTGGACCAGGTATTCCTTCTGTTGTGGCGTATCCGAAAAGGAGTCAGACCAGCACTGCAGATAGTGACCTCAAAGAAGATGGAATTTCCTCCCGGAAATCAACTGGCAGTGCTGTTGGAGGAAAGGGAATTGCTCCAGCCAGTCCCATGCTTGGGAATGCAAGTAATCCTAATAAGGCGGATATTCCTGAACGCAAGAAAAGCTCCACTGTCCCTAGTAGTAACACAGCATCTGGTGGAATGACACGACGAAATACTTATGTTTGCAGTGAGAGAACTACAGATGATAGACACTCAGTGATTCAGAATGGCAAAGAAAACAGCACTATTCCTGATCAGAGAACTCCAGTTGCTTCAACACACAGTATCAGTAGTGCAGCCACCCCAGATCGAATCCGCTTCCCAAGAGGCACTGCCAGTCGTAGCACTTTCCACGGCCAGCCCCGGGAACGGCGAACCGCAACATATAATGGCCCTCCTGCCTCTCCCAGCCTGTCCCATGAAGCCACACCATTGTCCCAGACTCGAAGCCGAGGCTCCACTACTCTCTTTAGTAAATTAACTTCAAAACTCACAAGGAGTCGCAATGTATCTGCTAAGCAAAAAGATGAAAACAAAGAAGCAAAGCCTCGATCCCTACGCTTCACCTGGAGCATGAAAACCACTAGTTCAATGGATCCCGGGGACATGATGCGGGAAATCCGCAAAGTGTTGGACGCCAATAACTGCGACTATGAGCAGAGGGAGCGCTTCTTGCTCTTCTGCGTCCACGGAGATGGGCACGCGGAGAACCTCGTGCAGTGGGAAATGGAAGTGTGCAAGCTGCCAAGACTGTCTCTGAACGGGGTCCGGTTTAAGCGGATATCGGGGACATCCATAGCCTTCAAAAATATTGCTTCCAAAATTGCCAATGAGCTAAAGCTGTAACCCAGTGATTATGATGTAAATTAAGTAGCAAGTAAAGTGTTTTCCTGAACACTGATGGAAATGTATAGAATAATATTTAGGCAATAACGTCTGCATCTTCTAAATCATGAAATTAAAGTCTGAGGACGAGAGCACGCCTGGGAGCGAAAGCTGGCCTTTTTTCTACGAATGCACTACATTAAAGATGTGCAACCTATGCGCCCCCTGCCCTACTTCCGTTACCCTGAGAGTCGGCGTGTGGCCCCATCTCCATGTGCCTCCCGTCTGGGTGGGTGTGAGAGTGGACGGTATGTGTGTGAAGTGGTGTATATGGAAGCATCTCCCTACACTGGCAGCCAGTCATTACTAGTACCTCTGCGGGAGATCATCCGGTGCTAAAACATTACAGTTGCCAAGGAGGAAAATACTGAATGACTGCTAAGAATTAACCTTAAGACCAGTTCATAGTTAATACAGGTTTACAGTTCATGCCTGTGGTTTTGTGTTTGTTGTTTTGTGTTTTTTTAGTGCAAAAGGTTTAAATTTATAGTTGTGAACATTGCTTGTGTGTGTTTTTCTAAGTAGATTCACAAGATAATTAAAAATTCACTTTTTCTCAGGT	MSTRTPLPTVNERDTENHTSHGDGRQEVTSRTSRSGARCRNSIASCADEQPHIGNYRLLKTIGKGNFAKVKLARHILTGREVAIKIIDKTQLNPTSLQKLFREVRIMKILNHPNIVKLFEVIETEKTLYLIMEYASGGEVFDYLVAHGRMKEKEARSKFRQIVSAVQYCHQKRIVHRDLKAENLLLDADMNIKIADFGFSNEFTVGGKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKRFLVLNPIKRGTLEQIMKDRWINAGHEEDELKPFVEPELDISDQKRIDIMVGMGYSQEEIQESLSKMKYDEITATYLLLGRKSSELDASDSSSSSNLSLAKVRPSSDLNNSTGQSPHHKVQRSVSSSQKQRRYSDHAGPAIPSVVAYPKRSQTSTADGDLKEDGISSRKSSGSAVGGKGIAPASPMLGNASNPNKADIPERKKSSTVPSSNTASGGMTRRNTYVCSERTTADRHSVIQNGKENSTIPDQRTPVASTHSISSAATPDRIRFPRGTASRSTFHGQPRERRTATYNGPPASPSLSHEATPLSQTRSRGSTNLFSKLTSKLTRSRNVSAEQKDENKEAKPRSLRFTWSMKTTSSMDPGDMMREIRKVLDANNCDYEQRERFLLFCVHGDGHAENLVQWEMEVCKLPRLSLNGVRFKRISGTSIAFKNIASKIANELKL	YRLLKTIGKGNFAKVKLARHILTGREVAIKIIDKTQLNPTSLQKLFREVRIMKILNHPNIVKLFEVIETQKTLYLIMEYASGGKVFDYLVAHGRMKEKEARSKFRQIVSAVQYCHQKRIVHRDLKAENLLLDADMNIKIADFGFSNEFTVGGKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKRFLVLNPIKRGTLEQIMKDRWI	Known - Refseq
MARK2	SK120	CAMK	CAMKL	MARK	N	CGGCGGTGGTGGCGGCCATGTTGGGAGCAGCAGGTCCGGCGGCGGCTGCCTGTGTGCCGGGCGCGGAGCAGTGCCGCTGAGGGCAGGGGAGGAGCGAGGCAGGCGGCCGGCTGCGGCGGCAGAGAGTAGGCGGAGCGGCGCGGCCCGGCCGAAAGGCGGCACAGCCCAGCCGGGGGTCGGGGGGGTGCGGTCCGGAGCCGCTCGGAGCCGGCGCGGCCTAGCCCGAGCGGCGCATCCCCGGGCTGGCGTGAGCGGCTGCCCGGCCTCCCCGCACCCCCGGCCGGGGCCCATGCGGCGGGTGCTCCTGCTGTGAGAAGCCCCGCCCGGCCGGGCTCCGCGCCTTCCCTTCCCTCCCTTCCTCCAAGCTTCTCGGTTCCCTCCCCCGAGATACCGGCGCCATGTCCAGCGCTCGGACCCCCCTACCCACGCTGAACGAGAGGGACACGGAGCAGCCCACCTTGGGACACCTTGACTCCAAGCCCAGCAGTAAGTCCAACATGATTCGGGGCCGCAACTCAGCCACCTCTGCTGATGAGCAGCCCCACATTGGAAACTACCGGCTCCTCAAGACCATTGGCAAGGGTAATTTTGCCAAGGTGAAGTTGGCCCGACACATCCTGACTGGGAAAGAGGTAGCTGTGAAGATCATTGACAAGACTCAACTGAACTCCTCCAGCCTCCAGAAACTATTCCGCGAAGTAAGAATAATGAAGGTTTTGAATCATCCCAACATAGTTAAATTATTTGAAGTGATTGAGACTGAGAAAACGCTCTACCTTGTCATGGAGTACGCTAGTGGCGGAGAGGTATTTGATTACCTAGTGGCTCATGGCAGGATGAAAGAAAAAGAGGCTCGAGCCAAATTCCGCCAGATAGTGTCTGCTGTGCAGTACTGTCACCAGAAGTTTATTGTCCATAGAGACTTAAAGGCAGAAAACCTGCTCTTGGATGCTGATATGAACATCAAGATTGCAGACTTTGGCTTCAGCAATGAATTCACCTTTGGGAACAAGCTGGACACCTTCTGTGGCAGTCCCCCTTATGCTGCCCCAGAACTCTTCCAGGGCAAAAAATATGATGGACCCGAGGTGGATGTGTGGAGCCTAGGAGTTATCCTCTATACACTGGTCAGCGGATCCCTGCCTTTTGATGGACAGAACCTCAAGGAGCTGCGGGAACGGGTACTGAGGGGAAAATACCGTATTCCATTCTACATGTCCACGGACTGTGAAAACCTGCTTAAGAAATTTCTCATTCTTAATCCCAGCAAGAGAGGCACTTTAGAGCAAATCATGAAAGATCGATGGATGAATGTGGGTCACGAAGATGATGAACTAAAGCCTTACGTGGAGCCACTCCCTGACTACAAGGACCCCCGGCGGACAGAGCTGATGGTGTCCATGGGTTATACACGGGAAGAGATCCAGGACTCGCTGGTGGGCCAGAGATACAACGAGGTGATGGCCACCTATCTGCTCCTGGGCTACAAGAGCTCCGAGCTGGAAGGCGACACCATCACCCTGAAACCCCGGCCTTCAGCTGATCTAACCAATAGCAGCGCCCAATTCCCATCCCACAAGGTACAGCGAAGCGTGTCGGCCAATCCCAAGCAGCGGCGCTTCAGCGACCAGGCTGGTCCTGCCATTCCCACCTCTAATTCTTACTCTAAGAAGACTCAGAGTAACAACGCAGAAAATAAGCGGCCTGAGGAGGACCGGGAGTCAGGGCGGAAAGCCAGCAGCACAGCCAAGGTGCCTGCCAGCCCCCTGCCCGGTCTGGAGAGGAAGAAGACCACCCCAACCCCCTCCACGAACAGCGTCCTCTCCACCAGCACAAATCGAAGCAGGAATTCCCCACTTTTGGAGCGGGCCAGCCTCGGCCAGGCCTCCATCCAGAATGGCAAAGACAGCCTAACCATGCCAGGGTCCCGGGCCTCCACGGCTTCTGCTTCTGCCGCAGTCTCTGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCGGCCTCCGTGCACCCCAACAAGGCCTCTGGGCTGCCCCCCACGGAGAGTAACTGTGAGGTGCCGCGGCCCAGCACAGCCCCCCAGCGTGTCCCTGTTGCCTCCCCATCCGCCCACAACATCAGCAGCAGTGGTGGAGCCCCAGACCGAACTAACTTCCCCCGGGGTGTGTCCAGCCGAAGCACCTTCCATGCTGGGCAGCTCCGACAGGTGCGGGACCAGCAGAATTTGCCCTACGGTGTGACCCCAGCCTCTCCCTCTGGCCACAGCCAGGGCCGGCGGGGGGCCTCTGGGAGCATCTTCAGCAAGTTCACCTCCAAGTTTGTACGCAGAAATCTGTCTTTCAGGTTTGCCAGAAGGAACCTGAATGAACCTGAAAGCAAAGACCGAGTGGAGACGCTCAGACCTCACGTGGTGGGCAGTGGCGGCAACGACAAAGAAAAGGAAGAATTTCGGGAGGCCAAGCCCCGCTCCCTCCGCTTCACGTGGAGTATGAAGACCACGAGCTCCATGGAGCCCAACGAGATGATGCGGGAGATCCGCAAGGTGCTGGACGCGAACAGCTGCCAGAGCGAGCTGCATGAGAAGTACATGCTGCTGTGCATGCACGGCACGCCGGGCCACGAGGACTTCGTGCAGTGGGAGATGGAGGTGTGCAAACTGCCGCGGCTCTCTCTCAACGGGGTTCGATTTAAGCGGATATCGGGCACCTCCATGGCCTTCAAAAACATTGCCTCCAAAATAGCCAACGAGCTGAAGCTTTAACAGGCTGCCAGGAGCGGGGGCGGCGGGGGCGGGCCAGCTGGACGGGCTGCCGGCCGTGCGCCGCCCCACCTGGGCGAGACTGCAGCGATGGATTGGTGTGTCTCCCTGCTGGCACTTCTCCCCTCCCTGGCCCTTCTCAGTTTTCTCCCACATTCACCCCTGCCCAGAGATTCCCCCTTCTCCTCTCCCCTACTGGAGGCAAAGGAAGGGGAGGGTGGATGGGGGGGCAGGGCTCCCCCTCGGTACTGCGGTTGCACAGAGTATTTCGCCTAAACCAAGAAATTTTTTATTACCAAAAAGA	MSSARTPLPTLNERDTEQPTLGHLDSKPSSKSNMIRGRNSATSADEQPHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNHPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAENLLLDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKFLILNPSKRGTLEQIMKDRWMNVGHEDDELKPYVEPLPDYKDPRRTELMVSMGYTREEIQDSLVGQRYNEVMATYLLLGYKSSELEGDTITLKPRPSADLTNSSAQFPSHKVQRSVSANPKQRRFSDQAGPAIPTSNSYSKKTQSNNAENKRPEEDRESGRKASSTAKVPASPLPGLERKKTTPTPSTNSVLSTSTNRSRNSPLLERASLGQASIQNGKDSLTMPGSRASTASASAAVSAARPRQHQKSMSASVHPNKASGLPPTESNCEVPRPSTAPQRVPVASPSAHNISSSGGAPDRTNFPRGVSSRSTFHAGQLRQVRDQQNLPYGVTPASPSGHSQGRRGASGSIFSKFTSKFVRRNLSFRFARRNLNEPESKDRVETLRPHVVGSGGNDKEKEEFREAKPRSLRFTWSMKTTSSMEPNEMMREIRKVLDANSCQSELHEKYMLLCMHGTPGHEDFVQWEMEVCKLPRLSLNGVRFKRISGTSMAFKNIASKIANELKL	YRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNHPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAENLLLDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKFLILNPSKRGTLEQIMKDRWM	Known - RefseqBioPerl-1.007002/t/data/test.txt000444000766000024       107513155576321 16413 0ustar00cjfieldsstaff000000000000>Test
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTBioPerl-1.007002/t/data/test.waba000444000766000024     15116313155576321 16552 0ustar00cjfieldsstaff000000000000U57623.c1 align 40.9% of 3833 pair1_hs.fa U57623:33-2971 + pair1_mm.fa.U02884:242-3687 +
agctatgatggcgtcacagtactccagcctgggagacacagcga-gagactttgtctctaaaa------------------------------------aataataataaaataaaaagttcaatgaaacaatacacccaaagccctcagcatgcaataaatagcaagacaaggcaggtcttattt-ttactgaaagtgcttagta-aactatacagtg-acaaaccaccgcacaacaggctctcgaaaggaggcagcaaattacccaaaagtg-caggcggcttgctagt-gtgcacaggccaaagaaagggcggcaggtggggaaggcagccat------------------gggccttgaagagctgaccgaattggcagaatttctgcaggaggggagctgggaacgacctgagctaaagctcggagctgtgcgaagaaaccggaaaagcccagagcacttgcaggggcgggtggggagctagatggtggggtggggtggggacggaggagggc-ca-gcaggagacattccgcagggaggggcaagcacgtgtgaggcgggc--ggggcgcgaagggtcaggcttttgctcaaaacaggcagaggacaaggtcagctcagccgcagaccgagccgctggtgactgtctccgccaccaggcagtgagagtgaagggagagcgcgacctctgaagcccgctagactaagcttgcaatctgagctccattcaccccctcctatttcttgagaccttgtcagttcccctgtgagcctcggactcacttgta-aa-acgaggacagatgcccgt----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gccagaa-g-tcaaccagagctttccccggcgtgggcaccagcccaagggcg-ttttgttttctagtctcatctctgctctgacgctaagctcaaagagggactgggggacgggaagatatccaccatggatgcgccctagatctcgggctggtgtcggctgttccttctcagattccagagtgtctagaggccaggaaagggagaaggtcctaccagcctggggtagggactcgggggccagg-cactg-gcgctgacgcagg-ctagcagggcgccactggctggtc-cccacccacctcggtgggt-tgggggatgggcgcaccagcccctcctgggtgagccctagcctggggcttcctatttcgggagccgggggcgtgggccacgtctcctcatgtgatgcgagggctatttaaagcggcagcccgggcagggagccgccg-tcggagcccttgcacgcctgctctcttgtagcttctctcagcctagcccagcatcactatggtggacgctttcctgggcacctggaagctagtggacagcaagaatttcgatgactacatgaagtcactcggtgagcaagccgcggggctcaggatgttgg-----------------------cttggggactggctggtggcgtgcctagccccacgcagcactcctgccgcatccctcctggttaagactggggaataggggagcgcggagatggcagcctggcctagagcaggt--------------------ggggcctgttcagagggggctttggtggtccaaatctggttagagaccacggtagggaggtggtggaaggaggcagctgtg-----------------tgggaggctctttccaggaag-agggatatgtgatttggaggtaggaggagggtttggataaagaacactgatcacaggaaagggagtgtagccaggggagaaaaagaacaggggcatgggtagtttagaaattggaggagactgaacccagaaagggaatggggcagccagggagtgtacaatgatgtaaacaagtaggaaatacctaggaggaaaaagattagtggggaaaaaactgtggatcagtgaatcagatatgagaaggacgtaagacaggaacctgcagtaagcagcaatccccatctctgc---tt-ggttagggaagagaattcttgctggagaatgccctttctcaccagccagtctgaccttgtcctgcagtctatgtatccaggccttcatcactgtctgtgagcctcgtggtagggtggggcaagaggcccatgatcagctgggcctttcctgcaac-ccaa-ggctcacc-tatctgtgcgaggggtaggcag-agaaagccattggacttctgatgtgcagtagagggtccca-aggcaaggtcaagacctgggagggaggatcactggtttaggaggatgtggagaactcctgtggtgttgggatggagaagaatcaggattcaaagaatctcac-aggtgaggaacttggagattccca-tacca-tctagttcaacagggaaactgaaaccaggagagtagaaatgtattataacaattccacagcagagccaatatgaaaatctaaggtttctagatctgta-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------acccagagctcttcccactaccctacaggccctgcgagtgggaagaaaagtagaaactgcttagctaatgattgacctcagcccttcttctactgctttgggcttagatggagag---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gtcaaagctctcaacggcctctaccctatcttg--------------ggcgctatgcccagtaattctaggcaggcagtcattct-tagaggagcagcccccagcccccacgaacacagcccagcagctattgggaagttggaatgcccagatttagttcctccttccaaagctgggccagagctgagtct-tgaattgagctgcaacaactttacc-attctt-gttcccttattctgccccg-agttggg-tcagcgggctg-gtctccctgaagtcctgttatctttcagcagcttatgttaaggcagccagcattctcatcgtaggaatggaaagcctgggaaaataccctcctcagctctcagtaagtagtgctggcttcatttctaagtagaacccagatctccctgagtctcctaaattctgtcagctcaatattcttagtttctcttggttcagaccctcactcatcccgcagtggtttccttttcaaacactccatacctctgggtagatcctaagtgaacag
agccagagcagcggcacacagctgtaacccaggagacagaggcaggagaatctttagttcaaggtcaacccctgctacacattgagatgctgacttggtaataatta-aacagaaactgctgaactaaggaataggctccactgaggttccct-tactcacctgtaaaaaggggatgataccacctaccaacgaaaaagttgagtgtgaccatgccctgaagtaggctacaaccatcaatagtcgggtcttatttaataacgtactttaaggtgacaagcagtctagtggcagaagtcaggggaaaaaactgacttcagcagagggtcgcggctttccgggagttaaggtggccgaggccggaagaaccctctgaatagaca-aa-ttgt-c-ttcgcggagtgaagaacgaccctggcacaagctcagaggtcagtaaataaagc-ctgaagcgctttcaggcagcggcgacgggtgggactg-----------------------cggagaaaggcgcaggcgggagacattccgcagggaggggctagcacgtgtggggctagcatgagggaagcaaggtcacg-ttctccgc-cagcagg-tgaggcgctgggcagctcagccatccgcggtgtccaaggcaactcttttc---------cact-tgtctggtaggagcaagagggctc-aaaggccactagaccatgctctctgtccaggctcca---attcttttttacttacggcgaccgcgtca-ttcctctccgagcctctgagcctcttctacaagaagaggacataggaccgttgagatgggtttttgggtaaaggcccttgctgtcaagccttgacaaccccagtttgatacgtgggacccacacggtggaagcagagaagggactcccgcgagttacaacgaacgccccagtctcccaccccttccccataagtacgcctacacgagcatacacaatataagaataaaaccacagcgaattaaaaaacaaggcggcagaaggatcaagcggcg-tttctccagcgt-ggcaccagctcaagggcgagtttcctttc-agt-------------------------------------------------------------------------------------------------------------------------------atggccgggggatgctctacttgggttgcgggaagcgccccgcagccaggccagggatgggttagatggcaccaacaggaccgcgggcgccgctgacgtaggcgacgggagggctgtgggggatgggc-c-ccagccctt--tgcgggagtgcaagcc-ccggcttcctatttcgggagcgaggggtgtgggccac-tttcatcatgtgatgcgagggctatttaaagaggctgtcc-agccgggagctgcggttctcagtgcctgctcgcctcctcactcatcg-----------------------caccatggcggacgcctttgtcggtacctggaagctagtggacagcaagaattttgatgactacatgaagtcactcggtgagcga-acgaacggcgcaggatctagggtcaggagggccggcaaggcggtcttggcgctgagctcccagggggagtgcccccatg-tgc-ctcccgcaagctcctagccagtccagac-agggaatactgaggtgcggag--ggtggcctgggctgaagccactccactccaccccaccccaccccggcctcctgggaggggggtgtcgcggtccaagcttggcgagcctcgtagct--ggaggggaagggtagaggcagctgtggccgcagaggtccgggatgggagg--ctttctaggaagcagtg-taggtgatccggaggt-gga--------------aaggggaggga-aagaagggcgggaggctggccgcaggagaaggcaaagaggagcat-ggtggtccagaa----------attgaattccgaaagggaatagagcagcta-ggagtgtacag-----------------------------------agcct-ggaggaagactaaagaaaatcagtgaattccatctgggaagaggtgaagatacagccaggcagtcagcaacaagccctacccctccatgttggggtagtgaagaggcctctctctggaagatgccctggttc-tca-ccagcctgaccttcacctacagtgtgtgcagcca-cccctgggatcagtcggagacgctgctgctagagcagggcaagacgaccacta-cacatagg-cttcccggccgcaccagtcggccaccggatcagtgctggggatagggtgaagaaagc----------ctgggatcgagcagagggtgtcagaagaaaggtgaagagctatgaagggaga-gtgtggctt-gg-ggctgggga-aa-ttgtgtggtgtgggcggtgacacaacgcctttaaccagcactctgggaagcagaggcaggtgaatctcccgagttctaggcctggtctatacagaga-gaattccaggacag-ccaggactacacagagaaaccatgtcttgaaaaaaaaaagaaaggaagagtcccatgatttacttaataggaagacagcttgggacacatgagctcatcgcctcataggaaagcccaggatttctttttgaagactgaactagagccttgtgcatgccccctactgctgagttatactccccactcacacacacacacacacacaccctctttttactctgtgtaacaggttctcactaacttccccaggttggctttgatcttgtaacctgccatctcggccttccaaatagttgagaacccagaactacctagagttcttcccatt------------tcaacagtggggaatgtcacatgaaccacttatccaa-ga-cggccccagcccttcctttcttgccttgagcttagataaagacctctacctgcggagtccctggctatatcatcctggtctaggaggctggggcagggaaaacaggactgtgtcatgcctgagctagcttccactccgtcttccccgggaaggagggctggaatcggacatgttgagggatgtgtgtagttgcctctcacctacttccagctcttctctgaaacaggcccacaaagcaatttgtccttttggtttggggaatggaacccaaggccctttgcccgtgctaagcaagcactgcgactgctgaaccacatctccagacagggctcccaccggcacctaccctaccctgaggctctccaggaaggcagctggtcttgtcttttaagacagggttttactgtgtatccctggctctcctggaactccctaa-ggagaccaggtcctgtt-gtctctgcctctcccgcactggggttagaggtatgagcccacacccagctagttggctgtcaagttagggagtactagattacctgggcttagttctgtttcactgagctgccgctgccttcctagacttctttttgcctcagggcatgttgtc-ttcaggccattgt---------------------------------------------------------------tctgtgggtgctgaacccagctttagtcag-gggactgaaattctatttagcctaaaaatatcgacaggctgaaggccagta--aagtctagatgcaccccagcttccagcagtaactggcttcactggcaccctacacctacctgtaggtgggtcctgggaaaacag
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLQQQQQQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTT312312312312312312312312312HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLQQQQQQQQQQQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLQQQQQQQQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHQQQQQQQQQQQQQQQQQHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTT231231231231231231231231231231123123123123TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ1231231231231231231TTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL231231231231231231231231231231231231231231QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ231231231231231231231231231231231QQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
U57623.c2 align 43.7% of 4211 pair1_hs.fa U57623:3021-6913 + pair1_mm.fa.U02884:3704-6847 +
gcctgactcatcctgataccaaggggcaatgccaagttcctcactggccaagcaagggtgggctgacagcataacagcagaggcagcccctgcccctcctgctgtagacctagggctctcaaggggcaaagaggtcccgtctagtaccagtgaccacaggcacaactgctggcct---ggattgagtatgtgctggacagaatcgcccagtgaaaatagtcaacagttttggagccgaggttcaaatctatgtcagtagtttattctctttgaattt-----------------------------------------------------------------------------------------------------------------------------------------------------cgacaagacact-tcgcactcttcattgtaaactg--gggat-aatctacgcttcgaggctgttacaagcattaagtaaaacaacccatgtagggcatgtgcagagtacctagcttccagcaagcactatgtagccaggtacatttggagactttacac-acaccacctcactacactgggctgcctcctgcctcacctttg-------------------------------------------ccttggaaga-cagttcaatgttaagctgctggggggagagggggcagtcatgattagttctttgttctttacttggttgcaggacacttaggactttgcccagtacccaaggaagccatgcttgggtcaggaagagagtctctgtaaagccttagactgggagtcaggagacgggtttgagtctaactca-ttgttgctaccgctttaggctcctcctgaatctgcacaataggacaaatacttcctttgta-c-ctaactcctagatcatagataacaggctttgaaaatgatgggttgccatgtataagggacaagagcactaacacttcttag-tttcagggtaaaaacttccaaagttggaaaactcctatgcctaaggctttggaagggaaagtctatgtttctcttctttcctcagccttattcctaaggctttgagagcttttcaggtgccctggaaggcagccttatgctccagccttgggaggtagtatagctgagcacttaagcaagctctggactcagacaattctgggcttcaatc-tcagatttgtgaccctgggctttacctctgtttttgtatctgtaacgtggaaacagtcttcagaagaacaggaagaactaaatgagataacatgtacagttcttactacacaaaaagctcatagtacttaatagtagctttttttttttttttttgagatggaatctcactctgttggctaggctggagtgcagtggcacaatctcgactcactgcaacctccacctcctaggttcaagcaattctcagcctcagcctcctgagtagctgggattacaggcacataccaccacatctggctaatttttt-gtatttttagtagagacgggtttcaccatattggccag-gctggtcttaaactcctggcctcatgtgatccgcctgccttggcctcccaaagtgtgattacaggcgtgagccaccacacttggcccaatagtagcttattctaatcccagctctgccactgacttgctatggcactgctgttccttaagtatctctcatctaatgggatcagttatctgtgttcaccaaacagaactaagcgcaagactgaattttaaaattcccatgca-aaggctttgaaagatacagtcctccacttccccatacccaggcctgagagttattcattgagtttcttgtacactgcttctctaccccagctcatatactcataac-ct-tccccctaccctcaggtgtgggttttgctaccaggcaggtggccagcatgaccaagcctaccacaatcatcgaaaagaatggggacattctcaccctaaaaacacacagcaccttcaagaacacagagatcagctttaagttgggggtggagttcgatgagacaacagcagatgacaggaaggtcaaggtaagtcagggaaacaggggtggggaatggagagtgctgagactctaaaagagaataggctggtagtcttggctccctgg-tattgcaccctgaggggcagactatcatggggaatttacatgaaacaagattcataaagcctgtgtagtgctggaatgccactgatgctaaatacatg-tcagttctgtcctcttgttttcttccctcccttcttgggattcatctattgtctgcctc-ggaatgggcagcacagagccaggatgttcttctgacctcagtatctactccagctccagctgggtgaccctgt---gcaaggtatgcagtagctct-aggtttctttccccttccatagatggagagttatgtggccatggctgtgacctgaagtgctttaggaatgatgcccagaagtcagggccctccactgagtgaggtcattgtgacctccagcagcaaaaaaggcagccaggaactagaagc-acctactcagatgccgcttca-act-tctaactcccagacatggccaatgaccctgacaaactatttccagtgttgccagctgacaggca-------ggaaagagctatgttccgtgatagggcattcaccttgtcatgaatgtgtttgcagtgtctcccaccaagccttagcccctcctcccagggttctatcaccctgcagtggctgtcttggcagcttgc-ctcagccttccaggccaggcatgggagcgagagaacttaagggctttgacctctatagggtgtccctatagcagtgttctat-catgacactatcattcagccccatcagctgtttcctcttcctcatagctgtccccagaaagaacagg---------------------------------------------------atcacacaggtggctggcagcagagctggggatggtgcccaaagatggcagtctaccttggataaaggtggctgccccaccacctgctcatacctccttggacttgcctactttctcaaggggcaagaaccccaattaaacacaata--gc-cctgtggaatgcctagggcaaaaatatctactctgagtaggcaaaaaaaactaggggaat-gagaacaaggagtaaggtaaggataaaaaagagcacactaaga-gacaggcctcataccccttatcacctaaacaatacacagaaccttctcagattctcctactgaaccaccttgctcatcaggatcccttagcctggccttgtggcccccaaactcct--aggaaagagagctggaagagctgccaaatgagaaccagctgatgtatgtatgctggcagcacccagagctgaggaaccacttcaagggcatcca------------------------------gtcacaggactttgtggttgctgccctcttgttggctaa-agaggtcacatgatgtggaccaagaaaaggtgtaggaatacagggcaggaagtctaattatccaatacttcctatcactaagggtcttttagacattatgtggactaaccacaaggctggataaagattctcaggactactcctcctcctcagtcagtctttcccagggatagactagtaaatcccacctgtatctgaggggaccaggctacgggaatcacctagagtacagataagtgtctgtcttgaaggcttgtggtacttctcagagccaggctctctggctccaccatactgcctgcctctccctccttgcctaatatctgaaggcctcttccccagaaaggcagtagtggagcagaggctggaggtgaactagatgtcttgcagggatagctgggaggcggattgcctgagctcttgtcctcacaccatcactagtttgggtcaaaggctgtgtcctctgtggcccagtgtccagaccccaccctgcccctcaattcctgactaagatcacagctcaggcctctaccctctttccacagtccattgtgacactggatggagggaaacttgttcacctgcagaaatgggacgggcaagagaccacacttgtgcgggagctaattgatggaaaactcatcctggtaagatgggca
gcccaactcacacagataccagtaggcaaagccaagcctctcact------------------------tcttgctgtgtagccaaagctcctgacttatcctatagaaccaaaggt-tcttaggacaaagcagcccagcctagtttaagtgacttcaagcacagatggtggcttcaagggtagagtatgttattccaagaatgatatagtgagactaaaagagagtttgggaatctatg-tcactaaactcggatta-tttatttacttagcctttttgagacagggtttcactatagcccatactctggaagctacgcagcccaagctggccttgaattctcggcatttcccctgctccagtcccctgcctcttgagtgagattctaggggagtcaccatgcttggcccgtttgactttggctaagacagcaccgtgtctcagcctcgtttgtaaatggaaactataaagcttaggtttagggctgtcccaagga-t-act-tggcca-ccacttagagcttgtgcagtgtgcacagcttgcagcag------------------------------atgcacaataccatagccttatattgggctgcctcctgccacatcgctgaggatggctcagagtgtgctggggccagacgacaggtagtcaaccatggaagattccaggaaagctactaacccaaagcaccaaaggcttgac-ccaaggggtctgtgaactttacctgcttgagggacacctgggaccttgcctaggactcag--------------------------------atccaatgattatgtcaggagtctccccagggacttccaagtcatgcagttgtcgctacttttttcagc-cct-ctacgtctg--tggta-gac-aagac-tcctttgtatctctaac--------------caggaggctttgaaactga--cgctgccatacagacggca-gagagcact-gc-tgtctcagttttctgggtggaaa---------tgggagacgacccttgtccaggggactctagaaggcagttgacg-atctcttggttcttcagtcctgtt-ctgtgtgttcaggag------------------------------------------------actagaagccagcgggt-acccagctctggagcgacacagtgcttagcagcttccatctgaattgtgaccctg-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttcacatctacaaaatcttccaggggcaggactgcgtgaggggctggctatgtggctcacaccccatggtaccttccttgccgctgttgccgaccctgccct-gcatccacatgtctcatatttgacatgag-------------------------------------------------------------------------------------------------------tttaacagctgccgagctaagggaaagagcta-agggaatgagaaaatggccccacacaaagacgtgggccactgag-gatcgccttccccatgcctaggccacaaactt-ctctttgggtct-atata-ac-acgtctctaccctacctaatgtgtcctcaactatctgcccctgcccttaggtgtgggctttgccaccaggcaggtggctagcatgaccaagcctactaccatcatcgagaagaacggggatactatcaccataaagacacaaagtaccttcaagaacacagagatcaactttcagctgggaatagagttcgacgaggtgacagcagatgaccggaaggtcaaggtgagtcagag-aa-agggga-tggagggcactg-gatggaacaccacagggtaagaggctggccctcttagctccttggctttttaaccccaaggggcagg-----------------------------ttcataaagcctgctcagtgctgcgatggcccagggactaagtataagctctggcc--------tgttttcttctc-accttcctgggaaggatctatcagctgtcactggagtgggcag--cagagccaagatattcttccgacct-tgt-gc--ctccagctccagctgggtgaccttgtacaccaaggtacccagtggctctgagg-------------------------acatcagcagccatggctgtgacctgaagtgttttaggaatgatgcccagaagtcagtg--ctctac--agcgaggtcatcctg-gctctggcagcagaggaggcagctgggaacaacaagctgagttctatccacaggtttcctgctctgtagctcccaggctagaccactgaccggaacaaactgtttccagtgccaccagttgacaggcacctgcgtttaccaacaggagtgctgttgggtgtccatagtctcttcaagtatttattt-aagggtatgggagggagtgtctacctccagtgatgctcagttatctcatggtggttatcttcttagcagcttgctcaaaatctcccagcactgg---gccacgcacagaactaagtaacatctgtatctataggttgtccttata-cagtatcctctacatcacaacccta-aaattcatctcttcagctctttcctcctcacagttgcccccagaaagaacagggtaggtaccaaccagtcttgcagttacagaggcgctaaagcccagcccaggaccacacagcaagctggaagtgaagatccccaaggcgccctgctgcaccctgctccaccacat-------------gtcccacctac-c-tacatctttgaacttgccatcttccttgagagaccagatttcacattaaatataacagtggtccactgggatgtct---------------------------------------ggacaatggggaatgaagattccagaaggtggaatatagacaggaaagagatgagtgacagccatcacctt-tctagactcctaccgacaaaccctgcttag-ctctccttctga---------------------------------cctgcaactcccaaattcctaaagcagatagatttggggcagctgcccaacacgaactagctga-g-a--taggctggcagcaccaaggaccgaatggtcactggagctagagctagagaacactccaaggatgcctgggtccttggtccaaggaccttgcaattgccgctcttttgccagttaagggaggtcacatggtagaaacaa---------------------------aagtctaatttgccaata-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tatcaaggctgagctgcctgccatgcccactgccagagggcc-ccgcccctgcagagcagga---------------------------------agcttgggcagctgggctggaggtgggctgtctgctgatcccagcaccatcactggttaggttcctggtttg--------------------------------------------tcctggctctggtcacagcttagg-ctct-gtctctttccacagtcactggtgacgctggacggaggcaaactcatccatgtgcagaagtggaacgggcaggagacaacactaactagggagctagttgacgggaaactcatcctggtaagatgggca
231231231231231231231231231231231231231231231TTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL23123123123123123123123123TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLL2312312312312312312312312QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL23123123123123123123TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL12312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312312HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL31231231231231231231231231231QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTHHHHHHHHHHHHHHHHHHTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT12312312312312312312312331231123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123
U57623.c3 align 50.3% of 2218 pair1_hs.fa U57623:7003-9170 + pair1_mm.fa.U02884:6891-8711 +
gctgggacaagagagtggttgtgggtcagggtggtatcaggtgggaatttttctgtgtagtggctttggactcacacaggccggaactcaaatcttaccttataggctacatgactgtgggcaaatcaccttttccaagtgcaactgtaaaacgggtattaataataccaaccttgtagggctgctgggaagcctgtaagagacagtgtatgcacagcacaaagca-tcact-gat-tgaggaacacagcaggtgctccatgtcctttgtttgctcttcctgtgtttctaccttgcctcacctcaggaagaagtagaaaacagggccaaatctgatcccaggccctctaggaggggctcccattgcctatctcagcattccctttcctctcctccctaggactgcattgtcacttgcagggacaggctcgtgactggtggggacactgaatga-cagtacagtcctttcttccccattctagtcctac-cccattttcatgctttctatgtctggcctactgaaactacttgactactgcttgggtaggaagtaccacagccaggctggcagatctgttcaagcttggggacttcacttggagaatctagccttgactgaattccccccagacccagggagagcagccaactgtggattctgcctaaccacagggcctcaggttttcacctaggcatcttcactgcacaccttcttgggtcagcataacctgttaactgcattcttgtactcatgtgggacaggggtccccttgaagtttggaatgaggtgcctagctttggtggggatgtgatatgcaggaccaaattctcagtggcagctgaactatggtgaggccatgggtctggctctatgatgccagaccggatagtgggaggtacagggctctggccctggcactactctaagttagggaaggattggagttagtacccaaacacagtcctttcctgagtctctggatatttttcctatttgtc-aac-tatatgccaggcaccatcttagacactaaggatgaagaagccaaatggtataagggaaggaaaaacactcaggtcttgaccaaattacttcctctctaaaggctc-gttttt--tccaaatctctaaaataagaattacaatgcctgtcttaaggatttgctgtgcatatcagaaaaaaaaaattatgtatgtatacacacacacacacacacacacacacatacatacttgccggcactggtaggtctcagtgaca-attatcaggaggaagggagggtagaatgctcgcaatg-gtgttcctggctc-ccac-cccccatctc-actctgtctttccttccagacactcacccacggcactgcagtttgcactcgcacttacgagaaagaggcatgacctgactgcactgttgctgac----tactactctgccaatcggctacccctcgactcagcaccacattgcctcat--ttct-tcctctg-cattttgtac-aa-atccacgaattcttctggggtcaggtgccactgaccgggatcc-agttccagttcccatggtgtatgtggttttttttttttttttttaactgcactcatagggtgctctgaggtcaataaagcagagccaaggccacccagttgccttttggcctttggtaacataactctgggagtcttggtttatcctgtgtgtcagagagtg-ggcagaaataacggcctgaaggttactgaggaagaagcactggatgggagactgaaatggacagtctcggagc-ctgttaatcagctgatcaccttacacatttaataataaaagagctgtacctacacgttgcctttacactgcccc-----------------ccctccatggtcaaatgacctagttcagtcagtgatggggcttccccaggtttggctattgaactgtcacttcaggcccatcctacactga-aa-gctc-ttgggt-ctggctgttctctgtgaaatgctgtagtctctccctttccagaattcaggttcagggca-cagaacccaggcttgtaccatggtggtgggaga-aaatgaccactggccaagaggactgctgacctgtgcaccaggctagtacttatgactacaaattcttactgcttctctaatcaactctgagggaagagggcatctgatcattacaaaagggagggcttataagtgat
actaggacaagagag-----------------------------gcaggggt-ggggtcctggctgtggatttacacaggtcttggttcaagcatcagtctaaaggctatctgac-aacacataaccttcaagggccactgaaatgg-------------------------------gggctgctgggaggcc----------agtgtattcagagtccaaagcactggccaaatgggaagaacgcagtaggcacccacaaacacttcctcctgcttgctgt----------------tccctgggaagaggcagaaagcaggacc-agt-agatcccaggctggagaggagcagctgccat-----------------cctctcccctcctgagtagaaatgca-ggagtc-tgcaggaccaagtgtgtgcctggtgggcactgccagggagcagccccctccttactcacaattttgtctactgctcctggcttcctg-gaaatatctattgtcta------------------------gctaggaggtgatacaaccaggcctgcagatctgct---------------------------------ttgggacaagtttgaaagcatccctggaatagtccctacatcctcgtaggactgtac-ctgggccaggagcatggaccacaatgtcagcatcacagacctgggtcgctcagtggaacccactgattgca------tattcacatgagactggggttcccactgagttagaagtgaagggcctagctctggaagggaggtaacaaagaggatcatgttcac-taggtagctagagtaaggtgaggccatggct-gggctctacagtgccaga------------------------------------atactgcatgttaggggagg-gagga-aaagttggc-agcttagcagtttctcaaggctctgttcttatcacccgtttgtctgccacatacaccaggcacccccttaggca-----ggtgctgaaatgaacacaaaggaggaacaggaatgtact-ggatcttgaccagtttacctcctctctcaagggcctatttttcccccaaatctctaaaatgctaattataa--catct-taaaagatttg-------tatcagaaaaaaaa-----------------------------------------------------------gtaaagtgcctggcacacagtaggtgctcaagtgctggtcaggatgagggtggggagcactccctcctctgctctgccccatctgaaacctgtctttctttctagactctcactcatggcagtgtggtgagcactcggacttatgagaaggaggcgtgacctggctgctccgtcactgaccgcccgctcctctgccaactggccacccctcagctcagcaccatgctgcctcatggttttcccctctgacattttgtataaacattcttgggttgggat-ttttctggagatacggggcatcagcctggacccagttcctactatgtatgtggtttatttttt------aaaactgtatccaaagggtgctccaaggtcaataaagcagaaccaaggccacccagttgtct-------------------------------gtctttggtcctcctttcctgtgtgtcaggttgaaatgaaggcctataggtcacctgggaagcagcactgtcaaggag-ccg-agtggacaggctcaaggctcagttagg-----------------------------gaacagtagcacctatgtaatacccttacactgacctgccaaggctcagagaagctagctgtcattctagcatctatgcaagcccttacactggcctgcccatggcagagcagctggctgtcactgtgtggctatttcacattcatcctgcacagacattcctggatttgctgtatggtgtgctgtggtcaccctctctctagagtacaggctcaggacatcaaggtccaggtgtgaacaactgtggtgggaggtgactgctaagagtcgcccactcatgcccagcaagtccccagggttacaaatacaagggaaagcggtc---------------------------------------atcactatggaagagaaggtttatgagtaat
312312312312312TTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTHHHHHHHHHHHHHHHHTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTT231231231231231231231231231231231231TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL312312312312312312312312TTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTHHHHHHHHHHHHHHTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL3123123123123123123123123123123123123123123123123123123123123123123123123123123123123123123QQQQLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHTTTTTTLLLLLLLLLLLLLL312312312312312312312312312312312312312312312312TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTT3123123123123123123123123123123123123QQQQQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT2312312312312312312312312312312
X57152.c1 align 46.8% of 7572 pair9_hs.fa X57152:3-5844 + pair9_mm.fa.X80685:631-7367 +
ctgtcggttggggtcctacttttacataacgcccccacaatgcccttcgccttcctcaacgtggcccccgctccaagcccattttctggagccaggaatccactctgtgggttaggaaaggccctcaggaggc-ggagggaaacctgtggaatgccgagaagccgtgtaatgaaataacggtcacggcctggcccctcaccattactctgaccagggttcgaag-----------------------gtcacacttagagcctaaggggaaatggagaagtgcaaagggacgag------cagaatggctggcaccacctcaggttagcgcactgggacgttcca-gttctcacaccgcccaccccaccccacccaagtcctacgca-cggagccaag-ccg-cacctctcccctcatgaggcaggagccccggaggaaacagtacgcccgtcaagggtctctggcgggactgattcgcactaggggcccaacaggcaataaggacccagcggattggccgaggataggccagtcccctgggcagcagcgccgcgccgggactagaggggaacgtgaggaga-gctgcggaaagagatccagcctggctc-cctcctttccccgccctaagtcagcctcttcacccagtgagcacaaaactgtattgcccagactcccgggccccg-a-acgccatacctggcttccgcttccggtggcttctcgttgtgccccgcccgcaagcgccctcctccgggccttcgtgacagccag-gtcgtgcgcgggtcatcctgggattggtagttcg-ctttctctcatttagccagtttctttctctaccggggactccgtgtcccggcatccaccgcggcacctgac-c--cttggcgcttgcgtgttgccctcttccccaccctccctaatttccact------------ccccccaccccacttcgcctgccgcggtcgggtccgcggcctgcgctgtagcggtcgccgccgttccctggaagtagcaacttccctaccccaccccagtcctggtccccgtccagccggtgagtctgaagtcgtcgctgctccgagtcccttgtcgctgggagcggcacatggggtctccggactttgatgt-ggggcgggggaggaagcgaccaggtccg-gcacgaaggagggagaggtggcctgaggagcggaggggggatgtgtggattccggtgaaagggacctgacaat-c-gcc--c-ccaaccc-gtgagaaaaggaggagcccagttcttgcttgagaatgataaacttggaaacccttgggaaaggcgtgggggtcatgcagagacttgtattggtagggagcctgagtcgaggtccctgccggagttgacacagaggagagagggccctggccttcgggagctccagggatgtgggtcgggctggtgggtcaaagtatctg-ttggcttctttcaagtggtgg-gaccccaaagaatgtttaacttcaaagaaaaggggctgagatgtaaattagaggagctggagaggagtgcttcagagtttgggttgctttaagaaagggtggttccgaattctcccgtggttggagggccgaatgtgggaggagggaggataccagaggcagggaaggagaacttgagctttactgac--actgttctt-tttc-tagctgacgtgaagatgagcagctcagaggaggtgtcctggatttcctggttctgtgggctccgtggcaatgaattcttctgtgaagtgagttctcttcaacc-tccctacttgccagcttcacatatcttcccaccagacgttccttcacatattccacttctacactgttctcttacatgctatttgaaaacttcctatcagcaaagagtcccccctataaaccccgacgaacctgtgctaaagtggcaaaactggggcccaagtcctgagtctgccaccgtccagcaatataacgttgggctagtcaatttgtgtctttttcttttttttgagactgggtctcactctgtcaccgaggctggagggtagtggtgcgatctcggcttactgccacctctgcctcccaggttcaagcgattctcctgctccagcctcccaagtagctgggattacaagtgcctgccaccatgcctggctaatttttgtatttttagtagagacagggtttcactatgttggcaaggctggtctcgaactccagacctcagggtgatctgcctgcctcgggcctcccaaagtgctgggattacaggcgtgagcattgcgcccggcctgtatcttttgttactaaagtggcactgctagtacttgtctcaggtggcctttaggaaaactgaaatgctacacattgaaatgttttg-------------------------------------------ttcagaaaccatgctgttcagcttccacc-ttccttagccagctgagaggacaaaactggttcctagagacgggatacaggagtggagtagggacaaagatcttggaaaagaatgtctaa-gaaaaag-a-ttgctgtatctacttatccttagaaaagaaaagccaaagcttttatgggagagagtgtaggtgaactagggagagacacaagtacttctgctgagttgggagtgagaaacaagcacaacagatgcagttgtgttgatgataaggcatcacttagagcattttgcccaggtcaaagatgaggattttgata-tgggttc--cctcttggcttccatgt-cctgacaggtggatgaagactacatccaggacaaatttaatcttactggactcaatgagcaggtccctcactatcgacaagctctagacatgatcttggacctggagcctggtgaggcaccctcagggttgtt---------------------------------------------ttgtgtgtgtgcgtgcactatttttctcttc-aaat-ctctattcacttgcctgaattttgccaaatttcctttggttctctgatttctttaaccccaaattcatgctttattttgatcctccacctgactcttgtctagt-tttgtgacgtatatcacttgttctcatgttttctaaatccgcaattcagacctattccaaaatgcgtttcctcag-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ggtctggtttgttgtctgtttctcctgctttgcaccttccagtctagagtttcatcttctgcattgacattgttgcagttatgtattgaggagggagttgggagggagagcaaggagcagaggctgaaaaggtgtgaggggaaggcagagctgtcttcgtttgatgcaagggtcagaagcccaggtttctgggtcccatgcccagatgttggatggggtaaggcccaaaagtaggtgctaggcaaactgaatagcccgcagcccctggatatgggcagggcacctaggaaagctgaaaaacaagtagttgcatttggccgggctgtggttcagatgaagaactggaagacaaccccaaccagagtgacctgattgagcaggcagccgagatgctttatggattgatccacgcccgctacatccttaccaaccgtggcatcgcccagatggtgaggcctctctgctcctacctgcctccttctgagcagtaagagacacaggttcctgcagcaagaagtcatgtttaagccctgtttaaggaagctagctgagaagaggggaagaaccccagaacttgggcctgggaattgaattctgattgggggtcatcctgaagggattgttttcagggagggagac-agaccttgaatcagagagttgtgatagactgcctcttcctcaaggaacaaacaacaaatggctctgatggtttgtagccctgccctaatttggaagaaaggcaacacagaagtttgagagcccatctagtccagagaagggggcctctggacagagttggaaggagtgccgacagagttggtatgggttgggctgcgaagggagttgc-ctcttctttacat-ct-acctgccaaccccttccattgtattcacctcagttggaaaagtaccagcaaggagactttggttactgtcctcgtgtgtactgtgagaaccagccaatgcttcccattggtgagtgttgaagaagggaaaggaaagcaccgtgtggcagtcttatgggaaggagttggggctcaacacattggagcctgagtcctgaggggaggttaggtaggaatagggggatacctggcctgctgagtctggctg----tctcccaggcctttcagacatcccaggtgaagccatggtgaagctctactgccccaagtgcatggatgtgtacacacccaagtcatcaagacaccatcacacggatggcgcctacttcggcactggtttccctcacatgctcttcatggtgcatcccgagtaccggcccaagagacctgccaaccagtttgtgcccaggtagggagcagggagagtcattaagggtcaaaggaaaggcccaagatcccccagagaggggaggacagggcatggccctttcttgaggtctgcttctcccagaatcagggcatctccctgctgagtgactgtgggaaagttatttgattatctgtgc-ttgagttacc----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttattgtagaatgttcttgagctgagaagttgggaaccacgaggctttagctctgagcaggtccat-----------------------------------------------------------------------------------------------------------------------------agaggagctcaggtgg-ggaggtgggaatgcaggtgactggcagggcctggatggggctcatgctgctgcctctctgacctctgccctggcctaggctctacggtttcaagatccatccgatggcctaccagctgcagctccaagccgccagcaacttcaagagcccagtcaagacgattcgctgattccctcccccacctgtcctgcagtctttgtcttttccttt-cttttttgccaccctttcaggaaccctgtatggtttttagtttaaattaaaggagtcgttatcgtggtgggaatatgaaataaagtagaagaaaaggccatgagctagtctgctggtgcttgctgttggggaagggaaggtgatggtgtgttggactccaggggccctcatggcccagcccaccctccccagattgaaaaccaggacagatttgtgctcagtggat-tgggtggtgtttttagtatggagcagaacagaattcctaggactgcgtgtgatgaaatgcaaggtcaaaaggaaaagacaaagcatatttcaaagatgagaaatatttgtttggatatctatgactgtctgtttatactgtaaggggcttaatcagcagctccatcttttagttttagttctaaaggaaaagtag-cctaaagtcagtataactaaagggtggaacgaggtgggacaaggtccggaattgctgctcagtgatgtgtgtgtgcctgccgctggtggagctgagactgctcactctcagaaggatggggatgcttgatttcctggccaggttgtcccagcacagtggggattggccctgttgtatgacgaagacagcacatggtggcagagatagatactaacccatggactttccaagggagggaataggtctttggagggtatgcaagacaaaggtagacactggataaagaacccggtagtgcccaggtattaccccatctgggccattactcccacactcaggaaccagacgttgtgggtgaggacatgctgtccctcctgccaagta-ataacttccttccca-gccaggatcctgccccaagtaggaatatagctctgcatttacagcagctcctgctcagac--cttgtcaaaaccaccctgcagcttaggattaaggagcatggtcacaggaaggtggggtttcagggcatcccctcaggaactgcccatctccccagaattccaaaatgaaggtccatatgcttgtaggtgtgctggtcatggtgggctca-cagtaggaaagggtaagtggggcccaggggcagggaggg
ctgtcggttggggtcctgcttttacataacgcccccacaatgcccttcgcc--------------------------------------------------accctccgcgttcagaaagactctgaggacacagtggggagacctgtgggatgccgaggagctgtgagatgaagtaac-atcacgg--ttacccctcaccactgctctgagcagggtttgaagaacagtcagggtcatcagcacaactctctaccccag-ctctgaggagatggagaagtacaaagggacaagcggcggcagaatggctggccccacctcaggttagctcgcaggg-cggtccaggttctcacgcagcgtgcacagctcagcgcatcccaagcacacccgacctaagtccctcaccacaactctgcgcatgccggagcccgagcgcactctgt----------------------------------------------------------------cgcgggcctggcga-gaga-accaggatcccgtgggttggcctggcacagggaagagggagaaaaaaaagcaaaggcaactgagggagcacc-gcagggatgacaatcagcccgaggacctacccggcagctt-agcgag-cctaacaagactatatttcccaggcttcctggtcgggaagaccccctgctccgcttccgcttccggtggcgcctcggttcgccccgccc-ccag-gccttcctctagggcctcgcggcttagagagtcatgcgcgggtcctcttgggattggtagtttgtcttccccccatttcgtcagtttctctctgccgacgggactacatctcccggcgtccacggaggtagggggcggttcttagcgcctgc-cgttgccct-tttctcaccc-aaatcctcaccagtttccagtggccccccccctccctacttcgtctgctgcggccgggtcggctttttgcgctgtagtggtctctgcggttccttggaagca-cagctccccttccccgccccagtcccagtccccgtccggccggtgagtgtggggttgtccccgcgtcgagtgcc-cgtccctgggcgcggcac-tctggttggagctcctcgatgtgggggcgacgaaggaagtgaccgggtcggtagccgaaggaggtcgggggccctgggcgagaggaggcggcttttggggacgctcgtgagacccacagaagtgtggtgccttcgccaaccctgcgagtgcagga-gaggccggctc-tg-ttggggaaaatgaacttcggaagccttgggacaggcgccaggaacatgcaggcacctgcggtggtggggagccggagccgagggccctgtcgcggctgacatggaggggagaggggcctggctttgaggagcgccagggacgagggtc-------------acactaacagatcaggacctgtcattttctggaaagtagcgaaacttattgccagcacactgcaagggggctgaggtgaaggagagaagcttg-ga-ga-tgcttcagaggccgggatccttcaagcctggctggactcagattcttccgttgtt-gtggagaatgtgtgggaggagggaagagacaaga----------aacagcttggtctccacttacttaacgctcttctttcacagcggacataaagatgagtagctctgaggaggtgtcctggatttcctggttctgtgggctccgtggtaatgaattcttctgtgaggtgagtttaggtcggccaactccacatgcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ctcgatgttttattttatgttgtttgagagcagatttc----------------------------gacggaactcactatgcagcctagactggccttgaactcctggcagtcctacttcctcagtctcctgagt-gctaggatttcaaggttttgtcaatatgcatggctaacagaggtacctct-------------------------------------------------------------------------------------------------------------------------------------------------------------------gggtgaccactaggataattaaaatatttcatgttaaagttgggtaatgtgcaaagcccggtggcttcagtagaaaattataaatgcctttcagaaactaaactgtttagccttcatgattcccaagtcttcaactcagagagtttgctatccccaaga-agatggcaagtgcggtttctaaaataagcttgtgtcgaag-ctgaataatgtctatgtctttgctggagatggttagcctta-aagaaagggcctgcagtttttatgagacttc--------------------------agtacctctgcagaattggga--------ataggacacgagaggtgacttggctgaggataagacatctcttgg--------gcccaggtggaagatgggccttcctatattattttcaaccccttggcttccctgtgcccg-taggtggatgaagactacatccaggacaaatttaatcttactggactcaatgagcaggtgcctcactatcgacaagctctggacatgatcttagacctggaacctggtaatgtgcccttagggttgttgctgactgtggggttggtgataaagtgtgcactcccctccataggtgctttgttttcattttcttctggtctctgctcactggcctcttgaggtggttg-ttgtgggaggtggaaactgggttttcttttttcttt-ttcatatatatatattttatgtatataagcacactaaagctgtacaggtggttgtga-gcct-tcatgtggttgctgggaattgaatttaggaactctgctctcgagtcaaacccgctcactcagtccctgctcactctggcccaaagatttatttattattataaataaatacactgtaactgttttcagacacaccagaagagggcatcagatcccattacagatggttgtgagccaccatgtggttgctgggatttgaactcaggaccttaggaagagcagtcagtgctcttaaccgctgagccatctctctggcccgagacaggttttcttgggtagccttgtctgttctagaactcattctgtagaccagcctgtccttgaactcacagagatctgcttgtctctgcctcctgagtactggatcacagactggcttgcttcttgaatttctaaatttccttttaataatccagctctctctcctatccccagatcccttgctcctgtcttttctcccccacctcaaggcccaagcattcataacccaaactggactttaccccttggtctttctgccctgctttcgatggctgagtcgtggcacacacagcagtgcttggcttcttcactgttttgattccttatgactcttgctttgtctccaagctctctgaaagtagctcagttctggttcgtaacgatagtttcctctcgggtttggtgtgctgctgcctcttcccctctgctgctctagag-ggcctcctctgcgtttgtgtgtttacatttacttactgtgaaaagag-aggcaggcagagactaaag-------aggaacacagagaaggccctgccgagcagtcttgctttg-tagaagaatcaaaagcccaggtttctgggtcagatgtatagatgatgggtagggcaaggctcagaaacaggtactagagaaactgga-ggcgc-caccttgcaggtaaggtggggttaccctggaaaactaaacaagcggccaccccacccacgtt--------ttcagatgaagagctggaagacaaccccaaccagagcgacttgatcgaacaggcagctgagatgctttatgggttgatccacgcccgctacatcctcaccaaccgaggcatcgcacaaatggtgaggc-------------tctg-ctccttct--gcaggaagggaaacaggtgcatg-ggtccg-aggcctggttcctacctg-gcaaggagcgtggcagaggagagagggagagacccagagc-tggg-ctgaggagtgaatcctcactcagggtcccattgaa-gg--tgttttaaggaagggagatgaaaccggaaaacgaaggagtttg-----------------cagggaacaaatagcaaatggcccctgggctctgcag-actgccc-cacaaag--gaaaggc-ac-ttg-agtttgaggacctatctcg-acagag-agggggcttctagtcagaagtgggagacatgggg-------------gggggggaccatgaaatgagttgagattgcctcttcatgctcacccaccagtcccttctgttttacacaccttagttggaaaagtaccagcagggagactttggctactgtcctcgtgtatactgtgagaaccagccaatgcttcctatcggtgagtgttgaa----------------------------------agccagaagctgccttactgtac-tcagtgcccgagtcct-ttgggaggttggggagcgcta--gggatacctggtctgc--agtctggctgtctatctcccaggcctttcagacatcccaggcgaggccatggtgaaactctactgccccaagtgcatggacgtgtacacacccaagtcctccagacaccaccacacggacggcgcatacttcggcactggtttccctcacatgctcttcatggtgcatccagagtaccggcccaagcgacctgccaaccagtttgtacccaggtagggagcaaagacagtcacaaaggatcaaag-----agccaaggt-ctagagagaattgaggaca-agcatagccctttcttgaggcttgcctatcccaaagtcagggctttttcctgctgagtggctg-ggg-aagttacttgcttgtgagtccattttcttatctatgaagcagggatgccaacagtacctgcctagcaacagttttaaatgtatggcacttgactatttaaacagtgactgttgctgttcccattttggatgcttagctttgtgatttagtgagacttatcatcctggtatctttttttttactgtataccaggggagaaagattctattttgaacaggtactaaatcttcttttttttttttttttttttttttccgagacagggtttctctgtgtagctctggctgtcctggaactcactttgtagatcaggctggcctcaaactcagaaatccgcctgcctctgcctcccaagtgctgggattaaaggcatgtgccaccatgcccggcagtactaaatcttaataaatttgaaatttcctgtgtgggttggaagtttcccctggcctcatgcctgccaaaccatcctctctctctgagctatactttcactgtgagtttttggttggttggttggtttggcacaggtgttgtgagaggcacagggaatgtttttttttttaagatttatttatttatttatttatttatttatttatttatttatttattatatgtaagtacactgtagctgtcctcagacactccagaagagggagtcagatcttgttacggatggttgtgagccaccatgtggttgctgggatttgaacttccgacctttggaagagcagtcgccatctcaccagcccccacagggaatgtttgacagggtcgttgttggctaagttgatctcaagctataaataagactataaatgaggcacgcattacctggcctggaattttaattttagtggatgtttatggta-catttttttaagctgggga-tggttacacaaggggaggcagaggtaagcagatctctttattttgagccaaggccctgttagacacagaagccctgtcttgaaaaactagcccctccccaaataagagaaagagagagacatgtttcatgtattcatgtgcaaggagattggggtcctgtggagtcgatgtgaggaggctgggatggggttggccg-cactggcagagctagcagagagcttaccgtgctgcctctctga-c-ct-ccttcacccaggctctatggtttcaagatccatccaatggcttaccagctgcagctccaagccgccagcaacttcaagagcccagtcaagactattcgctgattgcc-cacccacctctccctctgtctgtgacaccaccattcctctgctgccaccctttcaggaagtc--tatggtttttagtttaaattaaaggaattgttactgtggtgggaatatgaaataaag--gaagaaaaggccatgagct-gtctcctactgtgtgttgctggggtcgggaagg-ggtgggctactgcactccagggaccctcttgctctagcccatcttccctaggttggaagc-agcccagattgcggcttcatgaatctgtaccatgtacagatagtgtgtcagagcagcact-ctagg-ttgggtgagcgcaagtgcaggattgaagggaaaggtttcagaggttggagaacatctgctctcttggggctg-tggctgtggctg-ctg--tagacttcatgggaagt--------------cccctcagtcttgctgttaaagggaatgtaaccctacagtaaataaaactgga---------gaggaggca-gagagccccaactgttgctcagtggtgtctgtgtgccccctgctgggagacctgaga--gc-c-gtctggaaaaggttggaaggcttg-tct-ctggccaacctctcccagcataatgggggccaagcctactgtgtg-ggtggacagcaggtagtggcagagacaggt--------------ccctgaagtgggggtacaggccttt-caaggcatg-tcta-ggatgaagacacctgataaagagccagctggtgctcttctgtggcct---------------------acacaggaaccagacaatgtgggtgaggacaggc-cttcttcctgccaa-tagatgacttcctcctctggtcaggatcttgcctcaggcaggagtgcacctctgcacccacagcagtttctgctcagactgcctgtcaaacccattctgcctctgaagatca--------------agaaaggtggggctt-ggggta-ctttgtgggagttgctcctctcccccaaattccataatgagggcccgcgtgcttgtaggtatgctgaccatggtgggctttgcgatggggaagggtaagt-aagaccagggtctgggagga
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL2312312312312312312312312312312312312312HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHQQQQQQQQQQQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLL312312312312312312312312312QQQQQQHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL231231231231231231231231231231LLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLQQQQQQQQQQQQHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL231231231231231231231231231231231231231231231231231231231231231231231231231231231231231TTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL3123123123123123123123123TTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ3123123123123123123123123123LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTT123123123123123123123TTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH12312312312312312312312312312312312312312312312312QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLL31231231231231231231231231231231231231LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTT31231231231231231231231231231231231231231231231231231231231231231231231231231231231231231231231231231231231231231231231231231231TTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTT1231231231231231231231LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH3123123123123123123123TTTTTLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHH12312312312312312312312312312312312312312312HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL3123123123123123123123123123123123123123123123LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL231231231231231TTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL2312312312312312312312312312312312312312312312312312312312312311231231231231231231123123123123123123123
BioPerl-1.007002/t/data/test.xls000444000766000024     13500013155576321 16436 0ustar00cjfieldsstaff000000000000ÐÏࡱá>þÿ	Xþÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿýÿÿÿ[	

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Kinase DomainNoveltyNKnown - LiteratureKnown - RefseqA6SK001Atypical¹CCGCCGGCCGGGGCCGCTGGCTGCACTCAGCGCCGGAGCCGGGAGCTAGCGGCCGCCGCCATGTCCCACCAGACCGGCATCCAAGCAAGTGAAGATGTTAAAGAGATCTTTGCCAGAGCCAGAAATGGAAAGTACAGACTTCTGAAAATATCTATTGAAAATGAGCAACTTGTGATTGGATCATATAGTCAGCCTTCAGATTCCTGGGATAAGGATTATGATTCCTTTGTTTTACCCCTGTTGGAGGACAAACAACCATGCTATATATTATTCAGGTTAGATTCTCAGAATGCCCAGGGATATGAATGGATATTCATTGCATGGTCTCCAGATCATTCTCATGTTCGTCAAAAAATGTTGTATGCAGCAACAAGAGCAACTCTGAAGAAGGAATTTGGAGGTGGCCACATTAAAGATGAAGTATTTGGAACAGTAAAGGAAGATGTATCATTACATGGATATAAAAAATACTTGCTGTCACAATCTTCCCCTGCCCCACTGACTGCAGCTGAGGAAGAACTACGACAGATTAAAATCAATGAGGTACAGACTGACGTGGGTGTGGACACTAAGCATCAAACACTACAAGGAGTAGCATTTCCCATTTCTCGAGAAGCCTTTCAGGCTTTGGAAAAATTGAATAATAGACAGCTCAACTATGTGCAGTTGGAAATAGATATAAAAAATGAAATTATAATTTTGGCCAACACAACAAATACAGAACTGAAAGATTTGCCAAAGAGGATTCCCAAGGATTCAGCTCGTTACCATTTCTTTCTGTATAAACATTCCCATGAAGGAGACTATTTAGAGTCCATAGTTTTTATTTATTCAATGCCTGGATACACATGCAGTATAAGAGAGCGGATGCTGTATTCTAGCTGCAAGAGCCGTCTGCTAGAAATTGTAGAAAGACAACTACAAATGGATGTAATTAGAAAGATCGAGATAGACAATGGGGATGAGTTGACTGCAGACTTCCTTTATGAAGAAGTACATCCCAAGCAGCATGCACACAAGCAAAGTTTTGCAAAACCAAAAGGTCCTGCAGGAAAAAGAGGAATTCGAAGACTAATTAGGGGCCCAGCGGAAACTGAAGCTACTACTGATTAAAGTCATCACATTAAACATTGTAATACTAGTTTTTTAAAAGTCCAGCTTTTAGTACAGGAGAACTGAAATCATTCCATGTTGATATAAAGTAGGGAAAAAAATTGTACTTTTTGGAAAATAGCACTTTTCACTTCTGTGTGTTTTTAAAATTAATGTTATAGAAGACTCATGATTTCTATTTTTGAGTTAAAGCTAGAAAAGGGTTCAACATAATGTTTAATTTTGTCACACTGTTTTCATAGCGTTGATTCCACACTTCAAATACTTCTTAAAATTTTATACAGTTGGGCCAGTTCTAGAAAGTCTGATGTCTCAAAGGGTAAACTTACTACTTTCTTGTGGGACAGAAAGACCTTAAAATATTCATATTACTTAATGAATATGTTAAGGACCAGGCTAGAGTATTTTCTAAGCTGGAAACTTAGTGTGCCTTGGAAAAGGCCGCAAGTTGCTTACTCCGAGTAGCTGTGCTAGCTCTGTCAGACTGTAGGATCATGTCTGCAACTTTTAGAAATAGTGCTTTATATTGCAGCAGTCTTTTATATTTGACTTTTTTTTAATAGCATTAAAATTGCAGATCAGCTCACTCTGAAACTTTAAGGGTACCAGATATTTTCTATACTGCAGGATTTCTGATGACATTGAAAGACTTTAAACAGCCTTAGTAAATTATCTTTCTAATGCTCTGTGAGGCCAAACATTTATGTTCAGATTGAAATTTAAATTAATATCATTCAAAAGGAAACAAAAAATGTTGAGTTTTAAAAATCAGGATTGACTTTTTTCTCCAAAACCATACATTTATGGGCAAATTGTGTTCTTTATCACTTCCGAGCAAATACTCAGATTTAAAATTACTTTAAAGTCCTGGTACTTAACAGGCTAACGTAGATAAACACCTTAATAATCTCAGTTAATACTGTATTTCAAAACACATTTAACTGTTTTCTAATGCTTTGCATTATCAGTTACAACCTAGAGAGATTTTGAGCCTCATATTTCTTTGATACTTGAAATAGAGGGAGCTAGAACACTTAATGTTTAATCTGTTAAACCTGCTGCAAGAGCCATAACTTTGAGGCATTTTCTAAATGAACTGTGGGGATCCAGGATTTGTAATTTCTTGATCTAAACTTTATGCTGCATAAATCACTTATCGGAAATGCACATTTCATAGTGTGAAGCACTCATTTCTAAACCTTATTATCTAAGGTAATATATGCACCTTTCAGAAATTTGTGTTCGAGTAAGTAAAGCATATTAGAATAATTGTGGGTTGACAGATTTTTAAAATAGAATTTAGAGTATTTGGGGTTTTGTTTGTTTACAAATAATCAGACTATAATATTTAAACATGCAAAATAACTGACAATAATGTTGCACTTGTTTACTAAAGATATAAGTTGTTCCATGGGTGTACACGTAGACAGACACACATACACCCAAATTATTGCATTAAGAATCCTGGAGCAGACCATAGCTGAAGCTGTTATTTTCAGTCAGGAAGACTACCTGTCATGAAGGTATAAAATAATTTAGAAGTGAATGTTTTTCTGTACCATCTATGTGCAATTATACTCTAAATTCCACTACACTACATTAAAGTAAATGGACATTCCAGAATATAGATGTGATTATAGTCTTAAACTAATTATTATTAAACCAATGATTGCTGAAAATCAGTGATGCATTTGTTATAGAGTATAACTCATCGTTTACAGTATGTTTTAGTTGGCAGTATCATACCTAGATGGTGAATAACATATTCCCAGTAAATTTATATAGCAGTGAAGAATTACATGCCTTCTGGTGGACATTTTATAAGTGCATTTTATATCACAATAAAAATTTTTTCTCTTTAAAAAAAAAAAACAAGAAAAAAAAAAAA]MAHQTGIHATEELKEFFAKARAGSVRLIKVVIEDEQLVLGASQEPVGRWDQDYDRAVLPLLDAQQPCYLLYRLDSQNAQGFEWLFLAWSPDNSPVRLKMLYAATRATVKKEFGGGHIKDELFGTVKDDLSFAGYQKHLSSCAAPAPLTSAERELQQIRINEVKTEISVESKHQTLQGLAFPLQPEAQRALQQLKQKMVNYIQMKLDLERETIELVHTEPTDVAQLPSRVPRDAARYHFFLYKHTHEGDPLESVVFIYSMPGYKCSIKERMLYSSCKSRLLDSVEQDFHLEIAKKIEIGDGAELTAEFLYDEVHPKQHAFKQAFAKPKGPGGKRGHKRLIRGPGENGDDS^MSHQTGIQASEDVKEIFARARNGKYRLLKISIENEQLVIGSYSQPSDSWDKDYDSFVLPLLEDKQPCYILFRLDSQNAQGYEWIFIAWSPDHSHVRQKMLYAATRATLKKEFGGGHIKDEVFGTVKEDVSLHGYKKYLLSQSSPAPLTAAEEELRQIKINEVQTDVGVDTKHQTLQGVAFPISREAFQALEKLNNRQLNYVQLEIDIKNEIIILANTTNTELKDLPKRIPKDSARYHFFLYKHSHEGDYLESIVFIYSMPGYTCSIRERMLYSSCKSRLLEIVERQLQMDVIRKIEIDNGDELTADFLYEEVHPKQHAHKQSFAKPKGPAGKRGIRRLIRGPAETEATTD A6rSK512&GACAGCCTCCGCCACATCCTCCACCTCTCTTGGTCCAGCGAGCGTTGCCGGGCCAGGGTCAAGCGGAGGGCTCCGACGGCGCGGACGGAGCGAAGCGCCGAGCCATGGCGCACCAAACGGGCATCCACGCCACGGAAGAGCTGAAGGAATTCTTTGCCAAGGCACGGGCTGGCTCTGTGCGGCTCATCAAGGTTGTGATTGAGGACGAGCAGCTCGTGCTGGGTGCCTCGCAGGAGCCAGTAGGCCGCTGGGATCAGGACTATGACAGGGCCGTGCTGCCACTGCTGGACGCCCAGCAGCCCTGCTACCTGCTCTACCGCCTCGACTCACAGAATGCTCAGGGCTTCGAATGGCTCTTCCTCGCCTGGTCGCCTGATAACTCCCCCGTGCGGCTGAAGATGCTGTACGCGGCCACGCGGGCCACAGTGAAAAAGGAGTTTGGAGGTGGCCACATCAAGGATGAGCTCTTCGGGACTGTGAAGGATGACCTCTCTTTTGCTGGGTACCAGAAACACCTGTCGTCCTGTGCGGCACCTGCCCCGCTGACCTCGGCTGAGAGAGAGCTCCAGCAGATCCGCATTAACGAGGTGAAGACAGAGATCAGTGTGGAAAGCAAGCACCAGACCCTGCAGGGCCTCGCCTTCCCCCTGCAGCCTGAGGCCCAGCGGGCACTCCAGCAGCTCAAGCAGAAAATGGTCAACTACATCCAGATGAAGCTGGACCTAGAGCGGGAAACCATTGAGCTGGTGCACACAGAGCCCACGGATGTGGCCCAGCTGCCCTCCCGGGTGCCCCGAGATGCTGCCCGCTACCACTTCTTCCTCTACAAGCACACCCATGAGGGCGACCCCCTTGAGTCTGTAGTGTTCATCTACTCCATGCCGGGGTACAAGTGCAGCATCAAGGAGCGAATGCTCTACTCCAGCTGCAAGAGCCGCCTCCTCGACTCCGTGGAGCAGGACTTCCATCTGGAGATCGCCAAGAAAATTGAGATTGGCGATGGGGCAGAGCTGACGGCAGAGTTCCTCTACGACGAGGTGCACCCCAAGCAACACGCCTTCAAGCAGGCCTTCGCCAAGCCCAAGGGCCCAGGGGGCAAGCGGGGCCATAAGCGCCTCATCCGCGGCCCGGGTGAAAATGGGGATGACAGCTAGGAGGCTGGAGCAGGGCCGGCCACGTGTGGACTGTGGGGCTGCCCACCTTCCGCTCCCTGCCACCATCCTCCTTCCTGGGCTCCAGGAAAGTGTTTCTGGGAGGTCAGGAGGGCTGGCAGCTGAACGCACTTGCAGCGTCCGAGGGCCACCGGGCTGGCATTTTGTGACCCTTCCCTGTTGCTGTCCCTGCATCTCGTCTGTGTGCCCAGGGTGTCCGGGGACCCTGCCTGGCTGGCTTAAGGGGGCTGGGTCAGGGGCCTGGCATGAACCTGGCCTCCCGGGGAGCTGAGACTAGGGTCCCAGCACAGCCCAGAAACCTTTGGCCACAAGAAGTGGGGTCAGTCAGGGCTGGGGCAGGGGTCACTGCAGTTTGGGATGGTTGAATGCTGTATTTTCTAAAGAATAAAATATTTTTAAATCCAMKCAMK2CaMK2dSK703YQLFEELGKGAFSVVRRCMKIPTGQGYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGFHYLVFDLVTGGELFEDIVAREYYSEADASHCIQQILESVNHCHLNGIVHRDLKPENLLLASKSKGAAVKLADFGLAIEVQGDQQAWFGFAGTPGYLSPEVLRKDPYGKPVDMWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPAKRITASEALKHPWIÜATGGCTTCGACCACCACCTGCACCAGGTTCACGGACGAGTATCAGCTTTTCGAGGAGCTTGGAAAGGGGGCATTCTCAGTGGTGAGAAGATGTATGAAAATTCCTACTGGACAAGGATATGCTGCCAAAATTATCAACACCAAAAAGCTTTCTGCTAGGGATCATCAGAAACTAGAAAGAGAAGCTAGAATCTGCCGTCTTTTGAAGCACCCTAATATTGTGCGACTTCATGATAGCATATCAGAAGAGGGCTTTCACTACTTGGTGTTTGATTTAGTTACTGGAGGTGAACTGTTTGAAGACATAGTGGCAAGAGAATACTACAGTGAAGCTGATGCCAGTCATTGTATACAGCAGATTCTAGAAAGTGTTAATCATTGTCACCTAAATGGCATAGTTCACAGGGACCTGAAGCCTGAGAATTTGCTTTTAGCTAGCAAATCCAAGGGAGCAGCTGTGAAATTGGCAGACTTTGGCTTAGCCATAGAAGTTCAAGGGGACCAGCAGGCGTGGTTTGGTTTTGCTGGCACACCTGGATATCTTTCTCCAGAAGTTTTACGTAAAGATCCTTATGGAAAGCCAGTGGATATGTGGGCATGTGGTGTCATTCTCTATATTCTACTTGTGGGGTATCCACCCTTCTGGGATGAAGACCAACACAGACTCTATCAGCAGATCAAGGCTGGAGCTTATGATTTTCCATCACCAGAATGGGACACGGTGACTCCTGAAGCCAAAGACCTCATCAATAAAATGCTTACTATCAACCCTGCCAAACGCATCACAGCCTCAGAGGCACTGAAGCACCCATGGATCTGTCAACGTTCTACTGTTGCTTCCATGATGCACAGACAGGAGACTGTAGACTGCTTGAAGAAATTTAATGCTAGAAGAAAACTAAAGGGTGCCATCTTGACAACTATGCTGGCTACAAGGAATTTCTCAGCAGCCAAGAGTTTGTTGAAGAAACCAGATGGAGTAAAGGAGTCAACTGAGAGTTCAAATACAACAATTGAGGATGAAGATGTGAAAGCACGAAAGCAAGAGATTATCAAAGTCACTGAACAACTGATCGAAGCTATCAACAATGGGGACTTTGAAGCCTACACAAAAATCTGTGACCCAGGCCTTACTGCTTTTGAACCTGAAGCTTTGGGTAATTTAGTGGAAGGGATGGATTTTCACCGATTCTACTTTGAAAATGCTTTGTCCAAAAGCAATAAACCAATCCACACTATTATTCTAAACCCTCATGTACATCTGGTAGGGGATGATGCCGCCTGCATAGCATATATTAGGCTCACACAGTACATGGATGGCAGTGGAATGCCAAAGACAATGCAGTCAGAAGAGACTCGTGTGTGGCACCGCCGGGATGGAAAGTGGCAGAATGTTCATTTTCATCGCTCGGGGTCACCAACAGTACCCATCAAGCCACCCTGTATTCCAAATGGGAAAGAAAACTTCTCAGGAGGCACCTCTTTGTGGCAAAACATCTGAóMASTTTCTRFTDEYQLFEELGKGAFSVVRRCMKIPTGQGYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGFHYLVFDLVTGGELFEDIVAREYYSEADASHCIQQILESVNHCHLNGIVHRDLKPENLLLASKSKGAAVKLADFGLAIEVQGDQQAWFGFAGTPGYLSPEVLRKDPYGKPVDMWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPAKRITASEALKHPWICQRSTVASMMHRQETVDCLKKFNARRKLKGAILTTMLATRNFSAAKSLLKKPDGVKESTESSNTTIEDEDVKARKQEIIKVTEQLIEAINNGDFEAYTKICDPGLTAFEPEALGNLVEGMDFHRFYFENALSKSNKPIHTIILNPHVHLVGDDAACIAYIRLTQYMDGSGMPKTMQSEETRVWHRRDGKWQNVHFHRSGSPTVPIKPPCIPNGKENFSGGTSLWQNIAMPKa1SK032CAMKLAMPKGGCAGACTCAGTTCCTGGAGAAAGATGGCGACAGCCGAGAAGCAGAAACACGACGGGCGGGTGAAGATCGGCCACTACATTCTGGGTGACACGCTGGGGGTCGGCACCTTCGGCAAAGTGAAGGTTGGCAAACATGAATTGACTGGGCATAAAGTAGCTGTGAAGATACTCAATCGACAGAAGATTCGGAGCCTTGATGTGGTAGGAAAAATCCGCAGAGAAATTCAGAACCTCAAGCTTTTCAGGCATCCTCATATAATTAAACTGTACCAGGTCATCAGTACACCATCTGATATTTTCATGGTGATGGAATATGTCTCAGGAGGAGAGCTATTTGATTATATCTGTAAGAATGGAAGGCTGGATGAAAAAGAAAGTCGGCGTCTGTTCCAACAGATCCTTTCTGGT<  GTGGATTATTGTCACAGGCATATGGTGGTCCATAGAGATTTGAAACCTGAAAATGTCCTGCTTGATGCACACATGAATGCAAAGATAGCTGATTTTGGTCTTTCAAACATGATGTCAGATGGTGAATTTTTAAGAACAAGTTGTGGCTCACCCAACTATGCTGCACCAGAAGTAATTTCAGGAAGATTGTATGCAGGCCCAGAGGTAGATATATGGAGCAGTGGGGTTATTCTCTATGCTTTATTATGTGGAACCCTTCCATTTGATGATGACCATGTGCCAACTCTTTTTAAGAAGATATGTGATGGGATCTTCTATACCCCTCAATATTTAAATCCTTCTGTGATTAGCCTTTTGAAACATATGCTGCAGGTGGATCCCATGAAGAGGGCCTCAATCAAAGATATCAGGGAACATGAATGGTTTAAACAGGACCTTCCAAAATATCTCTTTCCTGAGGATCCATCATATAGTTCAACCATGATTGATGATGAAGCCTTAAAAGAAGTATGTGAAAAGTTTGAGTGCTCAGAAGAGGAAGTTCTCAGCTGTCTTTACAACAGAAATCACCAGGATCCTTTGGCAGTTGCCTACCATCTCATAATAGATAACAGGAGAATAATGAATGAAGCCAAAGATTTCTATTTGGCGACAAGCCCACCTGATTCTTTTCTTGATGATCATCACCTGACTCGGCCCCATCCTGAAAGAGTACCATTCTTGGTTGCTGAAACACCAAGGGCACGCCATACCCTTGATGAATTAAATCCACAGAAATCCAAACACCAAGGTGTAAGGAAAGCAAAATGGCATTTAGGAATTAGAAGTCAAAGTCGACCAAATGATATTATGGCAGAAGTATGTAGAGCAATCAAACAATTGGATTATGAATGGAAGGTTGTAAACCCATATTATTTGCGTGTACGAAGGAAGAATCCTGTGACAAGCACTTACTCCAAAATGAGTCTACAGTTATACCAAGTGGATAGTAGAACTTATCTACTGGATTTCCGTAGTATTGATGATGAAATTACAGAAGCCAAATCAGGGACTGCTACTCCACAGAGATCGGGATCAGTTAGCAACTATCGATCTTGCCAAAGGAGTGATTCAGATGCTGAGGCTCAAGGAAAATCCTCAGAAGTTTCTCTTACCTCATCTGTGACCTCACTTGACTCTTCTCCTGTTGACCTAACTCCAAGACCTGGAAGTCACACAATAGAATTTTTTGAGATGTGTGCAAATCTAATTAAAATTCTTGCACAATAAACAGAAAACTTTGCTTATTTCTTTTGCAGCAATAAGCATGCATAATAAGTCACAGCCAAATGCTTCCATTTGTAATCAAGTTATACATAATTATAACCGAGGGCTGGCGTTTTGGAATCGAATTTCGACAGGGATTGGAACATGATTTATAGTTAAAAGCCTAATATCGAGAAATGAATTAAGATCA&MATAEKQKHDGRVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKNGRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRASIKDIREHEWFKQDLPKYLFPEDPSYSSTMIDDEALKEVCEKFECSEEEVLSCLYNRNHQDPLAVAYHLIIDNRRIMNEAKDFYLATSPPDSFLDDHHLTRPHPERVPFLVAETPRARHTLDELNPQKSKHQGVRKAKWHLGIRSQSRPNDIMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTYSKMSLQLYQVDSRTYLLDFRSIDDEITEAKSGTATPQRSGSVSNYRSCQRSDSDAEAQGKSSEVSLTSSVTSLDSSPVDLTPRPGSHTIEFFEMCANLIKILAQýYILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKNGRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRASIKDIREHEWFAMPKa2SK0339	GGTAGCGGCGGCGGCGGCGGCTAGCGGAGCGGCAGGCGGTGGAGCGAGGCCGCGCGCGCCGAAGATGGCTGAGAAGCAGAAGCACGACGGGCGGGTGAAGATCGGACACTACGTGCTGGGCGACACGCTGGGCGTCGGCACCTTCGGCAAAGTGAAGATTGGAGAACATCAATTAACAGGCCATAAAGTGGCAGTTAAAATCTTAAATAGACAGAAGATTCGCAGTTTAGATGTTGTTGGAAAAATAAAACGAGAAATTCAAAATCTAAAACTCTTTCGTCATCCTCATATTATCAAACTATACCAGGTGATCAGCACTCCAACAGATTTTTTTATGGTAATGGAATATGTGTCTGGAGGTGAATTATTTGACTACATCTGTAAGCATGGACGGGTTGAAGAGATGGAAGCCAGGCGGCTCTTTCAGCAGATTCTGTCTGCTGTGGATTACTGTCATAGGCATATGGTTGTTCATCGAGACCTGAAACCAGAGAATGTCCTGTTGGATGCACACATGAATGCCAAGATAGCCGATTTCGGATTATCTAATATGATGTCAGATGGTGAATTTCTGAGAACTAGTTGCGGATCTCCAAATTATACAGCACCTGAAGTCATCTCAGGCAGATTGTATGCAGGTCCTGAAGTTGATATCTGGAGCTGTGGTGTTATCTTGTATGCTCTTCTTTGTGGCACCCTCCCATTTGATGATGAGCATGTACCTACGTTATTTAAGAAGATCCGAGGGGGTGTCTTTTATATCCCAGAATATCTCAATCGTTCTGTCGCCACTCTCCTGATGCATATGCTGCAGGTTGACCCACTGAAACGAGCAACTATCAAAGACATAAGAGAGCATGAATGGTTTAAACAAGGTTTGCCCAGTTACTTATTTCCTGAAGACCCTTCCTATGATGCTAACGTCATTGATGATGAGGCTGTGAAAGAAGTGTGTGAAAAATTTGAATGTACAGAATCAGAAGTAATGAACAGTTTATATAGTGGTGACCCTCAAGACCAGCTTGCAGTGGCTTATCATCTTATCATTGACAATCGGAGAATAATGAACCAAGCCAGTGAGTTCTACCTCGCCTCTAGTCCTCCATCTGGTTCTTTTATGGATGATAGTGCCATGCATATTCCCCCAGGCCTGAAACCTCATCCAGAAAGGATGCCACCTCTTATAGCAGACAGCCCCAAAGCAAGATGTCCATTGGATGCACTGAATACGACTAAGCCCAAATCTTTAGCTGTGAAAAAAGCCAAGTGGCGTCAAGGAATCCGAAGTCAGAGCAAACCGTATGACATTATGGCTGAAGTTTACCGAGCTATGAAGCAGCTGGATTTTGAATGGAAGGTAGTGAATGCATACCATCTTCGTGTAAGAAGAAAAAATCCAGTGACTGGCAATTACGTGAAAATGAGCTTACAACTTTACCTGGTTGATAACAGGAGCTATCTTTTGGACTTTAAAAGCATTGATGATGAAGTAGTGGAGCAGAGATCTGGTTCCTCAACACCTCAGCGTTCCTGTTCTGCTGCTGGCTTACACAGACCAAGATCAAGTTTTGATTCCACAACTGCAGAGAGCCATTCACTTTCTGGCTCTCTCACTGGCTCTTTGACCGGAAGCACATTGTCTTCAGTTTCACCTCGCCTGGGCAGTCACACCATGGATTTTTTTGAAATGTGTGCCAGTCTGATTACTACTTTAGCCCGTTGATCTGTCTCTAGTTTCTTTCTGTTATTGCACTATGAAAATCAGTTATATTCTTTAAATTTTTATCTTACTTTTGGATAATATCCACTGCAATACTAATTGAGAAACATGAATTATTTCCAGGGGCACACAATGCTATTGAAATTACTGAAAACAAAATATCTGACATCTTATTTACTTGTAGAAATCTGTAATTCTATTGTGCCTATGATAAATTCACATAGGCAATATCTTTAATAGGTTAATATCAATGAAGATTTTTAATTACAATAATGAGTTCACTACAGACGATTAACACACCACACTGGCGAACCATCTCAATGTAAGGGTGGTTTGGCAACACCTCCTTGCTTTGCTGTTTGGTGTAGTAAATCTAGTTTACTTCCTAAATTTCAGTAGGCTTTATGCTGTGTTTATCGCCCAATTTATTTTAACAAAAGAAGATTAAAAAGTAAAGAACCACGAGTAAGATATTATTTAAATGTTGAAATCTTAAAACCTGCCTCCAAGATTTCAGAAGCCAAGTTTTTCTAACAGTATTTGTACAAATACTGCCTAGTGTATTCAACAGAAGACTGTGGTCATGTAACAGGTAACCACAATTTTCAGGTTTCTTAAAAACAGCTGTAACTAACTCAGGA(MAEKQKHDGRVKIGHYVLGDTLGVGTFGKVKIGEHQLTGHKVAVKILNRQKIRSLDVVGKIKREIQNLKLFRHPHIIKLYQVISTPTDFFMVMEYVSGGELFDYICKHGRVEEMEARRLFQQILSAVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYTAPEVISGRLYAGPEVDIWSCGVILYALLCGTLPFDDEHVPTLFKKIRGGVFYIPEYLNRSVATLLMHMLQVDPLKRATIKDIREHEWFKQGLPSYLFPEDPSYDANVIDDEAVKEVCEKFECTESEVMNSLYSGDPQDQLAVAYHLIIDNRRIMNQASEFYLASSPPSGSFMDDSAMHIPPGLKPHPERMPPLIADSPKARCPLDALNTTKPKSLAVKKAKWRQGIRSQSKPYDIMAEVYRAMKQLDFEWKVVNAYHLRVRRKNPVTGNYVKMSLQLYLVDNRSYLLDFKSIDDEVVEQRSGSSTPQRSCSAAGLHRPRSSFDSTTAESHSLSGSLTGSLTGSTLSSVSPRLGSHTMDFFEMCASLITTLARýYVLGDTLGVGTFGKVKIGEHQLTGHKVAVKILNRQKIRSLDVVGKIKREIQNLKLFRHPHIIKLYQVISTPTDFFMVMEYVSGGELFDYICKHGRVEEMEARRLFQQILSAVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYTAPEVISGRLYAGPEVDIWSCGVILYALLCGTLPFDDEHVPTLFKKIRGGVFYIPEYLNRSVATLLMHMLQVDPLKRATIKDIREHEWFMARKMARK2SK120÷CGGCGGTGGTGGCGGCCATGTTGGGAGCAGCAGGTCCGGCGGCGGCTGCCTGTGTGCCGGGCGCGGAGCAGTGCCGCTGAGGGCAGGGGAGGAGCGAGGCAGGCGGCCGGCTGCGGCGGCAGAGAGTAGGCGGAGCGGCGCGGCCCGGCCGAAAGGCGGCACAGCCCAGCCGGGGGTCGGGGGGGTGCGGTCCGGAGCCGCTCGGAGCCGGCGCGGCCTAGCCCGAGCGGCGCATCCCCGGGCTGGCGTGAGCGGCTGCCCGGCCTCCCCGCACCCCCGGCCGGGGCCCATGCGGCGGGTGCTCCTGCTGTGAGAAGCCCCGCCCGGCCGGGCTCCGCGCCTTCCCTTCCCTCCCTTCCTCCAAGCTTCTCGGTTCCCTCCCCCGAGATACCGGCGCCATGTCCAGCGCTCGGACCCCCCTACCCACGCTGAACGAGAGGGACACGGAGCAGCCCACCTTGGGACACCTTGACTCCAAGCCCAGCAGTAAGTCCAACATGATTCGGGGCCGCAACTCAGCCACCTCTGCTGATGAGCAGCCCCACATTGGAAACTACCGGCTCCTCAAGACCATTGGCAAGGGTAATTTTGCCAAGGTGAAGTTGGCCCGACACATCCTGACTGGGAAAGAGGTAGCTGTGAAGATCATTGACAAGACTCAACTGAACTCCTCCAGCCTCCAGAAACTATTCCGCGAAGTAAGAATAATGAAGGTTTTGAATCATCCCAACATAGTTAAATTATTTGAAGTGATTGAGACTGAGAAAACGCTCTACCTTGTCATGGAGTACGCTAGTGGCGGAGAGGTATTTGATTACCTAGTGGCTCATGGCAGGATGAAAGAAAAAGAGGCTCGAGCCAAATTCCGCCAGATAGTGTCTGCTGTGCAGTACTGTCACCAGAAGTTTATTGTCCATAGAGACTTAAAGGCAGAAAACCTGCTCTTGGATGCTGATATGAACATCAAGATTGCAGACTTTGGCTTCAGCAATGAATTCACCTTTGGGAACAAGCTGGACACCTTCTGTGGCAGTCCCCCTTATGCTGCCCCAGAACTCTTCCAGGGCAAAAAATATGATGGACCCGAGGTGGATGTGTGGAGCCTAGGAGTTATCCTCTATACACTGGTCAGCGGATCCCTGCCTTTTGATGGACAGAACCTCAAGGAGCTGCGGGAACGGGTACTGAGGGGAAAATACCGTATTCCATTCTACATGTCCACGGACTGTGAAAACCTGCTTAAGAAATTTCTCATTCTTAATCCCAGCAAGAGAGGCACTTTAGAGCAAATCATGAAAGATCGATGGATGAATGTGGGTCACGAAGATGATGAACTAAAGCCTTACGTGGAGCCACTCCCTGACTACAAGGACCCCCGGCGGACAGAGCTGATGGTGTCCATGGGTTATACACGGGAAGAGATCCAGGACTCGCTGGTGGGCCAGAGATACAACGAGGTGATGGCCACCTATCTGCTCCTGGGCTACAAGAGCTCCGAGCTGGAAGGCGACACCATCACCCTGAAACCCCGGCCTTCAGCTGATCTAACCAATAGCAGCGCCCAATTCCCATCCCACAAGGTACAGCGAAGCGTGTCGGCCAATCCCAAGCAGCGGCGCTTCAGCGACCAGGCTGGTCCTGCCATTCCCACCTCTAATTCTTACTCTAAGAAGACTCAGAGTAACAACGCAGAAAATAAGCGGCCTGAGGAGGACCGGGAGTCAGGGCGGAAAGCCAGCAGCACAGCCAAGGTGCCTGCCAGCCCCCTGCCCGGTCTGGAGAGGAAGAAGACCACCCCAACCCCCTCCACGAACAGCGTCCTCTCCACCAGCACAAATCGAAGCAGGAATTCCCCACTTTTGGAGCGGGCCAGCCTCGGCCAGGCCTCCATCCAGAATGGCAAAGACAGCCTAACCATGCCAGGGTCCCGGGCCTCCACGGCTTCTGCTTCTGCCGCAGTCTCTGCGGCCCGGCCCCGCCAGCACCAGAAATCCATGTCGGCCTCCGTGCACCCCAACAAGGCCTCTGGGCTGCCCCCCACGGAGAGTAACTGTGAGGTGCCGCGGCCCAGCACAGCCCCCCAGCGTGTCCCTGTTGCCTCCCCATCCGCCCACAACATCAGCAGCAGTGGTGGAGCCCCAGACCGAACTAACTTCCCCCGGGGTGTGTCCAGCCGAAGCACCTTCCATGCTGGGCAGCTCCGACAGGTGCGGGACCAGCAGAATTTGCCCTACGGTGTGACCCCAGCCTCTCCCTCTGGCCACAGCCAGGGCCGGCGGGGGGCCTCTGGGAGCATCTTCAGCAAGTTCACCTCCAAGTTTGTACGCAGAAATCTGTCTTTCAGGTTTGCCAGAAGGAACCTGAATGAACCTGAAAGCAAAGACCGAGTGGAGACGCTCAGACCTCACGTGGTGGGCAGTGGCGGCAACGACAAAGAAAAGGAAGAATTTCGGGAGGCCAAGCCCCGCTCCCTCCGCTTCACGTGGAGTATGAAGACCACGAGCTCCATGGAGCCCAACGAGATGATGCGGGAGATCCGCAAGGTGCTGGACGCGAACAGCTGCCAGAGCGAGCTGCATGAGAAGTACATGCTGCTGTGCATGCACGGCACGCCGGGCCACGAGGACTTCGTGCAGTGGGAGATGGAGGTGTGCAAACTGCCGCGGCTCTCTCTCAACGGGGTTCGATTTAAGCGGATATCGGGCACCTCCATGGCCTTCAAAAACATTGCCTCCAAAAT<  AGCCAACGAGCTGAAGCTTTAACAGGCTGCCAGGAGCGGGGGCGGCGGGGGCGGGCCAGCTGGACGGGCTGCCGGCCGTGCGCCGCCCCACCTGGGCGAGACTGCAGCGATGGATTGGTGTGTCTCCCTGCTGGCACTTCTCCCCTCCCTGGCCCTTCTCAGTTTTCTCCCACATTCACCCCTGCCCAGAGATTCCCCCTTCTCCTCTCCCCTACTGGAGGCAAAGGAAGGGGAGGGTGGATGGGGGGGCAGGGCTCCCCCTCGGTACTGCGGTTGCACAGAGTATTTCGCCTAAACCAAGAAATTTTTTATTACCAAAAAGAMSSARTPLPTLNERDTEQPTLGHLDSKPSSKSNMIRGRNSATSADEQPHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNHPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAENLLLDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKFLILNPSKRGTLEQIMKDRWMNVGHEDDELKPYVEPLPDYKDPRRTELMVSMGYTREEIQDSLVGQRYNEVMATYLLLGYKSSELEGDTITLKPRPSADLTNSSAQFPSHKVQRSVSANPKQRRFSDQAGPAIPTSNSYSKKTQSNNAENKRPEEDRESGRKASSTAKVPASPLPGLERKKTTPTPSTNSVLSTSTNRSRNSPLLERASLGQASIQNGKDSLTMPGSRASTASASAAVSAARPRQHQKSMSASVHPNKASGLPPTESNCEVPRPSTAPQRVPVASPSAHNISSSGGAPDRTNFPRGVSSRSTFHAGQLRQVRDQQNLPYGVTPASPSGHSQGRRGASGSIFSKFTSKFVRRNLSFRFARRNLNEPESKDRVETLRPHVVGSGGNDKEKEEFREAKPRSLRFTWSMKTTSSMEPNEMMREIRKVLDANSCQSELHEKYMLLCMHGTPGHEDFVQWEMEVCKLPRLSLNGVRFKRISGTSMAFKNIASKIANELKLüYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNHPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAENLLLDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKFLILNPSKRGTLEQIMKDRWMMARK3SK096bGACGGCCCGGGCCAGGCCCGGGATCTAGAACGGCCGTAGGGGGAAGGGAGCCGCCCTCCCCACGGCGCCTTTTCGGAACTGCCGTGGACTCGAGGACGCTGGTCGCCGGCCTCCTAGGGCTGTGCTGTTTTGTTTTGACCCTCGCATTGTGCAGAATTAAAGTGCAGTAAAATGTCCACTAGGACCCCATTGCCAACGGTGAATGAACGAGACACTGAAAACCACACGTCACATGGAGATGGGCGTCAAGAAGTTACCTCTCGTACCAGCCGCTCAGGAGCTCGGTGTAGAAACTCTATAGCCTCCTGTGCAGATGAACAACCTCACATCGGAAACTACAGACTGTTGAAAACAATCGGCAAGGGGAATTTTGCAAAAGTAAAATTGGCAAGACATATCCTTACAGGCAGAGAGGTTGCAATAAAAATAATTGACAAAACTCAGTTGAATCCAACAAGTCTACAAAAGCTCTTCAGAGAAGTAAGAATAATGAAGATTTTAAATCATCCCAATATAGTGAAGTTATTCGAAGTCATTGAAACTCAAAAAACACTCTACCTAATCATGGAATATGCAAGTGGAGGTAAAGTATTTGACTATTTGGTTGCACATGGCAGGATGAAGGAAAAAGAAGCAAGATCTAAATTTAGACAGATTGTGTCTGCAGTTCAATACTGCCATCAGAAACGGATCGTACATCGAGACCTCAAGGCTGAAAATCTATTGTTAGATGCCGATATGAACATTAAAATAGCAGATTTCGGTTTTAGCAATGAATTTACTGTTGGCGGTAAACTCGACACGTTTTGTGGCAGTCCTCCATACGCAGCACCTGAGCTCTTCCAGGGCAAGAAATATGACGGGCCAGAAGTGGATGTGTGGAGTCTGGGGGTCATTTTATACACACTAGTCAGTGGCTCACTTCCCTTTGATGGGCAAAACCTAAAGGAACTGAGAGAGAGAGTATTAAGAGGGAAATACAGAATTCCCTTCTACATGTCTACAGACTGTGAAAACCTTCTCAAACGTTTCCTGGTGCTAAATCCAATTAAACGCGGCACTCTAGAGCAAATCATGAAGGACAGGTGGATCAATGCAGGGCATGAAGAAGATGAACTCAAACCATTTGTTGAACCAGAGCTAGACATCTCAGACCAAAAAAGAATAGATATTATGGTGGGAATGGGATATTCACAAGAAGAAATTCAAGAATCTCTTAGTAAGATGAAATACGATGAAATCACAGCTACATATTTGTTATTGGGGAGAAAATCTTCAGAGGTTAGGCCGAGCAGTGATCTCAACAACAGTACTGGCCAGTCTCCTCACCACAAAGTGCAGAGAAGTGTTTCTTCAAGCCAAAAGCAAAGACGCTACAGTGACCATGCTGGACCAGGTATTCCTTCTGTTGTGGCGTATCCGAAAAGGAGTCAGACCAGCACTGCAGATAGTGACCTCAAAGAAGATGGAATTTCCTCCCGGAAATCAACTGGCAGTGCTGTTGGAGGAAAGGGAATTGCTCCAGCCAGTCCCATGCTTGGGAATGCAAGTAATCCTAATAAGGCGGATATTCCTGAACGCAAGAAAAGCTCCACTGTCCCTAGTAGTAACACAGCATCTGGTGGAATGACACGACGAAATACTTATGTTTGCAGTGAGAGAACTACAGATGATAGACACTCAGTGATTCAGAATGGCAAAGAAAACAGCACTATTCCTGATCAGAGAACTCCAGTTGCTTCAACACACAGTATCAGTAGTGCAGCCACCCCAGATCGAATCCGCTTCCCAAGAGGCACTGCCAGTCGTAGCACTTTCCACGGCCAGCCCCGGGAACGGCGAACCGCAACATATAATGGCCCTCCTGCCTCTCCCAGCCTGTCCCATGAAGCCACACCATTGTCCCAGACTCGAAGCCGAGGCTCCACTACTCTCTTTAGTAAATTAACTTCAAAACTCACAAGGAGTCGCAATGTATCTGCTAAGCAAAAAGATGAAAACAAAGAAGCAAAGCCTCGATCCCTACGCTTCACCTGGAGCATGAAAACCACTAGTTCAATGGATCCCGGGGACATGATGCGGGAAATCCGCAAAGTGTTGGACGCCAATAACTGCGACTATGAGCAGAGGGAGCGCTTCTTGCTCTTCTGCGTCCACGGAGATGGGCACGCGGAGAACCTCGTGCAGTGGGAAATGGAAGTGTGCAAGCTGCCAAGACTGTCTCTGAACGGGGTCCGGTTTAAGCGGATATCGGGGACATCCATAGCCTTCAAAAATATTGCTTCCAAAATTGCCAATGAGCTAAAGCTGTAACCCAGTGATTATGATGTAAATTAAGTAGCAAGTAAAGTGTTTTCCTGAACACTGATGGAAATGTATAGAATAATATTTAGGCAATAACGTCTGCATCTTCTAAATCATGAAATTAAAGTCTGAGGACGAGAGCACGCCTGGGAGCGAAAGCTGGCCTTTTTTCTACGAATGCACTACATTAAAGATGTGCAACCTATGCGCCCCCTGCCCTACTTCCGTTACCCTGAGAGTCGGCGTGTGGCCCCATCTCCATGTGCCTCCCGTCTGGGTGGGTGTGAGAGTGGACGGTATGTGTGTGAAGTGGTGTATATGGAAGCATCTCCCTACACTGGCAGCCAGTCATTACTAGTACCTCTGCGGGAGATCATCCGGTGCTAAAACATTACAGTTGCCAAGGAGGAAAATACTGAATGACTGCTAAGAATTAACCTTAAGACCAGTTCATAGTTAATACAGGTTTACAGTTCATGCCTGTGGTTTTGTGTTTGTTGTTTTGTGTTTTTTTAGTGCAAAAGGTTTAAATTTATAGTTGTGAACATTGCTTGTGTGTGTTTTTCTAAGTAGATTCACAAGATAATTAAAAATTCACTTTTTCTCAGGTÙMSTRTPLPTVNERDTENHTSHGDGRQEVTSRTSRSGARCRNSIASCADEQPHIGNYRLLKTIGKGNFAKVKLARHILTGREVAIKIIDKTQLNPTSLQKLFREVRIMKILNHPNIVKLFEVIETEKTLYLIMEYASGGEVFDYLVAHGRMKEKEARSKFRQIVSAVQYCHQKRIVHRDLKAENLLLDADMNIKIADFGFSNEFTVGGKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKRFLVLNPIKRGTLEQIMKDRWINAGHEEDELKPFVEPELDISDQKRIDIMVGMGYSQEEIQESLSKMKYDEITATYLLLGRKSSELDASDSSSSSNLSLAKVRPSSDLNNSTGQSPHHKVQRSVSSSQKQRRYSDHAGPAIPSVVAYPKRSQTSTADGDLKEDGISSRKSSGSAVGGKGIAPASPMLGNASNPNKADIPERKKSSTVPSSNTASGGMTRRNTYVCSERTTADRHSVIQNGKENSTIPDQRTPVASTHSISSAATPDRIRFPRGTASRSTFHGQPRERRTATYNGPPASPSLSHEATPLSQTRSRGSTNLFSKLTSKLTRSRNVSAEQKDENKEAKPRSLRFTWSMKTTSSMDPGDMMREIRKVLDANNCDYEQRERFLLFCVHGDGHAENLVQWEMEVCKLPRLSLNGVRFKRISGTSIAFKNIASKIANELKLüYRLLKTIGKGNFAKVKLARHILTGREVAIKIIDKTQLNPTSLQKLFREVRIMKILNHPNIVKLFEVIETQKTLYLIMEYASGGKVFDYLVAHGRMKEKEARSKFRQIVSAVQYCHQKRIVHRDLKAENLLLDADMNIKIADFGFSNEFTVGGKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKRFLVLNPIKRGTLEQIMKDRWIOtherCaMKK2SK482CAMKKMetaÔ
GAGCCGAGCCGAGCTGGGGGCGCAGACGCGGAGGCGGCGGCGGCGCGGAGCCCAGGTGGCTCCGTGCCGGATGGGAGTGCCCCAGTGTGCTGGATGAAGCTGGCGCATGCACCATGTCATCATGTGTCTCTAGCCAGCCCAGCAGCAACCGGGCCGCCCCCCAGGATGAGCTGGGGGGCAGGGGCAGCAGCAGCAGCGAAAGCCAGAAGCCCTGTGAGGCCCTGCGGGGCCTCTCATCCTTGAGCATCCACCTGGGCATGGAGTCCTTCATTGTGGTCACCGAGTGTGAGCCGGGCTGTGCTGTGGACCTCGGCTTGGCGCGGGACCGGCCCCTGGAGGCCGATGGCCAAGAGGTCCCCCTTGACACCTCCGGGTCCCAGGCCCGGCCCCACCTCTCCGGTCGCAAGCTGTCTCTGCAAGAGCGGTCCCAGGGTGGGCTGGCAGCCGGTGGCAGCCTGGACATGAACGGACGCTGCATCTGCCCGTCCCTGCCCTACTCACCCGTCAGCTCCCCGCAGTCCTCGCCTCGGCTGCCCCGGCGGCCGACAGTGGAGTCTCACCACGTCTCCATCACGGGTATGCAGGACTGTGTGCAGCTGAATCAGTATACCCTGAAGGATGAAATTGGAAAGGGCTCCTATGGTGTCGTCAAGTTGGCCTACAATGAAAATGACAATACCTACTATGCAATGAAGGTGCTGTCCAAAAAGAAGCTGATCCGGCAGGCCGCTTTTCCACGTCGCCCTCCACCCCGAGGCACCCGGCCAGCTCCTGGAGGCTGCATCCAGCCCAGGGGCCCCATTGAGCAGGTGTACCAGGAAATTGCCATCCTCAAGAAGCTGGACCACCCCAATGTGGTGAAGCTGGTGGAGGTCCTGGATGACCCCAATGAGGACCATCTGTACATGGTGTTCGAACTGGTCAACCAAGGGCCCGTGATGGAAGTGCCCACCCTCAAACCACTCTCTGAAGACCAGGCCCGTTTCTACTTCCAGGATCTGATCAAAGGCATCGAGTACTTACACTACCAGAAGATCATCCACCGTGACATCAAACCTTCCAACCTCCTGGTCGGAGAAGATGGGCACATCAAGATCGCTGACTTTGGTGTGAGCAATGAATTCAAGGGCAGTGACGCGCTCCTCTCCAACTACGTGGGCACGCCCGCCTTCATGGCTCCCGAGTCGCTCTCTGAGACCCGCAAGATCTTCTCTGGGAAGGCCAAGGATGTTTGGGCCATGGGTGTGACACTATACTGCTTTGTCTTTGGCCAGTGCCCATTCATGGACGAGCGGATCATGTGTTTACACAGTAAGATCAAGAGTCAGGCCCTGGAATTTCCAGACCAGCCCGACATAGCTGAGGACTTGAAGGACCTGATCACCCGTATGCTGGACAAGAACCCCGAGTCGAGGATCGTGGTGCCGGAAATCAAGCTGCACCCCTGGGTCACGAGGCATGGGGCGGAGCCGTTGCCGTCGGAGGATGAGAACTGCACGCTGGTCGAAGTGACTGAAGAGGAGGTCGAGAACTCAGTCAAACACATTCCCAGCTTGGCAACCGTGATCCTGGTGAAGACCATGATACGTAAACGCTCCTTTGGGAACCCATTCGAGGGCAGCCGGCGGGAGGAACGCTCACTGTCAGCGCCTGGAAACTTGCTCACCAAAAAACCAACCAGGGAATGTGAGTCCCTGTCTGAGCTCAAGGAAGCAAGGCAGCGAAGACAACCTCCAGGGCACCGACCCGCCCCCCGTGGGGGAGGAGGAAGTGCTCTTGTGAGAGGCAGTCCCTGCGTGGAAAGTTGCTGGGCCCCCGCCCCCGGCTCCCCCGCACGCATGCATCCACTGCGGCCGGAGGAGGCCATGGAGCCCGAGTAGCTGCCTGGATCGCTCGACCTCGCATGCGCGCCGCGTCGCCTCTGGGGGGCTGCTGCACCGCGTTTCCATAGCAGCATGTCCTACGGAAACCCAGCACGTGTGTTTCCATAGCAGCATGTCTGCAACCCAGACGCGGTGTGTAGAGCCTCGATCGTCATCTCTGGTTATTTGTTTTTTCCTTTGTTGTTTTAAAGGGACAAAAAAAAAAAAGGACTGACTCCATAGCTCGACCGTGGCCGCTGGCTGGCTGGACAGGCGGGTGTGAGGAGTTGCAGACCCAAACCCACGTGCATTTTGGGACAATTGCTTTTTAAAACGTTTTTATGCCAAAAATCCTTCATTGTGATTTTCAGAACCACGTCAGATATACCAAGTGACTGTGTGTGGGGTTTGACAACTGTGGAAAGGCGAGCAGAAAACTCCGGCGGTCTGAGGCCATGGAGGTGGTTGCTGCATTTGAGAGGGAGTAGGGGGCTAGATGTGGCTCCTAGTGCAAACCGGAAACCATGGCACCTTCCAGAGCCGTGGTCTCAAGGAGTCAGAGCAGGGAGCTTTGATGCAACTTATTTGTAAGAAGGATTTTTAAATTTTTTATGGGTAGAATTGTAGTCAGGAAAACAGAAAGGGCTTGAAATTTAATAAGTGCTGCTGGAGGGGATTTTCCAAGCCTGGAAGGGTATTCAGCAGCTGTGGTGGGGAAAGATTTCTCCTGAAAGACTGAACGTGTTTCTTCATGACAGCTGCTCAAAGCAGGTTTCTGAGATAGCTGACCGAGCTCTGGTAAATCTCTTTGTCAAATTACGAAAACTTCAGGGCGAAATCCTATGCTTCCATGTACATTACATGGCTTAAGTTAAACAAAAACATTTTTCAAGTCTCTAACTAGAGTGAALMSSCVSSQPSSNRAAPQDELGGRGSSSSESQKPCEALRGLSSLSIHLGMESFIVVTECEPGCAVDLGLARDRPLEADGQEVPLDTSGSQARPHLSGRKLSLQERSQGGLAAGGSLDM<NGRCICPSLPYSPVSSPQSSPRLPRRPTVESHHVSITGMQDCVQLNQYTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAAFPRRPPPRGTRPAPGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNYVGTPAFMAPESLSETRKIFSGKAKDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWVTRHGAEPLPSEDENCTLVEVTEEEVENSVKHIPSLATVILVKTMIRKRSFGNPFEGSRREERSLSAPGNLLTKKPTRECESLSELKEARQRRQPPGHRPAPRGGGGSALVRGSPCVESCWAPAPGSPARMHPLRPEEAMEPEYTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAAFPRRPPPRGTRPAPGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNYVGTPAFMAPESLSETRKIFSGKAKDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWV
PseudogeneYA6ps1SK752¢CCGCCGGCCGGGGCCGCTGGCTGCACTCAGCGCCGGAGCCGGGAGCTAGCGGCCGCCGCCATGTCCCACCAGACCGGCATCCAAGCAAGTGAAGATGTTAAAGAGATCTTTGCCAGAGCCAGAAATGGAAAGTACAGACTTCTGAAAATATCTATTGAAAATGAGCAACTTGTGATTGGATCATATAGTCAGCCTTCAGATTCCTGGGATAAGGATTATGATTCCTTTGTTTTACCCCTGTTGGAGGACAAACAACCATGCTATATATTATTCAGGTTAGATTCTCAGAATGCCCAGGGATATGAATGGATATTCATTGCATGGTCTCCAGATCATTCTCATGTTCGTCAAAAAATGTTGTATGCAGCAACAAGAGCAACTCTGAAGAAGGAATTTGGAGGTGGCCACATTAAAGATGAAATATTTGGAACAGTAAAGGAAGATGTATCATTACATGGATATAAAAAATACTTGCTGTCACAATCTTCCCCTGCCCCACTGACTGCAGCTGAGGAAGAATTACGACAGATTAAAATCAATGAGGTACAGACTGACGTGGGTGTGGACACTAAGCATCAAACACTACAAGGAGTAGCATTTCCCATTTCTCGAGAAGCCTTTCAGGCTTTGGAAAAATTGAATAACAGACAGCTCAACTATGTGCAGTTGGAAATAGATATAAAAAATGAAATTATAATTTTGGCCAACACAACAAATACAGAACTGAAAGATTTGCCAAAGAGGATTCCCAAGGATTCAGCTCGTTACCATTTCTTTCTGTATAAACATTCCCATGAAGGAGACTATTTAGAGTCCATAGTTNTTATTTATTCAATGCCTGGATACACATGCAGTATAAGAGAGCGGATGCTGTATTCTAGCTGCAAGAGCCCTCTGCTAGAAATTGTAGAAAGACAACTACAAATGGATGTAATTAGAAAGATCGAGATAGACAATGGGGATGAGTTGACTGCAGACTTCCTTTATGAAGAAGTACATCCCAAGCAGCAGGCACACAAGCAAAGTTTTGCAAAACCAAAAGGTCCTGCAGGAAAAAGAGGAATTCGAAGACTAATTAGGGGCCCAGCGGAAACTGAAGCTACTACTGATTAAAGTCGTCACATTAAACATTGCAATACTAGTTTTTTAAAAGTCCAGCTTTTAGTACAGGAGAACTGAAATCATTCCATGTTGATATAAAGTAGGGAAAAACATTGTACTTTTTGGAAAATAGCACTTTTCACTTCTGTGTGTTTTTAAAATTAATGTTATAGAAGACTCATGATTTCTATTTTTGAGTTAAAGCTAGAAAAGGGTTCAACATAATGTTTAATTTTGTCACACTGTTTTCATAGTGTTGATTCCACACTTCAAATACTTCTTAAAATTTTATACAGTTGGGCCAGCTCTAGAAAGTCTGATGTCTCAAAGGGTAAACTTACTACTTTCTTGTGGGACAGAAGGACCTTAAAATATTCATATTACTTAATGAATATGTTAAGGACCAGGCTAGAGTATTTTCTAAGCTGGAAACTTAGTGTGCCTCGGAAAAGGCCGCAAGTTGCTTACTCCGAGTAGCTGTGCTAGCTCTGTCAGACTGTAGGATCATGTCTGCAACTTTTAGAAATAGTGCTTTATATTGCAGCAGTCTTTTATATTTGACTTTTTTTTTAATAGCATTAAAATTGCAGATCAGCTCACTCTGAAACTTTAAGGGTACCAGATATTTTCTATACTGCAGGATTTCTAATGACATTGAAAGACTTTTAAACAGCCTTAGTAAATTATCTTTCTAATGCTCTGTGAGGCCAAACATTTATGTTCAGATTGAAATTTAAATTAATATCATTCAAAAGGAAACAAAAAATGTTGAGTTTTAAAAATCAGGATTGACTTTTTTCTCCAAAACCATACATTTATAGGCAAATTGTGTTCTTTATCACTTCTGAGCAAATACTCAGATTTAAAATTACTTTAAAGTCCTGGTACTTAACAGGCTAACGTAGATAAACACCTTAATAATCTCAGTTAATACTGTATTTCAAAACACATTTAACTGTTTTCTAATGCTTTGCATTATCAGTTACAACCTAGAGAGATTTTGAGCCTCATATTTCTTTGATACTTGAAATAGAGGGAGCTAGAACACTTAATGTTTAATCTGTTAAACCTGCTGCAAGAGCCATAACTTTGAGGCATTTTCTAAATGAACTGTGGGGATCCAGGATTTGTAATTTCTTGATCTAAACTTTATGCTGCATAAATCACTTATCGGAAATGCACATTTCATAGTGTGAAGCACTCATTTCTAAACCTTATTATCTAAGGTAATATATGCACCTTTCAGAAATTTGTGTTCGAGTAAGTAAAGCATATTAGAATAATTATGGGTTGACAGATTTTTAAAATAGAATTTAGAGTATTTGTGTGGGGTTTTGTTTGTTTACAAATAATCAGACTATAATATTTAAACATGCAAAATAACTGAGAATAATGTTGCACTTGTTTACTAAAGATATAAGTTGTTCCATGGGTGTACACGTAGACAGACACACATACACCCAAATTATTGCATTAAGAATCCTGGAGCAGACCATAGCTGAAGCTGTTATTTTCAGTCAGGAAGACTACCTGTCATGAAGGTATACAATAATTTAGAAGTGAATGTTTTTCTGTACCATCTATGTGCAATTATACTCTAAATTCCACTACACTACATTAAAGTAAATGGACATTCCAGAATATAGATGTGATTATAGTCTTAAACTAATTATTAAACCAATGATTGCTGAAAATCAGTGATGCATTTGTTATAGAGTATAACTCATCGTTTACAGTATGTTTTAGTTGGCAGTATCATACCTAGATGGTGAATAACATATTCCCAGTAAATTTATATAGCAGTGAAGAATTACATGCCTTCTGGTGGACATTTTATAAGTGCATTTTATATCACAATAAAATTTTTTCTCTTTAA ùTCCCACCAGACCTGCATCCAAGCAAGTGAAGATGTTAAAGAGATCNNNGCCAGAGCCAGAAATGGAAAGTACAGACCTCTGAAAATATCTATTGAAAATGGGCAACTTATGATTGGATCATATNNNCAGCCTTCAGATTCCTGGGATAACGATTATGATTCCTTTGTTTTACCCCTGTTGGAGGACAAACAACTGTGCTATATATTATTCAGGTTAGATTCTCAGAATGCCCAGGGATATGAATGGATATTCATTGCATGGTTTCCAGATCATTCTCATGTCCGTCAAAAAAGGTTATATGCAGCAACAAGAGCAACTCTGGAAAAGGAATCTGGAGGTGGCCACGTTAAAGATGAAGTATTTGGAACAGTAAAGGAAGATGTATCATTACATGGATATAAAAAATGTTTGCTCTCACAATCTTCCCCTGCCCCACTGACTGCAGCTGAGGAAGAATTANNNGACATTAAAATCAATGAGGTACAGACTGACGTGGGTGTGGACGCTAAGCATCAAACACTACAAGGAGTAGCATTTCCTATTTCTCGAGAAGCTTTTCAGGCTTTGGAAAAAATAAATAACNNNCTGAACTATGTGCAGTTGGAAATAAACATAAAAAATGAAATTATAATTTTGGCCAACACAACAAATACAGAACTAAAAGATTTGCCAAAGAGGATTCCCAAGGATTCAGCTCGTTACCATTTCTTTCTGTATAAACATTCCCATGAAGGAGACTATTTAGAGTCCATAGTTTTTATCTATTCAATGCCCAGATACACATGCAGTATAAGAGAACGGATGCTGTATTCTAGCTGCAAGAGCCCTCTGCTAGAAATTGTAGAAAGACAACTANNNGTTGTAATGGATGTAATTAGAAAGATTGAGATAGACAATGAGGATTAGTTGACTTCAGACTTCCTTTGTGAAGAAGAAGTACATCCCAAGCAGCATGCAGGAAAAAGAAGAATTCGAAGACTAATTAGGGGCCCAGCGGAAAATGAAGCTACTACTGATSSHQTCIQASEDVKEIXARARNGKYRPLKISIENGQLMIGSYXQPSDSWDNDYDSFVLPLLEDKQLCYILFRLDSQNAQGYEWIFIAWFPDHSHVRQKRLYAATRATLEKESGGGHVKDEVFGTVKEDVSLHGYKKCLLSQSSPAPLTAAEEELXDIKINEVQTDVGVDAKHQTLQGVAFPISREAFQALEKINNXLNYVQLEINIKNEIIILANTTNTELKDLPKRIPKDSARYHFFLYKHSHEGDYLESIVFIYSMPRYTCSIRERMLYSSCKSPLLEIVERQLXVVMDVIRKIEIDNED*LTSDFLCEEEVHPKQHAGKRRIRRLIRGPAENEATTD_MSHQTGIQASEDVKEIFARARNGKYRLLKISIENEQLVIGSYSQPSDSWDKDYDSFVLPLLEDKQPCYILFRLDSQNAQGYEWIFIAWSPDHSHVRQKMLYAATRATLKKEFGGGHIKDEIFGTVKEDVSLHGYKKYLLSQSSPAPLTAAEEELRQIKINEVQTDVGVDTKHQTLQGVAFPISREAFQALEKLNNRQLNYVQLEIDIKNEIIILANTTNTELKDLPKRIPKDSARYHFFLYKHSHEGDYLESIVXIYSMPGYTCSIRERMLYSSCKSPLLEIVERQLQMDVIRKIEIDNGDELTADFLYEEVHPKQQAHKQSFAKPKGPAGKRGIRRLIRGPAETEATTD*A6ps2SK766ÿB0¿ÿ[pÛ·¿ÿšv°Ÿ&{¿ÿs:+¿ÿÉM]t2]Æ¢k¿ÿ¦€"&°€ü€;¦0 tT€È¿ÿ¦ptTTtT¿ÿ¦PhisR`gocav Ôtp¤¿ÿ¦p;sÔ¸¿ÿ«y¿ÿ«z°\¿ÿ©ÐtT¿ÿ«y2PÉ8¿ÿ¦àn²HÊ,jà0¿ÿ¦à-@¿ÿ©Ð¿ÿ¦àp¨°€Œ<Àÿÿÿÿ
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YÔ’y*c‡ˆVÈZSV4AŠN£]l‰8®V£s#i­Bn#Âe¶¨ÜF©æéá(Š§zM5>䣪æ7ïˆfKeV¶-×TRI”,‰\âc]{¯iÌ“°+E·‘½ÝÊè-º:Òñ.zÝ´’”ë.:ĸw]»6ÑR4©â’ÂFŠ5•\7c¯CäAÔ–%çÅ&)ÕV[mµÕV[mµÕV[mµÕøÕ¿<€TEXT¶ÇxÁÁJÄ0Ðû)ï:¥IZCY¼¦±'iH‹àÞÀƉ"ˆøÍ/lzÙXÓ‹f1rhv#„À–Ø‚„lu”}€¤B`û¥õi| ̯.aÞéwši+_Ä·ŸSªÇ{©ˆ¼ç)‰¹WZáÌÑaè°¸sÄR®ôx\R^-÷üØ5¾àãRË}—úyÜo¦kDZÓR¶Ø5`ËÖ'OJ+¦{%¥5ðI/JBioPerl-1.007002/t/data/test1.blasttab3000444000766000024       160013155576321 17526 0ustar00cjfieldsstaff000000000000# BLASTP 2.0MP-WashU [04-May-2006] [linux26-i686-ILP32F64 2006-05-09T11:47:08]
# Start: 3:11:00 PM CEST May 21, 2008
# Parameters:
#   topcomboN=5
#   links
#   E=0.0001
#   mformat=3
#   V=5
#   B=5
# Database: test_orfs.fa
#   Title: test_orfs.fa
#   Posted: 11:50:04 AM CEST May 14, 2008
#   Created: 11:50:04 AM CEST May 14, 2008
#   Letters: 9460
#   Records: 307
# Query: 000086_1606_1131
# Fields: qid	sid	E	N	Sprime	S	alignlen	nident	npos	nmism	pcident	pcpos	qgaps	qgaplen	sgaps	sgaplen	qframe	qstart	qend	sframe	sstart	send	group	links
000086_1606_1131	000086_1606_1131	1.7e-11	1	50.12	128	21	21	21	0	100.00	100.00	0	0	0	0	+0	1	21	+0	1	21	1	(1)
000086_1606_1131	000269_0423_3271	5.4e-06	1	31.81	76	22	17	18	1	77.27	81.82	2	2	2	2	+0	1	20	+0	2	21	1	(1)
000086_1606_1131	000780_0082_2331	6.9e-06	1	31.46	75	23	17	19	2	73.91	82.61	3	3	1	1	+0	1	20	+0	2	23	1	(1)
# EXIT: [000086_1606_1131]: 0
BioPerl-1.007002/t/data/test1.wublastp000444000766000024       626713155576321 17526 0ustar00cjfieldsstaff000000000000BLASTP 2.0MP-WashU [04-May-2006] [linux26-i686-ILP32F64 2006-05-09T11:47:08]

Copyright (C) 1996-2006 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2006) http://blast.wustl.edu

Query=  000086_1606_1131 this is your fake desc
        (21 letters)

Database:  test_orfs.fa
           307 sequences; 9460 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done

                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

000086_1606_1131 [64 - 2] (REVERSE SENSE) length=64 uaccn...   128  1.7e-11   1
000269_0423_3271 [1 - 78] length=78 uaccno=ER8QEOW01BBHO5       76  5.4e-06   1
000780_0082_2331 [1 - 78] length=78 uaccno=ER8QEOW01AHI8T       75  6.9e-06   1


>000086_1606_1131 [64 - 2] (REVERSE SENSE) length=64 uaccno=ER8QEOW01D7AWT
        Length = 21

 Score = 128 (50.1 bits), Expect = 1.7e-11, P = 1.7e-11, Group = 1
 Identities = 21/21 (100%), Positives = 21/21 (100%)
 Links = (1)

Query:     1 THITHTYTHITHTSHTHHTHR 21
             THITHTYTHITHTSHTHHTHR
Sbjct:     1 THITHTYTHITHTSHTHHTHR 21


>000269_0423_3271 [1 - 78] length=78 uaccno=ER8QEOW01BBHO5
        Length = 26

 Score = 76 (31.8 bits), Expect = 5.4e-06, P = 5.4e-06, Group = 1
 Identities = 17/22 (77%), Positives = 18/22 (81%)
 Links = (1)

Query:     1 THITHTYTHITHT-SHTH-HTH 20
             TH THTYTH THT +HTH HTH
Sbjct:     2 TH-THTYTH-THTQTHTHAHTH 21


>000780_0082_2331 [1 - 78] length=78 uaccno=ER8QEOW01AHI8T
        Length = 26

 Score = 75 (31.5 bits), Expect = 6.9e-06, P = 6.9e-06, Group = 1
 Identities = 17/23 (73%), Positives = 19/23 (82%)
 Links = (1)

Query:     1 THI-THTYTHITHT-SHTH-HTH 20
             THI THT+TH THT +HTH HTH
Sbjct:     2 THIHTHTHTH-THTHTHTHTHTH 23


Parameters:
  B=5
  V=5
  E=0.0001
  links
  topcomboN=5

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.324   0.122   0.430    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E    S W   T  X   E2     S2
   +0      0       21        21   9.7e-05  71 3  11 22  0.40    21
                                                    29  0.44    22


Statistics:

  Database:  test_orfs.fa
   Title:  test_orfs.fa
   Posted:  11:50:04 AM CEST May 14, 2008
   Created:  11:50:04 AM CEST May 14, 2008
   Format:  XDF-1
   # of letters in database:  9460
   # of sequences in database:  307
   # of database sequences satisfying E:  3
  No. of states in DFA:  208 (22 KB)
  Total size of DFA:  39 KB (2056 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  2
  Search cpu time:  0.00u 0.02s 0.02t   Elapsed:  00:00:00
  Total cpu time:  0.00u 0.02s 0.02t   Elapsed:  00:00:00
  Start:  Wed May 21 22:50:32 2008   End:  Wed May 21 22:50:32 2008
BioPerl-1.007002/t/data/test2.infernal000444000766000024       572413155576321 17461 0ustar00cjfieldsstaff000000000000# cmsearch :: search a sequence database with an RNA CM
# INFERNAL 1.0 (January 2009)
# Copyright (C) 2009 HHMI Janelia Farm Research Campus
# Freely distributed under the GNU General Public License (GPLv3)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# command:    cmsearch my.cm tosearch.300Kb.db
# date:       Tue May 19 11:36:34 2009
# num seqs:   1
# dbsize(Mb): 0.600000
#
# Pre-search info for CM 1: trna.5-1
#
#                                  cutoffs            predictions     
#                            -------------------  --------------------
# rnd  mod  alg  cfg   beta     E value   bit sc     surv     run time
# ---  ---  ---  ---  -----  ----------  -------  -------  -----------
    1   cm  cyk  loc  1e-07     100.010     3.84   0.0183  00:02:34.47
    2   cm  ins  loc  1e-15       1.000    11.92   0.0001  00:00:13.89
# ---  ---  ---  ---  -----  ----------  -------  -------  -----------
  all    -    -    -      -           -        -        -  00:02:48.36
#

CM: trna.5-1
>example

  Plus strand results:

 Query = 1 - 72, Target = 101 - 173
 Score = 78.06, E = 3.133e-21, P = 2.906e-26, GC =  53

           (((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______
         1 gCcgacAUaGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUu 59      
           GC::A::UAGC:CAGU GG AG:GCGCCAG:CUG+++A:CUGGAGGUCC:G:GUUCGAU 
       101 GCGGAUUUAGCUCAGUuGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUC 160     

           >>>>>))))))):
        60 CcccGUgucgGca 72      
           C:C:G::U::GCA
       161 CACAGAAUUCGCA 173     


 Query = 1 - 72, Target = 70822 - 70891
 Score = 12.47, E = 0.6752, P = 6.263e-06, GC =  53

           (((((((,,<<<<_______>>>>,<<<<<_______>>>>>,,,,,~~~~~~)))))))
         1 gCcgacAUaGcgcAgUGGuAgcgCgccagccUgucAagcuggAGgUC*[17]*UgucgGc 71      
            C:G :AU+GCG:A+UGG  :CGCGC    C  UCAA +++GA +UC      U: C:G 
     70822 UCUGCUAUGGCGUAAUGGCCACGCGC----CCAUCAACAAAGAUAUC*[19]*UAACAGG 70890   

           :
        72 a 72      
           A
     70891 A 70891   


  Minus strand results:

 Query = 1 - 72, Target = 15124 - 15083
 Score = 12.93, E = 0.4841, P = 4.491e-06, GC =  48

           (((((((,,~~~~~~,,,,,<<<<<_______>>>>>))))))):
         1 gCcgacAUa*[33]*AGgUCCgggGUUCGAUuCcccGUgucgGca 72      
           GCC: :AUA      A G CC::GG UCG  UCC::GU: :GGC+
     15124 GCCAGUAUA*[ 5]*AUGCCCUAGGAUCG--UCCUAGUAAUGGCG 15083   


#
# Post-search info for CM 1: trna.5-1
#
#                              number of hits       surv fraction  
#                            -------------------  -----------------
# rnd  mod  alg  cfg   beta    expected   actual  expected   actual
# ---  ---  ---  ---  -----  ----------  -------  --------  -------
    1   cm  cyk  loc  1e-07     100.010       70    0.0183   0.0152
    2   cm  ins  loc  1e-15       1.000        3    0.0001   0.0003
#
# expected time    actual time
# -------------  -------------
    00:02:48.36    00:02:42.00
//
#
# CPU time: 157.69u 1.65s 00:02:39.34 Elapsed: 00:02:43
BioPerl-1.007002/t/data/test2.raw000444000766000024        55513155576321 16431 0ustar00cjfieldsstaff000000000000MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVV
VMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVK
KLFVGALKDDHDEQSIRDYFQHFGNIVDNIVIDKETGKKRGFAFVEFDDYDPVDKVVLQK
QHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGN
NWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGND
FGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY

BioPerl-1.007002/t/data/test_badlf.gcg000444000766000024        56313155576321 17445 0ustar00cjfieldsstaff000000000000 REFORMAT of: b124_sp.pep  check: -1  from: 1  to: 146  January 28, 1999 16:22

 (No documentation)

b124_sp.pep  Length: 146  January 28, 1999 16:22  Type: P  Check: 5250  ..

       1  VXCAAEFDFM EKETPLRYTK TLLLPVVLVV FVAIVRKIIS DMWGVLAKQQ 

      51  THVRKHQFDH GELVYHALQL LAYTALGILI MRLKLFLTPY MCVMASLICS 

     101  RQLFGWLFCK VHPGAIVFVI LAAMSIQGSA NLQTQWKSTA SLALETBioPerl-1.007002/t/data/test_clear_range.fastq000444000766000024        35213155576321 21211 0ustar00cjfieldsstaff000000000000@HWI-EAS83:2:1:7:345#0/1
CTTCNGGTGTTACAAACTCTCGTGGTGTGACGGGCGGTGTGTAC
+
ZZZUDQTZZZZZZZXZXZZZZTVTRZZXFVYQENVRVTYQFQZW
@HWI-EAS83:2:1:7:574#0/1
ACGCNTGTCAATCTCTTTCTTCGGATAAGTCCTCGAGCTATTAG
+
\\VVDWX\\\\\\\\\\\\\\\XT\ZZ\T\\\\\X\Z\\\\\\V
BioPerl-1.007002/t/data/test_data.axt000444000766000024        62013155576321 17334 0ustar00cjfieldsstaff0000000000000 chr19 3001012 3001075 chr11 70568380 70568443 - 3500
TCAGCTCATAAATCACCTCCTGCCACAAGCCTGGCCTGGTCCCAGGAGAGTGTCCAGGCTCAGA
TCTGTTCATAAACCACCTGCCATGACAAGCCTGGCCTGTTCCCAAGACAATGTCCAGGCTCAGA

1 chr19 3008279 3008357 chr11 70573976 70574054 - 3900
CACAATCTTCACATTGAGATCCTGAGTTGCTGATCAGAATGGAAGGCTGAGCTAAGATGAGCGACGAGGCAATGTCACA
CACAGTCTTCACATTGAGGTACCAAGTTGTGGATCAGAATGGAAAGCTAGGCTATGATGAGGGACAGTGCGCTGTCACABioPerl-1.007002/t/data/test_singlets.cns.fastq000444000766000024      1516613155576321 21432 0ustar00cjfieldsstaff000000000000@gi|65306796|gb|AY948116.1|
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaagt
gcATAGCTTAGAAGAAAGCCTtgcaatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnattatgaaggtataaaatctGTTATAAGTAATCATGCGATAGAGAgTATttacatg
aatgaattagatattatcgctatgataaaacaaagTGCTTtaaagtTAAGTGCTGATGAA
atcattgctgannnnnnnnnnnagggatttgtagaatATGTCAAAAGTTGCCACCGCTCA
TTGCAATCCTAAAAAACAACCTGCATTAAACCACAATGATAGAaccaacgannnnnctaa
gacaatcactaaagAACTTACgcatttaaatgaatactcttgcactagcgatgaagtgcg
taagaacatagaaaggCTTTATAAAAAAGCTTATGAAAATTTTTATAAATATTGTGAAAA
TAAGAatggtttagctaaaagtggaannnnnnnnnnnnnnnnaaattttactaaaaaaga
aaaatgttatcacgagtttatnnnnnnnnnnnnnnnnnntactacaatggagcaatgcca
agAGcttacgcAAAAaatcGCAGAGCTTACAGGATTTACACCTTtacaagttgtaatnnn
nnnnnnnnnnntaagtgAGAATGCTAAAGGGGAAAAacaaacnnnnnnnnnnnnnnnngc
ggtattttttacactcgataacannnnnnnnnnnnnnnnnagacgtgaagcaagtttgaa
taaagccaatcttagcaaaatacaAACcctaaccgcacaaagtttaaaaatggagcgtGG
AGCTAATCGCTACGAGAAtaacgaaaagnnnnnnnnnnnnatacaagattataaaacata
cgctcnnnnntaagaacaagaaaaagcatTACTTCaaagAataCAAGAACAAGAGCATAA
ATTAACGCAaatggccctagaattgaannnnnnnnnnaaagagatacaagacaaggctaa
agagttaaaatcgaaagaaaACGAATTACAAGCGAAAATAGAGCAacAtcaaaaacatat
acaaaatttagAactAGGACACGAAAGAgctttaaAggaacttacacaagagtttgaaaa
nnnnnnnnnnnnnnnnnaaaacattttAACCTTTGGAAAATACAACGCCaaagtnnnnnn
agactatcagttaacaaagaatgctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
naacaaagagcttgaatatttaAAATttgaatatCATAaagtcaaagatgaacgagatan
tttaaaaactttgtttgaGGCACACAAAACAAAAAATGTTaaatnnnnnnnnngactaaa
agaaatagGCAAATGGTGtgaaaaaaatttaagnnnnnngcagttaaaagaaatatttcc
attaaaannnnnnnnnnnnnnaaaagagcttaaatatcaaagaGCTTTTGAaaattcTTT
TGAACAAGCAAaaAGAAACGATagagggttTGGGTTTAGCAGATAGTTTTCTTTtttggt
gctttagcaaatcgcacctgttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nctgagTGCGTAGCACGGAAGACGGAcaaagcccaccgccctagaaaaaaaattactcaa
ctttttttgttTTTTCTCTCGCGCGCGtacgcgtacnnnnnnnnnnnnnnnnnnnnnnnn
nnnttcttatttttagggggctttctaagccctatatnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnacgacaaaattctac
tattaaaacgnnaaaattctactattaaggggagaaaattctactattaaaacgacaaaa
tatttgacaaataTtgtttTAATATACTACAATAAAAAATCCGCCTTGAGTTTTCACTCt
tggcggaaatttaTCAATCAAGGCTAACTATGAAACgacatantaagcgttttgtgagat
tatacctaaaatttaggttttttaagcttaaagttgaannatttttctagcaaaaccgca
ggggCagagaaGCCCCTTGCCTTGATTGTCTTACTTTGGATATGCAAATGAGCGAAATAG
TTAAATATAATAATGATtttaatcttttannnnnncctgaaCTTAAAGCCATACAAATGG
atatgtnnntggctattatctcactaaccaaagannnnnnagaaaatacgccatttttaa
aaaagnnnnttaaccctgatagaAGAAAAATAATTATTCCGCAAAAGAAGTTTATTgaat
tatgtcggttaaannnnnnnnnnnnnnactataaagAAATTTTCTTTGCCATTGATGATT
GcttgaaaaaactttgcaattttcttatttcataccaannnnnnnnnnnnnnnatttATA
ATTTTGTTTGTTTTGAAGaagcaaatattattgnnnnnnnnnnnnatataacTTTACAAA
GTCGTTTTTACGATATGATAATAAataaaaaatttggtttcacagcctttgaattagccg
aatttgcagaacttnnnnnnnnnnnnnnnnnaactttatacagacttttAAAGCAATTTA
GAACCACAggcAAAgcttattttgagtgggaagaatnnnnnnngattatgaaaatacCTG
AAAATTATCGTCAAATAGATATAGACCAAAGaattttaaaannnnnnnnnaaagaactTT
CTAAAGAACGCTATCTTTTTGACCAAATCAGAgtgcctttTAAAaatcttgcttatgaaa
AAgaAaaaaccgcagggcgtgggcgcggcnnnnnnnnnncaggtattagctttactttTA
AACCtgAAAATATCCAAATGCAAAAGCTAGAAAATGAAAGTCAAAAAATAATgagcgatg
agcaaaaatatttaaagattntaaacaATATGAAACTTAATCAAGTTAGAtttgattatA
ATGACAAGCTTTGGCAATttaacgattttgatnttgatgaatttaaaattaTTGCAATag
AGCTTGTAagagatgaatacgagaannnnnnnnnnggaaatcatatgcacTTTAATGCTA
aaaatcaagagcagttttttaaaaTGATTGAAACCTTTAGAAAAGGTATtaggnnnnnnn
nnnnnnnnnnnntatctttaaaggatacaagctatccgccacttgtgccaagtgtcgagc
ntgtaaggggtgcaaccccttaaccCcactaataaaaatcaactaAAAtcaataaatgat
ttttttgattnnnnnn
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?BBB
BBEEEEEEEEEEEEEEEEEEEB?????!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!??????????????????BBEEEEHEEEHHHHHHHHHHHHHHHEEBEEEBBBBBBB
BBBBBBBBBBBBBBBBBBBBBB?????????????EEEEEBBBBBBEEEEEEEEEEEEEE
???????????!!!!!!!!!!!????????????BBBEEEEHHHHHHEEEEHKKNNNNQQ
QQNNNNNNNNNNNNQQNKNKKKKHHHKKKKKHHHHHHHHEEEEBBBBBB??!!!!!???B
BBBBBBBBBBBBBBEEEEEEEBBB????????BBBBBBB???????BBBBBBBBBBB???
?????????BB???BBEEEEEEHHHHHHHHKNNNKKKKNNQNNNNNNKKKKKKKKHEEHH
HKKHEBBBBBBBBBBBBBBBBBB???!!!!!!!!!!!!!!!!??????????????BBBB
BBBBBBB??????????????!!!!!!!!!!!!!!!!!!???????????BBBBBBBBBB
BBEEBBBBBBBEEEEBBBBEEEEEHHHEEEEEHHHHEEEEEEEEBBBBB????????!!!
!!!!!!!!!!!?BBBBBEEEEEEEEEEEEEEEEEEEB?????!!!!!!!!!!!!!!!!??
???????????????????????!!!!!!!!!!!!!!!!!????????????????????
??BBB??????BBBBBBBBBBBBBEEEBBBBBBBBB????BBBBBBBBB????BBBBBEE
EEEHHEEEEEEEEEEEEEBBBBB?????!!!!!!!!!!!!????????????????????
?????!!!!!+????BBBBBBBBBBBBBBEEEEEEBBBBEBBBEHHHHKKKKKKHHHHHH
HHKKHHHHEBBBB??????????????!!!!!!!!!!?????????BBBBBBBBBBBBBB
BB??????????????BBBBEEEHHHKKKKKKKKKKHHHHHEEEEBBEBBB?????????
???BBBBBBBBEBBBEEEEEEEEEEEEEBBBBBBBEBBBB????????????????????
!!!!!!!!!!!!!!!!!???????BBBEEHHHHHHHHHHHHHEEEEEEEBBB??!!!!!!
?????????????????????????!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!????????????BBBBBBBBBEEEEBBBBBBBBEEEEBBBBBBBBB????????????!
???????????????BBBEHHHHHHEEEEEEEEEEEEEEEBBB?!!!!!!!!!???????
?BBBBBBBEEEEEEEEEEBBBBBBBB???????!!!!!!???BBBBBBBBBBBBBBBBBB
BBBB???!!!!!!!!!!!!!!?????BBBBBBBBBBBBBBBBBEEEEEEEEBBBBBBEEE
EHHHHHHHEEEBBEEEEEEEEEBBBB???BEEEEEEEEEEEEEEEEEEEEEEEEB??BBB
BBB???????????????????!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!BBBBBEEEEEEEEEEEEEEEEEEEE???????????BBBBBBBBBBBBBBBBBBB????
??????????BEEEEEEEEEEEEEEEEBBBBBBBB?!!!!!!!!!!!!!!!!!!!!!!!!
!!!?????????BBBBBBBBBBBBBBBB?????????!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!)))))))))))))))
))))))))))!!???????????????BBBBBBBBBB????????????BBB????????
?????????BBBBEBBBBBEEEEEEEEEEEHHHHHHKKHHHHHHEHHHHHHHHHHEEEEB
B????????B?BBEEEEHHHHHHHHHHHHHHHHHEEBB????!?????????????????
?????????????BBBBBBBBBBBBBBBBBBBB?????!!?????????????BBBBBBB
BBBBEBBBBBBEEEEEEEEEEEEEEEEHKHHKNNNNNNNNNNNKKKKNNNNNNKKKHEEE
EEEEHHHHHHHHEEEEEBBBBBBBBB???!!!!!!??BBBBEEEEEEEEEEEEEEEEEEE
BB????!!!?????????????????????????!!!!!!????????????????????
?????!!!!??????????????HHHKKKKKQQQNNNNNNNNNNNNNNHHHEEEEE????
?????????????!!!!!!!!!!!!!!?????????EEEEEEHHHHHHHHHHEEEEEEEE
E????BB??????BBBBBBBBBBBBBBBBB????????!!!!!!!!!!!!!!!BBBBEEE
EEEEEEEEHHHHHHHHHHBBBB???????????!!!!!!!!!!!!???BBBBEEEEEEEH
HHHKKNNNNNKKKHHHHEEEEEEEBBBBBB???????????????????BBBB???????
??????????????!!!!!!!!!!!!!!!!!????????????BBBBBBEEEEHHHEEEE
EEEEEEEEBBBEEEBBBB??????????????????!!!!!!!??BBBBBBBBBBBBEEE
EHHHHHKKHHEEEEHHKKKKKKHHHHEEEEEBBBBBBBB??!!!!!!!!!BBBBBBBBEE
HHHHHHHKKNNNNNNHHHHKKKKHHEEEEEEEBB???BBBEEEEBBBBBBBBBBBBBBBB
EEBBEBBBBBBBBBBBBBBBBBBBB????!!!!!!!!!!????????BBBBBBBBBBBEE
EEEEBBEEEHHHEEEEEEEEEEKHHHKNQQQNNNKKKKKKKKKKKKKEEEEEB??BBBBB
BBBBBBBBBBBBBBBB????!????BBEEEEEEEEEEEEEEEEEEEEEEEBB?BBBBBBE
EEEEEEEHHHHEEEEEEEBBBBBB????????!??????????BBBBBBBBEEEEEEEBB
EEEEEEEEBBBBBBBB?????????!!!!!!!!!!?BBBBBBBBBBBBBBEEEEEEEEEE
B??????????BBBB???????BBEEHHKKKKKKKKHHHHHHHHHHHEEBB??!!!!!!!
!!!!!!!!!!!!???????????????????????BB???????????????????????
!??????????????????????BBEBBBBBBBBBBBBBBBBBBBEEEBB??????????
??????????!!!!!!
BioPerl-1.007002/t/data/test_singlets.maq000444000766000024     11066213155576321 20325 0ustar00cjfieldsstaff00000000000065306796|gb|AY948116.1|_57_240_13/2	gi|65306796|gb|AY948116.1|	57	+	184	18	99	78	78	0	0	1	0	25	AAGTGCATAGCTTAGAAGAAAGCCT	YYYYYYYYYWYYYYWWYWWUWYYWW
65306796|gb|AY948116.1|_58_177_20/1	gi|65306796|gb|AY948116.1|	58	+	120	18	99	78	78	0	0	1	0	25	AGTGCATAGCTTAGAAGAAAGCCTT	YYYYYYYYYWYYYYYYYWWYWWYWY
|65306796|gb|AY948116.1|_63_202_8/2	gi|65306796|gb|AY948116.1|	63	+	140	18	99	78	78	0	0	1	0	25	ATAGCTTAGAAGAAAGCCTTGCAAT	YYYYYYYYYYWYYYYYYYYSYWWQQ
5306796|gb|AY948116.1|_125_324_25/2	gi|65306796|gb|AY948116.1|	125	+	200	18	99	78	78	0	0	1	0	25	ATTATGAAGGTATAAAATCTGTTAT	YYYYYYYYYYYYYYYWYWWYWYYWW
5306796|gb|AY948116.1|_143_319_3f/2	gi|65306796|gb|AY948116.1|	143	+	177	18	99	78	78	0	0	1	0	25	CTGTTATAAGTAATCATGCGATAGA	YYYYYYYYYYYYYYYYYYYSYWYSY
5306796|gb|AY948116.1|_145_306_2d/1	gi|65306796|gb|AY948116.1|	145	+	162	18	99	78	78	0	0	1	0	25	GTTATAAGTAATCATGCGATAGAGA	YYYYYYYYYYYYYWYYYYWUWWYWY
5306796|gb|AY948116.1|_149_317_73/2	gi|65306796|gb|AY948116.1|	149	+	169	18	99	78	78	0	0	1	0	25	TAAGTAATCATGCGATAGAGAGTAT	YYYYYYYYYWYYYYYWYYWWYYYSY
65306796|gb|AY948116.1|_58_177_20/2	gi|65306796|gb|AY948116.1|	153	-	-120	18	99	78	78	0	0	1	0	25	TAATCATGCGATAGAGAGTATTTAC	QQWWYWWYYWWYYYYWYYYYYYYYY
5306796|gb|AY948116.1|_171_331_5a/1	gi|65306796|gb|AY948116.1|	171	+	161	18	99	78	78	0	0	1	0	25	TATTTACATGAATGAATTAGATATT	YYYYYYYYYYYYYYYYWYYSYYYWW
|65306796|gb|AY948116.1|_63_202_8/1	gi|65306796|gb|AY948116.1|	178	-	-140	18	99	78	78	0	0	1	0	25	ATGAATGAATTAGATATTATCGCTA	YSYYWWYYYYYYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_196_351_32/2	gi|65306796|gb|AY948116.1|	196	+	156	18	99	78	78	0	0	1	0	25	ATCGCTATGATAAAACAAAGTGCTT	YYYYYYYYYYYYYYYYWYYWYWWQQ
5306796|gb|AY948116.1|_216_381_36/2	gi|65306796|gb|AY948116.1|	216	+	166	18	99	78	78	0	0	1	0	25	TGCTTTAAAGTTAAGTGCTGATGAA	YYYYYYYYYYYYYYYYYWWYWYYWW
65306796|gb|AY948116.1|_57_240_13/1	gi|65306796|gb|AY948116.1|	216	-	-184	18	99	78	78	0	0	1	0	25	TGCTTTAAAGTTAAGTGCTGATGAA	WWYYWYWWYYYYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_227_417_78/1	gi|65306796|gb|AY948116.1|	227	+	191	18	99	78	78	0	0	1	0	25	TAAGTGCTGATGAAATCATTGCTGA	YYYYYYYYYYYYYYYYYYWUWWYWY
5306796|gb|AY948116.1|_263_431_4a/1	gi|65306796|gb|AY948116.1|	263	+	169	18	99	78	78	0	0	1	0	25	AGGGATTTGTAGAATATGTCAAAAG	YYYYYYYYYYYYYYWWYYWYWWYWW
5306796|gb|AY948116.1|_275_459_16/1	gi|65306796|gb|AY948116.1|	275	+	185	18	99	78	78	0	0	1	0	25	AATATGTCAAAAGTTGCCACCGCTC	YYYYYYYYYWYYYWYYWYWYWWYWY
5306796|gb|AY948116.1|_278_467_3a/1	gi|65306796|gb|AY948116.1|	278	+	190	18	99	78	78	0	0	1	0	25	ATGTCAAAAGTTGCCACCGCTCATT	YYYYYYYYYYYYYYYYYWWUWWYSU
5306796|gb|AY948116.1|_145_306_2d/2	gi|65306796|gb|AY948116.1|	282	-	-162	18	99	78	78	0	0	1	0	25	CAAAAGTTGCCACCGCTCATTGCAA	YWYYWYWYWYYYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_292_484_58/2	gi|65306796|gb|AY948116.1|	292	+	193	18	99	78	78	0	0	1	0	25	CACCGCTCATTGCAATCCTAAAAAA	YYYYYYYYYYYYYYWWYYYSYYYWW
5306796|gb|AY948116.1|_149_317_73/1	gi|65306796|gb|AY948116.1|	293	-	-169	18	99	78	78	0	0	1	0	25	ACCGCTCATTGCAATCCTAAAAAAC	USYYWWWWYWWYYYWYYYYYYYYYY
5306796|gb|AY948116.1|_143_319_3f/1	gi|65306796|gb|AY948116.1|	295	-	-177	18	99	78	78	0	0	1	0	25	CGCTCATTGCAATCCTAAAAAACAA	WWYYYWWYYWYYYYYWYYYYYYYYY
5306796|gb|AY948116.1|_299_483_56/2	gi|65306796|gb|AY948116.1|	299	+	185	18	99	78	78	0	0	1	0	25	CATTGCAATCCTAAAAAACAACCTG	YYYYYYYYYYWYYYWWYYWUWYYSY
5306796|gb|AY948116.1|_125_324_25/1	gi|65306796|gb|AY948116.1|	300	-	-200	18	99	78	78	0	0	1	0	25	ATTGCAATCCTAAAAAACAACCTGC	WWYWWUWYYWYYYYYWYYYYYYYYY
5306796|gb|AY948116.1|_171_331_5a/2	gi|65306796|gb|AY948116.1|	307	-	-161	18	99	78	78	0	0	1	0	25	TCCTAAAAAACAACCTGCATTAAAC	QQWWWYWWYWWYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_315_506_75/2	gi|65306796|gb|AY948116.1|	315	+	192	18	99	78	78	0	0	1	0	25	AACAACCTGCATTAAACCACAATGA	YYYYYYYYYWYYYYWWYYWWYWYWY
5306796|gb|AY948116.1|_319_475_6c/2	gi|65306796|gb|AY948116.1|	319	+	157	18	99	78	78	0	0	1	0	25	ACCTGCATTAAACCACAATGATAGA	YYYYYYYYYYYYYYYYWYWUWWYWY
5306796|gb|AY948116.1|_325_461_38/1	gi|65306796|gb|AY948116.1|	325	+	137	18	99	78	78	0	0	1	0	25	ATTAAACCACAATGATAGAACCAAC	YYYYYYYYYYYYYWYYYYWYWWWQQ
5306796|gb|AY948116.1|_196_351_32/1	gi|65306796|gb|AY948116.1|	327	-	-156	18	99	78	78	0	0	1	0	25	TAAACCACAATGATAGAACCAACGA	WWYYWUWWYYYYYYYWYYYYYYYYY
5306796|gb|AY948116.1|_216_381_36/1	gi|65306796|gb|AY948116.1|	357	-	-166	18	99	78	78	0	0	1	0	25	CTAAGACAATCACTAAAGAACTTAC	WWYWWWYYYWWYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_360_547_3e/2	gi|65306796|gb|AY948116.1|	360	+	188	18	99	78	78	0	0	1	0	25	AGACAATCACTAAAGAACTTACGCA	YYYYYYYYYYWYYYYYYYYSYWYSY
5306796|gb|AY948116.1|_375_561_46/2	gi|65306796|gb|AY948116.1|	375	+	187	18	99	78	78	0	0	1	0	25	AACTTACGCATTTAAATGAATACTC	YYYYYYYYYWYYYYYYYWWUWWYSY
5306796|gb|AY948116.1|_227_417_78/2	gi|65306796|gb|AY948116.1|	393	-	-191	18	99	78	78	0	0	1	0	25	AATACTCTTGCACTAGCGATGAAGT	QQWWWWYYYWWYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_263_431_4a/2	gi|65306796|gb|AY948116.1|	407	-	-169	18	99	78	78	0	0	1	0	25	AGCGATGAAGTGCGTAAGAACATAG	YWYYWUWYWYYYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_430_615_42/1	gi|65306796|gb|AY948116.1|	430	+	186	18	99	78	78	0	0	1	0	25	AGAAAGGCTTTATAAAAAAGCTTAT	YYYYYYYYYYWYYYWWYWWYWWYSU
5306796|gb|AY948116.1|_275_459_16/2	gi|65306796|gb|AY948116.1|	435	-	-185	18	99	78	78	0	0	1	0	25	GGCTTTATAAAAAAGCTTATGAAAA	YWYWWUWWYWYWYYYWYYYYYYYYY
5306796|gb|AY948116.1|_325_461_38/2	gi|65306796|gb|AY948116.1|	437	-	-137	18	99	78	78	0	0	1	0	25	CTTTATAAAAAAGCTTATGAAAATT	YSYWWUWWYYYYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_278_467_3a/2	gi|65306796|gb|AY948116.1|	443	-	-190	18	99	78	78	0	0	1	0	25	AAAAAAGCTTATGAAAATTTTTATA	USYWWWWYYYYYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_319_475_6c/1	gi|65306796|gb|AY948116.1|	451	-	-157	18	99	78	78	0	0	1	0	25	TTATGAAAATTTTTATAAATATTGT	QQWWWUWWYWWYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_452_644_4b/2	gi|65306796|gb|AY948116.1|	452	+	193	18	99	78	78	0	0	1	0	25	TATGAAAATTTTTATAAATATTGTG	YYYYYYYYYYYYYWYYYYYSYWYWY
5306796|gb|AY948116.1|_299_483_56/1	gi|65306796|gb|AY948116.1|	459	-	-185	18	99	78	78	0	0	1	0	25	ATTTTTATAAATATTGTGAAAATAA	YWYWWYWWYYYWYYYYYYYYYYYYY
5306796|gb|AY948116.1|_292_484_58/1	gi|65306796|gb|AY948116.1|	460	-	-193	18	99	78	78	0	0	1	0	25	TTTTTATAAATATTGTGAAAATAAG	USYYWWYYWYYYYYWYYYYYYYYYY
5306796|gb|AY948116.1|_461_636_37/2	gi|65306796|gb|AY948116.1|	461	+	176	18	99	78	78	0	0	1	0	25	TTTTATAAATATTGTGAAAATAAGA	YYYYYYYYYYYYYYWWYWWUWWYSU
65306796|gb|AY948116.1|_479_649_c/1	gi|65306796|gb|AY948116.1|	479	+	171	18	99	78	78	0	0	1	0	25	AATAAGAATGGTTTAGCTAAAAGTG	YYYYYYYYYYWYYYWWYWWYWWWQQ
5306796|gb|AY948116.1|_315_506_75/1	gi|65306796|gb|AY948116.1|	482	-	-192	18	99	78	78	0	0	1	0	25	AAGAATGGTTTAGCTAAAAGTGGAA	YSYYYSYYWYYYYYYWYYYYYYYYY
5306796|gb|AY948116.1|_360_547_3e/1	gi|65306796|gb|AY948116.1|	523	-	-188	18	99	78	78	0	0	1	0	25	AAATTTTACTAAAAAAGAAAAATGT	YWYYYSYYYYYYYYWYYYYYYYYYY
5306796|gb|AY948116.1|_375_561_46/1	gi|65306796|gb|AY948116.1|	537	-	-187	18	99	78	78	0	0	1	0	25	AAGAAAAATGTTATCACGAGTTTAT	WWYWYSYYYWWYYYYWYYYYYYYYY
5306796|gb|AY948116.1|_580_743_2f/1	gi|65306796|gb|AY948116.1|	580	+	164	18	99	78	78	0	0	1	0	25	TACTACAATGGAGCAATGCCAAGAG	YYYYYYYYYWYYYYYWYWWYWWWQQ
5306796|gb|AY948116.1|_430_615_42/2	gi|65306796|gb|AY948116.1|	591	-	-186	18	99	78	78	0	0	1	0	25	AGCAATGCCAAGAGCTTACGCAAAA	WWYWWYWWYWWYYYYYYYYYYYYYY
65306796|gb|AY948116.1|_603_785_2/2	gi|65306796|gb|AY948116.1|	603	+	183	18	99	78	78	0	0	1	0	25	AGCTTACGCAAAAAATCGCAGAGCT	YYYYYYYYYWYYYYYYYYWYWYYSU
5306796|gb|AY948116.1|_461_636_37/1	gi|65306796|gb|AY948116.1|	612	-	-176	18	99	78	78	0	0	1	0	25	AAAAAATCGCAGAGCTTACAGGATT	WWYYYWYYYYYWYYYYYYYYYYYYY
5306796|gb|AY948116.1|_452_644_4b/1	gi|65306796|gb|AY948116.1|	620	-	-193	18	99	78	78	0	0	1	0	25	GCAGAGCTTACAGGATTTACACCTT	YWYWWUWWYWWYYYYYYYYYYYYYY
65306796|gb|AY948116.1|_479_649_c/2	gi|65306796|gb|AY948116.1|	625	-	-171	18	99	78	78	0	0	1	0	25	GCTTACAGGATTTACACCTTTACAA	QQWWWWWYYYYYYYYWYYYYYYYYY
5306796|gb|AY948116.1|_633_845_6b/2	gi|65306796|gb|AY948116.1|	633	+	213	18	99	78	78	0	0	1	0	25	GATTTACACCTTTACAAGTTGTAAT	YYYYYYYYYYYYYWYYWYWWWYYSU
5306796|gb|AY948116.1|_672_807_65/2	gi|65306796|gb|AY948116.1|	672	+	136	18	99	78	78	0	0	1	0	25	TAAGTGAGAATGCTAAAGGGGAAAA	YYYYYYYYYYWYYWYWYYYSYYYSY
5306796|gb|AY948116.1|_673_829_15/1	gi|65306796|gb|AY948116.1|	673	+	157	18	99	78	78	0	0	1	0	25	AAGTGAGAATGCTAAAGGGGAAAAA	YYYYYYYYYWYYYWYYWYYWWWYWY
5306796|gb|AY948116.1|_678_858_72/1	gi|65306796|gb|AY948116.1|	678	+	181	18	99	78	78	0	0	1	0	25	AGAATGCTAAAGGGGAAAAACAAAC	YYYYYYYYYWYYYYYYYYWUWWWQQ
5306796|gb|AY948116.1|_580_743_2f/2	gi|65306796|gb|AY948116.1|	719	-	-164	18	99	78	78	0	0	1	0	25	GCGGTATTTTTTACACTCGATAACA	USYWWYWYWYYYYYYYYYYYYYYYY
65306796|gb|AY948116.1|_603_785_2/1	gi|65306796|gb|AY948116.1|	761	-	-183	18	99	78	78	0	0	1	0	25	AGACGTGAAGCAAGTTTGAATAAAG	USYYWYWYWYYYYYYWYYYYYYYYY
5306796|gb|AY948116.1|_672_807_65/1	gi|65306796|gb|AY948116.1|	783	-	-136	18	99	78	78	0	0	1	0	25	AAGCCAATCTTAGCAAAATACAAAC	YWYYYSYYYYYYYYWYYYYYYYYYY
5306796|gb|AY948116.1|_792_964_79/2	gi|65306796|gb|AY948116.1|	792	+	173	18	99	78	78	0	0	1	0	25	TTAGCAAAATACAAACCCTAACCGC	YYYYYYYYYYWYYYYYYYWUWWYWY
5306796|gb|AY948116.1|_673_829_15/2	gi|65306796|gb|AY948116.1|	805	-	-157	18	99	78	78	0	0	1	0	25	AACCCTAACCGCACAAAGTTTAAAA	YWYYYSYYYWYYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_633_845_6b/1	gi|65306796|gb|AY948116.1|	821	-	-213	18	99	78	78	0	0	1	0	25	AGTTTAAAAATGGAGCGTGGAGCTA	USYWYWYYYYYYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_678_858_72/2	gi|65306796|gb|AY948116.1|	834	-	-181	18	99	78	78	0	0	1	0	25	AGCGTGGAGCTAATCGCTACGAGAA	USYWWYWYYYYYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_839_973_44/1	gi|65306796|gb|AY948116.1|	839	+	135	18	99	78	78	0	0	1	0	25	GGAGCTAATCGCTACGAGAATAACG	YYYYYYYYYYWYYYWWYYWYWYYWY
306796|gb|AY948116.1|_844_1031_1e/2	gi|65306796|gb|AY948116.1|	844	+	188	18	99	78	78	0	0	1	0	25	TAATCGCTACGAGAATAACGAAAAG	YYYYYYYYYWYYYWYYYYYWYYYSY
306796|gb|AY948116.1|_881_1061_7b/2	gi|65306796|gb|AY948116.1|	881	+	181	18	99	78	78	0	0	1	0	25	ATACAAGATTATAAAACATACGCTC	YYYYYYYYYYWYYYYWYYWYWWWQQ
306796|gb|AY948116.1|_904_1068_68/1	gi|65306796|gb|AY948116.1|	904	+	165	130	7	-1	78	0	0	0	0	25	TCAATTTAAGAACAAGAAAAAGCAT	YYYYYYYYYYYYYYYWYWWYWWWQQ
306796|gb|AY948116.1|_910_1065_60/1	gi|65306796|gb|AY948116.1|	911	+	155	18	99	61	61	1	30	0	1	25	tAAGAACAAGAAAAAGCATTACTTC	+YYYYYYYYYYYYWYYYYYSYWWQQ
306796|gb|AY948116.1|_916_1071_76/2	gi|65306796|gb|AY948116.1|	916	+	156	18	99	78	78	0	0	1	0	25	ACAAGAAAAAGCATTACTTCAAAGA	YYYYYYYYYWYYYYWWYWWWYWWQQ
306796|gb|AY948116.1|_930_1108_2e/1	gi|65306796|gb|AY948116.1|	930	+	179	18	99	78	78	0	0	1	0	25	TACTTCAAAGAATACAAGAACAAGA	YYYYYYYYYYYYYYYYYYYSYYYSY
5306796|gb|AY948116.1|_792_964_79/1	gi|65306796|gb|AY948116.1|	940	-	-173	18	99	78	78	0	0	1	0	25	AATACAAGAACAAGAGCATAAATTA	WWYWWUWYYYYYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_944_1116_e/1	gi|65306796|gb|AY948116.1|	944	+	173	18	99	78	78	0	0	1	0	25	CAAGAACAAGAGCATAAATTAACGC	YYYYYYYYYYYYYWYYWYYSYYYSY
306796|gb|AY948116.1|_945_1120_52/1	gi|65306796|gb|AY948116.1|	945	+	176	18	99	78	78	0	0	1	0	25	AAGAACAAGAGCATAAATTAACGCA	YYYYYYYYYYWYYYYYWYYWYWWQQ
5306796|gb|AY948116.1|_839_973_44/2	gi|65306796|gb|AY948116.1|	949	-	-135	18	99	78	78	0	0	1	0	25	ACAAGAGCATAAATTAACGCAAATG	USYWWYWYWYYWYYYYYYYYYYYYY
306796|gb|AY948116.1|_963_1092_23/1	gi|65306796|gb|AY948116.1|	963	+	130	18	99	78	78	0	0	1	0	25	TAACGCAAATGGCCCTAGAATTGAA	YYYYYYYYYYWYYWYWYYYSYYYWW
306796|gb|AY948116.1|_998_1182_7c/1	gi|65306796|gb|AY948116.1|	998	+	185	18	99	78	78	0	0	1	0	25	AAAGAGATACAAGACAAGGCTAAAG	YYYYYYYYYYWYYWYWYYYWWWYWY
306796|gb|AY948116.1|_844_1031_1e/1	gi|65306796|gb|AY948116.1|	1007	-	-188	18	99	78	78	0	0	1	0	25	CAAGACAAGGCTAAAGAGTTAAAAT	WWYYWYWYYWWYYYWYYYYYYYYYY
06796|gb|AY948116.1|_1032_1194_30/2	gi|65306796|gb|AY948116.1|	1032	+	163	18	99	78	78	0	0	1	0	25	CGAAAGAAAACGAATTACAAGCGAA	YYYYYYYYYYYYYYYYYYWWWWYSY
306796|gb|AY948116.1|_881_1061_7b/1	gi|65306796|gb|AY948116.1|	1037	-	-181	18	99	78	78	0	0	1	0	25	GAAAACGAATTACAAGCGAAAATAG	WWYWWYWYYWWYYYYWYYYYYYYYY
306796|gb|AY948116.1|_910_1065_60/2	gi|65306796|gb|AY948116.1|	1041	-	-155	18	99	78	61	0	0	1	0	25	ACGAATTACAAGCGAAAATAGAGCA	WWYYWYWYYWWYYYYYYYYYYYYYY
306796|gb|AY948116.1|_904_1068_68/2	gi|65306796|gb|AY948116.1|	1044	-	-165	18	78	78	78	0	0	1	0	25	AATTACAAGCGAAAATAGAGCAACA	QQWWWUWYYWWYYYYYYYYYYYYYY
306796|gb|AY948116.1|_916_1071_76/1	gi|65306796|gb|AY948116.1|	1047	-	-156	18	99	78	78	0	0	1	0	25	TACAAGCGAAAATAGAGCAACATCA	YWYWWWYYYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_963_1092_23/2	gi|65306796|gb|AY948116.1|	1068	-	-130	18	99	78	78	0	0	1	0	25	ATCAAAAACATATACAAAATTTAGA	YSYWWYWYYWWYYYYYYYYYYYYYY
306796|gb|AY948116.1|_930_1108_2e/2	gi|65306796|gb|AY948116.1|	1084	-	-179	18	99	78	78	0	0	1	0	25	AAATTTAGAACTAGGACACGAAAGA	QQWWWYWYYYYYYYYYYYYYYYYYY
5306796|gb|AY948116.1|_944_1116_e/2	gi|65306796|gb|AY948116.1|	1092	-	-173	18	99	78	78	0	0	1	0	25	AACTAGGACACGAAAGAGCTTTAAA	YWYWWYWYYYYYYYYWYYYYYYYYY
306796|gb|AY948116.1|_945_1120_52/2	gi|65306796|gb|AY948116.1|	1096	-	-176	18	99	78	78	0	0	1	0	25	AGGACACGAAAGAGCTTTAAAGGAA	WWYYYWYYYWWYYYYYYYYYYYYYY
306796|gb|AY948116.1|_1116_1298_7/1	gi|65306796|gb|AY948116.1|	1116	+	183	18	99	78	78	0	0	1	0	25	AGGAACTTACACAAGAGTTTGAAAA	YYYYYYYYYYYYYYWWYYYWWYYWW
306796|gb|AY948116.1|_998_1182_7c/2	gi|65306796|gb|AY948116.1|	1158	-	-185	18	99	78	78	0	0	1	0	25	AAAACATTTTAACCTTTGGAAAATA	QQWWWWWYWYYYYYWYYYYYYYYYY
306796|gb|AY948116.1|_1165_1307_5/1	gi|65306796|gb|AY948116.1|	1165	+	143	18	99	78	78	0	0	1	0	25	TTTAACCTTTGGAAAATACAACGCC	YYYYYYYYYYYYYYYYWYYSYWYSU
06796|gb|AY948116.1|_1168_1364_14/1	gi|65306796|gb|AY948116.1|	1168	+	197	18	99	78	78	0	0	1	0	25	AACCTTTGGAAAATACAACGCCAAA	YYYYYYYYYYYYYYYYWYYSYWYSY
06796|gb|AY948116.1|_1032_1194_30/1	gi|65306796|gb|AY948116.1|	1170	-	-163	18	99	78	78	0	0	1	0	25	CCTTTGGAAAATACAACGCCAAAGT	YWYYWUWYYWYWYYYYYYYYYYYYY
06796|gb|AY948116.1|_1201_1398_29/2	gi|65306796|gb|AY948116.1|	1201	+	198	18	99	78	78	0	0	1	0	25	AGACTATCAGTTAACAAAGAATGCT	YYYYYYYYYYYYYYYYWYWUWWYWW
06796|gb|AY948116.1|_1262_1447_6f/2	gi|65306796|gb|AY948116.1|	1262	+	186	18	99	78	78	0	0	1	0	25	AACAAAGAGCTTGAATATTTAAAAT	YYYYYYYYYWYYYYWWYYYSYYYSU
306796|gb|AY948116.1|_1116_1298_7/2	gi|65306796|gb|AY948116.1|	1274	-	-183	18	99	78	78	0	0	1	0	25	GAATATTTAAAATTTGAATATCATA	USYYYSYYYWWYYYYWYYYYYYYYY
306796|gb|AY948116.1|_1165_1307_5/2	gi|65306796|gb|AY948116.1|	1283	-	-143	18	99	78	78	0	0	1	0	25	AAATTTGAATATCATAAAGTCAAAG	YSYWWWYYWYYWYYYYYYYYYYYYY
06796|gb|AY948116.1|_1295_1444_18/2	gi|65306796|gb|AY948116.1|	1295	+	150	18	99	78	78	0	0	1	0	25	CATAAAGTCAAAGATGAACGAGATA	YYYYYYYYYYYYYYYYYWWYWYYSY
06796|gb|AY948116.1|_1321_1511_62/1	gi|65306796|gb|AY948116.1|	1321	+	191	18	99	78	78	0	0	1	0	25	TTTAAAAACTTTGTTTGAGGCACAC	YYYYYYYYYWYYYWYYWYYWWYYSY
06796|gb|AY948116.1|_1336_1508_1c/2	gi|65306796|gb|AY948116.1|	1336	+	173	18	99	78	78	0	0	1	0	25	TGAGGCACACAAAACAAAAAATGTT	YYYYYYYYYYYYYWYWYYYWWWYSU
06796|gb|AY948116.1|_1339_1491_33/1	gi|65306796|gb|AY948116.1|	1339	+	153	18	99	78	78	0	0	1	0	25	GGCACACAAAACAAAAAATGTTAAA	YYYYYYYYYYWYYYYYYYWWWYYSY
06796|gb|AY948116.1|_1168_1364_14/2	gi|65306796|gb|AY948116.1|	1340	-	-197	18	99	78	78	0	0	1	0	25	GCACACAAAACAAAAAATGTTAAAT	QQWWWWWWYWWYYYYWYYYYYYYYY
06796|gb|AY948116.1|_1201_1398_29/1	gi|65306796|gb|AY948116.1|	1374	-	-198	18	99	78	78	0	0	1	0	25	GACTAAAAGAAATAGGCAAATGGTG	QQWWWYWYYYYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_1382_1538_40/2	gi|65306796|gb|AY948116.1|	1382	+	157	18	99	78	78	0	0	1	0	25	GAAATAGGCAAATGGTGTGAAAAAA	YYYYYYYYYYWYYYYYYYYSYWWQQ
06796|gb|AY948116.1|_1389_1563_3c/1	gi|65306796|gb|AY948116.1|	1389	+	175	18	99	78	78	0	0	1	0	25	GCAAATGGTGTGAAAAAAATTTAAG	YYYYYYYYYYYYYYYYYYWYWWWQQ
06796|gb|AY948116.1|_1295_1444_18/1	gi|65306796|gb|AY948116.1|	1420	-	-150	18	99	78	78	0	0	1	0	25	GCAGTTAAAAGAAATATTTCCATTA	QQWWYSYYYWWYYYYYYYYYYYYYY
06796|gb|AY948116.1|_1262_1447_6f/1	gi|65306796|gb|AY948116.1|	1423	-	-186	18	99	78	78	0	0	1	0	25	GTTAAAAGAAATATTTCCATTAAAA	WWYWYWYYWYYWYYYWYYYYYYYYY
06796|gb|AY948116.1|_1462_1646_1a/2	gi|65306796|gb|AY948116.1|	1462	+	185	18	99	78	78	0	0	1	0	25	AAAAGAGCTTAAATATCAAAGAGCT	YYYYYYYYYYWYYYYYYYYSYWWQQ
06796|gb|AY948116.1|_1339_1491_33/2	gi|65306796|gb|AY948116.1|	1467	-	-153	18	99	78	78	0	0	1	0	25	AGCTTAAATATCAAAGAGCTTTTGA	WWYWWYWYYYYYYYYWYYYYYYYYY
06796|gb|AY948116.1|_1336_1508_1c/1	gi|65306796|gb|AY948116.1|	1484	-	-173	18	99	78	78	0	0	1	0	25	GCTTTTGAAAATTCTTTTGAACAAG	WWYYYSYYYWWYYYYYYYYYYYYYY
06796|gb|AY948116.1|_1321_1511_62/2	gi|65306796|gb|AY948116.1|	1487	-	-191	18	99	78	78	0	0	1	0	25	TTTGAAAATTCTTTTGAACAAGCAA	YWYWYSYYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_1498_1676_4e/2	gi|65306796|gb|AY948116.1|	1498	+	179	18	99	78	78	0	0	1	0	25	TTTTGAACAAGCAAAAAGAAACGAT	YYYYYYYYYYWYYYYYYWWYWYYSU
306796|gb|AY948116.1|_1502_1651_d/2	gi|65306796|gb|AY948116.1|	1502	+	150	18	99	78	78	0	0	1	0	25	GAACAAGCAAAAAGAAACGATAGAG	YYYYYYYYYYWYYYYYYWWYWYYSY
06796|gb|AY948116.1|_1382_1538_40/1	gi|65306796|gb|AY948116.1|	1514	-	-157	18	99	78	78	0	0	1	0	25	AGAAACGATAGAGGGTTTGGGTTTA	USYWYSYYYWYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_1530_1707_77/1	gi|65306796|gb|AY948116.1|	1530	+	178	18	99	78	78	0	0	1	0	25	TTGGGTTTAGCAGATAGTTTTCTTT	YYYYYYYYYYYYYWYWYYYWWWWQQ
306796|gb|AY948116.1|_1531_1682_1/2	gi|65306796|gb|AY948116.1|	1531	+	152	18	99	78	78	0	0	1	0	25	TGGGTTTAGCAGATAGTTTTCTTTT	YYYYYYYYYWYYYYYYYWWYWYYSU
06796|gb|AY948116.1|_1389_1563_3c/2	gi|65306796|gb|AY948116.1|	1539	-	-175	18	99	78	78	0	0	1	0	25	GCAGATAGTTTTCTTTTTTGGTGCT	QQWWYWWWYWYWYYWYYYYYYYYYY
06796|gb|AY948116.1|_1558_1716_59/2	gi|65306796|gb|AY948116.1|	1558	+	159	18	99	78	78	0	0	1	0	25	GGTGCTTTAGCAAATCGCACCTGTT	YYYYYYYYYYYYYYYYYYWWWWYWY
306796|gb|AY948116.1|_1622_1777_6/2	gi|65306796|gb|AY948116.1|	1622	+	156	18	99	78	78	0	0	1	0	25	CTGAGTGCGTAGCACGGAAGACGGA	YYYYYYYYYYYYYYYYYWWWYWYWY
06796|gb|AY948116.1|_1462_1646_1a/1	gi|65306796|gb|AY948116.1|	1622	-	-185	18	99	78	78	0	0	1	0	25	CTGAGTGCGTAGCACGGAAGACGGA	USYWYSYYWYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_1502_1651_d/1	gi|65306796|gb|AY948116.1|	1627	-	-150	18	99	78	78	0	0	1	0	25	TGCGTAGCACGGAAGACGGACAAAG	YSYYWUWYYWWYYYYYYYYYYYYYY
06796|gb|AY948116.1|_1498_1676_4e/1	gi|65306796|gb|AY948116.1|	1652	-	-179	18	99	78	78	0	0	1	0	25	CCCACCGCCCTAGAAAAAAAATTAC	WWYWWUWYYWWYYYYYYYYYYYYYY
306796|gb|AY948116.1|_1531_1682_1/1	gi|65306796|gb|AY948116.1|	1658	-	-152	18	99	78	78	0	0	1	0	25	GCCCTAGAAAAAAAATTACTCAACT	WWYYWYWYYWYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_1530_1707_77/2	gi|65306796|gb|AY948116.1|	1683	-	-178	18	99	78	78	0	0	1	0	25	TTTTTTGTTTTTTCTCTCGCGCGCG	YSYYYSYYYWWYYYYWYYYYYYYYY
06796|gb|AY948116.1|_1691_1870_2b/1	gi|65306796|gb|AY948116.1|	1691	+	180	18	78	78	0	0	0	1	0	25	TTTTTCTCTCGCGCGCGTACGCGTA	YYYYYYYYYYWYYYYYYWWYWYYSU
06796|gb|AY948116.1|_1558_1716_59/1	gi|65306796|gb|AY948116.1|	1692	-	-159	18	99	78	78	0	0	1	0	25	TTTTCTCTCGCGCGCGTACGCGTAC	USYWYWYYYYYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_1744_1934_27/1	gi|65306796|gb|AY948116.1|	1744	+	191	18	99	78	78	0	0	1	0	25	TTCTTATTTTTAGGGGGCTTTCTAA	YYYYYYYYYYYYYYYYYYWYWWWQQ
306796|gb|AY948116.1|_1622_1777_6/1	gi|65306796|gb|AY948116.1|	1753	-	-156	18	99	78	78	0	0	1	0	25	TTAGGGGGCTTTCTAAGCCCTATAT	QQWWYSYYYWWYYYYWYYYYYYYYY
06796|gb|AY948116.1|_1802_1954_24/1	gi|65306796|gb|AY948116.1|	1846	+	109	18	0	0	0	0	0	3	0	25	ACGACAAAATTCTACTATTAAAACG	YYYYYYYYYYWYYWYYYWWYWWWQQ
06796|gb|AY948116.1|_1691_1870_2b/2	gi|65306796|gb|AY948116.1|	1846	-	-180	18	0	0	0	0	0	3	0	25	ACGACAAAATTCTACTATTAAAACG	YWYWYSYYYWYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_1873_2073_63/2	gi|65306796|gb|AY948116.1|	1873	+	201	18	99	78	78	0	0	1	0	25	AAAATTCTACTATTAAGGGGAGAAA	YYYYYYYYYWYYYYYYWYWYWYYWW
306796|gb|AY948116.1|_1888_2018_3/2	gi|65306796|gb|AY948116.1|	1888	+	131	18	99	78	78	0	0	1	0	25	AGGGGAGAAAATTCTACTATTAAAA	YYYYYYYYYYYYYWYYYWWYWYYWY
06796|gb|AY948116.1|_1744_1934_27/2	gi|65306796|gb|AY948116.1|	1910	-	-191	18	99	78	78	0	0	1	0	25	AAACGACAAAATATTTGACAAATAT	QQWWWUWYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_1802_1954_24/2	gi|65306796|gb|AY948116.1|	1930	-	-109	18	61	61	0	1	30	0	1	25	AATATTGTTTTAATATACTACAATA	USYYYWWYYWWYYYYYYYYYYYYYY
06796|gb|AY948116.1|_1934_2078_49/1	gi|65306796|gb|AY948116.1|	1934	+	145	18	99	61	61	1	30	0	1	25	TTGTTTTAATATACTACAATAAAAA	YYYYYYYYYWYYYYYWYWWYWWWQQ
06796|gb|AY948116.1|_1940_2118_35/2	gi|65306796|gb|AY948116.1|	1940	+	179	18	99	61	61	1	30	0	1	25	TAATATACTACAATAAAAAATCCGC	YYYYYYYYYYYYYYYYYWWUWWWQQ
306796|gb|AY948116.1|_1951_2136_0/2	gi|65306796|gb|AY948116.1|	1951	+	186	18	99	78	78	0	0	1	0	25	AATAAAAAATCCGCCTTGAGTTTTC	YYYYYYYYYYWYYYYYYYWWWWWQQ
06796|gb|AY948116.1|_1955_2172_10/2	gi|65306796|gb|AY948116.1|	1955	+	218	18	99	78	78	0	0	1	0	25	AAAAATCCGCCTTGAGTTTTCACTC	YYYYYYYYYYYYYYYWYYYSYWYWY
06796|gb|AY948116.1|_1957_2161_55/1	gi|65306796|gb|AY948116.1|	1957	+	205	18	99	78	78	0	0	1	0	25	AAATCCGCCTTGAGTTTTCACTCTT	YYYYYYYYYYYYYYYYWYWYWWWQQ
06796|gb|AY948116.1|_1966_2156_2a/1	gi|65306796|gb|AY948116.1|	1966	+	191	18	99	78	78	0	0	1	0	25	TTGAGTTTTCACTCTTGGCGGAAAT	YYYYYYYYYWYYYYYYYYWYWWYSY
306796|gb|AY948116.1|_1990_2157_4/1	gi|65306796|gb|AY948116.1|	1990	+	168	18	99	78	78	0	0	1	0	25	TTTATCAATCAAGGCTAACTATGAA	YYYYYYYYYYYYYYYWYYYSYWWQQ
06796|gb|AY948116.1|_1992_2129_51/2	gi|65306796|gb|AY948116.1|	1992	+	138	18	99	78	78	0	0	1	0	25	TATCAATCAAGGCTAACTATGAAAC	YYYYYYYYYYWYYYYYYYYSYYYSU
306796|gb|AY948116.1|_1888_2018_3/1	gi|65306796|gb|AY948116.1|	1994	-	-131	18	99	78	78	0	0	1	0	25	TCAATCAAGGCTAACTATGAAACGA	WWYYYSYYYYYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_1998_2143_67/1	gi|65306796|gb|AY948116.1|	1998	+	146	18	99	78	78	0	0	1	0	25	TCAAGGCTAACTATGAAACGACATA	YYYYYYYYYYYYYYYYYYWUWYYSY
06796|gb|AY948116.1|_2024_2222_5c/2	gi|65306796|gb|AY948116.1|	2024	+	199	18	99	78	78	0	0	1	0	25	TAAGCGTTTTGTGAGATTATACCTA	YYYYYYYYYYYYYYYWYWWWYWYWW
06796|gb|AY948116.1|_1873_2073_63/1	gi|65306796|gb|AY948116.1|	2049	-	-201	18	99	78	78	0	0	1	0	25	AAATTTAGGTTTTTTAAGCTTAAAG	USYYWUWWYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_1934_2078_49/2	gi|65306796|gb|AY948116.1|	2054	-	-145	18	99	78	61	0	0	1	0	25	TAGGTTTTTTAAGCTTAAAGTTGAA	USYWWUWYYWYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_2081_2254_22/1	gi|65306796|gb|AY948116.1|	2081	+	174	18	99	78	78	0	0	1	0	25	ATTTTTCTAGCAAAACCGCAGGGGC	YYYYYYYYYYYYYYYYYYYSYWYWW
06796|gb|AY948116.1|_1940_2118_35/1	gi|65306796|gb|AY948116.1|	2094	-	-179	18	99	78	61	0	0	1	0	25	AACCGCAGGGGCAGAGAAGCCCCTT	USYYWUWWYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_1992_2129_51/1	gi|65306796|gb|AY948116.1|	2105	-	-138	18	99	78	78	0	0	1	0	25	CAGAGAAGCCCCTTGCCTTGATTGT	USYWWYWWYWWYYYYYYYYYYYYYY
306796|gb|AY948116.1|_1951_2136_0/1	gi|65306796|gb|AY948116.1|	2112	-	-186	18	99	78	78	0	0	1	0	25	GCCCCTTGCCTTGATTGTCTTACTT	YSYWYSYYWYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_1998_2143_67/2	gi|65306796|gb|AY948116.1|	2119	-	-146	18	99	78	78	0	0	1	0	25	GCCTTGATTGTCTTACTTTGGATAT	YWYWWYWYWYYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_2128_2314_31/2	gi|65306796|gb|AY948116.1|	2128	+	187	18	99	78	61	0	0	1	0	25	GTCTTACTTTGGATATGCAAATGAG	YYYYYYYYYYWYYYYWYYWUWWYSY
06796|gb|AY948116.1|_2129_2328_19/1	gi|65306796|gb|AY948116.1|	2129	+	200	18	99	78	78	0	0	1	0	25	TCTTACTTTGGATATGCAAATGAGC	YYYYYYYYYYYYYYYYWYWUWWYWY
06796|gb|AY948116.1|_1966_2156_2a/2	gi|65306796|gb|AY948116.1|	2132	-	-191	18	99	78	78	0	0	1	0	25	TACTTTGGATATGCAAATGAGCGAA	USYWYSYYYWYYYYYWYYYYYYYYY
306796|gb|AY948116.1|_1990_2157_4/2	gi|65306796|gb|AY948116.1|	2133	-	-168	18	99	78	78	0	0	1	0	25	ACTTTGGATATGCAAATGAGCGAAA	YSYYYWYYYWYYYYYWYYYYYYYYY
06796|gb|AY948116.1|_1957_2161_55/2	gi|65306796|gb|AY948116.1|	2137	-	-205	18	99	78	78	0	0	1	0	25	TGGATATGCAAATGAGCGAAATAGT	YWYWYWWYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_1955_2172_10/1	gi|65306796|gb|AY948116.1|	2148	-	-218	18	99	78	78	0	0	1	0	25	ATGAGCGAAATAGTTAAATATAATA	WWYWWYWWYWYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2153_2336_1d/1	gi|65306796|gb|AY948116.1|	2153	+	184	18	99	78	78	0	0	1	0	25	CGAAATAGTTAAATATAATAATGAT	YYYYYYYYYYWYYWYYYYWYWWWQQ
06796|gb|AY948116.1|_2162_2328_57/1	gi|65306796|gb|AY948116.1|	2162	+	167	18	99	78	78	0	0	1	0	25	TAAATATAATAATGATTTTAATCTT	YYYYYYYYYYYYYYYYYYYWWWYSU
06796|gb|AY948116.1|_2165_2331_66/2	gi|65306796|gb|AY948116.1|	2165	+	167	18	99	78	78	0	0	1	0	25	ATATAATAATGATTTTAATCTTTTA	YYYYYYYYYWYYYYWWYYWUWYYWY
06796|gb|AY948116.1|_2196_2392_5d/1	gi|65306796|gb|AY948116.1|	2196	+	197	18	99	78	78	0	0	1	0	25	CCTGAACTTAAAGCCATACAAATGG	YYYYYYYYYYWYYYYYYYYSYWWQQ
06796|gb|AY948116.1|_2024_2222_5c/1	gi|65306796|gb|AY948116.1|	2198	-	-199	18	99	78	78	0	0	1	0	25	TGAACTTAAAGCCATACAAATGGAT	YSYYWWYYYWWYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2202_2401_6d/1	gi|65306796|gb|AY948116.1|	2202	+	200	18	99	78	78	0	0	1	0	25	CTTAAAGCCATACAAATGGATATGT	YYYYYYYYYYWYYYYYWYWWYWYWY
06796|gb|AY948116.1|_2081_2254_22/2	gi|65306796|gb|AY948116.1|	2230	-	-174	18	99	78	78	0	0	1	0	25	TGGCTATTATCTCACTAACCAAAGA	YWYWYWYYWYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2261_2430_12/2	gi|65306796|gb|AY948116.1|	2261	+	170	18	99	78	78	0	0	1	0	25	AGAAAATACGCCATTTTTAAAAAAG	YYYYYYYYYYYYYWYWYYWWYYYWY
06796|gb|AY948116.1|_2128_2314_31/1	gi|65306796|gb|AY948116.1|	2290	-	-187	18	99	61	61	1	30	0	1	25	TTAACCCTGATAGAAGAAAAATAAT	YWYWYSYYYWWYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2304_2478_39/2	gi|65306796|gb|AY948116.1|	2304	+	175	18	99	78	78	0	0	1	0	25	AGAAAAATAATTATTCCGCAAAAGA	YYYYYYYYYWYYYYYWYYWYWYYSY
06796|gb|AY948116.1|_2129_2328_19/2	gi|65306796|gb|AY948116.1|	2304	-	-200	18	99	78	78	0	0	1	0	25	AGAAAAATAATTATTCCGCAAAAGA	YWYWYWWYYWWYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2162_2328_57/2	gi|65306796|gb|AY948116.1|	2304	-	-167	18	99	78	78	0	0	1	0	25	AGAAAAATAATTATTCCGCAAAAGA	USYWWWYYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2165_2331_66/1	gi|65306796|gb|AY948116.1|	2307	-	-167	18	99	78	78	0	0	1	0	25	AAAATAATTATTCCGCAAAAGAAGT	WWYWWUWWYWYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_2312_2478_48/2	gi|65306796|gb|AY948116.1|	2312	+	167	18	99	78	78	0	0	1	0	25	AATTATTCCGCAAAAGAAGTTTATT	YYYYYYYYYWYYYYYYWYYWYWWQQ
06796|gb|AY948116.1|_2153_2336_1d/2	gi|65306796|gb|AY948116.1|	2312	-	-184	18	99	78	78	0	0	1	0	25	AATTATTCCGCAAAAGAAGTTTATT	YSYYWWWYYWWYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2329_2493_2c/1	gi|65306796|gb|AY948116.1|	2329	+	165	18	99	78	78	0	0	1	0	25	AGTTTATTGAATTATGTCGGTTAAA	YYYYYYYYYYYYYYYYYWWUWWYWY
06796|gb|AY948116.1|_2196_2392_5d/2	gi|65306796|gb|AY948116.1|	2368	-	-197	18	99	78	78	0	0	1	0	25	ACTATAAAGAAATTTTCTTTGCCAT	YSYWWUWWYYYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_2377_2544_5e/1	gi|65306796|gb|AY948116.1|	2377	+	168	18	99	78	78	0	0	1	0	25	AAATTTTCTTTGCCATTGATGATTG	YYYYYYYYYWYYYWYYWYWWYYYWY
06796|gb|AY948116.1|_2202_2401_6d/2	gi|65306796|gb|AY948116.1|	2377	-	-200	18	99	78	78	0	0	1	0	25	AAATTTTCTTTGCCATTGATGATTG	QQWWWWYYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2383_2537_43/2	gi|65306796|gb|AY948116.1|	2383	+	155	18	99	78	78	0	0	1	0	25	TCTTTGCCATTGATGATTGCTTGAA	YYYYYYYYYYYYYYWWYWWUWWYSU
06796|gb|AY948116.1|_2261_2430_12/1	gi|65306796|gb|AY948116.1|	2406	-	-170	18	99	78	78	0	0	1	0	25	AAAAAACTTTGCAATTTTCTTATTT	WWYYYWYYWYYWYYYYYYYYYYYYY
06796|gb|AY948116.1|_2414_2548_54/1	gi|65306796|gb|AY948116.1|	2414	+	135	18	99	78	78	0	0	1	0	25	TTGCAATTTTCTTATTTCATACCAA	YYYYYYYYYYWYYYYYYWWWWYYSU
06796|gb|AY948116.1|_2304_2478_39/1	gi|65306796|gb|AY948116.1|	2454	-	-175	18	99	78	78	0	0	1	0	25	ATTTATAATTTTGTTTGTTTTGAAG	QQWWWWWYYWWYYYWYYYYYYYYYY
06796|gb|AY948116.1|_2312_2478_48/1	gi|65306796|gb|AY948116.1|	2454	-	-167	18	99	78	78	0	0	1	0	25	ATTTATAATTTTGTTTGTTTTGAAG	YSYWYWYYYWYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2458_2654_74/2	gi|65306796|gb|AY948116.1|	2458	+	197	18	99	78	78	0	0	1	0	25	ATAATTTTGTTTGTTTTGAAGAAGC	YYYYYYYYYWYYYWYYYWWYWYYSU
06796|gb|AY948116.1|_2329_2493_2c/2	gi|65306796|gb|AY948116.1|	2469	-	-165	18	99	78	78	0	0	1	0	25	TGTTTTGAAGAAGCAAATATTATTG	USYYYWYYWYYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_2506_2676_7a/1	gi|65306796|gb|AY948116.1|	2506	+	171	18	99	78	78	0	0	1	0	25	ATATAACTTTACAAAGTCGTTTTTA	YYYYYYYYYWYYYYYWYYWYWWYWY
06796|gb|AY948116.1|_2509_2658_34/1	gi|65306796|gb|AY948116.1|	2509	+	150	18	99	78	78	0	0	1	0	25	TAACTTTACAAAGTCGTTTTTACGA	YYYYYYYYYYYYYYYYWYYSYWWQQ
06796|gb|AY948116.1|_2383_2537_43/1	gi|65306796|gb|AY948116.1|	2513	-	-155	18	99	78	78	0	0	1	0	25	TTTACAAAGTCGTTTTTACGATATG	YWYYYWYYYWYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2377_2544_5e/2	gi|65306796|gb|AY948116.1|	2520	-	-168	18	99	78	78	0	0	1	0	25	AGTCGTTTTTACGATATGATAATAA	WWYWYSYYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2414_2548_54/2	gi|65306796|gb|AY948116.1|	2524	-	-135	18	99	78	78	0	0	1	0	25	GTTTTTACGATATGATAATAAATAA	YWYYWUWYWYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2526_2710_53/2	gi|65306796|gb|AY948116.1|	2526	+	185	18	99	78	78	0	0	1	0	25	TTTTACGATATGATAATAAATAAAA	YYYYYYYYYYYYYWYYWYYWYYYSU
06796|gb|AY948116.1|_2549_2708_4d/2	gi|65306796|gb|AY948116.1|	2549	+	160	18	99	78	78	0	0	1	0	25	AAAATTTGGTTTCACAGCCTTTGAA	YYYYYYYYYYYYYYYYYYYSYWYSU
06796|gb|AY948116.1|_2570_2722_4c/1	gi|65306796|gb|AY948116.1|	2570	+	153	18	99	78	78	0	0	1	0	25	TGAATTAGCCGAATTTGCAGAACTT	YYYYYYYYYYWYYYYYYWWYWYYSU
06796|gb|AY948116.1|_2612_2792_21/2	gi|65306796|gb|AY948116.1|	2612	+	181	18	99	78	61	0	0	1	0	25	AACTTTATACAGACTTTTAAAGCAA	YYYYYYYYYYYYYYYYWYYWWWYSU
06796|gb|AY948116.1|_2624_2822_5b/1	gi|65306796|gb|AY948116.1|	2624	+	199	18	99	78	78	0	0	1	0	25	ACTTTTAAAGCAATTTAGAACCACA	YYYYYYYYYYYYYYYYYYYWWYYSY
06796|gb|AY948116.1|_2458_2654_74/1	gi|65306796|gb|AY948116.1|	2630	-	-197	18	99	78	78	0	0	1	0	25	AAAGCAATTTAGAACCACAGGCAAA	WWYYWWYYYYYYYYYWYYYYYYYYY
06796|gb|AY948116.1|_2509_2658_34/2	gi|65306796|gb|AY948116.1|	2634	-	-150	18	99	78	78	0	0	1	0	25	CAATTTAGAACCACAGGCAAAGCTT	YSYYYSYYYYYYYYYWYYYYYYYYY
06796|gb|AY948116.1|_2506_2676_7a/2	gi|65306796|gb|AY948116.1|	2652	-	-171	18	99	78	78	0	0	1	0	25	AAAGCTTATTTTGAGTGGGAAGAAT	YSYYYSYYWYYWYYWYYYYYYYYYY
06796|gb|AY948116.1|_2549_2708_4d/1	gi|65306796|gb|AY948116.1|	2684	-	-160	18	99	78	78	0	0	1	0	25	GATTATGAAAATACCTGAAAATTAT	YWYWWUWWYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2526_2710_53/1	gi|65306796|gb|AY948116.1|	2686	-	-185	18	99	78	78	0	0	1	0	25	TTATGAAAATACCTGAAAATTATCG	USYYWUWWYYYWYYYWYYYYYYYYY
06796|gb|AY948116.1|_2570_2722_4c/2	gi|65306796|gb|AY948116.1|	2698	-	-153	18	99	78	78	0	0	1	0	25	CTGAAAATTATCGTCAAATAGATAT	YWYWWYWWYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2702_2884_64/1	gi|65306796|gb|AY948116.1|	2702	+	183	18	99	78	78	0	0	1	0	25	AAATTATCGTCAAATAGATATAGAC	YYYYYYYYYYYYYYYYWYWWWYYSY
06796|gb|AY948116.1|_2707_2804_41/2	gi|65306796|gb|AY948116.1|	2707	+	98	18	99	78	78	0	0	1	0	25	ATCGTCAAATAGATATAGACCAAAG	YYYYYYYYYYYYYYWWYYYSYYYSU
06796|gb|AY948116.1|_2715_2892_6a/2	gi|65306796|gb|AY948116.1|	2715	+	178	18	99	78	78	0	0	1	0	25	ATAGATATAGACCAAAGAATTTTAA	YYYYYYYYYWYYYYYWYYWWYYYSY
06796|gb|AY948116.1|_2717_2903_3b/1	gi|65306796|gb|AY948116.1|	2717	+	187	18	99	78	78	0	0	1	0	25	AGATATAGACCAAAGAATTTTAAAA	YYYYYYYYYYYYYYYYYYYSYWWQQ
06796|gb|AY948116.1|_2751_2931_47/2	gi|65306796|gb|AY948116.1|	2751	+	181	18	99	61	61	1	30	0	1	25	AAAGAACTTTCTAAAGAACGCTATC	YYYYYYYYYWYYYYYYWYYSYWYSU
06796|gb|AY948116.1|_2751_2927_70/2	gi|65306796|gb|AY948116.1|	2751	+	177	18	99	61	61	1	30	0	1	25	AAAGAACTTTCTAAAGAACGCTATC	YYYYYYYYYWYYYYYWYWWWWYYWW
06796|gb|AY948116.1|_2759_2911_28/2	gi|65306796|gb|AY948116.1|	2759	+	153	18	99	61	61	1	30	0	1	25	TTCTAAAGAACGCTATCTTTTTGAC	YYYYYYYYYYYYYWYYYYYSYWYWY
06796|gb|AY948116.1|_2761_2927_45/2	gi|65306796|gb|AY948116.1|	2761	+	167	18	99	61	61	1	30	0	1	25	CTAAAGAACGCTATCTTTTTGACCA	YYYYYYYYYYYYYYYWYWWUWWYSY
06796|gb|AY948116.1|_2612_2792_21/1	gi|65306796|gb|AY948116.1|	2768	-	-181	18	99	61	61	1	30	0	1	25	ACGCTATCTTTTTGACCAAATCAGA	USYWYWWWYWWYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2770_2956_1b/2	gi|65306796|gb|AY948116.1|	2770	+	187	18	99	61	61	1	30	0	1	25	GCTATCTTTTTGACCAAATCAGAGT	YYYYYYYYYYYYYWYYYYYSYWWQQ
06796|gb|AY948116.1|_2707_2804_41/1	gi|65306796|gb|AY948116.1|	2780	-	-98	18	99	78	78	0	0	1	0	25	TGACCAAATCAGAGTGCCTTTTAAA	USYYWYWWYWYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_2624_2822_5b/2	gi|65306796|gb|AY948116.1|	2798	-	-199	18	99	78	78	0	0	1	0	25	TTTTAAAAATCTTGCTTATGAAAAA	WWYYYSYYWYYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_2801_2960_26/2	gi|65306796|gb|AY948116.1|	2801	+	160	18	99	78	78	0	0	1	0	25	TAAAAATCTTGCTTATGAAAAAGAA	YYYYYYYYYWYYYYWWYYYWWWYSU
06796|gb|AY948116.1|_2821_2986_1f/1	gi|65306796|gb|AY948116.1|	2821	+	166	18	99	78	78	0	0	1	0	25	AAGAAAAAACCGCAGGGCGTGGGCG	YYYYYYYYYYYYYYYWYWWYWYYSY
06796|gb|AY948116.1|_2825_2992_6e/2	gi|65306796|gb|AY948116.1|	2825	+	168	18	99	61	61	1	30	0	1	25	AAAAACCGCAGGGCGTGGGCGCGGC	YYYYYYYYYWYYYYWWYYWUWWYSY
06796|gb|AY948116.1|_2702_2884_64/2	gi|65306796|gb|AY948116.1|	2860	-	-183	18	99	78	78	0	0	1	0	25	CAGGTATTAGCTTTACTTTTAAACC	WWYYYWYYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2715_2892_6a/1	gi|65306796|gb|AY948116.1|	2868	-	-178	18	99	78	78	0	0	1	0	25	AGCTTTACTTTTAAACCTGAAAATA	WWYWWYWWYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2717_2903_3b/2	gi|65306796|gb|AY948116.1|	2879	-	-187	18	99	78	78	0	0	1	0	25	TAAACCTGAAAATATCCAAATGCAA	WWYYWUWWYWYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_2759_2911_28/1	gi|65306796|gb|AY948116.1|	2887	-	-153	18	99	78	61	0	0	1	0	25	AAAATATCCAAATGCAAAAGCTAGA	YWYWWUWYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2890_3076_4f/2	gi|65306796|gb|AY948116.1|	2890	+	187	18	99	78	78	0	0	1	0	25	ATATCCAAATGCAAAAGCTAGAAAA	YYYYYYYYYYYYYYWWYYYSYYYSY
06796|gb|AY948116.1|_2761_2927_45/1	gi|65306796|gb|AY948116.1|	2903	-	-167	18	99	78	61	0	0	1	0	25	AAAGCTAGAAAATGAAAGTCAAAAA	YWYWWWWYWYYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_2751_2927_70/1	gi|65306796|gb|AY948116.1|	2903	-	-177	18	99	78	61	0	0	1	0	25	AAAGCTAGAAAATGAAAGTCAAAAA	YWYWYSYYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2751_2931_47/1	gi|65306796|gb|AY948116.1|	2907	-	-181	18	99	78	61	0	0	1	0	25	CTAGAAAATGAAAGTCAAAAAATAA	USYWYWWYWYYWYYYWYYYYYYYYY
306796|gb|AY948116.1|_2908_3068_9/1	gi|65306796|gb|AY948116.1|	2908	+	161	18	99	78	78	0	0	1	0	25	TAGAAAATGAAAGTCAAAAAATAAT	YYYYYYYYYYYYYYYYYYWYWWYSU
306796|gb|AY948116.1|_2909_3032_a/2	gi|65306796|gb|AY948116.1|	2909	+	124	18	99	78	78	0	0	1	0	25	AGAAAATGAAAGTCAAAAAATAATG	YYYYYYYYYYYYYYWWYYWWYWWQQ
06796|gb|AY948116.1|_2770_2956_1b/1	gi|65306796|gb|AY948116.1|	2932	-	-187	18	99	78	61	0	0	1	0	25	TGAGCGATGAGCAAAAATATTTAAA	WWYWYSYYYYYYYYWYYYYYYYYYY
06796|gb|AY948116.1|_2801_2960_26/1	gi|65306796|gb|AY948116.1|	2936	-	-160	18	99	78	78	0	0	1	0	25	CGATGAGCAAAAATATTTAAAGATT	QQWWYSYYWYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2821_2986_1f/2	gi|65306796|gb|AY948116.1|	2962	-	-166	18	99	78	78	0	0	1	0	25	TAAACAATATGAAACTTAATCAAGT	USYWWUWYYWYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_2966_3121_61/2	gi|65306796|gb|AY948116.1|	2966	+	156	18	99	78	78	0	0	1	0	25	CAATATGAAACTTAATCAAGTTAGA	YYYYYYYYYYWYYYWWYYYWYYYSY
06796|gb|AY948116.1|_2825_2992_6e/1	gi|65306796|gb|AY948116.1|	2968	-	-168	18	99	78	61	0	0	1	0	25	ATATGAAACTTAATCAAGTTAGATT	YWYYYWYYYWWYYYYWYYYYYYYYY
06796|gb|AY948116.1|_2987_3171_11/2	gi|65306796|gb|AY948116.1|	2987	+	185	18	99	78	78	0	0	1	0	25	TAGATTTGATTATAATGACAAGCTT	YYYYYYYYYYYYYYWWYYYSYWYSU
06796|gb|AY948116.1|_2994_3156_69/2	gi|65306796|gb|AY948116.1|	2994	+	163	18	99	78	78	0	0	1	0	25	GATTATAATGACAAGCTTTGGCAAT	YYYYYYYYYYWYYWYYWYWUWWYWW
06796|gb|AY948116.1|_3000_3167_3d/2	gi|65306796|gb|AY948116.1|	3000	+	168	18	99	78	78	0	0	1	0	25	AATGACAAGCTTTGGCAATTTAACG	YYYYYYYYYWYYYYWWYYYSYWWQQ
306796|gb|AY948116.1|_2909_3032_a/1	gi|65306796|gb|AY948116.1|	3008	-	-124	18	99	78	78	0	0	1	0	25	GCTTTGGCAATTTAACGATTTTGAT	YSYWWWYYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_3034_3217_71/1	gi|65306796|gb|AY948116.1|	3034	+	184	18	99	78	78	0	0	1	0	25	TTGATGAATTTAAAATTATTGCAAT	YYYYYYYYYYYYYYYYYYWWYYYWY
306796|gb|AY948116.1|_2908_3068_9/2	gi|65306796|gb|AY948116.1|	3044	-	-161	18	99	78	78	0	0	1	0	25	TAAAATTATTGCAATAGAGCTTGTA	QQWWWWWYYYYWYYYWYYYYYYYYY
06796|gb|AY948116.1|_2890_3076_4f/1	gi|65306796|gb|AY948116.1|	3052	-	-187	18	99	78	78	0	0	1	0	25	TTGCAATAGAGCTTGTAAGAGATGA	WWYWWWWYYYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_3061_3240_f/1	gi|65306796|gb|AY948116.1|	3061	+	180	18	99	78	78	0	0	1	0	25	AGCTTGTAAGAGATGAATACGAGAA	YYYYYYYYYYYYYYYYYYWYWYYWW
306796|gb|AY948116.1|_3096_3266_b/2	gi|65306796|gb|AY948116.1|	3096	+	171	18	99	78	78	0	0	1	0	25	GGAAATCATATGCACTTTAATGCTA	YYYYYYYYYYYYYYYYYYWUWWWQQ
06796|gb|AY948116.1|_2966_3121_61/1	gi|65306796|gb|AY948116.1|	3097	-	-156	18	99	78	78	0	0	1	0	25	GAAATCATATGCACTTTAATGCTAA	YSYWWWWWYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_3111_3290_5f/1	gi|65306796|gb|AY948116.1|	3111	+	180	18	99	78	78	0	0	1	0	25	TTTAATGCTAAAAATCAAGAGCAGT	YYYYYYYYYYYYYWYWYYWYWWYSY
06796|gb|AY948116.1|_2994_3156_69/1	gi|65306796|gb|AY948116.1|	3132	-	-163	18	99	78	78	0	0	1	0	25	CAGTTTTTTAAAATGATTGAAACCT	YWYWYSYYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_3000_3167_3d/1	gi|65306796|gb|AY948116.1|	3143	-	-168	18	99	78	78	0	0	1	0	25	AATGATTGAAACCTTTAGAAAAGGT	YSYWWYWYYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_3145_3288_17/1	gi|65306796|gb|AY948116.1|	3145	+	144	18	99	78	78	0	0	1	0	25	TGATTGAAACCTTTAGAAAAGGTAT	YYYYYYYYYWYYYYYYWYWUWYYWY
06796|gb|AY948116.1|_2987_3171_11/1	gi|65306796|gb|AY948116.1|	3147	-	-185	18	99	78	78	0	0	1	0	25	ATTGAAACCTTTAGAAAAGGTATTA	USYYYSYYYYYWYYYYYYYYYYYYY
06796|gb|AY948116.1|_3149_3310_50/2	gi|65306796|gb|AY948116.1|	3149	+	162	18	99	78	78	0	0	1	0	25	TGAAACCTTTAGAAAAGGTATTAGG	YYYYYYYYYYYYYYYYYYYSYYYWY
06796|gb|AY948116.1|_3034_3217_71/2	gi|65306796|gb|AY948116.1|	3193	-	-184	18	99	78	78	0	0	1	0	25	TATCTTTAAAGGATACAAGCTATCC	WWYWWUWYYYYWYYYWYYYYYYYYY
306796|gb|AY948116.1|_3061_3240_f/2	gi|65306796|gb|AY948116.1|	3216	-	-180	18	99	78	78	0	0	1	0	25	CCGCCACTTGTGCCAAGTGTCGAGC	WWYYYSYYWYYYYYYYYYYYYYYYY
306796|gb|AY948116.1|_3096_3266_b/1	gi|65306796|gb|AY948116.1|	3242	-	-171	18	99	78	78	0	0	1	0	25	TGTAAGGGGTGCAACCCCTTAACCC	YWYWYSYYYYYWYYYYYYYYYYYYY
06796|gb|AY948116.1|_3145_3288_17/2	gi|65306796|gb|AY948116.1|	3264	-	-144	18	99	78	78	0	0	1	0	25	CCCCACTAATAAAAATCAACTAAAA	USYWWUWYYWYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_3111_3290_5f/2	gi|65306796|gb|AY948116.1|	3266	-	-180	18	99	78	78	0	0	1	0	25	CCACTAATAAAAATCAACTAAAATC	WWYYYWWWYYYYYYYYYYYYYYYYY
06796|gb|AY948116.1|_3149_3310_50/1	gi|65306796|gb|AY948116.1|	3286	-	-162	18	99	78	78	0	0	1	0	25	AAATCAATAAATGATTTTTTTGATT	USYYYSYYYWYYYYWYYYYYYYYYY
BioPerl-1.007002/t/data/test_space.embl000444000766000024        67513155576321 17653 0ustar00cjfieldsstaff000000000000ID   TEST standard; DNA; 10 BP.
XX
AC   TEST;
XX
DT   09-APR-2015
XX
DE   Test of space before quoted qualifier.
XX
XX
FH   Key             Location/Qualifiers
FT   CDS             1..10
FT                   /*tag= x
FT                   /gene= "someT"
FT                   /product= "somewordandt extthatisquite lon
FT                   gandthereforewraps"
XX
SQ   Sequence 10 BP; 10 A; 0 C; 0 G; 9 T; 0 U; 0 Other;
     aaaaaaaaaa       10
//
BioPerl-1.007002/t/data/testaln.arp000444000766000024      6235513155576321 17101 0ustar00cjfieldsstaff000000000000[Profile]

     Title="mtDNA sequences in the Senegalese Mandenka (hypervariable region 1)"

	 #Data from :
	 #Graven, L., Passarino, G., Semino, O., Boursot, P., Santachiara-Benerecetti, A. S., 
	 #Langaney, A., and Excoffier, L., 1995, Evolutionary correlation between 
	 #control region sequence and RFLP diversity pattern in the mitochondrial genome 
	 #of a Senegalese sample, Mol. Biol. Evol. 12(2):334-345

     NbSamples=1

          	GenotypicData=0 
          	DataType=DNA
          	LocusSeparator=NONE
		MissingData='?'

[Data]

     [[Samples]]

 		SampleName="Mandenka"
	   	#Reference: Graven et al. 1995 Mol. Biol. Evol. 12:334-345.
	   	SampleSize=119
	   	SampleData= {
01   6     ATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACTATCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCATCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCTTTCTCGTCCCCATGGATGACCCCCC
02   2     ???????????????????????????????????????????TCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCCATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCATCCTTAACAGTACATGGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCC?
03   10    ??????????????????????????TTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATCTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCATACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC		
04   1     ????????????????????????????????????????????????????????????????????????????????????????ACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCCCCTCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCATCCTTAACAGTACATGGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTCCTCGTCCCCATGGATGACCCCC?
05   1     ???????????????????????????????????TTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAGCAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
06   4     ??????????????????????????TTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCCATGTATTTCGTACATTACTGCCAGCCACCATGAATATCGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGTCA-CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCACGGATGACCCCC?  
07   1     ????????????????????TTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA??????????????????????????????ATGCTTACAAGCAAGTACAGCAATCGACCCTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
08   2     ??????????????????????????????????????TCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGCACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCTCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGTCA-CCCCTTACCCATTAGGATATCAACAAACCTACCCGCCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCC?
09   1     ?????????????????????TCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATCGTACGGTACCATAAATACTTCACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCC??
10   7     ??????????????????????????????AACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
11   2     ????????????????????????????????CTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATCGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
12   7     ??????????????????????????????????????????TTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCTCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAGGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
13   1     ????????????????????????????????????????TGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATCTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCATACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCACGGATGACCCCCC		
14   1     ??????????????????????????????????????????TTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGCACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCTCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCATTAGGATATCAACAAACCTACCCGCCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCC?
15   2     ???????????????????????????????????????????????????????????????????GTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCC?
16   3     ??????????????????????????TTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
17   1     ????????????????????TTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATCTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCATACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGA??????
18   3     ????????????????????????????????????????TGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGCACGGTACCATAAATACTTAACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCTCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCATTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGAT????????
19   1     ??????????????????????????????????????TCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACAGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGTCA-CCTCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCACGGATGACCCCC?
20   1     ??????????????????????????????????????????????????????????????????GGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACAGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCCCCTCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGTCA-CCTCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCACGGATGACCCCCC
21   2     ???????????????????????????????ACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACAGTACCATAAATACTTGACTACCTGTAGTACATAAAAACTCAAC--CCACATCAAAA-----CCCTGCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTGTCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGCACATAAAGTCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
22   1     ???????????????????????????????ACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
23   3     ?????????????????????????ATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATCGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAGCCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCGATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTCACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
24   1     ????????????????????????????????????????????????????????????????????TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGCACAGCAATCAACCCTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGCCCCCATGGATGACCCCC?
25   3     ??????????????????????????????AACTATTCTCTGTTCTTTCATGGGGAAGCGGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGCACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCTCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCATTAGGATATCAACAAACCTACCCGCCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
26   1     ??????????????????????????????AACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCAACATGAATATTGCACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCTCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCATTAGGATATCAACAAACCTACCCGCCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
27   2     ?????????????????????????????AAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTATCCATCCTTAACAGTACATGGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
28   3     ???????????????????????????????????TTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATCTCGTACATTACTGCCAGCCACCATGAATATTGTACAGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAA???????????CCCCCATGCTTACAAGCAAGCACAGCGATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTGCCCATCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTTGTCCCCATGGATGAC?????
29   2     ????????????????????????????????CTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGCACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAA????????????????????????????????????????????????????????????????????????CCAAAGCCA-CCCCTTACCCATTAGGATATCAACAAACCTACCCGCCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
30   1     ??????????????????????????????AACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGCACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAC--CCACATCAAAA-----CCCTCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCATTAGGATATCAACAAACCTACCCRCCCTTAACAGTACATAGCACATAAAACCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCC?
31   1     ??????????????????????????????????????TCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCA???????????????CCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCATCCTTAACAGTACATGGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
32   1     ??????????????????????????????????????????TTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCAACATGAATATTGTACAGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAACAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTGCAGTCAAATCCTTTCTCGCCCCCATGGATGACCCCCC
33   2     ?????????????????????????????????????????????TTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATCGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCTCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGCCCCCAT????????????
34   1     ?????????????????????????????????????????????????????????GCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATCGTACGGTACCATAAATACTTGACTACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCGCCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGCCCCCATGGATGACCCCCC
35   2     ??????????????????????????????????????????????????????????????????GGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCAACATGAATATTGCACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCTCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCATTAGAATATCAACAAACCTACCCGCCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCC?
36   1     ??????????????????????????????????????????????????????????????????GGTACCACCCAAGTATTGACTCACCCATCAACAACCGCCATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAACCAACCTTCAACTATCACACATCAACTGCAACTCCAAGGCCA-CCCCTTACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
37   2     ??????????????????????????????????????TCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAATCCAAT--CCACATCAAAA-----CCCCCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
38   1     ?????????????????????????????????????????????TTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATCGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGCACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGCCCCCATGGATGACCCCCC
39   1     ??????????????????????????????????????????????????????????????????GGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCTCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGCCCCCATGGATGACCCCCC
40   3     ????????????????????????????????????TCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCAGCATGAATATTGCACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCTCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCATTAGGATATCAACAAACCTACCCGCCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCC?
41   1     ??????????????????????????????????????????????????????????????????GGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATCTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAACAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCATCCTTAACAGTACATGGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
42   1     ????????????????????????????????????????????????????????????????????????????????????????????ATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCATACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
43   1     ??????????????????????????????????????????????????????????????????????CCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATCGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCTAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGCACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGCCCCC??????????????
44   2     ??????????????????????????????????????????????????????????????????GGTGCCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCAACATGAATATTGTACAGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAACAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAGACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTTCAGTCAAATCCCTTCTCGCCCCCATGGATGACCCCCC
45   2     ???????????????????????????????????TTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGCACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCTCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCATTAGGATATCAACAAACCTACCCGCCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCC???
46   1     ?????????????????????????????????????CTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGCACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCC?
47   1     ??????????????????????????????????????????????????????????????????GGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCAGCATGAATATTGCACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCTCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCATTAGAATATCAACAAACCTACCCGCCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCC??????????????
48   2     ????????????????????????????????????????TGTTCTTTCATGGGGAAGCAGATTTGGGTGCCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCC?
49   1     ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATTAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCTACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCTTTCTCGTCCCCATGGATGACCCCCC
50   1     ????????????????????TTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAACAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGCCCCCATGG??????????
51   1     ??????????????????????????????????????????????????????????????????GGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAACAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCATCCTTAACAGTACATGGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
52   3     ???????????????????????????????????????????????????????AAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGCACGGTACCATAAATACTTAACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCTCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCATTAGGATATCAACAAACCTACCCGCCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCC??
53   1     ??????????????????????????????????????????TTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGAATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCC?
54   2     ??????????????????????????????????????????????????????????????????GGTGCCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCC?
55   1     ???????????????????????????????????????????????????????????????????????????????????????????????AACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGCCCCCATGGATGACCCCCC
56   2     ??????????????????????????????????????????????????????????????????GGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCTCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGCCCCCATGGATGACCCCCC
57   1     ???????????????????????????????????????????????????GGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATCGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAG?ATATCAACAAACCTACCCACCCTTAACAGYACATAGYACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGYCCCCATGGATGACCCCCC
58   1     ???????????????????????????????????????????????TCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGTCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCC?
59   2     ??????????????????????????????????????????????????????????????????GGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTCACCCACTAGGATATCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGAT????????
60   1     ???????????????????????????????????????????????????????????AGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAAT--CCACATCAAAA-----CCTTCCCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA-CCCCTTACCCATTAGGATATCAACAAACCTACCCGCCCTTAACAGTACATAGCACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGCCCCCATGGATGACCCCC?
}
BioPerl-1.007002/t/data/testaln.clustalw000444000766000024      1031013155576321 20135 0ustar00cjfieldsstaff000000000000CLUSTAL W (1.74) multiple sequence alignment


P84139                MNEGEHQIKLDELFEKLLRARKIFKNKDVLRHSYTPKDLPLRHEQIETLAQILVPVLRGE
P814153               MNEGMHQIKLDVLFEKLLRARKIFKNKDVLRHSYTPKDLPHRHEQIETLAQILVPVLRGE
P851414               ------------------------------------------------------------
P841414               ------------------------------------------------------------
BAB68554              --------------------MLTEDDKQLIQHVWEKVLEHQEDFGAEALERMFIVYPSTK
gb|443893|124775      -MRFRFGVVVPPAVAGARPELLVVGSRPELG-RWEPRGAVRLRPAGTAAGDGALALQEPG
                                                                                  

P84139                TPSNIFVYG-KTGTGKTVTVK-FVTEELKRISEKYNIPVDVIYINCEIVDTHYRVLANIV
P814153               TPSNIFVYG-KTGTGKTVTVK-FVTEELKRISEKYNIPVDVIYINCEIVDTHYRVLANIV
P851414               -MKIVWCGH-ACFLVEDRGTK-ILIDPYPDVDEDRIGKVDYILQTHEHMD-HYGKTPLIA
P841414               -MKIVWCGH-ACFLVEDRGTK-ILIDPYPDVDEDRIGKVDYILVTHEHMD-HYGKTPLIA
BAB68554              TYFPHFDLHHDSEQIRHHGKK-VVGALGDAVKHIDNLSATLSELSNLHCY-NLRVDPVNF
gb|443893|124775      LWLGEVELA-AEEAAQDGAEPGRVDTFWYKFLKREPGGELSWEGNGPHHDRCCTYNENNL
                                     .       :      . .           .               

P84139                NYFKDETGIGVPMVGWPTDEVYAKLKQVIDMKERFVIIVLDEIDKLVKKSGDEVLYSLTR
P814153               NYFKDETGIEVPMVGWPTDEVYAKLKQVIDMKERFVIIVLDEIDKLVKKSGDEVLYSLTR
P851414               KLSD--------------------------------------------------------
P841414               KLSD--------------------------------------------------------
BAB68554              KLLSHCFQVVLGAHLG--REYTPQVQVAYDKFLAAVSAVLAEKYR---------------
gb|443893|124775      VDGVYCLPIG---HWGEATGHTNEMKHTTDFYFNIAGHQAMHYSRILPNIWLGSCPRQVE
                                                                                  

P84139                INTELKRAKVSVIGISNDLKFKEYLDPRVLSSLSEEEVVFPPYDANQLRDILTQRAEEAF
P814153               INTELKRAKVSVIGISNDLKFKEYLDPRVLSSLSEEEVVFPPYDANQLRDILTQRAEEAF
P851414               ------------------------------------------------------------
P841414               ------------------------------------------------------------
BAB68554              ------------------------------------------------------------
gb|443893|124775      HVTIKLKHELGITAVMN-FQTEWDIVQNSSGCNRYPEPMTPDTMIKLYREEGLAYIWMP-
                                                                                  

P84139                YPGVLDEGVIPLCAALAAREHGDARKALDLLRVAGEIAEREGASKVTEKHVWKAQEKIEQ
P814153               YPGVLDEGVIPLCAALAAREHGDARKALDLLRVAGEIAEREGASKVTEKHVWKAQEKIEQ
P851414               ------------------------------------------------------------
P841414               ------------------------------------------------------------
BAB68554              ------------------------------------------------------------
gb|443893|124775      TPDMSTEGRVQMLPQAVCLLHALLEKGHIVY-----VHCNAGVGRSTAAVCGWLQYVMGW
                                                                                  

P84139                DMMEEVIKTRPLQSKVLLYAIVLLDENGDLPANTGDVYAVYRELCEYIDLEPLTQRRISD
P814153               DMMEEVIKTLPLQSKVLLYAIVLLDENGDLPANTGDVYAVYRELCEYIDLEPLTQRRISD
P851414               ------------------------------------------------------------
P841414               ------------------------------------------------------------
BAB68554              ------------------------------------------------------------
gb|443893|124775      NLRKVQYFLMAKRPAVYIDEEALARAQEDFFQKFGKVRSSVCSL----------------
                                                                                  

P84139                LINELDMLGIINAKVVSKGRYGRTKEIRLNVTSYKIRNVLRYDYSIQPLLTISLKSEQRR
P814153               LINELDMLGIINAKVVSKGRYGRTKEIRLMVTSYKIRNVLRYDYSIQPLLTISLKSEQRR
P851414               ------------------------------------------------------------
P841414               ------------------------------------------------------------
BAB68554              ------------------------------------------------------------
gb|443893|124775      ------------------------------------------------------------
                                                                                  

P84139                LI
P814153               LI
P851414               --
P841414               --
BAB68554              --
gb|443893|124775      --
                        
BioPerl-1.007002/t/data/testaln.fasta000444000766000024      1105113155576321 17400 0ustar00cjfieldsstaff000000000000>AK1H_ECOLI/114-431 DESCRIPTION HERE
CPDSINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDPVEKLLAVG-HYLESTVDIAE
STRRIAASRIP------A-DHMVLMAGFTAGN-EKGELVVLGRNGSDYSAAVLAACLRAD
CCEIWTDVNGVYTCDP-------------RQVPDARLLKSMSYQEAMELSY--FGAKVLH
PRTITPIAQFQIPCLIKNTGNPQAPGTL-IG--ASRDEDELP----VKGISNLN------
NMAMFSVSGP-GMKGMVGMAARVFAAMS-------RARISVVLITQSSSEYSISFCVPQS
DCVRAERAMLEEFY-----LELKEGLLEPLAVAERLAIISV-VGDGLRTLRGISAKF---
---FAALARANINIVAIA
>AKH_HAEIN 114-431
-----------------VEDAVKATIDCRGEKLSIAMMKAWFEARGY-S--VHIVDPVKQ
LLAKG-GYLESSVEIEESTKRVDAANIA--K-DKVVLMAGF---TAGNEKGELVLLGRNG
SDYSAAC-----------------LAACLGASVCEIWTDVDGVYTCDP--RLVPDARLLP
TLSYREAMELSYFGAKVIHPRTIGPLLPQNIPCVIKNTGNPSAPGSI-ID--GNVKSESL
Q----VKGITNLDNLAMFNVSGPGMQGM---VGMASRVFSAMSGAGISVILITQSSSEYS
---ISFCVPVKSAEVAKTVLETEFA-----NELNEHQLEPIEVIKDLSIISV-VGDGMKQ
AKGIAARF------FSALAQANISIVAIA
>AKH1_MAIZE/117-440
-----------------ATESFSDFVVGHGELWSAQMLSYAIQKSGT-P--CSWMDTREV
LVVNPSGANQVDPDYLESEKRLEKWFSRC-P-AETIIATGF---IASTPENIPTTLKRDG
SDFSAAI-----------------IGSLVKARQVTIWTDVDGVFSADP--RKVSEAVILS
TLSYQEAWEMSYFGANVLHPRTIIPVMKYNIPIVIRNIFNTSAPGTM-IC--QQPANENG
DLEACVKAFATIDKLALVNVEGTGMAGV---PGTANAIFGAVKDVGANVIMISQASSEHS
---VCFAVPEKEVALVSAALHARFR-----EALAAGRLSKVEVIHNCSILAT-VGLRMAS
TPGVSATL------FDALAKANINVRAIA
>AK2H_ECOLI/112-431
-----------------INDAVYAEVVGHGEVWSARLMSAVLNQQG-----LPAAWLDAR
EFLRAERAAQPQVDEGLSYPLLQQLLVQH-P-GKRLVVTGF---ISRNNAGETVLLGRNG
SDYSATQ-----------------IGALAGVSRVTIWSDVAGVYSADP--RKVKDACLLP
LLRLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIERVLASGTGARI
VTSHDDVCLI-EFQVPASQDFKLAHKEI--DQILKRAQVRPLAVGVHNDRQLLQFCYTSE
VADSALKILDEAG---------LPGELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQ
PVEFTWQSDDGISLVAVL
>AK1_BACSU/66-374
-----------------ISPREQDLLLSCGETISSVVFTSMLLDNGVKA--AALTGAQAG
FLTNDQHTNAKIIEMKPER--LFSVLAN----HDAVVVAGF---QGATEKGDTTTIGRGG
SDTSAAA-----------------LGAAVDAEYIDIFTDVEGVMTADP--RVVENAKPLP
VVTYTEICNLAYQGAKVISPRAVEIAMQAKVPIRVRSTYS-NDKGTLVTSHHSSKVGSDV
FERLITGIAH-VKDVTQFKVPAKIGQYN-----VQTEVFKAMANAGISVDFFNITPSEIV
YTVAGNKTETAQR------------ILMDMGYDPMVTRNCAKVSAVGAGIMGVPGVTSKI
------VSALSEKEIPILQSA
>AK2_BACST/63-370
-----------------KRE--MDMLLSTGEQVSIALLAMSLHEKGYKA--VSLTGWQAG
ITTEEMHGNARIMNIDTT--RIRRCLDE----GAIVIVAGF---QGVTETGEITTLGRGG
SDTTAVA-----------------LAAALKAEKCDIYTDVTGVFTTDP--RYVKTARKIK
EISYDEMLELANLGAGVLHPRAVEFAKNYEVPLEVRSSME-NERGTMVK--EEVSMEQHL
IVRGIAFEDQ-VTRVTVVGIEKYLQSVA--------TIFTALANRGINVDIIIQNA----
----------------TNSETAS--VSFSIRTEDLPETLQVLQ-------------ALEG
ADVHYESGLAKVSI-VGSGMISNPGVAARV------FEVLADQGIEIKMVS
>AK2_BACSU/63-373
-----------------KRE--MDMLLATGEQVTISLLSMALQEKGYDA--VSYTGWQAG
IRTEAIHGNARITDIDTS--VLADQLEK----GKIVIVAGF---QGMTEDCEITTLGRGG
SDTTAVA-----------------LAAALKVDKCDIYTDVPGVFTTDP--RYVKSARKLE
GISYDEMLELANLGAGVLHPRAVEFAKNYQVPLEVRSSTE-TEAGTLIE--EESSMEQNL
IVRGIAFEDQ-ITRVTIYGLTSGLTTLS--------TIFTTLAKRNINVDIIIQTQ----
----------------AEDKTG---ISFSVKTEDADQTVAVLEEYK---------DALEF
EKIETESKLAKVSI-VGSGMVSNPGVAAEM------FAVLAQKNILIKMVS
>AKAB_CORFL/63-379
-----------------ARE--MDMLLTAGERISNALVAMAIESLGAEA--QSFTGSQAG
VLTTERHGNARIVDVTPG--RVREALDE----GKICIVAGF--QGVNKETRDVTTLGRGG
SDTTAVA-----------------LAAALNADVCEIYSDVDGVYTADP--RIVPNAQKLE
KLSFEEMLELAAVGSKILVLRSVEYARAFNVPLRVRSSYS-NDPGTLIAGSMEDIPVEEA
VLTGVATDKS-EAKVTVLGISDKPGEAA--------KVFRALADAEINIDMVLQNV----
----------------SSVEDGTTDITFTCPRADGRRAMEILKKLQ---------VQGNW
TNVLYDDQVDKVSL-VGAGMKSHPGVTAEF------MEALRDVNVNIELIS
>AKAB_MYCSM/63-379
-----------------PRE--MDMLLTAGERISNALVAMAIESLGAQA--RSFTGSQAG
VITTGTHGNAKIIDVTPG--RLRDALDE----GQIVLVAGF--QGVSQDSKDVTTLGRGG
SDTTAVA-----------------VAAALDADVCEIYTDVDGIFTADP--RIVPNARHLD
TVSFEEMLEMAACGAKVLMLRCVEYARRYNVPIHVRSSYS-DKPGTIVKGSIEDIPMEDA
ILTGVAHDRS-EAKVTVVGLPDVPGYAA--------KVFRAVAEADVNIDMVLQNI----
----------------SKIEDGKTDITFTCARDNGPRAVEKLSALK---------SEIGF
SQVLYDDHIGKVSL-IGAGMRSHPGVTATF------CEALAEAGINIDLIS
>AK3_ECOLI/106-407
-----------------TSPALTDELVSHGELMSTLLFVEILRERD--V--QAQWFDVRK
VMRTNDRFGRAEPDIAALAELAALQLLPR-LNEGLVITQGF---IGSENKGRTTTLGRGG
SDYTAAL-----------------LAEALHASRVDIWTDVPGIYTTDP--RVVSAAKRID
EIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFRA
LAL--RRNQT-LLTLHSLNMLHSRGFLA--------EVFGILARHNISVDLITTSEVSVA
LTLDTTGSTSTG----------DTLLTQSLLMELSALCRVEVEEGLALVALIG-------
---NDLSKACGVGKEVF
>AK_YEAST/134-472 A COMMENT FOR YEAST
-----------------VSSRTVDLVMSCGEKLSCLFMTALCNDRGCKAKYVDLSHIVPS
DFSASALDNSFYTFLVQALKEKLAPFVSA-KERIVPVFTGF---FGLVPTGLLNGVGRGY
TDLCAAL-----------------IAVAVNADELQVWKEVDGIFTADP--RKVPEARLLD
SVTPEEASELTYYGSEVIHPFTMEQVIRAKIPIRIKNVQNPLGNGTIIYPDNVAKKGEST
PPHPPENLSS----SFYEKRKRGATAITTKN----DIFVINIHSNKKTLSHGFLAQIFTI
LDKYKLVVDLISTSEVHVSMALPIPDADS-LKSLRQAEEKLRILGSVDITKKLSIVSLVG
KHMKQYIGIAG---TMFTTLAEEGINIEMIS
BioPerl-1.007002/t/data/testaln.fastq000444000766000024       524213155576321 17405 0ustar00cjfieldsstaff000000000000@FC12044_91407_8_200_406_24
GTTAGCTCCCACCTTAAGATGTTTA
+FC12044_91407_8_200_406_24
SXXTXXXXXXXXXTTSUXSSXKTMQ
@FC12044_91407_8_200_720_610
CTCTGTGGCACCCCATCCCTCACTT
+FC12044_91407_8_200_720_610
OXXXXXXXXXXXXXXXXXTSXQTXU
@FC12044_91407_8_200_345_133
GATTTTTTAACAATAAACGTACATA
+FC12044_91407_8_200_345_133
OQTOOSFORTFFFIIOFFFFFFFFF
@FC12044_91407_8_200_106_131
GTTGCCCAGGCTCGTCTTGAACTCC
+FC12044_91407_8_200_106_131
XXXXXXXXXXXXXXSXXXXISTXQS
@FC12044_91407_8_200_916_471
TGATTGAAGGTAGGGTAGCATACTG
+FC12044_91407_8_200_916_471
XXXXXXXXXXXXXXXUXXUSXXTXW
@FC12044_91407_8_200_57_85
GCTCCAATAGCGCAGAGGAAACCTG
+FC12044_91407_8_200_57_85
XFXMXSXXSXXXOSQROOSROFQIQ
@FC12044_91407_8_200_10_437
GCTGCTTGGGAGGCTGAGGCAGGAG
+FC12044_91407_8_200_10_437
USXSXXXXXXUXXXSXQXXUQXXKS
@FC12044_91407_8_200_154_436
AGACCTTTGGATACAATGAACGACT
+FC12044_91407_8_200_154_436
MKKMQTSRXMSQTOMRFOOIFFFFF
@FC12044_91407_8_200_336_64
AGGGAATTTTAGAGGAGGGCTGCCG
+FC12044_91407_8_200_336_64
STQMOSXSXSQXQXXKXXXKFXFFK
@FC12044_91407_8_200_620_233
TCTCCATGTTGGTCAGGCTGGTCTC
+FC12044_91407_8_200_620_233
XXXXXXXXXXXXXXXXXXXXXSXSW
@FC12044_91407_8_200_902_349
TGAACGTCGAGACGCAAGGCCCGCC
+FC12044_91407_8_200_902_349
XMXSSXMXXSXQSXTSQXFKSKTOF
@FC12044_91407_8_200_40_618
CTGTCCCCACGGCGGGGGGGCCTGG
+FC12044_91407_8_200_40_618
TXXXXSXXXXXXXXXXXXXRKFOXS
@FC12044_91407_8_200_83_511
GATGTACTCTTACACCCAGACTTTG
+FC12044_91407_8_200_83_511
SOXXXXXUXXXXXXQKQKKROOQSU
@FC12044_91407_8_200_76_246
TCAAGGGTGGATCTTGGCTCCCAGT
+FC12044_91407_8_200_76_246
XTXTUXXXXXRXXXTXXSUXSRFXQ
@FC12044_91407_8_200_303_427
TTGCGACAGAGTTTTGCTCTTGTCC
+FC12044_91407_8_200_303_427
XXQROXXXXIXFQXXXOIQSSXUFF
@FC12044_91407_8_200_31_299
TCTGCTCCAGCTCCAAGACGCCGCC
+FC12044_91407_8_200_31_299
XRXTSXXXRXXSXQQOXQTSQSXKQ
@FC12044_91407_8_200_553_135
TACGGAGCCGCGGGCGGGAAAGGCG
+FC12044_91407_8_200_553_135
XSQQXXXXXXXXXXSXXMFFQXTKU
@FC12044_91407_8_200_139_74
CCTCCCAGGTTCAAGCGATTATCCT
+FC12044_91407_8_200_139_74
RMXUSXTXXQXXQUXXXSQISISSO
@FC12044_91407_8_200_108_33
GTCATGGCGGCCCGCGCGGGGAGCG
+FC12044_91407_8_200_108_33
OOOSSXXSXXOMKMOFMKFOKFFFF
@FC12044_91407_8_200_980_965
ACAGTGGGTTCTTAAAGAAGAGTCG
+FC12044_91407_8_200_980_965
TOSSRXXXSSMSXMOMXIRXOXFFS
@FC12044_91407_8_200_981_857
AACGAGGGGCGCGACTTGACCTTGG
+FC12044_91407_8_200_981_857
RXMSSXXXXSXQXQXFSXQFQKMXS
@FC12044_91407_8_200_8_865
TTTCCCACCCCAGGAAGCCTTGGAC
+FC12044_91407_8_200_8_865
XXXFKOROMKOORMIMRIIKKORFF
@FC12044_91407_8_200_292_484
TCAGCCTCCGTGCCCAGCCCACTCC
+FC12044_91407_8_200_292_484
XQXOSXXXXXUXXXXIXXXXQTOXF
@FC12044_91407_8_200_675_16
CTCGGGAGGCTGAGGCAGGGGGGTT
+FC12044_91407_8_200_675_16
OXTXXXSXXQXXOXXKMXXMXOKQF
@FC12044_91407_8_200_285_136
CCAAATCTTGAATTGTAGCTCCCCT
+FC12044_91407_8_200_285_136
OSXOQXXXXXSXXUXXTXXXXTRMS
BioPerl-1.007002/t/data/testaln.list000444000766000024         7113155576321 17175 0ustar00cjfieldsstaff000000000000BAB68554
gb|443893|124775
P814153
P84139
P841414
P851414
BioPerl-1.007002/t/data/testaln.mase000444000766000024       175313155576321 17217 0ustar00cjfieldsstaff000000000000;; saved by seaview on Wed Jan  7 11:14:33 1998
;;# of segments=14 all seqs
;; 25,25 27,27 30,30 96,96 98,98 117,117 149,149 160,160 164,164 173,173
;; 258,258 282,282 289,289 291,291
;no comment
AK1H_ECOLI
CPDSINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDPVEKLLAVG-HYLESTVDIAE
STRRIAASRIP------A-DHMVLMAGFTAGN-EKGELVVLGRNGSDYSAAVLAACLRAD
CCEIWTDVNGVYTCDP-------------RQVPDARLLKSMSYQEAMELSY--FGAKVLH
PRTITPIAQFQIPCLIKNTGNPQAPGTL-IG--ASRDEDELP----VKGISNLN------
NMAMFSVSGP-GMKGMVGMAARVFAAMS-------RARISVVLITQSSSEYSISFCVPQS
DCVRAERAMLEEFY-----LELKEGLLEPLAVAERLAIISV-VGDGLRTLRGISAKF---
---FAALARANINIVAIA
;no comment
AKH_HAEIN
-----------------VEDAVKATIDCRGEKLSIAMMKAWFEARGY-S--VHIVDPVKQ
LLAKG-GYLESSVEIEESTKRVDAANIA--K-DKVVLMAGF---TAGNEKGELVLLGRNG
SDYSAAC-----------------LAACLGASVCEIWTDVDGVYTCDP--RLVPDARLLP
TLSYREAMELSYFGAKVIHPRTIGPLLPQNIPCVIKNTGNPSAPGSI-ID--GNVKSESL
Q----VKGITNLDNLAMFNVSGPGMQGM---VGMASRVFSAMSGAGISVILITQSSSEYS
---ISFCVPVKSAEVAKTVLETEFA-----NELNEHQLEPIEVIKDLSIISV-VGDGMKQ
AKGIAARF------FSALAQAN
BioPerl-1.007002/t/data/testaln.mega000444000766000024       255713155576321 17206 0ustar00cjfieldsstaff000000000000#mega
!Title: Amino acid sequences of hemoglobin alpha chains;
!Format datatype=protein identical=. indel=-;

[
M. Nei and S. Kumar (2000) Molecular Evolution and Phylogenetics.  
Oxford University Press. New York.
Data for Example 2.1.
]



#Human    V-LSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHF-DL SHGSAQVKGH 
#Horse    ....A..... .....S...G .......... .....G.... .......... ........A. 
#Cow      ....A...G. .........G ..A....... .......... .......... .......... 
#Kangaroo ....A...GH ...I.....G .....A..G. ..T.H..... .......... ......IQA. 
#Newt     MK..AE..H. ..TT.DHIKG .EEAL..... F...T.L.A. R....AK... .E..SFLHS. 
#Carp     S...DK..AA ..I..A.ISP K.DDI..... G..LTVY.Q. ....A.WA.. .P..GP..-. 

#Human    GKKVA-DALT NAVAHVDDMP NALSALSDLH AHKLRVDPVN FKLLSHCLLV TLAAHLPAEF 
#Horse    .......G.. L..G.L..L. G...D..N.. .......... .........S ...V...ND. 
#Cow      .A....A... K..E.L..L. G...E..... .......... ......S... ...S...SD. 
#Kangaroo ...I.....G Q..E.I..L. GT..K..... .......... .......... .F....GDA. 
#Newt     ....M.G..S .....I..ID A..CK...K. .QD.M...A. .PK.A.NI.. VMGI..K.HL 
#Carp     ....IMG.VG D..SKI..LV GG.AS..E.. .S......A. ..I.ANHIV. GIMFY..GD. 

#Human    TPAVHASLDK FLASVSTVLT SKYR
#Horse    .......... ..S....... ....
#Cow      .......... ...N...... ....
#Kangaroo ..E....... ...A...... ....
#Newt     .YP..C.V.. ..DV.GH... ....
#Carp     P.E..M.V.. .FQNLALA.S E...

BioPerl-1.007002/t/data/testaln.metafasta000444000766000024        22113155576321 20204 0ustar00cjfieldsstaff000000000000>test1/3-25
CDEFHIJKLMNOPQRSTUVWXYZ
&hydrophobic
I & OIOIJOIIOOIOOOOUIIX
&structural
ABAEEIEIJEIIEOAEEAAUIAX
>test1/3-23
CDEFHIJKLMNOPQRSTUVWX--
BioPerl-1.007002/t/data/testaln.msf000444000766000024      1612413155576321 17075 0ustar00cjfieldsstaff000000000000
NoName   MSF: 16  Type: P  Fri May 25 11:28:34 2001  Check: 00 ..

 Name: 1433_LYCES/9-246  Len:    242  Check:  2603  Weight:  1.00
 Name: 1434_LYCES/6-243  Len:    242  Check:  2257  Weight:  1.00
 Name: 143R_ARATH/7-245  Len:    242  Check:  3905  Weight:  1.00
 Name: 143B_VICFA/7-242  Len:    242  Check:  2825  Weight:  1.00
 Name: 143E_HUMAN/4-239  Len:    242  Check:  2034  Weight:  1.00
 Name: BMH1_YEAST/4-240  Len:    242  Check:  7237  Weight:  1.00
 Name: RA24_SCHPO/6-241  Len:    242  Check:  3762  Weight:  1.00
 Name: RA25_SCHPO/5-240  Len:    242  Check:  2995  Weight:  1.00
 Name: 1431_ENTHI/4-239  Len:    242  Check:  2213  Weight:  1.00
 Name: 1432_ENTHI/4-238  Len:    242  Check:  8344  Weight:  1.00
 Name: 1433_CAEEL/5-237  Len:    242  Check:  1241  Weight:  1.00
 Name: 143Z_DROME/6-239  Len:    242  Check:  8864  Weight:  1.00
 Name: 1433_XENLA/1-227  Len:    242  Check:  8793  Weight:  1.00
 Name: 143T_HUMAN/3-236  Len:    242  Check:  6034  Weight:  1.00
 Name: 143F_MOUSE/3-240  Len:    242  Check:  5185  Weight:  1.00
 Name: 143S_HUMAN/3-238  Len:    242  Check:  1679  Weight:  1.00

//


1433_LYCES/9-246      REENVYMAKL ADRAESDEEM VEFMEKVSNS LGS.EELTVE ERNLLSVAYK 
1434_LYCES/6-243      REENVYLAKL AEQAERYEEM IEFMEKVAKT ADV.EELTVE ERNLLSVAYK 
143R_ARATH/7-245      RDQYVYMAKL AEQAERYEEM VQFMEQLVTG ATPAEELTVE ERNLLSVAYK 
143B_VICFA/7-242      RENFVYIAKL AEQAERYEEM VDSMKNVANL DV...ELTIE ERNLLSVGYK 
143E_HUMAN/4-239      REDLVYQAKL AEQAERYDEM VESMKKVAGM DV...ELTVE ERNLLSVAYK 
BMH1_YEAST/4-240      REDSVYLAKL AEQAERYEEM VENMKTVASS GQ...ELSVE ERNLLSVAYK 
RA24_SCHPO/6-241      REDAVYLAKL AEQAERYEGM VENMKSVAST DQ...ELTVE ERNLLSVAYK 
RA25_SCHPO/5-240      RENSVYLAKL AEQAERYEEM VENMKKVACS ND...KLSVE ERNLLSVAYK 
1431_ENTHI/4-239      REDCVYTAKL AEQSERYDEM VQCMKQVAEM EA...ELSIE ERNLLSVAYK 
1432_ENTHI/4-238      REDLVYLSKL AEQSERYEEM VQYMKQVAEM GT...ELSVE ERNLISVAYK 
1433_CAEEL/5-237      VEELVQRAKL AEQAERYDDM AAAMKKVTEQ GQ...ELSNE ERNLLSVAYK 
143Z_DROME/6-239      KEELVQKAKL AEQSERYDDM AQAMKSVTET GV...ELSNE ERNLLSVAYK 
1433_XENLA/1-227      .......AKL SEQAERYDDM AASMKAVTEL GA...ELSNE ERNLLSVAYK 
143T_HUMAN/3-236      KTELIQKAKL AEQAERYDDM ATCMKAVTEQ GA...ELSNE ERNLLSVAYK 
143F_MOUSE/3-240      REQLLQRARL AEQAERYDDM ASAMKAVTEL NE...PLSNE DRNLLSVAYK 
143S_HUMAN/3-238      RASLIQKAKL AEQAERYEDM AAFMKGAVEK GE...ELSCE ERNLLSVAYK 


1433_LYCES/9-246      NVIGARRASW RIISSIEQKE ESRG.NEEHV NSIREYRSKI ENELSKICDG 
1434_LYCES/6-243      NVIGARRASW RIISSIEQKE ESRG.NEDHV NTIKEYRSKI EADLSKICDG 
143R_ARATH/7-245      NVIGSLRAAW RIVSSIEQKE ESRK.NDEHV SLVKDYRSKV ESELSSVCSG 
143B_VICFA/7-242      NVIGARRASW RILSSIEQKE ESKG.NDVNA KRIKEYRHKV ETELSNICID 
143E_HUMAN/4-239      NVIGARRASW RIISSIEQKE ENKG.GEDKL KMIREYRQMV ETELKLICCD 
BMH1_YEAST/4-240      NVIGARRASW RIVSSIEQKE ESKEKSEHQV ELICSYRSKI ETELTKISDD 
RA24_SCHPO/6-241      NVIGARRASW RIVSSIEQKE ESKG.NTAQV ELIKEYRQKI EQELDTICQD 
RA25_SCHPO/5-240      NIIGARRASW RIISSIEQKE ESRG.NTRQA ALIKEYRKKI EDELSDICHD 
1431_ENTHI/4-239      NVIGAKRASW RIISSLEQKE QAKG.NDKHV EIIKGYRAKI EKELSTCCDD 
1432_ENTHI/4-238      NVVGSRRASW RIISSLEQKE QAKG.NTQRV ELIKTYRAKI EQELSQKCDD 
1433_CAEEL/5-237      NVVGARRSSW RVISSIEQKT EG...SEKKQ QLAKEYRVKV EQELNDICQD 
143Z_DROME/6-239      NVVGARRSSW RVISSIEQKT EA...SARKQ QLAREYRERV EKELREICYE 
1433_XENLA/1-227      NVVGARRSSW RVISSIEQKT EG...NDKRQ QMAREYREKV ETELQDICKD 
143T_HUMAN/3-236      NVVGGRRSAW RVISSIEQKT DT...SDKKL QLIKDYREKV ESELRSICTT 
143F_MOUSE/3-240      NVVGARRSSW RVISSIEQKT MADG.NEKKL EKVKAYREKI EKELETVCND 
143S_HUMAN/3-238      NVVGGQRAAW RVLSSIEQKS NEEG.SEEKG PEVREYREKV ETELQGVCDT 


1433_LYCES/9-246      ILKLLDSKLI PSA..TSGDS KVFYLKMKGD YHRYLAEFKT GAERKEAAES 
1434_LYCES/6-243      ILSLLESNLI PSA..STAES KVFHLKMKGD YHRYLAEFKT GTERKEAAEN 
143R_ARATH/7-245      ILKLLDSHLI PSA..GASES KVFYLKMKGD YHRYMAEFKS GDERKTAAED 
143B_VICFA/7-242      VMRVIDEHLI PSA..AAGES TVFYYKMKGD YYRYLAEFKT GNEKKEAGDQ 
143E_HUMAN/4-239      ILDVLDKHLI PAA..NTGES KVFYYKMKGD YHRYLAEFAT GNDRKEAAEN 
BMH1_YEAST/4-240      ILSVLDSHLI PSA..TTGES KVFYYKMKGD YHRYLAEFSS GDAREKATNA 
RA24_SCHPO/6-241      ILTVLEKHLI PNA..ASAES KVFYYKMKGD YYRYLAEFAV GEKRQHSADQ 
RA25_SCHPO/5-240      VLSVLEKHLI PAA..TTGES KVFYYKMKGD YYRYLAEFTV GEVCKEAADS 
1431_ENTHI/4-239      VLKVIQENLL PKA..STSES KVFFKKMEGD YYRYFAEFTV DEKRKEVADK 
1432_ENTHI/4-238      VLKIITEFLL KNS..TSIES KVFFKKMEGD YYRYYAEFTV DEKRKEVADK 
1433_CAEEL/5-237      VLKLLDEFLI VKA..GAAES KAFYLKMKGD YYRYLAEVAS .EDRAAVVEK 
143Z_DROME/6-239      VLGLLDKYLI PKA..SNPES KVFYLKMKGD YYRYLAEVAT GDARNTVVDD 
1433_XENLA/1-227      VLDLLDRFLV PNA..TPPES KVFYLKMKGD YYRYLSEVAS GDSKQETVAS 
143T_HUMAN/3-236      VLELLDKYLI ANA..TNPES KVFYLKMKGD YFRYLAEVAC GDDRKQTIDN 
143F_MOUSE/3-240      VLALLDKFLI KNCNDFQYES KVFYLKMKGD YYRYLAEVAS GEKKNSVVEA 
143S_HUMAN/3-238      VLGLLDSHLI KEA..GDAES RVFYLKMKGD YYRYLAEVAT GDDKKRIIDS 


1433_LYCES/9-246      TLTAYKAAQD IASAELAPTH PIRLGLALNF SVFYYEILNS PDRACNLAKQ 
1434_LYCES/6-243      TLLAYKSAQD IALAELAPTH PIRLGLALNF SVFYYEILNS PDRACNLAKQ 
143R_ARATH/7-245      TMLAYKAAQD IAAADMAPTH PIRLGLALNF SVFYYEILNS SDKACNMAKQ 
143B_VICFA/7-242      SMKAYESATT AAEAELPPTH PIRLGLALNF SVFYYEILNS PERACHLAKQ 
143E_HUMAN/4-239      SLVAYKAASD IAMTELPPTH PIRLGLALNF SVFYYEILNS PDRACRLAKA 
BMH1_YEAST/4-240      SLEAYKTASE IATTELPPTH PIRLGLALNF SVFYYEIQNS PDKACHLAKQ 
RA24_SCHPO/6-241      SLEGYKAASE IATAELAPTH PIRLGLALNF SVFYYEILNS PDRACYLAKQ 
RA25_SCHPO/5-240      SLEAYKAASD IAVAELPPTD PMRLGLALNF SVFYYEILDS PESACHLAKQ 
1431_ENTHI/4-239      SLAAYTEATE ISNAELAPTH PIRLGLALNF SVFYFEIMND ADKACQLAKQ 
1432_ENTHI/4-238      SLAAYQEATD TA.ASLVPTH PIRLGLALNF SVFYYQIMND ADKACQLAKE 
1433_CAEEL/5-237      SQKAYQEALD IAKDKMQPTH PIRLGLALNF SVFYYEILNT PEHACQLAKQ 
143Z_DROME/6-239      SQTAYQDAFD ISKGKMQPTH PIRLGLALNF SVFYYEILNS PDKACQLAKQ 
1433_XENLA/1-227      SQQAYQEAFE ISKSEMQPTH PIRLGLALNF SVFYYEILNS PEKACSLAKS 
143T_HUMAN/3-236      SQGAYQEAFD ISKKEMQPTH PIRLGLALNF SVFYYEILNN PELACTLAKT 
143F_MOUSE/3-240      SEAAYKEAFE ISKEHMQPTH PIRLGLALNF SVFYYEIQNA PEQACLLAKQ 
143S_HUMAN/3-238      ARSAYQEAMD ISKKEMPPTN PIRLGLALNF SVFHYEIANS PEEAISLAKT 


1433_LYCES/9-246      AFDEAIAELD TLGEESYKDS TLIMQLLRDN LTLWTSDMQD DG 
1434_LYCES/6-243      AFDEAISELD TLGEESYKDS TLIMQLLRDN LTLWTSDNAD DV 
143R_ARATH/7-245      AFEEAIAELD TLGEESYKDS TLIMQLLRDN LTLWTSDYAG AD 
143B_VICFA/7-242      AFDEAISELD TLNEESYKDS TLIMQLLRDN LTLWTSDIPE DG 
143E_HUMAN/4-239      AFDDAIAELD TLSEESYKDS TLIMQLLRDN LTLWTSDMQG DG 
BMH1_YEAST/4-240      AFDDAIAELD TLSEESYKDS TLIMQLLRDN LTLWTSDMSE SG 
RA24_SCHPO/6-241      AFDEAISELD SLSEESYKDS TLIMQLLRDN LTLWTSDAEY SA 
RA25_SCHPO/5-240      VFDEAISELD SLSEESYKDS TLIMQLLRDN LTLWTSDAEY NQ 
1431_ENTHI/4-239      AFDDAIAKLD EVPENMYKDS TLIMQLLRDN LTLWTSDACD EE 
1432_ENTHI/4-238      AFDEAIQKLD EVPEESYKES TLIMQLLRDN LTLWTSDMGD DE 
1433_CAEEL/5-237      AFDDAIAELD TLNEDSYKDS TLIMQLLRDN LTLWTSDVGA ED 
143Z_DROME/6-239      AFDDAIAELD TLNEDSYKDS TLIMQLLRDN LTLWTSDTQG DE 
1433_XENLA/1-227      AFDEAIRELD TLNEESYKDS TLIMQLLRDN LTLWTSENQG EE 
143T_HUMAN/3-236      AFDEAIAELD TLNEDSYKDS TLIMQLLRDN LTLWTSDSAG EE 
143F_MOUSE/3-240      AFDDAIAELD TLNEDSYKDS TLIMQLLRDN LTLWTSDQQD EE 
143S_HUMAN/3-238      TFDEAMADLH TLSEDSYKDS TLIMQLLRDN LTLWTADNAG EE 


BioPerl-1.007002/t/data/testaln.nexus000444000766000024       105313155576321 17425 0ustar00cjfieldsstaff000000000000#NEXUS
[TITLE: Four Anthropoidea]

begin data;
dimensions ntax=4 nchar=50;
format interleave datatype=RNA missing=N gap=-;

matrix
'Homo sapiens'      AGUCGAGUC---GCAGAAACGCAUGAC-GAC
Pan_paniscus        AGUCGCGUCG--GCAGAAACGCAUGACGGAC
Gorilla_gorilla     AGUCGCGUCG--GCAGAUACGCAUCACGGAC
Pongo_pigmaeus      AGUCGCGUCGAAGCAGA--CGCAUGACGGAC

'Homo sapiens'      CACAUUUU-CCUUGCAAAG
Pan_paniscus        CACAUCAU-CCUUGCAAAG
Gorilla_gorilla     -ACAUCAUCCCUCGCAGAG
Pongo_pigmaeus      CACAUCAUCCCUUGCAGAG
;

endblock;
begin assumptions;
options deftype=unord;
BioPerl-1.007002/t/data/testaln.pfam000444000766000024      1016013155576321 17225 0ustar00cjfieldsstaff0000000000001433_LYCES/9-246    REENVYMAKLADRAESDEEMVEFMEKVSNSLGS.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKICDGILKLLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFKTGAERKEAAESTLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDMQDDG
1434_LYCES/6-243    REENVYLAKLAEQAERYEEMIEFMEKVAKTADV.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVNTIKEYRSKIEADLSKICDGILSLLESNLIPSA..STAESKVFHLKMKGDYHRYLAEFKTGTERKEAAENTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAISELDTLGEESYKDSTLIMQLLRDNLTLWTSDNADDV
143R_ARATH/7-245    RDQYVYMAKLAEQAERYEEMVQFMEQLVTGATPAEELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NDEHVSLVKDYRSKVESELSSVCSGILKLLDSHLIPSA..GASESKVFYLKMKGDYHRYMAEFKSGDERKTAAEDTMLAYKAAQDIAAADMAPTHPIRLGLALNFSVFYYEILNSSDKACNMAKQAFEEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDYAGAD
143B_VICFA/7-242    RENFVYIAKLAEQAERYEEMVDSMKNVANLDV...ELTIEERNLLSVGYKNVIGARRASWRILSSIEQKEESKG.NDVNAKRIKEYRHKVETELSNICIDVMRVIDEHLIPSA..AAGESTVFYYKMKGDYYRYLAEFKTGNEKKEAGDQSMKAYESATTAAEAELPPTHPIRLGLALNFSVFYYEILNSPERACHLAKQAFDEAISELDTLNEESYKDSTLIMQLLRDNLTLWTSDIPEDG
143E_HUMAN/4-239    REDLVYQAKLAEQAERYDEMVESMKKVAGMDV...ELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKG.GEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAA..NTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDG
BMH1_YEAST/4-240    REDSVYLAKLAEQAERYEEMVENMKTVASSGQ...ELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKEKSEHQVELICSYRSKIETELTKISDDILSVLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFSSGDAREKATNASLEAYKTASEIATTELPPTHPIRLGLALNFSVFYYEIQNSPDKACHLAKQAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMSESG
RA24_SCHPO/6-241    REDAVYLAKLAEQAERYEGMVENMKSVASTDQ...ELTVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKG.NTAQVELIKEYRQKIEQELDTICQDILTVLEKHLIPNA..ASAESKVFYYKMKGDYYRYLAEFAVGEKRQHSADQSLEGYKAASEIATAELAPTHPIRLGLALNFSVFYYEILNSPDRACYLAKQAFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYSA
RA25_SCHPO/5-240    RENSVYLAKLAEQAERYEEMVENMKKVACSND...KLSVEERNLLSVAYKNIIGARRASWRIISSIEQKEESRG.NTRQAALIKEYRKKIEDELSDICHDVLSVLEKHLIPAA..TTGESKVFYYKMKGDYYRYLAEFTVGEVCKEAADSSLEAYKAASDIAVAELPPTDPMRLGLALNFSVFYYEILDSPESACHLAKQVFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYNQ
1431_ENTHI/4-239    REDCVYTAKLAEQSERYDEMVQCMKQVAEMEA...ELSIEERNLLSVAYKNVIGAKRASWRIISSLEQKEQAKG.NDKHVEIIKGYRAKIEKELSTCCDDVLKVIQENLLPKA..STSESKVFFKKMEGDYYRYFAEFTVDEKRKEVADKSLAAYTEATEISNAELAPTHPIRLGLALNFSVFYFEIMNDADKACQLAKQAFDDAIAKLDEVPENMYKDSTLIMQLLRDNLTLWTSDACDEE
1432_ENTHI/4-238    REDLVYLSKLAEQSERYEEMVQYMKQVAEMGT...ELSVEERNLISVAYKNVVGSRRASWRIISSLEQKEQAKG.NTQRVELIKTYRAKIEQELSQKCDDVLKIITEFLLKNS..TSIESKVFFKKMEGDYYRYYAEFTVDEKRKEVADKSLAAYQEATDTA.ASLVPTHPIRLGLALNFSVFYYQIMNDADKACQLAKEAFDEAIQKLDEVPEESYKESTLIMQLLRDNLTLWTSDMGDDE
1433_CAEEL/5-237    VEELVQRAKLAEQAERYDDMAAAMKKVTEQGQ...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...SEKKQQLAKEYRVKVEQELNDICQDVLKLLDEFLIVKA..GAAESKAFYLKMKGDYYRYLAEVAS.EDRAAVVEKSQKAYQEALDIAKDKMQPTHPIRLGLALNFSVFYYEILNTPEHACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDVGAED
143Z_DROME/6-239    KEELVQKAKLAEQSERYDDMAQAMKSVTETGV...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEA...SARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKA..SNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDE
1433_XENLA/1-227    .......AKLSEQAERYDDMAASMKAVTELGA...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...NDKRQQMAREYREKVETELQDICKDVLDLLDRFLVPNA..TPPESKVFYLKMKGDYYRYLSEVASGDSKQETVASSQQAYQEAFEISKSEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKSAFDEAIRELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGEE
143T_HUMAN/3-236    KTELIQKAKLAEQAERYDDMATCMKAVTEQGA...ELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDT...SDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEE
143F_MOUSE/3-240    REQLLQRARLAEQAERYDDMASAMKAVTELNE...PLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADG.NEKKLEKVKAYREKIEKELETVCNDVLALLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEHMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEE
143S_HUMAN/3-238    RASLIQKAKLAEQAERYEDMAAFMKGAVEKGE...ELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEG.SEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEA..GDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEE
BioPerl-1.007002/t/data/testaln.phylip000444000766000024        40313155576321 17546 0ustar00cjfieldsstaff0000000000004 50
Homo sapie AGUCGAGUC---GCAGAAACGCAUGAC-GACC
Pan panisc AGUCGCGUCG--GCAGAAACGCAUGACGGACC
Gorilla go AGUCGCGUCG--GCAGAUACGCAUCACGGAC-
Pongo pigm AGUCGCGUCGAAGCAGA--CGCAUGACGGACC
 
ACAUUUU-CCUUGCAAAG
ACAUCAU-CCUUGCAAAG
ACAUCAUCCCUCGCAGAG
ACAUCAUCCCUUGCAGAG
BioPerl-1.007002/t/data/testaln.po000444000766000024      3033113155576321 16722 0ustar00cjfieldsstaff000000000000VERSION=clustalw
NAME=NoName
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SOURCENAME=P841414
SOURCEINFO=60 154 0 -1 
SOURCENAME=BAB68554
SOURCEINFO=141 42 0 -1 
SOURCENAME=gb|443893|124775
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P:L566S5A567
V:L567S0S1A570
M:L568S5A569
F:L569S0S1A572
T:L570S5A571
P:L571L572S0S1S5
P:L573S0S1A575
D:L573S5A574
Y:L574S0S1A577
T:L575S5A576
D:L576S0S1A579
M:L577S5A578
A:L578S0S1A581
I:L579S5A580
N:L580S0S1A583
K:L581S5A582
Q:L582S0S1A585
L:L583S5A584
L:L584S0S1A587
Y:L585S5A586
R:L586L587S0S1S5
D:L588S0S1A590
E:L588S5A589
I:L589S0S1A592
E:L590S5A591
L:L591S0S1A594
G:L592S5A593
T:L593S0S1A596
L:L594S5A595
Q:L595S0S1A598
A:L596S5A597
R:L597S0S1A600
Y:L598S5A599
A:L599S0S1A602
I:L600S5A601
E:L601S0S1A604
W:L602S5A603
E:L603S0S1A606
M:L604S5A605
A:L605S0S1A608
P:L606S5A607
F:L607S0S1
Y:L609S0S1A611
T:L608S5A610
P:L610L611S0S1S5
G:L612S0S1A614
D:L612S5A613
V:L613S0S1A616
M:L614S5A615
L:L615S0S1A618
S:L616S5A617
D:L617S0S1A620
T:L618S5A619
E:L619L620S0S1S5
G:L621S0S1S5
V:L622S0S1A624
R:L622S5A623
I:L623S0S1A626
V:L624S5A625
P:L625S0S1A628
Q:L626S5A627
L:L627S0S1A630
M:L628S5A629
C:L629S0S1A632
L:L630S5A631
A:L631S0S1A634
P:L632S5A633
A:L633S0S1A636
Q:L634S5A635
L:L635S0S1A638
A:L636S5A637
A:L637S0S1A640
V:L638S5A639
A:L639S0S1A642
C:L640S5A641
R:L641S0S1A644
L:L642S5A643
E:L643S0S1A646
L:L644S5A645
H:L645L646S0S1S5
G:L647S0S1A649
A:L647S5A648
D:L648S0S1A651
L:L649S5A650
A:L650S0S1A653
L:L651S5A652
R:L652S0S1A655
E:L653S5A654
K:L654L655S0S1S5
A:L656S0S1A658
G:L656S5A657
L:L657S0S1A660
H:L658S5A659
D:L659S0S1A662
I:L660S5A661
L:L661S0S1A664
V:L662S5A663
L:L663S0S1A666
Y:L664S5A665
R:L665S0S1
V:L667S0S1
A:L668S0S1
G:L669S0S1
E:L670S0S1
I:L671S0S1A673
V:L666S5A672
A:L672S0S1A675
H:L673S5A674
E:L674S0S1A677
C:L675S5A676
R:L676S0S1A679
N:L677S5A678
E:L678S0S1A681
A:L679S5A680
G:L680L681S0S1S5
A:L682S0S1A684
V:L682S5A683
S:L683S0S1A686
G:L684S5A685
K:L685S0S1A688
R:L686S5A687
V:L687S0S1A690
S:L688S5A689
T:L689L690S0S1S5
E:L691S0S1A693
A:L691S5A692
K:L692S0S1A695
A:L693S5A694
H:L694S0S1A697
V:L695S5A696
V:L696S0S1A699
C:L697S5A698
W:L698S0S1A701
G:L699S5A700
K:L700S0S1A703
W:L701S5A702
A:L702S0S1A705
L:L703S5A704
Q:L704L705S0S1S5
E:L706S0S1A708
Y:L706S5A707
K:L707S0S1A710
V:L708S5A709
I:L709S0S1A712
M:L710S5A711
E:L711S0S1A714
G:L712S5A713
Q:L713S0S1A716
W:L714S5A715
D:L715S0S1A718
N:L716S5A717
M:L717S0S1A720
L:L718S5A719
M:L719S0S1A722
R:L720S5A721
E:L721S0S1A724
K:L722S5A723
E:L723S0S1A726
V:L724S5A725
V:L725S0S1A728
Q:L726S5A727
I:L727S0S1A730
Y:L728S5A729
K:L729S0S1A732
F:L730S5A731
T:L731S0S1A734
L:L732S5A733
R:L733S0A736
L:L733S1A737
M:L734S5A735
P:L735L736S0S1A739
A:L737S5A738
L:L738S0S1A741
K:L739S5A740
Q:L740S0S1A743
R:L741S5A742
S:L742S0S1A745
P:L743S5A744
K:L744S0S1A747
A:L745S5A746
V:L746L747S0S1S5
L:L748S0S1A750
Y:L748S5A749
L:L749S0S1A752
I:L750S5A751
Y:L751S0S1A754
D:L752S5A753
A:L753S0S1A756
E:L754S5A755
I:L755S0S1A758
E:L756S5A757
V:L757S0S1A760
A:L758S5A759
L:L759L760S0S1S5
L:L761S0S1A763
A:L761S5A762
D:L762S0S1A765
R:L763S5A764
E:L764S0S1A767
A:L765S5A766
N:L766S0S1A769
Q:L767S5A768
G:L768S0S1A771
E:L769S5A770
D:L770L771S0S1S5
L:L772S0S1A774
F:L772S5A773
P:L773S0S1A776
F:L774S5A775
A:L775S0S1A778
Q:L776S5A777
N:L777S0S1A780
K:L778S5A779
T:L779S0S1A782
F:L780S5A781
G:L781L782S0S1S5
D:L783S0S1A785
K:L783S5A784
V:L784L785S0S1S5
Y:L786S0S1A788
R:L786S5A787
A:L787S0S1A790
S:L788S5A789
V:L789S0S1A792
S:L790S5A791
Y:L791S0S1A794
V:L792S5A793
R:L793S0S1A796
C:L794S5A795
E:L795S0S1A798
S:L796S5A797
L:L797L798S0S1S5
C:L799S0S1
E:L800S0S1
Y:L801S0S1
I:L802S0S1
D:L803S0S1
L:L804S0S1
E:L805S0S1
P:L806S0S1
L:L807S0S1
T:L808S0S1
Q:L809S0S1
R:L810S0S1
R:L811S0S1
I:L812S0S1
S:L813S0S1
D:L814S0S1
L:L815S0S1
I:L816S0S1
N:L817S0S1
E:L818S0S1
L:L819S0S1
D:L820S0S1
M:L821S0S1
L:L822S0S1
G:L823S0S1
I:L824S0S1
I:L825S0S1
N:L826S0S1
A:L827S0S1
K:L828S0S1
V:L829S0S1
V:L830S0S1
S:L831S0S1
K:L832S0S1
G:L833S0S1
R:L834S0S1
Y:L835S0S1
G:L836S0S1
R:L837S0S1
T:L838S0S1
K:L839S0S1
E:L840S0S1
I:L841S0S1
R:L842S0S1
L:L843S0S1
N:L844S0A846
M:L844S1A845
V:L845L846S0S1
T:L847S0S1
S:L848S0S1
Y:L849S0S1
K:L850S0S1
I:L851S0S1
R:L852S0S1
N:L853S0S1
V:L854S0S1
L:L855S0S1
R:L856S0S1
Y:L857S0S1
D:L858S0S1
Y:L859S0S1
S:L860S0S1
I:L861S0S1
Q:L862S0S1
P:L863S0S1
L:L864S0S1
L:L865S0S1
T:L866S0S1
I:L867S0S1
S:L868S0S1
L:L869S0S1
K:L870S0S1
S:L871S0S1
E:L872S0S1
Q:L873S0S1
R:L874S0S1
R:L875S0S1
L:L876S0S1
I:L877S0S1
BioPerl-1.007002/t/data/testaln.prodom000444000766000024      1105513155576321 17606 0ustar00cjfieldsstaff000000000000ID   1184 p2000.1                           57 seq.
AC   PD001000
KW   CB21(6) CB22(5) CB23(3)  // CHLOROPHYLL PROTEIN PRECURSOR BINDING PHOTOSYSTEM II TRANSIT PEPTIDE I TYPE 
LA   36
AL P04777|CB21_ARATH       1    33 0.59 MAASTMALSSPA-FAGKAVNLS--PAASEVLGSGRV
AL P04778|CB22_ARATH       1    33 0.59 MAASTMALSSPA-FAGKAVKLS--PAASEVLGSGRV
AL P13851|CB21_SINAL       1    33 0.77 MAASTMALSSPA-FAGKAVKLS--PGASEVFGTGRV
AL Q39142|Q39142_ARATH     1    33 0.77 MAASTMALSSPA-LTGKAVKLS--PAASEVFGTGRI
AL O22669|O22669_PANGI     1    33 0.91 MAASTMALSSPS-FAGMAVKVA--PSSSELFGSGRI
AL P92919|P92919_APIGR     1    33 0.91 MAASTMALSSPA-LAGKAVKVA--PSSSELFGNGRV
AL P04780|CB22_PETSP       1    32 0.70 MAAATMALSSST-FAGKVVKLS--PSSSEITGNGK.
AL Q41447|Q41447_SOLTU     1    32 0.70 MAAATMALSSST-FAGKAVKLS--PSSSEITGNGR.
AL P12469|CB23_NICPL       1    33 0.31 MAASTMALSSSS-FAGKAVKLS--PSSSEITGNGKV
AL O64446|O64446_NICSY     1    33 0.31 MAASTMALSSSS-FAGKAVKLS--PSSSEITGNGKV
AL P27496|CB25_TOBAC       1    33 0.38 MAAATMALSSSS-FAGKAVKLS--PSSSEITGNGKV
AL O64450|O64450_NICSY     1    33 0.45 MAASTMALSSSS-FVGKAVKLS--PSSSEITGNGKV
AL P27495|CB24_TOBAC       1    33 0.49 MAASTMALSSPS-FAGKAVKLS--PSSSEITGNGKV
AL P04781|CB23_PETSP       1    33 0.63 MAATTMALSSSS-FAGKAVKLS--SSSSEITGNGKV
AL P07369|CB2G_LYCES       1    33 0.66 MATSTMALSSST-FAGKAVKLS--PSSSEITGNGRV
AL P04783|CB25_PETSP       1    32 0.80 MAAATMALSSPS-FAGKAVKFS--PSSSEITGNGK.
AL P27493|CB22_TOBAC       1    33 0.24 MAAATMALSSPS-FAGQAVKLS--PSAPEITGNGRV
AL O64444|O64444_NICSY     1    33 0.24 MAASTMALSSPS-FAGQAVKLS--PSAPEITGNGRV
AL O64442|O64442_NICSY     1    33 0.21 MAAATMALSSPS-FAGQAVKLS--PSASEITGNGRV
AL O64443|O64443_NICSY     1    33 0.21 MAAATMALSSPS-FAGQAVKLS--PSASEITGNGRV
AL Q41423|Q41423_SOLTU     1    33 0.21 MAAATMALSSPS-FAGQAVKLS--PSASEITGNGRI
AL O64445|O64445_NICSY     1    33 0.28 MAASTMALSSPS-FAGQAVKLS--PSASEITGNGRV
AL P07370|CB2B_LYCES       1    33 0.24 MAAATMALSSPS-FAGQAVKLS--PSASEISGNGRI
AL Q41421|Q41421_SOLTU     1    33 0.24 MAAATMALSSPS-FAGQAVKLS--PSASEISGNGRI
AL Q41422|Q41422_SOLTU     1    33 0.24 MAAATMALSSPS-FAGQAVKLS--PSASEISGNGRI
AL Q41425|Q41425_SOLTU     1    33 0.35 MAASTMALSSPS-FAGQAVKLS--PSASEISGNGRI
AL Q41424|Q41424_SOLTU     1    33 0.45 MAASTMALSSPS-FAGQAVKLS--PSTSEITGNGRI
AL P27491|CB27_TOBAC       1    32 0.59 MTASTMALSSPS-FAGNAVKLS--PSSSEITGNGK.
AL O64449|O64449_NICSY     1    32 0.59 MTASTMALSSPS-FAGNAVKLS--PSSSEITGNGK.
AL O64448|O64448_NICSY     1    33 0.98 MAAATMSLSSPS-FAGKAVKLS--PSSYEIIGNGKV
AL Q32291|Q32291_GOSHI     1    33 1.29 MASTTMALSSPS-FAGKAVKFS--PSTPEIQGTGRV
AL P12333|CB21_SPIOL       1    33 0.77 MASSTMALSSPS-LAGKAVKLG--PTASEIIGEGRI
AL O04686|O04686_MESCR     1    33 0.77 MASSTMALSSPS-LAGKMVKLA--PTASEILGEGRI
AL O04685|O04685_MESCR     1    33 0.84 MASSTMALSSPS-FAGKAVKLS--PTASETLGEGRI
AL O04687|O04687_MESCR     1    33 0.94 MASSAMALSSPS-LAGKAVKLN--PTTSQILGEGRI
AL Q40961|Q40961_PRUPE     1    33 1.29 MASSTMALSSPS-LAGQAVKLG--SSVSNIVGEGRI
AL P27492|CB21_TOBAC       1    32 0.80 MAASTTALSSP--FAGKAVKLS--PSSSEVTGNGKV
AL P12470|CB25_NICPL       1    32 0.80 MAASTTALSSP--FAGKAVKLS--PSSSEVTGNGKV
AL O64447|O64447_NICSY     1    32 1.11 MASSTMALSSS--FAGKAVKLS--PSSSEITGNGKV
AL Q40247|Q40247_LACSA     1    32 1.32 MAASTMALSSP--FAGQAVKTS--PSSSELFGNGRV
AL Q40185|Q40185_LEMGI     1    32 1.95 .MAASMALSSPS-LVGKAVKLA--PAASEVFGEGRV
AL P08963|CB22_HORVU       1    33 2.02 MAAATMALSSST-FAGKAVKNL--SSSSEVQGDARV
AL P04779|CB21_PETSP       1    32 1.57 MAAATMALSSSS-FAGKAVNV---PSSSEITRNGKV
AL P04782|CB24_PETSP       1    31 1.57 MAAATMAISSSS-FAGKAVNV---PSSSQITGNGK.
AL Q39141|Q39141_ARATH     1    31 2.19 MASSTMALSSPA-FAGKAVK----PAASDVLGSGRV
AL P09755|CB22_SOYBN       1    32 1.18 MAASTMALSSSS-LAGQAMKLA--PSTPEL-GVGRV
AL Q43437|Q43437_SOYBN     1    32 1.18 MAASTMALSSSS-LAGQAIKLA--PSTPEL-GVGRV
AL O48657|O48657_FAGCR     1    32 1.43 MAASTMALSSPS-LAGKAVKLA--PSTPEL-NVGRV
AL O81391|O81391_MEDSA     1    31 1.53 MAASSMALSSPT-LAGKPVKLT--PSSQEL-GAAR.
AL Q9ZP08|Q9ZP08_CICAR     1    31 1.53 MAASSMALSSPT-LAGKPVKLS--PSSQEL-GASR.
AL P09756|CB23_SOYBN       3    31 1.81 .AASSMALSSPS-LAGKAVKLG--PSAPEV-GRV..
AL Q39831|Q39831_SOYBN     3    31 1.81 .AASSMALSSPS-LAGKAVKLG--PSAPEV-GRV..
AL P04784|CB21_WHEAT       1    32 1.74 MAATTMSLSSSS-FAGKAVKNL--PSSA-LIGDARV
AL O24401|O24401_WHEAT     1    32 1.74 MAAATMSLSSST-FAGKAVKNV--PSLA-LLGEARV
AL Q40065|Q40065_HORVU     1    32 1.78 MAATTMYLSSST-FAGKAVKNV--PLSA-LFGEARV
AL P27490|CB28_PEA         1    31 3.34 MAASSMALSSPT-LTGKPVETSANPSSQELGG....
AL O24226|O24226_ORYSA     1    30 3.62 MAASTMALSSPAALAGKAV------ANAKVFGEGRV
CO                                      MAASTMALSSPS-FAGKAVKLS--PSSSEITGNGRV
//
BioPerl-1.007002/t/data/testaln.psi000444000766000024     20123113155576321 17116 0ustar00cjfieldsstaff000000000000               QUERY  MAWDMCNQDSESVWSDIECAALVGEDQPLCPDLPELDLSELDVNDLDTDS
         PRGC1_HUMAN   MAWDMCNQDSESVWSDIECAALVGEDQPLCPDLPELDLSELDVNDLDTDS
        Q4W5M7_HUMAN   MAWDMCNQDSESVWSDIECAALVGEDQPLCPDLPELDLSELDVNDLDTDS
        Q5RBY0_PONPY   MAWDMCNQDSESVWSDIECAALVGEDQPLCPDLPELDLSELDVNDLDTDS
           PRGC1_PIG   MAWDMCNQD--SVWTDIECAALVGEDQPLCPDLPELDLSELDVNDLDTDS
           PRGC1_RAT   MAWDMCSQD--SVWSDIECAALVGEDQPLCPDLPELDLSELDVNDLDTDS
         PRGC1_BOVIN   MAWDMCNQD--SVWSDIECAALVGEDQPLCPDLPELDLSELDVNDLDTDS
        Q4L229_BOVIN   MAWDMCNQD--SVWSDIECAALVGEDQPLCPDLPELDLSELDVNDLDTDS
         PRGC1_MOUSE   MAWDMCSQD--SVWSDIECAALVGEDQPLCPDLPELDLSELDVNDLDTDS
        Q3UP72_MOUSE   MAWDMCSQD--SVWSDIECAALVGEDQPLCPDLPELDLSELDVNDLDTDS
        Q60GU0_CHICK   MAWDMCNQD--SVWSDIECAALVGEDQPLCPDLPELDLSELDVNDLDADS
          Q5QHW4_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4R5X5_MACFA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q58FA1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3Y595_FUGRU   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG1_HUMAN   MAWDMCNQDSESVWSDIECAALVGEDQPLCPDLPELDLSELDVNDLDTDS
        Q3LIG2_MOUSE   MAWDMCSQD--SVWSDIECAALVGEDQPLCPDLPELDLSELDVNDLDTDS
        Q6R2I4_SPETR   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4SAM8_TETNG   MAWDRCNQD--SVWRELECAALVGEDQPLCPDLPELDLSELDVSDLDADS
          Q811R2_RAT   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSDFDSAT
        Q8TAL0_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8TDE4_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSDFDSAT
        Q8VHJ7_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSDFDSAT
        Q86YN5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSDFDSAT
        Q8N1N9_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSDFDSAT
        Q86YN3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSDFDSAT
        Q8TDE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSDFDSAT
        Q86YN6_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSDFDSAT
        Q86YN4_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSDFDSAT
        Q8C1C0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSDFDSPT
        Q76N31_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV66_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV67_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3U5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BZE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q91YW8_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3W1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NZN1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q80TW6_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW3_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4RQH2_TETNG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BUJ3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6VAC1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H3_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5U183_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NPA7_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM1_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IH74_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM0_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9VN24_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q7QA91_ANOGA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW5_PIG   MAWDMCNQD--SVWTDIECAALVGEDQPLCPDLPELDLSELDVNDLDTDS
        Q52MY8_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H2_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSDFDSVN
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

               QUERY  FLGGLKWCSDQSEIISNQYNNEPSNIFEKIDEENEANLLAVLTETLDSLP
         PRGC1_HUMAN   FLGGLKWCSDQSEIISNQYNNEPSNIFEKIDEENEANLLAVLTETLDSLP
        Q4W5M7_HUMAN   FLGGLKWCSDQSEIISNQYNNEPSNIFEKIDEENEANLLAVLTETLDSLP
        Q5RBY0_PONPY   FLGGLKWCSDQSEIISNQYNNEPSNIFEKIDEENEANLLAVLTETLDSLP
           PRGC1_PIG   FLGGLKWCSDQSEIISNQYNNEPSNIFEKIDEENEANLLAVLTETLDSLP
           PRGC1_RAT   FLGGLKWCSDQSEIISNQYNNEPANIFEKIDEENEANLLAVLTETLDSLP
         PRGC1_BOVIN   FLGGLKWCSDQSEIISNQYNNEPSNIFEKIDEENEANLLAVLTETLDSLP
        Q4L229_BOVIN   FLGGLKWCSDQSEIISNQYNNEPSNIFEKIDEENEANLLAVLTETLDSLP
         PRGC1_MOUSE   FLGGLKWCSDQSEIISNQYNNEPANIFEKIDEENEANLLAVLTETLDSLP
        Q3UP72_MOUSE   FLGGLKWCSDQSEIISNQYNNEPANIFEKIDEENEANLLAVLTETLDSLP
        Q60GU0_CHICK   FLGGLKWYSDQSEVISSQYSNEPANIFEKIDEENEANLLAVLTETLDSIP
          Q5QHW4_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4R5X5_MACFA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q58FA1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3Y595_FUGRU   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDEENEANLLAVLTETLDSIP
        Q3LIG1_HUMAN   FLGGLKWCSDQSEIISNQYNNEPSNIFEKIDEENEANLLAVLTETLDSLP
        Q3LIG2_MOUSE   FLGGLKWCSDQSEIISNQYNNEPANIFEKIDEENEANLLAVLTETLDSLP
        Q6R2I4_SPETR   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4SAM8_TETNG   FLGGLKWYSDQSEIISAQYGNEASNLFEKIDEENEANLLAVLTETLDSIP
          Q811R2_RAT   CFGELQWCPETSETEPSQYSPDDSEFFQ-IDSENEA-LLAALTKTLDDIP
        Q8TAL0_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8TDE4_HUMAN   CFGELQWCPENSETEPNQYSPDDSELFQ-IDSENEA-LLAELTKTLDDIP
        Q8VHJ7_MOUSE   CFGELQWCPETSETEPSQYSPDDSELFQ-IDSENEA-LLAALTKTLDDIP
        Q86YN5_HUMAN   CFGELQWCPENSETEPNQYSPDDSELFQ-IDSENEA-LLAELTKTLDDIP
        Q8N1N9_HUMAN   CFGELQWCPENSETEPNQYSPDDSELFQ-IDSENEA-LLAELTKTLDDIP
        Q86YN3_HUMAN   CFGELQWCPENSETEPNQYSPDDSELFQ-IDSENEA-LLAELTKTLDDIP
        Q8TDE5_HUMAN   CFGELQWCPENSETEPNQYSPDDSELFQ-IDSENEA-LLAELTKTLDDIP
        Q86YN6_HUMAN   CFGELQWCPENSETEPNQYSPDDSELFQ-IDSENEA-LLAELTKTLDDIP
        Q86YN4_HUMAN   CFGELQWCPENSETEPNQYSPDDSELFQ-IDSENEA-LLAELTKTLDDIP
        Q8C1C0_MOUSE   CFGELQWCPETSETEPSQYSPDDSELFQ-IDSENEA-LLAALTKTLDDIP
        Q76N31_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV66_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV67_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3U5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BZE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q91YW8_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3W1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NZN1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q80TW6_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW3_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4RQH2_TETNG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BUJ3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6VAC1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H3_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5U183_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NPA7_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM1_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IH74_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM0_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9VN24_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q7QA91_ANOGA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW5_PIG   FLGGLKWCSDQSEIISNQYNNEPSNIFEXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H2_BRARE   CLSELHWCNEQSDHSPAQYSAGDPELFE---EEN-AALLAALTDSLDGIV
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

               QUERY  VDEDGLPSFDALTDGDVTTDNEASPSSMPDGTPPPQEAEEPSLLKKLLLA
         PRGC1_HUMAN   VDEDGLPSFDALTDGDVTTDNEASPSSMPDGTPPPQEAEEPSLLKKLLLA
        Q4W5M7_HUMAN   VDEDGLPSFDALTDGDVTTDNEASPSSMPDGTPPPQEAEEPSLLKKLLLA
        Q5RBY0_PONPY   VDEDGLPSFDALTDGDVTTDNEASPSSMPDGTPPPQEAEEPSLLKKLLLA
           PRGC1_PIG   VDEDGLPSFDALTDGDVTTENEASPSSMPDGTPPPQEAEEPSLLKKLLLA
           PRGC1_RAT   VDEDGLPSFDALTDGDVTTDNEASPSSMPDGTPPPQEAEEPSLLKKLLLA
         PRGC1_BOVIN   VDEDGLPSFDALTDGDVTTENEASPSSMPDGTPPPQEAEEPSLLKKLLLA
        Q4L229_BOVIN   VDEDGLPSFDALTDGDVTTENEASPSSMPDGTPPPQEAEEPSLLKKLLLA
         PRGC1_MOUSE   VDEDGLPSFDALTDGAVTTDNEASPSSMPDGTPPPQEAEEPSLLKKLLLA
        Q3UP72_MOUSE   VDEDGLPSFDALTDGAVTTDNEASPSSMPDGTPPPQEAEEPSLLKKLLLA
        Q60GU0_CHICK   VDEDGLPSFDALTDGDVTNEHDASPSPMPDGTPPPQEAEEPSLLKKLLLA
          Q5QHW4_PIG   XXXXXXXXXDALTDGDVTTENEASPSSMPDGTPPPQEAEEPSLLKKLLLA
        Q4R5X5_MACFA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q58FA1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3Y595_FUGRU   VDEDGLPSFEALADGDVTNASDRSCPSSPDGSPRTPEPEEPSLLKKLLLA
        Q3LIG1_HUMAN   VDEDGLPSFDALTDGDVTTDNEASPSSMPDGTPPPQEAEEPSLLKKLLLA
        Q3LIG2_MOUSE   VDEDGLPSFDALTDGAVTTDNEASPSSMPDGTPPPQEAEEPSLLKKLLLA
        Q6R2I4_SPETR   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4SAM8_TETNG   VDEDGLPSFEALADGDVTNASDRSCPSSPGGSPRTPEPEEPSLLKKLLLA
          Q811R2_RAT   EDDVGLAAFPGLDEGDTPSCTPASPAPLSVPPSPASEVDELSLLQKLLLA
        Q8TAL0_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8TDE4_HUMAN   EDDVGLAAFPALDGGDALSCTAPPSPAPEKPSAPAPEVDELSL-------
        Q8VHJ7_MOUSE   EDDVGLAAFPELDEGDTPSCTAPPSPTLERLLSPASDVDELSLLQKLLLA
        Q86YN5_HUMAN   EDDVGLAAFPALDGGDALSCTAPPSPAPEKPSAPAPEVDELSLLQKLLLA
        Q8N1N9_HUMAN   EDDVGLAAFPALDGGDALSCTAPPSPAPEKPSAPAPEVDELSLLQKLLLA
        Q86YN3_HUMAN   EDDVGLAAFPALDGGDALSCTAPPSPAPEKPSAPAPEVDELSLLQKLLLA
        Q8TDE5_HUMAN   EDDVGLAAFPALDGGDALSCTAPPSPAPEKPSAPAPEVDELSLLQKLLLA
        Q86YN6_HUMAN   EDDVGLAAFPALDGGDALSCTAPPSPAPEKPSAPAPEVDELSLLQKLLLA
        Q86YN4_HUMAN   EDDVGLAAFPALDGGDALSCTAPPSPAPEKPSAPAPEVDELSLLQKLLLA
        Q8C1C0_MOUSE   EDDVGLAAFPELDEGDTPSCTAPPSPTLERLLSPASDVDELSLLQKLLLA
        Q76N31_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV66_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV67_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3U5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BZE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q91YW8_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3W1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NZN1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q80TW6_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW3_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4RQH2_TETNG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BUJ3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6VAC1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H3_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5U183_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NPA7_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM1_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IH74_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM0_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9VN24_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q7QA91_ANOGA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW5_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXA
        Q800H2_BRARE   EDGVGLSVFPSLGDEPEEGEEEEDDLPMESEPLPSPETEDPSLLKKLLLT
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

               QUERY  PANTQLSYNECSGLSTQNHANHNHRIRTNPAIVKTENSWSNKAKSICQQQ
         PRGC1_HUMAN   PANTQLSYNECSGLSTQNHANHNHRIRTNPAIVKTENSWSNKAKSICQQQ
        Q4W5M7_HUMAN   PANTQLSYNECSGLSTQNHANHNHRIRTNPAIVKTENSWSNKAKSICQQQ
        Q5RBY0_PONPY   PANTQLSYNECSGLSTQNHANHNHRIRTNPAIVKTENSWSNKAKSICQQQ
           PRGC1_PIG   PANTQLSYNECSGLSTQNHANHNHRIRTNPAVVKTENSWSNKAKSICQQQ
           PRGC1_RAT   PANTQLSYNECSGLSTQNHANHTHRIRTNPAIVKTENSWSNKAKSICQQQ
         PRGC1_BOVIN   PANTQLSYNECSGLSTQNHANHNHRIRTNPAVVKTENSWSNKAKSICQQQ
        Q4L229_BOVIN   PANTQLSYNECSGLSTQNHANHNHRIRTNPAVVKTENSWSNKAKSICQQQ
         PRGC1_MOUSE   PANTQLSYNECSGLSTQNHANHTHRIRTNPAIVKTENSWSNKAKSICQQQ
        Q3UP72_MOUSE   PANTQLSYNECSGLSTQNHANHTHRIRTNPAIVKTENSWSNKAKSICQQQ
        Q60GU0_CHICK   PANTQLNYNECSGLSTQNHANTNHRIRTSPVVVKTENSWSNKAKSICQQQ
          Q5QHW4_PIG   PANTQLSYNECSGLSTQNHANHNHRIRTNPAVVKTENSWSNKAKSICQQQ
        Q4R5X5_MACFA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q58FA1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3Y595_FUGRU   PANSQLSYNQYTGGQAQNHASSNHRIRPPPAVVKMESTWNGKARGSSQQN
        Q3LIG1_HUMAN   PANTQLSYNECSGLSTQNHANHNHRIRTNPAIVKTENSWSNKAKSICQQQ
        Q3LIG2_MOUSE   PANTQLSYNECSGLSTQNHANHTHRIRTNPAIVKTENSWSNKAKSICQQQ
        Q6R2I4_SPETR   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4SAM8_TETNG   PANSQLSYNQYTGGKAQNHASSNHRIRPPPAVVKMESPWNGKSRGCSQQN
          Q811R2_RAT   TSSPTASSDALKDGATWSQTSLSS--RSQRPCVKVDGTQDKKTPML----
        Q8TAL0_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8TDE4_HUMAN   ----------------------------------ADSTQDKKAPMM----
        Q8VHJ7_MOUSE   TSSPTASSDALKDGATWSQTSLSS--RSQRPCVKVDGTQDKKTPTL----
        Q86YN5_HUMAN   T-----SYPTSSSDTQKEGTAWRQRSKSQRPCVKADSTQDKKAPMM----
        Q8N1N9_HUMAN   T-----SYPTSSSDTQKEGTAWRQRSKSQRPCVKADSTQDKKAPMM----
        Q86YN3_HUMAN   T-----SYPTSSSDTQKEGTAWRQRSKSQRPCVKADSTQDKKAPMM----
        Q8TDE5_HUMAN   T-----SYPTSSSDTQKEGTAWRQRSKSQRPCVKADSTQDKKAPMM----
        Q86YN6_HUMAN   T-----SYPTSSSDTQKEGTAWRQRSKSQRPCVKADSTQDKKAPMM----
        Q86YN4_HUMAN   T-----SYPTSSSDTQKEGTAWRQRSKSQRPCVKADSTQDKKAPMM----
        Q8C1C0_MOUSE   TSSPTASSDALKDGATWSQTSLSS--RSQRPCVKVDGTQDKKTPTL----
        Q76N31_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV66_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV67_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3U5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BZE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q91YW8_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3W1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NZN1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q80TW6_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW3_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4RQH2_TETNG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BUJ3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6VAC1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXWSNKAKSICQQQ
        Q800H3_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5U183_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NPA7_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM1_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IH74_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM0_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9VN24_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q7QA91_ANOGA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW5_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   PANSQLSYNQYPGGKAQNHAASNQRIRPAPSCIKTENPWNSKPRGAC-PN
        Q800H2_BRARE   PPNVPVGLESHKDSGVHRHSSRNQHVKPVRPVLKXXXXXXXXXXXXXXXX
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

               QUERY  KPQRRPCSELLKYLTTNDDPPHTKPTENRNSSRDKCTSKKKSHTQSQSQH
         PRGC1_HUMAN   KPQRRPCSELLKYLTTNDDPPHTKPTENRNSSRDKCTSKKKSHTQSQSQH
        Q4W5M7_HUMAN   KPQRRPCSELLKYLTTNDDPPHTKPTENRNSSRDKCTSKKKSHTQSQSQH
        Q5RBY0_PONPY   KPQRRPCSELLKYLTTNDDPPHTKPTENRNSSRDKCTSKKKSHTQSQSQH
           PRGC1_PIG   KPQRRPCSELLKYLTTNDDPPHTKPTETRNSSRDKCTSKKKAHTQSQSQH
           PRGC1_RAT   KPQRRPCSELLKYLTTNDDPPHTKPTENRNSSRDKCASKKKSHTQPQSQH
         PRGC1_BOVIN   KPQRRPCSELLKYLTTNDDPPHTKPTENRNSSRDKCTSKKKAHTQSQTQH
        Q4L229_BOVIN   KPQRRPCSELLKYLTTNDDPPHTKPTENRNSSRDKCTSKKKAHTQSQTQH
         PRGC1_MOUSE   KPQRRPCSELLKYLTTNDDPPHTKPTENRNSSRDKCASKKKSHTQPQSQH
        Q3UP72_MOUSE   KPQRRPCSELLKYLTTNDDPPHTKPTENRNSSRDKCASKKKSHTQPQSQH
        Q60GU0_CHICK   KPQRRPCSELLKYLTTNDDPPQTKPAENRNSSKEKCTSKRKPHLQSQTNH
          Q5QHW4_PIG   KPQRRPCSELLKYLTTNDDPPHTKPTETRNSSRDKCTSKKKAHTQSQSQH
        Q4R5X5_MACFA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q58FA1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3Y595_FUGRU   RPVRRHCTELLKYLTATDDILHAKNNDAKGTSRDKSGLGL ----------
        Q3LIG1_HUMAN   KPQRRPCSELLKYLTTNDDPPHTKPTENRNSSRDKCTSKKKSHTQSQSQH
        Q3LIG2_MOUSE   KPQRRPCSELLKYLTTNDDPPHTKPTENRNSSRDKCASKKKSHTQPQSQH
        Q6R2I4_SPETR   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4SAM8_TETNG   RPVRRHCTELLKYLTATDDILHPKASEAKGTSRDKS--------------
          Q811R2_RAT   RSQSRPCTELHKHLTSVLPCPRGKA-------------------------
        Q8TAL0_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8TDE4_HUMAN   QSQSRSCTELHKHLTSAQCCLQ----------------------------
        Q8VHJ7_MOUSE   RAQSRPCTELHKHLTSVLPCPRVKA-------------------------
        Q86YN5_HUMAN   QSQSRSCTELHKHLTSAQCCLQ----------------------------
        Q8N1N9_HUMAN   QSQSRSCTELHKHLTSAQCCLQ----------------------------
        Q86YN3_HUMAN   QSQSRSCTELHKHLTSAQCCLQ----------------------------
        Q8TDE5_HUMAN   QSQSRSCTELHKHLTSAQCCLQ----------------------------
        Q86YN6_HUMAN   QSQSRSCTELHKHLTSAQCCLQ----------------------------
        Q86YN4_HUMAN   QSQSRSCTELHKHLTSAQCCLQ----------------------------
        Q8C1C0_MOUSE   RAQSRPCTELHKHLTSVLPCPRVKA-------------------------
        Q76N31_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV66_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV67_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3U5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BZE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q91YW8_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3W1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NZN1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q80TW6_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW3_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4RQH2_TETNG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BUJ3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6VAC1_SHEEP   KPQRRPCSELLKYLTTNDDPPHTKPTENRNSSRDKCTSKKKAHTQSQTQH
        Q800H3_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5U183_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NPA7_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM1_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IH74_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM0_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9VN24_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q7QA91_ANOGA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW5_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   RSMRRPCTELLKYLTSSDEAFQTKAGEAKSTXXXXXXXXXXXXXXXXXXX
        Q800H2_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

               QUERY  LQAKPTTLSLPLTPESPNDPKGSPFENKTIERTLSVELSGTAGLTPPTTP
         PRGC1_HUMAN   LQAKPTTLSLPLTPESPNDPKGSPFENKTIERTLSVELSGTAGLTPPTTP
        Q4W5M7_HUMAN   LQAKPTTLSLPLTPESPNDPKGSPFENKTIERTLSVELSGTAGLTPPTTP
        Q5RBY0_PONPY   LQAKPTTLSLPLTPESPNDPKGSPFENKTIERTLSVELSGTAGLTPPTTP
           PRGC1_PIG   LQAKPTSLSLPLTPESPNDPKGSPFENKTIERTLSVELSGTAGLTPPTTP
           PRGC1_RAT   AQAKPTTLSLPLTPESPNDPKGSPFENKTIERTLSVELSGTAGLTPPTTP
         PRGC1_BOVIN   LQAKPTTLSLPLTPESPNDPKGSPFENKTIERTLSVELSGTAGLTPPTTP
        Q4L229_BOVIN   LQAKPTTLSLPLTPESPNDPKGSPFENKTIERTLSVELSGTAGLTPPTTP
         PRGC1_MOUSE   AQAKPTTLSLPLTPESPNDPKGSPFENKTIERTLSVELSGTAGLTPPTTP
        Q3UP72_MOUSE   AQAKPTTLSLPLTPESPNDPKGSPFENKTIERTLSVELSGTAGLTPPTTP
        Q60GU0_CHICK   LQAKPTSLSLPLTPESPNDPKGSPFENKTIEQTLSVELSGTAGLTPPTTP
          Q5QHW4_PIG   LQAKPTSLSLPLTPESPNDPKGSPFENKTIERTLSVELSGTAGLTPPTTP
        Q4R5X5_MACFA   XXAKPTTLSLPLTPESPNDPKGSPFENKTIERTLSVELSGTAGLTPPTTP
        Q58FA1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3Y595_FUGRU   --AKPTTLPLPLTPESPNDHKGSPFENKTIERTLSVEIAGTPGLTPPTTP
        Q3LIG1_HUMAN   LQAKPTTLSLPLTPESPNXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG2_MOUSE   AQAKPTTLSLPLTPESPNXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6R2I4_SPETR   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLSGTAGLTPPTTP
        Q4SAM8_TETNG   --AKPTTLPLPLTPESPNDHKGSPFENKAIERTLSVEIAGTP--DRRQPV
          Q811R2_RAT   ----PRCLMLAL---SQSDPLG----KKSFEESLTVELCGTAGLTPPTTP
        Q8TAL0_HUMAN   XXXXPRCLMLALSQSDPT------FGKKSFEQTLTVELCGTAGLTPPTTP
        Q8TDE4_HUMAN   ----PRCLMLALSQSDPT------FGKKSFEQTLTVELCGTAGLTPPTTP
        Q8VHJ7_MOUSE   -----RCLMLAL---SQSDSLG----KKSFEESLTVELCGTAGLTPPTTP
        Q86YN5_HUMAN   ----PRCLMLALSQSDPT------FGKKSFEQTLTVELCGTAGLTPPTTP
        Q8N1N9_HUMAN   ----PRCLMLALSQSDPT------FGKKSFEQTLTVELCGTAGLTPPTTP
        Q86YN3_HUMAN   ----PRCLMLALSQSDPT------FGKKSFEQTLTVELCGTAGLTPPTTP
        Q8TDE5_HUMAN   ----PRCLMLALSQSDPT------FGKKSFEQTLTVELCGTAGLTPPTTP
        Q86YN6_HUMAN   ----PRCLMLALSQSDPT------FGKKSFEQTLTVELCGTAGLTPPTTP
        Q86YN4_HUMAN   ----PRCLMLALSQSDPT------FGKKSFEQTLTVELCGTAGLTPPTTP
        Q8C1C0_MOUSE   -----RCLMLAL---SQSDSLG----RKSFEESLTVELCGTAGLTPPTTP
        Q76N31_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV66_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV67_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3U5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BZE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q91YW8_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3W1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NZN1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q80TW6_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW3_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4RQH2_TETNG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BUJ3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6VAC1_SHEEP   LQAKPTTLSLPLTPESPNDPKGSPFENKTIERTLSVELSGTAGLXXXXXX
        Q800H3_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXYANKPFEQTLCMELCGTAGLTPPTTP
        Q5U183_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NPA7_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM1_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IH74_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM0_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9VN24_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q7QA91_ANOGA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW5_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H2_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG0_MOUSE   XXXKPTTLSLPLTPESPNDPKGSPFENKTIERTLSVELSGXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

               QUERY  PHKANQDNPFRASPKLKSSCKTVVPPPSKKPRYSESSGTQGNNSTKKGPE
         PRGC1_HUMAN   PHKANQDNPFRASPKLKSSCKTVVPPPSKKPRYSESSGTQGNNSTKKGPE
        Q4W5M7_HUMAN   PHKANQDNPFRASPKLKSSCKTVVPPPSKKPRYSESSGTQGNNSTKKGPE
        Q5RBY0_PONPY   PHKANQDNPFRASPKLKSSCKTVVPPPSKKPRYSESSGTQGNNSTKKGPE
           PRGC1_PIG   PHKANQDNPFRASPKLKPPCKTVVPPPSKKTRYSESSGTHGNNSTKKGPE
           PRGC1_RAT   PHKANQDNPFKASPKLKPSCKTVVPPPTKRARYSECSGTQGSHSTKKGPE
         PRGC1_BOVIN   PHKANQDNPFRASPKLKPSCKTVVPPPSKKARYSESSCTQGSNSTKKGPE
        Q4L229_BOVIN   PHKANQDNPFRASPKLKPSCKTVVPPPSKKARYSESSCTQGSNSTKKGPE
         PRGC1_MOUSE   PHKANQDNPFKASPKLKPSCKTVVPPPTKRARYSECSGTQGSHSTKKGPE
        Q3UP72_MOUSE   PHKANQDNPFKASPKLKPSCKTVVPPPTKRARYSECSGTQGSHSTKKGPE
        Q60GU0_CHICK   PHKANQDNPFRTSPKPKSSCKTV-APPSKKPRYSESSGSQGNNPVKKGPE
          Q5QHW4_PIG   PHKANQDNPFRASPKLKPPCKTVVPPPSKKTRYSESSGTHGNNSTKKGPE
        Q4R5X5_MACFA   PHKANQDNPFRASPKPKSSCKTVVPPPSKKPRYSESSGTQGNNSTKKGPE
        Q58FA1_SHEEP   XHKANQDNPFRASPKLKPSCKTVVPPPAKKARYSESSGTQGSNSTKKGPE
        Q3Y595_FUGRU   PHKASQENPFKASLKTKLSSCSSSAFVCKRARLSESGPGAGGGPIRKGPE
        Q3LIG1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG2_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6R2I4_SPETR   PHKANQDNPFRASPKPKSSCKTVVPPPSKKARYSESSGTQGNNSTKKGPE
        Q4SAM8_TETNG   WNRFCGASRKRESQTFPKNQERVTAPACKRARLSEPGPAAPAPGARKGPE
          Q811R2_RAT   PYKPMEEDPFKQDTKHSPGQDTAPSLPSPETLQLTATPGASHKLPKRHPE
        Q8TAL0_HUMAN   PYKPTEEDPFKPDIKHSLGKEIALSLPSPEGLSLKATPGAAHKLPKKHPE
        Q8TDE4_HUMAN   PYKPTEEDPFKPDIKHSLGKEIALSLPSPEGLSLKATPGAAHKLPKKHPE
        Q8VHJ7_MOUSE   PYKPMEEDPFKPDTKLSPGQDTAPSLPSPEALPLTATPGASHKLPKRHPE
        Q86YN5_HUMAN   PYKPTEEDPFKPDIKHSLGKEIALSLPSPEGLSLKATPGAAHKLPKKHPE
        Q8N1N9_HUMAN   PYKPTEEDPFKPDIKHSLGKEIALSLPSPEGLSLKATPGAAHKLPKKHPE
        Q86YN3_HUMAN   PYKPTEEDPFKPDIKHSLGKEIALSLPSPEGLSLKATPGAAHKLPKKHPE
        Q8TDE5_HUMAN   PYKPTEEDPFKPDIKHSLGKEIALSLPSPEGLSLKATPGAAHKLPKKHPE
        Q86YN6_HUMAN   PYKPTEEDPFKPDIKHSLGKEIALSLPSPEGLSLKATPGAAHKLPKKHPE
        Q86YN4_HUMAN   PYKPTEEDPFKPDIKHSLGKEIALSLPSPEGLSLKATPGAAHKLPKKHPE
        Q8C1C0_MOUSE   PYKPMEEDPFKPDTKLSPGQDTAPSLPSPEALPLTATPGASHKLPKRHPE
        Q76N31_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV66_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV67_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3U5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BZE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q91YW8_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3W1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NZN1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q80TW6_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW3_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4RQH2_TETNG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BUJ3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6VAC1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H3_BRARE   PHKPVEDELFK---------------PDAKADLSTKSSCLMRANMRKLPE
        Q5U183_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NPA7_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM1_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IH74_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM0_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9VN24_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q7QA91_ANOGA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW5_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H2_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

               QUERY  QSELYAQLSKSSVLTGGHEERKTKRPSLRLFGDHDYCQSINSKTEILINI
         PRGC1_HUMAN   QSELYAQLSKSSVLTGGHEERKTKRPSLRLFGDHDYCQSINSKTEILINI
        Q4W5M7_HUMAN   QSELYAQLSKSSVLTGGHEERKTKRPSLRLFGDHDYCQSINSKTEILINI
        Q5RBY0_PONPY   QSELYAQLSKSSVLTGGHEERKTKRPSLRLFGDHDYCQSINSKTEILINI
           PRGC1_PIG   QSELYAQLSKTSALGGGHEERKARRPSLRLFGDHDYCQSINSKAEILINI
           PRGC1_RAT   QSELYAQLSKSSVLSRGHEERKTKRPSLRLFGDHDYCQSVNSKTDILINI
         PRGC1_BOVIN   QSELYAQLSKTSVLTSGHEERKAKRPSLRLFGDHDYCQSINSKTEILVST
        Q4L229_BOVIN   QSELYAQLSKTSVLTSGHEERKAKRPSLRLFGDHDYCQSINSKTEILVST
         PRGC1_MOUSE   QSELYAQLSKSSGLSRGHEERKTKRPSLRLFGDHDYCQSLNSKTDILINI
        Q3UP72_MOUSE   QSELYAQLSKSSGLSRGHEERKTKRPSLRLFGDHDYCQSLNSKTDILINI
        Q60GU0_CHICK   QTELYAQLSKTTALSSGHEERKTKRPSLRLFGDHDYCQSVNSKSEIHIKI
          Q5QHW4_PIG   QSELYAQLSKTSALGGGHEERKARRPSLRLFGDHDYCQSINSKAEILINI
        Q4R5X5_MACFA   QSELYAQLSKSTVLTGGHEERKTKRHSLRLFGDHDYCQSINSKTEILIHI
        Q58FA1_SHEEP   QSESYAQLSKTSVLTSGHEERKAKRPSLRLFGDHDYCQSINSKTEILVSI
        Q3Y595_FUGRU   QTELYAQLSKASTALGGPEERRSKRAAPRGYSDHDYCQASAKKDSAALVP
        Q3LIG1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG2_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6R2I4_SPETR   QSELYAQLSKSSVPSSGHEERKAKRPSPRLFGDHDYCQSINSKTEILLHV
        Q4SAM8_TETNG   QTELYAQLSKASTARGHRSSGSSQRAASRRHSDHDYCQASAGKDSVTMTT
          Q811R2_RAT   RSELLSHLQHAT--TQPVSQAGQKRPFSCSFGDHDYCQVIRPEAAL----
        Q8TAL0_HUMAN   RSELLSHLRHATAQPA--SQAGQKRPFSCSFGDHDYCQVLRPEGVL----
        Q8TDE4_HUMAN   RSELLSHLRHATAQPA--SQAGQKRPFSCSFGDHDYCQVLRPEGVL----
        Q8VHJ7_MOUSE   RSELLSHLQHAT--TQPVSQAGQKRPFSCSFGDHDYCQVLRPEAAL----
        Q86YN5_HUMAN   RSELLSHLRHATAQPA--SQAGQKRPFSCSFGDHDYCQVLRPEGVL----
        Q8N1N9_HUMAN   RSELLSHLRHATAQPA--SQAGQKRPFSCSFGDHDYCQVLRPEGVL----
        Q86YN3_HUMAN   RSELLSHLRHATAQPA--SQAGQKRPFSCSFGDHDYCQVLRPEGVL----
        Q8TDE5_HUMAN   RSELLSHLRHATAQPA--SQAGQKRPFSCSFGDHDYCQVLRPEGVL----
        Q86YN6_HUMAN   RSELLSHLRHATAQPA--SQAGQKRPFSCSFGDHDYCQVLRPEGVL----
        Q86YN4_HUMAN   RSELLSHLRHATAQPA--SQAGQKRPFSCSFGDHDYCQVLRPEGVL----
        Q8C1C0_MOUSE   RSELLSHLQHAT--TQPVSQAGQKRPFSCSFGDHDYCQVLRPEAAL----
        Q76N31_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV66_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV67_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3U5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BZE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q91YW8_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3W1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NZN1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q80TW6_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW3_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4RQH2_TETNG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BUJ3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6VAC1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H3_BRARE   QTELYAQLRR ----MGQTGDIDSKGGTQRAYGDHDYCLGESRKTTAVLNG
        Q5U183_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NPA7_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM1_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IH74_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM0_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9VN24_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q7QA91_ANOGA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW5_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H2_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

               QUERY  SQELQDSRQLENKDVSSDWQGQICSSTDSDQCYLRETLEASKQVSPCSTR
         PRGC1_HUMAN   SQELQDSRQLENKDVSSDWQGQICSSTDSDQCYLRETLEASKQVSPCSTR
        Q4W5M7_HUMAN   SQELQDSRQLENKDVSSDWQGQICSSTDSDQCYLRETLEASKQVSPCSTR
        Q5RBY0_PONPY   SQELQDSRQLENKDVSSDWQGQICSSTDSDQCYLRETLEASKQVSPCSTR
           PRGC1_PIG   SQELHDSRQLDSKDAASDWQRQMCSSTDSDQCYLTETSEASRQVSPGSAR
           PRGC1_RAT   SQELQDSRQLDFKDASCDWQGHICSSTDSSQCYLRETLEASKQVSPCSTR
         PRGC1_BOVIN   SQELHDSRQLENKDASSNGPGQIHSSTDSDPCYLRETAEVSRQVSPGSTR
        Q4L229_BOVIN   SQELHDSRQLENKDASSNGPGQIHSSTDSDPCYLRETAEVSRQVSPGSTR
         PRGC1_MOUSE   SQELQDSRQLDFKDASCDWQGHICSSTDSGQCYLRETLEASKQVSPCSTR
        Q3UP72_MOUSE   SQELQDSRQLDFKDASCDWQGHICSSTDSGQCYLRETLEASKQVSPCSTR
        Q60GU0_CHICK   SQELQDSRQLEFKDSSPGWQCQICSSLEQDQYFKKETLQTSKQGSQGNNR
          Q5QHW4_PIG   SQELHDSRQLDSKDAASDWQRQMCSSTDSDQCYLTETSEASRQVSPGSAR
        Q4R5X5_MACFA   SQELQDSRQLENKDVSSDWQGQICSSTDSDQCYLRETSEASKQVSPCSTR
        Q58FA1_SHEEP   SQELHDSRQLENKDASSNGPGQIHSSTDSDLCYLRETAEVSRQVSPGSTR
        Q3Y595_FUGRU   TVGRVEDGHVECKDSAMPPEQQDLSSVDGKAAPARPSGDDEDQLQTCASR
        Q3LIG1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG2_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6R2I4_SPETR   SQELPDSRQLDYKDASSAWQGQICSSTDSDQLYLRETLEASKQVSPCGTR
        Q4SAM8_TETNG   AAMTAEDGHVECKDLAMPPSSSSSSPPSSSPPPKASSGPSAEQQNPSSAR
          Q811R2_RAT   --QRKVLRSWEPIKVHLEDLAHQGATLPVETKTPRREADQNCDPTP-KDS
        Q8TAL0_HUMAN   --QRKVLRSWEPSGVHLDWPQQGAPWAEA- QAPGREEDRSCDAGAPPKDS
        Q8TDE4_HUMAN   --QRKVLRSWEPSGVHLDWPQQGAPWAEA- QAPGREEDRSCDAGAPPKDS
        Q8VHJ7_MOUSE   --QRKVLRSWEPIGVHLEDLAQQGAPLPTETKAPRR--EANQNCDPTKDS
        Q86YN5_HUMAN   --QRKVLRSWEPSGVHLDWPQQGAPWAEA- QAPGREEDRSCDAGAPPKDS
        Q8N1N9_HUMAN   --QRKVLRSWEPSGVHLDWPQQGAPWAEA- QAPGREEDRSCDAGAPPKDS
        Q86YN3_HUMAN   --QRKVLRSWEPSGVHLDWPQQGAPWAEA- QAPGREEDRSCDAGAPPKDS
        Q8TDE5_HUMAN   --QRKVLRSWEPSGVHLDWPQQGAPWAEA- QAPGREEDRSCDAGAPPKDS
        Q86YN6_HUMAN   --QRKVLRSWEPSGVHLDWPQQGAPWAEA- QAPGREEDRSCDAGAPPKDS
        Q86YN4_HUMAN   --QRKVLRSWEPSGVHLDWPQQGAPWAEA- QAPGREEDRSCDAGAPPKDS
        Q8C1C0_MOUSE   --QRKVLRSWEPIGVHLEDLAQQGAPLPTETKAPRR--EANQNCDPTKDS
        Q76N31_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV66_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV67_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3U5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BZE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q91YW8_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3W1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NZN1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q80TW6_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW3_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4RQH2_TETNG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BUJ3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6VAC1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H3_BRARE   SQ------------------------------------------------
        Q5U183_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NPA7_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM1_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IH74_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM0_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9VN24_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q7QA91_ANOGA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW5_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H2_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

               QUERY  KQLQDQEIRAELNKHFGHPSQAVFDDEADKTGELRDSDFSNEQFSKLPMF
         PRGC1_HUMAN   KQLQDQEIRAELNKHFGHPSQAVFDDEADKTGELRDSDFSNEQFSKLPMF
        Q4W5M7_HUMAN   KQLQDQEIRAELNKHFGHPSQAVFDDEADKTGELRDSDFSNEQFSKLPMF
        Q5RBY0_PONPY   KQLQDQEIRAELDKHFGHPSQAVFDDEADKTSELRDSDFSNEQFSKLPMF
           PRGC1_PIG   KQLQDQEIRAELNKHFGHPSQAVFDDEADKTSELRDSDFSNEQFSKLPMF
           PRGC1_RAT   KQLQDQEIRAELNKHFGHPSQAVFDDKVDKTSELRDGNFSNEQFSKLPVF
         PRGC1_BOVIN   KQLQDQEIRAELNKHFGHPSQAVFDDKADKTSELRDSDFSNEQFSKLPMF
        Q4L229_BOVIN   KQLQDQEIRAELNKHFGHPSQAVFDDKADKTSELRDSDFSNEQFSKLPMF
         PRGC1_MOUSE   KQLQDQEIRAELNKHFGHPCQAVFDDKSDKTSELRDGDFSNEQFSKLPVF
        Q3UP72_MOUSE   KQLQDQEIRAELNKHFGHPCQAVFDDKSDKTSELRDGDFSNEQFSKLPVF
        Q60GU0_CHICK   KQLQDQEIRAELNKHFGHPSQAVFDEEADKTGELRDSDYSNEQFSKLPMF
          Q5QHW4_PIG   KQLQDQEIRAELNKHFGHPSQAVFDDEADKTSELRDSDFSNEQFSKLPMF
        Q4R5X5_MACFA   KQLQDQEIRAELNKHFGHPSQAVFDDEADKTSELRDSDFSNEQFSKLPMF
        Q58FA1_SHEEP   KQLQDQEIRAELNKHFGHPSQAVFDDKADRTSELRDSDFSNEQFSKLPMF
        Q3Y595_FUGRU   KLLRDNQIRAELNKHFGHPLQALYSQXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG2_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6R2I4_SPETR   KQLQDQEIRAELNKHFGHPSQAVFDDEADKTSELRDSDFSNEQFSKLPMF
        Q4SAM8_TETNG   KLLRDNEIRAELNKHFGPPLQALYSQGREPVGEGEDSYYPH----RLPSY
          Q811R2_RAT   MQLRDHEIRASLTKHFG---------------------------------
        Q8TAL0_HUMAN   TLLRDHEIRASLTKHFG---------------------------------
        Q8TDE4_HUMAN   TLLRDHEIRASLTKHFG---------------------------------
        Q8VHJ7_MOUSE   MQLRDHEIRASLTKHFG---------------------------------
        Q86YN5_HUMAN   TLLRDHEIRASLTKHFG---------------------------------
        Q8N1N9_HUMAN   TLLRDHEIRASLTKHFG---------------------------------
        Q86YN3_HUMAN   TLLRDHEIRASLTKHFG---------------------------------
        Q8TDE5_HUMAN   TLLRDHEIRASLTKHFG---------------------------------
        Q86YN6_HUMAN   TLLRDHEIRASLTKHFG---------------------------------
        Q86YN4_HUMAN   TLLRDHEIRASLTKHFG---------------------------------
        Q8C1C0_MOUSE   MQLRDHEIRASLTKHFG---------------------------------
        Q76N31_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV66_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV67_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3U5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BZE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q91YW8_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3W1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NZN1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q80TW6_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW3_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4RQH2_TETNG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BUJ3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6VAC1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H3_BRARE   --------------------------------------------------
        Q5U183_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NPA7_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM1_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IH74_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM0_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9VN24_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q7QA91_ANOGA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW5_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H2_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

               QUERY  INSGLAMDGLFDDSEDESDKLSYPWDGTQSYSLFNVSPSCSSFNSPCRDS
         PRGC1_HUMAN   INSGLAMDGLFDDSEDESDKLSYPWDGTQSYSLFNVSPSCSSFNSPCRDS
        Q4W5M7_HUMAN   INSGLAMDGLFDDSEDESDKLSYPWDGTQSYSLFNVSPSCSSFNSPCRDS
        Q5RBY0_PONPY   INSGLAMDGLFDDSEDESDKLSYPWDGTQSYSLFNVSPSCSSFNSPCRDS
           PRGC1_PIG   INSGLAMDGLFDDSEDESDKLNSPWDGTQSYSLFDVSPSCSSFNSPCRDS
           PRGC1_RAT   INSGLAMDGLFDDSEDENDKLSYPWDGTQSYSLFDVSPSCSSFNSPCRDS
         PRGC1_BOVIN   INSGLAMDGLFDDSEDESDKLNSPWDGTQSYSLFDVSPSCSSFNSPCRDS
        Q4L229_BOVIN   INSGLAMDGLFDDSEDESDKLNSPWDGTQSYSLFDVSPSCSSFNSPCRDS
         PRGC1_MOUSE   INSGLAMDGLFDDSEDESDKLSYPWDGTQPYSLFDVSPSCSSFNSPCRDS
        Q3UP72_MOUSE   INSGLAMDGLFDDSEDESDKLSYPWDGTQPYSLFDVSPSCSSFNSPCRDS
        Q60GU0_CHICK   INSGLAMDGLFDDSEDESDKLCYPWDGTQSYSLFDVSPSCSSFNSPCRDS
          Q5QHW4_PIG   INSGLAMDGLFDDSEDESDKLNSPWDGTQSYSLFDVSPSCSSFNSPCRDS
        Q4R5X5_MACFA   INSGLAMDGLFDDSEDESDKLSYPWDGTQSYSLFNVSPSCSSFNSPCRDS
        Q58FA1_SHEEP   INSGLAMDGLFDDSEDESDKLNSPWDGTQSYSLFDVSPSCSSFNSPCRDS
        Q3Y595_FUGRU   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG2_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6R2I4_SPETR   INSGLAMDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4SAM8_TETNG   LHPGLPFHEELELAQDREGRSLYPWEGTPLDLLFDRSPSCPSSCSPSRGS
          Q811R2_RAT   --------------------------------------------------
        Q8TAL0_HUMAN   --------------------------------------------------
        Q8TDE4_HUMAN   --------------------------------------------------
        Q8VHJ7_MOUSE   --------------------------------------------------
        Q86YN5_HUMAN   --------------------------------------------------
        Q8N1N9_HUMAN   --------------------------------------------------
        Q86YN3_HUMAN   --------------------------------------------------
        Q8TDE5_HUMAN   --------------------------------------------------
        Q86YN6_HUMAN   --------------------------------------------------
        Q86YN4_HUMAN   --------------------------------------------------
        Q8C1C0_MOUSE   --------------------------------------------------
        Q76N31_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV66_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV67_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3U5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BZE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q91YW8_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3W1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NZN1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q80TW6_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW3_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4RQH2_TETNG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BUJ3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6VAC1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H3_BRARE   --------------------------------------------------
        Q5U183_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NPA7_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM1_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IH74_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM0_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9VN24_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q7QA91_ANOGA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW5_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H2_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

               QUERY  VSPPKSLFSQRPQRMRSRSRSFSRHRSCSRSPYSRSRSRSPGSRSSSRSC
         PRGC1_HUMAN   VSPPKSLFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4W5M7_HUMAN   VSPPKSLFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5RBY0_PONPY   VSPPKSLFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           PRGC1_PIG   VSPPKSLFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           PRGC1_RAT   VSPPKSLF------------------------------------------
         PRGC1_BOVIN   VSPPKSLF------------------------------------------
        Q4L229_BOVIN   VSPPKSLF------------------------------------------
         PRGC1_MOUSE   VSPPKSLFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3UP72_MOUSE   VSPPKSLFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q60GU0_CHICK   VSPPKSLFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW4_PIG   VSPPKSLFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4R5X5_MACFA   VSPPKSLFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q58FA1_SHEEP   VSPPKSLFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3Y595_FUGRU   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG2_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6R2I4_SPETR   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4SAM8_TETNG   I-------------------------------------------------
          Q811R2_RAT   --------------------------------------------------
        Q8TAL0_HUMAN   --------------------------------------------------
        Q8TDE4_HUMAN   --------------------------------------------------
        Q8VHJ7_MOUSE   --------------------------------------------------
        Q86YN5_HUMAN   --------------------------------------------------
        Q8N1N9_HUMAN   --------------------------------------------------
        Q86YN3_HUMAN   --------------------------------------------------
        Q8TDE5_HUMAN   --------------------------------------------------
        Q86YN6_HUMAN   --------------------------------------------------
        Q86YN4_HUMAN   --------------------------------------------------
        Q8C1C0_MOUSE   --------------------------------------------------
        Q76N31_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV66_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV67_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3U5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BZE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q91YW8_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3W1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NZN1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q80TW6_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW3_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4RQH2_TETNG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BUJ3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6VAC1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H3_BRARE   --------------------------------------------------
        Q5U183_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NPA7_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM1_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IH74_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM0_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9VN24_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q7QA91_ANOGA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW5_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H2_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

               QUERY  YYYESSHYRHRTHRNSPLYVRSRSRSPYSRRPRYDSYEEYQHERLKREEY
         PRGC1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4W5M7_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5RBY0_PONPY   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           PRGC1_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           PRGC1_RAT   --------------------------------------------------
         PRGC1_BOVIN   -------------------------------------EEYQHERLKREEY
        Q4L229_BOVIN   -------------------------------------EEYQHERLKREEY
         PRGC1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3UP72_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q60GU0_CHICK   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW4_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4R5X5_MACFA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q58FA1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3Y595_FUGRU   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG2_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6R2I4_SPETR   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4SAM8_TETNG   --------------------------------------------------
          Q811R2_RAT   --------------------------------------------------
        Q8TAL0_HUMAN   --------------------------------------------------
        Q8TDE4_HUMAN   --------------------------------------------------
        Q8VHJ7_MOUSE   --------------------------------------------------
        Q86YN5_HUMAN   --------------------------------------------------
        Q8N1N9_HUMAN   --------------------------------------------------
        Q86YN3_HUMAN   --------------------------------------------------
        Q8TDE5_HUMAN   --------------------------------------------------
        Q86YN6_HUMAN   --------------------------------------------------
        Q86YN4_HUMAN   --------------------------------------------------
        Q8C1C0_MOUSE   --------------------------------------------------
        Q76N31_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV66_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5VV67_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3U5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BZE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q91YW8_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6P3W1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NZN1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q80TW6_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW3_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4RQH2_TETNG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9BUJ3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6VAC1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H3_BRARE   --------------------------------------------------
        Q5U183_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NPA7_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM1_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IH74_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM0_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9VN24_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q7QA91_ANOGA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW5_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H2_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

               QUERY  RREYEKRESERAKQRERQRQKAIEERRVIYVGKIRPDTTRTELRDRFEVF
         PRGC1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4W5M7_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5RBY0_PONPY   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           PRGC1_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           PRGC1_RAT   ---------------------------VIYVGKIRPDTTRTELRDRFEVF
         PRGC1_BOVIN   RREYEKRESERAKQRERQRQKAIEERRVIYVGKIRPDTTRTELRDRFEVF
        Q4L229_BOVIN   RREYEKRESERAKQRERQRQKAIEERRVIYVGKIRPDTTRTELRDRFEVF
         PRGC1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3UP72_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q60GU0_CHICK   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW4_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4R5X5_MACFA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q58FA1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3Y595_FUGRU   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG2_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6R2I4_SPETR   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4SAM8_TETNG   ---------------------------VVYVGRLRSDCTRTELKRRFEVF
          Q811R2_RAT   ---------------------------VVYIRNLSGDMSSRELKKRFEVF
        Q8TAL0_HUMAN   ---------------------------VVYIQNLSSDMSSRELKRRFEVF
        Q8TDE4_HUMAN   ---------------------------VVYIQNLSSDMSSRELKRRFEVF
        Q8VHJ7_MOUSE   ---------------------------VVYIRNLSSDMSSRELKKRFEVF
        Q86YN5_HUMAN   ---------------------------VVYIQNLSSDMSSRELKRRFEVF
        Q8N1N9_HUMAN   ---------------------------VVYIQNLSSDMSSRELKRRFEVF
        Q86YN3_HUMAN   ---------------------------VVYIQNLSSDMSSRELKRRFEVF
        Q8TDE5_HUMAN   ---------------------------VVYIQNLSSDMSSRELKRRFEVF
        Q86YN6_HUMAN   ---------------------------VVYIQNLSSDMSSRELKRRFEVF
        Q86YN4_HUMAN   ---------------------------VVYIQNLSSDMSSRELKRRFEVF
        Q8C1C0_MOUSE   ---------------------------VVYIRNLSSDMSSRELKKRFEVF
        Q76N31_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXVVFIGKIPGRMTRSELKQRFSVF
        Q5VV66_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXVVFIGKIPGRMTRSELKQRFSVF
        Q5VV67_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXVVFIGKIPGRMTRSELKQRFSVF
        Q6P3U5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXVVFIGKIPGRMTRSELKQRFSVF
        Q9BZE5_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXVVFIGKIPGRMTRSELKQRFSVF
        Q91YW8_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXVVFIGKIPGRMTRSELKQRFSVF
        Q6P3W1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXVVFIGKIPGRMTRSELKQRFSVF
        Q6NZN1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXVVFIGKIPGRMTRSELKQRFSVF
        Q80TW6_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXVVFIGKIPGRMTRSELKQRFSVF
          Q5QHW3_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXELRDRFEVF
        Q4RQH2_TETNG   XXXXXXXXXXXXXXXXXXXXXXXXXXXVVYVGRIRGTMTQKELGERFSLF
        Q9BUJ3_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXVVFIGKIPGRMTRSELKQRFSVF
        Q6VAC1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H3_BRARE   ---------------------------VIYIHNLPSSVTQTMLRKRFEAF
        Q5U183_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXIVYVGRIEQETTKEILRRKFLPY
        Q6NPA7_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXIVYVGRIEQETTKEILRRKFLPY
        Q8IPM1_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXIVYVGRIEQETTKEILRRKFLPY
        Q8IH74_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXIVYVGRIEQETTKEILRRKFLPY
        Q8IPM0_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXIVYVGRIEQETTKEILRRKFLPY
        Q9VN24_DROME   XXXXXXXXXXXXXXXXXXXXXXXXXXXIVYVGRIEQETTKEILRRKFLPY
        Q7QA91_ANOGA   XXXXXXXXXXXXXXXXXXXXXXXXXXXIVYVGRLESTTRKEDLQQKFQPY
          Q5QHW5_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H2_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXYIKHLPDDITDDRLREIFEPF

               QUERY  GEIEECTVNLRDDGDSYGFITYRYTCDAFAALENGYTLRRSNETDFELYF
         PRGC1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4W5M7_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5RBY0_PONPY   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           PRGC1_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           PRGC1_RAT   GEIEECTVNLRDDGDSYGFITYRYTCDAFAALENGYTLRRSNETDFELYF
         PRGC1_BOVIN   GEIEECTVNLRDDGDSYGFITYRYTCDAFAALENGYTLRRSNETDFELYF
        Q4L229_BOVIN   GEIEECTVNLRDDGDSYGFITYRYTCDAFAALENGYTLRRSNETDFELYF
         PRGC1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3UP72_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q60GU0_CHICK   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW4_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4R5X5_MACFA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q58FA1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3Y595_FUGRU   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG2_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6R2I4_SPETR   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4SAM8_TETNG   GEIEECAVNLRDDGDNFGFITYRYTCDAFAALENGHTLRRSDEPQFELCF
          Q811R2_RAT   GEIVECQVLRRKRGQKHGFITFRCSEHAALSVRNGATLRKRNEPSFHLSY
        Q8TAL0_HUMAN   GEIEECEVLTRNRGEKYGFITYRCSEHAALSLTKGAALRKRNEPSFQLSY
        Q8TDE4_HUMAN   GEIEECEVLTRNRGEKYGFITYRCSEHAALSLTKGAALRKRNEPSFQLSY
        Q8VHJ7_MOUSE   GEIVECQVLTRKRGQKHGFITFRCSEHAALSVRNGATLRKRNEPSFHLSY
        Q86YN5_HUMAN   GEIEECEVLTRNRGEKYGFITYRCSEHAALSLTKGAALRKRNEPSFQLSY
        Q8N1N9_HUMAN   GEIEECEVLTRNRGEKYGFITYRCSEHAALSLTKGAALRKRNEPSFQLSY
        Q86YN3_HUMAN   GEIEECEVLTRNRGEKYGFITYRCSEHAALSLTKGAALRKRNEPSFQLSY
        Q8TDE5_HUMAN   GEIEECEVLTRNRGEKYGFITYRCSEHAALSLTKGAALRKRNEPSFQLSY
        Q86YN6_HUMAN   GEIEECEVLTRNRGEKYGFITYRCSEHAALSLTKGAALRKRNEPSFQLSY
        Q86YN4_HUMAN   GEIEECEVLTRNRGEKYGFITYRCSEHAALSLTKGAALRKRNEPSFQLSY
        Q8C1C0_MOUSE   GEIVECQVLTRKRGQKHGFITFRCSEHAALSVRNGATLRKRNEPSFHLSY
        Q76N31_HUMAN   GEIEECTIHFRVQGDNYGFVTYRYAEEAFAAIESGHKLRQADEQPFDLCF
        Q5VV66_HUMAN   GEIEECTIHFRVQGDNYGFVTYRYAEEAFAAIESGHKLRQADEQPFDLCF
        Q5VV67_HUMAN   GEIEECTIHFRVQGDNYGFVTYRYAEEAFAAIESGHKLRQADEQPFDLCF
        Q6P3U5_HUMAN   GEIEECTIHFRVQGDNYGFVTYRYAEEAFAAIESGHKLRQADEQPFDLCF
        Q9BZE5_HUMAN   GEIEECTIHFRVQGDNYGFVTYRYAEEAFAAIESGHKLRQADEQPFDLCF
        Q91YW8_MOUSE   GEIEECTIHFRVQGDNYGFVTYRYAEEAFAAIESGHKLRQADEQPFDLCF
        Q6P3W1_HUMAN   GEIEECTIHFRVQGDNYGFVTYRYAEEAFAAIESGHKLRQADEQPFDLCF
        Q6NZN1_MOUSE   GEIEECTIHFRVQGDNYGFVTYRYAEEAFAAIESGHKLRQADEQPFDLCF
        Q80TW6_MOUSE   GEIEECTIHFRVQGDNYGFVTYRYAEEAFAAIESGHKLRQADEQPFDLCF
          Q5QHW3_PIG   GEIEECTVNLRDDGDSYGFITYRYTCDAFAALENGYTLRRSNETDFELYF
        Q4RQH2_TETNG   GEIEDCTLHFRNHGDNYGFVTYYDTKDAFAAIENGSKLRKPDELPFDLCF
        Q9BUJ3_HUMAN   GEIEECTIHFRVQGDNYGFVTYRYAEEAFAAIESGHKLRQADEQPFDLCF
        Q6VAC1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H3_BRARE   GHPEDCKVVIKKE-ERCGVITLRHTQ-------NGQTSRHRWDLLGPSGG
        Q5U183_DROME   GSIKQITIHYKENGMKYGFVTYERAQDAFTAIDTSH--RDSQISMYDISF
        Q6NPA7_DROME   GSIKQITIHYKENGMKYGFVTYERAQDAFTAIDTSH--RDSQISMYDISF
        Q8IPM1_DROME   GSIKQITIHYKENGMKYGFVTYERAQDAFTAIDTSH--RDSQISMYDISF
        Q8IH74_DROME   GSIKQITIHYKENGMKYGFVTYERAQDAFTAIDTSH--RDSQISMYDISF
        Q8IPM0_DROME   GSIKQITIHYKENGMKYGFVTYERAQDAFTAIDTSH--RDSQISMYDISF
        Q9VN24_DROME   GSIKQITIHYKENGMKYGFVTYERAQDAFTAIDTSH--RDSQISMYDISF
        Q7QA91_ANOGA   GKIVKITLHMKANGSRYGFVTFEKPQHAYDAIDARGT--DPNLRNYDVSF
          Q5QHW5_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H2_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   GKITSCAIMKEPNGKGFAFVCFEDKQHASAALRNGHPLEHSAKPLYXXXX

               QUERY  CGRKQFFKSNYADLDSNSDDFDPASTKSKYDSLDFDSLLKEAQRSLRR
         PRGC1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4W5M7_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q5RBY0_PONPY   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           PRGC1_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           PRGC1_RAT   CGRKQFFKSNYADLDSNSDDFDPASTKSKYDSLDFDSLLKEAQRSLRR
         PRGC1_BOVIN   CGRKQFFKSNYADLDSNSDDFDPACIKSKYDSLDFDSLLKEAQRSLRR
        Q4L229_BOVIN   CGRKQFFKSNYADLDSNSDDFDPACIKSKYDSLDFDSLLKEAQRSLRR
         PRGC1_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3UP72_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q60GU0_CHICK   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW4_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4R5X5_MACFA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q58FA1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3Y595_FUGRU   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG1_HUMAN   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG2_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6R2I4_SPETR   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4SAM8_TETNG   GGQKQFCKSHYADLDSHSDDFDPASTKSKYGSLDFDSLLREAQRSLRX
          Q811R2_RAT   GGLRHFRWPRYTDYDPTSEESLPSSGKSKYEAMDFDSLLKEAQQSLHX
        Q8TAL0_HUMAN   GGLRHLGWPRYTDYXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8TDE4_HUMAN   GGLRHFCWPRYTDYDSNSEEALPASGKSKYEAMDFDSLLKEAQQSLHX
        Q8VHJ7_MOUSE   GGLRHFRWPRYTDYDPTSEESLPSSGKSKYEAMDFDSLLKEAQQSLHX
        Q86YN5_HUMAN   GGLRHFCWPRYTDYXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8N1N9_HUMAN   GGLRHFCWPRYTDYDSNSEEALPASGKSKYEAMDFDSLLKEAQQSLHX
        Q86YN3_HUMAN   GGLRHFCWPRYTDYXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8TDE5_HUMAN   GGLRHFCWPRYTDYDSNSEEALPASGKSKYEAMDFDSLLKEAQQSLHX
        Q86YN6_HUMAN   GGLRHFCWPRYTDYDSNSEEALPASGKSKYEAMDFDSLLKEAQQSLHX
        Q86YN4_HUMAN   GGLRHFCWPRYTDYDSNSEEALPASGKSKYEAMDFDSLLKEAQQSLHX
        Q8C1C0_MOUSE   GGLRHFRWPRYTDYDPTSEESLPSSGKSKYEAMDFDSLLKEAQQSLHX
        Q76N31_HUMAN   GGRRQFCKRSYSDLDSNREDFDPAPVKSKFDSLDFDTLLKQAQKNLRR
        Q5VV66_HUMAN   GGRRQFCKRSYSDLDSNREDFDPAPVKSKFDSLDFDTLLKQAQKNLRR
        Q5VV67_HUMAN   GGRRQFCKRSYSDLDSNREDFDPAPVKSKFDSLDFDTLLKQAQKNLRR
        Q6P3U5_HUMAN   GGRRQFCKRSYSDLDSNREDFDPAPVKSKFDSLDFDTLLKQAQKNLRR
        Q9BZE5_HUMAN   GGRRQFCKRSYSDLDSNREDFDPAPVKSKFDSLDFDTLLKQAQKNLRR
        Q91YW8_MOUSE   GGRRQFCKRSYSDLDSNREDFDPAPVKSKFDSLDFDTLLKQAQKNLRR
        Q6P3W1_HUMAN   GGRRQFCKRSYSDLDSNREDFDPAPVKSKFDSLDFDTLLKQAQKNLRR
        Q6NZN1_MOUSE   GGRRQFCKRSYSDLDSNREDFDPAPVKSKFDSLDFDTLLKQAQKNLRR
        Q80TW6_MOUSE   GGRRQFCKRSYSDLDSNREDFDPAPVKSKFDSLDFDTLLKQAQKNLRR
          Q5QHW3_PIG   CGRKQFFKSNYADLDSNSDDFDPASTKSKYDSLDFDSLLKEAQRSLRX
        Q4RQH2_TETNG   GGRRQFCQTSYADLDS-STEYEPFPAKGKFHALDFDTLLKQAQQNLKR
        Q9BUJ3_HUMAN   GGRRQFCKRSYSDLDSNREDFDPAPVRAXXXXXXXXXXXXXXXXXXXX
        Q6VAC1_SHEEP   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H3_BRARE   NGSRRFGRKRYIDLDEAG----PGPVKSKYDALDFDALLKEAQRSLHR
        Q5U183_DROME   GGRRAFCRSSYADLDNAGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q6NPA7_DROME   GGRRAFCRSSYADLDNAGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM1_DROME   GGRRAFCRSSYADLDNAGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IH74_DROME   GGRRAFCRSSYADLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q8IPM0_DROME   GGRRAFCRSSYADLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q9VN24_DROME   GGRRAFCRSSYADLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q7QA91_ANOGA   GGRRAFCRTQYADLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          Q5QHW5_PIG   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q52MY8_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q800H2_BRARE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q3LIG0_MOUSE   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
        Q4QA88_LEIMA   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
BioPerl-1.007002/t/data/testaln.selex000444000766000024      1133113155576321 17423 0ustar00cjfieldsstaff000000000000#=SQ HSFAU  1.00 - - 0..0:0 H.sapiens fau mRNA
#=SQ HSFAU1 1.00 - - 0..0:0 H.sapiens fau 1 gene

HSFAU  ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc
HSFAU1 ctaccattttccctctcgattctatatgtacactcgggacaagttctcct

HSFAU  gccaatatgcagctctttgtccgcgcccaggagctacacaccttcgaggt
HSFAU1 gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg

HSFAU  gaccggccaggaaacggtcgcccagatcaaggctcatgtagcctcactgg
HSFAU1 gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc

HSFAU  agggcattgccccggaagatcaagtcgtgctcctggcaggcgcgcccctg
HSFAU1 tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac

HSFAU  gaggatgaggccactctgggccagtgcggggtggaggccctgactaccct
HSFAU1 accggttctccatccccgcagcgtagcccggaacatggtagctgccatct

HSFAU  ggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
HSFAU1 ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgccccg

HSFAU  gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaag
HSFAU1 tcctgcgcgagctgctgcccaggcaggttcgccggtgcgagcgtaaaggg

HSFAU  aagaagaagaagacaggtcgggctaagcggcggatgcagtacaaccggcg
HSFAU1 gcggagctaggactgccttgggcggtacaaatagcagggaaccgcgcggt

HSFAU  ctttgtcaacgttgtgcccacctttggcaagaagaagggccccaatgcca
HSFAU1 cgctcagcagtgacgtgacacgcagcccacggtctgtactgacgcgccct

HSFAU  actcttaagtcttttgtaattctggctttctctaataaaaaagccactta
HSFAU1 cgcttcttcctctttctcgactccatcttcgcggtagctgggaccgccgt

HSFAU  gttcagtcaaaaaaaaaa                                
HSFAU1 tcaggtaagaatggggccttggctggatccgaagggcttgtagcaggttg

HSFAU                                                    
HSFAU1 gctgcggggtcagaaggcgcggggggaaccgaagaacggggcctgctccg

HSFAU                                                    
HSFAU1 tggccctgctccagtccctatccgaactccttgggaggcactggccttcc

HSFAU                                                    
HSFAU1 gcacgtgagccgccgcgaccaccatcccgtcgcgatcgtttctggaccgc

HSFAU                                                    
HSFAU1 tttccactcccaaatctcctttatcccagagcatttcttggcttctctta

HSFAU                                                    
HSFAU1 caagccgtcttttctttactcagtcgccaatatgcagctctttgtccgcg

HSFAU                                                    
HSFAU1 cccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcccag

HSFAU                                                    
HSFAU1 atcaaggtaaggctgcttggtgcgccctgggttccattttcttgtgctct

HSFAU                                                    
HSFAU1 tcactctcgcggcccgagggaacgcttacgagccttatctttccctgtag

HSFAU                                                    
HSFAU1 gctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgct

HSFAU                                                    
HSFAU1 cctggcaggcgcgcccctggaggatgaggccactctgggccagtgcgggg

HSFAU                                                    
HSFAU1 tggaggccctgactaccctggaagtagcaggccgcatgcttggaggtgag

HSFAU                                                    
HSFAU1 tgagagaggaatgttctttgaagtaccggtaagcgtctagtgagtgtggg

HSFAU                                                    
HSFAU1 gtgcatagtcctgacagctgagtgtcacacctatggtaatagagtacttc

HSFAU                                                    
HSFAU1 tcactgtcttcagttcagagtgattcttcctgtttacatccctcatgttg

HSFAU                                                    
HSFAU1 aacacagacgtccatgggagactgagccagagtgtagttgtatttcagtc

HSFAU                                                    
HSFAU1 acatcacgagatcctagtctggttatcagcttccacactaaaaattaggt

HSFAU                                                    
HSFAU1 cagaccaggccccaaagtgctctataaattagaagctggaagatcctgaa

HSFAU                                                    
HSFAU1 atgaaacttaagatttcaaggtcaaatatctgcaactttgttctcattac

HSFAU                                                    
HSFAU1 ctattgggcgcagcttctctttaaaggcttgaattgagaaaagaggggtt

HSFAU                                                    
HSFAU1 ctgctgggtggcaccttcttgctcttacctgctggtgccttcctttccca

HSFAU                                                    
HSFAU1 ctacaggtaaagtccatggttccctggcccgtgctggaaaagtgagaggt

HSFAU                                                    
HSFAU1 cagactcctaaggtgagtgagagtattagtggtcatggtgttaggacttt

HSFAU                                                    
HSFAU1 ttttcctttcacagctaaaccaagtccctgggctcttactcggtttgcct

HSFAU                                                    
HSFAU1 tctccctccctggagatgagcctgagggaagggatgctaggtgtggaaga

HSFAU                                                    
HSFAU1 caggaaccagggcctgattaaccttcccttctccaggtggccaaacagga

HSFAU                                                    
HSFAU1 gaagaagaagaagaagacaggtcgggctaagcggcggatgcagtacaacc

HSFAU                                                    
HSFAU1 ggcgctttgtcaacgttgtgcccacctttggcaagaagaagggccccaat

HSFAU                                                    
HSFAU1 gccaactcttaagtcttttgtaattctggctttctctaataaaaaagcca

HSFAU                                                    
HSFAU1 cttagttcagtcatcgcattgtttcatctttacttgcaaggcctcaggga

HSFAU                  
HSFAU1 gaggtgtgcttctcgg
BioPerl-1.007002/t/data/testaln.stockholm000444000766000024      4673113155576321 20322 0ustar00cjfieldsstaff000000000000# STOCKHOLM 1.0
#=GF ID   14-3-3
#=GF AC   PF00244
#=GF DE   14-3-3 proteins
#=GF AU   Finn RD
#=GF AL   Clustalw
#=GF SE   Prosite
#=GF GA   25 25
#=GF TC   35.40 35.40
#=GF NC   8.80 8.80
#=GF BM   hmmbuild -f HMM SEED
#=GF BM   hmmcalibrate --seed 0 HMM
#=GF RN   [1]
#=GF RM   95327195
#=GF RT   Structure of a 14-3-3 protein and implications for
#=GF RT   coordination of multiple signalling pathways. 
#=GF RA   Xiao B, Smerdon SJ, Jones DH, Dodson GG, Soneji Y, Aitken
#=GF RA   A, Gamblin SJ; 
#=GF RL   Nature 1995;376:188-191.
#=GF RN   [2]
#=GF RM   95327196
#=GF RT   Crystal structure of the zeta isoform of the 14-3-3
#=GF RT   protein. 
#=GF RA   Liu D, Bienkowska J, Petosa C, Collier RJ, Fu H, Liddington
#=GF RA   R; 
#=GF RL   Nature 1995;376:191-194.
#=GF RN   [3]
#=GF RM   96182649
#=GF RT   Interaction of 14-3-3 with signaling proteins is mediated
#=GF RT   by the recognition of phosphoserine. 
#=GF RA   Muslin AJ, Tanner JW, Allen PM, Shaw AS; 
#=GF RL   Cell 1996;84:889-897.
#=GF RN   [4]
#=GF RM   97424374
#=GF RT   The 14-3-3 protein binds its target proteins with a common
#=GF RT   site located towards the C-terminus. 
#=GF RA   Ichimura T, Ito M, Itagaki C, Takahashi M, Horigome T,
#=GF RA   Omata S, Ohno S, Isobe T 
#=GF RL   FEBS Lett 1997;413:273-276.
#=GF RN   [5]
#=GF RM   96394689
#=GF RT   Molecular evolution of the 14-3-3 protein family. 
#=GF RA   Wang W, Shakes DC 
#=GF RL   J Mol Evol 1996;43:384-398.
#=GF RN   [6]
#=GF RM   96300316
#=GF RT   Function of 14-3-3 proteins. 
#=GF RA   Jin DY, Lyu MS, Kozak CA, Jeang KT 
#=GF RL   Nature 1996;382:308-308.
#=GF DR   PROSITE; PDOC00633;
#=GF DR   SMART; 14_3_3;
#=GF DR   PRINTS; PR00305;
#=GF DR   SCOP; 1a4o; fa;
#=GF DR   INTERPRO; IPR000308;
#=GF SQ   16
#=GS 1433_LYCES/9-246  AC P93209
#=GS 1431_ENTHI/4-239  AC P42648
#=GS 1432_ENTHI/4-238  AC P42649
#=GS 1434_LYCES/6-243  AC P42652
#=GS 143B_VICFA/7-242  AC P42654
#=GS 1433_CAEEL/5-237  AC P41932
#=GS 143Z_DROME/6-239  AC P29310
#=GS 1433_XENLA/1-227  AC P29309
#=GS 143E_HUMAN/4-239  AC P42655
#=GS 143F_MOUSE/3-240  AC P11576
#=GS 143R_ARATH/7-245  AC P42647
#=GS 143S_HUMAN/3-238  AC P31947
#=GS 143T_HUMAN/3-236  AC P27348
#=GS BMH1_YEAST/4-240  AC P29311
#=GS RA24_SCHPO/6-241  AC P42656
#=GS RA25_SCHPO/5-240  AC P42657
1433_LYCES/9-246             REENVYMAKLADRAESDEEMVEFMEKVSNSLGS.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKICDGILKLLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFKTGAERKEAAESTLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDMQDDG
1434_LYCES/6-243             REENVYLAKLAEQAERYEEMIEFMEKVAKTADV.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVNTIKEYRSKIEADLSKICDGILSLLESNLIPSA..STAESKVFHLKMKGDYHRYLAEFKTGTERKEAAENTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAISELDTLGEESYKDSTLIMQLLRDNLTLWTSDNADDV
143R_ARATH/7-245             RDQYVYMAKLAEQAERYEEMVQFMEQLVTGATPAEELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NDEHVSLVKDYRSKVESELSSVCSGILKLLDSHLIPSA..GASESKVFYLKMKGDYHRYMAEFKSGDERKTAAEDTMLAYKAAQDIAAADMAPTHPIRLGLALNFSVFYYEILNSSDKACNMAKQAFEEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDYAGAD
143B_VICFA/7-242             RENFVYIAKLAEQAERYEEMVDSMKNVANLDV...ELTIEERNLLSVGYKNVIGARRASWRILSSIEQKEESKG.NDVNAKRIKEYRHKVETELSNICIDVMRVIDEHLIPSA..AAGESTVFYYKMKGDYYRYLAEFKTGNEKKEAGDQSMKAYESATTAAEAELPPTHPIRLGLALNFSVFYYEILNSPERACHLAKQAFDEAISELDTLNEESYKDSTLIMQLLRDNLTLWTSDIPEDG
143E_HUMAN/4-239             REDLVYQAKLAEQAERYDEMVESMKKVAGMDV...ELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKG.GEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAA..NTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDG
BMH1_YEAST/4-240             REDSVYLAKLAEQAERYEEMVENMKTVASSGQ...ELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKEKSEHQVELICSYRSKIETELTKISDDILSVLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFSSGDAREKATNASLEAYKTASEIATTELPPTHPIRLGLALNFSVFYYEIQNSPDKACHLAKQAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMSESG
RA24_SCHPO/6-241             REDAVYLAKLAEQAERYEGMVENMKSVASTDQ...ELTVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKG.NTAQVELIKEYRQKIEQELDTICQDILTVLEKHLIPNA..ASAESKVFYYKMKGDYYRYLAEFAVGEKRQHSADQSLEGYKAASEIATAELAPTHPIRLGLALNFSVFYYEILNSPDRACYLAKQAFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYSA
RA25_SCHPO/5-240             RENSVYLAKLAEQAERYEEMVENMKKVACSND...KLSVEERNLLSVAYKNIIGARRASWRIISSIEQKEESRG.NTRQAALIKEYRKKIEDELSDICHDVLSVLEKHLIPAA..TTGESKVFYYKMKGDYYRYLAEFTVGEVCKEAADSSLEAYKAASDIAVAELPPTDPMRLGLALNFSVFYYEILDSPESACHLAKQVFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYNQ
1431_ENTHI/4-239             REDCVYTAKLAEQSERYDEMVQCMKQVAEMEA...ELSIEERNLLSVAYKNVIGAKRASWRIISSLEQKEQAKG.NDKHVEIIKGYRAKIEKELSTCCDDVLKVIQENLLPKA..STSESKVFFKKMEGDYYRYFAEFTVDEKRKEVADKSLAAYTEATEISNAELAPTHPIRLGLALNFSVFYFEIMNDADKACQLAKQAFDDAIAKLDEVPENMYKDSTLIMQLLRDNLTLWTSDACDEE
1432_ENTHI/4-238             REDLVYLSKLAEQSERYEEMVQYMKQVAEMGT...ELSVEERNLISVAYKNVVGSRRASWRIISSLEQKEQAKG.NTQRVELIKTYRAKIEQELSQKCDDVLKIITEFLLKNS..TSIESKVFFKKMEGDYYRYYAEFTVDEKRKEVADKSLAAYQEATDTA.ASLVPTHPIRLGLALNFSVFYYQIMNDADKACQLAKEAFDEAIQKLDEVPEESYKESTLIMQLLRDNLTLWTSDMGDDE
1433_CAEEL/5-237             VEELVQRAKLAEQAERYDDMAAAMKKVTEQGQ...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...SEKKQQLAKEYRVKVEQELNDICQDVLKLLDEFLIVKA..GAAESKAFYLKMKGDYYRYLAEVAS.EDRAAVVEKSQKAYQEALDIAKDKMQPTHPIRLGLALNFSVFYYEILNTPEHACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDVGAED
143Z_DROME/6-239             KEELVQKAKLAEQSERYDDMAQAMKSVTETGV...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEA...SARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKA..SNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDE
1433_XENLA/1-227             .......AKLSEQAERYDDMAASMKAVTELGA...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...NDKRQQMAREYREKVETELQDICKDVLDLLDRFLVPNA..TPPESKVFYLKMKGDYYRYLSEVASGDSKQETVASSQQAYQEAFEISKSEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKSAFDEAIRELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGEE
143T_HUMAN/3-236             KTELIQKAKLAEQAERYDDMATCMKAVTEQGA...ELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDT...SDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEE
143F_MOUSE/3-240             REQLLQRARLAEQAERYDDMASAMKAVTELNE...PLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADG.NEKKLEKVKAYREKIEKELETVCNDVLALLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEHMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEE
143S_HUMAN/3-238             RASLIQKAKLAEQAERYEDMAAFMKGAVEKGE...ELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEG.SEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEA..GDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEE
//
# STOCKHOLM 1.0
#=GF ID   14-3-3
#=GF AC   PF00245
#=GF DE   14-3-3 proteins
#=GF AU   Finn RD
#=GF AL   Clustalw
#=GF SE   Prosite
#=GF GA   25 25
#=GF TC   35.40 35.40
#=GF NC   8.80 8.80
#=GF BM   hmmbuild -f HMM SEED
#=GF BM   hmmcalibrate --seed 0 HMM
#=GF RN   [1]
#=GF RM   95327195
#=GF RT   Structure of a 14-3-3 protein and implications for
#=GF RT   coordination of multiple signalling pathways. 
#=GF RA   Xiao B, Smerdon SJ, Jones DH, Dodson GG, Soneji Y, Aitken
#=GF RA   A, Gamblin SJ; 
#=GF RL   Nature 1995;376:188-191.
#=GF RN   [2]
#=GF RM   95327196
#=GF RT   Crystal structure of the zeta isoform of the 14-3-3
#=GF RT   protein. 
#=GF RA   Liu D, Bienkowska J, Petosa C, Collier RJ, Fu H, Liddington
#=GF RA   R; 
#=GF RL   Nature 1995;376:191-194.
#=GF RN   [3]
#=GF RM   96182649
#=GF RT   Interaction of 14-3-3 with signaling proteins is mediated
#=GF RT   by the recognition of phosphoserine. 
#=GF RA   Muslin AJ, Tanner JW, Allen PM, Shaw AS; 
#=GF RL   Cell 1996;84:889-897.
#=GF RN   [4]
#=GF RM   97424374
#=GF RT   The 14-3-3 protein binds its target proteins with a common
#=GF RT   site located towards the C-terminus. 
#=GF RA   Ichimura T, Ito M, Itagaki C, Takahashi M, Horigome T,
#=GF RA   Omata S, Ohno S, Isobe T 
#=GF RL   FEBS Lett 1997;413:273-276.
#=GF RN   [5]
#=GF RM   96394689
#=GF RT   Molecular evolution of the 14-3-3 protein family. 
#=GF RA   Wang W, Shakes DC 
#=GF RL   J Mol Evol 1996;43:384-398.
#=GF RN   [6]
#=GF RM   96300316
#=GF RT   Function of 14-3-3 proteins. 
#=GF RA   Jin DY, Lyu MS, Kozak CA, Jeang KT 
#=GF RL   Nature 1996;382:308-308.
#=GF DR   PROSITE; PDOC00633;
#=GF DR   SMART; 14_3_3;
#=GF DR   PRINTS; PR00305;
#=GF DR   SCOP; 1a4o; fa;
#=GF DR   INTERPRO; IPR000308;
#=GF SQ   16
#=GS 1433_LYCES/9-246  AC P93209
#=GS 1431_ENTHI/4-239  AC P42648
#=GS 1432_ENTHI/4-238  AC P42649
#=GS 1434_LYCES/6-243  AC P42652
#=GS 143B_VICFA/7-242  AC P42654
#=GS 1433_CAEEL/5-237  AC P41932
#=GS 143Z_DROME/6-239  AC P29310
#=GS 1433_XENLA/1-227  AC P29309
#=GS 143E_HUMAN/4-239  AC P42655
#=GS 143F_MOUSE/3-240  AC P11576
#=GS 143R_ARATH/7-245  AC P42647
#=GS 143S_HUMAN/3-238  AC P31947
#=GS 143T_HUMAN/3-236  AC P27348
#=GS BMH1_YEAST/4-240  AC P29311
#=GS RA24_SCHPO/6-241  AC P42656
#=GS RA25_SCHPO/5-240  AC P42657
1433_LYCES/9-246             REENVYMAKLADRAESDEEMVEFMEKVSNSLGS.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKICDGILKLLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFKTGAERKEAAESTLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDMQDDG
1434_LYCES/6-243             REENVYLAKLAEQAERYEEMIEFMEKVAKTADV.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVNTIKEYRSKIEADLSKICDGILSLLESNLIPSA..STAESKVFHLKMKGDYHRYLAEFKTGTERKEAAENTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAISELDTLGEESYKDSTLIMQLLRDNLTLWTSDNADDV
143R_ARATH/7-245             RDQYVYMAKLAEQAERYEEMVQFMEQLVTGATPAEELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NDEHVSLVKDYRSKVESELSSVCSGILKLLDSHLIPSA..GASESKVFYLKMKGDYHRYMAEFKSGDERKTAAEDTMLAYKAAQDIAAADMAPTHPIRLGLALNFSVFYYEILNSSDKACNMAKQAFEEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDYAGAD
143B_VICFA/7-242             RENFVYIAKLAEQAERYEEMVDSMKNVANLDV...ELTIEERNLLSVGYKNVIGARRASWRILSSIEQKEESKG.NDVNAKRIKEYRHKVETELSNICIDVMRVIDEHLIPSA..AAGESTVFYYKMKGDYYRYLAEFKTGNEKKEAGDQSMKAYESATTAAEAELPPTHPIRLGLALNFSVFYYEILNSPERACHLAKQAFDEAISELDTLNEESYKDSTLIMQLLRDNLTLWTSDIPEDG
143E_HUMAN/4-239             REDLVYQAKLAEQAERYDEMVESMKKVAGMDV...ELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKG.GEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAA..NTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDG
BMH1_YEAST/4-240             REDSVYLAKLAEQAERYEEMVENMKTVASSGQ...ELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKEKSEHQVELICSYRSKIETELTKISDDILSVLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFSSGDAREKATNASLEAYKTASEIATTELPPTHPIRLGLALNFSVFYYEIQNSPDKACHLAKQAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMSESG
RA24_SCHPO/6-241             REDAVYLAKLAEQAERYEGMVENMKSVASTDQ...ELTVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKG.NTAQVELIKEYRQKIEQELDTICQDILTVLEKHLIPNA..ASAESKVFYYKMKGDYYRYLAEFAVGEKRQHSADQSLEGYKAASEIATAELAPTHPIRLGLALNFSVFYYEILNSPDRACYLAKQAFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYSA
RA25_SCHPO/5-240             RENSVYLAKLAEQAERYEEMVENMKKVACSND...KLSVEERNLLSVAYKNIIGARRASWRIISSIEQKEESRG.NTRQAALIKEYRKKIEDELSDICHDVLSVLEKHLIPAA..TTGESKVFYYKMKGDYYRYLAEFTVGEVCKEAADSSLEAYKAASDIAVAELPPTDPMRLGLALNFSVFYYEILDSPESACHLAKQVFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYNQ
1431_ENTHI/4-239             REDCVYTAKLAEQSERYDEMVQCMKQVAEMEA...ELSIEERNLLSVAYKNVIGAKRASWRIISSLEQKEQAKG.NDKHVEIIKGYRAKIEKELSTCCDDVLKVIQENLLPKA..STSESKVFFKKMEGDYYRYFAEFTVDEKRKEVADKSLAAYTEATEISNAELAPTHPIRLGLALNFSVFYFEIMNDADKACQLAKQAFDDAIAKLDEVPENMYKDSTLIMQLLRDNLTLWTSDACDEE
1432_ENTHI/4-238             REDLVYLSKLAEQSERYEEMVQYMKQVAEMGT...ELSVEERNLISVAYKNVVGSRRASWRIISSLEQKEQAKG.NTQRVELIKTYRAKIEQELSQKCDDVLKIITEFLLKNS..TSIESKVFFKKMEGDYYRYYAEFTVDEKRKEVADKSLAAYQEATDTA.ASLVPTHPIRLGLALNFSVFYYQIMNDADKACQLAKEAFDEAIQKLDEVPEESYKESTLIMQLLRDNLTLWTSDMGDDE
1433_CAEEL/5-237             VEELVQRAKLAEQAERYDDMAAAMKKVTEQGQ...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...SEKKQQLAKEYRVKVEQELNDICQDVLKLLDEFLIVKA..GAAESKAFYLKMKGDYYRYLAEVAS.EDRAAVVEKSQKAYQEALDIAKDKMQPTHPIRLGLALNFSVFYYEILNTPEHACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDVGAED
143Z_DROME/6-239             KEELVQKAKLAEQSERYDDMAQAMKSVTETGV...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEA...SARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKA..SNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDE
1433_XENLA/1-227             .......AKLSEQAERYDDMAASMKAVTELGA...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...NDKRQQMAREYREKVETELQDICKDVLDLLDRFLVPNA..TPPESKVFYLKMKGDYYRYLSEVASGDSKQETVASSQQAYQEAFEISKSEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKSAFDEAIRELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGEE
143T_HUMAN/3-236             KTELIQKAKLAEQAERYDDMATCMKAVTEQGA...ELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDT...SDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEE
143F_MOUSE/3-240             REQLLQRARLAEQAERYDDMASAMKAVTELNE...PLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADG.NEKKLEKVKAYREKIEKELETVCNDVLALLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEHMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEE
143S_HUMAN/3-238             RASLIQKAKLAEQAERYEDMAAFMKGAVEKGE...ELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEG.SEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEA..GDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEE
//
# STOCKHOLM 1.0
#=GF ID   14-3-3
#=GF AC   PF00246
#=GF DE   14-3-3 proteins
#=GF AU   Finn RD
#=GF AL   Clustalw
#=GF SE   Prosite
#=GF GA   25 25
#=GF TC   35.40 35.40
#=GF NC   8.80 8.80
#=GF BM   hmmbuild -f HMM SEED
#=GF BM   hmmcalibrate --seed 0 HMM
#=GF RN   [1]
#=GF RM   95327195
#=GF RT   Structure of a 14-3-3 protein and implications for
#=GF RT   coordination of multiple signalling pathways. 
#=GF RA   Xiao B, Smerdon SJ, Jones DH, Dodson GG, Soneji Y, Aitken
#=GF RA   A, Gamblin SJ; 
#=GF RL   Nature 1995;376:188-191.
#=GF RN   [2]
#=GF RM   95327196
#=GF RT   Crystal structure of the zeta isoform of the 14-3-3
#=GF RT   protein. 
#=GF RA   Liu D, Bienkowska J, Petosa C, Collier RJ, Fu H, Liddington
#=GF RA   R; 
#=GF RL   Nature 1995;376:191-194.
#=GF RN   [3]
#=GF RM   96182649
#=GF RT   Interaction of 14-3-3 with signaling proteins is mediated
#=GF RT   by the recognition of phosphoserine. 
#=GF RA   Muslin AJ, Tanner JW, Allen PM, Shaw AS; 
#=GF RL   Cell 1996;84:889-897.
#=GF RN   [4]
#=GF RM   97424374
#=GF RT   The 14-3-3 protein binds its target proteins with a common
#=GF RT   site located towards the C-terminus. 
#=GF RA   Ichimura T, Ito M, Itagaki C, Takahashi M, Horigome T,
#=GF RA   Omata S, Ohno S, Isobe T 
#=GF RL   FEBS Lett 1997;413:273-276.
#=GF RN   [5]
#=GF RM   96394689
#=GF RT   Molecular evolution of the 14-3-3 protein family. 
#=GF RA   Wang W, Shakes DC 
#=GF RL   J Mol Evol 1996;43:384-398.
#=GF RN   [6]
#=GF RM   96300316
#=GF RT   Function of 14-3-3 proteins. 
#=GF RA   Jin DY, Lyu MS, Kozak CA, Jeang KT 
#=GF RL   Nature 1996;382:308-308.
#=GF DR   PROSITE; PDOC00633;
#=GF DR   SMART; 14_3_3;
#=GF DR   PRINTS; PR00305;
#=GF DR   SCOP; 1a4o; fa;
#=GF DR   INTERPRO; IPR000308;
#=GF SQ   16
#=GS 1433_LYCES/9-246  AC P93209
#=GS 1431_ENTHI/4-239  AC P42648
#=GS 1432_ENTHI/4-238  AC P42649
#=GS 1434_LYCES/6-243  AC P42652
#=GS 143B_VICFA/7-242  AC P42654
#=GS 1433_CAEEL/5-237  AC P41932
#=GS 143Z_DROME/6-239  AC P29310
#=GS 1433_XENLA/1-227  AC P29309
#=GS 143E_HUMAN/4-239  AC P42655
#=GS 143F_MOUSE/3-240  AC P11576
#=GS 143R_ARATH/7-245  AC P42647
#=GS 143S_HUMAN/3-238  AC P31947
#=GS 143T_HUMAN/3-236  AC P27348
#=GS BMH1_YEAST/4-240  AC P29311
#=GS RA24_SCHPO/6-241  AC P42656
#=GS RA25_SCHPO/5-240  AC P42657
1433_LYCES/9-246             REENVYMAKLADRAESDEEMVEFMEKVSNSLGS.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKICDGILKLLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFKTGAERKEAAESTLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDMQDDG
1434_LYCES/6-243             REENVYLAKLAEQAERYEEMIEFMEKVAKTADV.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVNTIKEYRSKIEADLSKICDGILSLLESNLIPSA..STAESKVFHLKMKGDYHRYLAEFKTGTERKEAAENTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAISELDTLGEESYKDSTLIMQLLRDNLTLWTSDNADDV
143R_ARATH/7-245             RDQYVYMAKLAEQAERYEEMVQFMEQLVTGATPAEELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NDEHVSLVKDYRSKVESELSSVCSGILKLLDSHLIPSA..GASESKVFYLKMKGDYHRYMAEFKSGDERKTAAEDTMLAYKAAQDIAAADMAPTHPIRLGLALNFSVFYYEILNSSDKACNMAKQAFEEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDYAGAD
143B_VICFA/7-242             RENFVYIAKLAEQAERYEEMVDSMKNVANLDV...ELTIEERNLLSVGYKNVIGARRASWRILSSIEQKEESKG.NDVNAKRIKEYRHKVETELSNICIDVMRVIDEHLIPSA..AAGESTVFYYKMKGDYYRYLAEFKTGNEKKEAGDQSMKAYESATTAAEAELPPTHPIRLGLALNFSVFYYEILNSPERACHLAKQAFDEAISELDTLNEESYKDSTLIMQLLRDNLTLWTSDIPEDG
143E_HUMAN/4-239             REDLVYQAKLAEQAERYDEMVESMKKVAGMDV...ELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKG.GEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAA..NTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDG
BMH1_YEAST/4-240             REDSVYLAKLAEQAERYEEMVENMKTVASSGQ...ELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKEKSEHQVELICSYRSKIETELTKISDDILSVLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFSSGDAREKATNASLEAYKTASEIATTELPPTHPIRLGLALNFSVFYYEIQNSPDKACHLAKQAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMSESG
RA24_SCHPO/6-241             REDAVYLAKLAEQAERYEGMVENMKSVASTDQ...ELTVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKG.NTAQVELIKEYRQKIEQELDTICQDILTVLEKHLIPNA..ASAESKVFYYKMKGDYYRYLAEFAVGEKRQHSADQSLEGYKAASEIATAELAPTHPIRLGLALNFSVFYYEILNSPDRACYLAKQAFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYSA
RA25_SCHPO/5-240             RENSVYLAKLAEQAERYEEMVENMKKVACSND...KLSVEERNLLSVAYKNIIGARRASWRIISSIEQKEESRG.NTRQAALIKEYRKKIEDELSDICHDVLSVLEKHLIPAA..TTGESKVFYYKMKGDYYRYLAEFTVGEVCKEAADSSLEAYKAASDIAVAELPPTDPMRLGLALNFSVFYYEILDSPESACHLAKQVFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYNQ
1431_ENTHI/4-239             REDCVYTAKLAEQSERYDEMVQCMKQVAEMEA...ELSIEERNLLSVAYKNVIGAKRASWRIISSLEQKEQAKG.NDKHVEIIKGYRAKIEKELSTCCDDVLKVIQENLLPKA..STSESKVFFKKMEGDYYRYFAEFTVDEKRKEVADKSLAAYTEATEISNAELAPTHPIRLGLALNFSVFYFEIMNDADKACQLAKQAFDDAIAKLDEVPENMYKDSTLIMQLLRDNLTLWTSDACDEE
1432_ENTHI/4-238             REDLVYLSKLAEQSERYEEMVQYMKQVAEMGT...ELSVEERNLISVAYKNVVGSRRASWRIISSLEQKEQAKG.NTQRVELIKTYRAKIEQELSQKCDDVLKIITEFLLKNS..TSIESKVFFKKMEGDYYRYYAEFTVDEKRKEVADKSLAAYQEATDTA.ASLVPTHPIRLGLALNFSVFYYQIMNDADKACQLAKEAFDEAIQKLDEVPEESYKESTLIMQLLRDNLTLWTSDMGDDE
1433_CAEEL/5-237             VEELVQRAKLAEQAERYDDMAAAMKKVTEQGQ...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...SEKKQQLAKEYRVKVEQELNDICQDVLKLLDEFLIVKA..GAAESKAFYLKMKGDYYRYLAEVAS.EDRAAVVEKSQKAYQEALDIAKDKMQPTHPIRLGLALNFSVFYYEILNTPEHACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDVGAED
143Z_DROME/6-239             KEELVQKAKLAEQSERYDDMAQAMKSVTETGV...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEA...SARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKA..SNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDE
1433_XENLA/1-227             .......AKLSEQAERYDDMAASMKAVTELGA...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...NDKRQQMAREYREKVETELQDICKDVLDLLDRFLVPNA..TPPESKVFYLKMKGDYYRYLSEVASGDSKQETVASSQQAYQEAFEISKSEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKSAFDEAIRELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGEE
143T_HUMAN/3-236             KTELIQKAKLAEQAERYDDMATCMKAVTEQGA...ELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDT...SDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEE
143F_MOUSE/3-240             REQLLQRARLAEQAERYDDMASAMKAVTELNE...PLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADG.NEKKLEKVKAYREKIEKELETVCNDVLALLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEHMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEE
143S_HUMAN/3-238             RASLIQKAKLAEQAERYEDMAAFMKGAVEKGE...ELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEG.SEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEA..GDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEE
//
BioPerl-1.007002/t/data/testaln.xmfa000444000766000024       422413155576321 17221 0ustar00cjfieldsstaff000000000000>1:1-598 + chrY
TCCAAGTCGGCTTTATGTTTGCTTCTGCCAGGCATTCTAGATGCCCCATGTCTAGGATCT
CTTTAGGCAGGAGAGAGGGTGATGGTGTAGGAGGACCCATTTCTTGGCTTGCAGATTCCA
ATAATAAAAAAGTCACAGATTTAAACCCCAAACTTTGATGAAATGCAGGTCTAGGGTTTT
AAAATATAATGAGAGTTAAATACTTTTGTATTTTCTTCATCCAGAGATGGGGCAAGCTTC
CTCATCTGCTCGTTCATGGGTGATTTATATTTTCCCCACTCCATCCTTTTCCTAAGGTAT
TTTTTTTTTAGGGACAATGGCTTTTTGCAGAGTACTCAGTTCCAGCTCCGGGGGCACCGG
TTGAGCCCTTACCGTCCTGCCCCTAAACATCCAGACCTCAAGTTAGAGAGGGGAGTAACA
TTTGGGGGGTGCCCACACCTAGGAGGACCAATCCTTCTGGTTTCCTTAGGGATGCAGGAA
TTTGGGGGGGGGGGGCTCAGTGCTAAAACCAGTAGAGTCCTGGGCAAACGAGTATGACTG
AAGATGCTTTGAACACCCTAGCGTTATGTCGATCGCATGCATCGTAGTGTCGCTGATG
>2:5000-5534 - chr17
TGCAGATTGGCCTT-TGTTTCGTTTTTC-AAGCGTT-TAAA--CGCCTTGCCTAAGAATC
TTTT--GCAGGGAAGGGGATAGTGAACTGGGAAAACCTGGCTCTTCCTTTCGAGATTCCA
GTAACAAACATGTCATAACTATAAACGCCAAACTTGG--AGAGCGCAGGAATGGAAGGTC
AAACACCAATGAGAGTTAGATGGTTTTGGGTTT----------------------GCT--
CTAGTCTGCACG-------GTGCTCCCCGTCCCCTCACGTCCGTGCTTTTCCTCAGGATG
ATGCCTTGCCAGAACACCGGTGTGCTGCAAGGTGCTCAGCTCCAAATCGGGCTGCACCGC
TTCAGCTTTCCCCATCCAGCCA--ACGCAGGAAGGCCTGGAGCTACAGAGTTTAGAGCCA
TCTCTCCGCTGCTCAT--------TAACCAACCATTCCAGCT-------GTCTGTAGTGG
GTTTTTTTCTT----CTCTACACTAAAATGAGGACAGTCCAGGCCCTTTG--TTAGACTG
AAGATGCTTTGAACACCCTAGCGTTATGTCGATCGCATGCATCGTAGTGTCGCTGATG
>3:19000-19537 - chr7
TCCAGACTGTCTTT-TGCTCCCTTTTTCCGAGCATT-TAAAAATACCATGCCTAAGAATC
TTTT--GCAGGGAAGGGGATAGCGAGCTGGGAAGGCCTATTTCTTCATTTCGAGATTCTG
GTAATAAACATGTCATAAATATAAATGCCAAACTCCG--GAAATGCAGGTGTAGAGCGTC
AGATTCTATTTGGACTTAAATGATGTGGTGTTTT---------------------GCT--
CTAATTTCTACC-------GTGCTCTCCGTTCC-TCAAGTCCATGCATTTCCTTAGGGTG
CTGCCTTTCCAGAGTACTGGTATGCTGCAGGGTGCTCAGTTCCACATCTGTCTGCACTAT
TTCAAAGTTTCCC-TCCAGCCC--ACACAACTATGCCTAGAGCTA--GAGGTTAGAACCG
TCTGTCCA-TGCTCTT--------TAACCAACCACTCCAGAT-------AGGTGTGGTGG
TTTTTTTTTTTTTTTCTCTGTACTAAAATTAGGACAGTCCAGGCCTGTTG--TTAGACCA
AAGATGCTTTGAACACCCTAGCGTTATGTCGATCGCATGCATCGTAGTGTCGCTGATG
= score = 111
>1:1000-1059 + chrY
CACTCTAATAGTAAAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCAT
>2:6000-6055 + chr17
CACTCTAATACTAAACTTTCTTTTCCTCTCCACA----CTTTACTTTAATTACATCCCAT
>3:20000-20055 - chr12
CACTCTAATAGTAAAGTTTCTT----TGTGCAGAAGCTCTTAGTTTTAATTAGATCCCAT
= score = 11
>TelAviv_01:1-9 + TelAviv_01
AAAAAAAAA
BioPerl-1.007002/t/data/testaln2.arp000444000766000024       220313155576321 17125 0ustar00cjfieldsstaff000000000000[Profile] 
 Title="An example of DNA sequence data" 
 NbSamples=3 
 GenotypicData=0 
 DataType=DNA 
 LocusSeparator=NONE 
[Data] 
 [[Samples]] 
  SampleName="Population 1" 
  SampleSize=6 
  SampleData= { 
 000 3 GACTCTCTACGTAGCATCCGATGACGATA 
 001 1 GACTGTCTGCGTAGCATACGACGACGATA 
 002 2 GCCTGTCTGCGTAGCATAGGATGACGATA 
  } 
  SampleName="Population 2" 
  SampleSize=8 
  SampleData= { 
 000 1 GACTCTCTACGTAGCATCCGATGACGATA 
 001 1 GACTGTCTGCGTAGCATACGACGACGATA 
 002 1 GCCTGTCTGCGTAGCATAGGATGACGATA 
 003 1 GCCTGTCTGCCTAGCATACGATCACGATA 
 004 1 GCCTGTCTGCGTACCATACGATGACGATA 
 005 1 GCCTGTCCGCGTAGCGTACGATGACGATA 
 006 1 GCCCGTGTGCGTAGCATACGATGGCGATA 
 007 1 GCCTGTCTGCGTAGCATGCGACGACGATA 
  } 
  SampleName="Population 3" 
  SampleSize=6 
  SampleData= { 
 023 1 GCCTGTCTGCGTAGCATACGATGACGGTA 
 024 1 GCCTGTCTGCGTAGCGTACGATGACGATA 
 025 1 GCCTGTCTGCGTAGCATACGATGACGATA 
 026 1 GCCTGTCCGCGTAGCATACGGTGACGGTA 
 027 1 GCCTGTCTGCGTGGCATACGATGACGATG 
 028 1 GCCTGTCTGCGTAGCATACGATGACGATA 
  } 
[[Structure]] 
  StructureName="A group of 3 populations analyzed for DNA" 
  NbGroups=1 
  Group= { 
   "Population 1" 
   "Population 2" 
   "Population 3" 
  } 
BioPerl-1.007002/t/data/testaln2.fasta000444000766000024      1430613155576321 17470 0ustar00cjfieldsstaff000000000000>AK1H_ECOLI/114-431 DESCRIPTION HERE
CPDSINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDPVEKLLAVG-HYLESTVDIAE
STRRIAASRIP------A-DHMVLMAGFTAGN-EKGELVVLGRNGSDYSAAVLAACLRAD
CCEIWTDVNGVYTCDP-------------RQVPDARLLKSMSYQEAMELSY--FGAKVLH
PRTITPIAQFQIPCLIKNTGNPQAPGTL-IG--ASRDEDELP----VKGISNLN------
NMAMFSVSGP-GMKGMVGMAARVFAAMS-------RARISVVLITQSSSEYSISFCVPQS
DCVRAERAMLEEFY-----LELKEGLLEPLAVAERLAIISV-VGDGLRTLRGISAKF---
---FAALARANINIVAIA
>AK1H_ECOLI_dup1 DESCRIPTION HERE
CPDSINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDPVEKLLAVG-HYLESTVDIAE
STRRIAASRIP------A-DHMVLMAGFTAGN-EKGELVVLGRNGSDYSAAVLAACLRAD
CCEIWTDVNGVYTCDP-------------RQVPDARLLKSMSYQEAMELSY--FGAKVLH
PRTITPIAQFQIPCLIKNTGNPQAPGTL-IG--ASRDEDELP----VKGISNLN------
NMAMFSVSGP-GMKGMVGMAARVFAAMS-------RARISVVLITQSSSEYSISFCVPQS
DCVRAERAMLEEFY-----LELKEGLLEPLAVAERLAIISV-VGDGLRTLRGISAKF---
---FAALARANINIVAIA
>AK1H_ECOLI_dup2 DESCRIPTION HERE
CPDSINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDPVEKLLAVG-HYLESTVDIAE
STRRIAASRIP------A-DHMVLMAGFTAGN-EKGELVVLGRNGSDYSAAVLAACLRAD
CCEIWTDVNGVYTCDP-------------RQVPDARLLKSMSYQEAMELSY--FGAKVLH
PRTITPIAQFQIPCLIKNTGNPQAPGTL-IG--ASRDEDELP----VKGISNLN------
NMAMFSVSGP-GMKGMVGMAARVFAAMS-------RARISVVLITQSSSEYSISFCVPQS
DCVRAERAMLEEFY-----LELKEGLLEPLAVAERLAIISV-VGDGLRTLRGISAKF---
---FAALARANINIVAIA
>AK1H_ECOLI_dup3_head_gap DESCRIPTION HERE
---SINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDPVEKLLAVG-HYLESTVDIAE
STRRIAASRIP------A-DHMVLMAGFTAGN-EKGELVVLGRNGSDYSAAVLAACLRAD
CCEIWTDVNGVYTCDP-------------RQVPDARLLKSMSYQEAMELSY--FGAKVLH
PRTITPIAQFQIPCLIKNTGNPQAPGTL-IG--ASRDEDELP----VKGISNLN------
NMAMFSVSGP-GMKGMVGMAARVFAAMS-------RARISVVLITQSSSEYSISFCVPQS
DCVRAERAMLEEFY-----LELKEGLLEPLAVAERLAIISV-VGDGLRTLRGISAKF---
---FAALARANINIV---
>AK1H_ECOLI_dup4_end_gap DESCRIPTION HERE
CPDSINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDPVEKLLAVG-HYLESTVDIAE
STRRIAASRIP------A-DHMVLMAGFTAGN-EKGELVVLGRNGSDYSAAVLAACLRAD
CCEIWTDVNGVYTCDP-------------RQVPDARLLKSMSYQEAMELSY--FGAKVLH
PRTITPIAQFQIPCLIKNTGNPQAPGTL-IG--ASRDEDELP----VKGISNLN------
NMAMFSVSGP-GMKGMVGMAARVFAAMS-------RARISVVLITQSSSEYSISFCVPQS
DCVRAERAMLEEFY-----LELKEGLLEPLAVAERLAIISV-VGDGLRTLRGISAKF---
---FAALARANINIV---
>AKH_HAEIN 114-431
-----------------VEDAVKATIDCRGEKLSIAMMKAWFEARGY-S--VHIVDPVKQ
LLAKG-GYLESSVEIEESTKRVDAANIA--K-DKVVLMAGF---TAGNEKGELVLLGRNG
SDYSAAC-----------------LAACLGASVCEIWTDVDGVYTCDP--RLVPDARLLP
TLSYREAMELSYFGAKVIHPRTIGPLLPQNIPCVIKNTGNPSAPGSI-ID--GNVKSESL
Q----VKGITNLDNLAMFNVSGPGMQGM---VGMASRVFSAMSGAGISVILITQSSSEYS
---ISFCVPVKSAEVAKTVLETEFA-----NELNEHQLEPIEVIKDLSIISV-VGDGMKQ
AKGIAARF------FSALAQANISIVAIA
>AKH1_MAIZE/117-440
-----------------ATESFSDFVVGHGELWSAQMLSYAIQKSGT-P--CSWMDTREV
LVVNPSGANQVDPDYLESEKRLEKWFSRC-P-AETIIATGF---IASTPENIPTTLKRDG
SDFSAAI-----------------IGSLVKARQVTIWTDVDGVFSADP--RKVSEAVILS
TLSYQEAWEMSYFGANVLHPRTIIPVMKYNIPIVIRNIFNTSAPGTM-IC--QQPANENG
DLEACVKAFATIDKLALVNVEGTGMAGV---PGTANAIFGAVKDVGANVIMISQASSEHS
---VCFAVPEKEVALVSAALHARFR-----EALAAGRLSKVEVIHNCSILAT-VGLRMAS
TPGVSATL------FDALAKANINVRAIA
>AK2H_ECOLI/112-431
-----------------INDAVYAEVVGHGEVWSARLMSAVLNQQG-----LPAAWLDAR
EFLRAERAAQPQVDEGLSYPLLQQLLVQH-P-GKRLVVTGF---ISRNNAGETVLLGRNG
SDYSATQ-----------------IGALAGVSRVTIWSDVAGVYSADP--RKVKDACLLP
LLRLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIERVLASGTGARI
VTSHDDVCLI-EFQVPASQDFKLAHKEI--DQILKRAQVRPLAVGVHNDRQLLQFCYTSE
VADSALKILDEAG---------LPGELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQ
PVEFTWQSDDGISLVAVL
>AK1_BACSU/66-374
-----------------ISPREQDLLLSCGETISSVVFTSMLLDNGVKA--AALTGAQAG
FLTNDQHTNAKIIEMKPER--LFSVLAN----HDAVVVAGF---QGATEKGDTTTIGRGG
SDTSAAA-----------------LGAAVDAEYIDIFTDVEGVMTADP--RVVENAKPLP
VVTYTEICNLAYQGAKVISPRAVEIAMQAKVPIRVRSTYS-NDKGTLVTSHHSSKVGSDV
FERLITGIAH-VKDVTQFKVPAKIGQYN-----VQTEVFKAMANAGISVDFFNITPSEIV
YTVAGNKTETAQR------------ILMDMGYDPMVTRNCAKVSAVGAGIMGVPGVTSKI
------VSALSEKEIPILQSA
>AK2_BACST/63-370
-----------------KRE--MDMLLSTGEQVSIALLAMSLHEKGYKA--VSLTGWQAG
ITTEEMHGNARIMNIDTT--RIRRCLDE----GAIVIVAGF---QGVTETGEITTLGRGG
SDTTAVA-----------------LAAALKAEKCDIYTDVTGVFTTDP--RYVKTARKIK
EISYDEMLELANLGAGVLHPRAVEFAKNYEVPLEVRSSME-NERGTMVK--EEVSMEQHL
IVRGIAFEDQ-VTRVTVVGIEKYLQSVA--------TIFTALANRGINVDIIIQNA----
----------------TNSETAS--VSFSIRTEDLPETLQVLQ-------------ALEG
ADVHYESGLAKVSI-VGSGMISNPGVAARV------FEVLADQGIEIKMVS
>AK2_BACSU/63-373
-----------------KRE--MDMLLATGEQVTISLLSMALQEKGYDA--VSYTGWQAG
IRTEAIHGNARITDIDTS--VLADQLEK----GKIVIVAGF---QGMTEDCEITTLGRGG
SDTTAVA-----------------LAAALKVDKCDIYTDVPGVFTTDP--RYVKSARKLE
GISYDEMLELANLGAGVLHPRAVEFAKNYQVPLEVRSSTE-TEAGTLIE--EESSMEQNL
IVRGIAFEDQ-ITRVTIYGLTSGLTTLS--------TIFTTLAKRNINVDIIIQTQ----
----------------AEDKTG---ISFSVKTEDADQTVAVLEEYK---------DALEF
EKIETESKLAKVSI-VGSGMVSNPGVAAEM------FAVLAQKNILIKMVS
>AKAB_CORFL/63-379
-----------------ARE--MDMLLTAGERISNALVAMAIESLGAEA--QSFTGSQAG
VLTTERHGNARIVDVTPG--RVREALDE----GKICIVAGF--QGVNKETRDVTTLGRGG
SDTTAVA-----------------LAAALNADVCEIYSDVDGVYTADP--RIVPNAQKLE
KLSFEEMLELAAVGSKILVLRSVEYARAFNVPLRVRSSYS-NDPGTLIAGSMEDIPVEEA
VLTGVATDKS-EAKVTVLGISDKPGEAA--------KVFRALADAEINIDMVLQNV----
----------------SSVEDGTTDITFTCPRADGRRAMEILKKLQ---------VQGNW
TNVLYDDQVDKVSL-VGAGMKSHPGVTAEF------MEALRDVNVNIELIS
>AKAB_MYCSM/63-379
-----------------PRE--MDMLLTAGERISNALVAMAIESLGAQA--RSFTGSQAG
VITTGTHGNAKIIDVTPG--RLRDALDE----GQIVLVAGF--QGVSQDSKDVTTLGRGG
SDTTAVA-----------------VAAALDADVCEIYTDVDGIFTADP--RIVPNARHLD
TVSFEEMLEMAACGAKVLMLRCVEYARRYNVPIHVRSSYS-DKPGTIVKGSIEDIPMEDA
ILTGVAHDRS-EAKVTVVGLPDVPGYAA--------KVFRAVAEADVNIDMVLQNI----
----------------SKIEDGKTDITFTCARDNGPRAVEKLSALK---------SEIGF
SQVLYDDHIGKVSL-IGAGMRSHPGVTATF------CEALAEAGINIDLIS
>AK3_ECOLI/106-407
-----------------TSPALTDELVSHGELMSTLLFVEILRERD--V--QAQWFDVRK
VMRTNDRFGRAEPDIAALAELAALQLLPR-LNEGLVITQGF---IGSENKGRTTTLGRGG
SDYTAAL-----------------LAEALHASRVDIWTDVPGIYTTDP--RVVSAAKRID
EIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFRA
LAL--RRNQT-LLTLHSLNMLHSRGFLA--------EVFGILARHNISVDLITTSEVSVA
LTLDTTGSTSTG----------DTLLTQSLLMELSALCRVEVEEGLALVALIG-------
---NDLSKACGVGKEVF
>AK_YEAST/134-472 A COMMENT FOR YEAST
-----------------VSSRTVDLVMSCGEKLSCLFMTALCNDRGCKAKYVDLSHIVPS
DFSASALDNSFYTFLVQALKEKLAPFVSA-KERIVPVFTGF---FGLVPTGLLNGVGRGY
TDLCAAL-----------------IAVAVNADELQVWKEVDGIFTADP--RKVPEARLLD
SVTPEEASELTYYGSEVIHPFTMEQVIRAKIPIRIKNVQNPLGNGTIIYPDNVAKKGEST
PPHPPENLSS----SFYEKRKRGATAITTKN----DIFVINIHSNKKTLSHGFLAQIFTI
LDKYKLVVDLISTSEVHVSMALPIPDADS-LKSLRQAEEKLRILGSVDITKKLSIVSLVG
KHMKQYIGIAG---TMFTTLAEEGINIEMIS
BioPerl-1.007002/t/data/testdat.exonerate000444000766000024       613713155576321 20263 0ustar00cjfieldsstaff000000000000C4 Alignment display:
  Model: est2genome
  Raw score: 1615
  Aligned positions 65->416 of query
  Aligned positions 0->939 of target

Query: ln27 
Target: Contig124

  66 : GTGATGTAGGAAAGAAGCCGGCTGGGACTGGCGCGGTGATATCGACGTGA : 115
       |||||||||||||||| |||||||||||||||||||||||||||||||||
   1 : GTGATGTAGGAAAGAAACCGGCTGGGACTGGCGCGGTGATATCGACGTGA :  50

 116 : TTGTTCATGCTGCCGCTAGGCTGGGAGTCTTCAAGGCGACAGGCATCGCT : 165
       ||||||||||||||||||||||||||||||||||||||||||||||||||
  51 : TTGTTCATGCTGCCGCTAGGCTGGGAGTCTTCAAGGCGACAGGCATCGCT : 100

 166 : GCAATAAGTGTCTCGTGGATTGTC  <<<< Intron 1 <<<<  CAAT : 193
       ||||||||||||||||||||||||         53 bp        ||||
 101 : GCAATAAGTGTCTCGTGGATTGTCct..................acCAAT : 181

 194 : TGTTTAGAGCAAGCCAAACACCAAGCAGTATCCATACCCATATCAATCAT : 243
       ||||||||||||||||||||||||||||||||||||||||||||||||||
 182 : TGTTTAGAGCAAGCCAAACACCAAGCAGTATCCATACCCATATCAATCAT : 231

 244 : AGTCATTTTGAGCGGTATTGTGTCGGGCCAAGAGTGATTGTAGATGTAGA : 293
       ||||||||||||||||||||||||||||||||||||||||||||||||||
 232 : AGTCATTTTGAGCGGTATTGTGTCGGGCCAAGAGTGATTGTAGATGTAGA : 281

 294 : AGGGTAAAGAAAACGGGGCTGTTACAAGACAAAGGAGAAGAGAGTCGTCC : 343
       ||||||||||||||||||||||||||||||||||||||||||||||||||
 282 : AGGGTAAAGAAAACGGGGCTGTTACAAGACAAAGGAGAAGAGAGTCGTCC : 331

 344 : GAGGGAGTTAGTGATGGGGAGAGTCGAAATGC  <<<< Intron 2 << : 375
       ||||||||||||||||||||||||||||||||        535 bp    
 332 : GAGGGAGTTAGTGATGGGGAGAGTCGAAATGCct................ : 898

 376 : <<  CTACACCAGGCTGCAATATTCTCGCCTATAATTCTGCGCTT : 416
           |||||||||||||||||||||||||||||||||||||||||
 899 : ..acCTACACCAGGCTGCAATATTCTCGCCTATAATTCTGCGCTT : 939

cigar: ln27 65 416 - Contig124 0 939 + 1615 M 124 D 53 M 186 D 535 M 41
C4 Alignment display:
  Model: est2genome
  Raw score: 1152
  Aligned positions 385->644 of query
  Aligned positions 900->1296 of target

Query: ln74
Target: Contig275

  386 : CTTGGGGTCCTTCTCCGATTCACTGCTTCCACCGCTGCTGCCGC  <<<< :  429
        ||||||||||||||||||||||||||||||||||||||||||||      
  901 : CTTGGGGTCCTTCTCCGATTCACTGCTTCCACCGCTGCTGCCGCct.... :  997

  430 :  Intron 1 <<<<  ACTTTTGCAAAATGAAGACATTTTCCCTCTTACC :  463
           53 bp        ||||||||||||||||||||||||||||||||||
  998 : ..............acACTTTTGCAAAATGAAGACATTTTCCCTCTTACC : 1031

  464 : ACCCCACTTTTCCAAGGCGTCCTTGACGCTCTTACTGTTTTTGTACATTT :  513
        ||||||||||||||||||||||||||||||||||||||||||||||||||
 1032 : ACCCCACTTTTCCAAGGCGTCCTTGACGCTCTTACTGTTTTTGTACATTT : 1081

  514 : GAGCACAATCAATGTAGGTGTACCCGGTCTTCAAGGCTGAGACGAGATGC :  563
        ||||||||||||||||||||||||||||||||||||||||||||||||||
 1082 : GAGCACAATCAATGTAGGTGTACCCGGTCTTCAAGGCTGAGACGAGATGC : 1131

  564 : TCAACGCATTCCTTGCCGTAGTGGGTGGTGC  <<<< Intron 2 <<< :  594
        |||||||||||||||||||||||||||||||         84 bp     
 1132 : TCAACGCATTCCTTGCCGTAGTGGGTGGTGCct................. : 1246

  595 : <  CAAGACCAAACCCAATTTTGGGGATCTTGACACCATCATTGAGAGTT :  641
           |||||||||||||||||||||||||||||||||||||||||||||||
 1247 : .acCAAGACCAAACCCAATTTTGGGGATCTTGACACCATCATTGAGAGTT : 1293

  642 : ATG :  644
        |||
 1294 : ATG : 1296

cigar: ln74 385 644 - Contig275 900 1296 + 1152 M 44 D 53 M 165 D 84 M 50
BioPerl-1.007002/t/data/testdata.crossmatch000444000766000024      1027213155576321 20613 0ustar00cjfieldsstaff000000000000cross_match 34_1_5_MSX1DF.seq msx1_ens2.fasta -alignments 
cross_match version 0.990329

Run date:time  080103:101214
Query file(s):  34_1_5_MSX1DF.seq
Subject file(s):   msx1_ens2.fasta
Presumed sequence type: DNA

Pairwise comparison algorithm: banded Smith-Waterman

Score matrix (set by value of penalty: -2)
    A   C   G   T   N   X
A   1  -2  -2  -2   0  -3
C  -2   1  -2  -2   0  -3
G  -2  -2   1  -2   0  -3
T  -2  -2  -2   1   0  -3
N   0   0   0   0   0   0
X  -3  -3  -3  -3   0  -3

Gap penalties: gap_init: -4, gap_ext: -3, ins_gap_ext: -3, del_gap_ext: -3, 
Using complexity-adjusted scores. Assumed background frequencies:
 A: 0.250  C: 0.250  G: 0.250  T: 0.250  N: 0.000  X: 0.000  

minmatch: 14, maxmatch: 14, max_group_size: 20, minscore: 30, bandwidth: 14, indexwordsize: 10
vector_bound: 0
word_raw: 0
masklevel: 80

Sequence file: 34_1_5_MSX1DF.seq    1 entries
Residue counts:
  A      123
  C      148
  G      170
  N        1
  T      161
Total    603

NO QUALITY FILE 34_1_5_MSX1DF.seq.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15.
Maximal single base matches (low complexity regions):

 538  1.37 0.51 0.34  C:\Program       19   603 (0)    msx1_ens2     2824  3409 (3856)  

  C:\Program          19 TCCCAA-CGTCTAAGACTGAGCCATTAA-GTGGACTCCAGGTGCCCAAGG 66
                               -      i              -                     
  msx1_ens2         2824 TCCCAAACGTCTAGGACTGAGCCATTAAAGTGGACTCCAGGTGCCCAAGG 2873

  C:\Program          67 CGGTTCGCTCCAAGGCCTCACGGCCCCCTGGCTGCTCTACTCAGAGAACA 116
                                                                           
  msx1_ens2         2874 CGGTTCGCTCCAAGGCCTCACGGCCCCCTGGCTGCTCTACTCAGAGAACA 2923

  C:\Program         117 CGCTCGGAGATATTTCAGGAGCACGGGAAATTCCCAAGTTTTCCTCGTTT 166
                                                                           
  msx1_ens2         2924 CGCTCGGAGATATTTCAGGAGCACGGGAAATTCCCAAGTTTTCCTCGTTT 2973

  C:\Program         167 CCTCCGATTATTTTGCTCGGCATAATAGCAGCCAGATTTCAATGGCGTGA 216
                                                                           
  msx1_ens2         2974 CCTCCGATTATTTTGCTCGGCATAATAGCAGCCAGATTTCAATGGCGTGA 3023

  C:\Program         217 TGCTGAGGAATGATTTTTATCTGGGGATTAAACGTCTTTGAAAGGCCAGT 266
                                                                           
  msx1_ens2         3024 TGCTGAGGAATGATTTTTATCTGGGGATTAAACGTCTTTGAAAGGCCAGT 3073

  C:\Program         267 CCCTCCCTAAGCCTAATGGCCGGAGAAGGTGGCCCCGCTCTGGGTTGTCG 316
                                                                           
  msx1_ens2         3074 CCCTCCCTAAGCCTAATGGCCGGAGAAGGTGGCCCCGCTCTGGGTTGTCG 3123

  C:\Program         317 CCGCTGAAGGGAGTGACGTTTCTCTCGGCGCCCGCCCCTCGGGCGGCCCG 366
                                                                           
  msx1_ens2         3124 CCGCTGAAGGGAGTGACGTTTCTCTCGGCGCCCGCCCCTCGGGCGGCCCG 3173

  C:\Program         367 GCGGAAAGCTAGTTGGGGGCCAAGCGCTTCCCGGACTCCCGGTGGCCTCC 416
                                                                           
  msx1_ens2         3174 GCGGAAAGCTAGTTGGGGGCCAAGCGCTTCCCGGACTCCCGGTGGCCTCC 3223

  C:\Program         417 AGCAGGGAAGAAGCGGGGTGTTAACACGAGATTTCGTTTTGACTCACATC 466
                                                                -          
  msx1_ens2         3224 AGCAGGGAAGAAGCGGGGTGTTAACACGAGATTTCGTTT-GACTCACATC 3272

  C:\Program         467 CTGGTGGTCTGAAAGTCCAAAGGATCGTTGTGTTTTCTTTGTTTAGTCAT 516
                                                                     v  iv 
  msx1_ens2         3273 CTGGTGGTCTGAAAGTCCAAAGGATCGTTGTGTTTTCTTTGTTTTGTTTT 3322

  C:\Program         517 GTTTNTTCTGTTTGTTTGTGGTTGTTTTTTAGAGAGGTGTGAAAAAATGC 566
                             ?                                             
  msx1_ens2         3323 GTTTTTTCTGTTTGTTTGTGGTTGTTTTTTAGAGAGGTGTGAAAAAATGC 3372

  C:\Program         567 ATACTTAGGGCAAAACCGCGGTGGTGAA-CATCTTCGA 603
                                  -       vvv        -         
  msx1_ens2         3373 ATACTTAGG-CAAAACCCGCGTGGTGAAACATCTTCGA 3409

Transitions / transversions = 0.40 (2 / 5)
Gap_init rate = 0.01 (5 / 586), avg. gap size = 1.00 (5 / 5)  


1 matching entries (first file).

Discrepancy summary:
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
BioPerl-1.007002/t/data/testdbaccnums.out000444000766000024      3357613155576321 20316 0ustar00cjfieldsstaff000000000000BLASTP 2.2.4 [Aug-26-2002]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.
RID: 1036160600-011802-21377
Query= test_result
         (8 letters)

Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF 
           1,220,597 sequences; 388,937,031 total letters



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gb|NP_065733.1|CYT19 (NM_020682) Cyt19 protein; likely ortholog of r...    31   0.18 
emb|XP_053690.4|Cyt19 (XM_053690) similar to Cyt19 protein; likely or...    31   0.18 
dbj|NP_056277.2|DKFZP586L0724 (NM_015462) DKFZP586L0724 protein [Homo sapiens...    21   113  
pir||T14789 hypothetical protein DKFZp586L0724.1 - human >gi|581...    21   113  
prf||XP_064862.2 (XM_064862) similar to pheromone receptor [Homo...    21   152  
pdb|BAB13968.1|1 (AK022138) unnamed protein product [Homo sapiens]      21   204  
sp|Q16478|GLK5_HUMAN Glutamate receptor, ionotropic kainate 5 pr...    21   204  
pat|US|NP_002079.2 (NM_002088) glutamate receptor, ionotropic, kai...    21   204  
bbs|NP_079463.2| (NM_025187) hypothetical protein FLJ12076 [Homo...    21   204  
gnl|db1|NP_002444.1 (NM_002453) mitochondrial translational initiat...    21   204  
ref|XP_051877.1| (XM_051877) similar to NS1-binding protein-like...    20   274  
lcl|AAH16829.1| (BC016829) Unknown (protein for IMAGE:413...    20   274  
gi|1|gb|NP_065733.1|CYT19 (NM_020682) Cyt19 protein; likely ortholog of r...    31   0.18 
gi|2|emb|XP_053690.4|Cyt19 (XM_053690) similar to Cyt19 protein; likely or...    31   0.18 
gi|3|dbj|NP_056277.2|DKFZP586L0724 (NM_015462) DKFZP586L0724 protein [Homo sapiens...    21   113  
gi|4|pir||T14789 hypothetical protein DKFZp586L0724.1 - human >gi|581...    21   113  
gi|5|prf||XP_064862.2 (XM_064862) similar to pheromone receptor [Homo...    21   152  
gi|6|pdb|BAB13968.1|1 (AK022138) unnamed protein product [Homo sapiens]      21   204  
gi|7|sp|Q16478|GLK5_HUMAN Glutamate receptor, ionotropic kainate 5 pr...    21   204  
gi|8|pat|US|NP_002079.2 (NM_002088) glutamate receptor, ionotropic, kai...    21   204  
gi|9|bbs|NP_079463.2| (NM_025187) hypothetical protein FLJ12076 [Homo...    21   204  
gi|10|gnl|db1|NP_002444.1 (NM_002453) mitochondrial translational initiat...    21   204  
gi|11|ref|XP_051877.1| (XM_051877) similar to NS1-binding protein-like...    20   274  
gi|12|lcl|AAH16829.1| (BC016829) Unknown (protein for IMAGE:413...    20   274  
MY_test_ID (BC016829) Unknown (protein for IMAGE:413...    20   274  

ALIGNMENTS
>pir||T14789 hypothetical protein DKFZp586L0724.1 - human
 emb|CAB53709.1| (AL110271) hypothetical protein [Homo sapiens]
 gb|AAH01726.1|AAH01726 (BC001726) Similar to DKFZP586L0724 protein [Homo sapiens]
          Length = 314

 Score = 21.4 bits (43), Expect =   113
 Identities = 6/8 (75%), Positives = 7/8 (87%)

Query: 1   LMFDANFT 8
           L+ DANFT
Sbjct: 247 LLLDANFT 254


>gb|NP_065733.1|CYT19 (NM_020682) Cyt19 protein; likely ortholog of rat methyltransferase
           Cyt19; S-adenosylmethionine:arsenic (III)
           methyltransferase [Homo sapiens]
 gb|AAG09731.1|AF226730_1 (AF226730) Cyt19 [Homo sapiens]
          Length = 338

 Score = 30.8 bits (65), Expect = 0.18
 Identities = 8/8 (100%), Positives = 8/8 (100%)

Query: 1   LMFDANFT 8
           LMFDANFT
Sbjct: 286 LMFDANFT 293


>emb|XP_053690.4|Cyt19 (XM_053690) similar to Cyt19 protein; likely ortholog of rat
           methyltransferase Cyt19; S-adenosylmethionine:arsenic
           (III) methyltransferase [Homo sapiens]
          Length = 375

 Score = 30.8 bits (65), Expect = 0.18
 Identities = 8/8 (100%), Positives = 8/8 (100%)

Query: 1   LMFDANFT 8
           LMFDANFT
Sbjct: 286 LMFDANFT 293


>dbj|NP_056277.2|DKFZP586L0724 (NM_015462) DKFZP586L0724 protein [Homo sapiens]
 dbj|BAB14647.1| (AK023702) unnamed protein product [Homo sapiens]
          Length = 719

 Score = 21.4 bits (43), Expect =   113
 Identities = 6/8 (75%), Positives = 7/8 (87%)

Query: 1   LMFDANFT 8
           L+ DANFT
Sbjct: 652 LLLDANFT 659


>prf||XP_064862.2 (XM_064862) similar to pheromone receptor [Homo sapiens]
          Length = 370

 Score = 21.0 bits (42), Expect =   152
 Identities = 5/5 (100%), Positives = 5/5 (100%)

Query: 2   MFDAN 6
           MFDAN
Sbjct: 348 MFDAN 352


>pdb|BAB13968.1|1 (AK022138) unnamed protein product [Homo sapiens]
          Length = 258

 Score = 20.6 bits (41), Expect =   204
 Identities = 5/5 (100%), Positives = 5/5 (100%)

Query: 1  LMFDA 5
          LMFDA
Sbjct: 45 LMFDA 49


>sp|Q16478|GLK5_HUMAN Glutamate receptor, ionotropic kainate 5 precursor (Glutamate
           receptor KA-2) (KA2) (Excitatory amino acid receptor 2)
           (EAA2)
 pir||I57936 glutamate receptor subunit - human
 gb|AAB22591.1| (S40369) glutamate receptor subunit; EAA2; excitatory amino acid
           receptor 2 [Homo sapiens]
          Length = 980

 Score = 20.6 bits (41), Expect =   204
 Identities = 5/5 (100%), Positives = 5/5 (100%)

Query: 1   LMFDA 5
           LMFDA
Sbjct: 306 LMFDA 310


>pat|US|NP_002079.2 (NM_002088) glutamate receptor, ionotropic, kainate 5 [Homo
           sapiens]
 emb|CAC80547.1| (AJ249209) kainate receptor subunit KA2a [Homo sapiens]
          Length = 981

 Score = 20.6 bits (41), Expect =   204
 Identities = 5/5 (100%), Positives = 5/5 (100%)

Query: 1   LMFDA 5
           LMFDA
Sbjct: 306 LMFDA 310


>bbs|NP_079463.2| (NM_025187) hypothetical protein FLJ12076 [Homo sapiens]
 sp|Q9BSU1|U183_HUMAN UPF0183 protein
 gb|AAH04556.1|AAH04556 (BC004556) Similar to CG7083 gene product [Homo sapiens]
 gb|AAK96888.1| (AF176088) lin-10-like protein [Homo sapiens]
          Length = 422

 Score = 20.6 bits (41), Expect =   204
 Identities = 5/5 (100%), Positives = 5/5 (100%)

Query: 1  LMFDA 5
          LMFDA
Sbjct: 67 LMFDA 71



 Score = 16.8 bits (32), Expect =  2880
 Identities = 4/5 (80%), Positives = 5/5 (100%)

Query: 2   MFDAN 6
           +FDAN
Sbjct: 296 LFDAN 300


>gnl|db1|NP_002444.1 (NM_002453) mitochondrial translational initiation factor 2
           precursor; IF-2mt [Homo sapiens]
 sp|P46199|IF2M_HUMAN Translation initiation factor IF-2, mitochondrial precursor
           (IF-2Mt) (IF-2(Mt))
 pir||A55628 translation initiation factor IF-2 precursor, mitochondrial - human
 gb|AAA67038.1| (L34600) initiation factor 2 [Homo sapiens]
 gb|AAM14617.1|AF494407_1 (AF494407) mitochondrial translation-initiation factor 2 [Homo
           sapiens]
 gb|AAM70196.1| (AF495546) translation initiation factor 2 [Homo sapiens]
          Length = 727

 Score = 20.6 bits (41), Expect =   204
 Identities = 5/6 (83%), Positives = 5/6 (83%)

Query: 1   LMFDAN 6
           LMFD N
Sbjct: 398 LMFDEN 403


>ref|XP_051877.1| (XM_051877) similar to NS1-binding protein-like protein [Homo
          sapiens]
 dbj|BAA74873.1| (AB020657) KIAA0850 protein [Homo sapiens]
 emb|CAB72329.1| (AL078644) bG279B7.1.1 (NS1-binding protein (KIAA0850, BTB/POZ
          domain and Kelch motifs containing protein)) [Homo
          sapiens]
 gb|AAG43485.1| (AF205218) NS1-binding protein-like protein [Homo sapiens]
          Length = 642

 Score = 20.2 bits (40), Expect =   274
 Identities = 6/8 (75%), Positives = 6/8 (75%), Gaps = 1/8 (12%)

Query: 1  LMF-DANF 7
          LMF D NF
Sbjct: 7  LMFEDENF 14


>lcl|AAH16829.1| (BC016829) Unknown (protein for IMAGE:4132295) [Homo sapiens]
          Length = 391

 Score = 20.2 bits (40), Expect =   274
 Identities = 5/6 (83%), Positives = 5/6 (83%)

Query: 3  FDANFT 8
          FD NFT
Sbjct: 32 FDTNFT 37

>gi|1|gb|NP_065733.1|CYT19 (NM_020682) Cyt19 protein; likely ortholog of rat methyltransferase
           Cyt19; S-adenosylmethionine:arsenic (III)
           methyltransferase [Homo sapiens]
 gb|AAG09731.1|AF226730_1 (AF226730) Cyt19 [Homo sapiens]
          Length = 338

 Score = 30.8 bits (65), Expect = 0.18
 Identities = 8/8 (100%), Positives = 8/8 (100%)

Query: 1   LMFDANFT 8
           LMFDANFT
Sbjct: 286 LMFDANFT 293


>gi|2|emb|XP_053690.4|Cyt19 (XM_053690) similar to Cyt19 protein; likely ortholog of rat
           methyltransferase Cyt19; S-adenosylmethionine:arsenic
           (III) methyltransferase [Homo sapiens]
          Length = 375

 Score = 30.8 bits (65), Expect = 0.18
 Identities = 8/8 (100%), Positives = 8/8 (100%)

Query: 1   LMFDANFT 8
           LMFDANFT
Sbjct: 286 LMFDANFT 293


>gi|3|dbj|NP_056277.2|DKFZP586L0724 (NM_015462) DKFZP586L0724 protein [Homo sapiens]
 dbj|BAB14647.1| (AK023702) unnamed protein product [Homo sapiens]
          Length = 719

 Score = 21.4 bits (43), Expect =   113
 Identities = 6/8 (75%), Positives = 7/8 (87%)

Query: 1   LMFDANFT 8
           L+ DANFT
Sbjct: 652 LLLDANFT 659


>gi|4|pir||T14789 hypothetical protein DKFZp586L0724.1 - human
 emb|CAB53709.1| (AL110271) hypothetical protein [Homo sapiens]
 gb|AAH01726.1|AAH01726 (BC001726) Similar to DKFZP586L0724 protein [Homo sapiens]
          Length = 314

 Score = 21.4 bits (43), Expect =   113
 Identities = 6/8 (75%), Positives = 7/8 (87%)

Query: 1   LMFDANFT 8
           L+ DANFT
Sbjct: 247 LLLDANFT 254


>gi|5|prf||XP_064862.2 (XM_064862) similar to pheromone receptor [Homo sapiens]
          Length = 370

 Score = 21.0 bits (42), Expect =   152
 Identities = 5/5 (100%), Positives = 5/5 (100%)

Query: 2   MFDAN 6
           MFDAN
Sbjct: 348 MFDAN 352


>gi|6|pdb|BAB13968.1|1 (AK022138) unnamed protein product [Homo sapiens]
          Length = 258

 Score = 20.6 bits (41), Expect =   204
 Identities = 5/5 (100%), Positives = 5/5 (100%)

Query: 1  LMFDA 5
          LMFDA
Sbjct: 45 LMFDA 49


>gi|7|sp|Q16478|GLK5_HUMAN Glutamate receptor, ionotropic kainate 5 precursor (Glutamate
           receptor KA-2) (KA2) (Excitatory amino acid receptor 2)
           (EAA2)
 pir||I57936 glutamate receptor subunit - human
 gb|AAB22591.1| (S40369) glutamate receptor subunit; EAA2; excitatory amino acid
           receptor 2 [Homo sapiens]
          Length = 980

 Score = 20.6 bits (41), Expect =   204
 Identities = 5/5 (100%), Positives = 5/5 (100%)

Query: 1   LMFDA 5
           LMFDA
Sbjct: 306 LMFDA 310


>gi|8|pat|US|NP_002079.2 (NM_002088) glutamate receptor, ionotropic, kainate 5 [Homo
           sapiens]
 emb|CAC80547.1| (AJ249209) kainate receptor subunit KA2a [Homo sapiens]
          Length = 981

 Score = 20.6 bits (41), Expect =   204
 Identities = 5/5 (100%), Positives = 5/5 (100%)

Query: 1   LMFDA 5
           LMFDA
Sbjct: 306 LMFDA 310


>gi|9|bbs|NP_079463.2| (NM_025187) hypothetical protein FLJ12076 [Homo sapiens]
 sp|Q9BSU1|U183_HUMAN UPF0183 protein
 gb|AAH04556.1|AAH04556 (BC004556) Similar to CG7083 gene product [Homo sapiens]
 gb|AAK96888.1| (AF176088) lin-10-like protein [Homo sapiens]
          Length = 422

 Score = 20.6 bits (41), Expect =   204
 Identities = 5/5 (100%), Positives = 5/5 (100%)

Query: 1  LMFDA 5
          LMFDA
Sbjct: 67 LMFDA 71



 Score = 16.8 bits (32), Expect =  2880
 Identities = 4/5 (80%), Positives = 5/5 (100%)

Query: 2   MFDAN 6
           +FDAN
Sbjct: 296 LFDAN 300


>gi|10|gnl|db1|NP_002444.1 (NM_002453) mitochondrial translational initiation factor 2
           precursor; IF-2mt [Homo sapiens]
 sp|P46199|IF2M_HUMAN Translation initiation factor IF-2, mitochondrial precursor
           (IF-2Mt) (IF-2(Mt))
 pir||A55628 translation initiation factor IF-2 precursor, mitochondrial - human
 gb|AAA67038.1| (L34600) initiation factor 2 [Homo sapiens]
 gb|AAM14617.1|AF494407_1 (AF494407) mitochondrial translation-initiation factor 2 [Homo
           sapiens]
 gb|AAM70196.1| (AF495546) translation initiation factor 2 [Homo sapiens]
          Length = 727

 Score = 20.6 bits (41), Expect =   204
 Identities = 5/6 (83%), Positives = 5/6 (83%)

Query: 1   LMFDAN 6
           LMFD N
Sbjct: 398 LMFDEN 403


>gi|11|ref|XP_051877.1| (XM_051877) similar to NS1-binding protein-like protein [Homo
          sapiens]
 dbj|BAA74873.1| (AB020657) KIAA0850 protein [Homo sapiens]
 emb|CAB72329.1| (AL078644) bG279B7.1.1 (NS1-binding protein (KIAA0850, BTB/POZ
          domain and Kelch motifs containing protein)) [Homo
          sapiens]
 gb|AAG43485.1| (AF205218) NS1-binding protein-like protein [Homo sapiens]
          Length = 642

 Score = 20.2 bits (40), Expect =   274
 Identities = 6/8 (75%), Positives = 6/8 (75%), Gaps = 1/8 (12%)

Query: 1  LMF-DANF 7
          LMF D NF
Sbjct: 7  LMFEDENF 14


>gi|12|lcl|AAH16829.1| (BC016829) Unknown (protein for IMAGE:4132295) [Homo sapiens]
          Length = 391

 Score = 20.2 bits (40), Expect =   274
 Identities = 5/6 (83%), Positives = 5/6 (83%)

Query: 3  FDANFT 8
          FD NFT
Sbjct: 32 FDTNFT 37

>MY_test_ID (BC016829) Unknown (protein for IMAGE:4132295) [Homo sapiens]
          Length = 391

 Score = 20.2 bits (40), Expect =   274
 Identities = 5/6 (83%), Positives = 5/6 (83%)

Query: 3  FDANFT 8
          FD NFT
Sbjct: 32 FDTNFT 37


  Database: All non-redundant GenBank CDS
  translations+PDB+SwissProt+PIR+PRF
    Posted date:  Oct 31, 2002  3:52 AM
  Number of letters in database: 388,937,031
  Number of sequences in database:  1,220,597
  
Lambda     K      H
   0.328    0.274     1.77 

Gapped
Lambda     K      H
   0.294    0.110    0.610 


Matrix: PAM30
Gap Penalties: Existence: 9, Extension: 1
Number of Hits to DB: 660,045
Number of Sequences: 1220597
Number of extensions: 3731
Number of successful extensions: 3028
Number of sequences better than 200000.0: 2850
Number of HSP's better than 200000.0 without gapping: 2850
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 3028
length of query: 8
length of database: 35,444,647
effective HSP length: 0
effective length of query: 9
effective length of database: 35,444,647
effective search space: 319001823
effective search space used: 319001823
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 35 (14.8 bits)
X3: 58 (24.6 bits)
S1: 18 (10.4 bits)
S2: 18 (10.8 bits)


BioPerl-1.007002/t/data/testfile.erpin000444000766000024       152413155576321 17550 0ustar00cjfieldsstaff000000000000
Training set:	"/home/Administrator/pyrR.epn":
		40 sequences of length 43
Cutoff:		1.00  

Database:	"AE016879.fna"
		5227266 nucleotides to be processed in 1 sequence
		ATGC ratios: 0.322  0.324  0.176  0.178
E-value at cutoff 1.0 for 5.2Mb double strand data: 4.59e-02

>gi|30260185|gb|AE016879.1| Bacillus anthracis str. Ames, complete genome
FW   1 5181155..5181183  30.36  1.68e-05
CTTT.aacc--.CAACC.CCGTGA.GGTTG.a.GAAG
>gi|30260185|gb|AE016879.1| Bacillus anthracis str. Ames, complete genome
RC   1 3709092..3709121  28.97  5.61e-05
CTTT.taatt-.CAGTC.CTGTGA.GACCG.g.AAAG
RC   2 3710524..3710553  27.97  1.31e-04
TTTT.aaatg-.TAGTC.CTGTGA.GGCTG.c.CAAA
RC   3 3711223..3711251  31.64  4.44e-06
CTTT.aaca--.CAGCC.CCGTGA.GGTTG.a.GAAG

-------- at level 1 --------
10454532 bases processed
cutoff: 1.00
6 config. per site
10 hits
4 independent hits

BioPerl-1.007002/t/data/testfuzzy.genbank000444000766000024       646313155576321 20317 0ustar00cjfieldsstaff000000000000LOCUS       DDU63596      310 bp    DNA             INV       14-MAY-1999
DEFINITION  Dictyostelium discoideum Tdd-4 transposable element flanking
            sequence, clone p427/428 right end.
ACCESSION   U63596
NID         g2393749
KEYWORDS    .
SOURCE      Dictyostelium discoideum.
  ORGANISM  Dictyostelium discoideum
            Eukaryota; Dictyosteliida; Dictyostelium.
REFERENCE   1  (bases 1 to 310)
  AUTHORS   Wells,D.J.
  TITLE     Tdd-4, a DNA transposon of Dictyostelium that encodes proteins
            similar to LTR retroelement integrases
  JOURNAL   Nucleic Acids Res. 27 (11), 2408-2415 (1999)
REFERENCE   2  (bases 1 to 310)
  AUTHORS   Wells,D.J. and Welker,D.L.
  TITLE     Dictyostelium discoideum Tdd-4 transposable element, right end
            flanking sequence from clone p427/428
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 310)
  AUTHORS   Wells,D.J. and Welker,D.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JUL-1996) Biology, Utah State Univ., Logan, UT
            84322-5305, USA
FEATURES             Location/Qualifiers
     source          1..310
                     /organism="Dictyostelium discoideum"
                     /strain="AX4"
                     /db_xref="taxon:44689"
                     /clone="p427/428"
     misc_feature    5.12
                     /note="Fuzzy location"
     misc_feature    <5..12
                     /note="Fuzzy location2"
     misc_feature    5>..12
                     /note="Fuzzy location3"
     misc_feature    5..<12
                     /note="Fuzzy location4"
     misc_feature    5..12>
                     /note="Fuzzy location5"
     misc_feature    <5..12>
                     /note="Fuzzy location6"
     misc_feature    5.12>
                     /note="Fuzzy location7"
     misc_feature    <5.12>
                     /note="Fuzzy location8"
     misc_feature    5>.12>
                     /note="Fuzzy location9"
     misc_feature    5.<12
                     /note="Fuzzy location10"
     misc_feature    5.60..<120
                     /note="Fuzzy location11"
     misc_feature    5^9..>200
                     /note="Fuzzy location12"
     misc_feature    5.10..12.15
                     /note="Fuzzy location13"
     misc_feature    5.10
                     /note="Fuzzy location14"
     misc_feature    join(J00194:(100..202),1..245,300..422)
                     /note="Location partly in another entry"
     misc_feature    complement(join(1..30,30.40,4^8,40.30..90))
	             /note="complement of join"
     misc_feature    order(1..30, 31..40)
		     /note="location uses order"
     misc_feature    order(AF183172.1:1..30, 31..40)
		     /note="location uses order in another sequence"
     misc_feature    order(AF183172.1:<1..30, 31..>342)
		     /note="uses order and fuzzy locs in another sequence"
     mRNA            join(complement(83202..83329),84248..84996)
BASE COUNT      118 a     46 c     67 g     79 t
ORIGIN      
        1 gtgacagttg gctgtcagac atacaatgat tgtttagaag aggagaagat tgatccggag
       61 taccgtgata gtattttaaa aactatgaaa gcgggaatac ttaatggtaa actagttaga
      121 ttatgtgacg tgccaagggg tgtagatgta gaaattgaaa caactggtct aaccgattca
      181 gaaggagaaa gtgaatcaaa agaagaagag tgatgatgaa tagccaccat tactgcatac
      241 tgtagccctt acccttgtcg caccattagc cattaataaa aataaaaaat tatataaaaa
      301 ttacacccat 
//
BioPerl-1.007002/t/data/tiny.stk000444000766000024        15513155576321 16357 0ustar00cjfieldsstaff000000000000# STOCKHOLM 1.0
#=GF AU    HMMER 2.3.2

a        SEQENCEQQQQQ
b        PRTEINAACIDQ
#=GC RF  xxxxxxxxxxxx
//
BioPerl-1.007002/t/data/tmhmm.out000444000766000024       104513155576321 16543 0ustar00cjfieldsstaff000000000000# my_sequence_id Length: 178
# my_sequence_id Number of predicted TMHs:  3
# my_sequence_id Exp number of AAs in TMHs: 69.58306
# my_sequence_id Exp number, first 60 AAs:  8.42188
# my_sequence_id Total prob of N-in:        0.07306
my_sequence_id	TMHMM2.0	outside	     1    53
my_sequence_id	TMHMM2.0	TMhelix	    54    76
my_sequence_id	TMHMM2.0	inside	    77   115
my_sequence_id	TMHMM2.0	TMhelix	   116   138
my_sequence_id	TMHMM2.0	outside	   139   150
my_sequence_id	TMHMM2.0	TMhelix	   151   173
my_sequence_id	TMHMM2.0	inside	   174   178    
BioPerl-1.007002/t/data/tmp.fst000444000766000024       113013155576321 16201 0ustar00cjfieldsstaff000000000000>TEST00001                                    EOL
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
>TEST00002                                    EOL
ccccccccccccccccccccccccccccccccccccccccccccccccc
ccccccccccccccccccccccccccccccccccccccccccccccccc
>TEST00003                                    EOL
ggggggggggggggggggggggggggggggggggggggggggggggggg
ggggggggggggggggggggggggggggggggggggggggggggggggg
>TEST00004                                    EOL
ttttttttttttttttttttttttttttttttttttttttttttttttt
ttttttttttttttttttttttttttttttttttttttttttttttttt
BioPerl-1.007002/t/data/tol-2010-02-18.nhx000444000766000024   1363735713155576322 17364 0ustar00cjfieldsstaff000000000000(((aquifex[&&NHX:TOL=59615],calderobacterium[&&NHX:TOL=59616],hydrogenobacter[&&NHX:TOL=59617],thermocrinis[&&NHX:TOL=59618],hydrogenothermus[&&NHX:TOL=59619],persephonella[&&NHX:TOL=59620],sulfurihydrogenibium[&&NHX:TOL=59621],balnearium[&&NHX:TOL=59622],desulfurobacterium[&&NHX:TOL=59623],thermovibrio[&&NHX:TOL=59624])aquificae[&&NHX:TOL=2285],(thermotoga[&&NHX:TOL=59625],fervidobacterium[&&NHX:TOL=59626],geotoga[&&NHX:TOL=59627],marinitoga[&&NHX:TOL=59628],petrotoga[&&NHX:TOL=59629],thermosipho[&&NHX:TOL=59630])thermotogae[&&NHX:TOL=2286],(thermodesulfobacterium[&&NHX:TOL=59633],thermodesulfatator[&&NHX:TOL=59634])thermodesulfobacteria[&&NHX:TOL=2287],chrysiogenes arsenatis[&&NHX:TOL=59595],(nitospira[&&NHX:TOL=59651],leptospirillum[&&NHX:TOL=59652],magnetobacterium[&&NHX:TOL=59653],thermodesulfovibrio[&&NHX:TOL=59654])nitrospira[&&NHX:TOL=59597],(deferribacter[&&NHX:TOL=59655],denitrovibrio[&&NHX:TOL=59656],flexistipes[&&NHX:TOL=59657],geovibrio[&&NHX:TOL=59658],synergistes[&&NHX:TOL=59659],caldithrix[&&NHX:TOL=59660])deferribacteres[&&NHX:TOL=59598],(chloroflexus[&&NHX:TOL=59641],chloronema[&&NHX:TOL=59642],heliothrix[&&NHX:TOL=59643],roseiflexus[&&NHX:TOL=59644],oscillochloris[&&NHX:TOL=59645],herpetosiphon[&&NHX:TOL=59646],anaerolinea[&&NHX:TOL=59647],caldilinea[&&NHX:TOL=59648])chloroflexi[&&NHX:TOL=2289],(thermomicrobium roseum[&&NHX:TOL=59649],thermomicrobium fosteri[&&NHX:TOL=59650])thermomicrobium[&&NHX:TOL=59596],((fibrobacter succinogenes succinogenes[&&NHX:TOL=60128],fibrobacter succinogenes elongatus[&&NHX:TOL=60129])fibrobacter succinogenes[&&NHX:TOL=60126],fibrobacter intestinalis[&&NHX:TOL=60127])fibrobacteres[&&NHX:TOL=2300],((rhodospirillales[&&NHX:TOL=57769],rickettsiales[&&NHX:TOL=57770],rhodobacterales[&&NHX:TOL=57771],sphingomonadales[&&NHX:TOL=57772],caulobacterales[&&NHX:TOL=57773],rhizobiales[&&NHX:TOL=57774],parvularcula bermudensis[&&NHX:TOL=57775],kordiimonas gwangyangensis[&&NHX:TOL=57776])alpha proteobacteria[&&NHX:TOL=2303],beta proteobacteria[&&NHX:TOL=2304],gamma proteobacteria[&&NHX:TOL=2306],(desulfarculus baarsii[&&NHX:TOL=65512],desulfovibrionales[&&NHX:TOL=65513],desulfobacterales[&&NHX:TOL=65514],desulfurellales[&&NHX:TOL=65515],desulfuromonales[&&NHX:TOL=65518],syntrophobacterales[&&NHX:TOL=65519],bdellovibrionales[&&NHX:TOL=65520],myxococcales[&&NHX:TOL=65521])delta proteobacteria[&&NHX:TOL=2305],((campylobacter[&&NHX:TOL=121972],arcobacter[&&NHX:TOL=121973],dehalospirillum[&&NHX:TOL=121974],sulfurospirillum[&&NHX:TOL=121975])campylobacteraceae[&&NHX:TOL=121971],(helicobacter[&&NHX:TOL=121977],sulfurimonas[&&NHX:TOL=121978],thiovulum[&&NHX:TOL=121979],wolinella[&&NHX:TOL=121980])helicobacteraceae[&&NHX:TOL=121976],(nautilia[&&NHX:TOL=121982],caminibacter[&&NHX:TOL=121983])nautiliaceae[&&NHX:TOL=121981],hydrogenimonas thermophila[&&NHX:TOL=121984])epsilon proteobacteria[&&NHX:TOL=57768])proteobacteria[&&NHX:TOL=2302],(planctomyces[&&NHX:TOL=60112],gemmata[&&NHX:TOL=60113],isosphaera[&&NHX:TOL=60114],pirellula[&&NHX:TOL=60115])planctomycetes[&&NHX:TOL=2298],(chlamydia[&&NHX:TOL=60116],chlamydophila[&&NHX:TOL=60117],neochlamydia[&&NHX:TOL=60118],parachlamydia[&&NHX:TOL=60119],rhabdochlamydia[&&NHX:TOL=60120],simkania[&&NHX:TOL=60121],waddlia[&&NHX:TOL=60122])chlamydiae[&&NHX:TOL=59600],(borrelia[&&NHX:TOL=24812],brachyspira[&&NHX:TOL=24821],brevinema[&&NHX:TOL=24813],clevelandina[&&NHX:TOL=24814],cristispira[&&NHX:TOL=24815],diplocalyx[&&NHX:TOL=24816],hollandina[&&NHX:TOL=24817],leptonema[&&NHX:TOL=24822],leptospira[&&NHX:TOL=24823],pillotina[&&NHX:TOL=24818],serpulina[&&NHX:TOL=24820],spirochaeta[&&NHX:TOL=24811],treponema[&&NHX:TOL=24819])spirochaetes[&&NHX:TOL=2301],(acetofilamentum[&&NHX:TOL=60146],acetomicrobium[&&NHX:TOL=60147],acetothermus[&&NHX:TOL=60148],alistipes[&&NHX:TOL=60149],anaerophaga[&&NHX:TOL=60150],anaerorhabdus[&&NHX:TOL=60151],bacteroides[&&NHX:TOL=60152],belliella[&&NHX:TOL=60185],dysgonomonas[&&NHX:TOL=60153],marinilabilia[&&NHX:TOL=60154],megamonas[&&NHX:TOL=60155],porphyromonas[&&NHX:TOL=60156],prevotella[&&NHX:TOL=60157],rikenella[&&NHX:TOL=60158],tannerella[&&NHX:TOL=60159],aequorivita[&&NHX:TOL=60160],arenibacter[&&NHX:TOL=60161],bergeyella[&&NHX:TOL=60162],blattabacterium[&&NHX:TOL=60163],capnocytophaga[&&NHX:TOL=60164],cellulophaga[&&NHX:TOL=60165],chitinophaga[&&NHX:TOL=60186],chryseobacterium[&&NHX:TOL=60166],coenonia[&&NHX:TOL=60167],crenothrix[&&NHX:TOL=60187],croceibacter[&&NHX:TOL=60168],cyclobacterium[&&NHX:TOL=60188],cytophaga[&&NHX:TOL=60189],dyadobacter[&&NHX:TOL=60190],empedobacter[&&NHX:TOL=60169],flammeovirga[&&NHX:TOL=60191],flavobacterium[&&NHX:TOL=60170],flectobacillus[&&NHX:TOL=60192],flexibacter[&&NHX:TOL=60193],flexithrix[&&NHX:TOL=60194],gelidibacter[&&NHX:TOL=60171],gillisia[&&NHX:TOL=60172],haliscomenobacter[&&NHX:TOL=60195],hongiella[&&NHX:TOL=60196],hymenobacter[&&NHX:TOL=60197],lewinella[&&NHX:TOL=60198],meniscus[&&NHX:TOL=60199],mesonia[&&NHX:TOL=60173],microscilla[&&NHX:TOL=60200],muricauda[&&NHX:TOL=60174],myroides[&&NHX:TOL=60175],ornithobacterium[&&NHX:TOL=60176],pedobacter[&&NHX:TOL=60201],persicobacter[&&NHX:TOL=60202],polaribacter[&&NHX:TOL=60177],psychroflexus[&&NHX:TOL=60178],psychroserpens[&&NHX:TOL=60179],reichenbachia[&&NHX:TOL=60203],rhodothermus[&&NHX:TOL=60204],riemerella[&&NHX:TOL=60180],runella[&&NHX:TOL=60205],salegentibacter[&&NHX:TOL=60181],salinibacter[&&NHX:TOL=60206],saprospira[&&NHX:TOL=60207],sphingobacterium[&&NHX:TOL=60208],spirosoma[&&NHX:TOL=60209],sporocytophaga[&&NHX:TOL=60210],tenacibaculum[&&NHX:TOL=60182],thermonema[&&NHX:TOL=60211],toxothrix[&&NHX:TOL=60212],weeksella[&&NHX:TOL=60183],zobellia[&&NHX:TOL=60184])bacteroidetes[&&NHX:TOL=59602],(chlorobium[&&NHX:TOL=59681],ancalochloris[&&NHX:TOL=59682],chlorobaculum[&&NHX:TOL=59683],chloroherpeton[&&NHX:TOL=59684],pelodictyon[&&NHX:TOL=59685],prosthecochloris[&&NHX:TOL=59686])chlorobi[&&NHX:TOL=59599],(acidimicrobium ferrooxidans[&&NHX:TOL=59934],((actinobaculum[&&NHX:TOL=59935],actinomyces[&&NHX:TOL=59584],arcanobacterium[&&NHX:TOL=59936],mobiluncus[&&NHX:TOL=59946],varibaculum[&&NHX:TOL=59957])actinomycineae[&&NHX:TOL=60032],(corynebacterium[&&NHX:TOL=59587],dietzia[&&NHX:TOL=59988],gordonia[&&NHX:TOL=59991],mycobacterium[&&NHX:TOL=59591],nocardia[&&NHX:TOL=59592],rhodococcus[&&NHX:TOL=60012],skermania[&&NHX:TOL=60017],tsukamurella[&&NHX:TOL=60024],williamsia[&&NHX:TOL=60027])corynebacterineae[&&NHX:TOL=60033],(agreia[&&NHX:TOL=59967],agrococcus[&&NHX:TOL=59968],agromyces[&&NHX:TOL=59969],arsenicicoccus[&&NHX:TOL=59970],arthrobacter[&&NHX:TOL=59585],beutenbergia[&&NHX:TOL=59973],bogoriella[&&NHX:TOL=59960],brachybacterium[&&NHX:TOL=59974],brevibacterium[&&NHX:TOL=59975],cellulomonas[&&NHX:TOL=59978],cellulosimicrobium[&&NHX:TOL=59979],citricoccus[&&NHX:TOL=59938],clavibacter[&&NHX:TOL=59980],cryobacterium[&&NHX:TOL=59982],curtobacterium[&&NHX:TOL=59983],demetria[&&NHX:TOL=59961],dermabacter[&&NHX:TOL=59985],dermacoccus[&&NHX:TOL=59986],dermatophilus[&&NHX:TOL=59987],frigoribacterium[&&NHX:TOL=59989],georgenia[&&NHX:TOL=59990],intrasporangium[&&NHX:TOL=59992],janibacter[&&NHX:TOL=59993],jonesia[&&NHX:TOL=59994],kineosphaera[&&NHX:TOL=59995],knoellia[&&NHX:TOL=59996],kocuria[&&NHX:TOL=59945],kytococcus[&&NHX:TOL=59997],leifsonia[&&NHX:TOL=59998],leucobacter[&&NHX:TOL=59999],microbacterium[&&NHX:TOL=60000],micrococcus[&&NHX:TOL=59589],mycetocola[&&NHX:TOL=60001],nesterenkonia[&&NHX:TOL=59947],nostocoidia[&&NHX:TOL=60002],oerskovia[&&NHX:TOL=60003],okibacterium[&&NHX:TOL=60004],ornithinicoccus[&&NHX:TOL=60005],ornithinimicrobium[&&NHX:TOL=60006],plantibacter[&&NHX:TOL=60008],promicromonospora[&&NHX:TOL=60009],rarobacter[&&NHX:TOL=60010],rathayibacter[&&NHX:TOL=60011],renibacterium[&&NHX:TOL=59949],rhodoglobus[&&NHX:TOL=60013],rothia[&&NHX:TOL=59950],salana[&&NHX:TOL=60014],salinibacterium[&&NHX:TOL=60015],sanguibacter[&&NHX:TOL=60016],stomatococcus[&&NHX:TOL=59955],subtercola[&&NHX:TOL=60019],terrabacter[&&NHX:TOL=60020],terracoccus[&&NHX:TOL=60021],tetrasphaera[&&NHX:TOL=60022],tropheryma[&&NHX:TOL=60023],xylanibacterium[&&NHX:TOL=60028],xylanimonas[&&NHX:TOL=60029],yania[&&NHX:TOL=59958])micrococcineae[&&NHX:TOL=60034],(actinoplanes[&&NHX:TOL=59966],asanoa[&&NHX:TOL=59971],catellatospora[&&NHX:TOL=59976],catenuloplanes[&&NHX:TOL=59977],couchioplanes[&&NHX:TOL=59981],dactylosporangium[&&NHX:TOL=59984],micromonospora[&&NHX:TOL=59590],pilimelia[&&NHX:TOL=60007],spirilliplanes[&&NHX:TOL=60018],verrucosispora[&&NHX:TOL=60025],virgisporangium[&&NHX:TOL=60026])micromonosporineae[&&NHX:TOL=60035],(aeromicrobium[&&NHX:TOL=60037],actinopolymorpha[&&NHX:TOL=60038],friedmanniella[&&NHX:TOL=60039],kribbella[&&NHX:TOL=60040],luteococcus[&&NHX:TOL=60041],marmoricola[&&NHX:TOL=60042],microlunatus[&&NHX:TOL=60043],micropruina[&&NHX:TOL=60044],nocardioides[&&NHX:TOL=60045],propionibacterium[&&NHX:TOL=60046],propionicimonas[&&NHX:TOL=60047],propioniferax[&&NHX:TOL=60048],propionimicrobium[&&NHX:TOL=60049],tessaracoccus[&&NHX:TOL=60050])propionibacterineae[&&NHX:TOL=60036],(actinoalloteichus[&&NHX:TOL=60052],actinokineospora[&&NHX:TOL=60053],actinopolyspora[&&NHX:TOL=60054],actinosynnema[&&NHX:TOL=60055],amycolatopsis[&&NHX:TOL=60056],crossiella[&&NHX:TOL=60057],kibdelosporangium[&&NHX:TOL=60058],kutzneria[&&NHX:TOL=60059],lechevalieria[&&NHX:TOL=60060],lentzea[&&NHX:TOL=60061],prauserella[&&NHX:TOL=60062],pseudonocardia[&&NHX:TOL=60063],saccharomonospora[&&NHX:TOL=60064],saccharopolyspora[&&NHX:TOL=60065],saccharothrix[&&NHX:TOL=60066],streptoalloteichus[&&NHX:TOL=60067],thermobispora[&&NHX:TOL=60068],thermocrispum[&&NHX:TOL=60069])pseudonocardineae[&&NHX:TOL=60051],(kitasatospora[&&NHX:TOL=60071],streptomyces[&&NHX:TOL=60072],streptoverticillium[&&NHX:TOL=60073])streptomycineae[&&NHX:TOL=60070],(acrocarpospora[&&NHX:TOL=60075],actinomadura[&&NHX:TOL=60076],herbidospora[&&NHX:TOL=60077],microbispora[&&NHX:TOL=60078],microtetraspora[&&NHX:TOL=60079],nocardiopsis[&&NHX:TOL=60080],nonomuraea[&&NHX:TOL=60081],planobispora[&&NHX:TOL=60082],planomonospora[&&NHX:TOL=60083],planotetraspora[&&NHX:TOL=60084],spirillospora[&&NHX:TOL=60085],streptomonospora[&&NHX:TOL=60086],streptosporangium[&&NHX:TOL=60087],thermobifida[&&NHX:TOL=60088],thermomonospora[&&NHX:TOL=60089])streptosporangineae[&&NHX:TOL=60074],(acidothermus[&&NHX:TOL=60091],blastococcus[&&NHX:TOL=60092],cryptosporangium[&&NHX:TOL=60093],frankia[&&NHX:TOL=60094],geodermatophilus[&&NHX:TOL=60095],kineococcus[&&NHX:TOL=60096],kineosporia[&&NHX:TOL=60097],microsphaera[&&NHX:TOL=60099],modestobacter[&&NHX:TOL=60098],sporichthya[&&NHX:TOL=60100])frankineae[&&NHX:TOL=60090],(glycomyces harbinensis[&&NHX:TOL=60242],glycomyces rutgersensis[&&NHX:TOL=60243],glycomyces tenuis[&&NHX:TOL=60244])glycomyces[&&NHX:TOL=60101])actinomycetales[&&NHX:TOL=59965],(atopobium[&&NHX:TOL=59937],collinsella[&&NHX:TOL=59939],coriobacterium[&&NHX:TOL=59941],cryptobacterium[&&NHX:TOL=59942],denitrobacterium[&&NHX:TOL=59943],eggerthella[&&NHX:TOL=59944],olsenella[&&NHX:TOL=59948],slackia[&&NHX:TOL=59952])coriobacteriales[&&NHX:TOL=60030],(conexibacter[&&NHX:TOL=59940],rubrobacter[&&NHX:TOL=59951],solirubrobacter[&&NHX:TOL=59953],thermoleophilum[&&NHX:TOL=59956])rubrobacterales[&&NHX:TOL=60031],(actinocorallia[&&NHX:TOL=60103],aeriscardovia[&&NHX:TOL=60104],bifidobacterium[&&NHX:TOL=60105],falcivibrio[&&NHX:TOL=60106],gardnerella[&&NHX:TOL=60107],parascardovia[&&NHX:TOL=60108],pelczaria[&&NHX:TOL=60109],scardovia[&&NHX:TOL=60110],turicella[&&NHX:TOL=60111])bifidobacteriales[&&NHX:TOL=60102])actinobacteria[&&NHX:TOL=59583],((deinococcus radiodurans[&&NHX:TOL=122689],deinococcus geothermalis[&&NHX:TOL=122690],deinococcus grandis[&&NHX:TOL=122691],deinococcus indicus[&&NHX:TOL=122692],deinococcus murrayi[&&NHX:TOL=122693],deinococcus proteolyticus[&&NHX:TOL=122694],deinococcus radiopugnans[&&NHX:TOL=122695])deinococcus[&&NHX:TOL=59635],(thermus aquaticus[&&NHX:TOL=122696],thermus antranikianii[&&NHX:TOL=122697],thermus brockianus[&&NHX:TOL=122698],thermus filiformis[&&NHX:TOL=122699],thermus igniterrae[&&NHX:TOL=122700],thermus oshimai[&&NHX:TOL=122701],thermus scotoductus[&&NHX:TOL=122702],thermus thermophilus[&&NHX:TOL=122703])thermus[&&NHX:TOL=59636],marinithermus hydrothermalis[&&NHX:TOL=59637],(meiothermus ruber[&&NHX:TOL=122704],meiothermus cerbereus[&&NHX:TOL=122705],meiothermus chliarophilus[&&NHX:TOL=122706],meiothermus silvanus[&&NHX:TOL=122707],meiothermus taiwanensis[&&NHX:TOL=122708])meiothermus[&&NHX:TOL=59638],oceanithermus profundus[&&NHX:TOL=59639],vulcanithermus mediatlanticus[&&NHX:TOL=59640])deinococcusthermus[&&NHX:TOL=2288],((chamaesiphon[&&NHX:TOL=2309],chroococcus[&&NHX:TOL=2310],cyanobacterium[&&NHX:TOL=2311],cyanobium[&&NHX:TOL=2312],cyanothece[&&NHX:TOL=2313],dactylococcopsis[&&NHX:TOL=2314],gloeobacter[&&NHX:TOL=2315],gloeocapsa[&&NHX:TOL=2316],gloeothece[&&NHX:TOL=2317],microcystis[&&NHX:TOL=2318],prochlorococcus[&&NHX:TOL=2319],prochloron[&&NHX:TOL=2320],synechococcus[&&NHX:TOL=2321],synechocystis[&&NHX:TOL=2322])subsection i[&&NHX:TOL=2308],(cyanocystis[&&NHX:TOL=2324],dermocarpella[&&NHX:TOL=2325],stanieria[&&NHX:TOL=2326],xenococcus[&&NHX:TOL=2327],chroococcidiopsis[&&NHX:TOL=2328],myxosarcina[&&NHX:TOL=2329],pleurocapsa[&&NHX:TOL=2330])subsection ii[&&NHX:TOL=2323],(arthrospira[&&NHX:TOL=2332],borzia[&&NHX:TOL=2333],crinalium[&&NHX:TOL=2334],geitlerinema[&&NHX:TOL=2335],halospirulina[&&NHX:TOL=59680],leptolyngbya[&&NHX:TOL=2336],limnothrix[&&NHX:TOL=2337],lyngbya[&&NHX:TOL=2338],microcoleus[&&NHX:TOL=2339],oscillatoria[&&NHX:TOL=2340],planktothrix[&&NHX:TOL=2341],prochlorothrix[&&NHX:TOL=2342],pseudanabaena[&&NHX:TOL=2343],spirulina[&&NHX:TOL=2344],starria[&&NHX:TOL=2345],symploca[&&NHX:TOL=2346],trichodesmium[&&NHX:TOL=2347],tychonema[&&NHX:TOL=2348])subsection iii[&&NHX:TOL=2331],(anabaena[&&NHX:TOL=2351],anabaenopsis[&&NHX:TOL=2352],aphanizomenon[&&NHX:TOL=2353],calothrix[&&NHX:TOL=2361],cyanospira[&&NHX:TOL=2354],cylindrospermopsis[&&NHX:TOL=2355],cylindrospermum[&&NHX:TOL=2356],nodularia[&&NHX:TOL=2357],nostoc[&&NHX:TOL=2358],rivularia[&&NHX:TOL=2362],scytonema[&&NHX:TOL=2359],tolypothrix[&&NHX:TOL=2363])subsection iv[&&NHX:TOL=2349],(chlorogloeopsis[&&NHX:TOL=2365],fischerella[&&NHX:TOL=2366],geitleria[&&NHX:TOL=2367],iyengariella[&&NHX:TOL=2368],nostochopsis[&&NHX:TOL=2369],stigonema[&&NHX:TOL=2370])subsection v[&&NHX:TOL=2364])cyanobacteria[&&NHX:TOL=2290],((((acetivibrio[&&NHX:TOL=59690],acidaminobacter[&&NHX:TOL=59691],alkaliphilus[&&NHX:TOL=59692],anaerobacter[&&NHX:TOL=59693],anaerotruncus[&&NHX:TOL=59694],bryantella[&&NHX:TOL=59695],caloramator[&&NHX:TOL=59696],caloranaerobacter[&&NHX:TOL=59697],caminicella[&&NHX:TOL=59698],clostridium[&&NHX:TOL=59699],coprobacillus[&&NHX:TOL=59700],dorea[&&NHX:TOL=59701],faecalibacterium[&&NHX:TOL=59702],hespellia[&&NHX:TOL=59703],natronincola[&&NHX:TOL=59704],oxobacter[&&NHX:TOL=59705],parasporobacterium[&&NHX:TOL=59706],sarcina[&&NHX:TOL=59707],soehngenia[&&NHX:TOL=59708],tepidibacter[&&NHX:TOL=59710],thermobrachium[&&NHX:TOL=59711],thermohalobacter[&&NHX:TOL=59712],tindallia[&&NHX:TOL=59713])clostridiaceae[&&NHX:TOL=59689],(acetitomaculum[&&NHX:TOL=59715],anaerofilum[&&NHX:TOL=59716],anaerostipes[&&NHX:TOL=59717],butyrivibrio[&&NHX:TOL=59718],catenibacterium[&&NHX:TOL=59719],catonella[&&NHX:TOL=59720],coprococcus[&&NHX:TOL=59721],johnsonella[&&NHX:TOL=59722],lachnobacterium[&&NHX:TOL=59723],lachnospira[&&NHX:TOL=59724],pseudobutyrivibrio[&&NHX:TOL=59725],roseburia[&&NHX:TOL=59726],ruminococcus[&&NHX:TOL=59727],shuttleworthia[&&NHX:TOL=59728],sporobacterium[&&NHX:TOL=59729])lachnospiraceae[&&NHX:TOL=59714],(anaerococcus[&&NHX:TOL=59731],filifactor[&&NHX:TOL=59732],finegoldia[&&NHX:TOL=59733],fusibacter[&&NHX:TOL=59734],gallicola[&&NHX:TOL=59735],helcococcus[&&NHX:TOL=59736],micromonas[&&NHX:TOL=59737],peptoniphilus[&&NHX:TOL=59738],peptostreptococcus[&&NHX:TOL=59739],sedimentibacter[&&NHX:TOL=59740],sporanaerobacter[&&NHX:TOL=59741],tissierella[&&NHX:TOL=59742])peptostreptococcaceae[&&NHX:TOL=59730],(acetobacterium[&&NHX:TOL=59744],anaerovorax[&&NHX:TOL=59745],eubacterium[&&NHX:TOL=59746],mogibacterium[&&NHX:TOL=59747],pseudoramibacter[&&NHX:TOL=59748])eubacteriaceae[&&NHX:TOL=59743],(carboxydothermus[&&NHX:TOL=59752],dehalobacter[&&NHX:TOL=59753],desulfitobacterium[&&NHX:TOL=59754],desulfonispora[&&NHX:TOL=59755],desulfosporosinus[&&NHX:TOL=59756],desulfotomaculum[&&NHX:TOL=59757],pelotomaculum[&&NHX:TOL=59758],peptococcus[&&NHX:TOL=59759],syntrophobotulus[&&NHX:TOL=59760],thermoterrabacterium[&&NHX:TOL=59761])peptococcaceae[&&NHX:TOL=59751],(heliobacillus[&&NHX:TOL=59763],heliobacterium[&&NHX:TOL=59764],heliophilum[&&NHX:TOL=59765],heliorestis[&&NHX:TOL=59766])heliobacteriaceae[&&NHX:TOL=59762],(acetonema[&&NHX:TOL=59768],acidaminococcus[&&NHX:TOL=59769],allisonella[&&NHX:TOL=59770],anaeroarcus[&&NHX:TOL=59771],anaeroglobus[&&NHX:TOL=59772],anaeromusa[&&NHX:TOL=59773],anaerosinus[&&NHX:TOL=59774],anaerovibrio[&&NHX:TOL=59775],centipeda[&&NHX:TOL=59776],dendrosporobacter[&&NHX:TOL=59777],dialister[&&NHX:TOL=59778],megasphaera[&&NHX:TOL=59779],mitsuokella[&&NHX:TOL=59780],papillibacter[&&NHX:TOL=59781],pectinatus[&&NHX:TOL=59782],phascolarctobacterium[&&NHX:TOL=59783],propionispira[&&NHX:TOL=59784],propionispora[&&NHX:TOL=59785],quinella[&&NHX:TOL=59786],schwartzia[&&NHX:TOL=59787],selenomonas[&&NHX:TOL=59788],sporomusa[&&NHX:TOL=59789],succiniclasticum[&&NHX:TOL=59790],succinispira[&&NHX:TOL=59791],veillonella[&&NHX:TOL=59792],zymophilus[&&NHX:TOL=59793])acidaminococcaceae[&&NHX:TOL=59767],(acetogenium[&&NHX:TOL=59795],aminobacterium[&&NHX:TOL=59796],aminomonas[&&NHX:TOL=59797],anaerobaculum[&&NHX:TOL=59798],anaerobranca[&&NHX:TOL=59799],caldicellulosiruptor[&&NHX:TOL=59800],carboxydocella[&&NHX:TOL=59801],dethiosulfovibrio[&&NHX:TOL=59802],pelospora[&&NHX:TOL=59803],syntrophospora[&&NHX:TOL=59804],syntrophothermus[&&NHX:TOL=59805],thermoaerobacter[&&NHX:TOL=59806],thermanaerovibrio[&&NHX:TOL=59807],thermohydrogenium[&&NHX:TOL=59808],thermosyntropha[&&NHX:TOL=59809])syntrophomonadaceae[&&NHX:TOL=59794])clostridiales[&&NHX:TOL=59688],(ammonifex[&&NHX:TOL=59810],caldanaerobacter[&&NHX:TOL=59811],carboxydobrachium[&&NHX:TOL=59812],coprothermobacter[&&NHX:TOL=59813],gelria[&&NHX:TOL=59814],moorella[&&NHX:TOL=59815],sporotomaculum[&&NHX:TOL=59816],thermacetogenium[&&NHX:TOL=59817],thermanaeromonas[&&NHX:TOL=59818],thermoanaerobacter[&&NHX:TOL=59819],thermoanaerobacterium[&&NHX:TOL=59820],thermoanaerobium[&&NHX:TOL=59821],thermovenabulum[&&NHX:TOL=59822],thermodesulfobium[&&NHX:TOL=59823])thermoanaerobacteriales[&&NHX:TOL=59749],(acetohalobium[&&NHX:TOL=59825],halanaerobacter[&&NHX:TOL=59826],halanaerobium[&&NHX:TOL=59827],halonatronum[&&NHX:TOL=59828],halobacteroides[&&NHX:TOL=59829],halocella[&&NHX:TOL=59830],halothermothrix[&&NHX:TOL=59831],natroniella[&&NHX:TOL=59832],orenia[&&NHX:TOL=59833],selenihalanaerobacter[&&NHX:TOL=59834],sporohalobacter[&&NHX:TOL=59835])haloanaerobiales[&&NHX:TOL=59824])clostridia[&&NHX:TOL=59687],(acholeplasma[&&NHX:TOL=59837],anaeroplasma[&&NHX:TOL=59838],asteroleplasma[&&NHX:TOL=59839],entomoplasma[&&NHX:TOL=59840],eperythrozoon[&&NHX:TOL=59841],haemobartonella[&&NHX:TOL=59842],mesoplasma[&&NHX:TOL=59843],mycoplasma[&&NHX:TOL=59844],phytoplasma[&&NHX:TOL=59845],spiroplasma[&&NHX:TOL=59846],ureaplasma[&&NHX:TOL=59847],(bulleidia[&&NHX:TOL=59849],erysipelothrix[&&NHX:TOL=59850],holdemania[&&NHX:TOL=59851],solobacterium[&&NHX:TOL=59852])erysipelotrichaceae[&&NHX:TOL=59848])mollicutes[&&NHX:TOL=59750],((alicyclobacillus[&&NHX:TOL=59854],ammoniphilus[&&NHX:TOL=59855],amphibacillus[&&NHX:TOL=59856],aneurinibacillus[&&NHX:TOL=59857],anoxybacillus[&&NHX:TOL=59858],bacillus[&&NHX:TOL=59859],brevibacillus[&&NHX:TOL=59860],brochothrix[&&NHX:TOL=59861],caryophanon[&&NHX:TOL=59862],exiguobacterium[&&NHX:TOL=59863],filibacter[&&NHX:TOL=59864],filobacillus[&&NHX:TOL=59865],gemella[&&NHX:TOL=59866],geobacillus[&&NHX:TOL=59867],gracilibacillus[&&NHX:TOL=59868],halobacillus[&&NHX:TOL=59869],jeotgalibacillus[&&NHX:TOL=59870],jeotgalicoccus[&&NHX:TOL=59871],kurthia[&&NHX:TOL=59872],lentibacillus[&&NHX:TOL=59873],listeria[&&NHX:TOL=59874],macrococcus[&&NHX:TOL=59875],marinibacillus[&&NHX:TOL=59876],marinococcus[&&NHX:TOL=59877],oceanobacillus[&&NHX:TOL=59878],oxalophagus[&&NHX:TOL=59879],paenibacillus[&&NHX:TOL=59880],paraliobacillus[&&NHX:TOL=59881],pasteuria[&&NHX:TOL=59882],planococcus[&&NHX:TOL=59883],planomicrobium[&&NHX:TOL=59884],saccharococcus[&&NHX:TOL=59885],salibacillus[&&NHX:TOL=59886],salinicoccus[&&NHX:TOL=59887],sporolactobacillus[&&NHX:TOL=59888],sporosarcina[&&NHX:TOL=59889],staphylococcus[&&NHX:TOL=59890],sulfobacillus[&&NHX:TOL=59891],thermicanus[&&NHX:TOL=59892],thermoactinomyces[&&NHX:TOL=59893],thermobacillus[&&NHX:TOL=59894],turicibacter[&&NHX:TOL=59895],ureibacillus[&&NHX:TOL=59896],virgibacillus[&&NHX:TOL=59897])bacillales[&&NHX:TOL=59836],(abiotrophia[&&NHX:TOL=59899],acetoanaerobium[&&NHX:TOL=59900],aerococcus[&&NHX:TOL=59901],agitococcus[&&NHX:TOL=59902],alkalibacterium[&&NHX:TOL=59903],allofustis[&&NHX:TOL=59904],alloiococcus[&&NHX:TOL=59905],atopobacter[&&NHX:TOL=59906],carnobacterium[&&NHX:TOL=59907],desemzia[&&NHX:TOL=59908],dolosicoccus[&&NHX:TOL=59909],dolosigranulum[&&NHX:TOL=59910],enterococcus[&&NHX:TOL=59911],eremococcus[&&NHX:TOL=59912],facklamia[&&NHX:TOL=59913],globicatella[&&NHX:TOL=59914],granulicatella[&&NHX:TOL=59915],ignavigranum[&&NHX:TOL=59916],isobaculum[&&NHX:TOL=59917],lactobacillus[&&NHX:TOL=59918],lactococcus[&&NHX:TOL=59919],lactosphaera[&&NHX:TOL=59920],leuconostoc[&&NHX:TOL=59921],marinilactibacillus[&&NHX:TOL=59922],melissococcus[&&NHX:TOL=59923],oenococcus[&&NHX:TOL=59924],oscillospira[&&NHX:TOL=59925],paralactobacillus[&&NHX:TOL=59926],pediococcus[&&NHX:TOL=59927],streptococcus[&&NHX:TOL=59928],syntrophococcus[&&NHX:TOL=59929],tetragenococcus[&&NHX:TOL=59930],trichococcus[&&NHX:TOL=59931],vagococcus[&&NHX:TOL=59932],weissella[&&NHX:TOL=59933])lactobacillales[&&NHX:TOL=59898])bacilli[&&NHX:TOL=59853])firmicutes[&&NHX:TOL=2291],(fusobacterium[&&NHX:TOL=60213],ilyobacter[&&NHX:TOL=60214],leptotrichia[&&NHX:TOL=60215],propionigenium[&&NHX:TOL=60216],sebaldella[&&NHX:TOL=60217],streptobacillus[&&NHX:TOL=60218],sneathia[&&NHX:TOL=60219],cetobacterium ceti[&&NHX:TOL=60220])fusobacteria[&&NHX:TOL=59603],(opitutus[&&NHX:TOL=60221],prosthecobacter[&&NHX:TOL=60222],verrucomicrobium[&&NHX:TOL=60223],victivallis[&&NHX:TOL=60224],xiphinematobacter[&&NHX:TOL=60225])verrucomicrobia[&&NHX:TOL=2296],(acidobacterium capsulatum[&&NHX:TOL=60130],geothrix fermentans[&&NHX:TOL=60131],holophaga foetida[&&NHX:TOL=60132])acidobacteria[&&NHX:TOL=59601],(dictyoglomus thermophilum[&&NHX:TOL=60226],dictyoglomus turgidum[&&NHX:TOL=60227])dictyoglomi[&&NHX:TOL=59604],gemmatimonas aurantiaca[&&NHX:TOL=2292])eubacteria[&&NHX:TOL=2],((((prasinophytes[&&NHX:TOL=20567],((chlorophyceae[&&NHX:TOL=20570],trebouxiophyceae[&&NHX:TOL=20571])[&&NHX:TOL=20569],ulvophyceae[&&NHX:TOL=20572])[&&NHX:TOL=20568],(chlorokybales[&&NHX:TOL=20574],(klebsormidiales[&&NHX:TOL=20576],(((zygnemataceae[&&NHX:TOL=21728],mesotaeniaceae[&&NHX:TOL=21729])[&&NHX:TOL=21727],((gonatozygaceae[&&NHX:TOL=21732],closteriaceae[&&NHX:TOL=21733],peniaceae[&&NHX:TOL=21734])[&&NHX:TOL=21731],desmidiaceae[&&NHX:TOL=21735])[&&NHX:TOL=21730])zygnematales[&&NHX:TOL=20578],((((chara[&&NHX:TOL=20586],lamprothamnium[&&NHX:TOL=20587])[&&NHX:TOL=20585],(lychnothamnus[&&NHX:TOL=20589],nitellopsis[&&NHX:TOL=20590])[&&NHX:TOL=20588])[&&NHX:TOL=20584],(nitella[&&NHX:TOL=20593],tolypella[&&NHX:TOL=20592])[&&NHX:TOL=20591])charales[&&NHX:TOL=20580],coleochaetales[&&NHX:TOL=20581],(marchantiomorpha[&&NHX:TOL=20595],((notothylas[&&NHX:TOL=21561],(((anthoceros[&&NHX:TOL=21565],(sphaerosporoceros[&&NHX:TOL=21567],(leiosporoceros[&&NHX:TOL=21569],folioceros[&&NHX:TOL=21570])[&&NHX:TOL=21568])[&&NHX:TOL=21566])[&&NHX:TOL=21564],(mesoceros[&&NHX:TOL=21572],phaeoceros[&&NHX:TOL=21573])[&&NHX:TOL=21571])anthocerotaceae[&&NHX:TOL=21563],(dendroceros[&&NHX:TOL=21575],megaceros[&&NHX:TOL=21576])dendrocerotaceae[&&NHX:TOL=21574])[&&NHX:TOL=21562])anthocerotophyta[&&NHX:TOL=20597],((sphagnopsida[&&NHX:TOL=21578],takakiales[&&NHX:TOL=21579],(andreaeopsida[&&NHX:TOL=21581],(oedipodiaceae[&&NHX:TOL=21583],polytrichopsida[&&NHX:TOL=21584],(tetraphidopsida[&&NHX:TOL=21586],(diphysiales[&&NHX:TOL=21589],(funariales[&&NHX:TOL=21591],(timmiales[&&NHX:TOL=21593],(encalyptales[&&NHX:TOL=21595],((grimmiales[&&NHX:TOL=21598],seligeriales[&&NHX:TOL=21599],archidiales[&&NHX:TOL=21600])[&&NHX:TOL=21597],(pottiales[&&NHX:TOL=21602],dicranales[&&NHX:TOL=21603])[&&NHX:TOL=21601])dicraniidae[&&NHX:TOL=21596],((orthotrichales[&&NHX:TOL=21606],splachnales[&&NHX:TOL=21607])[&&NHX:TOL=21605],(hedwigiales[&&NHX:TOL=21609],bryales[&&NHX:TOL=21610],(rhizogoniales[&&NHX:TOL=21612],(hookeriales[&&NHX:TOL=21614],hypnales[&&NHX:TOL=21615])[&&NHX:TOL=21613])[&&NHX:TOL=21611])[&&NHX:TOL=21608])bryidae[&&NHX:TOL=21604])[&&NHX:TOL=21594])[&&NHX:TOL=21592])[&&NHX:TOL=21590])bryopsida[&&NHX:TOL=21587])[&&NHX:TOL=21585])peristomate mosses[&&NHX:TOL=21582])[&&NHX:TOL=21580])bryophyta[&&NHX:TOL=20599],(horneophytopsida[&&NHX:EXT=Y:TOL=20601],(aglaophyton major[&&NHX:EXT=Y:TOL=20603],(rhyniopsida[&&NHX:EXT=Y:TOL=20605],((lycopodiaceae[&&NHX:TOL=134087],(selaginella[&&NHX:TOL=134089],isoëtes[&&NHX:TOL=134090])selaginellidae[&&NHX:TOL=134088])lycopodiopsida[&&NHX:TOL=20607],(eophyllophyton bellum[&&NHX:EXT=Y:TOL=20609],psilophyton dawsonii[&&NHX:EXT=Y:TOL=20610],((cladoxylopsida[&&NHX:EXT=Y:TOL=20613],((((((((((((((((polypodiaceae[&&NHX:TOL=21677],davalliaceae[&&NHX:TOL=21679])[&&NHX:TOL=94188],oleandraceae[&&NHX:TOL=94189])[&&NHX:TOL=94187],tectariaceae[&&NHX:TOL=94190])[&&NHX:TOL=94186],lomariopsidaceae[&&NHX:TOL=94191])[&&NHX:TOL=94185],dryopteridaceae[&&NHX:TOL=21681])eupolypods i[&&NHX:TOL=94184],(thelypteridaceae[&&NHX:TOL=21683],(blechnaceae[&&NHX:TOL=21682],onocleaceae[&&NHX:TOL=94194])[&&NHX:TOL=94193],aspleniaceae[&&NHX:TOL=21684],woodsiaceae[&&NHX:TOL=94195])eupolypods ii[&&NHX:TOL=94192])[&&NHX:TOL=21673],(((((((hemionitids[&&NHX:TOL=133569],(cheilanthes leucopoda[&&NHX:TOL=133578],notholaena nigricans[&&NHX:TOL=133587],notholaena solitaria[&&NHX:TOL=133588],(notholaena standleyi[&&NHX:TOL=133579],(((notholaena aureolina[&&NHX:TOL=133618],notholaena jaliscana[&&NHX:TOL=133620])[&&NHX:TOL=133633],notholaena brachypus[&&NHX:TOL=133619],notholaena ochracea[&&NHX:TOL=133622])notholaena aureolina clade[&&NHX:TOL=133580],(cheiloplecton rigidum[&&NHX:TOL=133581],((((notholaena grayi[&&NHX:TOL=133594],notholaena aliena[&&NHX:TOL=133589])[&&NHX:TOL=133624],(notholaena rosei[&&NHX:TOL=133597],notholaena montieliae[&&NHX:TOL=133621])[&&NHX:TOL=140242])[&&NHX:TOL=133623],(notholaena schaffneri[&&NHX:TOL=133598],((notholaena rigida[&&NHX:TOL=133596],(notholaena nealleyi[&&NHX:TOL=133595],notholaena brevistipes[&&NHX:TOL=133592])[&&NHX:TOL=140577])[&&NHX:TOL=133627],(notholaena aschenborniana[&&NHX:TOL=133590],notholaena galeottii[&&NHX:TOL=133593])[&&NHX:TOL=140578])[&&NHX:TOL=133626])[&&NHX:TOL=133625],notholaena trichomanoides[&&NHX:TOL=133599],notholaena weatherbiana[&&NHX:TOL=133600],notholaena brachycaulis[&&NHX:TOL=133591],notholaena affinis[&&NHX:TOL=133601])core notholaena i[&&NHX:TOL=133616],(notholaena greggii[&&NHX:TOL=133608],((notholaena lemmonii[&&NHX:TOL=133610],notholaena meridionalis[&&NHX:TOL=133612])[&&NHX:TOL=133629],notholaena californica[&&NHX:TOL=133603])[&&NHX:TOL=133628],((notholaena neglecta[&&NHX:TOL=133613],notholaena bryopoda[&&NHX:TOL=133602],notholaena jacalensis[&&NHX:TOL=133609])[&&NHX:TOL=133631],(notholaena copelandii[&&NHX:TOL=133605],notholaena candida[&&NHX:TOL=133604])[&&NHX:TOL=133632],notholaena sulphurea[&&NHX:TOL=133614])[&&NHX:TOL=133630],notholaena cubensis[&&NHX:TOL=133615],notholaena ekmanii[&&NHX:TOL=133606],notholaena galapagensis[&&NHX:TOL=133607],notholaena leonina[&&NHX:TOL=133611])core notholaena ii[&&NHX:TOL=133617])core notholaena[&&NHX:TOL=133582])[&&NHX:TOL=133585])[&&NHX:TOL=133584],notholaena aurantiaca[&&NHX:TOL=133586])[&&NHX:TOL=133583])notholaenids[&&NHX:TOL=133570])[&&NHX:TOL=133568],((pellaeids[&&NHX:TOL=133573],myriopterids[&&NHX:TOL=133574])[&&NHX:TOL=133572],skinneri clade[&&NHX:TOL=133575])[&&NHX:TOL=133571])[&&NHX:TOL=133567],bommeriids[&&NHX:TOL=133576])[&&NHX:TOL=133566],doryopteris ludens clade[&&NHX:TOL=133577])cheilanthoids[&&NHX:TOL=133070],adiantoids[&&NHX:TOL=133071])[&&NHX:TOL=133069],(ceratopteridoids[&&NHX:TOL=133074],pteridoids[&&NHX:TOL=133073])[&&NHX:TOL=133072])[&&NHX:TOL=133068],cryptogrammoids[&&NHX:TOL=133075])pteridaceae[&&NHX:TOL=29352],dennstaedtiaceae[&&NHX:TOL=21688])[&&NHX:TOL=21672],lindsaeaceae[&&NHX:TOL=21689],saccolomataceae[&&NHX:TOL=94196])polypodiales[&&NHX:TOL=21671],((dicksoniaceae[&&NHX:TOL=21695],cibotiaceae[&&NHX:TOL=94198],cyatheaceae[&&NHX:TOL=21696],metaxyaceae[&&NHX:TOL=21692])[&&NHX:TOL=94197],thyrsopteridaceae[&&NHX:TOL=94199],((plagiogyriaceae[&&NHX:TOL=21697],culcitaceae[&&NHX:TOL=94202])[&&NHX:TOL=94201],loxomataceae[&&NHX:TOL=21694])[&&NHX:TOL=94200])cyatheales[&&NHX:TOL=21690])[&&NHX:TOL=27842],((salviniaceae[&&NHX:TOL=21702],hydropteris[&&NHX:EXT=Y:TOL=21703])[&&NHX:TOL=21699],marsileaceae[&&NHX:TOL=21704])salviniales[&&NHX:TOL=21698])core leptosporangiates[&&NHX:TOL=33127],((anemiaceae[&&NHX:TOL=133882],schizaeaceae[&&NHX:TOL=133881])[&&NHX:TOL=133884],lygodiaceae[&&NHX:TOL=133883])schizaeales[&&NHX:TOL=21705])[&&NHX:TOL=21670],((matoniaceae[&&NHX:TOL=21709],dipteridaceae[&&NHX:TOL=21707])[&&NHX:TOL=94173],gleicheniaceae[&&NHX:TOL=21710])gleicheniales[&&NHX:TOL=27840],hymenophyllaceae[&&NHX:TOL=21711])[&&NHX:TOL=33126],tempskyaceae[&&NHX:EXT=Y:TOL=21719],psalixochlaenaceae[&&NHX:EXT=Y:TOL=21716],sermayaceae[&&NHX:EXT=Y:TOL=21715],anachoropteridaceae[&&NHX:EXT=Y:TOL=21717],botryopteridaceae[&&NHX:EXT=Y:TOL=21714],tedeleaceae[&&NHX:EXT=Y:TOL=21713],osmundaceae[&&NHX:TOL=33128])polypodiidae[&&NHX:TOL=21666],equisetum[&&NHX:TOL=33130],(((((((((((ptisana squamosa[&&NHX:TOL=134205],(ptisana sambucina[&&NHX:TOL=134207],(ptisana costulisora[&&NHX:TOL=56776],ptisana melanesica[&&NHX:TOL=56778])[&&NHX:TOL=134208])[&&NHX:TOL=134206])[&&NHX:TOL=134204],(ptisana pellucida[&&NHX:TOL=134210],ptisana sylvatica[&&NHX:TOL=134211])[&&NHX:TOL=134209],ptisana mertensiana[&&NHX:TOL=134212])[&&NHX:TOL=134203],(ptisana attenuata[&&NHX:TOL=56842],marattia rolandiprincipis[&&NHX:TOL=56779])[&&NHX:TOL=134213],ptisana howeana[&&NHX:TOL=134214])[&&NHX:TOL=134202],(ptisana salicina[&&NHX:TOL=134216],ptisana smithii[&&NHX:TOL=134217])[&&NHX:TOL=134215])[&&NHX:TOL=134201],(ptisana oreades[&&NHX:TOL=134219],ptisana obesa[&&NHX:TOL=134220])[&&NHX:TOL=134218])[&&NHX:TOL=134200],ptisana purpurascens[&&NHX:TOL=56775])[&&NHX:TOL=134199],ptisana fraxinea[&&NHX:TOL=56774],marattia koordersii[&&NHX:TOL=134280],ptisana platybasis[&&NHX:TOL=134281],ptisana novoguineensis[&&NHX:TOL=134282],ptisana grandifolia[&&NHX:TOL=134283],ptisana ternatea[&&NHX:TOL=134284])ptisana[&&NHX:TOL=56761],(eupodium kaulfussii[&&NHX:TOL=134222],(eupodium laeve[&&NHX:TOL=56763],marattia pittieri[&&NHX:TOL=134224])[&&NHX:TOL=134223])eupodium[&&NHX:TOL=134221])[&&NHX:TOL=134198],(christensenia aesculifolia[&&NHX:TOL=56838],(((((angiopteris itoi[&&NHX:TOL=56744],((angiopteris hokouensis[&&NHX:TOL=56747],angiopteris caudata[&&NHX:TOL=56748],angiopteris bipinnata[&&NHX:TOL=56749],angiopteris cadierei[&&NHX:TOL=56750],angiopteris henryi[&&NHX:TOL=56751],angiopteris chingii[&&NHX:TOL=134230])[&&NHX:TOL=56745],angiopteris tonkinensis[&&NHX:TOL=56746])[&&NHX:TOL=134229])archangiopteris[&&NHX:TOL=56743],(angiopteris angustifolia[&&NHX:TOL=134231],angiopteris rapensis[&&NHX:TOL=134232],angiopteris caudatiformis[&&NHX:TOL=134233],angiopteris hypoleuca[&&NHX:TOL=134234],angiopteris monstruosa[&&NHX:TOL=56758],angiopteris annamensis[&&NHX:TOL=56757],(angiopteris lygodiifolia[&&NHX:TOL=56756],angiopteris fokiensis[&&NHX:TOL=134236])[&&NHX:TOL=134235],angiopteris elliptica[&&NHX:TOL=56755],angiopteris evecta[&&NHX:TOL=56754],angiopteris teysmanniana[&&NHX:TOL=134285],angiopteris chauliodonta[&&NHX:TOL=134286])[&&NHX:TOL=56753])[&&NHX:TOL=134228],angiopteris smithii[&&NHX:TOL=56759])[&&NHX:TOL=134248],(angiopteris boninensis[&&NHX:TOL=134238],angiopteris durvilleana[&&NHX:TOL=134239])[&&NHX:TOL=134237])angiopteris[&&NHX:TOL=56742],(((marattia alata[&&NHX:TOL=56781],marattia weinmanniifolia[&&NHX:TOL=56768])[&&NHX:TOL=134250],marattia douglassii[&&NHX:TOL=56782])[&&NHX:TOL=56780],((marattia interposita[&&NHX:TOL=56767],marattia excavata[&&NHX:TOL=56764],marattia chiricana[&&NHX:TOL=56766])[&&NHX:TOL=134242],(marattia cicutifolia[&&NHX:TOL=56770],marattia laxa[&&NHX:TOL=56769])[&&NHX:TOL=134243])[&&NHX:TOL=134241])marattia[&&NHX:TOL=134240])[&&NHX:TOL=134226])[&&NHX:TOL=134225])[&&NHX:TOL=56741],((((((danaea falcata[&&NHX:TOL=56790],danaea vivax[&&NHX:TOL=56791])[&&NHX:TOL=56789],(danaea acuminata[&&NHX:TOL=56792],danaea riparia[&&NHX:TOL=56843])[&&NHX:TOL=134244])[&&NHX:TOL=56788],((danaea wendlandii[&&NHX:TOL=56795],danaea oblanceolata[&&NHX:TOL=56796])[&&NHX:TOL=56794],danaea alata[&&NHX:TOL=56797])[&&NHX:TOL=56793])[&&NHX:TOL=56787],((((danaea mazeana[&&NHX:TOL=56802],danaea jenmanii[&&NHX:TOL=56803],danaea moritziana[&&NHX:TOL=56804],danaea excurrens[&&NHX:TOL=56844],danaea humilis[&&NHX:TOL=56846],danaea cuspidata[&&NHX:TOL=134245])[&&NHX:TOL=56801],danaea urbanii[&&NHX:TOL=56805])[&&NHX:TOL=56800],(danaea carillensis[&&NHX:TOL=56807],danaea crispa[&&NHX:TOL=56808])[&&NHX:TOL=56806])[&&NHX:TOL=56799],(danaea trichomanoides[&&NHX:TOL=56809],danaea imbricata[&&NHX:TOL=56845],danaea plicata[&&NHX:TOL=56847],danaea tenera[&&NHX:TOL=56848])[&&NHX:TOL=134246])[&&NHX:TOL=56798],danaea bicolor[&&NHX:TOL=56849])holodanaea[&&NHX:TOL=56786],((danaea cartilaginea[&&NHX:TOL=56823],danaea nigrescens[&&NHX:TOL=56824])[&&NHX:TOL=56822],((((danaea media[&&NHX:TOL=56815],danaea nodosa[&&NHX:TOL=56816])[&&NHX:TOL=56814],(danaea grandifolia[&&NHX:TOL=56818],danaea longicaudata[&&NHX:TOL=56819])[&&NHX:TOL=56817])[&&NHX:TOL=56813],danaea kalevala[&&NHX:TOL=56820])[&&NHX:TOL=56812],danaea erecta[&&NHX:TOL=56821])[&&NHX:TOL=56811],danaea latipinna[&&NHX:TOL=56850],danaea ushana[&&NHX:TOL=56851])danaea[&&NHX:TOL=56810])[&&NHX:TOL=56785],(((((danaea arbuscula[&&NHX:TOL=56831],danaea polymorpha[&&NHX:TOL=56832],danaea ulei[&&NHX:TOL=56852],danaea geniculata[&&NHX:TOL=56853],danaea linguacervina[&&NHX:TOL=56854])[&&NHX:TOL=56828],danaea bipinnata[&&NHX:TOL=56829])[&&NHX:TOL=134247],danaea leprieurii[&&NHX:TOL=56833])[&&NHX:TOL=56827],(danaea trifoliata[&&NHX:TOL=56835],danaea antillensis[&&NHX:TOL=56836])[&&NHX:TOL=56834])[&&NHX:TOL=56826],danaea simplicifolia[&&NHX:TOL=56837])arthrodanaea[&&NHX:TOL=56825])danaea[&&NHX:TOL=56784])marattiaceae[&&NHX:TOL=134249],(psaronius  scolecopteris[&&NHX:EXT=Y:TOL=56840],asterotheca[&&NHX:EXT=Y:TOL=56855])asterothecaceae[&&NHX:EXT=Y:TOL=56839])marattiales[&&NHX:TOL=21664])[&&NHX:TOL=33124],(ophioglossaceae[&&NHX:TOL=21665],psilotaceae[&&NHX:TOL=21662])psilotidae[&&NHX:TOL=33131])[&&NHX:TOL=33123],zygopteridales[&&NHX:EXT=Y:TOL=21661],stauropteridales[&&NHX:EXT=Y:TOL=21660])polypodiopsida[&&NHX:TOL=20615])[&&NHX:TOL=20612],(pertica varia[&&NHX:EXT=Y:TOL=20617],(aneurophytales[&&NHX:EXT=Y:TOL=20619],archaeopteridales[&&NHX:EXT=Y:TOL=20620],protopityales[&&NHX:EXT=Y:TOL=20621],(calamopityaceae[&&NHX:EXT=Y:TOL=20624],hydraspermaceae[&&NHX:EXT=Y:TOL=20625],(lyginopteridaceae[&&NHX:EXT=Y:TOL=20627],(medullosaceae[&&NHX:EXT=Y:TOL=20629],(cycads[&&NHX:TOL=20631],callistophytaceae[&&NHX:EXT=Y:TOL=20632],(((taxaceae[&&NHX:TOL=21618],cupressaceae[&&NHX:TOL=21619],cephalotaxaceae[&&NHX:TOL=21620])[&&NHX:TOL=21617],sciadopityaceae[&&NHX:TOL=21621],podocarpaceae[&&NHX:TOL=21622],araucariaceae[&&NHX:TOL=21623],(((((((((pinus ponderosa[&&NHX:TOL=27207],pinus devoniana[&&NHX:TOL=27208],pinus durangensis[&&NHX:TOL=27209],pinus engelmannii[&&NHX:TOL=27212],pinus douglasiana[&&NHX:TOL=27213],pinus maximinoi[&&NHX:TOL=27214],pinus cooperi[&&NHX:TOL=27215],pinus coulteri[&&NHX:TOL=27216],pinus torreyana[&&NHX:TOL=27217],pinus sabineana[&&NHX:TOL=27218],pinus jeffreyi[&&NHX:TOL=27219])[&&NHX:TOL=27205],pinus hartwegii[&&NHX:TOL=27206],pinus montezumae[&&NHX:TOL=27210],pinus pseudostrobus[&&NHX:TOL=27211])subsection ponderosae[&&NHX:TOL=21645],((pinus attenuata[&&NHX:TOL=27229],pinus muricata[&&NHX:TOL=27230],pinus radiata[&&NHX:TOL=27231])[&&NHX:TOL=27225],((pinus cubensis[&&NHX:TOL=27235],pinus occidentalis[&&NHX:TOL=27236])[&&NHX:TOL=27227],(pinus pungens[&&NHX:TOL=27237],pinus rigida[&&NHX:TOL=27238],pinus taeda[&&NHX:TOL=27239],pinus serotina[&&NHX:TOL=27240])[&&NHX:TOL=27228],pinus lawsonii[&&NHX:TOL=27232],pinus lumholtzii[&&NHX:TOL=27233],pinus teocote[&&NHX:TOL=27234],pinus patula[&&NHX:TOL=27241],pinus pringlei[&&NHX:TOL=27242],pinus greggii[&&NHX:TOL=27243],pinus oocarpa[&&NHX:TOL=27244],pinus herrerae[&&NHX:TOL=27245],pinus palustris[&&NHX:TOL=27246],pinus caribaea[&&NHX:TOL=27247],pinus elliottii[&&NHX:TOL=27248],pinus echinata[&&NHX:TOL=27249],pinus leiophylla[&&NHX:TOL=27250],pinus jaliscana[&&NHX:TOL=27251],pinus praetermissa[&&NHX:TOL=27252])[&&NHX:TOL=27226])subsection australes[&&NHX:TOL=21649])[&&NHX:TOL=21644],((pinus clausa[&&NHX:TOL=27222],pinus virginiana[&&NHX:TOL=27223])[&&NHX:TOL=27220],pinus contorta[&&NHX:TOL=27221],pinus banksiana[&&NHX:TOL=27224])subsection contortae[&&NHX:TOL=21643])section trifoliae[&&NHX:TOL=27108],(((((pinus yunnanensis[&&NHX:TOL=27255],pinus densata[&&NHX:TOL=27256])[&&NHX:TOL=27253],pinus kesiya[&&NHX:TOL=27258])[&&NHX:TOL=27259],pinus tabuliformis[&&NHX:TOL=27254],pinus thunbergii[&&NHX:TOL=27257],pinus luchuensis[&&NHX:TOL=27260],pinus hwangshanensis[&&NHX:TOL=27261],pinus taiwanensis[&&NHX:TOL=27262])[&&NHX:TOL=27106],((pinus uncinata[&&NHX:TOL=27266],pinus mugo[&&NHX:TOL=27267])[&&NHX:TOL=27264],pinus sylvestris[&&NHX:TOL=27265],pinus densiflora[&&NHX:TOL=27268])[&&NHX:TOL=27263],((pinus merkusii[&&NHX:TOL=27273],pinus massoniana[&&NHX:TOL=27274])[&&NHX:TOL=27271],pinus tropicalis[&&NHX:TOL=27272])[&&NHX:TOL=27270],pinus resinosa[&&NHX:TOL=27275],pinus nigra[&&NHX:TOL=27276])subsection pinus[&&NHX:TOL=27269],(((pinus halepensis[&&NHX:TOL=27284],pinus brutia[&&NHX:TOL=27285])[&&NHX:TOL=27279],pinus pinaster[&&NHX:TOL=27280],pinus pinea[&&NHX:TOL=27281],pinus canariensis[&&NHX:TOL=27282],pinus roxburghii[&&NHX:TOL=27283])[&&NHX:TOL=27277],pinus heldreichii[&&NHX:TOL=27278])subsection pinaster[&&NHX:TOL=27107])section pinus[&&NHX:TOL=27105])subgenus pinus[&&NHX:TOL=21637],((((((((pinus armandii[&&NHX:TOL=27185],pinus cembra[&&NHX:TOL=27186],pinus morrisonicola[&&NHX:TOL=27187],pinus pumila[&&NHX:TOL=27188],pinus sibirica[&&NHX:TOL=27195],pinus fenzeliana[&&NHX:TOL=27201],pinus bhutanica[&&NHX:TOL=27202],pinus koraiensis[&&NHX:TOL=27203],pinus wallichiana[&&NHX:TOL=27204])[&&NHX:TOL=27181],(pinus lambertiana[&&NHX:TOL=27197],pinus parviflora[&&NHX:TOL=27198],pinus albicaulis[&&NHX:TOL=27199])[&&NHX:TOL=27196])[&&NHX:TOL=27200],pinus monticola[&&NHX:TOL=27193])[&&NHX:TOL=27194],((pinus strobus[&&NHX:TOL=27189],pinus chiapensis[&&NHX:TOL=27190])[&&NHX:TOL=27183],(pinus ayacahuite[&&NHX:TOL=27191],pinus flexilis[&&NHX:TOL=27192])[&&NHX:TOL=27184])[&&NHX:TOL=27182])[&&NHX:TOL=27179],pinus peuce[&&NHX:TOL=27180])subsection strobus[&&NHX:TOL=27118],pinus krempfii[&&NHX:TOL=27117])[&&NHX:TOL=27112],((pinus bungeana[&&NHX:TOL=27164],pinus gerardiana[&&NHX:TOL=27165])[&&NHX:TOL=27162],pinus squamata[&&NHX:TOL=27163])subsection gerardianae[&&NHX:TOL=27111])section quinquefoliae[&&NHX:TOL=27109],(((((pinus cembroides[&&NHX:TOL=27158],pinus remota[&&NHX:TOL=27159])[&&NHX:TOL=27153],(pinus johannis[&&NHX:TOL=27156],pinus culminicola[&&NHX:TOL=27157])[&&NHX:TOL=27154])[&&NHX:TOL=27151],(pinus monophylla[&&NHX:TOL=27160],pinus quadrifolia[&&NHX:TOL=27161])[&&NHX:TOL=27152],pinus edulis[&&NHX:TOL=27155])[&&NHX:TOL=27146],(pinus pinceana[&&NHX:TOL=27771],pinus maximartinezii[&&NHX:TOL=27772])[&&NHX:TOL=27770],pinus rzedowskii[&&NHX:TOL=27773])subsection cembroides[&&NHX:TOL=27769],(pinus nelsonii[&&NHX:TOL=27116],(pinus balfouriana[&&NHX:TOL=27142],(pinus longaeva[&&NHX:TOL=27144],pinus aristata[&&NHX:TOL=27145])[&&NHX:TOL=27143])subsection balfourianae[&&NHX:TOL=27115])[&&NHX:TOL=27113])section parrya[&&NHX:TOL=27110])subgenus strobus[&&NHX:TOL=21639])pinus[&&NHX:TOL=21626],picea[&&NHX:TOL=21627],cathaya[&&NHX:TOL=21628])[&&NHX:TOL=27099],((((pseudotsuga wilsoniana[&&NHX:TOL=27123],pseudotsuga sinensis[&&NHX:TOL=27124])[&&NHX:TOL=27121],pseudotsuga japonica[&&NHX:TOL=27122])[&&NHX:TOL=27119],(pseudotsuga menziesii[&&NHX:TOL=27125],pseudotsuga macrocarpa[&&NHX:TOL=27126])[&&NHX:TOL=27120])pseudotsuga[&&NHX:TOL=21630],((larix laricina[&&NHX:TOL=27129],larix lyallii[&&NHX:TOL=27130],larix occidentalis[&&NHX:TOL=27131])[&&NHX:TOL=27127],(larix griffithiana[&&NHX:TOL=27132],(larix potaninii[&&NHX:TOL=27138],larix gmelinii[&&NHX:TOL=27137],larix kaempferi[&&NHX:TOL=27136],larix russica[&&NHX:TOL=27135],larix decidua[&&NHX:TOL=27134])[&&NHX:TOL=27133],larix mastersiana[&&NHX:TOL=27139])[&&NHX:TOL=27128])larix[&&NHX:TOL=21629])[&&NHX:TOL=27104])[&&NHX:TOL=27100],cedrus[&&NHX:TOL=21631],((abies[&&NHX:TOL=21632],keteleeria[&&NHX:TOL=21633])[&&NHX:TOL=27101],(tsuga[&&NHX:TOL=21634],pseudolarix[&&NHX:TOL=21635])[&&NHX:TOL=27102])[&&NHX:TOL=27103])pinaceae[&&NHX:TOL=21624])conifers[&&NHX:TOL=20634],cordaitopsida[&&NHX:EXT=Y:TOL=20635])[&&NHX:TOL=20633],glossopteridaceae[&&NHX:EXT=Y:TOL=20636],czekanowskiaceae[&&NHX:EXT=Y:TOL=20637],ginkgos[&&NHX:TOL=20638],peltaspermaceae[&&NHX:EXT=Y:TOL=20639],corystospermaceae[&&NHX:EXT=Y:TOL=20640],caytoniaceae[&&NHX:EXT=Y:TOL=20641],(pentoxylales[&&NHX:EXT=Y:TOL=20643],bennettitales[&&NHX:EXT=Y:TOL=20644],((ephedra alata[&&NHX:TOL=27463],ephedra altissima[&&NHX:TOL=27464],ephedra americana[&&NHX:TOL=27465],ephedra antisyphilitica[&&NHX:TOL=27466],ephedra aphylla[&&NHX:TOL=27467],ephedra aspera[&&NHX:TOL=27468],ephedra boelckei[&&NHX:TOL=27469],ephedra breana[&&NHX:TOL=27470],ephedra californica[&&NHX:TOL=27471],ephedra chilensis[&&NHX:TOL=27472],ephedra compacta[&&NHX:TOL=27473],ephedra coryi[&&NHX:TOL=27474],ephedra cutleri[&&NHX:TOL=27475],ephedra distachya[&&NHX:TOL=27476],ephedra equisetina[&&NHX:TOL=27477],ephedra fasciculata[&&NHX:TOL=27478],ephedra fedtschenkoae[&&NHX:TOL=27479],ephedra foeminea[&&NHX:TOL=27480],ephedra foliata[&&NHX:TOL=27481],ephedra fragilis[&&NHX:TOL=27482],ephedra frustillata[&&NHX:TOL=27483],ephedra funerea[&&NHX:TOL=27484],ephedra gerardiana[&&NHX:TOL=27485],ephedra gracilis[&&NHX:TOL=27486],ephedra holoptera[&&NHX:TOL=27487],ephedra intermedia[&&NHX:TOL=27488],ephedra lepidosperma[&&NHX:TOL=27489],ephedra likiangensis[&&NHX:TOL=27490],ephedra lomatolepis[&&NHX:TOL=27491],ephedra major[&&NHX:TOL=27492],ephedra minuta[&&NHX:TOL=27493],ephedra monosperma[&&NHX:TOL=27494],ephedra multiflora[&&NHX:TOL=27495],ephedra nevadensis[&&NHX:TOL=27496],ephedra ochreata[&&NHX:TOL=27497],ephedra oxyphylla[&&NHX:TOL=27498],ephedra pachyclada[&&NHX:TOL=27499],ephedra pedunculata[&&NHX:TOL=27500],ephedra przewalski[&&NHX:TOL=27501],ephedra rupestris[&&NHX:TOL=27502],ephedra sarcocapa[&&NHX:TOL=27503],ephedra saxatilis[&&NHX:TOL=27504],ephedra sinica[&&NHX:TOL=27505],ephedra strobilacea[&&NHX:TOL=27506],ephedra torreyana[&&NHX:TOL=27507],ephedra triandra[&&NHX:TOL=27508],ephedra trifurca[&&NHX:TOL=27509],ephedra trifurcata[&&NHX:TOL=27510],ephedra tweediana[&&NHX:TOL=27511],ephedra viridis[&&NHX:TOL=27512])ephedra[&&NHX:TOL=21721],(welwitschia mirabilis[&&NHX:TOL=21723],(gnetum acutum[&&NHX:TOL=27513],gnetum africanum[&&NHX:TOL=27514],gnetum arobreum[&&NHX:TOL=27515],gnetum bosavicum[&&NHX:TOL=27516],gnetum buchholzianum[&&NHX:TOL=27517],gnetum camporum[&&NHX:TOL=27518],gnetum cleistostachyum[&&NHX:TOL=27519],gnetum contractum[&&NHX:TOL=27520],gnetum costatum[&&NHX:TOL=27521],gnetum cuspidatum[&&NHX:TOL=27522],gnetum diminutum[&&NHX:TOL=27523],gnetum globosum[&&NHX:TOL=27524],gnetum gnemon[&&NHX:TOL=27525],gnetum gnemonoides[&&NHX:TOL=27526],gnetum gracilipes[&&NHX:TOL=27527],gnetum hainanense[&&NHX:TOL=27528],gnetum klossii[&&NHX:TOL=27529],gnetum latifolium[&&NHX:TOL=27530],gnetum leptostachyum[&&NHX:TOL=27531],gnetum leyboldii[&&NHX:TOL=27532],gnetum lofuense[&&NHX:TOL=27533],gnetum loerzingii[&&NHX:TOL=27534],gnetum macrostachyum[&&NHX:TOL=27535],gnetum microcarpum[&&NHX:TOL=27536],gnetum montanum[&&NHX:TOL=27537],gnetum neglectum[&&NHX:TOL=27538],gnetum nodiflorum[&&NHX:TOL=27539],gnetum oblongum[&&NHX:TOL=27540],gnetum oxycarpum[&&NHX:TOL=27541],gnetum paniculatum[&&NHX:TOL=27542],gnetum parvifolium[&&NHX:TOL=27543],gnetum pendulum[&&NHX:TOL=27544],gnetum raya[&&NHX:TOL=27545],gnetum ridleyi[&&NHX:TOL=27546],gnetum schwackeanum[&&NHX:TOL=27547],gnetum tenuifolium[&&NHX:TOL=27548],gnetum ula[&&NHX:TOL=27549],gnetum urens[&&NHX:TOL=27550],gnetum venosum[&&NHX:TOL=27551])gnetum[&&NHX:TOL=21724])[&&NHX:TOL=21722])gnetales[&&NHX:TOL=20645],(amborella trichopoda[&&NHX:TOL=20652],((((((aristolochiaceae[&&NHX:TOL=21536],((saururus cernuus[&&NHX:TOL=133650],saururus chinensis[&&NHX:TOL=133651],anemopsis californica[&&NHX:TOL=133652],gymnotheca chinensis[&&NHX:TOL=133653],gymnotheca involucrata[&&NHX:TOL=133654],houttuynia cordata[&&NHX:TOL=133655])saururaceae[&&NHX:TOL=21539],piperaceae[&&NHX:TOL=21538])[&&NHX:TOL=21537],(hydnora[&&NHX:TOL=133656],prosopanche[&&NHX:TOL=133657])hydnoraceae[&&NHX:TOL=21540])piperales[&&NHX:TOL=20674],(((bubbia[&&NHX:TOL=21544],belliolum[&&NHX:TOL=21545],exospermum[&&NHX:TOL=21546],zygogynum[&&NHX:TOL=21547])[&&NHX:TOL=21543],drimys[&&NHX:TOL=21548],tetrathalamus[&&NHX:TOL=21549],pseudowintera[&&NHX:TOL=21550],tasmannia[&&NHX:TOL=21551],takhtajania[&&NHX:TOL=21552])winteraceae[&&NHX:TOL=21542],(canella[&&NHX:TOL=21554],capiscodendron[&&NHX:TOL=21555],cinnamodendron[&&NHX:TOL=21556],cinnamosma[&&NHX:TOL=21557],pleodendron[&&NHX:TOL=21558],warburgia[&&NHX:TOL=21559])canellaceae[&&NHX:TOL=21553])canellales[&&NHX:TOL=20673])[&&NHX:TOL=27067],((((degeneriaceae[&&NHX:TOL=21323],himantandraceae[&&NHX:TOL=21324])[&&NHX:TOL=21322],magnoliaceae[&&NHX:TOL=21326],(eupomatiaceae[&&NHX:TOL=21320],annonaceae[&&NHX:TOL=21321])[&&NHX:TOL=21319])[&&NHX:TOL=51245],myristicaceae[&&NHX:TOL=21325])magnoliales[&&NHX:TOL=20671],(calycanthaceae[&&NHX:TOL=21308],((siparunaceae[&&NHX:TOL=21311],(gomortega nitida[&&NHX:TOL=21313],atherospermataceae[&&NHX:TOL=21314])[&&NHX:TOL=21312])[&&NHX:TOL=21310],hernandiaceae[&&NHX:TOL=21315],monimiaceae[&&NHX:TOL=21316],lauraceae[&&NHX:TOL=21317])[&&NHX:TOL=21309])laurales[&&NHX:TOL=20672])[&&NHX:TOL=27066])magnoliids[&&NHX:TOL=20670],(hedyosmum[&&NHX:TOL=20686],(ascarina[&&NHX:TOL=20688],(sarcandra[&&NHX:TOL=20690],chloranthus[&&NHX:TOL=20691])[&&NHX:TOL=20689])[&&NHX:TOL=20687])chloranthaceae[&&NHX:TOL=20669],((ceratophyllum platyacanthum[&&NHX:TOL=20656],(ceratophyllum demersum[&&NHX:TOL=20658],(ceratophyllum echinatum[&&NHX:TOL=20660],ceratophyllum submersum[&&NHX:TOL=20661])[&&NHX:TOL=20659])[&&NHX:TOL=20657])[&&NHX:TOL=20655],(ceratophyllum muricatum[&&NHX:TOL=20663],ceratophyllum tanaiticum[&&NHX:TOL=20664])[&&NHX:TOL=20662])ceratophyllaceae[&&NHX:TOL=20667],(((((butomaceae[&&NHX:TOL=21344],(alismataceae[&&NHX:TOL=21346],limnocharitaceae[&&NHX:TOL=21347])[&&NHX:TOL=21345])[&&NHX:TOL=21343],(hydrocharitaceae[&&NHX:TOL=21349],najadaceae[&&NHX:TOL=21350])[&&NHX:TOL=21348])[&&NHX:TOL=21342],(aponogetonaceae[&&NHX:TOL=21352],(scheuchzeriaceae[&&NHX:TOL=21354],((posidoniaceae[&&NHX:TOL=21357],(cymodoceaceae[&&NHX:TOL=21359],ruppiaceae[&&NHX:TOL=21360])[&&NHX:TOL=21358])[&&NHX:TOL=21356],((juncaginaceae[&&NHX:TOL=21363],lilaeaceae[&&NHX:TOL=21364])[&&NHX:TOL=21362],(zosteraceae[&&NHX:TOL=21366],(potamogetonaceae[&&NHX:TOL=21368],zannichelliaceae[&&NHX:TOL=21369])[&&NHX:TOL=21367])[&&NHX:TOL=21365])[&&NHX:TOL=21361])[&&NHX:TOL=21355])[&&NHX:TOL=21353])[&&NHX:TOL=21351])alismatanae[&&NHX:TOL=21329],(gymnostachys[&&NHX:TOL=21371],(orontieae[&&NHX:TOL=21373],(pothoideae[&&NHX:TOL=21375],(lasieae[&&NHX:TOL=21377],(calla[&&NHX:TOL=21379],(philodendroideae[&&NHX:TOL=21381],aroideae[&&NHX:TOL=21382])[&&NHX:TOL=21380])[&&NHX:TOL=21378])[&&NHX:TOL=21376])[&&NHX:TOL=21374])[&&NHX:TOL=21372])aranae[&&NHX:TOL=21330])[&&NHX:TOL=21328],((alstroemeriaceae[&&NHX:TOL=21490],campynemataceae[&&NHX:TOL=21491],colchicaceae[&&NHX:TOL=21492],liliaceae[&&NHX:TOL=21493],luzuriagaceae[&&NHX:TOL=21494],melanthiaceae[&&NHX:TOL=21495],philesiaceae[&&NHX:TOL=21496],ripogonaceae[&&NHX:TOL=21497],smilacaceae[&&NHX:TOL=21498])liliales[&&NHX:TOL=21332],(agapanthaceae[&&NHX:TOL=21419],agavaceae[&&NHX:TOL=21420],alliaceae[&&NHX:TOL=21421],amaryllidaceae[&&NHX:TOL=21422],anemarrhenaceae[&&NHX:TOL=21423],anthericaceae[&&NHX:TOL=21424],aphyllanthaceae[&&NHX:TOL=21425],asparagaceae[&&NHX:TOL=21426],asphodelaceae[&&NHX:TOL=21427],asteliaceae[&&NHX:TOL=21428],behniaceae[&&NHX:TOL=21429],blandfordiaceae[&&NHX:TOL=21430],boryaceae[&&NHX:TOL=21431],convallariaceae[&&NHX:TOL=21432],doryanthaceae[&&NHX:TOL=21433],hemerocallidaceae[&&NHX:TOL=21434],herreriaceae[&&NHX:TOL=21435],hesperocallidaceae[&&NHX:TOL=21436],(oziroeoideae[&&NHX:TOL=21449],(urgineoideae[&&NHX:TOL=21451],(ornithogaloideae[&&NHX:TOL=21453],hyacinthoideae[&&NHX:TOL=21454])[&&NHX:TOL=21452])[&&NHX:TOL=21450])hyacinthaceae[&&NHX:TOL=21437],hypoxidaceae[&&NHX:TOL=21438],iridaceae[&&NHX:TOL=21439],ixioliriaceae[&&NHX:TOL=21440],lanariaceae[&&NHX:TOL=21441],laxmaniaceae[&&NHX:TOL=21442],orchidaceae[&&NHX:TOL=21443],tecophiliaceae[&&NHX:TOL=21444],themidaceae[&&NHX:TOL=21445],xanthorrhoeaceae[&&NHX:TOL=21446],xeronemataceae[&&NHX:TOL=21447])asparagales[&&NHX:TOL=21333],(cyclanthaceae[&&NHX:TOL=21500],pandanaceae[&&NHX:TOL=21501],stemonaceae[&&NHX:TOL=21502],triuridaceae[&&NHX:TOL=21503],velloziaceae[&&NHX:TOL=21504])pandanales[&&NHX:TOL=21334],(burmanniaceae[&&NHX:TOL=21483],dioscoreaceae[&&NHX:TOL=21484],nartheciaceae[&&NHX:TOL=21485],taccaceae[&&NHX:TOL=21486],thismiaceae[&&NHX:TOL=21487],trichopodaceae[&&NHX:TOL=21488])dioscoreales[&&NHX:TOL=21335],((nypoideae[&&NHX:TOL=21384],(calamoideae[&&NHX:TOL=21386],(((livistoninae[&&NHX:TOL=21390],thrinacinae1[&&NHX:TOL=21391])[&&NHX:TOL=21389],((borasseae[&&NHX:TOL=21394],coryphinae[&&NHX:TOL=21395])[&&NHX:TOL=21393],(phoeniceae[&&NHX:TOL=21397],(sabalinae[&&NHX:TOL=21399],thrinacinae2[&&NHX:TOL=21400])[&&NHX:TOL=21398])[&&NHX:TOL=21396])[&&NHX:TOL=21392])[&&NHX:TOL=21388],((ceroxyleae[&&NHX:TOL=21403],phytelephantoideae[&&NHX:TOL=21404])[&&NHX:TOL=21402],((caryoteae[&&NHX:TOL=21407],iriarteae[&&NHX:TOL=21408])[&&NHX:TOL=21406],((hyophorbeae[&&NHX:TOL=21411],cyclospatheae[&&NHX:TOL=21412])[&&NHX:TOL=21410],(podococceae[&&NHX:TOL=21414],arecinae[&&NHX:TOL=21415],cocoeae[&&NHX:TOL=21416],geonomeae[&&NHX:TOL=21417])[&&NHX:TOL=21413])[&&NHX:TOL=21409])[&&NHX:TOL=21405])[&&NHX:TOL=21401])[&&NHX:TOL=21387])[&&NHX:TOL=21385])arecanae[&&NHX:TOL=21337],((musaceae[&&NHX:TOL=21506],(strelitziaceae[&&NHX:TOL=21508],(lowiaceae[&&NHX:TOL=21510],(heliconiaceae[&&NHX:TOL=21512],((costaceae[&&NHX:TOL=21515],zingiberaceae[&&NHX:TOL=21516])[&&NHX:TOL=21514],(cannaceae[&&NHX:TOL=21518],marantaceae[&&NHX:TOL=21519])[&&NHX:TOL=21517])[&&NHX:TOL=21513])[&&NHX:TOL=21511])[&&NHX:TOL=21509])[&&NHX:TOL=21507])zingiberanae[&&NHX:TOL=21339],((((pontederiaceae[&&NHX:TOL=21459],commelinaceae[&&NHX:TOL=21460])[&&NHX:TOL=21458],hanguanaceae[&&NHX:TOL=21461])[&&NHX:TOL=21457],(haemodoraceae[&&NHX:TOL=21463],philydraceae[&&NHX:TOL=21464])[&&NHX:TOL=21462])[&&NHX:TOL=21456],((bromeliaceae[&&NHX:TOL=21467],rapateaceae[&&NHX:TOL=21468])[&&NHX:TOL=21466],(eriocaulaceae[&&NHX:TOL=21470],(cyperaceae[&&NHX:TOL=21472],(typhaceae[&&NHX:TOL=21474],(flagellariaceae[&&NHX:TOL=21476],(restionaceae[&&NHX:TOL=21478],(joinvilleaceae[&&NHX:TOL=21480],poaceae[&&NHX:TOL=21481])[&&NHX:TOL=21479])[&&NHX:TOL=21477])[&&NHX:TOL=21475])[&&NHX:TOL=21473])[&&NHX:TOL=21471])[&&NHX:TOL=21469])[&&NHX:TOL=21465])commelinanae[&&NHX:TOL=21340])[&&NHX:TOL=21338])[&&NHX:TOL=21336])[&&NHX:TOL=21331])monocotyledons[&&NHX:TOL=20668],(((papaveraceae[&&NHX:TOL=21015],euptelea[&&NHX:TOL=21016],(circaeasteraceae[&&NHX:TOL=21018],lardizabalaceae[&&NHX:TOL=21019],(menispermaceae[&&NHX:TOL=21021],(berberidaceae[&&NHX:TOL=21023],ranunculaceae[&&NHX:TOL=21024])[&&NHX:TOL=21022])[&&NHX:TOL=21020])[&&NHX:TOL=21017])ranunculales[&&NHX:TOL=20706],(((platanus[&&NHX:TOL=21011],proteaceae[&&NHX:TOL=21012])[&&NHX:TOL=21010],nelumbo[&&NHX:TOL=21013])proteales[&&NHX:TOL=20708],sabia[&&NHX:TOL=20709],(trochodendraceae[&&NHX:TOL=20710],(((buxus[&&NHX:TOL=57792],notobuxus[&&NHX:TOL=57793])[&&NHX:TOL=57796],((pachysandra[&&NHX:TOL=57794],styloceras[&&NHX:TOL=57799])[&&NHX:TOL=57798],sarcococca[&&NHX:TOL=57795])[&&NHX:TOL=57797])buxaceae[&&NHX:TOL=20712],didymeles[&&NHX:TOL=20713])buxales[&&NHX:TOL=20711],((gunneraceae[&&NHX:TOL=20694],myrothamnaceae[&&NHX:TOL=20695])gunnerales[&&NHX:TOL=20693],((olacaceae[&&NHX:TOL=21277],(santalaceae[&&NHX:TOL=21279],opiliaceae[&&NHX:TOL=21280],(loranthaceae[&&NHX:TOL=21282],schoepfia[&&NHX:TOL=21283],misodendraceae[&&NHX:TOL=21284])[&&NHX:TOL=21281])[&&NHX:TOL=21278])santalales[&&NHX:TOL=20697],(((((saxifragaceae[&&NHX:TOL=59669],grossulariaceae[&&NHX:TOL=59670])[&&NHX:TOL=59668],(iteaceae[&&NHX:TOL=59672],pterostemonaceae[&&NHX:TOL=59673])[&&NHX:TOL=59671])saxifragaceae alliance[&&NHX:TOL=59667],(crassulaceae[&&NHX:TOL=59675],haloragaceae including aphanopetalum[&&NHX:TOL=59676])[&&NHX:TOL=59674])[&&NHX:TOL=59666],paeoniaceae[&&NHX:TOL=59677])[&&NHX:TOL=21302],altingiaceae[&&NHX:TOL=21303],cercidiphyllaceae[&&NHX:TOL=21305],hamamelidaceae[&&NHX:TOL=21306],daphniphyllaceae[&&NHX:TOL=59678],peridiscaceae[&&NHX:TOL=59679])saxifragales[&&NHX:TOL=20698],(aextoxicon punctatum[&&NHX:TOL=20959],(berberidopsis corallina[&&NHX:TOL=20961],streptothamnus moorei[&&NHX:TOL=20962],berberidopsis beckleri[&&NHX:TOL=20963])berberidopsidaceae[&&NHX:TOL=20960])berberidopsidales[&&NHX:TOL=20699],((((((((cercis[&&NHX:TOL=60293],(adenolobus[&&NHX:TOL=67063],(griffonia[&&NHX:TOL=60295],brenierea bauhinia[&&NHX:TOL=60296],(gigasiphon[&&NHX:TOL=60297],(tylosema[&&NHX:TOL=60298],(barklya[&&NHX:TOL=60299],lysiphyllum phanera lasiobema piliostigma[&&NHX:TOL=60300])[&&NHX:TOL=67066])[&&NHX:TOL=67065])[&&NHX:TOL=67064])[&&NHX:TOL=60294])[&&NHX:TOL=67062])cercideae[&&NHX:TOL=60233],(((prioria[&&NHX:TOL=65307],oxystigma[&&NHX:TOL=65308])prioria clade[&&NHX:TOL=60366],(daniella[&&NHX:TOL=60368],(hymenaea[&&NHX:TOL=60369],guibourtia[&&NHX:TOL=60384],(baikiaea[&&NHX:TOL=65310],sindora[&&NHX:TOL=65311])detarium clade[&&NHX:TOL=65309])[&&NHX:TOL=60383])detarieae sensu stricto[&&NHX:TOL=60367],(endertia[&&NHX:TOL=60381],(tamarindus[&&NHX:TOL=60371],afzelia intsia[&&NHX:TOL=60372],amherstia[&&NHX:TOL=60373],crudia[&&NHX:TOL=60382],hymenostegia[&&NHX:TOL=60374],brownea[&&NHX:TOL=65312],humboldtia[&&NHX:TOL=65313],(berlinia[&&NHX:TOL=60376],anthonotha[&&NHX:TOL=65314],englerodendron[&&NHX:TOL=65315],(julbernardia[&&NHX:TOL=65316],brachystegia[&&NHX:TOL=65317],tetraberlinia[&&NHX:TOL=65318],bikinia[&&NHX:TOL=65319],icuria[&&NHX:TOL=65320],aphanocalyx[&&NHX:TOL=65321],michelsonia[&&NHX:TOL=65322])babjit clade[&&NHX:TOL=60378])macrolobieae clade[&&NHX:TOL=60375])[&&NHX:TOL=60370])amherstieae clade[&&NHX:TOL=60380])detarieae sensu lato[&&NHX:TOL=60235],((subtribe duparquetiinae duparquetia[&&NHX:TOL=65323],(poeppigia baudouinia eligmocarpus mendoravia[&&NHX:TOL=60385],(distemonanthus apuleia[&&NHX:TOL=60387],(storkeilla subtribe labicheinae labichea petalostylis[&&NHX:TOL=60389],(koompassia martiodendron androcalymma kalappia[&&NHX:TOL=60391],(zenia[&&NHX:TOL=60393],uittienia dialium dicornynia[&&NHX:TOL=60394])[&&NHX:TOL=60392])[&&NHX:TOL=60390])[&&NHX:TOL=60388])[&&NHX:TOL=60386])subtribe dialiinae[&&NHX:TOL=65324])cassieae sensu lato pro parte[&&NHX:TOL=60237],((umtiza clade[&&NHX:TOL=60346],(cassieae sensu stricto chamaecrista senna cassia[&&NHX:TOL=60348],(pterogyne group[&&NHX:TOL=65337],caesalpinia group[&&NHX:TOL=65338])[&&NHX:TOL=65336],batesia group[&&NHX:TOL=65339],(moldenhawera group[&&NHX:TOL=65341],(tachigali group[&&NHX:TOL=65343],(corepeltophorum group[&&NHX:TOL=65345],(dimorphandra group[&&NHX:TOL=65347],(mimoseae pentaclethera group[&&NHX:TOL=65162],mimoseae dinizia group[&&NHX:TOL=67070],parkieae pro parte 1[&&NHX:TOL=67071],mimoseae pro parte[&&NHX:TOL=65164],(parkieae pro parte 2[&&NHX:TOL=65166],acacia subgenus acacia[&&NHX:TOL=65167],mimoseae piptadenia group[&&NHX:TOL=65168],(acacia subgenus aculeiferum[&&NHX:TOL=65170],(ingeae[&&NHX:TOL=65172],acacia subgenus phyllodineae[&&NHX:TOL=65173])[&&NHX:TOL=65171])[&&NHX:TOL=65169])[&&NHX:TOL=65165])mimosoideae[&&NHX:TOL=60351])[&&NHX:TOL=65346])[&&NHX:TOL=65344])[&&NHX:TOL=65342])[&&NHX:TOL=65340])[&&NHX:TOL=60347])caesalpinieae s.l. & s.s. cassieae sensu stricto mimosoideae[&&NHX:TOL=60239],((sophoreae pro parte a dipterygeae[&&NHX:TOL=60326],swartzieae sensu stricto[&&NHX:TOL=60327])[&&NHX:TOL=60325],((cladrastis[&&NHX:TOL=67059],pickeringia[&&NHX:TOL=67060],styphnolobium[&&NHX:TOL=67061])cladrastis clade[&&NHX:TOL=60329],(sophoreae pro parte c swartzieae pro parte[&&NHX:TOL=60332],dalbergieae pro parte a sophoreae pro parte d[&&NHX:TOL=60333],((sophoreae pro parte acosmium ormosia diplotropis etc.[&&NHX:TOL=66016],(brongniartieae incl. cyclolobium poecilanthe[&&NHX:TOL=66018],((sophoreae sens. strict. sophora maackia etc.[&&NHX:TOL=66021],euchresteae[&&NHX:TOL=66022],thermopsideae[&&NHX:TOL=66023])[&&NHX:TOL=66020],(podalyrieae[&&NHX:TOL=66025],(crotalarieae[&&NHX:TOL=66027],genisteae[&&NHX:TOL=66028])[&&NHX:TOL=66026])[&&NHX:TOL=66024])[&&NHX:TOL=66019])[&&NHX:TOL=66017])genistoid clade[&&NHX:TOL=60334],sophoreae pro parte b[&&NHX:TOL=60331])[&&NHX:TOL=60345],((amorphoid clade[&&NHX:TOL=66392],daleoid clade[&&NHX:TOL=66393])amorpheae[&&NHX:TOL=66386],(adesmia clade[&&NHX:TOL=66388],(pterocarpus clade[&&NHX:TOL=66390],dalbergia clade[&&NHX:TOL=66391])[&&NHX:TOL=66389])dalbergioid sensu stricto clade[&&NHX:TOL=66387])dalbergioid sensu lato clade[&&NHX:TOL=60336],((((indigofereae[&&NHX:TOL=66394],(millettieae abreae phaseoleae pro parte[&&NHX:TOL=66396],phaseoleae sensu stricto desmodieae psoraleeae[&&NHX:TOL=66397])[&&NHX:TOL=66395])millettioid sensu lato clade[&&NHX:TOL=60341],((glycyrrhiza[&&NHX:TOL=66490],afgekia[&&NHX:TOL=67072],callerya[&&NHX:TOL=67073],wisteria[&&NHX:TOL=67074],((galegeae sensu lato[&&NHX:TOL=66493],hedysaroid clade[&&NHX:TOL=66494])[&&NHX:TOL=66492],(((cicereae[&&NHX:TOL=66498],galega[&&NHX:TOL=66499])[&&NHX:TOL=66497],(trifolieae[&&NHX:TOL=66501],fabeae[&&NHX:TOL=66502])[&&NHX:TOL=66500])[&&NHX:TOL=66496],parochetus[&&NHX:TOL=66503])vicioids[&&NHX:TOL=66495])[&&NHX:TOL=66491])irlc inverted repeatlacking clade[&&NHX:TOL=60358],((sesbania[&&NHX:TOL=66504],loteae sensu lato[&&NHX:TOL=67067])[&&NHX:TOL=66505],robinieae[&&NHX:TOL=67068])robinioid clade[&&NHX:TOL=60365])hologalegina[&&NHX:TOL=60342])[&&NHX:TOL=60340],mirbelioid sensu lato clade[&&NHX:TOL=60343])[&&NHX:TOL=60339],baphioid clade[&&NHX:TOL=60344])[&&NHX:TOL=60338])[&&NHX:TOL=60330])[&&NHX:TOL=60328])papilionoideae[&&NHX:TOL=60240])[&&NHX:TOL=60238])[&&NHX:TOL=60236])[&&NHX:TOL=60234])fabaceae[&&NHX:TOL=21093],polygalaceae[&&NHX:TOL=21094],quillaja[&&NHX:TOL=21095],(cadellia[&&NHX:TOL=66581],guilfoylia[&&NHX:TOL=66582],recchia[&&NHX:TOL=66583],stylobasium[&&NHX:TOL=66584],suriana[&&NHX:TOL=66585])surianaceae[&&NHX:TOL=21096])fabales[&&NHX:TOL=21030],((rosaceae[&&NHX:TOL=21252],(barbeyaceae[&&NHX:TOL=21248],dirachmaceae[&&NHX:TOL=21249],elaeagnaceae[&&NHX:TOL=21250],rhamnaceae[&&NHX:TOL=21251],(ulmaceae[&&NHX:TOL=21254],(((urticaceae[&&NHX:TOL=21257],cecropiaceae[&&NHX:TOL=21259])[&&NHX:TOL=27081],moraceae[&&NHX:TOL=21258])[&&NHX:TOL=27082],(cannabaceae[&&NHX:TOL=21256],celtidaceae[&&NHX:TOL=21255])[&&NHX:TOL=27085])[&&NHX:TOL=27083])[&&NHX:TOL=21253])[&&NHX:TOL=27084])rosales[&&NHX:TOL=21029],((nothofagus[&&NHX:TOL=21099],(fagaceae[&&NHX:TOL=21098],(((ticodendraceae[&&NHX:TOL=21101],betulaceae[&&NHX:TOL=21102])[&&NHX:TOL=27078],casuarinaceae[&&NHX:TOL=21103])[&&NHX:TOL=27077],(rhoipteleaceae[&&NHX:TOL=21105],juglandaceae[&&NHX:TOL=21104])[&&NHX:TOL=27079],myricaceae[&&NHX:TOL=21106])[&&NHX:TOL=21100])[&&NHX:TOL=27076])fagales[&&NHX:TOL=21027],(anisophylleaceae[&&NHX:TOL=21085],(coriariaceae[&&NHX:TOL=21087],corynocarpaceae[&&NHX:TOL=21088])[&&NHX:TOL=26896],cucurbitaceae[&&NHX:TOL=21089],((tetramelaceae[&&NHX:TOL=21091],datiscaceae[&&NHX:TOL=21090])[&&NHX:TOL=26894],begoniaceae[&&NHX:TOL=21086])[&&NHX:TOL=26895])cucurbitales[&&NHX:TOL=21028])[&&NHX:TOL=139680])[&&NHX:TOL=139679])[&&NHX:TOL=139678],(((((salicaceae[&&NHX:TOL=21112],scyphostegia borneensis[&&NHX:TOL=68360])[&&NHX:TOL=68359],(tetrathylacium[&&NHX:TOL=68568],(lunania[&&NHX:TOL=68570],(((casearia sect. piparea[&&NHX:TOL=68574],ryania[&&NHX:TOL=68575])[&&NHX:TOL=68573],trichostephanus[&&NHX:TOL=68576])[&&NHX:TOL=68572],(osmelia[&&NHX:TOL=68578],pseudosmelia moluccana[&&NHX:TOL=68579],ophiobotrys zenkeri[&&NHX:TOL=68580])[&&NHX:TOL=68577],((euceraea[&&NHX:TOL=68583],neoptychocarpus[&&NHX:TOL=68584])[&&NHX:TOL=68582],(casearia[&&NHX:TOL=68586],laetia[&&NHX:TOL=68587],zuelania guidonia[&&NHX:TOL=68588],hecatostemon completus[&&NHX:TOL=68589],samyda[&&NHX:TOL=68590])[&&NHX:TOL=68585])[&&NHX:TOL=68581])[&&NHX:TOL=68571])[&&NHX:TOL=68569])samydaceae[&&NHX:TOL=68361])[&&NHX:TOL=68358],achariaceae[&&NHX:TOL=21113],(violaceae[&&NHX:TOL=21115],(passifloraceae[&&NHX:TOL=21117],turneraceae[&&NHX:TOL=21118],malesherbiaceae[&&NHX:TOL=21119])[&&NHX:TOL=21116])[&&NHX:TOL=21114],(clusiaceae[&&NHX:TOL=21121],podostemaceae[&&NHX:TOL=21123],hypericaceae[&&NHX:TOL=21124])[&&NHX:TOL=21120],(balanops[&&NHX:TOL=21126],((chrysobalanaceae[&&NHX:TOL=21129],euphronia[&&NHX:TOL=21130])[&&NHX:TOL=21128],(dichapetalaceae[&&NHX:TOL=21132],trigoniaceae[&&NHX:TOL=21133])[&&NHX:TOL=21131])[&&NHX:TOL=21127])[&&NHX:TOL=21125],(erythroxylaceae[&&NHX:TOL=21135],rhizophoraceae[&&NHX:TOL=21136])[&&NHX:TOL=21134],(malpighiaceae[&&NHX:TOL=21137],elatinaceae[&&NHX:TOL=21143])[&&NHX:TOL=27080],rafflesiaceae[&&NHX:TOL=51179],pandaceae[&&NHX:TOL=21138],putranjivaceae[&&NHX:TOL=21139],phyllantaceae[&&NHX:TOL=21140],picrodendraceae[&&NHX:TOL=21141],euphorbiaceae[&&NHX:TOL=21142],ixonanthaceae[&&NHX:TOL=21144],(((lacistema krukovii[&&NHX:TOL=68342],lacistema macbridei[&&NHX:TOL=68343],lacistema nena[&&NHX:TOL=68344],lacistema aggregatum[&&NHX:TOL=68345],lacistema hasslerianum[&&NHX:TOL=68346])[&&NHX:TOL=68341],(lacistema grandifolium[&&NHX:TOL=68348],lacistema pubescens[&&NHX:TOL=68349],lacistema serrulatum[&&NHX:TOL=68350],lacistema robustum[&&NHX:TOL=68351],lacistema lucidum[&&NHX:TOL=68352],lacistema polystachyum[&&NHX:TOL=68353])[&&NHX:TOL=68347])lacistema[&&NHX:TOL=68340],(lozania klugii[&&NHX:TOL=68355],lozania mutisiana[&&NHX:TOL=68356],lozania pittieri[&&NHX:TOL=68357])lozania[&&NHX:TOL=68354])lacistemataceae[&&NHX:TOL=21145],linaceae[&&NHX:TOL=21146],lophopyxis maingayi[&&NHX:TOL=21147],ctenolophonaceae[&&NHX:TOL=21148],(ochnaceae[&&NHX:TOL=21149],medusagynaceae[&&NHX:TOL=27073],quiinaceae[&&NHX:TOL=27074])[&&NHX:TOL=27075],irvingiaceae[&&NHX:TOL=21150],bonnetiaceae[&&NHX:TOL=21151],peridiscaceae[&&NHX:TOL=21152],phyllanthaceae[&&NHX:TOL=21153],caryocaraceae[&&NHX:TOL=21154],pseudanthaceae[&&NHX:TOL=21155],goupiaceae[&&NHX:TOL=21156],humiriaceae[&&NHX:TOL=21157])malpighiales[&&NHX:TOL=21033],(brunellia[&&NHX:TOL=21240],cephalotus follicularis[&&NHX:TOL=21241],cunoniaceae[&&NHX:TOL=21242],elaeocarpaceae[&&NHX:TOL=21243],(connaraceae[&&NHX:TOL=21245],oxalidaceae[&&NHX:TOL=21246])[&&NHX:TOL=21244])oxalidales[&&NHX:TOL=21032])[&&NHX:TOL=139682],(((celastraceae[&&NHX:TOL=21076],parnassiaceae[&&NHX:TOL=21077])[&&NHX:TOL=21075],lepidobotryaceae[&&NHX:TOL=21078])celastrales[&&NHX:TOL=21034],(afrostyrax[&&NHX:TOL=139688],hua[&&NHX:TOL=139689])huaceae[&&NHX:TOL=21035])[&&NHX:TOL=139683])[&&NHX:TOL=139681])[&&NHX:TOL=139677],(krameria[&&NHX:TOL=21274],zygophyllaceae[&&NHX:TOL=21275])zygophyllales[&&NHX:TOL=21031])fabidae[&&NHX:TOL=21026],(((melianthaceae[&&NHX:TOL=21108],geraniaceae[&&NHX:TOL=21109],vivianiaceae[&&NHX:TOL=21110])geraniales[&&NHX:TOL=21041],((((alzateaceae[&&NHX:TOL=21192],((oliniaceae[&&NHX:TOL=21195],penaeaceae[&&NHX:TOL=21196])[&&NHX:TOL=21194],rhynchocalycaceae[&&NHX:TOL=21197])[&&NHX:TOL=21193])[&&NHX:TOL=21191],(memecylaceae[&&NHX:TOL=21199],melastomataceae[&&NHX:TOL=21200])[&&NHX:TOL=21198])[&&NHX:TOL=21190],((heteropyxidaceae[&&NHX:TOL=21203],psiloxylaceae[&&NHX:TOL=21204])[&&NHX:TOL=21202],(vochysiaceae[&&NHX:TOL=21206],myrtaceae[&&NHX:TOL=21207])[&&NHX:TOL=21205])[&&NHX:TOL=21201])[&&NHX:TOL=21189],(((jussiaeeae[&&NHX:TOL=21214],(hauyeae[&&NHX:TOL=21216],((fuchsieae[&&NHX:TOL=21219],circaeeae[&&NHX:TOL=21220])[&&NHX:TOL=21218],(lopezieae[&&NHX:TOL=21222],((chamaenerion[&&NHX:TOL=21227],(epilobium[&&NHX:TOL=21229],(((zauschneria[&&NHX:TOL=21233],boisduvalia[&&NHX:TOL=21234])[&&NHX:TOL=21232],currania[&&NHX:TOL=21235])[&&NHX:TOL=21231],cordylophorum[&&NHX:TOL=21236],xerolobium[&&NHX:TOL=21237],crossostigma[&&NHX:TOL=21238])[&&NHX:TOL=21230])[&&NHX:TOL=21228])epilobieae[&&NHX:TOL=21224],onagreae[&&NHX:TOL=21225])[&&NHX:TOL=21223])[&&NHX:TOL=21221])[&&NHX:TOL=21217])[&&NHX:TOL=21215])onagraceae[&&NHX:TOL=21210],lythraceae[&&NHX:TOL=21211])[&&NHX:TOL=21209],combretaceae[&&NHX:TOL=21212])[&&NHX:TOL=21208])myrtales[&&NHX:TOL=21046])[&&NHX:TOL=139685],((((crossosomataceae[&&NHX:TOL=21081],stachyuraceae[&&NHX:TOL=21082])[&&NHX:TOL=21080],staphyleaceae[&&NHX:TOL=21083])[&&NHX:TOL=27796],(((strasburgeria robusta[&&NHX:TOL=21043],ixerba brexioides[&&NHX:TOL=21044])[&&NHX:TOL=27797],geissoloma marginatum[&&NHX:TOL=21045])[&&NHX:TOL=27798],aphloia theiformis[&&NHX:TOL=21037])[&&NHX:TOL=27799])crossosomatales[&&NHX:TOL=21042],((picramnia[&&NHX:TOL=21039],alvaradoa[&&NHX:TOL=21040])picramniaceae[&&NHX:TOL=21038],(((((tapiscia sinensis[&&NHX:TOL=21048],huertea[&&NHX:TOL=139635])tapisciaceae[&&NHX:TOL=139634],dipentodontaceae[&&NHX:TOL=93754])[&&NHX:TOL=93753],(gerrardina foliosa[&&NHX:TOL=93756],gerrardina eylesiana[&&NHX:TOL=93757])gerrardina[&&NHX:TOL=93755])huerteales[&&NHX:TOL=139633],(((akaniaceae[&&NHX:TOL=21054],tropaeolaceae[&&NHX:TOL=21055])[&&NHX:TOL=21053],((caricaceae[&&NHX:TOL=21058],moringaceae[&&NHX:TOL=21059])[&&NHX:TOL=21057],(setchellanthaceae[&&NHX:TOL=21061],limnanthaceae[&&NHX:TOL=21062],((bataceae[&&NHX:TOL=21065],salvadoraceae[&&NHX:TOL=21066])[&&NHX:TOL=21064],koeberliniaceae[&&NHX:TOL=21067],(brassicaceae[&&NHX:TOL=21069],gyrostemonaceae[&&NHX:TOL=21070],pentadiplandraceae[&&NHX:TOL=21071],resedaceae[&&NHX:TOL=21072],tovariaceae[&&NHX:TOL=21073])[&&NHX:TOL=21068])[&&NHX:TOL=21063])[&&NHX:TOL=21060])[&&NHX:TOL=21056])brassicales[&&NHX:TOL=21049],((((malvoideae[&&NHX:TOL=21161],bombacoideae[&&NHX:TOL=21162])malvatheca[&&NHX:TOL=21160],sterculioideae[&&NHX:TOL=21163],brownlowioideae[&&NHX:TOL=21164],dombeyoideae[&&NHX:TOL=21165],tilioideae[&&NHX:TOL=21166],helicteroideae[&&NHX:TOL=21167])malvadendrina[&&NHX:TOL=21159],(byttnerioideae[&&NHX:TOL=21169],grewioideae[&&NHX:TOL=21170])byttneriina[&&NHX:TOL=21168])core malvales[&&NHX:TOL=21172],((bixaceae[&&NHX:TOL=21175],diegodendraceae[&&NHX:TOL=21176])[&&NHX:TOL=21174],cochlospermaceae[&&NHX:TOL=21177])[&&NHX:TOL=21173],(((dipterocarpaceae[&&NHX:TOL=21181],sarcolaenaceae[&&NHX:TOL=21182])[&&NHX:TOL=21180],cistaceae[&&NHX:TOL=21183])[&&NHX:TOL=21179],muntingiaceae[&&NHX:TOL=21184])[&&NHX:TOL=21178],sphaerosepalaceae[&&NHX:TOL=21185],thymelaeaceae[&&NHX:TOL=21186],neuradaceae[&&NHX:TOL=21187])malvales[&&NHX:TOL=21050])[&&NHX:TOL=139636])[&&NHX:TOL=139632],((((abrahamia [&&NHX:TOL=133387],actinocheita[&&NHX:TOL=133388],amphipterygium[&&NHX:TOL=133389],anacardium[&&NHX:TOL=133390],androtium[&&NHX:TOL=133391],apterokarpos[&&NHX:TOL=133392],astronium[&&NHX:TOL=133393],baronia[&&NHX:TOL=133394],blepharocarya[&&NHX:TOL=133395],bonetiella[&&NHX:TOL=133396],bouea[&&NHX:TOL=133397],buchanania[&&NHX:TOL=133398],campnosperma[&&NHX:TOL=133399],campylopetalum[&&NHX:TOL=133400],cardenasiodendron[&&NHX:TOL=133401],comocladia[&&NHX:TOL=133402],cotinus[&&NHX:TOL=133403],dobinea[&&NHX:TOL=133404],drimycarpus[&&NHX:TOL=133405],euroschinus[&&NHX:TOL=133406],fegimanra[&&NHX:TOL=133407],faguetia[&&NHX:TOL=133408],gluta [&&NHX:TOL=133409],haplorhus[&&NHX:TOL=133410],heeria[&&NHX:TOL=133411],hermogenodendron [&&NHX:TOL=133412],holigarna[&&NHX:TOL=133413],laurophyllus[&&NHX:TOL=133414],lithrea[&&NHX:TOL=133415],loxopterygium[&&NHX:TOL=133416],loxostylis[&&NHX:TOL=133417],malosma[&&NHX:TOL=133418],mangifera[&&NHX:TOL=133419],mauria[&&NHX:TOL=133420],melanochyla[&&NHX:TOL=133421],melanococca[&&NHX:TOL=133422],metopium[&&NHX:TOL=133423],micronychia[&&NHX:TOL=133424],mosquitoxylum[&&NHX:TOL=133425],myracrodruon[&&NHX:TOL=133426],nothopegia[&&NHX:TOL=133427],ochoterenaea[&&NHX:TOL=133428],orthopterygium[&&NHX:TOL=133429],ozoroa[&&NHX:TOL=133430],pachycormus[&&NHX:TOL=133431],parishia[&&NHX:TOL=133432],pentaspadon[&&NHX:TOL=133433],pistacia[&&NHX:TOL=133434],protorhus[&&NHX:TOL=133435],pseudosmodingium[&&NHX:TOL=133436],rhodosphaera[&&NHX:TOL=133437],rhus[&&NHX:TOL=133438],schinopsis[&&NHX:TOL=133439],schinus[&&NHX:TOL=133440],searsia[&&NHX:TOL=133441],semecarpus[&&NHX:TOL=133442],smodingium[&&NHX:TOL=133443],sorindeia[&&NHX:TOL=133444],swintonia[&&NHX:TOL=133445],thyrsodium[&&NHX:TOL=133446],toxicodendron[&&NHX:TOL=133447],trichoscypha[&&NHX:TOL=133448])anacardioideae[&&NHX:TOL=133386],(allospondias[&&NHX:TOL=133450],antrocaryon[&&NHX:TOL=133451],choerospondias[&&NHX:TOL=133452],cyrtocarpa[&&NHX:TOL=133453],dracontomelon[&&NHX:TOL=133454],haematostaphis[&&NHX:TOL=133455],haplospondias[&&NHX:TOL=133456],harpephyllum[&&NHX:TOL=133457],koordersiodendron[&&NHX:TOL=133458],lannea[&&NHX:TOL=133459],operculicarya[&&NHX:TOL=133460],pegia[&&NHX:TOL=133461],pleiogynium[&&NHX:TOL=133462],poupartia[&&NHX:TOL=133463],poupartiopsis [&&NHX:TOL=133464],pseudospondias[&&NHX:TOL=133465],sclerocarya[&&NHX:TOL=133466],solenocarpus[&&NHX:TOL=133467],spondias[&&NHX:TOL=133468],tapirira[&&NHX:TOL=133469])spondioideae[&&NHX:TOL=133449])anacardiaceae[&&NHX:TOL=21262],burseraceae[&&NHX:TOL=21263])[&&NHX:TOL=21261],biebersteiniaceae[&&NHX:TOL=21264],kirkiaceae[&&NHX:TOL=21265],(meliaceae[&&NHX:TOL=21267],rutaceae[&&NHX:TOL=21268],simaroubaceae[&&NHX:TOL=21269])[&&NHX:TOL=21266],nitrariaceae[&&NHX:TOL=21270],peganaceae[&&NHX:TOL=21271],sapindaceae[&&NHX:TOL=21272])sapindales[&&NHX:TOL=21051])[&&NHX:TOL=21047])[&&NHX:TOL=139687])[&&NHX:TOL=139686])malvidae[&&NHX:TOL=139684])rosids[&&NHX:TOL=20701],vitaceae[&&NHX:TOL=20700])[&&NHX:TOL=52339],((((polygonaceae[&&NHX:TOL=20973],plumbaginaceae[&&NHX:TOL=20974])[&&NHX:TOL=20972],(frankenia[&&NHX:TOL=20970],tamaricaceae[&&NHX:TOL=20971])[&&NHX:TOL=20969],(droseraceae[&&NHX:TOL=20978],(((ancistrocladus[&&NHX:TOL=59580],dioncophyllaceae[&&NHX:TOL=20976])[&&NHX:TOL=20977],drosophyllum lusitanicum[&&NHX:TOL=59581])[&&NHX:TOL=20979],nepenthes[&&NHX:TOL=59582])[&&NHX:TOL=20980])[&&NHX:TOL=20975])noncore caryophyllales[&&NHX:TOL=20968],rhabdodendron[&&NHX:TOL=20967],(simmondsia chinensis[&&NHX:TOL=20966],(((((((sarcobatus vermiculatus[&&NHX:TOL=66586],sarcobatus baileyi[&&NHX:TOL=66587])sarcobatus[&&NHX:TOL=21002],agdestis clematidea[&&NHX:TOL=59574])[&&NHX:TOL=21001],nyctaginaceae[&&NHX:TOL=59575],(gisekia[&&NHX:TOL=20999],petiveria alliacea[&&NHX:TOL=59576])[&&NHX:TOL=20994],phytolaccaceae[&&NHX:TOL=20993],aizoaceae[&&NHX:TOL=21000])[&&NHX:TOL=20995],barbeuia madagascariensis[&&NHX:TOL=59577])[&&NHX:TOL=21003],(portulacaceae[&&NHX:TOL=20988],cactaceae[&&NHX:TOL=20989],didiereaceae[&&NHX:TOL=20992],basellaceae[&&NHX:TOL=20990],halophytum ameghinoi[&&NHX:TOL=20991],molluginaceae[&&NHX:TOL=20998])[&&NHX:TOL=27071],limeum[&&NHX:TOL=20997],lophiocarpus[&&NHX:TOL=21004],corbichonia[&&NHX:TOL=21005],stegnosperma[&&NHX:TOL=59578])[&&NHX:TOL=20996],((achatocarpaceae[&&NHX:TOL=20986],amaranthaceae[&&NHX:TOL=59579])[&&NHX:TOL=20985],caryophyllaceae[&&NHX:TOL=20984])[&&NHX:TOL=20983])[&&NHX:TOL=20987],(physena[&&NHX:TOL=21007],asteropeia[&&NHX:TOL=21008])[&&NHX:TOL=21006])core caryophyllales[&&NHX:TOL=20965])[&&NHX:TOL=66550])caryophyllales[&&NHX:TOL=20703],dilleniaceae[&&NHX:TOL=20702])[&&NHX:TOL=52158],(((curtisia[&&NHX:TOL=23084],grubbia[&&NHX:TOL=20784])grubbiaceae[&&NHX:TOL=23085],(cornus[&&NHX:TOL=20785],alangium[&&NHX:TOL=23086])cornaceae[&&NHX:TOL=23087],((nyssa[&&NHX:TOL=20786],davidia[&&NHX:TOL=23088],camptotheca[&&NHX:TOL=23089])nyssoids[&&NHX:TOL=23090],(mastixia[&&NHX:TOL=23092],diplopanax[&&NHX:TOL=23093])mastixioids[&&NHX:TOL=23091])nyssaceae[&&NHX:TOL=23094],(hydrangeaceae[&&NHX:TOL=20789],loasaceae[&&NHX:TOL=20790])[&&NHX:TOL=20788],hydrostachys[&&NHX:TOL=20787])cornales[&&NHX:TOL=20719],((balsaminaceae[&&NHX:TOL=20806],marcgraviaceae[&&NHX:TOL=20807],pellicieraceae[&&NHX:TOL=20808],tetrameristaceae[&&NHX:TOL=20809])[&&NHX:TOL=20805],((((fouquieria leonilae[&&NHX:TOL=66513],fouquieria ochoterenae[&&NHX:TOL=66514],fouquieria macdougalii[&&NHX:TOL=66515],fouquieria diguetii[&&NHX:TOL=66516],fouquieria burragei[&&NHX:TOL=66517],fouquieria formosa[&&NHX:TOL=66518],fouquieria splendens[&&NHX:TOL=66519],fouquieria shrevei[&&NHX:TOL=66520])fouquieria fouquieria[&&NHX:TOL=66524],(fouquieria fasciculata[&&NHX:TOL=66521],fouquieria purpusii[&&NHX:TOL=66522])fouquieria bronnia[&&NHX:TOL=66525],fouquieria idria columnaris[&&NHX:TOL=66523])fouquieria[&&NHX:TOL=20811],((cantua[&&NHX:TOL=22990],bonplandia[&&NHX:TOL=22991],cobaea[&&NHX:TOL=22992])cobeaoideae[&&NHX:TOL=22986],acanthogilia gloriosa[&&NHX:TOL=22988],((((saltugilia australis[&&NHX:TOL=23047],saltugilia latimeri[&&NHX:TOL=23048],saltugilia caruifolia[&&NHX:TOL=23049],saltugilia splendens[&&NHX:TOL=23050])saltugilia[&&NHX:TOL=22998],(lathrocasis tenerrima[&&NHX:TOL=22996],((allophyllum[&&NHX:TOL=22993],(navarretia[&&NHX:TOL=22994],((((collomia larsenii[&&NHX:TOL=111781],collomia rawsoniana[&&NHX:TOL=111782],collomia debilis[&&NHX:TOL=111780],collomia mazama[&&NHX:TOL=111783])[&&NHX:TOL=133941],(collomia tenella[&&NHX:TOL=111790],collomia wilkenii[&&NHX:TOL=111793],collomia linearis[&&NHX:TOL=111792],collomia biflora[&&NHX:TOL=111779],collomia grandiflora[&&NHX:TOL=111791],collomia macrocalyx[&&NHX:TOL=111789],collomia renacta[&&NHX:TOL=111788])[&&NHX:TOL=133944])[&&NHX:TOL=133945],(collomia tinctoria[&&NHX:TOL=111786],collomia tracyi[&&NHX:TOL=111787])[&&NHX:TOL=133943])[&&NHX:TOL=133946],(collomia heterophylla[&&NHX:TOL=111784],collomia diversifolia[&&NHX:TOL=111785])[&&NHX:TOL=133942])collomia[&&NHX:TOL=22995])[&&NHX:TOL=23015])[&&NHX:TOL=23014],(gilia[&&NHX:TOL=22997],gilisenium hueberi[&&NHX:EXT=Y:TOL=23024])[&&NHX:TOL=23025])[&&NHX:TOL=133950])[&&NHX:TOL=23021])gilieae[&&NHX:TOL=23013],(aliciella[&&NHX:TOL=23008],(((ipomopsis[&&NHX:TOL=23029],(microgilia minutiflora[&&NHX:TOL=23028],((langloisia setosissima     [&&NHX:TOL=23026],loeseliastrum[&&NHX:TOL=23027])[&&NHX:TOL=23030],eriastrum[&&NHX:TOL=23031])[&&NHX:TOL=23032])[&&NHX:TOL=23033])[&&NHX:TOL=23034],bryantiella[&&NHX:TOL=23011],(loeselia[&&NHX:TOL=23006],dayia[&&NHX:TOL=23009])[&&NHX:TOL=133949])[&&NHX:TOL=133948],giliastrum[&&NHX:TOL=23010])[&&NHX:TOL=133947])loeselieae[&&NHX:TOL=22989])[&&NHX:TOL=133952],((linanthus[&&NHX:TOL=22999],(gymnosteris[&&NHX:TOL=23000],(leptosiphon[&&NHX:TOL=23001],(microsteris gracilis[&&NHX:TOL=23002],phlox[&&NHX:TOL=23003])[&&NHX:TOL=23020])[&&NHX:TOL=23019])[&&NHX:TOL=23018])phlocideae[&&NHX:TOL=23017],(polemonium[&&NHX:TOL=22987],polemonipollis majewskii[&&NHX:EXT=Y:TOL=23022])polemonieae[&&NHX:TOL=23023])[&&NHX:TOL=133951])polemonioideae[&&NHX:TOL=23012])polemoniaceae[&&NHX:TOL=20812])[&&NHX:TOL=27140],((((actinidiaceae[&&NHX:TOL=20837],roridulaceae[&&NHX:TOL=20838])[&&NHX:TOL=20836],sarraceniaceae[&&NHX:TOL=20839])[&&NHX:TOL=20835],(ericaceae[&&NHX:TOL=20841],cyrillaceae[&&NHX:TOL=20842],clethraceae[&&NHX:TOL=20843])[&&NHX:TOL=20840])core ericales[&&NHX:TOL=20834],lecythidaceae[&&NHX:TOL=20833],sapotaceae[&&NHX:TOL=20832],styracaceae[&&NHX:TOL=20831],diapensiaceae[&&NHX:TOL=20830],symplocaceae[&&NHX:TOL=20829],(lissocarpa[&&NHX:TOL=20827],ebenaceae[&&NHX:TOL=20828])[&&NHX:TOL=20826],(maesaceae[&&NHX:TOL=20820],(theophrastaceae[&&NHX:TOL=20822],(primulaceae[&&NHX:TOL=20824],myrsinaceae[&&NHX:TOL=20825])[&&NHX:TOL=20823])[&&NHX:TOL=20821])primuloid families[&&NHX:TOL=20819],theaceae[&&NHX:TOL=20818],(ternstroemiaceae[&&NHX:TOL=20814],pentaphylax[&&NHX:TOL=20815],ficalhoa laurifolia[&&NHX:TOL=20816],sladenia[&&NHX:TOL=20817])[&&NHX:TOL=20813])[&&NHX:TOL=20810])[&&NHX:TOL=27141])ericales[&&NHX:TOL=20720],(((((hydrolea[&&NHX:TOL=20952],sphenoclea[&&NHX:TOL=20953],montiniaceae[&&NHX:TOL=20954])[&&NHX:TOL=20951],(solanaceae[&&NHX:TOL=20956],convolvulaceae[&&NHX:TOL=20957])[&&NHX:TOL=20955])solanales[&&NHX:TOL=20725],(plocosperma[&&NHX:TOL=20857],carlemanniaceae[&&NHX:TOL=20859],((myxopyrum[&&NHX:TOL=20914],(nyctanthes[&&NHX:TOL=20916],dimetra craibiana[&&NHX:TOL=20917])[&&NHX:TOL=20915])[&&NHX:TOL=20913],fontanesia[&&NHX:TOL=20918],(abeliophyllum distichum[&&NHX:TOL=20920],forsythia[&&NHX:TOL=20921])[&&NHX:TOL=20919],((menodora[&&NHX:TOL=20924],jasminum[&&NHX:TOL=20925])[&&NHX:TOL=20923],((ligustrum[&&NHX:TOL=20928],syringa[&&NHX:TOL=20929])[&&NHX:TOL=20927],((comoranthus[&&NHX:TOL=20932],schrebera[&&NHX:TOL=20933])[&&NHX:TOL=20931],(fraxinus[&&NHX:TOL=20935],(chionanthus[&&NHX:TOL=20937],forestiera[&&NHX:TOL=20938],haenianthus[&&NHX:TOL=20939],hesperelaea palmeri[&&NHX:EXT=Y:TOL=20940],noronhia[&&NHX:TOL=20941],priogymnanthus[&&NHX:TOL=20942],olea[&&NHX:TOL=20943],(nestegis[&&NHX:TOL=20945],notelaea[&&NHX:TOL=20946],osmanthus[&&NHX:TOL=20947],phillyrea[&&NHX:TOL=20948],picconia excelsa[&&NHX:TOL=20949])[&&NHX:TOL=20944])[&&NHX:TOL=20936])[&&NHX:TOL=20934])[&&NHX:TOL=20930])[&&NHX:TOL=20926])[&&NHX:TOL=20922])oleaceae[&&NHX:TOL=20858],tetrachondraceae[&&NHX:TOL=20882],(((((((gesnerieae[&&NHX:TOL=20889],gloxinieae[&&NHX:TOL=20890])[&&NHX:TOL=20888],episcieae[&&NHX:TOL=20891])[&&NHX:TOL=20887],sinningieae[&&NHX:TOL=20892])[&&NHX:TOL=20886],((beslerieae[&&NHX:TOL=20895],napeantheae[&&NHX:TOL=20896])[&&NHX:TOL=20894],coronanthereae[&&NHX:TOL=20897])[&&NHX:TOL=20893])gesnerioideae[&&NHX:TOL=20885],((((((cyrtandreae[&&NHX:TOL=20904],trichosporeae1[&&NHX:TOL=20905])[&&NHX:TOL=20903],trichosporeae2[&&NHX:TOL=20906])[&&NHX:TOL=20902],didymocarpeae1[&&NHX:TOL=20907])[&&NHX:TOL=20901],didymocarpeae2[&&NHX:TOL=20908])[&&NHX:TOL=20900],didymocarpeae3[&&NHX:TOL=20909])[&&NHX:TOL=20899],titanotricheae[&&NHX:TOL=20910])cyrtandroideae[&&NHX:TOL=20898])[&&NHX:TOL=20884],klugieae[&&NHX:TOL=20911])gesneriaceae[&&NHX:TOL=20861],(((((((((((((((ruellia amplexicaulis[&&NHX:TOL=103639],ruellia angustiflora[&&NHX:TOL=103640],ruellia biolleyi[&&NHX:TOL=103641],ruellia breedlovei[&&NHX:TOL=103642],ruellia brevifolia[&&NHX:TOL=103643],ruellia chartacea[&&NHX:TOL=103644],ruellia costata[&&NHX:TOL=103645],ruellia eumorphantha[&&NHX:TOL=103646],ruellia fulgens[&&NHX:TOL=103647],ruellia fulgida[&&NHX:TOL=103648],ruellia gracilis[&&NHX:TOL=103649],ruellia grantii[&&NHX:TOL=103650],ruellia haenkeana[&&NHX:TOL=103651],ruellia ischnopoda[&&NHX:TOL=103652],ruellia jussieuoides[&&NHX:TOL=103653],ruellia longipedunculata[&&NHX:TOL=103654],ruellia macrophylla[&&NHX:TOL=103655],ruellia matudae[&&NHX:TOL=103656],ruellia menthoides[&&NHX:TOL=103657],ruellia nitida[&&NHX:TOL=103658],ruellia oaxacana[&&NHX:TOL=103659],ruellia pearcei[&&NHX:TOL=103660],ruellia pedunculosa[&&NHX:TOL=103661],ruellia pennellii[&&NHX:TOL=103662],ruellia proxima[&&NHX:TOL=103663],ruellia puri[&&NHX:TOL=103664],ruellia pygmea[&&NHX:TOL=103665],ruellia riopalenquensis[&&NHX:TOL=103666],ruellia rubra[&&NHX:TOL=103667],ruellia ruiziana[&&NHX:TOL=103668],ruellia sanguiea[&&NHX:TOL=103669],ruellia saulensis[&&NHX:TOL=103670],ruellia stemonacanthoides[&&NHX:TOL=103671],ruellia terminale[&&NHX:TOL=103672])physiruellia clade[&&NHX:TOL=65582],(ruellia blechum[&&NHX:TOL=103673],ruellia longepetiolata[&&NHX:TOL=103674],ruellia maya[&&NHX:TOL=103675],ruellia menthifolia[&&NHX:TOL=103676],ruellia tuxtlensis[&&NHX:TOL=103677])blechum clade[&&NHX:TOL=96989])[&&NHX:TOL=103637],(ruellia asperula[&&NHX:TOL=103678],ruellia floribunda[&&NHX:TOL=103679],ruellia galeottii[&&NHX:TOL=103680],ruellia inundata[&&NHX:TOL=103681],ruellia paniculata[&&NHX:TOL=103682],ruellia standleyi[&&NHX:TOL=103683])ruellia inundata clade[&&NHX:TOL=96991])[&&NHX:TOL=103636],(ruellia adenocalyx[&&NHX:TOL=103684],ruellia alboviolacea[&&NHX:TOL=103685],ruellia amoena[&&NHX:TOL=103686],ruellia beyrichiana[&&NHX:TOL=103687],ruellia bulbifera[&&NHX:TOL=103688],ruellia densa[&&NHX:TOL=103689],ruellia donnellsmithii[&&NHX:TOL=103690],ruellia eriocalyx[&&NHX:TOL=103691],ruellia erythropus[&&NHX:TOL=103692],ruellia foetida[&&NHX:TOL=103693],ruellia geminiflora[&&NHX:TOL=103694],ruellia hapalotricha[&&NHX:TOL=103695],ruellia hookeriana[&&NHX:TOL=103696],ruellia humboldtiana[&&NHX:TOL=103697],ruellia incompta[&&NHX:TOL=103698],ruellia leucantha[&&NHX:TOL=103699],ruellia longifilamentosa[&&NHX:TOL=103700],ruellia magnifora[&&NHX:TOL=103701],ruellia matagalpae[&&NHX:TOL=103702],ruellia mcvaughii[&&NHX:TOL=103703],ruellia novogaliciana[&&NHX:TOL=103704],ruellia petiolaris[&&NHX:TOL=103705],ruellia salviaefolius[&&NHX:TOL=103706],ruellia spissa[&&NHX:TOL=103707],ruellia tarapotana[&&NHX:TOL=103708],ruellia tomentosa[&&NHX:TOL=103709],ruellia tubiflora[&&NHX:TOL=103710],ruellia verbasciformis[&&NHX:TOL=103711],ruellia villosa[&&NHX:TOL=103712],ruellia yurimaguensis[&&NHX:TOL=103713])ebracteolate clade[&&NHX:TOL=96997],(ruellia brittoniana[&&NHX:TOL=103714],ruellia ciliatiflora[&&NHX:TOL=103715],ruellia coerulea[&&NHX:TOL=103716],ruellia drummondiana[&&NHX:TOL=103717],ruellia edwardsae[&&NHX:TOL=103718],ruellia hygrophila[&&NHX:TOL=103719],ruellia jimulcensis[&&NHX:TOL=103720],ruellia lactea[&&NHX:TOL=103721],ruellia macrosolen[&&NHX:TOL=103722],ruellia malaca[&&NHX:TOL=103723],ruellia metzae[&&NHX:TOL=103724],ruellia morongii[&&NHX:TOL=103725],ruellia nudiflora[&&NHX:TOL=103726],ruellia runyonii[&&NHX:TOL=103727],ruellia tuberosa[&&NHX:TOL=103728])euruellia clade[&&NHX:TOL=96993],(ruellia acutangula[&&NHX:TOL=103729],ruellia elegans[&&NHX:TOL=103730],ruellia eurycodon[&&NHX:TOL=103731],ruellia exserta[&&NHX:TOL=103732],ruellia inflata[&&NHX:TOL=103733],ruellia steyermarkii[&&NHX:TOL=103734],ruellia subsessilis[&&NHX:TOL=103735])ruellia inflata clade[&&NHX:TOL=96995],(ruellia bourgaei[&&NHX:TOL=103736],ruellia conzattii[&&NHX:TOL=103737],ruellia fruticosa[&&NHX:TOL=103738],ruellia jaliscana[&&NHX:TOL=103739],ruellia pringlei[&&NHX:TOL=103740],ruellia speciosa[&&NHX:TOL=103741])ruellia jaliscana clade[&&NHX:TOL=96996],(ruellia harveyana[&&NHX:TOL=103742],ruellia multifolia[&&NHX:TOL=103743],ruellia nobilis[&&NHX:TOL=103744],ruellia pilosa[&&NHX:TOL=103745])ruellia harveyana clade[&&NHX:TOL=96998],(ruellia caroliniensis[&&NHX:TOL=103746],ruellia humilis[&&NHX:TOL=103747],ruellia purshiana[&&NHX:TOL=103748],ruellia strepens[&&NHX:TOL=103749])ruellia humilis clade[&&NHX:TOL=103638])new world ruellia[&&NHX:TOL=65577],(ruellia anaticollis[&&NHX:TOL=103750],ruellia ansericollis[&&NHX:TOL=103751],ruellia cordata[&&NHX:TOL=103752],ruellia detonsa[&&NHX:TOL=103753],ruellia discifolia[&&NHX:TOL=103754],ruellia geayi[&&NHX:TOL=103755],ruellia insignis[&&NHX:TOL=103756],ruellia latisepala[&&NHX:TOL=103757],ruellia linearibracteolata[&&NHX:TOL=103758],ruellia malacophylla[&&NHX:TOL=103759],ruellia megachlamys[&&NHX:TOL=103760],ruellia patula[&&NHX:TOL=103761])african ruellia[&&NHX:TOL=65578])ruellia s. l.[&&NHX:TOL=65583],(acanthopale albosetulosa[&&NHX:TOL=103762],acanthopale azaleoides[&&NHX:TOL=103763],acanthopale buchholzii[&&NHX:TOL=103764],acanthopale confertiflora[&&NHX:TOL=103765],acanothpale decempedalis[&&NHX:TOL=103766],acanthopale laxiflora[&&NHX:TOL=103767],acanthopale pubescens[&&NHX:TOL=103768])acanthopale[&&NHX:TOL=96975])[&&NHX:TOL=96977],((((brillantaisia[&&NHX:TOL=65588],(hemigraphis  strobilanthes  relatives[&&NHX:TOL=65590],hygrophila[&&NHX:TOL=65591])[&&NHX:TOL=65589])[&&NHX:TOL=65587],bravaisia[&&NHX:TOL=65592])[&&NHX:TOL=65586],(((calacanthus[&&NHX:TOL=65596],suessenguthia[&&NHX:TOL=65597])[&&NHX:TOL=65595],sanchezia[&&NHX:TOL=65598])[&&NHX:TOL=65594],louteridium[&&NHX:TOL=65599])[&&NHX:TOL=65593])[&&NHX:TOL=65585],(((duosperma[&&NHX:TOL=65603],dyschoriste[&&NHX:TOL=65604])[&&NHX:TOL=65602],petalidium[&&NHX:TOL=65605])[&&NHX:TOL=65601],(mimulopsis[&&NHX:TOL=65607],mellera[&&NHX:TOL=65608])[&&NHX:TOL=65606])[&&NHX:TOL=65600])[&&NHX:TOL=65584])[&&NHX:TOL=65574],dischistocalyx[&&NHX:TOL=65609])[&&NHX:TOL=65573],pararuellia[&&NHX:TOL=65610],phaulopsis[&&NHX:TOL=65611])ruellieae[&&NHX:TOL=52296],(((((new world justicioids[&&NHX:TOL=52328],diclipterinae[&&NHX:TOL=52329])[&&NHX:TOL=52327],old world justicioids[&&NHX:TOL=52330])[&&NHX:TOL=52326],tetramerium lineage[&&NHX:TOL=52331])[&&NHX:TOL=102739],(ptyssiglottis[&&NHX:TOL=55563],(isoglossa  conocalyx[&&NHX:TOL=55564],(brachystephanus i[&&NHX:TOL=65569],(brachystephanus ii[&&NHX:TOL=65571],brachystephanus iii  nw isoglossinae stenostephanus razisea habracanthus kalbreyeriella[&&NHX:TOL=65572])[&&NHX:TOL=65570])[&&NHX:TOL=65568])core isoglossinae[&&NHX:TOL=52332])[&&NHX:TOL=65567])[&&NHX:TOL=102738],pseuderanthemum lineage[&&NHX:TOL=52333])justicieae[&&NHX:TOL=52290])[&&NHX:TOL=52291],(whitfieldieae[&&NHX:TOL=52297],(andrographideae[&&NHX:TOL=52298],barlerieae[&&NHX:TOL=52292])[&&NHX:TOL=68863])[&&NHX:TOL=68862])ruellioideae[&&NHX:TOL=52295],neuracanthus[&&NHX:TOL=52299])[&&NHX:TOL=52294],(((((((acanthus eminens[&&NHX:TOL=69133],acanthus ilicifolius[&&NHX:TOL=69134],acanthus longifolius[&&NHX:TOL=69135],acanthus mollis[&&NHX:TOL=69136],acanthus montanus[&&NHX:TOL=69137],acanthus pubescens[&&NHX:TOL=69138],acanthus sennii [&&NHX:TOL=69139],acanthus spinosus[&&NHX:TOL=69140],blepharis dhofarensis[&&NHX:TOL=69141])acanthus clade[&&NHX:TOL=52304],(acanthopsis carduifolia[&&NHX:TOL=69142],acanthopsis hoffmannseggiana[&&NHX:TOL=69143],acanthopsis disperma[&&NHX:TOL=69144])acanthopsis[&&NHX:TOL=52311])[&&NHX:TOL=52310],(blepharis acuminata [&&NHX:TOL=69145],blepharis asteracanthus [&&NHX:TOL=69146],blepharis buchneri [&&NHX:TOL=69147],blepharis calcitrapa [&&NHX:TOL=69148],blepharis diversipina[&&NHX:TOL=69149],blepharis edulis[&&NHX:TOL=69150],blepharis integrifolia[&&NHX:TOL=69151],blepharis katangensis [&&NHX:TOL=69152],blepharis maderaspatensis [&&NHX:TOL=69153],blepharis natalensis [&&NHX:TOL=69154],blepharis sinuata[&&NHX:TOL=69155],blepharis subvolubilis [&&NHX:TOL=69156],blepharis tenuiramea [&&NHX:TOL=69157],blepharis trispina [&&NHX:TOL=69158])blepharis[&&NHX:TOL=52312])[&&NHX:TOL=52309],cynarospermum asperrimum[&&NHX:TOL=52313])crown clade[&&NHX:TOL=52308],(crossandrella dusenii[&&NHX:TOL=52315],streptosiphon hirsutus [&&NHX:TOL=52316],(sclerochiton harveyanus [&&NHX:TOL=69159],sclerochiton ilicifolius [&&NHX:TOL=69160],sclerochiton triacanthus [&&NHX:TOL=69161],sclerochiton vogelii[&&NHX:TOL=69162])sclerochiton[&&NHX:TOL=52317])sclerochiton clade[&&NHX:TOL=52314])[&&NHX:TOL=52307],(crossandra greenstockii [&&NHX:TOL=69163],crossandra horrida [&&NHX:TOL=69164],crossandra infundibuliformis[&&NHX:TOL=69165],crossandra longipes [&&NHX:TOL=69166],crossandra pungens [&&NHX:TOL=69167],crossandra strobilifera[&&NHX:TOL=69168])crossandra[&&NHX:TOL=52318])one lipped corolla lineage[&&NHX:TOL=52306],((achyrocalyx decaryi[&&NHX:TOL=69169],stenandrium afromontanum[&&NHX:TOL=69170],stenandrium guineensis[&&NHX:TOL=69171],stenandrium humile[&&NHX:TOL=69172],stenandrium thompsonii[&&NHX:TOL=69173],stenandrium warneckei[&&NHX:TOL=69174])stenandriopsis clade[&&NHX:TOL=52320],((aphelandra verticillata [&&NHX:TOL=69175],holographis ehrenbergiana [&&NHX:TOL=69176],holographis pallida [&&NHX:TOL=69177],holographis velutifolia[&&NHX:TOL=69178],neriacanthus purdieanus [&&NHX:TOL=69179],salpixantha coccinea [&&NHX:TOL=69180],stenandrium mandioccanum [&&NHX:TOL=69181],stenandrium pilosulum[&&NHX:TOL=69182])stenandrium clade[&&NHX:TOL=52322],(aphelandra aurantiaca [&&NHX:TOL=69183],aphelandra boyacensis [&&NHX:TOL=69184],aphelandra campanensis [&&NHX:TOL=69185],aphelandra castanifolia [&&NHX:TOL=69186],aphelandra dolichantha [&&NHX:TOL=69187],aphelandra fasciculata [&&NHX:TOL=69188],aphelandra fernandezii [&&NHX:TOL=69189],aphelandra golfodulcensis [&&NHX:TOL=69190],aphelandra gigantiflora [&&NHX:TOL=69191],aphelandra guerrerensis [&&NHX:TOL=69192],aphelandra hylaea [&&NHX:TOL=69193],aphelandra impressa [&&NHX:TOL=69194],aphelandra lasia [&&NHX:TOL=69195],aphelandra leonardii [&&NHX:TOL=69196],aphelandra maculata[&&NHX:TOL=69197],aphelandra maximiliana [&&NHX:TOL=69198],aphelandra rubra [&&NHX:TOL=69199],aphelandra runcinata [&&NHX:TOL=69200],aphelandra speciosa [&&NHX:TOL=69201],aphelandra squarrosa [&&NHX:TOL=69202],aphelandra tetragona  [&&NHX:TOL=69203],aphelandra tonduzii [&&NHX:TOL=69204],aphelandra tridentata [&&NHX:TOL=69205],encephalosphaera lasiandra [&&NHX:TOL=69206],geissomeria longiflora [&&NHX:TOL=69207],geissomeria tetragona [&&NHX:TOL=69208],neriacanthus grandiflorus [&&NHX:TOL=69209],neriacanthus lehmannianus [&&NHX:TOL=69210],rhombochlamys rosulata [&&NHX:TOL=69211])other new world acantheae[&&NHX:TOL=52323])[&&NHX:TOL=52321])two lipped corolla lineage[&&NHX:TOL=52319])acantheae[&&NHX:TOL=52300])core acanthaceae[&&NHX:TOL=68861],(avicennia[&&NHX:TOL=52288],((thunbergia[&&NHX:TOL=110642],meyenia[&&NHX:TOL=110649],pseudocalyx[&&NHX:TOL=110643])[&&NHX:TOL=110647],anomacanthus[&&NHX:TOL=110646],mendoncia[&&NHX:TOL=110645])thunbergioideae[&&NHX:TOL=52301])[&&NHX:TOL=68864])[&&NHX:TOL=52293],nelsonioideae[&&NHX:TOL=52302])acanthaceae[&&NHX:TOL=20878],calceolariaceae[&&NHX:TOL=20862],scrophulariaceae[&&NHX:TOL=20863],buddlejaceae[&&NHX:TOL=20864],myoporaceae[&&NHX:TOL=20865],plantaginaceae[&&NHX:TOL=20866],bignoniaceae[&&NHX:TOL=20867],pedaliaceae[&&NHX:TOL=20868],paulowniaceae[&&NHX:TOL=20869],orobanchaceae[&&NHX:TOL=20870],martyniaceae[&&NHX:TOL=20871],lentibulariaceae[&&NHX:TOL=20872],verbenaceae[&&NHX:TOL=20873],lamiaceae[&&NHX:TOL=20874],cyclocheilaceae[&&NHX:TOL=20875],byblidaceae[&&NHX:TOL=20876],phrymaceae[&&NHX:TOL=20879],schlegeliaceae[&&NHX:TOL=20880],stilbaceae[&&NHX:TOL=20881])core lamiales[&&NHX:TOL=20860])lamiales[&&NHX:TOL=20726],(rubiaceae[&&NHX:TOL=20850],(gelsemiaceae[&&NHX:TOL=20852],apocynaceae[&&NHX:TOL=20853],loganiaceae[&&NHX:TOL=20854],gentianaceae[&&NHX:TOL=20855])[&&NHX:TOL=20851])gentianales[&&NHX:TOL=20724],boraginaceae[&&NHX:TOL=20723],vahlia[&&NHX:TOL=20729])[&&NHX:TOL=27069],(eucommia ulmoides[&&NHX:TOL=20845],(aucuba[&&NHX:TOL=20847],garrya[&&NHX:TOL=20848])garryaceae[&&NHX:TOL=20846])garryales[&&NHX:TOL=20727],oncotheca[&&NHX:TOL=20728],icacinaceae[&&NHX:TOL=20732])euasterids i lamiids[&&NHX:TOL=20722],(((campanulaceae[&&NHX:TOL=20767],pentaphragma[&&NHX:TOL=20768],(roussea[&&NHX:TOL=20770],carpodetaceae[&&NHX:TOL=20771])[&&NHX:TOL=20769],donatia[&&NHX:TOL=20772],stylidiaceae[&&NHX:TOL=20773],phelline[&&NHX:TOL=20774],argophyllaceae[&&NHX:TOL=20775],alseuosmiaceae[&&NHX:TOL=20776],(menyanthaceae[&&NHX:TOL=20778],((((huarpea[&&NHX:TOL=120448],barnadesia[&&NHX:TOL=120449])[&&NHX:TOL=120447],((chuquiraga[&&NHX:TOL=120457],doniophyton[&&NHX:TOL=120458])[&&NHX:TOL=120456],(((arnaldoa[&&NHX:TOL=120453],fulcaldea[&&NHX:TOL=120454])[&&NHX:TOL=120452],dasyphyllum subg. archidasyphyllum[&&NHX:TOL=120455])[&&NHX:TOL=120451],schlechtendalia[&&NHX:TOL=120445])[&&NHX:TOL=121192])[&&NHX:TOL=121191],duseniella[&&NHX:TOL=120446],dasyphyllum subg. dasyphyllum[&&NHX:TOL=120450])barnadesioideae[&&NHX:TOL=22864],((((aphyllocladus[&&NHX:TOL=120114],plazia[&&NHX:TOL=120115])[&&NHX:TOL=120113],(onoseris[&&NHX:TOL=120117],lycoseris[&&NHX:TOL=120118])[&&NHX:TOL=120116],gypothamnium[&&NHX:TOL=120237],urmenetea[&&NHX:TOL=120238])onoserideae[&&NHX:TOL=120088],(((((acourtia[&&NHX:TOL=120122],((perezia[&&NHX:TOL=120124],panphalea[&&NHX:TOL=120241])[&&NHX:TOL=120240],(nassauvia[&&NHX:TOL=120125],triptilion[&&NHX:TOL=120253])[&&NHX:TOL=120262])[&&NHX:TOL=120123])[&&NHX:TOL=120121],(jungia[&&NHX:TOL=120127],(trixis[&&NHX:TOL=120129],(dolichlasium[&&NHX:TOL=120130],ameghinoa[&&NHX:TOL=120242])[&&NHX:TOL=120264])[&&NHX:TOL=120128],holocheilus[&&NHX:TOL=120245])[&&NHX:TOL=120126])[&&NHX:TOL=120120],(leucheria[&&NHX:TOL=120131],(polyachyrus[&&NHX:TOL=120252],moscharia[&&NHX:TOL=120249])[&&NHX:TOL=120266])[&&NHX:TOL=120265])[&&NHX:TOL=120119],(proustia[&&NHX:TOL=120133],lophopappus[&&NHX:TOL=120134])[&&NHX:TOL=120132],berylsimpsonia[&&NHX:TOL=120259],burkartia[&&NHX:TOL=120243],calopappus[&&NHX:TOL=120263],(calorezia nutans[&&NHX:TOL=133894],calorezia prenanthoides[&&NHX:TOL=133895])calorezia[&&NHX:TOL=120260],cephalopappus[&&NHX:TOL=120244],leunisia[&&NHX:TOL=120246],macrachaenium gracile[&&NHX:TOL=120247],marticorenia foliosa[&&NHX:TOL=120248],oxyphyllum ulicinum[&&NHX:TOL=120250],pleocarphus revolutus[&&NHX:TOL=120251],criscia stricta[&&NHX:TOL=120267])nassauvieae[&&NHX:TOL=69939],((((gerbera[&&NHX:TOL=120137],leibnitzia[&&NHX:TOL=120255])[&&NHX:TOL=121874],chaptalia[&&NHX:TOL=120138])[&&NHX:TOL=120136],(brachyclados[&&NHX:TOL=120140],((trichocline aurea[&&NHX:TOL=133897],trichocline spathulata[&&NHX:TOL=133898])sect. amblysperma[&&NHX:TOL=133896],(trichocline auriculata[&&NHX:TOL=133900],trichocline beckeri[&&NHX:TOL=133901],trichocline boecheri[&&NHX:TOL=133902],trichocline catharinensis[&&NHX:TOL=133903],trichocline caulescens[&&NHX:TOL=133904],trichocline cineraria[&&NHX:TOL=133905],trichocline dealbata[&&NHX:TOL=133906],trichocline deserticola[&&NHX:TOL=133907],trichocline exscapa[&&NHX:TOL=133908],trichocline heterophylla[&&NHX:TOL=133909],trichocline humilis[&&NHX:TOL=133910],trichocline incana[&&NHX:TOL=133911],trichocline linearifolia[&&NHX:TOL=133912],trichocline macrocephala[&&NHX:TOL=133913],trichoclne macrorhiza[&&NHX:TOL=133914],trichocline maxima[&&NHX:TOL=133915],trichocline plicata[&&NHX:TOL=133916],trichocline reptans[&&NHX:TOL=133917],trichocline sinuata[&&NHX:TOL=133918],trichocline speciosa[&&NHX:TOL=133919])sect. trichocline[&&NHX:TOL=133899])trichocline[&&NHX:TOL=120141])[&&NHX:TOL=120139])[&&NHX:TOL=120135],((chaetanthera lanata[&&NHX:TOL=134028],chaetanthera spathulifolia[&&NHX:TOL=134029],chaetanthera villosa[&&NHX:TOL=134030])subgenus carmelita[&&NHX:TOL=134020],subgenus glandulosa[&&NHX:TOL=134021],((chaetanthera apiculata[&&NHX:TOL=134033],((chaetanthera revoluta[&&NHX:TOL=134036],chaetanthera dioica[&&NHX:TOL=134037])[&&NHX:TOL=134035],(chaetanthera sphaeroidalis[&&NHX:TOL=134039],chaetanthera pulvinata[&&NHX:TOL=134040])[&&NHX:TOL=134038])[&&NHX:TOL=134034],chaetanthera pentacaenoides[&&NHX:TOL=134041],chaetanthera acerosa[&&NHX:TOL=134042],(chaetanthera cochlearifolia[&&NHX:TOL=134044],chaetanthera stuebelii[&&NHX:TOL=134045],chaetanthera boliviensis[&&NHX:TOL=134046])[&&NHX:TOL=134043])subgenus egania[&&NHX:TOL=134023],(((chaetanthera pusilla[&&NHX:TOL=134049],chaetanthera planiseta[&&NHX:TOL=134050])[&&NHX:TOL=134048],chaetanthera lycopodioides[&&NHX:TOL=134051])[&&NHX:TOL=134047],(chaetanthera gnaphalioides[&&NHX:TOL=134053],chaetanthera minuta[&&NHX:TOL=134054])[&&NHX:TOL=134052])subgenus oriastrum[&&NHX:TOL=134024])[&&NHX:TOL=134022],((chaetanthera australis[&&NHX:TOL=134057],chaetanthera moenchioides[&&NHX:TOL=134058])[&&NHX:TOL=134056],chaetanthera ciliata[&&NHX:TOL=134061],chaetanthera euphrasioides[&&NHX:TOL=134059],chaetanthera flabellata[&&NHX:TOL=134064],chaetanthera incana[&&NHX:TOL=134060],chaetanthera tenella[&&NHX:TOL=134062],((chaetanthera leptocephala[&&NHX:TOL=134063],(chaetanthera linearis[&&NHX:TOL=134065],chaetanthera microphylla[&&NHX:TOL=134066])[&&NHX:TOL=134025])[&&NHX:TOL=134072],chaetanthera perpusilla[&&NHX:TOL=134067])[&&NHX:TOL=134071],(chaetanthera peruviana[&&NHX:TOL=134069],chaetanthera chiquianensis[&&NHX:TOL=134070])[&&NHX:TOL=134068])subgenus euchatanthera[&&NHX:TOL=134055],(chaetanthera serrata[&&NHX:TOL=134073],chaetanthera elegans[&&NHX:TOL=134074],chaetanthera brachylepis[&&NHX:TOL=134075],chaetanthera chilensis[&&NHX:TOL=134076],chaetanthera valdiviana[&&NHX:TOL=134077])subgenus proselia[&&NHX:TOL=134026],(((chaetanthera glabrata[&&NHX:TOL=134080],chaetanthera limbata[&&NHX:TOL=134081])[&&NHX:TOL=134079],chaetanthera kalinae[&&NHX:TOL=134082])[&&NHX:TOL=134078],chaetanthera renifolia[&&NHX:TOL=134083],(chaetanthera flabellifolia[&&NHX:TOL=134085],chaetanthera splendens[&&NHX:TOL=134086])[&&NHX:TOL=134084])subgenus tylloma[&&NHX:TOL=134027])chaetanthera[&&NHX:TOL=120146],adenocaulon[&&NHX:TOL=120142],(((mutisia lanata[&&NHX:TOL=133956],mutisia campanulata[&&NHX:TOL=133957],mutisia wurdackii[&&NHX:TOL=133958],mutisia coccinea[&&NHX:TOL=133959],mutisia speciosa[&&NHX:TOL=133960],mutisia rimbachii[&&NHX:TOL=133961],mutisia acuminata[&&NHX:TOL=133962],mutisia vicia[&&NHX:TOL=133963],mutisia hieronymi[&&NHX:TOL=133964],mutisia grandiflora[&&NHX:TOL=133965],mutisia microcephala[&&NHX:TOL=133966],mutisia sodiroi[&&NHX:TOL=133967],mutisia pulcherrima[&&NHX:TOL=133968],mutisia stuebelii[&&NHX:TOL=133969],mutisia venusta[&&NHX:TOL=133970],mutisia microphylla[&&NHX:TOL=133971],mutisia microneura[&&NHX:TOL=133972],mutisia lehmannii[&&NHX:TOL=133973],mutisia ochroleuca[&&NHX:TOL=133974],mutisia intermedia[&&NHX:TOL=133975],mutisia clematis[&&NHX:TOL=133976])section mutisia[&&NHX:TOL=133955],(mutisia kurtzii[&&NHX:TOL=133978],mutisia orbignyana[&&NHX:TOL=133979],mutisia linifolia[&&NHX:TOL=133980])section isantha[&&NHX:TOL=133977],(mutisia acerosa[&&NHX:TOL=133982],mutisia linearifolia[&&NHX:TOL=133983],mutisia mathewsii[&&NHX:TOL=133984],mutisia tridens[&&NHX:TOL=133985],mutisia subulata[&&NHX:TOL=133986],mutisia friesiana[&&NHX:TOL=133987],mutisia rosea[&&NHX:TOL=133988])section holophyllum[&&NHX:TOL=133981],(mutisia comptoniaefolia[&&NHX:TOL=133990],mutisia ledifolia[&&NHX:TOL=133991],mutisia homoeantha[&&NHX:TOL=133992])section fruticosa[&&NHX:TOL=133989],(mutisia lutzii[&&NHX:TOL=133994],mutisia spectabilis[&&NHX:TOL=133995],mutisia hamata[&&NHX:TOL=133996],mutisia retrorsa[&&NHX:TOL=133997],mutisia decurrens[&&NHX:TOL=133998],mutisia alata[&&NHX:TOL=133999],mutisia cochabambensis[&&NHX:TOL=134000],mutisia mandoniana[&&NHX:TOL=134001],mutisia andersonii[&&NHX:TOL=134002],mutisia hastata[&&NHX:TOL=134003],mutisia saltensis[&&NHX:TOL=134004],mutisia arequipensis[&&NHX:TOL=134005],mutisia lanigera[&&NHX:TOL=134006],mutisia splendens[&&NHX:TOL=134007],mutisia subspinosa[&&NHX:TOL=134008],mutisia sinuata[&&NHX:TOL=134009])section guariruma[&&NHX:TOL=133993],(mutisia oligodon[&&NHX:TOL=134011],mutisia macrophylla[&&NHX:TOL=134012],mutisia involucrata[&&NHX:TOL=134013],mutisia spinosa[&&NHX:TOL=134014],mutisia ilicifolia[&&NHX:TOL=134015],mutisia araucana[&&NHX:TOL=134016],mutisia cana[&&NHX:TOL=134017],mutisia latifolia[&&NHX:TOL=134018],mutisia brachyantha[&&NHX:TOL=134019])section ovata[&&NHX:TOL=134010])mutisia[&&NHX:TOL=120144],pachylaena[&&NHX:TOL=120145])[&&NHX:TOL=120143],lulia[&&NHX:TOL=120256],uechtritzia[&&NHX:TOL=120257],eriachaenium magellanicum[&&NHX:TOL=120258])mutisieae[&&NHX:TOL=69940])[&&NHX:TOL=120087])mutisioideae[&&NHX:TOL=22866],(((hyaloseris[&&NHX:TOL=120093],dinoseris[&&NHX:TOL=120094])[&&NHX:TOL=120092],(duidaea[&&NHX:TOL=120096],gongylolepis[&&NHX:TOL=120097])[&&NHX:TOL=120095])[&&NHX:TOL=120091],stifftia[&&NHX:TOL=120098],achnopogon[&&NHX:TOL=120272],glossarion[&&NHX:TOL=120273],eurydochus[&&NHX:TOL=120274],neblinaea[&&NHX:TOL=120275],quelchia[&&NHX:TOL=120276])stifftioideae[&&NHX:TOL=118971],(((((stenopadus[&&NHX:TOL=120102],stomatochaeta[&&NHX:TOL=120103])[&&NHX:TOL=120101],chimantaea[&&NHX:TOL=120104])[&&NHX:TOL=120100],wunderlichia[&&NHX:TOL=120105])wunderlichieae[&&NHX:TOL=120099],((ianthopappus[&&NHX:TOL=120108],hyalis[&&NHX:TOL=120109])[&&NHX:TOL=120107],(nouelia[&&NHX:TOL=120111],leucomeris[&&NHX:TOL=120112])[&&NHX:TOL=120110])hyalideae[&&NHX:TOL=120106])wunderlichioideae[&&NHX:TOL=118974],((((richterago[&&NHX:TOL=104540],cnicothamnus[&&NHX:TOL=104539])[&&NHX:TOL=120147],gochnatia[&&NHX:TOL=104538])[&&NHX:TOL=120090],cyclolepis[&&NHX:TOL=104537])gochnatioideae[&&NHX:TOL=22869],(hecastocleis shockleyi[&&NHX:TOL=22871],((((brachylaena[&&NHX:TOL=128555],tarchonanthus[&&NHX:TOL=128556])[&&NHX:TOL=128554],oldenburgia[&&NHX:TOL=128557])tarchonantheae[&&NHX:TOL=104541],(((cardopatium[&&NHX:TOL=128571],cousiniopsis[&&NHX:TOL=128572])cardopatiinae[&&NHX:TOL=128558],(acantholepis[&&NHX:TOL=128573],echinops[&&NHX:TOL=128574])echinopinae[&&NHX:TOL=128559],((atractylodes[&&NHX:TOL=128576],(atractylis[&&NHX:TOL=128578],carlina[&&NHX:TOL=128579])[&&NHX:TOL=128577])[&&NHX:TOL=128575],tugarinovia[&&NHX:TOL=128580])carlininae[&&NHX:TOL=128560],(((((((((oligochaeta[&&NHX:TOL=128587],myopordon[&&NHX:TOL=128588])[&&NHX:TOL=128586],rhaponticum[&&NHX:TOL=128589],leuzea[&&NHX:TOL=128590],acroptilon[&&NHX:TOL=128591])[&&NHX:TOL=128585],(((crocodylum[&&NHX:TOL=128595],(carduncellus[&&NHX:TOL=128597],(femeniasia[&&NHX:TOL=128599],phonus[&&NHX:TOL=128600])[&&NHX:TOL=128598])[&&NHX:TOL=128596])[&&NHX:TOL=128594],carthamus[&&NHX:TOL=128601])[&&NHX:TOL=128593],centaurea[&&NHX:TOL=128602])[&&NHX:TOL=128592],psephellus[&&NHX:TOL=128603],(plagiobasis[&&NHX:TOL=128605],(russowia[&&NHX:TOL=128607],amberboa[&&NHX:TOL=128608])[&&NHX:TOL=128606])[&&NHX:TOL=128604],(karvandarina[&&NHX:TOL=128610],callicephalus[&&NHX:TOL=128611])[&&NHX:TOL=128609],rhaponticoides[&&NHX:TOL=128612],centaurothamnus[&&NHX:TOL=128613],cheirolophus[&&NHX:TOL=128614],crupina[&&NHX:TOL=128615],(serratula[&&NHX:TOL=128617],mantisalca[&&NHX:TOL=128618])[&&NHX:TOL=128616],(nikitinia[&&NHX:TOL=128620],klasea[&&NHX:TOL=128621])[&&NHX:TOL=128619],tricholepis[&&NHX:TOL=128622],volutaria[&&NHX:TOL=128623],zoegea[&&NHX:TOL=128624])[&&NHX:TOL=128562],stilozophus[&&NHX:TOL=128625])[&&NHX:TOL=128584],schischkinia[&&NHX:TOL=128626])centaureinae[&&NHX:TOL=128583],((((carduus[&&NHX:TOL=128633],cirsium[&&NHX:TOL=128634],tyrimnus[&&NHX:TOL=128631])[&&NHX:TOL=128632],silybum[&&NHX:TOL=128635])[&&NHX:TOL=128629],notobasis[&&NHX:TOL=128636],pycnomon[&&NHX:TOL=128637])[&&NHX:TOL=128628],cynara[&&NHX:TOL=128640],galactites[&&NHX:TOL=128638],lamyropsis[&&NHX:TOL=128639],ptilostemon[&&NHX:TOL=128641])[&&NHX:TOL=128627])[&&NHX:TOL=128582],(((((jurinea[&&NHX:TOL=128647],saussurea3[&&NHX:TOL=128650])[&&NHX:TOL=128646],(dolomiaea[&&NHX:TOL=128652],saussurea2[&&NHX:TOL=128653])[&&NHX:TOL=128651])[&&NHX:TOL=128645],(saussurea1[&&NHX:TOL=128655],polytaxis[&&NHX:TOL=128656])[&&NHX:TOL=128654])[&&NHX:TOL=128644],((cousinia3[&&NHX:TOL=128659],arctium[&&NHX:TOL=128660])[&&NHX:TOL=128658],((hypacanthium[&&NHX:TOL=128663],schmalhausenia[&&NHX:TOL=128664])[&&NHX:TOL=128662],cousinia2[&&NHX:TOL=128665])[&&NHX:TOL=128661])[&&NHX:TOL=128657])[&&NHX:TOL=128643],cousinia1[&&NHX:TOL=128666])[&&NHX:TOL=128642])[&&NHX:TOL=128581],berardia[&&NHX:TOL=128676],staehelina[&&NHX:TOL=128677],(((lamyropappus[&&NHX:TOL=128670],olgaea[&&NHX:TOL=128671],syreitschikovia[&&NHX:TOL=128672],synurus[&&NHX:TOL=128673])[&&NHX:TOL=128669],alfredia[&&NHX:TOL=128674])[&&NHX:TOL=128668],onopordum[&&NHX:TOL=128675])[&&NHX:TOL=128667])[&&NHX:TOL=128685],(amphoricarpos[&&NHX:TOL=128679],(chardinia[&&NHX:TOL=128681],(xeranthemum[&&NHX:TOL=128683],siebera[&&NHX:TOL=128684])[&&NHX:TOL=128682])[&&NHX:TOL=128680])[&&NHX:TOL=128678])carduinae[&&NHX:TOL=128563])cardueae[&&NHX:TOL=104543],(dicoma[&&NHX:TOL=128564],macledium[&&NHX:TOL=128565],cloiselia[&&NHX:TOL=128566],pasaccardoa[&&NHX:TOL=128567],erythrocephalum[&&NHX:TOL=128568],pleiotaxis[&&NHX:TOL=128569],gladiopappus[&&NHX:TOL=128570])dicomeae[&&NHX:TOL=104544])[&&NHX:TOL=104542])carduoideae[&&NHX:TOL=22873],(((diaspananthus[&&NHX:TOL=120463],ainsliaea[&&NHX:TOL=120464])[&&NHX:TOL=120462],catamixis baccharoides[&&NHX:TOL=133823],macroclinidium[&&NHX:TOL=120459],myripnois[&&NHX:TOL=120461],pertya[&&NHX:TOL=120460])pertyoideae[&&NHX:TOL=22879],(gymnarrhena micrantha[&&NHX:TOL=22881],(((gundelia tournefortii[&&NHX:TOL=22885],cichorieae[&&NHX:TOL=22886])[&&NHX:TOL=22985],arctotideae[&&NHX:TOL=22887],(liabeae[&&NHX:TOL=22889],vernonieae[&&NHX:TOL=22890])[&&NHX:TOL=22888])cichorioideae[&&NHX:TOL=22883],(corymbium glabrum[&&NHX:TOL=22892],(senecionodae[&&NHX:TOL=27897],(((astereae[&&NHX:TOL=22902],anthemideae[&&NHX:TOL=22903])[&&NHX:TOL=22900],gnaphalieae[&&NHX:TOL=22901])[&&NHX:TOL=22897],calenduleae[&&NHX:TOL=22898])asterodae[&&NHX:TOL=22896],((((duhaldea[&&NHX:TOL=121195],(caesulia[&&NHX:TOL=121197],blumea[&&NHX:TOL=121198])[&&NHX:TOL=121196])[&&NHX:TOL=121194],((schizogyne[&&NHX:TOL=121201],vierea[&&NHX:TOL=121202],pulicaria1[&&NHX:TOL=121203],rhanterium[&&NHX:TOL=121204])[&&NHX:TOL=121200],(xerolekia[&&NHX:TOL=121206],buphthalmum[&&NHX:TOL=121207])[&&NHX:TOL=121205],((inula1[&&NHX:TOL=121210],pentanema[&&NHX:TOL=121211],chrysophthalmum[&&NHX:TOL=121212],amblyocarpum[&&NHX:TOL=121213])[&&NHX:TOL=121209],(carpesium[&&NHX:TOL=121215],telekia[&&NHX:TOL=121216])[&&NHX:TOL=121214],inula2[&&NHX:TOL=121217])[&&NHX:TOL=121208],((pulicaria2[&&NHX:TOL=121220],(dittrichia[&&NHX:TOL=121222],jasonia[&&NHX:TOL=121223])[&&NHX:TOL=121221])[&&NHX:TOL=121219],((pallenis[&&NHX:TOL=121226],asteriscus[&&NHX:TOL=121227],ighermia[&&NHX:TOL=121228])[&&NHX:TOL=121225],anvillea[&&NHX:TOL=121229])[&&NHX:TOL=121224])[&&NHX:TOL=121218])[&&NHX:TOL=121199])inulinae[&&NHX:TOL=121193],plucheinae[&&NHX:TOL=121230])inuleae[&&NHX:TOL=22907],(((helenieae[&&NHX:TOL=22910],(((chrysanthellum[&&NHX:TOL=104500],diodontium[&&NHX:TOL=104501],eryngiophyllum[&&NHX:TOL=104502],glossocardia[&&NHX:TOL=104503],isostigma[&&NHX:TOL=104504],trioncinia[&&NHX:TOL=104505])chrysanthellinae[&&NHX:TOL=104496],(bidens[&&NHX:TOL=104506],coreocarpus[&&NHX:TOL=104507],coreopsis[&&NHX:TOL=104508],cosmos[&&NHX:TOL=104509],cyathomone[&&NHX:TOL=104510],dahlia[&&NHX:TOL=104511],dicranocarpus[&&NHX:TOL=104512],ericentrodea[&&NHX:TOL=104513],fitchia[&&NHX:TOL=104514],goldmanella[&&NHX:TOL=104515],henricksonia[&&NHX:TOL=104516],heterosperma[&&NHX:TOL=104517],hidalgoa[&&NHX:TOL=104518],megalodonta[&&NHX:TOL=104519],moonia[&&NHX:TOL=104520],narvalina[&&NHX:TOL=104521],oparanthus[&&NHX:TOL=104522],petrobium[&&NHX:TOL=104523],selleophytum[&&NHX:TOL=104524],thelesperma[&&NHX:TOL=104525])coreopsidinae[&&NHX:TOL=104497],(koehneola[&&NHX:TOL=104526],pinillosia[&&NHX:TOL=104527],tetraperone[&&NHX:TOL=104528])pinillosiinae[&&NHX:TOL=104498],staurochlamys[&&NHX:TOL=104499])coreopsideae[&&NHX:TOL=22912],(((((achyropappus[&&NHX:TOL=104474],amauriopsis[&&NHX:TOL=104475],apostates[&&NHX:TOL=104476],bahia[&&NHX:TOL=104477],bartlettia[&&NHX:TOL=104478],chaetymenia[&&NHX:TOL=104479],chamaechaenactis[&&NHX:TOL=104480],espejoa[&&NHX:TOL=104481],florestina[&&NHX:TOL=104482],holoschkuhria[&&NHX:TOL=104483],hymenopappus[&&NHX:TOL=104484],hymenothrix[&&NHX:TOL=104485],hypericophyllum[&&NHX:TOL=104486],loxothysanus[&&NHX:TOL=104487],palafoxia[&&NHX:TOL=104488],peucephyllum[&&NHX:TOL=104489],platyschkuhria[&&NHX:TOL=104490],psathyrotopsis[&&NHX:TOL=104491],schkuhria[&&NHX:TOL=104492],thymopsis[&&NHX:TOL=104493])bahieae[&&NHX:TOL=22920],(orochaenactis[&&NHX:TOL=104566],chaenactis[&&NHX:TOL=104567],dimeresia[&&NHX:TOL=104568])chaenactideae[&&NHX:TOL=22921])[&&NHX:TOL=22918],(clappinae[&&NHX:TOL=104572],coulterellinae[&&NHX:TOL=104569],jaumeinae[&&NHX:TOL=104573],flaveriinae[&&NHX:TOL=104574],((tagetes[&&NHX:TOL=120382],hydropectis[&&NHX:TOL=120383])[&&NHX:TOL=120381],(adenophyllum[&&NHX:TOL=120386],(dysodiopsis[&&NHX:TOL=120388],(strotheria[&&NHX:TOL=120390],thymophylla[&&NHX:TOL=120391])[&&NHX:TOL=120389])[&&NHX:TOL=120387])[&&NHX:TOL=120385],((dyssodia[&&NHX:TOL=120396],gymnolaena[&&NHX:TOL=120397],boeberoides[&&NHX:TOL=120394])[&&NHX:TOL=120393],comaclinium[&&NHX:TOL=120399],schizotrichia[&&NHX:TOL=120400])[&&NHX:TOL=120392],((leucactinia[&&NHX:TOL=120404],urbinella[&&NHX:TOL=120405])[&&NHX:TOL=120403],bajacalia[&&NHX:TOL=120406])[&&NHX:TOL=120402],nicolletia[&&NHX:TOL=120408],(porophyllum[&&NHX:TOL=120410],pectis[&&NHX:TOL=120411])[&&NHX:TOL=120409],chrysactinia[&&NHX:TOL=120412],boeberastrum[&&NHX:TOL=120414],(harnackia[&&NHX:TOL=120416],lescaillea[&&NHX:TOL=120417])[&&NHX:TOL=120415])pectidinae[&&NHX:TOL=104571],varillinae[&&NHX:TOL=104570],pseudoclappia[&&NHX:TOL=104575],oxypappus[&&NHX:TOL=104576],arnicastrum[&&NHX:TOL=104577],jamesianthus[&&NHX:TOL=104578])tageteae[&&NHX:TOL=22919])[&&NHX:TOL=22916],(heptanthinae[&&NHX:TOL=104471],enydrinae[&&NHX:TOL=104472],neurolaeninae[&&NHX:TOL=104473])neurolaeneae[&&NHX:TOL=22917])[&&NHX:TOL=22914],polymnieae[&&NHX:TOL=22922],(((montanoinae[&&NHX:TOL=104445],(((((melanthera[&&NHX:TOL=104601],(((wedelia[&&NHX:TOL=104624],elaphandra[&&NHX:TOL=104587])[&&NHX:TOL=120430],(oyedaea[&&NHX:TOL=104605],steiractinia[&&NHX:TOL=104616])[&&NHX:TOL=120431])[&&NHX:TOL=120429],zexmenia[&&NHX:TOL=104626],zyzyxia[&&NHX:TOL=104627])[&&NHX:TOL=120428],(wollastonia[&&NHX:TOL=104625],lipochaeta[&&NHX:TOL=104599])[&&NHX:TOL=120432],perymenium[&&NHX:TOL=104609],lundellianthus[&&NHX:TOL=104600])[&&NHX:TOL=120425],(clibadium[&&NHX:TOL=104582],lantanopsis[&&NHX:TOL=104596],riencourtia[&&NHX:TOL=104613])[&&NHX:TOL=120434])[&&NHX:TOL=120424],wamalchitamia[&&NHX:TOL=104623],(rensonia[&&NHX:TOL=104612],perymeniopsis[&&NHX:TOL=104608])[&&NHX:TOL=120435],tilesia[&&NHX:TOL=104619],(sphagneticola[&&NHX:TOL=104615],trigonopterum[&&NHX:TOL=104620])[&&NHX:TOL=120436],eclipta[&&NHX:TOL=104586])[&&NHX:TOL=120420],((oblivia[&&NHX:TOL=104603],otopappus[&&NHX:TOL=104604],tuxtla[&&NHX:TOL=104622])[&&NHX:TOL=120438],(((lasianthaea[&&NHX:TOL=104597],synedrella[&&NHX:TOL=104617])[&&NHX:TOL=120441],damnxanthodium[&&NHX:TOL=104583])[&&NHX:TOL=120440],delilia[&&NHX:TOL=104584])[&&NHX:TOL=120439],synedrellopsis[&&NHX:TOL=104618])[&&NHX:TOL=120437])[&&NHX:TOL=120419],((monactis[&&NHX:TOL=104602],idiopappus[&&NHX:TOL=104592],kingianthus[&&NHX:TOL=104595])[&&NHX:TOL=120443],podanthus[&&NHX:TOL=104611])[&&NHX:TOL=120442],leptocarpha[&&NHX:TOL=104598],baltimora[&&NHX:TOL=104579],blainvillea[&&NHX:TOL=104580],dimerostemma[&&NHX:TOL=104585],fenixia[&&NHX:TOL=104590],iogeton[&&NHX:TOL=104593],jefea[&&NHX:TOL=104594],schizoptera[&&NHX:TOL=104614],eleutheranthera[&&NHX:TOL=104588],exomiocarpon[&&NHX:TOL=104589],calyptocarpus[&&NHX:TOL=104581],hoffmanniella[&&NHX:TOL=104591],pascalia[&&NHX:TOL=104606],pentalepis[&&NHX:TOL=104607],plagiolophus[&&NHX:TOL=104610],tuberculocarpus[&&NHX:TOL=104621])ecliptinae[&&NHX:TOL=104446])[&&NHX:TOL=104444],((((ambrosiinae1[&&NHX:TOL=104452],(((acmella[&&NHX:TOL=104668],oxycarpha[&&NHX:TOL=104669],salmea[&&NHX:TOL=104670],spilanthes[&&NHX:TOL=104671],tetranthus[&&NHX:TOL=104672])spilanthinae[&&NHX:TOL=104455],(echinacea[&&NHX:TOL=104689],heliopsis[&&NHX:TOL=104690],philactis[&&NHX:TOL=104691],sanvitalia[&&NHX:TOL=104692],tehuana[&&NHX:TOL=104693],trichocoryne[&&NHX:TOL=104694],zinnia[&&NHX:TOL=104695])zinniinae[&&NHX:TOL=104456])[&&NHX:TOL=104454],((aldama[&&NHX:TOL=104696],alvordia[&&NHX:TOL=104697],bahiopsis[&&NHX:TOL=104698],calanticaria[&&NHX:TOL=104699],helianthus[&&NHX:TOL=104700],heliomeris[&&NHX:TOL=104701],hymenostephium[&&NHX:TOL=104702],iostephane[&&NHX:TOL=104703],lagascea[&&NHX:TOL=104704],pappobolus[&&NHX:TOL=104705],phoebanthus[&&NHX:TOL=104706],rhysolepis[&&NHX:TOL=104707],sclerocarpus[&&NHX:TOL=104708],simsia[&&NHX:TOL=104709],stuessya[&&NHX:TOL=104710],syncretocarpus[&&NHX:TOL=104711],tithonia[&&NHX:TOL=104712],viguiera[&&NHX:TOL=104713])helianthinae[&&NHX:TOL=104458],((hybridella[&&NHX:TOL=104714],zaluzania[&&NHX:TOL=104715])zaluzaniinae[&&NHX:TOL=104460],(chromolepidinae[&&NHX:TOL=104462],(dugesiinae[&&NHX:TOL=104464],ambrosiinae2[&&NHX:TOL=104465])[&&NHX:TOL=104463])[&&NHX:TOL=104461])[&&NHX:TOL=104459])[&&NHX:TOL=104457])[&&NHX:TOL=104453],((((enceliopsis[&&NHX:TOL=104717],geraea[&&NHX:TOL=104719])[&&NHX:TOL=120368],encelia[&&NHX:TOL=104716])[&&NHX:TOL=120367],flourensia[&&NHX:TOL=104718])[&&NHX:TOL=120366],helianthella[&&NHX:TOL=104720])enceliinae[&&NHX:TOL=104466])[&&NHX:TOL=104451],((ratibida[&&NHX:TOL=104721],rudbeckia[&&NHX:TOL=104722])rudbeckiinae[&&NHX:TOL=104468],(((((berlandiera[&&NHX:TOL=104723],engelmannia[&&NHX:TOL=104726])[&&NHX:TOL=120372],(lindheimera[&&NHX:TOL=104727],silphium[&&NHX:TOL=104728])[&&NHX:TOL=120373])[&&NHX:TOL=120371],((wyethia[&&NHX:TOL=120376],balsamorhiza[&&NHX:TOL=120377])[&&NHX:TOL=120375],chrysogonum[&&NHX:TOL=104725])[&&NHX:TOL=120374])[&&NHX:TOL=120370],borrichia[&&NHX:TOL=104724])[&&NHX:TOL=120369],vigethia[&&NHX:TOL=104729])engelmanniinae[&&NHX:TOL=104469])[&&NHX:TOL=104467])[&&NHX:TOL=104450],(((squamopappus[&&NHX:TOL=104731],podachaenium[&&NHX:TOL=104730])[&&NHX:TOL=104735],verbesina[&&NHX:TOL=104733])[&&NHX:TOL=104734],tetrachyron[&&NHX:TOL=104732])verbesininae[&&NHX:TOL=104470])[&&NHX:TOL=104449],rojasianthinae[&&NHX:TOL=104448])[&&NHX:TOL=104447])heliantheae[&&NHX:TOL=22924],((desmanthodiinae[&&NHX:TOL=105487],(bebbia[&&NHX:TOL=105489],cymophora[&&NHX:TOL=105490],dyscritothamnus[&&NHX:TOL=105491],tetragonotheca[&&NHX:TOL=105492],tridax[&&NHX:TOL=105493])dyscritothamninae[&&NHX:TOL=105488],(carramboa[&&NHX:TOL=105500],espeletia[&&NHX:TOL=105501],tamananthus[&&NHX:TOL=105502])espeletiinae[&&NHX:TOL=105494],(alepidocline[&&NHX:TOL=105503],alloispermum[&&NHX:TOL=105504],aphanactis[&&NHX:TOL=105505],faxonia[&&NHX:TOL=105506],galinsoga[&&NHX:TOL=105507],oteiza[&&NHX:TOL=105508],sabazia[&&NHX:TOL=105509],schistocarpha[&&NHX:TOL=105510],selloa[&&NHX:TOL=105511])galinsoginae[&&NHX:TOL=105495],guardiolinae[&&NHX:TOL=105496],jaegeriinae[&&NHX:TOL=105497],(acanthospermum[&&NHX:TOL=105512],lecocarpus[&&NHX:TOL=105513],melampodium[&&NHX:TOL=105514])melampodiinae[&&NHX:TOL=105498],(axiniphyllum[&&NHX:TOL=105515],guizotia[&&NHX:TOL=105516],ichthyothere[&&NHX:TOL=105517],micractis[&&NHX:TOL=105518],milleria[&&NHX:TOL=105519],rumfordia[&&NHX:TOL=105520],sigesbeckia[&&NHX:TOL=105521],smallanthus[&&NHX:TOL=105522],stachycephalum[&&NHX:TOL=105523],trigonospermum[&&NHX:TOL=105524],unxia[&&NHX:TOL=105525])milleriinae[&&NHX:TOL=105499])millerieae[&&NHX:TOL=22926],(madieae[&&NHX:TOL=22928],(((galeana[&&NHX:TOL=105527],villanova[&&NHX:TOL=105528])galeaninae[&&NHX:TOL=105526],lycapsinae[&&NHX:TOL=105529],(amauria[&&NHX:TOL=105531],eutetras[&&NHX:TOL=105532],pericome[&&NHX:TOL=105533],perityle[&&NHX:TOL=105534])peritylinae[&&NHX:TOL=105530])perityleae[&&NHX:TOL=22930],(hofmeisteriinae[&&NHX:TOL=105535],oxylobinae[&&NHX:TOL=105536],mikaniinae[&&NHX:TOL=105537],trichocoroninae[&&NHX:TOL=105538],adenostemmatinae[&&NHX:TOL=105539],fleischmanniinae[&&NHX:TOL=105540],ageratinae[&&NHX:TOL=105541],eupatoriinae[&&NHX:TOL=105542],liatrinae[&&NHX:TOL=105543],praxelinae[&&NHX:TOL=105544],gyptidinae[&&NHX:TOL=105545],disynaphiinae[&&NHX:TOL=105546],ayapaninae[&&NHX:TOL=105547],alomiinae[&&NHX:TOL=105548],critoniinae[&&NHX:TOL=105549],hebecliinae[&&NHX:TOL=105550],neomirandeinae[&&NHX:TOL=105551])eupatorieae[&&NHX:TOL=22931])[&&NHX:TOL=22929])[&&NHX:TOL=22927])[&&NHX:TOL=22925])[&&NHX:TOL=22923])[&&NHX:TOL=22913])phytomelanin cypsela clade[&&NHX:TOL=22911])[&&NHX:TOL=22909],feddeeae[&&NHX:TOL=118976])[&&NHX:TOL=118975],(athroisminae[&&NHX:TOL=105552],anisopappinae[&&NHX:TOL=105553],centipedinae[&&NHX:TOL=105554])athroismeae[&&NHX:TOL=22908])[&&NHX:TOL=22905])helianthodae[&&NHX:TOL=22899])asteroideae[&&NHX:TOL=27898])[&&NHX:TOL=22891])[&&NHX:TOL=22882])[&&NHX:TOL=22880])[&&NHX:TOL=22878])[&&NHX:TOL=22872])[&&NHX:TOL=22870])[&&NHX:TOL=118973])[&&NHX:TOL=118972])[&&NHX:TOL=22865])asteraceae[&&NHX:TOL=20780],calyceraceae[&&NHX:TOL=20781],goodeniaceae[&&NHX:TOL=20782])[&&NHX:TOL=20779])[&&NHX:TOL=20777])asterales[&&NHX:TOL=20736],((mackinlayaceae[&&NHX:TOL=27177],apiaceae[&&NHX:TOL=20746],araliaceae[&&NHX:TOL=20747],pittosporaceae[&&NHX:TOL=20748],myodocarpaceae[&&NHX:TOL=27178])[&&NHX:TOL=20745],(griselinia littoralis[&&NHX:TOL=20754],griselinia lucida[&&NHX:TOL=20755],griselinia jodinifolia[&&NHX:TOL=20756],griselinia scandens[&&NHX:TOL=20757],griselinia carlomunozii[&&NHX:TOL=20758],griselinia racemosa[&&NHX:TOL=20759],griselinia ruscifolia[&&NHX:TOL=20760])griselinia[&&NHX:TOL=20749],torricellia[&&NHX:TOL=20750],melanophylla[&&NHX:TOL=20751],aralidium pinnatifidum[&&NHX:TOL=20752],pennantia[&&NHX:TOL=27176])apiales[&&NHX:TOL=20741],(((((adoxa moschatellina[&&NHX:TOL=23604],tetradoxa omeiensis[&&NHX:TOL=23605])[&&NHX:TOL=23603],sinadoxa corydalifolia[&&NHX:TOL=23606])[&&NHX:TOL=23608],sambucus[&&NHX:TOL=23607])[&&NHX:TOL=23601],viburnum[&&NHX:TOL=23602])adoxaceae[&&NHX:TOL=20799],((weigela[&&NHX:TOL=23581],diervilla[&&NHX:TOL=23582])diervilleae[&&NHX:TOL=20794],(((triosteum[&&NHX:TOL=23609],lonicera[&&NHX:TOL=23610],leycestaria[&&NHX:TOL=23611],symphoricarpos[&&NHX:TOL=23612])[&&NHX:TOL=23618],heptacodium[&&NHX:TOL=23617])caprifolieae[&&NHX:TOL=20793],((linnaea borealis[&&NHX:TOL=23613],(dipelta[&&NHX:TOL=23619],diplodipelta[&&NHX:EXT=Y:TOL=23620])[&&NHX:TOL=23614],kolkwitzia[&&NHX:TOL=23615],abelia[&&NHX:TOL=23616])linnaeeae[&&NHX:TOL=20795],((acanthocalyx[&&NHX:TOL=23583],(morina[&&NHX:TOL=23585],cryprtothladia[&&NHX:TOL=23586])[&&NHX:TOL=23584])morinaceae[&&NHX:TOL=20796],((dipsacaceae[&&NHX:TOL=23590],triplostegia glandulifera[&&NHX:TOL=23591])[&&NHX:TOL=20798],(patrinia[&&NHX:TOL=23588],(nardostachys[&&NHX:TOL=23589],((valerianella[&&NHX:TOL=23598],fedia[&&NHX:TOL=23599])[&&NHX:TOL=23597],(centranthus[&&NHX:TOL=23595],valeriana[&&NHX:TOL=23593],plectritis[&&NHX:TOL=23596])[&&NHX:TOL=23600])[&&NHX:TOL=23594])[&&NHX:TOL=23587])valerianaceae[&&NHX:TOL=20797])[&&NHX:TOL=23592])valerina[&&NHX:TOL=23578])linnina[&&NHX:TOL=23579])[&&NHX:TOL=23580])caprifoliaceae[&&NHX:TOL=20792])dipsacales[&&NHX:TOL=20743],quintinia[&&NHX:TOL=27168],bruniaceae[&&NHX:TOL=20742],columellia[&&NHX:TOL=20733],tribeles australis[&&NHX:TOL=20740],eremosyne pectinata[&&NHX:TOL=20738],escalloniaceae[&&NHX:TOL=20739],sphenostemon[&&NHX:TOL=50853],paracryphia alticola[&&NHX:TOL=50854],polyosmaceae[&&NHX:TOL=50855],desfontainia spinosa[&&NHX:TOL=50856])[&&NHX:TOL=27166],((aquifoliaceae[&&NHX:TOL=20762],helwingia[&&NHX:TOL=20764],phyllonoma[&&NHX:TOL=20765])[&&NHX:TOL=27175],(stemonuraceae[&&NHX:TOL=27173],cardiopteridaceae[&&NHX:TOL=20730])[&&NHX:TOL=27174])aquifoliales[&&NHX:TOL=20735])euasterids ii campanulids[&&NHX:TOL=20734])euasterids[&&NHX:TOL=20721])asterids[&&NHX:TOL=20704])[&&NHX:TOL=20696])core eudicots[&&NHX:TOL=20714])[&&NHX:TOL=27068])[&&NHX:TOL=20707])[&&NHX:TOL=20705],cytinaceae[&&NHX:TOL=20715],balanophoraceae[&&NHX:TOL=20716],cynomorium[&&NHX:TOL=20717])eudicots[&&NHX:TOL=20666])[&&NHX:TOL=20649],(austrobaileya[&&NHX:TOL=20677],(trimenia[&&NHX:TOL=20679],(illicium[&&NHX:TOL=20681],(kadsura[&&NHX:TOL=20683],schisandra[&&NHX:TOL=20684])schisandraceae[&&NHX:TOL=20682])[&&NHX:TOL=20680])[&&NHX:TOL=20678])austrobaileyales[&&NHX:TOL=20650])[&&NHX:TOL=50857],((nuphar[&&NHX:TOL=21525],(barclaya[&&NHX:TOL=21527],(ondinea purpurea[&&NHX:TOL=21529],(nymphaea[&&NHX:TOL=21531],(euryale ferox[&&NHX:TOL=21533],victoria[&&NHX:TOL=21534])[&&NHX:TOL=21532])[&&NHX:TOL=21530])[&&NHX:TOL=21528])[&&NHX:TOL=21526])[&&NHX:TOL=21524],(cabomba[&&NHX:TOL=21522],brasenia[&&NHX:TOL=21523])[&&NHX:TOL=21521])nymphaeaceae[&&NHX:TOL=20651])[&&NHX:TOL=20648])angiosperms[&&NHX:TOL=20646])[&&NHX:TOL=20642])[&&NHX:TOL=20630])[&&NHX:TOL=20628])[&&NHX:TOL=20626])spermatopsida[&&NHX:TOL=20622])[&&NHX:TOL=20618])[&&NHX:TOL=20616])[&&NHX:TOL=20611])[&&NHX:TOL=20608])[&&NHX:TOL=20606])[&&NHX:TOL=20604])[&&NHX:TOL=20602])[&&NHX:TOL=20600])[&&NHX:TOL=20598])[&&NHX:TOL=20596])embryophytes[&&NHX:TOL=20582])[&&NHX:TOL=20579])[&&NHX:TOL=20577])[&&NHX:TOL=20575])streptophyta[&&NHX:TOL=20573])green plants[&&NHX:TOL=2382],(cyanidium[&&NHX:TOL=21777],porphyridiales[&&NHX:TOL=21778],compsopogonales[&&NHX:TOL=21779],bangiales[&&NHX:TOL=21780],(ahnfeltiales[&&NHX:TOL=21737],hildenbrandiales[&&NHX:TOL=21738],((corallinales[&&NHX:TOL=21741],rhodogorgonales[&&NHX:TOL=21742])[&&NHX:TOL=21740],(acrochaetiales[&&NHX:TOL=21744],batrachospermales[&&NHX:TOL=21745],nemaliales[&&NHX:TOL=21746],palmariales[&&NHX:TOL=21747])[&&NHX:TOL=21743])[&&NHX:TOL=21739],(bonnemaisoniales[&&NHX:TOL=21749],(ceramiaceae[&&NHX:TOL=23527],(dasyaceae[&&NHX:TOL=23529],delesseriaceae[&&NHX:TOL=23530],(bostrychioideae[&&NHX:TOL=57080],rhodomeloideae[&&NHX:TOL=57081],polysiphonioideae[&&NHX:TOL=57082])rhodomelaceae[&&NHX:TOL=23531])[&&NHX:TOL=23528])ceramiales[&&NHX:TOL=21750],((((((european clade[&&NHX:TOL=21763],indopacificcaribbean clade[&&NHX:TOL=21764])[&&NHX:TOL=21762],suhria clade[&&NHX:TOL=21765])[&&NHX:TOL=21761],gelidium pusillum[&&NHX:TOL=21766])[&&NHX:TOL=21760],gelidium coulteri clade[&&NHX:TOL=21767],indopacific ii clade[&&NHX:TOL=21768])[&&NHX:TOL=21759],porphyroglossum[&&NHX:TOL=21769],capreolia clade[&&NHX:TOL=21770],ptilophora clade[&&NHX:TOL=21771])gelidium[&&NHX:TOL=21758],(pterocladiella[&&NHX:TOL=21773],pterocladia[&&NHX:TOL=21774])[&&NHX:TOL=21772],(parviphycus[&&NHX:TOL=56974],gelidiella[&&NHX:TOL=56975])[&&NHX:TOL=21775])gelidiales[&&NHX:TOL=21751],gigartinales[&&NHX:TOL=21752],gracilariales[&&NHX:TOL=21753],halymeniales[&&NHX:TOL=21754],plocamiales[&&NHX:TOL=21755],rhodymeniales[&&NHX:TOL=21756])[&&NHX:TOL=21748])florideophyceae[&&NHX:TOL=21781])rhodophyta[&&NHX:TOL=2381])[&&NHX:TOL=124795],glaucophytes[&&NHX:TOL=2407])archaeplastida plantae[&&NHX:TOL=121168],((((((((((arkarua[&&NHX:EXT=Y:TOL=19227],helicoplacus[&&NHX:EXT=Y:TOL=19228],edrioasteroidea[&&NHX:EXT=Y:TOL=19229],((((fourcirclet crinoids[&&NHX:TOL=19244],(((cladida[&&NHX:EXT=Y:TOL=19248],articulata[&&NHX:TOL=19249])[&&NHX:TOL=19247],flexibilia[&&NHX:EXT=Y:TOL=19250])[&&NHX:TOL=19246],camerata[&&NHX:EXT=Y:TOL=19251])[&&NHX:TOL=19245])[&&NHX:TOL=19243],disparida[&&NHX:EXT=Y:TOL=19252])crinoidea[&&NHX:TOL=19232],blastoidea[&&NHX:EXT=Y:TOL=19233])pelmatozoa[&&NHX:TOL=19231],(((ophiuroidea[&&NHX:TOL=19236],(paleozoic asteroids[&&NHX:EXT=Y:TOL=24774],(calliasterellidae[&&NHX:EXT=Y:TOL=24775],(compasteridae[&&NHX:EXT=Y:TOL=24776],(trichasteropsida[&&NHX:EXT=Y:TOL=24777],((brisingida[&&NHX:TOL=24779],forcipulatida[&&NHX:TOL=24778])forcipulatacea[&&NHX:TOL=24786],((spinulosida[&&NHX:TOL=24784],velatida[&&NHX:TOL=24783])spinulosacea[&&NHX:TOL=24792],((notomyotida[&&NHX:TOL=24781],valvatida[&&NHX:TOL=24780])[&&NHX:TOL=24790],paxillosida[&&NHX:TOL=24782])valvatacea[&&NHX:TOL=24791])[&&NHX:TOL=24788])[&&NHX:TOL=24789])[&&NHX:TOL=24787])[&&NHX:TOL=24793])ambuloasteroidea[&&NHX:TOL=24785],concentricycloidea[&&NHX:TOL=24794])asteroidea[&&NHX:TOL=19238])[&&NHX:TOL=27777],(chinianasteridae[&&NHX:EXT=Y:TOL=24267],(villebrunasteridae[&&NHX:EXT=Y:TOL=24268],archegonasteridae[&&NHX:EXT=Y:TOL=24269])[&&NHX:EXT=Y:TOL=24273],archophiactinidae[&&NHX:EXT=Y:TOL=24270],helianthasteridae[&&NHX:EXT=Y:TOL=24271])somasteroidea[&&NHX:EXT=Y:TOL=24272])asterozoa[&&NHX:TOL=19235],(((apodida[&&NHX:TOL=19254],(elasipodida[&&NHX:TOL=19256],(aspidochirotida[&&NHX:TOL=19258],(molpadiida[&&NHX:TOL=19260],(dendrochirotida[&&NHX:TOL=19262],dactylochirotida[&&NHX:TOL=19263])[&&NHX:TOL=19261])[&&NHX:TOL=19259])[&&NHX:TOL=19257])[&&NHX:TOL=19255])[&&NHX:TOL=19253],eupyrgidae[&&NHX:TOL=19264],gephyrothuriidae[&&NHX:TOL=19265])holothuroidea[&&NHX:TOL=19240],echinoidea[&&NHX:TOL=19241])echinozoa[&&NHX:TOL=19239])eleutherozoa[&&NHX:TOL=19234])[&&NHX:TOL=19230])echinodermata[&&NHX:TOL=2497],(planctosphaeridae[&&NHX:TOL=19337],((cephalodiscidae[&&NHX:TOL=19340],rhabdopleuridae[&&NHX:TOL=19341],atubaridae[&&NHX:TOL=19342])pterobranchia[&&NHX:TOL=19339],(ptychoderidae[&&NHX:TOL=19344],harrimaniidae[&&NHX:TOL=19345],spengelidae[&&NHX:TOL=19346],saxipendiidae[&&NHX:TOL=19347])enteropneusta[&&NHX:TOL=19343])[&&NHX:TOL=19338])hemichordata[&&NHX:TOL=2498])[&&NHX:TOL=2496],(calcichordata[&&NHX:EXT=Y:TOL=14819],((octacnemidae[&&NHX:TOL=114489],((ascidiidae[&&NHX:TOL=114496],corellidae[&&NHX:TOL=114497],agnesiidae[&&NHX:TOL=114499],perophoridae[&&NHX:TOL=114500])phlebobranchiata[&&NHX:TOL=114490],(doliolidae[&&NHX:TOL=114503],salpidae[&&NHX:TOL=114504],pyrosomatidae[&&NHX:TOL=114505])thaliacea[&&NHX:TOL=114501])[&&NHX:TOL=114517],cionidae[&&NHX:TOL=114494],diazonidae[&&NHX:TOL=114492],(styelidae[&&NHX:TOL=114508],pyuridae[&&NHX:TOL=114509],molgulidae[&&NHX:TOL=114510])stolidobranchiata[&&NHX:TOL=114507],sorberacea[&&NHX:TOL=114511],(clavelinidae[&&NHX:TOL=114513],didemnidae[&&NHX:TOL=114514],polyclinidae[&&NHX:TOL=114515])aplousobranchiata[&&NHX:TOL=114512],appendicularia[&&NHX:TOL=114516])urochordata[&&NHX:TOL=14821],((cephalochordata[&&NHX:TOL=14824],yunnanozoon[&&NHX:EXT=Y:TOL=14825])[&&NHX:TOL=14823],((gilpichthys[&&NHX:EXT=Y:TOL=15928],(myxinikela[&&NHX:EXT=Y:TOL=15930],(eptatretus[&&NHX:TOL=15932],paramyxine[&&NHX:TOL=15933],(myxine[&&NHX:TOL=15935],neomyxine[&&NHX:TOL=15936])myxinidae[&&NHX:TOL=15934])node 2[&&NHX:TOL=15931])node 1[&&NHX:TOL=15929])hyperotreti[&&NHX:TOL=14828],(((((((lampetra[&&NHX:TOL=15913],lethenteron[&&NHX:TOL=15914])[&&NHX:TOL=15912],entosphenus[&&NHX:TOL=15915])[&&NHX:TOL=15911],tetrapleurodon[&&NHX:TOL=15916],eudontomyzon[&&NHX:TOL=15917],ichthyomyzon[&&NHX:TOL=15918],petromyzon[&&NHX:TOL=15919],caspiomyzon[&&NHX:TOL=15920],(geotria[&&NHX:TOL=15922],mordacia[&&NHX:TOL=15923])[&&NHX:TOL=15921])node 3[&&NHX:TOL=15910],pipiscius[&&NHX:EXT=Y:TOL=15924])node 2[&&NHX:TOL=15909],mayomyzon[&&NHX:EXT=Y:TOL=15925])node 1[&&NHX:TOL=15908],hardistiella[&&NHX:EXT=Y:TOL=15926])hyperoartia[&&NHX:TOL=14831],euconodonta[&&NHX:EXT=Y:TOL=14832],((((((((((((psammosteidae[&&NHX:EXT=Y:TOL=16927],protaspididae[&&NHX:EXT=Y:TOL=16928])[&&NHX:TOL=16926],pteraspididae[&&NHX:EXT=Y:TOL=16929])[&&NHX:TOL=16925],protopteraspididae[&&NHX:EXT=Y:TOL=16930])[&&NHX:TOL=16924],anchipteraspididae[&&NHX:EXT=Y:TOL=16931])heterostraci node 2[&&NHX:TOL=16923],(cyathaspidida[&&NHX:EXT=Y:TOL=16933],amphiaspidida[&&NHX:EXT=Y:TOL=16934])heterostraci node1[&&NHX:TOL=16932])[&&NHX:TOL=16922],tolypelepidida[&&NHX:EXT=Y:TOL=16935])[&&NHX:TOL=16921],traquairaspidiformes[&&NHX:EXT=Y:TOL=16936])[&&NHX:TOL=16920],lepidaspis[&&NHX:EXT=Y:TOL=16937])heterostraci[&&NHX:EXT=Y:TOL=16904],(eriptychius americanus[&&NHX:EXT=Y:TOL=16917],eriptychius orvigi[&&NHX:EXT=Y:TOL=16918])eriptychiida[&&NHX:EXT=Y:TOL=16905])pteraspidomorphi node 2[&&NHX:TOL=16903],(astraspis desiderata[&&NHX:EXT=Y:TOL=16914],astraspis splendens[&&NHX:EXT=Y:TOL=16915])astraspida[&&NHX:EXT=Y:TOL=16906])pteraspidomorphi node 1[&&NHX:TOL=16902],(arandaspis[&&NHX:EXT=Y:TOL=16909],porophoraspis[&&NHX:EXT=Y:TOL=16910],sacabambaspis[&&NHX:EXT=Y:TOL=16911],andinaspis[&&NHX:EXT=Y:TOL=16912])arandaspida[&&NHX:EXT=Y:TOL=16907])pteraspidomorphi[&&NHX:EXT=Y:TOL=14834],thelodonti[&&NHX:EXT=Y:TOL=14835],(((((lasanius[&&NHX:EXT=Y:TOL=15370],birkenia[&&NHX:EXT=Y:TOL=15371])anaspida node 3[&&NHX:TOL=15369],rhyncholepis[&&NHX:EXT=Y:TOL=15372])anaspida node 2[&&NHX:TOL=15368],pterygolepis[&&NHX:EXT=Y:TOL=15373])anaspida node 1[&&NHX:TOL=15367],pharyngolepis[&&NHX:EXT=Y:TOL=15374])anaspida[&&NHX:EXT=Y:TOL=14837],(((((huananaspidiformes[&&NHX:EXT=Y:TOL=15902],polybranchiaspidiformes[&&NHX:EXT=Y:TOL=15903])galeaspida node 3[&&NHX:TOL=15901],eugaleaspidiformes[&&NHX:EXT=Y:TOL=15904])galeaspida node 2[&&NHX:TOL=15900],xiushuiaspis[&&NHX:EXT=Y:TOL=15905])galeaspida node 1[&&NHX:TOL=15899],hanyangaspis[&&NHX:EXT=Y:TOL=15906])galeaspida[&&NHX:EXT=Y:TOL=14839],((pituriaspis[&&NHX:EXT=Y:TOL=16899],neeyambaspis[&&NHX:EXT=Y:TOL=16900])pituriaspida[&&NHX:EXT=Y:TOL=14841],(((((((thyestiida[&&NHX:EXT=Y:TOL=16890],kiaeraspidida[&&NHX:EXT=Y:TOL=16891])node 5[&&NHX:TOL=16889],benneviaspidida[&&NHX:EXT=Y:TOL=16892])node 4[&&NHX:TOL=16888],zenaspidida[&&NHX:EXT=Y:TOL=16893])node 3[&&NHX:TOL=16887],cephalaspidida[&&NHX:EXT=Y:TOL=16894])cornuata[&&NHX:TOL=16886],hemicyclaspis[&&NHX:EXT=Y:TOL=16895])node 2[&&NHX:TOL=16885],hirella[&&NHX:EXT=Y:TOL=16896])node 1[&&NHX:TOL=16884],ateleaspis[&&NHX:EXT=Y:TOL=16897])osteostraci[&&NHX:EXT=Y:TOL=14842],(((((onychodontiformes[&&NHX:EXT=Y:TOL=14942],coelacanthimorpha[&&NHX:TOL=14943],(porolepimorpha[&&NHX:EXT=Y:TOL=14946],dipnoi[&&NHX:TOL=14947])[&&NHX:TOL=14945],(rhizodontimorpha[&&NHX:EXT=Y:TOL=14949],(osteolepimorpha[&&NHX:EXT=Y:TOL=14951],(((((((((((((((((((eothyrididae[&&NHX:EXT=Y:TOL=14955],caseidae[&&NHX:EXT=Y:TOL=14956])caseasauria[&&NHX:TOL=14954],(varanopseidae[&&NHX:EXT=Y:TOL=14958],(ophiacodontidae[&&NHX:EXT=Y:TOL=14960],(edaphosauridae[&&NHX:EXT=Y:TOL=14962],(haptodus garnettensis[&&NHX:EXT=Y:TOL=14964],(palaeohatteria[&&NHX:EXT=Y:TOL=14966],(pantelosaurus[&&NHX:EXT=Y:TOL=14968],(cutleria[&&NHX:EXT=Y:TOL=14970],(sphenacodontidae[&&NHX:EXT=Y:TOL=14972],(biarmosuchia[&&NHX:EXT=Y:TOL=15022],eotitanosuchia[&&NHX:EXT=Y:TOL=15023],dinocephalia[&&NHX:EXT=Y:TOL=15024],anomodontia[&&NHX:EXT=Y:TOL=15025],(gorgonopsia[&&NHX:EXT=Y:TOL=15027],(therocephalia[&&NHX:EXT=Y:TOL=15029],(diviniidae[&&NHX:EXT=Y:TOL=15031],(triconodonts[&&NHX:EXT=Y:TOL=15989],(((tachyglossus aculeatus[&&NHX:TOL=16251],zaglossus bruijni[&&NHX:TOL=16252],zaglossus bartoni[&&NHX:TOL=117704],zaglossus attenboroughi[&&NHX:TOL=117705])tachyglossidae[&&NHX:TOL=16250],ornithorhynchus anatinus[&&NHX:TOL=16253])monotremata[&&NHX:TOL=15991],multituberculata[&&NHX:EXT=Y:TOL=15992],((didelphimorphia[&&NHX:TOL=16242],paucituberculata[&&NHX:TOL=16243],microbiotheria[&&NHX:TOL=16244],dasyuromorphia[&&NHX:TOL=16245],peramelemorphia[&&NHX:TOL=16246],notoryctemorphia[&&NHX:TOL=16247],diprotodontia[&&NHX:TOL=16248])marsupialia[&&NHX:TOL=15994],(palaeoryctoids[&&NHX:EXT=Y:TOL=15996],(((cingulata[&&NHX:TOL=16153],((megalonychidae[&&NHX:TOL=16156],bradypodidae[&&NHX:TOL=16157])folivora[&&NHX:TOL=16155],vermilingua[&&NHX:TOL=16158])pilosa[&&NHX:TOL=16154])edentata[&&NHX:TOL=15953],(epoicotheriidae[&&NHX:EXT=Y:TOL=16270],metacheiromyidae[&&NHX:EXT=Y:TOL=16271],(eurotamandua[&&NHX:EXT=Y:TOL=16274],(eomanis[&&NHX:EXT=Y:TOL=16276],necromanis[&&NHX:EXT=Y:TOL=16277],patriomanis[&&NHX:EXT=Y:TOL=16278],manis manis crassicaudata[&&NHX:TOL=16279],manis manis pentadactyla[&&NHX:TOL=16280],manis paramanis javanica[&&NHX:TOL=16281])maninae[&&NHX:TOL=16275],((manis smutsia gigantea[&&NHX:TOL=16284],manis smutsia temminckii[&&NHX:TOL=16285])[&&NHX:TOL=16283],(manis phataginus tricuspis[&&NHX:TOL=16287],manis uromanis tetradactyla[&&NHX:TOL=16288])[&&NHX:TOL=16286])smutsiinae african pangolins[&&NHX:TOL=16282])manidae[&&NHX:TOL=16272])pholidota[&&NHX:TOL=15954])[&&NHX:TOL=15952],((((ochotonidae[&&NHX:TOL=16226],leporidae[&&NHX:TOL=16227])lagomorpha[&&NHX:TOL=15958],(((((spalacinae[&&NHX:TOL=16526],rhizomyinae[&&NHX:TOL=16527],myospalacinae[&&NHX:TOL=50658])spalacidae[&&NHX:TOL=16525],(platacanthomyinae[&&NHX:TOL=16530],(((dendromurinae[&&NHX:TOL=16531],cricetomyinae[&&NHX:TOL=16529])[&&NHX:TOL=50661],petromyscinae[&&NHX:TOL=16543],mystromyinae[&&NHX:TOL=16542])[&&NHX:TOL=50660],nesomyinae[&&NHX:TOL=16541])nesomyidae[&&NHX:TOL=50659],(((phloeomys[&&NHX:TOL=50695],batomys[&&NHX:TOL=50696],crateromys[&&NHX:TOL=50697],carpomys[&&NHX:TOL=50698])phloeomyini[&&NHX:TOL=50694],((((rattus[&&NHX:TOL=50732],berylmys[&&NHX:TOL=50733],tarsomys[&&NHX:TOL=50734],limnomys[&&NHX:TOL=50735],abditomys[&&NHX:TOL=50736],bullimus[&&NHX:TOL=50737],bandicota[&&NHX:TOL=50738],sundamys[&&NHX:TOL=50739])[&&NHX:TOL=50731],(niviventer[&&NHX:TOL=50741],(dacnomys[&&NHX:TOL=50743],leopoldamys[&&NHX:TOL=50744])[&&NHX:TOL=50742])[&&NHX:TOL=50740])[&&NHX:TOL=50730],maxomys[&&NHX:TOL=50745])rattini[&&NHX:TOL=50729],((((((tokudaia[&&NHX:TOL=50792],apodemus[&&NHX:TOL=129885])apodemini[&&NHX:TOL=50789],malacomyini[&&NHX:TOL=50788])[&&NHX:TOL=129884],((praomys[&&NHX:TOL=50701],mastomys[&&NHX:TOL=50702],zelotomys[&&NHX:TOL=50703],hylomyscus[&&NHX:TOL=50704],myomys[&&NHX:TOL=50705],stenocephalomys[&&NHX:TOL=50706],colomys[&&NHX:TOL=50707],heimyscus[&&NHX:TOL=50708])praomyini[&&NHX:TOL=50700],murini[&&NHX:TOL=129886])[&&NHX:TOL=50709])[&&NHX:TOL=129883],vandeleuria[&&NHX:TOL=129887])[&&NHX:TOL=129882],(millardini[&&NHX:TOL=50793],((lemniscomys[&&NHX:TOL=50712],arvicanthis[&&NHX:TOL=50713],rhabdomys[&&NHX:TOL=50714],aethomys[&&NHX:TOL=50715],(stochomys[&&NHX:TOL=50717],hybomys[&&NHX:TOL=50718])[&&NHX:TOL=50716],desmomys[&&NHX:TOL=50719],pelomys[&&NHX:TOL=50720],mylomys[&&NHX:TOL=50721],grammomys[&&NHX:TOL=50723],oenomys[&&NHX:TOL=50725],thallomys[&&NHX:TOL=50724])arvicanthini[&&NHX:TOL=50711],(otomys[&&NHX:TOL=50727],parotomys[&&NHX:TOL=50728])otomyini[&&NHX:TOL=50726])arvicanthine group[&&NHX:TOL=50710])[&&NHX:TOL=129888])[&&NHX:TOL=129881],((((chrotomys[&&NHX:TOL=50749],archboldomys[&&NHX:TOL=50750],rhynchomys[&&NHX:TOL=50751],celaenomys[&&NHX:TOL=50752])shrew rats[&&NHX:TOL=50748],apomys[&&NHX:TOL=50753])philippine old endemics ii[&&NHX:TOL=50747],(hyomys[&&NHX:TOL=50755],anisomys[&&NHX:TOL=50756],(chiruromys[&&NHX:TOL=50758],pogonomys[&&NHX:TOL=50759])[&&NHX:TOL=50757],coccymys[&&NHX:TOL=50760],macruromys[&&NHX:TOL=50761],mallomys[&&NHX:TOL=50762])new guinea group[&&NHX:TOL=50754],((leporillus[&&NHX:TOL=50765],conilurus[&&NHX:TOL=50766],mesembriomys[&&NHX:TOL=50767])[&&NHX:TOL=50764],(mastacomys[&&NHX:TOL=50769],pseudomys[&&NHX:TOL=50770],notomys[&&NHX:TOL=50771])[&&NHX:TOL=50768],zyzomys[&&NHX:TOL=50772],uromys[&&NHX:TOL=50773],leggadina[&&NHX:TOL=50774],(hydromys[&&NHX:TOL=50776],parahydromys[&&NHX:TOL=50777])[&&NHX:TOL=50775],(neohydromys[&&NHX:TOL=50779],mayermys[&&NHX:TOL=50780],pseudohydromys[&&NHX:TOL=50781])[&&NHX:TOL=50778],xeromys[&&NHX:TOL=50782],crossomys[&&NHX:TOL=50783],leptomys[&&NHX:TOL=50784],(solomys[&&NHX:TOL=50786],melomys[&&NHX:TOL=50787])[&&NHX:TOL=50785])[&&NHX:TOL=50763])hydromyini[&&NHX:TOL=50746],chiropodomys[&&NHX:TOL=129890])[&&NHX:TOL=129889])[&&NHX:TOL=129880])[&&NHX:TOL=129879])murinae[&&NHX:TOL=16536],(gerbillinae[&&NHX:TOL=16539],(acomys[&&NHX:TOL=50795],deomys[&&NHX:TOL=50796],lophuromys[&&NHX:TOL=50797],uranomys[&&NHX:TOL=50798])deomyinae[&&NHX:TOL=16538])[&&NHX:TOL=50662],lophiomyinae[&&NHX:TOL=16532])muridae[&&NHX:TOL=16533],calomyscinae[&&NHX:TOL=16540],(cricetinae[&&NHX:TOL=16546],arvicolinae[&&NHX:TOL=16547],(neotominae[&&NHX:TOL=16550],(((sigmodon alstoni[&&NHX:TOL=16594],(sigmodon toltecus[&&NHX:TOL=65507],sigmodon peruanus[&&NHX:TOL=16605],(sigmodon mascotensis[&&NHX:TOL=65508],sigmodon hispidus[&&NHX:TOL=65509],sigmodon arizonae[&&NHX:TOL=16599])[&&NHX:TOL=16603],sigmodon inopinatus[&&NHX:TOL=16601],sigmodon ochrognathus[&&NHX:TOL=16604],(sigmodon alleni[&&NHX:TOL=16598],sigmodon hirsutus[&&NHX:TOL=65510])[&&NHX:TOL=16600],(sigmodon leucotis[&&NHX:TOL=16602],sigmodon fulviventer[&&NHX:TOL=16596])[&&NHX:TOL=65511])[&&NHX:TOL=16597])sigmodon[&&NHX:TOL=16582],(neusticomys mussoi[&&NHX:TOL=16499],neusticomys venezuelae[&&NHX:TOL=16500],(neusticomys peruviensis[&&NHX:TOL=16502],neusticomys oyapocki[&&NHX:TOL=16503],(neusticomys monticolus[&&NHX:TOL=16505],(chibchanomys trichotis[&&NHX:TOL=16507],(anotomys leander[&&NHX:TOL=16509],(((ichthyomys tweedii[&&NHX:TOL=16513],ichthyomys hydrobates[&&NHX:TOL=16514])[&&NHX:TOL=16512],ichthyomys stolzmanni[&&NHX:TOL=16515],ichthyomys pitteri[&&NHX:TOL=16516])ichthyomys[&&NHX:TOL=16511],((rheomys hartmani[&&NHX:TOL=16519],rheomys thomasi[&&NHX:TOL=16520])[&&NHX:TOL=16518],(rheomys underwoodi[&&NHX:TOL=16522],rheomys mexicanus[&&NHX:TOL=16523])[&&NHX:TOL=16521])rheomys[&&NHX:TOL=16517])[&&NHX:TOL=16510])[&&NHX:TOL=16508])[&&NHX:TOL=16506])[&&NHX:TOL=16504])[&&NHX:TOL=16501])ichthyomyini[&&NHX:TOL=16583])[&&NHX:TOL=50664],((abrawayaomys[&&NHX:TOL=16607],aepeomys[&&NHX:TOL=16608],chilomys[&&NHX:TOL=16609],phaenomys[&&NHX:TOL=16611],rhagomys[&&NHX:TOL=16612],(rhipidomys[&&NHX:TOL=16613],thomasomys[&&NHX:TOL=50677])[&&NHX:TOL=16614],wilfredomys[&&NHX:TOL=16615])thomasomyine group and sigmodontinae incertae sedis[&&NHX:TOL=16585],(wiedomys[&&NHX:TOL=16622],cholomys[&&NHX:EXT=Y:TOL=16623])wiedomyini[&&NHX:TOL=16586],(scolomys[&&NHX:TOL=16555],(megalomys[&&NHX:TOL=16566],oryzomys[&&NHX:TOL=16572],oecomys[&&NHX:TOL=16573],megaoryzomys[&&NHX:EXT=Y:TOL=16575],(((neacomys[&&NHX:TOL=16559],microryzomys[&&NHX:TOL=16558])[&&NHX:TOL=50668],oligoryzomys[&&NHX:TOL=16574])[&&NHX:TOL=50667],((holochilus[&&NHX:TOL=16563],pseudoryzomys[&&NHX:TOL=16565])[&&NHX:TOL=50669],lundomys[&&NHX:TOL=16564])[&&NHX:TOL=16562],((nectomys[&&NHX:TOL=16569],amphinectomys[&&NHX:TOL=16570])[&&NHX:TOL=16568],nesoryzomys[&&NHX:TOL=16571],(sigmodontomys[&&NHX:TOL=16576],melanomys[&&NHX:TOL=16567])[&&NHX:TOL=50671])[&&NHX:TOL=50670])[&&NHX:TOL=50666])[&&NHX:TOL=16560],zygodontomys[&&NHX:TOL=50672])oryzomyini[&&NHX:TOL=16587],((((((calomys venustus[&&NHX:TOL=16636],calomys bolivae[&&NHX:TOL=16637],calomys callosus[&&NHX:TOL=16638],calomys tener[&&NHX:TOL=16639],calomys callidus[&&NHX:TOL=16640])[&&NHX:TOL=16635],calomys hummelincki[&&NHX:TOL=16641])[&&NHX:TOL=16634],calomys musculinus[&&NHX:TOL=16642],calomys laucha[&&NHX:TOL=16643])[&&NHX:TOL=16633],calomys lepidus[&&NHX:TOL=16644])[&&NHX:TOL=16632],calomys sorellus[&&NHX:TOL=16645])calomys[&&NHX:TOL=16675],((eligmodontia morgani[&&NHX:TOL=16649],eligmodontia typus[&&NHX:TOL=16650],eligmodontia moreni[&&NHX:TOL=16651],eligmodontia puerulus[&&NHX:TOL=16652])eligmodontia[&&NHX:TOL=16677],((graomys griseoflavus[&&NHX:TOL=16665],graomys dorae[&&NHX:EXT=Y:TOL=16666],graomys domorum[&&NHX:TOL=16667],graomys edithae[&&NHX:TOL=16668])graomys[&&NHX:TOL=16680],((phyllotis wolffsohni[&&NHX:TOL=16706],(((((((phyllotis xanthopygus[&&NHX:TOL=16717],phyllotis limatus[&&NHX:TOL=16718],phyllotis bonaeriensis[&&NHX:TOL=16724])[&&NHX:TOL=16716],(phyllotis darwini[&&NHX:TOL=16720],phyllotis magister[&&NHX:TOL=16721])[&&NHX:TOL=16719])[&&NHX:TOL=16715],phyllotis osgoodi[&&NHX:TOL=16722])[&&NHX:TOL=16714],phyllotis caprinus[&&NHX:TOL=16723])phyllotis darwini species group[&&NHX:TOL=16713],phyllotis definitus[&&NHX:TOL=16725])[&&NHX:TOL=16712],((phyllotis amicus[&&NHX:TOL=16710],phyllotis gerbillus[&&NHX:TOL=16708])[&&NHX:TOL=50689],phyllotis andium[&&NHX:TOL=16711])[&&NHX:TOL=16709])[&&NHX:TOL=50688],(phyllotis haggardi[&&NHX:TOL=16727],phyllotis osilae[&&NHX:TOL=16728])[&&NHX:TOL=16726])[&&NHX:TOL=50687])phyllotis[&&NHX:TOL=16683],(((auliscomys boliviensis[&&NHX:TOL=16627],(auliscomys sublimis[&&NHX:TOL=16629],auliscomys pictus[&&NHX:TOL=16630])[&&NHX:TOL=16628])auliscomys[&&NHX:TOL=16685],galenomys garleppi[&&NHX:TOL=16686])auliscomys group[&&NHX:TOL=16684],(loxodontomys micropus[&&NHX:TOL=16672],loxodontomys formosus[&&NHX:EXT=Y:TOL=16673])loxodontomys[&&NHX:TOL=16692])[&&NHX:TOL=50673],chinchillula sahamae[&&NHX:TOL=16687])[&&NHX:TOL=16682],salinomys[&&NHX:TOL=16681],tapecomys[&&NHX:TOL=50674])[&&NHX:TOL=16678],(andalgalomys pearsoni[&&NHX:TOL=16662],andalgalomys olrogi[&&NHX:TOL=16664],andalgalomys roigi[&&NHX:TOL=16663])andalgalomys[&&NHX:TOL=50675])[&&NHX:TOL=16676],ichthyurodon[&&NHX:EXT=Y:TOL=16694],olympicomys[&&NHX:EXT=Y:TOL=16693])phyllotini[&&NHX:TOL=16592],andinomys edax[&&NHX:TOL=16690],punomys[&&NHX:TOL=16591],((reithrodon typicus[&&NHX:TOL=16704],reithrodon auritus[&&NHX:TOL=16703])reithrodon[&&NHX:TOL=16700],panchomys[&&NHX:EXT=Y:TOL=16698])[&&NHX:TOL=50676],irenomys tarsalis[&&NHX:TOL=16689],(euneomys chinchilloides[&&NHX:TOL=16654],euneomys petersoni[&&NHX:TOL=16655],euneomys mordax[&&NHX:TOL=16656])euneomys[&&NHX:TOL=16699],neotomys[&&NHX:TOL=16701],((abrothrix[&&NHX:TOL=16490],chroeomys[&&NHX:TOL=16491])[&&NHX:TOL=16489],(chelemys[&&NHX:TOL=16494],pearsonomys[&&NHX:TOL=16496],geoxus[&&NHX:TOL=16497],notiomys[&&NHX:TOL=16495])[&&NHX:TOL=16492])abrothicine group[&&NHX:TOL=16488],((((akodon sensu stricto[&&NHX:TOL=16479],necromys[&&NHX:TOL=16480])[&&NHX:TOL=16478],thalpomys[&&NHX:TOL=16481])[&&NHX:TOL=16477],lenoxus[&&NHX:TOL=16483])[&&NHX:TOL=16475],dankomys[&&NHX:EXT=Y:TOL=16484],blarinomys[&&NHX:TOL=16485],podoxomys[&&NHX:TOL=16486],juscelinomys[&&NHX:TOL=16487],oxymycterus[&&NHX:TOL=16482],bibimys[&&NHX:TOL=16579],(scapteromys[&&NHX:TOL=16578],kunsia[&&NHX:TOL=16590])[&&NHX:TOL=50678])akodontini[&&NHX:TOL=16589],delomys[&&NHX:TOL=16610],juliomys[&&NHX:TOL=50679])oryzomyalia[&&NHX:TOL=16584])sigmodontinae[&&NHX:TOL=16548],(nyctomys[&&NHX:TOL=16617],otonyctomys[&&NHX:TOL=16618],tylomys[&&NHX:TOL=16619],ototylomys[&&NHX:TOL=16620])tylomyinae[&&NHX:TOL=16551])[&&NHX:TOL=50663])cricetidae[&&NHX:TOL=16545])eumuroida[&&NHX:TOL=16528])muroidea[&&NHX:TOL=16461],dipodoidea[&&NHX:TOL=16463])suborder myodonta[&&NHX:TOL=50665],(pedetoidae[&&NHX:TOL=16465],anomaluroidae[&&NHX:TOL=16464])suborder anomaluromorpha[&&NHX:TOL=65349],(geomyoidea[&&NHX:TOL=16462],castoridae[&&NHX:TOL=16457])suborder castorimorpha[&&NHX:TOL=65350])[&&NHX:TOL=16453],theridomorpha[&&NHX:EXT=Y:TOL=16458],((aplodontiidae[&&NHX:TOL=16455],((((callosciurus[&&NHX:TOL=16733],dremomys[&&NHX:TOL=16734],exilisciurus[&&NHX:TOL=16735],glyphotes[&&NHX:TOL=16736],hyosciurus[&&NHX:TOL=16737],lariscus[&&NHX:TOL=16738],menetes[&&NHX:TOL=16739],nannosciurus[&&NHX:TOL=16740],prosciurillus[&&NHX:TOL=16741],rubrisciurus[&&NHX:TOL=16742],tamiops[&&NHX:TOL=16743],sundasciurus[&&NHX:TOL=16744])callosciurini[&&NHX:TOL=16809],funambulini[&&NHX:TOL=16810])callosciurinae[&&NHX:TOL=50690],((((spermophilus[&&NHX:TOL=16777],cynomys[&&NHX:TOL=16775],(((((marmota himalyana[&&NHX:TOL=16755],marmota sibirica[&&NHX:TOL=16756])[&&NHX:TOL=16754],marmota camtschatica[&&NHX:TOL=16757])[&&NHX:TOL=16753],(marmota bobak[&&NHX:TOL=16759],marmota baibacina[&&NHX:TOL=16760])[&&NHX:TOL=16758])[&&NHX:TOL=16752],marmota broweri[&&NHX:TOL=16761],(marmota caudata[&&NHX:TOL=16763],marmota menzbieri[&&NHX:TOL=16764])[&&NHX:TOL=16762],marmota marmota[&&NHX:TOL=16765],marmota monax[&&NHX:TOL=16766])[&&NHX:TOL=16751],(marmota flaviventris[&&NHX:TOL=16768],(marmota caligata[&&NHX:TOL=16770],marmota vancouverensis[&&NHX:TOL=16771])[&&NHX:TOL=16769],marmota olympus[&&NHX:TOL=16772])[&&NHX:TOL=16767])marmota[&&NHX:TOL=16776],ammospermophilus[&&NHX:TOL=16774])[&&NHX:TOL=50693],tamias[&&NHX:TOL=16778],sciurotamias[&&NHX:TOL=16779])marmotini[&&NHX:TOL=16811],((epixerus[&&NHX:TOL=16799],heliosciurus[&&NHX:TOL=16800],protoxerus[&&NHX:TOL=16801])protoxerina[&&NHX:TOL=16813],(funisciurus[&&NHX:TOL=16746],myosciurus[&&NHX:TOL=16748],paraxerus[&&NHX:TOL=16749])funisciurina[&&NHX:TOL=50692])protoxerini[&&NHX:TOL=50691])[&&NHX:TOL=50681],(atlantoxerus getulus[&&NHX:TOL=16819],spermophilopsis leptodactylus[&&NHX:TOL=16820],xerus[&&NHX:TOL=16821])xerini[&&NHX:TOL=16817])xerinae[&&NHX:TOL=50680],(((rheithrosciurus[&&NHX:TOL=16803],(sciurus[&&NHX:TOL=16805],(microsciurus[&&NHX:TOL=16781],syntheosciurus[&&NHX:TOL=16782])microsciurini[&&NHX:TOL=16812])[&&NHX:TOL=50685])sciurini[&&NHX:TOL=16815],tamiasciurini[&&NHX:TOL=16816])[&&NHX:TOL=50684],(aeretes[&&NHX:TOL=16784],aeromys[&&NHX:TOL=16785],belomys[&&NHX:TOL=16786],biswamoyopterus[&&NHX:TOL=16787],eupetaurus[&&NHX:TOL=16788],glaucomys[&&NHX:TOL=16789],hylopetes[&&NHX:TOL=16790],iomys[&&NHX:TOL=16791],petaurillus[&&NHX:TOL=16792],petaurista[&&NHX:TOL=16793],petinomys[&&NHX:TOL=16794],pteromys[&&NHX:TOL=16795],pteromyscus[&&NHX:TOL=16796],trogopterus[&&NHX:TOL=16797])pteromyini[&&NHX:TOL=16807])sciurinae[&&NHX:TOL=50683])[&&NHX:TOL=16808],ratufinae[&&NHX:TOL=16814],sciurillinae[&&NHX:TOL=50686])sciuridae[&&NHX:TOL=16456])[&&NHX:TOL=16454],gliridae[&&NHX:TOL=16467])sciuromorpha[&&NHX:TOL=65351],(ctenodactylidae[&&NHX:TOL=16466],(franimorpha[&&NHX:EXT=Y:TOL=16469],bathyergomorpha[&&NHX:TOL=16470],hystricomorpha[&&NHX:TOL=16471],phiomorpha[&&NHX:TOL=16472],caviomorpha[&&NHX:TOL=16473])infraorder hystricognathi[&&NHX:TOL=16468])suborder hystricomorpha[&&NHX:TOL=65352])rodentia[&&NHX:TOL=15959])glires[&&NHX:TOL=15957],(((elephantulus brachyrhynchus[&&NHX:TOL=30129],elephantulus edwardii[&&NHX:TOL=30117],elephantulus fuscipes[&&NHX:TOL=30118],elephantulus fuscus[&&NHX:TOL=30119],elephantulus intufi[&&NHX:TOL=30120],elephantulus myurus[&&NHX:TOL=30121],elephantulus revoili[&&NHX:TOL=30122],elephantulus rufescens[&&NHX:TOL=30124],elephantulus rupestris[&&NHX:TOL=30125])[&&NHX:TOL=16235],((petrodromus tetradactylus[&&NHX:TOL=16236],elephantulus rozeti[&&NHX:TOL=30123])[&&NHX:TOL=30132],macroscelides proboscideus[&&NHX:TOL=16234])[&&NHX:TOL=30131])[&&NHX:TOL=30130],(rhynchocyon chrysopygus[&&NHX:TOL=30126],rhynchocyon cirnei[&&NHX:TOL=30127],rhynchocyon petersi[&&NHX:TOL=30128])rhynchocyon[&&NHX:TOL=16239],metoldobotes[&&NHX:EXT=Y:TOL=16229],herodotius[&&NHX:EXT=Y:TOL=16230],hiwegicyon[&&NHX:EXT=Y:TOL=16231],pronasilio[&&NHX:EXT=Y:TOL=16232],palaeothentoides[&&NHX:EXT=Y:TOL=16233],myohyrax[&&NHX:EXT=Y:TOL=16237],protypotheroides[&&NHX:EXT=Y:TOL=16238],mylomygale[&&NHX:EXT=Y:TOL=16240])macroscelididae[&&NHX:TOL=15960])[&&NHX:TOL=15956],((((((((((((callithrix[&&NHX:TOL=16308],cebuella[&&NHX:TOL=16309])[&&NHX:TOL=16307],leontopithecus[&&NHX:TOL=16310])[&&NHX:TOL=16306],saguinus[&&NHX:TOL=16311])[&&NHX:TOL=16305],callimico[&&NHX:TOL=16312])[&&NHX:TOL=16304],(cebus[&&NHX:TOL=16314],saimiri[&&NHX:TOL=16315])[&&NHX:TOL=16313])[&&NHX:TOL=16303],(aotus[&&NHX:TOL=16317],callicebus[&&NHX:TOL=16318])[&&NHX:TOL=16316])[&&NHX:TOL=16302],((pithecia[&&NHX:TOL=16321],(cacajao[&&NHX:TOL=16323],chiropotes[&&NHX:TOL=16324])[&&NHX:TOL=16322])[&&NHX:TOL=16320],(alouatta[&&NHX:TOL=16326],((ateles[&&NHX:TOL=16329],lagothrix[&&NHX:TOL=16330])[&&NHX:TOL=16328],brachyteles[&&NHX:TOL=16331])[&&NHX:TOL=16327])[&&NHX:TOL=16325])[&&NHX:TOL=16319])platyrrhini[&&NHX:TOL=16292],((((macaca[&&NHX:TOL=16383],((cercocebus[&&NHX:TOL=16386],mandrillus[&&NHX:TOL=16387])[&&NHX:TOL=16385],(papio[&&NHX:TOL=16389],theropithecus[&&NHX:TOL=16390])[&&NHX:TOL=16388])[&&NHX:TOL=16384])[&&NHX:TOL=16382],(((cercopithecus[&&NHX:TOL=16394],erythrocebus[&&NHX:TOL=16395])[&&NHX:TOL=16393],miopithecus[&&NHX:TOL=16396])[&&NHX:TOL=16392],allenopithecus[&&NHX:TOL=16397])[&&NHX:TOL=16391])[&&NHX:TOL=16381],((collobus[&&NHX:TOL=16400],procolobus[&&NHX:TOL=16401])[&&NHX:TOL=16399],(pygathrix[&&NHX:TOL=16403],((simias[&&NHX:TOL=16406],nasalis[&&NHX:TOL=16407])[&&NHX:TOL=16405],presbytis[&&NHX:TOL=16408])[&&NHX:TOL=16404])[&&NHX:TOL=16402])[&&NHX:TOL=16398])cercopithecidae[&&NHX:TOL=16297],(((pongo abelii[&&NHX:TOL=65353],pongo pygmaeus[&&NHX:TOL=65354])pongo[&&NHX:TOL=16410],(((pan paniscus[&&NHX:TOL=26564],pan troglodytes[&&NHX:TOL=26565])pan[&&NHX:TOL=16413],(ardipithecus[&&NHX:EXT=Y:TOL=16415],(australopithecus[&&NHX:EXT=Y:TOL=16417],(homo sapiens[&&NHX:TOL=16421],homo erectus[&&NHX:EXT=Y:TOL=16422],homo ergaster[&&NHX:EXT=Y:TOL=16423],homo rudolfensis[&&NHX:EXT=Y:TOL=16424],homo habilis[&&NHX:EXT=Y:TOL=16425])homo[&&NHX:TOL=16418])[&&NHX:TOL=16416])[&&NHX:TOL=16414])[&&NHX:TOL=16412],(gorilla beringei[&&NHX:TOL=65355],gorilla gorilla[&&NHX:TOL=65356])gorilla[&&NHX:TOL=16419])[&&NHX:TOL=16411])hominidae[&&NHX:TOL=16299],((((((hylobates agilis[&&NHX:TOL=16433],hylobates lar[&&NHX:TOL=16434],hylobates muelleri[&&NHX:TOL=16435])[&&NHX:TOL=16432],hylobates moloch[&&NHX:TOL=16436])[&&NHX:TOL=16431],hylobates pileatus[&&NHX:TOL=16437])[&&NHX:TOL=16430],hylobates klossii[&&NHX:TOL=16438])hylobates[&&NHX:TOL=16429],bunopithecus hoolock[&&NHX:TOL=16439])[&&NHX:TOL=16428],symphalangus syndactylus[&&NHX:TOL=16440],(nomascus gabriellae[&&NHX:TOL=112090],nomascus hainanus[&&NHX:TOL=112091],nomascus leucogenys[&&NHX:TOL=112092],nomascus siki[&&NHX:TOL=112093],nomascus concolor[&&NHX:TOL=16441])nomascus[&&NHX:TOL=112088])hylobatidae[&&NHX:TOL=16300])[&&NHX:TOL=16298])catarrhini[&&NHX:TOL=16293])[&&NHX:TOL=16291],(((tarsius bancanus[&&NHX:TOL=16375],tarsius syrichta[&&NHX:TOL=16376])[&&NHX:TOL=16374],(tarsius pumilus[&&NHX:TOL=16378],tarsius tarsier[&&NHX:TOL=16379],tarsius dianae[&&NHX:TOL=108146],tarsius sangirensis[&&NHX:TOL=108147],tarsius pelengensis[&&NHX:TOL=108148],tarsius lariang[&&NHX:TOL=108149])sulawesi tarsiers[&&NHX:TOL=16377],tarsius eocaenus[&&NHX:EXT=Y:TOL=108150],afrotarsius chatrathi[&&NHX:EXT=Y:TOL=108151],tarsius thailandicus[&&NHX:EXT=Y:TOL=108152])[&&NHX:TOL=108145],xanthrorhysis tabrumi[&&NHX:EXT=Y:TOL=108153])tarsius[&&NHX:TOL=16294])[&&NHX:TOL=16290],((((((lemur catta[&&NHX:TOL=16338],(hapalemur aureus[&&NHX:TOL=23779],hapalemur griseus[&&NHX:TOL=23780],hapalemur simus[&&NHX:TOL=23781])gentle lemurs[&&NHX:TOL=16339])[&&NHX:TOL=16337],(eulemur coronatus[&&NHX:TOL=23783],eulemur macaco[&&NHX:TOL=23784],eulemur mongoz[&&NHX:TOL=23785],eulemur rubriventer[&&NHX:TOL=23786],eulemur fulvus[&&NHX:TOL=16340])[&&NHX:TOL=23788],varecia variegata[&&NHX:TOL=16341],pachylemur insignis[&&NHX:EXT=Y:TOL=30116])lemuridae[&&NHX:TOL=16335],(((avahi laniger[&&NHX:TOL=16347],(propithecus diadema[&&NHX:TOL=23800],propithecus tattersalli[&&NHX:TOL=23801],propithecus verreauxi[&&NHX:TOL=23802])sifakas[&&NHX:TOL=16349],indri indri indri[&&NHX:TOL=16350])indridae[&&NHX:TOL=16346],(archaeoindris fontoynonti[&&NHX:EXT=Y:TOL=23806],(palaeopropithecus ingens[&&NHX:EXT=Y:TOL=23807],palaeopropithecus maximus[&&NHX:EXT=Y:TOL=23811])[&&NHX:TOL=23812],babakotia radofilai[&&NHX:EXT=Y:TOL=23808],(mesopropithecus globiceps[&&NHX:EXT=Y:TOL=23809],mesopropithecus pithecoides[&&NHX:EXT=Y:TOL=23810],mesopropithecus dolichobrachion[&&NHX:EXT=Y:TOL=23813])[&&NHX:EXT=Y:TOL=23805])palaeopropithecidae[&&NHX:EXT=Y:TOL=23803])[&&NHX:TOL=23804],(hadropithecus stenognathus[&&NHX:EXT=Y:TOL=23834],archaeolemur edwardsi[&&NHX:EXT=Y:TOL=23833],archaeolemur majori[&&NHX:EXT=Y:TOL=23835])archaeolemuridae[&&NHX:EXT=Y:TOL=23832])[&&NHX:TOL=23836])[&&NHX:TOL=16334],((((microcebus murinus[&&NHX:TOL=23777],microcebus rufus[&&NHX:TOL=23778])mouse lemurs[&&NHX:TOL=16354],mirza coquereli[&&NHX:TOL=16355])[&&NHX:TOL=16353],(cheirogaleus major[&&NHX:TOL=23775],cheirogaleus medius[&&NHX:TOL=23776])dwarf lemurs[&&NHX:TOL=16356])[&&NHX:TOL=16352],(allocebus trichotis[&&NHX:TOL=16358],phaner furcifer[&&NHX:TOL=16359])[&&NHX:TOL=16357])cheirogaleidae[&&NHX:TOL=16351],(lepilemur dorsalis[&&NHX:TOL=23793],lepilemur ruficaudatus[&&NHX:TOL=23794],lepilemur edwardsi[&&NHX:TOL=23795],lepilemur leucopus[&&NHX:TOL=23796],lepilemur mustelinus[&&NHX:TOL=23797],lepilemur microdon[&&NHX:TOL=23798],lepilemur septentrionalis[&&NHX:TOL=23799])lepilemur[&&NHX:TOL=16343],(megaladapis grandidieri[&&NHX:EXT=Y:TOL=23792],megaladapis edwardsi[&&NHX:EXT=Y:TOL=23791],megaladapis madagascariensis[&&NHX:EXT=Y:TOL=23790])koala lemurs[&&NHX:EXT=Y:TOL=23789])[&&NHX:TOL=16333],(daubentonia madagascariensis[&&NHX:TOL=16345],daubentonia robusta[&&NHX:EXT=Y:TOL=23829])[&&NHX:TOL=23830])lemuriformes[&&NHX:TOL=23814],karanisia clarki[&&NHX:EXT=Y:TOL=52136],((galago demidoff[&&NHX:TOL=23825],galago zanzibaricus[&&NHX:TOL=23826],galago moholi[&&NHX:TOL=23823],galago alleni[&&NHX:TOL=23831],galago senegalensis[&&NHX:TOL=23824],(otolemur crassicaudatus[&&NHX:TOL=23827],otolemur garnettii[&&NHX:TOL=23828])greater bush babies[&&NHX:TOL=16364],(euoticus elegantulus[&&NHX:TOL=23818],euoticus inustus[&&NHX:TOL=23819])needleclawed bush babies[&&NHX:TOL=16365])galagidae[&&NHX:TOL=16361],saharagalago misrensis[&&NHX:EXT=Y:TOL=52137],wadilemur elegans[&&NHX:EXT=Y:TOL=52138],komba robustus[&&NHX:EXT=Y:TOL=52139],(loris tardigradus[&&NHX:TOL=16369],arctocebus calabarensis[&&NHX:TOL=23815],(nycticebus coucang[&&NHX:TOL=23816],nycticebus pygmaeus[&&NHX:TOL=23817])slow lorises[&&NHX:TOL=16371],nycticeboides simpsoni[&&NHX:EXT=Y:TOL=52140],perodicticus potto[&&NHX:TOL=16372])lorisidae[&&NHX:TOL=16366])lorisiformes[&&NHX:TOL=16360])strepsirrhini[&&NHX:TOL=16295])primates[&&NHX:TOL=15963],(((urogale everetti[&&NHX:TOL=16828],anathana ellioti[&&NHX:TOL=16826],(tupaia belangeri[&&NHX:TOL=50801],tupaia chrysogaster[&&NHX:TOL=50802],tupaia dorsalis[&&NHX:TOL=50803],tupaia glis[&&NHX:TOL=50804],tupaia gracilis[&&NHX:TOL=50805],tupaia javanica[&&NHX:TOL=50806],tupaia longipes[&&NHX:TOL=50807],tupaia minor[&&NHX:TOL=50808],tupaia moellendorffi[&&NHX:TOL=50818],tupaia montana[&&NHX:TOL=50809],tupaia nicobarica[&&NHX:TOL=50810],tupaia palawanensis[&&NHX:TOL=50811],tupaia picta[&&NHX:TOL=50812],tupaia splendidula[&&NHX:TOL=50813],tupaia tana[&&NHX:TOL=50814],tupaia miocenica[&&NHX:EXT=Y:TOL=50819],palaeotupaia sivalicus[&&NHX:EXT=Y:TOL=50820])tupaia[&&NHX:TOL=16825])[&&NHX:TOL=50800],eodendrogale parvum[&&NHX:EXT=Y:TOL=16823],(dendrogale melanura[&&NHX:TOL=50815],dendrogale murina[&&NHX:TOL=50816])dendrogale[&&NHX:TOL=16827])[&&NHX:TOL=50799],ptilocercus lowii[&&NHX:TOL=16829],prodendrogale yunnanica[&&NHX:EXT=Y:TOL=16824])scandentia[&&NHX:TOL=15964])[&&NHX:TOL=15962],((megachiroptera[&&NHX:TOL=16076],(icaronycteris[&&NHX:EXT=Y:TOL=16078],(archaeonycteris[&&NHX:EXT=Y:TOL=16080],(hassianycteris[&&NHX:EXT=Y:TOL=16082],(palaeochiropteryx[&&NHX:EXT=Y:TOL=16084],(emballonuroidea[&&NHX:TOL=16087],(((rhinopomatidae[&&NHX:TOL=16128],craseonycteridae[&&NHX:TOL=16129])rhinopomatoidea[&&NHX:TOL=16090],(nycteridae[&&NHX:TOL=16123],(megadermatidae[&&NHX:TOL=16125],(rhinolophinae[&&NHX:TOL=16120],hipposiderinae[&&NHX:TOL=16121])rhinolophidae[&&NHX:TOL=16126])[&&NHX:TOL=16124])rhinolophoidea[&&NHX:TOL=16091])[&&NHX:TOL=16089],((((mormoopidae[&&NHX:TOL=16115],noctilionidae[&&NHX:TOL=16116])[&&NHX:TOL=16114],phyllostomidae[&&NHX:TOL=16117])[&&NHX:TOL=16113],mystacinidae[&&NHX:TOL=16118])noctilionoidea[&&NHX:TOL=16093],((myzopodidae[&&NHX:TOL=16106],(thyropteridae[&&NHX:TOL=16108],(furipteridae[&&NHX:TOL=16110],natalidae[&&NHX:TOL=16111])[&&NHX:TOL=16109])[&&NHX:TOL=16107])nataloidea[&&NHX:TOL=16095],(((tomopeatinae[&&NHX:TOL=16100],molossinae[&&NHX:TOL=16101])molossidae[&&NHX:TOL=16103],antrozoidae[&&NHX:TOL=16104])molossoidea[&&NHX:TOL=16097],(vespertilioninae[&&NHX:TOL=16131],(miniopterinae[&&NHX:TOL=16133],(myotinae[&&NHX:TOL=16135],(muriniae[&&NHX:TOL=16137],kerivoulinae[&&NHX:TOL=16138])[&&NHX:TOL=16136])[&&NHX:TOL=16134])[&&NHX:TOL=16132])vespertilionidae[&&NHX:TOL=16140])[&&NHX:TOL=16096])[&&NHX:TOL=16094])[&&NHX:TOL=16092])[&&NHX:TOL=16088])microchiroptera[&&NHX:TOL=16085])[&&NHX:TOL=16083])[&&NHX:TOL=16081])[&&NHX:TOL=16079])[&&NHX:TOL=16077])chiroptera[&&NHX:TOL=15966],(paromomyidae[&&NHX:EXT=Y:TOL=16142],(plagiomenidae[&&NHX:EXT=Y:TOL=16144],(mixodectidae[&&NHX:EXT=Y:TOL=16146],(dermotherium[&&NHX:EXT=Y:TOL=16148],(cynocephalus variegatus[&&NHX:TOL=16150],cynocephalus volans[&&NHX:TOL=16151])[&&NHX:TOL=16149])galeopithecidae[&&NHX:TOL=16147])[&&NHX:TOL=16145])[&&NHX:TOL=16143])dermoptera[&&NHX:TOL=15967])[&&NHX:TOL=15965])[&&NHX:TOL=15961],(erinaceidae[&&NHX:TOL=16211],solenodontidae[&&NHX:TOL=16220],soricidae[&&NHX:TOL=16223],(((micropotamogale lamottei[&&NHX:TOL=60274],micropotamogale ruwenzorii[&&NHX:TOL=60275])micropotamogale[&&NHX:TOL=60272],potamogale velox[&&NHX:TOL=60278])potamogalinae[&&NHX:TOL=60271],((hemicentetes semispinosus[&&NHX:TOL=60281],tenrec ecaudatus[&&NHX:TOL=60287],(echinops telfairi[&&NHX:TOL=60290],setifer setosus[&&NHX:TOL=60284])[&&NHX:TOL=60303])tenrecinae spiny tenrecs [&&NHX:TOL=60279],(((oryzorictes hova[&&NHX:TOL=60268],oryzorictes talpoides[&&NHX:TOL=60269],oryzorictes tetradactylus[&&NHX:TOL=60270])oryzorictes[&&NHX:TOL=60266],((microgale brevicaudata[&&NHX:TOL=60253],microgale cowani[&&NHX:TOL=60255],microgale dobsoni[&&NHX:TOL=60256],microgale drouhardi[&&NHX:TOL=60309],microgale dryas[&&NHX:TOL=60257],microgale fotsifotsy[&&NHX:TOL=60310],microgale gracilis[&&NHX:TOL=60258],microgale gymnorhyncha[&&NHX:TOL=60311],microgale longicaudata[&&NHX:TOL=60259],microgale monticola[&&NHX:TOL=60312],microgale nasoloi[&&NHX:TOL=60313],microgale parvula[&&NHX:TOL=60260],microgale principula[&&NHX:TOL=60261],microgale pulla[&&NHX:TOL=60262],microgale pusilla[&&NHX:TOL=60263],microgale soricoides[&&NHX:TOL=60314],microgale taiva[&&NHX:TOL=60315],microgale talazaci[&&NHX:TOL=60264],microgale thomasi[&&NHX:TOL=60265])microgale[&&NHX:TOL=60252],limnogale mergulus[&&NHX:TOL=60251])[&&NHX:TOL=69962])oryzorictinae[&&NHX:TOL=60248],(geogale aurita[&&NHX:TOL=60247],parageogale[&&NHX:EXT=Y:TOL=60304])geogalinae[&&NHX:TOL=60308],erythrozootes[&&NHX:EXT=Y:TOL=60306],protenrec[&&NHX:EXT=Y:TOL=60307])soft tenrecs[&&NHX:TOL=60302])malagasy tenrecs[&&NHX:TOL=60301])tenrecidae[&&NHX:TOL=16224],talpidae[&&NHX:TOL=16213],(calcochloris obtusirostris[&&NHX:TOL=16178],eremitalpa granti[&&NHX:TOL=16179],(cryptochloris wintoni[&&NHX:TOL=16181],cryptochloris zyli[&&NHX:TOL=16182])[&&NHX:TOL=16180],((amblysomus julianae[&&NHX:TOL=16185],amblysomus gunningi[&&NHX:TOL=16186])amblysomus neamblysomus[&&NHX:TOL=16184],(amblysomus iris[&&NHX:TOL=16188],amblysomus septentrionalis[&&NHX:TOL=16189],amblysomus hottentotus[&&NHX:TOL=16190])amblysomus amblysomus[&&NHX:TOL=16187])south african golden moles[&&NHX:TOL=16183],(chlorotalpa tytonis[&&NHX:TOL=16192],chlorotalpa leucorhina[&&NHX:TOL=16193],chlorotalpa sclateri[&&NHX:TOL=16194],chlorotalpa duthieae[&&NHX:TOL=16195],chlorotalpa arendsi[&&NHX:TOL=16196])african golden moles[&&NHX:TOL=16191],(chrysospalax trevelyani[&&NHX:TOL=16198],chrysospalax villosus[&&NHX:TOL=16199])large golden moles[&&NHX:TOL=16197],(chrysochloris visagei[&&NHX:TOL=16201],chrysochloris stuhlmanni[&&NHX:TOL=16202],chrysochloris asiatica[&&NHX:TOL=16203])cape golden moles[&&NHX:TOL=16200])chrysochloridae[&&NHX:TOL=16206],adapisoriculidae[&&NHX:EXT=Y:TOL=16205],sespedectidae[&&NHX:EXT=Y:TOL=16207],amphilemuridae[&&NHX:EXT=Y:TOL=16208],adapisoricidae[&&NHX:EXT=Y:TOL=16209],creotarsidae[&&NHX:EXT=Y:TOL=16210],proscalopidae[&&NHX:EXT=Y:TOL=16212],dimylidae[&&NHX:EXT=Y:TOL=16214],otlestidae[&&NHX:EXT=Y:TOL=16215],geolabididae[&&NHX:EXT=Y:TOL=16216],nesophontidae[&&NHX:EXT=Y:TOL=16217],micropternodontidae[&&NHX:EXT=Y:TOL=16218],apternodontidae[&&NHX:EXT=Y:TOL=16219],plesiosoricidae[&&NHX:EXT=Y:TOL=16221],nyctitheriidae[&&NHX:EXT=Y:TOL=16222])insectivora[&&NHX:TOL=15968],(creodonta[&&NHX:EXT=Y:TOL=15970],((viverravidae[&&NHX:EXT=Y:TOL=16004],nimravidae[&&NHX:EXT=Y:TOL=16005],((acinonyx jubatus[&&NHX:TOL=123524],caracal caracal[&&NHX:TOL=123525],(catopuma badia[&&NHX:TOL=123527],catopuma temminckii[&&NHX:TOL=123528])catopuma[&&NHX:TOL=123526],(felis bieti[&&NHX:TOL=123530],felis catus[&&NHX:TOL=123531],felis chaus[&&NHX:TOL=123532],felis manul[&&NHX:TOL=123533],felis margarita[&&NHX:TOL=123534],felis nigripes[&&NHX:TOL=123535],felis silvestris[&&NHX:TOL=123536])felis[&&NHX:TOL=123529],(leopardus braccatus[&&NHX:TOL=123538],leopardus colocolo[&&NHX:TOL=123539],leopardus geoffroyi[&&NHX:TOL=123540],leopardus guigna[&&NHX:TOL=123541],leopardus jacobitus[&&NHX:TOL=123542],leopardus pajeros[&&NHX:TOL=123543],leopardus pardalis[&&NHX:TOL=123544],leopardus tigrinus[&&NHX:TOL=123545],leopardus wiedii[&&NHX:TOL=123546])leopardus[&&NHX:TOL=123537],leptailurus serval[&&NHX:TOL=123547],(lynx canadensis[&&NHX:TOL=123549],lynx lynx[&&NHX:TOL=123550],lynx pardinus[&&NHX:TOL=123551],lynx rufus[&&NHX:TOL=123552])lynx[&&NHX:TOL=123548],pardofelis marmorata[&&NHX:TOL=123553],(prionailurus bengalensis[&&NHX:TOL=123555],prionailurus iriomotensis[&&NHX:TOL=123556],prionailurus planiceps[&&NHX:TOL=123557],prionailurus rubiginosus[&&NHX:TOL=123558],prionailurus viverrinus[&&NHX:TOL=123559])prionailurus[&&NHX:TOL=123554],profelis aurata[&&NHX:TOL=123560],(puma yagouaroundi[&&NHX:TOL=123563],puma concolor[&&NHX:TOL=123562])puma[&&NHX:TOL=123561])felinae[&&NHX:TOL=123610],((panthera leo[&&NHX:TOL=123566],panthera onca[&&NHX:TOL=123567],panthera pardus[&&NHX:TOL=123568],panthera tigris[&&NHX:TOL=123569])panthera[&&NHX:TOL=123565],neofelis nebulosa[&&NHX:TOL=123564],uncia uncia[&&NHX:TOL=123570])pantherinae[&&NHX:TOL=123611])felidae[&&NHX:TOL=16006],viverridae[&&NHX:TOL=16007],herpestidae[&&NHX:TOL=16008],hyaenidae[&&NHX:TOL=16009],nandinia binotata[&&NHX:TOL=16010],eupleridae[&&NHX:TOL=123669])feliformia[&&NHX:TOL=16003],(miacidae[&&NHX:EXT=Y:TOL=16012],canidae[&&NHX:TOL=16013],ailurus fulgens[&&NHX:TOL=123869],amphicyonidae[&&NHX:EXT=Y:TOL=16014],(ursus americanus[&&NHX:TOL=123665],ursus arctos[&&NHX:TOL=123666],ursus maritimus[&&NHX:TOL=123667],ursus thibetanus[&&NHX:TOL=123668],ailuropoda melanoleuca[&&NHX:TOL=123660],helarctos malayanus[&&NHX:TOL=123661],melursus ursinus[&&NHX:TOL=123662],tremarctos ornatus[&&NHX:TOL=123663])ursidae[&&NHX:TOL=16015],hemicyonidae[&&NHX:EXT=Y:TOL=16016],mephitidae[&&NHX:TOL=123833],mustelidae[&&NHX:TOL=16017],procyonidae[&&NHX:TOL=16018],((cystophora cristata[&&NHX:TOL=123791],erignathus barbatus[&&NHX:TOL=123792],halichoerus grypus[&&NHX:TOL=123793],histriophoca fasciata[&&NHX:TOL=123794],hydrurga leptonyx[&&NHX:TOL=123795],leptonychotes weddellii[&&NHX:TOL=123796],lobodon carcinophaga[&&NHX:TOL=123797],(mirounga angustirostris[&&NHX:TOL=123799],mirounga leonina[&&NHX:TOL=123800])mirounga[&&NHX:TOL=123798],(monachus monachus[&&NHX:TOL=123802],monachus schauinslandi[&&NHX:TOL=123803],monachus tropicalis[&&NHX:EXT=Y:TOL=123804])monachus[&&NHX:TOL=123801],ommatophoca rossii[&&NHX:TOL=123805],pagophilus groenlandicus[&&NHX:TOL=123806],(phoca vitulina[&&NHX:TOL=123809],phoca largha[&&NHX:TOL=123808])phoca[&&NHX:TOL=123807],(pusa caspica[&&NHX:TOL=123811],pusa hispida[&&NHX:TOL=123812],pusa sibirica[&&NHX:TOL=123813])pusa[&&NHX:TOL=123810])phocidae[&&NHX:TOL=16020],odobenus rosmarus[&&NHX:TOL=123814],otariidae[&&NHX:TOL=16021])pinnipedia phocoidea[&&NHX:TOL=16019])caniformia[&&NHX:TOL=16011])carnivora[&&NHX:TOL=15971])[&&NHX:TOL=15969],(condylarthra[&&NHX:EXT=Y:TOL=15973],((((((babyrousa babyrussa[&&NHX:TOL=51280],hylochoerus meinertzhageni[&&NHX:TOL=51283],(phacochoerus africanus[&&NHX:TOL=51282],(phacochoerus aethiopicus delamerei[&&NHX:TOL=51756],phacochoerus aethiopicus aethiopicus[&&NHX:EXT=Y:TOL=51757])phacochoerus aethiopicus[&&NHX:TOL=51281])phacochoerus[&&NHX:TOL=51717],(potamochoerus porcus[&&NHX:TOL=51284],potamochoerus larvatus[&&NHX:TOL=51285])potamochoerus[&&NHX:TOL=51718],(sus barbatus[&&NHX:TOL=51287],sus salvanius[&&NHX:TOL=51288],sus scrofa[&&NHX:TOL=51289],sus verrucosus[&&NHX:TOL=51290],sus bucculentus[&&NHX:TOL=51291],sus cebifrons[&&NHX:TOL=51292],sus celebensis[&&NHX:TOL=51293],sus heureni[&&NHX:TOL=51294],sus oliveri[&&NHX:TOL=124450],sus philippensis[&&NHX:TOL=51295],sus timoriensis[&&NHX:TOL=51296])sus[&&NHX:TOL=51286],celebochoerus[&&NHX:EXT=Y:TOL=51723],eumaiochoerus[&&NHX:EXT=Y:TOL=51727],hippohyus[&&NHX:EXT=Y:TOL=51728],hippopotamodon[&&NHX:EXT=Y:TOL=51729],kolpochoerus[&&NHX:EXT=Y:TOL=51732],korynochoerus[&&NHX:EXT=Y:TOL=51733],metridiochoerus[&&NHX:EXT=Y:TOL=51740],microstonyx[&&NHX:EXT=Y:TOL=51741],molarochoerus[&&NHX:EXT=Y:TOL=51863],potamochoeroides[&&NHX:EXT=Y:TOL=51747],propotamochoerus[&&NHX:EXT=Y:TOL=51748],sinohyus[&&NHX:EXT=Y:TOL=51749],sivahyus[&&NHX:EXT=Y:TOL=51751],stylochoerus[&&NHX:EXT=Y:TOL=51752])suinae[&&NHX:TOL=51862],cainochoerus[&&NHX:EXT=Y:TOL=51722],(chleuastochoerus[&&NHX:EXT=Y:TOL=51724],dubiotherium[&&NHX:EXT=Y:TOL=51726],hyotherium[&&NHX:EXT=Y:TOL=51730])hyotheriinae[&&NHX:EXT=Y:TOL=51857],(nguruwe[&&NHX:EXT=Y:TOL=51743],kenyasus[&&NHX:EXT=Y:TOL=51731],kubanochoerus[&&NHX:EXT=Y:TOL=51734],libycochoerus[&&NHX:EXT=Y:TOL=51735],megalochoerus[&&NHX:EXT=Y:TOL=51739])kubanochoerinae[&&NHX:EXT=Y:TOL=51858],(bunolistriodon[&&NHX:EXT=Y:TOL=51721],eurolistriodon[&&NHX:EXT=Y:TOL=51860],listriodon[&&NHX:EXT=Y:TOL=51736],lopholistriodon[&&NHX:EXT=Y:TOL=51738])listriodontinae[&&NHX:EXT=Y:TOL=51859],namachoerus[&&NHX:EXT=Y:TOL=51742],(aureliachoerus[&&NHX:EXT=Y:TOL=51720],palaeochoerus[&&NHX:EXT=Y:TOL=51745],yunnanochoerus[&&NHX:EXT=Y:TOL=51754])palaeochoerinae[&&NHX:EXT=Y:TOL=51719],siamochoerus[&&NHX:EXT=Y:TOL=51861],sinapriculus[&&NHX:EXT=Y:TOL=51758],(conohyus[&&NHX:EXT=Y:TOL=51725],lophochoerus[&&NHX:EXT=Y:TOL=51737],notochoerus[&&NHX:EXT=Y:TOL=51744],nyanzachoerus[&&NHX:EXT=Y:TOL=51806],parachleuastochoerus[&&NHX:EXT=Y:TOL=51746],sivachoerus[&&NHX:EXT=Y:TOL=51750],tetraconodon[&&NHX:EXT=Y:TOL=51753])tetraconodontinae[&&NHX:EXT=Y:TOL=51805])suidae[&&NHX:TOL=30339],(odoichoerus[&&NHX:EXT=Y:TOL=51864],(catagonus wagneri[&&NHX:TOL=50860],tayassu pecari[&&NHX:TOL=50858],pecari tajacu[&&NHX:TOL=50859],argyrohyus[&&NHX:EXT=Y:TOL=51866],brasiliochoerus[&&NHX:EXT=Y:TOL=51867],chaenohyus[&&NHX:EXT=Y:TOL=51868],cynorca[&&NHX:EXT=Y:TOL=51869],dyseohyus[&&NHX:EXT=Y:TOL=51870],egatochoerus[&&NHX:EXT=Y:TOL=51871],hesperhys[&&NHX:EXT=Y:TOL=51872],mylohyus[&&NHX:EXT=Y:TOL=51873],perchoerus[&&NHX:EXT=Y:TOL=51874],platygonus[&&NHX:EXT=Y:TOL=51875],prosthennops[&&NHX:EXT=Y:TOL=51876],thinohyus[&&NHX:EXT=Y:TOL=51877])tayassuinae[&&NHX:TOL=51865],(barberahyus[&&NHX:EXT=Y:TOL=51882],doliochoerus[&&NHX:EXT=Y:TOL=51879],pecarichoerus[&&NHX:EXT=Y:TOL=51881],schizochoerus[&&NHX:EXT=Y:TOL=51883],taucanamo[&&NHX:EXT=Y:TOL=51880])doliochoerinae[&&NHX:EXT=Y:TOL=51878])tayassuidae[&&NHX:TOL=30341],xenohyus[&&NHX:EXT=Y:TOL=50861])[&&NHX:TOL=33122],(kenyapotamus[&&NHX:EXT=Y:TOL=30364],hexaprotodon[&&NHX:EXT=Y:TOL=30365],choeropsis liberiensis[&&NHX:TOL=30367],trilobophorus afarensis[&&NHX:EXT=Y:TOL=30374],(hippopotamus amphibius[&&NHX:TOL=30366],hippopotamus gorgops[&&NHX:EXT=Y:TOL=30370],hippopotamus kaisensis[&&NHX:EXT=Y:TOL=30371],hippopotamus laloumena[&&NHX:EXT=Y:TOL=30373],hippopotamus lemerlei[&&NHX:EXT=Y:TOL=30377],hippopotamus antiquus[&&NHX:EXT=Y:TOL=30380],hippopotamus creutzburgi[&&NHX:EXT=Y:TOL=30386],hippopotamus melitensis[&&NHX:EXT=Y:TOL=30387])[&&NHX:TOL=30376])hippopotamidae[&&NHX:TOL=30340],(((((camelus dromedarius[&&NHX:TOL=30349],camelus bactrianus[&&NHX:TOL=30350],procamelus[&&NHX:EXT=Y:TOL=52069],megatylopus[&&NHX:EXT=Y:TOL=52070],titanotylopus[&&NHX:EXT=Y:TOL=52071],megacamelus[&&NHX:EXT=Y:TOL=52072],gigantocamelus[&&NHX:EXT=Y:TOL=52114])camelini[&&NHX:TOL=30348],(lama guanicoe[&&NHX:TOL=30344],lama glama[&&NHX:TOL=30345],lama pacos[&&NHX:TOL=30346],vicugna vicugna[&&NHX:TOL=30347],hemiauchenia[&&NHX:EXT=Y:TOL=52073],pliauchenia[&&NHX:EXT=Y:TOL=52074],alforjas[&&NHX:EXT=Y:TOL=52075],blancocamelus[&&NHX:EXT=Y:TOL=52076],camelops[&&NHX:EXT=Y:TOL=52077],palaeolama[&&NHX:EXT=Y:TOL=52078],eulamaops[&&NHX:EXT=Y:TOL=52079],aepycamelus[&&NHX:EXT=Y:TOL=52087])lamini[&&NHX:TOL=30343],dyseotylopus[&&NHX:EXT=Y:TOL=52080],delahomeryx[&&NHX:EXT=Y:TOL=52089],hesperocamelus[&&NHX:EXT=Y:TOL=52090])camelinae[&&NHX:TOL=52068],(floridatragulus[&&NHX:EXT=Y:TOL=52097],aguascalientia[&&NHX:EXT=Y:TOL=52098])floridatragulinae[&&NHX:EXT=Y:TOL=52111],(paramiolabis[&&NHX:EXT=Y:TOL=52093],miolabis[&&NHX:EXT=Y:TOL=52092],cuyamacamelus[&&NHX:EXT=Y:TOL=52099],nothotylopus[&&NHX:EXT=Y:TOL=52081],capricamelus[&&NHX:EXT=Y:TOL=52109])miolabinae[&&NHX:EXT=Y:TOL=52113],(tanymykter[&&NHX:EXT=Y:TOL=52082],protolabis[&&NHX:EXT=Y:TOL=52084],michenia[&&NHX:EXT=Y:TOL=52083])protolabinae[&&NHX:EXT=Y:TOL=52112],(stenomylus[&&NHX:EXT=Y:TOL=52094],blickomylus[&&NHX:EXT=Y:TOL=52095],rakomylus[&&NHX:EXT=Y:TOL=52096],pseudolabis[&&NHX:EXT=Y:TOL=52107],miotylopus[&&NHX:EXT=Y:TOL=52100])stenomylinae[&&NHX:EXT=Y:TOL=52110],poebrodon[&&NHX:EXT=Y:TOL=52101],hidrosotherium[&&NHX:EXT=Y:TOL=52102],poebrotherium[&&NHX:EXT=Y:TOL=52103],paralabis[&&NHX:EXT=Y:TOL=52104],paratylopus[&&NHX:EXT=Y:TOL=52105],oxydactylus[&&NHX:EXT=Y:TOL=52085],australocamelus[&&NHX:EXT=Y:TOL=52086],priscocamelus[&&NHX:EXT=Y:TOL=52088],nothokemas[&&NHX:EXT=Y:TOL=52091],gentilicamelus[&&NHX:EXT=Y:TOL=52106])camelidae[&&NHX:TOL=30342],oromerycidae[&&NHX:EXT=Y:TOL=50863])[&&NHX:TOL=52108],protoceratidae[&&NHX:EXT=Y:TOL=30352],xiphodontidae[&&NHX:EXT=Y:TOL=30358])tylopoda[&&NHX:TOL=50862],((((bovinae[&&NHX:TOL=51150],((((alcelaphus buselaphus[&&NHX:TOL=50983],sigmoceros lichtensteinii[&&NHX:TOL=50991])[&&NHX:TOL=51158],(connochaetes taurinus[&&NHX:TOL=50985],connochaetes gnou[&&NHX:TOL=50986])[&&NHX:TOL=50984],(damaliscus lunatus[&&NHX:TOL=50988],damaliscus hunteri[&&NHX:TOL=50989],damaliscus pygargus[&&NHX:TOL=50990])[&&NHX:TOL=50987],damalops[&&NHX:EXT=Y:TOL=52585],oreonagor[&&NHX:EXT=Y:TOL=52586],parestigorgon[&&NHX:EXT=Y:TOL=52587],parmularius[&&NHX:EXT=Y:TOL=52588],rabaticeras[&&NHX:EXT=Y:TOL=52589],rhynotragus[&&NHX:EXT=Y:TOL=52590],rusingoryx[&&NHX:EXT=Y:TOL=52591])alcelaphinae[&&NHX:TOL=51157],(addax nasomaculatus[&&NHX:TOL=51122],hippotragus equinus[&&NHX:TOL=51124],hippotragus leucophaeus[&&NHX:EXT=Y:TOL=51125],hippotragus niger[&&NHX:TOL=51126],(oryx dammah[&&NHX:TOL=51128],oryx gazella[&&NHX:TOL=51129],oryx leucoryx[&&NHX:TOL=51130])[&&NHX:TOL=51127],praedamalis[&&NHX:EXT=Y:TOL=52583],wellsiana[&&NHX:EXT=Y:TOL=52584])hippotraginae[&&NHX:TOL=51159])[&&NHX:TOL=51156],(((ammotragus lervia[&&NHX:TOL=51064],budorcas taxicolor[&&NHX:TOL=51065],(capra caucasica[&&NHX:TOL=51067],capra cylindricornis[&&NHX:TOL=51068],capra hircus[&&NHX:TOL=51070],capra falconeri[&&NHX:TOL=51069],capra nubiana[&&NHX:TOL=51072],(capra pyrenaica[&&NHX:TOL=51073],capra ibex[&&NHX:TOL=51071])[&&NHX:TOL=120565],capra sibirica[&&NHX:TOL=51074],capra walie[&&NHX:TOL=51075])capra[&&NHX:TOL=51066],(hemitragus hylocrius[&&NHX:TOL=51077],hemitragus jayakari[&&NHX:TOL=51078],hemitragus jemlahicus[&&NHX:TOL=51079])hemitragus[&&NHX:TOL=51076],(ovis ammon[&&NHX:TOL=51090],ovis aries[&&NHX:TOL=51091],ovis canadensis[&&NHX:TOL=51092],ovis dalli[&&NHX:TOL=51093],ovis nivicola[&&NHX:TOL=51094],ovis vignei[&&NHX:TOL=51095])ovis[&&NHX:TOL=51089],(pseudois nayaur[&&NHX:TOL=51097],pseudois schaeferi[&&NHX:TOL=51098])pseudois[&&NHX:TOL=51096])[&&NHX:TOL=52124],((naemorhedus baileyi[&&NHX:TOL=51081],naemorhedus caudatus[&&NHX:TOL=51082],naemorhedus crispus[&&NHX:TOL=51083],naemorhedus goral[&&NHX:TOL=51084],naemorhedus sumatraensis[&&NHX:TOL=51085],naemorhedus swinhoei[&&NHX:TOL=51086])naemorhedus[&&NHX:TOL=51080],oreamnos americanus[&&NHX:TOL=51087],ovibos moschatus[&&NHX:TOL=51088])[&&NHX:TOL=52125],(rupicapra pyrenaica[&&NHX:TOL=51100],rupicapra rupicapra[&&NHX:TOL=51101])rupicapra[&&NHX:TOL=51099],(benicerus[&&NHX:EXT=Y:TOL=52477],boopsis[&&NHX:EXT=Y:TOL=52478],bootherium[&&NHX:EXT=Y:TOL=52519],capraoryx[&&NHX:EXT=Y:TOL=52479],caprotragoides[&&NHX:EXT=Y:TOL=52480],criotherium[&&NHX:EXT=Y:TOL=52481],damalavus[&&NHX:EXT=Y:TOL=52482],euceratherium[&&NHX:EXT=Y:TOL=52483],gallogoral[&&NHX:EXT=Y:TOL=52484],myotragus[&&NHX:EXT=Y:TOL=52485],oioceros[&&NHX:EXT=Y:TOL=52486],lyrocerus[&&NHX:EXT=Y:TOL=52487],makapania[&&NHX:EXT=Y:TOL=52488],megalovis[&&NHX:EXT=Y:TOL=52489],mesembriacerus[&&NHX:EXT=Y:TOL=52490],neotragocerus[&&NHX:EXT=Y:TOL=52491],nesogoral[&&NHX:EXT=Y:TOL=52492],norbertia[&&NHX:EXT=Y:TOL=52493],numidocapra[&&NHX:EXT=Y:TOL=52494],olonbulukia[&&NHX:EXT=Y:TOL=52495],pachygazella[&&NHX:EXT=Y:TOL=52496],pachytragus[&&NHX:EXT=Y:TOL=52497],palaeoreas[&&NHX:EXT=Y:TOL=52498],palaeoryx[&&NHX:EXT=Y:TOL=52499],paraprotoryx[&&NHX:EXT=Y:TOL=52500],parapseudotragus[&&NHX:EXT=Y:TOL=52501],parurmiatherium[&&NHX:EXT=Y:TOL=52502],praeovibos[&&NHX:EXT=Y:TOL=52503],preptoceras[&&NHX:EXT=Y:TOL=52638],procamptoceras[&&NHX:EXT=Y:TOL=52504],prosinotragus[&&NHX:EXT=Y:TOL=52505],protoryx[&&NHX:EXT=Y:TOL=52506],pseudotragus[&&NHX:EXT=Y:TOL=52507],samotragus[&&NHX:EXT=Y:TOL=52508],sinocapra[&&NHX:EXT=Y:TOL=52509],sinopalaeoceros[&&NHX:EXT=Y:TOL=52510],sinotragus[&&NHX:EXT=Y:TOL=52511],sivacapra[&&NHX:EXT=Y:TOL=52512],soergelia[&&NHX:EXT=Y:TOL=52521],sporadotragus[&&NHX:EXT=Y:TOL=52513],symbos[&&NHX:EXT=Y:TOL=52520],tethytragus[&&NHX:EXT=Y:TOL=52514],tossunnoria[&&NHX:EXT=Y:TOL=52515],tsaidamotherium[&&NHX:EXT=Y:TOL=52516],turcocerus[&&NHX:EXT=Y:TOL=52517],urmiatherium[&&NHX:EXT=Y:TOL=52518])fossil caprinae[&&NHX:EXT=Y:TOL=52476])caprinae[&&NHX:TOL=51161],pantholops hodgsonii[&&NHX:TOL=51025])[&&NHX:TOL=51160],aepyceros melampus[&&NHX:TOL=50982],((cephalophus callipygus[&&NHX:TOL=51104],cephalophus weynsi[&&NHX:TOL=51119],cephalophus ogilbyi[&&NHX:TOL=51114])[&&NHX:TOL=52121],(cephalophus harveyi[&&NHX:TOL=51106],cephalophus natalensis[&&NHX:TOL=51111],cephalophus nigrifrons[&&NHX:TOL=51113],cephalophus rufilatus[&&NHX:TOL=51116])[&&NHX:TOL=52122],(cephalophus spadix[&&NHX:TOL=51118],cephalophus silvicultor[&&NHX:TOL=51117],cephalophus dorsalis[&&NHX:TOL=51105])[&&NHX:TOL=52123],cephalophus adersi[&&NHX:TOL=51103],cephalophus jentinki[&&NHX:TOL=51107],cephalophus leucogaster[&&NHX:TOL=51108],cephalophus maxwellii[&&NHX:TOL=51109],cephalophus monticola[&&NHX:TOL=51110],cephalophus niger[&&NHX:TOL=51112],cephalophus rubidus[&&NHX:TOL=51115],cephalophus zebra[&&NHX:TOL=51120],sylvicapra grimmia[&&NHX:TOL=51121])cephalophinae[&&NHX:TOL=51163],(((redunca arundinum[&&NHX:TOL=51139],redunca fulvorufula[&&NHX:TOL=51141],redunca redunca[&&NHX:TOL=51142])[&&NHX:TOL=51138],(kobus ellipsiprymnus[&&NHX:TOL=51133],kobus kob[&&NHX:TOL=51134],kobus leche[&&NHX:TOL=51135],kobus megaceros[&&NHX:TOL=51136],kobus vardonii[&&NHX:TOL=51137])[&&NHX:TOL=51132],(cambayella[&&NHX:EXT=Y:TOL=52573],dorcadoxa[&&NHX:EXT=Y:TOL=52574],gangicobus[&&NHX:EXT=Y:TOL=52575],hydaspicobus[&&NHX:EXT=Y:TOL=52576],kobikeryx[&&NHX:EXT=Y:TOL=52577],menelikia[&&NHX:EXT=Y:TOL=52578],sivacobus[&&NHX:EXT=Y:TOL=52579],sivadenota[&&NHX:EXT=Y:TOL=52580],thaleroceros[&&NHX:EXT=Y:TOL=52581],vishnucobus[&&NHX:EXT=Y:TOL=52582])fossil reduncinae[&&NHX:EXT=Y:TOL=52731])reduncinae[&&NHX:TOL=51165],pelea capreolus[&&NHX:TOL=51131])[&&NHX:TOL=51164],(ammodorcas clarkei[&&NHX:TOL=50992],antidorcas marsupialis[&&NHX:TOL=50993],antilope cervicapra[&&NHX:TOL=50994],dorcatragus megalotis[&&NHX:TOL=50995],(gazella arabica[&&NHX:TOL=50997],gazella bennettii[&&NHX:TOL=50998],gazella bilkis[&&NHX:TOL=50999],gazella cuvieri[&&NHX:TOL=51000],gazella dama[&&NHX:TOL=51001],gazella dorcas[&&NHX:TOL=51002],gazella gazella[&&NHX:TOL=51003],gazella granti[&&NHX:TOL=51004],gazella leptoceros[&&NHX:TOL=51005],gazella rufifrons[&&NHX:TOL=51006],gazella rufina[&&NHX:TOL=51007],gazella saudiya[&&NHX:TOL=51008],gazella soemmerringii[&&NHX:TOL=51009],gazella spekei[&&NHX:TOL=51010],gazella subgutturosa[&&NHX:TOL=51011],gazella thomsonii[&&NHX:TOL=51012])gazella[&&NHX:TOL=50996],litocranius walleri[&&NHX:TOL=51013],(madoqua guentheri[&&NHX:TOL=51015],madoqua kirkii[&&NHX:TOL=51016],madoqua piacentinii[&&NHX:TOL=51017],madoqua saltiana[&&NHX:TOL=51018])madoqua[&&NHX:TOL=51014],ourebia ourebi[&&NHX:TOL=51024],(procapra gutturosa[&&NHX:TOL=51027],procapra picticaudata[&&NHX:TOL=51028],procapra przewalskii[&&NHX:TOL=51029])procapra[&&NHX:TOL=51026],(raphicerus campestris[&&NHX:TOL=51031],raphicerus melanotis[&&NHX:TOL=51032],raphicerus sharpei[&&NHX:TOL=51033])raphicerus[&&NHX:TOL=51030],saiga tatarica[&&NHX:TOL=51034],antilospira[&&NHX:EXT=Y:TOL=52467],dorcadoryx[&&NHX:EXT=Y:TOL=52461],gazellospira[&&NHX:EXT=Y:TOL=52471],hispanodorcas[&&NHX:EXT=Y:TOL=52464],nisidorcas[&&NHX:EXT=Y:TOL=52465],ouzocerus[&&NHX:EXT=Y:TOL=52460],parastrepsiceros[&&NHX:EXT=Y:TOL=52469],prostrepsiceros[&&NHX:EXT=Y:TOL=52459],protragelaphus[&&NHX:EXT=Y:TOL=52462],qurliqnoria[&&NHX:EXT=Y:TOL=52463],sinapocerus[&&NHX:EXT=Y:TOL=52466],sinoreas[&&NHX:EXT=Y:TOL=52468],spirocerus[&&NHX:EXT=Y:TOL=52470],tragospira[&&NHX:EXT=Y:TOL=52472])antilopinae[&&NHX:TOL=51166],(neotragus batesi[&&NHX:TOL=51020],neotragus moschatus[&&NHX:TOL=51021],neotragus pygmaeus[&&NHX:TOL=51022])neotragus[&&NHX:TOL=51019],oreotragus oreotragus[&&NHX:TOL=51023])[&&NHX:TOL=51154],(damalacra[&&NHX:EXT=Y:TOL=52451],fenhoryx[&&NHX:EXT=Y:TOL=52454],homoiodorcas[&&NHX:EXT=Y:TOL=52473],hypsodontus[&&NHX:EXT=Y:TOL=52442],kabulicornis[&&NHX:EXT=Y:TOL=52450],kubanotragus[&&NHX:EXT=Y:TOL=52443],namibiomeryx[&&NHX:EXT=Y:TOL=52441],palaeotragiscus[&&NHX:EXT=Y:TOL=52474],parabubalis[&&NHX:EXT=Y:TOL=52455],pontoceros[&&NHX:EXT=Y:TOL=52452],procobus[&&NHX:EXT=Y:TOL=52445],prodamaliscus[&&NHX:EXT=Y:TOL=52446],pseudoeotragus[&&NHX:EXT=Y:TOL=52444],samodorcas[&&NHX:EXT=Y:TOL=52447],shaanxispira[&&NHX:EXT=Y:TOL=52448],torticornis[&&NHX:EXT=Y:TOL=52449],tyrrhenotragus[&&NHX:EXT=Y:TOL=52475],vishnumeryx[&&NHX:EXT=Y:TOL=52453])miscellaneous fossil bovids[&&NHX:EXT=Y:TOL=52722])bovidae[&&NHX:TOL=50878],(moschus berezovskii[&&NHX:TOL=50924],moschus chrysogaster[&&NHX:TOL=50925],moschus cupreus[&&NHX:TOL=51144],moschus fuscus[&&NHX:TOL=50926],moschus leucogaster[&&NHX:TOL=51145],moschus moschiferus[&&NHX:TOL=50927],micromeryx[&&NHX:EXT=Y:TOL=52354])moschidae[&&NHX:TOL=50871],(((((axis axis[&&NHX:TOL=50929],axis calamianensis[&&NHX:TOL=51408],axis kuhlii[&&NHX:TOL=51409],axis porcinus[&&NHX:TOL=50932])axis[&&NHX:TOL=51169],(rucervus duvaucelii[&&NHX:TOL=50936],rucervus schomburgki[&&NHX:EXT=Y:TOL=50941])[&&NHX:TOL=51170])[&&NHX:TOL=108170],((dama dama[&&NHX:TOL=50945],dama mesopotamica[&&NHX:TOL=50946])dama[&&NHX:TOL=50944],((cervus elaphus[&&NHX:TOL=50937],cervus nippon[&&NHX:TOL=50940],cervus albirostris[&&NHX:TOL=50934],cervus mariannus[&&NHX:TOL=50939],cervus alfredi[&&NHX:TOL=50935],cervus timorensis[&&NHX:TOL=50942],cervus unicolor[&&NHX:TOL=50943])[&&NHX:TOL=50933],(elaphurus davidianus[&&NHX:TOL=50947],cervus eldii[&&NHX:TOL=50938])[&&NHX:TOL=51171])[&&NHX:TOL=108172])[&&NHX:TOL=108171],(allocaenelaphus[&&NHX:EXT=Y:TOL=52596],arvernoceros[&&NHX:EXT=Y:TOL=52597],candiacervus[&&NHX:EXT=Y:TOL=52598],cervocerus novorossiae[&&NHX:EXT=Y:TOL=108178],croizetoceros[&&NHX:EXT=Y:TOL=52599],eucladoceros[&&NHX:EXT=Y:TOL=52600],megaceroides[&&NHX:EXT=Y:TOL=52601],megaloceros[&&NHX:EXT=Y:TOL=52602],neomegaloceros[&&NHX:EXT=Y:TOL=52603],nesoleipoceros[&&NHX:EXT=Y:TOL=52604],orchonoceros[&&NHX:EXT=Y:TOL=52605],praemegaceros[&&NHX:EXT=Y:TOL=52606],praesinomegaceros[&&NHX:EXT=Y:TOL=52607],psekupsoceros[&&NHX:EXT=Y:TOL=52608],sangamona[&&NHX:EXT=Y:TOL=52609],sinomegaceros[&&NHX:EXT=Y:TOL=52610])miscellaneous fossil old world deer[&&NHX:EXT=Y:TOL=52595])old world deer[&&NHX:TOL=51168],(elaphodus cephalophus[&&NHX:TOL=50949],(eostyloceros[&&NHX:EXT=Y:TOL=52382],megamuntiacus vuquangensis[&&NHX:TOL=51175],metacervulus[&&NHX:EXT=Y:TOL=52386],(muntiacus atherodes[&&NHX:TOL=50951],muntiacus crinifrons[&&NHX:TOL=50952],muntiacus feae[&&NHX:TOL=50953],muntiacus gongshanensis[&&NHX:TOL=50954],muntiacus muntjak[&&NHX:TOL=50955],muntiacus putaoensis[&&NHX:TOL=51172],muntiacus reevesi[&&NHX:TOL=50956],muntiacus rooseveltorum[&&NHX:TOL=51173],muntiacus truongsonensis[&&NHX:TOL=51174],muntiacus leilaoensis[&&NHX:EXT=Y:TOL=108179])muntiacus[&&NHX:TOL=52387],paracervulus[&&NHX:EXT=Y:TOL=52390])muntjacs[&&NHX:TOL=50950])[&&NHX:TOL=108169])[&&NHX:TOL=51167],(((capreolus capreolus[&&NHX:TOL=50960],capreolus pygargus[&&NHX:TOL=50961])capreolus[&&NHX:TOL=50959],hydropotes inermis[&&NHX:TOL=50948])[&&NHX:TOL=108173],((blastocerus dichotomus[&&NHX:TOL=50958],(hippocamelus antisensis[&&NHX:TOL=50963],hippocamelus bisulcus[&&NHX:TOL=50964])hippocamelus[&&NHX:TOL=50962],(mazama americana[&&NHX:TOL=50966],mazama bororo[&&NHX:TOL=124451],mazama bricenii[&&NHX:TOL=50967],mazama chunyi[&&NHX:TOL=50968],mazama gouazoupira[&&NHX:TOL=50969],mazama nana[&&NHX:TOL=50970],mazama rufina[&&NHX:TOL=50971])mazama[&&NHX:TOL=50965],(odocoileus hemionus[&&NHX:TOL=50973],odocoileus virginianus[&&NHX:TOL=50974])odocoileus[&&NHX:TOL=50972],ozotoceros bezoarticus[&&NHX:TOL=50975],(pudu mephistophiles[&&NHX:TOL=50977],pudu puda[&&NHX:TOL=50978])pudu[&&NHX:TOL=50976])[&&NHX:TOL=108175],rangifer tarandus[&&NHX:TOL=50979])[&&NHX:TOL=108177],alces alces[&&NHX:TOL=50957],agalmaceros[&&NHX:EXT=Y:TOL=52614],antifer[&&NHX:EXT=Y:TOL=52615],bretzia[&&NHX:EXT=Y:TOL=52616],cervalces[&&NHX:EXT=Y:TOL=52617],charitoceros[&&NHX:EXT=Y:TOL=52618],eocoileus[&&NHX:EXT=Y:TOL=108180],epieuryceros[&&NHX:EXT=Y:TOL=108181],morenelaphus[&&NHX:EXT=Y:TOL=52619],navahoceros[&&NHX:EXT=Y:TOL=52620],paraceros[&&NHX:EXT=Y:TOL=108182],pavlodaria[&&NHX:EXT=Y:TOL=52621],procapreolus[&&NHX:EXT=Y:TOL=52622])[&&NHX:TOL=51176],(acteocemas[&&NHX:EXT=Y:TOL=52379],amphiprox[&&NHX:EXT=Y:TOL=52380],cervavitulus[&&NHX:EXT=Y:TOL=52395],dicrocerus[&&NHX:EXT=Y:TOL=52381],euprox[&&NHX:EXT=Y:TOL=52383],heteroprox[&&NHX:EXT=Y:TOL=52384],lagomeryx[&&NHX:EXT=Y:TOL=52385],lucentia[&&NHX:EXT=Y:TOL=52396],muva[&&NHX:EXT=Y:TOL=52397],oschinotherium[&&NHX:EXT=Y:TOL=52388],palaeoplatycerus[&&NHX:EXT=Y:TOL=52389],paradicrocerus[&&NHX:EXT=Y:TOL=52391],platycemas[&&NHX:EXT=Y:TOL=52392],procervulus[&&NHX:EXT=Y:TOL=52393],pseudalces[&&NHX:EXT=Y:TOL=52611],stephanocemas[&&NHX:EXT=Y:TOL=52394],tamanalces[&&NHX:EXT=Y:TOL=52612],torontoceros[&&NHX:EXT=Y:TOL=52613])miscellaneous fossil cervids[&&NHX:EXT=Y:TOL=108174])cervidae[&&NHX:TOL=50875])[&&NHX:TOL=51149],(canthumeryx[&&NHX:EXT=Y:TOL=52399],climacoceras[&&NHX:EXT=Y:TOL=52400],georgiomeryx[&&NHX:EXT=Y:TOL=52435],(birgerbohlinia[&&NHX:EXT=Y:TOL=52402],bramatherium[&&NHX:EXT=Y:TOL=52403],bohlinia[&&NHX:EXT=Y:TOL=52404],csakvarotherium[&&NHX:EXT=Y:TOL=52405],decennatherium[&&NHX:EXT=Y:TOL=52406],(giraffa camelopardalis[&&NHX:TOL=50980],giraffa gracilis[&&NHX:EXT=Y:TOL=52430],giraffa jumae[&&NHX:EXT=Y:TOL=52434],giraffa priscilla[&&NHX:EXT=Y:TOL=52432],giraffa punjabiensis[&&NHX:EXT=Y:TOL=52433],giraffa pygmaea[&&NHX:EXT=Y:TOL=52431],giraffa sivalensis[&&NHX:EXT=Y:TOL=52429],giraffa stillei[&&NHX:EXT=Y:TOL=52436])giraffa[&&NHX:TOL=52407],helladotherium[&&NHX:EXT=Y:TOL=52409],honanotherium[&&NHX:EXT=Y:TOL=52410],hydaspitherium[&&NHX:EXT=Y:TOL=52411],karsimatherium[&&NHX:EXT=Y:TOL=52412],macedonitherium[&&NHX:EXT=Y:TOL=52413],mitilanotherium[&&NHX:EXT=Y:TOL=52414],okapia johnstoni[&&NHX:TOL=50981],praepalaeotragus[&&NHX:EXT=Y:TOL=52416],palaeotragus[&&NHX:EXT=Y:TOL=52417],samotherium[&&NHX:EXT=Y:TOL=52418],sivatherium[&&NHX:EXT=Y:TOL=52419],sogdianotherium[&&NHX:EXT=Y:TOL=52420],vishnutherium[&&NHX:EXT=Y:TOL=52421])giraffidae[&&NHX:TOL=52401],giraffokeryx[&&NHX:EXT=Y:TOL=52408],injanatherium[&&NHX:EXT=Y:TOL=52422],lorancameryx[&&NHX:EXT=Y:TOL=52423],nyanzameryx[&&NHX:EXT=Y:TOL=52424],orangemeryx[&&NHX:EXT=Y:TOL=52437],progiraffa[&&NHX:EXT=Y:TOL=52425],propalaeomeryx[&&NHX:EXT=Y:TOL=52426],propalaeoryx[&&NHX:EXT=Y:TOL=52427],sperrgebietomeryx[&&NHX:EXT=Y:TOL=52438],teruelia[&&NHX:EXT=Y:TOL=52428])giraffoidea[&&NHX:TOL=50877],((antilocapra americana americana[&&NHX:TOL=52672],antilocapra americana mexicana[&&NHX:TOL=52673],antilocapra americana peninsularis[&&NHX:TOL=52674],antilocapra americana sonoriensis[&&NHX:TOL=52675])antilocapra americana[&&NHX:TOL=50872],capromeryx[&&NHX:EXT=Y:TOL=52376],ceratomeryx[&&NHX:EXT=Y:TOL=52375],cosoryx[&&NHX:EXT=Y:TOL=52363],hayoceros[&&NHX:EXT=Y:TOL=52369],hexameryx[&&NHX:EXT=Y:TOL=52373],hexobelomeryx[&&NHX:EXT=Y:TOL=52370],ilingoceros[&&NHX:EXT=Y:TOL=52366],merriamoceros[&&NHX:EXT=Y:TOL=52360],merycodus[&&NHX:EXT=Y:TOL=52359],osbornoceros[&&NHX:EXT=Y:TOL=52365],ottoceros[&&NHX:EXT=Y:TOL=52371],paracosoryx[&&NHX:EXT=Y:TOL=52361],plioceros[&&NHX:EXT=Y:TOL=52372],proantilocapra[&&NHX:EXT=Y:TOL=52374],ramoceros[&&NHX:EXT=Y:TOL=52362],sphenophalos[&&NHX:EXT=Y:TOL=52367],stockoceros[&&NHX:EXT=Y:TOL=52378],subantilocapra[&&NHX:EXT=Y:TOL=52364],tetrameryx[&&NHX:EXT=Y:TOL=52377],texoceros[&&NHX:EXT=Y:TOL=52368])antilocapridae[&&NHX:TOL=52358],(andegameryx[&&NHX:EXT=Y:TOL=52456],blastomeryx[&&NHX:EXT=Y:TOL=52352],bugtimeryx[&&NHX:EXT=Y:TOL=52457],dremotherium[&&NHX:EXT=Y:TOL=52355],eumeryx[&&NHX:EXT=Y:TOL=52349],hanhaicerus[&&NHX:EXT=Y:TOL=52440],hispanomeryx[&&NHX:EXT=Y:TOL=52353],hoplitomerycidae[&&NHX:EXT=Y:TOL=50874],longirostromeryx[&&NHX:EXT=Y:TOL=52357],machaeromeryx[&&NHX:EXT=Y:TOL=52356],palaeohypsodontus[&&NHX:EXT=Y:TOL=52340],palaeomerycidae[&&NHX:EXT=Y:TOL=50873],rutitherium[&&NHX:EXT=Y:TOL=52350],walangania[&&NHX:EXT=Y:TOL=52351])miscellaneous fossil pecorans[&&NHX:EXT=Y:TOL=52439])pecora[&&NHX:TOL=51143],((hyemoschus aquaticus[&&NHX:TOL=50920],moschiola meminna[&&NHX:TOL=50921],(tragulus javanicus[&&NHX:TOL=50922],tragulus williamsoni[&&NHX:TOL=51182],tragulus kanchil[&&NHX:TOL=51183])[&&NHX:TOL=51181],(tragulus napu[&&NHX:TOL=50923],tragulus nigricans[&&NHX:TOL=51185])[&&NHX:TOL=51184],tragulus versicolor[&&NHX:TOL=51186],siamotragulus sanyathanai[&&NHX:EXT=Y:TOL=51187],yunnanotherium[&&NHX:EXT=Y:TOL=51188],dorcatherium[&&NHX:EXT=Y:TOL=51189],dorcabune[&&NHX:EXT=Y:TOL=51190],archaeotragulus krabiensis[&&NHX:EXT=Y:TOL=51178])tragulidae[&&NHX:TOL=50866],lophiomerycidae[&&NHX:EXT=Y:TOL=50869])[&&NHX:TOL=51177],bachitheriidae[&&NHX:EXT=Y:TOL=50868],climacoceratidae[&&NHX:EXT=Y:TOL=50876],gelocidae[&&NHX:EXT=Y:TOL=50870],gobiocerus[&&NHX:EXT=Y:TOL=52348],hypertragulidae[&&NHX:EXT=Y:TOL=50865],leptomerycidae[&&NHX:EXT=Y:TOL=50867])ruminantia[&&NHX:TOL=16001],((agriochoerus[&&NHX:EXT=Y:TOL=30357],diplobunops[&&NHX:EXT=Y:TOL=30356],protoreodon[&&NHX:EXT=Y:TOL=30355])agriochoeridae[&&NHX:EXT=Y:TOL=30354],aksyiria[&&NHX:EXT=Y:TOL=52067],amphimerycidae[&&NHX:EXT=Y:TOL=50864],(anoplotherium[&&NHX:EXT=Y:TOL=52709],catodontherium[&&NHX:EXT=Y:TOL=52717],dacrytherium[&&NHX:EXT=Y:TOL=52716],deilotherium[&&NHX:EXT=Y:TOL=52712],diplartiopus[&&NHX:EXT=Y:TOL=52713],diplobune[&&NHX:EXT=Y:TOL=52710],ephelcomenus[&&NHX:EXT=Y:TOL=52711],hyracodontherium[&&NHX:EXT=Y:TOL=52714],leptotheridium[&&NHX:EXT=Y:TOL=52718],robiacina[&&NHX:EXT=Y:TOL=52707],robiatherium[&&NHX:EXT=Y:TOL=52708])anoplotheriidae[&&NHX:EXT=Y:TOL=33103],anthracotheriidae[&&NHX:EXT=Y:TOL=30368],(caenomeryx[&&NHX:EXT=Y:TOL=51239],cainotherium[&&NHX:EXT=Y:TOL=51240],oxacron[&&NHX:EXT=Y:TOL=51235],paroxacron[&&NHX:EXT=Y:TOL=51236],plesiomeryx[&&NHX:EXT=Y:TOL=51238])cainotheriidae[&&NHX:EXT=Y:TOL=33102],cebochoeridae[&&NHX:EXT=Y:TOL=30375],(amphirhagatherium[&&NHX:EXT=Y:TOL=33113],choeropotamus[&&NHX:EXT=Y:TOL=33106],cuisitherium[&&NHX:EXT=Y:TOL=33115],hallebune[&&NHX:EXT=Y:TOL=33112],haplobunodon[&&NHX:EXT=Y:TOL=33108],lophiobunodon[&&NHX:EXT=Y:TOL=33109],masillabune[&&NHX:EXT=Y:TOL=33114],parabunodon[&&NHX:EXT=Y:TOL=33116],rhagatherium[&&NHX:EXT=Y:TOL=33111],tapirulus[&&NHX:EXT=Y:TOL=33110],thaumastognathus[&&NHX:EXT=Y:TOL=33107])choeropotamidae[&&NHX:EXT=Y:TOL=30362],dichobunidae[&&NHX:EXT=Y:TOL=30369],entelodontidae[&&NHX:EXT=Y:TOL=33105],helohyidae[&&NHX:EXT=Y:TOL=33099],merycoidodontidae[&&NHX:EXT=Y:TOL=30353],mixtotheriidae[&&NHX:EXT=Y:TOL=33101],raoellidae[&&NHX:EXT=Y:TOL=30361],sanitheriidae[&&NHX:EXT=Y:TOL=33098])miscellaneous fossil artiodactyls[&&NHX:EXT=Y:TOL=52715])artiodactyla[&&NHX:TOL=15976],((agorophiidae[&&NHX:EXT=Y:TOL=16058],(kogiidae[&&NHX:TOL=16060],physeteridae[&&NHX:TOL=16059])physeteroidea[&&NHX:TOL=23130],dalpiazinidae[&&NHX:EXT=Y:TOL=16064],((((((phocoenidae[&&NHX:TOL=16072],albireonidae[&&NHX:EXT=Y:TOL=16069])[&&NHX:TOL=23132],monodontidae [&&NHX:TOL=16070])[&&NHX:TOL=23128],delphinidae [&&NHX:TOL=16071])delphinoidea[&&NHX:TOL=23129],kentriodontidae[&&NHX:EXT=Y:TOL=16068])[&&NHX:TOL=23133],(pontoporiidae[&&NHX:TOL=16074],iniidae [&&NHX:TOL=16073])[&&NHX:TOL=23131])[&&NHX:TOL=23134],lipotidae[&&NHX:TOL=23135],ziphiidae[&&NHX:TOL=16061],(squalodelphidae[&&NHX:EXT=Y:TOL=16063],platanistidae[&&NHX:TOL=16065])[&&NHX:TOL=23137],squalodontidae[&&NHX:EXT=Y:TOL=16062],(eoplatanistidae[&&NHX:EXT=Y:TOL=16066],eurhinodelphidae[&&NHX:EXT=Y:TOL=16067])[&&NHX:TOL=23136])[&&NHX:TOL=23138])odontoceti[&&NHX:TOL=16025],(llanocetidae[&&NHX:EXT=Y:TOL=16027],mammalodontidae[&&NHX:EXT=Y:TOL=16029],kekenodontidae[&&NHX:EXT=Y:TOL=16030],((((notiocetus[&&NHX:EXT=Y:TOL=16045],palaeocetus[&&NHX:EXT=Y:TOL=16046],balaenoptera musculus[&&NHX:TOL=16047],balaenoptera physalus[&&NHX:TOL=16048],balaenoptera borealis[&&NHX:TOL=16049],balaenoptera edeni[&&NHX:TOL=16050],balaenoptera acutorostrata[&&NHX:TOL=16051],plesiocetus[&&NHX:EXT=Y:TOL=16052],idiocetus[&&NHX:EXT=Y:TOL=16053],megaptera novaeangliae[&&NHX:TOL=16054],megapteropsis[&&NHX:EXT=Y:TOL=16055],burtinopsis[&&NHX:EXT=Y:TOL=16056])balaenopteridae[&&NHX:TOL=16032],eschrichtius robustus grey whale[&&NHX:TOL=16033],caperea marginata pygmy right whale[&&NHX:TOL=16034],(morenocetus[&&NHX:EXT=Y:TOL=16037],balaenula[&&NHX:EXT=Y:TOL=16038],protobalaena[&&NHX:EXT=Y:TOL=16039],mesoteras[&&NHX:EXT=Y:TOL=16040],balaena mysticetus[&&NHX:TOL=16041],eubalaena glacialis[&&NHX:TOL=16042],eubalaena australis[&&NHX:TOL=16043])balaenidae[&&NHX:TOL=16035])[&&NHX:TOL=23139],cetotheriidae[&&NHX:EXT=Y:TOL=16031])[&&NHX:TOL=23144],aetiocetidae[&&NHX:EXT=Y:TOL=16028])[&&NHX:TOL=23140])mysticeti[&&NHX:TOL=16024],archaeoceti[&&NHX:EXT=Y:TOL=16023])cetacea[&&NHX:TOL=15977])[&&NHX:TOL=15975],(palaeorycteropus[&&NHX:EXT=Y:TOL=16878],archaeorycteropus[&&NHX:EXT=Y:TOL=16879],myorycteropus[&&NHX:EXT=Y:TOL=16880],orycteropus afer[&&NHX:TOL=16881],leptorycteropus[&&NHX:EXT=Y:TOL=16882])tubulidentata[&&NHX:TOL=15978],((equidae[&&NHX:TOL=16255],palaeotheriidae[&&NHX:EXT=Y:TOL=16256],brontotheriidae[&&NHX:EXT=Y:TOL=16257],anchilophidae[&&NHX:EXT=Y:TOL=16258],eomoropidae[&&NHX:EXT=Y:TOL=16259],chalicotheriidae[&&NHX:EXT=Y:TOL=16260],hyracodontidae[&&NHX:EXT=Y:TOL=16261],rhinocerotidae[&&NHX:TOL=16262],helaletidae[&&NHX:EXT=Y:TOL=16263],isectolophidae[&&NHX:EXT=Y:TOL=16264],lophiodontidae[&&NHX:EXT=Y:TOL=16265],deperetellidae[&&NHX:EXT=Y:TOL=16266],lophialetidae[&&NHX:EXT=Y:TOL=16267],tapiridae[&&NHX:TOL=16268])perissodactyla[&&NHX:TOL=15980],((seggeurius[&&NHX:EXT=Y:TOL=16168],(pliohyracidae[&&NHX:EXT=Y:TOL=16170],(procavia capensis[&&NHX:TOL=16172],heterohyrax brucei[&&NHX:TOL=16173],(dendrohyrax dorsalis[&&NHX:TOL=16160],dendrohyrax arboreus[&&NHX:TOL=16162])dendrohyrax[&&NHX:TOL=16174],prohyrax[&&NHX:EXT=Y:TOL=16175],gigantohyrax[&&NHX:EXT=Y:TOL=16176])procaviidae[&&NHX:TOL=16171])[&&NHX:TOL=16169])hyracoidea[&&NHX:TOL=15982],((prorastomus[&&NHX:EXT=Y:TOL=16831],(eotheroides[&&NHX:EXT=Y:TOL=16835],(sirenotherium[&&NHX:EXT=Y:TOL=16837],(miodugong[&&NHX:EXT=Y:TOL=16839],(protosiren[&&NHX:EXT=Y:TOL=16841],((prototherium[&&NHX:EXT=Y:TOL=16844],paralitherium[&&NHX:EXT=Y:TOL=16845],halitherium[&&NHX:EXT=Y:TOL=16846],crenatosiren[&&NHX:EXT=Y:TOL=16847],thalattosiren[&&NHX:EXT=Y:TOL=16848])halitheriinae[&&NHX:TOL=16843],((caribosiren[&&NHX:EXT=Y:TOL=16851],metaxytherium[&&NHX:EXT=Y:TOL=16852],dusisiren[&&NHX:EXT=Y:TOL=16853],hesperosiren[&&NHX:EXT=Y:TOL=16854],hydrodamalis gigas[&&NHX:EXT=Y:TOL=16855])hydrodamalinae[&&NHX:TOL=16850],((anomotherium[&&NHX:EXT=Y:TOL=16858],miosiren[&&NHX:EXT=Y:TOL=16859])miosireninae[&&NHX:TOL=16857],((((dioplotherium[&&NHX:EXT=Y:TOL=16864],rytiodus[&&NHX:EXT=Y:TOL=16865])[&&NHX:TOL=16863],xenosiren[&&NHX:EXT=Y:TOL=16866])[&&NHX:TOL=16862],corystosiren[&&NHX:EXT=Y:TOL=16867])rytiodontinae[&&NHX:TOL=16861],(indosiren[&&NHX:EXT=Y:TOL=16869],dugong dugon[&&NHX:TOL=16870])dugonginae[&&NHX:TOL=16868])[&&NHX:TOL=16860])[&&NHX:TOL=16856])[&&NHX:TOL=16849])[&&NHX:TOL=16842])[&&NHX:TOL=16840])[&&NHX:TOL=16838])[&&NHX:TOL=16836])dugongidae[&&NHX:TOL=16832],(potamosiren[&&NHX:EXT=Y:TOL=16872],ribodon[&&NHX:EXT=Y:TOL=16873],trichechus inunguis[&&NHX:TOL=16874],trichechus manatus[&&NHX:TOL=16875],trichechus senegalensis[&&NHX:TOL=16876])trichechidae[&&NHX:TOL=16833])sirenia[&&NHX:TOL=15984],desmostylia[&&NHX:EXT=Y:TOL=15985],embrythopoda[&&NHX:EXT=Y:TOL=15986],(numidotheriidae[&&NHX:EXT=Y:TOL=16443],moeritheriidae[&&NHX:EXT=Y:TOL=16444],barytheriidae[&&NHX:EXT=Y:TOL=16445],deinotheriidae[&&NHX:EXT=Y:TOL=16446],(mammutidae[&&NHX:EXT=Y:TOL=16448],gomphotheriidae[&&NHX:EXT=Y:TOL=16449],stegodontidae[&&NHX:EXT=Y:TOL=16450],(primelephas[&&NHX:EXT=Y:TOL=22664],(mammuthus columbi[&&NHX:EXT=Y:TOL=60660],mammuthus exilis[&&NHX:EXT=Y:TOL=60661],mammuthus jeffersonii[&&NHX:EXT=Y:TOL=60662],mammuthus lamarmorae[&&NHX:EXT=Y:TOL=60665],mammuthus meridionalis[&&NHX:EXT=Y:TOL=60663],mammuthus primigenius[&&NHX:EXT=Y:TOL=60664])mammuthus[&&NHX:EXT=Y:TOL=22665],elephas maximus[&&NHX:TOL=22666],loxodonta africana[&&NHX:TOL=22667])elephantidae[&&NHX:TOL=16451])elephantiformes[&&NHX:TOL=16447])proboscidea[&&NHX:TOL=15987])[&&NHX:TOL=15983])[&&NHX:TOL=15981])[&&NHX:TOL=15979])[&&NHX:TOL=15974])[&&NHX:TOL=15972])[&&NHX:TOL=15955])eutheria[&&NHX:TOL=15997])[&&NHX:TOL=15995])[&&NHX:TOL=15993])[&&NHX:TOL=15990])mammalia[&&NHX:TOL=15040],procynosuchidae[&&NHX:EXT=Y:TOL=15032],galesauridae[&&NHX:EXT=Y:TOL=15033],thrinaxodontidae[&&NHX:EXT=Y:TOL=15034],cynognathidae[&&NHX:EXT=Y:TOL=15035],gomphodonts[&&NHX:EXT=Y:TOL=15036],chiniquodontidae[&&NHX:EXT=Y:TOL=15037],probainognathidae[&&NHX:EXT=Y:TOL=15038],tritheledontidae[&&NHX:EXT=Y:TOL=15039])cynodontia[&&NHX:TOL=15030])[&&NHX:TOL=15028])theriodontia[&&NHX:TOL=15026])therapsida[&&NHX:TOL=14973])sphenacodontoidea[&&NHX:TOL=14971])[&&NHX:TOL=14969])[&&NHX:TOL=14967])[&&NHX:TOL=14965])sphenacodontia[&&NHX:TOL=14963])[&&NHX:TOL=14961])[&&NHX:TOL=14959])eupelycosauria[&&NHX:TOL=14957])synapsida[&&NHX:TOL=14845],((mesosauridae[&&NHX:EXT=Y:TOL=14848],(millerettidae[&&NHX:EXT=Y:TOL=14850],((acleistorhinus[&&NHX:EXT=Y:TOL=14853],lanthanosuchidae[&&NHX:EXT=Y:TOL=14854])[&&NHX:TOL=14852],(macroleter[&&NHX:EXT=Y:TOL=14856],nyctiphruretia[&&NHX:EXT=Y:TOL=14857],(pareiasauria[&&NHX:EXT=Y:TOL=14859],procolophonoidea[&&NHX:EXT=Y:TOL=14860])[&&NHX:TOL=14858],(proganochelys[&&NHX:EXT=Y:TOL=17618],(pleurodira[&&NHX:TOL=17620],(kayentachelys[&&NHX:EXT=Y:TOL=17622],((pleurosternidae[&&NHX:EXT=Y:TOL=17625],baenidae[&&NHX:EXT=Y:TOL=17626])paracryptodira[&&NHX:TOL=17624],(plesiochelyidae[&&NHX:EXT=Y:TOL=17628],(meiolaniidae[&&NHX:EXT=Y:TOL=17630],polycryptodira[&&NHX:TOL=17631])centrocryptodira[&&NHX:TOL=17629])eucryptodira[&&NHX:TOL=17627])selmacryptodira[&&NHX:TOL=17623])cryptodira[&&NHX:TOL=17621])casichelydia[&&NHX:TOL=17619])testudines[&&NHX:TOL=14861])[&&NHX:TOL=14855])[&&NHX:TOL=14851])[&&NHX:TOL=14849])anapsida[&&NHX:TOL=14847],(captorhinidae[&&NHX:EXT=Y:TOL=14863],(protorothyrididae[&&NHX:EXT=Y:TOL=14865],(((((((((((((((((((((((pisanosaurus[&&NHX:EXT=Y:TOL=15728],(lesothosaurus[&&NHX:EXT=Y:TOL=15730],((scutellosaurus[&&NHX:EXT=Y:TOL=15733],(emausaurus[&&NHX:EXT=Y:TOL=15735],(stegosauria[&&NHX:EXT=Y:TOL=15737],(scelidosaurus[&&NHX:EXT=Y:TOL=15777],(minmi[&&NHX:EXT=Y:TOL=15771],((struthiosaurus[&&NHX:EXT=Y:TOL=15796],(animantarx[&&NHX:EXT=Y:TOL=15798],edmontonia[&&NHX:EXT=Y:TOL=15799])[&&NHX:TOL=15797],(panoplosaurus[&&NHX:EXT=Y:TOL=15801],(sauropelta[&&NHX:EXT=Y:TOL=15803],silvisaurus[&&NHX:EXT=Y:TOL=15804])[&&NHX:TOL=15802])[&&NHX:TOL=15800])[&&NHX:TOL=15795],anoplosaurus[&&NHX:EXT=Y:TOL=15805],niobrarasaurus[&&NHX:EXT=Y:TOL=15806],nodosaurus[&&NHX:EXT=Y:TOL=15807],pawpawsaurus[&&NHX:EXT=Y:TOL=15808],prioconodon[&&NHX:EXT=Y:TOL=15809],stegopelta[&&NHX:EXT=Y:TOL=15810],texasetes[&&NHX:EXT=Y:TOL=15811])nodosauridae[&&NHX:EXT=Y:TOL=15772],(((gargoyleosaurus[&&NHX:EXT=Y:TOL=15814],(hylaeosaurus[&&NHX:EXT=Y:TOL=15816],mymoorapelta[&&NHX:EXT=Y:TOL=15817])[&&NHX:TOL=15815])[&&NHX:TOL=15813],(gastonia[&&NHX:EXT=Y:TOL=15819],(hoplitosaurus[&&NHX:EXT=Y:TOL=15821],polacanthus[&&NHX:EXT=Y:TOL=15822])[&&NHX:TOL=15820])[&&NHX:TOL=15818])polacanthidae[&&NHX:EXT=Y:TOL=15774],((cedarpelta[&&NHX:EXT=Y:TOL=15780],(shamosaurus[&&NHX:EXT=Y:TOL=15782],(ankylosaurus[&&NHX:EXT=Y:TOL=15784],((saichania[&&NHX:EXT=Y:TOL=15787],tarchia[&&NHX:EXT=Y:TOL=15788])[&&NHX:TOL=15786],(euoplocephalus[&&NHX:EXT=Y:TOL=15790],pinacosaurus[&&NHX:EXT=Y:TOL=15791])[&&NHX:TOL=15789])[&&NHX:TOL=15785])[&&NHX:TOL=15783])[&&NHX:TOL=15781])[&&NHX:TOL=15779],nodocephalosaurus[&&NHX:EXT=Y:TOL=15792],talarurus[&&NHX:EXT=Y:TOL=15793],tsagantegia[&&NHX:EXT=Y:TOL=15794])ankylosauridae[&&NHX:EXT=Y:TOL=15775])[&&NHX:TOL=15773])ankylosauria[&&NHX:EXT=Y:TOL=15778])ankylosauromorpha[&&NHX:EXT=Y:TOL=15738])[&&NHX:TOL=15736])[&&NHX:TOL=15734])thyreophora[&&NHX:TOL=15732],(ornithopoda[&&NHX:EXT=Y:TOL=15740],(pachycephalosauria[&&NHX:EXT=Y:TOL=15742],ceratopsia[&&NHX:EXT=Y:TOL=15743])marginocephalia[&&NHX:TOL=15741])neornithischia[&&NHX:TOL=15739])[&&NHX:TOL=15731])[&&NHX:TOL=15729])ornithischia[&&NHX:EXT=Y:TOL=15723],(((riojasaurus[&&NHX:EXT=Y:TOL=15746],((yunnanosaurus[&&NHX:EXT=Y:TOL=15749],massospondylus[&&NHX:EXT=Y:TOL=15750])[&&NHX:TOL=15748],(lufengosaurus[&&NHX:EXT=Y:TOL=15752],(sellosaurus[&&NHX:EXT=Y:TOL=15754],plateosaurus[&&NHX:EXT=Y:TOL=15755])[&&NHX:TOL=15753])[&&NHX:TOL=15751])[&&NHX:TOL=15747])prosauropoda[&&NHX:TOL=15745],sauropoda[&&NHX:EXT=Y:TOL=15756])sauropodomorpha[&&NHX:EXT=Y:TOL=15725],(eoraptor[&&NHX:EXT=Y:TOL=15758],(herrerasauridae[&&NHX:EXT=Y:TOL=15760],(ceratosauria[&&NHX:EXT=Y:TOL=15762],((torvosauridae[&&NHX:EXT=Y:TOL=15765],spinosauridae[&&NHX:EXT=Y:TOL=15766])[&&NHX:TOL=15764],(allosauroidea[&&NHX:EXT=Y:TOL=15768],(ornitholestes[&&NHX:EXT=Y:TOL=15705],compsognathidae[&&NHX:EXT=Y:TOL=15706],(((alvarezsauridae[&&NHX:EXT=Y:TOL=15710],ornithomimidae[&&NHX:EXT=Y:TOL=15711])[&&NHX:TOL=15709],therizinosauridae[&&NHX:EXT=Y:TOL=15712])[&&NHX:TOL=15708],(((stokesosaurus clevelandi[&&NHX:EXT=Y:TOL=15892],itemirus medullaris[&&NHX:EXT=Y:TOL=15893])[&&NHX:TOL=15891],labocania anomala[&&NHX:EXT=Y:TOL=15894],siamotyrannus isanensis[&&NHX:EXT=Y:TOL=15895],((aublysodon molnari[&&NHX:EXT=Y:TOL=15874],alectrosaurus olseni[&&NHX:EXT=Y:TOL=15875],kirtland shale aublysodontine[&&NHX:EXT=Y:TOL=15876])aublysodontinae[&&NHX:EXT=Y:TOL=15873],(alioramus remotus[&&NHX:EXT=Y:TOL=15878],(shanshanosaurus houyanshanensis[&&NHX:EXT=Y:TOL=15880],(albertosaurus sarcophagus[&&NHX:EXT=Y:TOL=15882],gorgosaurus libratus[&&NHX:EXT=Y:TOL=15883],(daspletosaurus torosus[&&NHX:EXT=Y:TOL=15885],two medicine tyrannosaurine[&&NHX:EXT=Y:TOL=15886],(tarbosaurus bataar[&&NHX:EXT=Y:TOL=15888],tyrannosaurus rex[&&NHX:EXT=Y:TOL=15889])[&&NHX:EXT=Y:TOL=15887])[&&NHX:EXT=Y:TOL=15884])[&&NHX:EXT=Y:TOL=15881])[&&NHX:EXT=Y:TOL=15879])tyrannosaurinae[&&NHX:EXT=Y:TOL=15877])tyrannosauridae[&&NHX:EXT=Y:TOL=15896])tyrannosauroidea[&&NHX:EXT=Y:TOL=15714],(oviraptorosauria[&&NHX:EXT=Y:TOL=15716],((dromaeosauridae[&&NHX:EXT=Y:TOL=15719],troodontidae[&&NHX:EXT=Y:TOL=15720])[&&NHX:TOL=15718],(archaeopteryx[&&NHX:EXT=Y:TOL=15824],(confuciusornithidae[&&NHX:EXT=Y:TOL=15826],(enantiornithes[&&NHX:EXT=Y:TOL=15828],((patagopteryx[&&NHX:EXT=Y:TOL=15831],hesperornithiformes[&&NHX:EXT=Y:TOL=15832],ichthyornithiformes[&&NHX:EXT=Y:TOL=15833])[&&NHX:TOL=15830],(((struthio camelus[&&NHX:TOL=26289],struthio molybdophanes[&&NHX:TOL=100853])struthio[&&NHX:TOL=100852],(((((casuarius casuarius[&&NHX:TOL=57549],casuarius bennetti[&&NHX:TOL=57550],casuarius unappendiculatus[&&NHX:TOL=57552])casuariidae[&&NHX:TOL=26287],dromaius novaehollandiae[&&NHX:TOL=26288])[&&NHX:TOL=26286],((apteryx owenii[&&NHX:TOL=57547],apteryx haastii[&&NHX:TOL=57548])spotted kiwis[&&NHX:TOL=57571],((apteryx rowi[&&NHX:TOL=57573],apteryx mantelli[&&NHX:TOL=57574])[&&NHX:TOL=57572],apteryx australis[&&NHX:TOL=57575])brown kiwis[&&NHX:TOL=57546])apterygidae[&&NHX:TOL=26285])[&&NHX:TOL=57570],(mullerornis[&&NHX:EXT=Y:TOL=57563],aepyornis[&&NHX:EXT=Y:TOL=57564])aepyornithidae[&&NHX:EXT=Y:TOL=57562])[&&NHX:TOL=57627],(rhea americana[&&NHX:TOL=57553],pterocnemia pennata[&&NHX:TOL=57554])rheidae[&&NHX:TOL=26290],((((tinamotis pentlandii[&&NHX:TOL=57544],tinamotis ingoufi[&&NHX:TOL=57545])tinamotis[&&NHX:TOL=57543],(eudromia elegans[&&NHX:TOL=57541],eudromia formosa[&&NHX:TOL=57542])eudromia[&&NHX:TOL=57540])[&&NHX:TOL=57539],(((taoniscus nanus[&&NHX:TOL=57512],((((nothura chacoensis[&&NHX:TOL=57519],nothura maculosa[&&NHX:TOL=57522])[&&NHX:TOL=57623],nothura darwinii[&&NHX:TOL=57521])[&&NHX:TOL=57518],nothura minor[&&NHX:TOL=57517])[&&NHX:TOL=57622],nothura boraquira[&&NHX:TOL=57516])nothura[&&NHX:TOL=57514])[&&NHX:TOL=57620],((((nothoprocta curvirostris[&&NHX:TOL=57529],nothoprocta perdicaria[&&NHX:TOL=57530])[&&NHX:TOL=57528],(nothoprocta pentlandii[&&NHX:TOL=57532],nothoprocta taczanowskii[&&NHX:TOL=57525])[&&NHX:TOL=57625])[&&NHX:TOL=57527],(nothoprocta ornata[&&NHX:TOL=57535],nothoprocta kalinowskii[&&NHX:TOL=57536])[&&NHX:TOL=57534])[&&NHX:TOL=57624],nothoprocta cinerascens[&&NHX:TOL=57533])nothoprocta[&&NHX:TOL=57524])[&&NHX:TOL=57619],(rhynchotus rufescens[&&NHX:TOL=57538],rhynchotus maculicollis[&&NHX:TOL=94857])rhynchotus[&&NHX:TOL=100851])[&&NHX:TOL=57618])nothurinae aridland tinamous[&&NHX:TOL=57523],((((((((((crypturellus transfasciatus[&&NHX:TOL=57509],crypturellus cinnamomeus[&&NHX:TOL=57510])[&&NHX:TOL=57508],crypturellus undulatus[&&NHX:TOL=57474])[&&NHX:TOL=57613],crypturellus strigulosus[&&NHX:TOL=57493])[&&NHX:TOL=57612],(((((((crypturellus bartletti[&&NHX:TOL=57482],crypturellus brevirostris[&&NHX:TOL=57483])[&&NHX:TOL=57481],crypturellus casiquiare[&&NHX:TOL=57484])[&&NHX:TOL=57480],crypturellus variegatus[&&NHX:TOL=57485],crypturellus noctivagus[&&NHX:TOL=57486])[&&NHX:TOL=57479],crypturellus erythropus[&&NHX:TOL=57487])[&&NHX:TOL=57478],crypturellus duidae[&&NHX:TOL=57488])[&&NHX:TOL=57477],crypturellus atrocapillus[&&NHX:TOL=57490])[&&NHX:TOL=57611],crypturellus soui[&&NHX:TOL=57506])[&&NHX:TOL=57610])[&&NHX:TOL=57609],crypturellus boucardi[&&NHX:TOL=57496])[&&NHX:TOL=57608],((crypturellus cinereus[&&NHX:TOL=57504],crypturellus berlepschi[&&NHX:TOL=57505])[&&NHX:TOL=57503],crypturellus ptaritepui[&&NHX:TOL=57507])[&&NHX:TOL=57614])[&&NHX:TOL=57607],((crypturellus parvirostris[&&NHX:TOL=57500],crypturellus tataupa[&&NHX:TOL=57501])[&&NHX:TOL=57499],crypturellus obsoletus[&&NHX:TOL=57502])[&&NHX:TOL=57498])[&&NHX:TOL=57606],crypturellus kerriae[&&NHX:TOL=57495])crypturellus[&&NHX:TOL=57473],((tinamus major[&&NHX:TOL=57468],tinamus guttatus[&&NHX:TOL=57470])[&&NHX:TOL=57615],((tinamus solitarius[&&NHX:TOL=57467],tinamus tao[&&NHX:TOL=57469])[&&NHX:TOL=57617],tinamus osgoodi[&&NHX:TOL=57471])[&&NHX:TOL=57616])tinamus[&&NHX:TOL=57464])[&&NHX:TOL=57605],(nothocercus julius[&&NHX:TOL=57459],(nothocercus nigrocapillus[&&NHX:TOL=57461],nothocercus bonapartei[&&NHX:TOL=57462])[&&NHX:TOL=57460])nothocercus[&&NHX:TOL=57458])tinaminae forest tinamous[&&NHX:TOL=57621])tinamiformes[&&NHX:TOL=15838],(((pachyornis[&&NHX:EXT=Y:TOL=57560],((euryapteryx[&&NHX:EXT=Y:TOL=57559],emeus[&&NHX:EXT=Y:TOL=57558])[&&NHX:TOL=57568],anomalopteryx[&&NHX:EXT=Y:TOL=57556])[&&NHX:TOL=57567])[&&NHX:TOL=57566],dinornis[&&NHX:EXT=Y:TOL=57561])[&&NHX:TOL=57565],megalapteryx[&&NHX:EXT=Y:TOL=57557])dinornithidae[&&NHX:EXT=Y:TOL=57555])[&&NHX:TOL=15839])palaeognathae[&&NHX:TOL=15837],((((((dendrocygna viduata[&&NHX:TOL=89126],dendrocygna autumnalis[&&NHX:TOL=89127],dendrocygna guttata[&&NHX:TOL=89128],dendrocygna arborea[&&NHX:TOL=89129],dendrocygna bicolor[&&NHX:TOL=89130],dendrocygna eytoni[&&NHX:TOL=89131],dendrocygna arcuata[&&NHX:TOL=89132],dendrocygna javanica[&&NHX:TOL=89133])dendrocygna[&&NHX:TOL=89125],thalassornis leuconotus[&&NHX:TOL=89134],cereopsis novaehollandiae[&&NHX:TOL=89135],(anser cygnoides[&&NHX:TOL=89137],anser fabalis[&&NHX:TOL=89138],anser serrirostris[&&NHX:TOL=129472],anser brachyrhynchus[&&NHX:TOL=89139],anser anser[&&NHX:TOL=89140],anser albifrons[&&NHX:TOL=89141],anser erythropus[&&NHX:TOL=89142],anser indicus[&&NHX:TOL=89143])anser[&&NHX:TOL=89136],(chen caerulescens[&&NHX:TOL=89145],chen rossii[&&NHX:TOL=89146],chen canagica[&&NHX:TOL=89147])chen[&&NHX:TOL=89144],(branta canadensis[&&NHX:TOL=89149],branta hutchinsii[&&NHX:TOL=89150],branta sandvicensis[&&NHX:TOL=89151],branta bernicla[&&NHX:TOL=89152],branta leucopsis[&&NHX:TOL=89153],branta ruficollis[&&NHX:TOL=89154])branta[&&NHX:TOL=89148],coscoroba coscoroba[&&NHX:TOL=89155],(cygnus atratus[&&NHX:TOL=89157],cygnus melancoryphus[&&NHX:TOL=89158],cygnus olor[&&NHX:TOL=89159],cygnus buccinator[&&NHX:TOL=89160],cygnus columbianus[&&NHX:TOL=89161],cygnus cygnus[&&NHX:TOL=89162])cygnus[&&NHX:TOL=89156],stictonetta naevosa[&&NHX:TOL=89163],hymenolaimus malacorhynchos[&&NHX:TOL=89164],(tachyeres patachonicus[&&NHX:TOL=89166],tachyeres pteneres[&&NHX:TOL=89167],tachyeres brachypterus[&&NHX:TOL=89168],tachyeres leucocephalus[&&NHX:TOL=89169])tachyeres[&&NHX:TOL=89165],merganetta armata[&&NHX:TOL=89170],plectropterus gambensis[&&NHX:TOL=89171],(sarkidiornis melanotos[&&NHX:TOL=89173],sarkidiornis sylvicola[&&NHX:TOL=89174])sarkidiornis[&&NHX:TOL=89172],cyanochen cyanoptera[&&NHX:TOL=89175],alopochen aegyptiaca[&&NHX:TOL=89176],neochen jubata[&&NHX:TOL=89177],(chloephaga melanoptera[&&NHX:TOL=89179],chloephaga picta[&&NHX:TOL=89180],chloephaga hybrida[&&NHX:TOL=89181],chloephaga poliocephala[&&NHX:TOL=89182],chloephaga rubidiceps[&&NHX:TOL=89183])chloephaga[&&NHX:TOL=89178],(tadorna tadorna[&&NHX:TOL=89185],tadorna radjah[&&NHX:TOL=89186],tadorna ferruginea[&&NHX:TOL=89187],tadorna cana[&&NHX:TOL=89188],tadorna tadornoides[&&NHX:TOL=89189],tadorna variegata[&&NHX:TOL=89190])tadorna[&&NHX:TOL=89184],malacorhynchus membranaceus[&&NHX:TOL=89191],salvadorina waigiuensis[&&NHX:TOL=89192],cairina moschata[&&NHX:TOL=89193],asarcornis scutulata[&&NHX:TOL=89194],pteronetta hartlaubii[&&NHX:TOL=89195],(aix sponsa[&&NHX:TOL=89198],aix galericulata[&&NHX:TOL=89197])aix[&&NHX:TOL=89196],chenonetta jubata[&&NHX:TOL=89199],(nettapus auritus[&&NHX:TOL=89201],nettapus coromandelianus[&&NHX:TOL=89202],nettapus pulchellus[&&NHX:TOL=89203])nettapus[&&NHX:TOL=89200],amazonetta brasiliensis[&&NHX:TOL=89204],callonetta leucophrys[&&NHX:TOL=89205],lophonetta specularioides[&&NHX:TOL=89206],speculanas specularis[&&NHX:TOL=89207],(anas capensis[&&NHX:TOL=89209],anas strepera[&&NHX:TOL=89210],anas falcata[&&NHX:TOL=89211],anas sibilatrix[&&NHX:TOL=89212],anas penelope[&&NHX:TOL=89213],anas americana[&&NHX:TOL=89214],anas sparsa[&&NHX:TOL=89215],anas rubripes[&&NHX:TOL=89216],anas platyrhynchos[&&NHX:TOL=89217],anas diazi[&&NHX:TOL=89218],anas fulvigula[&&NHX:TOL=89219],anas wyvilliana[&&NHX:TOL=89220],anas laysanensis[&&NHX:TOL=89221],anas luzonica[&&NHX:TOL=89222],anas superciliosa[&&NHX:TOL=89223],anas poecilorhyncha[&&NHX:TOL=89224],anas zonorhyncha[&&NHX:TOL=89225],anas undulata[&&NHX:TOL=89226],anas melleri[&&NHX:TOL=89227],anas discors[&&NHX:TOL=89228],anas cyanoptera[&&NHX:TOL=89229],anas smithii[&&NHX:TOL=89230],anas platalea[&&NHX:TOL=89231],anas rhynchotis[&&NHX:TOL=89232],anas clypeata[&&NHX:TOL=89233],anas bernieri[&&NHX:TOL=89234],anas gibberifrons[&&NHX:TOL=89235],anas albogularis[&&NHX:TOL=129672],anas gracilis[&&NHX:TOL=89236],anas castanea[&&NHX:TOL=89237],anas aucklandica[&&NHX:TOL=89238],anas nesiotis[&&NHX:TOL=129473],anas chlorotis[&&NHX:TOL=129474],anas bahamensis[&&NHX:TOL=89239],anas erythrorhyncha[&&NHX:TOL=89240],anas flavirostris[&&NHX:TOL=89241],anas andium[&&NHX:TOL=89242],anas georgica[&&NHX:TOL=89243],anas acuta[&&NHX:TOL=89244],anas eatoni[&&NHX:TOL=89245],anas querquedula[&&NHX:TOL=89246],anas formosa[&&NHX:TOL=89247],anas crecca[&&NHX:TOL=89248],anas carolinensis[&&NHX:TOL=89249],anas versicolor[&&NHX:TOL=89250],anas puna[&&NHX:TOL=89251],anas hottentota[&&NHX:TOL=89252])anas[&&NHX:TOL=89208],marmaronetta angustirostris[&&NHX:TOL=89253],(netta rufina[&&NHX:TOL=89255],netta peposaca[&&NHX:TOL=89256],netta erythrophthalma[&&NHX:TOL=89257])netta[&&NHX:TOL=89254],(aythya valisineria[&&NHX:TOL=89259],aythya americana[&&NHX:TOL=89260],aythya ferina[&&NHX:TOL=89261],aythya australis[&&NHX:TOL=89262],aythya innotata[&&NHX:TOL=89263],aythya baeri[&&NHX:TOL=89264],aythya nyroca[&&NHX:TOL=89265],aythya novaeseelandiae[&&NHX:TOL=89266],aythya collaris[&&NHX:TOL=89267],aythya fuligula[&&NHX:TOL=89268],aythya marila[&&NHX:TOL=89269],aythya affinis[&&NHX:TOL=89270])aythya[&&NHX:TOL=89258],polysticta stelleri[&&NHX:TOL=89271],(somateria fischeri[&&NHX:TOL=89273],somateria spectabilis[&&NHX:TOL=89274],somateria mollissima[&&NHX:TOL=89275])somateria[&&NHX:TOL=89272],histrionicus histrionicus[&&NHX:TOL=89276],(melanitta perspicillata[&&NHX:TOL=89278],melanitta fusca[&&NHX:TOL=89279],melanitta deglandi[&&NHX:TOL=89280],melanitta nigra[&&NHX:TOL=89281],melanitta americana[&&NHX:TOL=89282])melanitta[&&NHX:TOL=89277],clangula hyemalis[&&NHX:TOL=89283],(bucephala albeola[&&NHX:TOL=89285],bucephala clangula[&&NHX:TOL=89286],bucephala islandica[&&NHX:TOL=89287])bucephala[&&NHX:TOL=89284],mergellus albellus[&&NHX:TOL=89288],lophodytes cucullatus[&&NHX:TOL=89289],(mergus octosetaceus[&&NHX:TOL=89291],mergus merganser[&&NHX:TOL=89292],mergus serrator[&&NHX:TOL=89293],mergus squamatus[&&NHX:TOL=89294])mergus[&&NHX:TOL=89290],heteronetta atricapilla[&&NHX:TOL=89295],nomonyx dominicus[&&NHX:TOL=89296],(oxyura jamaicensis[&&NHX:TOL=89298],oxyura ferruginea[&&NHX:TOL=89299],oxyura vittata[&&NHX:TOL=89300],oxyura australis[&&NHX:TOL=89301],oxyura maccoa[&&NHX:TOL=89302],oxyura leucocephala[&&NHX:TOL=89303])oxyura[&&NHX:TOL=89297],biziura lobata[&&NHX:TOL=89304])anatidae[&&NHX:TOL=26293],anseranas semipalmata[&&NHX:TOL=26294])[&&NHX:TOL=26292],(anhima cornuta[&&NHX:TOL=89122],chauna chavaria[&&NHX:TOL=89123],chauna torquata[&&NHX:TOL=89124])anhimidae[&&NHX:TOL=26295])anseriformes[&&NHX:TOL=15841],((((((aepypodius arfakianus[&&NHX:TOL=57632],aepypodius bruijnii[&&NHX:TOL=57633])aepypodius[&&NHX:TOL=57631],alectura lathami[&&NHX:TOL=57634])[&&NHX:TOL=57630],leipoa ocellata[&&NHX:TOL=57635],(talegalla cuvieri[&&NHX:TOL=57637],talegalla fuscirostris[&&NHX:TOL=57638],talegalla jobiensis[&&NHX:TOL=57639])talegalla[&&NHX:TOL=57636])mound builders[&&NHX:TOL=57629],macrocephalon maleo[&&NHX:TOL=57640])[&&NHX:TOL=57628],((megapodius laperouse[&&NHX:TOL=57643],megapodius nicobariensis[&&NHX:TOL=57644],megapodius bernsteinii[&&NHX:TOL=57645],(megapodius tenimberensis[&&NHX:TOL=57647],megapodius cumingii[&&NHX:TOL=57648])[&&NHX:TOL=57646],megapodius geelvinkianus[&&NHX:TOL=57649],((((megapodius forstenii[&&NHX:TOL=57654],megapodius freycinet[&&NHX:TOL=57655])[&&NHX:TOL=57653],megapodius decollatus[&&NHX:TOL=57656])[&&NHX:TOL=57652],(megapodius eremita[&&NHX:TOL=57658],megapodius reinwardt[&&NHX:TOL=57659])[&&NHX:TOL=57657])[&&NHX:TOL=57651],(megapodius pritchardii[&&NHX:TOL=57661],megapodius layardi[&&NHX:TOL=57662])[&&NHX:TOL=57660])[&&NHX:TOL=57650])megapodius[&&NHX:TOL=57642],eulipoa wallacei[&&NHX:TOL=57663])[&&NHX:TOL=57641])megapodiidae[&&NHX:TOL=26297],((((((pauxi pauxi[&&NHX:TOL=88652],pauxi unicornis[&&NHX:TOL=88653])pauxi[&&NHX:TOL=88651],(mitu tomentosum[&&NHX:TOL=88647],mitu salvini[&&NHX:TOL=88648],mitu tuberosum[&&NHX:TOL=88649],mitu mitu[&&NHX:TOL=88650])mitu[&&NHX:TOL=88646],nothocrax urumutum[&&NHX:TOL=88645])[&&NHX:TOL=103222],(crax rubra[&&NHX:TOL=88655],crax alberti[&&NHX:TOL=88656],crax daubentoni[&&NHX:TOL=88657],crax alector[&&NHX:TOL=88658],crax globulosa[&&NHX:TOL=88659],crax fasciolata[&&NHX:TOL=88660],crax blumenbachii[&&NHX:TOL=88661])crax[&&NHX:TOL=88654])[&&NHX:TOL=103221],oreophasis derbianus[&&NHX:TOL=88644],(ortalis vetula[&&NHX:TOL=88604],ortalis cinereiceps[&&NHX:TOL=88605],ortalis garrula[&&NHX:TOL=88606],ortalis ruficauda[&&NHX:TOL=88607],ortalis erythroptera[&&NHX:TOL=88608],ortalis wagleri[&&NHX:TOL=88609],ortalis poliocephala[&&NHX:TOL=88610],ortalis canicollis[&&NHX:TOL=88611],ortalis leucogastra[&&NHX:TOL=88612],ortalis guttata[&&NHX:TOL=88613],ortalis araucuan[&&NHX:TOL=88614],ortalis squamata[&&NHX:TOL=88615],ortalis columbiana[&&NHX:TOL=88616],ortalis motmot[&&NHX:TOL=88617],ortalis ruficeps[&&NHX:TOL=88618],ortalis superciliaris[&&NHX:TOL=88619])ortalis[&&NHX:TOL=88603])[&&NHX:TOL=103220],(((aburria aburri[&&NHX:TOL=88639],(pipile pipile[&&NHX:TOL=88637],pipile jacutinga[&&NHX:TOL=88638],pipile cumanensis[&&NHX:TOL=129451],pipile cujubi[&&NHX:TOL=129452])pipile[&&NHX:TOL=88636])[&&NHX:TOL=103224],(penelope argyrotis[&&NHX:TOL=88621],penelope barbata[&&NHX:TOL=88622],penelope ortoni[&&NHX:TOL=88623],penelope montagnii[&&NHX:TOL=88624],penelope marail[&&NHX:TOL=88625],penelope superciliaris[&&NHX:TOL=88626],penelope dabbenei[&&NHX:TOL=88627],penelope purpurascens[&&NHX:TOL=88628],penelope perspicax[&&NHX:TOL=88629],penelope albipennis[&&NHX:TOL=88630],penelope jacquacu[&&NHX:TOL=88631],penelope obscura[&&NHX:TOL=88632],penelope pileata[&&NHX:TOL=88633],penelope ochrogaster[&&NHX:TOL=88634],penelope jacucaca[&&NHX:TOL=88635])penelope[&&NHX:TOL=88620])[&&NHX:TOL=103223],penelopina nigra[&&NHX:TOL=88643],(chamaepetes goudotii[&&NHX:TOL=88641],chamaepetes unicolor[&&NHX:TOL=88642])chamaepetes[&&NHX:TOL=88640])[&&NHX:TOL=103219])cracidae[&&NHX:TOL=26299],(((((((bambusicola fytchii[&&NHX:TOL=88705],bambusicola thoracicus[&&NHX:TOL=88706])bambusicola[&&NHX:TOL=57160],(gallus gallus[&&NHX:TOL=88707],gallus sonneratii[&&NHX:TOL=88708],gallus lafayetii[&&NHX:TOL=88709],gallus varius[&&NHX:TOL=88710])gallus[&&NHX:TOL=57162])[&&NHX:TOL=57159],(francolinus francolinus[&&NHX:TOL=88711],francolinus pictus[&&NHX:TOL=88712],francolinus pintadeanus[&&NHX:TOL=88713],francolinus pondicerianus[&&NHX:TOL=88714],francolinus gularis[&&NHX:TOL=88715])francolinus[&&NHX:TOL=57164])[&&NHX:TOL=57158],(((bonasa umbellus[&&NHX:TOL=57172],(((((dendragapus obscurus[&&NHX:TOL=129453],dendragapus fuliginosus[&&NHX:TOL=129454])dendragapus[&&NHX:TOL=57179],(tympanuchus phasianellus[&&NHX:TOL=88718],tympanuchus pallidicinctus[&&NHX:TOL=88719],tympanuchus cupido[&&NHX:TOL=88720])tympanuchus[&&NHX:TOL=57184])[&&NHX:TOL=57178],(centrocercus urophasianus[&&NHX:TOL=88716],centrocercus minimus[&&NHX:TOL=88717])centrocercus[&&NHX:TOL=57242])[&&NHX:TOL=57176],((falcipennis falcipennis[&&NHX:TOL=88721],falcipennis canadensis[&&NHX:TOL=88722])falcipennis[&&NHX:TOL=57189],(lyrurus mlokosiewiczi[&&NHX:TOL=88833],lyrurus tetrix[&&NHX:TOL=88834])lyrurus[&&NHX:TOL=88832])[&&NHX:TOL=57186])[&&NHX:TOL=57174],(lagopus lagopus[&&NHX:TOL=88728],lagopus muta[&&NHX:TOL=88727],lagopus leucura[&&NHX:TOL=88726])lagopus[&&NHX:TOL=57201])[&&NHX:TOL=57173])[&&NHX:TOL=57167],(meleagris gallopavo[&&NHX:TOL=88729],meleagris ocellata[&&NHX:TOL=88730])meleagris[&&NHX:TOL=57202])[&&NHX:TOL=57166],((alectoris graeca[&&NHX:TOL=88763],alectoris chukar[&&NHX:TOL=88764],alectoris magna[&&NHX:TOL=88765],alectoris philbyi[&&NHX:TOL=88766],alectoris barbara[&&NHX:TOL=88767],alectoris rufa[&&NHX:TOL=88768],alectoris melanocephala[&&NHX:TOL=88769])alectoris[&&NHX:TOL=57428],pucrasia macrolopha[&&NHX:TOL=57441],(polyplectron chalcurum[&&NHX:TOL=88770],polyplectron inopinatum[&&NHX:TOL=88771],polyplectron germaini[&&NHX:TOL=88772],polyplectron bicalcaratum[&&NHX:TOL=88773],polyplectron malacense[&&NHX:TOL=88774],polyplectron schleiermacheri[&&NHX:TOL=88775],polyplectron napoleonis[&&NHX:TOL=88776])polyplectron[&&NHX:TOL=57448],(afropavo congensis[&&NHX:TOL=57451],(pavo cristatus[&&NHX:TOL=88761],pavo muticus[&&NHX:TOL=88762])pavo[&&NHX:TOL=57452])[&&NHX:TOL=57457],((((lophura leucomelanos[&&NHX:TOL=88743],lophura nycthemera[&&NHX:TOL=88744],lophura edwardsi[&&NHX:TOL=88745],lophura hatinhensis[&&NHX:TOL=88746],lophura swinhoii[&&NHX:TOL=88747],lophura hoogerwerfi[&&NHX:TOL=88748],lophura inornata[&&NHX:TOL=88749],lophura erythrophthalma[&&NHX:TOL=88750],lophura ignita[&&NHX:TOL=88751],lophura diardi[&&NHX:TOL=88752],lophura bulweri[&&NHX:TOL=88753])lophura[&&NHX:TOL=57443],(crossoptilon crossoptilon[&&NHX:TOL=88739],crossoptilon harmani[&&NHX:TOL=88740],crossoptilon mantchuricum[&&NHX:TOL=88741],crossoptilon auritum[&&NHX:TOL=88742])crossoptilon[&&NHX:TOL=57444],catreus wallichi[&&NHX:TOL=57445],(chrysolophus pictus[&&NHX:TOL=88754],chrysolophus amherstiae[&&NHX:TOL=88755])chrysolophus[&&NHX:TOL=57447],((syrmaticus ellioti[&&NHX:TOL=88734],syrmaticus humiae[&&NHX:TOL=88735],syrmaticus mikado[&&NHX:TOL=88736],syrmaticus soemmerringii[&&NHX:TOL=88737],syrmaticus reevesii[&&NHX:TOL=88738])syrmaticus[&&NHX:TOL=57446],(phasianus colchicus[&&NHX:TOL=57208],phasianus versicolor[&&NHX:TOL=129471])phasianus[&&NHX:TOL=129470])[&&NHX:TOL=57456])[&&NHX:TOL=57455],(perdix perdix[&&NHX:TOL=88731],perdix dauurica[&&NHX:TOL=88732],perdix hodgsoniae[&&NHX:TOL=88733])perdix[&&NHX:TOL=57207])[&&NHX:TOL=57204],(tragopan melanocephalus[&&NHX:TOL=88756],tragopan satyra[&&NHX:TOL=88757],tragopan blythii[&&NHX:TOL=88758],tragopan temminckii[&&NHX:TOL=88759],tragopan caboti[&&NHX:TOL=88760])tragopan[&&NHX:TOL=57209])[&&NHX:TOL=57203])[&&NHX:TOL=57454])[&&NHX:TOL=57165])[&&NHX:TOL=57157],(ammoperdix griseogularis[&&NHX:TOL=88785],ammoperdix heyi[&&NHX:TOL=88786])ammoperdix[&&NHX:TOL=57425],anurophasis monorthonyx[&&NHX:TOL=57432],(arborophila torqueola[&&NHX:TOL=88800],arborophila rufogularis[&&NHX:TOL=88801],arborophila atrogularis[&&NHX:TOL=88802],arborophila crudigularis[&&NHX:TOL=88803],arborophila mandellii[&&NHX:TOL=88804],arborophila brunneopectus[&&NHX:TOL=88805],arborophila rufipectus[&&NHX:TOL=88806],arborophila gingica[&&NHX:TOL=88807],arborophila davidi[&&NHX:TOL=88808],arborophila cambodiana[&&NHX:TOL=88809],arborophila diversa[&&NHX:TOL=88810],arborophila campbelli[&&NHX:TOL=88811],arborophila rolli[&&NHX:TOL=88812],arborophila sumatrana[&&NHX:TOL=88813],arborophila orientalis[&&NHX:TOL=88814],arborophila javanica[&&NHX:TOL=88815],arborophila rubrirostris[&&NHX:TOL=88816],arborophila hyperythra[&&NHX:TOL=88817],arborophila ardens[&&NHX:TOL=88818],arborophila charltonii[&&NHX:TOL=88819],arborophila chloropus[&&NHX:TOL=88820])arborophila[&&NHX:TOL=57434],argusianus argus[&&NHX:TOL=57450],caloperdix oculeus[&&NHX:TOL=57435],(coturnix coturnix[&&NHX:TOL=88777],coturnix japonica[&&NHX:TOL=88778],coturnix coromandelica[&&NHX:TOL=88779],coturnix delegorguei[&&NHX:TOL=88780],coturnix pectoralis[&&NHX:TOL=88781],coturnix ypsilophora[&&NHX:TOL=88782])coturnix[&&NHX:TOL=57212],(excalfactoria adansonii[&&NHX:TOL=88784],excalfactoria chinensis[&&NHX:TOL=88783])excalfactoria[&&NHX:TOL=135894],dendroperdix sephaena[&&NHX:TOL=88848],(galloperdix spadicea[&&NHX:TOL=88823],galloperdix lunulata[&&NHX:TOL=88824],galloperdix bicalcarata[&&NHX:TOL=88825])galloperdix[&&NHX:TOL=57439],haematortyx sanguiniceps[&&NHX:TOL=57436],ithaginis cruentus[&&NHX:TOL=57440],lerwa lerwa[&&NHX:TOL=57424],(lophophorus impejanus[&&NHX:TOL=88826],lophophorus sclateri[&&NHX:TOL=88827],lophophorus lhuysii[&&NHX:TOL=88828])lophophorus[&&NHX:TOL=57442],margaroperdix madagascariensis[&&NHX:TOL=57430],melanoperdix niger[&&NHX:TOL=57431],(peliperdix lathami[&&NHX:TOL=88836],peliperdix coqui[&&NHX:TOL=88837],peliperdix albogularis[&&NHX:TOL=88838],peliperdix schlegelii[&&NHX:TOL=88839])peliperdix[&&NHX:TOL=88835],(perdicula asiatica[&&NHX:TOL=88796],perdicula argoondah[&&NHX:TOL=88797],perdicula erythrorhyncha[&&NHX:TOL=88798],perdicula manipurensis[&&NHX:TOL=88799])perdicula[&&NHX:TOL=57433],(pternistis squamatus[&&NHX:TOL=88850],pternistis ahantensis[&&NHX:TOL=88851],pternistis griseostriatus[&&NHX:TOL=88852],pternistis hildebrandti[&&NHX:TOL=88853],pternistis bicalcaratus[&&NHX:TOL=88854],pternistis icterorhynchus[&&NHX:TOL=88855],pternistis clappertoni[&&NHX:TOL=88856],pternistis harwoodi[&&NHX:TOL=88857],pternistis swierstrai[&&NHX:TOL=88858],pternistis camerunensis[&&NHX:TOL=88859],pternistis nobilis[&&NHX:TOL=88860],pternistis jacksoni[&&NHX:TOL=88861],pternistis castaneicollis[&&NHX:TOL=88862],pternistis ochropectus[&&NHX:TOL=88863],pternistis erckelii[&&NHX:TOL=88864],pternistis hartlaubi[&&NHX:TOL=88865],pternistis adspersus[&&NHX:TOL=88866],pternistis capensis[&&NHX:TOL=88867],pternistis natalensis[&&NHX:TOL=88868],pternistis leucoscepus[&&NHX:TOL=88869],pternistis rufopictus[&&NHX:TOL=88870],pternistis afer[&&NHX:TOL=88871],pternistis swainsonii[&&NHX:TOL=88872])pternistis[&&NHX:TOL=88849],(ptilopachus petrosus[&&NHX:TOL=88821],ptilopachus nahani[&&NHX:TOL=88822])ptilopachus[&&NHX:TOL=57438],rheinardia ocellata[&&NHX:TOL=57449],(rhizothera longirostris[&&NHX:TOL=88794],rhizothera dulitensis[&&NHX:TOL=88795])rhizothera[&&NHX:TOL=57429],rollulus rouloul[&&NHX:TOL=57437],(scleroptila streptophora[&&NHX:TOL=88841],scleroptila africana[&&NHX:TOL=88842],scleroptila levaillantii[&&NHX:TOL=88843],scleroptila finschi[&&NHX:TOL=88844],scleroptila shelleyi[&&NHX:TOL=88845],scleroptila psilolaema[&&NHX:TOL=88846],scleroptila levaillantoides[&&NHX:TOL=88847])scleroptila[&&NHX:TOL=88840],(tetrao parvirostris[&&NHX:TOL=88724],tetrao urogallus[&&NHX:TOL=88725])tetrao[&&NHX:TOL=88723],(tetraogallus caucasicus[&&NHX:TOL=88787],tetraogallus caspius[&&NHX:TOL=88788],tetraogallus himalayensis[&&NHX:TOL=88789],tetraogallus tibetanus[&&NHX:TOL=88790],tetraogallus altaicus[&&NHX:TOL=88791])tetraogallus[&&NHX:TOL=57426],(tetraophasis obscurus[&&NHX:TOL=88792],tetraophasis szechenyii[&&NHX:TOL=88793])tetraophasis[&&NHX:TOL=57427],(tetrastes bonasia[&&NHX:TOL=88830],tetrastes sewerzowi[&&NHX:TOL=88831])tetrastes[&&NHX:TOL=88829],xenoperdix udzungwensis[&&NHX:TOL=88873])phasianidae[&&NHX:TOL=26302],((dendrortyx barbatus[&&NHX:TOL=88669],dendrortyx macroura[&&NHX:TOL=88670],dendrortyx leucophrys[&&NHX:TOL=88671])dendrortyx[&&NHX:TOL=88668],oreortyx pictus[&&NHX:TOL=88672],(callipepla squamata[&&NHX:TOL=88674],callipepla douglasii[&&NHX:TOL=88675],(callipepla gambelii[&&NHX:TOL=88677],callipepla californica[&&NHX:TOL=88676])[&&NHX:TOL=110584])callipepla[&&NHX:TOL=88673],philortyx fasciatus[&&NHX:TOL=88678],(colinus virginianus[&&NHX:TOL=88680],colinus nigrogularis[&&NHX:TOL=88681],colinus leucopogon[&&NHX:TOL=88682],colinus cristatus[&&NHX:TOL=88683])colinus[&&NHX:TOL=88679],(odontophorus gujanensis[&&NHX:TOL=88685],odontophorus capueira[&&NHX:TOL=88686],odontophorus melanotis[&&NHX:TOL=88687],odontophorus erythrops[&&NHX:TOL=88688],odontophorus atrifrons[&&NHX:TOL=88689],odontophorus hyperythrus[&&NHX:TOL=88690],odontophorus melanonotus[&&NHX:TOL=88691],odontophorus speciosus[&&NHX:TOL=88692],odontophorus dialeucos[&&NHX:TOL=88693],odontophorus strophium[&&NHX:TOL=88694],odontophorus columbianus[&&NHX:TOL=88695],odontophorus leucolaemus[&&NHX:TOL=88696],odontophorus balliviani[&&NHX:TOL=88697],odontophorus stellatus[&&NHX:TOL=88698],odontophorus guttatus[&&NHX:TOL=88699])odontophorus[&&NHX:TOL=88684],dactylortyx thoracicus[&&NHX:TOL=88700],(cyrtonyx montezumae[&&NHX:TOL=88702],cyrtonyx ocellatus[&&NHX:TOL=88703])cyrtonyx[&&NHX:TOL=88701],rhynchortyx cinctus[&&NHX:TOL=88704])odontophoridae[&&NHX:TOL=26303])[&&NHX:TOL=26301],(agelastes meleagrides[&&NHX:TOL=88662],agelastes niger[&&NHX:TOL=88663],numida meleagris[&&NHX:TOL=88664],guttera plumifera[&&NHX:TOL=88665],guttera pucherani[&&NHX:TOL=88666],acryllium vulturinum[&&NHX:TOL=88667])numididae[&&NHX:TOL=26304])[&&NHX:TOL=26300])[&&NHX:TOL=26298])galliformes[&&NHX:TOL=26296])galloanserae[&&NHX:TOL=15840],(((((((acanthisitta chloris[&&NHX:TOL=83937],xenicus longipes[&&NHX:TOL=83938],xenicus gilviventris[&&NHX:TOL=83939])acanthisittidae[&&NHX:TOL=68000],(((((pitta arquata[&&NHX:TOL=83953],pitta granatina[&&NHX:TOL=83954],pitta ussheri[&&NHX:TOL=83956],pitta venusta[&&NHX:TOL=83955],pitta erythrogaster[&&NHX:TOL=83951],pitta dohertyi[&&NHX:TOL=83952],pitta kochi[&&NHX:TOL=83950])[&&NHX:TOL=108282],(pitta elliotii[&&NHX:TOL=83947],pitta gurneyi[&&NHX:TOL=83949],pitta cyanea[&&NHX:TOL=83946],pitta baudii[&&NHX:TOL=83957],pitta guajana[&&NHX:TOL=83948],pitta caerulea[&&NHX:TOL=83945],pitta schneideri[&&NHX:TOL=83944],pitta nipalensis[&&NHX:TOL=83941],pitta soror[&&NHX:TOL=83942],pitta oatesi[&&NHX:TOL=83943],pitta phayrei[&&NHX:TOL=83940])[&&NHX:TOL=108281],(pitta angolensis[&&NHX:TOL=83962],pitta brachyura[&&NHX:TOL=83964],pitta moluccensis[&&NHX:TOL=83966],pitta nympha[&&NHX:TOL=83965],pitta versicolor[&&NHX:TOL=83971],pitta elegans[&&NHX:TOL=83968],pitta vigorsii[&&NHX:TOL=83969],pitta anerythra[&&NHX:TOL=83972],pitta megarhyncha[&&NHX:TOL=83967],pitta reichenowi[&&NHX:TOL=83963],pitta sordida[&&NHX:TOL=83958],pitta steerii[&&NHX:TOL=83960],pitta iris[&&NHX:TOL=83970],pitta superba[&&NHX:TOL=83961],pitta maxima[&&NHX:TOL=83959])[&&NHX:TOL=108283])pitta[&&NHX:TOL=67974],((((philepitta castanea[&&NHX:TOL=83973],philepitta schlegeli[&&NHX:TOL=83974])[&&NHX:TOL=84873],(neodrepanis coruscans[&&NHX:TOL=83975],neodrepanis hypoxantha[&&NHX:TOL=83976])[&&NHX:TOL=84874])philepittidae[&&NHX:TOL=67977],(pseudocalyptomena graueri[&&NHX:TOL=83991],((psarisomus dalhousiae[&&NHX:TOL=83984],corydon sumatranus[&&NHX:TOL=83990])[&&NHX:TOL=110618],(((serilophus lunatus[&&NHX:TOL=83985],cymbirhynchus macrorhynchos[&&NHX:TOL=83983])[&&NHX:TOL=108279],(eurylaimus ochromalus[&&NHX:TOL=83987],eurylaimus javanicus[&&NHX:TOL=83986])eurylaimus[&&NHX:TOL=84877])[&&NHX:TOL=108278],(sarcophanops samarensis[&&NHX:TOL=83989],sarcophanops steerii[&&NHX:TOL=83988])sarcophanops[&&NHX:TOL=110653])[&&NHX:TOL=110652])[&&NHX:TOL=108277])[&&NHX:TOL=108276])[&&NHX:TOL=108275],sapayoa aenigma[&&NHX:TOL=67975],((calyptomena viridis[&&NHX:TOL=83980],calyptomena hosii[&&NHX:TOL=83981],calyptomena whiteheadi[&&NHX:TOL=83982])calyptomena[&&NHX:TOL=84876],(smithornis capensis[&&NHX:TOL=83977],smithornis sharpei[&&NHX:TOL=83978],smithornis rufolateralis[&&NHX:TOL=83979])smithornis[&&NHX:TOL=84875])[&&NHX:TOL=108273])eurylaimidae broadbills[&&NHX:TOL=67978])eurylaimides[&&NHX:TOL=67973],((((((((masius chrysopterus[&&NHX:TOL=83993],(corapipo gutturalis[&&NHX:TOL=83995],corapipo leucorrhoa[&&NHX:TOL=83996],corapipo altera[&&NHX:TOL=108203])corapipo[&&NHX:TOL=83994])[&&NHX:TOL=139059],ilicura militaris[&&NHX:TOL=83992])[&&NHX:TOL=139058],((chiroxiphia linearis[&&NHX:TOL=84020],chiroxiphia lanceolata[&&NHX:TOL=84021],chiroxiphia pareola[&&NHX:TOL=84022],chiroxiphia boliviana[&&NHX:TOL=84023],chiroxiphia caudata[&&NHX:TOL=84024])chiroxiphia[&&NHX:TOL=84019],(antilophia bokermanni[&&NHX:TOL=84017],antilophia galeata[&&NHX:TOL=84018])antilophia[&&NHX:TOL=84016])[&&NHX:TOL=139060])[&&NHX:TOL=139057],(xenopipo atronitens[&&NHX:TOL=84030],(chloropipo holochlora[&&NHX:TOL=84026],chloropipo flavicapilla[&&NHX:TOL=84027],chloropipo unicolor[&&NHX:TOL=84028],chloropipo uniformis[&&NHX:TOL=84029])chloropipo[&&NHX:TOL=84025])[&&NHX:TOL=139061])[&&NHX:TOL=139056],((manacus manacus[&&NHX:TOL=84012],manacus candei[&&NHX:TOL=84013],manacus vitellinus[&&NHX:TOL=84014],manacus aurantiacus[&&NHX:TOL=84015])manacus[&&NHX:TOL=84011],(heterocercus aurantiivertex[&&NHX:TOL=84032],heterocercus flavivertex[&&NHX:TOL=84033],heterocercus linteatus[&&NHX:TOL=84034])heterocercus[&&NHX:TOL=84031],(pipra aureola[&&NHX:TOL=84037],pipra filicauda[&&NHX:TOL=84038],pipra fasciicauda[&&NHX:TOL=84039])pipra[&&NHX:TOL=84035],(lepidothrix coronata[&&NHX:TOL=84003],lepidothrix isidorei[&&NHX:TOL=84004],lepidothrix coeruleocapilla[&&NHX:TOL=84005],lepidothrix nattereri[&&NHX:TOL=84006],lepidothrix vilasboasi[&&NHX:TOL=84007],lepidothrix iris[&&NHX:TOL=84008],lepidothrix serena[&&NHX:TOL=84009],lepidothrix suavissima[&&NHX:TOL=84010])lepidothrix[&&NHX:TOL=84002],((machaeropterus deliciosus[&&NHX:TOL=83998],machaeropterus regulus[&&NHX:TOL=83999],machaeropterus striolatus[&&NHX:TOL=84000],machaeropterus pyrocephalus[&&NHX:TOL=84001])machaeropterus[&&NHX:TOL=83997],(dixiphia pipra pipra[&&NHX:TOL=84036],(pipra rubrocapilla[&&NHX:TOL=84044],pipra erythrocephala[&&NHX:TOL=84043],pipra mentalis[&&NHX:TOL=84041],pipra chloromeros[&&NHX:TOL=84042],pipra cornuta[&&NHX:TOL=84040])pipra part 2[&&NHX:TOL=139121])[&&NHX:TOL=139120])[&&NHX:TOL=139119])[&&NHX:TOL=139062])[&&NHX:TOL=139055],((tyranneutes stolzmanni[&&NHX:TOL=84649],tyranneutes virescens[&&NHX:TOL=84650])tyranneutes[&&NHX:TOL=84648],(neopelma chrysocephalum[&&NHX:TOL=84643],neopelma sulphureiventer[&&NHX:TOL=84644],neopelma pallescens[&&NHX:TOL=84645],neopelma aurifrons[&&NHX:TOL=84646],neopelma chrysolophum[&&NHX:TOL=84647])neopelma[&&NHX:TOL=84642])[&&NHX:TOL=139065])pipridae[&&NHX:TOL=67995],((((((cephalopterus glabricollis[&&NHX:TOL=84163],cephalopterus ornatus[&&NHX:TOL=84164],cephalopterus penduliger[&&NHX:TOL=84165])cephalopterus[&&NHX:TOL=84162],perissocephalus tricolor[&&NHX:TOL=84161],pyroderus scutatus[&&NHX:TOL=84160])[&&NHX:TOL=108265],querula purpurata[&&NHX:TOL=84158])[&&NHX:TOL=108263],haematoderus militaris[&&NHX:TOL=84159],(cotinga amabilis[&&NHX:TOL=84121],cotinga ridgwayi[&&NHX:TOL=84122],cotinga nattererii[&&NHX:TOL=84123],cotinga maynana[&&NHX:TOL=84124],cotinga cotinga[&&NHX:TOL=84125],cotinga maculata[&&NHX:TOL=84126],cotinga cayana[&&NHX:TOL=84127])cotinga[&&NHX:TOL=84120],(procnias tricarunculatus[&&NHX:TOL=84129],procnias albus[&&NHX:TOL=84130],procnias averano[&&NHX:TOL=84131],procnias nudicollis[&&NHX:TOL=84132])procnias[&&NHX:TOL=84128],((tijuca condita[&&NHX:TOL=84134],tijuca atra[&&NHX:TOL=84135])tijuca[&&NHX:TOL=84133],(lipaugus weberi[&&NHX:TOL=84137],lipaugus fuscocinereus[&&NHX:TOL=84138],lipaugus uropygialis[&&NHX:TOL=84139],lipaugus unirufus[&&NHX:TOL=84140],lipaugus vociferans[&&NHX:TOL=84141],lipaugus lanioides[&&NHX:TOL=84142],lipaugus streptophorus[&&NHX:TOL=84143])lipaugus[&&NHX:TOL=84136])[&&NHX:TOL=108266],(((gymnoderus foetidus[&&NHX:TOL=84157],conioptilon mcilhennyi[&&NHX:TOL=84144])[&&NHX:TOL=108269],((carpodectes hopkei[&&NHX:TOL=84154],carpodectes nitidus[&&NHX:TOL=84155],carpodectes antoniae[&&NHX:TOL=84156])carpodectes[&&NHX:TOL=84153],(xipholena punicea[&&NHX:TOL=84150],xipholena lamellipennis[&&NHX:TOL=84151],xipholena atropurpurea[&&NHX:TOL=84152])xipholena[&&NHX:TOL=84149])[&&NHX:TOL=108270])[&&NHX:TOL=108268],porphyrolaema porphyrolaema[&&NHX:TOL=84148])[&&NHX:TOL=139118])[&&NHX:TOL=108257],(carpornis melanocephala[&&NHX:TOL=84098],carpornis cucullata[&&NHX:TOL=84099])carpornis[&&NHX:TOL=84097],(((phoenicircus nigricollis[&&NHX:TOL=84118],phoenicircus carnifex[&&NHX:TOL=84119])phoenicircus[&&NHX:TOL=84117],(rupicola rupicola[&&NHX:TOL=84115],rupicola peruvianus[&&NHX:TOL=84116])rupicola[&&NHX:TOL=84114])[&&NHX:TOL=108258],(snowornis subalaris[&&NHX:TOL=84146],snowornis cryptolophus[&&NHX:TOL=84147])snowornis[&&NHX:TOL=84145])[&&NHX:TOL=139074],(((phytotoma raimondii[&&NHX:TOL=84094],phytotoma rutila[&&NHX:TOL=84095],phytotoma rara[&&NHX:TOL=84096])phytotoma[&&NHX:TOL=84093],((doliornis remseni[&&NHX:TOL=84091],doliornis sclateri[&&NHX:TOL=84092])doliornis[&&NHX:TOL=84090],(ampelion rufaxilla[&&NHX:TOL=84087],ampelion rubrocristatus[&&NHX:TOL=84088])ampelion[&&NHX:TOL=84086])[&&NHX:TOL=108271])[&&NHX:TOL=108260],zaratornis stresemanni[&&NHX:TOL=84089])[&&NHX:TOL=139073])[&&NHX:TOL=139066],((pipreola riefferii[&&NHX:TOL=84101],pipreola intermedia[&&NHX:TOL=84102],pipreola arcuata[&&NHX:TOL=84103],pipreola aureopectus[&&NHX:TOL=84104],pipreola jucunda[&&NHX:TOL=84105],pipreola lubomirskii[&&NHX:TOL=84106],pipreola pulchra[&&NHX:TOL=84107],pipreola frontalis[&&NHX:TOL=84108],pipreola chlorolepidota[&&NHX:TOL=84109],pipreola formosa[&&NHX:TOL=84110],pipreola whitelyi[&&NHX:TOL=84111])pipreola[&&NHX:TOL=84100],ampelioides tschudii[&&NHX:TOL=84113])[&&NHX:TOL=108259],(phibalura flavirostris[&&NHX:TOL=84084],phibalura boliviana[&&NHX:TOL=84085])phibalura[&&NHX:TOL=84083])cotingidae[&&NHX:TOL=67999],calyptura cristata[&&NHX:TOL=84571],(((((tityra inquisitor[&&NHX:TOL=84046],tityra cayana[&&NHX:TOL=84047],tityra semifasciata[&&NHX:TOL=84048])tityra[&&NHX:TOL=84045],(((pachyramphus viridis[&&NHX:TOL=84065],pachyramphus xanthogenys[&&NHX:TOL=84066],pachyramphus versicolor[&&NHX:TOL=84067],pachyramphus spodiurus[&&NHX:TOL=84068],pachyramphus rufus[&&NHX:TOL=84069],pachyramphus castaneus[&&NHX:TOL=84070],pachyramphus cinnamomeus[&&NHX:TOL=84071],pachyramphus polychopterus[&&NHX:TOL=84072],pachyramphus marginatus[&&NHX:TOL=84073],pachyramphus albogriseus[&&NHX:TOL=84074],pachyramphus major[&&NHX:TOL=84075],pachyramphus surinamus[&&NHX:TOL=84076])pachyramphus[&&NHX:TOL=84064],(platypsaris aglaiae[&&NHX:TOL=84078],platypsaris homochrous[&&NHX:TOL=84079],platypsaris minor[&&NHX:TOL=84080],platypsaris validus[&&NHX:TOL=84081],platypsaris niger[&&NHX:TOL=84082])platypsaris[&&NHX:TOL=84077])[&&NHX:TOL=108261],xenopsaris albinucha[&&NHX:TOL=84063])[&&NHX:TOL=139075])[&&NHX:TOL=108245],(iodopleura pipra[&&NHX:TOL=84057],iodopleura fusca[&&NHX:TOL=84058],iodopleura isabellae[&&NHX:TOL=84059])iodopleura[&&NHX:TOL=84056])[&&NHX:TOL=108248],(((laniisoma buckleyi[&&NHX:TOL=84062],laniisoma elegans[&&NHX:TOL=84061])laniisoma[&&NHX:TOL=84060],(laniocera rufescens[&&NHX:TOL=84054],laniocera hypopyrra[&&NHX:TOL=84055])laniocera[&&NHX:TOL=84053])[&&NHX:TOL=139078],(schiffornis major[&&NHX:TOL=84050],schiffornis turdina[&&NHX:TOL=84051],schiffornis virescens[&&NHX:TOL=84052])schiffornis[&&NHX:TOL=84049])[&&NHX:TOL=139077])[&&NHX:TOL=139117],oxyruncus cristatus[&&NHX:TOL=67997],(((myiobius villosus[&&NHX:TOL=84635],myiobius sulphureipygius[&&NHX:TOL=84636],myiobius barbatus[&&NHX:TOL=84637],myiobius mastacalis[&&NHX:TOL=84638],myiobius atricaudus[&&NHX:TOL=84639])myiobius[&&NHX:TOL=84634],terenotriccus erythrurus[&&NHX:TOL=84640])[&&NHX:TOL=139102],(onychorhynchus coronatus[&&NHX:TOL=84630],onychorhynchus mexicanus[&&NHX:TOL=84631],onychorhynchus occidentalis[&&NHX:TOL=84632],onychorhynchus swainsoni[&&NHX:TOL=84633])onychorhynchus[&&NHX:TOL=84629])[&&NHX:TOL=139101])tityridae[&&NHX:TOL=67996],(((((((((((agriornis montanus[&&NHX:TOL=84738],agriornis albicauda[&&NHX:TOL=84739],agriornis lividus[&&NHX:TOL=84740],agriornis micropterus[&&NHX:TOL=84741],agriornis murinus[&&NHX:TOL=84742])agriornis[&&NHX:TOL=84737],neoxolmis rufiventris[&&NHX:TOL=84759],(myiotheretes striaticollis[&&NHX:TOL=84753],myiotheretes pernix[&&NHX:TOL=84754],myiotheretes fumigatus[&&NHX:TOL=84755],myiotheretes fuscorufus[&&NHX:TOL=84756])myiotheretes[&&NHX:TOL=84752])[&&NHX:TOL=138986],((xolmis pyrope[&&NHX:TOL=84744],xolmis cinereus[&&NHX:TOL=84745],xolmis coronatus[&&NHX:TOL=84746],xolmis velatus[&&NHX:TOL=84747],xolmis irupero[&&NHX:TOL=84748],xolmis rubetra[&&NHX:TOL=84749],xolmis salinarum[&&NHX:TOL=84750])xolmis[&&NHX:TOL=84743],heteroxolmis dominicana[&&NHX:TOL=84751])[&&NHX:TOL=139081])[&&NHX:TOL=138985],(polioxolmis rufipennis[&&NHX:TOL=84758],cnemarchus erythropygius[&&NHX:TOL=84757])[&&NHX:TOL=138987])[&&NHX:TOL=138984],(hymenops perspicillatus[&&NHX:TOL=84720],(knipolegus striaticeps[&&NHX:TOL=84709],knipolegus hudsoni[&&NHX:TOL=84710],knipolegus poecilocercus[&&NHX:TOL=84711],knipolegus signatus[&&NHX:TOL=84712],knipolegus cyanirostris[&&NHX:TOL=84713],knipolegus poecilurus[&&NHX:TOL=84714],knipolegus orenocensis[&&NHX:TOL=84715],knipolegus aterrimus[&&NHX:TOL=84716],knipolegus franciscanus[&&NHX:TOL=84717],knipolegus lophotes[&&NHX:TOL=84718],knipolegus nigerrimus[&&NHX:TOL=84719])knipolegus[&&NHX:TOL=84708])[&&NHX:TOL=138990],(lessonia rufa[&&NHX:TOL=84706],lessonia oreas[&&NHX:TOL=84707])lessonia[&&NHX:TOL=84705],(satrapa icterophrys[&&NHX:TOL=84722],(muscisaxicola frontalis[&&NHX:TOL=84736],muscisaxicola fluviatilis[&&NHX:TOL=84724],muscisaxicola maculirostris[&&NHX:TOL=84725],muscisaxicola griseus[&&NHX:TOL=84726],muscisaxicola juninensis[&&NHX:TOL=84727],muscisaxicola cinereus[&&NHX:TOL=84728],muscisaxicola albifrons[&&NHX:TOL=84729],muscisaxicola flavinucha[&&NHX:TOL=84730],muscisaxicola rufivertex[&&NHX:TOL=84731],muscisaxicola maclovianus[&&NHX:TOL=84732],muscisaxicola albilora[&&NHX:TOL=84733],muscisaxicola alpinus[&&NHX:TOL=84734],muscisaxicola capistratus[&&NHX:TOL=84735])muscisaxicola[&&NHX:TOL=84723])[&&NHX:TOL=138988])xolmiini[&&NHX:TOL=138982],(((((lathrotriccus euleri[&&NHX:TOL=84654],lathrotriccus griseipectus[&&NHX:TOL=84655])lathrotriccus[&&NHX:TOL=84653],(aphanotriccus capitalis[&&NHX:TOL=84657],aphanotriccus audax[&&NHX:TOL=84658])aphanotriccus[&&NHX:TOL=84656],(xenotriccus callizonus[&&NHX:TOL=84661],xenotriccus mexicanus[&&NHX:TOL=84662])xenotriccus[&&NHX:TOL=84660])[&&NHX:TOL=139083],cnemotriccus fuscatus[&&NHX:TOL=84659])[&&NHX:TOL=138994],ochthornis littoralis[&&NHX:TOL=84721],(((contopus cooperi[&&NHX:TOL=84671],contopus pertinax[&&NHX:TOL=84672],contopus lugubris[&&NHX:TOL=84673],contopus fumigatus[&&NHX:TOL=84674],contopus ochraceus[&&NHX:TOL=84675],contopus sordidulus[&&NHX:TOL=84676],contopus virens[&&NHX:TOL=84677],contopus cinereus[&&NHX:TOL=84678],contopus punensis[&&NHX:TOL=84679],contopus albogularis[&&NHX:TOL=84680],contopus nigrescens[&&NHX:TOL=84681],contopus caribaeus[&&NHX:TOL=84682],contopus hispaniolensis[&&NHX:TOL=84683],contopus pallidus[&&NHX:TOL=84684],contopus latirostris[&&NHX:TOL=84685])contopus[&&NHX:TOL=84670],(empidonax flaviventris[&&NHX:TOL=84687],empidonax virescens[&&NHX:TOL=84688],empidonax traillii[&&NHX:TOL=84689],empidonax alnorum[&&NHX:TOL=84690],empidonax albigularis[&&NHX:TOL=84691],empidonax minimus[&&NHX:TOL=84692],empidonax hammondii[&&NHX:TOL=84693],empidonax oberholseri[&&NHX:TOL=84694],empidonax wrightii[&&NHX:TOL=84695],empidonax affinis[&&NHX:TOL=84696],empidonax difficilis[&&NHX:TOL=84697],empidonax occidentalis[&&NHX:TOL=84698],empidonax flavescens[&&NHX:TOL=84699],empidonax fulvifrons[&&NHX:TOL=84700],empidonax atriceps[&&NHX:TOL=84701])empidonax[&&NHX:TOL=84686])[&&NHX:TOL=138997],(mitrephanes phaeocercus[&&NHX:TOL=84668],mitrephanes olivaceus[&&NHX:TOL=84669])mitrephanes[&&NHX:TOL=84667],(sayornis phoebe[&&NHX:TOL=84664],sayornis nigricans[&&NHX:TOL=84665],sayornis saya[&&NHX:TOL=84666])sayornis[&&NHX:TOL=84663])[&&NHX:TOL=138995])[&&NHX:TOL=138992],(myiophobus cryptoxanthus[&&NHX:TOL=84538],myiophobus fasciatus[&&NHX:TOL=84539])myiophobus[&&NHX:TOL=84530])contopini[&&NHX:TOL=139112])[&&NHX:TOL=138991],((arundinicola leucocephala[&&NHX:TOL=84766],colonia colonus[&&NHX:TOL=84786],(pyrocephalus rubinus[&&NHX:TOL=84703],pyrocephalus nanus[&&NHX:TOL=84704])pyrocephalus[&&NHX:TOL=84702],(fluvicola pica[&&NHX:TOL=84763],fluvicola albiventer[&&NHX:TOL=84764],fluvicola nengeta[&&NHX:TOL=84765])fluvicola[&&NHX:TOL=84762],((alectrurus tricolor[&&NHX:TOL=84768],alectrurus risora[&&NHX:TOL=84769])alectrurus[&&NHX:TOL=84767],gubernetes yetapa[&&NHX:TOL=84760])[&&NHX:TOL=139003])[&&NHX:TOL=139000],(sublegatus arenarum[&&NHX:TOL=84522],sublegatus obscurior[&&NHX:TOL=84523],sublegatus modestus[&&NHX:TOL=84524])sublegatus[&&NHX:TOL=84521],(myiophobus flavicans[&&NHX:TOL=84531],myiophobus phoenicomitra[&&NHX:TOL=84532],myiophobus roraimae[&&NHX:TOL=84534],myiophobus inornatus[&&NHX:TOL=84533])myiophobus part 2[&&NHX:TOL=139084],(tumbezia salvini[&&NHX:TOL=84770],(ochthoeca piurae[&&NHX:TOL=84784],ochthoeca leucophrys[&&NHX:TOL=84783],ochthoeca oenanthoides[&&NHX:TOL=84782],ochthoeca fumicolor[&&NHX:TOL=84781],ochthoeca rufipectoralis[&&NHX:TOL=84780],ochthoeca thoracica[&&NHX:TOL=84779],ochthoeca nigrita[&&NHX:TOL=84778],ochthoeca cinnamomeiventris[&&NHX:TOL=84777],ochthoeca spodionota[&&NHX:TOL=84773])ochthoeca[&&NHX:TOL=84771])[&&NHX:TOL=139004])fluvicolini[&&NHX:TOL=138998],(colorhamphus parvirostris[&&NHX:TOL=84785],(silvicultrix ochthoeca frontalis[&&NHX:TOL=84772],silvicultrix ochthoeca jelskii[&&NHX:TOL=84776],silvicultrix ochthoeca diadema[&&NHX:TOL=84775],silvicultrix ochthoeca pulchella[&&NHX:TOL=84774])silvicultrix ochthoeca[&&NHX:TOL=139114])[&&NHX:TOL=139113],muscipipra vetula[&&NHX:TOL=84761])fluvicolinae[&&NHX:TOL=139005],(attila phoenicurus[&&NHX:TOL=84866],attila cinnamomeus[&&NHX:TOL=84867],attila torridus[&&NHX:TOL=84868],attila citriniventris[&&NHX:TOL=84869],attila bolivianus[&&NHX:TOL=84870],attila rufus[&&NHX:TOL=84871],attila spadiceus[&&NHX:TOL=84872])attila[&&NHX:TOL=84865],((ramphotrigon fuscicauda[&&NHX:TOL=84864],ramphotrigon ruficauda[&&NHX:TOL=84863],ramphotrigon megacephalum[&&NHX:TOL=84862])ramphotrigon[&&NHX:TOL=84861],deltarhynchus flammulatus[&&NHX:TOL=84860],(conopias albovittatus[&&NHX:TOL=84799],conopias parvus[&&NHX:TOL=84800],conopias trivirgatus[&&NHX:TOL=84801],conopias cinchoneti[&&NHX:TOL=84802])conopias[&&NHX:TOL=84798],phelpsia inornata[&&NHX:TOL=84790])[&&NHX:TOL=139085],((((casiornis rufus[&&NHX:TOL=84835],casiornis fuscus[&&NHX:TOL=84836])casiornis[&&NHX:TOL=84834],(rhytipterna simplex[&&NHX:TOL=84828],rhytipterna immunda[&&NHX:TOL=84829],rhytipterna holerythra[&&NHX:TOL=84830])rhytipterna[&&NHX:TOL=84827])[&&NHX:TOL=139026],(sirystes sibilator[&&NHX:TOL=84832],sirystes albogriseus[&&NHX:TOL=84833])sirystes[&&NHX:TOL=84831])[&&NHX:TOL=139025],(myiarchus semirufus[&&NHX:TOL=84838],myiarchus yucatanensis[&&NHX:TOL=84839],myiarchus barbirostris[&&NHX:TOL=84840],myiarchus tuberculifer[&&NHX:TOL=84841],myiarchus swainsoni[&&NHX:TOL=84842],myiarchus venezuelensis[&&NHX:TOL=84843],myiarchus panamensis[&&NHX:TOL=84844],myiarchus ferox[&&NHX:TOL=84845],myiarchus apicalis[&&NHX:TOL=84846],myiarchus cephalotes[&&NHX:TOL=84847],myiarchus phaeocephalus[&&NHX:TOL=84848],myiarchus cinerascens[&&NHX:TOL=84849],myiarchus nuttingi[&&NHX:TOL=84850],myiarchus crinitus[&&NHX:TOL=84851],myiarchus tyrannulus[&&NHX:TOL=84852],myiarchus magnirostris[&&NHX:TOL=84853],myiarchus nugator[&&NHX:TOL=84854],myiarchus validus[&&NHX:TOL=84855],myiarchus sagrae[&&NHX:TOL=84856],myiarchus stolidus[&&NHX:TOL=84857],myiarchus antillarum[&&NHX:TOL=84858],myiarchus oberi[&&NHX:TOL=84859])myiarchus[&&NHX:TOL=84837])myiarchini[&&NHX:TOL=139024],((pitangus sulphuratus[&&NHX:TOL=84796],philohydor lictor[&&NHX:TOL=84797])[&&NHX:TOL=139023],(((griseotyrannus aurantioatrocristatus[&&NHX:TOL=84812],empidonomus varius[&&NHX:TOL=84811])[&&NHX:TOL=139008],(tyrannus niveigularis[&&NHX:TOL=84814],tyrannus albogularis[&&NHX:TOL=84815],tyrannus melancholicus[&&NHX:TOL=84816],tyrannus couchii[&&NHX:TOL=84817],tyrannus vociferans[&&NHX:TOL=84818],tyrannus crassirostris[&&NHX:TOL=84819],tyrannus verticalis[&&NHX:TOL=84820],tyrannus forficatus[&&NHX:TOL=84821],tyrannus savana[&&NHX:TOL=84822],tyrannus tyrannus[&&NHX:TOL=84823],tyrannus dominicensis[&&NHX:TOL=84824],tyrannus cubensis[&&NHX:TOL=84825],tyrannus caudifasciatus[&&NHX:TOL=84826])tyrannus[&&NHX:TOL=84813])[&&NHX:TOL=139007],(myiozetetes cayanensis[&&NHX:TOL=84792],myiozetetes similis[&&NHX:TOL=84793],myiozetetes granadensis[&&NHX:TOL=84794],myiozetetes luteiventris[&&NHX:TOL=84795])myiozetetes[&&NHX:TOL=84791],((tyrannopsis sulphurea[&&NHX:TOL=84810],megarynchus pitangua[&&NHX:TOL=84809])[&&NHX:TOL=139022],(myiodynastes hemichrysus[&&NHX:TOL=84804],myiodynastes chrysocephalus[&&NHX:TOL=84805],myiodynastes bairdii[&&NHX:TOL=84806],myiodynastes luteiventris[&&NHX:TOL=84807],myiodynastes maculatus[&&NHX:TOL=84808])myiodynastes[&&NHX:TOL=84803])[&&NHX:TOL=139021])[&&NHX:TOL=139019],machetornis rixosa[&&NHX:TOL=84788],legatus leucophaius[&&NHX:TOL=84789])tyrannini[&&NHX:TOL=139115])[&&NHX:TOL=139012],muscigralla brevicauda[&&NHX:TOL=84787])[&&NHX:TOL=139011],((pyrrhomyias cinnamomeus[&&NHX:TOL=84651],hirundinea ferruginea[&&NHX:TOL=84652])[&&NHX:TOL=139045],(myiotriccus ornatus[&&NHX:TOL=84540],(myiophobus ochraceiventris[&&NHX:TOL=84537],myiophobus pulcher[&&NHX:TOL=84535],myiophobus lintoni[&&NHX:TOL=84536])myiophobus part 3[&&NHX:TOL=139088])[&&NHX:TOL=139087])hirundineinae[&&NHX:TOL=139044],((((((uromyias agraphia[&&NHX:TOL=84438],uromyias agilis[&&NHX:TOL=84439])uromyias[&&NHX:TOL=84437],(anairetes nigrocristatus[&&NHX:TOL=84431],anairetes reguloides[&&NHX:TOL=84432],anairetes alpinus[&&NHX:TOL=84433],anairetes flavirostris[&&NHX:TOL=84434],anairetes parulus[&&NHX:TOL=84435],anairetes fernandezianus[&&NHX:TOL=84436])anairetes[&&NHX:TOL=84430])[&&NHX:TOL=139034],((pseudocolopteryx dinelliana[&&NHX:TOL=84455],pseudocolopteryx sclateri[&&NHX:TOL=84456],pseudocolopteryx acutipennis[&&NHX:TOL=84457],pseudocolopteryx flaviventris[&&NHX:TOL=84458])pseudocolopteryx[&&NHX:TOL=84454],(serpophaga cinerea[&&NHX:TOL=84441],serpophaga hypoleuca[&&NHX:TOL=84442],serpophaga nigricans[&&NHX:TOL=84443],serpophaga subcristata[&&NHX:TOL=84444],serpophaga munda[&&NHX:TOL=84445])serpophaga[&&NHX:TOL=84440])[&&NHX:TOL=139036],(polystictus superciliaris[&&NHX:TOL=84451],polystictus pectoralis[&&NHX:TOL=84452])polystictus[&&NHX:TOL=84450],culicivora caudacuta[&&NHX:TOL=84542])[&&NHX:TOL=139033],mecocerculus leucophrys[&&NHX:TOL=84423])[&&NHX:TOL=139032],(capsiempis flaveola[&&NHX:TOL=84449],((phaeomyias murina[&&NHX:TOL=84447],phaeomyias tumbezana[&&NHX:TOL=84448])phaeomyias[&&NHX:TOL=84446],(phyllomyias fasciatus[&&NHX:TOL=84371],phyllomyias griseiceps[&&NHX:TOL=84379],phyllomyias griseocapilla[&&NHX:TOL=84378],phyllomyias weedeni[&&NHX:TOL=129851],phyllomyias urichi[&&NHX:TOL=84376],phyllomyias sclateri[&&NHX:TOL=84377],phyllomyias nigrocapillus[&&NHX:TOL=84381])phyllomyias[&&NHX:TOL=84370])[&&NHX:TOL=139038],nesotriccus ridgwayi[&&NHX:TOL=84453])[&&NHX:TOL=139037],(elaenia martinica[&&NHX:TOL=84395],elaenia flavogaster[&&NHX:TOL=84394],elaenia spectabilis[&&NHX:TOL=84396],elaenia ridleyana[&&NHX:TOL=84397],elaenia albiceps[&&NHX:TOL=84398],elaenia parvirostris[&&NHX:TOL=84399],elaenia mesoleuca[&&NHX:TOL=84400],elaenia strepera[&&NHX:TOL=84401],elaenia gigas[&&NHX:TOL=84402],elaenia pelzelni[&&NHX:TOL=84403],elaenia cristata[&&NHX:TOL=84404],elaenia chiriquensis[&&NHX:TOL=84405],elaenia ruficeps[&&NHX:TOL=84406],elaenia frantzii[&&NHX:TOL=84407],elaenia obscura[&&NHX:TOL=84408],elaenia dayi[&&NHX:TOL=84409],elaenia pallatangae[&&NHX:TOL=84410],elaenia fallax[&&NHX:TOL=84411])elaenia[&&NHX:TOL=84393],((suiriri suiriri[&&NHX:TOL=84420],suiriri islerorum[&&NHX:TOL=84422])suiriri[&&NHX:TOL=84419],((myiopagis gaimardii[&&NHX:TOL=84386],myiopagis caniceps[&&NHX:TOL=84387],myiopagis olallai[&&NHX:TOL=84388],myiopagis subplacens[&&NHX:TOL=84389],myiopagis flavivertex[&&NHX:TOL=84390],myiopagis viridicata[&&NHX:TOL=84391],myiopagis cotta[&&NHX:TOL=84392])myiopagis[&&NHX:TOL=84385],tyrannulus elatus[&&NHX:TOL=84384])[&&NHX:TOL=139086])[&&NHX:TOL=139040],pseudelaenia leucospodia[&&NHX:TOL=84469])elaenini[&&NHX:TOL=139030],((((ornithion semiflavum[&&NHX:TOL=84413],ornithion brunneicapillus[&&NHX:TOL=84414],ornithion inerme[&&NHX:TOL=84415])ornithion[&&NHX:TOL=84412],(camptostoma imberbe[&&NHX:TOL=84417],camptostoma obsoletum[&&NHX:TOL=84418])camptostoma[&&NHX:TOL=84416])[&&NHX:TOL=139042],(tyranniscus phyllomyias burmeisteri[&&NHX:TOL=84372],tyranniscus phyllomyias zeledoni[&&NHX:TOL=84373],tyranniscus phyllomyias uropygialis[&&NHX:TOL=84383],tyranniscus phyllomyias virescens[&&NHX:TOL=84374],tyranniscus phyllomyias plumbeiceps[&&NHX:TOL=84380],tyranniscus phyllomyias cinereiceps[&&NHX:TOL=84382],tyranniscus phyllomyias reiseri[&&NHX:TOL=84375])tyranniscus phyllomyias[&&NHX:TOL=139104],(mecocerculus poecilocercus[&&NHX:TOL=84425],mecocerculus calopterus[&&NHX:TOL=84427],mecocerculus hellmayri[&&NHX:TOL=84426],mecocerculus stictopterus[&&NHX:TOL=84429],mecocerculus minor[&&NHX:TOL=84428])mecocerculus part 2[&&NHX:TOL=139105])[&&NHX:TOL=139103],(stigmatura napensis[&&NHX:TOL=84471],stigmatura bahiae[&&NHX:TOL=84472],stigmatura budytoides[&&NHX:TOL=84473],stigmatura gracilis[&&NHX:TOL=84474])stigmatura[&&NHX:TOL=84470],((euscarthmus meloryphus[&&NHX:TOL=84467],euscarthmus rufomarginatus[&&NHX:TOL=84468])euscarthmus[&&NHX:TOL=84466],(inezia tenuirostris[&&NHX:TOL=84526],inezia inornata[&&NHX:TOL=84527],inezia subflava[&&NHX:TOL=84528],inezia caudata[&&NHX:TOL=84529])inezia[&&NHX:TOL=84525])[&&NHX:TOL=139048],(zimmerius villarejoi[&&NHX:TOL=84480],zimmerius gracilipes[&&NHX:TOL=84481],zimmerius chrysops[&&NHX:TOL=84482],zimmerius flavidifrons[&&NHX:TOL=84483],zimmerius viridiflavus[&&NHX:TOL=84484],zimmerius vilissimus[&&NHX:TOL=84476],zimmerius improbus[&&NHX:TOL=84477],zimmerius bolivianus[&&NHX:TOL=84478],zimmerius cinereicapilla[&&NHX:TOL=84479])zimmerius[&&NHX:TOL=84475])euscarthmini[&&NHX:TOL=139041])elaeninae[&&NHX:TOL=139028])[&&NHX:TOL=139010],(piprites griseiceps[&&NHX:TOL=84568],piprites chloris[&&NHX:TOL=84569],piprites pileata[&&NHX:TOL=84570])piprites[&&NHX:TOL=84567],(((platyrinchus saturatus[&&NHX:TOL=84622],platyrinchus cancrominus[&&NHX:TOL=84623],platyrinchus mystaceus[&&NHX:TOL=84624],platyrinchus coronatus[&&NHX:TOL=84625],platyrinchus flavigularis[&&NHX:TOL=84626],platyrinchus platyrhynchos[&&NHX:TOL=84627],platyrinchus leucoryphus[&&NHX:TOL=84628])platyrinchus[&&NHX:TOL=84621],neopipo cinnamomea[&&NHX:TOL=84641])[&&NHX:TOL=139106],((((((oncostoma cinereigulare[&&NHX:TOL=84577],oncostoma olivaceum[&&NHX:TOL=84578])oncostoma[&&NHX:TOL=84576],(lophotriccus pileatus[&&NHX:TOL=84580],lophotriccus eulophotes[&&NHX:TOL=84581],lophotriccus vitiosus[&&NHX:TOL=84582],lophotriccus galeatus[&&NHX:TOL=84583])lophotriccus[&&NHX:TOL=84579],(myiornis auricularis[&&NHX:TOL=84572],myiornis albiventris[&&NHX:TOL=84573],myiornis atricapillus[&&NHX:TOL=84574],myiornis ecaudatus[&&NHX:TOL=84575])myiornis[&&NHX:TOL=84565],atalotriccus lophotriccus pilaris[&&NHX:TOL=84584],(hemitriccus diops[&&NHX:TOL=84544],hemitriccus obsoletus[&&NHX:TOL=84545],hemitriccus flammulatus[&&NHX:TOL=84546],hemitriccus minor[&&NHX:TOL=84547],hemitriccus spodiops[&&NHX:TOL=84548],hemitriccus josephinae[&&NHX:TOL=84549],hemitriccus zosterops[&&NHX:TOL=84550],hemitriccus griseipectus[&&NHX:TOL=84551],hemitriccus minimus[&&NHX:TOL=84552],hemitriccus orbitatus[&&NHX:TOL=84553],hemitriccus iohannis[&&NHX:TOL=84554],hemitriccus striaticollis[&&NHX:TOL=84555],hemitriccus nidipendulus[&&NHX:TOL=84556],hemitriccus margaritaceiventer[&&NHX:TOL=84557],hemitriccus inornatus[&&NHX:TOL=84558],hemitriccus granadensis[&&NHX:TOL=84559],hemitriccus mirandae[&&NHX:TOL=84560],hemitriccus cinnamomeipectus[&&NHX:TOL=84561],hemitriccus kaempferi[&&NHX:TOL=84562],hemitriccus rufigularis[&&NHX:TOL=84563],hemitriccus furcatus[&&NHX:TOL=84564])hemitriccus[&&NHX:TOL=84543])[&&NHX:TOL=139046],((poecilotriccus ruficeps[&&NHX:TOL=84586],poecilotriccus luluae[&&NHX:TOL=84587],poecilotriccus albifacies[&&NHX:TOL=84588],poecilotriccus capitalis[&&NHX:TOL=84589],poecilotriccus senex[&&NHX:TOL=84590],poecilotriccus russatus[&&NHX:TOL=84591],poecilotriccus plumbeiceps[&&NHX:TOL=84592],poecilotriccus fumifrons[&&NHX:TOL=84593],poecilotriccus latirostris[&&NHX:TOL=84594],poecilotriccus sylvia[&&NHX:TOL=84595],poecilotriccus calopterus[&&NHX:TOL=84596],poecilotriccus pulchellus[&&NHX:TOL=84597])poecilotriccus[&&NHX:TOL=84585],(todirostrum maculatum[&&NHX:TOL=84600],todirostrum poliocephalum[&&NHX:TOL=84601],todirostrum cinereum[&&NHX:TOL=84602],todirostrum viridanum[&&NHX:TOL=84603],todirostrum pictum[&&NHX:TOL=84604],todirostrum chrysocrotaphum[&&NHX:TOL=84605],todirostrum nigriceps[&&NHX:TOL=84606])todirostrum[&&NHX:TOL=84599])[&&NHX:TOL=139050])todirostrini[&&NHX:TOL=139049],(((tolmomyias sulphurescens[&&NHX:TOL=84614],tolmomyias traylori[&&NHX:TOL=84615],tolmomyias assimilis[&&NHX:TOL=84616],tolmomyias flavotectus[&&NHX:TOL=84617],tolmomyias poliocephalus[&&NHX:TOL=84618],tolmomyias flaviventris[&&NHX:TOL=84619],tolmomyias viridiceps[&&NHX:TOL=84620])tolmomyias[&&NHX:TOL=84613],(rhynchocyclus brevirostris[&&NHX:TOL=84609],rhynchocyclus olivaceus[&&NHX:TOL=84610],rhynchocyclus pacificus[&&NHX:TOL=84611],rhynchocyclus fulvipectus[&&NHX:TOL=84612])rhynchocyclus[&&NHX:TOL=84608])[&&NHX:TOL=139094],((cnipodectes subbrunneus[&&NHX:TOL=129529],cnipodectes superrufus[&&NHX:TOL=129530])cnipodectes[&&NHX:TOL=84607],taeniotriccus andrei[&&NHX:TOL=84598])[&&NHX:TOL=139100])rhynchocyclini[&&NHX:TOL=139107])[&&NHX:TOL=139116],(((corythopis torquatus[&&NHX:TOL=84464],corythopis delalandi[&&NHX:TOL=84465])corythopis[&&NHX:TOL=84463],(pseudotriccus pelzelni[&&NHX:TOL=84460],pseudotriccus simplex[&&NHX:TOL=84461],pseudotriccus ruficeps[&&NHX:TOL=84462])pseudotriccus[&&NHX:TOL=84459])[&&NHX:TOL=139097],((leptopogon amaurocephalus[&&NHX:TOL=84517],leptopogon superciliaris[&&NHX:TOL=84518],leptopogon rufipectus[&&NHX:TOL=84519],leptopogon taczanowskii[&&NHX:TOL=84520])leptopogon[&&NHX:TOL=84516],(mionectes striaticollis[&&NHX:TOL=84511],mionectes olivaceus[&&NHX:TOL=84512],mionectes oleagineus[&&NHX:TOL=84513],mionectes macconnelli[&&NHX:TOL=84514],mionectes rufiventris[&&NHX:TOL=84515])mionectes[&&NHX:TOL=84510])[&&NHX:TOL=139099],((phylloscartes ventralis[&&NHX:TOL=84494],phylloscartes ceciliae[&&NHX:TOL=84495],phylloscartes kronei[&&NHX:TOL=84496],phylloscartes beckeri[&&NHX:TOL=84497],phylloscartes flavovirens[&&NHX:TOL=84498],phylloscartes virescens[&&NHX:TOL=84499],phylloscartes gualaquizae[&&NHX:TOL=84500],phylloscartes nigrifrons[&&NHX:TOL=84501],phylloscartes superciliaris[&&NHX:TOL=84502],phylloscartes flaviventris[&&NHX:TOL=84503],phylloscartes parkeri[&&NHX:TOL=84504],phylloscartes roquettei[&&NHX:TOL=84505],phylloscartes paulista[&&NHX:TOL=84506],phylloscartes oustaleti[&&NHX:TOL=84507],phylloscartes difficilis[&&NHX:TOL=84508],phylloscartes sylviolus[&&NHX:TOL=84509])phylloscartes[&&NHX:TOL=84493],(pogonotriccus poecilotis[&&NHX:TOL=84486],pogonotriccus chapmani[&&NHX:TOL=84487],pogonotriccus ophthalmicus[&&NHX:TOL=84488],pogonotriccus orbitalis[&&NHX:TOL=84489],pogonotriccus venezuelanus[&&NHX:TOL=84490],pogonotriccus lanyoni[&&NHX:TOL=84491],pogonotriccus eximius[&&NHX:TOL=84492])pogonotriccus[&&NHX:TOL=84485])[&&NHX:TOL=139098])pipromorphini[&&NHX:TOL=139095])[&&NHX:TOL=139092],tachuris rubrigastra[&&NHX:TOL=84541])[&&NHX:TOL=139090])rhynchocyclinae[&&NHX:TOL=139089])tyrannidae[&&NHX:TOL=67998])tyranni[&&NHX:TOL=67994],((melanopareia torquata[&&NHX:TOL=86104],melanopareia maximiliani[&&NHX:TOL=86105],melanopareia maranonica[&&NHX:TOL=86106],melanopareia elegans[&&NHX:TOL=86107])melanopareia[&&NHX:TOL=67981],((((neoctantes niger[&&NHX:TOL=85836],myrmorchilus strigilatus[&&NHX:TOL=85896],microrhopias quixensis[&&NHX:TOL=85913],(epinecrophylla myrmotherula leucophthalma[&&NHX:TOL=85874],epinecrophylla myrmotherula fulviventris[&&NHX:TOL=85872])epinecrophylla myrmotherula[&&NHX:TOL=138833],(myrmeciza atrothorax[&&NHX:TOL=85994],myrmeciza pelzelni[&&NHX:TOL=85991])myrmeciza part 2[&&NHX:TOL=111021])microrhopini[&&NHX:TOL=108285],((myrmochanes hemileucus[&&NHX:TOL=85969],((myrmotherula hauxwelli[&&NHX:TOL=85869],myrmotherula guttata[&&NHX:TOL=85870])[&&NHX:TOL=110996],myrmotherula gularis[&&NHX:TOL=85871],(myrmotherula gutturalis[&&NHX:TOL=85873],(myrmotherula fjeldsaai[&&NHX:TOL=85876],myrmotherula haematonota[&&NHX:TOL=85875],myrmotherula spodionota[&&NHX:TOL=85877])[&&NHX:TOL=110998],myrmotherula ornata[&&NHX:TOL=85878],myrmotherula erythrura[&&NHX:TOL=85879])[&&NHX:TOL=110997],(myrmotherula surinamensis[&&NHX:TOL=85861],myrmotherula longicauda[&&NHX:TOL=85866],myrmotherula brachyura[&&NHX:TOL=85860],myrmotherula ignota[&&NHX:TOL=85859],myrmotherula pacifica[&&NHX:TOL=85863],myrmotherula  multostriata[&&NHX:TOL=85862],myrmotherula cherriei[&&NHX:TOL=85864],myrmotherula klagesi[&&NHX:TOL=85865],myrmotherula ambigua[&&NHX:TOL=85867],myrmotherula sclateri[&&NHX:TOL=85868])streaked antwrens[&&NHX:TOL=111001],myrmotherula luctuosa[&&NHX:TOL=85881],myrmotherula schisticolor[&&NHX:TOL=85882],myrmotherula sunensis[&&NHX:TOL=85883],myrmotherula minor[&&NHX:TOL=85884],myrmotherula iheringi[&&NHX:TOL=85887],myrmotherula fluminensis[&&NHX:TOL=85888],myrmotherula grisea[&&NHX:TOL=85889],(myrmotherula unicolor[&&NHX:TOL=85890],myrmotherula snowi[&&NHX:TOL=85891])[&&NHX:TOL=110999],myrmotherula assimilis[&&NHX:TOL=85894])myrmotherula[&&NHX:TOL=85858])[&&NHX:TOL=111000],((formicivora iheringi[&&NHX:TOL=85915],formicivora erythronotos[&&NHX:TOL=85916],formicivora grisea[&&NHX:TOL=85917],formicivora intermedia[&&NHX:TOL=85918],formicivora serrana[&&NHX:TOL=85919],formicivora littoralis[&&NHX:TOL=85920],formicivora melanogaster[&&NHX:TOL=85921],formicivora rufa[&&NHX:TOL=85922],formicivora grantsaui[&&NHX:TOL=129455])formicivora[&&NHX:TOL=85914],(myrmotherula menetriesii[&&NHX:TOL=85893],(myrmotherula longipennis[&&NHX:TOL=85885],myrmotherula urosticta[&&NHX:TOL=85886])[&&NHX:TOL=111004],myrmotherula axillaris[&&NHX:TOL=85880],myrmotherula behni[&&NHX:TOL=85892])myrmotherula part 2[&&NHX:TOL=111003])[&&NHX:TOL=111002])formicivorini[&&NHX:TOL=108299],(((phaenostictus mcleannani[&&NHX:TOL=86025],(pithys castaneus[&&NHX:TOL=86003],pithys albifrons[&&NHX:TOL=86004])pithys[&&NHX:TOL=86002])[&&NHX:TOL=111005],((((gymnopithys leucaspis[&&NHX:TOL=86006],gymnopithys rufigula[&&NHX:TOL=86007],gymnopithys salvini[&&NHX:TOL=86008],gymnopithys lunulatus[&&NHX:TOL=86009])gymnopithys[&&NHX:TOL=86005],(rhegmatorhina gymnops[&&NHX:TOL=86011],rhegmatorhina berlepschi[&&NHX:TOL=86012],rhegmatorhina hoffmannsi[&&NHX:TOL=86013],rhegmatorhina cristata[&&NHX:TOL=86014],rhegmatorhina melanosticta[&&NHX:TOL=86015])rhegmatorhina[&&NHX:TOL=86010])[&&NHX:TOL=108302],(phlegopsis erythroptera[&&NHX:TOL=86022],phlegopsis nigromaculata[&&NHX:TOL=86023])phlegopsis[&&NHX:TOL=86021])[&&NHX:TOL=138835],hylophylax poecilinotus[&&NHX:TOL=86020])[&&NHX:TOL=138834],skutchia borbae[&&NHX:TOL=86024])professional antfollowing birds[&&NHX:TOL=108301],(((cercomacra cinerascens[&&NHX:TOL=85941],cercomacra brasiliana[&&NHX:TOL=85942],cercomacra tyrannina[&&NHX:TOL=85943],cercomacra laeta[&&NHX:TOL=85944],cercomacra parkeri[&&NHX:TOL=85945],cercomacra nigrescens[&&NHX:TOL=85946],cercomacra serva[&&NHX:TOL=85947],cercomacra nigricans[&&NHX:TOL=85948],cercomacra carbonaria[&&NHX:TOL=85949],cercomacra melanaria[&&NHX:TOL=85950],cercomacra manu[&&NHX:TOL=85951],cercomacra ferdinandi[&&NHX:TOL=85952])cercomacra[&&NHX:TOL=85940],(myrmeciza hemimelaena[&&NHX:TOL=85993],myrmeciza castanea[&&NHX:TOL=85992])myrmeciza part 3[&&NHX:TOL=111022])[&&NHX:TOL=111006],((drymophila ferruginea[&&NHX:TOL=85925],drymophila rubricollis[&&NHX:TOL=85926],drymophila genei[&&NHX:TOL=85927],drymophila ochropyga[&&NHX:TOL=85928],drymophila malura[&&NHX:TOL=85929],drymophila squamata[&&NHX:TOL=85930],drymophila devillei[&&NHX:TOL=85931],drymophila caudata[&&NHX:TOL=85932])drymophila[&&NHX:TOL=85924],(hypocnemis cantator[&&NHX:TOL=85964],hypocnemis flavescens[&&NHX:TOL=129571],hypocnemis peruviana[&&NHX:TOL=129572],hypocnemis subflava[&&NHX:TOL=129573],hypocnemis ochrogyna[&&NHX:TOL=129574],hypocnemis striata[&&NHX:TOL=129575],hypocnemis hypoxantha[&&NHX:TOL=85965])hypocnemis[&&NHX:TOL=85963])[&&NHX:TOL=111007])[&&NHX:TOL=108303])pithyini[&&NHX:TOL=108300],((((((myrmeciza melanoceps[&&NHX:TOL=85995],myrmeciza goeldii[&&NHX:TOL=85996])[&&NHX:TOL=111013],(myrmeciza immaculata[&&NHX:TOL=85999],myrmeciza fortis[&&NHX:TOL=85998])[&&NHX:TOL=111014])myrmeciza part 4[&&NHX:TOL=111012],(percnostola arenarum[&&NHX:TOL=85974],percnostola rufifrons[&&NHX:TOL=85973])percnostola[&&NHX:TOL=85972])[&&NHX:TOL=111011],(pyriglena leuconota[&&NHX:TOL=85954],pyriglena atra[&&NHX:TOL=85955],pyriglena leucoptera[&&NHX:TOL=85956])pyriglena[&&NHX:TOL=85953],((myrmoborus leucophrys[&&NHX:TOL=85959],myrmoborus lugubris[&&NHX:TOL=85960],myrmoborus myotherinus[&&NHX:TOL=85961],myrmoborus melanurus[&&NHX:TOL=85962])myrmoborus[&&NHX:TOL=85958],percnostola lophotes[&&NHX:TOL=85975])[&&NHX:TOL=111009],gymnocichla nudiceps[&&NHX:TOL=85970],((myrmeciza berlepschi[&&NHX:TOL=85990],(myrmeciza nigricauda[&&NHX:TOL=85989],myrmeciza laemosticta[&&NHX:TOL=85988])[&&NHX:TOL=111025])[&&NHX:TOL=111024],myrmeciza exsul[&&NHX:TOL=85983],myrmeciza griseiceps[&&NHX:TOL=86000],(myrmeciza disjuncta[&&NHX:TOL=85981],myrmeciza longipes[&&NHX:TOL=85982])[&&NHX:TOL=138840])myrmeciza[&&NHX:TOL=111015])[&&NHX:TOL=138837],(myrmeciza loricata[&&NHX:TOL=85986],myrmeciza squamosa[&&NHX:TOL=85987],myrmeciza ferruginea[&&NHX:TOL=85984],myrmeciza ruficauda[&&NHX:TOL=85985])myrmeciza part 5[&&NHX:TOL=111023],((hypocnemoides maculicauda[&&NHX:TOL=85967],hypocnemoides melanopogon[&&NHX:TOL=85968])hypocnemoides[&&NHX:TOL=85966],(hylophylax naevioides[&&NHX:TOL=86017],hylophylax naevius[&&NHX:TOL=86018],hylophylax punctulatus[&&NHX:TOL=86019])hylophylax[&&NHX:TOL=86016])[&&NHX:TOL=108306])[&&NHX:TOL=138836],(sclateria naevia[&&NHX:TOL=85971],((schistocichla schistacea[&&NHX:TOL=85977],schistocichla leucostigma[&&NHX:TOL=85978],schistocichla humaythae[&&NHX:TOL=129576],schistocichla brunneiceps[&&NHX:TOL=129577],schistocichla rufifacies[&&NHX:TOL=129578],schistocichla saturata[&&NHX:TOL=129579],schistocichla caurensis[&&NHX:TOL=85979])schistocichla[&&NHX:TOL=85976],myrmeciza hyperythra[&&NHX:TOL=85997])[&&NHX:TOL=111016])[&&NHX:TOL=108298])pyriglenini[&&NHX:TOL=111008],(megastictus margaritatus[&&NHX:TOL=85835],(thamnomanes ardesiacus[&&NHX:TOL=85853],thamnomanes saturninus[&&NHX:TOL=85854],thamnomanes caesius[&&NHX:TOL=85855],thamnomanes schistogynus[&&NHX:TOL=85856])thamnomanes[&&NHX:TOL=85852],dichrozona cincta[&&NHX:TOL=85895],((taraba major[&&NHX:TOL=85798],(cymbilaimus lineatus[&&NHX:TOL=85788],cymbilaimus sanctaemariae[&&NHX:TOL=85789])cymbilaimus[&&NHX:TOL=85787])[&&NHX:TOL=111017],((hypoedaleus guttatus[&&NHX:TOL=85790],batara cinerea[&&NHX:TOL=85791])[&&NHX:TOL=108290],((mackenziaena severa[&&NHX:TOL=85793],mackenziaena leachii[&&NHX:TOL=85794])mackenziaena[&&NHX:TOL=85792],(frederickena unduligera[&&NHX:TOL=85796],frederickena viridis[&&NHX:TOL=85797])frederickena[&&NHX:TOL=85795])[&&NHX:TOL=108291])[&&NHX:TOL=108289])large antshrikes[&&NHX:TOL=108288],(((((thamnophilus atrinucha[&&NHX:TOL=85823],thamnophilus bridgesi[&&NHX:TOL=85813])[&&NHX:TOL=108223],((((thamnophilus aethiops[&&NHX:TOL=85818],thamnophilus aroyae[&&NHX:TOL=85822])[&&NHX:TOL=108230],thamnophilus unicolor[&&NHX:TOL=85819],thamnophilus caerulescens[&&NHX:TOL=85832])[&&NHX:TOL=108228],(thamnophilus cryptoleucus[&&NHX:TOL=85817],thamnophilus nigrocinereus[&&NHX:TOL=85816])[&&NHX:TOL=108232],(thamnophilus punctatus[&&NHX:TOL=85824],thamnophilus sticturus[&&NHX:TOL=85826],thamnophilus pelzelni[&&NHX:TOL=85827],thamnophilus ambiguus[&&NHX:TOL=85828],thamnophilus stictocephalus[&&NHX:TOL=85825])[&&NHX:TOL=108233],(thamnophilus nigriceps[&&NHX:TOL=85814],thamnophilus praecox[&&NHX:TOL=85815])[&&NHX:TOL=108235],thamnophilus amazonicus[&&NHX:TOL=85829],(thamnophilus insignis[&&NHX:TOL=85831],thamnophilus divisorius[&&NHX:TOL=85830])[&&NHX:TOL=108237])[&&NHX:TOL=108225],(thamnophilus murinus[&&NHX:TOL=85821],thamnophilus schistaceus[&&NHX:TOL=85820])[&&NHX:TOL=108238])[&&NHX:TOL=108224])solid plumage thamnophilus[&&NHX:TOL=108222],(thamnophilus doliatus[&&NHX:TOL=85808],(thamnophilus ruficapillus[&&NHX:TOL=85834],thamnophilus torquatus[&&NHX:TOL=85833])[&&NHX:TOL=108241],(((thamnophilus palliatus[&&NHX:TOL=85812],thamnophilus tenuepunctatus[&&NHX:TOL=85811])[&&NHX:TOL=108244],thamnophilus multistriatus[&&NHX:TOL=85810])[&&NHX:TOL=108243],thamnophilus zarumae[&&NHX:TOL=85809])[&&NHX:TOL=108242])barred plumage thamnophilus[&&NHX:TOL=108239])thamnophilus[&&NHX:TOL=85807],((sakesphorus cristatus[&&NHX:TOL=85801],sakesphorus bernardi[&&NHX:TOL=85802],sakesphorus canadensis[&&NHX:TOL=85800])[&&NHX:TOL=111020],sakesphorus melanonotus[&&NHX:TOL=85803],sakesphorus melanothorax[&&NHX:TOL=85804])sakesphorus[&&NHX:TOL=85799])[&&NHX:TOL=138838],(((dysithamnus stictothorax[&&NHX:TOL=85843],dysithamnus mentalis[&&NHX:TOL=85844],dysithamnus striaticeps[&&NHX:TOL=85845],dysithamnus puncticeps[&&NHX:TOL=85846],dysithamnus xanthopterus[&&NHX:TOL=85847],dysithamnus occidentalis[&&NHX:TOL=85848],dysithamnus plumbeus[&&NHX:TOL=85849])dysithamnus[&&NHX:TOL=85842],(herpsilochmus pileatus[&&NHX:TOL=85898],herpsilochmus sellowi[&&NHX:TOL=85899],herpsilochmus atricapillus[&&NHX:TOL=85900],herpsilochmus motacilloides[&&NHX:TOL=85901],herpsilochmus parkeri[&&NHX:TOL=85902],herpsilochmus sticturus[&&NHX:TOL=85903],herpsilochmus dugandi[&&NHX:TOL=85904],herpsilochmus stictocephalus[&&NHX:TOL=85905],herpsilochmus dorsimaculatus[&&NHX:TOL=85906],herpsilochmus roraimae[&&NHX:TOL=85907],herpsilochmus pectoralis[&&NHX:TOL=85908],herpsilochmus longirostris[&&NHX:TOL=85909],herpsilochmus gentryi[&&NHX:TOL=85910],herpsilochmus axillaris[&&NHX:TOL=85911],herpsilochmus rufimarginatus[&&NHX:TOL=85912])herpsilochmus[&&NHX:TOL=85897])[&&NHX:TOL=108293],sakesphorus luctuosus[&&NHX:TOL=85805])[&&NHX:TOL=138839])[&&NHX:TOL=111018])thamnophilini[&&NHX:TOL=108286],(clytoctantes atrogularis[&&NHX:TOL=85838],clytoctantes alixii[&&NHX:TOL=85839])clytoctantes[&&NHX:TOL=85837],rhopornis ardesiacus[&&NHX:TOL=85957],stymphalornis acutirostris[&&NHX:TOL=85923],xenornis setifrons[&&NHX:TOL=85840])thamnophilinae[&&NHX:TOL=108296],(myrmornis torquata[&&NHX:TOL=86001],(pygiptila stellaris[&&NHX:TOL=85857],thamnistes anabatinus[&&NHX:TOL=85841])[&&NHX:TOL=108295])myrmornithinae[&&NHX:TOL=108294])[&&NHX:TOL=138832],(terenura maculata[&&NHX:TOL=85934],terenura sicki[&&NHX:TOL=85935],terenura callinota[&&NHX:TOL=85936],terenura humeralis[&&NHX:TOL=85937],terenura sharpei[&&NHX:TOL=85938],terenura spodioptila[&&NHX:TOL=85939])terenura[&&NHX:TOL=85933],biatas nigropectus[&&NHX:TOL=85806])thamnophilidae[&&NHX:TOL=67983],((conopophaga lineata[&&NHX:TOL=86026],conopophaga cearae[&&NHX:TOL=86027],conopophaga aurita[&&NHX:TOL=86028],conopophaga roberti[&&NHX:TOL=86029],conopophaga peruviana[&&NHX:TOL=86030],conopophaga ardesiaca[&&NHX:TOL=86031],conopophaga castaneiceps[&&NHX:TOL=86032],conopophaga melanops[&&NHX:TOL=86033],conopophaga melanogaster[&&NHX:TOL=86034])conopophaga[&&NHX:TOL=67984],(pittasoma rufopileatum[&&NHX:TOL=86069],pittasoma michleri[&&NHX:TOL=86068])pittasoma[&&NHX:TOL=86067])conopophagidae[&&NHX:TOL=110659],(((grallaria squamigera[&&NHX:TOL=86036],grallaria gigantea[&&NHX:TOL=86037],grallaria excelsa[&&NHX:TOL=86038],grallaria varia[&&NHX:TOL=86039],grallaria alleni[&&NHX:TOL=86040],grallaria guatimalensis[&&NHX:TOL=86041],grallaria chthonia[&&NHX:TOL=86042],grallaria haplonota[&&NHX:TOL=86043],grallaria dignissima[&&NHX:TOL=86044],grallaria eludens[&&NHX:TOL=86045],grallaria ruficapilla[&&NHX:TOL=86046],grallaria watkinsi[&&NHX:TOL=86047],grallaria bangsi[&&NHX:TOL=86048],grallaria kaestneri[&&NHX:TOL=86049],grallaria andicolus[&&NHX:TOL=86050],grallaria griseonucha[&&NHX:TOL=86051],grallaria rufocinerea[&&NHX:TOL=86052],grallaria ridgelyi[&&NHX:TOL=86053],grallaria nuchalis[&&NHX:TOL=86054],grallaria carrikeri[&&NHX:TOL=86055],grallaria albigula[&&NHX:TOL=86056],grallaria flavotincta[&&NHX:TOL=86057],grallaria hypoleuca[&&NHX:TOL=86058],grallaria przewalskii[&&NHX:TOL=86059],grallaria capitalis[&&NHX:TOL=86060],grallaria erythroleuca[&&NHX:TOL=86061],grallaria rufula[&&NHX:TOL=86062],grallaria blakei[&&NHX:TOL=86063],grallaria quitensis[&&NHX:TOL=86064],grallaria milleri[&&NHX:TOL=86065],grallaria erythrotis[&&NHX:TOL=86066])grallaria[&&NHX:TOL=86035],(((hylopezus perspicillatus[&&NHX:TOL=86071],hylopezus macularius[&&NHX:TOL=86072],hylopezus auricularis[&&NHX:TOL=86073],hylopezus dives[&&NHX:TOL=86074],hylopezus fulviventris[&&NHX:TOL=86075],hylopezus berlepschi[&&NHX:TOL=86076],hylopezus ochroleucus[&&NHX:TOL=86077],hylopezus nattereri[&&NHX:TOL=86078])hylopezus[&&NHX:TOL=86070],(myrmothera simplex[&&NHX:TOL=86080],myrmothera campanisona[&&NHX:TOL=86081])myrmothera[&&NHX:TOL=86079])[&&NHX:TOL=108256],(grallaricula flavirostris[&&NHX:TOL=86083],grallaricula loricata[&&NHX:TOL=86084],grallaricula cucullata[&&NHX:TOL=86085],grallaricula peruviana[&&NHX:TOL=86086],grallaricula ochraceifrons[&&NHX:TOL=86087],grallaricula ferrugineipectus[&&NHX:TOL=86088],grallaricula leymebambae[&&NHX:TOL=86089],grallaricula nana[&&NHX:TOL=86090],grallaricula lineifrons[&&NHX:TOL=86091])grallaricula[&&NHX:TOL=86082])[&&NHX:TOL=108255])grallariidae[&&NHX:TOL=67986],(((((scelorchilus rubecula[&&NHX:TOL=86098],scelorchilus albicollis[&&NHX:TOL=86099])scelorchilus[&&NHX:TOL=86097],(pteroptochos castaneus[&&NHX:TOL=86094],pteroptochos tarnii[&&NHX:TOL=86095],pteroptochos megapodius[&&NHX:TOL=86096])pteroptochos[&&NHX:TOL=86093])[&&NHX:TOL=138805],(((teledromas fuscus[&&NHX:TOL=86101],rhinocrypta lanceolata[&&NHX:TOL=86100])[&&NHX:TOL=138808],acropternis orthonyx[&&NHX:TOL=86092])[&&NHX:TOL=138807],liosceles thoracicus[&&NHX:TOL=86102])[&&NHX:TOL=138806])[&&NHX:TOL=138804],psilorhamphus guttatus[&&NHX:TOL=86108],((eugralla paradoxa[&&NHX:TOL=86112],(scytalopus iraiensis[&&NHX:TOL=86115],scytalopus diamantinensis[&&NHX:TOL=129852],scytalopus speluncae[&&NHX:TOL=86116],scytalopus pachecoi[&&NHX:TOL=129465],scytalopus novacapitalis[&&NHX:TOL=86117],scytalopus indigoticus[&&NHX:TOL=86118],scytalopus psychopompus[&&NHX:TOL=86119],scytalopus bolivianus[&&NHX:TOL=86120],scytalopus atratus[&&NHX:TOL=86121],scytalopus sanctaemartae[&&NHX:TOL=86122],scytalopus femoralis[&&NHX:TOL=86123],scytalopus micropterus[&&NHX:TOL=86124],scytalopus vicinior[&&NHX:TOL=86125],scytalopus robbinsi[&&NHX:TOL=86126],scytalopus chocoensis[&&NHX:TOL=86127],scytalopus rodriguezi[&&NHX:TOL=129466],scytalopus stilesi[&&NHX:TOL=129467],scytalopus panamensis[&&NHX:TOL=86128],scytalopus argentifrons[&&NHX:TOL=86129],scytalopus caracae[&&NHX:TOL=86130],scytalopus meridanus[&&NHX:TOL=86131],scytalopus latebricola[&&NHX:TOL=86132],scytalopus spillmanni[&&NHX:TOL=86133],scytalopus parkeri[&&NHX:TOL=86134],scytalopus parvirostris[&&NHX:TOL=86135],scytalopus acutirostris[&&NHX:TOL=86136],scytalopus unicolor[&&NHX:TOL=86137],scytalopus fuscicauda[&&NHX:TOL=86138],scytalopus griseicollis[&&NHX:TOL=86139],scytalopus canus[&&NHX:TOL=86140],scytalopus affinis[&&NHX:TOL=86141],scytalopus altirostris[&&NHX:TOL=86142],scytalopus urubambae[&&NHX:TOL=86143],scytalopus schulenbergi[&&NHX:TOL=86144],scytalopus simonsi[&&NHX:TOL=86145],scytalopus zimmeri[&&NHX:TOL=86146],scytalopus superciliaris[&&NHX:TOL=86147],scytalopus magellanicus[&&NHX:TOL=86148],scytalopus fuscus[&&NHX:TOL=86149],scytalopus latrans[&&NHX:TOL=86150],scytalopus macropus[&&NHX:TOL=86151],scytalopus infasciatus[&&NHX:TOL=86152])scytalopus[&&NHX:TOL=86114])[&&NHX:TOL=138810],myornis senilis[&&NHX:TOL=86113],(merulaxis stresemanni[&&NHX:TOL=86110],merulaxis ater[&&NHX:TOL=86111])merulaxis[&&NHX:TOL=86109])[&&NHX:TOL=138809])rhinocryptidae[&&NHX:TOL=67988],(((formicarius colma[&&NHX:TOL=86154],formicarius analis[&&NHX:TOL=86155],formicarius moniliger[&&NHX:TOL=86156],formicarius hoffmanni[&&NHX:TOL=86157],formicarius rufifrons[&&NHX:TOL=86158],formicarius nigricapillus[&&NHX:TOL=86159],formicarius rufipectus[&&NHX:TOL=86160])formicarius[&&NHX:TOL=86153],(chamaeza campanisona[&&NHX:TOL=86162],chamaeza nobilis[&&NHX:TOL=86163],chamaeza meruloides[&&NHX:TOL=86164],chamaeza ruficauda[&&NHX:TOL=86165],chamaeza turdina[&&NHX:TOL=86166],chamaeza mollissima[&&NHX:TOL=86167])chamaeza[&&NHX:TOL=86161])formicariidae[&&NHX:TOL=67990],(((sclerurus mexicanus[&&NHX:TOL=86492],sclerurus rufigularis[&&NHX:TOL=86493],sclerurus albigularis[&&NHX:TOL=86494],sclerurus caudacutus[&&NHX:TOL=86495],sclerurus scansor[&&NHX:TOL=86496],sclerurus guatemalensis[&&NHX:TOL=86497])sclerurus[&&NHX:TOL=86385],(((geositta tenuirostris[&&NHX:TOL=86172],geositta cunicularia[&&NHX:TOL=86169])[&&NHX:TOL=138800],geositta peruviana[&&NHX:TOL=86174])[&&NHX:TOL=138799],((geositta maritima[&&NHX:TOL=86173],geositta antarctica[&&NHX:TOL=86171],geositta saxicolina[&&NHX:TOL=86175],geositta isabellina[&&NHX:TOL=86177])[&&NHX:TOL=138802],(geositta rufipennis[&&NHX:TOL=86176],geositta punensis[&&NHX:TOL=86170])[&&NHX:TOL=138803],geositta crassirostris[&&NHX:TOL=86178],geositta geobates poecilopterus[&&NHX:TOL=86179])[&&NHX:TOL=138801])geositta[&&NHX:TOL=86168])scleruridae[&&NHX:TOL=108325],(((((((((((upucerthia jelskii[&&NHX:TOL=86181],upucerthia validirostris[&&NHX:TOL=86182])[&&NHX:TOL=111205],(upucerthia dumetaria[&&NHX:TOL=86184],upucerthia albigula[&&NHX:TOL=86183])[&&NHX:TOL=111206])upucerthia[&&NHX:TOL=86180],(cinclodes excelsior[&&NHX:TOL=86193],cinclodes aricomae[&&NHX:TOL=86194],cinclodes fuscus[&&NHX:TOL=86195],cinclodes comechingonus[&&NHX:TOL=86196],cinclodes pabsti[&&NHX:TOL=86197],cinclodes olrogi[&&NHX:TOL=86198],cinclodes oustaleti[&&NHX:TOL=86199],cinclodes patagonicus[&&NHX:TOL=86200],cinclodes antarcticus[&&NHX:TOL=86201],cinclodes taczanowskii[&&NHX:TOL=86202],cinclodes nigrofumosus[&&NHX:TOL=86203],cinclodes atacamensis[&&NHX:TOL=86204],cinclodes palliatus[&&NHX:TOL=86205])cinclodes[&&NHX:TOL=86192])[&&NHX:TOL=108315],((furnarius minor[&&NHX:TOL=86207],furnarius figulus[&&NHX:TOL=86208],furnarius leucopus[&&NHX:TOL=86209],furnarius cinnamomeus[&&NHX:TOL=86210],furnarius longirostris[&&NHX:TOL=86211],furnarius torridus[&&NHX:TOL=86212],furnarius rufus[&&NHX:TOL=86213],furnarius cristatus[&&NHX:TOL=86214])furnarius[&&NHX:TOL=86206],upucerthia serrana[&&NHX:TOL=86185],lochmias nematura[&&NHX:TOL=86498],(phleocryptes melanops[&&NHX:TOL=86347],limnornis curvirostris[&&NHX:TOL=86351])[&&NHX:TOL=108314])[&&NHX:TOL=138775])[&&NHX:TOL=108312],((pseudocolaptes lawrencii[&&NHX:TOL=86376],pseudocolaptes johnsoni[&&NHX:TOL=86377],pseudocolaptes boissonneautii[&&NHX:TOL=86378])pseudocolaptes[&&NHX:TOL=86375],((tarphonomus upucerthia certhioides[&&NHX:TOL=86189],tarphonomus upucerthia harterti[&&NHX:TOL=86188])[&&NHX:TOL=111207],premnornis guttuligera[&&NHX:TOL=86359])[&&NHX:TOL=138782])[&&NHX:TOL=108316])[&&NHX:TOL=138774],(((aphrastura masafuerae[&&NHX:TOL=86217],aphrastura spinicauda[&&NHX:TOL=86218])aphrastura[&&NHX:TOL=86216],(((leptasthenura fuliginiceps[&&NHX:TOL=86220],leptasthenura yanacensis[&&NHX:TOL=86221],leptasthenura platensis[&&NHX:TOL=86222],leptasthenura aegithaloides[&&NHX:TOL=86223],leptasthenura striolata[&&NHX:TOL=86224],leptasthenura pileata[&&NHX:TOL=86225],leptasthenura xenothorax[&&NHX:TOL=86226],leptasthenura striata[&&NHX:TOL=86227],leptasthenura andicola[&&NHX:TOL=86228],leptasthenura setaria[&&NHX:TOL=86229])leptasthenura[&&NHX:TOL=86219],sylviorthorhynchus desmursii[&&NHX:TOL=86215])[&&NHX:TOL=138776],(((schoeniophylax phryganophilus[&&NHX:TOL=86265],(certhiaxis mustelinus[&&NHX:TOL=86327],certhiaxis cinnamomeus[&&NHX:TOL=86328])certhiaxis[&&NHX:TOL=86326])[&&NHX:TOL=138795],((synallaxis castanea[&&NHX:TOL=86271],synallaxis unirufa[&&NHX:TOL=86270],synallaxis kollari[&&NHX:TOL=86268],synallaxis candei[&&NHX:TOL=86267],synallaxis chinchipensis[&&NHX:TOL=86300],synallaxis stictothorax[&&NHX:TOL=86299],synallaxis zimmeri[&&NHX:TOL=86298],synallaxis albilora[&&NHX:TOL=86297],synallaxis maranonica[&&NHX:TOL=86296],synallaxis gujanensis[&&NHX:TOL=86295],synallaxis cabanisi[&&NHX:TOL=86294],synallaxis moesta[&&NHX:TOL=86293],synallaxis macconnelli[&&NHX:TOL=86292],synallaxis propinqua[&&NHX:TOL=86291],synallaxis tithys[&&NHX:TOL=86290],synallaxis brachyura[&&NHX:TOL=86289],synallaxis erythrothorax[&&NHX:TOL=86288],synallaxis cherriei[&&NHX:TOL=86287],synallaxis rutilans[&&NHX:TOL=86286],synallaxis spixi[&&NHX:TOL=86285],synallaxis hypospodia[&&NHX:TOL=86284],synallaxis albigularis[&&NHX:TOL=86283],synallaxis albescens[&&NHX:TOL=86282],synallaxis courseni[&&NHX:TOL=86281],synallaxis azarae[&&NHX:TOL=86280],synallaxis frontalis[&&NHX:TOL=86279],synallaxis subpudica[&&NHX:TOL=86278],synallaxis cinerascens[&&NHX:TOL=86277],synallaxis cinnamomea[&&NHX:TOL=86276],synallaxis infuscata[&&NHX:TOL=86275],synallaxis cinerea[&&NHX:TOL=86274],synallaxis ruficapilla[&&NHX:TOL=86273],synallaxis fuscorufa[&&NHX:TOL=86272])synallaxis[&&NHX:TOL=86266],gyalophylax hellmayri[&&NHX:TOL=86302])[&&NHX:TOL=138796],siptornopsis hypochondriaca[&&NHX:TOL=86301],poecilurus synallaxis scutatus[&&NHX:TOL=86269])[&&NHX:TOL=108330],(spartonoica maluroides[&&NHX:TOL=86348],(pseudoseisura cristata[&&NHX:TOL=86371],pseudoseisura unirufa[&&NHX:TOL=86372],pseudoseisura lophotes[&&NHX:TOL=86373],pseudoseisura gutturalis[&&NHX:TOL=86374])pseudoseisura[&&NHX:TOL=86370],asthenes cactorum[&&NHX:TOL=86249])[&&NHX:TOL=138784],(phacellodomus rufifrons[&&NHX:TOL=86335],phacellodomus inornatus[&&NHX:TOL=86336],phacellodomus sibilatrix[&&NHX:TOL=86337],phacellodomus striaticeps[&&NHX:TOL=86338],phacellodomus striaticollis[&&NHX:TOL=86339],phacellodomus maculipectus[&&NHX:TOL=86340],phacellodomus dorsalis[&&NHX:TOL=86341],phacellodomus ruber[&&NHX:TOL=86342],phacellodomus erythrophthalmus[&&NHX:TOL=86343],phacellodomus ferrugineigula[&&NHX:TOL=86344])phacellodomus[&&NHX:TOL=86334],((((schizoeaca perijana[&&NHX:TOL=86231],schizoeaca fuliginosa[&&NHX:TOL=86232],schizoeaca vilcabambae[&&NHX:TOL=86233],schizoeaca coryi[&&NHX:TOL=86234],schizoeaca griseomurina[&&NHX:TOL=86235],schizoeaca palpebralis[&&NHX:TOL=86236],schizoeaca helleri[&&NHX:TOL=86237],schizoeaca harterti[&&NHX:TOL=86238])schizoeaca[&&NHX:TOL=86230],oreophylax moreirae[&&NHX:TOL=86239])[&&NHX:TOL=108331],(asthenes pyrrholeuca[&&NHX:TOL=86241],asthenes humicola[&&NHX:TOL=86243],asthenes humilis[&&NHX:TOL=86250],asthenes urubambensis[&&NHX:TOL=86261],asthenes patagonica[&&NHX:TOL=86244],asthenes pudibunda[&&NHX:TOL=86245],asthenes ottonis[&&NHX:TOL=86246],asthenes heterura[&&NHX:TOL=86247],asthenes modesta[&&NHX:TOL=86248],asthenes dorbignyi[&&NHX:TOL=86251],asthenes arequipae[&&NHX:TOL=86252],asthenes huancavelicae[&&NHX:TOL=86253],asthenes berlepschi[&&NHX:TOL=86254],asthenes steinbachi[&&NHX:TOL=86255],asthenes luizae[&&NHX:TOL=86256],asthenes wyatti[&&NHX:TOL=86257],asthenes sclateri[&&NHX:TOL=86258],asthenes anthoides[&&NHX:TOL=86259],asthenes hudsoni[&&NHX:TOL=86260],asthenes flammulata[&&NHX:TOL=86262],asthenes virgata[&&NHX:TOL=86263],asthenes maculicauda[&&NHX:TOL=86264])asthenes[&&NHX:TOL=86240])[&&NHX:TOL=111209],asthenes baeri[&&NHX:TOL=86242])[&&NHX:TOL=138785],hellmayrea gularis[&&NHX:TOL=86303],(((((roraimia adusta[&&NHX:TOL=86363],(thripophaga cherriei[&&NHX:TOL=86330],thripophaga macroura[&&NHX:TOL=86331],thripophaga fusciceps[&&NHX:TOL=86332],thripophaga berlepschi[&&NHX:TOL=86333])thripophaga[&&NHX:TOL=86329])[&&NHX:TOL=138791],siptornis striaticollis[&&NHX:TOL=86354])[&&NHX:TOL=138790],(limnoctites rectirostris[&&NHX:TOL=86350],(cranioleuca marcapatae[&&NHX:TOL=86305],cranioleuca albiceps[&&NHX:TOL=86306],cranioleuca vulpina[&&NHX:TOL=86307],cranioleuca dissita[&&NHX:TOL=86308],cranioleuca vulpecula[&&NHX:TOL=86309],cranioleuca sulphurifera[&&NHX:TOL=86310],cranioleuca subcristata[&&NHX:TOL=86311],cranioleuca pyrrhophia[&&NHX:TOL=86312],cranioleuca henricae[&&NHX:TOL=86313],cranioleuca obsoleta[&&NHX:TOL=86314],cranioleuca pallida[&&NHX:TOL=86315],cranioleuca semicinerea[&&NHX:TOL=86316],cranioleuca albicapilla[&&NHX:TOL=86317],cranioleuca erythrops[&&NHX:TOL=86318],cranioleuca demissa[&&NHX:TOL=86319],cranioleuca hellmayri[&&NHX:TOL=86320],cranioleuca curtata[&&NHX:TOL=86321],cranioleuca antisiensis[&&NHX:TOL=86322],cranioleuca baroni[&&NHX:TOL=86323],cranioleuca gutturata[&&NHX:TOL=86324],cranioleuca muelleri[&&NHX:TOL=86325])cranioleuca[&&NHX:TOL=86304])[&&NHX:TOL=108328])[&&NHX:TOL=138789],(metopothrix aurantiaca[&&NHX:TOL=86355],(xenerpestes singularis[&&NHX:TOL=86357],xenerpestes minlosi[&&NHX:TOL=86358])xenerpestes[&&NHX:TOL=86356])[&&NHX:TOL=138792])[&&NHX:TOL=138788],acrobatornis fonsecai[&&NHX:TOL=86364])[&&NHX:TOL=138787],(anumbius annumbi[&&NHX:TOL=86352],coryphistera alaudina[&&NHX:TOL=86353])[&&NHX:TOL=108311])[&&NHX:TOL=108309])[&&NHX:TOL=108333])[&&NHX:TOL=108308],((margarornis rubiginosus[&&NHX:TOL=86366],margarornis stellatus[&&NHX:TOL=86367],margarornis bellulus[&&NHX:TOL=86368],margarornis squamiger[&&NHX:TOL=86369])margarornis[&&NHX:TOL=86365],(premnoplex tatei[&&NHX:TOL=86361],premnoplex brunnescens[&&NHX:TOL=86362])premnoplex[&&NHX:TOL=86360])[&&NHX:TOL=138793])[&&NHX:TOL=138783])[&&NHX:TOL=108307],(((((anabacerthia variegaticeps[&&NHX:TOL=86446],anabacerthia striaticollis[&&NHX:TOL=86447],anabacerthia amaurotis[&&NHX:TOL=86448])anabacerthia[&&NHX:TOL=86380],((syndactyla guttulata[&&NHX:TOL=86449],syndactyla subalaris[&&NHX:TOL=86450],syndactyla rufosuperciliata[&&NHX:TOL=86451],syndactyla ruficollis[&&NHX:TOL=86452])syndactyla[&&NHX:TOL=86381],(simoxenops striatus[&&NHX:TOL=86454],simoxenops ucayalae[&&NHX:TOL=86455])simoxenops[&&NHX:TOL=86453])[&&NHX:TOL=138794])[&&NHX:TOL=108323],megaxenops parnaguae[&&NHX:TOL=86504])[&&NHX:TOL=108322],((philydor ruficaudatum[&&NHX:TOL=86460],philydor fuscipenne[&&NHX:TOL=86461],philydor erythrocercum[&&NHX:TOL=86462],philydor erythropterum[&&NHX:TOL=86463],philydor lichtensteini[&&NHX:TOL=86464],philydor novaesi[&&NHX:TOL=86465],philydor atricapillus[&&NHX:TOL=86466],philydor rufum[&&NHX:TOL=86467],philydor pyrrhodes[&&NHX:TOL=86468],philydor dimidiatum[&&NHX:TOL=86469])philydor[&&NHX:TOL=86382],heliobletus contaminatus[&&NHX:TOL=86499])[&&NHX:TOL=108324],(anabazenops fuscus[&&NHX:TOL=86471],anabazenops dorsalis[&&NHX:TOL=86472])anabazenops[&&NHX:TOL=86470])[&&NHX:TOL=108321],cichlocolaptes leucophrus[&&NHX:TOL=86473],(((thripadectes ignobilis[&&NHX:TOL=86474],thripadectes rufobrunneus[&&NHX:TOL=86475],thripadectes melanorhynchus[&&NHX:TOL=86476],thripadectes holostictus[&&NHX:TOL=86477],thripadectes virgaticeps[&&NHX:TOL=86478],thripadectes flammulatus[&&NHX:TOL=86479],thripadectes scrutator[&&NHX:TOL=86480])thripadectes[&&NHX:TOL=86383],(((automolus ochrolaemus[&&NHX:TOL=86481],automolus infuscatus[&&NHX:TOL=86482],automolus paraensis[&&NHX:TOL=86483],automolus leucophthalmus[&&NHX:TOL=86484],automolus lammi[&&NHX:TOL=129853],automolus melanopezus[&&NHX:TOL=86485],automolus roraimae[&&NHX:TOL=86486],automolus rubiginosus[&&NHX:TOL=86487],automolus rufipileatus[&&NHX:TOL=86488])automolus[&&NHX:TOL=86384],(hylocryptus rectirostris[&&NHX:TOL=86490],hylocryptus erythrocephalus[&&NHX:TOL=86491])hylocryptus[&&NHX:TOL=86489])[&&NHX:TOL=138779],(hyloctistes subulatus[&&NHX:TOL=86458],hyloctistes virgatus[&&NHX:TOL=86459])hyloctistes[&&NHX:TOL=86457])[&&NHX:TOL=138778])[&&NHX:TOL=108319],ancistrops strigilatus[&&NHX:TOL=86456])[&&NHX:TOL=138777])[&&NHX:TOL=108318])[&&NHX:TOL=108332],clibanornis dendrocolaptoides[&&NHX:TOL=86345],((((ochetorhynchus phoenicurus[&&NHX:TOL=86190],upucerthia ruficaudus[&&NHX:TOL=86186])[&&NHX:TOL=111203],(chilia melanura[&&NHX:TOL=86191],upucerthia andaecola[&&NHX:TOL=86187])[&&NHX:TOL=111204])[&&NHX:TOL=111202],microxenops xenops milleri[&&NHX:TOL=86500])[&&NHX:TOL=138781],pygarrhichas albogularis[&&NHX:TOL=86505])[&&NHX:TOL=138780])[&&NHX:TOL=138773],berlepschia rikeri[&&NHX:TOL=86379])[&&NHX:TOL=138772],(xenops rutilans[&&NHX:TOL=86503],xenops minutus[&&NHX:TOL=86502],xenops tenuirostris[&&NHX:TOL=86501])xenops[&&NHX:TOL=86386])furnariidae[&&NHX:TOL=67993],(((((lepidocolaptes leucogaster[&&NHX:TOL=86433],lepidocolaptes souleyetii[&&NHX:TOL=86434],lepidocolaptes angustirostris[&&NHX:TOL=86435],lepidocolaptes affinis[&&NHX:TOL=86436],lepidocolaptes lacrymiger[&&NHX:TOL=86437],lepidocolaptes squamatus[&&NHX:TOL=86438],lepidocolaptes albolineatus[&&NHX:TOL=86439],lepidocolaptes falcinellus[&&NHX:TOL=108204])lepidocolaptes[&&NHX:TOL=86432],(xiphorhynchus picus[&&NHX:TOL=86418],xiphorhynchus kienerii[&&NHX:TOL=86419],xiphorhynchus obsoletus[&&NHX:TOL=86420],xiphorhynchus ocellatus[&&NHX:TOL=86422],xiphorhynchus chunchotambo[&&NHX:TOL=129854],xiphorhynchus fuscus[&&NHX:TOL=86421],xiphorhynchus elegans[&&NHX:TOL=86423],xiphorhynchus spixii[&&NHX:TOL=86424],xiphorhynchus pardalotus[&&NHX:TOL=86425],xiphorhynchus guttatus[&&NHX:TOL=86426],xiphorhynchus susurrans[&&NHX:TOL=86427],xiphorhynchus flavigaster[&&NHX:TOL=86428],xiphorhynchus lachrymosus[&&NHX:TOL=86429],xiphorhynchus erythropygius[&&NHX:TOL=86430],xiphorhynchus triangularis[&&NHX:TOL=86431])xiphorhynchus[&&NHX:TOL=86417],drymornis bridgesii[&&NHX:TOL=86399],(campylorhamphus pucherani[&&NHX:TOL=86441],campylorhamphus trochilirostris[&&NHX:TOL=86442],campylorhamphus falcularius[&&NHX:TOL=86443],campylorhamphus pusillus[&&NHX:TOL=86444],campylorhamphus procurvoides[&&NHX:TOL=86445])campylorhamphus[&&NHX:TOL=86440])[&&NHX:TOL=111216],((dendrexetastes rufigula[&&NHX:TOL=86401],nasica longirostris[&&NHX:TOL=86400])[&&NHX:TOL=111218],(((xiphocolaptes promeropirhynchus[&&NHX:TOL=86407],xiphocolaptes albicollis[&&NHX:TOL=86408],xiphocolaptes falcirostris[&&NHX:TOL=86409],xiphocolaptes major[&&NHX:TOL=86410])xiphocolaptes[&&NHX:TOL=86406],(hylexetastes perrotii[&&NHX:TOL=86403],hylexetastes uniformis[&&NHX:TOL=86404],hylexetastes brigidai[&&NHX:TOL=129580],hylexetastes stresemanni[&&NHX:TOL=86405])hylexetastes[&&NHX:TOL=86402])[&&NHX:TOL=111219],(dendrocolaptes sanctithomae[&&NHX:TOL=86412],dendrocolaptes certhia[&&NHX:TOL=86413],dendrocolaptes hoffmannsi[&&NHX:TOL=86414],dendrocolaptes picumnus[&&NHX:TOL=86415],dendrocolaptes platyrostris[&&NHX:TOL=86416])dendrocolaptes[&&NHX:TOL=86411])[&&NHX:TOL=138798])[&&NHX:TOL=111217])[&&NHX:TOL=111215],glyphorynchus spirurus[&&NHX:TOL=86398])[&&NHX:TOL=138797],((dendrocincla tyrannina[&&NHX:TOL=86388],dendrocincla fuliginosa[&&NHX:TOL=86389],dendrocincla turdina[&&NHX:TOL=86390],dendrocincla anabatina[&&NHX:TOL=86391],dendrocincla homochroa[&&NHX:TOL=86392],dendrocincla merula[&&NHX:TOL=86393])dendrocincla[&&NHX:TOL=86387],((deconychura stictolaema[&&NHX:TOL=86396],deconychura longicauda[&&NHX:TOL=86395])deconychura[&&NHX:TOL=86394],sittasomus griseicapillus[&&NHX:TOL=86397])[&&NHX:TOL=111214])[&&NHX:TOL=111213])dendrocolaptidae[&&NHX:TOL=67992])[&&NHX:TOL=110662])[&&NHX:TOL=110661])[&&NHX:TOL=67989])[&&NHX:TOL=67987])[&&NHX:TOL=67985])furnarii[&&NHX:TOL=67980])tyrannides new world suboscines[&&NHX:TOL=67979])suboscines[&&NHX:TOL=26445],((((((((((poecilodryas albispecularis[&&NHX:TOL=79276],poecilodryas cinereifrons[&&NHX:TOL=79277],poecilodryas brachyura[&&NHX:TOL=79278],poecilodryas hypoleuca[&&NHX:TOL=79279],poecilodryas superciliosa[&&NHX:TOL=79280],poecilodryas cerviniventris[&&NHX:TOL=79281],poecilodryas placens[&&NHX:TOL=79282],poecilodryas albonotata[&&NHX:TOL=79283])poecilodryas[&&NHX:TOL=79275],(peneothello sigillata[&&NHX:TOL=79285],peneothello cryptoleuca[&&NHX:TOL=79286],peneothello cyanus[&&NHX:TOL=79287],peneothello bimaculata[&&NHX:TOL=79288])peneothello[&&NHX:TOL=79284],peneoenanthe pulverulenta[&&NHX:TOL=79289],(tregellasia leucops[&&NHX:TOL=79291],tregellasia capito[&&NHX:TOL=79292])tregellasia[&&NHX:TOL=79290],(eopsaltria australis[&&NHX:TOL=79294],eopsaltria griseogularis[&&NHX:TOL=79295],eopsaltria georgiana[&&NHX:TOL=79296],eopsaltria flaviventris[&&NHX:TOL=79297])eopsaltria[&&NHX:TOL=79293],(melanodryas cucullata[&&NHX:TOL=79299],melanodryas vittata[&&NHX:TOL=79300])melanodryas[&&NHX:TOL=79298],(pachycephalopsis hattamensis[&&NHX:TOL=79302],pachycephalopsis poliosoma[&&NHX:TOL=79303])pachycephalopsis[&&NHX:TOL=79301],monachella muelleriana[&&NHX:TOL=79304],(microeca papuana[&&NHX:TOL=79306],microeca griseoceps[&&NHX:TOL=79307],microeca flavovirescens[&&NHX:TOL=79308],microeca flavigaster[&&NHX:TOL=79309],microeca hemixantha[&&NHX:TOL=79310],microeca fascinans[&&NHX:TOL=79311])microeca[&&NHX:TOL=79305],eugerygone rubra[&&NHX:TOL=79312],(petroica rosea[&&NHX:TOL=79314],petroica rodinogaster[&&NHX:TOL=79315],petroica archboldi[&&NHX:TOL=79316],petroica bivittata[&&NHX:TOL=79317],petroica phoenicea[&&NHX:TOL=79318],petroica multicolor[&&NHX:TOL=79319],petroica boodang[&&NHX:TOL=79320],petroica goodenovii[&&NHX:TOL=79321],petroica macrocephala[&&NHX:TOL=79322],petroica australis[&&NHX:TOL=79323],petroica traversi[&&NHX:TOL=79324])petroica[&&NHX:TOL=79313],(drymodes superciliaris[&&NHX:TOL=79326],drymodes brunneopygia[&&NHX:TOL=79327])drymodes[&&NHX:TOL=79325],(amalocichla sclateriana[&&NHX:TOL=79329],amalocichla incerta[&&NHX:TOL=79330])amalocichla[&&NHX:TOL=79328])petroicidae[&&NHX:TOL=67954],(((irenidae[&&NHX:TOL=67279],(nectariniidae[&&NHX:TOL=67281],dicaeidae[&&NHX:TOL=67282])[&&NHX:TOL=67280],((((((((parulidae[&&NHX:TOL=67291],((((((((cacicus haemorrhous[&&NHX:TOL=67423],(clypicterus oseryi[&&NHX:TOL=67661],ocyalus latirostris[&&NHX:TOL=67662])[&&NHX:TOL=67660])[&&NHX:TOL=67659],(cacicus chrysonotous[&&NHX:TOL=67424],cacicus leucoramphus[&&NHX:TOL=77458])[&&NHX:TOL=77457])[&&NHX:TOL=67422],((cacicus uropygialis[&&NHX:TOL=67426],cacicus microrhynchus[&&NHX:TOL=77460])[&&NHX:TOL=77459],cacicus cela[&&NHX:TOL=67427])[&&NHX:TOL=67425])[&&NHX:TOL=67421],(cacicus sclateri[&&NHX:TOL=67429],cacicus chrysopterus[&&NHX:TOL=67430])[&&NHX:TOL=67428])[&&NHX:TOL=67658],cacicus solitarius[&&NHX:TOL=67663])[&&NHX:TOL=67657],cacicus koepckeae[&&NHX:TOL=67664],cacicus melanicterus[&&NHX:TOL=67665])cacicus[&&NHX:TOL=67377],(((psarocolius angustifrons[&&NHX:TOL=67433],psarocolius atrovirens[&&NHX:TOL=67434])[&&NHX:TOL=67432],zarhynchus wagleri[&&NHX:TOL=67435])[&&NHX:TOL=67431],(((((psarocolius montezuma[&&NHX:TOL=67439],(psarocolius bifasciatus[&&NHX:TOL=67440],psarocolius yuracares[&&NHX:TOL=77462])[&&NHX:TOL=77461])[&&NHX:TOL=67438],psarocolius cassini[&&NHX:TOL=67655])[&&NHX:TOL=67654],psarocolius guatimozinus[&&NHX:TOL=67656])[&&NHX:TOL=67653],psarocolius viridis[&&NHX:TOL=67441])[&&NHX:TOL=67437],psarocolius decumanus[&&NHX:TOL=67442])[&&NHX:TOL=67436])psarocolius[&&NHX:TOL=67378])[&&NHX:TOL=67376],amblycercus holosericeus[&&NHX:TOL=67379],(((((((((((icterus cayanensis cayanensis[&&NHX:TOL=67452],icterus chrysocephalus[&&NHX:TOL=67453])[&&NHX:TOL=67451],(icterus cayanensis pyrrhopterus[&&NHX:TOL=67455],icterus cayanensis periporphyrus[&&NHX:TOL=67456])[&&NHX:TOL=67454])[&&NHX:TOL=67450],icterus bonana[&&NHX:TOL=67461])[&&NHX:TOL=67501],(icterus oberi[&&NHX:TOL=67458],icterus laudabilis[&&NHX:TOL=67459])[&&NHX:TOL=67457])[&&NHX:TOL=67449],icterus dominicensis portoricensis[&&NHX:TOL=67460])[&&NHX:TOL=67500],(icterus dominicensis melanopsis[&&NHX:TOL=67463],icterus dominicensis northropi[&&NHX:TOL=67464])[&&NHX:TOL=67462])[&&NHX:TOL=67447],(icterus prosthemelas[&&NHX:TOL=67466],(icterus spurius[&&NHX:TOL=67467],icterus fuertesi[&&NHX:TOL=77464])[&&NHX:TOL=77463])[&&NHX:TOL=67465])[&&NHX:TOL=67446],icterus cucullatus[&&NHX:TOL=67468])[&&NHX:TOL=67445],icterus wagleri[&&NHX:TOL=67469])[&&NHX:TOL=67444],(((((((icterus nigrogularis[&&NHX:TOL=67486],icterus gularis[&&NHX:TOL=67487])[&&NHX:TOL=67485],icterus auratus[&&NHX:TOL=67488])[&&NHX:TOL=67484],(icterus galbula[&&NHX:TOL=67493],icterus abeillei[&&NHX:TOL=77466])[&&NHX:TOL=77465])[&&NHX:TOL=67504],(icterus pustulatus[&&NHX:TOL=67491],icterus bullockii[&&NHX:TOL=67492])[&&NHX:TOL=67490])[&&NHX:TOL=67482],icterus leucopteryx[&&NHX:TOL=67489])[&&NHX:TOL=67503],((icterus graduacauda[&&NHX:TOL=67496],icterus chrysater[&&NHX:TOL=67497])[&&NHX:TOL=67495],icterus parisorum[&&NHX:TOL=67498])[&&NHX:TOL=67494])[&&NHX:TOL=67480],(((icterus icterus[&&NHX:TOL=67474],(icterus jamacaii[&&NHX:TOL=67475],icterus croconotus[&&NHX:TOL=77468])[&&NHX:TOL=77467])[&&NHX:TOL=67473],(icterus pectoralis[&&NHX:TOL=67477],icterus graceannae[&&NHX:TOL=67478])[&&NHX:TOL=67476])[&&NHX:TOL=67472],icterus mesomelas[&&NHX:TOL=67479])[&&NHX:TOL=67471])[&&NHX:TOL=67502])[&&NHX:TOL=67499],icterus maculialatus[&&NHX:TOL=67470],icterus auricapillus[&&NHX:TOL=77469])icterus[&&NHX:TOL=67380],(((((((((pseudoleistes guirahuro[&&NHX:TOL=67527],pseudoleistes virescens[&&NHX:TOL=67528])pseudoleistes[&&NHX:TOL=67389],xanthopsar flavus[&&NHX:TOL=67390])[&&NHX:TOL=67388],(chrysomus icterocephalus[&&NHX:TOL=67529],chrysomus ruficapillus[&&NHX:TOL=67530])chrysomus[&&NHX:TOL=67391])[&&NHX:TOL=67387],(agelaioides badius[&&NHX:TOL=77764],agelaioides oreopsar[&&NHX:TOL=77763])agelaioides[&&NHX:TOL=67420])[&&NHX:TOL=67386],((agelasticus cyanopus[&&NHX:TOL=67532],agelasticus xanthophthalmus[&&NHX:TOL=67533])[&&NHX:TOL=67531],agelasticus thilius[&&NHX:TOL=67534])agelasticus[&&NHX:TOL=67393])[&&NHX:TOL=67385],gnorimopsar chopi[&&NHX:TOL=67394],((curaeus curaeus[&&NHX:TOL=77841],curaeus forbesi[&&NHX:TOL=77842])curaeus[&&NHX:TOL=67396],amblyramphus holosericeus[&&NHX:TOL=67397])[&&NHX:TOL=67395])[&&NHX:TOL=67384],((gymnomystax mexicanus[&&NHX:TOL=67401],hypopyrrhus pyrohypogaster[&&NHX:TOL=67402])[&&NHX:TOL=67400],lampropsar tanagrinus[&&NHX:TOL=67403])[&&NHX:TOL=67399],macroagelaius[&&NHX:TOL=77836])[&&NHX:TOL=67383],(((quiscalus quiscula[&&NHX:TOL=67519],(((quiscalus major[&&NHX:TOL=67523],quiscalus mexicanus[&&NHX:TOL=67524])[&&NHX:TOL=67522],quiscalus niger[&&NHX:TOL=67525])[&&NHX:TOL=67521],quiscalus lugubris[&&NHX:TOL=67526])[&&NHX:TOL=67520],quiscalus palustris[&&NHX:TOL=77474],quiscalus nicaraguensis[&&NHX:TOL=77475])quiscalus[&&NHX:TOL=67407],euphagus[&&NHX:TOL=67408])[&&NHX:TOL=67406],((agelaius tricolor[&&NHX:TOL=67506],(agelaius phoeniceus[&&NHX:TOL=67507],agelaius assimilis[&&NHX:TOL=77471])[&&NHX:TOL=77470])[&&NHX:TOL=67505],(agelaius xanthomus[&&NHX:TOL=67509],agelaius humeralis[&&NHX:TOL=67510])[&&NHX:TOL=67508])agelaius[&&NHX:TOL=67409],(dives atroviolacea[&&NHX:TOL=67814],dives dives[&&NHX:TOL=67815],dives warszewiczi[&&NHX:TOL=67816])dives[&&NHX:TOL=67410],((((molothrus ater[&&NHX:TOL=67514],molothrus bonariensis[&&NHX:TOL=67515])[&&NHX:TOL=67513],molothrus aeneus[&&NHX:TOL=67516])[&&NHX:TOL=67512],molothrus oryzivora[&&NHX:TOL=67517])[&&NHX:TOL=67511],molothrus rufoaxillaris[&&NHX:TOL=67518])molothrus[&&NHX:TOL=67411])[&&NHX:TOL=67405])[&&NHX:TOL=67382],nesopsar nigerrimus[&&NHX:TOL=67412])[&&NHX:TOL=67381],((xanthocephalus xanthocephalus[&&NHX:TOL=67415],dolichonyx oryzivorus[&&NHX:TOL=67416])[&&NHX:TOL=67414],(sturnella bellicosa[&&NHX:TOL=67535],sturnella loyca[&&NHX:TOL=67809],sturnella militaris[&&NHX:TOL=67810],((sturnella magna[&&NHX:TOL=67537],sturnella lilianae[&&NHX:TOL=67808])[&&NHX:TOL=67812],sturnella neglecta[&&NHX:TOL=67813])[&&NHX:TOL=67811],sturnella superciliaris[&&NHX:TOL=77472],sturnella defilippii[&&NHX:TOL=77473])sturnella[&&NHX:TOL=67417])[&&NHX:TOL=67413])icteridae[&&NHX:TOL=67292])[&&NHX:TOL=67290],emberizidae[&&NHX:TOL=67293],(thraupidae[&&NHX:TOL=67295],cardinalidae [&&NHX:TOL=67296])[&&NHX:TOL=67294])[&&NHX:TOL=67289],(calcarius[&&NHX:TOL=67297],plectrophenax[&&NHX:TOL=68255])[&&NHX:TOL=68254])[&&NHX:TOL=67288],fringillidae[&&NHX:TOL=67298])nineprimaried oscines[&&NHX:TOL=67287],motacillidae[&&NHX:TOL=67299])[&&NHX:TOL=67286],passeridae[&&NHX:TOL=67300])[&&NHX:TOL=67285],ploceidae[&&NHX:TOL=67301])[&&NHX:TOL=67284],(prunellidae[&&NHX:TOL=67303],peucedramus taeniatus[&&NHX:TOL=67304])[&&NHX:TOL=67302])[&&NHX:TOL=67283])passeroidea[&&NHX:TOL=67278],((sittidae[&&NHX:TOL=68149],(certhiidae[&&NHX:TOL=68151],(troglodytidae[&&NHX:TOL=68153],polioptilidae[&&NHX:TOL=68154])[&&NHX:TOL=68152])[&&NHX:TOL=68150])certhioidea[&&NHX:TOL=67306],((bombycillidae[&&NHX:TOL=68155],hypocoliidae[&&NHX:TOL=68250])[&&NHX:TOL=68249],((cinclidae[&&NHX:TOL=68158],(turdidae[&&NHX:TOL=68160],muscicapidae[&&NHX:TOL=68161])[&&NHX:TOL=68159])[&&NHX:TOL=68157],(rhabdornis[&&NHX:TOL=68163],buphagus[&&NHX:TOL=80928],sturnidae[&&NHX:TOL=68165],mimidae[&&NHX:TOL=68166])[&&NHX:TOL=68162])[&&NHX:TOL=68156])muscicapoidea[&&NHX:TOL=67307])[&&NHX:TOL=67305],promeropidae[&&NHX:TOL=68167])[&&NHX:TOL=67277],regulidae[&&NHX:TOL=67951],hyliota[&&NHX:TOL=67952],((stenostiridae[&&NHX:TOL=68169],(paridae[&&NHX:TOL=68171],remizidae[&&NHX:TOL=68172])[&&NHX:TOL=68170])[&&NHX:TOL=68168],((alaudidae[&&NHX:TOL=68175],panurus[&&NHX:TOL=68176])[&&NHX:TOL=68174],(nicator[&&NHX:TOL=68178],(sphenoeacus[&&NHX:TOL=68180],achaetops[&&NHX:TOL=68181])[&&NHX:TOL=68179],macrosphenus[&&NHX:TOL=68182],bradypterus victorini[&&NHX:TOL=68183],melocichla[&&NHX:TOL=68184],(acrocephalidae[&&NHX:TOL=68186],(donacobius[&&NHX:TOL=68188],megaluridae[&&NHX:TOL=68189])[&&NHX:TOL=68187])[&&NHX:TOL=68185],(hirundinidae[&&NHX:TOL=68191],pycnonotidae[&&NHX:TOL=68192],(cettiidae[&&NHX:TOL=68194],aegithalidae[&&NHX:TOL=68195],hylia[&&NHX:TOL=68196])[&&NHX:TOL=68193],phylloscopidae[&&NHX:TOL=68197])[&&NHX:TOL=68190],cisticolidae[&&NHX:TOL=68198],timaliidae[&&NHX:TOL=68199])[&&NHX:TOL=68177])[&&NHX:TOL=68173])sylvioidea[&&NHX:TOL=67276])[&&NHX:TOL=67950],(((chaetops aurantius[&&NHX:TOL=79390],chaetops frenatus[&&NHX:TOL=79391])chaetopidae[&&NHX:TOL=79389],(androphobus viridis[&&NHX:TOL=79176],psophodes[&&NHX:TOL=79177],eupetes macrocerus[&&NHX:TOL=79183],(ptilorrhoa[&&NHX:TOL=68209],(cinclosoma punctatum[&&NHX:TOL=79200],cinclosoma castanotum[&&NHX:TOL=79201],cinclosoma cinnamomeum[&&NHX:TOL=79202],cinclosoma castaneothorax[&&NHX:TOL=79203],cinclosoma ajax[&&NHX:TOL=79204])cinclosoma[&&NHX:TOL=79199])[&&NHX:TOL=125359])eupetidae[&&NHX:TOL=79175])[&&NHX:TOL=125358],picathartidae[&&NHX:TOL=67953])[&&NHX:TOL=125357])passerida[&&NHX:TOL=29223],(daphoenositta[&&NHX:TOL=68200],campephagidae[&&NHX:TOL=68201],colluricincla[&&NHX:TOL=68202],falcunculus[&&NHX:TOL=68203],pachycephalidae[&&NHX:TOL=68204],(oreoica[&&NHX:TOL=68206],pitohui[&&NHX:TOL=68207])[&&NHX:TOL=68205],paramythia[&&NHX:TOL=68208],(erpornis[&&NHX:TOL=68211],vireonidae[&&NHX:TOL=68212])[&&NHX:TOL=68210],(oriolidae[&&NHX:TOL=68214],sphecotheres[&&NHX:TOL=68215])[&&NHX:TOL=68213],((((cracticidae[&&NHX:TOL=68220],gymnorhina[&&NHX:TOL=68221])[&&NHX:TOL=68219],strepera[&&NHX:TOL=68222])[&&NHX:TOL=68218],artamidae[&&NHX:TOL=68223])[&&NHX:TOL=68217],aegithinidae[&&NHX:TOL=68224],(malaconotinae[&&NHX:TOL=68226],dryoscopus[&&NHX:TOL=68227])[&&NHX:TOL=68225],(batis[&&NHX:TOL=68229],lanioturdus[&&NHX:TOL=68230])[&&NHX:TOL=68228],(vangidae[&&NHX:TOL=68232],prionopidae[&&NHX:TOL=68233])[&&NHX:TOL=68231])[&&NHX:TOL=68216],(dicruridae[&&NHX:TOL=68235],rhipiduridae[&&NHX:TOL=68236],((laniidae[&&NHX:TOL=68239],corvidae[&&NHX:TOL=68240])[&&NHX:TOL=68238],paradisaeidae[&&NHX:TOL=68241],(struthidea[&&NHX:TOL=68243],corcorax[&&NHX:TOL=68244])[&&NHX:TOL=68242],melampitta[&&NHX:TOL=68245],(monarchidae[&&NHX:TOL=68247],grallina[&&NHX:TOL=68248])[&&NHX:TOL=68246])[&&NHX:TOL=68237])[&&NHX:TOL=68234])corvoidea[&&NHX:TOL=67955])[&&NHX:TOL=67949],melanocharitidae[&&NHX:TOL=67956],callaeatidae[&&NHX:TOL=67957],cnemophilinae[&&NHX:TOL=67958])[&&NHX:TOL=67948],orthonychidae[&&NHX:TOL=67959])[&&NHX:TOL=67947],pomatostomidae[&&NHX:TOL=67960])[&&NHX:TOL=67946],(maluridae[&&NHX:TOL=67962],dasyornis[&&NHX:TOL=67963],acanthizidae[&&NHX:TOL=67964],(meliphagidae[&&NHX:TOL=67966],pardalotidae[&&NHX:TOL=67967])[&&NHX:TOL=67965])meliphagoidea[&&NHX:TOL=67961])[&&NHX:TOL=67945],(ptilonorhynchidae[&&NHX:TOL=67970],climacteridae[&&NHX:TOL=67969])[&&NHX:TOL=67968])[&&NHX:TOL=67944],(menuridae[&&NHX:TOL=67971],atrichornithidae[&&NHX:TOL=67972])menuroidea[&&NHX:TOL=29224])oscines[&&NHX:TOL=29222])[&&NHX:TOL=67943])passeriformes[&&NHX:TOL=15868],((((((((((((((((ara ararauna[&&NHX:TOL=91596],ara glaucogularis[&&NHX:TOL=91597],ara militaris[&&NHX:TOL=91598],ara ambiguus[&&NHX:TOL=91599],ara chloropterus[&&NHX:TOL=91600],ara rubrogenys[&&NHX:TOL=91601],ara severus[&&NHX:TOL=91602],ara macao[&&NHX:TOL=91603])ara[&&NHX:TOL=91595],orthopsittaca manilata[&&NHX:TOL=91604],(primolius couloni[&&NHX:TOL=91606],primolius maracana[&&NHX:TOL=91607],primolius auricollis[&&NHX:TOL=91608])primolius[&&NHX:TOL=91605])[&&NHX:TOL=103462],cyanopsitta spixii[&&NHX:TOL=91594])[&&NHX:TOL=103461],(nandayus nenday[&&NHX:TOL=91638],(aratinga acuticaudata[&&NHX:TOL=91616],aratinga jandaya[&&NHX:TOL=91629],aratinga solstitialis[&&NHX:TOL=91628],aratinga auricapillus[&&NHX:TOL=91630],aratinga holochlora[&&NHX:TOL=91617],aratinga brevipes[&&NHX:TOL=91618],aratinga rubritorquis[&&NHX:TOL=91619],aratinga strenua[&&NHX:TOL=91620],aratinga wagleri[&&NHX:TOL=91621],aratinga mitrata[&&NHX:TOL=91622],aratinga erythrogenys[&&NHX:TOL=91623],aratinga finschi[&&NHX:TOL=91624],aratinga euops[&&NHX:TOL=91626],aratinga chloroptera[&&NHX:TOL=91627],aratinga nana[&&NHX:TOL=91632],aratinga astec[&&NHX:TOL=91633],aratinga canicularis[&&NHX:TOL=91634],aratinga weddellii[&&NHX:TOL=91631],aratinga aurea[&&NHX:TOL=91635],aratinga cactorum[&&NHX:TOL=91637],aratinga pertinax[&&NHX:TOL=91636])aratinga[&&NHX:TOL=91615],cyanoliseus patagonus[&&NHX:TOL=91640])[&&NHX:TOL=103493])[&&NHX:TOL=103492],(guaruba guarouba[&&NHX:TOL=91614],diopsittaca nobilis[&&NHX:TOL=91609])[&&NHX:TOL=103463])[&&NHX:TOL=103491],((anodorhynchus hyacinthinus[&&NHX:TOL=91592],anodorhynchus leari[&&NHX:TOL=91593])anodorhynchus[&&NHX:TOL=91591],aratinga leucophthalma[&&NHX:TOL=91625])[&&NHX:TOL=103494])[&&NHX:TOL=103490],(enicognathus ferrugineus[&&NHX:TOL=91664],enicognathus leptorhynchus[&&NHX:TOL=91665])enicognathus[&&NHX:TOL=91663],(rhynchopsitta pachyrhyncha[&&NHX:TOL=91611],rhynchopsitta terrisi[&&NHX:TOL=91612])rhynchopsitta[&&NHX:TOL=91610],(((pyrrhura picta[&&NHX:TOL=91648],pyrrhura amazonum[&&NHX:TOL=135887],pyrrhura roseifrons[&&NHX:TOL=135888],pyrrhura lucianii[&&NHX:TOL=135889])[&&NHX:TOL=135886],(pyrrhura pfrimeri[&&NHX:TOL=91650],(pyrrhura leucotis[&&NHX:TOL=91649],pyrrhura griseipectus[&&NHX:TOL=129457])[&&NHX:TOL=129456])[&&NHX:TOL=103465],pyrrhura emma[&&NHX:TOL=91652])[&&NHX:TOL=103464],pyrrhura cruentata[&&NHX:TOL=91642],((pyrrhura melanura[&&NHX:TOL=91655],pyrrhura albipectus[&&NHX:TOL=91658])[&&NHX:TOL=103467],pyrrhura rhodocephala[&&NHX:TOL=91661],pyrrhura orcesi[&&NHX:TOL=91656],pyrrhura hoffmanni[&&NHX:TOL=91662],pyrrhura rupicola[&&NHX:TOL=91657],(pyrrhura lepida[&&NHX:TOL=91645],(pyrrhura frontalis[&&NHX:TOL=91644],pyrrhura devillei[&&NHX:TOL=91643])[&&NHX:TOL=103469],pyrrhura perlata[&&NHX:TOL=91646],pyrrhura molinae[&&NHX:TOL=91647])[&&NHX:TOL=103468])[&&NHX:TOL=103466],pyrrhura egregia[&&NHX:TOL=91654],pyrrhura viridicata[&&NHX:TOL=91653],pyrrhura calliptera[&&NHX:TOL=91659],pyrrhura hoematotis[&&NHX:TOL=91660])pyrrhura[&&NHX:TOL=91641])[&&NHX:TOL=103306],((pionites melanocephalus[&&NHX:TOL=91706],pionites leucogaster[&&NHX:TOL=91707])pionites[&&NHX:TOL=91705],deroptyus accipitrinus[&&NHX:TOL=91765])[&&NHX:TOL=103470])[&&NHX:TOL=103458],(psilopsiagon aymara[&&NHX:TOL=91670],psilopsiagon aurifrons[&&NHX:TOL=91671])psilopsiagon[&&NHX:TOL=91669])[&&NHX:TOL=103305],(forpus cyanopygius[&&NHX:TOL=91677],forpus passerinus[&&NHX:TOL=91678],forpus xanthopterygius[&&NHX:TOL=91679],forpus conspicillatus[&&NHX:TOL=91680],forpus modestus[&&NHX:TOL=91681],forpus coelestis[&&NHX:TOL=91682],forpus xanthops[&&NHX:TOL=91683])forpus[&&NHX:TOL=91676])[&&NHX:TOL=103457],(((((graydidascalus brachyurus[&&NHX:TOL=91722],salvatoria xanthops[&&NHX:TOL=91750])[&&NHX:TOL=103474],(((((amazona ventralis[&&NHX:TOL=91735],amazona leucocephala[&&NHX:TOL=91733],amazona vittata[&&NHX:TOL=91739])[&&NHX:TOL=103478],amazona collaria[&&NHX:TOL=91734])[&&NHX:TOL=103477],amazona agilis[&&NHX:TOL=91738],amazona albifrons[&&NHX:TOL=91736])[&&NHX:TOL=103476],(amazona pretrei[&&NHX:TOL=91741],amazona tucumana[&&NHX:TOL=91740])[&&NHX:TOL=103479],amazona vinacea[&&NHX:TOL=91760],amazona festiva[&&NHX:TOL=91749],((amazona oratrix[&&NHX:TOL=91753],amazona aestiva[&&NHX:TOL=91752],amazona auropalliata[&&NHX:TOL=91754],amazona ochrocephala[&&NHX:TOL=91755],amazona barbadensis[&&NHX:TOL=91751])[&&NHX:TOL=103481],(amazona versicolor[&&NHX:TOL=91761],amazona arausiaca[&&NHX:TOL=91762])[&&NHX:TOL=103482])[&&NHX:TOL=103480],(amazona farinosa[&&NHX:TOL=91759],amazona kawalli[&&NHX:TOL=91758])[&&NHX:TOL=103483],(amazona rhodocorytha[&&NHX:TOL=91747],amazona dufresniana[&&NHX:TOL=91746])[&&NHX:TOL=103484],((amazona viridigenalis[&&NHX:TOL=91742],amazona finschi[&&NHX:TOL=91743])[&&NHX:TOL=103486],amazona autumnalis[&&NHX:TOL=91744])[&&NHX:TOL=103485],(((amazona guildingii[&&NHX:TOL=91763],amazona amazonica[&&NHX:TOL=91756])[&&NHX:TOL=103489],amazona brasiliensis[&&NHX:TOL=91748])[&&NHX:TOL=103488],amazona imperialis[&&NHX:TOL=91764])[&&NHX:TOL=103487],amazona diadema[&&NHX:TOL=91745],amazona xantholora[&&NHX:TOL=91737],amazona mercenaria[&&NHX:TOL=91757])amazona[&&NHX:TOL=91732],(pionus menstruus[&&NHX:TOL=91724],pionus sordidus[&&NHX:TOL=91725],pionus maximiliani[&&NHX:TOL=91726],pionus tumultuosus[&&NHX:TOL=91727],pionus seniloides[&&NHX:TOL=91728],pionus senilis[&&NHX:TOL=91729],pionus chalcopterus[&&NHX:TOL=91730],pionus fuscus[&&NHX:TOL=91731])pionus[&&NHX:TOL=91723])[&&NHX:TOL=103475])[&&NHX:TOL=103310],triclaria malachitacea[&&NHX:TOL=91766])[&&NHX:TOL=103309],(pionopsitta vulturina[&&NHX:TOL=91709],pionopsitta aurantiocephala[&&NHX:TOL=91710],pionopsitta haematotis[&&NHX:TOL=91711],pionopsitta pulchra[&&NHX:TOL=91712],pionopsitta barrabandi[&&NHX:TOL=91713],pionopsitta pyrilia[&&NHX:TOL=91714],pionopsitta caica[&&NHX:TOL=91715],pionopsitta pileata[&&NHX:TOL=91716])pionopsitta[&&NHX:TOL=91708])[&&NHX:TOL=103472],((myiopsitta monachus[&&NHX:TOL=91667],myiopsitta luchsi[&&NHX:TOL=91668])myiopsitta[&&NHX:TOL=91666],(brotogeris sanctithomae[&&NHX:TOL=91692],brotogeris chrysoptera[&&NHX:TOL=91691],brotogeris cyanoptera[&&NHX:TOL=91690],brotogeris jugularis[&&NHX:TOL=91689],brotogeris pyrrhoptera[&&NHX:TOL=91688],brotogeris chiriri[&&NHX:TOL=91687],brotogeris versicolurus[&&NHX:TOL=91686],brotogeris tirica[&&NHX:TOL=91685])brotogeris[&&NHX:TOL=91684])[&&NHX:TOL=103307])[&&NHX:TOL=103471])[&&NHX:TOL=103456],((bolborhynchus lineola[&&NHX:TOL=91673],bolborhynchus orbygnesius[&&NHX:TOL=91674],bolborhynchus ferrugineifrons[&&NHX:TOL=91675])bolborhynchus[&&NHX:TOL=91672],(nannopsittaca panychlora[&&NHX:TOL=91694],nannopsittaca dachilleae[&&NHX:TOL=91695])nannopsittaca[&&NHX:TOL=91693])[&&NHX:TOL=103473])[&&NHX:TOL=103455],leptosittaca branickii[&&NHX:TOL=91639],ognorhynchus icterotis[&&NHX:TOL=91613],(touit batavicus[&&NHX:TOL=91697],touit huetii[&&NHX:TOL=91698],touit costaricensis[&&NHX:TOL=91699],touit dilectissimus[&&NHX:TOL=91700],touit purpuratus[&&NHX:TOL=91701],touit melanonotus[&&NHX:TOL=91702],touit surdus[&&NHX:TOL=91703],touit stictopterus[&&NHX:TOL=91704])touit[&&NHX:TOL=91696],(hapalopsittaca amazonina[&&NHX:TOL=91718],hapalopsittaca melanotis[&&NHX:TOL=91719],hapalopsittaca fuertesi[&&NHX:TOL=91720],hapalopsittaca pyrrhops[&&NHX:TOL=91721])hapalopsittaca[&&NHX:TOL=91717])arini[&&NHX:TOL=103304],(psittrichas fulgidus[&&NHX:TOL=91458],(coracopsis vasa[&&NHX:TOL=91577],coracopsis nigra[&&NHX:TOL=91578])coracopsis[&&NHX:TOL=91576])[&&NHX:TOL=103312],(((eolophus roseicapilla[&&NHX:TOL=91782],(cacatua tenuirostris[&&NHX:TOL=91786],cacatua pastinator[&&NHX:TOL=91787],cacatua sanguinea[&&NHX:TOL=91788],cacatua goffiniana[&&NHX:TOL=91789],cacatua ducorpsii[&&NHX:TOL=91790],cacatua haematuropygia[&&NHX:TOL=91791],cacatua leadbeateri[&&NHX:TOL=91792],cacatua sulphurea[&&NHX:TOL=91793],cacatua galerita[&&NHX:TOL=91794],cacatua ophthalmica[&&NHX:TOL=91795],cacatua alba[&&NHX:TOL=91796],cacatua moluccensis[&&NHX:TOL=91797])cacatua[&&NHX:TOL=91785])[&&NHX:TOL=103314],probosciger aterrimus[&&NHX:TOL=91783])[&&NHX:TOL=103313],(calyptorhynchus banksii[&&NHX:TOL=91776],calyptorhynchus lathami[&&NHX:TOL=91777],calyptorhynchus funereus[&&NHX:TOL=91778],calyptorhynchus latirostris[&&NHX:TOL=91779],calyptorhynchus baudinii[&&NHX:TOL=91780])calyptorhynchus[&&NHX:TOL=91775],callocephalon fimbriatum[&&NHX:TOL=91781],nymphicus hollandicus[&&NHX:TOL=91784])cacatuinae[&&NHX:TOL=26408],(psittacus erithacus[&&NHX:TOL=91579],(poicephalus fuscicollis[&&NHX:TOL=91581],poicephalus robustus[&&NHX:TOL=91582],poicephalus gulielmi[&&NHX:TOL=91583],poicephalus meyeri[&&NHX:TOL=91584],poicephalus rueppellii[&&NHX:TOL=91585],poicephalus cryptoxanthus[&&NHX:TOL=91586],poicephalus crassus[&&NHX:TOL=91587],poicephalus rufiventris[&&NHX:TOL=91588],poicephalus senegalus[&&NHX:TOL=91589],poicephalus flavifrons[&&NHX:TOL=91590])poicephalus[&&NHX:TOL=91580])[&&NHX:TOL=103315],(bolbopsittacus lunulatus[&&NHX:TOL=91774],(cyclopsitta diophthalma[&&NHX:TOL=91768],cyclopsitta gulielmitertii[&&NHX:TOL=91769])cyclopsitta[&&NHX:TOL=91767])[&&NHX:TOL=103317],((psittacella brehmii[&&NHX:TOL=91517],psittacella picta[&&NHX:TOL=91518],psittacella modesta[&&NHX:TOL=91519],psittacella madaraszi[&&NHX:TOL=91520])psittacella[&&NHX:TOL=91516],psittinus cyanurus[&&NHX:TOL=91521],(geoffroyus geoffroyi[&&NHX:TOL=91523],geoffroyus simplex[&&NHX:TOL=91524],geoffroyus heteroclitus[&&NHX:TOL=91525])geoffroyus[&&NHX:TOL=91522],(loriculus vernalis[&&NHX:TOL=91460],loriculus beryllinus[&&NHX:TOL=91461],loriculus philippensis[&&NHX:TOL=91462],loriculus camiguinensis[&&NHX:TOL=129503],loriculus galgulus[&&NHX:TOL=91463],loriculus stigmatus[&&NHX:TOL=91464],loriculus amabilis[&&NHX:TOL=91465],loriculus sclateri[&&NHX:TOL=129504],loriculus catamene[&&NHX:TOL=91466],loriculus aurantiifrons[&&NHX:TOL=91467],loriculus tener[&&NHX:TOL=91468],loriculus exilis[&&NHX:TOL=91469],loriculus pusillus[&&NHX:TOL=91470],loriculus flosculus[&&NHX:TOL=91471])loriculus[&&NHX:TOL=91459])[&&NHX:TOL=103318],(micropsitta keiensis[&&NHX:TOL=91473],micropsitta geelvinkiana[&&NHX:TOL=91474],micropsitta pusio[&&NHX:TOL=91475],micropsitta meeki[&&NHX:TOL=91476],micropsitta finschii[&&NHX:TOL=91477],micropsitta bruijnii[&&NHX:TOL=91478])micropsitta[&&NHX:TOL=91472])[&&NHX:TOL=26407],((prioniturus montanus[&&NHX:TOL=91527],prioniturus waterstradti[&&NHX:TOL=129507],prioniturus platenae[&&NHX:TOL=91528],prioniturus luconensis[&&NHX:TOL=91529],prioniturus discurus[&&NHX:TOL=91530],prioniturus verticalis[&&NHX:TOL=91531],prioniturus flavicans[&&NHX:TOL=91532],prioniturus platurus[&&NHX:TOL=91533],prioniturus mada[&&NHX:TOL=91534])prioniturus[&&NHX:TOL=91526],((tanygnathus megalorynchos[&&NHX:TOL=91536],tanygnathus lucionensis[&&NHX:TOL=91537],tanygnathus gramineus[&&NHX:TOL=91538],tanygnathus sumatranus[&&NHX:TOL=91539])tanygnathus[&&NHX:TOL=91535],eclectus roratus[&&NHX:TOL=91540],(psittacula eupatria[&&NHX:TOL=91553],psittacula krameri[&&NHX:TOL=91554],psittacula echo[&&NHX:TOL=91555],psittacula himalayana[&&NHX:TOL=91556],psittacula finschii[&&NHX:TOL=91557],psittacula cyanocephala[&&NHX:TOL=91558],psittacula roseata[&&NHX:TOL=91559],psittacula columboides[&&NHX:TOL=91560],psittacula calthropae[&&NHX:TOL=91561],psittacula derbiana[&&NHX:TOL=91562],psittacula alexandri[&&NHX:TOL=91563],psittacula caniceps[&&NHX:TOL=91564],psittacula longicauda[&&NHX:TOL=91565])psittacula[&&NHX:TOL=91552])[&&NHX:TOL=103320],(((alisterus amboinensis[&&NHX:TOL=91546],alisterus chloropterus[&&NHX:TOL=91547],alisterus scapularis[&&NHX:TOL=91548])alisterus[&&NHX:TOL=91545],(aprosmictus jonquillaceus[&&NHX:TOL=91550],aprosmictus erythropterus[&&NHX:TOL=91551])aprosmictus[&&NHX:TOL=91549])[&&NHX:TOL=103322],(polytelis swainsonii[&&NHX:TOL=91542],polytelis anthopeplus[&&NHX:TOL=91543],polytelis alexandrae[&&NHX:TOL=91544])polytelis[&&NHX:TOL=91541])[&&NHX:TOL=103321])psittaculini[&&NHX:TOL=103319],(((platycercus caledonicus[&&NHX:TOL=91493],platycercus elegans[&&NHX:TOL=91494],platycercus eximius[&&NHX:TOL=129707],platycercus adscitus[&&NHX:TOL=91495],platycercus venustus[&&NHX:TOL=129708],platycercus icterotis[&&NHX:TOL=91496])platycercus[&&NHX:TOL=91492],(psephotus haematonotus[&&NHX:TOL=91499],psephotus varius[&&NHX:TOL=91500],psephotus dissimilis[&&NHX:TOL=91501],psephotus chrysopterygius[&&NHX:TOL=91502])psephotus[&&NHX:TOL=91498],barnardius zonarius[&&NHX:TOL=91491],(pezoporus occidentalis[&&NHX:TOL=91514],pezoporus wallicus[&&NHX:TOL=91515])pezoporus[&&NHX:TOL=91513],(neophema chrysostoma[&&NHX:TOL=91505],neophema elegans[&&NHX:TOL=91506],neophema petrophila[&&NHX:TOL=91507],neophema chrysogaster[&&NHX:TOL=91508],neophema pulchella[&&NHX:TOL=91509],neophema splendida[&&NHX:TOL=91510])neophema[&&NHX:TOL=91504],lathamus discolor[&&NHX:TOL=91511],northiella haematogaster[&&NHX:TOL=91497],purpureicephalus spurius[&&NHX:TOL=91490],(prosopeia splendens[&&NHX:TOL=91480],prosopeia personata[&&NHX:TOL=91481],prosopeia tabuensis[&&NHX:TOL=91482])prosopeia[&&NHX:TOL=91479],(eunymphicus cornutus[&&NHX:TOL=91483],eunymphicus uvaeensis[&&NHX:TOL=135862])eunymphicus[&&NHX:TOL=135861])[&&NHX:TOL=103324],(cyanoramphus saisseti[&&NHX:TOL=91485],cyanoramphus cookii[&&NHX:TOL=91486],cyanoramphus unicolor[&&NHX:TOL=91487],cyanoramphus auriceps[&&NHX:TOL=91488],cyanoramphus forbesi[&&NHX:TOL=129505],cyanoramphus malherbi[&&NHX:TOL=129506],cyanoramphus novaezelandiae[&&NHX:TOL=91489],cyanoramphus hochstetteri[&&NHX:TOL=129706])cyanoramphus[&&NHX:TOL=91484])platycercini[&&NHX:TOL=103323],((((((neopsittacus musschenbroekii[&&NHX:TOL=91863],neopsittacus pullicauda[&&NHX:TOL=91864])neopsittacus[&&NHX:TOL=91862],oreopsittacus arfaki[&&NHX:TOL=91861],(charmosyna palmarum[&&NHX:TOL=91848],charmosyna rubrigularis[&&NHX:TOL=91849],charmosyna meeki[&&NHX:TOL=91850],charmosyna toxopei[&&NHX:TOL=91851],charmosyna multistriata[&&NHX:TOL=91852],charmosyna wilhelminae[&&NHX:TOL=91853],charmosyna rubronotata[&&NHX:TOL=91854],charmosyna placentis[&&NHX:TOL=91855],charmosyna amabilis[&&NHX:TOL=91856],charmosyna margarethae[&&NHX:TOL=91857],charmosyna pulchella[&&NHX:TOL=91858],charmosyna josefinae[&&NHX:TOL=91859],charmosyna papou[&&NHX:TOL=91860])charmosyna[&&NHX:TOL=91847],(glossopsitta concinna[&&NHX:TOL=91844],glossopsitta pusilla[&&NHX:TOL=91845],glossopsitta porphyrocephala[&&NHX:TOL=91846])glossopsitta[&&NHX:TOL=91843],(vini australis[&&NHX:TOL=91838],vini kuhlii[&&NHX:TOL=91839],vini stepheni[&&NHX:TOL=91840],vini peruviana[&&NHX:TOL=91841],vini ultramarina[&&NHX:TOL=91842])vini[&&NHX:TOL=91837],phigys solitarius[&&NHX:TOL=91836],(lorius garrulus[&&NHX:TOL=91830],lorius domicella[&&NHX:TOL=91831],lorius lory[&&NHX:TOL=91832],lorius hypoinochrous[&&NHX:TOL=91833],lorius albidinucha[&&NHX:TOL=91834],lorius chlorocercus[&&NHX:TOL=91835])lorius[&&NHX:TOL=91829],(psitteuteles versicolor[&&NHX:TOL=91826],psitteuteles iris[&&NHX:TOL=91827],psitteuteles goldiei[&&NHX:TOL=91828])psitteuteles[&&NHX:TOL=91825],(trichoglossus ornatus[&&NHX:TOL=91812],trichoglossus forsteni[&&NHX:TOL=91813],trichoglossus weberi[&&NHX:TOL=91814],trichoglossus capistratus[&&NHX:TOL=91815],trichoglossus haematodus[&&NHX:TOL=91816],trichoglossus rosenbergii[&&NHX:TOL=91817],trichoglossus moluccanus[&&NHX:TOL=91818],trichoglossus rubritorquis[&&NHX:TOL=91819],trichoglossus euteles[&&NHX:TOL=91820],trichoglossus flavoviridis[&&NHX:TOL=91821],trichoglossus johnstoniae[&&NHX:TOL=91822],trichoglossus rubiginosus[&&NHX:TOL=91823],trichoglossus chlorolepidotus[&&NHX:TOL=91824])trichoglossus[&&NHX:TOL=91811],pseudeos fuscata[&&NHX:TOL=91810],(eos histrio[&&NHX:TOL=91804],eos squamata[&&NHX:TOL=91805],eos rubra[&&NHX:TOL=91806],eos reticulata[&&NHX:TOL=91807],eos cyanogenia[&&NHX:TOL=91808],eos semilarvata[&&NHX:TOL=91809])eos[&&NHX:TOL=91803],(chalcopsitta atra[&&NHX:TOL=91799],chalcopsitta duivenbodei[&&NHX:TOL=91800],chalcopsitta sintillata[&&NHX:TOL=91801],chalcopsitta cardinalis[&&NHX:TOL=91802])chalcopsitta[&&NHX:TOL=91798])loriinae[&&NHX:TOL=56964],melopsittacus undulatus[&&NHX:TOL=91512])[&&NHX:TOL=103328],(psittaculirostris salvadorii[&&NHX:TOL=91773],psittaculirostris edwardsii[&&NHX:TOL=91772],psittaculirostris desmarestii[&&NHX:TOL=91771])psittaculirostris[&&NHX:TOL=91770])[&&NHX:TOL=103327],(agapornis canus[&&NHX:TOL=91567],agapornis pullarius[&&NHX:TOL=91568],agapornis taranta[&&NHX:TOL=91569],agapornis swindernianus[&&NHX:TOL=91570],agapornis roseicollis[&&NHX:TOL=91571],agapornis fischeri[&&NHX:TOL=91572],agapornis personatus[&&NHX:TOL=91573],agapornis lilianae[&&NHX:TOL=91574],agapornis nigrigenis[&&NHX:TOL=91575])agapornis[&&NHX:TOL=91566])[&&NHX:TOL=103326],neopsephotus bourkii[&&NHX:TOL=91503])[&&NHX:TOL=103325])[&&NHX:TOL=103188],((nestor notabilis[&&NHX:TOL=91455],nestor meridionalis[&&NHX:TOL=91456])nestor[&&NHX:TOL=91454],strigops habroptila[&&NHX:TOL=91457])[&&NHX:TOL=103189])psittacidae[&&NHX:TOL=26406])[&&NHX:TOL=123192],(((((((daptrius ater[&&NHX:TOL=66404],(milvago chimachima[&&NHX:TOL=66468],milvago chimango[&&NHX:TOL=66469])milvago[&&NHX:TOL=66405])[&&NHX:TOL=66403],(phalcoboenus carunculatus[&&NHX:TOL=66470],phalcoboenus megalopterus[&&NHX:TOL=66471],phalcoboenus albogularis[&&NHX:TOL=66472],phalcoboenus australis[&&NHX:TOL=66473])phalcoboenus[&&NHX:TOL=66406])[&&NHX:TOL=66402],ibycter americanus[&&NHX:TOL=66407])[&&NHX:TOL=66401],(caracara cheriway[&&NHX:TOL=66474],caracara lutosa[&&NHX:EXT=Y:TOL=66475],caracara plancus[&&NHX:TOL=66476])caracara[&&NHX:TOL=66408])[&&NHX:TOL=66400],spiziapteryx circumcincta[&&NHX:TOL=66409])[&&NHX:TOL=66399],((microhierax caerulescens[&&NHX:TOL=66477],microhierax fringillarius[&&NHX:TOL=66478],microhierax latifrons[&&NHX:TOL=66479],microhierax erythrogenys[&&NHX:TOL=66480],microhierax melanoleucos[&&NHX:TOL=66481])microhierax[&&NHX:TOL=66411],(polihierax semitorquatus[&&NHX:TOL=66482],polihierax insignis[&&NHX:TOL=66483])polihierax[&&NHX:TOL=66412],(falco naumanni[&&NHX:TOL=66419],falco tinnunculus[&&NHX:TOL=66420],falco rupicolus[&&NHX:TOL=135859],falco newtoni[&&NHX:TOL=66421],falco punctatus[&&NHX:TOL=66422],falco araeus[&&NHX:TOL=66423],falco moluccensis[&&NHX:TOL=66424],falco cenchroides[&&NHX:TOL=66425],falco sparverius[&&NHX:TOL=66426],falco rupicoloides[&&NHX:TOL=66427],falco alopex[&&NHX:TOL=66428],falco ardosiaceus[&&NHX:TOL=66429],falco dickinsoni[&&NHX:TOL=66430],falco zoniventris[&&NHX:TOL=66431],falco chicquera[&&NHX:TOL=66432],falco vespertinus[&&NHX:TOL=66433],falco amurensis[&&NHX:TOL=66434],falco eleonorae[&&NHX:TOL=66435],falco concolor[&&NHX:TOL=66436],falco femoralis[&&NHX:TOL=66437],falco columbarius[&&NHX:TOL=66438],falco rufigularis[&&NHX:TOL=66439],falco deiroleucus[&&NHX:TOL=66440],falco subbuteo[&&NHX:TOL=66441],falco cuvierii[&&NHX:TOL=66442],falco severus[&&NHX:TOL=66443],falco longipennis[&&NHX:TOL=66444],falco novaeseelandiae[&&NHX:TOL=66445],falco berigora[&&NHX:TOL=66446],falco hypoleucos[&&NHX:TOL=66447],falco subniger[&&NHX:TOL=66448],falco biarmicus[&&NHX:TOL=66449],falco jugger[&&NHX:TOL=66450],falco cherrug[&&NHX:TOL=66451],falco rusticolus[&&NHX:TOL=66452],falco mexicanus[&&NHX:TOL=66453],falco peregrinus[&&NHX:TOL=66454],falco pelegrinoides[&&NHX:TOL=66455],falco fasciinucha[&&NHX:TOL=66456])falco[&&NHX:TOL=66413])[&&NHX:TOL=66410])[&&NHX:TOL=66398],(herpetotheres cachinnans[&&NHX:TOL=66415],(micrastur ruficollis[&&NHX:TOL=66484],micrastur plumbeus[&&NHX:TOL=66485],micrastur gilvicollis[&&NHX:TOL=66486],micrastur mirandollei[&&NHX:TOL=66487],micrastur semitorquatus[&&NHX:TOL=66488],micrastur buckleyi[&&NHX:TOL=66489],micrastur mintoni[&&NHX:TOL=102313])micrastur[&&NHX:TOL=66416])[&&NHX:TOL=66414])falconidae[&&NHX:TOL=26379])[&&NHX:TOL=123198],(cariama cristata[&&NHX:TOL=90238],chunga burmeisteri[&&NHX:TOL=90239])cariamidae[&&NHX:TOL=26320],(((((((nyctyornis athertoni[&&NHX:TOL=92708],nyctyornis amictus[&&NHX:TOL=92707])[&&NHX:TOL=92706],meropogon forsteni[&&NHX:TOL=92709],(merops breweri[&&NHX:TOL=92711],merops muelleri[&&NHX:TOL=92712],merops gularis[&&NHX:TOL=92713],merops hirundineus[&&NHX:TOL=92714],merops pusillus[&&NHX:TOL=92715],merops variegatus[&&NHX:TOL=92716],merops oreobates[&&NHX:TOL=92717],merops bulocki[&&NHX:TOL=92718],merops bullockoides[&&NHX:TOL=92719],merops revoilii[&&NHX:TOL=92720],merops albicollis[&&NHX:TOL=92721],merops boehmi[&&NHX:TOL=92722],merops orientalis[&&NHX:TOL=92723],merops persicus[&&NHX:TOL=92724],merops superciliosus[&&NHX:TOL=92725],merops philippinus[&&NHX:TOL=92726],merops ornatus[&&NHX:TOL=92727],merops viridis[&&NHX:TOL=92728],merops leschenaulti[&&NHX:TOL=92729],merops apiaster[&&NHX:TOL=92730],merops malimbicus[&&NHX:TOL=92731],merops nubicus[&&NHX:TOL=92732],merops nubicoides[&&NHX:TOL=92733])merops[&&NHX:TOL=92710])meropidae[&&NHX:TOL=26433],(((hylomanes momotula[&&NHX:TOL=92734],aspatha gularis[&&NHX:TOL=92735],(momotus mexicanus[&&NHX:TOL=92737],momotus momota[&&NHX:TOL=92738],momotus aequatorialis[&&NHX:TOL=92739])momotus[&&NHX:TOL=92736],(baryphthengus martii[&&NHX:TOL=92741],baryphthengus ruficapillus[&&NHX:TOL=92742])baryphthengus[&&NHX:TOL=92740],(electron carinatum[&&NHX:TOL=92744],electron platyrhynchum[&&NHX:TOL=92745])electron[&&NHX:TOL=92743],eumomota superciliosa[&&NHX:TOL=92746])momotidae[&&NHX:TOL=26437],((((halcyon coromanda[&&NHX:TOL=92686],halcyon smyrnensis[&&NHX:TOL=92687],halcyon cyanoventris[&&NHX:TOL=92688],halcyon badia[&&NHX:TOL=92689],halcyon pileata[&&NHX:TOL=92690],halcyon leucocephala[&&NHX:TOL=92691],halcyon albiventris[&&NHX:TOL=92692],halcyon chelicuti[&&NHX:TOL=92693],halcyon malimbica[&&NHX:TOL=92694],halcyon senegalensis[&&NHX:TOL=92695],halcyon senegaloides[&&NHX:TOL=92696])halcyon[&&NHX:TOL=66576],(pelargopsis capensis[&&NHX:TOL=92697],pelargopsis melanorhyncha[&&NHX:TOL=92698],pelargopsis amauroptera[&&NHX:TOL=92699])pelargopsis[&&NHX:TOL=66577])[&&NHX:TOL=66575],lacedo pulchella[&&NHX:TOL=66574],caridonax fulgidus[&&NHX:TOL=92701],((cittura cyanotis[&&NHX:TOL=66563],(tanysiptera galatea[&&NHX:TOL=92643],tanysiptera ellioti[&&NHX:TOL=92644],tanysiptera riedelii[&&NHX:TOL=92645],tanysiptera carolinae[&&NHX:TOL=92646],tanysiptera hydrocharis[&&NHX:TOL=92647],tanysiptera sylvia[&&NHX:TOL=92648],tanysiptera nigriceps[&&NHX:TOL=92649],tanysiptera nympha[&&NHX:TOL=92650],tanysiptera danae[&&NHX:TOL=92651])tanysiptera[&&NHX:TOL=66564])[&&NHX:TOL=66562],(actenoides monachus[&&NHX:TOL=92652],actenoides princeps[&&NHX:TOL=92653],actenoides bougainvillei[&&NHX:TOL=92654],actenoides lindsayi[&&NHX:TOL=92655],actenoides hombroni[&&NHX:TOL=92656],actenoides concretus[&&NHX:TOL=92657])actenoides[&&NHX:TOL=66565],((todiramphus recurvirostris[&&NHX:TOL=92672],todiramphus australasia[&&NHX:TOL=92673],todiramphus tutus[&&NHX:TOL=92674],todiramphus ruficollaris[&&NHX:TOL=92675],todiramphus veneratus[&&NHX:TOL=92676],todiramphus gambieri[&&NHX:TOL=92677],todiramphus godeffroyi[&&NHX:TOL=92678],todiramphus pyrrhopygius[&&NHX:TOL=92679],todiramphus nigrocyaneus[&&NHX:TOL=92658],todiramphus winchelli[&&NHX:TOL=92659],todiramphus diops[&&NHX:TOL=92660],todiramphus lazuli[&&NHX:TOL=92661],todiramphus macleayii[&&NHX:TOL=92662],todiramphus albonotatus[&&NHX:TOL=92663],todiramphus leucopygius[&&NHX:TOL=92664],todiramphus farquhari[&&NHX:TOL=92665],todiramphus funebris[&&NHX:TOL=92666],todiramphus chloris[&&NHX:TOL=92667],todiramphus enigma[&&NHX:TOL=92668],todiramphus cinnamominus[&&NHX:TOL=92669],todiramphus saurophagus[&&NHX:TOL=92670],todiramphus sanctus[&&NHX:TOL=92671])todiramphus[&&NHX:TOL=66567],(syma torotoro[&&NHX:TOL=92680],syma megarhyncha[&&NHX:TOL=92681])syma[&&NHX:TOL=66568])[&&NHX:TOL=66566],(((dacelo novaeguineae[&&NHX:TOL=92682],dacelo leachii[&&NHX:TOL=92683],dacelo tyro[&&NHX:TOL=92684],dacelo gaudichaud[&&NHX:TOL=92685])dacelo[&&NHX:TOL=66571],clytoceyx rex[&&NHX:TOL=66572])[&&NHX:TOL=66570],melidora macrorrhina[&&NHX:TOL=66573])[&&NHX:TOL=66569])[&&NHX:TOL=66561])daceloninae[&&NHX:TOL=66560],(((alcedo euryzona[&&NHX:TOL=92622],((alcedo meninting[&&NHX:TOL=92627],alcedo hercules[&&NHX:TOL=92630])[&&NHX:TOL=105744],((alcedo quadribrachys[&&NHX:TOL=92623],alcedo semitorquata[&&NHX:TOL=92629])[&&NHX:TOL=105746],(alcedo coerulescens[&&NHX:TOL=92621],alcedo atthis[&&NHX:TOL=92628])[&&NHX:TOL=105747])[&&NHX:TOL=105745])[&&NHX:TOL=105743])[&&NHX:TOL=105742],(ceyx fallax[&&NHX:TOL=92633],((alcedo pusilla[&&NHX:TOL=92626],(alcedo azurea[&&NHX:TOL=92624],alcedo websteri[&&NHX:TOL=92625])[&&NHX:TOL=105751])[&&NHX:TOL=105750],(ceyx melanurus[&&NHX:TOL=92632],(ceyx erithaca[&&NHX:TOL=92631],(ceyx lepidus[&&NHX:TOL=92634],(alcedo argentata[&&NHX:TOL=92620],alcedo cyanopectus[&&NHX:TOL=92619])[&&NHX:TOL=105755])[&&NHX:TOL=105754])[&&NHX:TOL=105753])[&&NHX:TOL=105752])[&&NHX:TOL=105749])[&&NHX:TOL=105748])[&&NHX:TOL=105741],(((alcedo vintsioides[&&NHX:TOL=92618],(alcedo cristata[&&NHX:TOL=92616],alcedo thomensis[&&NHX:TOL=92617],alcedo nais[&&NHX:TOL=92615])[&&NHX:TOL=105756])[&&NHX:TOL=105739],alcedo leucogaster[&&NHX:TOL=92614])[&&NHX:TOL=105738],(ispidina picta[&&NHX:TOL=92704],ispidina lecontei[&&NHX:TOL=92703],ispidina madagascariensis[&&NHX:TOL=92705])ispidina[&&NHX:TOL=92702])[&&NHX:TOL=105736])alcedininae[&&NHX:TOL=66552],((megaceryle lugubris[&&NHX:TOL=92635],(megaceryle maxima[&&NHX:TOL=92636],(megaceryle torquata[&&NHX:TOL=92637],megaceryle alcyon[&&NHX:TOL=92638])[&&NHX:TOL=105774])[&&NHX:TOL=105773])megaceryle[&&NHX:TOL=66556],((chloroceryle amazona[&&NHX:TOL=92642],(chloroceryle aenea[&&NHX:TOL=92639],(chloroceryle inda[&&NHX:TOL=92640],chloroceryle americana[&&NHX:TOL=92641])[&&NHX:TOL=105776])[&&NHX:TOL=105775])chloroceryle[&&NHX:TOL=66558],ceryle rudis[&&NHX:TOL=66559])[&&NHX:TOL=66557])cerylinae[&&NHX:TOL=66555])alcedinidae[&&NHX:TOL=26439])[&&NHX:TOL=26435],(((todus mexicanus[&&NHX:TOL=57578],todus todus[&&NHX:TOL=57579])[&&NHX:TOL=57577],todus subulatus[&&NHX:TOL=57580])[&&NHX:TOL=57576],(todus angustirostris[&&NHX:TOL=57582],todus multicolor[&&NHX:TOL=57583])[&&NHX:TOL=57581])todidae[&&NHX:TOL=26438])[&&NHX:TOL=123197],(((coracias garrulus[&&NHX:TOL=57585],coracias abyssinicus[&&NHX:TOL=57586],coracias caudatus[&&NHX:TOL=57587],coracias spatulatus[&&NHX:TOL=57588],coracias naevius[&&NHX:TOL=57589],coracias benghalensis[&&NHX:TOL=57590],coracias temminckii[&&NHX:TOL=57591],coracias cyanogaster[&&NHX:TOL=57592])coracias[&&NHX:TOL=57584],(eurystomus orientalis[&&NHX:TOL=57597],eurystomus azureus[&&NHX:TOL=57596],eurystomus gularis[&&NHX:TOL=57595],eurystomus glaucurus[&&NHX:TOL=57594])eurystomus[&&NHX:TOL=57593])coraciidae[&&NHX:TOL=26443],((geobiastes squamiger[&&NHX:TOL=57602],brachypteracias leptosomus[&&NHX:TOL=57603])brachypteracias[&&NHX:TOL=57601],uratelornis chimaera[&&NHX:TOL=57604],(atelornis pittoides[&&NHX:TOL=57600],atelornis crossleyi[&&NHX:TOL=57599])atelornis[&&NHX:TOL=57598])brachypteraciidae[&&NHX:TOL=26444])[&&NHX:TOL=26442])coraciiformes[&&NHX:TOL=56738],((((bucco macrodactylus[&&NHX:TOL=93698],bucco tamatia[&&NHX:TOL=93699],bucco noanamae[&&NHX:TOL=93700],bucco capensis[&&NHX:TOL=93701])bucco[&&NHX:TOL=93697],(nystalus radiatus[&&NHX:TOL=93703],nystalus chacuru[&&NHX:TOL=93704],nystalus striolatus[&&NHX:TOL=93705],nystalus maculatus[&&NHX:TOL=93706],nystalus striatipectus[&&NHX:TOL=93707])nystalus[&&NHX:TOL=93702],hypnelus ruficollis[&&NHX:TOL=93708],(malacoptila striata[&&NHX:TOL=93710],malacoptila fusca[&&NHX:TOL=93711],malacoptila semicincta[&&NHX:TOL=93712],malacoptila fulvogularis[&&NHX:TOL=93713],malacoptila rufa[&&NHX:TOL=93714],malacoptila panamensis[&&NHX:TOL=93715],malacoptila mystacalis[&&NHX:TOL=93716])malacoptila[&&NHX:TOL=93709],micromonacha lanceolata[&&NHX:TOL=93717],(nonnula rubecula[&&NHX:TOL=93719],nonnula sclateri[&&NHX:TOL=93720],nonnula brunnea[&&NHX:TOL=93721],nonnula frontalis[&&NHX:TOL=93722],nonnula ruficapilla[&&NHX:TOL=93723],nonnula amaurocephala[&&NHX:TOL=93724])nonnula[&&NHX:TOL=93718],chelidoptera tenebrosa[&&NHX:TOL=93725],hapaloptila castanea[&&NHX:TOL=93726],(monasa atra[&&NHX:TOL=93728],monasa nigrifrons[&&NHX:TOL=93729],monasa morphoeus[&&NHX:TOL=93730],monasa flavirostris[&&NHX:TOL=93731])monasa[&&NHX:TOL=93727],(notharchus tectus[&&NHX:TOL=93696],notharchus macrorhynchos[&&NHX:TOL=129464],notharchus hyperrhynchus[&&NHX:TOL=93692],notharchus swainsoni[&&NHX:TOL=93693],notharchus pectoralis[&&NHX:TOL=93694],notharchus ordii[&&NHX:TOL=93695])notharchus[&&NHX:TOL=93691])bucconidae[&&NHX:TOL=26413],((galbula albirostris[&&NHX:TOL=93733],galbula cyanicollis[&&NHX:TOL=93734],galbula ruficauda[&&NHX:TOL=93735],galbula galbula[&&NHX:TOL=93736],galbula pastazae[&&NHX:TOL=93737],galbula tombacea[&&NHX:TOL=93738],galbula cyanescens[&&NHX:TOL=93739],galbula chalcothorax[&&NHX:TOL=93740],galbula leucogastra[&&NHX:TOL=93741],galbula dea[&&NHX:TOL=93742])galbula[&&NHX:TOL=93732],jacamaralcyon tridactyla[&&NHX:TOL=93743],(brachygalba salmoni[&&NHX:TOL=93745],brachygalba goeringi[&&NHX:TOL=93746],brachygalba lugubris[&&NHX:TOL=93747],brachygalba albogularis[&&NHX:TOL=93748])brachygalba[&&NHX:TOL=93744],(galbalcyrhynchus leucotis[&&NHX:TOL=93750],galbalcyrhynchus purusianus[&&NHX:TOL=93751])galbalcyrhynchus[&&NHX:TOL=93749],jacamerops aureus[&&NHX:TOL=93752])galbulidae[&&NHX:TOL=26414])[&&NHX:TOL=26412],(((((((gymnobucco bonapartei[&&NHX:TOL=93381],gymnobucco sladeni[&&NHX:TOL=93382],gymnobucco peli[&&NHX:TOL=93383],gymnobucco calvus[&&NHX:TOL=93384])gymnobucco[&&NHX:TOL=93380],(stactolaema leucotis[&&NHX:TOL=93386],stactolaema whytii[&&NHX:TOL=93387],stactolaema olivacea[&&NHX:TOL=93389],stactolaema anchietae[&&NHX:TOL=93388])stactolaema[&&NHX:TOL=93385])[&&NHX:TOL=125368],buccanodon duchaillui[&&NHX:TOL=93400])[&&NHX:TOL=125379],(((lybius undatus[&&NHX:TOL=93409],lybius leucocephalus[&&NHX:TOL=93411],lybius chaplini[&&NHX:TOL=93412],lybius rubrifacies[&&NHX:TOL=93413],lybius guifsobalito[&&NHX:TOL=93414],lybius torquatus[&&NHX:TOL=93415],lybius vieilloti[&&NHX:TOL=93410],lybius minor[&&NHX:TOL=93417],lybius bidentatus[&&NHX:TOL=93418],lybius dubius[&&NHX:TOL=93419],lybius melanopterus[&&NHX:TOL=93416],lybius rolleti[&&NHX:TOL=93420])lybius[&&NHX:TOL=93408],(tricholaema hirsuta[&&NHX:TOL=93402],tricholaema frontata[&&NHX:TOL=93404],tricholaema leucomelas[&&NHX:TOL=93405],tricholaema diademata[&&NHX:TOL=93403],tricholaema lachrymosa[&&NHX:TOL=93406],tricholaema melanocephala[&&NHX:TOL=93407])tricholaema[&&NHX:TOL=93401])[&&NHX:TOL=125370],(pogoniulus scolopaceus[&&NHX:TOL=93391],pogoniulus simplex[&&NHX:TOL=93392],pogoniulus leucomystax[&&NHX:TOL=93393],pogoniulus coryphaeus[&&NHX:TOL=93394],pogoniulus atroflavus[&&NHX:TOL=93395],pogoniulus subsulphureus[&&NHX:TOL=93396],pogoniulus bilineatus[&&NHX:TOL=93397],pogoniulus makawai[&&NHX:TOL=129527],pogoniulus pusillus[&&NHX:TOL=93398],pogoniulus chrysoconus[&&NHX:TOL=93399])pogoniulus[&&NHX:TOL=93390])[&&NHX:TOL=125369],(trachyphonus purpuratus[&&NHX:TOL=93422],trachyphonus vaillantii[&&NHX:TOL=93423],trachyphonus erythrocephalus[&&NHX:TOL=93424],trachyphonus margaritatus[&&NHX:TOL=93425],trachyphonus darnaudii[&&NHX:TOL=93426])trachyphonus[&&NHX:TOL=93421])african barbets[&&NHX:TOL=26417],((((((aulacorhynchus wagleri[&&NHX:TOL=129813],aulacorhynchus prasinus[&&NHX:TOL=93290],aulacorhynchus caeruleogularis[&&NHX:TOL=129814],aulacorhynchus cognatus[&&NHX:TOL=129815],aulacorhynchus lautus[&&NHX:TOL=129816],aulacorhynchus griseigularis[&&NHX:TOL=129817],aulacorhynchus albivitta[&&NHX:TOL=129818],aulacorhynchus atrogularis[&&NHX:TOL=129819],aulacorhynchus sulcatus[&&NHX:TOL=93291],aulacorhynchus calorhynchus[&&NHX:TOL=93292],aulacorhynchus derbianus[&&NHX:TOL=93293],aulacorhynchus haematopygus[&&NHX:TOL=93294],aulacorhynchus huallagae[&&NHX:TOL=93295],aulacorhynchus coeruleicinctis[&&NHX:TOL=93296])aulacorhynchus[&&NHX:TOL=93289],(selenidera spectabilis[&&NHX:TOL=93313],selenidera culik[&&NHX:TOL=93314],selenidera reinwardtii[&&NHX:TOL=93315],selenidera nattereri[&&NHX:TOL=93316],selenidera gouldii[&&NHX:TOL=93317],selenidera maculirostris[&&NHX:TOL=93318])selenidera[&&NHX:TOL=93312])[&&NHX:TOL=125377],(andigena hypoglauca[&&NHX:TOL=93320],andigena laminirostris[&&NHX:TOL=93321],andigena cucullata[&&NHX:TOL=93322],andigena nigrirostris[&&NHX:TOL=93323])andigena[&&NHX:TOL=93319])[&&NHX:TOL=125376],(pteroglossus viridis[&&NHX:TOL=93298],pteroglossus inscriptus[&&NHX:TOL=93299],pteroglossus bitorquatus[&&NHX:TOL=93300],pteroglossus azara[&&NHX:TOL=93301],pteroglossus mariae[&&NHX:TOL=93302],pteroglossus aracari[&&NHX:TOL=93303],pteroglossus castanotis[&&NHX:TOL=93304],pteroglossus pluricinctus[&&NHX:TOL=93305],pteroglossus torquatus[&&NHX:TOL=93306],pteroglossus sanguineus[&&NHX:TOL=93307],pteroglossus erythropygius[&&NHX:TOL=93308],pteroglossus frantzii[&&NHX:TOL=93309],pteroglossus beauharnaesii[&&NHX:TOL=93310],pteroglossus bailloni[&&NHX:TOL=93311])pteroglossus[&&NHX:TOL=93297])[&&NHX:TOL=125375],(ramphastos dicolorus[&&NHX:TOL=93325],ramphastos vitellinus[&&NHX:TOL=93326],ramphastos citreolaemus[&&NHX:TOL=93327],ramphastos brevis[&&NHX:TOL=93328],ramphastos sulfuratus[&&NHX:TOL=93329],ramphastos toco[&&NHX:TOL=93330],ramphastos tucanus[&&NHX:TOL=93331],ramphastos swainsonii[&&NHX:TOL=93332],ramphastos ambiguus[&&NHX:TOL=93333])ramphastos[&&NHX:TOL=93324])ramphastidae[&&NHX:TOL=26419],(((capito aurovirens[&&NHX:TOL=93335],capito wallacei[&&NHX:TOL=93336],capito maculicoronatus[&&NHX:TOL=93337],capito squamatus[&&NHX:TOL=93338],capito hypoleucus[&&NHX:TOL=93339],capito dayi[&&NHX:TOL=93340],capito brunneipectus[&&NHX:TOL=93341],capito niger[&&NHX:TOL=93342],capito auratus[&&NHX:TOL=93343],capito quinticolor[&&NHX:TOL=93344])capito[&&NHX:TOL=93334],(eubucco richardsoni[&&NHX:TOL=93346],eubucco bourcierii[&&NHX:TOL=93347],eubucco tucinkae[&&NHX:TOL=93348],eubucco versicolor[&&NHX:TOL=93349])eubucco[&&NHX:TOL=93345])[&&NHX:TOL=125378],(semnornis ramphastinus[&&NHX:TOL=93351],semnornis frantzii[&&NHX:TOL=93352])semnornis[&&NHX:TOL=93350])new world barbets[&&NHX:TOL=26420])[&&NHX:TOL=26418])[&&NHX:TOL=26416],(((megalaima virens[&&NHX:TOL=93355],megalaima lagrandieri[&&NHX:TOL=93356],megalaima zeylanica[&&NHX:TOL=93357],megalaima lineata[&&NHX:TOL=93358],megalaima viridis[&&NHX:TOL=93359],megalaima faiostricta[&&NHX:TOL=93360],megalaima corvina[&&NHX:TOL=93361],megalaima chrysopogon[&&NHX:TOL=93362],megalaima rafflesii[&&NHX:TOL=93363],megalaima mystacophanos[&&NHX:TOL=93364],megalaima javensis[&&NHX:TOL=93365],megalaima flavifrons[&&NHX:TOL=93366],megalaima franklinii[&&NHX:TOL=93367],megalaima oorti[&&NHX:TOL=93368],megalaima annamensis[&&NHX:TOL=129820],megalaima faber[&&NHX:TOL=129525],megalaima nuchalis[&&NHX:TOL=129526],megalaima asiatica[&&NHX:TOL=93369],megalaima monticola[&&NHX:TOL=93370],megalaima incognita[&&NHX:TOL=93371],megalaima henricii[&&NHX:TOL=93372],megalaima armillaris[&&NHX:TOL=93373],megalaima pulcherrima[&&NHX:TOL=93374],megalaima australis[&&NHX:TOL=93375],megalaima eximia[&&NHX:TOL=93376],megalaima malabarica[&&NHX:TOL=129821],megalaima rubricapillus[&&NHX:TOL=93377],megalaima haemacephala[&&NHX:TOL=93378])megalaima[&&NHX:TOL=93354],psilopogon pyrolophus[&&NHX:TOL=93353])[&&NHX:TOL=125381],caloramphus fuliginosus[&&NHX:TOL=93379])asian barbets[&&NHX:TOL=125380])[&&NHX:TOL=125366],(((prodotiscus insignis[&&NHX:TOL=93443],prodotiscus zambesiae[&&NHX:TOL=93444],prodotiscus regulus[&&NHX:TOL=93445])prodotiscus[&&NHX:TOL=93442],melichneutes robustus[&&NHX:TOL=93446],(indicator pumilio[&&NHX:TOL=93428],indicator willcocksi[&&NHX:TOL=93429],indicator meliphilus[&&NHX:TOL=93430],indicator exilis[&&NHX:TOL=93431],indicator conirostris[&&NHX:TOL=93432],indicator minor[&&NHX:TOL=93433],indicator maculatus[&&NHX:TOL=93434],indicator variegatus[&&NHX:TOL=93435],indicator xanthonotus[&&NHX:TOL=93436],indicator archipelagicus[&&NHX:TOL=93437],indicator indicator[&&NHX:TOL=93438])indicator[&&NHX:TOL=93427],(melignomon zenkeri[&&NHX:TOL=93440],melignomon eisentrauti[&&NHX:TOL=93441])melignomon[&&NHX:TOL=93439])indicatoridae[&&NHX:TOL=26422],((picumnus innominatus[&&NHX:TOL=93448],picumnus aurifrons[&&NHX:TOL=93449],picumnus lafresnayi[&&NHX:TOL=93450],picumnus pumilus[&&NHX:TOL=93451],picumnus exilis[&&NHX:TOL=93452],picumnus nigropunctatus[&&NHX:TOL=93453],picumnus sclateri[&&NHX:TOL=93454],picumnus squamulatus[&&NHX:TOL=93455],picumnus spilogaster[&&NHX:TOL=93456],picumnus minutissimus[&&NHX:TOL=93457],picumnus pygmaeus[&&NHX:TOL=93458],picumnus steindachneri[&&NHX:TOL=93459],picumnus varzeae[&&NHX:TOL=93460],picumnus cirratus[&&NHX:TOL=93461],picumnus dorbignyanus[&&NHX:TOL=93462],picumnus temminckii[&&NHX:TOL=93463],picumnus albosquamatus[&&NHX:TOL=93464],picumnus fuscus[&&NHX:TOL=93465],picumnus rufiventris[&&NHX:TOL=93466],picumnus limae[&&NHX:TOL=93467],picumnus fulvescens[&&NHX:TOL=93468],picumnus nebulosus[&&NHX:TOL=93469],picumnus castelnau[&&NHX:TOL=93470],picumnus subtilis[&&NHX:TOL=93471],picumnus olivaceus[&&NHX:TOL=93472],picumnus granadensis[&&NHX:TOL=93473],picumnus cinnamomeus[&&NHX:TOL=93474])picumnus[&&NHX:TOL=93447],(jynx torquilla[&&NHX:TOL=93476],jynx ruficollis[&&NHX:TOL=93477])jynx[&&NHX:TOL=93475],(sasia africana[&&NHX:TOL=93479],sasia abnormis[&&NHX:TOL=93480],sasia ochracea[&&NHX:TOL=93481])sasia[&&NHX:TOL=93478],nesoctites micromegas[&&NHX:TOL=93482],leuconerpes candidus[&&NHX:TOL=93483],(melanerpes lewis[&&NHX:TOL=93485],melanerpes herminieri[&&NHX:TOL=93486],melanerpes portoricensis[&&NHX:TOL=93487],melanerpes erythrocephalus[&&NHX:TOL=93488],melanerpes formicivorus[&&NHX:TOL=93489],melanerpes cruentatus[&&NHX:TOL=93490],melanerpes flavifrons[&&NHX:TOL=93491],melanerpes chrysauchen[&&NHX:TOL=93492],melanerpes pulcher[&&NHX:TOL=93493],melanerpes pucherani[&&NHX:TOL=93494],melanerpes cactorum[&&NHX:TOL=93495],melanerpes striatus[&&NHX:TOL=93496],melanerpes radiolatus[&&NHX:TOL=93497],melanerpes chrysogenys[&&NHX:TOL=93498],melanerpes hypopolius[&&NHX:TOL=93499],melanerpes pygmaeus[&&NHX:TOL=93500],melanerpes rubricapillus[&&NHX:TOL=93501],melanerpes uropygialis[&&NHX:TOL=93502],melanerpes hoffmannii[&&NHX:TOL=93503],melanerpes aurifrons[&&NHX:TOL=93504],melanerpes carolinus[&&NHX:TOL=93505],melanerpes superciliaris[&&NHX:TOL=93506])melanerpes[&&NHX:TOL=93484],(sphyrapicus thyroideus[&&NHX:TOL=93508],sphyrapicus varius[&&NHX:TOL=93509],sphyrapicus nuchalis[&&NHX:TOL=93510],sphyrapicus ruber[&&NHX:TOL=93511])sphyrapicus[&&NHX:TOL=93507],xiphidiopicus percussus[&&NHX:TOL=93512],(campethera punctuligera[&&NHX:TOL=93514],campethera bennettii[&&NHX:TOL=93515],campethera scriptoricauda[&&NHX:TOL=93516],campethera nubica[&&NHX:TOL=93517],campethera abingoni[&&NHX:TOL=93518],campethera mombassica[&&NHX:TOL=93519],campethera notata[&&NHX:TOL=93520],campethera cailliautii[&&NHX:TOL=93521],campethera maculosa[&&NHX:TOL=93522],campethera tullbergi[&&NHX:TOL=93523],campethera nivosa[&&NHX:TOL=93524],campethera caroli[&&NHX:TOL=93525])campethera[&&NHX:TOL=93513],geocolaptes olivaceus[&&NHX:TOL=93526],(dendropicos elachus[&&NHX:TOL=93528],dendropicos poecilolaemus[&&NHX:TOL=93529],dendropicos abyssinicus[&&NHX:TOL=93530],dendropicos fuscescens[&&NHX:TOL=93531],dendropicos gabonensis[&&NHX:TOL=93532],dendropicos stierlingi[&&NHX:TOL=93533],dendropicos namaquus[&&NHX:TOL=93534],dendropicos xantholophus[&&NHX:TOL=93535],dendropicos pyrrhogaster[&&NHX:TOL=93536],dendropicos elliotii[&&NHX:TOL=93537],dendropicos goertae[&&NHX:TOL=93538],dendropicos griseocephalus[&&NHX:TOL=93539])dendropicos[&&NHX:TOL=93527],(dendrocopos hyperythrus[&&NHX:TOL=93541],dendrocopos temminckii[&&NHX:TOL=93542],dendrocopos maculatus[&&NHX:TOL=93543],dendrocopos ramsayi[&&NHX:TOL=129528],dendrocopos moluccensis[&&NHX:TOL=93544],dendrocopos nanus[&&NHX:TOL=93545],dendrocopos kizuki[&&NHX:TOL=93546],dendrocopos canicapillus[&&NHX:TOL=93547],dendrocopos minor[&&NHX:TOL=93548],dendrocopos macei[&&NHX:TOL=93549],dendrocopos analis[&&NHX:TOL=129849],dendrocopos atratus[&&NHX:TOL=93550],dendrocopos auriceps[&&NHX:TOL=93551],dendrocopos mahrattensis[&&NHX:TOL=93552],dendrocopos dorae[&&NHX:TOL=93553],dendrocopos cathpharius[&&NHX:TOL=93554],dendrocopos darjellensis[&&NHX:TOL=93555],dendrocopos medius[&&NHX:TOL=93556],dendrocopos leucotos[&&NHX:TOL=93557],dendrocopos himalayensis[&&NHX:TOL=93558],dendrocopos assimilis[&&NHX:TOL=93559],dendrocopos syriacus[&&NHX:TOL=93560],dendrocopos leucopterus[&&NHX:TOL=93561],dendrocopos major[&&NHX:TOL=93562])dendrocopos[&&NHX:TOL=93540],(picoides obsoletus[&&NHX:TOL=93564],picoides mixtus[&&NHX:TOL=93565],picoides lignarius[&&NHX:TOL=93566],picoides scalaris[&&NHX:TOL=93567],picoides nuttallii[&&NHX:TOL=93568],picoides pubescens[&&NHX:TOL=93569],picoides villosus[&&NHX:TOL=93570],picoides arizonae[&&NHX:TOL=93571],picoides stricklandi[&&NHX:TOL=93572],picoides borealis[&&NHX:TOL=93573],picoides albolarvatus[&&NHX:TOL=93574],picoides tridactylus[&&NHX:TOL=93575],picoides dorsalis[&&NHX:TOL=93576],picoides arcticus[&&NHX:TOL=93577])picoides[&&NHX:TOL=93563],(veniliornis callonotus[&&NHX:TOL=93579],veniliornis dignus[&&NHX:TOL=93580],veniliornis nigriceps[&&NHX:TOL=93581],veniliornis fumigatus[&&NHX:TOL=93582],veniliornis passerinus[&&NHX:TOL=93583],veniliornis frontalis[&&NHX:TOL=93584],veniliornis spilogaster[&&NHX:TOL=93585],veniliornis sanguineus[&&NHX:TOL=93586],veniliornis kirkii[&&NHX:TOL=93587],veniliornis affinis[&&NHX:TOL=93588],veniliornis chocoensis[&&NHX:TOL=93589],veniliornis cassini[&&NHX:TOL=93590],veniliornis maculifrons[&&NHX:TOL=93591])veniliornis[&&NHX:TOL=93578],(piculus simplex[&&NHX:TOL=93593],piculus callopterus[&&NHX:TOL=93594],piculus leucolaemus[&&NHX:TOL=93595],piculus litae[&&NHX:TOL=93596],piculus flavigula[&&NHX:TOL=93597],piculus chrysochloros[&&NHX:TOL=93598],piculus aurulentus[&&NHX:TOL=93599],piculus rubiginosus[&&NHX:TOL=93600],piculus auricularis[&&NHX:TOL=93602],piculus rivolii[&&NHX:TOL=93603])piculus[&&NHX:TOL=93592],(chrysoptilus atricollis[&&NHX:TOL=93605],chrysoptilus punctigula[&&NHX:TOL=93606],chrysoptilus melanochloros[&&NHX:TOL=93607])chrysoptilus[&&NHX:TOL=93604],(colaptes auratus[&&NHX:TOL=93609],colaptes chrysoides[&&NHX:TOL=93610],colaptes fernandinae[&&NHX:TOL=93611],colaptes pitius[&&NHX:TOL=93612],colaptes rupicola[&&NHX:TOL=93613],colaptes campestris[&&NHX:TOL=93614])colaptes[&&NHX:TOL=93608],(celeus brachyurus[&&NHX:TOL=93616],celeus loricatus[&&NHX:TOL=93617],celeus undatus[&&NHX:TOL=93618],celeus grammicus[&&NHX:TOL=93619],celeus castaneus[&&NHX:TOL=93620],celeus elegans[&&NHX:TOL=93621],celeus lugubris[&&NHX:TOL=93622],celeus flavescens[&&NHX:TOL=93623],celeus flavus[&&NHX:TOL=93624],celeus spectabilis[&&NHX:TOL=93625],celeus obrieni[&&NHX:TOL=93626],celeus torquatus[&&NHX:TOL=93627])celeus[&&NHX:TOL=93615],(dryocopus galeatus[&&NHX:TOL=93629],dryocopus schulzi[&&NHX:TOL=93630],dryocopus lineatus[&&NHX:TOL=93631],dryocopus pileatus[&&NHX:TOL=93632],dryocopus javensis[&&NHX:TOL=93633],dryocopus hodgei[&&NHX:TOL=93634],dryocopus martius[&&NHX:TOL=93635])dryocopus[&&NHX:TOL=93628],(campephilus pollens[&&NHX:TOL=93637],campephilus haematogaster[&&NHX:TOL=93638],campephilus rubricollis[&&NHX:TOL=93639],campephilus robustus[&&NHX:TOL=93640],campephilus melanoleucos[&&NHX:TOL=93641],campephilus guatemalensis[&&NHX:TOL=93642],campephilus gayaquilensis[&&NHX:TOL=93643],campephilus leucopogon[&&NHX:TOL=93644],campephilus magellanicus[&&NHX:TOL=93645],campephilus principalis[&&NHX:TOL=93646],campephilus imperialis[&&NHX:TOL=93647])campephilus[&&NHX:TOL=93636],(picus miniaceus[&&NHX:TOL=93649],picus puniceus[&&NHX:TOL=93650],picus chlorolophus[&&NHX:TOL=93651],picus mentalis[&&NHX:TOL=93652],picus flavinucha[&&NHX:TOL=93653],picus viridanus[&&NHX:TOL=93654],picus vittatus[&&NHX:TOL=93655],picus xanthopygaeus[&&NHX:TOL=93656],picus squamatus[&&NHX:TOL=93657],picus awokera[&&NHX:TOL=93658],picus viridis[&&NHX:TOL=93659],picus vaillantii[&&NHX:TOL=93660],picus rabieri[&&NHX:TOL=93661],picus erythropygius[&&NHX:TOL=93662],picus canus[&&NHX:TOL=93663])picus[&&NHX:TOL=93648],(dinopium rafflesii[&&NHX:TOL=93665],dinopium shorii[&&NHX:TOL=93666],dinopium javanense[&&NHX:TOL=93667],dinopium benghalense[&&NHX:TOL=93668])dinopium[&&NHX:TOL=93664],(chrysocolaptes lucidus[&&NHX:TOL=93670],chrysocolaptes stricklandi[&&NHX:TOL=129850],chrysocolaptes festivus[&&NHX:TOL=93671])chrysocolaptes[&&NHX:TOL=93669],(gecinulus viridis[&&NHX:TOL=93673],gecinulus grantia[&&NHX:TOL=93674])gecinulus[&&NHX:TOL=93672],sapheopipo noguchii[&&NHX:TOL=93675],(blythipicus pyrrhotis[&&NHX:TOL=93677],blythipicus rubiginosus[&&NHX:TOL=93678])blythipicus[&&NHX:TOL=93676],reinwardtipicus validus[&&NHX:TOL=93679],(meiglyptes tristis[&&NHX:TOL=93681],meiglyptes jugularis[&&NHX:TOL=93682],meiglyptes tukki[&&NHX:TOL=93683])meiglyptes[&&NHX:TOL=93680],(hemicircus canente[&&NHX:TOL=93686],hemicircus concretus[&&NHX:TOL=93685])hemicircus[&&NHX:TOL=93684],(mulleripicus fulvus[&&NHX:TOL=93688],mulleripicus funebris[&&NHX:TOL=93689],mulleripicus pulverulentus[&&NHX:TOL=93690])mulleripicus[&&NHX:TOL=93687])picidae[&&NHX:TOL=26423])[&&NHX:TOL=26421])[&&NHX:TOL=26415])piciformes[&&NHX:TOL=26411])[&&NHX:TOL=123196],(((upupa epops[&&NHX:TOL=92747],upupa africana[&&NHX:TOL=92748],upupa marginata[&&NHX:TOL=92749])upupa[&&NHX:TOL=26429],((phoeniculus castaneiceps[&&NHX:TOL=92751],phoeniculus bollei[&&NHX:TOL=92752],phoeniculus purpureus[&&NHX:TOL=92753],phoeniculus somaliensis[&&NHX:TOL=92754],phoeniculus damarensis[&&NHX:TOL=92755],phoeniculus granti[&&NHX:TOL=92756])phoeniculus[&&NHX:TOL=92750],(rhinopomastus aterrimus[&&NHX:TOL=92758],rhinopomastus cyanomelas[&&NHX:TOL=92759],rhinopomastus minor[&&NHX:TOL=92760])rhinopomastus[&&NHX:TOL=92757])phoeniculidae[&&NHX:TOL=26430])[&&NHX:TOL=26428],(((tockus alboterminatus[&&NHX:TOL=92762],tockus bradfieldi[&&NHX:TOL=92763],tockus fasciatus[&&NHX:TOL=92764],tockus hemprichii[&&NHX:TOL=92765],tockus pallidirostris[&&NHX:TOL=92766],tockus nasutus[&&NHX:TOL=92767],tockus monteiri[&&NHX:TOL=92768],tockus erythrorhynchus[&&NHX:TOL=92769],tockus damarensis[&&NHX:TOL=135864],tockus rufirostris[&&NHX:TOL=135865],tockus ruahae[&&NHX:TOL=135866],tockus kempi[&&NHX:TOL=135867],tockus leucomelas[&&NHX:TOL=92770],tockus flavirostris[&&NHX:TOL=92771],tockus deckeni[&&NHX:TOL=92772],tockus jacksoni[&&NHX:TOL=92773],tockus hartlaubi[&&NHX:TOL=92774],tockus camurus[&&NHX:TOL=92775])tockus[&&NHX:TOL=92761],(anorrhinus tickelli[&&NHX:TOL=92777],anorrhinus austeni[&&NHX:TOL=129520],anorrhinus galeritus[&&NHX:TOL=92778])anorrhinus[&&NHX:TOL=92776],tropicranus albocristatus[&&NHX:TOL=92779],(ocyceros griseus[&&NHX:TOL=92781],ocyceros gingalensis[&&NHX:TOL=92782],ocyceros birostris[&&NHX:TOL=92783])ocyceros[&&NHX:TOL=92780],(anthracoceros coronatus[&&NHX:TOL=92785],anthracoceros albirostris[&&NHX:TOL=92786],anthracoceros marchei[&&NHX:TOL=92787],anthracoceros malayanus[&&NHX:TOL=92788],anthracoceros montani[&&NHX:TOL=92789])anthracoceros[&&NHX:TOL=92784],(buceros bicornis[&&NHX:TOL=92791],buceros rhinoceros[&&NHX:TOL=92792],buceros hydrocorax[&&NHX:TOL=92793])buceros[&&NHX:TOL=92790],rhinoplax vigil[&&NHX:TOL=92794],(penelopides panini[&&NHX:TOL=92796],penelopides manillae[&&NHX:TOL=129524],penelopides mindorensis[&&NHX:TOL=129521],penelopides samarensis[&&NHX:TOL=129522],penelopides affinis[&&NHX:TOL=129523],penelopides exarhatus[&&NHX:TOL=92797])penelopides[&&NHX:TOL=92795],berenicornis comatus[&&NHX:TOL=92798],(aceros nipalensis[&&NHX:TOL=92800],aceros cassidix[&&NHX:TOL=92801],aceros corrugatus[&&NHX:TOL=92802],aceros waldeni[&&NHX:TOL=92803],aceros leucocephalus[&&NHX:TOL=92804])aceros[&&NHX:TOL=92799],(rhyticeros plicatus[&&NHX:TOL=92806],rhyticeros narcondami[&&NHX:TOL=92807],rhyticeros subruficollis[&&NHX:TOL=92808],rhyticeros undulatus[&&NHX:TOL=92809],rhyticeros everetti[&&NHX:TOL=92810])rhyticeros[&&NHX:TOL=92805],(ceratogymna atrata[&&NHX:TOL=92812],ceratogymna elata[&&NHX:TOL=92813])ceratogymna[&&NHX:TOL=92811],(bycanistes fistulator[&&NHX:TOL=92815],bycanistes bucinator[&&NHX:TOL=92816],bycanistes cylindricus[&&NHX:TOL=92817],bycanistes albotibialis[&&NHX:TOL=92818],bycanistes subcylindricus[&&NHX:TOL=92819],bycanistes brevis[&&NHX:TOL=92820])bycanistes[&&NHX:TOL=92814])bucerotidae[&&NHX:TOL=26431],(bucorvus abyssinicus[&&NHX:TOL=92822],bucorvus leadbeateri[&&NHX:TOL=92823])bucorvus[&&NHX:TOL=92821])[&&NHX:TOL=103217])bucerotiformes[&&NHX:TOL=26427])[&&NHX:TOL=123195],(((harpactes fasciatus[&&NHX:TOL=92574],harpactes kasumba[&&NHX:TOL=92575],harpactes diardii[&&NHX:TOL=92576],harpactes ardens[&&NHX:TOL=92577],harpactes whiteheadi[&&NHX:TOL=92578],harpactes orrhophaeus[&&NHX:TOL=92579],harpactes duvaucelii[&&NHX:TOL=92580],harpactes oreskios[&&NHX:TOL=92581],harpactes erythrocephalus[&&NHX:TOL=92582],harpactes wardi[&&NHX:TOL=92583])harpactes[&&NHX:TOL=92573],(apaloderma narina[&&NHX:TOL=92567],apaloderma aequatoriale[&&NHX:TOL=92568],apaloderma vittatum[&&NHX:TOL=92569])apaloderma[&&NHX:TOL=92566],(apalharpactes mackloti[&&NHX:TOL=92571],apalharpactes reinwardtii[&&NHX:TOL=92572])apalharpactes[&&NHX:TOL=92570])[&&NHX:TOL=124978],(priotelus roseigaster[&&NHX:TOL=92585],priotelus temnurus[&&NHX:TOL=92586])priotelus[&&NHX:TOL=92584],(trogon melanocephalus[&&NHX:TOL=92588],trogon citreolus[&&NHX:TOL=92589],trogon viridis[&&NHX:TOL=92590],trogon chionurus[&&NHX:TOL=92591],trogon bairdii[&&NHX:TOL=92592],trogon surrucura[&&NHX:TOL=92593],trogon curucui[&&NHX:TOL=92594],trogon violaceus[&&NHX:TOL=92595],trogon caligatus[&&NHX:TOL=92596],trogon mexicanus[&&NHX:TOL=92597],trogon elegans[&&NHX:TOL=92598],trogon collaris[&&NHX:TOL=92599],trogon personatus[&&NHX:TOL=92600],trogon rufus[&&NHX:TOL=92601],trogon massena[&&NHX:TOL=92602],trogon clathratus[&&NHX:TOL=92603],trogon melanurus[&&NHX:TOL=92604],trogon mesurus[&&NHX:TOL=92605],trogon comptus[&&NHX:TOL=92606])trogon[&&NHX:TOL=92587],((pharomachrus auriceps[&&NHX:TOL=92610],pharomachrus antisianus[&&NHX:TOL=92613],pharomachrus pavoninus[&&NHX:TOL=92609],pharomachrus fulgidus[&&NHX:TOL=92611],pharomachrus mocinno[&&NHX:TOL=92612])pharomachrus[&&NHX:TOL=92608],euptilotis neoxenus[&&NHX:TOL=92607])[&&NHX:TOL=124993])trogonidae[&&NHX:TOL=26426])[&&NHX:TOL=123194],leptosomus discolor[&&NHX:TOL=26441])[&&NHX:TOL=123193],((sagittarius serpentarius[&&NHX:TOL=26377],((((((((circus[&&NHX:TOL=57812],accipiter[&&NHX:TOL=57800])[&&NHX:TOL=57880],(melierax[&&NHX:TOL=57843],micronisus[&&NHX:TOL=57844])[&&NHX:TOL=65528])[&&NHX:TOL=57879],megatriorchis[&&NHX:TOL=57842],erythrotriorchis[&&NHX:TOL=57816],urotriorchis[&&NHX:TOL=57864],kaupifalco[&&NHX:TOL=57836],macheiramphus[&&NHX:TOL=57841],(((haliastur[&&NHX:TOL=57825],milvus[&&NHX:TOL=57845])[&&NHX:TOL=57871],(ichthyophaga[&&NHX:TOL=57833],haliaeetus[&&NHX:TOL=57824])[&&NHX:TOL=57872])[&&NHX:TOL=57870],((((((parabuteo[&&NHX:TOL=57850],buteo[&&NHX:TOL=57807],geranoaetus[&&NHX:TOL=57819],leucopternis[&&NHX:TOL=57838],asturina[&&NHX:TOL=57803])[&&NHX:TOL=57876],(buteogallus[&&NHX:TOL=57808],harpyhaliaetus[&&NHX:TOL=57829])[&&NHX:TOL=57877],busarellus[&&NHX:TOL=57805])[&&NHX:TOL=57875],(rostrhamus[&&NHX:TOL=57855],geranospiza[&&NHX:TOL=57820])[&&NHX:TOL=57878])[&&NHX:TOL=57874],ictinia[&&NHX:TOL=57835])[&&NHX:TOL=57873],harpagus[&&NHX:TOL=65525])[&&NHX:TOL=57869],butastur[&&NHX:TOL=57806])[&&NHX:TOL=57868])[&&NHX:TOL=65529])[&&NHX:TOL=65527],(spizastur[&&NHX:TOL=57859],aquila[&&NHX:TOL=57802],stephanoaetus[&&NHX:TOL=57860],polemaetus[&&NHX:TOL=57853],oroaetus[&&NHX:TOL=57849],ictinaetus[&&NHX:TOL=57834],lophaetus[&&NHX:TOL=57839],hieraaetus[&&NHX:TOL=57832],spizaetus[&&NHX:TOL=57858])[&&NHX:TOL=57881])[&&NHX:TOL=57867],(harpyopsis[&&NHX:TOL=57830],(morphnus[&&NHX:TOL=57846],harpia[&&NHX:TOL=57828])[&&NHX:TOL=65530])[&&NHX:TOL=57882])[&&NHX:TOL=57866],((((trigonoceps[&&NHX:TOL=57863],(aegypius[&&NHX:TOL=57801],torgos[&&NHX:TOL=57862])[&&NHX:TOL=57888])[&&NHX:TOL=57887],sarcogyps[&&NHX:TOL=57856])[&&NHX:TOL=57886],(necrosyrtes[&&NHX:TOL=57847],gyps[&&NHX:TOL=57823])[&&NHX:TOL=57889])[&&NHX:TOL=57885],(((terathopius[&&NHX:TOL=57861],(dryotriorchis[&&NHX:TOL=57813],circaetus[&&NHX:TOL=57811])[&&NHX:TOL=57893])[&&NHX:TOL=57892],pithecophaga[&&NHX:TOL=57852])[&&NHX:TOL=57891],spilornis[&&NHX:TOL=57857])[&&NHX:TOL=57890])[&&NHX:TOL=57884])[&&NHX:TOL=57865],(elanus[&&NHX:TOL=57815],gampsonyx[&&NHX:TOL=57818],chelictinia[&&NHX:TOL=57809],((((((lophoictinia[&&NHX:TOL=57840],hamirostra[&&NHX:TOL=57826])[&&NHX:TOL=57899],(elanoides[&&NHX:TOL=57814],aviceda[&&NHX:TOL=57804])[&&NHX:TOL=65532])[&&NHX:TOL=57898],(pernis[&&NHX:TOL=57851],henicopernis[&&NHX:TOL=57831])[&&NHX:TOL=65533])[&&NHX:TOL=57897],(leptodon[&&NHX:TOL=57837],chondrohierax[&&NHX:TOL=57810])[&&NHX:TOL=57900])[&&NHX:TOL=57896],(((neophron[&&NHX:TOL=57848],gypaetus[&&NHX:TOL=57821])[&&NHX:TOL=57903],eutriorchis[&&NHX:TOL=57817])[&&NHX:TOL=65534],gypohierax[&&NHX:TOL=57822])[&&NHX:TOL=57901])[&&NHX:TOL=57895],polyboroides[&&NHX:TOL=57854])[&&NHX:TOL=57894])[&&NHX:TOL=65531])accipitridae[&&NHX:TOL=26375],(pandion haliaetus[&&NHX:TOL=26376],pandion cristatus[&&NHX:TOL=129679])pandion[&&NHX:TOL=129678])[&&NHX:TOL=57763])[&&NHX:TOL=57762],(coragyps atratus[&&NHX:TOL=89856],sarcoramphus papa[&&NHX:TOL=89857],gymnogyps californianus[&&NHX:TOL=89858],vultur gryphus[&&NHX:TOL=89859],(cathartes aura[&&NHX:TOL=89853],cathartes burrovianus[&&NHX:TOL=89854],cathartes melambrotus[&&NHX:TOL=89855])cathartes[&&NHX:TOL=89852])cathartidae[&&NHX:TOL=26378])accipitriformes[&&NHX:TOL=123200],(((megascops flammeolus[&&NHX:TOL=100896],megascops asio[&&NHX:TOL=100897],megascops kennicottii[&&NHX:TOL=100898],megascops seductus[&&NHX:TOL=100899],megascops cooperi[&&NHX:TOL=100900],megascops trichopsis[&&NHX:TOL=100901],megascops choliba[&&NHX:TOL=100902],megascops roboratus[&&NHX:TOL=100903],megascops koepckeae[&&NHX:TOL=100904],megascops clarkii[&&NHX:TOL=100905],megascops colombianus[&&NHX:TOL=129460],megascops barbarus[&&NHX:TOL=100906],megascops ingens[&&NHX:TOL=100907],megascops petersoni[&&NHX:TOL=100908],megascops marshalli[&&NHX:TOL=100909],megascops watsonii[&&NHX:TOL=100910],megascops guatemalae[&&NHX:TOL=100911],megascops centralis[&&NHX:TOL=100912],megascops hoyi[&&NHX:TOL=100913],megascops atricapilla[&&NHX:TOL=100914],megascops sanctaecatarinae[&&NHX:TOL=100915],megascops roraimae[&&NHX:TOL=100916],megascops nudipes[&&NHX:TOL=100917],megascops albogularis[&&NHX:TOL=100918])megascops[&&NHX:TOL=100895],pyrroglaux podargina[&&NHX:TOL=100919],gymnoglaux lawrencii[&&NHX:TOL=100920],(ptilopsis leucotis[&&NHX:TOL=100922],ptilopsis granti[&&NHX:TOL=100923])ptilopsis[&&NHX:TOL=100921],mimizuku gurneyi[&&NHX:TOL=100924],(bubo scandiacus[&&NHX:TOL=100926],bubo virginianus[&&NHX:TOL=100927],bubo magellanicus[&&NHX:TOL=100928],bubo bubo[&&NHX:TOL=100929],bubo bengalensis[&&NHX:TOL=129513],bubo ascalaphus[&&NHX:TOL=100930],bubo capensis[&&NHX:TOL=100931],bubo africanus[&&NHX:TOL=100932],bubo cinerascens[&&NHX:TOL=100933],bubo poensis[&&NHX:TOL=100934],bubo vosseleri[&&NHX:TOL=100935],bubo nipalensis[&&NHX:TOL=100936],bubo sumatranus[&&NHX:TOL=100937],bubo shelleyi[&&NHX:TOL=100938],bubo lacteus[&&NHX:TOL=100939],bubo coromandus[&&NHX:TOL=100940],bubo leucostictus[&&NHX:TOL=100941],bubo philippensis[&&NHX:TOL=100942],bubo blakistoni[&&NHX:TOL=100943])bubo[&&NHX:TOL=100925],(ketupa zeylonensis[&&NHX:TOL=100945],ketupa flavipes[&&NHX:TOL=100946],ketupa ketupu[&&NHX:TOL=100947])ketupa[&&NHX:TOL=100944],(scotopelia peli[&&NHX:TOL=100949],scotopelia ussheri[&&NHX:TOL=100950],scotopelia bouvieri[&&NHX:TOL=100951])scotopelia[&&NHX:TOL=100948],(strix seloputo[&&NHX:TOL=100953],strix ocellata[&&NHX:TOL=100954],strix leptogrammica[&&NHX:TOL=100955],strix aluco[&&NHX:TOL=100956],strix nivicola[&&NHX:TOL=129805],strix butleri[&&NHX:TOL=100957],strix occidentalis[&&NHX:TOL=100958],strix varia[&&NHX:TOL=100959],strix fulvescens[&&NHX:TOL=100960],strix hylophila[&&NHX:TOL=100961],strix chacoensis[&&NHX:TOL=100962],strix rufipes[&&NHX:TOL=100963],strix uralensis[&&NHX:TOL=100964],strix davidi[&&NHX:TOL=100965],strix nebulosa[&&NHX:TOL=100966],strix woodfordii[&&NHX:TOL=100967],strix virgata[&&NHX:TOL=100968],strix albitarsis[&&NHX:TOL=100969],strix nigrolineata[&&NHX:TOL=100970],strix huhula[&&NHX:TOL=100971])strix[&&NHX:TOL=100952],jubula lettii[&&NHX:TOL=100972],lophostrix cristata[&&NHX:TOL=100973],(pulsatrix perspicillata[&&NHX:TOL=100975],pulsatrix koeniswaldiana[&&NHX:TOL=100976],pulsatrix melanota[&&NHX:TOL=100977])pulsatrix[&&NHX:TOL=100974],surnia ulula[&&NHX:TOL=100978],(glaucidium passerinum[&&NHX:TOL=100980],glaucidium brodiei[&&NHX:TOL=100981],glaucidium perlatum[&&NHX:TOL=100982],glaucidium californicum[&&NHX:TOL=100983],glaucidium gnoma[&&NHX:TOL=100984],glaucidium hoskinsii[&&NHX:TOL=100985],glaucidium costaricanum[&&NHX:TOL=100986],glaucidium jardinii[&&NHX:TOL=100987],glaucidium nubicola[&&NHX:TOL=100988],glaucidium bolivianum[&&NHX:TOL=100989],glaucidium palmarum[&&NHX:TOL=100990],glaucidium sanchezi[&&NHX:TOL=100991],glaucidium mooreorum[&&NHX:TOL=100992],glaucidium griseiceps[&&NHX:TOL=100993],glaucidium parkeri[&&NHX:TOL=100994],glaucidium hardyi[&&NHX:TOL=100995],glaucidium minutissimum[&&NHX:TOL=100996],glaucidium brasilianum[&&NHX:TOL=100997],glaucidium peruanum[&&NHX:TOL=100998],glaucidium nana[&&NHX:TOL=100999],glaucidium siju[&&NHX:TOL=101000],glaucidium tephronotum[&&NHX:TOL=101001],glaucidium sjostedti[&&NHX:TOL=101002],glaucidium cuculoides[&&NHX:TOL=101003],glaucidium castanopterum[&&NHX:TOL=101004],glaucidium radiatum[&&NHX:TOL=101005],glaucidium castanonotum[&&NHX:TOL=101006],glaucidium capense[&&NHX:TOL=101007],glaucidium albertinum[&&NHX:TOL=129514])glaucidium[&&NHX:TOL=100979],xenoglaux loweryi[&&NHX:TOL=101008],micrathene whitneyi[&&NHX:TOL=101009],(athene noctua[&&NHX:TOL=101011],athene brama[&&NHX:TOL=101012],athene cunicularia[&&NHX:TOL=101013])athene[&&NHX:TOL=101010],heteroglaux blewitti[&&NHX:TOL=101014],(aegolius funereus[&&NHX:TOL=101016],aegolius acadicus[&&NHX:TOL=101017],aegolius ridgwayi[&&NHX:TOL=101018],aegolius harrisii[&&NHX:TOL=101019])aegolius[&&NHX:TOL=101015],(ninox rufa[&&NHX:TOL=101021],ninox burhani[&&NHX:TOL=101022],ninox strenua[&&NHX:TOL=101023],ninox connivens[&&NHX:TOL=101024],ninox rudolfi[&&NHX:TOL=101025],ninox novaeseelandiae[&&NHX:TOL=101027],ninox scutulata[&&NHX:TOL=101028],ninox obscura[&&NHX:TOL=129807],ninox affinis[&&NHX:TOL=101029],ninox superciliaris[&&NHX:TOL=101030],ninox philippensis[&&NHX:TOL=101031],ninox ochracea[&&NHX:TOL=101032],ninox ios[&&NHX:TOL=101033],ninox hypogramma[&&NHX:TOL=129808],ninox squamipila[&&NHX:TOL=101034],ninox forbesi[&&NHX:TOL=129809],ninox natalis[&&NHX:TOL=101035],ninox theomacha[&&NHX:TOL=101036],ninox meeki[&&NHX:TOL=101037],ninox punctulata[&&NHX:TOL=101038],ninox variegata[&&NHX:TOL=101039],ninox odiosa[&&NHX:TOL=101040],ninox jacquinoti[&&NHX:TOL=101041],ninox sumbensis[&&NHX:TOL=101042])ninox[&&NHX:TOL=101020],uroglaux dimorpha[&&NHX:TOL=101043],(pseudoscops grammicus[&&NHX:TOL=101045],pseudoscops clamator[&&NHX:TOL=101046])pseudoscops[&&NHX:TOL=101044],nesasio solomonensis[&&NHX:TOL=101047],(asio stygius[&&NHX:TOL=101049],asio otus[&&NHX:TOL=101050],asio abyssinicus[&&NHX:TOL=101051],asio madagascariensis[&&NHX:TOL=101052],asio flammeus[&&NHX:TOL=101053],asio capensis[&&NHX:TOL=101054])asio[&&NHX:TOL=101048],(otus angelinae[&&NHX:TOL=100864],otus mentawi[&&NHX:TOL=100865],otus bakkamoena[&&NHX:TOL=100866],otus lettia[&&NHX:TOL=129803],otus semitorques[&&NHX:TOL=129804],otus lempiji[&&NHX:TOL=129806],otus fuliginosus[&&NHX:TOL=100867],otus megalotis[&&NHX:TOL=100868],otus silvicola[&&NHX:TOL=100869],otus mirus[&&NHX:TOL=100870],otus longicornis[&&NHX:TOL=100871],otus mindorensis[&&NHX:TOL=100872],otus brucei[&&NHX:TOL=100873],otus senegalensis[&&NHX:TOL=100874],otus scops[&&NHX:TOL=100875],otus sunia[&&NHX:TOL=100876],otus magicus[&&NHX:TOL=100877],otus sulaensis[&&NHX:TOL=100878],otus siaoensis[&&NHX:TOL=100879],otus mantananensis[&&NHX:TOL=100880],otus elegans[&&NHX:TOL=100881],otus manadensis[&&NHX:TOL=100882],otus collari[&&NHX:TOL=100883],otus beccarii[&&NHX:TOL=100884],otus insularis[&&NHX:TOL=100885],otus umbra[&&NHX:TOL=100886],otus alius[&&NHX:TOL=100887],otus pembaensis[&&NHX:TOL=100888],otus pauliani[&&NHX:TOL=100889],otus capnodes[&&NHX:TOL=129512],otus moheliensis[&&NHX:TOL=100890],otus mayottensis[&&NHX:TOL=100891],otus madagascariensis[&&NHX:TOL=100892],otus rutilus[&&NHX:TOL=100893],otus hartlaubi[&&NHX:TOL=100894],otus sagittatus[&&NHX:TOL=100855],otus rufescens[&&NHX:TOL=100856],otus thilohoffmanni[&&NHX:TOL=100857],otus icterorhynchus[&&NHX:TOL=100858],otus ireneae[&&NHX:TOL=100859],otus balli[&&NHX:TOL=100860],otus alfredi[&&NHX:TOL=100861],otus spilocephalus[&&NHX:TOL=100862],otus brookii[&&NHX:TOL=100863])otus[&&NHX:TOL=100854])strigidae[&&NHX:TOL=56736],((phodilus badius[&&NHX:TOL=68553],phodilus assimilis[&&NHX:TOL=129711],phodilus prigoginei[&&NHX:TOL=68554])phodilus[&&NHX:TOL=68551],(tyto alba[&&NHX:TOL=68555],tyto javanica[&&NHX:TOL=68561],tyto deroepstorffi[&&NHX:TOL=129712],tyto aurantia[&&NHX:TOL=68556],tyto capensis[&&NHX:TOL=68557],tyto longimembris[&&NHX:TOL=129508],tyto glaucops[&&NHX:TOL=68558],tyto inexspectata[&&NHX:TOL=68559],tyto manusi[&&NHX:TOL=68560],tyto nigrobrunnea[&&NHX:TOL=68562],tyto novaehollandiae[&&NHX:TOL=68563],tyto rosenbergii[&&NHX:TOL=68564],tyto sororcula[&&NHX:TOL=68565],tyto soumagnei[&&NHX:TOL=68566],tyto tenebricosa[&&NHX:TOL=68567])tyto[&&NHX:TOL=68552])tytonidae[&&NHX:TOL=56737])strigiformes[&&NHX:TOL=26388],((colius striatus[&&NHX:TOL=92559],colius leucocephalus[&&NHX:TOL=92560],colius castanotus[&&NHX:TOL=92561],colius colius[&&NHX:TOL=92562])colius[&&NHX:TOL=92558],(urocolius indicus[&&NHX:TOL=92565],urocolius macrourus[&&NHX:TOL=92564])urocolius[&&NHX:TOL=92563])coliidae[&&NHX:TOL=26425])land birds[&&NHX:TOL=26410],(((((((((alle alle[&&NHX:TOL=90566],alca torda[&&NHX:TOL=90567],(uria aalge[&&NHX:TOL=90565],uria lomvia[&&NHX:TOL=90564])uria[&&NHX:TOL=90563])[&&NHX:TOL=103383],(cepphus grylle[&&NHX:TOL=90569],cepphus columba[&&NHX:TOL=90570],cepphus carbo[&&NHX:TOL=90571])cepphus[&&NHX:TOL=90568],(brachyramphus marmoratus[&&NHX:TOL=90573],brachyramphus perdix[&&NHX:TOL=90574],brachyramphus brevirostris[&&NHX:TOL=90575])brachyramphus[&&NHX:TOL=90572],(synthliboramphus hypoleucus[&&NHX:TOL=90577],synthliboramphus craveri[&&NHX:TOL=90578],synthliboramphus antiquus[&&NHX:TOL=90579],synthliboramphus wumizusume[&&NHX:TOL=90580])synthliboramphus[&&NHX:TOL=90576])[&&NHX:TOL=103382],(((aethia psittacula[&&NHX:TOL=90583],aethia pusilla[&&NHX:TOL=90584],aethia pygmaea[&&NHX:TOL=90585],aethia cristatella[&&NHX:TOL=90586])aethia[&&NHX:TOL=90582],ptychoramphus aleuticus[&&NHX:TOL=90581])[&&NHX:TOL=103385],((fratercula arctica[&&NHX:TOL=90589],fratercula corniculata[&&NHX:TOL=90590],fratercula cirrhata[&&NHX:TOL=90591])fratercula[&&NHX:TOL=90588],cerorhinca monocerata[&&NHX:TOL=90587])[&&NHX:TOL=103386])[&&NHX:TOL=103384])alcidae[&&NHX:TOL=26357],(stercorarius chilensis[&&NHX:TOL=90837],stercorarius maccormicki[&&NHX:TOL=90838],stercorarius antarcticus[&&NHX:TOL=90839],stercorarius skua[&&NHX:TOL=90840],stercorarius pomarinus[&&NHX:TOL=90841],stercorarius parasiticus[&&NHX:TOL=90842],stercorarius longicaudus[&&NHX:TOL=90843])stercorarius[&&NHX:TOL=90836])[&&NHX:TOL=103069],((((((((((sterna dougallii[&&NHX:TOL=90657],sterna striata[&&NHX:TOL=90658])[&&NHX:TOL=103405],sterna sumatrana[&&NHX:TOL=90659])[&&NHX:TOL=103404],((sterna vittata[&&NHX:TOL=90664],sterna hirundinacea[&&NHX:TOL=90660])[&&NHX:TOL=103407],sterna paradisaea[&&NHX:TOL=90663])[&&NHX:TOL=103406])[&&NHX:TOL=103403],sterna hirundo[&&NHX:TOL=90661])[&&NHX:TOL=103402],(sterna trudeaui[&&NHX:TOL=90667],sterna forsteri[&&NHX:TOL=90666])[&&NHX:TOL=103408],(((sterna lunata[&&NHX:TOL=90677],sterna anaethetus[&&NHX:TOL=90678])[&&NHX:TOL=103411],sterna fuscata[&&NHX:TOL=90679])[&&NHX:TOL=103410],sterna aleutica[&&NHX:TOL=90676])[&&NHX:TOL=103409],(((sterna eurygnatha[&&NHX:TOL=90652],sterna sandvicensis[&&NHX:TOL=90651])[&&NHX:TOL=103414],sterna elegans[&&NHX:TOL=90649])[&&NHX:TOL=103413],(sterna bengalensis[&&NHX:TOL=90650],sterna maxima[&&NHX:TOL=90654])[&&NHX:TOL=103415],sterna bergii[&&NHX:TOL=90655],sterna bernsteini[&&NHX:TOL=90653])[&&NHX:TOL=103412],sterna aurantia[&&NHX:TOL=90656],sterna virgata[&&NHX:TOL=90665])sterna[&&NHX:TOL=90646],(chlidonias hybrida[&&NHX:TOL=90682],(chlidonias leucopterus[&&NHX:TOL=90683],chlidonias niger[&&NHX:TOL=90684])[&&NHX:TOL=103416],chlidonias albostriatus[&&NHX:TOL=90680],chlidonias repressa[&&NHX:TOL=90662],chlidonias acuticauda[&&NHX:TOL=90675])chlidonias[&&NHX:TOL=90681])[&&NHX:TOL=103371],gelochelidon nilotica[&&NHX:TOL=90647],hydroprogne caspia[&&NHX:TOL=90648],larosterna inca[&&NHX:TOL=90694])[&&NHX:TOL=103370],phaetusa simplex[&&NHX:TOL=90685],(sternula saundersi[&&NHX:TOL=90669],(sternula albifrons[&&NHX:TOL=90668],sternula nereis[&&NHX:TOL=90673])[&&NHX:TOL=103417],(sternula antillarum[&&NHX:TOL=90670],sternula superciliaris[&&NHX:TOL=90671])[&&NHX:TOL=103418],sternula lorata[&&NHX:TOL=90672],sternula balaenarum[&&NHX:TOL=90674])sternula[&&NHX:TOL=103372])[&&NHX:TOL=103369],((creagrus furcatus[&&NHX:TOL=90642],rhodostethia rosea[&&NHX:TOL=90640])[&&NHX:TOL=103378],((((larus saundersi[&&NHX:TOL=90631],(larus serranus[&&NHX:TOL=90632],((larus hartlaubii[&&NHX:TOL=90623],larus cirrocephalus[&&NHX:TOL=90622])[&&NHX:TOL=103389],(larus brunnicephalus[&&NHX:TOL=90621],larus ridibundus[&&NHX:TOL=90628])[&&NHX:TOL=103390])[&&NHX:TOL=103388],(larus scopulinus[&&NHX:TOL=90625],larus bulleri[&&NHX:TOL=90626],larus novaehollandiae[&&NHX:TOL=90624])[&&NHX:TOL=103391],larus philadelphia[&&NHX:TOL=90630],larus genei[&&NHX:TOL=90629],larus maculipennis[&&NHX:TOL=90627])[&&NHX:TOL=103387],larus minutus[&&NHX:TOL=90638],((larus audouinii[&&NHX:TOL=90603],larus melanocephalus[&&NHX:TOL=90633],larus relictus[&&NHX:TOL=90634],larus leucophthalmus[&&NHX:TOL=90600],larus hemprichii[&&NHX:TOL=90601],larus ichthyaetus[&&NHX:TOL=90620])[&&NHX:TOL=103393],((larus modestus[&&NHX:TOL=90598],larus scoresbii[&&NHX:TOL=90593])[&&NHX:TOL=103395],(larus atricilla[&&NHX:TOL=90636],(larus fuliginosus[&&NHX:TOL=90635],larus pipixcan[&&NHX:TOL=90637])[&&NHX:TOL=103397])[&&NHX:TOL=103396])[&&NHX:TOL=103394],((((larus armenicus[&&NHX:TOL=90617],larus dominicanus[&&NHX:TOL=90607],larus marinus[&&NHX:TOL=90606],larus argentatus[&&NHX:TOL=90614],larus smithsonianus[&&NHX:TOL=129496],larus cachinnans[&&NHX:TOL=90616],larus michahellis[&&NHX:TOL=129497],larus californicus[&&NHX:TOL=90605],larus glaucescens[&&NHX:TOL=90608],larus fuscus[&&NHX:TOL=90619],larus schistisagus[&&NHX:TOL=90618],larus thayeri[&&NHX:TOL=90613],larus glaucoides[&&NHX:TOL=90612],larus hyperboreus[&&NHX:TOL=90611])[&&NHX:TOL=103401],larus livens[&&NHX:TOL=90610],larus occidentalis[&&NHX:TOL=90609])[&&NHX:TOL=103400],larus delawarensis[&&NHX:TOL=90604])[&&NHX:TOL=103399],larus canus[&&NHX:TOL=90602])[&&NHX:TOL=103398],larus heermanni[&&NHX:TOL=90599],larus crassirostris[&&NHX:TOL=90597],larus pacificus[&&NHX:TOL=90594],larus belcheri[&&NHX:TOL=90595],larus atlanticus[&&NHX:TOL=90596])[&&NHX:TOL=103392],larus vegae[&&NHX:TOL=90615])larus[&&NHX:TOL=90592],(rissa tridactyla[&&NHX:TOL=90644],rissa brevirostris[&&NHX:TOL=90645])rissa[&&NHX:TOL=90643])[&&NHX:TOL=103377],pagophila eburnea[&&NHX:TOL=90639])[&&NHX:TOL=103376],xema sabini[&&NHX:TOL=90641])[&&NHX:TOL=103375])[&&NHX:TOL=103374],gygis alba[&&NHX:TOL=90693],(rynchops niger[&&NHX:TOL=90696],rynchops flavirostris[&&NHX:TOL=90697],rynchops albicollis[&&NHX:TOL=90698])rynchops[&&NHX:TOL=90695])[&&NHX:TOL=103368],((anous stolidus[&&NHX:TOL=90687],(anous tenuirostris[&&NHX:TOL=90688],anous minutus[&&NHX:TOL=90689])[&&NHX:TOL=103419])anous[&&NHX:TOL=90686],(procelsterna cerulea[&&NHX:TOL=90691],procelsterna albivitta[&&NHX:TOL=90692])procelsterna[&&NHX:TOL=90690])[&&NHX:TOL=103379])laridae[&&NHX:TOL=26358])[&&NHX:TOL=26356],(((rhinoptilus africanus[&&NHX:TOL=90550],rhinoptilus cinctus[&&NHX:TOL=90551],rhinoptilus chalcopterus[&&NHX:TOL=90552],rhinoptilus bitorquatus[&&NHX:TOL=90553])rhinoptilus[&&NHX:TOL=90549],((stiltia isabella[&&NHX:TOL=90554],(glareola pratincola[&&NHX:TOL=90556],glareola maldivarum[&&NHX:TOL=90557],glareola nordmanni[&&NHX:TOL=90558],glareola ocularis[&&NHX:TOL=90559],glareola nuchalis[&&NHX:TOL=90560],glareola cinerea[&&NHX:TOL=90561],glareola lactea[&&NHX:TOL=90562])glareola[&&NHX:TOL=90555])[&&NHX:TOL=103381],(cursorius cursor[&&NHX:TOL=90543],cursorius somalensis[&&NHX:TOL=90544],cursorius rufus[&&NHX:TOL=90545],cursorius temminckii[&&NHX:TOL=90546],cursorius coromandelicus[&&NHX:TOL=90547])cursorius[&&NHX:TOL=90542])[&&NHX:TOL=103380])glareolidae[&&NHX:TOL=26355],dromas ardeola[&&NHX:TOL=90864])[&&NHX:TOL=103070])[&&NHX:TOL=26354],((turnix sylvaticus[&&NHX:TOL=90700],turnix maculosus[&&NHX:TOL=90701],turnix hottentottus[&&NHX:TOL=90702],turnix nanus[&&NHX:TOL=135860],turnix tanki[&&NHX:TOL=90703],turnix ocellatus[&&NHX:TOL=90704],turnix suscitator[&&NHX:TOL=90705],turnix nigricollis[&&NHX:TOL=90706],turnix melanogaster[&&NHX:TOL=90707],turnix castanotus[&&NHX:TOL=90708],turnix olivii[&&NHX:TOL=90709],turnix varius[&&NHX:TOL=90710],turnix worcesteri[&&NHX:TOL=90711],turnix everetti[&&NHX:TOL=90712],turnix pyrrhothorax[&&NHX:TOL=90713],turnix velox[&&NHX:TOL=90714])turnix[&&NHX:TOL=90699],ortyxelos meiffrenii[&&NHX:TOL=90715])turnicidae[&&NHX:TOL=26359])lari[&&NHX:TOL=26353],(((((((((calidris tenuirostris[&&NHX:TOL=90808],calidris canutus[&&NHX:TOL=90809],calidris alba[&&NHX:TOL=90810],calidris pusilla[&&NHX:TOL=90811],calidris mauri[&&NHX:TOL=90812],calidris ruficollis[&&NHX:TOL=90813],calidris minuta[&&NHX:TOL=90814],calidris temminckii[&&NHX:TOL=90815],calidris subminuta[&&NHX:TOL=90816],calidris minutilla[&&NHX:TOL=90817],calidris fuscicollis[&&NHX:TOL=90818],calidris bairdii[&&NHX:TOL=90819],calidris melanotos[&&NHX:TOL=90820],calidris acuminata[&&NHX:TOL=90821],calidris ferruginea[&&NHX:TOL=90822],calidris maritima[&&NHX:TOL=90823],calidris ptilocnemis[&&NHX:TOL=90824],calidris alpina[&&NHX:TOL=90825])calidris[&&NHX:TOL=90807],aphriza virgata[&&NHX:TOL=90806])[&&NHX:TOL=103353],eurynorhynchus pygmeus[&&NHX:TOL=90827])[&&NHX:TOL=103352],philomachus pugnax[&&NHX:TOL=90830],limicola falcinellus[&&NHX:TOL=90828],(tryngites subruficollis[&&NHX:TOL=90829],micropalama himantopus[&&NHX:TOL=90826])[&&NHX:TOL=103355])[&&NHX:TOL=103351],(arenaria interpres[&&NHX:TOL=90804],arenaria melanocephala[&&NHX:TOL=90805])arenaria[&&NHX:TOL=90803])[&&NHX:TOL=103350],((((heteroscelus brevipes[&&NHX:TOL=90798],heteroscelus incanus[&&NHX:TOL=90799])heteroscelus[&&NHX:TOL=90797],(tringa erythropus[&&NHX:TOL=90783],tringa totanus[&&NHX:TOL=90784],tringa stagnatilis[&&NHX:TOL=90785],tringa nebularia[&&NHX:TOL=90786],tringa guttifer[&&NHX:TOL=90787],tringa melanoleuca[&&NHX:TOL=90788],tringa flavipes[&&NHX:TOL=90789],tringa ochropus[&&NHX:TOL=90790],tringa solitaria[&&NHX:TOL=90791],tringa glareola[&&NHX:TOL=90792])tringa[&&NHX:TOL=90782])[&&NHX:TOL=103360],catoptrophorus semipalmatus[&&NHX:TOL=90800])[&&NHX:TOL=103359],(actitis hypoleucos[&&NHX:TOL=90795],actitis macularius[&&NHX:TOL=90796])actitis[&&NHX:TOL=90794],xenus cinereus[&&NHX:TOL=90793],(phalaropus tricolor[&&NHX:TOL=90832],phalaropus lobatus[&&NHX:TOL=90833],phalaropus fulicarius[&&NHX:TOL=90834])phalaropus[&&NHX:TOL=90831])[&&NHX:TOL=103356],((((gallinago solitaria[&&NHX:TOL=90746],gallinago hardwickii[&&NHX:TOL=90747],gallinago nemoricola[&&NHX:TOL=90748],gallinago stenura[&&NHX:TOL=90749],gallinago megala[&&NHX:TOL=90750],gallinago nigripennis[&&NHX:TOL=90751],gallinago macrodactyla[&&NHX:TOL=90752],gallinago media[&&NHX:TOL=90753],gallinago gallinago[&&NHX:TOL=90754],gallinago delicata[&&NHX:TOL=90755],gallinago paraguaiae[&&NHX:TOL=90756],gallinago andina[&&NHX:TOL=90757],gallinago nobilis[&&NHX:TOL=90758],gallinago undulata[&&NHX:TOL=90759],gallinago stricklandii[&&NHX:TOL=90760],gallinago jamesoni[&&NHX:TOL=90761],gallinago imperialis[&&NHX:TOL=90762])gallinago[&&NHX:TOL=90745],(coenocorypha aucklandica[&&NHX:TOL=90742],coenocorypha pusilla[&&NHX:TOL=90743])coenocorypha[&&NHX:TOL=90741])[&&NHX:TOL=103363],(scolopax rusticola[&&NHX:TOL=90733],scolopax mira[&&NHX:TOL=90734],scolopax saturata[&&NHX:TOL=90735],scolopax rosenbergii[&&NHX:TOL=90736],scolopax bukidnonensis[&&NHX:TOL=90737],scolopax celebensis[&&NHX:TOL=90738],scolopax rochussenii[&&NHX:TOL=90739],scolopax minor[&&NHX:TOL=90740])scolopax[&&NHX:TOL=90732])[&&NHX:TOL=103362],(lymnocryptes minimus[&&NHX:TOL=90744],(limnodromus griseus[&&NHX:TOL=90764],limnodromus scolopaceus[&&NHX:TOL=90765],limnodromus semipalmatus[&&NHX:TOL=90766])limnodromus[&&NHX:TOL=90763])[&&NHX:TOL=103364])[&&NHX:TOL=103361])[&&NHX:TOL=103348],(limosa limosa[&&NHX:TOL=90768],limosa haemastica[&&NHX:TOL=90769],limosa lapponica[&&NHX:TOL=90770],limosa fedoa[&&NHX:TOL=90771])limosa[&&NHX:TOL=90767])[&&NHX:TOL=103347],((numenius minutus[&&NHX:TOL=90773],numenius borealis[&&NHX:TOL=90774],numenius phaeopus[&&NHX:TOL=90775],numenius tahitiensis[&&NHX:TOL=90776],numenius tenuirostris[&&NHX:TOL=90777],numenius arquata[&&NHX:TOL=90778],numenius madagascariensis[&&NHX:TOL=90779],numenius americanus[&&NHX:TOL=90780])numenius[&&NHX:TOL=90772],bartramia longicauda[&&NHX:TOL=90781])[&&NHX:TOL=103365],(prosobonia leucoptera[&&NHX:TOL=90802],aechmorhynchus parvirostris[&&NHX:TOL=90801])[&&NHX:TOL=103366])scolopacidae[&&NHX:TOL=26368],((((((irediparra gallinacea[&&NHX:TOL=90720],microparra capensis[&&NHX:TOL=90716])[&&NHX:TOL=103343],metopidius indicus[&&NHX:TOL=90722])[&&NHX:TOL=103342],(actophilornis africanus[&&NHX:TOL=90718],actophilornis albinucha[&&NHX:TOL=90719])[&&NHX:TOL=90717])[&&NHX:TOL=103341],((jacana spinosa[&&NHX:TOL=90724],jacana jacana[&&NHX:TOL=90725])[&&NHX:TOL=90723],hydrophasianus chirurgus[&&NHX:TOL=90721])[&&NHX:TOL=103344])jacanidae[&&NHX:TOL=26363],(rostratula benghalensis[&&NHX:TOL=90726],rostratula australis[&&NHX:TOL=129495],nycticryphes semicollaris[&&NHX:TOL=90727])rostratulidae[&&NHX:TOL=26364])[&&NHX:TOL=26362],(pedionomus torquatus[&&NHX:TOL=26366],((thinocorus orbignyianus[&&NHX:TOL=90730],thinocorus rumicivorus[&&NHX:TOL=90731])[&&NHX:TOL=103346],(attagis gayi[&&NHX:TOL=90728],attagis malouinus[&&NHX:TOL=90729])[&&NHX:TOL=103345])thinocoridae[&&NHX:TOL=26367])[&&NHX:TOL=26365])[&&NHX:TOL=26361])scolopaci[&&NHX:TOL=26360])[&&NHX:TOL=26352],(((((((((charadrius obscurus[&&NHX:TOL=90466],charadrius hiaticula[&&NHX:TOL=90467],charadrius semipalmatus[&&NHX:TOL=90468],charadrius placidus[&&NHX:TOL=90469],charadrius dubius[&&NHX:TOL=90470],charadrius wilsonia[&&NHX:TOL=90471],charadrius vociferus[&&NHX:TOL=90472],charadrius melodus[&&NHX:TOL=90473],charadrius thoracicus[&&NHX:TOL=90474],charadrius pecuarius[&&NHX:TOL=90475],charadrius sanctaehelenae[&&NHX:TOL=90476],charadrius tricollaris[&&NHX:TOL=90477],charadrius forbesi[&&NHX:TOL=90478],charadrius marginatus[&&NHX:TOL=90479],charadrius alexandrinus[&&NHX:TOL=90480],charadrius nivosus[&&NHX:TOL=90481],charadrius javanicus[&&NHX:TOL=90482],charadrius ruficapillus[&&NHX:TOL=90483],charadrius peronii[&&NHX:TOL=90484],charadrius pallidus[&&NHX:TOL=90485],charadrius collaris[&&NHX:TOL=90486],charadrius alticola[&&NHX:TOL=90487],charadrius falklandicus[&&NHX:TOL=90488],charadrius bicinctus[&&NHX:TOL=90489],charadrius mongolus[&&NHX:TOL=90490],charadrius leschenaultii[&&NHX:TOL=90491],charadrius asiaticus[&&NHX:TOL=90492],charadrius veredus[&&NHX:TOL=90493],charadrius modestus[&&NHX:TOL=90495],charadrius montanus[&&NHX:TOL=90496])charadrius[&&NHX:TOL=90465],((thinornis rubricollis[&&NHX:TOL=90499],thinornis novaeseelandiae[&&NHX:TOL=90500])thinornis[&&NHX:TOL=90498],elseyornis melanops[&&NHX:TOL=90501])[&&NHX:TOL=103336])[&&NHX:TOL=103335],eudromias morinellus[&&NHX:TOL=90494])[&&NHX:TOL=103334],phegornis mitchellii[&&NHX:TOL=90504])[&&NHX:TOL=103333],oreopholus ruficollis[&&NHX:TOL=90502])[&&NHX:TOL=103332],(((peltohyas australis[&&NHX:TOL=90497],anarhynchus frontalis[&&NHX:TOL=90503])[&&NHX:TOL=103339],erythrogonys cinctus[&&NHX:TOL=90459])[&&NHX:TOL=103338],((vanellus vanellus[&&NHX:TOL=90436],vanellus crassirostris[&&NHX:TOL=90437],vanellus armatus[&&NHX:TOL=90438],vanellus spinosus[&&NHX:TOL=90439],vanellus duvaucelii[&&NHX:TOL=90440],vanellus tectus[&&NHX:TOL=90441],vanellus malabaricus[&&NHX:TOL=90442],vanellus albiceps[&&NHX:TOL=90443],vanellus lugubris[&&NHX:TOL=90444],vanellus melanopterus[&&NHX:TOL=90445],vanellus coronatus[&&NHX:TOL=90446],vanellus senegallus[&&NHX:TOL=90447],vanellus melanocephalus[&&NHX:TOL=90448],vanellus superciliosus[&&NHX:TOL=90449],vanellus cinereus[&&NHX:TOL=90450],vanellus indicus[&&NHX:TOL=90451],vanellus macropterus[&&NHX:TOL=90452],vanellus tricolor[&&NHX:TOL=90453],vanellus miles[&&NHX:TOL=90454],vanellus gregarius[&&NHX:TOL=90455],vanellus leucurus[&&NHX:TOL=90456],vanellus chilensis[&&NHX:TOL=90457],vanellus resplendens[&&NHX:TOL=90458])vanellus[&&NHX:TOL=90435],hoploxypterus cayanus[&&NHX:TOL=90505])[&&NHX:TOL=103340])[&&NHX:TOL=103337])charadriidae[&&NHX:TOL=26345],((((himantopus himantopus[&&NHX:TOL=90507],himantopus leucocephalus[&&NHX:TOL=90508],himantopus mexicanus[&&NHX:TOL=90509],himantopus melanurus[&&NHX:TOL=90510],himantopus novaezelandiae[&&NHX:TOL=90511])himantopus[&&NHX:TOL=90506],cladorhynchus leucocephalus[&&NHX:TOL=90512])[&&NHX:TOL=103330],(recurvirostra avosetta[&&NHX:TOL=90514],recurvirostra americana[&&NHX:TOL=90515],recurvirostra novaehollandiae[&&NHX:TOL=90516],recurvirostra andina[&&NHX:TOL=90517])recurvirostra[&&NHX:TOL=90513])recurvirostridae[&&NHX:TOL=26347],((haematopus leucopodus[&&NHX:TOL=90518],haematopus ater[&&NHX:TOL=90519],haematopus bachmani[&&NHX:TOL=90520],haematopus palliatus[&&NHX:TOL=90521],haematopus moquini[&&NHX:TOL=90522],haematopus ostralegus[&&NHX:TOL=90523],haematopus finschi[&&NHX:TOL=90524],haematopus longirostris[&&NHX:TOL=90525],haematopus unicolor[&&NHX:TOL=90526],haematopus chathamensis[&&NHX:TOL=129494],haematopus fuliginosus[&&NHX:TOL=90527])haematopus[&&NHX:TOL=26348],ibidorhyncha struthersii[&&NHX:TOL=90863])[&&NHX:TOL=103331])[&&NHX:TOL=26346],(pluvialis apricaria[&&NHX:TOL=90461],pluvialis fulva[&&NHX:TOL=90462],pluvialis dominica[&&NHX:TOL=90463],pluvialis squatarola[&&NHX:TOL=90464])pluvialis[&&NHX:TOL=90460])[&&NHX:TOL=26344],pluvianus aegyptius[&&NHX:TOL=90548])[&&NHX:TOL=103329],(((burhinus oedicnemus[&&NHX:TOL=90529],burhinus indicus[&&NHX:TOL=129696],burhinus senegalensis[&&NHX:TOL=90530],burhinus vermiculatus[&&NHX:TOL=90531],burhinus capensis[&&NHX:TOL=90532],burhinus bistriatus[&&NHX:TOL=90533],burhinus superciliaris[&&NHX:TOL=90534],burhinus grallarius[&&NHX:TOL=90535])burhinus[&&NHX:TOL=90528],(esacus neglectus[&&NHX:TOL=90537],esacus recurvirostris[&&NHX:TOL=90538])esacus[&&NHX:TOL=90536])burhinidae[&&NHX:TOL=26350],((chionis albus[&&NHX:TOL=90539],chionis minor[&&NHX:TOL=90540])chionis[&&NHX:TOL=26351],pluvianellus socialis[&&NHX:TOL=103074])[&&NHX:TOL=103073])[&&NHX:TOL=26349])charadrii[&&NHX:TOL=26343])charadriiformes[&&NHX:TOL=26342])[&&NHX:TOL=123201],((((((((balearica pavonina[&&NHX:TOL=90085],balearica regulorum[&&NHX:TOL=90084])balearica[&&NHX:TOL=90083],(grus leucogeranus[&&NHX:TOL=90070],(((grus antigone[&&NHX:TOL=90072],(grus rubicunda[&&NHX:TOL=90073],grus vipio[&&NHX:TOL=90074])[&&NHX:TOL=103783])[&&NHX:TOL=103782],(grus canadensis[&&NHX:TOL=90071],(grus carunculata[&&NHX:TOL=90069],(anthropoides paradiseus[&&NHX:TOL=90082],anthropoides virgo[&&NHX:TOL=90081])anthropoides[&&NHX:TOL=90080])[&&NHX:TOL=103773])[&&NHX:TOL=103781])[&&NHX:TOL=107367],(grus japonensis[&&NHX:TOL=90079],(grus americana[&&NHX:TOL=90077],(grus grus[&&NHX:TOL=90075],(grus monacha[&&NHX:TOL=90076],grus nigricollis[&&NHX:TOL=90078])[&&NHX:TOL=103780])[&&NHX:TOL=103784])[&&NHX:TOL=103771])[&&NHX:TOL=103779])[&&NHX:TOL=90068])[&&NHX:TOL=107366])gruidae[&&NHX:TOL=26312],aramus guarauna[&&NHX:TOL=26311])[&&NHX:TOL=26310],(psophia crepitans[&&NHX:TOL=90086],psophia leucoptera[&&NHX:TOL=90087],psophia viridis[&&NHX:TOL=90088])psophiidae[&&NHX:TOL=26313])[&&NHX:TOL=26309],(((podica senegalensis[&&NHX:TOL=90089],(heliornis fulica[&&NHX:TOL=90091],heliopais personatus[&&NHX:TOL=90090])[&&NHX:TOL=107369])heliornithidae[&&NHX:TOL=26315],(sarothrura pulchra[&&NHX:TOL=90278],sarothrura elegans[&&NHX:TOL=90279],sarothrura rufa[&&NHX:TOL=90280],sarothrura lugens[&&NHX:TOL=90281],sarothrura boehmi[&&NHX:TOL=90282],sarothrura affinis[&&NHX:TOL=90283],sarothrura insularis[&&NHX:TOL=90284],sarothrura ayresi[&&NHX:TOL=90285],sarothrura watersi[&&NHX:TOL=90286])sarothrura[&&NHX:TOL=90277])[&&NHX:TOL=108994],((nesoclopeus woodfordi[&&NHX:TOL=90125],nesoclopeus poecilopterus[&&NHX:TOL=90126])nesoclopeus[&&NHX:TOL=90124],(gallirallus australis[&&NHX:TOL=90128],gallirallus calayanensis[&&NHX:TOL=90129],gallirallus lafresnayanus[&&NHX:TOL=90130],gallirallus sylvestris[&&NHX:TOL=90131],gallirallus okinawae[&&NHX:TOL=90132],gallirallus torquatus[&&NHX:TOL=90133],gallirallus insignis[&&NHX:TOL=90134],gallirallus philippensis[&&NHX:TOL=90135],gallirallus owstoni[&&NHX:TOL=90136],gallirallus rovianae[&&NHX:TOL=90137],gallirallus striatus[&&NHX:TOL=90138])gallirallus[&&NHX:TOL=90127],(rallus longirostris[&&NHX:TOL=90140],rallus elegans[&&NHX:TOL=90141],rallus wetmorei[&&NHX:TOL=90142],rallus limicola[&&NHX:TOL=90143],rallus aequatorialis[&&NHX:TOL=90144],rallus semiplumbeus[&&NHX:TOL=90145],rallus antarcticus[&&NHX:TOL=90146],rallus aquaticus[&&NHX:TOL=90147],rallus indicus[&&NHX:TOL=129694],rallus caerulescens[&&NHX:TOL=90148],rallus madagascariensis[&&NHX:TOL=90149])rallus[&&NHX:TOL=90139],(lewinia mirifica[&&NHX:TOL=90151],lewinia pectoralis[&&NHX:TOL=90152],lewinia muelleri[&&NHX:TOL=90153])lewinia[&&NHX:TOL=90150],dryolimnas cuvieri[&&NHX:TOL=90154],(crex crex[&&NHX:TOL=90157],crex egregia[&&NHX:TOL=90156])crex[&&NHX:TOL=90155],rougetius rougetii[&&NHX:TOL=90158],aramidopsis plateni[&&NHX:TOL=90159],atlantisia rogersi[&&NHX:TOL=90160],(aramides mangle[&&NHX:TOL=90162],aramides axillaris[&&NHX:TOL=90163],aramides cajanea[&&NHX:TOL=90164],aramides wolfi[&&NHX:TOL=90165],aramides ypecaha[&&NHX:TOL=90166],aramides saracura[&&NHX:TOL=90167],aramides calopterus[&&NHX:TOL=90168])aramides[&&NHX:TOL=90161],amaurolimnas concolor[&&NHX:TOL=90169],(gymnocrex rosenbergii[&&NHX:TOL=90171],gymnocrex talaudensis[&&NHX:TOL=90172],gymnocrex plumbeiventris[&&NHX:TOL=90173])gymnocrex[&&NHX:TOL=90170],(amaurornis akool[&&NHX:TOL=90175],amaurornis isabellina[&&NHX:TOL=90176],amaurornis olivacea[&&NHX:TOL=90177],amaurornis moluccana[&&NHX:TOL=129695],amaurornis magnirostris[&&NHX:TOL=90178],amaurornis phoenicurus[&&NHX:TOL=90179],amaurornis flavirostra[&&NHX:TOL=90180],amaurornis olivieri[&&NHX:TOL=90181])amaurornis[&&NHX:TOL=90174],(porzana bicolor[&&NHX:TOL=90183],porzana parva[&&NHX:TOL=90184],porzana pusilla[&&NHX:TOL=90185],porzana porzana[&&NHX:TOL=90186],porzana fluminea[&&NHX:TOL=90187],porzana carolina[&&NHX:TOL=90188],porzana spiloptera[&&NHX:TOL=90189],porzana albicollis[&&NHX:TOL=90190],porzana fusca[&&NHX:TOL=90191],porzana paykullii[&&NHX:TOL=90192],porzana tabuensis[&&NHX:TOL=90193],porzana atra[&&NHX:TOL=90194],porzana flaviventer[&&NHX:TOL=90195],porzana cinerea[&&NHX:TOL=90196])porzana[&&NHX:TOL=90182],aenigmatolimnas marginalis[&&NHX:TOL=90197],cyanolimnas cerverai[&&NHX:TOL=90198],(neocrex colombiana[&&NHX:TOL=90200],neocrex erythrops[&&NHX:TOL=90201])neocrex[&&NHX:TOL=90199],(pardirallus maculatus[&&NHX:TOL=90203],pardirallus nigricans[&&NHX:TOL=90204],pardirallus sanguinolentus[&&NHX:TOL=90205])pardirallus[&&NHX:TOL=90202],eulabeornis castaneoventris[&&NHX:TOL=90206],habroptila wallacii[&&NHX:TOL=90207],megacrex inepta[&&NHX:TOL=90208],gallicrex cinerea[&&NHX:TOL=90209],(porphyrio porphyrio[&&NHX:TOL=90211],porphyrio madagascariensis[&&NHX:TOL=90212],porphyrio hochstetteri[&&NHX:TOL=90213],porphyrio alleni[&&NHX:TOL=90214],porphyrio martinicus[&&NHX:TOL=90215],porphyrio flavirostris[&&NHX:TOL=90216])porphyrio[&&NHX:TOL=90210],(gallinula silvestris[&&NHX:TOL=90218],gallinula comeri[&&NHX:TOL=129493],gallinula nesiotis[&&NHX:EXT=Y:TOL=90219],gallinula chloropus[&&NHX:TOL=90220],gallinula tenebrosa[&&NHX:TOL=90221],gallinula angulata[&&NHX:TOL=90222],gallinula melanops[&&NHX:TOL=90223],gallinula ventralis[&&NHX:TOL=90224],gallinula mortierii[&&NHX:TOL=90225])gallinula[&&NHX:TOL=90217],(fulica cristata[&&NHX:TOL=90227],fulica atra[&&NHX:TOL=90228],fulica alai[&&NHX:TOL=90229],fulica americana[&&NHX:TOL=90230],fulica caribaea[&&NHX:TOL=90231],fulica leucoptera[&&NHX:TOL=90232],fulica ardesiaca[&&NHX:TOL=90233],fulica armillata[&&NHX:TOL=90234],fulica rufifrons[&&NHX:TOL=90235],fulica gigantea[&&NHX:TOL=90236],fulica cornuta[&&NHX:TOL=90237])fulica[&&NHX:TOL=90226],(coturnicops exquisitus[&&NHX:TOL=90093],coturnicops noveboracensis[&&NHX:TOL=90094],coturnicops notatus[&&NHX:TOL=90095])coturnicops[&&NHX:TOL=90092],(canirallus oculeus[&&NHX:TOL=90097],canirallus kioloides[&&NHX:TOL=90098])canirallus[&&NHX:TOL=90096],himantornis haematopus[&&NHX:TOL=90099],micropygia schomburgkii[&&NHX:TOL=90100],(rallina rubra[&&NHX:TOL=90102],rallina leucospila[&&NHX:TOL=90103],rallina forbesi[&&NHX:TOL=90104],rallina mayri[&&NHX:TOL=90105],rallina tricolor[&&NHX:TOL=90106],rallina canningi[&&NHX:TOL=90107],rallina fasciata[&&NHX:TOL=90108],rallina eurizonoides[&&NHX:TOL=90109])rallina[&&NHX:TOL=90101],anurolimnas castaneiceps[&&NHX:TOL=90110],(laterallus viridis[&&NHX:TOL=90112],laterallus fasciatus[&&NHX:TOL=90113],laterallus melanophaius[&&NHX:TOL=90114],laterallus levraudi[&&NHX:TOL=90115],laterallus ruber[&&NHX:TOL=90116],laterallus albigularis[&&NHX:TOL=90117],laterallus exilis[&&NHX:TOL=90118],laterallus jamaicensis[&&NHX:TOL=90119],laterallus tuerosi[&&NHX:TOL=90120],laterallus spilonotus[&&NHX:TOL=90121],laterallus leucopyrrhus[&&NHX:TOL=90122],laterallus xenopterus[&&NHX:TOL=90123])laterallus[&&NHX:TOL=90111])rallidae[&&NHX:TOL=26316])[&&NHX:TOL=107368])gruiformes[&&NHX:TOL=26307],((rhinortha chlorophaea[&&NHX:TOL=91957],(((ceuthmochares aereus[&&NHX:TOL=129709],ceuthmochares australis[&&NHX:TOL=129710])ceuthmochares[&&NHX:TOL=91958],((taccocua leschenaultii[&&NHX:TOL=91959],(zanclostomus javanicus[&&NHX:TOL=91960],(phaenicophaeus curvirostris[&&NHX:TOL=91963],(phaenicophaeus sumatranus[&&NHX:TOL=91965],phaenicophaeus pyrrhocephalus[&&NHX:TOL=91964],(phaenicophaeus viridirostris[&&NHX:TOL=91966],phaenicophaeus diardi[&&NHX:TOL=91967],phaenicophaeus tristis[&&NHX:TOL=91968])[&&NHX:TOL=103852])[&&NHX:TOL=103850])phaenicophaeus[&&NHX:TOL=91962])[&&NHX:TOL=108194])[&&NHX:TOL=103818],rhamphococcyx calyorhynchus[&&NHX:TOL=91961],(dasylophus cumingi[&&NHX:TOL=91970],dasylophus superciliosus[&&NHX:TOL=91971])dasylophus[&&NHX:TOL=91969],(clamator coromandus[&&NHX:TOL=91973],(clamator glandarius[&&NHX:TOL=91974],(clamator levaillantii[&&NHX:TOL=91975],clamator jacobinus[&&NHX:TOL=91976])[&&NHX:TOL=103855])[&&NHX:TOL=103854])clamator[&&NHX:TOL=91972],((coccycua minuta[&&NHX:TOL=91978],(coccycua pumila[&&NHX:TOL=91979],coccycua cinerea[&&NHX:TOL=91980])[&&NHX:TOL=103856])coccycua[&&NHX:TOL=91977],((piaya cayana[&&NHX:TOL=91983],piaya melanogaster[&&NHX:TOL=91982])piaya[&&NHX:TOL=91981],((coccyzus melacoryphus[&&NHX:TOL=91985],((coccyzus americanus[&&NHX:TOL=91986],coccyzus euleri[&&NHX:TOL=91987])[&&NHX:TOL=103859],(coccyzus minor[&&NHX:TOL=91988],coccyzus ferrugineus[&&NHX:TOL=91989])[&&NHX:TOL=103860])[&&NHX:TOL=103858])[&&NHX:TOL=103857],(coccyzus erythropthalmus[&&NHX:TOL=91990],coccyzus lansbergi[&&NHX:TOL=91991],((coccyzus pluvialis[&&NHX:TOL=91992],coccyzus rufigularis[&&NHX:TOL=91993])[&&NHX:TOL=103864],(coccyzus vetula[&&NHX:TOL=91994],coccyzus vieilloti[&&NHX:TOL=91996],(coccyzus merlini[&&NHX:TOL=91995],coccyzus longirostris[&&NHX:TOL=91997])[&&NHX:TOL=103867])[&&NHX:TOL=103865])[&&NHX:TOL=103863])[&&NHX:TOL=103861])coccyzus[&&NHX:TOL=91984])[&&NHX:TOL=103824])arboreal new world cuckoos[&&NHX:TOL=103823])[&&NHX:TOL=103817])phaenicophaeini[&&NHX:TOL=103816],(pachycoccyx audeberti[&&NHX:TOL=91998],(microdynamis parva[&&NHX:TOL=91999],(eudynamys scolopaceus[&&NHX:TOL=92001],eudynamys melanorhynchus[&&NHX:TOL=92002],eudynamys orientalis[&&NHX:TOL=92003])eudynamys[&&NHX:TOL=92000])[&&NHX:TOL=103827],urodynamis taitensis[&&NHX:TOL=92004],scythrops novaehollandiae[&&NHX:TOL=92005],(((chrysococcyx maculatus[&&NHX:TOL=92007],chrysococcyx xanthorhynchus[&&NHX:TOL=92008])[&&NHX:TOL=108197],(chrysococcyx caprius[&&NHX:TOL=92009],chrysococcyx klaas[&&NHX:TOL=92010],(chrysococcyx flavigularis[&&NHX:TOL=92011],chrysococcyx cupreus[&&NHX:TOL=92012])[&&NHX:TOL=108199])african glossy cuckoos[&&NHX:TOL=108198])[&&NHX:TOL=108196],(chrysococcyx megarhynchus[&&NHX:TOL=92013],chrysococcyx basalis[&&NHX:TOL=92014],chrysococcyx osculans[&&NHX:TOL=92015],chrysococcyx ruficollis[&&NHX:TOL=92016],chrysococcyx lucidus[&&NHX:TOL=92017],chrysococcyx meyeri[&&NHX:TOL=92018],chrysococcyx minutillus[&&NHX:TOL=92019])australian and new guinea glossy cuckoos[&&NHX:TOL=108200])chrysococcyx[&&NHX:TOL=92006],(((cacomantis pallidus[&&NHX:TOL=92022],cacomantis leucolophus[&&NHX:TOL=92023])[&&NHX:TOL=103906],((cacomantis castaneiventris[&&NHX:TOL=92024],cacomantis flabelliformis[&&NHX:TOL=92025])[&&NHX:TOL=103908],cacomantis sonneratii[&&NHX:TOL=92026],(cacomantis merulinus[&&NHX:TOL=92027],cacomantis passerinus[&&NHX:TOL=92028],(cacomantis sepulcralis[&&NHX:TOL=92030],cacomantis variolosus[&&NHX:TOL=92029])[&&NHX:TOL=103912])[&&NHX:TOL=103910])[&&NHX:TOL=103907])cacomantis[&&NHX:TOL=92021],((cercococcyx mechowi[&&NHX:TOL=92033],(cercococcyx olivinus[&&NHX:TOL=92034],cercococcyx montanus[&&NHX:TOL=92035])[&&NHX:TOL=103914])cercococcyx[&&NHX:TOL=92032],(surniculus velutinus[&&NHX:TOL=92038],surniculus lugubris[&&NHX:TOL=92037],surniculus dicruroides[&&NHX:TOL=129713],surniculus musschenbroeki[&&NHX:TOL=129714])surniculus[&&NHX:TOL=92036],((((hierococcyx sparverioides[&&NHX:TOL=92041],hierococcyx varius[&&NHX:TOL=92042])[&&NHX:TOL=103923],hierococcyx bocki[&&NHX:TOL=129802])[&&NHX:TOL=129801],(hierococcyx hyperythrus[&&NHX:TOL=92043],(hierococcyx pectoralis[&&NHX:TOL=92045],hierococcyx fugax[&&NHX:TOL=92046],hierococcyx nisicolor[&&NHX:TOL=92047])[&&NHX:TOL=103925])[&&NHX:TOL=103924])[&&NHX:TOL=103920],hierococcyx vagans[&&NHX:TOL=92040])hierococcyx[&&NHX:TOL=92039],(cuculus clamosus[&&NHX:TOL=92049],(cuculus solitarius[&&NHX:TOL=92050],(cuculus poliocephalus[&&NHX:TOL=92051],cuculus crassirostris[&&NHX:TOL=92052],(cuculus micropterus[&&NHX:TOL=92053],((cuculus rochii[&&NHX:TOL=92054],cuculus gularis[&&NHX:TOL=92055])[&&NHX:TOL=103932],(cuculus canorus[&&NHX:TOL=92057],(cuculus saturatus[&&NHX:TOL=129510],cuculus optatus[&&NHX:TOL=92056],cuculus lepidus[&&NHX:TOL=129511])[&&NHX:TOL=129509])[&&NHX:TOL=103933])[&&NHX:TOL=103931])[&&NHX:TOL=103930])[&&NHX:TOL=103928])[&&NHX:TOL=103927])cuculus[&&NHX:TOL=92048])[&&NHX:TOL=103832])[&&NHX:TOL=103831])cuculini[&&NHX:TOL=108195])[&&NHX:TOL=103815])cuculinae[&&NHX:TOL=103814],(((carpococcyx viridis[&&NHX:TOL=91945],carpococcyx radiceus[&&NHX:TOL=91944],carpococcyx renauldi[&&NHX:TOL=91946])southeast asian ground cuckoos[&&NHX:TOL=91943],((coua cristata[&&NHX:TOL=91948],(coua caerulea[&&NHX:TOL=91950],coua verreauxi[&&NHX:TOL=91949])[&&NHX:TOL=103840])[&&NHX:TOL=103839],(coua ruficeps[&&NHX:TOL=91951],(coua reynaudii[&&NHX:TOL=91952],(coua coquereli[&&NHX:TOL=91953],coua cursor[&&NHX:TOL=91954])[&&NHX:TOL=103844],(coua gigas[&&NHX:TOL=91955],coua delalandei[&&NHX:EXT=Y:TOL=103847],coua serriana[&&NHX:TOL=91956])[&&NHX:TOL=103845])[&&NHX:TOL=103842])[&&NHX:TOL=103841])couas[&&NHX:TOL=91947])couinae[&&NHX:TOL=103813],((centropus milo[&&NHX:TOL=91913],(centropus ateralbus[&&NHX:TOL=91914],(centropus menbeki[&&NHX:TOL=91915],centropus chalybeus[&&NHX:TOL=91916])[&&NHX:TOL=103870])[&&NHX:TOL=103869])[&&NHX:TOL=103868],(centropus unirufus[&&NHX:TOL=91917],centropus chlororhynchos[&&NHX:TOL=91918],(centropus melanops[&&NHX:TOL=91919],(centropus steerii[&&NHX:TOL=91920],centropus rectunguis[&&NHX:TOL=91921])[&&NHX:TOL=103875])[&&NHX:TOL=103874],(centropus celebensis[&&NHX:TOL=91922],(((centropus anselli[&&NHX:TOL=91923],centropus leucogaster[&&NHX:TOL=91924])[&&NHX:TOL=103879],(centropus senegalensis[&&NHX:TOL=91925],(centropus monachus[&&NHX:TOL=91926],(centropus cupreicaudus[&&NHX:TOL=91927],centropus superciliosus[&&NHX:TOL=91928])[&&NHX:TOL=103882])[&&NHX:TOL=103881])[&&NHX:TOL=108193])[&&NHX:TOL=103878],((centropus nigrorufus[&&NHX:TOL=91931],(centropus sinensis[&&NHX:TOL=91932],centropus andamanensis[&&NHX:TOL=91941])[&&NHX:TOL=103885])[&&NHX:TOL=103884],(centropus toulou[&&NHX:TOL=91933],centropus goliath[&&NHX:TOL=91934],centropus violaceus[&&NHX:TOL=91938],(centropus bernsteini[&&NHX:TOL=91939],centropus phasianinus[&&NHX:TOL=91940])[&&NHX:TOL=103892],(centropus grillii[&&NHX:TOL=91935],(centropus viridis[&&NHX:TOL=91936],centropus bengalensis[&&NHX:TOL=91937])[&&NHX:TOL=103890])[&&NHX:TOL=103889])[&&NHX:TOL=103886])[&&NHX:TOL=103883])[&&NHX:TOL=103877])[&&NHX:TOL=103876])[&&NHX:TOL=103871])centropus[&&NHX:TOL=91912])[&&NHX:TOL=108192],((guira guira[&&NHX:TOL=91898],(crotophaga major[&&NHX:TOL=91895],(crotophaga ani[&&NHX:TOL=91896],crotophaga sulcirostris[&&NHX:TOL=91897])[&&NHX:TOL=103835])anis[&&NHX:TOL=91894])crotophaginae[&&NHX:TOL=103806],((((geococcyx californianus[&&NHX:TOL=91906],geococcyx velox[&&NHX:TOL=91905])geococcyx[&&NHX:TOL=91904],((neomorphus rufipennis[&&NHX:TOL=91910],neomorphus pucheranii[&&NHX:TOL=91911])[&&NHX:TOL=103837],(neomorphus radiolosus[&&NHX:TOL=91909],(neomorphus geoffroyi[&&NHX:TOL=91908],neomorphus squamiger[&&NHX:TOL=129459])[&&NHX:TOL=129458])[&&NHX:TOL=103836])neomorphus[&&NHX:TOL=91907])[&&NHX:TOL=103810],morococcyx erythropygus[&&NHX:TOL=91903])[&&NHX:TOL=103809],(tapera naevia[&&NHX:TOL=91899],(dromococcyx phasianellus[&&NHX:TOL=91902],dromococcyx pavoninus[&&NHX:TOL=91901])[&&NHX:TOL=91900])[&&NHX:TOL=103808])neomorphinae[&&NHX:TOL=103807])[&&NHX:TOL=103805])cuculidae[&&NHX:TOL=26409])[&&NHX:TOL=123204],((ardeotis arabs[&&NHX:TOL=90241],ardeotis kori[&&NHX:TOL=90242],ardeotis nigriceps[&&NHX:TOL=90243],ardeotis australis[&&NHX:TOL=90244])ardeotis[&&NHX:TOL=90240],otis tarda[&&NHX:TOL=90245],(chlamydotis undulata[&&NHX:TOL=90247],chlamydotis macqueenii[&&NHX:TOL=90248])chlamydotis[&&NHX:TOL=90246],(neotis denhami[&&NHX:TOL=90250],neotis ludwigii[&&NHX:TOL=90251],neotis heuglinii[&&NHX:TOL=90252],neotis nuba[&&NHX:TOL=90253])neotis[&&NHX:TOL=90249],(eupodotis senegalensis[&&NHX:TOL=90255],eupodotis barrowii[&&NHX:TOL=90256],eupodotis caerulescens[&&NHX:TOL=90257],eupodotis vigorsii[&&NHX:TOL=90258],eupodotis rueppellii[&&NHX:TOL=90259],eupodotis humilis[&&NHX:TOL=90260])eupodotis[&&NHX:TOL=90254],(lophotis savilei[&&NHX:TOL=90262],lophotis gindiana[&&NHX:TOL=90263],lophotis ruficrista[&&NHX:TOL=90264])lophotis[&&NHX:TOL=90261],(afrotis afraoides[&&NHX:TOL=90266],afrotis afra[&&NHX:TOL=90267])afrotis[&&NHX:TOL=90265],(lissotis hartlaubii[&&NHX:TOL=90269],lissotis melanogaster[&&NHX:TOL=90270])lissotis[&&NHX:TOL=90268],houbaropsis bengalensis[&&NHX:TOL=90271],sypheotides indica[&&NHX:TOL=90272],tetrax tetrax[&&NHX:TOL=90273])otididae[&&NHX:TOL=26321])[&&NHX:TOL=123203],(((((((((thalassarche chlororhynchos[&&NHX:TOL=89323],((thalassarche chrysostoma[&&NHX:TOL=89324],thalassarche melanophrys[&&NHX:TOL=89325])[&&NHX:TOL=103227],(thalassarche bulleri[&&NHX:TOL=89326],thalassarche cauta[&&NHX:TOL=89322])[&&NHX:TOL=103228])[&&NHX:TOL=103226])thalassarche[&&NHX:TOL=89321],(phoebetria palpebrata[&&NHX:TOL=89319],phoebetria fusca[&&NHX:TOL=89320])phoebetria[&&NHX:TOL=89318])[&&NHX:TOL=103225],((diomedea exulans[&&NHX:TOL=89316],diomedea epomophora[&&NHX:TOL=89317])diomedea[&&NHX:TOL=89315],(((phoebastria immutabilis[&&NHX:TOL=89311],phoebastria nigripes[&&NHX:TOL=89312])[&&NHX:TOL=103231],phoebastria albatrus[&&NHX:TOL=89314])[&&NHX:TOL=103230],phoebastria irrorata[&&NHX:TOL=89313])phoebastria[&&NHX:TOL=89310])[&&NHX:TOL=103229])diomedeidae[&&NHX:TOL=26383],(((((((((((pterodroma macroptera[&&NHX:TOL=89346],pterodroma lessonii[&&NHX:TOL=89347])[&&NHX:TOL=103238],pterodroma incerta[&&NHX:TOL=89348])[&&NHX:TOL=103237],pterodroma magentae[&&NHX:TOL=89350])[&&NHX:TOL=103236],((pterodroma feae[&&NHX:TOL=89354],pterodroma cahow[&&NHX:TOL=89355])[&&NHX:TOL=103240],pterodroma hasitata[&&NHX:TOL=89356])[&&NHX:TOL=103239])[&&NHX:TOL=103235],pterodroma mollis[&&NHX:TOL=89352])[&&NHX:TOL=103234],(pterodroma neglecta[&&NHX:TOL=89359],((pterodroma externa[&&NHX:TOL=89357],pterodroma phaeopygia[&&NHX:TOL=89366])[&&NHX:TOL=103243],pterodroma inexpectata[&&NHX:TOL=89367])[&&NHX:TOL=103242])[&&NHX:TOL=103241])[&&NHX:TOL=103233],((pterodroma cookii[&&NHX:TOL=89374],pterodroma longirostris[&&NHX:TOL=89376])[&&NHX:TOL=103245],pterodroma hypoleuca[&&NHX:TOL=89371])[&&NHX:TOL=103244])[&&NHX:TOL=103232],pterodroma nigripennis[&&NHX:TOL=89369])[&&NHX:TOL=103271],pterodroma solandri[&&NHX:TOL=89349],pterodroma ultima[&&NHX:TOL=89351],pterodroma madeira[&&NHX:TOL=89353],pterodroma occulta[&&NHX:TOL=89358],pterodroma heraldica[&&NHX:TOL=89360],pterodroma arminjoniana[&&NHX:TOL=89361],pterodroma atrata[&&NHX:TOL=89362],pterodroma alba[&&NHX:TOL=89363],pterodroma baraui[&&NHX:TOL=89364],pterodroma sandwichensis[&&NHX:TOL=89365],pterodroma cervicalis[&&NHX:TOL=89368],pterodroma axillaris[&&NHX:TOL=89370],pterodroma leucoptera[&&NHX:TOL=89372],pterodroma brevipes[&&NHX:TOL=89373],pterodroma defilippiana[&&NHX:TOL=89375],pterodroma pycrofti[&&NHX:TOL=89377])pterodroma[&&NHX:TOL=89345],((((halobaena caerulea[&&NHX:TOL=89336],(((pachyptila vittata[&&NHX:TOL=89338],(pachyptila salvini[&&NHX:TOL=89339],pachyptila desolata[&&NHX:TOL=89340])[&&NHX:TOL=103256])[&&NHX:TOL=103255],pachyptila turtur[&&NHX:TOL=89342])[&&NHX:TOL=103254],pachyptila belcheri[&&NHX:TOL=89341],pachyptila crassirostris[&&NHX:TOL=89343])pachyptila[&&NHX:TOL=89337])[&&NHX:TOL=103253],((((procellaria aequinoctialis[&&NHX:TOL=89384],procellaria parkinsoni[&&NHX:TOL=89386])[&&NHX:TOL=103259],procellaria westlandica[&&NHX:TOL=89387])[&&NHX:TOL=103258],procellaria cinerea[&&NHX:TOL=89383],procellaria conspicillata[&&NHX:TOL=89385])procellaria[&&NHX:TOL=89382],(bulweria bulwerii[&&NHX:TOL=89413],bulweria fallax[&&NHX:TOL=89414])bulweria[&&NHX:TOL=89412])[&&NHX:TOL=103257])[&&NHX:TOL=103252],((((puffinus gravis[&&NHX:TOL=89411],puffinus griseus[&&NHX:TOL=89407],(puffinus creatopus[&&NHX:TOL=89409],puffinus carneipes[&&NHX:TOL=89410])[&&NHX:TOL=103264])[&&NHX:TOL=103261],(puffinus pacificus[&&NHX:TOL=89394],puffinus bulleri[&&NHX:TOL=89395])[&&NHX:TOL=103263])[&&NHX:TOL=103272],((((puffinus huttoni[&&NHX:TOL=89402],puffinus gavia[&&NHX:TOL=89401])[&&NHX:TOL=129480],(((puffinus lherminieri[&&NHX:TOL=89403],puffinus persicus[&&NHX:TOL=129674],puffinus baroli[&&NHX:TOL=129479])[&&NHX:TOL=129481],puffinus assimilis[&&NHX:TOL=89406])[&&NHX:TOL=103269],puffinus bailloni[&&NHX:TOL=129477],puffinus opisthomelas[&&NHX:TOL=89399],puffinus puffinus[&&NHX:TOL=89396],puffinus newelli[&&NHX:TOL=129476],(puffinus yelkouan[&&NHX:TOL=89397],puffinus mauretanicus[&&NHX:TOL=89398])[&&NHX:TOL=129482])[&&NHX:TOL=103268])[&&NHX:TOL=103267],(puffinus nativitatis[&&NHX:TOL=89393],puffinus subalaris[&&NHX:TOL=129478])[&&NHX:TOL=129483])[&&NHX:TOL=103266],(calonectris leucomelas[&&NHX:TOL=89389],calonectris diomedea[&&NHX:TOL=89390],calonectris edwardsii[&&NHX:TOL=89391])calonectris[&&NHX:TOL=89388])[&&NHX:TOL=103265],puffinus auricularis[&&NHX:TOL=89400],puffinus bannermani[&&NHX:TOL=89404],puffinus heinrothi[&&NHX:TOL=89405],puffinus tenuirostris[&&NHX:TOL=89408])puffinus[&&NHX:TOL=89392],(pseudobulweria aterrima[&&NHX:TOL=89379],pseudobulweria rostrata[&&NHX:TOL=89380],pseudobulweria becki[&&NHX:TOL=129475],pseudobulweria macgillivrayi[&&NHX:TOL=89381])pseudobulweria[&&NHX:TOL=89378],aphrodroma brevirostris[&&NHX:TOL=89344])[&&NHX:TOL=103260])[&&NHX:TOL=103246],(((((fulmarus glacialoides[&&NHX:TOL=89331],fulmarus glacialis[&&NHX:TOL=89332])fulmarus[&&NHX:TOL=89330],(macronectes giganteus[&&NHX:TOL=89328],macronectes halli[&&NHX:TOL=89329])macronectes[&&NHX:TOL=89327])[&&NHX:TOL=103251],daption capense[&&NHX:TOL=89334])[&&NHX:TOL=103250],thalassoica antarctica[&&NHX:TOL=89333])[&&NHX:TOL=103249],pagodroma nivea[&&NHX:TOL=89335])[&&NHX:TOL=103248])[&&NHX:TOL=103270])procellariidae[&&NHX:TOL=26384],(pelecanoides garnotii[&&NHX:TOL=89440],((pelecanoides magellani[&&NHX:TOL=89441],pelecanoides georgicus[&&NHX:TOL=89442])[&&NHX:TOL=103282],pelecanoides urinatrix[&&NHX:TOL=89443])[&&NHX:TOL=103281])pelecanoides[&&NHX:TOL=89439])[&&NHX:TOL=103218])[&&NHX:TOL=26382],((((garrodia nereis[&&NHX:TOL=89419],pelagodroma marina[&&NHX:TOL=89420])[&&NHX:TOL=103275],(fregetta tropica[&&NHX:TOL=89422],fregetta grallaria[&&NHX:TOL=89423])fregetta[&&NHX:TOL=89421])[&&NHX:TOL=103274],(oceanites oceanicus[&&NHX:TOL=89416],oceanites maorianus[&&NHX:TOL=89417],oceanites gracilis[&&NHX:TOL=89418])oceanites[&&NHX:TOL=89415])[&&NHX:TOL=103273],nesofregetta fuliginosa[&&NHX:TOL=89424],(((oceanodroma leucorhoa[&&NHX:TOL=89431],oceanodroma tristrami[&&NHX:TOL=89433])[&&NHX:TOL=103277],(oceanodroma furcata[&&NHX:TOL=89438],hydrobates pelagicus[&&NHX:TOL=89425])[&&NHX:TOL=103278])[&&NHX:TOL=103276],(oceanodroma melania[&&NHX:TOL=89434],(oceanodroma tethys[&&NHX:TOL=89428],oceanodroma microsoma[&&NHX:TOL=89427])[&&NHX:TOL=103280])[&&NHX:TOL=103279],oceanodroma castro[&&NHX:TOL=89429],oceanodroma monteiroi[&&NHX:TOL=135858],oceanodroma monorhis[&&NHX:TOL=89430],oceanodroma markhami[&&NHX:TOL=89432],oceanodroma matsudairae[&&NHX:TOL=89435],oceanodroma homochroa[&&NHX:TOL=89436],oceanodroma hornbyi[&&NHX:TOL=89437])oceanodroma[&&NHX:TOL=89426])hydrobatidae[&&NHX:TOL=26385])procellariiformes[&&NHX:TOL=26381],((aptenodytes forsteri[&&NHX:TOL=57224],aptenodytes patagonicus[&&NHX:TOL=57223])aptenodytes[&&NHX:TOL=57222],((pygoscelis adeliae[&&NHX:TOL=57227],(pygoscelis papua[&&NHX:TOL=57229],pygoscelis antarcticus[&&NHX:TOL=57230])[&&NHX:TOL=57228])pygoscelis[&&NHX:TOL=57226],((eudyptula minor[&&NHX:TOL=57252],(spheniscus magellanicus[&&NHX:TOL=57217],spheniscus demersus[&&NHX:TOL=57216],(spheniscus humboldti[&&NHX:TOL=57219],spheniscus mendiculus[&&NHX:TOL=57220])[&&NHX:TOL=57218])[&&NHX:TOL=57253])spheniscus[&&NHX:TOL=57215],(megadyptes antipodes[&&NHX:TOL=57232],(eudyptes pachyrhynchus[&&NHX:TOL=57234],eudyptes sclateri[&&NHX:TOL=57236],eudyptes chrysocome[&&NHX:TOL=57237],eudyptes chrysolophus[&&NHX:TOL=57239])eudyptes[&&NHX:TOL=57233])[&&NHX:TOL=57244])[&&NHX:TOL=57231])[&&NHX:TOL=57243])spheniscidae[&&NHX:TOL=26387])[&&NHX:TOL=123209],(((anastomus oscitans[&&NHX:TOL=89671],anastomus lamelligerus[&&NHX:TOL=89672])anastomus[&&NHX:TOL=89670],(leptoptilos javanicus[&&NHX:TOL=89686],leptoptilos dubius[&&NHX:TOL=89687],leptoptilos crumeniferus[&&NHX:TOL=89688])leptoptilos[&&NHX:TOL=89685],(mycteria americana[&&NHX:TOL=89666],(mycteria ibis[&&NHX:TOL=89668],(mycteria leucocephala[&&NHX:TOL=89669],mycteria cinerea[&&NHX:TOL=89667])[&&NHX:TOL=103295])[&&NHX:TOL=103294])mycteria[&&NHX:TOL=89665],(ciconia nigra[&&NHX:TOL=89674],((ciconia episcopus[&&NHX:TOL=89676],ciconia stormi[&&NHX:TOL=89677])[&&NHX:TOL=103297],ciconia abdimii[&&NHX:TOL=89675])[&&NHX:TOL=103296],((ciconia boyciana[&&NHX:TOL=89680],ciconia ciconia[&&NHX:TOL=89679])[&&NHX:TOL=103299],ciconia maguari[&&NHX:TOL=89678])[&&NHX:TOL=103298])ciconia[&&NHX:TOL=89673],((ephippiorhynchus asiaticus[&&NHX:TOL=89682],ephippiorhynchus senegalensis[&&NHX:TOL=89683])ephippiorhynchus[&&NHX:TOL=89681],jabiru mycteria[&&NHX:TOL=89684])[&&NHX:TOL=103300])ciconiidae[&&NHX:TOL=26332],(((((((morus serrator[&&NHX:TOL=57667],morus capensis[&&NHX:TOL=57668])[&&NHX:TOL=57666],morus bassanus[&&NHX:TOL=57669])morus[&&NHX:TOL=57665],papasula abbotti[&&NHX:TOL=57670])[&&NHX:TOL=57664],((((sula variegata[&&NHX:TOL=57675],sula nebouxii[&&NHX:TOL=57676])[&&NHX:TOL=57674],(sula dactylatra[&&NHX:TOL=57696],sula granti[&&NHX:TOL=57697])[&&NHX:TOL=57677])[&&NHX:TOL=57673],sula leucogaster[&&NHX:TOL=57678])[&&NHX:TOL=57672],sula sula[&&NHX:TOL=57679])sula[&&NHX:TOL=57671])sulidae[&&NHX:TOL=26335],((anhinga anhinga[&&NHX:TOL=57692],anhinga melanogaster[&&NHX:TOL=57693],anhinga novaehollandiae[&&NHX:TOL=57694],anhinga rufa[&&NHX:TOL=57695])anhingidae[&&NHX:TOL=26337],((phalacrocorax capensis[&&NHX:TOL=57707],(phalacrocorax carbo[&&NHX:TOL=57710],phalacrocorax lucidus[&&NHX:TOL=102312])[&&NHX:TOL=103502])[&&NHX:TOL=57738],((phalacrocorax featherstoni[&&NHX:TOL=57715],phalacrocorax punctatus[&&NHX:TOL=57731])[&&NHX:TOL=57740],phalacrocorax aristotelis[&&NHX:TOL=57700])[&&NHX:TOL=57739],(phalacrocorax varius[&&NHX:TOL=57736],phalacrocorax sulcirostris[&&NHX:TOL=57734])[&&NHX:TOL=57741],(phalacrocorax urile[&&NHX:TOL=57735],phalacrocorax pelagicus[&&NHX:TOL=57728])[&&NHX:TOL=57742],((phalacrocorax onslowi[&&NHX:TOL=57727],phalacrocorax chalconotus[&&NHX:TOL=57712])[&&NHX:TOL=57744],phalacrocorax campbelli[&&NHX:TOL=57706])[&&NHX:TOL=57743],phalacrocorax albiventer[&&NHX:TOL=57699],phalacrocorax atriceps[&&NHX:TOL=57701],phalacrocorax auritus[&&NHX:TOL=57702],phalacrocorax bougainvillii[&&NHX:TOL=57703],phalacrocorax bransfieldensis[&&NHX:TOL=57704],phalacrocorax brasilianus[&&NHX:TOL=57705],phalacrocorax capillatus[&&NHX:TOL=57709],phalacrocorax carunculatus[&&NHX:TOL=57711],phalacrocorax colensoi[&&NHX:TOL=57713],phalacrocorax fuscescens[&&NHX:TOL=57716],phalacrocorax fuscicollis[&&NHX:TOL=57717],phalacrocorax gaimardi[&&NHX:TOL=57718],phalacrocorax georgianus[&&NHX:TOL=57719],phalacrocorax harrisi[&&NHX:TOL=57720],phalacrocorax magellanicus[&&NHX:TOL=57721],phalacrocorax neglectus[&&NHX:TOL=57723],phalacrocorax nigrogularis[&&NHX:TOL=57725],phalacrocorax penicillatus[&&NHX:TOL=57729],phalacrocorax perspicillatus[&&NHX:EXT=Y:TOL=57730],phalacrocorax ranfurlyi[&&NHX:TOL=57733],phalacrocorax verrucosus[&&NHX:TOL=57737],microcarbo africanus[&&NHX:TOL=57698],microcarbo coronatus[&&NHX:TOL=57714],microcarbo melanoleucos[&&NHX:TOL=57722],microcarbo niger[&&NHX:TOL=57724],microcarbo pygmeus[&&NHX:TOL=57732])phalacrocoracidae[&&NHX:TOL=26338])[&&NHX:TOL=26336])[&&NHX:TOL=26334],(((fregata andrewsi[&&NHX:TOL=57682],fregata minor[&&NHX:TOL=57683])[&&NHX:TOL=57681],(fregata aquila[&&NHX:TOL=57685],fregata magnificens[&&NHX:TOL=57686])[&&NHX:TOL=57684])[&&NHX:TOL=57680],fregata ariel[&&NHX:TOL=57687])fregatidae[&&NHX:TOL=26339])[&&NHX:TOL=26333],(((balaeniceps rex[&&NHX:TOL=26328],(pelecanus onocrotalus[&&NHX:TOL=89583],pelecanus rufescens[&&NHX:TOL=89584],pelecanus philippensis[&&NHX:TOL=89585],pelecanus crispus[&&NHX:TOL=89586],pelecanus conspicillatus[&&NHX:TOL=89587],pelecanus erythrorhynchos[&&NHX:TOL=89588],pelecanus occidentalis[&&NHX:TOL=89589],pelecanus thagus[&&NHX:TOL=89590])pelecanus[&&NHX:TOL=26329])[&&NHX:TOL=26327],scopus umbretta[&&NHX:TOL=26330])[&&NHX:TOL=26326],(((threskiornis aethiopicus[&&NHX:TOL=89543],threskiornis bernieri[&&NHX:TOL=129484],threskiornis melanocephalus[&&NHX:TOL=89544],threskiornis molucca[&&NHX:TOL=89545],threskiornis spinicollis[&&NHX:TOL=89546])threskiornis[&&NHX:TOL=89542],(pseudibis papillosa[&&NHX:TOL=89548],pseudibis davisoni[&&NHX:TOL=89549],pseudibis gigantea[&&NHX:TOL=89550])pseudibis[&&NHX:TOL=89547],(geronticus eremita[&&NHX:TOL=89552],geronticus calvus[&&NHX:TOL=89553])geronticus[&&NHX:TOL=89551],nipponia nippon[&&NHX:TOL=89554],(bostrychia olivacea[&&NHX:TOL=89556],bostrychia bocagei[&&NHX:TOL=89557],bostrychia rara[&&NHX:TOL=89558],bostrychia hagedash[&&NHX:TOL=89559],bostrychia carunculata[&&NHX:TOL=89560])bostrychia[&&NHX:TOL=89555],(theristicus caerulescens[&&NHX:TOL=89562],theristicus caudatus[&&NHX:TOL=89563],theristicus melanopis[&&NHX:TOL=89564])theristicus[&&NHX:TOL=89561],cercibis oxycerca[&&NHX:TOL=89565],mesembrinibis cayennensis[&&NHX:TOL=89566],phimosus infuscatus[&&NHX:TOL=89567],(eudocimus ruber[&&NHX:TOL=89570],eudocimus albus[&&NHX:TOL=89569])eudocimus[&&NHX:TOL=89568],(plegadis falcinellus[&&NHX:TOL=89572],plegadis chihi[&&NHX:TOL=89573],plegadis ridgwayi[&&NHX:TOL=89574])plegadis[&&NHX:TOL=89571],lophotibis cristata[&&NHX:TOL=89575],(platalea leucorodia[&&NHX:TOL=89577],platalea minor[&&NHX:TOL=89578],platalea alba[&&NHX:TOL=89579],platalea regia[&&NHX:TOL=89580],platalea flavipes[&&NHX:TOL=89581],platalea ajaja[&&NHX:TOL=89582])platalea[&&NHX:TOL=89576])threskiornithidae[&&NHX:TOL=26325],((((syrigma sibilatrix[&&NHX:TOL=89649],(egretta intermedia[&&NHX:TOL=89651],egretta picata[&&NHX:TOL=89652],egretta novaehollandiae[&&NHX:TOL=89653],egretta rufescens[&&NHX:TOL=89654],egretta ardesiaca[&&NHX:TOL=89655],egretta vinaceigula[&&NHX:TOL=89656],egretta tricolor[&&NHX:TOL=89657],egretta caerulea[&&NHX:TOL=89658],egretta thula[&&NHX:TOL=89659],egretta garzetta[&&NHX:TOL=89660],egretta gularis[&&NHX:TOL=89661],egretta dimorpha[&&NHX:TOL=89662],egretta sacra[&&NHX:TOL=89663],egretta eulophotes[&&NHX:TOL=89664])egretta[&&NHX:TOL=89650])[&&NHX:TOL=103288],((ardea cinerea[&&NHX:TOL=89637],ardea herodias[&&NHX:TOL=89638],ardea cocoi[&&NHX:TOL=89639],ardea pacifica[&&NHX:TOL=89640],ardea melanocephala[&&NHX:TOL=89641],ardea humbloti[&&NHX:TOL=89642],ardea insignis[&&NHX:TOL=89643],ardea sumatrana[&&NHX:TOL=89644],ardea goliath[&&NHX:TOL=89645],ardea purpurea[&&NHX:TOL=89646],ardea alba[&&NHX:TOL=89647],ardea modesta[&&NHX:TOL=129677])ardea[&&NHX:TOL=89636],(bubulcus ibis[&&NHX:TOL=89635],bubulcus coromandus[&&NHX:TOL=129676])bubulcus[&&NHX:TOL=129675])[&&NHX:TOL=103286],(butorides virescens[&&NHX:TOL=89625],butorides sundevalli[&&NHX:TOL=89626],butorides striata[&&NHX:TOL=89627])butorides[&&NHX:TOL=89624],(nycticorax nycticorax[&&NHX:TOL=89622],nycticorax caledonicus[&&NHX:TOL=89621])nycticorax[&&NHX:TOL=89620],nyctanassa violacea[&&NHX:TOL=89623])[&&NHX:TOL=103290],(((botaurus stellaris[&&NHX:TOL=89601],botaurus poiciloptilus[&&NHX:TOL=89602],botaurus lentiginosus[&&NHX:TOL=89603],botaurus pinnatus[&&NHX:TOL=89604])botaurus[&&NHX:TOL=89600],(ixobrychus involucris[&&NHX:TOL=89606],ixobrychus exilis[&&NHX:TOL=89607],ixobrychus minutus[&&NHX:TOL=89608],ixobrychus dubius[&&NHX:TOL=129673],ixobrychus sinensis[&&NHX:TOL=89610],ixobrychus eurhythmus[&&NHX:TOL=89611],ixobrychus cinnamomeus[&&NHX:TOL=89612],ixobrychus sturmii[&&NHX:TOL=89613])ixobrychus[&&NHX:TOL=89605])[&&NHX:TOL=103285],zebrilus undulatus[&&NHX:TOL=89599])[&&NHX:TOL=103284])[&&NHX:TOL=103289],cochlearius cochlearius[&&NHX:TOL=89598],((tigrisoma lineatum[&&NHX:TOL=89594],tigrisoma fasciatum[&&NHX:TOL=89595],tigrisoma mexicanum[&&NHX:TOL=89596])tigrisoma[&&NHX:TOL=89593],tigriornis leucolopha[&&NHX:TOL=89592])[&&NHX:TOL=103291],(ardeola ralloides[&&NHX:TOL=89629],ardeola grayii[&&NHX:TOL=89630],ardeola bacchus[&&NHX:TOL=89631],ardeola speciosa[&&NHX:TOL=89632],ardeola idae[&&NHX:TOL=89633],ardeola rufiventris[&&NHX:TOL=89634])ardeola[&&NHX:TOL=89628],(gorsachius magnificus[&&NHX:TOL=89616],gorsachius goisagi[&&NHX:TOL=89617],gorsachius melanolophus[&&NHX:TOL=89618],gorsachius leuconotus[&&NHX:TOL=89619])gorsachius[&&NHX:TOL=89615],dupetor flavicollis[&&NHX:TOL=89614],pilherodius pileatus[&&NHX:TOL=89648],zonerodius heliosylus[&&NHX:TOL=89591],agamia agami[&&NHX:TOL=89597])ardeidae[&&NHX:TOL=26331])[&&NHX:TOL=123174])[&&NHX:TOL=123173])pelecaniformes[&&NHX:TOL=57152])[&&NHX:TOL=26323])[&&NHX:TOL=123208],(gavia stellata[&&NHX:TOL=89305],((gavia adamsii[&&NHX:TOL=89309],gavia immer[&&NHX:TOL=89308])[&&NHX:TOL=103302],(gavia arctica[&&NHX:TOL=89306],gavia pacifica[&&NHX:TOL=89307])[&&NHX:TOL=103303])[&&NHX:TOL=103301])gaviidae[&&NHX:TOL=26386])water birds[&&NHX:TOL=123207],((((((((tauraco fischeri[&&NHX:TOL=91873],tauraco livingstonii[&&NHX:TOL=91869])[&&NHX:TOL=103798],tauraco corythaix[&&NHX:TOL=91871])[&&NHX:TOL=103797],tauraco persa[&&NHX:TOL=91868])[&&NHX:TOL=103796],tauraco schalowi[&&NHX:TOL=91870],tauraco schuettii[&&NHX:TOL=91872],tauraco bannermani[&&NHX:TOL=91876],tauraco hartlaubi[&&NHX:TOL=91878],tauraco ruspolii[&&NHX:TOL=91880])[&&NHX:TOL=91867],tauraco leucotis[&&NHX:TOL=91879],(tauraco leucolophus[&&NHX:TOL=91875],tauraco erythrolophus[&&NHX:TOL=91877])[&&NHX:TOL=103799],(tauraco macrorhynchus[&&NHX:TOL=91874],(musophaga rossae[&&NHX:TOL=91885],musophaga violacea[&&NHX:TOL=91886])[&&NHX:TOL=91884])[&&NHX:TOL=103800])[&&NHX:TOL=103795],(tauraco porphyreolophus[&&NHX:TOL=91881],ruwenzorornis johnstoni[&&NHX:TOL=91883])[&&NHX:TOL=103801])[&&NHX:TOL=103794],(((corythaixoides personatus[&&NHX:TOL=91888],corythaixoides concolor[&&NHX:TOL=91889])[&&NHX:TOL=91887],(crinifer piscator[&&NHX:TOL=91893],crinifer zonurus[&&NHX:TOL=91892])[&&NHX:TOL=91891])[&&NHX:TOL=103803],corythaixoides leucogaster[&&NHX:TOL=91890])[&&NHX:TOL=103802])[&&NHX:TOL=103793],corythaeola cristata[&&NHX:TOL=91882])musophagidae[&&NHX:TOL=26401])[&&NHX:TOL=123206])[&&NHX:TOL=123202],opisthocomus hoazin[&&NHX:TOL=26402],((((gymnophaps albertisii[&&NHX:TOL=91196],gymnophaps mada[&&NHX:TOL=91197],gymnophaps stalkeri[&&NHX:TOL=129705],gymnophaps solomonensis[&&NHX:TOL=91198])gymnophaps[&&NHX:TOL=91195],lopholaimus antarcticus[&&NHX:TOL=91192],(hemiphaga novaeseelandiae[&&NHX:TOL=91193],hemiphaga chathamensis[&&NHX:TOL=129502])hemiphaga[&&NHX:TOL=129501])[&&NHX:TOL=108434],((alectroenas madagascariensis[&&NHX:TOL=91152],alectroenas sganzini[&&NHX:TOL=91153],alectroenas pulcherrima[&&NHX:TOL=91154])alectroenas[&&NHX:TOL=91151],drepanoptila holosericea[&&NHX:TOL=91150],(ptilinopus rivoli[&&NHX:TOL=91136],ptilinopus solomonensis[&&NHX:TOL=91137],ptilinopus viridis[&&NHX:TOL=91138],ptilinopus eugeniae[&&NHX:TOL=91139],ptilinopus iozonus[&&NHX:TOL=91140],ptilinopus insolitus[&&NHX:TOL=91141],ptilinopus hyogastrus[&&NHX:TOL=91142],ptilinopus granulifrons[&&NHX:TOL=91143],ptilinopus melanospilus[&&NHX:TOL=91144],ptilinopus nainus[&&NHX:TOL=91145],ptilinopus arcanus[&&NHX:TOL=91146],ptilinopus victor[&&NHX:TOL=91147],ptilinopus luteovirens[&&NHX:TOL=91148],ptilinopus layardi[&&NHX:TOL=91149],ptilinopus cinctus[&&NHX:TOL=91100],ptilinopus dohertyi[&&NHX:TOL=91101],ptilinopus porphyreus[&&NHX:TOL=91102],ptilinopus marchei[&&NHX:TOL=91103],ptilinopus merrilli[&&NHX:TOL=91104],ptilinopus occipitalis[&&NHX:TOL=91105],ptilinopus fischeri[&&NHX:TOL=91106],ptilinopus jambu[&&NHX:TOL=91107],ptilinopus subgularis[&&NHX:TOL=91108],ptilinopus leclancheri[&&NHX:TOL=91109],ptilinopus bernsteinii[&&NHX:TOL=91110],ptilinopus magnificus[&&NHX:TOL=91111],ptilinopus perlatus[&&NHX:TOL=91112],ptilinopus ornatus[&&NHX:TOL=91113],ptilinopus tannensis[&&NHX:TOL=91114],ptilinopus aurantiifrons[&&NHX:TOL=91115],ptilinopus wallacii[&&NHX:TOL=91116],ptilinopus superbus[&&NHX:TOL=91117],ptilinopus perousii[&&NHX:TOL=91118],ptilinopus porphyraceus[&&NHX:TOL=91119],ptilinopus pelewensis[&&NHX:TOL=91120],ptilinopus rarotongensis[&&NHX:TOL=91121],ptilinopus roseicapilla[&&NHX:TOL=91122],ptilinopus regina[&&NHX:TOL=91123],ptilinopus richardsii[&&NHX:TOL=91124],ptilinopus purpuratus[&&NHX:TOL=91125],ptilinopus chalcurus[&&NHX:TOL=91126],ptilinopus coralensis[&&NHX:TOL=91127],ptilinopus greyii[&&NHX:TOL=91128],ptilinopus huttoni[&&NHX:TOL=91129],ptilinopus dupetithouarsii[&&NHX:TOL=91130],ptilinopus mercierii[&&NHX:TOL=91131],ptilinopus insularis[&&NHX:TOL=91132],ptilinopus coronulatus[&&NHX:TOL=91133],ptilinopus pulchellus[&&NHX:TOL=91134],ptilinopus monacha[&&NHX:TOL=91135])ptilinopus[&&NHX:TOL=91099])[&&NHX:TOL=108453],(ducula poliocephala[&&NHX:TOL=91156],ducula forsteni[&&NHX:TOL=91157],ducula mindorensis[&&NHX:TOL=91158],ducula radiata[&&NHX:TOL=91159],ducula carola[&&NHX:TOL=91160],ducula aenea[&&NHX:TOL=91161],ducula nicobarica[&&NHX:TOL=129703],ducula perspicillata[&&NHX:TOL=91162],ducula neglecta[&&NHX:TOL=129704],ducula concinna[&&NHX:TOL=91163],ducula pacifica[&&NHX:TOL=91164],ducula oceanica[&&NHX:TOL=91165],ducula aurorae[&&NHX:TOL=91166],ducula galeata[&&NHX:TOL=91167],ducula rubricera[&&NHX:TOL=91168],ducula myristicivora[&&NHX:TOL=91169],ducula rufigaster[&&NHX:TOL=91170],ducula basilica[&&NHX:TOL=91171],ducula finschii[&&NHX:TOL=91172],ducula chalconota[&&NHX:TOL=91173],ducula pistrinaria[&&NHX:TOL=91174],ducula rosacea[&&NHX:TOL=91175],ducula whartoni[&&NHX:TOL=91176],ducula pickeringii[&&NHX:TOL=91177],ducula latrans[&&NHX:TOL=91178],ducula brenchleyi[&&NHX:TOL=91179],ducula bakeri[&&NHX:TOL=91180],ducula goliath[&&NHX:TOL=91181],ducula pinon[&&NHX:TOL=91182],ducula melanochroa[&&NHX:TOL=91183],ducula mullerii[&&NHX:TOL=91184],ducula zoeae[&&NHX:TOL=91185],ducula badia[&&NHX:TOL=91186],ducula lacernulata[&&NHX:TOL=91187],ducula cineracea[&&NHX:TOL=91188],ducula bicolor[&&NHX:TOL=91189],ducula luctuosa[&&NHX:TOL=129500],ducula spilorrhoa[&&NHX:TOL=91190],ducula subflavescens[&&NHX:TOL=91191])ducula[&&NHX:TOL=91155],(treron fulvicollis[&&NHX:TOL=91075],treron olax[&&NHX:TOL=91076],treron vernans[&&NHX:TOL=91077],treron bicinctus[&&NHX:TOL=91078],treron pompadora[&&NHX:TOL=91079],treron affinis[&&NHX:TOL=129698],treron phayrei[&&NHX:TOL=129699],treron chloropterus[&&NHX:TOL=129700],treron axillaris[&&NHX:TOL=129701],treron aromaticus[&&NHX:TOL=129702],treron curvirostra[&&NHX:TOL=91080],treron griseicauda[&&NHX:TOL=91081],treron teysmannii[&&NHX:TOL=91082],treron floris[&&NHX:TOL=91083],treron psittaceus[&&NHX:TOL=91084],treron capellei[&&NHX:TOL=91085],treron phoenicopterus[&&NHX:TOL=91086],treron waalia[&&NHX:TOL=91087],treron australis[&&NHX:TOL=91088],treron griveaudi[&&NHX:TOL=91089],treron calvus[&&NHX:TOL=91090],treron pembaensis[&&NHX:TOL=91091],treron sanctithomae[&&NHX:TOL=91092],treron apicauda[&&NHX:TOL=91093],treron oxyurus[&&NHX:TOL=91094],treron seimundi[&&NHX:TOL=91095],treron sphenurus[&&NHX:TOL=91096],treron sieboldii[&&NHX:TOL=91097],treron formosae[&&NHX:TOL=91098])treron[&&NHX:TOL=91074],((oena capensis[&&NHX:TOL=90956],(turtur chalcospilos[&&NHX:TOL=90951],turtur abyssinicus[&&NHX:TOL=90952],turtur afer[&&NHX:TOL=90953],turtur tympanistria[&&NHX:TOL=90954],turtur brehmeri[&&NHX:TOL=90955])turtur[&&NHX:TOL=90950])[&&NHX:TOL=108437],(chalcophaps stephani[&&NHX:TOL=90958],chalcophaps indica[&&NHX:TOL=90959],chalcophaps longirostris[&&NHX:TOL=129697])chalcophaps[&&NHX:TOL=90957])[&&NHX:TOL=108436],(phapitreron amethystinus[&&NHX:TOL=91071],phapitreron cinereiceps[&&NHX:TOL=91072],phapitreron brunneiceps[&&NHX:TOL=129499],phapitreron leucotis[&&NHX:TOL=91073])phapitreron[&&NHX:TOL=91070],caloenas nicobarica[&&NHX:TOL=91044],(pezophaps solitaria[&&NHX:EXT=Y:TOL=108451],raphus cucullatus[&&NHX:EXT=Y:TOL=108452])[&&NHX:TOL=108450],trugon terrestris[&&NHX:TOL=90972],(goura cristata[&&NHX:TOL=91066],goura scheepmakeri[&&NHX:TOL=91067],goura victoria[&&NHX:TOL=91068])goura[&&NHX:TOL=91065],didunculus strigirostris[&&NHX:TOL=91069],otidiphaps nobilis[&&NHX:TOL=91064],((petrophassa albipennis[&&NHX:TOL=90975],petrophassa rufipennis[&&NHX:TOL=90976])petrophassa[&&NHX:TOL=90974],(phaps chalcoptera[&&NHX:TOL=90964],phaps elegans[&&NHX:TOL=90965],phaps histrionica[&&NHX:TOL=90966])phaps[&&NHX:TOL=90963],(geophaps plumifera[&&NHX:TOL=90969],geophaps scripta[&&NHX:TOL=90970],geophaps smithii[&&NHX:TOL=90971])geophaps[&&NHX:TOL=90968],(geopelia cuneata[&&NHX:TOL=90978],geopelia striata[&&NHX:TOL=90979],geopelia maugei[&&NHX:TOL=90980],geopelia humeralis[&&NHX:TOL=90981],geopelia placida[&&NHX:TOL=90982])geopelia[&&NHX:TOL=90977],leucosarcia melanoleuca[&&NHX:TOL=90973],(gallicolumba luzonica[&&NHX:TOL=91046],gallicolumba crinigera[&&NHX:TOL=91047],gallicolumba platenae[&&NHX:TOL=91048],gallicolumba keayi[&&NHX:TOL=91049],gallicolumba menagei[&&NHX:TOL=91050],gallicolumba rufigula[&&NHX:TOL=91051],gallicolumba tristigmata[&&NHX:TOL=91052],gallicolumba hoedtii[&&NHX:TOL=91053],gallicolumba jobiensis[&&NHX:TOL=91054],gallicolumba kubaryi[&&NHX:TOL=91055],gallicolumba erythroptera[&&NHX:TOL=91056],gallicolumba xanthonura[&&NHX:TOL=91057],gallicolumba stairi[&&NHX:TOL=91058],gallicolumba sanctaecrucis[&&NHX:TOL=91059],gallicolumba salamonis[&&NHX:TOL=91060],gallicolumba rubescens[&&NHX:TOL=91061],gallicolumba beccarii[&&NHX:TOL=91062],gallicolumba canifrons[&&NHX:TOL=91063])gallicolumba[&&NHX:TOL=91045],(henicophaps albifrons[&&NHX:TOL=90961],henicophaps foersteri[&&NHX:TOL=90962])henicophaps[&&NHX:TOL=90960],ocyphaps lophotes[&&NHX:TOL=90967])[&&NHX:TOL=108438],cryptophaps poecilorrhoa[&&NHX:TOL=91194])[&&NHX:TOL=108431],(((columbina passerina[&&NHX:TOL=91001],columbina minuta[&&NHX:TOL=91002],columbina buckleyi[&&NHX:TOL=91003],columbina talpacoti[&&NHX:TOL=91004],columbina picui[&&NHX:TOL=91005],columbina cruziana[&&NHX:TOL=91006],columbina cyanopis[&&NHX:TOL=91007])columbina[&&NHX:TOL=91000],(scardafella inca[&&NHX:TOL=90998],scardafella squammata[&&NHX:TOL=90999])scardafella[&&NHX:TOL=90997],(metriopelia ceciliae[&&NHX:TOL=90984],metriopelia morenoi[&&NHX:TOL=90985],metriopelia melanoptera[&&NHX:TOL=90986],metriopelia aymara[&&NHX:TOL=90987])metriopelia[&&NHX:TOL=90983],uropelia campestris[&&NHX:TOL=90988])[&&NHX:TOL=108440],(claravis pretiosa[&&NHX:TOL=91009],claravis godefrida[&&NHX:TOL=91010],claravis mondetoura[&&NHX:TOL=91011])claravis[&&NHX:TOL=91008])[&&NHX:TOL=108454],(((((macropygia unchall[&&NHX:TOL=90936],macropygia amboinensis[&&NHX:TOL=90937],macropygia magna[&&NHX:TOL=90938],macropygia rufipennis[&&NHX:TOL=90939],macropygia nigrirostris[&&NHX:TOL=90940],macropygia mackinlayi[&&NHX:TOL=90941],macropygia ruficeps[&&NHX:TOL=90942])macropygia[&&NHX:TOL=90935],(turacoena manadensis[&&NHX:TOL=90948],turacoena modesta[&&NHX:TOL=90949])turacoena[&&NHX:TOL=90947])[&&NHX:TOL=108446],(reinwardtoena reinwardtii[&&NHX:TOL=90944],reinwardtoena browni[&&NHX:TOL=90945],reinwardtoena crassirostris[&&NHX:TOL=90946])reinwardtoena[&&NHX:TOL=90943])[&&NHX:TOL=108445],(columba sjostedti[&&NHX:TOL=90880],columba thomensis[&&NHX:TOL=90881],columba pollenii[&&NHX:TOL=90882],columba hodgsonii[&&NHX:TOL=90883],columba albinucha[&&NHX:TOL=90884],columba pulchricollis[&&NHX:TOL=90885],columba elphinstonii[&&NHX:TOL=90886],columba torringtoni[&&NHX:TOL=90887],columba punicea[&&NHX:TOL=90888],columba argentina[&&NHX:TOL=90889],columba palumboides[&&NHX:TOL=90890],columba janthina[&&NHX:TOL=90891],columba vitiensis[&&NHX:TOL=90892],columba leucomela[&&NHX:TOL=90893],columba pallidiceps[&&NHX:TOL=90894],columba delegorguei[&&NHX:TOL=90895],columba iriditorques[&&NHX:TOL=90896],columba malherbii[&&NHX:TOL=90897],columba larvata[&&NHX:TOL=90898],columba livia[&&NHX:TOL=90866],columba rupestris[&&NHX:TOL=90867],columba leuconota[&&NHX:TOL=90868],columba guinea[&&NHX:TOL=90869],columba albitorques[&&NHX:TOL=90870],columba oenas[&&NHX:TOL=90871],columba eversmanni[&&NHX:TOL=90872],columba oliviae[&&NHX:TOL=90873],columba palumbus[&&NHX:TOL=90874],columba trocaz[&&NHX:TOL=90875],columba bollii[&&NHX:TOL=90876],columba junoniae[&&NHX:TOL=90877],columba unicincta[&&NHX:TOL=90878],columba arquatrix[&&NHX:TOL=90879])columba[&&NHX:TOL=90865],(((((streptopelia hypopyrrha[&&NHX:TOL=90921],streptopelia turtur[&&NHX:TOL=90919])[&&NHX:TOL=108458],streptopelia orientalis[&&NHX:TOL=90922])[&&NHX:TOL=108457],streptopelia bitorquata[&&NHX:TOL=90923],streptopelia tranquebarica[&&NHX:TOL=90931])[&&NHX:TOL=108456],((((streptopelia decaocto[&&NHX:TOL=90924],streptopelia roseogrisea[&&NHX:TOL=90925])[&&NHX:TOL=108462],streptopelia decipiens[&&NHX:TOL=90927])[&&NHX:TOL=108461],streptopelia semitorquata[&&NHX:TOL=90928])[&&NHX:TOL=108460],(streptopelia capicola[&&NHX:TOL=90929],streptopelia vinacea[&&NHX:TOL=90930])[&&NHX:TOL=108463])[&&NHX:TOL=108459],streptopelia lugens[&&NHX:TOL=90920],streptopelia reichenowi[&&NHX:TOL=90926])[&&NHX:TOL=108455],(streptopelia chinensis[&&NHX:TOL=90933],streptopelia senegalensis[&&NHX:TOL=90934])[&&NHX:TOL=108464],(streptopelia picturata[&&NHX:TOL=90932],nesoenas mayeri[&&NHX:TOL=90917])[&&NHX:TOL=108465])streptopelia[&&NHX:TOL=90918],(patagioenas leucocephala[&&NHX:TOL=90900],patagioenas squamosa[&&NHX:TOL=90901],patagioenas speciosa[&&NHX:TOL=90902],patagioenas picazuro[&&NHX:TOL=90903],patagioenas corensis[&&NHX:TOL=90904],patagioenas maculosa[&&NHX:TOL=90905],patagioenas fasciata[&&NHX:TOL=90906],patagioenas araucana[&&NHX:TOL=90907],patagioenas caribaea[&&NHX:TOL=90908],patagioenas cayennensis[&&NHX:TOL=90909],patagioenas flavirostris[&&NHX:TOL=90910],patagioenas oenops[&&NHX:TOL=90911],patagioenas inornata[&&NHX:TOL=90912],patagioenas plumbea[&&NHX:TOL=90913],patagioenas subvinacea[&&NHX:TOL=90914],patagioenas nigrirostris[&&NHX:TOL=90915],patagioenas goodsoni[&&NHX:TOL=90916])patagioenas[&&NHX:TOL=90899],ectopistes migratorius[&&NHX:EXT=Y:TOL=108444])[&&NHX:TOL=108443],((leptotila verreauxi[&&NHX:TOL=91013],leptotila megalura[&&NHX:TOL=91014],leptotila rufaxilla[&&NHX:TOL=91015],leptotila plumbeiceps[&&NHX:TOL=91016],leptotila pallida[&&NHX:TOL=91017],leptotila battyi[&&NHX:TOL=91018],leptotila wellsi[&&NHX:TOL=91019],leptotila jamaicensis[&&NHX:TOL=91020],leptotila cassini[&&NHX:TOL=91021],leptotila ochraceiventris[&&NHX:TOL=91022],leptotila conoveri[&&NHX:TOL=91023])leptotila[&&NHX:TOL=91012],((((zenaida macroura[&&NHX:TOL=90990],zenaida graysoni[&&NHX:TOL=90991])[&&NHX:TOL=108468],zenaida auriculata[&&NHX:TOL=90992],zenaida galapagoensis[&&NHX:TOL=90994])[&&NHX:TOL=108467],zenaida aurita[&&NHX:TOL=90993])[&&NHX:TOL=108466],(zenaida asiatica[&&NHX:TOL=90995],zenaida meloda[&&NHX:TOL=90996])[&&NHX:TOL=108469])zenaida[&&NHX:TOL=90989],(geotrygon lawrencii[&&NHX:TOL=91025],geotrygon carrikeri[&&NHX:TOL=91026],geotrygon costaricensis[&&NHX:TOL=91027],geotrygon goldmani[&&NHX:TOL=91028],geotrygon saphirina[&&NHX:TOL=91029],geotrygon veraguensis[&&NHX:TOL=91030],geotrygon purpurata[&&NHX:TOL=91031],geotrygon caniceps[&&NHX:TOL=91032],geotrygon leucometopia[&&NHX:TOL=91033],geotrygon versicolor[&&NHX:TOL=91034],geotrygon albifacies[&&NHX:TOL=91035],geotrygon chiriquensis[&&NHX:TOL=91036],geotrygon linearis[&&NHX:TOL=91037],geotrygon frenata[&&NHX:TOL=91038],geotrygon chrysia[&&NHX:TOL=91039],geotrygon mystacea[&&NHX:TOL=91040],geotrygon violacea[&&NHX:TOL=91041],geotrygon montana[&&NHX:TOL=91042])geotrygon[&&NHX:TOL=91024],starnoenas cyanocephala[&&NHX:TOL=91043])[&&NHX:TOL=108448])[&&NHX:TOL=108442])columbidae[&&NHX:TOL=26404],((syrrhaptes tibetanus[&&NHX:TOL=90846],syrrhaptes paradoxus[&&NHX:TOL=90847])[&&NHX:TOL=90845],(pterocles alchata[&&NHX:TOL=90849],pterocles namaqua[&&NHX:TOL=90850],pterocles exustus[&&NHX:TOL=90851],pterocles senegallus[&&NHX:TOL=90852],pterocles orientalis[&&NHX:TOL=90853],pterocles gutturalis[&&NHX:TOL=90854],pterocles coronatus[&&NHX:TOL=90855],pterocles decoratus[&&NHX:TOL=90856],pterocles personatus[&&NHX:TOL=90857],pterocles lichtensteinii[&&NHX:TOL=90858],pterocles indicus[&&NHX:TOL=90859],pterocles quadricinctus[&&NHX:TOL=90860],pterocles bicinctus[&&NHX:TOL=90861],pterocles burchelli[&&NHX:TOL=90862])[&&NHX:TOL=90848])pteroclididae[&&NHX:TOL=90844],(phaethon aethereus[&&NHX:TOL=57688],(phaethon lepturus[&&NHX:TOL=57691],phaethon rubricauda[&&NHX:TOL=57690])[&&NHX:TOL=57689])phaethontidae[&&NHX:TOL=26340],(((trochilidae[&&NHX:TOL=26392],(apodidae[&&NHX:TOL=56962],hemiprocnidae[&&NHX:TOL=56963])[&&NHX:TOL=26393])apodiformes[&&NHX:TOL=26391],((((aegotheles wallaciii[&&NHX:TOL=65369],(aegotheles archboldi[&&NHX:TOL=65367],aegotheles albertisi albertisi[&&NHX:TOL=66911])[&&NHX:TOL=66910],aegotheles albertisi salvadorii[&&NHX:TOL=66912])[&&NHX:TOL=65366],(aegotheles bennettii[&&NHX:TOL=65371],aegotheles cristatus[&&NHX:TOL=65372])[&&NHX:TOL=65370],aegotheles crinifrons[&&NHX:TOL=65373])[&&NHX:TOL=65365],(aegotheles tatei[&&NHX:TOL=65375],aegotheles insignis[&&NHX:TOL=65376])[&&NHX:TOL=65374])[&&NHX:TOL=65364],(aegotheles novaezealandiae[&&NHX:EXT=Y:TOL=65378],aegotheles savesi[&&NHX:TOL=65379])[&&NHX:TOL=65377])aegotheles[&&NHX:TOL=26394])[&&NHX:TOL=107600],((((eurostopodus argus[&&NHX:TOL=92079],eurostopodus mystacalis[&&NHX:TOL=92080],eurostopodus diabolicus[&&NHX:TOL=92081],eurostopodus papuensis[&&NHX:TOL=92082],eurostopodus archboldi[&&NHX:TOL=92083],eurostopodus temminckii[&&NHX:TOL=92084],eurostopodus macrotis[&&NHX:TOL=92085])eurostopodus[&&NHX:TOL=92078],((macrodipteryx longipennis[&&NHX:TOL=92152],macrodipteryx vexillarius[&&NHX:TOL=92153])macrodipteryx[&&NHX:TOL=92151],macropsalis forcipata[&&NHX:TOL=92160],eleothreptus anomalus[&&NHX:TOL=92161],(chordeiles pusillus[&&NHX:TOL=92066],chordeiles rupestris[&&NHX:TOL=92067],chordeiles acutipennis[&&NHX:TOL=92068],chordeiles minor[&&NHX:TOL=92069],chordeiles gundlachii[&&NHX:TOL=92070])chordeiles[&&NHX:TOL=92065],(lurocalis semitorquatus[&&NHX:TOL=92072],lurocalis rufiventris[&&NHX:TOL=92073])lurocalis[&&NHX:TOL=92071],(nyctiprogne vielliardi[&&NHX:TOL=92075],nyctiprogne leucopyga[&&NHX:TOL=92076])nyctiprogne[&&NHX:TOL=92074],podager nacunda[&&NHX:TOL=92077],veles binotatus[&&NHX:TOL=92086],nyctidromus albicollis[&&NHX:TOL=92087],((hydropsalis climacocerca[&&NHX:TOL=92155],hydropsalis torquata[&&NHX:TOL=92156])hydropsalis[&&NHX:TOL=92154],(uropsalis segmentata[&&NHX:TOL=92158],uropsalis lyra[&&NHX:TOL=92159])uropsalis[&&NHX:TOL=92157])[&&NHX:TOL=107352],(caprimulgus carolinensis[&&NHX:TOL=92096],caprimulgus rufus[&&NHX:TOL=92097],caprimulgus cubanensis[&&NHX:TOL=92098],caprimulgus salvini[&&NHX:TOL=92099],caprimulgus badius[&&NHX:TOL=92100],caprimulgus sericocaudatus[&&NHX:TOL=92101],caprimulgus ridgwayi[&&NHX:TOL=92102],caprimulgus vociferus[&&NHX:TOL=92103],caprimulgus noctitherus[&&NHX:TOL=92104],caprimulgus saturatus[&&NHX:TOL=92105],caprimulgus longirostris[&&NHX:TOL=92106],caprimulgus cayennensis[&&NHX:TOL=92107],caprimulgus candicans[&&NHX:TOL=92108],caprimulgus maculicaudus[&&NHX:TOL=92109],caprimulgus parvulus[&&NHX:TOL=92110],caprimulgus heterurus[&&NHX:TOL=129516],caprimulgus anthonyi[&&NHX:TOL=92111],caprimulgus maculosus[&&NHX:TOL=92112],caprimulgus nigrescens[&&NHX:TOL=92113],caprimulgus whitelyi[&&NHX:TOL=92114],caprimulgus hirundinaceus[&&NHX:TOL=92115],caprimulgus ruficollis[&&NHX:TOL=92116],caprimulgus indicus[&&NHX:TOL=92117],caprimulgus jotaka[&&NHX:TOL=129810],caprimulgus europaeus[&&NHX:TOL=92118],caprimulgus fraenatus[&&NHX:TOL=92119],caprimulgus rufigena[&&NHX:TOL=92120],caprimulgus aegyptius[&&NHX:TOL=92121],caprimulgus mahrattensis[&&NHX:TOL=92122],caprimulgus centralasicus[&&NHX:TOL=92123],caprimulgus nubicus[&&NHX:TOL=92124],caprimulgus eximius[&&NHX:TOL=92125],caprimulgus atripennis[&&NHX:TOL=92126],caprimulgus macrurus[&&NHX:TOL=92127],caprimulgus meesi[&&NHX:TOL=129517],caprimulgus andamanicus[&&NHX:TOL=129518],caprimulgus manillensis[&&NHX:TOL=92128],caprimulgus celebensis[&&NHX:TOL=92129],caprimulgus donaldsoni[&&NHX:TOL=92130],caprimulgus nigriscapularis[&&NHX:TOL=92131],caprimulgus pectoralis[&&NHX:TOL=92132],caprimulgus poliocephalus[&&NHX:TOL=92133],caprimulgus ruwenzorii[&&NHX:TOL=92134],caprimulgus asiaticus[&&NHX:TOL=92135],caprimulgus madagascariensis[&&NHX:TOL=92136],caprimulgus natalensis[&&NHX:TOL=92137],caprimulgus solala[&&NHX:TOL=92138],caprimulgus inornatus[&&NHX:TOL=92139],caprimulgus stellatus[&&NHX:TOL=92140],caprimulgus affinis[&&NHX:TOL=92141],caprimulgus tristigma[&&NHX:TOL=92142],caprimulgus concretus[&&NHX:TOL=92143],caprimulgus pulchellus[&&NHX:TOL=92144],caprimulgus prigoginei[&&NHX:TOL=92145],caprimulgus enarratus[&&NHX:TOL=92146],caprimulgus batesi[&&NHX:TOL=92147],caprimulgus climacurus[&&NHX:TOL=92148],caprimulgus clarus[&&NHX:TOL=92149],caprimulgus fossii[&&NHX:TOL=92150])caprimulgus[&&NHX:TOL=92095],(nyctiphrynus mcleodii[&&NHX:TOL=92091],nyctiphrynus yucatanicus[&&NHX:TOL=92092],nyctiphrynus ocellatus[&&NHX:TOL=92093],nyctiphrynus rosenbergi[&&NHX:TOL=92094])nyctiphrynus[&&NHX:TOL=92090],siphonorhis brewsteri[&&NHX:TOL=92089],phalaenoptilus nuttallii[&&NHX:TOL=92088])[&&NHX:TOL=107351])caprimulgidae[&&NHX:TOL=26398],((podargus ocellatus[&&NHX:TOL=92163],podargus papuensis[&&NHX:TOL=92164],podargus strigoides[&&NHX:TOL=92165])podargus[&&NHX:TOL=92162],(batrachostomus auritus[&&NHX:TOL=92168],batrachostomus harterti[&&NHX:TOL=92169],batrachostomus septimus[&&NHX:TOL=92170],batrachostomus stellatus[&&NHX:TOL=92171],batrachostomus moniliger[&&NHX:TOL=92172],batrachostomus hodgsoni[&&NHX:TOL=92173],batrachostomus poliolophus[&&NHX:TOL=92174],batrachostomus mixtus[&&NHX:TOL=129515],batrachostomus javensis[&&NHX:TOL=92175],batrachostomus cornutus[&&NHX:TOL=92176])batrachostomus[&&NHX:TOL=92167],rigidipenna inexpectatus[&&NHX:TOL=107353])podargidae[&&NHX:TOL=26400])[&&NHX:TOL=107602],(nyctibius grandis[&&NHX:TOL=92058],nyctibius aethereus[&&NHX:TOL=92059],nyctibius jamaicensis[&&NHX:TOL=92060],nyctibius griseus[&&NHX:TOL=92061],(nyctibius leucopterus[&&NHX:TOL=92063],nyctibius maculosus[&&NHX:TOL=92062])[&&NHX:TOL=107601],nyctibius bracteatus[&&NHX:TOL=92064])nyctibius[&&NHX:TOL=26397],steatornis caripensis[&&NHX:TOL=26399])caprimulgiformes[&&NHX:TOL=56965])[&&NHX:TOL=26389],(eurypyga helias[&&NHX:TOL=26318],rhynochetos jubatus[&&NHX:TOL=26319])[&&NHX:TOL=26317],(monias benschi[&&NHX:TOL=90276],mesitornis unicolor[&&NHX:TOL=90275],mesitornis variegatus[&&NHX:TOL=90274])mesitornithidae[&&NHX:TOL=26322],(((tachybaptus rufolavatus[&&NHX:TOL=89445],tachybaptus ruficollis[&&NHX:TOL=89446],tachybaptus novaehollandiae[&&NHX:TOL=89447],tachybaptus pelzelnii[&&NHX:TOL=89448],tachybaptus dominicus[&&NHX:TOL=89449])tachybaptus[&&NHX:TOL=89444],(podilymbus podiceps[&&NHX:TOL=89451],podilymbus gigas[&&NHX:TOL=89452])podilymbus[&&NHX:TOL=89450],(rollandia rolland[&&NHX:TOL=89454],rollandia microptera[&&NHX:TOL=89455])rollandia[&&NHX:TOL=89453],(poliocephalus poliocephalus[&&NHX:TOL=89457],poliocephalus rufopectus[&&NHX:TOL=89458])poliocephalus[&&NHX:TOL=89456],(podiceps major[&&NHX:TOL=89460],podiceps grisegena[&&NHX:TOL=89461],podiceps cristatus[&&NHX:TOL=89462],podiceps auritus[&&NHX:TOL=89463],podiceps nigricollis[&&NHX:TOL=89464],podiceps occipitalis[&&NHX:TOL=89465],podiceps taczanowskii[&&NHX:TOL=89466],podiceps gallardoi[&&NHX:TOL=89467])podiceps[&&NHX:TOL=89459],(aechmophorus occidentalis[&&NHX:TOL=89469],aechmophorus clarkii[&&NHX:TOL=89470])aechmophorus[&&NHX:TOL=89468])podicipedidae[&&NHX:TOL=26371],(phoenicopterus roseus[&&NHX:TOL=89471],phoenicopterus ruber[&&NHX:TOL=89472],phoenicopterus chilensis[&&NHX:TOL=89473],phoeniconaias minor[&&NHX:TOL=89474],phoenicoparrus andinus[&&NHX:TOL=89475],phoenicoparrus jamesi[&&NHX:TOL=89476])phoenicopteridae[&&NHX:TOL=26370])[&&NHX:TOL=26369])neoaves[&&NHX:TOL=26305])neognathae[&&NHX:TOL=26291])neornithes[&&NHX:TOL=15834])euornithes true birds[&&NHX:TOL=15829])[&&NHX:TOL=15827])[&&NHX:TOL=15825])aves[&&NHX:TOL=15721])[&&NHX:TOL=15717])maniraptora[&&NHX:TOL=15715])[&&NHX:TOL=15713])[&&NHX:TOL=15707])coelurosauria[&&NHX:TOL=15769])[&&NHX:TOL=15767])tetanurae[&&NHX:TOL=15763])[&&NHX:TOL=15761])[&&NHX:TOL=15759])theropoda[&&NHX:TOL=15726])saurischia[&&NHX:TOL=15724])dinosauria[&&NHX:TOL=14883],pterosauria[&&NHX:EXT=Y:TOL=14882])[&&NHX:TOL=14881],lagosuchis[&&NHX:EXT=Y:TOL=14880])[&&NHX:TOL=14879],ornithosuchidae[&&NHX:EXT=Y:TOL=14878])[&&NHX:TOL=14877],euparkeria[&&NHX:EXT=Y:TOL=14876])[&&NHX:TOL=14875],parasuchia[&&NHX:EXT=Y:TOL=14874])[&&NHX:TOL=14873],aetosauria[&&NHX:EXT=Y:TOL=14872])[&&NHX:TOL=14871],rauisuchia[&&NHX:EXT=Y:TOL=14870])[&&NHX:TOL=14869],crocodylomorpha[&&NHX:TOL=14868])archosauria[&&NHX:TOL=14900],proterochapmsia[&&NHX:EXT=Y:TOL=14899])[&&NHX:TOL=14898],erythrosuchia[&&NHX:EXT=Y:TOL=14897])[&&NHX:TOL=14896],proterosuchia[&&NHX:EXT=Y:TOL=14895])[&&NHX:TOL=14894],prolacertiformes[&&NHX:EXT=Y:TOL=14893])[&&NHX:TOL=14892],trilophosauria[&&NHX:EXT=Y:TOL=14891])[&&NHX:TOL=14890],rhynchosauria[&&NHX:EXT=Y:TOL=14889])[&&NHX:TOL=14888],choristodera[&&NHX:EXT=Y:TOL=14887])[&&NHX:TOL=14886],placodontia[&&NHX:EXT=Y:TOL=14885])archosauromorpha[&&NHX:TOL=14916],(saurosternon[&&NHX:EXT=Y:TOL=14928],paliguana[&&NHX:EXT=Y:TOL=14929],(kuehneosauridae[&&NHX:EXT=Y:TOL=14931],((((tropidurinae[&&NHX:TOL=17574],leiocephalinae[&&NHX:TOL=17575],liolaeminae[&&NHX:TOL=17576])tropiduridae[&&NHX:TOL=17573],(leiolepidinae[&&NHX:TOL=17578],chamaeleonidae[&&NHX:TOL=17579],agaminae[&&NHX:TOL=17580])acrodonta[&&NHX:TOL=17577],corytophanidae[&&NHX:TOL=17581],crotaphytidae[&&NHX:TOL=17582],hoplocercidae[&&NHX:TOL=17583],polychridae[&&NHX:TOL=17584],opluridae[&&NHX:TOL=17585],iguaninae[&&NHX:TOL=17586],((sand lizards[&&NHX:TOL=17590],phrynosoma[&&NHX:TOL=17591])[&&NHX:TOL=17589],petrosaurus[&&NHX:TOL=17592],(uta[&&NHX:TOL=17594],(urosaurus[&&NHX:TOL=17596],(sator[&&NHX:TOL=17598],sceloporus[&&NHX:TOL=17599])[&&NHX:TOL=17597])[&&NHX:TOL=17595])sceloporus group[&&NHX:TOL=17593])phrynosomatidae[&&NHX:TOL=17587])iguania[&&NHX:TOL=17559],(gekkota[&&NHX:TOL=17561],dibamidae[&&NHX:TOL=17562],serpentes[&&NHX:TOL=17563],amphisbaenia[&&NHX:TOL=17564],(scincoidea[&&NHX:TOL=17566],lacertoidea[&&NHX:TOL=17567])scincomorpha[&&NHX:TOL=17565],(anguidae[&&NHX:TOL=17569],xenosauridae[&&NHX:TOL=17570],varanoidea[&&NHX:TOL=17571])anguimorpha[&&NHX:TOL=17568])scleroglossa[&&NHX:TOL=17560])squamata[&&NHX:TOL=14933],(gephyrosaurus[&&NHX:EXT=Y:TOL=14935],sphenodontida[&&NHX:TOL=14936])rhynchocephalia[&&NHX:TOL=14934])lepidosauria[&&NHX:TOL=14932])[&&NHX:TOL=14930])lepidosauromorpha[&&NHX:TOL=14917],sauropterygia[&&NHX:EXT=Y:TOL=14915],ichthyosauria[&&NHX:EXT=Y:TOL=14914])sauria[&&NHX:TOL=14913],claudiosaurus[&&NHX:EXT=Y:TOL=14912],younginiformes[&&NHX:EXT=Y:TOL=14911],heleosuchus[&&NHX:EXT=Y:TOL=14910],galesphyrus[&&NHX:EXT=Y:TOL=14909],heleosaurus[&&NHX:EXT=Y:TOL=14908])[&&NHX:TOL=14907],apsisaurus[&&NHX:EXT=Y:TOL=14906])[&&NHX:TOL=14905],coelurosauravus[&&NHX:EXT=Y:TOL=14904])[&&NHX:TOL=14903],araeoscelidia[&&NHX:EXT=Y:TOL=14902])diapsida[&&NHX:TOL=14866])[&&NHX:TOL=14864])romeriida[&&NHX:TOL=14862])reptilia[&&NHX:TOL=14846])amniota[&&NHX:TOL=14990],diadectomorpha[&&NHX:EXT=Y:TOL=14991])[&&NHX:TOL=14989],solenodonsaurus janenschi[&&NHX:EXT=Y:TOL=14992])reptiliomorpha[&&NHX:TOL=14988],(((((((triadobatrachus massinoti[&&NHX:EXT=Y:TOL=16962],(prosalirus bitis[&&NHX:EXT=Y:TOL=106168],vieraella herbsti[&&NHX:EXT=Y:TOL=16964],notobatrachus degiustoi[&&NHX:EXT=Y:TOL=16965],(((ascaphus truei[&&NHX:TOL=106170],ascaphus montanus[&&NHX:TOL=106171])ascaphus[&&NHX:TOL=16966],((leiopelma markhami[&&NHX:EXT=Y:TOL=17147],leiopelma auroraensis[&&NHX:EXT=Y:TOL=17148],leiopelma hochstetteri[&&NHX:TOL=17149])[&&NHX:TOL=17146],(leiopelma waitomoensis[&&NHX:EXT=Y:TOL=17151],leiopelma archeyi[&&NHX:TOL=17153],(leiopelma pakeka[&&NHX:TOL=43175],leiopelma hamiltoni[&&NHX:TOL=17152])[&&NHX:TOL=43174])[&&NHX:TOL=17150])leiopelma[&&NHX:TOL=16968])[&&NHX:TOL=106169],(eodiscoglossus santonjae[&&NHX:EXT=Y:TOL=16970],eodiscoglossus oxoniensis[&&NHX:EXT=Y:TOL=106176],(((barbourula busuangensis[&&NHX:TOL=37802],barbourula kalimantanensis[&&NHX:TOL=37803])barbourula[&&NHX:TOL=17005],(((bombina maxima[&&NHX:TOL=37798],bombina fortinuptialis[&&NHX:TOL=37797],bombina microdeladigitora[&&NHX:TOL=37799])[&&NHX:TOL=133689],bombina lichuanensis[&&NHX:TOL=42205])subgenus grobina[&&NHX:TOL=133688],(bombina orientalis[&&NHX:TOL=37800],(bombina bombina[&&NHX:TOL=37796],(bombina pachypus[&&NHX:TOL=43191],bombina variegata[&&NHX:TOL=37801])[&&NHX:TOL=133692])[&&NHX:TOL=133691])subgenus bombina[&&NHX:TOL=133690])bombina[&&NHX:TOL=17004])bombinatoridae[&&NHX:TOL=16971],(spondylophryne[&&NHX:EXT=Y:TOL=17049],scotiophryne[&&NHX:EXT=Y:TOL=17050],prodiscoglossus[&&NHX:EXT=Y:TOL=17051],pelophilus[&&NHX:EXT=Y:TOL=17052],paradiscoglossus[&&NHX:EXT=Y:TOL=17053],latonia[&&NHX:EXT=Y:TOL=17054],baranophrys[&&NHX:EXT=Y:TOL=17055],(alytes cisternasii[&&NHX:TOL=37516],alytes dickhilleni[&&NHX:TOL=37517],alytes maurus[&&NHX:TOL=38211],alytes muletensis[&&NHX:TOL=37518],alytes obstetricans[&&NHX:TOL=37519])alytes[&&NHX:TOL=17056],(discoglossus galganoi[&&NHX:TOL=49931],discoglossus montalenti[&&NHX:TOL=37520],discoglossus nigriventer[&&NHX:TOL=37521],discoglossus pictus[&&NHX:TOL=37522],discoglossus sardus[&&NHX:TOL=37523],discoglossus jeanneae[&&NHX:TOL=42204])discoglossus[&&NHX:TOL=17057])discoglossidae[&&NHX:TOL=16973])[&&NHX:TOL=106172],(((rhadinosteus parvus[&&NHX:EXT=Y:TOL=106174],(chelomophrynus bayi[&&NHX:EXT=Y:TOL=17526],((rhinophrynus dorsalis[&&NHX:TOL=17528],rhinophrynus sp.[&&NHX:EXT=Y:TOL=17529])rhinophrynus[&&NHX:TOL=17527],(eorhinophrynus sp.[&&NHX:EXT=Y:TOL=133698],eorhinophrynus septentrionalis[&&NHX:EXT=Y:TOL=133699])eorhinophrynus[&&NHX:EXT=Y:TOL=17524])[&&NHX:TOL=133687])[&&NHX:TOL=17525])rhinophrynidae[&&NHX:TOL=16982],((cordicephalus[&&NHX:EXT=Y:TOL=17411],eoxenopoides[&&NHX:EXT=Y:TOL=17412],saltenia[&&NHX:EXT=Y:TOL=17413],shomronella[&&NHX:EXT=Y:TOL=17414],thoraciliacus[&&NHX:EXT=Y:TOL=17415])pipids[&&NHX:EXT=Y:TOL=16984],(albionbatrachus[&&NHX:EXT=Y:TOL=17377],lithobatrachus[&&NHX:EXT=Y:TOL=17378],neusibatrachus[&&NHX:EXT=Y:TOL=17379],palaeobatrachus[&&NHX:EXT=Y:TOL=17380],pliobatrachus[&&NHX:EXT=Y:TOL=17381])palaeobatrachidae[&&NHX:EXT=Y:TOL=16985],(((xenopus amieti[&&NHX:TOL=42169],xenopus andrei[&&NHX:TOL=42170],xenopus borealis[&&NHX:TOL=42171],xenopus boumbaensis[&&NHX:TOL=42172],xenopus clivii[&&NHX:TOL=42173],xenopus fraseri[&&NHX:TOL=42174],xenopus gilli[&&NHX:TOL=42175],xenopus laevis[&&NHX:TOL=50173],xenopus largeni[&&NHX:TOL=42176],xenopus longipes[&&NHX:TOL=42177],xenopus muelleri[&&NHX:TOL=42178],xenopus pascuali[&&NHX:EXT=Y:TOL=17402],xenopus pygmaeus[&&NHX:TOL=42179],xenopus ruwenzoriensis[&&NHX:TOL=42180],xenopus vestitus[&&NHX:TOL=42181],xenopus wittei[&&NHX:TOL=42182])xenopus[&&NHX:TOL=17401],(silurana epitropicalis[&&NHX:TOL=42183],silurana petersii[&&NHX:TOL=50174],silurana tropicalis[&&NHX:TOL=42184])silurana[&&NHX:TOL=17403])[&&NHX:TOL=17399],xenopus romeri[&&NHX:TOL=17404],((hymenochirus[&&NHX:TOL=17407],pseudhymenochirus merlini[&&NHX:TOL=17408])[&&NHX:TOL=17406],pipa[&&NHX:TOL=17409])[&&NHX:TOL=17405])pipidae[&&NHX:TOL=16986])pipimorpha[&&NHX:TOL=16983])pipoidea[&&NHX:TOL=16981],(((aralobatrachus[&&NHX:EXT=Y:TOL=17061],eopelobates[&&NHX:EXT=Y:TOL=17062],kizylkuma[&&NHX:EXT=Y:TOL=17063])eopelobatinae[&&NHX:EXT=Y:TOL=16977],(((scaphiopus holbrookii[&&NHX:TOL=42199],scaphiopus hurterii[&&NHX:TOL=42200])[&&NHX:TOL=106214],scaphiopus couchii[&&NHX:TOL=43178])scaphiopus[&&NHX:TOL=17387],(spea bombifrons[&&NHX:TOL=42201],spea hammondii[&&NHX:TOL=43184],spea intermontana[&&NHX:TOL=42202],spea multiplicata[&&NHX:TOL=42203])spea[&&NHX:TOL=17388])scaphiopodidae[&&NHX:TOL=106213],((macropelobates[&&NHX:EXT=Y:TOL=17384],(pelobates cultripes[&&NHX:TOL=42195],pelobates fuscus[&&NHX:TOL=42196],pelobates syriacus[&&NHX:TOL=42197],pelobates varaldii[&&NHX:TOL=42198])pelobates[&&NHX:TOL=17385])pelobatidae[&&NHX:TOL=16979],(propelodytes[&&NHX:EXT=Y:TOL=17390],(miopelodytes[&&NHX:EXT=Y:TOL=17392],(pelodytes caucasicus[&&NHX:TOL=17394],pelodytes ibericus[&&NHX:TOL=43177],(pelodytes arevacus[&&NHX:EXT=Y:TOL=17396],pelodytes punctatus[&&NHX:TOL=17397])[&&NHX:TOL=17395])pelodytes[&&NHX:TOL=17393])[&&NHX:TOL=17391])pelodytidae[&&NHX:TOL=16980],(atympanophrys[&&NHX:TOL=50022],brachytarsophrys[&&NHX:TOL=17285],leptobrachella[&&NHX:TOL=17286],leptobrachium[&&NHX:TOL=38149],leptobrachium[&&NHX:TOL=17287],leptolalax[&&NHX:TOL=17288],megophrys[&&NHX:TOL=17289],ophryophryne[&&NHX:TOL=38185],oreolalax[&&NHX:TOL=42209],scutiger[&&NHX:TOL=17290],vibrissaphora[&&NHX:TOL=38206])megophryidae[&&NHX:TOL=16978])[&&NHX:TOL=106211])pelobatoidea[&&NHX:TOL=16976],(((((limnomedusa macroglossa[&&NHX:TOL=17168],hydrolaetare[&&NHX:TOL=49227],telmatobiidae[&&NHX:TOL=38265],(adenomera[&&NHX:TOL=17160],(edalorhina[&&NHX:TOL=17162],(hydrolaetare[&&NHX:TOL=17164],(leptodactylus[&&NHX:TOL=17166],((lithodytes[&&NHX:TOL=17170],(paratelmatobius[&&NHX:TOL=17172],((physalaemus aguirrei[&&NHX:TOL=17204],(physalaemus albifrons[&&NHX:TOL=17206],(physalaemus albonotatus[&&NHX:TOL=17208],(physalaemus barrioi[&&NHX:TOL=17210],(physalaemus biligonigerus[&&NHX:TOL=17212],(physalaemus bokermanni[&&NHX:TOL=17214],(physalaemus centralis[&&NHX:TOL=17216],(physalaemus cicada[&&NHX:TOL=17218],(physalaemus coloradorum[&&NHX:TOL=17220],(physalaemus crombiei[&&NHX:TOL=17222],(physalaemus cuvieri[&&NHX:TOL=17224],(physalaemus enesefae[&&NHX:TOL=17226],(physalaemus ephippifer[&&NHX:TOL=17228],(physalaemus evangelistai[&&NHX:TOL=17230],(physalaemus fernandezae[&&NHX:TOL=17232],(physalaemus fischeri[&&NHX:TOL=17234],(physalaemus fuscomaculatus[&&NHX:TOL=17236],(physalaemus gracilis[&&NHX:TOL=17238],(physalaemus henselii[&&NHX:TOL=17240],(physalaemus jordanensis[&&NHX:TOL=17242],(physalaemus kroyeri[&&NHX:TOL=17244],(physalaemus lisei[&&NHX:TOL=17246],(physalaemus maculiventris[&&NHX:TOL=17248],(physalaemus moreirae[&&NHX:TOL=17250],(physalaemus nanus[&&NHX:TOL=17252],(physalaemus nattereri[&&NHX:TOL=17254],(physalaemus obtectus[&&NHX:TOL=17256],(physalaemus olfersii[&&NHX:TOL=17258],(physalaemus petersi[&&NHX:TOL=17260],(physalaemus pustulatus[&&NHX:TOL=17262],(physalaemus pustulosus[&&NHX:TOL=17264],(physalaemus riograndensis[&&NHX:TOL=17266],(physalaemus santafecinus[&&NHX:TOL=17268],(physalaemus signifer[&&NHX:TOL=17270],physalaemus soaresi[&&NHX:TOL=17271])[&&NHX:TOL=17269])[&&NHX:TOL=17267])[&&NHX:TOL=17265])[&&NHX:TOL=17263])[&&NHX:TOL=17261])[&&NHX:TOL=17259])[&&NHX:TOL=17257])[&&NHX:TOL=17255])[&&NHX:TOL=17253])[&&NHX:TOL=17251])[&&NHX:TOL=17249])[&&NHX:TOL=17247])[&&NHX:TOL=17245])[&&NHX:TOL=17243])[&&NHX:TOL=17241])[&&NHX:TOL=17239])[&&NHX:TOL=17237])[&&NHX:TOL=17235])[&&NHX:TOL=17233])[&&NHX:TOL=17231])[&&NHX:TOL=17229])[&&NHX:TOL=17227])[&&NHX:TOL=17225])[&&NHX:TOL=17223])[&&NHX:TOL=17221])[&&NHX:TOL=17219])[&&NHX:TOL=17217])[&&NHX:TOL=17215])[&&NHX:TOL=17213])[&&NHX:TOL=17211])[&&NHX:TOL=17209])[&&NHX:TOL=17207])[&&NHX:TOL=17205])physalaemus[&&NHX:TOL=17174],(pleurodema[&&NHX:TOL=17176],(pseudopaludicola[&&NHX:TOL=17178],vanzolinius[&&NHX:TOL=17179])[&&NHX:TOL=17177])[&&NHX:TOL=17175])[&&NHX:TOL=17173])[&&NHX:TOL=17171])[&&NHX:TOL=17169])[&&NHX:TOL=17167])[&&NHX:TOL=17165])[&&NHX:TOL=17163])[&&NHX:TOL=17161])leptodactylinae[&&NHX:TOL=17158],hylodinae[&&NHX:TOL=17157],ceratophryinae[&&NHX:TOL=17155],eleutherodactylinae[&&NHX:TOL=17156],(brachycephalus ephippium[&&NHX:TOL=17007],psyllophryne didactyla[&&NHX:TOL=17008])brachycephalidae[&&NHX:TOL=16940],((rhinoderma darwinii[&&NHX:TOL=17521],rhinoderma rufum[&&NHX:TOL=17522])rhinoderma[&&NHX:TOL=16948],insuetophrynus acarpicus[&&NHX:TOL=38305])rhinodermatidae[&&NHX:TOL=133826],(alsodes[&&NHX:TOL=38266],batrachyla[&&NHX:TOL=38289],hylorina sylvatica[&&NHX:TOL=38304],eusophus[&&NHX:TOL=38295],atelognathus[&&NHX:TOL=38278])alsodidae[&&NHX:TOL=133825],(odontophrynus[&&NHX:TOL=48384],macrogenioglottus alipioi[&&NHX:TOL=48383],proceratophrys[&&NHX:TOL=48394])odontophrynidae[&&NHX:TOL=133734],(aromobates[&&NHX:TOL=17041],colostethus[&&NHX:TOL=17042],dendrobates[&&NHX:TOL=17043],epipedobates[&&NHX:TOL=17044],mannophryne[&&NHX:TOL=17045],minyobates[&&NHX:TOL=17046],phyllobates[&&NHX:TOL=17047])dendrobatidae[&&NHX:TOL=16956],((stefania[&&NHX:TOL=17084],fritziana[&&NHX:TOL=17085],flectonotus[&&NHX:TOL=17086],cryptobatrachus[&&NHX:TOL=17087],hemiphractus[&&NHX:TOL=17088],gastrotheca[&&NHX:TOL=17089],amphignathodon[&&NHX:TOL=17090])hemiphractinae[&&NHX:TOL=17079],(triprion[&&NHX:TOL=17092],trachycephalus[&&NHX:TOL=17093],sphaenorhynchus[&&NHX:TOL=17094],ptychohyla[&&NHX:TOL=17095],pternohyla[&&NHX:TOL=17096],proacris[&&NHX:EXT=Y:TOL=17097],plectrohyla[&&NHX:TOL=17098],phyllodytes[&&NHX:TOL=17099],phrynohyas[&&NHX:TOL=17100],osteopilus[&&NHX:TOL=17101],osteocephalus[&&NHX:TOL=17102],ololygon[&&NHX:TOL=17103],nyctimantis[&&NHX:TOL=17104],corythomantis[&&NHX:TOL=17105],calyptahyla[&&NHX:TOL=17106],argenteohyla[&&NHX:TOL=17107],aplatodiscus[&&NHX:TOL=17108],aparasphenodon[&&NHX:TOL=17109],anotheca[&&NHX:TOL=17110],pseudacris[&&NHX:TOL=17111],limnaeodus[&&NHX:TOL=17112],acris[&&NHX:TOL=17113],hyla[&&NHX:TOL=17114],smilisca[&&NHX:TOL=17115],allophryne[&&NHX:TOL=17116])hylinae[&&NHX:TOL=17080],(austrlobatrachus[&&NHX:EXT=Y:TOL=17118],litoria[&&NHX:TOL=17119],cyclorana[&&NHX:TOL=17120],nyctimystes[&&NHX:TOL=17121])pelodryadinae[&&NHX:TOL=17081],(phrynomedusa[&&NHX:TOL=17123],agalychnis[&&NHX:TOL=17124],phyllomedusa[&&NHX:TOL=17125],pachymedusa[&&NHX:TOL=17126])phyllomedusinae[&&NHX:TOL=17082])hylidae[&&NHX:TOL=16950],((centrolene[&&NHX:TOL=17037],hyalinobatrachium[&&NHX:TOL=17038],cochranella[&&NHX:TOL=17039])centrolenidae[&&NHX:TOL=16952],allophryne ruthveni[&&NHX:TOL=16939])[&&NHX:TOL=133736],(adenomus[&&NHX:TOL=33247],altiphrynoides malcolmi[&&NHX:TOL=33162],andinophryne[&&NHX:TOL=33163],ansonia[&&NHX:TOL=33167],atelophryniscus chrysophorus[&&NHX:TOL=33187],(atelopus andinus[&&NHX:TOL=43194],atelopus angelito[&&NHX:TOL=43195],atelopus arsyecue[&&NHX:TOL=43196],atelopus arthuri[&&NHX:TOL=33188],atelopus balios[&&NHX:TOL=33189],atelopus bomolochos[&&NHX:TOL=33190],atelopus boulengeri[&&NHX:TOL=33191],atelopus carauta[&&NHX:TOL=33192],atelopus carbonerensis[&&NHX:TOL=33193],atelopus carrikeri[&&NHX:TOL=33194],atelopus certus[&&NHX:TOL=33195],atelopus chiriquiensis[&&NHX:TOL=33196],atelopus chocoensis[&&NHX:TOL=43197],atelopus chrysocorallus[&&NHX:TOL=33197],atelopus coynei[&&NHX:TOL=33198],atelopus cruciger[&&NHX:TOL=33199],atelopus dimorphus[&&NHX:TOL=43198],atelopus ebenoides[&&NHX:TOL=33200],atelopus elegans[&&NHX:TOL=33201],atelopus erythropus[&&NHX:TOL=33202],atelopus eusebianus[&&NHX:TOL=33203],atelopus exiguus[&&NHX:TOL=43199],atelopus farci[&&NHX:TOL=33204],atelopus famelicus[&&NHX:TOL=33205],atelopus flavescens[&&NHX:TOL=33206],atelopus franciscus[&&NHX:TOL=33207],atelopus galactogaster[&&NHX:TOL=33208],atelopus glyphus[&&NHX:TOL=33209],atelopus guanujo[&&NHX:TOL=43200],atelopus guitarraensis[&&NHX:TOL=43201],atelopus halihelos[&&NHX:TOL=33210],atelopus ignescens[&&NHX:TOL=43202],atelopus laetissimus[&&NHX:TOL=33211],atelopus karrikeri[&&NHX:TOL=33212],atelopus limosus[&&NHX:TOL=43203],atelopus longibrachius[&&NHX:TOL=33213],atelopus longirostris[&&NHX:TOL=33214],atelopus lozanoi[&&NHX:TOL=43204],atelopus lynchi[&&NHX:TOL=33215],atelopus mandingues[&&NHX:TOL=43205],atelopus mindoensis[&&NHX:TOL=33216],atelopus minutulus[&&NHX:TOL=33217],atelopus mucubajiensis[&&NHX:TOL=33218],atelopus muisca[&&NHX:TOL=33219],atelopus nahumae[&&NHX:TOL=33220],atelopus nanay[&&NHX:TOL=43206],atelopus nepiozomus[&&NHX:TOL=33221],atelopus nicefori[&&NHX:TOL=33222],atelopus oxyrhynchus[&&NHX:TOL=33223],atelopus pachydermus[&&NHX:TOL=33224],atelopus palmatus[&&NHX:TOL=33225],atelopus pedimarmoratus[&&NHX:TOL=33226],atelopus peruensis[&&NHX:TOL=33227],atelopus petriruizi[&&NHX:TOL=43207],atelopus pictiventris[&&NHX:TOL=33228],atelopus pinangoi[&&NHX:TOL=33229],atelopus planispina[&&NHX:TOL=33230],atelopus pulcher[&&NHX:TOL=43208],atelopus quimbaya[&&NHX:TOL=33231],atelopus reticulatus[&&NHX:TOL=43209],atelopus sanjosei[&&NHX:TOL=33232],atelopus seminiferus[&&NHX:TOL=33233],atelopus senex[&&NHX:TOL=33234],atelopus sernai[&&NHX:TOL=33235],atelopus simulatus[&&NHX:TOL=33236],atelopus siranus[&&NHX:TOL=43210],atelopus sonsonensis[&&NHX:TOL=43211],atelopus sorianoi[&&NHX:TOL=33237],atelopus spumarius[&&NHX:TOL=33238],atelopus spurrelli[&&NHX:TOL=33239],atelopus subornatus[&&NHX:TOL=33240],atelopus tamaensis[&&NHX:TOL=33241],atelopus tricolor[&&NHX:TOL=33242],atelopus varius[&&NHX:TOL=33243],atelopus vogli[&&NHX:TOL=43212],atelopus walkeri[&&NHX:TOL=33244],atelopus zeteki[&&NHX:TOL=33245])atelopus[&&NHX:TOL=17011],(bufo achalensis[&&NHX:TOL=23176],bufo achavali[&&NHX:TOL=49400],bufo acutirostris[&&NHX:TOL=23177],bufo ailaoanus[&&NHX:TOL=23178],bufo alvarius[&&NHX:TOL=23179],bufo amabilis[&&NHX:TOL=23180],bufo amatolicus[&&NHX:TOL=23181],bufo amboroensis[&&NHX:TOL=23182],bufo anderssoni[&&NHX:TOL=23184],bufo andrewsi[&&NHX:TOL=23185],bufo angusticeps[&&NHX:TOL=23186],bufo arabicus[&&NHX:TOL=23187],bufo arborescandens[&&NHX:TOL=23188],bufo arenarum[&&NHX:TOL=23189],bufo arequipensis[&&NHX:TOL=23190],bufo arunco[&&NHX:TOL=23191],bufo asmarae[&&NHX:TOL=23192],bufo asper[&&NHX:TOL=23193],bufo aspinius[&&NHX:TOL=23194],bufo atacamensis[&&NHX:TOL=23195],bufo atukoralei[&&NHX:TOL=23196],bufo bankorensis[&&NHX:TOL=23197],bufo beddomii[&&NHX:TOL=23199],bufo beebei[&&NHX:TOL=23200],bufo beiranus[&&NHX:TOL=23201],bufo bergi[&&NHX:TOL=23202],bufo biporcatus[&&NHX:TOL=23203],bufo blanfordii[&&NHX:TOL=23204],bufo blombergi[&&NHX:TOL=23205],bufo bocourti[&&NHX:TOL=23206],bufo brauni[&&NHX:TOL=23208],bufo brevirostris[&&NHX:TOL=23209],bufo brongersmai[&&NHX:TOL=23210],bufo buchneri[&&NHX:TOL=23211],bufo bufo[&&NHX:TOL=23212],bufo burmanus[&&NHX:TOL=23213],bufo caeruleostictus[&&NHX:TOL=23214],bufo calamita[&&NHX:TOL=23215],bufo camerunensis[&&NHX:TOL=23217],bufo campbelli[&&NHX:TOL=23218],bufo canaliferus[&&NHX:TOL=23219],bufo castaneoticus[&&NHX:TOL=23221],bufo cavifrons[&&NHX:TOL=23223],bufo celebensis[&&NHX:TOL=23224],bufo ceratophrys[&&NHX:TOL=23225],bufo chavin[&&NHX:TOL=23226],bufo chudeaui[&&NHX:TOL=23227],bufo claviger[&&NHX:TOL=23228],bufo coccifer[&&NHX:TOL=23229],bufo compactilis[&&NHX:TOL=23231],bufo coniferus[&&NHX:TOL=23232],bufo cophotis[&&NHX:TOL=23233],bufo corynetes[&&NHX:TOL=23234],bufo cristatus[&&NHX:TOL=23235],bufo cristiglans[&&NHX:TOL=23236],bufo cristinae[&&NHX:TOL=23237],bufo crocus[&&NHX:TOL=49401],bufo crucifer[&&NHX:TOL=23238],bufo cryptotympanicus[&&NHX:TOL=23239],bufo cycladen[&&NHX:TOL=23240],bufo cyphosus[&&NHX:TOL=23241],bufo damaranus[&&NHX:TOL=23242],bufo danatensis[&&NHX:TOL=23243],bufo danielae[&&NHX:TOL=23244],bufo dapsilis[&&NHX:TOL=23245],bufo dhufarensis[&&NHX:TOL=23247],bufo diptychus[&&NHX:TOL=23248],bufo divergens[&&NHX:TOL=23249],bufo djohongensis[&&NHX:TOL=23250],bufo dodsoni[&&NHX:TOL=23251],bufo dombensis[&&NHX:TOL=23252],bufo dorbignyi[&&NHX:TOL=23253],bufo fastidiosus[&&NHX:TOL=23256],bufo fenoulheti[&&NHX:TOL=23257],bufo fernandezae[&&NHX:TOL=23258],bufo fissipes[&&NHX:TOL=23259],bufo fuliginatus[&&NHX:TOL=23263],bufo funereus[&&NHX:TOL=23264],bufo gabbi[&&NHX:TOL=23266],bufo galeatus[&&NHX:TOL=23267],bufo gallardoi[&&NHX:TOL=23268],bufo gargarizans[&&NHX:TOL=23269],bufo gariepensis[&&NHX:TOL=23270],bufo garmani[&&NHX:TOL=23271],bufo gemmifer[&&NHX:TOL=23272],bufo glaberrimus[&&NHX:TOL=23273],bufo gnustae[&&NHX:TOL=23274],bufo gracilipes[&&NHX:TOL=23275],bufo grandisonae[&&NHX:TOL=23276],bufo granulosus[&&NHX:TOL=23277],bufo guentheri[&&NHX:TOL=23278],bufo guttatus[&&NHX:TOL=23280],bufo gutturalis[&&NHX:TOL=23281],bufo hadramautinus[&&NHX:TOL=23282],bufo haematiticus[&&NHX:TOL=23283],bufo himalayanus[&&NHX:TOL=23285],bufo hoeschi[&&NHX:TOL=23286],bufo holdridgei[&&NHX:TOL=23287],bufo hololius[&&NHX:TOL=23288],(((((((((((bufo houstonensis[&&NHX:TOL=23289],bufo americanus[&&NHX:TOL=23183],bufo velatus[&&NHX:TOL=133672],bufo fowleri[&&NHX:TOL=23261])[&&NHX:TOL=133671],(bufo hemiophrys[&&NHX:TOL=23284],bufo baxteri[&&NHX:TOL=23198])[&&NHX:TOL=133673])[&&NHX:TOL=133670],bufo woodhousii[&&NHX:TOL=23429])[&&NHX:TOL=133669],bufo terrestris[&&NHX:TOL=23407])[&&NHX:TOL=133668],(bufo californicus[&&NHX:TOL=23216],bufo microscaphus[&&NHX:TOL=23336])[&&NHX:TOL=133674])[&&NHX:TOL=133667],bufo cognatus[&&NHX:TOL=23230])[&&NHX:TOL=133666],bufo speciosus[&&NHX:TOL=23391])[&&NHX:TOL=133665],(bufo kelloggi[&&NHX:TOL=23304],bufo retiformis[&&NHX:TOL=23378],bufo debilis[&&NHX:TOL=23246])bufo debilis group[&&NHX:TOL=133675])[&&NHX:TOL=133664],bufo quercicus[&&NHX:TOL=23373])[&&NHX:TOL=133663],bufo punctatus[&&NHX:TOL=23369])[&&NHX:TOL=133662],(bufo nelsoni[&&NHX:TOL=23342],bufo exsul[&&NHX:TOL=23255],bufo canorus[&&NHX:TOL=23220],bufo boreas[&&NHX:TOL=23207])bufo boreas group[&&NHX:TOL=133680])nearctic bufo clade[&&NHX:TOL=133679],bufo hypomelas[&&NHX:TOL=23290],bufo ibarrai[&&NHX:TOL=23291],bufo ictericus[&&NHX:TOL=23292],bufo inca[&&NHX:TOL=23293],bufo intermedius[&&NHX:TOL=23294],bufo inyangae[&&NHX:TOL=23295],bufo iserni[&&NHX:TOL=23296],bufo japonicus[&&NHX:TOL=23297],bufo jimi[&&NHX:TOL=23298],bufo justinianoi[&&NHX:TOL=23299],bufo juxtasper[&&NHX:TOL=23300],bufo kabischi[&&NHX:TOL=23301],bufo kassasii[&&NHX:TOL=23302],bufo kavangensis[&&NHX:TOL=23303],bufo kerinyagae[&&NHX:TOL=23305],bufo kisoloensis[&&NHX:TOL=23306],bufo kotagamai[&&NHX:TOL=23307],bufo koynayensis[&&NHX:TOL=23308],bufo kumquat[&&NHX:TOL=23309],bufo langanoensis[&&NHX:TOL=23310],bufo latastii[&&NHX:TOL=23311],bufo latifrons[&&NHX:TOL=23312],bufo lemairii[&&NHX:TOL=23313],bufo leucomyos[&&NHX:TOL=23315],bufo limensis[&&NHX:TOL=23316],bufo lindneri[&&NHX:TOL=23317],(bufo longinasus[&&NHX:TOL=23318],bufo lemur[&&NHX:TOL=23314],bufo florentinoi[&&NHX:TOL=133686],bufo peltocephalus[&&NHX:TOL=23357],bufo gundlachi[&&NHX:TOL=23279],bufo fluviaticus[&&NHX:TOL=23260],bufo empusus[&&NHX:TOL=23254],bufo taladai[&&NHX:TOL=23406],bufo cataulaciceps[&&NHX:TOL=23222],bufo fractus[&&NHX:TOL=23262],bufo fustiger[&&NHX:TOL=23265])peltophryne[&&NHX:TOL=133685],bufo lonnbergi[&&NHX:TOL=23319],bufo luetkenii[&&NHX:TOL=23320],bufo lughenisis[&&NHX:TOL=23321],bufo lughensis[&&NHX:TOL=23322],bufo luristanicus[&&NHX:TOL=23323],bufo macrocristatus[&&NHX:TOL=23324],bufo macrotis[&&NHX:TOL=23325],bufo maculatus[&&NHX:TOL=23326],bufo margaritifer[&&NHX:TOL=23327],bufo marinus[&&NHX:TOL=23328],bufo marmoreus[&&NHX:TOL=23329],bufo mauritanicus[&&NHX:TOL=23330],bufo mazatlanensis[&&NHX:TOL=23331],bufo melanochlorus[&&NHX:TOL=23332],bufo melanopleura[&&NHX:TOL=23333],bufo melanostictus[&&NHX:TOL=23334],bufo mexicanus[&&NHX:TOL=23335],bufo microtympanum[&&NHX:TOL=23337],bufo minshanicus[&&NHX:TOL=23338],bufo mocquardi[&&NHX:TOL=23339],bufo nasicus[&&NHX:TOL=23340],bufo nebulifer[&&NHX:TOL=23341],bufo nesiotes[&&NHX:TOL=23343],bufo noellerti[&&NHX:TOL=23344],bufo nyikae[&&NHX:TOL=23345],bufo oblongus[&&NHX:TOL=23346],bufo occidentalis[&&NHX:TOL=23347],bufo ocellatus[&&NHX:TOL=23348],bufo olivaceus[&&NHX:TOL=23349],bufo pageoti[&&NHX:TOL=23350],bufo pantherinus[&&NHX:TOL=23351],bufo paracnemis[&&NHX:TOL=23352],bufo pardalis[&&NHX:TOL=23353],bufo parietalis[&&NHX:TOL=23354],bufo parkeri[&&NHX:TOL=23355],bufo parvus[&&NHX:TOL=23356],bufo pentoni[&&NHX:TOL=23358],bufo periglenes[&&NHX:TOL=23359],bufo peripatetes[&&NHX:TOL=23360],bufo perplexus[&&NHX:TOL=23361],bufo perreti[&&NHX:TOL=23362],bufo pewzowi[&&NHX:TOL=23363],bufo philippinicus[&&NHX:TOL=23364],bufo poeppigii[&&NHX:TOL=23365],bufo poweri[&&NHX:TOL=23366],bufo proboscideus[&&NHX:TOL=23367],bufo pseudoraddei[&&NHX:TOL=23368],bufo pygmaeus[&&NHX:TOL=23370],bufo quadriporcatus[&&NHX:TOL=23371],bufo quechua[&&NHX:TOL=23372],bufo raddei[&&NHX:TOL=23374],bufo rangeri[&&NHX:TOL=23375],bufo reesi[&&NHX:TOL=23376],bufo regularis[&&NHX:TOL=23377],bufo robinsoni[&&NHX:TOL=23379],bufo roqueanus[&&NHX:TOL=23380],bufo rubropunctatus[&&NHX:TOL=23381],bufo rufus[&&NHX:TOL=23382],bufo rumbolli[&&NHX:TOL=23383],bufo scaber[&&NHX:TOL=23384],bufo schmidti[&&NHX:TOL=23385],bufo schneideri[&&NHX:TOL=23386],bufo scitulus[&&NHX:TOL=49402],bufo sclerocephalus[&&NHX:TOL=23387],bufo scorteccii[&&NHX:TOL=23388],bufo silentvalleyensis[&&NHX:TOL=23389],bufo simus[&&NHX:TOL=23390],bufo spiculatus[&&NHX:TOL=23392],bufo spinulosus[&&NHX:TOL=23393],bufo stanlaii[&&NHX:TOL=23394],bufo steindachneri[&&NHX:TOL=23395],bufo stejnegeri[&&NHX:TOL=23396],bufo sternosignatus[&&NHX:TOL=23397],bufo stomaticus[&&NHX:TOL=23398],bufo stuarti[&&NHX:TOL=23399],bufo sumatranus[&&NHX:TOL=23400],bufo superciliaris[&&NHX:TOL=23401],bufo surdus[&&NHX:TOL=23402],bufo tacanensis[&&NHX:TOL=23403],bufo taiensis[&&NHX:TOL=23404],bufo taitanus[&&NHX:TOL=23405],bufo tibetanus[&&NHX:TOL=23408],bufo tihamicus[&&NHX:TOL=23409],bufo togoensis[&&NHX:TOL=23410],bufo torrenticola[&&NHX:TOL=23411],bufo tuberculatus[&&NHX:TOL=23412],bufo tuberosus[&&NHX:TOL=23413],bufo turkanae[&&NHX:TOL=23414],bufo tutelarius[&&NHX:TOL=23415],bufo urunguensis[&&NHX:TOL=23416],bufo uzunguensis[&&NHX:TOL=23417],bufo valhallae[&&NHX:TOL=23418],bufo valliceps[&&NHX:TOL=23419],bufo variegatus[&&NHX:TOL=23420],bufo vellardi[&&NHX:TOL=23421],bufo veraguensis[&&NHX:TOL=23422],bufo verrucosissimus[&&NHX:TOL=23423],bufo vertebralis[&&NHX:TOL=23424],bufo villiersi[&&NHX:TOL=23425],bufo viridis[&&NHX:TOL=23426],bufo vittatus[&&NHX:TOL=23427],bufo wolongensis[&&NHX:TOL=23428],bufo xeros[&&NHX:TOL=23430])bufo[&&NHX:TOL=17012],bufoides meghalayanus[&&NHX:TOL=17013],capensibufo[&&NHX:TOL=17014],crepidophryne epiotica[&&NHX:TOL=33252],dendrophryniscus[&&NHX:TOL=17016],didynamipus sjostedti[&&NHX:TOL=33260],frostius pernambucensis[&&NHX:TOL=33261],leptophryne[&&NHX:TOL=17019],melanophryniscus[&&NHX:TOL=17020],mertensophryne micranotis[&&NHX:TOL=33276],laurentophryne parkeri[&&NHX:TOL=33262],metaphryniscus sosae[&&NHX:TOL=33277],nectophryne[&&NHX:TOL=17022],nectophrynoides[&&NHX:TOL=17023],nimbaphrynoides[&&NHX:TOL=33285],oreophrynella[&&NHX:TOL=17024],(osornophryne bufoniformis[&&NHX:TOL=33294],osornophryne antisana[&&NHX:TOL=33295],osornophryne guacamayo[&&NHX:TOL=33296],osornophryne percrassa[&&NHX:TOL=33297],osornophryne sumacoensis[&&NHX:TOL=33298],osornophryne talipes[&&NHX:TOL=33299])osornophryne[&&NHX:TOL=17025],parapelophryne scalptus[&&NHX:TOL=33300],pedostibes[&&NHX:TOL=17026],pelophryne[&&NHX:TOL=17027],pseudobufo subasper[&&NHX:TOL=17029],rhamphophryne[&&NHX:TOL=17030],schismaderma carens[&&NHX:TOL=17031],spinophrynoides osgoodi[&&NHX:TOL=36537],stephopaedes[&&NHX:TOL=17032],truebella[&&NHX:TOL=17033],werneria[&&NHX:TOL=17034],wolterstorffina[&&NHX:TOL=17035])bufonidae[&&NHX:TOL=16941])hyloidea[&&NHX:TOL=106196],((((pseudohemisus[&&NHX:TOL=17293],scaphiophryne[&&NHX:TOL=17294])scaphiophryninae[&&NHX:TOL=17292],((asterophrys[&&NHX:TOL=17297],barygenys[&&NHX:TOL=17298],hylophorbus[&&NHX:TOL=17299],pherohapsis[&&NHX:TOL=17300],phrynomantis[&&NHX:TOL=17301],xenobatrachus[&&NHX:TOL=17302],xenorhina[&&NHX:TOL=17303])asterophryinae[&&NHX:TOL=17296],(anodonthyla[&&NHX:TOL=17310],cophyla[&&NHX:TOL=17311],madecassophryne[&&NHX:TOL=17312],mantipus[&&NHX:TOL=17313],paracophyla[&&NHX:TOL=17314],platypelis[&&NHX:TOL=17315],plethodontohyla[&&NHX:TOL=17316],rhombophryne[&&NHX:TOL=17317],stumpffia[&&NHX:TOL=17318])cophylinae[&&NHX:TOL=17309],(calluela[&&NHX:TOL=17320],dyscophus[&&NHX:TOL=17321])dyscophinae[&&NHX:TOL=17319],(choerophryne[&&NHX:TOL=17323],cophixalus[&&NHX:TOL=17324],copiula[&&NHX:TOL=17325],genyophryne[&&NHX:TOL=17326],oreophryne[&&NHX:TOL=17327],sphenophryne[&&NHX:TOL=17328])genyophryninae[&&NHX:TOL=17322],(holophryne[&&NHX:TOL=17330],melanobatrachus[&&NHX:TOL=17331],parhoplophryne[&&NHX:TOL=17332])melanobatrachinae[&&NHX:TOL=17329],(arcovomer[&&NHX:TOL=17334],chaperina[&&NHX:TOL=17335],chiasmocleis[&&NHX:TOL=17336],ctenophryne[&&NHX:TOL=17337],dasypops[&&NHX:TOL=17338],dermatonotus[&&NHX:TOL=17339],elachistocleis[&&NHX:TOL=17340],gastrophryne[&&NHX:TOL=17341],gastrophrynoides[&&NHX:TOL=17342],glossostoma[&&NHX:TOL=17343],glyphoglossus[&&NHX:TOL=17344],hamptophryne[&&NHX:TOL=17345],hypopachus[&&NHX:TOL=17346],hyophryne[&&NHX:TOL=17347],kalophrynus[&&NHX:TOL=17348],kaloula[&&NHX:TOL=17349],metaphrynella[&&NHX:TOL=17350],microhyla[&&NHX:TOL=17351],myersiella[&&NHX:TOL=17352],otophryne[&&NHX:TOL=17353],phrynella[&&NHX:TOL=17354],ramanella[&&NHX:TOL=17355],relictivomer[&&NHX:TOL=17356],stereocyclops[&&NHX:TOL=17357],synapturanus[&&NHX:TOL=17358],syncope[&&NHX:TOL=17359],uperodon[&&NHX:TOL=17360])microhylinae[&&NHX:TOL=17333],phrynomerus[&&NHX:TOL=17361])scoptanura[&&NHX:TOL=17295])microhylidae[&&NHX:TOL=16954],(((hemisus brachydactylum[&&NHX:TOL=17070],hemisus guineensis[&&NHX:TOL=17071],hemisus guttatus[&&NHX:TOL=17072],hemisus marmoratus[&&NHX:TOL=17073],hemisus microscaphus[&&NHX:TOL=17074],hemisus olivaceus[&&NHX:TOL=17075],hemisus perreti[&&NHX:TOL=17076],hemisus wittei[&&NHX:TOL=17077])hemisus[&&NHX:TOL=16955],(breviceps[&&NHX:TOL=17305],callulina[&&NHX:TOL=17306],probreviceps[&&NHX:TOL=17307],spelaeophryne[&&NHX:TOL=17308])brevicipitinae[&&NHX:TOL=17304])node m[&&NHX:TOL=133705],(((astylosternus[&&NHX:TOL=16992],leptodactylodon[&&NHX:TOL=16993],nyctibates[&&NHX:TOL=16994],scotobleps[&&NHX:TOL=16995],trichobatrachus[&&NHX:TOL=16996])astylosterninae[&&NHX:TOL=16991],(arthroleptis[&&NHX:TOL=16998],cardioglossa[&&NHX:TOL=16999],schoutedenella[&&NHX:TOL=17000])arthroleptinae[&&NHX:TOL=16997])arthroleptidae[&&NHX:TOL=16957],((callixalus[&&NHX:TOL=17129],chrysobatrachus[&&NHX:TOL=17130],cryptothylax[&&NHX:TOL=17131],heterixalus[&&NHX:TOL=17132],hyperolius[&&NHX:TOL=17133],opisthothylax[&&NHX:TOL=17134],tachycnemis[&&NHX:TOL=17135])hyperoliinae[&&NHX:TOL=17128],(afrixalus[&&NHX:TOL=17137],kassina[&&NHX:TOL=17138],kassinula[&&NHX:TOL=17139],phlyctimantis[&&NHX:TOL=17140],tornierella[&&NHX:TOL=17141])kassininae[&&NHX:TOL=17136],(acanthixalus[&&NHX:TOL=17143],leptopelis[&&NHX:TOL=17144])leptopelinae[&&NHX:TOL=17142])hyperoliidae[&&NHX:TOL=16959])node o[&&NHX:TOL=133706])node n[&&NHX:TOL=133704])brevicipitiforms[&&NHX:TOL=133702],((afrana[&&NHX:TOL=41219],amietia vertebralis[&&NHX:TOL=41230],amnirana[&&NHX:TOL=41222],amolops[&&NHX:TOL=17430],aubria[&&NHX:TOL=17431],chaparana[&&NHX:TOL=40956],conraua[&&NHX:TOL=17434],euphlyctis[&&NHX:TOL=40974],elachyglossa gyldenstolpei[&&NHX:TOL=17436],fejervarya[&&NHX:TOL=40978],hildebrandtia[&&NHX:TOL=17437],hoplobatrachus[&&NHX:TOL=41000],huia[&&NHX:TOL=41005],indirana[&&NHX:TOL=41010],ingerana[&&NHX:TOL=41020],lankanectes corrugatus[&&NHX:TOL=41029],lanzarana largeni[&&NHX:TOL=17438],limnonectes[&&NHX:TOL=41030],meristogenys[&&NHX:TOL=41076],micrixalus[&&NHX:TOL=17439],minervarya sahyadris[&&NHX:TOL=50201],nannophrys[&&NHX:TOL=17440],nanorana[&&NHX:TOL=17443],nyctibatrachus[&&NHX:TOL=17441],occidozyga[&&NHX:TOL=17444],paa[&&NHX:TOL=41119],((platymantis acrochorda[&&NHX:TOL=41144],platymantis aculeodactyla[&&NHX:TOL=41145],platymantis akarithyma[&&NHX:TOL=41146],platymantis banahao[&&NHX:TOL=50211],platymantis batantae[&&NHX:TOL=41147],platymantis boulengeri[&&NHX:TOL=41148],platymantis browni[&&NHX:TOL=50212],platymantis cheesmanae[&&NHX:TOL=41149],platymantis cornuta[&&NHX:TOL=41150],platymantis corrugata[&&NHX:TOL=41151],platymantis dorsalis[&&NHX:TOL=41152],platymantis gilliardi[&&NHX:TOL=41153],platymantis guentheri[&&NHX:TOL=41154],platymantis guppyi[&&NHX:TOL=41155],platymantis hazelae[&&NHX:TOL=41156],platymantis ingeri[&&NHX:TOL=41157],platymantis insulata[&&NHX:TOL=41158],platymantis isarog[&&NHX:TOL=50213],platymantis lawtoni[&&NHX:TOL=41159],platymantis levigata[&&NHX:TOL=41160],platymantis luzonensis[&&NHX:TOL=50214],platymantis macrops[&&NHX:TOL=41161],platymantis macrosceles[&&NHX:TOL=50215],platymantis magna[&&NHX:TOL=41162],platymantis mamusiorum[&&NHX:TOL=50216],platymantis meyeri[&&NHX:TOL=41163],platymantis mimica[&&NHX:TOL=41164],platymantis mimula[&&NHX:TOL=50217],platymantis montana[&&NHX:TOL=50218],platymantis myersi[&&NHX:TOL=41165],platymantis naomiae[&&NHX:TOL=50219],platymantis neckeri[&&NHX:TOL=41166],platymantis negrosensis[&&NHX:TOL=50220],platymantis nexipus[&&NHX:TOL=50221],platymantis panayensis[&&NHX:TOL=50222],platymantis papuensis[&&NHX:TOL=41167],platymantis parkeri[&&NHX:TOL=41168],platymantis pelewensis[&&NHX:TOL=50223],platymantis polillensis[&&NHX:TOL=41169],platymantis punctata[&&NHX:TOL=41170],platymantis pygmaea[&&NHX:TOL=50224],platymantis rabori[&&NHX:TOL=50225],platymantis rhipiphalca[&&NHX:TOL=41171],platymantis schmidti[&&NHX:TOL=41172],platymantis sierramadrensis[&&NHX:TOL=50226],platymantis solomonis[&&NHX:TOL=41173],platymantis spelaea[&&NHX:TOL=50227],platymantis subterrestris[&&NHX:TOL=41174],platymantis vitiana[&&NHX:TOL=41175],platymantis vitiensis[&&NHX:TOL=41176],platymantis weberi[&&NHX:TOL=41177])platymantis[&&NHX:TOL=17446],palmatorappia solomonis[&&NHX:TOL=17445],ceratobatrachus guentheri[&&NHX:TOL=17433],(discodeles bufoniformis[&&NHX:TOL=40969],discodeles guppyi[&&NHX:TOL=40970],discodeles malukuna[&&NHX:TOL=40971],discodeles opisthodon[&&NHX:TOL=40972],discodeles vogti[&&NHX:TOL=40973])discodeles[&&NHX:TOL=17435],(batrachylodes elegans[&&NHX:TOL=40948],batrachylodes gigas[&&NHX:TOL=40949],batrachylodes mediodiscus[&&NHX:TOL=40950],batrachylodes minutus[&&NHX:TOL=40951],batrachylodes montanus[&&NHX:TOL=40952],batrachylodes trossulus[&&NHX:TOL=40953],batrachylodes vertebralis[&&NHX:TOL=40954],batrachylodes wolfi[&&NHX:TOL=40955])batrachylodes[&&NHX:TOL=17432])platymantines[&&NHX:TOL=133661],pterorana khare[&&NHX:TOL=41241],ptychadena[&&NHX:TOL=17447],pyxicephalus[&&NHX:TOL=17448],sphaerotheca[&&NHX:TOL=41242],staurois[&&NHX:TOL=17450],strongylopus[&&NHX:TOL=17451],tomopterna[&&NHX:TOL=17452],((rana sauteri[&&NHX:TOL=50555],rana sangzhiensis[&&NHX:TOL=50554],rana sanguinea[&&NHX:TOL=50553],rana temporaria[&&NHX:TOL=50581],rana sakuraii[&&NHX:TOL=50552],rana rugosa[&&NHX:TOL=50550],rana raniceps[&&NHX:TOL=50548],rana pyrenaica[&&NHX:TOL=50547],rana pueblae[&&NHX:TOL=50545],rana psaltes[&&NHX:TOL=50544],rana pleuraden[&&NHX:TOL=50541],rana pirica[&&NHX:TOL=50539],rana picturata[&&NHX:TOL=50538],rana persimilis[&&NHX:TOL=50537],rana papua[&&NHX:TOL=50535],rana ornativentris[&&NHX:TOL=50533],rana omeimontis[&&NHX:TOL=50530],rana okinavana[&&NHX:TOL=50529],rana oatesii[&&NHX:TOL=50527],rana novaeguineae[&&NHX:TOL=50526],rana nigrovittata[&&NHX:TOL=50525],rana nigrotympanica[&&NHX:TOL=50524],rana nasuta[&&NHX:TOL=50520],rana narina[&&NHX:TOL=50519],rana multidenticulata[&&NHX:TOL=50517],rana morafkai[&&NHX:TOL=50516],rana montivaga[&&NHX:TOL=50515],rana moluccana[&&NHX:TOL=50514],rana moellendorffi[&&NHX:TOL=50513],rana miopus[&&NHX:TOL=50512],rana minima[&&NHX:TOL=50511],rana milleti[&&NHX:TOL=50510],rana melanomenta[&&NHX:TOL=50508],rana megatympanum[&&NHX:TOL=50507],rana maritima[&&NHX:TOL=50506],rana margariana[&&NHX:TOL=50505],rana margaretae[&&NHX:TOL=50504],rana maosonensis[&&NHX:TOL=50503],rana mangyanum[&&NHX:TOL=50502],rana malabarica[&&NHX:TOL=50501],rana macrops[&&NHX:TOL=50499],rana macrodactyla[&&NHX:TOL=50497],rana macrocnemis[&&NHX:TOL=50496],rana luzonensis[&&NHX:TOL=50495],rana lungshengensis[&&NHX:TOL=50493],rana luctuosa[&&NHX:TOL=50492],rana longicrus[&&NHX:TOL=50491],rana livida[&&NHX:TOL=50490],rana limosespinal[&&NHX:TOL=50489],rana leptoglossa[&&NHX:TOL=50487],rana leporipes[&&NHX:TOL=50486],rana latouchii[&&NHX:TOL=50485],rana laterimaculata[&&NHX:TOL=50484],rana latastei[&&NHX:TOL=50482],rana kurtmuelleri[&&NHX:TOL=50481],rana kunyuensis[&&NHX:TOL=50480],rana kuangwuensis[&&NHX:TOL=50479],rana kreffti[&&NHX:TOL=50478],rana kampeni[&&NHX:TOL=50477],rana johnsi[&&NHX:TOL=50475],rana johni[&&NHX:TOL=50474],rana jingdongensis[&&NHX:TOL=50473],rana jimiensis[&&NHX:TOL=50472],rana japonica[&&NHX:TOL=50471],rana italica[&&NHX:TOL=50470],rana ishikawae[&&NHX:TOL=50469],rana igorota[&&NHX:TOL=50468],rana iberica[&&NHX:TOL=50467],rana humeralis[&&NHX:TOL=50466],rana huanrenensis[&&NHX:TOL=50464],rana hosii[&&NHX:TOL=50463],rana honnorati[&&NHX:TOL=50462],rana holtzi[&&NHX:TOL=50461],rana holsti[&&NHX:TOL=50460],rana hmongorum[&&NHX:TOL=50459],rana hispanica[&&NHX:TOL=50458],rana hejiangensis[&&NHX:TOL=50457],rana hainanensis[&&NHX:TOL=50455],((((rana saharica[&&NHX:TOL=17492],rana perezi[&&NHX:TOL=17493])[&&NHX:TOL=17491],(rana epeirotica[&&NHX:TOL=17495],(rana shqiperica[&&NHX:TOL=17497],(rana lessonae[&&NHX:TOL=17499],(rana cretensis[&&NHX:TOL=17501],(rana cerigensis[&&NHX:TOL=17503],(rana bedriagae[&&NHX:TOL=17505],rana ridibunda[&&NHX:TOL=17506])[&&NHX:TOL=17504])[&&NHX:TOL=17502])[&&NHX:TOL=17500])[&&NHX:TOL=17498])[&&NHX:TOL=17496])[&&NHX:TOL=17494])[&&NHX:TOL=17490],rana terentievi[&&NHX:TOL=17507])western palearctic water frogs[&&NHX:TOL=17479],(rana fukiensis[&&NHX:TOL=17470],rana hubeiensis[&&NHX:TOL=17471],rana lateralis[&&NHX:TOL=17472],rana nigrolineata[&&NHX:TOL=17473],rana nigromaculata[&&NHX:TOL=17474],rana plancyi[&&NHX:TOL=17475],rana porosa[&&NHX:TOL=17476],rana shuchinae[&&NHX:TOL=17477])eastern palearctic water frogs[&&NHX:TOL=17480])rana pelophylax[&&NHX:TOL=17424],rana schmackeri[&&NHX:TOL=50556],rana scutigera[&&NHX:TOL=50557],rana senchalensis[&&NHX:TOL=50558],rana siberu[&&NHX:TOL=50563],rana signata[&&NHX:TOL=50565],rana similis[&&NHX:TOL=50566],rana sinica[&&NHX:TOL=50567],rana spinidactyla[&&NHX:TOL=50569],rana spinulosa[&&NHX:TOL=50570],rana subaspera[&&NHX:TOL=50571],rana supragrisea[&&NHX:TOL=50572],rana supranarina[&&NHX:TOL=50573],rana swinhoana[&&NHX:TOL=50574],rana tagoi[&&NHX:TOL=50576],rana taipehensis[&&NHX:TOL=50578],rana temporalis[&&NHX:TOL=50580],rana tenggerensis[&&NHX:TOL=50582],rana tiannanensis[&&NHX:TOL=50584],rana tientaiensis[&&NHX:TOL=50585],rana tipanan[&&NHX:TOL=50586],rana trankieni[&&NHX:TOL=50588],rana tsushimensis[&&NHX:TOL=50589],rana utsunomiyaorum[&&NHX:TOL=50590],rana varians[&&NHX:TOL=50592],rana versabilis[&&NHX:TOL=50593],rana volkerjane[&&NHX:TOL=50596],rana weiningensis[&&NHX:TOL=50598],rana wuchuanensis[&&NHX:TOL=50599],rana zhengi[&&NHX:TOL=50601],rana zhenhaiensis[&&NHX:TOL=50602],rana guentheri[&&NHX:TOL=50454],rana grisea[&&NHX:TOL=50452],rana grandocula[&&NHX:TOL=50451],rana graminea[&&NHX:TOL=50450],rana grahami[&&NHX:TOL=50449],rana graeca[&&NHX:TOL=50448],rana gracilis[&&NHX:TOL=50447],rana glandulosa[&&NHX:TOL=50446],rana garritor[&&NHX:TOL=50445],rana garoensis[&&NHX:TOL=50444],rana florensis[&&NHX:TOL=50442],rana fasciata[&&NHX:TOL=50441],rana faber[&&NHX:TOL=50440],rana exiliversabilis[&&NHX:TOL=50439],rana everetti[&&NHX:TOL=50438],rana esculenta[&&NHX:TOL=50437],rana erythraea[&&NHX:TOL=50436],rana emelijanovi[&&NHX:TOL=50434],rana elberti[&&NHX:TOL=50433],rana dybowskii[&&NHX:TOL=50432],rana demarchii[&&NHX:TOL=50430],rana debussyi[&&NHX:TOL=50429],rana daunchina[&&NHX:TOL=50428],rana daorum[&&NHX:TOL=50427],rana danieli[&&NHX:TOL=50426],rana dalmatina[&&NHX:TOL=50425],rana daemeli[&&NHX:TOL=50424],rana curtipes[&&NHX:TOL=50423],rana cubitalis[&&NHX:TOL=50422],rana crassiovis[&&NHX:TOL=50420],rana cordofana[&&NHX:TOL=50419],rana chosenica[&&NHX:TOL=50417],rana chloronota[&&NHX:TOL=50416],rana chitwanensis[&&NHX:TOL=50415],rana chichicuahutla[&&NHX:TOL=50414],rana chevronta[&&NHX:TOL=50413],rana chensinensis[&&NHX:TOL=50412],rana charlesdarwini[&&NHX:TOL=50411],rana chapaensis[&&NHX:TOL=50410],rana chaochiaoensis[&&NHX:TOL=50409],rana chalconota[&&NHX:TOL=50408],rana celebensis[&&NHX:TOL=50406],rana camerani[&&NHX:TOL=50402],rana caldwelli[&&NHX:TOL=50401],rana brownorum[&&NHX:TOL=50399],rana bergeri[&&NHX:TOL=50397],rana baramica[&&NHX:TOL=50395],rana bannanica[&&NHX:TOL=50394],rana banaorum[&&NHX:TOL=50393],rana bacboensis[&&NHX:TOL=50392],rana aurata[&&NHX:TOL=50390],rana aurantiaca[&&NHX:TOL=50389],rana attigua[&&NHX:TOL=50388],rana asiatica[&&NHX:TOL=50387],rana arvalis[&&NHX:TOL=50386],rana arfaki[&&NHX:TOL=50385],rana archotaphus[&&NHX:TOL=50384],rana anlungensis[&&NHX:TOL=50383],rana andersonii[&&NHX:TOL=50382],rana amurensis[&&NHX:TOL=50381],rana adenopleura[&&NHX:TOL=50380],(rana boylii[&&NHX:TOL=50398],rana aurora[&&NHX:TOL=50391],rana draytonii[&&NHX:TOL=50431],rana cascadae[&&NHX:TOL=50404],rana luteiventris[&&NHX:TOL=50494],rana muscosa[&&NHX:TOL=50518],rana pretiosa[&&NHX:TOL=50543])amerana[&&NHX:TOL=67137])laurasiarana[&&NHX:TOL=67136],((rana sylvatica[&&NHX:TOL=50575],(rana clamitans[&&NHX:TOL=50418],rana catesbeiana[&&NHX:TOL=50405],rana grylio[&&NHX:TOL=50453],rana heckscheri[&&NHX:TOL=50456],rana okaloossae[&&NHX:TOL=50528],rana septentrionalis[&&NHX:TOL=50559],rana virgatipes[&&NHX:TOL=50595])aquarana[&&NHX:TOL=67138])[&&NHX:TOL=67183],((((rana warszewitschii[&&NHX:TOL=50597],rana vibicaria[&&NHX:TOL=50594])trypheropsis[&&NHX:TOL=67144],rana maculata[&&NHX:TOL=50500])levirana[&&NHX:TOL=67143],(rana bwana[&&NHX:TOL=50400],rana juliani[&&NHX:TOL=50476],rana palmipes[&&NHX:TOL=50534],rana vaillanti[&&NHX:TOL=50591],rana species 1[&&NHX:TOL=67146])lithobates[&&NHX:TOL=67145])ranula[&&NHX:TOL=67142],((rana sierramadrensis[&&NHX:TOL=50564],(rana pustulosa[&&NHX:TOL=50546],rana tarahumarae[&&NHX:TOL=50577],rana zweifeli[&&NHX:TOL=50603],rana psilonota[&&NHX:TOL=67141])zweifelia[&&NHX:TOL=67140])torrentirana[&&NHX:TOL=67139],((rana pipiens[&&NHX:TOL=17425],(rana dunni[&&NHX:TOL=67149],rana chiricahuensis[&&NHX:TOL=67150],rana montezumae[&&NHX:TOL=67151],rana subaquavocalis[&&NHX:TOL=67152],rana species 2[&&NHX:TOL=67153])lacusirana[&&NHX:TOL=67148])stertirana[&&NHX:TOL=67147],((rana capito[&&NHX:TOL=67157],rana areolata[&&NHX:TOL=67158],rana palustris[&&NHX:TOL=67159],rana sevosa[&&NHX:TOL=50560])nenirana[&&NHX:TOL=67156],(rana berlandieri[&&NHX:TOL=67162],rana macroglossa[&&NHX:TOL=50498],rana blairi[&&NHX:TOL=67163],rana forreri[&&NHX:TOL=67164],rana magnaocularis[&&NHX:TOL=67165],rana neovolcanica[&&NHX:TOL=67166],rana omiltemana[&&NHX:TOL=67167],rana onca[&&NHX:TOL=67168],rana spectabilis[&&NHX:TOL=67169],rana s. sphenocephala[&&NHX:TOL=67170],rana s. utricularia[&&NHX:TOL=67171],rana taylori[&&NHX:TOL=67172],rana tlaloci[&&NHX:TOL=67173],rana yavapaiensis[&&NHX:TOL=67174],rana species 3[&&NHX:TOL=67175],rana species 4[&&NHX:TOL=67176],rana species 5[&&NHX:TOL=67177],rana species 6[&&NHX:TOL=67178],rana species 7[&&NHX:TOL=67179],rana species 8[&&NHX:TOL=67180])scurrilirana[&&NHX:TOL=67161])[&&NHX:TOL=67155])pantherana[&&NHX:TOL=67186])[&&NHX:TOL=67185],rana megapoda[&&NHX:TOL=50375],rana fisheri[&&NHX:EXT=Y:TOL=50604],rana miadis[&&NHX:TOL=50509])sierrana[&&NHX:TOL=67184])novirana[&&NHX:TOL=67182])rana[&&NHX:TOL=67181])raninae[&&NHX:TOL=17428],(anhydrophryne rattrayi[&&NHX:TOL=17454],arthroleptella[&&NHX:TOL=17455],arthroleptides[&&NHX:TOL=17456],cacosterum[&&NHX:TOL=17457],dimorphognathus africanus[&&NHX:TOL=17458],ericabatrachus baleensis[&&NHX:TOL=40845],microbatrachella capensis[&&NHX:TOL=40846],natalobatrachus bonebergi[&&NHX:TOL=40847],nothophryne broadleyi[&&NHX:TOL=40848],petropedetes[&&NHX:TOL=17462],phrynobatrachus[&&NHX:TOL=17463],phrynodon sandersoni[&&NHX:TOL=17464],poyntonia paludicola[&&NHX:TOL=40920])petropedetinae[&&NHX:TOL=17453],(laurentomantis[&&NHX:TOL=17466],(mantella bernhardi[&&NHX:TOL=23433],((mantella cowanii[&&NHX:TOL=23435],(mantella haraldmeieri[&&NHX:TOL=23438],(mantella nigricans[&&NHX:TOL=23442],mantella baroni[&&NHX:TOL=23432])[&&NHX:TOL=23526])[&&NHX:TOL=23525])[&&NHX:TOL=23524],((mantella laevigata[&&NHX:TOL=23439],(mantella expectata[&&NHX:TOL=23437],(mantella betsileo[&&NHX:TOL=23434],mantella viridis[&&NHX:TOL=23444])[&&NHX:TOL=23519])[&&NHX:TOL=23518])[&&NHX:TOL=23517],(mantella aurantiaca[&&NHX:TOL=23431],((mantella crocea[&&NHX:TOL=23436],mantella milotympanum[&&NHX:TOL=23441])[&&NHX:TOL=23522],(mantella madagascariensis[&&NHX:TOL=23440],mantella pulchra[&&NHX:TOL=23443])[&&NHX:TOL=23523])[&&NHX:TOL=23521])[&&NHX:TOL=23520])[&&NHX:TOL=23516])[&&NHX:TOL=23515])mantella[&&NHX:TOL=17467],mantidactylus[&&NHX:TOL=17468])mantellinae[&&NHX:TOL=17465])ranidae[&&NHX:TOL=16958],(philautus[&&NHX:TOL=17509],(aglyptodactylus[&&NHX:TOL=17511],boophis[&&NHX:TOL=17512],buergeria[&&NHX:TOL=17513],chirixalus[&&NHX:TOL=17514],chiromantis[&&NHX:TOL=17515],nyctixalus[&&NHX:TOL=17516],polypedates[&&NHX:TOL=17517],rhacophorus[&&NHX:TOL=17518],theloderma[&&NHX:TOL=17519])rhacophorinae[&&NHX:TOL=17510])rhacophoridae[&&NHX:TOL=16960])ranoidea[&&NHX:TOL=16953])node z[&&NHX:TOL=106195],(((adelotus[&&NHX:TOL=17273],heleioporus[&&NHX:TOL=17274],kyarranus[&&NHX:TOL=17275],lechriodus[&&NHX:TOL=17276],limnodynastes[&&NHX:TOL=17277],megistolotis[&&NHX:TOL=17278],mixophyes[&&NHX:TOL=17279],neobatrachus[&&NHX:TOL=17280],notaden[&&NHX:TOL=17281],philoria[&&NHX:TOL=17282])limnodynastinae[&&NHX:TOL=16944],(arenophryne[&&NHX:TOL=17363],assa[&&NHX:TOL=17364],crinia[&&NHX:TOL=17365],geocrinia[&&NHX:TOL=17366],indobatrachus[&&NHX:EXT=Y:TOL=17367],myobatrachus[&&NHX:TOL=17368],paracrinia[&&NHX:TOL=17369],pseudophryne[&&NHX:TOL=17370],rheobatrachus[&&NHX:TOL=17371],taudactylus[&&NHX:TOL=17372],uperoleia[&&NHX:TOL=17373])myobatrachinae[&&NHX:TOL=16946])myobatrachidae[&&NHX:TOL=106194],(caudiverbera caudiverbera[&&NHX:TOL=38294],telmatobufo[&&NHX:TOL=49396])calyptocephalellidae[&&NHX:TOL=133824])myobatrachoidea[&&NHX:TOL=133834])node y[&&NHX:TOL=106193],(nasikabatrachus sahyadrensis[&&NHX:TOL=43176],((sooglossus gardineri[&&NHX:TOL=17532],sooglossus sechellensis[&&NHX:TOL=17533])[&&NHX:TOL=17531],nesomantis thomasseti[&&NHX:TOL=17534])sooglossidae[&&NHX:TOL=16947])sooglossoidea[&&NHX:TOL=106192])node x[&&NHX:TOL=106191],(heleophryne hewitti[&&NHX:TOL=37804],heleophryne natalensis[&&NHX:TOL=17065],heleophryne orientalis[&&NHX:TOL=43169],heleophryne purcelli[&&NHX:TOL=17066],heleophryne regis[&&NHX:TOL=17067],heleophryne rosei[&&NHX:TOL=17068])heleophryne[&&NHX:TOL=16942])neobatrachia[&&NHX:TOL=16987])acosmanura[&&NHX:TOL=106173])pipanura[&&NHX:TOL=16974])bombinanura[&&NHX:TOL=16967])anura[&&NHX:TOL=16963])[&&NHX:TOL=106167])salientia[&&NHX:TOL=14938],((((((((((((((bolitoglossa[&&NHX:TOL=66007],pseudoeurycea[&&NHX:TOL=66014])[&&NHX:TOL=70058],chiropterotriton[&&NHX:TOL=68787])[&&NHX:TOL=70057],thorius[&&NHX:TOL=66015])[&&NHX:TOL=70056],(((bradytriton silus[&&NHX:TOL=68780],oedipina[&&NHX:TOL=65951])[&&NHX:TOL=70069],nototriton[&&NHX:TOL=65958])[&&NHX:TOL=70068],(nyctanolis pernix[&&NHX:TOL=68791],dendrotriton[&&NHX:TOL=68788])[&&NHX:TOL=70070])[&&NHX:TOL=70067])[&&NHX:TOL=70055],cryptotriton[&&NHX:TOL=65952])supergenus bolitoglossa[&&NHX:TOL=68802],((batrachoseps attenuatus[&&NHX:TOL=65914],(((((batrachoseps gregarius[&&NHX:TOL=65922],batrachoseps stebbinsi[&&NHX:TOL=65923])[&&NHX:TOL=65921],batrachoseps simatus[&&NHX:TOL=65924])[&&NHX:TOL=65920],batrachoseps nigriventris[&&NHX:TOL=65925])batrachoseps nigriventris group[&&NHX:TOL=65918],(batrachoseps gabrieli[&&NHX:TOL=65928],(((((batrachoseps minor[&&NHX:TOL=65934],batrachoseps major[&&NHX:TOL=65935])[&&NHX:TOL=65933],batrachoseps incognitus[&&NHX:TOL=65936])[&&NHX:TOL=65932],batrachoseps pacificus[&&NHX:TOL=65937])[&&NHX:TOL=65931],batrachoseps luciae[&&NHX:TOL=65938])[&&NHX:TOL=65930],batrachoseps gavilanensis[&&NHX:TOL=65939])[&&NHX:TOL=65929])batrachoseps pacificus group[&&NHX:TOL=65927])[&&NHX:TOL=65917],(((batrachoseps relictus[&&NHX:TOL=65943],batrachoseps kawia[&&NHX:TOL=65944])[&&NHX:TOL=65942],batrachoseps regius[&&NHX:TOL=65945])[&&NHX:TOL=65941],batrachoseps diabolicus[&&NHX:TOL=65946])batrachoseps relictus group[&&NHX:TOL=65940])[&&NHX:TOL=65916])batrachoseps batrachoseps[&&NHX:TOL=65910],((batrachoseps campi[&&NHX:TOL=65907],batrachoseps robustus[&&NHX:TOL=65908])[&&NHX:TOL=65906],batrachoseps wrightorum[&&NHX:TOL=65909])batrachoseps plethopsis[&&NHX:TOL=65905])supergenus batrachoseps[&&NHX:TOL=65947])bolitoglossinae[&&NHX:TOL=15532],(((gyrinophilus[&&NHX:TOL=66379],stereochilus marginatus[&&NHX:TOL=66380])[&&NHX:TOL=66378],pseudotriton[&&NHX:TOL=72989])[&&NHX:TOL=78583],eurycea[&&NHX:TOL=66529],haideotriton wallacei[&&NHX:TOL=77428])spelerpinae[&&NHX:TOL=66377],hemidactylium scutatum[&&NHX:TOL=15534])[&&NHX:TOL=66374],((((phaeognathus hubrichti[&&NHX:TOL=15468],(desmognathus wrighti[&&NHX:TOL=15470],(desmognathus aeneus[&&NHX:TOL=15472],((desmognathus marmoratus[&&NHX:TOL=15475],desmognathus quadramaculatus[&&NHX:TOL=15476])[&&NHX:TOL=15474],(desmognathus imitator[&&NHX:TOL=15478],((((desmognathus carolinensis[&&NHX:TOL=15483],desmognathus orestes[&&NHX:TOL=15484])[&&NHX:TOL=15482],desmognathus ocoee[&&NHX:TOL=15485])[&&NHX:TOL=15481],desmognathus ochrophaeus[&&NHX:TOL=15486])[&&NHX:TOL=15480],((desmognathus fuscus 1[&&NHX:TOL=15489],desmognathus auriculatus[&&NHX:TOL=15490])[&&NHX:TOL=15488],(((desmognathus fuscus 2[&&NHX:TOL=15494],(desmognathus monticola[&&NHX:TOL=15496],desmognathus apalachicolae[&&NHX:TOL=15497])[&&NHX:TOL=15495])[&&NHX:TOL=15493],(desmognathus conanti[&&NHX:TOL=15499],desmognathus santeetlah[&&NHX:TOL=15500])[&&NHX:TOL=15498])[&&NHX:TOL=15492],(desmognathus brimleyorum[&&NHX:TOL=15502],desmognathus welteri[&&NHX:TOL=15503])[&&NHX:TOL=15501])[&&NHX:TOL=15491])[&&NHX:TOL=15487])[&&NHX:TOL=15479])[&&NHX:TOL=15477])[&&NHX:TOL=15473])[&&NHX:TOL=15471])[&&NHX:TOL=15469])desmognathus[&&NHX:TOL=15529],((((aneides ferreus[&&NHX:TOL=15610],aneides flavipunctatus[&&NHX:TOL=15611])[&&NHX:TOL=15609],aneides lugubris[&&NHX:TOL=15612])[&&NHX:TOL=15608],aneides hardii[&&NHX:TOL=15613])[&&NHX:TOL=15607],aneides aeneus[&&NHX:TOL=15614])[&&NHX:TOL=15606],karsenia koreana[&&NHX:TOL=68771])[&&NHX:TOL=68799],hydromantes[&&NHX:TOL=68770],ensatina eschscholtzii[&&NHX:TOL=15536])[&&NHX:TOL=69091],plethodon[&&NHX:TOL=66383])plethodontinae[&&NHX:TOL=15533])plethodontidae[&&NHX:TOL=15441],(((amphiuma tridactylum[&&NHX:TOL=15430],amphiuma means[&&NHX:TOL=15431])[&&NHX:TOL=15429],amphiuma pholeter[&&NHX:TOL=15432])[&&NHX:TOL=15428],amphiuma antica[&&NHX:EXT=Y:TOL=15433],amphiuma jepseni[&&NHX:EXT=Y:TOL=15434],proamphiuma cretacea[&&NHX:EXT=Y:TOL=15435])amphiumidae[&&NHX:TOL=15440])[&&NHX:TOL=15439],((rhyacotriton variegatus[&&NHX:TOL=15647],rhyacotriton cascadae[&&NHX:TOL=15648])[&&NHX:TOL=15646],(rhyacotriton kezeri[&&NHX:TOL=15650],rhyacotriton olympicus[&&NHX:TOL=15651])[&&NHX:TOL=15649])rhyacotritonidae[&&NHX:TOL=15450])[&&NHX:TOL=66418],(((((((((ambystoma texanum[&&NHX:TOL=15380],ambystoma barbouri[&&NHX:TOL=15381])[&&NHX:TOL=15379],(ambystoma cingulatum[&&NHX:TOL=15383],ambystoma annulatum[&&NHX:TOL=15384])[&&NHX:TOL=15382])[&&NHX:TOL=15378],ambystoma mabeei[&&NHX:TOL=15385])[&&NHX:TOL=15377],(((ambystoma opacum[&&NHX:TOL=15389],ambystoma jeffersonianum[&&NHX:TOL=15390])[&&NHX:TOL=15388],(ambystoma macrodactylum[&&NHX:TOL=15392],ambystoma laterale[&&NHX:TOL=15393])[&&NHX:TOL=15391])[&&NHX:TOL=15387],(ambystoma californiense[&&NHX:TOL=15395],(((ambystoma larmaensis[&&NHX:TOL=15399],ambystoma granulosum[&&NHX:TOL=15400],rhyacosiredon altimirani[&&NHX:TOL=15401],rhyacosiredon rivularis[&&NHX:TOL=15402])[&&NHX:TOL=15398],ambystoma dumerilii[&&NHX:TOL=15403])[&&NHX:TOL=15397],(ambystoma velasci[&&NHX:TOL=15405],ambystoma tigrinum[&&NHX:TOL=15406],ambystoma flavipiperatum[&&NHX:TOL=15407],ambystoma rosaceum[&&NHX:TOL=15408],ambystoma amblycephalum[&&NHX:TOL=15409],ambystoma andersoni[&&NHX:TOL=15410],ambystoma ordinarium[&&NHX:TOL=15411],ambystoma taylori[&&NHX:TOL=15412],ambystoma mexicanum[&&NHX:TOL=15413])[&&NHX:TOL=15404])[&&NHX:TOL=15396])[&&NHX:TOL=15394])[&&NHX:TOL=15386])[&&NHX:TOL=15376],((ambystoma maculatum[&&NHX:TOL=15416],ambystoma gracile[&&NHX:TOL=15417])[&&NHX:TOL=15415],ambystoma talpoideum[&&NHX:TOL=15418])[&&NHX:TOL=15414])[&&NHX:TOL=15375],ambystoma bombypellum[&&NHX:TOL=15419],ambystoma lacustre[&&NHX:TOL=15420],rhyacosiredon leorae[&&NHX:TOL=15421],rhyacosiredon zempoalaensis[&&NHX:TOL=15422],ambystoma hibbardi[&&NHX:EXT=Y:TOL=15423],ambystoma kansaense[&&NHX:EXT=Y:TOL=15424],ambystoma minshalli[&&NHX:EXT=Y:TOL=15425],ambystoma tiheni[&&NHX:EXT=Y:TOL=15426],amphitriton brevis[&&NHX:EXT=Y:TOL=15427])ambystomatidae[&&NHX:TOL=15448],((dicamptodon aterrimus[&&NHX:TOL=15505],(dicamptodon copei[&&NHX:TOL=15507],(dicamptodon ensatus[&&NHX:TOL=15509],dicamptodon tenebrosus[&&NHX:TOL=15510])[&&NHX:TOL=15508])[&&NHX:TOL=15506])[&&NHX:TOL=15504],ambystomichnus montanensis[&&NHX:EXT=Y:TOL=15511],bargmannia wettsteini[&&NHX:EXT=Y:TOL=15512],chrysotriton tiheni[&&NHX:EXT=Y:TOL=15513],geyeriella mertensi[&&NHX:EXT=Y:TOL=15514],wolterstorffiella wiggeri[&&NHX:EXT=Y:TOL=15515])dicamptodontidae[&&NHX:TOL=15447])[&&NHX:TOL=15446],(((salamandrina terdigitata[&&NHX:TOL=91371],salamandrina perspicillata[&&NHX:TOL=91372])salamandrina[&&NHX:TOL=15663],((((salamandra algira[&&NHX:TOL=82685],(salamandra infraimmaculata[&&NHX:TOL=82688],salamandra salamandra[&&NHX:TOL=15657],salamandra lanzai[&&NHX:TOL=82690],salamandra corsica[&&NHX:TOL=82692],salamandra atra[&&NHX:TOL=15656])[&&NHX:TOL=91370])salamandra[&&NHX:TOL=82684],lyciasalamandra[&&NHX:TOL=82693])[&&NHX:TOL=15655],(chioglossa lusitanica[&&NHX:TOL=15660],mertensiella caucasica[&&NHX:TOL=15661])[&&NHX:TOL=82683])[&&NHX:TOL=15653],((pleurodeles[&&NHX:TOL=15666],(echinotriton[&&NHX:TOL=82710],tylototriton[&&NHX:TOL=15667])[&&NHX:TOL=82709])[&&NHX:TOL=15665],((notophthalmus[&&NHX:TOL=15683],taricha[&&NHX:TOL=15684])[&&NHX:TOL=15682],(euproctus[&&NHX:TOL=82782],((lissotriton[&&NHX:TOL=82784],mesotriton alpestris[&&NHX:TOL=87636])[&&NHX:TOL=87635],(((ommatotriton[&&NHX:TOL=82763],neurergus[&&NHX:TOL=82764])[&&NHX:TOL=82762],(calotriton[&&NHX:TOL=91377],triturus[&&NHX:TOL=82771])[&&NHX:TOL=82788])[&&NHX:TOL=82787],(cynops[&&NHX:TOL=15679],(paramesotriton[&&NHX:TOL=15680],pachytriton[&&NHX:TOL=15681],paramesotriton laoensis[&&NHX:TOL=82747])[&&NHX:TOL=94252])[&&NHX:TOL=15678])[&&NHX:TOL=82786])[&&NHX:TOL=15675])[&&NHX:TOL=15668])[&&NHX:TOL=82706])[&&NHX:TOL=15664])[&&NHX:TOL=15652])[&&NHX:TOL=82682],archaeotriton[&&NHX:EXT=Y:TOL=15685],chelotriton[&&NHX:EXT=Y:TOL=15686],koalliella[&&NHX:EXT=Y:TOL=15687],megalotriton[&&NHX:EXT=Y:TOL=15688],oligosemia[&&NHX:EXT=Y:TOL=15689],palaeopleurodeles[&&NHX:EXT=Y:TOL=15690],procynops[&&NHX:EXT=Y:TOL=15691])salamandridae[&&NHX:TOL=15445])[&&NHX:TOL=15444],(((necturus lewisi[&&NHX:TOL=15632],((necturus maculosus[&&NHX:TOL=15635],(necturus beyeri[&&NHX:TOL=15637],necturus alabamensis[&&NHX:TOL=15638])[&&NHX:TOL=15636])[&&NHX:TOL=15634],necturus punctatus[&&NHX:TOL=15639])[&&NHX:TOL=15633])[&&NHX:TOL=15631],proteus anguineus[&&NHX:TOL=15640])[&&NHX:TOL=15630],mioproteus caucasicus[&&NHX:EXT=Y:TOL=15641],necturus krausei[&&NHX:EXT=Y:TOL=15642],orthophyia longa[&&NHX:EXT=Y:TOL=15643],proteus bavaricus[&&NHX:EXT=Y:TOL=15644])proteidae[&&NHX:TOL=15449])[&&NHX:TOL=15443])[&&NHX:TOL=15438],(((siren intermedia[&&NHX:TOL=15694],siren lacertina[&&NHX:TOL=15695])[&&NHX:TOL=15693],pseudobranchus striatus[&&NHX:TOL=15696])[&&NHX:TOL=15692],habrosaurus dilatus[&&NHX:EXT=Y:TOL=15697],pseudobranchus robustus[&&NHX:EXT=Y:TOL=15698],pseudobranchus vetustus[&&NHX:EXT=Y:TOL=15699],siren dunni[&&NHX:EXT=Y:TOL=15700],siren hesterna[&&NHX:EXT=Y:TOL=15701],siren miotexana[&&NHX:EXT=Y:TOL=15702])sirenidae[&&NHX:TOL=15454])[&&NHX:TOL=66417],((((((((liua tsinpaensis[&&NHX:TOL=65828],liua shihi[&&NHX:TOL=65829])[&&NHX:TOL=15519],(((batrachuperus longdongensis[&&NHX:TOL=65832],batrachuperus pinchonii[&&NHX:TOL=65833])[&&NHX:TOL=65831],batrachuperus tibetanus[&&NHX:TOL=65834])[&&NHX:TOL=65830],batrachuperus yenyuanensis[&&NHX:TOL=65835],batrachuperus karlschmidti[&&NHX:TOL=68937],batrachuperus taibaiensis[&&NHX:TOL=68938])[&&NHX:TOL=15520])[&&NHX:TOL=15518],(salamandrella schrenckii[&&NHX:TOL=68940],salamandrella keyserlingii[&&NHX:TOL=65845])[&&NHX:TOL=68939])[&&NHX:TOL=65827],hynobius[&&NHX:TOL=15525])[&&NHX:TOL=65826],pachyhynobius shangchengensis[&&NHX:TOL=15527])[&&NHX:TOL=65825],(ranodon sibericus[&&NHX:TOL=15522],(paradactylodon gorganensis[&&NHX:TOL=65842],paradactylodon mustersi[&&NHX:TOL=65843],paradactylodon persicus[&&NHX:TOL=68967])[&&NHX:TOL=15523])[&&NHX:TOL=15521])[&&NHX:TOL=65824],(onychodactylus fischeri[&&NHX:TOL=65844],onychodactylus japonicus[&&NHX:TOL=68969])[&&NHX:TOL=68968],protohynobius puxiongensis[&&NHX:TOL=68971],(pseudohynobius shuichengensis[&&NHX:TOL=68973],pseudohynobius flavomaculatus[&&NHX:TOL=68974])[&&NHX:TOL=68972])hynobiidae[&&NHX:TOL=15453],((cryptobranchus alleghaniensis[&&NHX:TOL=15460],(andrias japonicus[&&NHX:TOL=15462],andrias davidianus[&&NHX:TOL=15463])[&&NHX:TOL=15461])[&&NHX:TOL=15459],andrias scheuchzeri[&&NHX:EXT=Y:TOL=15464],cryptobranchus guildayi[&&NHX:EXT=Y:TOL=15465],cryptobranchus saskatchewanensi[&&NHX:EXT=Y:TOL=15466])cryptobranchidae[&&NHX:TOL=15452])[&&NHX:TOL=15451])[&&NHX:TOL=15437],batrachosauaroididae[&&NHX:EXT=Y:TOL=15455],karauridae[&&NHX:EXT=Y:TOL=15456],prosirenidae[&&NHX:EXT=Y:TOL=15457],scapherpetontidae[&&NHX:EXT=Y:TOL=15458])caudata[&&NHX:TOL=14939])batrachia[&&NHX:TOL=133659],albanerpetontidae[&&NHX:EXT=Y:TOL=133660],gymnophiona[&&NHX:TOL=14940])living amphibians[&&NHX:TOL=14997],lysorophia[&&NHX:EXT=Y:TOL=14998])[&&NHX:TOL=14996],microsauria[&&NHX:EXT=Y:TOL=14999])[&&NHX:TOL=14995],nectridea[&&NHX:EXT=Y:TOL=15000])[&&NHX:TOL=14994],(aistopoda[&&NHX:EXT=Y:TOL=15002],adelogyrinidae[&&NHX:EXT=Y:TOL=15003])[&&NHX:TOL=15001])amphibia[&&NHX:TOL=14993])tetrapoda[&&NHX:TOL=14987],westlothiana[&&NHX:EXT=Y:TOL=15004])[&&NHX:TOL=14986],(urumqia liudaowanensis[&&NHX:EXT=Y:TOL=17540],kotlassia[&&NHX:EXT=Y:TOL=17541],utegenia shpinari[&&NHX:EXT=Y:TOL=17542],((discosauriscus pulcherrimus[&&NHX:EXT=Y:TOL=17549],discosauriscus austriacus[&&NHX:EXT=Y:TOL=17550])discosauriscus[&&NHX:EXT=Y:TOL=17544],ariekanerpeton sigalovi[&&NHX:EXT=Y:TOL=17545],(seymouria sanjuanensis[&&NHX:EXT=Y:TOL=17552],seymouria baylorensis[&&NHX:EXT=Y:TOL=17553],seymouria grandis[&&NHX:EXT=Y:TOL=17554])seymouria[&&NHX:EXT=Y:TOL=17546])[&&NHX:TOL=17543])seymouriamorpha[&&NHX:EXT=Y:TOL=15005])[&&NHX:TOL=14985],embolomeri[&&NHX:EXT=Y:TOL=15006],gephyrostegidae[&&NHX:EXT=Y:TOL=15007])[&&NHX:TOL=14984],whatcheeria[&&NHX:EXT=Y:TOL=15008])[&&NHX:TOL=14983],((((((((zatrachydidae[&&NHX:EXT=Y:TOL=17611],(branchiosauridae[&&NHX:EXT=Y:TOL=68335],micromelerpetontidae[&&NHX:EXT=Y:TOL=68336],((trematopidae[&&NHX:EXT=Y:TOL=68338],dissorophidae[&&NHX:EXT=Y:TOL=68339])[&&NHX:TOL=68544],amphibamidae[&&NHX:EXT=Y:TOL=68337])[&&NHX:TOL=68543])dissorophoidea[&&NHX:EXT=Y:TOL=17607])[&&NHX:TOL=137624],(eryopidae[&&NHX:EXT=Y:TOL=17610],archegosauridae[&&NHX:EXT=Y:TOL=17615])[&&NHX:TOL=137625])[&&NHX:TOL=137623],iberospondylus[&&NHX:EXT=Y:TOL=137626])[&&NHX:TOL=137622],(edopidae[&&NHX:EXT=Y:TOL=17602],cochleosauridae[&&NHX:EXT=Y:TOL=17603])edopoidea[&&NHX:TOL=17601])[&&NHX:TOL=137621],capetus[&&NHX:EXT=Y:TOL=137627])[&&NHX:TOL=137620],dendrerpeton[&&NHX:EXT=Y:TOL=17605])[&&NHX:TOL=137619],balanerpeton[&&NHX:EXT=Y:TOL=137628])euskelia[&&NHX:TOL=137618],(dvinosauria[&&NHX:EXT=Y:TOL=17613],(rhinesuchidae[&&NHX:EXT=Y:TOL=137629],(capitosauria[&&NHX:EXT=Y:TOL=137631],(trematosauridae[&&NHX:EXT=Y:TOL=137633],(metoposauroidea[&&NHX:EXT=Y:TOL=137635],(rhytidosteidae[&&NHX:EXT=Y:TOL=137637],brachyopoidea[&&NHX:EXT=Y:TOL=137638])[&&NHX:TOL=137636])[&&NHX:TOL=137634])trematosauria[&&NHX:TOL=137632])[&&NHX:TOL=137630])stereospondyli[&&NHX:EXT=Y:TOL=17616])limnarchia[&&NHX:TOL=17612])temnospondyli[&&NHX:EXT=Y:TOL=15009])[&&NHX:TOL=14982],colosteidae[&&NHX:EXT=Y:TOL=15010])[&&NHX:TOL=14981],(baphetes bohemicus[&&NHX:EXT=Y:TOL=15950],baphetes kirkbyi[&&NHX:EXT=Y:TOL=15948],baphetes lintonensis[&&NHX:EXT=Y:TOL=15949],baphetes planiceps[&&NHX:EXT=Y:TOL=15947],eucritta melanolimnetes[&&NHX:EXT=Y:TOL=58012],kyrinion martilli[&&NHX:EXT=Y:TOL=58013],loxomma acutirhinus[&&NHX:EXT=Y:TOL=15941],loxomma allmani[&&NHX:EXT=Y:TOL=15940],loxomma rankini[&&NHX:EXT=Y:TOL=15942],megalocephalus lineolatus[&&NHX:EXT=Y:TOL=15946],megalocephalus pachycephalus[&&NHX:EXT=Y:TOL=15945],spathicephalus mirus[&&NHX:EXT=Y:TOL=15943],spathicephalus pereger[&&NHX:EXT=Y:TOL=15944])baphetidae[&&NHX:EXT=Y:TOL=15011])[&&NHX:TOL=14980],crassigyrinus scoticus[&&NHX:EXT=Y:TOL=15012])[&&NHX:TOL=14979],tulerpeton[&&NHX:EXT=Y:TOL=15013])[&&NHX:TOL=14978],hynerpeton[&&NHX:EXT=Y:TOL=15014])[&&NHX:TOL=14977],ichthyostega[&&NHX:EXT=Y:TOL=15015],acanthostega gunnari[&&NHX:EXT=Y:TOL=15016])[&&NHX:TOL=14976],(ventastega[&&NHX:EXT=Y:TOL=15018],metaxygnathus[&&NHX:EXT=Y:TOL=15019])[&&NHX:TOL=15017])[&&NHX:TOL=14975],elginerpeton[&&NHX:EXT=Y:TOL=15020])terrestrial vertebrates[&&NHX:TOL=14952])[&&NHX:TOL=14950])[&&NHX:TOL=14948])sarcopterygii[&&NHX:TOL=14922],(polypteridae[&&NHX:TOL=68708],((cheirolepidiformes[&&NHX:EXT=Y:TOL=68720],(dorypteridae[&&NHX:EXT=Y:TOL=68746],platysomidae[&&NHX:EXT=Y:TOL=68745],chilodontidae[&&NHX:EXT=Y:TOL=68744],bobastraniidae[&&NHX:EXT=Y:TOL=68743],redfieldiidae[&&NHX:EXT=Y:TOL=68742],stegotrachelidae[&&NHX:EXT=Y:TOL=68741],aesopichthyidae[&&NHX:EXT=Y:TOL=68740],rhadinichthyidae[&&NHX:EXT=Y:TOL=68739],rhabdolepidae[&&NHX:EXT=Y:TOL=68738],pygopteridae[&&NHX:EXT=Y:TOL=68737],palaeoniscidae[&&NHX:EXT=Y:TOL=68736],elonichthyidae[&&NHX:EXT=Y:TOL=68735],commentryidae[&&NHX:EXT=Y:TOL=68734],birgeriidae[&&NHX:EXT=Y:TOL=68733],acrolepidae[&&NHX:EXT=Y:TOL=68732],aeduellidae[&&NHX:EXT=Y:TOL=68731])palaeonisciformes[&&NHX:EXT=Y:TOL=68721],tarrasiiformes[&&NHX:EXT=Y:TOL=68722],guildayichthyiformes[&&NHX:EXT=Y:TOL=68723],phanerorhynchiformes[&&NHX:EXT=Y:TOL=68724],saurichthyiformes[&&NHX:EXT=Y:TOL=68725],(peipiaosteidae[&&NHX:EXT=Y:TOL=68747],chondrosteidae[&&NHX:EXT=Y:TOL=68748],acipenseridae[&&NHX:TOL=68749],polyodontidae[&&NHX:TOL=68750])acipenseriformes[&&NHX:TOL=68726],ptycholepiformes[&&NHX:EXT=Y:TOL=68727],pholidopleuriformes[&&NHX:EXT=Y:TOL=68728],(cephaloxenidae[&&NHX:EXT=Y:TOL=68751],colobodontidae[&&NHX:EXT=Y:TOL=68752],platysiagidae[&&NHX:EXT=Y:TOL=68753],peltopleuridae[&&NHX:EXT=Y:TOL=68754],cleithrolepidae[&&NHX:EXT=Y:TOL=68755],perleididae[&&NHX:EXT=Y:TOL=68756],thoracopteridae[&&NHX:EXT=Y:TOL=68757])perleidiformes[&&NHX:EXT=Y:TOL=68729],luganoiiformes[&&NHX:EXT=Y:TOL=68730])chondrostei[&&NHX:TOL=15043],(pachycormiformes[&&NHX:EXT=Y:TOL=15053],aspidorhynchiformes[&&NHX:EXT=Y:TOL=15051],pycnodontiformes[&&NHX:EXT=Y:TOL=15049],semionotiformes[&&NHX:EXT=Y:TOL=15045],macrosemiiformes[&&NHX:EXT=Y:TOL=68711],lepisosteiformes[&&NHX:TOL=68712],(((amiiformes[&&NHX:TOL=15047],ionoscopiformes[&&NHX:EXT=Y:TOL=68716])[&&NHX:TOL=68719],parasemionotiformes[&&NHX:EXT=Y:TOL=68714])halecomorphi[&&NHX:TOL=68718],(araripichthyidae[&&NHX:EXT=Y:TOL=68704],tselfatiformes[&&NHX:EXT=Y:TOL=15067],pholidophoriformes[&&NHX:EXT=Y:TOL=15068],leptolepidiformes[&&NHX:EXT=Y:TOL=15069],(allothrissopidae[&&NHX:EXT=Y:TOL=68870],occithrissopidae[&&NHX:EXT=Y:TOL=68871],cladocyclidae[&&NHX:EXT=Y:TOL=68872],saurodontidae[&&NHX:EXT=Y:TOL=68873],ichthyodectidae[&&NHX:EXT=Y:TOL=68874])ichthyodectiformes[&&NHX:EXT=Y:TOL=68793],(((elopidae[&&NHX:TOL=68837],megalopidae[&&NHX:TOL=68838])elopiformes[&&NHX:TOL=68833],(albulidae[&&NHX:TOL=68839],halosauridae[&&NHX:TOL=68840],notacanthidae[&&NHX:TOL=68841])albuliformes[&&NHX:TOL=68834],(anguillidae[&&NHX:TOL=68842],heterenchelyidae[&&NHX:TOL=68843],moringuidae[&&NHX:TOL=68844],chlopsidae[&&NHX:TOL=68845],myrocongridae[&&NHX:TOL=68846],muraenidae[&&NHX:TOL=68847],synaphobranchidae[&&NHX:TOL=68848],ophichthidae[&&NHX:TOL=68849],colocongridae[&&NHX:TOL=68850],derichthyidae[&&NHX:TOL=68851],muraenesocidae[&&NHX:TOL=68852],nemichthyidae[&&NHX:TOL=68853],congridae[&&NHX:TOL=68854],nettastomatidae[&&NHX:TOL=68855],serrivomeridae[&&NHX:TOL=68856])anguilliformes[&&NHX:TOL=68835],(cyematidae[&&NHX:TOL=68857],saccopharyngidae[&&NHX:TOL=68858],eurypharyngidae[&&NHX:TOL=68859],monognathidae[&&NHX:TOL=68860])saccopharyngiformes[&&NHX:TOL=68836])elopomorpha[&&NHX:TOL=15073],(kuyangichthidae[&&NHX:EXT=Y:TOL=15127],(lycopteridae[&&NHX:EXT=Y:TOL=15129],((plesiolycoptera daqingensis[&&NHX:EXT=Y:TOL=15134],(yanbiania wangqingica[&&NHX:EXT=Y:TOL=15136],((eohiodon rosei[&&NHX:EXT=Y:TOL=15141],eohiodon woodruffi[&&NHX:EXT=Y:TOL=15142])eohiodon[&&NHX:EXT=Y:TOL=15138],(hiodon consteniorum[&&NHX:EXT=Y:TOL=15146],(hiodon tergisus[&&NHX:TOL=15148],hiodon alosoides[&&NHX:TOL=15149])[&&NHX:TOL=15147])hiodon[&&NHX:TOL=15139])[&&NHX:TOL=15137])[&&NHX:TOL=15135])hiodontiformes[&&NHX:TOL=15131],(osteoglossidae[&&NHX:TOL=68865],pantodontidae[&&NHX:TOL=68866],notopteridae[&&NHX:TOL=68867],mormyridae[&&NHX:TOL=68868],gymnarchidae[&&NHX:TOL=68869])osteoglossiformes[&&NHX:TOL=15132])[&&NHX:TOL=15130])[&&NHX:TOL=68875])osteoglossomorpha[&&NHX:TOL=15071],(((gonorhynchiformes[&&NHX:TOL=15056],(chanoides[&&NHX:EXT=Y:TOL=15058],(cypriniformes[&&NHX:TOL=15060],(((((prochilodontidae[&&NHX:TOL=15099],curimatidae[&&NHX:TOL=15100])[&&NHX:TOL=15098],(chilodontidae[&&NHX:TOL=15102],anostomidae[&&NHX:TOL=15103])[&&NHX:TOL=15101])[&&NHX:TOL=15097],(ctenoluciidae[&&NHX:TOL=15105],hepsetidae[&&NHX:TOL=15106],erythrinidae[&&NHX:TOL=15107],lebiasinidae[&&NHX:TOL=15108])[&&NHX:TOL=15104],hemiodontidae[&&NHX:TOL=15109],parodontidae[&&NHX:TOL=15110],gasteropelecidae[&&NHX:TOL=15111],crenuchidae[&&NHX:TOL=15112],characidae[&&NHX:TOL=15113])[&&NHX:TOL=15096],(citharinidae[&&NHX:TOL=15115],distichodontidae[&&NHX:TOL=15116])[&&NHX:TOL=15114])characiformes[&&NHX:TOL=15062],((gymnotidae[&&NHX:TOL=15118],((rhamphichthyidae[&&NHX:TOL=15121],hypopomidae[&&NHX:TOL=15122])[&&NHX:TOL=15120],(sternopygidae[&&NHX:TOL=15124],apteronotidae[&&NHX:TOL=15125])[&&NHX:TOL=15123])[&&NHX:TOL=15119])gymnotiformes[&&NHX:TOL=15064],(diplomystidae[&&NHX:TOL=15186],(hypsidoridae[&&NHX:EXT=Y:TOL=15188],siluroidea[&&NHX:TOL=15189],((nematogenyidae[&&NHX:TOL=15194],trichomycteridae[&&NHX:TOL=15195])[&&NHX:TOL=15193],(((((((hoplosternum punctatum[&&NHX:TOL=15357],hoplosternum magdalenae[&&NHX:TOL=15356],hoplosternum littorale[&&NHX:TOL=15355])hoplosternum[&&NHX:TOL=15336],(dianema longibarbis[&&NHX:TOL=15352],dianema urostriatum[&&NHX:TOL=15353])dianema[&&NHX:TOL=15337])[&&NHX:TOL=15335],(megalechis personata[&&NHX:TOL=15364],megalechis thoracata[&&NHX:TOL=15365])megalechis[&&NHX:TOL=15338])[&&NHX:TOL=15334],(lepthoplosternum pectorale[&&NHX:TOL=15359],lepthoplosternum beni[&&NHX:TOL=15360],lepthoplosternum altamazonicum[&&NHX:TOL=15361],lepthoplosternum tordilho[&&NHX:TOL=15362])lepthoplosternum[&&NHX:TOL=15339])[&&NHX:TOL=15333],(callichthys callichthys[&&NHX:TOL=15347],more callichthys species to be described[&&NHX:TOL=21842])callichthys[&&NHX:TOL=15340])[&&NHX:TOL=15332],((aspidoras albater[&&NHX:TOL=15313],aspidoras brunneus[&&NHX:TOL=15314],aspidoras carvalhoi[&&NHX:TOL=15315],aspidoras eurycephalus[&&NHX:TOL=15316],aspidoras fuscoguttatus[&&NHX:TOL=15317],aspidoras lakoi[&&NHX:TOL=15318],aspidoras maculosus[&&NHX:TOL=15319],aspidoras menezesi[&&NHX:TOL=15320],aspidoras pauciradiatus[&&NHX:TOL=15321],aspidoras poecilus[&&NHX:TOL=15322],aspidoras raimundi[&&NHX:TOL=15323],aspidoras rochai[&&NHX:TOL=15324],aspidoras spilotus[&&NHX:TOL=15325],aspidoras virgulatus[&&NHX:TOL=15326])aspidoras[&&NHX:TOL=15342],((corydoras garbei[&&NHX:TOL=15349],etc.[&&NHX:TOL=15350])corydoras[&&NHX:TOL=15344],(brochis britskii[&&NHX:TOL=15328],brochis multiradiatus[&&NHX:TOL=15329],brochis splendens[&&NHX:TOL=15330])brochis[&&NHX:TOL=15345])[&&NHX:TOL=15343])[&&NHX:TOL=15341])callichthyidae[&&NHX:TOL=15197],(scoloplacidae[&&NHX:TOL=15199],(astroblepidae[&&NHX:TOL=15201],loricariidae[&&NHX:TOL=15202])[&&NHX:TOL=15200])[&&NHX:TOL=15198])[&&NHX:TOL=15196])loricarioids[&&NHX:TOL=15192],cetopsidae[&&NHX:TOL=15190],((amblycipitidae[&&NHX:TOL=15204],(akysidae[&&NHX:TOL=15206],sisoridae[&&NHX:TOL=15207])[&&NHX:TOL=15205])sisoroids[&&NHX:TOL=15203],bagridae[&&NHX:TOL=15228],schilbidae[&&NHX:TOL=50919],austroglanididae[&&NHX:TOL=15227],claroteidae[&&NHX:TOL=15224],lacantunia enigmatica[&&NHX:TOL=15229],malapteruridae[&&NHX:TOL=15225],(mochokus[&&NHX:TOL=57790],(mochokiella paynei[&&NHX:TOL=57789],(acanthocleithron chapini[&&NHX:TOL=128963],(microsynodontis[&&NHX:TOL=57791],synodontis[&&NHX:TOL=57788],((atopodontus adriaensi[&&NHX:TOL=108379],(atopochilus[&&NHX:TOL=108404],euchilichthys[&&NHX:TOL=108430])[&&NHX:TOL=108429])[&&NHX:TOL=108378],chiloglanis[&&NHX:TOL=57784])chiloglanidinae[&&NHX:TOL=69225])[&&NHX:TOL=108377])[&&NHX:TOL=129167])[&&NHX:TOL=108375])mochokidae[&&NHX:TOL=15214],amphiliidae[&&NHX:TOL=15226],(astephus[&&NHX:EXT=Y:TOL=68922],(trogloglanis pattersoni[&&NHX:TOL=69910],(((ictalurus furcatus[&&NHX:TOL=69926],ictalurus lambda[&&NHX:EXT=Y:TOL=69927])[&&NHX:TOL=69925],ictalurus balsanus[&&NHX:TOL=69928])ictalurus furcatus group[&&NHX:TOL=69924],ictalurus rhaeas[&&NHX:EXT=Y:TOL=69929],(ictalurus australis[&&NHX:TOL=69931],ictalurus dugesii[&&NHX:TOL=69932],ictalurus echinatus[&&NHX:EXT=Y:TOL=69933],ictalurus lupus[&&NHX:TOL=69934],ictalurus mexicanus[&&NHX:TOL=69935],ictalurus pricei[&&NHX:TOL=69936],ictalurus punctatus[&&NHX:TOL=69937],ictalurus spodius[&&NHX:EXT=Y:TOL=69938])ictalurus punctatus group[&&NHX:TOL=69930])ictalurus[&&NHX:TOL=68925],((((((ameiurus melas[&&NHX:TOL=69827],ameiurus nebulosus[&&NHX:TOL=69828])[&&NHX:TOL=69826],ameiurus serracanthus[&&NHX:TOL=69829])[&&NHX:TOL=69825],ameiurus brunneus[&&NHX:TOL=69830])[&&NHX:TOL=69824],(ameiurus catus[&&NHX:TOL=69833],ameiurus platycephalus[&&NHX:TOL=69834])[&&NHX:TOL=69832])[&&NHX:TOL=69837],ameiurus natalis[&&NHX:TOL=69831])ameiurus[&&NHX:TOL=68927],((((((((((noturus elegans[&&NHX:TOL=69889],noturus trautmani[&&NHX:TOL=69921])[&&NHX:TOL=79167],(noturus baileyi[&&NHX:TOL=69887],noturus hildebrandi[&&NHX:TOL=69888])[&&NHX:TOL=69886])[&&NHX:TOL=69885],(noturus fasciatus[&&NHX:TOL=69890],(noturus stanauli[&&NHX:TOL=69919],noturus crypticus[&&NHX:TOL=69923])[&&NHX:TOL=79168])[&&NHX:TOL=69922])[&&NHX:TOL=69884],(noturus maydeni[&&NHX:TOL=79166],noturus albater[&&NHX:TOL=69883])[&&NHX:TOL=79165])[&&NHX:TOL=79164],((((((noturus stigmosus[&&NHX:TOL=69871],noturus gladiator[&&NHX:TOL=69870])[&&NHX:TOL=69869],noturus munitus[&&NHX:TOL=69872])[&&NHX:TOL=69868],noturus placidus[&&NHX:TOL=69873])[&&NHX:TOL=69867],noturus eleutherus[&&NHX:TOL=69874])[&&NHX:TOL=69866],(noturus flavater[&&NHX:TOL=69876],noturus furiosus[&&NHX:TOL=69877])[&&NHX:TOL=69875])[&&NHX:TOL=69865],noturus flavipinnis[&&NHX:TOL=69879])[&&NHX:TOL=69863],(noturus taylori[&&NHX:TOL=69891],noturus miurus[&&NHX:TOL=69880])[&&NHX:TOL=79163])[&&NHX:TOL=69861],((noturus phaeus[&&NHX:TOL=69902],(noturus funebris[&&NHX:TOL=69900],noturus leptacanthus[&&NHX:TOL=69901])[&&NHX:TOL=69899])[&&NHX:TOL=69898],((noturus gilberti[&&NHX:TOL=69897],(noturus insignis[&&NHX:TOL=69896],noturus species[&&NHX:TOL=69895])[&&NHX:TOL=69894])[&&NHX:TOL=69893],(noturus flavus[&&NHX:TOL=69907],(noturus gyrinus[&&NHX:TOL=69905],noturus lachneri[&&NHX:TOL=69906])[&&NHX:TOL=69904])[&&NHX:TOL=69903])[&&NHX:TOL=69892])[&&NHX:TOL=79162])[&&NHX:TOL=69860],noturus nocturnus[&&NHX:TOL=69909])[&&NHX:TOL=69859],noturus exilis[&&NHX:TOL=69908])noturus[&&NHX:TOL=68930],(prietella lundbergi[&&NHX:TOL=69912],prietella phreatophila[&&NHX:TOL=69913])prietella[&&NHX:TOL=68931])[&&NHX:TOL=68929],(pylodictis olivaris[&&NHX:TOL=69915],satan eurystomus[&&NHX:TOL=69917])[&&NHX:TOL=68932])[&&NHX:TOL=68928])[&&NHX:TOL=68926])[&&NHX:TOL=68923])ictaluridae[&&NHX:TOL=15230],cranoglanidae[&&NHX:TOL=15235],pangasiidae[&&NHX:TOL=15231],clariidae[&&NHX:TOL=15223],siluridae[&&NHX:TOL=15232],chacidae[&&NHX:TOL=15234],plotosidae[&&NHX:TOL=15233],(ariidae[&&NHX:TOL=15209],ancharius[&&NHX:TOL=15210])[&&NHX:TOL=52218],titanoglanis[&&NHX:TOL=15212],(((acanthodoras cataphractus[&&NHX:TOL=112566],acanthodoras depressus[&&NHX:TOL=112567],acanthodoras spinosissimus[&&NHX:TOL=112568])acanthodoras[&&NHX:TOL=112531],(agamyxis albomaculatus[&&NHX:TOL=112564],agamyxis pectinifrons[&&NHX:TOL=112565])agamyxis[&&NHX:TOL=112532],(amblydoras affinis[&&NHX:TOL=112569],amblydoras bolivarensis[&&NHX:TOL=112570],amblydoras gonzalezi[&&NHX:TOL=112571],amblydoras monitor[&&NHX:TOL=112572],amblydoras nauticus[&&NHX:TOL=112573],amblydoras truncatus[&&NHX:TOL=112574])amblydoras[&&NHX:TOL=112533],(anadoras grypus[&&NHX:TOL=112575],anadoras regani[&&NHX:TOL=112576],anadoras weddellii[&&NHX:TOL=112577])anadoras[&&NHX:TOL=112534],anduzedoras oxyrhynchus[&&NHX:TOL=112535],astrodoras asterifrons[&&NHX:TOL=112536],centrochir crocodili[&&NHX:TOL=112537],(centrodoras brachiatus[&&NHX:TOL=112581],centrodoras hasemani[&&NHX:TOL=112582])centrodoras[&&NHX:TOL=112538],doraops zuloagai[&&NHX:TOL=112539],(doras carinatus[&&NHX:TOL=112584],doras dionae[&&NHX:EXT=Y:TOL=112585],doras micropoeus[&&NHX:TOL=112586])doras[&&NHX:TOL=112540],franciscodoras marmoratus[&&NHX:TOL=112541],(hassar affinis[&&NHX:TOL=112588],hassar orestis[&&NHX:TOL=112589],hassar wilderi[&&NHX:TOL=112590])hassar[&&NHX:TOL=112542],(hemidoras morrisi[&&NHX:TOL=112591],hemidoras stenopeltis[&&NHX:TOL=112592])hemidoras[&&NHX:TOL=112543],hypodoras forficulatus[&&NHX:TOL=112544],kalyptodoras bahiensis[&&NHX:TOL=112545],(leptodoras acipenserinus[&&NHX:TOL=112595],leptodoras cataniai[&&NHX:TOL=112596],leptodoras copei[&&NHX:TOL=112597],leptodoras hasemani[&&NHX:TOL=112598],leptodoras juruensis[&&NHX:TOL=112599],leptodoras linnelli[&&NHX:TOL=112600],leptodoras myersi[&&NHX:TOL=112601],leptodoras nelsoni[&&NHX:TOL=112602],leptodoras praelongus[&&NHX:TOL=112603],leptodoras rogersae[&&NHX:TOL=112604])leptodoras[&&NHX:TOL=112546],lithodoras dorsalis[&&NHX:TOL=112547],(megalodoras guayoensis[&&NHX:TOL=112562],megalodoras uranoscopus[&&NHX:TOL=112563])megalodoras[&&NHX:TOL=112548],merodoras nheco[&&NHX:TOL=112549],(nemadoras elongatus[&&NHX:TOL=112607],nemadoras hemipeltis[&&NHX:TOL=112608],nemadoras humeralis[&&NHX:TOL=112609],nemadoras leporhinus[&&NHX:TOL=112610],nemadoras trimaculatus[&&NHX:TOL=112611])nemadoras[&&NHX:TOL=112550],(opsodoras boulengeri[&&NHX:TOL=112612],opsodoras morei[&&NHX:TOL=112613],opsodoras stuebelii[&&NHX:TOL=112614],opsodoras ternetzi[&&NHX:TOL=112615])opsodoras[&&NHX:TOL=112551],orinocodoras eigenmanni[&&NHX:TOL=112552],(oxydoras kneri[&&NHX:TOL=112617],oxydoras niger[&&NHX:TOL=112618],oxydoras sifontesi[&&NHX:TOL=112619])oxydoras[&&NHX:TOL=112553],(physopyxis ananas[&&NHX:TOL=112620],physopyxis cristata[&&NHX:TOL=112621],physopyxis lyra[&&NHX:TOL=112622])physopyxis[&&NHX:TOL=112554],(platydoras armatulus[&&NHX:TOL=112623],platydoras costatus[&&NHX:TOL=112624],platydoras hancockii[&&NHX:TOL=112625])platydoras[&&NHX:TOL=112555],(pterodoras granulosus[&&NHX:TOL=112626],pterodoras rivasi[&&NHX:TOL=112627])pterodoras[&&NHX:TOL=112556],(rhinodoras boehlkei[&&NHX:TOL=112628],rhinodoras dorbignyi[&&NHX:TOL=112629],rhinodoras thomersoni[&&NHX:TOL=112630])rhinodoras[&&NHX:TOL=112557],(rhynchodoras castilloi[&&NHX:TOL=112631],rhynchodoras woodsi[&&NHX:TOL=112632],rhynchodoras xingui[&&NHX:TOL=112633])rhynchodoras[&&NHX:TOL=112558],scorpiodoras heckelii[&&NHX:TOL=112559],(trachydoras brevis[&&NHX:TOL=112643],trachydoras microstomus[&&NHX:TOL=112635],trachydoras nattereri[&&NHX:TOL=112636],trachydoras paraguayensis[&&NHX:TOL=112637],trachydoras steindachneri[&&NHX:TOL=112638])trachydoras[&&NHX:TOL=112560],wertheimeria maculata[&&NHX:TOL=112561],doras fimbriatus[&&NHX:TOL=112640],doras punctatus[&&NHX:TOL=112641],oxydoras eigenmanni[&&NHX:TOL=112642])doradidae[&&NHX:TOL=15216],auchenipteridae[&&NHX:TOL=15217])doradoids[&&NHX:TOL=15211],((pseudobunocephalus bifidus[&&NHX:TOL=15237],pseudobunocephalus iheringii[&&NHX:TOL=15238],pseudobunocephalus rugosus[&&NHX:TOL=15239],pseudobunocephalus amazonicus[&&NHX:TOL=15240],pseudobunocephalus quadriradiatus[&&NHX:TOL=15241],pseudobunocephalus lundbergi[&&NHX:TOL=15242])pseudobunocephalus[&&NHX:TOL=15252],(acanthobunocephalus nicoi[&&NHX:TOL=15254],(((bunocephalus verrucosus[&&NHX:TOL=15279],bunocephalus aleuropsis[&&NHX:TOL=15280],bunocephalus coracoideus[&&NHX:TOL=15281],bunocephalus knerii[&&NHX:TOL=15282],bunocephalus amaurus[&&NHX:TOL=15283],bunocephalus chamaizelus[&&NHX:TOL=15284],bunocephalus doriae[&&NHX:TOL=15285],bunocephalus colombianus[&&NHX:TOL=15286],bunocephalus larai[&&NHX:TOL=15287])bunocephalus[&&NHX:TOL=15257],(amaralia hypsiura[&&NHX:TOL=15246],amaralia oviraptor[&&NHX:TOL=15247])amaralia[&&NHX:TOL=15258])bunocephalini[&&NHX:TOL=15256],((pterobunocephalus depressus[&&NHX:TOL=15303],pterobunocephalus dolichurus[&&NHX:TOL=15304])pterobunocephalus[&&NHX:TOL=15260],((platystacus cotylephorus[&&NHX:TOL=15263],((aspredinichthtys filamentosus[&&NHX:TOL=15249],aspredinichthtys tibicen[&&NHX:TOL=15250])aspredinichthys[&&NHX:TOL=15265],aspredo aspredo[&&NHX:TOL=15266])[&&NHX:TOL=15264])aspredini[&&NHX:TOL=15262],((xyliphius magdalenae[&&NHX:TOL=15306],xyliphius barbatus[&&NHX:TOL=15307],xyliphius melanopterus[&&NHX:TOL=15308],xyliphius lepturus[&&NHX:TOL=15309],xyliphius lombarderoi[&&NHX:TOL=15310],xyliphius kryptos[&&NHX:TOL=15311])xyliphius[&&NHX:TOL=15268],((hoplomyzon atrizona[&&NHX:TOL=15295],hoplomyzon papillatus[&&NHX:TOL=15296],hoplomyzon sexpapilostoma[&&NHX:TOL=15297])hoplomyzon[&&NHX:TOL=15270],(micromyzon akamai[&&NHX:TOL=15272],(dupouyichthys sapito[&&NHX:TOL=15274],(ernstichthys anduzei[&&NHX:TOL=15291],ernstichthys megistus[&&NHX:TOL=15292],ernstichthys intonsus[&&NHX:TOL=15293])ernstichthys[&&NHX:TOL=15275])[&&NHX:TOL=15273])[&&NHX:TOL=15271])hoplomyzontini[&&NHX:TOL=15269])[&&NHX:TOL=15267])[&&NHX:TOL=15261])[&&NHX:TOL=15259])[&&NHX:TOL=15255])[&&NHX:TOL=15253])aspredinidae[&&NHX:TOL=15208],conorhynchos[&&NHX:TOL=15218],(heptapteridae[&&NHX:TOL=15220],pimelodidae[&&NHX:TOL=15221],pseudopimelodidae[&&NHX:TOL=15222])pimelodoids[&&NHX:TOL=15219])[&&NHX:TOL=15191])siluroidei[&&NHX:TOL=15187])siluriformes[&&NHX:TOL=15065])[&&NHX:TOL=15063])[&&NHX:TOL=15061])otophysi[&&NHX:TOL=15059])[&&NHX:TOL=15057])ostariophysi[&&NHX:TOL=15077],clupeomorpha[&&NHX:TOL=15075])ostarioclupeomorpha[&&NHX:TOL=68703],(((argentinoidei[&&NHX:TOL=15167],salmonoidei[&&NHX:TOL=15168],((osmeridae[&&NHX:TOL=15159],salangidae[&&NHX:TOL=15160],sundasalangidae[&&NHX:TOL=15161])osmeroidea[&&NHX:TOL=15158],(retropinnidae[&&NHX:TOL=15163],lepidogalaxias salamandroides[&&NHX:TOL=15164],galaxiidae[&&NHX:TOL=15165])galaxioidea[&&NHX:TOL=15162])osmeroidei[&&NHX:TOL=15169])salmoniformes[&&NHX:TOL=15080],((((((esox reichertii[&&NHX:TOL=33149],esox lucius[&&NHX:TOL=33150])[&&NHX:TOL=33148],esox masquinongy[&&NHX:TOL=33151])[&&NHX:TOL=33147],(esox niger[&&NHX:TOL=33153],esox americanus[&&NHX:TOL=33154])[&&NHX:TOL=33152])[&&NHX:TOL=33146],novumbra[&&NHX:TOL=33155])[&&NHX:TOL=33145],dallia[&&NHX:TOL=33156])[&&NHX:TOL=33144],(umbra krameri[&&NHX:TOL=33158],(umbra pygmae[&&NHX:TOL=33160],umbra limi[&&NHX:TOL=33161])[&&NHX:TOL=33159])[&&NHX:TOL=33157])esociformes[&&NHX:TOL=15081])protacanthopterygii[&&NHX:TOL=15079],(stenopterygii[&&NHX:TOL=15083],ateleopodomorpha[&&NHX:TOL=68899],(cyclosquamata[&&NHX:TOL=15085],((((neoscopelus[&&NHX:TOL=15182],solivomer[&&NHX:TOL=15183])[&&NHX:TOL=15181],scopelengys[&&NHX:TOL=15184])neoscopelidae[&&NHX:TOL=15173],(myctophinae[&&NHX:TOL=15176],(notolychnus[&&NHX:TOL=15178],remaining lampanyctinae[&&NHX:TOL=15179])lympanyctinae[&&NHX:TOL=15177])myctophidae[&&NHX:TOL=15174])scopelomorpha[&&NHX:TOL=15087],((((((((elassomatiformes[&&NHX:TOL=68762],mugiliformes[&&NHX:TOL=68763],synbranchiformes[&&NHX:TOL=68764],(hippocampus[&&NHX:TOL=67270],gasterosteoidei[&&NHX:TOL=68769])gasterosteiformes[&&NHX:TOL=68765],atheriniformes[&&NHX:TOL=68766],beloniformes[&&NHX:TOL=68767],cyprinodontiformes[&&NHX:TOL=68768])smegmamorpha[&&NHX:TOL=52147],ophidiiformes[&&NHX:TOL=21986],((cretatriacanthidae[&&NHX:EXT=Y:TOL=93824],(plectocretacicidae[&&NHX:EXT=Y:TOL=93826],protriacanthidae[&&NHX:EXT=Y:TOL=93827])[&&NHX:TOL=93825])[&&NHX:TOL=93823],(triacanthodidae[&&NHX:TOL=93829],((triacanthidae[&&NHX:TOL=93832],(moclaybalistidae[&&NHX:EXT=Y:TOL=93834],((bolcabalistidae[&&NHX:EXT=Y:TOL=93837],eospinidae[&&NHX:EXT=Y:TOL=93838])[&&NHX:TOL=93836],((balistidae[&&NHX:TOL=93841],monacanthidae[&&NHX:TOL=93842])[&&NHX:TOL=93840],(spinacanthidae[&&NHX:EXT=Y:TOL=93844],(protobalistidae[&&NHX:EXT=Y:TOL=93846],(aracanidae[&&NHX:TOL=93848],ostraciidae[&&NHX:TOL=93849])[&&NHX:TOL=93847])[&&NHX:TOL=93845])[&&NHX:TOL=93843])[&&NHX:TOL=93839])[&&NHX:TOL=93835])[&&NHX:TOL=93833])[&&NHX:TOL=93831],(eoplectidae[&&NHX:EXT=Y:TOL=93851],(triodontidae[&&NHX:TOL=93853],(zignoichthyidae[&&NHX:EXT=Y:TOL=94204],((tetraodontidae[&&NHX:TOL=93856],diodontidae[&&NHX:TOL=93857])[&&NHX:TOL=94206],molidae[&&NHX:TOL=93858])[&&NHX:TOL=94205])[&&NHX:TOL=94203])[&&NHX:TOL=93852])[&&NHX:TOL=93850])[&&NHX:TOL=93830])[&&NHX:TOL=93828])tetraodontiformes[&&NHX:TOL=52153],pleuronectiformes[&&NHX:TOL=52152],dactylopteriformes[&&NHX:TOL=52151],scorpaeniformes[&&NHX:TOL=52150],batrachoidiformes[&&NHX:TOL=21988],perciformes[&&NHX:TOL=52149],((sladenia[&&NHX:TOL=52115],(lophiodes[&&NHX:TOL=52117],(lophiomus[&&NHX:TOL=52119],lophius[&&NHX:TOL=52120])[&&NHX:TOL=52118])[&&NHX:TOL=52116])lophiidae[&&NHX:TOL=21990],((((tetrabrachium ocellatum[&&NHX:TOL=21994],(((antennarius striatus[&&NHX:TOL=52046],antennarius hispidus[&&NHX:TOL=52047])antennarius striatus group[&&NHX:TOL=52020],((antennarius nummifer[&&NHX:TOL=52048],((antennarius coccineus[&&NHX:TOL=52051],antennarius bermudensis[&&NHX:TOL=52052],antennarius sanguineus[&&NHX:TOL=52053])[&&NHX:TOL=52050],(antennarius duescus[&&NHX:TOL=52055],antennarius analis[&&NHX:TOL=52056])[&&NHX:TOL=52054])[&&NHX:TOL=52049],antennarius dorhensis[&&NHX:TOL=52057],antennarius rosaceus[&&NHX:TOL=52058])antennarius nummifer group[&&NHX:TOL=52026],antennarius biocellatus[&&NHX:TOL=52028],(antennarius randalli[&&NHX:TOL=52065],antennarius pauciradiatus[&&NHX:TOL=52066])antennarius pauciradiatus group[&&NHX:TOL=52029])[&&NHX:TOL=52025],((antennarius pictus[&&NHX:TOL=52030],antennarius maculatus[&&NHX:TOL=52031],antennarius commersoni[&&NHX:TOL=52032],(antennarius multiocellatus[&&NHX:TOL=52034],antennarius pardalis[&&NHX:TOL=52035])[&&NHX:TOL=52033])antennarius pictus group[&&NHX:TOL=52022],(antennarius indicus[&&NHX:TOL=52036],(antennarius radiosus[&&NHX:TOL=52038],((antennarius scriptissimus[&&NHX:TOL=52041],antennarius avalonis[&&NHX:TOL=52042])[&&NHX:TOL=52040],(antennarius ocellatus[&&NHX:TOL=52044],antennarius senegalensis[&&NHX:TOL=52045])[&&NHX:TOL=52043])[&&NHX:TOL=52060])[&&NHX:TOL=52059])anennarius ocellatus group[&&NHX:TOL=52024])[&&NHX:TOL=52021])antennarius[&&NHX:TOL=52009],(nudiantennarius[&&NHX:TOL=52008],(antennatus[&&NHX:TOL=52007],(kuiterichthys[&&NHX:TOL=52005],(allenichthys[&&NHX:TOL=52004],(lophiocharon[&&NHX:TOL=52003],(echinophryne[&&NHX:TOL=52002],(phyllophryne[&&NHX:TOL=52001],(rhycherus[&&NHX:TOL=52000],(histiophryne[&&NHX:TOL=51999],tathicarpus[&&NHX:TOL=51998])[&&NHX:TOL=52019])[&&NHX:TOL=52018])[&&NHX:TOL=52017])[&&NHX:TOL=52016])[&&NHX:TOL=52015])[&&NHX:TOL=52014])[&&NHX:TOL=52013])[&&NHX:TOL=52011])[&&NHX:TOL=52010])antennariidae[&&NHX:TOL=21993])[&&NHX:TOL=21992],lophichthys boschmai[&&NHX:TOL=22059])[&&NHX:TOL=22058],(brachionichthys[&&NHX:TOL=53717],sympterichthys[&&NHX:TOL=111377])brachionichthyidae[&&NHX:TOL=21996])antennarioidei[&&NHX:TOL=21991],((chaunacops[&&NHX:TOL=53718],chaunax[&&NHX:TOL=53719])chaunacidae[&&NHX:TOL=21997],((solocisquama[&&NHX:TOL=52134],halieutaea[&&NHX:TOL=52129],halieutichthys[&&NHX:TOL=52130],(((zalieutes[&&NHX:TOL=52135],ogcocephalus[&&NHX:TOL=52133])[&&NHX:TOL=52216],malthopsis[&&NHX:TOL=52132])[&&NHX:TOL=52215],halicmetus[&&NHX:TOL=52131])[&&NHX:TOL=52214],dibranchus[&&NHX:TOL=52128],(halieutopsis[&&NHX:TOL=52127],coelophrys[&&NHX:TOL=52126])[&&NHX:TOL=52217])ogcocephalidae[&&NHX:TOL=22028],((centrophryne spinulosa[&&NHX:TOL=22009],(ceratias[&&NHX:TOL=56880],cryptopsaras[&&NHX:TOL=56881])ceratiidae[&&NHX:TOL=22010])[&&NHX:TOL=52341],((himantolophus groenlandicusgroup[&&NHX:TOL=56925],(himantolophus appeliigroup[&&NHX:TOL=56924],(himantolophus nigricornisgroup[&&NHX:TOL=56923],(himantolophus albinaresgroup[&&NHX:TOL=56922],himantolophus cornifergroup[&&NHX:TOL=56921])[&&NHX:TOL=110602])[&&NHX:TOL=110601])[&&NHX:TOL=110600])himantolophus[&&NHX:TOL=22004],((diceratias[&&NHX:TOL=56919],bufoceratias[&&NHX:TOL=56920])diceratiidae[&&NHX:TOL=22006],(((melanocetus eustalus[&&NHX:TOL=56913],melanocetus johnsonii[&&NHX:TOL=56914],melanocetus niger[&&NHX:TOL=56916],melanocetus rossi[&&NHX:TOL=56917])[&&NHX:TOL=56918],melanocetus murrayi[&&NHX:TOL=56915])melanocetus[&&NHX:TOL=22003],(((lasiognathus[&&NHX:TOL=56734],thaumatichthys[&&NHX:TOL=56733])thaumatichthyidae[&&NHX:TOL=22007],(lophodolos[&&NHX:TOL=56905],(pentherichthys[&&NHX:TOL=56908],(chaenophryne[&&NHX:TOL=56898],(spiniphryne[&&NHX:TOL=56911],oneirodes[&&NHX:TOL=56907],dermatias[&&NHX:TOL=56902],danaphryne[&&NHX:TOL=56901],microlophichthys[&&NHX:TOL=56906],phyllorhinichthys[&&NHX:TOL=56909],tyrannophryne[&&NHX:TOL=56912],(dolopichthys[&&NHX:TOL=56903],bertella[&&NHX:TOL=56897])[&&NHX:TOL=110595],(puck[&&NHX:TOL=56910],chirophryne[&&NHX:TOL=56899],leptacanthichthys[&&NHX:TOL=56904],ctenochirichthys[&&NHX:TOL=56900])[&&NHX:TOL=110596])[&&NHX:TOL=110593])[&&NHX:TOL=110592])[&&NHX:TOL=110591])oneirodidae[&&NHX:TOL=22026])[&&NHX:TOL=110589],((caulophryne[&&NHX:TOL=56878],robia[&&NHX:TOL=56879])caulophrynidae[&&NHX:TOL=22025],((neoceratias spinifer[&&NHX:TOL=22002],(gigantactis[&&NHX:TOL=56926],rhynchactis[&&NHX:TOL=56927])gigantactinidae[&&NHX:TOL=22011])[&&NHX:TOL=22052],(photocorynus[&&NHX:TOL=56932],(haplophryne[&&NHX:TOL=56930],(acentrophryne[&&NHX:TOL=56928],(borophryne[&&NHX:TOL=56929],linophryne[&&NHX:TOL=56931])[&&NHX:TOL=110599])[&&NHX:TOL=110598])[&&NHX:TOL=110597])linophrynidae[&&NHX:TOL=22027])[&&NHX:TOL=57753])[&&NHX:TOL=110590])[&&NHX:TOL=110588])[&&NHX:TOL=110587])[&&NHX:TOL=110586])[&&NHX:TOL=110585])ceratioidei[&&NHX:TOL=22000])[&&NHX:TOL=21999])[&&NHX:TOL=21998])[&&NHX:TOL=22045])lophiiformes[&&NHX:TOL=21989])percomorpha[&&NHX:TOL=52146],beryciformes[&&NHX:TOL=52145])[&&NHX:TOL=52144],zeiformes[&&NHX:TOL=52143])[&&NHX:TOL=52142],stephanoberyciformes[&&NHX:TOL=52141])acanthopterygii[&&NHX:TOL=15094],(bregmacerotidae[&&NHX:TOL=118961],euclichthyidae[&&NHX:TOL=118962],gadidae[&&NHX:TOL=118963],lotidae[&&NHX:TOL=118964],macrouridae[&&NHX:TOL=118965],melanonidae[&&NHX:TOL=118966],merlucciidae[&&NHX:TOL=118967],moridae[&&NHX:TOL=118968],muraenolepididae[&&NHX:TOL=118969],phycidae[&&NHX:TOL=118970])gadiformes[&&NHX:TOL=15093],percopsiformes[&&NHX:TOL=68761])[&&NHX:TOL=15092],polymixiiformes[&&NHX:TOL=15091])[&&NHX:TOL=15090],lampridiformes[&&NHX:TOL=15089])acanthomorpha[&&NHX:TOL=15088])[&&NHX:TOL=15086])[&&NHX:TOL=15084])neoteleostei[&&NHX:TOL=15082])euteleostei[&&NHX:TOL=15078])[&&NHX:TOL=15076])[&&NHX:TOL=15070])teleostei[&&NHX:TOL=15054])halecostomi[&&NHX:TOL=68717])neopterygii[&&NHX:TOL=68710])[&&NHX:TOL=68709])actinopterygii[&&NHX:TOL=14923])osteichthyes[&&NHX:TOL=14921],acanthodii[&&NHX:EXT=Y:TOL=14924])teleostomi[&&NHX:TOL=14920],chondrichthyes[&&NHX:TOL=14925])node 1[&&NHX:TOL=14919],placodermi[&&NHX:EXT=Y:TOL=14926])gnathostomata[&&NHX:TOL=14843])node 3[&&NHX:TOL=14840])node 2[&&NHX:TOL=14838])[&&NHX:TOL=14836])node 1[&&NHX:TOL=14833])vertebrata[&&NHX:TOL=14829])craniata[&&NHX:TOL=14826])[&&NHX:TOL=14822])[&&NHX:TOL=14820])chordata[&&NHX:TOL=2499])deuterostomia[&&NHX:TOL=2466],((((((((podura[&&NHX:TOL=10351],(onychiurinae[&&NHX:TOL=50879],tetrodontophorinae[&&NHX:TOL=50880])onychiuridae[&&NHX:TOL=10352],hypogastruridae[&&NHX:TOL=10353],brachystomellidae[&&NHX:TOL=10354],odontellidae[&&NHX:TOL=10355],(caputanurininae[&&NHX:TOL=50881],frieseinae[&&NHX:TOL=50882],morulininae[&&NHX:TOL=50883],neanurinae[&&NHX:TOL=50884],pseudachorutinae[&&NHX:TOL=50885],uchidanurinae[&&NHX:TOL=50886])neanuridae[&&NHX:TOL=10356])poduromorpha[&&NHX:TOL=10327],(katiannidae[&&NHX:TOL=10359],spinothecidae[&&NHX:TOL=10360],bourletiellidae[&&NHX:TOL=10361],mackenziella psocoides[&&NHX:TOL=10362],(bothriovulsus[&&NHX:TOL=50887],calvatomina[&&NHX:TOL=50888],dicyrtoma[&&NHX:TOL=50889],dicyrtomina[&&NHX:TOL=50890],gibberathrix[&&NHX:TOL=50891],jordanathrix[&&NHX:TOL=50892],papirioides[&&NHX:TOL=50893],ptenothrix[&&NHX:TOL=50894])dicyrtomidae[&&NHX:TOL=10364],sminthuridae[&&NHX:TOL=10363],sminthurididae[&&NHX:TOL=10358],sturmius[&&NHX:TOL=10365],arrhopalitidae[&&NHX:TOL=10366])symphypleona[&&NHX:TOL=10328],(neelus[&&NHX:TOL=10345],neelides[&&NHX:TOL=10346],megalothorax[&&NHX:TOL=10347],acanthothorax pratensis[&&NHX:TOL=10348],zelandothorax novaezealandiae[&&NHX:TOL=10349])neelidae[&&NHX:TOL=10329],isotogastrura[&&NHX:TOL=10330],(anurophorinae[&&NHX:TOL=50895],proisotominae[&&NHX:TOL=50896],isotominae[&&NHX:TOL=50897],pachyotominae[&&NHX:TOL=50898])isotomidae[&&NHX:TOL=10331],protentomobrya walkeri[&&NHX:EXT=Y:TOL=10332],coenaletes[&&NHX:TOL=10333],actaletidae[&&NHX:TOL=10334],microfalcula delamarei[&&NHX:TOL=10335],paronellidae[&&NHX:TOL=10336],(orchesellinae[&&NHX:TOL=50899],entomobryinae[&&NHX:TOL=50900],lepidocyrtinae[&&NHX:TOL=50901],seirinae[&&NHX:TOL=50902])entomobryidae[&&NHX:TOL=10337],oncobrya decepta[&&NHX:EXT=Y:TOL=10338],rhyniella praecursor[&&NHX:EXT=Y:TOL=10339],cyphoderidae[&&NHX:TOL=10340],((antennacyrtus[&&NHX:TOL=50903],aphaenomurus[&&NHX:TOL=50904],entomocerus[&&NHX:TOL=50905],lasofinius[&&NHX:TOL=50906],lepidophorella[&&NHX:TOL=50907],lethemurus[&&NHX:TOL=50908],monodontocerus[&&NHX:TOL=50909],neophorella[&&NHX:TOL=50910],novacerus[&&NHX:TOL=50911],plutomurus[&&NHX:TOL=50912],pogonognathellus[&&NHX:TOL=50913],pseudolepidophorella[&&NHX:TOL=50914],tomocerina[&&NHX:TOL=50915],tomocerus[&&NHX:TOL=50916],tomolonus[&&NHX:TOL=50917],tritomurus[&&NHX:TOL=50918])tomoceridae[&&NHX:TOL=10342],oncopoduridae[&&NHX:TOL=10343])[&&NHX:TOL=10341])collembola[&&NHX:TOL=8202],(((sinentomon chui[&&NHX:TOL=26869],sinentomon erythranum[&&NHX:TOL=26870],sinentomon yoroi[&&NHX:TOL=26871])sinentomon[&&NHX:TOL=14439],(fujientomon dicestum[&&NHX:TOL=26872],fujientomon primum[&&NHX:TOL=26873])fujientomon[&&NHX:TOL=14440])sinentomata[&&NHX:TOL=14438],((hesperentomon[&&NHX:TOL=26899],huhentomon[&&NHX:TOL=26900],ionescuellum[&&NHX:TOL=26901])hesperentomidae[&&NHX:TOL=14446],(condeellum[&&NHX:TOL=26902],hinomotentomon[&&NHX:TOL=26903],neocondeellum[&&NHX:TOL=26904],paracondeellum[&&NHX:TOL=26905],protentomon[&&NHX:TOL=26906],proturentomon[&&NHX:TOL=26907])protentomidae[&&NHX:TOL=14447],(acerella[&&NHX:TOL=26908],acerentomon[&&NHX:TOL=26909],acerentuloides[&&NHX:TOL=26910],acerentulus[&&NHX:TOL=26911],alaskaentomon[&&NHX:TOL=26912],amazonentulus[&&NHX:TOL=26913],amphientulus[&&NHX:TOL=26914],andinentulus[&&NHX:TOL=26915],australentulus[&&NHX:TOL=26916],baculentulus[&&NHX:TOL=26917],berberentulus[&&NHX:TOL=26918],bolivaridia[&&NHX:TOL=26919],brasilentulus[&&NHX:TOL=26920],brasilidia[&&NHX:TOL=26921],callientomon[&&NHX:TOL=26922],chosonentulus[&&NHX:TOL=26923],delamarentulus[&&NHX:TOL=26924],filientomon[&&NHX:TOL=26925],fjellbergella[&&NHX:TOL=26926],gracilentulus[&&NHX:TOL=26927],huashanentulus[&&NHX:TOL=26928],imadateiella[&&NHX:TOL=26929],kenyentulus[&&NHX:TOL=26930],madagascaridia[&&NHX:TOL=26931],maderentulus[&&NHX:TOL=26932],najtentulus[&&NHX:TOL=26933],neobaculentulus[&&NHX:TOL=26934],nienna[&&NHX:TOL=26935],nipponentomon[&&NHX:TOL=26936],noldo[&&NHX:TOL=26937],nosekiella[&&NHX:TOL=26938],notentulus[&&NHX:TOL=26939],orinentomon[&&NHX:TOL=26940],paracerella[&&NHX:TOL=26941],podolinella[&&NHX:TOL=26942],polyadenum[&&NHX:TOL=26943],proacerella[&&NHX:TOL=26944],silvestridia[&&NHX:TOL=26945],sugaentulus[&&NHX:TOL=26946],tasmanentulus[&&NHX:TOL=26947],tuxenentulus[&&NHX:TOL=26948],tuxenidia[&&NHX:TOL=26949],verrucoentomon[&&NHX:TOL=26950],vesiculentomon[&&NHX:TOL=26951],vindobonella[&&NHX:TOL=26952],wenyingia[&&NHX:TOL=26953],yamatentomon[&&NHX:TOL=26954],yavanna[&&NHX:TOL=26955],yichunentulus[&&NHX:TOL=26956],yinentulus[&&NHX:TOL=26957],zangentulus[&&NHX:TOL=26958])acerentomidae[&&NHX:TOL=14448])acerentomata[&&NHX:TOL=14445],(antelientomon[&&NHX:TOL=14443],(anisentomon[&&NHX:TOL=26959],eosentomon[&&NHX:TOL=26960],isoentomon[&&NHX:TOL=26961],madagascarentomon[&&NHX:TOL=26962],neanisentomon[&&NHX:TOL=26963],paranisentomon[&&NHX:TOL=26964],pseudanisentomon[&&NHX:TOL=26965],styletoentomon[&&NHX:TOL=26966],zhongguohentomon[&&NHX:TOL=26967])eosentomidae[&&NHX:TOL=14444])eosentomata[&&NHX:TOL=14442])protura[&&NHX:TOL=8203])[&&NHX:TOL=8201],(campodeidae[&&NHX:TOL=10413],procampodeidae[&&NHX:TOL=10414],projapygidae[&&NHX:TOL=10415],anajapygidae[&&NHX:TOL=10416],japygidae[&&NHX:TOL=10417],heterojapygidae[&&NHX:TOL=10418],dinjapygidae[&&NHX:TOL=10419],evalljapygidae[&&NHX:TOL=10420],parajapygidae[&&NHX:TOL=10421],onychojapyx schmidti[&&NHX:EXT=Y:TOL=10422],plioprojapyx primitivus[&&NHX:EXT=Y:TOL=10423])diplura[&&NHX:TOL=8204],((((meinertellidae[&&NHX:TOL=8271],machilidae[&&NHX:TOL=8272],triassomachilis uralensis[&&NHX:EXT=Y:TOL=8273])machiloidea[&&NHX:TOL=8270],(lepidodasypus sharovi[&&NHX:EXT=Y:TOL=8275],dasyleptus noli[&&NHX:EXT=Y:TOL=8276],dasyleptus lucasi[&&NHX:EXT=Y:TOL=8277],dasyleptus brongniarti[&&NHX:EXT=Y:TOL=8278])monura[&&NHX:TOL=8274])[&&NHX:TOL=8269],cercopodata[&&NHX:EXT=Y:TOL=8279])archaeognatha[&&NHX:TOL=8207],((lepidothrichidae[&&NHX:TOL=14531],nicoletiidae[&&NHX:TOL=14532],lepismatidae[&&NHX:TOL=14533],maindroniidae[&&NHX:TOL=14534])thysanura[&&NHX:TOL=8209],((((diaphanoptera[&&NHX:EXT=Y:TOL=10387],philiasptilon[&&NHX:EXT=Y:TOL=10388])diaphanopteridae[&&NHX:TOL=10386],(prochoroptera[&&NHX:EXT=Y:TOL=10390],euchoroptera[&&NHX:EXT=Y:TOL=10391])prochoropteridae[&&NHX:TOL=10389],elmoa[&&NHX:EXT=Y:TOL=10392],(parelmoa[&&NHX:EXT=Y:TOL=10394],pseudelmoa[&&NHX:EXT=Y:TOL=10395],uralia[&&NHX:EXT=Y:TOL=10396])parelmoidae[&&NHX:TOL=10393],paruralia[&&NHX:EXT=Y:TOL=10397],(martynovia[&&NHX:EXT=Y:TOL=10399],eumartynovia[&&NHX:EXT=Y:TOL=10400],phaneroneura[&&NHX:EXT=Y:TOL=10401])martynoviidae[&&NHX:TOL=10398],biarmohymen[&&NHX:EXT=Y:TOL=10402],asthenohymen[&&NHX:EXT=Y:TOL=10403],rhaphidiopsis[&&NHX:EXT=Y:TOL=10404],parabrodia[&&NHX:EXT=Y:TOL=10405],diapha[&&NHX:EXT=Y:TOL=10406],elmodiapha[&&NHX:EXT=Y:TOL=10407],paradiapha[&&NHX:EXT=Y:TOL=10408],permodiapha[&&NHX:EXT=Y:TOL=10409],protodiapha[&&NHX:EXT=Y:TOL=10410],stenodiapha[&&NHX:EXT=Y:TOL=10411])diaphanopterodea[&&NHX:EXT=Y:TOL=8259],(((dictyoneura[&&NHX:EXT=Y:TOL=13536],cleffia[&&NHX:EXT=Y:TOL=13537],dictyoneurula[&&NHX:EXT=Y:TOL=13538],goldenbergia[&&NHX:EXT=Y:TOL=13539],kallenbergia[&&NHX:EXT=Y:TOL=13540],macrodictya[&&NHX:EXT=Y:TOL=13541],microdictya[&&NHX:EXT=Y:TOL=13542],polioptenus[&&NHX:EXT=Y:TOL=13543],rotundopteris[&&NHX:EXT=Y:TOL=13544],sagenoptera[&&NHX:EXT=Y:TOL=13545],schmidtopteron[&&NHX:EXT=Y:TOL=13546],siberiodictya[&&NHX:EXT=Y:TOL=13547],stenodictya[&&NHX:EXT=Y:TOL=13548],stenodictyoneura[&&NHX:EXT=Y:TOL=13549],stilbocrocis[&&NHX:EXT=Y:TOL=13550])dictyoneuridae[&&NHX:EXT=Y:TOL=13466],(lithomantis[&&NHX:EXT=Y:TOL=13578],lusiella[&&NHX:EXT=Y:TOL=13579],synarmoge[&&NHX:EXT=Y:TOL=13580])lithomanteidae[&&NHX:EXT=Y:TOL=13467],(megaptilus[&&NHX:EXT=Y:TOL=13590],lithoptilus[&&NHX:EXT=Y:TOL=13591])megaptilidae[&&NHX:EXT=Y:TOL=13468],((calvertiella[&&NHX:EXT=Y:TOL=13530],carrizopteryx[&&NHX:EXT=Y:TOL=13531],moravia[&&NHX:EXT=Y:TOL=13532],moraviptera[&&NHX:EXT=Y:TOL=13533],sharovia[&&NHX:EXT=Y:TOL=13534])calvertiellidae[&&NHX:EXT=Y:TOL=13470],archaemegaptilus[&&NHX:EXT=Y:TOL=13471],(eugereon[&&NHX:EXT=Y:TOL=13555],dictyoptilus[&&NHX:EXT=Y:TOL=13556],peromaptera[&&NHX:EXT=Y:TOL=13557],sandiella[&&NHX:EXT=Y:TOL=13558],valdeania[&&NHX:EXT=Y:TOL=13559])eugereonidae[&&NHX:EXT=Y:TOL=13472])[&&NHX:TOL=13469],(lycocercus[&&NHX:EXT=Y:TOL=13582],apopappus[&&NHX:EXT=Y:TOL=13583],lycodemas[&&NHX:EXT=Y:TOL=13584],lycodus[&&NHX:EXT=Y:TOL=13585],madera[&&NHX:EXT=Y:TOL=13586],notorachis[&&NHX:EXT=Y:TOL=13587],polycreagra[&&NHX:EXT=Y:TOL=13588])lycocercidae[&&NHX:EXT=Y:TOL=13473],(graphiptilus[&&NHX:EXT=Y:TOL=13564],rhabdoptilus[&&NHX:EXT=Y:TOL=13565])graphiptilidae[&&NHX:EXT=Y:TOL=13474],(breyeria[&&NHX:EXT=Y:TOL=13525],hasala[&&NHX:EXT=Y:TOL=13526],megaptiloides[&&NHX:EXT=Y:TOL=13527],stobbsia[&&NHX:EXT=Y:TOL=13528])breyeriidae[&&NHX:EXT=Y:TOL=13475],(tchirkovaea[&&NHX:EXT=Y:TOL=13612],paimbia[&&NHX:EXT=Y:TOL=13613])tchirkovaeidae[&&NHX:EXT=Y:TOL=13476],(homoioptera[&&NHX:EXT=Y:TOL=13567],adolarryia[&&NHX:EXT=Y:TOL=13568],boltopruvostia[&&NHX:EXT=Y:TOL=13569],larryia[&&NHX:EXT=Y:TOL=13570],mazonopterum[&&NHX:EXT=Y:TOL=13571],mazothairos[&&NHX:EXT=Y:TOL=13572],parathesoneura[&&NHX:EXT=Y:TOL=13573],scepasma[&&NHX:EXT=Y:TOL=13574],thesoneura[&&NHX:EXT=Y:TOL=13575],turneropterum[&&NHX:EXT=Y:TOL=13576])homoiopteridae[&&NHX:EXT=Y:TOL=13477],mecynostomata[&&NHX:EXT=Y:TOL=13478],(fouquea[&&NHX:EXT=Y:TOL=13561],neofouquea[&&NHX:EXT=Y:TOL=13562])fouqueidae[&&NHX:EXT=Y:TOL=13479],eubleptus[&&NHX:EXT=Y:TOL=13480],(spilaptera[&&NHX:EXT=Y:TOL=13593],abaptilon[&&NHX:EXT=Y:TOL=13594],baeoneura[&&NHX:EXT=Y:TOL=13595],becquerelia[&&NHX:EXT=Y:TOL=13596],delitzschala bitterfeldensis[&&NHX:EXT=Y:TOL=13597],dunbaria[&&NHX:EXT=Y:TOL=13598],epitethe[&&NHX:EXT=Y:TOL=13599],homaloneura[&&NHX:EXT=Y:TOL=13600],lamproptilia[&&NHX:EXT=Y:TOL=13601],mcluckiepteron[&&NHX:EXT=Y:TOL=13602],neuburgia[&&NHX:EXT=Y:TOL=13603],palaeoptilus[&&NHX:EXT=Y:TOL=13604],paradunbaria[&&NHX:EXT=Y:TOL=13605],permiakovia[&&NHX:EXT=Y:TOL=13606],sheltoweeptera[&&NHX:EXT=Y:TOL=13607],spiloptilus[&&NHX:EXT=Y:TOL=13608],tectoptilus[&&NHX:EXT=Y:TOL=13609],vorkutoneura[&&NHX:EXT=Y:TOL=13610])spilapteridae[&&NHX:EXT=Y:TOL=13481],(elmoboria[&&NHX:EXT=Y:TOL=13552],oboria[&&NHX:EXT=Y:TOL=13553])elmoboriidae[&&NHX:EXT=Y:TOL=13482])[&&NHX:TOL=13465],kansasia[&&NHX:EXT=Y:TOL=13483],mammia[&&NHX:EXT=Y:TOL=13484],mecynoptera[&&NHX:EXT=Y:TOL=13485],mecynostomites[&&NHX:EXT=Y:TOL=13486],monsteropterum[&&NHX:EXT=Y:TOL=13487],palaiotaptus[&&NHX:EXT=Y:TOL=13488],palapteris[&&NHX:EXT=Y:TOL=13489],paramecynostoma[&&NHX:EXT=Y:TOL=13490],paramegaptilus[&&NHX:EXT=Y:TOL=13491],platephemera[&&NHX:EXT=Y:TOL=13492],propalingenia[&&NHX:EXT=Y:TOL=13493],pseudomecynostoma[&&NHX:EXT=Y:TOL=13494],psychroptilus[&&NHX:EXT=Y:TOL=13495],pteronidia[&&NHX:EXT=Y:TOL=13496],rochdalia[&&NHX:EXT=Y:TOL=13497],saarlandia[&&NHX:EXT=Y:TOL=13498],sabitaptus[&&NHX:EXT=Y:TOL=13499],schedoneura[&&NHX:EXT=Y:TOL=13500],severinopsis[&&NHX:EXT=Y:TOL=13501],titanodictya[&&NHX:EXT=Y:TOL=13502],turnbullia[&&NHX:EXT=Y:TOL=13503],althansia[&&NHX:EXT=Y:TOL=13504],ametretus[&&NHX:EXT=Y:TOL=13505],amousus[&&NHX:EXT=Y:TOL=13506],anagesthes[&&NHX:EXT=Y:TOL=13507],anthracosta[&&NHX:EXT=Y:TOL=13508],asiodictya[&&NHX:EXT=Y:TOL=13509],bathytaptus[&&NHX:EXT=Y:TOL=13510],bojoptera[&&NHX:EXT=Y:TOL=13511],boltonocosta[&&NHX:EXT=Y:TOL=13512],catadyesthus[&&NHX:EXT=Y:TOL=13513],compsoneura[&&NHX:EXT=Y:TOL=13514],diexodus[&&NHX:EXT=Y:TOL=13515],eumecoptera[&&NHX:EXT=Y:TOL=13516],eurydictyella[&&NHX:EXT=Y:TOL=13517],eurythmopteryx[&&NHX:EXT=Y:TOL=13518],gegenemene[&&NHX:EXT=Y:TOL=13519],haplophlebium[&&NHX:EXT=Y:TOL=13520],heolus[&&NHX:EXT=Y:TOL=13521],idoptilus[&&NHX:EXT=Y:TOL=13522],jongmansia[&&NHX:EXT=Y:TOL=13523])paleodictyoptera[&&NHX:EXT=Y:TOL=8260],(aspidothorax[&&NHX:EXT=Y:TOL=13076],anchineura[&&NHX:EXT=Y:TOL=13077],aspidohymen[&&NHX:EXT=Y:TOL=13078],aykhal[&&NHX:EXT=Y:TOL=13079],corydaloides[&&NHX:EXT=Y:TOL=13080],brodioptera[&&NHX:EXT=Y:TOL=13081],foriria[&&NHX:EXT=Y:TOL=13082],(sphecoptera[&&NHX:EXT=Y:TOL=13084],cyclocelis[&&NHX:EXT=Y:TOL=13085])sphecopteridae[&&NHX:TOL=13083],ischnoptilus[&&NHX:EXT=Y:TOL=13086],(mischoptera[&&NHX:EXT=Y:TOL=13088],psilothorax[&&NHX:EXT=Y:TOL=13089])mischopteridae[&&NHX:TOL=13087],(protohymen[&&NHX:EXT=Y:TOL=13091],ivahymen[&&NHX:EXT=Y:TOL=13092],permohymen[&&NHX:EXT=Y:TOL=13093])protohymenidae[&&NHX:TOL=13090],(scytohymen[&&NHX:EXT=Y:TOL=13095],tshekardohymen[&&NHX:EXT=Y:TOL=13096])scytohymenidae[&&NHX:TOL=13094],(bardohymen[&&NHX:EXT=Y:TOL=13098],actinohymen[&&NHX:EXT=Y:TOL=13099],alexahymen[&&NHX:EXT=Y:TOL=13100],calohymen[&&NHX:EXT=Y:TOL=13101],sylvohymen[&&NHX:EXT=Y:TOL=13102])bardohymenidae[&&NHX:TOL=13097],moravohymen[&&NHX:EXT=Y:TOL=13103],(eubrodia[&&NHX:EXT=Y:TOL=13105],brodia[&&NHX:EXT=Y:TOL=13106])brodiidae[&&NHX:TOL=13104],ancoptera[&&NHX:EXT=Y:TOL=13107],(vorkutia[&&NHX:EXT=Y:TOL=13109],sibiriohymen[&&NHX:EXT=Y:TOL=13110])vorkutiidae[&&NHX:TOL=13108],alectoneura[&&NHX:EXT=Y:TOL=13111],hana[&&NHX:EXT=Y:TOL=13112],(anconeura[&&NHX:EXT=Y:TOL=13114],arcioneura[&&NHX:EXT=Y:TOL=13115])arcioneuridae[&&NHX:TOL=13113],cauloptera[&&NHX:EXT=Y:TOL=13116],engisoptera[&&NHX:EXT=Y:TOL=13117],lameereites[&&NHX:EXT=Y:TOL=13118])megasecoptera[&&NHX:EXT=Y:TOL=8261],((permothemis[&&NHX:EXT=Y:TOL=13617],ideliella[&&NHX:EXT=Y:TOL=13618],pauciramus[&&NHX:EXT=Y:TOL=13619],permothemidia[&&NHX:EXT=Y:TOL=13620])permothemistidae[&&NHX:TOL=13616],(diathema[&&NHX:EXT=Y:TOL=13622],diathemidia[&&NHX:EXT=Y:TOL=13623])diathemidae[&&NHX:TOL=13621])permothemistida[&&NHX:EXT=Y:TOL=8262])paleodictyopteroidea[&&NHX:EXT=Y:TOL=8264],(((siphlonuridae[&&NHX:TOL=10766],baetidae[&&NHX:TOL=10767],oniscigastridae[&&NHX:TOL=10768],ameletopsidae[&&NHX:TOL=10769],ametropodidae[&&NHX:TOL=10770])baetoidea[&&NHX:TOL=10765],(coloburiscidae[&&NHX:TOL=10772],oligoneuriidae[&&NHX:TOL=10773],isonychiidae[&&NHX:TOL=10774],heptageniidae[&&NHX:TOL=10775])heptagenioidea[&&NHX:TOL=10771],leptophlebiidae[&&NHX:TOL=10776],(behningiidae[&&NHX:TOL=10778],potamanthidae[&&NHX:TOL=10779],euthyplociidae[&&NHX:TOL=10780],polymitarcydae[&&NHX:TOL=10781],ephemeridae[&&NHX:TOL=10782],palingeniidae[&&NHX:TOL=10783])ephemeroidea[&&NHX:TOL=10777])schistonota[&&NHX:TOL=10764],((ephemerellidae[&&NHX:TOL=10786],leptohyphidae[&&NHX:TOL=10787],tricorythidae[&&NHX:TOL=10788])ephemerelloidea[&&NHX:TOL=10785],(neoephemeridae[&&NHX:TOL=10790],baetiscidae[&&NHX:TOL=10791],caenidae[&&NHX:TOL=10792],prosopistomatidae[&&NHX:TOL=10793])caenoidea[&&NHX:TOL=10789])pannota[&&NHX:TOL=10784])ephemeroptera[&&NHX:TOL=8265],(protodonata[&&NHX:EXT=Y:TOL=13265],(protanisoptera[&&NHX:EXT=Y:TOL=13267],triadophlebiomorpha[&&NHX:EXT=Y:TOL=13268],(protozygoptera[&&NHX:EXT=Y:TOL=13270],archizygoptera[&&NHX:EXT=Y:TOL=13271])[&&NHX:TOL=13269],(zygoptera[&&NHX:TOL=13273],(anisozygoptera[&&NHX:TOL=13275],anisoptera[&&NHX:TOL=13276])[&&NHX:TOL=13274])[&&NHX:TOL=13272])[&&NHX:TOL=13266])odonata[&&NHX:TOL=8266],((((((((((((amphigerontia alticola[&&NHX:TOL=35186],amphigerontia anchonae[&&NHX:TOL=35187],amphigerontia bifasciata[&&NHX:TOL=35188],amphigerontia birabeni[&&NHX:TOL=35189],amphigerontia boliviana[&&NHX:TOL=35190],amphigerontia contaminata[&&NHX:TOL=35191],amphigerontia diffusa[&&NHX:TOL=35192],amphigerontia feai[&&NHX:TOL=35193],amphigerontia guiyangica[&&NHX:TOL=35194],amphigerontia hyalina[&&NHX:TOL=35195],amphigerontia incerta[&&NHX:TOL=35196],amphigerontia infernicola[&&NHX:TOL=35197],amphigerontia intermedia[&&NHX:TOL=35198],amphigerontia jezoensis[&&NHX:TOL=35199],amphigerontia lata[&&NHX:TOL=35200],amphigerontia lhasana[&&NHX:TOL=35201],amphigerontia limpida[&&NHX:TOL=35202],amphigerontia minutissima[&&NHX:TOL=35203],amphigerontia montivaga[&&NHX:TOL=35204],amphigerontia nadleri[&&NHX:TOL=35205],amphigerontia namiana[&&NHX:TOL=35206],amphigerontia nervosa[&&NHX:TOL=35207],amphigerontia petiolata[&&NHX:TOL=35208],amphigerontia shanxiensis[&&NHX:TOL=35209],amphigerontia sicyoides[&&NHX:TOL=35210],amphigerontia tincta[&&NHX:TOL=35211],amphigerontia titschacki[&&NHX:TOL=35212],amphigerontia umbrata[&&NHX:TOL=35213],amphigerontia unacrodonta[&&NHX:TOL=35214],amphigerontia voeltzkowi[&&NHX:TOL=35215])amphigerontia[&&NHX:TOL=35103],(anomaloblaste spinivalva[&&NHX:TOL=35216],anomaloblaste treubia[&&NHX:TOL=35217])anomaloblaste[&&NHX:TOL=35104],(blaste alfineta[&&NHX:TOL=35218],blaste alluaudi[&&NHX:TOL=35219],blaste amazonica[&&NHX:TOL=35220],blaste angolensis[&&NHX:TOL=35221],blaste angusta[&&NHX:TOL=35222],blaste angustipennis[&&NHX:TOL=35223],blaste annellus[&&NHX:TOL=35224],blaste aptera[&&NHX:TOL=35225],blaste arabica[&&NHX:TOL=35226],blaste auricularia[&&NHX:TOL=35227],blaste balli[&&NHX:TOL=35228],blaste basilewskyi[&&NHX:TOL=35229],blaste betschi[&&NHX:TOL=35230],blaste bicuspis[&&NHX:TOL=35231],blaste binotata[&&NHX:TOL=35232],blaste bistriata[&&NHX:TOL=35233],blaste bridarollii[&&NHX:TOL=35234],blaste capricornuta[&&NHX:TOL=35235],blaste castala[&&NHX:TOL=35236],blaste caudata[&&NHX:TOL=35237],blaste cinerea[&&NHX:TOL=35238],blaste cockerelli[&&NHX:TOL=35239],blaste conspurcata[&&NHX:TOL=35240],blaste cornuta[&&NHX:TOL=35241],blaste cyclota[&&NHX:TOL=35242],blaste cyprica[&&NHX:TOL=35243],blaste didyma[&&NHX:TOL=35244],blaste dundoensis[&&NHX:TOL=35245],blaste edwardi[&&NHX:TOL=35246],blaste euryphylla[&&NHX:TOL=35247],blaste falcifer[&&NHX:TOL=35248],blaste falsa[&&NHX:TOL=35249],blaste fasciata[&&NHX:TOL=35250],blaste forcepata[&&NHX:TOL=35251],blaste forficula[&&NHX:TOL=35252],blaste furcilla[&&NHX:TOL=35253],blaste fuscoptera[&&NHX:TOL=35254],blaste fusimera[&&NHX:TOL=35255],blaste garciorum[&&NHX:TOL=35256],blaste hamata[&&NHX:TOL=35257],blaste immobilis[&&NHX:TOL=35258],blaste lignicola[&&NHX:TOL=35259],blaste ligula[&&NHX:TOL=35260],blaste longicauda[&&NHX:TOL=35261],blaste longipennis[&&NHX:TOL=35262],blaste longispina[&&NHX:TOL=35263],blaste longivalva[&&NHX:TOL=35264],blaste lunnulata[&&NHX:TOL=35265],blaste lusambaensis[&&NHX:TOL=35266],blaste lyriphallus[&&NHX:TOL=35267],blaste machadoi[&&NHX:TOL=35268],blaste macrops[&&NHX:TOL=35269],blaste macrura[&&NHX:TOL=35270],blaste magnifica[&&NHX:TOL=35271],blaste martini[&&NHX:TOL=35272],blaste medleri[&&NHX:TOL=35273],blaste membranosa[&&NHX:TOL=35274],blaste memorialis[&&NHX:TOL=35275],blaste monserrati[&&NHX:TOL=35276],blaste muhni[&&NHX:TOL=35277],blaste nairobensis[&&NHX:TOL=35278],blaste nana[&&NHX:TOL=35279],blaste neotenica[&&NHX:TOL=35280],blaste nubeculosa[&&NHX:TOL=35281],blaste nubilistigma[&&NHX:TOL=35282],blaste obscura[&&NHX:TOL=35283],blaste obtusa[&&NHX:TOL=35284],blaste octofaria[&&NHX:TOL=35285],blaste opposita[&&NHX:TOL=35286],blaste oregona[&&NHX:TOL=35287],blaste osceola[&&NHX:TOL=35288],blaste osella[&&NHX:TOL=35289],blaste pallida[&&NHX:TOL=35290],blaste panops[&&NHX:TOL=35291],blaste pauliani[&&NHX:TOL=35292],blaste peringueyi[&&NHX:TOL=35293],blaste persimilis[&&NHX:TOL=35294],blaste phrynae[&&NHX:TOL=35295],blaste plaumanni[&&NHX:TOL=35296],blaste polioptera[&&NHX:TOL=35297],blaste posticata[&&NHX:TOL=35298],blaste pseudozonata[&&NHX:TOL=35299],blaste pusilla[&&NHX:TOL=35300],blaste quadrimaculata[&&NHX:TOL=35301],blaste quieta[&&NHX:TOL=35302],blaste richardsi[&&NHX:TOL=35303],blaste rotundata[&&NHX:TOL=35304],blaste sarda[&&NHX:TOL=35305],blaste serrata[&&NHX:TOL=35306],blaste similis[&&NHX:TOL=35307],blaste simillima[&&NHX:TOL=35308],blaste smilivirgata[&&NHX:TOL=35309],blaste squarrosa[&&NHX:TOL=35310],blaste stuckenbergi[&&NHX:TOL=35311],blaste subapterous[&&NHX:TOL=35312],blaste subquieta[&&NHX:TOL=35313],blaste suffusa[&&NHX:TOL=35314],blaste taylori[&&NHX:TOL=35315],blaste tillyardi[&&NHX:TOL=35316],blaste togoensis[&&NHX:TOL=35317],blaste triagularum[&&NHX:TOL=35318],blaste ukingana[&&NHX:TOL=35319],blaste vadoni[&&NHX:TOL=35320],blaste verticalis[&&NHX:TOL=35321],blaste viettei[&&NHX:TOL=35322],blaste vilhenai[&&NHX:TOL=35323],blaste virgata[&&NHX:TOL=35324],blaste yigongensis[&&NHX:TOL=35325])blaste[&&NHX:TOL=35105],(blastopsocidus acutus[&&NHX:TOL=35326],blastopsocidus affinis[&&NHX:TOL=35327],blastopsocidus areolatus[&&NHX:TOL=35328],blastopsocidus brasiliensis[&&NHX:TOL=35329],blastopsocidus caudatus[&&NHX:TOL=35330],blastopsocidus cristatus[&&NHX:TOL=35331],blastopsocidus flavidus[&&NHX:TOL=35332],blastopsocidus maculatus[&&NHX:TOL=35333],blastopsocidus marginalis[&&NHX:TOL=35334],blastopsocidus montanus[&&NHX:TOL=35335],blastopsocidus pictus[&&NHX:TOL=35336],blastopsocidus pini[&&NHX:TOL=35337],blastopsocidus quinquedentatus[&&NHX:TOL=35338],blastopsocidus strictus[&&NHX:TOL=35339],blastopsocidus wittmeri[&&NHX:TOL=35340])blastopsocidus[&&NHX:TOL=35106],(blastopsocus angustus[&&NHX:TOL=35341],blastopsocus goodrichi[&&NHX:TOL=35342],blastopsocus johnstoni[&&NHX:TOL=35343],blastopsocus lithinus[&&NHX:TOL=35344],blastopsocus mockfordi[&&NHX:TOL=35345],blastopsocus semistriatus[&&NHX:TOL=35346],blastopsocus uncinatus[&&NHX:TOL=35347],blastopsocus variabilis[&&NHX:TOL=35348],blastopsocus walshi[&&NHX:TOL=35349])blastopsocus[&&NHX:TOL=35107],chaetopsocidus sturmi[&&NHX:TOL=35108],chilopsocus macrochilus[&&NHX:TOL=35109],disopsocus megacheilus[&&NHX:TOL=35110],elaphopsocus glaphyrostigma[&&NHX:TOL=35111],elytropsocus coleoptratus[&&NHX:TOL=35112],(epiblaste glandacea[&&NHX:TOL=35355],epiblaste huananiensis[&&NHX:TOL=35356])epiblaste[&&NHX:TOL=35113],euclismioides inocellata[&&NHX:TOL=35114],(indoblaste discoloba[&&NHX:TOL=35358],indoblaste lawuensis[&&NHX:TOL=35359],indoblaste lienhardi[&&NHX:TOL=35360],indoblaste sastrawani[&&NHX:TOL=35361])indoblaste[&&NHX:TOL=35115],(javablaste aidab[&&NHX:TOL=35362],javablaste merapiensis[&&NHX:TOL=35363])javablaste[&&NHX:TOL=35116],(kaindipsocus emarginatus[&&NHX:TOL=35364],kaindipsocus marksae[&&NHX:TOL=35365],kaindipsocus mixtus[&&NHX:TOL=35366])kaindipsocus[&&NHX:TOL=35117],(lasiopsocus brevipilosus[&&NHX:TOL=35367],lasiopsocus dicellus[&&NHX:TOL=35368],lasiopsocus hollowayi[&&NHX:TOL=35369],lasiopsocus michaelseni[&&NHX:TOL=35370],lasiopsocus simulatus[&&NHX:TOL=35371])lasiopsocus[&&NHX:TOL=35118],metagerontia tribulosa[&&NHX:TOL=35119],(neoblaste alticola[&&NHX:TOL=35373],neoblaste ancistroides[&&NHX:TOL=35374],neoblaste brunnea[&&NHX:TOL=35375],neoblaste complexa[&&NHX:TOL=35376],neoblaste cubitalis[&&NHX:TOL=35377],neoblaste flavae[&&NHX:TOL=35378],neoblaste fujianensis[&&NHX:TOL=35379],neoblaste guangdongensis[&&NHX:TOL=35380],neoblaste harpophylla[&&NHX:TOL=35381],neoblaste javensis[&&NHX:TOL=35382],neoblaste octogona[&&NHX:TOL=35383],neoblaste ovalis[&&NHX:TOL=35384],neoblaste papillosa[&&NHX:TOL=35385],neoblaste parasetosa[&&NHX:TOL=35386],neoblaste partibilis[&&NHX:TOL=35387],neoblaste pinicola[&&NHX:TOL=35388],neoblaste profunda[&&NHX:TOL=35389],neoblaste quinquedentata[&&NHX:TOL=35390],neoblaste rectangula[&&NHX:TOL=35391],neoblaste schizopetala[&&NHX:TOL=35392],neoblaste setosa[&&NHX:TOL=35393],neoblaste soehardjani[&&NHX:TOL=35394],neoblaste timorensis[&&NHX:TOL=35395],neoblaste tricornis[&&NHX:TOL=35396],neoblaste umbonalis[&&NHX:TOL=35397])neoblaste[&&NHX:TOL=35120],(neopsocopsis hirticornis[&&NHX:TOL=35398],neopsocopsis longiptera[&&NHX:TOL=35399])neopsocopsis[&&NHX:TOL=35121],(pentablaste auctachila[&&NHX:TOL=35400],pentablaste clavata[&&NHX:TOL=35401],pentablaste jinxiuica[&&NHX:TOL=35402],pentablaste lanceolata[&&NHX:TOL=35403],pentablaste longicaudata[&&NHX:TOL=35404],pentablaste lushanensis[&&NHX:TOL=35405],pentablaste minuscula[&&NHX:TOL=35406],pentablaste obconica[&&NHX:TOL=35407],pentablaste pentasticha[&&NHX:TOL=35408],pentablaste tetraedrica[&&NHX:TOL=35409])pentablaste[&&NHX:TOL=35122],(stylatopsocus biuncialis[&&NHX:TOL=35410],stylatopsocus campanulinus[&&NHX:TOL=35411])stylatopsocus[&&NHX:TOL=35123])amphigerontiinae[&&NHX:TOL=50645],((atrichadenotecnum nudum[&&NHX:TOL=35715],atrichadenotecnum quadripunctatum[&&NHX:TOL=35716],atrichadenotecnum quinquepunctatum[&&NHX:TOL=35717],atrichadenotecnum ryukyuense[&&NHX:TOL=35718],atrichadenotecnum tayal[&&NHX:TOL=35719],atrichadenotecnum yoshizawai[&&NHX:TOL=35720])atrichadenotecnum[&&NHX:TOL=35151],(cycetes collessi[&&NHX:TOL=35618],cycetes thyrsophoroides[&&NHX:TOL=35619])cycetes[&&NHX:TOL=35142],(brachinodiscus cinctipes[&&NHX:TOL=35143],cyclotus microcorneus[&&NHX:TOL=35144],diplacanthoda bouvieri[&&NHX:TOL=35145],(metylophorus barretti[&&NHX:TOL=35623],metylophorus bicornutus[&&NHX:TOL=35624],metylophorus bishopi[&&NHX:TOL=35625],metylophorus brevantenninus[&&NHX:TOL=35626],metylophorus cabanae[&&NHX:TOL=35627],metylophorus calcaratus[&&NHX:TOL=35628],metylophorus camptodontus[&&NHX:TOL=35629],metylophorus contaminatus[&&NHX:TOL=35630],metylophorus ctenatus[&&NHX:TOL=35631],metylophorus cuneatus[&&NHX:TOL=35632],metylophorus cyclotus[&&NHX:TOL=35633],metylophorus daedaleus[&&NHX:TOL=35634],metylophorus denticulatus[&&NHX:TOL=35635],metylophorus diplodurus[&&NHX:TOL=35636],metylophorus dongbeicus[&&NHX:TOL=35637],metylophorus elongatus[&&NHX:TOL=35638],metylophorus fasciatus[&&NHX:TOL=35639],metylophorus fuscatus[&&NHX:TOL=35640],metylophorus giganteus[&&NHX:TOL=35641],metylophorus hemiphaeopterus[&&NHX:TOL=35642],metylophorus hengshanicus[&&NHX:TOL=35643],metylophorus hispidus[&&NHX:TOL=35644],metylophorus javensis[&&NHX:TOL=35645],metylophorus jinciensis[&&NHX:TOL=35646],metylophorus latespinosus[&&NHX:TOL=35647],metylophorus lisae[&&NHX:TOL=35648],metylophorus longicaudatus[&&NHX:TOL=35649],metylophorus lushanensis[&&NHX:TOL=35650],metylophorus maculosus[&&NHX:TOL=35651],metylophorus marmoreus[&&NHX:TOL=35652],metylophorus medicornutus[&&NHX:TOL=35653],metylophorus megistus[&&NHX:TOL=35654],metylophorus mendax[&&NHX:TOL=35655],metylophorus nebulifer[&&NHX:TOL=35656],metylophorus nebulosus[&&NHX:TOL=35657],metylophorus novaescotiae[&&NHX:TOL=35658],metylophorus paranebulosus[&&NHX:TOL=35659],metylophorus plebius[&&NHX:TOL=35660],metylophorus pleiotomus[&&NHX:TOL=35661],metylophorus purus[&&NHX:TOL=35662],metylophorus rotundatus[&&NHX:TOL=35663],metylophorus symmetricus[&&NHX:TOL=35664],metylophorus theresopolitanus[&&NHX:TOL=35665],metylophorus tricornis[&&NHX:TOL=35666],metylophorus trivalvis[&&NHX:TOL=35667],metylophorus uncorneus[&&NHX:TOL=35668],metylophorus wui[&&NHX:TOL=35669],metylophorus wuyinicus[&&NHX:TOL=35670],metylophorus xizangensis[&&NHX:TOL=35671],metylophorus yanezi[&&NHX:TOL=35672])metylophorus[&&NHX:TOL=35146],(ophthalmopsocus forficularis[&&NHX:TOL=35673],ophthalmopsocus ocularis[&&NHX:TOL=35674],ophthalmopsocus pallidus[&&NHX:TOL=35675])ophthalmopsocus[&&NHX:TOL=35147],(pearmania collarti[&&NHX:TOL=35676],pearmania crenulata[&&NHX:TOL=35677],pearmania fucata[&&NHX:TOL=35678],pearmania incuria[&&NHX:TOL=35679],pearmania lapidicola[&&NHX:TOL=35680],pearmania nebulosa[&&NHX:TOL=35681],pearmania rutshuruana[&&NHX:TOL=35682],pearmania tangana[&&NHX:TOL=35683],pearmania usambarana[&&NHX:TOL=35684],pearmania wittei[&&NHX:TOL=35685])pearmania[&&NHX:TOL=35148],(pilipsocus angolensis[&&NHX:TOL=35686],pilipsocus areolatus[&&NHX:TOL=35687],pilipsocus congolensis[&&NHX:TOL=35688],pilipsocus ghesquierei[&&NHX:TOL=35689],pilipsocus intricatus[&&NHX:TOL=35690],pilipsocus lepesmei[&&NHX:TOL=35691],pilipsocus machadoi[&&NHX:TOL=35692],pilipsocus vilhenai[&&NHX:TOL=35693])pilipsocus[&&NHX:TOL=35149])metylophorini[&&NHX:TOL=50648],(atropsocus atratus[&&NHX:TOL=35152],cryptopsocus cynostigmus[&&NHX:TOL=35153],(hyalopsocus contrarius[&&NHX:TOL=35723],hyalopsocus floridanus[&&NHX:TOL=35724],hyalopsocus gardinii[&&NHX:TOL=35725],hyalopsocus morio[&&NHX:TOL=35726],hyalopsocus striatus[&&NHX:TOL=35727])hyalopsocus[&&NHX:TOL=35154],(psocus alticolus[&&NHX:TOL=35728],psocus bipunctatus[&&NHX:TOL=35729],psocus crosbyi[&&NHX:TOL=35730],psocus cyllarus[&&NHX:TOL=35731],psocus dolorosus[&&NHX:TOL=35732],psocus illotus[&&NHX:TOL=35733],psocus incomptus[&&NHX:TOL=35734],psocus jeanneli[&&NHX:TOL=35735],psocus lapidarius[&&NHX:TOL=35736],psocus leidyi[&&NHX:TOL=35737],psocus mucronicaudatus[&&NHX:TOL=35738],psocus omissus[&&NHX:TOL=35739],psocus oneitus[&&NHX:TOL=35740],psocus rizali[&&NHX:TOL=35741],psocus saghaliensis[&&NHX:TOL=35742],psocus socialis[&&NHX:TOL=35743],psocus vannivalvulus[&&NHX:TOL=35744])psocus[&&NHX:TOL=35155],sacopsocus quadricornis[&&NHX:TOL=35156])psocini[&&NHX:TOL=50649],((atlantopsocus adustus[&&NHX:TOL=35746],atlantopsocus parvidens[&&NHX:TOL=35747],atlantopsocus personatus[&&NHX:TOL=35748],atlantopsocus semicircularis[&&NHX:TOL=35749],atlantopsocus triangularis[&&NHX:TOL=35750])atlantopsocus[&&NHX:TOL=35157],barrowia insularis[&&NHX:TOL=35158],(camelopsocus bactrianus[&&NHX:TOL=35752],camelopsocus hiemalis[&&NHX:TOL=35753],camelopsocus monticolus[&&NHX:TOL=35754],camelopsocus similis[&&NHX:TOL=35755],camelopsocus tucsonensis[&&NHX:TOL=35756])camelopsocus[&&NHX:TOL=35159],cephalopsocus cassideus[&&NHX:TOL=35160],(clematostigma brevistylus[&&NHX:TOL=35758],clematostigma excavatum[&&NHX:TOL=35759],clematostigma forcipatum[&&NHX:TOL=35760],clematostigma fumatum[&&NHX:TOL=35761],clematostigma hyalinum[&&NHX:TOL=35762],clematostigma indicum[&&NHX:TOL=35763],clematostigma lunulatum[&&NHX:TOL=35764],clematostigma maculiceps[&&NHX:TOL=35765],clematostigma paraguayense[&&NHX:TOL=35766],clematostigma sasmoko[&&NHX:TOL=35767],clematostigma striatum[&&NHX:TOL=35768],clematostigma subcostale[&&NHX:TOL=35769],clematostigma vinctum[&&NHX:TOL=35770])clematostigma[&&NHX:TOL=35161],(conothoracalis corollata[&&NHX:TOL=35771],conothoracalis enneagona[&&NHX:TOL=35772],conothoracalis guangxiica[&&NHX:TOL=35773],conothoracalis longimucronata[&&NHX:TOL=35774],conothoracalis perbella[&&NHX:TOL=35775],conothoracalis quinaria[&&NHX:TOL=35776],conothoracalis shilinica[&&NHX:TOL=35777],conothoracalis turriformis[&&NHX:TOL=35778],conothoracalis unciformis[&&NHX:TOL=35779])conothoracalis[&&NHX:TOL=35162],(copostigma bilineatum[&&NHX:TOL=35780],copostigma collinum[&&NHX:TOL=35781],copostigma dispersum[&&NHX:TOL=35782],copostigma dorsopunctatum[&&NHX:TOL=35783],copostigma gracilisura[&&NHX:TOL=35784],copostigma gressitti[&&NHX:TOL=35785],copostigma hyalinum[&&NHX:TOL=35786],copostigma insularum[&&NHX:TOL=35787],copostigma majus[&&NHX:TOL=35788],copostigma mara[&&NHX:TOL=35789],copostigma marosticum[&&NHX:TOL=35790],copostigma montanum[&&NHX:TOL=35791],copostigma natewa[&&NHX:TOL=35792],copostigma ouvea[&&NHX:TOL=35793],copostigma sitivanum[&&NHX:TOL=35794],copostigma trimaculatum[&&NHX:TOL=35795],copostigma vitiense[&&NHX:TOL=35796])copostigma[&&NHX:TOL=35163],fashenglianus albimaculatus[&&NHX:TOL=35164],hybopsocus bisipolaris[&&NHX:TOL=35165],(indiopsocus abouchaari[&&NHX:TOL=35799],indiopsocus acraeus[&&NHX:TOL=35800],indiopsocus affinis[&&NHX:TOL=35801],indiopsocus alticola[&&NHX:TOL=35802],indiopsocus bisignatus[&&NHX:TOL=35803],indiopsocus camagueyensis[&&NHX:TOL=35804],indiopsocus campestris[&&NHX:TOL=35805],indiopsocus caraibensis[&&NHX:TOL=35806],indiopsocus ceterus[&&NHX:TOL=35807],indiopsocus coquilletti[&&NHX:TOL=35808],indiopsocus cristatus[&&NHX:TOL=35809],indiopsocus cubanus[&&NHX:TOL=35810],indiopsocus dentatus[&&NHX:TOL=35811],indiopsocus denticulatus[&&NHX:TOL=35812],indiopsocus etiennei[&&NHX:TOL=35813],indiopsocus expansus[&&NHX:TOL=35814],indiopsocus fittkaui[&&NHX:TOL=35815],indiopsocus hilburni[&&NHX:TOL=35816],indiopsocus infumatus[&&NHX:TOL=35817],indiopsocus jamaicensis[&&NHX:TOL=35818],indiopsocus microvariegatus[&&NHX:TOL=35819],indiopsocus nebulosus[&&NHX:TOL=35820],indiopsocus obrieni[&&NHX:TOL=35821],indiopsocus palisadensis[&&NHX:TOL=35822],indiopsocus pallidus[&&NHX:TOL=35823],indiopsocus paranensis[&&NHX:TOL=35824],indiopsocus pulcher[&&NHX:TOL=35825],indiopsocus rosalesi[&&NHX:TOL=35826],indiopsocus sinuatistigma[&&NHX:TOL=35827],indiopsocus texanus[&&NHX:TOL=35828],indiopsocus ubiquitus[&&NHX:TOL=35829],indiopsocus variegatus[&&NHX:TOL=35830])indiopsocus[&&NHX:TOL=35166],(javapsocus intimadentatus[&&NHX:TOL=35831],javapsocus smithersi[&&NHX:TOL=35832],javapsocus soegiri[&&NHX:TOL=35833],javapsocus ungulatus[&&NHX:TOL=35834])javapsocus[&&NHX:TOL=35167],(loensia bannaensis[&&NHX:TOL=35835],loensia beijingensis[&&NHX:TOL=35836],loensia bicolor[&&NHX:TOL=35837],loensia bifurcata[&&NHX:TOL=35838],loensia binalis[&&NHX:TOL=35839],loensia conspersa[&&NHX:TOL=35840],loensia corollidenta[&&NHX:TOL=35841],loensia excrescens[&&NHX:TOL=35842],loensia falcata[&&NHX:TOL=35843],loensia fasciata[&&NHX:TOL=35844],loensia folivalva[&&NHX:TOL=35845],loensia fuscimacula[&&NHX:TOL=35846],loensia glabridorsum[&&NHX:TOL=35847],loensia hengshanica[&&NHX:TOL=35848],loensia infundibularis[&&NHX:TOL=35849],loensia maculosa[&&NHX:TOL=35850],loensia moesta[&&NHX:TOL=35851],loensia octogona[&&NHX:TOL=35852],loensia pearmani[&&NHX:TOL=35853],loensia pycnacantha[&&NHX:TOL=35854],loensia schoenemanni[&&NHX:TOL=35855],loensia sexcornuta[&&NHX:TOL=35856],loensia spicata[&&NHX:TOL=35857],loensia spissa[&&NHX:TOL=35858],loensia stigmatoidea[&&NHX:TOL=35859],loensia taeniana[&&NHX:TOL=35860],loensia teretiuscula[&&NHX:TOL=35861],loensia turriformis[&&NHX:TOL=35862],loensia variegata[&&NHX:TOL=35863])loensia[&&NHX:TOL=35168],(mecampsis changbaiensis[&&NHX:TOL=35864],mecampsis cinctifemur[&&NHX:TOL=35865],mecampsis dolichosa[&&NHX:TOL=35866],mecampsis insolita[&&NHX:TOL=35867],mecampsis laconia[&&NHX:TOL=35868],mecampsis lata[&&NHX:TOL=35869],mecampsis magnifica[&&NHX:TOL=35870],mecampsis multimacularis[&&NHX:TOL=35871],mecampsis ophiocephais[&&NHX:TOL=35872],mecampsis pindapoiensis[&&NHX:TOL=35873],mecampsis septangulata[&&NHX:TOL=35874],mecampsis undulata[&&NHX:TOL=35875],mecampsis unita[&&NHX:TOL=35876])mecampsis[&&NHX:TOL=35169],(oreopsocus buholzeri[&&NHX:TOL=35877],oreopsocus digitatus[&&NHX:TOL=35878],oreopsocus leptocephalus[&&NHX:TOL=35879],oreopsocus montanus[&&NHX:TOL=35880],oreopsocus sexangularis[&&NHX:TOL=35881])oreopsocus[&&NHX:TOL=35170],pseudoptycta pinicola[&&NHX:TOL=35171],(psocidus albostigmus[&&NHX:TOL=35883],psocidus apertus[&&NHX:TOL=35884],psocidus cataratae[&&NHX:TOL=35885],psocidus bifurcatus[&&NHX:TOL=35886],psocidus etiennei[&&NHX:TOL=35887],psocidus guilinensis[&&NHX:TOL=35888],psocidus hainanensis[&&NHX:TOL=35889],psocidus luotongshanicus[&&NHX:TOL=35890],psocidus manausensis[&&NHX:TOL=35891],psocidus murphyi[&&NHX:TOL=35892],psocidus samchiensis[&&NHX:TOL=35893],psocidus strictus[&&NHX:TOL=35894],psocidus trifasciatus[&&NHX:TOL=35895],psocidus validus[&&NHX:TOL=35896],psocidus zanzibarensis[&&NHX:TOL=35897],psocidus acourti[&&NHX:TOL=35898],psocidus albovarius[&&NHX:TOL=35899],psocidus aldai[&&NHX:TOL=35900],psocidus annulipes[&&NHX:TOL=35901],psocidus arenosus[&&NHX:TOL=35902],psocidus aztecanus[&&NHX:TOL=35903],psocidus bicruris[&&NHX:TOL=35904],psocidus biguttatus[&&NHX:TOL=35905],psocidus borneensis[&&NHX:TOL=35906],psocidus burmeisteri[&&NHX:TOL=35907],psocidus coniostigma[&&NHX:TOL=35908],psocidus consitus[&&NHX:TOL=35909],psocidus cuencanus[&&NHX:TOL=35910],psocidus dilutus[&&NHX:TOL=35911],psocidus ditatus[&&NHX:TOL=35912],psocidus divisus[&&NHX:TOL=35913],psocidus elegantulus[&&NHX:TOL=35914],psocidus femoratus[&&NHX:TOL=35915],psocidus flavonimbatus[&&NHX:TOL=35916],psocidus formosanus[&&NHX:TOL=35917],psocidus funerulus[&&NHX:TOL=35918],psocidus fuscatus[&&NHX:TOL=35919],psocidus ghesquierei[&&NHX:TOL=35920],psocidus gloriosus[&&NHX:TOL=35921],psocidus gomezi[&&NHX:TOL=35922],psocidus grisescens[&&NHX:TOL=35923],psocidus guttulatus[&&NHX:TOL=35924],psocidus hirsutus[&&NHX:TOL=35925],psocidus irroratus[&&NHX:TOL=35926],psocidus jacobsoni[&&NHX:TOL=35927],psocidus japonicus[&&NHX:TOL=35928],psocidus javanicus[&&NHX:TOL=35929],psocidus komiensis[&&NHX:TOL=35930],psocidus kotzbaueri[&&NHX:TOL=35931],psocidus lacroixi[&&NHX:TOL=35932],psocidus lestagei[&&NHX:TOL=35933],psocidus lobatus[&&NHX:TOL=35934],psocidus longicaudis[&&NHX:TOL=35935],psocidus longifolius[&&NHX:TOL=35936],psocidus masinus[&&NHX:TOL=35937],psocidus mouldsi[&&NHX:TOL=35938],psocidus multiplex[&&NHX:TOL=35939],psocidus nanyuensis[&&NHX:TOL=35940],psocidus nexus[&&NHX:TOL=35941],psocidus nigeriensis[&&NHX:TOL=35942],psocidus nigricornis[&&NHX:TOL=35943],psocidus nubilus[&&NHX:TOL=35944],psocidus oblitus[&&NHX:TOL=35945],psocidus oxyurus[&&NHX:TOL=35946],psocidus parilla[&&NHX:TOL=35947],psocidus parishi[&&NHX:TOL=35948],psocidus pellucidus[&&NHX:TOL=35949],psocidus peregrans[&&NHX:TOL=35950],psocidus proctus[&&NHX:TOL=35951],psocidus proi[&&NHX:TOL=35952],psocidus punctaticeps[&&NHX:TOL=35953],psocidus quadrisignatus[&&NHX:TOL=35954],psocidus reidi[&&NHX:TOL=35955],psocidus relativus[&&NHX:TOL=35956],psocidus salai[&&NHX:TOL=35957],psocidus sauteri[&&NHX:TOL=35958],psocidus schmidti[&&NHX:TOL=35959],psocidus segmentatus[&&NHX:TOL=35960],psocidus serrei[&&NHX:TOL=35961],psocidus signifer[&&NHX:TOL=35962],psocidus similaris[&&NHX:TOL=35963],psocidus simplex[&&NHX:TOL=35964],psocidus tacaoensis[&&NHX:TOL=35965],psocidus tateokanus[&&NHX:TOL=35966],psocidus tergatus[&&NHX:TOL=35967],psocidus ternatus[&&NHX:TOL=35968],psocidus venustus[&&NHX:TOL=35969],psocidus viscayanus[&&NHX:TOL=35970],psocidus vitalisi[&&NHX:TOL=35971],psocidus zikani[&&NHX:TOL=35972],psocidus zonatus[&&NHX:TOL=35973])psocidus[&&NHX:TOL=35172],(psocomesites bimaculatus[&&NHX:TOL=35974],psocomesites continuatus[&&NHX:TOL=35975],psocomesites guangzhouensis[&&NHX:TOL=35976],psocomesites laricolus[&&NHX:TOL=35977],psocomesites multidontatus[&&NHX:TOL=35978],psocomesites spinosus[&&NHX:TOL=35979],psocomesites sturmi[&&NHX:TOL=35980],psocomesites trifurcatus[&&NHX:TOL=35981])psocomesites[&&NHX:TOL=35173],(ptycta aaroni[&&NHX:TOL=35982],ptycta afasciata[&&NHX:TOL=35983],ptycta anacantha[&&NHX:TOL=35984],ptycta angulata[&&NHX:TOL=35985],ptycta angustifrons[&&NHX:TOL=35986],ptycta apicalis[&&NHX:TOL=35987],ptycta apicantha[&&NHX:TOL=35988],ptycta apicanthoides[&&NHX:TOL=35989],ptycta arandae[&&NHX:TOL=35990],ptycta aschekei[&&NHX:TOL=35991],ptycta australis[&&NHX:TOL=35992],ptycta badonneli[&&NHX:TOL=35993],ptycta bebea[&&NHX:TOL=35994],ptycta biloba[&&NHX:TOL=35995],ptycta blanci[&&NHX:TOL=35996],ptycta breuschi[&&NHX:TOL=35997],ptycta bulbosa[&&NHX:TOL=35998],ptycta buettikeri[&&NHX:TOL=35999],ptycta caboverdensis[&&NHX:TOL=36000],ptycta campbelli[&&NHX:TOL=36001],ptycta chekei[&&NHX:TOL=36002],ptycta chubsugulensis[&&NHX:TOL=36003],ptycta cogani[&&NHX:TOL=36004],ptycta johnsoni[&&NHX:TOL=68935],ptycta cruciata[&&NHX:TOL=36005],ptycta curvata[&&NHX:TOL=36006],ptycta curviclava[&&NHX:TOL=36007],ptycta deltoides[&&NHX:TOL=36008],ptycta descarpentriesi[&&NHX:TOL=36009],ptycta diacantha[&&NHX:TOL=36010],ptycta diadela[&&NHX:TOL=36011],ptycta diastema[&&NHX:TOL=36012],ptycta dichotoma[&&NHX:TOL=36013],ptycta dicrosa[&&NHX:TOL=36014],ptycta disclera[&&NHX:TOL=36015],ptycta distincta[&&NHX:TOL=36016],ptycta distinguenda[&&NHX:TOL=36017],ptycta drepana[&&NHX:TOL=36018],ptycta elegantula[&&NHX:TOL=36019],ptycta elena[&&NHX:TOL=36020],ptycta emarginata[&&NHX:TOL=36021],ptycta episcia[&&NHX:TOL=36022],ptycta flavipalpi[&&NHX:TOL=36023],ptycta floresensis[&&NHX:TOL=36024],ptycta frayorgensis[&&NHX:TOL=36025],ptycta frogneri[&&NHX:TOL=36026],ptycta frontalis[&&NHX:TOL=36027],ptycta furcata[&&NHX:TOL=36028],ptycta giffardi[&&NHX:TOL=36029],ptycta glossoptera[&&NHX:TOL=36030],ptycta grucheti[&&NHX:TOL=36031],ptycta gynegonia[&&NHX:TOL=36032],ptycta gyroflexa[&&NHX:TOL=36033],ptycta haleakalae[&&NHX:TOL=36034],ptycta hardyi[&&NHX:TOL=36035],ptycta hawaiiensis[&&NHX:TOL=36036],ptycta heterogamias[&&NHX:TOL=36037],ptycta hollowayae[&&NHX:TOL=36038],ptycta iaoensis[&&NHX:TOL=36039],ptycta improcera[&&NHX:TOL=36040],ptycta incerta[&&NHX:TOL=36041],ptycta incurvata[&&NHX:TOL=36042],ptycta isabelae[&&NHX:TOL=36043],ptycta kaala[&&NHX:TOL=36044],ptycta kauaiensis[&&NHX:TOL=36045],ptycta kenyensis[&&NHX:TOL=36046],ptycta kiboschoensis[&&NHX:TOL=36047],ptycta krakatau[&&NHX:TOL=36048],ptycta laevidorsum[&&NHX:TOL=36049],ptycta lanaiensis[&&NHX:TOL=36050],ptycta lemniscata[&&NHX:TOL=36051],ptycta leucothorax[&&NHX:TOL=36052],ptycta lineata[&&NHX:TOL=36053],ptycta lobata[&&NHX:TOL=36054],ptycta lobophora[&&NHX:TOL=36055],ptycta longicaulis[&&NHX:TOL=36056],ptycta longipennis[&&NHX:TOL=36057],ptycta longispinosa[&&NHX:TOL=36058],ptycta lugosensis[&&NHX:TOL=36059],ptycta lunulata[&&NHX:TOL=36060],ptycta maculata[&&NHX:TOL=36061],ptycta maculifrons[&&NHX:TOL=36062],ptycta maculosa[&&NHX:TOL=36063],ptycta marianensis[&&NHX:TOL=36064],ptycta marta[&&NHX:TOL=36065],ptycta merapiensis[&&NHX:TOL=36066],ptycta microctena[&&NHX:TOL=36067],ptycta microglena[&&NHX:TOL=36068],ptycta micromaculata[&&NHX:TOL=36069],ptycta molokaiensis[&&NHX:TOL=36070],ptycta monticola[&&NHX:TOL=36071],ptycta muogamarra[&&NHX:TOL=36072],ptycta nadleri[&&NHX:TOL=36073],ptycta nitens[&&NHX:TOL=36074],ptycta novohibernica[&&NHX:TOL=36075],ptycta oahuensis[&&NHX:TOL=36076],ptycta obscura[&&NHX:TOL=36077],ptycta oceanica[&&NHX:TOL=36078],ptycta oligocantha[&&NHX:TOL=36079],ptycta palikea[&&NHX:TOL=36080],ptycta pallida[&&NHX:TOL=36081],ptycta paralobata[&&NHX:TOL=36082],ptycta pardena[&&NHX:TOL=36083],ptycta parvidentata[&&NHX:TOL=36084],ptycta parvula[&&NHX:TOL=36085],ptycta pauliani[&&NHX:TOL=36086],ptycta pearmani[&&NHX:TOL=36087],ptycta pedina[&&NHX:TOL=36088],ptycta peleae[&&NHX:TOL=36089],ptycta perkinsi[&&NHX:TOL=36090],ptycta persimilis[&&NHX:TOL=36091],ptycta picta[&&NHX:TOL=36092],ptycta pikeloi[&&NHX:TOL=36093],ptycta pitallo[&&NHX:TOL=36094],ptycta placophora[&&NHX:TOL=36095],ptycta platyclava[&&NHX:TOL=36096],ptycta polluta[&&NHX:TOL=36097],ptycta polyacantha[&&NHX:TOL=36098],ptycta precincta[&&NHX:TOL=36099],ptycta prosta[&&NHX:TOL=36100],ptycta pulchra[&&NHX:TOL=36101],ptycta pupukea[&&NHX:TOL=36102],ptycta quadrimaculata[&&NHX:TOL=36103],ptycta reticulata[&&NHX:TOL=36104],ptycta revoluta[&&NHX:TOL=36105],ptycta rhina[&&NHX:TOL=36106],ptycta sardjani[&&NHX:TOL=36107],ptycta schillei[&&NHX:TOL=36108],ptycta schisma[&&NHX:TOL=36109],ptycta schneideri[&&NHX:TOL=36110],ptycta serrata[&&NHX:TOL=36111],ptycta seyrigi[&&NHX:TOL=36112],ptycta simulator[&&NHX:TOL=36113],ptycta stena[&&NHX:TOL=36114],ptycta stenomedia[&&NHX:TOL=36115],ptycta striatoptera[&&NHX:TOL=36116],ptycta swezeyi[&&NHX:TOL=36117],ptycta sylvestris[&&NHX:TOL=36118],ptycta tachardiae[&&NHX:TOL=36119],ptycta tapensis[&&NHX:TOL=36120],ptycta telma[&&NHX:TOL=36121],ptycta tikala[&&NHX:TOL=36122],ptycta timorensis[&&NHX:TOL=36123],ptycta trullifera[&&NHX:TOL=36124],ptycta tsutsumii[&&NHX:TOL=36125],ptycta umbrata[&&NHX:TOL=36126],ptycta unica[&&NHX:TOL=36127],ptycta vaga[&&NHX:TOL=36128],ptycta verticalis[&&NHX:TOL=36129],ptycta vittipennis[&&NHX:TOL=36130],ptycta williamsorum[&&NHX:TOL=36131],ptycta ypsilon[&&NHX:TOL=36132],ptycta zimmermani[&&NHX:TOL=36133],ptycta recava[&&NHX:TOL=68936])ptycta[&&NHX:TOL=35174],sciadionopsocus fenzelianae[&&NHX:TOL=35175],(steleops barrerai[&&NHX:TOL=36135],steleops conipata[&&NHX:TOL=36136],steleops elegans[&&NHX:TOL=36137],steleops lichenatus[&&NHX:TOL=36138],steleops maculatus[&&NHX:TOL=36139],steleops monticola[&&NHX:TOL=36140],steleops ortegae[&&NHX:TOL=36141],steleops pedunculatus[&&NHX:TOL=36142],steleops pulcher[&&NHX:TOL=36143],steleops punctipennis[&&NHX:TOL=36144],steleops purus[&&NHX:TOL=36145],steleops tambopata[&&NHX:TOL=36146],steleops wygodzinskyi[&&NHX:TOL=36147])steleops[&&NHX:TOL=35176],(symbiopsocus chaulommaus[&&NHX:TOL=36148],symbiopsocus diplocyclus[&&NHX:TOL=36149],symbiopsocus hastatus[&&NHX:TOL=36150],symbiopsocus leptocladus[&&NHX:TOL=36151],symbiopsocus quadripartitus[&&NHX:TOL=36152],symbiopsocus subrhombeus[&&NHX:TOL=36153])symbiopsocus[&&NHX:TOL=35177],(tanystigma bifurcatum[&&NHX:TOL=36154],tanystigma dubium[&&NHX:TOL=36155],tanystigma edwardsi[&&NHX:TOL=36156],tanystigma elongatum[&&NHX:TOL=36157],tanystigma inglewoodense[&&NHX:TOL=36158],tanystigma latimentulum[&&NHX:TOL=36159],tanystigma longitibia[&&NHX:TOL=36160],tanystigma notiale[&&NHX:TOL=36161],tanystigma paulum[&&NHX:TOL=36162],tanystigma striatifrons[&&NHX:TOL=36163],tanystigma tardipes[&&NHX:TOL=36164],tanystigma valvula[&&NHX:TOL=36165])tanystigma[&&NHX:TOL=35178],(trichadenopsocus aduncatus[&&NHX:TOL=36166],trichadenopsocus alternatus[&&NHX:TOL=36167],trichadenopsocus ampullaceus[&&NHX:TOL=36168],trichadenopsocus dactylinus[&&NHX:TOL=36169],trichadenopsocus digitatus[&&NHX:TOL=36170],trichadenopsocus jaculatorus[&&NHX:TOL=36171],trichadenopsocus jinxiuensis[&&NHX:TOL=36172],trichadenopsocus multangularis[&&NHX:TOL=36173],trichadenopsocus multicuspidatus[&&NHX:TOL=36174],trichadenopsocus paululus[&&NHX:TOL=36175],trichadenopsocus quadruplex[&&NHX:TOL=36176],trichadenopsocus stipulatus[&&NHX:TOL=36177],trichadenopsocus subrotundus[&&NHX:TOL=36178],trichadenopsocus subscalaris[&&NHX:TOL=36179],trichadenopsocus trichotomus[&&NHX:TOL=36180],trichadenopsocus uniformis[&&NHX:TOL=36181])trichadenopsocus[&&NHX:TOL=35179],(trichadenotecnum adika[&&NHX:TOL=36182],trichadenotecnum aggrogatum[&&NHX:TOL=36183],trichadenotecnum album[&&NHX:TOL=36184],trichadenotecnum alexanderae[&&NHX:TOL=36185],trichadenotecnum alinguum[&&NHX:TOL=36186],trichadenotecnum amamiense[&&NHX:TOL=36187],trichadenotecnum angolense[&&NHX:TOL=36188],trichadenotecnum apertum[&&NHX:TOL=36189],trichadenotecnum arciforme[&&NHX:TOL=36190],trichadenotecnum baishanzuicum[&&NHX:TOL=36191],trichadenotecnum bidens[&&NHX:TOL=36192],trichadenotecnum bidentatum[&&NHX:TOL=36193],trichadenotecnum bigyrans[&&NHX:TOL=36194],trichadenotecnum bitenatum[&&NHX:TOL=36195],trichadenotecnum bromoense[&&NHX:TOL=36196],trichadenotecnum bucciniforme[&&NHX:TOL=36197],trichadenotecnum calycoideum[&&NHX:TOL=36198],trichadenotecnum castrum[&&NHX:TOL=36199],trichadenotecnum cheahae[&&NHX:TOL=36200],trichadenotecnum chinense[&&NHX:TOL=36201],trichadenotecnum circulare[&&NHX:TOL=36202],trichadenotecnum circularoides[&&NHX:TOL=36203],trichadenotecnum colesae[&&NHX:TOL=36204],trichadenotecnum corniculum[&&NHX:TOL=36205],trichadenotecnum decui[&&NHX:TOL=36206],trichadenotecnum desolatum[&&NHX:TOL=36207],trichadenotecnum diplodurum[&&NHX:TOL=36208],trichadenotecnum distinctum[&&NHX:TOL=36209],trichadenotecnum dobhanense[&&NHX:TOL=36210],trichadenotecnum dolabratum[&&NHX:TOL=36211],trichadenotecnum emeishanense[&&NHX:TOL=36212],trichadenotecnum enderleini[&&NHX:TOL=36213],trichadenotecnum falx[&&NHX:TOL=36214],trichadenotecnum felix[&&NHX:TOL=36215],trichadenotecnum furcalingum[&&NHX:TOL=36216],trichadenotecnum fuscipenne[&&NHX:TOL=36217],trichadenotecnum galihi[&&NHX:TOL=36218],trichadenotecnum gallicum[&&NHX:TOL=36219],trichadenotecnum germanicum[&&NHX:TOL=36220],trichadenotecnum germinatum[&&NHX:TOL=36221],trichadenotecnum godavarense[&&NHX:TOL=36222],trichadenotecnum gombakense[&&NHX:TOL=36223],trichadenotecnum gonzalezi[&&NHX:TOL=36224],trichadenotecnum guandongicum[&&NHX:TOL=36225],trichadenotecnum gutianum[&&NHX:TOL=36226],trichadenotecnum hammani[&&NHX:TOL=36227],trichadenotecnum himalayense[&&NHX:TOL=36228],trichadenotecnum imperatorium[&&NHX:TOL=36229],trichadenotecnum imrum[&&NHX:TOL=36230],trichadenotecnum incognitum[&&NHX:TOL=36231],trichadenotecnum innuptum[&&NHX:TOL=36232],trichadenotecnum isocaulum[&&NHX:TOL=36233],trichadenotecnum krucilense[&&NHX:TOL=36234],trichadenotecnum kumejimense[&&NHX:TOL=36235],trichadenotecnum kunmingicum[&&NHX:TOL=36236],trichadenotecnum latebrachium[&&NHX:TOL=36237],trichadenotecnum laticornutum[&&NHX:TOL=36238],trichadenotecnum magnomixtum[&&NHX:TOL=36239],trichadenotecnum majus[&&NHX:TOL=36240],trichadenotecnum malayense[&&NHX:TOL=36241],trichadenotecnum mamillatum[&&NHX:TOL=36242],trichadenotecnum marginatum[&&NHX:TOL=36243],trichadenotecnum maroccanum[&&NHX:TOL=36244],trichadenotecnum masoni[&&NHX:TOL=36245],trichadenotecnum mclachlani[&&NHX:TOL=36246],trichadenotecnum medium[&&NHX:TOL=36247],trichadenotecnum merum[&&NHX:TOL=36248],trichadenotecnum minisexmaculatum[&&NHX:TOL=36249],trichadenotecnum minutum[&&NHX:TOL=36250],trichadenotecnum mixtum[&&NHX:TOL=36251],trichadenotecnum monodactylinum[&&NHX:TOL=36252],trichadenotecnum nebulosum[&&NHX:TOL=36253],trichadenotecnum nothoapertum[&&NHX:TOL=36254],trichadenotecnum obliquidens[&&NHX:TOL=36255],trichadenotecnum obsitum[&&NHX:TOL=36256],trichadenotecnum obsubulatum[&&NHX:TOL=36257],trichadenotecnum okinawense[&&NHX:TOL=36258],trichadenotecnum opiparipardale[&&NHX:TOL=36259],trichadenotecnum pardoides[&&NHX:TOL=36260],trichadenotecnum pardus[&&NHX:TOL=36261],trichadenotecnum percussum[&&NHX:TOL=36262],trichadenotecnum pergracilum[&&NHX:TOL=36263],trichadenotecnum pichincha[&&NHX:TOL=36264],trichadenotecnum pictipenne[&&NHX:TOL=36265],trichadenotecnum pokhariense[&&NHX:TOL=36266],trichadenotecnum pseudomedium[&&NHX:TOL=36267],trichadenotecnum punctipenne[&&NHX:TOL=36268],trichadenotecnum qingshuicum[&&NHX:TOL=36269],trichadenotecnum quadrispinosum[&&NHX:TOL=36270],trichadenotecnum quaesitum[&&NHX:TOL=36271],trichadenotecnum rachimi[&&NHX:TOL=36272],trichadenotecnum rectangulum[&&NHX:TOL=36273],trichadenotecnum resupinum[&&NHX:TOL=36274],trichadenotecnum rhomboides[&&NHX:TOL=36275],trichadenotecnum roesleri[&&NHX:TOL=36276],trichadenotecnum santosai[&&NHX:TOL=36277],trichadenotecnum sclerotum[&&NHX:TOL=36278],trichadenotecnum scoparium[&&NHX:TOL=36279],trichadenotecnum scobiculare[&&NHX:TOL=36280],trichadenotecnum sexpunctatum[&&NHX:TOL=36281],trichadenotecnum sexpunctellum[&&NHX:TOL=36282],trichadenotecnum simile[&&NHX:TOL=36283],trichadenotecnum sinuatum[&&NHX:TOL=36284],trichadenotecnum slossonae[&&NHX:TOL=36285],trichadenotecnum soekarmanni[&&NHX:TOL=36286],trichadenotecnum soenarti[&&NHX:TOL=36287],trichadenotecnum spiniserrulum[&&NHX:TOL=36288],trichadenotecnum spuristipiatum[&&NHX:TOL=36289],trichadenotecnum stipiatum[&&NHX:TOL=36290],trichadenotecnum sufflatum[&&NHX:TOL=36291],trichadenotecnum sylvaticum[&&NHX:TOL=36292],trichadenotecnum takahashii[&&NHX:TOL=36293],trichadenotecnum tenuispinum[&&NHX:TOL=36294],trichadenotecnum thallodailum[&&NHX:TOL=36295],trichadenotecnum thortoni[&&NHX:TOL=36296],trichadenotecnum trigonophyllum[&&NHX:TOL=36297],trichadenotecnum umbratum[&&NHX:TOL=36298],trichadenotecnum uncorne[&&NHX:TOL=36299],trichadenotecnum univittatum[&&NHX:TOL=36300],trichadenotecnum vaughani[&&NHX:TOL=36301],trichadenotecnum wuxiacum[&&NHX:TOL=36302],trichadenotecnum xizangicum[&&NHX:TOL=36303],trichadenotecnum yaeyamense[&&NHX:TOL=36304],trichadenotecnum yamatomajus[&&NHX:TOL=36305],trichadenotecnum yonaguniense[&&NHX:TOL=36306])trichadenotecnum[&&NHX:TOL=35180])ptyctini[&&NHX:TOL=50650],((sigmatoneura albostriata[&&NHX:TOL=35694],sigmatoneura antenniflava[&&NHX:TOL=35695],sigmatoneura baiyunica[&&NHX:TOL=35696],sigmatoneura basalis[&&NHX:TOL=35697],sigmatoneura brachyura[&&NHX:TOL=35698],sigmatoneura chinensis[&&NHX:TOL=35699],sigmatoneura clara[&&NHX:TOL=35700],sigmatoneura coronata[&&NHX:TOL=35701],sigmatoneura ellipsoidalis[&&NHX:TOL=35702],sigmatoneura flaviventris[&&NHX:TOL=35703],sigmatoneura formosa[&&NHX:TOL=35704],sigmatoneura kilbei[&&NHX:TOL=35705],sigmatoneura macroloba[&&NHX:TOL=35706],sigmatoneura mitsuhashiana[&&NHX:TOL=35707],sigmatoneura octofasciata[&&NHX:TOL=35708],sigmatoneura orientalis[&&NHX:TOL=35709],sigmatoneura phaeothera[&&NHX:TOL=35710],sigmatoneura scitula[&&NHX:TOL=35711],sigmatoneura spicata[&&NHX:TOL=35712],sigmatoneura subcostalis[&&NHX:TOL=35713],sigmatoneura triaristata[&&NHX:TOL=35714])sigmatoneura[&&NHX:TOL=35150],podopterocus longicornis[&&NHX:TOL=35135])sigmatoneurini[&&NHX:TOL=136820],(dictyopsocus pennicornis[&&NHX:TOL=35181],gigantopsocus metallicus[&&NHX:TOL=35182],(poecilopsocus anticus[&&NHX:TOL=36309],poecilopsocus beaveri[&&NHX:TOL=36310],poecilopsocus bishopi[&&NHX:TOL=36311],poecilopsocus calocoroides[&&NHX:TOL=36312],poecilopsocus cinctus[&&NHX:TOL=36313],poecilopsocus iridescens[&&NHX:TOL=36314],poecilopsocus leucotelus[&&NHX:TOL=36315],poecilopsocus pulcher[&&NHX:TOL=36316],poecilopsocus richardsi[&&NHX:TOL=36317])poecilopsocus[&&NHX:TOL=35183],(cerastipsocus aldretei[&&NHX:TOL=35412],cerastipsocus beaveri[&&NHX:TOL=35413],cerastipsocus bogotanus[&&NHX:TOL=35414],cerastipsocus brasilianus[&&NHX:TOL=35415],cerastipsocus claripennis[&&NHX:TOL=35416],cerastipsocus coloratus[&&NHX:TOL=35417],cerastipsocus consocius[&&NHX:TOL=35418],cerastipsocus cornutus[&&NHX:TOL=35419],cerastipsocus cubanus[&&NHX:TOL=35420],cerastipsocus dubius[&&NHX:TOL=35421],cerastipsocus fuscipennis[&&NHX:TOL=35422],cerastipsocus iguazuensis[&&NHX:TOL=35423],cerastipsocus infectus[&&NHX:TOL=35424],cerastipsocus kilbei[&&NHX:TOL=35425],cerastipsocus macrostigmatus[&&NHX:TOL=35426],cerastipsocus moestus[&&NHX:TOL=35427],cerastipsocus ochraceocristatus[&&NHX:TOL=35428],cerastipsocus pallidinervis[&&NHX:TOL=35429],cerastipsocus reductus[&&NHX:TOL=35430],cerastipsocus rufus[&&NHX:TOL=35431],cerastipsocus rugosus[&&NHX:TOL=35432],cerastipsocus sivorii[&&NHX:TOL=35433],cerastipsocus tostus[&&NHX:TOL=35434],cerastipsocus trifasciatus[&&NHX:TOL=35435],cerastipsocus venosus[&&NHX:TOL=35436],cerastipsocus vestustus[&&NHX:TOL=35437],cerastipsocus willineri[&&NHX:TOL=35438])cerastipsocus[&&NHX:TOL=35124],ceratostigma gracile[&&NHX:TOL=35125],cervopsocus medialis[&&NHX:TOL=35126],(clematoscenea apta[&&NHX:TOL=35441],clematoscenea biloba[&&NHX:TOL=35442],clematoscenea biroi[&&NHX:TOL=35443],clematoscenea dimorpha[&&NHX:TOL=35444],clematoscenea goilala[&&NHX:TOL=35445],clematoscenea gressitti[&&NHX:TOL=35446],clematoscenea josephinae[&&NHX:TOL=35447],clematoscenea lemniscata[&&NHX:TOL=35448],clematoscenea longitarsus[&&NHX:TOL=35449],clematoscenea macalpinei[&&NHX:TOL=35450],clematoscenea mosomensis[&&NHX:TOL=35451],clematoscenea newi[&&NHX:TOL=35452],clematoscenea pulchra[&&NHX:TOL=35453],clematoscenea yunnanica[&&NHX:TOL=35454])clematoscenea[&&NHX:TOL=35127],(dactylopsocus fumigatus[&&NHX:TOL=35455],dactylopsocus similis[&&NHX:TOL=35456])dactylopsocus[&&NHX:TOL=35128],(dinopsocus atratus[&&NHX:TOL=35457],dinopsocus semicoloratus[&&NHX:TOL=35458])dinopsocus[&&NHX:TOL=35129],(eremopsocus crassicornis[&&NHX:TOL=35459],eremopsocus flagellicornis[&&NHX:TOL=35460],eremopsocus flavatus[&&NHX:TOL=35461],eremopsocus infumatus[&&NHX:TOL=35462],eremopsocus mockfordi[&&NHX:TOL=35463],eremopsocus nigripes[&&NHX:TOL=35464])eremopsocus[&&NHX:TOL=35130],(ghesquierella cantralli[&&NHX:TOL=35465],ghesquierella ealensis[&&NHX:TOL=35466],ghesquierella sjoestedti[&&NHX:TOL=35467])ghesquierella[&&NHX:TOL=35131],(longivalvus dictyodromus[&&NHX:TOL=35468],longivalvus hyalospilus[&&NHX:TOL=35469],longivalvus lagenarius[&&NHX:TOL=35470],longivalvus pleuranthus[&&NHX:TOL=35471],longivalvus radiatus[&&NHX:TOL=35472],longivalvus shennongicus[&&NHX:TOL=35473])longivalvus[&&NHX:TOL=35132],lubricus dayaoshanensis[&&NHX:TOL=35133],(neopsocus rhenanus[&&NHX:TOL=35475],neopsocus tunesicus[&&NHX:TOL=35476])neopsocus[&&NHX:TOL=35134],pogonopsocus octofaris[&&NHX:TOL=35136],propsococerastis jiangkouensis[&&NHX:TOL=35137],pseudoclematus xanthoznatus[&&NHX:TOL=35138],(psococerastis albimaculata[&&NHX:TOL=35481],psococerastis amazonica[&&NHX:TOL=35482],psococerastis ampullaris[&&NHX:TOL=35483],psococerastis annae[&&NHX:TOL=35484],psococerastis asiatica[&&NHX:TOL=35485],psococerastis aspinosa[&&NHX:TOL=35486],psococerastis assamensis[&&NHX:TOL=35487],psococerastis aurata[&&NHX:TOL=35488],psococerastis baihuashanensis[&&NHX:TOL=35489],psococerastis baishanzuica[&&NHX:TOL=35490],psococerastis bakeri[&&NHX:TOL=35491],psococerastis bengalensis[&&NHX:TOL=35492],psococerastis betulisuga[&&NHX:TOL=35493],psococerastis bispinosa[&&NHX:TOL=35494],psococerastis bomiensis[&&NHX:TOL=35495],psococerastis boseiensis[&&NHX:TOL=35496],psococerastis brachyneura[&&NHX:TOL=35497],psococerastis brachypoda[&&NHX:TOL=35498],psococerastis breviollis[&&NHX:TOL=35499],psococerastis callangana[&&NHX:TOL=35500],psococerastis capitata[&&NHX:TOL=35501],psococerastis capitulatis[&&NHX:TOL=35502],psococerastis chebalingensis[&&NHX:TOL=35503],psococerastis collessi[&&NHX:TOL=35504],psococerastis cosmoptera[&&NHX:TOL=35505],psococerastis curvivalvae[&&NHX:TOL=35506],psococerastis cuspidata[&&NHX:TOL=35507],psococerastis deflecta[&&NHX:TOL=35508],psococerastis denticuligis[&&NHX:TOL=35509],psococerastis dicoccis[&&NHX:TOL=35510],psococerastis discalis[&&NHX:TOL=35511],psococerastis dissidens[&&NHX:TOL=35512],psococerastis duoipunctata[&&NHX:TOL=35513],psococerastis emeiensis[&&NHX:TOL=35514],psococerastis exilis[&&NHX:TOL=35515],psococerastis fasciata[&&NHX:TOL=35516],psococerastis fenestralis[&&NHX:TOL=35517],psococerastis ficivorella[&&NHX:TOL=35518],psococerastis flavistigma[&&NHX:TOL=35519],psococerastis fluctimarginalis[&&NHX:TOL=35520],psococerastis formosa[&&NHX:TOL=35521],psococerastis fortunae[&&NHX:TOL=35522],psococerastis fuelleborni[&&NHX:TOL=35523],psococerastis galeata[&&NHX:TOL=35524],psococerastis gansuiensis[&&NHX:TOL=35525],psococerastis ghesquierei[&&NHX:TOL=35526],psococerastis gibbosa[&&NHX:TOL=35527],psococerastis golfita[&&NHX:TOL=35528],psococerastis gracilescens[&&NHX:TOL=35529],psococerastis guangxiensis[&&NHX:TOL=35530],psococerastis guizhouensis[&&NHX:TOL=35531],psococerastis hageni[&&NHX:TOL=35532],psococerastis hainanensis[&&NHX:TOL=35533],psococerastis huangshanensis[&&NHX:TOL=35534],psococerastis huapingana[&&NHX:TOL=35535],psococerastis hunanensis[&&NHX:TOL=35536],psococerastis inqequimagna[&&NHX:TOL=35537],psococerastis joannisi[&&NHX:TOL=35538],psococerastis kurokiana[&&NHX:TOL=35539],psococerastis lassbergi[&&NHX:TOL=35540],psococerastis lifashengi[&&NHX:TOL=35541],psococerastis linearis[&&NHX:TOL=35542],psococerastis lombokensis[&&NHX:TOL=35543],psococerastis longifurcata[&&NHX:TOL=35544],psococerastis luroris[&&NHX:TOL=35545],psococerastis luzonensis[&&NHX:TOL=35546],psococerastis macrotaenialis[&&NHX:TOL=35547],psococerastis mali[&&NHX:TOL=35548],psococerastis malleata[&&NHX:TOL=35549],psococerastis martensi[&&NHX:TOL=35550],psococerastis melanostigma[&&NHX:TOL=35551],psococerastis microdonta[&&NHX:TOL=35552],psococerastis moganshanensis[&&NHX:TOL=35553],psococerastis murudensis[&&NHX:TOL=35554],psococerastis nepalensis[&&NHX:TOL=35555],psococerastis nigriventris[&&NHX:TOL=35556],psococerastis nilae[&&NHX:TOL=35557],psococerastis nirvana[&&NHX:TOL=35558],psococerastis nubila[&&NHX:TOL=35559],psococerastis opulenta[&&NHX:TOL=35560],psococerastis orientalis[&&NHX:TOL=35561],psococerastis pandurata[&&NHX:TOL=35562],psococerastis paraguayana[&&NHX:TOL=35563],psococerastis parallelica[&&NHX:TOL=35564],psococerastis parasinensis[&&NHX:TOL=35565],psococerastis pelesi[&&NHX:TOL=35566],psococerastis pellucidatis[&&NHX:TOL=35567],psococerastis phanerosticta[&&NHX:TOL=35568],psococerastis pictiventris[&&NHX:TOL=35569],psococerastis pingtangensis[&&NHX:TOL=35570],psococerastis pingxiangensis[&&NHX:TOL=35571],psococerastis platynota[&&NHX:TOL=35572],psococerastis platypis[&&NHX:TOL=35573],psococerastis platyraphis[&&NHX:TOL=35574],psococerastis platytaenia[&&NHX:TOL=35575],psococerastis plicata[&&NHX:TOL=35576],psococerastis polygonalis[&&NHX:TOL=35577],psococerastis polystictis[&&NHX:TOL=35578],psococerastis protractis[&&NHX:TOL=35579],psococerastis psaronipunctata[&&NHX:TOL=35580],psococerastis punctulosa[&&NHX:TOL=35581],psococerastis pyralina[&&NHX:TOL=35582],psococerastis pyralinella[&&NHX:TOL=35583],psococerastis pyriformis[&&NHX:TOL=35584],psococerastis quadrisecta[&&NHX:TOL=35585],psococerastis quinidentata[&&NHX:TOL=35586],psococerastis rhondae[&&NHX:TOL=35587],psococerastis ryukyuensis[&&NHX:TOL=35588],psococerastis sangzhiensis[&&NHX:TOL=35589],psococerastis scissilis[&&NHX:TOL=35590],psococerastis sexpunctata[&&NHX:TOL=35591],psococerastis shanxiensis[&&NHX:TOL=35592],psococerastis shennongjiana[&&NHX:TOL=35593],psococerastis sinensis[&&NHX:TOL=35594],psococerastis spatiosis[&&NHX:TOL=35595],psococerastis stictica[&&NHX:TOL=35596],psococerastis stipularis[&&NHX:TOL=35597],psococerastis stulticaulis[&&NHX:TOL=35598],psococerastis taprobanes[&&NHX:TOL=35599],psococerastis thomasseti[&&NHX:TOL=35600],psococerastis tianmushanensis[&&NHX:TOL=35601],psococerastis tibetensis[&&NHX:TOL=35602],psococerastis tokyoensis[&&NHX:TOL=35603],psococerastis trichotoma[&&NHX:TOL=35604],psococerastis trilobata[&&NHX:TOL=35605],psococerastis turriformis[&&NHX:TOL=35606],psococerastis urceolaris[&&NHX:TOL=35607],psococerastis venigra[&&NHX:TOL=35608],psococerastis venimaculis[&&NHX:TOL=35609],psococerastis weijuni[&&NHX:TOL=35610],psococerastis yunnanensis[&&NHX:TOL=35611],psococerastis yuwan[&&NHX:TOL=35612],psococerastis zambeziana[&&NHX:TOL=35613],psococerastis zayuensis[&&NHX:TOL=35614],psococerastis zhaoi[&&NHX:TOL=35615])psococerastis[&&NHX:TOL=35139],setopsocus magnus[&&NHX:TOL=35140],sundapsocus robertsoni[&&NHX:TOL=35141],(thyrsophorus formosus[&&NHX:TOL=36318],thyrsophorus speciosus[&&NHX:TOL=36319],thyrsophorus trabeatus[&&NHX:TOL=36320])thyrsophorus[&&NHX:TOL=35184],(thyrsopsocus aequatorialis[&&NHX:TOL=36321],thyrsopsocus angularis[&&NHX:TOL=36322],thyrsopsocus bellulus[&&NHX:TOL=36323],thyrsopsocus bellus[&&NHX:TOL=36324],thyrsopsocus bolivari[&&NHX:TOL=36325],thyrsopsocus brasiliensis[&&NHX:TOL=36326],thyrsopsocus elegans[&&NHX:TOL=36327],thyrsopsocus fairchildi[&&NHX:TOL=36328],thyrsopsocus newi[&&NHX:TOL=36329],thyrsopsocus peruanus[&&NHX:TOL=36330],thyrsopsocus pretiosus[&&NHX:TOL=36331],thyrsopsocus psocoides[&&NHX:TOL=36332],thyrsopsocus stigmaticus[&&NHX:TOL=36333])thyrsopsocus[&&NHX:TOL=35185])thyrsophorini[&&NHX:TOL=50651])psocinae[&&NHX:TOL=50646])psocidae[&&NHX:TOL=14482],(gyromyus gyrus[&&NHX:TOL=36351],(lichenomima ampla[&&NHX:TOL=36352],lichenomima argentina[&&NHX:TOL=36353],lichenomima ariasi[&&NHX:TOL=36354],lichenomima burgeoni[&&NHX:TOL=36355],lichenomima cameruna[&&NHX:TOL=36356],lichenomima capeneri[&&NHX:TOL=36357],lichenomima cervantesi[&&NHX:TOL=36358],lichenomima chelata[&&NHX:TOL=36359],lichenomima clypeofasciata[&&NHX:TOL=36360],lichenomima coloradensis[&&NHX:TOL=36361],lichenomima conspersa[&&NHX:TOL=36362],lichenomima corniculata[&&NHX:TOL=36363],lichenomima cylindra[&&NHX:TOL=36364],lichenomima elongata[&&NHX:TOL=36365],lichenomima excavata[&&NHX:TOL=36366],lichenomima fasciata[&&NHX:TOL=36367],lichenomima fenestrata[&&NHX:TOL=36368],lichenomima gibbulosa[&&NHX:TOL=36369],lichenomima guineensis[&&NHX:TOL=36370],lichenomima hamata[&&NHX:TOL=36371],lichenomima hangzhouensis[&&NHX:TOL=36372],lichenomima harpeodes[&&NHX:TOL=36373],lichenomima indica[&&NHX:TOL=36374],lichenomima intermedia[&&NHX:TOL=36375],lichenomima leucospila[&&NHX:TOL=36376],lichenomima lugens[&&NHX:TOL=36377],lichenomima machadoi[&&NHX:TOL=36378],lichenomima maxima[&&NHX:TOL=36379],lichenomima medialis[&&NHX:TOL=36380],lichenomima merapi[&&NHX:TOL=36381],lichenomima muscosa[&&NHX:TOL=36382],lichenomima onca[&&NHX:TOL=36383],lichenomima orbiculata[&&NHX:TOL=36384],lichenomima oxycera[&&NHX:TOL=36385],lichenomima pattoni[&&NHX:TOL=36386],lichenomima pauliani[&&NHX:TOL=36387],lichenomima posterior[&&NHX:TOL=36388],lichenomima pulchella[&&NHX:TOL=36389],lichenomima punctipennis[&&NHX:TOL=36390],lichenomima sanguensis[&&NHX:TOL=36391],lichenomima schoutedeni[&&NHX:TOL=36392],lichenomima sparsa[&&NHX:TOL=36393],lichenomima sumatrana[&&NHX:TOL=36394],lichenomima thorntoni[&&NHX:TOL=36395],lichenomima timmei[&&NHX:TOL=36396],lichenomima tridens[&&NHX:TOL=36397],lichenomima unicornis[&&NHX:TOL=36398],lichenomima varia[&&NHX:TOL=36399])lichenomima[&&NHX:TOL=36694],lophomyus bidigitatus[&&NHX:TOL=36400],(lophopterygella antennalis[&&NHX:TOL=36401],lophopterygella bellula[&&NHX:TOL=36402],lophopterygella bursulipennis[&&NHX:TOL=36403],lophopterygella camelina[&&NHX:TOL=36404],lophopterygella cincticornis[&&NHX:TOL=36405],lophopterygella haitiensis[&&NHX:TOL=36406],lophopterygella lobata[&&NHX:TOL=36407],lophopterygella petersi[&&NHX:TOL=36408],lophopterygella ridderi[&&NHX:TOL=36409],lophopterygella spilota[&&NHX:TOL=36410])lophopterygella[&&NHX:TOL=36695],(mouldsia barbarae[&&NHX:TOL=36411],mouldsia inocellata[&&NHX:TOL=36412],mouldsia marmorata[&&NHX:TOL=36413])mouldsia[&&NHX:TOL=36696],(myopsocus aenulus[&&NHX:TOL=36414],myopsocus africanus[&&NHX:TOL=36415],myopsocus albiceps[&&NHX:TOL=36416],myopsocus albomaculatus[&&NHX:TOL=36417],myopsocus albus[&&NHX:TOL=36418],myopsocus aldabrensis[&&NHX:TOL=36419],myopsocus alticola[&&NHX:TOL=36420],myopsocus ambiguus[&&NHX:TOL=36421],myopsocus amicus[&&NHX:TOL=36422],myopsocus angolensis[&&NHX:TOL=36423],myopsocus angulatus[&&NHX:TOL=36424],myopsocus anomalus[&&NHX:TOL=36425],myopsocus antillanus[&&NHX:TOL=36426],myopsocus apicalis[&&NHX:TOL=36427],myopsocus ascoides[&&NHX:TOL=36428],myopsocus australis[&&NHX:TOL=36429],myopsocus bakeri[&&NHX:TOL=36430],myopsocus basupuensis[&&NHX:TOL=36431],myopsocus bellus[&&NHX:TOL=36432],myopsocus bipunctatus[&&NHX:TOL=36433],myopsocus bomasa[&&NHX:TOL=36434],myopsocus brunneigena[&&NHX:TOL=36435],myopsocus brunneipes[&&NHX:TOL=36436],myopsocus ciliifer[&&NHX:TOL=36437],myopsocus cinctus[&&NHX:TOL=36438],myopsocus cinereus[&&NHX:TOL=36439],myopsocus circularis[&&NHX:TOL=36440],myopsocus clarki[&&NHX:TOL=36441],myopsocus clunius[&&NHX:TOL=36442],myopsocus congolensis[&&NHX:TOL=36443],myopsocus corticola[&&NHX:TOL=36444],myopsocus corticosus[&&NHX:TOL=36445],myopsocus cryptus[&&NHX:TOL=36446],myopsocus cubanus[&&NHX:TOL=36447],myopsocus dentatus[&&NHX:TOL=36448],myopsocus dispar[&&NHX:TOL=36449],myopsocus eatoni[&&NHX:TOL=36450],myopsocus enderleini[&&NHX:TOL=36451],myopsocus fenestratus[&&NHX:TOL=36452],myopsocus fraternus[&&NHX:TOL=36453],myopsocus furcatus[&&NHX:TOL=36454],myopsocus graptus[&&NHX:TOL=36455],myopsocus gregarius[&&NHX:TOL=36456],myopsocus gressitti[&&NHX:TOL=36457],myopsocus hickmani[&&NHX:TOL=36458],myopsocus hoskinsi[&&NHX:TOL=36459],myopsocus incomptus[&&NHX:TOL=36460],myopsocus javensis[&&NHX:TOL=36461],myopsocus kolbei[&&NHX:TOL=36462],myopsocus lichenosus[&&NHX:TOL=36463],myopsocus lineatus[&&NHX:TOL=36464],myopsocus lombokensis[&&NHX:TOL=36465],myopsocus longicauda[&&NHX:TOL=36466],myopsocus longigena[&&NHX:TOL=36467],myopsocus loriai[&&NHX:TOL=36468],myopsocus luteolus[&&NHX:TOL=36469],myopsocus lyrifer[&&NHX:TOL=36470],myopsocus maculatus[&&NHX:TOL=36471],myopsocus magnificus[&&NHX:TOL=36472],myopsocus marginatus[&&NHX:TOL=36473],myopsocus medleri[&&NHX:TOL=36474],myopsocus megops[&&NHX:TOL=36475],myopsocus minor[&&NHX:TOL=36476],myopsocus minutus[&&NHX:TOL=36477],myopsocus mjoebergi[&&NHX:TOL=36478],myopsocus muscosus[&&NHX:TOL=36479],myopsocus napuka[&&NHX:TOL=36480],myopsocus nigeriensis[&&NHX:TOL=36481],myopsocus obscurus[&&NHX:TOL=36482],myopsocus opunohu[&&NHX:TOL=36483],myopsocus ornatus[&&NHX:TOL=36484],myopsocus palauensis[&&NHX:TOL=36485],myopsocus pallidus[&&NHX:TOL=36486],myopsocus parvus[&&NHX:TOL=36487],myopsocus peltatus[&&NHX:TOL=36488],myopsocus pennyi[&&NHX:TOL=36489],myopsocus personatus[&&NHX:TOL=36490],myopsocus pilipes[&&NHX:TOL=36491],myopsocus placidulus[&&NHX:TOL=36492],myopsocus platyvalvula[&&NHX:TOL=36493],myopsocus pluviosus[&&NHX:TOL=36494],myopsocus preclarus[&&NHX:TOL=36495],myopsocus pulchellus[&&NHX:TOL=36496],myopsocus punctatoides[&&NHX:TOL=36497],myopsocus punctatus[&&NHX:TOL=36498],myopsocus quadrisetosus[&&NHX:TOL=36499],myopsocus rastafari[&&NHX:TOL=36500],myopsocus reptus[&&NHX:TOL=36501],myopsocus rimosus[&&NHX:TOL=36502],myopsocus sagitta[&&NHX:TOL=36503],myopsocus samoanus[&&NHX:TOL=36504],myopsocus scabiosus[&&NHX:TOL=36505],myopsocus setosus[&&NHX:TOL=36506],myopsocus spatulatus[&&NHX:TOL=36507],myopsocus speciosus[&&NHX:TOL=36508],myopsocus splendidus[&&NHX:TOL=36509],myopsocus taurus[&&NHX:TOL=36510],myopsocus thecatus[&&NHX:TOL=36511],myopsocus toxeres[&&NHX:TOL=36512],myopsocus tropicus[&&NHX:TOL=36513],myopsocus unduosus[&&NHX:TOL=36514],myopsocus venustus[&&NHX:TOL=36515],myopsocus vespertilio[&&NHX:TOL=36516],myopsocus vilazi[&&NHX:TOL=36517],myopsocus yunnanicus[&&NHX:TOL=36518],myopsocus zimmermani[&&NHX:TOL=36519])myopsocus[&&NHX:TOL=36697],(polygonomyus scapiformis[&&NHX:TOL=36520],polygonomyus sexangulus[&&NHX:TOL=36521],polygonomyus sinicus[&&NHX:TOL=36522])polygonomyus[&&NHX:TOL=36698],(smithersia angusta[&&NHX:TOL=36523],smithersia hermosa[&&NHX:TOL=36524],smithersia hermosoides[&&NHX:TOL=36525],smithersia newi[&&NHX:TOL=36526])smithersia[&&NHX:TOL=36699])myopsocidae[&&NHX:TOL=14484])[&&NHX:TOL=50653],((anopistoscena specularifrons[&&NHX:TOL=35065],cyclohemipsocus chinensis[&&NHX:TOL=35066],(hemipsocus africanus[&&NHX:TOL=35067],hemipsocus chloroticus[&&NHX:TOL=35068],hemipsocus fasciatus[&&NHX:TOL=35069],hemipsocus funebris[&&NHX:TOL=35070],hemipsocus luridus[&&NHX:TOL=35071],hemipsocus maculatus[&&NHX:TOL=35072],hemipsocus massulatus[&&NHX:TOL=35073],hemipsocus mauritianus[&&NHX:TOL=35074],hemipsocus ornatus[&&NHX:TOL=35075],hemipsocus pallidus[&&NHX:TOL=35076],hemipsocus parallelicus[&&NHX:TOL=35077],hemipsocus pardus[&&NHX:TOL=35078],hemipsocus pretiosus[&&NHX:TOL=35079],hemipsocus roseus[&&NHX:TOL=35080],hemipsocus rubellis[&&NHX:TOL=35081],hemipsocus selysi[&&NHX:TOL=35082],hemipsocus turneri[&&NHX:TOL=35083])hemipsocus[&&NHX:TOL=35063],(metahemipsocus bellatulus[&&NHX:TOL=35084],metahemipsocus bicuspidatus[&&NHX:TOL=35085],metahemipsocus bimaculatus[&&NHX:TOL=35086],metahemipsocus brachydicrus[&&NHX:TOL=35087],metahemipsocus cunestus[&&NHX:TOL=35088],metahemipsocus flabellatus[&&NHX:TOL=35089],metahemipsocus guangxiensis[&&NHX:TOL=35090],metahemipsocus iteraus[&&NHX:TOL=35091],metahemipsocus longicornis[&&NHX:TOL=35092],metahemipsocus longifurcus[&&NHX:TOL=35093],metahemipsocus octofarius[&&NHX:TOL=35094],metahemipsocus recurvicornis[&&NHX:TOL=35095],metahemipsocus scitulus[&&NHX:TOL=35096],metahemipsocus spilopterus[&&NHX:TOL=35097],metahemipsocus tenuatus[&&NHX:TOL=35098],metahemipsocus tianmushanicus[&&NHX:TOL=35099],metahemipsocus trimerus[&&NHX:TOL=35100],metahemipsocus vitellinus[&&NHX:TOL=35101],metahemipsocus yunnanicus[&&NHX:TOL=35102])metahemipsocus[&&NHX:TOL=35064])hemipsocidae[&&NHX:TOL=14481],(psilopsocus malayanus[&&NHX:TOL=36335],psilopsocus manus[&&NHX:TOL=36336],psilopsocus mimulus[&&NHX:TOL=36338],psilopsocus marmoratus[&&NHX:TOL=36337],psilopsocus nebulosus[&&NHX:TOL=36339],psilopsocus nigricornis[&&NHX:TOL=36340],psilopsocus parvus[&&NHX:TOL=36341])psilopsocus[&&NHX:TOL=14483])[&&NHX:TOL=136813])psocetae[&&NHX:TOL=30220],(((trichopsocus australis[&&NHX:TOL=34117],trichopsocus brincki[&&NHX:TOL=34118],trichopsocus chilensis[&&NHX:TOL=34119],trichopsocus clarus[&&NHX:TOL=34120],trichopsocus coloratus[&&NHX:TOL=34121],trichopsocus dalii[&&NHX:TOL=34122],trichopsocus difficilis[&&NHX:TOL=34123],trichopsocus fastuosus[&&NHX:TOL=34124],trichopsocus marmoratus[&&NHX:TOL=34125])trichopsocus[&&NHX:TOL=14476],(((haplophallus africanus[&&NHX:TOL=33428],haplophallus basilewskyi[&&NHX:TOL=33429],haplophallus boninensis[&&NHX:TOL=33430],haplophallus chilensis[&&NHX:TOL=33431],haplophallus chinensis[&&NHX:TOL=33432],haplophallus clarus[&&NHX:TOL=33433],haplophallus comptoni[&&NHX:TOL=33434],haplophallus cubitalis[&&NHX:TOL=33435],haplophallus emmus[&&NHX:TOL=33436],haplophallus fenestristigma[&&NHX:TOL=33437],haplophallus fuscipennis[&&NHX:TOL=33438],haplophallus fuscistigma[&&NHX:TOL=33439],haplophallus insignis[&&NHX:TOL=33440],haplophallus leopardina[&&NHX:TOL=33442],haplophallus leptus[&&NHX:TOL=33443],haplophallus maculatus[&&NHX:TOL=33444],haplophallus oblongatus[&&NHX:TOL=33445],haplophallus orientalis[&&NHX:TOL=33446],haplophallus rhabdocladus[&&NHX:TOL=33447],haplophallus separatus[&&NHX:TOL=33448],haplophallus sinus[&&NHX:TOL=33449],haplophallus subclarus[&&NHX:TOL=33450],haplophallus talilus[&&NHX:TOL=33451],haplophallus tandus[&&NHX:TOL=33452],haplophallus thorntoni[&&NHX:TOL=33453],haplophallus trachopetalus[&&NHX:TOL=33454],haplophallus trepticus[&&NHX:TOL=33455],haplophallus wongae[&&NHX:TOL=33456])haplophallus[&&NHX:TOL=37440],((garcialdretia veracruzensis[&&NHX:TOL=136805],garcialdretia jareviana[&&NHX:TOL=136806],garcialdretia chiapensis[&&NHX:TOL=136807],garcialdretia boricuensis[&&NHX:TOL=136808],garcialdretia jamaicensis[&&NHX:TOL=136809],garcialdretia dardana[&&NHX:TOL=136810])garcialdretia[&&NHX:TOL=136060],(philotarsus fraternus[&&NHX:TOL=33458],philotarsus kwakiutl[&&NHX:TOL=33460],philotarsus parviceps[&&NHX:TOL=33461],philotarsus picicornis[&&NHX:TOL=33462],philotarsus sinensis[&&NHX:TOL=33463],philotarsus thorntoni[&&NHX:TOL=33464],philotarsus zangdaicus[&&NHX:TOL=33465],philotarsus zangxiaoicus[&&NHX:TOL=33466])philotarsus[&&NHX:TOL=37441])[&&NHX:TOL=136804])philotarsinae[&&NHX:TOL=50637],((aaroniella achrysa[&&NHX:TOL=33467],aaroniella andrei[&&NHX:TOL=33468],aaroniella antennata[&&NHX:TOL=33469],aaroniella badonneli[&&NHX:TOL=33470],aaroniella bakeri[&&NHX:TOL=33471],aaroniella betschi[&&NHX:TOL=33472],aaroniella bruchi[&&NHX:TOL=33473],aaroniella caribe[&&NHX:TOL=33474],aaroniella chamelana[&&NHX:TOL=33475],aaroniella crista[&&NHX:TOL=33476],aaroniella curtifurca[&&NHX:TOL=33477],aaroniella dentata[&&NHX:TOL=33478],aaroniella festiva[&&NHX:TOL=33479],aaroniella flexa[&&NHX:TOL=33480],aaroniella galapagensis[&&NHX:TOL=33481],aaroniella glabra[&&NHX:TOL=33482],aaroniella glossoptera[&&NHX:TOL=33483],aaroniella grandiocula[&&NHX:TOL=33484],aaroniella gressitti[&&NHX:TOL=33485],aaroniella guttulata[&&NHX:TOL=33486],aaroniella gyratigra[&&NHX:TOL=33487],aaroniella hoffmannae[&&NHX:TOL=33488],aaroniella howensis[&&NHX:TOL=33489],aaroniella kepongensis[&&NHX:TOL=33490],aaroniella lobata[&&NHX:TOL=33491],aaroniella lombokensis[&&NHX:TOL=33492],aaroniella maculosa[&&NHX:TOL=33493],aaroniella madecassa[&&NHX:TOL=33494],aaroniella maligawa[&&NHX:TOL=33495],aaroniella mauritiensis[&&NHX:TOL=33496],aaroniella montana[&&NHX:TOL=33497],aaroniella multipunctata[&&NHX:TOL=33498],aaroniella nebulosa[&&NHX:TOL=33499],aaroniella pardina[&&NHX:TOL=33500],aaroniella pedunculata[&&NHX:TOL=33501],aaroniella pterosoma[&&NHX:TOL=33502],aaroniella pulchra[&&NHX:TOL=33503],aaroniella rawlingsi[&&NHX:TOL=33504],aaroniella recta[&&NHX:TOL=33505],aaroniella reunionensis[&&NHX:TOL=33506],aaroniella samoana[&&NHX:TOL=33507],aaroniella serialis[&&NHX:TOL=33508],aaroniella sinuosa[&&NHX:TOL=33509],aaroniella spenceri[&&NHX:TOL=33510],aaroniella stictica[&&NHX:TOL=33511],aaroniella sudarmani[&&NHX:TOL=33512],aaroniella ternata[&&NHX:TOL=33513],aaroniella trukensis[&&NHX:TOL=33514])aaroniella[&&NHX:TOL=37442],(philotarsopsis acraea[&&NHX:TOL=33515],philotarsopsis albicrus[&&NHX:TOL=33516],philotarsopsis alticola[&&NHX:TOL=33517],philotarsopsis basipunctata[&&NHX:TOL=33518],philotarsopsis brevis[&&NHX:TOL=33519],philotarsopsis bundoorensis[&&NHX:TOL=33520],philotarsopsis cruciclypeus[&&NHX:TOL=33521],philotarsopsis decora[&&NHX:TOL=33522],philotarsopsis elongata[&&NHX:TOL=33523],philotarsopsis fenestrata[&&NHX:TOL=33524],philotarsopsis guttata[&&NHX:TOL=33525],philotarsopsis kaindiensis[&&NHX:TOL=33526],philotarsopsis lemsidia[&&NHX:TOL=33527],philotarsopsis manoides[&&NHX:TOL=33528],philotarsopsis manus[&&NHX:TOL=33529],philotarsopsis medialis[&&NHX:TOL=33530],philotarsopsis mouldsi[&&NHX:TOL=33531],philotarsopsis novitas[&&NHX:TOL=33532],philotarsopsis ornata[&&NHX:TOL=33533],philotarsopsis paraguttata[&&NHX:TOL=33534],philotarsopsis parda[&&NHX:TOL=33535],philotarsopsis pseudosigma[&&NHX:TOL=33536],philotarsopsis reducta[&&NHX:TOL=33537],philotarsopsis setosa[&&NHX:TOL=33538],philotarsopsis sigma[&&NHX:TOL=33539],philotarsopsis sigmoides[&&NHX:TOL=33540],philotarsopsis stigmata[&&NHX:TOL=33541],philotarsopsis triangulum[&&NHX:TOL=33542],philotarsopsis virgata[&&NHX:TOL=33543])philotarsopsis[&&NHX:TOL=37443],(tarsophilus aequabilis[&&NHX:TOL=33544],tarsophilus lineatus[&&NHX:TOL=33545])tarsophilus[&&NHX:TOL=37444])aaroniellinae[&&NHX:TOL=50638])philotarsidae[&&NHX:TOL=30251],(callistoptera anna[&&NHX:TOL=34134],((calopsocus apicatus[&&NHX:TOL=34135],calopsocus cumulus[&&NHX:TOL=34136],calopsocus furcatus[&&NHX:TOL=34137],calopsocus gorokensis[&&NHX:TOL=34138],calopsocus guttatus[&&NHX:TOL=34139],calopsocus infelix[&&NHX:TOL=34140],calopsocus iridescens[&&NHX:TOL=34141],calopsocus javanus[&&NHX:TOL=34142],calopsocus koridensis[&&NHX:TOL=34143],calopsocus maculatus[&&NHX:TOL=34144],calopsocus marginatus[&&NHX:TOL=34145],calopsocus ovatus[&&NHX:TOL=34146],calopsocus pallistigma[&&NHX:TOL=34147],calopsocus reticulatus[&&NHX:TOL=34148],calopsocus reticuloides[&&NHX:TOL=34149],calopsocus rizali[&&NHX:TOL=34150],calopsocus solomonensis[&&NHX:TOL=34151],calopsocus yatesi[&&NHX:TOL=34152])calopsocus[&&NHX:TOL=38104],calosema browningae[&&NHX:TOL=34153],(cyclopsocus gressitti[&&NHX:TOL=34154],cyclopsocus hyalinus[&&NHX:TOL=34155],cyclopsocus hyaloides[&&NHX:TOL=34156],cyclopsocus navasi[&&NHX:TOL=34157],cyclopsocus straatmani[&&NHX:TOL=34158])cyclopsocus[&&NHX:TOL=38105],dendropsocus swartensis[&&NHX:TOL=34159],nemupsocus lobatus[&&NHX:TOL=34160],(neurosema alobum[&&NHX:TOL=34161],neurosema apicale[&&NHX:TOL=34162],neurosema dimorphum[&&NHX:TOL=34163],neurosema pulchroides[&&NHX:TOL=34164],neurosema pulchrum[&&NHX:TOL=34165])neurosema[&&NHX:TOL=38106],(torrepsocus novoguinensis[&&NHX:TOL=34166],torrepsocus pulleni[&&NHX:TOL=34167])torrepsocus[&&NHX:TOL=38107])calopsocinae[&&NHX:TOL=50634])calopsocidae[&&NHX:TOL=14474],(bryopsocus angulatus[&&NHX:TOL=33718],bryopsocus townsendi[&&NHX:TOL=33719])bryopsocus[&&NHX:TOL=30253],(((allocaecilius albidorsualis[&&NHX:TOL=33747],allocaecilius arcuatus[&&NHX:TOL=33748],allocaecilius biaduncus[&&NHX:TOL=33749],allocaecilius elongatus[&&NHX:TOL=33750],allocaecilius fusciceps[&&NHX:TOL=33751],allocaecilius gombakensis[&&NHX:TOL=33752],allocaecilius guangdongicus[&&NHX:TOL=33753],allocaecilius heterothorax[&&NHX:TOL=33754],allocaecilius maculatus[&&NHX:TOL=33755],allocaecilius selangorensis[&&NHX:TOL=33756],allocaecilius sinensis[&&NHX:TOL=33757],allocaecilius smithersi[&&NHX:TOL=33758],allocaecilius tenuilongus[&&NHX:TOL=33759])allocaecilius[&&NHX:TOL=33720],(allopsocus marginalis[&&NHX:TOL=33760],allopsocus medialis[&&NHX:TOL=33761])allopsocus[&&NHX:TOL=33721],(chorocaecilius brunellus[&&NHX:TOL=33762],chorocaecilius decemdentatus[&&NHX:TOL=33763])chorocaecilius[&&NHX:TOL=33722],(cladioneura foliata[&&NHX:TOL=33764],cladioneura pulchripennis[&&NHX:TOL=33765],cladioneura punctata[&&NHX:TOL=33766])cladioneura[&&NHX:TOL=33723],diplocaecilius peyrierasi[&&NHX:TOL=33724],(heterocaecilius abacutidens[&&NHX:TOL=33768],heterocaecilius adamsi[&&NHX:TOL=33769],heterocaecilius aequabilis[&&NHX:TOL=33770],heterocaecilius analis[&&NHX:TOL=33771],heterocaecilius anareolatus[&&NHX:TOL=33772],heterocaecilius anomalus[&&NHX:TOL=33773],heterocaecilius badonneli[&&NHX:TOL=33774],heterocaecilius bidigitatus[&&NHX:TOL=33775],heterocaecilius brevifurca[&&NHX:TOL=33776],heterocaecilius challengerius[&&NHX:TOL=33777],heterocaecilius circulicellus[&&NHX:TOL=33778],heterocaecilius deloneurous[&&NHX:TOL=33779],heterocaecilius dentalis[&&NHX:TOL=33780],heterocaecilius fasciatus[&&NHX:TOL=33781],heterocaecilius flaviformis[&&NHX:TOL=33782],heterocaecilius fumosus[&&NHX:TOL=33783],heterocaecilius fuscipalpus[&&NHX:TOL=33784],heterocaecilius fuscus[&&NHX:TOL=33785],heterocaecilius gressitti[&&NHX:TOL=33786],heterocaecilius hepaticivenus[&&NHX:TOL=33787],heterocaecilius hoplites[&&NHX:TOL=33788],heterocaecilius huananensis[&&NHX:TOL=33789],heterocaecilius huaxiensis[&&NHX:TOL=33790],heterocaecilius jinghongicus[&&NHX:TOL=33791],heterocaecilius kobus[&&NHX:TOL=33792],heterocaecilius lachlani[&&NHX:TOL=33793],heterocaecilius leei[&&NHX:TOL=33794],heterocaecilius liangi[&&NHX:TOL=33795],heterocaecilius liaoi[&&NHX:TOL=33796],heterocaecilius longipenna[&&NHX:TOL=33797],heterocaecilius longispinus[&&NHX:TOL=33798],heterocaecilius maculans[&&NHX:TOL=33799],heterocaecilius maculifrons[&&NHX:TOL=33800],heterocaecilius maculosus[&&NHX:TOL=33801],heterocaecilius madecassus[&&NHX:TOL=33802],heterocaecilius marginatus[&&NHX:TOL=33803],heterocaecilius mecotrichus[&&NHX:TOL=33804],heterocaecilius minotus[&&NHX:TOL=33805],heterocaecilius montanus[&&NHX:TOL=33806],heterocaecilius mouldsi[&&NHX:TOL=33807],heterocaecilius nepalensis[&&NHX:TOL=33808],heterocaecilius nigricans[&&NHX:TOL=33809],heterocaecilius ocraceus[&&NHX:TOL=33810],heterocaecilius octomaculatus[&&NHX:TOL=33811],heterocaecilius odontothelus[&&NHX:TOL=33812],heterocaecilius orientalis[&&NHX:TOL=33813],heterocaecilius ornatus[&&NHX:TOL=33814],heterocaecilius papillatus[&&NHX:TOL=33815],heterocaecilius papillosus[&&NHX:TOL=33816],heterocaecilius paulicellus[&&NHX:TOL=33817],heterocaecilius phimus[&&NHX:TOL=33818],heterocaecilius piceus[&&NHX:TOL=33819],heterocaecilius platokeratis[&&NHX:TOL=33820],heterocaecilius pseudoanomalus[&&NHX:TOL=33821],heterocaecilius quadrangulus[&&NHX:TOL=33822],heterocaecilius reticulatus[&&NHX:TOL=33823],heterocaecilius rhadnus[&&NHX:TOL=33824],heterocaecilius rotundus[&&NHX:TOL=33825],heterocaecilius rufolinearis[&&NHX:TOL=33826],heterocaecilius solocipennis[&&NHX:TOL=33827],heterocaecilius stenokeratis[&&NHX:TOL=33828],heterocaecilius stiliger[&&NHX:TOL=33829],heterocaecilius taipingensis[&&NHX:TOL=33830],heterocaecilius tartareus[&&NHX:TOL=33831],heterocaecilius tectus[&&NHX:TOL=33832],heterocaecilius unimaculatus[&&NHX:TOL=33833],heterocaecilius uruguayensis[&&NHX:TOL=33834],heterocaecilius variabilis[&&NHX:TOL=33835])heterocaecilius[&&NHX:TOL=33725],(kerocaecilius circulicellus[&&NHX:TOL=33836],kerocaecilius costatus[&&NHX:TOL=33837],kerocaecilius cunninghamius[&&NHX:TOL=33838],kerocaecilius curtiangulus[&&NHX:TOL=33839],kerocaecilius dianxiensis[&&NHX:TOL=33840],kerocaecilius ganglioneus[&&NHX:TOL=33841],kerocaecilius grammocephalus[&&NHX:TOL=33842],kerocaecilius grandis[&&NHX:TOL=33843],kerocaecilius kongdongshanicus[&&NHX:TOL=33844],kerocaecilius louguantaiensis[&&NHX:TOL=33845],kerocaecilius luridicapitus[&&NHX:TOL=33846],kerocaecilius minisculus[&&NHX:TOL=33847],kerocaecilius pachyoceratus[&&NHX:TOL=33848],kerocaecilius phaeolomus[&&NHX:TOL=33849],kerocaecilius tenuicornutus[&&NHX:TOL=33850])kerocaecilius[&&NHX:TOL=33726],(levucaecilius albicrus[&&NHX:TOL=33851],levucaecilius apicalis[&&NHX:TOL=33852],levucaecilius greenwoodi[&&NHX:TOL=33853],levucaecilius hilli[&&NHX:TOL=33854],levucaecilius panicus[&&NHX:TOL=33855],levucaecilius pictus[&&NHX:TOL=33856],levucaecilius simplex[&&NHX:TOL=33857],levucaecilius veitchi[&&NHX:TOL=33858],levucaecilius volatus[&&NHX:TOL=33859])levucaecilius[&&NHX:TOL=33727],(lobocaecilius arcuatus[&&NHX:TOL=33860],lobocaecilius bifurcus[&&NHX:TOL=33861],lobocaecilius carinifex[&&NHX:TOL=33862],lobocaecilius cynara[&&NHX:TOL=33863],lobocaecilius drepanus[&&NHX:TOL=33864],lobocaecilius fennecus[&&NHX:TOL=33865],lobocaecilius ligur[&&NHX:TOL=33866],lobocaecilius longifurca[&&NHX:TOL=33867],lobocaecilius monicus[&&NHX:TOL=33868],lobocaecilius mouaputa[&&NHX:TOL=33869],lobocaecilius nigrens[&&NHX:TOL=33870],lobocaecilius nigroides[&&NHX:TOL=33871],lobocaecilius pahangensis[&&NHX:TOL=33872],lobocaecilius perductivirgus[&&NHX:TOL=33873],lobocaecilius pilosus[&&NHX:TOL=33874],lobocaecilius quadripartitus[&&NHX:TOL=33875],lobocaecilius thorntoni[&&NHX:TOL=33876],lobocaecilius vanuensis[&&NHX:TOL=33877],lobocaecilius viridis[&&NHX:TOL=33878])lobocaecilius[&&NHX:TOL=33728],(mepleres alettae[&&NHX:TOL=33879],mepleres avisonus[&&NHX:TOL=33880],mepleres bifasciatus[&&NHX:TOL=33881],mepleres circularis[&&NHX:TOL=33882],mepleres clarkei[&&NHX:TOL=33883],mepleres cornutus[&&NHX:TOL=33884],mepleres crennulatus[&&NHX:TOL=33885],mepleres decolor[&&NHX:TOL=33886],mepleres fasciatus[&&NHX:TOL=33887],mepleres forcipiformus[&&NHX:TOL=33888],mepleres fuscistigma[&&NHX:TOL=33889],mepleres gressitti[&&NHX:TOL=33890],mepleres hollowayi[&&NHX:TOL=33891],mepleres hyalinus[&&NHX:TOL=33892],mepleres immaculatus[&&NHX:TOL=33893],mepleres indicus[&&NHX:TOL=33894],mepleres insularis[&&NHX:TOL=33895],mepleres limbatus[&&NHX:TOL=33896],mepleres lomus[&&NHX:TOL=33897],mepleres longicellus[&&NHX:TOL=33898],mepleres longitudinalis[&&NHX:TOL=33899],mepleres lunai[&&NHX:TOL=33900],mepleres maculatus[&&NHX:TOL=33901],mepleres medialis[&&NHX:TOL=33902],mepleres megops[&&NHX:TOL=33903],mepleres morimotoi[&&NHX:TOL=33904],mepleres nigroguttatus[&&NHX:TOL=33905],mepleres ocellatus[&&NHX:TOL=33906],mepleres oresbius[&&NHX:TOL=33907],mepleres ornatus[&&NHX:TOL=33908],mepleres pallidus[&&NHX:TOL=33909],mepleres papillosus[&&NHX:TOL=33910],mepleres parvicellus[&&NHX:TOL=33911],mepleres pictus[&&NHX:TOL=33912],mepleres pisiformis[&&NHX:TOL=33913],mepleres plenimacularis[&&NHX:TOL=33914],mepleres posticus[&&NHX:TOL=33915],mepleres proboscideus[&&NHX:TOL=33916],mepleres procurrens[&&NHX:TOL=33917],mepleres pseudornatus[&&NHX:TOL=33918],mepleres radialis[&&NHX:TOL=33919],mepleres raphalis[&&NHX:TOL=33920],mepleres rotundatus[&&NHX:TOL=33921],mepleres sakishimensis[&&NHX:TOL=33922],mepleres similis[&&NHX:TOL=33923],mepleres sinicus[&&NHX:TOL=33924],mepleres solenocerus[&&NHX:TOL=33925],mepleres submarginalis[&&NHX:TOL=33926],mepleres suella[&&NHX:TOL=33927],mepleres suzukii[&&NHX:TOL=33928],mepleres tanei[&&NHX:TOL=33929],mepleres transversus[&&NHX:TOL=33930],mepleres tuberculatus[&&NHX:TOL=33931],mepleres ulterior[&&NHX:TOL=33932],mepleres unitus[&&NHX:TOL=33933],mepleres urbanus[&&NHX:TOL=33934],mepleres venusae[&&NHX:TOL=33935],mepleres vilus[&&NHX:TOL=33936],mepleres watti[&&NHX:TOL=33937],mepleres yeni[&&NHX:TOL=33938],mepleres yenoides[&&NHX:TOL=33939],mepleres yunnanicus[&&NHX:TOL=33940])mepleres[&&NHX:TOL=33729],(mesocaecilius bellus[&&NHX:TOL=33941],mesocaecilius decorosus[&&NHX:TOL=33942],mesocaecilius elegans[&&NHX:TOL=33943],mesocaecilius euryopterus[&&NHX:TOL=33944],mesocaecilius lepidus[&&NHX:TOL=33945],mesocaecilius pictipennis[&&NHX:TOL=33946],mesocaecilius quadrimaculatus[&&NHX:TOL=33947])mesocaecilius[&&NHX:TOL=33730],(neocaecilius campanula[&&NHX:TOL=33948],neocaecilius dardanus[&&NHX:TOL=33949],neocaecilius dybasi[&&NHX:TOL=33950],neocaecilius granulatus[&&NHX:TOL=33951],neocaecilius mutatus[&&NHX:TOL=33952],neocaecilius qianshanensis[&&NHX:TOL=33953])neocaecilius[&&NHX:TOL=33731],(ophiodopelma anocellum[&&NHX:TOL=33954],ophiodopelma fluctosum[&&NHX:TOL=33955],ophiodopelma glyptocephalum[&&NHX:TOL=33956],ophiodopelma hieroglyphicum[&&NHX:TOL=33957],ophiodopelma multipunctatum[&&NHX:TOL=33958],ophiodopelma ornatipenne[&&NHX:TOL=33959],ophiodopelma permaculatum[&&NHX:TOL=33960],ophiodopelma pictipenna[&&NHX:TOL=33961],ophiodopelma polyspilum[&&NHX:TOL=33962],ophiodopelma semiceps[&&NHX:TOL=33963])ophiodopelma[&&NHX:TOL=33732],(orbocaecilius argutus[&&NHX:TOL=33964],orbocaecilius bicruris[&&NHX:TOL=33965],orbocaecilius bifarius[&&NHX:TOL=33966],orbocaecilius brachystigmus[&&NHX:TOL=33967],orbocaecilius dasoceratus[&&NHX:TOL=33968],orbocaecilius duodecidentus[&&NHX:TOL=33969],orbocaecilius imparilis[&&NHX:TOL=33970],orbocaecilius longicornis[&&NHX:TOL=33971],orbocaecilius sedecimidentus[&&NHX:TOL=33972],orbocaecilius vulturius[&&NHX:TOL=33973],orbocaecilius xihuicus[&&NHX:TOL=33974])orbocaecilius[&&NHX:TOL=33733],(phallocaecilius hirsutus[&&NHX:TOL=33975],phallocaecilius sentosus[&&NHX:TOL=33976])phallocaecilius[&&NHX:TOL=33734],phyllocaecilius atrichus[&&NHX:TOL=33735],platyocaecilius parallelivenius[&&NHX:TOL=33736],(pseudocaecilius africanus[&&NHX:TOL=33979],pseudocaecilius angustus[&&NHX:TOL=33980],pseudocaecilius bibulbus[&&NHX:TOL=33981],pseudocaecilius bicostatus[&&NHX:TOL=33982],pseudocaecilius brevicornis[&&NHX:TOL=33983],pseudocaecilius ceratocercus[&&NHX:TOL=33984],pseudocaecilius citricola[&&NHX:TOL=33985],pseudocaecilius claggi[&&NHX:TOL=33986],pseudocaecilius clunialis[&&NHX:TOL=33987],pseudocaecilius cornutus[&&NHX:TOL=33988],pseudocaecilius cribrarius[&&NHX:TOL=33989],pseudocaecilius danaus[&&NHX:TOL=33990],pseudocaecilius euryocercus[&&NHX:TOL=33991],pseudocaecilius fletcheri[&&NHX:TOL=33992],pseudocaecilius formosanus[&&NHX:TOL=33993],pseudocaecilius funestus[&&NHX:TOL=33994],pseudocaecilius galactozonalis[&&NHX:TOL=33995],pseudocaecilius helicoides[&&NHX:TOL=33996],pseudocaecilius hispidus[&&NHX:TOL=33997],pseudocaecilius immaculatus[&&NHX:TOL=33998],pseudocaecilius inaequalis[&&NHX:TOL=33999],pseudocaecilius innotatus[&&NHX:TOL=34000],pseudocaecilius kagoshimensis[&&NHX:TOL=34001],pseudocaecilius katmanduensis[&&NHX:TOL=34002],pseudocaecilius lanatus[&&NHX:TOL=34003],pseudocaecilius largicellus[&&NHX:TOL=34004],pseudocaecilius machadoi[&&NHX:TOL=34005],pseudocaecilius maculosus[&&NHX:TOL=34006],pseudocaecilius marshalli[&&NHX:TOL=34007],pseudocaecilius medianicostatus[&&NHX:TOL=34008],pseudocaecilius molestus[&&NHX:TOL=34009],pseudocaecilius monotaeniatus[&&NHX:TOL=34010],pseudocaecilius morstatti[&&NHX:TOL=34011],pseudocaecilius nitoris[&&NHX:TOL=34012],pseudocaecilius otiosus[&&NHX:TOL=34013],pseudocaecilius papillaris[&&NHX:TOL=34014],pseudocaecilius paraornatus[&&NHX:TOL=34015],pseudocaecilius plagiozonalis[&&NHX:TOL=34016],pseudocaecilius productus[&&NHX:TOL=34017],pseudocaecilius pusillus[&&NHX:TOL=34018],pseudocaecilius ranus[&&NHX:TOL=34019],pseudocaecilius serratus[&&NHX:TOL=34020],pseudocaecilius setifer[&&NHX:TOL=34021],pseudocaecilius sexdentatus[&&NHX:TOL=34022],pseudocaecilius similis[&&NHX:TOL=34023],pseudocaecilius tahitiensis[&&NHX:TOL=34024],pseudocaecilius tenellus[&&NHX:TOL=34025],pseudocaecilius testaceus[&&NHX:TOL=34026],pseudocaecilius undecimimaculatus[&&NHX:TOL=34027],pseudocaecilius utricularis[&&NHX:TOL=34028],pseudocaecilius venimaculatus[&&NHX:TOL=34029],pseudocaecilius villosus[&&NHX:TOL=34030],pseudocaecilius wellsae[&&NHX:TOL=34031],pseudocaecilius zonatus[&&NHX:TOL=34032])pseudocaecilius[&&NHX:TOL=33737],(scottiella compta[&&NHX:TOL=34033],scottiella hirsuticornis[&&NHX:TOL=34034],scottiella micans[&&NHX:TOL=34035])scottiella[&&NHX:TOL=33738],(scytopsocopsis corniculata[&&NHX:TOL=34036],scytopsocopsis hirtipenna[&&NHX:TOL=34037],scytopsocopsis quadrangula[&&NHX:TOL=34038],scytopsocopsis wuxiaensis[&&NHX:TOL=34039])scytopsocopsis[&&NHX:TOL=33739],(scytopsocus coriaceus[&&NHX:TOL=34040],scytopsocus difficilis[&&NHX:TOL=34041],scytopsocus fluminis[&&NHX:TOL=34042],scytopsocus fuscus[&&NHX:TOL=34043],scytopsocus medialis[&&NHX:TOL=34044])scytopsocus[&&NHX:TOL=33740],thelocaecilius mecokeratus[&&NHX:TOL=33741],(trichocaecilius dayaoshanicus[&&NHX:TOL=34046],trichocaecilius delicatus[&&NHX:TOL=34047],trichocaecilius octodontus[&&NHX:TOL=34048],trichocaecilius tianmushanicus[&&NHX:TOL=34049])trichocaecilius[&&NHX:TOL=33742],(trimerocaecilius becheti[&&NHX:TOL=34050],trimerocaecilius popovi[&&NHX:TOL=34051])trimerocaecilius[&&NHX:TOL=33743])pseudocaeciliinae[&&NHX:TOL=50643],((austropsocus antennalis[&&NHX:TOL=34052],austropsocus apicipunctatus[&&NHX:TOL=34053],austropsocus australis[&&NHX:TOL=34054],austropsocus baeus[&&NHX:TOL=34055],austropsocus chathamensis[&&NHX:TOL=34056],austropsocus cornutus[&&NHX:TOL=34057],austropsocus costalis[&&NHX:TOL=34058],austropsocus cuneatus[&&NHX:TOL=34059],austropsocus delli[&&NHX:TOL=34060],austropsocus fasciatus[&&NHX:TOL=34061],austropsocus froggatti[&&NHX:TOL=34062],austropsocus hyalinus[&&NHX:TOL=34063],austropsocus insularis[&&NHX:TOL=34064],austropsocus micans[&&NHX:TOL=34065],austropsocus nimbosus[&&NHX:TOL=34066],austropsocus nitidus[&&NHX:TOL=34067],austropsocus novoguinensis[&&NHX:TOL=34068],austropsocus occidentalis[&&NHX:TOL=34069],austropsocus omega[&&NHX:TOL=34070],austropsocus perforatus[&&NHX:TOL=34071],austropsocus productus[&&NHX:TOL=34072],austropsocus punctatus[&&NHX:TOL=34073],austropsocus ramsayi[&&NHX:TOL=34074],austropsocus salmoni[&&NHX:TOL=34075],austropsocus sinuosus[&&NHX:TOL=34076],austropsocus strabus[&&NHX:TOL=34077],austropsocus suffusus[&&NHX:TOL=34078],austropsocus thapsinus[&&NHX:TOL=34079],austropsocus tibialis[&&NHX:TOL=34080],austropsocus venosus[&&NHX:TOL=34081],austropsocus viridis[&&NHX:TOL=34082],austropsocus xuthus[&&NHX:TOL=34083])austropsocus[&&NHX:TOL=33744],novopsocus stenopterus[&&NHX:TOL=33745],(zelandopsocus astictus[&&NHX:TOL=34085],zelandopsocus balius[&&NHX:TOL=34086],zelandopsocus bifidus[&&NHX:TOL=34087],zelandopsocus chroicus[&&NHX:TOL=34088],zelandopsocus cumulus[&&NHX:TOL=34089],zelandopsocus dialecus[&&NHX:TOL=34090],zelandopsocus diargemus[&&NHX:TOL=34091],zelandopsocus diides[&&NHX:TOL=34092],zelandopsocus formosellus[&&NHX:TOL=34093],zelandopsocus fulvus[&&NHX:TOL=34094],zelandopsocus furfurosus[&&NHX:TOL=34095],zelandopsocus gilvus[&&NHX:TOL=34096],zelandopsocus graptus[&&NHX:TOL=34097],zelandopsocus helvus[&&NHX:TOL=34098],zelandopsocus hemiptenus[&&NHX:TOL=34099],zelandopsocus humidus[&&NHX:TOL=34100],zelandopsocus justus[&&NHX:TOL=34101],zelandopsocus kuscheli[&&NHX:TOL=34102],zelandopsocus litus[&&NHX:TOL=34103],zelandopsocus loxus[&&NHX:TOL=34104],zelandopsocus luridus[&&NHX:TOL=34105],zelandopsocus marmor[&&NHX:TOL=34106],zelandopsocus ochrus[&&NHX:TOL=34107],zelandopsocus oropedius[&&NHX:TOL=34108],zelandopsocus perilegnes[&&NHX:TOL=34109],zelandopsocus perinesus[&&NHX:TOL=34110],zelandopsocus poecilus[&&NHX:TOL=34111],zelandopsocus tectus[&&NHX:TOL=34112],zelandopsocus translucidus[&&NHX:TOL=34113],zelandopsocus varianus[&&NHX:TOL=34114],zelandopsocus venustus[&&NHX:TOL=34115])zelandopsocus[&&NHX:TOL=33746])zelandopsocinae[&&NHX:TOL=50644])pseudocaeciliidae[&&NHX:TOL=14475])[&&NHX:TOL=136811],((ausysium joyceorum[&&NHX:TOL=33546],gondwanapsocus australis[&&NHX:TOL=33547],howeanum huberi[&&NHX:TOL=33548],metelipsocus qinghaiensis[&&NHX:TOL=33549],moapsocus angelicus[&&NHX:TOL=33550],onychophallus diemenensis[&&NHX:TOL=33551],psocophloea sarahae[&&NHX:TOL=33552],(sinelipsocus villosus[&&NHX:TOL=33586],sinelipsocus yangi[&&NHX:TOL=33587])sinelipsocus[&&NHX:TOL=33553],telmopsocus waldheimensis[&&NHX:TOL=33554],(trichoelipsocus brachypterus[&&NHX:TOL=33589],trichoelipsocus sanxianicus[&&NHX:TOL=33590])trichoelipsocus[&&NHX:TOL=33555],villopsocus tasmaniensis[&&NHX:TOL=33556],(cuneopalpus cyanops[&&NHX:TOL=33557],(drymopsocus brunneus[&&NHX:TOL=33593],drymopsocus carrilloi[&&NHX:TOL=33594],drymopsocus flavus[&&NHX:TOL=33595],drymopsocus griseus[&&NHX:TOL=33596],drymopsocus valdiviensis[&&NHX:TOL=33597])drymopsocus[&&NHX:TOL=33558],(elipsocus abdominalis[&&NHX:TOL=33598],elipsocus abnormis[&&NHX:TOL=33599],elipsocus alettae[&&NHX:TOL=33600],elipsocus alpinus[&&NHX:TOL=33601],elipsocus annulatus[&&NHX:TOL=33602],elipsocus azoricus[&&NHX:TOL=33603],elipsocus boops[&&NHX:TOL=33604],elipsocus brincki[&&NHX:TOL=33605],elipsocus capensis[&&NHX:TOL=33606],elipsocus coloripennis[&&NHX:TOL=33607],elipsocus fasciatus[&&NHX:TOL=33608],elipsocus guentheri[&&NHX:TOL=33609],elipsocus hyalinus[&&NHX:TOL=33610],elipsocus ignobilis[&&NHX:TOL=33611],elipsocus impressus[&&NHX:TOL=33612],elipsocus kuriliensis[&&NHX:TOL=33613],elipsocus labralis[&&NHX:TOL=33614],elipsocus lanceloticus[&&NHX:TOL=33615],elipsocus marplatensis[&&NHX:TOL=33616],elipsocus mbizianus[&&NHX:TOL=33617],elipsocus modestus[&&NHX:TOL=33618],elipsocus moebiusi[&&NHX:TOL=33619],elipsocus nuptialis[&&NHX:TOL=33620],elipsocus obscurus[&&NHX:TOL=33621],elipsocus oligotrichus[&&NHX:TOL=33622],elipsocus pumilis[&&NHX:TOL=33623],elipsocus pusillus[&&NHX:TOL=33624],elipsocus rubrostigma[&&NHX:TOL=33625],elipsocus ustulatus[&&NHX:TOL=33626],elipsocus viridimicans[&&NHX:TOL=33627])elipsocus[&&NHX:TOL=33559],(hemineura bigoti[&&NHX:TOL=33628],hemineura blascoi[&&NHX:TOL=33629],hemineura clunialis[&&NHX:TOL=33630],hemineura dispar[&&NHX:TOL=33631],hemineura hispanica[&&NHX:TOL=33632],hemineura sclerophallina[&&NHX:TOL=33633],hemineura trudiae[&&NHX:TOL=33634],hemineura turanica[&&NHX:TOL=33635],hemineura wittmeri[&&NHX:TOL=33636])hemineura[&&NHX:TOL=33560],(kilauella debilis[&&NHX:TOL=33637],kilauella erythrosticta[&&NHX:TOL=33638],kilauella frigida[&&NHX:TOL=33639],kilauella inaequifusca[&&NHX:TOL=33640],kilauella micramaura[&&NHX:TOL=33641],kilauella psylloides[&&NHX:TOL=33642],kilauella vinosa[&&NHX:TOL=33643])kilauella[&&NHX:TOL=33561],(palistreptus brevipennis[&&NHX:TOL=33644],palistreptus cinctifrons[&&NHX:TOL=33645],palistreptus fuscicosta[&&NHX:TOL=33646],palistreptus fuscifrons[&&NHX:TOL=33647],palistreptus heterothorax[&&NHX:TOL=33648],palistreptus hyalinus[&&NHX:TOL=33649],palistreptus inconstans[&&NHX:TOL=33650],palistreptus lobatus[&&NHX:TOL=33651],palistreptus longipennis[&&NHX:TOL=33652],palistreptus microvalvus[&&NHX:TOL=33653],palistreptus montanus[&&NHX:TOL=33654],palistreptus nigriceps[&&NHX:TOL=33655],palistreptus oahuensis[&&NHX:TOL=33656],palistreptus oligotarsus[&&NHX:TOL=33657],palistreptus pallithorax[&&NHX:TOL=33658],palistreptus pictifrons[&&NHX:TOL=33659],palistreptus setosus[&&NHX:TOL=33660],palistreptus sextus[&&NHX:TOL=33661],palistreptus swezeyi[&&NHX:TOL=33662],palistreptus valvulus[&&NHX:TOL=33663])palistreptus[&&NHX:TOL=33562],sabulopsocus tractuosus[&&NHX:TOL=33563])elipsocinae[&&NHX:TOL=50639],(clinopsocus smithersi[&&NHX:TOL=33564],(palmicola aphrodite[&&NHX:TOL=33666],palmicola pumilis[&&NHX:TOL=33667],palmicola robinae[&&NHX:TOL=33668],palmicola solitarius[&&NHX:TOL=33669],palmicola vinai[&&NHX:TOL=33670])palmicola[&&NHX:TOL=33565],(pseudopsocus acarinatus[&&NHX:TOL=33671],pseudopsocus carinatus[&&NHX:TOL=33672],pseudopsocus fusciceps[&&NHX:TOL=33673],pseudopsocus lichenophilus[&&NHX:TOL=33674],pseudopsocus meridionalis[&&NHX:TOL=33675],pseudopsocus rostocki[&&NHX:TOL=33676],pseudopsocus subtilis[&&NHX:TOL=33677])pseudopsocus[&&NHX:TOL=33566],reuterella helvimacula[&&NHX:TOL=33567])pseudopsocinae[&&NHX:TOL=50640],((antarctopsocus daviesi[&&NHX:TOL=33679],antarctopsocus jeanneli[&&NHX:TOL=33680])antarctopsocus[&&NHX:TOL=33568],(pentacladus eucalypti[&&NHX:TOL=33681],pentacladus marmoratus[&&NHX:TOL=33682])pentacladus[&&NHX:TOL=33569],(propsocus pallipes[&&NHX:TOL=33683],propsocus pulchripennis[&&NHX:TOL=33684])propsocus[&&NHX:TOL=33570],sandrapsocus clarki[&&NHX:TOL=33571],(spilopsocus annulatus[&&NHX:TOL=33686],spilopsocus avius[&&NHX:TOL=33687],spilopsocus colliensis[&&NHX:TOL=33688],spilopsocus masseyi[&&NHX:TOL=33689],spilopsocus parvus[&&NHX:TOL=33690],spilopsocus ruidus[&&NHX:TOL=33691],spilopsocus serratus[&&NHX:TOL=33692],spilopsocus stigmaticus[&&NHX:TOL=33693])spilopsocus[&&NHX:TOL=33572])propsocinae[&&NHX:TOL=50641],((nepiomorpha annulata[&&NHX:TOL=33694],nepiomorpha brasiliana[&&NHX:TOL=33695],nepiomorpha cingulata[&&NHX:TOL=33696],nepiomorpha crucifera[&&NHX:TOL=33697],nepiomorpha dolosa[&&NHX:TOL=33698],nepiomorpha pallida[&&NHX:TOL=33699],nepiomorpha peripsocoides[&&NHX:TOL=33700],nepiomorpha phragmitella[&&NHX:TOL=33701])nepiomorpha[&&NHX:TOL=33573],(nothopsocus badonneli[&&NHX:TOL=33702],nothopsocus cinqueportsae[&&NHX:TOL=33703],nothopsocus cooki[&&NHX:TOL=33704],nothopsocus defoei[&&NHX:TOL=33705],nothopsocus oxyurus[&&NHX:TOL=33706],nothopsocus selkirki[&&NHX:TOL=33707],nothopsocus skottsbergi[&&NHX:TOL=33708])nothopsocus[&&NHX:TOL=33574],paedomorpha gayi[&&NHX:TOL=33575],(roesleria achocallae[&&NHX:TOL=33710],roesleria desertica[&&NHX:TOL=33711])roesleria[&&NHX:TOL=33576])nepiomorphinae[&&NHX:TOL=50642],(lesneia capensis[&&NHX:TOL=33712],lesneia nigra[&&NHX:TOL=33713],lesneia pulchra[&&NHX:TOL=33714],lesneia stuckenbergi[&&NHX:TOL=33715])lesneia[&&NHX:TOL=33577],yuntapsocus hollowayi[&&NHX:TOL=33578])elipsocidae[&&NHX:TOL=30252],((bicuspidatus guangdongensis[&&NHX:TOL=34180],bicuspidatus pulchipunctatus[&&NHX:TOL=34181],bicuspidatus sigillatus[&&NHX:TOL=34182])bicuspidatus[&&NHX:TOL=34168],(campanulatus jaculatorius[&&NHX:TOL=34183],campanulatus lagenarius[&&NHX:TOL=34184])campanulatus[&&NHX:TOL=34169],(coniperipsocus jindingensis[&&NHX:TOL=34185],coniperipsocus melanolomus[&&NHX:TOL=34186],coniperipsocus minutissimus[&&NHX:TOL=34187],coniperipsocus porosus[&&NHX:TOL=34188],coniperipsocus proceridentalis[&&NHX:TOL=34189],coniperipsocus quadrifascius[&&NHX:TOL=34190],coniperipsocus yuae[&&NHX:TOL=34191])coniperipsocus[&&NHX:TOL=34170],(cycloperipsocus diplocyclus[&&NHX:TOL=34192],cycloperipsocus edwardsi[&&NHX:TOL=34193],cycloperipsocus norfolkensis[&&NHX:TOL=34194],cycloperipsocus pangi[&&NHX:TOL=34195])cycloperipsocus[&&NHX:TOL=34171],(diplopsocus albostigmus[&&NHX:TOL=34196],diplopsocus anoplus[&&NHX:TOL=34197],diplopsocus chebalingicus[&&NHX:TOL=34198],diplopsocus circularis[&&NHX:TOL=34199],diplopsocus cupressicolus[&&NHX:TOL=34200],diplopsocus dachigamensis[&&NHX:TOL=34201],diplopsocus fasciatus[&&NHX:TOL=34202],diplopsocus fujianicus[&&NHX:TOL=34203],diplopsocus hainanensis[&&NHX:TOL=34204],diplopsocus huananensis[&&NHX:TOL=34205],diplopsocus irregularis[&&NHX:TOL=34206],diplopsocus jiangxiensis[&&NHX:TOL=34207],diplopsocus liupanshanensis[&&NHX:TOL=34208],diplopsocus lophacanthus[&&NHX:TOL=34209],diplopsocus magniocellatus[&&NHX:TOL=34210],diplopsocus melanostictus[&&NHX:TOL=34211],diplopsocus ningmingicus[&&NHX:TOL=34212],diplopsocus oblongus[&&NHX:TOL=34213],diplopsocus palmiformis[&&NHX:TOL=34214],diplopsocus parabolicus[&&NHX:TOL=34215],diplopsocus parviocellatus[&&NHX:TOL=34216],diplopsocus phaeophlebicus[&&NHX:TOL=34217],diplopsocus phagococcus[&&NHX:TOL=34218],diplopsocus philopinnus[&&NHX:TOL=34219],diplopsocus punctigaster[&&NHX:TOL=34220],diplopsocus quadrangulus[&&NHX:TOL=34221],diplopsocus resupinatus[&&NHX:TOL=34222],diplopsocus rhombeus[&&NHX:TOL=34223],diplopsocus scrobiculatus[&&NHX:TOL=34224],diplopsocus selene[&&NHX:TOL=34225],diplopsocus shanxiensis[&&NHX:TOL=34226],diplopsocus sichuanicus[&&NHX:TOL=34227],diplopsocus similaris[&&NHX:TOL=34228],diplopsocus sinensis[&&NHX:TOL=34229],diplopsocus sylvaticus[&&NHX:TOL=34230],diplopsocus tibeticus[&&NHX:TOL=34231],diplopsocus xilingxiaensis[&&NHX:TOL=34232],diplopsocus yangi[&&NHX:TOL=34233])diplopsocus[&&NHX:TOL=34172],(kaestneriella ecuatoriana[&&NHX:TOL=34234],kaestneriella fumosa[&&NHX:TOL=34235],kaestneriella guatemalensis[&&NHX:TOL=34236],kaestneriella maculosa[&&NHX:TOL=34237],kaestneriella mexicana[&&NHX:TOL=34238],kaestneriella minor[&&NHX:TOL=34239],kaestneriella obscura[&&NHX:TOL=34240],kaestneriella occidentalis[&&NHX:TOL=34241],kaestneriella pacifica[&&NHX:TOL=34242],kaestneriella pilosa[&&NHX:TOL=34243],kaestneriella setosa[&&NHX:TOL=34244],kaestneriella similis[&&NHX:TOL=34245],kaestneriella tenebrosa[&&NHX:TOL=34246])kaestneriella[&&NHX:TOL=34173],orbiperipsocus fractiflexus[&&NHX:TOL=34174],(pericupsocus cuspidatus[&&NHX:TOL=34248],pericupsocus digitalis[&&NHX:TOL=34249])pericupsocus[&&NHX:TOL=34175],(peripsocus acuminatus[&&NHX:TOL=34250],peripsocus africanus[&&NHX:TOL=34251],peripsocus alachuae[&&NHX:TOL=34252],peripsocus alboguttatus[&&NHX:TOL=34253],peripsocus ammonus[&&NHX:TOL=34254],peripsocus angolensis[&&NHX:TOL=34255],peripsocus annectens[&&NHX:TOL=34256],peripsocus annulatus[&&NHX:TOL=34257],peripsocus anura[&&NHX:TOL=34258],peripsocus apicatus[&&NHX:TOL=34259],peripsocus apiculatus[&&NHX:TOL=34260],peripsocus attenuatus[&&NHX:TOL=34261],peripsocus australis[&&NHX:TOL=34262],peripsocus badimaculatus[&&NHX:TOL=34263],peripsocus baishanzuicus[&&NHX:TOL=34264],peripsocus baiyunshanicus[&&NHX:TOL=34265],peripsocus balli[&&NHX:TOL=34266],peripsocus barunus[&&NHX:TOL=34267],peripsocus beijingensis[&&NHX:TOL=34268],peripsocus bhaktai[&&NHX:TOL=34269],peripsocus biacanthus[&&NHX:TOL=34270],peripsocus bifasciarius[&&NHX:TOL=34271],peripsocus bifasciatus[&&NHX:TOL=34272],peripsocus bifidus[&&NHX:TOL=34273],peripsocus bilobatus[&&NHX:TOL=34274],peripsocus bivari[&&NHX:TOL=34275],peripsocus bonnieae[&&NHX:TOL=34276],peripsocus brachyura[&&NHX:TOL=34277],peripsocus brinchangensis[&&NHX:TOL=34278],peripsocus brunneus[&&NHX:TOL=34279],peripsocus bucephalus[&&NHX:TOL=34280],peripsocus bucerus[&&NHX:TOL=34281],peripsocus bulbus[&&NHX:TOL=34282],peripsocus camerunus[&&NHX:TOL=34283],peripsocus cassideus[&&NHX:TOL=34284],peripsocus caudatus[&&NHX:TOL=34285],peripsocus chamelanus[&&NHX:TOL=34286],peripsocus changbaishanicus[&&NHX:TOL=34287],peripsocus chekei[&&NHX:TOL=34288],peripsocus circinus[&&NHX:TOL=34289],peripsocus coccophagus[&&NHX:TOL=34290],peripsocus conoidalis[&&NHX:TOL=34291],peripsocus consobrinus[&&NHX:TOL=34292],peripsocus constrictus[&&NHX:TOL=34293],peripsocus corollaris[&&NHX:TOL=34294],peripsocus crassicosta[&&NHX:TOL=34295],peripsocus crenulatus[&&NHX:TOL=34296],peripsocus curviclavus[&&NHX:TOL=34297],peripsocus cylindratus[&&NHX:TOL=34298],peripsocus decellei[&&NHX:TOL=34299],peripsocus decurvatus[&&NHX:TOL=34300],peripsocus denticulatus[&&NHX:TOL=34301],peripsocus didymus[&&NHX:TOL=34302],peripsocus disdentus[&&NHX:TOL=34303],peripsocus dolichophallus[&&NHX:TOL=34304],peripsocus dongbeiensis[&&NHX:TOL=34305],peripsocus duodecimidentus[&&NHX:TOL=34306],peripsocus elongatus[&&NHX:TOL=34307],peripsocus equispineus[&&NHX:TOL=34308],peripsocus exilis[&&NHX:TOL=34309],peripsocus falsipictus[&&NHX:TOL=34310],peripsocus ferrugineus[&&NHX:TOL=34311],peripsocus fici[&&NHX:TOL=34312],peripsocus forcipatus[&&NHX:TOL=34313],peripsocus forficatus[&&NHX:TOL=34314],peripsocus fornicalis[&&NHX:TOL=34315],peripsocus frimensis[&&NHX:TOL=34316],peripsocus fulvescens[&&NHX:TOL=34317],peripsocus furcellatus[&&NHX:TOL=34318],peripsocus ghesquierei[&&NHX:TOL=34319],peripsocus grandispineus[&&NHX:TOL=34320],peripsocus guandishanicus[&&NHX:TOL=34321],peripsocus guttulatus[&&NHX:TOL=34322],peripsocus hainanensis[&&NHX:TOL=34323],peripsocus hamiltonae[&&NHX:TOL=34324],peripsocus haplacanthus[&&NHX:TOL=34325],peripsocus hedinianus[&&NHX:TOL=34326],peripsocus hickmani[&&NHX:TOL=34327],peripsocus hinduensis[&&NHX:TOL=34328],peripsocus hollowayi[&&NHX:TOL=34329],peripsocus hongkongensis[&&NHX:TOL=34330],peripsocus huashanensis[&&NHX:TOL=34331],peripsocus hutsoni[&&NHX:TOL=34332],peripsocus hyalinus[&&NHX:TOL=34333],peripsocus ignis[&&NHX:TOL=34334],peripsocus incertus[&&NHX:TOL=34335],peripsocus incoloratus[&&NHX:TOL=34336],peripsocus inflatus[&&NHX:TOL=34337],peripsocus intricatus[&&NHX:TOL=34338],peripsocus jianfenglingicus[&&NHX:TOL=34339],peripsocus jiangxiensis[&&NHX:TOL=34340],peripsocus jilinicus[&&NHX:TOL=34341],peripsocus jinggangshanicus[&&NHX:TOL=34342],peripsocus jinshaanensis[&&NHX:TOL=34343],peripsocus jinxiuensis[&&NHX:TOL=34344],peripsocus juniperi[&&NHX:TOL=34345],peripsocus kashmirensis[&&NHX:TOL=34346],peripsocus keniensis[&&NHX:TOL=34347],peripsocus kunmingiensis[&&NHX:TOL=34348],peripsocus laoshanicus[&&NHX:TOL=34349],peripsocus laricis[&&NHX:TOL=34350],peripsocus latispineus[&&NHX:TOL=34351],peripsocus leleupi[&&NHX:TOL=34352],peripsocus leptorrhizus[&&NHX:TOL=34353],peripsocus lifashengi[&&NHX:TOL=34354],peripsocus limi[&&NHX:TOL=34355],peripsocus longifurcus[&&NHX:TOL=34356],peripsocus longivalvus[&&NHX:TOL=34357],peripsocus louguantaiensis[&&NHX:TOL=34358],peripsocus lunaris[&&NHX:TOL=34359],peripsocus luotongshanicus[&&NHX:TOL=34360],peripsocus machadoi[&&NHX:TOL=34361],peripsocus macrosiphus[&&NHX:TOL=34362],peripsocus maculosus[&&NHX:TOL=34363],peripsocus madecassus[&&NHX:TOL=34364],peripsocus madescens[&&NHX:TOL=34365],peripsocus madidus[&&NHX:TOL=34366],peripsocus magnimammus[&&NHX:TOL=34367],peripsocus maoricus[&&NHX:TOL=34368],peripsocus marginatus[&&NHX:TOL=34369],peripsocus medifasciarius[&&NHX:TOL=34370],peripsocus medimacularis[&&NHX:TOL=34371],peripsocus medispineus[&&NHX:TOL=34372],peripsocus megalophus[&&NHX:TOL=34373],peripsocus melaleucae[&&NHX:TOL=34374],peripsocus menieri[&&NHX:TOL=34375],peripsocus meridionalis[&&NHX:TOL=34376],peripsocus microcheilius[&&NHX:TOL=34377],peripsocus milleri[&&NHX:TOL=34378],peripsocus milloti[&&NHX:TOL=34379],peripsocus mingshanicus[&&NHX:TOL=34380],peripsocus minimus[&&NHX:TOL=34381],peripsocus minutus[&&NHX:TOL=34382],peripsocus mirabilis[&&NHX:TOL=34383],peripsocus mokotensis[&&NHX:TOL=34384],peripsocus monticola[&&NHX:TOL=34385],peripsocus morulops[&&NHX:TOL=34386],peripsocus mutilatus[&&NHX:TOL=34387],peripsocus nanjingensis[&&NHX:TOL=34388],peripsocus nanus[&&NHX:TOL=34389],peripsocus nasutus[&&NHX:TOL=34390],peripsocus nebulosus[&&NHX:TOL=34391],peripsocus neglectus[&&NHX:TOL=34392],peripsocus nigrescens[&&NHX:TOL=34393],peripsocus notialis[&&NHX:TOL=34394],peripsocus nubifer[&&NHX:TOL=34395],peripsocus octoidentus[&&NHX:TOL=34396],peripsocus oculatus[&&NHX:TOL=34397],peripsocus oculimacularis[&&NHX:TOL=34398],peripsocus odontopetalus[&&NHX:TOL=34399],peripsocus oligodontus[&&NHX:TOL=34400],peripsocus optimalis[&&NHX:TOL=34401],peripsocus orbiculatus[&&NHX:TOL=34402],peripsocus orebius[&&NHX:TOL=34403],peripsocus orientalis[&&NHX:TOL=34404],peripsocus oxydontus[&&NHX:TOL=34405],peripsocus pallidus[&&NHX:TOL=34406],peripsocus papillatus[&&NHX:TOL=34407],peripsocus parareicherti[&&NHX:TOL=34408],peripsocus paraspinosus[&&NHX:TOL=34409],peripsocus parvulus[&&NHX:TOL=34410],peripsocus parvus[&&NHX:TOL=34411],peripsocus pauliani[&&NHX:TOL=34412],peripsocus pediformis[&&NHX:TOL=34413],peripsocus pembanus[&&NHX:TOL=34414],peripsocus peruanus[&&NHX:TOL=34415],peripsocus phacellodomi[&&NHX:TOL=34416],peripsocus phaeochilus[&&NHX:TOL=34417],peripsocus phaeopterus[&&NHX:TOL=34418],peripsocus pictus[&&NHX:TOL=34419],peripsocus placidus[&&NHX:TOL=34420],peripsocus plagiotropus[&&NHX:TOL=34421],peripsocus platyopterus[&&NHX:TOL=34422],peripsocus plstylpus[&&NHX:TOL=34423],peripsocus plurimaculatus[&&NHX:TOL=34424],peripsocus polygonalis[&&NHX:TOL=34425],peripsocus polyoacanthus[&&NHX:TOL=34426],peripsocus potosi[&&NHX:TOL=34427],peripsocus pseudoquercicola[&&NHX:TOL=34428],peripsocus pumilus[&&NHX:TOL=34429],peripsocus qingchengshanicus[&&NHX:TOL=34430],peripsocus qingdaoensis[&&NHX:TOL=34431],peripsocus quadratiprocessus[&&NHX:TOL=34432],peripsocus quadripunctatus[&&NHX:TOL=34433],peripsocus quadratridentalis[&&NHX:TOL=34434],peripsocus quattuordecimus[&&NHX:TOL=34435],peripsocus quercicola[&&NHX:TOL=34436],peripsocus reduncus[&&NHX:TOL=34437],peripsocus reflexibilis[&&NHX:TOL=34438],peripsocus reicherti[&&NHX:TOL=34439],peripsocus rhombicus[&&NHX:TOL=34440],peripsocus rhomboacanthus[&&NHX:TOL=34441],peripsocus roseus[&&NHX:TOL=34442],peripsocus scalpratus[&&NHX:TOL=34443],peripsocus scapiformis[&&NHX:TOL=34444],peripsocus sclerotus[&&NHX:TOL=34445],peripsocus sedecimidentalis[&&NHX:TOL=34446],peripsocus setosus[&&NHX:TOL=34447],peripsocus sexidentus[&&NHX:TOL=34448],peripsocus shilinensis[&&NHX:TOL=34449],peripsocus siculiformis[&&NHX:TOL=34450],peripsocus similis[&&NHX:TOL=34451],peripsocus spinosus[&&NHX:TOL=34452],peripsocus spissospilus[&&NHX:TOL=34453],peripsocus stagnivagus[&&NHX:TOL=34454],peripsocus stegeri[&&NHX:TOL=34455],peripsocus stenopterus[&&NHX:TOL=34456],peripsocus stigmatus[&&NHX:TOL=34457],peripsocus stigmostigmus[&&NHX:TOL=34458],peripsocus stipiatus[&&NHX:TOL=34459],peripsocus subfasciatus[&&NHX:TOL=34460],peripsocus subtilis[&&NHX:TOL=34461],peripsocus subtristis[&&NHX:TOL=34462],peripsocus suffitus[&&NHX:TOL=34463],peripsocus suoxiyuicus[&&NHX:TOL=34464],peripsocus sydneyensis[&&NHX:TOL=34465],peripsocus taipingensis[&&NHX:TOL=34466],peripsocus terricolis[&&NHX:TOL=34467],peripsocus teutonicus[&&NHX:TOL=34468],peripsocus tillyardi[&&NHX:TOL=34469],peripsocus tinctus[&&NHX:TOL=34470],peripsocus togoensis[&&NHX:TOL=34471],peripsocus transivenus[&&NHX:TOL=34472],peripsocus tredecimus[&&NHX:TOL=34473],peripsocus trigonoispineus[&&NHX:TOL=34474],peripsocus tristis[&&NHX:TOL=34475],peripsocus umbrosus[&&NHX:TOL=34476],peripsocus uncinatus[&&NHX:TOL=34477],peripsocus undecimidentus[&&NHX:TOL=34478],peripsocus undulatus[&&NHX:TOL=34479],peripsocus uniformis[&&NHX:TOL=34480],peripsocus vacoasensis[&&NHX:TOL=34481],peripsocus valvulus[&&NHX:TOL=34482],peripsocus variatus[&&NHX:TOL=34483],peripsocus varidentatus[&&NHX:TOL=34484],peripsocus vescus[&&NHX:TOL=34485],peripsocus viriosus[&&NHX:TOL=34486],peripsocus weinigeri[&&NHX:TOL=34487],peripsocus wuhoi[&&NHX:TOL=34488],peripsocus wuyishanicus[&&NHX:TOL=34489],peripsocus xanthochilus[&&NHX:TOL=34490],peripsocus xihuensis[&&NHX:TOL=34491],peripsocus yongi[&&NHX:TOL=34492],peripsocus yuleki[&&NHX:TOL=34493],peripsocus zhangispineus[&&NHX:TOL=34494],peripsocus zhangliani[&&NHX:TOL=34495],peripsocus ziguiensis[&&NHX:TOL=34496])peripsocus[&&NHX:TOL=34176],(periterminalis badonneli[&&NHX:TOL=34497],periterminalis cryptomeriae[&&NHX:TOL=34498],periterminalis hiatus[&&NHX:TOL=34499],periterminalis lata[&&NHX:TOL=34500],periterminalis longicuspis[&&NHX:TOL=34501],periterminalis scapifurca[&&NHX:TOL=34502],periterminalis shanxiensis[&&NHX:TOL=34503])periterminalis[&&NHX:TOL=34177],(properipsocus bicornis[&&NHX:TOL=34504],properipsocus gracilis[&&NHX:TOL=34505],properipsocus laticorneus[&&NHX:TOL=34506],properipsocus quadartus[&&NHX:TOL=34507])properipsocus[&&NHX:TOL=34178],(turriperipsocus chiangensis[&&NHX:TOL=34508],turriperipsocus cunninghamiae[&&NHX:TOL=34509],turriperipsocus cupressisugus[&&NHX:TOL=34510],turriperipsocus decemidentatus[&&NHX:TOL=34511],turriperipsocus hypsodontus[&&NHX:TOL=34512],turriperipsocus leshanensis[&&NHX:TOL=34513])turriperipsocus[&&NHX:TOL=34179])peripsocidae[&&NHX:TOL=14473],(belipsocus chiquibulensis[&&NHX:TOL=34514],ectianoculus baishanzuicus[&&NHX:TOL=34515],(ectopsocopsis annulata[&&NHX:TOL=34522],ectopsocopsis anura[&&NHX:TOL=34523],ectopsocopsis badonneli[&&NHX:TOL=34524],ectopsocopsis baidichengensis[&&NHX:TOL=34525],ectopsocopsis balli[&&NHX:TOL=34526],ectopsocopsis beijingensis[&&NHX:TOL=34527],ectopsocopsis biporosa[&&NHX:TOL=34528],ectopsocopsis biunciata[&&NHX:TOL=34529],ectopsocopsis brevimanubria[&&NHX:TOL=34530],ectopsocopsis bulbiapicia[&&NHX:TOL=34531],ectopsocopsis clavellata[&&NHX:TOL=34532],ectopsocopsis cognata[&&NHX:TOL=34533],ectopsocopsis corbiformis[&&NHX:TOL=34534],ectopsocopsis crassiuncata[&&NHX:TOL=34535],ectopsocopsis cryptomeriae[&&NHX:TOL=34536],ectopsocopsis curtinervis[&&NHX:TOL=34537],ectopsocopsis daqingshanensis[&&NHX:TOL=34538],ectopsocopsis decorata[&&NHX:TOL=34539],ectopsocopsis flavipedia[&&NHX:TOL=34540],ectopsocopsis gannanensis[&&NHX:TOL=34541],ectopsocopsis granulosa[&&NHX:TOL=34542],ectopsocopsis guangdongensis[&&NHX:TOL=34543],ectopsocopsis jiangxiensis[&&NHX:TOL=34544],ectopsocopsis lunai[&&NHX:TOL=34545],ectopsocopsis luteolicapita[&&NHX:TOL=34546],ectopsocopsis mozambica[&&NHX:TOL=34547],ectopsocopsis phaeostictoa[&&NHX:TOL=34548],ectopsocopsis pinisuga[&&NHX:TOL=34549],ectopsocopsis sarmentiformis[&&NHX:TOL=34550],ectopsocopsis septentrionalis[&&NHX:TOL=34551],ectopsocopsis spathulata[&&NHX:TOL=34552],ectopsocopsis spatiosimanubra[&&NHX:TOL=34553],ectopsocopsis tenuimanubria[&&NHX:TOL=34554],ectopsocopsis terricolis[&&NHX:TOL=34555],ectopsocopsis trimaculata[&&NHX:TOL=34556],ectopsocopsis xerophylla[&&NHX:TOL=34557])ectopsocopsis[&&NHX:TOL=34516],(ectopsocus acutistigma[&&NHX:TOL=34558],ectopsocus adelphos[&&NHX:TOL=34559],ectopsocus aethiops[&&NHX:TOL=34560],ectopsocus albiceps[&&NHX:TOL=34561],ectopsocus aldretei[&&NHX:TOL=34562],ectopsocus amblyura[&&NHX:TOL=34563],ectopsocus amphithrix[&&NHX:TOL=34564],ectopsocus anisodontus[&&NHX:TOL=34565],ectopsocus annandalei[&&NHX:TOL=34566],ectopsocus argus[&&NHX:TOL=34567],ectopsocus australis[&&NHX:TOL=34568],ectopsocus axillaris[&&NHX:TOL=34569],ectopsocus baliosus[&&NHX:TOL=34570],ectopsocus barlowi[&&NHX:TOL=34571],ectopsocus basalis[&&NHX:TOL=34572],ectopsocus bengalensis[&&NHX:TOL=34573],ectopsocus berlesii[&&NHX:TOL=34574],ectopsocus bicaudatus[&&NHX:TOL=34575],ectopsocus bifurcatus[&&NHX:TOL=34576],ectopsocus biuncialis[&&NHX:TOL=34577],ectopsocus boharti[&&NHX:TOL=34578],ectopsocus briggsi[&&NHX:TOL=34579],ectopsocus brinchangensis[&&NHX:TOL=34580],ectopsocus brunneus[&&NHX:TOL=34581],ectopsocus californicus[&&NHX:TOL=34582],ectopsocus cetratus[&&NHX:TOL=34583],ectopsocus chiapensis[&&NHX:TOL=34584],ectopsocus chiapensoides[&&NHX:TOL=34585],ectopsocus cinctus[&&NHX:TOL=34586],ectopsocus cirratus[&&NHX:TOL=34587],ectopsocus cluniatus[&&NHX:TOL=34588],ectopsocus coccophilus[&&NHX:TOL=34589],ectopsocus columbianus[&&NHX:TOL=34590],ectopsocus comitus[&&NHX:TOL=34591],ectopsocus comptus[&&NHX:TOL=34592],ectopsocus coronatus[&&NHX:TOL=34593],ectopsocus crinitus[&&NHX:TOL=34594],ectopsocus cristatus[&&NHX:TOL=34595],ectopsocus decenipunctatus[&&NHX:TOL=34596],ectopsocus denervus[&&NHX:TOL=34597],ectopsocus denotatus[&&NHX:TOL=34598],ectopsocus denudatus[&&NHX:TOL=34599],ectopsocus dialeptus[&&NHX:TOL=34600],ectopsocus dicroglossus[&&NHX:TOL=34601],ectopsocus downesi[&&NHX:TOL=34602],ectopsocus drepanus[&&NHX:TOL=34603],ectopsocus edwardsi[&&NHX:TOL=34604],ectopsocus eertmoedi[&&NHX:TOL=34605],ectopsocus equidentus[&&NHX:TOL=34606],ectopsocus erosus[&&NHX:TOL=34607],ectopsocus ewarti[&&NHX:TOL=34608],ectopsocus exastis[&&NHX:TOL=34609],ectopsocus fenestratus[&&NHX:TOL=34610],ectopsocus ferrugineiceps[&&NHX:TOL=34611],ectopsocus flaviceps[&&NHX:TOL=34612],ectopsocus formosus[&&NHX:TOL=34613],ectopsocus froggatti[&&NHX:TOL=34614],ectopsocus fullawayi[&&NHX:TOL=34615],ectopsocus fumidus[&&NHX:TOL=34616],ectopsocus furcatus[&&NHX:TOL=34617],ectopsocus gentingensis[&&NHX:TOL=34618],ectopsocus gracilis[&&NHX:TOL=34619],ectopsocus gradatus[&&NHX:TOL=34620],ectopsocus gyroancistrus[&&NHX:TOL=34621],ectopsocus halcrowi[&&NHX:TOL=34622],ectopsocus hartleyi[&&NHX:TOL=34623],ectopsocus hawaiensis[&&NHX:TOL=34624],ectopsocus heurni[&&NHX:TOL=34625],ectopsocus himalayanus[&&NHX:TOL=34626],ectopsocus hirsutus[&&NHX:TOL=34627],ectopsocus lhypandrus[&&NHX:TOL=34628],ectopsocus ignotus[&&NHX:TOL=34629],ectopsocus inclinans[&&NHX:TOL=34630],ectopsocus innotatus[&&NHX:TOL=34631],ectopsocus inornatus[&&NHX:TOL=34632],ectopsocus insularis[&&NHX:TOL=34633],ectopsocus intersitus[&&NHX:TOL=34634],ectopsocus isodentus[&&NHX:TOL=34635],ectopsocus kepongensis[&&NHX:TOL=34636],ectopsocus lambus[&&NHX:TOL=34637],ectopsocus leteusistrius[&&NHX:TOL=34638],ectopsocus longisetosus[&&NHX:TOL=34639],ectopsocus longitudinalis[&&NHX:TOL=34640],ectopsocus lubensis[&&NHX:TOL=34641],ectopsocus luridus[&&NHX:TOL=34642],ectopsocus machadoi[&&NHX:TOL=34643],ectopsocus macrotaenious[&&NHX:TOL=34644],ectopsocus maculatus[&&NHX:TOL=34645],ectopsocus maculosus[&&NHX:TOL=34646],ectopsocus maindroni[&&NHX:TOL=34647],ectopsocus marginatus[&&NHX:TOL=34648],ectopsocus meridionalis[&&NHX:TOL=34649],ectopsocus mexicanus[&&NHX:TOL=34650],ectopsocus mirus[&&NHX:TOL=34651],ectopsocus musae[&&NHX:TOL=34652],ectopsocus myrmecophilus[&&NHX:TOL=34653],ectopsocus nerens[&&NHX:TOL=34654],ectopsocus nidicolus[&&NHX:TOL=34655],ectopsocus nyingchiensis[&&NHX:TOL=34656],ectopsocus obscurus[&&NHX:TOL=34657],ectopsocus ornatoides[&&NHX:TOL=34658],ectopsocus ornatus[&&NHX:TOL=34659],ectopsocus pacificus[&&NHX:TOL=34660],ectopsocus paraplesius[&&NHX:TOL=34661],ectopsocus parmatus[&&NHX:TOL=34662],ectopsocus pauliani[&&NHX:TOL=34663],ectopsocus pearmani[&&NHX:TOL=34664],ectopsocus pectinatus[&&NHX:TOL=34665],ectopsocus perkinsi[&&NHX:TOL=34666],ectopsocus perplexus[&&NHX:TOL=34667],ectopsocus petersi[&&NHX:TOL=34668],ectopsocus pictus[&&NHX:TOL=34669],ectopsocus piger[&&NHX:TOL=34670],ectopsocus pilosoides[&&NHX:TOL=34671],ectopsocus pilosus[&&NHX:TOL=34672],ectopsocus predanus[&&NHX:TOL=34673],ectopsocus proctus[&&NHX:TOL=34674],ectopsocus pseudosalpinx[&&NHX:TOL=34675],ectopsocus psychodelicus[&&NHX:TOL=34676],ectopsocus pteridii[&&NHX:TOL=34677],ectopsocus pumilis[&&NHX:TOL=34678],ectopsocus punctatus[&&NHX:TOL=34679],ectopsocus quadratiapicius[&&NHX:TOL=34680],ectopsocus quadrisetus[&&NHX:TOL=34681],ectopsocus ramburi[&&NHX:TOL=34682],ectopsocus ribagai[&&NHX:TOL=34683],ectopsocus richardsi[&&NHX:TOL=34684],ectopsocus ridderi[&&NHX:TOL=34685],ectopsocus rileyae[&&NHX:TOL=34686],ectopsocus russulus[&&NHX:TOL=34687],ectopsocus salpinx[&&NHX:TOL=34688],ectopsocus separatus[&&NHX:TOL=34689],ectopsocus setulosus[&&NHX:TOL=34690],ectopsocus similis[&&NHX:TOL=34691],ectopsocus speciosus[&&NHX:TOL=34692],ectopsocus spiculatus[&&NHX:TOL=34693],ectopsocus spilocephalus[&&NHX:TOL=34694],ectopsocus spilotus[&&NHX:TOL=34695],ectopsocus stictus[&&NHX:TOL=34696],ectopsocus strauchi[&&NHX:TOL=34697],ectopsocus striatellus[&&NHX:TOL=34698],ectopsocus strictifoliatus[&&NHX:TOL=34699],ectopsocus sumatrensis[&&NHX:TOL=34700],ectopsocus tenellus[&&NHX:TOL=34701],ectopsocus thibaudi[&&NHX:TOL=34702],ectopsocus thoi[&&NHX:TOL=34703],ectopsocus thorntoni[&&NHX:TOL=34704],ectopsocus thysanus[&&NHX:TOL=34705],ectopsocus tinctus[&&NHX:TOL=34706],ectopsocus titschacki[&&NHX:TOL=34707],ectopsocus triangulus[&&NHX:TOL=34708],ectopsocus tuxtlarum[&&NHX:TOL=34709],ectopsocus uncinatus[&&NHX:TOL=34710],ectopsocus unipunctatus[&&NHX:TOL=34711],ectopsocus vachoni[&&NHX:TOL=34712],ectopsocus vacuus[&&NHX:TOL=34713],ectopsocus vannus[&&NHX:TOL=34714],ectopsocus variabilis[&&NHX:TOL=34715],ectopsocus venosus[&&NHX:TOL=34716],ectopsocus veracruzensis[&&NHX:TOL=34717],ectopsocus vilhenai[&&NHX:TOL=34718],ectopsocus villosus[&&NHX:TOL=34719],ectopsocus vishnyakovae[&&NHX:TOL=34720],ectopsocus waterstradti[&&NHX:TOL=34721],ectopsocus yongi[&&NHX:TOL=34722],ectopsocus yucatanus[&&NHX:TOL=34723],ectopsocus zayuensis[&&NHX:TOL=34724],ectopsocus zimmermani[&&NHX:TOL=34725])ectopsocus[&&NHX:TOL=34517],(estipulaceus daliensis[&&NHX:TOL=34726],estipulaceus longivalvus[&&NHX:TOL=34727],estipulaceus mecophyllus[&&NHX:TOL=34728],estipulaceus multiserratus[&&NHX:TOL=34729],estipulaceus polyspilus[&&NHX:TOL=34730],estipulaceus subulifolius[&&NHX:TOL=34731],estipulaceus trimaculatus[&&NHX:TOL=34732])estipulaceus[&&NHX:TOL=34518],mascaropsocus spinosus[&&NHX:TOL=34519])ectopsocidae[&&NHX:TOL=14472],(cyclolachesillus ningxiaensis[&&NHX:TOL=34734],(((anomopsocus amabilis[&&NHX:TOL=34753],anomopsocus radiolosus[&&NHX:TOL=34754])anomopsocus[&&NHX:TOL=34735],antilachesilla insulana[&&NHX:TOL=34736],(graphocaecilius enderleini[&&NHX:TOL=34756],graphocaecilius interpretatus[&&NHX:TOL=34757],graphocaecilius lacteus[&&NHX:TOL=34758],graphocaecilius luridus[&&NHX:TOL=34759],graphocaecilius peruvianus[&&NHX:TOL=34760],graphocaecilius pictus[&&NHX:TOL=34761],graphocaecilius trypetoides[&&NHX:TOL=34762],graphocaecilius vartyi[&&NHX:TOL=34763])graphocaecilius[&&NHX:TOL=34737],mesolachesilla aragua[&&NHX:TOL=34738],(nanolachesilla brevihirta[&&NHX:TOL=34765],nanolachesilla chelata[&&NHX:TOL=34766],nanolachesilla haitiana[&&NHX:TOL=34767],nanolachesilla hirundo[&&NHX:TOL=34768],nanolachesilla hirundoides[&&NHX:TOL=34769],nanolachesilla nanciae[&&NHX:TOL=34770],nanolachesilla normalis[&&NHX:TOL=34771])nanolachesilla[&&NHX:TOL=34739],(notolachesilla avispana[&&NHX:TOL=34772],notolachesilla maracana[&&NHX:TOL=34773])notolachesilla[&&NHX:TOL=34740],(prolachesilla callangana[&&NHX:TOL=34774],prolachesilla mediana[&&NHX:TOL=34775],prolachesilla mexicana[&&NHX:TOL=34776],prolachesilla pallida[&&NHX:TOL=34777],prolachesilla panamensis[&&NHX:TOL=34778],prolachesilla pilosa[&&NHX:TOL=34779],prolachesilla poblana[&&NHX:TOL=34780],prolachesilla terricola[&&NHX:TOL=34781],prolachesilla ticana[&&NHX:TOL=34782])prolachesilla[&&NHX:TOL=34741],(tricholachesilla alata[&&NHX:TOL=34783],tricholachesilla vampira[&&NHX:TOL=34784])tricholachesilla[&&NHX:TOL=34742])graphocaeciliini[&&NHX:TOL=50632],eolachesilla chilensis[&&NHX:TOL=34743])eolachesillinae[&&NHX:TOL=50631],(ceratolachesillus quinquecornus[&&NHX:TOL=34744],(dicrolachesillus dichodolichnus[&&NHX:TOL=34787],dicrolachesillus qianshanensis[&&NHX:TOL=34788],dicrolachesillus wutaishanensis[&&NHX:TOL=34789])dicrolachesillus[&&NHX:TOL=34745],(hemicaecilius bogotanus[&&NHX:TOL=34790],hemicaecilius venezolanus[&&NHX:TOL=34791])hemicaecilius[&&NHX:TOL=34746],(homoeolachesilla pinnulata[&&NHX:TOL=34792],homoeolachesilla tibetana[&&NHX:TOL=34793])homoeolachesilla[&&NHX:TOL=34747],(lachesilla abiesicola[&&NHX:TOL=34794],lachesilla aculeata[&&NHX:TOL=34795],lachesilla acuminata[&&NHX:TOL=34796],lachesilla acuminiforceps[&&NHX:TOL=34797],lachesilla acutiloba[&&NHX:TOL=34798],lachesilla aethiopica[&&NHX:TOL=34799],lachesilla ajuscana[&&NHX:TOL=34800],lachesilla albertina[&&NHX:TOL=34801],lachesilla aldretei[&&NHX:TOL=34802],lachesilla alpejia[&&NHX:TOL=34803],lachesilla alpha[&&NHX:TOL=34804],lachesilla amarilla[&&NHX:TOL=34805],lachesilla ambigua[&&NHX:TOL=34806],lachesilla anahuacensis[&&NHX:TOL=34807],lachesilla andra[&&NHX:TOL=34808],lachesilla anna[&&NHX:TOL=34809],lachesilla annulata[&&NHX:TOL=34810],lachesilla anomala[&&NHX:TOL=34811],lachesilla anura[&&NHX:TOL=34812],lachesilla aquilina[&&NHX:TOL=34813],lachesilla arida[&&NHX:TOL=34814],lachesilla arimensis[&&NHX:TOL=34815],lachesilla arnae[&&NHX:TOL=34816],lachesilla aspera[&&NHX:TOL=34817],lachesilla asperiforceps[&&NHX:TOL=34818],lachesilla badonneli[&&NHX:TOL=34819],lachesilla bahiana[&&NHX:TOL=34820],lachesilla belemensis[&&NHX:TOL=34821],lachesilla bernardi[&&NHX:TOL=34822],lachesilla beta[&&NHX:TOL=34823],lachesilla bicornata[&&NHX:TOL=34824],lachesilla bifurcata[&&NHX:TOL=34825],lachesilla bilobata[&&NHX:TOL=34826],lachesilla bilunaris[&&NHX:TOL=34827],lachesilla bimaculata[&&NHX:TOL=34828],lachesilla bonaerensis[&&NHX:TOL=34829],lachesilla bottimeri[&&NHX:TOL=34830],lachesilla braheicola[&&NHX:TOL=34831],lachesilla brasiliensis[&&NHX:TOL=34832],lachesilla braticagua[&&NHX:TOL=34833],lachesilla breviforceps[&&NHX:TOL=34834],lachesilla brinchangensis[&&NHX:TOL=34835],lachesilla broadheadi[&&NHX:TOL=34836],lachesilla buettikeri[&&NHX:TOL=34837],lachesilla bugiriana[&&NHX:TOL=34838],lachesilla caecilioides[&&NHX:TOL=34839],lachesilla cameruna[&&NHX:TOL=34840],lachesilla capreola[&&NHX:TOL=34841],lachesilla caribe[&&NHX:TOL=34842],lachesilla carinata[&&NHX:TOL=34843],lachesilla carinatoides[&&NHX:TOL=34844],lachesilla carioca[&&NHX:TOL=34845],lachesilla castrii[&&NHX:TOL=34846],lachesilla castroi[&&NHX:TOL=34847],lachesilla centralis[&&NHX:TOL=34848],lachesilla chamula[&&NHX:TOL=34849],lachesilla chapmani[&&NHX:TOL=34850],lachesilla chiapensis[&&NHX:TOL=34851],lachesilla chilensis[&&NHX:TOL=34852],lachesilla chiricahua[&&NHX:TOL=34853],lachesilla chrysostigma[&&NHX:TOL=34854],lachesilla cintalapa[&&NHX:TOL=34855],lachesilla cladiumicola[&&NHX:TOL=34856],lachesilla columnaris[&&NHX:TOL=34857],lachesilla concava[&&NHX:TOL=34858],lachesilla contraforcepeta[&&NHX:TOL=34859],lachesilla convexa[&&NHX:TOL=34860],lachesilla corbalanae[&&NHX:TOL=34861],lachesilla cornisterna[&&NHX:TOL=34862],lachesilla cornuta[&&NHX:TOL=34863],lachesilla corona[&&NHX:TOL=34864],lachesilla crutifurca[&&NHX:TOL=34865],lachesilla cuala[&&NHX:TOL=34866],lachesilla cuna[&&NHX:TOL=34867],lachesilla cupressicola[&&NHX:TOL=34868],lachesilla curviforceps[&&NHX:TOL=34869],lachesilla curvipila[&&NHX:TOL=34870],lachesilla dasylirionicola[&&NHX:TOL=34871],lachesilla delta[&&NHX:TOL=34872],lachesilla denticulata[&&NHX:TOL=34873],lachesilla denticuliforceps[&&NHX:TOL=34874],lachesilla dilatiforceps[&&NHX:TOL=34875],lachesilla dimorpha[&&NHX:TOL=34876],lachesilla disjuncta[&&NHX:TOL=34877],lachesilla dispariforceps[&&NHX:TOL=34878],lachesilla dividiforceps[&&NHX:TOL=34879],lachesilla dominicaensis[&&NHX:TOL=34880],lachesilla dona[&&NHX:TOL=34881],lachesilla ecuatoriana[&&NHX:TOL=34882],lachesilla eertmoedi[&&NHX:TOL=34883],lachesilla estradaorum[&&NHX:TOL=34884],lachesilla falcata[&&NHX:TOL=34885],lachesilla falcicula[&&NHX:TOL=34886],lachesilla filicicola[&&NHX:TOL=34887],lachesilla floridana[&&NHX:TOL=34888],lachesilla forcepeta[&&NHX:TOL=34889],lachesilla furcata[&&NHX:TOL=34890],lachesilla fusca[&&NHX:TOL=34891],lachesilla fuscipalpis[&&NHX:TOL=34892],lachesilla gamma[&&NHX:TOL=34893],lachesilla garciai[&&NHX:TOL=34894],lachesilla gigantea[&&NHX:TOL=34895],lachesilla gladiata[&&NHX:TOL=34896],lachesilla gracilis[&&NHX:TOL=34897],lachesilla graminicola[&&NHX:TOL=34898],lachesilla grandis[&&NHX:TOL=34899],lachesilla greeni[&&NHX:TOL=34900],lachesilla gridellii[&&NHX:TOL=34901],lachesilla guatemalensis[&&NHX:TOL=34902],lachesilla guayaquilensis[&&NHX:TOL=34903],lachesilla guentheri[&&NHX:TOL=34904],lachesilla gurneyi[&&NHX:TOL=34905],lachesilla hermosa[&&NHX:TOL=34906],lachesilla hirsuta[&&NHX:TOL=34907],lachesilla huasteca[&&NHX:TOL=34908],lachesilla iguazuensis[&&NHX:TOL=34909],lachesilla intrans[&&NHX:TOL=34910],lachesilla jeanae[&&NHX:TOL=34911],lachesilla juniperana[&&NHX:TOL=34912],lachesilla kahuziana[&&NHX:TOL=34913],lachesilla kathrynae[&&NHX:TOL=34914],lachesilla keniensis[&&NHX:TOL=34915],lachesilla kerzhneri[&&NHX:TOL=34916],lachesilla kikerensis[&&NHX:TOL=34917],lachesilla kola[&&NHX:TOL=34918],lachesilla laciniosiforceps[&&NHX:TOL=34919],lachesilla latinerva[&&NHX:TOL=34920],lachesilla leonilae[&&NHX:TOL=34921],lachesilla lienhardi[&&NHX:TOL=34922],lachesilla lingua[&&NHX:TOL=34923],lachesilla loisae[&&NHX:TOL=34924],lachesilla maculata[&&NHX:TOL=34925],lachesilla maculipenna[&&NHX:TOL=34926],lachesilla madecassa[&&NHX:TOL=34927],lachesilla magna[&&NHX:TOL=34928],lachesilla magnifica[&&NHX:TOL=34929],lachesilla major[&&NHX:TOL=34930],lachesilla maracayensis[&&NHX:TOL=34931],lachesilla marginata[&&NHX:TOL=34932],lachesilla mariateresae[&&NHX:TOL=34933],lachesilla mathieui[&&NHX:TOL=34934],lachesilla mattogrossensis[&&NHX:TOL=34935],lachesilla maya[&&NHX:TOL=34936],lachesilla mayorgae[&&NHX:TOL=34937],lachesilla megaforcepeta[&&NHX:TOL=34938],lachesilla meinanderi[&&NHX:TOL=34939],lachesilla merzi[&&NHX:TOL=34940],lachesilla mexica[&&NHX:TOL=34941],lachesilla michiliensis[&&NHX:TOL=34942],lachesilla microplatyclatae[&&NHX:TOL=34943],lachesilla micrura[&&NHX:TOL=34944],lachesilla mockfordi[&&NHX:TOL=34945],lachesilla mombachensis[&&NHX:TOL=34946],lachesilla mongolica[&&NHX:TOL=34947],lachesilla monocera[&&NHX:TOL=34948],lachesilla monticola[&&NHX:TOL=34949],lachesilla mucronata[&&NHX:TOL=34950],lachesilla muncunilli[&&NHX:TOL=34951],lachesilla mutabilis[&&NHX:TOL=34952],lachesilla nadleri[&&NHX:TOL=34953],lachesilla neoleonensis[&&NHX:TOL=34954],lachesilla nevermanni[&&NHX:TOL=34955],lachesilla newi[&&NHX:TOL=34956],lachesilla nigripalpa[&&NHX:TOL=34957],lachesilla nita[&&NHX:TOL=34958],lachesilla novemimaculata[&&NHX:TOL=34959],lachesilla nubilis[&&NHX:TOL=34960],lachesilla nubiloides[&&NHX:TOL=34961],lachesilla nuptialis[&&NHX:TOL=34962],lachesilla oaxacana[&&NHX:TOL=34963],lachesilla obrieni[&&NHX:TOL=34964],lachesilla otomi[&&NHX:TOL=34965],lachesilla pachyura[&&NHX:TOL=34966],lachesilla pacifica[&&NHX:TOL=34967],lachesilla pallida[&&NHX:TOL=34968],lachesilla palmera[&&NHX:TOL=34969],lachesilla palmicola[&&NHX:TOL=34970],lachesilla papillata[&&NHX:TOL=34971],lachesilla patula[&&NHX:TOL=34972],lachesilla patzunensis[&&NHX:TOL=34973],lachesilla paulista[&&NHX:TOL=34974],lachesilla pedicularia[&&NHX:TOL=34975],lachesilla penta[&&NHX:TOL=34976],lachesilla pereirorum[&&NHX:TOL=34977],lachesilla perezi[&&NHX:TOL=34978],lachesilla picticeps[&&NHX:TOL=34979],lachesilla picticepsoides[&&NHX:TOL=34980],lachesilla pigmentithorax[&&NHX:TOL=34981],lachesilla pinicola[&&NHX:TOL=34982],lachesilla platycladae[&&NHX:TOL=34983],lachesilla punctata[&&NHX:TOL=34984],lachesilla quercicola[&&NHX:TOL=34985],lachesilla quercus[&&NHX:TOL=34986],lachesilla querpina[&&NHX:TOL=34987],lachesilla rectiforceps[&&NHX:TOL=34988],lachesilla rectigladia[&&NHX:TOL=34989],lachesilla regiomontana[&&NHX:TOL=34990],lachesilla rena[&&NHX:TOL=34991],lachesilla renicula[&&NHX:TOL=34992],lachesilla reyesi[&&NHX:TOL=34993],lachesilla rhizophila[&&NHX:TOL=34994],lachesilla riegeli[&&NHX:TOL=34995],lachesilla rossica[&&NHX:TOL=34996],lachesilla rufa[&&NHX:TOL=34997],lachesilla rugosa[&&NHX:TOL=34998],lachesilla ruizabreorum[&&NHX:TOL=34999],lachesilla sabinae[&&NHX:TOL=35000],lachesilla salamana[&&NHX:TOL=35001],lachesilla sandersoni[&&NHX:TOL=35002],lachesilla sauteri[&&NHX:TOL=35003],lachesilla sclera[&&NHX:TOL=35004],lachesilla septenaria[&&NHX:TOL=35005],lachesilla silvatica[&&NHX:TOL=35006],lachesilla smithersi[&&NHX:TOL=35007],lachesilla soaresi[&&NHX:TOL=35008],lachesilla sola[&&NHX:TOL=35009],lachesilla sommermanae[&&NHX:TOL=35010],lachesilla sonamarga[&&NHX:TOL=35011],lachesilla sulcata[&&NHX:TOL=35012],lachesilla tanaidana[&&NHX:TOL=35013],lachesilla tapanatepeca[&&NHX:TOL=35014],lachesilla tapiabarqueroi[&&NHX:TOL=35015],lachesilla taxodicola[&&NHX:TOL=35016],lachesilla tectorum[&&NHX:TOL=35017],lachesilla tehuautlensis[&&NHX:TOL=35018],lachesilla tekwaensis[&&NHX:TOL=35019],lachesilla teresiana[&&NHX:TOL=35020],lachesilla texcocana[&&NHX:TOL=35021],lachesilla thorntoni[&&NHX:TOL=35022],lachesilla torulosa[&&NHX:TOL=35023],lachesilla trinidadensis[&&NHX:TOL=35024],lachesilla tropica[&&NHX:TOL=35025],lachesilla trujillensis[&&NHX:TOL=35026],lachesilla trunca[&&NHX:TOL=35027],lachesilla tuita[&&NHX:TOL=35028],lachesilla turneri[&&NHX:TOL=35029],lachesilla typhicola[&&NHX:TOL=35030],lachesilla ultima[&&NHX:TOL=35031],lachesilla valvula[&&NHX:TOL=35032],lachesilla veneper[&&NHX:TOL=35033],lachesilla wongae[&&NHX:TOL=35034],lachesilla xalapensis[&&NHX:TOL=35035],lachesilla ximaensis[&&NHX:TOL=35036],lachesilla yakima[&&NHX:TOL=35037],lachesilla yanomami[&&NHX:TOL=35038],lachesilla yanomamioides[&&NHX:TOL=35039],lachesilla yucateca[&&NHX:TOL=35040],lachesilla yuccalnicola[&&NHX:TOL=35041],lachesilla zapoteca[&&NHX:TOL=35042],lachesilla zeta[&&NHX:TOL=35043])lachesilla[&&NHX:TOL=34748],(nadleria alpha[&&NHX:TOL=35044],nadleria gamma[&&NHX:TOL=35045],nadleria mariateresae[&&NHX:TOL=35046],nadleria mockfordi[&&NHX:TOL=35047])nadleria[&&NHX:TOL=34749],zangilachesilla apterostigma[&&NHX:TOL=34750],(zonolachesillus ambipullus[&&NHX:TOL=35049],zonolachesillus aterilineus[&&NHX:TOL=35050],zonolachesillus bicornis[&&NHX:TOL=35051],zonolachesillus crassibasius[&&NHX:TOL=35052],zonolachesillus exilicellus[&&NHX:TOL=35053],zonolachesillus lomatomelus[&&NHX:TOL=35054],zonolachesillus oxyurus[&&NHX:TOL=35055],zonolachesillus parvus[&&NHX:TOL=35056],zonolachesillus preductifascus[&&NHX:TOL=35057],zonolachesillus retimaculus[&&NHX:TOL=35058],zonolachesillus spadiceilabius[&&NHX:TOL=35059],zonolachesillus wenxianensis[&&NHX:TOL=35060])zonolachesillus[&&NHX:TOL=34751])lachesillinae[&&NHX:TOL=50633])lachesillidae[&&NHX:TOL=14471],(acmomesopsocus tibeticus[&&NHX:TOL=33329],(aphanomesopsocus bipunctatus[&&NHX:TOL=33330],aphanomesopsocus furvus[&&NHX:TOL=33331],aphanomesopsocus fuscus[&&NHX:TOL=33332])aphanomesopsocus[&&NHX:TOL=37433],(conomesopsocus melanostigmus[&&NHX:TOL=33333],conomesopsocus meniscatus[&&NHX:TOL=33334])conomesopsocus[&&NHX:TOL=37434],(cyrtopsochus canariensis[&&NHX:TOL=33335],cyrtopsochus gibbosus[&&NHX:TOL=33336],cyrtopsochus irroratus[&&NHX:TOL=33337],cyrtopsochus nasutus[&&NHX:TOL=33338],cyrtopsochus pustulatus[&&NHX:TOL=33339],cyrtopsochus truncatus[&&NHX:TOL=33340])cyrtopsochus[&&NHX:TOL=37435],hexacyrtoma capense[&&NHX:TOL=33341],idatenopsocus orientalis[&&NHX:TOL=33342],mesopsocidus alienatus[&&NHX:TOL=33343],(mesopsocopsis occidentalis[&&NHX:TOL=33344],mesopsocopsis reticulata[&&NHX:TOL=33345],mesopsocopsis setosa[&&NHX:TOL=33346])mesopsocopsis[&&NHX:TOL=37436],(mesopsocus acutilobus[&&NHX:TOL=33347],mesopsocus alatus[&&NHX:TOL=33348],mesopsocus angolanus[&&NHX:TOL=33349],mesopsocus apterus[&&NHX:TOL=33350],mesopsocus atlasicus[&&NHX:TOL=33351],mesopsocus badhysi[&&NHX:TOL=33352],mesopsocus balachowskyi[&&NHX:TOL=33353],mesopsocus blancae[&&NHX:TOL=33354],mesopsocus brachyonematus[&&NHX:TOL=33355],mesopsocus broadheadi[&&NHX:TOL=33356],mesopsocus carthaginensis[&&NHX:TOL=33357],mesopsocus clarki[&&NHX:TOL=33358],mesopsocus corniculatus[&&NHX:TOL=33359],mesopsocus curvimarginatus[&&NHX:TOL=33360],mesopsocus dichotomus[&&NHX:TOL=33361],mesopsocus difficilis[&&NHX:TOL=33362],mesopsocus diopsis[&&NHX:TOL=33363],mesopsocus dislobus[&&NHX:TOL=33364],mesopsocus duboscqui[&&NHX:TOL=33365],mesopsocus enderleini[&&NHX:TOL=33366],mesopsocus fenestristigma[&&NHX:TOL=33367],mesopsocus fuscifrons[&&NHX:TOL=33368],mesopsocus gabonensis[&&NHX:TOL=33369],mesopsocus giganteus[&&NHX:TOL=33370],mesopsocus graecus[&&NHX:TOL=33371],mesopsocus helveticus[&&NHX:TOL=33372],mesopsocus hiemalis[&&NHX:TOL=33373],mesopsocus hongkongensis[&&NHX:TOL=33374],mesopsocus immunis[&&NHX:TOL=33375],mesopsocus incomitatus[&&NHX:TOL=33376],mesopsocus jiensis[&&NHX:TOL=33377],mesopsocus jinicus[&&NHX:TOL=33378],mesopsocus kopetdaghensis[&&NHX:TOL=33379],mesopsocus laricolus[&&NHX:TOL=33380],mesopsocus laterimaculatus[&&NHX:TOL=33381],mesopsocus laticeps[&&NHX:TOL=33382],mesopsocus latreillei[&&NHX:TOL=33383],mesopsocus lienhardi[&&NHX:TOL=33384],mesopsocus marikovskyi[&&NHX:TOL=33385],mesopsocus meinanderi[&&NHX:TOL=33386],mesopsocus mockfordi[&&NHX:TOL=33387],mesopsocus montinus[&&NHX:TOL=33388],mesopsocus neimongolicus[&&NHX:TOL=33389],mesopsocus nigrimaculatus[&&NHX:TOL=33390],mesopsocus nigrostigma[&&NHX:TOL=33391],mesopsocus nitidifrons[&&NHX:TOL=33392],mesopsocus phaeodematus[&&NHX:TOL=33393],mesopsocus propinquus[&&NHX:TOL=33394],mesopsocus salignus[&&NHX:TOL=33395],mesopsocus similis[&&NHX:TOL=33396],mesopsocus smithersi[&&NHX:TOL=33397],mesopsocus stenopterus[&&NHX:TOL=33398],mesopsocus strongylotus[&&NHX:TOL=33399],mesopsocus tetensi[&&NHX:TOL=33400],mesopsocus thorntoni[&&NHX:TOL=33401],mesopsocus troodos[&&NHX:TOL=33402],mesopsocus tumorosus[&&NHX:TOL=33403],mesopsocus unipunctatus[&&NHX:TOL=33404],mesopsocus vernus[&&NHX:TOL=33405],mesopsocus wardi[&&NHX:TOL=33406],mesopsocus yemenitus[&&NHX:TOL=33407],mesopsocus yeni[&&NHX:TOL=33408],mesopsocus ypsilon[&&NHX:TOL=33409])mesopsocus[&&NHX:TOL=37437],(metapsocus brevilobus[&&NHX:TOL=33410],metapsocus kolbei[&&NHX:TOL=33411],metapsocus wittmeri[&&NHX:TOL=33412])metapsocus[&&NHX:TOL=37438],microtrichipsocus shiffi[&&NHX:TOL=33413],newipsocus termitiformis[&&NHX:TOL=33414],oegomesoposcus guangxiensis[&&NHX:TOL=33415],psoculidus ricei[&&NHX:TOL=33416],psoculus neglectus[&&NHX:TOL=33417],(rhinopsocus arduus[&&NHX:TOL=33418],rhinopsocus badonneli[&&NHX:TOL=33419],rhinopsocus cincinnatus[&&NHX:TOL=33420],rhinopsocus distinctus[&&NHX:TOL=33421],rhinopsocus gibber[&&NHX:TOL=33422])rhinopsocus[&&NHX:TOL=37439])mesopsocidae[&&NHX:TOL=14480])[&&NHX:TOL=136812])homilopsocidea[&&NHX:TOL=14479],(((asiopsocus meridionalis[&&NHX:TOL=30811],asiopsocus mongolicus[&&NHX:TOL=30812],asiopsocus sonorensis[&&NHX:TOL=30813],asiopsocus tehuacanus[&&NHX:TOL=30814],asiopsocus vanharteni[&&NHX:TOL=30815],asiopsocus wulingshanensis[&&NHX:TOL=30816])asiopsocus[&&NHX:TOL=38108],(notiopsocus aldretei[&&NHX:TOL=30817],notiopsocus angulatus[&&NHX:TOL=30818],notiopsocus facilis[&&NHX:TOL=30819],notiopsocus machadoi[&&NHX:TOL=30820],notiopsocus neotropicus[&&NHX:TOL=30821],notiopsocus rufus[&&NHX:TOL=30822],notiopsocus simplex[&&NHX:TOL=30823],notiopsocus vilhenai[&&NHX:TOL=30824])notiopsocus[&&NHX:TOL=38109],pronotiopsocus amazonicus[&&NHX:TOL=30825])asiopsocidae[&&NHX:TOL=30390],((anoculaticaeca chuanshaanica[&&NHX:TOL=30826],hageniola solitaria[&&NHX:TOL=30827],(amphicaecilius daqingshanicus[&&NHX:TOL=30865],amphicaecilius floribundus[&&NHX:TOL=30866],amphicaecilius pulchellus[&&NHX:TOL=30867],amphicaecilius pulcherrimus[&&NHX:TOL=30868])amphicaecilius[&&NHX:TOL=30828],(((epicaecilius pilipennis[&&NHX:TOL=31515],epicaecilius smithersorum[&&NHX:TOL=31516],epicaecilius variegatus[&&NHX:TOL=31517])epicaecilius[&&NHX:TOL=30852],orocaecilius chiapensis[&&NHX:TOL=30853])epicaeciliini[&&NHX:TOL=50621],((coryphosmila bushi[&&NHX:TOL=31168],coryphosmila dolabrata[&&NHX:TOL=31169],coryphosmila jacobsoni[&&NHX:TOL=31170],coryphosmila morosa[&&NHX:TOL=31171],coryphosmila rubicunda[&&NHX:TOL=31172],coryphosmila soehardjani[&&NHX:TOL=31173])coryphosmila[&&NHX:TOL=30848],(coryphaca fasciata[&&NHX:TOL=31165],coryphaca inka[&&NHX:TOL=31166],coryphaca matona[&&NHX:TOL=31167])coryphaca[&&NHX:TOL=30847],protodypsocus fissiceps[&&NHX:TOL=30849],(stenocaecilius analis[&&NHX:TOL=31175],stenocaecilius andromimus[&&NHX:TOL=31176],stenocaecilius angustipennis[&&NHX:TOL=31177],stenocaecilius antennalis[&&NHX:TOL=31178],stenocaecilius antillanus[&&NHX:TOL=31179],stenocaecilius arotellus[&&NHX:TOL=31180],stenocaecilius australis[&&NHX:TOL=31181],stenocaecilius bamboutensis[&&NHX:TOL=31182],stenocaecilius benoiti[&&NHX:TOL=31183],stenocaecilius caboverdensis[&&NHX:TOL=31184],stenocaecilius casarum[&&NHX:TOL=31185],stenocaecilius congolensis[&&NHX:TOL=31186],stenocaecilius crassicornis[&&NHX:TOL=31187],stenocaecilius decolor[&&NHX:TOL=31188],stenocaecilius dundoensis[&&NHX:TOL=31189],stenocaecilius elongatus[&&NHX:TOL=31190],stenocaecilius fallax[&&NHX:TOL=31191],stenocaecilius fuscicornis[&&NHX:TOL=31192],stenocaecilius gilvus[&&NHX:TOL=31193],stenocaecilius glossopterus[&&NHX:TOL=31194],stenocaecilius griveaudi[&&NHX:TOL=31195],stenocaecilius guineensis[&&NHX:TOL=31196],stenocaecilius insularum[&&NHX:TOL=31197],stenocaecilius insulatus[&&NHX:TOL=31198],stenocaecilius kivuensis[&&NHX:TOL=31199],stenocaecilius lineatus[&&NHX:TOL=31200],stenocaecilius linguipennis[&&NHX:TOL=31201],stenocaecilius lucidus[&&NHX:TOL=31202],stenocaecilius lundensis[&&NHX:TOL=31203],stenocaecilius machadoi[&&NHX:TOL=31204],stenocaecilius marianus[&&NHX:TOL=31205],stenocaecilius moffiensis[&&NHX:TOL=31206],stenocaecilius oxycopeus[&&NHX:TOL=31207],stenocaecilius pacificus[&&NHX:TOL=31208],stenocaecilius petchkovskya[&&NHX:TOL=31209],stenocaecilius photophilus[&&NHX:TOL=31210],stenocaecilius pictifrons[&&NHX:TOL=31211],stenocaecilius propinquifallax[&&NHX:TOL=31212],stenocaecilius quercus[&&NHX:TOL=31213],stenocaecilius rutshuruanus[&&NHX:TOL=31214],stenocaecilius suturalis[&&NHX:TOL=31215],stenocaecilius transversalis[&&NHX:TOL=31216],stenocaecilius turneri[&&NHX:TOL=31217],stenocaecilius vilhenai[&&NHX:TOL=31218],stenocaecilius voov[&&NHX:TOL=31219])stenocaecilius[&&NHX:TOL=30850],(valenzuela abiectus[&&NHX:TOL=31220],valenzuela adrianae[&&NHX:TOL=31221],valenzuela albiceps[&&NHX:TOL=31222],valenzuela albimaculatus[&&NHX:TOL=31223],valenzuela albipes[&&NHX:TOL=31224],valenzuela albofasciatus[&&NHX:TOL=31225],valenzuela albomarginatus[&&NHX:TOL=31226],valenzuela albus[&&NHX:TOL=31227],valenzuela alcinus[&&NHX:TOL=31228],valenzuela alticola[&&NHX:TOL=31229],valenzuela ambiguus[&&NHX:TOL=31230],valenzuela amicus[&&NHX:TOL=31231],valenzuela andeanus[&&NHX:TOL=31232],valenzuela andinus[&&NHX:TOL=31233],valenzuela angustiplumalus[&&NHX:TOL=31234],valenzuela ankaratrensis[&&NHX:TOL=31235],valenzuela annulicornis[&&NHX:TOL=31236],valenzuela anomalus[&&NHX:TOL=31237],valenzuela apicatus[&&NHX:TOL=31238],valenzuela aridus[&&NHX:TOL=31239],valenzuela astovensis[&&NHX:TOL=31240],valenzuela atricornis[&&NHX:TOL=31241],valenzuela badiostigma[&&NHX:TOL=31242],valenzuela baishanzuicus[&&NHX:TOL=31243],valenzuela baliensis[&&NHX:TOL=31244],valenzuela bambusae[&&NHX:TOL=31245],valenzuela bataviensis[&&NHX:TOL=31246],valenzuela bengalensis[&&NHX:TOL=31247],valenzuela bermudensis[&&NHX:TOL=31248],valenzuela bicolorinervus[&&NHX:TOL=31249],valenzuela bicoloripes[&&NHX:TOL=31250],valenzuela bicolorus[&&NHX:TOL=31251],valenzuela bifoliolatus[&&NHX:TOL=31252],valenzuela biminiensis[&&NHX:TOL=31253],valenzuela boggianii[&&NHX:TOL=31254],valenzuela bombensis[&&NHX:TOL=31255],valenzuela boreus[&&NHX:TOL=31256],valenzuela borneensis[&&NHX:TOL=31257],valenzuela brunneimaculatus[&&NHX:TOL=31258],valenzuela brunneoflavus[&&NHX:TOL=31259],valenzuela brunneonitens[&&NHX:TOL=31260],valenzuela burmeisteri[&&NHX:TOL=31261],valenzuela cabrerai[&&NHX:TOL=31262],valenzuela caligoniodes[&&NHX:TOL=31263],valenzuela caligonus[&&NHX:TOL=31264],valenzuela caloclypeus[&&NHX:TOL=31265],valenzuela canei[&&NHX:TOL=31266],valenzuela caribensis[&&NHX:TOL=31267],valenzuela carneangularis[&&NHX:TOL=31268],valenzuela carriloi[&&NHX:TOL=31269],valenzuela castellus[&&NHX:TOL=31270],valenzuela chilozonus[&&NHX:TOL=31271],valenzuela chrysopterus[&&NHX:TOL=31272],valenzuela cinalus[&&NHX:TOL=31273],valenzuela cincticornis[&&NHX:TOL=31274],valenzuela citrinus[&&NHX:TOL=31275],valenzuela claripennis[&&NHX:TOL=31276],valenzuela claristigma[&&NHX:TOL=31277],valenzuela clarivenus[&&NHX:TOL=31278],valenzuela clayae[&&NHX:TOL=31279],valenzuela coei[&&NHX:TOL=31280],valenzuela collarti[&&NHX:TOL=31281],valenzuela columbianus[&&NHX:TOL=31282],valenzuela complexus[&&NHX:TOL=31283],valenzuela confluens[&&NHX:TOL=31284],valenzuela conspicuus[&&NHX:TOL=31285],valenzuela cornutus[&&NHX:TOL=31286],valenzuela corsicus[&&NHX:TOL=31287],valenzuela croesus[&&NHX:TOL=31288],valenzuela cuboideus[&&NHX:TOL=31289],valenzuela cuspidatus[&&NHX:TOL=31290],valenzuela cyrtospilus[&&NHX:TOL=31291],valenzuela dayongicus[&&NHX:TOL=31292],valenzuela deceptor[&&NHX:TOL=31293],valenzuela delamarei[&&NHX:TOL=31294],valenzuela delicatulus[&&NHX:TOL=31295],valenzuela descolei[&&NHX:TOL=31296],valenzuela despaxi[&&NHX:TOL=31297],valenzuela dicornis[&&NHX:TOL=31298],valenzuela dificilis[&&NHX:TOL=31299],valenzuela dinghuensis[&&NHX:TOL=31300],valenzuela diploideus[&&NHX:TOL=31301],valenzuela distinctus[&&NHX:TOL=31302],valenzuela dives[&&NHX:TOL=31303],valenzuela dolichostigmus[&&NHX:TOL=31304],valenzuela dubius[&&NHX:TOL=31305],valenzuela eastopi[&&NHX:TOL=31306],valenzuela elegans[&&NHX:TOL=31307],valenzuela elegantoides[&&NHX:TOL=31308],valenzuela equivocatus[&&NHX:TOL=31309],valenzuela erythrostigma[&&NHX:TOL=31310],valenzuela erythrozonalis[&&NHX:TOL=31311],valenzuela estriatus[&&NHX:TOL=31312],valenzuela excavatus[&&NHX:TOL=31313],valenzuela farrelli[&&NHX:TOL=31314],valenzuela fasciatus[&&NHX:TOL=31315],valenzuela fasciipennis[&&NHX:TOL=31316],valenzuela flavibrunneus[&&NHX:TOL=31317],valenzuela flavidorsalis[&&NHX:TOL=31318],valenzuela flavidus[&&NHX:TOL=31319],valenzuela flavipennis[&&NHX:TOL=31320],valenzuela flavistigma[&&NHX:TOL=31321],valenzuela flavus[&&NHX:TOL=31322],valenzuela florinaevus[&&NHX:TOL=31323],valenzuela foramilulosus[&&NHX:TOL=31324],valenzuela fortis[&&NHX:TOL=31325],valenzuela fortunatus[&&NHX:TOL=31326],valenzuela fraternus[&&NHX:TOL=31327],valenzuela fuligineneurus[&&NHX:TOL=31328],valenzuela furculatus[&&NHX:TOL=31329],valenzuela fuscipennis[&&NHX:TOL=31330],valenzuela fuscolineus[&&NHX:TOL=31331],valenzuela fusicangularis[&&NHX:TOL=31332],valenzuela gemmatus[&&NHX:TOL=31333],valenzuela ghesquierei[&&NHX:TOL=31334],valenzuela gonostigma[&&NHX:TOL=31335],valenzuela gracilentus[&&NHX:TOL=31336],valenzuela gracilis[&&NHX:TOL=31337],valenzuela graminis[&&NHX:TOL=31338],valenzuela grandivalvus[&&NHX:TOL=31339],valenzuela granulosus[&&NHX:TOL=31340],valenzuela gutianshanicus[&&NHX:TOL=31341],valenzuela gynapterus[&&NHX:TOL=31342],valenzuela hainanensis[&&NHX:TOL=31343],valenzuela hemipsocoides[&&NHX:TOL=31344],valenzuela heptimacularus[&&NHX:TOL=31345],valenzuela himalayanus[&&NHX:TOL=31346],valenzuela hivesi[&&NHX:TOL=31347],valenzuela huangi[&&NHX:TOL=31348],valenzuela hubeiensis[&&NHX:TOL=31349],valenzuela hyperboreus[&&NHX:TOL=31350],valenzuela ilamensis[&&NHX:TOL=31351],valenzuela imbecillus[&&NHX:TOL=31352],valenzuela imitator[&&NHX:TOL=31353],valenzuela incoloratus[&&NHX:TOL=31354],valenzuela incurviusculus[&&NHX:TOL=31355],valenzuela indicator[&&NHX:TOL=31356],valenzuela indicus[&&NHX:TOL=31357],valenzuela inornatus[&&NHX:TOL=31358],valenzuela inquinatus[&&NHX:TOL=31359],valenzuela insidiosus[&&NHX:TOL=31360],valenzuela isochasialis[&&NHX:TOL=31361],valenzuela itremoensis[&&NHX:TOL=31362],valenzuela jamaicensis[&&NHX:TOL=31363],valenzuela javanus[&&NHX:TOL=31364],valenzuela juniperorum[&&NHX:TOL=31365],valenzuela kamakurensis[&&NHX:TOL=31366],valenzuela kamatembanus[&&NHX:TOL=31367],valenzuela kansuensis[&&NHX:TOL=31368],valenzuela kraussi[&&NHX:TOL=31369],valenzuela kunashirensis[&&NHX:TOL=31370],valenzuela labratus[&&NHX:TOL=31371],valenzuela labrostylus[&&NHX:TOL=31372],valenzuela lemniscellus[&&NHX:TOL=31373],valenzuela leuroceps[&&NHX:TOL=31374],valenzuela lochloosae[&&NHX:TOL=31375],valenzuela longistylus[&&NHX:TOL=31376],valenzuela longulus[&&NHX:TOL=31377],valenzuela luachimensis[&&NHX:TOL=31378],valenzuela luridus[&&NHX:TOL=31379],valenzuela luteovenosus[&&NHX:TOL=31380],valenzuela machadoi[&&NHX:TOL=31381],valenzuela macromelaus[&&NHX:TOL=31382],valenzuela maculistigma[&&NHX:TOL=31383],valenzuela magnioculus[&&NHX:TOL=31384],valenzuela manteri[&&NHX:TOL=31385],valenzuela marginalis[&&NHX:TOL=31386],valenzuela marginatus[&&NHX:TOL=31387],valenzuela marginilacutus[&&NHX:TOL=31388],valenzuela maritimus[&&NHX:TOL=31389],valenzuela mclareni[&&NHX:TOL=31390],valenzuela medialunatus[&&NHX:TOL=31391],valenzuela medimacularis[&&NHX:TOL=31392],valenzuela megalocystis[&&NHX:TOL=31393],valenzuela megalodichotomus[&&NHX:TOL=31394],valenzuela melanocnemis[&&NHX:TOL=31395],valenzuela metasequoiae[&&NHX:TOL=31396],valenzuela mexcalensis[&&NHX:TOL=31397],valenzuela mexicanus[&&NHX:TOL=31398],valenzuela micanopi[&&NHX:TOL=31399],valenzuela micans[&&NHX:TOL=31400],valenzuela microcystus[&&NHX:TOL=31401],valenzuela milloti[&&NHX:TOL=31402],valenzuela minutoculus[&&NHX:TOL=31403],valenzuela miocensis[&&NHX:TOL=31404],valenzuela mjoebergi[&&NHX:TOL=31405],valenzuela mockfordi[&&NHX:TOL=31406],valenzuela mueggenburgi[&&NHX:TOL=31407],valenzuela multimaculatus[&&NHX:TOL=31408],valenzuela myrmicaformis[&&NHX:TOL=31409],valenzuela nadleri[&&NHX:TOL=31410],valenzuela nebuloides[&&NHX:TOL=31411],valenzuela nebulomaculatus[&&NHX:TOL=31412],valenzuela nebulosoides[&&NHX:TOL=31413],valenzuela nebulosus[&&NHX:TOL=31414],valenzuela nigricornis[&&NHX:TOL=31415],valenzuela nigritibia[&&NHX:TOL=31416],valenzuela nigroticta[&&NHX:TOL=31417],valenzuela obliquus[&&NHX:TOL=31418],valenzuela obscuripennis[&&NHX:TOL=31419],valenzuela obscurus[&&NHX:TOL=31420],valenzuela ochroleucus[&&NHX:TOL=31421],valenzuela oculatus[&&NHX:TOL=31422],valenzuela okamotoi[&&NHX:TOL=31423],valenzuela olitorius[&&NHX:TOL=31424],valenzuela oyamai[&&NHX:TOL=31425],valenzuela pakistanensis[&&NHX:TOL=31426],valenzuela pallidobrunneus[&&NHX:TOL=31427],valenzuela paradistinctus[&&NHX:TOL=31428],valenzuela paraguayensis[&&NHX:TOL=31429],valenzuela paramonus[&&NHX:TOL=31430],valenzuela parbatensis[&&NHX:TOL=31431],valenzuela patellaris[&&NHX:TOL=31432],valenzuela pauliani[&&NHX:TOL=31433],valenzuela pectinatus[&&NHX:TOL=31434],valenzuela pelmus[&&NHX:TOL=31435],valenzuela perplexus[&&NHX:TOL=31436],valenzuela peyrierasi[&&NHX:TOL=31437],valenzuela phaeocephalus[&&NHX:TOL=31438],valenzuela phaeopterellus[&&NHX:TOL=31439],valenzuela phaeopterus[&&NHX:TOL=31440],valenzuela phaeozanalis[&&NHX:TOL=31441],valenzuela piceus[&&NHX:TOL=31442],valenzuela pinicola[&&NHX:TOL=31443],valenzuela plagioerythrinus[&&NHX:TOL=31444],valenzuela platytaenius[&&NHX:TOL=31445],valenzuela podacromelas[&&NHX:TOL=31446],valenzuela podacrophaeus[&&NHX:TOL=31447],valenzuela posticoides[&&NHX:TOL=31448],valenzuela posticus[&&NHX:TOL=31449],valenzuela protritus[&&NHX:TOL=31450],valenzuela pseudanalis[&&NHX:TOL=31451],valenzuela pteridii[&&NHX:TOL=31452],valenzuela pubes[&&NHX:TOL=31453],valenzuela pugioniformis[&&NHX:TOL=31454],valenzuela pulchellus[&&NHX:TOL=31455],valenzuela purpureus[&&NHX:TOL=31456],valenzuela pycnacanthus[&&NHX:TOL=31457],valenzuela quadrimaculatus[&&NHX:TOL=31458],valenzuela quaternatus[&&NHX:TOL=31459],valenzuela quinarius[&&NHX:TOL=31460],valenzuela rhenanus[&&NHX:TOL=31461],valenzuela rodriguezi[&&NHX:TOL=31462],valenzuela roseus[&&NHX:TOL=31463],valenzuela rosor[&&NHX:TOL=31464],valenzuela rubinii[&&NHX:TOL=31465],valenzuela rubiventer[&&NHX:TOL=31466],valenzuela sanchezlabradori[&&NHX:TOL=31467],valenzuela scriptus[&&NHX:TOL=31468],valenzuela serpentinus[&&NHX:TOL=31469],valenzuela shixingensis[&&NHX:TOL=31470],valenzuela signatipennis[&&NHX:TOL=31471],valenzuela similipennis[&&NHX:TOL=31472],valenzuela similis[&&NHX:TOL=31473],valenzuela simplex[&&NHX:TOL=31474],valenzuela singularis[&&NHX:TOL=31475],valenzuela sinuofasciatus[&&NHX:TOL=31476],valenzuela soleili[&&NHX:TOL=31477],valenzuela spiloerythrinus[&&NHX:TOL=31478],valenzuela spissicornis[&&NHX:TOL=31479],valenzuela stenopterus[&&NHX:TOL=31480],valenzuela stigmatus[&&NHX:TOL=31481],valenzuela striolatus[&&NHX:TOL=31482],valenzuela stuckenbergi[&&NHX:TOL=31483],valenzuela subelegans[&&NHX:TOL=31484],valenzuela subflavus[&&NHX:TOL=31485],valenzuela sublineatus[&&NHX:TOL=31486],valenzuela subnebulosus[&&NHX:TOL=31487],valenzuela subundulatus[&&NHX:TOL=31488],valenzuela suffusus[&&NHX:TOL=31489],valenzuela sulciformis[&&NHX:TOL=31490],valenzuela tamiami[&&NHX:TOL=31491],valenzuela thiemei[&&NHX:TOL=31492],valenzuela totonacus[&&NHX:TOL=31493],valenzuela traceus[&&NHX:TOL=31494],valenzuela trifolius[&&NHX:TOL=31495],valenzuela trigonostigma[&&NHX:TOL=31496],valenzuela trigonus[&&NHX:TOL=31497],valenzuela trimaculatus[&&NHX:TOL=31498],valenzuela trukensis[&&NHX:TOL=31499],valenzuela tuberculatus[&&NHX:TOL=31500],valenzuela umbratus[&&NHX:TOL=31501],valenzuela umbripennis[&&NHX:TOL=31502],valenzuela vau[&&NHX:TOL=31503],valenzuela velectus[&&NHX:TOL=31504],valenzuela veracruzensis[&&NHX:TOL=31505],valenzuela villiersi[&&NHX:TOL=31506],valenzuela virgatus[&&NHX:TOL=31507],valenzuela vitellinus[&&NHX:TOL=31508],valenzuela vittidorsum[&&NHX:TOL=31509],valenzuela wolffhuegelianus[&&NHX:TOL=31510],valenzuela wui[&&NHX:TOL=31511],valenzuela wuxiaensis[&&NHX:TOL=31512],valenzuela wuyishanicus[&&NHX:TOL=31513],valenzuela zhejiangicus[&&NHX:TOL=31514])valenzuela[&&NHX:TOL=30851])coryphacini[&&NHX:TOL=50622],((kodamaius anaimalaicus[&&NHX:TOL=31088],kodamaius acinacostigmus[&&NHX:TOL=31089],kodamaius acisostigmus[&&NHX:TOL=31090],kodamaius ampyostigmus[&&NHX:TOL=31091],kodamaius angolensis[&&NHX:TOL=31092],kodamaius besucheti[&&NHX:TOL=31093],kodamaius brachycladus[&&NHX:TOL=31094],kodamaius brevicornis[&&NHX:TOL=31095],kodamaius cerastigmus[&&NHX:TOL=31096],kodamaius chinensis[&&NHX:TOL=31097],kodamaius collarti[&&NHX:TOL=31098],kodamaius conostigmus[&&NHX:TOL=31099],kodamaius cuboides[&&NHX:TOL=31100],kodamaius curtifurcus[&&NHX:TOL=31101],kodamaius curtus[&&NHX:TOL=31102],kodamaius curvativalvus[&&NHX:TOL=31103],kodamaius curvatus[&&NHX:TOL=31104],kodamaius directus[&&NHX:TOL=31105],kodamaius furvus[&&NHX:TOL=31106],kodamaius grandicornis[&&NHX:TOL=31107],kodamaius guizhouensis[&&NHX:TOL=31108],kodamaius ikomai[&&NHX:TOL=31109],kodamaius immeneus[&&NHX:TOL=31110],kodamaius ingenicellus[&&NHX:TOL=31111],kodamaius jiangxiensis[&&NHX:TOL=31112],kodamaius khasiensis[&&NHX:TOL=31113],kodamaius lamottei[&&NHX:TOL=31114],kodamaius latifurcus[&&NHX:TOL=31115],kodamaius loebli[&&NHX:TOL=31116],kodamaius longifurcus[&&NHX:TOL=31117],kodamaius macrostigma[&&NHX:TOL=31118],kodamaius maeandropetalus[&&NHX:TOL=31119],kodamaius mingshuii[&&NHX:TOL=31120],kodamaius mirabundus[&&NHX:TOL=31121],kodamaius obovatus[&&NHX:TOL=31122],kodamaius pilosus[&&NHX:TOL=31123],kodamaius pini[&&NHX:TOL=31124],kodamaius shixingicus[&&NHX:TOL=31125],kodamaius stipiatus[&&NHX:TOL=31126],kodamaius tibetensis[&&NHX:TOL=31127],kodamaius trapezius[&&NHX:TOL=31128],kodamaius trigonicus[&&NHX:TOL=31129],kodamaius wittmeri[&&NHX:TOL=31130],kodamaius yunnanicus[&&NHX:TOL=31131])kodamaius[&&NHX:TOL=30838],(pericaecilius singularis[&&NHX:TOL=31132],pericaecilius vaughani[&&NHX:TOL=31133],pericaecilius werneri[&&NHX:TOL=31134])pericaecilius[&&NHX:TOL=30839],thorntoniella lalea[&&NHX:TOL=30840],(asiocaecilius abbreviatus[&&NHX:TOL=31136],asiocaecilius assamensis[&&NHX:TOL=31137],asiocaecilius bhutanensis[&&NHX:TOL=31138],asiocaecilius comorensis[&&NHX:TOL=31139],asiocaecilius narmadus[&&NHX:TOL=31140],asiocaecilius okanus[&&NHX:TOL=31141],asiocaecilius singaporensis[&&NHX:TOL=31142])asiocaecilius[&&NHX:TOL=30841],(austrocaecilius alettae[&&NHX:TOL=31143],austrocaecilius parviramosus[&&NHX:TOL=31144])austrocaecilius[&&NHX:TOL=30842],(isophanopsis albofasciata[&&NHX:TOL=31145],isophanopsis annus[&&NHX:TOL=31146],isophanopsis interrupta[&&NHX:TOL=31147])isophanopsis[&&NHX:TOL=30843],lienhardiella dahli[&&NHX:TOL=30844],maoripsocopsis sumatrensis[&&NHX:TOL=30845],(maoripsocus aequalis[&&NHX:TOL=31150],maoripsocus africanus[&&NHX:TOL=31151],maoripsocus concavistigma[&&NHX:TOL=31152],maoripsocus dimorphus[&&NHX:TOL=31153],maoripsocus ericifoliae[&&NHX:TOL=31154],maoripsocus fastigatus[&&NHX:TOL=31155],maoripsocus frater[&&NHX:TOL=31156],maoripsocus griseus[&&NHX:TOL=31157],maoripsocus juneae[&&NHX:TOL=31158],maoripsocus koriflae[&&NHX:TOL=31159],maoripsocus lobatus[&&NHX:TOL=31160],maoripsocus macrostigma[&&NHX:TOL=31161],maoripsocus semifuscatus[&&NHX:TOL=31162],maoripsocus tugloensis[&&NHX:TOL=31163],maoripsocus wilsoni[&&NHX:TOL=31164])maoripsocus[&&NHX:TOL=30846])kodamaiini[&&NHX:TOL=50623],(dypsocopsis nathani[&&NHX:TOL=30835],(caecilius acrorbiculatus[&&NHX:TOL=30878],caecilius albonigrus[&&NHX:TOL=30879],caecilius ampullaceus[&&NHX:TOL=30880],caecilius anothylacus[&&NHX:TOL=30881],caecilius apiciglobosus[&&NHX:TOL=30882],caecilius arcuatus[&&NHX:TOL=30883],caecilius baeonaevus[&&NHX:TOL=30884],caecilius bannaicus[&&NHX:TOL=30885],caecilius bhimtalensis[&&NHX:TOL=30886],caecilius biahuashanicus[&&NHX:TOL=30887],caecilius bicarinatus[&&NHX:TOL=30888],caecilius bicruris[&&NHX:TOL=30889],caecilius biviminalis[&&NHX:TOL=30890],caecilius borealis[&&NHX:TOL=30891],caecilius brunneistigmus[&&NHX:TOL=30892],caecilius brunneolus[&&NHX:TOL=30893],caecilius callianthus[&&NHX:TOL=30894],caecilius calvatus[&&NHX:TOL=30895],caecilius calycinus[&&NHX:TOL=30896],caecilius ceratostictus[&&NHX:TOL=30897],caecilius cerinifullus[&&NHX:TOL=30898],caecilius changbaishanensis[&&NHX:TOL=30899],caecilius colossostigmus[&&NHX:TOL=30900],caecilius confusus[&&NHX:TOL=30901],caecilius connveaus[&&NHX:TOL=30902],caecilius corniculatus[&&NHX:TOL=30903],caecilius cornospilus[&&NHX:TOL=30904],caecilius craspedodrmus[&&NHX:TOL=30905],caecilius cuneatus[&&NHX:TOL=30906],caecilius cylindostigmus[&&NHX:TOL=30907],caecilius divulgatus[&&NHX:TOL=30908],caecilius emeishanensis[&&NHX:TOL=30909],caecilius enderleini[&&NHX:TOL=30910],caecilius ephippioideus[&&NHX:TOL=30911],caecilius exilis[&&NHX:TOL=30912],caecilius exquisitus[&&NHX:TOL=30913],caecilius extenuatus[&&NHX:TOL=30914],caecilius ferreus[&&NHX:TOL=30915],caecilius fibris[&&NHX:TOL=30916],caecilius flavicosta[&&NHX:TOL=30917],caecilius forficatus[&&NHX:TOL=30918],caecilius furcimaculatus[&&NHX:TOL=30919],caecilius fuscopterus[&&NHX:TOL=30920],caecilius genospilus[&&NHX:TOL=30921],caecilius guangxiensis[&&NHX:TOL=30922],caecilius guilinensis[&&NHX:TOL=30923],caecilius guizhouicus[&&NHX:TOL=30924],caecilius hapalotrichus[&&NHX:TOL=30925],caecilius hebetatus[&&NHX:TOL=30926],caecilius hengshanicus[&&NHX:TOL=30927],caecilius hornei[&&NHX:TOL=30928],caecilius huazhongicus[&&NHX:TOL=30929],caecilius hyalinonemus[&&NHX:TOL=30930],caecilius hyalinulus[&&NHX:TOL=30931],caecilius hylophilus[&&NHX:TOL=30932],caecilius hyperozonalis[&&NHX:TOL=30933],caecilius hypozonalis[&&NHX:TOL=30934],caecilius immensifascus[&&NHX:TOL=30935],caecilius immensus[&&NHX:TOL=30936],caecilius inclinans[&&NHX:TOL=30937],caecilius indecorus[&&NHX:TOL=30938],caecilius infurcus[&&NHX:TOL=30939],caecilius jilinensis[&&NHX:TOL=30940],caecilius jinganicus[&&NHX:TOL=30941],caecilius jinggangshanicus[&&NHX:TOL=30942],caecilius jini[&&NHX:TOL=30943],caecilius jinxiuensis[&&NHX:TOL=30944],caecilius jiugongshanicus[&&NHX:TOL=30945],caecilius lateralis[&&NHX:TOL=30946],caecilius laterimacularis[&&NHX:TOL=30947],caecilius latissimus[&&NHX:TOL=30948],caecilius latreillei[&&NHX:TOL=30949],caecilius lazikoensis[&&NHX:TOL=30950],caecilius leptopterus[&&NHX:TOL=30951],caecilius linearis[&&NHX:TOL=30952],caecilius liui[&&NHX:TOL=30953],caecilius liupanshanicus[&&NHX:TOL=30954],caecilius loculatus[&&NHX:TOL=30955],caecilius longiansatus[&&NHX:TOL=30956],caecilius longiantennus[&&NHX:TOL=30957],caecilius longiglobis[&&NHX:TOL=30958],caecilius longlingensis[&&NHX:TOL=30959],caecilius loratus[&&NHX:TOL=30960],caecilius loteolus[&&NHX:TOL=30961],caecilius luojiashanicus[&&NHX:TOL=30962],caecilius madecassus[&&NHX:TOL=30963],caecilius magnivalvus[&&NHX:TOL=30964],caecilius malleatus[&&NHX:TOL=30965],caecilius manubriatus[&&NHX:TOL=30966],caecilius marcidus[&&NHX:TOL=30967],caecilius martensi[&&NHX:TOL=30968],caecilius mecodactylus[&&NHX:TOL=30969],caecilius mecostigmus[&&NHX:TOL=30970],caecilius medivittatus[&&NHX:TOL=30971],caecilius medogensis[&&NHX:TOL=30972],caecilius meridionalis[&&NHX:TOL=30973],caecilius mixtus[&&NHX:TOL=30974],caecilius montanus[&&NHX:TOL=30975],caecilius mustangensis[&&NHX:TOL=30976],caecilius myriospilus[&&NHX:TOL=30977],caecilius nanningensis[&&NHX:TOL=30978],caecilius nanyuensis[&&NHX:TOL=30979],caecilius octofarius[&&NHX:TOL=30980],caecilius oegospilus[&&NHX:TOL=30981],caecilius optilohyalinus[&&NHX:TOL=30982],caecilius oxyopterus[&&NHX:TOL=30983],caecilius parifurcus[&&NHX:TOL=30984],caecilius paurifurcus[&&NHX:TOL=30985],caecilius paurosphaerus[&&NHX:TOL=30986],caecilius parvulus[&&NHX:TOL=30987],caecilius persimilaris[&&NHX:TOL=30988],caecilius pinalis[&&NHX:TOL=30989],caecilius plagosus[&&NHX:TOL=30990],caecilius platostigmus[&&NHX:TOL=30991],caecilius platytaenus[&&NHX:TOL=30992],caecilius plautifascus[&&NHX:TOL=30993],caecilius plautus[&&NHX:TOL=30994],caecilius plumimaculatus[&&NHX:TOL=30995],caecilius polymorphis[&&NHX:TOL=30996],caecilius psaronicircularis[&&NHX:TOL=30997],caecilius punctulosus[&&NHX:TOL=30998],caecilius qiannaniensis[&&NHX:TOL=30999],caecilius qingchengshanicus[&&NHX:TOL=31000],caecilius qinlingensis[&&NHX:TOL=31001],caecilius qiongshanensis[&&NHX:TOL=31002],caecilius quadraticellus[&&NHX:TOL=31003],caecilius quadriglobis[&&NHX:TOL=31004],caecilius quaterimaculus[&&NHX:TOL=31005],caecilius reductus[&&NHX:TOL=31006],caecilius replcatus[&&NHX:TOL=31007],caecilius resupinatus[&&NHX:TOL=31008],caecilius sagittalis[&&NHX:TOL=31009],caecilius scalpratus[&&NHX:TOL=31010],caecilius scitulus[&&NHX:TOL=31011],caecilius seychellensis[&&NHX:TOL=31012],caecilius seyrigi[&&NHX:TOL=31013],caecilius shanjinicus[&&NHX:TOL=31014],caecilius shanxiensis[&&NHX:TOL=31015],caecilius shennongjiaicus[&&NHX:TOL=31016],caecilius shouothylacus[&&NHX:TOL=31017],caecilius sigmoideus[&&NHX:TOL=31018],caecilius similaris[&&NHX:TOL=31019],caecilius sinuatus[&&NHX:TOL=31020],caecilius solus[&&NHX:TOL=31021],caecilius sordidus[&&NHX:TOL=31022],caecilius spadicitaensis[&&NHX:TOL=31023],caecilius spiciformis[&&NHX:TOL=31024],caecilius spinosus[&&NHX:TOL=31025],caecilius sporadicus[&&NHX:TOL=31026],caecilius stenostigmus[&&NHX:TOL=31027],caecilius stigmatophorus[&&NHX:TOL=31028],caecilius stolidus[&&NHX:TOL=31029],caecilius sylvaticus[&&NHX:TOL=31030],caecilius terminatus[&&NHX:TOL=31031],caecilius terrestris[&&NHX:TOL=31032],caecilius tongshanicus[&&NHX:TOL=31033],caecilius trinatus[&&NHX:TOL=31034],caecilius tripunctatus[&&NHX:TOL=31035],caecilius trullatus[&&NHX:TOL=31036],caecilius truncatulus[&&NHX:TOL=31037],caecilius tsaratananensis[&&NHX:TOL=31038],caecilius uncinellus[&&NHX:TOL=31039],caecilius unus[&&NHX:TOL=31040],caecilius wittei[&&NHX:TOL=31041],caecilius wudangshanicus[&&NHX:TOL=31042],caecilius wulingshanicus[&&NHX:TOL=31043],caecilius xanthochilus[&&NHX:TOL=31044],caecilius ximaicus[&&NHX:TOL=31045],caecilius yadongicus[&&NHX:TOL=31046],caecilius yigongensis[&&NHX:TOL=31047],caecilius yoshizawai[&&NHX:TOL=31048],caecilius zhamogensis[&&NHX:TOL=31049],caecilius zhangliangi[&&NHX:TOL=31050],caecilius zhuangshani[&&NHX:TOL=31051])caecilius[&&NHX:TOL=30834],(dypsocus abaxialis[&&NHX:TOL=31053],dypsocus abruptus[&&NHX:TOL=31054],dypsocus acuminatus[&&NHX:TOL=31055],dypsocus ambuotrichus[&&NHX:TOL=31056],dypsocus apicatus[&&NHX:TOL=31057],dypsocus binervis[&&NHX:TOL=31058],dypsocus brevivalvus[&&NHX:TOL=31059],dypsocus capitivalvus[&&NHX:TOL=31060],dypsocus cervinus[&&NHX:TOL=31061],dypsocus cestrocephalus[&&NHX:TOL=31062],dypsocus coleoptratus[&&NHX:TOL=31063],dypsocus corporaali[&&NHX:TOL=31064],dypsocus cornutus[&&NHX:TOL=31065],dypsocus deplanatus[&&NHX:TOL=31066],dypsocus fortis[&&NHX:TOL=31067],dypsocus fucosus[&&NHX:TOL=31068],dypsocus latus[&&NHX:TOL=31069],dypsocus longidigitalis[&&NHX:TOL=31070],dypsocus longivalvus[&&NHX:TOL=31071],dypsocus minisculus[&&NHX:TOL=31072],dypsocus septemfidus[&&NHX:TOL=31073],dypsocus stenotalis[&&NHX:TOL=31074],dypsocus tappanensis[&&NHX:TOL=31075])dypsocus[&&NHX:TOL=30836],(isophanes angolensis[&&NHX:TOL=31076],isophanes capeneri[&&NHX:TOL=31077],isophanes cyclostigma[&&NHX:TOL=31078],isophanes decipiens[&&NHX:TOL=31079],isophanes fengduensis[&&NHX:TOL=31080],isophanes luteus[&&NHX:TOL=31081],isophanes orientalis[&&NHX:TOL=31082],isophanes oxyostigma[&&NHX:TOL=31083],isophanes palliatus[&&NHX:TOL=31084],isophanes platystigma[&&NHX:TOL=31085],isophanes sinensis[&&NHX:TOL=31086],isophanes yangi[&&NHX:TOL=31087])isophanes[&&NHX:TOL=30837])caeciliusini[&&NHX:TOL=50624],(phymocaecilius fuscifascus[&&NHX:TOL=30874],phymocaecilius guizhouensis[&&NHX:TOL=30875],phymocaecilius puniceifascus[&&NHX:TOL=30876],phymocaecilius subulosus[&&NHX:TOL=30877])phymocaecilius[&&NHX:TOL=30833],parvialacaecilia hebeiensis[&&NHX:TOL=30832],(licaecilius mangshiensis[&&NHX:TOL=30871],licaecilius triradiatus[&&NHX:TOL=30872])licaecilius[&&NHX:TOL=30831],disialacaecilia ningxiaensis[&&NHX:TOL=30830],bivalvicaecilia longiansa[&&NHX:TOL=30829])caeciliusinae[&&NHX:TOL=50620],aphyopsocus prolixus[&&NHX:TOL=30854],((chilenocaecilius nestae[&&NHX:TOL=31520],chilenocaecilius ornatipennis[&&NHX:TOL=31521])chilenocaecilius[&&NHX:TOL=30855],(enderleinella anocella[&&NHX:TOL=31522],enderleinella aureola[&&NHX:TOL=31523],enderleinella biaristata[&&NHX:TOL=31524],enderleinella binata[&&NHX:TOL=31525],enderleinella calta[&&NHX:TOL=31526],enderleinella ceylonica[&&NHX:TOL=31527],enderleinella cochleativalva[&&NHX:TOL=31528],enderleinella concava[&&NHX:TOL=31529],enderleinella constrictivalva[&&NHX:TOL=31530],enderleinella decurvata[&&NHX:TOL=31531],enderleinella dilatativalva[&&NHX:TOL=31532],enderleinella emeishanana[&&NHX:TOL=31533],enderleinella explanata[&&NHX:TOL=31534],enderleinella flavata[&&NHX:TOL=31535],enderleinella gramica[&&NHX:TOL=31536],enderleinella hainanana[&&NHX:TOL=31537],enderleinella huangshanana[&&NHX:TOL=31538],enderleinella hylobius[&&NHX:TOL=31539],enderleinella kurilensis[&&NHX:TOL=31540],enderleinella lurida[&&NHX:TOL=31541],enderleinella monosospaera[&&NHX:TOL=31542],enderleinella netropetala[&&NHX:TOL=31543],enderleinella obsoleta[&&NHX:TOL=31544],enderleinella occidentalis[&&NHX:TOL=31545],enderleinella ooidea[&&NHX:TOL=31546],enderleinella paulivalvacea[&&NHX:TOL=31547],enderleinella phaeocephala[&&NHX:TOL=31548],enderleinella prolongata[&&NHX:TOL=31549],enderleinella pyriformis[&&NHX:TOL=31550],enderleinella qingchengshanana[&&NHX:TOL=31551],enderleinella ruberifasciatria[&&NHX:TOL=31552],enderleinella setosivalva[&&NHX:TOL=31553],enderleinella sphenoidalis[&&NHX:TOL=31554],enderleinella sylvihabita[&&NHX:TOL=31555],enderleinella tenella[&&NHX:TOL=31556],enderleinella tianmushanana[&&NHX:TOL=31557],enderleinella trapezia[&&NHX:TOL=31558],enderleinella unicolor[&&NHX:TOL=31559],enderleinella yangi[&&NHX:TOL=31560],enderleinella yunnanana[&&NHX:TOL=31561])enderleinella[&&NHX:TOL=30856],mockfordiella mascarenensis[&&NHX:TOL=30857],(paracaecilius altus[&&NHX:TOL=31563],paracaecilius alutaceus[&&NHX:TOL=31564],paracaecilius basidentatus[&&NHX:TOL=31565],paracaecilius beijingicus[&&NHX:TOL=31566],paracaecilius berlandi[&&NHX:TOL=31567],paracaecilius cardaleae[&&NHX:TOL=31568],paracaecilius chebalinganus[&&NHX:TOL=31569],paracaecilius cinnamomus[&&NHX:TOL=31570],paracaecilius copiosus[&&NHX:TOL=31571],paracaecilius cyanops[&&NHX:TOL=31572],paracaecilius globiclypeus[&&NHX:TOL=31573],paracaecilius gulingicus[&&NHX:TOL=31574],paracaecilius hallae[&&NHX:TOL=31575],paracaecilius hilli[&&NHX:TOL=31576],paracaecilius japanus[&&NHX:TOL=31577],paracaecilius jilinicus[&&NHX:TOL=31578],paracaecilius lacteus[&&NHX:TOL=31579],paracaecilius lativalvis[&&NHX:TOL=31580],paracaecilius lemuris[&&NHX:TOL=31581],paracaecilius lingnanensis[&&NHX:TOL=31582],paracaecilius longicellus[&&NHX:TOL=31583],paracaecilius lucidus[&&NHX:TOL=31584],paracaecilius macrops[&&NHX:TOL=31585],paracaecilius megistus[&&NHX:TOL=31586],paracaecilius megops[&&NHX:TOL=31587],paracaecilius meniscoides[&&NHX:TOL=31588],paracaecilius mokotensis[&&NHX:TOL=31589],paracaecilius navasi[&&NHX:TOL=31590],paracaecilius niumatus[&&NHX:TOL=31591],paracaecilius novoguineensis[&&NHX:TOL=31592],paracaecilius oxystigma[&&NHX:TOL=31593],paracaecilius pallicornis[&&NHX:TOL=31594],paracaecilius pallidus[&&NHX:TOL=31595],paracaecilius papillatus[&&NHX:TOL=31596],paracaecilius parviareola[&&NHX:TOL=31597],paracaecilius pygmaeus[&&NHX:TOL=31598],paracaecilius seltus[&&NHX:TOL=31599],paracaecilius socialis[&&NHX:TOL=31600],paracaecilius sphaericus[&&NHX:TOL=31601],paracaecilius translucidus[&&NHX:TOL=31602],paracaecilius tripetatus[&&NHX:TOL=31603],paracaecilius wittei[&&NHX:TOL=31604],paracaecilius zelandicus[&&NHX:TOL=31605])paracaecilius[&&NHX:TOL=30858],(xanthocaecilius anahuacensis[&&NHX:TOL=31606],xanthocaecilius bilineatus[&&NHX:TOL=31607],xanthocaecilius brevicornis[&&NHX:TOL=31608],xanthocaecilius costaricensis[&&NHX:TOL=31609],xanthocaecilius eroticus[&&NHX:TOL=31610],xanthocaecilius falciferrens[&&NHX:TOL=31611],xanthocaecilius fasciatus[&&NHX:TOL=31612],xanthocaecilius granulosus[&&NHX:TOL=31613],xanthocaecilius macrops[&&NHX:TOL=31614],xanthocaecilius microphthalmus[&&NHX:TOL=31615],xanthocaecilius montserratensis[&&NHX:TOL=31616],xanthocaecilius obscurus[&&NHX:TOL=31617],xanthocaecilius pallidus[&&NHX:TOL=31618],xanthocaecilius papillatus[&&NHX:TOL=31619],xanthocaecilius quillayute[&&NHX:TOL=31620],xanthocaecilius silvaticus[&&NHX:TOL=31621],xanthocaecilius simplex[&&NHX:TOL=31622],xanthocaecilius sommermanae[&&NHX:TOL=31623],xanthocaecilius uniformis[&&NHX:TOL=31624])xanthocaecilius[&&NHX:TOL=30859])paracaeciliinae[&&NHX:TOL=50625],((fuelleborniella capensis[&&NHX:TOL=31625],fuelleborniella distincta[&&NHX:TOL=31626],fuelleborniella dubia[&&NHX:TOL=31627],fuelleborniella fulva[&&NHX:TOL=31628],fuelleborniella fusca[&&NHX:TOL=31629],fuelleborniella intermedia[&&NHX:TOL=31630],fuelleborniella mimula[&&NHX:TOL=31631],fuelleborniella nigricornis[&&NHX:TOL=31632],fuelleborniella nimbensis[&&NHX:TOL=31633],fuelleborniella nyassica[&&NHX:TOL=31634],fuelleborniella parva[&&NHX:TOL=31635],fuelleborniella tuberculata[&&NHX:TOL=31636])fuelleborniella[&&NHX:TOL=30860],(smithersiella anomala[&&NHX:TOL=31637],smithersiella nigrostigma[&&NHX:TOL=31638])smithersiella[&&NHX:TOL=30861],(ypsiloneura kirkpatricki[&&NHX:TOL=31639],ypsiloneura monostyla[&&NHX:TOL=31640])ypsiloneura[&&NHX:TOL=30862])fuelleborniellinae[&&NHX:TOL=50626])caeciliusidae[&&NHX:TOL=14467],(((kolbia bakeri[&&NHX:TOL=31660],kolbia davadshamci[&&NHX:TOL=31661],kolbia fusconervosa[&&NHX:TOL=31662],kolbia hummeli[&&NHX:TOL=31663],kolbia immaculata[&&NHX:TOL=31664],kolbia maculipennis[&&NHX:TOL=31665],kolbia madagascariensis[&&NHX:TOL=31666],kolbia punctata[&&NHX:TOL=31667],kolbia quisquiliarum[&&NHX:TOL=31668])kolbia[&&NHX:TOL=31641],(pseudokolbea immaculata[&&NHX:TOL=31669],pseudokolbea nigrisetosa[&&NHX:TOL=31670],pseudokolbea phaea[&&NHX:TOL=31671],pseudokolbea xanthoptera[&&NHX:TOL=31672])pseudokolbea[&&NHX:TOL=31642])kolbiini[&&NHX:TOL=50628],schizopechus marshalli[&&NHX:TOL=31643],capillopsocus smithersorum[&&NHX:TOL=31644],(brachypsocus badonneli[&&NHX:TOL=31645],(dasypsocus angolensis[&&NHX:TOL=31676],dasypsocus brachyops[&&NHX:TOL=31677],dasypsocus brunneus[&&NHX:TOL=31678],dasypsocus chillcotti[&&NHX:TOL=31679],dasypsocus congolensis[&&NHX:TOL=31680],dasypsocus nigrifrons[&&NHX:TOL=31681],dasypsocus paolettii[&&NHX:TOL=31682],dasypsocus pilosus[&&NHX:TOL=31683],dasypsocus roesleri[&&NHX:TOL=31684],dasypsocus solox[&&NHX:TOL=31685])dasypsocus[&&NHX:TOL=31646])dasypsocini[&&NHX:TOL=50629],(polypsocus bimaculatus[&&NHX:TOL=31686],polypsocus coleopterus[&&NHX:TOL=31687],polypsocus collinsi[&&NHX:TOL=31688],polypsocus corruptus[&&NHX:TOL=31689],polypsocus delunatus[&&NHX:TOL=31690],polypsocus desectus[&&NHX:TOL=31691],polypsocus falcifer[&&NHX:TOL=31692],polypsocus fasciatus[&&NHX:TOL=31693],polypsocus fastosus[&&NHX:TOL=31694],polypsocus fuscopterus[&&NHX:TOL=31695],polypsocus fuscus[&&NHX:TOL=31696],polypsocus griseolineatus[&&NHX:TOL=31697],polypsocus lineatus[&&NHX:TOL=31698],polypsocus lunulatus[&&NHX:TOL=31699],polypsocus nervulosus[&&NHX:TOL=31700],polypsocus ohausianus[&&NHX:TOL=31701],polypsocus quadriguttatus[&&NHX:TOL=31702],polypsocus selenius[&&NHX:TOL=31703],polypsocus serpentinus[&&NHX:TOL=31704],polypsocus suffuscus[&&NHX:TOL=31705],polypsocus unicolor[&&NHX:TOL=31706])polypsocus[&&NHX:TOL=31647],(afropsocus natalensis[&&NHX:TOL=31658],(amphipsocus aliflavidus[&&NHX:TOL=31757],amphipsocus amplus[&&NHX:TOL=31758],amphipsocus angusticruris[&&NHX:TOL=31759],amphipsocus arciatus[&&NHX:TOL=31760],amphipsocus armeniacus[&&NHX:TOL=31761],amphipsocus artus[&&NHX:TOL=31762],amphipsocus attenuatus[&&NHX:TOL=31763],amphipsocus bicolor[&&NHX:TOL=31764],amphipsocus bicoloripennis[&&NHX:TOL=31765],amphipsocus biconvexus[&&NHX:TOL=31766],amphipsocus bipunctatus[&&NHX:TOL=31767],amphipsocus callani[&&NHX:TOL=31768],amphipsocus camerunus[&&NHX:TOL=31769],amphipsocus cerasostigmus[&&NHX:TOL=31770],amphipsocus cognatus[&&NHX:TOL=31771],amphipsocus confusus[&&NHX:TOL=31772],amphipsocus connexus[&&NHX:TOL=31773],amphipsocus cornostigmus[&&NHX:TOL=31774],amphipsocus cuangoensis[&&NHX:TOL=31775],amphipsocus daozhulanicus[&&NHX:TOL=31776],amphipsocus declivimaculatus[&&NHX:TOL=31777],amphipsocus derroni[&&NHX:TOL=31778],amphipsocus disgregus[&&NHX:TOL=31779],amphipsocus dispar[&&NHX:TOL=31780],amphipsocus dubius[&&NHX:TOL=31781],amphipsocus erythroanatus[&&NHX:TOL=31782],amphipsocus erythrostigma[&&NHX:TOL=31783],amphipsocus facetus[&&NHX:TOL=31784],amphipsocus fasciatus[&&NHX:TOL=31785],amphipsocus flavidus[&&NHX:TOL=31786],amphipsocus fluctosus[&&NHX:TOL=31787],amphipsocus formosanus[&&NHX:TOL=31788],amphipsocus frontirutilus[&&NHX:TOL=31789],amphipsocus fusimus[&&NHX:TOL=31790],amphipsocus ghesquierei[&&NHX:TOL=31791],amphipsocus gibbosus[&&NHX:TOL=31792],amphipsocus glandaceus[&&NHX:TOL=31793],amphipsocus guangxiensis[&&NHX:TOL=31794],amphipsocus gutianshanus[&&NHX:TOL=31795],amphipsocus heterothrix[&&NHX:TOL=31796],amphipsocus hildebrandti[&&NHX:TOL=31797],amphipsocus intrans[&&NHX:TOL=31798],amphipsocus iridescens[&&NHX:TOL=31799],amphipsocus japonicus[&&NHX:TOL=31800],amphipsocus javensis[&&NHX:TOL=31801],amphipsocus jinggangshanensis[&&NHX:TOL=31802],amphipsocus limbatus[&&NHX:TOL=31803],amphipsocus longgangiensis[&&NHX:TOL=31804],amphipsocus lushanensis[&&NHX:TOL=31805],amphipsocus macrochilus[&&NHX:TOL=31806],amphipsocus maculiceps[&&NHX:TOL=31807],amphipsocus maculidorsum[&&NHX:TOL=31808],amphipsocus maculipennis[&&NHX:TOL=31809],amphipsocus madagascariensis[&&NHX:TOL=31810],amphipsocus maequilongus[&&NHX:TOL=31811],amphipsocus magnus[&&NHX:TOL=31812],amphipsocus mangiferae[&&NHX:TOL=31813],amphipsocus medogicus[&&NHX:TOL=31814],amphipsocus mendax[&&NHX:TOL=31815],amphipsocus minor[&&NHX:TOL=31816],amphipsocus montanus[&&NHX:TOL=31817],amphipsocus mucronatus[&&NHX:TOL=31818],amphipsocus nigricollis[&&NHX:TOL=31819],amphipsocus notus[&&NHX:TOL=31820],amphipsocus oligophlebius[&&NHX:TOL=31821],amphipsocus oppositus[&&NHX:TOL=31822],amphipsocus orbiculatus[&&NHX:TOL=31823],amphipsocus orophilus[&&NHX:TOL=31824],amphipsocus pallidus[&&NHX:TOL=31825],amphipsocus pandus[&&NHX:TOL=31826],amphipsocus parilis[&&NHX:TOL=31827],amphipsocus parvus[&&NHX:TOL=31828],amphipsocus perbellus[&&NHX:TOL=31829],amphipsocus perbrevis[&&NHX:TOL=31830],amphipsocus phoenicophlebius[&&NHX:TOL=31831],amphipsocus pictus[&&NHX:TOL=31832],amphipsocus pilosus[&&NHX:TOL=31833],amphipsocus purpureus[&&NHX:TOL=31834],amphipsocus rectivenis[&&NHX:TOL=31835],amphipsocus rotundus[&&NHX:TOL=31836],amphipsocus rubrostigma[&&NHX:TOL=31837],amphipsocus seyrigi[&&NHX:TOL=31838],amphipsocus similis[&&NHX:TOL=31839],amphipsocus smaragdinus[&&NHX:TOL=31840],amphipsocus stipiatus[&&NHX:TOL=31841],amphipsocus strumosus[&&NHX:TOL=31842],amphipsocus sulciformis[&&NHX:TOL=31843],amphipsocus transinervalis[&&NHX:TOL=31844],amphipsocus tricostatus[&&NHX:TOL=31845],amphipsocus unitoides[&&NHX:TOL=31846],amphipsocus unitus[&&NHX:TOL=31847],amphipsocus vittatus[&&NHX:TOL=31848],amphipsocus voeltzkowi[&&NHX:TOL=31849],amphipsocus wanxianicus[&&NHX:TOL=31850],amphipsocus wuzhishanicus[&&NHX:TOL=31851],amphipsocus xanthozonus[&&NHX:TOL=31852],amphipsocus yunnanicus[&&NHX:TOL=31853])amphipsocus[&&NHX:TOL=31653],(amphipsocopsis sogai[&&NHX:TOL=31755],amphipsocopsis surculosa[&&NHX:TOL=31756])amphipsocopsis[&&NHX:TOL=31652],(complaniamphus acutulus[&&NHX:TOL=31707],complaniamphus apicifuscus[&&NHX:TOL=31708],complaniamphus atrimaculatus[&&NHX:TOL=31709],complaniamphus fascigrus[&&NHX:TOL=31710],complaniamphus loratus[&&NHX:TOL=31711])complaniamphus[&&NHX:TOL=31648],(ctenopsocus annulicornis[&&NHX:TOL=31746],ctenopsocus bicoloripes[&&NHX:TOL=31747],ctenopsocus fuscipes[&&NHX:TOL=31748],ctenopsocus pallipes[&&NHX:TOL=31749],ctenopsocus similis[&&NHX:TOL=31750],ctenopsocus tibialis[&&NHX:TOL=31751])ctenopsocus[&&NHX:TOL=31650],(harpezoneura ambigua[&&NHX:TOL=31854],harpezoneura difficilis[&&NHX:TOL=31855],harpezoneura distincta[&&NHX:TOL=31856],harpezoneura indotata[&&NHX:TOL=31857],harpezoneura intermedia[&&NHX:TOL=31858],harpezoneura lateralis[&&NHX:TOL=31859],harpezoneura limbata[&&NHX:TOL=31860],harpezoneura madagascariensis[&&NHX:TOL=31861],harpezoneura montana[&&NHX:TOL=31862],harpezoneura multifurcata[&&NHX:TOL=31863],harpezoneura nigeriensis[&&NHX:TOL=31864],harpezoneura pallens[&&NHX:TOL=31865],harpezoneura pilosa[&&NHX:TOL=31866],harpezoneura speciosa[&&NHX:TOL=31867],harpezoneura stigmalis[&&NHX:TOL=31868])harpezoneura[&&NHX:TOL=31654],pentathyrsus vespertilio[&&NHX:TOL=31655],(taeniostigma baiyerense[&&NHX:TOL=31712],taeniostigma biconvexum[&&NHX:TOL=31713],taeniostigma bimaculatum[&&NHX:TOL=31714],taeniostigma cacuminalium[&&NHX:TOL=31715],taeniostigma campylodromum[&&NHX:TOL=31716],taeniostigma elongatum[&&NHX:TOL=31717],taeniostigma euneurum[&&NHX:TOL=31718],taeniostigma exoletum[&&NHX:TOL=31719],taeniostigma flavescens[&&NHX:TOL=31720],taeniostigma genuflexum[&&NHX:TOL=31721],taeniostigma guangdonganum[&&NHX:TOL=31722],taeniostigma hamatum[&&NHX:TOL=31723],taeniostigma ingens[&&NHX:TOL=31724],taeniostigma irianum[&&NHX:TOL=31725],taeniostigma longicrurium[&&NHX:TOL=31726],taeniostigma malayanum[&&NHX:TOL=31727],taeniostigma montanum[&&NHX:TOL=31728],taeniostigma nigricorne[&&NHX:TOL=31729],taeniostigma perkinsi[&&NHX:TOL=31730],taeniostigma phaeostigma[&&NHX:TOL=31731],taeniostigma platozona[&&NHX:TOL=31732],taeniostigma pulcha[&&NHX:TOL=31733],taeniostigma pyrrhospilum[&&NHX:TOL=31734],taeniostigma reticularium[&&NHX:TOL=31735],taeniostigma scariosum[&&NHX:TOL=31736],taeniostigma scotocaula[&&NHX:TOL=31737],taeniostigma sibilense[&&NHX:TOL=31738],taeniostigma stipatum[&&NHX:TOL=31739],taeniostigma stramineum[&&NHX:TOL=31740],taeniostigma strigulosum[&&NHX:TOL=31741],taeniostigma ternidentalium[&&NHX:TOL=31742],taeniostigma tibiale[&&NHX:TOL=31743],taeniostigma trickettae[&&NHX:TOL=31744],taeniostigma trinotatum[&&NHX:TOL=31745])taeniostigma[&&NHX:TOL=31649],(tagalopsocus hyalinus[&&NHX:TOL=31752],tagalopsocus luzonensis[&&NHX:TOL=31753],tagalopsocus phaeostigmus[&&NHX:TOL=31754])tagalopsocus[&&NHX:TOL=31651],(siniamphipsocus acutus[&&NHX:TOL=31870],siniamphipsocus aureus[&&NHX:TOL=31871],siniamphipsocus beijianicus[&&NHX:TOL=31872],siniamphipsocus bellulus[&&NHX:TOL=31873],siniamphipsocus betulicolus[&&NHX:TOL=31874],siniamphipsocus biconjugarus[&&NHX:TOL=31875],siniamphipsocus bilinearis[&&NHX:TOL=31876],siniamphipsocus changbaishanicus[&&NHX:TOL=31877],siniamphipsocus chiloscotius[&&NHX:TOL=31878],siniamphipsocus deltoides[&&NHX:TOL=31879],siniamphipsocus dichasialis[&&NHX:TOL=31880],siniamphipsocus emeiensis[&&NHX:TOL=31881],siniamphipsocus flavifrontus[&&NHX:TOL=31882],siniamphipsocus huashanensis[&&NHX:TOL=31883],siniamphipsocus mecocephalus[&&NHX:TOL=31884],siniamphipsocus pedatus[&&NHX:TOL=31885],siniamphipsocus pertenius[&&NHX:TOL=31886],siniamphipsocus platyocheilus[&&NHX:TOL=31887],siniamphipsocus sunae[&&NHX:TOL=31888],siniamphipsocus yangzijiangensis[&&NHX:TOL=31889])siniamphipsocus[&&NHX:TOL=31656],(xenopsocus africanus[&&NHX:TOL=31890],xenopsocus curvatus[&&NHX:TOL=31891],xenopsocus hagenii[&&NHX:TOL=31892])xenopsocus[&&NHX:TOL=31657])amphipsocini[&&NHX:TOL=50630],(calocaecilius apertus[&&NHX:TOL=31894],calocaecilius decipiens[&&NHX:TOL=31895])calocaecilius[&&NHX:TOL=31659])amphipsocidae[&&NHX:TOL=14469],((cubipilis anchorocaulis[&&NHX:TOL=31900],cubipilis aphidiformis[&&NHX:TOL=31901],cubipilis baishanzuensis[&&NHX:TOL=31902],cubipilis beijingensis[&&NHX:TOL=31903],cubipilis bicoloratus[&&NHX:TOL=31904],cubipilis chebalingensis[&&NHX:TOL=31905],cubipilis coronatus[&&NHX:TOL=31906],cubipilis cunnatus[&&NHX:TOL=31907],cubipilis denivalvis[&&NHX:TOL=31908],cubipilis falcatus[&&NHX:TOL=31909],cubipilis fastigiatus[&&NHX:TOL=31910],cubipilis flavicapitus[&&NHX:TOL=31911],cubipilis furcimaculatus[&&NHX:TOL=31912],cubipilis gannanensis[&&NHX:TOL=31913],cubipilis hamaocaulis[&&NHX:TOL=31914],cubipilis leucoresbius[&&NHX:TOL=31915],cubipilis locularis[&&NHX:TOL=31916],cubipilis macrostigmis[&&NHX:TOL=31917],cubipilis majusculus[&&NHX:TOL=31918],cubipilis mesozonalis[&&NHX:TOL=31919],cubipilis orbiculatus[&&NHX:TOL=31920],cubipilis ovalimacularis[&&NHX:TOL=31921],cubipilis palmatus[&&NHX:TOL=31922],cubipilis pellucidus[&&NHX:TOL=31923],cubipilis phaeostigmis[&&NHX:TOL=31924],cubipilis platytaenius[&&NHX:TOL=31925],cubipilis pyriformis[&&NHX:TOL=31926],cubipilis quaternatus[&&NHX:TOL=31927],cubipilis spilipsocius[&&NHX:TOL=31928],cubipilis tianmushanensis[&&NHX:TOL=31929],cubipilis trinotatus[&&NHX:TOL=31930],cubipilis yuensis[&&NHX:TOL=31931])cubipilis[&&NHX:TOL=31896],(graphopsocus borealis[&&NHX:TOL=31932],graphopsocus choui[&&NHX:TOL=31933],graphopsocus cruciatus[&&NHX:TOL=31934],graphopsocus epicharis[&&NHX:TOL=31935],graphopsocus euneurus[&&NHX:TOL=31936],graphopsocus evanidus[&&NHX:TOL=31937],graphopsocus flavipunctatus[&&NHX:TOL=31938],graphopsocus infirmus[&&NHX:TOL=31939],graphopsocus intrans[&&NHX:TOL=31940],graphopsocus leptostigmus[&&NHX:TOL=31941],graphopsocus liaoningensis[&&NHX:TOL=31942],graphopsocus luojiashanensis[&&NHX:TOL=31943],graphopsocus megistigmus[&&NHX:TOL=31944],graphopsocus mexicanus[&&NHX:TOL=31945],graphopsocus obcuneatus[&&NHX:TOL=31946],graphopsocus panduratus[&&NHX:TOL=31947],graphopsocus platynotus[&&NHX:TOL=31948],graphopsocus putuoshanensis[&&NHX:TOL=31949],graphopsocus shaanxiensis[&&NHX:TOL=31950],graphopsocus sinuolatus[&&NHX:TOL=31951],graphopsocus subaequalis[&&NHX:TOL=31952],graphopsocus urceolatus[&&NHX:TOL=31953])graphopsocus[&&NHX:TOL=31897],(malostenopsocus cubitalis[&&NHX:TOL=31954],malostenopsocus expansus[&&NHX:TOL=31955],malostenopsocus immaculatus[&&NHX:TOL=31956],malostenopsocus intertextus[&&NHX:TOL=31957],malostenopsocus mucronatus[&&NHX:TOL=31958],malostenopsocus parallelinervius[&&NHX:TOL=31959],malostenopsocus plurifasciatus[&&NHX:TOL=31960],malostenopsocus sulphurepterus[&&NHX:TOL=31961],malostenopsocus yunnanicus[&&NHX:TOL=31962])malostenopsocus[&&NHX:TOL=31898],(stenopsocus adisoemartoi[&&NHX:TOL=31963],stenopsocus albipileus[&&NHX:TOL=31964],stenopsocus albus[&&NHX:TOL=31965],stenopsocus angustifurcus[&&NHX:TOL=31966],stenopsocus angustistriatus[&&NHX:TOL=31967],stenopsocus anthracinus[&&NHX:TOL=31968],stenopsocus apertus[&&NHX:TOL=31969],stenopsocus aureus[&&NHX:TOL=31970],stenopsocus bellatulus[&&NHX:TOL=31971],stenopsocus betulus[&&NHX:TOL=31972],stenopsocus bicoloriceps[&&NHX:TOL=31973],stenopsocus biconicus[&&NHX:TOL=31974],stenopsocus biconvexus[&&NHX:TOL=31975],stenopsocus bimaculatus[&&NHX:TOL=31976],stenopsocus bipunctatus[&&NHX:TOL=31977],stenopsocus bombusus[&&NHX:TOL=31978],stenopsocus brachychelus[&&NHX:TOL=31979],stenopsocus brachycladus[&&NHX:TOL=31980],stenopsocus brevicapitus[&&NHX:TOL=31981],stenopsocus brevivalvaris[&&NHX:TOL=31982],stenopsocus capacimacularus[&&NHX:TOL=31983],stenopsocus cassideus[&&NHX:TOL=31984],stenopsocus ceuthozibrinus[&&NHX:TOL=31985],stenopsocus changbaishanicus[&&NHX:TOL=31986],stenopsocus chusanensis[&&NHX:TOL=31987],stenopsocus concisus[&&NHX:TOL=31988],stenopsocus dactylinus[&&NHX:TOL=31989],stenopsocus dichospilus[&&NHX:TOL=31990],stenopsocus dictyodromus[&&NHX:TOL=31991],stenopsocus disphaeroides[&&NHX:TOL=31992],stenopsocus dissimilis[&&NHX:TOL=31993],stenopsocus emeishanicus[&&NHX:TOL=31994],stenopsocus eucallus[&&NHX:TOL=31995],stenopsocus externus[&&NHX:TOL=31996],stenopsocus fanjingshanicus[&&NHX:TOL=31997],stenopsocus faungi[&&NHX:TOL=31998],stenopsocus flavifrons[&&NHX:TOL=31999],stenopsocus flavinigrus[&&NHX:TOL=32000],stenopsocus floralis[&&NHX:TOL=32001],stenopsocus foliaceus[&&NHX:TOL=32002],stenopsocus formosanus[&&NHX:TOL=32003],stenopsocus frontalis[&&NHX:TOL=32004],stenopsocus frontimaculatus[&&NHX:TOL=32005],stenopsocus fulivertex[&&NHX:TOL=32006],stenopsocus gansuensis[&&NHX:TOL=32007],stenopsocus genostictus[&&NHX:TOL=32008],stenopsocus gibbulosus[&&NHX:TOL=32009],stenopsocus gracilimaculatus[&&NHX:TOL=32010],stenopsocus gracillimus[&&NHX:TOL=32011],stenopsocus guizhouiensis[&&NHX:TOL=32012],stenopsocus hemiostictus[&&NHX:TOL=32013],stenopsocus hexagonus[&&NHX:TOL=32014],stenopsocus huangshanicus[&&NHX:TOL=32015],stenopsocus hunanicus[&&NHX:TOL=32016],stenopsocus immaculatus[&&NHX:TOL=32017],stenopsocus isotomus[&&NHX:TOL=32018],stenopsocus jocosus[&&NHX:TOL=32019],stenopsocus kunmingiensis[&&NHX:TOL=32020],stenopsocus lachlani[&&NHX:TOL=32021],stenopsocus lacteus[&&NHX:TOL=32022],stenopsocus laterimaculatus[&&NHX:TOL=32023],stenopsocus lifashengi[&&NHX:TOL=32024],stenopsocus liuae[&&NHX:TOL=32025],stenopsocus liupanshanensis[&&NHX:TOL=32026],stenopsocus longicuspis[&&NHX:TOL=32027],stenopsocus longitudinalis[&&NHX:TOL=32028],stenopsocus macrocheirus[&&NHX:TOL=32029],stenopsocus maculosus[&&NHX:TOL=32030],stenopsocus makii[&&NHX:TOL=32031],stenopsocus maximalis[&&NHX:TOL=32032],stenopsocus melanocephalus[&&NHX:TOL=32033],stenopsocus metastictus[&&NHX:TOL=32034],stenopsocus naevicapitatus[&&NHX:TOL=32035],stenopsocus nepalensis[&&NHX:TOL=32036],stenopsocus niger[&&NHX:TOL=32037],stenopsocus nigricellus[&&NHX:TOL=32038],stenopsocus obscurus[&&NHX:TOL=32039],stenopsocus oculimaculatus[&&NHX:TOL=32040],stenopsocus pallidus[&&NHX:TOL=32041],stenopsocus parviforficatus[&&NHX:TOL=32042],stenopsocus pavonicus[&&NHX:TOL=32043],stenopsocus paxillivalvaris[&&NHX:TOL=32044],stenopsocus percussus[&&NHX:TOL=32045],stenopsocus periostictus[&&NHX:TOL=32046],stenopsocus perspicuus[&&NHX:TOL=32047],stenopsocus phaeostigmus[&&NHX:TOL=32048],stenopsocus phaneostriatus[&&NHX:TOL=32049],stenopsocus pilosus[&&NHX:TOL=32050],stenopsocus platynotus[&&NHX:TOL=32051],stenopsocus platyocephalus[&&NHX:TOL=32052],stenopsocus podorphus[&&NHX:TOL=32053],stenopsocus polyceratus[&&NHX:TOL=32054],stenopsocus pygmaeus[&&NHX:TOL=32055],stenopsocus radimaculatus[&&NHX:TOL=32056],stenopsocus revolutus[&&NHX:TOL=32057],stenopsocus rubellus[&&NHX:TOL=32058],stenopsocus shennongjiaensis[&&NHX:TOL=32059],stenopsocus sichuanicus[&&NHX:TOL=32060],stenopsocus signatipennis[&&NHX:TOL=32061],stenopsocus silvaticus[&&NHX:TOL=32062],stenopsocus spongiosus[&&NHX:TOL=32063],stenopsocus stigmaticus[&&NHX:TOL=32064],stenopsocus striolatus[&&NHX:TOL=32065],stenopsocus symipsarous[&&NHX:TOL=32066],stenopsocus thermophilus[&&NHX:TOL=32067],stenopsocus tibialis[&&NHX:TOL=32068],stenopsocus tonkinensis[&&NHX:TOL=32069],stenopsocus tribulbus[&&NHX:TOL=32070],stenopsocus tripartibilis[&&NHX:TOL=32071],stenopsocus trisetus[&&NHX:TOL=32072],stenopsocus turgidus[&&NHX:TOL=32073],stenopsocus uniformis[&&NHX:TOL=32074],stenopsocus wuxiaensis[&&NHX:TOL=32075],stenopsocus xanthophaeus[&&NHX:TOL=32076],stenopsocus xanthostigmus[&&NHX:TOL=32077],stenopsocus xiangxiensis[&&NHX:TOL=32078],stenopsocus xilingxianicus[&&NHX:TOL=32079],stenopsocus zoantus[&&NHX:TOL=32080])stenopsocus[&&NHX:TOL=31899])stenopsocidae[&&NHX:TOL=14468],(((dasydemella aragua[&&NHX:TOL=32085],dasydemella cirrata[&&NHX:TOL=32086],dasydemella citramans[&&NHX:TOL=32087],dasydemella colossa[&&NHX:TOL=32088],dasydemella crassistigma[&&NHX:TOL=32089],dasydemella dezayasi[&&NHX:TOL=32090],dasydemella difflusa[&&NHX:TOL=32091],dasydemella estrita[&&NHX:TOL=32092],dasydemella formosa[&&NHX:TOL=32093],dasydemella gynopeza[&&NHX:TOL=32094],dasydemella kraepelini[&&NHX:TOL=32095],dasydemella montana[&&NHX:TOL=32096],dasydemella obrienorum[&&NHX:TOL=32097],dasydemella planistigma[&&NHX:TOL=32098],dasydemella septenpunctata[&&NHX:TOL=32099],dasydemella setosa[&&NHX:TOL=32100],dasydemella sichuanana[&&NHX:TOL=32101],dasydemella silvestrii[&&NHX:TOL=32102],dasydemella stigmata[&&NHX:TOL=32103],dasydemella stipitiformis[&&NHX:TOL=32104],dasydemella xiaochuni[&&NHX:TOL=32105],dasydemella yalinana[&&NHX:TOL=32106])dasydemella[&&NHX:TOL=38110],(matsumuraiella auriformis[&&NHX:TOL=32107],matsumuraiella calocephala[&&NHX:TOL=32108],matsumuraiella compressa[&&NHX:TOL=32109],matsumuraiella enderleini[&&NHX:TOL=32110],matsumuraiella guichengana[&&NHX:TOL=32111],matsumuraiella maculosa[&&NHX:TOL=32112],matsumuraiella perducta[&&NHX:TOL=32113],matsumuraiella quadripunctata[&&NHX:TOL=32114],matsumuraiella radiopicta[&&NHX:TOL=32115],matsumuraiella wangae[&&NHX:TOL=32116])matsumuraiella[&&NHX:TOL=38111],(teliapsocus conterminus[&&NHX:TOL=32117],teliapsocus distinctus[&&NHX:TOL=32118])teliapsocus[&&NHX:TOL=38112])dasydemellinae[&&NHX:TOL=50627],ptenopsila delicatella[&&NHX:TOL=32119])dasydemellidae[&&NHX:TOL=30392])caeciliusoidea[&&NHX:TOL=30391])caeciliusetae[&&NHX:TOL=30254],(((auroropsocus conoidalis[&&NHX:TOL=32124],auroropsocus cyclocarpus[&&NHX:TOL=32125],auroropsocus flavidus[&&NHX:TOL=32126],auroropsocus fumeus[&&NHX:TOL=32127],auroropsocus orientis[&&NHX:TOL=32128],auroropsocus setotus[&&NHX:TOL=32129],auroropsocus spatiosifurcatus[&&NHX:TOL=32130],auroropsocus strenus[&&NHX:TOL=32131])auroropsocus[&&NHX:TOL=38113],(dolabellopsocus apiatus[&&NHX:TOL=32133],dolabellopsocus carcinus[&&NHX:TOL=32134],dolabellopsocus catenatus[&&NHX:TOL=32135],dolabellopsocus ctenatus[&&NHX:TOL=32136],dolabellopsocus digitatus[&&NHX:TOL=32137],dolabellopsocus ecuadorensis[&&NHX:TOL=32138],dolabellopsocus eertmoedi[&&NHX:TOL=32139],dolabellopsocus flavipennis[&&NHX:TOL=32140],dolabellopsocus furcatus[&&NHX:TOL=32141],dolabellopsocus guttatus[&&NHX:TOL=32142],dolabellopsocus incertus[&&NHX:TOL=32143],dolabellopsocus intermedius[&&NHX:TOL=32144],dolabellopsocus lobatus[&&NHX:TOL=32145],dolabellopsocus maculatus[&&NHX:TOL=32146],dolabellopsocus maculosus[&&NHX:TOL=32147],dolabellopsocus pectenatus[&&NHX:TOL=32148],dolabellopsocus pictus[&&NHX:TOL=32149],dolabellopsocus pygmaeus[&&NHX:TOL=32150],dolabellopsocus roseus[&&NHX:TOL=32151],dolabellopsocus similis[&&NHX:TOL=32152],dolabellopsocus spinosus[&&NHX:TOL=32153])dolabellopsocus[&&NHX:TOL=38114],(isthmopsocus barbatus[&&NHX:TOL=32154],isthmopsocus breviceps[&&NHX:TOL=32155],isthmopsocus hylonomus[&&NHX:TOL=32156],isthmopsocus imperfectus[&&NHX:TOL=32157],isthmopsocus lanceatus[&&NHX:TOL=32158],isthmopsocus luridus[&&NHX:TOL=32159],isthmopsocus ornatus[&&NHX:TOL=32160],isthmopsocus radulatus[&&NHX:TOL=32161],isthmopsocus speculatus[&&NHX:TOL=32162])isthmopsocus[&&NHX:TOL=38115])dolabellapsocidae[&&NHX:TOL=14465],(neurostigma chaetocephalum[&&NHX:TOL=32164],neurostigma dispositum[&&NHX:TOL=32165],neurostigma enderleini[&&NHX:TOL=32166],neurostigma furcivenula[&&NHX:TOL=32167],neurostigma paucivenosum[&&NHX:TOL=32168],neurostigma radiatum[&&NHX:TOL=32169],neurostigma roesleri[&&NHX:TOL=32170],neurostigma xanthopterum[&&NHX:TOL=32171])neurostigma[&&NHX:TOL=30256],((cladiopsocus africanus[&&NHX:TOL=32174],cladiopsocus clarus[&&NHX:TOL=32175],cladiopsocus distinctus[&&NHX:TOL=32176],cladiopsocus dolosus[&&NHX:TOL=32177],cladiopsocus domesticus[&&NHX:TOL=32178],cladiopsocus fuscus[&&NHX:TOL=32179],cladiopsocus garciai[&&NHX:TOL=32180],cladiopsocus interruptus[&&NHX:TOL=32181],cladiopsocus mockfordi[&&NHX:TOL=32182],cladiopsocus multimaculatus[&&NHX:TOL=32183],cladiopsocus ocotensis[&&NHX:TOL=32184],cladiopsocus prionotus[&&NHX:TOL=32185],cladiopsocus ramulosus[&&NHX:TOL=32186],cladiopsocus roesleri[&&NHX:TOL=32187],cladiopsocus termitophilus[&&NHX:TOL=32188],cladiopsocus uncinatus[&&NHX:TOL=32189])cladiopsocus[&&NHX:TOL=38116],(spurostigma cuba[&&NHX:TOL=32190],spurostigma dominica[&&NHX:TOL=32191],spurostigma epiroticum[&&NHX:TOL=32192],spurostigma guyana[&&NHX:TOL=32193],spurostigma hispaniola[&&NHX:TOL=32194],spurostigma insula[&&NHX:TOL=32195],spurostigma jimenezi[&&NHX:TOL=32196],spurostigma mesembria[&&NHX:TOL=32197],spurostigma nesiotis[&&NHX:TOL=32198],spurostigma panamense[&&NHX:TOL=32199],spurostigma portoricense[&&NHX:TOL=32200])spurostigma[&&NHX:TOL=38117])cladiopsocidae[&&NHX:TOL=14464],((euplocania amabilis[&&NHX:TOL=32207],euplocania badonneli[&&NHX:TOL=32208],euplocania cerata[&&NHX:TOL=32209],euplocania greeni[&&NHX:TOL=32210],euplocania maculata[&&NHX:TOL=32211],euplocania marginata[&&NHX:TOL=32212],euplocania picta[&&NHX:TOL=32213],euplocania pictaoides[&&NHX:TOL=32214],euplocania zelayensis[&&NHX:TOL=32215])euplocania[&&NHX:TOL=38118],(loneura amazonica[&&NHX:TOL=32216],loneura boliviana[&&NHX:TOL=32217],loneura brasiliensis[&&NHX:TOL=32218],loneura crenata[&&NHX:TOL=32219],loneura erwini[&&NHX:TOL=32220],loneura leonilae[&&NHX:TOL=32221],loneura leinhardi[&&NHX:TOL=32222],loneura maesi[&&NHX:TOL=32223],loneura meridionalis[&&NHX:TOL=32224],loneura mombachensis[&&NHX:TOL=32225],loneura ocotensis[&&NHX:TOL=32226],loneura quinaria[&&NHX:TOL=32227],loneura raramuri[&&NHX:TOL=32228],loneura splendida[&&NHX:TOL=32229])loneura[&&NHX:TOL=38119],perucania longiareola[&&NHX:TOL=32230],ptiloneura bidorsalis[&&NHX:TOL=32231],ptiloneuropsis immaculata[&&NHX:TOL=32232],(triplocania ariasi[&&NHX:TOL=32233],triplocania bifida[&&NHX:TOL=32234],triplocania brailovskyana[&&NHX:TOL=32235],triplocania calcarata[&&NHX:TOL=32236],triplocania caudata[&&NHX:TOL=32237],triplocania caudatoides[&&NHX:TOL=32238],triplocania cervantesi[&&NHX:TOL=32239],triplocania chiquibulensis[&&NHX:TOL=32240],triplocania chulumanensis[&&NHX:TOL=32241],triplocania columbiana[&&NHX:TOL=32242],triplocania furcata[&&NHX:TOL=32243],triplocania immaculata[&&NHX:TOL=32244],triplocania lunulata[&&NHX:TOL=32245],triplocania lurida[&&NHX:TOL=32246],triplocania maesi[&&NHX:TOL=32247],triplocania magnifica[&&NHX:TOL=32248],triplocania marginepicta[&&NHX:TOL=32249],triplocania obscura[&&NHX:TOL=32250],triplocania reflexa[&&NHX:TOL=32251],triplocania robusta[&&NHX:TOL=32252],triplocania rondoniensis[&&NHX:TOL=32253],triplocania saslayensis[&&NHX:TOL=32254],triplocania spinosa[&&NHX:TOL=32255],triplocania tambopatensis[&&NHX:TOL=32256],triplocania umbrata[&&NHX:TOL=32257],triplocania vazquezae[&&NHX:TOL=32258])triplocania[&&NHX:TOL=38120])ptiloneuridae[&&NHX:TOL=14466],((bertkauia crosbyana[&&NHX:TOL=32274],bertkauia lepicidinaria[&&NHX:TOL=32275],bertkauia loebli[&&NHX:TOL=32276],bertkauia lucifuga[&&NHX:TOL=32277],bertkauia marusiki[&&NHX:TOL=32278],bertkauia miniscula[&&NHX:TOL=32279],bertkauia remyi[&&NHX:TOL=32280],bertkauia reticularis[&&NHX:TOL=32281])bertkauia[&&NHX:TOL=32259],(cubitiglabra dayaoshanana[&&NHX:TOL=32282],cubitiglabra polyphebia[&&NHX:TOL=32283],cubitiglabra quadripunctata[&&NHX:TOL=32284])cubitiglabra[&&NHX:TOL=32260],(dichoepipsocus dictyodromus[&&NHX:TOL=32285],dichoepipsocus micropterus[&&NHX:TOL=32286],dichoepipsocus thimphuensis[&&NHX:TOL=32287])dichoepipsocus[&&NHX:TOL=32261],(dicropsocus complexus[&&NHX:TOL=32288],dicropsocus montanus[&&NHX:TOL=32289],dicropsocus rugosus[&&NHX:TOL=32290])dicropsocus[&&NHX:TOL=32262],dimidistriata longicapita[&&NHX:TOL=32132],(epipsocopsis angolensis[&&NHX:TOL=32291],epipsocopsis apicalis[&&NHX:TOL=32292],epipsocopsis basalis[&&NHX:TOL=32293],epipsocopsis cameronensis[&&NHX:TOL=32294],epipsocopsis cincta[&&NHX:TOL=32295],epipsocopsis completa[&&NHX:TOL=32296],epipsocopsis conspersa[&&NHX:TOL=32297],epipsocopsis corollifer[&&NHX:TOL=32298],epipsocopsis costalis[&&NHX:TOL=32299],epipsocopsis delicata[&&NHX:TOL=32300],epipsocopsis dubia[&&NHX:TOL=32301],epipsocopsis dugani[&&NHX:TOL=32302],epipsocopsis fasciata[&&NHX:TOL=32303],epipsocopsis formosa[&&NHX:TOL=32304],epipsocopsis fumipennis[&&NHX:TOL=32305],epipsocopsis greeni[&&NHX:TOL=32306],epipsocopsis hakgalensis[&&NHX:TOL=32307],epipsocopsis hyalina[&&NHX:TOL=32308],epipsocopsis longiceps[&&NHX:TOL=32309],epipsocopsis machadoi[&&NHX:TOL=32310],epipsocopsis maclurei[&&NHX:TOL=32311],epipsocopsis macrostigma[&&NHX:TOL=32312],epipsocopsis maculata[&&NHX:TOL=32313],epipsocopsis magna[&&NHX:TOL=32314],epipsocopsis mouldsi[&&NHX:TOL=32315],epipsocopsis murca[&&NHX:TOL=32316],epipsocopsis murphyi[&&NHX:TOL=32317],epipsocopsis nebulifera[&&NHX:TOL=32318],epipsocopsis nubilipennis[&&NHX:TOL=32319],epipsocopsis obuduensis[&&NHX:TOL=32320],epipsocopsis paraselena[&&NHX:TOL=32321],epipsocopsis peradenayensis[&&NHX:TOL=32322],epipsocopsis prominens[&&NHX:TOL=32323],epipsocopsis punctata[&&NHX:TOL=32324],epipsocopsis sclerota[&&NHX:TOL=32325],epipsocopsis selena[&&NHX:TOL=32326],epipsocopsis setosa[&&NHX:TOL=32327],epipsocopsis serpentina[&&NHX:TOL=32328],epipsocopsis singaporensis[&&NHX:TOL=32329],epipsocopsis spatulata[&&NHX:TOL=32330],epipsocopsis stuckenbergi[&&NHX:TOL=32331],epipsocopsis taprobanensis[&&NHX:TOL=32332],epipsocopsis thailandensis[&&NHX:TOL=32333],epipsocopsis truncatula[&&NHX:TOL=32334],epipsocopsis vilhenai[&&NHX:TOL=32335])epipsocopsis[&&NHX:TOL=32263],(epipsocus acanthus[&&NHX:TOL=32336],epipsocus africanus[&&NHX:TOL=32337],epipsocus argentinus[&&NHX:TOL=32338],epipsocus argutus[&&NHX:TOL=32339],epipsocus atratus[&&NHX:TOL=32340],epipsocus badonneli[&&NHX:TOL=32341],epipsocus beguiristaini[&&NHX:TOL=32342],epipsocus blandus[&&NHX:TOL=32343],epipsocus borgmeieri[&&NHX:TOL=32344],epipsocus bullocki[&&NHX:TOL=32345],epipsocus euryocephalus[&&NHX:TOL=32346],epipsocus fasciicornis[&&NHX:TOL=32347],epipsocus foliatus[&&NHX:TOL=32348],epipsocus fuscareolatus[&&NHX:TOL=32349],epipsocus hageni[&&NHX:TOL=32350],epipsocus latistigma[&&NHX:TOL=32351],epipsocus maculithorax[&&NHX:TOL=32352],epipsocus marginatus[&&NHX:TOL=32353],epipsocus meruleus[&&NHX:TOL=32354],epipsocus nepos[&&NHX:TOL=32355],epipsocus opticus[&&NHX:TOL=32356],epipsocus pennyi[&&NHX:TOL=32357],epipsocus pereirai[&&NHX:TOL=32358],epipsocus petenensis[&&NHX:TOL=32359],epipsocus phaeus[&&NHX:TOL=32360],epipsocus pinnatus[&&NHX:TOL=32361],epipsocus quurcus[&&NHX:TOL=32362],epipsocus rhabdolepis[&&NHX:TOL=32363],epipsocus roraimensis[&&NHX:TOL=32364],epipsocus scotothoracalis[&&NHX:TOL=32365],epipsocus serenus[&&NHX:TOL=32366],epipsocus spatulatus[&&NHX:TOL=32367],epipsocus stictus[&&NHX:TOL=32368],epipsocus stigmaticus[&&NHX:TOL=32369],epipsocus uniformis[&&NHX:TOL=32370],epipsocus verrucosus[&&NHX:TOL=32371],epipsocus viiv[&&NHX:TOL=32372],epipsocus willineri[&&NHX:TOL=32373],epipsocus xanthothoracalis[&&NHX:TOL=32374])epipsocus[&&NHX:TOL=32264],(goja acuphallica[&&NHX:TOL=32375],goja aviceps[&&NHX:TOL=32376],goja bimaculata[&&NHX:TOL=32377],goja bogotana[&&NHX:TOL=32378],goja brailovskyana[&&NHX:TOL=32379],goja chilensis[&&NHX:TOL=32380],goja circumvittata[&&NHX:TOL=32381],goja cornuta[&&NHX:TOL=32382],goja cubitalis[&&NHX:TOL=32383],goja curvata[&&NHX:TOL=32384],goja ditata[&&NHX:TOL=32385],goja eertmoedi[&&NHX:TOL=32386],goja erwini[&&NHX:TOL=32387],goja guatemalensis[&&NHX:TOL=32388],goja herrerae[&&NHX:TOL=32389],goja latiphallica[&&NHX:TOL=32390],goja longiareola[&&NHX:TOL=32391],goja longispinosa[&&NHX:TOL=32392],goja martinezi[&&NHX:TOL=32393],goja medellini[&&NHX:TOL=32394],goja mockfordi[&&NHX:TOL=32395],goja molinai[&&NHX:TOL=32396],goja montieli[&&NHX:TOL=32397],goja moyai[&&NHX:TOL=32398],goja nebulosa[&&NHX:TOL=32399],goja obrienorum[&&NHX:TOL=32400],goja ochoterenae[&&NHX:TOL=32401],goja ocotensis[&&NHX:TOL=32402],goja oculatissima[&&NHX:TOL=32403],goja omiltemensis[&&NHX:TOL=32404],goja pallida[&&NHX:TOL=32405],goja pechi[&&NHX:TOL=32406],goja picta[&&NHX:TOL=32407],goja plaumanni[&&NHX:TOL=32408],goja poblana[&&NHX:TOL=32409],goja reticulata[&&NHX:TOL=32410],goja reticulatoides[&&NHX:TOL=32411],goja robusta[&&NHX:TOL=32412],goja semiaptera[&&NHX:TOL=32413],goja spiculata[&&NHX:TOL=32414],goja spinosissima[&&NHX:TOL=32415],goja ticana[&&NHX:TOL=32416],goja trinidadensis[&&NHX:TOL=32417],goja venezuelensis[&&NHX:TOL=32418],goja vittata[&&NHX:TOL=32419])goja[&&NHX:TOL=32265],(heteroepipsocus brevicellus[&&NHX:TOL=32420],heteroepipsocus inornatus[&&NHX:TOL=32421],heteroepipsocus longicellus[&&NHX:TOL=32422],heteroepipsocus maculatus[&&NHX:TOL=32423])heteroepipsocus[&&NHX:TOL=32266],(hinduipsocus annulipes[&&NHX:TOL=32424],hinduipsocus atratus[&&NHX:TOL=32425],hinduipsocus coleoptratus[&&NHX:TOL=32426],hinduipsocus hongkongensis[&&NHX:TOL=32427])hinduipsocus[&&NHX:TOL=32267],liratepipsocus jinghongicus[&&NHX:TOL=32268],(mesepipsocus andrewsi[&&NHX:TOL=32429],mesepipsocus antillanus[&&NHX:TOL=32430],mesepipsocus arborescens[&&NHX:TOL=32431],mesepipsocus bordoni[&&NHX:TOL=32432],mesepipsocus brasilianus[&&NHX:TOL=32433],mesepipsocus brasiliensis[&&NHX:TOL=32434],mesepipsocus brevistigma[&&NHX:TOL=32435],mesepipsocus broadheadi[&&NHX:TOL=32436],mesepipsocus brunellus[&&NHX:TOL=32437],mesepipsocus campanulatus[&&NHX:TOL=32438],mesepipsocus capitulatus[&&NHX:TOL=32439],mesepipsocus clarus[&&NHX:TOL=32440],mesepipsocus fuscatus[&&NHX:TOL=32441],mesepipsocus fuscivenatus[&&NHX:TOL=32442],mesepipsocus icarus[&&NHX:TOL=32443],mesepipsocus latiphallus[&&NHX:TOL=32444],mesepipsocus mobilis[&&NHX:TOL=32445],mesepipsocus mockfordi[&&NHX:TOL=32446],mesepipsocus newi[&&NHX:TOL=32447],mesepipsocus niger[&&NHX:TOL=32448],mesepipsocus obscurus[&&NHX:TOL=32449],mesepipsocus peruanus[&&NHX:TOL=32450],mesepipsocus proctus[&&NHX:TOL=32451],mesepipsocus roesleri[&&NHX:TOL=32452],mesepipsocus roncadorensis[&&NHX:TOL=32453],mesepipsocus semiclarus[&&NHX:TOL=32454],mesepipsocus sinuatus[&&NHX:TOL=32455],mesepipsocus taitubai[&&NHX:TOL=32456],mesepipsocus tambopatensis[&&NHX:TOL=32457],mesepipsocus umbratus[&&NHX:TOL=32458])mesepipsocus[&&NHX:TOL=32269],metepipsocus beijingicus[&&NHX:TOL=32270],(odontopsocus badonneli[&&NHX:TOL=32460],odontopsocus compactus[&&NHX:TOL=32461],odontopsocus orghidani[&&NHX:TOL=32462])odontopsocus[&&NHX:TOL=32271],(spordoepipsocus imperforatus[&&NHX:TOL=32463],spordoepipsocus perforatus[&&NHX:TOL=32464],spordoepipsocus subtilis[&&NHX:TOL=32465])spordoepipsocus[&&NHX:TOL=32272],valvepipsocus diodematus[&&NHX:TOL=32273])epipsocidae[&&NHX:TOL=14463],parepipsocus obscurus[&&NHX:TOL=50619])epipsocetae[&&NHX:TOL=30255])[&&NHX:TOL=30219],((archipsocopsis[&&NHX:TOL=32467],archipsocus[&&NHX:TOL=32468])archipsocinae[&&NHX:TOL=50635],(notarchipsocus[&&NHX:TOL=32469],pararchipsocus[&&NHX:TOL=32470],pseudoarchipsocus[&&NHX:TOL=32471])pararchipsocinae[&&NHX:TOL=50636])archipsocidae[&&NHX:TOL=14477])psocomorpha[&&NHX:TOL=30218],((((((((((haematopinus acuticeps[&&NHX:TOL=69530],haematopinus apri[&&NHX:TOL=69531],haematopinus asini[&&NHX:TOL=69532],haematopinus bufali[&&NHX:TOL=69533],haematopinus breviculus[&&NHX:TOL=69534],haematopinus channabasavannai[&&NHX:TOL=69535],haematopinus eurysternus[&&NHX:TOL=69536],haematopinus gorgonis[&&NHX:TOL=69537],haematopinus jeannereti[&&NHX:TOL=69538],haematopinus ludwigi[&&NHX:TOL=69539],haematopinus longus[&&NHX:TOL=69540],haematopinus latus[&&NHX:TOL=69541],haematopinus meinertzhageni[&&NHX:TOL=69542],haematopinus nigricantis[&&NHX:TOL=69543],haematopinus oliveri[&&NHX:TOL=69544],haematopinus oryx[&&NHX:TOL=69545],haematopinus phacochoeri[&&NHX:TOL=69546],haematopinus quadripertusus[&&NHX:TOL=69547],haematopinus suis[&&NHX:TOL=69548],haematopinus tuberculatus[&&NHX:TOL=69549],haematopinus taurotragi[&&NHX:TOL=69550])haematopinus[&&NHX:TOL=13671],hybophthirus notophallus[&&NHX:TOL=13670])[&&NHX:TOL=72061],((ratemia asiatica[&&NHX:TOL=69773],ratemia bassoni[&&NHX:TOL=69774],ratemia squamulata[&&NHX:TOL=69775])ratemia[&&NHX:TOL=13658],((((prolinognathus aethiopicus[&&NHX:TOL=69805],prolinognathus arcuatus[&&NHX:TOL=69806],prolinognathus caviaecapensis[&&NHX:TOL=69807],prolinognathus faini[&&NHX:TOL=69808],prolinognathus foleyi[&&NHX:TOL=69809],prolinognathus ferrisi[&&NHX:TOL=69810],prolinognathus leptocephalus[&&NHX:TOL=69811],prolinognathus schulzi[&&NHX:TOL=69812])prolinognathus[&&NHX:TOL=69273],(linognathus africanus[&&NHX:TOL=69577],linognathus angasi[&&NHX:TOL=69578],linognathus angulatus[&&NHX:TOL=69579],linognathus armatus[&&NHX:TOL=69580],linognathus aepycerus[&&NHX:TOL=69581],linognathus antidorcitis[&&NHX:TOL=69582],linognathus antennatus[&&NHX:TOL=69583],linognathus bedfordi[&&NHX:TOL=69584],linognathus bhatii[&&NHX:TOL=69585],linognathus brevicornis[&&NHX:TOL=69586],linognathus breviceps[&&NHX:TOL=69587],linognathus contractus[&&NHX:TOL=69588],linognathus cervicaprae[&&NHX:TOL=69589],linognathus digitalis[&&NHX:TOL=69590],linognathus damaliscus[&&NHX:TOL=69591],linognathus damarensis[&&NHX:TOL=69592],linognathus elblae[&&NHX:TOL=69593],linognathus euchore[&&NHX:TOL=69594],linognathus fahrenholzi[&&NHX:TOL=69595],linognathus fenneci[&&NHX:TOL=69596],linognathus fractus[&&NHX:TOL=69597],linognathus gorgonus[&&NHX:TOL=69598],linognathus geigyi[&&NHX:TOL=69599],linognathus gonolobatus[&&NHX:TOL=69600],linognathus gnu[&&NHX:TOL=69601],linognathus hippotragi[&&NHX:TOL=69602],linognathus kimi[&&NHX:TOL=69603],linognathus limnotragi[&&NHX:TOL=69604],linognathus lewisi[&&NHX:TOL=69605],linognathus nesotragi[&&NHX:TOL=69606],linognathus nevilli[&&NHX:TOL=69607],linognathus ourebiae[&&NHX:TOL=69608],linognathus oryx[&&NHX:TOL=69609],linognathus oviformis[&&NHX:TOL=69610],linognathus ovillus[&&NHX:TOL=69611],linognathus pedalis[&&NHX:TOL=69612],linognathus peleus[&&NHX:TOL=69613],linognathus panamensis[&&NHX:TOL=69614],linognathus pithodes[&&NHX:TOL=69615],linognathus petasmatus[&&NHX:TOL=69616],linognathus reduncae[&&NHX:TOL=69617],linognathus raphiceri[&&NHX:TOL=69618],linognathus saccatus[&&NHX:TOL=69619],linognathus sosninae[&&NHX:TOL=69620],linognathus stenopsis[&&NHX:TOL=69621],linognathus spicatus[&&NHX:TOL=69622],linognathus setosus[&&NHX:TOL=69623],linognathus tibialis[&&NHX:TOL=69624],linognathus taeniotrichus[&&NHX:TOL=69625],linognathus taurotragus[&&NHX:TOL=69626],linognathus vituli[&&NHX:TOL=69627],linognathus vulpis[&&NHX:TOL=69628],linognathus zumpti[&&NHX:TOL=69629])linognathus[&&NHX:TOL=69258])[&&NHX:TOL=72095],(solenopotes burmeisteri[&&NHX:TOL=69779],solenopotes binipilosus[&&NHX:TOL=69780],solenopotes capillatus[&&NHX:TOL=69781],solenopotes capreoli[&&NHX:TOL=69782],solenopotes ferrisi[&&NHX:TOL=69783],solenopotes hologastrus[&&NHX:TOL=69784],solenopotes muntiacus[&&NHX:TOL=69785],solenopotes natalensis[&&NHX:TOL=69786],solenopotes tarandi[&&NHX:TOL=69787])solenopotes[&&NHX:TOL=69280])linognathidae[&&NHX:TOL=13651],(((microthoracius cameli[&&NHX:TOL=69632],microthoracius minor[&&NHX:TOL=69633],microthoracius mazzai[&&NHX:TOL=69634],microthoracius praelongiceps[&&NHX:TOL=69635])microthoracius[&&NHX:TOL=13660],(((antarctophthirus callorhini[&&NHX:TOL=69285],antarctophthirus lobodontis[&&NHX:TOL=69286],antarctophthirus mawsoni[&&NHX:TOL=69287],antarctophthirus microchir[&&NHX:TOL=69288],antarctophthirus ogmorhini[&&NHX:TOL=69289],antarctophthirus trichechi[&&NHX:TOL=69290])antarctophthirus[&&NHX:TOL=69235],(lepidophthirus macrorhini[&&NHX:TOL=69560],lepidophthirus piriformis[&&NHX:TOL=69561])lepidophthirus[&&NHX:TOL=69256])[&&NHX:TOL=72098],echinophthirius horridus[&&NHX:TOL=69300],latagophthirus rauschi[&&NHX:TOL=69576],(proechinophthirus fluctus[&&NHX:TOL=69813],proechinophthirus zumpti[&&NHX:TOL=69814])proechinophthirus[&&NHX:TOL=69271])echinophthiriidae[&&NHX:TOL=13661])[&&NHX:TOL=72097],(neolinognathus elephantuli[&&NHX:TOL=69667],neolinognathus praelautus[&&NHX:TOL=69668])neolinognathus[&&NHX:TOL=13654])[&&NHX:TOL=72096])[&&NHX:TOL=72062])[&&NHX:TOL=13657])[&&NHX:TOL=13656],((hamophthirius galeopitheci[&&NHX:TOL=13655],((pedicinus albidus[&&NHX:TOL=69753],pedicinus ancoratus[&&NHX:TOL=69754],pedicinus badii[&&NHX:TOL=69755],pedicinus colobi[&&NHX:TOL=69756],pedicinus cercocebi[&&NHX:TOL=69757],pedicinus cynopitheci[&&NHX:TOL=69758],pedicinus eurygaster[&&NHX:TOL=69759],pedicinus ferrisi[&&NHX:TOL=69760],pedicinus hamadryas[&&NHX:TOL=69761],pedicinus miopitheci[&&NHX:TOL=69762],pedicinus obtusus[&&NHX:TOL=69763],pedicinus pictus[&&NHX:TOL=69764],pedicinus patas[&&NHX:TOL=69765],pedicinus veri[&&NHX:TOL=69766])pedicinus[&&NHX:TOL=13667],pecaroecus javalii[&&NHX:TOL=13668],((pediculus humanus[&&NHX:TOL=69669],pediculus mjöbergi[&&NHX:TOL=69670],pediculus schaeffi[&&NHX:TOL=69671])pediculus[&&NHX:TOL=13672],(pthirus gorillae[&&NHX:TOL=69672],pthirus pubis[&&NHX:TOL=69673])pthirus[&&NHX:TOL=13666])[&&NHX:TOL=72087])[&&NHX:TOL=13662])[&&NHX:TOL=72065],((cuyana maurii[&&NHX:TOL=69298],(lemurpediculus petterorum[&&NHX:TOL=69558],lemurpediculus verruculosus[&&NHX:TOL=69559])lemurpediculus[&&NHX:TOL=69254],typhlomyophthirus bifoliatus[&&NHX:TOL=69798],(((scipio aulacodi[&&NHX:TOL=69776],scipio breviceps[&&NHX:TOL=69777],scipio tripedatus[&&NHX:TOL=69778])scipio[&&NHX:TOL=69279],((phthirpediculus avahidis[&&NHX:TOL=69770],phthirpediculus brygooi[&&NHX:TOL=69771],phthirpediculus propitheci[&&NHX:TOL=69772])phthirpediculus[&&NHX:TOL=69268],(galeophthirus caviae[&&NHX:TOL=69385],((docophthirus acinetus[&&NHX:TOL=69299],lagidiophthirus parvus[&&NHX:TOL=69557])[&&NHX:TOL=72071],((eulinognathus aculeatus[&&NHX:TOL=69301],eulinognathus allactagae[&&NHX:TOL=69302],eulinognathus americanus[&&NHX:TOL=69303],eulinognathus alactaguli[&&NHX:TOL=69304],eulinognathus bolivianus[&&NHX:TOL=69306],eulinognathus biuncatus[&&NHX:TOL=69307],eulinognathus cardiocranius[&&NHX:TOL=69308],eulinognathus dipodis[&&NHX:TOL=69309],eulinognathus denticulatus[&&NHX:TOL=69310],eulinognathus euchoreutae[&&NHX:TOL=69311],eulinognathus elateri[&&NHX:TOL=69312],eulinognathus eremodipodis[&&NHX:TOL=69313],eulinognathus gentilis[&&NHX:TOL=69314],eulinognathus hilli[&&NHX:TOL=69315],eulinognathus hepperi[&&NHX:TOL=69316],eulinognathus hesperius[&&NHX:TOL=69317],eulinognathus hypogeomydis[&&NHX:TOL=69318],eulinognathus inermis[&&NHX:TOL=69319],eulinognathus jaculi[&&NHX:TOL=69320],eulinognathus lophiomydis[&&NHX:TOL=69321],eulinognathus lawrensis[&&NHX:TOL=69322],eulinognathus pygerethmi[&&NHX:TOL=69323],eulinognathus patagonicus[&&NHX:TOL=69324],eulinognathus scirtopodae[&&NHX:TOL=69325],eulinognathus tokmaki[&&NHX:TOL=69326],eulinognathus torquatus[&&NHX:TOL=69327],eulinognathus wernecki[&&NHX:TOL=69328])eulinognathus[&&NHX:TOL=69242],((fahrenholzia boleni[&&NHX:TOL=69305],fahrenholzia ehrlichi[&&NHX:TOL=69374],fahrenholzia fairchildi[&&NHX:TOL=69375],fahrenholzia ferrisi[&&NHX:TOL=69376],fahrenholzia hertigi[&&NHX:TOL=69377],fahrenholzia microcephala[&&NHX:TOL=69378],fahrenholzia pinnata[&&NHX:TOL=69379],fahrenholzia reducta[&&NHX:TOL=69380],fahrenholzia schwartzi[&&NHX:TOL=69381],fahrenholzia tribulosa[&&NHX:TOL=69382],fahrenholzia texana[&&NHX:TOL=69383],fahrenholzia zacatecae[&&NHX:TOL=69384])fahrenholzia[&&NHX:TOL=69243],(haemodipsus africanus[&&NHX:TOL=69522],haemodipsus conformalis[&&NHX:TOL=69523],haemodipsus leporis[&&NHX:TOL=69524],haemodipsus lyriocephalus[&&NHX:TOL=69525],haemodipsus setoni[&&NHX:TOL=69526],haemodipsus ventricosus[&&NHX:TOL=69527])haemodipsus[&&NHX:TOL=69247])[&&NHX:TOL=72073])[&&NHX:TOL=72072])[&&NHX:TOL=72070])[&&NHX:TOL=72069])[&&NHX:TOL=72068])[&&NHX:TOL=72067],(proenderleinellus calva[&&NHX:TOL=69769],((linognathoides baibacinae[&&NHX:TOL=69565],linognathoides citelli[&&NHX:TOL=69566],linognathoides cynomyis[&&NHX:TOL=69567],linognathoides faurei[&&NHX:TOL=69568],linognathoides laeviusculus[&&NHX:TOL=69569],linognathoides marmotae[&&NHX:TOL=69570],linognathoides palaearctus[&&NHX:TOL=69571],linognathoides pectinifer[&&NHX:TOL=69572],linognathoides relictus[&&NHX:TOL=69573],linognathoides schizodactylus[&&NHX:TOL=69574],linognathoides traubi[&&NHX:TOL=69575])linognathoides[&&NHX:TOL=69257],(((johnsonpthirus chlorotalpae[&&NHX:TOL=69552],johnsonpthirus heliosciuri[&&NHX:TOL=69553],johnsonpthirus keniae[&&NHX:TOL=69554],johnsonpthirus suahelicus[&&NHX:TOL=69555],johnsonpthirus spinosissimus[&&NHX:TOL=69556])johnsonpthirus[&&NHX:TOL=69251],((abrocomaphthirus chilensis[&&NHX:TOL=69283],abrocomaphthirus longus[&&NHX:TOL=69284])abrocomaphthirus[&&NHX:TOL=69233],ctenophthirus cercomydis[&&NHX:TOL=69820])[&&NHX:TOL=72078])[&&NHX:TOL=72077],(microphthirus uncinatus[&&NHX:TOL=69630],((polyplax acomydis[&&NHX:TOL=69674],polyplax antennata[&&NHX:TOL=69675],polyplax arvicanthis[&&NHX:TOL=69676],polyplax asiatica[&&NHX:TOL=69677],polyplax alaskensis[&&NHX:TOL=69678],polyplax auricularis[&&NHX:TOL=69679],polyplax abyssinica[&&NHX:TOL=69680],polyplax brachyuromyis[&&NHX:TOL=69681],polyplax blanfordi[&&NHX:TOL=69682],polyplax borealis[&&NHX:TOL=69683],polyplax brachyrrhyncha[&&NHX:TOL=69684],polyplax bureschi[&&NHX:TOL=69685],polyplax biseriata[&&NHX:TOL=69686],polyplax bullimae[&&NHX:TOL=69687],polyplax chinensis[&&NHX:TOL=69688],polyplax caluri[&&NHX:TOL=69689],polyplax cummingsi[&&NHX:TOL=69690],polyplax calomysci[&&NHX:TOL=69691],polyplax cannomydis[&&NHX:TOL=69692],polyplax cutchicus[&&NHX:TOL=69693],polyplax dacnomydis[&&NHX:TOL=69694],polyplax deomydis[&&NHX:TOL=69695],polyplax dolichura[&&NHX:TOL=69696],polyplax dentaticornis[&&NHX:TOL=69697],polyplax ellobii[&&NHX:TOL=69698],polyplax eropepli[&&NHX:TOL=69699],polyplax expressa[&&NHX:TOL=69700],polyplax grammomydis[&&NHX:TOL=69701],polyplax gerbilli[&&NHX:TOL=69702],polyplax gracilis[&&NHX:TOL=69703],polyplax guatemalensis[&&NHX:TOL=69704],polyplax hannswrangeli[&&NHX:TOL=69705],polyplax hoogstraali[&&NHX:TOL=69706],polyplax hopkinsi[&&NHX:TOL=69707],polyplax humae[&&NHX:TOL=69708],polyplax hurrianicus[&&NHX:TOL=69709],polyplax indica[&&NHX:TOL=69710],polyplax insulsa[&&NHX:TOL=69711],polyplax jonesi[&&NHX:TOL=69712],polyplax kondana[&&NHX:TOL=69713],polyplax kaiseri[&&NHX:TOL=69714],polyplax miacantha[&&NHX:TOL=69715],polyplax melasmothrixi[&&NHX:TOL=69716],polyplax meridionalis[&&NHX:TOL=69717],polyplax myotomydis[&&NHX:TOL=69718],polyplax nesomydis[&&NHX:TOL=69719],polyplax opimi[&&NHX:TOL=69720],polyplax oxyrrhyncha[&&NHX:TOL=69721],polyplax otomydis[&&NHX:TOL=69722],polyplax paradoxa[&&NHX:TOL=69723],polyplax phthisica[&&NHX:TOL=69724],polyplax phloemydis[&&NHX:TOL=69725],polyplax plesia[&&NHX:TOL=69726],polyplax praecisa[&&NHX:TOL=69727],polyplax pricei[&&NHX:TOL=69728],polyplax praomydis[&&NHX:TOL=69729],polyplax parataterae[&&NHX:TOL=69730],polyplax qiuae[&&NHX:TOL=69731],polyplax rhizomydis[&&NHX:TOL=69732],polyplax reclinata[&&NHX:TOL=69733],polyplax roseinnesi[&&NHX:TOL=69734],polyplax subtaterae[&&NHX:TOL=69735],polyplax sindensis[&&NHX:TOL=69736],polyplax smallwoodae[&&NHX:TOL=69737],polyplax solivaga[&&NHX:TOL=69738],polyplax spinigera[&&NHX:TOL=69739],polyplax stephensi[&&NHX:TOL=69740],polyplax spinulosa[&&NHX:TOL=69741],polyplax serrata[&&NHX:TOL=69742],polyplax steatomydis[&&NHX:TOL=69743],polyplax thamnomydis[&&NHX:TOL=69744],polyplax tarsomydis[&&NHX:TOL=69745],polyplax taterae[&&NHX:TOL=69746],polyplax vacillata[&&NHX:TOL=69747],polyplax vicina[&&NHX:TOL=69748],polyplax visenda[&&NHX:TOL=69749],polyplax waterstoni[&&NHX:TOL=69750],polyplax wallacei[&&NHX:TOL=69751],polyplax werneri[&&NHX:TOL=69752])polyplax[&&NHX:TOL=69270],((neohaematopinus appressus[&&NHX:TOL=69636],neohaematopinus batuanae[&&NHX:TOL=69637],neohaematopinus chinensis[&&NHX:TOL=69638],neohaematopinus ceylonicus[&&NHX:TOL=69639],neohaematopinus cognatus[&&NHX:TOL=69640],neohaematopinus callosciuri[&&NHX:TOL=69641],neohaematopinus citellinus[&&NHX:TOL=69642],neohaematopinus capitaneus[&&NHX:TOL=69643],neohaematopinus elbeli[&&NHX:TOL=69644],neohaematopinus echinatus[&&NHX:TOL=69645],neohaematopinus griseicolus[&&NHX:TOL=69646],neohaematopinus inornatus[&&NHX:TOL=69647],neohaematopinus kinabalensis[&&NHX:TOL=69648],neohaematopinus menetensis[&&NHX:TOL=69649],neohaematopinus neotomae[&&NHX:TOL=69650],neohaematopinus pallidus[&&NHX:TOL=69651],neohaematopinus pacificus[&&NHX:TOL=69652],neohaematopinus pteromydis[&&NHX:TOL=69653],neohaematopinus pansus[&&NHX:TOL=69654],neohaematopinus petauristae[&&NHX:TOL=69655],neohaematopinus qadrii[&&NHX:TOL=69656],neohaematopinus robustus[&&NHX:TOL=69657],neohaematopinus rupestis[&&NHX:TOL=69658],neohaematopinus sciurinus[&&NHX:TOL=69659],neohaematopinus sciuropteri[&&NHX:TOL=69660],neohaematopinus sciuri[&&NHX:TOL=69661],neohaematopinus sundasciuri[&&NHX:TOL=69662],neohaematopinus spilosomae[&&NHX:TOL=69663],neohaematopinus semifasciatus[&&NHX:TOL=69664],neohaematopinus setosus[&&NHX:TOL=69665],neohaematopinus syriacus[&&NHX:TOL=69666])neohaematopinus[&&NHX:TOL=69262],((lemurphthirus galagus[&&NHX:TOL=69562],lemurphthirus stigmosus[&&NHX:TOL=69563],lemurphthirus vincenti[&&NHX:TOL=69564])lemurphthirus[&&NHX:TOL=69255],sathrax durus[&&NHX:TOL=69788])[&&NHX:TOL=72085])[&&NHX:TOL=72084])[&&NHX:TOL=72083])[&&NHX:TOL=72079])[&&NHX:TOL=72076])[&&NHX:TOL=72075])[&&NHX:TOL=72074])[&&NHX:TOL=72066])polyplacidae[&&NHX:TOL=13650],(((schizophthirus aethogliris[&&NHX:TOL=69789],schizophthirus dryomydis[&&NHX:TOL=69790],schizophthirus gliris[&&NHX:TOL=69791],schizophthirus graphiuri[&&NHX:TOL=69792],schizophthirus jaczewskii[&&NHX:TOL=69793],schizophthirus pleurophaeus[&&NHX:TOL=69794],schizophthirus similes[&&NHX:TOL=69795],schizophthirus singularis[&&NHX:TOL=69796],schizophthirus sicistae[&&NHX:TOL=69797])schizophthirus[&&NHX:TOL=69278],haematopinoides squamosus[&&NHX:TOL=69528])[&&NHX:TOL=72088],((ancistroplax crocidurae[&&NHX:TOL=69291],ancistroplax chodsigoae[&&NHX:TOL=69292],ancistroplax nasuta[&&NHX:TOL=69294],ancistroplax nepalensis[&&NHX:TOL=69293],ancistroplax taiwanensis[&&NHX:TOL=69295])ancistroplax[&&NHX:TOL=69234],(paradoxophthirus emarginata[&&NHX:TOL=69768],((hoplopleura abeli[&&NHX:TOL=69387],hoplopleura arboricola[&&NHX:TOL=69386],hoplopleura affinis[&&NHX:TOL=69388],hoplopleura argentina[&&NHX:TOL=69389],hoplopleura aethomydis[&&NHX:TOL=69390],hoplopleura aitkeni[&&NHX:TOL=69391],hoplopleura akanezumi[&&NHX:TOL=69392],hoplopleura andina[&&NHX:TOL=69393],hoplopleura angulata[&&NHX:TOL=69394],hoplopleura apomydis[&&NHX:TOL=69395],hoplopleura alticola[&&NHX:TOL=69396],hoplopleura acanthopus[&&NHX:TOL=69397],hoplopleura arizonensis[&&NHX:TOL=69398],hoplopleura bidentata[&&NHX:TOL=69399],hoplopleura blanfordi[&&NHX:TOL=69400],hoplopleura brasiliensis[&&NHX:TOL=69401],hoplopleura biseriata[&&NHX:TOL=69402],hoplopleura captiosa[&&NHX:TOL=69403],hoplopleura calabyi[&&NHX:TOL=69404],hoplopleura cricetuli[&&NHX:TOL=69405],hoplopleura confuciana[&&NHX:TOL=69406],hoplopleura delticola[&&NHX:TOL=69425],hoplopleura chilensis[&&NHX:TOL=69407],hoplopleura colomydis[&&NHX:TOL=69408],hoplopleura cooki[&&NHX:TOL=69409],hoplopleura chippauxi[&&NHX:TOL=69410],hoplopleura capensis[&&NHX:TOL=69411],hoplopleura cryptica[&&NHX:TOL=69412],hoplopleura cornata[&&NHX:TOL=69413],hoplopleura chrysocomi[&&NHX:TOL=69414],hoplopleura contigua[&&NHX:TOL=69415],hoplopleura cutchicus[&&NHX:TOL=69416],hoplopleura chrotomydis[&&NHX:TOL=69417],hoplopleura dendromuris[&&NHX:TOL=69418],hoplopleura difficilis[&&NHX:TOL=69419],hoplopleura disgrega[&&NHX:TOL=69420],hoplopleura diaphora[&&NHX:TOL=69421],hoplopleura dissicula[&&NHX:TOL=69422],hoplopleura dissimilis[&&NHX:TOL=69423],hoplopleura distorta[&&NHX:TOL=69424],hoplopleura edentula[&&NHX:TOL=69426],hoplopleura enormis[&&NHX:TOL=69427],hoplopleura emphereia[&&NHX:TOL=69428],hoplopleura erismata[&&NHX:TOL=69429],hoplopleura erratica[&&NHX:TOL=69430],hoplopleura exima[&&NHX:TOL=69431],hoplopleura fonsecai[&&NHX:TOL=69432],hoplopleura ferrisi[&&NHX:TOL=69433],hoplopleura funambuli[&&NHX:TOL=69434],hoplopleura gyomydis[&&NHX:TOL=69435],hoplopleura griseoflavae[&&NHX:TOL=69436],hoplopleura handleyi[&&NHX:TOL=69437],hoplopleura himalayana[&&NHX:TOL=69438],hoplopleura himenezumi[&&NHX:TOL=69439],hoplopleura hesperomydis[&&NHX:TOL=69440],hoplopleura hispida[&&NHX:TOL=69441],hoplopleura hirsuta[&&NHX:TOL=69442],hoplopleura hybomyis[&&NHX:TOL=69443],hoplopleura indiscreta[&&NHX:TOL=69444],hoplopleura inagakii[&&NHX:TOL=69445],hoplopleura imparata[&&NHX:TOL=69446],hoplopleura ingens[&&NHX:TOL=69447],hoplopleura inusitata[&&NHX:TOL=69448],hoplopleura inexpectans[&&NHX:TOL=69452],hoplopleura intermedia[&&NHX:TOL=69451],hoplopleura ismailiae[&&NHX:TOL=69450],hoplopleura irritans[&&NHX:TOL=69449],hoplopleura johnsonae[&&NHX:TOL=69453],hoplopleura khandala[&&NHX:TOL=69454],hoplopleura kondana[&&NHX:TOL=69455],hoplopleura karachiensis[&&NHX:TOL=69456],hoplopleura kitti[&&NHX:TOL=69457],hoplopleura laticeps[&&NHX:TOL=69458],hoplopleura longula[&&NHX:TOL=69459],hoplopleura meridionidis[&&NHX:TOL=69460],hoplopleura mendezi[&&NHX:TOL=69461],hoplopleura malabarica[&&NHX:TOL=69462],hoplopleura mulleri[&&NHX:TOL=69463],hoplopleura maniculata[&&NHX:TOL=69464],hoplopleura mendozana[&&NHX:TOL=69465],hoplopleura misionalis[&&NHX:TOL=69466],hoplopleura minasensis[&&NHX:TOL=69467],hoplopleura oxymycteri[&&NHX:TOL=69482],hoplopleura mastacomydis[&&NHX:TOL=69468],hoplopleura musseri[&&NHX:TOL=69469],hoplopleura multilobata[&&NHX:TOL=69470],hoplopleura minuta[&&NHX:TOL=69471],hoplopleura mylomydis[&&NHX:TOL=69472],hoplopleura malaysiana[&&NHX:TOL=69473],hoplopleura myomyis[&&NHX:TOL=69474],hoplopleura neumanni[&&NHX:TOL=69475],hoplopleura nesoryzomydis[&&NHX:TOL=69476],hoplopleura nasvikae[&&NHX:TOL=69477],hoplopleura ochotonae[&&NHX:TOL=69478],hoplopleura ondatraria[&&NHX:TOL=69479],hoplopleura oenomydis[&&NHX:TOL=69480],hoplopleura orinocoi[&&NHX:TOL=69481],hoplopleura oryzomydis[&&NHX:TOL=69483],hoplopleura onychomydis[&&NHX:TOL=69484],hoplopleura pacifica[&&NHX:TOL=69485],hoplopleura patersoni[&&NHX:TOL=69486],hoplopleura pavlovskyi[&&NHX:TOL=69487],hoplopleura pahari[&&NHX:TOL=69488],hoplopleura pelomydis[&&NHX:TOL=69489],hoplopleura phaiomydis[&&NHX:TOL=69490],hoplopleura pectinata[&&NHX:TOL=69491],hoplopleura quadridentata[&&NHX:TOL=69492],hoplopleura reducta[&&NHX:TOL=69493],hoplopleura ramgarh[&&NHX:TOL=69494],hoplopleura rajah[&&NHX:TOL=69495],hoplopleura rukenyae[&&NHX:TOL=69496],hoplopleura rimae[&&NHX:TOL=69497],hoplopleura reithrodontomyis[&&NHX:TOL=69498],hoplopleura spiculifer[&&NHX:TOL=69499],hoplopleura sicata[&&NHX:TOL=69500],hoplopleura sinhgarh[&&NHX:TOL=69501],hoplopleura sembeli[&&NHX:TOL=69502],hoplopleura similis[&&NHX:TOL=69503],hoplopleura somereni[&&NHX:TOL=69504],hoplopleura spicula[&&NHX:TOL=69505],hoplopleura sciuricola[&&NHX:TOL=69506],hoplopleura scotinomydis[&&NHX:TOL=69507],hoplopleura setzeri[&&NHX:TOL=69508],hoplopleura scapteromydis[&&NHX:TOL=69509],hoplopleura silvula[&&NHX:TOL=69510],hoplopleura sahyadri[&&NHX:TOL=69511],hoplopleura trispinosa[&&NHX:TOL=69512],hoplopleura tiptoni[&&NHX:TOL=69513],hoplopleura traubi[&&NHX:TOL=69514],hoplopleura thurmanae[&&NHX:TOL=69515],hoplopleura travassosi[&&NHX:TOL=69516],hoplopleura uromydis[&&NHX:TOL=69517],hoplopleura varia[&&NHX:TOL=69518],hoplopleura veprecula[&&NHX:TOL=69519],hoplopleura vietnamensis[&&NHX:TOL=69520],hoplopleura zelotomydis[&&NHX:TOL=69521])hoplopleura[&&NHX:TOL=69249],(pterophthirus audax[&&NHX:TOL=69815],pterophthirus alata[&&NHX:TOL=69816],pterophthirus imitans[&&NHX:TOL=69817],pterophthirus splendida[&&NHX:TOL=69818],pterophthirus wernecki[&&NHX:TOL=69819])pterophthirus[&&NHX:TOL=69274])[&&NHX:TOL=72091])[&&NHX:TOL=72090])[&&NHX:TOL=72089])hoplopleuridae[&&NHX:TOL=13653],(phthirunculus sumatranus[&&NHX:TOL=69767],(((atopophthirus setosus[&&NHX:TOL=69297],atopophthirus emersoni[&&NHX:TOL=69296])atopophthirus[&&NHX:TOL=69236],mirophthirus liae[&&NHX:TOL=69631])[&&NHX:TOL=72093],((enderleinellus arizonensis[&&NHX:TOL=69329],enderleinellus blagoveshtchenskyi[&&NHX:TOL=69330],enderleinellus brasiliensis[&&NHX:TOL=69331],enderleinellus corrugatus[&&NHX:TOL=69332],enderleinellus deppei[&&NHX:TOL=69333],enderleinellus dolichocephalus[&&NHX:TOL=69334],enderleinellus dremomydis[&&NHX:TOL=69335],enderleinellus disparilis[&&NHX:TOL=69336],enderleinellus euxeri[&&NHX:TOL=69337],enderleinellus extremus[&&NHX:TOL=69338],enderleinellus ferrisi[&&NHX:TOL=69339],enderleinellus gambiani[&&NHX:TOL=69340],enderleinellus hondurensis[&&NHX:TOL=69341],enderleinellus heliosciuri[&&NHX:TOL=69342],enderleinellus insularis[&&NHX:TOL=69343],enderleinellus kaibabensis[&&NHX:TOL=69344],enderleinellus kelloggi[&&NHX:TOL=69345],enderleinellus kumadai[&&NHX:TOL=69346],enderleinellus krochinae[&&NHX:TOL=69347],enderleinellus longiceps[&&NHX:TOL=69348],enderleinellus larisci[&&NHX:TOL=69349],enderleinellus mexicanus[&&NHX:TOL=69350],enderleinellus malaysianus[&&NHX:TOL=69351],enderleinellus menetensis[&&NHX:TOL=69352],enderleinellus marmotae[&&NHX:TOL=69353],enderleinellus microsciuri[&&NHX:TOL=69354],enderleinellus nannosciuri[&&NHX:TOL=69355],enderleinellus nishimarui[&&NHX:TOL=69356],enderleinellus urosciuri[&&NHX:TOL=69371],enderleinellus nitzschi[&&NHX:TOL=69357],enderleinellus nayaritensis[&&NHX:TOL=69358],enderleinellus oculatus[&&NHX:TOL=69359],enderleinellus osborni[&&NHX:TOL=69360],enderleinellus paralongiceps[&&NHX:TOL=69361],enderleinellus propinquus[&&NHX:TOL=69362],enderleinellus pratti[&&NHX:TOL=69363],enderleinellus platyspicatus[&&NHX:TOL=69364],enderleinellus puvensis[&&NHX:TOL=69365],enderleinellus replicates[&&NHX:TOL=69366],enderleinellus sciurotamiasis[&&NHX:TOL=69367],enderleinellus suturalis[&&NHX:TOL=69368],enderleinellus tamiasis[&&NHX:TOL=69369],enderleinellus tamiasciuri[&&NHX:TOL=69370],enderleinellus venezuelae[&&NHX:TOL=69372],enderleinellus zonatus[&&NHX:TOL=69373])enderleinellus[&&NHX:TOL=69241],(werneckia africana[&&NHX:TOL=69799],werneckia funisciuri[&&NHX:TOL=69800],werneckia minuta[&&NHX:TOL=69801],werneckia nigeriensis[&&NHX:TOL=69802],werneckia paraxeri[&&NHX:TOL=69803])werneckia[&&NHX:TOL=69282])[&&NHX:TOL=72094])[&&NHX:TOL=72092])enderleinellidae[&&NHX:TOL=13652])[&&NHX:TOL=72086])[&&NHX:TOL=72064])anoplura[&&NHX:TOL=13871],(haematomyzus elephantis[&&NHX:TOL=13876],haematomyzus hopkinsi[&&NHX:TOL=13877],haematomyzus porci[&&NHX:TOL=70947])haematomyzus[&&NHX:TOL=13872])[&&NHX:TOL=13870],(((bovicola bovicola alpinus[&&NHX:TOL=75844],bovicola werneckiella aspilopygus[&&NHX:TOL=75845],bovicola bovicola bovis[&&NHX:TOL=75846],bovicola lepikentron breviceps[&&NHX:TOL=75847],bovicola bovicola caprae[&&NHX:TOL=75848],bovicola bovicola concavifrons[&&NHX:TOL=75849],bovicola holakartikos crassipes[&&NHX:TOL=75850],bovicola werneckiella equi[&&NHX:TOL=75851],bovicola werneckiella fulvus[&&NHX:TOL=75852],bovicola spinibovicola hemitragi[&&NHX:TOL=75853],bovicola bovicola jellisoni[&&NHX:TOL=75854],bovicola bovicola limbatus[&&NHX:TOL=75855],bovicola bovicola longicornis[&&NHX:TOL=75856],bovicola spinibovicola multispinosus[&&NHX:TOL=75857],bovicola werneckiella neglectus[&&NHX:TOL=75858],bovicola werneckiella ocellatus[&&NHX:TOL=75859],bovicola bovicola oreamnidis[&&NHX:TOL=75860],bovicola bovicola ovis[&&NHX:TOL=75861],bovicola bisonicola sedecimdecembrii[&&NHX:TOL=75862],bovicola bovicola tarandi[&&NHX:TOL=75863],bovicola bovicola tibialis[&&NHX:TOL=75864],bovicola werneckiella zebrae[&&NHX:TOL=75865],bovicola werneckiella zuluensis[&&NHX:TOL=75866])bovicola[&&NHX:TOL=75843],(cebidicola armatus[&&NHX:TOL=75868],cebidicola extrarius[&&NHX:TOL=75869],cebidicola semiarmatus[&&NHX:TOL=75870])cebidicola[&&NHX:TOL=75867],(damalinia damalinia adenota[&&NHX:TOL=75872],damalinia cervicola annectens[&&NHX:TOL=75873],damalinia damalinia appendiculata[&&NHX:TOL=75874],damalinia damalinia baxi[&&NHX:TOL=75875],damalinia damalinia chorleyi[&&NHX:TOL=75876],damalinia cervicola cordillerai[&&NHX:TOL=75877],damalinia damalinia crenelata[&&NHX:TOL=75878],damalinia damalinia dimorpha[&&NHX:TOL=75879],damalinia damalinia fahrenholzi[&&NHX:TOL=75880],damalinia cervicola forficula[&&NHX:TOL=75881],damalinia damalinia harrisoni[&&NHX:TOL=75882],damalinia cervicola hendrickxi[&&NHX:TOL=75883],damalinia damalinia hilli[&&NHX:TOL=75884],damalinia cervicola hopkinsi[&&NHX:TOL=75885],damalinia cervicola hydropotis[&&NHX:TOL=75886],damalinia cervicola lerouxi[&&NHX:TOL=75887],damalinia cervicola maai[&&NHX:TOL=75888],damalinia cervicola martinaglia[&&NHX:TOL=75889],damalinia cervicola meyeri[&&NHX:TOL=75890],damalinia cervicola muntiaca[&&NHX:TOL=75891],damalinia cervicola natalensis[&&NHX:TOL=75892],damalinia damalinia neotheileri[&&NHX:TOL=75893],damalinia damalinia orientalis[&&NHX:TOL=75894],damalinia damalinia ornata[&&NHX:TOL=75895],damalinia damalinia pelea[&&NHX:TOL=75896],damalinia cervicola reduncae[&&NHX:TOL=75897],damalinia damalinia semitheileri[&&NHX:TOL=75898],damalinia cervicola siamensis[&&NHX:TOL=75899],damalinia damalinia theileri[&&NHX:TOL=75900],damalinia damalinia thompsoni[&&NHX:TOL=75901],damalinia cervicola trabeculae[&&NHX:TOL=75902],damalinia tragulicola traguli[&&NHX:TOL=75903],damalinia cervicola ugandae[&&NHX:TOL=75904])damalinia[&&NHX:TOL=75871],(dasyonyx dasyonyx bedfordi[&&NHX:TOL=75906],dasyonyx neodasyonyx capensis[&&NHX:TOL=75907],dasyonyx dasyonyx dendrohyracis[&&NHX:TOL=75908],dasyonyx neodasyonyx diacanthus[&&NHX:TOL=75909],dasyonyx dasyonyx guineensis[&&NHX:TOL=75910],dasyonyx dasyonyx hopkinsi[&&NHX:TOL=75911],dasyonyx dasyonyx minor[&&NHX:TOL=75912],dasyonyx neodasyonyx nairobiensis[&&NHX:TOL=75913],dasyonyx dasyonyx oculatus[&&NHX:TOL=75914],dasyonyx dasyonyx ovalis[&&NHX:TOL=75915],dasyonyx neodasyonyx ruficeps[&&NHX:TOL=75916],dasyonyx dasyonyx smallwoodae[&&NHX:TOL=75917],dasyonyx neodasyonyx transvaalensis[&&NHX:TOL=75918],dasyonyx dasyonyx ugandensis[&&NHX:TOL=75919],dasyonyx dasyonyx validus[&&NHX:TOL=75920],dasyonyx neodasyonyx waterbergensis[&&NHX:TOL=75921])dasyonyx[&&NHX:TOL=75905],(eurytrichodectes machadoi[&&NHX:TOL=75923],eurytrichodectes paradoxus[&&NHX:TOL=75924])eurytrichodectes[&&NHX:TOL=75922],(eutrichophilus andersoni[&&NHX:TOL=75926],eutrichophilus australis[&&NHX:TOL=75927],eutrichophilus cercolabes[&&NHX:TOL=75928],eutrichophilus claytoni[&&NHX:TOL=75929],eutrichophilus comitans[&&NHX:TOL=75930],eutrichophilus cordiceps[&&NHX:TOL=75931],eutrichophilus duellmani[&&NHX:TOL=75932],eutrichophilus emersoni[&&NHX:TOL=75933],eutrichophilus exiguus[&&NHX:TOL=75934],eutrichophilus guyanensis[&&NHX:TOL=75935],eutrichophilus hershkovitzi[&&NHX:TOL=75936],eutrichophilus koopmani[&&NHX:TOL=75937],eutrichophilus lobatus[&&NHX:TOL=75938],eutrichophilus maximus[&&NHX:TOL=75939],eutrichophilus mexicanus[&&NHX:TOL=75940],eutrichophilus minor[&&NHX:TOL=75941],eutrichophilus moojeni[&&NHX:TOL=75942],eutrichophilus paraguayensis[&&NHX:TOL=75943],eutrichophilus setosus[&&NHX:TOL=75944])eutrichophilus[&&NHX:TOL=75925],(felicola paradoxuroecus acuticeps[&&NHX:TOL=75946],felicola suricatoecus acutirostris[&&NHX:TOL=75947],felicola paradoxuroecus africanus[&&NHX:TOL=75948],felicola lorisicola americanus[&&NHX:TOL=75949],felicola paradoxuroecus aspidorhynchus[&&NHX:TOL=75950],felicola suricatoecus bedfordi[&&NHX:TOL=75951],felicola paradoxuroecus bengalensis[&&NHX:TOL=75952],felicola lorisicola braziliensis[&&NHX:TOL=75953],felicola lorisicola caffra[&&NHX:TOL=75954],felicola felicola calogaleus[&&NHX:TOL=75955],felicola felicola congoensis[&&NHX:TOL=75956],felicola suricatoecus cooleyi[&&NHX:TOL=75957],felicola felicola cynictis[&&NHX:TOL=75958],felicola suricatoecus decipiens[&&NHX:TOL=75959],felicola suricatoecus fahrenholzi[&&NHX:TOL=75960],felicola lorisicola felis[&&NHX:TOL=75961],felicola suricatoecus fennecus[&&NHX:TOL=75962],felicola felicola genettae[&&NHX:TOL=75963],felicola suricatoecus guinlei[&&NHX:TOL=75964],felicola felicola helogale[&&NHX:TOL=75965],felicola felicola helogaloidis[&&NHX:TOL=75966],felicola lorisicola hercynianus[&&NHX:TOL=75967],felicola felicola hopkinsi[&&NHX:TOL=75968],felicola felicola inaequalis[&&NHX:TOL=75969],felicola lorisicola isidoroi[&&NHX:TOL=75970],felicola paradoxuroecus juccii[&&NHX:TOL=75971],felicola paradoxuroecus laticeps[&&NHX:TOL=75972],felicola paradoxuroecus lenicornis[&&NHX:TOL=75973],felicola felicola liberiae[&&NHX:TOL=75974],felicola suricatoecus macrurus[&&NHX:TOL=75975],felicola lorisicola malaysianus[&&NHX:TOL=75976],felicola felicola minimus[&&NHX:TOL=75977],felicola lorisicola mjoebergi[&&NHX:TOL=75978],felicola paradoxuroecus mungos[&&NHX:TOL=75979],felicola paradoxuroecus neoafricanus[&&NHX:TOL=75980],felicola lorisicola neofelis[&&NHX:TOL=75981],felicola felicola occidentalis[&&NHX:TOL=75982],felicola lorisicola oncae[&&NHX:TOL=75983],felicola paradoxuroecus paralaticeps[&&NHX:TOL=75984],felicola paradoxuroecus philippinensis[&&NHX:TOL=75985],felicola suricatoecus pygidialis[&&NHX:TOL=75986],felicola suricatoecus quadraticeps[&&NHX:TOL=75987],felicola felicola rahmi[&&NHX:TOL=75988],felicola felicola robertsi[&&NHX:TOL=75989],felicola felicola rohani[&&NHX:TOL=75990],felicola felicola setosus[&&NHX:TOL=75991],felicola lorisicola siamensis[&&NHX:TOL=75992],felicola lorisicola similis[&&NHX:TOL=75993],felicola lorisicola spenceri[&&NHX:TOL=75994],felicola felicola subrostratus[&&NHX:TOL=75995],felicola lorisicola sudamericanus[&&NHX:TOL=75996],felicola paradoxuroecus sumatrensis[&&NHX:TOL=75997],felicola felicola viverriculae[&&NHX:TOL=75998],felicola suricatoecus vulpis[&&NHX:TOL=75999],felicola paradoxuroecus wernecki[&&NHX:TOL=76000],felicola felicola zeylonicus[&&NHX:TOL=76001])felicola[&&NHX:TOL=75945],(lutridia lutridia exilis[&&NHX:TOL=76106],lutridia neolutridia lutrae[&&NHX:TOL=76107],lutridia lutridia matschiei[&&NHX:TOL=76108])lutridia[&&NHX:TOL=76105],((((((thomomydoecus thomomydoecus jamesbeeri[&&NHX:TOL=76197],thomomydoecus thomomydoecus zacatecae[&&NHX:TOL=76208])[&&NHX:TOL=76366],thomomydoecus thomomydoecus asymmetricus[&&NHX:TOL=76190],thomomydoecus thomomydoecus birneyi[&&NHX:TOL=76192],thomomydoecus thomomydoecus dickermani[&&NHX:TOL=76194],thomomydoecus thomomydoecus genowaysi[&&NHX:TOL=76195],thomomydoecus thomomydoecus greeri[&&NHX:TOL=76196],thomomydoecus thomomydoecus johnhafneri[&&NHX:TOL=76198],thomomydoecus thomomydoecus markhafneri[&&NHX:TOL=76199],thomomydoecus thomomydoecus minor[&&NHX:TOL=76200],thomomydoecus thomomydoecus neocopei[&&NHX:TOL=76201],thomomydoecus thomomydoecus orizabae[&&NHX:TOL=76202],thomomydoecus thomomydoecus peregrini[&&NHX:TOL=76203],thomomydoecus thomomydoecus potteri[&&NHX:TOL=76204],thomomydoecus thomomydoecus timmi[&&NHX:TOL=76205],thomomydoecus thomomydoecus williamsi[&&NHX:TOL=76207])[&&NHX:TOL=76365],thomomydoecus jamespattonius barbarae[&&NHX:TOL=76191],thomomydoecus jamespattonius arleneae[&&NHX:TOL=76189],thomomydoecus jamespattonius wardi[&&NHX:TOL=76206])[&&NHX:TOL=76364],thomomydoecus jamespattonius byersi[&&NHX:TOL=76193])thomomydoecus[&&NHX:TOL=13865],(((((((((((((((((geomydoecus geomydoecus californicus[&&NHX:TOL=76016],geomydoecus geomydoecus centralis[&&NHX:TOL=76017],geomydoecus geomydoecus albati[&&NHX:TOL=76004])[&&NHX:TOL=13689],(geomydoecus geomydoecus angularis[&&NHX:TOL=76007],geomydoecus geomydoecus bajaiensis[&&NHX:TOL=76009],geomydoecus geomydoecus clausonae[&&NHX:TOL=76023])[&&NHX:TOL=13693])[&&NHX:TOL=13688],geomydoecus geomydoecus subcalifornicus[&&NHX:TOL=76082])[&&NHX:TOL=13687],(geomydoecus geomydoecus limitaris limitaris[&&NHX:TOL=76054],(geomydoecus geomydoecus limitaris bakeri[&&NHX:TOL=76052],geomydoecus geomydoecus grahamensis[&&NHX:TOL=76043])[&&NHX:TOL=13700],geomydoecus geomydoecus limitaris halli[&&NHX:TOL=76053],geomydoecus geomydoecus limitaris tolteci[&&NHX:TOL=76055],geomydoecus geomydoecus aurei[&&NHX:TOL=76008],geomydoecus geomydoecus actuosi[&&NHX:TOL=76003],geomydoecus geomydoecus sinaloae[&&NHX:TOL=76080],geomydoecus geomydoecus crovelloi[&&NHX:TOL=76031],geomydoecus geomydoecus warmanae[&&NHX:TOL=76099],geomydoecus geomydoecus guadalupensis[&&NHX:TOL=76044])[&&NHX:TOL=13698],(geomydoecus geomydoecus shastensis[&&NHX:TOL=76079],geomydoecus geomydoecus hueyi[&&NHX:TOL=76047])[&&NHX:TOL=13711])[&&NHX:TOL=13686],(geomydoecus geomydoecus welleri welleri[&&NHX:TOL=76101],geomydoecus geomydoecus welleri multilineatus[&&NHX:TOL=76100])[&&NHX:TOL=76370])[&&NHX:TOL=13685],geomydoecus geomydoecus umbrini[&&NHX:TOL=76095],geomydoecus geomydoecus jaliscoensis[&&NHX:TOL=76050],(geomydoecus geomydoecus extimi[&&NHX:TOL=76038],geomydoecus geomydoecus nayaritensis[&&NHX:TOL=76063])[&&NHX:TOL=13719])[&&NHX:TOL=13684],geomydoecus geomydoecus musculi[&&NHX:TOL=76061])[&&NHX:TOL=13683],geomydoecus geomydoecus cliftoni[&&NHX:TOL=76024])[&&NHX:TOL=13682],geomydoecus geomydoecus quadridentatus[&&NHX:TOL=76076])[&&NHX:TOL=13681],geomydoecus geomydoecus geomydis[&&NHX:TOL=76042],geomydoecus geomydoecus oklahomensis[&&NHX:TOL=76066],geomydoecus geomydoecus nebrathkensis[&&NHX:TOL=76064],geomydoecus geomydoecus spickai[&&NHX:TOL=76081],geomydoecus geomydoecus heaneyi[&&NHX:TOL=76045],(geomydoecus geomydoecus subgeomydis[&&NHX:TOL=76083],geomydoecus geomydoecus ewingi[&&NHX:TOL=76036])[&&NHX:TOL=13730],geomydoecus geomydoecus dalgleishi[&&NHX:TOL=76033])[&&NHX:TOL=13680],geomydoecus geomydoecus illinoensis[&&NHX:TOL=76049])[&&NHX:TOL=13679],(geomydoecus geomydoecus oregonus[&&NHX:TOL=76067],geomydoecus geomydoecus idahoensis[&&NHX:TOL=76048])[&&NHX:TOL=13735])[&&NHX:TOL=13678],((geomydoecus geomydoecus telli[&&NHX:TOL=76086],geomydoecus geomydoecus veracruzensis[&&NHX:TOL=76098],(geomydoecus geomydoecus coronadoi coronadoi[&&NHX:TOL=76026],geomydoecus geomydoecus coronadoi saccharalis[&&NHX:TOL=76027],geomydoecus geomydoecus coronadoi submerriami[&&NHX:TOL=76028])[&&NHX:TOL=76367])[&&NHX:TOL=13739],geomydoecus geomydoecus merriami[&&NHX:TOL=76058],geomydoecus geomydoecus polydentatus polydentatus[&&NHX:TOL=76074],geomydoecus geomydoecus polydentatus angustirostris[&&NHX:TOL=76073])[&&NHX:TOL=13738])[&&NHX:TOL=13677],(geomydoecus geomydoecus expansus[&&NHX:TOL=76037],geomydoecus geomydoecus martini[&&NHX:TOL=76056])[&&NHX:TOL=13749])[&&NHX:TOL=13676],((geomydoecus geomydoecus truncatus[&&NHX:TOL=76094],geomydoecus geomydoecus neotruncatus[&&NHX:TOL=76065])[&&NHX:TOL=13753],(geomydoecus geomydoecus scleritus[&&NHX:TOL=76077],geomydoecus geomydoecus mobilensis[&&NHX:TOL=76060])[&&NHX:TOL=13756])[&&NHX:TOL=13752])[&&NHX:TOL=13675],(((geomydoecus geomydoecus bulleri bulleri[&&NHX:TOL=76012],geomydoecus geomydoecus bulleri melanuri[&&NHX:TOL=76014],((geomydoecus geomydoecus bulleri intermedius[&&NHX:TOL=76013],geomydoecus geomydoecus nadleri[&&NHX:TOL=76062])[&&NHX:TOL=13765],geomydoecus geomydoecus burti[&&NHX:TOL=76015])[&&NHX:TOL=13764])[&&NHX:TOL=13761],((((geomydoecus geomydoecus traubi[&&NHX:TOL=76092],geomydoecus geomydoecus mexicanus[&&NHX:TOL=76059])[&&NHX:TOL=13772],(geomydoecus geomydoecus fulvescens[&&NHX:TOL=76040],(geomydoecus geomydoecus perotensis irolonis[&&NHX:TOL=76071],geomydoecus geomydoecus perotensis perotensis[&&NHX:TOL=76072])[&&NHX:TOL=76369])[&&NHX:TOL=13775])[&&NHX:TOL=13771],(geomydoecus geomydoecus mcgregori[&&NHX:TOL=76057],(geomydoecus geomydoecus wernecki wernecki[&&NHX:TOL=76103],geomydoecus geomydoecus wernecki planiceps[&&NHX:TOL=76102])[&&NHX:TOL=13782])[&&NHX:TOL=13780])[&&NHX:TOL=13770],geomydoecus geomydoecus alcorni[&&NHX:TOL=76005])[&&NHX:TOL=13769])[&&NHX:TOL=13760],geomydoecus geomydoecus trichopi[&&NHX:TOL=76093])[&&NHX:TOL=13759],(geomydoecus geomydoecus texanus tropicalis[&&NHX:TOL=76088],geomydoecus geomydoecus texanus texanus[&&NHX:TOL=76087],(geomydoecus geomydoecus ustulati clarkii[&&NHX:TOL=76096],geomydoecus geomydoecus ustulati ustulati[&&NHX:TOL=76097],geomydoecus geomydoecus tamaulipensis[&&NHX:TOL=76085],(geomydoecus geomydoecus subnubili[&&NHX:TOL=76084],(((((geomydoecus geomydoecus chapini[&&NHX:TOL=76018],geomydoecus geomydoecus hoffmanni[&&NHX:TOL=76046])[&&NHX:TOL=13802],geomydoecus geomydoecus yucatanensis[&&NHX:TOL=76104])[&&NHX:TOL=13800],geomydoecus geomydoecus copei[&&NHX:TOL=76025])[&&NHX:TOL=13798],((geomydoecus geomydoecus chiapensis[&&NHX:TOL=76020],geomydoecus geomydoecus pygacanthi[&&NHX:TOL=76075])[&&NHX:TOL=13806],(geomydoecus geomydoecus alleni[&&NHX:TOL=76006],geomydoecus geomydoecus jonesi[&&NHX:TOL=76051])[&&NHX:TOL=13809])[&&NHX:TOL=13805])[&&NHX:TOL=13797],((geomydoecus geomydoecus panamensis panamensis[&&NHX:TOL=76069],geomydoecus geomydoecus panamensis dariensis[&&NHX:TOL=76068],geomydoecus geomydoecus setzeri[&&NHX:TOL=76078],geomydoecus geomydoecus davidhafneri[&&NHX:TOL=76034])[&&NHX:TOL=13813],(geomydoecus geomydoecus costaricensis[&&NHX:TOL=76029],geomydoecus geomydoecus cherriei[&&NHX:TOL=76019])[&&NHX:TOL=13818])[&&NHX:TOL=13812])[&&NHX:TOL=13796])[&&NHX:TOL=13794])[&&NHX:TOL=13790])[&&NHX:TOL=13787])[&&NHX:TOL=13674],geomydoecus geomydoecus tolucae[&&NHX:TOL=76091],geomydoecus geomydoecus fulvi[&&NHX:TOL=76041],geomydoecus geomydoecus chihuahuae chihuahuae[&&NHX:TOL=76021],geomydoecus geomydoecus chihuahuae emersoni[&&NHX:TOL=76022],geomydoecus geomydoecus pattoni[&&NHX:TOL=76070],(geomydoecus thaelerius thomomyus[&&NHX:TOL=76090],geomydoecus thaelerius craigi[&&NHX:TOL=76030],geomydoecus thaelerius biagiae[&&NHX:TOL=76011],(geomydoecus thaelerius betleyae[&&NHX:TOL=76010],geomydoecus thaelerius thaeleri[&&NHX:TOL=76089])[&&NHX:TOL=13830],geomydoecus thaelerius dakotensis[&&NHX:TOL=76032],geomydoecus thaelerius fuchsi[&&NHX:TOL=76039],geomydoecus thaelerius duchesnensis[&&NHX:TOL=76035])[&&NHX:TOL=13826])geomydoecus[&&NHX:TOL=13866])[&&NHX:TOL=13864],(neotrichodectes conepaticola arizonae[&&NHX:TOL=76110],neotrichodectes trigonodectes barbarae[&&NHX:TOL=76111],neotrichodectes conepaticola chilensis[&&NHX:TOL=76112],neotrichodectes lakshminarayanella cummingsi[&&NHX:TOL=76113],neotrichodectes lakshminarayanella gastrodes[&&NHX:TOL=76114],neotrichodectes conepaticola interruptofasciatus[&&NHX:TOL=76115],neotrichodectes neotrichodectes mephitidis[&&NHX:TOL=76116],neotrichodectes neotrichodectes minutus[&&NHX:TOL=76117],neotrichodectes neotrichodectes osborni[&&NHX:TOL=76118],neotrichodectes nasuicola pallidus[&&NHX:TOL=76119],neotrichodectes conepaticola semistriatus[&&NHX:TOL=76120],neotrichodectes neotrichodectes thoracicus[&&NHX:TOL=76121],neotrichodectes neotrichodectes wolffhuegeli[&&NHX:TOL=76122])neotrichodectes[&&NHX:TOL=76109])neotrichodectinae[&&NHX:TOL=13924],(paratrichodectes ovalis[&&NHX:TOL=76124],paratrichodectes ugandensis[&&NHX:TOL=76125],paratrichodectes zorillae[&&NHX:TOL=76126])paratrichodectes[&&NHX:TOL=76123],(procavicola procavicola affinis[&&NHX:TOL=76128],procavicola condylocephalus bedfordi bedfordi[&&NHX:TOL=76129],procavicola condylocephalus bedfordi dissimilis[&&NHX:TOL=76130],procavicola procavicola brucei[&&NHX:TOL=76131],procavicola procavicola eichleri[&&NHX:TOL=76132],procavicola procavicola emarginatus[&&NHX:TOL=76133],procavicola procavicola furca[&&NHX:TOL=76134],procavicola procavicola heterohyracis[&&NHX:TOL=76135],procavicola condylocephalus hopkinsi[&&NHX:TOL=76136],procavicola condylocephalus lindfieldi[&&NHX:TOL=76137],procavicola procavicola lopesi lopesi[&&NHX:TOL=76138],procavicola procavicola lopesi vicinus[&&NHX:TOL=76139],procavicola procavicola mokeetsi[&&NHX:TOL=76140],procavicola procavicola natalensis[&&NHX:TOL=76141],procavicola procavicola parvus[&&NHX:TOL=76142],procavicola procavicola pretoriensis[&&NHX:TOL=76143],procavicola procavicola shoanus[&&NHX:TOL=76144],procavicola procavicola sternatus[&&NHX:TOL=76145],procavicola procavicola subparvus[&&NHX:TOL=76146],procavicola procavicola thorntoni[&&NHX:TOL=76147],procavicola procavicola ugandensis[&&NHX:TOL=76148],procavicola condylocephalus univirgatus[&&NHX:TOL=76149])procavicola[&&NHX:TOL=76127],(procaviphilus meganarionoides africanus[&&NHX:TOL=76151],procaviphilus meganarionoides angolensis[&&NHX:TOL=76152],procaviphilus meganarionoides colobi[&&NHX:TOL=76153],procaviphilus meganarionoides congoensis[&&NHX:TOL=76154],procaviphilus procaviphilus dubius[&&NHX:TOL=76155],procaviphilus procaviphilus ferrisi ferrisi[&&NHX:TOL=76156],procaviphilus procaviphilus ferrisi granuloides[&&NHX:TOL=76157],procaviphilus procaviphilus ferrisi hindei[&&NHX:TOL=76158],procaviphilus procaviphilus granulatus[&&NHX:TOL=76159],procaviphilus procaviphilus harrisi[&&NHX:TOL=76160],procaviphilus meganarionoides jordani[&&NHX:TOL=76161],procaviphilus meganarionoides major[&&NHX:TOL=76162],procaviphilus meganarionoides muesebecki[&&NHX:TOL=76163],procaviphilus meganarionoides neumanni baculatus[&&NHX:TOL=76164],procaviphilus meganarionoides neumanni neumanni[&&NHX:TOL=76165],procaviphilus procaviphilus robertsi[&&NHX:TOL=76166],procaviphilus meganarionoides sclerotis[&&NHX:TOL=76167],procaviphilus meganarionoides scutifer[&&NHX:TOL=76168],procaviphilus meganarionoides serraticus[&&NHX:TOL=76169],procaviphilus meganarionoides tendeiroi[&&NHX:TOL=76170])procaviphilus[&&NHX:TOL=76150],(protelicola hyaenae[&&NHX:TOL=76172],protelicola intermedius[&&NHX:TOL=76173])protelicola[&&NHX:TOL=76171],(stachiella divaricata[&&NHX:TOL=76175],stachiella emeryi[&&NHX:TOL=76176],stachiella ermineae[&&NHX:TOL=76177],stachiella fallax[&&NHX:TOL=76178],stachiella jacobi[&&NHX:TOL=76179],stachiella kingi[&&NHX:TOL=76180],stachiella larseni[&&NHX:TOL=76181],stachiella martis[&&NHX:TOL=76182],stachiella mustelae[&&NHX:TOL=76183],stachiella octomaculatus[&&NHX:TOL=76184],stachiella potus[&&NHX:TOL=76185],stachiella retusa[&&NHX:TOL=76186],stachiella salfii[&&NHX:TOL=76187])stachiella[&&NHX:TOL=76174],(trichodectes canis[&&NHX:TOL=76210],trichodectes emersoni[&&NHX:TOL=76211],trichodectes euarctidos[&&NHX:TOL=76212],trichodectes galictidis[&&NHX:TOL=76213],trichodectes kuntzi[&&NHX:TOL=76214],trichodectes melis[&&NHX:TOL=76215],trichodectes pinguis[&&NHX:TOL=76216],trichodectes vosseleri[&&NHX:TOL=76217])trichodectes[&&NHX:TOL=76209],(tricholipeurus aepycerus[&&NHX:TOL=76219],tricholipeurus albimarginatus[&&NHX:TOL=76220],tricholipeurus antidorcus[&&NHX:TOL=76221],tricholipeurus balanicus[&&NHX:TOL=76222],tricholipeurus bedfordi[&&NHX:TOL=76223],tricholipeurus clayae[&&NHX:TOL=76224],tricholipeurus conectens[&&NHX:TOL=76225],tricholipeurus cornutus[&&NHX:TOL=76226],tricholipeurus dorcelaphi[&&NHX:TOL=76227],tricholipeurus elongatus[&&NHX:TOL=76228],tricholipeurus indicus[&&NHX:TOL=76229],tricholipeurus lineatus[&&NHX:TOL=76230],tricholipeurus lipeuroides[&&NHX:TOL=76231],tricholipeurus longiceps[&&NHX:TOL=76232],tricholipeurus moschatus[&&NHX:TOL=76233],tricholipeurus ourebiae[&&NHX:TOL=76234],tricholipeurus pakenhami[&&NHX:TOL=76235],tricholipeurus parallelus[&&NHX:TOL=76236],tricholipeurus parkeri[&&NHX:TOL=76237],tricholipeurus spinifer[&&NHX:TOL=76238],tricholipeurus victoriae[&&NHX:TOL=76239],tricholipeurus zaganseeri[&&NHX:TOL=76240])tricholipeurus[&&NHX:TOL=76218],werneckodectes ferrisi[&&NHX:TOL=76241])trichodectidae[&&NHX:TOL=13861],((acidoproctus emersoni[&&NHX:TOL=72996],acidoproctus fuligulae[&&NHX:TOL=72997],acidoproctus gottwaldhirschi[&&NHX:TOL=72998],acidoproctus hilli[&&NHX:TOL=72999],acidoproctus kelloggi[&&NHX:TOL=73000],acidoproctus maximus[&&NHX:TOL=73001],acidoproctus moschatae[&&NHX:TOL=73002],acidoproctus rostratus[&&NHX:TOL=73003],acidoproctus taschenbergi[&&NHX:TOL=73004])acidoproctus[&&NHX:TOL=72995],(acutifrons australis[&&NHX:TOL=73006],acutifrons caracarensis[&&NHX:TOL=73007],acutifrons chimango[&&NHX:TOL=73008],acutifrons colombianus[&&NHX:TOL=73009],acutifrons connectens[&&NHX:TOL=73010],acutifrons megalopterus[&&NHX:TOL=73011],acutifrons mexicanus[&&NHX:TOL=73012],acutifrons orbiculatus[&&NHX:TOL=73013],acutifrons ruficollidis[&&NHX:TOL=73014],acutifrons similis[&&NHX:TOL=73015],acutifrons titschacki[&&NHX:TOL=73016],acutifrons vieirai[&&NHX:TOL=73017])acutifrons[&&NHX:TOL=73005],(aegypoecus africanus[&&NHX:TOL=73019],aegypoecus brevicollis[&&NHX:TOL=73020],aegypoecus clayae[&&NHX:TOL=73021],aegypoecus hopkinsi[&&NHX:TOL=73022],aegypoecus jordani[&&NHX:TOL=73023],aegypoecus perspicuus[&&NHX:TOL=73024],aegypoecus trigonoceps[&&NHX:TOL=73025])aegypoecus[&&NHX:TOL=73018],(alcedoecus alatoclypeatus[&&NHX:TOL=73027],alcedoecus annulatus[&&NHX:TOL=73028],alcedoecus capistratus[&&NHX:TOL=73029],alcedoecus chelicutii[&&NHX:TOL=73030],alcedoecus constrictus[&&NHX:TOL=73031],alcedoecus delphax[&&NHX:TOL=73032],alcedoecus incisus[&&NHX:TOL=73033],alcedoecus latigenitalis[&&NHX:TOL=73034],alcedoecus minor[&&NHX:TOL=73035],alcedoecus mossambicanus[&&NHX:TOL=73036],alcedoecus mystacinus[&&NHX:TOL=73037],alcedoecus neorientalis[&&NHX:TOL=73038],alcedoecus nepalensis[&&NHX:TOL=73039],alcedoecus orientalis[&&NHX:TOL=73040],alcedoecus sanctus[&&NHX:TOL=73041],alcedoecus senegalensis[&&NHX:TOL=73042],alcedoecus setosus[&&NHX:TOL=73043],alcedoecus sumatranus[&&NHX:TOL=73044])alcedoecus[&&NHX:TOL=73026],(alcedoffula aeneae[&&NHX:TOL=73046],alcedoffula alcedinis[&&NHX:TOL=73047],alcedoffula alcyonae[&&NHX:TOL=73048],alcedoffula brachialis[&&NHX:TOL=73049],alcedoffula brelihi[&&NHX:TOL=73050],alcedoffula carvalhoi[&&NHX:TOL=73051],alcedoffula ceycis[&&NHX:TOL=73052],alcedoffula chocoana[&&NHX:TOL=73053],alcedoffula columbiana[&&NHX:TOL=73054],alcedoffula cristata[&&NHX:TOL=73055],alcedoffula duplicata[&&NHX:TOL=73056],alcedoffula elongata[&&NHX:TOL=73057],alcedoffula extumida[&&NHX:TOL=73058],alcedoffula luzonica[&&NHX:TOL=73059],alcedoffula machera[&&NHX:TOL=73060],alcedoffula madagascariensis[&&NHX:TOL=73061],alcedoffula mahigir[&&NHX:TOL=73062],alcedoffula neoguineensis[&&NHX:TOL=73063],alcedoffula theresae[&&NHX:TOL=73064])alcedoffula[&&NHX:TOL=73045],(anaticola angustolimbatus[&&NHX:TOL=73066],anaticola anseris[&&NHX:TOL=73067],anaticola asymmetricus[&&NHX:TOL=73068],anaticola australis[&&NHX:TOL=73069],anaticola beieri[&&NHX:TOL=73070],anaticola branderi[&&NHX:TOL=73071],anaticola breviceps[&&NHX:TOL=73072],anaticola buccinator[&&NHX:TOL=73073],anaticola cairinensis[&&NHX:TOL=73074],anaticola candidus[&&NHX:TOL=73075],anaticola chaetodens[&&NHX:TOL=73076],anaticola clangulae[&&NHX:TOL=73077],anaticola coloratus[&&NHX:TOL=73078],anaticola constrictus[&&NHX:TOL=73079],anaticola crassicornis[&&NHX:TOL=73080],anaticola cygnopsis[&&NHX:TOL=73081],anaticola delacouri[&&NHX:TOL=73082],anaticola dissonus[&&NHX:TOL=73083],anaticola ernstmayri[&&NHX:TOL=73084],anaticola gambensis[&&NHX:TOL=73085],anaticola jamesi[&&NHX:TOL=73086],anaticola klockenhoffi[&&NHX:TOL=73087],anaticola magnificus[&&NHX:TOL=73088],anaticola marginella[&&NHX:TOL=73089],anaticola megaceros[&&NHX:TOL=73090],anaticola mergiserrati[&&NHX:TOL=73091],anaticola parviceps[&&NHX:TOL=73092],anaticola phoenicopteri[&&NHX:TOL=73093],anaticola rheinwaldi[&&NHX:TOL=73094],anaticola tadornae[&&NHX:TOL=73095],anaticola tamarae[&&NHX:TOL=73096],anaticola thoracicus[&&NHX:TOL=73097],anaticola tordae[&&NHX:TOL=73098])anaticola[&&NHX:TOL=73065],(anatoecus clayae[&&NHX:TOL=73100],anatoecus cygni[&&NHX:TOL=73101],anatoecus dentatus[&&NHX:TOL=73102],anatoecus icterodes[&&NHX:TOL=73103],anatoecus keleri[&&NHX:TOL=73104],anatoecus keymeri[&&NHX:TOL=73105],anatoecus monteiroi[&&NHX:TOL=73106],anatoecus penicillatus[&&NHX:TOL=73107],anatoecus pygaspis[&&NHX:TOL=73108],anatoecus regina[&&NHX:TOL=73109])anatoecus[&&NHX:TOL=73099],(aquanirmus americanus[&&NHX:TOL=73111],aquanirmus australis[&&NHX:TOL=73112],aquanirmus bahli[&&NHX:TOL=73113],aquanirmus bucomfishi[&&NHX:TOL=73114],aquanirmus chamberlini[&&NHX:TOL=73115],aquanirmus colymbinus[&&NHX:TOL=73116],aquanirmus emersoni[&&NHX:TOL=73117],aquanirmus occidentalis[&&NHX:TOL=73118],aquanirmus podicepis[&&NHX:TOL=73119],aquanirmus podilymbus[&&NHX:TOL=73120],aquanirmus rollandii[&&NHX:TOL=73121],aquanirmus runcinatus[&&NHX:TOL=73122])aquanirmus[&&NHX:TOL=73110],(ardeicola ababae[&&NHX:TOL=73124],ardeicola aequalis[&&NHX:TOL=73125],ardeicola africanus[&&NHX:TOL=73126],ardeicola ajajae[&&NHX:TOL=73127],ardeicola ardeae[&&NHX:TOL=73128],ardeicola asiaticus[&&NHX:TOL=73129],ardeicola atratus[&&NHX:TOL=73130],ardeicola australis[&&NHX:TOL=73131],ardeicola bicolor[&&NHX:TOL=73132],ardeicola botauri[&&NHX:TOL=73133],ardeicola buettikeri[&&NHX:TOL=73134],ardeicola burmanus[&&NHX:TOL=73135],ardeicola capitatus[&&NHX:TOL=73136],ardeicola castaneus[&&NHX:TOL=73137],ardeicola celeris[&&NHX:TOL=73138],ardeicola ciconiae[&&NHX:TOL=73139],ardeicola clayae[&&NHX:TOL=73140],ardeicola cruris[&&NHX:TOL=73141],ardeicola cruscula[&&NHX:TOL=73142],ardeicola dennelli[&&NHX:TOL=73143],ardeicola dissourae[&&NHX:TOL=73144],ardeicola elongata[&&NHX:TOL=73145],ardeicola emersoni[&&NHX:TOL=73146],ardeicola epiphanes[&&NHX:TOL=73147],ardeicola exilis[&&NHX:TOL=73148],ardeicola expallidus[&&NHX:TOL=73149],ardeicola fissomaculatus[&&NHX:TOL=73150],ardeicola florida[&&NHX:TOL=73151],ardeicola freemani[&&NHX:TOL=73152],ardeicola geronticorum[&&NHX:TOL=73153],ardeicola goisagi[&&NHX:TOL=73154],ardeicola gracilentus[&&NHX:TOL=73155],ardeicola hardayali[&&NHX:TOL=73156],ardeicola harrisoni[&&NHX:TOL=73157],ardeicola hopkinsi[&&NHX:TOL=73158],ardeicola ibis[&&NHX:TOL=73159],ardeicola indicus[&&NHX:TOL=73160],ardeicola intermedia[&&NHX:TOL=73161],ardeicola ixobrychae[&&NHX:TOL=73162],ardeicola keleri[&&NHX:TOL=73163],ardeicola keniensis[&&NHX:TOL=73164],ardeicola lepidus[&&NHX:TOL=73165],ardeicola leucoproctus[&&NHX:TOL=73166],ardeicola leucosoma[&&NHX:TOL=73167],ardeicola loculator[&&NHX:TOL=73168],ardeicola macroceros[&&NHX:TOL=73169],ardeicola maculatus[&&NHX:TOL=73170],ardeicola meinertzhageni[&&NHX:TOL=73171],ardeicola melanopis[&&NHX:TOL=73172],ardeicola neopallidus[&&NHX:TOL=73173],ardeicola nigra[&&NHX:TOL=73174],ardeicola nippon[&&NHX:TOL=73175],ardeicola nyctanassa[&&NHX:TOL=73176],ardeicola ovisignatus[&&NHX:TOL=73177],ardeicola pilgrimi[&&NHX:TOL=73178],ardeicola plataleae[&&NHX:TOL=73179],ardeicola porrectus[&&NHX:TOL=73180],ardeicola praegracilis[&&NHX:TOL=73181],ardeicola praelongus[&&NHX:TOL=73182],ardeicola pseudoraphidius[&&NHX:TOL=73183],ardeicola rhaphidius[&&NHX:TOL=73184],ardeicola robusta[&&NHX:TOL=73185],ardeicola senegalensis[&&NHX:TOL=73186],ardeicola signatus[&&NHX:TOL=73187],ardeicola smithersi[&&NHX:TOL=73188],ardeicola stellaris[&&NHX:TOL=73189],ardeicola tantali[&&NHX:TOL=73190],ardeicola theristicus[&&NHX:TOL=73191])ardeicola[&&NHX:TOL=73123],(ardeiphagus cochlearius[&&NHX:TOL=73193],ardeiphagus salmoni[&&NHX:TOL=73194],ardeiphagus similis[&&NHX:TOL=73195])ardeiphagus[&&NHX:TOL=73192],(auricotes affinis[&&NHX:TOL=73197],auricotes aliger[&&NHX:TOL=73198],auricotes artutus[&&NHX:TOL=73199],auricotes avifissus[&&NHX:TOL=73200],auricotes bellus[&&NHX:TOL=73201],auricotes candidus[&&NHX:TOL=73202],auricotes caputilongus[&&NHX:TOL=73203],auricotes carpophagae[&&NHX:TOL=73204],auricotes celebeensis[&&NHX:TOL=73205],auricotes clayae[&&NHX:TOL=73206],auricotes clissoldi[&&NHX:TOL=73207],auricotes coloceroides[&&NHX:TOL=73208],auricotes crespoi[&&NHX:TOL=73209],auricotes declinatus[&&NHX:TOL=73210],auricotes decolor[&&NHX:TOL=73211],auricotes diasi[&&NHX:TOL=73212],auricotes emersoni[&&NHX:TOL=73213],auricotes fiadeiroi[&&NHX:TOL=73214],auricotes ivoi[&&NHX:TOL=73215],auricotes javanensis[&&NHX:TOL=73216],auricotes keiensis[&&NHX:TOL=73217],auricotes kurodai[&&NHX:TOL=73218],auricotes lacunosus[&&NHX:TOL=73219],auricotes lativenter[&&NHX:TOL=73220],auricotes lekaguli[&&NHX:TOL=73221],auricotes limbatus[&&NHX:TOL=73222],auricotes longifrons[&&NHX:TOL=73223],auricotes marshalli[&&NHX:TOL=73224],auricotes meinertzhageni[&&NHX:TOL=73225],auricotes melanesicus[&&NHX:TOL=73226],auricotes myristicivorae[&&NHX:TOL=73227],auricotes neobritannicus[&&NHX:TOL=73228],auricotes neoclayae[&&NHX:TOL=73229],auricotes neoguineensis[&&NHX:TOL=73230],auricotes obscurus[&&NHX:TOL=73231],auricotes pazmartinae[&&NHX:TOL=73232],auricotes pellucidus[&&NHX:TOL=73233],auricotes petiscai[&&NHX:TOL=73234],auricotes philippinensis[&&NHX:TOL=73235],auricotes polynesicus[&&NHX:TOL=73236],auricotes quadraticeps[&&NHX:TOL=73237],auricotes radiatus[&&NHX:TOL=73238],auricotes retrosutus[&&NHX:TOL=73239],auricotes robustus[&&NHX:TOL=73240],auricotes rotundus[&&NHX:TOL=73241],auricotes salomonensis[&&NHX:TOL=73242],auricotes samoensis[&&NHX:TOL=73243],auricotes setosus[&&NHX:TOL=73244],auricotes silvai[&&NHX:TOL=73245],auricotes stefani[&&NHX:TOL=73246],auricotes stricticlypeus[&&NHX:TOL=73247],auricotes transversalis[&&NHX:TOL=73248])auricotes[&&NHX:TOL=73196],(austrogoniodes antarcticus[&&NHX:TOL=73250],austrogoniodes bicornutus[&&NHX:TOL=73251],austrogoniodes bifasciatus[&&NHX:TOL=73252],austrogoniodes brevipes[&&NHX:TOL=73253],austrogoniodes concii[&&NHX:TOL=73254],austrogoniodes cristati[&&NHX:TOL=73255],austrogoniodes demersus[&&NHX:TOL=73256],austrogoniodes gressitti[&&NHX:TOL=73257],austrogoniodes hamiltoni[&&NHX:TOL=73258],austrogoniodes keleri[&&NHX:TOL=73259],austrogoniodes macquariensis[&&NHX:TOL=73260],austrogoniodes mawsoni[&&NHX:TOL=73261],austrogoniodes metoecus[&&NHX:TOL=73262],austrogoniodes strutheus[&&NHX:TOL=73263],austrogoniodes waterstoni[&&NHX:TOL=73264])austrogoniodes[&&NHX:TOL=73249],(austrophilopterus andigenae[&&NHX:TOL=73266],austrophilopterus calorhynchus[&&NHX:TOL=73267],austrophilopterus cancellosus[&&NHX:TOL=73268],austrophilopterus castanotus[&&NHX:TOL=73269],austrophilopterus caurensis[&&NHX:TOL=73270],austrophilopterus cuvieri[&&NHX:TOL=73271],austrophilopterus dimorphus[&&NHX:TOL=73272],austrophilopterus flavirostris[&&NHX:TOL=73273],austrophilopterus incae[&&NHX:TOL=73274],austrophilopterus megathorax[&&NHX:TOL=73275],austrophilopterus microgaster[&&NHX:TOL=73276],austrophilopterus minor[&&NHX:TOL=73277],austrophilopterus minutus[&&NHX:TOL=73278],austrophilopterus pacificus[&&NHX:TOL=73279],austrophilopterus sanguineus[&&NHX:TOL=73280],austrophilopterus seminirmus[&&NHX:TOL=73281],austrophilopterus similis[&&NHX:TOL=73282],austrophilopterus spinosus[&&NHX:TOL=73283],austrophilopterus subsimilis[&&NHX:TOL=73284],austrophilopterus sulcatus[&&NHX:TOL=73285],austrophilopterus tenuicapitis[&&NHX:TOL=73286],austrophilopterus torquatus[&&NHX:TOL=73287],austrophilopterus truncatus[&&NHX:TOL=73288])austrophilopterus[&&NHX:TOL=73265],bedfordiella unica[&&NHX:TOL=73289],(bizarrifrons clayae[&&NHX:TOL=73291],bizarrifrons francisi[&&NHX:TOL=73292],bizarrifrons juruani[&&NHX:TOL=73293],bizarrifrons maculatus[&&NHX:TOL=73294],bizarrifrons magus[&&NHX:TOL=73295],bizarrifrons meinertzhageni[&&NHX:TOL=73296],bizarrifrons picturatus[&&NHX:TOL=73297])bizarrifrons[&&NHX:TOL=73290],(bothriometopus macrocnemis[&&NHX:TOL=73299],bothriometopus simillimus[&&NHX:TOL=73300])bothriometopus[&&NHX:TOL=73298],(brueelia abbasi[&&NHX:TOL=73302],brueelia abrupta[&&NHX:TOL=73303],brueelia acuminata[&&NHX:TOL=73304],brueelia acutangulata[&&NHX:TOL=73305],brueelia addoloratoi[&&NHX:TOL=73306],brueelia affinis[&&NHX:TOL=73307],brueelia afzali[&&NHX:TOL=73308],brueelia albida[&&NHX:TOL=73309],brueelia albiventris[&&NHX:TOL=73310],brueelia alexandrii[&&NHX:TOL=73311],brueelia altaica[&&NHX:TOL=73312],brueelia amazonae[&&NHX:TOL=73313],brueelia americana[&&NHX:TOL=73314],brueelia amsel[&&NHX:TOL=73315],brueelia anamariae[&&NHX:TOL=73316],brueelia angulata[&&NHX:TOL=73317],brueelia angustifrons[&&NHX:TOL=73318],brueelia annae[&&NHX:TOL=73319],brueelia antennatus[&&NHX:TOL=73320],brueelia antimarginalis[&&NHX:TOL=73321],brueelia antiqua[&&NHX:TOL=73322],brueelia anumbii[&&NHX:TOL=73323],brueelia apiastri[&&NHX:TOL=73324],brueelia argentina[&&NHX:TOL=73325],brueelia argula[&&NHX:TOL=73326],brueelia astrildae[&&NHX:TOL=73327],brueelia atherae[&&NHX:TOL=73328],brueelia athertona[&&NHX:TOL=73329],brueelia atricapilla[&&NHX:TOL=73330],brueelia audax[&&NHX:TOL=73331],brueelia avinus[&&NHX:TOL=73332],brueelia badia[&&NHX:TOL=73333],brueelia balati[&&NHX:TOL=73334],brueelia bicurvata[&&NHX:TOL=73335],brueelia biguttata[&&NHX:TOL=73336],brueelia biocellata[&&NHX:TOL=73337],brueelia bisetacea[&&NHX:TOL=73338],brueelia blagovescenskyi[&&NHX:TOL=73339],brueelia boae[&&NHX:TOL=73340],brueelia bonariensis[&&NHX:TOL=73341],brueelia borini[&&NHX:TOL=73342],brueelia brachythorax[&&NHX:TOL=73343],brueelia brasiliensis[&&NHX:TOL=73344],brueelia breueri[&&NHX:TOL=73345],brueelia brevipennis[&&NHX:TOL=73346],brueelia brevipes[&&NHX:TOL=73347],brueelia brueliodes[&&NHX:TOL=73348],brueelia brunneinucha[&&NHX:TOL=73349],brueelia buettikeri[&&NHX:TOL=73350],brueelia bullockoda[&&NHX:TOL=73351],brueelia busharae[&&NHX:TOL=73352],brueelia calandrellae[&&NHX:TOL=73353],brueelia cambayensis[&&NHX:TOL=73354],brueelia capitus[&&NHX:TOL=73355],brueelia carrikeri[&&NHX:TOL=73356],brueelia cedrorum[&&NHX:TOL=73357],brueelia chayanh[&&NHX:TOL=73358],brueelia chelydensis[&&NHX:TOL=73359],brueelia chiguanca[&&NHX:TOL=73360],brueelia chilchil[&&NHX:TOL=73361],brueelia chrysomytris[&&NHX:TOL=73362],brueelia clayae[&&NHX:TOL=73363],brueelia concavus[&&NHX:TOL=73364],brueelia coniceps[&&NHX:TOL=73365],brueelia conocephalus[&&NHX:TOL=73366],brueelia corydalla[&&NHX:TOL=73367],brueelia cruciata[&&NHX:TOL=73368],brueelia cruscula[&&NHX:TOL=73369],brueelia cubana[&&NHX:TOL=73370],brueelia cucullata[&&NHX:TOL=73371],brueelia currucae[&&NHX:TOL=73372],brueelia cyanea[&&NHX:TOL=73373],brueelia cyclothorax[&&NHX:TOL=73374],brueelia daumae[&&NHX:TOL=73375],brueelia decumana[&&NHX:TOL=73376],brueelia deficiens[&&NHX:TOL=73377],brueelia delicata[&&NHX:TOL=73378],brueelia densilimba[&&NHX:TOL=73379],brueelia diaprepes[&&NHX:TOL=73380],brueelia dicruri[&&NHX:TOL=73381],brueelia docilis[&&NHX:TOL=73382],brueelia docophoroides[&&NHX:TOL=73383],brueelia domestica[&&NHX:TOL=73384],brueelia dorsale[&&NHX:TOL=73385],brueelia ductilis[&&NHX:TOL=73386],brueelia effronte[&&NHX:TOL=73387],brueelia eichleri[&&NHX:TOL=73388],brueelia elbeli[&&NHX:TOL=73389],brueelia embernagrae[&&NHX:TOL=73390],brueelia emersoni[&&NHX:TOL=73391],brueelia erythropteri[&&NHX:TOL=73392],brueelia eustigma[&&NHX:TOL=73393],brueelia exigua[&&NHX:TOL=73394],brueelia ferianci[&&NHX:TOL=73395],brueelia flinti[&&NHX:TOL=73396],brueelia fulmeki[&&NHX:TOL=73397],brueelia fuscopleura[&&NHX:TOL=73398],brueelia galapagensis[&&NHX:TOL=73399],brueelia ginginianus[&&NHX:TOL=73400],brueelia glandarii[&&NHX:TOL=73401],brueelia glizi[&&NHX:TOL=73402],brueelia gobiensis[&&NHX:TOL=73403],brueelia goertae[&&NHX:TOL=73404],brueelia goniocotes[&&NHX:TOL=73405],brueelia goniodes[&&NHX:TOL=73406],brueelia gracilis[&&NHX:TOL=73407],brueelia grandalae[&&NHX:TOL=73408],brueelia guatemalensis[&&NHX:TOL=73409],brueelia gulabitilyar[&&NHX:TOL=73410],brueelia guldum[&&NHX:TOL=73411],brueelia haftorni[&&NHX:TOL=73412],brueelia hamatofasciata[&&NHX:TOL=73413],brueelia hectica[&&NHX:TOL=73414],brueelia hopkinsi[&&NHX:TOL=73415],brueelia humphreyi[&&NHX:TOL=73416],brueelia husaini[&&NHX:TOL=73417],brueelia iliaci[&&NHX:TOL=73418],brueelia ilmasae[&&NHX:TOL=73419],brueelia immaculata[&&NHX:TOL=73420],brueelia imponderabilica[&&NHX:TOL=73421],brueelia impressifrons[&&NHX:TOL=73422],brueelia incerta[&&NHX:TOL=73423],brueelia indonesiana[&&NHX:TOL=73424],brueelia infrequens[&&NHX:TOL=73425],brueelia infuscata[&&NHX:TOL=73426],brueelia interposita[&&NHX:TOL=73427],brueelia jacobi[&&NHX:TOL=73428],brueelia juno[&&NHX:TOL=73429],brueelia keleri[&&NHX:TOL=73430],brueelia kistiakowskyi[&&NHX:TOL=73431],brueelia kluzi[&&NHX:TOL=73432],brueelia koslovae[&&NHX:TOL=73433],brueelia kratochvili[&&NHX:TOL=73434],brueelia lais[&&NHX:TOL=73435],brueelia laticeps[&&NHX:TOL=73436],brueelia latifasciata[&&NHX:TOL=73437],brueelia leucocephala[&&NHX:TOL=73438],brueelia limbata[&&NHX:TOL=73439],brueelia limpidus[&&NHX:TOL=73440],brueelia locustellae[&&NHX:TOL=73441],brueelia lonchurae[&&NHX:TOL=73442],brueelia longa[&&NHX:TOL=73443],brueelia longiabdominalis[&&NHX:TOL=73444],brueelia longifrons[&&NHX:TOL=73445],brueelia longipes[&&NHX:TOL=73446],brueelia longisternus[&&NHX:TOL=73447],brueelia lullulae[&&NHX:TOL=73448],brueelia magellanica[&&NHX:TOL=73449],brueelia magnini[&&NHX:TOL=73450],brueelia mahrastran[&&NHX:TOL=73451],brueelia marcoi[&&NHX:TOL=73452],brueelia marginata[&&NHX:TOL=73453],brueelia marginella[&&NHX:TOL=73454],brueelia matvejevi[&&NHX:TOL=73455],brueelia mauroi[&&NHX:TOL=73456],brueelia mediterranea[&&NHX:TOL=73457],brueelia meinertzhageni[&&NHX:TOL=73458],brueelia melanococa[&&NHX:TOL=73459],brueelia melanocoryphae[&&NHX:TOL=73460],brueelia menuraelyrae[&&NHX:TOL=73461],brueelia merulensis[&&NHX:TOL=73462],brueelia mimas[&&NHX:TOL=73463],brueelia minor[&&NHX:TOL=73464],brueelia mirabile[&&NHX:TOL=73465],brueelia modularis[&&NHX:TOL=73466],brueelia mollii[&&NHX:TOL=73467],brueelia mongolica[&&NHX:TOL=73468],brueelia moreli[&&NHX:TOL=73469],brueelia moriona[&&NHX:TOL=73470],brueelia multipunctata[&&NHX:TOL=73471],brueelia munda[&&NHX:TOL=73472],brueelia munia[&&NHX:TOL=73473],brueelia museiberolinensis[&&NHX:TOL=73474],brueelia myiophoneae[&&NHX:TOL=73475],brueelia nawabi[&&NHX:TOL=73476],brueelia nebulosa[&&NHX:TOL=73477],brueelia neoatricapillae[&&NHX:TOL=73478],brueelia neoeichleri[&&NHX:TOL=73479],brueelia neotropicalis[&&NHX:TOL=73480],brueelia nesiotes[&&NHX:TOL=73481],brueelia nigrosignata[&&NHX:TOL=73482],brueelia nipalensis[&&NHX:TOL=73483],brueelia niquitaoi[&&NHX:TOL=73484],brueelia nitzschi[&&NHX:TOL=73485],brueelia nivalis[&&NHX:TOL=73486],brueelia niveus[&&NHX:TOL=73487],brueelia novofacies[&&NHX:TOL=73488],brueelia nuda[&&NHX:TOL=73489],brueelia olivacea[&&NHX:TOL=73490],brueelia ornatissima[&&NHX:TOL=73491],brueelia oudhensis[&&NHX:TOL=73492],brueelia ovalis[&&NHX:TOL=73493],brueelia oxypyga[&&NHX:TOL=73494],brueelia pagodarum[&&NHX:TOL=73495],brueelia pakistanaise[&&NHX:TOL=73496],brueelia pallida[&&NHX:TOL=73497],brueelia pallidula[&&NHX:TOL=73498],brueelia papuana[&&NHX:TOL=73499],brueelia paraboliceps[&&NHX:TOL=73500],brueelia parabolocybe[&&NHX:TOL=73501],brueelia parae[&&NHX:TOL=73502],brueelia paratricapillae[&&NHX:TOL=73503],brueelia parviguttata[&&NHX:TOL=73504],brueelia pelikani[&&NHX:TOL=73505],brueelia pengya[&&NHX:TOL=73506],brueelia peninsularis[&&NHX:TOL=73507],brueelia perforata[&&NHX:TOL=73508],brueelia perisoreus[&&NHX:TOL=73509],brueelia persimilis[&&NHX:TOL=73510],brueelia perwienae[&&NHX:TOL=73511],brueelia picturata[&&NHX:TOL=73512],brueelia piechockii[&&NHX:TOL=73513],brueelia plocea[&&NHX:TOL=73514],brueelia pointu[&&NHX:TOL=73515],brueelia propinqua[&&NHX:TOL=73516],brueelia pseudopicturata[&&NHX:TOL=73517],brueelia ptiliogonis[&&NHX:TOL=73518],brueelia punjabensis[&&NHX:TOL=73519],brueelia pyrrhularum[&&NHX:TOL=73520],brueelia quadrangularis[&&NHX:TOL=73521],brueelia rhamphocelii[&&NHX:TOL=73522],brueelia rhinocichlae[&&NHX:TOL=73523],brueelia rhipidura[&&NHX:TOL=73524],brueelia rosickyi[&&NHX:TOL=73525],brueelia rotundata[&&NHX:TOL=73526],brueelia rotundifrons[&&NHX:TOL=73527],brueelia rotundifrontalis[&&NHX:TOL=73528],brueelia ruficapilla[&&NHX:TOL=73529],brueelia saghirae[&&NHX:TOL=73530],brueelia saliemi[&&NHX:TOL=73531],brueelia sallei[&&NHX:TOL=73532],brueelia saltatora[&&NHX:TOL=73533],brueelia satelles[&&NHX:TOL=73534],brueelia sayacae[&&NHX:TOL=73535],brueelia schistacea[&&NHX:TOL=73536],brueelia scotocercae[&&NHX:TOL=73537],brueelia sehri[&&NHX:TOL=73538],brueelia semiannulata[&&NHX:TOL=73539],brueelia setifer[&&NHX:TOL=73540],brueelia sexmaculata[&&NHX:TOL=73541],brueelia sexytanum[&&NHX:TOL=73542],brueelia sibirica[&&NHX:TOL=73543],brueelia similis[&&NHX:TOL=73544],brueelia solitaria[&&NHX:TOL=73545],brueelia stadleri[&&NHX:TOL=73546],brueelia stenozona[&&NHX:TOL=73547],brueelia sternotransversa[&&NHX:TOL=73548],brueelia sternotypicus[&&NHX:TOL=73549],brueelia straminea[&&NHX:TOL=73550],brueelia stresemanni[&&NHX:TOL=73551],brueelia subacuta[&&NHX:TOL=73552],brueelia subis[&&NHX:TOL=73553],brueelia subtilis[&&NHX:TOL=73554],brueelia tasniemae[&&NHX:TOL=73555],brueelia taulis[&&NHX:TOL=73556],brueelia tenuis[&&NHX:TOL=73557],brueelia tersinae[&&NHX:TOL=73558],brueelia theresae[&&NHX:TOL=73559],brueelia tovornikae[&&NHX:TOL=73560],brueelia trinidadensis[&&NHX:TOL=73561],brueelia tristis[&&NHX:TOL=73562],brueelia trithorax[&&NHX:TOL=73563],brueelia turdinulae[&&NHX:TOL=73564],brueelia uncinosa[&&NHX:TOL=73565],brueelia vaneki[&&NHX:TOL=73566],brueelia varia[&&NHX:TOL=73567],brueelia variegata[&&NHX:TOL=73568],brueelia ventratum[&&NHX:TOL=73569],brueelia violacea[&&NHX:TOL=73570],brueelia virgata[&&NHX:TOL=73571],brueelia viscivori[&&NHX:TOL=73572],brueelia vulgata[&&NHX:TOL=73573],brueelia weberi[&&NHX:TOL=73574],brueelia xanthocephali[&&NHX:TOL=73575],brueelia xanthocollis[&&NHX:TOL=73576],brueelia xilitla[&&NHX:TOL=73577],brueelia zavattariornis[&&NHX:TOL=73578],brueelia zeropunctata[&&NHX:TOL=73579],brueelia zohrae[&&NHX:TOL=73580],brueelia zootherae[&&NHX:TOL=73581])brueelia[&&NHX:TOL=73301],(bucerocophorus latifrons[&&NHX:TOL=73583],bucerocophorus pachycnemis[&&NHX:TOL=73584],bucerocophorus watsoni[&&NHX:TOL=73585])bucerocophorus[&&NHX:TOL=73582],(buceroemersonia brelihi[&&NHX:TOL=73587],buceroemersonia clarkei[&&NHX:TOL=73588])buceroemersonia[&&NHX:TOL=73586],(buceronirmus albescens[&&NHX:TOL=73590],buceronirmus albipes[&&NHX:TOL=73591],buceronirmus arcellus[&&NHX:TOL=73592],buceronirmus deignani[&&NHX:TOL=73593],buceronirmus grandiceps[&&NHX:TOL=73594],buceronirmus longicuneatus[&&NHX:TOL=73595],buceronirmus orientalis[&&NHX:TOL=73596],buceronirmus taurus[&&NHX:TOL=73597],buceronirmus thompsoni[&&NHX:TOL=73598],buceronirmus trabeculus[&&NHX:TOL=73599],buceronirmus zonatus[&&NHX:TOL=73600])buceronirmus[&&NHX:TOL=73589],bucorvellus docophorus[&&NHX:TOL=73601],(buerelius longiceps[&&NHX:TOL=73603],buerelius subsimus[&&NHX:TOL=73604])buerelius[&&NHX:TOL=73602],(campanulotes bidentatus[&&NHX:TOL=73606],campanulotes bisetosus[&&NHX:TOL=73607],campanulotes campanulatus[&&NHX:TOL=73608],campanulotes clayae[&&NHX:TOL=73609],campanulotes compar[&&NHX:TOL=73610],campanulotes costaricensis[&&NHX:TOL=73611],campanulotes delicatus[&&NHX:TOL=73612],campanulotes drosti[&&NHX:TOL=73613],campanulotes durdeni[&&NHX:TOL=73614],campanulotes elegans[&&NHX:TOL=73615],campanulotes flavirostris[&&NHX:TOL=73616],campanulotes flavus[&&NHX:TOL=73617],campanulotes frenatus[&&NHX:TOL=73618],campanulotes geopeliae[&&NHX:TOL=73619],campanulotes heteroceros[&&NHX:TOL=73620],campanulotes madeirensis[&&NHX:TOL=73621],campanulotes rotundatus[&&NHX:TOL=73622],campanulotes silvestris[&&NHX:TOL=73623])campanulotes[&&NHX:TOL=73605],(capraiella fulva[&&NHX:TOL=73625],capraiella masumae[&&NHX:TOL=73626],capraiella piageti[&&NHX:TOL=73627],capraiella sabzak[&&NHX:TOL=73628],capraiella subcuspidata[&&NHX:TOL=73629])capraiella[&&NHX:TOL=73624],caracaricola chimangophilus[&&NHX:TOL=73630],(carduiceps cingulatus[&&NHX:TOL=73632],carduiceps clayae[&&NHX:TOL=73633],carduiceps fulvofasciatus[&&NHX:TOL=73634],carduiceps lapponicus[&&NHX:TOL=73635],carduiceps meinertzhageni[&&NHX:TOL=73636],carduiceps scalaris[&&NHX:TOL=73637],carduiceps subscalaris[&&NHX:TOL=73638],carduiceps zonarius[&&NHX:TOL=73639])carduiceps[&&NHX:TOL=73631],centropodiella borneoensis[&&NHX:TOL=73640],(chelopistes bicolor[&&NHX:TOL=73642],chelopistes calvus[&&NHX:TOL=73643],chelopistes chamaepetes[&&NHX:TOL=73644],chelopistes costaricensis[&&NHX:TOL=73645],chelopistes craxae[&&NHX:TOL=73646],chelopistes dendrortyx[&&NHX:TOL=73647],chelopistes elongatus[&&NHX:TOL=73648],chelopistes erythrops[&&NHX:TOL=73649],chelopistes eximius[&&NHX:TOL=73650],chelopistes guttatus[&&NHX:TOL=73651],chelopistes heterurus[&&NHX:TOL=73652],chelopistes hyperythra[&&NHX:TOL=73653],chelopistes jacquacu[&&NHX:TOL=73654],chelopistes latafrons[&&NHX:TOL=73655],chelopistes lervicola[&&NHX:TOL=73656],chelopistes leucolaema[&&NHX:TOL=73657],chelopistes longicephalus[&&NHX:TOL=73658],chelopistes longipes[&&NHX:TOL=73659],chelopistes longisetosus[&&NHX:TOL=73660],chelopistes macropoda[&&NHX:TOL=73661],chelopistes melanonotus[&&NHX:TOL=73662],chelopistes meleagridis[&&NHX:TOL=73663],chelopistes mexicanus[&&NHX:TOL=73664],chelopistes minutus[&&NHX:TOL=73665],chelopistes oculari[&&NHX:TOL=73666],chelopistes peruviana[&&NHX:TOL=73667],chelopistes phasiani[&&NHX:TOL=73668],chelopistes pilosus[&&NHX:TOL=73669],chelopistes quadratus[&&NHX:TOL=73670],chelopistes rotundus[&&NHX:TOL=73671],chelopistes setosus[&&NHX:TOL=73672],chelopistes stigmatus[&&NHX:TOL=73673],chelopistes subquadratus[&&NHX:TOL=73674],chelopistes texanus[&&NHX:TOL=73675])chelopistes[&&NHX:TOL=73641],(cirrophthirius mysigma[&&NHX:TOL=73677],cirrophthirius recurvirostrae[&&NHX:TOL=73678],cirrophthirius testudinarius[&&NHX:TOL=73679])cirrophthirius[&&NHX:TOL=73676],(colilipeurus colius[&&NHX:TOL=73681],colilipeurus obscurior[&&NHX:TOL=73682],colilipeurus pallidior[&&NHX:TOL=73683],colilipeurus radiatus[&&NHX:TOL=73684])colilipeurus[&&NHX:TOL=73680],(colinicola docophoroides[&&NHX:TOL=73686],colinicola mearnsi[&&NHX:TOL=73687],colinicola numidianus[&&NHX:TOL=73688],colinicola opimus[&&NHX:TOL=73689],colinicola pallida[&&NHX:TOL=73690],colinicola philortyx[&&NHX:TOL=73691],colinicola similis[&&NHX:TOL=73692],colinicola subtenuis[&&NHX:TOL=73693])colinicola[&&NHX:TOL=73685],(coloceras absimile[&&NHX:TOL=73695],coloceras aduncum[&&NHX:TOL=73696],coloceras aegypticum[&&NHX:TOL=73697],coloceras aethiopicum[&&NHX:TOL=73698],coloceras alloceratum[&&NHX:TOL=73699],coloceras apicaudae[&&NHX:TOL=73700],coloceras aplopeliae[&&NHX:TOL=73701],coloceras benoiti[&&NHX:TOL=73702],coloceras brelihi[&&NHX:TOL=73703],coloceras britannicum[&&NHX:TOL=73704],coloceras bychovskyi[&&NHX:TOL=73705],coloceras carrikeri[&&NHX:TOL=73706],coloceras castroi[&&NHX:TOL=73707],coloceras chinense[&&NHX:TOL=73708],coloceras clayae[&&NHX:TOL=73709],coloceras clypeatum[&&NHX:TOL=73710],coloceras damicorne[&&NHX:TOL=73711],coloceras doreyanus[&&NHX:TOL=73712],coloceras elbeli[&&NHX:TOL=73713],coloceras emersoni[&&NHX:TOL=73714],coloceras fasciatum[&&NHX:TOL=73715],coloceras fradei[&&NHX:TOL=73716],coloceras funebreae[&&NHX:TOL=73717],coloceras furcatum[&&NHX:TOL=73718],coloceras geopeliae[&&NHX:TOL=73719],coloceras grande[&&NHX:TOL=73720],coloceras guinea[&&NHX:TOL=73721],coloceras harrisoni[&&NHX:TOL=73722],coloceras hemiphagae[&&NHX:TOL=73723],coloceras hilli[&&NHX:TOL=73724],coloceras hoogstraali[&&NHX:TOL=73725],coloceras indicum[&&NHX:TOL=73726],coloceras israelensis[&&NHX:TOL=73727],coloceras laticlypeatus[&&NHX:TOL=73728],coloceras lativentris[&&NHX:TOL=73729],coloceras liviae[&&NHX:TOL=73730],coloceras menadense[&&NHX:TOL=73731],coloceras museihalense[&&NHX:TOL=73732],coloceras neoindicum [&&NHX:TOL=73733],coloceras nitens[&&NHX:TOL=73734],coloceras novaeseelandiae[&&NHX:TOL=73735],coloceras orientalis[&&NHX:TOL=73736],coloceras piageti[&&NHX:TOL=73737],coloceras piriformis[&&NHX:TOL=73738],coloceras procerum[&&NHX:TOL=73739],coloceras pugioclavatus[&&NHX:TOL=73740],coloceras quadraticus[&&NHX:TOL=73741],coloceras restinctus[&&NHX:TOL=73742],coloceras santhomae[&&NHX:TOL=73743],coloceras savoi[&&NHX:TOL=73744],coloceras setosum[&&NHX:TOL=73745],coloceras stephanii[&&NHX:TOL=73746],coloceras streptopeliae[&&NHX:TOL=73747],coloceras tandani[&&NHX:TOL=73748],coloceras taschenbergi[&&NHX:TOL=73749],coloceras temporalis[&&NHX:TOL=73750],coloceras tenue[&&NHX:TOL=73751],coloceras theresae[&&NHX:TOL=73752],coloceras thomensis[&&NHX:TOL=73753],coloceras tovornikae[&&NHX:TOL=73754],coloceras truncatum[&&NHX:TOL=73755],coloceras turturis[&&NHX:TOL=73756],coloceras uchidai[&&NHX:TOL=73757],coloceras unchalli[&&NHX:TOL=73758])coloceras[&&NHX:TOL=73694],(columbicola adamsi[&&NHX:TOL=73760],columbicola altamimiae[&&NHX:TOL=73761],columbicola angustus[&&NHX:TOL=73762],columbicola bacillus[&&NHX:TOL=73763],columbicola baculoides[&&NHX:TOL=73764],columbicola beccarii[&&NHX:TOL=73765],columbicola becheti[&&NHX:TOL=73766],columbicola brygooi[&&NHX:TOL=73767],columbicola capicolae[&&NHX:TOL=73768],columbicola carrikeri[&&NHX:TOL=73769],columbicola cavifrons[&&NHX:TOL=73770],columbicola cicchinoi[&&NHX:TOL=73771],columbicola claviformis[&&NHX:TOL=73772],columbicola clayae[&&NHX:TOL=73773],columbicola columbae[&&NHX:TOL=73774],columbicola curtus[&&NHX:TOL=73775],columbicola deboomi[&&NHX:TOL=73776],columbicola drowni[&&NHX:TOL=73777],columbicola effeminatus[&&NHX:TOL=73778],columbicola elbeli[&&NHX:TOL=73779],columbicola emersoni[&&NHX:TOL=73780],columbicola exilicornis[&&NHX:TOL=73781],columbicola extinctus[&&NHX:TOL=73782],columbicola fortis[&&NHX:TOL=73783],columbicola fradei[&&NHX:TOL=73784],columbicola fradeorum[&&NHX:TOL=73785],columbicola fulmeki[&&NHX:TOL=73786],columbicola gourae[&&NHX:TOL=73787],columbicola gracilicapitis[&&NHX:TOL=73788],columbicola grandiusculus[&&NHX:TOL=73789],columbicola guimaraesi[&&NHX:TOL=73790],columbicola gymnopeliae[&&NHX:TOL=73791],columbicola harrisoni[&&NHX:TOL=73792],columbicola hoogstraali[&&NHX:TOL=73793],columbicola insularis[&&NHX:TOL=73794],columbicola keleri[&&NHX:TOL=73795],columbicola longantennatus[&&NHX:TOL=73796],columbicola longiceps[&&NHX:TOL=73797],columbicola longisetaceus[&&NHX:TOL=73798],columbicola macrourae[&&NHX:TOL=73799],columbicola mckeani[&&NHX:TOL=73800],columbicola meinertzhageni[&&NHX:TOL=73801],columbicola meridionalis[&&NHX:TOL=73802],columbicola mjoebergi[&&NHX:TOL=73803],columbicola obliteratus[&&NHX:TOL=73804],columbicola oenae[&&NHX:TOL=73805],columbicola orientalis[&&NHX:TOL=73806],columbicola paradoxus[&&NHX:TOL=73807],columbicola parvus[&&NHX:TOL=73808],columbicola passerinae[&&NHX:TOL=73809],columbicola phoenicopterae[&&NHX:TOL=73810],columbicola senegalensis[&&NHX:TOL=73811],columbicola sphenurus[&&NHX:TOL=73812],columbicola streptopeliae[&&NHX:TOL=73813],columbicola stresemanni[&&NHX:TOL=73814],columbicola taschenbergi[&&NHX:TOL=73815],columbicola tasmaniensis[&&NHX:TOL=73816],columbicola tendeiroi[&&NHX:TOL=73817],columbicola theresae[&&NHX:TOL=73818],columbicola timmermanni[&&NHX:TOL=73819],columbicola timorensis[&&NHX:TOL=73820],columbicola triangularis[&&NHX:TOL=73821],columbicola tschulyschman[&&NHX:TOL=73822],columbicola turturis[&&NHX:TOL=73823],columbicola veigasimoni[&&NHX:TOL=73824],columbicola vitiensis[&&NHX:TOL=73825],columbicola waggermani[&&NHX:TOL=73826],columbicola waltheri[&&NHX:TOL=73827],columbicola wardi[&&NHX:TOL=73828],columbicola xavieri[&&NHX:TOL=73829])columbicola[&&NHX:TOL=73759],(cotingacola dimorpha[&&NHX:TOL=73831],cotingacola fitzpatricki[&&NHX:TOL=73832],cotingacola gracilis[&&NHX:TOL=73833],cotingacola meridae[&&NHX:TOL=73834],cotingacola parmipapillae[&&NHX:TOL=73835],cotingacola rupicolae[&&NHX:TOL=73836],cotingacola stotzi[&&NHX:TOL=73837],cotingacola tergalis[&&NHX:TOL=73838])cotingacola[&&NHX:TOL=73830],(craspedonirmus atricolor[&&NHX:TOL=73840],craspedonirmus colymbinus[&&NHX:TOL=73841],craspedonirmus immer[&&NHX:TOL=73842])craspedonirmus[&&NHX:TOL=73839],(craspedorrhynchus americanus[&&NHX:TOL=73844],craspedorrhynchus aquilinus[&&NHX:TOL=73845],craspedorrhynchus brevicapitis[&&NHX:TOL=73846],craspedorrhynchus buteonis[&&NHX:TOL=73847],craspedorrhynchus candidus[&&NHX:TOL=73848],craspedorrhynchus chicquerae[&&NHX:TOL=73849],craspedorrhynchus cicatricosus[&&NHX:TOL=73850],craspedorrhynchus cornutus[&&NHX:TOL=73851],craspedorrhynchus dilatatus[&&NHX:TOL=73852],craspedorrhynchus fasciati[&&NHX:TOL=73853],craspedorrhynchus femoralis[&&NHX:TOL=73854],craspedorrhynchus fraterculus[&&NHX:TOL=73855],craspedorrhynchus genitalis[&&NHX:TOL=73856],craspedorrhynchus gypohieracis[&&NHX:TOL=73857],craspedorrhynchus haematopus[&&NHX:TOL=73858],craspedorrhynchus halieti[&&NHX:TOL=73859],craspedorrhynchus hirsutus[&&NHX:TOL=73860],craspedorrhynchus hopkinsi[&&NHX:TOL=73861],craspedorrhynchus insolitus[&&NHX:TOL=73862],craspedorrhynchus intermedius[&&NHX:TOL=73863],craspedorrhynchus leucogaster[&&NHX:TOL=73864],craspedorrhynchus macrocephalus[&&NHX:TOL=73865],craspedorrhynchus melittoscopus[&&NHX:TOL=73866],craspedorrhynchus naevius[&&NHX:TOL=73867],craspedorrhynchus nipalensis[&&NHX:TOL=73868],craspedorrhynchus nisi[&&NHX:TOL=73869],craspedorrhynchus obscurus[&&NHX:TOL=73870],craspedorrhynchus pachypus[&&NHX:TOL=73871],craspedorrhynchus platystomus[&&NHX:TOL=73872],craspedorrhynchus ranjhae[&&NHX:TOL=73873],craspedorrhynchus reichelti[&&NHX:TOL=73874],craspedorrhynchus robustisetosus[&&NHX:TOL=73875],craspedorrhynchus rotundatus[&&NHX:TOL=73876],craspedorrhynchus spathulatus[&&NHX:TOL=73877],craspedorrhynchus subbuteonis[&&NHX:TOL=73878],craspedorrhynchus subhaematopus[&&NHX:TOL=73879],craspedorrhynchus transversifrons[&&NHX:TOL=73880],craspedorrhynchus triangularis[&&NHX:TOL=73881],craspedorrhynchus tubulus[&&NHX:TOL=73882],craspedorrhynchus umbrosus[&&NHX:TOL=73883])craspedorrhynchus[&&NHX:TOL=73843],(cuclotocephalus extraneus[&&NHX:TOL=73885],cuclotocephalus secundus[&&NHX:TOL=73886],cuclotocephalus similis[&&NHX:TOL=73887])cuclotocephalus[&&NHX:TOL=73884],(cuclotogaster acuminatus[&&NHX:TOL=73889],cuclotogaster aethiopicus[&&NHX:TOL=73890],cuclotogaster arabicus[&&NHX:TOL=73891],cuclotogaster barbara[&&NHX:TOL=73892],cuclotogaster bicalcaratus[&&NHX:TOL=73893],cuclotogaster cameratus[&&NHX:TOL=73894],cuclotogaster cinereus[&&NHX:TOL=73895],cuclotogaster erckelii[&&NHX:TOL=73896],cuclotogaster gedgii[&&NHX:TOL=73897],cuclotogaster haydocki[&&NHX:TOL=73898],cuclotogaster heterogrammicus[&&NHX:TOL=73899],cuclotogaster heterographus[&&NHX:TOL=73900],cuclotogaster heyi[&&NHX:TOL=73901],cuclotogaster hopkinsi[&&NHX:TOL=73902],cuclotogaster hungerfordi[&&NHX:TOL=73903],cuclotogaster insolitus[&&NHX:TOL=73904],cuclotogaster maculipes[&&NHX:TOL=73905],cuclotogaster madagascariensis[&&NHX:TOL=73906],cuclotogaster maranensis[&&NHX:TOL=73907],cuclotogaster meinertzhageni[&&NHX:TOL=73908],cuclotogaster moucheti[&&NHX:TOL=73909],cuclotogaster nigromarginatus[&&NHX:TOL=73910],cuclotogaster notatus[&&NHX:TOL=73911],cuclotogaster obscurior[&&NHX:TOL=73912],cuclotogaster occidentalis[&&NHX:TOL=73913],cuclotogaster opimus[&&NHX:TOL=73914],cuclotogaster phayrei[&&NHX:TOL=73915],cuclotogaster placentella[&&NHX:TOL=73916],cuclotogaster pternistis[&&NHX:TOL=73917],cuclotogaster rosalindae[&&NHX:TOL=73918],cuclotogaster sephaenae[&&NHX:TOL=73919],cuclotogaster spinicaudatus[&&NHX:TOL=73920],cuclotogaster subinsolitus[&&NHX:TOL=73921],cuclotogaster synoicus[&&NHX:TOL=73922],cuclotogaster tetraogallus[&&NHX:TOL=73923],cuclotogaster theresae[&&NHX:TOL=73924],cuclotogaster ugandanus[&&NHX:TOL=73925],cuclotogaster zumpti[&&NHX:TOL=73926])cuclotogaster[&&NHX:TOL=73888],(cuculicola acutus[&&NHX:TOL=73928],cuculicola atopus[&&NHX:TOL=73929],cuculicola concolor[&&NHX:TOL=73930],cuculicola coromandus[&&NHX:TOL=73931],cuculicola dilatatofasciatus[&&NHX:TOL=73932],cuculicola erythropthalmus[&&NHX:TOL=73933],cuculicola hardayali[&&NHX:TOL=73934],cuculicola jamilae[&&NHX:TOL=73935],cuculicola kui[&&NHX:TOL=73936],cuculicola latirostris[&&NHX:TOL=73937],cuculicola limbatus[&&NHX:TOL=73938],cuculicola lipeuriformis[&&NHX:TOL=73939],cuculicola pallidus[&&NHX:TOL=73940],cuculicola philippensis[&&NHX:TOL=73941],cuculicola sculptus[&&NHX:TOL=73942],cuculicola sinensis[&&NHX:TOL=73943],cuculicola splendidus[&&NHX:TOL=73944],cuculicola vagata[&&NHX:TOL=73945])cuculicola[&&NHX:TOL=73927],(cuculoecus africanus[&&NHX:TOL=73947],cuculoecus angulatus[&&NHX:TOL=73948],cuculoecus coccygii[&&NHX:TOL=73949],cuculoecus distinctus[&&NHX:TOL=73950],cuculoecus emarginatus[&&NHX:TOL=73951],cuculoecus laticlypeatus[&&NHX:TOL=73952],cuculoecus latifrons[&&NHX:TOL=73953],cuculoecus maruhashi[&&NHX:TOL=73954],cuculoecus obcordatus[&&NHX:TOL=73955],cuculoecus piayae[&&NHX:TOL=73956])cuculoecus[&&NHX:TOL=73946],(cummingsiella ambigua[&&NHX:TOL=73958],cummingsiella aurea[&&NHX:TOL=73959],cummingsiella brelihi[&&NHX:TOL=73960],cummingsiella breviclypeata[&&NHX:TOL=73961],cummingsiella longirostricola[&&NHX:TOL=73962],cummingsiella ovalis[&&NHX:TOL=73963])cummingsiella[&&NHX:TOL=73957],dahlemhornia asymmetrica[&&NHX:TOL=73964],(degeeriella africana[&&NHX:TOL=73966],degeeriella aquilarum[&&NHX:TOL=73967],degeeriella beaufacies[&&NHX:TOL=73968],degeeriella camtschaticus[&&NHX:TOL=73969],degeeriella carrikeri[&&NHX:TOL=73970],degeeriella carruthi[&&NHX:TOL=73971],degeeriella castanea[&&NHX:TOL=73972],degeeriella deignani[&&NHX:TOL=73973],degeeriella discocephalus[&&NHX:TOL=73974],degeeriella elani[&&NHX:TOL=73975],degeeriella elbeli[&&NHX:TOL=73976],degeeriella emersoni[&&NHX:TOL=73977],degeeriella epustulata[&&NHX:TOL=73978],degeeriella frater[&&NHX:TOL=73979],degeeriella fulva[&&NHX:TOL=73980],degeeriella fusca[&&NHX:TOL=73981],degeeriella guimaraesi[&&NHX:TOL=73982],degeeriella gypsivorum[&&NHX:TOL=73983],degeeriella haydocki[&&NHX:TOL=73984],degeeriella hopkinsi[&&NHX:TOL=73985],degeeriella leucopleura[&&NHX:TOL=73986],degeeriella manariensis[&&NHX:TOL=73987],degeeriella meinertzhageni[&&NHX:TOL=73988],degeeriella mookerjeei[&&NHX:TOL=73989],degeeriella nisus[&&NHX:TOL=73990],degeeriella paleata[&&NHX:TOL=73991],degeeriella phlyctopygus[&&NHX:TOL=73992],degeeriella pricei[&&NHX:TOL=73993],degeeriella punctifer[&&NHX:TOL=73994],degeeriella quatei[&&NHX:TOL=73995],degeeriella regalis[&&NHX:TOL=73996],degeeriella rima[&&NHX:TOL=73997],degeeriella rufa[&&NHX:TOL=73998],degeeriella stelleri[&&NHX:TOL=73999],degeeriella storeri[&&NHX:TOL=74000],degeeriella tendeiroi[&&NHX:TOL=74001],degeeriella traylori[&&NHX:TOL=74002],degeeriella vagans[&&NHX:TOL=74003])degeeriella[&&NHX:TOL=73965],(discocorpus cephalosus[&&NHX:TOL=74005],discocorpus furculus[&&NHX:TOL=74006],discocorpus intermedius[&&NHX:TOL=74007],discocorpus mexicanus[&&NHX:TOL=74008],discocorpus microgenitalis[&&NHX:TOL=74009])discocorpus[&&NHX:TOL=74004],(docophoroides brevis[&&NHX:TOL=74011],docophoroides ferrisi[&&NHX:TOL=74012],docophoroides harrisoni[&&NHX:TOL=74013],docophoroides levequei[&&NHX:TOL=74014],docophoroides murphyi[&&NHX:TOL=74015],docophoroides niethammeri[&&NHX:TOL=74016],docophoroides pacificus[&&NHX:TOL=74017],docophoroides simplex[&&NHX:TOL=74018])docophoroides[&&NHX:TOL=74010],(echinophilopterus angustoclypeatus[&&NHX:TOL=74020],echinophilopterus brygooi[&&NHX:TOL=74021],echinophilopterus buphthalmus[&&NHX:TOL=74022],echinophilopterus chapini[&&NHX:TOL=74023],echinophilopterus clayae[&&NHX:TOL=74024],echinophilopterus emersoni[&&NHX:TOL=74025],echinophilopterus forficuloides[&&NHX:TOL=74026],echinophilopterus inexpectatus[&&NHX:TOL=74027],echinophilopterus protrusus[&&NHX:TOL=74028])echinophilopterus[&&NHX:TOL=74019],(emersoniella bracteata[&&NHX:TOL=74030],emersoniella galateae[&&NHX:TOL=74031],emersoniella halcyonis[&&NHX:TOL=74032],emersoniella regis[&&NHX:TOL=74033])emersoniella[&&NHX:TOL=74029],episbates pederiformis[&&NHX:TOL=74034],(esthiopterum africanum[&&NHX:TOL=74036],esthiopterum brevicephalum[&&NHX:TOL=74037],esthiopterum elbeli[&&NHX:TOL=74038],esthiopterum giganteum[&&NHX:TOL=74039],esthiopterum gruis[&&NHX:TOL=74040],esthiopterum indicum[&&NHX:TOL=74041],esthiopterum maximum[&&NHX:TOL=74042],esthiopterum paradiseum[&&NHX:TOL=74043],esthiopterum tataupa[&&NHX:TOL=74044])esthiopterum[&&NHX:TOL=74035],(falcolipeurus affulgeus[&&NHX:TOL=74046],falcolipeurus assessor[&&NHX:TOL=74047],falcolipeurus conflictus[&&NHX:TOL=74048],falcolipeurus frater[&&NHX:TOL=74049],falcolipeurus hopkinsi[&&NHX:TOL=74050],falcolipeurus jocabundus[&&NHX:TOL=74051],falcolipeurus josephi[&&NHX:TOL=74052],falcolipeurus lineatus[&&NHX:TOL=74053],falcolipeurus longiphallus[&&NHX:TOL=74054],falcolipeurus marginalis[&&NHX:TOL=74055],falcolipeurus monilis[&&NHX:TOL=74056],falcolipeurus quadriguttatus[&&NHX:TOL=74057],falcolipeurus quadripunctatus[&&NHX:TOL=74058],falcolipeurus quadripustulatus[&&NHX:TOL=74059],falcolipeurus secretarius[&&NHX:TOL=74060],falcolipeurus sulcifrons[&&NHX:TOL=74061],falcolipeurus suturalis[&&NHX:TOL=74062],falcolipeurus ternatus[&&NHX:TOL=74063],falcolipeurus yasminae[&&NHX:TOL=74064])falcolipeurus[&&NHX:TOL=74045],(falcolius elbeli[&&NHX:TOL=74066],falcolius jordani[&&NHX:TOL=74067],falcolius samarensis[&&NHX:TOL=74068])falcolius[&&NHX:TOL=74065],(forficuloecus emersoni[&&NHX:TOL=74070],forficuloecus forficula[&&NHX:TOL=74071],forficuloecus greeni[&&NHX:TOL=74072],forficuloecus meinertzhageni[&&NHX:TOL=74073],forficuloecus palmai[&&NHX:TOL=74074],forficuloecus pilgrimi[&&NHX:TOL=74075])forficuloecus[&&NHX:TOL=74069],(formicaphagus angustifrons[&&NHX:TOL=74077],formicaphagus arnoldi[&&NHX:TOL=74078],formicaphagus brevifrons[&&NHX:TOL=74079],formicaphagus clypeatus[&&NHX:TOL=74080],formicaphagus donpetersi[&&NHX:TOL=74081],formicaphagus magnus[&&NHX:TOL=74082],formicaphagus minutus[&&NHX:TOL=74083],formicaphagus picturatus[&&NHX:TOL=74084],formicaphagus pittasomae[&&NHX:TOL=74085],formicaphagus rhamphasti[&&NHX:TOL=74086],formicaphagus splendidus[&&NHX:TOL=74087])formicaphagus[&&NHX:TOL=74076],(formicaricola analoides[&&NHX:TOL=74089],formicaricola willisi[&&NHX:TOL=74090])formicaricola[&&NHX:TOL=74088],(fulicoffula americana[&&NHX:TOL=74092],fulicoffula colasbelcouri[&&NHX:TOL=74093],fulicoffula comstocki[&&NHX:TOL=74094],fulicoffula distincta[&&NHX:TOL=74095],fulicoffula gallinula[&&NHX:TOL=74096],fulicoffula heliornis[&&NHX:TOL=74097],fulicoffula longipila[&&NHX:TOL=74098],fulicoffula lurida[&&NHX:TOL=74099],fulicoffula obstinata[&&NHX:TOL=74100],fulicoffula personata[&&NHX:TOL=74101],fulicoffula rallina[&&NHX:TOL=74102],fulicoffula rotundata[&&NHX:TOL=74103],fulicoffula saturatior[&&NHX:TOL=74104],fulicoffula stammeri[&&NHX:TOL=74105])fulicoffula[&&NHX:TOL=74091],(furnariphilus griffithsi[&&NHX:TOL=74107],furnariphilus pagei[&&NHX:TOL=74108],furnariphilus parkeri[&&NHX:TOL=74109])furnariphilus[&&NHX:TOL=74106],galliphilopterus brunneopectus[&&NHX:TOL=74110],(goniocotes afer[&&NHX:TOL=74112],goniocotes afropavo[&&NHX:TOL=74113],goniocotes albidus[&&NHX:TOL=74114],goniocotes castaneicollis[&&NHX:TOL=74115],goniocotes chapini[&&NHX:TOL=74116],goniocotes chrysocephalus[&&NHX:TOL=74117],goniocotes clayae[&&NHX:TOL=74118],goniocotes congolensis[&&NHX:TOL=74119],goniocotes coxatus[&&NHX:TOL=74120],goniocotes crassicauda[&&NHX:TOL=74121],goniocotes creber[&&NHX:TOL=74122],goniocotes crossoptiloni[&&NHX:TOL=74123],goniocotes diasi[&&NHX:TOL=74124],goniocotes diplogonus[&&NHX:TOL=74125],goniocotes eurygaster[&&NHX:TOL=74126],goniocotes gallinae[&&NHX:TOL=74127],goniocotes gregarius[&&NHX:TOL=74128],goniocotes haplogonus[&&NHX:TOL=74129],goniocotes ictiorhynchi[&&NHX:TOL=74130],goniocotes ignitus[&&NHX:TOL=74131],goniocotes jirufti[&&NHX:TOL=74132],goniocotes keleri[&&NHX:TOL=74133],goniocotes keniensis[&&NHX:TOL=74134],goniocotes kivuensis[&&NHX:TOL=74135],goniocotes maculatus[&&NHX:TOL=74136],goniocotes mayuri[&&NHX:TOL=74137],goniocotes megalocephalus[&&NHX:TOL=74138],goniocotes microcephalus[&&NHX:TOL=74139],goniocotes microthorax[&&NHX:TOL=74140],goniocotes nahanii[&&NHX:TOL=74141],goniocotes obscurus[&&NHX:TOL=74142],goniocotes pallidiflavus[&&NHX:TOL=74143],goniocotes pallidomaculatus[&&NHX:TOL=74144],goniocotes parviceps[&&NHX:TOL=74145],goniocotes plumiferae[&&NHX:TOL=74146],goniocotes pternistis[&&NHX:TOL=74147],goniocotes pucherani[&&NHX:TOL=74148],goniocotes punctatus[&&NHX:TOL=74149],goniocotes pusillus[&&NHX:TOL=74150],goniocotes rectangulatus[&&NHX:TOL=74151],goniocotes reticulatus[&&NHX:TOL=74152],goniocotes rotundiceps[&&NHX:TOL=74153],goniocotes schraderi[&&NHX:TOL=74154],goniocotes shelleyii[&&NHX:TOL=74155],goniocotes tetraophasis[&&NHX:TOL=74156],goniocotes vulturini[&&NHX:TOL=74157])goniocotes[&&NHX:TOL=74111],(goniodes aepypodius[&&NHX:TOL=74159],goniodes agelastes[&&NHX:TOL=74160],goniodes ammoperdix[&&NHX:TOL=74161],goniodes antennatus[&&NHX:TOL=74162],goniodes arfakianus[&&NHX:TOL=74163],goniodes argus[&&NHX:TOL=74164],goniodes assimilis[&&NHX:TOL=74165],goniodes astrocephalus[&&NHX:TOL=74166],goniodes australis[&&NHX:TOL=74167],goniodes bambusicolus[&&NHX:TOL=74168],goniodes bifurcus[&&NHX:TOL=74169],goniodes biordinatus[&&NHX:TOL=74170],goniodes bituberculatus[&&NHX:TOL=74171],goniodes bonasus[&&NHX:TOL=74172],goniodes capitatus[&&NHX:TOL=74173],goniodes centrocerci[&&NHX:TOL=74174],goniodes cervinicornis[&&NHX:TOL=74175],goniodes chloropus[&&NHX:TOL=74176],goniodes chrysolophi[&&NHX:TOL=74177],goniodes colchici[&&NHX:TOL=74178],goniodes columbianus[&&NHX:TOL=74179],goniodes confusio[&&NHX:TOL=74180],goniodes coronatus[&&NHX:TOL=74181],goniodes corpulentus[&&NHX:TOL=74182],goniodes costatus[&&NHX:TOL=74183],goniodes crassipes[&&NHX:TOL=74184],goniodes crossoptilon[&&NHX:TOL=74185],goniodes cupido[&&NHX:TOL=74186],goniodes curtiprothorax[&&NHX:TOL=74187],goniodes curvicornis[&&NHX:TOL=74188],goniodes diardi[&&NHX:TOL=74189],goniodes discogaster[&&NHX:TOL=74190],goniodes dispar[&&NHX:TOL=74191],goniodes dissimilis[&&NHX:TOL=74192],goniodes dolani[&&NHX:TOL=74193],goniodes emersoni[&&NHX:TOL=74194],goniodes eurygaster[&&NHX:TOL=74195],goniodes fissus[&&NHX:TOL=74196],goniodes gigas[&&NHX:TOL=74197],goniodes graecus[&&NHX:TOL=74198],goniodes gutterae[&&NHX:TOL=74199],goniodes hopkinsi[&&NHX:TOL=74200],goniodes humiae[&&NHX:TOL=74201],goniodes inaequalis[&&NHX:TOL=74202],goniodes indicus[&&NHX:TOL=74203],goniodes intermedius[&&NHX:TOL=74204],goniodes isogenos[&&NHX:TOL=74205],goniodes ithaginis[&&NHX:TOL=74206],goniodes keleri[&&NHX:TOL=74207],goniodes klockenhoffi[&&NHX:TOL=74208],goniodes lagopi[&&NHX:TOL=74209],goniodes leipoae[&&NHX:TOL=74210],goniodes leucurus[&&NHX:TOL=74211],goniodes longus[&&NHX:TOL=74212],goniodes lootensi[&&NHX:TOL=74213],goniodes lophurus[&&NHX:TOL=74214],goniodes macrocephalus[&&NHX:TOL=74215],goniodes major[&&NHX:TOL=74216],goniodes megaceros[&&NHX:TOL=74217],goniodes meinertzhageni[&&NHX:TOL=74218],goniodes merriamanus[&&NHX:TOL=74219],goniodes meyi[&&NHX:TOL=74220],goniodes minimus[&&NHX:TOL=74221],goniodes minor[&&NHX:TOL=74222],goniodes montschadskyi[&&NHX:TOL=74223],goniodes moucheti[&&NHX:TOL=74224],goniodes nebraskensis[&&NHX:TOL=74225],goniodes neokeleri[&&NHX:TOL=74226],goniodes numidae[&&NHX:TOL=74227],goniodes ocellatus[&&NHX:TOL=74228],goniodes ocrea[&&NHX:TOL=74229],goniodes oreophilus[&&NHX:TOL=74230],goniodes ortygis[&&NHX:TOL=74231],goniodes ovoidalis[&&NHX:TOL=74232],goniodes pavonis[&&NHX:TOL=74233],goniodes phasidus[&&NHX:TOL=74234],goniodes pictus[&&NHX:TOL=74235],goniodes plumiferae[&&NHX:TOL=74236],goniodes processus[&&NHX:TOL=74237],goniodes reichenowii[&&NHX:TOL=74238],goniodes retractus[&&NHX:TOL=74239],goniodes rhynchortyx[&&NHX:TOL=74240],goniodes schoutedenii[&&NHX:TOL=74241],goniodes scleroptilus[&&NHX:TOL=74242],goniodes sectus[&&NHX:TOL=74243],goniodes securiger[&&NHX:TOL=74244],goniodes sinensis[&&NHX:TOL=74245],goniodes soueefi[&&NHX:TOL=74246],goniodes spinicornis[&&NHX:TOL=74247],goniodes squamatus[&&NHX:TOL=74248],goniodes stefani[&&NHX:TOL=74249],goniodes submamillatus[&&NHX:TOL=74250],goniodes talegallae[&&NHX:TOL=74251],goniodes temporalis[&&NHX:TOL=74252],goniodes tetraonis[&&NHX:TOL=74253],goniodes tetraophasis[&&NHX:TOL=74254],goniodes tibetanus[&&NHX:TOL=74255],goniodes tragopan[&&NHX:TOL=74256],goniodes wilsoni[&&NHX:TOL=74257],goniodes zairensis[&&NHX:TOL=74258])goniodes[&&NHX:TOL=74158],haffneria grandis[&&NHX:TOL=74259],(halipeurus halipeurus abnormis[&&NHX:TOL=74261],halipeurus halipeurus angusticeps angusticeps[&&NHX:TOL=74262],halipeurus halipeurus angusticeps fosteri[&&NHX:TOL=74263],halipeurus halipeurus attenuatus[&&NHX:TOL=74264],halipeurus halipeurus bulweriae[&&NHX:TOL=74265],halipeurus halipeurus consimilis[&&NHX:TOL=74266],halipeurus halipeurus diversus[&&NHX:TOL=74267],halipeurus halipeurus fallacis[&&NHX:TOL=74268],halipeurus halipeurus falsus falsus[&&NHX:TOL=74269],halipeurus halipeurus falsus pacificus[&&NHX:TOL=74270],halipeurus halipeurus forficulatus[&&NHX:TOL=74271],halipeurus halipeurus gravis[&&NHX:TOL=74272],halipeurus halipeurus heraldicus[&&NHX:TOL=74273],halipeurus halipeurus kermadecensis[&&NHX:TOL=74274],halipeurus halipeurus leucophryna[&&NHX:TOL=74275],halipeurus halipeurus marquesanus[&&NHX:TOL=74276],halipeurus halipeurus mirabilis[&&NHX:TOL=74277],halipeurus halipeurus mundae[&&NHX:TOL=74278],halipeurus synnautes nesofregettae[&&NHX:TOL=74279],halipeurus halipeurus noctivagus[&&NHX:TOL=74280],halipeurus synnautes pelagicus[&&NHX:TOL=74281],halipeurus halipeurus placodus[&&NHX:TOL=74282],halipeurus halipeurus priapulus[&&NHX:TOL=74283],halipeurus halipeurus procellariae[&&NHX:TOL=74284],halipeurus anamias raphanus[&&NHX:TOL=74285],halipeurus halipeurus sawadai[&&NHX:TOL=74286],halipeurus halipeurus spadix[&&NHX:TOL=74287],halipeurus halipeurus subclavus[&&NHX:TOL=74288],halipeurus halipeurus theresae[&&NHX:TOL=74289],halipeurus halipeurus thompsoni[&&NHX:TOL=74290],halipeurus halipeurus turtur[&&NHX:TOL=74291])halipeurus[&&NHX:TOL=74260],(harrisoniella copei[&&NHX:TOL=74293],harrisoniella densa[&&NHX:TOL=74294],harrisoniella ferox[&&NHX:TOL=74295],harrisoniella hopkinsi[&&NHX:TOL=74296])harrisoniella[&&NHX:TOL=74292],(heptapsogaster acutiventris[&&NHX:TOL=74298],heptapsogaster albigularis[&&NHX:TOL=74299],heptapsogaster andinae[&&NHX:TOL=74300],heptapsogaster benii[&&NHX:TOL=74301],heptapsogaster bolivianus[&&NHX:TOL=74302],heptapsogaster boliviensis[&&NHX:TOL=74303],heptapsogaster boraquirae[&&NHX:TOL=74304],heptapsogaster boultoni[&&NHX:TOL=74305],heptapsogaster brasiliensis[&&NHX:TOL=74306],heptapsogaster callaoi[&&NHX:TOL=74307],heptapsogaster carrikeri[&&NHX:TOL=74308],heptapsogaster chacoensis[&&NHX:TOL=74309],heptapsogaster chinirii[&&NHX:TOL=74310],heptapsogaster costaricensis[&&NHX:TOL=74311],heptapsogaster crenulatus[&&NHX:TOL=74312],heptapsogaster crucis[&&NHX:TOL=74313],heptapsogaster dilatatus[&&NHX:TOL=74314],heptapsogaster favus[&&NHX:TOL=74315],heptapsogaster femininus[&&NHX:TOL=74316],heptapsogaster frielingi[&&NHX:TOL=74317],heptapsogaster garleppi[&&NHX:TOL=74318],heptapsogaster grandis[&&NHX:TOL=74319],heptapsogaster idoneus[&&NHX:TOL=74320],heptapsogaster inexpectatus[&&NHX:TOL=74321],heptapsogaster insperatus[&&NHX:TOL=74322],heptapsogaster julius[&&NHX:TOL=74323],heptapsogaster keleri[&&NHX:TOL=74324],heptapsogaster latacephalus[&&NHX:TOL=74325],heptapsogaster latithorax[&&NHX:TOL=74326],heptapsogaster lunulatus[&&NHX:TOL=74327],heptapsogaster magdalenae[&&NHX:TOL=74328],heptapsogaster mandibularis[&&NHX:TOL=74329],heptapsogaster minor[&&NHX:TOL=74330],heptapsogaster minutus[&&NHX:TOL=74331],heptapsogaster modestae[&&NHX:TOL=74332],heptapsogaster motilonensis[&&NHX:TOL=74333],heptapsogaster nigriceps[&&NHX:TOL=74334],heptapsogaster noctivagi[&&NHX:TOL=74335],heptapsogaster nothocercae[&&NHX:TOL=74336],heptapsogaster odontophorae[&&NHX:TOL=74337],heptapsogaster oliverioi[&&NHX:TOL=74338],heptapsogaster parvulus[&&NHX:TOL=74339],heptapsogaster pentlandi[&&NHX:TOL=74340],heptapsogaster rotundatus[&&NHX:TOL=74341],heptapsogaster sexpunctatus[&&NHX:TOL=74342],heptapsogaster sexsetosus[&&NHX:TOL=74343],heptapsogaster sinuensis[&&NHX:TOL=74344],heptapsogaster stultus[&&NHX:TOL=74345],heptapsogaster subdilatatus[&&NHX:TOL=74346],heptapsogaster subminutus[&&NHX:TOL=74347],heptapsogaster subteres[&&NHX:TOL=74348],heptapsogaster tapicollae[&&NHX:TOL=74349],heptapsogaster temporalis[&&NHX:TOL=74350],heptapsogaster teres[&&NHX:TOL=74351],heptapsogaster tesselatus[&&NHX:TOL=74352],heptapsogaster testudo[&&NHX:TOL=74353],heptapsogaster truncatus[&&NHX:TOL=74354],heptapsogaster tuxtlae[&&NHX:TOL=74355],heptapsogaster undulatus[&&NHX:TOL=74356],heptapsogaster yapurae[&&NHX:TOL=74357])heptapsogaster[&&NHX:TOL=74297],(hopkinsiella clavigera[&&NHX:TOL=74359],hopkinsiella haydocki[&&NHX:TOL=74360],hopkinsiella hopkinsi[&&NHX:TOL=74361])hopkinsiella[&&NHX:TOL=74358],(ibidoecus acutulus[&&NHX:TOL=74363],ibidoecus australis[&&NHX:TOL=74364],ibidoecus bimaculatus[&&NHX:TOL=74365],ibidoecus bisignatus[&&NHX:TOL=74366],ibidoecus clausus[&&NHX:TOL=74367],ibidoecus clayae[&&NHX:TOL=74368],ibidoecus dennelli[&&NHX:TOL=74369],ibidoecus dianae[&&NHX:TOL=74370],ibidoecus fissisignatus[&&NHX:TOL=74371],ibidoecus flavus[&&NHX:TOL=74372],ibidoecus heterogenitalis[&&NHX:TOL=74373],ibidoecus hians[&&NHX:TOL=74374],ibidoecus iberoamericanus[&&NHX:TOL=74375],ibidoecus insularis[&&NHX:TOL=74376],ibidoecus longiclypeatus[&&NHX:TOL=74377],ibidoecus meinertzhageni[&&NHX:TOL=74378],ibidoecus phimosus[&&NHX:TOL=74379],ibidoecus plataleae[&&NHX:TOL=74380],ibidoecus plegadii[&&NHX:TOL=74381],ibidoecus scolopaceus[&&NHX:TOL=74382],ibidoecus tandani[&&NHX:TOL=74383],ibidoecus threskiornis[&&NHX:TOL=74384],ibidoecus vicinus[&&NHX:TOL=74385])ibidoecus[&&NHX:TOL=74362],(incidifrons armillatus[&&NHX:TOL=74387],incidifrons curvitrabeculatus[&&NHX:TOL=74388],incidifrons dissimilis[&&NHX:TOL=74389],incidifrons emersoni[&&NHX:TOL=74390],incidifrons flavopunctatus[&&NHX:TOL=74391],incidifrons fulicae[&&NHX:TOL=74392],incidifrons gallinulae[&&NHX:TOL=74393],incidifrons leucopterae[&&NHX:TOL=74394],incidifrons monachus[&&NHX:TOL=74395],incidifrons porzanae[&&NHX:TOL=74396],incidifrons ralli[&&NHX:TOL=74397],incidifrons transpositus[&&NHX:TOL=74398])incidifrons[&&NHX:TOL=74386],(kelloggia agonus[&&NHX:TOL=74400],kelloggia boucardi[&&NHX:TOL=74401],kelloggia brevipes[&&NHX:TOL=74402],kelloggia caquetae[&&NHX:TOL=74403],kelloggia chocoanus[&&NHX:TOL=74404],kelloggia clayae[&&NHX:TOL=74405],kelloggia colombianus[&&NHX:TOL=74406],kelloggia coniceps[&&NHX:TOL=74407],kelloggia dimorphus[&&NHX:TOL=74408],kelloggia genitalis[&&NHX:TOL=74409],kelloggia heterurus[&&NHX:TOL=74410],kelloggia idoneus[&&NHX:TOL=74411],kelloggia inconspicuus[&&NHX:TOL=74412],kelloggia intermedius[&&NHX:TOL=74413],kelloggia latifrons[&&NHX:TOL=74414],kelloggia latithorax[&&NHX:TOL=74415],kelloggia mendax[&&NHX:TOL=74416],kelloggia mexicanus[&&NHX:TOL=74417],kelloggia mirabilis[&&NHX:TOL=74418],kelloggia nigriceps[&&NHX:TOL=74419],kelloggia obsoletus[&&NHX:TOL=74420],kelloggia ribeiroi[&&NHX:TOL=74421],kelloggia romainei[&&NHX:TOL=74422],kelloggia strigulosus[&&NHX:TOL=74423],kelloggia undulatus[&&NHX:TOL=74424])kelloggia[&&NHX:TOL=74399],(kodocephalon bradicephalum[&&NHX:TOL=74426],kodocephalon latum[&&NHX:TOL=74427],kodocephalon suborbiculatum[&&NHX:TOL=74428])kodocephalon[&&NHX:TOL=74425],(labicotes guttatus[&&NHX:TOL=74430],labicotes kourii[&&NHX:TOL=74431])labicotes[&&NHX:TOL=74429],(lagopoecus affinis[&&NHX:TOL=74433],lagopoecus californicus[&&NHX:TOL=74434],lagopoecus choui[&&NHX:TOL=74435],lagopoecus colchicus[&&NHX:TOL=74436],lagopoecus crossoptiloni[&&NHX:TOL=74437],lagopoecus gambelii[&&NHX:TOL=74438],lagopoecus gibsoni[&&NHX:TOL=74439],lagopoecus heterotypus[&&NHX:TOL=74440],lagopoecus irinae[&&NHX:TOL=74441],lagopoecus kozuii[&&NHX:TOL=74442],lagopoecus lophophori[&&NHX:TOL=74443],lagopoecus lyrurus[&&NHX:TOL=74444],lagopoecus meinertzhageni[&&NHX:TOL=74445],lagopoecus obscurus[&&NHX:TOL=74446],lagopoecus ovatus[&&NHX:TOL=74447],lagopoecus pallidovittatus[&&NHX:TOL=74448],lagopoecus perplexus[&&NHX:TOL=74449],lagopoecus sinensis[&&NHX:TOL=74450],lagopoecus tetrastei[&&NHX:TOL=74451],lagopoecus tragopani[&&NHX:TOL=74452],lagopoecus umbellus[&&NHX:TOL=74453],lagopoecus waterstoni[&&NHX:TOL=74454])lagopoecus[&&NHX:TOL=74432],(lamprocorpus hirsutus[&&NHX:TOL=74456],lamprocorpus spinosus[&&NHX:TOL=74457])lamprocorpus[&&NHX:TOL=74455],(lipeurus alexandermuelleri[&&NHX:TOL=74459],lipeurus boonsongi[&&NHX:TOL=74460],lipeurus brunneipictus[&&NHX:TOL=74461],lipeurus caponis[&&NHX:TOL=74462],lipeurus charltonii[&&NHX:TOL=74463],lipeurus crassus[&&NHX:TOL=74464],lipeurus crinitus[&&NHX:TOL=74465],lipeurus deignani[&&NHX:TOL=74466],lipeurus dekkeri[&&NHX:TOL=74467],lipeurus delta[&&NHX:TOL=74468],lipeurus differens[&&NHX:TOL=74469],lipeurus epsilon[&&NHX:TOL=74470],lipeurus eurycnemis[&&NHX:TOL=74471],lipeurus fimbriatus[&&NHX:TOL=74472],lipeurus fradei[&&NHX:TOL=74473],lipeurus hamatus[&&NHX:TOL=74474],lipeurus introductus[&&NHX:TOL=74475],lipeurus jonesi[&&NHX:TOL=74476],lipeurus keleri[&&NHX:TOL=74477],lipeurus latifasciatus[&&NHX:TOL=74478],lipeurus lawrensis[&&NHX:TOL=74479],lipeurus lewisi[&&NHX:TOL=74480],lipeurus maculosus[&&NHX:TOL=74481],lipeurus meyeri[&&NHX:TOL=74482],lipeurus moluccensis[&&NHX:TOL=74483],lipeurus namalaius[&&NHX:TOL=74484],lipeurus nodosus[&&NHX:TOL=74485],lipeurus numidae[&&NHX:TOL=74486],lipeurus palauensis[&&NHX:TOL=74487],lipeurus parkeri[&&NHX:TOL=74488],lipeurus parumsetosus[&&NHX:TOL=74489],lipeurus pavo[&&NHX:TOL=74490],lipeurus phasidus[&&NHX:TOL=74491],lipeurus polyplectron[&&NHX:TOL=74492],lipeurus raymondi[&&NHX:TOL=74493],lipeurus rheinardia[&&NHX:TOL=74494],lipeurus sarissa[&&NHX:TOL=74495],lipeurus schoutedeni[&&NHX:TOL=74496],lipeurus silvai[&&NHX:TOL=74497],lipeurus sinuatus[&&NHX:TOL=74498],lipeurus talautensis[&&NHX:TOL=74499],lipeurus tropicalis[&&NHX:TOL=74500],lipeurus tsade[&&NHX:TOL=74501])lipeurus[&&NHX:TOL=74458],(lunaceps actophilus[&&NHX:TOL=74503],lunaceps cabanisi[&&NHX:TOL=74504],lunaceps clayae[&&NHX:TOL=74505],lunaceps drosti[&&NHX:TOL=74506],lunaceps falcinellus[&&NHX:TOL=74507],lunaceps haematopi[&&NHX:TOL=74508],lunaceps holophaeus[&&NHX:TOL=74509],lunaceps incoenis[&&NHX:TOL=74510],lunaceps limosella[&&NHX:TOL=74511],lunaceps nereis[&&NHX:TOL=74512],lunaceps numenii hopkinsi[&&NHX:TOL=74513],lunaceps numenii lissmanni[&&NHX:TOL=74514],lunaceps numenii numenii[&&NHX:TOL=74515],lunaceps numenii oliveri[&&NHX:TOL=74516],lunaceps numenii phaeopi[&&NHX:TOL=74517],lunaceps numenii proximus[&&NHX:TOL=74518],lunaceps numenii rileyi[&&NHX:TOL=74519],lunaceps parabolicus[&&NHX:TOL=74520],lunaceps paschalis[&&NHX:TOL=74521],lunaceps timmermanni[&&NHX:TOL=74522],lunaceps wilsoni[&&NHX:TOL=74523])lunaceps[&&NHX:TOL=74502],(megaginus emarginatus[&&NHX:TOL=74525],megaginus felisae[&&NHX:TOL=74526],megaginus simplex[&&NHX:TOL=74527],megaginus sordidus[&&NHX:TOL=74528],megaginus tataupensis[&&NHX:TOL=74529],megaginus tessellatus[&&NHX:TOL=74530])megaginus[&&NHX:TOL=74524],(megapeostus alterus[&&NHX:TOL=74532],megapeostus arcaeceps[&&NHX:TOL=74533],megapeostus asymmetricus[&&NHX:TOL=74534],megapeostus clypeiceps[&&NHX:TOL=74535],megapeostus fuscus[&&NHX:TOL=74536],megapeostus heptarthrogastriformis[&&NHX:TOL=74537],megapeostus heterurus[&&NHX:TOL=74538],megapeostus multiplex[&&NHX:TOL=74539],megapeostus parvigenitalis[&&NHX:TOL=74540],megapeostus petersi[&&NHX:TOL=74541],megapeostus platycephalus[&&NHX:TOL=74542],megapeostus ruficipitis[&&NHX:TOL=74543],megapeostus secundus[&&NHX:TOL=74544])megapeostus[&&NHX:TOL=74531],(megapodiella nakatae[&&NHX:TOL=74546],megapodiella parkeri[&&NHX:TOL=74547],megapodiella talegallae[&&NHX:TOL=74548])megapodiella[&&NHX:TOL=74545],(meinertzhageniella lata[&&NHX:TOL=74550],meinertzhageniella schubarti[&&NHX:TOL=74551])meinertzhageniella[&&NHX:TOL=74549],(meropoecus caprai[&&NHX:TOL=74553],meropoecus debeauxi[&&NHX:TOL=74554],meropoecus eichleri[&&NHX:TOL=74555],meropoecus emersoni[&&NHX:TOL=74556],meropoecus meropis[&&NHX:TOL=74557],meropoecus mossambicensis[&&NHX:TOL=74558],meropoecus smithi[&&NHX:TOL=74559])meropoecus[&&NHX:TOL=74552],(mulcticola balati[&&NHX:TOL=74561],mulcticola deignani[&&NHX:TOL=74562],mulcticola hypoleucus[&&NHX:TOL=74563],mulcticola macrocephalus[&&NHX:TOL=74564],mulcticola minutus[&&NHX:TOL=74565],mulcticola nacunda[&&NHX:TOL=74566],mulcticola orientalis[&&NHX:TOL=74567],mulcticola pectoralis[&&NHX:TOL=74568],mulcticola scotornis[&&NHX:TOL=74569],mulcticola tenuiceps[&&NHX:TOL=74570],mulcticola vexillarius[&&NHX:TOL=74571],mulcticola wolffi[&&NHX:TOL=74572])mulcticola[&&NHX:TOL=74560],(nakicola madagascarinus[&&NHX:TOL=74574],nakicola mesitinus[&&NHX:TOL=74575])nakicola[&&NHX:TOL=74573],(naubates guenterion clypeatus[&&NHX:TOL=74577],naubates guenterion damma[&&NHX:TOL=74578],naubates naubates fuliginosus[&&NHX:TOL=74579],naubates naubates harrisoni[&&NHX:TOL=74580],naubates guenterion heteroproctus[&&NHX:TOL=74581],naubates guenterion lessonii[&&NHX:TOL=74582],naubates guenterion prioni[&&NHX:TOL=74583],naubates guenterion pterodromi[&&NHX:TOL=74584],naubates naubates thieli[&&NHX:TOL=74585],naubates guenterion ultimae[&&NHX:TOL=74586])naubates[&&NHX:TOL=74576],(neophilopterus abdimius[&&NHX:TOL=74588],neophilopterus completus[&&NHX:TOL=74589],neophilopterus episcopi[&&NHX:TOL=74590],neophilopterus heteropygus[&&NHX:TOL=74591],neophilopterus horridus[&&NHX:TOL=74592],neophilopterus incompletus[&&NHX:TOL=74593],neophilopterus indicus[&&NHX:TOL=74594],neophilopterus jabiraui[&&NHX:TOL=74595],neophilopterus phillipsi[&&NHX:TOL=74596],neophilopterus platyclypeatus[&&NHX:TOL=74597],neophilopterus sarae[&&NHX:TOL=74598],neophilopterus subincompletus[&&NHX:TOL=74599],neophilopterus tricolor[&&NHX:TOL=74600],neophilopterus unifasciatus[&&NHX:TOL=74601])neophilopterus[&&NHX:TOL=74587],(neopsittaconirmus abnormis[&&NHX:TOL=74603],neopsittaconirmus africanus[&&NHX:TOL=74604],neopsittaconirmus albidus[&&NHX:TOL=74605],neopsittaconirmus albus[&&NHX:TOL=74606],neopsittaconirmus andrettae[&&NHX:TOL=74607],neopsittaconirmus anodis[&&NHX:TOL=74608],neopsittaconirmus borgiolii[&&NHX:TOL=74609],neopsittaconirmus capreolus[&&NHX:TOL=74610],neopsittaconirmus chandabani[&&NHX:TOL=74611],neopsittaconirmus circumfasciatus[&&NHX:TOL=74612],neopsittaconirmus clayae[&&NHX:TOL=74613],neopsittaconirmus difficilis[&&NHX:TOL=74614],neopsittaconirmus elbeli[&&NHX:TOL=74615],neopsittaconirmus emersoni[&&NHX:TOL=74616],neopsittaconirmus eos[&&NHX:TOL=74617],neopsittaconirmus femoratus[&&NHX:TOL=74618],neopsittaconirmus gracilis[&&NHX:TOL=74619],neopsittaconirmus hoogstraali[&&NHX:TOL=74620],neopsittaconirmus inexpectatus[&&NHX:TOL=74621],neopsittaconirmus interruptofasciatus[&&NHX:TOL=74622],neopsittaconirmus jobiensis[&&NHX:TOL=74623],neopsittaconirmus kea[&&NHX:TOL=74624],neopsittaconirmus lybartota[&&NHX:TOL=74625],neopsittaconirmus meinertzhageni[&&NHX:TOL=74626],neopsittaconirmus palaeornis[&&NHX:TOL=74627],neopsittaconirmus pallipes[&&NHX:TOL=74628],neopsittaconirmus piageti[&&NHX:TOL=74629],neopsittaconirmus shanahani[&&NHX:TOL=74630],neopsittaconirmus strepsiceros[&&NHX:TOL=74631],neopsittaconirmus trinoton[&&NHX:TOL=74632],neopsittaconirmus wardi[&&NHX:TOL=74633])neopsittaconirmus[&&NHX:TOL=74602],nesiotinus demersus[&&NHX:TOL=74634],(nothocotus centralis[&&NHX:TOL=74636],nothocotus distinctus[&&NHX:TOL=74637],nothocotus genitalis[&&NHX:TOL=74638],nothocotus parvithorax[&&NHX:TOL=74639],nothocotus subsimilis[&&NHX:TOL=74640])nothocotus[&&NHX:TOL=74635],nyctibicola longirostris[&&NHX:TOL=74641],(ornicholax alienus[&&NHX:TOL=74643],ornicholax boliviensis[&&NHX:TOL=74644],ornicholax felisae[&&NHX:TOL=74645],ornicholax olfersi[&&NHX:TOL=74646],ornicholax robustus[&&NHX:TOL=74647])ornicholax[&&NHX:TOL=74642],(ornithobius bucephalus[&&NHX:TOL=74649],ornithobius cygni[&&NHX:TOL=74650],ornithobius fuscus[&&NHX:TOL=74651],ornithobius goniopleurus[&&NHX:TOL=74652],ornithobius hexophthalmus[&&NHX:TOL=74653],ornithobius mathisi[&&NHX:TOL=74654],ornithobius waterstoni[&&NHX:TOL=74655])ornithobius[&&NHX:TOL=74648],(osculotes curta[&&NHX:TOL=74657],osculotes macropoda[&&NHX:TOL=74658])osculotes[&&NHX:TOL=74656],(otidoecus antilogus[&&NHX:TOL=74660],otidoecus bedfordi[&&NHX:TOL=74661],otidoecus carpi[&&NHX:TOL=74662],otidoecus dimorphus[&&NHX:TOL=74663],otidoecus dissimilis[&&NHX:TOL=74664],otidoecus elliotti[&&NHX:TOL=74665],otidoecus houbarae[&&NHX:TOL=74666],otidoecus kori[&&NHX:TOL=74667],otidoecus neotidis[&&NHX:TOL=74668],otidoecus turmalis[&&NHX:TOL=74669])otidoecus[&&NHX:TOL=74659],(oxylipeurus abdominalis[&&NHX:TOL=74671],oxylipeurus aepypodius[&&NHX:TOL=74672],oxylipeurus agriocharis[&&NHX:TOL=74673],oxylipeurus angustifrons[&&NHX:TOL=74674],oxylipeurus annamensis[&&NHX:TOL=74675],oxylipeurus appendiculatus[&&NHX:TOL=74676],oxylipeurus araucuanus[&&NHX:TOL=74677],oxylipeurus baileyi[&&NHX:TOL=74678],oxylipeurus bridgesi[&&NHX:TOL=74679],oxylipeurus burmeisteri[&&NHX:TOL=74680],oxylipeurus callipeplus[&&NHX:TOL=74681],oxylipeurus caquetae[&&NHX:TOL=74682],oxylipeurus ceratornis[&&NHX:TOL=74683],oxylipeurus chiniri[&&NHX:TOL=74684],oxylipeurus clavatus[&&NHX:TOL=74685],oxylipeurus colchicus[&&NHX:TOL=74686],oxylipeurus concolor[&&NHX:TOL=74687],oxylipeurus connectens[&&NHX:TOL=74688],oxylipeurus corpulentus[&&NHX:TOL=74689],oxylipeurus costaricensis[&&NHX:TOL=74690],oxylipeurus craxae[&&NHX:TOL=74691],oxylipeurus crossoptilon[&&NHX:TOL=74692],oxylipeurus dentatus[&&NHX:TOL=74693],oxylipeurus ellipticus[&&NHX:TOL=74694],oxylipeurus forcipatus[&&NHX:TOL=74695],oxylipeurus formosanus[&&NHX:TOL=74696],oxylipeurus garrulae[&&NHX:TOL=74697],oxylipeurus globicerus[&&NHX:TOL=74698],oxylipeurus guajirensis[&&NHX:TOL=74699],oxylipeurus guttatus[&&NHX:TOL=74700],oxylipeurus gutterae[&&NHX:TOL=74701],oxylipeurus hamatus[&&NHX:TOL=74702],oxylipeurus heiji[&&NHX:TOL=74703],oxylipeurus hierophasis[&&NHX:TOL=74704],oxylipeurus himalayensis[&&NHX:TOL=74705],oxylipeurus hoogstraali[&&NHX:TOL=74706],oxylipeurus huilensis[&&NHX:TOL=74707],oxylipeurus importunuus[&&NHX:TOL=74708],oxylipeurus inaequalis[&&NHX:TOL=74709],oxylipeurus inexpectatus[&&NHX:TOL=74710],oxylipeurus ischnocephalus[&&NHX:TOL=74711],oxylipeurus ithaginis[&&NHX:TOL=74712],oxylipeurus laticapitis[&&NHX:TOL=74713],oxylipeurus longiantennatus[&&NHX:TOL=74714],oxylipeurus longus[&&NHX:TOL=74715],oxylipeurus megalops[&&NHX:TOL=74716],oxylipeurus melanotis[&&NHX:TOL=74717],oxylipeurus mesopelios[&&NHX:TOL=74718],oxylipeurus minor[&&NHX:TOL=74719],oxylipeurus montezumae[&&NHX:TOL=74720],oxylipeurus nitzschi[&&NHX:TOL=74721],oxylipeurus ocellatus[&&NHX:TOL=74722],oxylipeurus ovaticephalus[&&NHX:TOL=74723],oxylipeurus paraguayensis[&&NHX:TOL=74724],oxylipeurus parvirostris[&&NHX:TOL=74725],oxylipeurus pauxus[&&NHX:TOL=74726],oxylipeurus penelope[&&NHX:TOL=74727],oxylipeurus perijanus[&&NHX:TOL=74728],oxylipeurus piagetinus[&&NHX:TOL=74729],oxylipeurus polytrapezius[&&NHX:TOL=74730],oxylipeurus postemarginatus[&&NHX:TOL=74731],oxylipeurus pucrasia[&&NHX:TOL=74732],oxylipeurus quadripapulus[&&NHX:TOL=74733],oxylipeurus quinimammulus[&&NHX:TOL=74734],oxylipeurus reevesi[&&NHX:TOL=74735],oxylipeurus rhizothera[&&NHX:TOL=74736],oxylipeurus rhynchoti[&&NHX:TOL=74737],oxylipeurus robustus[&&NHX:TOL=74738],oxylipeurus ruficaudatus[&&NHX:TOL=74739],oxylipeurus sanctaemartae[&&NHX:TOL=74740],oxylipeurus sinemammulus[&&NHX:TOL=74741],oxylipeurus sinuosus[&&NHX:TOL=74742],oxylipeurus soemmerringii[&&NHX:TOL=74743],oxylipeurus songprakobi[&&NHX:TOL=74744],oxylipeurus spangleri[&&NHX:TOL=74745],oxylipeurus tenuicapitis[&&NHX:TOL=74746],oxylipeurus tenuis[&&NHX:TOL=74747],oxylipeurus tetraonis[&&NHX:TOL=74748],oxylipeurus tetraophasis[&&NHX:TOL=74749],oxylipeurus tropicoperdix[&&NHX:TOL=74750],oxylipeurus uchidai[&&NHX:TOL=74751],oxylipeurus unicolor[&&NHX:TOL=74752],oxylipeurus venezuelanus[&&NHX:TOL=74753],oxylipeurus vicentei[&&NHX:TOL=74754],oxylipeurus volsellus[&&NHX:TOL=74755])oxylipeurus[&&NHX:TOL=74670],pachyskelotes orthopleurus[&&NHX:TOL=74756],(paraclisis confidens[&&NHX:TOL=74758],paraclisis diomedeae[&&NHX:TOL=74759],paraclisis giganticola[&&NHX:TOL=74760],paraclisis hyalina[&&NHX:TOL=74761],paraclisis miriceps[&&NHX:TOL=74762],paraclisis obscura[&&NHX:TOL=74763])paraclisis[&&NHX:TOL=74757],(paragoniocotes abnormis[&&NHX:TOL=74765],paragoniocotes acutifrons[&&NHX:TOL=74766],paragoniocotes anomalus[&&NHX:TOL=74767],paragoniocotes aratingae[&&NHX:TOL=74768],paragoniocotes costalimai[&&NHX:TOL=74769],paragoniocotes fasciatus[&&NHX:TOL=74770],paragoniocotes fulvofasciatus[&&NHX:TOL=74771],paragoniocotes grandis[&&NHX:TOL=74772],paragoniocotes gripocephalus[&&NHX:TOL=74773],paragoniocotes guajirensis[&&NHX:TOL=74774],paragoniocotes heterogenitalis[&&NHX:TOL=74775],paragoniocotes intermedius[&&NHX:TOL=74776],paragoniocotes ligulatus[&&NHX:TOL=74777],paragoniocotes limai[&&NHX:TOL=74778],paragoniocotes longulufrons[&&NHX:TOL=74779],paragoniocotes mercenarius[&&NHX:TOL=74780],paragoniocotes meridionalis[&&NHX:TOL=74781],paragoniocotes mexicanus[&&NHX:TOL=74782],paragoniocotes microgaster[&&NHX:TOL=74783],paragoniocotes militaris[&&NHX:TOL=74784],paragoniocotes mirabilis[&&NHX:TOL=74785],paragoniocotes molinae[&&NHX:TOL=74786],paragoniocotes nanus[&&NHX:TOL=74787],paragoniocotes neivai[&&NHX:TOL=74788],paragoniocotes nevadensis[&&NHX:TOL=74789],paragoniocotes nirmoides[&&NHX:TOL=74790],paragoniocotes pyrrhurae[&&NHX:TOL=74791],paragoniocotes rotundus[&&NHX:TOL=74792],paragoniocotes scutula[&&NHX:TOL=74793],paragoniocotes semicingulatus[&&NHX:TOL=74794],paragoniocotes tenuigaster[&&NHX:TOL=74795],paragoniocotes venezolanus[&&NHX:TOL=74796])paragoniocotes[&&NHX:TOL=74764],(paroncophorus cephalotes[&&NHX:TOL=74798],paroncophorus javanicus[&&NHX:TOL=74799],paroncophorus major[&&NHX:TOL=74800])paroncophorus[&&NHX:TOL=74797],(passonomedea emersoni[&&NHX:TOL=74802],passonomedea hopkinsi[&&NHX:TOL=74803])passonomedea[&&NHX:TOL=74801],(pectenosoma angusta[&&NHX:TOL=74805],pectenosoma cinnamomea[&&NHX:TOL=74806],pectenosoma meserythra[&&NHX:TOL=74807],pectenosoma noctivagi[&&NHX:TOL=74808],pectenosoma parva[&&NHX:TOL=74809],pectenosoma punensis[&&NHX:TOL=74810],pectenosoma salvini[&&NHX:TOL=74811],pectenosoma subparva[&&NHX:TOL=74812],pectenosoma verrucosa[&&NHX:TOL=74813],pectenosoma yapurae[&&NHX:TOL=74814])pectenosoma[&&NHX:TOL=74804],(pectinopygus acutifrons[&&NHX:TOL=74816],pectinopygus acutofasciatus[&&NHX:TOL=74817],pectinopygus afer[&&NHX:TOL=74818],pectinopygus anhingae[&&NHX:TOL=74819],pectinopygus annulatus[&&NHX:TOL=74820],pectinopygus aquaticus[&&NHX:TOL=74821],pectinopygus australis[&&NHX:TOL=74822],pectinopygus bassani[&&NHX:TOL=74823],pectinopygus bifasciatus[&&NHX:TOL=74824],pectinopygus brevicornis[&&NHX:TOL=74825],pectinopygus carunculatus[&&NHX:TOL=74826],pectinopygus crenatus[&&NHX:TOL=74827],pectinopygus dispar[&&NHX:TOL=74828],pectinopygus excornis[&&NHX:TOL=74829],pectinopygus farallonii[&&NHX:TOL=74830],pectinopygus forcipatus[&&NHX:TOL=74831],pectinopygus forficulatus[&&NHX:TOL=74832],pectinopygus fregatiphagus[&&NHX:TOL=74833],pectinopygus garbei[&&NHX:TOL=74834],pectinopygus gracilicornis[&&NHX:TOL=74835],pectinopygus grubeni[&&NHX:TOL=74836],pectinopygus gyricornis[&&NHX:TOL=74837],pectinopygus gyroceras[&&NHX:TOL=74838],pectinopygus insularis[&&NHX:TOL=74839],pectinopygus kosswigi[&&NHX:TOL=74840],pectinopygus magellanicus[&&NHX:TOL=74841],pectinopygus makundi[&&NHX:TOL=74842],pectinopygus maritimus[&&NHX:TOL=74843],pectinopygus minor[&&NHX:TOL=74844],pectinopygus nannopteri[&&NHX:TOL=74845],pectinopygus occidentalis[&&NHX:TOL=74846],pectinopygus punctatus[&&NHX:TOL=74847],pectinopygus setosus[&&NHX:TOL=74848],pectinopygus socotranus[&&NHX:TOL=74849],pectinopygus sulae[&&NHX:TOL=74850],pectinopygus timmermanni[&&NHX:TOL=74851],pectinopygus tordoffi[&&NHX:TOL=74852],pectinopygus turbinatus[&&NHX:TOL=74853],pectinopygus varius[&&NHX:TOL=74854])pectinopygus[&&NHX:TOL=74815],(pelmatocerandra enderleini[&&NHX:TOL=74856],pelmatocerandra flinti[&&NHX:TOL=74857],pelmatocerandra setosa[&&NHX:TOL=74858])pelmatocerandra[&&NHX:TOL=74855],(penenirmus affectator[&&NHX:TOL=74860],penenirmus albiventris[&&NHX:TOL=74861],penenirmus arcticus[&&NHX:TOL=74862],penenirmus arcus[&&NHX:TOL=74863],penenirmus auritus[&&NHX:TOL=74864],penenirmus barusi[&&NHX:TOL=74865],penenirmus bidentatus[&&NHX:TOL=74866],penenirmus buresi[&&NHX:TOL=74867],penenirmus campephili[&&NHX:TOL=74868],penenirmus copiosus[&&NHX:TOL=74869],penenirmus deductoris[&&NHX:TOL=74870],penenirmus desertus[&&NHX:TOL=74871],penenirmus digitiformis[&&NHX:TOL=74872],penenirmus fallax[&&NHX:TOL=74873],penenirmus fringalaudae[&&NHX:TOL=74874],penenirmus gentilis[&&NHX:TOL=74875],penenirmus guineensis[&&NHX:TOL=74876],penenirmus gulosus[&&NHX:TOL=74877],penenirmus heteroscelis[&&NHX:TOL=74878],penenirmus hibari[&&NHX:TOL=74879],penenirmus immaculatus[&&NHX:TOL=74880],penenirmus incurvatus[&&NHX:TOL=74881],penenirmus jungens[&&NHX:TOL=74882],penenirmus kuxi[&&NHX:TOL=74883],penenirmus leucomelan[&&NHX:TOL=74884],penenirmus limbatus[&&NHX:TOL=74885],penenirmus longuliceps[&&NHX:TOL=74886],penenirmus maculipes[&&NHX:TOL=74887],penenirmus marginatus[&&NHX:TOL=74888],penenirmus mirinotatus[&&NHX:TOL=74889],penenirmus nirmoideus[&&NHX:TOL=74890],penenirmus panamensis[&&NHX:TOL=74891],penenirmus pari[&&NHX:TOL=74892],penenirmus patevi[&&NHX:TOL=74893],penenirmus pavlovskyi[&&NHX:TOL=74894],penenirmus phylloscopi[&&NHX:TOL=74895],penenirmus pici[&&NHX:TOL=74896],penenirmus pikulai[&&NHX:TOL=74897],penenirmus priniae[&&NHX:TOL=74898],penenirmus quadripustulatus[&&NHX:TOL=74899],penenirmus rafflesi[&&NHX:TOL=74900],penenirmus rarus[&&NHX:TOL=74901],penenirmus reconditus[&&NHX:TOL=74902],penenirmus serrahnensis[&&NHX:TOL=74903],penenirmus serrilimbus[&&NHX:TOL=74904],penenirmus silvicultrix[&&NHX:TOL=74905],penenirmus solitarius[&&NHX:TOL=74906],penenirmus speciosus[&&NHX:TOL=74907],penenirmus stactolaemae[&&NHX:TOL=74908],penenirmus visendus[&&NHX:TOL=74909],penenirmus zeylanicus[&&NHX:TOL=74910],penenirmus zumpti[&&NHX:TOL=74911])penenirmus[&&NHX:TOL=74859],(perineus circumfasciatus[&&NHX:TOL=74913],perineus concinnoides[&&NHX:TOL=74914],perineus concinnus[&&NHX:TOL=74915],perineus macronecti[&&NHX:TOL=74916],perineus nigrolimbatus[&&NHX:TOL=74917],perineus oblongus[&&NHX:TOL=74918])perineus[&&NHX:TOL=74912],(philoceanus amadoni[&&NHX:TOL=74920],philoceanus annuliventris[&&NHX:TOL=74921],philoceanus becki[&&NHX:TOL=74922],philoceanus fasciatus[&&NHX:TOL=74923],philoceanus garrodiae[&&NHX:TOL=74924],philoceanus robertsi[&&NHX:TOL=74925])philoceanus[&&NHX:TOL=74919],(philopterus acrocephalus[&&NHX:TOL=74927],philopterus acutior[&&NHX:TOL=74928],philopterus agelaii[&&NHX:TOL=74929],philopterus albidus[&&NHX:TOL=74930],philopterus alexanderkoenigi[&&NHX:TOL=74931],philopterus alienus[&&NHX:TOL=74932],philopterus americanus[&&NHX:TOL=74933],philopterus arboreus[&&NHX:TOL=74934],philopterus atratus[&&NHX:TOL=74935],philopterus barypthenga[&&NHX:TOL=74936],philopterus belskayae[&&NHX:TOL=74937],philopterus bijae[&&NHX:TOL=74938],philopterus binedictae[&&NHX:TOL=74939],philopterus bischoffi[&&NHX:TOL=74940],philopterus breviformis[&&NHX:TOL=74941],philopterus bruneri[&&NHX:TOL=74942],philopterus capillatus[&&NHX:TOL=74943],philopterus cardinalis[&&NHX:TOL=74944],philopterus carrikeri[&&NHX:TOL=74945],philopterus cincli[&&NHX:TOL=74946],philopterus citrinellae[&&NHX:TOL=74947],philopterus claviformis[&&NHX:TOL=74948],philopterus clayae[&&NHX:TOL=74949],philopterus coarctatus[&&NHX:TOL=74950],philopterus comatus[&&NHX:TOL=74951],philopterus confusio[&&NHX:TOL=74952],philopterus corvi[&&NHX:TOL=74953],philopterus cotingae[&&NHX:TOL=74954],philopterus craigi[&&NHX:TOL=74955],philopterus crassipes[&&NHX:TOL=74956],philopterus cubensis[&&NHX:TOL=74957],philopterus cumulatus[&&NHX:TOL=74958],philopterus curvirostrae[&&NHX:TOL=74959],philopterus dalgleishi[&&NHX:TOL=74960],philopterus dathei[&&NHX:TOL=74961],philopterus davuricae[&&NHX:TOL=74962],philopterus dennyii[&&NHX:TOL=74963],philopterus depressus[&&NHX:TOL=74964],philopterus desertus[&&NHX:TOL=74965],philopterus diasi[&&NHX:TOL=74966],philopterus domesticus[&&NHX:TOL=74967],philopterus dumani[&&NHX:TOL=74968],philopterus emersoni[&&NHX:TOL=74969],philopterus emiliae[&&NHX:TOL=74970],philopterus erythrini[&&NHX:TOL=74971],philopterus eurasiaticus[&&NHX:TOL=74972],philopterus excisus[&&NHX:TOL=74973],philopterus extraneus[&&NHX:TOL=74974],philopterus fedorenkoae[&&NHX:TOL=74975],philopterus festivus[&&NHX:TOL=74976],philopterus fortunatus[&&NHX:TOL=74977],philopterus fringillae[&&NHX:TOL=74978],philopterus frontosus[&&NHX:TOL=74979],philopterus fuscatus[&&NHX:TOL=74980],philopterus fuscoventralis[&&NHX:TOL=74981],philopterus garrulae[&&NHX:TOL=74982],philopterus garruli[&&NHX:TOL=74983],philopterus goshikidori[&&NHX:TOL=74984],philopterus grandiceps[&&NHX:TOL=74985],philopterus guttatus[&&NHX:TOL=74986],philopterus hamatus[&&NHX:TOL=74987],philopterus hansmuenchi[&&NHX:TOL=74988],philopterus hanzaki[&&NHX:TOL=74989],philopterus hercynicus[&&NHX:TOL=74990],philopterus himalayanus[&&NHX:TOL=74991],philopterus hispaniolensis[&&NHX:TOL=74992],philopterus hiyodori[&&NHX:TOL=74993],philopterus hungaricus[&&NHX:TOL=74994],philopterus husinae[&&NHX:TOL=74995],philopterus hypocolii[&&NHX:TOL=74996],philopterus indefinitus[&&NHX:TOL=74997],philopterus insulicola[&&NHX:TOL=74998],philopterus irkutensis[&&NHX:TOL=74999],philopterus isabellinae[&&NHX:TOL=75000],philopterus kalkalichi[&&NHX:TOL=75001],philopterus kansensis[&&NHX:TOL=75002],philopterus kayanobori[&&NHX:TOL=75003],philopterus kekilovae[&&NHX:TOL=75004],philopterus kolla[&&NHX:TOL=75005],philopterus lahorensis[&&NHX:TOL=75006],philopterus latitemporus[&&NHX:TOL=75007],philopterus leptomelas[&&NHX:TOL=75008],philopterus linariae[&&NHX:TOL=75009],philopterus lineatus[&&NHX:TOL=75010],philopterus macgregori[&&NHX:TOL=75011],philopterus major[&&NHX:TOL=75012],philopterus markevichi[&&NHX:TOL=75013],philopterus martinezi[&&NHX:TOL=75014],philopterus melanocoryphae[&&NHX:TOL=75015],philopterus microsomaticus[&&NHX:TOL=75016],philopterus minutus[&&NHX:TOL=75017],philopterus mirificus[&&NHX:TOL=75018],philopterus mirus[&&NHX:TOL=75019],philopterus mitsusui[&&NHX:TOL=75020],philopterus modularis[&&NHX:TOL=75021],philopterus momotula[&&NHX:TOL=75022],philopterus mongolus[&&NHX:TOL=75023],philopterus montani[&&NHX:TOL=75024],philopterus mugimaki[&&NHX:TOL=75025],philopterus mukudori[&&NHX:TOL=75026],philopterus nativus[&&NHX:TOL=75027],philopterus necopinatus[&&NHX:TOL=75028],philopterus neomajor[&&NHX:TOL=75029],philopterus neotropicalis[&&NHX:TOL=75030],philopterus novaezealandiae[&&NHX:TOL=75031],philopterus ocellatus[&&NHX:TOL=75032],philopterus oenanthe[&&NHX:TOL=75033],philopterus orinocensis[&&NHX:TOL=75034],philopterus ornatus[&&NHX:TOL=75035],philopterus osborni[&&NHX:TOL=75036],philopterus osculolimbatus[&&NHX:TOL=75037],philopterus pallescens[&&NHX:TOL=75038],philopterus palmai[&&NHX:TOL=75039],philopterus panamensis[&&NHX:TOL=75040],philopterus parvulus[&&NHX:TOL=75041],philopterus passerinus[&&NHX:TOL=75042],philopterus pavidus[&&NHX:TOL=75043],philopterus peripariphilus[&&NHX:TOL=75044],philopterus petrinus[&&NHX:TOL=75045],philopterus phillipi[&&NHX:TOL=75046],philopterus phoenicuri[&&NHX:TOL=75047],philopterus phylloscopi[&&NHX:TOL=75048],philopterus picae[&&NHX:TOL=75049],philopterus picatae[&&NHX:TOL=75050],philopterus piezorhinae[&&NHX:TOL=75051],philopterus platypsarus[&&NHX:TOL=75052],philopterus pleschankae[&&NHX:TOL=75053],philopterus prionitis[&&NHX:TOL=75054],philopterus ptilostomi[&&NHX:TOL=75055],philopterus quadraticeps[&&NHX:TOL=75056],philopterus quiscali[&&NHX:TOL=75057],philopterus rapax[&&NHX:TOL=75058],philopterus raptori[&&NHX:TOL=75059],philopterus reginae[&&NHX:TOL=75060],philopterus reguli[&&NHX:TOL=75061],philopterus residuus[&&NHX:TOL=75062],philopterus rhodospizae[&&NHX:TOL=75063],philopterus roehreri[&&NHX:TOL=75064],philopterus rotundatus[&&NHX:TOL=75065],philopterus rubeculae[&&NHX:TOL=75066],philopterus rufus[&&NHX:TOL=75067],philopterus rutteri[&&NHX:TOL=75068],philopterus sabia[&&NHX:TOL=75069],philopterus sartajae[&&NHX:TOL=75070],philopterus sclerotifrons[&&NHX:TOL=75071],philopterus shakushigi[&&NHX:TOL=75072],philopterus sialii[&&NHX:TOL=75073],philopterus sibiricus[&&NHX:TOL=75074],philopterus sittae[&&NHX:TOL=75075],philopterus smogorzewskyi[&&NHX:TOL=75076],philopterus solus[&&NHX:TOL=75077],philopterus spinosus[&&NHX:TOL=75078],philopterus stadleri[&&NHX:TOL=75079],philopterus stegmanni[&&NHX:TOL=75080],philopterus stepposus[&&NHX:TOL=75081],philopterus subitus[&&NHX:TOL=75082],philopterus taigaicus[&&NHX:TOL=75083],philopterus taigensis[&&NHX:TOL=75084],philopterus thryptocephalus[&&NHX:TOL=75085],philopterus thuringiacus[&&NHX:TOL=75086],philopterus timmermanni[&&NHX:TOL=75087],philopterus titicacae[&&NHX:TOL=75088],philopterus tityra[&&NHX:TOL=75089],philopterus topicalis[&&NHX:TOL=75090],philopterus trabecula[&&NHX:TOL=75091],philopterus trigonophorus[&&NHX:TOL=75092],philopterus troglodytis[&&NHX:TOL=75093],philopterus tropicalis[&&NHX:TOL=75094],philopterus turdi[&&NHX:TOL=75095],philopterus turkmenicus[&&NHX:TOL=75096],philopterus underwoodi[&&NHX:TOL=75097],philopterus unifarius[&&NHX:TOL=75098],philopterus urocissae[&&NHX:TOL=75099],philopterus vernus[&&NHX:TOL=75100],philopterus vittati[&&NHX:TOL=75101],philopterus vultuosus[&&NHX:TOL=75102],philopterus zerini[&&NHX:TOL=75103],philopterus zlotorzyckae[&&NHX:TOL=75104],philopterus zohrae[&&NHX:TOL=75105],philopterus zulfi[&&NHX:TOL=75106])philopterus[&&NHX:TOL=74926],(physconella cinerea[&&NHX:TOL=75108],physconella emersoni[&&NHX:TOL=75109],physconella genitalis[&&NHX:TOL=75110],physconella hamata[&&NHX:TOL=75111],physconella julia[&&NHX:TOL=75112],physconella kelloggi[&&NHX:TOL=75113],physconella nothocercae[&&NHX:TOL=75114],physconella subsimilis[&&NHX:TOL=75115])physconella[&&NHX:TOL=75107],(physconelloides anolaimae[&&NHX:TOL=75117],physconelloides australiensis[&&NHX:TOL=75118],physconelloides ceratoceps[&&NHX:TOL=75119],physconelloides cubanus[&&NHX:TOL=75120],physconelloides emersoni[&&NHX:TOL=75121],physconelloides eurysema[&&NHX:TOL=75122],physconelloides galapagensis[&&NHX:TOL=75123],physconelloides johnsoni[&&NHX:TOL=75124],physconelloides moyeri[&&NHX:TOL=75125],physconelloides perijae[&&NHX:TOL=75126],physconelloides robbinsi[&&NHX:TOL=75127],physconelloides rufaxilla[&&NHX:TOL=75128],physconelloides spenceri[&&NHX:TOL=75129],physconelloides strangeri[&&NHX:TOL=75130],physconelloides wisemani[&&NHX:TOL=75131],physconelloides zenaidurae[&&NHX:TOL=75132])physconelloides[&&NHX:TOL=75116],(picicola acutus[&&NHX:TOL=75134],picicola angolensis[&&NHX:TOL=75135],picicola australis[&&NHX:TOL=75136],picicola bimaculatus[&&NHX:TOL=75137],picicola campethera[&&NHX:TOL=75138],picicola candidus[&&NHX:TOL=75139],picicola capitatus[&&NHX:TOL=75140],picicola cuniculariae[&&NHX:TOL=75141],picicola emersoni[&&NHX:TOL=75142],picicola foedus[&&NHX:TOL=75143],picicola fusca[&&NHX:TOL=75144],picicola grundespectus[&&NHX:TOL=75145],picicola magnus[&&NHX:TOL=75146],picicola malaya[&&NHX:TOL=75147],picicola marginatulus[&&NHX:TOL=75148],picicola meinertzhageni[&&NHX:TOL=75149],picicola nitzschii[&&NHX:TOL=75150],picicola obscurus[&&NHX:TOL=75151],picicola orpheus[&&NHX:TOL=75152],picicola porisma[&&NHX:TOL=75153],picicola quadripustulosus[&&NHX:TOL=75154],picicola regulus[&&NHX:TOL=75155],picicola roberti[&&NHX:TOL=75156],picicola rufa[&&NHX:TOL=75157],picicola snodgrassi[&&NHX:TOL=75158],picicola striata[&&NHX:TOL=75159],picicola superciliosa[&&NHX:TOL=75160],picicola thripias[&&NHX:TOL=75161],picicola usheri[&&NHX:TOL=75162])picicola[&&NHX:TOL=75133],(podargoecus papuensis[&&NHX:TOL=75164],podargoecus strigoides[&&NHX:TOL=75165],podargoecus tasmaniensis[&&NHX:TOL=75166])podargoecus[&&NHX:TOL=75163],(pseudocophorus antennatus[&&NHX:TOL=75168],pseudocophorus chasmorhynchus[&&NHX:TOL=75169],pseudocophorus decoratus[&&NHX:TOL=75170],pseudocophorus perijanus[&&NHX:TOL=75171],pseudocophorus peruvianus[&&NHX:TOL=75172])pseudocophorus[&&NHX:TOL=75167],(pseudolipeurus bonapartei[&&NHX:TOL=75174],pseudolipeurus carrikeri[&&NHX:TOL=75175],pseudolipeurus conspicuus[&&NHX:TOL=75176],pseudolipeurus dubius[&&NHX:TOL=75177],pseudolipeurus garleppi[&&NHX:TOL=75178],pseudolipeurus grandis[&&NHX:TOL=75179],pseudolipeurus longipes[&&NHX:TOL=75180],pseudolipeurus macconelli[&&NHX:TOL=75181],pseudolipeurus macrogenitalis[&&NHX:TOL=75182],pseudolipeurus megaceros[&&NHX:TOL=75183],pseudolipeurus peruvianus[&&NHX:TOL=75184],pseudolipeurus plumbeus[&&NHX:TOL=75185],pseudolipeurus sanctaemartae[&&NHX:TOL=75186],pseudolipeurus serratae[&&NHX:TOL=75187],pseudolipeurus similis[&&NHX:TOL=75188],pseudolipeurus subsimilis[&&NHX:TOL=75189],pseudolipeurus taoi[&&NHX:TOL=75190],pseudolipeurus theresae[&&NHX:TOL=75191],pseudolipeurus tinami[&&NHX:TOL=75192],pseudolipeurus verendus[&&NHX:TOL=75193])pseudolipeurus[&&NHX:TOL=75173],(pseudonirmus charcoti[&&NHX:TOL=75195],pseudonirmus gurlti[&&NHX:TOL=75196],pseudonirmus lubugris[&&NHX:TOL=75197])pseudonirmus[&&NHX:TOL=75194],(pseudophilopterus grandior[&&NHX:TOL=75199],pseudophilopterus hirsutus[&&NHX:TOL=75200],pseudophilopterus notivagus[&&NHX:TOL=75201],pseudophilopterus obsoletus[&&NHX:TOL=75202],pseudophilopterus perijanus[&&NHX:TOL=75203],pseudophilopterus similis[&&NHX:TOL=75204],pseudophilopterus tinami[&&NHX:TOL=75205])pseudophilopterus[&&NHX:TOL=75198],(psittaconirmus psittaconirmus australis[&&NHX:TOL=75207],psittaconirmus psittaconirmus cardinalis[&&NHX:TOL=75208],psittaconirmus psittaconirmus charmosynae[&&NHX:TOL=75209],psittaconirmus psittaconirmus chlorocerci[&&NHX:TOL=75210],psittaconirmus psittaconirmus comis[&&NHX:TOL=75211],psittaconirmus psittaconirmus forficuloides[&&NHX:TOL=75212],psittaconirmus psittaconirmus harrisoni[&&NHX:TOL=75213],psittaconirmus psittaconirmus hellenthali[&&NHX:TOL=75214],psittaconirmus psittaconirmus johnstoniae[&&NHX:TOL=75215],psittaconirmus xenopsittaconirmus kulmani[&&NHX:TOL=75216],psittaconirmus psittaconirmus launceloti[&&NHX:TOL=75217],psittaconirmus parapsittaconirmus micropsittae[&&NHX:TOL=75218],psittaconirmus psittaconirmus neumanni[&&NHX:TOL=75219],psittaconirmus psittaconirmus opopsittae[&&NHX:TOL=75220],psittaconirmus psittaconirmus zinki[&&NHX:TOL=75221])psittaconirmus[&&NHX:TOL=75206],(psittoecus eos[&&NHX:TOL=75223],psittoecus hoogstraali[&&NHX:TOL=75224],psittoecus mollisoni[&&NHX:TOL=75225],psittoecus vanzolinii[&&NHX:TOL=75226],psittoecus waterstoni[&&NHX:TOL=75227])psittoecus[&&NHX:TOL=75222],(pterocotes aberrans[&&NHX:TOL=75229],pterocotes costaricensis[&&NHX:TOL=75230],pterocotes cylindratus[&&NHX:TOL=75231],pterocotes immaculatus[&&NHX:TOL=75232],pterocotes inexpectatus[&&NHX:TOL=75233],pterocotes julius[&&NHX:TOL=75234],pterocotes nothocercae[&&NHX:TOL=75235],pterocotes solitarius[&&NHX:TOL=75236],pterocotes taoi[&&NHX:TOL=75237],pterocotes tergalis[&&NHX:TOL=75238],pterocotes undulatus[&&NHX:TOL=75239])pterocotes[&&NHX:TOL=75228],(quadraceps acuticeps[&&NHX:TOL=75241],quadraceps adustus[&&NHX:TOL=75242],quadraceps aethereus[&&NHX:TOL=75243],quadraceps alcae[&&NHX:TOL=75244],quadraceps alexandrinus[&&NHX:TOL=75245],quadraceps alpha[&&NHX:TOL=75246],quadraceps altoasiaticum[&&NHX:TOL=75247],quadraceps ambestrix[&&NHX:TOL=75248],quadraceps anagrapsus[&&NHX:TOL=75249],quadraceps annosus[&&NHX:TOL=75250],quadraceps annulatus[&&NHX:TOL=75251],quadraceps antiquus[&&NHX:TOL=75252],quadraceps apophoretus[&&NHX:TOL=75253],quadraceps assimilis[&&NHX:TOL=75254],quadraceps auratus[&&NHX:TOL=75255],quadraceps australis[&&NHX:TOL=75256],quadraceps baliola[&&NHX:TOL=75257],quadraceps bicuspis[&&NHX:TOL=75258],quadraceps birostris[&&NHX:TOL=75259],quadraceps boephilus[&&NHX:TOL=75260],quadraceps brunneus[&&NHX:TOL=75261],quadraceps bryki[&&NHX:TOL=75262],quadraceps burhinoides[&&NHX:TOL=75263],quadraceps carrikeri[&&NHX:TOL=75264],quadraceps caspius[&&NHX:TOL=75265],quadraceps cedemajori[&&NHX:TOL=75266],quadraceps charadrii[&&NHX:TOL=75267],quadraceps chorleyi[&&NHX:TOL=75268],quadraceps coenocoryphae[&&NHX:TOL=75269],quadraceps connexus[&&NHX:TOL=75270],quadraceps crassipedalis[&&NHX:TOL=75271],quadraceps cucullatus[&&NHX:TOL=75272],quadraceps dasi[&&NHX:TOL=75273],quadraceps decipiens[&&NHX:TOL=75274],quadraceps dominella[&&NHX:TOL=75275],quadraceps dressleri[&&NHX:TOL=75276],quadraceps eggelingi[&&NHX:TOL=75277],quadraceps ellipticus[&&NHX:TOL=75278],quadraceps elongatus[&&NHX:TOL=75279],quadraceps eugrammicus[&&NHX:TOL=75280],quadraceps falcigerus[&&NHX:TOL=75281],quadraceps fimbriatus[&&NHX:TOL=75282],quadraceps fissus[&&NHX:TOL=75283],quadraceps furvus[&&NHX:TOL=75284],quadraceps galachrysiae[&&NHX:TOL=75285],quadraceps geminus[&&NHX:TOL=75286],quadraceps giebeli[&&NHX:TOL=75287],quadraceps grallarius[&&NHX:TOL=75288],quadraceps guimaraesi[&&NHX:TOL=75289],quadraceps hancocki[&&NHX:TOL=75290],quadraceps hasei[&&NHX:TOL=75291],quadraceps helgovauki[&&NHX:TOL=75292],quadraceps hemichrous[&&NHX:TOL=75293],quadraceps hiaticulae[&&NHX:TOL=75294],quadraceps hopkinsi[&&NHX:TOL=75295],quadraceps hoplopteri[&&NHX:TOL=75296],quadraceps hospes[&&NHX:TOL=75297],quadraceps houri[&&NHX:TOL=75298],quadraceps impar[&&NHX:TOL=75299],quadraceps incai[&&NHX:TOL=75300],quadraceps insignis[&&NHX:TOL=75301],quadraceps junceus[&&NHX:TOL=75302],quadraceps kekra[&&NHX:TOL=75303],quadraceps kilimandjarensis[&&NHX:TOL=75304],quadraceps kirghizicus[&&NHX:TOL=75305],quadraceps kosswigi[&&NHX:TOL=75306],quadraceps kuscheli[&&NHX:TOL=75307],quadraceps lahorensis[&&NHX:TOL=75308],quadraceps latus[&&NHX:TOL=75309],quadraceps legatus[&&NHX:TOL=75310],quadraceps lineatus[&&NHX:TOL=75311],quadraceps longicollis[&&NHX:TOL=75312],quadraceps macrocephalus[&&NHX:TOL=75313],quadraceps major[&&NHX:TOL=75314],quadraceps maritimus[&&NHX:TOL=75315],quadraceps meinertzhageni[&&NHX:TOL=75316],quadraceps mutschekiepchen[&&NHX:TOL=75317],quadraceps neoaustralis[&&NHX:TOL=75318],quadraceps niethammeri[&&NHX:TOL=75319],quadraceps nigrolimbatus[&&NHX:TOL=75320],quadraceps normifer[&&NHX:TOL=75321],quadraceps novaeseelandiae[&&NHX:TOL=75322],quadraceps nycthemerus[&&NHX:TOL=75323],quadraceps obliquus[&&NHX:TOL=75324],quadraceps obscurus[&&NHX:TOL=75325],quadraceps obtusus[&&NHX:TOL=75326],quadraceps ochropi[&&NHX:TOL=75327],quadraceps orarius[&&NHX:TOL=75328],quadraceps ornatus[&&NHX:TOL=75329],quadraceps ornatus antarcticus[&&NHX:TOL=75330],quadraceps ornatus fuscolaminulatus[&&NHX:TOL=75331],quadraceps ornatus lineolatus[&&NHX:TOL=75332],quadraceps ornatus ornatus[&&NHX:TOL=75333],quadraceps ornatus paulschulzei[&&NHX:TOL=75334],quadraceps ornatus striolatus[&&NHX:TOL=75335],quadraceps pacificus[&&NHX:TOL=75336],quadraceps paludicola[&&NHX:TOL=75337],quadraceps parvopallidus[&&NHX:TOL=75338],quadraceps phaeonotus[&&NHX:TOL=75339],quadraceps phalaropi[&&NHX:TOL=75340],quadraceps pictus[&&NHX:TOL=75341],quadraceps praestans[&&NHX:TOL=75342],quadraceps princeps[&&NHX:TOL=75343],quadraceps ptyadis[&&NHX:TOL=75344],quadraceps punctatus clayae[&&NHX:TOL=75345],quadraceps punctatus felix[&&NHX:TOL=75346],quadraceps punctatus lingulatus[&&NHX:TOL=75347],quadraceps punctatus pallidus[&&NHX:TOL=75348],quadraceps punctatus punctatus[&&NHX:TOL=75349],quadraceps punctatus regressus[&&NHX:TOL=75350],quadraceps punctatus schuezi[&&NHX:TOL=75351],quadraceps punctatus sublingulatus[&&NHX:TOL=75352],quadraceps punctatus ventosus[&&NHX:TOL=75353],quadraceps punctifer[&&NHX:TOL=75354],quadraceps punensis[&&NHX:TOL=75355],quadraceps quadrisetaceus[&&NHX:TOL=75356],quadraceps ravus[&&NHX:TOL=75357],quadraceps renschi[&&NHX:TOL=75358],quadraceps rheinwaldi[&&NHX:TOL=75359],quadraceps ridgwayi[&&NHX:TOL=75360],quadraceps rubricollis[&&NHX:TOL=75361],quadraceps ruficollis[&&NHX:TOL=75362],quadraceps schusteri[&&NHX:TOL=75363],quadraceps sellatus[&&NHX:TOL=75364],quadraceps semifissus[&&NHX:TOL=75365],quadraceps semipalmatus[&&NHX:TOL=75366],quadraceps senegalensis[&&NHX:TOL=75367],quadraceps separatus[&&NHX:TOL=75368],quadraceps signatus[&&NHX:TOL=75369],quadraceps similis[&&NHX:TOL=75370],quadraceps sinensis[&&NHX:TOL=75371],quadraceps solitarius[&&NHX:TOL=75372],quadraceps stellaepolaris[&&NHX:TOL=75373],quadraceps strepsilaris[&&NHX:TOL=75374],quadraceps thapari[&&NHX:TOL=75375],quadraceps titicacae[&&NHX:TOL=75376],quadraceps titschacki[&&NHX:TOL=75377],quadraceps umbrinus[&&NHX:TOL=75378],quadraceps vaginalis[&&NHX:TOL=75379],quadraceps waterstoni[&&NHX:TOL=75380],quadraceps zephyra[&&NHX:TOL=75381])quadraceps[&&NHX:TOL=75240],(rallicola rallicola acutifrons[&&NHX:TOL=75383],rallicola rallicola advenus[&&NHX:TOL=75384],rallicola rallicola affinis[&&NHX:TOL=75385],rallicola rallicola africana[&&NHX:TOL=75386],rallicola rallicola anabacerthia[&&NHX:TOL=75387],rallicola rallicola andinus[&&NHX:TOL=75388],rallicola rallicola antioquensis[&&NHX:TOL=75389],rallicola rallicola aramides[&&NHX:TOL=75390],rallicola rallicola bedfordi[&&NHX:TOL=75391],rallicola rallicola bipustulatus[&&NHX:TOL=75392],rallicola rallicola bisetosus[&&NHX:TOL=75393],rallicola rallicola bournei[&&NHX:TOL=75394],rallicola rallicola californicus[&&NHX:TOL=75395],rallicola rallicola campbelli[&&NHX:TOL=75396],rallicola rallicola carrikeri[&&NHX:TOL=75397],rallicola rallicola centropus[&&NHX:TOL=75398],rallicola rallicola cephalosa[&&NHX:TOL=75399],rallicola rallicola certhia[&&NHX:TOL=75400],rallicola rallicola chunchotambo[&&NHX:TOL=75401],rallicola rallicola clayae[&&NHX:TOL=75402],rallicola rallicola colombiana[&&NHX:TOL=75403],rallicola rallicola cornutae[&&NHX:TOL=75404],rallicola rallicola cuspidatus[&&NHX:TOL=75405],rallicola rallicola deckeri[&&NHX:TOL=75406],rallicola rallicola elliotti[&&NHX:TOL=75407],rallicola rallicola ewingi[&&NHX:TOL=75408],rallicola rallicola exiguifrons[&&NHX:TOL=75409],rallicola huiacola extinctus[&&NHX:TOL=75410],rallicola rallicola ferrisi[&&NHX:TOL=75411],rallicola rallicola flavescens[&&NHX:TOL=75412],rallicola rallicola foedus[&&NHX:TOL=75413],rallicola rallicola fulicae[&&NHX:TOL=75414],rallicola rallicola fuliginosa[&&NHX:TOL=75415],rallicola rallicola funebris[&&NHX:TOL=75416],rallicola aptericola gadowi[&&NHX:TOL=75417],rallicola aptericola gracilentus[&&NHX:TOL=75418],rallicola rallicola gracilis[&&NHX:TOL=75419],rallicola rallicola guami[&&NHX:TOL=75420],rallicola rallicola guimaraesi[&&NHX:TOL=75421],rallicola rallicola hambleri[&&NHX:TOL=75422],rallicola rallicola harrisoni[&&NHX:TOL=75423],rallicola rallicola harveyi[&&NHX:TOL=75424],rallicola rallicola haydocki[&&NHX:TOL=75425],rallicola rallicola heterocephala[&&NHX:TOL=75426],rallicola rallicola hirsuta[&&NHX:TOL=75427],rallicola rallicola hoogstraali[&&NHX:TOL=75428],rallicola rallicola hylactiphaga[&&NHX:TOL=75429],rallicola rallicola indicus[&&NHX:TOL=75430],rallicola rallicola inexpectata[&&NHX:TOL=75431],rallicola rallicola insulana[&&NHX:TOL=75432],rallicola rallicola irediparrae[&&NHX:TOL=75433],rallicola rallicola kelloggi[&&NHX:TOL=75434],rallicola rallicola keymerae[&&NHX:TOL=75435],rallicola rallicola lachrymosa[&&NHX:TOL=75436],rallicola rallicola laticephala[&&NHX:TOL=75437],rallicola rallicola leeae[&&NHX:TOL=75438],rallicola rallicola leucopterae[&&NHX:TOL=75439],rallicola rallicola longifrons[&&NHX:TOL=75440],rallicola rallicola lugens[&&NHX:TOL=75441],rallicola rallicola lyali[&&NHX:TOL=75442],rallicola rallicola maculatus[&&NHX:TOL=75443],rallicola rallicola mallophagulus[&&NHX:TOL=75444],rallicola rallicola minhaensis[&&NHX:TOL=75445],rallicola rallicola minutus[&&NHX:TOL=75446],rallicola rallicola mooreae[&&NHX:TOL=75447],rallicola rallicola mortieri[&&NHX:TOL=75448],rallicola rallicola mystax[&&NHX:TOL=75449],rallicola rallicola ortygometrae[&&NHX:TOL=75450],rallicola rallicola palmai[&&NHX:TOL=75451],rallicola rallicola parani[&&NHX:TOL=75452],rallicola rallicola parvigenitalis[&&NHX:TOL=75453],rallicola rallicola philippensis[&&NHX:TOL=75454],rallicola rallicola piageti[&&NHX:TOL=75455],rallicola rallicola picirostris[&&NHX:TOL=75456],rallicola aptericola pilgrimi[&&NHX:TOL=75457],rallicola rallicola pipraphaga[&&NHX:TOL=75458],rallicola rallicola porzanae[&&NHX:TOL=75459],rallicola rallicola pratti[&&NHX:TOL=75460],rallicola rallicola quadraticeps[&&NHX:TOL=75461],rallicola aptericola rodericki[&&NHX:TOL=75462],rallicola rallicola sarothurae[&&NHX:TOL=75463],rallicola rallicola scapanoides[&&NHX:TOL=75464],rallicola rallicola subporzanae[&&NHX:TOL=75465],rallicola rallicola sulcatus[&&NHX:TOL=75466],rallicola rallicola tabuensis[&&NHX:TOL=75467],rallicola rallicola takahe[&&NHX:TOL=75468],rallicola rallicola taylori[&&NHX:TOL=75469],rallicola rallicola tergalis[&&NHX:TOL=75470],rallicola rallicola thompsoni[&&NHX:TOL=75471],rallicola rallicola titicacae[&&NHX:TOL=75472],rallicola rallicola tompkinsi[&&NHX:TOL=75473],rallicola rallicola triangularis[&&NHX:TOL=75474],rallicola rallicola unguiculatus[&&NHX:TOL=75475],rallicola rallicola villiersi[&&NHX:TOL=75476],rallicola rallicola wernecki[&&NHX:TOL=75477],rallicola rallicola zumpti[&&NHX:TOL=75478])rallicola[&&NHX:TOL=75382],(rhopaloceras abbreviatus[&&NHX:TOL=75480],rhopaloceras almeidai[&&NHX:TOL=75481],rhopaloceras bonaparti[&&NHX:TOL=75482],rhopaloceras brevitemporalis[&&NHX:TOL=75483],rhopaloceras carrikeri[&&NHX:TOL=75484],rhopaloceras cinereus[&&NHX:TOL=75485],rhopaloceras genitalis[&&NHX:TOL=75486],rhopaloceras heterogenitalis[&&NHX:TOL=75487],rhopaloceras laticeps[&&NHX:TOL=75488],rhopaloceras oniscus[&&NHX:TOL=75489],rhopaloceras pennaticeps[&&NHX:TOL=75490],rhopaloceras rudimentarius[&&NHX:TOL=75491],rhopaloceras spatulata[&&NHX:TOL=75492],rhopaloceras undulatus[&&NHX:TOL=75493],rhopaloceras variegatus[&&NHX:TOL=75494])rhopaloceras[&&NHX:TOL=75479],(rhynonirmus carrikeri[&&NHX:TOL=75496],rhynonirmus helvolus[&&NHX:TOL=75497],rhynonirmus infuscatus[&&NHX:TOL=75498],rhynonirmus kingi[&&NHX:TOL=75499],rhynonirmus medius[&&NHX:TOL=75500],rhynonirmus parsonsae[&&NHX:TOL=75501],rhynonirmus scolopacis[&&NHX:TOL=75502],rhynonirmus stenurae[&&NHX:TOL=75503])rhynonirmus[&&NHX:TOL=75495],rotundiceps cordatus[&&NHX:TOL=75504],(saemundssonia saemundssonia acutipecta[&&NHX:TOL=75506],saemundssonia saemundssonia africana africana[&&NHX:TOL=75507],saemundssonia saemundssonia africana senegalla[&&NHX:TOL=75508],saemundssonia saemundssonia africana sycophanta[&&NHX:TOL=75509],saemundssonia saemundssonia alaskensis[&&NHX:TOL=75510],saemundssonia saemundssonia albemarlensis[&&NHX:TOL=75511],saemundssonia saemundssonia anisorhamphos[&&NHX:TOL=75512],saemundssonia saemundssonia antarctica[&&NHX:TOL=75513],saemundssonia saemundssonia australis[&&NHX:TOL=75514],saemundssonia saemundssonia bakeri[&&NHX:TOL=75515],saemundssonia saemundssonia bicolor[&&NHX:TOL=75516],saemundssonia saemundssonia brevicornis[&&NHX:TOL=75517],saemundssonia saemundssonia calva[&&NHX:TOL=75518],saemundssonia saemundssonia camura[&&NHX:TOL=75519],saemundssonia saemundssonia celidoxa[&&NHX:TOL=75520],saemundssonia saemundssonia cephalus[&&NHX:TOL=75521],saemundssonia saemundssonia chathamensis[&&NHX:TOL=75522],saemundssonia saemundssonia clayae[&&NHX:TOL=75523],saemundssonia saemundssonia conica conica[&&NHX:TOL=75524],saemundssonia saemundssonia conica naumanni[&&NHX:TOL=75525],saemundssonia saemundssonia desolata[&&NHX:TOL=75526],saemundssonia puffinoecus enderleini[&&NHX:TOL=75527],saemundssonia saemundssonia euryrhyncha[&&NHX:TOL=75528],saemundssonia saemundssonia fraterculae[&&NHX:TOL=75529],saemundssonia saemundssonia furca[&&NHX:TOL=75530],saemundssonia saemundssonia gaini[&&NHX:TOL=75531],saemundssonia saemundssonia gelochelidoni[&&NHX:TOL=75532],saemundssonia saemundssonia grylle[&&NHX:TOL=75533],saemundssonia saemundssonia haemastica[&&NHX:TOL=75534],saemundssonia saemundssonia haematopi[&&NHX:TOL=75535],saemundssonia saemundssonia hexagona[&&NHX:TOL=75536],saemundssonia saemundssonia hopkinsi[&&NHX:TOL=75537],saemundssonia saemundssonia incisa[&&NHX:TOL=75538],saemundssonia saemundssonia inexspectata[&&NHX:TOL=75539],saemundssonia saemundssonia insolita[&&NHX:TOL=75540],saemundssonia saemundssonia integer[&&NHX:TOL=75541],saemundssonia puffinoecus jamaicensis[&&NHX:TOL=75542],saemundssonia saemundssonia keleri[&&NHX:TOL=75543],saemundssonia puffinoecus kosswigi[&&NHX:TOL=75544],saemundssonia saemundssonia kratochvili[&&NHX:TOL=75545],saemundssonia saemundssonia lari[&&NHX:TOL=75546],saemundssonia saemundssonia laticaudata[&&NHX:TOL=75547],saemundssonia saemundssonia limosae[&&NHX:TOL=75548],saemundssonia saemundssonia lobaticeps[&&NHX:TOL=75549],saemundssonia saemundssonia lockleyi[&&NHX:TOL=75550],saemundssonia saemundssonia marina[&&NHX:TOL=75551],saemundssonia saemundssonia media[&&NHX:TOL=75552],saemundssonia saemundssonia melanocephalus[&&NHX:TOL=75553],saemundssonia saemundssonia merguli[&&NHX:TOL=75554],saemundssonia saemundssonia meridiana[&&NHX:TOL=75555],saemundssonia saemundssonia minitrans[&&NHX:TOL=75556],saemundssonia puffinoecus minor[&&NHX:TOL=75557],saemundssonia saemundssonia montereyi[&&NHX:TOL=75558],saemundssonia saemundssonia nereis[&&NHX:TOL=75559],saemundssonia saemundssonia niethammeri[&&NHX:TOL=75560],saemundssonia saemundssonia occidentalis[&&NHX:TOL=75561],saemundssonia saemundssonia olrogi[&&NHX:TOL=75562],saemundssonia puffinoecus orientalis[&&NHX:TOL=75563],saemundssonia saemundssonia parvigenitalis[&&NHX:TOL=75564],saemundssonia saemundssonia paucisetosa[&&NHX:TOL=75565],saemundssonia puffinoecus persica[&&NHX:TOL=75566],saemundssonia puffinoecus peusi[&&NHX:TOL=75567],saemundssonia saemundssonia phaetona[&&NHX:TOL=75568],saemundssonia saemundssonia platycephalus[&&NHX:TOL=75569],saemundssonia saemundssonia platygaster[&&NHX:TOL=75570],saemundssonia saemundssonia platygaster ashi[&&NHX:TOL=75571],saemundssonia saemundssonia platygaster balati[&&NHX:TOL=75572],saemundssonia saemundssonia platygaster cordiceps[&&NHX:TOL=75573],saemundssonia saemundssonia platygaster frater[&&NHX:TOL=75574],saemundssonia saemundssonia platygaster islandica[&&NHX:TOL=75575],saemundssonia saemundssonia platygaster jadwigae[&&NHX:TOL=75576],saemundssonia saemundssonia platygaster mollis[&&NHX:TOL=75577],saemundssonia saemundssonia platygaster nitzschi[&&NHX:TOL=75578],saemundssonia saemundssonia platygaster pastoris[&&NHX:TOL=75579],saemundssonia saemundssonia platygaster platygaster[&&NHX:TOL=75580],saemundssonia saemundssonia platygaster semivittata[&&NHX:TOL=75581],saemundssonia saemundssonia platygaster stenrami[&&NHX:TOL=75582],saemundssonia saemundssonia platygaster temporalis[&&NHX:TOL=75583],saemundssonia saemundssonia platygaster theresae[&&NHX:TOL=75584],saemundssonia saemundssonia procax[&&NHX:TOL=75585],saemundssonia saemundssonia producta[&&NHX:TOL=75586],saemundssonia saemundssonia pterodromae[&&NHX:TOL=75587],saemundssonia puffinoecus puellula[&&NHX:TOL=75588],saemundssonia saemundssonia remota[&&NHX:TOL=75589],saemundssonia saemundssonia sagulata[&&NHX:TOL=75590],saemundssonia saemundssonia scolopacisphaeopodis brelihi[&&NHX:TOL=75591],saemundssonia saemundssonia scolopacisphaeopodis humeralis[&&NHX:TOL=75592],saemundssonia saemundssonia scolopacisphaeopodis nearctica[&&NHX:TOL=75593],saemundssonia saemundssonia scolopacisphaeopodis scolopacisphaeopodis[&&NHX:TOL=75594],saemundssonia saemundssonia snyderi[&&NHX:TOL=75595],saemundssonia saemundssonia solitariae[&&NHX:TOL=75596],saemundssonia saemundssonia stammeri[&&NHX:TOL=75597],saemundssonia saemundssonia sternae[&&NHX:TOL=75598],saemundssonia saemundssonia thalassidromae[&&NHX:TOL=75599],saemundssonia saemundssonia thompsoni[&&NHX:TOL=75600],saemundssonia saemundssonia tricolor[&&NHX:TOL=75601],saemundssonia saemundssonia tringae[&&NHX:TOL=75602],saemundssonia saemundssonia uppalensis[&&NHX:TOL=75603],saemundssonia puffinoecus valida[&&NHX:TOL=75604],saemundssonia saemundssonia virilis[&&NHX:TOL=75605],saemundssonia saemundssonia weidneri[&&NHX:TOL=75606],saemundssonia saemundssonia wumisuzume[&&NHX:TOL=75607])saemundssonia[&&NHX:TOL=75505],(splendoroffula ampullacea[&&NHX:TOL=75609],splendoroffula benoiti[&&NHX:TOL=75610],splendoroffula contaminata[&&NHX:TOL=75611],splendoroffula corythaeolae[&&NHX:TOL=75612],splendoroffula distincta[&&NHX:TOL=75613],splendoroffula ruwenzorornis[&&NHX:TOL=75614],splendoroffula sachtlebeni[&&NHX:TOL=75615],splendoroffula subtilis[&&NHX:TOL=75616],splendoroffula tauracobia[&&NHX:TOL=75617],splendoroffula theresae[&&NHX:TOL=75618],splendoroffula turacina[&&NHX:TOL=75619])splendoroffula[&&NHX:TOL=75608],(strigiphilus acadicus[&&NHX:TOL=75621],strigiphilus aitkeni[&&NHX:TOL=75622],strigiphilus barbatus[&&NHX:TOL=75623],strigiphilus boomae[&&NHX:TOL=75624],strigiphilus bramae[&&NHX:TOL=75625],strigiphilus capensis[&&NHX:TOL=75626],strigiphilus ceblebrachys[&&NHX:TOL=75627],strigiphilus chilensis[&&NHX:TOL=75628],strigiphilus crenulatus[&&NHX:TOL=75629],strigiphilus crucigerus[&&NHX:TOL=75630],strigiphilus cursitans[&&NHX:TOL=75631],strigiphilus cursor[&&NHX:TOL=75632],strigiphilus desertae[&&NHX:TOL=75633],strigiphilus elutus[&&NHX:TOL=75634],strigiphilus garylarsoni[&&NHX:TOL=75635],strigiphilus goniodicerus[&&NHX:TOL=75636],strigiphilus heterocerus[&&NHX:TOL=75637],strigiphilus heterogenitalis[&&NHX:TOL=75638],strigiphilus heterurus[&&NHX:TOL=75639],strigiphilus jardini[&&NHX:TOL=75640],strigiphilus ketupae[&&NHX:TOL=75641],strigiphilus laticephalus[&&NHX:TOL=75642],strigiphilus lophostrix[&&NHX:TOL=75643],strigiphilus macrogenitalis[&&NHX:TOL=75644],strigiphilus marshalli[&&NHX:TOL=75645],strigiphilus microgenitalis[&&NHX:TOL=75646],strigiphilus nemoralis[&&NHX:TOL=75647],strigiphilus oculatus[&&NHX:TOL=75648],strigiphilus otus[&&NHX:TOL=75649],strigiphilus pallidus[&&NHX:TOL=75650],strigiphilus petersoni[&&NHX:TOL=75651],strigiphilus portigi[&&NHX:TOL=75652],strigiphilus remotus[&&NHX:TOL=75653],strigiphilus riparius[&&NHX:TOL=75654],strigiphilus rostratus[&&NHX:TOL=75655],strigiphilus schemskei[&&NHX:TOL=75656],strigiphilus siamensis[&&NHX:TOL=75657],strigiphilus speotyti[&&NHX:TOL=75658],strigiphilus splendens[&&NHX:TOL=75659],strigiphilus strigis[&&NHX:TOL=75660],strigiphilus syrnii[&&NHX:TOL=75661],strigiphilus tuleskovi[&&NHX:TOL=75662],strigiphilus vapidus[&&NHX:TOL=75663],strigiphilus virgo[&&NHX:TOL=75664],strigiphilus whitei[&&NHX:TOL=75665],strigiphilus zumpti[&&NHX:TOL=75666])strigiphilus[&&NHX:TOL=75620],(strongylocotes abdominalis[&&NHX:TOL=75668],strongylocotes albigularis[&&NHX:TOL=75669],strongylocotes berlepschi[&&NHX:TOL=75670],strongylocotes columbianus[&&NHX:TOL=75671],strongylocotes complanatus[&&NHX:TOL=75672],strongylocotes cordiceps[&&NHX:TOL=75673],strongylocotes fimbriatus[&&NHX:TOL=75674],strongylocotes glabrous[&&NHX:TOL=75675],strongylocotes idoneus[&&NHX:TOL=75676],strongylocotes interruptus[&&NHX:TOL=75677],strongylocotes limai[&&NHX:TOL=75678],strongylocotes lipogonus[&&NHX:TOL=75679],strongylocotes nirmoides[&&NHX:TOL=75680],strongylocotes noctivagi[&&NHX:TOL=75681],strongylocotes orbicularis[&&NHX:TOL=75682],strongylocotes spinosus[&&NHX:TOL=75683],strongylocotes subconiceps[&&NHX:TOL=75684],strongylocotes subspinosus[&&NHX:TOL=75685],strongylocotes taoi[&&NHX:TOL=75686],strongylocotes tinami[&&NHX:TOL=75687],strongylocotes variegatus[&&NHX:TOL=75688],strongylocotes wernecki[&&NHX:TOL=75689])strongylocotes[&&NHX:TOL=75667],(struthiolipeurus andinus[&&NHX:TOL=75691],struthiolipeurus chilensis[&&NHX:TOL=75692],struthiolipeurus nandu[&&NHX:TOL=75693],struthiolipeurus renschi[&&NHX:TOL=75694],struthiolipeurus stresemanni[&&NHX:TOL=75695],struthiolipeurus struthionis[&&NHX:TOL=75696])struthiolipeurus[&&NHX:TOL=75690],(sturnidoecus acuminatus[&&NHX:TOL=75698],sturnidoecus acutifrons[&&NHX:TOL=75699],sturnidoecus aeneas[&&NHX:TOL=75700],sturnidoecus affinis[&&NHX:TOL=75701],sturnidoecus afzali[&&NHX:TOL=75702],sturnidoecus atharea[&&NHX:TOL=75703],sturnidoecus avivorax[&&NHX:TOL=75704],sturnidoecus bannoo[&&NHX:TOL=75705],sturnidoecus bituberculatus[&&NHX:TOL=75706],sturnidoecus blandus[&&NHX:TOL=75707],sturnidoecus boeevi[&&NHX:TOL=75708],sturnidoecus borobodur[&&NHX:TOL=75709],sturnidoecus caligineus[&&NHX:TOL=75710],sturnidoecus capensis[&&NHX:TOL=75711],sturnidoecus capitis[&&NHX:TOL=75712],sturnidoecus carpodaci[&&NHX:TOL=75713],sturnidoecus carrikeri[&&NHX:TOL=75714],sturnidoecus chendoola[&&NHX:TOL=75715],sturnidoecus chilchil[&&NHX:TOL=75716],sturnidoecus clayae[&&NHX:TOL=75717],sturnidoecus continuus[&&NHX:TOL=75718],sturnidoecus distinguendus[&&NHX:TOL=75719],sturnidoecus eichleri[&&NHX:TOL=75720],sturnidoecus femoratus[&&NHX:TOL=75721],sturnidoecus fragilis[&&NHX:TOL=75722],sturnidoecus galbula[&&NHX:TOL=75723],sturnidoecus graculae[&&NHX:TOL=75724],sturnidoecus guldum[&&NHX:TOL=75725],sturnidoecus hudeci[&&NHX:TOL=75726],sturnidoecus husaini[&&NHX:TOL=75727],sturnidoecus intermedius[&&NHX:TOL=75728],sturnidoecus irritans[&&NHX:TOL=75729],sturnidoecus lopesi[&&NHX:TOL=75730],sturnidoecus meinertzhageni[&&NHX:TOL=75731],sturnidoecus melodicus[&&NHX:TOL=75732],sturnidoecus minor[&&NHX:TOL=75733],sturnidoecus neoacutifrons[&&NHX:TOL=75734],sturnidoecus neointermedius[&&NHX:TOL=75735],sturnidoecus obsoletus[&&NHX:TOL=75736],sturnidoecus opeca[&&NHX:TOL=75737],sturnidoecus orientalis[&&NHX:TOL=75738],sturnidoecus parvifrons[&&NHX:TOL=75739],sturnidoecus pastoris[&&NHX:TOL=75740],sturnidoecus peguensis[&&NHX:TOL=75741],sturnidoecus perunensis[&&NHX:TOL=75742],sturnidoecus pflegeri[&&NHX:TOL=75743],sturnidoecus philippensis[&&NHX:TOL=75744],sturnidoecus quadrilineatus[&&NHX:TOL=75745],sturnidoecus radui[&&NHX:TOL=75746],sturnidoecus raji[&&NHX:TOL=75747],sturnidoecus refractariolus[&&NHX:TOL=75748],sturnidoecus regalis[&&NHX:TOL=75749],sturnidoecus rehanae[&&NHX:TOL=75750],sturnidoecus rostratus[&&NHX:TOL=75751],sturnidoecus ruficeps[&&NHX:TOL=75752],sturnidoecus saleimi[&&NHX:TOL=75753],sturnidoecus sarwatae[&&NHX:TOL=75754],sturnidoecus senegalensis[&&NHX:TOL=75755],sturnidoecus sexualis[&&NHX:TOL=75756],sturnidoecus simplex[&&NHX:TOL=75757],sturnidoecus stresemanni[&&NHX:TOL=75758],sturnidoecus sturni[&&NHX:TOL=75759],sturnidoecus subacutus[&&NHX:TOL=75760],sturnidoecus textoris[&&NHX:TOL=75761],sturnidoecus theresae[&&NHX:TOL=75762],sturnidoecus tulackovae[&&NHX:TOL=75763],sturnidoecus wittei[&&NHX:TOL=75764],sturnidoecus xanthops[&&NHX:TOL=75765],sturnidoecus zahrae[&&NHX:TOL=75766],sturnidoecus zoophilic[&&NHX:TOL=75767])sturnidoecus[&&NHX:TOL=75697],(syrrhaptoecus alchatae[&&NHX:TOL=75769],syrrhaptoecus angulatus[&&NHX:TOL=75770],syrrhaptoecus bedfordi[&&NHX:TOL=75771],syrrhaptoecus brevifrons[&&NHX:TOL=75772],syrrhaptoecus declivis[&&NHX:TOL=75773],syrrhaptoecus digonus[&&NHX:TOL=75774],syrrhaptoecus emahusaini[&&NHX:TOL=75775],syrrhaptoecus excisus[&&NHX:TOL=75776],syrrhaptoecus falcatus[&&NHX:TOL=75777],syrrhaptoecus mitratus[&&NHX:TOL=75778],syrrhaptoecus obtusus[&&NHX:TOL=75779],syrrhaptoecus pallasi[&&NHX:TOL=75780],syrrhaptoecus paradoxus[&&NHX:TOL=75781],syrrhaptoecus tibetanus[&&NHX:TOL=75782],syrrhaptoecus uncinosus[&&NHX:TOL=75783],syrrhaptoecus waterstoni[&&NHX:TOL=75784])syrrhaptoecus[&&NHX:TOL=75768],(theresiella clayae[&&NHX:TOL=75786],theresiella gemina[&&NHX:TOL=75787],theresiella hitchcocki[&&NHX:TOL=75788])theresiella[&&NHX:TOL=75785],(tinamotaecola andinae[&&NHX:TOL=75790],tinamotaecola elegans[&&NHX:TOL=75791],tinamotaecola wardi[&&NHX:TOL=75792],tinamotaecola zyskowskii[&&NHX:TOL=75793])tinamotaecola[&&NHX:TOL=75789],(trabeculus aviator[&&NHX:TOL=75795],trabeculus flemingi[&&NHX:TOL=75796],trabeculus fuscoclypeatus[&&NHX:TOL=75797],trabeculus hexakon[&&NHX:TOL=75798],trabeculus mirabilis[&&NHX:TOL=75799],trabeculus schillingi[&&NHX:TOL=75800])trabeculus[&&NHX:TOL=75794],(trichodopeostus aculeatus[&&NHX:TOL=75802],trichodopeostus crassus[&&NHX:TOL=75803],trichodopeostus grandior[&&NHX:TOL=75804],trichodopeostus praegracilis[&&NHX:TOL=75805],trichodopeostus spinosus[&&NHX:TOL=75806])trichodopeostus[&&NHX:TOL=75801],trichophilopterus babakotophilus[&&NHX:TOL=75807],(trogoniella aequatoriale[&&NHX:TOL=75809],trogoniella apaloderma[&&NHX:TOL=75810])trogoniella[&&NHX:TOL=75808],(trogoninirmus curucui[&&NHX:TOL=75812],trogoninirmus eleganus[&&NHX:TOL=75813],trogoninirmus hastiformis[&&NHX:TOL=75814],trogoninirmus insolitus[&&NHX:TOL=75815],trogoninirmus laticephalus[&&NHX:TOL=75816],trogoninirmus melanurus[&&NHX:TOL=75817],trogoninirmus odontopleuron[&&NHX:TOL=75818],trogoninirmus pharomacrus[&&NHX:TOL=75819],trogoninirmus strigilatus[&&NHX:TOL=75820])trogoninirmus[&&NHX:TOL=75811],(turnicola angustissimus[&&NHX:TOL=75822],turnicola nigrolineatus[&&NHX:TOL=75823],turnicola platyclypeatus[&&NHX:TOL=75824])turnicola[&&NHX:TOL=75821],(turturicola arabica[&&NHX:TOL=75826],turturicola clayae[&&NHX:TOL=75827],turturicola cruzesilvai[&&NHX:TOL=75828],turturicola puylaerti[&&NHX:TOL=75829],turturicola salimalii[&&NHX:TOL=75830],turturicola sudanicus[&&NHX:TOL=75831],turturicola thompsoni[&&NHX:TOL=75832],turturicola verheyeni[&&NHX:TOL=75833])turturicola[&&NHX:TOL=75825],upupicola upupae[&&NHX:TOL=75834],(vernoniella bergi[&&NHX:TOL=75836],vernoniella biprosapiae[&&NHX:TOL=75837],vernoniella guimaraesi[&&NHX:TOL=75838],vernoniella macgregori[&&NHX:TOL=75839])vernoniella[&&NHX:TOL=75835],wilsoniella absita[&&NHX:TOL=75840])philopteridae[&&NHX:TOL=13859])ischnocera[&&NHX:TOL=13873])[&&NHX:TOL=13869],(((((boopia aquilonia[&&NHX:TOL=70032],boopia bettongia[&&NHX:TOL=70033],boopia biseriata[&&NHX:TOL=70034],boopia doriana[&&NHX:TOL=70035],boopia dubia[&&NHX:TOL=70036],boopia emersoni[&&NHX:TOL=70037],boopia grandis[&&NHX:TOL=70038],boopia greeni[&&NHX:TOL=70039],boopia lukoschusi[&&NHX:TOL=70040],boopia minuta[&&NHX:TOL=70041],boopia mjoebergi[&&NHX:TOL=70042],boopia murrayi[&&NHX:TOL=70043],boopia notafusca[&&NHX:TOL=70044],boopia occidua[&&NHX:TOL=70045],boopia tarsata[&&NHX:TOL=70046],boopia uncinata[&&NHX:TOL=70047])boopia[&&NHX:TOL=70022],(heterodoxus alatus[&&NHX:TOL=70808],heterodoxus ampullatus[&&NHX:TOL=70809],heterodoxus ancoratus[&&NHX:TOL=70810],heterodoxus briscoei[&&NHX:TOL=70811],heterodoxus calabyi[&&NHX:TOL=70812],heterodoxus closei[&&NHX:TOL=70813],heterodoxus harrisoni[&&NHX:TOL=70814],heterodoxus maai[&&NHX:TOL=70821],heterodoxus hughendensis[&&NHX:TOL=70815],heterodoxus insularis[&&NHX:TOL=70816],heterodoxus insulatus[&&NHX:TOL=70817],heterodoxus keleri[&&NHX:TOL=70818],heterodoxus lesoueefi[&&NHX:TOL=70819],heterodoxus longitarsus[&&NHX:TOL=70820],heterodoxus macropus[&&NHX:TOL=70822],heterodoxus maynesi[&&NHX:TOL=70823],heterodoxus mitratus[&&NHX:TOL=70824],heterodoxus murrayi[&&NHX:TOL=70825],heterodoxus octoseriatus[&&NHX:TOL=70826],heterodoxus orarius[&&NHX:TOL=70827],heterodoxus pygidialis[&&NHX:TOL=70828],heterodoxus quadriseriatus[&&NHX:TOL=70829],heterodoxus spiniger[&&NHX:TOL=70830],heterodoxus ualabati[&&NHX:TOL=70831])heterodoxus[&&NHX:TOL=70023],(latumcephalum greeni[&&NHX:TOL=70832],latumcephalum lesoueefi[&&NHX:TOL=70833],latumcephalum macropus[&&NHX:TOL=70834],latumcephalum tenax[&&NHX:TOL=70835])latumcephalum[&&NHX:TOL=70024],(macropophila biarcuata[&&NHX:TOL=70836],macropophila breviarcuata[&&NHX:TOL=70837],macropophila clayae[&&NHX:TOL=70838],macropophila forcipata[&&NHX:TOL=70839])macropophila[&&NHX:TOL=70025],paraboopia flava[&&NHX:TOL=70026],(paraheterodoxus calcaratus[&&NHX:TOL=70840],paraheterodoxus erinaceus[&&NHX:TOL=70841],paraheterodoxus insignis[&&NHX:TOL=70842])paraheterodoxus[&&NHX:TOL=70027],(phacogalia brevispinosa[&&NHX:TOL=70843],phacogalia spinosa[&&NHX:TOL=70844])phacogalia[&&NHX:TOL=70028],therodoxus oweni[&&NHX:TOL=70029])boopiidae[&&NHX:TOL=13639],((actornithophilus ardeolae[&&NHX:TOL=70970],actornithophilus bicolor[&&NHX:TOL=70971],actornithophilus canuti[&&NHX:TOL=70972],actornithophilus ceruleus[&&NHX:TOL=70973],actornithophilus crinitus[&&NHX:TOL=70974],actornithophilus erinaceus[&&NHX:TOL=70975],actornithophilus flumineus[&&NHX:TOL=70976],actornithophilus gracilis[&&NHX:TOL=70977],actornithophilus grandiceps[&&NHX:TOL=70978],actornithophilus himantopi[&&NHX:TOL=70979],actornithophilus hoplopteri[&&NHX:TOL=70980],actornithophilus incisus[&&NHX:TOL=70981],actornithophilus kilauensis[&&NHX:TOL=70982],actornithophilus lacustris[&&NHX:TOL=70983],actornithophilus limarius[&&NHX:TOL=70984],actornithophilus limosae[&&NHX:TOL=70985],actornithophilus lyallpurensis[&&NHX:TOL=70986],actornithophilus mexicanus[&&NHX:TOL=70987],actornithophilus multisetosus[&&NHX:TOL=70988],actornithophilus nodularis[&&NHX:TOL=70989],actornithophilus ocellatus[&&NHX:TOL=70990],actornithophilus ochraceus[&&NHX:TOL=70991],actornithophilus paludosus[&&NHX:TOL=70992],actornithophilus patellatus[&&NHX:TOL=70993],actornithophilus pauliani[&&NHX:TOL=70994],actornithophilus pediculoides[&&NHX:TOL=70995],actornithophilus piceus lari[&&NHX:TOL=70996],actornithophilus piceus piceus[&&NHX:TOL=70997],actornithophilus pustulosus[&&NHX:TOL=70998],actornithophilus sabulosus[&&NHX:TOL=70999],actornithophilus sedes[&&NHX:TOL=71000],actornithophilus spinulosus[&&NHX:TOL=71001],actornithophilus stictus[&&NHX:TOL=71002],actornithophilus tetralicis[&&NHX:TOL=71003],actornithophilus totani[&&NHX:TOL=71004],actornithophilus umbrinus[&&NHX:TOL=71005],actornithophilus uniseriatus[&&NHX:TOL=71006])actornithophilus[&&NHX:TOL=70969],afrimenopon waar[&&NHX:TOL=71007],(amyrsidea cracimenopon aburris[&&NHX:TOL=71009],amyrsidea argimenopon afropavo[&&NHX:TOL=71010],amyrsidea argimenopon agelastes[&&NHX:TOL=71011],amyrsidea argimenopon borgesferreirai[&&NHX:TOL=71012],amyrsidea cracimenopon caquetae[&&NHX:TOL=71013],amyrsidea desumenopon complicata[&&NHX:TOL=71014],amyrsidea cracimenopon cracis[&&NHX:TOL=71015],amyrsidea numidimenopon desousai[&&NHX:TOL=71016],amyrsidea amyrsidea elbeli[&&NHX:TOL=71017],amyrsidea argimenopon francolinus[&&NHX:TOL=71018],amyrsidea argimenopon fulvomaculata[&&NHX:TOL=71019],amyrsidea cracimenopon garruli[&&NHX:TOL=71020],amyrsidea desumenopon gujanensis[&&NHX:TOL=71021],amyrsidea desumenopon hyperythra[&&NHX:TOL=71022],amyrsidea argimenopon impejani[&&NHX:TOL=71023],amyrsidea cracimenopon jacquacu[&&NHX:TOL=71024],amyrsidea argimenopon jacutica[&&NHX:TOL=71025],amyrsidea argimenopon lagopi[&&NHX:TOL=71026],amyrsidea argimenopon lativulvata[&&NHX:TOL=71027],amyrsidea numidimenopon lopesi[&&NHX:TOL=71028],amyrsidea argimenopon minuta[&&NHX:TOL=71029],amyrsidea cracimenopon mituensis[&&NHX:TOL=71030],amyrsidea argimenopon nicobariensis[&&NHX:TOL=71031],amyrsidea amyrsidea oculeae[&&NHX:TOL=71032],amyrsidea cracimenopon pauxis[&&NHX:TOL=71033],amyrsidea argimenopon perdicis[&&NHX:TOL=71034],amyrsidea argimenopon phaeostoma[&&NHX:TOL=71035],amyrsidea argimenopon phalloides[&&NHX:TOL=71036],amyrsidea numidimenopon plumiferae[&&NHX:TOL=71037],amyrsidea argimenopon polytricha[&&NHX:TOL=71038],amyrsidea argimenopon powelli[&&NHX:TOL=71039],amyrsidea desumenopon praegracilis[&&NHX:TOL=71040],amyrsidea cracimenopon purpurascens[&&NHX:TOL=71041],amyrsidea desumenopon ricaurtei[&&NHX:TOL=71042],amyrsidea cracimenopon rogersi[&&NHX:TOL=71043],amyrsidea argimenopon rolluli[&&NHX:TOL=71044],amyrsidea cracimenopon rubra[&&NHX:TOL=71045],amyrsidea cracimenopon semicracis[&&NHX:TOL=71046],amyrsidea cracimenopon simplex[&&NHX:TOL=71047],amyrsidea cracimenopon sixiola[&&NHX:TOL=71048],amyrsidea desumenopon speciosa[&&NHX:TOL=71049],amyrsidea cracimenopon spicula[&&NHX:TOL=71050],amyrsidea cracimenopon steineri[&&NHX:TOL=71051],amyrsidea argimenopon sternosetosa[&&NHX:TOL=71052],amyrsidea argimenopon subaequale[&&NHX:TOL=71053],amyrsidea argimenopon tetraogalli[&&NHX:TOL=71054],amyrsidea argimenopon tibetani[&&NHX:TOL=71055],amyrsidea argimenopon triseriata[&&NHX:TOL=71056],amyrsidea argimenopon uniseriata[&&NHX:TOL=71057],amyrsidea amyrsidea ventralis[&&NHX:TOL=71058],amyrsidea numidimenopon vulturini[&&NHX:TOL=71059],amyrsidea cracimenopon wagleri[&&NHX:TOL=71060])amyrsidea[&&NHX:TOL=71008],ancistrona vagelli[&&NHX:TOL=71061],(apterygon dumosum[&&NHX:TOL=71063],apterygon hintoni[&&NHX:TOL=71064],apterygon mirum[&&NHX:TOL=71065])apterygon[&&NHX:TOL=71062],(ardeiphilus floridae[&&NHX:TOL=71067],ardeiphilus incertus[&&NHX:TOL=71068],ardeiphilus trochioxus[&&NHX:TOL=71069],ardeiphilus vittatus[&&NHX:TOL=71070])ardeiphilus[&&NHX:TOL=71066],(austromenopon aegialitidis[&&NHX:TOL=71072],austromenopon affine[&&NHX:TOL=71073],austromenopon alpinum[&&NHX:TOL=71074],austromenopon atrofulvum[&&NHX:TOL=71075],austromenopon beckii[&&NHX:TOL=71076],austromenopon brevifimbriatum[&&NHX:TOL=71077],austromenopon bulweriae[&&NHX:TOL=71078],austromenopon confine[&&NHX:TOL=71079],austromenopon corporosum[&&NHX:TOL=71080],austromenopon crocatum[&&NHX:TOL=71081],austromenopon cursorium[&&NHX:TOL=71082],austromenopon decorosum[&&NHX:TOL=71083],austromenopon durisetosum[&&NHX:TOL=71084],austromenopon echinatum[&&NHX:TOL=71085],austromenopon edwardsi[&&NHX:TOL=71086],austromenopon elliotti[&&NHX:TOL=71087],austromenopon enigki[&&NHX:TOL=71088],austromenopon erilis[&&NHX:TOL=71089],austromenopon fuscofasciatum[&&NHX:TOL=71090],austromenopon gregariae[&&NHX:TOL=71091],austromenopon haematopi[&&NHX:TOL=71092],austromenopon hatutuense[&&NHX:TOL=71093],austromenopon himantopi[&&NHX:TOL=71094],austromenopon hystriculum[&&NHX:TOL=71095],austromenopon icterum[&&NHX:TOL=71096],austromenopon leucurae[&&NHX:TOL=71097],austromenopon limosae[&&NHX:TOL=71098],austromenopon longithoracicum[&&NHX:TOL=71099],austromenopon lutescens[&&NHX:TOL=71100],austromenopon madagascariensis[&&NHX:TOL=71101],austromenopon meyeri[&&NHX:TOL=71102],austromenopon micrandrum[&&NHX:TOL=71103],austromenopon narboroughi[&&NHX:TOL=71104],austromenopon navigans[&&NHX:TOL=71105],austromenopon nigropleurum[&&NHX:TOL=71106],austromenopon oceanodromae[&&NHX:TOL=71107],austromenopon ossifragae[&&NHX:TOL=71108],austromenopon paululum[&&NHX:TOL=71109],austromenopon pelagicum[&&NHX:TOL=71110],austromenopon phaeopodis[&&NHX:TOL=71111],austromenopon pinguis[&&NHX:TOL=71112],austromenopon popellus[&&NHX:TOL=71113],austromenopon sachtlebeni[&&NHX:TOL=71114],austromenopon sohni[&&NHX:TOL=71115],austromenopon spenceri[&&NHX:TOL=71116],austromenopon squatarolae[&&NHX:TOL=71117],austromenopon stammeri[&&NHX:TOL=71118],austromenopon transversum[&&NHX:TOL=71119])austromenopon[&&NHX:TOL=71071],(bonomiella afra[&&NHX:TOL=71121],bonomiella beieri[&&NHX:TOL=71122],bonomiella columbae[&&NHX:TOL=71123],bonomiella concii[&&NHX:TOL=71124],bonomiella insolitunguicolata[&&NHX:TOL=71125])bonomiella[&&NHX:TOL=71120],(bucerocolpocephalum deignani[&&NHX:TOL=71127],bucerocolpocephalum emersoni[&&NHX:TOL=71128])bucerocolpocephalum[&&NHX:TOL=71126],(bucerophagus africanus[&&NHX:TOL=71130],bucerophagus forcipatus[&&NHX:TOL=71131],bucerophagus productus[&&NHX:TOL=71132])bucerophagus[&&NHX:TOL=71129],(cavifera abdita[&&NHX:TOL=71134],cavifera senta[&&NHX:TOL=71135])cavifera[&&NHX:TOL=71133],(chapinia acutovulvata[&&NHX:TOL=71137],chapinia blakei[&&NHX:TOL=71138],chapinia boonsongi[&&NHX:TOL=71139],chapinia bucerotis[&&NHX:TOL=71140],chapinia camuri[&&NHX:TOL=71141],chapinia clayae[&&NHX:TOL=71142],chapinia fasciati[&&NHX:TOL=71143],chapinia hirta[&&NHX:TOL=71144],chapinia hoplai[&&NHX:TOL=71145],chapinia lophocerus[&&NHX:TOL=71146],chapinia lydae[&&NHX:TOL=71147],chapinia malayensis[&&NHX:TOL=71148],chapinia muesebecki[&&NHX:TOL=71149],chapinia robusta[&&NHX:TOL=71150],chapinia traylori[&&NHX:TOL=71151],chapinia waniti[&&NHX:TOL=71152],chapinia wenzeli[&&NHX:TOL=71153])chapinia[&&NHX:TOL=71136],(ciconiphilus africanus[&&NHX:TOL=71155],ciconiphilus butoridiphagus[&&NHX:TOL=71156],ciconiphilus cygni[&&NHX:TOL=71157],ciconiphilus decimfasciatus[&&NHX:TOL=71158],ciconiphilus euxenuri[&&NHX:TOL=71159],ciconiphilus matosi[&&NHX:TOL=71160],ciconiphilus pectiniventris[&&NHX:TOL=71161],ciconiphilus quadripustulatus[&&NHX:TOL=71162],ciconiphilus temporalis[&&NHX:TOL=71163])ciconiphilus[&&NHX:TOL=71154],(clayia afra[&&NHX:TOL=71165],clayia chapini[&&NHX:TOL=71166],clayia clappertoni[&&NHX:TOL=71167],clayia congensis[&&NHX:TOL=71168],clayia cruzi[&&NHX:TOL=71169],clayia distincta[&&NHX:TOL=71170],clayia kassaica[&&NHX:TOL=71171],clayia kenyensis[&&NHX:TOL=71172],clayia mjoebergi[&&NHX:TOL=71173],clayia moucheti[&&NHX:TOL=71174],clayia nahani[&&NHX:TOL=71175],clayia nobilis[&&NHX:TOL=71176],clayia phasida[&&NHX:TOL=71177],clayia plumifera[&&NHX:TOL=71178],clayia shelleyii[&&NHX:TOL=71179],clayia spinosa[&&NHX:TOL=71180],clayia squamata[&&NHX:TOL=71181],clayia subcruzi[&&NHX:TOL=71182],clayia subtheresae[&&NHX:TOL=71183],clayia theresae[&&NHX:TOL=71184],clayia transvaaliensis[&&NHX:TOL=71185],clayia wernecki[&&NHX:TOL=71186],clayia whyteii[&&NHX:TOL=71187],clayia zairensis[&&NHX:TOL=71188],clayia zumpti[&&NHX:TOL=71189])clayia[&&NHX:TOL=71164],(colimenopon hamatum[&&NHX:TOL=71191],colimenopon urocolius[&&NHX:TOL=71192])colimenopon[&&NHX:TOL=71190],(colpocephalum aculeatum[&&NHX:TOL=71194],colpocephalum aethiopicae[&&NHX:TOL=71195],colpocephalum africanum[&&NHX:TOL=71196],colpocephalum ajajae[&&NHX:TOL=71197],colpocephalum alecturae[&&NHX:TOL=71198],colpocephalum angolensis[&&NHX:TOL=71199],colpocephalum angulaticeps[&&NHX:TOL=71200],colpocephalum apivorus[&&NHX:TOL=71201],colpocephalum appendiculatum[&&NHX:TOL=71202],colpocephalum arfakiani[&&NHX:TOL=71203],colpocephalum asiatici[&&NHX:TOL=71204],colpocephalum ateri[&&NHX:TOL=71205],colpocephalum barbati[&&NHX:TOL=71206],colpocephalum benoiti[&&NHX:TOL=71207],colpocephalum berigorae[&&NHX:TOL=71208],colpocephalum brachysomum[&&NHX:TOL=71209],colpocephalum californici[&&NHX:TOL=71210],colpocephalum cayennensis[&&NHX:TOL=71211],colpocephalum ceciliae[&&NHX:TOL=71212],colpocephalum chelictiniae[&&NHX:TOL=71213],colpocephalum chloropi[&&NHX:TOL=71214],colpocephalum cholibae[&&NHX:TOL=71215],colpocephalum clayellum[&&NHX:TOL=71216],colpocephalum cooki[&&NHX:TOL=71217],colpocephalum cristatae[&&NHX:TOL=71218],colpocephalum crotophagicola[&&NHX:TOL=71219],colpocephalum cucullare[&&NHX:TOL=71220],colpocephalum davisoni[&&NHX:TOL=71221],colpocephalum ecaudati[&&NHX:TOL=71222],colpocephalum emersoni[&&NHX:TOL=71223],colpocephalum eremitae[&&NHX:TOL=71224],colpocephalum eucarenum[&&NHX:TOL=71225],colpocephalum falconii[&&NHX:TOL=71226],colpocephalum ferrisi[&&NHX:TOL=71227],colpocephalum flavescens[&&NHX:TOL=71228],colpocephalum foetens[&&NHX:TOL=71229],colpocephalum fradei[&&NHX:TOL=71230],colpocephalum fregili[&&NHX:TOL=71231],colpocephalum freycineti[&&NHX:TOL=71232],colpocephalum fusconigrum[&&NHX:TOL=71233],colpocephalum gallinulae[&&NHX:TOL=71234],colpocephalum germanum[&&NHX:TOL=71235],colpocephalum griffoneae[&&NHX:TOL=71236],colpocephalum gypsi[&&NHX:TOL=71237],colpocephalum haematopi[&&NHX:TOL=71238],colpocephalum harpiprioni[&&NHX:TOL=71239],colpocephalum harterti[&&NHX:TOL=71240],colpocephalum heterosoma[&&NHX:TOL=71241],colpocephalum hoffmanni[&&NHX:TOL=71242],colpocephalum holzenthali[&&NHX:TOL=71243],colpocephalum ibicter[&&NHX:TOL=71244],colpocephalum ignotum[&&NHX:TOL=71245],colpocephalum imperialis[&&NHX:TOL=71246],colpocephalum impressum[&&NHX:TOL=71247],colpocephalum inaequale[&&NHX:TOL=71248],colpocephalum indi[&&NHX:TOL=71249],colpocephalum infuscati[&&NHX:TOL=71250],colpocephalum javensis[&&NHX:TOL=71251],colpocephalum kelloggi[&&NHX:TOL=71252],colpocephalum krappi[&&NHX:TOL=71253],colpocephalum lamelligeri[&&NHX:TOL=71254],colpocephalum lathami[&&NHX:TOL=71255],colpocephalum leptopygos[&&NHX:TOL=71256],colpocephalum leucocephali[&&NHX:TOL=71257],colpocephalum longicaudum[&&NHX:TOL=71258],colpocephalum longissimum[&&NHX:TOL=71259],colpocephalum lyali[&&NHX:TOL=71260],colpocephalum maculatum[&&NHX:TOL=71261],colpocephalum maculosum[&&NHX:TOL=71262],colpocephalum maguari[&&NHX:TOL=71263],colpocephalum majesticum[&&NHX:TOL=71264],colpocephalum maleonis[&&NHX:TOL=71265],colpocephalum marabu[&&NHX:TOL=71266],colpocephalum megalops[&&NHX:TOL=71267],colpocephalum megalopteri[&&NHX:TOL=71268],colpocephalum melanocephalae[&&NHX:TOL=71269],colpocephalum milvi[&&NHX:TOL=71270],colpocephalum mycteriae[&&NHX:TOL=71271],colpocephalum nanum[&&NHX:TOL=71272],colpocephalum napiforme[&&NHX:TOL=71273],colpocephalum nigrae[&&NHX:TOL=71274],colpocephalum nipponi[&&NHX:TOL=71275],colpocephalum occidentalis[&&NHX:TOL=71276],colpocephalum occipitale[&&NHX:TOL=71277],colpocephalum oreas[&&NHX:TOL=71278],colpocephalum orientalis[&&NHX:TOL=71279],colpocephalum osborni[&&NHX:TOL=71280],colpocephalum oscitansi[&&NHX:TOL=71281],colpocephalum oxycercae[&&NHX:TOL=71282],colpocephalum papuensis[&&NHX:TOL=71283],colpocephalum parumpilosum[&&NHX:TOL=71284],colpocephalum pectinatum[&&NHX:TOL=71285],colpocephalum penicillatum[&&NHX:TOL=71286],colpocephalum percnopteri[&&NHX:TOL=71287],colpocephalum phalcoboeni[&&NHX:TOL=71288],colpocephalum phasianini[&&NHX:TOL=71289],colpocephalum pilgrimi[&&NHX:TOL=71290],colpocephalum plataleae[&&NHX:TOL=71291],colpocephalum polonum[&&NHX:TOL=71292],colpocephalum polybori[&&NHX:TOL=71293],colpocephalum pricei[&&NHX:TOL=71294],colpocephalum pulverulenti[&&NHX:TOL=71295],colpocephalum pygidiale[&&NHX:TOL=71296],colpocephalum rosei[&&NHX:TOL=71297],colpocephalum salimalii[&&NHX:TOL=71298],colpocephalum satellitum[&&NHX:TOL=71299],colpocephalum scalariforme[&&NHX:TOL=71300],colpocephalum scharfi[&&NHX:TOL=71301],colpocephalum scopinum[&&NHX:TOL=71302],colpocephalum sinensis[&&NHX:TOL=71303],colpocephalum smithi[&&NHX:TOL=71304],colpocephalum spineum[&&NHX:TOL=71305],colpocephalum spinicollis[&&NHX:TOL=71306],colpocephalum strangei[&&NHX:TOL=71307],colpocephalum stricklandi[&&NHX:TOL=71308],colpocephalum subpenicillatum[&&NHX:TOL=71309],colpocephalum subzebra[&&NHX:TOL=71310],colpocephalum subzerafae[&&NHX:TOL=71311],colpocephalum talegallae[&&NHX:TOL=71312],colpocephalum tandani[&&NHX:TOL=71313],colpocephalum tausi[&&NHX:TOL=71314],colpocephalum tetraophasis[&&NHX:TOL=71315],colpocephalum thoracicum[&&NHX:TOL=71316],colpocephalum tibiale[&&NHX:TOL=71317],colpocephalum tirkhan[&&NHX:TOL=71318],colpocephalum trachelioti[&&NHX:TOL=71319],colpocephalum trichosum[&&NHX:TOL=71320],colpocephalum trispinum[&&NHX:TOL=71321],colpocephalum tristis[&&NHX:TOL=71322],colpocephalum turbinatum[&&NHX:TOL=71323],colpocephalum uchidi[&&NHX:TOL=71324],colpocephalum unciferum[&&NHX:TOL=71325],colpocephalum wilhelmi[&&NHX:TOL=71326],colpocephalum zebra[&&NHX:TOL=71327],colpocephalum zerafae[&&NHX:TOL=71328])colpocephalum[&&NHX:TOL=71193],(comatomenopon dichromanassae[&&NHX:TOL=71330],comatomenopon elbeli[&&NHX:TOL=71331],comatomenopon elongatum[&&NHX:TOL=71332],comatomenopon exilis[&&NHX:TOL=71333],comatomenopon grayi[&&NHX:TOL=71334],comatomenopon ibis[&&NHX:TOL=71335],comatomenopon thulae[&&NHX:TOL=71336],comatomenopon xenicum[&&NHX:TOL=71337])comatomenopon[&&NHX:TOL=71329],coramenopon coracopsis[&&NHX:TOL=71338],(ctenigogus erinaceimorphus[&&NHX:TOL=71340],ctenigogus secundarius[&&NHX:TOL=71341])ctenigogus[&&NHX:TOL=71339],cuculimenopon pallidi[&&NHX:TOL=71342],(cuculiphilus falcophilus alternatus[&&NHX:TOL=71344],cuculiphilus falcophilus cathartaepapae[&&NHX:TOL=71345],cuculiphilus cuculiphilus decoratus[&&NHX:TOL=71346],cuculiphilus cuculiphilus fasciativentris[&&NHX:TOL=71347],cuculiphilus cuculiphilus fasciatus[&&NHX:TOL=71348],cuculiphilus aegypiphilus gypsis[&&NHX:TOL=71349],cuculiphilus cuculiphilus hototogisu[&&NHX:TOL=71350],cuculiphilus carrikeria megaspinus[&&NHX:TOL=71351],cuculiphilus cuculiphilus platygaster[&&NHX:TOL=71352],cuculiphilus falcophilus punctatus[&&NHX:TOL=71353],cuculiphilus cuculiphilus snodgrassi[&&NHX:TOL=71354],cuculiphilus cuculiphilus upak[&&NHX:TOL=71355],cuculiphilus falcophilus zonatus[&&NHX:TOL=71356])cuculiphilus[&&NHX:TOL=71343],(dennyus collodennyus adamsae[&&NHX:TOL=71358],dennyus dennyus aequatorialis[&&NHX:TOL=71359],dennyus dennyus australis[&&NHX:TOL=71360],dennyus collodennyus boothi[&&NHX:TOL=71361],dennyus dennyus brevicapitis[&&NHX:TOL=71362],dennyus dennyus bruneri[&&NHX:TOL=71363],dennyus dennyus brunneitorques[&&NHX:TOL=71364],dennyus collodennyus carljonesi carljonesi[&&NHX:TOL=71365],dennyus collodennyus carljonesi forresteri[&&NHX:TOL=71366],dennyus collodennyus carljonesi fosteri[&&NHX:TOL=71367],dennyus collodennyus collinsi[&&NHX:TOL=71368],dennyus dennyus cypsiurus[&&NHX:TOL=71369],dennyus collodennyus distinctus distinctus[&&NHX:TOL=71370],dennyus collodennyus distinctus timjonesi[&&NHX:TOL=71371],dennyus dennyus dubius[&&NHX:TOL=71372],dennyus ctenodennyus elbeli[&&NHX:TOL=71373],dennyus collodennyus elliotti[&&NHX:TOL=71374],dennyus collodennyus emersoni[&&NHX:TOL=71375],dennyus collodennyus ferrisi[&&NHX:TOL=71376],dennyus collodennyus francicus[&&NHX:TOL=71377],dennyus takamatsuia giganteus[&&NHX:TOL=71378],dennyus dennyus gossei[&&NHX:TOL=71379],dennyus collodennyus hahnae[&&NHX:TOL=71380],dennyus dennyus hirundinis[&&NHX:TOL=71381],dennyus dennyus intonsus[&&NHX:TOL=71382],dennyus collodennyus kristinae[&&NHX:TOL=71383],dennyus dennyus limbus[&&NHX:TOL=71384],dennyus takamatsuia major[&&NHX:TOL=71385],dennyus collodennyus medwayi[&&NHX:TOL=71386],dennyus dennyus meridionalis[&&NHX:TOL=71387],dennyus dennyus richmondi[&&NHX:TOL=71388],dennyus dennyus rotundocapitis[&&NHX:TOL=71389],dennyus dennyus semicollaris[&&NHX:TOL=71390],dennyus collodennyus simberloffi[&&NHX:TOL=71391],dennyus dennyus similis[&&NHX:TOL=71392],dennyus collodennyus singhi[&&NHX:TOL=71393],dennyus collodennyus somadikartai[&&NHX:TOL=71394],dennyus ctenodennyus southwoodi[&&NHX:TOL=71395],dennyus ctenodennyus spiniger[&&NHX:TOL=71396],dennyus dennyus spininotus[&&NHX:TOL=71397],dennyus collodennyus tarburtoni[&&NHX:TOL=71398],dennyus collodennyus theresae[&&NHX:TOL=71399],dennyus collodennyus thompsoni[&&NHX:TOL=71400],dennyus dennyus vauxi[&&NHX:TOL=71401],dennyus dennyus vonarxi[&&NHX:TOL=71402],dennyus collodennyus wellsi[&&NHX:TOL=71403],dennyus collodennyus wraggi[&&NHX:TOL=71404])dennyus[&&NHX:TOL=71357],(dicteisia abdominalis[&&NHX:TOL=71406],dicteisia gracilis[&&NHX:TOL=71407],dicteisia keleri[&&NHX:TOL=71408],dicteisia palamedeae[&&NHX:TOL=71409],dicteisia tristis[&&NHX:TOL=71410])dicteisia[&&NHX:TOL=71405],(eidmanniella albescens[&&NHX:TOL=71412],eidmanniella eurygaster[&&NHX:TOL=71413],eidmanniella nancyae[&&NHX:TOL=71414],eidmanniella pellucida[&&NHX:TOL=71415],eidmanniella pustulosa[&&NHX:TOL=71416])eidmanniella[&&NHX:TOL=71411],elbelia validi[&&NHX:TOL=71417],(eomenopon beeri[&&NHX:TOL=71419],eomenopon cardinalis[&&NHX:TOL=71420],eomenopon chlorocerci[&&NHX:TOL=71421],eomenopon clissoldi[&&NHX:TOL=71422],eomenopon concinnae[&&NHX:TOL=71423],eomenopon denticulatum[&&NHX:TOL=71424],eomenopon greeni[&&NHX:TOL=71425],eomenopon mirzai[&&NHX:TOL=71426],eomenopon patoni[&&NHX:TOL=71427],eomenopon placentis[&&NHX:TOL=71428],eomenopon pulchellae[&&NHX:TOL=71429],eomenopon ryani[&&NHX:TOL=71430],eomenopon semilunare[&&NHX:TOL=71431],eomenopon sintillatae[&&NHX:TOL=71432],eomenopon spinimentum[&&NHX:TOL=71433],eomenopon wilsoni[&&NHX:TOL=71434])eomenopon[&&NHX:TOL=71418],epiara dimorpha[&&NHX:TOL=71435],eucolpocephalum femorale[&&NHX:TOL=71436],(eureum cimicoides[&&NHX:TOL=71438],eureum ewingi[&&NHX:TOL=71439],eureum hasegawai[&&NHX:TOL=71440],eureum mumfordi[&&NHX:TOL=71441],eureum pacificum[&&NHX:TOL=71442],eureum pygostyli[&&NHX:TOL=71443],eureum salangane[&&NHX:TOL=71444],eureum spenceri[&&NHX:TOL=71445],eureum yepezi[&&NHX:TOL=71446])eureum[&&NHX:TOL=71437],(falcomenopon boonsongi[&&NHX:TOL=71448],falcomenopon erythrogonysi[&&NHX:TOL=71449])falcomenopon[&&NHX:TOL=71447],(franciscoloa franciscoloa aterrimi[&&NHX:TOL=71451],franciscoloa franciscoloa erythropteri[&&NHX:TOL=71452],franciscoloa franciscoloa fulgidi[&&NHX:TOL=71453],franciscoloa franciscoloa funerei[&&NHX:TOL=71454],franciscoloa cacamenopon hodsoni[&&NHX:TOL=71455],franciscoloa cacamenopon kimi[&&NHX:TOL=71456],franciscoloa franciscoloa leadbeateri[&&NHX:TOL=71457],franciscoloa franciscoloa magnifici[&&NHX:TOL=71458],franciscoloa franciscoloa pallida[&&NHX:TOL=71459],franciscoloa franciscoloa rorati[&&NHX:TOL=71460],franciscoloa franciscoloa roseicapillae[&&NHX:TOL=71461],franciscoloa franciscoloa temporale[&&NHX:TOL=71462],franciscoloa franciscoloa thompsoni[&&NHX:TOL=71463])franciscoloa[&&NHX:TOL=71450],fregatiella aurifasciata[&&NHX:TOL=71464],(gruimenopon canadense[&&NHX:TOL=71466],gruimenopon longum[&&NHX:TOL=71467])gruimenopon[&&NHX:TOL=71465],(heleonomus abdominalis[&&NHX:TOL=71469],heleonomus assimilis[&&NHX:TOL=71470],heleonomus cornutus[&&NHX:TOL=71471],heleonomus elbeli[&&NHX:TOL=71472],heleonomus furgalai[&&NHX:TOL=71473],heleonomus harrisoni[&&NHX:TOL=71474],heleonomus laveryi[&&NHX:TOL=71475],heleonomus macilentus[&&NHX:TOL=71476],heleonomus sami[&&NHX:TOL=71477],heleonomus semiluctus[&&NHX:TOL=71478])heleonomus[&&NHX:TOL=71468],(heterokodeia aratingae[&&NHX:TOL=71480],heterokodeia auricapilli[&&NHX:TOL=71481],heterokodeia chiriri[&&NHX:TOL=71482],heterokodeia guimaraesi[&&NHX:TOL=71483],heterokodeia maracanae[&&NHX:TOL=71484],heterokodeia severae[&&NHX:TOL=71485],heterokodeia spinosa[&&NHX:TOL=71486],heterokodeia subsimilis[&&NHX:TOL=71487])heterokodeia[&&NHX:TOL=71479],(heteromenopon heteromenopon anodorhynchi[&&NHX:TOL=71489],heteromenopon heteromenopon aurifrons[&&NHX:TOL=71490],heteromenopon heteromenopon clayae[&&NHX:TOL=71491],heteromenopon heteromenopon jugularis[&&NHX:TOL=71492],heteromenopon keamenopon kalamundae[&&NHX:TOL=71493],heteromenopon keamenopon kea[&&NHX:TOL=71494],heteromenopon heteromenopon laticapitis[&&NHX:TOL=71495],heteromenopon heteromenopon macrurum[&&NHX:TOL=71496],heteromenopon heteromenopon militaris[&&NHX:TOL=71497],heteromenopon heteromenopon passerini[&&NHX:TOL=71498],heteromenopon heteromenopon pictae[&&NHX:TOL=71499],heteromenopon heteromenopon pionopsittae[&&NHX:TOL=71500],heteromenopon keamenopon psittacum[&&NHX:TOL=71501],heteromenopon heteromenopon sincipitalis[&&NHX:TOL=71502],heteromenopon heteromenopon viridicatae[&&NHX:TOL=71503])heteromenopon[&&NHX:TOL=71488],hoazineus armiferus[&&NHX:TOL=71504],(hohorstiella andina[&&NHX:TOL=71506],hohorstiella asiatica[&&NHX:TOL=71507],hohorstiella corpulenta[&&NHX:TOL=71508],hohorstiella ectootoca[&&NHX:TOL=71509],hohorstiella frontalis[&&NHX:TOL=71510],hohorstiella gigantea[&&NHX:TOL=71511],hohorstiella lata[&&NHX:TOL=71512],hohorstiella menadensis[&&NHX:TOL=71513],hohorstiella modesta[&&NHX:TOL=71514],hohorstiella paladinella[&&NHX:TOL=71515],hohorstiella passerina[&&NHX:TOL=71516],hohorstiella radovskyi[&&NHX:TOL=71517],hohorstiella songprakobi[&&NHX:TOL=71518],hohorstiella streptopeliae[&&NHX:TOL=71519],hohorstiella sylvatica[&&NHX:TOL=71520],hohorstiella tandani[&&NHX:TOL=71521],hohorstiella tenorioae[&&NHX:TOL=71522],hohorstiella timorensis[&&NHX:TOL=71523],hohorstiella turturis[&&NHX:TOL=71524],hohorstiella tympanistriae[&&NHX:TOL=71525],hohorstiella unicolor[&&NHX:TOL=71526])hohorstiella[&&NHX:TOL=71505],(holomenopon acutae[&&NHX:TOL=71528],holomenopon boehmi[&&NHX:TOL=71529],holomenopon brevithoracicum[&&NHX:TOL=71530],holomenopon bucephalae[&&NHX:TOL=71531],holomenopon cairinae[&&NHX:TOL=71532],holomenopon clauseni[&&NHX:TOL=71533],holomenopon clypeilargum[&&NHX:TOL=71534],holomenopon goliath[&&NHX:TOL=71535],holomenopon leucoxanthum[&&NHX:TOL=71536],holomenopon loomisii[&&NHX:TOL=71537],holomenopon maxbeieri[&&NHX:TOL=71538],holomenopon obscurum[&&NHX:TOL=71539],holomenopon setigerum[&&NHX:TOL=71540],holomenopon tadornae[&&NHX:TOL=71541],holomenopon transvaalense[&&NHX:TOL=71542],holomenopon tumidum[&&NHX:TOL=71543])holomenopon[&&NHX:TOL=71527],(kaysius cotingae[&&NHX:TOL=71545],kaysius emersoni[&&NHX:TOL=71546],kaysius tityrus[&&NHX:TOL=71547])kaysius[&&NHX:TOL=71544],(kelerimenopon kelerimenopon aepypodi[&&NHX:TOL=71549],kelerimenopon kelerimenopon ciliatum[&&NHX:TOL=71550],kelerimenopon kelerimenopon clayae[&&NHX:TOL=71551],kelerimenopon kelerimenopon crassispinum[&&NHX:TOL=71552],kelerimenopon kelerimenopon eichleri[&&NHX:TOL=71553],kelerimenopon kelerimenopon fuscirostris[&&NHX:TOL=71554],kelerimenopon lorimenopon galeritae[&&NHX:TOL=71555],kelerimenopon lorimenopon geoffroyi[&&NHX:TOL=71556],kelerimenopon kelerimenopon indonesiensis[&&NHX:TOL=71557],kelerimenopon lorimenopon longipes[&&NHX:TOL=71558],kelerimenopon kelerimenopon minus[&&NHX:TOL=71559],kelerimenopon lorimenopon psittaculae[&&NHX:TOL=71560],kelerimenopon kelerimenopon sanfilippoi[&&NHX:TOL=71561],kelerimenopon kelerimenopon thompsoni[&&NHX:TOL=71562],kelerimenopon kelerimenopon tongaensis[&&NHX:TOL=71563])kelerimenopon[&&NHX:TOL=71548],(kurodaia conciella acadicae[&&NHX:TOL=71565],kurodaia conciella caputonis[&&NHX:TOL=71566],kurodaia kurodaia cheelae[&&NHX:TOL=71567],kurodaia conciella crassiceps[&&NHX:TOL=71568],kurodaia conciella cryptostigmatia[&&NHX:TOL=71569],kurodaia conciella deignani[&&NHX:TOL=71570],kurodaia conciella flammei[&&NHX:TOL=71571],kurodaia kurodaia fulvofasciata[&&NHX:TOL=71572],kurodaia conciella gnomae[&&NHX:TOL=71573],kurodaia kurodaia haliaeeti[&&NHX:TOL=71574],kurodaia kurodaia koepckei[&&NHX:TOL=71575],kurodaia conciella longipes[&&NHX:TOL=71576],kurodaia kurodaia macrocybe[&&NHX:TOL=71577],kurodaia conciella magna[&&NHX:TOL=71578],kurodaia conciella painei[&&NHX:TOL=71579],kurodaia conciella panjabensis[&&NHX:TOL=71580],kurodaia kurodaia parvula[&&NHX:TOL=71581],kurodaia conciella platyclypeatum[&&NHX:TOL=71582],kurodaia kurodaia quatei[&&NHX:TOL=71583],kurodaia conciella scotopeliae[&&NHX:TOL=71584],kurodaia conciella subpachygaster[&&NHX:TOL=71585],kurodaia conciella tordoi[&&NHX:TOL=71586])kurodaia[&&NHX:TOL=71564],(longimenopon dominicanum[&&NHX:TOL=71588],longimenopon elliotti[&&NHX:TOL=71589],longimenopon galeatum[&&NHX:TOL=71590],longimenopon infans[&&NHX:TOL=71591],longimenopon puffinus[&&NHX:TOL=71592],longimenopon shiraii[&&NHX:TOL=71593])longimenopon[&&NHX:TOL=71587],(machaerilaemus americanus[&&NHX:TOL=71595],machaerilaemus clayae[&&NHX:TOL=71596],machaerilaemus complexus[&&NHX:TOL=71597],machaerilaemus cyanocittae[&&NHX:TOL=71598],machaerilaemus diglossae[&&NHX:TOL=71599],machaerilaemus gigas[&&NHX:TOL=71600],machaerilaemus hawaiiensis[&&NHX:TOL=71601],machaerilaemus hirsutus[&&NHX:TOL=71602],machaerilaemus laticapitus[&&NHX:TOL=71603],machaerilaemus laticorpus[&&NHX:TOL=71604],machaerilaemus maestus[&&NHX:TOL=71605],machaerilaemus malleus[&&NHX:TOL=71606],machaerilaemus plocei[&&NHX:TOL=71607],machaerilaemus raggianae[&&NHX:TOL=71608],machaerilaemus tangarae[&&NHX:TOL=71609])machaerilaemus[&&NHX:TOL=71594],(menacanthus abdominalis[&&NHX:TOL=71611],menacanthus aburris[&&NHX:TOL=71612],menacanthus aeedonis[&&NHX:TOL=71613],menacanthus affinis[&&NHX:TOL=71614],menacanthus agilis[&&NHX:TOL=71615],menacanthus alaudae[&&NHX:TOL=71616],menacanthus albicans[&&NHX:TOL=71617],menacanthus albicaudus[&&NHX:TOL=71618],menacanthus annuliventer[&&NHX:TOL=71619],menacanthus arctifasciatus[&&NHX:TOL=71620],menacanthus aurocapillus[&&NHX:TOL=71621],menacanthus balfouri[&&NHX:TOL=71622],menacanthus boliviensis[&&NHX:TOL=71623],menacanthus brachygaster[&&NHX:TOL=71624],menacanthus brevispinus[&&NHX:TOL=71625],menacanthus camelinus[&&NHX:TOL=71626],menacanthus campephili[&&NHX:TOL=71627],menacanthus caudatus[&&NHX:TOL=71628],menacanthus chaparensis[&&NHX:TOL=71629],menacanthus chrysophaeus[&&NHX:TOL=71630],menacanthus cincinnatus[&&NHX:TOL=71631],menacanthus colinus[&&NHX:TOL=71632],menacanthus coniceps[&&NHX:TOL=71633],menacanthus cornuceps[&&NHX:TOL=71634],menacanthus cornutus[&&NHX:TOL=71635],menacanthus crateropus[&&NHX:TOL=71636],menacanthus curuccae[&&NHX:TOL=71637],menacanthus daubentoni[&&NHX:TOL=71638],menacanthus dendroicae[&&NHX:TOL=71639],menacanthus dennisi[&&NHX:TOL=71640],menacanthus distinctus[&&NHX:TOL=71641],menacanthus eichleri[&&NHX:TOL=71642],menacanthus eisenachensis[&&NHX:TOL=71643],menacanthus elbeli[&&NHX:TOL=71644],menacanthus eurysternus[&&NHX:TOL=71645],menacanthus exilis[&&NHX:TOL=71646],menacanthus exsanguis[&&NHX:TOL=71647],menacanthus extraneus[&&NHX:TOL=71648],menacanthus falcatus[&&NHX:TOL=71649],menacanthus fasciatus[&&NHX:TOL=71650],menacanthus fertilis[&&NHX:TOL=71651],menacanthus foxi[&&NHX:TOL=71652],menacanthus genitalis[&&NHX:TOL=71653],menacanthus geothlypis[&&NHX:TOL=71654],menacanthus gonophaeus[&&NHX:TOL=71655],menacanthus hilensis[&&NHX:TOL=71656],menacanthus infumatus[&&NHX:TOL=71657],menacanthus kaddoui[&&NHX:TOL=71658],menacanthus kalatitar[&&NHX:TOL=71659],menacanthus laticephalus[&&NHX:TOL=71660],menacanthus latus[&&NHX:TOL=71661],menacanthus leistidis[&&NHX:TOL=71662],menacanthus longipalpis[&&NHX:TOL=71663],menacanthus longispinus[&&NHX:TOL=71664],menacanthus lyali[&&NHX:TOL=71665],menacanthus machadoi[&&NHX:TOL=71666],menacanthus mamola[&&NHX:TOL=71667],menacanthus menura[&&NHX:TOL=71668],menacanthus meridionalis[&&NHX:TOL=71669],menacanthus merisuoi[&&NHX:TOL=71670],menacanthus mikadokiji[&&NHX:TOL=71671],menacanthus mituensis[&&NHX:TOL=71672],menacanthus montagnii[&&NHX:TOL=71673],menacanthus nelsoni[&&NHX:TOL=71674],menacanthus nogoma[&&NHX:TOL=71675],menacanthus nothoproctae[&&NHX:TOL=71676],menacanthus numidae[&&NHX:TOL=71677],menacanthus obsoleti[&&NHX:TOL=71678],menacanthus orioli[&&NHX:TOL=71679],menacanthus ortalidis[&&NHX:TOL=71680],menacanthus pallidulus[&&NHX:TOL=71681],menacanthus pallipes[&&NHX:TOL=71682],menacanthus pauxensis[&&NHX:TOL=71683],menacanthus perijanus[&&NHX:TOL=71684],menacanthus phasiani[&&NHX:TOL=71685],menacanthus pici[&&NHX:TOL=71686],menacanthus picicola[&&NHX:TOL=71687],menacanthus pipilensis[&&NHX:TOL=71688],menacanthus pricei[&&NHX:TOL=71689],menacanthus pusillus[&&NHX:TOL=71690],menacanthus quiscali[&&NHX:TOL=71691],menacanthus ralli[&&NHX:TOL=71692],menacanthus robustus[&&NHX:TOL=71693],menacanthus samaipatae[&&NHX:TOL=71694],menacanthus setifer[&&NHX:TOL=71695],menacanthus sinuatus[&&NHX:TOL=71696],menacanthus stramineus[&&NHX:TOL=71697],menacanthus stubbei[&&NHX:TOL=71698],menacanthus sturnellae[&&NHX:TOL=71699],menacanthus takayamai[&&NHX:TOL=71700],menacanthus tarsatus[&&NHX:TOL=71701],menacanthus tenuifrons[&&NHX:TOL=71702],menacanthus tyranni[&&NHX:TOL=71703],menacanthus unicolor[&&NHX:TOL=71704],menacanthus valenciae[&&NHX:TOL=71705],menacanthus werneri[&&NHX:TOL=71706])menacanthus[&&NHX:TOL=71610],(menopon carrikeri[&&NHX:TOL=71708],menopon clayae[&&NHX:TOL=71709],menopon deryloi[&&NHX:TOL=71710],menopon ferrisi[&&NHX:TOL=71711],menopon gallinae[&&NHX:TOL=71712],menopon hopkinsi[&&NHX:TOL=71713],menopon interpositum[&&NHX:TOL=71714],menopon jellisoni[&&NHX:TOL=71715],menopon kuntzi[&&NHX:TOL=71716],menopon pallens[&&NHX:TOL=71717],menopon spinulosum[&&NHX:TOL=71718],menopon subgallinae[&&NHX:TOL=71719])menopon[&&NHX:TOL=71707],(meromenopon brevicolle[&&NHX:TOL=71721],meromenopon incisum[&&NHX:TOL=71722],meromenopon marshalli[&&NHX:TOL=71723],meromenopon meropis[&&NHX:TOL=71724])meromenopon[&&NHX:TOL=71720],(microctenia crucis[&&NHX:TOL=71726],microctenia guimaraesi[&&NHX:TOL=71727],microctenia heterocephalus[&&NHX:TOL=71728],microctenia major[&&NHX:TOL=71729],microctenia soaresi[&&NHX:TOL=71730],microctenia tibialis[&&NHX:TOL=71731])microctenia[&&NHX:TOL=71725],mimemamenopon zumpti[&&NHX:TOL=71732],(myrsidea abhorrens[&&NHX:TOL=71734],myrsidea abidae[&&NHX:TOL=71735],myrsidea aegithali[&&NHX:TOL=71736],myrsidea aenigma[&&NHX:TOL=71737],myrsidea aitkeni[&&NHX:TOL=71738],myrsidea albiceps[&&NHX:TOL=71739],myrsidea amandava[&&NHX:TOL=71740],myrsidea ananthakrishnani[&&NHX:TOL=71741],myrsidea anaspila[&&NHX:TOL=71742],myrsidea anathorax[&&NHX:TOL=71743],myrsidea antiqua[&&NHX:TOL=71744],myrsidea aquilonia[&&NHX:TOL=71745],myrsidea arafura[&&NHX:TOL=71746],myrsidea argentina[&&NHX:TOL=71747],myrsidea assamensis[&&NHX:TOL=71748],myrsidea australiensis[&&NHX:TOL=71749],myrsidea bakeri[&&NHX:TOL=71750],myrsidea bakttitar[&&NHX:TOL=71751],myrsidea balati[&&NHX:TOL=71752],myrsidea balteri[&&NHX:TOL=71753],myrsidea bedfordi[&&NHX:TOL=71754],myrsidea bennetti[&&NHX:TOL=71755],myrsidea bharat[&&NHX:TOL=71756],myrsidea bhutanensis[&&NHX:TOL=71757],myrsidea birmensis[&&NHX:TOL=71758],myrsidea bonariensis[&&NHX:TOL=71759],myrsidea borneoensis[&&NHX:TOL=71760],myrsidea brevipes[&&NHX:TOL=71761],myrsidea breviterga[&&NHX:TOL=71762],myrsidea breviventris[&&NHX:TOL=71763],myrsidea brunnea[&&NHX:TOL=71764],myrsidea bubalornithis[&&NHX:TOL=71765],myrsidea buxtoni[&&NHX:TOL=71766],myrsidea capensis[&&NHX:TOL=71767],myrsidea carrikeri[&&NHX:TOL=71768],myrsidea cecilae[&&NHX:TOL=71769],myrsidea chiapensis[&&NHX:TOL=71770],myrsidea chilchil[&&NHX:TOL=71771],myrsidea cinerea[&&NHX:TOL=71772],myrsidea clamosae[&&NHX:TOL=71773],myrsidea clayae[&&NHX:TOL=71774],myrsidea coerebicola[&&NHX:TOL=71775],myrsidea coloiopsis[&&NHX:TOL=71776],myrsidea comosa[&&NHX:TOL=71777],myrsidea conspicua[&&NHX:TOL=71778],myrsidea cornicis[&&NHX:TOL=71779],myrsidea crassipes[&&NHX:TOL=71780],myrsidea cucullaris[&&NHX:TOL=71781],myrsidea cyanopycae[&&NHX:TOL=71782],myrsidea cyrtostigma[&&NHX:TOL=71783],myrsidea dauurica[&&NHX:TOL=71784],myrsidea destructor[&&NHX:TOL=71785],myrsidea devastator[&&NHX:TOL=71786],myrsidea diffusa[&&NHX:TOL=71787],myrsidea dissimilis[&&NHX:TOL=71788],myrsidea dorotheae[&&NHX:TOL=71789],myrsidea downsi[&&NHX:TOL=71790],myrsidea dukhunensis[&&NHX:TOL=71791],myrsidea duplicata[&&NHX:TOL=71792],myrsidea eisentrauti[&&NHX:TOL=71793],myrsidea elbeli[&&NHX:TOL=71794],myrsidea elegans[&&NHX:TOL=71795],myrsidea emersoni[&&NHX:TOL=71796],myrsidea eremialis[&&NHX:TOL=71797],myrsidea erythrocephali[&&NHX:TOL=71798],myrsidea estrildae[&&NHX:TOL=71799],myrsidea eurocephali[&&NHX:TOL=71800],myrsidea extranea[&&NHX:TOL=71801],myrsidea fallax[&&NHX:TOL=71802],myrsidea flavescens[&&NHX:TOL=71803],myrsidea flavida[&&NHX:TOL=71804],myrsidea flavirostrata[&&NHX:TOL=71805],myrsidea franciscoloi[&&NHX:TOL=71806],myrsidea funerea[&&NHX:TOL=71807],myrsidea fusca[&&NHX:TOL=71808],myrsidea fuscicapilla[&&NHX:TOL=71809],myrsidea fuscomarginata[&&NHX:TOL=71810],myrsidea grallinae[&&NHX:TOL=71811],myrsidea grandiceps[&&NHX:TOL=71812],myrsidea guimaraesi[&&NHX:TOL=71813],myrsidea himalayensis[&&NHX:TOL=71814],myrsidea hirsuta[&&NHX:TOL=71815],myrsidea hopkinsi[&&NHX:TOL=71816],myrsidea iliaci[&&NHX:TOL=71817],myrsidea imbricata[&&NHX:TOL=71818],myrsidea incerta[&&NHX:TOL=71819],myrsidea indigenella[&&NHX:TOL=71820],myrsidea indivisa[&&NHX:TOL=71821],myrsidea insolita[&&NHX:TOL=71822],myrsidea insularis[&&NHX:TOL=71823],myrsidea insulsa[&&NHX:TOL=71824],myrsidea integra[&&NHX:TOL=71825],myrsidea intermedia[&&NHX:TOL=71826],myrsidea interrupta[&&NHX:TOL=71827],myrsidea invadens[&&NHX:TOL=71828],myrsidea ishizawai[&&NHX:TOL=71829],myrsidea islandica[&&NHX:TOL=71830],myrsidea isostoma[&&NHX:TOL=71831],myrsidea jonnyvonbergeni[&&NHX:TOL=71832],myrsidea karyi[&&NHX:TOL=71833],myrsidea keniensis[&&NHX:TOL=71834],myrsidea kikuchii[&&NHX:TOL=71835],myrsidea laciniaesternata[&&NHX:TOL=71836],myrsidea laciniata[&&NHX:TOL=71837],myrsidea latifrons[&&NHX:TOL=71838],myrsidea ledgeri[&&NHX:TOL=71839],myrsidea lehmensicki[&&NHX:TOL=71840],myrsidea lengerkeni[&&NHX:TOL=71841],myrsidea longipecta[&&NHX:TOL=71842],myrsidea luroris[&&NHX:TOL=71843],myrsidea lyali[&&NHX:TOL=71844],myrsidea macraidoia[&&NHX:TOL=71845],myrsidea macrorhynchicola[&&NHX:TOL=71846],myrsidea magnidens[&&NHX:TOL=71847],myrsidea major[&&NHX:TOL=71848],myrsidea malayensis[&&NHX:TOL=71849],myrsidea manipurensis[&&NHX:TOL=71850],myrsidea meinertzhageni[&&NHX:TOL=71851],myrsidea melanorum[&&NHX:TOL=71852],myrsidea mellori[&&NHX:TOL=71853],myrsidea mendesi[&&NHX:TOL=71854],myrsidea mera[&&NHX:TOL=71855],myrsidea mexicana[&&NHX:TOL=71856],myrsidea minuscula[&&NHX:TOL=71857],myrsidea mirabile[&&NHX:TOL=71858],myrsidea mirabilis[&&NHX:TOL=71859],myrsidea monilegeri[&&NHX:TOL=71860],myrsidea montana[&&NHX:TOL=71861],myrsidea nigra[&&NHX:TOL=71862],myrsidea novabritannica[&&NHX:TOL=71863],myrsidea nuristaniensis[&&NHX:TOL=71864],myrsidea obovata[&&NHX:TOL=71865],myrsidea orientalis[&&NHX:TOL=71866],myrsidea ovatula[&&NHX:TOL=71867],myrsidea pachycephalae[&&NHX:TOL=71868],myrsidea palloris[&&NHX:TOL=71869],myrsidea patkaiensis[&&NHX:TOL=71870],myrsidea pectinata[&&NHX:TOL=71871],myrsidea peninsularis[&&NHX:TOL=71872],myrsidea philippinensis[&&NHX:TOL=71873],myrsidea piageti[&&NHX:TOL=71874],myrsidea picae[&&NHX:TOL=71875],myrsidea picta[&&NHX:TOL=71876],myrsidea pilosa[&&NHX:TOL=71877],myrsidea pricei[&&NHX:TOL=71878],myrsidea prionopsis[&&NHX:TOL=71879],myrsidea proterva[&&NHX:TOL=71880],myrsidea psittaci[&&NHX:TOL=71881],myrsidea ptilorhynchi[&&NHX:TOL=71882],myrsidea ptilostomi[&&NHX:TOL=71883],myrsidea pullula[&&NHX:TOL=71884],myrsidea pungens[&&NHX:TOL=71885],myrsidea pycnonoti[&&NHX:TOL=71886],myrsidea quadrifasciata[&&NHX:TOL=71887],myrsidea quadrimaculata[&&NHX:TOL=71888],myrsidea queleae[&&NHX:TOL=71889],myrsidea regius[&&NHX:TOL=71890],myrsidea ridulosa[&&NHX:TOL=71891],myrsidea robsoni[&&NHX:TOL=71892],myrsidea rohi[&&NHX:TOL=71893],myrsidea rustica[&&NHX:TOL=71894],myrsidea salimalii[&&NHX:TOL=71895],myrsidea satbhai[&&NHX:TOL=71896],myrsidea saturata[&&NHX:TOL=71897],myrsidea schizotergum[&&NHX:TOL=71898],myrsidea seguyi[&&NHX:TOL=71899],myrsidea sehri[&&NHX:TOL=71900],myrsidea seminuda[&&NHX:TOL=71901],myrsidea serini[&&NHX:TOL=71902],myrsidea shirakii[&&NHX:TOL=71903],myrsidea siamensis[&&NHX:TOL=71904],myrsidea sikkimensis[&&NHX:TOL=71905],myrsidea simplex[&&NHX:TOL=71906],myrsidea sindianus[&&NHX:TOL=71907],myrsidea singularis[&&NHX:TOL=71908],myrsidea sjoestedti[&&NHX:TOL=71909],myrsidea somaliensis[&&NHX:TOL=71910],myrsidea splendenticola[&&NHX:TOL=71911],myrsidea srivastava[&&NHX:TOL=71912],myrsidea stenodesma[&&NHX:TOL=71913],myrsidea strangeri[&&NHX:TOL=71914],myrsidea strobilisternata[&&NHX:TOL=71915],myrsidea struthidea[&&NHX:TOL=71916],myrsidea subanaspila[&&NHX:TOL=71917],myrsidea subcoracis[&&NHX:TOL=71918],myrsidea subdissimilis[&&NHX:TOL=71919],myrsidea sultanpurensis[&&NHX:TOL=71920],myrsidea takayamai[&&NHX:TOL=71921],myrsidea tchagrae[&&NHX:TOL=71922],myrsidea teraokai[&&NHX:TOL=71923],myrsidea textoris[&&NHX:TOL=71924],myrsidea thailandensis[&&NHX:TOL=71925],myrsidea thoracica[&&NHX:TOL=71926],myrsidea tibetana[&&NHX:TOL=71927],myrsidea timmermanni[&&NHX:TOL=71928],myrsidea trinoton[&&NHX:TOL=71929],myrsidea tristicola[&&NHX:TOL=71930],myrsidea trithorax[&&NHX:TOL=71931],myrsidea troglodyti[&&NHX:TOL=71932],myrsidea tropicalis[&&NHX:TOL=71933],myrsidea ugandanus[&&NHX:TOL=71934],myrsidea urocissae[&&NHX:TOL=71935],myrsidea varia[&&NHX:TOL=71936],myrsidea victrix[&&NHX:TOL=71937],myrsidea viduae[&&NHX:TOL=71938],myrsidea vincula[&&NHX:TOL=71939],myrsidea vinlandica[&&NHX:TOL=71940],myrsidea woltersi[&&NHX:TOL=71941])myrsidea[&&NHX:TOL=71733],neomenopon pteroclurus[&&NHX:TOL=71942],(nosopon atyeoi[&&NHX:TOL=71944],nosopon australiense[&&NHX:TOL=71945],nosopon casteli[&&NHX:TOL=71946],nosopon chanabense[&&NHX:TOL=71947],nosopon clayae[&&NHX:TOL=71948],nosopon haliasturis[&&NHX:TOL=71949],nosopon krappi[&&NHX:TOL=71950],nosopon lucidum[&&NHX:TOL=71951],nosopon milvus[&&NHX:TOL=71952])nosopon[&&NHX:TOL=71943],numidicola antennatus[&&NHX:TOL=71953],(odoriphila clayae[&&NHX:TOL=71955],odoriphila dekeyseri[&&NHX:TOL=71956],odoriphila phoeniculi[&&NHX:TOL=71957])odoriphila[&&NHX:TOL=71954],(osborniella clayae[&&NHX:TOL=71959],osborniella crotophagae[&&NHX:TOL=71960],osborniella guiraensis[&&NHX:TOL=71961],osborniella pectinifera[&&NHX:TOL=71962],osborniella sulcirostriae[&&NHX:TOL=71963])osborniella[&&NHX:TOL=71958],(pacifimenopon fuscatae[&&NHX:TOL=71965],pacifimenopon gressitti[&&NHX:TOL=71966],pacifimenopon nelsoni[&&NHX:TOL=71967],pacifimenopon shanahani[&&NHX:TOL=71968])pacifimenopon[&&NHX:TOL=71964],(piagetiella africana[&&NHX:TOL=71970],piagetiella bursaepelecani[&&NHX:TOL=71971],piagetiella caputincisum[&&NHX:TOL=71972],piagetiella chilensis[&&NHX:TOL=71973],piagetiella incomposita[&&NHX:TOL=71974],piagetiella peralis[&&NHX:TOL=71975],piagetiella titan[&&NHX:TOL=71976],piagetiella transitans[&&NHX:TOL=71977],piagetiella vigua[&&NHX:TOL=71978])piagetiella[&&NHX:TOL=71969],(plegadiphilus cayennensis[&&NHX:TOL=71980],plegadiphilus eudocimus[&&NHX:TOL=71981],plegadiphilus geronticus[&&NHX:TOL=71982],plegadiphilus mamillatus[&&NHX:TOL=71983],plegadiphilus plegadis[&&NHX:TOL=71984],plegadiphilus threskiornis[&&NHX:TOL=71985],plegadiphilus zumpti[&&NHX:TOL=71986])plegadiphilus[&&NHX:TOL=71979],podargiphilus burmensis[&&NHX:TOL=71987],(pseudomenopon australis[&&NHX:TOL=71989],pseudomenopon bracofortei[&&NHX:TOL=71990],pseudomenopon carrikeri[&&NHX:TOL=71991],pseudomenopon cinereum[&&NHX:TOL=71992],pseudomenopon concretum[&&NHX:TOL=71993],pseudomenopon crecis[&&NHX:TOL=71994],pseudomenopon dolium[&&NHX:TOL=71995],pseudomenopon grebenjukae[&&NHX:TOL=71996],pseudomenopon lanceolatum[&&NHX:TOL=71997],pseudomenopon mcclurei[&&NHX:TOL=71998],pseudomenopon meinertzhageni[&&NHX:TOL=71999],pseudomenopon pflegeri[&&NHX:TOL=72000],pseudomenopon phoenicuri[&&NHX:TOL=72001],pseudomenopon pilgrimi[&&NHX:TOL=72002],pseudomenopon pilosum[&&NHX:TOL=72003],pseudomenopon qadrii[&&NHX:TOL=72004],pseudomenopon ralliculae[&&NHX:TOL=72005],pseudomenopon rostratulae[&&NHX:TOL=72006],pseudomenopon scopulacorne[&&NHX:TOL=72007],pseudomenopon stresemanni[&&NHX:TOL=72008])pseudomenopon[&&NHX:TOL=71988],(psittacobrosus amazonicus[&&NHX:TOL=72010],psittacobrosus ambiguus[&&NHX:TOL=72011],psittacobrosus anduzei[&&NHX:TOL=72012],psittacobrosus aratingae[&&NHX:TOL=72013],psittacobrosus brotogerisi[&&NHX:TOL=72014],psittacobrosus burmeisteri[&&NHX:TOL=72015],psittacobrosus carrikeri[&&NHX:TOL=72016],psittacobrosus dalgleishi[&&NHX:TOL=72017],psittacobrosus farinosae[&&NHX:TOL=72018],psittacobrosus forpi[&&NHX:TOL=72019],psittacobrosus genitalis[&&NHX:TOL=72020],psittacobrosus hyacinthini[&&NHX:TOL=72021],psittacobrosus kelloggi[&&NHX:TOL=72022],psittacobrosus mitratae[&&NHX:TOL=72023],psittacobrosus molinae[&&NHX:TOL=72024],psittacobrosus nandayi[&&NHX:TOL=72025],psittacobrosus patagoni[&&NHX:TOL=72026],psittacobrosus pyrrhurae[&&NHX:TOL=72027],psittacobrosus rubrogenysi[&&NHX:TOL=72028],psittacobrosus versicoluri[&&NHX:TOL=72029])psittacobrosus[&&NHX:TOL=72009],(psittacomenopon bifurcatum[&&NHX:TOL=72057],psittacomenopon gulielmi[&&NHX:TOL=72058],psittacomenopon heterocephalum[&&NHX:TOL=72059],psittacomenopon impar[&&NHX:TOL=72060])psittacomenopon[&&NHX:TOL=72030],pterophilus sudanensis[&&NHX:TOL=72031],quateia irianensis[&&NHX:TOL=72032],rediella mirabilis[&&NHX:TOL=72033],(somaphantus kingi[&&NHX:TOL=72035],somaphantus lusius[&&NHX:TOL=72036],somaphantus spencei[&&NHX:TOL=72037])somaphantus[&&NHX:TOL=72034],(trinoton aculeatum[&&NHX:TOL=72039],trinoton alopochen[&&NHX:TOL=72040],trinoton anserinum[&&NHX:TOL=72041],trinoton emersoni[&&NHX:TOL=72042],trinoton femoratum[&&NHX:TOL=72043],trinoton fluviatile[&&NHX:TOL=72044],trinoton gambensis[&&NHX:TOL=72045],trinoton intermedium[&&NHX:TOL=72046],trinoton laveryi[&&NHX:TOL=72047],trinoton madagascariense[&&NHX:TOL=72048],trinoton nigrum[&&NHX:TOL=72049],trinoton querquedulae[&&NHX:TOL=72050],trinoton straeleni[&&NHX:TOL=72051])trinoton[&&NHX:TOL=72038],(turacoeca bedfordi[&&NHX:TOL=72053],turacoeca leucotis[&&NHX:TOL=72054],turacoeca scleroderma[&&NHX:TOL=72055],turacoeca subrotunda[&&NHX:TOL=72056])turacoeca[&&NHX:TOL=72052])menoponidae[&&NHX:TOL=13638])[&&NHX:TOL=50655],((chinchillophaga clayae[&&NHX:TOL=72099],(cummingsia cummingsia albujai[&&NHX:TOL=72101],cummingsia cummingsia barkleyae[&&NHX:TOL=72102],cummingsia acanthomenopon gardneri[&&NHX:TOL=72103],cummingsia cummingsia inopinata[&&NHX:TOL=72104],cummingsia cummingsia intermedia[&&NHX:TOL=72105],cummingsia cummingsia izori[&&NHX:TOL=72106],cummingsia cummingsia maculata[&&NHX:TOL=72107],cummingsia cummingsia micheneri[&&NHX:TOL=72108],cummingsia acanthomenopon peramydis[&&NHX:TOL=72109],cummingsia cummingsia perezi[&&NHX:TOL=72110])cummingsia[&&NHX:TOL=72100],harrisonia uncinata[&&NHX:TOL=72111],hoplomyophilus nativus[&&NHX:TOL=72112],(philandesia chinchillae[&&NHX:TOL=72114],philandesia maurii[&&NHX:TOL=72115],philandesia mazzai[&&NHX:TOL=72116],philandesia townsendi[&&NHX:TOL=72117])philandesia[&&NHX:TOL=72113],trimenopon hispidum[&&NHX:TOL=72118])trimenoponidae[&&NHX:TOL=13642],((abrocomophaga chilensis[&&NHX:TOL=70854],abrocomophaga emmonsae[&&NHX:TOL=70855],abrocomophaga hellenthali[&&NHX:TOL=70856])abrocomophaga[&&NHX:TOL=70845],(aotiella aotophilus[&&NHX:TOL=70857],aotiella hershkovitzi[&&NHX:TOL=70858])aotiella[&&NHX:TOL=70846],(gliricola gliricola aequatorialis[&&NHX:TOL=70905],gliricola gliricola arboricola[&&NHX:TOL=70906],gliricola hutiaphilus armatus[&&NHX:TOL=70907],gliricola gliricola brasiliensis[&&NHX:TOL=70908],gliricola gliricola brooksae[&&NHX:TOL=70909],gliricola gliricola calcaratus[&&NHX:TOL=70910],gliricola hutiaphilus capromydis[&&NHX:TOL=70911],gliricola gliricola columbanus[&&NHX:TOL=70912],gliricola hutiaphilus cubanus[&&NHX:TOL=70913],gliricola gliricola cutkompi[&&NHX:TOL=70914],gliricola gliricola decurtatus[&&NHX:TOL=70915],gliricola gliricola distinctus[&&NHX:TOL=70916],gliricola gliricola echimydis[&&NHX:TOL=70917],gliricola hutiaphilus ewingi[&&NHX:TOL=70918],gliricola gliricola fonsecai[&&NHX:TOL=70919],gliricola gliricola halli[&&NHX:TOL=70920],gliricola gliricola handleyi[&&NHX:TOL=70921],gliricola gliricola humilis[&&NHX:TOL=70922],gliricola gliricola lindolphoi[&&NHX:TOL=70923],gliricola longicollis[&&NHX:TOL=70924],gliricola gliricola maculatus[&&NHX:TOL=70925],gliricola gliricola marajoensis[&&NHX:TOL=70926],gliricola gliricola mendezi[&&NHX:TOL=70927],gliricola gliricola mesomydis[&&NHX:TOL=70928],gliricola gliricola mirandai[&&NHX:TOL=70929],gliricola hutiaphilus omahonyi[&&NHX:TOL=70930],gliricola gliricola palladius[&&NHX:TOL=70931],gliricola gliricola panamensis[&&NHX:TOL=70932],gliricola gliricola paraensis[&&NHX:TOL=70933],gliricola hutiaphilus pinei[&&NHX:TOL=70934],gliricola gliricola pintoi[&&NHX:TOL=70935],gliricola gliricola porcelli[&&NHX:TOL=70936],gliricola gliricola quadrisetosus[&&NHX:TOL=70937],gliricola hutiaphilus rabbi[&&NHX:TOL=70938],gliricola hutiaphilus schwartzi[&&NHX:TOL=70939],gliricola gliricola sylvatica[&&NHX:TOL=70940],gliricola gliricola tiptoni[&&NHX:TOL=70941],gliricola gliricola venezuelanus[&&NHX:TOL=70942],gliricola gliricola vogelsangi[&&NHX:TOL=70943],gliricola gliricola wenzeli[&&NHX:TOL=70944],gliricola hutiaphilus wernecki[&&NHX:TOL=70945],gliricola gliricola woodmani[&&NHX:TOL=70946])gliricola[&&NHX:TOL=70847],(gyropus cercomydis[&&NHX:TOL=70859],gyropus cruzi[&&NHX:TOL=70860],gyropus diplomys[&&NHX:TOL=70861],gyropus elongatus[&&NHX:TOL=70862],gyropus emersoni[&&NHX:TOL=70863],gyropus freitasi[&&NHX:TOL=70864],gyropus lenti distinctus[&&NHX:TOL=70865],gyropus lenti lenti[&&NHX:TOL=70866],gyropus limai[&&NHX:TOL=70867],gyropus lineatus[&&NHX:TOL=70868],gyropus longus[&&NHX:TOL=70869],gyropus martini iheringi[&&NHX:TOL=70870],gyropus martini martini[&&NHX:TOL=70871],gyropus martini matthaeensis[&&NHX:TOL=70872],gyropus mesoamericanus[&&NHX:TOL=70873],gyropus ovalis[&&NHX:TOL=70874],gyropus parasetosus[&&NHX:TOL=70875],gyropus parvus[&&NHX:TOL=70876],gyropus persetosus[&&NHX:TOL=70877],gyropus ribeiroi[&&NHX:TOL=70878],gyropus scalaris[&&NHX:TOL=70879],gyropus setifer[&&NHX:TOL=70880],gyropus setosus[&&NHX:TOL=70881],gyropus thompsoni[&&NHX:TOL=70882],gyropus travassosi[&&NHX:TOL=70883],gyropus wernecki[&&NHX:TOL=70884])gyropus[&&NHX:TOL=70848],(macrogyropus amplexans[&&NHX:TOL=70885],macrogyropus costalimai[&&NHX:TOL=70886],macrogyropus dicotylis[&&NHX:TOL=70887],macrogyropus heteronychus[&&NHX:TOL=70888],macrogyropus longisetis[&&NHX:TOL=70889])macrogyropus[&&NHX:TOL=70849],(monothoracius almeidai[&&NHX:TOL=70890],monothoracius penidoi[&&NHX:TOL=70891])monothoracius[&&NHX:TOL=70850],(phtheiropoios centralis[&&NHX:TOL=70892],phtheiropoios ewingi[&&NHX:TOL=70893],phtheiropoios forficulatus[&&NHX:TOL=70894],phtheiropoios gracilipes[&&NHX:TOL=70895],phtheiropoios lagotis[&&NHX:TOL=70896],phtheiropoios latipollicaris[&&NHX:TOL=70897],phtheiropoios mendocinus[&&NHX:TOL=70898],phtheiropoios nematophallus[&&NHX:TOL=70899],phtheiropoios pearsoni[&&NHX:TOL=70900],phtheiropoios pollicaris[&&NHX:TOL=70901],phtheiropoios rionegrensis[&&NHX:TOL=70902],phtheiropoios tucumanus[&&NHX:TOL=70903],phtheiropoios wetmorei[&&NHX:TOL=70904])phtheiropoios[&&NHX:TOL=70851],pitrufquenia coypus[&&NHX:TOL=70852],protogyropus normalis[&&NHX:TOL=70853])gyropidae[&&NHX:TOL=13643])[&&NHX:TOL=50656])[&&NHX:TOL=50654],(((ricinus alphaaurigae[&&NHX:TOL=72120],ricinus arcuatus[&&NHX:TOL=72121],ricinus australis[&&NHX:TOL=72122],ricinus balati[&&NHX:TOL=72123],ricinus borin[&&NHX:TOL=72124],ricinus brelihi[&&NHX:TOL=72125],ricinus brevicapitis[&&NHX:TOL=72126],ricinus butleri[&&NHX:TOL=72127],ricinus calcarii[&&NHX:TOL=72128],ricinus carolynae[&&NHX:TOL=72129],ricinus cherriei[&&NHX:TOL=72130],ricinus clayae[&&NHX:TOL=72131],ricinus complicatus[&&NHX:TOL=72132],ricinus dalgleishi[&&NHX:TOL=72133],ricinus dendroicae[&&NHX:TOL=72134],ricinus diffusus[&&NHX:TOL=72135],ricinus dolichocephalus[&&NHX:TOL=72136],ricinus elongatus[&&NHX:TOL=72137],ricinus emersoni[&&NHX:TOL=72138],ricinus fasciatus[&&NHX:TOL=72139],ricinus flavicans[&&NHX:TOL=72140],ricinus frenatus[&&NHX:TOL=72141],ricinus fringillae[&&NHX:TOL=72142],ricinus gibbus[&&NHX:TOL=72143],ricinus invadens[&&NHX:TOL=72144],ricinus ivanovi[&&NHX:TOL=72145],ricinus leptosomus[&&NHX:TOL=72146],ricinus maculatus[&&NHX:TOL=72147],ricinus major[&&NHX:TOL=72148],ricinus mandibulatus[&&NHX:TOL=72149],ricinus marginatus[&&NHX:TOL=72150],ricinus meinertzhageni[&&NHX:TOL=72151],ricinus microcephalus[&&NHX:TOL=72152],ricinus mollisoni[&&NHX:TOL=72153],ricinus mugimaki[&&NHX:TOL=72154],ricinus muscisaxicolae[&&NHX:TOL=72155],ricinus myiarchi[&&NHX:TOL=72156],ricinus pallens[&&NHX:TOL=72157],ricinus pessimalis[&&NHX:TOL=72158],ricinus pflegeri[&&NHX:TOL=72159],ricinus picturatus[&&NHX:TOL=72160],ricinus piechockii[&&NHX:TOL=72161],ricinus polioptilus[&&NHX:TOL=72162],ricinus praetextus[&&NHX:TOL=72163],ricinus ramphoceli[&&NHX:TOL=72164],ricinus rubeculae[&&NHX:TOL=72165],ricinus seiuri[&&NHX:TOL=72166],ricinus serratus[&&NHX:TOL=72167],ricinus sittae[&&NHX:TOL=72168],ricinus sorus[&&NHX:TOL=72169],ricinus subangulatus[&&NHX:TOL=72170],ricinus subdiffusus[&&NHX:TOL=72171],ricinus subhastatus[&&NHX:TOL=72172],ricinus sucinaceus[&&NHX:TOL=72173],ricinus tanagraephilus[&&NHX:TOL=72174],ricinus thoracicus[&&NHX:TOL=72175],ricinus timmermanni[&&NHX:TOL=72176],ricinus tinctus[&&NHX:TOL=72177],ricinus tragus[&&NHX:TOL=72178],ricinus tugarinovi[&&NHX:TOL=72179],ricinus uragi[&&NHX:TOL=72180],ricinus vagus[&&NHX:TOL=72181],ricinus vireoensis[&&NHX:TOL=72182],ricinus volatiniae[&&NHX:TOL=72183],ricinus wolfi[&&NHX:TOL=72184])ricinus[&&NHX:TOL=72119],(trochiliphagus abdominalis[&&NHX:TOL=72186],trochiliphagus austini[&&NHX:TOL=72187],trochiliphagus brevicephalus[&&NHX:TOL=72188],trochiliphagus grandior[&&NHX:TOL=72189],trochiliphagus hirsutus[&&NHX:TOL=72190],trochiliphagus irazuensis[&&NHX:TOL=72191],trochiliphagus jiminezi[&&NHX:TOL=72192],trochiliphagus latitemporalis[&&NHX:TOL=72193],trochiliphagus lazulus[&&NHX:TOL=72194],trochiliphagus lineatus[&&NHX:TOL=72195],trochiliphagus mellivorus[&&NHX:TOL=72196],trochiliphagus mexicanus[&&NHX:TOL=72197],trochiliphagus peruanus[&&NHX:TOL=72198])trochiliphagus[&&NHX:TOL=72185],(trochiloecetes abdominalis[&&NHX:TOL=72200],trochiloecetes aglaeacti[&&NHX:TOL=72201],trochiloecetes angustifrons[&&NHX:TOL=72202],trochiloecetes aureoventridis[&&NHX:TOL=72203],trochiloecetes bolivianus[&&NHX:TOL=72204],trochiloecetes coartatia[&&NHX:TOL=72205],trochiloecetes columbianus[&&NHX:TOL=72206],trochiloecetes complexus[&&NHX:TOL=72207],trochiloecetes cubanensis[&&NHX:TOL=72208],trochiloecetes doratophorus[&&NHX:TOL=72209],trochiloecetes emeliae[&&NHX:TOL=72210],trochiloecetes fasciatus[&&NHX:TOL=72211],trochiloecetes grandior[&&NHX:TOL=72212],trochiloecetes illumani[&&NHX:TOL=72213],trochiloecetes insularis[&&NHX:TOL=72214],trochiloecetes latitemporis[&&NHX:TOL=72215],trochiloecetes malvasae[&&NHX:TOL=72216],trochiloecetes mandibularis[&&NHX:TOL=72217],trochiloecetes multicarinae[&&NHX:TOL=72218],trochiloecetes naevius[&&NHX:TOL=72219],trochiloecetes ochoterenai[&&NHX:TOL=72220],trochiloecetes oenonae[&&NHX:TOL=72221],trochiloecetes pinguis[&&NHX:TOL=72222],trochiloecetes prominens[&&NHX:TOL=72223],trochiloecetes quibdoensis[&&NHX:TOL=72224],trochiloecetes rhodopis[&&NHX:TOL=72225],trochiloecetes rupununi[&&NHX:TOL=72226],trochiloecetes sauli[&&NHX:TOL=72227],trochiloecetes simplex[&&NHX:TOL=72228],trochiloecetes trinidadensis[&&NHX:TOL=72229])trochiloecetes[&&NHX:TOL=72199])ricinidae[&&NHX:TOL=13641],(laemobothrion laemobothrion vulturis[&&NHX:TOL=70968],laemobothrion laemobothrion tinnunculi[&&NHX:TOL=70967],laemobothrion eulaemobothrion simile[&&NHX:TOL=70966],laemobothrion eulaemobothrion setigerum[&&NHX:TOL=70965],laemobothrion eulaemobothrion plegadilymanticum[&&NHX:TOL=70964],laemobothrion eulaemobothrion pallescens[&&NHX:TOL=70963],laemobothrion eulaemobothrion opisthocomi[&&NHX:TOL=70962],laemobothrion eulaemobothrion nocturnum[&&NHX:TOL=70961],laemobothrion laemobothrion maximum[&&NHX:TOL=70960],laemobothrion eulaemobothrion kelloggi[&&NHX:TOL=70959],laemobothrion eulaemobothrion jabiruensis[&&NHX:TOL=70958],laemobothrion eulaemobothrion gracile[&&NHX:TOL=70957],laemobothrion laemobothrion glutinans[&&NHX:TOL=70956],laemobothrion eulaemobothrion eurypygae[&&NHX:TOL=70955],laemobothrion eulaemobothrion emarginatum[&&NHX:TOL=70954],laemobothrion eulaemobothrion cubense[&&NHX:TOL=70953],laemobothrion eulaemobothrion chloropodis[&&NHX:TOL=70952],laemobothrion eulaemobothrion blagoveshtchenskyi[&&NHX:TOL=70951],laemobothrion eulaemobothrion biswasi[&&NHX:TOL=70950],laemobothrion eulaemobothrion atrum[&&NHX:TOL=70949])laemobothrion[&&NHX:TOL=13640])[&&NHX:TOL=50657])amblycera[&&NHX:TOL=13874])phthiraptera[&&NHX:TOL=8237],(((belapha globifer[&&NHX:TOL=32674],belapha schoutedeni[&&NHX:TOL=32675])belapha[&&NHX:TOL=32665],(belaphopsocus badonneli[&&NHX:TOL=32676],belaphopsocus murphyi[&&NHX:TOL=32677],belaphopsocus vilhenai[&&NHX:TOL=32678])belaphopsocus[&&NHX:TOL=32666],(belaphotroctes alleni[&&NHX:TOL=32679],belaphotroctes angolensis[&&NHX:TOL=32680],belaphotroctes antennalis[&&NHX:TOL=32681],belaphotroctes atlanticus[&&NHX:TOL=32682],belaphotroctes badonneli[&&NHX:TOL=32683],belaphotroctes brunneus[&&NHX:TOL=32684],belaphotroctes fallax[&&NHX:TOL=32685],belaphotroctes ghesquierei[&&NHX:TOL=32686],belaphotroctes hermosus[&&NHX:TOL=32687],belaphotroctes major[&&NHX:TOL=32688],belaphotroctes mimulus[&&NHX:TOL=32689],belaphotroctes ocularis[&&NHX:TOL=32690],belaphotroctes remyi[&&NHX:TOL=32691],belaphotroctes simberloffi[&&NHX:TOL=32692],belaphotroctes simulans[&&NHX:TOL=32693],belaphotroctes striatus[&&NHX:TOL=32694],belaphotroctes traegardhi[&&NHX:TOL=32695],belaphotroctes vaginatus[&&NHX:TOL=32696])belaphotroctes[&&NHX:TOL=32667],chaetotroctes lenkoi[&&NHX:TOL=32668],embidopsocopsis newi[&&NHX:TOL=32669],(embidopsocus angolensis[&&NHX:TOL=32699],embidopsocus antennalis[&&NHX:TOL=32700],embidopsocus bousemani[&&NHX:TOL=32701],embidopsocus brasiliensis[&&NHX:TOL=32702],embidopsocus citrensis[&&NHX:TOL=32703],embidopsocus congolensis[&&NHX:TOL=32704],embidopsocus cubanus[&&NHX:TOL=32705],embidopsocus distinctus[&&NHX:TOL=32706],embidopsocus echinus[&&NHX:TOL=32707],embidopsocus enderleini[&&NHX:TOL=32708],embidopsocus femoralis[&&NHX:TOL=32709],embidopsocus flexuosus[&&NHX:TOL=32710],embidopsocus frater[&&NHX:TOL=32711],embidopsocus granulosus[&&NHX:TOL=32712],embidopsocus hainanicus[&&NHX:TOL=32713],embidopsocus intermedius[&&NHX:TOL=32714],embidopsocus jikuni[&&NHX:TOL=32715],embidopsocus kumaonensis[&&NHX:TOL=32716],embidopsocus laticeps[&&NHX:TOL=32717],embidopsocus leucomelas[&&NHX:TOL=32718],embidopsocus luteus[&&NHX:TOL=32719],embidopsocus machadoi[&&NHX:TOL=32720],embidopsocus mendax[&&NHX:TOL=32721],embidopsocus mexicanus[&&NHX:TOL=32722],embidopsocus minor[&&NHX:TOL=32723],embidopsocus needhami[&&NHX:TOL=32724],embidopsocus oleaginus[&&NHX:TOL=32725],embidopsocus pallidus[&&NHX:TOL=32726],embidopsocus paradoxus[&&NHX:TOL=32727],embidopsocus pauliani[&&NHX:TOL=32728],embidopsocus pilosus[&&NHX:TOL=32729],embidopsocus sacchari[&&NHX:TOL=32730],embidopsocus similis[&&NHX:TOL=32731],embidopsocus thorntoni[&&NHX:TOL=32732],embidopsocus trichurensis[&&NHX:TOL=32733],embidopsocus trifasciatus[&&NHX:TOL=32734],embidopsocus vilhenai[&&NHX:TOL=32735],embidopsocus virgatus[&&NHX:TOL=32736],embidopsocus zhouyaoi[&&NHX:TOL=32737])embidopsocus[&&NHX:TOL=32670],troctulus machadoi[&&NHX:TOL=32671])embidopsocinae[&&NHX:TOL=50614],((liposcelis abdominalis[&&NHX:TOL=32739],liposcelis aconae[&&NHX:TOL=32740],liposcelis albothoracica[&&NHX:TOL=32741],liposcelis alticolis[&&NHX:TOL=32742],liposcelis ambigua[&&NHX:TOL=32743],liposcelis angolensis[&&NHX:TOL=32744],liposcelis annulata[&&NHX:TOL=32745],liposcelis anomala[&&NHX:TOL=32746],liposcelis antennatoides[&&NHX:TOL=32747],liposcelis arenicola[&&NHX:TOL=32748],liposcelis australis[&&NHX:TOL=32749],liposcelis ayosae[&&NHX:TOL=32750],liposcelis barrai[&&NHX:TOL=32751],liposcelis bengalensis[&&NHX:TOL=32752],liposcelis bicolor[&&NHX:TOL=32753],liposcelis bicoloripes[&&NHX:TOL=32754],liposcelis bogotana[&&NHX:TOL=32755],liposcelis borbonensis[&&NHX:TOL=32756],liposcelis bostrychophila[&&NHX:TOL=32757],liposcelis bouilloni[&&NHX:TOL=32758],liposcelis broadheadi[&&NHX:TOL=32759],liposcelis brunnea[&&NHX:TOL=32760],liposcelis canariensis[&&NHX:TOL=32761],liposcelis castrii[&&NHX:TOL=32762],liposcelis chilensis[&&NHX:TOL=32763],liposcelis cibaritica[&&NHX:TOL=32764],liposcelis compacta[&&NHX:TOL=32765],liposcelis corrodens[&&NHX:TOL=32766],liposcelis decolor[&&NHX:TOL=32767],liposcelis delamarei[&&NHX:TOL=32768],liposcelis deltachi[&&NHX:TOL=32769],liposcelis dentata[&&NHX:TOL=32770],liposcelis desertica[&&NHX:TOL=32771],liposcelis dichromis[&&NHX:TOL=32772],liposcelis discalis[&&NHX:TOL=32773],liposcelis distincta[&&NHX:TOL=32774],liposcelis divinatoria[&&NHX:TOL=32775],liposcelis edaphica[&&NHX:TOL=32776],liposcelis elegantis[&&NHX:TOL=32777],liposcelis entomophila[&&NHX:TOL=32778],liposcelis exigua[&&NHX:TOL=32779],liposcelis fallax[&&NHX:TOL=32780],liposcelis fasciata[&&NHX:TOL=32781],liposcelis flavida[&&NHX:TOL=32782],liposcelis formicaria[&&NHX:TOL=32783],liposcelis fusciceps[&&NHX:TOL=32784],liposcelis globiceps[&&NHX:TOL=32785],liposcelis guentheri[&&NHX:TOL=32786],liposcelis hirsuta[&&NHX:TOL=32787],liposcelis hirsutoides[&&NHX:TOL=32788],liposcelis jilinica[&&NHX:TOL=32789],liposcelis keleri[&&NHX:TOL=32790],liposcelis kidderi[&&NHX:TOL=32791],liposcelis kyrosensis[&&NHX:TOL=32792],liposcelis lacinia[&&NHX:TOL=32793],liposcelis laoshanensis[&&NHX:TOL=32794],liposcelis laparvensis[&&NHX:TOL=32795],liposcelis lenkoi[&&NHX:TOL=32796],liposcelis liparoides[&&NHX:TOL=32797],liposcelis lunai[&&NHX:TOL=32798],liposcelis machadoi[&&NHX:TOL=32799],liposcelis maculata[&&NHX:TOL=32800],liposcelis maracayensis[&&NHX:TOL=32801],liposcelis marginepunctata[&&NHX:TOL=32802],liposcelis mendax[&&NHX:TOL=32803],liposcelis meridionalis[&&NHX:TOL=32804],liposcelis mimula[&&NHX:TOL=32805],liposcelis minuta[&&NHX:TOL=32806],liposcelis mira[&&NHX:TOL=32807],liposcelis montamargensis[&&NHX:TOL=32808],liposcelis myrmecophila[&&NHX:TOL=32809],liposcelis nasus[&&NHX:TOL=32810],liposcelis naturalis[&&NHX:TOL=32811],liposcelis nigra[&&NHX:TOL=32812],liposcelis nigritibia[&&NHX:TOL=32813],liposcelis nigrocincta[&&NHX:TOL=32814],liposcelis nigrofasciata[&&NHX:TOL=32815],liposcelis nuptialis[&&NHX:TOL=32816],liposcelis obscura[&&NHX:TOL=32817],liposcelis orghidani[&&NHX:TOL=32818],liposcelis ornata[&&NHX:TOL=32819],liposcelis pacifica[&&NHX:TOL=32820],liposcelis paeta[&&NHX:TOL=32821],liposcelis paetula[&&NHX:TOL=32822],liposcelis palatina[&&NHX:TOL=32823],liposcelis pallens[&&NHX:TOL=32824],liposcelis pallida[&&NHX:TOL=32825],liposcelis parvula[&&NHX:TOL=32826],liposcelis pauliani[&&NHX:TOL=32827],liposcelis pearmani[&&NHX:TOL=32828],liposcelis perforata[&&NHX:TOL=32829],liposcelis picta[&&NHX:TOL=32830],liposcelis plesiopuber[&&NHX:TOL=32831],liposcelis prenolepidis[&&NHX:TOL=32832],liposcelis priesneri[&&NHX:TOL=32833],liposcelis puber[&&NHX:TOL=32834],liposcelis pubescens[&&NHX:TOL=32835],liposcelis pulchra[&&NHX:TOL=32836],liposcelis purpurea[&&NHX:TOL=32837],liposcelis reticulata[&&NHX:TOL=32838],liposcelis romeralensis[&&NHX:TOL=32839],liposcelis rufa[&&NHX:TOL=32840],liposcelis rufiornata[&&NHX:TOL=32841],liposcelis rugosa[&&NHX:TOL=32842],liposcelis sculptimacula[&&NHX:TOL=32843],liposcelis semicaeca[&&NHX:TOL=32844],liposcelis setosa[&&NHX:TOL=32845],liposcelis silvarum[&&NHX:TOL=32846],liposcelis similis[&&NHX:TOL=32847],liposcelis sinica[&&NHX:TOL=32848],liposcelis tamminensis[&&NHX:TOL=32849],liposcelis tetrops[&&NHX:TOL=32850],liposcelis transvaalensis[&&NHX:TOL=32851],liposcelis tricolor[&&NHX:TOL=32852],liposcelis triocellata[&&NHX:TOL=32853],liposcelis uxoris[&&NHX:TOL=32854],liposcelis villosa[&&NHX:TOL=32855],liposcelis yangi[&&NHX:TOL=32856],liposcelis yunnaniensis[&&NHX:TOL=32857])liposcelis[&&NHX:TOL=32672],troglotroctes ashmoleorum[&&NHX:TOL=32673])liposcelidinae[&&NHX:TOL=50615])liposcelididae[&&NHX:TOL=14455],(((nanopsocus falsus[&&NHX:TOL=32578],nanopsocus longicornis[&&NHX:TOL=32579],nanopsocus oceanicus[&&NHX:TOL=32580],nanopsocus pictus[&&NHX:TOL=32581],nanopsocus trifasciatus[&&NHX:TOL=32582])nanopsocus[&&NHX:TOL=38123],(psylloneura pygmaea[&&NHX:TOL=32583],psylloneura simbangana[&&NHX:TOL=32584],psylloneura ugandana[&&NHX:TOL=32585])psylloneura[&&NHX:TOL=38124],(tapinella aliena[&&NHX:TOL=32586],tapinella baliensis[&&NHX:TOL=32587],tapinella bannana[&&NHX:TOL=32588],tapinella bicolorata[&&NHX:TOL=32589],tapinella campanensis[&&NHX:TOL=32590],tapinella candida[&&NHX:TOL=32591],tapinella castanea[&&NHX:TOL=32592],tapinella chamelana[&&NHX:TOL=32593],tapinella clypeola[&&NHX:TOL=32594],tapinella columbiana[&&NHX:TOL=32595],tapinella curvata[&&NHX:TOL=32596],tapinella curvatoides[&&NHX:TOL=32597],tapinella dichromoptera[&&NHX:TOL=32598],tapinella fasciata[&&NHX:TOL=32599],tapinella formosana[&&NHX:TOL=32600],tapinella francesca[&&NHX:TOL=32601],tapinella fusca[&&NHX:TOL=32602],tapinella gamma[&&NHX:TOL=32603],tapinella glyptops[&&NHX:TOL=32604],tapinella huangi[&&NHX:TOL=32605],tapinella levuka[&&NHX:TOL=32606],tapinella maculata[&&NHX:TOL=32607],tapinella madagascariensis[&&NHX:TOL=32608],tapinella maracana[&&NHX:TOL=32609],tapinella mariana[&&NHX:TOL=32610],tapinella nebulosa[&&NHX:TOL=32611],tapinella negreai[&&NHX:TOL=32612],tapinella olmeca[&&NHX:TOL=32613],tapinella ornaticeps[&&NHX:TOL=32614],tapinella picta[&&NHX:TOL=32615],tapinella picticeps[&&NHX:TOL=32616],tapinella pictipenna[&&NHX:TOL=32617],tapinella qutangxiana[&&NHX:TOL=32618],tapinella spinosa[&&NHX:TOL=32619],tapinella squamosa[&&NHX:TOL=32620],tapinella stenomedia[&&NHX:TOL=32621],tapinella trilineata[&&NHX:TOL=32622],tapinella tuila[&&NHX:TOL=32623],tapinella unicolorata[&&NHX:TOL=32624],tapinella vittata[&&NHX:TOL=32625])tapinella[&&NHX:TOL=38125])tapinellinae[&&NHX:TOL=50612],(antilopsocus nadleri[&&NHX:TOL=32626],leptotroctes pelesi[&&NHX:TOL=32627],nymphotroctes denisi[&&NHX:TOL=32628],(pachytroctes achrostus[&&NHX:TOL=32629],pachytroctes aegyptius[&&NHX:TOL=32630],pachytroctes aglyphus[&&NHX:TOL=32631],pachytroctes ambiguus[&&NHX:TOL=32632],pachytroctes aurantiacus[&&NHX:TOL=32633],pachytroctes australis[&&NHX:TOL=32634],pachytroctes bicoloripes[&&NHX:TOL=32635],pachytroctes brasilianus[&&NHX:TOL=32636],pachytroctes brunneus[&&NHX:TOL=32637],pachytroctes dayae[&&NHX:TOL=32638],pachytroctes dichromoscelis[&&NHX:TOL=32639],pachytroctes ealensis[&&NHX:TOL=32640],pachytroctes grannulosus[&&NHX:TOL=32641],pachytroctes infuscatus[&&NHX:TOL=32642],pachytroctes insularis[&&NHX:TOL=32643],pachytroctes ixtapaensis[&&NHX:TOL=32644],pachytroctes maculosus[&&NHX:TOL=32645],pachytroctes neoleonensis[&&NHX:TOL=32646],pachytroctes nivecinctus[&&NHX:TOL=32647],pachytroctes pacificus[&&NHX:TOL=32648],pachytroctes robustus[&&NHX:TOL=32649],pachytroctes rugosus[&&NHX:TOL=32650],pachytroctes sericeus[&&NHX:TOL=32651],pachytroctes sinuosus[&&NHX:TOL=32652],pachytroctes tapinelloides[&&NHX:TOL=32653],pachytroctes velutinus[&&NHX:TOL=32654],pachytroctes viettei[&&NHX:TOL=32655])pachytroctes[&&NHX:TOL=38126],(peritroctes angolensis[&&NHX:TOL=32656],peritroctes bengalensis[&&NHX:TOL=32657],peritroctes cochinensis[&&NHX:TOL=32658],peritroctes etiennei[&&NHX:TOL=32659],peritroctes natalensis[&&NHX:TOL=32660],peritroctes trifasciatus[&&NHX:TOL=32661])peritroctes[&&NHX:TOL=38127],(psacadium bilimbatum[&&NHX:TOL=32662],psacadium georgi[&&NHX:TOL=32663])psacadium[&&NHX:TOL=38128],psyllotroctes plaumanni[&&NHX:TOL=32664])pachytroctinae[&&NHX:TOL=50613])pachytroctidae[&&NHX:TOL=14456])[&&NHX:TOL=30259],((badonnelia castrii[&&NHX:TOL=32554],badonnelia granulosa[&&NHX:TOL=32555],badonnelia similis[&&NHX:TOL=32556],badonnelia testacea[&&NHX:TOL=32557],badonnelia titei[&&NHX:TOL=32558])badonnelia[&&NHX:TOL=38121],(sphaeropsocopsis argentina[&&NHX:TOL=32559],sphaeropsocopsis chilensis[&&NHX:TOL=32560],sphaeropsocopsis microps[&&NHX:TOL=32561],sphaeropsocopsis myrtleae[&&NHX:TOL=32562],sphaeropsocopsis recens[&&NHX:TOL=32563],sphaeropsocopsis reisi[&&NHX:TOL=32564],sphaeropsocopsis spinosa[&&NHX:TOL=32565],sphaeropsocopsis valdiviensis[&&NHX:TOL=32566],sphaeropsocopsis valeriae[&&NHX:TOL=32567])sphaeropsocopsis[&&NHX:TOL=38122],sphaeropsocus kuenowii[&&NHX:TOL=137532],[&&NHX:TOL=137533])sphaeropsocidae[&&NHX:TOL=14457])nanopsocetae[&&NHX:TOL=30258],(((ancylentomus apicidealbatus[&&NHX:TOL=32930],(amphientomum acuminatum[&&NHX:TOL=32970],amphientomum aelleni[&&NHX:TOL=32971],amphientomum annulicorne[&&NHX:TOL=32972],amphientomum annulitibia[&&NHX:TOL=32973],amphientomum dimorphum[&&NHX:TOL=32974],amphientomum ectostriolatis[&&NHX:TOL=32975],amphientomum flexuosum[&&NHX:TOL=32976],amphientomum hieroglyphicum[&&NHX:TOL=32977],amphientomum indentatum[&&NHX:TOL=32978],amphientomum loebli[&&NHX:TOL=32979],amphientomum mimulum[&&NHX:TOL=32980],amphientomum montanum[&&NHX:TOL=32981],amphientomum pauliani[&&NHX:TOL=32982],amphientomum punctatum[&&NHX:TOL=32983],amphientomum simile[&&NHX:TOL=32984],amphientomum striaticeps[&&NHX:TOL=32985])amphientomum[&&NHX:TOL=32931],compressionis introvenis[&&NHX:TOL=32932],(diamphipsocus acaudatus[&&NHX:TOL=32987],diamphipsocus concoloratus[&&NHX:TOL=32988],diamphipsocus fulvus[&&NHX:TOL=32989],diamphipsocus grammostictous[&&NHX:TOL=32990],diamphipsocus shanxiesis[&&NHX:TOL=32991],diamphipsocus signatus[&&NHX:TOL=32992],diamphipsocus weihuai[&&NHX:TOL=32993],diamphipsocus xanthocephalus[&&NHX:TOL=32994])diamphipsocus[&&NHX:TOL=32933],(hemiseopsis alettae[&&NHX:TOL=32995],hemiseopsis fuelleborni[&&NHX:TOL=32996],hemiseopsis machadoi[&&NHX:TOL=32997],hemiseopsis obscura[&&NHX:TOL=32998])hemiseopsis[&&NHX:TOL=32934],(lithoseopsis cervantesi[&&NHX:TOL=32999],lithoseopsis chamelensis[&&NHX:TOL=33000],lithoseopsis elongata[&&NHX:TOL=33001],lithoseopsis hellmani[&&NHX:TOL=33002],lithoseopsis hystrix[&&NHX:TOL=33003],lithoseopsis insularis[&&NHX:TOL=33004],lithoseopsis tuitensis[&&NHX:TOL=33005])lithoseopsis[&&NHX:TOL=32935],(marcenendius illustris[&&NHX:TOL=33006],marcenendius nostras[&&NHX:TOL=33007])marcenendius[&&NHX:TOL=32936],neoseopsis nuda[&&NHX:TOL=32937],(nephax angolensis[&&NHX:TOL=33009],nephax capensis[&&NHX:TOL=33010],nephax fortunatus[&&NHX:TOL=33011],nephax nepalensis[&&NHX:TOL=33012],nephax sofadanus[&&NHX:TOL=33013])nephax[&&NHX:TOL=32938],(paramphientomum cordatum[&&NHX:TOL=33014],paramphientomum magnimanubrum[&&NHX:TOL=33015],paramphientomum malayense[&&NHX:TOL=33016],paramphientomum nanum[&&NHX:TOL=33017],paramphientomum nietneri[&&NHX:TOL=33018],paramphientomum nigriceps[&&NHX:TOL=33019],paramphientomum sinuosum[&&NHX:TOL=33020],paramphientomum striatum[&&NHX:TOL=33021],paramphientomum triangulum[&&NHX:TOL=33022],paramphientomum tristrigatum[&&NHX:TOL=33023],paramphientomum yumyum[&&NHX:TOL=33024])paramphientomum[&&NHX:TOL=32939],(pseudoseopsis elegans[&&NHX:TOL=33025],pseudoseopsis marginepunctata[&&NHX:TOL=33026],pseudoseopsis usambarana[&&NHX:TOL=33027],pseudoseopsis venezuelensis[&&NHX:TOL=33028],pseudoseopsis vilhenai[&&NHX:TOL=33029])pseudoseopsis[&&NHX:TOL=32940],(seopsis ardoi[&&NHX:TOL=33030],seopsis badia[&&NHX:TOL=33031],seopsis beijingensis[&&NHX:TOL=33032],seopsis chinensis[&&NHX:TOL=33033],seopsis concava[&&NHX:TOL=33034],seopsis cycloptera[&&NHX:TOL=33035],seopsis eucalla[&&NHX:TOL=33036],seopsis guibeiensis[&&NHX:TOL=33037],seopsis hirtella[&&NHX:TOL=33038],seopsis humphreysi[&&NHX:TOL=33039],seopsis incisa[&&NHX:TOL=33040],seopsis longisquama[&&NHX:TOL=33041],seopsis luzonica[&&NHX:TOL=33042],seopsis magna[&&NHX:TOL=33043],seopsis metallops[&&NHX:TOL=33044],seopsis metodicra[&&NHX:TOL=33045],seopsis multisquama[&&NHX:TOL=33046],seopsis nanjingensis[&&NHX:TOL=33047],seopsis pavonia[&&NHX:TOL=33048],seopsis qinlingensis[&&NHX:TOL=33049],seopsis superba[&&NHX:TOL=33050],seopsis termitophila[&&NHX:TOL=33051],seopsis tricolor[&&NHX:TOL=33052],seopsis vasantasena[&&NHX:TOL=33053])seopsis[&&NHX:TOL=32941],(seopsocus acuminatus[&&NHX:TOL=33054],seopsocus albiceps[&&NHX:TOL=33055],seopsocus annulipes[&&NHX:TOL=33056],seopsocus fasciatus[&&NHX:TOL=33057],seopsocus lacandonicus[&&NHX:TOL=33058],seopsocus rafaeli[&&NHX:TOL=33059],seopsocus rotundatus[&&NHX:TOL=33060])seopsocus[&&NHX:TOL=32942],stigmatopathus horvathi[&&NHX:TOL=32943],(stimulopalpus acutipinnatus[&&NHX:TOL=33062],stimulopalpus angustivalvus[&&NHX:TOL=33063],stimulopalpus africanus[&&NHX:TOL=33064],stimulopalpus baeoivalvus[&&NHX:TOL=33065],stimulopalpus biocellatus[&&NHX:TOL=33066],stimulopalpus brunneus[&&NHX:TOL=33067],stimulopalpus changjiangicus[&&NHX:TOL=33068],stimulopalpus cochleatus[&&NHX:TOL=33069],stimulopalpus concinnus[&&NHX:TOL=33070],stimulopalpus conflexus[&&NHX:TOL=33071],stimulopalpus distinctus[&&NHX:TOL=33072],stimulopalpus dolichogonus[&&NHX:TOL=33073],stimulopalpus erromerus[&&NHX:TOL=33074],stimulopalpus estipitatus[&&NHX:TOL=33075],stimulopalpus exilis[&&NHX:TOL=33076],stimulopalpus furcatus[&&NHX:TOL=33077],stimulopalpus galactospilus[&&NHX:TOL=33078],stimulopalpus heteroideus[&&NHX:TOL=33079],stimulopalpus huashanensis[&&NHX:TOL=33080],stimulopalpus immediatus[&&NHX:TOL=33081],stimulopalpus introcurvus[&&NHX:TOL=33082],stimulopalpus isoneurus[&&NHX:TOL=33083],stimulopalpus japonicus[&&NHX:TOL=33084],stimulopalpus medifascus[&&NHX:TOL=33085],stimulopalpus mimeticus[&&NHX:TOL=33086],stimulopalpus peltatus[&&NHX:TOL=33087],stimulopalpus pentospilus[&&NHX:TOL=33088],stimulopalpus phaeospilus[&&NHX:TOL=33089],stimulopalpus polychaetus[&&NHX:TOL=33090],stimulopalpus psednopetalus[&&NHX:TOL=33091])stimulopalpus[&&NHX:TOL=32944],(syllysis caudata[&&NHX:TOL=33092],syllysis erato[&&NHX:TOL=33093],syllysis ritusamhara[&&NHX:TOL=33094],syllysis samarangana[&&NHX:TOL=33095],syllysis sinipennis[&&NHX:TOL=33096])syllysis[&&NHX:TOL=32945],yinia capitinigra[&&NHX:TOL=32946])amphientominae[&&NHX:TOL=50618],((cymatopsocus emarginatus[&&NHX:TOL=32959],cymatopsocus enderleini[&&NHX:TOL=32960],cymatopsocus enigmaticus[&&NHX:TOL=32961],cymatopsocus maculatus[&&NHX:TOL=32962],cymatopsocus opalinus[&&NHX:TOL=32963])cymatopsocus[&&NHX:TOL=32928],(tineomorpha angolana[&&NHX:TOL=32964],tineomorpha greeniana[&&NHX:TOL=32965],tineomorpha jacobsoniana[&&NHX:TOL=32966],tineomorpha murphyi[&&NHX:TOL=32967],tineomorpha timahensis[&&NHX:TOL=32968])tineomorpha[&&NHX:TOL=32929])tineomorphinae[&&NHX:TOL=50617],(ancylopsocus fortuosus[&&NHX:TOL=32947],ancylopsocus ganquanensis[&&NHX:TOL=32948],ancylopsocus longinervus[&&NHX:TOL=32949],ancylopsocus macrurus[&&NHX:TOL=32950])ancylopsocus[&&NHX:TOL=32921],antivulgaris jainfenglingensis[&&NHX:TOL=32922],(biocellientomia bitrigata[&&NHX:TOL=32952],biocellientomia diplosticta[&&NHX:TOL=32953])biocellientomia[&&NHX:TOL=32923],(cornutientomus curtifurcis[&&NHX:TOL=32955],cornutientomus illepidotus[&&NHX:TOL=32954])cornutientomus[&&NHX:TOL=32924],lifashengia zhongshani[&&NHX:TOL=32925],neuroseopsis mecodichis[&&NHX:TOL=32926],yunientomia ditaenia[&&NHX:TOL=32927])amphientomidae[&&NHX:TOL=14458],(compsocus elegans[&&NHX:TOL=32880],electrentomopsis variegata[&&NHX:TOL=32881])compsocidae[&&NHX:TOL=14462],((epitroctes calypso[&&NHX:TOL=32870],epitroctes pluvialis[&&NHX:TOL=32871],epitroctes sanguineus[&&NHX:TOL=32872],epitroctes sanvito[&&NHX:TOL=32873],epitroctes tuxtlarum[&&NHX:TOL=32874])epitroctes[&&NHX:TOL=38130],manicapsocus alettae[&&NHX:TOL=32875],nothoentomum palpale[&&NHX:TOL=32876],phallopsocus carminatus[&&NHX:TOL=32877])electrentomidae[&&NHX:TOL=30263],(musapsocoides nadleri[&&NHX:TOL=32884],(musapsocus birkenholzi[&&NHX:TOL=32885],musapsocus creole[&&NHX:TOL=32886],musapsocus huastecanus[&&NHX:TOL=32887],musapsocus insularis[&&NHX:TOL=32888],musapsocus mockfordi[&&NHX:TOL=32889],musapsocus newi[&&NHX:TOL=32890],musapsocus simlae[&&NHX:TOL=32891],musapsocus tabascensis[&&NHX:TOL=32892])musapsocus[&&NHX:TOL=38131])musapsocidae[&&NHX:TOL=14459],(chelyopsocus garganicus[&&NHX:TOL=32862],(philedaphia aphrodite[&&NHX:TOL=32863],philedaphia hauseri[&&NHX:TOL=32864])philedaphia[&&NHX:TOL=38129],protroctopsocus enigmaticus[&&NHX:TOL=32865],reticulopsocus besucheti[&&NHX:TOL=137504])protroctopsocidae[&&NHX:TOL=30262],((coleotroctellus burckhardti[&&NHX:TOL=32899],coleotroctellus loebli[&&NHX:TOL=32900],coleotroctellus sui[&&NHX:TOL=32901],coleotroctellus venosus[&&NHX:TOL=32902])coleotroctellus[&&NHX:TOL=38132],selenopsocus schwendingeri[&&NHX:TOL=32903],(thaipsocus bau[&&NHX:TOL=32904],thaipsocus borneensis[&&NHX:TOL=32905],thaipsocus doisuthep[&&NHX:TOL=32906],thaipsocus orientalis[&&NHX:TOL=32907],thaipsocus sarawakensis[&&NHX:TOL=32908],thaipsocus siamensis[&&NHX:TOL=32909],thaipsocus thamluang[&&NHX:TOL=32910])thaipsocus[&&NHX:TOL=38133],(troctopsocopsis intermedia[&&NHX:TOL=32911],troctopsocopsis jamaicensis[&&NHX:TOL=32912],troctopsocopsis luciensis[&&NHX:TOL=32913],troctopsocopsis martinica[&&NHX:TOL=32914],troctopsocopsis obscura[&&NHX:TOL=32915])troctopsocopsis[&&NHX:TOL=38134],(troctopsoculus brasiliensis[&&NHX:TOL=32916],troctopsoculus morenus[&&NHX:TOL=32917])troctopsoculus[&&NHX:TOL=38135],(troctopsocus bicolor[&&NHX:TOL=32918],troctopsocus separatus[&&NHX:TOL=32919],troctopsocus similis[&&NHX:TOL=32920])troctopsocus[&&NHX:TOL=38136])troctopsocidae[&&NHX:TOL=14460])amphientometae[&&NHX:TOL=30260])troctomorpha[&&NHX:TOL=30257])[&&NHX:TOL=30217],((((((anomocopeus chrysops[&&NHX:TOL=30394],anomocopeus nasutus[&&NHX:TOL=30395])anomocopeus[&&NHX:TOL=30393],(cerobasis albipes[&&NHX:TOL=30397],cerobasis alfredi[&&NHX:TOL=30398],cerobasis alpha[&&NHX:TOL=30399],cerobasis amorosa[&&NHX:TOL=30400],cerobasis annulata[&&NHX:TOL=30401],cerobasis australica[&&NHX:TOL=30402],cerobasis caboverdensis[&&NHX:TOL=30403],cerobasis canariensis[&&NHX:TOL=30404],cerobasis captiva[&&NHX:TOL=30405],cerobasis clarionensis[&&NHX:TOL=30406],cerobasis denticulata[&&NHX:TOL=30407],cerobasis ericacea[&&NHX:TOL=30408],cerobasis guestfalica[&&NHX:TOL=30409],cerobasis harteni[&&NHX:TOL=30410],cerobasis insularis[&&NHX:TOL=30411],cerobasis intermedia[&&NHX:TOL=30412],cerobasis lambda[&&NHX:TOL=30413],cerobasis lapidicola[&&NHX:TOL=30414],cerobasis longicornis[&&NHX:TOL=30424],cerobasis maculiceps[&&NHX:TOL=30415],cerobasis maderensis[&&NHX:TOL=30416],cerobasis maya[&&NHX:TOL=30417],cerobasis nigra[&&NHX:TOL=30418],cerobasis pineticola[&&NHX:TOL=30419],cerobasis recta[&&NHX:TOL=30420],cerobasis rosae[&&NHX:TOL=30421],cerobasis socotrae[&&NHX:TOL=30422],cerobasis treptica[&&NHX:TOL=30423])cerobasis[&&NHX:TOL=30396],helminotrogia bipunctata[&&NHX:TOL=30425],(lepinotus angolensis[&&NHX:TOL=30427],lepinotus fuscus[&&NHX:TOL=30437],lepinotus indicus[&&NHX:TOL=30428],lepinotus inquilinus[&&NHX:TOL=30429],lepinotus lepinotoides[&&NHX:TOL=30430],lepinotus machadoi[&&NHX:TOL=30431],lepinotus patruelis[&&NHX:TOL=30432],lepinotus reticulatus[&&NHX:TOL=30433],lepinotus stoneae[&&NHX:TOL=30434],lepinotus tasmaniensis[&&NHX:TOL=30435],lepinotus vermicularis[&&NHX:TOL=30436])lepinotus[&&NHX:TOL=30426],myrmicodipnella aptera[&&NHX:TOL=30438],phlebotrogia chinensis[&&NHX:TOL=30439],spinatropos philippi[&&NHX:TOL=30440],(trogium apterum[&&NHX:TOL=30442],trogium braheicola[&&NHX:TOL=30443],trogium evansorum[&&NHX:TOL=30448],trogium lapidarium[&&NHX:TOL=30444],trogium picticeps[&&NHX:TOL=30445],trogium pulsatorium[&&NHX:TOL=30446],trogium stellatum[&&NHX:TOL=30447])trogium[&&NHX:TOL=30441])trogiidae[&&NHX:TOL=14451],(balliella ealensis[&&NHX:TOL=30453],(eosilla denervosa[&&NHX:TOL=30460],eosilla jacobsoni[&&NHX:TOL=30461])eosilla[&&NHX:TOL=30454],(psoquilla infuscata[&&NHX:TOL=30462],psoquilla marginepunctata[&&NHX:TOL=30463])psoquilla[&&NHX:TOL=30455],rhyopsocidus niger[&&NHX:TOL=30456],rhyopsoculus mexicanus[&&NHX:TOL=30457],(rhyopsocus afer[&&NHX:TOL=30466],rhyopsocus bentonae[&&NHX:TOL=30467],rhyopsocus bicornis[&&NHX:TOL=30468],rhyopsocus calakmulensis[&&NHX:TOL=30469],rhyopsocus concavus[&&NHX:TOL=30470],rhyopsocus conformis[&&NHX:TOL=30471],rhyopsocus confusus[&&NHX:TOL=30472],rhyopsocus disparilis[&&NHX:TOL=30473],rhyopsocus eclipticus[&&NHX:TOL=30474],rhyopsocus grandiphallus[&&NHX:TOL=30475],rhyopsocus maculosus[&&NHX:TOL=30476],rhyopsocus madagascariensis[&&NHX:TOL=30477],rhyopsocus micropterus[&&NHX:TOL=30478],rhyopsocus nidicola[&&NHX:TOL=30479],rhyopsocus ocotensis[&&NHX:TOL=30480],rhyopsocus orthatus[&&NHX:TOL=30481],rhyopsocus pandanicola[&&NHX:TOL=30482],rhyopsocus peregrinus[&&NHX:TOL=30483],rhyopsocus plesiafer[&&NHX:TOL=30484],rhyopsocus spheciophilus[&&NHX:TOL=30485],rhyopsocus texanus[&&NHX:TOL=30486])rhyopsocus[&&NHX:TOL=30458])psoquillidae[&&NHX:TOL=14452])[&&NHX:TOL=30389],(((thylacella acutipennis[&&NHX:TOL=30507],thylacella angulifrons[&&NHX:TOL=30508],thylacella angustipennis[&&NHX:TOL=30509],thylacella annulata[&&NHX:TOL=30510],thylacella congolensis[&&NHX:TOL=30511],thylacella cubana[&&NHX:TOL=30512],thylacella eversiana[&&NHX:TOL=30513],thylacella fasciata[&&NHX:TOL=30514],thylacella fasciifrons[&&NHX:TOL=30515],thylacella fenestrata[&&NHX:TOL=30516],thylacella huautlensis[&&NHX:TOL=30517],thylacella immaculata[&&NHX:TOL=30518],thylacella madagascariensis[&&NHX:TOL=30519],thylacella montana[&&NHX:TOL=30520],thylacella pilipennis[&&NHX:TOL=30521],thylacella similis[&&NHX:TOL=30522],thylacella trifurcata[&&NHX:TOL=30523],thylacella vitripennis[&&NHX:TOL=30524])thylacella[&&NHX:TOL=30488],pseudothylacus acisopterus[&&NHX:TOL=30487])thylacellinae[&&NHX:TOL=30799],((lepium chrysochlorum[&&NHX:TOL=30526],lepium enderleini[&&NHX:TOL=30527],lepium luridum[&&NHX:TOL=30528])lepium[&&NHX:TOL=30490],illepidopsocus yunnanicus[&&NHX:TOL=30489],neolepidopsocus chinensis[&&NHX:TOL=30491],(nepticulomima biroiana[&&NHX:TOL=30530],nepticulomima bothriata[&&NHX:TOL=30531],nepticulomima brasiliensis[&&NHX:TOL=30532],nepticulomima campechensis[&&NHX:TOL=30533],nepticulomima jacobsoni[&&NHX:TOL=30538],nepticulomima cavagnaroi[&&NHX:TOL=30534],nepticulomima chalcomelas[&&NHX:TOL=30535],nepticulomima essigkeana[&&NHX:TOL=30536],nepticulomima hoesemanni[&&NHX:TOL=30537],nepticulomima latisquama[&&NHX:TOL=30539],nepticulomima lineata[&&NHX:TOL=30540],nepticulomima lusiae[&&NHX:TOL=30541],nepticulomima orientalis[&&NHX:TOL=30542],nepticulomima penicillata[&&NHX:TOL=30543],nepticulomima pulvillata[&&NHX:TOL=30544],nepticulomima sakuntala[&&NHX:TOL=30545],nepticulomima saltuaria[&&NHX:TOL=30546],nepticulomima scottiana[&&NHX:TOL=30547],nepticulomima sumatrensis[&&NHX:TOL=30548],nepticulomima tridentata[&&NHX:TOL=30549],nepticulomima uniformis[&&NHX:TOL=30550])nepticulomima[&&NHX:TOL=30492],(notolepium brasiliense[&&NHX:TOL=30551],notolepium paraguayense[&&NHX:TOL=30552])notolepium[&&NHX:TOL=30493],parasoa haploneura[&&NHX:TOL=30494],(perientomum acutipenne[&&NHX:TOL=30554],perientomum argentatum[&&NHX:TOL=30555],perientomum ceylonicum[&&NHX:TOL=30556],perientomum chrysargyrium[&&NHX:TOL=30557],perientomum greeni[&&NHX:TOL=30560],perientomum gregarium[&&NHX:TOL=30561],perientomum corticola[&&NHX:TOL=30558],perientomum fucatum[&&NHX:TOL=30559],perientomum griseifrons[&&NHX:TOL=30562],perientomum morosum[&&NHX:TOL=30563],perientomum notatum[&&NHX:TOL=30564],perientomum trichopteryx[&&NHX:TOL=30565],perientomum triste[&&NHX:TOL=30566])perientomum[&&NHX:TOL=30495],proentomum personatum[&&NHX:TOL=30496],(soa angolana[&&NHX:TOL=30568],soa dahliana[&&NHX:TOL=30569],soa enderleini[&&NHX:TOL=30570],soa flaviterminata[&&NHX:TOL=30571],soa reticulata[&&NHX:TOL=30572],soa violacea[&&NHX:TOL=30573])soa[&&NHX:TOL=30497])perientominae[&&NHX:TOL=30794],((echmepteryx acuminata[&&NHX:TOL=30578],echmepteryx acutipennis[&&NHX:TOL=30579],echmepteryx aesculana[&&NHX:TOL=30580],echmepteryx albigena[&&NHX:TOL=30581],echmepteryx alpha[&&NHX:TOL=30582],echmepteryx angusta[&&NHX:TOL=30583],echmepteryx annulitibia[&&NHX:TOL=30584],echmepteryx anomala[&&NHX:TOL=30585],echmepteryx aperta[&&NHX:TOL=30586],echmepteryx argenta[&&NHX:TOL=30587],echmepteryx argentofasciata[&&NHX:TOL=30588],echmepteryx armillata[&&NHX:TOL=30589],echmepteryx atlantica[&&NHX:TOL=30590],echmepteryx barba[&&NHX:TOL=30591],echmepteryx bicolor[&&NHX:TOL=30592],echmepteryx bishopi[&&NHX:TOL=30593],echmepteryx brunnea[&&NHX:TOL=30594],echmepteryx carolinensis[&&NHX:TOL=30595],echmepteryx chagosensis[&&NHX:TOL=30596],echmepteryx chekei[&&NHX:TOL=30597],echmepteryx desquamata[&&NHX:TOL=30598],echmepteryx diexquadra[&&NHX:TOL=30599],echmepteryx dryas[&&NHX:TOL=30600],echmepteryx dybasi[&&NHX:TOL=30601],echmepteryx falco[&&NHX:TOL=30602],echmepteryx fastigata[&&NHX:TOL=30603],echmepteryx frontalis[&&NHX:TOL=30604],echmepteryx fuscata[&&NHX:TOL=30605],echmepteryx gumpi[&&NHX:TOL=30606],echmepteryx hageni[&&NHX:TOL=30607],echmepteryx hamiltoni[&&NHX:TOL=30608],echmepteryx hartmeyeri[&&NHX:TOL=30609],echmepteryx hebes[&&NHX:TOL=30610],echmepteryx hieroglyphica[&&NHX:TOL=30611],echmepteryx howensis[&&NHX:TOL=30612],echmepteryx humphreysi[&&NHX:TOL=30613],echmepteryx intermedia[&&NHX:TOL=30614],echmepteryx lacinipennis[&&NHX:TOL=30615],echmepteryx lawrencei[&&NHX:TOL=30616],echmepteryx lealae[&&NHX:TOL=30617],echmepteryx lineata[&&NHX:TOL=30618],echmepteryx lunulata[&&NHX:TOL=30619],echmepteryx lurida[&&NHX:TOL=30620],echmepteryx lutosa[&&NHX:TOL=30621],echmepteryx macgregori[&&NHX:TOL=30622],echmepteryx maculimargo[&&NHX:TOL=30623],echmepteryx madagascariensis[&&NHX:TOL=30624],echmepteryx mahensis[&&NHX:TOL=30625],echmepteryx malayensis[&&NHX:TOL=30626],echmepteryx mihira[&&NHX:TOL=30627],echmepteryx montana[&&NHX:TOL=30628],echmepteryx monticola[&&NHX:TOL=30629],echmepteryx muscicolis[&&NHX:TOL=30630],echmepteryx nigra[&&NHX:TOL=30631],echmepteryx nigrapalpa[&&NHX:TOL=30632],echmepteryx pacifica[&&NHX:TOL=30633],echmepteryx pallida[&&NHX:TOL=30634],echmepteryx pauliani[&&NHX:TOL=30635],echmepteryx picta[&&NHX:TOL=30636],echmepteryx picticeps[&&NHX:TOL=30637],echmepteryx pinnula[&&NHX:TOL=30638],echmepteryx pletschi[&&NHX:TOL=30639],echmepteryx psyche[&&NHX:TOL=30640],echmepteryx punctulata[&&NHX:TOL=30641],echmepteryx quadrilineata[&&NHX:TOL=30642],echmepteryx rara[&&NHX:TOL=30643],echmepteryx renoides[&&NHX:TOL=30644],echmepteryx schrankeli[&&NHX:TOL=30645],echmepteryx scotti[&&NHX:TOL=30646],echmepteryx sericea[&&NHX:TOL=30647],echmepteryx similis[&&NHX:TOL=30648],echmepteryx stylesi[&&NHX:TOL=30649],echmepteryx submontana[&&NHX:TOL=30650],echmepteryx symmetrolepis[&&NHX:TOL=30651],echmepteryx terricolis[&&NHX:TOL=30652],echmepteryx unicolor[&&NHX:TOL=30653],echmepteryx uniformis[&&NHX:TOL=30654],echmepteryx vitiensis[&&NHX:TOL=30655],echmepteryx yanezi[&&NHX:TOL=30656],echmepteryx youngi[&&NHX:TOL=30657])echmepteryx[&&NHX:TOL=30499],(cyptophania alutacea[&&NHX:TOL=30574],cyptophania bifurcata[&&NHX:TOL=30575],cyptophania hirsuta[&&NHX:TOL=30576],cyptophania marginata[&&NHX:TOL=30577])cyptophania[&&NHX:TOL=30498],(lepidopsocus aureus[&&NHX:TOL=30658],lepidopsocus cinctus[&&NHX:TOL=30659],lepidopsocus cuneatus[&&NHX:TOL=30660],lepidopsocus curtoisi[&&NHX:TOL=30661],lepidopsocus delius[&&NHX:TOL=30662],lepidopsocus dindus[&&NHX:TOL=30663],lepidopsocus euaensis[&&NHX:TOL=30664],lepidopsocus fasciatus[&&NHX:TOL=30665],lepidopsocus fuscus[&&NHX:TOL=30666],lepidopsocus hopkinsi[&&NHX:TOL=30667],lepidopsocus immaculatus[&&NHX:TOL=30668],lepidopsocus maculatus[&&NHX:TOL=30669],lepidopsocus magnus[&&NHX:TOL=30670],lepidopsocus major[&&NHX:TOL=30671],lepidopsocus marmoratus[&&NHX:TOL=30672],lepidopsocus nausoriensis[&&NHX:TOL=30673],lepidopsocus nepticulides[&&NHX:TOL=30674],lepidopsocus ochreus[&&NHX:TOL=30675],lepidopsocus oweni[&&NHX:TOL=30676],lepidopsocus pallidus[&&NHX:TOL=30677],lepidopsocus pelmus[&&NHX:TOL=30678],lepidopsocus pictus[&&NHX:TOL=30679],lepidopsocus pretiosus[&&NHX:TOL=30680],lepidopsocus pseudomaculatus[&&NHX:TOL=30681],lepidopsocus ruptus[&&NHX:TOL=30682],lepidopsocus samus[&&NHX:TOL=30683],lepidopsocus savuensis[&&NHX:TOL=30684],lepidopsocus similis[&&NHX:TOL=30685],lepidopsocus stradus[&&NHX:TOL=30686],lepidopsocus sudarmani[&&NHX:TOL=30687],lepidopsocus tibialis[&&NHX:TOL=30688],lepidopsocus tongensis[&&NHX:TOL=30689],lepidopsocus torus[&&NHX:TOL=30690],lepidopsocus vittatus[&&NHX:TOL=30691])lepidopsocus[&&NHX:TOL=30500])lepidopsocinae[&&NHX:TOL=30795],((neolepolepis caribensis[&&NHX:TOL=30694],neolepolepis leticiae[&&NHX:TOL=30695],neolepolepis occidentalis[&&NHX:TOL=30696],neolepolepis xerica[&&NHX:TOL=30697])neolepolepis[&&NHX:TOL=30502],(echinopsocus erinaceus[&&NHX:TOL=30692],echinopsocus grayi[&&NHX:TOL=30693])echinopsocus[&&NHX:TOL=30501],(pteroxanium evansi[&&NHX:TOL=30698],pteroxanium forcepetum[&&NHX:TOL=30699],pteroxanium funebre[&&NHX:TOL=30700],pteroxanium insularum[&&NHX:TOL=30701],pteroxanium kelloggi[&&NHX:TOL=30702],pteroxanium marrisi[&&NHX:TOL=30703],pteroxanium oaxacanum[&&NHX:TOL=30704],pteroxanium ralstonae[&&NHX:TOL=30705])pteroxanium[&&NHX:TOL=30503],scolopama halterata[&&NHX:TOL=30504])echinopsocinae[&&NHX:TOL=30796],(lepolepis bicolor[&&NHX:TOL=30802],lepolepis ceylonica[&&NHX:TOL=30803],lepolepis columbiensis[&&NHX:TOL=30804],lepolepis graemei[&&NHX:TOL=30805],lepolepis pateriformis[&&NHX:TOL=30806],lepolepis picta[&&NHX:TOL=30807])lepolepis[&&NHX:TOL=30801])lepidopsocidae[&&NHX:TOL=30215])atropetae[&&NHX:TOL=30214],((dorypteryx domestica[&&NHX:TOL=30718],dorypteryx longipennis[&&NHX:TOL=30719],dorypteryx pallida[&&NHX:TOL=30720])dorypteryx[&&NHX:TOL=30713],pseudopsyllipsocus gangliigerus[&&NHX:TOL=30714],pseudorypteryx mexicana[&&NHX:TOL=30715],(psocathropos astizi[&&NHX:TOL=30723],psocathropos cameriferus[&&NHX:TOL=30724],psocathropos cuttackae[&&NHX:TOL=30725],psocathropos domesticus[&&NHX:TOL=30726],psocathropos dyadoclemus[&&NHX:TOL=30727],psocathropos lachlani[&&NHX:TOL=30728],psocathropos pilipennis[&&NHX:TOL=30729],psocathropos pleurotaenus[&&NHX:TOL=30730],psocathropos purpuripsarous[&&NHX:TOL=30731],psocathropos sinensis[&&NHX:TOL=30732],psocathropos termitorum[&&NHX:TOL=30733],psocathropos tridymus[&&NHX:TOL=30734])psocathropos[&&NHX:TOL=30716],(psyllipsocus batuensis[&&NHX:TOL=30735],psyllipsocus bombayensis[&&NHX:TOL=30736],psyllipsocus chamela[&&NHX:TOL=30737],psyllipsocus chiquibulensis[&&NHX:TOL=30738],psyllipsocus collarti[&&NHX:TOL=30739],psyllipsocus decui[&&NHX:TOL=30740],psyllipsocus delamarei[&&NHX:TOL=30741],psyllipsocus dorae[&&NHX:TOL=30742],psyllipsocus dubius[&&NHX:TOL=30743],psyllipsocus edentulus[&&NHX:TOL=30744],psyllipsocus garciamolinai[&&NHX:TOL=30745],psyllipsocus hirsutus[&&NHX:TOL=30746],psyllipsocus hyalinus[&&NHX:TOL=30747],psyllipsocus maculatus[&&NHX:TOL=30748],psyllipsocus metamicropterus[&&NHX:TOL=30749],psyllipsocus minutissimus[&&NHX:TOL=30750],psyllipsocus monticolus[&&NHX:TOL=30751],psyllipsocus neoleonensis[&&NHX:TOL=30752],psyllipsocus oculatus[&&NHX:TOL=30753],psyllipsocus orghidani[&&NHX:TOL=30754],psyllipsocus ornatus[&&NHX:TOL=30755],psyllipsocus ramburii[&&NHX:TOL=30756],psyllipsocus sanxiaensis[&&NHX:TOL=30757],psyllipsocus sauteri[&&NHX:TOL=30758],psyllipsocus sinicus[&&NHX:TOL=30759],psyllipsocus spinosus[&&NHX:TOL=30760],psyllipsocus variabilis[&&NHX:TOL=30761],psyllipsocus youngi[&&NHX:TOL=30762],psyllipsocus yucatan[&&NHX:TOL=30763])psyllipsocus[&&NHX:TOL=30717])psyllipsocetae[&&NHX:TOL=14453])[&&NHX:TOL=30388],(((prionoglaris dactyloides[&&NHX:TOL=30765],prionoglaris lindbergi[&&NHX:TOL=30767],prionoglaris stygia[&&NHX:TOL=30766])prionoglaris[&&NHX:TOL=30764],(speleketor flocki[&&NHX:TOL=30771],speleketor irwini[&&NHX:TOL=30772],speleketor pictus[&&NHX:TOL=30773])speleketor[&&NHX:TOL=30770])[&&NHX:TOL=30797],siamoglaris zebrina[&&NHX:TOL=30768],sensitibilla strinatii[&&NHX:TOL=30769])prionoglarididae[&&NHX:TOL=14454])trogiomorpha[&&NHX:TOL=14450])psocodea[&&NHX:TOL=8235],((merothripidae[&&NHX:TOL=14522],uzelothripidae[&&NHX:TOL=14523],aeolothripidae[&&NHX:TOL=14524],adeheterothripidae[&&NHX:TOL=14525],heterothripidae[&&NHX:TOL=14526],thripidae[&&NHX:TOL=14527],fauriellidae[&&NHX:TOL=14528])terebrantia[&&NHX:TOL=14521],phlaeothripidae[&&NHX:TOL=14529])thysanoptera[&&NHX:TOL=8238],(((psyllidae[&&NHX:TOL=10978],calophyidae[&&NHX:TOL=10979],phacopteronidae[&&NHX:TOL=10980],homotomidae[&&NHX:TOL=10981],carsidaridae[&&NHX:TOL=10982],triozidae[&&NHX:TOL=10983])psylloidea[&&NHX:TOL=10977],(aleurodicinae[&&NHX:TOL=65522],aleyrodinae[&&NHX:TOL=65523])aleyrodidae[&&NHX:TOL=10984],((((adelgidae[&&NHX:TOL=11123],mesozoicaphididae[&&NHX:EXT=Y:TOL=11124],elektraphididae[&&NHX:EXT=Y:TOL=11125])[&&NHX:TOL=11122],phylloxeridae[&&NHX:TOL=11126])phylloxeroidea[&&NHX:TOL=11008],(oviparosiphidae[&&NHX:EXT=Y:TOL=11012],(((((aphidounguis[&&NHX:TOL=11083],byrsocryptoides[&&NHX:TOL=11084],colopha[&&NHX:TOL=11085],colophina[&&NHX:TOL=11086],eriosoma[&&NHX:TOL=11087],gharesia[&&NHX:TOL=11088],grylloprociphilus[&&NHX:TOL=133565],hemipodaphis[&&NHX:TOL=11089],paracolopha[&&NHX:TOL=11090],shizoneura[&&NHX:TOL=11091],schizoneurata[&&NHX:TOL=11092],shizoneurella[&&NHX:TOL=11093])eriosomatini[&&NHX:TOL=11074],(kaltenbachiella[&&NHX:TOL=11114],tetraneura[&&NHX:TOL=11115])tetraneurini[&&NHX:TOL=11075])eriosomatinae[&&NHX:TOL=11073],((aploneura[&&NHX:TOL=11095],forda[&&NHX:TOL=11096],geoica[&&NHX:TOL=11097],smynthurodes[&&NHX:TOL=11098])fordini[&&NHX:TOL=11077],(melaphis[&&NHX:TOL=11100],nurudea[&&NHX:TOL=11101],schlechtendalia[&&NHX:TOL=11102])melaphidini[&&NHX:TOL=11078])fordinae[&&NHX:TOL=11076],((epipemphigus[&&NHX:TOL=11104],mordvilkoja[&&NHX:TOL=11105],pemphigus[&&NHX:TOL=11106],thecabius[&&NHX:TOL=11107])pemphigini[&&NHX:TOL=11080],(gootiella[&&NHX:TOL=11109],pachypappa[&&NHX:TOL=11110],pachypapella[&&NHX:TOL=11111],prociphilus[&&NHX:TOL=11112])prociphilini[&&NHX:TOL=11081])pemphiginae[&&NHX:TOL=11079])pemphigidae[&&NHX:TOL=11015],anoeciidae[&&NHX:TOL=11016],(aleurodaphis[&&NHX:TOL=11046],((nipponaphidini[&&NHX:TOL=11049],hormaphidini[&&NHX:TOL=11050])[&&NHX:TOL=11048],(((((astegopterx[&&NHX:TOL=11057],(pseudoregma[&&NHX:TOL=11059],ceratovacuna[&&NHX:TOL=11060])[&&NHX:TOL=11058])[&&NHX:TOL=11056],chaitoregma[&&NHX:TOL=11061])[&&NHX:TOL=11055],(ceratoglyphina bambusae[&&NHX:TOL=11068],ceratoglyphina bengalensis[&&NHX:TOL=11069],ceratoglyphina styracicola[&&NHX:TOL=11070])ceratoglyphina[&&NHX:TOL=11062])[&&NHX:TOL=11054],glyphinaphis[&&NHX:TOL=11063])[&&NHX:TOL=11053],(cerataphis[&&NHX:TOL=11065],tuberaphis[&&NHX:TOL=11066])[&&NHX:TOL=11064])cerataphidini[&&NHX:TOL=11051])[&&NHX:TOL=11047])hormaphididae[&&NHX:TOL=11017])[&&NHX:TOL=11014],(tajmyraphididae[&&NHX:EXT=Y:TOL=11019],((mindaridae[&&NHX:TOL=11022],((drepanosiphinae[&&NHX:TOL=11042],phyllaphidinae[&&NHX:TOL=11043],chaitophorinae[&&NHX:TOL=11044])drepanosiphidae[&&NHX:TOL=11024],thelaxidae[&&NHX:TOL=11025])[&&NHX:TOL=11023])[&&NHX:TOL=11021],phloeomyzidae[&&NHX:TOL=11026],(greenideidae[&&NHX:TOL=11028],((baltichaitophorinae[&&NHX:TOL=11034],pterocommatinae[&&NHX:TOL=11035],(aphidini[&&NHX:TOL=11037],(rhopalosiphina[&&NHX:TOL=11039],macrosiphina[&&NHX:TOL=11040])macrosiphini[&&NHX:TOL=11038])aphidinae[&&NHX:TOL=11036])aphididae[&&NHX:TOL=11030],lachnidae[&&NHX:TOL=11031])[&&NHX:TOL=11029])[&&NHX:TOL=11027])[&&NHX:TOL=11020])[&&NHX:TOL=11018])[&&NHX:TOL=11013])aphidoidea[&&NHX:TOL=11009])[&&NHX:TOL=11007],(shaposhnikoviidae[&&NHX:EXT=Y:TOL=11117],(palaeoaphididae[&&NHX:EXT=Y:TOL=11119],canadaphididae[&&NHX:EXT=Y:TOL=11120])[&&NHX:TOL=11118])canadaphidoidea[&&NHX:EXT=Y:TOL=11010])aphidomorpha[&&NHX:TOL=10985],(margarodidae[&&NHX:TOL=10987],ortheziidae[&&NHX:TOL=10988],phenacoleachiidae[&&NHX:TOL=10989],pseudococcidae[&&NHX:TOL=10990],eriococcidae[&&NHX:TOL=10991],dactylopiidae[&&NHX:TOL=10992],kermesidae[&&NHX:TOL=10993],aclerdidae[&&NHX:TOL=10994],stictococcidae[&&NHX:TOL=10995],asterolecaniidae[&&NHX:TOL=10996],cerococcidae[&&NHX:TOL=10997],lecanodiaspididae[&&NHX:TOL=10998],coccidae[&&NHX:TOL=10999],kerriidae[&&NHX:TOL=11000],phoenicococcidae[&&NHX:TOL=11001],conchaspididae[&&NHX:TOL=11002],beesoniidae[&&NHX:TOL=11003],halimococcidae[&&NHX:TOL=11004],diaspididae[&&NHX:TOL=11005])coccoidea[&&NHX:TOL=10986])sternorrhyncha[&&NHX:TOL=10800],((((tettigarctidae[&&NHX:TOL=10822],cicadidae[&&NHX:TOL=10823])cicadoidea[&&NHX:TOL=10821],((cercopidae[&&NHX:TOL=10826],aphrophoridae[&&NHX:TOL=10827],machaerotidae[&&NHX:TOL=10828],clastopteridae[&&NHX:TOL=10829])cercopoidea[&&NHX:TOL=10825],(cicadellidae[&&NHX:TOL=10853],(melizoderidae[&&NHX:TOL=10855],(aetalionidae[&&NHX:TOL=10857],membracidae[&&NHX:TOL=10858])[&&NHX:TOL=10856])[&&NHX:TOL=10854])membracoidea[&&NHX:TOL=10830])[&&NHX:TOL=10824])cicadomorpha[&&NHX:TOL=10820],(achilidae[&&NHX:TOL=10836],achilixiidae[&&NHX:TOL=10839],acanaloniidae[&&NHX:TOL=10843],cixiidae[&&NHX:TOL=10833],delphacidae[&&NHX:TOL=10832],derbidae[&&NHX:TOL=10837],dictyopharidae[&&NHX:TOL=10838],eurybrachidae[&&NHX:TOL=10847],flatidae[&&NHX:TOL=10845],fulgoridae[&&NHX:TOL=10835],gengidae[&&NHX:TOL=10850],hypochthonellidae[&&NHX:TOL=10851],issidae[&&NHX:TOL=10844],kinnaridae[&&NHX:TOL=10840],lophopidae[&&NHX:TOL=10848],meenoplidae[&&NHX:TOL=10834],nogodinidae[&&NHX:TOL=10846],ricaniidae[&&NHX:TOL=10849],tettigometridae[&&NHX:TOL=10841],tropiduchidae[&&NHX:TOL=10842])fulgoromorpha[&&NHX:TOL=10831])auchenorrhyncha[&&NHX:TOL=10802],((((oiophysella[&&NHX:TOL=23621],oiophysa[&&NHX:TOL=23623])[&&NHX:TOL=23633],(xenophysella[&&NHX:TOL=23625],xenophyes[&&NHX:TOL=23626])[&&NHX:TOL=23635])[&&NHX:TOL=23634],((peloridium[&&NHX:TOL=23622],(kuscheloides[&&NHX:TOL=23632],(peloridora[&&NHX:TOL=23630],pantinia[&&NHX:TOL=23631])[&&NHX:TOL=23636])[&&NHX:TOL=23641])[&&NHX:TOL=23640],(hemiodoecellus[&&NHX:TOL=23629],(howeria[&&NHX:TOL=23624],((hemiowoodwardia[&&NHX:TOL=23627],hemiodoecus[&&NHX:TOL=23628])[&&NHX:TOL=23638],hackeriella[&&NHX:TOL=10891])[&&NHX:TOL=23639])[&&NHX:TOL=23643])[&&NHX:TOL=23642])[&&NHX:TOL=23637])peloridiidae[&&NHX:TOL=10804],(((alienates[&&NHX:TOL=30174],boreostolus[&&NHX:TOL=30176],brevidorsus[&&NHX:TOL=30177],ciucephalus[&&NHX:TOL=30191],didymocephalus[&&NHX:TOL=30192],embolorrhinus[&&NHX:TOL=30179],enicocephalus[&&NHX:TOL=30180],euchelichir[&&NHX:TOL=30193],henicocorinus[&&NHX:TOL=30194],henschiella[&&NHX:TOL=30181],hoplitocoris[&&NHX:TOL=30175],hymenocoris[&&NHX:TOL=30166],lysenicocephalus[&&NHX:TOL=30195],monteithostolus[&&NHX:TOL=30196],murphyanella[&&NHX:TOL=30197],neoncylocotis[&&NHX:TOL=30198],oncylocotis[&&NHX:TOL=30182],phallopirates[&&NHX:TOL=30199],phthirocoris[&&NHX:TOL=30183],phthirocorisella[&&NHX:TOL=30200],pseudenicocephalus[&&NHX:TOL=30184],systelloderes[&&NHX:TOL=30167],timahocoris[&&NHX:TOL=30201],tornocrusus[&&NHX:TOL=30202],vuorilinna[&&NHX:TOL=30203])enicocephalidae[&&NHX:TOL=10899],(aenictocoris[&&NHX:TOL=30185],aenictopechys[&&NHX:TOL=30187],australostolus[&&NHX:TOL=30204],lomagostus[&&NHX:TOL=30189],maoristolus[&&NHX:TOL=30186],megenicocephalus[&&NHX:TOL=30190],nymphocoris[&&NHX:TOL=30188])aenictopecheidae[&&NHX:TOL=10900])enicocephalomorpha[&&NHX:TOL=10807],((ceratocombidae[&&NHX:TOL=10893],dipsocoridae[&&NHX:TOL=10894],hypsipterygidae[&&NHX:TOL=10895],schizopteridae[&&NHX:TOL=10896],stemmocryptidae[&&NHX:TOL=10897])dipsocoromorpha[&&NHX:TOL=10809],((mesoveliidae[&&NHX:TOL=10902],(hebridae[&&NHX:TOL=10904],((paraphrynoveliidae[&&NHX:TOL=10907],(macroveliidae[&&NHX:TOL=10909],hydrometridae[&&NHX:TOL=10910])[&&NHX:TOL=10908])[&&NHX:TOL=10906],(hermatobatidae[&&NHX:TOL=10912],(veliidae[&&NHX:TOL=10914],gerridae[&&NHX:TOL=10915])[&&NHX:TOL=10913])[&&NHX:TOL=10911])[&&NHX:TOL=10905])[&&NHX:TOL=10903])gerromorpha[&&NHX:TOL=10811],(((nepidae[&&NHX:TOL=10925],belostomatidae[&&NHX:TOL=10926])[&&NHX:TOL=10924],((ochteridae[&&NHX:TOL=10929],gelastocoridae[&&NHX:TOL=10930])[&&NHX:TOL=10928],corixidae[&&NHX:TOL=10931],aphelocheiridae[&&NHX:TOL=10935],potamocoridae[&&NHX:TOL=10934],naucoridae[&&NHX:TOL=10933],(notonectidae[&&NHX:TOL=10937],(pleidae[&&NHX:TOL=10939],helotrephidae[&&NHX:TOL=10940])[&&NHX:TOL=10938])[&&NHX:TOL=10936])[&&NHX:TOL=27098])nepomorpha[&&NHX:TOL=10814],((((leptosaldinae[&&NHX:TOL=136080],(leotichiini[&&NHX:TOL=136082],leptopodini[&&NHX:TOL=136083])leptopodinae[&&NHX:TOL=136081])leptopodidae[&&NHX:TOL=10918],omaniidae[&&NHX:TOL=10919])[&&NHX:TOL=10917],(aepophilidae[&&NHX:TOL=10921],(((saldini[&&NHX:TOL=136075],saldoidini[&&NHX:TOL=136076])[&&NHX:TOL=136074],saldunculini[&&NHX:TOL=136077])saldinae[&&NHX:TOL=136073],chiloxantinae[&&NHX:TOL=136078],saldoniinae[&&NHX:EXT=Y:TOL=136079])saldidae[&&NHX:TOL=10922])[&&NHX:TOL=10920])leptopodomorpha[&&NHX:TOL=10815],(((aradidae[&&NHX:TOL=10943],termitaphididae[&&NHX:TOL=10944])aradoidea[&&NHX:TOL=10942],(((alydidae[&&NHX:TOL=10971],coreidae[&&NHX:TOL=10972],hyocephalidae[&&NHX:TOL=10973],rhopalidae[&&NHX:TOL=10974],stenocephalidae[&&NHX:TOL=10975])coreoidea[&&NHX:TOL=10970],(berytidae[&&NHX:TOL=10961],colobathristidae[&&NHX:TOL=10962],idiostolidae[&&NHX:TOL=10963],lygaeidae[&&NHX:TOL=10964],malcidae[&&NHX:TOL=10965],piesmatidae[&&NHX:TOL=10966])lygaeoidea[&&NHX:TOL=10960],(largidae[&&NHX:TOL=10968],pyrrhocoridae[&&NHX:TOL=10969])pyrrhocoroidea[&&NHX:TOL=10967])[&&NHX:TOL=57778],(urostylididae[&&NHX:TOL=10959],(saileriolidae[&&NHX:TOL=136066],(acanthosomatidae[&&NHX:TOL=10946],(tessaratomidae[&&NHX:TOL=10957],dinidoridae[&&NHX:TOL=10950],(cydnidae[&&NHX:TOL=136069],thaumastellidae[&&NHX:TOL=136071],parastrachiinae[&&NHX:TOL=137372])cydnidae s. lat.[&&NHX:TOL=10949],(corimelaenidae[&&NHX:TOL=136070],lestoniidae[&&NHX:TOL=10951],phloeidae[&&NHX:TOL=10954],(scutelleridae[&&NHX:TOL=10956],plataspididae[&&NHX:TOL=10955])[&&NHX:TOL=136072],pentatomidae[&&NHX:TOL=10953],canopidae[&&NHX:TOL=10948],megarididae[&&NHX:TOL=137373])[&&NHX:TOL=137371])[&&NHX:TOL=136068])[&&NHX:TOL=136067])[&&NHX:TOL=136065])pentatomoidea[&&NHX:TOL=10945])trichophora[&&NHX:TOL=57777])pentatomomorpha[&&NHX:TOL=10818],((pachynomidae[&&NHX:TOL=10861],(hammacerinae[&&NHX:TOL=118717],(((holoptilinae[&&NHX:TOL=118721],phymatinae[&&NHX:TOL=118722],phimophorinae[&&NHX:TOL=118723],elasmodeminae[&&NHX:TOL=118724])[&&NHX:TOL=118720],centrocneminae[&&NHX:TOL=118725])phymatine complex[&&NHX:TOL=118719],(harpactorinae[&&NHX:TOL=118727],physoderinae[&&NHX:TOL=118728],((saicinae[&&NHX:TOL=118731],visayanocorinae[&&NHX:TOL=118732],emesinae[&&NHX:TOL=118733])[&&NHX:TOL=118730],(tribelocephalinae[&&NHX:TOL=118735],ectrichodiinae[&&NHX:TOL=118736])[&&NHX:TOL=118734])[&&NHX:TOL=118729],reduviinae[&&NHX:TOL=118737],vesciinae[&&NHX:TOL=118738],stenopodainae[&&NHX:TOL=118739],triatominae[&&NHX:TOL=118740],peiratinae[&&NHX:TOL=118741],pseudocetherinae[&&NHX:TOL=118742],(salyavatinae[&&NHX:TOL=118744],sphaeridopinae[&&NHX:TOL=118745])[&&NHX:TOL=118743],cetherinae[&&NHX:TOL=118746])[&&NHX:TOL=118726])[&&NHX:TOL=118718],chryxinae[&&NHX:TOL=118747],bactrodinae[&&NHX:TOL=118748],manangocorinae[&&NHX:TOL=118749])reduviidae[&&NHX:TOL=10862])[&&NHX:TOL=10860],(velocipedidae[&&NHX:TOL=10864],((microphysidae[&&NHX:TOL=10867],(joppeicidae[&&NHX:TOL=10869],(thaumastocoridae[&&NHX:TOL=10871],(miridae[&&NHX:TOL=10873],tingidae[&&NHX:TOL=10874])[&&NHX:TOL=10872])[&&NHX:TOL=10870])[&&NHX:TOL=10868])[&&NHX:TOL=10866],((medocostidae[&&NHX:TOL=10877],nabidae[&&NHX:TOL=10878])[&&NHX:TOL=10876],(lasiochilidae[&&NHX:TOL=10880],(plokiophilidae[&&NHX:TOL=10882],(lyctocoridae[&&NHX:TOL=10884],(anthocoridae[&&NHX:TOL=10886],(cimicidae[&&NHX:TOL=10888],polyctenidae[&&NHX:TOL=10889])[&&NHX:TOL=10887])[&&NHX:TOL=10885])[&&NHX:TOL=10883])[&&NHX:TOL=10881])[&&NHX:TOL=10879])[&&NHX:TOL=10875])[&&NHX:TOL=10865])[&&NHX:TOL=10863])cimicomorpha[&&NHX:TOL=10817])[&&NHX:TOL=10816])[&&NHX:TOL=136063])[&&NHX:TOL=136062])[&&NHX:TOL=10810])[&&NHX:TOL=10808])heteroptera[&&NHX:TOL=10805])[&&NHX:TOL=10803])[&&NHX:TOL=10801])hemiptera[&&NHX:TOL=8239])hemipteroid assemblage[&&NHX:TOL=8242],(((((sialidae[&&NHX:TOL=12997],((chloroniella[&&NHX:TOL=12980],((neurhermes[&&NHX:TOL=12983],protohermes[&&NHX:TOL=12984])protohermes lineage[&&NHX:TOL=12982],((acanthacorydalis[&&NHX:TOL=12987],(neoneuromus[&&NHX:TOL=12989],neuromus[&&NHX:TOL=12990])[&&NHX:TOL=12988])neuromus lineage[&&NHX:TOL=12986],((platyneuromus honduranus[&&NHX:TOL=13071],platyneuromus reflexus[&&NHX:TOL=13072],platyneuromus soror[&&NHX:TOL=13073],platyneuromus species a[&&NHX:TOL=13074])platyneuromus[&&NHX:TOL=12992],((chloronia absona[&&NHX:TOL=13002],chloronia antilliensis[&&NHX:TOL=13003],chloronia banksiana[&&NHX:TOL=13004],chloronia bogotana[&&NHX:TOL=13005],chloronia convergens[&&NHX:TOL=13006],chloronia corripiens[&&NHX:TOL=13007],chloronia gaianii[&&NHX:TOL=13008],chloronia gloriosoi[&&NHX:TOL=13009],chloronia hieroglyphica[&&NHX:TOL=13010],chloronia marthae[&&NHX:TOL=13011],chloronia mexicana[&&NHX:TOL=13012],chloronia mirifica[&&NHX:TOL=13013],chloronia osae[&&NHX:TOL=13014],chloronia pallida[&&NHX:TOL=13015],chloronia pennyi[&&NHX:TOL=13016],chloronia plaumanni[&&NHX:TOL=13017],chloronia zacapa[&&NHX:TOL=13018])chloronia[&&NHX:TOL=12994],((corydalus cephalotes[&&NHX:TOL=13021],corydalus hecate[&&NHX:TOL=13022])[&&NHX:TOL=13020],(corydalus ecuadorianus[&&NHX:TOL=13024],((corydalus colombianus[&&NHX:TOL=13027],corydalus amazonas[&&NHX:TOL=13028])[&&NHX:TOL=13026],((corydalus flinti[&&NHX:TOL=13031],(corydalus arpi[&&NHX:TOL=13033],corydalus ignotus[&&NHX:TOL=13034])[&&NHX:TOL=13032])[&&NHX:TOL=13030],(corydalus affinis[&&NHX:TOL=13036],((corydalus nubilus[&&NHX:TOL=13039],corydalus tesselatus[&&NHX:TOL=13040])[&&NHX:TOL=13038],(corydalus australis[&&NHX:TOL=13042],corydalus diasi[&&NHX:TOL=13043],(corydalus imperiosus[&&NHX:TOL=13045],corydalus tridentatus[&&NHX:TOL=13046])[&&NHX:TOL=13044],(corydalus batesii[&&NHX:TOL=13048],corydalus holzenthali[&&NHX:TOL=13049],corydalus longicornis[&&NHX:TOL=13050],corydalus neblinensis[&&NHX:TOL=13051],corydalus parvus[&&NHX:TOL=13052],corydalus primitivus[&&NHX:TOL=13053],(corydalus clauseni[&&NHX:TOL=13055],(corydalus armatus[&&NHX:TOL=13057],corydalus peruvianus[&&NHX:TOL=13058])[&&NHX:TOL=13056])[&&NHX:TOL=13054],(corydalus flavicornis[&&NHX:TOL=13060],((corydalus cornutus[&&NHX:TOL=13063],corydalus texanus[&&NHX:TOL=13064])[&&NHX:TOL=13062],(corydalus luteus[&&NHX:TOL=13066],(corydalus bidenticulatus[&&NHX:TOL=13068],corydalus magnus[&&NHX:TOL=13069])[&&NHX:TOL=13067])[&&NHX:TOL=13065])[&&NHX:TOL=13061])[&&NHX:TOL=13059])[&&NHX:TOL=13047])[&&NHX:TOL=13041])[&&NHX:TOL=13037])[&&NHX:TOL=13035])[&&NHX:TOL=13029])[&&NHX:TOL=13025])[&&NHX:TOL=13023])corydalus[&&NHX:TOL=12995])[&&NHX:TOL=12993])corydalus lineage[&&NHX:TOL=12991])[&&NHX:TOL=12985])[&&NHX:TOL=12981])corydalinae[&&NHX:TOL=12999],chauliodinae[&&NHX:TOL=13000])corydalidae[&&NHX:TOL=12998])megaloptera[&&NHX:TOL=8218],(raphidiidae[&&NHX:TOL=14486],inocelliidae[&&NHX:TOL=14487])raphidioptera[&&NHX:TOL=8219],(((dilaridae[&&NHX:TOL=13135],(berothidae[&&NHX:TOL=13137],mantispidae[&&NHX:TOL=13138])[&&NHX:TOL=13136])[&&NHX:TOL=13134],((((((silveira marshalli[&&NHX:TOL=13255],silveira occultus[&&NHX:TOL=13256])[&&NHX:TOL=13254],silveira rufus[&&NHX:TOL=13257])[&&NHX:TOL=13253],silveira jordani[&&NHX:TOL=13258])silveira[&&NHX:TOL=13212],((cabralis n.sp.[&&NHX:TOL=26897],cabralis gloriosus[&&NHX:TOL=26898])cabralis[&&NHX:TOL=13214],(zygophlebius pseudosilveira[&&NHX:TOL=13260],(zygophlebius zebra[&&NHX:TOL=13262],zygophlebius leoninus[&&NHX:TOL=13263])[&&NHX:TOL=13261])zygophlebius[&&NHX:TOL=13215])[&&NHX:TOL=13213])zygophlebiinae[&&NHX:TOL=13211],((((balmes notabilis[&&NHX:TOL=13222],balmes birmanus[&&NHX:TOL=13223])[&&NHX:TOL=13221],balmes terissinus[&&NHX:TOL=13224])[&&NHX:TOL=13220],balmes formosus[&&NHX:TOL=13225])balmes[&&NHX:TOL=13217],(psychopsis gallardi[&&NHX:TOL=13228],(psychopsis coelivaga[&&NHX:TOL=13230],((psychopsis meyricki[&&NHX:TOL=13233],psychopsis insolens[&&NHX:TOL=13234])[&&NHX:TOL=13232],(psychopsis illidgei[&&NHX:TOL=13236],(psychopsis gracilis[&&NHX:TOL=13238],(psychopsis dumigani[&&NHX:TOL=13240],(psychopsis maculipennis[&&NHX:TOL=13242],(psychopsis margarita[&&NHX:TOL=13244],(psychopsis elegans[&&NHX:TOL=13246],(psychopsis mimica[&&NHX:TOL=13248],(psychopsis barnardi[&&NHX:TOL=13250],psychopsis tillyardi[&&NHX:TOL=13251])[&&NHX:TOL=13249])[&&NHX:TOL=13247])[&&NHX:TOL=13245])[&&NHX:TOL=13243])[&&NHX:TOL=13241])[&&NHX:TOL=13239])[&&NHX:TOL=13237])[&&NHX:TOL=13235])[&&NHX:TOL=13231])[&&NHX:TOL=13229])psychopsis[&&NHX:TOL=13218])psychopsinae[&&NHX:TOL=13216])psychopsidae[&&NHX:TOL=13140],(nymphidae[&&NHX:TOL=13142],(nemopteridae[&&NHX:TOL=13144],(myrmeleontidae[&&NHX:TOL=13146],ascalaphidae[&&NHX:TOL=13147])[&&NHX:TOL=13145])[&&NHX:TOL=13143])[&&NHX:TOL=13141])[&&NHX:TOL=13139])[&&NHX:TOL=13133],coniopterygidae[&&NHX:TOL=13148],ithonidae[&&NHX:TOL=13149],osmylidae[&&NHX:TOL=13150],neurorthidae[&&NHX:TOL=13151],sisyridae[&&NHX:TOL=13152],(adelphohemerobius[&&NHX:TOL=13158],(carobius[&&NHX:TOL=13160],((((hemerobius[&&NHX:TOL=13165],nesobiella[&&NHX:TOL=13166])[&&NHX:TOL=13164],(wesmaelius[&&NHX:TOL=13168],hemerobiella[&&NHX:TOL=13169])[&&NHX:TOL=13167])[&&NHX:TOL=13163],biramus[&&NHX:TOL=13170])[&&NHX:TOL=13162],(notherobius[&&NHX:TOL=13172],((nomerobius[&&NHX:TOL=13175],(neosympherobius[&&NHX:TOL=13177],sympherobius[&&NHX:TOL=13178])[&&NHX:TOL=13176])[&&NHX:TOL=13174],((psychobiella[&&NHX:TOL=13181],(notiobiella[&&NHX:TOL=13183],(psectra[&&NHX:TOL=13185],(anapsectra[&&NHX:TOL=13187],zachobiella[&&NHX:TOL=13188])[&&NHX:TOL=13186])[&&NHX:TOL=13184])[&&NHX:TOL=13182])[&&NHX:TOL=13180],((conchopterella[&&NHX:TOL=13191],(austromegalomus[&&NHX:TOL=13193],drepanacra[&&NHX:TOL=13194])[&&NHX:TOL=13192])[&&NHX:TOL=13190],(megalomus[&&NHX:TOL=13196],((neuronema[&&NHX:TOL=13199],(gayomyia[&&NHX:TOL=13201],drepanepteryx[&&NHX:TOL=13202])[&&NHX:TOL=13200])[&&NHX:TOL=13198],(noius[&&NHX:TOL=13204],(nusalala[&&NHX:TOL=13206],(megalomina[&&NHX:TOL=13208],micromus[&&NHX:TOL=13209])[&&NHX:TOL=13207])[&&NHX:TOL=13205])[&&NHX:TOL=13203])[&&NHX:TOL=13197])[&&NHX:TOL=13195])[&&NHX:TOL=13189])[&&NHX:TOL=13179])[&&NHX:TOL=13173])[&&NHX:TOL=13171])[&&NHX:TOL=13161])[&&NHX:TOL=13159])hemerobiidae[&&NHX:TOL=13153],(nothochrysinae[&&NHX:TOL=118750],apochrysinae[&&NHX:TOL=118751],chrysopinae[&&NHX:TOL=118752])chrysopidae[&&NHX:TOL=13154],polystoechotidae[&&NHX:TOL=13155],rapismatidae[&&NHX:TOL=13156])neuroptera[&&NHX:TOL=8220])[&&NHX:TOL=8217],((((((((((((((((sphaerites dimidiatus[&&NHX:TOL=104028],sphaerites glabratus[&&NHX:TOL=104029],sphaerites nitidus[&&NHX:TOL=104030],sphaerites opacus[&&NHX:TOL=104031],sphaerites politus[&&NHX:TOL=104032])sphaerites[&&NHX:TOL=9220],(((onthophilus[&&NHX:TOL=9451],epiechinus[&&NHX:TOL=9452],peploglyptus[&&NHX:TOL=9453],vuattoxinus[&&NHX:TOL=9454],sigillum[&&NHX:TOL=9455],sculptura[&&NHX:TOL=9456],glymma[&&NHX:TOL=9457])onthophilinae[&&NHX:TOL=9376],(anapleus compactus[&&NHX:TOL=9235],anapleus nakanei[&&NHX:TOL=9236],(anapleus hagai[&&NHX:TOL=9238],anapleus marginatus[&&NHX:TOL=9239])[&&NHX:TOL=9237],(anapleus nomurai[&&NHX:TOL=9241],anapleus raddai[&&NHX:TOL=9242])[&&NHX:TOL=9240])anapleini[&&NHX:TOL=9377],(((((((eucurtiopsis adebratti[&&NHX:TOL=107455],eucurtiopsis brendelli[&&NHX:TOL=107456],eucurtiopsis carinatus[&&NHX:TOL=107457],eucurtiopsis chungi[&&NHX:TOL=107458],eucurtiopsis danielssoni[&&NHX:TOL=107459],eucurtiopsis elongatus[&&NHX:TOL=107460],eucurtiopsis gomyi[&&NHX:TOL=107461],eucurtiopsis hammondi[&&NHX:TOL=107462],eucurtiopsis hiranoi[&&NHX:TOL=107463],eucurtiopsis kanaari[&&NHX:TOL=107464],eucurtiopsis marinae[&&NHX:TOL=107465],eucurtiopsis mazuri[&&NHX:TOL=107466],eucurtiopsis mirabilis[&&NHX:TOL=107467],eucurtiopsis ohtanii[&&NHX:TOL=107468],eucurtiopsis tishechkini[&&NHX:TOL=107469],eucurtiopsis reichenspergeri[&&NHX:TOL=107470],eucurtiopsis viennai[&&NHX:TOL=107471],eucurtiopsis zecki[&&NHX:TOL=107472])eucurtiopsis[&&NHX:TOL=9255],(orectoscelis attenuatus[&&NHX:TOL=107473],orectoscelis aurolepidus[&&NHX:TOL=107474],orectoscelis blackburni[&&NHX:TOL=107475],orectoscelis circularis[&&NHX:TOL=107476],orectoscelis duboulaii[&&NHX:TOL=107477],orectoscelis dumogae[&&NHX:TOL=107478],orectoscelis halmaherae[&&NHX:TOL=107479],orectoscelis howdeni[&&NHX:TOL=107480],orectoscelis humeralis[&&NHX:TOL=107481],orectoscelis kovariki[&&NHX:TOL=107482],orectoscelis marginicollis[&&NHX:TOL=107483],orectoscelis obliquus[&&NHX:TOL=107484],orectoscelis okei[&&NHX:TOL=107485],orectoscelis peninsularis[&&NHX:TOL=107486],orectoscelis punctatus[&&NHX:TOL=107487],orectoscelis shihoae[&&NHX:TOL=107488],orectoscelis ubirr[&&NHX:TOL=107489],orectoscelis westwoodi[&&NHX:TOL=107490])orectoscelis[&&NHX:TOL=9256],(pheidoliphila acutistria[&&NHX:TOL=107491],pheidoliphila arriagadai[&&NHX:TOL=107492],pheidoliphila bifida[&&NHX:TOL=107493],pheidoliphila carbo[&&NHX:TOL=107494],pheidoliphila dahlgreni[&&NHX:TOL=107495],pheidoliphila finnigana[&&NHX:TOL=107496],pheidoliphila granulata[&&NHX:TOL=107497],pheidoliphila kapleri[&&NHX:TOL=107498],pheidoliphila lackneri[&&NHX:TOL=107499],pheidoliphila macmillani[&&NHX:TOL=107500],pheidoliphila magna[&&NHX:TOL=107501],pheidoliphila micra[&&NHX:TOL=107502],pheidoliphila minuta[&&NHX:TOL=107503],pheidoliphila oharai[&&NHX:TOL=107504],pheidoliphila penatii[&&NHX:TOL=107505],pheidoliphila pseudocephala[&&NHX:TOL=107506],pheidoliphila ruginota[&&NHX:TOL=107507],pheidoliphila rugosa[&&NHX:TOL=107508],pheidoliphila secqi[&&NHX:TOL=107509],pheidoliphila sternalis[&&NHX:TOL=107510],pheidoliphila storeyi[&&NHX:TOL=107511],pheidoliphila suturalis[&&NHX:TOL=107512],pheidoliphila unita[&&NHX:TOL=107513],pheidoliphila verityi[&&NHX:TOL=107514],pheidoliphila wenzeli[&&NHX:TOL=107515],pheidoliphila yelamosi[&&NHX:TOL=107516])pheidoliphila[&&NHX:TOL=9257],(ceratohister ankylonotum[&&NHX:TOL=107448],ceratohister cornutus[&&NHX:TOL=107449],ceratohister demotus[&&NHX:TOL=107450],ceratohister leai[&&NHX:TOL=107451],ceratohister pheidoliphilus[&&NHX:TOL=107452])ceratohister[&&NHX:TOL=9258],(gomyopsis kuscheli[&&NHX:TOL=9254],papuopsis andersoni[&&NHX:TOL=107445])[&&NHX:TOL=107595],teretriopsis theryi[&&NHX:TOL=107442])[&&NHX:TOL=9253],(((chlamydonia punctinota[&&NHX:TOL=107431],chlamydonia eucurtiopsoides[&&NHX:TOL=107430],chlamydonia fauveli[&&NHX:TOL=107432])[&&NHX:TOL=108213],chlamydonia inflata[&&NHX:TOL=107426],chlamydonia densa[&&NHX:TOL=107427],((chlamydonia erectipilosa[&&NHX:TOL=107429],chlamydonia stellata[&&NHX:TOL=107428])[&&NHX:TOL=108215],chlamydonia foveata[&&NHX:TOL=107425])[&&NHX:TOL=108214])[&&NHX:TOL=108212],((((((chlamydonia sinuata[&&NHX:TOL=107434],chlamydonia terapoides[&&NHX:TOL=107433])[&&NHX:TOL=108221],chlamydonia angulata[&&NHX:TOL=107437],chlamydonia dzumacensis[&&NHX:TOL=107435],chlamydonia volans[&&NHX:TOL=107436])[&&NHX:TOL=108220],chlamydonia wenzeli[&&NHX:TOL=107438])[&&NHX:TOL=108219],chlamydonia coutume[&&NHX:TOL=107422],chlamydonia gomyi[&&NHX:TOL=107423])[&&NHX:TOL=108218],chlamydonia sol[&&NHX:TOL=107421])[&&NHX:TOL=108217],chlamydonia tjibaoui[&&NHX:TOL=107424])[&&NHX:TOL=108216])chlamydonia[&&NHX:TOL=107420])[&&NHX:TOL=107594],kanakopsis amieuensis[&&NHX:TOL=107439])[&&NHX:TOL=107593],quasimodopsis riedeli[&&NHX:TOL=107417])[&&NHX:TOL=107592],(eucurtia comata[&&NHX:TOL=9261],((chlamydopsis baloghi[&&NHX:TOL=107525],chlamydopsis caledoniae[&&NHX:TOL=107529],((chlamydopsis epipleuralis[&&NHX:TOL=107544],((chlamydopsis convexa[&&NHX:TOL=107536],(((chlamydopsis dispersa[&&NHX:TOL=107542],(((chlamydopsis ectatommae[&&NHX:TOL=107543],chlamydopsis jayawijaya[&&NHX:TOL=107549],chlamydopsis kununurra[&&NHX:TOL=107550],(chlamydopsis degallieri[&&NHX:TOL=107539],chlamydopsis loculosa[&&NHX:TOL=107556],(chlamydopsis lawrencei[&&NHX:TOL=107553],(chlamydopsis monteithi[&&NHX:TOL=107563],chlamydopsis setifera[&&NHX:TOL=107580])[&&NHX:TOL=107816])[&&NHX:TOL=107815],chlamydopsis mallee[&&NHX:TOL=107560],(chlamydopsis pecki[&&NHX:TOL=107571],chlamydopsis variolosa[&&NHX:TOL=107589])[&&NHX:TOL=107817],(chlamydopsis australis[&&NHX:TOL=107524],chlamydopsis lepida[&&NHX:TOL=107555],(chlamydopsis bifovaecollis[&&NHX:TOL=107527],chlamydopsis nielseni[&&NHX:TOL=107566])[&&NHX:TOL=107819])[&&NHX:TOL=107818],chlamydopsis myrmecophila[&&NHX:TOL=107565])[&&NHX:TOL=107814],(chlamydopsis acutricha[&&NHX:TOL=107521],(chlamydopsis bataviae[&&NHX:TOL=107526],chlamydopsis lucifer[&&NHX:TOL=107558])[&&NHX:TOL=107821])[&&NHX:TOL=107820],chlamydopsis papuae[&&NHX:TOL=107569])[&&NHX:TOL=107813],((chlamydopsis burnetta[&&NHX:TOL=107528],chlamydopsis contorta[&&NHX:TOL=107534],chlamydopsis pluriseta[&&NHX:TOL=107573],chlamydopsis zborowskii[&&NHX:TOL=107591])[&&NHX:TOL=107823],chlamydopsis pilosipes[&&NHX:TOL=107572])[&&NHX:TOL=107822])[&&NHX:TOL=107812],((chlamydopsis crowcrofti[&&NHX:TOL=107538],chlamydopsis macmillani[&&NHX:TOL=107559],chlamydopsis nullarbor[&&NHX:TOL=107567],(chlamydopsis latipennis[&&NHX:TOL=107551],chlamydopsis latipes[&&NHX:TOL=107552])[&&NHX:TOL=107826])[&&NHX:TOL=107825],chlamydopsis rotunda[&&NHX:TOL=107577])[&&NHX:TOL=107824],chlamydopsis weiri[&&NHX:TOL=107590])[&&NHX:TOL=107811])[&&NHX:TOL=107810],(chlamydopsis formicicola[&&NHX:TOL=107546],chlamydopsis striatella[&&NHX:TOL=107583])[&&NHX:TOL=107827])[&&NHX:TOL=107809],(chlamydopsis carinota[&&NHX:TOL=107531],((chlamydopsis mormolyce[&&NHX:TOL=107564],(((chlamydopsis carinicollis[&&NHX:TOL=107530],chlamydopsis coronis[&&NHX:TOL=107537],chlamydopsis erupta[&&NHX:TOL=107545],chlamydopsis pygidialis[&&NHX:TOL=107574],(chlamydopsis agilis[&&NHX:TOL=107522],(chlamydopsis inaequalis[&&NHX:TOL=107547],chlamydopsis longipes[&&NHX:TOL=107557])[&&NHX:TOL=107835])[&&NHX:TOL=107834],chlamydopsis serricollis[&&NHX:TOL=107579],(chlamydopsis convergens[&&NHX:TOL=107535],chlamydopsis transversa[&&NHX:TOL=107586])[&&NHX:TOL=107836],chlamydopsis setipennis[&&NHX:TOL=107581])[&&NHX:TOL=107833],(chlamydopsis dimorpha[&&NHX:TOL=107541],chlamydopsis reticulata[&&NHX:TOL=107576])[&&NHX:TOL=107837])[&&NHX:TOL=107832],chlamydopsis strigicollis[&&NHX:TOL=107585])[&&NHX:TOL=107831],(chlamydopsis leai[&&NHX:TOL=107554],(chlamydopsis rana[&&NHX:TOL=107575],(chlamydopsis antennata[&&NHX:TOL=107523],chlamydopsis trichonota[&&NHX:TOL=107587])[&&NHX:TOL=107840])[&&NHX:TOL=107839],chlamydopsis striatipennis[&&NHX:TOL=107584],(chlamydopsis compressipes[&&NHX:TOL=107533],chlamydopsis pallida[&&NHX:TOL=107568])[&&NHX:TOL=107841])[&&NHX:TOL=107838])[&&NHX:TOL=107830],chlamydopsis tuberculata[&&NHX:TOL=107588])[&&NHX:TOL=107829])[&&NHX:TOL=107828])[&&NHX:TOL=107808])[&&NHX:TOL=107807],(chlamydopsis inquilina[&&NHX:TOL=107548],(chlamydopsis cavicollis[&&NHX:TOL=107532],(chlamydopsis matthewsi[&&NHX:TOL=107562],(chlamydopsis detecti[&&NHX:TOL=107540],chlamydopsis storeyi[&&NHX:TOL=107582])[&&NHX:TOL=107845])[&&NHX:TOL=107844])[&&NHX:TOL=107843])[&&NHX:TOL=107842])[&&NHX:TOL=107806],chlamydopsis sculptus[&&NHX:TOL=107578])[&&NHX:TOL=107805],chlamydopsis mareeba[&&NHX:TOL=107561])[&&NHX:TOL=107804],chlamydopsis parallelus[&&NHX:TOL=107570])chlamydopsis[&&NHX:TOL=9259],(ectatommiphila glabra[&&NHX:TOL=107517],ectatommiphila opaca[&&NHX:TOL=107518])ectatommiphila[&&NHX:TOL=9260])[&&NHX:TOL=107597])[&&NHX:TOL=107596])chlamydopsinae[&&NHX:TOL=9386],((saprinodes[&&NHX:TOL=9473],notosaprinus[&&NHX:TOL=9474],saprinus[&&NHX:TOL=9475],myrmeosaprinus[&&NHX:TOL=9476],satrapister[&&NHX:TOL=9477],phoxonotus[&&NHX:TOL=9478],euspilotus[&&NHX:TOL=9479],xerosaprinus[&&NHX:TOL=9480],geomysaprinus[&&NHX:TOL=9481],chelyoxenus[&&NHX:TOL=9482],aphelosternus[&&NHX:TOL=9483],styphrus[&&NHX:TOL=9484],zorius[&&NHX:TOL=9485],chalcionellus[&&NHX:TOL=9486],pholioxenus[&&NHX:TOL=9487],axelinus[&&NHX:TOL=9488],saprinillus[&&NHX:TOL=9489],hypocacculus[&&NHX:TOL=9490],chivaenius[&&NHX:TOL=9491],hypocaccus[&&NHX:TOL=9492],exaesiopus[&&NHX:TOL=9493],neopachylopus[&&NHX:TOL=9494],pachylopus[&&NHX:TOL=9495],paravolvulus[&&NHX:TOL=9496],reichardtiolus[&&NHX:TOL=9497],ammostyphrus[&&NHX:TOL=9498],gnathoncus[&&NHX:TOL=9499],eremosaprinus[&&NHX:TOL=9500],tomogenius[&&NHX:TOL=9501],paramyrmetes[&&NHX:TOL=9502],myrmetes[&&NHX:TOL=9503],reichardtia[&&NHX:TOL=9504],eopachylopus[&&NHX:TOL=9505],xenonychus[&&NHX:TOL=9506],philothus[&&NHX:TOL=9507],ptenophilothis[&&NHX:TOL=9508],paraphilothis[&&NHX:TOL=9509],xenophilothis[&&NHX:TOL=9510],terametopon[&&NHX:TOL=9511],monachister[&&NHX:TOL=9512],philoxenus[&&NHX:TOL=9513])saprininae[&&NHX:TOL=9380],((niponius andrewesi[&&NHX:TOL=9428],niponius bicolor[&&NHX:TOL=9429],niponius canalicollis[&&NHX:TOL=9430],niponius foveicollis[&&NHX:TOL=9431],niponius furcatus[&&NHX:TOL=9432],niponius himalayensis[&&NHX:TOL=9433],niponius impressicollis[&&NHX:TOL=9434],niponius interstitialis[&&NHX:TOL=9435],niponius obtusiceps[&&NHX:TOL=9436],niponius osorioceps[&&NHX:TOL=9437],niponius parvulus[&&NHX:TOL=9438],niponius piceae[&&NHX:TOL=9439],niponius polinae[&&NHX:TOL=9440],niponius punjabensis[&&NHX:TOL=9441],niponius simplicipygus[&&NHX:TOL=9442],niponius striaticeps[&&NHX:TOL=9443],niponius substriatus[&&NHX:TOL=9444],niponius tamanukii[&&NHX:TOL=9445],niponius unidentatus[&&NHX:TOL=9446],niponius unistrius[&&NHX:TOL=9447],niponius yamasakii[&&NHX:TOL=9448],niponius variabilis[&&NHX:TOL=9449])niponiinae[&&NHX:TOL=9382],(athomalus[&&NHX:TOL=9459],cryptomalus[&&NHX:TOL=9460],diplostix[&&NHX:TOL=9461],pachylomalus[&&NHX:TOL=9462],platylomalus[&&NHX:TOL=9463],xestipyge[&&NHX:TOL=9464],coomanister[&&NHX:TOL=9465],carcinops[&&NHX:TOL=9466],eutriptus[&&NHX:TOL=9467],australomalus[&&NHX:TOL=9468],eulomalus[&&NHX:TOL=9469],paromalus[&&NHX:TOL=9470],kissister[&&NHX:TOL=9471])paromalini[&&NHX:TOL=9383])[&&NHX:TOL=9381],(triballodes[&&NHX:TOL=9244],antongilus[&&NHX:TOL=9245],(geocolus[&&NHX:TOL=9247],bacanius[&&NHX:TOL=9248])[&&NHX:TOL=9246],(chaetobacanius[&&NHX:TOL=9250],abraeomorphus[&&NHX:TOL=9251])[&&NHX:TOL=9249])bacaniini[&&NHX:TOL=9384],(abraeini[&&NHX:TOL=9226],acritomorphini[&&NHX:TOL=9227],(acritini[&&NHX:TOL=9229],plegaderini[&&NHX:TOL=9230])[&&NHX:TOL=9228],((coptotrophis[&&NHX:TOL=104025],trypanaeus[&&NHX:TOL=104026],xylonaeus[&&NHX:TOL=104027])trypanaeinae[&&NHX:TOL=9232],teretriini[&&NHX:TOL=9233])[&&NHX:TOL=9231])abraeinae[&&NHX:TOL=9385])[&&NHX:TOL=9379],(dendrophilus californicus[&&NHX:TOL=9263],dendrophilus opacus[&&NHX:TOL=9264],dendrophilus proditor[&&NHX:TOL=9265],dendrophilus punctatus[&&NHX:TOL=9266],dendrophilus pygmaeus[&&NHX:TOL=9267],dendrophilus sulcatus[&&NHX:TOL=9268],dendrophilus tularensis[&&NHX:TOL=9269],dendrophilus xavieri[&&NHX:TOL=9270])dendrophilini[&&NHX:TOL=9387],((epierus[&&NHX:TOL=9515],plagiogramma[&&NHX:TOL=9516],pseudepierus[&&NHX:TOL=9517],stictostix[&&NHX:TOL=9518],parepierus[&&NHX:TOL=9519],scaphidister[&&NHX:TOL=9520],tribalus[&&NHX:TOL=9521],tribalasia[&&NHX:TOL=9522],idolia[&&NHX:TOL=9523],sphaericosoma[&&NHX:TOL=9524],caerosternus[&&NHX:TOL=9525])tribalinae[&&NHX:TOL=9389],(((atribalus[&&NHX:TOL=9401],rhypochares[&&NHX:TOL=9402],margarinotus[&&NHX:TOL=9403],macrolister[&&NHX:TOL=9404],pachylister[&&NHX:TOL=9405],hister[&&NHX:TOL=9406],merohister[&&NHX:TOL=9407],neohister[&&NHX:TOL=9408],spilodiscus[&&NHX:TOL=9409],zabromorphus[&&NHX:TOL=9410],teinotarsus[&&NHX:TOL=9411],campylorhabdus[&&NHX:TOL=9412],neosantalus[&&NHX:TOL=9413],contipus[&&NHX:TOL=9414],eugrammicus[&&NHX:TOL=9415],exorhabdus[&&NHX:TOL=9416],omotropis[&&NHX:TOL=9417],epiglyptus[&&NHX:TOL=9418],psiloscelis[&&NHX:TOL=9419],eudiplister[&&NHX:TOL=9420],atholus[&&NHX:TOL=9421],asiaster[&&NHX:TOL=9422],seitzister[&&NHX:TOL=9423],coptosternus[&&NHX:TOL=9424],hubenthalia[&&NHX:TOL=9425],megalocraerus[&&NHX:TOL=9426])histerini[&&NHX:TOL=9393],(alienister[&&NHX:TOL=9272],aneuterapus[&&NHX:TOL=9273],aristomorphus[&&NHX:TOL=9274],attalister[&&NHX:TOL=9275],aphanister[&&NHX:TOL=9276],anasynodites[&&NHX:TOL=9277],alloiodites[&&NHX:TOL=9278],aemulister[&&NHX:TOL=9279],bastactister[&&NHX:TOL=9280],cachexia[&&NHX:TOL=9281],chelonosternus[&&NHX:TOL=9282],coelister[&&NHX:TOL=9283],colonides[&&NHX:TOL=9284],cyclechinus[&&NHX:TOL=9285],chelyocephalus[&&NHX:TOL=9286],cossyphodister[&&NHX:TOL=9287],cheilister[&&NHX:TOL=9288],clientister[&&NHX:TOL=9289],convivister[&&NHX:TOL=9290],chrysetaerius[&&NHX:TOL=9291],daptesister[&&NHX:TOL=9292],daitrosister[&&NHX:TOL=9293],discoscelis[&&NHX:TOL=9294],ecclisister[&&NHX:TOL=9295],enicosoma[&&NHX:TOL=9296],euxenister[&&NHX:TOL=9297],eurysister[&&NHX:TOL=9298],euclasea[&&NHX:TOL=9299],eretmotus[&&NHX:TOL=9300],ecitonister[&&NHX:TOL=9301],fistulaster[&&NHX:TOL=9302],glyptosister[&&NHX:TOL=9303],gallaster[&&NHX:TOL=9304],hetaerimorphus[&&NHX:TOL=9305],hemicolonides[&&NHX:TOL=9306],hetaerius[&&NHX:TOL=9307],hetaeriobius[&&NHX:TOL=9308],hetaeriodes[&&NHX:TOL=9309],hippeutister[&&NHX:TOL=9310],hesperodromus[&&NHX:TOL=9311],homalopygus[&&NHX:TOL=9312],inquilinister[&&NHX:TOL=9313],iugulister[&&NHX:TOL=9314],kleptisister[&&NHX:TOL=9315],latronister[&&NHX:TOL=9316],leptosister[&&NHX:TOL=9317],lissosternus[&&NHX:TOL=9318],mecistostethus[&&NHX:TOL=9319],morphetaerius[&&NHX:TOL=9320],murexus[&&NHX:TOL=9321],nomadister[&&NHX:TOL=9322],notocoelis[&&NHX:TOL=9323],mesynodites[&&NHX:TOL=9324],nevermannister[&&NHX:TOL=9325],metasynodites[&&NHX:TOL=9326],monotonodites[&&NHX:TOL=9327],nymphister[&&NHX:TOL=9328],oudaimosister[&&NHX:TOL=9329],oaristes[&&NHX:TOL=9330],opadosister[&&NHX:TOL=9331],panoplitellus[&&NHX:TOL=9332],pselaphister[&&NHX:TOL=9333],pterotister[&&NHX:TOL=9334],poneralister[&&NHX:TOL=9335],pulvinister[&&NHX:TOL=9336],parasynodites[&&NHX:TOL=9337],plagioscelis[&&NHX:TOL=9338],paratropinus[&&NHX:TOL=9339],psalidister[&&NHX:TOL=9340],paroecister[&&NHX:TOL=9341],procolonides[&&NHX:TOL=9342],pinaxister[&&NHX:TOL=9343],plaumannister[&&NHX:TOL=9344],parodites[&&NHX:TOL=9345],reninoides[&&NHX:TOL=9346],reninopsis[&&NHX:TOL=9347],reninus[&&NHX:TOL=9348],sterncoelopsis[&&NHX:TOL=9349],synoditinus[&&NHX:TOL=9350],symphilister[&&NHX:TOL=9351],scapicoelis[&&NHX:TOL=9352],scapolister[&&NHX:TOL=9353],synoditulus[&&NHX:TOL=9354],sternocoelis[&&NHX:TOL=9355],synetister[&&NHX:TOL=9356],satrapes[&&NHX:TOL=9357],teratolister[&&NHX:TOL=9358],teratosoma[&&NHX:TOL=9359],troglosternus[&&NHX:TOL=9360],tubulister[&&NHX:TOL=9361],tylois[&&NHX:TOL=9362],terapus[&&NHX:TOL=9363],thaumataerius[&&NHX:TOL=9364],tarsilister[&&NHX:TOL=9365],termitoxenus[&&NHX:TOL=9366],termitolister[&&NHX:TOL=9367],trichoreninus[&&NHX:TOL=9368],ulkeus[&&NHX:TOL=9369],ulkeopsis[&&NHX:TOL=9370],wasmannister[&&NHX:TOL=9371],voratister[&&NHX:TOL=9372],xylostega[&&NHX:TOL=9373],xenister[&&NHX:TOL=9374])hetaeriinae[&&NHX:TOL=9394])[&&NHX:TOL=9392],platysomatini[&&NHX:TOL=9395],(hololeptini[&&NHX:TOL=9397],exosternini[&&NHX:TOL=9398],omalodini[&&NHX:TOL=9399])[&&NHX:TOL=9396])histerinae[&&NHX:TOL=9390])[&&NHX:TOL=9388])[&&NHX:TOL=9378])histeridae[&&NHX:TOL=9223],(syntelia davidis[&&NHX:TOL=104033],syntelia histeroides[&&NHX:TOL=104034],syntelia indica[&&NHX:TOL=104035],syntelia mazuri[&&NHX:TOL=104036],syntelia mexicana[&&NHX:TOL=104037],syntelia sinica[&&NHX:TOL=104038],syntelia westwoodi[&&NHX:TOL=104039])syntelia[&&NHX:TOL=9222])[&&NHX:TOL=9221])histeroidea[&&NHX:TOL=9075],((helophorus empleurus[&&NHX:TOL=60696],helophorus eutrichelophorus[&&NHX:TOL=60697],helophorus gephelophorus[&&NHX:TOL=60698],helophorus helophorus[&&NHX:TOL=60699],helophorus kyphohelophorus[&&NHX:TOL=60700],helophorus lihelophorus[&&NHX:TOL=60701],helophorus orphelophorus[&&NHX:TOL=60702],helophorus rhopalohelophorus[&&NHX:TOL=60703],helophorus thaumhelophorus[&&NHX:TOL=60704],helophorus transithelophorus[&&NHX:TOL=60705],helophorus trichohelophorus[&&NHX:TOL=60706])helophorus[&&NHX:TOL=9210],(epimetopus[&&NHX:TOL=60713],eumetopus[&&NHX:TOL=60714],eupotemus[&&NHX:TOL=60715])epimetopidae[&&NHX:TOL=9211],(georissus georissus[&&NHX:TOL=60717],georissus neogeorissus[&&NHX:TOL=60718],georissus nipponogeorissus[&&NHX:TOL=60719])georissus[&&NHX:TOL=9212],hydrochus[&&NHX:TOL=9213],spercheus[&&NHX:TOL=9214],(((penitus[&&NHX:EXT=Y:TOL=60744],(phelea[&&NHX:TOL=60757],paranacaena[&&NHX:TOL=60756],paracymus[&&NHX:TOL=60755],notohydrus[&&NHX:TOL=60754],notionotus[&&NHX:TOL=60753],hebauerina[&&NHX:TOL=60752],grodum[&&NHX:TOL=60751],enigmata[&&NHX:TOL=60750],(crenitis acrenitis[&&NHX:TOL=60748],crenitis crenitis[&&NHX:TOL=60749])crenitis[&&NHX:TOL=60747],anacaena[&&NHX:TOL=60746])anacaenini[&&NHX:TOL=60745],((allocotocerus[&&NHX:TOL=60759],(berosus berosus[&&NHX:TOL=60761],berosus enoplurus[&&NHX:TOL=60762],berosus phelerosus[&&NHX:TOL=60763])berosus[&&NHX:TOL=60760],derallus[&&NHX:TOL=60764],hemiosus[&&NHX:TOL=60765],regimbartia[&&NHX:TOL=60766])berosini[&&NHX:TOL=60758],(amphiops[&&NHX:TOL=60768],apurebium[&&NHX:TOL=60769],chaetarthria[&&NHX:TOL=60770],guyanobius[&&NHX:TOL=60771],hemisphaera[&&NHX:TOL=60772],thysanarthria[&&NHX:TOL=60773],venezuelobium[&&NHX:TOL=60774])chaetarthriini[&&NHX:TOL=60767])[&&NHX:TOL=107957],((acidocerus[&&NHX:TOL=60777],(agraphydrus agraphydrus[&&NHX:TOL=60779],agraphydrus gymnhelochares[&&NHX:TOL=60780])agraphydrus[&&NHX:TOL=60778],chasmogenus[&&NHX:TOL=60781],cymbiodyta[&&NHX:TOL=60782],dieroxenus[&&NHX:TOL=60783],enochrella[&&NHX:TOL=60784],(enochrus enochrus[&&NHX:TOL=60786],enochrus holcophilydrus[&&NHX:TOL=60787],enochrus hugoscottia[&&NHX:TOL=60788],enochrus hydatotrephis[&&NHX:TOL=60789],enochrus lumetus[&&NHX:TOL=60790],enochrus methydrus[&&NHX:TOL=60791])enochrus[&&NHX:TOL=60785],gemelus[&&NHX:TOL=60792],guaramacalus[&&NHX:TOL=60793],helobata[&&NHX:TOL=60794],(helochares batochares[&&NHX:TOL=60796],helochares helochares[&&NHX:TOL=60797],helochares helocharimorphus[&&NHX:TOL=60798],helochares hydrobaticus[&&NHX:TOL=60799],helochares sindolus[&&NHX:TOL=60800])helochares[&&NHX:TOL=60795],helocombus[&&NHX:TOL=60801],helopeltarium[&&NHX:TOL=60802],megagraphydrus[&&NHX:TOL=60803],omniops[&&NHX:TOL=60804],peltochares[&&NHX:TOL=60805],quadriops[&&NHX:TOL=60806],troglochares[&&NHX:TOL=60807])acidocerina[&&NHX:TOL=60776],globulosis[&&NHX:TOL=60808],(hybogralius[&&NHX:TOL=60812],hydramara[&&NHX:TOL=60813],hydrobius[&&NHX:TOL=60814],limnocyclus[&&NHX:TOL=60815],limnoxenus[&&NHX:TOL=60816])hydrobiusina[&&NHX:TOL=60811],((hydrobiomorpha brownephilus[&&NHX:TOL=60819],hydrobiomorpha hydrobiomorpha[&&NHX:TOL=60820])hydrobiomorpha[&&NHX:TOL=60818],hydrochara[&&NHX:TOL=60821],(hydrophilus dibolocelus[&&NHX:TOL=60823],hydrophilus hydrophilus[&&NHX:TOL=60824],hydrophilus temnopterus[&&NHX:TOL=60825])hydrophilus[&&NHX:TOL=60822],(sternolophus neosternolophus[&&NHX:TOL=60827],sternolophus sternolophus[&&NHX:TOL=60828])sternolophus[&&NHX:TOL=60826],(tropisternus homostethus[&&NHX:TOL=60830],tropisternus pleurhomus[&&NHX:TOL=60831],tropisternus pristoternus[&&NHX:TOL=60832],tropisternus strepitornus[&&NHX:TOL=60833],tropisternus tropisternus[&&NHX:TOL=60834])tropisternus[&&NHX:TOL=60829])hydrophilina[&&NHX:TOL=60817])hydrophilini[&&NHX:TOL=60775],(arabhydrus[&&NHX:TOL=60836],beralitra[&&NHX:TOL=60837],gentilina[&&NHX:TOL=60838],hydrophilomima[&&NHX:TOL=60839],(laccobius compsolaccobius[&&NHX:TOL=60841],laccobius cyclolaccobius[&&NHX:TOL=60842],laccobius dimorpholaccobius[&&NHX:TOL=60843],laccobius glyptolaccobius[&&NHX:TOL=60844],laccobius hydroxenus[&&NHX:TOL=60845],laccobius laccobius[&&NHX:TOL=60846],laccobius microlaccobius[&&NHX:TOL=60847],laccobius notoberosus[&&NHX:TOL=60848],laccobius yateberosus[&&NHX:TOL=60849])laccobius[&&NHX:TOL=60840],oocyclus[&&NHX:TOL=60850],ophthalmocyclus[&&NHX:TOL=60851],(pelthydrus globipelthydrus[&&NHX:TOL=60853],pelthydrus pelthydrus[&&NHX:TOL=60854])pelthydrus[&&NHX:TOL=60852],scoliopsis[&&NHX:TOL=60855],tritonus[&&NHX:TOL=60856])laccobiini[&&NHX:TOL=60835],(ametor[&&NHX:TOL=60858],anticura[&&NHX:TOL=60859],cylomissus[&&NHX:TOL=60860],hydrocassis[&&NHX:TOL=60861],sperchopsis[&&NHX:TOL=60862])sperchopsini[&&NHX:TOL=60857])hydrophilinae[&&NHX:TOL=9216],((andotypus[&&NHX:TOL=60864],coelostomopsis[&&NHX:TOL=60865])andotypini[&&NHX:TOL=60863],(borborophorus[&&NHX:TOL=60867],petasopsis[&&NHX:TOL=60868])borborophorini[&&NHX:TOL=60866],(adolopus[&&NHX:TOL=60870],badioglobus[&&NHX:TOL=60871],bourdonnaisia[&&NHX:TOL=60872],coeloctenus[&&NHX:TOL=60873],coelofletium[&&NHX:TOL=60874],(coelostoma coelostoma[&&NHX:TOL=60876],coelostoma hammacoelostoma[&&NHX:TOL=60877],coelostoma holocoelostoma[&&NHX:TOL=60878],coelostoma lachnocoelostoma[&&NHX:TOL=60879])coelostoma[&&NHX:TOL=60875],cyclotypus[&&NHX:TOL=60880],cyloma[&&NHX:TOL=60881],dactylosternum[&&NHX:TOL=60882],dactylostethus[&&NHX:TOL=60883],elocomosta[&&NHX:TOL=60884],galapagodacnum[&&NHX:TOL=60885],hemikruia[&&NHX:TOL=60886],hydroglobus[&&NHX:TOL=60887],kruia[&&NHX:TOL=60888],lachnodacnum[&&NHX:TOL=60889],phaenonotum[&&NHX:TOL=60890],phaenostoma[&&NHX:TOL=60891],rhachiostethus[&&NHX:TOL=60892],toma[&&NHX:TOL=60893])coelostomatini[&&NHX:TOL=60869],(acaryon[&&NHX:TOL=60895],agna[&&NHX:TOL=60896],agnaeformia[&&NHX:TOL=60897],anchorosternum[&&NHX:TOL=60898],armostus[&&NHX:TOL=60899],australocyon[&&NHX:TOL=60900],bolbonotum[&&NHX:TOL=60901],cenebriophilus[&&NHX:TOL=60902],cercillum[&&NHX:TOL=60903],cercyodes[&&NHX:TOL=60904],(cercyon acycreon[&&NHX:TOL=60906],cercyon arcocercyon[&&NHX:TOL=60907],cercyon cercyon[&&NHX:TOL=60908],cercyon clinocercyon[&&NHX:TOL=60909],cercyon conocercyon[&&NHX:TOL=60910],cercyon dicyrtocercyon[&&NHX:TOL=60911],cercyon himalcercyon[&&NHX:TOL=60912],cercyon oedocercyon[&&NHX:TOL=60913],cercyon paracercyon[&&NHX:TOL=60914],cercyon paracycreon[&&NHX:TOL=60915],cercyon prostercyon[&&NHX:TOL=60916])cercyon[&&NHX:TOL=60905],ceronocyton[&&NHX:TOL=60917],cetiocyon[&&NHX:TOL=60918],chledocyon[&&NHX:TOL=60919],colerus[&&NHX:TOL=60920],cryptopleurum[&&NHX:TOL=60921],cycreon[&&NHX:TOL=60922],cycrillum[&&NHX:TOL=60923],cyrtonion[&&NHX:TOL=60924],delimetrium[&&NHX:TOL=60925],deltostethus[&&NHX:TOL=60926],emmidolium[&&NHX:TOL=60927],ercycodes[&&NHX:TOL=60928],gillisius[&&NHX:TOL=60929],kahanga[&&NHX:TOL=60930],kanala[&&NHX:TOL=60931],megasternum[&&NHX:TOL=60932],moraphilus[&&NHX:TOL=60933],morastus[&&NHX:TOL=60934],motonerus[&&NHX:TOL=60935],nipponocercyon[&&NHX:TOL=60936],nitidulodes[&&NHX:TOL=60937],notocercyon[&&NHX:TOL=60938],oosternum[&&NHX:TOL=60939],oreocyon[&&NHX:TOL=60940],pachysternum[&&NHX:TOL=60941],pacrillum[&&NHX:TOL=60942],parastromus[&&NHX:TOL=60943],paroosternum[&&NHX:TOL=60944],pelocyon[&&NHX:TOL=60945],pelosoma[&&NHX:TOL=60946],peltocercyon[&&NHX:TOL=60947],pilocnema[&&NHX:TOL=60948],platycyon[&&NHX:TOL=60949],pseucyon[&&NHX:TOL=60950],pseudocercyon[&&NHX:TOL=60951],pseudoosternum[&&NHX:TOL=60952],pyretus[&&NHX:TOL=60953],quadristernum[&&NHX:TOL=60954],sacosternum[&&NHX:TOL=60955],tectosternum[&&NHX:TOL=60956])megasternini[&&NHX:TOL=60894],(aculomicrus[&&NHX:TOL=60958],heteryon[&&NHX:TOL=60959],lala[&&NHX:TOL=60960],litrosurus[&&NHX:TOL=60961],mircogioton[&&NHX:TOL=60962],nannomicrus[&&NHX:TOL=60963],noteropagus[&&NHX:TOL=60964],omicrogiton[&&NHX:TOL=60965],omicrus[&&NHX:TOL=60966],oreomicrus[&&NHX:TOL=60967],paromicrus[&&NHX:TOL=60968],peratogonus[&&NHX:TOL=60969],psalitrus[&&NHX:TOL=60970],stanmalcolmia[&&NHX:TOL=60971],tylomicrus[&&NHX:TOL=60972])omicrini[&&NHX:TOL=60957],(mucetum[&&NHX:TOL=60974],(rhombosternum[&&NHX:TOL=60976],protosternum[&&NHX:TOL=60975])[&&NHX:TOL=107956])protosternini[&&NHX:TOL=60973],(cylorygmus[&&NHX:TOL=60978],eurygmus[&&NHX:TOL=60979],pseudohydrobius[&&NHX:TOL=60980],pseudorygmodus[&&NHX:TOL=60981],rygmodus[&&NHX:TOL=60982],rygmostralia[&&NHX:TOL=60983],saphydrus[&&NHX:TOL=60984])rygmodini[&&NHX:TOL=60977],sphaeridium[&&NHX:TOL=60985],(afrotormus[&&NHX:TOL=60989],exydrus[&&NHX:TOL=60990],hydrostygnus[&&NHX:TOL=60991],tormissus[&&NHX:TOL=60992],tormus[&&NHX:TOL=60993])tormissini[&&NHX:TOL=60988])sphaeridiinae        [&&NHX:TOL=9217])[&&NHX:TOL=107788],horelophus[&&NHX:TOL=9215],(horelophopsis avita[&&NHX:TOL=108142],horelophopsis hanseni[&&NHX:TOL=108143])horelophopsis[&&NHX:TOL=105740],angarolarva[&&NHX:EXT=Y:TOL=105757],aposphinctus[&&NHX:EXT=Y:TOL=105758],creniphilites[&&NHX:EXT=Y:TOL=105759],cretohelophorus[&&NHX:EXT=Y:TOL=105760],cretosperchus[&&NHX:EXT=Y:TOL=105761],escheria[&&NHX:EXT=Y:TOL=105762],hydrobiites[&&NHX:EXT=Y:TOL=105763],hydrophilites[&&NHX:EXT=Y:TOL=105764],hydrophilopsia[&&NHX:EXT=Y:TOL=105765],hydrophilopsis[&&NHX:EXT=Y:TOL=105766],mesohelophorus[&&NHX:EXT=Y:TOL=105767],mesosperchus[&&NHX:EXT=Y:TOL=105768],mesydra[&&NHX:EXT=Y:TOL=105769],paraspercheus[&&NHX:EXT=Y:TOL=105770],polysitum[&&NHX:EXT=Y:TOL=105771],zetemenos[&&NHX:EXT=Y:TOL=105772])hydrophilidae[&&NHX:TOL=107787])hydrophiloidea[&&NHX:TOL=9224])[&&NHX:TOL=107948],(((((oomtelecopon[&&NHX:TOL=107690],coelometopon[&&NHX:TOL=28055])coelometoponini[&&NHX:TOL=107688],(haptaenida[&&NHX:TOL=107692],hydraenida[&&NHX:TOL=28058],parhydraenida[&&NHX:TOL=28059])hydraenidini[&&NHX:TOL=107691],(adelphydraena[&&NHX:TOL=28068],(hydraena hydraena[&&NHX:TOL=107698],hydraena hydraenopsis[&&NHX:TOL=107699])hydraena[&&NHX:TOL=28069])hydraenini[&&NHX:TOL=107695],((limnebius bilimneus[&&NHX:TOL=107703],limnebius limnebius[&&NHX:TOL=107704])limnebius[&&NHX:TOL=28067],laeliana[&&NHX:TOL=28066])limnebiini[&&NHX:TOL=107700],(davidraena[&&NHX:TOL=107706],gondraena[&&NHX:TOL=107707],madagaster[&&NHX:TOL=107708])madagastrini[&&NHX:TOL=107705],(discozantaena[&&NHX:TOL=107710],(parhydraena parhydraena[&&NHX:TOL=107713],parhydraena decarthrocerus[&&NHX:TOL=28061])parhydraena[&&NHX:TOL=28060],pneuminion[&&NHX:TOL=107714],protozantaena[&&NHX:TOL=107715])parhydraenini[&&NHX:TOL=107709])hydraeninae[&&NHX:TOL=28049],(ginkgoscia[&&NHX:TOL=107716],(enicocerus[&&NHX:TOL=107719],(meropathus[&&NHX:TOL=28070],tympallopatrum[&&NHX:TOL=107722],(tympanogaster hygrotympanogaster[&&NHX:TOL=107754],tympanogaster topotympanogaster[&&NHX:TOL=107755],tympanogaster plesiotympanogaster[&&NHX:TOL=107756])tympanogaster[&&NHX:TOL=28071])meropathina[&&NHX:TOL=107720],neochthebius[&&NHX:TOL=28053],(aulacochthebius[&&NHX:TOL=107727],gymnanthelius[&&NHX:TOL=107728],gymnochthebius[&&NHX:TOL=28050],hughleechia[&&NHX:TOL=28054],micragasma[&&NHX:TOL=28052],(ochthebius asiobates[&&NHX:TOL=107733],ochthebius ochthebius[&&NHX:TOL=107734])ochthebius[&&NHX:TOL=28051])ochthebiina[&&NHX:TOL=107726],protochthebius[&&NHX:TOL=107736])ochthebiini[&&NHX:TOL=107717],(edaphobates[&&NHX:TOL=107738],ochtheosus[&&NHX:TOL=107739])ochtheosini[&&NHX:TOL=107737])ochthebiinae[&&NHX:TOL=28048],(homalaena[&&NHX:TOL=28064],orchymontia[&&NHX:TOL=28065],podaena[&&NHX:TOL=28063])orchymontiinae[&&NHX:TOL=107740],(nucleotops[&&NHX:TOL=107745],(parasthetops[&&NHX:TOL=107748],sebasthetops[&&NHX:TOL=107749],mesoceration[&&NHX:TOL=28062],sicilicula[&&NHX:TOL=28056])parasthetopini[&&NHX:TOL=107746],prosthetops[&&NHX:TOL=28057],protosthetops[&&NHX:TOL=107752],pterosthetops[&&NHX:TOL=107753])prosthetopinae[&&NHX:TOL=107744],ochtebiites[&&NHX:EXT=Y:TOL=105925])hydraenidae[&&NHX:TOL=9615],(((acrotrichis[&&NHX:TOL=9628],actinopteryx[&&NHX:TOL=9722],chirostirca[&&NHX:TOL=9633],neotrichopteryx[&&NHX:TOL=107375],storicricha[&&NHX:TOL=107376])acrotrichini[&&NHX:TOL=107374],(baeocrara[&&NHX:TOL=9632],etronia[&&NHX:TOL=9728],(nephanes titan[&&NHX:TOL=9635],nephanes leaviusculus[&&NHX:TOL=9636],nephanes flaviventris[&&NHX:TOL=9637],nephanes truncatum[&&NHX:TOL=9638],nephanes puritanus[&&NHX:TOL=9639],nephanes vicksburgensis[&&NHX:TOL=9640],nephanes pubescens[&&NHX:TOL=9641],nephanes oregonus[&&NHX:TOL=9642])nephanes[&&NHX:TOL=9631],rioneta[&&NHX:TOL=9739],ptiliodes[&&NHX:TOL=9735],ptiliopcyna[&&NHX:TOL=9629],smicrus[&&NHX:TOL=9630])nephanini[&&NHX:TOL=107377])acrotrichinae[&&NHX:TOL=9623],(limulodes[&&NHX:TOL=9644],rodwayia[&&NHX:TOL=9645],paralimulodes wasmanni[&&NHX:TOL=9646],eulimulodes[&&NHX:TOL=9647],cephaloplectus[&&NHX:TOL=9648])cephaloplectinae[&&NHX:TOL=9624],(actidium[&&NHX:TOL=9703],(motschulskium[&&NHX:TOL=9704],nossidium[&&NHX:TOL=9702])nossidini[&&NHX:TOL=66526],micridium[&&NHX:TOL=9705],dilinium[&&NHX:TOL=9706],(ptilium sharpi[&&NHX:TOL=9744],ptilium columbianum[&&NHX:TOL=9745],ptilium humile[&&NHX:TOL=9746],ptilium obscurum[&&NHX:TOL=9747],ptilium hornianum[&&NHX:TOL=9748],ptilium fungicola[&&NHX:TOL=9749],ptilium truncatum[&&NHX:TOL=9750],ptilium sulcatum[&&NHX:TOL=9751],ptilium solidum[&&NHX:TOL=9752],ptilium tropicum[&&NHX:TOL=9753],ptilium smithsi[&&NHX:TOL=9754],ptilium rufotestaceum[&&NHX:TOL=9755],ptilium planum[&&NHX:TOL=9756],ptilium impressum[&&NHX:TOL=9757])ptilium[&&NHX:TOL=9707],ptenidium[&&NHX:TOL=9708],ptiliola[&&NHX:TOL=9709],millidium[&&NHX:TOL=9710],cissidium[&&NHX:TOL=9711],micridina[&&NHX:TOL=9712],oligella[&&NHX:TOL=9713],euryptilium[&&NHX:TOL=9714],ptiliolum[&&NHX:TOL=9715],bambara[&&NHX:TOL=9716],microptilium[&&NHX:TOL=9717],notoptenidium[&&NHX:TOL=9718],ptenidotonium[&&NHX:TOL=9719],dipentium[&&NHX:TOL=9720],gomyella[&&NHX:TOL=9721],africoptilium[&&NHX:TOL=9723],astatopteryx[&&NHX:TOL=9724],cnemodoxia[&&NHX:TOL=9725],cochliarion[&&NHX:TOL=9726],dybasina[&&NHX:TOL=9727],leaduadicus[&&NHX:TOL=9729],leptinla[&&NHX:TOL=9730],malkinella[&&NHX:TOL=9731],myrmicotrichis[&&NHX:TOL=9732],pterycodes[&&NHX:TOL=9733],(pteryx[&&NHX:TOL=9734],ptinella[&&NHX:TOL=9736],ptinellodes[&&NHX:TOL=9737])ptinellini[&&NHX:TOL=66527],pycnopteryx[&&NHX:TOL=9738],skidmorella[&&NHX:TOL=9740],urotriainus[&&NHX:TOL=9741],xenopteryx[&&NHX:TOL=9742],((nanosella fungi[&&NHX:TOL=9672],nanosella atrocephalus[&&NHX:TOL=9673],nanosella matthewsi[&&NHX:TOL=9674],nanosella panamensis[&&NHX:TOL=9675],nanosella robustus[&&NHX:TOL=9676])nanosella[&&NHX:TOL=9652],throscoptilium duryi[&&NHX:TOL=9653],porophila malkini[&&NHX:TOL=9654],suterina microcephala[&&NHX:TOL=9655],hydnosella globitheca[&&NHX:TOL=9656],cylindrosella dampfi[&&NHX:TOL=9657],(throscidium fairmairei[&&NHX:TOL=9697],throscidium germainii[&&NHX:TOL=9698])throscidium[&&NHX:TOL=9658],mikado[&&NHX:TOL=9659],kimoda[&&NHX:TOL=9660],(nellosana elegantula[&&NHX:TOL=9679],nellosana grandis[&&NHX:TOL=9680],nellosana intermedia[&&NHX:TOL=9681],nellosana minima[&&NHX:TOL=9682])nellosana[&&NHX:TOL=9661],kuschelidium[&&NHX:TOL=9662],(philagarica agilis[&&NHX:TOL=9688],philagarica parva[&&NHX:TOL=9689],philagarica pilosa[&&NHX:TOL=9690],philagarica parvicornis[&&NHX:TOL=9691])philagarica[&&NHX:TOL=9663],isolumpia[&&NHX:TOL=9664],paratuposa[&&NHX:TOL=9665],mycophagus[&&NHX:TOL=9666])nanosellini[&&NHX:TOL=9625])ptiliinae[&&NHX:TOL=9626])ptiliidae[&&NHX:TOL=9616])[&&NHX:TOL=29358],(((zeanecrophilus[&&NHX:TOL=29387],necrophilus[&&NHX:TOL=29386])necrophilinae[&&NHX:TOL=29378],(ecanus[&&NHX:TOL=29385],((ipelates[&&NHX:TOL=29382],lyrosoma[&&NHX:TOL=29383])[&&NHX:TOL=29381],(agyrtes agyrtecanus[&&NHX:TOL=105898],agyrtes agyrtes[&&NHX:TOL=105899])agyrtes[&&NHX:TOL=29384])[&&NHX:TOL=29380])agyrtinae[&&NHX:TOL=29377],(pteroloma[&&NHX:TOL=29388],apteroloma[&&NHX:TOL=29389])pterolomatinae[&&NHX:TOL=29379],mesecanus[&&NHX:EXT=Y:TOL=105879],miosilpha[&&NHX:EXT=Y:TOL=105880],ponomarenkia[&&NHX:EXT=Y:TOL=105881],sinosilphia[&&NHX:EXT=Y:TOL=105882])agyrtidae[&&NHX:TOL=9617],(((catopsolius[&&NHX:TOL=29464],eublackburniella[&&NHX:TOL=29465],myrmicholeva[&&NHX:TOL=29466],neopelatops[&&NHX:TOL=29467],ragytodes[&&NHX:TOL=29468],sphaeropelatops[&&NHX:TOL=29469])neopelatopini[&&NHX:TOL=29391],((afropelates joannae[&&NHX:TOL=87698],afropelates latitarsus[&&NHX:TOL=87699],afropelates leleupi[&&NHX:TOL=87700])afropelates[&&NHX:TOL=29442],(agyrtodes atropos[&&NHX:TOL=87701],agyrtodes bicolor[&&NHX:TOL=87702],agyrtodes crassus[&&NHX:TOL=87703],agyrtodes decoratus[&&NHX:TOL=87704],agyrtodes disparatus[&&NHX:TOL=87705],agyrtodes eucalypti[&&NHX:TOL=87706],agyrtodes hunuensis[&&NHX:TOL=87707],agyrtodes koebeli[&&NHX:TOL=87708],agyrtodes labralis[&&NHX:TOL=87709],agyrtodes monticola[&&NHX:TOL=87710],agyrtodes nebulosus[&&NHX:TOL=87711],agyrtodes nemoralis[&&NHX:TOL=87712],agyrtodes ovatus[&&NHX:TOL=87713],agyrtodes tasmanicus[&&NHX:TOL=87714],agyrtodes variegatus[&&NHX:TOL=87715])agyrtodes[&&NHX:TOL=29443],agyrtolasia[&&NHX:TOL=29444],chelagyrtodes crowsoni[&&NHX:TOL=29445],chiliopelates[&&NHX:TOL=29446],cholevomorpha[&&NHX:TOL=29447],dasypelates[&&NHX:TOL=29448],dictydiella[&&NHX:TOL=29449],eupelates[&&NHX:TOL=29450],gurvanocoleus[&&NHX:EXT=Y:TOL=29451],paragyrtodes[&&NHX:TOL=29452],ragytodina[&&NHX:TOL=29453],zeagyrtes[&&NHX:TOL=29454],zeagyrtoma[&&NHX:TOL=29455],zearagytodes[&&NHX:TOL=29456])agyrtodini[&&NHX:TOL=29392],(baeosilpha[&&NHX:TOL=29457],camiarites[&&NHX:TOL=29458],camiarus[&&NHX:TOL=29459],inocatops[&&NHX:TOL=29460],neocamiarus[&&NHX:TOL=29461],zenocolon[&&NHX:TOL=29462])camiarini[&&NHX:TOL=29393])camiarinae[&&NHX:TOL=29390],((catopocerus[&&NHX:TOL=29416],glacicavicola[&&NHX:TOL=29417])catopocerinae[&&NHX:TOL=29404],(((euliodes[&&NHX:TOL=29492],hinomoto[&&NHX:TOL=29493],hydnobius[&&NHX:TOL=29494],hydnodiaetus[&&NHX:TOL=29495],isocolon[&&NHX:TOL=29496],metahydnobius[&&NHX:TOL=29497],sogda[&&NHX:TOL=29498],(stereus deltocnemis[&&NHX:TOL=106768],stereus stereus[&&NHX:TOL=106769])stereus[&&NHX:TOL=29499],triarthron[&&NHX:TOL=29500])sogdini[&&NHX:TOL=29397],(dietta dietta[&&NHX:TOL=106756],dietta mesodietta[&&NHX:TOL=106757])dietta[&&NHX:TOL=29398],(afrocyrtusa[&&NHX:TOL=29501],afroleiodes[&&NHX:TOL=29502],anogdus[&&NHX:TOL=29503],chobautiella[&&NHX:TOL=29504],cyrtusa[&&NHX:TOL=29505],cyrtusamorpha[&&NHX:TOL=29506],(cyrtusoma cyrtusoma[&&NHX:TOL=106758],cyrtusoma paracyrtusoma[&&NHX:TOL=106759])cyrtusoma[&&NHX:TOL=29507],ecarinosphaerula[&&NHX:TOL=29508],hypoliodes[&&NHX:TOL=29509],incacyrtusa[&&NHX:TOL=29510],isoplastus[&&NHX:TOL=29511],leiodes[&&NHX:TOL=29512],liocyrtusa[&&NHX:TOL=29513],lionothus[&&NHX:TOL=29514],ovocyrtusa[&&NHX:TOL=29515],xanthosphaera[&&NHX:TOL=29516],zeadolopus[&&NHX:TOL=29517])leiodini[&&NHX:TOL=29399])[&&NHX:TOL=29396],((agaricophagus[&&NHX:TOL=29518],allocolenisia[&&NHX:TOL=29519],ansibaris[&&NHX:TOL=29520],cainosternum[&&NHX:TOL=29521],(colenis colenis[&&NHX:TOL=106760],colenis colenodes[&&NHX:TOL=106761])colenis[&&NHX:TOL=29522],colenisia[&&NHX:TOL=29523],dermatohomoeus[&&NHX:TOL=29524],neohydnobius[&&NHX:TOL=29525],perkovskius[&&NHX:TOL=29526],(pseudcolenis pseudcolenis[&&NHX:TOL=106762],pseudcolenis pseudcolenisia[&&NHX:TOL=106763])pseudcolenis[&&NHX:TOL=29527],zelodes[&&NHX:TOL=29528])pseudoliodini[&&NHX:TOL=29401],(aglyptinus[&&NHX:TOL=29529],creagrophorus[&&NHX:TOL=29531],cyrtusiola[&&NHX:TOL=29532],parabystus[&&NHX:TOL=29533],popeus[&&NHX:TOL=29534],scotocryptodes[&&NHX:TOL=29535],(scotocryptus scotocryptopsis[&&NHX:TOL=106766],scotocryptus scotocryptus[&&NHX:TOL=106767])scotocryptus[&&NHX:TOL=29536],synaristus[&&NHX:TOL=29537],termitoglobus[&&NHX:TOL=29538],pseudocyrtusiola[&&NHX:TOL=106764])scotocryptini[&&NHX:TOL=29402],(afroagathidium[&&NHX:TOL=29539],(agathidium agathidium[&&NHX:TOL=106748],agathidium chaetoceble[&&NHX:TOL=106749],agathidium cyphoceble[&&NHX:TOL=106750],agathidium euryceble[&&NHX:TOL=106751],agathidium macroceble[&&NHX:TOL=106752],agathidium microceble[&&NHX:TOL=106753],agathidium neoceble[&&NHX:TOL=106754],agathidium rhabdoelytrum[&&NHX:TOL=106755])agathidium[&&NHX:TOL=29540],amphicyllis[&&NHX:TOL=29541],anisotoma[&&NHX:TOL=29542],besuchetionella[&&NHX:TOL=29543],cyrtoplastus[&&NHX:TOL=29544],decuria[&&NHX:TOL=29545],gelae[&&NHX:TOL=29546],liodopria[&&NHX:TOL=29547],pseudoagathidium[&&NHX:TOL=29548],sphaeroliodes[&&NHX:TOL=29549],stetholiodes[&&NHX:TOL=29550])agathidiini[&&NHX:TOL=29403])[&&NHX:TOL=29400])leiodinae[&&NHX:TOL=29395])[&&NHX:TOL=29422],((colon chelicolon[&&NHX:TOL=106737],colon colon[&&NHX:TOL=106738],colon desmidocolon[&&NHX:TOL=106739],colon eurycolon[&&NHX:TOL=106740],colon mesagyrtes[&&NHX:TOL=106741],colon myloechus[&&NHX:TOL=106742],colon platycolon[&&NHX:TOL=106743],colon striatocolon[&&NHX:TOL=106744],colon tricolon[&&NHX:TOL=106745])colon[&&NHX:TOL=29487],(colonellus colonellus[&&NHX:TOL=106746],colonellus pentacolonellus[&&NHX:TOL=106747])colonellus[&&NHX:TOL=29488])coloninae[&&NHX:TOL=29405],((((anemadiola[&&NHX:TOL=106404],anemadus[&&NHX:TOL=106405],cholevodes[&&NHX:TOL=106406],speonemadus[&&NHX:TOL=106407])anemadina[&&NHX:TOL=29470],(eocatops eocatops[&&NHX:TOL=106408],eocatops eonemadus[&&NHX:TOL=106409])eocatops[&&NHX:TOL=29471],(araucaniopsis[&&NHX:TOL=106410],austrocholeva[&&NHX:TOL=106411],austronargus[&&NHX:TOL=106412],austronemadus[&&NHX:TOL=106413],catoposchema[&&NHX:TOL=106414],dissochaetus[&&NHX:TOL=106415],eunemadus[&&NHX:TOL=106416],falkocholeva[&&NHX:TOL=106417],falkonemadus[&&NHX:TOL=106418],nargiotes[&&NHX:TOL=106419],nargomorphus[&&NHX:TOL=106420],(nemadiolus nemadiolus[&&NHX:TOL=106422],nemadiolus reticulonemadiolus[&&NHX:TOL=106423],nemadiolus subnemadiolus[&&NHX:TOL=106424])nemadiolus[&&NHX:TOL=106421],nemadiopsis[&&NHX:TOL=106425],nemadotropis[&&NHX:TOL=106426],newtoniopsis[&&NHX:TOL=106427],nipponemadus[&&NHX:TOL=106428],paranemadus[&&NHX:TOL=106429],peckardia[&&NHX:TOL=106430],pseudonargiotes[&&NHX:TOL=106431],(pseudonemadus leptonemadus[&&NHX:TOL=106433],pseudonemaduspseudonemadus[&&NHX:TOL=106434],pseudonemadustriardronia[&&NHX:TOL=106435])pseudonemadus[&&NHX:TOL=106432],rangiola[&&NHX:TOL=106436])eunemadina[&&NHX:TOL=29472],(micronemadus[&&NHX:TOL=106437],(nemadus eonargus[&&NHX:TOL=106439],nemadus laferius[&&NHX:TOL=106440],nemadus nemadus[&&NHX:TOL=106441])nemadus[&&NHX:TOL=106438])nemadina[&&NHX:TOL=29473],(mesocolon[&&NHX:TOL=106442],paracatops[&&NHX:TOL=106443])paracatopina[&&NHX:TOL=29474])anemadini[&&NHX:TOL=29409],((attaephilus[&&NHX:TOL=106462],attumbra[&&NHX:TOL=106463],(catopsimorphus attiscurra[&&NHX:TOL=106465],catopsimorphus catopsimorphus[&&NHX:TOL=106466],catopsimorphus weiratherella[&&NHX:TOL=106467])catopsimorphus[&&NHX:TOL=106464],(choleva choleva[&&NHX:TOL=106469],choleva cholevopsis[&&NHX:TOL=106470],choleva protocatops[&&NHX:TOL=106471])choleva[&&NHX:TOL=106468],(nargus demochrus[&&NHX:TOL=106473],nargus eunargus[&&NHX:TOL=106474],nargus nargus[&&NHX:TOL=106475])nargus[&&NHX:TOL=106472],(philomessor attumbrinus[&&NHX:TOL=106477],philomessor philomessor[&&NHX:TOL=106478])philomessor[&&NHX:TOL=106476],prionochaeta[&&NHX:TOL=66209],takobiella[&&NHX:TOL=106479])cholevina[&&NHX:TOL=29475],(apocatops[&&NHX:TOL=106444],apterocatops[&&NHX:TOL=106445],catopidius[&&NHX:TOL=106446],catopodes[&&NHX:TOL=106447],catops[&&NHX:TOL=106448],catoptrichus[&&NHX:TOL=106449],chionocatops[&&NHX:TOL=106450],cholevinus[&&NHX:TOL=106451],dreposcia[&&NHX:TOL=106452],dzungarites[&&NHX:TOL=106453],fissocatops[&&NHX:TOL=106454],himalops[&&NHX:TOL=106455],mesocatops[&&NHX:TOL=106456],(rybinskiella eurybinskiella[&&NHX:TOL=106458],rybinskiella rybinskiella[&&NHX:TOL=106459],rybinskiella sintania[&&NHX:TOL=106460])rybinskiella[&&NHX:TOL=106457],sciodrepoides[&&NHX:TOL=106461])catopina[&&NHX:TOL=29476])cholevini[&&NHX:TOL=29410])[&&NHX:TOL=29423],(sciaphyes[&&NHX:TOL=29420],((antroherpon[&&NHX:TOL=106485],croatodirus[&&NHX:TOL=106486],hadesia[&&NHX:TOL=106487],leptomeson[&&NHX:TOL=106488],nauticiella[&&NHX:TOL=106489],parantrophilon[&&NHX:TOL=106490],remyella[&&NHX:TOL=106491],velebitodromus[&&NHX:TOL=106492])antroherponina[&&NHX:TOL=29477],(anillocharis[&&NHX:TOL=106493],anisoscapha[&&NHX:TOL=106494],antrodulus[&&NHX:TOL=106495],aphaobiella[&&NHX:TOL=106496],aphaobius[&&NHX:TOL=106497],aphaotus[&&NHX:TOL=106498],augustia[&&NHX:TOL=106499],bathyscia[&&NHX:TOL=106500],blattochaeta[&&NHX:TOL=106501],blattodromus[&&NHX:TOL=106502],cansiliella[&&NHX:TOL=106503],deelemaniella[&&NHX:TOL=106504],halbherria[&&NHX:TOL=106505],henrotiella[&&NHX:TOL=106506],hexaurus[&&NHX:TOL=106507],huetheriella[&&NHX:TOL=106508],(leonhardella leonhardella[&&NHX:TOL=106510],leonhardella leonhardellina[&&NHX:TOL=106511])leonhardella[&&NHX:TOL=106509],lessiniella[&&NHX:TOL=106512],lotharia[&&NHX:TOL=106513],netolitzkya[&&NHX:TOL=106514],orostygia[&&NHX:TOL=106515],oryotus[&&NHX:TOL=106516],(phaneropella epiroella[&&NHX:TOL=106518],phaneropella hittitia[&&NHX:TOL=106519],phaneropella phaneropella[&&NHX:TOL=106520],phaneropella uludagites[&&NHX:TOL=106521])phaneropella[&&NHX:TOL=106517],pholeuodromus[&&NHX:TOL=106522],(pholeuonopsis pholeuonopsis[&&NHX:TOL=106524],pholeuonopsis scotosites[&&NHX:TOL=106525],pholeuonopsis silphanillus[&&NHX:TOL=106526])pholeuonopsis[&&NHX:TOL=106523],pisidiella[&&NHX:TOL=106527],pretneria[&&NHX:TOL=106528],(proleonhardella pholeuonillus[&&NHX:TOL=106530],proleonhardella proleonhardella[&&NHX:TOL=106531])proleonhardella[&&NHX:TOL=106529],sinobathyscia[&&NHX:TOL=106532],speophyes[&&NHX:TOL=106533],tartariella[&&NHX:TOL=106534],weiratheria[&&NHX:TOL=106535])bathysciina[&&NHX:TOL=29478],(bathyscidius[&&NHX:TOL=106536],bathysciotes[&&NHX:TOL=106537],neobathyscia[&&NHX:TOL=106538],pseudobathyscidius[&&NHX:TOL=106539],ravasinia[&&NHX:TOL=106540],redensekia[&&NHX:TOL=106541],(speonesiotes albanella[&&NHX:TOL=106543],speonesiotes crivosiella[&&NHX:TOL=106544],speonesiotes kulzeria[&&NHX:TOL=106545],speonesiotes speonesiotes[&&NHX:TOL=106546])speonesiotes[&&NHX:TOL=106542],sphaerobathyscia[&&NHX:TOL=106547])bathysciotina[&&NHX:TOL=29479],(adelopidius[&&NHX:TOL=106548],albanodirus[&&NHX:TOL=106549],antrosedes[&&NHX:TOL=106550],apholeuonus[&&NHX:TOL=106551],astagobius[&&NHX:TOL=106552],balcanobius[&&NHX:TOL=106553],bathyscimorphus[&&NHX:TOL=106554],bathysciopsis[&&NHX:TOL=106555],beroniella[&&NHX:TOL=106556],bulgariella[&&NHX:TOL=106557],(ceuthmonocharis ceuthmonocharis[&&NHX:TOL=106559],ceuthmonocharis rectipenis[&&NHX:TOL=106560])ceuthmonocharis[&&NHX:TOL=106558],charonites[&&NHX:TOL=106561],elladoherpon[&&NHX:TOL=106562],genestiellina[&&NHX:TOL=106563],haplotropidius[&&NHX:TOL=106564],icharonia[&&NHX:TOL=106565],katobatizon[&&NHX:TOL=106566],laneyriella[&&NHX:TOL=106567],leonhardia[&&NHX:TOL=106568],leptodirus[&&NHX:TOL=106569],leptostagus[&&NHX:TOL=106570],parapropus[&&NHX:TOL=106571],petkovskiella[&&NHX:TOL=106572],pholeuonella[&&NHX:TOL=106573],pholeuonidius[&&NHX:TOL=106574],protobracharthron[&&NHX:TOL=106575],radziella[&&NHX:TOL=106576],roubaliella[&&NHX:TOL=106577],setnikia[&&NHX:TOL=106578],spelaeodromus[&&NHX:TOL=106579],spelaites[&&NHX:TOL=106580],speoplanes[&&NHX:TOL=106581])leptodirina[&&NHX:TOL=29480],(adelopsella[&&NHX:TOL=106582],albaniola[&&NHX:TOL=106583],anillochlamys[&&NHX:TOL=106584],antrocharis[&&NHX:TOL=106585],aranzadiella[&&NHX:TOL=106586],archeoboldoria[&&NHX:TOL=106587],atticiella[&&NHX:TOL=106588],babuniella[&&NHX:TOL=106589],banatiola[&&NHX:TOL=106590],bathysciella[&&NHX:TOL=106591],(bathysciola bathysciola[&&NHX:TOL=106593],bathysciola salfia[&&NHX:TOL=106594])bathysciola[&&NHX:TOL=106592],bellesia[&&NHX:TOL=106595],beronia[&&NHX:TOL=106596],beskovia[&&NHX:TOL=106597],besuchetiola[&&NHX:TOL=106598],bithyniella[&&NHX:TOL=106599],boldoria[&&NHX:TOL=106600],breuilia[&&NHX:TOL=106601],breuilites[&&NHX:TOL=106602],bureschiana[&&NHX:TOL=106603],canavesiella[&&NHX:TOL=106604],cantabrogeus[&&NHX:TOL=106605],capraiola[&&NHX:TOL=106606],cavazzutiella[&&NHX:TOL=106607],ceretophyes[&&NHX:TOL=106608],ceuthophyes[&&NHX:TOL=106609],closania[&&NHX:TOL=106610],coiffaitiola[&&NHX:TOL=106611],coreobathyscia[&&NHX:TOL=106612],cryptobathyscia[&&NHX:TOL=106613],cytodromus[&&NHX:TOL=106614],dalmatiola[&&NHX:TOL=106615],dellabeffaella[&&NHX:TOL=106616],diaprysius[&&NHX:TOL=106617],(drimeotus bihorites[&&NHX:TOL=106619],drimeotus drimeotinus[&&NHX:TOL=106620],drimeotus drimeotus[&&NHX:TOL=106621],drimeotus fericeus[&&NHX:TOL=106622],drimeotus trichopharis[&&NHX:TOL=106623])drimeotus[&&NHX:TOL=106618],eskualdunella[&&NHX:TOL=106624],espanoliella[&&NHX:TOL=106625],(euryspeonomus euryspeonomus[&&NHX:TOL=106627],euryspeonomus urbasolus[&&NHX:TOL=106628])euryspeonomus[&&NHX:TOL=106626],fusi[&&NHX:TOL=106629],gesciella[&&NHX:TOL=106630],hoffmannella[&&NHX:TOL=106631],hussonella[&&NHX:TOL=106632],insubriella[&&NHX:TOL=106633],iranobathyscia[&&NHX:TOL=106634],isereus[&&NHX:TOL=106635],josettekia[&&NHX:TOL=106636],karadeniziella[&&NHX:TOL=106637],lagariella[&&NHX:TOL=106638],leonesiella[&&NHX:TOL=106639],(magdelainella knirschiella[&&NHX:TOL=106641],magdelainella magdelainella[&&NHX:TOL=106642])magdelainella[&&NHX:TOL=106640],maroniella[&&NHX:TOL=106643],mehadiella[&&NHX:TOL=106644],monguzziella[&&NHX:TOL=106645],muelleriella[&&NHX:TOL=106646],naspunius[&&NHX:TOL=106647],notidocharis[&&NHX:TOL=106648],ochridiola[&&NHX:TOL=106649],oresigenus[&&NHX:TOL=106650],ovobathysciola[&&NHX:TOL=106651],pallaresiella[&&NHX:TOL=106652],pangaeoniola[&&NHX:TOL=106653],(parabathyscia ligurobathyscia[&&NHX:TOL=106655],parabathyscia parabathyscia[&&NHX:TOL=106656])parabathyscia[&&NHX:TOL=106654],paranillochlamys[&&NHX:TOL=106657],paraspeonomus[&&NHX:TOL=106658],parvospeonomus[&&NHX:TOL=106659],patriziella[&&NHX:TOL=106660],perriniella[&&NHX:TOL=106661],(phacomorphus phacomorphoides[&&NHX:TOL=106663],phacomorphus phacomorphus[&&NHX:TOL=106664])phacomorphus[&&NHX:TOL=106662],(pholeuon parapholeuon[&&NHX:TOL=106666],pholeuon pholeuon[&&NHX:TOL=106667])pholeuon[&&NHX:TOL=106665],protopholeuon[&&NHX:TOL=106668],pseudoboldoria[&&NHX:TOL=106669],pseudochlamys[&&NHX:TOL=106670],purkynella[&&NHX:TOL=106671],(quaestus amphogeus[&&NHX:TOL=106673],quaestus asturianella[&&NHX:TOL=106674],quaestus quaesticulus[&&NHX:TOL=106675],quaestus quaestus[&&NHX:TOL=106676],quaestus samanolla[&&NHX:TOL=106677],quaestus speogeus[&&NHX:TOL=106678])quaestus[&&NHX:TOL=106672],radevia[&&NHX:TOL=106679],rhodopiola[&&NHX:TOL=106680],royerella[&&NHX:TOL=106681],salgadoia[&&NHX:TOL=106682],sbordoniola[&&NHX:TOL=106683],sengletiola[&&NHX:TOL=106684],(sophrochaeta cernella[&&NHX:TOL=106686],sophrochaeta sophrochaeta[&&NHX:TOL=106687])sophrochaeta[&&NHX:TOL=106685],spelaeochlamys[&&NHX:TOL=106688],(speocharidius kobiella[&&NHX:TOL=106690],speocharidius speocharidius[&&NHX:TOL=106691])speocharidius[&&NHX:TOL=106689],speocharinus[&&NHX:TOL=106692],(speodiaetus ochsiella[&&NHX:TOL=106694],speodiaetus speodiaetus[&&NHX:TOL=106695])speodiaetus[&&NHX:TOL=106693],speonomidius[&&NHX:TOL=106696],speonomites[&&NHX:TOL=106697],(speonomus batinoscelis[&&NHX:TOL=106699],speonomus machaeroscelis[&&NHX:TOL=106700],speonomus metaspeonomus[&&NHX:TOL=106701],speonomus speonomus[&&NHX:TOL=106702])speonomus[&&NHX:TOL=106698],stygiophyes[&&NHX:TOL=106703],tismanella[&&NHX:TOL=106704],trapezodirus[&&NHX:TOL=106705],trocharanis[&&NHX:TOL=106706],(troglocharinus antrocharidius[&&NHX:TOL=106708],troglocharinus troglocharinus[&&NHX:TOL=106709])troglocharinus[&&NHX:TOL=106707],troglodromus[&&NHX:TOL=106710],troglophyes[&&NHX:TOL=106711],viallia[&&NHX:TOL=106712],vratzaniola[&&NHX:TOL=106713],zariquieyella[&&NHX:TOL=106714])pholeuina[&&NHX:TOL=29481],platycholeus[&&NHX:TOL=29482],(prospelaeobates[&&NHX:TOL=106715],(spelaeobates pretneriella[&&NHX:TOL=106717],spelaeobates spelaeobates[&&NHX:TOL=106718])spelaeobates[&&NHX:TOL=106716])spelaeobatina[&&NHX:TOL=29483],proleptodirina[&&NHX:TOL=106483],[&&NHX:TOL=106484])leptodirini[&&NHX:TOL=29407])[&&NHX:TOL=29424],((afrocatops[&&NHX:TOL=29489],chappuisiotes[&&NHX:TOL=29490],oritocatops[&&NHX:TOL=29491])oritocatopini[&&NHX:TOL=29412],(eucatops eucatops[&&NHX:TOL=106480],eucatops napocatops[&&NHX:TOL=106481],eucatops sphaerocatops[&&NHX:TOL=106482])eucatops[&&NHX:TOL=29413],(baryodirus[&&NHX:TOL=29484],(acrotrychiopsis[&&NHX:TOL=106719],adelopsis[&&NHX:TOL=106720],amplexella[&&NHX:TOL=106721],parapaulipalpina[&&NHX:TOL=106722],paulipalpina[&&NHX:TOL=106723],peckena[&&NHX:TOL=106724],(ptomaphagus adelops[&&NHX:TOL=106726],ptomaphagus appadelopsis[&&NHX:TOL=106727],ptomaphagus echinocoleus[&&NHX:TOL=106728],ptomaphagus merodiscus[&&NHX:TOL=106729],ptomaphagus ptomaphagus[&&NHX:TOL=106730],ptomaphagus synaulus[&&NHX:TOL=106731],ptomaphagus tupania[&&NHX:TOL=106732])ptomaphagus[&&NHX:TOL=106725])ptomaphagina[&&NHX:TOL=29485],(pandania[&&NHX:TOL=106733],proptomaphaginus[&&NHX:TOL=106734],ptomaphaginus[&&NHX:TOL=106735],ptomaphaminus[&&NHX:TOL=106736])ptomaphaginina[&&NHX:TOL=29486])ptomaphagini[&&NHX:TOL=29414])[&&NHX:TOL=29425])cholevinae[&&NHX:TOL=29406],(leptinillus[&&NHX:TOL=29551],leptinus[&&NHX:TOL=29552],platypsyllus[&&NHX:TOL=29553],silphopsyllus[&&NHX:TOL=29554])platypsyllinae[&&NHX:TOL=29415],mesagyrtoides[&&NHX:EXT=Y:TOL=106402],nyujwa[&&NHX:EXT=Y:TOL=106403])leiodidae[&&NHX:TOL=9618])[&&NHX:TOL=29354],((((arrhenopeplus[&&NHX:TOL=61234],cerapeplus[&&NHX:TOL=61237],kalissus[&&NHX:TOL=61238],micropeplus[&&NHX:TOL=61239],peplomicrus[&&NHX:TOL=61240],pseudokalissus[&&NHX:TOL=61241])micropeplinae[&&NHX:TOL=9760],empelus[&&NHX:TOL=9761],(glypholoma[&&NHX:TOL=61244],proglypholoma[&&NHX:TOL=61245])glypholomatinae[&&NHX:TOL=9762],microsilpha[&&NHX:TOL=9766],(((acidota[&&NHX:TOL=61865],altaiodromicus[&&NHX:TOL=61866],amphichroum[&&NHX:TOL=61867],anthobioides[&&NHX:TOL=61868],(anthobium anthobium[&&NHX:TOL=61870],anthobium prionothorax[&&NHX:TOL=61871])anthobium[&&NHX:TOL=61869],(anthophagus anthophagus[&&NHX:TOL=61873],anthophagus dimorphoschelus[&&NHX:TOL=61874],anthophagus phaganthus[&&NHX:TOL=61875])anthophagus[&&NHX:TOL=61872],arpedium[&&NHX:TOL=61876],artochia[&&NHX:TOL=61877],brathinus[&&NHX:TOL=61878],camioleum[&&NHX:TOL=61879],cylletron[&&NHX:TOL=61880],deinopteroloma[&&NHX:TOL=61881],deliphrosoma[&&NHX:TOL=61882],(deliphrum arpediopsis[&&NHX:TOL=61884],deliphrum deliphrum[&&NHX:TOL=61885])deliphrum[&&NHX:TOL=61883],emodensia[&&NHX:TOL=61886],eucnecosum[&&NHX:TOL=61887],(geodromicus brachydromicus[&&NHX:TOL=61889],geodromicus geodromicus[&&NHX:TOL=61890])geodromicus[&&NHX:TOL=61888],hygrodromicus[&&NHX:TOL=61891],hygrogeus[&&NHX:TOL=61892],(lesteva lesteva[&&NHX:TOL=61894],lesteva lestevidia[&&NHX:TOL=61895],lesteva lestevina[&&NHX:TOL=61896])lesteva[&&NHX:TOL=61893],liophilydrodes[&&NHX:TOL=61897],mannerheimia[&&NHX:TOL=61898],microedus[&&NHX:TOL=61899],olophrum[&&NHX:TOL=61900],omalorphanus[&&NHX:TOL=61901],orobanus[&&NHX:TOL=61902],orochares[&&NHX:TOL=61903],paramannerheimia[&&NHX:TOL=61904],paratrichodromeus[&&NHX:TOL=61905],pelecomalium[&&NHX:TOL=61906],philhydrodema[&&NHX:TOL=61907],philorinum[&&NHX:TOL=61908],(philydrodes minyphilydrodes[&&NHX:TOL=61910],philydrodes philydrodes[&&NHX:TOL=61911])philydrodes[&&NHX:TOL=61909],phlaeopterus[&&NHX:TOL=61912],phyllodrepoidea[&&NHX:TOL=61913],porrhodites[&&NHX:TOL=61914],tanyrhinus[&&NHX:TOL=61915],trichodromeus[&&NHX:TOL=61916],trigonodemus[&&NHX:TOL=61917],uenohadesina[&&NHX:TOL=61918],unamis[&&NHX:TOL=61919],vellica[&&NHX:TOL=61920],xenicopoda[&&NHX:TOL=61921])anthophagini[&&NHX:TOL=10103],(acrolocha[&&NHX:TOL=61922],acrulia[&&NHX:TOL=61923],acruliopsis[&&NHX:TOL=61924],allodrepa[&&NHX:TOL=61925],antarctotachinus[&&NHX:TOL=61926],anthobiomimus[&&NHX:TOL=61927],austrolophrum[&&NHX:TOL=61928],brouniellum[&&NHX:TOL=61929],(carcinocephalus carcinocephalus[&&NHX:TOL=61931],carcinocephalus scribaia[&&NHX:TOL=61932])carcinocephalus[&&NHX:TOL=61930],crymus[&&NHX:TOL=61933],dialycera[&&NHX:TOL=61934],dropephylla[&&NHX:TOL=61935],hapalaraea[&&NHX:TOL=61936],hypopycna[&&NHX:TOL=61937],(ischnoderus ischnoderus[&&NHX:TOL=61939],ischnoderus walkerellus[&&NHX:TOL=61940])ischnoderus[&&NHX:TOL=61938],leaskia[&&NHX:TOL=61941],macralymma[&&NHX:TOL=61942],metaxylostiba[&&NHX:TOL=61943],micralymma[&&NHX:TOL=61944],nesomalium[&&NHX:TOL=61945],nipponophloeostiba[&&NHX:TOL=61946],noumalia[&&NHX:TOL=61947],omaliomimus[&&NHX:TOL=61948],omaliopsis[&&NHX:TOL=61949],omalium[&&NHX:TOL=61950],omalonomus[&&NHX:TOL=61951],palpomalium[&&NHX:TOL=61952],paraphloeostiba[&&NHX:TOL=61953],(phloeonomus phloeonomodes[&&NHX:TOL=61955],phloeonomus phloeonomus[&&NHX:TOL=61956])phloeonomus[&&NHX:TOL=61954],phloeostiba[&&NHX:TOL=61957],phyllodrepa[&&NHX:TOL=61958],prosopaspis[&&NHX:TOL=61959],pycnoglypta[&&NHX:TOL=61960],selonomus[&&NHX:TOL=61961],stenomalium[&&NHX:TOL=61962],tetradelus[&&NHX:TOL=61963],ulommia[&&NHX:TOL=61964],xanthonomus[&&NHX:TOL=61965],xenanthobium[&&NHX:TOL=61966],xylodromus[&&NHX:TOL=61967],xylostiba[&&NHX:TOL=61968],zeolymma[&&NHX:TOL=61969])omaliini[&&NHX:TOL=10104],(eusphalerum eusphalerum[&&NHX:TOL=61971],eusphalerum pareusphalerum[&&NHX:TOL=61972])eusphalerum[&&NHX:TOL=10105],(brachygnathellus[&&NHX:TOL=61974],hadrognathus[&&NHX:TOL=61975])hadrognathini[&&NHX:TOL=10106],(corneolabium[&&NHX:TOL=61976],metacorneolabium[&&NHX:TOL=61977],paracorneolabium[&&NHX:TOL=61978])corneolabiini[&&NHX:TOL=10107],((archaeoboreaphilus[&&NHX:TOL=61980],boreaphilus[&&NHX:TOL=61981],caloboreaphilus[&&NHX:TOL=61982],gnathoryphium[&&NHX:TOL=61983],hypsonothrus[&&NHX:TOL=61984],niphetodops[&&NHX:TOL=61985])boreaphilina[&&NHX:TOL=61979],(altaioniphetodes[&&NHX:TOL=61987],coryphiocnemus[&&NHX:TOL=61988],coryphiodes[&&NHX:TOL=61989],coryphiomorphus[&&NHX:TOL=61990],coryphiopsis[&&NHX:TOL=61991],coryphium[&&NHX:TOL=61992],ephelinus[&&NHX:TOL=61993],eudectus[&&NHX:TOL=61994],haida[&&NHX:TOL=61995],holoboreaphilus[&&NHX:TOL=61996],murathus[&&NHX:TOL=61997],niphetodes[&&NHX:TOL=61998],occiephelinus[&&NHX:TOL=61999],ophthalmoniphetodes[&&NHX:TOL=62000],pareudectus[&&NHX:TOL=62001],planeboreaphilus[&&NHX:TOL=62002],platycoryphium[&&NHX:TOL=62003],pseudohaida[&&NHX:TOL=62004],subhaida[&&NHX:TOL=62005])coryphiina[&&NHX:TOL=61986])coryphiini[&&NHX:TOL=10108],(aphaenostemmus[&&NHX:TOL=62006],giulianium[&&NHX:TOL=62007],trigonobregma[&&NHX:TOL=62008])aphaenostemmini[&&NHX:TOL=10109])omaliinae[&&NHX:TOL=9764],((alloproteinus[&&NHX:TOL=62009],silphotelus[&&NHX:TOL=62010])silphotelini[&&NHX:TOL=10190],((nesoneus[&&NHX:TOL=62011],paranesoneus[&&NHX:TOL=62012])nesoneini[&&NHX:TOL=10192],((austrorhysus[&&NHX:TOL=62013],megarthroides[&&NHX:TOL=62014])austrorhysini[&&NHX:TOL=10194],((anepius[&&NHX:TOL=62015],eupsorus[&&NHX:TOL=62016])anepiini[&&NHX:TOL=10196],(megarthrus[&&NHX:TOL=62017],metopsia[&&NHX:TOL=62018],proteinus[&&NHX:TOL=62019])proteinini[&&NHX:TOL=10197])[&&NHX:TOL=10195])[&&NHX:TOL=10193])[&&NHX:TOL=10191])proteininae[&&NHX:TOL=9765])[&&NHX:TOL=9763],(neophonus[&&NHX:TOL=9773],(dasycerus[&&NHX:TOL=9772],(protopselaphus[&&NHX:TOL=9771],(ceroncinus[&&NHX:TOL=62020],greys[&&NHX:EXT=Y:TOL=62021],((amaurops[&&NHX:TOL=62024],amauropus[&&NHX:TOL=62025],arianops[&&NHX:TOL=62026],bergrothia[&&NHX:TOL=62027],orientamaurops[&&NHX:TOL=62028],paramaurops[&&NHX:TOL=62029],protamaurops[&&NHX:TOL=62030],pseudamaurops[&&NHX:TOL=62031],seracamaurops[&&NHX:TOL=62032],troglamaurops[&&NHX:TOL=62033],tropidamaurops[&&NHX:TOL=62034],zoufalia[&&NHX:TOL=62035])amauropini[&&NHX:TOL=62023],(baceysus[&&NHX:TOL=62037],batoxylomorpha[&&NHX:TOL=62038],coryphomobatrus[&&NHX:TOL=62039],euceroncinus[&&NHX:TOL=62040],pantobatrisus[&&NHX:EXT=Y:TOL=62041],temnodera[&&NHX:EXT=Y:TOL=62042],veddabatrus[&&NHX:TOL=62043],(ambicocerodes[&&NHX:TOL=62045],ambicoceropsis[&&NHX:TOL=62046],ambicocerus[&&NHX:TOL=62047],pseudambicocerus[&&NHX:TOL=62048])ambicocerina[&&NHX:TOL=62044],(acanthanops[&&NHX:TOL=62050],acanthicomus[&&NHX:TOL=62051],acanthocliarthrus[&&NHX:TOL=62052],adiastulus[&&NHX:TOL=62053],amblybatrisus[&&NHX:TOL=62054],anama[&&NHX:TOL=62055],ancistromus[&&NHX:TOL=62056],apobatrisus[&&NHX:TOL=62057],apocliarthrus[&&NHX:TOL=62058],apotrabisus[&&NHX:TOL=62059],arthmius[&&NHX:TOL=62060],arthromelodes[&&NHX:TOL=62061],(arthromelus arthromelus[&&NHX:TOL=62063],arthromelus euthiomelus[&&NHX:TOL=62064],arthromelus scaiomelus[&&NHX:TOL=62065])arthromelus[&&NHX:TOL=62062],(atheropterus atheropterus[&&NHX:TOL=62067],atheropterus echinotrabisus[&&NHX:TOL=62068],atheropterus paratrabisus[&&NHX:TOL=62069],atheropterus probatrisus[&&NHX:TOL=62070],atheropterus trabisellus[&&NHX:TOL=62071],atheropterus trabisidius[&&NHX:TOL=62072],atheropterus trabisinus[&&NHX:TOL=62073],atheropterus trabisomorphus[&&NHX:TOL=62074],atheropterus trabisonoma[&&NHX:TOL=62075],atheropterus trabisorites[&&NHX:TOL=62076])atheropterus[&&NHX:TOL=62066],babascenellus[&&NHX:TOL=62077],basitrodes[&&NHX:TOL=62078],batoctenus[&&NHX:TOL=62079],batoxyla[&&NHX:TOL=62080],(batriasymmodes batriasymmodes[&&NHX:TOL=62082],batriasymmodes extollodes[&&NHX:TOL=62083],batriasymmodes speleodes[&&NHX:TOL=62084])batriasymmodes[&&NHX:TOL=62081],batribolbus[&&NHX:TOL=62085],batricrator[&&NHX:TOL=62086],batrictenistes[&&NHX:TOL=62087],batrifigia[&&NHX:TOL=62088],batrinanda[&&NHX:TOL=62089],batriplica[&&NHX:TOL=62090],batrisaulax[&&NHX:TOL=62091],batriscenaulax[&&NHX:TOL=62092],(batriscenellus batriscenellinus[&&NHX:TOL=62094],batriscenellus batriscenellus[&&NHX:TOL=62095],batriscenellus coreoscenellus[&&NHX:TOL=62096],batriscenellus nipponoscenellus[&&NHX:TOL=62097],batriscenellus scaioscenellus[&&NHX:TOL=62098])batriscenellus[&&NHX:TOL=62093],batrisceninus[&&NHX:TOL=62099],batrisceniola[&&NHX:TOL=62100],batriscenites[&&NHX:TOL=62101],batriscenodes[&&NHX:TOL=62102],batrischema[&&NHX:TOL=62103],batrisiella[&&NHX:TOL=62104],batrisinus[&&NHX:TOL=62105],batrisiotes[&&NHX:TOL=62106],batrisocenus[&&NHX:TOL=62107],batrisochaetus[&&NHX:TOL=62108],(batrisochorus batrisochorus[&&NHX:TOL=62110],batrisochorus batristellus[&&NHX:TOL=62111])batrisochorus[&&NHX:TOL=62109],batrisoconnus[&&NHX:TOL=62112],batrisodella[&&NHX:TOL=62113],batrisodellus[&&NHX:TOL=62114],batrisodema[&&NHX:TOL=62115],(batrisodes babnormodes[&&NHX:TOL=62117],batrisodes batrisodes[&&NHX:TOL=62118],batrisodes declivodes[&&NHX:TOL=62119],batrisodes elytrodes[&&NHX:TOL=62120],batrisodes empinodes[&&NHX:TOL=62121],batrisodes excavodes[&&NHX:TOL=62122],batrisodes pubimodes[&&NHX:TOL=62123],batrisodes spifemodes[&&NHX:TOL=62124])batrisodes[&&NHX:TOL=62116],batrisodiola[&&NHX:TOL=62125],batrisodites[&&NHX:TOL=62126],batrisomalus[&&NHX:TOL=62127],batrisomellus[&&NHX:TOL=62128],batrisomicrus[&&NHX:TOL=62129],batrisomina[&&NHX:TOL=62130],batrisopachys[&&NHX:TOL=62131],batrisophyma[&&NHX:TOL=62132],batrisoplatus[&&NHX:TOL=62133],batrisoplisus[&&NHX:TOL=62134],batrisopsis[&&NHX:TOL=62135],batrisoschema[&&NHX:TOL=62136],batrisoxenus[&&NHX:TOL=62137],batristerus[&&NHX:TOL=62138],batristhenes[&&NHX:TOL=62139],batristidius[&&NHX:TOL=62140],batristilbus[&&NHX:TOL=62141],batristites[&&NHX:TOL=62142],batristogenius[&&NHX:TOL=62143],batrisus[&&NHX:TOL=62144],batrivitis[&&NHX:TOL=62145],batrixenus[&&NHX:TOL=62146],besuchetidia[&&NHX:TOL=62147],borneana[&&NHX:TOL=62148],bothriotelus[&&NHX:TOL=62149],camptomodes[&&NHX:TOL=62150],catoxyomus[&&NHX:TOL=62151],celisia[&&NHX:TOL=62152],ceroderma[&&NHX:TOL=62153],clarkeorites[&&NHX:TOL=62154],cliarthrinidius[&&NHX:TOL=62155],cliarthrinus[&&NHX:TOL=62156],cliarthrodes[&&NHX:TOL=62157],cliarthromorphus[&&NHX:TOL=62158],cliarthrus[&&NHX:TOL=62159],connodontinus[&&NHX:TOL=62160],(connodontus connodontites[&&NHX:TOL=62162],connodontus connodontus[&&NHX:TOL=62163])connodontus[&&NHX:TOL=62161],conogastridius[&&NHX:TOL=62164],conopygidia[&&NHX:TOL=62165],conuridius[&&NHX:TOL=62166],coryphomodes[&&NHX:TOL=62167],coryphomoides[&&NHX:TOL=62168],(coryphomus camptomidius[&&NHX:TOL=62170],coryphomus camptomites[&&NHX:TOL=62171],coryphomus coryphomellus[&&NHX:TOL=62172],coryphomus coryphomus[&&NHX:TOL=62173])coryphomus[&&NHX:TOL=62169],cratna[&&NHX:TOL=62174],cylindroma[&&NHX:TOL=62175],daintree[&&NHX:TOL=62176],diaposis[&&NHX:TOL=62177],diaugis[&&NHX:TOL=62178],ectotrabisus[&&NHX:TOL=62179],eleodimerina[&&NHX:TOL=62180],eleodimerodes[&&NHX:TOL=62181],eleodimerus[&&NHX:TOL=62182],eubatrisus[&&NHX:TOL=62183],exallidius[&&NHX:TOL=62184],exallomorpha[&&NHX:TOL=62185],exallus[&&NHX:TOL=62186],exechophyes[&&NHX:TOL=62187],exedrus[&&NHX:TOL=62188],franzorella[&&NHX:TOL=62189],gadgarra[&&NHX:TOL=62190],hemicliarthrus[&&NHX:TOL=62191],hingstoniella[&&NHX:TOL=62192],hulstaertites[&&NHX:TOL=62193],hyobontus[&&NHX:TOL=62194],hypochraeus[&&NHX:TOL=62195],iteticus[&&NHX:TOL=62196],jochmansiella[&&NHX:TOL=62197],kigatrodes[&&NHX:TOL=62198],korovodes[&&NHX:TOL=62199],(leleupia leleupia[&&NHX:TOL=62201],leleupia paraleleupia[&&NHX:TOL=62202])leleupia[&&NHX:TOL=62200],leleupiastes[&&NHX:TOL=62203],(leptobatrisus leptobatrisus[&&NHX:TOL=62205],leptobatrisus strongylomus[&&NHX:TOL=62206])leptobatrisus[&&NHX:TOL=62204],loebliella[&&NHX:TOL=62207],lukwangulorites[&&NHX:TOL=62208],macrodelphus[&&NHX:TOL=62209],madrasorites[&&NHX:TOL=62210],manniconnus[&&NHX:TOL=62211],megabatrus[&&NHX:TOL=62212],microbatrisodes[&&NHX:TOL=62213],mnia[&&NHX:TOL=62214],mossman[&&NHX:TOL=62215],nenemeca[&&NHX:TOL=62216],neotrabisus[&&NHX:TOL=62217],nesiotomina[&&NHX:TOL=62218],neurum[&&NHX:TOL=62219],odonticoscapus[&&NHX:TOL=62220],odontoconnus[&&NHX:TOL=62221],ophelius[&&NHX:TOL=62222],orropygia[&&NHX:TOL=62223],(oxarthrius baroxarthrius[&&NHX:TOL=62225],oxarthrius oxarthrius[&&NHX:TOL=62226])oxarthrius[&&NHX:TOL=62224],oxyomera[&&NHX:TOL=62227],oxyomites[&&NHX:TOL=62228],pachypygidia[&&NHX:TOL=62229],pachytrabisus[&&NHX:TOL=62230],panaphysis[&&NHX:TOL=62231],pantosiella[&&NHX:TOL=62232],parabatrisus[&&NHX:TOL=62233],passosiella[&&NHX:TOL=62234],petaloscapus[&&NHX:TOL=62235],physomerinus[&&NHX:TOL=62236],plocamarthrus[&&NHX:TOL=62237],podus[&&NHX:TOL=62238],procheilophorus[&&NHX:TOL=62239],pseudobatrisus[&&NHX:TOL=62240],pseudocliarthrus[&&NHX:TOL=62241],pseudoconnus[&&NHX:TOL=62242],pseudoctenistes[&&NHX:TOL=62243],pseudotrabisoides[&&NHX:TOL=62244],ruacorites[&&NHX:TOL=62245],ryxabis[&&NHX:TOL=62246],sathytes[&&NHX:TOL=62247],seydelites[&&NHX:TOL=62248],siteromina[&&NHX:TOL=62249],speobatrisodes[&&NHX:TOL=62250],spurgeon[&&NHX:TOL=62251],stenocliarthrus[&&NHX:TOL=62252],stictus[&&NHX:TOL=62253],sulcifigia[&&NHX:TOL=62254],syrbatomorphus[&&NHX:TOL=62255],(syrbatus syrbatidius[&&NHX:TOL=62257],syrbatus syrbatus[&&NHX:TOL=62258])syrbatus[&&NHX:TOL=62256],syrmocerus[&&NHX:TOL=62259],texamaurops[&&NHX:TOL=62260],tinaroo[&&NHX:TOL=62261],trabisodema[&&NHX:TOL=62262],trabisoides[&&NHX:TOL=62263],trabisostenus[&&NHX:TOL=62264],trabisoxenus[&&NHX:TOL=62265],tribasodema[&&NHX:TOL=62266],tribasodes[&&NHX:TOL=62267],tribasodites[&&NHX:TOL=62268],trichonomorphus[&&NHX:TOL=62269],trichopnites[&&NHX:TOL=62270],trisinarthrus[&&NHX:TOL=62271],trisiniotus[&&NHX:TOL=62272],trisinus[&&NHX:TOL=62273],typhlobatrisus[&&NHX:TOL=62274],typhlorites[&&NHX:TOL=62275],xenadiastus[&&NHX:TOL=62276],xenobasilewskyia[&&NHX:TOL=62277],xenobatrisus[&&NHX:TOL=62278],xenocliarthrus[&&NHX:TOL=62279],xenoconurus[&&NHX:TOL=62280],xenolejeunea[&&NHX:TOL=62281],xenomachadoella[&&NHX:TOL=62282],xenopygia[&&NHX:TOL=62283],xenopygiella[&&NHX:TOL=62284])batrisina[&&NHX:TOL=62049],leupelia[&&NHX:TOL=62285],(codonoderus[&&NHX:TOL=62289],pelulea[&&NHX:TOL=62290],peluleotes[&&NHX:TOL=62291],stilipalpus[&&NHX:TOL=62292])stilipalpina[&&NHX:TOL=62288])batrisini[&&NHX:TOL=62036],thaumastocephalus[&&NHX:TOL=62293])batrisitae[&&NHX:TOL=62022],((adranes[&&NHX:TOL=62298],(ambrosiger[&&NHX:TOL=62302],apoderiger[&&NHX:TOL=62303],micrapoderiger[&&NHX:TOL=62304],trymalius[&&NHX:TOL=62305])apoderigerina[&&NHX:TOL=62301],(claviger clavifer[&&NHX:TOL=62308],claviger claviger[&&NHX:TOL=62309])claviger[&&NHX:TOL=62306],(amphironchus[&&NHX:TOL=62312],anaclasiger[&&NHX:TOL=62313],ankarahitra[&&NHX:TOL=62314],archiclaviger[&&NHX:TOL=62315],articerodes[&&NHX:TOL=62316],articeronomus[&&NHX:TOL=62317],articeropsis[&&NHX:TOL=62318],articerus[&&NHX:TOL=62319],bironia[&&NHX:TOL=62320],cerylambus[&&NHX:TOL=62321],clavigerodes[&&NHX:TOL=62322],clavigeropsis[&&NHX:TOL=62323],colletocerus[&&NHX:TOL=62324],commatocerodes[&&NHX:TOL=62325],corynotopsis[&&NHX:TOL=62326],corynotus[&&NHX:TOL=62327],dejageria[&&NHX:TOL=62328],diartiger[&&NHX:TOL=62329],elasmatus[&&NHX:TOL=62330],fossiger[&&NHX:TOL=62331],fustiger[&&NHX:TOL=62332],fustigerillus[&&NHX:TOL=62333],fustigerinus[&&NHX:TOL=62334],fustigerodes[&&NHX:TOL=62335],fustigeromimus[&&NHX:TOL=62336],fustigeropsis[&&NHX:TOL=62337],gericlavodes[&&NHX:TOL=62338],gomyia[&&NHX:TOL=62339],hexamerodes[&&NHX:TOL=62340],ischyroceros[&&NHX:TOL=62341],kaisia[&&NHX:TOL=62342],leptocorynotus[&&NHX:TOL=62343],marofusiger[&&NHX:TOL=62344],mesoleptochir[&&NHX:TOL=62345],micrelytriger[&&NHX:TOL=62346],microfustigerinus[&&NHX:TOL=62347],nadarimanu[&&NHX:TOL=62348],nearticerodes[&&NHX:TOL=62349],neocorynotus[&&NHX:TOL=62350],neofustiger[&&NHX:TOL=62351],neofustigerinus[&&NHX:TOL=62352],neoradamopsis[&&NHX:TOL=62353],novoclaviger[&&NHX:TOL=62354],novofustiger[&&NHX:TOL=62355],palaeoclaviger[&&NHX:TOL=62356],paliger[&&NHX:TOL=62357],pararticerus[&&NHX:TOL=62358],paussiger[&&NHX:TOL=62359],platycerodes[&&NHX:TOL=62360],pseudacerus[&&NHX:TOL=62361],pseudoclavigerodes[&&NHX:TOL=62362],radamopsis[&&NHX:TOL=62363],rhynchoclaviger[&&NHX:TOL=62364],stenofustigerinus[&&NHX:TOL=62365],sufifer[&&NHX:TOL=62366],syrraphesina[&&NHX:TOL=62367],triartiger[&&NHX:TOL=62368],triceratomerus[&&NHX:TOL=62369],villofustiger[&&NHX:TOL=62370],xenalluaudia[&&NHX:TOL=62371],xenobesuchetia[&&NHX:TOL=62372],xenocelisia[&&NHX:TOL=62373],xenoleleupia[&&NHX:TOL=62374],xenomussardia[&&NHX:TOL=62375])clavigerodina[&&NHX:TOL=62311],dimerometopus[&&NHX:TOL=62376],disarthricerus[&&NHX:TOL=62379],(burgeonilla[&&NHX:TOL=62383],hadrophorus[&&NHX:TOL=62384],hoplitoxenus[&&NHX:TOL=62385],monodiger[&&NHX:TOL=62386])hoplitoxenina[&&NHX:TOL=62382],lunilla[&&NHX:TOL=62387],mastiger[&&NHX:TOL=62390],miroclaviger[&&NHX:TOL=62393],neoceratopsis[&&NHX:TOL=62396],neocerus[&&NHX:TOL=62399],(madara[&&NHX:TOL=62403],merinia[&&NHX:TOL=62404],pseudoradama[&&NHX:TOL=62405],radama[&&NHX:TOL=62406],radamellus[&&NHX:TOL=62407],radamides[&&NHX:TOL=62408],radamira[&&NHX:TOL=62409],semiclaviger[&&NHX:TOL=62410])radamina[&&NHX:TOL=62402],(antalaha[&&NHX:TOL=62412],theocerus[&&NHX:TOL=62413])theocerina[&&NHX:TOL=62411],(arnoldiella[&&NHX:TOL=62415],braunsiella[&&NHX:TOL=62416],eurycheiles[&&NHX:TOL=62417],soalala[&&NHX:TOL=62418],thysdariella[&&NHX:TOL=62419],thysdariopsis[&&NHX:TOL=62420],thysdarius[&&NHX:TOL=62421],trichomatosus[&&NHX:TOL=62422])thysdariina[&&NHX:TOL=62414])clavigerini[&&NHX:TOL=62297],colilodion[&&NHX:TOL=62423],tiracerus[&&NHX:TOL=62426])clavigeritae[&&NHX:TOL=62296],(cautinia[&&NHX:TOL=62430],eupsinoides[&&NHX:EXT=Y:TOL=62431],hetereuplectus[&&NHX:EXT=Y:TOL=62432],mehuinia[&&NHX:TOL=62433],monyx[&&NHX:EXT=Y:TOL=62434],nugator[&&NHX:EXT=Y:TOL=62435],philotrimium[&&NHX:TOL=62436],((acrodimerus[&&NHX:TOL=62439],anomozethodes[&&NHX:TOL=62440],anomozethus[&&NHX:TOL=62441],anozethopsis[&&NHX:TOL=62442],apozethopsus[&&NHX:TOL=62443],archaeozethus[&&NHX:TOL=62444],aulacozethus[&&NHX:TOL=62445],basilewskyozethus[&&NHX:TOL=62446],besucheteidos[&&NHX:TOL=62447],besuchetiozethus[&&NHX:TOL=62448],bolbozethus[&&NHX:TOL=62449],bythinoplectoides[&&NHX:TOL=62450],bythinoplectus[&&NHX:TOL=62451],cephalozethus[&&NHX:TOL=62452],couloniella[&&NHX:TOL=62453],decazethodes[&&NHX:TOL=62454],decazethus[&&NHX:TOL=62455],dichocoryna[&&NHX:TOL=62456],dichozethinus[&&NHX:TOL=62457],dimorphozethus[&&NHX:TOL=62458],diplomelinus[&&NHX:TOL=62459],echinozethus[&&NHX:TOL=62460],euplectomorphus[&&NHX:TOL=62461],hendecameros[&&NHX:TOL=62462],heptaleptus[&&NHX:TOL=62463],jeannelia[&&NHX:TOL=62464],leleupiozethus[&&NHX:TOL=62465],loebliozethus[&&NHX:TOL=62466],mecynozethus[&&NHX:TOL=62467],microzethinus[&&NHX:TOL=62468],microzethopsis[&&NHX:TOL=62469],neozethopsus[&&NHX:TOL=62470],nesiotozethus[&&NHX:TOL=62471],nipponozethus[&&NHX:TOL=62472],notozethus[&&NHX:TOL=62473],octomeros[&&NHX:TOL=62474],octozethodes[&&NHX:TOL=62475],octozethus[&&NHX:TOL=62476],opisthosphaera[&&NHX:TOL=62477],orazethus[&&NHX:TOL=62478],oxyzethodes[&&NHX:TOL=62479],oxyzethus[&&NHX:TOL=62480],pachyzethopsus[&&NHX:TOL=62481],petalozethopsis[&&NHX:TOL=62482],poeciloceras[&&NHX:TOL=62483],proboscites[&&NHX:TOL=62484],projeannelia[&&NHX:TOL=62485],protozethopsus[&&NHX:TOL=62486],pseudozethinus[&&NHX:TOL=62487],puripnozethus[&&NHX:TOL=62488],pyxidion[&&NHX:TOL=62489],rhinozethus[&&NHX:TOL=62490],schizocoryna[&&NHX:TOL=62491],selenozethus[&&NHX:TOL=62492],trizethopsis[&&NHX:TOL=62493],typhlozethodes[&&NHX:TOL=62494],typhlozethus[&&NHX:TOL=62495],urozethidius[&&NHX:TOL=62496],zethinomorphus[&&NHX:TOL=62497],zethinus[&&NHX:TOL=62498],zethopsinus[&&NHX:TOL=62499],zethopsiola[&&NHX:TOL=62500],zethopsoides[&&NHX:TOL=62501],zethopsus[&&NHX:TOL=62502])bythinoplectina[&&NHX:TOL=62438],(cerennea[&&NHX:TOL=62504],hughia[&&NHX:TOL=62505],megalocarpus[&&NHX:TOL=62506],nandius[&&NHX:TOL=62507],neopyxidicerus[&&NHX:TOL=62508],orlandia[&&NHX:TOL=62509],parapyxidicerus[&&NHX:TOL=62510],pyxidicerinus[&&NHX:TOL=62511],pyxidicerus[&&NHX:TOL=62512],pyxidizethus[&&NHX:TOL=62513])pyxidicerina[&&NHX:TOL=62503])bythinoplectini[&&NHX:TOL=62437],(barroeuplectoides[&&NHX:TOL=62515],ocabaraja[&&NHX:TOL=62516],octomicrellus[&&NHX:TOL=62517],octomicrites[&&NHX:TOL=62518],octomicrus[&&NHX:TOL=62519],tuberoplectus[&&NHX:TOL=62520])dimerini[&&NHX:TOL=62514],(acolonia[&&NHX:TOL=62522],(afroplectus afroplectaulax[&&NHX:TOL=62524],afroplectus afroplectidius[&&NHX:TOL=62525],afroplectus afroplectodes[&&NHX:TOL=62526],afroplectus afroplectus[&&NHX:TOL=62527])afroplectus[&&NHX:TOL=62523],anomoplectus[&&NHX:TOL=62528],austroeuplectus[&&NHX:TOL=62529],bothriocephalotes[&&NHX:TOL=62530],coptoplectus[&&NHX:TOL=62531],dissemoplectus[&&NHX:TOL=62532],dorrigo[&&NHX:TOL=62533],euplectamecia[&&NHX:TOL=62534],euplectus[&&NHX:TOL=62535],labroplectus[&&NHX:TOL=62536],leptoplectus[&&NHX:TOL=62537],mitrametopus[&&NHX:TOL=62538],okella[&&NHX:TOL=62539],plectoprotus[&&NHX:TOL=62540],pycnoplectus[&&NHX:TOL=62541],seleneuplectus[&&NHX:TOL=62542],tyxs[&&NHX:TOL=62543])euplectini[&&NHX:TOL=62521],(arctophysis[&&NHX:TOL=62545],auxenocerus[&&NHX:TOL=62546],balega[&&NHX:TOL=62547],barrojuba[&&NHX:TOL=62548],endytocera[&&NHX:TOL=62549],germainites[&&NHX:TOL=62550],jubomorphus[&&NHX:TOL=62551],jubus[&&NHX:TOL=62552],kuscheliotes[&&NHX:TOL=62553],macta[&&NHX:TOL=62554],phamisus[&&NHX:TOL=62555],pselaphomorphus[&&NHX:TOL=62556],sebaga[&&NHX:TOL=62557])jubini[&&NHX:TOL=62544],((mayetia mayetia[&&NHX:TOL=62560],mayetia metamayetia[&&NHX:TOL=62561],mayetia promayetia[&&NHX:TOL=62562])mayetia[&&NHX:TOL=62559],typhloleptodes[&&NHX:TOL=62563],typhloleptus[&&NHX:TOL=62564])mayetiini[&&NHX:TOL=62558],(hagnometopias[&&NHX:EXT=Y:TOL=62566],(barrometopia[&&NHX:TOL=62568],bibrax[&&NHX:TOL=62569],chandleria[&&NHX:TOL=62570],metopias[&&NHX:TOL=62571],metopiasoides[&&NHX:TOL=62572],metopiellus[&&NHX:TOL=62573],metopiosoma[&&NHX:TOL=62574],metopioxys[&&NHX:TOL=62575])metopiasina[&&NHX:TOL=62567],(rhinoscepsis rafrhisis[&&NHX:TOL=62578],rhinoscepsis rhinoscepsis[&&NHX:TOL=62579])rhinoscepsis[&&NHX:TOL=62576])metopiasini[&&NHX:TOL=62565],((aphilia[&&NHX:TOL=62583],apoterus[&&NHX:TOL=62584],bartle[&&NHX:TOL=62585],bibloporellus[&&NHX:TOL=62586],bibloporus[&&NHX:TOL=62587],chaetorhopalus[&&NHX:TOL=62588],epiplectus[&&NHX:TOL=62589],eupinion[&&NHX:TOL=62590],kuriporus[&&NHX:TOL=62591],narcissiella[&&NHX:TOL=62592],omobathus[&&NHX:TOL=62593],opisthosemus[&&NHX:TOL=62594],praeruptifrons[&&NHX:TOL=62595],typhlokahusia[&&NHX:TOL=62596])bibloporina[&&NHX:TOL=62582],(acetalius[&&NHX:TOL=62598],acotreba[&&NHX:TOL=62599],adalmus[&&NHX:TOL=62600],aloxomidus[&&NHX:TOL=62601],(aminosimus aminosimus[&&NHX:TOL=62603],aminosimus plectasymus[&&NHX:TOL=62604])aminosimus[&&NHX:TOL=62602],anotimus[&&NHX:TOL=62605],apheloplectus[&&NHX:TOL=62606],ararat[&&NHX:TOL=62607],(asymoplectus asymoplectodes[&&NHX:TOL=62609],asymoplectus asymoplectus[&&NHX:TOL=62610])asymoplectus[&&NHX:TOL=62608],aulaxus[&&NHX:TOL=62611],biblomelba[&&NHX:TOL=62612],biblomimus[&&NHX:TOL=62613],bibloplectinus[&&NHX:TOL=62614],bibloplectopsis[&&NHX:TOL=62615],(bibloplectus bibloplectodes[&&NHX:TOL=62617],bibloplectus bibloplectus[&&NHX:TOL=62618])bibloplectus[&&NHX:TOL=62616],bruxner[&&NHX:TOL=62619],calarus[&&NHX:TOL=62620],chichester[&&NHX:TOL=62621],cleland[&&NHX:TOL=62622],dalma[&&NHX:TOL=62623],dalmisus[&&NHX:TOL=62624],dandenong[&&NHX:TOL=62625],deroplectus[&&NHX:TOL=62626],diarrogus[&&NHX:TOL=62627],dungog[&&NHX:TOL=62628],eleusomatus[&&NHX:TOL=62629],epithematus[&&NHX:TOL=62630],euglyptus[&&NHX:TOL=62631],eungella[&&NHX:TOL=62632],euphiliops[&&NHX:TOL=62633],euplectina[&&NHX:TOL=62634],euplectodina[&&NHX:TOL=62635],euplectops[&&NHX:TOL=62636],euplectopsis[&&NHX:TOL=62637],(eutyphlus eutyphlus[&&NHX:TOL=62639],eutyphlus planityphlus[&&NHX:TOL=62640])eutyphlus[&&NHX:TOL=62638],fijiastes[&&NHX:TOL=62641],forinus[&&NHX:TOL=62642],gabata[&&NHX:TOL=62643],glastus[&&NHX:TOL=62644],gordon[&&NHX:TOL=62645],gubarra[&&NHX:TOL=62646],haploplectus[&&NHX:TOL=62647],hatchia[&&NHX:TOL=62648],humbertella[&&NHX:TOL=62649],(hypoplectus hypoplectinus[&&NHX:TOL=62651],hypoplectus hypoplectus[&&NHX:TOL=62652])hypoplectus[&&NHX:TOL=62650],joalah[&&NHX:TOL=62653],kapalga[&&NHX:TOL=62654],kenocoelus[&&NHX:TOL=62655],kioloa[&&NHX:TOL=62656],kyogle[&&NHX:TOL=62657],lioplectus[&&NHX:TOL=62658],(meliceria cyrtoplectus[&&NHX:TOL=62660],meliceria meliceria[&&NHX:TOL=62661])meliceria[&&NHX:TOL=62659],metaplectodes[&&NHX:TOL=62662],methorius[&&NHX:TOL=62663],mexigaster[&&NHX:TOL=62664],miallo[&&NHX:TOL=62665],microplectus[&&NHX:TOL=62666],millaa[&&NHX:TOL=62667],mirellus[&&NHX:TOL=62668],namssom[&&NHX:TOL=62669],neoplectidius[&&NHX:TOL=62670],neothesiastes[&&NHX:TOL=62671],nesiotoplectus[&&NHX:TOL=62672],noota[&&NHX:TOL=62673],omotimellus[&&NHX:TOL=62674],omotimiotes[&&NHX:TOL=62675],omotimus[&&NHX:TOL=62676],pachyeuplectus[&&NHX:TOL=62677],panaphantus[&&NHX:TOL=62678],paraphiliopsis[&&NHX:TOL=62679],paraplectus[&&NHX:TOL=62680],patreus[&&NHX:TOL=62681],perditadens[&&NHX:TOL=62682],periplectus[&&NHX:TOL=62683],philiopsis[&&NHX:TOL=62684],philoscotus[&&NHX:TOL=62685],piptoncus[&&NHX:TOL=62686],placodium[&&NHX:TOL=62687],plectiastes[&&NHX:TOL=62688],plectodytes[&&NHX:TOL=62689],plectomorphus[&&NHX:TOL=62690],plectophloeus[&&NHX:TOL=62691],prodalma[&&NHX:TOL=62692],pseudactium[&&NHX:TOL=62693],pseudomotimus[&&NHX:TOL=62694],pseudoplectus[&&NHX:TOL=62695],pteroplectus[&&NHX:TOL=62696],quotidiaplectus[&&NHX:TOL=62697],ramecia[&&NHX:TOL=62698],ramussia[&&NHX:TOL=62699],rhynchoplectus[&&NHX:TOL=62700],sagolonus[&&NHX:TOL=62701],sampsa[&&NHX:TOL=62702],saxet[&&NHX:TOL=62703],scabritia[&&NHX:TOL=62704],scotoplectus[&&NHX:TOL=62705],sealy[&&NHX:TOL=62706],thesiastes[&&NHX:TOL=62707],thesium[&&NHX:TOL=62708],tiliactus[&&NHX:TOL=62709],tooloom[&&NHX:TOL=62710],torvicia[&&NHX:TOL=62711],trigonoplectus[&&NHX:TOL=62712],trimiophanes[&&NHX:TOL=62713],trimioplectus[&&NHX:TOL=62714],trisignis[&&NHX:TOL=62715],vidamodes[&&NHX:TOL=62716],vidamus[&&NHX:TOL=62717],whitea[&&NHX:TOL=62718],whyanbeel[&&NHX:TOL=62719],xyts[&&NHX:TOL=62720],zelandius[&&NHX:TOL=62721])panaphantina[&&NHX:TOL=62597],(abdiunguis[&&NHX:TOL=62723],allodalminiastes[&&NHX:TOL=62724],amauronyx[&&NHX:TOL=62725],ambalavoa[&&NHX:TOL=62726],andiotes[&&NHX:TOL=62727],andiplectops[&&NHX:TOL=62728],ankavena[&&NHX:TOL=62729],anoplectus[&&NHX:TOL=62730],apotectus[&&NHX:TOL=62731],araucaniotes[&&NHX:TOL=62732],badensia[&&NHX:TOL=62733],barrengarry[&&NHX:TOL=62734],bithongabel[&&NHX:TOL=62735],bontomtes[&&NHX:TOL=62736],caligrua[&&NHX:TOL=62737],caligruacmes[&&NHX:TOL=62738],chrestomera[&&NHX:TOL=62739],clyde[&&NHX:TOL=62740],daliacmes[&&NHX:TOL=62741],(dalmina dalmina[&&NHX:TOL=62743],dalmina dalminiola[&&NHX:TOL=62744])dalmina[&&NHX:TOL=62742],dalminella[&&NHX:TOL=62745],dalminia[&&NHX:TOL=62746],dalminiastes[&&NHX:TOL=62747],dalminiomus[&&NHX:TOL=62748],damilinidius[&&NHX:TOL=62749],epullea[&&NHX:TOL=62750],etopias[&&NHX:TOL=62751],euplecterga[&&NHX:TOL=62752],fanoridius[&&NHX:TOL=62753],faronoma[&&NHX:TOL=62754],foveoscapha[&&NHX:TOL=62755],frutillariotes[&&NHX:TOL=62756],imeriniella[&&NHX:TOL=62757],jindabyne[&&NHX:TOL=62758],kerplectus[&&NHX:TOL=62759],macroplectus[&&NHX:TOL=62760],macroraffrayia[&&NHX:TOL=62761],meithton[&&NHX:TOL=62762],mexiplectus[&&NHX:TOL=62763],mildana[&&NHX:TOL=62764],morius[&&NHX:TOL=62765],namunia[&&NHX:TOL=62766],neoraffrayia[&&NHX:TOL=62767],nothoplectus[&&NHX:TOL=62768],oropodes[&&NHX:TOL=62769],panaramecia[&&NHX:TOL=62770],parapteracmes[&&NHX:TOL=62771],parepullea[&&NHX:TOL=62772],platyplectus[&&NHX:TOL=62773],plectostenus[&&NHX:TOL=62774],plectusodes[&&NHX:TOL=62775],protoplectus[&&NHX:TOL=62776],pseudeuplectus[&&NHX:TOL=62777],pseudocaligrua[&&NHX:TOL=62778],pteracmes[&&NHX:TOL=62779],pteracmidius[&&NHX:TOL=62780],raffrayia[&&NHX:TOL=62781],raffrayidius[&&NHX:TOL=62782],(raffrayites raffrayites[&&NHX:TOL=62784],raffrayites raffrayitidia[&&NHX:TOL=62785])raffrayites[&&NHX:TOL=62783],raffrayola[&&NHX:TOL=62786],(ranavala fanovana[&&NHX:TOL=62788],ranavala masoala[&&NHX:TOL=62789],ranavala ranavala[&&NHX:TOL=62790])ranavala[&&NHX:TOL=62787],ranavalidius[&&NHX:TOL=62791],ranavalodes[&&NHX:TOL=62792],stenoplectus[&&NHX:TOL=62793],tetrascapha[&&NHX:TOL=62794],thelotia[&&NHX:TOL=62795],thesiectus[&&NHX:TOL=62796],tiomomus[&&NHX:TOL=62797],trepacmes[&&NHX:TOL=62798],trichonyx[&&NHX:TOL=62799],trimiodytes[&&NHX:TOL=62800],tumucania[&&NHX:TOL=62801],typhloraffrayia[&&NHX:TOL=62802],unumgar[&&NHX:TOL=62803],verabarolus[&&NHX:TOL=62804],washpool[&&NHX:TOL=62805],xenogyna[&&NHX:TOL=62806],xenogynidia[&&NHX:TOL=62807])trichonychina[&&NHX:TOL=62722],(actiastes[&&NHX:TOL=62809],actionoma[&&NHX:TOL=62810],actium[&&NHX:TOL=62811],actizona[&&NHX:TOL=62812],allobrox[&&NHX:TOL=62813],allomelba[&&NHX:TOL=62814],alloplectus[&&NHX:TOL=62815],allotrimium[&&NHX:TOL=62816],amudrocerus[&&NHX:TOL=62817],aphiliops[&&NHX:TOL=62818],armidale[&&NHX:TOL=62819],cupila[&&NHX:TOL=62820],dalmomelba[&&NHX:TOL=62821],dalmoplectus[&&NHX:TOL=62822],dalmosanus[&&NHX:TOL=62823],dalmosella[&&NHX:TOL=62824],gayundah[&&NHX:TOL=62825],haasellia[&&NHX:TOL=62826],hanfordia[&&NHX:TOL=62827],hispanisella[&&NHX:TOL=62828],latomelba[&&NHX:TOL=62829],lemelba[&&NHX:TOL=62830],leptophiliops[&&NHX:TOL=62831],limoniates[&&NHX:TOL=62832],malleoceps[&&NHX:TOL=62833],(melba asymmelba[&&NHX:TOL=62835],melba cismelba[&&NHX:TOL=62836],melba frontelba[&&NHX:TOL=62837],melba melba[&&NHX:TOL=62838],melba rameloidea[&&NHX:TOL=62839],melba vertelba[&&NHX:TOL=62840])melba[&&NHX:TOL=62834],melbamima[&&NHX:TOL=62841],minibi[&&NHX:TOL=62842],neactium[&&NHX:TOL=62843],neodalmus[&&NHX:TOL=62844],paractium[&&NHX:TOL=62845],perimelba[&&NHX:TOL=62846],pilactium[&&NHX:TOL=62847],prophilus[&&NHX:TOL=62848],pseudotrimium[&&NHX:TOL=62849],quadrelba[&&NHX:TOL=62850],ramelbida[&&NHX:TOL=62851],sandersonella[&&NHX:TOL=62852],saulcyella[&&NHX:TOL=62853],simplona[&&NHX:TOL=62854],tomoplectus[&&NHX:TOL=62855],trimioarcus[&&NHX:TOL=62856],trimiodina[&&NHX:TOL=62857],trimiomelba[&&NHX:TOL=62858],trimiomorphus[&&NHX:TOL=62859],trimiopsis[&&NHX:TOL=62860],trimiosella[&&NHX:TOL=62861],trimiovillus[&&NHX:TOL=62862],trimium[&&NHX:TOL=62863],zibus[&&NHX:TOL=62864],zolium[&&NHX:TOL=62865],zonaira[&&NHX:TOL=62866])trimiina[&&NHX:TOL=62808])trichonychini[&&NHX:TOL=62581],(phtegnomus[&&NHX:TOL=62868],(austrorhexius[&&NHX:TOL=62872],(rhexius rafrhexius[&&NHX:TOL=62874],rhexius rhexinexus[&&NHX:TOL=62875],rhexius rhexius[&&NHX:TOL=62876])rhexius[&&NHX:TOL=62873])rhexiina[&&NHX:TOL=62871],(aboeurhexius[&&NHX:TOL=62878],adrogaster[&&NHX:TOL=62879],anarmodius[&&NHX:TOL=62880],aporhexius[&&NHX:TOL=62881],conoplectus[&&NHX:TOL=62882],euboarhexius[&&NHX:TOL=62883],eurhexius[&&NHX:TOL=62884],fletcherexius[&&NHX:TOL=62885],mesoplatus[&&NHX:TOL=62886],neosampa[&&NHX:TOL=62887],oropus[&&NHX:TOL=62888],platomesus[&&NHX:TOL=62889],rhexidius[&&NHX:TOL=62890],rhexinia[&&NHX:TOL=62891],rhexiola[&&NHX:TOL=62892],tomeplasus[&&NHX:TOL=62893],trogaster[&&NHX:TOL=62894],trogasteropsis[&&NHX:TOL=62895],xerhius[&&NHX:TOL=62896])trogastrina[&&NHX:TOL=62877])trogastrini[&&NHX:TOL=62867])euplectitae[&&NHX:TOL=62429],(delenda[&&NHX:TOL=62898],exeirarthra[&&NHX:TOL=62899],faronidiellus[&&NHX:TOL=62900],faronidius[&&NHX:TOL=62901],faronites[&&NHX:TOL=62902],faronitopsis[&&NHX:TOL=62903],faronus[&&NHX:TOL=62904],golasa[&&NHX:TOL=62905],golasidius[&&NHX:TOL=62906],golasina[&&NHX:TOL=62907],golasites[&&NHX:TOL=62908],logasa[&&NHX:TOL=62909],(megarafonus megarafonus[&&NHX:TOL=62911],megarafonus nafonus[&&NHX:TOL=62912],megarafonus nanorafonus[&&NHX:TOL=62913])megarafonus[&&NHX:TOL=62910],nugaculus[&&NHX:EXT=Y:TOL=62914],parafaronus[&&NHX:TOL=62915],prosagola[&&NHX:TOL=62916],sagola[&&NHX:TOL=62917],salagosa[&&NHX:TOL=62918],salagosita[&&NHX:TOL=62919],sonoma[&&NHX:TOL=62920],stenosagola[&&NHX:TOL=62921])faronitae[&&NHX:TOL=62897],((awas[&&NHX:TOL=62924],harmophorus[&&NHX:TOL=62925])arnylliini[&&NHX:TOL=62923],barrosellus[&&NHX:TOL=62926],(barybryaxis[&&NHX:EXT=Y:TOL=62930],(euphalepsus[&&NHX:TOL=62932],phalespoides[&&NHX:TOL=62933])baradina[&&NHX:TOL=62931],(acamaldes[&&NHX:TOL=62935],achilia[&&NHX:TOL=62936],achillidia[&&NHX:TOL=62937],achilliotes[&&NHX:TOL=62938],anabaxis[&&NHX:TOL=62939],anarmoxys[&&NHX:TOL=62940],anasidius[&&NHX:TOL=62941],anasopsis[&&NHX:TOL=62942],anchylarthron[&&NHX:TOL=62943],antipodebaxis[&&NHX:TOL=62944],arachis[&&NHX:TOL=62945],araneabaxis[&&NHX:TOL=62946],asanis[&&NHX:TOL=62947],atacamia[&&NHX:TOL=62948],atenisodus[&&NHX:TOL=62949],baraxina[&&NHX:TOL=62950],batraxis[&&NHX:TOL=62951],baxyridius[&&NHX:TOL=62952],baxyris[&&NHX:TOL=62953],berdura[&&NHX:TOL=62954],booloumba[&&NHX:TOL=62955],brachygluta[&&NHX:TOL=62956],braxyda[&&NHX:TOL=62957],briara[&&NHX:TOL=62958],briaraxis[&&NHX:TOL=62959],bryaxella[&&NHX:TOL=62960],bryaxina[&&NHX:TOL=62961],bryaxinella[&&NHX:TOL=62962],bryaxonoma[&&NHX:TOL=62963],bundjulung[&&NHX:TOL=62964],bunoderus[&&NHX:TOL=62965],byraxorites[&&NHX:TOL=62966],bythinogaster[&&NHX:TOL=62967],caligocara[&&NHX:TOL=62968],comatopselaphus[&&NHX:TOL=62969],cryptorhinula[&&NHX:TOL=62970],dicrobiotus[&&NHX:TOL=62971],diroptrus[&&NHX:TOL=62972],(drasinus drasinus[&&NHX:TOL=62974],drasinus paradrasinus[&&NHX:TOL=62975])drasinus[&&NHX:TOL=62973],ectopocerus[&&NHX:TOL=62976],ephymata[&&NHX:TOL=62977],eremomus[&&NHX:TOL=62978],ergasteriocerus[&&NHX:TOL=62979],eupifigia[&&NHX:TOL=62980],eupinella[&&NHX:TOL=62981],(eupines byraxis[&&NHX:TOL=62983],eupines eupines[&&NHX:TOL=62984])eupines[&&NHX:TOL=62982],eupinidius[&&NHX:TOL=62985],eupinogitus[&&NHX:TOL=62986],eupinolus[&&NHX:TOL=62987],eupinopsis[&&NHX:TOL=62988],eutrichites[&&NHX:TOL=62989],fagniezia[&&NHX:TOL=62990],gastrobothrus[&&NHX:TOL=62991],ghesquierites[&&NHX:TOL=62992],globa[&&NHX:TOL=62993],iluka[&&NHX:TOL=62994],leiochrotella[&&NHX:TOL=62995],leiochrotidius[&&NHX:TOL=62996],leptachillia[&&NHX:TOL=62997],leptorrachis[&&NHX:TOL=62998],mallanganee[&&NHX:TOL=62999],mallecoa[&&NHX:TOL=63000],malleecola[&&NHX:TOL=63001],mitona[&&NHX:TOL=63002],mundaring[&&NHX:TOL=63003],nisaxis[&&NHX:TOL=63004],noduliceps[&&NHX:TOL=63005],nondulia[&&NHX:TOL=63006],obricala[&&NHX:TOL=63007],paluma[&&NHX:TOL=63008],panabachia[&&NHX:TOL=63009],parachillia[&&NHX:TOL=63010],pedisinops[&&NHX:TOL=63011],physobryaxis[&&NHX:TOL=63012],physoplectus[&&NHX:TOL=63013],plectrobythus[&&NHX:TOL=63014],prosthecarthron[&&NHX:TOL=63015],pselaptus[&&NHX:TOL=63016],pseudachillia[&&NHX:TOL=63017],pseudachillidia[&&NHX:TOL=63018],pseudocamaldes[&&NHX:TOL=63019],(rabyxis pseudobaxyris[&&NHX:TOL=63021],rabyxis rabyxis[&&NHX:TOL=63022])rabyxis[&&NHX:TOL=63020],raxybis[&&NHX:TOL=63023],reichenbachella[&&NHX:TOL=63024],reichenbachia[&&NHX:TOL=63025],rougemontiella[&&NHX:TOL=63026],rybaxidia[&&NHX:TOL=63027],rybaxis[&&NHX:TOL=63028],scalenarthrus[&&NHX:TOL=63029],silillicus[&&NHX:TOL=63030],simkinion[&&NHX:TOL=63031],speobaxyris[&&NHX:TOL=63032],startes[&&NHX:TOL=63033],storeyella[&&NHX:TOL=63034],strombopsis[&&NHX:TOL=63035],tremissus[&&NHX:TOL=63036],tribatus[&&NHX:TOL=63037],triomicrus[&&NHX:TOL=63038],(trissemus apotrissemus[&&NHX:TOL=63040],trissemus corynecerus[&&NHX:TOL=63041],trissemus trissemidius[&&NHX:TOL=63042],trissemus trissemodes[&&NHX:TOL=63043],trissemus trissemus[&&NHX:TOL=63044])trissemus[&&NHX:TOL=63039],vasse[&&NHX:TOL=63045],wataranka[&&NHX:TOL=63046],wiangaree[&&NHX:TOL=63047],wollomombi[&&NHX:TOL=63048],woodenbong[&&NHX:TOL=63049],xenobryaxis[&&NHX:TOL=63050],xiphobythus[&&NHX:TOL=63051],xybarida[&&NHX:TOL=63052],xybaris[&&NHX:TOL=63053])brachyglutina[&&NHX:TOL=62934],((decarthron decarfuss[&&NHX:TOL=63056],decarthron decarthron[&&NHX:TOL=63057])decarthron[&&NHX:TOL=63055],euteleia[&&NHX:TOL=63058],raffrayolus[&&NHX:TOL=63059])decarthrina[&&NHX:TOL=63054],(eupsenina[&&NHX:TOL=63061],eupsenius[&&NHX:TOL=63062])eupseniina[&&NHX:TOL=63060])brachyglutini[&&NHX:TOL=62929],(antrobythus[&&NHX:TOL=63064],bathybythus[&&NHX:TOL=63065],bryaxis[&&NHX:TOL=63066],bythinus[&&NHX:TOL=63067],bythoxenites[&&NHX:TOL=63068],bythoxenus[&&NHX:TOL=63069],ceratobythus[&&NHX:TOL=63070],decatocerus[&&NHX:TOL=63071],gasparobythus[&&NHX:TOL=63072],glyphobythus[&&NHX:TOL=63073],leptobythus[&&NHX:TOL=63074],linderia[&&NHX:TOL=63075],machaerites[&&NHX:TOL=63076],machaerodes[&&NHX:TOL=63077],mangalobythus[&&NHX:TOL=63078],nonveilleria[&&NHX:TOL=63079],pauperobythus[&&NHX:TOL=63080],prionobythus[&&NHX:TOL=63081],(pselaptrichus pselaptrichus[&&NHX:TOL=63083],pselaptrichus vestitrichus[&&NHX:TOL=63084])pselaptrichus[&&NHX:TOL=63082],spelaeobythus[&&NHX:TOL=63085],speleochus[&&NHX:TOL=63086],subterrochus[&&NHX:TOL=63087],tychobythinus[&&NHX:TOL=63088],typhlobythus[&&NHX:TOL=63089],xenobythus[&&NHX:TOL=63090])bythinini[&&NHX:TOL=63063],plagiophorus[&&NHX:TOL=63091],(adrocerus[&&NHX:TOL=63095],basilewskydiella[&&NHX:TOL=63096],bredoella[&&NHX:TOL=63097],debeckeria[&&NHX:TOL=63098],enneameron[&&NHX:TOL=63099],goniaceroides[&&NHX:TOL=63100],goniacerus[&&NHX:TOL=63101],goniastes[&&NHX:TOL=63102],heptameron[&&NHX:TOL=63103],ipsimodes[&&NHX:TOL=63104],ipsimus[&&NHX:TOL=63105],kistneriella[&&NHX:TOL=63106],leleupites[&&NHX:TOL=63107],listriophorus[&&NHX:TOL=63108],microgmocerus[&&NHX:TOL=63109],notogmocerus[&&NHX:TOL=63110],ogmoceridius[&&NHX:TOL=63111],ogmocerodes[&&NHX:TOL=63112],ogmoceropsis[&&NHX:TOL=63113],ogmocerus[&&NHX:TOL=63114],paragoniastes[&&NHX:TOL=63115],parasimus[&&NHX:TOL=63116],vadonites[&&NHX:TOL=63117],xenogmocerodes[&&NHX:TOL=63118])goniacerini[&&NHX:TOL=63094],imirus[&&NHX:TOL=63119],((anoplobraxis[&&NHX:TOL=63124],auchenotropidius[&&NHX:TOL=63125],auchenotropis[&&NHX:TOL=63126],batriphysis[&&NHX:TOL=63127],batrisobryaxis[&&NHX:TOL=63128],brunomanseria[&&NHX:TOL=63129],bythinophysis[&&NHX:TOL=63130],bythonesiotes[&&NHX:TOL=63131],capnites[&&NHX:TOL=63132],dalmoburis[&&NHX:TOL=63133],dalmodes[&&NHX:TOL=63134],dalmomima[&&NHX:TOL=63135],dalmonexus[&&NHX:TOL=63136],dalmophysis[&&NHX:TOL=63137],globosulus[&&NHX:TOL=63138],iniocyphus[&&NHX:TOL=63139],leleupiella[&&NHX:TOL=63140],maya[&&NHX:TOL=63141],morana[&&NHX:TOL=63142],nipponobythus[&&NHX:TOL=63143],phybytharsis[&&NHX:TOL=63144],rugegius[&&NHX:TOL=63145],sogaella[&&NHX:TOL=63146],(sunorfa sunorfa[&&NHX:TOL=63148],sunorfa sunorfoides[&&NHX:TOL=63149])sunorfa[&&NHX:TOL=63147],takaorites[&&NHX:TOL=63150],trimicerus[&&NHX:TOL=63151])iniocyphina[&&NHX:TOL=63123],(acrocomus[&&NHX:TOL=63153],apoplectus[&&NHX:TOL=63154],natypleurus[&&NHX:TOL=63155],nedarassus[&&NHX:TOL=63156],simplicorfa[&&NHX:TOL=63157])natypleurina[&&NHX:TOL=63152])iniocyphini[&&NHX:TOL=63122],machadous[&&NHX:TOL=63158],(aulacobythus[&&NHX:TOL=63162],berlaraxis[&&NHX:TOL=63163],breguetiella[&&NHX:TOL=63164],bythinoderes[&&NHX:TOL=63165],bythinophanax[&&NHX:TOL=63166],cephalaxis[&&NHX:TOL=63167],craspedopterus[&&NHX:TOL=63168],delamarea[&&NHX:TOL=63169],ectoparyphidius[&&NHX:TOL=63170],ectoparyphodes[&&NHX:TOL=63171],ectoparyphus[&&NHX:TOL=63172],elaphobythus[&&NHX:TOL=63173],euharmophola[&&NHX:TOL=63174],gnesion[&&NHX:TOL=63175],goniomellus[&&NHX:TOL=63176],harmomima[&&NHX:TOL=63177],harmophola[&&NHX:TOL=63178],hypoparyphantus[&&NHX:TOL=63179],imtempus[&&NHX:TOL=63180],loebliobythus[&&NHX:TOL=63181],mechanicus[&&NHX:TOL=63182],mimoplectus[&&NHX:TOL=63183],neodeuterus[&&NHX:TOL=63184],oxygastrobythus[&&NHX:TOL=63185],pareuplectops[&&NHX:TOL=63186],paryphantellus[&&NHX:TOL=63187],paryphopterus[&&NHX:TOL=63188],phthartomicrus[&&NHX:TOL=63189],platycerobythus[&&NHX:TOL=63190],proterus[&&NHX:TOL=63191],pseudoterus[&&NHX:TOL=63192],rhamophorus[&&NHX:TOL=63193],rossites[&&NHX:TOL=63194],salpictomelus[&&NHX:TOL=63195],ulugurubythus[&&NHX:TOL=63196])proterini[&&NHX:TOL=63161],pygoxyon[&&NHX:TOL=63197],((prespelea fusjuguma[&&NHX:TOL=63202],prespelea prespelea[&&NHX:TOL=63203])prespelea[&&NHX:TOL=63201],speleobama[&&NHX:TOL=63204])speleobamini[&&NHX:TOL=63200],(atychodea[&&NHX:TOL=63206],custotychus[&&NHX:TOL=63207],cylindrarctus[&&NHX:TOL=63208],hesperotychus[&&NHX:TOL=63209],hyugatychus[&&NHX:TOL=63210],lucifotychus[&&NHX:TOL=63211],nearctitychus[&&NHX:TOL=63212],ouachitychus[&&NHX:TOL=63213],paratychus[&&NHX:TOL=63214],tainochus[&&NHX:TOL=63215],tychomorphus[&&NHX:TOL=63216],tychus[&&NHX:TOL=63217])tychini[&&NHX:TOL=63205],valda[&&NHX:TOL=63218])goniaceritae[&&NHX:TOL=62922],((caccoplectinus[&&NHX:TOL=63223],caccoplectus[&&NHX:TOL=63224],eichiella[&&NHX:TOL=63225],holozodinus[&&NHX:TOL=63226],holozodoides[&&NHX:TOL=63227],holozodus[&&NHX:TOL=63228],madabaxyris[&&NHX:TOL=63229],pachacuti[&&NHX:TOL=63230],rhytus[&&NHX:TOL=63231],sabarhytus[&&NHX:TOL=63232],tetraglyptinus[&&NHX:TOL=63233],tetraglyptus[&&NHX:TOL=63234],tolga[&&NHX:TOL=63235],woldenka[&&NHX:TOL=63236])arhytodini[&&NHX:TOL=63222],attapsenius[&&NHX:TOL=63237],(atinus[&&NHX:TOL=63241],biotus[&&NHX:TOL=63242],centrotoma[&&NHX:TOL=63243],chenniopsis[&&NHX:TOL=63244],chennium[&&NHX:TOL=63245],ctenicellus[&&NHX:TOL=63246],ctenisis[&&NHX:TOL=63247],ctenisodes[&&NHX:TOL=63248],ctenisomimus[&&NHX:TOL=63249],ctenisomorphus[&&NHX:TOL=63250],ctenisophanes[&&NHX:TOL=63251],ctenisophus[&&NHX:TOL=63252],ctenisoschema[&&NHX:TOL=63253],(ctenistes ctenistes[&&NHX:TOL=63255],ctenistes tecnesis[&&NHX:TOL=63256],ctenistes tecnesites[&&NHX:TOL=63257])ctenistes[&&NHX:TOL=63254],ctenistidius[&&NHX:TOL=63258],ctenistodes[&&NHX:EXT=Y:TOL=63259],ctenistodites[&&NHX:TOL=63260],daveyia[&&NHX:TOL=63261],(desimia desimia[&&NHX:TOL=63263],desimia desimiella[&&NHX:TOL=63264],desimia xenodesimia[&&NHX:TOL=63265])desimia[&&NHX:TOL=63262],edocranes[&&NHX:TOL=63266],enoptostomus[&&NHX:TOL=63267],epicaris[&&NHX:TOL=63268],gnorosus[&&NHX:TOL=63269],hynneophorus[&&NHX:TOL=63270],laphidioderomimus[&&NHX:TOL=63271],laphidioderus[&&NHX:TOL=63272],largeyeus[&&NHX:TOL=63273],metactenistes[&&NHX:TOL=63274],parastectenis[&&NHX:TOL=63275],poroderopsis[&&NHX:TOL=63276],poroderus[&&NHX:TOL=63277],sognorus[&&NHX:TOL=63278],stectenidius[&&NHX:TOL=63279])ctenistini[&&NHX:TOL=63240],(acmoeonotus[&&NHX:TOL=63281],apharina[&&NHX:TOL=63282],apharinodes[&&NHX:TOL=63283],filigerinus[&&NHX:TOL=63284],filigerodes[&&NHX:TOL=63285],hybocephalodes[&&NHX:TOL=63286],hybocephalus[&&NHX:TOL=63287],mecochelia[&&NHX:TOL=63288],(mestogaster mestogaster[&&NHX:TOL=63290],mestogaster mestogastridius[&&NHX:TOL=63291])mestogaster[&&NHX:TOL=63289],pseudapharina[&&NHX:TOL=63292],stipesa[&&NHX:TOL=63293])hybocephalini[&&NHX:TOL=63280],(algodontodes[&&NHX:TOL=63295],algodontus[&&NHX:TOL=63296],madontalgus[&&NHX:TOL=63297],odontalgus[&&NHX:TOL=63298],warrumbungle[&&NHX:TOL=63299])odontalgini[&&NHX:TOL=63294],(pachygastrodes[&&NHX:TOL=63301],pachygastrodirius[&&NHX:TOL=63302])pachygastrodini[&&NHX:TOL=63300],phalepsus[&&NHX:TOL=63303],(afropselaphus[&&NHX:TOL=63307],bellenden[&&NHX:TOL=63308],curculionellus[&&NHX:TOL=63309],dicentrius[&&NHX:TOL=63310],geopselaphus[&&NHX:TOL=63311],hirashimanymus[&&NHX:TOL=63312],kakadu[&&NHX:TOL=63313],mareeba[&&NHX:TOL=63314],margaris[&&NHX:TOL=63315],maydena[&&NHX:TOL=63316],mentraphus[&&NHX:TOL=63317],nabepselaphus[&&NHX:TOL=63318],neopselaphus[&&NHX:TOL=63319],peckiella[&&NHX:TOL=63320],(pselaphaulax neopselaphaulax[&&NHX:TOL=63322],pselaphaulax pselaphaulax[&&NHX:TOL=63323])pselaphaulax[&&NHX:TOL=63321],pselaphellus[&&NHX:TOL=63324],pselaphischnus[&&NHX:TOL=63325],pselaphogenius[&&NHX:TOL=63326],pselaphophus[&&NHX:TOL=63327],pselaphorites[&&NHX:TOL=63328],pselaphostomus[&&NHX:TOL=63329],pselaphotheseus[&&NHX:TOL=63330],pselaphotrichus[&&NHX:TOL=63331],pselaphus[&&NHX:TOL=63332],tyraphus[&&NHX:TOL=63333])pselaphini[&&NHX:TOL=63306],(leanymus[&&NHX:TOL=63335],schistodactylus[&&NHX:TOL=63336])schistodactylini[&&NHX:TOL=63334],(afrotyrus[&&NHX:TOL=63338],ancystrocerus[&&NHX:TOL=63339],aphanethrix[&&NHX:TOL=63340],brinckidiella[&&NHX:TOL=63341],chandleriella[&&NHX:TOL=63342],ctenotillus[&&NHX:TOL=63343],dacnotillus[&&NHX:TOL=63344],eudranes[&&NHX:TOL=63345],gasterotropis[&&NHX:TOL=63346],itombworites[&&NHX:TOL=63347],jardine[&&NHX:TOL=63348],machadoites[&&NHX:TOL=63349],neosintectes[&&NHX:TOL=63350],pselaphocerodes[&&NHX:TOL=63351],pselaphocerus[&&NHX:TOL=63352],pseudophanias[&&NHX:TOL=63353],raphitreodes[&&NHX:TOL=63354],raphitreus[&&NHX:TOL=63355],riphaterus[&&NHX:TOL=63356],saltisedes[&&NHX:TOL=63357],smilestethus[&&NHX:TOL=63358],stethotaphrus[&&NHX:TOL=63359],syntectodes[&&NHX:TOL=63360],tapiloites[&&NHX:TOL=63361],tmesiphorinus[&&NHX:TOL=63362],tmesiphorites[&&NHX:TOL=63363],tmesiphoroides[&&NHX:EXT=Y:TOL=63364],tmesiphoromimus[&&NHX:TOL=63365],tmesiphorus[&&NHX:TOL=63366],tropeogaster[&&NHX:TOL=63367],tyrocarius[&&NHX:TOL=63368],xenotmesiphorus[&&NHX:TOL=63369])tmesiphorini[&&NHX:TOL=63337],(cymbalizon[&&NHX:EXT=Y:TOL=63371],dantiscanus[&&NHX:EXT=Y:TOL=63372],deuterotyrus[&&NHX:EXT=Y:TOL=63373],pammiges[&&NHX:EXT=Y:TOL=63374],(camaldosis[&&NHX:TOL=63376],centrophthalmina[&&NHX:TOL=63377],centrophthalmus[&&NHX:TOL=63378],enantius[&&NHX:TOL=63379])centrophthalmina[&&NHX:TOL=63375],janusculus[&&NHX:TOL=63380],(acylobythus[&&NHX:TOL=63384],acylopselaphus[&&NHX:TOL=63385],acylotyrus[&&NHX:TOL=63386],apharus[&&NHX:TOL=63387],aploderina[&&NHX:TOL=63388],cercoceroides[&&NHX:TOL=63389],cercoceropsis[&&NHX:TOL=63390],cercocerulus[&&NHX:TOL=63391],circocerus[&&NHX:TOL=63392],elaphidipalpus[&&NHX:TOL=63393],ephimia[&&NHX:TOL=63394],googarna[&&NHX:TOL=63395],hamotidius[&&NHX:TOL=63396],hamotocellus[&&NHX:TOL=63397],hamotopsis[&&NHX:TOL=63398],(hamotus hamotoides[&&NHX:TOL=63400],hamotus hamotus[&&NHX:TOL=63401])hamotus[&&NHX:TOL=63399],himepion[&&NHX:TOL=63402],horniella[&&NHX:TOL=63403],motschtyrus[&&NHX:TOL=63404],phamisulus[&&NHX:TOL=63405],pselaphocompsus[&&NHX:TOL=63406],pseudohamotus[&&NHX:TOL=63407],pseudotychus[&&NHX:TOL=63408],somatipion[&&NHX:TOL=63409],swan[&&NHX:TOL=63410])somatipionina[&&NHX:TOL=63383],(abascantodes[&&NHX:TOL=63412],agatyrus[&&NHX:TOL=63413],anagonus[&&NHX:TOL=63414],anitra[&&NHX:TOL=63415],bansartiella[&&NHX:TOL=63416],(cedius cedius[&&NHX:TOL=63418],cedius sinistrocedius[&&NHX:TOL=63419])cedius[&&NHX:TOL=63417],ceophyllus[&&NHX:TOL=63420],chalcoplectus[&&NHX:TOL=63421],chasoke[&&NHX:TOL=63422],collacerothorax[&&NHX:TOL=63423],decumarellus[&&NHX:TOL=63424],durbos[&&NHX:TOL=63425],franziotus[&&NHX:TOL=63426],gerallus[&&NHX:TOL=63427],hamotulus[&&NHX:TOL=63428],indophodes[&&NHX:TOL=63429],kiera[&&NHX:TOL=63430],labomimus[&&NHX:TOL=63431],lasinus[&&NHX:TOL=63432],lethenomus[&&NHX:TOL=63433],linan[&&NHX:TOL=63434],marellus[&&NHX:TOL=63435],megatyrus[&&NHX:TOL=63436],mipseltyrus[&&NHX:TOL=63437],narrabeen[&&NHX:TOL=63438],neotyropsis[&&NHX:TOL=63439],neotyrus[&&NHX:TOL=63440],nesiotyrodes[&&NHX:TOL=63441],nomuraius[&&NHX:TOL=63442],palimbolus[&&NHX:TOL=63443],paralasinus[&&NHX:TOL=63444],phormiobius[&&NHX:TOL=63445],plesiotyrus[&&NHX:TOL=63446],pselaphodes[&&NHX:TOL=63447],pseudotyropsis[&&NHX:TOL=63448],rytus[&&NHX:TOL=63449],spilorhombus[&&NHX:TOL=63450],subulipalpus[&&NHX:TOL=63451],taiwanophodes[&&NHX:TOL=63452],tasmanityrus[&&NHX:TOL=63453],termitotyrus[&&NHX:TOL=63454],tyrinasius[&&NHX:TOL=63455],tyrodes[&&NHX:TOL=63456],tyrogatunus[&&NHX:TOL=63457],tyrogetus[&&NHX:TOL=63458],tyromacrus[&&NHX:TOL=63459],tyromorphus[&&NHX:TOL=63460],tyropsidius[&&NHX:TOL=63461],tyropsis[&&NHX:TOL=63462],tyrus[&&NHX:TOL=63463],vadoniotus[&&NHX:TOL=63464],zeatyrus[&&NHX:TOL=63465])tyrina[&&NHX:TOL=63411])tyrini[&&NHX:TOL=63370])pselaphitae[&&NHX:TOL=63221])pselaphinae[&&NHX:TOL=9770])[&&NHX:TOL=9769])[&&NHX:TOL=9768])[&&NHX:TOL=9767])omaliinae group[&&NHX:TOL=9759],((((((((gymnusa grandiceps[&&NHX:TOL=10080],((gymnusa brevicornis[&&NHX:TOL=10083],gymnusa atra[&&NHX:TOL=10084])[&&NHX:TOL=10082],((gymnusa variegata[&&NHX:TOL=10087],gymnusa pseudovariegata[&&NHX:TOL=10088])[&&NHX:TOL=10086],(gymnusa konopackii[&&NHX:TOL=10090],(gymnusa campbelli[&&NHX:TOL=10092],(gymnusa smetanai[&&NHX:TOL=10094],gymnusa inexspectata[&&NHX:TOL=10095])[&&NHX:TOL=10093])[&&NHX:TOL=10091])[&&NHX:TOL=10089])[&&NHX:TOL=10085])[&&NHX:TOL=10081])[&&NHX:TOL=10079],gymnusa miyashitai[&&NHX:TOL=10096])gymnusa[&&NHX:TOL=10098],stylogymnusa subantarctica[&&NHX:TOL=10099])gymnusini[&&NHX:TOL=9814],((((adinopsis flavicornis[&&NHX:TOL=10015],adinopsis devroeyi[&&NHX:TOL=10016],adinopsis africana[&&NHX:TOL=10017],adinopsis schoutedeni[&&NHX:TOL=10018],adinopsis rufobrunnea[&&NHX:TOL=10019],adinopsis cinnamomea[&&NHX:TOL=10020],adinopsis australis[&&NHX:TOL=10021],adinopsis bicornis[&&NHX:TOL=10022],adinopsis myllaenoides[&&NHX:TOL=10023],adinopsis angusta[&&NHX:TOL=10024],adinopsis ferruginea[&&NHX:TOL=10025],adinopsis braziliensis[&&NHX:TOL=10026],adinopsis ndumu[&&NHX:TOL=10027],adinopsis mmabolela[&&NHX:TOL=10028],adinopsis maraisi[&&NHX:TOL=10029],adinopsis hammondi[&&NHX:TOL=10030],adinopsis deckerti[&&NHX:TOL=10031],adinopsis cuspidata[&&NHX:TOL=10032],adinopsis nepalensis[&&NHX:TOL=10033],adinopsis groehni[&&NHX:EXT=Y:TOL=10034])adinopsis[&&NHX:TOL=10043],((((((deinopsis pulawskii[&&NHX:TOL=10051],deinopsis erosa[&&NHX:TOL=10052])[&&NHX:TOL=10050],deinopsis modesta[&&NHX:TOL=10053])[&&NHX:TOL=10049],deinopsis minor[&&NHX:TOL=10054])[&&NHX:TOL=10048],(((deinopsis texana[&&NHX:TOL=10058],deinopsis virginiana[&&NHX:TOL=10059])[&&NHX:TOL=10057],deinopsis illinoisensis[&&NHX:TOL=10060])[&&NHX:TOL=10056],(((deinopsis rhadina[&&NHX:TOL=10064],deinopsis harringtoni[&&NHX:TOL=10065])[&&NHX:TOL=10063],deinopsis canadensis[&&NHX:TOL=10066])[&&NHX:TOL=10062],deinopsis rapida[&&NHX:TOL=10067])[&&NHX:TOL=10061])[&&NHX:TOL=10055])[&&NHX:TOL=10047],deinopsis queenslandica[&&NHX:TOL=10068])[&&NHX:TOL=10046],deinopsis apicicornis[&&NHX:TOL=10069],deinopsis franki[&&NHX:TOL=10070],deinopsis stephani[&&NHX:TOL=10071])deinopsis[&&NHX:TOL=10042])[&&NHX:TOL=10041],(((metadeinopsis brunnea[&&NHX:TOL=10074],metadeinopsis matthewsi[&&NHX:TOL=10075])[&&NHX:TOL=10073],metadeinopsis longicornis[&&NHX:TOL=10076])[&&NHX:TOL=10072],metadeinopsis balli[&&NHX:TOL=10077],metadeinopsis ferox[&&NHX:TOL=10078])metadeinopsis[&&NHX:TOL=10044])[&&NHX:TOL=10040],(allodinopsis howdeni[&&NHX:TOL=10036],allodinopsis pecki[&&NHX:TOL=10037])allodinopsis[&&NHX:TOL=10045])deinopsini[&&NHX:TOL=9815])[&&NHX:TOL=9813],((congopsenius[&&NHX:TOL=63466],hamitopsenius[&&NHX:TOL=63467],mastopsenius[&&NHX:TOL=63468],megaxenistusa[&&NHX:TOL=63469],parrhinopsenius[&&NHX:TOL=63470],phorilimulus[&&NHX:TOL=63471],prorhinopsenius[&&NHX:TOL=63472],rhinotermopsenius[&&NHX:TOL=63473],schedolimulus[&&NHX:TOL=63474],schizelythron[&&NHX:TOL=63475],seeversia[&&NHX:TOL=63476],termitona[&&NHX:TOL=63477],termitopsenius[&&NHX:TOL=63478],trichopsenius[&&NHX:TOL=63479],xenistusa[&&NHX:TOL=63480])trichopseniini[&&NHX:TOL=9817],(ambracyptus[&&NHX:EXT=Y:TOL=63481],ampheida[&&NHX:TOL=63482],anacyptus[&&NHX:TOL=63483],dictyon[&&NHX:TOL=63484],kistnerium[&&NHX:TOL=63485],mesoporus[&&NHX:TOL=63486],mimodictyon[&&NHX:TOL=63487],paraconosoma[&&NHX:TOL=63488],paradictyon[&&NHX:TOL=63489])mesoporini[&&NHX:TOL=9818],(((amazonopora[&&NHX:TOL=63490],brachypronomaea[&&NHX:TOL=63491],bryothinusa[&&NHX:TOL=63492],dimonomera[&&NHX:TOL=63493],dysacrita[&&NHX:TOL=63494],lautaea[&&NHX:TOL=63495],myllaena[&&NHX:TOL=63496],paramyllaena[&&NHX:TOL=63497],philomina[&&NHX:TOL=63498],polypea[&&NHX:TOL=63499],rothium[&&NHX:TOL=63500])myllaenini[&&NHX:TOL=9821],(mataris[&&NHX:TOL=63501],nopromaea[&&NHX:TOL=63502],pronomaea[&&NHX:TOL=63503],pseudomniophila[&&NHX:TOL=63504],stenectinobregma[&&NHX:TOL=63505],stylopalpus[&&NHX:TOL=63506],tomoxelia[&&NHX:TOL=63507])pronomaeini[&&NHX:TOL=9822],(masuria masuria[&&NHX:TOL=63509],masuria oncosomechusa[&&NHX:TOL=63510])masuria[&&NHX:TOL=9824])[&&NHX:TOL=9820],((aenictocupidus[&&NHX:TOL=63512],aenictophila[&&NHX:TOL=63513],aenictoteras[&&NHX:TOL=63514],mimaenictus[&&NHX:TOL=63515],procantonnetia[&&NHX:TOL=63516],rosciszewskia[&&NHX:TOL=63517],steysborgia[&&NHX:TOL=63518],weiria[&&NHX:TOL=63519],weissflogia[&&NHX:TOL=63520])aenictoteratini[&&NHX:TOL=9826],(loeblius[&&NHX:TOL=63521],malaybergius[&&NHX:TOL=63522],malayloeblius[&&NHX:TOL=63523],parasahlbergius[&&NHX:TOL=63524],sahlbergius[&&NHX:TOL=63525])sahlbergiini[&&NHX:TOL=9827],(berghoffia[&&NHX:TOL=63526],dorylogaster[&&NHX:TOL=63527])dorylogastrini[&&NHX:TOL=9828],phyllodinarda[&&NHX:TOL=9829],((acrotona acrotona[&&NHX:TOL=63531],acrotona aremia[&&NHX:TOL=63532],acrotona arisota[&&NHX:TOL=63533],acrotona colpodota[&&NHX:TOL=63534],acrotona dolosota[&&NHX:TOL=63535],acrotona eurypronota[&&NHX:TOL=63536],acrotona neada[&&NHX:TOL=63537],acrotona reania[&&NHX:TOL=63538])acrotona[&&NHX:TOL=63530],acticola[&&NHX:TOL=63539],actocharina[&&NHX:TOL=63540],actophylla[&&NHX:TOL=63541],adda[&&NHX:TOL=63542],adota[&&NHX:TOL=63543],afrodotina[&&NHX:TOL=63544],afrooreobia[&&NHX:TOL=63545],afroplatyola[&&NHX:TOL=63546],aglaogaster[&&NHX:TOL=63547],agnosiusa[&&NHX:TOL=63548],alevonota[&&NHX:TOL=63549],alianta[&&NHX:TOL=63550],(aloconota aloconota[&&NHX:TOL=63552],aloconota disopora[&&NHX:TOL=63553],aloconota taphrodota[&&NHX:TOL=63554],aloconota terasota[&&NHX:TOL=63555])aloconota[&&NHX:TOL=63551],alomacrotona[&&NHX:TOL=63556],alomaina[&&NHX:TOL=63557],(alpinia alpinia[&&NHX:TOL=63559],alpinia petrammostiba[&&NHX:TOL=63560])alpinia[&&NHX:TOL=63558],amidobia[&&NHX:TOL=63561],amischa[&&NHX:TOL=63562],amphibolusa[&&NHX:TOL=63563],amriathaea[&&NHX:TOL=63564],anatheta[&&NHX:TOL=63565],angkorusa[&&NHX:TOL=63566],anisodota[&&NHX:TOL=63567],apagorea[&&NHX:TOL=63568],apphiana[&&NHX:TOL=63569],askeptoxenia[&&NHX:TOL=63570],(atheta acromyrmecoxene[&&NHX:TOL=63572],atheta acrotonida[&&NHX:TOL=63573],atheta alaobia[&&NHX:TOL=63574],atheta anopleta[&&NHX:TOL=63575],atheta arctostiba[&&NHX:TOL=63576],atheta atheta[&&NHX:TOL=63577],atheta attatheta[&&NHX:TOL=63578],atheta badura[&&NHX:TOL=63579],atheta bessobia[&&NHX:TOL=63580],atheta ceritaxa[&&NHX:TOL=63581],atheta chaetida[&&NHX:TOL=63582],atheta coprothassa[&&NHX:TOL=63583],atheta dabura[&&NHX:TOL=63584],atheta datomicra[&&NHX:TOL=63585],atheta delphota[&&NHX:TOL=63586],atheta diaprepota[&&NHX:TOL=63587],atheta dicolyota[&&NHX:TOL=63588],atheta dilacra[&&NHX:TOL=63589],atheta dimetrota[&&NHX:TOL=63590],atheta donesia[&&NHX:TOL=63591],atheta ekkliatheta[&&NHX:TOL=63592],atheta epimella[&&NHX:TOL=63593],atheta eubadura[&&NHX:TOL=63594],atheta eugluta[&&NHX:TOL=63595],atheta evaniodera[&&NHX:TOL=63596],atheta geostibops[&&NHX:TOL=63597],atheta hummleriella[&&NHX:TOL=63598],atheta hygroecia[&&NHX:TOL=63599],atheta hypsostiba[&&NHX:TOL=63600],atheta ischnoderoecia[&&NHX:TOL=63601],atheta lamiota[&&NHX:TOL=63602],atheta lampratheta[&&NHX:TOL=63603],atheta libanostiba[&&NHX:TOL=63604],atheta metadimetrota[&&NHX:TOL=63605],atheta microdota[&&NHX:TOL=63606],atheta microdotina[&&NHX:TOL=63607],atheta nemota[&&NHX:TOL=63608],atheta niphetodroma[&&NHX:TOL=63609],atheta oligatheta[&&NHX:TOL=63610],atheta oreostiba[&&NHX:TOL=63611],atheta orientatheta[&&NHX:TOL=63612],atheta oxypodera[&&NHX:TOL=63613],atheta paradota[&&NHX:TOL=63614],atheta parameotica[&&NHX:TOL=63615],atheta parametaxya[&&NHX:TOL=63616],atheta paramidobia[&&NHX:TOL=63617],atheta peliolurga[&&NHX:TOL=63618],atheta pelmatheta[&&NHX:TOL=63619],atheta phanerosphena[&&NHX:TOL=63620],atheta philacrotona[&&NHX:TOL=63621],atheta philhygra[&&NHX:TOL=63622],atheta polydota[&&NHX:TOL=63623],atheta poromicrodota[&&NHX:TOL=63624],atheta pseudhygroecia[&&NHX:TOL=63625],atheta pseudobessobia[&&NHX:TOL=63626],atheta pseudohygroecia[&&NHX:TOL=63627],atheta pseudoleptonia[&&NHX:TOL=63628],atheta pseudopasilia[&&NHX:TOL=63629],atheta pseudophilygra[&&NHX:TOL=63630],atheta pseudota[&&NHX:TOL=63631],atheta pseudothinoecia[&&NHX:TOL=63632],atheta rhagocneme[&&NHX:TOL=63633],atheta sepedomicra[&&NHX:TOL=63634],atheta sipalatheta[&&NHX:TOL=63635],atheta spelaeolla[&&NHX:TOL=63636],atheta stictatheta[&&NHX:TOL=63637],atheta stilbatheta[&&NHX:TOL=63638],atheta strobilocera[&&NHX:TOL=63639],atheta suensonia[&&NHX:TOL=63640],atheta synaloconota[&&NHX:TOL=63641],atheta tachynota[&&NHX:TOL=63642],atheta thinobaena[&&NHX:TOL=63643],atheta traumoecia[&&NHX:TOL=63644],atheta trochanterella[&&NHX:TOL=63645],atheta tropatheta[&&NHX:TOL=63646],atheta umbala[&&NHX:TOL=63647],atheta xenota[&&NHX:TOL=63648],atheta xestota[&&NHX:TOL=63649])atheta[&&NHX:TOL=63571],australoconota[&&NHX:TOL=63650],australoplatyola[&&NHX:TOL=63651],austropelioptera[&&NHX:TOL=63652],bellatheta bellatheta[&&NHX:TOL=63653],(berca aplestoglossa[&&NHX:TOL=63657],berca prosechoglossa[&&NHX:TOL=63658])berca[&&NHX:TOL=63656],bernhaueria[&&NHX:TOL=63659],boreophilia[&&NHX:TOL=63660],boreostiba[&&NHX:TOL=63661],borneoxenia[&&NHX:TOL=63662],brundinia[&&NHX:TOL=63663],caenogluta[&&NHX:TOL=63664],callicerus[&&NHX:TOL=63665],cantaberella[&&NHX:TOL=63666],chalcochara[&&NHX:TOL=63667],charicera[&&NHX:TOL=63668],charoxus[&&NHX:TOL=63669],chinecallicerus[&&NHX:TOL=63670],chionostiba[&&NHX:TOL=63671],chtamalota[&&NHX:TOL=63672],clusiota[&&NHX:TOL=63673],codoglossa[&&NHX:TOL=63674],cosmogastrusa[&&NHX:TOL=63675],crephalia[&&NHX:TOL=63676],ctenatheta[&&NHX:TOL=63677],dacrila[&&NHX:TOL=63678],dadobia[&&NHX:TOL=63679],dalotia[&&NHX:TOL=63680],delonusa[&&NHX:TOL=63681],diabainella[&&NHX:TOL=63682],dikraspedella[&&NHX:TOL=63683],dilobidiontura[&&NHX:TOL=63684],dinaraea[&&NHX:TOL=63685],dityloechusa[&&NHX:TOL=63686],dochmonota[&&NHX:TOL=63687],ealisbia[&&NHX:TOL=63688],earota[&&NHX:TOL=63689],eidmannotherium[&&NHX:TOL=63690],ektasitrachela[&&NHX:TOL=63691],(emmelostiba emmelostiba[&&NHX:TOL=63693],emmelostiba italiusa[&&NHX:TOL=63694])emmelostiba[&&NHX:TOL=63692],enalodroma[&&NHX:TOL=63695],enkoilogeneia[&&NHX:TOL=63696],erpachara[&&NHX:TOL=63697],euliodota[&&NHX:TOL=63698],eurodotina[&&NHX:TOL=63699],euromota[&&NHX:TOL=63700],exacrotona[&&NHX:TOL=63701],exaeretota[&&NHX:TOL=63702],fenyesia[&&NHX:TOL=63703],fernanstiba[&&NHX:TOL=63704],gaenima[&&NHX:TOL=63705],(gastropaga gastropaga[&&NHX:TOL=63707],gastropaga rougemontia[&&NHX:TOL=63708])gastropaga[&&NHX:TOL=63706],gastrosteata[&&NHX:TOL=63709],geopora[&&NHX:TOL=63710],(geostiba acanthosipalia[&&NHX:TOL=63712],geostiba anatologeostiba[&&NHX:TOL=63713],geostiba chondridiosipalia[&&NHX:TOL=63714],geostiba dichondrosipalia[&&NHX:TOL=63715],geostiba geostiba[&&NHX:TOL=63716],geostiba indatheta[&&NHX:TOL=63717],geostiba myoposipalia[&&NHX:TOL=63718],geostiba odontosipalia[&&NHX:TOL=63719],geostiba prionosipalia[&&NHX:TOL=63720],geostiba sibiota[&&NHX:TOL=63721],geostiba sipalotricha[&&NHX:TOL=63722],geostiba sphenosipalia[&&NHX:TOL=63723],geostiba tetratropogeostiba[&&NHX:TOL=63724],geostiba trachyglutosipalia[&&NHX:TOL=63725],geostiba triptychosipalia[&&NHX:TOL=63726],geostiba tropogastrosipalia[&&NHX:TOL=63727],geostiba typhlusida[&&NHX:TOL=63728])geostiba[&&NHX:TOL=63711],geostibasoma[&&NHX:TOL=63729],giachinusa[&&NHX:TOL=63730],goniusa[&&NHX:TOL=63731],halobrecta[&&NHX:TOL=63732],halobrecthina[&&NHX:TOL=63733],haplostylipera[&&NHX:TOL=63734],helichatheta[&&NHX:TOL=63735],heterostiba[&&NHX:TOL=63736],homia[&&NHX:TOL=63737],hovastiba[&&NHX:TOL=63738],hydrosmecta[&&NHX:TOL=63739],hylodesina[&&NHX:TOL=63740],idiocolyusa[&&NHX:TOL=63741],iotarphia[&&NHX:TOL=63742],irianusa[&&NHX:TOL=63743],ischnonota[&&NHX:TOL=63744],ischnothina[&&NHX:TOL=63745],kyrtoxyna[&&NHX:TOL=63746],lamprostiba[&&NHX:TOL=63747],lasiosomina[&&NHX:TOL=63748],leiodota[&&NHX:TOL=63749],lemuridota[&&NHX:TOL=63750],leptoglossula[&&NHX:TOL=63751],leptonia[&&NHX:TOL=63752],leptoporodota[&&NHX:TOL=63753],leptostiba[&&NHX:TOL=63754],leptotheta[&&NHX:TOL=63755],(liogluta anepsiota[&&NHX:TOL=63757],liogluta liogluta[&&NHX:TOL=63758],liogluta paraliogluta[&&NHX:TOL=63759])liogluta[&&NHX:TOL=63756],lomaella[&&NHX:TOL=63760],(longiprimitarsus longiprimitarsus[&&NHX:TOL=63762],longiprimitarsus penichradoxus[&&NHX:TOL=63763])longiprimitarsus[&&NHX:TOL=63761],lucuphilus[&&NHX:TOL=63764],lundbergia[&&NHX:TOL=63765],lypoglossa[&&NHX:TOL=63766],lyprocorrhe[&&NHX:TOL=63767],macrophthalmodites[&&NHX:TOL=63768],madecatheta[&&NHX:TOL=63769],madeirostiba[&&NHX:TOL=63770],makrakanthakneme[&&NHX:TOL=63771],malayanota[&&NHX:TOL=63772],mauritecia[&&NHX:TOL=63773],megonychiusa[&&NHX:TOL=63774],miathamia[&&NHX:TOL=63775],micratheta[&&NHX:TOL=63776],micrearota[&&NHX:TOL=63777],microcephalina[&&NHX:TOL=63778],microceratheta[&&NHX:TOL=63779],mimatheta[&&NHX:TOL=63780],mocyta[&&NHX:TOL=63781],mycetota[&&NHX:TOL=63782],nehemitropia[&&NHX:TOL=63783],neocallicerus[&&NHX:TOL=63784],neodinaraea[&&NHX:TOL=63785],neohilara[&&NHX:TOL=63786],neorhagocneme[&&NHX:TOL=63787],nepalota[&&NHX:TOL=63788],nikkostiba[&&NHX:TOL=63789],notatheta[&&NHX:TOL=63790],(notothecta kraatzia[&&NHX:TOL=63792],notothecta notothecta[&&NHX:TOL=63793],notothecta notothectina[&&NHX:TOL=63794])notothecta[&&NHX:TOL=63791],oligocharina[&&NHX:TOL=63795],ousipalia[&&NHX:TOL=63796],ousipaliaglossa[&&NHX:TOL=63797],outachyusa[&&NHX:TOL=63798],oxypodinus[&&NHX:TOL=63799],pachnida[&&NHX:TOL=63800],pachyatheta[&&NHX:TOL=63801],parademosoma[&&NHX:TOL=63802],paragoniusa[&&NHX:TOL=63803],paraleptonia[&&NHX:TOL=63804],paraleptusa[&&NHX:TOL=63805],paraloconota[&&NHX:TOL=63806],paranomusa[&&NHX:TOL=63807],paranopleta[&&NHX:TOL=63808],parapodoxya[&&NHX:TOL=63809],(pelioptera geostibida[&&NHX:TOL=63811],pelioptera pelioptera[&&NHX:TOL=63812],pelioptera phaediolia[&&NHX:TOL=63813])pelioptera[&&NHX:TOL=63810],peliopteronia[&&NHX:TOL=63814],peliusa[&&NHX:TOL=63815],phaenacrotona[&&NHX:TOL=63816],physetophallia[&&NHX:TOL=63817],pikrainusa[&&NHX:TOL=63818],planadota[&&NHX:TOL=63819],(plataraea alloceraea[&&NHX:TOL=63821],plataraea plataraea[&&NHX:TOL=63822])plataraea[&&NHX:TOL=63820],platyola[&&NHX:TOL=63823],platyolopsis[&&NHX:TOL=63824],pontomalota[&&NHX:TOL=63825],psammopora[&&NHX:TOL=63826],psammostiba[&&NHX:TOL=63827],pseudacrotona[&&NHX:TOL=63828],pseudoleptusa[&&NHX:TOL=63829],pseudomyrmedon[&&NHX:TOL=63830],pseudosemiris[&&NHX:TOL=63831],pujolia[&&NHX:TOL=63832],(pycnota parapycnota[&&NHX:TOL=63834],pycnota pycnota[&&NHX:TOL=63835])pycnota[&&NHX:TOL=63833],sableta[&&NHX:TOL=63836],saphocallus[&&NHX:TOL=63837],schistacme[&&NHX:TOL=63838],schistoglossa[&&NHX:TOL=63839],seeversiella[&&NHX:TOL=63840],serikasomina[&&NHX:TOL=63841],shamuheruna[&&NHX:TOL=63842],shigatheta[&&NHX:TOL=63843],sipaliopsis[&&NHX:TOL=63844],stethusa[&&NHX:TOL=63845],strigota[&&NHX:TOL=63846],strophogastra[&&NHX:TOL=63847],tarphiota[&&NHX:TOL=63848],thectonota[&&NHX:TOL=63849],thinusa[&&NHX:TOL=63850],tolypotheca[&&NHX:TOL=63851],tomoglossa[&&NHX:TOL=63852],tramiathaea[&&NHX:TOL=63853],trichiusa[&&NHX:TOL=63854],trichomicra[&&NHX:TOL=63855],trigonoglossina[&&NHX:TOL=63856],tropimenelytron[&&NHX:TOL=63857],tyloplatyola[&&NHX:TOL=63858],xenastenoglossa[&&NHX:TOL=63859],zyrathetoides[&&NHX:TOL=63860],(coptolimulus[&&NHX:TOL=63862],coptophilus[&&NHX:TOL=63863],coptotermoecia[&&NHX:TOL=63864],philobrunneus[&&NHX:TOL=63865])coptotermoeciina[&&NHX:TOL=63861],(microcerophilus[&&NHX:TOL=63867],microceroxenus[&&NHX:TOL=63868])microceroxenina[&&NHX:TOL=63866],nasutiphilus[&&NHX:TOL=63869],(eutaenoglossa[&&NHX:TOL=63873],litoglossa[&&NHX:TOL=63874],medeterusa[&&NHX:TOL=63875],platorischna[&&NHX:TOL=63876],pseudoxypoda[&&NHX:TOL=63877],schistogenia[&&NHX:TOL=63878],tacata[&&NHX:TOL=63879])schistogeniina[&&NHX:TOL=63872],(discerota[&&NHX:TOL=63881],taxicera[&&NHX:TOL=63882])taxicerina[&&NHX:TOL=63880],(neotermitotelus[&&NHX:TOL=63884],termitotelus[&&NHX:TOL=63885])termitotelina[&&NHX:TOL=63883],(thamiaraea miatharaea[&&NHX:TOL=63888],thamiaraea thamiaraea[&&NHX:TOL=63889])thamiaraea[&&NHX:TOL=63886])athetini[&&NHX:TOL=9830],((((aleochara heterochara[&&NHX:TOL=9899],aleochara aleochara s. str.[&&NHX:TOL=9900],aleochara aidochara[&&NHX:TOL=9901],aleochara euryodma[&&NHX:TOL=9902],aleochara ceranota[&&NHX:TOL=9903],(aleochara obscurella[&&NHX:TOL=9968],aleochara phycophila[&&NHX:TOL=9969],aleochara albopila[&&NHX:TOL=9970],aleochara fucicola[&&NHX:TOL=9971],aleochara puetzi[&&NHX:TOL=9972],aleochara littoralis[&&NHX:TOL=9973],aleochara pacifica[&&NHX:TOL=9974],aleochara curtidens[&&NHX:TOL=9975])aleochara emplenota[&&NHX:TOL=9904],(aleochara trisulcata[&&NHX:TOL=10002],aleochara zerchei[&&NHX:TOL=10003],aleochara nubis[&&NHX:TOL=10004])aleochara triochara[&&NHX:TOL=9905],(((((aleochara valida[&&NHX:TOL=9980],(aleochara opacella[&&NHX:TOL=9982],aleochara gracilis[&&NHX:TOL=9983])[&&NHX:TOL=9981],aleochara depressa[&&NHX:TOL=9984])[&&NHX:TOL=9979],aleochara duplicata[&&NHX:TOL=9985])[&&NHX:TOL=9978],aleochara wickhami[&&NHX:TOL=9986])[&&NHX:TOL=9977],((aleochara angusticollis[&&NHX:TOL=9989],aleochara asperata[&&NHX:TOL=9990])[&&NHX:TOL=9988],(aleochara brunneipennis[&&NHX:TOL=9992],aleochara ituriensis[&&NHX:TOL=9993])[&&NHX:TOL=9991])[&&NHX:TOL=9987],aleochara horni[&&NHX:TOL=9994],aleochara javana[&&NHX:TOL=9995])[&&NHX:TOL=9976],aleochara argentina[&&NHX:TOL=9996],aleochara comorensis[&&NHX:TOL=9997])aleochara maseochara[&&NHX:TOL=9906],(aleochara lobata[&&NHX:TOL=9963],aleochara lucifuga[&&NHX:TOL=9964],aleochara ocularis[&&NHX:TOL=9965],aleochara fenyesi[&&NHX:TOL=9966])aleochara echochara[&&NHX:TOL=9907],aleochara calochara[&&NHX:TOL=9908],aleochara mesochara[&&NHX:TOL=9909],aleochara xenochara s. l.[&&NHX:TOL=9910],aleochara rheochara[&&NHX:TOL=9911],(aleochara grisea[&&NHX:TOL=9999],aleochara punctatella[&&NHX:TOL=10000])aleochara polystomota[&&NHX:TOL=9912],((aleochara densissima[&&NHX:TOL=9916],(((aleochara bipustulata[&&NHX:TOL=9920],aleochara lindbergi[&&NHX:TOL=9921],aleochara bisolata[&&NHX:TOL=9922],aleochara verna[&&NHX:TOL=9923])[&&NHX:TOL=9919],(aleochara freyi[&&NHX:TOL=9925],(aleochara reinigi[&&NHX:TOL=9927],(aleochara suffusa[&&NHX:TOL=9929],aleochara brundini[&&NHX:TOL=9930])[&&NHX:TOL=9928])[&&NHX:TOL=9926])[&&NHX:TOL=9924])[&&NHX:TOL=9918],((aleochara binotata[&&NHX:TOL=9933],aleochara pauxilla[&&NHX:TOL=9934])[&&NHX:TOL=9932],((aleochara hluhluwe[&&NHX:TOL=9937],aleochara lineatocollis[&&NHX:TOL=9938])[&&NHX:TOL=9936],(aleochara sublaevipennis[&&NHX:TOL=9940],aleochara granulicauda[&&NHX:TOL=9941])[&&NHX:TOL=9939])[&&NHX:TOL=9935])[&&NHX:TOL=9931],(aleochara bilineata[&&NHX:TOL=9943],(aleochara notula[&&NHX:TOL=9945],((aleochara bimaculata[&&NHX:TOL=9948],(aleochara mutare[&&NHX:TOL=9950],aleochara solieri[&&NHX:TOL=9951])[&&NHX:TOL=9949])[&&NHX:TOL=9947],(aleochara salsipotens[&&NHX:TOL=9953],(aleochara sulcicollis[&&NHX:TOL=9955],aleochara squalithorax[&&NHX:TOL=9956])[&&NHX:TOL=9954])[&&NHX:TOL=9952])[&&NHX:TOL=9946])[&&NHX:TOL=9944])[&&NHX:TOL=9942])[&&NHX:TOL=9917])[&&NHX:TOL=9915],aleochara polychroma[&&NHX:TOL=9957],aleochara robusta[&&NHX:TOL=9958],aleochara pamirensis[&&NHX:TOL=9959],aleochara composita[&&NHX:TOL=9960],aleochara ? semicarinata[&&NHX:TOL=9961])aleochara coprochara[&&NHX:TOL=9913],aleochara megalogastria[&&NHX:TOL=9914])aleochara[&&NHX:TOL=9878],correa[&&NHX:TOL=9879],cratoacrochara[&&NHX:TOL=9880],creochara[&&NHX:TOL=9881],ilarochara[&&NHX:TOL=9882],leptogenophilus[&&NHX:TOL=9883],lyperosterochara[&&NHX:TOL=9884],(ocyota dubia[&&NHX:TOL=9894],ocyota fortepunctata[&&NHX:TOL=9895])ocyota[&&NHX:TOL=9885],oxybessoglossa[&&NHX:TOL=9886],palaeochara[&&NHX:TOL=9887],paraleochara[&&NHX:TOL=9888],paroxysmeme[&&NHX:TOL=9889],piochardia[&&NHX:TOL=9890],plesiochara[&&NHX:TOL=9891],pseudocalea brevicornis[&&NHX:TOL=9892])aleocharina[&&NHX:TOL=9874],(((compactopedia[&&NHX:TOL=10008],discoxenus[&&NHX:TOL=10009])[&&NHX:TOL=10007],emersonilla[&&NHX:TOL=10010])[&&NHX:TOL=10006],hirsitilla[&&NHX:TOL=10011])compactopediina[&&NHX:TOL=9875],hodoxenus sheasbyi[&&NHX:TOL=9876])aleocharini[&&NHX:TOL=9832],(acantoxyura[&&NHX:TOL=63891],aleochandria[&&NHX:TOL=63892],alloplandria[&&NHX:TOL=63893],bessoglossa[&&NHX:TOL=63894],borneusa[&&NHX:TOL=63895],brachidamorpha[&&NHX:TOL=63896],gonionycha[&&NHX:TOL=63897],palaeochara[&&NHX:TOL=63898],(heliconandria[&&NHX:TOL=63900],(hoplandria arrhenandria[&&NHX:TOL=63902],hoplandria genosema[&&NHX:TOL=63903],hoplandria hoplandria[&&NHX:TOL=63904],hoplandria lophomucter[&&NHX:TOL=63905],hoplandria platonica[&&NHX:TOL=63906])hoplandria[&&NHX:TOL=63901],leptandria[&&NHX:TOL=63907])hoplandriina[&&NHX:TOL=63899],(ditropandria[&&NHX:TOL=63909],ligulata[&&NHX:TOL=63910],microlia[&&NHX:TOL=63911],omoplandria[&&NHX:TOL=63912],paroplandria[&&NHX:TOL=63913],platandria[&&NHX:TOL=63914])platandriina[&&NHX:TOL=63908],pseudoplandria[&&NHX:TOL=63915])hoplandriini[&&NHX:TOL=9833])[&&NHX:TOL=9831],(daccordiusa[&&NHX:TOL=63918],trisporusa[&&NHX:TOL=63919],(aenictobia[&&NHX:TOL=63921],dentaphila[&&NHX:TOL=63922],tobiisima[&&NHX:TOL=63923],trichotobia[&&NHX:TOL=63924])aenictobiina[&&NHX:TOL=63920],(lomechusa[&&NHX:TOL=63926],lomechusoides[&&NHX:TOL=63927],lornechusula[&&NHX:TOL=63928],xenodusa[&&NHX:TOL=63929])lomechusina[&&NHX:TOL=63925],(abothrus[&&NHX:TOL=63931],acanthastilbus[&&NHX:TOL=63932],aenictocleptis[&&NHX:TOL=63933],aenictonia[&&NHX:TOL=63934],aenictozyras[&&NHX:TOL=63935],allardiana[&&NHX:TOL=63936],allodinarda[&&NHX:TOL=63937],amaurodera[&&NHX:TOL=63938],amazoncharis[&&NHX:TOL=63939],amblyoponiphilus[&&NHX:TOL=63940],anepipleuronia[&&NHX:TOL=63941],ankaratraella[&&NHX:TOL=63942],anommatochara[&&NHX:TOL=63943],anopsapterus[&&NHX:TOL=63944],anthropeltodonia[&&NHX:TOL=63945],apalonia[&&NHX:TOL=63946],apteranillus[&&NHX:TOL=63947],apteraphaenops[&&NHX:TOL=63948],astilbides[&&NHX:TOL=63949],aulacocephalonia[&&NHX:TOL=63950],borneozyras[&&NHX:TOL=63951],bothriocrata[&&NHX:TOL=63952],brachypteronia[&&NHX:TOL=63953],brachysipalia[&&NHX:TOL=63954],camerouniella[&&NHX:TOL=63955],cantaloubeia[&&NHX:TOL=63956],(catarractodes catarractodes[&&NHX:TOL=63958],catarractodes hyptiorrates[&&NHX:TOL=63959])catarractodes[&&NHX:TOL=63957],chaetosogonocephus[&&NHX:TOL=63960],conradsia[&&NHX:TOL=63961],creodonia[&&NHX:TOL=63962],dabra[&&NHX:TOL=63963],dabrosoma[&&NHX:TOL=63964],degalliera[&&NHX:TOL=63965],dentazyras[&&NHX:TOL=63966],deroleptus[&&NHX:TOL=63967],dinocoryna[&&NHX:TOL=63968],dinusella[&&NHX:TOL=63969],diplopleurus[&&NHX:TOL=63970],doratoporus[&&NHX:TOL=63971],dromacamatus[&&NHX:TOL=63972],dromanomma[&&NHX:TOL=63973],dromeciton[&&NHX:TOL=63974],drugia[&&NHX:TOL=63975],drusilla[&&NHX:TOL=63976],drusillota[&&NHX:TOL=63977],dysamblys[&&NHX:TOL=63978],ecitana[&&NHX:TOL=63979],ecitocala[&&NHX:TOL=63980],ecitocerus[&&NHX:TOL=63981],ecitocryptodes[&&NHX:TOL=63982],ecitocryptus[&&NHX:TOL=63983],ecitodiscus[&&NHX:TOL=63984],ecitodonia[&&NHX:TOL=63985],ecitoglossa[&&NHX:TOL=63986],ecitonia[&&NHX:TOL=63987],ecitonidia[&&NHX:TOL=63988],ecitonilla[&&NHX:TOL=63989],ecitopelta[&&NHX:TOL=63990],ecitophila[&&NHX:TOL=63991],ecitophiletus[&&NHX:TOL=63992],ecitophrura[&&NHX:TOL=63993],ecitoplectus[&&NHX:TOL=63994],ecitopolites[&&NHX:TOL=63995],ecitopora[&&NHX:TOL=63996],ecitotyphlus[&&NHX:TOL=63997],ecitoxenidia[&&NHX:TOL=63998],euryalusa[&&NHX:TOL=63999],eurydiotyphla[&&NHX:TOL=64000],falagonia[&&NHX:TOL=64001],falagonilla[&&NHX:TOL=64002],gallardoia[&&NHX:TOL=64003],gapia[&&NHX:TOL=64004],gramminopleurus[&&NHX:TOL=64005],gryptaulacus[&&NHX:TOL=64006],haplomyrmemonia[&&NHX:TOL=64007],heteroporus[&&NHX:TOL=64008],homalodonia[&&NHX:TOL=64009],kakodaimonia[&&NHX:TOL=64010],katanganella[&&NHX:TOL=64011],kenyanella[&&NHX:TOL=64012],kolwezia[&&NHX:TOL=64013],labidilla[&&NHX:TOL=64014],labidoculex[&&NHX:TOL=64015],lamprostenusa[&&NHX:TOL=64016],leiorhopala[&&NHX:TOL=64017],leleupidiella[&&NHX:TOL=64018],leptogenoxenus[&&NHX:TOL=64019],macrogerodonia[&&NHX:TOL=64020],madecazyras[&&NHX:TOL=64021],malaiseium[&&NHX:TOL=64022],manikaella[&&NHX:TOL=64023],maschwitzia[&&NHX:TOL=64024],meronera[&&NHX:TOL=64025],methneria[&&NHX:TOL=64026],methnerotherium[&&NHX:TOL=64027],microdonia[&&NHX:TOL=64028],mimoplandria[&&NHX:TOL=64029],monobothrus[&&NHX:TOL=64030],myrmechusa[&&NHX:TOL=64031],myrmechusina[&&NHX:TOL=64032],myrmecopella[&&NHX:TOL=64033],myrmecoxenia[&&NHX:TOL=64034],myrmedonota[&&NHX:TOL=64035],myrmigaster[&&NHX:TOL=64036],myrmoecia[&&NHX:TOL=64037],neocamacopalpus[&&NHX:TOL=64038],neolara[&&NHX:TOL=64039],neosmectonia[&&NHX:TOL=64040],neowroughtonilla[&&NHX:TOL=64041],ocyplanus[&&NHX:TOL=64042],orphnebius[&&NHX:TOL=64043],oxylidia[&&NHX:TOL=64044],(pachorhopala pachorhopala[&&NHX:TOL=64046],pachorhopala troposipalia[&&NHX:TOL=64047])pachorhopala[&&NHX:TOL=64045],papuanusa[&&NHX:TOL=64048],paramyrmoecia[&&NHX:TOL=64049],paraporus[&&NHX:TOL=64050],parastilbus[&&NHX:TOL=64051],pedinopleurus[&&NHX:TOL=64052],pella[&&NHX:TOL=64053],periergopus[&&NHX:TOL=64054],pheidologitonetes[&&NHX:TOL=64055],philastilbus[&&NHX:TOL=64056],philusina[&&NHX:TOL=64057],platyastilbus[&&NHX:TOL=64058],platyusa[&&NHX:TOL=64059],plesiadda[&&NHX:TOL=64060],porus[&&NHX:TOL=64061],propinquitas[&&NHX:TOL=64062],pseudastilbus[&&NHX:TOL=64063],pseudodinusa[&&NHX:TOL=64064],pseudodrusilla[&&NHX:TOL=64065],(pseudopachorhopala pachorhopaella[&&NHX:TOL=64067],pseudopachorhopala pachorhopalopsis[&&NHX:TOL=64068],pseudopachorhopala pseudopachorhopala[&&NHX:TOL=64069])pseudopachorhopala[&&NHX:TOL=64066],pseudoporus[&&NHX:TOL=64070],pseudothamiaraea[&&NHX:TOL=64071],quarternio[&&NHX:TOL=64072],rhopalybia[&&NHX:TOL=64073],rhoptrodinarda[&&NHX:TOL=64074],salutoporus[&&NHX:TOL=64075],scotodonia[&&NHX:TOL=64076],smectonia[&&NHX:TOL=64077],stenocyplanus[&&NHX:TOL=64078],stenopleurus[&&NHX:TOL=64079],stichodonia[&&NHX:TOL=64080],strabocephalium[&&NHX:TOL=64081],synthoracastilbus[&&NHX:TOL=64082],termitognathus[&&NHX:TOL=64083],terrecorvonia[&&NHX:TOL=64084],tetrabothrus[&&NHX:TOL=64085],tetradonella[&&NHX:TOL=64086],tetradonia[&&NHX:TOL=64087],tetragnypeta[&&NHX:TOL=64088],tetralophodes[&&NHX:TOL=64089],thlibopleurus[&&NHX:TOL=64090],thoracastilbus[&&NHX:TOL=64091],thoracophagus[&&NHX:TOL=64092],togpelenys[&&NHX:TOL=64093],trachydonia[&&NHX:TOL=64094],trachyota[&&NHX:TOL=64095],trichodonia[&&NHX:TOL=64096],tropiochara[&&NHX:TOL=64097],typhlonusa[&&NHX:TOL=64098],typhlozyras[&&NHX:TOL=64099],urodonia[&&NHX:TOL=64100],vertexprorogatio[&&NHX:TOL=64101],wasmannina[&&NHX:TOL=64102],wroughtonilla[&&NHX:TOL=64103],xesturida[&&NHX:TOL=64104],(zyras acanthocnemidonia[&&NHX:TOL=64106],zyras acrothoraconia[&&NHX:TOL=64107],zyras androdonia[&&NHX:TOL=64108],zyras anophthalmodonia[&&NHX:TOL=64109],zyras antronia[&&NHX:TOL=64110],zyras aplastonia[&&NHX:TOL=64111],zyras apostenonia[&&NHX:TOL=64112],zyras apterygodonia[&&NHX:TOL=64113],zyras aulacodonia[&&NHX:TOL=64114],zyras botsa[&&NHX:TOL=64115],zyras callodonia[&&NHX:TOL=64116],zyras cameronodonia[&&NHX:TOL=64117],zyras camonia[&&NHX:TOL=64118],zyras cephalodonia[&&NHX:TOL=64119],zyras colpodonia[&&NHX:TOL=64120],zyras craspa[&&NHX:TOL=64121],zyras crateodonia[&&NHX:TOL=64122],zyras ctenodonia[&&NHX:TOL=64123],zyras dentothalmonia[&&NHX:TOL=64124],zyras diaulaconia[&&NHX:TOL=64125],zyras euryalonia[&&NHX:TOL=64126],zyras eurydonia[&&NHX:TOL=64127],zyras euryncephalodonia[&&NHX:TOL=64128],zyras euryndonia[&&NHX:TOL=64129],zyras fealina[&&NHX:TOL=64130],zyras glossacantha[&&NHX:TOL=64131],zyras grammodonia[&&NHX:TOL=64132],zyras hylozyras[&&NHX:TOL=64133],zyras isothoracodonia[&&NHX:TOL=64134],zyras lastia[&&NHX:TOL=64135],zyras leptodonia[&&NHX:TOL=64136],zyras macrodonia[&&NHX:TOL=64137],zyras myrmelia[&&NHX:TOL=64138],zyras neotropopella[&&NHX:TOL=64139],zyras pachydonia[&&NHX:TOL=64140],zyras paragrammodonia[&&NHX:TOL=64141],zyras parophthalmonia[&&NHX:TOL=64142],zyras peltodonia[&&NHX:TOL=64143],zyras platydonia[&&NHX:TOL=64144],zyras polydonia[&&NHX:TOL=64145],zyras pycnodonia[&&NHX:TOL=64146],zyras remionea[&&NHX:TOL=64147],zyras rhopalodonia[&&NHX:TOL=64148],zyras rocnema[&&NHX:TOL=64149],zyras sinozyras[&&NHX:TOL=64150],zyras subversoris[&&NHX:TOL=64151],zyras synthoracodonia[&&NHX:TOL=64152],zyras taprodonia[&&NHX:TOL=64153],zyras termidonia[&&NHX:TOL=64154],zyras termitelia[&&NHX:TOL=64155],zyras termitodonia[&&NHX:TOL=64156],zyras trigonodonia[&&NHX:TOL=64157],zyras trigonozyras[&&NHX:TOL=64158],zyras tropidonia[&&NHX:TOL=64159],zyras visendor[&&NHX:TOL=64160],zyras zyras[&&NHX:TOL=64161],zyras zyrastilbus[&&NHX:TOL=64162])zyras[&&NHX:TOL=64105])myrmedoniina[&&NHX:TOL=63930],(havilandoxenus[&&NHX:TOL=64164],hodotermophilus[&&NHX:TOL=64165],iheringocantharus[&&NHX:TOL=64166],limulodilla[&&NHX:TOL=64167],longipedisymbia[&&NHX:TOL=64168],longipedoxenus[&&NHX:TOL=64169],termitonusa[&&NHX:TOL=64170],termitophagus[&&NHX:TOL=64171],termitosymbia[&&NHX:TOL=64172],termitozyras[&&NHX:TOL=64173],termophidoholus[&&NHX:TOL=64174])termitozyrina[&&NHX:TOL=64163])lomechusini[&&NHX:TOL=9834],(abrophaena[&&NHX:TOL=64175],achtherampla[&&NHX:TOL=64176],acrocyusa[&&NHX:TOL=64177],acrostiba[&&NHX:TOL=64178],afromeotica[&&NHX:TOL=64179],alfocalea[&&NHX:TOL=64180],alisalia[&&NHX:TOL=64181],amanota[&&NHX:TOL=64182],amarochara[&&NHX:TOL=64183],ambodina[&&NHX:TOL=64184],andinostiba[&&NHX:TOL=64185],anocalea[&&NHX:TOL=64186],antistydatusa[&&NHX:TOL=64187],apatelieida[&&NHX:TOL=64188],aphytopus[&&NHX:TOL=64189],apimela[&&NHX:TOL=64190],aspidobactrus[&&NHX:TOL=64191],australiusa[&&NHX:TOL=64192],austrocalea[&&NHX:TOL=64193],aylikusa[&&NHX:TOL=64194],bamona[&&NHX:TOL=64195],beijingusa[&&NHX:TOL=64196],betocalea[&&NHX:TOL=64197],blepharhymenus[&&NHX:TOL=64198],brachyusa[&&NHX:TOL=64199],brouniana[&&NHX:TOL=64200],caenopoda[&&NHX:TOL=64201],calodera[&&NHX:TOL=64202],cephalocousya[&&NHX:TOL=64203],chanoma[&&NHX:TOL=64204],chilodera[&&NHX:TOL=64205],chilomorpha[&&NHX:TOL=64206],chitosa[&&NHX:TOL=64207],cnemostyla[&&NHX:TOL=64208],colle[&&NHX:TOL=64209],cousya[&&NHX:TOL=64210],crataraea[&&NHX:TOL=64211],ctenopeuca[&&NHX:TOL=64212],dasygnypeta[&&NHX:TOL=64213],dasymera[&&NHX:TOL=64214],decusa[&&NHX:TOL=64215],demoglena[&&NHX:TOL=64216],derocala[&&NHX:TOL=64217],devia[&&NHX:TOL=64218],dexiogyia[&&NHX:TOL=64219],diacanthochara[&&NHX:TOL=64220],dinarda[&&NHX:TOL=64221],dinusa[&&NHX:TOL=64222],diploxenus[&&NHX:TOL=64223],dymerinx[&&NHX:TOL=64224],ecitodulus[&&NHX:TOL=64225],elaphromniusa[&&NHX:TOL=64226],euryalea[&&NHX:TOL=64227],euthorax[&&NHX:TOL=64228],feluva[&&NHX:TOL=64229],franzidota[&&NHX:TOL=64230],gastrolamprusa[&&NHX:TOL=64231],gastrorhopalus[&&NHX:TOL=64232],gennadota[&&NHX:TOL=64233],gnathusa[&&NHX:TOL=64234],gnypeta[&&NHX:TOL=64235],gnypetalia[&&NHX:TOL=64236],gnypetella[&&NHX:TOL=64237],gnypetoidea[&&NHX:TOL=64238],gnypetosoma[&&NHX:TOL=64239],gyronotus[&&NHX:TOL=64240],gyronycha[&&NHX:TOL=64241],haplochara[&&NHX:TOL=64242],haploglossa[&&NHX:TOL=64243],homoeusa[&&NHX:TOL=64244],hygropetrophila[&&NHX:TOL=64245],hygropora[&&NHX:TOL=64246],idiostiba[&&NHX:TOL=64247],ilyobates[&&NHX:TOL=64248],irmaria[&&NHX:TOL=64249],ischnoglossa[&&NHX:TOL=64250],(ischnopoda caliusa[&&NHX:TOL=64252],ischnopoda cathusya[&&NHX:TOL=64253],ischnopoda ischnopoda[&&NHX:TOL=64254],ischnopoda ischnopoderona[&&NHX:TOL=64255])ischnopoda[&&NHX:TOL=64251],ischyradelia[&&NHX:TOL=64256],ischyrocolpura[&&NHX:TOL=64257],kaweshkarusa[&&NHX:TOL=64258],leichusa[&&NHX:TOL=64259],leptobamona[&&NHX:TOL=64260],liometoxenus[&&NHX:TOL=64261],longipeltina[&&NHX:TOL=64262],losiusa[&&NHX:TOL=64263],makara[&&NHX:TOL=64264],maurachelia[&&NHX:TOL=64265],mecrona[&&NHX:TOL=64266],megocalea[&&NHX:TOL=64267],melanalia[&&NHX:TOL=64268],melvilloxenus[&&NHX:TOL=64269],meotica[&&NHX:TOL=64270],meoticaops[&&NHX:TOL=64271],meoticella[&&NHX:TOL=64272],metocalea[&&NHX:TOL=64273],mimobates[&&NHX:TOL=64274],mniusa[&&NHX:TOL=64275],myrmedonella[&&NHX:TOL=64276],myrmobiota[&&NHX:TOL=64277],neocalodera[&&NHX:TOL=64278],neodemosoma[&&NHX:TOL=64279],neodoxa[&&NHX:TOL=64280],neothetalia[&&NHX:TOL=64281],newtonusa[&&NHX:TOL=64282],nordenskjoldella[&&NHX:TOL=64283],ocalea[&&NHX:TOL=64284],ocyusa[&&NHX:TOL=64285],ocyustiba[&&NHX:TOL=64286],oligonotus[&&NHX:TOL=64287],oreuryalea[&&NHX:TOL=64288],oreusa[&&NHX:TOL=64289],(oxypoda atlantoxypoda[&&NHX:TOL=64291],oxypoda baeoglena[&&NHX:TOL=64292],oxypoda baptopoda[&&NHX:TOL=64293],oxypoda bessopora[&&NHX:TOL=64294],oxypoda canaroxypoda[&&NHX:TOL=64295],oxypoda cyrtonychochaeta[&&NHX:TOL=64296],oxypoda demosoma[&&NHX:TOL=64297],oxypoda deropoda[&&NHX:TOL=64298],oxypoda disochara[&&NHX:TOL=64299],oxypoda mycetodrepa[&&NHX:TOL=64300],oxypoda oxypoda[&&NHX:TOL=64301],oxypoda paroxypoda[&&NHX:TOL=64302],oxypoda podoxya[&&NHX:TOL=64303],oxypoda sedomoma[&&NHX:TOL=64304],oxypoda sphenoma[&&NHX:TOL=64305])oxypoda[&&NHX:TOL=64290],pachycerota[&&NHX:TOL=64306],parabainusa[&&NHX:TOL=64307],paradilacra[&&NHX:TOL=64308],paragnypeta[&&NHX:TOL=64309],parahydrosmecta[&&NHX:TOL=64310],paramarochara[&&NHX:TOL=64311],paraphyma[&&NHX:TOL=64312],paraphytopus[&&NHX:TOL=64313],parapimela[&&NHX:TOL=64314],paratachyusa[&&NHX:TOL=64315],parocalea[&&NHX:TOL=64316],(parocyusa parocyusa[&&NHX:TOL=64318],parocyusa tetralaucopora[&&NHX:TOL=64319])parocyusa[&&NHX:TOL=64317],pentanota[&&NHX:TOL=64320],phasmota[&&NHX:TOL=64321],phloeopora[&&NHX:TOL=64322],platysmarthrusa[&&NHX:TOL=64323],pnephorusa[&&NHX:TOL=64324],poikilnotha[&&NHX:TOL=64325],polyacanthode[&&NHX:TOL=64326],polylobinus[&&NHX:TOL=64327],polylobus[&&NHX:TOL=64328],porocallus[&&NHX:TOL=64329],poromniusa[&&NHX:TOL=64330],prymnorhopala[&&NHX:TOL=64331],pseudapimela[&&NHX:TOL=64332],pseudocyusa[&&NHX:TOL=64333],pseudognypeta[&&NHX:TOL=64334],pseudomeotica[&&NHX:TOL=64335],pseudomyllaena[&&NHX:TOL=64336],pseudophaena[&&NHX:TOL=64337],pyroglossa[&&NHX:TOL=64338],randa[&&NHX:TOL=64339],rechota[&&NHX:TOL=64340],rheobioma[&&NHX:TOL=64341],rhomphocallus[&&NHX:TOL=64342],rhopalotella[&&NHX:TOL=64343],saphoglossa[&&NHX:TOL=64344],smetanaetha[&&NHX:TOL=64345],somasterochara[&&NHX:TOL=64346],spanioda[&&NHX:TOL=64347],sphaenidatoma[&&NHX:TOL=64348],stichoglossa[&&NHX:TOL=64349],sytus[&&NHX:TOL=64350],tachyusa[&&NHX:TOL=64351],tectusa[&&NHX:TOL=64352],teliusa[&&NHX:TOL=64353],teratanytoma[&&NHX:TOL=64354],(thiasophila apatusa[&&NHX:TOL=64356],thiasophila thiasophila[&&NHX:TOL=64357])thiasophila[&&NHX:TOL=64355],thinonoma[&&NHX:TOL=64358],thripsophaga[&&NHX:TOL=64359],tomocoryphusa[&&NHX:TOL=64360],topikoglossa[&&NHX:TOL=64361],trichoglossina[&&NHX:TOL=64362],tricolpochila[&&NHX:TOL=64363],triglotta[&&NHX:TOL=64364],troglocyphodas[&&NHX:TOL=64365],weineria[&&NHX:TOL=64366],xenomma[&&NHX:TOL=64367],zoosetha[&&NHX:TOL=64368],barychara[&&NHX:TOL=64369])oxypodini[&&NHX:TOL=9835],(attonia[&&NHX:TOL=64372],autalia[&&NHX:TOL=64373],compsusa[&&NHX:TOL=64374],eudera[&&NHX:TOL=64375],gansia[&&NHX:TOL=64376],ophioglossa[&&NHX:TOL=64377],rhopalogastrum[&&NHX:TOL=64378])autaliini[&&NHX:TOL=9836],((demerilla[&&NHX:TOL=64380],demerina[&&NHX:TOL=64381],demerinda[&&NHX:TOL=64382],derelina[&&NHX:TOL=64383],derema[&&NHX:TOL=64384],deremilla[&&NHX:TOL=64385],dorylobactrus[&&NHX:TOL=64386],dorylobius[&&NHX:TOL=64387],dorylocerus[&&NHX:TOL=64388],dorylonilla[&&NHX:TOL=64389],dorylophila[&&NHX:TOL=64390],dorylostethus[&&NHX:TOL=64391],draconula[&&NHX:TOL=64392],emerda[&&NHX:TOL=64393],fossulopora[&&NHX:TOL=64394],kamptomerus[&&NHX:TOL=64395],koilomera[&&NHX:TOL=64396],lokomera[&&NHX:TOL=64397],macfieia[&&NHX:TOL=64398],medera[&&NHX:TOL=64399],nitinella[&&NHX:TOL=64400],notelyglypha[&&NHX:TOL=64401],ponerilla[&&NHX:TOL=64402],redema[&&NHX:TOL=64403],rhopalinda[&&NHX:TOL=64404],rodylopora[&&NHX:TOL=64405],rylodophila[&&NHX:TOL=64406])dorylophilina[&&NHX:TOL=64379],(mimanomma[&&NHX:TOL=64408],siafumimus[&&NHX:TOL=64409])mimanommatina[&&NHX:TOL=64407])mimanommatini[&&NHX:TOL=9837],(termitosius[&&NHX:TOL=64410],termitosuga[&&NHX:TOL=64411],(abroteles[&&NHX:TOL=64413],termitophya[&&NHX:TOL=64414])abrotelina[&&NHX:TOL=64412],(austrospirachtha[&&NHX:TOL=64416],coatonachthodes[&&NHX:TOL=64417],corotoca[&&NHX:TOL=64418],eburniola[&&NHX:TOL=64419],fulleroxenus[&&NHX:TOL=64420],nasutimimus[&&NHX:TOL=64421],nasutiptochus[&&NHX:TOL=64422],neoguinella[&&NHX:TOL=64423],nigriphilus[&&NHX:TOL=64424],oideprosoma[&&NHX:TOL=64425],spirachtha[&&NHX:TOL=64426],spirachthodes[&&NHX:TOL=64427],termitomimus[&&NHX:TOL=64428],termitoptocinus[&&NHX:TOL=64429],termitopula[&&NHX:TOL=64430],termitopullus[&&NHX:TOL=64431],thyreoxenus[&&NHX:TOL=64432],tumulipcinus[&&NHX:TOL=64433])corotocina[&&NHX:TOL=64415],(eburniogaster[&&NHX:TOL=64435],termitonidia[&&NHX:TOL=64436])eburniogastrina[&&NHX:TOL=64434],nasutitella[&&NHX:TOL=64437],sphuridaethes[&&NHX:TOL=64440],termitochara[&&NHX:TOL=64443],termitocupidus[&&NHX:TOL=64446],(idiogaster[&&NHX:TOL=64450],idioptochus[&&NHX:TOL=64451],leucoptochus[&&NHX:TOL=64452],melanoptochus[&&NHX:TOL=64453],millotoca[&&NHX:TOL=64454],neotermitogaster[&&NHX:TOL=64455],rhadinoxenus[&&NHX:TOL=64456],termella[&&NHX:TOL=64457],termitella[&&NHX:TOL=64458],termitellodes[&&NHX:TOL=64459],termitogaster[&&NHX:TOL=64460],termitoides[&&NHX:TOL=64461],termitomorpha[&&NHX:TOL=64462],termitonasus[&&NHX:TOL=64463],termitosyne[&&NHX:TOL=64464],termitosynodes[&&NHX:TOL=64465],trachopeplus[&&NHX:TOL=64466],xenogaster[&&NHX:TOL=64467],xenopelta[&&NHX:TOL=64468])termitogastrina[&&NHX:TOL=64449],(fonsechellus[&&NHX:TOL=64470],mormellus[&&NHX:TOL=64471],oecidiophilus[&&NHX:TOL=64472],parvidolum[&&NHX:TOL=64473],perlinctus[&&NHX:TOL=64474],termitoiceus[&&NHX:TOL=64475])termitoiceina[&&NHX:TOL=64469],termitopithus[&&NHX:TOL=64476],(affinoptochus[&&NHX:TOL=64480],australoptochus[&&NHX:TOL=64481],eutermitoptochus[&&NHX:TOL=64482],hospitaliptochus[&&NHX:TOL=64483],lacessiptochus[&&NHX:TOL=64484],paracorotoca[&&NHX:TOL=64485],termitoptochus[&&NHX:TOL=64486])termitoptochina[&&NHX:TOL=64479],(ptocholellus[&&NHX:TOL=64488],reginamimus[&&NHX:TOL=64489],termitozophilus[&&NHX:TOL=64490],termituncula[&&NHX:TOL=64491],timeparthenus[&&NHX:TOL=64492])timeparthenina[&&NHX:TOL=64487])corotocini[&&NHX:TOL=9838],((beyeria[&&NHX:TOL=64493],crematoxenus[&&NHX:TOL=64494],cryptomimus[&&NHX:TOL=64495],diploeciton[&&NHX:TOL=64496],ecitosius[&&NHX:TOL=64497],ecitotima[&&NHX:TOL=64498],neivaphilus[&&NHX:TOL=64499],neobeyeria[&&NHX:TOL=64500],philacamatus[&&NHX:TOL=64501],probeyeria[&&NHX:TOL=64502],pulicomorpha[&&NHX:TOL=64503])crematoxenini[&&NHX:TOL=9840],(labidopullus[&&NHX:TOL=104427],(acamatusinella[&&NHX:TOL=104429],ecitomerus[&&NHX:TOL=104430],ecitophanes[&&NHX:TOL=104431],ecitosoma[&&NHX:TOL=104432],leptanillophilus[&&NHX:TOL=104433],mimacamatus[&&NHX:TOL=104434])leptanillophilina[&&NHX:TOL=104428],(labidoglobus[&&NHX:TOL=104436],labidosphaerula[&&NHX:TOL=104437],mimeciton[&&NHX:TOL=104438],paramimeciton[&&NHX:TOL=104439],pseudomimeciton[&&NHX:TOL=104440])mimecitina[&&NHX:TOL=104435],(labidomimus[&&NHX:TOL=104442],mimonilla[&&NHX:TOL=104443])mimonillina[&&NHX:TOL=104441])leptanillophilini [&&NHX:TOL=9841])[&&NHX:TOL=9839],(diglotta[&&NHX:TOL=64504],paradiglotta[&&NHX:TOL=64505])diglottini[&&NHX:TOL=9842],digrammus miricollis[&&NHX:TOL=9843],(dorylocratus[&&NHX:TOL=104423],dorylomimus[&&NHX:TOL=104424],dorylonannus[&&NHX:TOL=104425],jeanneliusa[&&NHX:TOL=104426])dorylomimini[&&NHX:TOL=104422],drepanoxenus[&&NHX:TOL=9845],(campbellia[&&NHX:TOL=64510],ecitochara[&&NHX:TOL=64511],ecitodaemon[&&NHX:TOL=64512],ecitomorpha[&&NHX:TOL=64513],ecitophya[&&NHX:TOL=64514],ecitoschneirla[&&NHX:TOL=64515],ecitosymbia[&&NHX:TOL=64516],ecitoxenia[&&NHX:TOL=64517],retteneciton[&&NHX:TOL=64518],seeverseciton[&&NHX:TOL=64519])ecitocharini[&&NHX:TOL=9846],ecitogaster[&&NHX:TOL=9847],(eusteniamorpha[&&NHX:TOL=64522],(eustenidia eustenidia[&&NHX:TOL=64524],eustenidia microeustenidia[&&NHX:TOL=64525])eustenidia[&&NHX:TOL=64523])eusteniamorphini[&&NHX:TOL=9848],((akrincastiba[&&NHX:TOL=64526],aleodorus[&&NHX:TOL=64527],almoria[&&NHX:TOL=64528],ameipseusa[&&NHX:TOL=64529],anaulacaspis[&&NHX:TOL=64530],bohemiellina[&&NHX:TOL=64531],borboropora[&&NHX:TOL=64532],borneopora[&&NHX:TOL=64533],bryobiota[&&NHX:TOL=64534],cordalia[&&NHX:TOL=64535],dasytricheta[&&NHX:TOL=64536],drepanopora[&&NHX:TOL=64537],eccoptoglossa[&&NHX:TOL=64538],ecomorypora[&&NHX:TOL=64539],euphorbagria[&&NHX:TOL=64540],falagria[&&NHX:TOL=64541],falagrioma[&&NHX:TOL=64542],falagriota[&&NHX:TOL=64543],galafria[&&NHX:TOL=64544],guajira[&&NHX:TOL=64545],himalagria[&&NHX:TOL=64546],indomyrmecopora[&&NHX:TOL=64547],leptagria[&&NHX:TOL=64548],lissagria[&&NHX:TOL=64549],lophagria[&&NHX:TOL=64550],myrmecocephalus[&&NHX:TOL=64551],(myrmecopora amechanopora[&&NHX:TOL=64553],myrmecopora anatolagria[&&NHX:TOL=64554],myrmecopora euphorbiusa[&&NHX:TOL=64555],myrmecopora iliusa[&&NHX:TOL=64556],myrmecopora lamproxenusa[&&NHX:TOL=64557],myrmecopora myrmecopora[&&NHX:TOL=64558],myrmecopora paraxenusa[&&NHX:TOL=64559],myrmecopora xenusa[&&NHX:TOL=64560])myrmecopora[&&NHX:TOL=64552],pheifalagria[&&NHX:TOL=64561],pheigetoxenus[&&NHX:TOL=64562],plesiosipalia[&&NHX:TOL=64563],pyromecroma[&&NHX:TOL=64564],scytoglossa[&&NHX:TOL=64565],termitolara[&&NHX:TOL=64566],tropidera[&&NHX:TOL=64567])falagriini[&&NHX:TOL=9850],(dinardilla[&&NHX:TOL=64568],sceptobius[&&NHX:TOL=64569])sceptobiini[&&NHX:TOL=9851])[&&NHX:TOL=9849],(dicuspidoxenus[&&NHX:TOL=64570],dicuspiphilus[&&NHX:TOL=64571],dlefa[&&NHX:TOL=64572],felda[&&NHX:TOL=64573],fisiphila[&&NHX:TOL=64574],lefda[&&NHX:TOL=64575],pericapritoxenus[&&NHX:TOL=64576],tekalita[&&NHX:TOL=64577],termitobaena[&&NHX:TOL=64578])feldini[&&NHX:TOL=9852],(actocharis readingii[&&NHX:TOL=104388],aisthentusa[&&NHX:TOL=64579],ameristoglossa[&&NHX:TOL=64580],anamignusa[&&NHX:TOL=64581],andrikothelyna[&&NHX:TOL=64582],(anebolura anebolura[&&NHX:TOL=64584],anebolura deharvengina[&&NHX:TOL=64585],anebolura maresia[&&NHX:TOL=64586],anebolura oroussetina[&&NHX:TOL=64587])anebolura[&&NHX:TOL=64583],animobata[&&NHX:TOL=64588],anomalophaena[&&NHX:TOL=64589],(anomognathus anomognathus[&&NHX:TOL=64591],anomognathus mindoria[&&NHX:TOL=64592])anomognathus[&&NHX:TOL=64590],antithetusa[&&NHX:TOL=64593],apatelomixidota[&&NHX:TOL=64594],aphelusa[&&NHX:TOL=64595],aplopalpus[&&NHX:TOL=64596],aprosdoketusa[&&NHX:TOL=64597],arrostoryta[&&NHX:TOL=64598],asthenesita[&&NHX:TOL=64599],brachyda[&&NHX:TOL=64600],brachyglyptaglossa[&&NHX:TOL=64601],cajachara[&&NHX:TOL=64602],caloderina[&&NHX:TOL=64603],cantabrodytes[&&NHX:TOL=64604],caralepta[&&NHX:TOL=64605],cephalomalota[&&NHX:TOL=64606],(cephaloxynum cephaloxynum[&&NHX:TOL=64608],cephaloxynum ponticulus[&&NHX:TOL=64609])cephaloxynum[&&NHX:TOL=64607],chledophila[&&NHX:TOL=64610],coenonica[&&NHX:TOL=64611],cyllogerusa[&&NHX:TOL=64612],cyphea[&&NHX:TOL=64613],dianusa[&&NHX:TOL=64614],(diestota aphaenoglossa[&&NHX:TOL=64616],diestota apheloglossa[&&NHX:TOL=64617],diestota diestota[&&NHX:TOL=64618],diestota eutrichostygna[&&NHX:TOL=64619],diestota ocyupora[&&NHX:TOL=64620])diestota[&&NHX:TOL=64615],dimastiglossa[&&NHX:TOL=64621],dinardopsis[&&NHX:TOL=64622],dolichoderma[&&NHX:TOL=64623],drepanomastax[&&NHX:TOL=64624],eccoptogenia[&&NHX:TOL=64625],epamyktoglossa[&&NHX:TOL=64626],episemina[&&NHX:TOL=64627],episkilepta[&&NHX:TOL=64628],erastriusa[&&NHX:TOL=64629],eudiestota[&&NHX:TOL=64630],eumecognathus[&&NHX:TOL=64631],eupachytoma[&&NHX:TOL=64632],euryloxa[&&NHX:TOL=64633],(euryusa ectolabrus[&&NHX:TOL=64635],euryusa euryusa[&&NHX:TOL=64636])euryusa[&&NHX:TOL=64634],eusipalia[&&NHX:TOL=64637],gastrophaena[&&NHX:TOL=64638],herpastedia[&&NHX:TOL=64639],heterota[&&NHX:TOL=64640],holisomimus[&&NHX:TOL=64641],homalota[&&NHX:TOL=64642],homoiobrachida[&&NHX:TOL=64643],hoplomicra[&&NHX:TOL=64644],hygronomalota[&&NHX:TOL=64645],hygroptera[&&NHX:TOL=64646],kanakaloma[&&NHX:TOL=64647],lembonia[&&NHX:TOL=64648],(leptusa adexiopisalia[&&NHX:TOL=64650],leptusa adoxopisalia[&&NHX:TOL=64651],leptusa afroleptusa[&&NHX:TOL=64652],leptusa akratopisalia[&&NHX:TOL=64653],leptusa amalopisalia[&&NHX:TOL=64654],leptusa anisopisalia[&&NHX:TOL=64655],leptusa anomopisalia[&&NHX:TOL=64656],leptusa anosiopisalia[&&NHX:TOL=64657],leptusa aphaireleptusa[&&NHX:TOL=64658],leptusa baldopisalia[&&NHX:TOL=64659],leptusa boreoleptusa[&&NHX:TOL=64660],leptusa bothrydiopisalia[&&NHX:TOL=64661],leptusa bryopisalia[&&NHX:TOL=64662],leptusa chondrelytropisalia[&&NHX:TOL=64663],leptusa chondridiopisalia[&&NHX:TOL=64664],leptusa chondropisalia[&&NHX:TOL=64665],leptusa cidnopisalia[&&NHX:TOL=64666],leptusa comphopisalia[&&NHX:TOL=64667],leptusa craspedopisalia[&&NHX:TOL=64668],leptusa cryptopisalia[&&NHX:TOL=64669],leptusa cyllopisalia[&&NHX:TOL=64670],leptusa dendroleptusa[&&NHX:TOL=64671],leptusa drepanoleptusa[&&NHX:TOL=64672],leptusa dysleptusa[&&NHX:TOL=64673],leptusa ectinopisalia[&&NHX:TOL=64674],leptusa emmelopisalia[&&NHX:TOL=64675],leptusa entomophallopisalia[&&NHX:TOL=64676],leptusa eospisalia[&&NHX:TOL=64677],leptusa eremopisalia[&&NHX:TOL=64678],leptusa eucryptusa[&&NHX:TOL=64679],leptusa evaniopisalia[&&NHX:TOL=64680],leptusa exaeretopisalia[&&NHX:TOL=64681],leptusa gallopisalia[&&NHX:TOL=64682],leptusa geopisalia[&&NHX:TOL=64683],leptusa gnopheropisalia[&&NHX:TOL=64684],leptusa habropisalia[&&NHX:TOL=64685],leptusa halmaeusa[&&NHX:TOL=64686],leptusa hemipasilia[&&NHX:TOL=64687],leptusa heteroleptusa[&&NHX:TOL=64688],leptusa heterotyphlopasilia[&&NHX:TOL=64689],leptusa homopisalia[&&NHX:TOL=64690],leptusa ischnopisalia[&&NHX:TOL=64691],leptusa kochliodepisalia[&&NHX:TOL=64692],leptusa koilokoryphepisalia[&&NHX:TOL=64693],leptusa lasiopisalia[&&NHX:TOL=64694],leptusa lathripisalia[&&NHX:TOL=64695],leptusa leptopasilia[&&NHX:TOL=64696],leptusa leptusa[&&NHX:TOL=64697],leptusa liopisalia[&&NHX:TOL=64698],leptusa megacolypisalia[&&NHX:TOL=64699],leptusa melopisalia[&&NHX:TOL=64700],leptusa metaplasmopasilia[&&NHX:TOL=64701],leptusa microcolypisalia[&&NHX:TOL=64702],leptusa micropisalia[&&NHX:TOL=64703],leptusa myopopisalia[&&NHX:TOL=64704],leptusa nanoglossa[&&NHX:TOL=64705],leptusa nanopisalia[&&NHX:TOL=64706],leptusa neopisalia[&&NHX:TOL=64707],leptusa nesopisalia[&&NHX:TOL=64708],leptusa oligopisalia[&&NHX:TOL=64709],leptusa oncopisalia[&&NHX:TOL=64710],leptusa oreopisalia[&&NHX:TOL=64711],leptusa pachygastropisalia[&&NHX:TOL=64712],leptusa pachygluta[&&NHX:TOL=64713],leptusa parapisalia[&&NHX:TOL=64714],leptusa pasilia[&&NHX:TOL=64715],leptusa pisalia[&&NHX:TOL=64716],leptusa planepisalia[&&NHX:TOL=64717],leptusa protoleptusa[&&NHX:EXT=Y:TOL=64718],leptusa rhombopisalia[&&NHX:TOL=64719],leptusa roubaliusa[&&NHX:TOL=64720],leptusa scelopisalia[&&NHX:TOL=64721],leptusa scoliophallopisalia[&&NHX:TOL=64722],leptusa scolioplatypisalia[&&NHX:TOL=64723],leptusa stenoleptusa[&&NHX:TOL=64724],leptusa stictopisalia[&&NHX:TOL=64725],leptusa toxophallopisalia[&&NHX:TOL=64726],leptusa trichopasilia[&&NHX:TOL=64727],leptusa typhlopasilia[&&NHX:TOL=64728],leptusa ulitusa[&&NHX:TOL=64729])leptusa[&&NHX:TOL=64649],(linoglossa axinocolya[&&NHX:TOL=64731],linoglossa linoglossa[&&NHX:TOL=64732],linoglossa lophoglossa[&&NHX:TOL=64733])linoglossa[&&NHX:TOL=64730],lomaglossina[&&NHX:TOL=64734],madecusa[&&NHX:TOL=64735],megaloscapa[&&NHX:TOL=64736],megaparaglossa[&&NHX:TOL=64737],melainacnemisa[&&NHX:TOL=64738],metechonica[&&NHX:TOL=64739],methistemistiba[&&NHX:TOL=64740],microdinarda[&&NHX:TOL=64741],mimopisalia[&&NHX:TOL=64742],neactocharis[&&NHX:TOL=64743],neidosphena[&&NHX:TOL=64744],(nemoedia nemoedia[&&NHX:TOL=64746],nemoedia novocaledoniella[&&NHX:TOL=64747])nemoedia[&&NHX:TOL=64745],neocoenonica[&&NHX:TOL=64748],(neoleptusa neoleptusa[&&NHX:TOL=64750],neoleptusa physetotoma[&&NHX:TOL=64751])neoleptusa[&&NHX:TOL=64749],neomalota[&&NHX:TOL=64752],neosilusa[&&NHX:TOL=64753],omologlusa[&&NHX:TOL=64754],oroekklina[&&NHX:TOL=64755],oroussetiella[&&NHX:TOL=64756],panbrachyna[&&NHX:TOL=64757],parabrachida[&&NHX:TOL=64758],paractocharis[&&NHX:TOL=64759],paralinoglossa[&&NHX:TOL=64760],parasilusa[&&NHX:TOL=64761],pareudera[&&NHX:TOL=64762],paroxypodinus[&&NHX:TOL=64763],philoleptusa[&&NHX:TOL=64764],piescymnida[&&NHX:TOL=64765],(plesiomalota chaetopiezusa[&&NHX:TOL=64767],plesiomalota heteromalota[&&NHX:TOL=64768],plesiomalota leptosomaphya[&&NHX:TOL=64769],plesiomalota microchara[&&NHX:TOL=64770],plesiomalota microusa[&&NHX:TOL=64771],plesiomalota plesiomalota[&&NHX:TOL=64772])plesiomalota[&&NHX:TOL=64766],polytelusa[&&NHX:TOL=64773],pomariella[&&NHX:TOL=64774],psephothetemusa[&&NHX:TOL=64775],pseudomicrodota[&&NHX:TOL=64776],pseudopisalia[&&NHX:TOL=64777],pseudoplacusa[&&NHX:TOL=64778],pseudosilusa[&&NHX:TOL=64779],pseudostenusa[&&NHX:TOL=64780],rhopalocerina[&&NHX:TOL=64781],siagotanyx[&&NHX:TOL=64782],(silusa silusa[&&NHX:TOL=64784],silusa stenusa[&&NHX:TOL=64785])silusa[&&NHX:TOL=64783],solenoglossa[&&NHX:TOL=64786],sphendysglossa[&&NHX:TOL=64787],stenomastax[&&NHX:TOL=64788],stichostigma[&&NHX:TOL=64789],stictomadecassina[&&NHX:TOL=64790],sulepta[&&NHX:TOL=64791],tachiona[&&NHX:TOL=64792],tachychara[&&NHX:TOL=64793],tachyusida[&&NHX:TOL=64794],tahitia[&&NHX:TOL=64795],taraktomora[&&NHX:TOL=64796],thecturella[&&NHX:TOL=64797],thecturota[&&NHX:TOL=64798],thrichidryas[&&NHX:TOL=64799],trachystegosoma[&&NHX:TOL=64800],trichidryas[&&NHX:TOL=64801],tropoleptusa[&&NHX:TOL=64802],troposilusa[&&NHX:TOL=64803],typhlomalota[&&NHX:TOL=64804],xenobiota[&&NHX:TOL=64805],(austrasilida[&&NHX:TOL=64807],bolitochara[&&NHX:TOL=64808],epipedopora[&&NHX:TOL=64809],hongophila[&&NHX:TOL=64810],madegassochara[&&NHX:TOL=64811],neotobia[&&NHX:TOL=64812],phymatura[&&NHX:TOL=64813],pleurotobia[&&NHX:TOL=64814],prosoponotha[&&NHX:TOL=64815],pseudatheta[&&NHX:TOL=64816],silusida[&&NHX:TOL=64817],stictalia[&&NHX:TOL=64818],tanystetha[&&NHX:TOL=64819])bolitocharina[&&NHX:TOL=64806],(adelarthra[&&NHX:TOL=64821],afrobrachida[&&NHX:TOL=64822],agaricochara[&&NHX:TOL=64823],agaricomorpha[&&NHX:TOL=64824],brachida[&&NHX:TOL=64825],brachycantharus[&&NHX:TOL=64826],brachychara[&&NHX:TOL=64827],dactyloglossa[&&NHX:TOL=64828],encephalus[&&NHX:TOL=64829],eumicrota[&&NHX:TOL=64830],(gyrophaena agaricophaena[&&NHX:TOL=64832],gyrophaena enkentrophaena[&&NHX:TOL=64833],gyrophaena gyrophaena[&&NHX:TOL=64834],gyrophaena leptarthrophaena[&&NHX:TOL=64835],gyrophaena orphnebioidea[&&NHX:TOL=64836],gyrophaena phaenogyra[&&NHX:TOL=64837],gyrophaena razia[&&NHX:TOL=64838])gyrophaena[&&NHX:TOL=64831],mesophaena[&&NHX:TOL=64839],microbrachida[&&NHX:TOL=64840],neobrachida[&&NHX:TOL=64841],neobrachychara[&&NHX:TOL=64842],notiomerinx[&&NHX:TOL=64843],(phanerota acanthophaena[&&NHX:TOL=64845],phanerota phanerota[&&NHX:TOL=64846])phanerota[&&NHX:TOL=64844],probrachida[&&NHX:TOL=64847],pseudobrachida[&&NHX:TOL=64848],pseudoligota[&&NHX:TOL=64849],sternotropa[&&NHX:TOL=64850])gyrophaenina[&&NHX:TOL=64820])homalotini[&&NHX:TOL=9853],(benickia[&&NHX:TOL=64851],caloderella[&&NHX:TOL=64852],cryptocompsus[&&NHX:TOL=64853],heterotaxus[&&NHX:TOL=64854],hygrochara[&&NHX:TOL=64855],hygronoma[&&NHX:TOL=64856],pediculota[&&NHX:TOL=64857],platyepipedia[&&NHX:TOL=64858],protinodes[&&NHX:TOL=64859])hygronomini[&&NHX:TOL=9854],(akanthoystera[&&NHX:TOL=64860],baltioligota[&&NHX:EXT=Y:TOL=64861],cypha[&&NHX:TOL=64862],holobus[&&NHX:TOL=64863],liophaena[&&NHX:TOL=64864],microtachyporus[&&NHX:TOL=64865],nematoscelis[&&NHX:TOL=64866],neodecusa[&&NHX:TOL=64867],oligota[&&NHX:TOL=64868],oligusa[&&NHX:TOL=64869],typhlocyptus[&&NHX:TOL=64870])hypocyphtini[&&NHX:TOL=9855],leucocraspedum[&&NHX:TOL=9856],(amblopusa[&&NHX:TOL=64873],baeostethus[&&NHX:TOL=64874],diaulota[&&NHX:TOL=64875],halorhadinus[&&NHX:TOL=64876],liparocephalus[&&NHX:TOL=64877],moorea[&&NHX:TOL=64878],paramblopusa[&&NHX:TOL=64879],salinamexus[&&NHX:TOL=64880],thinobiosus[&&NHX:TOL=64881])liparocephalini[&&NHX:TOL=9857],pagla[&&NHX:TOL=9858],paradoxenusa silvestrii[&&NHX:TOL=9859],(philotermes[&&NHX:TOL=64886],pseudophilotermes[&&NHX:TOL=64887])philotermitini[&&NHX:TOL=9861],(arena[&&NHX:TOL=64888],cameronium[&&NHX:TOL=64889],(phytosus actosus[&&NHX:TOL=64891],phytosus euphytosus[&&NHX:TOL=64892],phytosus phytosus[&&NHX:TOL=64893])phytosus[&&NHX:TOL=64890])phytosini[&&NHX:TOL=9862],(euvira[&&NHX:TOL=64894],placusa[&&NHX:TOL=64895])placusini[&&NHX:TOL=9863],(austrointhus[&&NHX:TOL=64896],indinthus[&&NHX:TOL=64897],malayinthus[&&NHX:TOL=64898],pseudoperinthus[&&NHX:TOL=64899])pseudoperinthini[&&NHX:TOL=9864],(adoketoxenus[&&NHX:TOL=64900],aenictoxenus[&&NHX:TOL=64901],anommatophilus[&&NHX:TOL=64902],anommatoxenus[&&NHX:TOL=64903],cephaplakoxena[&&NHX:TOL=64904],delibius[&&NHX:TOL=64905],deliodes[&&NHX:TOL=64906],dorylotyphlus[&&NHX:TOL=64907],doryloxenus[&&NHX:TOL=64908],eupygostenus[&&NHX:TOL=64909],lydorus[&&NHX:TOL=64910],mandera[&&NHX:TOL=64911],mesomegaskela[&&NHX:TOL=64912],micropolemon[&&NHX:TOL=64913],mimocete[&&NHX:TOL=64914],neopygostenus[&&NHX:TOL=64915],odontoxenus[&&NHX:TOL=64916],pegestenus[&&NHX:TOL=64917],pogostenus[&&NHX:TOL=64918],prodeliodes[&&NHX:TOL=64919],pseudolydorus[&&NHX:TOL=64920],pygoplanus[&&NHX:TOL=64921],pygostenus[&&NHX:TOL=64922],sympolemon[&&NHX:TOL=64923],typhlopolemon[&&NHX:TOL=64924],typhloponemys[&&NHX:TOL=64925],xenidus[&&NHX:TOL=64926])pygostenini[&&NHX:TOL=9865],skatitoxenus[&&NHX:TOL=9866],(athexenia[&&NHX:TOL=64929],(termitodiscus[&&NHX:TOL=64933],termitogerrus[&&NHX:TOL=64934])termitodiscina[&&NHX:TOL=64932])termitodiscini[&&NHX:TOL=9867],((coptophysa[&&NHX:TOL=64936],coptophysella[&&NHX:TOL=64937],coptoxenus[&&NHX:TOL=64938],hetairotermes[&&NHX:TOL=64939],japanophilus[&&NHX:TOL=64940],sinophilus[&&NHX:TOL=64941],termitobra[&&NHX:TOL=64942])hetairotermitina[&&NHX:TOL=64935],(blapticoxenus[&&NHX:TOL=64944],paratermitosocius[&&NHX:TOL=64945],termitohospes[&&NHX:TOL=64946],termitosocius[&&NHX:TOL=64947],termitosodalis[&&NHX:TOL=64948])termitohospitina[&&NHX:TOL=64943])termitohospitini[&&NHX:TOL=9868],((alzada[&&NHX:TOL=64950],catalina[&&NHX:TOL=64951],eutermitophila[&&NHX:TOL=64952],gralloperinthus[&&NHX:TOL=64953],lauella[&&NHX:TOL=64954],macrognathellus[&&NHX:TOL=64955],paralauella[&&NHX:TOL=64956],paraperinthus[&&NHX:TOL=64957],perinthodes[&&NHX:TOL=64958],perinthus[&&NHX:TOL=64959],physoperinthus[&&NHX:TOL=64960],poduroides[&&NHX:TOL=64961],termitocola[&&NHX:TOL=64962],termitonicus[&&NHX:TOL=64963],termitopelta[&&NHX:TOL=64964])perinthina[&&NHX:TOL=64949],(chaetonannus[&&NHX:TOL=64966],eunannodes[&&NHX:TOL=64967],macrotrichurus[&&NHX:TOL=64968],nannellus[&&NHX:TOL=64969],nannusa[&&NHX:TOL=64970],termitocomes[&&NHX:TOL=64971],termitonannus[&&NHX:TOL=64972],termitonilla[&&NHX:TOL=64973])termitonannina[&&NHX:TOL=64965])termitonannini[&&NHX:TOL=9869],(coatonipulex[&&NHX:TOL=64974],dioxeuta[&&NHX:TOL=64975],macrotermophila[&&NHX:TOL=64976],macrotoxenus[&&NHX:TOL=64977],neodioxeuta[&&NHX:TOL=64978],neotermitotecna[&&NHX:TOL=64979],paratermitopulex[&&NHX:TOL=64980],physomilitaris[&&NHX:TOL=64981],polyteinia[&&NHX:TOL=64982],protermitobia[&&NHX:TOL=64983],termitobia[&&NHX:TOL=64984],termitolinus[&&NHX:TOL=64985],termitonda[&&NHX:TOL=64986],termitopaedia[&&NHX:TOL=64987],termitopulex[&&NHX:TOL=64988],termitotecna[&&NHX:TOL=64989],termitotropha[&&NHX:TOL=64990],termozyras[&&NHX:TOL=64991])termitopaediini[&&NHX:TOL=9870],((pseudotermitoecia[&&NHX:TOL=64993],termitana[&&NHX:TOL=64994],termitoecia[&&NHX:TOL=64995],termitospectrum[&&NHX:TOL=64996])termitospectrina[&&NHX:TOL=64992],(termitusa[&&NHX:TOL=64998],termitusodes[&&NHX:TOL=64999],thoracotusa[&&NHX:TOL=65000])termitusina[&&NHX:TOL=64997])termitusini[&&NHX:TOL=9871],trilobitideus[&&NHX:TOL=9872])[&&NHX:TOL=9825])[&&NHX:TOL=9819])[&&NHX:TOL=9816],akatastopsis papuana[&&NHX:TOL=104389],cordobanus mirabilis[&&NHX:TOL=104390],cryptonotopsis rougemonti[&&NHX:TOL=104397])aleocharinae[&&NHX:TOL=9777],(trichophya[&&NHX:TOL=9779],(habrocerus[&&NHX:TOL=61256],nomimocerus[&&NHX:TOL=61257])habrocerinae[&&NHX:TOL=9780])[&&NHX:TOL=9778])[&&NHX:TOL=9776],((derops[&&NHX:TOL=61276],(lacvietina[&&NHX:TOL=61280],megarthropsis[&&NHX:TOL=61281],nepaliodes[&&NHX:TOL=61282],peitawopsis[&&NHX:TOL=61283])megarthropsini[&&NHX:TOL=61279],(bolitobius[&&NHX:TOL=61285],bolitopunctus[&&NHX:TOL=61286],bryophacis[&&NHX:TOL=61287],bryoporus[&&NHX:TOL=61288],canariobolitobius[&&NHX:TOL=61289],carphacis[&&NHX:TOL=61290],ischnosoma[&&NHX:TOL=61291],(lordithon bobitobus[&&NHX:TOL=61293],lordithon lordithon[&&NHX:TOL=61294])lordithon[&&NHX:TOL=61292],mycetoporus[&&NHX:TOL=61295],neobolitobius[&&NHX:TOL=61296],parabolitobius[&&NHX:TOL=61297])mycetoporini[&&NHX:TOL=61284],(austrotachinus[&&NHX:TOL=61299],cilea[&&NHX:TOL=61300],cileoporus[&&NHX:TOL=61301],coproporus[&&NHX:TOL=61302],coprotachinus[&&NHX:TOL=61303],euconosoma[&&NHX:TOL=61304],lamprinodes[&&NHX:TOL=61305],lamprinus[&&NHX:TOL=61306],leucotachinus[&&NHX:TOL=61307],mimocyptus[&&NHX:TOL=61308],nitidotachinus[&&NHX:TOL=61309],olophrinus[&&NHX:TOL=61310],palaeosepedophilus[&&NHX:EXT=Y:TOL=61311],paracilea[&&NHX:TOL=61312],pseudotachinus[&&NHX:TOL=61313],sepedophilus[&&NHX:TOL=61314],symmixus[&&NHX:TOL=61315],tachinomorphus[&&NHX:TOL=61316],tachinoporus[&&NHX:TOL=61317],tachinoproporus[&&NHX:TOL=61318],(tachinus japanotachinus[&&NHX:TOL=61320],tachinus latotachinus[&&NHX:TOL=61321],tachinus tachinoderus[&&NHX:TOL=61322],tachinus tachinoplesius[&&NHX:TOL=61323],tachinus tachinus[&&NHX:TOL=61324])tachinus[&&NHX:TOL=61319],(tachyporus palporus[&&NHX:TOL=61326],tachyporus tachyporus[&&NHX:TOL=61327])tachyporus[&&NHX:TOL=61325],termitoplus[&&NHX:TOL=61328],urolitus[&&NHX:TOL=61329])tachyporini[&&NHX:TOL=61298],vatesus[&&NHX:TOL=61330],abscondus[&&NHX:EXT=Y:TOL=61269],cuneocharis[&&NHX:EXT=Y:TOL=61270],mesotachinus[&&NHX:EXT=Y:TOL=61271],mesotachyporus[&&NHX:EXT=Y:TOL=61272],ryvkinius[&&NHX:EXT=Y:TOL=61273],tachyporoides[&&NHX:EXT=Y:TOL=61274],undiatina[&&NHX:EXT=Y:TOL=61275])tachyporinae[&&NHX:TOL=9785],((charhyphus[&&NHX:TOL=61258],dytoscotes[&&NHX:TOL=61259],ecbletus[&&NHX:TOL=61260],(phloeocharis phloeocharis[&&NHX:TOL=61262],phloeocharis scotodytes[&&NHX:TOL=61263])phloeocharis[&&NHX:TOL=61261],phloeognathus[&&NHX:TOL=61264],pseudophloeocharis[&&NHX:TOL=61265],vicelva[&&NHX:TOL=61266])phloeocharinae[&&NHX:TOL=9783],olisthaerus[&&NHX:TOL=9784])[&&NHX:TOL=9782])[&&NHX:TOL=9781])[&&NHX:TOL=9775],(((cyparium[&&NHX:TOL=61346],(cerambyciscapha[&&NHX:TOL=61350],diatelium[&&NHX:TOL=61351],euscaphidium[&&NHX:TOL=61352],scaphidium[&&NHX:TOL=61353])scaphidiini[&&NHX:TOL=61349],(ascaphium[&&NHX:TOL=61355],episcaphium[&&NHX:TOL=61356],scaphium[&&NHX:TOL=61357])scaphiini[&&NHX:TOL=61354],(afroscaphium[&&NHX:TOL=61359],alexidia[&&NHX:TOL=61360],amalocera[&&NHX:TOL=61361],amaloceromorpha[&&NHX:TOL=61362],baeocera[&&NHX:TOL=61363],baeoceridium[&&NHX:TOL=61364],bertiscapha[&&NHX:TOL=61365],birocera[&&NHX:TOL=61366],bironium[&&NHX:TOL=61367],brachynoposoma[&&NHX:TOL=61368],brachynopus[&&NHX:TOL=61369],collartium[&&NHX:TOL=61370],curtoscaphosoma[&&NHX:TOL=61371],kasibaeocera[&&NHX:TOL=61372],kathetopodion[&&NHX:TOL=61373],mordelloscaphium[&&NHX:TOL=61374],nesoscapha[&&NHX:TOL=61375],notonewtonia[&&NHX:TOL=61376],paratoxidium[&&NHX:TOL=61377],pseudobironiella[&&NHX:TOL=61378],pseudobironium[&&NHX:TOL=61379],sapitia[&&NHX:TOL=61380],scaphicoma[&&NHX:TOL=61381],scaphischema[&&NHX:TOL=61382],scaphisoma[&&NHX:TOL=61383],scaphobaeocera[&&NHX:TOL=61384],scaphoxium[&&NHX:TOL=61385],sphaeroscapha[&&NHX:TOL=61386],spinoscapha[&&NHX:TOL=61387],termitoscaphium[&&NHX:TOL=61388],toxidium[&&NHX:TOL=61389],tritoxidium[&&NHX:TOL=61390],vickibella[&&NHX:TOL=61391],vituratella[&&NHX:TOL=61392],xotidium[&&NHX:TOL=61393],zinda[&&NHX:TOL=61394])scaphisomatini[&&NHX:TOL=61358])scaphidiinae[&&NHX:TOL=9793],(apatetica[&&NHX:TOL=61395],nodynus[&&NHX:TOL=61396])apateticinae[&&NHX:TOL=9795],(((eupiestus[&&NHX:TOL=61333],hypotelus[&&NHX:TOL=61334],parasiagonum[&&NHX:TOL=61335],piestoneus[&&NHX:TOL=61336],(piestus antropiestus[&&NHX:TOL=61338],piestus elytropiestus[&&NHX:TOL=61339],piestus lissopiestus[&&NHX:TOL=61340],piestus piestus[&&NHX:TOL=61341],piestus trachypiestus[&&NHX:TOL=61342],piestus zirophorus[&&NHX:TOL=61343])piestus[&&NHX:TOL=61337],prognathoides[&&NHX:TOL=61344],siagonium[&&NHX:TOL=61345])piestinae[&&NHX:TOL=9791],((renardia[&&NHX:TOL=66215],eleusis[&&NHX:TOL=92334],zeoleusis[&&NHX:TOL=92335])eleusinini[&&NHX:TOL=66213],sinolispinodes[&&NHX:EXT=Y:TOL=92189],(borolinus[&&NHX:TOL=92191],(leptochirus leptochirus[&&NHX:TOL=92193],leptochirus mesochirus[&&NHX:TOL=92194],leptochirus strongylochirus[&&NHX:TOL=92195],leptochirus tropiochirus[&&NHX:TOL=92196])leptochirus[&&NHX:TOL=92192],(priochirus barychirus[&&NHX:TOL=92198],priochirus cephalomerus[&&NHX:TOL=92199],priochirus euleptarthrus[&&NHX:TOL=92200],priochirus eutriacanthus[&&NHX:TOL=92201],priochirus exochirus[&&NHX:TOL=92202],priochirus leiochirus[&&NHX:TOL=92203],priochirus paraborolinus[&&NHX:TOL=92204],priochirus peucodontus[&&NHX:TOL=92205],priochirus plastus[&&NHX:TOL=92206],priochirus priochirus[&&NHX:TOL=92207],priochirus stigmatochirus[&&NHX:TOL=92208],priochirus syncampsochirus[&&NHX:TOL=92209])priochirus[&&NHX:TOL=92197],thoracochirus[&&NHX:TOL=92210])leptochirini[&&NHX:TOL=92190],(afrosorius[&&NHX:TOL=92212],afrotyphlopsis[&&NHX:TOL=92213],allogonus[&&NHX:TOL=92214],allosorius[&&NHX:TOL=92215],anancosorius[&&NHX:TOL=92216],andringitrana[&&NHX:TOL=92217],arpagonus[&&NHX:TOL=92218],atopocnemius[&&NHX:TOL=92219],bacillopsis[&&NHX:TOL=92220],baculopsis[&&NHX:TOL=92221],bothrys[&&NHX:TOL=92222],craspedus[&&NHX:TOL=92223],cylindrops[&&NHX:TOL=92224],cylindropsis[&&NHX:TOL=92225],edapholotrochus[&&NHX:TOL=92226],euparagonus[&&NHX:TOL=92227],fagelia[&&NHX:TOL=92228],gigarthrus[&&NHX:TOL=92229],gnatholotrochus[&&NHX:TOL=92230],heterocylindropsis[&&NHX:TOL=92231],heterosorius[&&NHX:TOL=92232],holotrochodes[&&NHX:TOL=92233],holotrochomorphus[&&NHX:TOL=92234],holotrochopsis[&&NHX:TOL=92235],(holotrochus holotrochus[&&NHX:TOL=92237],holotrochus scapulotrochus[&&NHX:TOL=92238])holotrochus[&&NHX:TOL=92236],idiocnemius[&&NHX:TOL=92239],indosorius[&&NHX:TOL=92240],kistneria[&&NHX:TOL=92241],leptotyphlopsis[&&NHX:TOL=92242],levasseuria[&&NHX:TOL=92243],lusitanopsis[&&NHX:TOL=92244],madecosorius[&&NHX:TOL=92245],madegassosorius[&&NHX:TOL=92246],mimogonellus[&&NHX:TOL=92247],mimogonia[&&NHX:TOL=92248],mimogonidius[&&NHX:TOL=92249],mimogonoderus[&&NHX:TOL=92250],mimogonus[&&NHX:TOL=92251],mimotrochus[&&NHX:TOL=92252],neocaledonopsis[&&NHX:TOL=92253],neosorius[&&NHX:TOL=92254],nepalocylindrops[&&NHX:TOL=92255],nototorchus[&&NHX:TOL=92256],oeophronistus[&&NHX:TOL=92257],oligotyphlopsis[&&NHX:TOL=92258],oryssomma[&&NHX:TOL=92259],osoriellus[&&NHX:TOL=92260],osoriocanthus[&&NHX:TOL=92261],osoriopsis[&&NHX:TOL=92262],osorius[&&NHX:TOL=92263],ouloglene[&&NHX:TOL=92264],paratorchus[&&NHX:TOL=92265],paratrochodes[&&NHX:TOL=92266],parosorius[&&NHX:TOL=92267],rhabdopsidius[&&NHX:TOL=92268],rhabdopsis[&&NHX:TOL=92269],saegerius[&&NHX:TOL=92270],tavakilianidia[&&NHX:TOL=92271],tetrosorius[&&NHX:TOL=92272],thoracogonus[&&NHX:TOL=92273],thoracoprius[&&NHX:TOL=92274],tumboecus[&&NHX:TOL=92275],typhlholotrochus[&&NHX:TOL=92276],typhlobledius[&&NHX:TOL=92277],typhloiulopsis[&&NHX:TOL=92278],typhlosorius[&&NHX:TOL=92279],witelsus[&&NHX:TOL=92280])osoriini[&&NHX:TOL=92211],((allotrochus[&&NHX:TOL=92283],(clavilispinus clavilispinus[&&NHX:TOL=92285],clavilispinus neolispinodes[&&NHX:TOL=92286])clavilispinus[&&NHX:TOL=92284],eulibia[&&NHX:TOL=92287],hospitalibia[&&NHX:TOL=92288],ischiopsaurus[&&NHX:TOL=92289],myrmelibia[&&NHX:TOL=92290],neolispinus[&&NHX:TOL=92291])clavilispinina[&&NHX:TOL=92282],(espeson[&&NHX:TOL=92293],(geomitopsis geomitopsis[&&NHX:TOL=92295],geomitopsis pseudogeomitopsis[&&NHX:TOL=92296])geomitopsis[&&NHX:TOL=92294],glyptoma[&&NHX:TOL=92297],lispinodes[&&NHX:TOL=92298],lispinomimus[&&NHX:TOL=92299],parespeson[&&NHX:TOL=92300],synaenictus[&&NHX:TOL=92301])glyptomina[&&NHX:TOL=92292],(liberiana[&&NHX:TOL=92303],lispinuncus[&&NHX:TOL=92304],(lispinus aulacolispinus[&&NHX:TOL=92306],lispinus lispinus[&&NHX:TOL=92307],lispinus paralispinus[&&NHX:TOL=92308],lispinus pseudolispinodes[&&NHX:TOL=92309],lispinus stictolispinus[&&NHX:TOL=92310])lispinus[&&NHX:TOL=92305],(nacaeus nacaeus[&&NHX:TOL=92312],nacaeus rumeba[&&NHX:TOL=92313])nacaeus[&&NHX:TOL=92311],(neolosus neolosus[&&NHX:TOL=92315],neolosus osholus[&&NHX:TOL=92316],neolosus relinda[&&NHX:TOL=92317])neolosus[&&NHX:TOL=92314],tannea[&&NHX:TOL=92318])lispinina[&&NHX:TOL=92302],(aneucamptus[&&NHX:TOL=92320],dirocephalus[&&NHX:TOL=92321],euctenopsia[&&NHX:TOL=92322],fauva[&&NHX:TOL=92323],mesotrochus[&&NHX:TOL=92324],pardirocephalus[&&NHX:TOL=92325],pselaphomimus[&&NHX:TOL=92326],rhopalopherus[&&NHX:TOL=92327],teiros[&&NHX:TOL=92328],tetrapleurus[&&NHX:TOL=92329],(thoracophorus leipophorus[&&NHX:TOL=92331],thoracophorus stilbogastrus[&&NHX:TOL=92332],thoracophorus thoracophorus[&&NHX:TOL=92333])thoracophorus[&&NHX:TOL=92330])thoracophorina[&&NHX:TOL=92319])thoracophorini[&&NHX:TOL=92281])osoriinae[&&NHX:TOL=9790])[&&NHX:TOL=9789],((deleaster[&&NHX:TOL=10113],(syntomium[&&NHX:TOL=10115],(oxypius[&&NHX:TOL=10117],euphanias[&&NHX:TOL=10118])[&&NHX:TOL=10116])[&&NHX:TOL=10114])[&&NHX:TOL=10112],(coprostygnus[&&NHX:TOL=10120],coprophilus[&&NHX:TOL=10121],homalotrichus[&&NHX:TOL=10122],((manda[&&NHX:TOL=10125],planeustomus[&&NHX:TOL=10126])[&&NHX:TOL=10124],(crassodemus[&&NHX:TOL=10128],((aploderus[&&NHX:TOL=10131],((eppelsheimius[&&NHX:TOL=10134],bledius[&&NHX:TOL=10135])[&&NHX:TOL=10133],(((blediotrogus[&&NHX:TOL=10139],pareiobledius[&&NHX:TOL=10140])[&&NHX:TOL=10138],(teropalpus[&&NHX:TOL=10142],(mimopaederus[&&NHX:TOL=10144],(ochthephilus[&&NHX:TOL=10146],(carpelimus[&&NHX:TOL=10148],xerophygus[&&NHX:TOL=10149],(thinodromus[&&NHX:TOL=10151],(trogactus[&&NHX:TOL=10153],apocellagria[&&NHX:TOL=10154])[&&NHX:TOL=10152])[&&NHX:TOL=10150])[&&NHX:TOL=10147])[&&NHX:TOL=10145])[&&NHX:TOL=10143])[&&NHX:TOL=10141])[&&NHX:TOL=10137],(neoxus[&&NHX:TOL=10156],(sciotrogus[&&NHX:TOL=10158],thinobius[&&NHX:TOL=10159])[&&NHX:TOL=10157])[&&NHX:TOL=10155])[&&NHX:TOL=10136])[&&NHX:TOL=10132])[&&NHX:TOL=10130],(sartallus[&&NHX:TOL=10161],((paraploderus[&&NHX:TOL=10164],parosus[&&NHX:TOL=10165])[&&NHX:TOL=10163],(platystethus[&&NHX:TOL=10167],(ecitoclimax[&&NHX:TOL=10169],(((hoplitodes[&&NHX:TOL=10173],(paroxytelopsis[&&NHX:TOL=10175],(anisopsis[&&NHX:TOL=10177],anisopsidius[&&NHX:TOL=10178])[&&NHX:TOL=10176])[&&NHX:TOL=10174])[&&NHX:TOL=10172],oxytelus[&&NHX:TOL=10179])[&&NHX:TOL=10171],(apocellus[&&NHX:TOL=10181],(rimba[&&NHX:TOL=10183],((oxytelopsis[&&NHX:TOL=10186],oncoparia[&&NHX:TOL=10187])[&&NHX:TOL=10185],anotylus[&&NHX:TOL=10188])[&&NHX:TOL=10184])[&&NHX:TOL=10182])[&&NHX:TOL=10180])[&&NHX:TOL=10170])[&&NHX:TOL=10168])[&&NHX:TOL=10166])[&&NHX:TOL=10162])[&&NHX:TOL=10160])[&&NHX:TOL=10129])[&&NHX:TOL=10127])[&&NHX:TOL=10123])[&&NHX:TOL=10119])oxytelinae[&&NHX:TOL=9792])[&&NHX:TOL=9788],trigonurus[&&NHX:TOL=9794])[&&NHX:TOL=9787],(((((arrowinus[&&NHX:TOL=107281],(antarctothius[&&NHX:TOL=65003],coomania[&&NHX:TOL=65004],diochus[&&NHX:TOL=65005])diochini[&&NHX:TOL=10245],maorothius[&&NHX:TOL=10246],(atrecus[&&NHX:TOL=65008],othius[&&NHX:TOL=65009],parothius[&&NHX:TOL=65010])othiini[&&NHX:TOL=10247],(platyprosopus megaprosopoda[&&NHX:TOL=65012],platyprosopus platyprosopus[&&NHX:TOL=65013])platyprosopus[&&NHX:TOL=10248],((amblyopinus[&&NHX:TOL=104382],amblyopinodes[&&NHX:TOL=104383],chilamblyopinus piceus[&&NHX:TOL=104384],edrabius[&&NHX:TOL=104385],megamblyopinus[&&NHX:TOL=104386],myotyphlus jansoni[&&NHX:TOL=104387])amblyopinina[&&NHX:TOL=10252],(amelinus[&&NHX:TOL=92336],amichrotus[&&NHX:TOL=92337],anisolinus[&&NHX:TOL=92338],barygnathus[&&NHX:TOL=92339],bombylodes[&&NHX:TOL=92340],diatrechus[&&NHX:TOL=92341],hesperoschema[&&NHX:TOL=92342],(hesperosoma euhesperosoma[&&NHX:TOL=92344],hesperosoma paramichrotus[&&NHX:TOL=92345])hesperosoma[&&NHX:TOL=92343],misantlius[&&NHX:TOL=92346],pammegus[&&NHX:TOL=92347],paratympanophorus[&&NHX:TOL=92348],philomyceta[&&NHX:TOL=92349],tolmerinus[&&NHX:TOL=92350],turgiditarsus[&&NHX:TOL=92351],tympanophorus[&&NHX:TOL=92352])anisolinina[&&NHX:TOL=10253],holisus[&&NHX:TOL=10254],(actinomorphus[&&NHX:TOL=92355],actinus[&&NHX:TOL=92356],afrorabigus[&&NHX:TOL=92357],agacerus[&&NHX:TOL=92358],atopocentrum[&&NHX:TOL=92359],belonuchus[&&NHX:TOL=92360],bisnius[&&NHX:TOL=92361],(cafius bryonomus[&&NHX:TOL=92363],cafius cafius[&&NHX:TOL=92364],cafius euremus[&&NHX:TOL=92365],cafius ifacus[&&NHX:TOL=92366],cafius platygonium[&&NHX:TOL=92367],cafius pseudoremus[&&NHX:TOL=92368])cafius[&&NHX:TOL=92362],chroaptomus[&&NHX:TOL=92369],craspedomerus[&&NHX:TOL=92370],diplostictus[&&NHX:TOL=92371],dorcophilonthus[&&NHX:TOL=92372],ecitophytes[&&NHX:TOL=92373],endeius[&&NHX:TOL=92374],(erichsonius erichsonius[&&NHX:TOL=92376],erichsonius sectophilonthus[&&NHX:TOL=92377])erichsonius[&&NHX:TOL=92375],flohria[&&NHX:TOL=92378],gabriopalpus[&&NHX:TOL=92379],gabrius[&&NHX:TOL=92380],gabronthus[&&NHX:TOL=92381],(glyphesthus aleioglyphesthus[&&NHX:TOL=92383],glyphesthus glyphesthus[&&NHX:TOL=92384])glyphesthus[&&NHX:TOL=92382],hesperomimus[&&NHX:TOL=92385],hesperopalpus[&&NHX:TOL=92386],hesperus[&&NHX:TOL=92387],hybridolinus[&&NHX:TOL=92388],jurecekia[&&NHX:TOL=92389],laetulonthus[&&NHX:TOL=92390],leptopeltus[&&NHX:TOL=92391],leucitus[&&NHX:TOL=92392],linoderus[&&NHX:TOL=92393],mentophilonthus[&&NHX:TOL=92394],(moeocerus moeocerus[&&NHX:TOL=92396],moeocerus polystictomoeocerus[&&NHX:TOL=92397])moeocerus[&&NHX:TOL=92395],mysolius[&&NHX:TOL=92398],neobisnius[&&NHX:TOL=92399],neoleucitus[&&NHX:TOL=92400],odontolinus[&&NHX:TOL=92401],ophionthus[&&NHX:TOL=92402],orthidus[&&NHX:TOL=92403],pachypelmopus[&&NHX:TOL=92404],paederallus[&&NHX:TOL=92405],paederomimus[&&NHX:TOL=92406],paracraspedomerus[&&NHX:TOL=92407],pescolinus[&&NHX:TOL=92408],peucoglyphus[&&NHX:TOL=92409],phileciton[&&NHX:TOL=92410],philonthus piezarthrus[&&NHX:TOL=92411],phucobius[&&NHX:TOL=92414],platyschema[&&NHX:TOL=92415],proxenobius[&&NHX:TOL=92416],pseudocraspedomerus[&&NHX:TOL=92417],pseudomoeocerus[&&NHX:TOL=92418],pterygolaetus[&&NHX:TOL=92419],rabigus[&&NHX:TOL=92420],remus[&&NHX:TOL=92421],scelotrichus[&&NHX:TOL=92422],shaverdolena[&&NHX:TOL=92423],sphaeriolinus[&&NHX:TOL=92424],sternotoxus[&&NHX:TOL=92425],stevensia[&&NHX:TOL=92426],taxiplagus[&&NHX:TOL=92427],thinocafius[&&NHX:TOL=92428],trachyphilonthus[&&NHX:TOL=92429],tropiopterius[&&NHX:TOL=92430],xanthodermus[&&NHX:TOL=92431],xenobius[&&NHX:TOL=92432])philonthina[&&NHX:TOL=10255],(acylohsellus[&&NHX:TOL=92433],(acylophorus acylophorus[&&NHX:TOL=92435],acylophorus amacylophorus[&&NHX:TOL=92436],acylophorus indoacylophorus[&&NHX:TOL=92437],acylophorus neoacylophorus[&&NHX:TOL=92438],acylophorus palpacylophorus[&&NHX:TOL=92439],acylophorus paracylophorus[&&NHX:TOL=92440])acylophorus[&&NHX:TOL=92434],anaquedius[&&NHX:TOL=92441],anchocerus[&&NHX:TOL=92442],astrapaeus[&&NHX:TOL=92443],beeria[&&NHX:TOL=92444],bolitogyrus[&&NHX:TOL=92445],cafioquedus[&&NHX:TOL=92446],cheilocolpus[&&NHX:TOL=92447],ctenandropus[&&NHX:TOL=92448],euristus[&&NHX:TOL=92449],euryporus[&&NHX:TOL=92450],heinzia[&&NHX:TOL=92451],hemiquedius[&&NHX:TOL=92452],heterothops[&&NHX:TOL=92453],indoquedius[&&NHX:TOL=92454],ioma[&&NHX:TOL=92455],(loncovilius lienturius[&&NHX:TOL=92457],loncovilius loncovilius[&&NHX:TOL=92458])loncovilius[&&NHX:TOL=92456],lonia[&&NHX:TOL=92459],mimosticus[&&NHX:TOL=92460],natalignathus[&&NHX:TOL=92461],paratolmerus[&&NHX:TOL=92462],parisanopus[&&NHX:TOL=92463],philonthellus[&&NHX:TOL=92464],pseudorientis[&&NHX:TOL=92465],quediocafus[&&NHX:TOL=92466],quediomacrus[&&NHX:TOL=92467],quediomimus[&&NHX:TOL=92468],quediopsis[&&NHX:TOL=92469],(quedius cyrtoquedius[&&NHX:TOL=92471],quedius distichalius[&&NHX:TOL=92472],quedius euryquedius[&&NHX:TOL=92473],quedius farus[&&NHX:TOL=92474],quedius megaquedius[&&NHX:TOL=92475],quedius microquedius[&&NHX:TOL=92476],quedius microsaurus[&&NHX:TOL=92477],quedius paraquedius[&&NHX:TOL=92478],quedius pridonius[&&NHX:TOL=92479],quedius quedionuchus[&&NHX:TOL=92480],quedius quediops[&&NHX:TOL=92481],quedius quedius[&&NHX:TOL=92482],quedius raphirus[&&NHX:TOL=92483])quedius[&&NHX:TOL=92470],quelaestrygon[&&NHX:TOL=92484],quetarsius[&&NHX:TOL=92485],quwatanabius[&&NHX:TOL=92486],rolla[&&NHX:TOL=92487],sphingoquedius[&&NHX:TOL=92488],strouhalium[&&NHX:TOL=92489],termitoquedius[&&NHX:TOL=92490],valdiviodes[&&NHX:TOL=92491],velleiopsis[&&NHX:TOL=92492],velleius[&&NHX:TOL=92493])quedina[&&NHX:TOL=10256],(abemus[&&NHX:TOL=92496],agelosus[&&NHX:TOL=92497],apecholinus[&&NHX:TOL=92498],apostenolinus[&&NHX:TOL=92499],aulacocypus[&&NHX:TOL=92500],bafutella[&&NHX:TOL=92501],collocypus[&&NHX:TOL=92502],creophilus[&&NHX:TOL=66211],(dinothenarus dinothenarus[&&NHX:TOL=92505],dinothenarus parabemus[&&NHX:TOL=92506])dinothenarus[&&NHX:TOL=92504],emus[&&NHX:TOL=92507],(eucibdelus eucibdelus[&&NHX:TOL=92509],eucibdelus neocibdelus[&&NHX:TOL=92510],eucibdelus pareucibdelus[&&NHX:TOL=92511])eucibdelus[&&NHX:TOL=92508],guillaumius[&&NHX:TOL=92512],hadropinus[&&NHX:TOL=92513],hadrotes[&&NHX:TOL=92514],leistotrophus[&&NHX:TOL=92515],liusus[&&NHX:TOL=92516],menoedius[&&NHX:TOL=92517],miobdelus[&&NHX:TOL=92518],naddia[&&NHX:TOL=92519],ocychinus[&&NHX:TOL=92520],(ocypus angulephallus[&&NHX:TOL=92522],ocypus matidus[&&NHX:TOL=92523],ocypus ocypus[&&NHX:TOL=92524],ocypus pseudocypus[&&NHX:TOL=92525])ocypus[&&NHX:TOL=92521],ontholestes[&&NHX:TOL=92526],palaestrinus[&&NHX:TOL=92527],pancarpius[&&NHX:TOL=92528],paragastrisus[&&NHX:TOL=92529],parapalaestrinus[&&NHX:TOL=92530],paraphytolinus[&&NHX:TOL=92531],philetaerius[&&NHX:TOL=92532],physetops[&&NHX:TOL=92533],phytolinus[&&NHX:TOL=92534],(platydracus chaetodracus[&&NHX:TOL=92536],platydracus chitocompsus[&&NHX:TOL=92537],platydracus nesiolinus[&&NHX:TOL=92538],platydracus paraplatydracus[&&NHX:TOL=92539],platydracus platydracus[&&NHX:TOL=92540],platydracus poikilodracus[&&NHX:TOL=92541],platydracus tropoplatydracus[&&NHX:TOL=92542])platydracus[&&NHX:TOL=92535],protocypus[&&NHX:TOL=92543],protogoerius[&&NHX:TOL=92544],rhynchocheilus[&&NHX:TOL=92545],rhyncocheilus[&&NHX:TOL=92546],saniderus[&&NHX:TOL=92547],sphaerobulbus[&&NHX:TOL=92548],sphaeromacrops[&&NHX:TOL=92549],staphylinus[&&NHX:TOL=92550],(tasgius rayacheila[&&NHX:TOL=92552],tasgius tasgius[&&NHX:TOL=92553])tasgius[&&NHX:TOL=92551],thinopinus[&&NHX:TOL=92554],thoracostrongylus[&&NHX:TOL=92555],trichocosmetes[&&NHX:TOL=92556],wasmannellus[&&NHX:TOL=92557])staphylinina[&&NHX:TOL=10257],atanygnathus[&&NHX:TOL=10258],(algon[&&NHX:TOL=10261],antimerus[&&NHX:TOL=10264],dysanellus[&&NHX:TOL=10265],elecatopselaphus[&&NHX:TOL=10266],((elmas strigella[&&NHX:TOL=107758],elmas strigiformis[&&NHX:TOL=107759])[&&NHX:TOL=107757],(elmas guianas[&&NHX:TOL=10218],(elmas lambas[&&NHX:TOL=10220],(elmas hibbsi[&&NHX:TOL=107760],(elmas panamaensis[&&NHX:TOL=107762],(elmas elassos[&&NHX:TOL=107764],(elmas elassoides[&&NHX:TOL=107766],elmas similis[&&NHX:TOL=107767])[&&NHX:TOL=107765])[&&NHX:TOL=107763],(elmas patillas[&&NHX:TOL=107769],(elmas spinosus[&&NHX:TOL=107771],(elmas falini[&&NHX:TOL=107773],elmas gigas[&&NHX:TOL=107774])[&&NHX:TOL=107772])[&&NHX:TOL=107770])[&&NHX:TOL=107768],(elmas hanleyi[&&NHX:TOL=107776],((elmas brooksi[&&NHX:TOL=107779],elmas esmeraldas[&&NHX:TOL=107780])[&&NHX:TOL=107778],(elmas lescheni[&&NHX:TOL=107782],(elmas windsori[&&NHX:TOL=107784],elmas costaricensis[&&NHX:TOL=107785])[&&NHX:TOL=107783])[&&NHX:TOL=107781])[&&NHX:TOL=107777])[&&NHX:TOL=107775])[&&NHX:TOL=107761])[&&NHX:TOL=10223])[&&NHX:TOL=10219])[&&NHX:TOL=10217],elmas modesta[&&NHX:TOL=107786])elmas[&&NHX:TOL=10267],gastrisus[&&NHX:TOL=10268],glenus[&&NHX:TOL=10269],hasumius[&&NHX:TOL=10270],(isanopus eptaskouros[&&NHX:TOL=133870],(isanopus sahlbergi[&&NHX:TOL=133872],isanopus tenuicornis[&&NHX:TOL=133873],(isanopus ashei[&&NHX:TOL=133875],(isanopus hinojosai[&&NHX:TOL=133877],isanopus sallaei[&&NHX:TOL=133878])[&&NHX:TOL=133876])[&&NHX:TOL=133874])[&&NHX:TOL=133871])isanopus[&&NHX:TOL=10272],nausicotus[&&NHX:TOL=10273],(nordus major[&&NHX:TOL=57006],((nordus amphivolos[&&NHX:TOL=57010],nordus longipes[&&NHX:TOL=57011])[&&NHX:TOL=57009],(nordus cribricollis[&&NHX:TOL=57013],(((nordus nigroscutellatus[&&NHX:TOL=57017],(nordus aeneiceps[&&NHX:TOL=57019],nordus gebieni[&&NHX:TOL=57020])[&&NHX:TOL=57018])[&&NHX:TOL=57016],(nordus facialis[&&NHX:TOL=57022],(nordus stomachoponos[&&NHX:TOL=57024],(nordus dichromos[&&NHX:TOL=57026],(nordus championi[&&NHX:TOL=57028],nordus fungicola[&&NHX:TOL=57029])[&&NHX:TOL=57027])[&&NHX:TOL=57025])[&&NHX:TOL=57023])[&&NHX:TOL=57021])[&&NHX:TOL=57015],((nordus elytisi[&&NHX:TOL=57032],nordus seferisi[&&NHX:TOL=57033])[&&NHX:TOL=57031],((nordus simplex[&&NHX:TOL=57036],(nordus velitaris[&&NHX:TOL=57038],(nordus diversiventris[&&NHX:TOL=57040],(nordus styloceros[&&NHX:TOL=57042],(nordus amazonicus[&&NHX:TOL=57044],nordus batesi[&&NHX:TOL=57045])[&&NHX:TOL=57043])[&&NHX:TOL=57041])[&&NHX:TOL=57039],((nordus solitarius[&&NHX:TOL=57048],nordus testaceus[&&NHX:TOL=57049])[&&NHX:TOL=57047],((nordus omios[&&NHX:TOL=57052],nordus terminalis[&&NHX:TOL=57053])[&&NHX:TOL=57051],(nordus xanthocerus[&&NHX:TOL=57055],nordus maculiceps[&&NHX:TOL=57056])[&&NHX:TOL=57054])[&&NHX:TOL=57050])[&&NHX:TOL=57046])[&&NHX:TOL=57037])[&&NHX:TOL=57035],((nordus densiventris[&&NHX:TOL=57059],(nordus periergos[&&NHX:TOL=57061],nordus semelius[&&NHX:TOL=57062])[&&NHX:TOL=57060])[&&NHX:TOL=57058],((nordus antennatus[&&NHX:TOL=57065],nordus banghaasi[&&NHX:TOL=57066])[&&NHX:TOL=57064],(nordus picticornis[&&NHX:TOL=57068],(nordus aeneipennis[&&NHX:TOL=57070],(nordus zischkai[&&NHX:TOL=57072],(nordus portokalis[&&NHX:TOL=57074],(nordus elegans[&&NHX:TOL=57076],(nordus cherylae[&&NHX:TOL=57078],nordus speciosus[&&NHX:TOL=57079])[&&NHX:TOL=57077])[&&NHX:TOL=57075])[&&NHX:TOL=57073])[&&NHX:TOL=57071])[&&NHX:TOL=57069])[&&NHX:TOL=57067])[&&NHX:TOL=57063])[&&NHX:TOL=57057])[&&NHX:TOL=57034])[&&NHX:TOL=57030])[&&NHX:TOL=57014])[&&NHX:TOL=57012])[&&NHX:TOL=57008])nordus[&&NHX:TOL=10274],ocyolinus[&&NHX:TOL=10275],oligotergus[&&NHX:TOL=10276],paraxenopygus[&&NHX:TOL=10278],phanolinopsis[&&NHX:TOL=10279],phanolinus[&&NHX:TOL=10280],((philothalpus fervidus[&&NHX:TOL=57389],(philothalpus chloropennis[&&NHX:TOL=57391],(philothalpus rufus[&&NHX:TOL=57393],philothalpus rugosus[&&NHX:TOL=57394])[&&NHX:TOL=57392])[&&NHX:TOL=57390])[&&NHX:TOL=57388],((philothalpus bilobus[&&NHX:TOL=57397],philothalpus mauroprasinus[&&NHX:TOL=57398])[&&NHX:TOL=57396],((philothalpus antennaria[&&NHX:TOL=57401],(philothalpus osanus[&&NHX:TOL=57403],(philothalpus brooksi[&&NHX:TOL=57405],philothalpus falini[&&NHX:TOL=57406])[&&NHX:TOL=57404])[&&NHX:TOL=57402])[&&NHX:TOL=57400],(philothalpus nitidus[&&NHX:TOL=57408],((philothalpus asymmetros[&&NHX:TOL=57411],(philothalpus mundus[&&NHX:TOL=57413],(philothalpus bicolor[&&NHX:TOL=57415],philothalpus pecki[&&NHX:TOL=57416])[&&NHX:TOL=57414])[&&NHX:TOL=57412])[&&NHX:TOL=57410],(philothalpus chotaenus[&&NHX:TOL=57418],philothalpus ecuadorensis[&&NHX:TOL=57419],philothalpus loksos[&&NHX:TOL=57420],philothalpus porphyros[&&NHX:TOL=57421],philothalpus portokalis[&&NHX:TOL=57422],philothalpus stravos[&&NHX:TOL=57423])[&&NHX:TOL=57417])[&&NHX:TOL=57409])[&&NHX:TOL=57407])[&&NHX:TOL=57399])[&&NHX:TOL=57395])philothalpus[&&NHX:TOL=10281],plociopterus[&&NHX:TOL=10282],prianophthalmus[&&NHX:TOL=10283],prionopedinus[&&NHX:TOL=10284],prionophilonthus[&&NHX:TOL=10285],rientis[&&NHX:TOL=10286],scaponopselaphus[&&NHX:TOL=10287],styngetus[&&NHX:TOL=10288],torobus[&&NHX:TOL=10289],triacrus[&&NHX:TOL=10290],tricholinus[&&NHX:TOL=10291],trigonopalpus[&&NHX:TOL=10292],trigonopselaphus[&&NHX:TOL=10293],xanthopygoides[&&NHX:TOL=10295],xanthopygus[&&NHX:TOL=10296],xenopygus[&&NHX:TOL=10297])xanthopygina[&&NHX:TOL=10259])staphylinini[&&NHX:TOL=10249],(achemia[&&NHX:TOL=65015],achmonia[&&NHX:TOL=65016],adhavara[&&NHX:TOL=65017],agerodes[&&NHX:TOL=65018],allolinus[&&NHX:TOL=65019],allotrichus[&&NHX:TOL=65020],andamania[&&NHX:TOL=65021],andelis[&&NHX:TOL=65022],archaites[&&NHX:TOL=65023],atopolinus[&&NHX:TOL=65024],australinus[&&NHX:TOL=65025],caecolinus[&&NHX:TOL=65026],calontholinus[&&NHX:TOL=65027],cibyra[&&NHX:TOL=65028],crinolinus[&&NHX:TOL=65029],cylindrinus[&&NHX:TOL=65030],dactylaptatus[&&NHX:TOL=65031],daolus[&&NHX:TOL=65032],denon[&&NHX:TOL=65033],dibothroglyptus[&&NHX:TOL=65034],domea[&&NHX:TOL=65035],eachamia[&&NHX:TOL=65036],elgonia[&&NHX:TOL=65037],enervia[&&NHX:TOL=65038],erymus[&&NHX:TOL=65039],eulissus[&&NHX:TOL=65040],faxilla[&&NHX:TOL=65041],gauropterus[&&NHX:TOL=65042],grevillia[&&NHX:TOL=65043],(gyrohypnus gyrohypnus[&&NHX:TOL=65045],gyrohypnus xenoxantholinus[&&NHX:TOL=65046])gyrohypnus[&&NHX:TOL=65044],(habrolinus habrolinus[&&NHX:TOL=65048],habrolinus timagenes[&&NHX:TOL=65049])habrolinus[&&NHX:TOL=65047],hesperolinus[&&NHX:TOL=65050],heterocinus[&&NHX:TOL=65051],heterolinus[&&NHX:TOL=65052],himmala[&&NHX:TOL=65053],holocorynus[&&NHX:TOL=65054],homalolinus[&&NHX:TOL=65055],homorocerus[&&NHX:TOL=65056],hypnogyra[&&NHX:TOL=65057],indolinus[&&NHX:TOL=65058],indomorphus[&&NHX:TOL=65059],lemiganus[&&NHX:TOL=65060],lepidophallus[&&NHX:TOL=65061],lepitacnus[&&NHX:TOL=65062],lepta[&&NHX:TOL=65063],leptacinellus[&&NHX:TOL=65064],(leptacinus chaetocinus[&&NHX:TOL=65066],leptacinus leptacinus[&&NHX:TOL=65068])leptacinus[&&NHX:TOL=65065],leptomicrus[&&NHX:TOL=65069],leptophius[&&NHX:TOL=65070],leurocorynus[&&NHX:TOL=65071],linohesperus[&&NHX:TOL=65072],linosomus[&&NHX:TOL=65073],liotesba[&&NHX:TOL=65074],lissohypnus[&&NHX:TOL=65075],lithocharodes[&&NHX:TOL=65076],maharadja[&&NHX:TOL=65077],mahavana[&&NHX:TOL=65078],manilla[&&NHX:TOL=65079],medhiama[&&NHX:TOL=65080],megalinus[&&NHX:TOL=65081],metocinus[&&NHX:TOL=65082],metolinus[&&NHX:TOL=65083],metosina[&&NHX:TOL=65084],microleptus[&&NHX:TOL=65085],microlinus[&&NHX:TOL=65086],mitomorphus[&&NHX:TOL=65087],neohypnus[&&NHX:TOL=65088],neoleptacinus[&&NHX:TOL=65089],neoxantholinus[&&NHX:TOL=65090],nepalinus[&&NHX:TOL=65091],nilla[&&NHX:TOL=65092],notolinus[&&NHX:TOL=65093],nudobius[&&NHX:TOL=65094],oculolabrus[&&NHX:TOL=65095],otagonia[&&NHX:TOL=65096],oxybleptes[&&NHX:TOL=65097],pachycorynus[&&NHX:TOL=65098],pahanghella[&&NHX:TOL=65099],paracorynus[&&NHX:TOL=65100],paratesba[&&NHX:TOL=65101],paulianella[&&NHX:TOL=65102],phacophallus[&&NHX:TOL=65103],platydromus[&&NHX:TOL=65104],plochionocerus[&&NHX:TOL=65105],pseudocorynus[&&NHX:TOL=65106],pseudoxantholinus[&&NHX:TOL=65107],queenslandina[&&NHX:TOL=65108],renda[&&NHX:TOL=65109],sagarmatha[&&NHX:TOL=65110],scytalinus[&&NHX:TOL=65111],someira[&&NHX:TOL=65112],somoleptus[&&NHX:TOL=65113],spaniolinus[&&NHX:TOL=65114],(stenistoderus leptoglenus[&&NHX:TOL=65116],stenistoderus stenistoderus[&&NHX:TOL=65117])stenistoderus[&&NHX:TOL=65115],stenolinus[&&NHX:TOL=65118],stictolinus[&&NHX:TOL=65119],sulawesina[&&NHX:TOL=65120],sumatera[&&NHX:TOL=65121],sungaria[&&NHX:TOL=65122],sylea[&&NHX:TOL=65123],symilla[&&NHX:TOL=65124],talliella[&&NHX:TOL=65125],tamilla[&&NHX:TOL=65126],tesba[&&NHX:TOL=65127],tetraulacus[&&NHX:TOL=65128],thyreocephalus[&&NHX:TOL=65129],tralichia[&&NHX:TOL=65130],ulisseus[&&NHX:TOL=65131],(vulda typhlodes[&&NHX:TOL=65133],vulda vulda[&&NHX:TOL=65134])vulda[&&NHX:TOL=65132],waitatia[&&NHX:TOL=65135],walesia[&&NHX:TOL=65136],whangareiella[&&NHX:TOL=65137],xanthocorynus[&&NHX:TOL=65138],(xantholinus afrolinus[&&NHX:TOL=65140],xantholinus calolinus[&&NHX:TOL=65141],xantholinus helicophallus[&&NHX:TOL=65142],xantholinus heterolius[&&NHX:TOL=65143],xantholinus idiolinus[&&NHX:TOL=65144],xantholinus meneidophallus[&&NHX:TOL=65145],xantholinus milichilinus[&&NHX:TOL=65146],xantholinus neoleptophallus[&&NHX:TOL=65147],xantholinus paracyclinus[&&NHX:TOL=65148],xantholinus polydontophallus[&&NHX:TOL=65149],xantholinus purrolinus[&&NHX:TOL=65150],xantholinus stenophallus[&&NHX:TOL=65151],xantholinus tetralinus[&&NHX:TOL=65152],xantholinus toxophallus[&&NHX:TOL=65153],xantholinus typhlolinus[&&NHX:TOL=65154],xantholinus xantholinus[&&NHX:TOL=65155])xantholinus[&&NHX:TOL=65139],xanthophius[&&NHX:TOL=65156],xestolinus[&&NHX:TOL=65157],yunna[&&NHX:TOL=65158],yunnella[&&NHX:TOL=65159],zenon[&&NHX:TOL=65160],zeteotomus[&&NHX:TOL=65161])xantholinini[&&NHX:TOL=10250],cretoquedius[&&NHX:EXT=Y:TOL=107277],laasbium[&&NHX:EXT=Y:TOL=107278],laostaphylinus[&&NHX:EXT=Y:TOL=107279],mesostaphylinus[&&NHX:EXT=Y:TOL=107280])staphylininae[&&NHX:TOL=9810],(miolithocharis[&&NHX:EXT=Y:TOL=61512],(coecoscopaeus[&&NHX:TOL=61514],((astenus astenognathus[&&NHX:TOL=61529],astenus astenopleuritus[&&NHX:TOL=61530],astenus astenus[&&NHX:TOL=61531],astenus eurysunius[&&NHX:TOL=61532],astenus mecognathus[&&NHX:TOL=61533],astenus neognathus[&&NHX:TOL=61534])astenus[&&NHX:TOL=61528],himastenus[&&NHX:TOL=61535],nazeris[&&NHX:TOL=61536],stilicastenus[&&NHX:TOL=61537],tetracanthognathus[&&NHX:TOL=61538])astenina[&&NHX:TOL=61527],(aderobium[&&NHX:TOL=61540],afrobium[&&NHX:TOL=61541],afrophitodum[&&NHX:TOL=61542],baryopsis[&&NHX:TOL=61543],biocrypta[&&NHX:TOL=61544],chetocephalus[&&NHX:TOL=61545],cryptafrum[&&NHX:TOL=61546],cryptofagiella[&&NHX:TOL=61547],cryptomirea[&&NHX:TOL=61548],dicax[&&NHX:TOL=61549],formicocephalus[&&NHX:TOL=61550],himalobium[&&NHX:TOL=61551],(homaeotarsus eucryptina[&&NHX:TOL=61553],homaeotarsus gastrolobium[&&NHX:TOL=61554],homaeotarsus hesperobium[&&NHX:TOL=61555],homaeotarsus homaeotarsus[&&NHX:TOL=61556],homaeotarsus homoeobium[&&NHX:TOL=61557],homaeotarsus nemoeotus[&&NHX:TOL=61558])homaeotarsus[&&NHX:TOL=61552],hyperomma[&&NHX:TOL=61559],lissobiops[&&NHX:TOL=61560],longiscapus[&&NHX:TOL=61561],macrodicax[&&NHX:TOL=61562],matropium[&&NHX:TOL=61563],monocrypta[&&NHX:TOL=61564],nitidicryptum[&&NHX:TOL=61565],noumea[&&NHX:TOL=61566],(ochthephilum ababactus[&&NHX:TOL=61568],ochthephilum astenobium[&&NHX:TOL=61569],ochthephilum cryptobiella[&&NHX:TOL=61570],ochthephilum neobactus[&&NHX:TOL=61571],ochthephilum ochthephilum[&&NHX:TOL=61572])ochthephilum[&&NHX:TOL=61567],ophitodum[&&NHX:TOL=61573],opithes[&&NHX:TOL=61574],pachycryptum[&&NHX:TOL=61575],prytocum[&&NHX:TOL=61576],pseudocryptobium[&&NHX:TOL=61577],pycnocrypta[&&NHX:TOL=61578],scopaeodes[&&NHX:TOL=61579],suniopsis[&&NHX:TOL=61580],tracypum[&&NHX:TOL=61581])cryptobiina[&&NHX:TOL=61539],(cylindroxystus[&&NHX:TOL=61583],neolindus[&&NHX:TOL=61584])cylindroxystina[&&NHX:TOL=61582],(acaratopus[&&NHX:TOL=61586],afracus[&&NHX:TOL=61587],afroscotonomus[&&NHX:TOL=61588],dolicaon[&&NHX:TOL=61589],gnathymenus[&&NHX:TOL=61590],jarrigeus[&&NHX:TOL=61591],laavsnartius[&&NHX:TOL=61592],leptobium[&&NHX:TOL=61593],liparopus[&&NHX:TOL=61594],pinobius[&&NHX:TOL=61595],plathypodema[&&NHX:TOL=61596],platydolicaon[&&NHX:TOL=61597],pseudobolitocharina[&&NHX:TOL=61598],scotonomus[&&NHX:TOL=61599],scotticus[&&NHX:TOL=61600],serrolabis[&&NHX:TOL=61601],stenopholea[&&NHX:TOL=61602],sudanus[&&NHX:TOL=61603])dolicaonina[&&NHX:TOL=61585],(cephalochetus[&&NHX:TOL=61605],(echiaster echiaster[&&NHX:TOL=61607],echiaster leptogenius[&&NHX:TOL=61608],echiaster polyasterellus[&&NHX:TOL=61609])echiaster[&&NHX:TOL=61606],haplonazeris[&&NHX:TOL=61610],malena[&&NHX:TOL=61611],myrmecosaurus[&&NHX:TOL=61612],ophryomedon[&&NHX:TOL=61613],pseudastenus[&&NHX:TOL=61614],ronetus[&&NHX:TOL=61615],santiagonius[&&NHX:TOL=61616],sclerochiton[&&NHX:TOL=61617],sphaeronum[&&NHX:TOL=61618],termitosaurus[&&NHX:TOL=61619],zonaster[&&NHX:TOL=61620])echiasterina[&&NHX:TOL=61604],(acalophaena[&&NHX:TOL=61622],(achenium achenium[&&NHX:TOL=61624],achenium chinachenium[&&NHX:TOL=61625],achenium micrachenium[&&NHX:TOL=61626])achenium[&&NHX:TOL=61623],attaxenus[&&NHX:TOL=61627],dacnochilus[&&NHX:TOL=61628],(domene canariomene[&&NHX:TOL=61630],domene domene[&&NHX:TOL=61631],domene lathromene[&&NHX:TOL=61632],domene macromene[&&NHX:TOL=61633],domene neodomene[&&NHX:TOL=61634],domene spelaeomene[&&NHX:TOL=61635])domene[&&NHX:TOL=61629],dysanabatium[&&NHX:TOL=61636],enallagium[&&NHX:TOL=61637],ganarus[&&NHX:TOL=61638],(lathrobium abletobium[&&NHX:TOL=61640],lathrobium apteralium[&&NHX:TOL=61641],lathrobium glyptomerodoschema[&&NHX:TOL=61642],lathrobium glyptomerus[&&NHX:TOL=61643],lathrobium lathrobioma[&&NHX:TOL=61644],lathrobium lathrobiopsis[&&NHX:TOL=61645],lathrobium lathrobium[&&NHX:TOL=61646],lathrobium lathrolepta[&&NHX:TOL=61647],lathrobium madecalobrathium[&&NHX:TOL=61648],lathrobium palaeolobrathium[&&NHX:EXT=Y:TOL=61649])lathrobium[&&NHX:TOL=61639],(lobrathium eulathrobium[&&NHX:TOL=61651],lobrathium lobrathium[&&NHX:TOL=61652],lobrathium paralobrathium[&&NHX:TOL=61653],lobrathium ponthrobium[&&NHX:TOL=61654])lobrathium[&&NHX:TOL=61650],micrillus[&&NHX:TOL=61655],neoscimbalium[&&NHX:TOL=61656],notobium[&&NHX:TOL=61657],paederopsis[&&NHX:TOL=61658],paulianidia[&&NHX:TOL=61659],phanophilus[&&NHX:TOL=61660],platybrathium[&&NHX:TOL=61661],platydomene[&&NHX:TOL=61662],pseudobium[&&NHX:TOL=61663],(pseudolathra allolathra[&&NHX:TOL=61665],pseudolathra pseudolathra[&&NHX:TOL=61666])pseudolathra[&&NHX:TOL=61664],scymbalium[&&NHX:TOL=61667],scymbalopsis[&&NHX:TOL=61668],stereocephalus[&&NHX:TOL=61669],sucoca[&&NHX:TOL=61670],tetartopeus[&&NHX:TOL=61671],throbalium[&&NHX:TOL=61672],tripectenopus[&&NHX:TOL=61673])lathrobiina[&&NHX:TOL=61621],((acanthoglossa acanthoglossa[&&NHX:TOL=61676],acanthoglossa cyclodesia[&&NHX:TOL=61677])acanthoglossa[&&NHX:TOL=61675],(achenomorphus achenomorphus[&&NHX:TOL=61679],achenomorphus aderocharis[&&NHX:TOL=61680],achenomorphus dorocharis[&&NHX:TOL=61681])achenomorphus[&&NHX:TOL=61678],achenopsis[&&NHX:TOL=61682],argoderus[&&NHX:TOL=61683],cephisella[&&NHX:TOL=61684],charichirus[&&NHX:TOL=61685],deroderus[&&NHX:TOL=61686],ecitocleptis[&&NHX:TOL=61687],ecitomedon[&&NHX:TOL=61688],eusclerus[&&NHX:TOL=61689],exomedon[&&NHX:TOL=61690],gourvesia[&&NHX:TOL=61691],hexamedon[&&NHX:TOL=61692],isocheilus[&&NHX:TOL=61693],(labrocharis labrocharis[&&NHX:TOL=61695],labrocharis labroporus[&&NHX:TOL=61696])labrocharis[&&NHX:TOL=61694],leiporaphes[&&NHX:TOL=61697],lithocharis[&&NHX:TOL=61698],luzea[&&NHX:TOL=61699],lypeticus[&&NHX:TOL=61700],malaisomedon[&&NHX:TOL=61701],malayanomedon[&&NHX:TOL=61702],medomonista[&&NHX:TOL=61703],(medon cryptoporus[&&NHX:TOL=61705],medon medon[&&NHX:TOL=61706],medon medonodonta[&&NHX:TOL=61707],medon mespalerus[&&NHX:TOL=61708],medon nitimedon[&&NHX:TOL=61709],medon platymedon[&&NHX:TOL=61710],medon tetramedon[&&NHX:TOL=61711])medon[&&NHX:TOL=61704],monocharis[&&NHX:TOL=61712],myrmecomedon[&&NHX:TOL=61713],neomedon[&&NHX:TOL=61714],neosclerus[&&NHX:TOL=61715],nesomedon[&&NHX:TOL=61716],ophiomedon[&&NHX:TOL=61717],ophioomma[&&NHX:TOL=61718],pachymedon[&&NHX:TOL=61719],panscopaeus[&&NHX:TOL=61720],parascopaeus[&&NHX:TOL=61721],perierpon[&&NHX:TOL=61722],pimus[&&NHX:TOL=61723],(pseudomedon euphonus[&&NHX:TOL=61725],pseudomedon pseudomedon[&&NHX:TOL=61726])pseudomedon[&&NHX:TOL=61724],sciocharis[&&NHX:TOL=61727],scioporus[&&NHX:TOL=61728],scopobium[&&NHX:TOL=61729],stilocharis[&&NHX:TOL=61730],stilomedon[&&NHX:TOL=61731],suniotrichus[&&NHX:TOL=61732],(sunius caloderma[&&NHX:TOL=61734],sunius hypomedon[&&NHX:TOL=61735],sunius sunius[&&NHX:TOL=61736],sunius trachysectus[&&NHX:TOL=61737])sunius[&&NHX:TOL=61733],surdomedon[&&NHX:TOL=61738],thinocharis[&&NHX:TOL=61739],xenomedon[&&NHX:TOL=61740])medonina[&&NHX:TOL=61674],(allopaederus[&&NHX:TOL=61742],ctenopaederus[&&NHX:TOL=61743],diplopaederus[&&NHX:TOL=61744],eupaederus[&&NHX:TOL=61745],lobopaederus[&&NHX:TOL=61746],madecapaederus[&&NHX:TOL=61747],megalopaederus[&&NHX:TOL=61748],oncopaederus[&&NHX:TOL=61749],oreopaederus[&&NHX:TOL=61750],pachypaederus[&&NHX:TOL=61751],paederidus[&&NHX:TOL=61752],(paederus anomalopaederus[&&NHX:TOL=61754],paederus eopaederus[&&NHX:TOL=61755],paederus gnathopaederus[&&NHX:TOL=61756],paederus harpopaederus[&&NHX:TOL=61757],paederus heteropaederus[&&NHX:TOL=61758],paederus neopaederus[&&NHX:TOL=61759],paederus nepalopaederus[&&NHX:TOL=61760],paederus oedopaederus[&&NHX:TOL=61761],paederus oreinopaederus[&&NHX:TOL=61762],paederus paederognathus[&&NHX:TOL=61763],paederus paederus[&&NHX:TOL=61764],paederus poederomorphus[&&NHX:TOL=61765],paederus pseudopaederus[&&NHX:TOL=61766])paederus[&&NHX:TOL=61753],parameropaederus[&&NHX:TOL=61767],uncopaederus[&&NHX:TOL=61768])paederina[&&NHX:TOL=61741],(euscopaeus[&&NHX:TOL=61770],medome[&&NHX:TOL=61771],micranops[&&NHX:TOL=61772],(orus leucorus[&&NHX:TOL=61774],orus orus[&&NHX:TOL=61775],orus pycnorus[&&NHX:TOL=61776])orus[&&NHX:TOL=61773],scopaeomerus[&&NHX:TOL=61777],(scopaeus asiascopaeus[&&NHX:TOL=61779],scopaeus hyperscopaeus[&&NHX:TOL=61780],scopaeus scopaeodera[&&NHX:TOL=61781],scopaeus scopaeoma[&&NHX:TOL=61782],scopaeus scopaeopsis[&&NHX:TOL=61783],scopaeus scopaeus[&&NHX:TOL=61784],scopaeus typhloscopaeus[&&NHX:TOL=61785])scopaeus[&&NHX:TOL=61778],typhloleleupius[&&NHX:TOL=61786])scopaeina[&&NHX:TOL=61769],(acrostilicus[&&NHX:TOL=61788],(eustilicus eustilicus[&&NHX:TOL=61790],eustilicus trochoderus[&&NHX:TOL=61791])eustilicus[&&NHX:TOL=61789],lathrorugilus[&&NHX:TOL=61792],medostilicus[&&NHX:TOL=61793],megastilicus[&&NHX:TOL=61794],pachystilicus[&&NHX:TOL=61795],(rugilus afrostilicus[&&NHX:TOL=61797],rugilus allostilicus[&&NHX:TOL=61798],rugilus cephalostilicus[&&NHX:TOL=61799],rugilus eurystilicus[&&NHX:TOL=61800],rugilus fossulostilicus[&&NHX:TOL=61801],rugilus hemistilicus[&&NHX:TOL=61802],rugilus heterostilicus[&&NHX:TOL=61803],rugilus mirostilicus[&&NHX:TOL=61804],rugilus parastilicus[&&NHX:TOL=61805],rugilus pedistilicus[&&NHX:TOL=61806],rugilus rugilus[&&NHX:TOL=61807],rugilus scabrostilicus[&&NHX:TOL=61808],rugilus tetragnathostilicus[&&NHX:TOL=61809])rugilus[&&NHX:TOL=61796],stilicoderus[&&NHX:TOL=61810],stiliderus[&&NHX:TOL=61811])stilicina[&&NHX:TOL=61787],((dibelonetes brachynetes[&&NHX:TOL=61814],dibelonetes dibelonetes[&&NHX:TOL=61815],dibelonetes heteronetes[&&NHX:TOL=61816],dibelonetes melanetes[&&NHX:TOL=61817])dibelonetes[&&NHX:TOL=61813],dibelophacis[&&NHX:TOL=61818],stamnoderus[&&NHX:TOL=61819],stilicopsis[&&NHX:TOL=61820],stiliphacis[&&NHX:TOL=61821],stilosaurus[&&NHX:TOL=61822],sunesta[&&NHX:TOL=61823],(suniocharis parasuniocharis[&&NHX:TOL=61825],suniocharis suniocharis[&&NHX:TOL=61826])suniocharis[&&NHX:TOL=61824],suniophacis[&&NHX:TOL=61827],suniosaurus[&&NHX:TOL=61828],xenaster[&&NHX:TOL=61829])stilicopsina[&&NHX:TOL=61812],(bolbophites[&&NHX:TOL=61516],diasimognathus[&&NHX:TOL=61517],ecitobium[&&NHX:TOL=61518],ecitonides[&&NHX:TOL=61519],ecitosaurus[&&NHX:TOL=61520],ecitotropis[&&NHX:TOL=61521],labidophites[&&NHX:TOL=61522],leleupirinia[&&NHX:TOL=61523],mimophites[&&NHX:TOL=61524],monista[&&NHX:TOL=61525],synecitonides[&&NHX:TOL=61526])paederini incertae sedis[&&NHX:TOL=61515])paederini[&&NHX:TOL=61513],((araeocerus[&&NHX:TOL=61832],galopinus[&&NHX:TOL=61833],gridellius[&&NHX:TOL=61834],lathropinus[&&NHX:TOL=61835],leleupauchmetes[&&NHX:TOL=61836],levasseurius[&&NHX:TOL=61837],metapinophilus[&&NHX:TOL=61838],mimopinophilus[&&NHX:TOL=61839],neopinophilus[&&NHX:TOL=61840],phinopilus[&&NHX:TOL=61841],pinocharis[&&NHX:TOL=61842],pinogalus[&&NHX:TOL=61843],pinonepalus[&&NHX:TOL=61844],pinophilinus[&&NHX:TOL=61845],pinophilus[&&NHX:TOL=61846],pinoragus[&&NHX:TOL=61847],pinoritus[&&NHX:TOL=61848],pinostygus[&&NHX:TOL=61849],taenodema[&&NHX:TOL=61850])pinophilina[&&NHX:TOL=61831],(neoprocirrus[&&NHX:TOL=61852],(oedichirus oedichiranus[&&NHX:TOL=61854],oedichirus oedichirus[&&NHX:TOL=61855])oedichirus[&&NHX:TOL=61853],oedodactylus[&&NHX:TOL=61856],(palaminus palaminus[&&NHX:TOL=61858],palaminus parapalaminus[&&NHX:TOL=61859])palaminus[&&NHX:TOL=61857],paraprocirrus[&&NHX:TOL=61860],(procirrus procirrinus[&&NHX:TOL=61862],procirrus procirrus[&&NHX:TOL=61863])procirrus[&&NHX:TOL=61861],pseudoprocirrus[&&NHX:TOL=61864])procirrina[&&NHX:TOL=61851])pinophilini[&&NHX:TOL=61830])paederinae[&&NHX:TOL=9811])[&&NHX:TOL=9809],(pseudopsis[&&NHX:TOL=10209],(nanobius[&&NHX:TOL=10211],(asemobius[&&NHX:TOL=10213],zalobius[&&NHX:TOL=10214])[&&NHX:TOL=10212])[&&NHX:TOL=10210])pseudopsinae[&&NHX:TOL=9808])[&&NHX:TOL=9807],(cephalotyphlus[&&NHX:TOL=61442],((allotyphlus allotyphlus[&&NHX:TOL=61447],allotyphlus moreotyphlus[&&NHX:TOL=61448])allotyphlus[&&NHX:TOL=61446],cyrtotyphlus[&&NHX:TOL=61449],(entomoculia entomoculia[&&NHX:TOL=61451],entomoculia stenotyphlus[&&NHX:TOL=61452])entomoculia[&&NHX:TOL=61450],(mesotyphlus acanthotyphlus[&&NHX:TOL=61454],mesotyphlus dexiotyphlus[&&NHX:TOL=61455],mesotyphlus mesotyphlus[&&NHX:TOL=61456],mesotyphlus teleotyphlus[&&NHX:TOL=61457])mesotyphlus[&&NHX:TOL=61453],neocyrtotyphlus[&&NHX:TOL=61458],(paratyphlus ischnotyphlus[&&NHX:TOL=61460],paratyphlus paratyphlus[&&NHX:TOL=61461])paratyphlus[&&NHX:TOL=61459])entomoculiini[&&NHX:TOL=61445],(afrotyphlus[&&NHX:TOL=61463],eotyphlus[&&NHX:TOL=61464],epalxotyphlus[&&NHX:TOL=61465],hesperotyphlus[&&NHX:TOL=61466],kenotyphlus[&&NHX:TOL=61467],kilimatyphlus[&&NHX:TOL=61468],(leptotyphlus anomotyphlus[&&NHX:TOL=61470],leptotyphlus leptotyphlus[&&NHX:TOL=61471],leptotyphlus odontotyphlus[&&NHX:TOL=61472],leptotyphlus porotyphlus[&&NHX:TOL=61473],leptotyphlus stigmotyphlus[&&NHX:TOL=61474],leptotyphlus subhesperotyphlus[&&NHX:TOL=61475])leptotyphlus[&&NHX:TOL=61469],newtonius[&&NHX:TOL=61476],portotyphlus[&&NHX:TOL=61477],sekotyphlus[&&NHX:TOL=61478])leptotyphlini[&&NHX:TOL=61462],(apotyphlus[&&NHX:TOL=61480],banatotyphlus[&&NHX:TOL=61481],(egeotyphlus egeotyphlus[&&NHX:TOL=61483],egeotyphlus epirotyphlus[&&NHX:TOL=61484])egeotyphlus[&&NHX:TOL=61482],gynotyphlus[&&NHX:TOL=61485],(metrotyphlus agnotyphlus[&&NHX:TOL=61487],metrotyphlus metrotyphlus[&&NHX:TOL=61488])metrotyphlus[&&NHX:TOL=61486],rhopalotyphlus[&&NHX:TOL=61489],venezillotyphlus[&&NHX:TOL=61490])metrotyphlini[&&NHX:TOL=61479],(apheliotyphlus[&&NHX:TOL=61492],cafrotyphlus[&&NHX:TOL=61493],cainotyphlus[&&NHX:TOL=61494],chiliotyphlus[&&NHX:TOL=61495],chionotyphlus[&&NHX:TOL=61496],cubanotyphlus[&&NHX:TOL=61497],eutyphlops[&&NHX:TOL=61498],heterotyphlus[&&NHX:TOL=61499],homeotyphlus[&&NHX:TOL=61500],idahotyphlus[&&NHX:TOL=61501],kladotyphlus[&&NHX:TOL=61502],macrotyphlus[&&NHX:TOL=61503],mayatyphlus[&&NHX:TOL=61504],megatyphlus[&&NHX:TOL=61505],neotyphlus[&&NHX:TOL=61506],oreinotyphlus[&&NHX:TOL=61507],paramacrotyphlus[&&NHX:TOL=61508],prototyphlus[&&NHX:TOL=61509],telotyphlus[&&NHX:TOL=61510],xenotyphlus[&&NHX:TOL=61511])neotyphlini[&&NHX:TOL=61491])leptotyphlinae[&&NHX:TOL=9806])[&&NHX:TOL=9805],(oxyporus[&&NHX:TOL=9803],((megalopinus gata[&&NHX:TOL=61432],megalopinus megalopinus[&&NHX:TOL=61433],megalopinus megalopsidiella[&&NHX:TOL=61434],megalopinus polycyrtopsidia[&&NHX:TOL=61435],megalopinus stylopodus[&&NHX:TOL=61436])megalopinus[&&NHX:TOL=9802],((alzadaesthetus[&&NHX:TOL=61397],(austroesthetus[&&NHX:TOL=61401],chilioesthetus[&&NHX:TOL=61402],mesoaesthetus[&&NHX:TOL=61403],nothoesthetus[&&NHX:TOL=61404],tasmanosthetus[&&NHX:TOL=61405])austroesthetini[&&NHX:TOL=61400],(coiffaitia[&&NHX:TOL=61407],ctenomastax[&&NHX:TOL=61408],edaphus[&&NHX:TOL=61409],euaesthetotyphlus[&&NHX:TOL=61410],euaesthetus[&&NHX:TOL=61411],macroturellus[&&NHX:TOL=61412],neocoiffaitia[&&NHX:TOL=61413],octavius[&&NHX:TOL=61414],phaenoctavius[&&NHX:TOL=61415],protopristus[&&NHX:TOL=61416],schatzmayrina[&&NHX:TOL=61417],tamotus[&&NHX:TOL=61418])euaesthetini[&&NHX:TOL=61406],(fenderia[&&NHX:TOL=61420],stictocranius[&&NHX:TOL=61421])fenderiini[&&NHX:TOL=61419],(edaphosoma[&&NHX:TOL=61423],libanoeuaesthetus[&&NHX:TOL=61424],nordenskioldia[&&NHX:TOL=61425])nordenskioldiini[&&NHX:TOL=61422],(agnosthaetus[&&NHX:TOL=61427],gerhardia[&&NHX:TOL=61428],stenaesthetus[&&NHX:TOL=61429],tyrannomastax[&&NHX:TOL=61430])stenaesthetini[&&NHX:TOL=61426])euaesthetinae[&&NHX:TOL=9801],(dianous[&&NHX:TOL=107359],(stenus hemistenus[&&NHX:TOL=107360],stenus hypostenus[&&NHX:TOL=107361],stenus metatesnus[&&NHX:TOL=107362],stenus stenus[&&NHX:TOL=107363],stenus tesnus[&&NHX:TOL=107364])stenus[&&NHX:TOL=107365])steninae[&&NHX:TOL=9800])[&&NHX:TOL=9799])[&&NHX:TOL=9798])[&&NHX:TOL=9797],solierius[&&NHX:TOL=9804])[&&NHX:TOL=9796])[&&NHX:TOL=9786])[&&NHX:TOL=9774])staphylinidae[&&NHX:TOL=9621],(hapsomela[&&NHX:EXT=Y:TOL=61032],((clidicus[&&NHX:TOL=61037],leptochromus[&&NHX:TOL=61038],palaeoleptochromus[&&NHX:EXT=Y:TOL=61039],papusus[&&NHX:TOL=61040])clidicini[&&NHX:TOL=61036],(ablepton[&&NHX:TOL=61042],leptomastax[&&NHX:TOL=61043],taurablepton[&&NHX:TOL=61044])leptomastacini[&&NHX:TOL=61041],(mastigus[&&NHX:TOL=61046],palaeostigus[&&NHX:TOL=61047],(stenomastigus acanthostigus[&&NHX:TOL=61049],stenomastigus stenomastigus[&&NHX:TOL=61050])stenomastigus[&&NHX:TOL=61048])mastigini[&&NHX:TOL=61045])mastiginae[&&NHX:TOL=61035],(((cephennium cephennarium[&&NHX:TOL=61054],cephennium cephennium[&&NHX:TOL=61055],cephennium geodytes[&&NHX:TOL=61056],cephennium macroderus[&&NHX:TOL=61057],cephennium neocephennium[&&NHX:TOL=61058],cephennium phennecium[&&NHX:TOL=61059])cephennium[&&NHX:TOL=61053],cephennodes[&&NHX:TOL=61060],cephennomicrus[&&NHX:TOL=61061],chelonoidum[&&NHX:TOL=61062],coatesia[&&NHX:TOL=61063],elacatophora[&&NHX:TOL=61064],etelea[&&NHX:TOL=61065],nanophthalmus[&&NHX:TOL=61066],neseuthia[&&NHX:TOL=61067],paracephennium[&&NHX:TOL=61068],paraneseuthia[&&NHX:TOL=61069],pseudocephennium[&&NHX:TOL=61070])cephenniini[&&NHX:TOL=61052],chevrolatia[&&NHX:TOL=61071],(allohoraeomorphus[&&NHX:TOL=61075],alloraphes[&&NHX:TOL=61076],anhoraeomorphus[&&NHX:TOL=61077],archiconnus[&&NHX:TOL=61078],borneosabahia[&&NHX:TOL=61079],brachycepsis[&&NHX:TOL=61080],catalinus[&&NHX:TOL=61081],chathamaenus[&&NHX:TOL=61082],euconnomorphus[&&NHX:TOL=61083],(euconnus alloconophron[&&NHX:TOL=61085],euconnus allonapochus[&&NHX:TOL=61086],euconnus androconnus[&&NHX:TOL=61087],euconnus anthicimorphus[&&NHX:TOL=61088],euconnus borneoconnus[&&NHX:TOL=61089],euconnus cephaloconnus[&&NHX:TOL=61090],euconnus cerviconnus[&&NHX:TOL=61091],euconnus cladoconnus[&&NHX:TOL=61092],euconnus dimorphoconnus[&&NHX:TOL=61093],euconnus drastophus[&&NHX:TOL=61094],euconnus euconnus[&&NHX:TOL=61095],euconnus euconophron[&&NHX:TOL=61096],euconnus eupentarius[&&NHX:TOL=61097],euconnus filonapochus[&&NHX:TOL=61098],euconnus heteroconnus[&&NHX:TOL=61099],euconnus heterotetramelus[&&NHX:TOL=61100],euconnus himaloconnus[&&NHX:TOL=61101],euconnus microconnus[&&NHX:TOL=61102],euconnus myrmecodytes[&&NHX:TOL=61103],euconnus napochus[&&NHX:TOL=61104],euconnus napoconnus[&&NHX:TOL=61105],euconnus neonapochus[&&NHX:TOL=61106],euconnus nepaloconnus[&&NHX:TOL=61107],euconnus noctophus[&&NHX:TOL=61108],euconnus nodoconnus[&&NHX:TOL=61109],euconnus palaeoconnus[&&NHX:TOL=61110],euconnus paranapochus[&&NHX:TOL=61111],euconnus paratetramelus[&&NHX:TOL=61112],euconnus psomophus[&&NHX:TOL=61113],euconnus pycnophus[&&NHX:TOL=61114],euconnus rhomboconnus[&&NHX:TOL=61115],euconnus scopophus[&&NHX:TOL=61116],euconnus scydmaenites[&&NHX:TOL=61117],euconnus smicrophus[&&NHX:TOL=61118],euconnus tetramelus[&&NHX:TOL=61119],euconnus ursoconnus[&&NHX:TOL=61120],euconnus xestophus[&&NHX:TOL=61121])euconnus[&&NHX:TOL=61084],heteroscydmus[&&NHX:TOL=61122],homoconnus[&&NHX:TOL=61123],horaeomorphus[&&NHX:TOL=61124],leptocharis[&&NHX:TOL=61125],loeblites[&&NHX:TOL=61126],lophioderus[&&NHX:TOL=61127],madagassoconnus[&&NHX:TOL=61128],maorinus[&&NHX:TOL=61129],microraphes[&&NHX:TOL=61130],(microscydmus delius[&&NHX:TOL=61132],microscydmus microscydmus[&&NHX:TOL=61133],microscydmus neladius[&&NHX:TOL=61134],microscydmus neoscydmus[&&NHX:TOL=61135])microscydmus[&&NHX:TOL=61131],mimoscydmus[&&NHX:TOL=61136],napochomorphus[&&NHX:TOL=61137],neuraphanax[&&NHX:TOL=61138],(neuraphes neuraphes[&&NHX:TOL=61140],neuraphes pararaphes[&&NHX:TOL=61141],neuraphes rhynchoraphes[&&NHX:TOL=61142])neuraphes[&&NHX:TOL=61139],neuraphomorphus[&&NHX:TOL=61143],oneila[&&NHX:TOL=61144],(parapseudoconnus neuraphomimus[&&NHX:TOL=61146],parapseudoconnus parapseudoconnus[&&NHX:TOL=61147])parapseudoconnus[&&NHX:TOL=61145],parascydmus[&&NHX:TOL=61148],parastenichnaphes[&&NHX:TOL=61149],parastenichnus[&&NHX:TOL=61150],protandroconnus[&&NHX:TOL=61151],protoconnus[&&NHX:TOL=61152],protoscydmus[&&NHX:TOL=61153],psepharobius[&&NHX:TOL=61154],pseudoraphes[&&NHX:TOL=61155],(sciacharis anthicimimus[&&NHX:TOL=61157],sciacharis magellanoconnus[&&NHX:TOL=61158],sciacharis sciacharis[&&NHX:TOL=61159],sciacharis valdivioconnus[&&NHX:TOL=61160])sciacharis[&&NHX:TOL=61156],scydmoraphes[&&NHX:TOL=61161],stenichnaphes[&&NHX:TOL=61162],stenichnoconnus[&&NHX:TOL=61163],stenichnodes[&&NHX:TOL=61164],stenichnoteras[&&NHX:TOL=61165],(stenichnus austrostenichnus[&&NHX:TOL=61167],stenichnus scydmaenichnus[&&NHX:TOL=61168],stenichnus scydmaenilla[&&NHX:TOL=61169],stenichnus stenichnus[&&NHX:TOL=61170])stenichnus[&&NHX:TOL=61166],(syndicus semisyndicus[&&NHX:TOL=61172],syndicus syndicus[&&NHX:TOL=61173])syndicus[&&NHX:TOL=61171],taphroscydmus[&&NHX:TOL=61174],venezolanoconnus[&&NHX:TOL=61175])cyrtoscydmini[&&NHX:TOL=61074],(eutheia[&&NHX:TOL=61177],eutheimorphus[&&NHX:TOL=61178],euthiconus[&&NHX:TOL=61179],paeneutheia[&&NHX:TOL=61180],protoeuthia[&&NHX:TOL=61181],veraphis[&&NHX:TOL=61182])eutheiini[&&NHX:TOL=61176],leptoscydmus[&&NHX:TOL=61183],plaumanniola[&&NHX:TOL=61186],(adrastia[&&NHX:TOL=61190],ceramphis[&&NHX:TOL=61191],clavigeroscydmus[&&NHX:TOL=61192],eudesis[&&NHX:TOL=61193],palaeoscydmaenus[&&NHX:TOL=61194],(pseudoeudesis afroeudesis[&&NHX:TOL=61196],pseudoeudesis oreoeudesis[&&NHX:TOL=61197],pseudoeudesis pseudoeudesis[&&NHX:TOL=61198])pseudoeudesis[&&NHX:TOL=61195],(scydmaenus afroscydmaenus[&&NHX:TOL=61200],scydmaenus agathelor[&&NHX:TOL=61201],scydmaenus alaudula[&&NHX:TOL=61202],scydmaenus androscydmaenus[&&NHX:TOL=61203],scydmaenus androscydmus[&&NHX:TOL=61204],scydmaenus archiscydmaenus[&&NHX:TOL=61205],scydmaenus armatoscydmaenus[&&NHX:TOL=61206],scydmaenus breviclavatoscydmaenus[&&NHX:TOL=61207],scydmaenus choleropsis[&&NHX:TOL=61208],scydmaenus cholerus[&&NHX:TOL=61209],scydmaenus conoscydmaenus[&&NHX:TOL=61210],scydmaenus corbulifer[&&NHX:TOL=61211],scydmaenus eustemmoides[&&NHX:TOL=61212],scydmaenus eustemmus[&&NHX:TOL=61213],scydmaenus geoscydmaenus[&&NHX:TOL=61214],scydmaenus heteroeustemmus[&&NHX:TOL=61215],scydmaenus heteromicrus[&&NHX:TOL=61216],scydmaenus kingius[&&NHX:TOL=61217],scydmaenus mascarensia[&&NHX:TOL=61218],scydmaenus mimoscydmaenus[&&NHX:TOL=61219],scydmaenus nepaloscydmaenus[&&NHX:TOL=61220],scydmaenus paraeustemmus[&&NHX:TOL=61221],scydmaenus parageoscydmaenus[&&NHX:TOL=61222],scydmaenus parallomicrus[&&NHX:TOL=61223],scydmaenus parascydmaenus[&&NHX:TOL=61224],scydmaenus pseudeumicrus[&&NHX:TOL=61225],scydmaenus scottiscydmaenus[&&NHX:TOL=61226],scydmaenus scydmaenus[&&NHX:TOL=61227],scydmaenus seychellinus[&&NHX:TOL=61228],scydmaenus termitoscydmaenus[&&NHX:TOL=61229],scydmaenus trapezoscydmaenus[&&NHX:TOL=61230])scydmaenus[&&NHX:TOL=61199])scydmaenini[&&NHX:TOL=61189],siamites[&&NHX:TOL=61231])scydmaeninae[&&NHX:TOL=61051],cryptodiodon[&&NHX:EXT=Y:TOL=61023],electroscydmaenus[&&NHX:EXT=Y:TOL=61024],hetereuthia[&&NHX:EXT=Y:TOL=61025],heuretus[&&NHX:EXT=Y:TOL=61026],microlynx[&&NHX:EXT=Y:TOL=61027],palaeomastigus[&&NHX:EXT=Y:TOL=61028],palaeothia[&&NHX:EXT=Y:TOL=61029],scydmaenoides[&&NHX:EXT=Y:TOL=61030],semnodioceras[&&NHX:EXT=Y:TOL=61031])scydmaenidae[&&NHX:TOL=9619],(((((necrodes[&&NHX:TOL=27006],diamesus[&&NHX:TOL=27007])[&&NHX:TOL=27002],(((((aclypea[&&NHX:TOL=27018],silpha[&&NHX:TOL=27019])[&&NHX:TOL=27014],(silpha ablattaria[&&NHX:TOL=27016],silpha phosphuga[&&NHX:TOL=27017])[&&NHX:TOL=27015])[&&NHX:TOL=27012],dendroxena[&&NHX:TOL=27013])[&&NHX:TOL=27008],(heterosilpha[&&NHX:TOL=27010],necrophila[&&NHX:TOL=27011])[&&NHX:TOL=27009])[&&NHX:TOL=27004],oiceoptoma[&&NHX:TOL=27005],heterotemna[&&NHX:TOL=27917])[&&NHX:TOL=27003])[&&NHX:TOL=27000],thanatophilus[&&NHX:TOL=27001])[&&NHX:TOL=26996],(ptomaphila[&&NHX:TOL=26998],oxelytrum[&&NHX:TOL=26999])[&&NHX:TOL=26997])silphinae[&&NHX:TOL=26994],nicrophorinae[&&NHX:TOL=26995])silphidae[&&NHX:TOL=9620])[&&NHX:TOL=29359])staphylinoidea[&&NHX:TOL=9076])staphyliniformia[&&NHX:TOL=9074],((glaresis alfierii[&&NHX:TOL=9555],glaresis arenata[&&NHX:TOL=9556],glaresis beckeri[&&NHX:TOL=9557],glaresis canadensis[&&NHX:TOL=9558],glaresis carthagensis[&&NHX:TOL=9559],glaresis cartwrighti[&&NHX:TOL=9560],glaresis ceballosi[&&NHX:TOL=9561],glaresis celiae[&&NHX:TOL=9562],glaresis clypeata[&&NHX:TOL=9563],glaresis confusa[&&NHX:TOL=9564],glaresis contrerasi[&&NHX:TOL=9565],glaresis dakotensis[&&NHX:TOL=9566],glaresis desperata[&&NHX:TOL=9567],glaresis ecostata[&&NHX:TOL=9568],glaresis exasperata[&&NHX:TOL=9569],glaresis foveolata[&&NHX:TOL=9570],glaresis freyi[&&NHX:TOL=9571],glaresis fritzi[&&NHX:TOL=9572],glaresis frustrata[&&NHX:TOL=9573],glaresis gineri[&&NHX:TOL=9574],glaresis handlirshci[&&NHX:TOL=9575],glaresis hispanus[&&NHX:TOL=9576],glaresis holmi[&&NHX:TOL=9577],glaresis howdeni[&&NHX:TOL=9578],glaresis impressicollis[&&NHX:TOL=9579],glaresis inducta[&&NHX:TOL=9580],glaresis kocheri[&&NHX:TOL=9581],glaresis koenigsbaueri[&&NHX:TOL=9582],glaresis longisternum[&&NHX:TOL=9583],glaresis lomii[&&NHX:TOL=9584],glaresis mandibularis[&&NHX:TOL=9585],glaresis maroccana[&&NHX:TOL=9586],glaresis mauritanica[&&NHX:TOL=9587],glaresis medialis[&&NHX:TOL=9588],glaresis mendica[&&NHX:TOL=9589],glaresis methneri[&&NHX:TOL=9590],glaresis minuta[&&NHX:TOL=9591],glaresis namibensis[&&NHX:TOL=9592],glaresis penrithae[&&NHX:TOL=9593],glaresis oxiana[&&NHX:TOL=9594],glaresis pardoi[&&NHX:TOL=9595],glaresis pardoalcaidei[&&NHX:TOL=9596],glaresis phoenicis[&&NHX:TOL=9597],glaresis porrecta[&&NHX:TOL=9598],glaresis quedenfeldti[&&NHX:TOL=9599],glaresis rufa[&&NHX:TOL=9600],glaresis texana[&&NHX:TOL=9601],glaresis tripolitana[&&NHX:TOL=9602],glaresis villiersi[&&NHX:TOL=9603],glaresis walzlae[&&NHX:TOL=9604],glaresis zarudniana[&&NHX:TOL=9605])glaresis[&&NHX:TOL=9529],((((((((leptaulax[&&NHX:TOL=104803],mastochilus[&&NHX:TOL=104804],odontotaenius[&&NHX:TOL=104805],passalus[&&NHX:TOL=104806],paxillus[&&NHX:TOL=104807],popilius[&&NHX:TOL=104808],proculus[&&NHX:TOL=104809],veturius[&&NHX:TOL=104810])passalinae[&&NHX:TOL=65643],(aulacocyclus[&&NHX:TOL=104811],ceracupes[&&NHX:TOL=104812],comacupes[&&NHX:TOL=104813],cylindrocaulus[&&NHX:TOL=104814],taeniocerus[&&NHX:TOL=104815])aulacocyclinae[&&NHX:TOL=65644])passalidae[&&NHX:TOL=9536],(((aesalus[&&NHX:TOL=65641],lucanobium[&&NHX:TOL=104762])aesalinae[&&NHX:TOL=104761],(nicagus[&&NHX:TOL=104764],ceratognathus[&&NHX:TOL=104765])nicaginae[&&NHX:TOL=104763],(sinodendron[&&NHX:TOL=104767],syndesus[&&NHX:TOL=104768],ceruchus[&&NHX:TOL=104769])syndesinae[&&NHX:TOL=104766],(dendroblax[&&NHX:TOL=104771],lamprima[&&NHX:TOL=104772],phalacrognathus[&&NHX:TOL=104773],streptocerus[&&NHX:TOL=104774])lampriminae[&&NHX:TOL=104770],(penichrolucanus[&&NHX:TOL=104776],brasilucanus[&&NHX:TOL=104777])penichrolucaninae[&&NHX:TOL=104775],(lucanus[&&NHX:TOL=65642],chiasognathus[&&NHX:TOL=104779],colophon[&&NHX:TOL=104780],cyclommatus[&&NHX:TOL=104781],dendezia[&&NHX:TOL=104782],dorcus[&&NHX:TOL=104783],figulus[&&NHX:TOL=104784],lissotes[&&NHX:TOL=104785],nigidus[&&NHX:TOL=104786],odontolabis[&&NHX:TOL=104787],pholiodotus[&&NHX:TOL=104788],platycerus[&&NHX:TOL=104789],prosopocoilus[&&NHX:TOL=104790],pseudodorcus[&&NHX:TOL=104791],rhaetulus[&&NHX:TOL=104792],rhyssonotus[&&NHX:TOL=104793],sclerostomus[&&NHX:TOL=104794],scortizus[&&NHX:TOL=104795],serrognathus[&&NHX:TOL=104796])lucaninae[&&NHX:TOL=104778])lucanidae[&&NHX:TOL=9538],(diphyllostoma fimbriata[&&NHX:TOL=65647],diphyllostoma linsleyi[&&NHX:TOL=104844],diphyllostoma nigricollis[&&NHX:TOL=104845])diphyllostoma[&&NHX:TOL=9539])[&&NHX:TOL=9537])[&&NHX:TOL=9535],(trox[&&NHX:TOL=65645],[&&NHX:TOL=65646],omorgus[&&NHX:TOL=104816],polynoncus[&&NHX:TOL=104817])trogidae[&&NHX:TOL=9540])[&&NHX:TOL=9534],((athyreus[&&NHX:TOL=104899],blackburnium[&&NHX:TOL=104900],bolbelasmus[&&NHX:TOL=104901],bolboceras[&&NHX:TOL=104902],bolbocerasoma[&&NHX:TOL=104903],elephastomus[&&NHX:TOL=104904],eucanthus[&&NHX:TOL=104905],neoathyreus[&&NHX:TOL=104906],odonteus[&&NHX:TOL=104915],[&&NHX:TOL=104916])bolboceratidae[&&NHX:TOL=9542],(pleocoma australis[&&NHX:TOL=67262],pleocoma badia[&&NHX:TOL=104818],pleocoma behrensi[&&NHX:TOL=104819],pleocoma bicolor[&&NHX:TOL=104820],pleocoma blaisdelli[&&NHX:TOL=104821],pleocoma carinata[&&NHX:TOL=104822],pleocoma conjungens[&&NHX:TOL=104823],pleocoma crinita[&&NHX:TOL=104824],pleocoma dubitabilis[&&NHX:TOL=104825],pleocoma fimbriata[&&NHX:TOL=104826],pleocoma hirticollis[&&NHX:TOL=104827],pleocoma hoppingi[&&NHX:TOL=104828],pleocoma linsleyi[&&NHX:TOL=104829],pleocoma marquai[&&NHX:TOL=104830],pleocoma minor[&&NHX:TOL=104831],pleocoma octopagina[&&NHX:TOL=104832],pleocoma oregonensis[&&NHX:TOL=104833],pleocoma puncticollis[&&NHX:TOL=104834],pleocoma rickseckeri[&&NHX:TOL=104835],pleocoma rubiginosa[&&NHX:TOL=104836],pleocoma shastensis[&&NHX:TOL=104837],pleocoma simi[&&NHX:TOL=104838],pleocoma sonomae[&&NHX:TOL=104839],pleocoma staff[&&NHX:TOL=104840],pleocoma trifoliata[&&NHX:TOL=104841],pleocoma tularensis[&&NHX:TOL=104842],pleocoma venturae[&&NHX:TOL=104843])pleocoma[&&NHX:TOL=9543])[&&NHX:TOL=9541])[&&NHX:TOL=9533],(amphicoma[&&NHX:TOL=104955],anthypna[&&NHX:TOL=104956],cratoscelis[&&NHX:TOL=104957],dasychaeta[&&NHX:TOL=104958],glaphyrus[&&NHX:TOL=104959],lichnia[&&NHX:TOL=104960],lichnanthe[&&NHX:TOL=104961],toxocerus[&&NHX:TOL=104962])glaphyridae[&&NHX:TOL=9544])[&&NHX:TOL=9532],((frickius[&&NHX:TOL=104921],taurocerastes[&&NHX:TOL=67258],anoplotrupes[&&NHX:TOL=104935],ceratotrupes[&&NHX:TOL=104924],chromogeotrupes[&&NHX:TOL=104926],geotrupes[&&NHX:TOL=65649],mycotrupes[&&NHX:TOL=104930],typhoeus[&&NHX:TOL=104932],lethrus[&&NHX:TOL=104934])geotrupidae[&&NHX:TOL=9546],(((anaides[&&NHX:TOL=104949],coelodes[&&NHX:TOL=104950],cryptogenius[&&NHX:TOL=104951],hybosorus[&&NHX:TOL=104952],liparochrus[&&NHX:TOL=104953],phaeochrous[&&NHX:TOL=104954])hybosoridae[&&NHX:TOL=9549],(ceratocanthus[&&NHX:TOL=67260],cloeotus[&&NHX:TOL=104945],cyphopisthes[&&NHX:TOL=104946],madrasostes[&&NHX:TOL=104947],philharmostes[&&NHX:TOL=104948])ceratocanthidae[&&NHX:TOL=9550])[&&NHX:TOL=9548],((codocera[&&NHX:TOL=104937],endognathus[&&NHX:TOL=104938],ochodaeus[&&NHX:TOL=65651],odontochodaeus[&&NHX:TOL=104939])ochodaeinae[&&NHX:TOL=65652],(chaetocanthus[&&NHX:TOL=104941],namibiotalpa[&&NHX:TOL=104942],pseudochodaeus[&&NHX:TOL=104943],synochodaeus[&&NHX:TOL=104944])chaetocanthinae[&&NHX:TOL=104940])ochodaeidae[&&NHX:TOL=9551])[&&NHX:TOL=9547])[&&NHX:TOL=9545])[&&NHX:TOL=9531],((aegialia[&&NHX:TOL=104964],aphodius[&&NHX:TOL=67264],ataenius[&&NHX:TOL=104965],aulonocnemis[&&NHX:TOL=104966],chiron[&&NHX:TOL=104967],corythoderus[&&NHX:TOL=104968],demarziella[&&NHX:TOL=104969],eremazus[&&NHX:TOL=104970],euparia[&&NHX:TOL=104971],oxyomus[&&NHX:TOL=104972],psammobius[&&NHX:TOL=104973],rhyparus[&&NHX:TOL=104974],rhyssemus[&&NHX:TOL=104975],saprus[&&NHX:TOL=104976],silluvia[&&NHX:TOL=104977],termitotrox[&&NHX:TOL=104978],thinorycter[&&NHX:TOL=104979])aphodiinae[&&NHX:TOL=104963],(alloscelus[&&NHX:TOL=104981],ateuchus[&&NHX:TOL=104982],canthon[&&NHX:TOL=104983],copris[&&NHX:TOL=104984],coptodactylus[&&NHX:TOL=104985],deltochilum[&&NHX:TOL=104986],dichotomius[&&NHX:TOL=104987],eucranium[&&NHX:TOL=104988],eurysternus[&&NHX:TOL=104989],gymnopleurus[&&NHX:TOL=104990],heliocopris[&&NHX:TOL=104991],melanocanthon[&&NHX:TOL=105088],oniticellus[&&NHX:TOL=104992],onitis[&&NHX:TOL=104993],onthophagus[&&NHX:TOL=104994],phanaeus[&&NHX:TOL=104995],pinotus[&&NHX:TOL=104996],scarabaeus[&&NHX:TOL=65653],sisyphus[&&NHX:TOL=104997])scarabaeinae[&&NHX:TOL=104980],(aegidiellus[&&NHX:TOL=105215],aegidinus[&&NHX:TOL=105216],aegidium[&&NHX:TOL=104999],chaetonyx[&&NHX:TOL=105000],orphnus[&&NHX:TOL=105001],paraegidium[&&NHX:TOL=105217])orphninae[&&NHX:TOL=104998],(pachypus caesus[&&NHX:TOL=105173],pachypus candidae[&&NHX:TOL=105174],pachypus demoflysi[&&NHX:TOL=105175])pachypus[&&NHX:TOL=105002],(allidiostoma bosqui[&&NHX:TOL=105156],allidiostoma halffteri[&&NHX:TOL=105157],allidiostoma hirtum[&&NHX:TOL=105158],allidiostoma landbecki[&&NHX:TOL=105159],allidiostoma monrosmuntanolae[&&NHX:TOL=105160],allidiostoma ramosae[&&NHX:TOL=105161],allidiostoma rufum[&&NHX:TOL=105162],allidiostoma simplicifrons[&&NHX:TOL=105163],allidiostoma strobeli[&&NHX:TOL=105164])allidiostoma[&&NHX:TOL=94855],dynamopus[&&NHX:TOL=105003],(aclopus[&&NHX:TOL=105005],neophaenognatha[&&NHX:TOL=105006],phaenognatha[&&NHX:TOL=105007],xenaclopus[&&NHX:TOL=105008])aclopinae[&&NHX:TOL=105004],(cheirotonus[&&NHX:TOL=105010],euchirus[&&NHX:TOL=105011],propomacrus[&&NHX:TOL=105012])euchirinae[&&NHX:TOL=105009],(oxychirus[&&NHX:TOL=105014],phaenomeris[&&NHX:TOL=105015])phaenomeridinae[&&NHX:TOL=105013],(ablabera[&&NHX:TOL=105017],automolus[&&NHX:TOL=105018],chasmatopterus[&&NHX:TOL=105019],dichelonyx[&&NHX:TOL=105020],diplotaxis[&&NHX:TOL=105021],heteronyx[&&NHX:TOL=105022],hoplia[&&NHX:TOL=105023],liparetrus[&&NHX:TOL=105024],macrodactylus[&&NHX:TOL=105025],maechidius[&&NHX:TOL=105026],melolontha[&&NHX:TOL=65655],pachydema[&&NHX:TOL=105027],phyllophaga[&&NHX:TOL=105028],phyllotocidium[&&NHX:TOL=105029],phyllotocus[&&NHX:TOL=105030],polyphylla[&&NHX:TOL=105087],serica[&&NHX:TOL=105031],systellopus[&&NHX:TOL=105032],xylonychus[&&NHX:TOL=105033])melolonthinae[&&NHX:TOL=105016],(adoretus[&&NHX:TOL=105035],anomala[&&NHX:TOL=105036],anoplognathus[&&NHX:TOL=105037],bolax[&&NHX:TOL=105038],cotalpa[&&NHX:TOL=105039],epectinaspis[&&NHX:TOL=94854],geniates[&&NHX:TOL=105040],pelidnota[&&NHX:TOL=105041],phyllopertha[&&NHX:TOL=105042],plusiotis[&&NHX:TOL=105043],popillia[&&NHX:TOL=105044],repsimus[&&NHX:TOL=105045],rutela[&&NHX:TOL=105046],spodochlamys[&&NHX:TOL=105047])rutelinae[&&NHX:TOL=105034],(agaocephala[&&NHX:TOL=105049],cryptodus[&&NHX:TOL=105050],cyclocephala[&&NHX:TOL=105051],dynastes[&&NHX:TOL=65654],dyscinetus[&&NHX:TOL=105052],golofa[&&NHX:TOL=105053],heteronychus[&&NHX:TOL=105054],hexodon[&&NHX:TOL=105055],ligyrus[&&NHX:TOL=105056],megasoma[&&NHX:TOL=105057],oryctes[&&NHX:TOL=105058],oryctoderus[&&NHX:TOL=105059],pentodon[&&NHX:TOL=105060],phileurus[&&NHX:TOL=105061],strategus[&&NHX:TOL=105062],xyloryctes[&&NHX:TOL=105063])dynastinae[&&NHX:TOL=105048],((incaina[&&NHX:TOL=133779],(osmodermatina[&&NHX:TOL=133780],(((gymnetina[&&NHX:TOL=133740],blaesiina[&&NHX:TOL=133741])gymnetini[&&NHX:TOL=105066],platygenina[&&NHX:TOL=136023],diplognathini[&&NHX:TOL=105067],(leucocelina[&&NHX:TOL=133739],euphoriina[&&NHX:TOL=133738],cetoniina[&&NHX:TOL=133737])cetoniini[&&NHX:TOL=105065],(goliathina[&&NHX:TOL=133770],dicronocephalina[&&NHX:TOL=133771],ichnestomatina[&&NHX:TOL=133772],coryphocerina[&&NHX:TOL=133773])goliathini[&&NHX:TOL=105072],((spilophorus cretosus[&&NHX:TOL=133783],spilophorus aurifer[&&NHX:TOL=133784],spilophorus cervinus[&&NHX:TOL=133785],spilophorus fernandesi[&&NHX:TOL=133786],spilophorus grandis[&&NHX:TOL=133787],spilophorus lugubris[&&NHX:TOL=133788],spilophorus maculatus[&&NHX:TOL=133789],spilophorus plagosus[&&NHX:TOL=133790])spilophorus[&&NHX:TOL=133742],(macroma[&&NHX:TOL=133791],campsiura[&&NHX:TOL=133792])macromina[&&NHX:TOL=133743],trogodina[&&NHX:TOL=133744],nyassinina[&&NHX:TOL=133745],heterogenina[&&NHX:TOL=133746],aspilina[&&NHX:TOL=133747],coenochilina[&&NHX:TOL=133748],cymophorina[&&NHX:TOL=133749],trichoplina[&&NHX:TOL=133750],oplostomatina[&&NHX:TOL=133751],telochilina[&&NHX:TOL=133752],genuchina[&&NHX:TOL=133753],pilinurgina[&&NHX:TOL=133754],goliathopsidina[&&NHX:TOL=133755],cremastocheilina[&&NHX:TOL=133756],lissogeniina[&&NHX:TOL=133757])cremastocheilini[&&NHX:TOL=105068],(taenioderina[&&NHX:TOL=133758],chalcotheina[&&NHX:TOL=133759])taenioderini[&&NHX:TOL=105070],(coptomiina[&&NHX:TOL=133760],anochiliina[&&NHX:TOL=133761],pantoliina[&&NHX:TOL=133762],stenotarsiina[&&NHX:TOL=133763],euchroeina[&&NHX:TOL=133764],doryscelina[&&NHX:TOL=133765],parachiliina[&&NHX:TOL=133766],heterophanina[&&NHX:TOL=133767],chromoptiliina[&&NHX:TOL=133768],heterosomatina[&&NHX:TOL=133769])stenotarsiini[&&NHX:TOL=105071],(schizorhinina[&&NHX:TOL=133774],lomapterina[&&NHX:TOL=133775])schizorhinini[&&NHX:TOL=105073],phaedimini[&&NHX:TOL=105069],xiphoscelidini[&&NHX:TOL=105085])[&&NHX:TOL=136022],cremastocheilus[&&NHX:TOL=136024])[&&NHX:TOL=136021])[&&NHX:TOL=136020])[&&NHX:TOL=136019],(((microvalgina[&&NHX:TOL=133781],valgina[&&NHX:TOL=133782])valgini[&&NHX:TOL=105075],cryptodontina[&&NHX:TOL=136025])[&&NHX:TOL=133776],trichiina[&&NHX:TOL=136026])trichiini[&&NHX:TOL=105074])cetoniinae[&&NHX:TOL=105064])scarabaeidae[&&NHX:TOL=9552])[&&NHX:TOL=9530],belohina inexpectata[&&NHX:TOL=104936])scarabaeoidea[&&NHX:TOL=9077])[&&NHX:TOL=9073],(((schizopodinae[&&NHX:TOL=9104],(julodinae[&&NHX:TOL=9106],(buprestinae[&&NHX:TOL=9108],agrilinae[&&NHX:TOL=9109])[&&NHX:TOL=9107])[&&NHX:TOL=9105])buprestoidea[&&NHX:TOL=9082],((acalyptomerus[&&NHX:TOL=29902],calyptomerus[&&NHX:TOL=29901],((clambus arizonicus[&&NHX:TOL=112501],clambus armadillo[&&NHX:TOL=112502],clambus arnetti[&&NHX:TOL=112503],clambus besucheti[&&NHX:TOL=112504],clambus caucasus[&&NHX:TOL=112505],clambus cilicicus[&&NHX:TOL=112506],clambus dux[&&NHX:TOL=112507],clambus evae[&&NHX:TOL=112508],clambus felix[&&NHX:TOL=112509],clambus filii[&&NHX:TOL=112510],clambus gibbulus[&&NHX:TOL=112511],clambus hayekae[&&NHX:TOL=112512],clambus howdeni[&&NHX:TOL=112513],clambus lohsei[&&NHX:TOL=112514],clambus minutus[&&NHX:TOL=112515],clambus nigrellus[&&NHX:TOL=112516],clambus nigriclavis[&&NHX:TOL=112517],clambus octobris[&&NHX:TOL=112518],clambus pallidulus[&&NHX:TOL=112519],clambus pilosellus[&&NHX:TOL=112520],clambus pubescens[&&NHX:TOL=112521],clambus punctulum[&&NHX:TOL=112522],clambus radula[&&NHX:TOL=112523],clambus seminulum[&&NHX:TOL=112524],clambus simsoni[&&NHX:TOL=112525],clambus smetanai[&&NHX:TOL=112526],clambus spangleri[&&NHX:TOL=112527],clambus vulneratus[&&NHX:TOL=112528],clambus sp. new zealand[&&NHX:TOL=112529],[&&NHX:TOL=112530])clambus[&&NHX:TOL=29903],loricaster[&&NHX:TOL=29904],sphaerothorax[&&NHX:TOL=29905])clambinae[&&NHX:TOL=105282])clambidae[&&NHX:TOL=9612],(declinia relicta[&&NHX:TOL=105275],declinia versicolor[&&NHX:TOL=105276])declinia[&&NHX:TOL=9610],(bisaya[&&NHX:TOL=29892],eucilodes[&&NHX:TOL=29893],eucinetella[&&NHX:TOL=29895],eucinetus[&&NHX:TOL=29894],euscaphurus[&&NHX:TOL=29896],jentozkus[&&NHX:TOL=29897],(noteucinetus nunni[&&NHX:TOL=105277],noteucinetus chilensis[&&NHX:TOL=105278],noteucinetus latipennis[&&NHX:TOL=105279])noteucinetus[&&NHX:TOL=65636],nycteus[&&NHX:TOL=29898],(proeuzkus pachys[&&NHX:TOL=105280],proeuzkus coecus[&&NHX:TOL=105281])proeuzkus[&&NHX:TOL=65637],tohlezkus[&&NHX:TOL=29900],mesocinetes[&&NHX:EXT=Y:TOL=107372],peltocoleops[&&NHX:EXT=Y:TOL=107373])eucinetidae[&&NHX:TOL=9611],(amplectopus[&&NHX:TOL=65640],byrrhopsis[&&NHX:TOL=105283],cyphanodes[&&NHX:TOL=105284],cyphanus[&&NHX:TOL=105285],cyphon[&&NHX:TOL=65638],cyphotelus[&&NHX:TOL=105286],elodes[&&NHX:TOL=105287],macrocyphon[&&NHX:TOL=105288],macrodascillus[&&NHX:TOL=105289],macrohelodes[&&NHX:TOL=105290],mesocyphon[&&NHX:TOL=105291],microcara[&&NHX:TOL=105292],ora[&&NHX:TOL=105293],peneveronatus[&&NHX:TOL=105294],pseudomicrorara[&&NHX:TOL=105295],prionocyphon[&&NHX:TOL=105296],veronatus[&&NHX:TOL=65639],stenocyphon[&&NHX:TOL=107244],[&&NHX:TOL=107245],scirtes[&&NHX:TOL=107370],[&&NHX:TOL=107371])scirtidae[&&NHX:TOL=9613])scirtoidea[&&NHX:TOL=9080],((byrrhidae[&&NHX:TOL=9112],elmidae[&&NHX:TOL=9120],(heteroceridae[&&NHX:TOL=9119],(((afrolimnichus[&&NHX:TOL=94078],bothriophorus[&&NHX:TOL=94079],byrrhinus[&&NHX:TOL=65666],caccothryptus[&&NHX:TOL=94080],cephalobyrrhinus[&&NHX:TOL=94081],chibidoronus[&&NHX:TOL=94082],corrinea[&&NHX:TOL=94083],cyclolimnichus[&&NHX:TOL=94084],ersachus[&&NHX:TOL=94085],eulimnichus[&&NHX:TOL=94086],euthryptus[&&NHX:TOL=94087],geolimnichus[&&NHX:TOL=94088],limnichites[&&NHX:TOL=92922],limnichoderus[&&NHX:TOL=92923],limnichomorphus[&&NHX:TOL=94089],limnichus[&&NHX:TOL=92924],mandersia[&&NHX:TOL=94090],paralimnichus[&&NHX:TOL=92925],pelochares[&&NHX:TOL=92926],phalacrichus[&&NHX:TOL=94091],physemus[&&NHX:TOL=92927],pseudothryptus[&&NHX:TOL=94092],resachus[&&NHX:TOL=94093],simplocarina[&&NHX:TOL=94094],tricholimnichus[&&NHX:TOL=94095],platypelochares[&&NHX:TOL=94096])limnichinae[&&NHX:TOL=94077],(parathroscinus[&&NHX:TOL=92929],cephalobyrrhus[&&NHX:TOL=92928],throscinus[&&NHX:TOL=92930],erichia[&&NHX:TOL=94098])cephalobyrrhinae[&&NHX:TOL=94097],hyphalus[&&NHX:TOL=65665],(mexico[&&NHX:TOL=92934],martinius[&&NHX:TOL=92933],pseudeucinetus[&&NHX:TOL=92932],acontosceles[&&NHX:TOL=92931],babalimnichus[&&NHX:TOL=94100])thaumastodinae[&&NHX:TOL=94099])limnichidae[&&NHX:TOL=9118],(dryopidae[&&NHX:TOL=9116],lutrochus[&&NHX:TOL=9117])[&&NHX:TOL=9115])[&&NHX:TOL=9114])[&&NHX:TOL=9113])[&&NHX:TOL=9111],(callirhipidae[&&NHX:TOL=9125],(brounia thoracica[&&NHX:TOL=29688],chelonarium[&&NHX:TOL=29686],pseudochelonarium[&&NHX:TOL=29687])chelonariidae[&&NHX:TOL=9126],cneoglossidae[&&NHX:TOL=9127],(eulichas[&&NHX:TOL=29915],stenocolus[&&NHX:TOL=29914])eulichadidae[&&NHX:TOL=9124],psephenidae[&&NHX:TOL=9122],ptilodactylidae[&&NHX:TOL=9123])[&&NHX:TOL=9121])byrrhoidea[&&NHX:TOL=9083],(((coptocera[&&NHX:TOL=91442],dascillus[&&NHX:TOL=91441],notodascillus[&&NHX:TOL=91443],haematodes[&&NHX:TOL=91444],pseudolichas[&&NHX:TOL=91445],sinocaulus[&&NHX:TOL=91446])dascillinae[&&NHX:TOL=105297],(anorus[&&NHX:TOL=91447],drilocephalus[&&NHX:TOL=91448],escalerina[&&NHX:TOL=91449],emmita[&&NHX:TOL=91450],genecerus[&&NHX:TOL=91451],karumia[&&NHX:TOL=91452],pleolobus[&&NHX:TOL=91453])karumiinae[&&NHX:TOL=105298])dascillidae[&&NHX:TOL=9183],(arrhaphipterus[&&NHX:TOL=29906],chamoerhipis[&&NHX:TOL=29907],polymerius[&&NHX:TOL=29908],ptiocerus[&&NHX:TOL=29909],rhipicera[&&NHX:TOL=29910],sandalus[&&NHX:TOL=29911])rhipiceridae[&&NHX:TOL=9184])dascilloidea[&&NHX:TOL=9081],(omalisidae[&&NHX:TOL=65694],podabrocephalus[&&NHX:TOL=65707],rhinorhipus[&&NHX:TOL=65703],((allopogonia[&&NHX:TOL=29916],artematopus[&&NHX:TOL=29917],carcinognathus[&&NHX:TOL=29918],ctesibius[&&NHX:TOL=29919],electribius[&&NHX:TOL=29920],eurypogon[&&NHX:TOL=29921],macropogon[&&NHX:TOL=29922])artematopodidae[&&NHX:TOL=9196],brachypsectra[&&NHX:TOL=65677],(elateridae[&&NHX:TOL=9190],(cerophytum[&&NHX:TOL=9194],eucnemidae[&&NHX:TOL=9192],throscidae[&&NHX:TOL=9193])[&&NHX:TOL=9191])[&&NHX:TOL=9189],(plastocerus[&&NHX:TOL=65690],(cantharidae[&&NHX:TOL=9199],drilidae[&&NHX:TOL=9202],lampyridae[&&NHX:TOL=9205],lycidae[&&NHX:TOL=9200],(blatchleya[&&NHX:TOL=29961],drilonius[&&NHX:TOL=29962],ginglymocladus[&&NHX:TOL=29963],matheteus[&&NHX:TOL=29964],malthomethes[&&NHX:TOL=29965],omethes[&&NHX:TOL=29966],symphyomethes[&&NHX:TOL=29967],troglomethes[&&NHX:TOL=29968])omethidae[&&NHX:TOL=9206],(acladocera[&&NHX:TOL=29925],adendrocera[&&NHX:TOL=29926],brasilocerus[&&NHX:TOL=29927],cenophengus[&&NHX:TOL=29928],cephalophrixothorax[&&NHX:TOL=29929],cydistus[&&NHX:TOL=29930],decamastinocerus[&&NHX:TOL=29931],dioptoma[&&NHX:TOL=29932],diplocladon[&&NHX:TOL=29933],distremocephalus[&&NHX:TOL=29934],eurymastinocerus[&&NHX:TOL=29935],euryopa[&&NHX:TOL=29936],euryognathus[&&NHX:TOL=29937],falsophrixothrix[&&NHX:TOL=29938],mastinocerus[&&NHX:TOL=29939],mastinomorphus[&&NHX:TOL=29940],mastinowittmerus[&&NHX:TOL=29941],microphengodes[&&NHX:TOL=29942],neophengus[&&NHX:TOL=29943],nephromma[&&NHX:TOL=29944],oxymastinocerus[&&NHX:TOL=29945],paramastinocerus[&&NHX:TOL=29946],paraptorthodius[&&NHX:TOL=29947],penicillophores[&&NHX:TOL=29948],phengodes[&&NHX:TOL=29949],phrixothrix[&&NHX:TOL=29950],pseudomastinocerus[&&NHX:TOL=29951],pseudophengodes[&&NHX:TOL=29952],ptorthodiellus[&&NHX:TOL=29953],ptorthodius[&&NHX:TOL=29954],rhagophthalmus[&&NHX:TOL=29955],spangleriella[&&NHX:TOL=29956],steneuropa[&&NHX:TOL=29957],stenophrixothrix[&&NHX:TOL=29958],taximastinocerus[&&NHX:TOL=29959],zarhipis[&&NHX:TOL=29960])phengodidae[&&NHX:TOL=9204],(pseudotelegeusis[&&NHX:TOL=29923],telegeusis[&&NHX:TOL=29924])telegeusidae[&&NHX:TOL=9203])[&&NHX:TOL=9198])[&&NHX:TOL=9197])[&&NHX:TOL=9188],rhagopthalmidae[&&NHX:TOL=107980])elateroidea[&&NHX:TOL=9084])elateriformia[&&NHX:TOL=9079],((derodontus[&&NHX:TOL=9186],laricobius[&&NHX:TOL=29674],nothoderodontus[&&NHX:TOL=29676],peltastica[&&NHX:TOL=29675])derodontidae[&&NHX:TOL=9086],(anobiidae[&&NHX:TOL=9102],((dysides[&&NHX:TOL=58102],apoleon[&&NHX:TOL=58103])dysidinae[&&NHX:TOL=58101],(polycaon[&&NHX:TOL=58105],melalgus[&&NHX:TOL=58106])polycaoninae[&&NHX:TOL=58104],(dinapate[&&NHX:TOL=58110],(xylomedes[&&NHX:TOL=58114],apate[&&NHX:TOL=58115],phonapate[&&NHX:TOL=58116],chilenius[&&NHX:TOL=58117])apatini[&&NHX:TOL=58113],(sinocalon[&&NHX:TOL=58119],calodectes[&&NHX:TOL=58120],calodrypta[&&NHX:TOL=58121],calopertha[&&NHX:TOL=58122],sinoxylon[&&NHX:TOL=58123],xyloperthodes[&&NHX:TOL=58124])sinoxylini[&&NHX:TOL=58118],(bostrichus[&&NHX:TOL=58126],dexicrates[&&NHX:TOL=58127],lichenophanes[&&NHX:TOL=58128],calopherus[&&NHX:TOL=58129],neoterius[&&NHX:TOL=58130],dolichobostrychus[&&NHX:TOL=58131],parabostrychus[&&NHX:TOL=58132],megabostrychus[&&NHX:TOL=58133],heterobostrychus[&&NHX:TOL=58134],bostrychopsis[&&NHX:TOL=58135],amphicerus[&&NHX:TOL=58136],apatides[&&NHX:TOL=58137],bostrychoplites[&&NHX:TOL=58138],micrapate[&&NHX:TOL=58139],bostrycharis[&&NHX:TOL=58140],sinoxylodes[&&NHX:TOL=58141],psicula[&&NHX:TOL=58142])bostrichini[&&NHX:TOL=58125],(xylomeira[&&NHX:TOL=58144],amintinus[&&NHX:TOL=58145],xyloprista[&&NHX:TOL=58146],dendrobiella[&&NHX:TOL=58147],paraxylogenes[&&NHX:TOL=58148],tetrapriocera[&&NHX:TOL=58149],xylogenes[&&NHX:TOL=58150],scobicia[&&NHX:TOL=58151],enneadesmus[&&NHX:TOL=58152],xylophorus[&&NHX:TOL=58153],ctenobostrychus[&&NHX:TOL=58154],xylobiops[&&NHX:TOL=58155],xyloblaptus[&&NHX:TOL=58156],xylodeleis[&&NHX:TOL=58157],xylocis[&&NHX:TOL=58158],xylotillus[&&NHX:TOL=58159],octodesmus[&&NHX:TOL=58160],xylodectes[&&NHX:TOL=58161],calonistes[&&NHX:TOL=58162],xyloperthella[&&NHX:TOL=58163],xylodrypta[&&NHX:TOL=58164],xylionulus[&&NHX:TOL=58165],xylion[&&NHX:TOL=58166],paraxylion[&&NHX:TOL=58167],mesoxylion[&&NHX:TOL=58168],plioxylion[&&NHX:TOL=58169],xylionopsis[&&NHX:TOL=58170],xylobosca[&&NHX:TOL=58171],calophagus[&&NHX:TOL=58172],xylothrips[&&NHX:TOL=58173],xylopsocus[&&NHX:TOL=58174],sifidius[&&NHX:TOL=58175],xylopertha[&&NHX:TOL=58176])xyloperthini[&&NHX:TOL=58143])bostrichinae[&&NHX:TOL=58109],(psoa[&&NHX:TOL=58178],psoidia[&&NHX:TOL=58179],coccographis[&&NHX:TOL=58180],stenomera[&&NHX:TOL=58181],heteropsoa[&&NHX:TOL=58182])psoinae[&&NHX:TOL=58177],(rhizoperthodes[&&NHX:TOL=58184],rhyzopertha[&&NHX:TOL=58185],stephanopachys[&&NHX:TOL=58186],prostephanus[&&NHX:TOL=58187],dinoderopsis[&&NHX:TOL=58188],dinoderus[&&NHX:TOL=58189])dinoderinae[&&NHX:TOL=58183],((lyctus[&&NHX:TOL=58192],acantholyctus[&&NHX:TOL=58193],lyctodon[&&NHX:TOL=58194],lyctoplites[&&NHX:TOL=58195],minthea[&&NHX:TOL=58196],lyctoxylon[&&NHX:TOL=58197])lyctini[&&NHX:TOL=58191],(trogoxylon[&&NHX:TOL=58199],triastaria[&&NHX:TOL=58200],lyctopsis[&&NHX:TOL=58201],lyctoderma[&&NHX:TOL=58202],cephalotoma[&&NHX:TOL=58203],phyllyctus[&&NHX:TOL=58204])trogoxylini[&&NHX:TOL=58198])lyctinae[&&NHX:TOL=58190],euderia[&&NHX:TOL=58205])bostrichidae[&&NHX:TOL=9101],dermestidae[&&NHX:TOL=9099],endecatomidae[&&NHX:TOL=9100],(derolathrus[&&NHX:TOL=29969],saphophagus[&&NHX:TOL=29970],sarothrias[&&NHX:TOL=29971])jacobsoniidae[&&NHX:TOL=9097],(nosodendron[&&NHX:TOL=29972],orphilus[&&NHX:TOL=29973])nosodendridae[&&NHX:TOL=9098])bostrichoidea[&&NHX:TOL=9087])bostrichiformia[&&NHX:TOL=9085],((atractocerus[&&NHX:TOL=29974],australymexylon[&&NHX:TOL=29975],elateroides[&&NHX:TOL=29976],lymexylon[&&NHX:TOL=29977],melittomma[&&NHX:TOL=29978],melittommopsis[&&NHX:TOL=29979],promelittomma[&&NHX:TOL=29980])lymexylidae[&&NHX:TOL=9090],(((sphaerosoma lamprosphaerula[&&NHX:TOL=120701],sphaerosoma arthrosphaerula[&&NHX:TOL=120702],sphaerosoma neosphaerula[&&NHX:TOL=120703],sphaerosoma sphaerosoma[&&NHX:TOL=120704])sphaerosoma[&&NHX:TOL=65850],((austrophthalma[&&NHX:TOL=139136],bicava[&&NHX:TOL=139137],corticaria[&&NHX:TOL=139138],corticarina[&&NHX:TOL=139139],corticaromus[&&NHX:TOL=139140],cortinicara[&&NHX:TOL=139141],fuchsina[&&NHX:TOL=139142],melanophthalma[&&NHX:TOL=139143],migneuxia[&&NHX:TOL=139144],paracaria[&&NHX:TOL=139145],rethusus[&&NHX:TOL=139146],succinimontia[&&NHX:EXT=Y:TOL=139147])corticariinae[&&NHX:TOL=139135],(adistemia[&&NHX:TOL=139149],akalyptoischion[&&NHX:TOL=139150],archelatrius[&&NHX:EXT=Y:TOL=139151],besuchetia[&&NHX:TOL=139152],cartodere[&&NHX:TOL=139153],dicastria[&&NHX:TOL=139154],dienerella[&&NHX:TOL=139155],enicmus[&&NHX:TOL=139156],euchionellus[&&NHX:TOL=139157],eufallia[&&NHX:TOL=139158],eufalloides[&&NHX:TOL=139159],herfordia[&&NHX:TOL=139160],latridius[&&NHX:TOL=139161],lithostygnus[&&NHX:TOL=139162],metophthalmoides[&&NHX:TOL=139163],metophthalmus[&&NHX:TOL=139164],mumfordia[&&NHX:TOL=139165],nalpaumia[&&NHX:TOL=139166],revelieria[&&NHX:TOL=139167],stephostethus[&&NHX:TOL=139168],thes[&&NHX:TOL=139169])latridiinae[&&NHX:TOL=139148],tetrameropsis[&&NHX:EXT=Y:TOL=139170])latridiidae[&&NHX:TOL=9172],(cerylonidae[&&NHX:TOL=9166],((antibothrus[&&NHX:TOL=139383],ascetoderes[&&NHX:TOL=139386],asosylus[&&NHX:TOL=139389],bothrideres[&&NHX:TOL=139390],chinikus[&&NHX:TOL=139393],cosmothorax[&&NHX:TOL=139394],craspedophilus[&&NHX:TOL=139395],cylindromicrus[&&NHX:TOL=139396],dastarcus[&&NHX:TOL=139397],pathodermus[&&NHX:TOL=139398],deretaphrus[&&NHX:TOL=139400],emmaglaeus[&&NHX:TOL=139403],erotylathris[&&NHX:TOL=139404],leptoglyphus[&&NHX:TOL=139407],lithophorus[&&NHX:TOL=139410],mabomus[&&NHX:TOL=139411],ogmoderes[&&NHX:TOL=139413],patroderes[&&NHX:TOL=139416],petalophora[&&NHX:TOL=139417],prolyctus[&&NHX:TOL=139418],machlotes[&&NHX:TOL=139419],pseudantibothrus[&&NHX:TOL=139421],pseudobothrideres[&&NHX:TOL=139422],pseudososylus[&&NHX:TOL=139423],roplyctus[&&NHX:TOL=139424],shekarus[&&NHX:TOL=139425],sosylus[&&NHX:TOL=139579],triboderus[&&NHX:TOL=139431])bothriderinae[&&NHX:TOL=139382],(oxylaemus[&&NHX:TOL=139433],rustleria[&&NHX:TOL=139436],sosylopsis[&&NHX:TOL=139437],sysolus[&&NHX:TOL=139438],teredolaemus[&&NHX:TOL=139439],teredomorphus[&&NHX:TOL=139440],teredus[&&NHX:TOL=139441])teredinae[&&NHX:TOL=139432],xylariophilus[&&NHX:TOL=139495],(abromus[&&NHX:TOL=139449],kocherius[&&NHX:TOL=139450],anommatus[&&NHX:TOL=139580])anommatinae[&&NHX:TOL=139444])bothrideridae[&&NHX:TOL=9165],((aphanocephalus[&&NHX:TOL=139176],fallia[&&NHX:TOL=139177],parafallia[&&NHX:TOL=139178],profallia[&&NHX:TOL=139179],solitarius[&&NHX:TOL=139180])aphanocephalinae[&&NHX:TOL=139175],(discoloma[&&NHX:TOL=65893],cassidoloma[&&NHX:TOL=139185])discolomatinae[&&NHX:TOL=139184],(dystheamon[&&NHX:TOL=139187],holophygus[&&NHX:TOL=139188],parmaschema[&&NHX:TOL=139189],notiophygus[&&NHX:TOL=139190],pachyplacus[&&NHX:TOL=139191],praviclava[&&NHX:TOL=139192])notiophyginae[&&NHX:TOL=139186],(katoporus[&&NHX:TOL=139194],pondonatus[&&NHX:TOL=139195])pondonatinae[&&NHX:TOL=139193],cephalophanus[&&NHX:TOL=139182])discolomatidae[&&NHX:TOL=9168])[&&NHX:TOL=139619],((chilocorini[&&NHX:TOL=65871],platynaspidini[&&NHX:TOL=65872],telsimini[&&NHX:TOL=136800],argentipilosini[&&NHX:TOL=136036],cephaloscymnini[&&NHX:TOL=136032],limnichopharini[&&NHX:TOL=136035],plotinini[&&NHX:TOL=136034],shirozuellini[&&NHX:TOL=136031],sticholotidini[&&NHX:TOL=136027],coccinellini[&&NHX:TOL=65875],discotomini[&&NHX:TOL=136051],halyziini[&&NHX:TOL=136049],singhikalia[&&NHX:TOL=136052],tytthaspidini[&&NHX:TOL=136050],cynegetini[&&NHX:TOL=136803],epilachnini[&&NHX:TOL=65876],epiverta[&&NHX:TOL=136055],eremochilus[&&NHX:TOL=136053],azyini[&&NHX:TOL=136041],coccidulini[&&NHX:TOL=65874],cranophorini[&&NHX:TOL=136037],exoplectrini[&&NHX:TOL=136038],lithophilini[&&NHX:TOL=136040],monocoryni[&&NHX:TOL=136039],noviini[&&NHX:TOL=65873],oryssomini[&&NHX:TOL=136802],poria[&&NHX:TOL=136801],aspidimerini[&&NHX:TOL=136045],brachiacanthini[&&NHX:TOL=136043],cryptognathini[&&NHX:TOL=136048],diomini[&&NHX:TOL=136798],hyperaspidini[&&NHX:TOL=136042],ortaliini[&&NHX:TOL=136056],selvadiini[&&NHX:TOL=136047],scymnini[&&NHX:TOL=136044],scymnillini[&&NHX:TOL=136046],stethorini[&&NHX:TOL=65877],(sukunahikonini[&&NHX:TOL=136029],(microweiseini[&&NHX:TOL=136030],serangiini[&&NHX:TOL=65878])[&&NHX:TOL=139595],carinodulini[&&NHX:TOL=136033])microweiseinae[&&NHX:TOL=139594])coccinellidae[&&NHX:TOL=9170],(periptyctinae[&&NHX:TOL=143231],(foadiini[&&NHX:TOL=65880],(cleidostethini[&&NHX:TOL=143298],(aenigmaticini[&&NHX:TOL=143300],(peltinodini[&&NHX:TOL=143340],corylophini[&&NHX:TOL=143318],teplinini[&&NHX:TOL=143323],orthoperini[&&NHX:TOL=143304],parmulini[&&NHX:TOL=143306],sericoderini[&&NHX:TOL=143315],rypobiini[&&NHX:TOL=143325])[&&NHX:TOL=143338])[&&NHX:TOL=143337])[&&NHX:TOL=143336])corylophinae[&&NHX:TOL=143293])corylophidae[&&NHX:TOL=9171],((holoparamecus[&&NHX:TOL=65897],cholovocera[&&NHX:TOL=120942],cholovocerida[&&NHX:TOL=120943],hexasternum[&&NHX:TOL=120944],latrapion[&&NHX:TOL=120945],lixella[&&NHX:TOL=120946],lycoperdinella[&&NHX:TOL=120947],merophysia[&&NHX:TOL=120948],pseudevolocera[&&NHX:TOL=120949],pseudoparamecus[&&NHX:TOL=120950],pythlarhinus[&&NHX:TOL=120951],reitteria[&&NHX:TOL=120952])merophysiinae[&&NHX:TOL=120941],(((((((((aphorista[&&NHX:TOL=120908],dapsa[&&NHX:TOL=120918],hylaia[&&NHX:TOL=120926],lycoperdina[&&NHX:TOL=120928],(pseudindalmus[&&NHX:TOL=120936],mycetina[&&NHX:TOL=120931])[&&NHX:TOL=120990],(acinaces[&&NHX:TOL=120903],amphix[&&NHX:TOL=120906],(beccariola[&&NHX:TOL=120911],(sinocymbachus[&&NHX:TOL=120937],cymbachus[&&NHX:TOL=120916])[&&NHX:TOL=120993],dryadites[&&NHX:TOL=120921])[&&NHX:TOL=120992])[&&NHX:TOL=120991],((((cymones[&&NHX:TOL=120917],callimodapsa[&&NHX:TOL=120914],indalmus[&&NHX:TOL=120927],malindus[&&NHX:TOL=120929],parindalmus[&&NHX:TOL=120933])[&&NHX:TOL=120997],(trycherus[&&NHX:TOL=120940],(chetryrus[&&NHX:TOL=120915],(microtrycherus[&&NHX:TOL=120930],haploscelis[&&NHX:TOL=120925])[&&NHX:TOL=121000])[&&NHX:TOL=120999])[&&NHX:TOL=120998],ancylopus[&&NHX:TOL=120907],avencymon[&&NHX:TOL=120910])[&&NHX:TOL=120996],(eumorphus[&&NHX:TOL=120923],platindalmus[&&NHX:TOL=120934])[&&NHX:TOL=121001],encymon[&&NHX:TOL=120922])[&&NHX:TOL=120995],((brachytrycherus[&&NHX:TOL=120912],(stictomela[&&NHX:TOL=120939],(amphistethus[&&NHX:TOL=120905],amphisternus[&&NHX:TOL=120904],cacodaemon[&&NHX:TOL=120913])[&&NHX:TOL=121004],spathomeles[&&NHX:TOL=120938])[&&NHX:TOL=121003],ohtaius[&&NHX:TOL=120932],stroheckeria[&&NHX:TOL=120986])[&&NHX:TOL=121002],gerstaeckerus[&&NHX:TOL=120924])[&&NHX:TOL=121011])[&&NHX:TOL=120994],polymus[&&NHX:TOL=120935])[&&NHX:TOL=120989],(((daulotypus[&&NHX:TOL=120920],daulis[&&NHX:TOL=120919])[&&NHX:TOL=121007],archipines[&&NHX:TOL=120909])[&&NHX:TOL=121006],achuarmychus[&&NHX:TOL=120902])[&&NHX:TOL=121005])lycoperdininae[&&NHX:TOL=120901],(epipocus[&&NHX:TOL=65896],epopterus[&&NHX:TOL=120883],anidrytus[&&NHX:TOL=120884],ephebus[&&NHX:TOL=120885])epipocinae[&&NHX:TOL=120882])[&&NHX:TOL=120985],(africanasaula[&&NHX:TOL=120961],chondria[&&NHX:TOL=120962],danae[&&NHX:TOL=120963],ectomychus[&&NHX:TOL=120964],paniegena[&&NHX:TOL=120965],perrisina[&&NHX:TOL=120966],saula[&&NHX:TOL=120967],stenotarsus[&&NHX:TOL=120968],tragoscelis[&&NHX:TOL=120969])stenotarsinae[&&NHX:TOL=120960])[&&NHX:TOL=120984],(endomychus[&&NHX:TOL=65895],bolbomorphus[&&NHX:TOL=120878],cyclotoma[&&NHX:TOL=120879],cyclotomima[&&NHX:TOL=120974],eucteanus[&&NHX:TOL=120880],meilichius[&&NHX:TOL=120881],opetius[&&NHX:TOL=120975])endomychinae[&&NHX:TOL=120877])[&&NHX:TOL=120983],(danascelis[&&NHX:TOL=120875],hadromychus[&&NHX:TOL=120876])danascelinae[&&NHX:TOL=120874])[&&NHX:TOL=120982],xenomycetes[&&NHX:TOL=120970],(cerasommatidia[&&NHX:TOL=120887],chileolobius[&&NHX:TOL=120888],eidoreus[&&NHX:TOL=120889],evolocera[&&NHX:TOL=120890],ibicarella[&&NHX:TOL=120891],microxenus[&&NHX:TOL=120892])eupsilobiinae[&&NHX:TOL=120886])[&&NHX:TOL=120981],((mycetaea[&&NHX:TOL=120954],agaricophilus[&&NHX:TOL=120955])mycetaeinae[&&NHX:TOL=120953],(phymaphoroides[&&NHX:EXT=Y:TOL=120898],((stethorhanis[&&NHX:TOL=120900],(rhanidea[&&NHX:TOL=120899],panaleies[&&NHX:TOL=120895],panamomus[&&NHX:TOL=120896])[&&NHX:TOL=121010],leiestes[&&NHX:TOL=120894])[&&NHX:TOL=121009],phymaphora[&&NHX:TOL=120897])[&&NHX:TOL=121008])leiestinae[&&NHX:TOL=120893])[&&NHX:TOL=120987])[&&NHX:TOL=120980],((dadocerus[&&NHX:TOL=120957],trochoideus[&&NHX:TOL=120959],pleganophorus[&&NHX:TOL=120958])pleganophorinae[&&NHX:TOL=120956],(bystus[&&NHX:TOL=65894],aclemmysa[&&NHX:TOL=120841],acritosoma[&&NHX:TOL=120842],afralexia[&&NHX:TOL=120843],anagaricophilus[&&NHX:TOL=120844],anamorphus[&&NHX:TOL=120845],anamycetaea[&&NHX:TOL=120846],asymbius[&&NHX:TOL=120847],austroclemmus[&&NHX:TOL=120848],baeochelys[&&NHX:TOL=120849],bryodryas[&&NHX:TOL=120850],bystodes[&&NHX:TOL=120851],catapotia[&&NHX:TOL=120852],clemmus[&&NHX:TOL=120853],coryphus[&&NHX:TOL=120854],cyrtomychus[&&NHX:TOL=120855],cysalemma[&&NHX:TOL=120973],dexialia[&&NHX:TOL=120856],dialexia[&&NHX:TOL=120857],discolomopsis[&&NHX:EXT=Y:TOL=120858],endocoelus[&&NHX:TOL=120859],erotendomychus[&&NHX:TOL=120860],exysma[&&NHX:TOL=120861],exysmodes[&&NHX:TOL=120976],geoendomychus[&&NHX:TOL=120862],idiophyes[&&NHX:TOL=120863],loeblia[&&NHX:TOL=120977],malagaricophilus[&&NHX:TOL=120864],micropsephodes[&&NHX:TOL=120865],micropsephus[&&NHX:TOL=120866],mychothenus[&&NHX:TOL=120867],papuella[&&NHX:TOL=120868],pararhymbus[&&NHX:TOL=120869],parasymbius[&&NHX:TOL=120870],rhymbillus[&&NHX:TOL=120871],rhymbomicrus[&&NHX:TOL=120872],symbiotes[&&NHX:TOL=120873])anamorphinae[&&NHX:TOL=120840])[&&NHX:TOL=121012])[&&NHX:TOL=120979])endomychidae[&&NHX:TOL=9169])[&&NHX:TOL=139620])cerylonid series[&&NHX:TOL=117918],tasmosalpingus[&&NHX:TOL=66068],agapytho[&&NHX:TOL=65848],cyclaxyra[&&NHX:TOL=65890],myrabolia[&&NHX:TOL=66043],priasilphidae[&&NHX:TOL=66055],biphyllidae[&&NHX:TOL=9164],boganiidae[&&NHX:TOL=9148],brachypteridae[&&NHX:TOL=9144],byturidae[&&NHX:TOL=9163],cavognathidae[&&NHX:TOL=9158],cryptophagidae[&&NHX:TOL=9159],(cucujus[&&NHX:TOL=29981],palaestes[&&NHX:TOL=29982],pediacus[&&NHX:TOL=29983],platisus[&&NHX:TOL=29984])cucujidae[&&NHX:TOL=9153],erotylidae[&&NHX:TOL=9162],helota[&&NHX:TOL=65903],hobartiidae[&&NHX:TOL=9157],laemophloeidae[&&NHX:TOL=9154],lamingtonium[&&NHX:TOL=66033],monotomidae[&&NHX:TOL=9147],nitidulidae[&&NHX:TOL=9145],(passandra[&&NHX:TOL=29677],ancistria[&&NHX:TOL=29678],nicolebertia[&&NHX:TOL=29679],passandrina[&&NHX:TOL=29680],aulonosoma[&&NHX:TOL=29681],taphroscelidia[&&NHX:TOL=29682],passandrella[&&NHX:TOL=29683],scalidiopsis[&&NHX:TOL=29684],catogenus[&&NHX:TOL=29685])passandridae[&&NHX:TOL=9152],phalacridae[&&NHX:TOL=9156],phloeostichidae[&&NHX:TOL=9150],propalticidae[&&NHX:TOL=9155],ericmodes[&&NHX:TOL=66060],silvanidae[&&NHX:TOL=9151],smicrips[&&NHX:TOL=66064],(protosphindus[&&NHX:TOL=66066],(odontosphindus[&&NHX:TOL=117660],(sphindiphorus[&&NHX:TOL=117661],(notosphindus[&&NHX:TOL=117857],(carinisphindus[&&NHX:TOL=117854],(sphindus[&&NHX:TOL=117858],(aspidiphorus[&&NHX:TOL=117853],(genisphindus[&&NHX:TOL=117856],eurysphindus[&&NHX:TOL=117855])[&&NHX:TOL=139611])[&&NHX:TOL=139610])[&&NHX:TOL=139609])[&&NHX:TOL=139608])sphindinae[&&NHX:TOL=117851])[&&NHX:TOL=139607])[&&NHX:TOL=139606])sphindidae[&&NHX:TOL=9143])cucujoidea[&&NHX:TOL=9092],(phloiophilidae[&&NHX:TOL=9134],trogossitidae[&&NHX:TOL=9135],chaetosomatidae[&&NHX:TOL=9136],cleridae[&&NHX:TOL=9137],acanthocnemidae[&&NHX:TOL=9138],phycosecidae[&&NHX:TOL=9139],melyridae[&&NHX:TOL=9140])cleroidea[&&NHX:TOL=9091],((archeocrypticidae[&&NHX:TOL=10301],pterogeniidae[&&NHX:TOL=10300])[&&NHX:TOL=10299],aderidae[&&NHX:TOL=10322],anthicidae[&&NHX:TOL=10323],boridae[&&NHX:TOL=30280],chalcodryidae[&&NHX:TOL=10313],ciidae[&&NHX:TOL=10303],colydiidae[&&NHX:TOL=10308],melandryidae[&&NHX:TOL=10305],meloidae[&&NHX:TOL=10320],monommatidae[&&NHX:TOL=10309],mordellidae[&&NHX:TOL=10306],mycetophagidae[&&NHX:TOL=10302],mycteridae[&&NHX:TOL=10324],oedemeridae[&&NHX:TOL=10318],perimylopidae[&&NHX:TOL=10312],(dryocora[&&NHX:TOL=29985],prostomis[&&NHX:TOL=29986])prostomidae[&&NHX:TOL=10316],pyrochroidae[&&NHX:TOL=30282],pythidae[&&NHX:TOL=30281],rhipiphoridae[&&NHX:TOL=10307],salpingidae[&&NHX:TOL=10325],scraptiidae[&&NHX:TOL=10321],(anelpistus[&&NHX:TOL=29989],cephaloon[&&NHX:TOL=29990],nematoplus[&&NHX:TOL=29991],scotodes[&&NHX:TOL=29992],stenocephaloon[&&NHX:TOL=29993],stenotrachelus[&&NHX:TOL=29994])stenotrachelidae[&&NHX:TOL=10319],(mallodrya[&&NHX:TOL=29987],synchroa[&&NHX:TOL=29988])synchroidae[&&NHX:TOL=10317],((laenini[&&NHX:TOL=133222],adeliini[&&NHX:TOL=133223],pycnocerini[&&NHX:TOL=133224],goniaderini[&&NHX:TOL=133225],lupropini[&&NHX:TOL=133226],(lagriina[&&NHX:TOL=133228],statirina[&&NHX:TOL=133229])lagriini[&&NHX:TOL=133227],chaerodini[&&NHX:TOL=133230],cossyphini[&&NHX:TOL=133231],belopini[&&NHX:TOL=133232])lagriinae[&&NHX:TOL=133221],nilioninae[&&NHX:TOL=133233],(cossyphodini[&&NHX:TOL=133235],cossyphoditini[&&NHX:TOL=133236],esemephini[&&NHX:TOL=133237],paramellonini[&&NHX:TOL=133238])cossyphodinae[&&NHX:TOL=133234],(archaeoglenini[&&NHX:TOL=133240],penetini[&&NHX:TOL=133241],phrenapatini[&&NHX:TOL=133242])phrenapatinae[&&NHX:TOL=133239],zolodininae[&&NHX:TOL=133243],(boromorphini[&&NHX:TOL=133245],caenocrypticini[&&NHX:TOL=133246],(actizetina[&&NHX:TOL=133248],cnemeplatiina[&&NHX:TOL=133249],rondoniellina[&&NHX:TOL=133250],thorictosomatina[&&NHX:TOL=133251])cnemeplatiini[&&NHX:TOL=133247],idisiini[&&NHX:TOL=133252],falsomycterini[&&NHX:TOL=133253],(klewariina[&&NHX:TOL=133255],lachnogyina[&&NHX:TOL=133256],netuschiliina[&&NHX:TOL=133257])lachnogyini[&&NHX:TOL=133254],vacronini[&&NHX:TOL=133258],stenosini[&&NHX:TOL=133259],zophosini[&&NHX:TOL=133260],erodiini[&&NHX:TOL=133261],adelostomini[&&NHX:TOL=133262],ceratanisini[&&NHX:TOL=133263],(hypomelina[&&NHX:TOL=133265],molurina[&&NHX:TOL=133266],oxurina[&&NHX:TOL=133267],phanerotomeina[&&NHX:TOL=133268],sepidiina[&&NHX:TOL=133269],trachynotina[&&NHX:TOL=133270])sepidiini[&&NHX:TOL=133264],akidini[&&NHX:TOL=133271],(calognathina[&&NHX:TOL=133273],cryptochilina[&&NHX:TOL=133274],homebiina[&&NHX:TOL=133275],horatomina[&&NHX:TOL=133276],vansoniina[&&NHX:TOL=133277])cryptochilini[&&NHX:TOL=133272],pimeliini[&&NHX:TOL=133278],anepsiini[&&NHX:TOL=133279],centriopterini[&&NHX:TOL=133280],nyctoporini[&&NHX:TOL=133281],elenophorini[&&NHX:TOL=133282],nycteliini[&&NHX:TOL=133283],physogasterini[&&NHX:TOL=133284],praociini[&&NHX:TOL=133285],coniontini[&&NHX:TOL=133286],branchini[&&NHX:TOL=133287],asidini[&&NHX:TOL=133288],cnemodinini[&&NHX:TOL=133289],trilobocarini[&&NHX:TOL=133290],epitragini[&&NHX:TOL=133291],edrotini[&&NHX:TOL=133292],phrynocarenini[&&NHX:TOL=133293],thinobatini[&&NHX:TOL=133294],evaniosomini[&&NHX:TOL=133295],adesmiini[&&NHX:TOL=133296],tentyriini[&&NHX:TOL=133297],kuhitangiini[&&NHX:TOL=133298],leptodini[&&NHX:TOL=133299])pimeliinae[&&NHX:TOL=133244],(palorini[&&NHX:TOL=133301],(eudysantina[&&NHX:TOL=133303],nycteropina[&&NHX:TOL=133304],toxicina[&&NHX:TOL=133305])toxicini[&&NHX:TOL=133302],bolitophagini[&&NHX:TOL=133306],tenebrionini[&&NHX:TOL=133307],centronopini[&&NHX:TOL=133308],titaenini[&&NHX:TOL=133309],(asphalina[&&NHX:TOL=133311],cyphaleina[&&NHX:TOL=133312],heleina[&&NHX:TOL=133313])heleini[&&NHX:TOL=133310],acropteronini[&&NHX:TOL=133314],alphitobiini[&&NHX:TOL=133315],triboliini[&&NHX:TOL=133316],ulomini[&&NHX:TOL=133317],helopini[&&NHX:TOL=133318],(aptilina[&&NHX:TOL=133320],helopinina[&&NHX:TOL=133321],micrantereina[&&NHX:TOL=133322],oncosomina[&&NHX:TOL=133323])helopinini[&&NHX:TOL=133319],amarygmini[&&NHX:TOL=133324],rhysopaussini[&&NHX:TOL=133325],cerenopini[&&NHX:TOL=133326],eulabini[&&NHX:TOL=133327],apocryphini[&&NHX:TOL=133328],scaurini[&&NHX:TOL=133329],scotobiini[&&NHX:TOL=133330],(blaptina[&&NHX:TOL=133332],gnaptorina[&&NHX:TOL=133333],gnaptorinina[&&NHX:TOL=133334],prosodina[&&NHX:TOL=133335],remipedellina[&&NHX:TOL=133336])blaptini[&&NHX:TOL=133331],praeugenini[&&NHX:TOL=133337],amphidorini[&&NHX:TOL=133338],(dendarina[&&NHX:TOL=133340],eurynotina[&&NHX:TOL=133341],leichenina[&&NHX:TOL=133342],loensina[&&NHX:TOL=133343],melambiina[&&NHX:TOL=133344],pedinina[&&NHX:TOL=133345],platynotina[&&NHX:TOL=133346],pythiopina[&&NHX:TOL=133347])pedinini[&&NHX:TOL=133339],(heterocheirina[&&NHX:TOL=133349],heterotarsina[&&NHX:TOL=133350],opatrina[&&NHX:TOL=133351],pachypterina[&&NHX:TOL=133352])opatrini[&&NHX:TOL=133348],platyscelidini[&&NHX:TOL=133353],dissonomini[&&NHX:TOL=133354],melanimini[&&NHX:TOL=133355])tenebrioninae[&&NHX:TOL=133300],((alleculina[&&NHX:TOL=133358],gonoderina[&&NHX:TOL=133359],mycetocharina[&&NHX:TOL=133360],xystropodina[&&NHX:TOL=133361])alleculini[&&NHX:TOL=133357],cteniopodini[&&NHX:TOL=133362])alleculinae[&&NHX:TOL=133356],((adelinina[&&NHX:TOL=133365],diaperina[&&NHX:TOL=133366])diaperini[&&NHX:TOL=133364],(brittonina[&&NHX:TOL=133368],hyociina[&&NHX:TOL=133369],uptonina[&&NHX:TOL=133370])hyociini[&&NHX:TOL=133367],ectychini[&&NHX:TOL=133371],crypticini[&&NHX:TOL=133372],phaleriini[&&NHX:TOL=133373],trachyscelini[&&NHX:TOL=133374],myrmechixenini[&&NHX:TOL=133375],hypophlaeini[&&NHX:TOL=133376],(anopidiina[&&NHX:TOL=133378],gnathidiina[&&NHX:TOL=133379])gnathidiini[&&NHX:TOL=133377],scaphidemini[&&NHX:TOL=133380],leiochrinini[&&NHX:TOL=133381])diaperinae[&&NHX:TOL=133363],(cnodalonini[&&NHX:TOL=133383],stenochiini[&&NHX:TOL=133384],talanini[&&NHX:TOL=133385])stenochiinae[&&NHX:TOL=133382])tenebrionidae[&&NHX:TOL=10315],tetratomidae[&&NHX:TOL=10304],trachelostenidae[&&NHX:TOL=10314],ulodidae[&&NHX:TOL=10311],zopheridae[&&NHX:TOL=10310])tenebrionoidea[&&NHX:TOL=9093],(bruchidae[&&NHX:TOL=29998],(aseminae[&&NHX:TOL=56882],cerambycinae[&&NHX:TOL=56883],disteniinae[&&NHX:TOL=56884],lamiinae[&&NHX:TOL=56885],lepturinae[&&NHX:TOL=56886],necydalinae[&&NHX:TOL=56887],parandrinae[&&NHX:TOL=56888],prioninae[&&NHX:TOL=56889],spondylinae[&&NHX:TOL=56890])cerambycidae[&&NHX:TOL=9129],chrysomelidae[&&NHX:TOL=9132],megalopodidae[&&NHX:TOL=9130],(aulacoscelis[&&NHX:TOL=29999],janbechynea[&&NHX:TOL=30000],orsodacne[&&NHX:TOL=30001])orsodacnidae[&&NHX:TOL=9131])chrysomeloidea[&&NHX:TOL=9094],(anthribidae[&&NHX:TOL=9175],attelabidae[&&NHX:TOL=9177],belidae[&&NHX:TOL=9176],brentidae[&&NHX:TOL=9178],caridae[&&NHX:TOL=9179],curculionidae[&&NHX:TOL=9181],ithycerus noveboracensis[&&NHX:TOL=9180],nemonychidae[&&NHX:TOL=9174])curculionoidea[&&NHX:TOL=9095])cucujiformia[&&NHX:TOL=9088])[&&NHX:TOL=9078])polyphaga[&&NHX:TOL=8870],(((lepicerus bufo[&&NHX:TOL=9060],lepicerus inaequalis[&&NHX:TOL=9059])lepicerus[&&NHX:TOL=9048],haplochelus georrisoides[&&NHX:EXT=Y:TOL=108335])lepiceridae[&&NHX:TOL=108334],(((delevea bertrandi[&&NHX:TOL=30004],delevea namibensis[&&NHX:TOL=30006])delevea[&&NHX:TOL=9065],satonius kurosawai[&&NHX:TOL=30003],(claudiella ingens[&&NHX:TOL=9069],(iapir borgmeieri[&&NHX:TOL=30007],iapir britskii[&&NHX:TOL=30008],iapir castalia[&&NHX:TOL=30009],iapir trombetensis[&&NHX:TOL=30010])iapir[&&NHX:TOL=9070],incoltorrida madagassica[&&NHX:TOL=9068],(torridincola congolesica[&&NHX:TOL=30134],torridincola natalesica[&&NHX:TOL=30135],torridincola rhodesica[&&NHX:TOL=9067])torridincola[&&NHX:TOL=30133],(ytu angra[&&NHX:TOL=30136],ytu artemis[&&NHX:TOL=30011],ytu athena[&&NHX:TOL=30012],ytu brutus[&&NHX:TOL=30013],ytu cleideae[&&NHX:TOL=30014],ytu cupidus[&&NHX:TOL=30015],ytu cuyaba[&&NHX:TOL=30137],ytu demeter[&&NHX:TOL=30016],ytu godayi[&&NHX:TOL=30138],ytu hephaestus[&&NHX:TOL=30017],ytu itati[&&NHX:TOL=30139],ytu mirandus[&&NHX:TOL=30140],ytu mirim[&&NHX:TOL=30141],ytu morpheus[&&NHX:TOL=30018],ytu phebo[&&NHX:TOL=30019],ytu reichardti[&&NHX:TOL=30020],ytu yaguar[&&NHX:TOL=30142],ytu ysypo[&&NHX:TOL=30021],ytu zeus[&&NHX:TOL=30022])ytu[&&NHX:TOL=9071])[&&NHX:TOL=9066])torridincolidae[&&NHX:TOL=9050],(((hydroscapha coomani[&&NHX:TOL=30023],hydroscapha granulum[&&NHX:TOL=30024],hydroscapha hunanensis[&&NHX:TOL=30026],hydroscapha jaechi[&&NHX:TOL=30027],hydroscapha mauretanica[&&NHX:TOL=30028],hydroscapha monticola[&&NHX:TOL=30029],hydroscapha natans[&&NHX:TOL=30030],hydroscapha nepalensis[&&NHX:TOL=30031],hydroscapha reichardti[&&NHX:TOL=30032],hydroscapha saboureaui[&&NHX:TOL=30033],hydroscapha satoi[&&NHX:TOL=30034],hydroscapha substrigosa[&&NHX:TOL=30035],hydroscapha takahashii[&&NHX:TOL=30036],hydroscapha turbinata[&&NHX:TOL=30037],hydroscapha jumaloni[&&NHX:TOL=113974])hydroscapha[&&NHX:TOL=9055],(scaphydra angra[&&NHX:TOL=30038],scaphydra hintoni[&&NHX:TOL=30039],scaphydra pygmaea[&&NHX:TOL=30040])scaphydra[&&NHX:TOL=9056],(yara dybasi[&&NHX:TOL=30041],yara vanini[&&NHX:TOL=30042])yara[&&NHX:TOL=9057])hydroscaphidae[&&NHX:TOL=9052],(sphaerius acaroides[&&NHX:TOL=26450],sphaerius africanus[&&NHX:TOL=26451],sphaerius alticola[&&NHX:TOL=26452],sphaerius coenensis[&&NHX:TOL=26453],sphaerius coomani[&&NHX:TOL=30043],sphaerius cribratus[&&NHX:TOL=30044],sphaerius favosus[&&NHX:TOL=30045],sphaerius gustavlohsei[&&NHX:TOL=26454],sphaerius hispanicus[&&NHX:TOL=26455],sphaerius humicola[&&NHX:TOL=26456],sphaerius laeviventris[&&NHX:TOL=30046],sphaerius madecassus[&&NHX:TOL=30047],sphaerius politus[&&NHX:TOL=26457],sphaerius obsoletus[&&NHX:TOL=30048],sphaerius ovensensis[&&NHX:TOL=26459],sphaerius papulosus[&&NHX:TOL=30049],sphaerius perlaevis[&&NHX:TOL=30050],sphaerius scutellaris[&&NHX:TOL=26460],sphaerius silvicola[&&NHX:TOL=26461],sphaerius spississimus[&&NHX:TOL=26462],sphaerius tesselatus[&&NHX:TOL=30051],sphaerius texanus[&&NHX:TOL=26463],sphaerius tropicus[&&NHX:TOL=30052])sphaeriusidae[&&NHX:TOL=9053])[&&NHX:TOL=9051])[&&NHX:TOL=9049])myxophaga[&&NHX:TOL=8871])[&&NHX:TOL=8869],(avocatinus elongatus[&&NHX:EXT=Y:TOL=29842],catinius pelta[&&NHX:EXT=Y:TOL=29843],catinoides rotundatus[&&NHX:EXT=Y:TOL=29844],macrocatinius brachycephalus[&&NHX:EXT=Y:TOL=29845],triassocatinius[&&NHX:EXT=Y:TOL=29846])catiniidae[&&NHX:EXT=Y:TOL=8872])[&&NHX:TOL=8868],(ademosyne[&&NHX:EXT=Y:TOL=29806],ademosynoides[&&NHX:EXT=Y:TOL=29807],cephalosyne capitata[&&NHX:EXT=Y:TOL=29808],dolichosyne[&&NHX:EXT=Y:TOL=29809],gnathosyne akkolkensis[&&NHX:EXT=Y:TOL=29810],grammositus[&&NHX:EXT=Y:TOL=29811],petrosyne liassica[&&NHX:EXT=Y:TOL=29812],platycrossos[&&NHX:EXT=Y:TOL=29813],polysitus[&&NHX:EXT=Y:TOL=29814],ranis[&&NHX:EXT=Y:TOL=29815],shepherdia[&&NHX:EXT=Y:TOL=29816],sphaerosyne globisa[&&NHX:EXT=Y:TOL=29817])ademosynidae[&&NHX:EXT=Y:TOL=8873])[&&NHX:TOL=8867],(camaricopterus ovalis[&&NHX:EXT=Y:TOL=30337],catabrycus hoplites[&&NHX:EXT=Y:TOL=29824],dikerocoleus divisus[&&NHX:EXT=Y:TOL=30338],hadeocoleodes calus[&&NHX:EXT=Y:TOL=29825],hadeocoleus[&&NHX:EXT=Y:TOL=29826],lethocoleus sternalis[&&NHX:EXT=Y:TOL=29827],malmelater priscus[&&NHX:EXT=Y:TOL=29828],parathnesidius oculatus[&&NHX:EXT=Y:TOL=29829],pesus prognathus[&&NHX:EXT=Y:TOL=29830],praesagus capitatus[&&NHX:EXT=Y:TOL=29831],salebrocoleus[&&NHX:EXT=Y:TOL=29832],salebroferus[&&NHX:EXT=Y:TOL=29833],schizophorinus punctatus[&&NHX:EXT=Y:TOL=29834],schizophoroides[&&NHX:EXT=Y:TOL=29835],schizophorus crassus[&&NHX:EXT=Y:TOL=29836],tersoides[&&NHX:EXT=Y:TOL=29837],tersus[&&NHX:EXT=Y:TOL=29838],thnesidius[&&NHX:EXT=Y:TOL=29839],triassocoleus[&&NHX:EXT=Y:TOL=29840],xyphosternum[&&NHX:EXT=Y:TOL=29841])schizophoridae[&&NHX:EXT=Y:TOL=8874])[&&NHX:TOL=8866],(((spanglerogyrus albiventris[&&NHX:TOL=8945])spanglerogyrus[&&NHX:TOL=8923],((gyrinus[&&NHX:TOL=8926],metagyrinus[&&NHX:TOL=8927],aulonogyrus[&&NHX:TOL=8928])[&&NHX:TOL=8925],heterogyrus[&&NHX:TOL=8929],(enhydrus[&&NHX:TOL=8931],((dineutus[&&NHX:TOL=8934],porrorhynchus[&&NHX:TOL=8935])[&&NHX:TOL=8933],(macrogyrus[&&NHX:TOL=8937],andogyrus[&&NHX:TOL=8938],(gyretes[&&NHX:TOL=8940],(orectochilus[&&NHX:TOL=8942],orectogyrus[&&NHX:TOL=8943])[&&NHX:TOL=8941])[&&NHX:TOL=8939])[&&NHX:TOL=8936])[&&NHX:TOL=8932])[&&NHX:TOL=8930])[&&NHX:TOL=8924])gyrinidae[&&NHX:TOL=8882],(peltodytes[&&NHX:TOL=8947],((brychius pacificus[&&NHX:TOL=117475],((brychius glabratus[&&NHX:TOL=117479],brychius elevatus[&&NHX:TOL=117478])[&&NHX:TOL=117481],(brychius hungerfordi[&&NHX:TOL=117476],brychius hornii[&&NHX:TOL=117477])[&&NHX:TOL=117482])[&&NHX:TOL=117480])brychius[&&NHX:TOL=8949],haliplus[&&NHX:TOL=8950])[&&NHX:TOL=8948])haliplidae[&&NHX:TOL=8884],((stygeonectes[&&NHX:EXT=Y:TOL=8913],necronecctes[&&NHX:EXT=Y:TOL=8914],exedia[&&NHX:EXT=Y:TOL=8915],pseudohydrophilus[&&NHX:EXT=Y:TOL=8916])necronectinae[&&NHX:EXT=Y:TOL=8912],coptoclava[&&NHX:EXT=Y:TOL=8917],(charonoscapha[&&NHX:EXT=Y:TOL=8919],charonoscaphidia[&&NHX:EXT=Y:TOL=8920])charonoscaphinae[&&NHX:EXT=Y:TOL=8918])coptoclavidae[&&NHX:EXT=Y:TOL=8896],meruidae[&&NHX:TOL=29297],parahygrobia natans[&&NHX:EXT=Y:TOL=8897],((phreatodytes[&&NHX:TOL=8955],(notomicrus[&&NHX:TOL=8957],(neohydrocoptus[&&NHX:TOL=8959],(pronoterus[&&NHX:TOL=8961],(noterus[&&NHX:TOL=8963],(synchortus[&&NHX:TOL=8965],(mesonoterus[&&NHX:TOL=8967],(renotus[&&NHX:TOL=8969],(siolius[&&NHX:TOL=8971],suphis[&&NHX:TOL=8972],(hydrocanthus[&&NHX:TOL=8974],(canthydrus[&&NHX:TOL=8976],suphisellus[&&NHX:TOL=8977])[&&NHX:TOL=8975])[&&NHX:TOL=8973])[&&NHX:TOL=8970])[&&NHX:TOL=8968])[&&NHX:TOL=8966])[&&NHX:TOL=8964])[&&NHX:TOL=8962])[&&NHX:TOL=8960])[&&NHX:TOL=8958])[&&NHX:TOL=8956])noteridae[&&NHX:TOL=8889],((amphizoa davidi[&&NHX:TOL=8903],(((amphizoa sinica[&&NHX:TOL=8907],amphizoa lecontei[&&NHX:TOL=8908])[&&NHX:TOL=8906],amphizoa striata[&&NHX:TOL=8909])[&&NHX:TOL=8905],amphizoa insolens[&&NHX:TOL=8910])[&&NHX:TOL=8904])amphizoidae[&&NHX:TOL=8891],((dytiscidae[&&NHX:TOL=8893],hygrobiidae[&&NHX:TOL=8894])[&&NHX:TOL=8892],aspidytidae[&&NHX:TOL=29299])[&&NHX:TOL=29298])[&&NHX:TOL=8890])[&&NHX:TOL=8888],liadytes[&&NHX:EXT=Y:TOL=8898],(((trachypachus holmbergi[&&NHX:TOL=8987],trachypachus gibbsii[&&NHX:TOL=8988],trachypachus zetterstedi[&&NHX:TOL=8989],trachypachus slevini[&&NHX:TOL=8990])trachypachus[&&NHX:TOL=8981],(systolosoma breve[&&NHX:TOL=8984],systolosoma lateritium[&&NHX:TOL=8985])systolosoma[&&NHX:TOL=8982])trachypachidae[&&NHX:TOL=8887],(((psydrus piceus[&&NHX:TOL=1786],nomius[&&NHX:TOL=1787],laccocenus ambiguus[&&NHX:TOL=1788])psydrini[&&NHX:TOL=84],melaenus[&&NHX:TOL=85],cymbionotum[&&NHX:TOL=86],((axonyina[&&NHX:TOL=884],((((craspedonotus[&&NHX:TOL=869],broscus[&&NHX:TOL=870])[&&NHX:TOL=868],(chaetobroscus[&&NHX:TOL=872],((zacotus[&&NHX:TOL=875],eobroscus[&&NHX:TOL=876])[&&NHX:TOL=874],((miscodera[&&NHX:TOL=879],broscodera[&&NHX:TOL=880])[&&NHX:TOL=878],broscosoma[&&NHX:TOL=881])[&&NHX:TOL=877])[&&NHX:TOL=873])[&&NHX:TOL=871])[&&NHX:TOL=867],sinobrosculus[&&NHX:TOL=882])broscina[&&NHX:TOL=886],(nothobroscina[&&NHX:TOL=888],(creobiina[&&NHX:TOL=890],barypina[&&NHX:TOL=891])[&&NHX:TOL=889])[&&NHX:TOL=887])[&&NHX:TOL=885])[&&NHX:TOL=883],ebertius[&&NHX:TOL=892])broscini[&&NHX:TOL=87],apotomus[&&NHX:TOL=88],((trechini[&&NHX:TOL=91],zolini[&&NHX:TOL=92],pogonini[&&NHX:TOL=93],((((((bembidion balli[&&NHX:TOL=378],bembidion foveum[&&NHX:TOL=379])[&&NHX:TOL=133793],((bembidion punctatostriatum[&&NHX:TOL=394],(bembidion lapponicum[&&NHX:TOL=393],(bembidion velox[&&NHX:TOL=392],(bembidion stenoderum[&&NHX:TOL=391],bembidion carinula[&&NHX:TOL=390])[&&NHX:TOL=133798])[&&NHX:TOL=133797])[&&NHX:TOL=133796])[&&NHX:TOL=133795],((bembidion argenteolum[&&NHX:TOL=384],bembidion semenovi[&&NHX:TOL=385])[&&NHX:TOL=133800],bembidion alaskense[&&NHX:TOL=382])[&&NHX:TOL=133799],(((bembidion inaequale[&&NHX:TOL=403],bembidion levettei[&&NHX:TOL=404])[&&NHX:TOL=133803],bembidion conicolle[&&NHX:TOL=401],bembidion litorale[&&NHX:TOL=400])[&&NHX:TOL=133802],bembidion zephyrum[&&NHX:TOL=398],bembidion hesperium[&&NHX:TOL=396],bembidion lorquinii[&&NHX:TOL=397])[&&NHX:TOL=133801])[&&NHX:TOL=133794])bembidion bracteon[&&NHX:TOL=367],(bembidion americanum[&&NHX:TOL=511],bembidion bifossulatum[&&NHX:TOL=512])bembidion ochthedromus[&&NHX:TOL=369],(bembidion aeneipes[&&NHX:TOL=533],bembidion aenulum[&&NHX:TOL=532],bembidion arizonae[&&NHX:TOL=131252],bembidion bowditchii[&&NHX:TOL=516],bembidion carinatum[&&NHX:TOL=527],bembidion chloropus[&&NHX:TOL=536],bembidion confusum[&&NHX:TOL=529],bembidion coxendix[&&NHX:TOL=526],bembidion durangoense[&&NHX:TOL=530],bembidion foraminosum[&&NHX:TOL=517],bembidion fusiforme[&&NHX:TOL=534],bembidion gebieni[&&NHX:TOL=522],bembidion japonicum[&&NHX:TOL=523],bembidion narzikulovi[&&NHX:TOL=520],bembidion persimile[&&NHX:TOL=521],bembidion robusticolle[&&NHX:TOL=525],bembidion sculpturatum[&&NHX:TOL=528],bembidion soederbomi[&&NHX:TOL=524],bembidion striatum[&&NHX:TOL=518],bembidion subfusum[&&NHX:TOL=535],bembidion suensoni[&&NHX:TOL=537],bembidion suturale[&&NHX:TOL=519])bembidion odontium[&&NHX:TOL=368],((bembidion chalceum[&&NHX:TOL=543],bembidion rothfelsi[&&NHX:TOL=105270],bembidion bellorum[&&NHX:TOL=105271],bembidion antiquum[&&NHX:TOL=545],bembidion louisella[&&NHX:TOL=105272])bembidion chalceum subgroup[&&NHX:TOL=132629],(bembidion rufotinctum[&&NHX:TOL=547],bembidion integrum[&&NHX:TOL=546],bembidion honestum[&&NHX:TOL=544],bembidion arenobilis[&&NHX:TOL=105274])bembidion honestum subgroup[&&NHX:TOL=132630])bembidion pseudoperyphus[&&NHX:TOL=370])bembidion odontium complex[&&NHX:TOL=133816],(bembidion ateradustum[&&NHX:TOL=131534],bembidion errans[&&NHX:TOL=131535],bembidion proprium[&&NHX:TOL=131536],(bembidion rotundicolle rotundicolle[&&NHX:TOL=131538],bembidion rotundicolle eustictum[&&NHX:TOL=131539])bembidion rotundicolle[&&NHX:TOL=131537])bembidion ananotaphus[&&NHX:TOL=23678],bembidion incisum[&&NHX:TOL=23719],((bembidion eburneonigrum[&&NHX:TOL=58071],bembidion engelhardti[&&NHX:TOL=58072],bembidion germainianum[&&NHX:TOL=58073],bembidion hirtipes[&&NHX:TOL=58074],bembidion parvum[&&NHX:TOL=58075],bembidion philippii[&&NHX:TOL=58076],bembidion ringueleti[&&NHX:TOL=58077],bembidion rufoplagiatum[&&NHX:TOL=58078],bembidion tucumanum[&&NHX:TOL=58079],bembidion uniforme[&&NHX:TOL=58080])bembidion antiperyphus[&&NHX:TOL=23713],(bembidion chilense[&&NHX:TOL=58085],bembidion loscondesi[&&NHX:TOL=58089],bembidion maculiferum[&&NHX:TOL=58088],bembidion negreanum[&&NHX:TOL=58087],bembidion spinolai[&&NHX:TOL=58086])bembidion antiperyphanes[&&NHX:TOL=23715],(bembidion cassinense[&&NHX:TOL=58083],bembidion mendocinum[&&NHX:TOL=58081],bembidion orregoi[&&NHX:TOL=58082])bembidion chilioperyphus[&&NHX:TOL=23714],bembidion mandibulare[&&NHX:TOL=23712])bembidion antiperyphus complex[&&NHX:TOL=133822],(bembidion platyderoides[&&NHX:TOL=132576],bembidion wollastoni[&&NHX:TOL=132577])bembidion apteromimus[&&NHX:TOL=132575],(bembidion algidum[&&NHX:TOL=132113],bembidion altestriatum[&&NHX:TOL=132114],bembidion amaurum[&&NHX:TOL=132115],bembidion amnicola[&&NHX:TOL=132116],bembidion bimaculatum[&&NHX:TOL=132117],bembidion chloreum[&&NHX:TOL=132118],(bembidion collutum collutum[&&NHX:TOL=132120],bembidion collutum nakanoshimense[&&NHX:TOL=132121],bembidion collutum semiluitum[&&NHX:TOL=132122])bembidion collutum[&&NHX:TOL=132119],bembidion exornatum[&&NHX:TOL=132123],bembidion gotoense[&&NHX:TOL=132124],bembidion infuscatum[&&NHX:TOL=132125],bembidion kazakhstanicum[&&NHX:TOL=132126],(bembidion ladas ladas[&&NHX:TOL=132128],bembidion ladas lehense[&&NHX:TOL=132129])bembidion ladas[&&NHX:TOL=132127],bembidion lenae[&&NHX:TOL=132130],bembidion lindbergi[&&NHX:TOL=132131],bembidion lunatum[&&NHX:TOL=132132],bembidion macropterum[&&NHX:TOL=132133],bembidion obenbergeri[&&NHX:TOL=132134],bembidion ocylum[&&NHX:TOL=132135],bembidion ovale[&&NHX:TOL=132136],(bembidion pamiricola pamiricola[&&NHX:TOL=132138],bembidion pamiricola beybienkoi[&&NHX:TOL=132139])bembidion pamiricola[&&NHX:TOL=132137],bembidion peleum[&&NHX:TOL=132140],bembidion postremum[&&NHX:TOL=132141],bembidion renoanum[&&NHX:TOL=132142],bembidion sajanum[&&NHX:TOL=132143],bembidion sapporense[&&NHX:TOL=132144],bembidion semiferrugineum[&&NHX:TOL=132145],(bembidion semilunium semilunium[&&NHX:TOL=132147],bembidion semilunium muchei[&&NHX:TOL=132148],bembidion semilunium serorum[&&NHX:TOL=132149])bembidion semilunium[&&NHX:TOL=132146],bembidion smirnovi[&&NHX:TOL=132150],bembidion sordidum[&&NHX:TOL=132151],bembidion umiatense[&&NHX:TOL=132152],bembidion ustum[&&NHX:TOL=132153])bembidion asioperyphus[&&NHX:TOL=357],(bembidion aureofuscum[&&NHX:TOL=131781],bembidion jaechi[&&NHX:TOL=131782])bembidion aureoplataphus[&&NHX:TOL=23692],(bembidion adductum[&&NHX:TOL=23774],bembidion crassicorne[&&NHX:TOL=23767],(bembidion humerale humerale[&&NHX:TOL=131588],bembidion humerale petribulirschi[&&NHX:TOL=131589])bembidion humerale[&&NHX:TOL=23766],bembidion jucundum[&&NHX:TOL=23773],bembidion mutatum[&&NHX:TOL=23769],bembidion oregonense[&&NHX:TOL=23772],bembidion pacificum[&&NHX:TOL=131590],bembidion paediscum[&&NHX:TOL=23765],bembidion pedicellatum[&&NHX:TOL=23771],bembidion praecinctum[&&NHX:TOL=23770],(bembidion quadrimaculatum quadrimaculatum[&&NHX:TOL=131591],bembidion quadrimaculatum caporiaccoi[&&NHX:TOL=131592],bembidion quadrimaculatum cardiaderum[&&NHX:TOL=131593],bembidion quadrimaculatum dubitans[&&NHX:TOL=131594],bembidion quadrimaculatum mandli[&&NHX:TOL=131595],bembidion quadrimaculatum oppositum[&&NHX:TOL=131596])bembidion quadrimaculatum[&&NHX:TOL=23763],(bembidion quadripustulatum quadripustulatum[&&NHX:TOL=131597],bembidion quadripustulatum afghanistanicum[&&NHX:TOL=131598],bembidion quadripustulatum hassani[&&NHX:TOL=131599],bembidion quadripustulatum iraniculum[&&NHX:TOL=131600],bembidion quadripustulatum trimaculatum[&&NHX:TOL=131601])bembidion quadripustulatum[&&NHX:TOL=23764],(bembidion sciakyi sciakyi[&&NHX:TOL=131602],bembidion sciakyi luguense[&&NHX:TOL=131603],bembidion sciakyi rinaldi[&&NHX:TOL=131604])bembidion sciakyi[&&NHX:TOL=23768],bembidion teres[&&NHX:TOL=131605])bembidion bembidion[&&NHX:TOL=23672],(bembidion abchasicum[&&NHX:TOL=131800],bembidion ascendens[&&NHX:TOL=131801],bembidion astrabadense[&&NHX:TOL=131802],bembidion atrocaeruleum[&&NHX:TOL=131803],bembidion atrox[&&NHX:TOL=131804],bembidion bactrianum[&&NHX:TOL=131805],bembidion beloborodovi[&&NHX:TOL=131806],bembidion brunoi[&&NHX:TOL=131807],(bembidion bugnioni bugnioni[&&NHX:TOL=131809],bembidion bugnioni cassolai[&&NHX:TOL=131810],bembidion bugnioni sclanoi[&&NHX:TOL=131811])bembidion bugnioni[&&NHX:TOL=131808],bembidion catharinae[&&NHX:TOL=131812],bembidion cimmerium[&&NHX:TOL=131813],bembidion coeruleum[&&NHX:TOL=131814],bembidion complanatum[&&NHX:TOL=131815],bembidion concoeruleum[&&NHX:TOL=131816],bembidion conforme[&&NHX:TOL=131817],bembidion cyaneum[&&NHX:TOL=131818],bembidion depressicolle[&&NHX:TOL=131819],bembidion depressum[&&NHX:TOL=131820],bembidion eleonorae[&&NHX:TOL=131821],bembidion fasciolatum[&&NHX:TOL=131822],(bembidion ferghanicum ferghanicum[&&NHX:TOL=131824],bembidion ferghanicum almasyi[&&NHX:TOL=131825])bembidion ferghanicum[&&NHX:TOL=131823],(bembidion geniculatum geniculatum[&&NHX:TOL=131827],bembidion geniculatum ayderense[&&NHX:TOL=131828],bembidion geniculatum claudejeannei[&&NHX:TOL=131829],bembidion geniculatum dilutipes[&&NHX:TOL=131830])bembidion geniculatum[&&NHX:TOL=131826],bembidion gerdi[&&NHX:TOL=131831],bembidion gotschii[&&NHX:TOL=131832],bembidion gredosanum[&&NHX:TOL=131833],bembidion grosclaudei[&&NHX:TOL=131834],bembidion hamanense[&&NHX:TOL=131835],bembidion josephi[&&NHX:TOL=131836],bembidion justinae[&&NHX:TOL=131837],bembidion kartalinicum[&&NHX:TOL=131838],bembidion leonense[&&NHX:TOL=131839],bembidion leonhardi[&&NHX:TOL=131840],bembidion livens[&&NHX:TOL=131841],bembidion longipes[&&NHX:TOL=131842],bembidion marggii[&&NHX:TOL=131843],bembidion meschniggi[&&NHX:TOL=131844],bembidion milosfassatii[&&NHX:TOL=131845],bembidion mingrelicum[&&NHX:TOL=131846],bembidion motzfeldi[&&NHX:TOL=131847],bembidion orinum[&&NHX:TOL=131848],bembidion paracomplanatum[&&NHX:TOL=131849],bembidion peliopterum[&&NHX:TOL=131850],bembidion penninum[&&NHX:TOL=131851],(bembidion piceocyaneum piceocyaneum[&&NHX:TOL=131853],bembidion piceocyaneum zaisanicum[&&NHX:TOL=131854])bembidion piceocyaneum[&&NHX:TOL=131852],bembidion pseudascendens[&&NHX:TOL=131855],bembidion pseudocyaneum[&&NHX:TOL=131856],bembidion relictum[&&NHX:TOL=131857],bembidion rhodopense[&&NHX:TOL=131858],bembidion rionicum[&&NHX:TOL=131859],(bembidion satanas satanas[&&NHX:TOL=131861],bembidion satanas mandlianum[&&NHX:TOL=131862])bembidion satanas[&&NHX:TOL=131860],bembidion scandens[&&NHX:TOL=131863],bembidion tabellatum[&&NHX:TOL=131864],bembidion tibiale[&&NHX:TOL=131865],bembidion toledanoi[&&NHX:TOL=131866],bembidion trabzonicum[&&NHX:TOL=131867],bembidion transcaucasicum[&&NHX:TOL=131868],(bembidion varicolor varicolor[&&NHX:TOL=131870],bembidion varicolor agurense[&&NHX:TOL=131871])bembidion varicolor[&&NHX:TOL=131869],bembidion vodozi[&&NHX:TOL=131872])bembidion bembidionetolitzkya[&&NHX:TOL=23697],bembidion panda[&&NHX:TOL=132490],(bembidion davaai[&&NHX:TOL=131776],bembidion hastii[&&NHX:TOL=131777],bembidion hiogoense[&&NHX:TOL=131778],bembidion virens[&&NHX:TOL=131779])bembidion blepharoplataphus[&&NHX:TOL=23689],(bembidion championi[&&NHX:TOL=23744],bembidion cyclodes[&&NHX:TOL=23740],bembidion dannieae[&&NHX:TOL=23742],bembidion erwini[&&NHX:TOL=23743],bembidion georgettae[&&NHX:TOL=23746],bembidion poculare[&&NHX:TOL=23739],bembidion sphaeroderum[&&NHX:TOL=23741],bembidion sphaeruliferum[&&NHX:TOL=131494])bembidion cyclolopha[&&NHX:TOL=23671],(bembidion assimile[&&NHX:TOL=131520],bembidion bisulcatum[&&NHX:TOL=131521],bembidion blandulum[&&NHX:TOL=131522],(bembidion clarkii clarkii[&&NHX:TOL=131524],bembidion clarkii magistrettii[&&NHX:TOL=131525])bembidion clarkii[&&NHX:TOL=131523],bembidion fumigatum[&&NHX:TOL=131526],bembidion hesperum[&&NHX:TOL=131527],bembidion loeffleri[&&NHX:TOL=131528],bembidion longipenne[&&NHX:TOL=131529],bembidion skoraszewskyi[&&NHX:TOL=131530],(bembidion transparens transparens[&&NHX:TOL=131532],bembidion transparens prostratum[&&NHX:TOL=131533])bembidion transparens[&&NHX:TOL=131531])bembidion diplocampa[&&NHX:TOL=23653],((bembidion whymperi[&&NHX:TOL=131634],bembidion azuayi[&&NHX:TOL=131608])bembidion whymperi group[&&NHX:TOL=133885],(bembidion mucubaji[&&NHX:TOL=132515],bembidion jimburae[&&NHX:TOL=131622],bembidion wardi[&&NHX:TOL=133858],bembidion walterrossii[&&NHX:TOL=133857])bembidion jimburae group[&&NHX:TOL=133886],(bembidion boyaca[&&NHX:TOL=133844],bembidion atillense[&&NHX:TOL=133843],bembidion camposi[&&NHX:TOL=131611],bembidion moreti[&&NHX:TOL=133851],bembidion pichincha[&&NHX:TOL=133854])bembidion camposi group[&&NHX:TOL=133887],bembidion andersoni[&&NHX:TOL=133842],(bembidion guaramacal[&&NHX:TOL=133850],bembidion georgeballi[&&NHX:TOL=133849],bembidion cosangaense[&&NHX:TOL=133848],bembidion pierrei[&&NHX:TOL=133855])bembidion georgeballi group[&&NHX:TOL=133888],(bembidion agonoides[&&NHX:TOL=133890],bembidion chimborazonum[&&NHX:TOL=131614],(bembidion paulinae[&&NHX:TOL=131625],bembidion paulinae bolvianum[&&NHX:TOL=133853])[&&NHX:TOL=133891],bembidion rogersi[&&NHX:TOL=132356],bembidion sanctaemarthae[&&NHX:TOL=132527],bembidion subapterum[&&NHX:TOL=132530])bembidion chimborazonum group[&&NHX:TOL=133889],(bembidion andinum[&&NHX:TOL=131607],bembidion achipungi[&&NHX:TOL=131606],bembidion allegroi[&&NHX:TOL=133841],bembidion bibliani[&&NHX:TOL=131609],bembidion bolivari[&&NHX:TOL=131610],bembidion callacalla[&&NHX:TOL=133845],bembidion carreli[&&NHX:TOL=131612],bembidion chilesi[&&NHX:TOL=131613],bembidion cocuyanum[&&NHX:TOL=133846],bembidion colombianum[&&NHX:TOL=133847],bembidion cotopaxi[&&NHX:TOL=131615],bembidion davidsoni[&&NHX:TOL=131616],bembidion espejoense[&&NHX:TOL=132504],bembidion fulvocinctum[&&NHX:TOL=131617],bembidion guamani[&&NHX:TOL=131619],bembidion humboldti[&&NHX:TOL=131620],bembidion illuchi[&&NHX:TOL=131621],bembidion mathani[&&NHX:TOL=131623],bembidion onorei[&&NHX:TOL=131624],bembidion oxapampa[&&NHX:TOL=133852],bembidion perraulti[&&NHX:TOL=131626],bembidion pyxidum[&&NHX:TOL=131627],bembidion quebrada[&&NHX:TOL=133856],bembidion rawlinsi[&&NHX:TOL=131628],bembidion saragurense[&&NHX:TOL=131629],bembidion sirinae[&&NHX:TOL=131630],bembidion sulfurarium[&&NHX:TOL=131631],bembidion vignai[&&NHX:TOL=131632],bembidion villagomesi[&&NHX:TOL=131633],bembidion youngi[&&NHX:TOL=131635])bembidion fulvocinctum  andinum group[&&NHX:TOL=133892])bembidion ecuadion[&&NHX:TOL=113128],(bembidion articulatoides[&&NHX:TOL=131454],(bembidion axillare axillare[&&NHX:TOL=131456],bembidion axillare euxinum[&&NHX:TOL=131457],bembidion axillare occiduum[&&NHX:TOL=131458])bembidion axillare[&&NHX:TOL=131455],(bembidion azurescens azurescens[&&NHX:TOL=131460],bembidion azurescens kurangense[&&NHX:TOL=131461])bembidion azurescens[&&NHX:TOL=131459],bembidion bulgani[&&NHX:TOL=131462],bembidion diligens[&&NHX:TOL=131463],bembidion eupages[&&NHX:TOL=131464],bembidion gobiense[&&NHX:TOL=131465],bembidion iliense[&&NHX:TOL=131466],bembidion inconspicuum[&&NHX:TOL=131467],bembidion karounense[&&NHX:TOL=131468],bembidion lais[&&NHX:TOL=131469],(bembidion latiplaga latiplaga[&&NHX:TOL=131471],bembidion latiplaga flavibase[&&NHX:TOL=131472],bembidion latiplaga mateui[&&NHX:TOL=131473])bembidion latiplaga[&&NHX:TOL=131470],bembidion minimum[&&NHX:TOL=131474],bembidion motschulskyi[&&NHX:TOL=131475],bembidion netolitzkyanum[&&NHX:TOL=131476],(bembidion normannum normannum[&&NHX:TOL=131478],bembidion normannum apfelbecki[&&NHX:TOL=131479],bembidion normannum mediterraneum[&&NHX:TOL=131480])bembidion normannum[&&NHX:TOL=131477],bembidion quadriplagiatum[&&NHX:TOL=131481],(bembidion tenellum tenellum[&&NHX:TOL=131483],bembidion tenellum buchariplaga[&&NHX:TOL=131484],bembidion tenellum pseudoplaga[&&NHX:TOL=131485],bembidion tenellum telemus[&&NHX:TOL=131486])bembidion tenellum[&&NHX:TOL=131482],bembidion transversum[&&NHX:TOL=131487],bembidion vile[&&NHX:TOL=131488],bembidion zagrosense[&&NHX:TOL=131489])bembidion emphanes[&&NHX:TOL=23668],bembidion megalops[&&NHX:TOL=132578],(bembidion alikhelicum[&&NHX:TOL=131894],(bembidion combustum combustum[&&NHX:TOL=131896],bembidion combustum lugubriveste[&&NHX:TOL=131897])bembidion combustum[&&NHX:TOL=131895],bembidion eques[&&NHX:TOL=131898],(bembidion fluviatile fluviatile[&&NHX:TOL=131900],bembidion fluviatile acragas[&&NHX:TOL=131901],bembidion fluviatile amplum[&&NHX:TOL=131902],bembidion fluviatile basale[&&NHX:TOL=131903],bembidion fluviatile exhibitum[&&NHX:TOL=131904],bembidion fluviatile pyrrium[&&NHX:TOL=131905],bembidion fluviatile richteri[&&NHX:TOL=131906],bembidion fluviatile unctulum[&&NHX:TOL=131907])bembidion fluviatile[&&NHX:TOL=131899],bembidion fulvipes[&&NHX:TOL=131908],(bembidion giganteum giganteum[&&NHX:TOL=131910],bembidion giganteum reinigi[&&NHX:TOL=131911])bembidion giganteum[&&NHX:TOL=131909],bembidion nobile[&&NHX:TOL=131912],(bembidion parallelipenne parallelipenne[&&NHX:TOL=131914],bembidion parallelipenne exisonum[&&NHX:TOL=131915],bembidion parallelipenne pseudoripicola[&&NHX:TOL=131916])bembidion parallelipenne[&&NHX:TOL=131913],bembidion regale[&&NHX:TOL=131917],bembidion ripicola[&&NHX:TOL=131918],(bembidion scapulare scapulare[&&NHX:TOL=131920],bembidion scapulare lomnickii[&&NHX:TOL=131921],bembidion scapulare oblongum[&&NHX:TOL=131922],bembidion scapulare tergluense[&&NHX:TOL=131923])bembidion scapulare[&&NHX:TOL=131919],(bembidion testaceum testaceum[&&NHX:TOL=131925],bembidion testaceum brevius[&&NHX:TOL=131926])bembidion testaceum[&&NHX:TOL=131924])bembidion euperyphus[&&NHX:TOL=23700],(bembidion aratum[&&NHX:TOL=372],bembidion dentelloides[&&NHX:TOL=23733],bembidion dentellum[&&NHX:TOL=423],bembidion graciliforme[&&NHX:TOL=427],bembidion immaturum[&&NHX:TOL=426],bembidion incrematum[&&NHX:TOL=425],bembidion ruthenum[&&NHX:TOL=23734],bembidion sibiricum[&&NHX:TOL=23735],bembidion starkii[&&NHX:TOL=23736],bembidion tinctum[&&NHX:TOL=424],bembidion scintillans[&&NHX:TOL=373],bembidion variegatum[&&NHX:TOL=482])bembidion eupetedromus[&&NHX:TOL=348],(bembidion affine[&&NHX:TOL=52639],bembidion barrense[&&NHX:TOL=132493],bembidion egens[&&NHX:TOL=52640],bembidion flavopictum[&&NHX:TOL=52641],bembidion fuchsii[&&NHX:TOL=52642],bembidion impotens[&&NHX:TOL=52643],bembidion mimus[&&NHX:TOL=52644],bembidion nogalesium[&&NHX:TOL=52645],bembidion timidum[&&NHX:TOL=52646],bembidion triviale[&&NHX:TOL=52647],bembidion versicolor[&&NHX:TOL=52648])bembidion furcacampa[&&NHX:TOL=23667],(bembidion spurcum[&&NHX:TOL=132618],bembidion blackburni[&&NHX:TOL=132619])bembidion gnatholymnaeum[&&NHX:TOL=132631],(bembidion alpineanum[&&NHX:TOL=23759],bembidion avidum[&&NHX:TOL=23760],bembidion concolor[&&NHX:TOL=23751],bembidion friebi[&&NHX:TOL=131780],bembidion hirmocaelum[&&NHX:TOL=23747],bembidion humboldtense[&&NHX:TOL=23755],bembidion nigrum[&&NHX:TOL=23748],bembidion quadrulum[&&NHX:TOL=23753],bembidion recticolle[&&NHX:TOL=23754],bembidion salebratum[&&NHX:TOL=23752],bembidion subaerarium[&&NHX:TOL=23762])bembidion hirmoplataphus[&&NHX:TOL=23690],(bembidion brevistriatum[&&NHX:TOL=23749],bembidion californicum[&&NHX:TOL=23761],bembidion marinianum[&&NHX:TOL=23757],bembidion quadratulum[&&NHX:TOL=23758],bembidion semistriatum[&&NHX:TOL=23750])bembidion hydriomicrus[&&NHX:TOL=23691],(((bembidion chalcodes[&&NHX:TOL=23575],bembidion interventor[&&NHX:TOL=441],bembidion laevibase[&&NHX:TOL=431],bembidion laticolle[&&NHX:TOL=433],bembidion nitidum[&&NHX:TOL=439],bembidion obliquulum[&&NHX:TOL=443],bembidion pogonoides[&&NHX:TOL=435],bembidion rufotibiellum[&&NHX:TOL=23576],bembidion vitiosum[&&NHX:TOL=437])bembidion eurytrachelus[&&NHX:TOL=131250],(bembidion levigatum[&&NHX:TOL=444],bembidion nipponicum[&&NHX:TOL=131249])bembidion hydrium[&&NHX:TOL=340])[&&NHX:TOL=133818],((bembidion almum almum[&&NHX:TOL=131272],bembidion almum protalmum[&&NHX:TOL=131273])bembidion almum[&&NHX:TOL=131271],bembidion difforme[&&NHX:TOL=131274],bembidion elbursicum[&&NHX:TOL=131275],bembidion leucolenum[&&NHX:TOL=131276],bembidion loricatum[&&NHX:TOL=131277],(bembidion luridicorne luridicorne[&&NHX:TOL=131279],bembidion luridicorne lamprinum[&&NHX:TOL=131280])bembidion luridicorne[&&NHX:TOL=131278],bembidion mundatum[&&NHX:TOL=131281],bembidion pygmaeum[&&NHX:TOL=131282],bembidion quailaicum[&&NHX:TOL=131283],(bembidion splendidum splendidum[&&NHX:TOL=131285],bembidion splendidum luteipes[&&NHX:TOL=131286],bembidion splendidum pincum[&&NHX:TOL=131287])bembidion splendidum[&&NHX:TOL=131284],bembidion wittmeri[&&NHX:TOL=131288])bembidion chlorodium[&&NHX:TOL=23649],(bembidion ambiguum[&&NHX:TOL=131257],bembidion cirtense[&&NHX:TOL=131258],bembidion gansuense[&&NHX:TOL=131259],(bembidion leucoscelis leucoscelis[&&NHX:TOL=131261],bembidion leucoscelis tripolitanum[&&NHX:TOL=131262])bembidion leucoscelis[&&NHX:TOL=131260],bembidion nigricorne[&&NHX:TOL=131263],bembidion palumboi[&&NHX:TOL=131264],(bembidion rugicolle rugicolle[&&NHX:TOL=131266],bembidion rugicolle sporadicum[&&NHX:TOL=131267])bembidion rugicolle[&&NHX:TOL=131265],bembidion striaticeps[&&NHX:TOL=131268],bembidion submutatum[&&NHX:TOL=131269],bembidion torosum[&&NHX:TOL=131270])bembidion neja[&&NHX:TOL=23644],(bembidion bodenheimeri[&&NHX:TOL=131289],bembidion dyschirinum[&&NHX:TOL=131290],(bembidion elevatum elevatum[&&NHX:TOL=131292],bembidion elevatum lamprosimile[&&NHX:TOL=131293])bembidion elevatum[&&NHX:TOL=131291],bembidion lampros[&&NHX:TOL=131294],bembidion ovoideum[&&NHX:TOL=131295],bembidion properans[&&NHX:TOL=131296],bembidion veneriatum[&&NHX:TOL=131297])bembidion metallina[&&NHX:TOL=23650])bembidion hydrium complex[&&NHX:TOL=133820],(bembidion aberdarense[&&NHX:TOL=132590],bembidion buxtoni[&&NHX:TOL=132591],bembidion celisi[&&NHX:TOL=132592],bembidion hypsipezum edwardsi[&&NHX:TOL=132593],(bembidion kenyense kenyense[&&NHX:TOL=132595],bembidion kenyense eborense[&&NHX:TOL=132596])bembidion kenyense[&&NHX:TOL=132594],bembidion mackinderi[&&NHX:TOL=132597],bembidion mus[&&NHX:TOL=132598],bembidion ruwenzoricum[&&NHX:TOL=132599],bembidion sjoestedti[&&NHX:TOL=132600])bembidion hypsipezum[&&NHX:TOL=132589],(bembidion csikii[&&NHX:TOL=131253],(bembidion kirschenhoferi kirschenhoferi[&&NHX:TOL=131255],bembidion kirschenhoferi annapurnae[&&NHX:TOL=131256])bembidion kirschenhoferi[&&NHX:TOL=131254])bembidion hoquedela[&&NHX:TOL=23654],(bembidion belousovi[&&NHX:TOL=132485],bembidion luisae[&&NHX:TOL=132486],bembidion pieroi[&&NHX:TOL=132487],bembidion shugela[&&NHX:TOL=132488],bembidion taguense[&&NHX:TOL=132489])bembidion josefia[&&NHX:TOL=132484],bembidion tigrinum[&&NHX:TOL=23696],(bembidion festivum[&&NHX:TOL=52261],bembidion horni[&&NHX:TOL=52260],bembidion mundum[&&NHX:TOL=52259])bembidion liocosmius[&&NHX:TOL=23695],(((((bembidion lindrothellum[&&NHX:TOL=131688],(bembidion lummi[&&NHX:TOL=464],bembidion chintimini[&&NHX:TOL=465])[&&NHX:TOL=133808])[&&NHX:TOL=133807],bembidion erasum[&&NHX:TOL=460])[&&NHX:TOL=133806],bembidion disjunctum[&&NHX:TOL=458])[&&NHX:TOL=133805],bembidion castum[&&NHX:TOL=456])[&&NHX:TOL=133804],((bembidion sequoiae[&&NHX:TOL=454],bembidion pseudoerasum[&&NHX:TOL=453])[&&NHX:TOL=133810],bembidion osculans[&&NHX:TOL=451])[&&NHX:TOL=133809])bembidion lionepha[&&NHX:TOL=343],bembidion quadriimpressum[&&NHX:TOL=23717],(bembidion abeillei[&&NHX:TOL=132427],bembidion eichleri[&&NHX:TOL=132428],bembidion laticeps[&&NHX:TOL=132429],bembidion nigropiceum[&&NHX:TOL=132430],bembidion utahense[&&NHX:TOL=132431])bembidion lymnaeum[&&NHX:TOL=23718],(bembidion aegyptiacum[&&NHX:TOL=131236],bembidion apicale[&&NHX:TOL=131237],bembidion discordans[&&NHX:TOL=131238],bembidion icterodes[&&NHX:TOL=131239],bembidion luniferum[&&NHX:TOL=131240],bembidion ochsi[&&NHX:TOL=131241],bembidion pogonopsis[&&NHX:TOL=131242],bembidion quadricolle[&&NHX:TOL=131243],bembidion splendens[&&NHX:TOL=131244],bembidion xanthacrum[&&NHX:TOL=131245],bembidion xanthoxanthum[&&NHX:TOL=131246])bembidion microserrullula[&&NHX:TOL=131235],(bembidion barkamense[&&NHX:TOL=22945],bembidion daxuense[&&NHX:TOL=22954],bembidion facchinii[&&NHX:TOL=22946],bembidion herbertfranzi[&&NHX:TOL=22952],bembidion jani[&&NHX:TOL=22951],bembidion luhuoense[&&NHX:TOL=22949],bembidion qinghaicum[&&NHX:TOL=22944],bembidion rebeccae[&&NHX:TOL=22947],bembidion schillhammeri[&&NHX:TOL=22950],bembidion schuelkei[&&NHX:TOL=131587],bembidion turnai[&&NHX:TOL=22953],bembidion wraseanum[&&NHX:TOL=22948])bembidion microsinocys[&&NHX:TOL=22941],bembidion punctatellum[&&NHX:TOL=23673],(bembidion constricticolle[&&NHX:TOL=131368],bembidion nudipenne[&&NHX:TOL=131387],bembidion nitidicolle[&&NHX:TOL=133880])bembidion neobembidion[&&NHX:TOL=133879],(bembidion satoi[&&NHX:TOL=131490],bembidion shimoyamai[&&NHX:TOL=131491])bembidion neoemphanes[&&NHX:TOL=23669],(bembidion assalemi[&&NHX:TOL=131636],(bembidion callosum callosum[&&NHX:TOL=131638],bembidion callosum paralaterale[&&NHX:TOL=131639],bembidion callosum subconnexum[&&NHX:TOL=131640])bembidion callosum[&&NHX:TOL=131637],bembidion cantalicum[&&NHX:TOL=131641],bembidion caucasicum[&&NHX:TOL=131642],bembidion deliae[&&NHX:TOL=131643],bembidion fortunatum[&&NHX:TOL=131644],bembidion genei[&&NHX:TOL=131645],bembidion glabrum[&&NHX:TOL=131646],bembidion grisvardi[&&NHX:TOL=131647],bembidion hauserianum[&&NHX:TOL=131648],bembidion ibericum[&&NHX:TOL=131649],bembidion illigeri[&&NHX:TOL=131650],bembidion laevipenne[&&NHX:TOL=131651],bembidion loefflerianum[&&NHX:TOL=131652],bembidion menetriesii[&&NHX:TOL=131653],bembidion pinkeri[&&NHX:TOL=131654],bembidion retipenne[&&NHX:TOL=131655],bembidion rufimacula[&&NHX:TOL=131656],(bembidion schmidti schmidti[&&NHX:TOL=131658],bembidion schmidti alluaudi[&&NHX:TOL=131659],bembidion schmidti jeannelianum[&&NHX:TOL=131660],bembidion schmidti mequignoni[&&NHX:TOL=131661],bembidion schmidti moses[&&NHX:TOL=131662],bembidion schmidti pseudocallosum[&&NHX:TOL=131663],bembidion schmidti subcallosum[&&NHX:TOL=131664],bembidion schmidti tibesticum[&&NHX:TOL=131665])bembidion schmidti[&&NHX:TOL=131657],bembidion seriatum[&&NHX:TOL=131666],(bembidion tetragrammum tetragrammum[&&NHX:TOL=131668],bembidion tetragrammum cycladicum[&&NHX:TOL=131669])bembidion tetragrammum[&&NHX:TOL=131667],bembidion tetrasemum[&&NHX:TOL=131670],bembidion turcicum[&&NHX:TOL=131671],(bembidion vseteckai vseteckai[&&NHX:TOL=131673],bembidion vseteckai adanae[&&NHX:TOL=131674],bembidion vseteckai dissimile[&&NHX:TOL=131675])bembidion vseteckai[&&NHX:TOL=131672])bembidion nepha[&&NHX:TOL=23683],(bembidion advena[&&NHX:TOL=133835],bembidion ignicola[&&NHX:TOL=132611],bembidion pacificum[&&NHX:TOL=133836],bembidion teres[&&NHX:TOL=133837],bembidion admirandum[&&NHX:TOL=132603],bembidion munroi[&&NHX:TOL=132601],bembidion rude[&&NHX:TOL=132613],bembidion waialeale[&&NHX:TOL=133811],bembidion smaragdinum[&&NHX:TOL=132614],bembidion fulgens[&&NHX:TOL=132609],bembidion auratum[&&NHX:TOL=132607],bembidion kauaiensis[&&NHX:TOL=132617],bembidion coecus[&&NHX:TOL=132616],bembidion perkinsi[&&NHX:TOL=132612],bembidion koebelei[&&NHX:TOL=132610],bembidion corticarium[&&NHX:TOL=132608],bembidion gagneorum[&&NHX:TOL=133813],bembidion paratomarium[&&NHX:TOL=133812],bembidion atomarium[&&NHX:TOL=132606],bembidion kamakou[&&NHX:TOL=133814],bembidion haleakalae[&&NHX:TOL=133815])bembidion nesocidium[&&NHX:TOL=132632],bembidion ainu[&&NHX:TOL=23681],bembidion ephippium[&&NHX:TOL=23662],(bembidion ejusmodi[&&NHX:TOL=131417],bembidion foveolatum[&&NHX:TOL=131418],(bembidion niloticum niloticum[&&NHX:TOL=131420],bembidion niloticum batesi[&&NHX:TOL=131421])bembidion niloticum[&&NHX:TOL=131419],(bembidion opulentum opulentum[&&NHX:TOL=131423],bembidion opulentum riverinae[&&NHX:TOL=131424],bembidion opulentum luzonicum[&&NHX:TOL=131425])bembidion opulentum[&&NHX:TOL=131422],bembidion tropicale[&&NHX:TOL=131426])bembidion notaphocampa[&&NHX:TOL=23660],(bembidion anthracinum[&&NHX:TOL=131443],bembidion bolsoni[&&NHX:TOL=131444],bembidion cekalovici[&&NHX:TOL=131437],bembidion cekalovicianum[&&NHX:TOL=131438],bembidion cupreostriatum[&&NHX:TOL=131439],bembidion delamarei[&&NHX:TOL=131445],bembidion grossepunctatum[&&NHX:TOL=131446],bembidion hornense[&&NHX:TOL=131440],bembidion jeannelicum[&&NHX:TOL=131447],bembidion marginatum[&&NHX:TOL=131448],bembidion nigritum[&&NHX:TOL=131449],bembidion obliteratum[&&NHX:TOL=131441],bembidion paralongulum[&&NHX:TOL=131450],bembidion sanandresi[&&NHX:TOL=131451],bembidion silvicola[&&NHX:TOL=131452],bembidion solieri[&&NHX:TOL=131442],bembidion topali[&&NHX:TOL=131453])bembidion nothocys[&&NHX:TOL=133861],(bembidion abnormale[&&NHX:TOL=131352],bembidion acticola[&&NHX:TOL=131353],bembidion aeneicolle[&&NHX:TOL=489],bembidion antarcticum[&&NHX:TOL=131354],bembidion approximatum[&&NHX:TOL=470],bembidion aricense[&&NHX:TOL=131355],bembidion armuelles[&&NHX:TOL=132492],bembidion aubei[&&NHX:TOL=131356],bembidion auxiliator[&&NHX:TOL=498],bembidion basiplagiatum[&&NHX:TOL=131357],bembidion bicolor[&&NHX:TOL=131358],bembidion bonariense[&&NHX:TOL=131359],bembidion brullei[&&NHX:TOL=131360],bembidion callens[&&NHX:TOL=131361],bembidion calverti[&&NHX:TOL=131362],bembidion castor[&&NHX:TOL=492],bembidion cayambense[&&NHX:TOL=131363],bembidion chaudoirianum[&&NHX:TOL=131364],bembidion cognatum[&&NHX:TOL=131365],bembidion coloradense[&&NHX:TOL=469],bembidion commissum[&&NHX:TOL=131366],bembidion consimile[&&NHX:TOL=131367],bembidion conspersum[&&NHX:TOL=472],bembidion constrictum[&&NHX:TOL=131369],bembidion consuetum[&&NHX:TOL=473],bembidion contractum[&&NHX:TOL=131370],bembidion convergens[&&NHX:TOL=131371],bembidion cordatum[&&NHX:TOL=486],bembidion cortes[&&NHX:TOL=132497],bembidion debiliceps[&&NHX:TOL=495],bembidion dejectum[&&NHX:TOL=131372],bembidion dorsale[&&NHX:TOL=471],bembidion evidens[&&NHX:TOL=474],bembidion fischeri[&&NHX:TOL=131373],bembidion flohri[&&NHX:TOL=131374],bembidion gabrielum[&&NHX:TOL=131375],bembidion galapagoense[&&NHX:TOL=131376],bembidion graphicum[&&NHX:TOL=494],bembidion hageni[&&NHX:TOL=131377],bembidion idoneum[&&NHX:TOL=475],bembidion igorot[&&NHX:TOL=131378],bembidion inconstans[&&NHX:TOL=131379],bembidion indistinctum[&&NHX:TOL=485],bembidion insulatum[&&NHX:TOL=487],bembidion intermedium[&&NHX:TOL=491],bembidion jacobianum[&&NHX:TOL=476],bembidion jacobseni[&&NHX:TOL=131380],bembidion kuscheli[&&NHX:TOL=131381],bembidion latebricola[&&NHX:TOL=490],bembidion lecontei[&&NHX:TOL=131382],bembidion lorenzi[&&NHX:TOL=131383],bembidion luculentum[&&NHX:TOL=131384],bembidion mirasoi[&&NHX:TOL=131385],bembidion mormon[&&NHX:TOL=131386],bembidion nigripes[&&NHX:TOL=496],bembidion nubiculosum[&&NHX:TOL=477],bembidion oberthueri[&&NHX:TOL=131388],bembidion obliquum[&&NHX:TOL=468],bembidion obscuromaculatum[&&NHX:TOL=131389],bembidion obtusangulum[&&NHX:TOL=131390],bembidion obtusidens[&&NHX:TOL=131391],bembidion operosum[&&NHX:TOL=500],bembidion patruele[&&NHX:TOL=497],bembidion pedestre[&&NHX:TOL=131392],bembidion pilatei[&&NHX:TOL=131393],bembidion pimanum[&&NHX:TOL=501],bembidion placitum[&&NHX:TOL=131394],(bembidion posticale posticale[&&NHX:TOL=131396],bembidion posticale platense[&&NHX:TOL=131397])bembidion posticale[&&NHX:TOL=131395],bembidion rapidum[&&NHX:TOL=488],bembidion regismontium[&&NHX:TOL=131398],bembidion scudderi[&&NHX:TOL=131399],bembidion semifasciatum[&&NHX:TOL=478],bembidion semiopacum[&&NHX:TOL=502],bembidion semipunctatum[&&NHX:TOL=493],bembidion serpentinum[&&NHX:TOL=131400],bembidion servillei[&&NHX:TOL=131401],bembidion sparsum[&&NHX:TOL=479],bembidion spretum[&&NHX:TOL=480],bembidion ugartei[&&NHX:TOL=131402],bembidion umbratum[&&NHX:TOL=484],bembidion unifasciatum[&&NHX:TOL=131403],bembidion varium[&&NHX:TOL=467],bembidion versutum[&&NHX:TOL=483],bembidion viridicolle[&&NHX:TOL=131404],bembidion vividum[&&NHX:TOL=131405],bembidion vulpecula[&&NHX:TOL=481])bembidion notaphus[&&NHX:TOL=347],(bembidion lonae[&&NHX:TOL=59631],bembidion pallideguttula[&&NHX:TOL=59632])bembidion nothonepha[&&NHX:TOL=23684],(bembidion angelieri[&&NHX:TOL=132425],bembidion bonniardae[&&NHX:TOL=132426])bembidion notoperyphus[&&NHX:TOL=23716],(bembidion adowanum[&&NHX:TOL=131927],(bembidion aetolicum aetolicum[&&NHX:TOL=131929],bembidion aetolicum taygetanum[&&NHX:TOL=131930])bembidion aetolicum[&&NHX:TOL=131928],bembidion africanum[&&NHX:TOL=131931],(bembidion atlanticum atlanticum[&&NHX:TOL=131933],bembidion atlanticum galbenum[&&NHX:TOL=131934],bembidion atlanticum leveillei[&&NHX:TOL=131935],bembidion atlanticum megaspilum[&&NHX:TOL=131936],bembidion atlanticum palaciosi[&&NHX:TOL=131937])bembidion atlanticum[&&NHX:TOL=131932],bembidion baehri[&&NHX:TOL=131938],bembidion cnemidotum[&&NHX:TOL=131939],(bembidion decorum decorum[&&NHX:TOL=131941],bembidion decorum bodemeyeri[&&NHX:TOL=131942],bembidion decorum caraffai[&&NHX:TOL=131943],bembidion decorum subconvexum[&&NHX:TOL=131944])bembidion decorum[&&NHX:TOL=131940],bembidion derelictum[&&NHX:TOL=131945],bembidion dolorosum[&&NHX:TOL=131946],bembidion drago[&&NHX:TOL=131947],bembidion echarouxi[&&NHX:TOL=131948],bembidion echigonum[&&NHX:TOL=131949],(bembidion hasurada hasurada[&&NHX:TOL=131951],bembidion hasurada pagmanicum[&&NHX:TOL=131952])bembidion hasurada[&&NHX:TOL=131950],bembidion hesperidum[&&NHX:TOL=131953],bembidion hiekei[&&NHX:TOL=131954],(bembidion ispartanum ispartanum[&&NHX:TOL=131956],bembidion ispartanum nairicum[&&NHX:TOL=131957])bembidion ispartanum[&&NHX:TOL=131955],bembidion leleupi[&&NHX:TOL=131958],bembidion maddisoni[&&NHX:TOL=131959],bembidion melanocerum[&&NHX:TOL=131960],bembidion meruanum[&&NHX:TOL=131961],bembidion merum[&&NHX:TOL=131962],bembidion modestum[&&NHX:TOL=131963],bembidion moritai[&&NHX:TOL=131964],bembidion muellermotzfeldi[&&NHX:TOL=131965],bembidion multipunctatum[&&NHX:TOL=131966],bembidion negrei[&&NHX:TOL=131967],(bembidion ortsi ortsi[&&NHX:TOL=131969],bembidion ortsi grabense[&&NHX:TOL=131970])bembidion ortsi[&&NHX:TOL=131968],bembidion roberti[&&NHX:TOL=131971],bembidion ocydromus rude[&&NHX:TOL=131972],(bembidion saxatile saxatile[&&NHX:TOL=131974],bembidion saxatile bimorsum[&&NHX:TOL=131975],bembidion saxatile caesareum[&&NHX:TOL=131976],bembidion saxatile devillei[&&NHX:TOL=131977],bembidion saxatile flavipalpe[&&NHX:TOL=131978],bembidion saxatile fuscomaculatum[&&NHX:TOL=131979],bembidion saxatile kuruschicum[&&NHX:TOL=131980],bembidion saxatile morsum[&&NHX:TOL=131981])bembidion saxatile[&&NHX:TOL=131973],bembidion schoenmanni[&&NHX:TOL=131982],bembidion scopulinum[&&NHX:TOL=131983],bembidion semilotum[&&NHX:TOL=131984],(bembidion siculum siculum[&&NHX:TOL=131986],bembidion siculum breiti[&&NHX:TOL=131987],bembidion siculum certans[&&NHX:TOL=131988],bembidion siculum durudense[&&NHX:TOL=131989],bembidion siculum smyrnense[&&NHX:TOL=131990],bembidion siculum winkleri[&&NHX:TOL=131991])bembidion siculum[&&NHX:TOL=131985],bembidion tolbonuri[&&NHX:TOL=131992],bembidion transsylvanicum[&&NHX:TOL=131993],bembidion uenoianum[&&NHX:TOL=131994],bembidion yunnanum[&&NHX:TOL=131995],bembidion zolotarewi[&&NHX:TOL=131996])bembidion ocydromus[&&NHX:TOL=364],(bembidion antennarium[&&NHX:TOL=131997],bembidion argaeicola[&&NHX:TOL=131998],bembidion babaulti[&&NHX:TOL=131999],bembidion baghlanicum[&&NHX:TOL=132000],bembidion balcanicum balcanicum[&&NHX:TOL=132001],bembidion circassicum[&&NHX:TOL=132002],(bembidion culminicola culminicola[&&NHX:TOL=132004],bembidion culminicola davatchii[&&NHX:TOL=132005])bembidion culminicola[&&NHX:TOL=132003],bembidion dieckmanni[&&NHX:TOL=132006],(bembidion dudichi dudichi[&&NHX:TOL=132008],bembidion dudichi tunetanum[&&NHX:TOL=132009])bembidion dudichi[&&NHX:TOL=132007],bembidion dyscheres[&&NHX:TOL=132010],(bembidion eucheres eucheres[&&NHX:TOL=132012],bembidion eucheres darvasicum[&&NHX:TOL=132013],bembidion eucheres michailovi[&&NHX:TOL=132014])bembidion eucheres[&&NHX:TOL=132011],bembidion fulvipenne[&&NHX:TOL=132015],bembidion gudenzii[&&NHX:TOL=132016],bembidion heinzi[&&NHX:TOL=132017],bembidion hissaricum[&&NHX:TOL=132018],bembidion hoberlandtianum[&&NHX:TOL=132019],bembidion iphigenia[&&NHX:TOL=132020],bembidion iranicum[&&NHX:TOL=132021],bembidion kabakovi[&&NHX:TOL=132022],bembidion karokhense[&&NHX:TOL=132023],bembidion khanakense[&&NHX:TOL=132024],bembidion kiritshenkoi[&&NHX:TOL=132025],bembidion kuhitangi[&&NHX:TOL=132026],bembidion kurdistanicum[&&NHX:TOL=132027],bembidion ledouxianum[&&NHX:TOL=132028],bembidion lobanovi[&&NHX:TOL=132029],bembidion lysander[&&NHX:TOL=132030],bembidion manfredschmidi[&&NHX:TOL=132031],bembidion martachemai[&&NHX:TOL=132032],bembidion marginipenne[&&NHX:TOL=132033],bembidion menander[&&NHX:TOL=132034],bembidion mirzayani[&&NHX:TOL=132035],bembidion notatum[&&NHX:TOL=132036],bembidion parsorum[&&NHX:TOL=132037],bembidion pindicum[&&NHX:TOL=132038],(bembidion praeustum praeustum[&&NHX:TOL=132040],bembidion praeustum fauveli[&&NHX:TOL=132041],bembidion praeustum viridifluum[&&NHX:TOL=132042])bembidion praeustum[&&NHX:TOL=132039],(bembidion reiseri reiseri[&&NHX:TOL=132044],bembidion reiseri vranense[&&NHX:TOL=132045])bembidion reiseri[&&NHX:TOL=132043],bembidion schermanni[&&NHX:TOL=132046],bembidion signatipenne[&&NHX:TOL=132047],bembidion stolfai[&&NHX:TOL=132048],(bembidion subcylindricum subcylindricum[&&NHX:TOL=132050],bembidion subcylindricum kuliabense[&&NHX:TOL=132051],bembidion subcylindricum kyros[&&NHX:TOL=132052])bembidion subcylindricum[&&NHX:TOL=132049],(bembidion tauricum tauricum[&&NHX:TOL=132054],bembidion tauricum frivaldszkyi[&&NHX:TOL=132055],bembidion tauricum weiratheri[&&NHX:TOL=132056])bembidion tauricum[&&NHX:TOL=132053],bembidion viduum[&&NHX:TOL=132057],(bembidion waziristanum waziristanum[&&NHX:TOL=132059],bembidion waziristanum murreense[&&NHX:TOL=132060])bembidion waziristanum[&&NHX:TOL=132058],bembidion xanthochiton[&&NHX:TOL=132061],bembidion xestum[&&NHX:TOL=132062])bembidion ocyturanes[&&NHX:TOL=23701],(bembidion caricum[&&NHX:TOL=131875],(bembidion hypocrita hypocrita[&&NHX:TOL=131877],bembidion hypocrita illyricum[&&NHX:TOL=131878],bembidion hypocrita normandi[&&NHX:TOL=131879])bembidion hypocrita[&&NHX:TOL=131876],bembidion israelita[&&NHX:TOL=131880],bembidion kempi[&&NHX:TOL=131881],bembidion manicatum[&&NHX:TOL=131882],bembidion semibraccatum[&&NHX:TOL=131883],(bembidion steinbuehleri steinbuehleri[&&NHX:TOL=131885],bembidion steinbuehleri gridellii[&&NHX:TOL=131886])bembidion steinbuehleri[&&NHX:TOL=131884],bembidion strictum[&&NHX:TOL=131887])bembidion omoperyphus[&&NHX:TOL=23698],(bembidion aethiopicum[&&NHX:TOL=131406],bembidion alsium[&&NHX:TOL=131407],bembidion altipeta[&&NHX:TOL=131408],bembidion kilimanum[&&NHX:TOL=131409],bembidion kivuanum[&&NHX:TOL=131410],bembidion mellissii[&&NHX:TOL=131411],bembidion mixtum[&&NHX:TOL=131412],bembidion scotti[&&NHX:TOL=131413],bembidion simienense[&&NHX:TOL=131414],bembidion sperans[&&NHX:TOL=131415],bembidion tropicum[&&NHX:TOL=131416])bembidion omotaphus[&&NHX:TOL=23659],((bembidion atrum[&&NHX:TOL=131427],bembidion epistomale[&&NHX:TOL=131428],bembidion punctigerum[&&NHX:TOL=131429],bembidion sexfoveatum[&&NHX:TOL=131430])bembidion notholopha[&&NHX:TOL=23663],(bembidion melanopodum[&&NHX:TOL=131431],bembidion penai[&&NHX:TOL=131432],bembidion renei[&&NHX:TOL=131433],bembidion rugosellum[&&NHX:TOL=131434],bembidion scitulum[&&NHX:TOL=131435],bembidion stricticolle[&&NHX:TOL=131436])bembidion pacmophena[&&NHX:TOL=23664])bembidion pacmophena complex[&&NHX:TOL=133838],(bembidion badakshanicum[&&NHX:TOL=132408],bembidion bucephalum[&&NHX:TOL=132409],bembidion ghilarovi[&&NHX:TOL=132410],bembidion glasunovi[&&NHX:TOL=132411],bembidion himalayanum[&&NHX:TOL=132412],bembidion jacobsoni[&&NHX:TOL=132413],bembidion kryzhanovskii[&&NHX:TOL=132414],bembidion kurram[&&NHX:TOL=132415],bembidion mesasiaticum[&&NHX:TOL=132416],bembidion mikitjukovi[&&NHX:TOL=132417],bembidion petrimagni[&&NHX:TOL=132418],bembidion platypterum[&&NHX:TOL=132419],bembidion punctulipenne[&&NHX:TOL=132420],bembidion roborowskii[&&NHX:TOL=132421],bembidion rufum[&&NHX:TOL=132422],bembidion zlotini[&&NHX:TOL=132423])bembidion pamirium[&&NHX:TOL=23709],bembidion heyrovskyi[&&NHX:TOL=23694],bembidion chinense[&&NHX:TOL=23674],(bembidion adygorum[&&NHX:TOL=132063],bembidion brunnicorne[&&NHX:TOL=132064],bembidion castaneipenne[&&NHX:TOL=132065],(bembidion dalmatinum dalmatinum[&&NHX:TOL=132067],bembidion dalmatinum haupti[&&NHX:TOL=132068],bembidion dalmatinum hybridum[&&NHX:TOL=132069],bembidion dalmatinum levantinum[&&NHX:TOL=132070],bembidion dalmatinum rufoguttatum[&&NHX:TOL=132071])bembidion dalmatinum[&&NHX:TOL=132066],(bembidion deletum deletum[&&NHX:TOL=132073],bembidion deletum schulerianum[&&NHX:TOL=132074])bembidion deletum[&&NHX:TOL=132072],bembidion dostali[&&NHX:TOL=132075],bembidion florentinum[&&NHX:TOL=132076],bembidion fraxator[&&NHX:TOL=132077],bembidion fuliginosum[&&NHX:TOL=132078],bembidion gautieri[&&NHX:TOL=132079],(bembidion grandipenne grandipenne[&&NHX:TOL=132081],bembidion grandipenne bulgardagense[&&NHX:TOL=132082],bembidion grandipenne freyi[&&NHX:TOL=132083])bembidion grandipenne[&&NHX:TOL=132080],bembidion hayachinense[&&NHX:TOL=132084],bembidion hikosanum[&&NHX:TOL=132085],bembidion imereticum[&&NHX:TOL=132086],bembidion italicum[&&NHX:TOL=132087],bembidion kulzeri[&&NHX:TOL=132088],bembidion lacrimans[&&NHX:TOL=132089],bembidion lacunarium[&&NHX:TOL=132090],bembidion lafertei[&&NHX:TOL=132091],bembidion latinum[&&NHX:TOL=132092],bembidion lirykense[&&NHX:TOL=132093],bembidion lulinense[&&NHX:TOL=132094],bembidion maroccanum[&&NHX:TOL=132095],(bembidion milleri milleri[&&NHX:TOL=132097],bembidion milleri carpathicum[&&NHX:TOL=132098],bembidion milleri kulti[&&NHX:TOL=132099],bembidion milleri pseudocarpathicum[&&NHX:TOL=132100],bembidion milleri vogesiacum[&&NHX:TOL=132101])bembidion milleri[&&NHX:TOL=132096],bembidion morvanianum[&&NHX:TOL=132102],bembidion olegleonidovici[&&NHX:TOL=132103],bembidion pallidicorne[&&NHX:TOL=132104],bembidion phryganobium[&&NHX:TOL=132105],bembidion platynoides[&&NHX:TOL=132106],bembidion stephensii[&&NHX:TOL=132107],bembidion texanum[&&NHX:TOL=132108],(bembidion weiratherianum weiratherianum[&&NHX:TOL=132110],bembidion weiratherianum cilicicum[&&NHX:TOL=132111],bembidion weiratherianum syriacum[&&NHX:TOL=132112])bembidion weiratherianum[&&NHX:TOL=132109])bembidion peryphanes[&&NHX:TOL=355],(bembidion caligatum[&&NHX:TOL=131888],bembidion lucifugum[&&NHX:TOL=131889],(bembidion monticola monticola[&&NHX:TOL=131891],bembidion monticola makolskii[&&NHX:TOL=131892],bembidion monticola ponticum[&&NHX:TOL=131893])bembidion monticola[&&NHX:TOL=131890])bembidion peryphiolus[&&NHX:TOL=23699],(bembidion ephippiger[&&NHX:TOL=132313],bembidion salinarium[&&NHX:TOL=132314],bembidion bakeri[&&NHX:TOL=132315],bembidion bryanti[&&NHX:TOL=132316],bembidion dammermani[&&NHX:TOL=132317],bembidion hammondianum[&&NHX:TOL=132318],bembidion linauense[&&NHX:TOL=132319],bembidion storkianum[&&NHX:TOL=132320],bembidion aegrum[&&NHX:TOL=132321],bembidion amurense[&&NHX:TOL=132322],bembidion angulicolle[&&NHX:TOL=132323],bembidion bandotaro[&&NHX:TOL=132324],bembidion chakrata[&&NHX:TOL=132325],bembidion charon[&&NHX:TOL=132326],bembidion chiriqui[&&NHX:TOL=132327],bembidion citulum[&&NHX:TOL=132328],bembidion ciudadense[&&NHX:TOL=132329],bembidion daviacum[&&NHX:TOL=132330],bembidion diabola[&&NHX:TOL=132331],bembidion dimidiatum[&&NHX:TOL=132332],bembidion edwardsi[&&NHX:TOL=132333],bembidion ehikoense[&&NHX:TOL=132334],bembidion eutherum[&&NHX:TOL=132335],bembidion farsense[&&NHX:TOL=132336],bembidion fassatii[&&NHX:TOL=132337],bembidion grapii[&&NHX:TOL=132338],bembidion hirtipalposum[&&NHX:TOL=132339],bembidion hoberlandti[&&NHX:TOL=132340],bembidion jeanneli[&&NHX:TOL=132341],bembidion kamikochii[&&NHX:TOL=132342],bembidion klapperichi[&&NHX:TOL=132343],bembidion lavernae[&&NHX:TOL=132344],bembidion macrogonum[&&NHX:TOL=132345],bembidion mexicanum[&&NHX:TOL=132346],bembidion ohkurai[&&NHX:TOL=132347],bembidion parepum[&&NHX:TOL=132348],bembidion pernotum[&&NHX:TOL=66460],bembidion phaedrum[&&NHX:TOL=132349],bembidion pseudolucillum[&&NHX:TOL=132350],bembidion quetzal[&&NHX:TOL=132351],(bembidion radians radians[&&NHX:TOL=132353],bembidion radians puetzi[&&NHX:TOL=132354],bembidion radians shaanxianum[&&NHX:TOL=132355])bembidion radians[&&NHX:TOL=132352],bembidion sanatum[&&NHX:TOL=132357],bembidion satellites[&&NHX:TOL=132358],bembidion shunichii[&&NHX:TOL=132359],bembidion sjoelanderi[&&NHX:TOL=132360],bembidion spectans[&&NHX:TOL=132361],bembidion sterbai[&&NHX:TOL=132362],bembidion submaculatum[&&NHX:TOL=374],bembidion torosiense[&&NHX:TOL=133863],bembidion trajectum[&&NHX:TOL=132363],bembidion umeyai[&&NHX:TOL=132364],bembidion vaillanti[&&NHX:TOL=132365],bembidion vernale[&&NHX:TOL=132366],bembidion vulcanium[&&NHX:TOL=132367],bembidion wutaishanense[&&NHX:TOL=132368])bembidion peryphodes[&&NHX:TOL=23705],(bembidion clarum[&&NHX:TOL=132369],bembidion endymion[&&NHX:TOL=132370],bembidion eurydice[&&NHX:TOL=132371])bembidion peryphophila[&&NHX:TOL=23707],((bembidion abbreviatum abbreviatum[&&NHX:TOL=132176],bembidion abbreviatum longicrum[&&NHX:TOL=132177],bembidion abbreviatum pulpani[&&NHX:TOL=132178],bembidion abbreviatum uvidum[&&NHX:TOL=132179])bembidion abbreviatum[&&NHX:TOL=132175],bembidion actuosum[&&NHX:TOL=132180],bembidion alaf[&&NHX:TOL=132181],bembidion alticola[&&NHX:TOL=132182],bembidion andreae[&&NHX:TOL=132183],(bembidion asiaeminoris asiaeminoris[&&NHX:TOL=132185],bembidion sevanense asiorum[&&NHX:TOL=132186])bembidion asiaeminoris[&&NHX:TOL=132184],bembidion bracculatum[&&NHX:TOL=132187],bembidion brittoni[&&NHX:TOL=132188],bembidion bruxellense[&&NHX:TOL=132189],bembidion captivorum[&&NHX:TOL=132190],bembidion consanguineum[&&NHX:TOL=132191],bembidion cordicolle[&&NHX:TOL=132192],(bembidion cruciatum cruciatum[&&NHX:TOL=132194],bembidion cruciatum albanicum[&&NHX:TOL=132195],bembidion cruciatum anglicanum[&&NHX:TOL=132196],bembidion cruciatum atlantis[&&NHX:TOL=132197],bembidion cruciatum baenningeri[&&NHX:TOL=132198],bembidion cruciatum bualei[&&NHX:TOL=132199],bembidion cruciatum dromioides[&&NHX:TOL=132200],bembidion cruciatum espinassei[&&NHX:TOL=132201],bembidion cruciatum hummleri[&&NHX:TOL=132202],bembidion cruciatum liberum[&&NHX:TOL=132203],bembidion cruciatum polonicum[&&NHX:TOL=132204],bembidion cruciatum quadriflammeum[&&NHX:TOL=132205],bembidion cruciatum subtypicum[&&NHX:TOL=132206],bembidion cruciatum tyrrhenicum[&&NHX:TOL=132207],bembidion cruciatum vorax[&&NHX:TOL=132208],bembidion cruciatum xanthomum[&&NHX:TOL=132209])bembidion cruciatum[&&NHX:TOL=132193],bembidion dauricum[&&NHX:TOL=132210],bembidion dilutipenne[&&NHX:TOL=132211],(bembidion distinguendum distinguendum[&&NHX:TOL=132213],bembidion distinguendum arrisi[&&NHX:TOL=132214],bembidion distinguendum lindrothi[&&NHX:TOL=132215],bembidion distinguendum meyeri[&&NHX:TOL=132216],bembidion distinguendum rupestroides[&&NHX:TOL=132217])bembidion distinguendum[&&NHX:TOL=132212],bembidion femoratum[&&NHX:TOL=132218],bembidion franzi[&&NHX:TOL=132219],bembidion gersdorfi[&&NHX:TOL=132220],(bembidion gilgit gilgit[&&NHX:TOL=132222],bembidion gilgit nuristanicum[&&NHX:TOL=132223],bembidion gilgit peratrum[&&NHX:TOL=132224])bembidion gilgit[&&NHX:TOL=132221],bembidion havelkai[&&NHX:TOL=132225],bembidion hispanicum[&&NHX:TOL=132226],bembidion incognitum[&&NHX:TOL=132227],(bembidion insidiosum insidiosum[&&NHX:TOL=132229],bembidion insidiosum betegara[&&NHX:TOL=132230],bembidion insidiosum clops[&&NHX:TOL=132231],bembidion insidiosum holdhausi[&&NHX:TOL=132232],bembidion insidiosum ixion[&&NHX:TOL=132233],bembidion insidiosum luntaka[&&NHX:TOL=132234])bembidion insidiosum[&&NHX:TOL=132228],(bembidion jedlickai jedlickai[&&NHX:TOL=132236],bembidion jedlickai turkestanicum[&&NHX:TOL=132237])bembidion jedlickai[&&NHX:TOL=132235],bembidion klapperichianum[&&NHX:TOL=132238],bembidion koikei[&&NHX:TOL=132239],bembidion kuznetsovi[&&NHX:TOL=132240],(bembidion ladakense ladakense[&&NHX:TOL=132242],bembidion ladakense baumi[&&NHX:TOL=132243],bembidion ladakense hazara[&&NHX:TOL=132244],bembidion ladakense naltarense[&&NHX:TOL=132245])bembidion ladakense[&&NHX:TOL=132241],bembidion languens[&&NHX:TOL=132246],(bembidion maritimum maritimum[&&NHX:TOL=132248],bembidion maritimum lusitanicum[&&NHX:TOL=132249])bembidion maritimum[&&NHX:TOL=132247],bembidion marussii[&&NHX:TOL=132250],bembidion massaicum[&&NHX:TOL=132251],bembidion misellum[&&NHX:TOL=132252],bembidion morawitzi[&&NHX:TOL=132253],bembidion nevadense[&&NHX:TOL=132254],(bembidion obscurellum obscurellum[&&NHX:TOL=132256],bembidion obscurellum corporaali[&&NHX:TOL=132257],bembidion obscurellum fumipenne[&&NHX:TOL=132258],bembidion obscurellum insperatum[&&NHX:TOL=132259],bembidion obscurellum thibeticum[&&NHX:TOL=132260],bembidion obscurellum turanicum[&&NHX:TOL=132261])bembidion obscurellum[&&NHX:TOL=132255],bembidion olemartini[&&NHX:TOL=132262],bembidion persicum[&&NHX:TOL=132263],(bembidion petrosum petrosum[&&NHX:TOL=132265],bembidion petrosum attuense[&&NHX:TOL=132266])bembidion petrosum[&&NHX:TOL=132264],bembidion plagiatum[&&NHX:TOL=132267],(bembidion poppii poppii[&&NHX:TOL=132269],bembidion poppii eugenes[&&NHX:TOL=132270],bembidion poppii pohlai[&&NHX:TOL=132271],bembidion poppii schalleri[&&NHX:TOL=132272])bembidion poppii[&&NHX:TOL=132268],bembidion pseudosiebkei[&&NHX:TOL=132273],bembidion psilodorum[&&NHX:TOL=132274],bembidion reichardti[&&NHX:TOL=132275],bembidion rickmersi[&&NHX:TOL=132276],bembidion rubidum[&&NHX:TOL=132277],bembidion rupicola[&&NHX:TOL=132278],bembidion satelles[&&NHX:TOL=132279],bembidion scottustulatum[&&NHX:TOL=132280],(bembidion scythicum scythicum[&&NHX:TOL=132282],bembidion scythicum imitator[&&NHX:TOL=132283])bembidion scythicum[&&NHX:TOL=132281],(bembidion sejunctum sejunctum[&&NHX:TOL=132285],bembidion sejunctum semiaureum[&&NHX:TOL=132286])bembidion sejunctum[&&NHX:TOL=132284],bembidion sillemi[&&NHX:TOL=132287],bembidion sogdianum[&&NHX:TOL=132288],bembidion solskyi[&&NHX:TOL=132289],(bembidion straussi straussi[&&NHX:TOL=132291],bembidion straussi gurwani[&&NHX:TOL=132292],bembidion straussi iridicyaneum[&&NHX:TOL=132293],bembidion straussi iridipiceum[&&NHX:TOL=132294])bembidion straussi[&&NHX:TOL=132290],bembidion striola[&&NHX:TOL=132295],bembidion subangustatum[&&NHX:TOL=132296],(bembidion subcostatum subcostatum[&&NHX:TOL=132298],bembidion subcostatum allepense[&&NHX:TOL=132299],bembidion subcostatum creticum[&&NHX:TOL=132300],bembidion subcostatum javurkovae[&&NHX:TOL=132301],bembidion subcostatum spartanum[&&NHX:TOL=132302],bembidion subcostatum vau[&&NHX:TOL=132303])bembidion subcostatum[&&NHX:TOL=132297],bembidion subimpressum[&&NHX:TOL=132304],bembidion sulcicolle[&&NHX:TOL=132305],bembidion taiyuanense[&&NHX:TOL=132306],(bembidion tetracolum tetracolum[&&NHX:TOL=132308],bembidion tetracolum brachypteron[&&NHX:TOL=132309],bembidion tetracolum pfefferi[&&NHX:TOL=132310],bembidion tetracolum uralense[&&NHX:TOL=132311])bembidion tetracolum[&&NHX:TOL=132307],bembidion transversale[&&NHX:TOL=66457],bembidion yukonum[&&NHX:TOL=132312])bembidion peryphus[&&NHX:TOL=23704],(bembidion andrewesi[&&NHX:TOL=131540],bembidion brancuccii[&&NHX:TOL=131541],bembidion cupido[&&NHX:TOL=131542],bembidion daliangi[&&NHX:TOL=131543],bembidion exquisitum[&&NHX:TOL=131544],bembidion goetzi[&&NHX:TOL=131545],bembidion hansi[&&NHX:TOL=131546],bembidion leptaleum[&&NHX:TOL=131547],bembidion perditum[&&NHX:TOL=131548])bembidion philochthemphanes[&&NHX:TOL=23679],((bembidion aeneum aeneum[&&NHX:TOL=131550],bembidion aeneum athalassicum[&&NHX:TOL=131551])bembidion aeneum[&&NHX:TOL=131549],bembidion antoinei[&&NHX:TOL=131552],bembidion baicalicum[&&NHX:TOL=131553],bembidion biguttatum[&&NHX:TOL=131554],bembidion cumanum[&&NHX:TOL=131555],bembidion decolor[&&NHX:TOL=131556],bembidion ellipticocurtum[&&NHX:TOL=131557],bembidion eregliense[&&NHX:TOL=131558],(bembidion escherichi escherichi[&&NHX:TOL=131560],bembidion escherichi erratum[&&NHX:TOL=131561],bembidion escherichi latiore[&&NHX:TOL=131562],bembidion escherichi paganettii[&&NHX:TOL=131563],bembidion escherichi subatratum[&&NHX:TOL=131564])bembidion escherichi[&&NHX:TOL=131559],bembidion fumatum[&&NHX:TOL=131565],bembidion gazella[&&NHX:TOL=131566],bembidion guadarramense[&&NHX:TOL=131567],bembidion guttula[&&NHX:TOL=131568],bembidion guttuloides[&&NHX:TOL=131569],bembidion hustachei[&&NHX:TOL=131570],bembidion inoptatum[&&NHX:TOL=131571],bembidion iricolor[&&NHX:TOL=131572],bembidion jacksoniense[&&NHX:TOL=131573],bembidion judaicum[&&NHX:TOL=131574],bembidion luigionii[&&NHX:TOL=131575],bembidion lunulatum[&&NHX:TOL=131576],bembidion lycicum[&&NHX:TOL=131577],bembidion mannerheimii[&&NHX:TOL=131578],(bembidion neresheimeri neresheimeri[&&NHX:TOL=131580],bembidion neresheimeri dagense[&&NHX:TOL=131581])bembidion neresheimeri[&&NHX:TOL=131579],bembidion netolitzkyi[&&NHX:TOL=131582],bembidion pallidiveste[&&NHX:TOL=131583],bembidion subplagiatum[&&NHX:TOL=131584],bembidion vicinum[&&NHX:TOL=131585],bembidion zaitzevi[&&NHX:TOL=131586])bembidion philochthus[&&NHX:TOL=23680],(bembidion abdelkrimi[&&NHX:TOL=131309],bembidion demidenkoae[&&NHX:TOL=131310],bembidion incommodum[&&NHX:TOL=131311],bembidion liliputanum[&&NHX:TOL=131312],bembidion minoum[&&NHX:TOL=131313],bembidion obtusum[&&NHX:TOL=131314],bembidion phoeniceum[&&NHX:TOL=131315],bembidion rectangulum[&&NHX:TOL=131316],bembidion tethys[&&NHX:TOL=131317])bembidion phyla[&&NHX:TOL=23648],((bembidion aeruginosum[&&NHX:TOL=131689],bembidion arcticum[&&NHX:TOL=131690],bembidion brachythorax[&&NHX:TOL=131691],bembidion breve[&&NHX:TOL=131692],bembidion complanulum[&&NHX:TOL=131693],bembidion compressum[&&NHX:TOL=131694],bembidion crenulatum[&&NHX:TOL=131695],bembidion daisetsuzanum[&&NHX:TOL=131696],bembidion difficile[&&NHX:TOL=131697],bembidion elatum[&&NHX:TOL=131698],bembidion farkaci[&&NHX:TOL=131699],bembidion farrarae[&&NHX:TOL=131700],(bembidion fellmanni fellmanni[&&NHX:TOL=131702],bembidion fellmanni deubeli[&&NHX:TOL=131703])bembidion fellmanni[&&NHX:TOL=131701],bembidion fujiyamai[&&NHX:TOL=131704],bembidion haruspex[&&NHX:TOL=131705],bembidion improvidens[&&NHX:TOL=131706],bembidion komareki[&&NHX:TOL=131707],bembidion kuprianovii[&&NHX:TOL=131708],bembidion laxatum[&&NHX:TOL=131709],bembidion manningense[&&NHX:TOL=131710],bembidion neocoerulescens[&&NHX:TOL=131711],bembidion nigrocoeruleum[&&NHX:TOL=131712],bembidion nuncaestimatum[&&NHX:TOL=131713],bembidion occultator[&&NHX:TOL=131714],bembidion placeranum[&&NHX:TOL=131715],bembidion quadrifoveolatum[&&NHX:TOL=131716],bembidion rosslandicum[&&NHX:TOL=131717],bembidion solanum[&&NHX:TOL=131718],(bembidion tetraporum tetraporum[&&NHX:TOL=131720],bembidion tetraporum kurokawense[&&NHX:TOL=131721])bembidion tetraporum[&&NHX:TOL=131719],bembidion viator[&&NHX:TOL=131722])bembidion plataphodes[&&NHX:TOL=23688],(bembidion altaicum[&&NHX:TOL=131723],bembidion asiaticum[&&NHX:TOL=131724],bembidion basicorne[&&NHX:TOL=131725],bembidion birulai[&&NHX:TOL=131726],bembidion carolinense[&&NHX:TOL=131727],bembidion coelestinum[&&NHX:TOL=131728],bembidion curtulatum[&&NHX:TOL=131729],bembidion darlingtonicum[&&NHX:TOL=131730],bembidion depressiusculum[&&NHX:TOL=131731],bembidion falsum[&&NHX:TOL=131732],(bembidion gebleri gebleri[&&NHX:TOL=131734],bembidion gebleri nakanei[&&NHX:TOL=131735],bembidion gebleri persuasum[&&NHX:TOL=131736],bembidion gebleri turbatum[&&NHX:TOL=131737])bembidion gebleri[&&NHX:TOL=131733],bembidion gordoni[&&NHX:TOL=131738],bembidion gratiosum[&&NHX:TOL=131739],bembidion habui[&&NHX:TOL=131740],bembidion hingstoni[&&NHX:TOL=131741],bembidion hiranoi[&&NHX:TOL=131742],bembidion hyperboraeorum[&&NHX:TOL=131743],bembidion infuscatipenne[&&NHX:TOL=131744],bembidion kalumae[&&NHX:TOL=131745],bembidion kishimotoi[&&NHX:TOL=131746],bembidion lucillum[&&NHX:TOL=131747],bembidion maeklini[&&NHX:TOL=131748],bembidion nivicola[&&NHX:TOL=131749],bembidion ohtsukai[&&NHX:TOL=131750],bembidion oppressum[&&NHX:TOL=131751],bembidion persephone[&&NHX:TOL=131752],bembidion pfizenmayeri[&&NHX:TOL=131753],bembidion planatum[&&NHX:TOL=131754],bembidion planiusculum[&&NHX:TOL=131755],bembidion pliculatum[&&NHX:TOL=131756],bembidion prasinum[&&NHX:TOL=131757],bembidion pluto[&&NHX:TOL=131758],bembidion rufinum[&&NHX:TOL=131759],(bembidion rusticum rusticum[&&NHX:TOL=131761],bembidion rusticum lenensoides[&&NHX:TOL=131762])bembidion rusticum[&&NHX:TOL=131760],bembidion shikokuense[&&NHX:TOL=131763],bembidion shilenkovi[&&NHX:TOL=131764],bembidion sierricola[&&NHX:TOL=131765],bembidion stillaguamish[&&NHX:TOL=131766],(bembidion sulcipenne sulcipenne[&&NHX:TOL=131768],bembidion sulcipenne hyperboroides[&&NHX:TOL=131769],bembidion sulcipenne prasinoides[&&NHX:TOL=131770])bembidion sulcipenne[&&NHX:TOL=131767],bembidion takasagonis[&&NHX:TOL=131771],bembidion vandykei[&&NHX:TOL=131772],bembidion vespertinum[&&NHX:TOL=131773],bembidion watanabei[&&NHX:TOL=131774],bembidion yoshikawai[&&NHX:TOL=131775])bembidion plataphus[&&NHX:TOL=23687])bembidion plataphus complex[&&NHX:TOL=133821],bembidion polites[&&NHX:TOL=23702],((bembidion basistriatum[&&NHX:TOL=131327],bembidion beesoni[&&NHX:TOL=131328],(bembidion bipunctatum bipunctatum[&&NHX:TOL=131330],bembidion bipunctatum alii[&&NHX:TOL=131331],bembidion bipunctatum biincisum[&&NHX:TOL=131332],bembidion bipunctatum laevifrons[&&NHX:TOL=131333],bembidion bipunctatum nivale[&&NHX:TOL=131334],bembidion bipunctatum pyritosum[&&NHX:TOL=131335],bembidion bipunctatum tectimundi[&&NHX:TOL=131336])bembidion bipunctatum[&&NHX:TOL=131329],bembidion capito[&&NHX:TOL=131337],bembidion flavoposticatum[&&NHX:TOL=131338],bembidion idriae[&&NHX:TOL=131339],bembidion laetum[&&NHX:TOL=131340],(bembidion quadrifossulatum quadrifossulatum[&&NHX:TOL=131342],bembidion quadrifossulatum coelesyriae[&&NHX:TOL=131343])bembidion quadrifossulatum[&&NHX:TOL=131341],bembidion trebinjense[&&NHX:TOL=131344])bembidion testedium[&&NHX:TOL=23656],(bembidion compactum[&&NHX:TOL=131318],bembidion coreanum[&&NHX:TOL=131319],bembidion davidi[&&NHX:TOL=131320],bembidion dufourii[&&NHX:TOL=131321],bembidion marthae[&&NHX:TOL=131322],(bembidion punctulatum punctulatum[&&NHX:TOL=131324],bembidion punctulatum bracteonoides[&&NHX:TOL=131325],bembidion punctulatum obscuripes[&&NHX:TOL=131326])bembidion punctulatum[&&NHX:TOL=131323])bembidion princidium[&&NHX:TOL=23655],bembidion ruficolle[&&NHX:TOL=23657],(bembidion crotchii[&&NHX:TOL=131345],bembidion kuesteri[&&NHX:TOL=131346],bembidion lachnophoroides[&&NHX:TOL=131347],bembidion pallidipenne[&&NHX:TOL=131348],bembidion paulinoi[&&NHX:TOL=131349])bembidion actedium[&&NHX:TOL=23658])bembidion princidium complex[&&NHX:TOL=133819],(bembidion cupreolum[&&NHX:TOL=131298],bembidion lamproides[&&NHX:TOL=131299])bembidion pseudometallina[&&NHX:TOL=23651],(bembidion dicksoniae[&&NHX:TOL=132580],bembidion evanescens[&&NHX:TOL=132581],bembidion fossor[&&NHX:TOL=132582],bembidion gemmulipennis[&&NHX:TOL=132583],bembidion grayanus[&&NHX:TOL=132584],bembidion nubigena[&&NHX:TOL=132585],bembidion rufosuffusus[&&NHX:TOL=132586],bembidion sublimbatus[&&NHX:TOL=132587],bembidion trechoides[&&NHX:TOL=132588])bembidion pseudophilochthus[&&NHX:TOL=132579],bembidion derbesi[&&NHX:TOL=23677],(bembidion amoenum[&&NHX:TOL=587],bembidion botezati[&&NHX:TOL=588],bembidion carnifex[&&NHX:TOL=589],bembidion chaudoirii[&&NHX:TOL=578],bembidion convexiusculum[&&NHX:TOL=590],bembidion convexulum[&&NHX:TOL=582],bembidion dagestanum[&&NHX:TOL=591],bembidion dormeyeri[&&NHX:TOL=592],bembidion gassneri[&&NHX:TOL=593],bembidion gilvipes[&&NHX:TOL=577],bembidion guttulatum[&&NHX:TOL=594],bembidion heydeni[&&NHX:TOL=595],bembidion irroratum[&&NHX:TOL=596],bembidion mandarin[&&NHX:TOL=597],bembidion morulum[&&NHX:TOL=584],bembidion muscicola[&&NHX:TOL=586],bembidion ovulum[&&NHX:TOL=598],bembidion praticola[&&NHX:TOL=585],bembidion roosevelti[&&NHX:TOL=131518],bembidion rubiginosum[&&NHX:TOL=580],bembidion schueppelii[&&NHX:TOL=131519],bembidion semicinctum[&&NHX:TOL=583],bembidion steini[&&NHX:TOL=599],bembidion variola[&&NHX:TOL=600],bembidion variolatum[&&NHX:TOL=601])bembidion semicampa[&&NHX:TOL=344],bembidion aliense[&&NHX:TOL=23682],(bembidion aspericolle[&&NHX:TOL=131492],bembidion subfasciatum[&&NHX:TOL=131493])bembidion talanes[&&NHX:TOL=23670],(bembidion avaricum[&&NHX:TOL=132154],bembidion consummatum[&&NHX:TOL=132155],bembidion delerei[&&NHX:TOL=132156],(bembidion kaschmirense kaschmirense[&&NHX:TOL=132158],bembidion kaschmirense dux[&&NHX:TOL=132159],bembidion kaschmirense ochropus[&&NHX:TOL=132160])bembidion kaschmirense[&&NHX:TOL=132157],(bembidion mckinleyi mckinleyi[&&NHX:TOL=132162],bembidion mckinleyi carneum[&&NHX:TOL=132163],bembidion mckinleyi scandicum[&&NHX:TOL=132164])bembidion mckinleyi[&&NHX:TOL=132161],bembidion ovalipenne[&&NHX:TOL=132165],bembidion pseudoconsumatum[&&NHX:TOL=132166],(bembidion terminale terminale[&&NHX:TOL=132168],bembidion terminale confinis[&&NHX:TOL=132169],bembidion terminale dardum[&&NHX:TOL=132170],bembidion terminale kirgisorum[&&NHX:TOL=132171],bembidion terminale pulcherrimum[&&NHX:TOL=132172],bembidion terminale tujngoli[&&NHX:TOL=132173])bembidion terminale[&&NHX:TOL=132167],bembidion vitalisi[&&NHX:TOL=132174])bembidion terminophanes[&&NHX:TOL=23703],(bembidion carpetanum[&&NHX:TOL=132372],bembidion corsicum[&&NHX:TOL=132373],bembidion dacicum[&&NHX:TOL=132374],bembidion glaciale[&&NHX:TOL=132375],(bembidion jacqueti jacqueti[&&NHX:TOL=132377],bembidion jacqueti apenninum[&&NHX:TOL=132378])bembidion jacqueti[&&NHX:TOL=132376],bembidion julianum[&&NHX:TOL=132379],(bembidion magellense magellense[&&NHX:TOL=132381],bembidion magellense alpicola[&&NHX:TOL=132382])bembidion magellense[&&NHX:TOL=132380],bembidion montanum[&&NHX:TOL=132383],(bembidion pyrenaeum pyrenaeum[&&NHX:TOL=132385],bembidion pyrenaeum poenini[&&NHX:TOL=132386])bembidion pyrenaeum[&&NHX:TOL=132384],bembidion rhaeticum[&&NHX:TOL=132387],(bembidion armeniacum armeniacum[&&NHX:TOL=132389],bembidion armeniacum kokandicum[&&NHX:TOL=132390])bembidion armeniacum[&&NHX:TOL=132388],bembidion braminum[&&NHX:TOL=132391],(bembidion gagates gagates[&&NHX:TOL=132393],bembidion gagates sindicum[&&NHX:TOL=132394])bembidion gagates[&&NHX:TOL=132392],bembidion kunarense[&&NHX:TOL=132395],bembidion montei[&&NHX:TOL=132396],bembidion seminskiense[&&NHX:TOL=132397],bembidion tizianoi[&&NHX:TOL=132398],(bembidion validum validum[&&NHX:TOL=132400],bembidion validum marquardti[&&NHX:TOL=132401])bembidion validum[&&NHX:TOL=132399],bembidion commotum[&&NHX:TOL=132402],bembidion modocianum[&&NHX:TOL=132403],bembidion nebraskense[&&NHX:TOL=132404],bembidion obscuripenne[&&NHX:TOL=132405],bembidion perbrevicolle[&&NHX:TOL=132406],bembidion ulkei[&&NHX:TOL=132407])bembidion testediolum[&&NHX:TOL=23708],(bembidion ajmonis ajmonis[&&NHX:TOL=131873],bembidion ajmonis staveni[&&NHX:TOL=131874])bembidion ajmonis[&&NHX:TOL=23706],(bembidion iridescens[&&NHX:TOL=131685],bembidion simplex[&&NHX:TOL=131686],bembidion trechiforme[&&NHX:TOL=131687])bembidion trechonepha[&&NHX:TOL=23685],(bembidion acutifrons[&&NHX:TOL=131504],bembidion ampliceps[&&NHX:TOL=131505],bembidion anguliferum[&&NHX:TOL=131506],bembidion atripes[&&NHX:TOL=131507],bembidion canadianum[&&NHX:TOL=131508],bembidion clemens[&&NHX:TOL=131509],bembidion concretum[&&NHX:TOL=131510],bembidion connivens[&&NHX:TOL=131511],bembidion doris[&&NHX:TOL=131512],bembidion foraticolle[&&NHX:TOL=131513],bembidion fortestriatum[&&NHX:TOL=67201],bembidion frontale[&&NHX:TOL=67202],bembidion politum[&&NHX:TOL=131514],bembidion pseudocautum[&&NHX:TOL=131515],bembidion scenicum[&&NHX:TOL=131516],bembidion siticum[&&NHX:TOL=131517])bembidion trepanedoris[&&NHX:TOL=23676],(bembidion articulatum[&&NHX:TOL=131495],bembidion bedelianum[&&NHX:TOL=131496],(bembidion maculatum maculatum[&&NHX:TOL=131498],bembidion maculatum atripenne[&&NHX:TOL=131499],bembidion maculatum serbicum[&&NHX:TOL=131500])bembidion maculatum[&&NHX:TOL=131497],bembidion octomaculatum[&&NHX:TOL=131501],bembidion sengleti[&&NHX:TOL=131502],bembidion xanthocerum[&&NHX:TOL=131503])bembidion trepanes[&&NHX:TOL=23675],(bembidion deplanatum[&&NHX:TOL=131783],bembidion eurygonum[&&NHX:TOL=131784],bembidion fugax[&&NHX:TOL=131785],bembidion grandiceps[&&NHX:TOL=131786],bembidion hysteron[&&NHX:TOL=131787],bembidion inaense[&&NHX:TOL=131788],bembidion infans[&&NHX:TOL=131789],bembidion kara[&&NHX:TOL=131790],bembidion liparum[&&NHX:TOL=131791],bembidion lissonotoides[&&NHX:TOL=131792],bembidion lissonotum[&&NHX:TOL=131793],bembidion miwai[&&NHX:TOL=131794],bembidion oxyglymma[&&NHX:TOL=131795],bembidion planum[&&NHX:TOL=67199],bembidion proteron[&&NHX:TOL=131796],bembidion rolandi[&&NHX:TOL=67200],bembidion taiwanum[&&NHX:TOL=131797],bembidion tambra[&&NHX:TOL=131798])bembidion trichoplataphus[&&NHX:TOL=23693],(bembidion musae[&&NHX:TOL=131350],bembidion orbiferum[&&NHX:TOL=131351])bembidion zeactedium[&&NHX:TOL=22965],(bembidion alacre[&&NHX:TOL=696],bembidion albescens[&&NHX:TOL=695],bembidion chalmeri[&&NHX:TOL=699],bembidion embersoni[&&NHX:TOL=698],bembidion tillyardi[&&NHX:TOL=697])bembidion zecillenus[&&NHX:TOL=198],(bembidion anchonoderus[&&NHX:TOL=131300],bembidion chalceipes[&&NHX:TOL=131301],bembidion hokitikense[&&NHX:TOL=131302],bembidion parviceps[&&NHX:TOL=131303],bembidion solitarium[&&NHX:TOL=131304],bembidion stewartense[&&NHX:TOL=131305],bembidion tekapoense[&&NHX:TOL=131306],bembidion urewerense[&&NHX:TOL=131307],bembidion wanakense[&&NHX:TOL=131308])bembidion zemetallina[&&NHX:TOL=22967],bembidion callipeplum[&&NHX:TOL=23711],bembidion actuarium[&&NHX:TOL=22966],(bembidion charile[&&NHX:TOL=131677],bembidion dehiscens[&&NHX:TOL=131678],bembidion granuliferum[&&NHX:TOL=131679],(bembidion maorinum maorinum[&&NHX:TOL=131681],bembidion maorinum levatum[&&NHX:TOL=131682])bembidion maorinum[&&NHX:TOL=131680],bembidion tairuense[&&NHX:TOL=131683],bembidion townsendi[&&NHX:TOL=131684])bembidion zeplataphus[&&NHX:TOL=131676],bembidion wickhami[&&NHX:TOL=132535],(bembidion chlorostictum[&&NHX:TOL=132494],bembidion cillenoides[&&NHX:TOL=132495],bembidion cordillerae[&&NHX:TOL=132496],bembidion cubanum[&&NHX:TOL=132498],bembidion cymindulum[&&NHX:TOL=132499],bembidion darlingtoni[&&NHX:TOL=132500],bembidion discoideum[&&NHX:TOL=132501],bembidion duvali[&&NHX:TOL=132502],bembidion equatoriale[&&NHX:TOL=132503],bembidion foveatum[&&NHX:TOL=132505],bembidion franiae[&&NHX:TOL=132506],bembidion holconotum[&&NHX:TOL=132507],bembidion irregulare[&&NHX:TOL=132509],bembidion ixtatan[&&NHX:TOL=132510],bembidion jamaicense[&&NHX:TOL=132511],bembidion leve[&&NHX:TOL=132512],bembidion limatum[&&NHX:TOL=132513],bembidion msignatum[&&NHX:TOL=132514],bembidion nahuala[&&NHX:TOL=132516],bembidion peruvianum[&&NHX:TOL=132517],bembidion peterseni[&&NHX:TOL=132518],bembidion pokharense[&&NHX:TOL=132519],bembidion portoricense[&&NHX:TOL=132520],bembidion proportionale[&&NHX:TOL=132521],bembidion psuchrum[&&NHX:TOL=132522],bembidion purulha[&&NHX:TOL=132523],bembidion putzeysi[&&NHX:TOL=132524],bembidion rucillum[&&NHX:TOL=132525],bembidion ryei[&&NHX:TOL=132526],bembidion sokolowskii[&&NHX:TOL=132528],bembidion speciense[&&NHX:TOL=132529],bembidion tesselatum[&&NHX:TOL=132531],bembidion tunuyanense[&&NHX:TOL=132532],bembidion turquinum[&&NHX:TOL=132533],bembidion uruguayense[&&NHX:TOL=132534])bembidion incertae sedis[&&NHX:TOL=23738])bembidion[&&NHX:TOL=194],(ocys andreae[&&NHX:TOL=131142],ocys beatricis[&&NHX:TOL=131143],ocys bedeli[&&NHX:TOL=131144],ocys crypticola[&&NHX:TOL=131145],ocys davatchii[&&NHX:TOL=131146],ocys elbursensis[&&NHX:TOL=131147],ocys harpaloides[&&NHX:TOL=131148],ocys hoffmanni[&&NHX:TOL=131149],ocys inguscioi[&&NHX:TOL=131150],ocys ledouxi[&&NHX:TOL=131151],ocys pecoudi[&&NHX:TOL=131152],ocys pennisii[&&NHX:TOL=131153],ocys peyerimhoffi[&&NHX:TOL=131154],ocys pravei[&&NHX:TOL=131155],ocys pseudopaphius[&&NHX:TOL=131156],(ocys quinquestriatus quinquestriatus[&&NHX:TOL=131158],ocys quinquestriatus berytensis[&&NHX:TOL=131159],ocys quinquestriatus subtilis[&&NHX:TOL=131160])ocys quinquestriatus[&&NHX:TOL=131157],(ocys reticulatus reticulatus[&&NHX:TOL=131162],ocys reticulatus croaticus[&&NHX:TOL=131163])ocys reticulatus[&&NHX:TOL=131161],ocys rotundipennis[&&NHX:TOL=131164],ocys soleymanensis[&&NHX:TOL=131165],ocys tachysoides[&&NHX:TOL=131166],ocys tassii[&&NHX:TOL=131167],ocys trechoides[&&NHX:TOL=131168])ocys[&&NHX:TOL=22955],(sinechostictus aeneoviridimicans[&&NHX:TOL=132433],sinechostictus afghanistanum[&&NHX:TOL=132434],sinechostictus arnosti[&&NHX:TOL=132435],(sinechostictus cameroni cameroni[&&NHX:TOL=132437],sinechostictus cameroni schawalleri[&&NHX:TOL=132438])sinechostictus cameroni[&&NHX:TOL=132436],sinechostictus chuji[&&NHX:TOL=132439],(sinechostictus cribrum cribrum[&&NHX:TOL=132441],sinechostictus cribrum stenacrum[&&NHX:TOL=132442])sinechostictus cribrum[&&NHX:TOL=132440],sinechostictus cyprium[&&NHX:TOL=132443],(sinechostictus dahlii dahlii[&&NHX:TOL=132445],sinechostictus dahlii laevigaster[&&NHX:TOL=132446],sinechostictus dahlii nordafricanum[&&NHX:TOL=132447])sinechostictus dahlii[&&NHX:TOL=132444],(sinechostictus decoratum decoratum[&&NHX:TOL=132449],sinechostictus decoratum barbarum[&&NHX:TOL=132450])sinechostictus decoratum[&&NHX:TOL=132448],sinechostictus doderoi[&&NHX:TOL=132451],sinechostictus effluviorum[&&NHX:TOL=132452],(sinechostictus elongatum elongatum[&&NHX:TOL=132454],sinechostictus elongatum tarsicum[&&NHX:TOL=132455])sinechostictus elongatum[&&NHX:TOL=132453],sinechostictus exaratum[&&NHX:TOL=132456],sinechostictus fontinale[&&NHX:TOL=132457],(sinechostictus frederici frederici[&&NHX:TOL=132459],sinechostictus frederici maghrebicum[&&NHX:TOL=132460])sinechostictus frederici[&&NHX:TOL=132458],sinechostictus galloisi[&&NHX:TOL=132461],sinechostictus ictis[&&NHX:TOL=132462],sinechostictus inustum[&&NHX:TOL=132463],sinechostictus kosti[&&NHX:TOL=132464],sinechostictus kyushuense[&&NHX:TOL=132465],(sinechostictus lederi lederi[&&NHX:TOL=132467],sinechostictus lederi anatolicum[&&NHX:TOL=132468])sinechostictus lederi[&&NHX:TOL=132466],sinechostictus millerianum[&&NHX:TOL=132469],sinechostictus moschatum[&&NHX:TOL=132470],(sinechostictus multisulcatum multisulcatum[&&NHX:TOL=132472],sinechostictus multisulcatum cariniger[&&NHX:TOL=132473])sinechostictus multisulcatum[&&NHX:TOL=132471],sinechostictus nakabusei[&&NHX:TOL=132474],sinechostictus nordmanni[&&NHX:TOL=132475],sinechostictus pendleburyi[&&NHX:TOL=132476],(sinechostictus ruficorne ruficorne[&&NHX:TOL=132478],sinechostictus ruficorne ganglbaueri[&&NHX:TOL=132479])sinechostictus ruficorne[&&NHX:TOL=132477],sinechostictus solarii[&&NHX:TOL=132480],(sinechostictus stomoides stomoides[&&NHX:TOL=132482],sinechostictus stomoides rousorum[&&NHX:TOL=132483])sinechostictus stomoides[&&NHX:TOL=132481])sinechostictus[&&NHX:TOL=132432],((amerizus oblonguloides[&&NHX:TOL=22960],amerizus oblongulus[&&NHX:TOL=132537],amerizus spectabilis[&&NHX:TOL=132538],amerizus wingatei[&&NHX:TOL=22958])amerizus amerizus[&&NHX:TOL=132536],((amerizus barkamensis barkamensis[&&NHX:TOL=132540],amerizus barkamensis zhanglaensis[&&NHX:TOL=132541])amerizus barkamensis[&&NHX:TOL=132539],amerizus baxiensis[&&NHX:TOL=132542],amerizus beatriciae[&&NHX:TOL=132543],amerizus bhutanensis[&&NHX:TOL=132544],amerizus bolivari[&&NHX:TOL=132545],amerizus camillae[&&NHX:TOL=132546],amerizus casalei[&&NHX:TOL=132547],amerizus deuvei[&&NHX:TOL=132548],amerizus eremita[&&NHX:TOL=132549],amerizus faizae[&&NHX:TOL=132550],amerizus ganesh[&&NHX:TOL=132551],amerizus garuda[&&NHX:TOL=132552],amerizus gongga[&&NHX:TOL=132553],amerizus gosainkundensis[&&NHX:TOL=132554],amerizus hubeiensis[&&NHX:TOL=132555],amerizus indecorus[&&NHX:TOL=132556],amerizus kashmiricus[&&NHX:TOL=132557],amerizus lassallei[&&NHX:TOL=132558],amerizus ledouxi[&&NHX:TOL=132559],amerizus macrocephalus[&&NHX:TOL=132560],amerizus markamensis[&&NHX:TOL=132561],amerizus martensi[&&NHX:TOL=132562],amerizus morvani[&&NHX:TOL=132563],amerizus mourzinei[&&NHX:TOL=132564],amerizus perraulti[&&NHX:TOL=132565],amerizus queinneci[&&NHX:TOL=132566],amerizus sabinae[&&NHX:TOL=132567],amerizus sarkimani[&&NHX:TOL=132568],amerizus schawalleri[&&NHX:TOL=132569],amerizus songpanensis[&&NHX:TOL=132570],amerizus turnai[&&NHX:TOL=132571],amerizus wittmeri[&&NHX:TOL=132572],amerizus wolongensis[&&NHX:TOL=132573],amerizus wrzecionkoi[&&NHX:TOL=132574])amerizus tiruka[&&NHX:TOL=22962])amerizus[&&NHX:TOL=22956],(asaphidion alaskanum[&&NHX:TOL=237],asaphidion angulicolle[&&NHX:TOL=131202],asaphidion austriacum[&&NHX:TOL=131203],(asaphidion caraboides caraboides[&&NHX:TOL=131204],asaphidion caraboides balcanicum[&&NHX:TOL=131205],asaphidion caraboides nebulosum[&&NHX:TOL=131206],asaphidion caraboides splendidum[&&NHX:TOL=131207],asaphidion caraboides varipes[&&NHX:TOL=131208])asaphidion caraboides[&&NHX:TOL=235],asaphidion championi[&&NHX:TOL=240],asaphidion cuprascens[&&NHX:TOL=242],asaphidion cupreum[&&NHX:TOL=131209],(asaphidion curtum curtum[&&NHX:TOL=131210],asaphidion curtum maroccanum[&&NHX:TOL=131211],asaphidion curtum delatorrei[&&NHX:TOL=131212])asaphidion curtum[&&NHX:TOL=236],(asaphidion cyanicorne cyanicorne[&&NHX:TOL=131213],asaphidion cyanicorne quarnerense[&&NHX:TOL=131214],asaphidion cyanicorne tyrolense[&&NHX:TOL=131215])asaphidion cyanicorne[&&NHX:TOL=233],asaphidion cyprium[&&NHX:TOL=131216],asaphidion domonense[&&NHX:TOL=131217],asaphidion elongatum[&&NHX:TOL=131218],asaphidion fabichi[&&NHX:TOL=131219],asaphidion festivum[&&NHX:TOL=234],asaphidion flavicorne[&&NHX:TOL=131220],asaphidion flavipes[&&NHX:TOL=230],asaphidion formosum[&&NHX:TOL=245],asaphidion fragile[&&NHX:TOL=131221],asaphidion ganglbaueri[&&NHX:TOL=131222],asaphidion granulatum[&&NHX:TOL=131223],asaphidion griseum[&&NHX:TOL=243],asaphidion indicum[&&NHX:TOL=246],asaphidion nadjae[&&NHX:TOL=131224],asaphidion obscurum[&&NHX:TOL=241],asaphidion ornatum[&&NHX:TOL=248],asaphidion pallipes[&&NHX:TOL=231],asaphidion pictum[&&NHX:TOL=131225],asaphidion rossii[&&NHX:TOL=232],asaphidion semilucidum[&&NHX:TOL=131226],asaphidion stierlini[&&NHX:TOL=131227],asaphidion substriatum[&&NHX:TOL=247],asaphidion subtile[&&NHX:TOL=131228],(asaphidion tenryuense tenryuense[&&NHX:TOL=131230],asaphidion tenryuense konoi[&&NHX:TOL=131231])asaphidion tenryuense[&&NHX:TOL=131229],asaphidion transcaspicum[&&NHX:TOL=131232],asaphidion triste[&&NHX:TOL=249],asaphidion ussuriense[&&NHX:TOL=131233],asaphidion viride[&&NHX:TOL=244],asaphidion weiratheri[&&NHX:TOL=131234],asaphidion yukonense[&&NHX:TOL=238])asaphidion[&&NHX:TOL=196],orzolina thalassophila[&&NHX:TOL=23730],sakagutia marina[&&NHX:TOL=131169],((cillenus alatus[&&NHX:TOL=131172],cillenus hoogstraali[&&NHX:TOL=131173],cillenus insularum[&&NHX:TOL=131174],cillenus lateralis[&&NHX:TOL=131175],cillenus palosverdes[&&NHX:TOL=131176])cillenus cillenus[&&NHX:TOL=131171],(cillenus albertisi[&&NHX:TOL=131178],cillenus formosanus[&&NHX:TOL=131179],cillenus sauteri[&&NHX:TOL=131180])cillenus armatocillenus[&&NHX:TOL=131177],(cillenus adelaidae[&&NHX:TOL=131182],cillenus albovirens[&&NHX:TOL=131183],cillenus angustatus[&&NHX:TOL=131184],cillenus flavescens[&&NHX:TOL=131185],cillenus foochowensis[&&NHX:TOL=131186],cillenus hebridarum[&&NHX:TOL=131187],cillenus leytensis[&&NHX:TOL=131188],cillenus mastersi[&&NHX:TOL=131189],cillenus seticornis[&&NHX:TOL=131190],cillenus sumaoi[&&NHX:TOL=131191],cillenus yokohamae[&&NHX:TOL=131192])cillenus desarmatocillenus[&&NHX:TOL=131181],cillenus sinicus[&&NHX:TOL=131193],(cillenus tokunoshimanus[&&NHX:TOL=131195],cillenus tsutsuii[&&NHX:TOL=131196])cillenus corallicillenus[&&NHX:TOL=131194],(cillenus aestuarii[&&NHX:TOL=131198],cillenus kasaharai[&&NHX:TOL=131199])cillenus novicillenus[&&NHX:TOL=131197])cillenus[&&NHX:TOL=131170],(caecidium trechomorphum[&&NHX:TOL=131200],caecidium yasudai[&&NHX:TOL=131201])caecidium[&&NHX:TOL=23729],phrypeus rickseckeri[&&NHX:TOL=195],(bembidarenas reicheellum[&&NHX:TOL=132620],bembidarenas setiventre[&&NHX:TOL=132621])bembidarenas[&&NHX:TOL=197])bembidiina[&&NHX:TOL=200],((((philipis quadraticollis[&&NHX:TOL=622],((philipis alticola[&&NHX:TOL=625],(philipis cooki[&&NHX:TOL=627],philipis laevigata[&&NHX:TOL=628])[&&NHX:TOL=626])[&&NHX:TOL=624],philipis heatherae[&&NHX:TOL=629])[&&NHX:TOL=623])[&&NHX:TOL=621],(philipis picea[&&NHX:TOL=631],philipis castanatea[&&NHX:TOL=632])[&&NHX:TOL=630],(((philipis unicolor[&&NHX:TOL=636],philipis atra[&&NHX:TOL=637])[&&NHX:TOL=635],philipis ruficollis[&&NHX:TOL=638])[&&NHX:TOL=634],(philipis inermis[&&NHX:TOL=640],(philipis reticulata[&&NHX:TOL=642],(philipis striata[&&NHX:TOL=644],(philipis spurgeoni[&&NHX:TOL=646],philipis planicola[&&NHX:TOL=647],(philipis thompsoni[&&NHX:TOL=649],philipis vicina[&&NHX:TOL=650],(philipis tribulationis[&&NHX:TOL=652],philipis trunci[&&NHX:TOL=653])[&&NHX:TOL=651])[&&NHX:TOL=648])[&&NHX:TOL=645])[&&NHX:TOL=643])[&&NHX:TOL=641])[&&NHX:TOL=639],((philipis laevis[&&NHX:TOL=656],philipis sulcata[&&NHX:TOL=657])[&&NHX:TOL=655],(philipis frerei[&&NHX:TOL=659],philipis subtropica[&&NHX:TOL=660])[&&NHX:TOL=658],philipis alutacea[&&NHX:TOL=661],((philipis rufescens[&&NHX:TOL=664],philipis perstriata[&&NHX:TOL=665])[&&NHX:TOL=663],(philipis ellioti[&&NHX:TOL=667],philipis agnicaptius[&&NHX:TOL=668],((philipis picta[&&NHX:TOL=671],philipis bicolor[&&NHX:TOL=672])[&&NHX:TOL=670],(philipis geoffreyi[&&NHX:TOL=674],philipis minor[&&NHX:TOL=675])[&&NHX:TOL=673],(philipis sinuata[&&NHX:TOL=677],(philipis distinguenda[&&NHX:TOL=679],philipis lustrans[&&NHX:TOL=680])[&&NHX:TOL=678])[&&NHX:TOL=676])[&&NHX:TOL=669])[&&NHX:TOL=666])[&&NHX:TOL=662])[&&NHX:TOL=654])[&&NHX:TOL=633])philipis[&&NHX:TOL=221],((xystosomus inflatus[&&NHX:TOL=684],xystosomus convexus[&&NHX:TOL=685])inflatus group[&&NHX:TOL=683],(xystosomus laevis[&&NHX:TOL=687],xystosomus paralaevis[&&NHX:TOL=688],xystosomus laevimicans[&&NHX:TOL=689],xystosomus niger[&&NHX:TOL=690],xystosomus tholus[&&NHX:TOL=691],xystosomus turgidus[&&NHX:TOL=692],xystosomus impressifrons[&&NHX:TOL=693])laevis group[&&NHX:TOL=686])xystosomus[&&NHX:TOL=222],((geballusa microtreta[&&NHX:TOL=608],geballusa oligotreta[&&NHX:TOL=609])microtreta group[&&NHX:TOL=607],(geballusa rex[&&NHX:TOL=611],geballusa polytreta[&&NHX:TOL=612],geballusa nannotreta[&&NHX:TOL=613])polytreta group[&&NHX:TOL=610])geballusa[&&NHX:TOL=223],(gouleta notiophiloides[&&NHX:TOL=615],gouleta spangleri[&&NHX:TOL=616],gouleta cayennense[&&NHX:TOL=617],gouleta gentryi[&&NHX:TOL=618])gouleta[&&NHX:TOL=224],((erwiniana bisulcifrons[&&NHX:TOL=267],erwiniana henryi[&&NHX:TOL=268],erwiniana baeza[&&NHX:TOL=269])erwiniana bisulcifrons group[&&NHX:TOL=251],(erwiniana crassa[&&NHX:TOL=273],erwiniana notesheje[&&NHX:TOL=274],erwiniana esheje[&&NHX:TOL=275],erwiniana parapara[&&NHX:TOL=276],erwiniana manusculptilis[&&NHX:TOL=277])erwiniana esheje group[&&NHX:TOL=252],erwiniana equanegrei[&&NHX:TOL=253],erwiniana negrei[&&NHX:TOL=254],(erwiniana hilaris[&&NHX:TOL=279],erwiniana belti[&&NHX:TOL=280],erwiniana para[&&NHX:TOL=281],erwiniana ampliata[&&NHX:TOL=282],erwiniana strigosa[&&NHX:TOL=283],erwiniana gruti[&&NHX:TOL=284],erwiniana nigripalpis[&&NHX:TOL=285],erwiniana angustia[&&NHX:TOL=286])erwiniana gruti group[&&NHX:TOL=255],erwiniana samiria[&&NHX:TOL=256],((erwiniana villiersi[&&NHX:TOL=309],erwiniana am[&&NHX:TOL=310])villiersi subgroup[&&NHX:TOL=308],(erwiniana indetecticostis[&&NHX:TOL=312],erwiniana nox[&&NHX:TOL=313])nox subgroup[&&NHX:TOL=311],(erwiniana apicisulcata[&&NHX:TOL=315],erwiniana parkeri[&&NHX:TOL=316],erwiniana hamatilis[&&NHX:TOL=317],erwiniana notparkeri[&&NHX:TOL=318])apiscisulcata subgroup[&&NHX:TOL=314],(erwiniana iris[&&NHX:TOL=320],erwiniana pfunorum[&&NHX:TOL=321],erwiniana quadrata[&&NHX:TOL=322])iris subgroup[&&NHX:TOL=319],(erwiniana protosculptilis[&&NHX:TOL=324],erwiniana misahualli[&&NHX:TOL=325],erwiniana depressisculptilis[&&NHX:TOL=326],erwiniana sculpticollis[&&NHX:TOL=327],erwiniana irisculptilis[&&NHX:TOL=328],erwiniana foveosculptilis[&&NHX:TOL=329],erwiniana punctisculptilis[&&NHX:TOL=330],erwiniana eugeneae[&&NHX:TOL=331])sulpticollis subgroup[&&NHX:TOL=323])erwiniana sculpticollis group[&&NHX:TOL=257],(erwiniana sulcicostis[&&NHX:TOL=333],erwiniana anterocostis[&&NHX:TOL=334],erwiniana anchicaya[&&NHX:TOL=335],erwiniana jefe[&&NHX:TOL=336])erwiniana sulcicostis group[&&NHX:TOL=258],(erwiniana exigupunctata[&&NHX:TOL=293],erwiniana ovatula[&&NHX:TOL=294],erwiniana grossipunctata[&&NHX:TOL=295],erwiniana batesi[&&NHX:TOL=296],erwiniana seriata[&&NHX:TOL=297],erwiniana sublaevis[&&NHX:TOL=298])erwiniana ovatula group[&&NHX:TOL=259],(erwiniana rosebudae[&&NHX:TOL=264],erwiniana aetholia[&&NHX:TOL=265])erwiniana aetholia group[&&NHX:TOL=260],(erwiniana jacupiranga[&&NHX:TOL=300],erwiniana parainsularis[&&NHX:TOL=301],erwiniana alticola[&&NHX:TOL=302],erwiniana wygo[&&NHX:TOL=303],erwiniana chiriboga[&&NHX:TOL=304])erwiniana parainsularis group[&&NHX:TOL=261],(erwiniana dannyi[&&NHX:TOL=288],erwiniana huacamayas[&&NHX:TOL=289])erwiniana huacamayas group[&&NHX:TOL=262])erwiniana[&&NHX:TOL=225])[&&NHX:TOL=220],(mioptachys[&&NHX:TOL=227],inpa[&&NHX:TOL=228])[&&NHX:TOL=226])xystosomina[&&NHX:TOL=201],anillina[&&NHX:TOL=205],(tachys[&&NHX:TOL=208],paratachys[&&NHX:TOL=209],elaphropus[&&NHX:TOL=210],pericompsus[&&NHX:TOL=211],tachyta[&&NHX:TOL=212],tasmanitachoides[&&NHX:TOL=213],costitachys[&&NHX:TOL=214],porotachys[&&NHX:TOL=215],meotachys[&&NHX:TOL=216],liotachys[&&NHX:TOL=217],polyderis[&&NHX:TOL=218],(micratopus[&&NHX:TOL=203],limnastis[&&NHX:TOL=204])[&&NHX:TOL=202])tachyina[&&NHX:TOL=206])bembidiini[&&NHX:TOL=94])trechitae[&&NHX:TOL=90],patrobini[&&NHX:TOL=95])[&&NHX:TOL=89],(((melisodera[&&NHX:TOL=171],moriodema[&&NHX:TOL=172],moriomorpha[&&NHX:TOL=173],celanida[&&NHX:TOL=174],rhaebolestes[&&NHX:TOL=175])melisoderina[&&NHX:TOL=161],(tropopterus[&&NHX:TOL=181],molopsida[&&NHX:TOL=182],pterogmus[&&NHX:TOL=183],teraphis[&&NHX:TOL=184],theprisa[&&NHX:TOL=185],trephisa[&&NHX:TOL=186],sitaphe[&&NHX:TOL=187])tropopterina[&&NHX:TOL=162],(meonis[&&NHX:TOL=177],raphetis[&&NHX:TOL=178],selenochilus[&&NHX:TOL=179])meonina[&&NHX:TOL=163],(amblytelus[&&NHX:TOL=166],(epelyx[&&NHX:TOL=168],dystrichothorax[&&NHX:TOL=169])[&&NHX:TOL=167])amblytelina[&&NHX:TOL=164])amblytelini[&&NHX:TOL=97],(((crepidogaster[&&NHX:TOL=1067],tyronia[&&NHX:TOL=1068],brachynillus[&&NHX:TOL=1069],crepidolomus[&&NHX:TOL=1070],crepidonellus[&&NHX:TOL=1071],crepidogastrillus[&&NHX:TOL=1072],crepidogastrinus[&&NHX:TOL=1073])crepidogastrini[&&NHX:TOL=70],((((((west african lineage[&&NHX:TOL=728],(indian lineage[&&NHX:TOL=730],(longipalpis lineage[&&NHX:TOL=732],(brachinoaptinus[&&NHX:TOL=734],(african lineage[&&NHX:TOL=736],aploa[&&NHX:TOL=737])[&&NHX:TOL=735])[&&NHX:TOL=733])[&&NHX:TOL=731])[&&NHX:TOL=729])[&&NHX:TOL=727],(aptinomimus[&&NHX:TOL=739],(cnecostolus[&&NHX:TOL=741],((((brachinus americanus[&&NHX:TOL=752],brachinus alexiguus[&&NHX:TOL=753])[&&NHX:TOL=751],brachinus microamericanus[&&NHX:TOL=754])[&&NHX:TOL=750],brachinus capnicus[&&NHX:TOL=755])[&&NHX:TOL=749],(((brachinus texanus[&&NHX:TOL=759],brachinus rhytiderus[&&NHX:TOL=760])[&&NHX:TOL=758],brachinus elongatulus[&&NHX:TOL=761])[&&NHX:TOL=757],(((brachinus sallei[&&NHX:TOL=765],(brachinus brunneus[&&NHX:TOL=767],brachinus melanarthrus[&&NHX:TOL=768])[&&NHX:TOL=766])[&&NHX:TOL=764],(brachinus grandis[&&NHX:TOL=770],(brachinus lateralis[&&NHX:TOL=772],brachinus aeger[&&NHX:TOL=773],brachinus chalchihuitlicue[&&NHX:TOL=774],brachinus arboreus[&&NHX:TOL=775],brachinus chirriador[&&NHX:TOL=776],brachinus adustipennis[&&NHX:TOL=777])[&&NHX:TOL=771])[&&NHX:TOL=769])[&&NHX:TOL=763],(((brachinus alternans[&&NHX:TOL=781],brachinus viridipennis[&&NHX:TOL=782])[&&NHX:TOL=780],brachinus rugipennis[&&NHX:TOL=783])[&&NHX:TOL=779],(brachinus costipennis[&&NHX:TOL=785],(brachinus kansanus[&&NHX:TOL=787],((brachinus hirsutus[&&NHX:TOL=790],brachinus pallidus[&&NHX:TOL=791])[&&NHX:TOL=789],(((brachinus cinctipennis[&&NHX:TOL=795],brachinus cibolensis[&&NHX:TOL=796])[&&NHX:TOL=794],((((brachinus kavanaughi[&&NHX:TOL=801],brachinus mexicanus[&&NHX:TOL=802])[&&NHX:TOL=800],brachinus quadripennis[&&NHX:TOL=803])[&&NHX:TOL=799],(brachinus javalinopsis[&&NHX:TOL=805],brachinus neglectus[&&NHX:TOL=806])[&&NHX:TOL=804])[&&NHX:TOL=798],(((brachinus phaeocerus[&&NHX:TOL=810],brachinus imporcitis[&&NHX:TOL=811])[&&NHX:TOL=809],(brachinus azureipennis[&&NHX:TOL=813],brachinus consanguineus[&&NHX:TOL=814])[&&NHX:TOL=812])[&&NHX:TOL=808],(brachinus oaxacensis[&&NHX:TOL=816],(brachinus patruelis[&&NHX:TOL=818],(brachinus conformis[&&NHX:TOL=820],(brachinus ovipennis[&&NHX:TOL=822],(brachinus tenuicollis[&&NHX:TOL=824],(brachinus cyanipennis[&&NHX:TOL=826],(brachinus medius[&&NHX:TOL=828],((brachinus gebhardis[&&NHX:TOL=831],brachinus galactoderus[&&NHX:TOL=832])[&&NHX:TOL=830],((brachinus fumans[&&NHX:TOL=835],brachinus puberulus[&&NHX:TOL=836])[&&NHX:TOL=834],(brachinus favicollis[&&NHX:TOL=838],(brachinus perplexus[&&NHX:TOL=840],(brachinus velutinus[&&NHX:TOL=842],brachinus imperialensis[&&NHX:TOL=843])[&&NHX:TOL=841])[&&NHX:TOL=839])[&&NHX:TOL=837])[&&NHX:TOL=833])[&&NHX:TOL=829])[&&NHX:TOL=827])[&&NHX:TOL=825])[&&NHX:TOL=823])[&&NHX:TOL=821])[&&NHX:TOL=819])[&&NHX:TOL=817])[&&NHX:TOL=815])[&&NHX:TOL=807])[&&NHX:TOL=797])[&&NHX:TOL=793],(((((((brachinus cordicollis[&&NHX:TOL=851],brachinus cyanochroaticus[&&NHX:TOL=852])[&&NHX:TOL=850],brachinus sublaevis[&&NHX:TOL=853])[&&NHX:TOL=849],brachinus ichapodopsis[&&NHX:TOL=854])[&&NHX:TOL=848],((brachinus oxygonus[&&NHX:TOL=857],brachinus fulminatus[&&NHX:TOL=858])[&&NHX:TOL=856],brachinus vulcanoides[&&NHX:TOL=859])[&&NHX:TOL=855])[&&NHX:TOL=847],brachinus janthinipennis[&&NHX:TOL=860])[&&NHX:TOL=846],brachinus mobilis[&&NHX:TOL=861])[&&NHX:TOL=845],(brachinus explosus[&&NHX:TOL=863],(brachinus aabaaba[&&NHX:TOL=865],brachinus sonorous[&&NHX:TOL=866])[&&NHX:TOL=864])[&&NHX:TOL=862])[&&NHX:TOL=844])[&&NHX:TOL=792])[&&NHX:TOL=788])[&&NHX:TOL=786])[&&NHX:TOL=784])[&&NHX:TOL=778])[&&NHX:TOL=762])[&&NHX:TOL=756])neobrachinus[&&NHX:TOL=742])[&&NHX:TOL=740])[&&NHX:TOL=738])[&&NHX:TOL=726],(branchynolomus[&&NHX:TOL=744],(brachinus[&&NHX:TOL=746],metabrachinus[&&NHX:TOL=747])[&&NHX:TOL=745])[&&NHX:TOL=743])brachinus[&&NHX:TOL=703],(brachinulus[&&NHX:TOL=705],aptinoderus[&&NHX:TOL=706])[&&NHX:TOL=704])brachinina[&&NHX:TOL=702],(((styphlodromus[&&NHX:TOL=710],styphlomerinus[&&NHX:TOL=711])[&&NHX:TOL=709],styphlomerus[&&NHX:TOL=712])[&&NHX:TOL=708],aptinus[&&NHX:TOL=713])aptinina[&&NHX:TOL=707])[&&NHX:TOL=701],(((aptinomorphus[&&NHX:TOL=717],(stenaptinus[&&NHX:TOL=719],pheropsophus[&&NHX:TOL=720])[&&NHX:TOL=718])[&&NHX:TOL=716],(pheropsophidius[&&NHX:TOL=722],protopheropsophus[&&NHX:TOL=723])[&&NHX:TOL=721])pheropsophina[&&NHX:TOL=715],mastax[&&NHX:TOL=724])[&&NHX:TOL=714])brachinini[&&NHX:TOL=71])brachinitae[&&NHX:TOL=99],(((((abacetus[&&NHX:TOL=51308],chlaeminus[&&NHX:TOL=51645])[&&NHX:TOL=68705],(aristopus[&&NHX:TOL=51306],cosmodiscus[&&NHX:TOL=51307])[&&NHX:TOL=51305],celioinkosa[&&NHX:TOL=51606],colpodichius[&&NHX:TOL=51602],cyrtomoscelis[&&NHX:TOL=51600],distrigidius[&&NHX:TOL=51309],haptoderodes[&&NHX:TOL=52166],holconotus[&&NHX:TOL=51304],haptoeridius[&&NHX:TOL=52167],inkosa[&&NHX:TOL=51605],(mateuellus troglobioticus[&&NHX:TOL=51313],(metabacetus arrowi[&&NHX:TOL=67930],metabacetus immarginatus[&&NHX:TOL=67931],metabacetus jeanneli[&&NHX:TOL=67932],metabacetus laotinus[&&NHX:TOL=67933],metabacetus perakianus[&&NHX:TOL=67934],metabacetus vandoesburgi[&&NHX:TOL=67935])metabacetus[&&NHX:TOL=51314])[&&NHX:TOL=51312],metaxys[&&NHX:TOL=51302],metaxellus[&&NHX:TOL=51303],(ecnomolaus clivinoides[&&NHX:TOL=68897],ecnomolaus dentitibiis[&&NHX:TOL=68898])ecnomolaus[&&NHX:TOL=51610],nelidus[&&NHX:TOL=51646],novillidius[&&NHX:TOL=51601],oodinkosa[&&NHX:TOL=51607],ophonichius[&&NHX:TOL=52168],pediomorphus[&&NHX:TOL=51310],pollicobius[&&NHX:TOL=51311],pioprosopus[&&NHX:TOL=51301],prostalomus[&&NHX:TOL=51603],pseudabacetus[&&NHX:TOL=51689],pterostillichus[&&NHX:TOL=51609],rhagadillius[&&NHX:TOL=51604],tiferonia[&&NHX:TOL=51611],trachelocyphus[&&NHX:TOL=52169],trachelocyphoides[&&NHX:TOL=52170])abacetini[&&NHX:TOL=51300],(((adrimus aenescens[&&NHX:TOL=67861],adrimus affinis[&&NHX:TOL=67862],adrimus balli[&&NHX:TOL=67863],adrimus claripes[&&NHX:TOL=67864],adrimus creparus[&&NHX:TOL=67865],adrimus elytralis[&&NHX:TOL=67866],adrimus fuscipes[&&NHX:TOL=67867],adrimus geminatus[&&NHX:TOL=67868],adrimus irideus[&&NHX:TOL=67869],adrimus latibasis[&&NHX:TOL=67870],adrimus longior[&&NHX:TOL=67871],adrimus matoanus[&&NHX:TOL=67872],adrimus microderus[&&NHX:TOL=67873],adrimus olivaceus[&&NHX:TOL=67874],adrimus paulensis[&&NHX:TOL=67875],adrimus proximus[&&NHX:TOL=67876],adrimus rufangulus[&&NHX:TOL=67877],adrimus suturalis[&&NHX:TOL=67878],adrimus uruguaicus[&&NHX:TOL=67879],adrimus ventralis[&&NHX:TOL=67880],adrimus virens[&&NHX:TOL=67881],adrimus viridescens[&&NHX:TOL=67882])adrimus[&&NHX:TOL=51483],(metoncidus gracilus[&&NHX:TOL=67373],metoncidus epiphytus[&&NHX:TOL=67372],metoncidus tenebrionides[&&NHX:TOL=67371])metoncidus[&&NHX:TOL=51488],(oxycrepis schadei[&&NHX:TOL=67562],oxycrepis leucocera[&&NHX:TOL=67563],oxycrepis brasiliensis[&&NHX:TOL=67564],oxycrepis cordata[&&NHX:TOL=67565])oxycrepis[&&NHX:TOL=51490],(stolonis dimidiaticornis[&&NHX:TOL=67842],stolonis martinezi[&&NHX:TOL=67843],stolonis willinki[&&NHX:TOL=67844],stolonis interceptus[&&NHX:TOL=67845],stolonis leucotelus[&&NHX:TOL=67846],stolonis fulvostigma[&&NHX:TOL=67847],stolonis notula[&&NHX:TOL=67848],stolonis leistoides[&&NHX:TOL=67849],stolonis laevicollis[&&NHX:TOL=67850],stolonis parvulus[&&NHX:TOL=67851],stolonis tapiai[&&NHX:TOL=67852],stolonis ovaticollis[&&NHX:TOL=67853],stolonis scortensis[&&NHX:TOL=67854],stolonis spinosus[&&NHX:TOL=67855],stolonis gracilis[&&NHX:TOL=67856],stolonis yasuni[&&NHX:TOL=67857],stolonis catenarius[&&NHX:TOL=67858],stolonis apicatus[&&NHX:TOL=67859])stolonis[&&NHX:TOL=51491],(loxandrus  accelerans[&&NHX:TOL=67734],loxandrus  aduncus[&&NHX:TOL=67735],loxandrus  agilis[&&NHX:TOL=67736],loxandrus  algidus[&&NHX:TOL=67737],loxandrus  brevicollis[&&NHX:TOL=67738],loxandrus  breviusculus[&&NHX:TOL=67739],loxandrus  calathinus[&&NHX:TOL=67740],loxandrus  celeris[&&NHX:TOL=67741],loxandrus  cervicalis[&&NHX:TOL=67742],loxandrus  cincinnati[&&NHX:TOL=67743],loxandrus  circulus[&&NHX:TOL=67744],loxandrus  collucens[&&NHX:TOL=67745],loxandrus  comptus[&&NHX:TOL=67746],loxandrus  concinnus[&&NHX:TOL=67747],loxandrus  contumax[&&NHX:TOL=67748],loxandrus  crenatus[&&NHX:TOL=67749],loxandrus  crenulatus[&&NHX:TOL=67750],loxandrus  cursitans[&&NHX:TOL=67751],loxandrus  duryi[&&NHX:TOL=67752],loxandrus  erraticus[&&NHX:TOL=67753],loxandrus  extendus[&&NHX:TOL=67754],loxandrus  floridanus[&&NHX:TOL=67755],loxandrus  fulgens[&&NHX:TOL=67756],loxandrus  gibbus[&&NHX:TOL=67757],loxandrus  infimus[&&NHX:TOL=67759],loxandrus  lateralis[&&NHX:TOL=67760],loxandrus  limatus[&&NHX:TOL=67761],loxandrus  lucens[&&NHX:TOL=67762],loxandrus  ludovicianus[&&NHX:TOL=67763],loxandrus  micans[&&NHX:TOL=67764],loxandrus  minor[&&NHX:TOL=67765],loxandrus  minutus[&&NHX:TOL=67766],loxandrus  mundus[&&NHX:TOL=67767],loxandrus  nitidulus[&&NHX:TOL=67768],loxandrus  pactinullus[&&NHX:TOL=67769],loxandrus  parallelus[&&NHX:TOL=67770],loxandrus  parvicollis[&&NHX:TOL=67771],loxandrus  parvulus[&&NHX:TOL=67772],loxandrus  piceolus[&&NHX:TOL=67773],loxandrus  piciventris[&&NHX:TOL=67774],loxandrus  pravitubus[&&NHX:TOL=67775],loxandrus  proximus[&&NHX:TOL=67776],loxandrus  rectangulus[&&NHX:TOL=67777],loxandrus  rectus[&&NHX:TOL=67778],loxandrus  reflexus[&&NHX:TOL=67779],loxandrus velocipes[&&NHX:TOL=67860])western hemisphere loxandrus[&&NHX:TOL=52155])amerilox clade[&&NHX:TOL=51619],((haploferonia simplex[&&NHX:TOL=51485],(homalonesiota karawari[&&NHX:TOL=67780],homalonesiota straneoi[&&NHX:TOL=67781])homolonesiota[&&NHX:TOL=51486],(nebrioferonia intermedia[&&NHX:TOL=67782],nebrioferonia strigitarsis[&&NHX:TOL=67783])nebrioferonia[&&NHX:TOL=51489],zeodera atra[&&NHX:TOL=51492],(loxandrus micantinus[&&NHX:TOL=67784],loxandrus brunneus[&&NHX:TOL=67785],loxandrus longiformis[&&NHX:TOL=67786],loxandrus quadricollis[&&NHX:TOL=67787],loxandrus australiensis[&&NHX:TOL=67788],loxandrus subiridescens[&&NHX:TOL=67789],loxandrus rufilabris[&&NHX:TOL=67790],loxandrus laevigatus[&&NHX:TOL=67791],loxandrus amplicollis[&&NHX:TOL=67792],loxandrus gagatinus[&&NHX:TOL=67793],loxandrus macleayi[&&NHX:TOL=67794],loxandrus australicus[&&NHX:TOL=67795],loxandrus subgagatinus[&&NHX:TOL=67796],loxandrus micantior[&&NHX:TOL=67797])austral loxandrus[&&NHX:TOL=52156])[&&NHX:TOL=51621],(feronista amaroides[&&NHX:TOL=67798],feronista minor[&&NHX:TOL=67799])feronista[&&NHX:TOL=51484])australox clade[&&NHX:TOL=51620])loxandrini[&&NHX:TOL=51299])gondwanalox clade[&&NHX:TOL=51599],((rhytisternus[&&NHX:TOL=51542],eurystomis castelnaui[&&NHX:TOL=51543])[&&NHX:TOL=51891],((cuneipectus foveatus[&&NHX:TOL=51809],cuneipectus frenchi[&&NHX:TOL=51810])cuneipectini[&&NHX:TOL=111],catadromus[&&NHX:TOL=29014])[&&NHX:TOL=77254],(setalidius attenuatus[&&NHX:TOL=52244],setalidius nigerimus[&&NHX:TOL=52245])setalidius[&&NHX:TOL=51545],euryabax colossus[&&NHX:TOL=51538],(holcaspis[&&NHX:TOL=51519],notolestus[&&NHX:TOL=51520],abacomorphus[&&NHX:TOL=51521],gourlayia[&&NHX:TOL=51522],darodilia[&&NHX:TOL=51523],liopasa[&&NHX:TOL=51524],(pachymorphus aereus[&&NHX:TOL=51829],(pachymorphus chalceus angulatus[&&NHX:TOL=51831],pachymorphus chalceus chalceus[&&NHX:TOL=51832],pachymorphus chalceus transandinus[&&NHX:TOL=51833])[&&NHX:TOL=51830],pachymorphus lucidus lucidus[&&NHX:TOL=51834],pachymorphus nebrioides[&&NHX:TOL=51835])pachymorphus[&&NHX:TOL=51555],(hypothecus flohri[&&NHX:TOL=67566],hybothecus mateui[&&NHX:TOL=67567],hybothecus incrassatus[&&NHX:TOL=67568],hybothecus aequatoria[&&NHX:TOL=67569],hybothecus anomala[&&NHX:TOL=67570],hybothecus sculptilis[&&NHX:TOL=67571])hybothecus[&&NHX:TOL=51564],(cophosomorpha[&&NHX:TOL=51662],wahlbergiana[&&NHX:TOL=51706])[&&NHX:TOL=51887],abacoleoptus[&&NHX:TOL=51525],platysmodes[&&NHX:TOL=51526],cratogaster[&&NHX:TOL=51527])holcaspis series[&&NHX:TOL=51518],(delinius[&&NHX:TOL=51514],nesites[&&NHX:TOL=51515],trigonotoma[&&NHX:TOL=51516],lesticus[&&NHX:TOL=51517],(rhytiferonia[&&NHX:TOL=51540],analoma[&&NHX:TOL=51657])[&&NHX:TOL=58002],euryaptus[&&NHX:TOL=51668])lesticus series[&&NHX:TOL=51512],((acanthoferonia[&&NHX:TOL=51498],castelnaudia[&&NHX:TOL=51499],crataferonia[&&NHX:TOL=51500],mecynognathus[&&NHX:TOL=51501],megadromus[&&NHX:TOL=51502],neofernia[&&NHX:TOL=51503],notabax monteithi[&&NHX:TOL=51504],nurus[&&NHX:TOL=51505],paranurus[&&NHX:TOL=51506],plocamostethus[&&NHX:TOL=51507],secatophus[&&NHX:TOL=51508],teropha[&&NHX:TOL=51509],omalosoma[&&NHX:TOL=51510],zeopoecilus[&&NHX:TOL=51511],loxogenius[&&NHX:TOL=67936])omalosoma series[&&NHX:TOL=51497],(((leiradira[&&NHX:TOL=51529],conchitella[&&NHX:TOL=51530],loxodactylus[&&NHX:TOL=51531],notonomus[&&NHX:TOL=51532],psegmatopterus[&&NHX:TOL=51533],sarticus[&&NHX:TOL=51534],(sphodrosomus saisseti[&&NHX:TOL=67685],sphodrosomus monteithi[&&NHX:TOL=67686])sphodrisomus[&&NHX:TOL=51535],platycaelus[&&NHX:TOL=51536],(pseudoceneus[&&NHX:TOL=51537],aulacopodus[&&NHX:TOL=51647])[&&NHX:TOL=67687])notonomus series[&&NHX:TOL=51528],(parhypates arctus[&&NHX:TOL=51842],(parhypates bonellii chiloensis[&&NHX:TOL=51844],parhypates bonellii bonellii[&&NHX:TOL=51845])[&&NHX:TOL=51843],parhypates chalybicolor[&&NHX:TOL=51846],parhypates convexipennis[&&NHX:TOL=51847],parhypates extenuatus[&&NHX:TOL=51848],parhypates irrequietus[&&NHX:TOL=51850],parhypates melaenus[&&NHX:TOL=51851],parhypates nunni[&&NHX:TOL=51852],parhypates rufipalpis[&&NHX:TOL=51853],parhypates sinuatipennis[&&NHX:TOL=51854],parhypates stenomus[&&NHX:TOL=51855],parhypates tenuistriatus[&&NHX:TOL=51856])parhypates[&&NHX:TOL=51596])[&&NHX:TOL=67840],((abropus carnifex[&&NHX:TOL=51321],(kuschelinus insularius[&&NHX:TOL=51322],metius[&&NHX:TOL=51320],(antarctiola laevigata[&&NHX:TOL=67886],antarctiola laevis[&&NHX:TOL=67887],antarctiola motschulskyi[&&NHX:TOL=67888],antarctiola amaroides[&&NHX:TOL=67889])antarctiola[&&NHX:TOL=51323])[&&NHX:TOL=67885])[&&NHX:TOL=51622],feroniola[&&NHX:TOL=51324])metiini[&&NHX:TOL=51319])[&&NHX:TOL=51624])[&&NHX:TOL=78584],rhabdotus reflexus[&&NHX:TOL=51539],((pterostichus s.str.[&&NHX:TOL=51353],(((leptoferonia falli[&&NHX:TOL=51385],(leptoferonia sphodrinus[&&NHX:TOL=51399],leptoferonia beyeri[&&NHX:TOL=51382])[&&NHX:TOL=67913],((((leptoferonia idahoae[&&NHX:TOL=51391],leptoferonia inanis[&&NHX:TOL=51392])[&&NHX:TOL=67911],(leptoferonia pemphredo[&&NHX:TOL=58006],leptpoferonia deino[&&NHX:TOL=58008])[&&NHX:TOL=107401])[&&NHX:TOL=67910],leptoferonia caligans[&&NHX:TOL=51383])[&&NHX:TOL=107400],((leptoferonia cochlearis[&&NHX:TOL=51384],(leptoferonia fenyesi fenyesi[&&NHX:TOL=51387],leptoferonia fenyesi fenderi[&&NHX:TOL=51386])[&&NHX:TOL=67897])[&&NHX:TOL=67896],(leptoferonia inopinus[&&NHX:TOL=51394],(((leptoferonia pumilus willamettensis[&&NHX:TOL=51397],leptoferonia pumilus pumilus[&&NHX:TOL=51398])[&&NHX:TOL=67899],leptoferonia infernalis[&&NHX:TOL=51393])[&&NHX:TOL=67898],(((leptoferonia humilis[&&NHX:TOL=51390],leptoferonia trinitensis[&&NHX:TOL=67902],leptoferonia enyo[&&NHX:TOL=58007])[&&NHX:TOL=67901],(leptoferonia lobatus[&&NHX:TOL=67904],leptoferonia fuchsi[&&NHX:TOL=51388],(leptoferonia mattolensis[&&NHX:TOL=51396],leptoferonia marinensis[&&NHX:TOL=51395])[&&NHX:TOL=67905])[&&NHX:TOL=107406])[&&NHX:TOL=67900],(((((leptoferonia stapedius[&&NHX:TOL=51400],leptoferonia yosemitensis[&&NHX:TOL=51402])[&&NHX:TOL=67909],leptoferonia hatchi[&&NHX:TOL=51389])[&&NHX:TOL=67908],leptoferonia blodgettensis[&&NHX:TOL=58005])[&&NHX:TOL=67907],leptoferonia angustus[&&NHX:TOL=51381])[&&NHX:TOL=107407],leptoferonia rothi[&&NHX:TOL=107408])[&&NHX:TOL=67906])[&&NHX:TOL=107405])[&&NHX:TOL=107404])[&&NHX:TOL=107403])[&&NHX:TOL=107402])[&&NHX:TOL=67892])leptoferonia[&&NHX:TOL=51380],(anilloferonia testaceus[&&NHX:TOL=51407],anilloferonia malkini[&&NHX:TOL=51406],anilloferonia rothi[&&NHX:TOL=51405],anilloferonia lanei[&&NHX:TOL=51404])anilloferonia[&&NHX:TOL=51403])[&&NHX:TOL=51481],(((hypherpes tristis[&&NHX:TOL=51475],hypherpes adoxus[&&NHX:TOL=51410])[&&NHX:TOL=67915],hypherpes morionides[&&NHX:TOL=51447])[&&NHX:TOL=67914],hypherpes alamedae[&&NHX:TOL=51411],hypherpes algidus[&&NHX:TOL=51412],hypherpes amethystinus[&&NHX:TOL=51413],hypherpes annosus[&&NHX:TOL=51414],hypherpes baldwini[&&NHX:TOL=51415],hypherpes barbarinus[&&NHX:TOL=51416],(hypherpes breviusculus mimus[&&NHX:TOL=51418],hypherpes breviusculus breviusculus[&&NHX:TOL=51417])[&&NHX:TOL=67916],hypherpes californicus[&&NHX:TOL=51419],hypherpes castaneus[&&NHX:TOL=51421],hypherpes castanipes[&&NHX:TOL=51422],hypherpes congestus[&&NHX:TOL=51423],hypherpes crenicollis[&&NHX:TOL=51424],hypherpes cuneatulus[&&NHX:TOL=51425],hypherpes diabolus[&&NHX:TOL=51426],hypherpes ecarinatus[&&NHX:TOL=51427],hypherpes esuriens[&&NHX:TOL=51428],hypherpes gliscans[&&NHX:TOL=51429],hypherpes gracilior[&&NHX:TOL=51430],hypherpes gregalis[&&NHX:TOL=51431],hypherpes herculaneus[&&NHX:TOL=51432],hypherpes hornii[&&NHX:TOL=51433],hypherpes humboldti[&&NHX:TOL=51434],hypherpes illustris[&&NHX:TOL=51435],hypherpes intectus[&&NHX:TOL=51437],hypherpes jacobinus[&&NHX:TOL=51439],hypherpes canallatus[&&NHX:TOL=51420],hypherpes isabellae[&&NHX:TOL=51438],hypherpes kansanus[&&NHX:TOL=51440],hypherpes laborans[&&NHX:TOL=51441],hypherpes lacertus[&&NHX:TOL=51442],hypherpes lama[&&NHX:TOL=51443],hypherpes lassulus[&&NHX:TOL=51444],hypherpes mercedianus[&&NHX:TOL=51445],(hypherpes miscellus[&&NHX:TOL=51446],hypherpes inermis[&&NHX:TOL=51436])[&&NHX:TOL=67917],hypherpes neobrunneus[&&NHX:TOL=51448],(hypherpes nigrocaeruleus[&&NHX:TOL=51449],hypherpes brachylobus[&&NHX:TOL=107410])[&&NHX:TOL=107409],hypherpes obsidianus[&&NHX:TOL=51450],hypherpes occultus[&&NHX:TOL=51451],hypherpes ordinarius[&&NHX:TOL=51452],hypherpes ovalipennis[&&NHX:TOL=51453],hypherpes panticulatus[&&NHX:TOL=51454],hypherpes parallelus[&&NHX:TOL=51455],hypherpes ybosqueti[&&NHX:TOL=51456],hypherpes pergracilis[&&NHX:TOL=51457],hypherpes placerensis[&&NHX:TOL=51458],hypherpes planctus[&&NHX:TOL=51459],hypherpes plutonicus[&&NHX:TOL=51460],hypherpes protensiformis[&&NHX:TOL=51461],hypherpes protensipennis[&&NHX:TOL=51462],hypherpes protractus[&&NHX:TOL=51463],hypherpes restrictus[&&NHX:TOL=51464],hypherpes scutellaris[&&NHX:TOL=51465],hypherpes sejungendus[&&NHX:TOL=51466],hypherpes setosus[&&NHX:TOL=51468],hypherpes sierranus[&&NHX:TOL=51469],hypherpes sponsor[&&NHX:TOL=51470],hypherpes spraguei[&&NHX:TOL=51471],hypherpes suffusus[&&NHX:TOL=51472],hypherpes tahoensis[&&NHX:TOL=51473],(hypherpes tarsalis[&&NHX:TOL=51474],hypherpes serripes[&&NHX:TOL=51467])[&&NHX:TOL=107411],hypherpes tuberculofemoratus[&&NHX:TOL=51476],hypherpes vandykei[&&NHX:TOL=51477],hypherpes vicinus[&&NHX:TOL=51478],hypherpes zunianus[&&NHX:TOL=51479],hypherpes menetriesii[&&NHX:TOL=67937],hypherpes lattini[&&NHX:TOL=107412])hypherpes[&&NHX:TOL=51354])hypherpes complex[&&NHX:TOL=51480],pterostichus cylindrocharis[&&NHX:TOL=51924],pterostichus orsonjohnsonus[&&NHX:TOL=51925],pterostichus georgeballius[&&NHX:TOL=51926],pterostichus carllindrothius[&&NHX:TOL=51927],pterostichus abea[&&NHX:TOL=51928],pterostichus haptotapinus[&&NHX:TOL=51929],pterostichus argutor[&&NHX:TOL=51930],pterostichus fukienostichus[&&NHX:TOL=51931],pterostichus pledarus[&&NHX:TOL=51932],pterostichus japeris[&&NHX:TOL=51933],pterostichus adelosia[&&NHX:TOL=51934],pterostichus moritapterus[&&NHX:TOL=51935],pterostichus melanius[&&NHX:TOL=51936],pterostichus lamenius[&&NHX:TOL=51937],pterostichus bothriopterus[&&NHX:TOL=51938],pterostichus platysma[&&NHX:TOL=51939],pterostichus morphnosoma[&&NHX:TOL=51940],pterostichus pseudomaseus[&&NHX:TOL=51941],pterostichus phonias[&&NHX:TOL=51942],pterostichus falsargutor[&&NHX:TOL=51943],pterostichus cryobius[&&NHX:TOL=51944],pterostichus pseudorites[&&NHX:TOL=51945],pterostichus unitrichus[&&NHX:TOL=51946],pterostichus neohaptoderus[&&NHX:TOL=51947],pterostichus morphohaptoderus[&&NHX:TOL=51948],pterostichus pseudohaptoderus[&&NHX:TOL=51949],pterostichus anomostichus[&&NHX:TOL=51950],pterostichus phaenoraphis[&&NHX:TOL=51951],pterostichus pseudosteropus[&&NHX:TOL=51952],pterostichus lyrothorax[&&NHX:TOL=51953],pterostichus oreoplatysma[&&NHX:TOL=51954],pterostichus asioplatysma[&&NHX:TOL=51955],pterostichus steropus[&&NHX:TOL=51956],pterostichus eosteropus[&&NHX:TOL=51957],pterostichus cophosus[&&NHX:TOL=51958],pterostichus sinosteropus[&&NHX:TOL=51959],pterostichus circinatus[&&NHX:TOL=51960],pterostichus lenapterus[&&NHX:TOL=51961],pterostichus feronidius[&&NHX:TOL=51962],pterostichus oreolyperus[&&NHX:TOL=51963],pterostichus tschitscherinea[&&NHX:TOL=51964],pterostichus jedlickaia[&&NHX:TOL=51965],pterostichus megabea[&&NHX:TOL=51966],pterostichus monoferonia[&&NHX:TOL=51967],pterostichus feronina[&&NHX:TOL=51968],pterostichus pseudoferonina[&&NHX:TOL=51969],pterostichus gastrosticta[&&NHX:TOL=51970],pterostichus paraferonia[&&NHX:TOL=51971],pterostichus metallophilus[&&NHX:TOL=51972],pterostichus petrophilus[&&NHX:TOL=51973],pterostichus chinapterus[&&NHX:TOL=51974],pterostichus cheporus[&&NHX:TOL=51975],pterostichus platypterus[&&NHX:TOL=51976],pterostichus pterostichus[&&NHX:TOL=51977],pterostichus kozyrevius[&&NHX:TOL=51978],pterostichus sphodroferonia[&&NHX:TOL=51979],pterostichus tinautius[&&NHX:TOL=51980],pterostichus lianoe[&&NHX:TOL=51981],pterostichus nialoe[&&NHX:TOL=51982],pterostichus micronialoe[&&NHX:TOL=51983],pterostichus koreonialoe[&&NHX:TOL=51984],pterostichus alecto[&&NHX:TOL=51985],pterostichus devilleinus[&&NHX:TOL=51986],pterostichus myosodus[&&NHX:TOL=51987],pterostichus plectes[&&NHX:TOL=51988],pterostichus aphaon[&&NHX:TOL=51989],pterostichus oreophilus[&&NHX:TOL=51990],pterostichus sinoreophilus[&&NHX:TOL=51991],pterostichus haplomaseus[&&NHX:TOL=51992],pterostichus eurymelanius[&&NHX:TOL=51993],pterostichus calopterus[&&NHX:TOL=51994],pterostichus ethira[&&NHX:TOL=51995],pterostichus pseudethira[&&NHX:TOL=51996],pterostichus steropanus[&&NHX:TOL=51997],pterostichus agastillus[&&NHX:TOL=67841])pterostichus[&&NHX:TOL=51895],((allotriopus s.str. brachypterus[&&NHX:TOL=51905],allotriopus s.str. ashei[&&NHX:TOL=51906],allotriopus s.str. hallbergi[&&NHX:TOL=51907],allotriopus s.str. hemingi[&&NHX:TOL=51908],allotriopus s.str. oscitans[&&NHX:TOL=51909],allotriopus s.str. serratipes[&&NHX:TOL=51910],allotriopus s.str. shpeleyi[&&NHX:TOL=51911],allotriopus s.str. whiteheadi[&&NHX:TOL=51912])allotriopus s.str.[&&NHX:TOL=51904],(allotriopus mayaferonia aeniola[&&NHX:TOL=51914],allotriopus mayaferonia triunfo[&&NHX:TOL=51915])allotriopus mayaferonia[&&NHX:TOL=51913])allotriopus[&&NHX:TOL=51653],(percolaus championi[&&NHX:TOL=51916],percolaus guillermo[&&NHX:TOL=51917])percolaus[&&NHX:TOL=51652])[&&NHX:TOL=67883],(cyclotrachelus  alabamensis[&&NHX:TOL=67688],cyclotrachelus  approximatus[&&NHX:TOL=67689],cyclotrachelus  brevoorti[&&NHX:TOL=67690],cyclotrachelus  dejeanellus[&&NHX:TOL=67691],cyclotrachelus  faber[&&NHX:TOL=67692],cyclotrachelus  freitagi[&&NHX:TOL=67693],cyclotrachelus  fucatus[&&NHX:TOL=67694],cyclotrachelus  hernandensis[&&NHX:TOL=67695],cyclotrachelus  iuvenis[&&NHX:TOL=67696],cyclotrachelus  laevipennis[&&NHX:TOL=67697],cyclotrachelus  levifaber[&&NHX:TOL=67698],cyclotrachelus  macrovulum[&&NHX:TOL=67699],cyclotrachelus  ovulum[&&NHX:TOL=67700],cyclotrachelus  parafaber[&&NHX:TOL=67701],cyclotrachelus  spoliatus[&&NHX:TOL=67702],cyclotrachelus  texensis[&&NHX:TOL=67703],cyclotrachelus  unicolor[&&NHX:TOL=67704],cyclotrachelus  vinctus[&&NHX:TOL=67705],cyclotrachelus  alabamae[&&NHX:TOL=67706],cyclotrachelus  alternans[&&NHX:TOL=67707],cyclotrachelus  blatchleyi[&&NHX:TOL=67708],cyclotrachelus  constrictus[&&NHX:TOL=67709],cyclotrachelus  convivus[&&NHX:TOL=67710],cyclotrachelus  engelmani[&&NHX:TOL=67711],cyclotrachelus  floridensis[&&NHX:TOL=67712],cyclotrachelus  furtivus[&&NHX:TOL=67713],cyclotrachelus  gigas[&&NHX:TOL=67714],cyclotrachelus  gravesi[&&NHX:TOL=67715],cyclotrachelus  gravidus[&&NHX:TOL=67716],cyclotrachelus  heros[&&NHX:TOL=67717],cyclotrachelus  hypherpiformis[&&NHX:TOL=67718],cyclotrachelus  incisus[&&NHX:TOL=67719],cyclotrachelus  iowensis[&&NHX:TOL=67720],cyclotrachelus  nonnitens[&&NHX:TOL=67721],cyclotrachelus  parasodalis[&&NHX:TOL=67722],cyclotrachelus  sallei[&&NHX:TOL=67723],cyclotrachelus  seximpressus[&&NHX:TOL=67724],cyclotrachelus  sigillatus[&&NHX:TOL=67725],cyclotrachelus  sinus[&&NHX:TOL=67726],cyclotrachelus sodalis colossus[&&NHX:TOL=67727],cyclotrachelus sodalis lodingi[&&NHX:TOL=67728],cyclotrachelus sodalis sodalis[&&NHX:TOL=67729],cyclotrachelus  substriatus[&&NHX:TOL=67730],cyclotrachelus  torvus deceptus[&&NHX:TOL=67731],cyclotrachelus  torvus torvus[&&NHX:TOL=67732],cyclotrachelus  whitcombi[&&NHX:TOL=67733])cyclotrachelus[&&NHX:TOL=51378],(piesmus submarginatus[&&NHX:TOL=51379],(stomis termitiformis[&&NHX:TOL=67800],stomis pumicatus[&&NHX:TOL=67801])stomis[&&NHX:TOL=51594],(gastrellarius blanchardi[&&NHX:TOL=51892],gastrellarius honestus[&&NHX:TOL=51893],gastrellarius unicarum[&&NHX:TOL=51894])gastrellarius[&&NHX:TOL=51593])[&&NHX:TOL=67884],poecilus[&&NHX:TOL=51630],stereocerus[&&NHX:TOL=51631],(((((lophoglossus gravis[&&NHX:TOL=51896],lophoglossus haldemanni[&&NHX:TOL=51897])[&&NHX:TOL=51921],lophoglossus substrenuus[&&NHX:TOL=51899])[&&NHX:TOL=51920],lophoglossus scrutator[&&NHX:TOL=51898])[&&NHX:TOL=51919],lophoglossus vernix[&&NHX:TOL=51901])[&&NHX:TOL=51918],lophoglossus tartaricus[&&NHX:TOL=51900])lophoglossus[&&NHX:TOL=51633],(xenion[&&NHX:TOL=51649],myas[&&NHX:TOL=51648],aristochroa[&&NHX:TOL=51650],aristochroodes[&&NHX:TOL=51659])[&&NHX:TOL=51902],((simodontus[&&NHX:TOL=51547],litarthrum[&&NHX:TOL=51548],setalis[&&NHX:TOL=51549],setalimorphus[&&NHX:TOL=51550],prosopogmus[&&NHX:TOL=51551],phenaulax[&&NHX:TOL=51552],gastrogmus[&&NHX:TOL=51553])australian series[&&NHX:TOL=51546],((((trirammatus unistriatus unistriatus[&&NHX:TOL=51840],trirammatus unistriatus nocticolor[&&NHX:TOL=51839],trirammatus unistriatus fulgidus[&&NHX:TOL=51841])[&&NHX:TOL=51838],trirammatus torqueotrochantus[&&NHX:TOL=51886],trirammatus selkirki[&&NHX:TOL=51836],trirammatus skottsbergi[&&NHX:TOL=51837],trirammatus chaudoiri[&&NHX:TOL=52239],trirammatus ignobilis[&&NHX:TOL=52240],trirammatus  lacordairei[&&NHX:TOL=52241])trirammatus[&&NHX:TOL=51558],pachythecus rubrocupreus[&&NHX:TOL=51559])[&&NHX:TOL=51557],(blennidus aratus[&&NHX:TOL=51811],blennidus blandus[&&NHX:TOL=51812],blennidus fontainei[&&NHX:TOL=51813],blennidus hebes[&&NHX:TOL=51814],blennidus inops[&&NHX:TOL=51815],blennidus mediolaevis[&&NHX:TOL=51816],blennidus meticulosus[&&NHX:TOL=51817],blennidus obscuripennis[&&NHX:TOL=51818],blennidus parvulus[&&NHX:TOL=51819],blennidus putzeysi[&&NHX:TOL=51820],blennidus rufescens[&&NHX:TOL=51821],blennidus somnians[&&NHX:TOL=51822],blennidus sublustris[&&NHX:TOL=51823])blennidus[&&NHX:TOL=51560],blenniventer violaceotinctus[&&NHX:TOL=51565],((neotalus portai[&&NHX:TOL=51568],(((abaris napoensis[&&NHX:TOL=51761],aberis striolata[&&NHX:TOL=51762])striolatagroup[&&NHX:TOL=51760],(abaris robustual[&&NHX:TOL=51764],((abaris notiophiloides[&&NHX:TOL=51767],abaris aquilonaria[&&NHX:TOL=51768])[&&NHX:TOL=51766],abaris aenea[&&NHX:TOL=51769],abaris erwini[&&NHX:TOL=51770])[&&NHX:TOL=51765])aeneagroup[&&NHX:TOL=51763],(abaris impunctata[&&NHX:TOL=51772],(abaris bigenera[&&NHX:TOL=51774],((abaris basistriata[&&NHX:TOL=51777],abaris metallica[&&NHX:TOL=51778])[&&NHX:TOL=51776],(abaris picipes[&&NHX:TOL=51780],abaris mina[&&NHX:TOL=51781])[&&NHX:TOL=51779])[&&NHX:TOL=51775])[&&NHX:TOL=51773])picipesgroup[&&NHX:TOL=51771])abaris sensu stricto[&&NHX:TOL=51759],((abaris bicolor[&&NHX:TOL=51784],abaris nobilis[&&NHX:TOL=51785])sedis mutabilis[&&NHX:TOL=51783],(abaris nitida[&&NHX:TOL=51787],(abaris franiai[&&NHX:TOL=51789],(abaris inflata[&&NHX:TOL=51791],(abaris tachypoides[&&NHX:TOL=51793],(abaris convexa[&&NHX:TOL=51795],abaris nigra[&&NHX:TOL=51796],(abaris inaequaloides[&&NHX:TOL=51798],(abaris opaca[&&NHX:TOL=51800],abaris splendidula[&&NHX:TOL=51801],abaris wardi[&&NHX:TOL=51802],abaris aequinoctialis[&&NHX:TOL=51803],abaris retiaria[&&NHX:TOL=51804])[&&NHX:TOL=51799])[&&NHX:TOL=51797])[&&NHX:TOL=51794])[&&NHX:TOL=51792])[&&NHX:TOL=51790])[&&NHX:TOL=51788])tachypoidesgroup[&&NHX:TOL=51786])abaridius[&&NHX:TOL=51782])abaris[&&NHX:TOL=51569])[&&NHX:TOL=51567],(pseudabarys brasiliensis[&&NHX:TOL=52227],pseudabarys columbicus[&&NHX:TOL=52228],pseudabarys lebasi[&&NHX:TOL=52229],pseudabarys mexicanus[&&NHX:TOL=52230],pseudabarys robustus[&&NHX:TOL=52231],pseudabarys substriatus[&&NHX:TOL=52232])pseudabarys[&&NHX:TOL=51570])abariform clade[&&NHX:TOL=51566],cynthidia[&&NHX:TOL=51571],eumara[&&NHX:TOL=51572],(plagioplatys vagans[&&NHX:TOL=51884],plagioplatys pseudoharpalus[&&NHX:TOL=51885])plagioplatys[&&NHX:TOL=51556],marsyas[&&NHX:TOL=51573],meropalpus[&&NHX:TOL=51574],bothynoproctus mattoensis[&&NHX:TOL=51575],(oribazus catenulatus[&&NHX:TOL=52233],oribazus quinquiestriatus[&&NHX:TOL=52234])oribazus[&&NHX:TOL=51576],apsaustodon segregatus[&&NHX:TOL=51577],(haplobothynus gounellei[&&NHX:TOL=52235],haplobothynus paranae[&&NHX:TOL=52236])haplobothynus[&&NHX:TOL=51578],euchroa[&&NHX:TOL=51579],microcephalus[&&NHX:TOL=51580],((argutoridius chilensis chilensis[&&NHX:TOL=51825],argutoridius chilensis ardens[&&NHX:TOL=51826],argutoridius chilensis chubutensis[&&NHX:TOL=51827])argutoridius chilensis[&&NHX:TOL=51824],argutoridius depressulus[&&NHX:TOL=51828])argutoridius[&&NHX:TOL=51581],(cephalostichus laticeps[&&NHX:TOL=52242],cephalostichus putzeysi[&&NHX:TOL=52243])cephalostichus[&&NHX:TOL=51582],(lobobrachus alternans[&&NHX:TOL=52237],lobobrachus lacerdae[&&NHX:TOL=52238])lobobrachus[&&NHX:TOL=51598])south american series[&&NHX:TOL=51554],((orthomus[&&NHX:TOL=51584],nesorthomus[&&NHX:TOL=51585],eutrichopus[&&NHX:TOL=51586],wolltinerfia[&&NHX:TOL=51587])[&&NHX:TOL=68706],(abacillodes[&&NHX:TOL=51608],abacillius[&&NHX:TOL=52165])[&&NHX:TOL=68707])african series[&&NHX:TOL=68148])euchroina[&&NHX:TOL=51298],cedrorum azoricus[&&NHX:TOL=51651],abacops rugipennis[&&NHX:TOL=51654],(abax[&&NHX:TOL=51655],(percus[&&NHX:TOL=51686],molops[&&NHX:TOL=51680])[&&NHX:TOL=78586])[&&NHX:TOL=78585],aphaonus[&&NHX:TOL=51658],camptoscelis[&&NHX:TOL=51660],chalcochrous[&&NHX:TOL=51661],crisimus[&&NHX:TOL=51663],cyrtoderus[&&NHX:TOL=51664],eucamptognathus[&&NHX:TOL=51666],eudromus[&&NHX:TOL=51667],eurypercus[&&NHX:TOL=51669],haptoderidius[&&NHX:TOL=51670],harpostomus[&&NHX:TOL=51672],henrotiochoromus[&&NHX:TOL=51673],henrotius[&&NHX:TOL=51674],hoplauchenium[&&NHX:TOL=51675],hoplodactylella[&&NHX:TOL=51676],licentius[&&NHX:TOL=51677],molopidius[&&NHX:TOL=51678],molopinus[&&NHX:TOL=51679],nirmala[&&NHX:TOL=51682],ogmophora[&&NHX:TOL=51683],oscadytes[&&NHX:TOL=51684],pedius[&&NHX:TOL=51685],peyrieraselus[&&NHX:TOL=51687],poecilinus madecassus[&&NHX:TOL=51688],rambousekiella[&&NHX:TOL=51690],speluncarius[&&NHX:TOL=51691],speomolops[&&NHX:TOL=51692],stenochoromus[&&NHX:TOL=51693],sthenocranion[&&NHX:TOL=51694],straneostichus[&&NHX:TOL=51695],styracoderus[&&NHX:TOL=51696],tanythrix[&&NHX:TOL=51697],taphoxomimus leleupi[&&NHX:TOL=51698],tapinopterus[&&NHX:TOL=51699],teratotarsa[&&NHX:TOL=51700],trichopedius[&&NHX:TOL=51701],troglorites[&&NHX:TOL=51703],tropidocerus[&&NHX:TOL=51704],typhlochoromus[&&NHX:TOL=51705],zariquieya[&&NHX:TOL=51707],(strigia[&&NHX:TOL=67938],parastrigia[&&NHX:TOL=67939],rathymus[&&NHX:TOL=67940])[&&NHX:TOL=51888])pterostichini[&&NHX:TOL=102],(((abacaelostus filicornis[&&NHX:TOL=51327],andrewesinulus[&&NHX:TOL=52160],apsidocnemus[&&NHX:TOL=51328],caecocaelus[&&NHX:TOL=51330],caelostomus[&&NHX:TOL=51331],camptogenys[&&NHX:TOL=52161],capabatus raffrayi[&&NHX:TOL=51334],crenulostrigus[&&NHX:TOL=52162],dactyleurys anomalus[&&NHX:TOL=51336],dactylinius punctipennis[&&NHX:TOL=51337],diachipteryx paradoxa[&&NHX:TOL=51338],diceromerus[&&NHX:TOL=51339],drymonaxus feanus[&&NHX:TOL=51332],feostoma irregulare[&&NHX:TOL=51341],hemitelestus[&&NHX:TOL=51342],hoplizomenus carinatus[&&NHX:TOL=51343],leleuporites[&&NHX:TOL=51344],madapelmus elongatus[&&NHX:TOL=51345],monodryxus crassus[&&NHX:TOL=52163],pachycaecus savanicola[&&NHX:TOL=51346],pachyroxochus[&&NHX:TOL=51347],platyxythrius[&&NHX:TOL=52164],stegazopteryx ivimkaensis[&&NHX:TOL=51351],stomonaxellus[&&NHX:TOL=51333],strigomerodes[&&NHX:TOL=51348],strigomerus[&&NHX:TOL=51349],trichillinus[&&NHX:TOL=51350])drimostomatina[&&NHX:TOL=51326],barylaus[&&NHX:TOL=51329],basilewskya[&&NHX:TOL=51708],cyrtolaus[&&NHX:TOL=51335],dromistomus[&&NHX:TOL=51340])drimostomatini[&&NHX:TOL=52157],(((catapiesis nitida[&&NHX:TOL=897],catapiesis attenuata[&&NHX:TOL=898],catapiesis columbica[&&NHX:TOL=899],catapiesis mexicana[&&NHX:TOL=900],catapiesis brasiliensis[&&NHX:TOL=901],catapiesis sulcipennis[&&NHX:TOL=902],catapiesis bartyrae[&&NHX:TOL=903],catapiesis tumida[&&NHX:TOL=904])catapiesis[&&NHX:TOL=896],homalomorpha castanea[&&NHX:TOL=905])catapieseini[&&NHX:TOL=105],((cratocerus monilicornis[&&NHX:TOL=51889],cratocerus sulcatus[&&NHX:TOL=51890])cratocerus[&&NHX:TOL=51316],(brachidius crassicornis[&&NHX:TOL=51318],oxyglychus laeviventris[&&NHX:TOL=51317])[&&NHX:TOL=51588])[&&NHX:TOL=52159])cratocerini[&&NHX:TOL=51315])[&&NHX:TOL=52171],(pseudamara[&&NHX:TOL=51637],amara[&&NHX:TOL=51638],zabrus[&&NHX:TOL=51639],aepsera[&&NHX:TOL=51640])zabrini[&&NHX:TOL=108],(chaetodactyla[&&NHX:TOL=51643],tshitsherinella[&&NHX:TOL=51642])chaetodactylini[&&NHX:TOL=51641],(microchiela denticollis[&&NHX:TOL=51807],microchiela picea[&&NHX:TOL=51808])microcheilini[&&NHX:TOL=51623],((((stereostoma usambaricum[&&NHX:TOL=29006],stereostoma titschacki[&&NHX:TOL=29005],stereostoma senegalense[&&NHX:TOL=29004],stereostoma sansibaricum[&&NHX:TOL=29003],stereostoma rhodesianum[&&NHX:TOL=29002],stereostoma praecellens[&&NHX:TOL=29001],stereostoma kuntzeni[&&NHX:TOL=29000],stereostoma jeanneli[&&NHX:TOL=28999],stereostoma interstitiale[&&NHX:TOL=28998],stereostoma ingens[&&NHX:TOL=28997],stereostoma inscisum[&&NHX:TOL=28996],stereostoma hirtipenne[&&NHX:TOL=28995],stereostoma guineense[&&NHX:TOL=28994],stereostoma girardi[&&NHX:TOL=28993],stereostoma erythraeum[&&NHX:TOL=28992],stereostoma ertli[&&NHX:TOL=28991],stereostoma corpulentum[&&NHX:TOL=28990],stereostoma conradti[&&NHX:TOL=28989],stereostoma clarkei[&&NHX:TOL=28988],stereostoma camerunum[&&NHX:TOL=28987],stereostoma balbisi[&&NHX:TOL=28986],stereostoma angolense[&&NHX:TOL=28985],stereostoma whitei[&&NHX:TOL=28984],stereostoma tenebriodes[&&NHX:TOL=28983],stereostoma stuhlmanni[&&NHX:TOL=28982],stereostoma solidum[&&NHX:TOL=28981],stereostoma punctisternum[&&NHX:TOL=28980],stereostoma punctatum[&&NHX:TOL=28979])stereostoma[&&NHX:TOL=26968],(morionidius charon[&&NHX:TOL=28931],morionidius doriae[&&NHX:TOL=28932],morionidius erebus[&&NHX:TOL=28933],morionidius inexpectatus[&&NHX:TOL=28934],morionidius insularis[&&NHX:TOL=28935])morionidius[&&NHX:TOL=28913])[&&NHX:TOL=28926],(buderes oberti[&&NHX:TOL=28914],((hyperectenus aenigmaticus[&&NHX:TOL=28929],hyperectenus minor[&&NHX:TOL=28930])hyperectenus[&&NHX:TOL=28915],(((moriosomus seticollis[&&NHX:TOL=28977],moriosomus motschulskyi[&&NHX:TOL=107415])[&&NHX:TOL=107414],moriosomus sylvestris[&&NHX:TOL=28978])moriosomus[&&NHX:TOL=28916],(hyperion schroetteri[&&NHX:TOL=28917],((morion angustus[&&NHX:TOL=28936],morion aridus[&&NHX:TOL=28937],morion attenuatus[&&NHX:TOL=28938],morion australis[&&NHX:TOL=28939],morion baloghi[&&NHX:TOL=28940],morion biroi[&&NHX:TOL=28941],morion bithynicus[&&NHX:TOL=28942],morion boliviensis[&&NHX:TOL=28943],morion boninensis[&&NHX:TOL=28944],morion brasiliensis[&&NHX:TOL=28945],morion brevior[&&NHX:TOL=28946],morion caledoniae[&&NHX:TOL=28947],morion congoensis[&&NHX:TOL=28948],morion constrictus[&&NHX:TOL=28949],morion cordatus[&&NHX:TOL=28950],morion costiger[&&NHX:TOL=28951],morion crassipes[&&NHX:TOL=28952],morion cucujoides[&&NHX:TOL=28953],morion cyclomus[&&NHX:TOL=28954],morion dalbertisi[&&NHX:TOL=28955],morion doriae[&&NHX:TOL=28956],morion germanus[&&NHX:TOL=28957],morion guineensis[&&NHX:TOL=28958],morion humeratus[&&NHX:TOL=28959],morion japonicus[&&NHX:TOL=28960],morion jordani[&&NHX:TOL=28961],morion lafertei[&&NHX:TOL=28962],morion longicollis[&&NHX:TOL=28964],morion longipennis[&&NHX:TOL=28963],morion luzonicus[&&NHX:TOL=28965],morion monilicornis[&&NHX:TOL=28966],morion novaehollandiae[&&NHX:TOL=28967],morion olympicus[&&NHX:TOL=28968],morion orientalis[&&NHX:TOL=28969],morion pachysomus[&&NHX:TOL=28970],morion parallelus[&&NHX:TOL=28971],morion piceus[&&NHX:TOL=28972],morion polynesiae[&&NHX:TOL=28973],morion simplex[&&NHX:TOL=28974],morion simulatus[&&NHX:TOL=28975],morion victoriae[&&NHX:TOL=28976])morion[&&NHX:TOL=28918],((megamorio basilewskyi[&&NHX:TOL=26970],megamorio camerunus[&&NHX:TOL=26971],megamorio congoensis[&&NHX:TOL=26972],megamorio feai[&&NHX:TOL=26973],megamorio gabonicus[&&NHX:TOL=26974],megamorio mniszechii[&&NHX:TOL=26975])megamorio[&&NHX:TOL=26969],platynodes westermanni[&&NHX:TOL=28919])[&&NHX:TOL=28920])[&&NHX:TOL=28921])[&&NHX:TOL=28922])[&&NHX:TOL=28923])[&&NHX:TOL=28924])[&&NHX:TOL=28925])morionini[&&NHX:TOL=103],cnemalobus[&&NHX:TOL=104])[&&NHX:TOL=67806],(dicaelindus[&&NHX:TOL=51634],melanchrous[&&NHX:TOL=51636],melanchiton[&&NHX:TOL=51635])melanchitonini[&&NHX:TOL=51644])pterostichite grade[&&NHX:TOL=51493],(idiomorphus[&&NHX:TOL=67941],perochnoristhus[&&NHX:TOL=67942])idiomorphini[&&NHX:TOL=129],(pelmatellina[&&NHX:TOL=1284],(((triplosarus[&&NHX:TOL=1212],((crasodactylus[&&NHX:TOL=1215],cenogmus[&&NHX:TOL=1216])[&&NHX:TOL=1214],hypharpax[&&NHX:TOL=1217])[&&NHX:TOL=1213])[&&NHX:TOL=1211],(gnathaphanus[&&NHX:TOL=1219],(((pseudoanisotarsus[&&NHX:TOL=1223],criniventer[&&NHX:TOL=1224])[&&NHX:TOL=1222],((anisotarsus[&&NHX:TOL=1227],(notiobia[&&NHX:TOL=1229],diatypus[&&NHX:TOL=1230])[&&NHX:TOL=1228])[&&NHX:TOL=1226],anisostichus[&&NHX:TOL=1231])[&&NHX:TOL=1225])[&&NHX:TOL=1221],(scybalicus[&&NHX:TOL=1233],((progonochaetus[&&NHX:TOL=1238],eudichirus[&&NHX:TOL=1239])[&&NHX:TOL=1237],(((phanagnathus[&&NHX:TOL=1243],(pseudognathaphanus[&&NHX:TOL=1245],(chydaeus[&&NHX:TOL=1247],(harpalomimetes[&&NHX:TOL=1249],rhysopus[&&NHX:TOL=1250])[&&NHX:TOL=1248])[&&NHX:TOL=1246])[&&NHX:TOL=1244])[&&NHX:TOL=1242],xestonotus[&&NHX:TOL=1251])[&&NHX:TOL=1241],(((((anisodactylus[&&NHX:TOL=1257],pseudanisodactylus[&&NHX:TOL=1258])[&&NHX:TOL=1256],(pseudhexatrichus[&&NHX:TOL=1260],hexatrichus[&&NHX:TOL=1261])[&&NHX:TOL=1259])[&&NHX:TOL=1255],(pseudodichirus[&&NHX:TOL=1263],gynandrotarsus[&&NHX:TOL=1264])[&&NHX:TOL=1262])[&&NHX:TOL=1254],(geopinus[&&NHX:TOL=1266],(anadaptus[&&NHX:TOL=1268],(spongopus[&&NHX:TOL=1270],(aplocentrus[&&NHX:TOL=1272],pseudaplocentrus[&&NHX:TOL=1273])[&&NHX:TOL=1271])[&&NHX:TOL=1269])[&&NHX:TOL=1267])[&&NHX:TOL=1265])[&&NHX:TOL=1253],((pseudamphasia[&&NHX:TOL=1276],amphasia[&&NHX:TOL=1277])[&&NHX:TOL=1275],((gynandromorphus[&&NHX:TOL=1280],diachromus[&&NHX:TOL=1281])[&&NHX:TOL=1279],dicheirus[&&NHX:TOL=1282])[&&NHX:TOL=1278])[&&NHX:TOL=1274])[&&NHX:TOL=1252])[&&NHX:TOL=1240])anisodactyloids[&&NHX:TOL=1234])[&&NHX:TOL=1232])[&&NHX:TOL=1220])[&&NHX:TOL=1218])[&&NHX:TOL=1210],allocinopus[&&NHX:TOL=1235])anisodactylina[&&NHX:TOL=1285],stenolophina[&&NHX:TOL=1286],harpalina[&&NHX:TOL=1287])harpalini[&&NHX:TOL=118],((platynus agilis[&&NHX:TOL=67666],platynus pecki[&&NHX:TOL=67667],platynus brunneomarginatus[&&NHX:TOL=67668],platynus decentis[&&NHX:TOL=67669],platynus lyratus[&&NHX:TOL=67670],platynus opaculus[&&NHX:TOL=67671],platynus ovipennis[&&NHX:TOL=67672],platynus parmarginatus[&&NHX:TOL=67673],platynus tenuicollis[&&NHX:TOL=67674],platynus trifoveolatus[&&NHX:TOL=67675],platynus angustatus[&&NHX:TOL=67676],platynus cincticollis[&&NHX:TOL=67677],platynus hypolithos[&&NHX:TOL=67678],platynus mannerheimii[&&NHX:TOL=67679],platynus prognathus[&&NHX:TOL=67680],platynus ovatulus[&&NHX:TOL=67681],platynus falli[&&NHX:TOL=67682],platynus megalops[&&NHX:TOL=67683],platynus rufiventris[&&NHX:TOL=67684])platynus[&&NHX:TOL=1709],(tetraleucus[&&NHX:TOL=1702],(((((((anchomenus yukihikoi[&&NHX:TOL=1719],anchomenus leucopus[&&NHX:TOL=1720])[&&NHX:TOL=1718],anchomenus virescens[&&NHX:TOL=1721])[&&NHX:TOL=1717],anchomenus cyaneus[&&NHX:TOL=1722])[&&NHX:TOL=1716],anchomenus dorsalis[&&NHX:TOL=1723])[&&NHX:TOL=1715],anchomenus dohrnii[&&NHX:TOL=1724])[&&NHX:TOL=1714],(anchomenus quadratus[&&NHX:TOL=1726],(anchomenus aeneolus[&&NHX:TOL=1728],(anchomenus funebris[&&NHX:TOL=1730],anchomenus capensis[&&NHX:TOL=1731])[&&NHX:TOL=1729])[&&NHX:TOL=1727])[&&NHX:TOL=1725])anchomenus[&&NHX:TOL=1704],(((sericoda quadripunctata[&&NHX:TOL=1754],sericoda lissoptera[&&NHX:TOL=1755])[&&NHX:TOL=1753],((sericoda obsoleta[&&NHX:TOL=1758],sericoda bogemannii[&&NHX:TOL=1759])[&&NHX:TOL=1757],(sericoda ceylonica[&&NHX:TOL=1761],(sericoda bembidioides[&&NHX:TOL=1763],sericoda montana[&&NHX:TOL=1764])[&&NHX:TOL=1762])[&&NHX:TOL=1760])[&&NHX:TOL=1756])sericoda[&&NHX:TOL=1706],((elliptoleus acutesculptus[&&NHX:TOL=1734],elliptoleus olisthopoides[&&NHX:TOL=1735])[&&NHX:TOL=1733],(elliptoleus corvus[&&NHX:TOL=1737],(elliptoleus curtulus[&&NHX:TOL=1739],(elliptoleus vixstriatus[&&NHX:TOL=1741],(elliptoleus balli[&&NHX:TOL=1743],elliptoleus tequilae[&&NHX:TOL=1744])[&&NHX:TOL=1742],(elliptoleus luteipes[&&NHX:TOL=1746],(elliptoleus zapotecorum[&&NHX:TOL=1748],(elliptoleus crepericornis[&&NHX:TOL=1750],elliptoleus whiteheadi[&&NHX:TOL=1751])[&&NHX:TOL=1749])[&&NHX:TOL=1747])[&&NHX:TOL=1745])[&&NHX:TOL=1740])[&&NHX:TOL=1738])[&&NHX:TOL=1736])elliptoleus[&&NHX:TOL=1707])[&&NHX:TOL=1705])[&&NHX:TOL=1703])anchomenus clade[&&NHX:TOL=1711])platynini[&&NHX:TOL=107],((((dicaelus purpuratus[&&NHX:TOL=30145],dicaelus costatus[&&NHX:TOL=30146],dicaelus crenatus[&&NHX:TOL=30147],dicaelus alternans[&&NHX:TOL=30148])dicaelus dicaelus[&&NHX:TOL=30144],(dicaelus politus[&&NHX:TOL=30150],dicaelus ambiguus[&&NHX:TOL=30151],dicaelus teter[&&NHX:TOL=30152],dicaelus furvus[&&NHX:TOL=30153],dicaelus elongatus[&&NHX:TOL=30154],dicaelus sculptilus[&&NHX:TOL=30155],dicaelus dilatatus[&&NHX:TOL=30156])dicaelus paradicaelus[&&NHX:TOL=30149],(dicaelus abbreviatus[&&NHX:TOL=30158],dicaelus chermocki[&&NHX:TOL=30159],dicaelus franclemonti[&&NHX:TOL=30160],dicaelus suffusus[&&NHX:TOL=30161],dicaelus laevipennis[&&NHX:TOL=30162])dicaelus liodicaelus[&&NHX:TOL=30157])dicaelus[&&NHX:TOL=30143],diplocheila[&&NHX:TOL=30163])dicaelina[&&NHX:TOL=30113],((lestignathina[&&NHX:TOL=30115],dicrochilina[&&NHX:TOL=30114])[&&NHX:TOL=30165],licinina[&&NHX:TOL=30112])[&&NHX:TOL=30164])licinini[&&NHX:TOL=114],geobaenini[&&NHX:TOL=30212],amorphomerini[&&NHX:TOL=133],orthogoniini[&&NHX:TOL=130],(oodini[&&NHX:TOL=115],panagaeini[&&NHX:TOL=116],chlaeniini[&&NHX:TOL=117],dercylini[&&NHX:TOL=51626],chaetogenyini[&&NHX:TOL=112],bascanini[&&NHX:TOL=109],((pseudagonica nitida[&&NHX:TOL=1589],(agonica simsoni[&&NHX:TOL=1603],agonica ovalipennis[&&NHX:TOL=1604],agonica victoriensis[&&NHX:TOL=1605])agonica[&&NHX:TOL=1590])agonicina[&&NHX:TOL=1588],(((eripidius franzi[&&NHX:TOL=1637],(eripus suturalis[&&NHX:TOL=1639],eripus subcaecus[&&NHX:TOL=1640],eripus microphthalmus[&&NHX:TOL=1641],eripus nitidus[&&NHX:TOL=1642],eripus scydmaenoides[&&NHX:TOL=1643],eripus oaxacanus[&&NHX:TOL=1644],eripus globipennis[&&NHX:TOL=1645],eripus breedlovei[&&NHX:TOL=1646])eripus s. str.[&&NHX:TOL=1638])eripus[&&NHX:TOL=1593],(((pelecidium sulcatum[&&NHX:TOL=1649],pelecidium sulcipenne[&&NHX:TOL=1650],pelecidium laevigatum[&&NHX:TOL=1651])pelecidium[&&NHX:TOL=1648],((pelecium striatipenne[&&NHX:TOL=1654],pelecium violaceum[&&NHX:TOL=1655],pelecium drakei[&&NHX:TOL=1656],pelecium tenellum[&&NHX:TOL=1657],pelecium parallelum[&&NHX:TOL=1658],pelecium punctatum[&&NHX:TOL=1659],pelecium longicolle[&&NHX:TOL=1660],pelecium brasiliense[&&NHX:TOL=1661])pelecium violaceum group[&&NHX:TOL=1653],pelecium cyanipes[&&NHX:TOL=1662],(pelecium renati[&&NHX:TOL=1664],pelecium striatum[&&NHX:TOL=1665])pelecium renati group[&&NHX:TOL=1663],(pelecium bolivianum[&&NHX:TOL=1667],pelecium atroviolaceum[&&NHX:TOL=1668],pelecium semistriatum[&&NHX:TOL=1669],pelecium punctatostriatum[&&NHX:TOL=1670])pelecium punctatostriatum group[&&NHX:TOL=1666],(pelecium paulae[&&NHX:TOL=1672],pelecium helenae[&&NHX:TOL=1673],pelecium purpureum[&&NHX:TOL=1674],pelecium rotundipenne[&&NHX:TOL=1675])pelecium rotundipenne group[&&NHX:TOL=1671],(pelecium refulgens[&&NHX:TOL=1677],pelecium fulgidum[&&NHX:TOL=1678],pelecium negrei[&&NHX:TOL=1679])pelecium refulgens group[&&NHX:TOL=1676],(pelecium foveicolle[&&NHX:TOL=1681],pelecium obtusum[&&NHX:TOL=1682],pelecium bisulcatum[&&NHX:TOL=1683],pelecium besckii[&&NHX:TOL=1684],pelecium faldermanni[&&NHX:TOL=1685])pelecium faldermanni group[&&NHX:TOL=1680],(pelecium laeve[&&NHX:TOL=1687],pelecium obscurum[&&NHX:TOL=1688],pelecium nicki[&&NHX:TOL=1689])pelecium laeve group[&&NHX:TOL=1686])pelecium s. str.[&&NHX:TOL=1652])pelecium[&&NHX:TOL=1595],(stricteripus impressus[&&NHX:TOL=1693],stricteripus peruvianus[&&NHX:TOL=1694],stricteripus banningeri[&&NHX:TOL=1695])stricteripus[&&NHX:TOL=1596])[&&NHX:TOL=1594])[&&NHX:TOL=1592],((ardistomopsis marginicollis[&&NHX:TOL=1607],ardistomopsis myrmex[&&NHX:TOL=1608],ardistomopsis ovicollis[&&NHX:TOL=1609],ardistomopsis andrewesi[&&NHX:TOL=1610],ardistomopsis batesi[&&NHX:TOL=1611])ardistomopsis[&&NHX:TOL=1598],((dyschiridium concinnum[&&NHX:TOL=1631],dyschiridium ebeninum[&&NHX:TOL=1632],dyschiridium lasti[&&NHX:TOL=1633],dyschiridium natalicum[&&NHX:TOL=1634],dyschiridium subdepressum[&&NHX:TOL=1635])dyschiridium[&&NHX:TOL=1600],(disphaericus alluaudi[&&NHX:TOL=1613],disphaericus benadirensis[&&NHX:TOL=1614],disphaericus carinulatus[&&NHX:TOL=1615],disphaericus clavicornis[&&NHX:TOL=1616],disphaericus conradti[&&NHX:TOL=1617],disphaericus deplanatus[&&NHX:TOL=1618],disphaericus gambianus[&&NHX:TOL=1619],disphaericus insulanus[&&NHX:TOL=1620],disphaericus katangensis[&&NHX:TOL=1621],disphaericus kolbei[&&NHX:TOL=1622],disphaericus meneghettii[&&NHX:TOL=1623],disphaericus multiporus[&&NHX:TOL=1624],disphaericus quangoanus[&&NHX:TOL=1625],disphaericus rhodesianus[&&NHX:TOL=1626],disphaericus silvestrii[&&NHX:TOL=1627],disphaericus tarsalis[&&NHX:TOL=1628],disphaericus zavattarii[&&NHX:TOL=1629])disphaericus[&&NHX:TOL=1601])[&&NHX:TOL=1599])[&&NHX:TOL=1597])peleciina[&&NHX:TOL=1591])peleciini[&&NHX:TOL=110])[&&NHX:TOL=51625],(physocrotaphini[&&NHX:TOL=125],(anthiini[&&NHX:TOL=127],helluonini[&&NHX:TOL=128])[&&NHX:TOL=126])[&&NHX:TOL=124],((dryptini[&&NHX:TOL=121],zuphiini[&&NHX:TOL=122])[&&NHX:TOL=120],(planetes[&&NHX:TOL=1177],(eunostus[&&NHX:TOL=1179],(ancystroglossus[&&NHX:TOL=1181],(trichognathus[&&NHX:TOL=1183],(galerita galerita[&&NHX:TOL=1205],((galerita forreri[&&NHX:TOL=1187],galerita reichardti[&&NHX:TOL=1188])[&&NHX:TOL=1186],((galerita atripes[&&NHX:TOL=1191],galerita janus[&&NHX:TOL=1192])[&&NHX:TOL=1190],(galerita mexicana[&&NHX:TOL=1194],(galerita bicolor[&&NHX:TOL=1196],(galerita lecontei bicoloripes[&&NHX:TOL=1198],(galerita lecontei lecontei[&&NHX:TOL=1200],(galerita lecontei veracrucis[&&NHX:TOL=1202],galerita lecontei tenebricosa[&&NHX:TOL=1203])[&&NHX:TOL=1201])[&&NHX:TOL=1199])g. lecontei[&&NHX:TOL=1197])[&&NHX:TOL=1195])[&&NHX:TOL=1193])[&&NHX:TOL=1189])galerita progaleritina[&&NHX:TOL=1206])galerita[&&NHX:TOL=1184])[&&NHX:TOL=1182])[&&NHX:TOL=1180])galeritina[&&NHX:TOL=1178])galeritini[&&NHX:TOL=123])[&&NHX:TOL=119],hexagoniini[&&NHX:TOL=131],(sphallomorpha[&&NHX:TOL=1775],(pseudomorpha[&&NHX:TOL=1777],((adelotopus[&&NHX:TOL=1780],(cainogenion[&&NHX:TOL=1782],paussotropus[&&NHX:TOL=1783])[&&NHX:TOL=1781])[&&NHX:TOL=1779],crytocephalomorpha[&&NHX:TOL=1784])[&&NHX:TOL=1778])[&&NHX:TOL=1776])pseudomorphini[&&NHX:TOL=106],ginema thomasi[&&NHX:TOL=30059],((((amphitasus[&&NHX:TOL=33133],(asklepia[&&NHX:TOL=33135],(aporesthus[&&NHX:TOL=33137],eucaerus[&&NHX:TOL=33138])[&&NHX:TOL=33136])[&&NHX:TOL=33134],lachnophorus[&&NHX:TOL=33139],stigmaphorus[&&NHX:TOL=33140],euphorticus[&&NHX:TOL=33141],(calybe sallei[&&NHX:TOL=52650],calybe laetula[&&NHX:TOL=52651])calybe[&&NHX:TOL=33142],selina[&&NHX:TOL=33143])lachnophorini[&&NHX:TOL=138],odacanthini[&&NHX:TOL=139])[&&NHX:TOL=137],calophaenini[&&NHX:TOL=140])[&&NHX:TOL=136],perigonini[&&NHX:TOL=141],(graphipterini[&&NHX:TOL=143],(mnuphorus[&&NHX:TOL=30054],cyclosomus[&&NHX:TOL=30055],cyclicus[&&NHX:TOL=30056],tetragonoderus[&&NHX:TOL=30057])cyclosomini[&&NHX:TOL=144],masoreini[&&NHX:TOL=145],sarothrocrepis[&&NHX:TOL=30058])[&&NHX:TOL=142],lebiini[&&NHX:TOL=146])lebiomorpha[&&NHX:TOL=134],ctenodactylini[&&NHX:TOL=51612])harpalinae[&&NHX:TOL=100])[&&NHX:TOL=98])[&&NHX:TOL=96])carabidae conjunctae[&&NHX:TOL=66],(((solenogenys funkei[&&NHX:TOL=1061],solenogenys thomsoni[&&NHX:TOL=1062])solenogenys[&&NHX:TOL=914],salcedia[&&NHX:TOL=915],(((schizogenius crenulatus crenulatus[&&NHX:TOL=924],schizogenius crenulatus chiapatecus[&&NHX:TOL=925])schizogenius crenulatus group[&&NHX:TOL=923],((schizogenius quinquesulcatus[&&NHX:TOL=928],(schizogenius szekessyi[&&NHX:TOL=930],schizogenius janae[&&NHX:TOL=931])[&&NHX:TOL=929])schizogenius quinquesulcatus group[&&NHX:TOL=927],(schizogenius impressicollis[&&NHX:TOL=933],(schizogenius sculptilis[&&NHX:TOL=935],((schizogenius suturalis[&&NHX:TOL=938],schizogenius maculatus[&&NHX:TOL=939])[&&NHX:TOL=937],(schizogenius impuncticollis[&&NHX:TOL=941],schizogenius tenuis[&&NHX:TOL=942])[&&NHX:TOL=940])[&&NHX:TOL=936])[&&NHX:TOL=934])schizogenius tenuis group[&&NHX:TOL=932])[&&NHX:TOL=926])[&&NHX:TOL=922],((schizogenius jacarensis[&&NHX:TOL=945],(((schizogenius optimus[&&NHX:TOL=949],schizogenius dyschirioides[&&NHX:TOL=950])[&&NHX:TOL=948],schizogenius clivinoides[&&NHX:TOL=951])[&&NHX:TOL=947],(schizogenius bicolor[&&NHX:TOL=953],schizogenius grossus[&&NHX:TOL=954])[&&NHX:TOL=952])schizogenius optimus group[&&NHX:TOL=946])[&&NHX:TOL=944],((schizogenius ferrugineus[&&NHX:TOL=957],schizogenius auripennis[&&NHX:TOL=958])schizogenius ferrugineus group[&&NHX:TOL=956],((schizogenius multipunctatus[&&NHX:TOL=961],(schizogenius negrei[&&NHX:TOL=963],(schizogenius basalis[&&NHX:TOL=965],schizogenius cearaensis[&&NHX:TOL=966])[&&NHX:TOL=964])[&&NHX:TOL=962])schizogenius basalis group[&&NHX:TOL=960],((schizogenius strigicollis[&&NHX:TOL=969],((schizogenius elongatus[&&NHX:TOL=972],schizogenius costiceps[&&NHX:TOL=973])schizogenius elongatus group[&&NHX:TOL=971],(schizogenius carinatus[&&NHX:TOL=975],schizogenius costipennis[&&NHX:TOL=976])schizogenius carinatus group[&&NHX:TOL=974])[&&NHX:TOL=970])[&&NHX:TOL=968],((schizogenius arechavaletae[&&NHX:TOL=979],schizogenius reichardti[&&NHX:TOL=980])schizogenius arechavaletae group[&&NHX:TOL=978],(((((schizogenius capitalis[&&NHX:TOL=986],schizogenius putzeysi[&&NHX:TOL=987])[&&NHX:TOL=985],(schizogenius lindrothi[&&NHX:TOL=989],schizogenius banningeri[&&NHX:TOL=990])[&&NHX:TOL=988])[&&NHX:TOL=984],schizogenius quadripunctatus[&&NHX:TOL=991])[&&NHX:TOL=983],(((schizogenius darlingtoni[&&NHX:TOL=995],schizogenius interstriatus[&&NHX:TOL=996])[&&NHX:TOL=994],schizogenius riparius[&&NHX:TOL=997])[&&NHX:TOL=993],schizogenius ocellatus[&&NHX:TOL=998])[&&NHX:TOL=992])schizogenius capitalis group[&&NHX:TOL=982],(schizogenius truquii[&&NHX:TOL=1000],(((schizogenius brevisetosus[&&NHX:TOL=1004],((schizogenius seticollis seticollis[&&NHX:TOL=1007],schizogenius seticollis vandykei[&&NHX:TOL=1008])[&&NHX:TOL=1006],((schizogenius pluripunctatus[&&NHX:TOL=1011],schizogenius kulti[&&NHX:TOL=1012])[&&NHX:TOL=1010],(schizogenius plurisetosus[&&NHX:TOL=1014],schizogenius multisetosus[&&NHX:TOL=1015])[&&NHX:TOL=1013])[&&NHX:TOL=1009])[&&NHX:TOL=1005])[&&NHX:TOL=1003],(schizogenius sallei[&&NHX:TOL=1017],(schizogenius tristriatus[&&NHX:TOL=1019],((schizogenius dilatus[&&NHX:TOL=1022],schizogenius tibialis[&&NHX:TOL=1023])[&&NHX:TOL=1021],(schizogenius amphibius[&&NHX:TOL=1025],(schizogenius planuloides[&&NHX:TOL=1027],(schizogenius ozarkensis[&&NHX:TOL=1029],schizogenius planulatus[&&NHX:TOL=1030])[&&NHX:TOL=1028])[&&NHX:TOL=1026])[&&NHX:TOL=1024])[&&NHX:TOL=1020])[&&NHX:TOL=1018])[&&NHX:TOL=1016])[&&NHX:TOL=1002],(schizogenius lineolatus[&&NHX:TOL=1032],((schizogenius pacificus[&&NHX:TOL=1035],(schizogenius chiricahuanus[&&NHX:TOL=1037],(schizogenius longipennis[&&NHX:TOL=1039],schizogenius neovalidus[&&NHX:TOL=1040])[&&NHX:TOL=1038])[&&NHX:TOL=1036])[&&NHX:TOL=1034],((schizogenius arimao[&&NHX:TOL=1043],(schizogenius emdeni[&&NHX:TOL=1045],schizogenius apicalis[&&NHX:TOL=1046])[&&NHX:TOL=1044])[&&NHX:TOL=1042],((schizogenius sulcifrons[&&NHX:TOL=1049],schizogenius litigiosus[&&NHX:TOL=1050])[&&NHX:TOL=1048],((schizogenius pygmaeus[&&NHX:TOL=1053],schizogenius scopaeus[&&NHX:TOL=1054])[&&NHX:TOL=1052],(schizogenius depressus[&&NHX:TOL=1056],(schizogenius falli[&&NHX:TOL=1058],schizogenius ochthocephalus[&&NHX:TOL=1059])[&&NHX:TOL=1057])[&&NHX:TOL=1055])[&&NHX:TOL=1051])[&&NHX:TOL=1047])[&&NHX:TOL=1041])[&&NHX:TOL=1033])[&&NHX:TOL=1031])[&&NHX:TOL=1001])schizogenius truquii group[&&NHX:TOL=999])[&&NHX:TOL=981])[&&NHX:TOL=977])[&&NHX:TOL=967])[&&NHX:TOL=959])[&&NHX:TOL=955])[&&NHX:TOL=943])schizogenius[&&NHX:TOL=916],clivina[&&NHX:TOL=917],(((neodyschirius[&&NHX:TOL=49575],cribrodyschirius[&&NHX:TOL=49576])[&&NHX:TOL=49574],setodyschirius[&&NHX:TOL=49577])[&&NHX:TOL=49573],(dyschirius[&&NHX:TOL=49579],(clivinopsis[&&NHX:TOL=49581],akephorus[&&NHX:TOL=49582],((dyschiriodes chiridysus[&&NHX:TOL=49585],dyschiriodes eudyschirius[&&NHX:TOL=49586])[&&NHX:TOL=49584],reicheiodes[&&NHX:TOL=49587])[&&NHX:TOL=49583],dyschiriodes antidyschirius[&&NHX:TOL=49588],((torretassoa[&&NHX:TOL=49591],(((d. chalybeus group[&&NHX:TOL=49595],d. heydeni group[&&NHX:TOL=49596])[&&NHX:TOL=49594],d. minutus group[&&NHX:TOL=49597],d. bengalensis group[&&NHX:TOL=49598],d. hessei group[&&NHX:TOL=49599])[&&NHX:TOL=49593],(((((dyschiriodes pallipennis[&&NHX:TOL=49605],dyschiriodes sellatus[&&NHX:TOL=49604])[&&NHX:TOL=49614],(dyschiriodes campicola[&&NHX:TOL=49607],dyschiriodes salivagans[&&NHX:TOL=49606])[&&NHX:TOL=49615])d. sellatus group[&&NHX:TOL=49603],d. nitidus group[&&NHX:TOL=49608])[&&NHX:TOL=49602],(d. filiformis group[&&NHX:TOL=49610],d. exochus group[&&NHX:TOL=49611])[&&NHX:TOL=49609])[&&NHX:TOL=49601],d. integer group[&&NHX:TOL=49612])[&&NHX:TOL=49600])dyschiriodes dyschiriodes[&&NHX:TOL=49592])[&&NHX:TOL=49590],dyschiriodes paradyschirius[&&NHX:TOL=49613])[&&NHX:TOL=49589])[&&NHX:TOL=49580])[&&NHX:TOL=49578])dyschiriina[&&NHX:TOL=918],aspidoglossa[&&NHX:TOL=52649])clivinini[&&NHX:TOL=64],scaritini[&&NHX:TOL=65])[&&NHX:TOL=63],((((metrius contractus contractus[&&NHX:TOL=134317],metrius contractus planatus[&&NHX:TOL=134318],metrius contractus sericeus[&&NHX:TOL=134319])metrius contractus[&&NHX:TOL=1360],metrius explodens[&&NHX:TOL=1361])metrius[&&NHX:TOL=134316],sinometrius turnai[&&NHX:TOL=134320])metriini[&&NHX:TOL=154],((((mystropomus regularis laevis[&&NHX:TOL=134321],mystropomus regularis regularis[&&NHX:TOL=134322])mystropomus regularis[&&NHX:TOL=1448],mystropomus subcostatus[&&NHX:TOL=1449])mystropomus[&&NHX:TOL=1402],((anentmetus pluto[&&NHX:TOL=1414],anentmetus spissicornis[&&NHX:TOL=1415])anentmetus[&&NHX:TOL=1412],crepidozaena gracilis[&&NHX:TOL=1544],(dhanya andrewesi[&&NHX:TOL=1417],dhanya bioculata[&&NHX:TOL=1418],dhanya cylindrella[&&NHX:TOL=1419],dhanya mulu[&&NHX:TOL=1420],dhanya parallela[&&NHX:TOL=1421],dhanya seminigra[&&NHX:TOL=1422])dhanya[&&NHX:TOL=1411],entomoantyx cyanipennis[&&NHX:TOL=1404],(eustra andrewesiana[&&NHX:TOL=56858],eustra bryanti[&&NHX:TOL=1426],eustra caeca[&&NHX:TOL=1427],eustra ceylanica[&&NHX:TOL=56859],eustra chinensis[&&NHX:TOL=1428],eustra crucifera[&&NHX:TOL=1429],(eustra csikii burmanensis[&&NHX:TOL=134329],eustra csikii csikii[&&NHX:TOL=134330])eustra csikii[&&NHX:TOL=1430],eustra deharvengi[&&NHX:TOL=52594],eustra gomyi[&&NHX:TOL=56860],eustra hammondi[&&NHX:TOL=56861],eustra honchongensi[&&NHX:TOL=1431],eustra indica[&&NHX:TOL=56862],eustra japonica[&&NHX:TOL=1432],eustra lao[&&NHX:TOL=56863],eustra lebretoni[&&NHX:TOL=1433],eustra leclerci[&&NHX:TOL=52593],(eustra matanga darlingtoni[&&NHX:TOL=134331],eustra matanga matanga[&&NHX:TOL=134332],eustra matanga negrosensis[&&NHX:TOL=134333])eustra matanga[&&NHX:TOL=1434],eustra nageli[&&NHX:TOL=134338],(eustra plagiata peguensis[&&NHX:TOL=134334],eustra plagiata plagiata[&&NHX:TOL=134335])eustra plagiata[&&NHX:TOL=1435],(eustra pseudomatanga cavernicola[&&NHX:TOL=134336],eustra pseudomatanga pseudomatanga[&&NHX:TOL=134337])eustra pseudomatanga[&&NHX:TOL=56864],eustra saripaensis[&&NHX:TOL=56865],eustra storki[&&NHX:TOL=56866],eustra taiwanica[&&NHX:TOL=56867],eustra troglophila[&&NHX:TOL=1436])eustra[&&NHX:TOL=1410],(filicerozaena bravoi[&&NHX:TOL=134339],filicerozaena callangaensis[&&NHX:TOL=134340],filicerozaena chiriboga[&&NHX:TOL=134341],filicerozaena cosangaensis[&&NHX:TOL=134342],filicerozaena flava[&&NHX:TOL=134343],filicerozaena leleuporum[&&NHX:TOL=134344],filicerozaena losi[&&NHX:TOL=134345],filicerozaena moreti[&&NHX:TOL=134346],filicerozaena tagliantii[&&NHX:TOL=134347],filicerozaena toureti[&&NHX:TOL=134348])filicerozaena[&&NHX:TOL=134324],(gibbozaena gibba[&&NHX:TOL=134349],gibbozaena mirabilis[&&NHX:TOL=134350])gibbozaena[&&NHX:TOL=134325],(goniotropis angulicollis[&&NHX:TOL=1474],goniotropis balli[&&NHX:TOL=134351],goniotropis barclayi[&&NHX:TOL=134352],goniotropis batesi[&&NHX:TOL=1475],goniotropis brasiliensis[&&NHX:TOL=1476],goniotropis cartagoensis[&&NHX:TOL=134353],goniotropis cayennensis[&&NHX:TOL=1477],goniotropis claritarsalis[&&NHX:TOL=134354],goniotropis cotopaxiensis[&&NHX:TOL=134355],goniotropis decelleri[&&NHX:TOL=134356],goniotropis ecuadorensis[&&NHX:TOL=134357],goniotropis guyanensis[&&NHX:TOL=134358],goniotropis kuntzeni[&&NHX:TOL=1479],(goniotropis morio parvimorio[&&NHX:TOL=134359],goniotropis morio morio[&&NHX:TOL=134360])goniotropis morio[&&NHX:TOL=1480],(goniotropis navattae boliviiensis[&&NHX:TOL=134362],goniotropis navattae navattae[&&NHX:TOL=134363])goniotropis navattae[&&NHX:TOL=134361],goniotropis omodon[&&NHX:TOL=134364],goniotropis parca[&&NHX:TOL=1484],goniotropis roubaudi[&&NHX:TOL=134365],goniotropis seriatoporoides[&&NHX:TOL=134366],goniotropis seriatoporus[&&NHX:TOL=134367],goniotropis setifer[&&NHX:TOL=1487],goniotropis simplicollis[&&NHX:TOL=134368],goniotropis tarsalis[&&NHX:TOL=134369],goniotropis taylorae[&&NHX:TOL=134370],goniotropis toulgoeti[&&NHX:TOL=134371])goniotropis[&&NHX:TOL=1472],inflatozaena inflatus[&&NHX:TOL=1512],(itamus castaneus[&&NHX:TOL=1438],itamus cavicola[&&NHX:TOL=1439],itamus dentatus[&&NHX:TOL=1440],itamus kaszabi[&&NHX:TOL=1441])itamus[&&NHX:TOL=1398],(microzaena angustior[&&NHX:TOL=1443],microzaena chrysomeloides[&&NHX:TOL=1444],microzaena levis[&&NHX:TOL=1445],microzaena madecassa[&&NHX:TOL=1446])microzaena[&&NHX:TOL=1401],(mimozaena virescens chrysomela[&&NHX:TOL=134372],mimozaena virescens virescens[&&NHX:TOL=134373])mimozaena virescens[&&NHX:TOL=1546],(((ozaena maxi[&&NHX:TOL=1452],ozaena moreti[&&NHX:TOL=52625])[&&NHX:TOL=52624],(ozaena linearis[&&NHX:TOL=1454],ozaena dentipes[&&NHX:TOL=1455],ozaena boucheri[&&NHX:TOL=52623])[&&NHX:TOL=1453])ozaena dentipes group[&&NHX:TOL=1451],((ozaena ecuadorica[&&NHX:TOL=1458],(ozaena elevata[&&NHX:TOL=1460],(ozaena lemoulti[&&NHX:TOL=1462],ozaena martinezi[&&NHX:TOL=1463])[&&NHX:TOL=1461])[&&NHX:TOL=1459])ozaena lemoulti group[&&NHX:TOL=1457],(ozaena grossa[&&NHX:TOL=1465],(ozaena manu[&&NHX:TOL=1467],ozaena convexa[&&NHX:TOL=1468])[&&NHX:TOL=1466])ozaena convexa group[&&NHX:TOL=1464])[&&NHX:TOL=1456])ozaena[&&NHX:TOL=1406],(pachyteles angustatus[&&NHX:TOL=1489],pachyteles aspericollis[&&NHX:TOL=1491],pachyteles bacillus[&&NHX:TOL=1492],pachyteles baleni[&&NHX:TOL=1493],pachyteles besckii[&&NHX:TOL=1494],pachyteles brunneus[&&NHX:TOL=1495],pachyteles castaneus[&&NHX:TOL=1496],pachyteles colasi[&&NHX:TOL=134374],pachyteles confusus[&&NHX:TOL=1497],pachyteles costaricensis[&&NHX:TOL=134375],pachyteles delauneyi[&&NHX:TOL=1498],pachyteles digiulioi[&&NHX:TOL=1499],pachyteles distinctus[&&NHX:TOL=1500],pachyteles excisus[&&NHX:TOL=1502],pachyteles filiformis[&&NHX:TOL=1503],pachyteles fuliginellus[&&NHX:TOL=1504],pachyteles fuscocephalus[&&NHX:TOL=134376],pachyteles fusculus[&&NHX:TOL=1506],pachyteles glaber[&&NHX:TOL=1508],pachyteles goniaderus[&&NHX:TOL=1509],pachyteles gyllenhalii[&&NHX:TOL=1510],pachyteles haroldi[&&NHX:TOL=1511],pachyteles lacordairei[&&NHX:TOL=1513],pachyteles mexicanus[&&NHX:TOL=1517],pachyteles modestus[&&NHX:TOL=1518],pachyteles nigripennis[&&NHX:TOL=1519],pachyteles parvicollis[&&NHX:TOL=1522],pachyteles peruvianus[&&NHX:TOL=1524],pachyteles politus[&&NHX:TOL=1525],pachyteles porrectus[&&NHX:TOL=1526],pachyteles praeustus[&&NHX:TOL=1527],pachyteles pseudovignai[&&NHX:TOL=134377],pachyteles punctulatus[&&NHX:TOL=1528],pachyteles semirufus[&&NHX:TOL=1529],pachyteles seriatus[&&NHX:TOL=1530],pachyteles seriepunctatus[&&NHX:TOL=1531],pachyteles striola[&&NHX:TOL=1532],pachyteles sulcipennis[&&NHX:TOL=1533],pachyteles tapajonus[&&NHX:TOL=1534],pachyteles trinidadensis[&&NHX:TOL=134378],pachyteles tuberculatus[&&NHX:TOL=1535],pachyteles undulatus[&&NHX:TOL=1536],pachyteles urrutiai[&&NHX:TOL=1537],pachyteles verruciger[&&NHX:TOL=1538],pachyteles verrucosus[&&NHX:TOL=1539],pachyteles vignai[&&NHX:TOL=1541])pachyteles[&&NHX:TOL=1405],(physea breyeri[&&NHX:TOL=134379],physea hirta[&&NHX:TOL=1548],physea latipes[&&NHX:TOL=1549],physea setosa[&&NHX:TOL=1550],physea testudinea[&&NHX:TOL=1551],physea tomentosa[&&NHX:TOL=1552])physea[&&NHX:TOL=1408],physeomorpha viana[&&NHX:TOL=1407],(platycerozaena bordoni[&&NHX:TOL=1556],platycerozaena brevicornis[&&NHX:TOL=1557],platycerozaena magna[&&NHX:TOL=1558],platycerozaena panamensis[&&NHX:TOL=1559])platycerozaena[&&NHX:TOL=1403],(proozaena cerdai[&&NHX:TOL=134380],proozaena enischnus[&&NHX:TOL=134381],proozaena flavonigra[&&NHX:TOL=134382],proozaena funcki[&&NHX:TOL=134383],proozaena lata[&&NHX:TOL=134384],proozaena longulus[&&NHX:TOL=134385],proozaena mooreae[&&NHX:TOL=134386],proozaena nigricornis[&&NHX:TOL=134387],proozaena parallelus[&&NHX:TOL=134388])proozaena[&&NHX:TOL=134326],(pseudozaena orientalis[&&NHX:TOL=1561],(pseudozaena tricostata opaca[&&NHX:TOL=134389],pseudozaena tricostata tenebrosa[&&NHX:TOL=134390],pseudozaena tricostata tricostata[&&NHX:TOL=134391])pseudozaena tricostata[&&NHX:TOL=1562])pseudozaena[&&NHX:TOL=1409],(scythropasus elongatus[&&NHX:TOL=1478],scythropasus napoensis[&&NHX:TOL=52626],scythropasus nicaraguensis[&&NHX:TOL=1481],scythropasus olivieri[&&NHX:TOL=1482],scythropasus rogerii[&&NHX:TOL=1485],scythropasus telefordi[&&NHX:TOL=52627])scythropasus[&&NHX:TOL=52569],(serratozaena longicornis[&&NHX:TOL=134392],serratozaena paraphysea[&&NHX:TOL=134393])serratozaena[&&NHX:TOL=134328],((sphaerostylus afrozaena acutangulus[&&NHX:TOL=1565],sphaerostylus afrozaena alluaudi[&&NHX:TOL=1566],sphaerostylus afrozaena feai[&&NHX:TOL=1568],sphaerostylus afrozaena guineensis[&&NHX:TOL=1569],sphaerostylus afrozaena insularis[&&NHX:TOL=1570],sphaerostylus afrozaena levis[&&NHX:TOL=1571],sphaerostylus afrozaena longipennis[&&NHX:TOL=1572],sphaerostylus afrozaena luteus[&&NHX:TOL=1573],sphaerostylus afrozaena striatus[&&NHX:TOL=1574],sphaerostylus afrozaena vadoni[&&NHX:TOL=1575])sphaerostylus afrozaena[&&NHX:TOL=1564],sphaerostylus ozaeniella bimaculatus[&&NHX:TOL=1567],(sphaerostylus sphaerostylus brevipennis[&&NHX:TOL=1577],sphaerostylus sphaerostylus ditomoides[&&NHX:TOL=1578],sphaerostylus sphaerostylus goryi[&&NHX:TOL=1579],sphaerostylus sphaerostylus punctutostriatus[&&NHX:TOL=1580])sphaerostylus sphaerostylus[&&NHX:TOL=1576])sphaerostylus[&&NHX:TOL=1399],(tachypeles arechavaletae[&&NHX:TOL=52571],tachypeles bechynei[&&NHX:TOL=134394],tachypeles boulardi[&&NHX:TOL=134395],tachypeles davidsoni[&&NHX:TOL=134396],tachypeles degallieri[&&NHX:TOL=134397],tachypeles durantoni[&&NHX:TOL=134398],tachypeles gonioderoides[&&NHX:TOL=134399],tachypeles hudsoni[&&NHX:TOL=134400],tachypeles laevigata[&&NHX:TOL=134401],tachypeles lecordieri[&&NHX:TOL=52572],tachypeles limonensis[&&NHX:TOL=134402],tachypeles moraguesi[&&NHX:TOL=134403],tachypeles moretellus[&&NHX:TOL=134404],tachypeles moretianus[&&NHX:TOL=134405],tachypeles oxyomus[&&NHX:TOL=134406],tachypeles parallelipipedus[&&NHX:TOL=134407],tachypeles pascoei[&&NHX:TOL=1523],tachypeles perraulti[&&NHX:TOL=134408],tachypeles rossii[&&NHX:TOL=134409],tachypeles seriepunctaoides[&&NHX:TOL=134410],tachypeles shushufindiensis[&&NHX:TOL=134411],tachypeles troglobioticus[&&NHX:TOL=134412])tachypeles[&&NHX:TOL=1490],(tropopsis biguttatus[&&NHX:TOL=1543],tropopsis marginicollis[&&NHX:TOL=1545])tropopsis[&&NHX:TOL=1542])ozaenina[&&NHX:TOL=134323])ozaenini[&&NHX:TOL=156],(eopaussus balticus[&&NHX:EXT=Y:TOL=27552],(protocerapterus incola[&&NHX:EXT=Y:TOL=27557],protocerapterus primigenius[&&NHX:EXT=Y:TOL=27556])protocerapterus[&&NHX:EXT=Y:TOL=27554],pleurarthropterus hermenaui[&&NHX:EXT=Y:TOL=134535],(succinarthropterus helmi[&&NHX:EXT=Y:TOL=27558],succinarthropterus kolbei[&&NHX:EXT=Y:TOL=27562],succinarthropterus kuehlii[&&NHX:EXT=Y:TOL=27563])succinarthropterus[&&NHX:EXT=Y:TOL=27555],(balticarthropterus nonsucineus[&&NHX:EXT=Y:TOL=135117],balticarthropterus andreei[&&NHX:EXT=Y:TOL=135118],balticarthropterus antiquus[&&NHX:EXT=Y:TOL=135119],balticarthropterus aterrimus[&&NHX:EXT=Y:TOL=135120],balticarthropterus balticus[&&NHX:EXT=Y:TOL=135121],balticarthropterus fritschi[&&NHX:EXT=Y:TOL=135122],balticarthropterus hagedorni[&&NHX:EXT=Y:TOL=135123],balticarthropterus nageli[&&NHX:EXT=Y:TOL=135124],balticarthropterus schaufussi[&&NHX:EXT=Y:TOL=135125],balticarthropterus simoni[&&NHX:EXT=Y:TOL=135126],balticarthropterus skwarrae[&&NHX:EXT=Y:TOL=135127],balticarthropterus subtilis[&&NHX:EXT=Y:TOL=135128])balticarthropterus[&&NHX:EXT=Y:TOL=135103],arthropterites klebsi[&&NHX:EXT=Y:TOL=135129],(cerapterites clavipetrus[&&NHX:EXT=Y:TOL=135131],cerapterites primaevus[&&NHX:EXT=Y:TOL=135132],cerapterites reichenspergerianus[&&NHX:EXT=Y:TOL=135133])cerapterites[&&NHX:EXT=Y:TOL=135130],acmarthropterus kuntzeni[&&NHX:EXT=Y:TOL=27565],(((carabidomemnus carabidoxus acutipennis[&&NHX:TOL=27445],carabidomemnus carabidoxus arthropteroides[&&NHX:TOL=27454],carabidomemnus carabidoxus baenningeri[&&NHX:TOL=27443],carabidomemnus carabidoxus besucheti[&&NHX:TOL=27442],carabidomemnus carabidoxus brachynoides[&&NHX:TOL=27441],carabidomemnus carabidoxus decellei[&&NHX:TOL=27440],carabidomemnus carabidoxus endroedyfilius[&&NHX:TOL=27439],carabidomemnus carabidoxus evansi[&&NHX:TOL=27438],carabidomemnus carabidoxus fulvescens[&&NHX:TOL=27437],carabidomemnus carabidoxus hargreavesi[&&NHX:TOL=27436],carabidomemnus carabidoxus jeanfoxae[&&NHX:TOL=27435],carabidomemnus carabidoxus kirbii[&&NHX:TOL=27434],carabidomemnus carabidoxus lecordieri[&&NHX:TOL=27433],carabidomemnus carabidoxus lunacarvalhoi[&&NHX:TOL=27432],carabidomemnus carabidoxus methneri[&&NHX:TOL=27431],carabidomemnus carabidoxus minutus[&&NHX:TOL=27430],carabidomemnus carabidoxus ozaenoides[&&NHX:TOL=27455],carabidomemnus carabidoxus seineri[&&NHX:TOL=27456],carabidomemnus carabidoxus vaticinus[&&NHX:TOL=27457],carabidomemnus carabidoxus vihenai[&&NHX:TOL=27458])carabidomemnus carabidoxus[&&NHX:TOL=27444],(carabidomemnus carabidomemnus feae[&&NHX:TOL=27452],carabidomemnus carabidomemnus hammondi[&&NHX:TOL=27451],carabidomemnus carabidomemnus ituriensis[&&NHX:TOL=27450],carabidomemnus carabidomemnus luluanus[&&NHX:TOL=27449],carabidomemnus carabidomemnus mollicellus[&&NHX:TOL=27448],carabidomemnus carabidomemnus pallidus[&&NHX:TOL=27453],carabidomemnus carabidomemnus reichenspergeri[&&NHX:TOL=27446])carabidomemnus carabidomemnus[&&NHX:TOL=27447])carabidomemnus[&&NHX:TOL=24842],(eohomopterus aequatoriensis[&&NHX:TOL=24891],eohomopterus centenarius[&&NHX:TOL=24890],eohomopterus paulmuelleri[&&NHX:EXT=Y:TOL=24892],eohomopterus poinari[&&NHX:EXT=Y:TOL=24893],eohomopterus bonfilsi[&&NHX:TOL=27420])eohomopterus[&&NHX:TOL=24889])[&&NHX:TOL=24841],(arthropterus abnormis[&&NHX:TOL=134417],arthropterus ambitiosus[&&NHX:TOL=134418],arthropterus angulatus[&&NHX:TOL=134419],arthropterus angulicornis[&&NHX:TOL=134420],arthropterus articularis[&&NHX:TOL=134421],arthropterus bisinuatus[&&NHX:TOL=134422],arthropterus brevicollis[&&NHX:TOL=134423],arthropterus brevis[&&NHX:TOL=134424],arthropterus brunni[&&NHX:TOL=134425],arthropterus cerapteroides[&&NHX:TOL=134426],arthropterus constricticeps[&&NHX:TOL=134427],arthropterus cribrosus[&&NHX:TOL=134428],arthropterus cylindricus[&&NHX:TOL=134429],arthropterus daemelianus[&&NHX:TOL=134430],arthropterus darlingensis[&&NHX:TOL=134431],arthropterus denudatus[&&NHX:TOL=134432],arthropterus depressus[&&NHX:TOL=134433],arthropterus discrepans[&&NHX:TOL=134434],arthropterus donovani[&&NHX:TOL=134435],arthropterus elongatulus[&&NHX:TOL=134436],arthropterus eruditulus[&&NHX:TOL=134437],arthropterus foveicollis[&&NHX:TOL=134438],arthropterus foveipennis[&&NHX:TOL=134439],arthropterus fraternus[&&NHX:TOL=134440],arthropterus geminus[&&NHX:TOL=134441],arthropterus hirtus[&&NHX:TOL=134442],arthropterus hopii[&&NHX:TOL=134443],arthropterus horni[&&NHX:TOL=134444],arthropterus howittensis[&&NHX:TOL=134445],arthropterus howittii[&&NHX:TOL=134446],arthropterus insidiosus[&&NHX:TOL=134447],arthropterus kingii[&&NHX:TOL=134448],arthropterus limitans[&&NHX:TOL=134449],arthropterus longicollis[&&NHX:TOL=134450],arthropterus macleaii[&&NHX:TOL=134451],arthropterus mastersii[&&NHX:TOL=134452],arthropterus negligens[&&NHX:TOL=134453],arthropterus nigricornis[&&NHX:TOL=134454],arthropterus novellus[&&NHX:TOL=134455],(arthropterus occidentalis occidentalis[&&NHX:TOL=134457],arthropterus occidentalis orientalis[&&NHX:TOL=134458])arthropterus occidentalis[&&NHX:TOL=134456],arthropterus ominosus[&&NHX:TOL=134459],arthropterus ovicollis[&&NHX:TOL=134460],arthropterus parallelocerus[&&NHX:TOL=134461],arthropterus pellax[&&NHX:TOL=134462],arthropterus pervicax[&&NHX:TOL=134463],arthropterus petax[&&NHX:TOL=134464],arthropterus piceus[&&NHX:TOL=134465],arthropterus planicornis[&&NHX:TOL=134466],arthropterus punctatissimus[&&NHX:TOL=134467],arthropterus puncticollis[&&NHX:TOL=134468],arthropterus queenslandiae[&&NHX:TOL=134469],arthropterus riverinae[&&NHX:TOL=134470],arthropterus rockhamptonensis[&&NHX:TOL=134471],(arthropterus schismaticus inconstans[&&NHX:TOL=134473],arthropterus schismaticus schismaticus[&&NHX:TOL=134474])arthropterus schismaticus[&&NHX:TOL=134472],arthropterus schroederi[&&NHX:TOL=134475],arthropterus secedens[&&NHX:TOL=134476],arthropterus simiolus[&&NHX:TOL=134477],arthropterus socius[&&NHX:TOL=134478],arthropterus spadiceus[&&NHX:TOL=134479],arthropterus subampliatus[&&NHX:TOL=134480],arthropterus subangulatus[&&NHX:TOL=134481],arthropterus subsulcatus[&&NHX:TOL=134482],arthropterus turneri[&&NHX:TOL=134483],arthropterus waterhousei[&&NHX:TOL=134484],arthropterus westwoodii[&&NHX:TOL=134485],arthropterus wilsoni[&&NHX:TOL=134486])arthropterus[&&NHX:TOL=65628],(cerapterus kolbei[&&NHX:TOL=134487],cerapterus cerapterus drescheri[&&NHX:TOL=134488],cerapterus cerapterus herrei[&&NHX:TOL=134489],cerapterus cerapterus horsefieldi[&&NHX:TOL=134490],(cerapterus cerapterus latipes latipes[&&NHX:TOL=134492],cerapterus cerapterus latipes singalensis[&&NHX:TOL=134493])cerapterus cerapterus latipes[&&NHX:TOL=134491],(cerapterus cerapterus quadrimaculatus austera[&&NHX:TOL=134495],cerapterus cerapterus quadrimaculatus quadrimaculatus[&&NHX:TOL=134496])cerapterus cerapterus quadrimaculatus[&&NHX:TOL=134494],cerapterus euthysoma benguelanus[&&NHX:TOL=134497],cerapterus euthysoma brancae[&&NHX:TOL=134498],cerapterus euthysoma burgeoni[&&NHX:TOL=134499],cerapterus euthysoma calaharicus[&&NHX:TOL=134500],(cerapterus euthysoma concolor concolor[&&NHX:TOL=134502],cerapterus euthysoma concolor virgula[&&NHX:TOL=134503])cerapterus euthysoma concolor[&&NHX:TOL=134501],(cerapterus euthysoma denoiti denoiti[&&NHX:TOL=134505],cerapterus euthysoma denoiti quadrilineatus[&&NHX:TOL=134506])cerapterus euthysoma denoiti[&&NHX:TOL=134504],cerapterus euthysoma horni[&&NHX:TOL=134507],cerapterus euthysoma immaculatus[&&NHX:TOL=134508],cerapterus euthysoma laceratus[&&NHX:TOL=134509],cerapterus euthysoma lafertei[&&NHX:TOL=134510],cerapterus euthysoma leoninus[&&NHX:TOL=134511],cerapterus euthysoma longihamus[&&NHX:TOL=134512],cerapterus euthysoma myrmedonum[&&NHX:TOL=134513],cerapterus euthysoma oblitus[&&NHX:TOL=134514],cerapterus euthysoma pseudoblitus[&&NHX:TOL=134515],cerapterus euthysoma punctatissimus[&&NHX:TOL=134516],cerapterus euthysoma pygmaeus[&&NHX:TOL=134517],cerapterus euthysoma stuhlmani[&&NHX:TOL=134518],(cerapterus euthysoma trinitalis nyassicus[&&NHX:TOL=134520],cerapterus euthysoma trinitatis parallelus[&&NHX:TOL=134521],cerapterus euthysoma trinitatis trinitatis[&&NHX:TOL=134522])cerapterus euthysoma trinitalis[&&NHX:TOL=134519],cerapterus orthopterus elongis[&&NHX:TOL=134523],cerapterus orthopterus hottentottus[&&NHX:TOL=134524],cerapterus orthopterus longipennis[&&NHX:TOL=134525],(cerapterus orthopterus pilipennis nigra[&&NHX:TOL=134527],cerapterus orthopterus pilipennis pilipennis[&&NHX:TOL=134528])cerapterus orthopterus pilipennis[&&NHX:TOL=134526],(cerapterus orthopterus smithii alluaudi[&&NHX:TOL=134530],cerapterus orthopterus smithii hamatus[&&NHX:TOL=134531],cerapterus orthopterus smithii smithi[&&NHX:TOL=134532])cerapterus orthopterus smithii[&&NHX:TOL=134529],cerapterus orthopterus splendidus[&&NHX:TOL=134533],cerapterus orthopterus stali[&&NHX:TOL=134534])cerapterus[&&NHX:TOL=24844],megalopaussus amplipennis[&&NHX:TOL=24845],mesarthropterus wasmanni[&&NHX:TOL=24846],((pentaplatarthus hyperpentarthrus schoutedeni[&&NHX:TOL=27424],(pentaplatarthus pentaplatarthus bottegi[&&NHX:TOL=135057],pentaplatarthus pentaplatarthus dollmani[&&NHX:TOL=135058],pentaplatarthus pentaplatarthus focki[&&NHX:TOL=135059],pentaplatarthus pentaplatarthus gestroi[&&NHX:TOL=135060],pentaplatarthus pentaplatarthus natalensis[&&NHX:TOL=135061],pentaplatarthus pentaplatarthus paussoides[&&NHX:TOL=135062],pentaplatarthus pentaplatarthus vandamii[&&NHX:TOL=135063])pentaplatarthus pentaplatarthus[&&NHX:TOL=135056])pentaplatarthus[&&NHX:TOL=24849],hexaplatarthus vadoni[&&NHX:TOL=24847])[&&NHX:TOL=24848],(homopterus hispaniolensis[&&NHX:EXT=Y:TOL=134656],homopterus lunacarvalhoi[&&NHX:TOL=134657],homopterus praemonens[&&NHX:TOL=134658],homopterus bolivianus[&&NHX:TOL=134659],homopterus brasiliensis[&&NHX:TOL=134660],homopterus honduriensis[&&NHX:TOL=134661],homopterus martinezi[&&NHX:TOL=134662],homopterus subcordatus[&&NHX:TOL=134663],homopterus amplificatus[&&NHX:TOL=134664],homopterus arrowi[&&NHX:TOL=134665],homopterus cunctans[&&NHX:TOL=134666],homopterus steinbachi[&&NHX:TOL=134667])homopterus[&&NHX:TOL=24850],((heteropaussus heteropaussus cardoni[&&NHX:TOL=134551],heteropaussus heteropaussus taprobanensis[&&NHX:TOL=134552],heteropaussus heteropaussus westermanni[&&NHX:TOL=134553])heteropaussus heteropaussus[&&NHX:TOL=134550],(heteropaussus janssenius brevicornis[&&NHX:TOL=134555],heteropaussus janssenius corintae[&&NHX:TOL=134556],heteropaussus janssenius hastatus[&&NHX:TOL=134557],heteropaussus janssenius laticornis[&&NHX:TOL=134558],heteropaussus janssenius oberthuri[&&NHX:TOL=134559],heteropaussus janssenius passoscarvalhoi[&&NHX:TOL=134560])heteropaussus janssenius[&&NHX:TOL=134554],(heteropaussus pleuropterinus allardi[&&NHX:TOL=134562],(heteropaussus pleuropterinus alternans alternans[&&NHX:TOL=134564],heteropaussus pleuropterinus alternans nigrita[&&NHX:TOL=134565])heteropaussus pleuropterinus alternans[&&NHX:TOL=134563],heteropaussus pleuropterinus angolensis[&&NHX:TOL=134566],heteropaussus pleuropterinus brueckelei[&&NHX:TOL=134567],heteropaussus pleuropterinus curvidens[&&NHX:TOL=134568],heteropaussus pleuropterinus dohrni[&&NHX:TOL=134569],heteropaussus pleuropterinus ferranti[&&NHX:TOL=134570],heteropaussus pleuropterinus flavolineatus[&&NHX:TOL=134571],heteropaussus pleuropterinus jeanneli[&&NHX:TOL=134572],heteropaussus pleuropterinus kivuensis[&&NHX:TOL=134573],heteropaussus pleuropterinus lujae[&&NHX:TOL=134574],heteropaussus pleuropterinus parallelicornis[&&NHX:TOL=134575],heteropaussus pleuropterinus quadricollis[&&NHX:TOL=134576],heteropaussus pleuropterinus rossi[&&NHX:TOL=134577],heteropaussus pleuropterinus simplex[&&NHX:TOL=134578],heteropaussus pleuropterinus trapezicollis[&&NHX:TOL=134579])heteropaussus pleuropterinus[&&NHX:TOL=134561])heteropaussus[&&NHX:TOL=24851],(((euplatyrhopalus aplustrifer[&&NHX:TOL=135064],euplatyrhopalus armicornis[&&NHX:TOL=135065],euplatyrhopalus macrophyllus[&&NHX:TOL=135066],euplatyrhopalus simonis[&&NHX:TOL=135067],euplatyrhopalus vexillifer[&&NHX:TOL=135068],euplatyrhopalus wasmanni[&&NHX:TOL=135069])euplatyrhopalus[&&NHX:TOL=24852],(lebioderus bakeri[&&NHX:TOL=135070],lebioderus candezei[&&NHX:TOL=135071],lebioderus dissimilis[&&NHX:TOL=135072],(lebioderus goryi bicolor[&&NHX:TOL=135074],lebioderus goryi goryi[&&NHX:TOL=135075])lebioderus goryi[&&NHX:TOL=135073],lebioderus javanus[&&NHX:TOL=135076],lebioderus percheronii[&&NHX:TOL=135077],lebioderus ritsemae[&&NHX:TOL=135078],lebioderus thaianus[&&NHX:TOL=135101],[&&NHX:TOL=135102])lebioderus[&&NHX:TOL=24853],(platyrhopalopsis platyrhopalides badgleyi[&&NHX:TOL=135079],(platyrhopalopsis platyrhopalopsis picteti[&&NHX:TOL=135081],platyrhopalopsis platyrhopalopsis mellei[&&NHX:TOL=135080])platyrhopalopsis platyrhopalopsis[&&NHX:TOL=135082])platyrhopalopsis[&&NHX:TOL=24854],((platyrhopalus platyrhopalus acutidens[&&NHX:TOL=135084],platyrhopalus platyrhopalus cardoni[&&NHX:TOL=135085],platyrhopalus platyrhopalus castelnaudi[&&NHX:TOL=135086],platyrhopalus platyrhopalus comottii[&&NHX:TOL=135087],platyrhopalus platyrhopalus davidis[&&NHX:TOL=135088],platyrhopalus platyrhopalus denticornis[&&NHX:TOL=135089],platyrhopalus platyrhopalus imadatei[&&NHX:TOL=135090],platyrhopalus platyrhopalus intermedius[&&NHX:TOL=135091],platyrhopalus platyrhopalus irregularis[&&NHX:TOL=135092],platyrhopalus platyrhopalus mandersi[&&NHX:TOL=135093],platyrhopalus platyrhopalus paussoides[&&NHX:TOL=135094],platyrhopalus platyrhopalus quinquepunctatus[&&NHX:TOL=135095],platyrhopalus platyrhopalus tonkinensis[&&NHX:TOL=135096],platyrhopalus platyrhopalus westwoodi[&&NHX:TOL=135097])platyrhopalus platyrhopalus[&&NHX:TOL=135083],(platyrhopalus stenorhopalus apicalus[&&NHX:TOL=134670],platyrhopalus stenorhopalus tridens[&&NHX:TOL=134671])platyrhopalus stenorhopalus[&&NHX:TOL=24856])platyrhopalus[&&NHX:TOL=24855])platyrhopalina[&&NHX:TOL=27425],((ceratoderus andrewesi[&&NHX:TOL=134537],ceratoderus bifasciatus[&&NHX:TOL=134538],ceratoderus klapperichi[&&NHX:TOL=134539],ceratoderus oberthuri[&&NHX:TOL=134540],ceratoderus palpalis[&&NHX:TOL=134541],ceratoderus tonkinensis[&&NHX:TOL=134542],ceratoderus venustus[&&NHX:TOL=134543])ceratoderus[&&NHX:TOL=24857],(merismoderus bensoni[&&NHX:TOL=134544],merismoderus borneensis[&&NHX:TOL=134545],merismoderus hamatocornis[&&NHX:TOL=134546])merismoderus[&&NHX:TOL=24859],(paussomorphus chevrolati[&&NHX:TOL=134547],paussomorphus conradsianus[&&NHX:TOL=134548],paussomorphus pauliani[&&NHX:TOL=134549])paussomorphus[&&NHX:TOL=24860])ceratoderina[&&NHX:TOL=24858],((granulopaussus granulatus[&&NHX:TOL=134674],granulopaussus leleupi[&&NHX:TOL=134675],granulopaussus reichenspergeri[&&NHX:TOL=134676],granulopaussus sankuruensis[&&NHX:TOL=134677])granulopaussus[&&NHX:TOL=134672],(hylopaussus gracilis[&&NHX:TOL=134894],hylopaussus sebakuanus[&&NHX:TOL=134895])hylopaussus[&&NHX:TOL=24874],(hylotorus basilweskyi[&&NHX:TOL=134678],hylotorus blanchardi[&&NHX:TOL=134679],hylotorus bucephalus[&&NHX:TOL=134680],hylotorus caroli[&&NHX:TOL=134681],hylotorus hottentottus[&&NHX:TOL=134682],hylotorus uelensis[&&NHX:TOL=134683])hylotorus[&&NHX:TOL=24875],leleupaussus tetramerus[&&NHX:TOL=27426],(paussus buettikeri[&&NHX:TOL=134684],paussus amphipaussus alienus[&&NHX:TOL=24861],(paussus anapaussus alluaudi[&&NHX:TOL=134685],paussus anapaussus cervinus[&&NHX:TOL=134686],paussus anapaussus dama[&&NHX:TOL=134687],paussus anapaussus elaphus[&&NHX:TOL=134688],paussus anapaussus perrieri[&&NHX:TOL=134689])paussus anapaussus[&&NHX:TOL=27427],(paussus apopaussus dedyckeri[&&NHX:TOL=134690],paussus apopaussus ghanensis[&&NHX:TOL=134691],paussus apopaussus latidens[&&NHX:TOL=134692],paussus apopaussus planifrons[&&NHX:TOL=134693],paussus apopaussus quadratidens[&&NHX:TOL=134694],(paussus apopaussus sikoranus grandidieri[&&NHX:TOL=134696],paussus apopaussus sikoranus sikoranus[&&NHX:TOL=134698])paussus apopaussus sikoranus[&&NHX:TOL=134695],paussus apopaussus striaticornis[&&NHX:TOL=134697])paussus apopaussus[&&NHX:TOL=24863],(paussus bathypaussus aldrovandi[&&NHX:TOL=134699],paussus bathypaussus cultratus[&&NHX:TOL=134700])paussus bathypaussus[&&NHX:TOL=24864],(paussus batillopaussus batillarius[&&NHX:TOL=134701],paussus batillopaussus cochlearius[&&NHX:TOL=134702],paussus batillopaussus fairmairei[&&NHX:TOL=134703],paussus batillopaussus leechi[&&NHX:TOL=134704],paussus batillopaussus tununguensis[&&NHX:TOL=134705])paussus batillopaussus[&&NHX:TOL=24865],(paussus bicornipaussus afraequatorialis[&&NHX:TOL=134706],paussus bicornipaussus audouini[&&NHX:TOL=134707],paussus bicornipaussus bicornis[&&NHX:TOL=134708],paussus bicornipaussus bituberculatus[&&NHX:TOL=134709],paussus bicornipaussus collarti[&&NHX:TOL=134710],paussus bicornipaussus exiguis[&&NHX:TOL=134711],paussus bicornipaussus kohli[&&NHX:TOL=134712],paussus bicornipaussus modestus[&&NHX:TOL=134713],paussus bicornipaussus planicornis[&&NHX:TOL=134714])paussus bicornipaussus[&&NHX:TOL=24866],(paussus cochliopaussus adjunctus[&&NHX:TOL=134715],paussus cochliopaussus angustulus[&&NHX:TOL=134716],paussus cochliopaussus anxius[&&NHX:TOL=134717],paussus cochliopaussus armicollis[&&NHX:TOL=134718],paussus cochliopaussus asperulus[&&NHX:TOL=134719],paussus cochliopaussus assmuthi[&&NHX:TOL=134720],paussus cochliopaussus atheruri[&&NHX:TOL=134721],paussus cochliopaussus aureofimbriatus[&&NHX:TOL=134722],paussus cochliopaussus basilewskyi[&&NHX:TOL=134723],paussus cochliopaussus benoiti[&&NHX:TOL=134724],paussus cochliopaussus bicolor[&&NHX:TOL=134725],paussus cochliopaussus borneensis[&&NHX:TOL=134726],paussus cochliopaussus bowringi[&&NHX:TOL=134727],paussus cochliopaussus boysi[&&NHX:TOL=134728],paussus cochliopaussus braunsi[&&NHX:TOL=134729],paussus cochliopaussus brittoni[&&NHX:TOL=134730],paussus cochliopaussus burchelianus[&&NHX:TOL=134731],paussus cochliopaussus cardoni[&&NHX:TOL=134732],paussus cochliopaussus celisi[&&NHX:TOL=134733],paussus cochliopaussus clarkei[&&NHX:TOL=134734],paussus cochliopaussus conradti[&&NHX:TOL=134735],paussus cochliopaussus corporaali[&&NHX:TOL=134736],paussus cochliopaussus crepidulae[&&NHX:TOL=134737],paussus cochliopaussus cucullatus[&&NHX:TOL=134738],paussus cochliopaussus cyathiger[&&NHX:TOL=134739],paussus cochliopaussus darlingtoni[&&NHX:TOL=134740],paussus cochliopaussus decellei[&&NHX:TOL=134741],paussus cochliopaussus denticulatus[&&NHX:TOL=134742],paussus cochliopaussus elizabethae[&&NHX:TOL=134743],paussus cochliopaussus escherichi[&&NHX:TOL=134744],paussus cochliopaussus excavatus[&&NHX:TOL=134745],paussus cochliopaussus fichtelii[&&NHX:TOL=134746],paussus cochliopaussus fissifrons[&&NHX:TOL=134747],paussus cochliopaussus foveifrons[&&NHX:TOL=134748],paussus cochliopaussus fulvus[&&NHX:TOL=134749],paussus cochliopaussus gazella[&&NHX:TOL=134750],paussus cochliopaussus glabripennis[&&NHX:TOL=134751],paussus cochliopaussus humbolti[&&NHX:TOL=134752],paussus cochliopaussus inexpectatus[&&NHX:TOL=134753],paussus cochliopaussus janssensi[&&NHX:TOL=134754],paussus cochliopaussus jerdani[&&NHX:TOL=134755],paussus cochliopaussus leleupi[&&NHX:TOL=134756],paussus cochliopaussus madurensis[&&NHX:TOL=134757],paussus cochliopaussus milloti[&&NHX:TOL=134758],paussus cochliopaussus milneedwardsi[&&NHX:TOL=134759],paussus cochliopaussus nauceras[&&NHX:TOL=134760],paussus cochliopaussus nobilis[&&NHX:TOL=134761],paussus cochliopaussus oberthuri[&&NHX:TOL=134762],paussus cochliopaussus opacus[&&NHX:TOL=134763],paussus cochliopaussus pacificus[&&NHX:TOL=134764],paussus cochliopaussus paulmuelleri[&&NHX:TOL=134765],paussus cochliopaussus perroti[&&NHX:TOL=134766],paussus cochliopaussus pierroni[&&NHX:TOL=134767],(paussus cochliopaussus pipitzi lateripunctatus[&&NHX:TOL=134769],paussus cochliopaussus pipitzi mollis[&&NHX:TOL=134770],paussus cochliopaussus pipitzi pictor[&&NHX:TOL=134771],paussus cochliopaussus pipitzi pipitzi[&&NHX:TOL=134772])paussus cochliopaussus pipitzi[&&NHX:TOL=134768],paussus cochliopaussus ploiophorus[&&NHX:TOL=134773],paussus cochliopaussus politus[&&NHX:TOL=134774],paussus cochliopaussus pseudocucullatus[&&NHX:TOL=134775],(paussus cochliopaussus quadricornis castanea[&&NHX:TOL=134777],paussus cochliopaussus quadricornis quadricornis[&&NHX:TOL=134778])paussus cochliopaussus quadricornis[&&NHX:TOL=134776],paussus cochliopaussus rawlinsi[&&NHX:TOL=134779],paussus cochliopaussus ricardojorgei[&&NHX:TOL=134780],paussus cochliopaussus rougemontianus[&&NHX:TOL=134781],paussus cochliopaussus ruber[&&NHX:TOL=134782],paussus cochliopaussus rufitarsus[&&NHX:TOL=134783],paussus cochliopaussus rugiceps[&&NHX:TOL=134784],(paussus cochliopaussus scyphus decorsei[&&NHX:TOL=134786],paussus cochliopaussus scyphus descarpentriesi[&&NHX:TOL=134787],paussus cochliopaussus scyphus scyphus[&&NHX:TOL=134788])paussus cochliopaussus scyphus[&&NHX:TOL=134785],paussus cochliopaussus semicuculatus[&&NHX:TOL=134789],paussus cochliopaussus semirufus[&&NHX:TOL=134790],paussus cochliopaussus seriesetosus[&&NHX:TOL=134791],paussus cochliopaussus seyriganus[&&NHX:TOL=134792],paussus cochliopaussus sicardi[&&NHX:TOL=134793],paussus cochliopaussus soleatus[&&NHX:TOL=134794],paussus cochliopaussus solidus[&&NHX:TOL=134795],paussus cochliopaussus stevensianus[&&NHX:TOL=134796],paussus cochliopaussus suavis[&&NHX:TOL=134797],paussus cochliopaussus testaceus[&&NHX:TOL=134798],paussus cochliopaussus thoracicus[&&NHX:TOL=134799],paussus cochliopaussus tibialis[&&NHX:TOL=134800],paussus cochliopaussus turcicus[&&NHX:TOL=134801],paussus cochliopaussus vadoni[&&NHX:TOL=134802],paussus cochliopaussus viator[&&NHX:TOL=134803],paussus cochliopaussus wellmanni[&&NHX:TOL=134804],paussus cochliopaussus wroughtoni[&&NHX:TOL=134805],paussus cochliopaussus brincki[&&NHX:TOL=134806],paussus cochliopaussus capillaceus[&&NHX:TOL=134807],paussus cochliopaussus dollmani[&&NHX:TOL=134808],paussus cochliopaussus laticollis[&&NHX:TOL=134809],paussus cochliopaussus lusotropicalis[&&NHX:TOL=134810],paussus cochliopaussus marshalli[&&NHX:TOL=134811],paussus cochliopaussus murrayi[&&NHX:TOL=134812],paussus cochliopaussus overlaeti[&&NHX:TOL=134813],paussus cochliopaussus penicillatus[&&NHX:TOL=134814],paussus cochliopaussus permutatus[&&NHX:TOL=134815],paussus cochliopaussus rugosus[&&NHX:TOL=134816],paussus cochliopaussus seydeli[&&NHX:TOL=134817],paussus cochliopaussus spiniceps[&&NHX:TOL=134818],paussus cochliopaussus ypsilopilos[&&NHX:TOL=134819],paussus cochliopaussus upembanus[&&NHX:TOL=134820])paussus cochliopaussus[&&NHX:TOL=24867],(paussus crenatopaussus cirenaicus[&&NHX:TOL=134821],paussus crenatopaussus colasi[&&NHX:TOL=134822],paussus crenatopaussus crenaticornis[&&NHX:TOL=134823],paussus crenatopaussus kochi[&&NHX:TOL=134824],paussus crenatopaussus piochardi[&&NHX:TOL=134825],paussus crenatopaussus scaliger[&&NHX:TOL=134826],paussus crenatopaussus serratulus[&&NHX:TOL=134827])paussus crenatopaussus[&&NHX:TOL=24868],(paussus curtisipaussus africanus[&&NHX:TOL=134828],paussus curtisipaussus bicoloricornis[&&NHX:TOL=134829],paussus curtisipaussus coronatus[&&NHX:TOL=134830],paussus curtisipaussus curtisii[&&NHX:TOL=134831],paussus curtisipaussus cylindricornis[&&NHX:TOL=134832],paussus curtisipaussus elongatus[&&NHX:TOL=134833],paussus curtisipaussus germari[&&NHX:TOL=134834],paussus curtisipaussus horikawae[&&NHX:TOL=134835],paussus curtisipaussus jacobsoni[&&NHX:TOL=134836],paussus curtisipaussus jousselini[&&NHX:TOL=134837],paussus curtisipaussus kjellanderi[&&NHX:TOL=134838],paussus curtisipaussus lamottei[&&NHX:TOL=134839],paussus curtisipaussus minor[&&NHX:TOL=134840],paussus curtisipaussus mirei[&&NHX:TOL=134841],paussus curtisipaussus pallidefulvus[&&NHX:TOL=134842],paussus curtisipaussus pasteuri[&&NHX:TOL=134843],paussus curtisipaussus raffrayi[&&NHX:TOL=134844],paussus curtisipaussus recticornis[&&NHX:TOL=134845],paussus curtisipaussus sauteri[&&NHX:TOL=134846],paussus curtisipaussus schaumii[&&NHX:TOL=134847],paussus curtisipaussus shuckardi[&&NHX:TOL=134848],paussus curtisipaussus sinicus[&&NHX:TOL=134849],paussus curtisipaussus spinolae[&&NHX:TOL=134850],paussus curtisipaussus telescopifer[&&NHX:TOL=134851],paussus curtisipaussus vanrooni[&&NHX:TOL=134852],paussus curtisipaussus wittei[&&NHX:TOL=134853])paussus curtispaussus[&&NHX:TOL=24869],(paussus edaphopaussus americanus[&&NHX:TOL=134854],paussus edaphopaussus avunculus[&&NHX:TOL=134855],paussus edaphopaussus burgeoni[&&NHX:TOL=134856],paussus edaphopaussus centurio[&&NHX:TOL=134857],paussus edaphopaussus dichrous[&&NHX:TOL=134858],paussus edaphopaussus eisentrauti[&&NHX:TOL=134859],paussus edaphopaussus goetzei[&&NHX:TOL=134860],paussus edaphopaussus laevifrons[&&NHX:TOL=134861],paussus edaphopaussus manni[&&NHX:TOL=134862],paussus edaphopaussus orientalis[&&NHX:TOL=134863],paussus edaphopaussus patrizii[&&NHX:TOL=134864],paussus edaphopaussus scorteccii[&&NHX:TOL=134865],paussus edaphopaussus simplicissimus[&&NHX:TOL=134866],paussus edaphopaussus stolzi[&&NHX:TOL=134867],paussus edaphopaussus tchadensis[&&NHX:TOL=134868],paussus edaphopaussus verticalis[&&NHX:TOL=134869],paussus edaphopaussus globiceps[&&NHX:TOL=134870],paussus edaphopaussus aristotelis[&&NHX:TOL=134871],paussus edaphopaussus cylindricollis[&&NHX:TOL=134872],paussus edaphopaussus henningsi[&&NHX:TOL=134873],paussus edaphopaussus inermis[&&NHX:TOL=134874],paussus edaphopaussus nudus[&&NHX:TOL=134875],paussus edaphopaussus procerus[&&NHX:TOL=134876],paussus edaphopaussus recorpus[&&NHX:TOL=134877],paussus edaphopaussus affinis[&&NHX:TOL=134878],paussus edaphopaussus cognatus[&&NHX:TOL=134879],paussus edaphopaussus hardwickii[&&NHX:TOL=134880],(paussus edaphopaussus hearseyanus hearseyanus[&&NHX:TOL=134882],paussus edaphopaussus hearseyanus parvicornis[&&NHX:TOL=134883])paussus edaphopaussus hearseyanus[&&NHX:TOL=134881],paussus edaphopaussus horni[&&NHX:TOL=134884],paussus edaphopaussus saundersii[&&NHX:TOL=134885],paussus edaphopaussus schiodtii[&&NHX:TOL=134886],(paussus edaphopaussus sesquisulcatus brevicornis[&&NHX:TOL=134888],paussus edaphopaussus sesquisulcatus sesquisulcatus[&&NHX:TOL=134889])paussus edaphopaussus sesquisulcatus[&&NHX:TOL=134887],paussus edaphopaussus sewelli[&&NHX:TOL=134890])paussus edaphopaussus[&&NHX:TOL=24870],paussus enneapaussus howa[&&NHX:TOL=24871],(paussus flagellopaussus biflagellatus[&&NHX:TOL=134891],paussus flagellopaussus favieri[&&NHX:TOL=134892],paussus flagellopaussus krelli[&&NHX:TOL=134893])paussus flagellopaussus[&&NHX:TOL=24873],paussus idupaussus pilicornis[&&NHX:TOL=24876],(paussus katapaussus adinventus[&&NHX:TOL=134920],paussus katapaussus aethiops[&&NHX:TOL=134921],paussus katapaussus arabicus[&&NHX:TOL=134922],paussus katapaussus armatus[&&NHX:TOL=134923],paussus katapaussus bayonii[&&NHX:TOL=134924],(paussus katapaussus clipes clipes[&&NHX:TOL=134926],paussus katapaussus clipes hirsutus[&&NHX:TOL=134927],paussus katapaussus clipes obscurus[&&NHX:TOL=134928],paussus katapaussus clipes propinquus[&&NHX:TOL=134929])paussus katapaussus clipes[&&NHX:TOL=134925],paussus katapaussus dissimulator[&&NHX:TOL=134930],paussus katapaussus moltonii[&&NHX:TOL=134931],paussus katapaussus nageli[&&NHX:TOL=134932],paussus katapaussus pseudosetosus[&&NHX:TOL=134933],paussus katapaussus setosus[&&NHX:TOL=134934],paussus katapaussus somaliae[&&NHX:TOL=134935],paussus katapaussus sphaerocerus[&&NHX:TOL=134936],paussus katapaussus spinicola[&&NHX:TOL=134937],paussus katapaussus thomsonii[&&NHX:TOL=134938],paussus katapaussus woerdeni[&&NHX:TOL=134939],paussus katapaussus chappuisi[&&NHX:TOL=134940],paussus katapaussus cornutus[&&NHX:TOL=134941],paussus katapaussus rusticus[&&NHX:TOL=134942],paussus katapaussus antinorii[&&NHX:TOL=134943],(paussus katapaussus humboldti humboldti[&&NHX:TOL=134945],paussus katapaussus humboldti laevicornis[&&NHX:TOL=134946])paussus katapaussus humboldti[&&NHX:TOL=134944])paussus katapaussus[&&NHX:TOL=24877],(paussus klugipaussus canteloubei[&&NHX:TOL=134947],paussus klugipaussus capreolus[&&NHX:TOL=134948],paussus klugipaussus comptus[&&NHX:TOL=134949],paussus klugipaussus distinguendus[&&NHX:TOL=134950],paussus klugipaussus klugii[&&NHX:TOL=134951],paussus klugipaussus lacrimans[&&NHX:TOL=134952],paussus klugipaussus latreillei[&&NHX:TOL=134953],paussus klugipaussus leroyi[&&NHX:TOL=134954],paussus klugipaussus linnavuori[&&NHX:TOL=134955],paussus klugipaussus olcesei[&&NHX:TOL=134956],paussus klugipaussus pseudoklugi[&&NHX:TOL=134957],paussus klugipaussus schoutedeni[&&NHX:TOL=134958],paussus klugipaussus subarcuatus[&&NHX:TOL=134959],paussus klugipaussus tigrinus[&&NHX:TOL=134960],paussus klugipaussus vexator[&&NHX:TOL=134961],paussus klugipaussus cerambyx[&&NHX:TOL=134962],paussus klugipaussus rougemonti[&&NHX:TOL=134963])paussus klugipaussus[&&NHX:TOL=24878],paussus latipaussus desneuxi[&&NHX:TOL=24879],(paussus lineatopaussus aenigma[&&NHX:TOL=134964],paussus lineatopaussus afzelii[&&NHX:TOL=134965],paussus lineatopaussus araneans[&&NHX:TOL=134966],paussus lineatopaussus camaxilensis[&&NHX:TOL=134967],paussus lineatopaussus concinnus[&&NHX:TOL=134968],paussus lineatopaussus decipiens[&&NHX:TOL=134969],paussus lineatopaussus degeeri[&&NHX:TOL=134970],paussus lineatopaussus heinrichi[&&NHX:TOL=134971],paussus lineatopaussus laetus[&&NHX:TOL=134972],paussus lineatopaussus lineatus[&&NHX:TOL=134973],paussus lineatopaussus moreirai[&&NHX:TOL=134974],paussus lineatopaussus natalis[&&NHX:TOL=134975],paussus lineatopaussus passosi[&&NHX:TOL=134976],paussus lineatopaussus pretoriensis[&&NHX:TOL=134977],paussus lineatopaussus semilineatus[&&NHX:TOL=134978],paussus lineatopaussus tenuiculus[&&NHX:TOL=134979],paussus lineatopaussus tenuis[&&NHX:TOL=134980])paussus lineatopaussus[&&NHX:TOL=24880],(paussus malgasipaussus aureovellus[&&NHX:TOL=134981],paussus malgasipaussus bekilyanus[&&NHX:TOL=134982],paussus malgasipaussus catalai[&&NHX:TOL=134983],paussus malgasipaussus jeannelianus[&&NHX:TOL=134984],(paussus malgasipaussus mucius kraatzi[&&NHX:TOL=134986],paussus malgasipaussus mucius mucius[&&NHX:TOL=134987])paussus malgasipaussus mucius[&&NHX:TOL=134985],paussus malgasipaussus seyrigi[&&NHX:TOL=134988],paussus malgasipaussus wasmanni[&&NHX:TOL=134989])paussus malgasipaussus[&&NHX:TOL=24881],(paussus manicanopaussus adeptus[&&NHX:TOL=134990],paussus manicanopaussus brevicornutus[&&NHX:TOL=134991],paussus manicanopaussus ceratoderinus[&&NHX:TOL=134992],paussus manicanopaussus citernii[&&NHX:TOL=134993],paussus manicanopaussus cuypersi[&&NHX:TOL=134994],paussus manicanopaussus fletcheri[&&NHX:TOL=134995],paussus manicanopaussus incultus[&&NHX:TOL=134996],paussus manicanopaussus intermedius[&&NHX:TOL=134997],paussus manicanopaussus kristenseni[&&NHX:TOL=134998],paussus manicanopaussus liber[&&NHX:TOL=134999],paussus manicanopaussus manicanus[&&NHX:TOL=135000],paussus manicanopaussus medleri[&&NHX:TOL=135001],paussus manicanopaussus planicollis[&&NHX:TOL=135002],paussus manicanopaussus spencii[&&NHX:TOL=135003],paussus manicanopaussus vollenhovii[&&NHX:TOL=135004])paussus manicanopaussus[&&NHX:TOL=24882],(paussus paussus affulgens[&&NHX:TOL=135005],paussus paussus barkeri[&&NHX:TOL=135006],paussus paussus burmeisteri[&&NHX:TOL=135007],paussus paussus dissidens[&&NHX:TOL=135008],paussus paussus linnaei[&&NHX:TOL=135009],paussus paussus microcephalus[&&NHX:TOL=135010],paussus paussus oertzeni[&&NHX:TOL=135011])paussus paussus[&&NHX:TOL=134673],(paussus scaphipaussus catoxanthus[&&NHX:TOL=135012],paussus scaphipaussus drescheri[&&NHX:TOL=135013],paussus scaphipaussus formosus[&&NHX:TOL=135014],paussus scaphipaussus hystrix[&&NHX:TOL=135015],paussus scaphipaussus kolbei[&&NHX:TOL=135016],paussus scaphipaussus occlusus[&&NHX:TOL=135017],paussus scaphipaussus tagalicus[&&NHX:TOL=135018],paussus scaphipaussus tristis[&&NHX:TOL=135019],paussus scaphipaussus waterhousei[&&NHX:TOL=135020])paussus scaphipaussus[&&NHX:TOL=24884],(paussus semipaussus andreae[&&NHX:TOL=135021],paussus semipaussus javanus[&&NHX:TOL=135022],paussus semipaussus kannegieteri[&&NHX:TOL=135023],paussus semipaussus lucasseni[&&NHX:TOL=135024],paussus semipaussus ludekingi[&&NHX:TOL=135025],paussus semipaussus nigrita[&&NHX:TOL=135026],paussus semipaussus pandamanus[&&NHX:TOL=135027],(paussus semipaussus ritsemae buitenzorgensis[&&NHX:TOL=135029],paussus semipaussus ritsemae ritsemae[&&NHX:TOL=135030])paussus semipaussus ritsemae[&&NHX:TOL=135028])paussus semipaussus[&&NHX:TOL=24885],(paussus spinicoxipaussus acuminicoxis[&&NHX:TOL=135031],paussus spinicoxipaussus arduus[&&NHX:TOL=135032],paussus spinicoxipaussus canaliculatus[&&NHX:TOL=135033],paussus spinicoxipaussus cridae[&&NHX:TOL=135034],paussus spinicoxipaussus damarinus[&&NHX:TOL=135035],paussus spinicoxipaussus mimus[&&NHX:TOL=135036],paussus spinicoxipaussus prestesjoannesi[&&NHX:TOL=135037],paussus spinicoxipaussus reductus[&&NHX:TOL=135038],paussus spinicoxipaussus spinicoxis[&&NHX:TOL=135039],paussus spinicoxipaussus suahelinus[&&NHX:TOL=135040],paussus spinicoxipaussus bohemani[&&NHX:TOL=135041],paussus spinicoxipaussus dohrnii[&&NHX:TOL=135042],paussus spinicoxipaussus fallax[&&NHX:TOL=135043],paussus spinicoxipaussus jeanneli[&&NHX:TOL=135044],paussus spinicoxipaussus massarti[&&NHX:TOL=135045],paussus spinicoxipaussus reichenspergeri[&&NHX:TOL=135046],paussus spinicoxipaussus cephalotes[&&NHX:TOL=135047])paussus spinicoxipaussus[&&NHX:TOL=24886],(paussus squamipaussus ambiguus[&&NHX:TOL=135048],paussus squamipaussus donisthorpei[&&NHX:TOL=135049],paussus squamipaussus hughscotti[&&NHX:TOL=135050],paussus squamipaussus roeri[&&NHX:TOL=135051],paussus squamipaussus signatipennis[&&NHX:TOL=135052],paussus squamipaussus squamicornis[&&NHX:TOL=135053])paussus squamipaussus[&&NHX:TOL=24887],(paussus trepopaussus bastinae[&&NHX:TOL=135054],paussus trepopaussus intuitivus[&&NHX:TOL=135055])paussus trepopaussus[&&NHX:TOL=24888])paussus[&&NHX:TOL=24883])paussina[&&NHX:TOL=24862])[&&NHX:TOL=27428])paussini[&&NHX:TOL=157],(protopaussus pristinus[&&NHX:EXT=Y:TOL=52631],(protopaussus archipaussus bakeri[&&NHX:TOL=52636],protopaussus archipaussus javanus[&&NHX:TOL=52635],protopaussus archipaussus jeanneli[&&NHX:TOL=52634],protopaussus archipaussus kaszabi[&&NHX:TOL=52633])protopaussus archipaussus[&&NHX:TOL=135098],(protopaussus protopaussus almorensis[&&NHX:TOL=52630],protopaussus protopaussus basilewskyi[&&NHX:TOL=135100],protopaussus protopaussus feae[&&NHX:TOL=52629],protopaussus protopaussus walkeri[&&NHX:TOL=52632])protopaussus protopaussus[&&NHX:TOL=135099])protopaussus[&&NHX:TOL=52628])[&&NHX:TOL=155])paussinae[&&NHX:TOL=49],(collyridini[&&NHX:TOL=78],megacephalini[&&NHX:TOL=79],ctenostomatini[&&NHX:TOL=80],manticorini[&&NHX:TOL=81],cicindelini[&&NHX:TOL=82])cicindelitae[&&NHX:TOL=53],nototylus fryi[&&NHX:TOL=50],(notiophilus[&&NHX:TOL=148],notiokasis chaudoiri[&&NHX:TOL=149],(pelophila rudis[&&NHX:TOL=1697],pelophila borealis[&&NHX:TOL=1698])pelophilini[&&NHX:TOL=150],(opisthius richardsoni[&&NHX:TOL=1394],paropisthius[&&NHX:TOL=1395])opisthiini[&&NHX:TOL=151],(leistus[&&NHX:TOL=1379],nippononebria[&&NHX:TOL=1380],nebria[&&NHX:TOL=1381],etc.[&&NHX:TOL=1382])nebriini[&&NHX:TOL=152])nebriitae[&&NHX:TOL=51],(carabini[&&NHX:TOL=73],(ceroglossus buqueti[&&NHX:TOL=57909],ceroglossus chilensis[&&NHX:TOL=57910],ceroglossus darwini[&&NHX:TOL=57911],ceroglossus guerini[&&NHX:TOL=57912],ceroglossus magellanicus[&&NHX:TOL=57913],ceroglossus ochsenii[&&NHX:TOL=57914],ceroglossus speciosus[&&NHX:TOL=57915],ceroglossus suturalis[&&NHX:TOL=57916])ceroglossus[&&NHX:TOL=74],(pamborus[&&NHX:TOL=1582],maoripamborus[&&NHX:TOL=1583])pamborini[&&NHX:TOL=75],(cychrus[&&NHX:TOL=1078],sphaeroderus[&&NHX:TOL=1079],scaphinotus[&&NHX:TOL=1080],cychropsis[&&NHX:TOL=1081])cychrini[&&NHX:TOL=76])carabitae[&&NHX:TOL=52],(loricera wollastoni[&&NHX:TOL=1336],(((loricera pilicornis[&&NHX:TOL=1340],(loricera decempunctata[&&NHX:TOL=1342],loricera foveata[&&NHX:TOL=1343])[&&NHX:TOL=1341])[&&NHX:TOL=1339],(loricera rotundicollis[&&NHX:TOL=1345],loricera aptena[&&NHX:TOL=1346])[&&NHX:TOL=1344])[&&NHX:TOL=1338],(loricera stevensi[&&NHX:TOL=1348],((loricera mirabilis[&&NHX:TOL=1351],loricera ovipennis[&&NHX:TOL=1352])[&&NHX:TOL=1350],loricera obsoleta[&&NHX:TOL=1353])[&&NHX:TOL=1349])[&&NHX:TOL=1347])[&&NHX:TOL=1337])loricerini[&&NHX:TOL=54],(omophron dentatum[&&NHX:TOL=57123],omophron baenningeri[&&NHX:TOL=57122],omophron tessellatum[&&NHX:TOL=57136],omophron ovale[&&NHX:TOL=57132],omophron sphaericum[&&NHX:TOL=57135],omophron solidum[&&NHX:TOL=57134],omophron robustum[&&NHX:TOL=57133],omophron brettinghamae[&&NHX:TOL=57137],omophron americanum[&&NHX:TOL=57121],omophron oblonguisculum[&&NHX:TOL=57131],omophron obliteratum[&&NHX:TOL=57130],omophron nitidum[&&NHX:TOL=57129],omophron mexicanum[&&NHX:TOL=57128],omophron labiatum[&&NHX:TOL=57127],omophron grossum[&&NHX:TOL=57126],omophron gratum[&&NHX:TOL=57125],omophron gilae[&&NHX:TOL=57124],(omophron phrator depressum[&&NHX:TOL=57140],omophron phrator grandidieri[&&NHX:TOL=57141],omophron phrator vitullatum[&&NHX:TOL=57139],omophron phrator multiguttatum[&&NHX:TOL=57142],omophron phrator rothschildi[&&NHX:TOL=57143],omophron phrator  schoutedeni[&&NHX:TOL=57144],omophron phrator variegatum variegatum[&&NHX:TOL=57145],omophron phrator variegatum boiteli[&&NHX:TOL=57146],omophron phrator variegatum sardoum[&&NHX:TOL=57147])omophron phrator[&&NHX:TOL=67267])omophron[&&NHX:TOL=55],(cicindis horni[&&NHX:TOL=911],archaeocindis johnbeckeri[&&NHX:TOL=912])cicindini[&&NHX:TOL=56],((diacheila arctica[&&NHX:TOL=1107],(diacheila polita[&&NHX:TOL=1109],diacheila fausti[&&NHX:TOL=1110])[&&NHX:TOL=1108])diacheila[&&NHX:TOL=1087],(((blethisa inexspectata[&&NHX:TOL=1093],blethisa julii[&&NHX:TOL=1094])[&&NHX:TOL=1092],((blethisa multipunctata[&&NHX:TOL=1097],blethisa oregonensis[&&NHX:TOL=1098])[&&NHX:TOL=1096],((blethisa tuberculata[&&NHX:TOL=1101],blethisa catenaria[&&NHX:TOL=1102])[&&NHX:TOL=1100],(blethisa eschscholtzi[&&NHX:TOL=1104],blethisa quadricollis[&&NHX:TOL=1105])[&&NHX:TOL=1103])[&&NHX:TOL=1099])[&&NHX:TOL=1095])blethisa[&&NHX:TOL=1089],(elaphrus lapponicus[&&NHX:TOL=1112],(((elaphrus splendidus[&&NHX:TOL=1116],(elaphrus japonicus[&&NHX:TOL=1118],(elaphrus pyrenoeus[&&NHX:TOL=1120],elaphrus uliginosus[&&NHX:TOL=1121])[&&NHX:TOL=1119])[&&NHX:TOL=1117])[&&NHX:TOL=1115],((elaphrus fuliginosus[&&NHX:TOL=1124],(elaphrus lindrothi[&&NHX:TOL=1126],elaphrus cicatricosus[&&NHX:TOL=1127])[&&NHX:TOL=1125])[&&NHX:TOL=1123],((elaphrus sibiricus[&&NHX:TOL=1130],elaphrus cupreus[&&NHX:TOL=1131])[&&NHX:TOL=1129],(elaphrus clairvillei[&&NHX:TOL=1133],(elaphrus laevigatus[&&NHX:TOL=1135],elaphrus olivaceous[&&NHX:TOL=1136])[&&NHX:TOL=1134])[&&NHX:TOL=1132])[&&NHX:TOL=1128])[&&NHX:TOL=1122])elaphrus neoelaphrus[&&NHX:TOL=1114],((elaphrus marginicollis[&&NHX:TOL=1139],((elaphrus lheritieri[&&NHX:TOL=1142],(elaphrus mimus[&&NHX:TOL=1144],elaphrus viridis[&&NHX:TOL=1145])[&&NHX:TOL=1143])[&&NHX:TOL=1141],(elaphrus hypocrita[&&NHX:TOL=1147],(elaphrus ruscarius[&&NHX:TOL=1149],((elaphrus lecontei[&&NHX:TOL=1152],(elaphrus californicus[&&NHX:TOL=1154],(elaphrus finitimus[&&NHX:TOL=1156],elaphrus americanus[&&NHX:TOL=1157])[&&NHX:TOL=1155])[&&NHX:TOL=1153])[&&NHX:TOL=1151],((elaphrus tuberculatus[&&NHX:TOL=1160],elaphrus riparius[&&NHX:TOL=1161])[&&NHX:TOL=1159],(elaphrus comatus[&&NHX:TOL=1163],(elaphrus parviceps[&&NHX:TOL=1165],elaphrus tibetanus[&&NHX:TOL=1166])[&&NHX:TOL=1164])[&&NHX:TOL=1162])[&&NHX:TOL=1158])[&&NHX:TOL=1150])[&&NHX:TOL=1148])[&&NHX:TOL=1146])[&&NHX:TOL=1140])elaphrus elaphrus[&&NHX:TOL=1138],(elaphrus punctatus[&&NHX:TOL=1168],(elaphrus aureus[&&NHX:TOL=1170],(elaphrus purpurans[&&NHX:TOL=1172],(elaphrus angusticollis[&&NHX:TOL=1174],elaphrus ulrichi[&&NHX:TOL=1175])[&&NHX:TOL=1173])[&&NHX:TOL=1171])[&&NHX:TOL=1169])elaphrus elaphroterus[&&NHX:TOL=1167])[&&NHX:TOL=1137])[&&NHX:TOL=1113])elaphrus[&&NHX:TOL=1090])[&&NHX:TOL=1088])elaphrini[&&NHX:TOL=57],((monolobus[&&NHX:TOL=1363],migadops[&&NHX:TOL=1364],migadopidius[&&NHX:TOL=1365],pseudomigadops[&&NHX:TOL=1366],antarctonomus[&&NHX:TOL=1367],aquilex[&&NHX:TOL=1368],lissopterus[&&NHX:TOL=1369],rhytidognathus[&&NHX:TOL=1370],calathosoma[&&NHX:TOL=1371],calyptogonia[&&NHX:TOL=1372],decogmus[&&NHX:TOL=1373],stichonotus[&&NHX:TOL=1374],nebriosoma[&&NHX:TOL=1375],loxomerus[&&NHX:TOL=1376])migadopini[&&NHX:TOL=58],amarotypus edwardsi[&&NHX:TOL=59])[&&NHX:TOL=65348],(promecognathus[&&NHX:TOL=1767],(axinidium[&&NHX:TOL=1769],paraxinidium[&&NHX:TOL=1770],(metaxinidium[&&NHX:TOL=1772],holaxinidium[&&NHX:TOL=1773])[&&NHX:TOL=1771])[&&NHX:TOL=1768])promecognathini[&&NHX:TOL=60],(siagona[&&NHX:TOL=2276],(luperca[&&NHX:TOL=2278],enceladus[&&NHX:TOL=2279])[&&NHX:TOL=2277])siagonini[&&NHX:TOL=61],(((((hiletus alluaudi[&&NHX:TOL=1324],hiletus nimba[&&NHX:TOL=1325])[&&NHX:TOL=1323],hiletus katanganus[&&NHX:TOL=1326])[&&NHX:TOL=1322],hiletus jeanneli[&&NHX:TOL=1327])[&&NHX:TOL=1321],(hiletus versutus[&&NHX:TOL=1329],hiletus fossulatus[&&NHX:TOL=1330])[&&NHX:TOL=1328])hiletus[&&NHX:TOL=1291],(((eucamaragnathus oxygonus[&&NHX:TOL=1296],eucamaragnathus fissipennis[&&NHX:TOL=1297])[&&NHX:TOL=1295],eucamaragnathus castelnaui[&&NHX:TOL=1298])[&&NHX:TOL=1294],(eucamaragnathus suberbiei[&&NHX:TOL=1300],(eucamaragnathus bocandei[&&NHX:TOL=1302],((eucamaragnathus borneensis[&&NHX:TOL=1305],(eucamaragnathus aterrimus[&&NHX:TOL=1307],((eucamaragnathus spiniger[&&NHX:TOL=1310],eucamaragnathus angulicollis[&&NHX:TOL=1311])[&&NHX:TOL=1309],eucamaragnathus sumatrensis[&&NHX:TOL=1312])[&&NHX:TOL=1308])[&&NHX:TOL=1306])[&&NHX:TOL=1304],(eucamaragnathus amapa[&&NHX:TOL=1314],(eucamaragnathus brasiliensis[&&NHX:TOL=1316],(eucamaragnathus jaws[&&NHX:TOL=1318],eucamaragnathus batesi[&&NHX:TOL=1319])[&&NHX:TOL=1317])[&&NHX:TOL=1315])[&&NHX:TOL=1313])[&&NHX:TOL=1303])[&&NHX:TOL=1301])[&&NHX:TOL=1299])eucamaragnathus[&&NHX:TOL=1292])hiletini[&&NHX:TOL=62],(gehringia olympica[&&NHX:TOL=68],(helenaea bisignata[&&NHX:TOL=57255],helenaea torretassoi[&&NHX:TOL=56967])helenaea[&&NHX:TOL=57254])gehringiini[&&NHX:TOL=56971],(leoglymmius lignarius[&&NHX:TOL=1791],sloanoglymmius planatus[&&NHX:TOL=1792],medisores abditus[&&NHX:TOL=1793],((dhysores thoreyi[&&NHX:TOL=1990],dhysores basilewskyi[&&NHX:TOL=1991],dhysores rhodesianus[&&NHX:TOL=1992],dhysores quadriimpressus[&&NHX:TOL=1993],dhysores pan[&&NHX:TOL=1994],dhysores liber[&&NHX:TOL=1995],dhysores biimpressus[&&NHX:TOL=1996])dhysores[&&NHX:TOL=1998],(neodhysores seximpressus[&&NHX:TOL=2002],neodhysores schreiberi[&&NHX:TOL=2003])neodhysores[&&NHX:TOL=1999],tangarona pensus[&&NHX:TOL=2000])dhysorina[&&NHX:TOL=1794],((rhysodes sulcatus[&&NHX:TOL=2272],rhysodes comes[&&NHX:TOL=2273])rhysodes[&&NHX:TOL=2236],kupeus arcuatus[&&NHX:TOL=2237],((kaveinga frontalis[&&NHX:TOL=2240],kaveinga stiletto[&&NHX:TOL=2241],kaveinga walfordi[&&NHX:TOL=2242])kaveinga angekiva[&&NHX:TOL=2247],(kaveinga orbitosa[&&NHX:TOL=2244],kaveinga bellorum[&&NHX:TOL=2245])kaveinga ingevaka[&&NHX:TOL=2248],(kaveinga setosa[&&NHX:TOL=2269],kaveinga lusca[&&NHX:TOL=2270])kaveinga vakeinga[&&NHX:TOL=2249],(kaveinga abbreviata[&&NHX:TOL=2252],kaveinga poggii[&&NHX:TOL=2253],kaveinga waai[&&NHX:TOL=2254],kaveinga fibulata[&&NHX:TOL=2255],kaveinga pignoris[&&NHX:TOL=2256],kaveinga kukum[&&NHX:TOL=2257],kaveinga nudicornis[&&NHX:TOL=2258],kaveinga ulteria[&&NHX:TOL=2259],kaveinga parva[&&NHX:TOL=2260],kaveinga cylindrica[&&NHX:TOL=2261],kaveinga lupata[&&NHX:TOL=2262],kaveinga okapa[&&NHX:TOL=2263],kaveinga marifuanga[&&NHX:TOL=2264],kaveinga occipitalis[&&NHX:TOL=2265],kaveinga histrio[&&NHX:TOL=2266],kaveinga strigiceps[&&NHX:TOL=2267])kaveinga kaveinga s. str.[&&NHX:TOL=2250])kaveinga[&&NHX:TOL=2238])rhysodina[&&NHX:TOL=1795],(((grouvellina tubericeps[&&NHX:TOL=1899],(((grouvellina montana[&&NHX:TOL=1903],grouvellina ranavalona[&&NHX:TOL=1904])[&&NHX:TOL=1902],((grouvellina gigas[&&NHX:TOL=1907],grouvellina hova[&&NHX:TOL=1908])[&&NHX:TOL=1906],grouvellina cuneata[&&NHX:TOL=1909])[&&NHX:TOL=1905])[&&NHX:TOL=1901],(grouvellina cooperi[&&NHX:TOL=1911],grouvellina edentata[&&NHX:TOL=1912])[&&NHX:TOL=1910])[&&NHX:TOL=1900],((grouvellina descarpentriesi[&&NHX:TOL=1915],(grouvellina radama[&&NHX:TOL=1917],(grouvellina divergens[&&NHX:TOL=1919],grouvellina grouvellei[&&NHX:TOL=1920])[&&NHX:TOL=1918])[&&NHX:TOL=1916])[&&NHX:TOL=1914],(grouvellina cinerea[&&NHX:TOL=1922],grouvellina dentipes[&&NHX:TOL=1923])[&&NHX:TOL=1921])[&&NHX:TOL=1913])[&&NHX:TOL=1898],grouvellina hexadon[&&NHX:TOL=1924])grouvellina[&&NHX:TOL=1805],(rhyzodiastes janus[&&NHX:TOL=1931],(rhyzodiastes montrouzieri[&&NHX:TOL=1926],rhyzodiastes proprius[&&NHX:TOL=1927],rhyzodiastes burnsi[&&NHX:TOL=1928],rhyzodiastes ovicollis[&&NHX:TOL=1929])rhyzodiastes rhyzoarca[&&NHX:TOL=1932],((rhyzodiastes pollinosus[&&NHX:TOL=1951],(rhyzodiastes raffrayi[&&NHX:TOL=1953],rhyzodiastes sulcicollis[&&NHX:TOL=1954],rhyzodiastes maritimus[&&NHX:TOL=1955])[&&NHX:TOL=1952],(rhyzodiastes guineensis[&&NHX:TOL=1957],rhyzodiastes singularis[&&NHX:TOL=1958],rhyzodiastes bipunctatus[&&NHX:TOL=1959],rhyzodiastes rimoganensis[&&NHX:TOL=1960],rhyzodiastes mirabilis[&&NHX:TOL=1961],rhyzodiastes indigens[&&NHX:TOL=1962],rhyzodiastes convergens[&&NHX:TOL=1963])[&&NHX:TOL=1956],(rhyzodiastes mishmicus[&&NHX:TOL=1965],rhyzodiastes waterhousei[&&NHX:TOL=1966],rhyzodiastes preorbitalis[&&NHX:TOL=1967])[&&NHX:TOL=1964],(rhyzodiastes myopicus[&&NHX:TOL=1969],(rhyzodiastes vadiceps[&&NHX:TOL=1971],(rhyzodiastes frater[&&NHX:TOL=1973],rhyzodiastes patruus[&&NHX:TOL=1974])[&&NHX:TOL=1972],(rhyzodiastes bifossulatus[&&NHX:TOL=1976],rhyzodiastes denticauda[&&NHX:TOL=1977])[&&NHX:TOL=1975])[&&NHX:TOL=1970])[&&NHX:TOL=1968],(rhyzodiastes gestroi[&&NHX:TOL=1979],rhyzodiastes propinquus[&&NHX:TOL=1980],rhyzodiastes bonsae[&&NHX:TOL=1981])[&&NHX:TOL=1978],(rhyzodiastes fairmairei[&&NHX:TOL=1983],rhyzodiastes spissicornis[&&NHX:TOL=1984],rhyzodiastes alveus[&&NHX:TOL=1985],rhyzodiastes fossulatus[&&NHX:TOL=1986])[&&NHX:TOL=1982])[&&NHX:TOL=1950],rhyzodiastes riedeli[&&NHX:TOL=1987],rhyzodiastes mindoro[&&NHX:TOL=1988])rhyzodiastes temoana[&&NHX:TOL=1933],(rhyzodiastes quadristriatus[&&NHX:TOL=1945],rhyzodiastes davidsoni[&&NHX:TOL=1946],rhyzodiastes nitidus[&&NHX:TOL=1947],rhyzodiastes menieri[&&NHX:TOL=1948],rhyzodiastes maderiensis[&&NHX:TOL=1949])rhyzodiastes rhyzostrix[&&NHX:TOL=1934],(rhyzodiastes pentacyclus[&&NHX:TOL=1939],rhyzodiastes parumcostatus[&&NHX:TOL=1940],rhyzodiastes liratus[&&NHX:TOL=1941],rhyzodiastes costatus[&&NHX:TOL=1942],rhyzodiastes suturalis[&&NHX:TOL=1943])rhyzodiastes rhyzodiastes s. str.[&&NHX:TOL=1935])rhyzodiastes[&&NHX:TOL=1806],((clinidium mexicanum[&&NHX:TOL=1888],clinidium balli[&&NHX:TOL=1889],clinidium triplehorni[&&NHX:TOL=1890],clinidium blomi[&&NHX:TOL=1891],clinidium iviei[&&NHX:TOL=1892],clinidium guatemalenum[&&NHX:TOL=1893],clinidium newtoni[&&NHX:TOL=1894],clinidium championi[&&NHX:TOL=1895],clinidium halffteri[&&NHX:TOL=1896],clinidium reyesi[&&NHX:TOL=1897])clinidium mexiclinidium[&&NHX:TOL=1809],clinidium extrarium[&&NHX:TOL=1810],(clinidium curvicosta[&&NHX:TOL=1817],clinidium chevrolati[&&NHX:TOL=1818],clinidium darlingtoni[&&NHX:TOL=1819],clinidium xenopodium[&&NHX:TOL=1820])clinidium tainoa[&&NHX:TOL=1811],((clinidium canaliculatum[&&NHX:TOL=1823],clinidium marginicolle[&&NHX:TOL=1824])[&&NHX:TOL=1822],((clinidium calcaratum[&&NHX:TOL=1827],(clinidium valentinei[&&NHX:TOL=1829],clinidium veneficum[&&NHX:TOL=1830])[&&NHX:TOL=1828])[&&NHX:TOL=1826],((clinidium baldufi[&&NHX:TOL=1833],clinidium apertum[&&NHX:TOL=1834])[&&NHX:TOL=1832],(clinidium rosenbergi[&&NHX:TOL=1836],clinidium sculptile[&&NHX:TOL=1837])[&&NHX:TOL=1835])[&&NHX:TOL=1831])[&&NHX:TOL=1825])clinidium arctoclinidium[&&NHX:TOL=1812],(clinidium impressum[&&NHX:TOL=1839],clinidium hammondi[&&NHX:TOL=1840],clinidium granatense[&&NHX:TOL=1841],clinidium incudis[&&NHX:TOL=1842],clinidium dubium[&&NHX:TOL=1843],clinidium insigne[&&NHX:TOL=1844],clinidium howdenorum[&&NHX:TOL=1845],clinidium boroquense[&&NHX:TOL=1846],clinidium integrum[&&NHX:TOL=1847],clinidium pilosum[&&NHX:TOL=1848],clinidium jolyi[&&NHX:TOL=1849],clinidium oberthueri[&&NHX:TOL=1850],clinidium alleni[&&NHX:TOL=1851],clinidium whiteheadi[&&NHX:TOL=1852],clinidium humboldti[&&NHX:TOL=1853],clinidium trionyx[&&NHX:TOL=1854],clinidium haitiense[&&NHX:TOL=1855],clinidium corbis[&&NHX:TOL=1856],clinidium jamaicense[&&NHX:TOL=1857],clinidium chiolinoi[&&NHX:TOL=1858],clinidium rossi[&&NHX:TOL=1859],clinidium dormans[&&NHX:TOL=1860],clinidium penicellatum[&&NHX:TOL=1861],clinidium segne[&&NHX:TOL=1862],clinidium kochalkai[&&NHX:TOL=1863],clinidium guildingii[&&NHX:TOL=1864],clinidium microfossatum[&&NHX:TOL=1865],clinidium smithsonianum[&&NHX:TOL=1866],clinidium planum[&&NHX:TOL=1867],clinidium rojasi[&&NHX:TOL=1868],clinidium bechyneorum[&&NHX:TOL=1869],clinidium excavatum[&&NHX:TOL=1870],clinidium pala[&&NHX:TOL=1871],clinidium mathani[&&NHX:TOL=1872],clinidium humile[&&NHX:TOL=1873],clinidium curvatum[&&NHX:TOL=1874],clinidium foveolatum[&&NHX:TOL=1875],clinidium cavicolle[&&NHX:TOL=1876],clinidium crater[&&NHX:TOL=1877],clinidium centrale[&&NHX:TOL=1878],clinidium validum[&&NHX:TOL=1879],clinidium spatulatum[&&NHX:TOL=1880],clinidium moldenkei[&&NHX:TOL=1881],clinidium sulcigaster[&&NHX:TOL=1882],clinidium argus[&&NHX:TOL=1883],clinidium beccari[&&NHX:TOL=1884],clinidium onorei[&&NHX:TOL=1885],clinidium gilloglyi[&&NHX:TOL=1886])clinidium clinidium s. str.[&&NHX:TOL=1813])clinidium[&&NHX:TOL=1807])clinidiina[&&NHX:TOL=1796],(xhosores figuratus[&&NHX:TOL=2007],(yamatosa kryzhanoskiji[&&NHX:TOL=2222],yamatosa longior[&&NHX:TOL=2223],yamatosa peninsularis[&&NHX:TOL=2224],yamatosa niponensis[&&NHX:TOL=2225],yamatosa kabakovi[&&NHX:TOL=2226],yamatosa arrowi[&&NHX:TOL=2227],yamatosa reitteri[&&NHX:TOL=2228],yamatosa draco[&&NHX:TOL=2229],yamatosa smetanorum[&&NHX:TOL=2230],yamatosa boysi[&&NHX:TOL=2231],yamatosa sinensis[&&NHX:TOL=2232])yamatosa[&&NHX:TOL=2008],shyrodes dohertyi[&&NHX:TOL=2009],srimara planicollis[&&NHX:TOL=2010],((plesioglymmius elegans[&&NHX:TOL=2218],plesioglymmius silus[&&NHX:TOL=2219],plesioglymmius compactus[&&NHX:TOL=2220])plesioglymmius plesioglymmius s. str.[&&NHX:TOL=2214],(plesioglymmius meridionalis[&&NHX:TOL=2207],plesioglymmius reichardti[&&NHX:TOL=2208],plesioglymmius compactus[&&NHX:TOL=2209])plesioglymmius ameroglymmius[&&NHX:TOL=2215],(plesioglymmius jugatus[&&NHX:TOL=2211],plesioglymmius negara[&&NHX:TOL=2212])plesioglymmius juxtaglymmius[&&NHX:TOL=2216])plesioglymmius[&&NHX:TOL=2011],(arrowina rostrata[&&NHX:TOL=2021],arrowina punctatolineata[&&NHX:TOL=2022],arrowina taprobanae[&&NHX:TOL=2023],arrowina pygmaea[&&NHX:TOL=2024],arrowina nilgiriensis[&&NHX:TOL=2025],arrowina anguliceps[&&NHX:TOL=2026])arrowina[&&NHX:TOL=2012],((omoglymmius africanus[&&NHX:TOL=2058],omoglymmius hemipunctatus[&&NHX:TOL=2059],omoglymmius javanicus[&&NHX:TOL=2060],omoglymmius germaini[&&NHX:TOL=2061],omoglymmius occultus[&&NHX:TOL=2062],omoglymmius ineditus[&&NHX:TOL=2063],omoglymmius rimatus[&&NHX:TOL=2064],omoglymmius inermis[&&NHX:TOL=2065])omoglymmius hemiglymmius[&&NHX:TOL=2046],(omoglymmius lewisi[&&NHX:TOL=2028],omoglymmius hamatus[&&NHX:TOL=2029],omoglymmius americanus[&&NHX:TOL=2030])omoglymmius boreoglymmius[&&NHX:TOL=2047],(((omoglymmius lederi[&&NHX:TOL=2190],omoglymmius crassiusculus[&&NHX:TOL=2191],omoglymmius subcaviceps[&&NHX:TOL=2192])[&&NHX:TOL=2189],(((omoglymmius krikkeni[&&NHX:TOL=2196],omoglymmius pilosus[&&NHX:TOL=2197])[&&NHX:TOL=2195],(omoglymmius hesperus[&&NHX:TOL=2199],(omoglymmius armatus[&&NHX:TOL=2201],omoglymmius strabus[&&NHX:TOL=2202])[&&NHX:TOL=2200])[&&NHX:TOL=2198])[&&NHX:TOL=2194],omoglymmius cristatus[&&NHX:TOL=2203])[&&NHX:TOL=2193])[&&NHX:TOL=2188],omoglymmius multicarinatus[&&NHX:TOL=2204],omoglymmius opacus[&&NHX:TOL=2205])omoglymmius pyxiglymmius[&&NHX:TOL=2048],(omoglymmius rugosus[&&NHX:TOL=2067],(omoglymmius oberthueri[&&NHX:TOL=2069],omoglymmius actae[&&NHX:TOL=2070],(omoglymmius insularis[&&NHX:TOL=2072],omoglymmius inaequalis[&&NHX:TOL=2073])[&&NHX:TOL=2071],(omoglymmius trisinuatus[&&NHX:TOL=2075],omoglymmius gorgo[&&NHX:TOL=2076])[&&NHX:TOL=2074])[&&NHX:TOL=2068])omoglymmius laminoglymmius[&&NHX:TOL=2049],(omoglymmius intrusus[&&NHX:TOL=2042],omoglymmius peckorum[&&NHX:TOL=2043],omoglymmius stylatus[&&NHX:TOL=2044])omoglymmius navitia[&&NHX:TOL=2050],(omoglymmius zimmermani[&&NHX:TOL=2032],omoglymmius okei[&&NHX:TOL=2033])omoglymmius caeconavitia[&&NHX:TOL=2051],(omoglymmius lineatus[&&NHX:TOL=2039],omoglymmius astraea[&&NHX:TOL=2040])omoglymmius indoglymmius[&&NHX:TOL=2052],(omoglymmius semioculatus[&&NHX:TOL=2078],omoglymmius greensladei[&&NHX:TOL=2079],omoglymmius hornabrooki[&&NHX:TOL=2080],omoglymmius offafinus[&&NHX:TOL=2081],omoglymmius lustrans[&&NHX:TOL=2082],omoglymmius fulgens[&&NHX:TOL=2083],omoglymmius toxopei[&&NHX:TOL=2084])omoglymmius nitiglymmius[&&NHX:TOL=2053],(omoglymmius sulcicollis[&&NHX:TOL=2180],omoglymmius microtis[&&NHX:TOL=2181],omoglymmius feae[&&NHX:TOL=2182],omoglymmius alticola[&&NHX:TOL=2183],omoglymmius longiceps[&&NHX:TOL=2184],omoglymmius cavifrons[&&NHX:TOL=2185],omoglymmius crenatus[&&NHX:TOL=2186],omoglymmius coomani[&&NHX:TOL=2187])omoglymmius orthoglymmius[&&NHX:TOL=2054],(omoglymmius nicobarensis[&&NHX:TOL=2035],omoglymmius hexagonus[&&NHX:TOL=2036],omoglymmius carinatus[&&NHX:TOL=2037])omoglymmius carinoglymmius[&&NHX:TOL=2055],(omoglymmius germari[&&NHX:TOL=2086],omoglymmius continuus[&&NHX:TOL=2087],omoglymmius malabaricus[&&NHX:TOL=2088],omoglymmius sakuraii[&&NHX:TOL=2089],omoglymmius laticeps[&&NHX:TOL=2090],omoglymmius bicarinatus[&&NHX:TOL=2091],omoglymmius bituberculatus[&&NHX:TOL=2092],omoglymmius summissus[&&NHX:TOL=2093],omoglymmius fringillus[&&NHX:TOL=2094],omoglymmius wittmeri[&&NHX:TOL=2095],omoglymmius gurneyi[&&NHX:TOL=2096],omoglymmius semperi[&&NHX:TOL=2097],omoglymmius oroensis[&&NHX:TOL=2098],omoglymmius ichthyocephalus[&&NHX:TOL=2099],omoglymmius viduus[&&NHX:TOL=2100],omoglymmius puncticornis[&&NHX:TOL=2101],omoglymmius tolai[&&NHX:TOL=2102],omoglymmius scopulinus[&&NHX:TOL=2103],omoglymmius vicinus[&&NHX:TOL=2104],omoglymmius ferrugatus[&&NHX:TOL=2105],omoglymmius classicus[&&NHX:TOL=2106],omoglymmius princeps[&&NHX:TOL=2107],omoglymmius lindrothi[&&NHX:TOL=2108],omoglymmius rusticus[&&NHX:TOL=2109],omoglymmius modicus[&&NHX:TOL=2110],omoglymmius manni[&&NHX:TOL=2111],omoglymmius regius[&&NHX:TOL=2112],omoglymmius vadosus[&&NHX:TOL=2113],omoglymmius crassicornis[&&NHX:TOL=2114],omoglymmius aristeus[&&NHX:TOL=2115],omoglymmius sabah[&&NHX:TOL=2116],omoglymmius amplus[&&NHX:TOL=2117],omoglymmius modiglianii[&&NHX:TOL=2118],omoglymmius morditus[&&NHX:TOL=2119],omoglymmius caelatus[&&NHX:TOL=2120],omoglymmius oceanicus[&&NHX:TOL=2121],omoglymmius batchianus[&&NHX:TOL=2122],omoglymmius humeralis[&&NHX:TOL=2123],omoglymmius renutus[&&NHX:TOL=2124],omoglymmius trepidus[&&NHX:TOL=2125],omoglymmius cavea[&&NHX:TOL=2126],omoglymmius philippensis[&&NHX:TOL=2127],omoglymmius imugani[&&NHX:TOL=2128],omoglymmius politus[&&NHX:TOL=2129],omoglymmius opticus[&&NHX:TOL=2130],omoglymmius duplex[&&NHX:TOL=2131],omoglymmius bouchardi[&&NHX:TOL=2132],omoglymmius nasalis[&&NHX:TOL=2133],omoglymmius wallacei[&&NHX:TOL=2134],omoglymmius data[&&NHX:TOL=2135],omoglymmius ephemeris[&&NHX:TOL=2136],omoglymmius mycteroides[&&NHX:TOL=2137],omoglymmius thoracicus[&&NHX:TOL=2138],omoglymmius coelebs[&&NHX:TOL=2139],omoglymmius malaicus[&&NHX:TOL=2140],omoglymmius fraudulentus[&&NHX:TOL=2141],omoglymmius nemoralis[&&NHX:TOL=2142],omoglymmius evasus[&&NHX:TOL=2143],omoglymmius brendelli[&&NHX:TOL=2144],omoglymmius sectatus[&&NHX:TOL=2145],omoglymmius seriatus[&&NHX:TOL=2146],omoglymmius gracilicornis[&&NHX:TOL=2147],omoglymmius consors[&&NHX:TOL=2148],omoglymmius hiekei[&&NHX:TOL=2149],omoglymmius quadruplex[&&NHX:TOL=2150],omoglymmius pectoralis[&&NHX:TOL=2151],omoglymmius tabulatus[&&NHX:TOL=2152],omoglymmius bucculatus[&&NHX:TOL=2153],omoglymmius patens[&&NHX:TOL=2154],omoglymmius solitarius[&&NHX:TOL=2155],omoglymmius impletus[&&NHX:TOL=2156],omoglymmius pulvinatus[&&NHX:TOL=2157],omoglymmius sedlaceki[&&NHX:TOL=2158],omoglymmius biroi[&&NHX:TOL=2159],omoglymmius cheesmanae[&&NHX:TOL=2160],omoglymmius asetatus[&&NHX:TOL=2161],omoglymmius quadraticollis[&&NHX:TOL=2162],omoglymmius gressitti[&&NHX:TOL=2163],omoglymmius repetitus[&&NHX:TOL=2164],omoglymmius follis[&&NHX:TOL=2165],omoglymmius iridescens[&&NHX:TOL=2166],omoglymmius craticulus[&&NHX:TOL=2167],omoglymmius planiceps[&&NHX:TOL=2168],omoglymmius sus[&&NHX:TOL=2169],omoglymmius monteithi[&&NHX:TOL=2170],omoglymmius cupedoides[&&NHX:TOL=2171],omoglymmius lentus[&&NHX:TOL=2172],omoglymmius capito[&&NHX:TOL=2173],omoglymmius largus[&&NHX:TOL=2174],omoglymmius auratus[&&NHX:TOL=2175],omoglymmius massa[&&NHX:TOL=2176],omoglymmius denticulatus[&&NHX:TOL=2177],omoglymmius emdomani[&&NHX:TOL=2178])omoglymmius omoglymmius s. str.[&&NHX:TOL=2056])omoglymmius[&&NHX:TOL=2013])omoglymmiina[&&NHX:TOL=1797])rhysodini[&&NHX:TOL=67])carabidae[&&NHX:TOL=8895])[&&NHX:TOL=29300],(triaplus macroplatus[&&NHX:TOL=8994],triaplus laticoxa[&&NHX:TOL=8995])triaplidae[&&NHX:EXT=Y:TOL=8899],colymbothetidae[&&NHX:EXT=Y:TOL=8900])adephaga[&&NHX:TOL=8875])[&&NHX:TOL=8865],(crowsoniella relicta[&&NHX:TOL=8998],((priacma serrata[&&NHX:TOL=9004],priacma corrupta[&&NHX:EXT=Y:TOL=29763],priacma longicapitis[&&NHX:EXT=Y:TOL=29764],priacma oculata[&&NHX:EXT=Y:TOL=29765],priacma striata[&&NHX:EXT=Y:TOL=29766])priacma[&&NHX:TOL=29762],((paracupes brasiliensis[&&NHX:TOL=29767],paracupes svitkoi[&&NHX:EXT=Y:TOL=29768])paracupes[&&NHX:TOL=9006],(cupes capitatus[&&NHX:TOL=30304],(tenomerga anguliscutis[&&NHX:TOL=9013],tenomerga cinerea[&&NHX:TOL=9010],tenomerga favella[&&NHX:TOL=9018],tenomerga gaolingziensis[&&NHX:TOL=29769],tenomerga japonica[&&NHX:TOL=9011],tenomerga kapnodes[&&NHX:TOL=9016],tenomerga kurasawai[&&NHX:TOL=29770],tenomerga leucophaea[&&NHX:TOL=9019],tenomerga moultoni[&&NHX:TOL=9017],tenomerga mucida[&&NHX:TOL=9014],tenomerga sibyllae[&&NHX:TOL=9015],tenomerga tianmuensis[&&NHX:TOL=29771],tenomerga trabecula[&&NHX:TOL=9012],tenomerga yamato[&&NHX:TOL=29772])tenomerga[&&NHX:TOL=9009],distocupes varians[&&NHX:TOL=9020],(adinolepis apodema[&&NHX:TOL=29773],adinolepis eumana[&&NHX:TOL=9022],adinolepis mathesonae[&&NHX:TOL=9023],adinolepis scalena[&&NHX:TOL=9025],adinolepis youanga[&&NHX:TOL=9024])adinolepis[&&NHX:TOL=9021],(ascioplaga mimeta[&&NHX:TOL=9027],ascioplaga sciasma[&&NHX:TOL=9028])ascioplaga[&&NHX:TOL=9026],(rhipsideigma adjuncta[&&NHX:TOL=9032],rhipsideigma cretaceotincta[&&NHX:TOL=9030],rhipsideigma lugubris[&&NHX:TOL=9033],rhipsideigma raffrayi[&&NHX:TOL=9031])rhipsideigma[&&NHX:TOL=9029],(prolixocupes latreillei[&&NHX:TOL=9037],prolixocupes lobiceps[&&NHX:TOL=9038])prolixocupes[&&NHX:TOL=9034])[&&NHX:TOL=9007])[&&NHX:TOL=9005],anaglyphites[&&NHX:EXT=Y:TOL=29774],cupidium abavum[&&NHX:EXT=Y:TOL=29775],mesocupes[&&NHX:EXT=Y:TOL=29776],mesocupoides[&&NHX:EXT=Y:TOL=29777],miocupes[&&NHX:EXT=Y:TOL=29786],priacmopsis adumbrata[&&NHX:EXT=Y:TOL=29778],pulchicupes jiensis[&&NHX:EXT=Y:TOL=29779])cupedidae[&&NHX:TOL=8999],micromalthus debilis[&&NHX:TOL=9000],((omma mastersi[&&NHX:TOL=9043],omma rutherfordi[&&NHX:TOL=29714],omma sagitta[&&NHX:TOL=9045],omma stanleyi[&&NHX:TOL=9044],omma aberratum[&&NHX:EXT=Y:TOL=29715],omma altajense[&&NHX:EXT=Y:TOL=29716],omma antennatum[&&NHX:EXT=Y:TOL=29717],omma avus[&&NHX:EXT=Y:TOL=29718],omma brevipes[&&NHX:EXT=Y:TOL=29719],omma gobiense[&&NHX:EXT=Y:TOL=29720],omma jurassicum[&&NHX:EXT=Y:TOL=29721],omma liassicum[&&NHX:EXT=Y:TOL=29722],omma pilosum[&&NHX:EXT=Y:TOL=29723],omma sibiricum[&&NHX:EXT=Y:TOL=29724],omma zitteli[&&NHX:EXT=Y:TOL=29725])omma[&&NHX:TOL=9042],(tetraphalerus wagneri[&&NHX:TOL=29732],tetraphalerus bruchi[&&NHX:TOL=29739],tetraphalerus antiquus[&&NHX:EXT=Y:TOL=29747],tetraphalerus bontsaganensis[&&NHX:EXT=Y:TOL=29735],tetraphalerus brevicapitis[&&NHX:EXT=Y:TOL=29738],tetraphalerus brevis[&&NHX:EXT=Y:TOL=29749],tetraphalerus collaris[&&NHX:EXT=Y:TOL=29734],tetraphalerus fentaiensis[&&NHX:EXT=Y:TOL=29753],tetraphalerus incertus[&&NHX:EXT=Y:TOL=29746],tetraphalerus glabratus[&&NHX:EXT=Y:TOL=29733],tetraphalerus grandis[&&NHX:EXT=Y:TOL=29744],tetraphalerus longicollis[&&NHX:EXT=Y:TOL=29736],tetraphalerus macilentus[&&NHX:EXT=Y:TOL=29752],tetraphalerus maximus[&&NHX:EXT=Y:TOL=29745],tetraphalerus mongolicus[&&NHX:EXT=Y:TOL=29750],tetraphalerus notatus[&&NHX:EXT=Y:TOL=29737],tetraphalerus ochotensis[&&NHX:EXT=Y:TOL=29742],tetraphalerus oligocenicus[&&NHX:EXT=Y:TOL=29740],tetraphalerus surrectus[&&NHX:EXT=Y:TOL=29751],tetraphalerus tenuipes[&&NHX:EXT=Y:TOL=29748],tetraphalerus verrucosus[&&NHX:EXT=Y:TOL=29741])tetraphalerus[&&NHX:TOL=9046],brochocoleus[&&NHX:EXT=Y:TOL=29754],cionocoleus[&&NHX:EXT=Y:TOL=29756],eurydictyon[&&NHX:EXT=Y:TOL=29757],lithocupes[&&NHX:EXT=Y:TOL=30302],notocupes[&&NHX:EXT=Y:TOL=30303],notocupoides[&&NHX:EXT=Y:TOL=29758],rhabdocupes[&&NHX:EXT=Y:TOL=29759],zygadenia[&&NHX:EXT=Y:TOL=29755])ommatidae[&&NHX:TOL=8997],(sikhotealinia zhiltsovae[&&NHX:TOL=107962],jurodes[&&NHX:EXT=Y:TOL=112039])jurodidae[&&NHX:TOL=112038],anthocoleus habiensis[&&NHX:EXT=Y:TOL=30320],bothynophora elegans[&&NHX:EXT=Y:TOL=30318],chalepocarabus elongatus[&&NHX:EXT=Y:TOL=30329],clathrocupes anthrilegnotus[&&NHX:EXT=Y:TOL=30310],clinomerus laticellus[&&NHX:EXT=Y:TOL=30319],cupedites minutissimus[&&NHX:EXT=Y:TOL=30323],doggeriopsis stonefieldiana[&&NHX:EXT=Y:TOL=30324],ensicupes guyanensis[&&NHX:EXT=Y:TOL=30326],euteticoleus radiatus[&&NHX:EXT=Y:TOL=30321],gansucupes attenuatus[&&NHX:EXT=Y:TOL=30327],hebeicoleus sertulatus[&&NHX:EXT=Y:TOL=30322],helopides hildsiensis[&&NHX:EXT=Y:TOL=30312],ironicus nothus[&&NHX:EXT=Y:TOL=30330],kakoselia anglia[&&NHX:EXT=Y:TOL=30331],katapontisus brodiei[&&NHX:EXT=Y:TOL=30332],kelidus bolbus[&&NHX:EXT=Y:TOL=30333],liassocupes[&&NHX:EXT=Y:TOL=30317],mesothoris[&&NHX:EXT=Y:TOL=29785],nannocurculionites carlsoni[&&NHX:EXT=Y:TOL=30313],parabuprestites rugulosus[&&NHX:EXT=Y:TOL=30314],paracurculionites parvulus[&&NHX:EXT=Y:TOL=30315],paradoggeria acuminata[&&NHX:EXT=Y:TOL=30325],pseudosilphites triassicus[&&NHX:EXT=Y:TOL=30311],sinocupes[&&NHX:EXT=Y:TOL=29791],stigmenamma heeri[&&NHX:EXT=Y:TOL=30316],synodus changnaensis[&&NHX:EXT=Y:TOL=30328],tenthyridium[&&NHX:EXT=Y:TOL=30334],tripocoleus rambulosus[&&NHX:EXT=Y:TOL=30336],zigadenia tuberculata[&&NHX:EXT=Y:TOL=30335])archostemata[&&NHX:TOL=8876])[&&NHX:TOL=8864],(asimma rara[&&NHX:EXT=Y:TOL=30293],cupesia[&&NHX:EXT=Y:TOL=30294],kirghizocupes cellulosus[&&NHX:EXT=Y:TOL=30295],moltenocupes townrowi[&&NHX:EXT=Y:TOL=30296],platycupes[&&NHX:EXT=Y:TOL=30297],procupes mandibularis[&&NHX:EXT=Y:TOL=30298],pterocupes[&&NHX:EXT=Y:TOL=30299],triadocupes[&&NHX:EXT=Y:TOL=30300])triadocupedidae[&&NHX:EXT=Y:TOL=8877])[&&NHX:TOL=8863],(erunakicupes[&&NHX:EXT=Y:TOL=29818],karakanocoleus[&&NHX:EXT=Y:TOL=29819],rhombocoleites adumbratus[&&NHX:EXT=Y:TOL=29820],rhombocoleus andreae[&&NHX:EXT=Y:TOL=29821],rossocoleus[&&NHX:EXT=Y:TOL=29822],schizotaldycupes[&&NHX:EXT=Y:TOL=29823])rhombocoleidae[&&NHX:EXT=Y:TOL=8878])[&&NHX:TOL=8862],(archicupes[&&NHX:EXT=Y:TOL=29796],cytocupes angustus[&&NHX:EXT=Y:TOL=29797],cytocupoides elongatus[&&NHX:EXT=Y:TOL=29798],eocupes[&&NHX:EXT=Y:TOL=29799],ichthyocupes[&&NHX:EXT=Y:TOL=29800],kaltanicupes[&&NHX:EXT=Y:TOL=29801],kaltanocoleus[&&NHX:EXT=Y:TOL=29802],permocupes[&&NHX:EXT=Y:TOL=29795],protocupes[&&NHX:EXT=Y:TOL=29803],protocupoides[&&NHX:EXT=Y:TOL=29804],tricupes[&&NHX:EXT=Y:TOL=30301],uralocupes major[&&NHX:EXT=Y:TOL=29805])permocupedidae[&&NHX:EXT=Y:TOL=8879])[&&NHX:TOL=8861],(labradorocoleus carpenteri[&&NHX:EXT=Y:TOL=30285],(liberocoleus[&&NHX:EXT=Y:TOL=29861],oborocoleus[&&NHX:EXT=Y:TOL=29862])oborocoleidae[&&NHX:EXT=Y:TOL=29860],(cryptocupes[&&NHX:EXT=Y:TOL=30290],simmondsia[&&NHX:EXT=Y:TOL=30292],taldycupes[&&NHX:EXT=Y:TOL=30289],tecticupes[&&NHX:EXT=Y:TOL=30291],tychticupes[&&NHX:EXT=Y:TOL=30287],tychticupoides grjasevi[&&NHX:EXT=Y:TOL=30288])taldycupedidae[&&NHX:EXT=Y:TOL=30286],(avocoleus[&&NHX:EXT=Y:TOL=29848],boscoleus blandus[&&NHX:EXT=Y:TOL=29849],eocoleus scaber[&&NHX:EXT=Y:TOL=29850],moravocoleus permianus[&&NHX:EXT=Y:TOL=29851],prosperocoleus prosperus[&&NHX:EXT=Y:TOL=29852],retelytron conopeum[&&NHX:EXT=Y:TOL=29853],sylvacoleodes admirandus[&&NHX:EXT=Y:TOL=29854],sylvacoleus[&&NHX:EXT=Y:TOL=29855],tshekardocoleus[&&NHX:EXT=Y:TOL=29856],umoricoleus perplex[&&NHX:EXT=Y:TOL=29857],uralocoleus[&&NHX:EXT=Y:TOL=29858],votocoleus submissus[&&NHX:EXT=Y:TOL=29859])tshekardocoleidae[&&NHX:EXT=Y:TOL=29847])protocoleoptera[&&NHX:EXT=Y:TOL=8880])coleoptera[&&NHX:TOL=8221])[&&NHX:TOL=8216],((((corioxenos acucyrtophallus[&&NHX:TOL=66628],corioxenos antestiae[&&NHX:TOL=66629],corioxenos raoi[&&NHX:TOL=66630])corioxenos[&&NHX:TOL=66627],loania canadensis[&&NHX:TOL=66631],mafagaa talhouki[&&NHX:TOL=66632],(malayaxenos kitaoka[&&NHX:TOL=66634],malayaxenos trapezonoti[&&NHX:TOL=66635])malayaxenos[&&NHX:TOL=66633],blissoxenos esaki[&&NHX:TOL=66636],viridipromontoxius vanharteni[&&NHX:TOL=66637],australoxenos yetmaniensis[&&NHX:TOL=66638],floridoxenos monroensis[&&NHX:TOL=66639],uniclavus zambezensis[&&NHX:TOL=66640],proceroxenos jordanicus[&&NHX:TOL=66641],(triozocera africana[&&NHX:TOL=66643],triozocera bedfordensis[&&NHX:TOL=66644],triozocera boharti[&&NHX:TOL=66645],triozocera ceylonesis[&&NHX:TOL=66646],triozocera cooloolaensis[&&NHX:TOL=66647],triozocera curvimaxllaria[&&NHX:TOL=66648],triozocera dundoana[&&NHX:TOL=66649],triozocera endrodyi[&&NHX:TOL=66650],triozocera gigantea[&&NHX:TOL=66651],triozocera innisfailensis[&&NHX:TOL=66652],triozocera katherinensis[&&NHX:TOL=66653],triozocera macrocysti[&&NHX:TOL=66654],triozocera maxi[&&NHX:TOL=66655],triozocera mexicana[&&NHX:TOL=66656],triozocera minor[&&NHX:TOL=66657],triozocera moorookensis[&&NHX:TOL=66658],triozocera papuana[&&NHX:TOL=66659],triozocera paulistana[&&NHX:TOL=66660],triozocera paradisea[&&NHX:TOL=66661],triozocera pugiopenis[&&NHX:TOL=66662],triozocera rydalmeriensis[&&NHX:TOL=66663],triozocera siamensis[&&NHX:TOL=66664],triozocera tecpanesis[&&NHX:TOL=66665],triozocera taxana[&&NHX:TOL=66666],triozocera vernalis[&&NHX:TOL=66667])triozocera[&&NHX:TOL=66642],(dundoxenos breviphelebos[&&NHX:TOL=66669],dundoxenos kinzelbachi[&&NHX:TOL=66670],dundoxenos vilhenai[&&NHX:TOL=66671])dundoxenos[&&NHX:TOL=66668])corioxenidae[&&NHX:TOL=14512],(bohartilla megalognatha[&&NHX:TOL=27086],bohartilla kinzelbachi[&&NHX:EXT=Y:TOL=27088])bohartilla[&&NHX:TOL=14513],((halictophagus abdominalis[&&NHX:TOL=66678],halictophagus acutus[&&NHX:TOL=66679],halictophagus agalliae[&&NHX:TOL=66680],halictophagus americanus[&&NHX:TOL=66681],halictophagus ancylophallus[&&NHX:TOL=66682],halictophagus angustipes[&&NHX:TOL=66683],halictophagus antennalus[&&NHX:TOL=66684],halictophagus australensis[&&NHX:TOL=66685],halictophagus barberi[&&NHX:TOL=66686],halictophagus besucheti[&&NHX:TOL=66687],halictophagus bidentatus[&&NHX:TOL=66688],halictophagus bipunctatus[&&NHX:TOL=66689],halictophagus calcaratus[&&NHX:TOL=66690],halictophagus callosus[&&NHX:TOL=66691],halictophagus chantaneeae[&&NHX:TOL=66692],halictophagus chinensis[&&NHX:TOL=66693],halictophagus chilensis[&&NHX:TOL=66694],halictophagus cladoceras[&&NHX:TOL=66695],halictophagus compactus[&&NHX:TOL=66696],halictophagus curtisi[&&NHX:TOL=66697],halictophagus desantisi[&&NHX:TOL=66698],halictophagus elongatus[&&NHX:TOL=66699],halictophagus endrodyi[&&NHX:TOL=66922],halictophagus eurycephalus[&&NHX:TOL=66700],halictophagus forthoodensis[&&NHX:TOL=66701],halictophagus fulmeki[&&NHX:TOL=66702],halictophagus ghanensis[&&NHX:TOL=66703],halictophagus gressitti[&&NHX:TOL=66704],halictophagus griveaudi[&&NHX:TOL=66705],halictophagus haydari[&&NHX:TOL=66706],halictophagus henriquei[&&NHX:TOL=66707],halictophagus hirashimai[&&NHX:TOL=66708],halictophagus indicus[&&NHX:TOL=66709],halictophagus insularum[&&NHX:TOL=66710],halictophagus iriomotensis[&&NHX:TOL=66711],halictophagus irwini[&&NHX:TOL=66712],halictophagus jacobsoni[&&NHX:TOL=66713],halictophagus javanensis[&&NHX:TOL=66714],halictophagus jordani[&&NHX:TOL=66715],halictophagus kinzelbachi[&&NHX:TOL=66716],halictophagus kuehnelti[&&NHX:TOL=66717],halictophagus languedoci[&&NHX:TOL=66718],halictophagus lappidae[&&NHX:TOL=66719],halictophagus longipenis[&&NHX:TOL=66720],halictophagus lopesi[&&NHX:TOL=66721],halictophagus mackayi[&&NHX:TOL=66722],halictophagus macrostelesi[&&NHX:TOL=66723],halictophagus malayanus[&&NHX:TOL=66724],halictophagus membraciphaga[&&NHX:TOL=66725],halictophagus minimus[&&NHX:TOL=66726],halictophagus minutus[&&NHX:TOL=66727],halictophagus moorookensis[&&NHX:TOL=66728],halictophagus naulti[&&NHX:TOL=66729],halictophagus omani[&&NHX:TOL=66730],halictophagus oncometopiae[&&NHX:TOL=66731],halictophagus orientalis[&&NHX:TOL=66732],halictophagus palmi[&&NHX:TOL=66733],halictophagus phaeodes[&&NHX:TOL=66734],halictophagus philaroniae[&&NHX:TOL=66735],halictophagus radiatus[&&NHX:TOL=66736],halictophagus bevipenis[&&NHX:TOL=66737],halictophagus samoanus[&&NHX:TOL=66738],halictophagus sararwakensis[&&NHX:TOL=66739],halictophagus scheveni[&&NHX:TOL=66740],halictophagus schwarzi[&&NHX:TOL=66741],halictophagus silwoodensis[&&NHX:TOL=66742],halictophagus stellatus[&&NHX:TOL=66743],halictophagus stenocrani[&&NHX:TOL=66744],halictophagus tenebrosus[&&NHX:TOL=66745],halictophagus thaiae[&&NHX:TOL=66746],halictophagus thoracicus[&&NHX:TOL=66747],halictophagus tryoni[&&NHX:TOL=66748],halictophagus uhleri[&&NHX:TOL=66749],halictophagus yaeyamanus[&&NHX:TOL=66750])halictophagus[&&NHX:TOL=66672],(stenocranophilus anomalocerus[&&NHX:TOL=66751],stenocranophilus dicranotropidis[&&NHX:TOL=66752],stenocranophilus canadensis[&&NHX:TOL=66753],stenocranophilus quadratus[&&NHX:TOL=66754],stenocranophilus perkinsiellae[&&NHX:TOL=66755])stenocranophilus[&&NHX:TOL=66673],(tridactylophagus buttonensis[&&NHX:TOL=66756],tridactylophagus borneoensis[&&NHX:TOL=66757],tridactylophagus canberraensis[&&NHX:TOL=66758],tridactylophagus ceylonensis[&&NHX:TOL=66759],tridactylophagus coniferus[&&NHX:TOL=66760],tridactylophagus harzi[&&NHX:TOL=66761],tridactylophagus maculatus[&&NHX:TOL=66762],tridactylophagus mysorensis[&&NHX:TOL=66763],tridactylophagus similis[&&NHX:TOL=66764],tridactylophagus sinensis[&&NHX:TOL=66765],tridactylophagus tartaria[&&NHX:TOL=66766])tridactylophagus[&&NHX:TOL=66674],(coriophagus adebratti[&&NHX:TOL=66767],coriophagus borneoensis[&&NHX:TOL=66768],coriophagus casui[&&NHX:TOL=66769],coriophagus gressittorum[&&NHX:TOL=66770],coriophagus latimanus[&&NHX:TOL=66771],coriophagus lockerbiensis[&&NHX:TOL=66772],coriophagus maai[&&NHX:TOL=66773],coriophagus madleri[&&NHX:TOL=66774],coriophagus monteithi[&&NHX:TOL=66775],coriophagus rieki[&&NHX:TOL=66776],coriophagus solomonensis[&&NHX:TOL=66777],coriophagus zanzibarae[&&NHX:TOL=66778])coriophagus[&&NHX:TOL=66675],dipterophagus daci[&&NHX:TOL=66676],blattodeaphagus beckmani[&&NHX:TOL=66677])halictophagidae[&&NHX:TOL=14514],(((elenchus butzei[&&NHX:TOL=66598],elenchus eastopi[&&NHX:TOL=66599],elenchus falcipennis[&&NHX:TOL=66600],elenchus koebelei[&&NHX:TOL=66601],elenchus japonicus[&&NHX:TOL=66602],elenchus leptodalphaxi[&&NHX:TOL=66603],elenchus lindbergi[&&NHX:TOL=66604],elenchus maorianus[&&NHX:TOL=66605],elenchus melanias[&&NHX:TOL=66606],elenchus mexicanus[&&NHX:TOL=66607],elenchus perkinsi[&&NHX:TOL=66608],elenchus solomonensis[&&NHX:TOL=66609],elenchus spangleri[&&NHX:TOL=66610],elenchus perkinsianus[&&NHX:TOL=66611],elenchus tenuicornis[&&NHX:TOL=66612],elenchus templetoni[&&NHX:TOL=66613],elenchus toyaphagus[&&NHX:TOL=66614],elenchus varleyi[&&NHX:TOL=66615])elenchus[&&NHX:TOL=66597],colacina insidiator[&&NHX:TOL=66616],(deinelenchus australensis[&&NHX:TOL=66618],deinelenchus deviatus[&&NHX:TOL=66619],deinelenchus berrimahensis[&&NHX:TOL=66620],deinelenchus hemifer[&&NHX:TOL=66621],deinelenchus nigeriensis[&&NHX:TOL=66622],deinelenchus sabahensis[&&NHX:TOL=66623])deinelenchus[&&NHX:TOL=66617],elencholax bismarckarum[&&NHX:TOL=66624],elencholax noonadanae[&&NHX:TOL=66625],protelencholax shleei[&&NHX:EXT=Y:TOL=66626])elenchidae[&&NHX:TOL=14516],((myrmecolax afurcifer[&&NHX:TOL=66783],myrmecolax blickenstaffi[&&NHX:TOL=66784],myrmecolax borgmeieri[&&NHX:TOL=66785],myrmecolax bifurcatus[&&NHX:TOL=66786],myrmecolax chantaneeae[&&NHX:TOL=66787],myrmecolax congoensis[&&NHX:TOL=66788],myrmecolax culionensis[&&NHX:TOL=66789],myrmecolax danielssoni[&&NHX:TOL=66790],myrmecolax flagellatus[&&NHX:TOL=66791],myrmecolax furcatus[&&NHX:TOL=66792],myrmecolax glaesi[&&NHX:TOL=66793],myrmecolax genitalis[&&NHX:TOL=66794],myrmecolax incautus[&&NHX:TOL=66795],myrmecolax kpelle[&&NHX:TOL=66796],myrmecolax leleupi[&&NHX:TOL=66797],myrmecolax lliberiensis[&&NHX:TOL=66798],myrmecolax longipes[&&NHX:TOL=66799],myrmecolax longipalpis[&&NHX:TOL=66800],myrmecolax lunai[&&NHX:TOL=66801],myrmecolax malayensis[&&NHX:TOL=66802],myrmecolax mano[&&NHX:TOL=66803],myrmecolax mymecinus[&&NHX:TOL=66804],myrmecolax nietneri[&&NHX:TOL=66805],myrmecolax odontognathus[&&NHX:TOL=66806],myrmecolax ogloblini[&&NHX:TOL=66807],myrmecolax parva[&&NHX:TOL=66808],myrmecolax philippinensis[&&NHX:TOL=66809],myrmecolax plantipes[&&NHX:TOL=66810],myrmecolax pseudolundensis[&&NHX:TOL=66811],myrmecolax rossi[&&NHX:TOL=66812],myrmecolax trinidadensis[&&NHX:TOL=66813],myrmecolax vardoni[&&NHX:TOL=66814])myrmecolax[&&NHX:TOL=66779],(stichotrema acutipennis[&&NHX:TOL=66815],stichotrema angolensis[&&NHX:TOL=66816],stichotrema anomalum[&&NHX:TOL=66817],stichotrema ambiguum[&&NHX:TOL=66818],stichotrema asahinai[&&NHX:TOL=66819],stichotrema barrosmachadoi[&&NHX:TOL=66820],stichotrema bassa[&&NHX:TOL=66821],stichotrema beckeri[&&NHX:TOL=66822],stichotrema boharti[&&NHX:TOL=66823],stichotrema capito[&&NHX:TOL=66824],stichotrema ceylonese[&&NHX:TOL=66825],stichotrema dallatorreanum[&&NHX:TOL=66826],stichotrema davao[&&NHX:TOL=66827],stichotrema dominicanum[&&NHX:TOL=66828],stichotrema ferenczi[&&NHX:TOL=66829],stichotrema fijiense[&&NHX:TOL=66830],stichotrema foxe[&&NHX:TOL=66831],stichotrema golias[&&NHX:TOL=66832],stichotrema neostichotrema gressitti[&&NHX:TOL=66833],stichotrema harleyi[&&NHX:TOL=66834],stichotrema hoberlandti[&&NHX:TOL=66835],stichotrema jeyasothiae[&&NHX:TOL=66836],stichotrema kaszabi[&&NHX:TOL=66837],stichotrema krombeini[&&NHX:TOL=66838],stichotrema kuranda[&&NHX:TOL=66839],stichotrema laticeps[&&NHX:TOL=66840],stichotrema lindbergi[&&NHX:TOL=66841],stichotrema longiflagellatum[&&NHX:TOL=66842],stichotrema malayanum[&&NHX:TOL=66843],stichotrema mendolong[&&NHX:TOL=66844],stichotrema mexicanum[&&NHX:TOL=66845],stichotrema minor[&&NHX:TOL=66846],stichotrema nasutum[&&NHX:TOL=66847],stichotrema pasteelsi[&&NHX:TOL=66848],stichotrema rectipennis[&&NHX:TOL=66849],stichotrema retrosum[&&NHX:TOL=66850],stichotrema rhipidocolaxoides[&&NHX:TOL=66851],stichotrema robertsoni[&&NHX:TOL=66852],stichotrema silvaticum[&&NHX:TOL=66853],stichotrema simile[&&NHX:TOL=66854],stichotrema székessyi[&&NHX:TOL=66855],stichotrema triblobulatum[&&NHX:TOL=66856],stichotrema triangulum[&&NHX:TOL=66857],stichotrema vilhenai[&&NHX:TOL=66858],stichotrema waterhousi[&&NHX:TOL=66859],stichotrema webbiense[&&NHX:TOL=66860],stichotrema weitschati[&&NHX:TOL=66861],stichotrema yasumatsui[&&NHX:TOL=66862])stichotrema[&&NHX:TOL=66780],(lychnocolax aerius[&&NHX:TOL=66863],lychnocolax hericarcalhensis[&&NHX:TOL=66864],lychnocolax champloni[&&NHX:TOL=66865],lychnocolax chiensis[&&NHX:TOL=66866],lychnocolax drysdalensis[&&NHX:TOL=66867],lychnocolax henricaralhensis[&&NHX:TOL=66868],lychnocolax hispanicus[&&NHX:TOL=66869],lychnocolax insularis[&&NHX:TOL=66870],lychnocolax lundensis[&&NHX:TOL=66871],lychnocolax maxillaris[&&NHX:TOL=66872],lychnocolax mindanao[&&NHX:TOL=66873],lychnocolax mindoro[&&NHX:TOL=66874],lychnocolax neobritannicus[&&NHX:TOL=66875],lychnocolax nigeriensis[&&NHX:TOL=66876],lychnocolax novaeguinea[&&NHX:TOL=66877],lychnocolax orientalis[&&NHX:TOL=66878],lychnocolax ovatus[&&NHX:TOL=66879],lychnocolax palpalis[&&NHX:TOL=66880],lychnocolax postorbis[&&NHX:TOL=66881],lychnocolax redinhai[&&NHX:TOL=66882],lychnocolax similis[&&NHX:TOL=66883],lychnocolax simplex[&&NHX:TOL=66884],lychnocolax solomon[&&NHX:TOL=66885],lychnocolax vilhenai[&&NHX:TOL=66886],lychnocolax wygodzinskyi[&&NHX:TOL=66887],lychnocolax vietnamicus[&&NHX:TOL=66888])lychnocolax[&&NHX:TOL=66781],(caenocholax brondzinski[&&NHX:TOL=66889],caenocholax dominicensis[&&NHX:TOL=66890],(caenocholax fenyesi texensis[&&NHX:TOL=66892],caenocholax fenyesi waloffi[&&NHX:TOL=66893])caenocholax fenyesi[&&NHX:TOL=66891],caenocholax pierci[&&NHX:TOL=66894])caenocholax[&&NHX:TOL=66782])myrmecolacidae[&&NHX:TOL=14517])[&&NHX:TOL=14515],(callipharixenos muiri[&&NHX:TOL=27701],callipharixenos siamensis[&&NHX:TOL=27702])callipharixenos[&&NHX:TOL=14518],stylopidae[&&NHX:TOL=14519])stylopidia[&&NHX:TOL=14510],((eoxenos laboulbenei[&&NHX:TOL=29430],congoxenos stami[&&NHX:TOL=29441],mengenilla chobauti[&&NHX:TOL=66588],mengenilla gracilipes[&&NHX:TOL=66589],mengenilla parvula[&&NHX:TOL=66590],mengenilla sinensis[&&NHX:TOL=66591],mengenilla kaszabi[&&NHX:TOL=66592],mengenilla marikovskii[&&NHX:TOL=66593],mengenilla arabica[&&NHX:TOL=66594],mengenilla orientalis[&&NHX:TOL=66595],mengenilla australiensis[&&NHX:TOL=66596])mengenillidae[&&NHX:TOL=14508],(mengea tertiaria[&&NHX:EXT=Y:TOL=29426],mengea mengei[&&NHX:EXT=Y:TOL=29427])mengeidae[&&NHX:EXT=Y:TOL=14509])mengenillidia[&&NHX:TOL=14507],protoxenos janzeni[&&NHX:EXT=Y:TOL=29428],cretostylops engeli[&&NHX:EXT=Y:TOL=29429])strepsiptera[&&NHX:TOL=8222],((((((((afrothaumalea[&&NHX:TOL=118040],androprosopa[&&NHX:TOL=118041],austrothaumalea[&&NHX:TOL=118042],niphta[&&NHX:TOL=118043],orphnephilina[&&NHX:TOL=118044],oterere oliveri[&&NHX:TOL=118045],protothaumalea[&&NHX:TOL=118046],thaumalea[&&NHX:TOL=118047],trichothaumalea[&&NHX:TOL=118048],mesothaumalea fossilis[&&NHX:EXT=Y:TOL=118049])thaumaleidae[&&NHX:TOL=10474],(simuliidae[&&NHX:TOL=10476],(ceratopogonidae[&&NHX:TOL=10478],chironomidae[&&NHX:TOL=10479])[&&NHX:TOL=10477])[&&NHX:TOL=10475])[&&NHX:TOL=10473],((asiodixa[&&NHX:TOL=118050],dixa[&&NHX:TOL=118051],dixella[&&NHX:TOL=118052],meringodixa chalonensis[&&NHX:TOL=118053],metadixa tritiara[&&NHX:TOL=118055],nothodixa[&&NHX:TOL=118054],syndixa[&&NHX:EXT=Y:TOL=118056],eucorethrina[&&NHX:EXT=Y:TOL=118057])dixidae[&&NHX:TOL=10481],((corethrella corethrella[&&NHX:TOL=111432],corethrella lutzomiops[&&NHX:TOL=111433],corethrella fossicorethrella[&&NHX:EXT=Y:TOL=111434])corethrella[&&NHX:TOL=10483],(chaoboridae[&&NHX:TOL=10486],culicidae[&&NHX:TOL=10485])[&&NHX:TOL=10484])[&&NHX:TOL=10482])[&&NHX:TOL=10480])culicomorpha[&&NHX:TOL=10494],(((bittacomorpha[&&NHX:TOL=118024],bittacomorphella[&&NHX:TOL=118025],probittacomorpha christenseni[&&NHX:EXT=Y:TOL=118026])bittacomorphinae[&&NHX:TOL=118023],(ptychoptera[&&NHX:TOL=118028],ptychopterula deleta[&&NHX:EXT=Y:TOL=118029])ptychopterinae[&&NHX:TOL=118027],brodilka mitchelli[&&NHX:EXT=Y:TOL=118030],sinoptychopterites paludus[&&NHX:EXT=Y:TOL=118031],zhiganka comitans[&&NHX:EXT=Y:TOL=118032])ptychopteridae[&&NHX:TOL=23976],(araucoderus gloriosus[&&NHX:TOL=111334],eutanyderus[&&NHX:TOL=111335],mischoderus[&&NHX:TOL=111337],nothoderus australiensis[&&NHX:TOL=111338],protanyderus[&&NHX:TOL=111435],protoplasa fitchii[&&NHX:TOL=111339],radinoderus[&&NHX:TOL=111340],tanyderus[&&NHX:TOL=111341],macrochile[&&NHX:EXT=Y:TOL=111336],nannotanyderus[&&NHX:EXT=Y:TOL=111342],praemacrochile[&&NHX:EXT=Y:TOL=111343])tanyderidae[&&NHX:TOL=23975])ptychopteromorpha[&&NHX:TOL=10497])[&&NHX:TOL=23995],((nymphomyia[&&NHX:TOL=10437],(blephariceridae[&&NHX:TOL=10435],deuterophlebia    [&&NHX:TOL=10436])[&&NHX:TOL=10434])blephariceromorpha[&&NHX:TOL=10490],(((cramptonomyia spenceri[&&NHX:TOL=118017],haruka elegans[&&NHX:TOL=118018],pachyneura[&&NHX:TOL=118019],pergratospes holoptica[&&NHX:TOL=118020],pivus sarus[&&NHX:EXT=Y:TOL=118021],tega karatavica[&&NHX:EXT=Y:TOL=118022])pachyneuridae[&&NHX:TOL=10432],(((bibio[&&NHX:TOL=118088],bibiodes[&&NHX:TOL=118089],dilophus[&&NHX:TOL=118090],penthetria[&&NHX:TOL=118091],plecia[&&NHX:TOL=118092],bibiodites confluens[&&NHX:EXT=Y:TOL=118093],clothonopsis miocenica[&&NHX:EXT=Y:TOL=118094],fushunoplecia eocenica[&&NHX:EXT=Y:TOL=118095],lithobibio styriacus[&&NHX:EXT=Y:TOL=118096],lithosomyia brevis[&&NHX:EXT=Y:TOL=118097],megeana hardyi[&&NHX:EXT=Y:TOL=118098])bibioninae[&&NHX:TOL=118087],(hesperinus[&&NHX:TOL=118100],longicornia tenuis[&&NHX:EXT=Y:TOL=118101])hesperinae[&&NHX:TOL=118099])bibionidae[&&NHX:TOL=10431],(cecidomyiidae[&&NHX:TOL=10428],sciaridae[&&NHX:TOL=10429],(((anisotricha[&&NHX:TOL=111397],chiletricha[&&NHX:TOL=111398],eratomyia[&&NHX:TOL=111399],insulatricha[&&NHX:TOL=111400],kenyatricha[&&NHX:TOL=111401],nepaletricha[&&NHX:TOL=111402],rhychoheterotricha[&&NHX:TOL=111403])chiletrichinae[&&NHX:TOL=111396],heterotricha[&&NHX:TOL=111420],(cabamofa[&&NHX:TOL=111405],colonomyia[&&NHX:TOL=111406],ohakunea[&&NHX:TOL=111407],rogambara[&&NHX:TOL=111408])ohakuneinae[&&NHX:TOL=111404],rangomarama[&&NHX:TOL=111422])rangomaramidae[&&NHX:TOL=111281],(lygistorrhinidae[&&NHX:TOL=111280],mycetophilidae[&&NHX:TOL=10430])[&&NHX:TOL=111409],(ditomyiidae[&&NHX:TOL=111278],diadocidiidae[&&NHX:TOL=111277],(bolitophilidae[&&NHX:TOL=111276],keroplatidae[&&NHX:TOL=111279])[&&NHX:TOL=111411])[&&NHX:TOL=111410])[&&NHX:TOL=111393],afrotricha[&&NHX:TOL=111412],freemanomyia[&&NHX:TOL=111413],loicia[&&NHX:TOL=111414],sciaropota[&&NHX:TOL=111415],sciarosoma[&&NHX:TOL=111416],starkomyia[&&NHX:TOL=111417],taxicnemis[&&NHX:TOL=111418])sciaroidea[&&NHX:TOL=111392])[&&NHX:TOL=111419])bibionomorpha[&&NHX:TOL=10499],(axymyia[&&NHX:TOL=118058],mesaxymyia[&&NHX:TOL=118059],protaxymyia melanoptera[&&NHX:TOL=118060],psocites[&&NHX:EXT=Y:TOL=118061])axymyiidae[&&NHX:TOL=24069],(((((canthyloscelis canthyloscelis[&&NHX:TOL=118009],canthyloscelis chiliscelis[&&NHX:TOL=118010],canthyloscelis araucoscelis[&&NHX:TOL=118011])canthyloscelis[&&NHX:TOL=118008],exiliscelis californiensis[&&NHX:TOL=118012],hyperoscelis[&&NHX:TOL=118013],spiloptera arctica[&&NHX:TOL=118014],synneuron[&&NHX:TOL=118015],prohyperoscelis jurassicus[&&NHX:EXT=Y:TOL=118016])canthyloscelidae[&&NHX:TOL=10507],scatopsidae[&&NHX:TOL=10506])[&&NHX:TOL=24097],(perissomma[&&NHX:TOL=111286],gurvaniella hosbayari[&&NHX:EXT=Y:TOL=111284],palaeoperissomma[&&NHX:EXT=Y:TOL=111285])perissommatidae[&&NHX:TOL=10509],(cretoseguya burmitica[&&NHX:EXT=Y:TOL=111272],(valeseguya disjuncta[&&NHX:EXT=Y:TOL=111274],valeseguya rieki[&&NHX:TOL=111275])valeseguya[&&NHX:TOL=111273])valeseguyidae[&&NHX:TOL=111271])psychodomorpha in part[&&NHX:TOL=24098],(psychodidae[&&NHX:TOL=24087],((tipulidae[&&NHX:TOL=23910],(diazosma hirtipennis[&&NHX:TOL=118266],nothotrichocera[&&NHX:TOL=118267],(trichocera saltrichocera[&&NHX:TOL=118269],trichocera trichocera[&&NHX:TOL=118270],trichocera oligotrichocera[&&NHX:EXT=Y:TOL=118271])trichocera[&&NHX:TOL=118268],(paracladura adura[&&NHX:TOL=118273],paracladura paracladura[&&NHX:TOL=118274],paracladura zedura[&&NHX:TOL=118275])paracladura[&&NHX:TOL=118272],archaeotrichocera ephemera[&&NHX:EXT=Y:TOL=118276],eotrichocera christinae[&&NHX:EXT=Y:TOL=118277],mailotrichocera jurassica[&&NHX:EXT=Y:TOL=118278],mesotrichocera laiyangensis[&&NHX:EXT=Y:TOL=118279],paleotrichocera mongolica[&&NHX:EXT=Y:TOL=118280],sinotrichocera parva[&&NHX:EXT=Y:TOL=118281],tanyochoreta[&&NHX:EXT=Y:TOL=118282],trichonomites aquaticus[&&NHX:EXT=Y:TOL=118283])trichoceridae[&&NHX:TOL=24095])tipulomorpha[&&NHX:TOL=24067],(anisopodidae[&&NHX:TOL=24065],((((opetiops alienus[&&NHX:TOL=111232],pantophthalmus[&&NHX:TOL=111233])pantophthalmidae[&&NHX:TOL=10441],((arthropeina[&&NHX:TOL=111234],coenomyoides[&&NHX:TOL=111235],solva[&&NHX:TOL=111236],xylomya[&&NHX:TOL=111237])xylomyidae[&&NHX:TOL=10443],(((parhadrestia atava[&&NHX:TOL=108704],parhadrestia curico[&&NHX:TOL=108705])[&&NHX:TOL=110639],cretaceogaster pygmaeus[&&NHX:EXT=Y:TOL=110640])parhadrestiinae[&&NHX:TOL=23954],((archilagarinus priscus[&&NHX:TOL=108475],archimyza ava[&&NHX:TOL=108476],barbiellinia[&&NHX:TOL=108477],(boreoides machiliformis[&&NHX:TOL=108868],boreoides subulatus[&&NHX:TOL=108869],boreoides tasmaniensis[&&NHX:TOL=108870])boreoides[&&NHX:TOL=108478],chiromyza[&&NHX:TOL=108479],clavimyia alticola[&&NHX:TOL=108480],hylorops[&&NHX:TOL=108481],(inopus brevicornis[&&NHX:TOL=108871],inopus flavus[&&NHX:TOL=108872],inopus geminus[&&NHX:TOL=108873],inopus grossus[&&NHX:TOL=108874],inopus hitchcocki[&&NHX:TOL=108875],inopus rubriceps[&&NHX:TOL=108876])inopus[&&NHX:TOL=108482],mapuchemyia[&&NHX:TOL=108483],mesomyza[&&NHX:TOL=108484],nonacris[&&NHX:TOL=108485],stenimantia carbonaria[&&NHX:TOL=108486],stenimas stemmiticalis[&&NHX:TOL=108487],tana[&&NHX:TOL=108488])chiromyzinae[&&NHX:TOL=23955],(((beridops[&&NHX:TOL=108500],hadrestia[&&NHX:TOL=108509],((beris alamaculata[&&NHX:TOL=108919],beris angustifacies[&&NHX:TOL=108920],beris annulipes[&&NHX:TOL=108921],beris basiflava[&&NHX:TOL=108922],beris burmanica[&&NHX:TOL=108923],beris chalybata[&&NHX:TOL=108924],beris clavipes[&&NHX:TOL=108925],beris crassitarsis[&&NHX:TOL=108926],beris cypria[&&NHX:TOL=108927],beris dolichocera[&&NHX:TOL=108928],beris emeishana[&&NHX:TOL=108929],beris excellens[&&NHX:TOL=108930],beris fuscipes[&&NHX:TOL=108931],beris gansuensis[&&NHX:TOL=108932],beris geniculata[&&NHX:TOL=108933],beris hauseri[&&NHX:TOL=111453],beris heptapotamica[&&NHX:TOL=108934],beris hildebrantae[&&NHX:TOL=108935],beris hirotui[&&NHX:TOL=108936],beris kovalevi[&&NHX:TOL=108937],beris luteipes[&&NHX:TOL=108938],beris luteistigma[&&NHX:TOL=108939],beris malaisei[&&NHX:TOL=108940],beris morrisii[&&NHX:TOL=108941],beris nebulosa[&&NHX:TOL=108942],beris potanini[&&NHX:TOL=108943],beris pulchripennis[&&NHX:TOL=108944],beris rex[&&NHX:TOL=108945],beris rozkosnyi[&&NHX:TOL=108946],beris schaposchnikowi[&&NHX:TOL=108947],beris similis[&&NHX:TOL=108948],beris strobli[&&NHX:TOL=108949],beris vallata[&&NHX:TOL=108950],beris ziminae[&&NHX:TOL=108951])beris[&&NHX:TOL=108501],draymonia nitida[&&NHX:TOL=108505])[&&NHX:TOL=111182],(microhadrestia minuta[&&NHX:TOL=108512],oplachantha[&&NHX:TOL=108515],(paraberismyia tzontehuitza[&&NHX:TOL=108516],((allognosta albifascia[&&NHX:TOL=108882],allognosta annulifemur[&&NHX:TOL=108883],allognosta assamensis[&&NHX:TOL=108884],allognosta basiflava[&&NHX:TOL=108885],allognosta brevicornis[&&NHX:TOL=108886],allognosta burmanica[&&NHX:TOL=108887],allognosta bwamba[&&NHX:TOL=108888],allognosta caloptera[&&NHX:TOL=108889],allognosta crassa[&&NHX:TOL=108890],allognosta crassitarsis[&&NHX:TOL=108891],allognosta flavimaculata[&&NHX:TOL=108892],allognosta flavofemoralis[&&NHX:TOL=108893],allognosta flavopleuralis[&&NHX:TOL=108894],allognosta fuscipennis[&&NHX:TOL=108895],allognosta fuscitarsis[&&NHX:TOL=108896],allognosta inermis[&&NHX:TOL=108897],allognosta japonica[&&NHX:TOL=108898],allognosta lativertex[&&NHX:TOL=108899],allognosta maculipleura[&&NHX:TOL=108900],allognosta maxima[&&NHX:TOL=108901],allognosta nigripes[&&NHX:TOL=108902],allognosta njombe[&&NHX:TOL=108903],allognosta obscuriventris[&&NHX:TOL=108904],allognosta orientalis[&&NHX:TOL=108905],allognosta partita[&&NHX:TOL=108906],allognosta philippina[&&NHX:TOL=108907],allognosta platypus[&&NHX:TOL=108908],allognosta pleuralis[&&NHX:TOL=108909],allognosta pulchella[&&NHX:TOL=108910],allognosta rufithorax[&&NHX:TOL=108911],allognosta shibuyai[&&NHX:TOL=108912],allognosta sichuanensis[&&NHX:TOL=108913],allognosta stigmaticalis[&&NHX:TOL=108914],allognosta stuckenbergae[&&NHX:TOL=108915],allognosta tessmanni[&&NHX:TOL=108916],allognosta vagans[&&NHX:TOL=108917],allognosta varians[&&NHX:TOL=108918])allognosta[&&NHX:TOL=108491],berismyia[&&NHX:TOL=108503])[&&NHX:TOL=111185])[&&NHX:TOL=111184],(arcuavena[&&NHX:TOL=108494],(beridella[&&NHX:TOL=108499],heteracanthia[&&NHX:TOL=108510])[&&NHX:TOL=111187])[&&NHX:TOL=111186])[&&NHX:TOL=111183])beris group[&&NHX:TOL=111181],(spartimas ornatipes[&&NHX:TOL=108518],(australoactina[&&NHX:TOL=108496],((chorisops caroli[&&NHX:TOL=108952],chorisops maculiala[&&NHX:TOL=108953],chorisops marginata[&&NHX:TOL=108954],chorisops masoni[&&NHX:TOL=108955],chorisops nagatomii[&&NHX:TOL=108956],chorisops separata[&&NHX:TOL=108957],chorisops tibialis[&&NHX:TOL=108958],chorisops tunisiae[&&NHX:TOL=108959],chorisops unita[&&NHX:TOL=108960])chorisops[&&NHX:TOL=108504],(((actina acutula[&&NHX:TOL=109943],actina amoena[&&NHX:TOL=109944],actina apicalis[&&NHX:TOL=109945],actina chalybea[&&NHX:TOL=109946],actina compta[&&NHX:TOL=109947],actina diadema[&&NHX:TOL=109948],actina flavicornis[&&NHX:TOL=109949],actina fraterna[&&NHX:TOL=109950],actina jezoensis[&&NHX:TOL=109951],actina maculipennis[&&NHX:TOL=109952],actina sapporo[&&NHX:TOL=109953],actina soldatowi[&&NHX:TOL=109954],actina spatulata[&&NHX:TOL=109955],actina varipes[&&NHX:TOL=109956],actina viridis[&&NHX:TOL=109957],actina xinzangensis[&&NHX:TOL=109958])actina[&&NHX:TOL=108489],australoberis[&&NHX:TOL=108497],mischomedia queenslandica[&&NHX:TOL=108878],(berisina[&&NHX:TOL=108502],(tytthoberis cuprea[&&NHX:TOL=108519],zealandoberis[&&NHX:TOL=108520])[&&NHX:TOL=111194])[&&NHX:TOL=111193])[&&NHX:TOL=111192],(aspartimas formosanus[&&NHX:TOL=108495],(archistratiomys[&&NHX:TOL=108493],(exaireta siliacea[&&NHX:TOL=108961],exaireta spinigera[&&NHX:TOL=108962])exaireta[&&NHX:TOL=108508],(anexaireta[&&NHX:TOL=108492],macromeracris[&&NHX:TOL=108511],smaragdinomyia magnifica[&&NHX:TOL=108517],((actinomyia eupodata[&&NHX:TOL=108879],actinomyia longicornis[&&NHX:TOL=108880],actinomyia novaeteutoniae[&&NHX:TOL=108881])actinomyia[&&NHX:TOL=108490],(neactina[&&NHX:TOL=108513],neoberis brasiliana[&&NHX:TOL=108514])[&&NHX:TOL=111199])[&&NHX:TOL=111198],(exairetina auricoma[&&NHX:TOL=108507],(benhamyia[&&NHX:TOL=108498],eumecacis clavigera[&&NHX:TOL=108506])[&&NHX:TOL=111201])[&&NHX:TOL=111200])[&&NHX:TOL=111197])[&&NHX:TOL=111196])[&&NHX:TOL=111195])[&&NHX:TOL=111191])[&&NHX:TOL=111190])[&&NHX:TOL=111189])actina group[&&NHX:TOL=111188])beridinae[&&NHX:TOL=23956],((anacanthella[&&NHX:TOL=108521],antissa cuprea[&&NHX:TOL=108522],antissella[&&NHX:TOL=108523],cyanauges[&&NHX:TOL=108524],discopteromyia[&&NHX:TOL=108525],(exodontha dubia[&&NHX:TOL=108963],exodontha luteipes[&&NHX:TOL=108964])exodontha[&&NHX:TOL=108526],(lecomyia caerulea[&&NHX:TOL=108965],lecomyia cyanea[&&NHX:TOL=108966],lecomyia notha[&&NHX:TOL=108967])lecomyia[&&NHX:TOL=108527])antissinae[&&NHX:TOL=23957],((abiomyia[&&NHX:TOL=108528],abrosiomyia[&&NHX:TOL=108529],acanthinomyia[&&NHX:TOL=108530],acyrocera argyraspis[&&NHX:TOL=108531],acyrocerops furcifera[&&NHX:TOL=108532],adraga[&&NHX:TOL=108533],ageiton ater[&&NHX:TOL=108534],aidomyia[&&NHX:TOL=108535],alliophleps elliptica[&&NHX:TOL=108536],anargemus basalis[&&NHX:TOL=108537],ankylacantha keiseri[&&NHX:TOL=108538],anomalocanthimyia[&&NHX:TOL=108539],apotomaspis nigeriana[&&NHX:TOL=108540],argyrobrithes[&&NHX:TOL=108541],(artemita amenides[&&NHX:TOL=108995],artemita argentea[&&NHX:TOL=108996],artemita aurata[&&NHX:TOL=108997],artemita banksi[&&NHX:TOL=108998],artemita bellardii[&&NHX:TOL=108999],artemita bequaerti[&&NHX:TOL=109000],artemita bicolor[&&NHX:TOL=109001],artemita brasiliana[&&NHX:TOL=109002],artemita centor[&&NHX:TOL=109003],artemita convexa[&&NHX:TOL=109004],artemita hieroglyphica[&&NHX:TOL=109005],artemita insularis[&&NHX:TOL=109006],artemita latifrons[&&NHX:TOL=109007],artemita nana[&&NHX:TOL=109008],artemita peruviana[&&NHX:TOL=109009],artemita podexargenteus[&&NHX:TOL=109010])artemita[&&NHX:TOL=108542],artemitomima mirabilis[&&NHX:TOL=108543],arthronemina curtilamelleta[&&NHX:TOL=108544],ashantina antennata[&&NHX:TOL=108545],aspidacantha[&&NHX:TOL=108546],aspidacanthina exigua[&&NHX:TOL=108547],asyncritula[&&NHX:TOL=108548],aulana[&&NHX:TOL=108549],(berkshiria albistylum[&&NHX:TOL=109011],berkshiria hungarica[&&NHX:TOL=109012])berkshiria[&&NHX:TOL=108550],bistinda castanea[&&NHX:TOL=108551],blastocera speciosa[&&NHX:TOL=108552],borboridea[&&NHX:TOL=108553],(brachyodina depressa[&&NHX:TOL=110522],brachyodina dorsata[&&NHX:TOL=110523],brachyodina insularis[&&NHX:TOL=110524],brachyodina metzi[&&NHX:TOL=110525],brachyodina niveioscula[&&NHX:TOL=110526],brachyodina tomentosa[&&NHX:TOL=110527])brachyodina[&&NHX:TOL=108554],brachyphleps tristis[&&NHX:TOL=108555],burmabrithes annulipes[&&NHX:TOL=108556],cactobia opuntae[&&NHX:TOL=108557],caenacantha bipartita[&&NHX:TOL=108558],camptopteromyia[&&NHX:TOL=108559],cardopomyia robusta[&&NHX:TOL=108560],cechorismenus flavicornis[&&NHX:TOL=108561],(chalcidomorphina argentea[&&NHX:TOL=109013],chalcidomorphina aurata[&&NHX:TOL=109014],chalcidomorphina planes[&&NHX:TOL=109015],chalcidomorphina terataspis[&&NHX:TOL=109016])chalcidomorphina[&&NHX:TOL=108562],charisina angustifrons[&&NHX:TOL=108563],chelonomima[&&NHX:TOL=108564],chlamydonotum nigreradiatum[&&NHX:TOL=108565],chlorophthalmyia brevicornis[&&NHX:TOL=108566],cibotogaster[&&NHX:TOL=108567],clarissimyia pallipes[&&NHX:TOL=108568],(cosmariomyia albarista[&&NHX:TOL=130323],cosmariomyia argyrosticta[&&NHX:TOL=130324],cosmariomyia pallidipennis[&&NHX:TOL=130325])cosmariomyia[&&NHX:TOL=108569],craspedometopon[&&NHX:TOL=108570],culcua[&&NHX:TOL=108571],cyclotaspis inornata[&&NHX:TOL=108572],cynipimorpha bilimecki[&&NHX:TOL=108573],dactylacantha plaumanni[&&NHX:TOL=108574],dactylodeictes[&&NHX:TOL=108575],dactylotinda saegeri[&&NHX:TOL=108576],damaromyia[&&NHX:TOL=108577],diademophora ruandaensis[&&NHX:TOL=108578],dialampsis argentata[&&NHX:TOL=108579],diargemus flavipes[&&NHX:TOL=108580],diastophthalmus flavimanus[&&NHX:TOL=108581],diplephippium[&&NHX:TOL=108582],diplopeltina skaifei[&&NHX:TOL=108583],dochmiocera aurilineata[&&NHX:TOL=108584],dolichodema[&&NHX:TOL=108585],drosimomyia[&&NHX:TOL=108586],ecchaetomyia nigrovittata[&&NHX:TOL=108587],eicochalcidina[&&NHX:TOL=108588],(eidalimus angustifrons[&&NHX:TOL=109017],eidalimus annulatus[&&NHX:TOL=109018],eidalimus flavicornis[&&NHX:TOL=109019],eidalimus fuscus[&&NHX:TOL=109020],eidalimus henshawi[&&NHX:TOL=109021],eidalimus insularum[&&NHX:TOL=109022],eidalimus lineatus[&&NHX:TOL=109023],eidalimus minutus[&&NHX:TOL=109024])eidalimus[&&NHX:TOL=108589],engicerus major[&&NHX:TOL=108590],enypnium[&&NHX:TOL=108591],eufijia[&&NHX:TOL=108592],(eupachygaster alexanderi[&&NHX:TOL=111381],eupachygaster flava[&&NHX:TOL=111382],eupachygaster lasiops[&&NHX:TOL=111383],eupachygaster subtarsalis[&&NHX:TOL=111455],eupachygaster tarsalis[&&NHX:TOL=111384])eupachygaster[&&NHX:TOL=108593],evaza[&&NHX:TOL=108594],gabaza[&&NHX:TOL=108595],glochinomyia albiseta[&&NHX:TOL=108596],gnesiomyia crassiseta[&&NHX:TOL=108597],gnorismomyia flavicornis[&&NHX:TOL=108598],gobertina[&&NHX:TOL=108599],goetghebueromyia paradoxa[&&NHX:TOL=108600],(gowdeyana albipilosa[&&NHX:TOL=111344],gowdeyana argenteus[&&NHX:TOL=111345],gowdeyana mirabilis[&&NHX:TOL=111346],gowdeyana punctifera[&&NHX:TOL=111347],gowdeyana ryckmani[&&NHX:TOL=111348],gowdeyana varipes[&&NHX:TOL=111349],gowdeyana vitrisetosus[&&NHX:TOL=111350])gowdeyana[&&NHX:TOL=108601],haplofijia simplex[&&NHX:TOL=108602],hermetiomima[&&NHX:TOL=108603],hexacraspis sexpinosa[&&NHX:TOL=108604],himantochaeta cultellata[&&NHX:TOL=108605],hypoceromys[&&NHX:TOL=108606],hypoxycera simplex[&&NHX:TOL=108607],hypselophrum cyphomyioides[&&NHX:TOL=108608],isomerocera[&&NHX:TOL=108609],keiseria[&&NHX:TOL=108610],kerteszmyia ecuadora[&&NHX:TOL=130326],kolomania[&&NHX:TOL=108611],lampetiopus umbrosus[&&NHX:TOL=108612],lasiodeictes niger[&&NHX:TOL=108613],lenomyia[&&NHX:TOL=108614],leucacron interruptum[&&NHX:TOL=108615],leveromyia[&&NHX:TOL=108616],ligyromyia columbiana[&&NHX:TOL=108617],lonchegaster[&&NHX:TOL=108618],lonchobrithes modestus[&&NHX:TOL=108619],lophoteles[&&NHX:TOL=108620],lyprotemyia[&&NHX:TOL=108621],maackiana[&&NHX:TOL=108622],madagascara seyrigi[&&NHX:TOL=108623],madagascarina beyeri[&&NHX:TOL=108624],manotes[&&NHX:TOL=108625],marangua pygmaea[&&NHX:TOL=108626],meristocera[&&NHX:TOL=108627],meristomeringella jamesi[&&NHX:TOL=108628],meristomeringina[&&NHX:TOL=108629],meristomerinx[&&NHX:TOL=108630],monacanthomyia[&&NHX:TOL=108631],mycterocera contigua[&&NHX:TOL=108632],myiocavia tomentosa[&&NHX:TOL=108633],nemodema nudibasis[&&NHX:TOL=108634],neoacanthina fasciata[&&NHX:TOL=108635],neochauna variabilis[&&NHX:TOL=108636],(neopachygaster africana[&&NHX:TOL=109959],neopachygaster admiranda[&&NHX:TOL=111459],neopachygaster basilewskyi[&&NHX:TOL=109960],neopachygaster biafra[&&NHX:TOL=109961],neopachygaster caucasica[&&NHX:TOL=111454],neopachygaster congoensis[&&NHX:TOL=109962],neopachygaster eisentrauti[&&NHX:TOL=109963],neopachygaster intermedia[&&NHX:TOL=109964],neopachygaster kiboensis[&&NHX:TOL=109965],neopachygaster maculicornis[&&NHX:TOL=109966],neopachygaster meromelaena[&&NHX:TOL=109967],neopachygaster occidentalis[&&NHX:TOL=109968],neopachygaster reniformis[&&NHX:TOL=109969],neopachygaster secernibilis[&&NHX:TOL=109970],neopachygaster stackelbergi[&&NHX:TOL=109971],neopachygaster stigma[&&NHX:TOL=109972],neopachygaster umbrifera[&&NHX:TOL=109973],neopachygaster valida[&&NHX:TOL=109974],neopachygaster vitrea[&&NHX:TOL=109975],neopachygaster wittei[&&NHX:TOL=109976])neopachygaster[&&NHX:TOL=108637],netrogramma consona[&&NHX:TOL=108638],nyplatys niger[&&NHX:TOL=108639],obrapa[&&NHX:TOL=108640],ornopyramis tener[&&NHX:TOL=108641],otionigera acuticornis[&&NHX:TOL=108642],oxymyia epacta[&&NHX:TOL=108643],pachyacantha crassiventris[&&NHX:TOL=108644],pachyberis stigmaticalis[&&NHX:TOL=108645],(pachygaster alpina[&&NHX:TOL=109025],pachygaster annulipes[&&NHX:TOL=109026],pachygaster atra[&&NHX:TOL=109027],pachygaster characta[&&NHX:TOL=109028],pachygaster dorsalis[&&NHX:TOL=109029],pachygaster emerita[&&NHX:TOL=111460],pachygaster flavimana[&&NHX:TOL=109030],pachygaster flavipennis[&&NHX:TOL=109031],pachygaster kerteszi[&&NHX:TOL=109032],pachygaster leachii[&&NHX:TOL=109033],pachygaster maura[&&NHX:TOL=109034],pachygaster montana[&&NHX:TOL=109035],pachygaster nigripes[&&NHX:TOL=109036],pachygaster piriventris[&&NHX:TOL=109037],pachygaster pulchra[&&NHX:TOL=109038],pachygaster subatra[&&NHX:TOL=111456],pachygaster wirthi[&&NHX:TOL=109039],pachygaster antiquus[&&NHX:EXT=Y:TOL=111457],pachygaster hymenaea[&&NHX:EXT=Y:TOL=111458])pachygaster[&&NHX:TOL=108646],panacridops varians[&&NHX:TOL=108647],panacris[&&NHX:TOL=108648],pangomyia[&&NHX:TOL=108649],paracanthinomyia argyrostriata[&&NHX:TOL=108650],paracechorismenus[&&NHX:TOL=108651],paradraga omnihirta[&&NHX:TOL=108652],(parastratiosphecomyia stratiosphecomyioides[&&NHX:TOL=130327],parastratiosphecomyia szechuanensis[&&NHX:TOL=130328])parastratiosphecomyia[&&NHX:TOL=108653],parevaza longa[&&NHX:TOL=108654],pedinocera longicornis[&&NHX:TOL=108655],pedinocerops[&&NHX:TOL=108656],pegadomyia[&&NHX:TOL=108657],peltina[&&NHX:TOL=108658],peratomastix australis[&&NHX:TOL=108659],physometopon[&&NHX:TOL=108660],pithomyia[&&NHX:TOL=108661],platylobium zurstrasseni[&&NHX:TOL=108662],platyna[&&NHX:TOL=108663],platynomorpha doryphora[&&NHX:TOL=108664],platynomyia[&&NHX:TOL=108665],popanomyia[&&NHX:TOL=108666],pristaspis truncata[&&NHX:TOL=108667],proegmenomyia metallica[&&NHX:TOL=108668],psapharomydops procerus[&&NHX:TOL=108669],psapharomys salebrosa[&&NHX:TOL=108670],psephiocera[&&NHX:TOL=108671],(pseudocyphomyia mimetica[&&NHX:TOL=108968],pseudocyphomyia n. sp.[&&NHX:TOL=108969])pseudocyphomyia[&&NHX:TOL=108672],pseudomeristomerinx nigricornis[&&NHX:TOL=108673],pseudoxymyia[&&NHX:TOL=108674],ptilinoxus fallax[&&NHX:TOL=108675],ptilocera[&&NHX:TOL=108676],raphanocera turanica[&&NHX:TOL=108677],rosapha[&&NHX:TOL=108678],rosaphula handschini[&&NHX:TOL=108679],salduba[&&NHX:TOL=108680],saldubella[&&NHX:TOL=108681],saruga[&&NHX:TOL=108682],sathroptera flavipes[&&NHX:TOL=108683],spaniomyia[&&NHX:TOL=108684],sphaerofijia evazaeformis[&&NHX:TOL=108685],steleoceromys anthracina[&&NHX:TOL=108686],sternobrithes[&&NHX:TOL=108687],stratiosphecomyia variegata[&&NHX:TOL=108688],strobilaspis[&&NHX:TOL=108689],strophognathus argentatus[&&NHX:TOL=108690],synaptochaeta digitata[&&NHX:TOL=108691],tegocera jamesi[&&NHX:TOL=108692],thopomyia[&&NHX:TOL=108693],thylacognathus lativentris[&&NHX:TOL=108694],tijucameru[&&NHX:TOL=111441],tinda[&&NHX:TOL=108695],tindacera quadrispinosa[&&NHX:TOL=108696],toxopeusomyia flavitarsis[&&NHX:TOL=108697],trichochaeta[&&NHX:TOL=108698],trigonocerina flaviventris[&&NHX:TOL=108699],vittiger schusei[&&NHX:TOL=108700],weimyia bispinosa[&&NHX:TOL=108701],xylopachygaster[&&NHX:TOL=108702],(zabrachia albipilum[&&NHX:TOL=108970],zabrachia annulifemur[&&NHX:TOL=108971],zabrachia barbata[&&NHX:TOL=108972],zabrachia beameri[&&NHX:TOL=108973],zabrachia hebicornuta[&&NHX:TOL=108974],zabrachia knowltoni[&&NHX:TOL=108975],zabrachia latigena[&&NHX:TOL=108976],zabrachia lopha[&&NHX:TOL=108977],zabrachia madagascariensis[&&NHX:TOL=108978],zabrachia magnicornis[&&NHX:TOL=108979],zabrachia mexicana[&&NHX:TOL=108980],zabrachia minutissima[&&NHX:TOL=108981],zabrachia occidentalis[&&NHX:TOL=108982],zabrachia parva[&&NHX:TOL=108983],zabrachia plicata[&&NHX:TOL=108984],zabrachia polita[&&NHX:TOL=108985],zabrachia pusilla[&&NHX:TOL=108986],zabrachia stackelbergi[&&NHX:TOL=108987],zabrachia stoichoides[&&NHX:TOL=108988],zabrachia tenella[&&NHX:TOL=108989],zabrachia yuccae[&&NHX:TOL=108990])zabrachia[&&NHX:TOL=108703])pachygastrinae[&&NHX:TOL=23958],((abasanistus[&&NHX:TOL=108706],abavus[&&NHX:TOL=108707],acropeltates[&&NHX:TOL=108708],(adoxomyia alashanica[&&NHX:TOL=109040],adoxomyia albopilosa[&&NHX:TOL=109041],adoxomyia appressa[&&NHX:TOL=109042],adoxomyia argentata[&&NHX:TOL=109043],adoxomyia argenteofasciata[&&NHX:TOL=109044],adoxomyia aureovittata[&&NHX:TOL=109045],adoxomyia bistriata[&&NHX:TOL=109046],adoxomyia brevispina[&&NHX:TOL=109047],adoxomyia cinerascens[&&NHX:TOL=109048],adoxomyia claripennis[&&NHX:TOL=109049],adoxomyia dahlii[&&NHX:TOL=109050],adoxomyia fenestrata[&&NHX:TOL=109051],adoxomyia flauipes[&&NHX:TOL=109052],adoxomyia formosana[&&NHX:TOL=109053],adoxomyia heminopla[&&NHX:TOL=109054],adoxomyia hermonensis[&&NHX:TOL=109055],adoxomyia hungshanensis[&&NHX:TOL=109056],adoxomyia lata[&&NHX:TOL=109057],adoxomyia lindneri[&&NHX:TOL=109058],adoxomyia lugubris[&&NHX:TOL=109059],adoxomyia marginata[&&NHX:TOL=109060],adoxomyia micheneri[&&NHX:TOL=109061],adoxomyia nigribarba[&&NHX:TOL=109062],adoxomyia obscuripennis[&&NHX:TOL=109063],adoxomyia palaestinensis[&&NHX:TOL=109064],adoxomyia pleskei[&&NHX:TOL=109065],adoxomyia portschinskii[&&NHX:TOL=109066],adoxomyia regularis[&&NHX:TOL=109067],adoxomyia ruficornis[&&NHX:TOL=109068],adoxomyia rustica[&&NHX:TOL=109069],adoxomyia sarudnyi[&&NHX:TOL=109070],adoxomyia socotrae[&&NHX:TOL=111444],adoxomyia subulata[&&NHX:TOL=109071],adoxomyia taxana[&&NHX:TOL=109073],adoxomyia tenuicornis[&&NHX:TOL=109072],adoxomyia transcaucasica[&&NHX:TOL=111462],adoxomyia weyrauchi[&&NHX:TOL=109074])adoxomyia[&&NHX:TOL=108709],(alopecuroceras atripluma[&&NHX:TOL=114864],alopecuroceras coloratum[&&NHX:TOL=114865])alopecuroceras[&&NHX:TOL=108710],amphilecta superba[&&NHX:TOL=108711],ampsalis[&&NHX:TOL=108712],anoamyia[&&NHX:TOL=108713],(auloceromyia pedunculata[&&NHX:TOL=111375],auloceromyia vespiformis[&&NHX:TOL=111376])auloceromyia[&&NHX:TOL=108714],caenocephaloides melanarius[&&NHX:TOL=108715],campeprosopa[&&NHX:TOL=108716],chrodonota[&&NHX:TOL=108717],(clitellaria aurofasciata[&&NHX:TOL=109075],clitellaria bergeri[&&NHX:TOL=109076],clitellaria bilineata[&&NHX:TOL=109077],clitellaria chikuni[&&NHX:TOL=109078],clitellaria crassistilus[&&NHX:TOL=109079],clitellaria ephippium[&&NHX:TOL=109080],clitellaria flavipilosa[&&NHX:TOL=109081],clitellaria ignifera[&&NHX:TOL=109082],clitellaria kunmingana[&&NHX:TOL=109083],clitellaria longipilosa[&&NHX:TOL=109084],clitellaria mediflava[&&NHX:TOL=109085],clitellaria nigra[&&NHX:TOL=109086],clitellaria obtusa[&&NHX:TOL=109087],clitellaria orientalis[&&NHX:TOL=109088],clitellaria pontica[&&NHX:TOL=109089],clitellaria stylata[&&NHX:TOL=109090])clitellaria[&&NHX:TOL=108718],(cyphomyia abana[&&NHX:TOL=109091],cyphomyia acuminata[&&NHX:TOL=109092],cyphomyia aczeli[&&NHX:TOL=109093],cyphomyia affinis[&&NHX:TOL=109094],cyphomyia albicaput[&&NHX:TOL=109095],cyphomyia albispina[&&NHX:TOL=109096],cyphomyia albitarsis[&&NHX:TOL=109097],cyphomyia albomaculata[&&NHX:TOL=109098],cyphomyia altifrons[&&NHX:TOL=109099],cyphomyia androgyna[&&NHX:TOL=109100],cyphomyia auriflamma[&&NHX:TOL=109101],cyphomyia aurifrons[&&NHX:TOL=109102],cyphomyia banksi[&&NHX:TOL=109103],cyphomyia bicarinata[&&NHX:TOL=109104],cyphomyia brevis[&&NHX:TOL=109105],cyphomyia chalybea[&&NHX:TOL=109106],cyphomyia chinensis[&&NHX:TOL=109107],cyphomyia chrysodota[&&NHX:TOL=109108],cyphomyia claripennis[&&NHX:TOL=109109],cyphomyia coprates[&&NHX:TOL=109110],cyphomyia curvispina[&&NHX:TOL=109111],cyphomyia cyanea[&&NHX:TOL=109112],cyphomyia dispar[&&NHX:TOL=109113],cyphomyia dominicana[&&NHX:TOL=109114],cyphomyia ecuadorensis[&&NHX:TOL=109115],cyphomyia erecta[&&NHX:TOL=109116],cyphomyia erectispinis[&&NHX:TOL=109117],cyphomyia fascipes[&&NHX:TOL=109118],cyphomyia fassli[&&NHX:TOL=109119],cyphomyia ferruginea[&&NHX:TOL=109120],cyphomyia flaviceps[&&NHX:TOL=109121],cyphomyia flavimana[&&NHX:TOL=109122],cyphomyia flavipennis[&&NHX:TOL=109123],cyphomyia formosa[&&NHX:TOL=109124],cyphomyia geniculata[&&NHX:TOL=109125],cyphomyia golbachi[&&NHX:TOL=109126],cyphomyia gracilicornis[&&NHX:TOL=109127],cyphomyia helvipennis[&&NHX:TOL=109128],cyphomyia hybrida[&&NHX:TOL=109129],cyphomyia imitans[&&NHX:TOL=109130],cyphomyia indica[&&NHX:TOL=109131],cyphomyia jamesi[&&NHX:TOL=109132],cyphomyia lasiophthalma[&&NHX:TOL=109133],cyphomyia leucocephala[&&NHX:TOL=109134],cyphomyia longicornis[&&NHX:TOL=109135],cyphomyia marginata[&&NHX:TOL=109136],cyphomyia marshalli[&&NHX:TOL=109137],cyphomyia neivai[&&NHX:TOL=109138],cyphomyia nigripes[&&NHX:TOL=109139],cyphomyia nigritarsis[&&NHX:TOL=109140],cyphomyia notabilis[&&NHX:TOL=109141],cyphomyia nubilipennis[&&NHX:TOL=109142],cyphomyia obscura[&&NHX:TOL=109143],cyphomyia obscuripalpis[&&NHX:TOL=109144],cyphomyia ochracea[&&NHX:TOL=109145],cyphomyia orientalis[&&NHX:TOL=109146],cyphomyia ornata[&&NHX:TOL=109147],cyphomyia picta[&&NHX:TOL=109148],cyphomyia pilosissima[&&NHX:TOL=109149],cyphomyia planifrons[&&NHX:TOL=109150],cyphomyia pseudomaculata[&&NHX:TOL=109151],cyphomyia pubiventris[&&NHX:TOL=109152],cyphomyia pulchella[&&NHX:TOL=109153],cyphomyia regularis[&&NHX:TOL=109154],cyphomyia rubra[&&NHX:TOL=109155],cyphomyia scalaris[&&NHX:TOL=109156],cyphomyia schwarzi[&&NHX:TOL=109157],cyphomyia shannoni[&&NHX:TOL=109158],cyphomyia simplex[&&NHX:TOL=109159],cyphomyia souzalopesi[&&NHX:TOL=109160],cyphomyia speciosa[&&NHX:TOL=109161],cyphomyia sulcifrons[&&NHX:TOL=109162],cyphomyia tomentosa[&&NHX:TOL=109163],cyphomyia unicolor[&&NHX:TOL=109164],cyphomyia varipes[&&NHX:TOL=109165],cyphomyia verticalis[&&NHX:TOL=109166],cyphomyia violacea[&&NHX:TOL=109167],cyphomyia whiteheadi[&&NHX:TOL=109168],cyphomyia wiedemanni[&&NHX:TOL=109169],cyphomyia willistoni[&&NHX:TOL=109170],cyphomyia xanthobasis[&&NHX:TOL=109171],cyphomyia ypsilon[&&NHX:TOL=109172],cyphomyia zernyi[&&NHX:TOL=109173])cyphomyia[&&NHX:TOL=108719],diaphorostylus[&&NHX:TOL=108720],dicyphoma[&&NHX:TOL=108721],dieuryneura stigma[&&NHX:TOL=108722],ditylometopa[&&NHX:TOL=108723],dysbiota[&&NHX:TOL=108724],elissoma[&&NHX:TOL=108725],eudmeta[&&NHX:TOL=108726],euryneura[&&NHX:TOL=108727],geranopus pupuratus[&&NHX:TOL=108728],grypomyia gracilis[&&NHX:TOL=108729],haplephippium[&&NHX:TOL=108730],homalarthria nigra[&&NHX:TOL=108731],labocerina atrata[&&NHX:TOL=108732],lagenosoma[&&NHX:TOL=108733],leucoptilum[&&NHX:TOL=108734],meringostylus[&&NHX:TOL=108735],mixoclitellaria maculipennis[&&NHX:TOL=108736],nigritomyia[&&NHX:TOL=108737],octarthria[&&NHX:TOL=108738],platopsomyia flavida[&&NHX:TOL=108739],progrypomyia nigra[&&NHX:TOL=108740],pycnomalla[&&NHX:TOL=108741],pycnothorax australis[&&NHX:TOL=108742],quichuamyia[&&NHX:TOL=111374],ruba[&&NHX:TOL=108743],syndipnomyia[&&NHX:TOL=108744])clitellariinae[&&NHX:TOL=23959],(((chaetohermetia[&&NHX:TOL=108745],chaetosargus[&&NHX:TOL=108746],(hermetia aeneipennis[&&NHX:TOL=109174],hermetia albipoda[&&NHX:TOL=109175],hermetia albitarsis[&&NHX:TOL=109176],hermetia amboyna[&&NHX:TOL=109177],hermetia ampulla[&&NHX:TOL=109178],hermetia amsarii[&&NHX:TOL=109179],hermetia anthidium[&&NHX:TOL=109180],hermetia aurata[&&NHX:TOL=109181],hermetia aurinotata[&&NHX:TOL=109182],hermetia austeni[&&NHX:TOL=109183],hermetia beebei[&&NHX:TOL=109184],hermetia bicolor[&&NHX:TOL=109185],hermetia borneensis[&&NHX:TOL=109186],hermetia brunettii[&&NHX:TOL=109187],hermetia burmeisteri[&&NHX:TOL=109188],hermetia callifera[&&NHX:TOL=109189],hermetia ceria[&&NHX:TOL=109190],hermetia ceriogaster[&&NHX:TOL=109191],hermetia cerioides[&&NHX:TOL=109192],hermetia chrysopila[&&NHX:TOL=109193],hermetia cingulata[&&NHX:TOL=109194],hermetia coarctata[&&NHX:TOL=109195],hermetia comstocki[&&NHX:TOL=109196],hermetia concinna[&&NHX:TOL=109197],hermetia condor[&&NHX:TOL=109198],hermetia confidens[&&NHX:TOL=109199],hermetia conjuncta[&&NHX:TOL=109200],hermetia cornithorax[&&NHX:TOL=109201],hermetia crabro[&&NHX:TOL=109202],hermetia currani[&&NHX:TOL=109203],hermetia eiseni[&&NHX:TOL=109204],hermetia femoralis[&&NHX:TOL=109205],hermetia fimbriata[&&NHX:TOL=109206],hermetia flavipes[&&NHX:TOL=109207],hermetia flavoscutata[&&NHX:TOL=109208],hermetia formica[&&NHX:TOL=109209],hermetia fulva[&&NHX:TOL=109210],hermetia geniculata[&&NHX:TOL=109211],hermetia goncalvesi[&&NHX:TOL=109212],hermetia hunteri[&&NHX:TOL=109213],hermetia illucens[&&NHX:TOL=109214],hermetia impressa[&&NHX:TOL=109215],hermetia inflata[&&NHX:TOL=109216],hermetia itatiaiensis[&&NHX:TOL=109217],hermetia jamesi[&&NHX:TOL=109218],hermetia laeta[&&NHX:TOL=109219],hermetia laglaizei[&&NHX:TOL=109220],hermetia lativentris[&&NHX:TOL=109221],hermetia malaana[&&NHX:TOL=109222],hermetia melanderi[&&NHX:TOL=109223],hermetia mitis[&&NHX:TOL=109224],hermetia myieriades[&&NHX:TOL=109225],hermetia nana[&&NHX:TOL=109226],hermetia nigra[&&NHX:TOL=109227],hermetia nigricornis[&&NHX:TOL=109228],hermetia pallidipes[&&NHX:TOL=109229],hermetia palmivora[&&NHX:TOL=109230],hermetia panamaensis[&&NHX:TOL=109231],hermetia panhagensis[&&NHX:TOL=111463],hermetia pectoralis[&&NHX:TOL=109232],hermetia pennicornis[&&NHX:TOL=109233],hermetia pterocausta[&&NHX:TOL=109234],hermetia pulchra[&&NHX:TOL=109235],hermetia reinhardi[&&NHX:TOL=109236],hermetia relicta[&&NHX:TOL=109237],hermetia remittens[&&NHX:TOL=109238],hermetia rufitarsis[&&NHX:TOL=109239],hermetia ryckmani[&&NHX:TOL=109240],hermetia samoensis[&&NHX:TOL=109241],hermetia scutellata[&&NHX:TOL=109242],hermetia sexmaculata[&&NHX:TOL=109243],hermetia sphecodes[&&NHX:TOL=109244],hermetia subpellucida[&&NHX:TOL=109245],hermetia teevani[&&NHX:TOL=109246],hermetia tincta[&&NHX:TOL=109247],hermetia virescens[&&NHX:TOL=109248],hermetia virgata[&&NHX:TOL=109249],hermetia woodleyi[&&NHX:TOL=111464])hermetia[&&NHX:TOL=108747],notohermetia pilifrons[&&NHX:TOL=108748],patagiomyia cyphomyioides[&&NHX:TOL=108749])hermetiinae[&&NHX:TOL=23960],(cacosis[&&NHX:TOL=108750],chromatopoda annulipes[&&NHX:TOL=108751],chrysochlora[&&NHX:TOL=108752],chrysochlorina[&&NHX:TOL=108753],labogastria pedunculata[&&NHX:TOL=108754],pelagomyia[&&NHX:TOL=108755],porpocera[&&NHX:TOL=108756],trichocercocera ptecticoides[&&NHX:TOL=108757])chrysochlorininae                    [&&NHX:TOL=108472])[&&NHX:TOL=23961],((acrochaeta[&&NHX:TOL=108758],amsaria sagittocera[&&NHX:TOL=108759],(cephalochrysa africana[&&NHX:TOL=109250],cephalochrysa albisquama[&&NHX:TOL=109251],cephalochrysa australis[&&NHX:TOL=109252],cephalochrysa calopa[&&NHX:TOL=109253],cephalochrysa canadensis[&&NHX:TOL=109254],cephalochrysa chrysidiformis[&&NHX:TOL=109255],cephalochrysa demeijerei[&&NHX:TOL=109256],cephalochrysa ferruginea[&&NHX:TOL=109257],cephalochrysa flavomarginata[&&NHX:TOL=109258],cephalochrysa gracilis[&&NHX:TOL=109259],cephalochrysa hovas[&&NHX:TOL=109260],cephalochrysa infuscata[&&NHX:TOL=109261],cephalochrysa maxima[&&NHX:TOL=109262],cephalochrysa nigra[&&NHX:TOL=109263],cephalochrysa nigricornis[&&NHX:TOL=109264],cephalochrysa rufibasis[&&NHX:TOL=109265],cephalochrysa rugulosa[&&NHX:TOL=109266],cephalochrysa sapphirina[&&NHX:TOL=109267],cephalochrysa similis[&&NHX:TOL=109268],cephalochrysa stenogaster[&&NHX:TOL=109269],cephalochrysa stigmatica[&&NHX:TOL=109270],cephalochrysa texana[&&NHX:TOL=109271])cephalochrysa[&&NHX:TOL=108760],(chloromyia bella[&&NHX:TOL=109272],chloromyia caeligera[&&NHX:TOL=109273],chloromyia cingulata[&&NHX:TOL=109274],chloromyia formosa[&&NHX:TOL=109275],chloromyia speciosa[&&NHX:TOL=109276],chloromyia tuberculata[&&NHX:TOL=109277])chloromyia[&&NHX:TOL=108761],chrysochromioides micropunctata[&&NHX:TOL=108762],dinosargus lateritius[&&NHX:TOL=108763],eumenogastrina angusta[&&NHX:TOL=108764],filiptschenkia sargoides[&&NHX:TOL=108765],formosargus[&&NHX:TOL=108766],gongrosargus[&&NHX:TOL=108767],himantigera[&&NHX:TOL=108768],lobisquama barbata[&&NHX:TOL=108769],(merosargus abana[&&NHX:TOL=109278],merosargus acutus[&&NHX:TOL=109279],merosargus aeneus[&&NHX:TOL=109280],merosargus akrei[&&NHX:TOL=109281],merosargus albidus[&&NHX:TOL=109282],merosargus albifascies[&&NHX:TOL=109283],merosargus albopictus[&&NHX:TOL=109284],merosargus alticola[&&NHX:TOL=109285],merosargus altifrons[&&NHX:TOL=109286],merosargus amethystinus[&&NHX:TOL=109287],merosargus ampulla[&&NHX:TOL=109288],merosargus andinus[&&NHX:TOL=109289],merosargus angulatus[&&NHX:TOL=109290],merosargus angustus[&&NHX:TOL=109291],merosargus antennatus[&&NHX:TOL=109292],merosargus anticus[&&NHX:TOL=109293],merosargus apicalis[&&NHX:TOL=109294],merosargus arcuatus[&&NHX:TOL=109295],merosargus atriannulatus[&&NHX:TOL=109296],merosargus aureonitens[&&NHX:TOL=109297],merosargus aurivena[&&NHX:TOL=109298],merosargus australis[&&NHX:TOL=109299],merosargus azureus[&&NHX:TOL=109300],merosargus banksi[&&NHX:TOL=109301],merosargus barbatus[&&NHX:TOL=109302],merosargus basalis[&&NHX:TOL=109303],merosargus beameri[&&NHX:TOL=109304],merosargus bequaerti[&&NHX:TOL=109305],merosargus bitaeniatus[&&NHX:TOL=109306],merosargus bituberculatus[&&NHX:TOL=109307],merosargus bivittatus[&&NHX:TOL=109308],merosargus brachiatus[&&NHX:TOL=109309],merosargus brunneus[&&NHX:TOL=109310],merosargus brunnipes[&&NHX:TOL=109311],merosargus bulbifrons[&&NHX:TOL=109312],merosargus cnigrum[&&NHX:TOL=109313],merosargus caeruleifrons[&&NHX:TOL=109314],merosargus calceolatus[&&NHX:TOL=109315],merosargus cingulatus[&&NHX:TOL=109316],merosargus citrinus[&&NHX:TOL=109317],merosargus complicatus[&&NHX:TOL=109318],merosargus concinnatus[&&NHX:TOL=109319],merosargus conopsoides[&&NHX:TOL=109320],merosargus contortus[&&NHX:TOL=109321],merosargus convexifrons[&&NHX:TOL=109322],merosargus coriaceus[&&NHX:TOL=109323],merosargus coxalis[&&NHX:TOL=109324],merosargus cyaneoscutellatus[&&NHX:TOL=109325],merosargus cyrtometopius[&&NHX:TOL=109326],merosargus dissimilis[&&NHX:TOL=109327],merosargus divisus[&&NHX:TOL=109328],merosargus dorsalis[&&NHX:TOL=109329],merosargus ecuadorensis[&&NHX:TOL=109330],merosargus elatus[&&NHX:TOL=109331],merosargus elongatus[&&NHX:TOL=109332],merosargus ethelia[&&NHX:TOL=109333],merosargus eunomus[&&NHX:TOL=109334],merosargus festivus[&&NHX:TOL=109335],merosargus flaviceps[&&NHX:TOL=109336],merosargus flavissimus[&&NHX:TOL=109337],merosargus flavitarsis[&&NHX:TOL=109338],merosargus flaviventris[&&NHX:TOL=109339],merosargus fraternus[&&NHX:TOL=109340],merosargus frontatus[&&NHX:TOL=109341],merosargus frosti[&&NHX:TOL=109342],merosargus fumipennis[&&NHX:TOL=109343],merosargus geminatus[&&NHX:TOL=109344],merosargus golbachi[&&NHX:TOL=109345],merosargus gorgona[&&NHX:TOL=109346],merosargus gowdeyi[&&NHX:TOL=109347],merosargus gracilior[&&NHX:TOL=109348],merosargus gracilis[&&NHX:TOL=109349],merosargus granulosus[&&NHX:TOL=109350],merosargus hansoni[&&NHX:TOL=109351],merosargus hoffmanni[&&NHX:TOL=109352],merosargus hyalopterus[&&NHX:TOL=109353],merosargus incanus[&&NHX:TOL=109354],merosargus insularis[&&NHX:TOL=109355],merosargus irwini[&&NHX:TOL=109356],merosargus lacrimosus[&&NHX:TOL=109357],merosargus lampronotus[&&NHX:TOL=109358],merosargus laniger[&&NHX:TOL=109359],merosargus lateromaculatus[&&NHX:TOL=109360],merosargus linearis[&&NHX:TOL=109361],merosargus longipes[&&NHX:TOL=109362],merosargus luridus[&&NHX:TOL=109363],merosargus lutzi[&&NHX:TOL=109364],merosargus lyricus[&&NHX:TOL=109365],merosargus megalopygus[&&NHX:TOL=109366],merosargus melanothorax[&&NHX:TOL=109367],merosargus mirabilis[&&NHX:TOL=109368],merosargus nebulifer[&&NHX:TOL=109369],merosargus nigribasis[&&NHX:TOL=109370],merosargus notatus[&&NHX:TOL=109371],merosargus obscurus[&&NHX:TOL=109372],merosargus obtusipennis[&&NHX:TOL=109373],merosargus opaliger[&&NHX:TOL=109374],merosargus orizabee[&&NHX:TOL=109375],merosargus pallidus[&&NHX:TOL=109376],merosargus pallifrons[&&NHX:TOL=109377],merosargus panamaensis[&&NHX:TOL=109378],merosargus par[&&NHX:TOL=109379],merosargus penai[&&NHX:TOL=109380],merosargus peruvianus[&&NHX:TOL=109381],merosargus pictipes[&&NHX:TOL=109382],merosargus pictithorax[&&NHX:TOL=109383],merosargus productus[&&NHX:TOL=109384],merosargus pseudolyricus[&&NHX:TOL=109385],merosargus pulcher[&&NHX:TOL=109386],merosargus quadratus[&&NHX:TOL=109387],merosargus quadrifasciatus[&&NHX:TOL=109388],merosargus robustus[&&NHX:TOL=109389],merosargus rossi[&&NHX:TOL=109390],merosargus rotundatus[&&NHX:TOL=109391],merosargus schildi[&&NHX:TOL=109392],merosargus scrobiculus[&&NHX:TOL=109393],merosargus sexmaculatus[&&NHX:TOL=109394],merosargus sexnotatus[&&NHX:TOL=109395],merosargus smaragdiferus[&&NHX:TOL=109396],merosargus spatulatus[&&NHX:TOL=109397],merosargus stamineus[&&NHX:TOL=109398],merosargus stigmaticus[&&NHX:TOL=109399],merosargus subinterruptus[&&NHX:TOL=109400],merosargus subobscurus[&&NHX:TOL=109401],merosargus supernitens[&&NHX:TOL=109402],merosargus taeniatus[&&NHX:TOL=109403],merosargus tangens[&&NHX:TOL=109404],merosargus telfordi[&&NHX:TOL=109405],merosargus tenebricosus[&&NHX:TOL=109406],merosargus tenuicornis[&&NHX:TOL=109407],merosargus terminalis[&&NHX:TOL=109408],merosargus transversus[&&NHX:TOL=109409],merosargus triangulatus[&&NHX:TOL=109410],merosargus tripartitus[&&NHX:TOL=109411],merosargus tristis[&&NHX:TOL=109412],merosargus tritaeniatus[&&NHX:TOL=109413],merosargus varicornis[&&NHX:TOL=109414],merosargus varicrus[&&NHX:TOL=109415],merosargus ventralis[&&NHX:TOL=109416],merosargus venustulus[&&NHX:TOL=109417],merosargus vertebratus[&&NHX:TOL=109418],merosargus viridis[&&NHX:TOL=109419],merosargus zeteki[&&NHX:TOL=109420])merosargus[&&NHX:TOL=108770],(microchrysa alessandrinorum[&&NHX:TOL=109421],microchrysa bicolor[&&NHX:TOL=109422],microchrysa bipars[&&NHX:TOL=109423],microchrysa calopa[&&NHX:TOL=109424],microchrysa circumscripta[&&NHX:TOL=109425],microchrysa congoensis[&&NHX:TOL=109426],microchrysa cyaneiventris[&&NHX:TOL=109427],microchrysa daccordii[&&NHX:TOL=109428],microchrysa deconinckae[&&NHX:TOL=109429],microchrysa dichoptica[&&NHX:TOL=109430],microchrysa dispar[&&NHX:TOL=109431],microchrysa edwardsi[&&NHX:TOL=109432],microchrysa elmari[&&NHX:TOL=109433],microchrysa flavicornis[&&NHX:TOL=109434],microchrysa flaviventris[&&NHX:TOL=109435],microchrysa flavomarginata[&&NHX:TOL=109436],microchrysa fuscistigma[&&NHX:TOL=109437],microchrysa ghesquierei[&&NHX:TOL=109438],microchrysa hemiochra[&&NHX:TOL=109439],microchrysa inversa[&&NHX:TOL=109440],microchrysa japonica[&&NHX:TOL=109441],microchrysa laodunensis[&&NHX:TOL=109442],microchrysa latifrons[&&NHX:TOL=109443],microchrysa loewi[&&NHX:TOL=109444],microchrysa macula[&&NHX:TOL=109445],microchrysa matengoensis[&&NHX:TOL=109446],microchrysa mokanshanensis[&&NHX:TOL=109447],microchrysa nigrimacula[&&NHX:TOL=109448],microchrysa nova[&&NHX:TOL=109449],microchrysa obscuriventris[&&NHX:TOL=109450],microchrysa polita[&&NHX:TOL=109451],microchrysa rozkosnyi[&&NHX:TOL=109452],microchrysa ruffoi[&&NHX:TOL=109453],microchrysa ruwenzoriensis[&&NHX:TOL=109454],microchrysa scutellaris[&&NHX:TOL=109455],microchrysa shanghaiensis[&&NHX:TOL=109456],microchrysa stuckenbergi[&&NHX:TOL=109457],microchrysa ussuriana[&&NHX:TOL=109458],microchrysa vertebrata[&&NHX:TOL=109459],microchrysa viridis[&&NHX:TOL=109460],microchrysa woodleyi[&&NHX:TOL=109461])microchrysa[&&NHX:TOL=108771],microptecticus[&&NHX:TOL=108772],microsargus stuckenbergi[&&NHX:TOL=108773],otochrysa bicolor[&&NHX:TOL=108774],paraptecticus[&&NHX:TOL=108775],(ptecticus abditis[&&NHX:TOL=109462],ptecticus aculeatus[&&NHX:TOL=109463],ptecticus adustus[&&NHX:TOL=109464],ptecticus aeneithorax[&&NHX:TOL=109465],ptecticus alticola[&&NHX:TOL=109466],ptecticus amapanus[&&NHX:TOL=109467],ptecticus amplior[&&NHX:TOL=109468],ptecticus annulipes[&&NHX:TOL=111445],ptecticus anomalopygus[&&NHX:TOL=109469],ptecticus archboldi[&&NHX:TOL=109470],ptecticus assamensis[&&NHX:TOL=109471],ptecticus aurifer[&&NHX:TOL=109472],ptecticus aurobrunneus[&&NHX:TOL=109473],ptecticus australis[&&NHX:TOL=109474],ptecticus bequaerti[&&NHX:TOL=109475],ptecticus bifidus[&&NHX:TOL=109476],ptecticus bilobatus[&&NHX:TOL=109477],ptecticus brevipennis[&&NHX:TOL=109478],ptecticus breviunguis[&&NHX:TOL=109479],ptecticus briani[&&NHX:TOL=109480],ptecticus brunescens[&&NHX:TOL=109481],ptecticus brunettii[&&NHX:TOL=109482],ptecticus ciliatus[&&NHX:TOL=109484],ptecticus cingulatus[&&NHX:TOL=109485],ptecticus complens[&&NHX:TOL=109486],ptecticus comstocki[&&NHX:TOL=109487],ptecticus concinnus[&&NHX:TOL=109488],ptecticus confusus[&&NHX:TOL=109489],ptecticus connectens[&&NHX:TOL=109490],ptecticus conopsoides[&&NHX:TOL=109491],ptecticus costaricensis[&&NHX:TOL=109492],ptecticus cyanifrons[&&NHX:TOL=109493],ptecticus danielsi[&&NHX:TOL=111446],ptecticus erectus[&&NHX:TOL=109494],ptecticus evansi[&&NHX:TOL=109495],ptecticus eximius[&&NHX:TOL=109496],ptecticus extensipes[&&NHX:TOL=109497],ptecticus ferrugineus[&&NHX:TOL=109498],ptecticus ficulnus[&&NHX:TOL=109499],ptecticus figlinus[&&NHX:TOL=109500],ptecticus flaviceps[&&NHX:TOL=109501],ptecticus flavifemoratus[&&NHX:TOL=109502],ptecticus fumipennis[&&NHX:TOL=111447],ptecticus furcatus[&&NHX:TOL=109503],ptecticus fuscipennis[&&NHX:TOL=109504],ptecticus gigliostosi[&&NHX:TOL=109505],ptecticus gilvus[&&NHX:TOL=109506],ptecticus glaucus[&&NHX:TOL=109507],ptecticus gracilipes[&&NHX:TOL=109508],ptecticus hansoni[&&NHX:TOL=109509],ptecticus helvolus[&&NHX:TOL=109510],ptecticus histrio[&&NHX:TOL=109511],ptecticus illustris[&&NHX:TOL=109512],ptecticus immaculatus[&&NHX:TOL=109513],ptecticus inops[&&NHX:TOL=109514],ptecticus insularis[&&NHX:TOL=109515],ptecticus intensivus[&&NHX:TOL=109516],ptecticus inversus[&&NHX:TOL=109517],ptecticus isabelensis[&&NHX:TOL=109518],ptecticus jamesi[&&NHX:TOL=109519],ptecticus japonicus[&&NHX:TOL=109520],ptecticus kambangensis[&&NHX:TOL=109521],ptecticus kerteszi[&&NHX:TOL=109522],ptecticus kraussi[&&NHX:TOL=109523],ptecticus lanei[&&NHX:TOL=109524],ptecticus linearis[&&NHX:TOL=109525],ptecticus longipennis[&&NHX:TOL=109526],ptecticus longipes[&&NHX:TOL=109527],ptecticus longispinus[&&NHX:TOL=111448],ptecticus maculatus[&&NHX:TOL=109528],ptecticus magnicornis[&&NHX:TOL=109529],ptecticus malayensis[&&NHX:TOL=109530],ptecticus matsumurae[&&NHX:TOL=109531],ptecticus melanothorax[&&NHX:TOL=109532],ptecticus melanurus[&&NHX:TOL=109533],ptecticus mesoxanthus[&&NHX:TOL=109534],ptecticus mexicanus[&&NHX:TOL=109535],ptecticus minimus[&&NHX:TOL=109536],ptecticus mirabilis[&&NHX:TOL=111449],ptecticus nebulifer[&&NHX:TOL=109537],ptecticus neoaffinis[&&NHX:TOL=109538],ptecticus niger[&&NHX:TOL=109539],ptecticus nigrifrons[&&NHX:TOL=109540],ptecticus nigritarsis[&&NHX:TOL=109541],ptecticus nigropygialis[&&NHX:TOL=109542],ptecticus nitidipennis[&&NHX:TOL=109543],ptecticus nodivena[&&NHX:TOL=109544],ptecticus ochraceus[&&NHX:TOL=109545],ptecticus okinawae[&&NHX:TOL=109546],ptecticus okinawaensus[&&NHX:TOL=109547],ptecticus palpalis[&&NHX:TOL=109548],ptecticus pangmapensis[&&NHX:TOL=111450],ptecticus papaunus[&&NHX:TOL=109549],ptecticus perochreus[&&NHX:TOL=109550],ptecticus petersoni[&&NHX:TOL=109551],ptecticus petiolatus[&&NHX:TOL=109552],ptecticus phillippinensis[&&NHX:TOL=111451],ptecticus polyxanthus[&&NHX:TOL=109553],ptecticus pomaceus[&&NHX:TOL=109554],ptecticus posticus[&&NHX:TOL=109555],ptecticus proximus[&&NHX:TOL=109556],ptecticus pseudohistrio[&&NHX:TOL=111442],ptecticus quadrifasciatus[&&NHX:TOL=109557],ptecticus queenslandicus[&&NHX:TOL=109558],ptecticus rectinervis[&&NHX:TOL=109559],ptecticus remeans[&&NHX:TOL=109560],ptecticus repensans[&&NHX:TOL=109561],ptecticus rhodesiae[&&NHX:TOL=109562],ptecticus rogans[&&NHX:TOL=109563],ptecticus rufipes[&&NHX:TOL=109564],ptecticus rufus[&&NHX:TOL=109565],ptecticus sackenii[&&NHX:TOL=109566],ptecticus sauteri[&&NHX:TOL=109567],ptecticus septentrionalis[&&NHX:TOL=109568],ptecticus serranus[&&NHX:TOL=109569],ptecticus shirakii[&&NHX:TOL=109570],ptecticus siamensis[&&NHX:TOL=109571],ptecticus simplex[&&NHX:TOL=109572],ptecticus sinchangensis[&&NHX:TOL=109573],ptecticus somereni[&&NHX:TOL=109574],ptecticus spatulatus[&&NHX:TOL=109575],ptecticus spatuloides[&&NHX:TOL=109576],ptecticus srilankai[&&NHX:TOL=111443],ptecticus subaustralis[&&NHX:TOL=109577],ptecticus substitutus[&&NHX:TOL=109578],ptecticus sumatranus[&&NHX:TOL=109579],ptecticus tarsalis[&&NHX:TOL=109580],ptecticus temasekianus[&&NHX:TOL=111452],ptecticus tenebrifer[&&NHX:TOL=109581],ptecticus tenuis[&&NHX:TOL=109582],ptecticus terminalis[&&NHX:TOL=109583],ptecticus testaceus[&&NHX:TOL=109584],ptecticus tricolor[&&NHX:TOL=109585],ptecticus tritus[&&NHX:TOL=109586],ptecticus trivittatus[&&NHX:TOL=109587],ptecticus violaceus[&&NHX:TOL=109588],ptecticus vitalisi[&&NHX:TOL=109589],ptecticus vulpianus[&&NHX:TOL=109590],ptecticus woodleyi[&&NHX:TOL=109591],ptecticus wulpii[&&NHX:TOL=109592],ptecticus xanthipes[&&NHX:TOL=109593],ptecticus zhejiangensis[&&NHX:TOL=109594])ptecticus[&&NHX:TOL=108776],ptectisargus[&&NHX:TOL=108777],sagaricera[&&NHX:TOL=108778],(sargus albibarbus[&&NHX:TOL=109595],sargus albopilosus[&&NHX:TOL=109596],sargus alchidas[&&NHX:TOL=109597],sargus analis[&&NHX:TOL=109598],sargus atrobasis[&&NHX:TOL=109599],sargus aureopilosus[&&NHX:TOL=109600],sargus aurora[&&NHX:TOL=109601],sargus baculventerus[&&NHX:TOL=109602],sargus bagosas[&&NHX:TOL=109603],sargus beppui[&&NHX:TOL=109604],sargus bipunctatus[&&NHX:TOL=109605],sargus brasiliensis[&&NHX:TOL=109606],sargus caerulapex[&&NHX:TOL=109607],sargus chrysis[&&NHX:TOL=109608],sargus circumcinctus[&&NHX:TOL=109609],sargus cirrhosus[&&NHX:TOL=109610],sargus citrinellus[&&NHX:TOL=109611],sargus clavatus[&&NHX:TOL=109612],sargus claviventris[&&NHX:TOL=109613],sargus concisus[&&NHX:TOL=109614],sargus contractus[&&NHX:TOL=109615],sargus cuprarius[&&NHX:TOL=109616],sargus cyaneus[&&NHX:TOL=109617],sargus darius[&&NHX:TOL=109618],sargus decorus[&&NHX:TOL=109619],sargus elegans[&&NHX:TOL=109620],sargus elongatulus[&&NHX:TOL=109621],sargus evansi[&&NHX:TOL=109622],sargus fasciatus[&&NHX:TOL=109623],sargus festivus[&&NHX:TOL=109624],sargus flavilatus[&&NHX:TOL=109625],sargus flavipes[&&NHX:TOL=109626],sargus flavopilosus[&&NHX:TOL=109627],sargus gemmifer[&&NHX:TOL=109628],sargus goliath[&&NHX:TOL=109629],sargus grandis[&&NHX:TOL=109630],sargus gselli[&&NHX:TOL=109631],sargus holosericeus[&&NHX:TOL=109632],sargus illuminata[&&NHX:TOL=109633],sargus inactus[&&NHX:TOL=109634],sargus inficitus[&&NHX:TOL=109635],sargus iridatus[&&NHX:TOL=109636],sargus isthmi[&&NHX:TOL=109637],sargus jaennickei[&&NHX:TOL=109638],sargus jamesi[&&NHX:TOL=109639],sargus jucundus[&&NHX:TOL=109640],sargus laetus[&&NHX:TOL=109641],sargus lateralis[&&NHX:TOL=109642],sargus lateritius[&&NHX:TOL=109643],sargus lateropictus[&&NHX:TOL=109644],sargus latipennis[&&NHX:TOL=109645],sargus latus[&&NHX:TOL=109646],sargus limbatus[&&NHX:TOL=109647],sargus lindneri[&&NHX:TOL=109648],sargus linearis[&&NHX:TOL=109649],sargus lucidus[&&NHX:TOL=109650],sargus macquaertii[&&NHX:TOL=109651],sargus mactans[&&NHX:TOL=109652],sargus maculatus[&&NHX:TOL=109653],sargus mandarinus[&&NHX:TOL=109654],sargus melleus[&&NHX:TOL=109655],sargus meracus[&&NHX:TOL=109656],sargus meridionalis[&&NHX:TOL=109657],sargus metallinus[&&NHX:TOL=109658],sargus molliculus[&&NHX:TOL=109659],sargus multicolor[&&NHX:TOL=109660],sargus nigripes[&&NHX:TOL=109661],sargus niphonensis[&&NHX:TOL=109662],sargus opulentus[&&NHX:TOL=109663],sargus parastenus[&&NHX:TOL=109664],sargus pavo[&&NHX:TOL=109665],sargus persimilis[&&NHX:TOL=109666],sargus petersoni[&&NHX:TOL=109667],sargus pleurotocus[&&NHX:TOL=109668],sargus polychromus[&&NHX:TOL=109669],sargus pseudoptecticus[&&NHX:TOL=109670],sargus ptecticoides[&&NHX:TOL=109671],sargus pubescens[&&NHX:TOL=109672],sargus punctatus[&&NHX:TOL=109673],sargus purpuratus[&&NHX:TOL=109674],sargus purpurea[&&NHX:TOL=109675],sargus rufibasis[&&NHX:TOL=109676],sargus ruficornis[&&NHX:TOL=109677],sargus rufifrons[&&NHX:TOL=109678],sargus rufipes[&&NHX:TOL=109679],sargus rufitarsis[&&NHX:TOL=109680],sargus schaeuffelei[&&NHX:TOL=109681],sargus seychellensis[&&NHX:TOL=109682],sargus speciosus[&&NHX:TOL=109683],sargus splendidus[&&NHX:TOL=109684],sargus stenus[&&NHX:TOL=109685],sargus stuckenbergi[&&NHX:TOL=109686],sargus tenuis[&&NHX:TOL=109687],sargus tenuiventris[&&NHX:TOL=109688],sargus thoracicus[&&NHX:TOL=109689],sargus transversus[&&NHX:TOL=109690],sargus tuberculatus[&&NHX:TOL=109691],sargus vandykei[&&NHX:TOL=109692],sargus viridiceps[&&NHX:TOL=109693],sargus viridis[&&NHX:TOL=109694],sargus viridistima[&&NHX:TOL=109695],sargus yerbabuena[&&NHX:TOL=109696])sargus[&&NHX:TOL=108779],stackelbergia chloromyioides[&&NHX:TOL=108780])sarginae[&&NHX:TOL=23962],(brachycara[&&NHX:TOL=108781],lasiopa[&&NHX:TOL=108782],((nemotelus abdominalis[&&NHX:TOL=110304],nemotelus acutirostris[&&NHX:TOL=110305],nemotelus aerosus[&&NHX:TOL=110306],nemotelus albifacies[&&NHX:TOL=110307],nemotelus albirostris[&&NHX:TOL=110308],nemotelus albitarsis[&&NHX:TOL=110309],nemotelus albiventris[&&NHX:TOL=110310],nemotelus alida[&&NHX:TOL=110311],nemotelus anchora[&&NHX:TOL=110312],nemotelus angustemarginatus[&&NHX:TOL=110313],nemotelus annulipes[&&NHX:TOL=110314],nemotelus arabistanicus[&&NHX:TOL=110315],nemotelus argentifer[&&NHX:TOL=110316],nemotelus armeniacus[&&NHX:TOL=110317],nemotelus aschuricus[&&NHX:TOL=110318],nemotelus atbassaricus[&&NHX:TOL=110319],nemotelus atriceps[&&NHX:TOL=110320],nemotelus aureus[&&NHX:TOL=110321],nemotelus barracloughi[&&NHX:TOL=110322],nemotelus basilaris[&&NHX:TOL=110323],nemotelus beckeri[&&NHX:TOL=110324],nemotelus bellulus[&&NHX:TOL=110325],nemotelus biodii[&&NHX:TOL=110326],nemotelus bipunctatus[&&NHX:TOL=110327],nemotelus bomynensis[&&NHX:TOL=110328],nemotelus bonnarius[&&NHX:TOL=110329],nemotelus brachystomus[&&NHX:TOL=110330],nemotelus brevirostris[&&NHX:TOL=110331],nemotelus bruesii[&&NHX:TOL=110332],nemotelus candidus[&&NHX:TOL=110333],nemotelus capensis[&&NHX:TOL=110334],nemotelus carthaginis[&&NHX:TOL=110335],nemotelus chaineyi[&&NHX:TOL=110336],nemotelus cheminii[&&NHX:TOL=110337],nemotelus cingulatus[&&NHX:TOL=110338],nemotelus clunipes[&&NHX:TOL=110339],nemotelus cochraneae[&&NHX:TOL=110340],nemotelus consentiens[&&NHX:TOL=110341],nemotelus crenatus[&&NHX:TOL=110342],nemotelus curdistanus[&&NHX:TOL=110343],nemotelus cylindricornis[&&NHX:TOL=110344],nemotelus cypriacus[&&NHX:TOL=110345],nemotelus dampfi[&&NHX:TOL=110346],nemotelus danielssoni[&&NHX:TOL=110347],nemotelus dentatus[&&NHX:TOL=110348],nemotelus dimidiatus[&&NHX:TOL=110349],nemotelus duofasciatus[&&NHX:TOL=110350],nemotelus exsul[&&NHX:TOL=110351],nemotelus exul[&&NHX:TOL=110352],nemotelus fasciatus[&&NHX:TOL=110353],nemotelus fasciventris[&&NHX:TOL=110354],nemotelus fozzeri[&&NHX:TOL=110355],nemotelus frontalis[&&NHX:TOL=110356],nemotelus frontosus[&&NHX:TOL=110357],nemotelus gobiensis[&&NHX:TOL=110358],nemotelus grootaerti[&&NHX:TOL=110359],nemotelus haemorrhous[&&NHX:TOL=110360],nemotelus hansoni[&&NHX:TOL=110361],nemotelus heptapotamicus[&&NHX:TOL=110362],nemotelus hirtulus[&&NHX:TOL=110363],nemotelus hyalinibasis[&&NHX:TOL=110364],nemotelus ilensis[&&NHX:TOL=110365],nemotelus imitator[&&NHX:TOL=110366],nemotelus immaculatus[&&NHX:TOL=110367],nemotelus inconspicuus[&&NHX:TOL=110368],nemotelus insularis[&&NHX:TOL=110369],nemotelus irwinorum[&&NHX:TOL=110370],nemotelus jakowlewi[&&NHX:TOL=110371],nemotelus kansensis[&&NHX:TOL=110372],nemotelus kaszabi[&&NHX:TOL=110373],nemotelus knowltoni[&&NHX:TOL=110374],nemotelus kugleri[&&NHX:TOL=110375],nemotelus lanatus[&&NHX:TOL=110376],nemotelus lasiops[&&NHX:TOL=110377],nemotelus latemarginatus[&&NHX:TOL=110378],nemotelus latiusculus[&&NHX:TOL=110379],nemotelus lativentris[&&NHX:TOL=110380],nemotelus leucorhynchus[&&NHX:TOL=110381],nemotelus londtorum[&&NHX:TOL=110382],nemotelus longirostris[&&NHX:TOL=110383],nemotelus maculiventris[&&NHX:TOL=110384],nemotelus madagascarensis[&&NHX:TOL=110385],nemotelus mandshuricus[&&NHX:TOL=110386],nemotelus marinus[&&NHX:TOL=110387],nemotelus matilei[&&NHX:TOL=110388],nemotelus megarhynchus[&&NHX:TOL=110389],nemotelus mersinae[&&NHX:TOL=110390],nemotelus mongolia[&&NHX:TOL=110391],nemotelus montanus[&&NHX:TOL=110392],nemotelus nanshanicus[&&NHX:TOL=110393],nemotelus nigribasis[&&NHX:TOL=110394],nemotelus nigrifrons[&&NHX:TOL=110395],nemotelus nigrimanus[&&NHX:TOL=110396],nemotelus niloticus[&&NHX:TOL=110397],nemotelus notatus[&&NHX:TOL=110398],nemotelus obscuripes[&&NHX:TOL=110399],nemotelus obtusirostris[&&NHX:TOL=110400],nemotelus pallipes[&&NHX:TOL=110401],nemotelus paludosus[&&NHX:TOL=110402],nemotelus pantherinus[&&NHX:TOL=110403],nemotelus pappi[&&NHX:TOL=110404],nemotelus personatus[&&NHX:TOL=110405],nemotelus planifrons[&&NHX:TOL=110406],nemotelus poecilorhynchus[&&NHX:TOL=110407],nemotelus proboscideus[&&NHX:TOL=110408],nemotelus przewalskii[&&NHX:TOL=110409],nemotelus pullus[&&NHX:TOL=110410],nemotelus punctatus[&&NHX:TOL=110411],nemotelus punctifacies[&&NHX:TOL=110412],nemotelus quadrinotatus[&&NHX:TOL=110413],nemotelus robertsonae[&&NHX:TOL=110414],nemotelus rudifranci[&&NHX:TOL=110415],nemotelus ruficornis[&&NHX:TOL=110416],nemotelus rufiventris[&&NHX:TOL=110417],nemotelus rufoabdominalis[&&NHX:TOL=110418],nemotelus rufus[&&NHX:TOL=110419],nemotelus rugosus[&&NHX:TOL=110420],nemotelus rumelicus[&&NHX:TOL=110421],nemotelus signatus[&&NHX:TOL=110422],nemotelus stellaris[&&NHX:TOL=110423],nemotelus stuckenbergi[&&NHX:TOL=110424],nemotelus subuliginosus[&&NHX:TOL=110425],nemotelus svenhedini[&&NHX:TOL=110426],nemotelus syriacus[&&NHX:TOL=110427],nemotelus transsylvanicus[&&NHX:TOL=110428],nemotelus tschorsnigi[&&NHX:TOL=110429],nemotelus turkestanicus[&&NHX:TOL=110430],nemotelus uliginosus[&&NHX:TOL=110431],nemotelus ventralis[&&NHX:TOL=110432],nemotelus victoriskusnezowi[&&NHX:TOL=110433],nemotelus zichyi[&&NHX:TOL=110434])nemotelus nemotelus[&&NHX:TOL=108857],(nemotelus albimarginatus[&&NHX:TOL=110435],nemotelus aldrichi[&&NHX:TOL=110436],nemotelus arator[&&NHX:TOL=110437],nemotelus aridus[&&NHX:TOL=110438],nemotelus aviceps[&&NHX:TOL=110439],nemotelus beameri[&&NHX:TOL=110440],nemotelus canadensis[&&NHX:TOL=110441],nemotelus catharistis[&&NHX:TOL=110442],nemotelus centralis[&&NHX:TOL=110443],nemotelus chilensis[&&NHX:TOL=110444],nemotelus chlorhimas[&&NHX:TOL=110445],nemotelus communis[&&NHX:TOL=110446],nemotelus congruens[&&NHX:TOL=110447],nemotelus contiguus[&&NHX:TOL=110448],nemotelus convexiceps[&&NHX:TOL=110449],nemotelus crinitus[&&NHX:TOL=110450],nemotelus diehli[&&NHX:TOL=110451],nemotelus eburneopictus[&&NHX:TOL=110452],nemotelus flavicornis[&&NHX:TOL=110453],nemotelus flavocingulatus[&&NHX:TOL=110454],nemotelus fuegensis[&&NHX:TOL=110455],nemotelus glaber[&&NHX:TOL=110456],nemotelus halophilus[&&NHX:TOL=110457],nemotelus hirsutissimus[&&NHX:TOL=110458],nemotelus incurvatus[&&NHX:TOL=110459],nemotelus jamesi[&&NHX:TOL=110460],nemotelus maculatus[&&NHX:TOL=110461],nemotelus magellanicus[&&NHX:TOL=110462],nemotelus melanderi[&&NHX:TOL=110463],nemotelus monensis[&&NHX:TOL=110464],nemotelus neotropicus[&&NHX:TOL=110465],nemotelus neuquenensis[&&NHX:TOL=110466],nemotelus nevadensis[&&NHX:TOL=110467],nemotelus niger[&&NHX:TOL=110468],nemotelus nigricornis[&&NHX:TOL=110469],nemotelus nigrinus[&&NHX:TOL=110470],nemotelus nudus[&&NHX:TOL=110471],nemotelus penai[&&NHX:TOL=110472],nemotelus peruvianus[&&NHX:TOL=110473],nemotelus picinus[&&NHX:TOL=110474],nemotelus poecilohimas[&&NHX:TOL=110475],nemotelus politus[&&NHX:TOL=110476],nemotelus polyposus[&&NHX:TOL=110477],nemotelus psilonotus[&&NHX:TOL=110478],nemotelus pulchricornis[&&NHX:TOL=110479],nemotelus pumilis[&&NHX:TOL=110480],nemotelus roedingeri[&&NHX:TOL=110481],nemotelus sabroskyi[&&NHX:TOL=110482],nemotelus shannoni[&&NHX:TOL=110483],nemotelus slossonae[&&NHX:TOL=110484],nemotelus sordidus[&&NHX:TOL=110485],nemotelus tenuistylus[&&NHX:TOL=110486],nemotelus tenuivena[&&NHX:TOL=110487],nemotelus thomae[&&NHX:TOL=110488],nemotelus titschacki[&&NHX:TOL=110489],nemotelus tristis[&&NHX:TOL=110490],nemotelus variabilis[&&NHX:TOL=110491],nemotelus vertebratus[&&NHX:TOL=110492],nemotelus wilfordhansoni[&&NHX:TOL=110493])nemotelus camptopelta[&&NHX:TOL=108858])nemotelus[&&NHX:TOL=108783],pselaphomyia[&&NHX:TOL=108784])nemotelinae[&&NHX:TOL=108473])[&&NHX:TOL=23965])[&&NHX:TOL=108471],((((caloparyphus amplus[&&NHX:TOL=109705],caloparyphus atriventris[&&NHX:TOL=109706],caloparyphus crotchi[&&NHX:TOL=109707],caloparyphus crucigerus[&&NHX:TOL=109708],caloparyphus currani[&&NHX:TOL=109709],caloparyphus decemmaculatus[&&NHX:TOL=109710],caloparyphus flaviventris[&&NHX:TOL=109711],caloparyphus greylockensis[&&NHX:TOL=109712],caloparyphus major[&&NHX:TOL=109713],caloparyphus mariposa[&&NHX:TOL=109714],caloparyphus pretiosus[&&NHX:TOL=109715],caloparyphus tetraspilus[&&NHX:TOL=109716])caloparyphus[&&NHX:TOL=108786],dicorymbimyia annulata[&&NHX:TOL=108787],((euparyphus albipilosus[&&NHX:TOL=109717],euparyphus apicalis[&&NHX:TOL=109718],euparyphus arizonae[&&NHX:TOL=109719],euparyphus carbonarius[&&NHX:TOL=109720],euparyphus elegans[&&NHX:TOL=109721],euparyphus elongatulus[&&NHX:TOL=109722],euparyphus lagunae[&&NHX:TOL=109723],euparyphus limbrocutris[&&NHX:TOL=109724],euparyphus monensis[&&NHX:TOL=109725],euparyphus mutabilis[&&NHX:TOL=109726],euparyphus stigmaticalis[&&NHX:TOL=109727],euparyphus tricolor[&&NHX:TOL=109728])euparyphus euparyphus[&&NHX:TOL=108853],(euparyphus ater[&&NHX:TOL=109729],euparyphus bistriatus[&&NHX:TOL=109730],euparyphus brasiliensis[&&NHX:TOL=109731],euparyphus brevicornis[&&NHX:TOL=109732],euparyphus cinctus[&&NHX:TOL=109733],euparyphus facialis[&&NHX:TOL=109734],euparyphus hamifer[&&NHX:TOL=109735],euparyphus peruvianus[&&NHX:TOL=109736],euparyphus sabroskyi[&&NHX:TOL=109737])euparyphus aochletus[&&NHX:TOL=108854],(euparyphus cataractus[&&NHX:TOL=109738],euparyphus ornatus[&&NHX:TOL=109739],euparyphus patagius[&&NHX:TOL=109740],euparyphus proxipalus[&&NHX:TOL=109741],euparyphus pygmaea[&&NHX:TOL=109742],euparyphus rothi[&&NHX:TOL=109743],euparyphus umbrulus[&&NHX:TOL=109744])euparyphus nigriparyphus[&&NHX:TOL=108855],(euparyphus nebulosus[&&NHX:TOL=109745],euparyphus pardalinus[&&NHX:TOL=109746])euparyphus parochletus[&&NHX:TOL=108856])euparyphus[&&NHX:TOL=108788],glariopsis brasiliana[&&NHX:TOL=108789],glaris mexicana[&&NHX:TOL=108790],hermionella seguyi[&&NHX:TOL=108791],(oxycera abyssinica[&&NHX:TOL=109747],oxycera adusta[&&NHX:TOL=109748],oxycera albomicans[&&NHX:TOL=109749],oxycera albovittata[&&NHX:TOL=109750],oxycera aldrichi[&&NHX:TOL=109751],oxycera analis[&&NHX:TOL=109752],oxycera apicalis[&&NHX:TOL=109753],oxycera approximata[&&NHX:TOL=109754],oxycera atra[&&NHX:TOL=109755],oxycera binotata[&&NHX:TOL=109756],oxycera centralis[&&NHX:TOL=109757],oxycera chikuni[&&NHX:TOL=109758],oxycera confinus[&&NHX:TOL=109759],oxycera dispar[&&NHX:TOL=109760],oxycera dives[&&NHX:TOL=109761],oxycera excellens[&&NHX:TOL=109762],oxycera fallenii[&&NHX:TOL=109763],oxycera fasciventris[&&NHX:TOL=109764],oxycera fenestrata[&&NHX:TOL=109765],oxycera flava[&&NHX:TOL=109766],oxycera flavopilosa[&&NHX:TOL=109767],oxycera fumipennis[&&NHX:TOL=109768],oxycera galeata[&&NHX:TOL=109769],oxycera germanica[&&NHX:TOL=109770],oxycera grancanariensis[&&NHX:TOL=109771],oxycera grata[&&NHX:TOL=109772],oxycera guangxiensis[&&NHX:TOL=109773],oxycera hirticeps[&&NHX:TOL=109774],oxycera hybrida[&&NHX:TOL=109775],oxycera insolata[&&NHX:TOL=109776],oxycera japonica[&&NHX:TOL=109777],oxycera kusigematii[&&NHX:TOL=109778],oxycera laniger[&&NHX:TOL=109779],oxycera latifrons[&&NHX:TOL=109780],oxycera leonina[&&NHX:TOL=109781],oxycera lii[&&NHX:TOL=109782],oxycera limbata[&&NHX:TOL=109783],oxycera locuples[&&NHX:TOL=109784],oxycera lyrifera[&&NHX:TOL=109785],oxycera madagassica[&&NHX:TOL=109786],oxycera manens[&&NHX:TOL=109787],oxycera marginata[&&NHX:TOL=109788],oxycera meigenii[&&NHX:TOL=109789],oxycera morrisii[&&NHX:TOL=109790],oxycera muscaria[&&NHX:TOL=109791],oxycera nana[&&NHX:TOL=109792],oxycera migricornis[&&NHX:TOL=109793],oxycera nigrisincipitalis[&&NHX:TOL=109794],oxycera nigriventris[&&NHX:TOL=109795],oxycera notata[&&NHX:TOL=109796],oxycera nubifera[&&NHX:TOL=109797],oxycera ochracea[&&NHX:TOL=109798],oxycera orientalis[&&NHX:TOL=109799],oxycera pardalina[&&NHX:TOL=109800],oxycera picta[&&NHX:TOL=109801],oxycera pseudoamoena[&&NHX:TOL=109802],oxycera pygmaea[&&NHX:TOL=109803],oxycera qinghensis[&&NHX:TOL=109804],oxycera quadripartita[&&NHX:TOL=109805],oxycera rara[&&NHX:TOL=109806],oxycera rufifrons[&&NHX:TOL=109807],oxycera semilimbata[&&NHX:TOL=109808],oxycera sibirica[&&NHX:TOL=109809],oxycera signata[&&NHX:TOL=109810],oxycera sinica[&&NHX:TOL=109811],oxycera stigmosa[&&NHX:TOL=109812],oxycera stuckenbergi[&&NHX:TOL=109813],oxycera submaculata[&&NHX:TOL=109814],oxycera sumbana[&&NHX:TOL=109815],oxycera tangi[&&NHX:TOL=109816],oxycera tenebricosa[&&NHX:TOL=109817],oxycera tenuis[&&NHX:TOL=109818],oxycera terminata[&&NHX:TOL=109819],oxycera tibialis[&&NHX:TOL=109820],oxycera torrentium[&&NHX:TOL=109821],oxycera turcica[&&NHX:TOL=111461],oxycera tricolor[&&NHX:TOL=109822],oxycera trilineata[&&NHX:TOL=109823],oxycera trispila[&&NHX:TOL=109824],oxycera variegata[&&NHX:TOL=109825],oxycera varipes[&&NHX:TOL=109826],oxycera vertipila[&&NHX:TOL=109827],oxycera whitei[&&NHX:TOL=109828],oxycera zambesina[&&NHX:TOL=109829])oxycera[&&NHX:TOL=108792],pachyptilum hennigi[&&NHX:TOL=108793],peritta melichlora[&&NHX:TOL=108794],stuckenbergiola jugorum[&&NHX:TOL=108795],vanoyia tenuicornis[&&NHX:TOL=108796])oxycerini[&&NHX:TOL=108785],(acanthasargus[&&NHX:TOL=108798],cyphoprosopa lindneri[&&NHX:TOL=108799],exochostoma[&&NHX:TOL=108800],hoplistopsis geminatus[&&NHX:TOL=108801],melanochroa dubia[&&NHX:TOL=108802],(myxosargus anomalus[&&NHX:TOL=109830],myxosargus braueri[&&NHX:TOL=109831],myxosargus fasciatus[&&NHX:TOL=109832],myxosargus knowltoni[&&NHX:TOL=109833],myxosargus melanaspis[&&NHX:TOL=109834],myxosargus mystaceus[&&NHX:TOL=109835],myxosargus nigricormis[&&NHX:TOL=109836],myxosargus pacificus[&&NHX:TOL=109837],myxosargus panamaensis[&&NHX:TOL=109838],myxosargus rugosifrons[&&NHX:TOL=109839],myxosargus scutellatus[&&NHX:TOL=109840],myxosargus texensis[&&NHX:TOL=109841])myxosargus[&&NHX:TOL=108803],(nothomyia alticola[&&NHX:TOL=109842],nothomyia bicolor[&&NHX:TOL=109843],nothomyia borgmeieri[&&NHX:TOL=109844],nothomyia brevis[&&NHX:TOL=109845],nothomyia calopus[&&NHX:TOL=109846],nothomyia fallax[&&NHX:TOL=109847],nothomyia fasciatipennis[&&NHX:TOL=109848],nothomyia flavipes[&&NHX:TOL=109849],nothomyia intensica[&&NHX:TOL=109850],nothomyia longisetosa[&&NHX:TOL=109851],nothomyia lopesi[&&NHX:TOL=109852],nothomyia metallica[&&NHX:TOL=109853],nothomyia nigra[&&NHX:TOL=109854],nothomyia parvicornis[&&NHX:TOL=109855],nothomyia scutellata[&&NHX:TOL=109856],nothomyia viridis[&&NHX:TOL=109857],nothomyia woodruffi[&&NHX:TOL=109858])nothomyia[&&NHX:TOL=108804],prosopochrysa[&&NHX:TOL=108805],rhaphiocerina hakiensis[&&NHX:TOL=108806])prosopochrysini[&&NHX:TOL=108797],(afrodontomyia[&&NHX:TOL=108808],alliocera graeca[&&NHX:TOL=108809],anopisthocrania zonata[&&NHX:TOL=108810],(anoplodonta fratella[&&NHX:TOL=109859],anoplodonta nigrirostris[&&NHX:TOL=109860])anoplodonta[&&NHX:TOL=108811],catatasis[&&NHX:TOL=108812],chloromelas[&&NHX:TOL=108813],crocutasis abyssinica[&&NHX:TOL=108814],cyrtopus[&&NHX:TOL=108815],dischizocera[&&NHX:TOL=108816],gongroneurina apidina[&&NHX:TOL=108817],(hedriodiscus binotatus[&&NHX:TOL=109861],hedriodiscus chloraspis[&&NHX:TOL=109862],hedriodiscus clypeatus[&&NHX:TOL=109863],hedriodiscus dorsalis[&&NHX:TOL=109864],hedriodiscus euchlorus[&&NHX:TOL=109865],hedriodiscus humilis[&&NHX:TOL=109866],hedriodiscus hydrolupus[&&NHX:TOL=109867],hedriodiscus infrapallidus[&&NHX:TOL=109868],hedriodiscus jacarellus[&&NHX:TOL=109869],hedriodiscus lefebvrei[&&NHX:TOL=109870],hedriodiscus leucogaster[&&NHX:TOL=109871],hedriodiscus lineatus[&&NHX:TOL=109872],hedriodiscus nudifrons[&&NHX:TOL=109873],hedriodiscus pallidiventris[&&NHX:TOL=109874],hedriodiscus prasinus[&&NHX:TOL=109875],hedriodiscus pulcher[&&NHX:TOL=109876],hedriodiscus punctifer[&&NHX:TOL=109877],hedriodiscus quadrilineatus[&&NHX:TOL=109878],hedriodiscus subcupratus[&&NHX:TOL=109879],hedriodiscus superpictus[&&NHX:TOL=109880],hedriodiscus tortugellus[&&NHX:TOL=109881],hedriodiscus trivittatus[&&NHX:TOL=109882],hedriodiscus truquii[&&NHX:TOL=109883],hedriodiscus turacellus[&&NHX:TOL=109884],hedriodiscus varipes[&&NHX:TOL=109885],hedriodiscus vertebratus[&&NHX:TOL=109886])hedriodiscus[&&NHX:TOL=108818],(hoplitimyia aleus[&&NHX:TOL=109887],hoplitimyia bellardii[&&NHX:TOL=109888],hoplitimyia clavata[&&NHX:TOL=109889],hoplitimyia constans[&&NHX:TOL=109890],hoplitimyia costalis[&&NHX:TOL=109891],hoplitimyia inbioensis[&&NHX:TOL=117910],hoplitimyia mutabilis[&&NHX:TOL=109892],hoplitimyia panamaensis[&&NHX:TOL=109893],hoplitimyia semiluna[&&NHX:TOL=109894],hoplitimyia subalba[&&NHX:TOL=109895],hoplitimyia taurina[&&NHX:TOL=109896])hoplitimyia[&&NHX:TOL=108819],metabasis rostratus[&&NHX:TOL=108820],nyassimyia[&&NHX:TOL=108821],(odontomyia adusta[&&NHX:TOL=109989],odontomyia aequalis[&&NHX:TOL=109990],odontomyia africana[&&NHX:TOL=109991],odontomyia albigenata[&&NHX:TOL=109992],odontomyia aldrichi[&&NHX:TOL=109993],odontomyia alini[&&NHX:TOL=109994],odontomyia alolena[&&NHX:TOL=109995],odontomyia altifrons[&&NHX:TOL=109996],odontomyia americana[&&NHX:TOL=109997],odontomyia amyris[&&NHX:TOL=109998],odontomyia anchorata[&&NHX:TOL=109999],odontomyia angulata[&&NHX:TOL=110000],odontomyia angusta[&&NHX:TOL=110001],odontomyia angustilimbata[&&NHX:TOL=110002],odontomyia annulata[&&NHX:TOL=110003],odontomyia annulipes[&&NHX:TOL=110004],odontomyia araneifera[&&NHX:TOL=110005],odontomyia arctuata[&&NHX:TOL=110006],odontomyia argentata[&&NHX:TOL=110007],odontomyia aterrima[&&NHX:TOL=110008],odontomyia atraria[&&NHX:TOL=110009],odontomyia atrodorsalis[&&NHX:TOL=110010],odontomyia atrovirens[&&NHX:TOL=110011],odontomyia aurata[&&NHX:TOL=110012],odontomyia aureovestis[&&NHX:TOL=110013],odontomyia aureovittata[&&NHX:TOL=110014],odontomyia australensis[&&NHX:TOL=110015],odontomyia azurea[&&NHX:TOL=110016],odontomyia bahamensis[&&NHX:TOL=110017],odontomyia barbata[&&NHX:TOL=110018],odontomyia bekily[&&NHX:TOL=110019],odontomyia bermudensis[&&NHX:TOL=110020],odontomyia bifascia[&&NHX:TOL=110021],odontomyia bimaculata[&&NHX:TOL=110022],odontomyia bipunctata[&&NHX:TOL=110023],odontomyia bipunctifacies[&&NHX:TOL=110024],odontomyia blastulaefrons[&&NHX:TOL=110025],odontomyia boharti[&&NHX:TOL=110026],odontomyia borealis[&&NHX:TOL=110027],odontomyia bulbifrons[&&NHX:TOL=110028],odontomyia calva[&&NHX:TOL=110029],odontomyia carinata[&&NHX:TOL=110030],odontomyia carinifacies[&&NHX:TOL=110031],odontomyia carnifex[&&NHX:TOL=110032],odontomyia cephalonica[&&NHX:TOL=110033],odontomyia chathamensis[&&NHX:TOL=110034],odontomyia chloris[&&NHX:TOL=110035],odontomyia chrysaner[&&NHX:TOL=110036],odontomyia cincta[&&NHX:TOL=110037],odontomyia cinctilineata[&&NHX:TOL=110038],odontomyia clarifrons[&&NHX:TOL=110039],odontomyia claripennis[&&NHX:TOL=110040],odontomyia cohaerens[&&NHX:TOL=110041],odontomyia colei[&&NHX:TOL=110042],odontomyia collarti[&&NHX:TOL=110043],odontomyia collina[&&NHX:TOL=110044],odontomyia confertissima[&&NHX:TOL=110045],odontomyia confusa[&&NHX:TOL=110046],odontomyia consobrina[&&NHX:TOL=110047],odontomyia coreana[&&NHX:TOL=110048],odontomyia cuthbersoni[&&NHX:TOL=110049],odontomyia cyanea[&&NHX:TOL=110050],odontomyia damascena[&&NHX:TOL=110051],odontomyia decipiens[&&NHX:TOL=110052],odontomyia disciclara[&&NHX:TOL=110053],odontomyia discolor[&&NHX:TOL=110054],odontomyia discolorata[&&NHX:TOL=110055],odontomyia disparina[&&NHX:TOL=110056],odontomyia dissimilis[&&NHX:TOL=110057],odontomyia dorsoangulata[&&NHX:TOL=110058],odontomyia elisabethae[&&NHX:TOL=110059],odontomyia emarginata[&&NHX:TOL=110060],odontomyia erecta[&&NHX:TOL=110061],odontomyia evansi[&&NHX:TOL=110062],odontomyia excocta[&&NHX:TOL=110063],odontomyia exigua[&&NHX:TOL=110064],odontomyia fasciata[&&NHX:TOL=110065],odontomyia fascipes[&&NHX:TOL=110066],odontomyia fiebrigi[&&NHX:TOL=110067],odontomyia filipjewi[&&NHX:TOL=110068],odontomyia finalis[&&NHX:TOL=110069],odontomyia flammiventris[&&NHX:TOL=110070],odontomyia flava[&&NHX:TOL=110071],odontomyia flavissima[&&NHX:TOL=110072],odontomyia foveifrons[&&NHX:TOL=110073],odontomyia frontalis[&&NHX:TOL=110074],odontomyia fulminans[&&NHX:TOL=110075],odontomyia fulviceps[&&NHX:TOL=110076],odontomyia fuscipennis[&&NHX:TOL=110077],odontomyia gagathina[&&NHX:TOL=110078],odontomyia garatas[&&NHX:TOL=110079],odontomyia grandimaculata[&&NHX:TOL=110080],odontomyia guianae[&&NHX:TOL=110081],odontomyia guizhouensis[&&NHX:TOL=110082],odontomyia halterata[&&NHX:TOL=110083],odontomyia herbacea[&&NHX:TOL=110084],odontomyia heterogastra[&&NHX:TOL=110085],odontomyia hirayamae[&&NHX:TOL=110086],odontomyia hirtocculata[&&NHX:TOL=110087],odontomyia hoodiana[&&NHX:TOL=110088],odontomyia hunteri[&&NHX:TOL=110089],odontomyia hydroleon[&&NHX:TOL=110090],odontomyia hydroleonoides[&&NHX:TOL=110091],odontomyia ialemus[&&NHX:TOL=110092],odontomyia icae[&&NHX:TOL=110093],odontomyia idahoensis[&&NHX:TOL=110094],odontomyia immiscens[&&NHX:TOL=110095],odontomyia inaequalis[&&NHX:TOL=110096],odontomyia inanimis[&&NHX:TOL=110097],odontomyia interrupta[&&NHX:TOL=110098],odontomyia jamesi[&&NHX:TOL=110099],odontomyia kamande[&&NHX:TOL=110100],odontomyia kashmirensis[&&NHX:TOL=110101],odontomyia kirchneri[&&NHX:TOL=110102],odontomyia kiricenoi[&&NHX:TOL=110103],odontomyia lamborni[&&NHX:TOL=110104],odontomyia lateremaculata[&&NHX:TOL=110105],odontomyia latatibia[&&NHX:TOL=110106],odontomyia limae[&&NHX:TOL=110107],odontomyia limbata[&&NHX:TOL=110108],odontomyia limbifacies[&&NHX:TOL=110109],odontomyia lineata[&&NHX:TOL=110110],odontomyia longicornis[&&NHX:TOL=110111],odontomyia lutatius[&&NHX:TOL=110112],odontomyia luteiceps[&&NHX:TOL=110113],odontomyia maculata[&&NHX:TOL=110114],odontomyia marginella[&&NHX:TOL=110115],odontomyia masaica[&&NHX:TOL=110116],odontomyia megacephala[&&NHX:TOL=110117],odontomyia melantera[&&NHX:TOL=110118],odontomyia microcera[&&NHX:TOL=110119],odontomyia microleon[&&NHX:TOL=110120],odontomyia microstoma[&&NHX:TOL=110121],odontomyia minima[&&NHX:TOL=110122],odontomyia mutica[&&NHX:TOL=110123],odontomyia neodorsalis[&&NHX:TOL=110124],odontomyia nexura[&&NHX:TOL=110125],odontomyia nigerrima[&&NHX:TOL=110126],odontomyia nigrinervis[&&NHX:TOL=110127],odontomyia nitidiceps[&&NHX:TOL=110128],odontomyia nitidissima[&&NHX:TOL=110129],odontomyia notatifrons[&&NHX:TOL=110130],odontomyia novaecaledoniae[&&NHX:TOL=110131],odontomyia novaeguineensis[&&NHX:TOL=110132],odontomyia nyassica[&&NHX:TOL=110133],odontomyia obscuripes[&&NHX:TOL=110134],odontomyia ochropa[&&NHX:TOL=110135],odontomyia okinawae[&&NHX:TOL=110136],odontomyia opertanea[&&NHX:TOL=110137],odontomyia ophyridfera[&&NHX:TOL=110138],odontomyia ornata[&&NHX:TOL=110139],odontomyia pachycephala[&&NHX:TOL=110140],odontomyia pachyceps[&&NHX:TOL=110141],odontomyia painteri[&&NHX:TOL=110142],odontomyia pallida[&&NHX:TOL=110143],odontomyia parallela[&&NHX:TOL=110144],odontomyia paralellina[&&NHX:TOL=110145],odontomyia pauliana[&&NHX:TOL=110146],odontomyia pectoralis[&&NHX:TOL=110147],odontomyia periscelis[&&NHX:TOL=110148],odontomyia peruviana[&&NHX:TOL=110149],odontomyia picea[&&NHX:TOL=110150],odontomyia picta[&&NHX:TOL=110151],odontomyia pictifrons[&&NHX:TOL=110152],odontomyia pilimana[&&NHX:TOL=110153],odontomyia pilosa[&&NHX:TOL=110154],odontomyia plebeja[&&NHX:TOL=110155],odontomyia poecilopoda[&&NHX:TOL=110156],odontomyia polycedes[&&NHX:TOL=110157],odontomyia proba[&&NHX:TOL=110158],odontomyia profuscata[&&NHX:TOL=110159],odontomyia pubescens[&&NHX:TOL=110160],odontomyia pulcherrima[&&NHX:TOL=110161],odontomyia quadrata[&&NHX:TOL=110162],odontomyia quadrinotata[&&NHX:TOL=110163],odontomyia rectifasciata[&&NHX:TOL=110164],odontomyia regisgeorgii[&&NHX:TOL=110165],odontomyia restricta[&&NHX:TOL=110166],odontomyia rhodaspis[&&NHX:TOL=110167],odontomyia rufifacies[&&NHX:TOL=110168],odontomyia rufipes[&&NHX:TOL=110169],odontomyia rufiventris[&&NHX:TOL=110170],odontomyia rufocera[&&NHX:TOL=110171],odontomyia rufoscutellata[&&NHX:TOL=110172],odontomyia saphyrina[&&NHX:TOL=110173],odontomyia schoutedeni[&&NHX:TOL=110174],odontomyia scutellata[&&NHX:TOL=110175],odontomyia seyrigi[&&NHX:TOL=110176],odontomyia shikokuana[&&NHX:TOL=110177],odontomyia siderogaster[&&NHX:TOL=110178],odontomyia sidneyensis[&&NHX:TOL=110179],odontomyia simplex[&&NHX:TOL=110180],odontomyia sinica[&&NHX:TOL=110181],odontomyia solennis[&&NHX:TOL=110182],odontomyia stigmaticalis[&&NHX:TOL=110183],odontomyia stricta[&&NHX:TOL=110184],odontomyia stylata[&&NHX:TOL=110185],odontomyia subdentata[&&NHX:TOL=110186],odontomyia subobscura[&&NHX:TOL=110187],odontomyia subpicta[&&NHX:TOL=110188],odontomyia thula[&&NHX:TOL=110189],odontomyia tigrina[&&NHX:TOL=110190],odontomyia timorensis[&&NHX:TOL=110191],odontomyia toxopeusi[&&NHX:TOL=110192],odontomyia transversa[&&NHX:TOL=110193],odontomyia triangulifera[&&NHX:TOL=110194],odontomyia tumida[&&NHX:TOL=110195],odontomyia uninigra[&&NHX:TOL=110196],odontomyia vanderwulpiana[&&NHX:TOL=110197],odontomyia vicina[&&NHX:TOL=110198],odontomyia virgo[&&NHX:TOL=110199],odontomyia viridana[&&NHX:TOL=110200],odontomyia vittata[&&NHX:TOL=110201],odontomyia xanthopus[&&NHX:TOL=110202],odontomyia yangi[&&NHX:TOL=110203])odontomyia[&&NHX:TOL=108822],(oplodontha albipennis[&&NHX:TOL=110619],oplodontha anodonta[&&NHX:TOL=110620],oplodontha anodontina[&&NHX:TOL=110621],oplodontha circumscripta[&&NHX:TOL=110622],oplodontha decellei[&&NHX:TOL=110623],oplodontha dispar[&&NHX:TOL=110624],oplodontha guerinii[&&NHX:TOL=110625],oplodontha impar[&&NHX:TOL=110626],oplodontha luzonensis[&&NHX:TOL=110627],oplodontha minuta[&&NHX:TOL=110628],oplodontha nigritula[&&NHX:TOL=110629],oplodontha oasina[&&NHX:TOL=110630],oplodontha picta[&&NHX:TOL=110631],oplodontha pulchriceps[&&NHX:TOL=110632],oplodontha punctifacies[&&NHX:TOL=110633],oplodontha rubrithorax[&&NHX:TOL=110634],oplodontha rufula[&&NHX:TOL=110635],oplodontha tangana[&&NHX:TOL=110636],oplodontha viridula[&&NHX:TOL=110637])oplodontha[&&NHX:TOL=108823],panamamyia silbergliedi[&&NHX:TOL=117911],pinaleus[&&NHX:TOL=108824],promeranisa[&&NHX:TOL=108825],(psellidotus abditis[&&NHX:TOL=109897],psellidotus annamariae[&&NHX:TOL=109898],psellidotus atrifascies[&&NHX:TOL=109899],psellidotus atriventris[&&NHX:TOL=109900],psellidotus auripes[&&NHX:TOL=109901],psellidotus aztecanus[&&NHX:TOL=109902],psellidotus bonariensis[&&NHX:TOL=109903],psellidotus caloceps[&&NHX:TOL=109904],psellidotus comma[&&NHX:TOL=109905],psellidotus concinnatus[&&NHX:TOL=109906],psellidotus connexus[&&NHX:TOL=109907],psellidotus dasyops[&&NHX:TOL=109908],psellidotus defectus[&&NHX:TOL=109909],psellidotus elegans[&&NHX:TOL=109910],psellidotus fascifrons[&&NHX:TOL=109911],psellidotus fenestratus[&&NHX:TOL=109912],psellidotus flavicornis[&&NHX:TOL=109913],psellidotus formosus[&&NHX:TOL=109914],psellidotus fulvicornis[&&NHX:TOL=109915],psellidotus gagatigaster[&&NHX:TOL=109916],psellidotus goniophorus[&&NHX:TOL=109917],psellidotus hieroglyphicus[&&NHX:TOL=109918],psellidotus hypomelas[&&NHX:TOL=109919],psellidotus inermis[&&NHX:TOL=109920],psellidotus inflatus[&&NHX:TOL=109921],psellidotus lucens[&&NHX:TOL=109922],psellidotus macalpini[&&NHX:TOL=109923],psellidotus maculifrons[&&NHX:TOL=109924],psellidotus meganticus[&&NHX:TOL=109925],psellidotus micheneri[&&NHX:TOL=109926],psellidotus nasiferus[&&NHX:TOL=109927],psellidotus novellus[&&NHX:TOL=109928],psellidotus obscurus[&&NHX:TOL=109929],psellidotus occipitalis[&&NHX:TOL=109930],psellidotus panamaensis[&&NHX:TOL=109931],psellidotus pictifrons[&&NHX:TOL=109932],psellidotus pictus[&&NHX:TOL=109933],psellidotus protrudens[&&NHX:TOL=109934],psellidotus robustus[&&NHX:TOL=109935],psellidotus rubricornis[&&NHX:TOL=109936],psellidotus rufipennis[&&NHX:TOL=109937],psellidotus similis[&&NHX:TOL=109938],psellidotus snowi[&&NHX:TOL=109939],psellidotus stonei[&&NHX:TOL=109940],psellidotus texasianus[&&NHX:TOL=109941],psellidotus viridis[&&NHX:TOL=109942])psellidotus[&&NHX:TOL=108826],rhingiopsis[&&NHX:TOL=108827],scapanocnema spatulipes[&&NHX:TOL=108828],stratiomyella nana[&&NHX:TOL=108829],(stratiomys adelpha[&&NHX:TOL=110212],stratiomys africana[&&NHX:TOL=110213],stratiomys annectans[&&NHX:TOL=110214],stratiomys apicalis[&&NHX:TOL=110215],stratiomys approximata[&&NHX:TOL=110216],stratiomys armeniaca[&&NHX:TOL=110217],stratiomys badia[&&NHX:TOL=110218],stratiomys barbata[&&NHX:TOL=110219],stratiomys barca[&&NHX:TOL=110220],stratiomys beresowskii[&&NHX:TOL=110221],stratiomys biguttata[&&NHX:TOL=110222],stratiomys bochariensis[&&NHX:TOL=110223],stratiomys browni[&&NHX:TOL=110224],stratiomys bruneri[&&NHX:TOL=110225],stratiomys canadensis[&&NHX:TOL=110226],stratiomys cenesia[&&NHX:TOL=110227],stratiomys chamaeleon[&&NHX:TOL=110228],stratiomys choui[&&NHX:TOL=110229],stratiomys concinna[&&NHX:TOL=110230],stratiomys conica[&&NHX:TOL=110231],stratiomys constricta[&&NHX:TOL=110232],stratiomys convexa[&&NHX:TOL=110233],stratiomys currani[&&NHX:TOL=110234],stratiomys deserticolor[&&NHX:TOL=110235],stratiomys diademata[&&NHX:TOL=110236],stratiomys discalis[&&NHX:TOL=110237],stratiomys discaloides[&&NHX:TOL=110238],stratiomys dissimilis[&&NHX:TOL=110239],stratiomys equestris[&&NHX:TOL=110240],stratiomys fenestrata[&&NHX:TOL=110241],stratiomys ferina[&&NHX:TOL=110242],stratiomys flavoscutellata[&&NHX:TOL=110243],stratiomys floridensis[&&NHX:TOL=110244],stratiomys fulvescens[&&NHX:TOL=110245],stratiomys griseata[&&NHX:TOL=110246],stratiomys hirsutissima[&&NHX:TOL=110247],stratiomys hispanica[&&NHX:TOL=110248],stratiomys hulli[&&NHX:TOL=110249],stratiomys jamesi[&&NHX:TOL=110250],stratiomys japonica[&&NHX:TOL=110251],stratiomys koslowi[&&NHX:TOL=110252],stratiomys laetimaculata[&&NHX:TOL=110253],stratiomys laevifrons[&&NHX:TOL=110254],stratiomys laticeps[&&NHX:TOL=110255],stratiomys lativentris[&&NHX:TOL=110256],stratiomys leucopsis[&&NHX:TOL=110257],stratiomys licenti[&&NHX:TOL=110258],stratiomys lindneriana[&&NHX:TOL=110259],stratiomys lineolata[&&NHX:TOL=110260],stratiomys longicornis[&&NHX:TOL=110261],stratiomys longifrons[&&NHX:TOL=110262],stratiomys lugubris[&&NHX:TOL=110263],stratiomys maculosa[&&NHX:TOL=110264],stratiomys mandshurica[&&NHX:TOL=110265],stratiomys meigenii[&&NHX:TOL=110266],stratiomys melanopsis[&&NHX:TOL=110267],stratiomys melastoma[&&NHX:TOL=110268],stratiomys micropilosa[&&NHX:TOL=110269],stratiomys mongolica[&&NHX:TOL=110270],stratiomys nevadae[&&NHX:TOL=110271],stratiomys nigerrima[&&NHX:TOL=110272],stratiomys nigrifrons[&&NHX:TOL=110273],stratiomys nigriventris[&&NHX:TOL=110274],stratiomys nobilis[&&NHX:TOL=110275],stratiomys norma[&&NHX:TOL=110276],stratiomys normula[&&NHX:TOL=110277],stratiomys nymphis[&&NHX:TOL=110278],stratiomys obesa[&&NHX:TOL=110279],stratiomys ohioensis[&&NHX:TOL=110280],stratiomys pallipes[&&NHX:TOL=110281],stratiomys pardalina[&&NHX:TOL=110282],stratiomys pellucida[&&NHX:TOL=110283],stratiomys portschinksyana[&&NHX:TOL=110284],stratiomys potamida[&&NHX:TOL=110285],stratiomys potanini[&&NHX:TOL=110286],stratiomys przewalskii[&&NHX:TOL=110287],stratiomys roborowwskii[&&NHX:TOL=110288],stratiomys rubricornis[&&NHX:TOL=110289],stratiomys ruficornis[&&NHX:TOL=110290],stratiomys rufipennis[&&NHX:TOL=110291],stratiomys rufiventris[&&NHX:TOL=110292],stratiomys sinensis[&&NHX:TOL=110293],stratiomys singularior[&&NHX:TOL=110294],stratiomys tularensis[&&NHX:TOL=110295],stratiomys validicornis[&&NHX:TOL=110296],stratiomys velutina[&&NHX:TOL=110297],stratiomys ventralis[&&NHX:TOL=110298],stratiomys virens[&&NHX:TOL=110299],stratiomys viridis[&&NHX:TOL=110300],stratiomys vittipennis[&&NHX:TOL=110301],stratiomys wagneri[&&NHX:TOL=110302],stratiomys zarudkyi[&&NHX:TOL=110303])stratiomys[&&NHX:TOL=108830],systegnum[&&NHX:TOL=108831],(zuerchermyia bequaerti[&&NHX:TOL=110528],zuerchermyia festiva[&&NHX:TOL=110529],zuerchermyia malachitis[&&NHX:TOL=110530],zuerchermyia princeps[&&NHX:TOL=110531],zuerchermyia pustulosa[&&NHX:TOL=110532])zuerchermyia[&&NHX:TOL=108832],zulumyia[&&NHX:TOL=108833])stratiomyini[&&NHX:TOL=108807])stratiomyinae[&&NHX:TOL=23964],(analcoceroides longicornis[&&NHX:TOL=108834],(analcocerus atriceps[&&NHX:TOL=109697],analcocerus orbitalis[&&NHX:TOL=109698],analcocerus taurus[&&NHX:TOL=109699])analcocerus[&&NHX:TOL=108835],anisoscapus[&&NHX:TOL=108836],basentidema[&&NHX:TOL=108837],brachythrix dileucostigma[&&NHX:TOL=108838],cyclophleps tenebrifera[&&NHX:TOL=108839],dactylothrix indicatrix[&&NHX:TOL=111436],dicamptocrana jorgenseni[&&NHX:TOL=108840],(dicranophora affinis[&&NHX:TOL=109700],dicranophora astuta[&&NHX:TOL=109701],dicranophora brevifurca[&&NHX:TOL=109702],dicranophora furcifera[&&NHX:TOL=109703],dicranophora picta[&&NHX:TOL=109704])dicranophora[&&NHX:TOL=108841],dolichothrix[&&NHX:TOL=108842],heptozus[&&NHX:TOL=108843],histriodroma[&&NHX:TOL=108844],hoplistes[&&NHX:TOL=108845],lysozus[&&NHX:TOL=108846],neanalcocerus[&&NHX:TOL=108847],neoraphiocera pipopiuna[&&NHX:TOL=111437],pezodontina[&&NHX:TOL=108848],phanerozus pampinus[&&NHX:TOL=108849],pseudocyclophleps[&&NHX:TOL=111438],pseudohistiodroma[&&NHX:TOL=111439],raphiocera[&&NHX:TOL=108850],rondonocera melanochrysa[&&NHX:TOL=111440],rhaphioceroides pendleburyi[&&NHX:TOL=108851],timorimyia bidentata[&&NHX:TOL=108852])raphiocerinae[&&NHX:TOL=23963])[&&NHX:TOL=108474])[&&NHX:TOL=108470])[&&NHX:TOL=23969])[&&NHX:TOL=23970])[&&NHX:TOL=23971])[&&NHX:TOL=23972],gigantoberis liaoningensis[&&NHX:EXT=Y:TOL=117912],montsecia martinezdelclosi[&&NHX:EXT=Y:TOL=117913])stratiomyidae[&&NHX:TOL=10444])[&&NHX:TOL=23918])stratiomyomorpha[&&NHX:TOL=23919],((arthropeas[&&NHX:TOL=118062],coenomyia[&&NHX:TOL=118063],dialysis[&&NHX:TOL=118064],exeretonevra[&&NHX:TOL=118065],heterostomus[&&NHX:TOL=118066],odontosabulus[&&NHX:TOL=118067],rachicerus[&&NHX:TOL=118068],xylophagus[&&NHX:TOL=118069],arthropiella eocenica[&&NHX:EXT=Y:TOL=118070],chrysothemis speciosa[&&NHX:EXT=Y:TOL=118072],ganeopteromyia calypso[&&NHX:EXT=Y:TOL=118073],habrosoma antiquum[&&NHX:EXT=Y:TOL=118071],lophyrophorus flabellatus[&&NHX:EXT=Y:TOL=118074],paleorachicerus formosus[&&NHX:EXT=Y:TOL=118075])xylophagidae[&&NHX:TOL=10440],(vermileonidae[&&NHX:TOL=10445],(rhagionidae[&&NHX:TOL=10447],(pelecorhynchidae[&&NHX:TOL=10449],(oreoleptis torrenticola[&&NHX:TOL=110658],((asuragina[&&NHX:TOL=118076],atherix[&&NHX:TOL=118077],atrichops[&&NHX:TOL=118078],dasyomma[&&NHX:TOL=118079],microphora angustifrons[&&NHX:TOL=118080],pachybates[&&NHX:TOL=118081],suragina[&&NHX:TOL=118082],suraginella macalpinei[&&NHX:TOL=118083],trichacantha[&&NHX:TOL=118084],athericites gordoni[&&NHX:EXT=Y:TOL=118085],succinatherix[&&NHX:EXT=Y:TOL=118086])athericidae[&&NHX:TOL=10451],tabanidae[&&NHX:TOL=10452])[&&NHX:TOL=23923])[&&NHX:TOL=110657])[&&NHX:TOL=23922])[&&NHX:TOL=23921])tabanomorpha[&&NHX:TOL=23920])[&&NHX:TOL=23924])[&&NHX:TOL=23884],(((acrocerinae[&&NHX:TOL=111378],(panopinae[&&NHX:TOL=111379],philopotinae[&&NHX:TOL=111380])[&&NHX:TOL=118198])acroceridae[&&NHX:TOL=10455],nemestrinidae[&&NHX:TOL=10456])nemestrinoidea[&&NHX:TOL=10454],(((asilidae[&&NHX:TOL=10460],(((apsilocephala longistyla[&&NHX:TOL=111429],apsilocephala vagabunda[&&NHX:EXT=Y:TOL=111430])apsilocephala[&&NHX:TOL=111238],clestenthia aberrans[&&NHX:TOL=111239],clestenthiella crassioccipitis[&&NHX:TOL=111240],burmapsilocephala cockerelli[&&NHX:EXT=Y:TOL=111431])apsilocephalidae[&&NHX:TOL=23891],(evocoa chilensis[&&NHX:TOL=23890],(scenopinidae[&&NHX:TOL=10462],(phycinae[&&NHX:TOL=24092],agapophytinae[&&NHX:TOL=24093],therevinae[&&NHX:TOL=24094])therevidae[&&NHX:TOL=10463])[&&NHX:TOL=23892])[&&NHX:TOL=23893])[&&NHX:TOL=10461],((((((apiophorinae[&&NHX:TOL=23997],ectyphinae[&&NHX:TOL=23996],mydinae[&&NHX:TOL=23998])[&&NHX:TOL=24005],diochlistinae[&&NHX:TOL=23999])[&&NHX:TOL=24006],anomalomydinae[&&NHX:TOL=24000])[&&NHX:TOL=24007],(syllegomydinaae[&&NHX:TOL=24001],(leptomydinae[&&NHX:TOL=24002],(cacatuopyginae[&&NHX:TOL=24003],rhopaliinae[&&NHX:TOL=24004])[&&NHX:TOL=24009])[&&NHX:TOL=24010])[&&NHX:TOL=24008])[&&NHX:TOL=24013],(tongamya[&&NHX:TOL=24014],(neorhaphiomidas[&&NHX:TOL=24016],megascelus[&&NHX:TOL=24015])[&&NHX:TOL=24017])megascelinae[&&NHX:TOL=24011],rhaphiomydinae[&&NHX:TOL=24012])mydidae[&&NHX:TOL=10465],apiocera[&&NHX:TOL=10466])[&&NHX:TOL=10464])[&&NHX:TOL=10459],((mythicomyiinae[&&NHX:TOL=23926],(oligodraninae[&&NHX:TOL=23927],(usiinae[&&NHX:TOL=23928],(toxophorinae[&&NHX:TOL=23929],(lordotinae[&&NHX:TOL=23930],(heterotropinae[&&NHX:TOL=23931],(bombyliinae[&&NHX:TOL=23932],(crocidinae[&&NHX:TOL=23933],(mariobezzinae[&&NHX:TOL=23934],(oniromyiinae[&&NHX:TOL=23935],(cythereinae[&&NHX:TOL=23936],(lomatiinae[&&NHX:TOL=23937],(anthracinae[&&NHX:TOL=23938],(tomomyzinae[&&NHX:TOL=23939],antoniinae[&&NHX:TOL=23940])[&&NHX:TOL=23941])[&&NHX:TOL=23942])[&&NHX:TOL=23943])[&&NHX:TOL=23944])[&&NHX:TOL=23945])[&&NHX:TOL=23946])[&&NHX:TOL=23947])[&&NHX:TOL=23948])[&&NHX:TOL=23949])[&&NHX:TOL=23950])[&&NHX:TOL=23951])[&&NHX:TOL=23952])[&&NHX:TOL=23953])bombyliidae[&&NHX:TOL=23894],(apystomyia elinguis[&&NHX:TOL=23897],(hilarimorpha[&&NHX:TOL=111241],hilarimorphites[&&NHX:EXT=Y:TOL=111242])hilarimorphidae[&&NHX:TOL=23896])[&&NHX:TOL=23895])[&&NHX:TOL=10467])asiloidea[&&NHX:TOL=10458],(((nemedina[&&NHX:TOL=111243],(atelestus[&&NHX:TOL=111245],(meghyperus[&&NHX:TOL=111247],acarteroptera[&&NHX:TOL=111248])[&&NHX:TOL=111246])[&&NHX:TOL=111244])atelestidae[&&NHX:TOL=23901],(hybotidae[&&NHX:TOL=23898],(empididae[&&NHX:TOL=10470],dolichopodidae[&&NHX:TOL=23899])[&&NHX:TOL=23902])[&&NHX:TOL=23925])empidoidea[&&NHX:TOL=10468],((((platypezidae[&&NHX:TOL=10514],(opetia[&&NHX:TOL=118102],lithopetia hirsuta[&&NHX:EXT=Y:TOL=118105],opetiala shatalkini[&&NHX:EXT=Y:TOL=118103],oppenheimiella baltica[&&NHX:EXT=Y:TOL=118104],pseudopetia[&&NHX:EXT=Y:TOL=118106])opetiidae[&&NHX:TOL=113123])[&&NHX:TOL=113122],((lonchoptera[&&NHX:TOL=111287],neolonchoptera[&&NHX:TOL=111288],homolonchoptera[&&NHX:TOL=111289],spilonchoptera[&&NHX:TOL=111290],lonchopterites[&&NHX:EXT=Y:TOL=111291],lonchopteromorpha[&&NHX:EXT=Y:TOL=111292])lonchopteridae[&&NHX:TOL=10516],((ironomyia nigromaculata[&&NHX:TOL=111249],cretonomyia pristina[&&NHX:EXT=Y:TOL=111250],eridomyia[&&NHX:EXT=Y:TOL=111251],hermaeomyia[&&NHX:EXT=Y:TOL=111252],lebambromyia acrai[&&NHX:EXT=Y:TOL=111253],palaeopetia laiyangensis[&&NHX:EXT=Y:TOL=111254])ironomyiidae[&&NHX:TOL=10518],phoridae[&&NHX:TOL=10521])[&&NHX:TOL=10517])[&&NHX:TOL=10515])platypezoidea[&&NHX:TOL=10513],(syrphidae[&&NHX:TOL=10523],(((chalarus absonus[&&NHX:TOL=54727],chalarus amazonensis[&&NHX:TOL=54728],chalarus angustifrons[&&NHX:TOL=54729],chalarus argenteus[&&NHX:TOL=54730],chalarus basalis[&&NHX:TOL=54731],chalarus beijingensis[&&NHX:TOL=54732],chalarus brevicaudis[&&NHX:TOL=54733],chalarus chilensis[&&NHX:TOL=54734],chalarus clarus[&&NHX:TOL=54735],chalarus connexus[&&NHX:TOL=54736],chalarus decorus[&&NHX:TOL=54737],chalarus delicatus[&&NHX:TOL=54738],chalarus elegantulus[&&NHX:TOL=54739],chalarus exiguus[&&NHX:TOL=54740],chalarus fimbriatus[&&NHX:TOL=54741],chalarus flosculus[&&NHX:TOL=54742],chalarus griseus[&&NHX:TOL=54743],chalarus gynocephalus[&&NHX:TOL=54744],chalarus holosericeus[&&NHX:TOL=54745],chalarus indistinctus[&&NHX:TOL=54746],chalarus irwini[&&NHX:TOL=128358],chalarus juliae[&&NHX:TOL=54747],chalarus latifrons[&&NHX:TOL=54748],chalarus lenkoi[&&NHX:TOL=54749],chalarus leticiae[&&NHX:TOL=54750],chalarus longicaudis[&&NHX:TOL=54751],chalarus magnalus[&&NHX:TOL=54752],chalarus obscurus[&&NHX:TOL=54753],chalarus orientalis[&&NHX:TOL=54754],chalarus parmenteri[&&NHX:TOL=54755],chalarus perplexus[&&NHX:TOL=54756],chalarus proprius[&&NHX:TOL=54757],chalarus pughi[&&NHX:TOL=54758],chalarus rectifrons[&&NHX:TOL=54759],chalarus spurius[&&NHX:TOL=54760],chalarus trilineatus[&&NHX:TOL=54761],chalarus triramosus[&&NHX:TOL=54762],chalarus unilacertus[&&NHX:TOL=54763],chalarus velutinus[&&NHX:TOL=54764],chalarus xanthopodus[&&NHX:TOL=54765],chalarus zanganus[&&NHX:TOL=54766],chalarus zlobini[&&NHX:TOL=54767],chalarus zyginae[&&NHX:TOL=54768])chalarus[&&NHX:TOL=54671],((verrallia andreei[&&NHX:EXT=Y:TOL=54715],verrallia aucta[&&NHX:TOL=54716],verrallia csikii[&&NHX:TOL=54717],verrallia exstincta[&&NHX:EXT=Y:TOL=54718],verrallia kerteszia[&&NHX:EXT=Y:TOL=54720],verrallia rebunensis[&&NHX:TOL=54721],verrallia spectabilis[&&NHX:TOL=54722],verrallia virginica[&&NHX:TOL=54723])verrallia[&&NHX:TOL=54673],(jassidophaga abscissa[&&NHX:TOL=54769],jassidophaga argentisegmentata[&&NHX:TOL=54770],jassidophaga armata[&&NHX:TOL=54771],jassidophaga beatricis[&&NHX:TOL=54772],jassidophaga chiiensis[&&NHX:TOL=54773],jassidophaga contracta[&&NHX:TOL=54774],jassidophaga eximia[&&NHX:TOL=54775],jassidophaga fasciata[&&NHX:TOL=54776],jassidophaga flavidipes[&&NHX:TOL=54777],jassidophaga guangxiensis[&&NHX:TOL=54778],jassidophaga hodosa[&&NHX:TOL=54779],jassidophaga japonica[&&NHX:TOL=54780],jassidophaga kurilensis[&&NHX:TOL=54781],jassidophaga makarkini[&&NHX:TOL=54782],jassidophaga nearctica[&&NHX:TOL=128360],jassidophaga pala[&&NHX:TOL=54783],jassidophaga pilosa[&&NHX:TOL=54784],jassidophaga plumbella[&&NHX:TOL=54785],jassidophaga pollinosa[&&NHX:TOL=54786],jassidophaga sidorenkoi[&&NHX:TOL=54788],jassidophaga speciosa[&&NHX:TOL=54789],jassidophaga triloba[&&NHX:TOL=54790],jassidophaga verrucosa[&&NHX:TOL=54791],jassidophaga villosa[&&NHX:TOL=54792])jassidophaga[&&NHX:TOL=54674],protoverrallia succinia[&&NHX:EXT=Y:TOL=54724])[&&NHX:TOL=54672])chalarinae[&&NHX:TOL=54640],((((protonephrocerus florissantius[&&NHX:EXT=Y:TOL=54693],protonephrocerus chiloensis[&&NHX:TOL=54694])protonephrocerus[&&NHX:TOL=54669],metanephrocerus collini[&&NHX:EXT=Y:TOL=54695])[&&NHX:TOL=54692],(nephrocerus acanthostylus[&&NHX:TOL=54696],nephrocerus atrapilus[&&NHX:TOL=54697],nephrocerus auritus[&&NHX:TOL=54698],nephrocerus corpulentus[&&NHX:TOL=54699],nephrocerus daeckei[&&NHX:TOL=54700],nephrocerus fatalis[&&NHX:TOL=54701],nephrocerus flavicornis[&&NHX:TOL=54702],nephrocerus flexus[&&NHX:TOL=54703],nephrocerus grandis[&&NHX:TOL=54704],nephrocerus japonicus[&&NHX:TOL=54705],nephrocerus lapponicus[&&NHX:TOL=54706],nephrocerus nevskajae[&&NHX:TOL=54707],nephrocerus oligocenicus[&&NHX:EXT=Y:TOL=54708],nephrocerus paektusanensis[&&NHX:TOL=54709],nephrocerus scutellatus[&&NHX:TOL=54710],nephrocerus slossonae[&&NHX:TOL=54711],nephrocerus spineus[&&NHX:TOL=54712],nephrocerus woodi[&&NHX:TOL=54713],nephrocerus zaitzevi[&&NHX:TOL=54714])nephrocerus[&&NHX:TOL=54670])nephrocerinae[&&NHX:TOL=54639],((pipunculus abnormis[&&NHX:TOL=54793],pipunculus albidus[&&NHX:TOL=54794],pipunculus amurensis[&&NHX:TOL=54795],pipunculus amuricus[&&NHX:TOL=54796],pipunculus apicarinus[&&NHX:TOL=54797],pipunculus avius[&&NHX:TOL=54798],pipunculus babai[&&NHX:TOL=54799],pipunculus basilicus[&&NHX:TOL=54801],pipunculus bulbistylus[&&NHX:TOL=54802],pipunculus calceatus[&&NHX:TOL=54803],pipunculus campestris[&&NHX:TOL=54804],pipunculus carlestolrai[&&NHX:TOL=54805],pipunculus cingulatus[&&NHX:TOL=54806],pipunculus curvitibiae[&&NHX:TOL=54807],pipunculus dentatus[&&NHX:TOL=54808],pipunculus denticeps[&&NHX:TOL=54809],pipunculus dimi[&&NHX:TOL=54810],pipunculus diuteus[&&NHX:TOL=54811],pipunculus elegans[&&NHX:TOL=128362],pipunculus elegantulus[&&NHX:TOL=54812],pipunculus emiliae[&&NHX:TOL=54813],pipunculus ferepauculus[&&NHX:TOL=54814],pipunculus fonsecai[&&NHX:TOL=54815],pipunculus fuscus[&&NHX:TOL=54816],pipunculus hastatus[&&NHX:TOL=54817],pipunculus hertzogi[&&NHX:TOL=54818],pipunculus horvathi[&&NHX:TOL=54819],pipunculus houghi[&&NHX:TOL=54820],pipunculus infandus[&&NHX:TOL=54821],pipunculus kondarensis[&&NHX:TOL=54822],pipunculus kotaneni[&&NHX:TOL=54823],pipunculus kozlovi[&&NHX:TOL=54824],pipunculus kurilensis[&&NHX:TOL=54825],pipunculus lenis[&&NHX:TOL=54826],pipunculus lichtwardti[&&NHX:TOL=54827],pipunculus luteicornis[&&NHX:TOL=54828],pipunculus magnicarinatus[&&NHX:TOL=54829],pipunculus maritimus[&&NHX:TOL=54830],pipunculus minutulus[&&NHX:TOL=54831],pipunculus mongolicus[&&NHX:TOL=54832],pipunculus monticola[&&NHX:TOL=128363],pipunculus nanus[&&NHX:TOL=54833],pipunculus nitor[&&NHX:TOL=54835],pipunculus nodus[&&NHX:TOL=54836],pipunculus oldenbergi[&&NHX:TOL=54837],pipunculus omissinervis[&&NHX:TOL=54838],pipunculus papulus[&&NHX:TOL=54839],pipunculus platystylus[&&NHX:TOL=54840],pipunculus pumilionis[&&NHX:TOL=54841],pipunculus rafaeli[&&NHX:TOL=54842],pipunculus rarus[&&NHX:TOL=54843],pipunculus sajanicus[&&NHX:TOL=54844],pipunculus stackelbergi[&&NHX:TOL=54846],pipunculus subvaripes[&&NHX:TOL=54847],pipunculus talgarensis[&&NHX:TOL=54848],pipunculus tanasijtshuki[&&NHX:TOL=54849],pipunculus tenuirostris[&&NHX:TOL=54850],pipunculus tibialis[&&NHX:TOL=54852],pipunculus torus[&&NHX:TOL=54853],pipunculus townsendi[&&NHX:TOL=54854],pipunculus ussuriensis[&&NHX:TOL=54855],pipunculus viduus[&&NHX:TOL=54857],pipunculus violovitshi[&&NHX:TOL=54858],pipunculus wolfi[&&NHX:TOL=128364],pipunculus xanthopodus[&&NHX:TOL=54859],pipunculus zaitzevi[&&NHX:TOL=54860],pipunculus zinovjevi[&&NHX:TOL=54861],pipunculus zlobini[&&NHX:TOL=54862],pipunculus zugmayeriae[&&NHX:TOL=54863])pipunculus[&&NHX:TOL=54641],((((cephalops argutus[&&NHX:TOL=54865],cephalops hemistilbus[&&NHX:TOL=54866],cephalops inchoatus[&&NHX:TOL=54867],cephalops pannonicus[&&NHX:TOL=54868])cephalops beckerias[&&NHX:TOL=54864],(cephalops abditus[&&NHX:TOL=54870],cephalops adamanteus[&&NHX:TOL=54871],cephalops aeneus[&&NHX:TOL=54872],cephalops albivillosus[&&NHX:TOL=54873],cephalops amapaensis[&&NHX:TOL=54874],cephalops amembranosus[&&NHX:TOL=54875],cephalops argenteus[&&NHX:TOL=54876],cephalops bequaerti[&&NHX:TOL=54877],cephalops boharti[&&NHX:TOL=54878],cephalops brasiliensis[&&NHX:TOL=54879],cephalops burmensis[&&NHX:TOL=54880],cephalops caeruleimontanus[&&NHX:TOL=54881],cephalops calcaratus[&&NHX:TOL=54882],cephalops callistus[&&NHX:TOL=54883],cephalops calvus[&&NHX:TOL=54884],cephalops candidulus[&&NHX:TOL=54885],cephalops cochleatus[&&NHX:TOL=54886],cephalops congoensis[&&NHX:TOL=54887],cephalops conjunctivus[&&NHX:TOL=54888],cephalops deminitens[&&NHX:TOL=54889],cephalops eximius[&&NHX:TOL=54890],cephalops flaviventris[&&NHX:TOL=54891],cephalops furnaceus[&&NHX:TOL=54892],cephalops grootaerti[&&NHX:TOL=54893],cephalops huashanensis[&&NHX:TOL=54894],cephalops inflatus[&&NHX:TOL=54895],cephalops innitidus[&&NHX:TOL=54896],cephalops javensis[&&NHX:TOL=54897],cephalops kalimus[&&NHX:TOL=54898],cephalops kunashiricus[&&NHX:TOL=54899],cephalops kurilensis[&&NHX:TOL=54900],cephalops laeviventris[&&NHX:TOL=54901],cephalops limatus[&&NHX:TOL=54902],cephalops longipennis[&&NHX:TOL=54903],cephalops longistylis[&&NHX:TOL=54904],cephalops lubuti[&&NHX:TOL=54905],cephalops lusingensis[&&NHX:TOL=54906],cephalops maculiventris[&&NHX:TOL=54907],cephalops multidenticulatus[&&NHX:TOL=54908],cephalops mundulus[&&NHX:TOL=54909],cephalops nagatomii[&&NHX:TOL=54910],cephalops nigricoxa[&&NHX:TOL=54911],cephalops nigrifrons[&&NHX:TOL=54912],cephalops nitidellus[&&NHX:TOL=54913],cephalops nitidus[&&NHX:TOL=54914],cephalops obtusus[&&NHX:TOL=54915],cephalops pacatus[&&NHX:TOL=54916],cephalops pallidipleura[&&NHX:TOL=54917],cephalops pallidivittipes[&&NHX:TOL=54918],cephalops pedernalensis[&&NHX:TOL=54919],cephalops pendleburyi[&&NHX:TOL=54920],cephalops perpaucus[&&NHX:TOL=54921],cephalops philippinensis[&&NHX:TOL=54922],cephalops ponti[&&NHX:TOL=54923],cephalops pulvillatus[&&NHX:TOL=54924],cephalops quasilubuti[&&NHX:TOL=54925],cephalops robustus[&&NHX:TOL=54926],cephalops talyshensis[&&NHX:TOL=54927],cephalops tibetanus[&&NHX:TOL=54928],cephalops turkmenorum[&&NHX:TOL=54929],cephalops validus[&&NHX:TOL=54930],cephalops villifemoralis[&&NHX:TOL=54931],cephalops villosiscutum[&&NHX:TOL=54932],cephalops vinnulus[&&NHX:TOL=54933],cephalops vittipes[&&NHX:TOL=54934],cephalops zululandicus[&&NHX:TOL=54935])cephalops cephalops[&&NHX:TOL=54869],(cephalops obtusinervis[&&NHX:TOL=54937],cephalops taiwanensis[&&NHX:TOL=54938])cephalops parabeckerias[&&NHX:TOL=54936],(cephalops acklandi[&&NHX:TOL=54940],cephalops acrothrix[&&NHX:TOL=54941],cephalops alienus[&&NHX:TOL=54942],cephalops amplus[&&NHX:TOL=54943],cephalops apletomeris[&&NHX:TOL=54944],cephalops ariadneae[&&NHX:TOL=54945],cephalops bellulus[&&NHX:TOL=54946],cephalops bicuspidis[&&NHX:TOL=54947],cephalops bifidus[&&NHX:TOL=54948],cephalops canutifrons[&&NHX:TOL=54949],cephalops carinatus[&&NHX:TOL=54950],cephalops cautus[&&NHX:TOL=54951],cephalops chauliosternum[&&NHX:TOL=54952],cephalops cornutus[&&NHX:TOL=54953],cephalops curvarmatus[&&NHX:TOL=54954],cephalops delomeris[&&NHX:TOL=54955],cephalops digitatus[&&NHX:TOL=54956],cephalops emeljanovi[&&NHX:TOL=54957],cephalops eufraternus[&&NHX:TOL=54958],cephalops euryhymenos[&&NHX:TOL=54959],cephalops extimus[&&NHX:TOL=54960],cephalops filicicola[&&NHX:TOL=54961],cephalops fraternus[&&NHX:TOL=54962],cephalops gnomus[&&NHX:TOL=54963],cephalops grandimembranus[&&NHX:TOL=54964],cephalops haleakalaae[&&NHX:TOL=54965],cephalops hardyi[&&NHX:TOL=54966],cephalops hawaiiensis[&&NHX:TOL=54967],cephalops holomelas[&&NHX:TOL=54968],cephalops injectivus[&&NHX:TOL=54969],cephalops inpaganus[&&NHX:TOL=54970],cephalops juvator[&&NHX:TOL=54971],cephalops juvencus[&&NHX:TOL=54972],cephalops laterisutilis[&&NHX:TOL=54973],cephalops libidinosus[&&NHX:TOL=54974],cephalops longiductulis[&&NHX:TOL=54975],cephalops longisetosus[&&NHX:TOL=54976],cephalops lucidus[&&NHX:TOL=54977],cephalops macrothrix[&&NHX:TOL=54978],cephalops magnimembrus[&&NHX:TOL=54979],cephalops mainensis[&&NHX:TOL=54980],cephalops megameris[&&NHX:TOL=54981],cephalops molokaiensis[&&NHX:TOL=54982],cephalops navus[&&NHX:TOL=54983],cephalops nigrotarsatus[&&NHX:TOL=54984],cephalops oahuensis[&&NHX:TOL=54985],cephalops obscuratus[&&NHX:TOL=54986],cephalops obstipus[&&NHX:TOL=54987],cephalops orestes[&&NHX:TOL=54988],cephalops paganus[&&NHX:TOL=54989],cephalops palawanensis[&&NHX:TOL=54990],cephalops pallipes[&&NHX:TOL=54991],cephalops papuaensis[&&NHX:TOL=54992],cephalops parmatus[&&NHX:TOL=54993],cephalops pauculus[&&NHX:TOL=54994],cephalops penepauculus[&&NHX:TOL=54995],cephalops penultimus[&&NHX:TOL=54996],cephalops perkinsiellae[&&NHX:TOL=54997],cephalops perspicuus[&&NHX:TOL=54998],cephalops phaethus[&&NHX:TOL=54999],cephalops proditus[&&NHX:TOL=55000],cephalops rotundipennis[&&NHX:TOL=55001],cephalops ruandensis[&&NHX:TOL=55002],cephalops saegeri[&&NHX:TOL=55003],cephalops sectus[&&NHX:TOL=55004],cephalops semifumosus[&&NHX:TOL=55005],cephalops shikotanicus[&&NHX:TOL=55006],cephalops signatus[&&NHX:TOL=55007],cephalops straminipes[&&NHX:TOL=55008],cephalops subultimus[&&NHX:TOL=55009],cephalops swezeyi[&&NHX:TOL=55010],cephalops terraereginensis[&&NHX:TOL=55011],cephalops terryi[&&NHX:TOL=55012],cephalops timberlakei[&&NHX:TOL=55013],cephalops titanus[&&NHX:TOL=55014],cephalops trichostylis[&&NHX:TOL=55015],cephalops ugandensis[&&NHX:TOL=55016],cephalops ultimus[&&NHX:TOL=55017],cephalops uluhe[&&NHX:TOL=55018],cephalops varius[&&NHX:TOL=55019],cephalops visendus[&&NHX:TOL=55020],cephalops xanthocnemis[&&NHX:TOL=55021])cephalops semicephalops[&&NHX:TOL=54939],cephalops artifrons[&&NHX:TOL=55023],cephalops buclavus[&&NHX:TOL=55024],cephalops chandiensis[&&NHX:TOL=55025],cephalops crassispinus[&&NHX:TOL=55026],cephalops excellens[&&NHX:TOL=55027],cephalops flavocinctus[&&NHX:TOL=55028],cephalops gansuensis[&&NHX:TOL=55029],cephalops gracilentus[&&NHX:TOL=55030],cephalops hirtifemurus[&&NHX:TOL=55031],cephalops incohatus[&&NHX:TOL=55032],cephalops kashmerensis[&&NHX:TOL=55033],cephalops kumaonensis[&&NHX:TOL=55034],cephalops kumatai[&&NHX:TOL=55035],cephalops longicaudus[&&NHX:TOL=55036],cephalops longistigmatis[&&NHX:TOL=55037],cephalops mashobraensis[&&NHX:TOL=55038],cephalops metallicus[&&NHX:TOL=55039],cephalops nigronitens[&&NHX:TOL=55040],cephalops orbiculatus[&&NHX:TOL=55041],cephalops seminitidus[&&NHX:TOL=55042],cephalops shanghaiensis[&&NHX:TOL=55043],cephalops shisanlingensis[&&NHX:TOL=55044],cephalops splendens[&&NHX:TOL=55045],cephalops yoshiyasui[&&NHX:TOL=55046])cephalops[&&NHX:TOL=54644],((cephalosphaera acuminata[&&NHX:TOL=55048],cephalosphaera appendiculata[&&NHX:TOL=55049],cephalosphaera fairchildi[&&NHX:TOL=55050],cephalosphaera furcata[&&NHX:TOL=55051],cephalosphaera germanica[&&NHX:TOL=55052],cephalosphaera guanacastensis[&&NHX:TOL=55053],cephalosphaera gymne[&&NHX:TOL=55054],cephalosphaera hirashimai[&&NHX:TOL=55055],cephalosphaera incomitata[&&NHX:TOL=55056],cephalosphaera insularis[&&NHX:TOL=55057],cephalosphaera inusitata[&&NHX:TOL=55058],cephalosphaera macroctenia[&&NHX:TOL=55059],cephalosphaera magnispinosa[&&NHX:TOL=55060],cephalosphaera mocaensis[&&NHX:TOL=55061],cephalosphaera pacaraima[&&NHX:TOL=55062],cephalosphaera panamaensis[&&NHX:TOL=55063],cephalosphaera prionotaina[&&NHX:TOL=55064],cephalosphaera procera[&&NHX:TOL=55065],cephalosphaera reducta[&&NHX:TOL=55066],cephalosphaera sapporoensis[&&NHX:TOL=55067],cephalosphaera tingens[&&NHX:TOL=55068],cephalosphaera xanthosternum[&&NHX:TOL=55069],cephalosphaera zumbadoi[&&NHX:TOL=55070])cephalosphaera cephalosphaera[&&NHX:TOL=55047],(cephalosphaera aequatorialis[&&NHX:TOL=55072],cephalosphaera arnaudi[&&NHX:TOL=55073],cephalosphaera biscaynei[&&NHX:TOL=55074],cephalosphaera boutropis[&&NHX:TOL=55075],cephalosphaera brevis[&&NHX:TOL=55076],cephalosphaera collarti[&&NHX:TOL=55077],cephalosphaera cristata[&&NHX:TOL=55078],cephalosphaera eukrenaina[&&NHX:TOL=55079],cephalosphaera filicera[&&NHX:TOL=55080],cephalosphaera jamaicensis[&&NHX:TOL=55081],cephalosphaera maxima[&&NHX:TOL=55082],cephalosphaera miriamae[&&NHX:TOL=55083],cephalosphaera pallidifemoralis[&&NHX:TOL=55084],cephalosphaera parthenopipis[&&NHX:TOL=55085],cephalosphaera patula[&&NHX:TOL=55086],cephalosphaera petila[&&NHX:TOL=55087],cephalosphaera santiagoensis[&&NHX:TOL=55088],cephalosphaera semispiralis[&&NHX:TOL=55089],cephalosphaera sylvana[&&NHX:TOL=55090],cephalosphaera vietnamensis[&&NHX:TOL=55091],cephalosphaera wauensis[&&NHX:TOL=55092])cephalosphaera neocephalosphaera[&&NHX:TOL=55071],cephalosphaera amboinalis[&&NHX:TOL=55094],cephalosphaera baltica[&&NHX:EXT=Y:TOL=55095],cephalosphaera hikosanus[&&NHX:TOL=55096],cephalosphaera honshuensis[&&NHX:TOL=55097],cephalosphaera immodica[&&NHX:TOL=55098],cephalosphaera kasparjani[&&NHX:TOL=55099],cephalosphaera motichoorensis[&&NHX:TOL=55100],cephalosphaera prolata[&&NHX:TOL=55101],cephalosphaera redunca[&&NHX:TOL=55102])cephalosphaera[&&NHX:TOL=54645])cephalopsini[&&NHX:TOL=54643],(((collinias fulvicaudus[&&NHX:TOL=54675],collinias heterostigmus[&&NHX:TOL=54676],collinias imparilis[&&NHX:TOL=54677],collinias leechi[&&NHX:TOL=54678],collinias limitaris[&&NHX:TOL=54679],collinias vitiensis[&&NHX:TOL=54680],collinias croceus[&&NHX:TOL=128351],collinias dolabratus[&&NHX:TOL=128352],collinias schlingeri[&&NHX:TOL=128353])collinias[&&NHX:TOL=54648],(microcephalops adunatus[&&NHX:TOL=55103],microcephalops angustifacies[&&NHX:TOL=55104],microcephalops anthracias[&&NHX:TOL=55105],microcephalops banksi[&&NHX:TOL=55106],microcephalops borneensis[&&NHX:TOL=55107],microcephalops brevicornis[&&NHX:TOL=55108],microcephalops conspectus[&&NHX:TOL=55109],microcephalops damasi[&&NHX:TOL=55110],microcephalops dolosus[&&NHX:TOL=55111],microcephalops exsertus[&&NHX:TOL=55112],microcephalops fimbriatus[&&NHX:TOL=55113],microcephalops floridae[&&NHX:TOL=55114],microcephalops griseus[&&NHX:TOL=55115],microcephalops homoeophanes[&&NHX:TOL=55116],microcephalops inermus[&&NHX:TOL=55117],microcephalops kurseongeniensis[&&NHX:TOL=55118],microcephalops latifrons[&&NHX:TOL=55119],microcephalops microdes[&&NHX:TOL=55120],microcephalops minisculus[&&NHX:TOL=55121],microcephalops montanus[&&NHX:TOL=55122],microcephalops mutuus[&&NHX:TOL=55123],microcephalops opacus[&&NHX:TOL=55124],microcephalops parafloridae[&&NHX:TOL=55125],microcephalops ravilateralis[&&NHX:TOL=55126],microcephalops rufopictus[&&NHX:TOL=55127],microcephalops spenceri[&&NHX:TOL=55128],microcephalops stenopsis[&&NHX:TOL=55129],microcephalops subaeneus[&&NHX:TOL=55130],microcephalops subdolosus[&&NHX:TOL=55131],microcephalops transversalis[&&NHX:TOL=55132],microcephalops williamsi[&&NHX:TOL=55133])microcephalops[&&NHX:TOL=54649])microcephalopsini[&&NHX:TOL=54647],((((eudorylas abdominalis[&&NHX:TOL=55568],eudorylas aberratus[&&NHX:TOL=55569],eudorylas ablus[&&NHX:TOL=55570],eudorylas abnorexitus[&&NHX:TOL=55571],eudorylas abnormalis[&&NHX:TOL=55572],eudorylas abruptus[&&NHX:TOL=55573],eudorylas absonditus[&&NHX:TOL=55574],eudorylas accedens[&&NHX:TOL=55575],eudorylas acroacanthus[&&NHX:TOL=55576],eudorylas acroapex[&&NHX:TOL=55577],eudorylas aculeatus[&&NHX:TOL=55578],eudorylas adunatus[&&NHX:TOL=55579],eudorylas aduncus[&&NHX:TOL=55580],eudorylas aemulus[&&NHX:TOL=55581],eudorylas aequus[&&NHX:TOL=55582],eudorylas aethiopicus[&&NHX:TOL=55583],eudorylas affinis[&&NHX:TOL=55584],eudorylas albinervis[&&NHX:TOL=55585],eudorylas albucus[&&NHX:TOL=55586],eudorylas alternatus[&&NHX:TOL=55587],eudorylas amanii[&&NHX:TOL=55588],eudorylas amitinus[&&NHX:TOL=55589],eudorylas amurensis[&&NHX:TOL=55590],eudorylas amuscarium[&&NHX:TOL=55591],eudorylas anaclastus[&&NHX:TOL=55592],eudorylas andinus[&&NHX:TOL=55593],eudorylas anfractus[&&NHX:TOL=55594],eudorylas angustimembranus[&&NHX:TOL=55595],eudorylas angustipennis[&&NHX:TOL=55596],eudorylas angustus[&&NHX:TOL=55597],eudorylas anomalus[&&NHX:TOL=55598],eudorylas antennalis[&&NHX:TOL=55599],eudorylas antillensis[&&NHX:TOL=55600],eudorylas apicalis[&&NHX:TOL=55601],eudorylas apiculatus[&&NHX:TOL=55602],eudorylas appendiculatus[&&NHX:TOL=55603],eudorylas aptus[&&NHX:TOL=55604],eudorylas aquavicinus[&&NHX:TOL=55605],eudorylas aquinoi[&&NHX:TOL=55606],eudorylas arcanus[&&NHX:TOL=55607],eudorylas arthurianus[&&NHX:TOL=55608],eudorylas arundani[&&NHX:TOL=55609],eudorylas arvazensis[&&NHX:TOL=55610],eudorylas ascitus[&&NHX:TOL=55611],eudorylas ashoroensis[&&NHX:TOL=55612],eudorylas atratus[&&NHX:TOL=55613],eudorylas attenuatus[&&NHX:TOL=55614],eudorylas auctus[&&NHX:TOL=55615],eudorylas barkalovi[&&NHX:TOL=55616],eudorylas barrettoi[&&NHX:TOL=55617],eudorylas bartaki[&&NHX:TOL=55618],eudorylas barueriensis[&&NHX:TOL=55619],eudorylas beckeri[&&NHX:TOL=55620],eudorylas beiyue[&&NHX:TOL=55621],eudorylas bentoni[&&NHX:TOL=55622],eudorylas bermeri[&&NHX:TOL=55623],eudorylas bharatiensis[&&NHX:TOL=55624],eudorylas bicolor[&&NHX:TOL=55625],eudorylas bicostalis[&&NHX:TOL=55626],eudorylas bidactylus[&&NHX:TOL=55627],eudorylas bilobus[&&NHX:TOL=55628],eudorylas bipertitus[&&NHX:TOL=55629],eudorylas biroi[&&NHX:TOL=55630],eudorylas bisetosus[&&NHX:TOL=55631],eudorylas blascoi[&&NHX:TOL=55632],eudorylas boliviensis[&&NHX:TOL=55633],eudorylas bredoi[&&NHX:TOL=55634],eudorylas brevisalus[&&NHX:TOL=55635],eudorylas brunnipennis[&&NHX:TOL=55636],eudorylas bulbosus[&&NHX:TOL=55637],eudorylas burmanicus[&&NHX:TOL=55638],eudorylas buscki[&&NHX:TOL=55639],eudorylas caccabatus[&&NHX:TOL=55640],eudorylas caledonicus[&&NHX:TOL=55641],eudorylas carpathicus[&&NHX:TOL=55642],eudorylas caudatus[&&NHX:TOL=55643],eudorylas cernuus[&&NHX:TOL=55644],eudorylas chilensis[&&NHX:TOL=55645],eudorylas chvalai[&&NHX:TOL=55646],eudorylas ciliatus[&&NHX:TOL=55647],eudorylas cinerascens[&&NHX:TOL=55648],eudorylas clausum[&&NHX:TOL=55649],eudorylas coei[&&NHX:TOL=55650],eudorylas collinus[&&NHX:TOL=55651],eudorylas coloratus[&&NHX:TOL=55652],eudorylas comparatus[&&NHX:TOL=55653],eudorylas concavus[&&NHX:TOL=55654],eudorylas concolor[&&NHX:TOL=55655],eudorylas conformis[&&NHX:TOL=55656],eudorylas consimilis[&&NHX:TOL=55657],eudorylas corbetti[&&NHX:TOL=55658],eudorylas cordatus[&&NHX:TOL=55659],eudorylas cornutus[&&NHX:TOL=55660],eudorylas costalis[&&NHX:TOL=55661],eudorylas cralimes[&&NHX:TOL=55662],eudorylas crassus[&&NHX:TOL=55663],eudorylas cressoni[&&NHX:TOL=55664],eudorylas cupreiventris[&&NHX:TOL=55665],eudorylas curtus[&&NHX:TOL=55666],eudorylas curvatus[&&NHX:TOL=55667],eudorylas curvicaudatus[&&NHX:TOL=55668],eudorylas cuspicornis[&&NHX:TOL=55669],eudorylas cycnus[&&NHX:TOL=55670],eudorylas dactylus[&&NHX:TOL=55671],eudorylas deansi[&&NHX:TOL=55672],eudorylas deceptor[&&NHX:TOL=55673],eudorylas decorus[&&NHX:TOL=55674],eudorylas definitus[&&NHX:TOL=55675],eudorylas delfinadoae[&&NHX:TOL=55676],eudorylas denotatus[&&NHX:TOL=55677],eudorylas devius[&&NHX:TOL=55678],eudorylas dextratus[&&NHX:TOL=55679],eudorylas dextrostylus[&&NHX:TOL=55680],eudorylas diagonalis[&&NHX:TOL=55681],eudorylas dichopticus[&&NHX:TOL=55682],eudorylas digitatus[&&NHX:TOL=55683],eudorylas discretus[&&NHX:TOL=55684],eudorylas disgregus[&&NHX:TOL=55685],eudorylas diversus[&&NHX:TOL=55686],eudorylas dives[&&NHX:TOL=55687],eudorylas dominicanensis[&&NHX:TOL=55688],eudorylas dominicensis[&&NHX:TOL=55689],eudorylas dorsispinosus[&&NHX:TOL=55690],eudorylas dreisbachi[&&NHX:TOL=55691],eudorylas duckei[&&NHX:TOL=55692],eudorylas dumicolus[&&NHX:TOL=55693],eudorylas duocollis[&&NHX:TOL=55694],eudorylas duplicatus[&&NHX:TOL=55695],eudorylas echinatus[&&NHX:TOL=55696],eudorylas elephas[&&NHX:TOL=55697],eudorylas encerus[&&NHX:TOL=55698],eudorylas ephippium[&&NHX:TOL=55699],eudorylas eremitus[&&NHX:TOL=55700],eudorylas eremnoptera[&&NHX:TOL=55701],eudorylas euciliatus[&&NHX:TOL=55702],eudorylas eulentiger[&&NHX:TOL=55703],eudorylas evanidus[&&NHX:TOL=55704],eudorylas excisus[&&NHX:TOL=55705],eudorylas expletirubus[&&NHX:TOL=55706],eudorylas extensus[&&NHX:TOL=55707],eudorylas facetus[&&NHX:TOL=55708],eudorylas falcatus[&&NHX:TOL=55709],eudorylas falcifer[&&NHX:TOL=55710],eudorylas falx[&&NHX:TOL=55711],eudorylas fascipes[&&NHX:TOL=55712],eudorylas filicornis[&&NHX:TOL=55713],eudorylas flavicornis[&&NHX:TOL=55714],eudorylas flavicrus[&&NHX:TOL=55715],eudorylas flavitarsis[&&NHX:TOL=55716],eudorylas flavitibia[&&NHX:TOL=55717],eudorylas flexus[&&NHX:TOL=55718],eudorylas fluviatilis[&&NHX:TOL=55719],eudorylas focus[&&NHX:TOL=55720],eudorylas fortis[&&NHX:TOL=55721],eudorylas fractus[&&NHX:TOL=55722],eudorylas fritzi[&&NHX:TOL=55723],eudorylas fukushimaensis[&&NHX:TOL=55724],eudorylas fumipennis[&&NHX:TOL=55725],eudorylas furvulus[&&NHX:TOL=55726],eudorylas fuscipennis[&&NHX:TOL=55727],eudorylas fuscipes[&&NHX:TOL=55728],eudorylas fuscitarsis[&&NHX:TOL=55729],eudorylas fuscitibia[&&NHX:TOL=55730],eudorylas fusculus[&&NHX:TOL=55731],eudorylas fustis[&&NHX:TOL=55732],eudorylas galeatus[&&NHX:TOL=55733],eudorylas garambensis[&&NHX:TOL=55734],eudorylas garhwalensis[&&NHX:TOL=55735],eudorylas gemellus[&&NHX:TOL=55736],eudorylas ghesquierei[&&NHX:TOL=55737],eudorylas gilvipes[&&NHX:TOL=55738],eudorylas globosus[&&NHX:TOL=55739],eudorylas goennersdorfensis[&&NHX:TOL=55740],eudorylas golbachi[&&NHX:TOL=55741],eudorylas gomesi[&&NHX:TOL=55742],eudorylas gorodkovi[&&NHX:TOL=55743],eudorylas grandis[&&NHX:TOL=55744],eudorylas gratiosus[&&NHX:TOL=55745],eudorylas gressitti[&&NHX:TOL=55746],eudorylas hadrosoma[&&NHX:TOL=55747],eudorylas hamatus[&&NHX:TOL=55748],eudorylas hardyi[&&NHX:TOL=55749],eudorylas harmstoni[&&NHX:TOL=55750],eudorylas harrisi[&&NHX:TOL=55751],eudorylas hasanicus[&&NHX:TOL=55752],eudorylas hokkaidoensis[&&NHX:TOL=55753],eudorylas huachucanus[&&NHX:TOL=55754],eudorylas hystricosus[&&NHX:TOL=55755],eudorylas ibericus[&&NHX:TOL=55756],eudorylas imbricatus[&&NHX:TOL=55757],eudorylas incisus[&&NHX:TOL=55758],eudorylas indiaensis[&&NHX:TOL=55759],eudorylas indivisus[&&NHX:TOL=55760],eudorylas inferus[&&NHX:TOL=55761],eudorylas inopsicolor[&&NHX:TOL=55762],eudorylas inornatus[&&NHX:TOL=55763],eudorylas insignis[&&NHX:TOL=55764],eudorylas jacksoni[&&NHX:TOL=55765],eudorylas jakuticus[&&NHX:TOL=55766],eudorylas javanensis[&&NHX:TOL=55767],eudorylas jenkinsoni[&&NHX:TOL=55768],eudorylas jesoensis[&&NHX:TOL=55769],eudorylas johnenae[&&NHX:TOL=55770],eudorylas kansensis[&&NHX:TOL=55771],eudorylas kaszabi[&&NHX:TOL=55772],eudorylas kataplisso[&&NHX:TOL=55773],eudorylas katonae[&&NHX:TOL=55774],eudorylas kerzhneri[&&NHX:TOL=55775],eudorylas khaziarensis[&&NHX:TOL=55776],eudorylas kondarensis[&&NHX:TOL=55777],eudorylas kovaljovi[&&NHX:TOL=55778],eudorylas kowarzi[&&NHX:TOL=55779],eudorylas kozaneki[&&NHX:TOL=55780],eudorylas lamellatus[&&NHX:TOL=55781],eudorylas largexitus[&&NHX:TOL=55782],eudorylas lasiofemoratus[&&NHX:TOL=55783],eudorylas latipennis[&&NHX:TOL=55784],eudorylas latistomachus[&&NHX:TOL=55785],eudorylas lautus[&&NHX:TOL=55786],eudorylas lentiger[&&NHX:TOL=55787],eudorylas lepus[&&NHX:TOL=55788],eudorylas liberia[&&NHX:TOL=55789],eudorylas libratus[&&NHX:TOL=55790],eudorylas ligo[&&NHX:TOL=55791],eudorylas lividus[&&NHX:TOL=55792],eudorylas loewii[&&NHX:TOL=55793],eudorylas longicornis[&&NHX:TOL=55794],eudorylas longifrons[&&NHX:TOL=55795],eudorylas longipilus[&&NHX:TOL=55796],eudorylas longispinus[&&NHX:TOL=55797],eudorylas longistigmus[&&NHX:TOL=55798],eudorylas longus[&&NHX:TOL=55799],eudorylas lopesi[&&NHX:TOL=55800],eudorylas ludhianaensis[&&NHX:TOL=55801],eudorylas luteipes[&&NHX:TOL=55802],eudorylas luteiventris[&&NHX:TOL=55803],eudorylas luteolus[&&NHX:TOL=55804],eudorylas luteopilus[&&NHX:TOL=55805],eudorylas macrocercus[&&NHX:TOL=55806],eudorylas major[&&NHX:TOL=55807],eudorylas malaisei[&&NHX:TOL=55808],eudorylas maleficus[&&NHX:TOL=55809],eudorylas mallee[&&NHX:TOL=55810],eudorylas manaliensis[&&NHX:TOL=55811],eudorylas maurus[&&NHX:TOL=55812],eudorylas mediterraneus[&&NHX:TOL=55813],eudorylas megacanthus[&&NHX:TOL=55814],eudorylas megacephalus[&&NHX:TOL=55815],eudorylas megasurstylus[&&NHX:TOL=55816],eudorylas melanotrichus[&&NHX:TOL=55817],eudorylas meniscatus[&&NHX:TOL=55818],eudorylas meristus[&&NHX:TOL=55819],eudorylas meruensis[&&NHX:TOL=55820],eudorylas mexicanus[&&NHX:TOL=55821],eudorylas michiganensis[&&NHX:TOL=55822],eudorylas mikenensis[&&NHX:TOL=55823],eudorylas minghlanii[&&NHX:TOL=55824],eudorylas minor[&&NHX:TOL=55825],eudorylas minutus[&&NHX:TOL=55826],eudorylas minymerus[&&NHX:TOL=55827],eudorylas misericors[&&NHX:TOL=55828],eudorylas modestus[&&NHX:TOL=55829],eudorylas modicus[&&NHX:TOL=55830],eudorylas moffattensis[&&NHX:TOL=55831],eudorylas monegrensis[&&NHX:TOL=55832],eudorylas mongolorum[&&NHX:TOL=55833],eudorylas montanus[&&NHX:TOL=55834],eudorylas montium[&&NHX:TOL=55835],eudorylas moragai[&&NHX:TOL=55836],eudorylas muiri[&&NHX:TOL=55837],eudorylas mutillatus[&&NHX:TOL=55838],eudorylas nasus[&&NHX:TOL=55839],eudorylas natalensis[&&NHX:TOL=55840],eudorylas nataliae[&&NHX:TOL=55841],eudorylas neimongolanus[&&NHX:TOL=55842],eudorylas nemoralis[&&NHX:TOL=55843],eudorylas nevadaensis[&&NHX:TOL=55844],eudorylas nigellus[&&NHX:TOL=55845],eudorylas nigripes[&&NHX:TOL=55846],eudorylas ningxiaensis[&&NHX:TOL=55847],eudorylas nomurai[&&NHX:TOL=55848],eudorylas nudus[&&NHX:TOL=55849],eudorylas obliquus[&&NHX:TOL=55850],eudorylas obscurus[&&NHX:TOL=55851],eudorylas occultus[&&NHX:TOL=55852],eudorylas ocularis[&&NHX:TOL=55853],eudorylas odontophorus[&&NHX:TOL=55854],eudorylas okalii[&&NHX:TOL=55855],eudorylas opinatus[&&NHX:TOL=55856],eudorylas opiparus[&&NHX:TOL=55857],eudorylas optabilis[&&NHX:TOL=55858],eudorylas orthogoninus[&&NHX:TOL=55859],eudorylas oscen[&&NHX:TOL=55860],eudorylas oshimaensis[&&NHX:TOL=55861],eudorylas oxianus[&&NHX:TOL=55862],eudorylas pachymerus[&&NHX:TOL=55863],eudorylas pallidiventris[&&NHX:TOL=55864],eudorylas pamirorum[&&NHX:TOL=55865],eudorylas pannonicus[&&NHX:TOL=55866],eudorylas paraappendiculatus[&&NHX:TOL=55867],eudorylas paranaensis[&&NHX:TOL=55868],eudorylas pardus[&&NHX:TOL=55869],eudorylas parens[&&NHX:TOL=55870],eudorylas parilis[&&NHX:TOL=55871],eudorylas partitus[&&NHX:TOL=55872],eudorylas parvifrons[&&NHX:TOL=55873],eudorylas parvulus[&&NHX:TOL=55874],eudorylas pectitibialis[&&NHX:TOL=55875],eudorylas penai[&&NHX:TOL=55876],eudorylas pennatus[&&NHX:TOL=55877],eudorylas peruensis[&&NHX:TOL=55878],eudorylas petalus[&&NHX:TOL=55879],eudorylas phallophylax[&&NHX:TOL=55880],eudorylas phatnomus[&&NHX:TOL=55881],eudorylas pilosus[&&NHX:TOL=55882],eudorylas pinjorensis[&&NHX:TOL=55883],eudorylas pinquis[&&NHX:TOL=55884],eudorylas piriformis[&&NHX:TOL=55885],eudorylas platytarsis[&&NHX:TOL=55886],eudorylas poantaensis[&&NHX:TOL=55887],eudorylas pondolandi[&&NHX:TOL=55888],eudorylas porrectus[&&NHX:TOL=55889],eudorylas posticus[&&NHX:TOL=55890],eudorylas productus[&&NHX:TOL=55891],eudorylas pusillus[&&NHX:TOL=55892],eudorylas quadratus[&&NHX:TOL=55893],eudorylas quadrifidus[&&NHX:TOL=55894],eudorylas quartarius[&&NHX:TOL=55895],eudorylas quinquepertitus[&&NHX:TOL=55896],eudorylas rectinervis[&&NHX:TOL=55897],eudorylas regalis[&&NHX:TOL=55898],eudorylas remiformis[&&NHX:TOL=55899],eudorylas remotus[&&NHX:TOL=55900],eudorylas restrictus[&&NHX:TOL=55901],eudorylas revolutus[&&NHX:TOL=55902],eudorylas rubidus[&&NHX:TOL=55903],eudorylas rubrus[&&NHX:TOL=55904],eudorylas rudis[&&NHX:TOL=55905],eudorylas rurestris[&&NHX:TOL=55906],eudorylas rusticus[&&NHX:TOL=55907],eudorylas sabroskyi[&&NHX:TOL=55908],eudorylas sauteri[&&NHX:TOL=55909],eudorylas scharffi[&&NHX:TOL=55910],eudorylas schreiteri[&&NHX:TOL=55911],eudorylas scissus[&&NHX:TOL=55912],eudorylas scotinus[&&NHX:TOL=55913],eudorylas scutellatus[&&NHX:TOL=55914],eudorylas semiopacus[&&NHX:TOL=55915],eudorylas separatus[&&NHX:TOL=55916],eudorylas serratus[&&NHX:TOL=55917],eudorylas setiformis[&&NHX:TOL=55918],eudorylas sherloukensis[&&NHX:TOL=55919],eudorylas similis[&&NHX:TOL=55920],eudorylas simulator[&&NHX:TOL=55921],eudorylas sinuosus[&&NHX:TOL=55922],eudorylas slovacus[&&NHX:TOL=55923],eudorylas soccatus[&&NHX:TOL=55924],eudorylas souzalopesi[&&NHX:TOL=55925],eudorylas spinosus[&&NHX:TOL=55926],eudorylas stackelbergi[&&NHX:TOL=55927],eudorylas stainsi[&&NHX:TOL=55928],eudorylas stigmaticus[&&NHX:TOL=55929],eudorylas straeleni[&&NHX:TOL=55930],eudorylas subfascipes[&&NHX:TOL=55931],eudorylas subjectus[&&NHX:TOL=55932],eudorylas subligo[&&NHX:TOL=55933],eudorylas subopacus[&&NHX:TOL=55934],eudorylas subterminalis[&&NHX:TOL=55935],eudorylas subvaralis[&&NHX:TOL=55936],eudorylas sulcatus[&&NHX:TOL=55937],eudorylas suwai[&&NHX:TOL=55938],eudorylas swanengi[&&NHX:TOL=55939],eudorylas tadzhikorum[&&NHX:TOL=55940],eudorylas tanasijtshuki[&&NHX:TOL=55941],eudorylas tanycerus[&&NHX:TOL=55942],eudorylas tanzaniensis[&&NHX:TOL=55943],eudorylas tarsalis[&&NHX:TOL=55944],eudorylas terminalis[&&NHX:TOL=55945],eudorylas terraboensis[&&NHX:TOL=55946],eudorylas thekkadiensis[&&NHX:TOL=55947],eudorylas tibiatus[&&NHX:TOL=55948],eudorylas titanus[&&NHX:TOL=55949],eudorylas totoflavus[&&NHX:TOL=55950],eudorylas trapezoides[&&NHX:TOL=55951],eudorylas triangularis[&&NHX:TOL=55952],eudorylas trigonus[&&NHX:TOL=55953],eudorylas tropidoapex[&&NHX:TOL=55954],eudorylas tshatkalensis[&&NHX:TOL=55955],eudorylas tshuki[&&NHX:TOL=55956],eudorylas tuberculatus[&&NHX:TOL=55957],eudorylas tucumanus[&&NHX:TOL=55958],eudorylas turneri[&&NHX:TOL=55959],eudorylas uki[&&NHX:TOL=55960],eudorylas umbrinus[&&NHX:TOL=55961],eudorylas unanimus[&&NHX:TOL=55962],eudorylas unicolor[&&NHX:TOL=55963],eudorylas venezuelensis[&&NHX:TOL=55964],eudorylas venturai[&&NHX:TOL=55965],eudorylas vicarius[&&NHX:TOL=55966],eudorylas vicinus[&&NHX:TOL=55967],eudorylas vidali[&&NHX:TOL=55968],eudorylas vierecki[&&NHX:TOL=55969],eudorylas vineti[&&NHX:TOL=55970],eudorylas vonderdunki[&&NHX:TOL=55971],eudorylas wahisi[&&NHX:TOL=55972],eudorylas willistoni[&&NHX:TOL=55973],eudorylas wittei[&&NHX:TOL=55974],eudorylas wygodzinskyi[&&NHX:TOL=55975],eudorylas youngi[&&NHX:TOL=55976],eudorylas yunnanensis[&&NHX:TOL=55977],eudorylas zaitzevi[&&NHX:TOL=55978],eudorylas zanclus[&&NHX:TOL=55979],eudorylas zermattensis[&&NHX:TOL=55980],eudorylas zonatus[&&NHX:TOL=55981],eudorylas zonellus[&&NHX:TOL=55982])eudorylas[&&NHX:TOL=54653],(clistoabdominalis ancylus[&&NHX:TOL=55983],clistoabdominalis angelikae[&&NHX:TOL=55984],clistoabdominalis beneficiens[&&NHX:TOL=55985],clistoabdominalis capillifascis[&&NHX:TOL=55986],clistoabdominalis carnatistylus[&&NHX:TOL=55987],clistoabdominalis collessi[&&NHX:TOL=55988],clistoabdominalis colophus[&&NHX:TOL=55989],clistoabdominalis condylostylus[&&NHX:TOL=55990],clistoabdominalis danielsi[&&NHX:TOL=55991],clistoabdominalis dasymelus[&&NHX:TOL=55992],clistoabdominalis digitatus[&&NHX:TOL=55993],clistoabdominalis dilatatus[&&NHX:TOL=55994],clistoabdominalis doczkali[&&NHX:TOL=55995],clistoabdominalis electus[&&NHX:TOL=55996],clistoabdominalis eutrichodes[&&NHX:TOL=55997],clistoabdominalis exallus[&&NHX:TOL=55998],clistoabdominalis gaban[&&NHX:TOL=55999],clistoabdominalis gremialis[&&NHX:TOL=56000],clistoabdominalis helluo[&&NHX:TOL=56001],clistoabdominalis imitator[&&NHX:TOL=56002],clistoabdominalis koebelei[&&NHX:TOL=56003],clistoabdominalis lambkinae[&&NHX:TOL=56004],clistoabdominalis lingulatus[&&NHX:TOL=56005],clistoabdominalis lomholdti[&&NHX:TOL=56006],clistoabdominalis macropygus[&&NHX:TOL=56007],clistoabdominalis mathiesoni[&&NHX:TOL=56008],clistoabdominalis monas[&&NHX:TOL=56009],clistoabdominalis nitidifrons[&&NHX:TOL=56010],clistoabdominalis nutatus[&&NHX:TOL=56011],clistoabdominalis octiparvus[&&NHX:TOL=56012],clistoabdominalis reipublicae[&&NHX:TOL=56013],clistoabdominalis roralis[&&NHX:TOL=56014],clistoabdominalis ruralis[&&NHX:TOL=56015],clistoabdominalis scalenus[&&NHX:TOL=56016],clistoabdominalis scintillatus[&&NHX:TOL=56017],clistoabdominalis sinaiensis[&&NHX:TOL=56018],clistoabdominalis spinitibialis[&&NHX:TOL=56019],clistoabdominalis subruralis[&&NHX:TOL=56020],clistoabdominalis tasmanicus[&&NHX:TOL=56021],clistoabdominalis tharra[&&NHX:TOL=56022],clistoabdominalis trochanteratus[&&NHX:TOL=56023],clistoabdominalis tumidus[&&NHX:TOL=56024],clistoabdominalis uniformis[&&NHX:TOL=56025],clistoabdominalis uzbekistanus[&&NHX:TOL=56026],clistoabdominalis yeatesi[&&NHX:TOL=56027])clistoabdominalis[&&NHX:TOL=54654])[&&NHX:TOL=54652],(((((claraeola adventitia[&&NHX:TOL=56028],claraeola agnosta[&&NHX:TOL=56029],claraeola alata[&&NHX:TOL=56030],claraeola amica[&&NHX:TOL=56031],claraeola anorhaebus[&&NHX:TOL=56032],claraeola celata[&&NHX:TOL=56033],claraeola clavata[&&NHX:TOL=56034],claraeola colossus[&&NHX:TOL=56035],claraeola conjuncta[&&NHX:TOL=56036],claraeola crassula[&&NHX:TOL=56037],claraeola cyclohirta[&&NHX:TOL=56038],claraeola cypriota[&&NHX:TOL=56039],claraeola discors[&&NHX:TOL=56040],claraeola erinys[&&NHX:TOL=56041],claraeola francoisi[&&NHX:TOL=56042],claraeola freyi[&&NHX:TOL=56043],claraeola gigantea[&&NHX:TOL=56044],claraeola gigas[&&NHX:TOL=56045],claraeola halterata[&&NHX:TOL=56046],claraeola koreana[&&NHX:TOL=56047],claraeola melanostola[&&NHX:TOL=56048],claraeola nigripennis[&&NHX:TOL=56049],claraeola oppleta[&&NHX:TOL=56050],claraeola palgongsana[&&NHX:TOL=56051],claraeola perpaucisquamosa[&&NHX:TOL=56052],claraeola robusta[&&NHX:TOL=56053],claraeola sicilis[&&NHX:TOL=56054],claraeola spargosis[&&NHX:TOL=56055],claraeola spinosa[&&NHX:TOL=56056],claraeola totoniger[&&NHX:TOL=56057],claraeola yingka[&&NHX:TOL=56058])claraeola[&&NHX:TOL=54659],(allomethus brimleyi[&&NHX:TOL=54681],allomethus catharinensis[&&NHX:TOL=54682],allomethus mysticus[&&NHX:TOL=54683],allomethus rotundicornis[&&NHX:TOL=54684],allomethus unicicolis[&&NHX:TOL=54685])allomethus[&&NHX:TOL=54660])[&&NHX:TOL=54658],(basileunculus aliciae[&&NHX:TOL=54686],(basileunculus interruptus[&&NHX:TOL=54687],basileunculus rex[&&NHX:TOL=54688])[&&NHX:TOL=56877])basileunculus[&&NHX:TOL=54661])[&&NHX:TOL=54657],((elmohardyia adunca[&&NHX:TOL=55493],elmohardyia amazona[&&NHX:TOL=55494],elmohardyia angustifrons[&&NHX:TOL=55495],elmohardyia aquinoi[&&NHX:TOL=55496],elmohardyia argentata[&&NHX:TOL=55497],elmohardyia argentocincta[&&NHX:TOL=55498],elmohardyia argyrogaster[&&NHX:TOL=55499],elmohardyia arnaudi[&&NHX:TOL=55500],elmohardyia arx[&&NHX:TOL=55501],elmohardyia atlantica[&&NHX:TOL=55502],elmohardyia bifida[&&NHX:TOL=55503],elmohardyia carrerai[&&NHX:TOL=55504],elmohardyia circulus[&&NHX:TOL=55505],elmohardyia concava[&&NHX:TOL=55506],elmohardyia conchulata[&&NHX:TOL=55507],elmohardyia congruens[&&NHX:TOL=55508],elmohardyia costaricana[&&NHX:TOL=55509],elmohardyia denigrata[&&NHX:TOL=55510],elmohardyia doelloi[&&NHX:TOL=55511],elmohardyia echinata[&&NHX:TOL=55512],elmohardyia eminula[&&NHX:TOL=55513],elmohardyia exserta[&&NHX:TOL=55514],elmohardyia galeata[&&NHX:TOL=55515],elmohardyia gowdeyi[&&NHX:TOL=55516],elmohardyia guimaraesi[&&NHX:TOL=55517],elmohardyia hispida[&&NHX:TOL=55518],elmohardyia immaculata[&&NHX:TOL=55519],elmohardyia inepta[&&NHX:TOL=55520],elmohardyia lanei[&&NHX:TOL=55521],elmohardyia lindneri[&&NHX:TOL=55522],elmohardyia maculata[&&NHX:TOL=55523],elmohardyia manaos[&&NHX:TOL=55524],elmohardyia merga[&&NHX:TOL=55525],elmohardyia oriximinaensis[&&NHX:TOL=55526],elmohardyia papaveroi[&&NHX:TOL=55527],elmohardyia parva[&&NHX:TOL=55528],elmohardyia praecipua[&&NHX:TOL=55529],elmohardyia replicata[&&NHX:TOL=55530],elmohardyia reversa[&&NHX:TOL=55531],elmohardyia roraimensis[&&NHX:TOL=55532],elmohardyia rosalyae[&&NHX:TOL=55533],elmohardyia scoliostylis[&&NHX:TOL=55534],elmohardyia spatulata[&&NHX:TOL=55535],elmohardyia spuria[&&NHX:TOL=55536],elmohardyia subnitella[&&NHX:TOL=55537],elmohardyia subtilis[&&NHX:TOL=55538],elmohardyia tingomariae[&&NHX:TOL=55539],elmohardyia tricuspis[&&NHX:TOL=55540],elmohardyia trinidadensis[&&NHX:TOL=55541],elmohardyia tuberosa[&&NHX:TOL=55542],elmohardyia valida[&&NHX:TOL=55543])elmohardyia[&&NHX:TOL=54663],(amazunculus besti[&&NHX:TOL=54689],amazunculus claripennis[&&NHX:TOL=54690],amazunculus corduligaster[&&NHX:TOL=138159],amazunculus deargentatus[&&NHX:TOL=138160],amazunculus duckei[&&NHX:TOL=138161],amazunculus platypodus[&&NHX:TOL=54691])amazunculus[&&NHX:TOL=54664])[&&NHX:TOL=54662])[&&NHX:TOL=54656],(dasydorylas australinus[&&NHX:TOL=56059],dasydorylas cinctus[&&NHX:TOL=56060],dasydorylas discoidalis[&&NHX:TOL=56061],dasydorylas dolichostigmus[&&NHX:TOL=56062],dasydorylas dorsalis[&&NHX:TOL=56063],dasydorylas eucalypti[&&NHX:TOL=56064],dasydorylas fallax[&&NHX:TOL=56065],dasydorylas filiformis[&&NHX:TOL=56066],dasydorylas gradus[&&NHX:TOL=56067],dasydorylas holosericeus[&&NHX:TOL=56068],dasydorylas horridus[&&NHX:TOL=56069],dasydorylas infissus[&&NHX:TOL=56070],dasydorylas lamellifer[&&NHX:TOL=56071],dasydorylas monothrix[&&NHX:TOL=56072],dasydorylas nigripedes[&&NHX:TOL=56073],dasydorylas orientalis[&&NHX:TOL=56074],dasydorylas quasidorsalis[&&NHX:TOL=56075],dasydorylas roseri[&&NHX:TOL=56076],dasydorylas setosilobus[&&NHX:TOL=56077],dasydorylas setosus[&&NHX:TOL=56078],dasydorylas sordidatus[&&NHX:TOL=56079])dasydorylas[&&NHX:TOL=54665])[&&NHX:TOL=54655])eudorylini[&&NHX:TOL=54651],((dorylomorpha laeta[&&NHX:TOL=55221],(dorylomorpha abdoflavus[&&NHX:TOL=55135],dorylomorpha burmanica[&&NHX:TOL=55136],dorylomorpha flavoscutellaris[&&NHX:TOL=55137],dorylomorpha indica[&&NHX:TOL=55138],dorylomorpha kambaitiensis[&&NHX:TOL=55139],dorylomorpha latifrons[&&NHX:TOL=55140],dorylomorpha malaisei[&&NHX:TOL=55141],dorylomorpha orientalis[&&NHX:TOL=55142],dorylomorpha similis[&&NHX:TOL=55143],dorylomorpha translucens[&&NHX:TOL=55144])dorylomorpha dorylomima[&&NHX:TOL=55134],((dorylomorpha abdochaetus[&&NHX:TOL=55167],dorylomorpha alaskensis[&&NHX:TOL=55168],dorylomorpha appendiculata[&&NHX:TOL=55169],dorylomorpha beckeri[&&NHX:TOL=55170],dorylomorpha caudelli[&&NHX:TOL=55171],dorylomorpha dispar[&&NHX:TOL=55172],dorylomorpha exilis[&&NHX:TOL=55173],dorylomorpha incognita[&&NHX:TOL=55174],dorylomorpha shatalkini[&&NHX:TOL=55175],dorylomorpha simplex[&&NHX:TOL=55176],dorylomorpha sinensis[&&NHX:TOL=55177],dorylomorpha tanasijtshuki[&&NHX:TOL=55178],dorylomorpha xanthocera[&&NHX:TOL=55179])dorylomorpha dorylomyia[&&NHX:TOL=55166],((dorylomorpha borealis[&&NHX:TOL=55216],dorylomorpha lenkoi[&&NHX:TOL=55217],dorylomorpha maculata[&&NHX:TOL=55218],dorylomorpha montivaga[&&NHX:TOL=55219],dorylomorpha reveloi[&&NHX:TOL=55220])dorylomorpha pipunculina[&&NHX:TOL=55215],((dorylomorpha aberrans[&&NHX:TOL=55146],dorylomorpha aczeli[&&NHX:TOL=55147],dorylomorpha amurensis[&&NHX:TOL=55148],dorylomorpha asiatica[&&NHX:TOL=55149],dorylomorpha atramontensis[&&NHX:TOL=55150],dorylomorpha confracta[&&NHX:TOL=55151],dorylomorpha confusa[&&NHX:TOL=55152],dorylomorpha extricata[&&NHX:TOL=55153],dorylomorpha extricatoides[&&NHX:TOL=55154],dorylomorpha imparata[&&NHX:TOL=55155],dorylomorpha improvisa[&&NHX:TOL=55156],dorylomorpha insulana[&&NHX:TOL=55157],dorylomorpha kurodakensis[&&NHX:TOL=55158],dorylomorpha neglecta[&&NHX:TOL=55159],dorylomorpha rectitermina[&&NHX:TOL=55160],dorylomorpha rufipes[&&NHX:TOL=55161],dorylomorpha spinosa[&&NHX:TOL=55162],dorylomorpha spinulosa[&&NHX:TOL=55163],dorylomorpha stenozona[&&NHX:TOL=55164],dorylomorpha valida[&&NHX:TOL=55165])dorylomorpha dorylomorpha[&&NHX:TOL=55145],(dorylomorpha albitarsis[&&NHX:TOL=55181],dorylomorpha albrechti[&&NHX:TOL=55182],dorylomorpha anderssoni[&&NHX:TOL=55183],dorylomorpha canadensis[&&NHX:TOL=55184],dorylomorpha clavata[&&NHX:TOL=55185],dorylomorpha clavifemora[&&NHX:TOL=55186],dorylomorpha clavipes[&&NHX:TOL=55187],dorylomorpha fennica[&&NHX:TOL=55188],dorylomorpha flavolateralis[&&NHX:TOL=55189],dorylomorpha flavomaculata[&&NHX:TOL=55190],dorylomorpha fulvitarsis[&&NHX:TOL=55191],dorylomorpha hackmani[&&NHX:TOL=55192],dorylomorpha haemorrhoidalis[&&NHX:TOL=55193],dorylomorpha hardyi[&&NHX:TOL=55194],dorylomorpha hungarica[&&NHX:TOL=55195],dorylomorpha infirmata[&&NHX:TOL=55196],dorylomorpha karelica[&&NHX:TOL=55197],dorylomorpha koreana[&&NHX:TOL=55198],dorylomorpha kuznetzovi[&&NHX:TOL=55199],dorylomorpha laticlavia[&&NHX:TOL=55200],dorylomorpha lautereri[&&NHX:TOL=55201],dorylomorpha mongolorum[&&NHX:TOL=55202],dorylomorpha occidens[&&NHX:TOL=55203],dorylomorpha onegensis[&&NHX:TOL=55204],dorylomorpha platystylis[&&NHX:TOL=55205],dorylomorpha praetermissa[&&NHX:TOL=55206],dorylomorpha sachalinensis[&&NHX:TOL=55207],dorylomorpha semiclavata[&&NHX:TOL=55208],dorylomorpha subclavata[&&NHX:TOL=55209],dorylomorpha tridentata[&&NHX:TOL=55210],dorylomorpha ussuriana[&&NHX:TOL=55211],dorylomorpha xanthopus[&&NHX:TOL=55212],dorylomorpha yamagishii[&&NHX:TOL=55213],dorylomorpha yanoi[&&NHX:TOL=55214])dorylomorpha dorylomyza[&&NHX:TOL=55180])[&&NHX:TOL=56876])[&&NHX:TOL=56875])[&&NHX:TOL=56874])dorylomorpha[&&NHX:TOL=54667],(tomosvaryella aegyptium[&&NHX:TOL=55222],tomosvaryella aeneiventris[&&NHX:TOL=55223],tomosvaryella africana[&&NHX:TOL=55224],tomosvaryella agnesea[&&NHX:TOL=55225],tomosvaryella albiseta[&&NHX:TOL=55226],tomosvaryella aliena[&&NHX:TOL=55227],tomosvaryella amazonensis[&&NHX:TOL=55228],tomosvaryella ancylostyla[&&NHX:TOL=55229],tomosvaryella angolensis[&&NHX:TOL=55230],tomosvaryella anomala[&&NHX:TOL=55231],tomosvaryella apicalis[&&NHX:TOL=55232],tomosvaryella appendipes[&&NHX:TOL=55233],tomosvaryella argentea[&&NHX:TOL=55234],tomosvaryella argenteiventris[&&NHX:TOL=55235],tomosvaryella argentifrons[&&NHX:TOL=55236],tomosvaryella argentosa[&&NHX:TOL=55237],tomosvaryella arguta[&&NHX:TOL=55238],tomosvaryella argyrata[&&NHX:TOL=55239],tomosvaryella argyratoides[&&NHX:TOL=55240],tomosvaryella armata[&&NHX:TOL=55241],tomosvaryella aurata[&&NHX:TOL=55242],tomosvaryella baderiensis[&&NHX:TOL=55243],tomosvaryella basalis[&&NHX:TOL=55244],tomosvaryella beameri[&&NHX:TOL=55245],tomosvaryella bidens[&&NHX:TOL=55246],tomosvaryella bissulca[&&NHX:TOL=55247],tomosvaryella botswanae[&&NHX:TOL=55248],tomosvaryella brachybasis[&&NHX:TOL=55249],tomosvaryella brachyscolops[&&NHX:TOL=55250],tomosvaryella brevidens[&&NHX:TOL=55251],tomosvaryella brevijuncta[&&NHX:TOL=55252],tomosvaryella bulganensis[&&NHX:TOL=55253],tomosvaryella caerulescens[&&NHX:TOL=55254],tomosvaryella cagiae[&&NHX:TOL=128354],tomosvaryella calcarata[&&NHX:TOL=55255],tomosvaryella caligata[&&NHX:TOL=55256],tomosvaryella chilensis[&&NHX:TOL=55257],tomosvaryella cilifemorata[&&NHX:TOL=55258],tomosvaryella cilifera[&&NHX:TOL=55259],tomosvaryella cilitarsis[&&NHX:TOL=55260],tomosvaryella claripennis[&&NHX:TOL=55261],tomosvaryella columbiana[&&NHX:TOL=55262],tomosvaryella comaousa[&&NHX:TOL=55263],tomosvaryella concavifronta[&&NHX:TOL=55264],tomosvaryella congoana[&&NHX:TOL=55265],tomosvaryella contorta[&&NHX:TOL=55266],tomosvaryella coquilletti[&&NHX:TOL=55267],tomosvaryella cornuta[&&NHX:TOL=55268],tomosvaryella corusca[&&NHX:TOL=128356],tomosvaryella crassifemorata[&&NHX:TOL=55269],tomosvaryella crinita[&&NHX:TOL=55270],tomosvaryella curta[&&NHX:TOL=55271],tomosvaryella curtissima[&&NHX:TOL=55272],tomosvaryella curvipatis[&&NHX:TOL=55273],tomosvaryella debruyni[&&NHX:TOL=55274],tomosvaryella deformis[&&NHX:TOL=55275],tomosvaryella dehraduniensis[&&NHX:TOL=55276],tomosvaryella demeyeri[&&NHX:TOL=55277],tomosvaryella denticulata[&&NHX:TOL=55278],tomosvaryella dentiterebra[&&NHX:TOL=55279],tomosvaryella deserticola[&&NHX:TOL=55280],tomosvaryella diffusa[&&NHX:TOL=55281],tomosvaryella disjuncta[&&NHX:TOL=55282],tomosvaryella dissimilis[&&NHX:TOL=55283],tomosvaryella dividua[&&NHX:TOL=55284],tomosvaryella docta[&&NHX:TOL=55285],tomosvaryella dongyue[&&NHX:TOL=55286],tomosvaryella ekyphysis[&&NHX:TOL=55287],tomosvaryella epichalca[&&NHX:TOL=55288],tomosvaryella equistylis[&&NHX:TOL=55289],tomosvaryella eusylvatica[&&NHX:TOL=55290],tomosvaryella exilidens[&&NHX:TOL=55291],tomosvaryella falkovitshi[&&NHX:TOL=55292],tomosvaryella femella[&&NHX:TOL=55293],tomosvaryella flavicrus[&&NHX:TOL=55294],tomosvaryella flavipes[&&NHX:TOL=55295],tomosvaryella flexa[&&NHX:TOL=55296],tomosvaryella floridensis[&&NHX:TOL=55297],tomosvaryella forchhammeri[&&NHX:TOL=55298],tomosvaryella forter[&&NHX:TOL=55299],tomosvaryella freidbergi[&&NHX:TOL=55300],tomosvaryella frontata[&&NHX:TOL=55301],tomosvaryella galapagensis[&&NHX:TOL=55302],tomosvaryella gazliensis[&&NHX:TOL=55303],tomosvaryella geniculata[&&NHX:TOL=55304],tomosvaryella genitalis[&&NHX:TOL=55305],tomosvaryella gibbosa[&&NHX:TOL=55306],tomosvaryella gobiensis[&&NHX:TOL=55307],tomosvaryella gussakovskyi[&&NHX:TOL=55308],tomosvaryella guwahatiensis[&&NHX:TOL=55309],tomosvaryella hactena[&&NHX:TOL=55310],tomosvaryella helwanensis[&&NHX:TOL=55311],tomosvaryella hildeae[&&NHX:TOL=55312],tomosvaryella hirticollis[&&NHX:TOL=55313],tomosvaryella hispanica[&&NHX:TOL=55314],tomosvaryella hissarica[&&NHX:TOL=55315],tomosvaryella hongorica[&&NHX:TOL=55316],tomosvaryella hortobagyiensis[&&NHX:TOL=55317],tomosvaryella hozretishiensis[&&NHX:TOL=55318],tomosvaryella immutata[&&NHX:TOL=55319],tomosvaryella inazumae[&&NHX:TOL=55320],tomosvaryella incompta[&&NHX:TOL=55321],tomosvaryella incondita[&&NHX:TOL=55322],tomosvaryella inconspicua[&&NHX:TOL=55323],tomosvaryella indica[&&NHX:TOL=55324],tomosvaryella inermis[&&NHX:TOL=55325],tomosvaryella inopinata[&&NHX:TOL=55326],tomosvaryella insulicola[&&NHX:TOL=55327],tomosvaryella israelensis[&&NHX:TOL=55328],tomosvaryella itoi[&&NHX:TOL=55329],tomosvaryella jubata[&&NHX:TOL=55330],tomosvaryella kalevala[&&NHX:TOL=128355],tomosvaryella karakalaensis[&&NHX:TOL=55331],tomosvaryella kashipurensis[&&NHX:TOL=55332],tomosvaryella kirghizorum[&&NHX:TOL=55333],tomosvaryella kondarensis[&&NHX:TOL=55334],tomosvaryella kuthyi[&&NHX:TOL=55335],tomosvaryella lata[&&NHX:TOL=55336],tomosvaryella laticlavia[&&NHX:TOL=55337],tomosvaryella latitarsis[&&NHX:TOL=55338],tomosvaryella leimonias[&&NHX:TOL=55339],tomosvaryella lepidipes[&&NHX:TOL=55340],tomosvaryella leri[&&NHX:TOL=55341],tomosvaryella limpidipennis[&&NHX:TOL=55342],tomosvaryella littoralis[&&NHX:TOL=55343],tomosvaryella longipygiamis[&&NHX:TOL=55344],tomosvaryella longiseta[&&NHX:TOL=55345],tomosvaryella longistyla[&&NHX:TOL=55346],tomosvaryella longula[&&NHX:TOL=55347],tomosvaryella luppovae[&&NHX:TOL=55348],tomosvaryella lynchi[&&NHX:TOL=55349],tomosvaryella lyneborgi[&&NHX:TOL=55350],tomosvaryella manauensis[&&NHX:TOL=55352],tomosvaryella mbuyensis[&&NHX:TOL=55353],tomosvaryella mediocris[&&NHX:TOL=55354],tomosvaryella membranacea[&&NHX:TOL=55355],tomosvaryella membranosa[&&NHX:TOL=55356],tomosvaryella mesasiatica[&&NHX:TOL=55357],tomosvaryella mesostena[&&NHX:TOL=55358],tomosvaryella mexicanensis[&&NHX:TOL=55359],tomosvaryella micronesiae[&&NHX:TOL=55360],tomosvaryella mimica[&&NHX:TOL=55361],tomosvaryella minacis[&&NHX:TOL=55362],tomosvaryella minima[&&NHX:TOL=55363],tomosvaryella miniscula[&&NHX:TOL=55364],tomosvaryella minutus[&&NHX:TOL=55365],tomosvaryella moala[&&NHX:TOL=128357],tomosvaryella mongolica[&&NHX:TOL=55366],tomosvaryella montana[&&NHX:TOL=55367],tomosvaryella montina[&&NHX:TOL=55368],tomosvaryella multisetae[&&NHX:TOL=55369],tomosvaryella mutata[&&NHX:TOL=55370],tomosvaryella nalaihiana[&&NHX:TOL=55371],tomosvaryella nartshukae[&&NHX:TOL=55372],tomosvaryella nigra[&&NHX:TOL=55373],tomosvaryella nigritula[&&NHX:TOL=55374],tomosvaryella nigronitida[&&NHX:TOL=55375],tomosvaryella nitens[&&NHX:TOL=55376],tomosvaryella nodosa[&&NHX:TOL=55377],tomosvaryella novaezealandiae[&&NHX:TOL=55378],tomosvaryella nyctias[&&NHX:TOL=55379],tomosvaryella oligoseta[&&NHX:TOL=55380],tomosvaryella olympicola[&&NHX:TOL=55381],tomosvaryella ornatitarsalis[&&NHX:TOL=55382],tomosvaryella orthocladia[&&NHX:TOL=55383],tomosvaryella oryzaetora[&&NHX:TOL=55384],tomosvaryella palliditarsis[&&NHX:TOL=55385],tomosvaryella parakuthyi[&&NHX:TOL=55386],tomosvaryella parvicuspis[&&NHX:TOL=55387],tomosvaryella pauca[&&NHX:TOL=55388],tomosvaryella pectinalis[&&NHX:TOL=55389],tomosvaryella pennatula[&&NHX:TOL=55390],tomosvaryella perissosceles[&&NHX:TOL=55391],tomosvaryella pernitida[&&NHX:TOL=55392],tomosvaryella perpusilla[&&NHX:TOL=55393],tomosvaryella pilosiventris[&&NHX:TOL=55394],tomosvaryella platensis[&&NHX:TOL=55395],tomosvaryella polita[&&NHX:TOL=55396],tomosvaryella propinqua[&&NHX:TOL=55397],tomosvaryella propria[&&NHX:TOL=55398],tomosvaryella prostata[&&NHX:TOL=55399],tomosvaryella pruinosa[&&NHX:TOL=55400],tomosvaryella pseudophanes[&&NHX:TOL=55401],tomosvaryella pterae[&&NHX:TOL=55402],tomosvaryella pulchra[&&NHX:TOL=55403],tomosvaryella pusilla[&&NHX:TOL=55404],tomosvaryella quadradentis[&&NHX:TOL=55405],tomosvaryella ramnagariensis[&&NHX:TOL=55406],tomosvaryella relicta[&&NHX:TOL=55407],tomosvaryella resurgens[&&NHX:TOL=55408],tomosvaryella robusta[&&NHX:TOL=55409],tomosvaryella rossica[&&NHX:TOL=55410],tomosvaryella ruwenzoriensis[&&NHX:TOL=55411],tomosvaryella sachtlebeni[&&NHX:TOL=55412],tomosvaryella santiagoensis[&&NHX:TOL=55413],tomosvaryella scalprata[&&NHX:TOL=55414],tomosvaryella scopulata[&&NHX:TOL=55415],tomosvaryella sedomensis[&&NHX:TOL=55416],tomosvaryella sentis[&&NHX:TOL=55417],tomosvaryella sepulta[&&NHX:TOL=55418],tomosvaryella setositora[&&NHX:TOL=55419],tomosvaryella shaoshanensis[&&NHX:TOL=55420],tomosvaryella sigillata[&&NHX:TOL=55421],tomosvaryella similis[&&NHX:TOL=55422],tomosvaryella singalensis[&&NHX:TOL=55423],tomosvaryella singula[&&NHX:TOL=55424],tomosvaryella singularis[&&NHX:TOL=55425],tomosvaryella singuloides[&&NHX:TOL=55426],tomosvaryella songinoensis[&&NHX:TOL=55427],tomosvaryella sonorensis[&&NHX:TOL=55428],tomosvaryella spangleri[&&NHX:TOL=55429],tomosvaryella speciosa[&&NHX:TOL=55430],tomosvaryella spectata[&&NHX:TOL=55431],tomosvaryella spicata[&&NHX:TOL=55432],tomosvaryella spiculata[&&NHX:TOL=55433],tomosvaryella spinea[&&NHX:TOL=55434],tomosvaryella spinigera[&&NHX:TOL=55435],tomosvaryella spinosa[&&NHX:TOL=55436],tomosvaryella spinulenta[&&NHX:TOL=55437],tomosvaryella spinulifera[&&NHX:TOL=55438],tomosvaryella stackelbergi[&&NHX:TOL=55439],tomosvaryella subafricana[&&NHX:TOL=55440],tomosvaryella subhectena[&&NHX:TOL=55441],tomosvaryella subnitens[&&NHX:TOL=55442],tomosvaryella subrobusta[&&NHX:TOL=55443],tomosvaryella subvirescens[&&NHX:TOL=55444],tomosvaryella sugonjaevi[&&NHX:TOL=55445],tomosvaryella sumbarensis[&&NHX:TOL=55446],tomosvaryella surstylae[&&NHX:TOL=55447],tomosvaryella sylvatica[&&NHX:TOL=55448],tomosvaryella sylvaticoides[&&NHX:TOL=55449],tomosvaryella sylvicola[&&NHX:TOL=55450],tomosvaryella synadelpha[&&NHX:TOL=55451],tomosvaryella synadelphoides[&&NHX:TOL=55452],tomosvaryella tadzhikorum[&&NHX:TOL=55453],tomosvaryella talyshensis[&&NHX:TOL=55454],tomosvaryella tanaitidis[&&NHX:TOL=55455],tomosvaryella tanasijtshuki[&&NHX:TOL=55456],tomosvaryella tattapaniensis[&&NHX:TOL=55457],tomosvaryella taurica[&&NHX:TOL=55458],tomosvaryella tecta[&&NHX:TOL=55459],tomosvaryella teligera[&&NHX:TOL=55460],tomosvaryella tenebricosa[&&NHX:TOL=55461],tomosvaryella tenera[&&NHX:TOL=55462],tomosvaryella teneroidea[&&NHX:TOL=55463],tomosvaryella tenuata[&&NHX:TOL=55464],tomosvaryella torosa[&&NHX:TOL=55465],tomosvaryella toxodentis[&&NHX:TOL=55466],tomosvaryella translata[&&NHX:TOL=55467],tomosvaryella transvaalensis[&&NHX:TOL=55468],tomosvaryella trichotibialis[&&NHX:TOL=55469],tomosvaryella tridens[&&NHX:TOL=55470],tomosvaryella trigona[&&NHX:TOL=55471],tomosvaryella trjapitzini[&&NHX:TOL=55472],tomosvaryella troangulatus[&&NHX:TOL=55473],tomosvaryella trochanterata[&&NHX:TOL=55474],tomosvaryella trochantericola[&&NHX:TOL=55475],tomosvaryella tuberculata[&&NHX:TOL=55476],tomosvaryella turgayica[&&NHX:TOL=55477],tomosvaryella turgida[&&NHX:TOL=55478],tomosvaryella ubsunurensis[&&NHX:TOL=55479],tomosvaryella unguiculatus[&&NHX:TOL=55480],tomosvaryella urdaensis[&&NHX:TOL=55481],tomosvaryella urgamalensis[&&NHX:TOL=55482],tomosvaryella utahensis[&&NHX:TOL=55483],tomosvaryella vagabunda[&&NHX:TOL=55484],tomosvaryella venezuelana[&&NHX:TOL=55485],tomosvaryella verrucula[&&NHX:TOL=55486],tomosvaryella vicina[&&NHX:TOL=55487],tomosvaryella virlai[&&NHX:TOL=55488],tomosvaryella vittigera[&&NHX:TOL=55489],tomosvaryella wilburi[&&NHX:TOL=55490],tomosvaryella xerophila[&&NHX:TOL=55491],tomosvaryella zimini[&&NHX:TOL=55492])tomosvaryella[&&NHX:TOL=54668])tomosvaryellini[&&NHX:TOL=54666],claraeosphaera suranganiensis[&&NHX:TOL=54725])[&&NHX:TOL=54650])[&&NHX:TOL=54646])[&&NHX:TOL=54642])pipunculinae[&&NHX:TOL=54638])[&&NHX:TOL=54637],(dorylas africanus[&&NHX:TOL=55545],pipunculus albinus[&&NHX:TOL=55546],pipunculus annulifemur[&&NHX:TOL=55547],dorylas artus[&&NHX:TOL=55548],dorylas chiiensis[&&NHX:TOL=55549],pipunculus cinereoaeneus[&&NHX:TOL=55550],pipunculus depauperatus[&&NHX:TOL=55551],pipunculus flavicrus[&&NHX:TOL=55552],dorylas gracilis[&&NHX:TOL=55553],dorylas hakuensis[&&NHX:TOL=55554],pipunculus mirabilis[&&NHX:TOL=55555],dorylas oshimensis[&&NHX:TOL=55556],dorilas dorilas parvicornis[&&NHX:TOL=55557],pipunculus risbeci[&&NHX:TOL=55558],dorylas rokotensis[&&NHX:TOL=55559],dorylas santaroi[&&NHX:TOL=55560],dorylas yakuensis[&&NHX:TOL=55561])pipunculidae of uncertain placement[&&NHX:TOL=56871])pipunculidae[&&NHX:TOL=10524])syrphoidea[&&NHX:TOL=10522])aschiza[&&NHX:TOL=10512],(((((micropezidae[&&NHX:TOL=10622],(((clisa[&&NHX:TOL=118248],cypselosoma gephyrae[&&NHX:TOL=118249],(formicosepsis formicosepsis[&&NHX:TOL=121766],formicosepsis lycosepsis[&&NHX:TOL=121767])formicosepsis[&&NHX:TOL=118250],cypselosomatites succini[&&NHX:EXT=Y:TOL=118264])cypselosomatinae[&&NHX:TOL=119814],((heloclusia apops flavitarsis[&&NHX:TOL=118253],heloclusia heloclusia imperfecta[&&NHX:TOL=118254])heloclusia[&&NHX:TOL=118252],latheticomyia[&&NHX:TOL=118255],macalpinella brevifacies[&&NHX:TOL=118256],polypathomyia stackelbergi[&&NHX:TOL=118257],(pseudopomyza dete collessi[&&NHX:TOL=118259],pseudopomyza pseudopomyza[&&NHX:TOL=118260])pseudopomyza[&&NHX:TOL=118258],pseudopomyzella flava[&&NHX:TOL=118261],rhinopomyzella[&&NHX:TOL=118262],tenuia[&&NHX:TOL=118263])pseudopomyzinae[&&NHX:TOL=119815],eopseudopomyza kuehni[&&NHX:EXT=Y:TOL=118265])cypselosomatidae[&&NHX:TOL=10625],(antillonerius[&&NHX:TOL=118284],chaetonerius[&&NHX:TOL=118285],derocephalus angusticollis[&&NHX:TOL=118286],eoloxozus sabroskyi[&&NHX:TOL=118287],eoneria[&&NHX:TOL=118288],glyphidops[&&NHX:TOL=118289],gymnonerius[&&NHX:TOL=118290],longina[&&NHX:TOL=118291],loxozus clavicornis[&&NHX:TOL=118292],nerius[&&NHX:TOL=118293],nipponerius femoratus[&&NHX:TOL=118294],odontoloxozus[&&NHX:TOL=118295],paranerius[&&NHX:TOL=118296],protonerius[&&NHX:TOL=118297],stypocladius appendiculatus[&&NHX:TOL=118298],telostylinus[&&NHX:TOL=118299],telostylus[&&NHX:TOL=118300])neriidae[&&NHX:TOL=10624])[&&NHX:TOL=10623])nerioidea[&&NHX:TOL=10530],((tanypezidae[&&NHX:TOL=10592],(nartshukia[&&NHX:TOL=111255],strongylophthalmyia[&&NHX:TOL=111256])strongylophthalmyiidae[&&NHX:TOL=10593])[&&NHX:TOL=10591],(((somatia aestiva[&&NHX:TOL=52176],somatia australis[&&NHX:TOL=52177],somatia carrerai[&&NHX:TOL=52178],somatia lanei[&&NHX:TOL=52179],somatia papaveroi[&&NHX:TOL=52180],somatia schildi[&&NHX:TOL=52181],somatia sophiston[&&NHX:TOL=52182])somatia[&&NHX:TOL=10596],psilidae[&&NHX:TOL=10597])[&&NHX:TOL=10595],(nothybus[&&NHX:TOL=10599],(diopsidae[&&NHX:TOL=10604],(syringogaster[&&NHX:TOL=111261],(megamerina[&&NHX:TOL=111257],protexara[&&NHX:TOL=111258],texara[&&NHX:TOL=111259],palaeotanypeza[&&NHX:EXT=Y:TOL=111260])megamerinidae[&&NHX:TOL=10602])[&&NHX:TOL=10601])[&&NHX:TOL=10600])[&&NHX:TOL=10598])[&&NHX:TOL=10594],(gobrya bacchoides[&&NHX:TOL=111424],gobrya cyanea[&&NHX:TOL=111425],gobrya cylindrica[&&NHX:TOL=111426],gobrya simulans[&&NHX:TOL=111427],gobrya syrphoides[&&NHX:TOL=111428])gobrya[&&NHX:TOL=111263])diopsoidea[&&NHX:TOL=10531])[&&NHX:TOL=10529],(conopidae[&&NHX:TOL=10533],((dasiops[&&NHX:TOL=118108],((chaetolonchaea[&&NHX:TOL=118107],earomyia[&&NHX:TOL=118109],lamprolonchaea[&&NHX:TOL=118110],protearomyia[&&NHX:TOL=118113],silvestrodasiops[&&NHX:TOL=118116])earomyini[&&NHX:TOL=119807],(lonchaea[&&NHX:TOL=118111],neosilba[&&NHX:TOL=118112],setisquamalonchaea[&&NHX:TOL=118114],silba[&&NHX:TOL=118115])lonchaeini[&&NHX:TOL=119808])lonchaeinae[&&NHX:TOL=119806])lonchaeidae[&&NHX:TOL=10672],((ulidiidae[&&NHX:TOL=10675],((plastotepritinae[&&NHX:TOL=122397],platystomatinae[&&NHX:TOL=122410],scolastinae[&&NHX:TOL=122442],trapherinae[&&NHX:TOL=122452],angelopteromyia[&&NHX:TOL=122556],apiola[&&NHX:TOL=122557],prosthiochaeta[&&NHX:TOL=130002],steyskaliella[&&NHX:TOL=130003])platystomatidae[&&NHX:TOL=10677],((acropyrgota flavescens[&&NHX:TOL=130068],adapsilia[&&NHX:TOL=130069],adapsona[&&NHX:TOL=130070],apyrgota[&&NHX:TOL=130071],boreothrinax[&&NHX:TOL=130072],campylocera[&&NHX:TOL=130073],cardiacera[&&NHX:TOL=130074],carrerapyrgota[&&NHX:TOL=130075],clemaxia[&&NHX:TOL=130076],commoniella[&&NHX:TOL=130078],congopyrgota[&&NHX:TOL=130077],descoleia terestrura[&&NHX:TOL=130686],diasteneura[&&NHX:TOL=130079],epice[&&NHX:TOL=130081],epicerella[&&NHX:TOL=130687],eupyrgota[&&NHX:TOL=130688],eumorphomyia bistrigata[&&NHX:TOL=130689],euphya[&&NHX:TOL=130082],facilina[&&NHX:TOL=130083],frontalia[&&NHX:TOL=130084],geloemyia[&&NHX:TOL=130690],hendelpyrgota longicornis[&&NHX:TOL=130085],hypotyphla[&&NHX:TOL=130086],hypotyphlina[&&NHX:TOL=130087],idiopyrgota setiventris[&&NHX:TOL=130088],leptopyrgota[&&NHX:TOL=130089],lopadops nigerrimus[&&NHX:TOL=130691],lygiohypotyphla[&&NHX:TOL=130090],maenomenus ensifer[&&NHX:TOL=130091],metropina[&&NHX:TOL=130092],neotoxura[&&NHX:TOL=130093],nicholsonia curvinervis[&&NHX:TOL=130094],osa[&&NHX:TOL=130095],peltodasia[&&NHX:TOL=130096],platynostira turbata[&&NHX:TOL=130097],plectrobrachis filigena[&&NHX:TOL=130692],porpomastix fasciolata[&&NHX:TOL=130693],prodalmannia variabilis[&&NHX:TOL=130098],prohypotyphla[&&NHX:TOL=130099],pyrgota[&&NHX:TOL=130100],pyrgotella changnoni[&&NHX:TOL=130101],pyrgotina[&&NHX:TOL=130102],pyrgotomyia ciliata[&&NHX:TOL=130103],pyrgotosoma flavidum[&&NHX:TOL=130694],sinolochmostylia sinica[&&NHX:TOL=130104],siridapha[&&NHX:TOL=130105],sphecomyiella[&&NHX:TOL=130106],stenopyrgota[&&NHX:TOL=130695],stirothrinax[&&NHX:TOL=130696],taeniomastix[&&NHX:TOL=130697],tephritocampylocera[&&NHX:TOL=130108],tephritohypotyphla[&&NHX:TOL=130109],tephritopyrgota[&&NHX:TOL=130110],teretrura[&&NHX:TOL=130698],toxopyrgota inclinata[&&NHX:TOL=130111],toxura[&&NHX:TOL=130112],trichempodia[&&NHX:TOL=130113],trichopeltia penicillaticoxa[&&NHX:TOL=130699],tropidothrinax boliviensis[&&NHX:TOL=130700],tylotrypes immsi[&&NHX:TOL=130701])pyrgotidae[&&NHX:TOL=10681],(blepharoneurinae[&&NHX:TOL=118192],phytalmiinae[&&NHX:TOL=118193],tachiniscinae[&&NHX:TOL=119721],(dacinae[&&NHX:TOL=118195],tephritinae[&&NHX:TOL=118196],trypetinae[&&NHX:TOL=118197])[&&NHX:TOL=118194])tephritidae[&&NHX:TOL=10679])[&&NHX:TOL=10678])[&&NHX:TOL=10676])[&&NHX:TOL=10674],(((automola[&&NHX:TOL=113480],epiplatea[&&NHX:TOL=113481],omomyia[&&NHX:TOL=113482])epiplateinae[&&NHX:TOL=113479],(beebeomyia[&&NHX:TOL=113485],batrachophthalmum rufiventre[&&NHX:TOL=113486],cladiscophleps[&&NHX:TOL=113487],coilometopia[&&NHX:TOL=113488],coniceps niger[&&NHX:TOL=113489],euolena[&&NHX:TOL=113490],hemixantha[&&NHX:TOL=113491],johnrichardia vockerothi[&&NHX:TOL=113492],macrostenomyia guerinii[&&NHX:TOL=113493],maerorichardia lugubris[&&NHX:TOL=113494],megalothoraca[&&NHX:TOL=113495],melanoloma[&&NHX:TOL=113496],neoidiotypa appendiculata[&&NHX:TOL=113497],ocaenicia nasuta[&&NHX:TOL=113498],odontomera[&&NHX:TOL=113499],odontomerella oxyptera[&&NHX:TOL=113500],oedematella czernyi[&&NHX:TOL=113501],ozaenina[&&NHX:TOL=113502],paneryma elongata[&&NHX:TOL=113503],poecilomyia[&&NHX:TOL=113504],richardia[&&NHX:TOL=113505],richardiodes[&&NHX:TOL=113506],sepsisoma[&&NHX:TOL=113507],setellia[&&NHX:TOL=113483],setellida caerulescens[&&NHX:TOL=113508],spheneuolena[&&NHX:TOL=113509],syntaces apicalis[&&NHX:TOL=113510])richardiinae[&&NHX:TOL=113484],pachysomites inermis[&&NHX:EXT=Y:TOL=113511],stenomyites fuscipennis[&&NHX:EXT=Y:TOL=113512],urortalis caudatus[&&NHX:EXT=Y:TOL=113513])richardiidae[&&NHX:TOL=10684],((eurygnathomyia bicolor[&&NHX:TOL=117995],(gorbunia insularis[&&NHX:TOL=117996],aenigmatomyia[&&NHX:TOL=117994],heloparia[&&NHX:TOL=117997],homaroides spiniventris[&&NHX:TOL=117998],maorina[&&NHX:TOL=117999],morgea[&&NHX:TOL=118000],palloptera[&&NHX:TOL=118001],pseudopyrgota caudata[&&NHX:TOL=118002],sciochthis uniseta[&&NHX:TOL=118003],temnosira[&&NHX:TOL=118004],toxonevra[&&NHX:TOL=118005])pallopterinae[&&NHX:TOL=119811],glaesolonchaea electrica[&&NHX:EXT=Y:TOL=118006],pallopterites electrica[&&NHX:EXT=Y:TOL=118007])pallopteridae[&&NHX:TOL=10686],((actenoptera[&&NHX:TOL=111351],neottiophilum praeustum[&&NHX:TOL=111365])neottiophilinae[&&NHX:TOL=119812],(allopiophila[&&NHX:TOL=111352],amphipogon[&&NHX:TOL=111353],bocainamyia[&&NHX:TOL=111364],centrophlebomyia furcata[&&NHX:TOL=111367],dasyphlebomyia stylata[&&NHX:TOL=111354],lasiopiophila pilosa[&&NHX:TOL=111355],mycetaulus[&&NHX:TOL=111356],neopiophila[&&NHX:TOL=111357],piophila[&&NHX:TOL=111358],piophilosoma[&&NHX:TOL=111368],prochyliza[&&NHX:TOL=111359],protopiophila[&&NHX:TOL=111360],protothyreophora[&&NHX:TOL=111369],pseudoseps signata[&&NHX:TOL=111363],pygopiophila sikorae[&&NHX:TOL=111361],stearibia nigriceps[&&NHX:TOL=111362],thyreophora cynophila[&&NHX:TOL=111366])piophilinae[&&NHX:TOL=119813])piophilidae[&&NHX:TOL=10687])[&&NHX:TOL=10685])[&&NHX:TOL=10683])[&&NHX:TOL=10673])tephritoidea[&&NHX:TOL=10534])[&&NHX:TOL=10532],ctenostylidae[&&NHX:TOL=111264])[&&NHX:TOL=10528],(((((cremifania[&&NHX:TOL=112681],procremifania[&&NHX:EXT=Y:TOL=112683])cremifaniinae[&&NHX:TOL=112678],(acrometopia[&&NHX:TOL=112685],anochthiphila[&&NHX:TOL=112686],chaetoleucopis[&&NHX:TOL=112687],chamaemyia[&&NHX:TOL=112688],leucochthiphila[&&NHX:TOL=112689],melametopia[&&NHX:TOL=112690],melanochthiphila[&&NHX:TOL=112691],notochthiphila[&&NHX:TOL=112692],ortalidina[&&NHX:TOL=112693],parapamecia[&&NHX:TOL=112694],(parochthiphila euestelia[&&NHX:TOL=112696],parochthiphila parochthiphila[&&NHX:TOL=112697])parochthiphila [&&NHX:TOL=112695],plunomia[&&NHX:TOL=112698],pseudodinia[&&NHX:TOL=112699],pseudoleucopis[&&NHX:TOL=112700])chamaemyiinae[&&NHX:TOL=112679],(anchioleucopis[&&NHX:TOL=112701],echinoleucopis[&&NHX:TOL=112702],leucopina[&&NHX:TOL=112703],(leucopis indioleucopis[&&NHX:TOL=112705],leucopis leucopella[&&NHX:TOL=112706],leucopis leucopis[&&NHX:TOL=112707],leucopis metaleucopis[&&NHX:TOL=112708],leucopis xenoleucopis[&&NHX:TOL=112709])leucopis[&&NHX:TOL=112704],leucopomyia[&&NHX:TOL=112710],lipoleucopis[&&NHX:TOL=112711],melaleucopis[&&NHX:TOL=112712],neoleucopis[&&NHX:TOL=112713])leucopinae[&&NHX:TOL=112680])chamaemyiidae[&&NHX:TOL=10620],(((arnomyia[&&NHX:TOL=112718],australinina[&&NHX:TOL=112719],caeniamima[&&NHX:TOL=112720],cainohomoneura[&&NHX:TOL=112721],celyphohomoneura[&&NHX:TOL=112753],cephaloconus[&&NHX:TOL=112722],cestrotus[&&NHX:TOL=112723],dioides[&&NHX:TOL=112724],eucyclosis[&&NHX:TOL=112725],euprosopomyia[&&NHX:TOL=112726],(homoneura chaetohomoneura[&&NHX:TOL=112728],homoneura drosomyia[&&NHX:TOL=112729],homoneura euhomoneura[&&NHX:TOL=112730],homoneura homoneura[&&NHX:TOL=112731],homoneura minettioides[&&NHX:TOL=112732],homoneura neohomoneura[&&NHX:TOL=112733],homoneura solomonia[&&NHX:TOL=112734],homoneura tarsohomoneura[&&NHX:TOL=112735])homoneura[&&NHX:TOL=112727],katalauxania[&&NHX:TOL=112736],longifrons[&&NHX:TOL=112737],(phobeticomyia phobeticomyia[&&NHX:TOL=112739],phobeticomyia poecilomyza[&&NHX:TOL=112740])phobeticomyia[&&NHX:TOL=112738],poichilus[&&NHX:TOL=112741],procestrotus[&&NHX:TOL=112742],prosopomyia[&&NHX:TOL=112743],prosopophorella[&&NHX:TOL=112744],tanyura[&&NHX:TOL=112745],teratocranum[&&NHX:TOL=112746],(trypetisoma trypaneoides[&&NHX:TOL=112748],trypetisoma trypetisoma[&&NHX:TOL=112749])trypetisoma[&&NHX:TOL=112747],wawu[&&NHX:TOL=112750],xenohomoneura[&&NHX:TOL=112751],zanjensiella[&&NHX:TOL=112752])homoneurinae[&&NHX:TOL=112714],(afrominettia[&&NHX:TOL=112755],agriphoneura[&&NHX:TOL=112756],allogriphoneura[&&NHX:TOL=112757],allominettia[&&NHX:TOL=112758],amblada[&&NHX:TOL=112759],aprochaetops[&&NHX:TOL=112760],asilostoma[&&NHX:TOL=112761],aulogastromyia[&&NHX:TOL=112762],bacilloflagellomera[&&NHX:TOL=112763],baliopteridion[&&NHX:TOL=112764],blepharolauxania[&&NHX:TOL=112765],calliopum[&&NHX:TOL=112766],camptoprosopella[&&NHX:TOL=112767],celypholauxania[&&NHX:TOL=112768],cephalella[&&NHX:TOL=112769],cerataulina[&&NHX:TOL=112770],ceratolauxania[&&NHX:TOL=112771],chaetocoelia[&&NHX:TOL=112772],chaetolauxania[&&NHX:TOL=112773],chaetominettia[&&NHX:TOL=112774],chamaelauxania[&&NHX:EXT=Y:TOL=112775],chilocryptus[&&NHX:TOL=112776],cnemacantha[&&NHX:TOL=112777],deceia[&&NHX:TOL=112778],depressa[&&NHX:TOL=112779],deutominettia[&&NHX:TOL=112780],diplochasma[&&NHX:TOL=112781],drepanephora[&&NHX:TOL=112782],dryomyzoides[&&NHX:TOL=112783],dryomyzothea[&&NHX:TOL=112784],dryosapromyza[&&NHX:TOL=112785],dyticomyia[&&NHX:TOL=112786],eolausanites[&&NHX:EXT=Y:TOL=112787],eriurgus[&&NHX:TOL=112788],eusapromyza[&&NHX:TOL=112789],evertomyia[&&NHX:TOL=112790],floriminettia[&&NHX:TOL=112791],freyia[&&NHX:TOL=112792],gauzania[&&NHX:TOL=112793],gibbolauxania[&&NHX:TOL=112794],griphominettia[&&NHX:TOL=112795],griphoneura[&&NHX:TOL=112796],griphoneuroides[&&NHX:TOL=112797],haakonia[&&NHX:TOL=112798],hemilauxania[&&NHX:EXT=Y:TOL=112799],hendelimyza[&&NHX:TOL=112800],himantopyga[&&NHX:TOL=112801],hirtodeceia[&&NHX:TOL=112802],holopticander[&&NHX:TOL=112803],homoeominettia[&&NHX:TOL=112804],hypagoga[&&NHX:TOL=112805],incurviseta[&&NHX:TOL=112806],isoclusia[&&NHX:TOL=112807],itomyia[&&NHX:TOL=112808],kertesziella[&&NHX:TOL=112809],kerteszomyia[&&NHX:TOL=112810],kimiella[&&NHX:TOL=112811],(lauxania callixania[&&NHX:TOL=112813],lauxania czernushka[&&NHX:TOL=112814],lauxania lauxania[&&NHX:TOL=112815])lauxania[&&NHX:TOL=112812],lauxanostegana[&&NHX:TOL=112816],(luzonomyza luzonomyza[&&NHX:TOL=112818],luzonomyza tetroxyrhina[&&NHX:TOL=112819])luzonomyza[&&NHX:TOL=112817],lyciovibrissina[&&NHX:TOL=112820],lyperomyia[&&NHX:TOL=112821],mallochomyza[&&NHX:TOL=112822],maquilingia[&&NHX:TOL=112823],marmarodeceia[&&NHX:TOL=112824],(meiosimyza lyciella[&&NHX:TOL=112826],meiosimyza meiosimyza[&&NHX:TOL=112827],meiosimyza shatalkinia[&&NHX:TOL=112828])meiosimyza[&&NHX:TOL=112825],melanina[&&NHX:TOL=112829],(melanomyza lauxaniella[&&NHX:TOL=112831],melanomyza melanomyza[&&NHX:TOL=112832])melanomyza[&&NHX:TOL=112830],melanopachycerina[&&NHX:TOL=112833],melinomyia[&&NHX:TOL=112834],mettinia[&&NHX:TOL=112835],(minettia frendelia[&&NHX:TOL=112837],minettia minettia[&&NHX:TOL=112838],minettia minettiella[&&NHX:TOL=112839],minettia plesiominettia[&&NHX:TOL=112840])minettia[&&NHX:TOL=112836],minilauxania[&&NHX:TOL=112841],mycterella[&&NHX:TOL=112842],neodeceia[&&NHX:TOL=112843],neogeomyza[&&NHX:TOL=112844],neogriphoneura[&&NHX:TOL=112845],neominettia[&&NHX:TOL=112846],neopachycerina[&&NHX:TOL=112847],neoparoecus[&&NHX:TOL=112848],neotrigonometopus[&&NHX:TOL=112849],neoxangelina[&&NHX:TOL=112850],nimettia[&&NHX:TOL=112851],noeetomima[&&NHX:TOL=112852],noonamyia[&&NHX:TOL=112853],ocellominettia[&&NHX:TOL=112854],oncodometopus[&&NHX:TOL=112855],pachycerina[&&NHX:TOL=112856],pachyopella[&&NHX:TOL=112857],panurgopsis[&&NHX:TOL=112858],paracestrotus[&&NHX:TOL=112859],paralauxania[&&NHX:TOL=112860],paranomina[&&NHX:TOL=112861],parapachycerina[&&NHX:TOL=112862],paraphysoclypeus[&&NHX:TOL=112863],peplominettia[&&NHX:TOL=112864],peplomyza[&&NHX:TOL=112865],physegenua[&&NHX:TOL=112866],physoclypeus[&&NHX:TOL=112867],platygraphium[&&NHX:TOL=112868],pleurigona[&&NHX:TOL=112869],poecilohetaerella[&&NHX:TOL=112870],poecilohetaerus[&&NHX:TOL=112871],poecilolycia[&&NHX:TOL=112872],poecilominettia[&&NHX:TOL=112873],prochaetops[&&NHX:TOL=112874],(prochaetopsis prochaetopsis[&&NHX:TOL=112876],prochaetopsis pseudoprochaetops[&&NHX:TOL=112877])prochaetopsis[&&NHX:TOL=112875],procrita[&&NHX:TOL=112878],prorhaphochaeta[&&NHX:TOL=112879],prosamyza[&&NHX:TOL=112880],protrigonometopus[&&NHX:TOL=112881],pseudocalliope[&&NHX:TOL=112882],pseudogriphoneura[&&NHX:TOL=112883],pseudolyciella[&&NHX:TOL=112884],pseudominettia[&&NHX:TOL=112885],rhabdolauxania[&&NHX:TOL=112886],rhagadolyra[&&NHX:TOL=112887],ritaemyia[&&NHX:TOL=112888],salebrifacies[&&NHX:TOL=112889],(sapromyza nannomyza[&&NHX:TOL=112891],sapromyza notiosapromyza[&&NHX:TOL=112892],sapromyza sapromyza[&&NHX:TOL=112893],sapromyza sapromyzosoma[&&NHX:TOL=112894],sapromyza schumannimyia[&&NHX:TOL=112895],sapromyza xenosapromyza[&&NHX:TOL=112896])sapromyza[&&NHX:TOL=112890],sciasminettia[&&NHX:TOL=112897],sciasmomyia[&&NHX:TOL=112898],sciosapromyza[&&NHX:TOL=112899],scutolauxania[&&NHX:TOL=112900],scutominettia[&&NHX:TOL=112901],setulina[&&NHX:TOL=112902],siphonophysa[&&NHX:TOL=112903],spathecerus[&&NHX:TOL=112904],steganolauxania[&&NHX:TOL=112905],steganopsis[&&NHX:TOL=112906],stenolauxania[&&NHX:TOL=112907],tauridion[&&NHX:TOL=112908],teratolauxania[&&NHX:TOL=112909],tibiominettia[&&NHX:TOL=112910],tricholauxania[&&NHX:TOL=112911],triconopsis[&&NHX:TOL=112912],trigonometopsis[&&NHX:TOL=112913],trigonometopus[&&NHX:TOL=112914],trisapromyza[&&NHX:TOL=112915],trivialia[&&NHX:TOL=112916],xangelina[&&NHX:TOL=112917],xeniconeura[&&NHX:TOL=112918],xenochaetina[&&NHX:TOL=112919],xenopterella[&&NHX:TOL=112920])lauxaniinae[&&NHX:TOL=112715])lauxaniidae[&&NHX:TOL=10616],(eurychoromyia     [&&NHX:TOL=10618],(acelyphus[&&NHX:TOL=112669],(celyphus celyphus [&&NHX:TOL=112671],celyphus hemiglobus[&&NHX:TOL=112672],celyphus paracelyphus[&&NHX:TOL=112673])celyphus[&&NHX:TOL=112670],chamaecelyphus[&&NHX:TOL=112674],idiocelyphus[&&NHX:TOL=112675],oocelyphus[&&NHX:TOL=112676],spaniocelyphus[&&NHX:TOL=112677])celyphidae[&&NHX:TOL=10619])[&&NHX:TOL=10617])[&&NHX:TOL=10615])lauxanioidea[&&NHX:TOL=10537],((lopa convexa[&&NHX:TOL=108405],((((((gluma nitida[&&NHX:TOL=110495],gluma musgravei[&&NHX:TOL=110496])[&&NHX:TOL=110494],gluma keyzeri[&&NHX:TOL=110497])gluma[&&NHX:TOL=108410],dasycoelopa australis[&&NHX:TOL=108411],(chaetocoelopa littoralis[&&NHX:TOL=110498],chaetocoelopa sydneyensis[&&NHX:TOL=110499])chaetocoelopa[&&NHX:TOL=108412])[&&NHX:TOL=108409],malacomyia sciomyzina[&&NHX:TOL=108413],coelopina anomala[&&NHX:TOL=108414])glumini[&&NHX:TOL=108408],(coelopa pilipes[&&NHX:TOL=110500],(coelopa vanduzeei[&&NHX:TOL=110502],((coelopa ursina[&&NHX:TOL=110505],coelopa alluaudi[&&NHX:TOL=110506])[&&NHX:TOL=110504],(coelopa nebularum[&&NHX:TOL=110508],coelopa frigida[&&NHX:TOL=110509])[&&NHX:TOL=110507])[&&NHX:TOL=110503])[&&NHX:TOL=110501],coelopa aequatorialis[&&NHX:TOL=110510],coelopa dasypoda[&&NHX:TOL=110511],coelopa orientalis[&&NHX:TOL=110512],coelopa stejnegeri[&&NHX:TOL=110513])coelopa[&&NHX:TOL=108415])[&&NHX:TOL=108407],(((this canus[&&NHX:TOL=108419],amma blancheae[&&NHX:TOL=108420])[&&NHX:TOL=108418],(rhis whitleyi[&&NHX:TOL=108421],coelopella popeae[&&NHX:TOL=110515])[&&NHX:TOL=110514])[&&NHX:TOL=108417],(coelopella curvipes[&&NHX:TOL=110516],(gen. nov[&&NHX:TOL=108425],((baeopterus philpotti[&&NHX:TOL=110517],baeopterus robustus[&&NHX:TOL=110518])baeopterus[&&NHX:TOL=108427],(icaridion debile[&&NHX:TOL=110519],icaridion nasutum[&&NHX:TOL=110520],icaridion nigrifrons[&&NHX:TOL=110521])icaridion[&&NHX:TOL=108428])[&&NHX:TOL=108426])[&&NHX:TOL=108424])[&&NHX:TOL=108422])ammini  coelopellini[&&NHX:TOL=108416])coelopinae[&&NHX:TOL=108406])coelopidae[&&NHX:TOL=10652],(((dryomyza[&&NHX:TOL=118117],dryope[&&NHX:TOL=118118],oedoparena[&&NHX:TOL=118119],paradryomyza[&&NHX:TOL=118120],pseudoneuroctena senilis[&&NHX:TOL=118121],steyskalomyza hasegawai[&&NHX:TOL=118122],palaeotimia ihoesti[&&NHX:EXT=Y:TOL=118123],prodryomyza electrica[&&NHX:EXT=Y:TOL=118124])dryomyzidae[&&NHX:TOL=10655],(cobergius[&&NHX:TOL=118133],dasysciomyza[&&NHX:TOL=118134],eurotocus australis[&&NHX:TOL=118135],helosciomyza[&&NHX:TOL=118136],napaeosciomyza[&&NHX:TOL=118137],polytocus[&&NHX:TOL=118138],sciogriphoneura[&&NHX:TOL=118139],scordalus femorata[&&NHX:TOL=118140],xenosciomyza[&&NHX:TOL=118141])helosciomyzidae[&&NHX:TOL=10656],sciomyzidae[&&NHX:TOL=10657])[&&NHX:TOL=10654],((apophorhynchus[&&NHX:TOL=118125],dactylissa digiticornis[&&NHX:TOL=118126],kroeberia[&&NHX:TOL=118127],lenkokroeberia[&&NHX:TOL=118128],mexicoa mexicana[&&NHX:TOL=118129],rhytidops[&&NHX:TOL=118130],ropalomera[&&NHX:TOL=118131],willistoniella[&&NHX:TOL=118132])ropalomeridae[&&NHX:TOL=10659],sepsidae[&&NHX:TOL=10660])[&&NHX:TOL=10658])[&&NHX:TOL=10653],(helcomyza[&&NHX:TOL=111265],maorimyia bipunctata[&&NHX:TOL=111266],paractora[&&NHX:TOL=111267],sphyrnoceps brunneus[&&NHX:TOL=111268])helcomyzidae[&&NHX:TOL=108373],(heterocheila buccata[&&NHX:TOL=111465],heterocheila hannai[&&NHX:TOL=111466])heterocheila[&&NHX:TOL=108372],huttonina[&&NHX:TOL=108402],(pelidnoptera fuscipennis[&&NHX:TOL=111467],pelidnoptera leptiformis[&&NHX:TOL=111468],pelidnoptera nigripennis[&&NHX:TOL=111469])pelidnoptera[&&NHX:TOL=108374])sciomyzoidea[&&NHX:TOL=10538],natalimyza[&&NHX:TOL=110651])[&&NHX:TOL=10536],(((((((phylloclusia lanceola [&&NHX:TOL=88234],(phylloclusia hendeli [&&NHX:TOL=88236],(phylloclusia steleocera [&&NHX:TOL=88238],(phylloclusia quadrivittata [&&NHX:TOL=88240],(phylloclusia nigroscutellum [&&NHX:TOL=88242],phylloclusia darlingi [&&NHX:TOL=88243])[&&NHX:TOL=88241])[&&NHX:TOL=88239])[&&NHX:TOL=88237])[&&NHX:TOL=88235])phylloclusia[&&NHX:TOL=27671],(tetrameringia pubescens[&&NHX:TOL=52184],tetrameringia ustulata[&&NHX:TOL=52185],tetrameringia aethiopica[&&NHX:TOL=52186],tetrameringia distoma[&&NHX:TOL=52187],tetrameringia borealis[&&NHX:TOL=88244],tetrameringia stuckenbergi[&&NHX:TOL=88245])tetrameringia[&&NHX:TOL=27672])[&&NHX:TOL=27696],(((apiochaeta connexa[&&NHX:TOL=139638],apiochaeta aterrima[&&NHX:TOL=139639])[&&NHX:TOL=139637],(((((((((apiochaeta pictipennis[&&NHX:TOL=139649],apiochaeta dacryodes[&&NHX:TOL=139650],apiochaeta similis[&&NHX:TOL=139651])[&&NHX:TOL=139648],(apiochaeta chiloensis[&&NHX:TOL=139653],apiochaeta philippii[&&NHX:TOL=139654])[&&NHX:TOL=139652])[&&NHX:TOL=139647],apiochaeta vitticollis[&&NHX:TOL=139655])[&&NHX:TOL=139646],apiochaeta excepta[&&NHX:TOL=139656],apiochaeta mallochi[&&NHX:TOL=139657],apiochaeta lenticula[&&NHX:TOL=139658])[&&NHX:TOL=139645],apiochaeta varia[&&NHX:TOL=139659])[&&NHX:TOL=139644],apiochaeta furcillata[&&NHX:TOL=139660])[&&NHX:TOL=139643],apiochaeta costalis[&&NHX:TOL=139661])[&&NHX:TOL=139642],apiochaeta bicolor[&&NHX:TOL=139662])[&&NHX:TOL=139641],apiochaeta tincticornis[&&NHX:TOL=139663])[&&NHX:TOL=139640])apiochaeta[&&NHX:TOL=27673],((clusia ciliata[&&NHX:TOL=121246],clusia czernyi[&&NHX:TOL=121247],clusia flava[&&NHX:TOL=121248],clusia intermedialis[&&NHX:TOL=121249],clusia japonica[&&NHX:TOL=121250],clusia lateralis[&&NHX:TOL=121251],clusia nigromaculata[&&NHX:TOL=121252],clusia occidentalis[&&NHX:TOL=121253],clusia okadomei[&&NHX:TOL=121254],clusia omogensis[&&NHX:TOL=121255],clusia sexlineata[&&NHX:TOL=121256],clusia tigrina[&&NHX:TOL=121257],clusia unita[&&NHX:TOL=121258])clusia[&&NHX:TOL=27675],melanoclusia bivibrissa[&&NHX:TOL=67805])[&&NHX:TOL=67804])[&&NHX:TOL=27699])clusiinae[&&NHX:TOL=27700],((chaetoclusia richardfreyi[&&NHX:TOL=67582],(chaetoclusia sabroskyi[&&NHX:TOL=67584],chaetoclusia nigromaculata[&&NHX:TOL=67585],(chaetoclusia quadrivittata[&&NHX:TOL=67587],(((chaetoclusia inbionella[&&NHX:TOL=67591],chaetoclusia longifilata[&&NHX:TOL=67592])[&&NHX:TOL=67590],chaetoclusia amplipenis[&&NHX:TOL=67593])[&&NHX:TOL=67589],(chaetoclusia centrofasciata[&&NHX:TOL=67595],chaetoclusia bakeri[&&NHX:TOL=67596])[&&NHX:TOL=67594],(chaetoclusia transversa[&&NHX:TOL=67598],(chaetoclusia furva[&&NHX:TOL=67600],chaetoclusia flava[&&NHX:TOL=67601],chaetoclusia xanthops[&&NHX:TOL=67602])[&&NHX:TOL=67599])[&&NHX:TOL=67597])[&&NHX:TOL=67588])[&&NHX:TOL=67586])[&&NHX:TOL=67652])chaetoclusia[&&NHX:TOL=27679],((procerosoma prominens[&&NHX:TOL=52199],procerosoma alini[&&NHX:TOL=52200])procerosoma[&&NHX:TOL=27694],sobarocephala[&&NHX:TOL=27670])[&&NHX:TOL=27695])sobarocephalinae[&&NHX:TOL=27693],(allometopon[&&NHX:TOL=27680],(electroclusiodes meuneri[&&NHX:EXT=Y:TOL=52201],electroclusiodes radiospinosa[&&NHX:EXT=Y:TOL=52202])electroclusiodes[&&NHX:EXT=Y:TOL=27688],(((craspedochaeta phaios[&&NHX:TOL=67603],craspedochaeta concinna[&&NHX:TOL=67604],(craspedochaeta fascipennis[&&NHX:TOL=67606],(craspedochaeta zongo[&&NHX:TOL=67608],(craspedochaeta pullipleura[&&NHX:TOL=67610],((craspedochaeta xanthonotum[&&NHX:TOL=67613],craspedochaeta loreto[&&NHX:TOL=67614],craspedochaeta trivittata[&&NHX:TOL=67615])[&&NHX:TOL=67612],(craspedochaeta biloba[&&NHX:TOL=67617],craspedochaeta chauliodon[&&NHX:TOL=67618])[&&NHX:TOL=67616],craspedochaeta brunneivibrissa[&&NHX:TOL=67619],craspedochaeta basalis[&&NHX:TOL=67620],craspedochaeta annulipes[&&NHX:TOL=67621])[&&NHX:TOL=67611])[&&NHX:TOL=67609])[&&NHX:TOL=67607])[&&NHX:TOL=67605])craspedochaeta concinna group[&&NHX:TOL=52207],(craspedochaeta apsilutea[&&NHX:TOL=67622],(craspedochaeta nigrithorax[&&NHX:TOL=67624],(craspedochaeta protomis[&&NHX:TOL=67626],(craspedochaeta feminea[&&NHX:TOL=67628],(craspedochaeta ornata[&&NHX:TOL=67630],(craspedochaeta festiva[&&NHX:TOL=67632],craspedochaeta pacaraima[&&NHX:TOL=67633])[&&NHX:TOL=67631],((craspedochaeta amazonensis[&&NHX:TOL=67636],(craspedochaeta melanosoma[&&NHX:TOL=67638],craspedochaeta claripennis[&&NHX:TOL=67639])[&&NHX:TOL=67637])[&&NHX:TOL=67635],(craspedochaeta candida[&&NHX:TOL=67641],craspedochaeta chela[&&NHX:TOL=67642],(craspedochaeta transversa[&&NHX:TOL=67644],(craspedochaeta weemsi[&&NHX:TOL=67646],(craspedochaeta pleuralis[&&NHX:TOL=67648],craspedochaeta synneura[&&NHX:TOL=67649],craspedochaeta pollostos[&&NHX:TOL=67650])[&&NHX:TOL=67647])[&&NHX:TOL=67645])[&&NHX:TOL=67643])[&&NHX:TOL=67640])[&&NHX:TOL=67634])[&&NHX:TOL=67629])[&&NHX:TOL=67627])[&&NHX:TOL=67625])[&&NHX:TOL=67623])craspedochaeta transversa group[&&NHX:TOL=52208],craspedochaeta biseta group[&&NHX:TOL=52209],craspedochaeta boettcheri[&&NHX:TOL=67651])craspedochaeta[&&NHX:TOL=27681],(heteromeringia[&&NHX:TOL=27682],(hendelia[&&NHX:TOL=27685],(((((clusiodes caledonicus[&&NHX:TOL=139694],clusiodes gentilis[&&NHX:TOL=139695])[&&NHX:TOL=139693],(clusiodes verticalis[&&NHX:TOL=139697],clusiodes apiculatus[&&NHX:TOL=139698])[&&NHX:TOL=139696])[&&NHX:TOL=139692],clusiodes americanus[&&NHX:TOL=139699])[&&NHX:TOL=139691],((clusiodes leucopeza[&&NHX:TOL=139702],clusiodes discostylus[&&NHX:TOL=139703])[&&NHX:TOL=139701],((clusiodes johnsoni[&&NHX:TOL=139706],clusiodes microcerus[&&NHX:TOL=139707],clusiodes albimanus[&&NHX:TOL=139708])[&&NHX:TOL=139705],clusiodes niger[&&NHX:TOL=139709])[&&NHX:TOL=139704])[&&NHX:TOL=139700])[&&NHX:TOL=139690],((((((clusiodes terminalis[&&NHX:TOL=139716],clusiodes apicalis[&&NHX:TOL=139717],clusiodes ater[&&NHX:TOL=139718])[&&NHX:TOL=139715],clusiodes freyi[&&NHX:TOL=139719])[&&NHX:TOL=139714],clusiodes caestus[&&NHX:TOL=139720])[&&NHX:TOL=139713],(clusiodes orbitalis[&&NHX:TOL=139722],(clusiodes nitidus[&&NHX:TOL=139724],(clusiodes pictipes[&&NHX:TOL=139726],clusiodes geomyzinus[&&NHX:TOL=139727])[&&NHX:TOL=139725])[&&NHX:TOL=139723])[&&NHX:TOL=139721])[&&NHX:TOL=139712],clusiodes tuomikoskii[&&NHX:TOL=139728])[&&NHX:TOL=139711],((clusiodes tobi[&&NHX:TOL=139731],(clusiodes flaveolus[&&NHX:TOL=139733],clusiodes ruficollis[&&NHX:TOL=139734])[&&NHX:TOL=139732])[&&NHX:TOL=139730],((clusiodes coconino[&&NHX:TOL=139737],clusiodes eremnos[&&NHX:TOL=139738],clusiodes leptadodemus[&&NHX:TOL=139739])[&&NHX:TOL=139736],(clusiodes clandestinus[&&NHX:TOL=139741],clusiodes gracilolobus[&&NHX:TOL=139742],clusiodes spinos[&&NHX:TOL=139743])[&&NHX:TOL=139740],clusiodes melanostomus[&&NHX:TOL=139744])[&&NHX:TOL=139735])[&&NHX:TOL=139729])[&&NHX:TOL=139710])clusiodes[&&NHX:TOL=27684])[&&NHX:TOL=27690])[&&NHX:TOL=27691])[&&NHX:TOL=27692])clusiodinae[&&NHX:TOL=27669])clusiidae[&&NHX:TOL=10628],((((afrodinia[&&NHX:TOL=112923],neoalticomerus[&&NHX:TOL=112924],odinia[&&NHX:TOL=112925],protodinia[&&NHX:EXT=Y:TOL=112926],turanodinia[&&NHX:TOL=112927])odiniinae[&&NHX:TOL=112921],(helgreelia[&&NHX:TOL=112928],lopesiodinia[&&NHX:TOL=112929],neoschildomyia[&&NHX:TOL=112930],neotraginops[&&NHX:TOL=112931],paratraginops[&&NHX:TOL=112932],pradomyia[&&NHX:TOL=112933],schildomyia[&&NHX:TOL=112934],shewellia[&&NHX:TOL=112935],traginops[&&NHX:TOL=112936])traginopinae[&&NHX:TOL=112922])odiniidae[&&NHX:TOL=10632],(agromyzidae[&&NHX:TOL=10634],fergusonina[&&NHX:TOL=10635])[&&NHX:TOL=10633])[&&NHX:TOL=10631],((((amnonthomyza[&&NHX:TOL=117893],amygdalops[&&NHX:TOL=117894],anagnota[&&NHX:TOL=117895],anthomyza[&&NHX:TOL=117896],apterosepsis basilewskyi[&&NHX:TOL=117897],barbarista[&&NHX:TOL=117898],cercagnota collini[&&NHX:TOL=117899],chamaebosca[&&NHX:TOL=117900],epischnomyia triarmigera[&&NHX:TOL=117914],fungomyza[&&NHX:TOL=117915],ischnomyia[&&NHX:TOL=117901],margdalops[&&NHX:TOL=117916],mumetopia[&&NHX:TOL=117902],paranthomyza[&&NHX:TOL=117903],receptrixa receptrix[&&NHX:TOL=117917],santhomyza[&&NHX:TOL=117904],stiphrosoma[&&NHX:TOL=117905],typhamyza bifasciata[&&NHX:TOL=117906],zealantha thorpei[&&NHX:TOL=117907],grimalantha vulnerata[&&NHX:EXT=Y:TOL=117908])anthomyzinae[&&NHX:TOL=117892],protanthomyzinae[&&NHX:EXT=Y:TOL=117909])anthomyzidae[&&NHX:TOL=10639],(anomalochaeta guttipennis[&&NHX:TOL=111293],geomyza[&&NHX:TOL=111294],opomyza[&&NHX:TOL=111295],scelomyza hirticornis[&&NHX:TOL=111296])opomyzidae[&&NHX:TOL=10638])[&&NHX:TOL=10637],(((neurochaeta[&&NHX:TOL=111302],nothoasteia[&&NHX:TOL=111303],anthoclusia[&&NHX:EXT=Y:TOL=111304])neurochaetidae[&&NHX:TOL=10645],(((diopsosoma prima[&&NHX:TOL=118152],marbenia peculiaris[&&NHX:TOL=118162],neoscutops[&&NHX:TOL=118160],parascutops maculipennis[&&NHX:TOL=118161],(periscelis myodris[&&NHX:TOL=118156],periscelis notioscelis fasciata[&&NHX:TOL=118157],periscelis periscelis[&&NHX:TOL=118158])periscelis[&&NHX:TOL=118155],scutops[&&NHX:TOL=118159])periscelidinae[&&NHX:TOL=121768],(cyamops[&&NHX:TOL=118151],podocera[&&NHX:TOL=121770],stenocyamops thaii[&&NHX:TOL=118163],stenomicra[&&NHX:TOL=118153])stenomicrinae[&&NHX:TOL=121769],planinasus[&&NHX:TOL=118154],procyamops succini[&&NHX:EXT=Y:TOL=118164])periscelididae[&&NHX:TOL=10644],(aulacigaster[&&NHX:TOL=111297],curiosimusca[&&NHX:TOL=111298],echidnocephalodes barbatus[&&NHX:TOL=111299],schizochroa[&&NHX:TOL=111300],protaulacigaster electra[&&NHX:EXT=Y:TOL=111301])aulacigastridae[&&NHX:TOL=10643])[&&NHX:TOL=10642])[&&NHX:TOL=10641],((auster pteridii[&&NHX:TOL=118142],camur willii[&&NHX:TOL=118143],lips collessii[&&NHX:TOL=118144],pous manicula[&&NHX:TOL=118145],stepta latipennis[&&NHX:TOL=118146],(teratomyza teratomyza[&&NHX:TOL=118148],teratomyza vitila[&&NHX:TOL=118149])teratomyza[&&NHX:TOL=118147],teratoptera chilensis[&&NHX:TOL=118150])teratomyzidae[&&NHX:TOL=10647],(xenasteia[&&NHX:TOL=10649],(anarista[&&NHX:TOL=118165],(asteia asteia[&&NHX:TOL=118167],asteia subanarista mahunkai[&&NHX:TOL=118168])asteia[&&NHX:TOL=118166],astiosoma[&&NHX:TOL=118169],bahamia longiceps[&&NHX:TOL=118170],bryania bipunctata[&&NHX:TOL=118171],leiomyza[&&NHX:TOL=118172],loewimyia[&&NHX:TOL=118173],phlebosotera[&&NHX:TOL=118174],sigaloessa[&&NHX:TOL=118175],tucumyia[&&NHX:TOL=118176],succinasteia carpenteri[&&NHX:EXT=Y:TOL=118177])asteiidae[&&NHX:TOL=10650])[&&NHX:TOL=10648])[&&NHX:TOL=10646],(nemo[&&NHX:TOL=111305],nemula[&&NHX:TOL=111306],ningula[&&NHX:TOL=111307])neminidae[&&NHX:TOL=111269])[&&NHX:TOL=10640])[&&NHX:TOL=10636])[&&NHX:TOL=10630],margo[&&NHX:TOL=111270])opomyzoidea[&&NHX:TOL=10541],(((tethinidae[&&NHX:TOL=10581],canacidae[&&NHX:TOL=10582])[&&NHX:TOL=10580],((cryptochetum[&&NHX:TOL=111309],librella demetrius[&&NHX:TOL=111311],phanerochaetum tuxeni[&&NHX:EXT=Y:TOL=111312])cryptochetidae[&&NHX:TOL=10588],(chloropidae[&&NHX:TOL=10589],milichiidae[&&NHX:TOL=10585])[&&NHX:TOL=110654])[&&NHX:TOL=10587])[&&NHX:TOL=10579],((australimyza[&&NHX:TOL=10576],inbiomyia[&&NHX:TOL=110656])[&&NHX:TOL=110655],carnidae[&&NHX:TOL=10578])[&&NHX:TOL=10575],((acartophthalmus bicolor[&&NHX:TOL=52172],acartophthalmus pusio[&&NHX:TOL=52264],acartophthalmus nigrinus[&&NHX:TOL=52265],acartophthalmus latrinalis[&&NHX:TOL=52173])acartophthalmus[&&NHX:TOL=52174],acartophthalmites tertiaria[&&NHX:EXT=Y:TOL=52266])acartophthalmidae[&&NHX:TOL=10629],((megabraula onerosa[&&NHX:TOL=108861],megabraula antecessor[&&NHX:TOL=108860])megabraula[&&NHX:TOL=108859],(braula coeca[&&NHX:TOL=108863],braula kohli[&&NHX:TOL=108864],braula orientalis[&&NHX:TOL=108865],braula pretoriensis[&&NHX:TOL=108866],braula schmitzi[&&NHX:TOL=108867])braula[&&NHX:TOL=108862])braulidae[&&NHX:TOL=10577])carnoidea[&&NHX:TOL=10542])[&&NHX:TOL=10540],((((aphaniosoma[&&NHX:TOL=118178],(chyromya chyromya[&&NHX:TOL=118180],chyromya somatiosoma[&&NHX:TOL=118181])chyromya[&&NHX:TOL=118179],gymnochyromyia[&&NHX:TOL=118182],gephyromyiella electrica[&&NHX:EXT=Y:TOL=118183])chyromyidae[&&NHX:TOL=10669],sphaeroceridae[&&NHX:TOL=10670])[&&NHX:TOL=10668],heleomyzidae[&&NHX:TOL=10663],mormotomyia hirsuta[&&NHX:TOL=10667],(azorastia[&&NHX:TOL=111331],nannodastia[&&NHX:TOL=111332])nannodastiidae[&&NHX:TOL=111313])sphaeroceroidea[&&NHX:TOL=10544],((axinota[&&NHX:TOL=111314],curtonotum[&&NHX:TOL=111315],cyrtona[&&NHX:TOL=111316])curtonotidae[&&NHX:TOL=10606],(((afrocamilla[&&NHX:TOL=111317],camilla[&&NHX:TOL=111318],katacamilla[&&NHX:TOL=111319],teratocamilla sinesita[&&NHX:TOL=111321],protocamilla succini[&&NHX:EXT=Y:TOL=111320])camillidae[&&NHX:TOL=10609],drosophilidae[&&NHX:TOL=10610])[&&NHX:TOL=10608],((campichoeta[&&NHX:TOL=111322],diastata[&&NHX:TOL=111323],euthychaeta spectabilis[&&NHX:TOL=111324],pareuthychaeta[&&NHX:EXT=Y:TOL=111325])diastatidae[&&NHX:TOL=10612],ephydridae[&&NHX:TOL=10613])[&&NHX:TOL=10611])[&&NHX:TOL=10607])ephydroidea[&&NHX:TOL=10545])[&&NHX:TOL=10543])[&&NHX:TOL=10539])[&&NHX:TOL=10535])acalyptratae[&&NHX:TOL=10527],(((scathophagidae[&&NHX:TOL=10557],(anthomyiidae[&&NHX:TOL=10559],((australofannia spiniclunis[&&NHX:TOL=111327],euryomma[&&NHX:TOL=111328],fannia[&&NHX:TOL=111329],piezura[&&NHX:TOL=111330])fanniidae[&&NHX:TOL=10561],muscidae[&&NHX:TOL=10562])[&&NHX:TOL=10560])[&&NHX:TOL=10558])muscoidea[&&NHX:TOL=10556],(mystacinobia zelandica[&&NHX:TOL=10567],(oestridae[&&NHX:TOL=10573],rhinophoridae[&&NHX:TOL=10571],sarcophagidae[&&NHX:TOL=10568],(exoristinae[&&NHX:TOL=57764],dexiinae[&&NHX:TOL=57765],phasiinae[&&NHX:TOL=57766],tachininae[&&NHX:TOL=57767])tachinidae[&&NHX:TOL=10572],calliphoridae[&&NHX:TOL=10566])[&&NHX:TOL=111390])oestroidea[&&NHX:TOL=10563])[&&NHX:TOL=111333],(glossina[&&NHX:TOL=10550],(hippoboscidae[&&NHX:TOL=10551],(streblidae[&&NHX:TOL=10553],nycteribiidae[&&NHX:TOL=10554])[&&NHX:TOL=10552])[&&NHX:TOL=111326])hippoboscoidea[&&NHX:TOL=10548])calyptratae[&&NHX:TOL=10546],((mallochianamyia cladostyla[&&NHX:TOL=119722],mallochianamyia fenestrata[&&NHX:TOL=119723],mallochianamyia flavitibia[&&NHX:TOL=119724],mallochianamyia furcata[&&NHX:TOL=119725],mallochianamyia gallina[&&NHX:TOL=119726],mallochianamyia latigena[&&NHX:TOL=119727],mallochianamyia magnipalpis[&&NHX:TOL=119728],mallochianamyia nigrohalterata[&&NHX:TOL=119729],mallochianamyia penai[&&NHX:TOL=119730],mallochianamyia setosa[&&NHX:TOL=119731],mallochianamyia truncata[&&NHX:TOL=119732],mallochianamyia vexans[&&NHX:TOL=119733])mallochianamyia[&&NHX:TOL=119718],(paraleucopis boydensis[&&NHX:TOL=119734],paraleucopis corvina[&&NHX:TOL=119735],paraleucopis mexicana[&&NHX:TOL=119736])paraleucopis[&&NHX:TOL=119719],schizostomyia atra[&&NHX:TOL=119720])unplaced acalyptratae[&&NHX:TOL=119717])schizophora[&&NHX:TOL=10525])cyclorrhapha[&&NHX:TOL=10471])eremoneura[&&NHX:TOL=23886])[&&NHX:TOL=10457])muscomorpha[&&NHX:TOL=10453])brachycera[&&NHX:TOL=10500])[&&NHX:TOL=24076])[&&NHX:TOL=24075])[&&NHX:TOL=24099])[&&NHX:TOL=24074])[&&NHX:TOL=24077])[&&NHX:TOL=23880])diptera[&&NHX:TOL=8226],(nannochoristidae[&&NHX:TOL=12964],(bittacidae[&&NHX:TOL=12966],(boreidae[&&NHX:TOL=12968],meropeidae[&&NHX:TOL=12969],(eomeropidae[&&NHX:TOL=12971],(apteropanorpidae[&&NHX:TOL=12973],(choristidae[&&NHX:TOL=12975],(panorpodidae[&&NHX:TOL=12977],panorpidae[&&NHX:TOL=12978])[&&NHX:TOL=12976])[&&NHX:TOL=12974])[&&NHX:TOL=12972])[&&NHX:TOL=12970])[&&NHX:TOL=12967])[&&NHX:TOL=12965])mecoptera[&&NHX:TOL=8227],(tungidae[&&NHX:TOL=14490],pulicidae[&&NHX:TOL=14491],rhopalopsyllidae[&&NHX:TOL=14492],malacopsyllidae[&&NHX:TOL=14493],vermipsyllidae[&&NHX:TOL=14494],hystrichopsyllidae[&&NHX:TOL=14495],coptopsyllidae[&&NHX:TOL=14496],pygiopsyllidae[&&NHX:TOL=14497],stephanocircidae[&&NHX:TOL=14498],macropsyllidae[&&NHX:TOL=14499],xyphiopsyllidae[&&NHX:TOL=14500],ancistropsyllidae[&&NHX:TOL=14501],chimaeropsyllidae[&&NHX:TOL=14502],ischnopsyllidae[&&NHX:TOL=14503],leptopsyllidae[&&NHX:TOL=14504],ceratopsyllidae[&&NHX:TOL=14505])siphonaptera[&&NHX:TOL=8228])[&&NHX:TOL=8225],(((cladochoristidae[&&NHX:EXT=Y:TOL=14621],microptysmatidae[&&NHX:EXT=Y:TOL=14622],prosepididontidae[&&NHX:EXT=Y:TOL=14623],protomeropidae[&&NHX:EXT=Y:TOL=14624],uraloptysmatidae[&&NHX:EXT=Y:TOL=14625])protomeropina[&&NHX:EXT=Y:TOL=14547],((rhyacophilidae[&&NHX:TOL=14586],hydrobiosidae[&&NHX:TOL=14585],glossosomatidae[&&NHX:TOL=14582],hydroptilidae[&&NHX:TOL=14583],( vitimotauliidae[&&NHX:EXT=Y:TOL=14569],taymyrelectronidae[&&NHX:EXT=Y:TOL=14570],kalophryganeidae[&&NHX:EXT=Y:TOL=14571],dysoneuridae[&&NHX:EXT=Y:TOL=14572],baissoferidae[&&NHX:EXT=Y:TOL=14573],(phryganopsychidae[&&NHX:TOL=14600],phryganeidae[&&NHX:TOL=14601],(plectrotarsidae[&&NHX:TOL=14603],((brachycentridae[&&NHX:TOL=14606],(oeconescidae[&&NHX:TOL=14608],(pisuliidae[&&NHX:TOL=14610],lepidostomatidae[&&NHX:TOL=14611])[&&NHX:TOL=14609])[&&NHX:TOL=14607])[&&NHX:TOL=14605],(rossianidae[&&NHX:TOL=14613],(limnephilidae[&&NHX:TOL=14615],(apataniidae[&&NHX:TOL=14617],uenoidae[&&NHX:TOL=14618],goeridae[&&NHX:TOL=14619])[&&NHX:TOL=14616])[&&NHX:TOL=14614])[&&NHX:TOL=14612])[&&NHX:TOL=14604])[&&NHX:TOL=14602])limnephiloidea[&&NHX:TOL=14574],((((odontoceridae[&&NHX:TOL=14590],atriplectididae[&&NHX:TOL=14591])[&&NHX:TOL=14589],philorhethridae[&&NHX:TOL=14592])[&&NHX:TOL=14588],limnocentropodidae[&&NHX:TOL=14593],(calamoceratidae[&&NHX:TOL=14595],(molannidae[&&NHX:TOL=14597],leptoceridae[&&NHX:TOL=14598])[&&NHX:TOL=14596])[&&NHX:TOL=14594])leptoceroidea[&&NHX:TOL=14576],tasmiidae[&&NHX:TOL=14577],(kokiriidae[&&NHX:TOL=14627],anomalopsychidae[&&NHX:TOL=14628],((calocidae[&&NHX:TOL=14631],chathamiidae[&&NHX:TOL=14632])[&&NHX:TOL=14630],(conoesucidae[&&NHX:TOL=14634],(helicophidae[&&NHX:TOL=14636],hydrosalpingidae[&&NHX:TOL=14637])[&&NHX:TOL=14635])[&&NHX:TOL=14633])[&&NHX:TOL=14629],(sericostomatidae[&&NHX:TOL=14639],(helicopsychidae[&&NHX:TOL=14641],(petrothrincidae[&&NHX:TOL=14643],(barbarochthonidae[&&NHX:TOL=14645],(beraeidae[&&NHX:TOL=14647],antipodoeciidae[&&NHX:TOL=14648])[&&NHX:TOL=14646])[&&NHX:TOL=14644])[&&NHX:TOL=14642])[&&NHX:TOL=14640])[&&NHX:TOL=14638])sericostomatoidea[&&NHX:TOL=14578])[&&NHX:TOL=14575])integripalpia[&&NHX:TOL=14551])[&&NHX:TOL=14548],(necrotauliidae[&&NHX:EXT=Y:TOL=14553],electralbertidae[&&NHX:EXT=Y:TOL=14554],philopotamidae[&&NHX:TOL=14555],(psychomyiidae[&&NHX:TOL=14557],xiphocentronidae[&&NHX:TOL=14558])[&&NHX:TOL=14556],((ecnomidae[&&NHX:TOL=14561],polycentropodidae[&&NHX:TOL=14562],(hydropsychidae[&&NHX:TOL=14564],arctopsychidae[&&NHX:TOL=14565])[&&NHX:TOL=14563])[&&NHX:TOL=14560],dipseudopsidae[&&NHX:TOL=14566])[&&NHX:TOL=14559],stenopsychidae[&&NHX:TOL=14567])annulipalpia[&&NHX:TOL=14549])[&&NHX:TOL=21890])trichoptera[&&NHX:TOL=8230],((((((((((((((((baronia brevicornis[&&NHX:TOL=12201],((hypermnestra helios[&&NHX:TOL=65392],((parnassius apollo[&&NHX:TOL=65428],(parnassius smintheus[&&NHX:TOL=65430],parnassius phoebus[&&NHX:TOL=65431],parnassius bremeri[&&NHX:TOL=65432])[&&NHX:TOL=65429],parnassius ruckbelii[&&NHX:TOL=65433])[&&NHX:TOL=65427],parnassius jacquemontii[&&NHX:TOL=65434],(parnassius nomion[&&NHX:TOL=65436],parnassius epaphus[&&NHX:TOL=65437])[&&NHX:TOL=65435],parnassius tianschanicus[&&NHX:TOL=65438],parnassius actius[&&NHX:TOL=65439],(parnassius apollonius[&&NHX:TOL=65441],parnassius honrathi[&&NHX:TOL=65442])[&&NHX:TOL=65440],(((parnassius acco[&&NHX:TOL=65446],((parnassius szechnyi[&&NHX:TOL=65449],parnassius cephalus[&&NHX:TOL=65450])[&&NHX:TOL=65448],parnassius maharaja[&&NHX:TOL=65451])[&&NHX:TOL=65447],parnassius schultei[&&NHX:TOL=65452],(parnassius huberi[&&NHX:TOL=65454],parnassius hannyngtoni[&&NHX:TOL=65455])[&&NHX:TOL=65453])[&&NHX:TOL=65445],(parnassius arcticus[&&NHX:TOL=65457],parnassius tenedius[&&NHX:TOL=65458])[&&NHX:TOL=65456])[&&NHX:TOL=65444],((((parnassius delphius[&&NHX:TOL=65463],parnassius maximius[&&NHX:TOL=65464])[&&NHX:TOL=65462],parnassius patricius[&&NHX:TOL=65465])[&&NHX:TOL=65461],(((parnassius staudingeri[&&NHX:TOL=65469],parnassius cardinal[&&NHX:TOL=65470])[&&NHX:TOL=65468],(parnassius stenosemus[&&NHX:TOL=65472],parnassius stoliczkanus[&&NHX:TOL=65473])[&&NHX:TOL=65471])[&&NHX:TOL=65467],parnassius hide[&&NHX:TOL=65474])[&&NHX:TOL=65466])[&&NHX:TOL=65460],(((parnassius charltonius[&&NHX:TOL=65478],parnassius inopinatus[&&NHX:TOL=65479])[&&NHX:TOL=65477],(parnassius acdestis[&&NHX:TOL=65481],(parnassius imperator[&&NHX:TOL=65483],parnassius augustis[&&NHX:TOL=65484])[&&NHX:TOL=65482])[&&NHX:TOL=65480])[&&NHX:TOL=65476],(parnassius autocrator[&&NHX:TOL=65486],parnassius loxias[&&NHX:TOL=65487])[&&NHX:TOL=65485])[&&NHX:TOL=65475])[&&NHX:TOL=65459],(parnassius hardwickii[&&NHX:TOL=65489],((parnassius boedromius[&&NHX:TOL=65492],(parnassius simo[&&NHX:TOL=65494],parnassius andreji[&&NHX:TOL=65495])[&&NHX:TOL=65493])[&&NHX:TOL=65491],parnassius simonius[&&NHX:TOL=65496])[&&NHX:TOL=65490])[&&NHX:TOL=65488],(parnassius mnemosyne[&&NHX:TOL=65498],parnassius ariadne[&&NHX:TOL=65499])[&&NHX:TOL=65497],parnassius stubbendorfii[&&NHX:TOL=65500],parnassius glacialis[&&NHX:TOL=65501],(parnassius eversmanni[&&NHX:TOL=65503],parnassius clodius[&&NHX:TOL=65504])[&&NHX:TOL=65502],parnassius nordmanni[&&NHX:TOL=65505],parnassius orleans[&&NHX:TOL=65506])[&&NHX:TOL=65443])parnassius[&&NHX:TOL=65393])parnassiini[&&NHX:TOL=65388],((((archon apollinaris[&&NHX:TOL=65402],archon apollinus[&&NHX:TOL=65403],archon bostanchii[&&NHX:TOL=118677])archon[&&NHX:TOL=65394],doritites bosniackii[&&NHX:EXT=Y:TOL=65424])[&&NHX:TOL=67918],(luehdorfia japonica[&&NHX:TOL=65404],(luehdorfia puziloi[&&NHX:TOL=65406],(luehdorfia taibai[&&NHX:TOL=65408],luehdorfia chinensis[&&NHX:TOL=65409])[&&NHX:TOL=65407])[&&NHX:TOL=65405])luehdorfia[&&NHX:TOL=65395])luehdorfiini[&&NHX:TOL=65390],(sericinus montela [&&NHX:TOL=65396],((bhutanitis thaidiana[&&NHX:TOL=65410],(bhutanitis lidderdalii[&&NHX:TOL=65412],bhutanitis mansfieldi[&&NHX:TOL=65413])[&&NHX:TOL=65411],bhutanitis ludlowi[&&NHX:TOL=65425])bhutanitis[&&NHX:TOL=65398],((zerynthia rumina[&&NHX:TOL=65414],zerynthia polyxena[&&NHX:TOL=65415])zerynthia[&&NHX:TOL=65400],(allancastria louristana[&&NHX:TOL=65416],(allancastria deyrollei[&&NHX:TOL=65418],(allancastria cretica[&&NHX:TOL=65420],(allancastria cerisy[&&NHX:TOL=65422],allancastria caucasica[&&NHX:TOL=65423])[&&NHX:TOL=65421])[&&NHX:TOL=65419])[&&NHX:TOL=65417])allancastria[&&NHX:TOL=65401])[&&NHX:TOL=65399])[&&NHX:TOL=65397])zerynthiini[&&NHX:TOL=65391],thaites ruminiana[&&NHX:EXT=Y:TOL=65426])[&&NHX:TOL=65389])parnassiinae[&&NHX:TOL=65387],(leptocircini[&&NHX:TOL=12207],(teinopalpus[&&NHX:TOL=12209],(troidini[&&NHX:TOL=12211],(papilionini[&&NHX:TOL=12212],(praepapilio colorado[&&NHX:EXT=Y:TOL=67802],praepapilio gracilis[&&NHX:EXT=Y:TOL=67803])praepapilio[&&NHX:EXT=Y:TOL=12200])[&&NHX:TOL=65384])[&&NHX:TOL=12210])[&&NHX:TOL=12208])papilioninae[&&NHX:TOL=12206])papilionidae[&&NHX:TOL=12177],(((pseudopontia paradoxa[&&NHX:TOL=12214],((leptidea amurensis[&&NHX:TOL=88432],leptidea duponcheli[&&NHX:TOL=88433],leptidea gigantea[&&NHX:TOL=88434],leptidea morsei[&&NHX:TOL=88435],leptidea reali[&&NHX:TOL=88436],leptidea sinapis[&&NHX:TOL=88437])leptidea[&&NHX:TOL=76371],((pseudopieris nehemia[&&NHX:TOL=77050],pseudopieris viridula[&&NHX:TOL=77051])pseudopieris[&&NHX:TOL=76372],(moschoneura pinthous[&&NHX:TOL=76373],(((dismorphia altis[&&NHX:TOL=77052],dismorphia arcadia[&&NHX:TOL=77081],dismorphia amphione[&&NHX:TOL=77053],dismorphia astyocha[&&NHX:TOL=77054],dismorphia boliviana[&&NHX:TOL=77055],dismorphia crisia[&&NHX:TOL=77056],dismorphia cubana[&&NHX:TOL=77057],dismorphia eunoe[&&NHX:TOL=77058],dismorphia hyposticta[&&NHX:TOL=77059],dismorphia laja[&&NHX:TOL=77060],dismorphia lelex[&&NHX:TOL=77061],dismorphia lewyi[&&NHX:TOL=77062],dismorphia lua[&&NHX:TOL=77063],dismorphia lycosura[&&NHX:TOL=77064],dismorphia lygdamis[&&NHX:TOL=77065],dismorphia lysis[&&NHX:TOL=77066],dismorphia medora[&&NHX:TOL=77067],dismorphia medorilla[&&NHX:TOL=77068],dismorphia melia[&&NHX:TOL=77069],dismorphia mirandola[&&NHX:TOL=77070],dismorphia niepelti[&&NHX:TOL=77071],dismorphia pseudolewyi[&&NHX:TOL=77072],dismorphia spio[&&NHX:TOL=77073],dismorphia teresa[&&NHX:TOL=77074],dismorphia thermesia[&&NHX:TOL=77075],dismorphia thermesina[&&NHX:TOL=77076],dismorphia theucharila[&&NHX:TOL=77077],dismorphia zaela[&&NHX:TOL=77078],dismorphia zathoe[&&NHX:TOL=77079],dismorphia n. sp.[&&NHX:TOL=77080])dismorphia[&&NHX:TOL=76374],(lieinix christa[&&NHX:TOL=77192],lieinix cinerascens[&&NHX:TOL=77193],lieinix lala[&&NHX:TOL=77194],lieinix neblina[&&NHX:TOL=77195],lieinix nemesis[&&NHX:TOL=77196],lieinix viridifascia[&&NHX:TOL=77197])lieinix[&&NHX:TOL=76375])[&&NHX:TOL=76381],((enantia albania[&&NHX:TOL=77183],enantia aloikea[&&NHX:TOL=77184],enantia citrinella[&&NHX:TOL=77185],enantia clarissa[&&NHX:TOL=77186],enantia jethrys[&&NHX:TOL=77187],enantia limnorina[&&NHX:TOL=77188],enantia lina[&&NHX:TOL=77189],enantia mazai[&&NHX:TOL=77190],enantia melite[&&NHX:TOL=77191])enantia[&&NHX:TOL=76376],(patia cordillera[&&NHX:TOL=77198],patia orise[&&NHX:TOL=77199],patia rhetes[&&NHX:TOL=77200])patia[&&NHX:TOL=76377])[&&NHX:TOL=76382])[&&NHX:TOL=76380])[&&NHX:TOL=76379])[&&NHX:TOL=76378])dismorphiinae[&&NHX:TOL=12215])[&&NHX:TOL=66506],((((nathalis iole[&&NHX:TOL=77258],nathalis plauta[&&NHX:TOL=77259])nathalis[&&NHX:TOL=76384],(kricogonia cabrerai[&&NHX:TOL=77260],kricogonia lyside[&&NHX:TOL=77261])kricogonia[&&NHX:TOL=76385])[&&NHX:TOL=76383],(((terias simulatrix[&&NHX:TOL=87359],terias blanda[&&NHX:TOL=87360],terias ada[&&NHX:TOL=87361],terias sari[&&NHX:TOL=87362],terias andersonii[&&NHX:TOL=87363],terias lacteola[&&NHX:TOL=87364],terias tilaha[&&NHX:TOL=87365],terias candida[&&NHX:TOL=87366],terias smilax[&&NHX:TOL=87367],terias sana[&&NHX:TOL=87368],terias alitha[&&NHX:TOL=88440],terias puella[&&NHX:TOL=88442],terias celebensis[&&NHX:TOL=88444],terias lombokiana[&&NHX:TOL=88445],terias sarilata[&&NHX:TOL=88446],terias tominia[&&NHX:TOL=88447],terias novopallida[&&NHX:TOL=88448],terias irena[&&NHX:TOL=93870],terias mandarinula[&&NHX:TOL=84931],terias regularis[&&NHX:TOL=84932],terias floricola[&&NHX:TOL=84933],terias hapale[&&NHX:TOL=84934],terias hecabe[&&NHX:TOL=84935],terias senegalensis[&&NHX:TOL=84936],terias upembana[&&NHX:TOL=84937])terias[&&NHX:TOL=76388],((pyrisitia chamberlaini[&&NHX:TOL=77224],pyrisitia dina[&&NHX:TOL=77225],pyrisitia euterpiformis[&&NHX:TOL=77226],pyrisitia leuce[&&NHX:TOL=77227],pyrisitia lisa[&&NHX:TOL=77228],pyrisitia messalina[&&NHX:TOL=77229],pyrisitia nise[&&NHX:TOL=77230],pyrisitia portoricensis[&&NHX:TOL=77231],pyrisitia proterpia[&&NHX:TOL=77232],pyrisitia pyro[&&NHX:TOL=77233],pyrisitia venusta[&&NHX:TOL=77234])pyrisitia[&&NHX:TOL=76390],(((eurema adamsi[&&NHX:TOL=77235],eurema agave[&&NHX:TOL=77236],eurema albula[&&NHX:TOL=77237],eurema amelia[&&NHX:TOL=77238],eurema arbela[&&NHX:TOL=77239],eurema brigitta[&&NHX:TOL=84929],eurema daira[&&NHX:TOL=77240],eurema desjardinsii[&&NHX:TOL=84930],eurema deva[&&NHX:TOL=77241],eurema elathea[&&NHX:TOL=77242],eurema fabiola[&&NHX:TOL=77243],eurema herla[&&NHX:TOL=87370],eurema laeta[&&NHX:TOL=87369],eurema lirina[&&NHX:TOL=77244],eurema lucina[&&NHX:TOL=77245],eurema mexicana[&&NHX:TOL=77246],eurema nigrocincta[&&NHX:TOL=77247],eurema paulina[&&NHX:TOL=77248],eurema phiale[&&NHX:TOL=77249],eurema reticulata[&&NHX:TOL=77250],eurema salome[&&NHX:TOL=77251],eurema tupuntenem[&&NHX:TOL=77252],eurema xanthochlora[&&NHX:TOL=77253])eurema[&&NHX:TOL=76392],(abaeis nicippe[&&NHX:TOL=77222],abaeis nicippiformis[&&NHX:TOL=77223])abaeis[&&NHX:TOL=76530])[&&NHX:TOL=76529],((leucidia brephos[&&NHX:TOL=77262],leucidia elvina[&&NHX:TOL=77263])leucidia[&&NHX:TOL=76394],teriocolias zelia[&&NHX:TOL=76395])[&&NHX:TOL=76393])[&&NHX:TOL=76391])[&&NHX:TOL=76389])eurema group[&&NHX:TOL=76387],((gandaca harina[&&NHX:TOL=88438],gandaca butyrosa[&&NHX:TOL=88439])gandaca[&&NHX:TOL=76397],(((gonepteryx amintha[&&NHX:TOL=88450],gonepteryx cleobule[&&NHX:TOL=88452],gonepteryx cleopatra[&&NHX:TOL=88453],gonepteryx farinosa[&&NHX:TOL=88454],gonepteryx maderensis[&&NHX:TOL=88455],gonepteryx mahaguru[&&NHX:TOL=88456],gonepteryx maxima[&&NHX:TOL=88457],gonepteryx palmae[&&NHX:TOL=88458],gonepteryx rhamni[&&NHX:TOL=88459])gonepteryx[&&NHX:TOL=76400],(dercas lycorias[&&NHX:TOL=88460],dercas verhuelli[&&NHX:TOL=88461])dercas[&&NHX:TOL=76401])[&&NHX:TOL=76399],((catopsilia florella[&&NHX:TOL=84897],catopsilia mabillei[&&NHX:TOL=84898],catopsilia thauruma[&&NHX:TOL=84899],catopsilia pyranthe[&&NHX:TOL=87352],catopsilia pomona[&&NHX:TOL=87353],catopsilia gorgophone[&&NHX:TOL=87354],catopsilia scylla[&&NHX:TOL=87355])catopsilia[&&NHX:TOL=76403],(((zerene cesonia[&&NHX:TOL=77201],zerene eurydice[&&NHX:TOL=77202])zerene[&&NHX:TOL=76406],(colias adelaidae[&&NHX:TOL=130229],colias aegidii[&&NHX:TOL=88487],colias aias[&&NHX:TOL=130230],colias alexandra[&&NHX:TOL=84914],colias alfacariensis[&&NHX:TOL=130231],colias alpherakii[&&NHX:TOL=88462],colias alta[&&NHX:TOL=130232],colias arida[&&NHX:TOL=88488],colias aurorina[&&NHX:TOL=88463],colias behrii[&&NHX:TOL=88489],colias berylla[&&NHX:TOL=88490],colias canadensis[&&NHX:TOL=84919],colias caucasica[&&NHX:TOL=88464],colias chlorocoma[&&NHX:TOL=88465],colias christina[&&NHX:TOL=84915],colias christophi[&&NHX:TOL=88466],colias chrysotheme[&&NHX:TOL=88467],colias cocandica[&&NHX:TOL=88468],colias croceus[&&NHX:TOL=84902],colias dimera[&&NHX:TOL=84905],colias diva[&&NHX:TOL=88491],colias dubia[&&NHX:TOL=88504],colias electo[&&NHX:TOL=84903],colias eogene[&&NHX:TOL=88470],colias erate[&&NHX:TOL=84904],colias erschoffii[&&NHX:TOL=88471],colias eurytheme[&&NHX:TOL=84906],colias euxanthe[&&NHX:TOL=84907],colias felderi[&&NHX:TOL=88503],colias fieldii[&&NHX:TOL=88472],colias flaveola[&&NHX:TOL=84908],colias gigantea[&&NHX:TOL=84924],colias grumi[&&NHX:TOL=130233],colias harfordii[&&NHX:TOL=84909],colias hecla[&&NHX:TOL=84918],colias heos[&&NHX:TOL=88473],colias hyale[&&NHX:TOL=88474],colias hyperborea[&&NHX:TOL=88475],colias interior[&&NHX:TOL=84925],colias lada[&&NHX:TOL=88492],colias ladakensis[&&NHX:TOL=88493],colias leechi[&&NHX:TOL=130234],colias lesbia[&&NHX:TOL=84910],colias marcopolo[&&NHX:TOL=88476],colias marnoana[&&NHX:TOL=130235],colias meadii[&&NHX:TOL=84916],colias minisni[&&NHX:TOL=130236],colias montium[&&NHX:TOL=88495],colias mossi[&&NHX:TOL=130237],colias myrmidone[&&NHX:TOL=88477],colias nastes[&&NHX:TOL=84921],colias nebulosa[&&NHX:TOL=88496],colias nilagiriensis[&&NHX:TOL=130238],colias nina[&&NHX:TOL=88505],colias occidentalis[&&NHX:TOL=84913],colias palaeno[&&NHX:TOL=84927],colias pelidne[&&NHX:TOL=84923],colias phicomone[&&NHX:TOL=88497],colias philodice[&&NHX:TOL=84911],colias poliographus[&&NHX:TOL=88478],colias ponteni[&&NHX:TOL=84912],colias regia[&&NHX:TOL=88479],colias romanovi[&&NHX:TOL=88480],colias sagartia[&&NHX:TOL=88498],colias scudderii[&&NHX:TOL=84922],colias shahfuladi[&&NHX:TOL=88499],colias sieversi[&&NHX:TOL=88482],colias sifanica[&&NHX:TOL=88500],colias staudingeri[&&NHX:TOL=88483],colias stoliczkana[&&NHX:TOL=88501],colias tamerlana[&&NHX:TOL=88502],colias thisoa[&&NHX:TOL=88484],colias thrasibulus[&&NHX:TOL=130239],colias tibetana[&&NHX:TOL=130240],colias tyche[&&NHX:TOL=84920],colias vauthierii[&&NHX:TOL=130241],colias wanda[&&NHX:TOL=130242],colias weberbaueri[&&NHX:TOL=130243],colias wiskotti[&&NHX:TOL=88486])colias[&&NHX:TOL=76407])[&&NHX:TOL=76405],((anteos clorinde[&&NHX:TOL=77203],anteos maerula[&&NHX:TOL=77204],anteos menippe[&&NHX:TOL=77205])anteos[&&NHX:TOL=76409],(((phoebis agarithe[&&NHX:TOL=77206],phoebis argante[&&NHX:TOL=77207],phoebis avellaneda[&&NHX:TOL=77208],phoebis bourkei[&&NHX:TOL=77209],phoebis editha[&&NHX:TOL=77210],phoebis neocypris[&&NHX:TOL=77211],phoebis philea[&&NHX:TOL=77212],phoebis sennae[&&NHX:TOL=77213])phoebis[&&NHX:TOL=76411],prestonia clarki[&&NHX:TOL=76532],rhabdodryas trite[&&NHX:TOL=76533])[&&NHX:TOL=76531],(aphrissa boisduvalii[&&NHX:TOL=77214],aphrissa fluminensis[&&NHX:TOL=77215],aphrissa godartiana[&&NHX:TOL=77216],aphrissa neleis[&&NHX:TOL=77217],aphrissa orbis[&&NHX:TOL=77218],aphrissa schausi[&&NHX:TOL=77219],aphrissa statira[&&NHX:TOL=77220],aphrissa wallacei[&&NHX:TOL=77221])aphrissa[&&NHX:TOL=76412])[&&NHX:TOL=76410])[&&NHX:TOL=76408])[&&NHX:TOL=76404])[&&NHX:TOL=76402])[&&NHX:TOL=76398])[&&NHX:TOL=76396])[&&NHX:TOL=76386])coliadinae[&&NHX:TOL=12217],(((hebomoia glaucippe[&&NHX:TOL=87438],hebomoia leucippe[&&NHX:TOL=87439])hebomoia[&&NHX:TOL=76429],(((colotis agoye[&&NHX:TOL=84946],colotis amata[&&NHX:TOL=84947],colotis antevippe[&&NHX:TOL=84948],colotis aurigineus[&&NHX:TOL=84949],colotis aurora[&&NHX:TOL=84950],colotis auxo[&&NHX:TOL=84951],colotis celimene[&&NHX:TOL=84952],colotis chrysonome[&&NHX:TOL=84953],colotis daira[&&NHX:TOL=84954],colotis danae[&&NHX:TOL=84955],colotis dissociatus[&&NHX:TOL=84956],colotis doubledayi[&&NHX:TOL=84957],colotis elgonensis[&&NHX:TOL=84958],colotis ephyia[&&NHX:TOL=84959],colotis eris[&&NHX:TOL=84960],colotis erone[&&NHX:TOL=84961],colotis etrida[&&NHX:TOL=88506],colotis eucharis[&&NHX:TOL=122563],colotis euippe[&&NHX:TOL=84962],colotis eunoma[&&NHX:TOL=84963],colotis evagore[&&NHX:TOL=84964],colotis evanthe[&&NHX:TOL=84965],colotis evanthides[&&NHX:TOL=84966],colotis evenina[&&NHX:TOL=84967],colotis fausta[&&NHX:TOL=84968],colotis guenei[&&NHX:TOL=84969],colotis halimede[&&NHX:TOL=84970],colotis hetaera[&&NHX:TOL=84971],colotis hildebrandti[&&NHX:TOL=84972],colotis incretus[&&NHX:TOL=122564],colotis ione[&&NHX:TOL=84973],colotis lais[&&NHX:TOL=84974],colotis liagore[&&NHX:TOL=84975],colotis mananhari[&&NHX:TOL=84976],colotis pallene[&&NHX:TOL=84977],colotis phisadia[&&NHX:TOL=84978],colotis pleione[&&NHX:TOL=84979],colotis protomedia[&&NHX:TOL=84980],colotis protractus[&&NHX:TOL=88507],colotis regina[&&NHX:TOL=84981],colotis rogersi[&&NHX:TOL=84982],colotis subfasciatus[&&NHX:TOL=84983],colotis ungemachi[&&NHX:TOL=84984],colotis venosa[&&NHX:TOL=84985],colotis vesta[&&NHX:TOL=84986],colotis vestalis[&&NHX:TOL=84987],colotis zoe[&&NHX:TOL=84988])colotis[&&NHX:TOL=76432],((nepheronia argia[&&NHX:TOL=84940],nepheronia buquetii[&&NHX:TOL=84941],nepheronia pharis[&&NHX:TOL=84942],nepheronia thalassina[&&NHX:TOL=84943])nepheronia[&&NHX:TOL=76434],(pareronia argolis[&&NHX:TOL=87440],pareronia avatar[&&NHX:TOL=87441],pareronia aviena[&&NHX:TOL=87442],pareronia boebera[&&NHX:TOL=87443],pareronia ceylanica[&&NHX:TOL=87444],pareronia chinki[&&NHX:TOL=87445],pareronia hippia[&&NHX:TOL=87446],pareronia jobaea[&&NHX:TOL=87447],pareronia nishayama[&&NHX:TOL=87448],pareronia paravatar[&&NHX:TOL=87449],pareronia phocaea[&&NHX:TOL=87450],pareronia tritaea[&&NHX:TOL=87451],pareronia valeria[&&NHX:TOL=87452])pareronia[&&NHX:TOL=76435])[&&NHX:TOL=76433],calopieris eulimene[&&NHX:TOL=76534])[&&NHX:TOL=76431],((gideona lucasi[&&NHX:TOL=76438],pinacopteryx eriphia[&&NHX:TOL=76439])[&&NHX:TOL=76437],((eronia cleodora[&&NHX:TOL=84944],eronia leda[&&NHX:TOL=84945])eronia[&&NHX:TOL=76441],(ixias flavipennis[&&NHX:TOL=87428],ixias malumsinicum[&&NHX:TOL=87429],ixias marianne[&&NHX:TOL=87430],ixias paluensis[&&NHX:TOL=87431],ixias piepersi[&&NHX:TOL=87432],ixias pyrene[&&NHX:TOL=87433],ixias reinwardti[&&NHX:TOL=87434],ixias venilla[&&NHX:TOL=87435],ixias vollenhovii[&&NHX:TOL=87436],ixias kuehni[&&NHX:TOL=87437])ixias[&&NHX:TOL=76442])[&&NHX:TOL=76440])[&&NHX:TOL=76436])[&&NHX:TOL=76430])colotis group[&&NHX:TOL=76413],((((((((((euchloe insularis[&&NHX:TOL=138192],euchloe crameri[&&NHX:TOL=88521])[&&NHX:TOL=138191],(euchloe melanochloros[&&NHX:TOL=138194],euchloe aegyptiaca[&&NHX:TOL=88516])[&&NHX:TOL=138193])[&&NHX:TOL=138190],(((euchloe simplonia[&&NHX:TOL=138198],euchloe ausonia[&&NHX:TOL=88517])[&&NHX:TOL=138197],euchloe persica[&&NHX:TOL=138199])[&&NHX:TOL=138196],euchloe ausonides[&&NHX:TOL=88518])[&&NHX:TOL=138195])[&&NHX:TOL=138189],(euchloe daphalis[&&NHX:TOL=138201],(((euchloe eversi[&&NHX:TOL=138205],euchloe sp. n. gran canaria[&&NHX:TOL=138206])[&&NHX:TOL=138204],(euchloe hesperidum[&&NHX:TOL=138208],euchloe belemia[&&NHX:TOL=88519])[&&NHX:TOL=138207])[&&NHX:TOL=138203],((euchloe creusa[&&NHX:TOL=88522],euchloe olympia[&&NHX:TOL=88528])[&&NHX:TOL=138210],(euchloe hyantis[&&NHX:TOL=88525],euchloe lotta[&&NHX:TOL=88526],euchloe guaymasensis[&&NHX:TOL=88524])[&&NHX:TOL=138211])[&&NHX:TOL=138209])[&&NHX:TOL=138202])[&&NHX:TOL=138200])[&&NHX:TOL=138188],euchloe falloui[&&NHX:TOL=88523])euchloe[&&NHX:TOL=76446],(zegris eupheme[&&NHX:TOL=88534],zegris fausti[&&NHX:TOL=88535],zegris pyrothoe[&&NHX:TOL=88536])zegris[&&NHX:TOL=76447])[&&NHX:TOL=76445],((anthocharis cethura[&&NHX:TOL=77264],anthocharis lanceolata[&&NHX:TOL=77265],anthocharis limonea[&&NHX:TOL=77266],anthocharis midea[&&NHX:TOL=77267],anthocharis sara[&&NHX:TOL=77268],anthocharis belia[&&NHX:TOL=88508],anthocharis bieti[&&NHX:TOL=88509],anthocharis cardamines[&&NHX:TOL=88510],anthocharis damone[&&NHX:TOL=88511],anthocharis gruneri[&&NHX:TOL=88512],anthocharis scolymus[&&NHX:TOL=88513],anthocharis stella[&&NHX:TOL=88514])anthocharis[&&NHX:TOL=76444],(iberochloe tagis[&&NHX:TOL=88529],iberochloe pechi[&&NHX:TOL=138213])iberochloe[&&NHX:TOL=138212])[&&NHX:TOL=138216])[&&NHX:TOL=76443],(elphinstonia tomyris[&&NHX:TOL=88530],elphinstonia transcaspica[&&NHX:TOL=88531],elphinstonia charlonia[&&NHX:TOL=88520])elphinstonia[&&NHX:TOL=138214])[&&NHX:TOL=138215],(eroessa chiliensis[&&NHX:TOL=76449],(cunizza hirlanda[&&NHX:TOL=76451],((hesperocharis anguitia[&&NHX:TOL=77270],hesperocharis costaricensis[&&NHX:TOL=77271],hesperocharis crocea[&&NHX:TOL=77272],hesperocharis emeris[&&NHX:TOL=77273],hesperocharis erota[&&NHX:TOL=77274],hesperocharis graphites[&&NHX:TOL=77275],hesperocharis leucania[&&NHX:TOL=77276],hesperocharis marchalii[&&NHX:TOL=77277],hesperocharis nera[&&NHX:TOL=77278],hesperocharis nereina[&&NHX:TOL=77279],hesperocharis paranensis[&&NHX:TOL=77280],hesperocharis ñambii[&&NHX:TOL=77281])hesperocharis[&&NHX:TOL=76453],(mathania agasicles[&&NHX:TOL=77282],mathania aureomaculata[&&NHX:TOL=77283],mathania carrizoi[&&NHX:TOL=77284],mathania leucothea[&&NHX:TOL=77285],mathania n. sp.[&&NHX:TOL=77286])mathania[&&NHX:TOL=76454])[&&NHX:TOL=76452])[&&NHX:TOL=76450])[&&NHX:TOL=76448])anthocharidini[&&NHX:TOL=76415],((leptosia nina[&&NHX:TOL=87375],leptosia alcesta[&&NHX:TOL=85122],leptosia hybrida[&&NHX:TOL=85123],leptosia marginea[&&NHX:TOL=85124],leptosia medusa[&&NHX:TOL=85125],leptosia nupta[&&NHX:TOL=85126],leptosia wigginsi[&&NHX:TOL=85127],leptosia lignea[&&NHX:TOL=93871])leptosia[&&NHX:TOL=76417],((elodina andropis[&&NHX:TOL=88874],elodina anticyra[&&NHX:TOL=88875],elodina argypheus[&&NHX:TOL=88876],elodina biaka[&&NHX:TOL=88877],elodina definita[&&NHX:TOL=88878],elodina hypatia[&&NHX:TOL=88879],elodina primularis[&&NHX:TOL=88881],elodina therasia[&&NHX:TOL=88882],elodina umbratica[&&NHX:TOL=88883],elodina dispar[&&NHX:TOL=88884],elodina egnatia[&&NHX:TOL=88885],elodina pseudanops[&&NHX:TOL=88886],elodina signata[&&NHX:TOL=88887],elodina parthia[&&NHX:TOL=87371],elodina angulipennis[&&NHX:TOL=87372],elodina padusa[&&NHX:TOL=87373],elodina perdita[&&NHX:TOL=87374],elodina sota[&&NHX:TOL=93873],[&&NHX:TOL=93874])elodina[&&NHX:TOL=76419],(((saletara liberia[&&NHX:TOL=76486],(appias catophaga albina[&&NHX:TOL=87401],appias catophaga nero[&&NHX:TOL=87402],appias catophaga paulina[&&NHX:TOL=87403],appias catophaga zarinda[&&NHX:TOL=93881],appias catophaga n. sp.[&&NHX:TOL=93882])appias catophaga[&&NHX:TOL=76487])[&&NHX:TOL=76485],(((appias glutophrissa drusilla[&&NHX:TOL=82807],appias glutophrissa punctifera[&&NHX:TOL=82808],appias glutophrissa epaphia[&&NHX:TOL=85060],appias glutophrissa lasti[&&NHX:TOL=85061],appias glutophrissa perlucens[&&NHX:TOL=85062],appias glutophrissa phaola[&&NHX:TOL=85063],appias glutophrissa sabina[&&NHX:TOL=85064],appias glutophrissa sylvia[&&NHX:TOL=85065])appias glutophrissa[&&NHX:TOL=76490],appias phrissura aegis[&&NHX:TOL=76491])[&&NHX:TOL=76489],aoa affinis[&&NHX:TOL=76492])[&&NHX:TOL=76488],udaiana cynis[&&NHX:TOL=76493],(appias appias libythea[&&NHX:TOL=87408],appias appias lyncida[&&NHX:TOL=87409],appias appias indra[&&NHX:TOL=87410],appias appias cardena[&&NHX:TOL=87411],appias appias melania[&&NHX:TOL=87412],appias appias celestina[&&NHX:TOL=87413],appias appias ada[&&NHX:TOL=87414],appias appias phoebe[&&NHX:TOL=87415],appias appias caeca[&&NHX:TOL=87416],appias appias hombroni[&&NHX:TOL=87417],appias appias ithome[&&NHX:TOL=87418],appias appias lalage[&&NHX:TOL=87419],appias appias leis[&&NHX:TOL=87420],appias appias mata[&&NHX:TOL=87421],appias appias nephele[&&NHX:TOL=87422],appias appias nupta[&&NHX:TOL=87423],appias appias placidia[&&NHX:TOL=87424],appias appias remedios[&&NHX:TOL=87425],appias appias waltraudae[&&NHX:TOL=87426],appias appias wardi[&&NHX:TOL=87427])appias appias[&&NHX:TOL=76494],(appias hiposcritia pandione[&&NHX:TOL=87406],appias hiposcritia lalassis[&&NHX:TOL=87407],appias hiposcritia urania[&&NHX:TOL=93879])appias hiposcritia[&&NHX:TOL=87404])appiadina[&&NHX:TOL=76421],(((ascia monuste[&&NHX:TOL=76456],((ganyra howarthi[&&NHX:TOL=77324],ganyra josephina[&&NHX:TOL=77325],ganyra phaloe[&&NHX:TOL=77326])ganyra[&&NHX:TOL=76458],((tatochila autodice[&&NHX:TOL=77287],tatochila distincta[&&NHX:TOL=77288],tatochila homeodice[&&NHX:TOL=77289],tatochila inversa[&&NHX:TOL=77290],tatochila mariae[&&NHX:TOL=77291],tatochila mercedis[&&NHX:TOL=77292],tatochila orthodice[&&NHX:TOL=77293],tatochila sagittata[&&NHX:TOL=77294],tatochila stigmadice[&&NHX:TOL=77295],tatochila theodice[&&NHX:TOL=77296],tatochila xanthodice[&&NHX:TOL=77297])tatochila[&&NHX:TOL=76460],(theochila maenacte[&&NHX:TOL=76462],(((pierphulia isabela[&&NHX:TOL=77308],pierphulia nysias[&&NHX:TOL=77309],pierphulia rosea[&&NHX:TOL=77310])pierphulia[&&NHX:TOL=76464],(piercolias coropunae[&&NHX:TOL=77305],piercolias forsteri[&&NHX:TOL=77306],piercolias huanaco[&&NHX:TOL=77307])piercolias[&&NHX:TOL=76536])[&&NHX:TOL=76535],((hypsochila argyrodice[&&NHX:TOL=77298],hypsochila galactodice[&&NHX:TOL=77299],hypsochila huemul[&&NHX:TOL=77300],hypsochila microdice[&&NHX:TOL=77301],hypsochila penai[&&NHX:TOL=77302],hypsochila wagenknechti[&&NHX:TOL=77303],hypsochila n. sp.[&&NHX:TOL=77304])hypsochila[&&NHX:TOL=76466],((infraphulia illimani[&&NHX:TOL=77311],infraphulia ilyodes[&&NHX:TOL=77312],infraphulia madeleinea[&&NHX:TOL=77313])infraphulia[&&NHX:TOL=76468],(phulia garleppi[&&NHX:TOL=77314],phulia nannophyes[&&NHX:TOL=77315],phulia nymphula[&&NHX:TOL=77316],phulia paranympha[&&NHX:TOL=77317])phulia[&&NHX:TOL=76469])[&&NHX:TOL=76467])[&&NHX:TOL=76465])[&&NHX:TOL=76463])[&&NHX:TOL=76461])[&&NHX:TOL=76459])[&&NHX:TOL=76457])[&&NHX:TOL=76455],((talbotia naganum[&&NHX:TOL=76472],(pieriballia viardi[&&NHX:TOL=76474],((itaballia demophile[&&NHX:TOL=77318],itaballia marana[&&NHX:TOL=77319],itaballia pandosia[&&NHX:TOL=77320])itaballia[&&NHX:TOL=76476],(perrhybris lorena[&&NHX:TOL=77321],perrhybris lypera[&&NHX:TOL=77322],perrhybris pamela[&&NHX:TOL=77323])perrhybris[&&NHX:TOL=76477])[&&NHX:TOL=76475])[&&NHX:TOL=76473])[&&NHX:TOL=76471],(((baltia butleri[&&NHX:TOL=88537],baltia shawii[&&NHX:TOL=88538])baltia[&&NHX:TOL=76480],((pontia beckerii[&&NHX:TOL=85024],pontia daplidice[&&NHX:TOL=85025],pontia distorta[&&NHX:TOL=85026],pontia glauconome[&&NHX:TOL=85027],pontia helice[&&NHX:TOL=85028],pontia protodice[&&NHX:TOL=85029],pontia sisymbrii[&&NHX:TOL=85030],pontia occidentalis[&&NHX:TOL=88539],pontia edusa[&&NHX:TOL=88541],pontia callidice[&&NHX:TOL=88542],pontia chloridice[&&NHX:TOL=88543])pontia[&&NHX:TOL=76481],miopieris[&&NHX:EXT=Y:TOL=76526])[&&NHX:TOL=76525])[&&NHX:TOL=76479],((leptophobia aripa[&&NHX:TOL=85032],leptophobia caesia[&&NHX:TOL=85033],leptophobia cinerea[&&NHX:TOL=85034],leptophobia diaguita[&&NHX:TOL=85035],leptophobia eleone[&&NHX:TOL=85036],leptophobia eleusis[&&NHX:TOL=85037],leptophobia erinna[&&NHX:TOL=85038],leptophobia eucosma[&&NHX:TOL=85039],leptophobia forsteri[&&NHX:TOL=85040],leptophobia gonzaga[&&NHX:TOL=85041],leptophobia helena[&&NHX:TOL=85042],leptophobia nephthis[&&NHX:TOL=85043],leptophobia olympia[&&NHX:TOL=85044],leptophobia penthica[&&NHX:TOL=85045],leptophobia philoma[&&NHX:TOL=85046],leptophobia pinara[&&NHX:TOL=85047],leptophobia tovaria[&&NHX:TOL=85048],3 undescribed species[&&NHX:TOL=85049])leptophobia[&&NHX:TOL=76483],((pieris brassicae[&&NHX:TOL=85018],pieris brassicoides[&&NHX:TOL=85019],pieris krueperi[&&NHX:TOL=85020],pieris napi[&&NHX:TOL=85021],pieris rapae[&&NHX:TOL=85022],pieris angelika[&&NHX:TOL=88544],pieris marginalis[&&NHX:TOL=88545],pieris oleracea[&&NHX:TOL=88546],pieris virginiensis[&&NHX:TOL=88547],pieris bowdeni[&&NHX:TOL=88548],pieris bryoniae[&&NHX:TOL=88549],pieris canidia[&&NHX:TOL=88550],pieris deota[&&NHX:TOL=88551],pieris dulcinea[&&NHX:TOL=88552],pieris ergane[&&NHX:TOL=88553],pieris euorientis[&&NHX:TOL=88554],pieris mahometana[&&NHX:TOL=88555],pieris melete[&&NHX:TOL=88556],pieris narina[&&NHX:TOL=88557],pieris nesis[&&NHX:TOL=88558],pieris ochsenheimeri[&&NHX:TOL=88559],pieris persis[&&NHX:TOL=88560],pieris pseudorapae[&&NHX:TOL=88561],pieris tadjika[&&NHX:TOL=88562],pieris manni[&&NHX:TOL=88566])pieris[&&NHX:TOL=76484],stolopsyche[&&NHX:EXT=Y:TOL=76528])[&&NHX:TOL=76527])[&&NHX:TOL=76482],glennia pylotis[&&NHX:TOL=76537])[&&NHX:TOL=76478])[&&NHX:TOL=76470],reliquia santamarta[&&NHX:TOL=76538])pierina[&&NHX:TOL=76423],(((cepora timnatha[&&NHX:TOL=88576],cepora iudith[&&NHX:TOL=87397],cepora nadina[&&NHX:TOL=87398],cepora nerissa[&&NHX:TOL=87399],cepora perimale[&&NHX:TOL=87400],cepora eurygonia[&&NHX:TOL=93883],cepora fora[&&NHX:TOL=93884],cepora aspasia[&&NHX:TOL=89066],cepora abnormis[&&NHX:TOL=88568],cepora boisduvaliana[&&NHX:TOL=88569],cepora celebensis[&&NHX:TOL=88570],cepora eperia[&&NHX:TOL=88571],cepora julia[&&NHX:TOL=88572],cepora laeta[&&NHX:TOL=88573],cepora licaea[&&NHX:TOL=88574],cepora temena[&&NHX:TOL=88575])cepora[&&NHX:TOL=76496],((prioneris autothisbe[&&NHX:TOL=88577],prioneris clemanthe[&&NHX:TOL=88578],prioneris cornelia[&&NHX:TOL=88579],prioneris philonome[&&NHX:TOL=88580],prioneris sita[&&NHX:TOL=88581],prioneris thestylis[&&NHX:TOL=88582])prioneris[&&NHX:TOL=76497],((mylothris aburi[&&NHX:TOL=107789],mylothris agathina[&&NHX:TOL=85067],mylothris alberici[&&NHX:TOL=85068],mylothris alcuana[&&NHX:TOL=85069],mylothris arabicus[&&NHX:TOL=85070],mylothris asphodelus[&&NHX:TOL=85071],mylothris atewa[&&NHX:TOL=85072],mylothris basalis[&&NHX:TOL=85073],mylothris bernice[&&NHX:TOL=85074],mylothris carcassoni[&&NHX:TOL=85075],mylothris celisi[&&NHX:TOL=85076],mylothris chloris[&&NHX:TOL=85077],mylothris citrina[&&NHX:TOL=85078],mylothris continua[&&NHX:TOL=85079],mylothris crawshayi[&&NHX:TOL=85080],mylothris croceus[&&NHX:TOL=85081],mylothris dimidiata[&&NHX:TOL=107790],mylothris elodina[&&NHX:TOL=85082],mylothris erlangeri[&&NHX:TOL=85083],mylothris ertli[&&NHX:TOL=85084],mylothris eximia[&&NHX:TOL=107791],mylothris flaviana[&&NHX:TOL=85085],mylothris hilara[&&NHX:TOL=85086],mylothris humbloti[&&NHX:TOL=85087],mylothris jacksoni[&&NHX:TOL=85088],mylothris kiellandi[&&NHX:TOL=85089],mylothris kilimensis[&&NHX:TOL=85090],mylothris kiwuensis[&&NHX:TOL=85091],mylothris knoopi[&&NHX:TOL=107792],mylothris leonora[&&NHX:TOL=85092],mylothris lucens[&&NHX:TOL=107793],mylothris mafuga[&&NHX:TOL=85093],mylothris mavunda[&&NHX:TOL=85094],mylothris mortoni[&&NHX:TOL=85095],mylothris ngaziya[&&NHX:TOL=85096],mylothris nubila[&&NHX:TOL=85097],mylothris ochracea[&&NHX:TOL=85098],mylothris ochrea[&&NHX:TOL=85099],mylothris phileris[&&NHX:TOL=85100],mylothris pluviata[&&NHX:TOL=85101],mylothris polychroma[&&NHX:TOL=85102],mylothris poppea[&&NHX:TOL=85103],mylothris primulina[&&NHX:TOL=107794],mylothris rembina[&&NHX:TOL=85104],mylothris rhodope[&&NHX:TOL=85105],mylothris ruandana[&&NHX:TOL=85106],mylothris rubricosta[&&NHX:TOL=85107],mylothris rueppellii[&&NHX:TOL=85108],mylothris sagala[&&NHX:TOL=85109],mylothris schoutedenii[&&NHX:TOL=85110],mylothris schumanni[&&NHX:TOL=85111],mylothris similis[&&NHX:TOL=85112],mylothris sjoestedti[&&NHX:TOL=85113],mylothris smithii[&&NHX:TOL=85114],mylothris spica[&&NHX:TOL=85115],mylothris splendens[&&NHX:TOL=85116],mylothris sulphurea[&&NHX:TOL=85117],mylothris superbus[&&NHX:TOL=85118],mylothris talboti[&&NHX:TOL=85119],mylothris trimenia[&&NHX:TOL=85120],mylothris yulei[&&NHX:TOL=85121])mylothris[&&NHX:TOL=76499],(((aporia acraea[&&NHX:TOL=88583],aporia agathon[&&NHX:TOL=88584],aporia bieti[&&NHX:TOL=88585],aporia crataegi[&&NHX:TOL=88586],aporia delavayi[&&NHX:TOL=88587],aporia gigantea[&&NHX:TOL=88588],aporia harrietae[&&NHX:TOL=88589],aporia hippia[&&NHX:TOL=88590],aporia howarthi[&&NHX:TOL=88591],aporia largeteaui[&&NHX:TOL=88592],aporia larraldei[&&NHX:TOL=88593],aporia leucodice[&&NHX:TOL=88594],aporia monbeigi[&&NHX:TOL=88595],aporia nabellica[&&NHX:TOL=88596],aporia nishimurai[&&NHX:TOL=124452],aporia potanini[&&NHX:TOL=88597],aporia procris[&&NHX:TOL=88598],aporia shinnooka[&&NHX:TOL=124453])aporia[&&NHX:TOL=76503],coliates[&&NHX:EXT=Y:TOL=76504])[&&NHX:TOL=76502],(((delias alberti[&&NHX:TOL=88888],delias albertisi[&&NHX:TOL=88889],delias alepa[&&NHX:TOL=88890],delias angabungana[&&NHX:TOL=88891],delias angiensis[&&NHX:TOL=88892],delias antara[&&NHX:TOL=88893],delias arabuana[&&NHX:TOL=88894],delias argentata[&&NHX:TOL=88895],delias aroae[&&NHX:TOL=88896],delias autumnalis[&&NHX:TOL=88897],delias awongkor[&&NHX:TOL=88898],delias bagoe[&&NHX:TOL=88899],delias bakeri[&&NHX:TOL=88900],delias balimensis[&&NHX:TOL=88901],delias biaka[&&NHX:TOL=88902],delias bobaga[&&NHX:TOL=88903],delias bornemannii[&&NHX:TOL=88904],delias bosnikiana[&&NHX:TOL=88905],delias bothwelli[&&NHX:TOL=88906],delias caliban[&&NHX:TOL=88907],delias callima[&&NHX:TOL=88908],delias callista[&&NHX:TOL=88909],delias campbelli[&&NHX:TOL=88910],delias caroli[&&NHX:TOL=88911],delias carstensziana[&&NHX:TOL=88912],delias acalis[&&NHX:TOL=87377],delias castaneus[&&NHX:TOL=88913],delias aganippe[&&NHX:TOL=87378],delias catisa[&&NHX:TOL=88914],delias agostina[&&NHX:TOL=87379],delias catocausta[&&NHX:TOL=88915],delias argenthona[&&NHX:TOL=87380],delias chimbu[&&NHX:TOL=88916],delias aruna[&&NHX:TOL=87381],delias citrona[&&NHX:TOL=88917],delias baracasa[&&NHX:TOL=87382],delias clathrata[&&NHX:TOL=88918],delias belladonna[&&NHX:TOL=87383],delias cuningputi[&&NHX:TOL=88919],delias descombesi[&&NHX:TOL=87384],delias cyclosticha[&&NHX:TOL=88920],delias ennia[&&NHX:TOL=87385],delias dice[&&NHX:TOL=88921],delias georgina[&&NHX:TOL=87386],delias discus[&&NHX:TOL=88922],delias harpalyce[&&NHX:TOL=87387],delias dixeyi[&&NHX:TOL=88923],delias hyparete[&&NHX:TOL=87388],delias dohertyi[&&NHX:TOL=88924],delias mysis[&&NHX:TOL=87389],delias doylei[&&NHX:TOL=88925],delias nigrina[&&NHX:TOL=87390],delias eichhorni[&&NHX:TOL=88926],delias ninus[&&NHX:TOL=87391],delias elongatus[&&NHX:TOL=88927],delias nysa[&&NHX:TOL=87392],delias endela[&&NHX:TOL=88928],delias pasithoe[&&NHX:TOL=87393],delias enniana[&&NHX:TOL=88929],delias singhapura[&&NHX:TOL=87394],delias eudiabolas[&&NHX:TOL=88930],delias euphemia[&&NHX:TOL=88931],delias eximia[&&NHX:TOL=88932],delias fascelis[&&NHX:TOL=88933],delias flavissima[&&NHX:TOL=88934],delias flavistriga[&&NHX:TOL=88935],delias frater[&&NHX:TOL=88936],delias gabia[&&NHX:TOL=88937],delias geraldina[&&NHX:TOL=88938],delias germana[&&NHX:TOL=88939],delias gilliardi[&&NHX:TOL=88940],delias hagenensis[&&NHX:TOL=88941],delias hallstromi[&&NHX:TOL=88942],delias hapalina[&&NHX:TOL=88943],delias heliophora[&&NHX:TOL=88944],delias heroni[&&NHX:TOL=88945],delias hyperapproximata[&&NHX:TOL=88946],delias hypomelas[&&NHX:TOL=88947],delias iltis[&&NHX:TOL=88948],delias imitator[&&NHX:TOL=88949],delias isocharis[&&NHX:TOL=88950],delias itamputi[&&NHX:TOL=88951],delias jordani[&&NHX:TOL=88952],delias kenricki[&&NHX:TOL=88953],delias klossi[&&NHX:TOL=88954],delias konokono[&&NHX:TOL=88955],delias kummeri[&&NHX:TOL=88956],delias ladas[&&NHX:TOL=88957],delias lecerfi[&&NHX:TOL=88958],delias leucias[&&NHX:TOL=88959],delias leucobalia[&&NHX:TOL=88960],delias ligata[&&NHX:TOL=88961],delias luctuosa[&&NHX:TOL=88962],delias lytaea[&&NHX:TOL=88963],delias madetes[&&NHX:TOL=88964],delias marguerita[&&NHX:TOL=88965],delias mariae[&&NHX:TOL=88966],delias maudei[&&NHX:TOL=88967],delias mavroneria[&&NHX:TOL=88968],delias meeki[&&NHX:TOL=88969],delias mesoblema[&&NHX:TOL=88970],delias messalina[&&NHX:TOL=88971],delias microsticha[&&NHX:TOL=88972],delias mira[&&NHX:TOL=88973],delias muliensis[&&NHX:TOL=88974],delias nais[&&NHX:TOL=88975],delias narses[&&NHX:TOL=88976],delias niepelti[&&NHX:TOL=88977],delias niewenhuisi[&&NHX:TOL=88978],delias nigropunctata[&&NHX:TOL=88979],delias oktanglap[&&NHX:TOL=88980],delias ornytion[&&NHX:TOL=88981],delias pheres[&&NHX:TOL=88982],delias phippsi[&&NHX:TOL=88983],delias pratti[&&NHX:TOL=88984],delias rileyi[&&NHX:TOL=88985],delias rosamontana[&&NHX:TOL=88986],delias sagessa[&&NHX:TOL=88987],delias salvini[&&NHX:TOL=88988],delias schoenbergi[&&NHX:TOL=88989],delias sphenodiscus[&&NHX:TOL=88990],delias subapicalis[&&NHX:TOL=88991],delias talboti[&&NHX:TOL=88992],delias thompsoni[&&NHX:TOL=88993],delias totila[&&NHX:TOL=88994],delias toxopei[&&NHX:TOL=88995],delias weiskei[&&NHX:TOL=88996],delias wollastoni[&&NHX:TOL=88997],delias yabensis[&&NHX:TOL=88998],delias zebra[&&NHX:TOL=88999],delias agoranis[&&NHX:TOL=89002],delias apatela[&&NHX:TOL=89003],delias auriantica[&&NHX:TOL=89004],delias belisama[&&NHX:TOL=89005],delias benasu[&&NHX:TOL=89006],delias berinda[&&NHX:TOL=89007],delias blanca[&&NHX:TOL=89008],delias brandti[&&NHX:TOL=89009],delias candida[&&NHX:TOL=89010],delias ceneus[&&NHX:TOL=89011],delias battana[&&NHX:TOL=93875],delias chrysomelaena[&&NHX:TOL=89012],delias kazueae[&&NHX:TOL=93876],delias crithoe[&&NHX:TOL=89013],delias shirozui[&&NHX:TOL=93877],delias diaphana[&&NHX:TOL=89014],delias surprisa[&&NHX:TOL=93878],delias dorimene[&&NHX:TOL=89015],delias dorylaea[&&NHX:TOL=89016],delias dumasi[&&NHX:TOL=89017],delias duris[&&NHX:TOL=89018],delias echidna[&&NHX:TOL=89019],delias eileenae[&&NHX:TOL=89020],delias ellipsis[&&NHX:TOL=89021],delias eschatia[&&NHX:TOL=89022],delias eucharis[&&NHX:TOL=89023],delias eumolpe[&&NHX:TOL=89024],delias fasciata[&&NHX:TOL=89025],delias fruhstorferi[&&NHX:TOL=89026],delias funerea[&&NHX:TOL=89027],delias hempeli[&&NHX:TOL=89028],delias henningia[&&NHX:TOL=89029],delias hippodamia[&&NHX:TOL=89030],delias isse[&&NHX:TOL=89031],delias joiceyi[&&NHX:TOL=89032],delias kuehni[&&NHX:TOL=89033],delias lativitta[&&NHX:TOL=89034],delias lemoulti[&&NHX:TOL=89035],delias levicki[&&NHX:TOL=89036],delias manuselensis[&&NHX:TOL=89037],delias mitisi[&&NHX:TOL=89038],delias momea[&&NHX:TOL=89039],delias nuydaorum[&&NHX:TOL=89040],delias oraia[&&NHX:TOL=89041],delias patrua[&&NHX:TOL=89042],delias periboea[&&NHX:TOL=89043],delias poecila[&&NHX:TOL=89044],delias prouti[&&NHX:TOL=89045],delias ribbei[&&NHX:TOL=89046],delias rosenbergi[&&NHX:TOL=89047],delias rothschildi[&&NHX:TOL=89048],delias sacha[&&NHX:TOL=89049],delias sambawana[&&NHX:TOL=89050],delias sanaca[&&NHX:TOL=89051],delias schmassmanni[&&NHX:TOL=89052],delias schuppi[&&NHX:TOL=89053],delias splendida[&&NHX:TOL=89054],delias stresemanni[&&NHX:TOL=89055],delias subviridis[&&NHX:TOL=89056],delias themis[&&NHX:TOL=89057],delias timorensis[&&NHX:TOL=89058],delias vidua[&&NHX:TOL=89059],delias vietnamensis[&&NHX:TOL=89060],delias wilemani[&&NHX:TOL=89061],delias woodi[&&NHX:TOL=89062],delias zebuda[&&NHX:TOL=89063],delias melusina[&&NHX:TOL=89064],delias laknekei[&&NHX:TOL=110606],[&&NHX:TOL=110607])delias[&&NHX:TOL=76507],(leuciacria acuta[&&NHX:TOL=88599],leuciacria olivei[&&NHX:TOL=88600])leuciacria[&&NHX:TOL=76506])[&&NHX:TOL=76505],((melete calymnia[&&NHX:TOL=82792],melete leucadia[&&NHX:TOL=82793],melete leucanthe[&&NHX:TOL=82794],melete lycimnia[&&NHX:TOL=82795],melete polyhymnia[&&NHX:TOL=82796],melete salacia[&&NHX:TOL=82797])melete[&&NHX:TOL=76509],((oligodonta[&&NHX:EXT=Y:TOL=76512],((leodonta dysoni[&&NHX:TOL=77329],leodonta tagaste[&&NHX:TOL=77330],leodonta tellane[&&NHX:TOL=77331],leodonta zenobia[&&NHX:TOL=77332],leodonta zenobina[&&NHX:TOL=77333])leodonta[&&NHX:TOL=76514],(pereute antodyca[&&NHX:TOL=82798],pereute callinice[&&NHX:TOL=82799],pereute callinira[&&NHX:TOL=82800],pereute charops[&&NHX:TOL=82801],pereute cheops[&&NHX:TOL=82802],pereute leucodrosime[&&NHX:TOL=82803],pereute lindemannae[&&NHX:TOL=82804],pereute swainsoni[&&NHX:TOL=82805],pereute telthusa[&&NHX:TOL=82806])pereute[&&NHX:TOL=76515])[&&NHX:TOL=76513])[&&NHX:TOL=76511],((neophasia terlooii[&&NHX:TOL=88601],neophasia menapia[&&NHX:TOL=88602])neophasia[&&NHX:TOL=76519],(eucheira socialis[&&NHX:TOL=76521],((catasticta affinis[&&NHX:TOL=77334],catasticta albofasciata[&&NHX:TOL=77335],catasticta amastris[&&NHX:TOL=77336],catasticta anaitis[&&NHX:TOL=77337],catasticta apaturina[&&NHX:TOL=77338],catasticta arborardens[&&NHX:TOL=77339],catasticta atahuallpa[&&NHX:TOL=77340],catasticta aureomaculata[&&NHX:TOL=77341],catasticta bithys[&&NHX:TOL=77342],catasticta cerberus[&&NHX:TOL=77343],catasticta chelidonis[&&NHX:TOL=77344],catasticta chrysolopha[&&NHX:TOL=77345],catasticta cinerea[&&NHX:TOL=77346],catasticta colla[&&NHX:TOL=77347],catasticta collina[&&NHX:TOL=77348],catasticta cora[&&NHX:TOL=77349],catasticta corcyra[&&NHX:TOL=77350],catasticta ctemene[&&NHX:TOL=77351],catasticta discalba[&&NHX:TOL=77352],catasticta distincta[&&NHX:TOL=77353],catasticta duida[&&NHX:TOL=77354],catasticta eurigania[&&NHX:TOL=77355],catasticta ferra[&&NHX:TOL=77356],catasticta flisa[&&NHX:TOL=77357],catasticta frontina[&&NHX:TOL=77358],catasticta fulva[&&NHX:TOL=77359],catasticta grisea[&&NHX:TOL=77360],catasticta hebra[&&NHX:TOL=77361],catasticta hegemon[&&NHX:TOL=77362],catasticta huancabamensis[&&NHX:TOL=77363],catasticta huebneri[&&NHX:TOL=77364],catasticta incerta[&&NHX:TOL=77365],catasticta lanceolata[&&NHX:TOL=77366],catasticta leucophaea[&&NHX:TOL=77367],catasticta lisa[&&NHX:TOL=77368],catasticta ludovici[&&NHX:TOL=77369],catasticta lycurgus[&&NHX:TOL=77370],catasticta manco[&&NHX:TOL=77371],catasticta marcapita[&&NHX:TOL=77372],catasticta modesta[&&NHX:TOL=77373],catasticta nimbata[&&NHX:TOL=77374],catasticta nimbice[&&NHX:TOL=77375],catasticta notha[&&NHX:TOL=77376],catasticta paucartambo[&&NHX:TOL=77377],catasticta pharnakia[&&NHX:TOL=77378],catasticta philais[&&NHX:TOL=77379],catasticta philodora[&&NHX:TOL=77380],catasticta philone[&&NHX:TOL=77381],catasticta philoscia[&&NHX:TOL=77382],catasticta philothea[&&NHX:TOL=77383],catasticta pieris[&&NHX:TOL=77384],catasticta pinava[&&NHX:TOL=77385],catasticta pluvius[&&NHX:TOL=77386],catasticta potameoides[&&NHX:TOL=77387],catasticta poujadei[&&NHX:TOL=77388],catasticta prioneris[&&NHX:TOL=77389],catasticta radiata[&&NHX:TOL=77390],catasticta reducta[&&NHX:TOL=77391],catasticta revancha[&&NHX:TOL=77392],catasticta rileya[&&NHX:TOL=77393],catasticta rosea[&&NHX:TOL=77394],catasticta scaeva[&&NHX:TOL=77395],catasticta scurra[&&NHX:TOL=77396],catasticta seitzi[&&NHX:TOL=77397],catasticta sella[&&NHX:TOL=77398],catasticta semiramis[&&NHX:TOL=77399],catasticta similis[&&NHX:TOL=77400],catasticta sinapina[&&NHX:TOL=77401],catasticta sisamnus[&&NHX:TOL=77402],catasticta smithia[&&NHX:TOL=77403],catasticta socorroensis[&&NHX:TOL=77404],catasticta striata[&&NHX:TOL=77405],catasticta suadela[&&NHX:TOL=77406],catasticta suasa[&&NHX:TOL=77407],catasticta superba[&&NHX:TOL=77408],catasticta susiana[&&NHX:TOL=77409],catasticta tamsa[&&NHX:TOL=77410],catasticta teutamis[&&NHX:TOL=77411],catasticta teutila[&&NHX:TOL=77412],catasticta theresa[&&NHX:TOL=77413],catasticta thomasorum[&&NHX:TOL=77414],catasticta toca[&&NHX:TOL=77415],catasticta tomyris[&&NHX:TOL=77416],catasticta tricolor[&&NHX:TOL=77417],catasticta troezene[&&NHX:TOL=77418],catasticta truncata[&&NHX:TOL=77419],catasticta uricoecheae[&&NHX:TOL=77420],catasticta vulnerata[&&NHX:TOL=77421],catasticta watkinsi[&&NHX:TOL=77422],catasticta n. sp. 1[&&NHX:TOL=77423],catasticta n. sp. 2[&&NHX:TOL=77424],catasticta n. sp. 3[&&NHX:TOL=77425],catasticta n. sp. 4[&&NHX:TOL=77426],catasticta n. sp. 5[&&NHX:TOL=77427])catasticta[&&NHX:TOL=76524],((charonias eurytele[&&NHX:TOL=77327],charonias theano[&&NHX:TOL=77328])charonias[&&NHX:TOL=76523],archonias brassolis[&&NHX:TOL=76517])[&&NHX:TOL=138027])[&&NHX:TOL=76522])[&&NHX:TOL=76520])[&&NHX:TOL=76518])[&&NHX:TOL=76510])[&&NHX:TOL=76508])[&&NHX:TOL=76500])[&&NHX:TOL=138026])[&&NHX:TOL=76498])[&&NHX:TOL=138025])aporiina[&&NHX:TOL=76425],((belenois albomaculatus[&&NHX:TOL=84990],belenois aldabrensis[&&NHX:TOL=84991],belenois anomala[&&NHX:TOL=84992],belenois antsianaka[&&NHX:TOL=84993],belenois aurota[&&NHX:TOL=84994],belenois calypso[&&NHX:TOL=84995],belenois crawshayi[&&NHX:TOL=84996],belenois creona[&&NHX:TOL=84997],belenois diminuta[&&NHX:TOL=84998],belenois gidica[&&NHX:TOL=84999],belenois grandidieri[&&NHX:TOL=85000],belenois hedyle[&&NHX:TOL=85001],belenois helcida[&&NHX:TOL=85002],belenois ianthe[&&NHX:TOL=85003],belenois larima[&&NHX:TOL=85004],belenois mabella[&&NHX:TOL=85005],belenois margaritacea[&&NHX:TOL=85006],belenois ogygia[&&NHX:TOL=85007],belenois raffrayi[&&NHX:TOL=85008],belenois rubrosignata[&&NHX:TOL=85009],belenois solilucis[&&NHX:TOL=85010],belenois subeida[&&NHX:TOL=85011],belenois sudanensis[&&NHX:TOL=85012],belenois theora[&&NHX:TOL=85013],belenois theuszi[&&NHX:TOL=85014],belenois thysa[&&NHX:TOL=85015],belenois victoria[&&NHX:TOL=85016],belenois zochalia[&&NHX:TOL=85017],belenois java[&&NHX:TOL=87395])belenois[&&NHX:TOL=76427],(dixeia capricornus[&&NHX:TOL=85050],dixeia cebron[&&NHX:TOL=85051],dixeia charina[&&NHX:TOL=85052],dixeia dixeyi[&&NHX:TOL=85053],dixeia doxo[&&NHX:TOL=85054],dixeia leucophanes[&&NHX:TOL=85055],dixeia orbona[&&NHX:TOL=85056],dixeia pigea[&&NHX:TOL=85057],dixeia piscicollis[&&NHX:TOL=85058],dixeia spilleri[&&NHX:TOL=85059])dixeia[&&NHX:TOL=76428])[&&NHX:TOL=76426])[&&NHX:TOL=76424])[&&NHX:TOL=76422])pierini[&&NHX:TOL=76420])[&&NHX:TOL=76418])[&&NHX:TOL=76416])[&&NHX:TOL=76414])pierinae[&&NHX:TOL=12216])[&&NHX:TOL=66507])pieridae[&&NHX:TOL=12176],((((((euselasia albomaculiga[&&NHX:TOL=104040],euselasia alcmena[&&NHX:TOL=104041],euselasia amblypodia[&&NHX:TOL=104042],euselasia amphidecta[&&NHX:TOL=104043],euselasia andreae[&&NHX:TOL=104044],euselasia angulata[&&NHX:TOL=104045],euselasia anica[&&NHX:TOL=104046],euselasia arbas[&&NHX:TOL=104047],euselasia archelaus[&&NHX:TOL=104048],euselasia argentea[&&NHX:TOL=104049],euselasia artos[&&NHX:TOL=104050],euselasia athena[&&NHX:TOL=104051],euselasia attrita[&&NHX:TOL=104052],euselasia aurantia[&&NHX:TOL=104053],euselasia aurantiaca[&&NHX:TOL=104054],euselasia authe[&&NHX:TOL=104055],euselasia baucis[&&NHX:TOL=104056],euselasia bettina[&&NHX:TOL=104057],euselasia bilineata[&&NHX:TOL=104058],euselasia brevicauda[&&NHX:TOL=104059],euselasia cafusa[&&NHX:TOL=104060],euselasia calligramma[&&NHX:TOL=104061],euselasia candaria[&&NHX:TOL=104062],euselasia cataleuca[&&NHX:TOL=104063],euselasia catoleuce[&&NHX:TOL=104064],euselasia charilis[&&NHX:TOL=104065],euselasia chinguala[&&NHX:TOL=104066],euselasia chrysippe[&&NHX:TOL=104067],euselasia clesa[&&NHX:TOL=104068],euselasia clithra[&&NHX:TOL=104069],euselasia corduena[&&NHX:TOL=104070],euselasia crinon[&&NHX:TOL=104071],euselasia cucuta[&&NHX:TOL=104072],euselasia cuprea[&&NHX:TOL=104073],euselasia cyanira[&&NHX:TOL=104074],euselasia cyanofusa[&&NHX:TOL=104075],euselasia dolichos[&&NHX:TOL=104076],euselasia dorina[&&NHX:TOL=104077],euselasia eberti[&&NHX:TOL=104078],euselasia effima[&&NHX:TOL=104079],euselasia ella[&&NHX:TOL=104080],euselasia erilis[&&NHX:TOL=104081],euselasia erythraea[&&NHX:TOL=104082],euselasia ethemon[&&NHX:TOL=104083],euselasia euboea[&&NHX:TOL=104084],euselasia eubotes[&&NHX:TOL=104085],euselasia eubule[&&NHX:TOL=104086],euselasia eucerus[&&NHX:TOL=104087],euselasia eucrates[&&NHX:TOL=104088],euselasia eucritus[&&NHX:TOL=104089],euselasia eugeon[&&NHX:TOL=104090],euselasia euhemerus[&&NHX:TOL=104091],euselasia eulione[&&NHX:TOL=104092],euselasia eumedia[&&NHX:TOL=104093],euselasia eumenes[&&NHX:TOL=104094],euselasia eumithres[&&NHX:TOL=104095],euselasia eunaeus[&&NHX:TOL=104096],euselasia euodias[&&NHX:TOL=104097],euselasia euoras[&&NHX:TOL=104098],euselasia eupatra[&&NHX:TOL=104099],euselasia euphaes[&&NHX:TOL=104100],euselasia euploea[&&NHX:TOL=104101],euselasia euriteus[&&NHX:TOL=104102],euselasia euromus[&&NHX:TOL=104103],euselasia eurymachus[&&NHX:TOL=104104],euselasia eurypus[&&NHX:TOL=104105],euselasia eustola[&&NHX:TOL=104106],euselasia eutaea[&&NHX:TOL=104107],euselasia eutychus[&&NHX:TOL=104108],euselasia euryone[&&NHX:TOL=104109],euselasia eusepus[&&NHX:TOL=104110],euselasia extensa[&&NHX:TOL=104111],euselasia fabia[&&NHX:TOL=104112],euselasia fervida[&&NHX:TOL=104113],euselasia fayneli[&&NHX:TOL=124676],euselasia fournierae[&&NHX:TOL=104114],euselasia gelanor[&&NHX:TOL=104115],euselasia gelon[&&NHX:TOL=104116],euselasia geon[&&NHX:TOL=104117],euselasia gordios[&&NHX:TOL=104118],euselasia gradata[&&NHX:TOL=104119],euselasia gyda[&&NHX:TOL=104120],euselasia hahneli[&&NHX:TOL=104121],euselasia hieronymi[&&NHX:TOL=104122],euselasia hygenius[&&NHX:TOL=104123],euselasia hypophaea[&&NHX:TOL=104124],euselasia ignitus[&&NHX:TOL=104125],euselasia illarina[&&NHX:TOL=104126],euselasia inconspicua[&&NHX:TOL=104127],euselasia inini[&&NHX:TOL=104128],euselasia issoria[&&NHX:TOL=104129],euselasia janigena[&&NHX:TOL=104130],euselasia jigginsi[&&NHX:TOL=104131],euselasia julia[&&NHX:TOL=104132],euselasia kartopus[&&NHX:TOL=104133],euselasia labdacus[&&NHX:TOL=104134],euselasia leucon[&&NHX:TOL=104135],euselasia leucophryna[&&NHX:TOL=104136],euselasia licinia[&&NHX:TOL=104137],euselasia lisias[&&NHX:TOL=104138],euselasia lycaeus[&&NHX:TOL=104139],euselasia lysimachus[&&NHX:TOL=104140],euselasia manoa[&&NHX:TOL=104141],euselasia mapatayna[&&NHX:TOL=104142],euselasia marica[&&NHX:TOL=104143],euselasia matuta[&&NHX:TOL=104144],euselasia mazaca[&&NHX:TOL=104145],euselasia melaphaea[&&NHX:TOL=104146],euselasia micaela[&&NHX:TOL=104147],euselasia michaeli[&&NHX:TOL=124677],euselasia midas[&&NHX:TOL=104148],euselasia mirania[&&NHX:TOL=104149],euselasia modesta[&&NHX:TOL=104150],euselasia murina[&&NHX:TOL=104151],euselasia mutator[&&NHX:TOL=104152],euselasia mys[&&NHX:TOL=104153],euselasia mystica[&&NHX:TOL=104154],euselasia nauca[&&NHX:TOL=104155],euselasia onorata[&&NHX:TOL=104156],euselasia opalescens[&&NHX:TOL=104157],euselasia opalina[&&NHX:TOL=104158],euselasia opimia[&&NHX:TOL=104159],euselasia orba[&&NHX:TOL=104160],euselasia orfita[&&NHX:TOL=104161],euselasia orion[&&NHX:TOL=104162],euselasia palla[&&NHX:TOL=104163],euselasia pance[&&NHX:TOL=104164],euselasia parca[&&NHX:TOL=104165],euselasia pellonia[&&NHX:TOL=104166],euselasia pellos[&&NHX:TOL=104167],euselasia pelor[&&NHX:TOL=104168],euselasia perisama[&&NHX:TOL=104169],euselasia phedica[&&NHX:TOL=104170],euselasia phelina[&&NHX:TOL=104171],euselasia pillaca[&&NHX:TOL=104172],euselasia pontasis[&&NHX:TOL=124678],euselasia portentosa[&&NHX:TOL=104173],euselasia praecipua[&&NHX:TOL=104174],euselasia praeclara[&&NHX:TOL=104175],euselasia procula[&&NHX:TOL=104176],euselasia pseudomys[&&NHX:TOL=104177],euselasia pullata[&&NHX:TOL=104178],euselasia pusilla[&&NHX:TOL=104179],euselasia rasonea[&&NHX:TOL=104180],euselasia rava[&&NHX:TOL=104181],euselasia regipennis[&&NHX:TOL=104182],euselasia rhodogyne[&&NHX:TOL=104183],euselasia rhodon[&&NHX:TOL=104184],euselasia rubrocilia[&&NHX:TOL=104185],euselasia saulina[&&NHX:TOL=104186],euselasia scotinosa[&&NHX:TOL=104187],euselasia seitzi[&&NHX:TOL=104188],euselasia serapis[&&NHX:TOL=104189],euselasia sergia[&&NHX:TOL=104190],euselasia subargentea[&&NHX:TOL=104191],euselasia tarinta[&&NHX:TOL=104192],euselasia teleclus[&&NHX:TOL=104193],euselasia thaumata[&&NHX:TOL=104194],euselasia thucydides[&&NHX:TOL=104195],euselasia thusnelda[&&NHX:TOL=104196],euselasia toppini[&&NHX:TOL=104197],euselasia uria[&&NHX:TOL=104198],euselasia urites[&&NHX:TOL=104199],euselasia utica[&&NHX:TOL=104200],euselasia uzita[&&NHX:TOL=104201],euselasia venezolana[&&NHX:TOL=104202],euselasia violacea[&&NHX:TOL=104203],euselasia violetta[&&NHX:TOL=104204],euselasia zara[&&NHX:TOL=104205],euselasia zena[&&NHX:TOL=104206])euselasia[&&NHX:TOL=103516],(hades hecamede[&&NHX:TOL=103519],hades noctula[&&NHX:TOL=103520])hades[&&NHX:TOL=103517],methone cecilia[&&NHX:TOL=103518])euselasiini[&&NHX:TOL=103506],styx infernalis[&&NHX:TOL=103507],corrachia leucoplaga[&&NHX:TOL=12219])euselasiinae[&&NHX:TOL=12220],((((eunogyra curupira[&&NHX:TOL=104223],eunogyra satyrus[&&NHX:TOL=104224])eunogyra[&&NHX:TOL=104207],((teratophthalma axilia[&&NHX:TOL=104225],teratophthalma bacche[&&NHX:TOL=104226],teratophthalma maenades[&&NHX:TOL=104227],teratophthalma monochroma[&&NHX:TOL=104228],teratophthalma phelina[&&NHX:TOL=104229])teratophthalma[&&NHX:TOL=104213],((mesosemia ackeryi[&&NHX:TOL=104260],mesosemia acuta[&&NHX:TOL=104261],mesosemia adida[&&NHX:TOL=104262],mesosemia ahava[&&NHX:TOL=104263],mesosemia albipuncta[&&NHX:TOL=104264],mesosemia amarantus[&&NHX:TOL=104265],mesosemia anceps[&&NHX:TOL=104266],mesosemia antaerice[&&NHX:TOL=104267],mesosemia araeostyla[&&NHX:TOL=104268],mesosemia asa[&&NHX:TOL=104269],mesosemia bahia[&&NHX:TOL=104270],mesosemia bella[&&NHX:TOL=104271],mesosemia carderi[&&NHX:TOL=104272],mesosemia carissima[&&NHX:TOL=104273],mesosemia ceropia[&&NHX:TOL=104274],mesosemia cippus[&&NHX:TOL=104275],mesosemia coelestis[&&NHX:TOL=104276],mesosemia cordillerensis[&&NHX:TOL=104277],mesosemia cyanira[&&NHX:TOL=104278],mesosemia cymotaxis[&&NHX:TOL=104279],mesosemia decolorata[&&NHX:TOL=104280],mesosemia dulcis[&&NHX:TOL=104281],mesosemia ephyne[&&NHX:TOL=104282],mesosemia epidius[&&NHX:TOL=104283],mesosemia erinnya[&&NHX:TOL=104284],mesosemia esmeralda[&&NHX:TOL=104285],mesosemia esperanza[&&NHX:TOL=104286],mesosemia eugenea[&&NHX:TOL=104287],mesosemia eumene[&&NHX:TOL=104288],mesosemia eurythmia[&&NHX:TOL=104289],mesosemia evias[&&NHX:TOL=104290],mesosemia friburgensis[&&NHX:TOL=104291],mesosemia gaudiolum[&&NHX:TOL=104292],mesosemia gemina[&&NHX:TOL=104293],mesosemia gertraudis[&&NHX:TOL=104294],mesosemia gneris[&&NHX:TOL=104295],mesosemia grandis[&&NHX:TOL=104296],mesosemia harveyi[&&NHX:TOL=104297],mesosemia hedwigis[&&NHX:TOL=104298],mesosemia hesperina[&&NHX:TOL=104299],mesosemia hypermegala[&&NHX:TOL=104300],mesosemia ibycus[&&NHX:TOL=104301],mesosemia impedita[&&NHX:TOL=104302],mesosemia inconspicua[&&NHX:TOL=104303],mesosemia isshia[&&NHX:TOL=104304],mesosemia jucunda[&&NHX:TOL=104305],mesosemia judicialis[&&NHX:TOL=104306],mesosemia kahuapayani[&&NHX:TOL=124719],mesosemia kwokii[&&NHX:TOL=104307],mesosemia lacernata[&&NHX:TOL=104308],mesosemia lamachus[&&NHX:TOL=104309],mesosemia lapillus[&&NHX:TOL=104310],mesosemia latizonata[&&NHX:TOL=104311],mesosemia loruhama[&&NHX:TOL=104312],mesosemia luperca[&&NHX:TOL=104313],mesosemia lycorias[&&NHX:TOL=104314],mesosemia macella[&&NHX:TOL=104315],mesosemia machaera[&&NHX:TOL=104316],mesosemia macrina[&&NHX:TOL=104317],mesosemia maeotis[&&NHX:TOL=104318],mesosemia magete[&&NHX:TOL=104319],mesosemia mamilia[&&NHX:TOL=104320],mesosemia mancia[&&NHX:TOL=104321],mesosemia mathania[&&NHX:TOL=104322],mesosemia mayi[&&NHX:TOL=104323],mesosemia meeda[&&NHX:TOL=104324],mesosemia mehida[&&NHX:TOL=104325],mesosemia melaene[&&NHX:TOL=104326],mesosemia melese[&&NHX:TOL=104327],mesosemia melpia[&&NHX:TOL=104328],mesosemia menoetes[&&NHX:TOL=104329],mesosemia mesoba[&&NHX:TOL=104330],mesosemia messeis[&&NHX:TOL=104331],mesosemia methion[&&NHX:TOL=104332],mesosemia metope[&&NHX:TOL=104333],mesosemia metuana[&&NHX:TOL=104334],mesosemia metura[&&NHX:TOL=104335],mesosemia mevania[&&NHX:TOL=104336],mesosemia minos[&&NHX:TOL=104337],mesosemia minutula[&&NHX:TOL=104338],mesosemia misipsa[&&NHX:TOL=104339],mesosemia modulata[&&NHX:TOL=104340],mesosemia moesia[&&NHX:TOL=104341],mesosemia mosera[&&NHX:TOL=104342],mesosemia myonia[&&NHX:TOL=104343],mesosemia myrmecias[&&NHX:TOL=104344],mesosemia naiadella[&&NHX:TOL=104345],mesosemia nerine[&&NHX:TOL=104346],mesosemia nyctea[&&NHX:TOL=104348],mesosemia nympharena[&&NHX:TOL=104347],mesosemia odice[&&NHX:TOL=104349],mesosemia olivencia[&&NHX:TOL=104350],mesosemia orbona[&&NHX:TOL=104351],mesosemia ozora[&&NHX:TOL=104352],mesosemia pacifica[&&NHX:TOL=104353],mesosemia pardalis[&&NHX:TOL=104354],mesosemia phace[&&NHX:TOL=104355],mesosemia philocles[&&NHX:TOL=104356],mesosemia praeculta[&&NHX:TOL=104357],mesosemia putli[&&NHX:TOL=104358],mesosemia quadrilineata[&&NHX:TOL=124720],mesosemia reba[&&NHX:TOL=104359],mesosemia rhodia[&&NHX:TOL=104360],mesosemia scotina[&&NHX:TOL=104361],mesosemia sibyllina[&&NHX:TOL=104366],mesosemia sifia[&&NHX:TOL=104362],mesosemia sirenia[&&NHX:TOL=104363],mesosemia steli[&&NHX:TOL=104364],mesosemia subtilis[&&NHX:TOL=104365],mesosemia synnephis[&&NHX:TOL=104367],mesosemia telegone[&&NHX:TOL=104368],mesosemia tenebricosa[&&NHX:TOL=104369],mesosemia teulem[&&NHX:TOL=104370],mesosemia thera[&&NHX:TOL=104371],mesosemia thetys[&&NHX:TOL=104372],mesosemia thyas[&&NHX:TOL=104373],mesosemia thymetus[&&NHX:TOL=104374],mesosemia ulrica[&&NHX:TOL=104375],mesosemia veneris[&&NHX:TOL=104376],mesosemia walteri[&&NHX:TOL=104377],mesosemia zanoa[&&NHX:TOL=104378],mesosemia zikla[&&NHX:TOL=104379],mesosemia zonalis[&&NHX:TOL=104380],mesosemia zorea[&&NHX:TOL=104381])mesosemia[&&NHX:TOL=104210],((leucochimona aequatorialis[&&NHX:TOL=104238],leucochimona anophthalma[&&NHX:TOL=104393],leucochimona hyphea[&&NHX:TOL=104239],leucochimona icare[&&NHX:TOL=104240],leucochimona iphias[&&NHX:TOL=104241],leucochimona lagora[&&NHX:TOL=104242],leucochimona lepida[&&NHX:TOL=104243],leucochimona matisca[&&NHX:TOL=104244],leucochimona molina[&&NHX:TOL=104245],leucochimona vestalis[&&NHX:TOL=104246])leucochimona[&&NHX:TOL=104208],(semomesia alyattes[&&NHX:TOL=104230],semomesia capanea[&&NHX:TOL=104231],semomesia croesus[&&NHX:TOL=104232],semomesia geminus[&&NHX:TOL=104233],semomesia macaris[&&NHX:TOL=104234],semomesia marisa[&&NHX:TOL=104235],semomesia nesti[&&NHX:TOL=104236],semomesia tenella[&&NHX:TOL=104237])semomesia[&&NHX:TOL=104212],((perophthalma lasciva[&&NHX:TOL=104247],perophthalma lasus[&&NHX:TOL=104248],perophthalma tullius[&&NHX:TOL=104249])perophthalma[&&NHX:TOL=104211],(mesophthalma idotea[&&NHX:TOL=104250],mesophthalma mirita[&&NHX:TOL=104251])mesophthalma[&&NHX:TOL=104209])[&&NHX:TOL=113118])[&&NHX:TOL=113117])[&&NHX:TOL=113116])[&&NHX:TOL=113115])mesosemiina[&&NHX:TOL=104221],(((hyphilaria anthias[&&NHX:TOL=104394],hyphilaria nicia[&&NHX:TOL=104395],hyphilaria parthenis[&&NHX:TOL=104396],hyphilaria thasus[&&NHX:TOL=104421])hyphilaria[&&NHX:TOL=104217],(napaea actoris[&&NHX:TOL=104416],napaea beltiana[&&NHX:TOL=104399],napaea calitra[&&NHX:TOL=104418],napaea elisae[&&NHX:TOL=104401],napaea eucharila[&&NHX:TOL=104402],napaea fratelloi[&&NHX:TOL=124708],napaea gynaecomorpha[&&NHX:TOL=124709],napaea heteroea[&&NHX:TOL=104420],napaea joinvilea[&&NHX:TOL=124710],napaea melampia[&&NHX:TOL=104403],napaea mellosa[&&NHX:TOL=124711],napaea merula[&&NHX:TOL=104404],napaea rufolimba[&&NHX:TOL=124712],napaea sylva[&&NHX:TOL=104410],napaea zikani[&&NHX:TOL=104415])napaea[&&NHX:TOL=104219])[&&NHX:TOL=124707],((voltinia agroeca[&&NHX:TOL=104398],voltinia cebrenia[&&NHX:TOL=124714],voltinia danforthi[&&NHX:TOL=104400],voltinia dramba[&&NHX:TOL=124721],voltinia phryxe[&&NHX:TOL=104409],voltinia radiata[&&NHX:TOL=104391],voltinia sanarita[&&NHX:TOL=104215],voltinia theata[&&NHX:TOL=104392],voltinia tumbesia[&&NHX:TOL=104413],voltinia umbra[&&NHX:TOL=104414])voltinia[&&NHX:TOL=104220],(((hermathena candidata[&&NHX:TOL=104258],hermathena eburna[&&NHX:TOL=124706],hermathena oweni[&&NHX:TOL=104259])hermathena[&&NHX:TOL=104216],(ithomiola bajotanos[&&NHX:TOL=124716],ithomiola buckleyi[&&NHX:TOL=104252],ithomiola calculosa[&&NHX:TOL=124717],ithomiola callixena[&&NHX:TOL=104253],ithomiola cribralis[&&NHX:TOL=124718],ithomiola floralis[&&NHX:TOL=104256],ithomiola neildi[&&NHX:TOL=104405],ithomiola nepos[&&NHX:TOL=104406],ithomiola orpheus[&&NHX:TOL=104407],ithomiola tanos[&&NHX:TOL=104411],ithomiola theages[&&NHX:TOL=104412])ithomiola[&&NHX:TOL=104218])[&&NHX:TOL=113121],ionotus alector[&&NHX:TOL=104417])[&&NHX:TOL=124715])[&&NHX:TOL=124713])napaeina[&&NHX:TOL=104222])mesosemiini[&&NHX:TOL=103508],(((alesa amesis[&&NHX:TOL=104529],alesa esmeralda[&&NHX:TOL=125194],alesa fournierae[&&NHX:TOL=104530],alesa hemiurga[&&NHX:TOL=104531],alesa lipara[&&NHX:TOL=104532],alesa prema[&&NHX:TOL=104533],alesa rothschildi[&&NHX:TOL=104534],alesa telephae[&&NHX:TOL=104535],alesa thelydrias[&&NHX:TOL=104536])alesa[&&NHX:TOL=104494],(eurybia albiseriata[&&NHX:TOL=104545],eurybia caerulescens[&&NHX:TOL=104546],eurybia carolina[&&NHX:TOL=104547],eurybia cyclopia[&&NHX:TOL=104548],eurybia dardus[&&NHX:TOL=104549],eurybia donna[&&NHX:TOL=104550],eurybia elvina[&&NHX:TOL=104551],eurybia franciscana[&&NHX:TOL=104552],eurybia halimede[&&NHX:TOL=104553],eurybia jemima[&&NHX:TOL=104554],eurybia juturna[&&NHX:TOL=104555],eurybia latifasciata[&&NHX:TOL=104556],eurybia lycisca[&&NHX:TOL=104557],eurybia misellivestis[&&NHX:TOL=104558],eurybia molochina[&&NHX:TOL=104559],eurybia nicaeus[&&NHX:TOL=104560],eurybia patrona[&&NHX:TOL=104561],eurybia pergaea[&&NHX:TOL=104562],eurybia rubeolata[&&NHX:TOL=104563],eurybia silaceana[&&NHX:TOL=104564],eurybia unxia[&&NHX:TOL=104565])eurybia[&&NHX:TOL=104495])eurybiini[&&NHX:TOL=103509],((amarynthis meneria[&&NHX:TOL=104628],amphiselenis chama[&&NHX:TOL=104629],(ancycluris aristodorus[&&NHX:TOL=104673],ancycluris aulestes[&&NHX:TOL=104674],ancycluris colubra[&&NHX:TOL=104675],ancycluris etias[&&NHX:TOL=104676],ancycluris formosissima[&&NHX:TOL=104677],ancycluris inca[&&NHX:TOL=104678],ancycluris jurgensenii[&&NHX:TOL=104679],ancycluris meliboeus[&&NHX:TOL=104680],ancycluris melior[&&NHX:TOL=104681],ancycluris miniola[&&NHX:TOL=104682],ancycluris mira[&&NHX:TOL=104683],ancycluris paetula[&&NHX:TOL=104684],ancycluris paramba[&&NHX:TOL=104685],ancycluris rubrofilum[&&NHX:TOL=104686],ancycluris tedea[&&NHX:TOL=104687],ancycluris n. sp.[&&NHX:TOL=104688])ancycluris[&&NHX:TOL=104630],(baeotis attali[&&NHX:TOL=104865],baeotis bacaenis[&&NHX:TOL=104866],baeotis bacaenita[&&NHX:TOL=104867],baeotis barce[&&NHX:TOL=104868],baeotis capreolus[&&NHX:TOL=104869],baeotis cephissa[&&NHX:TOL=104870],baeotis choroniensis[&&NHX:TOL=104871],baeotis creusis[&&NHX:TOL=104872],baeotis elegantula[&&NHX:TOL=104873],baeotis euprepes[&&NHX:TOL=104874],baeotis felix[&&NHX:TOL=104875],baeotis hisbon[&&NHX:TOL=104876],baeotis johannae[&&NHX:TOL=104877],baeotis kadenii[&&NHX:TOL=104878],baeotis melanis[&&NHX:TOL=104879],baeotis nesaea[&&NHX:TOL=104880],baeotis prima[&&NHX:TOL=104881],baeotis staudingeri[&&NHX:TOL=104882],baeotis sulphurea[&&NHX:TOL=104883],baeotis zonata[&&NHX:TOL=104884])baeotis[&&NHX:TOL=104631],barbicornis basilis[&&NHX:TOL=104632],(brachyglenis dinora[&&NHX:TOL=104853],brachyglenis dodone[&&NHX:TOL=104854],brachyglenis drymo[&&NHX:TOL=104855],brachyglenis esthema[&&NHX:TOL=104856])brachyglenis[&&NHX:TOL=104633],(caria castalia[&&NHX:TOL=105091],caria chrysame[&&NHX:TOL=105092],caria domitianus[&&NHX:TOL=105093],caria ino[&&NHX:TOL=105094],caria mantinea[&&NHX:TOL=105095],caria marsyas[&&NHX:TOL=105096],caria melino[&&NHX:TOL=105097],caria plutargus[&&NHX:TOL=105098],caria rhacotis[&&NHX:TOL=105099],caria sponsa[&&NHX:TOL=105100],caria stillaticia[&&NHX:TOL=105101],caria tabrenthia[&&NHX:TOL=105102],caria trochilus[&&NHX:TOL=105103],caria n. sp.[&&NHX:TOL=105104])caria[&&NHX:TOL=104635],(cariomothis chia[&&NHX:TOL=104917],cariomothis erotylus[&&NHX:TOL=104918],cariomothis erythromelas[&&NHX:TOL=104919],cariomothis poeciloptera[&&NHX:TOL=104920])cariomothis[&&NHX:TOL=104636],(cartea chiribiquetensis[&&NHX:TOL=125196],cartea ucayala[&&NHX:TOL=105165],cartea vitula[&&NHX:TOL=105166])cartea[&&NHX:TOL=104637],(chalodeta chaonitis[&&NHX:TOL=104887],chalodeta chelonis[&&NHX:TOL=104888],chalodeta chitinosa[&&NHX:TOL=104889],chalodeta chlosine[&&NHX:TOL=104890],chalodeta lypera[&&NHX:TOL=104891],chalodeta panurga[&&NHX:TOL=104892],chalodeta pescada[&&NHX:TOL=104893],chalodeta theodora[&&NHX:TOL=104894])chalodeta[&&NHX:TOL=104638],(chamaelimnas briola[&&NHX:TOL=105167],chamaelimnas cercides[&&NHX:TOL=105168],chamaelimnas cydonia[&&NHX:TOL=105169],chamaelimnas joviana[&&NHX:TOL=105170],chamaelimnas splendens[&&NHX:TOL=105171],chamaelimnas tircis[&&NHX:TOL=105172])chamaelimnas[&&NHX:TOL=104639],((seco aphanis[&&NHX:TOL=105178],(seco calagutis[&&NHX:TOL=105179],seco ocellata[&&NHX:TOL=105180])[&&NHX:TOL=113009])seco[&&NHX:TOL=105176],(((charis anius[&&NHX:TOL=105109],charis cadytis[&&NHX:TOL=105110])charis[&&NHX:TOL=104640],(calephelis acapulcoensis[&&NHX:TOL=105111],calephelis argyrodines[&&NHX:TOL=105112],calephelis arizonensis[&&NHX:TOL=105113],calephelis aymaran[&&NHX:TOL=105114],calephelis azteca[&&NHX:TOL=105115],calephelis bajaensis[&&NHX:TOL=105116],calephelis borealis[&&NHX:TOL=105117],calephelis braziliensis[&&NHX:TOL=105118],calephelis browni[&&NHX:TOL=105119],calephelis burgeri[&&NHX:TOL=105120],calephelis clenchi[&&NHX:TOL=105122],calephelis costaricicola[&&NHX:TOL=105123],calephelis dreisbachi[&&NHX:TOL=105124],calephelis exiguus[&&NHX:TOL=105125],calephelis freemani[&&NHX:TOL=105126],calephelis fulmen[&&NHX:TOL=105127],calephelis guatemala[&&NHX:TOL=105128],calephelis huasteca[&&NHX:TOL=105129],calephelis inca[&&NHX:TOL=105130],calephelis laverna[&&NHX:TOL=105132],calephelis matheri[&&NHX:TOL=105133],calephelis maya[&&NHX:TOL=105134],calephelis mexicana[&&NHX:TOL=105135],calephelis montezuma[&&NHX:TOL=105136],calephelis muticum[&&NHX:TOL=105137],calephelis nemesis[&&NHX:TOL=105138],calephelis nilus[&&NHX:TOL=105139],calephelis perditalis[&&NHX:TOL=105140],calephelis rawsoni[&&NHX:TOL=105141],calephelis sacapulas[&&NHX:TOL=105142],calephelis schausi[&&NHX:TOL=105143],calephelis sinaloensis[&&NHX:TOL=105144],calephelis sixola[&&NHX:TOL=105145],calephelis sodalis[&&NHX:TOL=105146],calephelis stallingsi[&&NHX:TOL=105147],calephelis tapuyo[&&NHX:TOL=105148],calephelis tikal[&&NHX:TOL=105149],((calephelis velutina[&&NHX:TOL=105150],calephelis iris[&&NHX:TOL=105131])[&&NHX:TOL=113013],calephelis candiope[&&NHX:TOL=105121])[&&NHX:TOL=113012],calephelis virginiensis[&&NHX:TOL=105151],calephelis wellingi[&&NHX:TOL=105152],calephelis wrighti[&&NHX:TOL=105153],calephelis yautepequensis[&&NHX:TOL=105154],calephelis yucatana[&&NHX:TOL=105155])calephelis[&&NHX:TOL=104634])[&&NHX:TOL=113011],(((detritivora nicolayi[&&NHX:TOL=105203],detritivora smalli[&&NHX:TOL=105208])[&&NHX:TOL=113015],(detritivora hermodora[&&NHX:TOL=105193],(detritivora gynaea[&&NHX:TOL=105192],(detritivora gallardi[&&NHX:TOL=105191],(detritivora barnesi[&&NHX:TOL=105183],(detritivora callaghani[&&NHX:TOL=105187],detritivora zama[&&NHX:TOL=105211])[&&NHX:TOL=113020])[&&NHX:TOL=113019])[&&NHX:TOL=113018])[&&NHX:TOL=113017])[&&NHX:TOL=113016])[&&NHX:TOL=113014],(detritivora argyrea[&&NHX:TOL=105181],((detritivora major[&&NHX:TOL=105198],(detritivora ma[&&NHX:TOL=105197],detritivora matic[&&NHX:TOL=105201])[&&NHX:TOL=113024])[&&NHX:TOL=113023],(detritivora cleonus[&&NHX:TOL=105189],(detritivora rocana[&&NHX:TOL=105206],((detritivora negro[&&NHX:TOL=105204],((detritivora ariquemes[&&NHX:TOL=105182],detritivora manu[&&NHX:TOL=105200])[&&NHX:TOL=113030],(detritivora humaita[&&NHX:TOL=105194],(detritivora iquitos[&&NHX:TOL=105196],(detritivora palcazu[&&NHX:TOL=105205],detritivora tefe[&&NHX:TOL=105210])[&&NHX:TOL=113033])[&&NHX:TOL=113032])[&&NHX:TOL=113031])[&&NHX:TOL=113029])[&&NHX:TOL=113028],(detritivora cacaulandia[&&NHX:TOL=105186],(detritivora manicore[&&NHX:TOL=105199],(detritivora ipiranga[&&NHX:TOL=105195],((detritivora cuiaba[&&NHX:TOL=105190],(detritivora maues[&&NHX:TOL=105202],detritivora tapajos[&&NHX:TOL=105209])[&&NHX:TOL=113039])[&&NHX:TOL=113038],((detritivora breves[&&NHX:TOL=105185],(detritivora caryatis[&&NHX:TOL=105188],detritivora brasilia[&&NHX:TOL=105184])[&&NHX:TOL=113042])[&&NHX:TOL=113041],detritivora santarem[&&NHX:TOL=105207])[&&NHX:TOL=113040])[&&NHX:TOL=113037])[&&NHX:TOL=113036])[&&NHX:TOL=113035])[&&NHX:TOL=113034])[&&NHX:TOL=113027])[&&NHX:TOL=113026])[&&NHX:TOL=113025])[&&NHX:TOL=113022])[&&NHX:TOL=113021])detritivora[&&NHX:TOL=104646])[&&NHX:TOL=113010])charis group[&&NHX:TOL=113008],(chorinea amazon[&&NHX:TOL=104746],chorinea batesii[&&NHX:TOL=104747],chorinea bogota[&&NHX:TOL=104748],chorinea gratiosa[&&NHX:TOL=104749],chorinea heliconides[&&NHX:TOL=104750],chorinea licursis[&&NHX:TOL=104751],chorinea octauius[&&NHX:TOL=104752],chorinea sylphina[&&NHX:TOL=104753])chorinea[&&NHX:TOL=104641],(colaciticus banghaasi[&&NHX:TOL=104885],colaciticus johnstoni[&&NHX:TOL=104886])colaciticus[&&NHX:TOL=104642],(crocozona coecias[&&NHX:TOL=105105],crocozona croceifasciata[&&NHX:TOL=105106],crocozona fasciata[&&NHX:TOL=105107],crocozona pheretima[&&NHX:TOL=105108])crocozona[&&NHX:TOL=104643],cyrenia martia[&&NHX:TOL=104644],(dachetola azora[&&NHX:TOL=104895],dachetola caligata[&&NHX:TOL=104896],dachetola pione[&&NHX:TOL=104897],dachetola virido[&&NHX:TOL=104898])dachetola[&&NHX:TOL=104645],(exoplisia cadmeis[&&NHX:TOL=104846],exoplisia hypochalybe[&&NHX:TOL=104847],exoplisia myrtis[&&NHX:TOL=104849])exoplisia[&&NHX:TOL=104647],isapis agyrtus[&&NHX:TOL=104648],(ithomeis aurantiaca[&&NHX:TOL=104754],ithomeis eulema[&&NHX:TOL=104755])ithomeis[&&NHX:TOL=104649],(lasaia aerugo[&&NHX:TOL=105218],lasaia agesilas[&&NHX:TOL=105219],lasaia arsis[&&NHX:TOL=105220],lasaia cutisca[&&NHX:TOL=105221],lasaia incoides[&&NHX:TOL=105222],lasaia kennethi[&&NHX:TOL=105223],lasaia maria[&&NHX:TOL=105224],lasaia maritima[&&NHX:TOL=105225],lasaia meris[&&NHX:TOL=105226],lasaia moeros[&&NHX:TOL=105227],lasaia oileus[&&NHX:TOL=105228],lasaia pseudomeris[&&NHX:TOL=105229],lasaia sessilis[&&NHX:TOL=105230],lasaia sula[&&NHX:TOL=105231])lasaia[&&NHX:TOL=104650],(lyropteryx apollonia[&&NHX:TOL=104736],lyropteryx diadocis[&&NHX:TOL=104737],lyropteryx lyra[&&NHX:TOL=104738],lyropteryx terpsichore[&&NHX:TOL=104739])lyropteryx[&&NHX:TOL=104651],(melanis aegates[&&NHX:TOL=105232],melanis alena[&&NHX:TOL=105233],melanis boyi[&&NHX:TOL=105234],melanis cephise[&&NHX:TOL=105235],melanis cercopes[&&NHX:TOL=105236],melanis cinaron[&&NHX:TOL=105237],melanis cratia[&&NHX:TOL=105238],melanis electron[&&NHX:TOL=105239],melanis herminae[&&NHX:TOL=105240],melanis hillapana[&&NHX:TOL=105241],melanis hodia[&&NHX:TOL=105242],melanis leucophlegma[&&NHX:TOL=105243],melanis lioba[&&NHX:TOL=105244],melanis lycea[&&NHX:TOL=105245],melanis marathon[&&NHX:TOL=105246],melanis melandra[&&NHX:TOL=105247],melanis melaniae[&&NHX:TOL=105248],melanis opites[&&NHX:TOL=105249],melanis passiena[&&NHX:TOL=105250],melanis pixe[&&NHX:TOL=105251],melanis seleukia[&&NHX:TOL=105252],melanis smithiae[&&NHX:TOL=105253],melanis unxia[&&NHX:TOL=105254],melanis vidali[&&NHX:TOL=105255],melanis volusia[&&NHX:TOL=105256],melanis xenia[&&NHX:TOL=105257],melanis yeda[&&NHX:TOL=105258])melanis[&&NHX:TOL=104652],(metacharis cuparina[&&NHX:TOL=104907],metacharis fergusi[&&NHX:TOL=124759],metacharis lucius[&&NHX:TOL=104908],metacharis nigrella[&&NHX:TOL=104909],metacharis ptolomaeus[&&NHX:TOL=104910],metacharis regalis[&&NHX:TOL=104911],metacharis syloes[&&NHX:TOL=104912],metacharis smalli[&&NHX:TOL=124760],metacharis victrix[&&NHX:TOL=104913],metacharis xanthocraspedum[&&NHX:TOL=104914])metacharis[&&NHX:TOL=104653],(monethe albertus[&&NHX:TOL=104857],monethe alphonsus[&&NHX:TOL=104858])monethe[&&NHX:TOL=104654],nahida coenoides[&&NHX:TOL=104655],(necyria bellona[&&NHX:TOL=104740],necyria duellona[&&NHX:TOL=104741],necyria ingaretha[&&NHX:TOL=104742],necyria larunda[&&NHX:TOL=124761])necyria[&&NHX:TOL=104656],nirodia belphegor[&&NHX:TOL=104657],notheme erota[&&NHX:TOL=104658],(panara aureizona[&&NHX:TOL=104756],panara jarbas[&&NHX:TOL=104757],panara ovifera[&&NHX:TOL=104758],panara phereclus[&&NHX:TOL=104759],panara soana[&&NHX:TOL=104760])panara[&&NHX:TOL=104659],(paraphthonia cteatus[&&NHX:TOL=104859],paraphthonia molione[&&NHX:TOL=104860])paraphthonia[&&NHX:TOL=104660],parcella amarynthina[&&NHX:TOL=104661],(pheles atricolor[&&NHX:TOL=104922],pheles bicolor[&&NHX:TOL=104923],pheles eulesca[&&NHX:TOL=104925],pheles heliconides[&&NHX:TOL=104927],pheles incerta[&&NHX:TOL=104928],pheles melanochroia[&&NHX:TOL=104929],pheles ochracea[&&NHX:TOL=104931],pheles strigosus[&&NHX:TOL=104933])pheles[&&NHX:TOL=104662],(rhetus arcius[&&NHX:TOL=104743],rhetus dysonii[&&NHX:TOL=104744],rhetus periander[&&NHX:TOL=104745])rhetus[&&NHX:TOL=104663],(riodina lycisca[&&NHX:TOL=105212],riodina lysippoides[&&NHX:TOL=105213],riodina lysippus[&&NHX:TOL=105214])riodina[&&NHX:TOL=104664],(siseme alectryo[&&NHX:TOL=105259],siseme aristoteles[&&NHX:TOL=105260],siseme atrytone[&&NHX:TOL=105261],siseme militaris[&&NHX:TOL=105262],siseme neurodes[&&NHX:TOL=105263],siseme pallas[&&NHX:TOL=105264],siseme peculiaris[&&NHX:TOL=105265],siseme pedias[&&NHX:TOL=105266],siseme pseudopallas[&&NHX:TOL=105267])siseme[&&NHX:TOL=104665],(syrmatia aethiops[&&NHX:TOL=104861],syrmatia astraea[&&NHX:TOL=104862],syrmatia lamia[&&NHX:TOL=104863],syrmatia nyx[&&NHX:TOL=104864])syrmatia[&&NHX:TOL=104666],(themone pais[&&NHX:TOL=104850],themone poecilia[&&NHX:TOL=104851],themone pulcherrima[&&NHX:TOL=104852])themone[&&NHX:TOL=104667])riodinini[&&NHX:TOL=103510],((chimastrum argentea[&&NHX:TOL=105367],chimastrum celina[&&NHX:TOL=105368])chimastrum[&&NHX:TOL=105299],(esthemopsis aeolia[&&NHX:TOL=105358],esthemopsis alicia[&&NHX:TOL=105359],esthemopsis clonia[&&NHX:TOL=105360],esthemopsis colaxes[&&NHX:TOL=105361],esthemopsis crystallina[&&NHX:TOL=105362],esthemopsis jesse[&&NHX:TOL=105363],esthemopsis macara[&&NHX:TOL=105364],esthemopsis pherephatte[&&NHX:TOL=105365],esthemopsis sericina[&&NHX:TOL=105366],esthemopsis talamanca[&&NHX:TOL=108368])esthemopsis[&&NHX:TOL=105300],(lucillella asterra[&&NHX:TOL=105312],lucillella camissa[&&NHX:TOL=105313],lucillella pomposa[&&NHX:TOL=105314],lucillella suberra[&&NHX:TOL=105315],lucillella splendida[&&NHX:TOL=108362])lucillella[&&NHX:TOL=105301],(mesene babosa[&&NHX:TOL=105316],mesene bigemmis[&&NHX:TOL=110613],mesene bomilcar[&&NHX:TOL=105317],mesene celetes[&&NHX:TOL=105318],mesene citrinella[&&NHX:TOL=105319],mesene croceella[&&NHX:TOL=105320],mesene cyneas[&&NHX:TOL=105321],mesene epaphus[&&NHX:TOL=105322],mesene florus[&&NHX:TOL=105323],mesene hyale[&&NHX:TOL=105324],mesene ingrumaensis[&&NHX:TOL=105325],mesene leucogyna[&&NHX:TOL=110612],mesene leucophrys[&&NHX:TOL=105326],mesene leucopus[&&NHX:TOL=105327],mesene margaretta[&&NHX:TOL=105328],mesene monostigma[&&NHX:TOL=105329],mesene mygdon[&&NHX:TOL=105330],mesene nepticula[&&NHX:TOL=105331],mesene nola[&&NHX:TOL=105332],mesene paraena[&&NHX:TOL=105333],mesene patawa[&&NHX:TOL=105334],mesene phareus[&&NHX:TOL=105335],mesene philonis[&&NHX:TOL=105336],mesene pyrippe[&&NHX:TOL=105337],mesene sardonyx[&&NHX:TOL=105338],mesene silaris[&&NHX:TOL=105339],mesene simplex[&&NHX:TOL=105340],mesene veleda[&&NHX:TOL=105341])mesene[&&NHX:TOL=105302],(mesenopsis albivitta[&&NHX:TOL=105342],mesenopsis briseis[&&NHX:TOL=105343],mesenopsis bryaxis[&&NHX:TOL=105344],mesenopsis melanochlora[&&NHX:TOL=105345],mesenopsis pulchella[&&NHX:TOL=105346])mesenopsis[&&NHX:TOL=105303],(panaropsis inaria[&&NHX:TOL=105424],panaropsis semiota[&&NHX:TOL=105425],panaropsis thyatira[&&NHX:TOL=105426],panaropsis elegans[&&NHX:TOL=105427])panaropsis[&&NHX:TOL=105304],(phaenochitonia cingulus[&&NHX:TOL=105441],phaenochitonia fuliginea[&&NHX:TOL=105442],phaenochitonia gallardi[&&NHX:TOL=105443],phaenochitonia ignipicta[&&NHX:TOL=105444],phaenochitonia pseudodebilis[&&NHX:TOL=105445],phaenochitonia pyrsodes[&&NHX:TOL=105446],phaenochitonia tale[&&NHX:TOL=105447])phaenochitonia[&&NHX:TOL=105305],(pirascca apolecta[&&NHX:TOL=105429],pirascca arbuscula[&&NHX:TOL=105430],pirascca crocostigma[&&NHX:TOL=105431],pirascca iasis[&&NHX:TOL=105432],pirascca interrupta[&&NHX:TOL=105433],pirascca patriciae[&&NHX:TOL=108358],pirascca phoenicura[&&NHX:TOL=105434],pirascca pluto[&&NHX:TOL=105435],pirascca polemistes[&&NHX:TOL=105436],pirascca pujarnii[&&NHX:TOL=124765],pirascca sagaris[&&NHX:TOL=105437],pirascca sticheli[&&NHX:TOL=105438],pirascca suapure[&&NHX:TOL=105439],pirascca tyriotes[&&NHX:TOL=105440])pirascca[&&NHX:TOL=105306],pterographium sicora[&&NHX:TOL=105307],(stichellia bocchoris[&&NHX:TOL=105369],stichellia cuneifascia[&&NHX:TOL=105370],stichellia dukinfieldia[&&NHX:TOL=105371],stichellia pelotensis[&&NHX:TOL=105372])stichellia[&&NHX:TOL=105308],(symmachia accusatrix[&&NHX:TOL=105373],symmachia aconia[&&NHX:TOL=105374],symmachia almeidai[&&NHX:TOL=105375],symmachia arcuata[&&NHX:TOL=105376],symmachia arion[&&NHX:TOL=105377],symmachia aurigera[&&NHX:TOL=105378],symmachia basilissa[&&NHX:TOL=105379],symmachia batesi[&&NHX:TOL=105380],symmachia busbyi[&&NHX:TOL=108356],symmachia calderoni[&&NHX:TOL=105381],symmachia calligrapha[&&NHX:TOL=105382],symmachia calliste[&&NHX:TOL=105383],symmachia elinas[&&NHX:TOL=105384],symmachia emeralda[&&NHX:TOL=108357],symmachia eraste[&&NHX:TOL=105385],symmachia exigua[&&NHX:TOL=105386],symmachia falcistriga[&&NHX:TOL=105387],symmachia fassli[&&NHX:TOL=105388],symmachia fulvicauda[&&NHX:TOL=105389],symmachia haeterina[&&NHX:TOL=105390],symmachia hazelana[&&NHX:TOL=105391],symmachia hippea[&&NHX:TOL=105392],symmachia hippodice[&&NHX:TOL=105393],symmachia hypochloris[&&NHX:TOL=124858],symmachia jugurtha[&&NHX:TOL=105394],symmachia juratrix[&&NHX:TOL=105395],symmachia leena[&&NHX:TOL=105396],symmachia leopardinum[&&NHX:TOL=105397],symmachia maeonius[&&NHX:TOL=105398],symmachia menetas[&&NHX:TOL=105399],symmachia mielkei[&&NHX:TOL=124766],symmachia miron[&&NHX:TOL=105400],symmachia multesima[&&NHX:TOL=105401],symmachia nemesis[&&NHX:TOL=105402],symmachia norina[&&NHX:TOL=105403],symmachia pardalia[&&NHX:TOL=105404],symmachia pardalis[&&NHX:TOL=105405],symmachia pena[&&NHX:TOL=110614],symmachia phaedra[&&NHX:TOL=105406],symmachia praxila[&&NHX:TOL=108366],symmachia probetor[&&NHX:TOL=105407],symmachia rita[&&NHX:TOL=105408],symmachia rubina[&&NHX:TOL=105409],symmachia rubrica[&&NHX:TOL=105410],symmachia satana[&&NHX:TOL=108364],symmachia sepyra[&&NHX:TOL=105411],symmachia splendida[&&NHX:TOL=105412],symmachia stigmosissima[&&NHX:TOL=105413],symmachia suevia[&&NHX:TOL=105414],symmachia technema[&&NHX:TOL=105415],symmachia threissa[&&NHX:TOL=105416],symmachia tigrina[&&NHX:TOL=105417],symmachia titania[&&NHX:TOL=105418],symmachia triangularis[&&NHX:TOL=105419],symmachia tricolor[&&NHX:TOL=105420],symmachia virgatula[&&NHX:TOL=105421],symmachia virgaurea[&&NHX:TOL=105422],symmachia xypete[&&NHX:TOL=105423])symmachia[&&NHX:TOL=105309],(xenandra agria[&&NHX:TOL=105347],xenandra ahrenholzi[&&NHX:TOL=108360],xenandra caeruleata[&&NHX:TOL=124767],xenandra desora[&&NHX:TOL=105348],xenandra helius[&&NHX:TOL=105350],xenandra nigrivenata[&&NHX:TOL=105352],xenandra pelopia[&&NHX:TOL=105353],xenandra poliotactis[&&NHX:TOL=105354],xenandra vulcanalis[&&NHX:TOL=105355])xenandra[&&NHX:TOL=105310],(xynia lilacina[&&NHX:TOL=105356],xynia lithosina[&&NHX:TOL=105357])xynias[&&NHX:TOL=105311])symmachiini[&&NHX:TOL=103511],((anteros acheus[&&NHX:TOL=105563],anteros aerosus[&&NHX:TOL=105564],anteros allectus[&&NHX:TOL=105565],anteros aurigans[&&NHX:TOL=105566],anteros bracteata[&&NHX:TOL=105567],anteros carausius[&&NHX:TOL=105568],anteros chrysoprasta[&&NHX:TOL=105569],anteros cruentatus[&&NHX:TOL=105570],anteros formosus[&&NHX:TOL=105571],anteros gentilis[&&NHX:TOL=105572],anteros kupris[&&NHX:TOL=105573],anteros lectabilis[&&NHX:TOL=105574],anteros nubosus[&&NHX:TOL=105575],anteros otho[&&NHX:TOL=105576],anteros principalis[&&NHX:TOL=105577],anteros renaldus[&&NHX:TOL=105578])anteros[&&NHX:TOL=105559],(helicopis cupido[&&NHX:TOL=105579],helicopis endymiaena[&&NHX:TOL=105580],helicopis gnidus[&&NHX:TOL=105581])helicopis[&&NHX:TOL=105560],(ourocnemis archytas[&&NHX:TOL=105582],ourocnemis boulleti[&&NHX:TOL=105583])ourocnemis[&&NHX:TOL=105561],(sarota acanthoides[&&NHX:TOL=105584],sarota acantus[&&NHX:TOL=105585],sarota chloropunctata[&&NHX:TOL=105586],sarota chocoensis[&&NHX:TOL=105587],sarota chrysus[&&NHX:TOL=105588],sarota completa[&&NHX:TOL=105589],sarota craspediodonta[&&NHX:TOL=105590],sarota estrada[&&NHX:TOL=105591],sarota gamelia[&&NHX:TOL=105592],sarota gyas[&&NHX:TOL=105593],sarota harveyi[&&NHX:TOL=105594],sarota lasciva[&&NHX:TOL=105595],sarota miranda[&&NHX:TOL=105596],sarota myrtea[&&NHX:TOL=105597],sarota neglecta[&&NHX:TOL=105598],sarota psaros[&&NHX:TOL=105599],sarota spicata[&&NHX:TOL=105600],sarota subtessellata[&&NHX:TOL=105601],sarota turrialbensis[&&NHX:TOL=105602],sarota willmotti[&&NHX:TOL=105603])sarota[&&NHX:TOL=105562])helicopini[&&NHX:TOL=103512],((((aricoris arenarum[&&NHX:TOL=105841],aricoris zachaeus[&&NHX:TOL=105862])[&&NHX:TOL=112095],((aricoris notialis[&&NHX:TOL=105858],aricoris chilensis[&&NHX:TOL=105845],aricoris cinericia[&&NHX:TOL=105846])[&&NHX:TOL=112097],((aricoris domina[&&NHX:TOL=105849],aricoris n. sp. 2[&&NHX:TOL=105864],((aricoris aurinia[&&NHX:TOL=105842],aricoris incana[&&NHX:TOL=105854])[&&NHX:TOL=112101],aricoris montana[&&NHX:TOL=105857])[&&NHX:TOL=112100])[&&NHX:TOL=112099],((aricoris caracensis[&&NHX:TOL=105843],(aricoris campestris[&&NHX:TOL=105844],aricoris erostratus[&&NHX:TOL=105851])[&&NHX:TOL=112104])[&&NHX:TOL=112103],(aricoris epulus[&&NHX:TOL=105850],aricoris propitia[&&NHX:TOL=105859])[&&NHX:TOL=112105],aricoris signata[&&NHX:TOL=105860],aricoris indistincta[&&NHX:TOL=105855],aricoris hubrichi[&&NHX:TOL=105853])[&&NHX:TOL=112102])[&&NHX:TOL=112098])[&&NHX:TOL=112096],((aricoris terias[&&NHX:TOL=105861],aricoris constantius[&&NHX:TOL=105848])[&&NHX:TOL=112107],(aricoris gauchoana[&&NHX:TOL=105852],(aricoris colchis[&&NHX:TOL=105847],(aricoris middletoni[&&NHX:TOL=105856],aricoris n. sp. 1[&&NHX:TOL=105863])[&&NHX:TOL=112110])[&&NHX:TOL=112109])[&&NHX:TOL=112108])[&&NHX:TOL=112106])aricoris[&&NHX:TOL=105811],(ariconias albinus[&&NHX:TOL=105865],ariconias glaphyra[&&NHX:TOL=105866])ariconias[&&NHX:TOL=105812])aricorina[&&NHX:TOL=105837],((((juditha odites[&&NHX:TOL=105896],((juditha pulcherrima[&&NHX:TOL=105897],juditha inambari[&&NHX:TOL=105893])[&&NHX:TOL=112114],(juditha dorilis[&&NHX:TOL=105892],(juditha naza[&&NHX:TOL=105895],(juditha azan[&&NHX:TOL=105890],(juditha molpe[&&NHX:TOL=105894],juditha caucana[&&NHX:TOL=105891])[&&NHX:TOL=112118])[&&NHX:TOL=112117])[&&NHX:TOL=112116])[&&NHX:TOL=112115])[&&NHX:TOL=112113])juditha[&&NHX:TOL=105813],(synargis anapis[&&NHX:TOL=105902],((synargis fenestrella[&&NHX:TOL=105909],(synargis phliasus[&&NHX:TOL=105918],synargis victrix[&&NHX:TOL=105924],synargis paulistina[&&NHX:TOL=105917])[&&NHX:TOL=112121])[&&NHX:TOL=112120],(((synargis chaonia[&&NHX:TOL=105906],(synargis pittheus[&&NHX:TOL=105919],(synargis agle[&&NHX:TOL=105901],(synargis ochra[&&NHX:TOL=105914],synargis dirca[&&NHX:TOL=105907])[&&NHX:TOL=112127])[&&NHX:TOL=112126])[&&NHX:TOL=112125])[&&NHX:TOL=112124],(synargis galena[&&NHX:TOL=105910],((synargis nymphidioides[&&NHX:TOL=105913],(synargis ethelinda[&&NHX:TOL=105908],synargis palaeste[&&NHX:TOL=105916])[&&NHX:TOL=112131])[&&NHX:TOL=112130],(synargis gela[&&NHX:TOL=105911],(synargis calyce[&&NHX:TOL=105905],(synargis mycone[&&NHX:TOL=105912],(synargis tytia[&&NHX:TOL=105923],(synargis abaris[&&NHX:TOL=105900],(synargis orestessa[&&NHX:TOL=105915],synargis soranus[&&NHX:TOL=105921])[&&NHX:TOL=112137])[&&NHX:TOL=112136])[&&NHX:TOL=112135])[&&NHX:TOL=112134])[&&NHX:TOL=112133])[&&NHX:TOL=112132])[&&NHX:TOL=112129])[&&NHX:TOL=112128])[&&NHX:TOL=112123],(synargis sylvarum[&&NHX:TOL=105922],(synargis regulus[&&NHX:TOL=105920],(synargis bisfasciata[&&NHX:TOL=105904],synargis axenus[&&NHX:TOL=105903])[&&NHX:TOL=112140])[&&NHX:TOL=112139])[&&NHX:TOL=112138])[&&NHX:TOL=112122])[&&NHX:TOL=112119])synargis[&&NHX:TOL=105815])[&&NHX:TOL=112112],(((thisbe molela[&&NHX:TOL=105887],thisbe rupestre[&&NHX:TOL=105888])[&&NHX:TOL=112142],(thisbe irenea[&&NHX:TOL=105885],(thisbe lycorias[&&NHX:TOL=105886],(thisbe hyalina[&&NHX:TOL=105883],(thisbe incubus[&&NHX:TOL=105884],thisbe ucubis[&&NHX:TOL=105889])[&&NHX:TOL=112146])[&&NHX:TOL=112145])[&&NHX:TOL=112144])[&&NHX:TOL=112143])thisbe[&&NHX:TOL=105816],((lemonias caligenea[&&NHX:TOL=105868],(lemonias egaensis[&&NHX:TOL=105869],lemonias zygia[&&NHX:TOL=105874])[&&NHX:TOL=112148])[&&NHX:TOL=112147],((lemonias stalachtioides[&&NHX:TOL=105872],lemonias sontella[&&NHX:TOL=105871])[&&NHX:TOL=112150],(lemonias ochracea[&&NHX:TOL=105870],(lemonias theodora[&&NHX:TOL=105873],lemonias albofasciata[&&NHX:TOL=105867])[&&NHX:TOL=112152])[&&NHX:TOL=112151])[&&NHX:TOL=112149])lemonias[&&NHX:TOL=105814])[&&NHX:TOL=112141])lemoniadina[&&NHX:TOL=105838],(((adelotypa annulifera[&&NHX:TOL=105995],adelotypa argiella[&&NHX:TOL=105996],adelotypa asemna[&&NHX:TOL=105998],adelotypa bolena[&&NHX:TOL=106000],adelotypa borsippa[&&NHX:TOL=106001],adelotypa curulis[&&NHX:TOL=106003],adelotypa malca[&&NHX:TOL=106013],adelotypa mollis[&&NHX:TOL=106014],adelotypa penthea[&&NHX:TOL=106016],adelotypa trinitatis[&&NHX:TOL=106019])adelotypa[&&NHX:TOL=105817],(calociasma ictericum[&&NHX:TOL=106047],calociasma laius[&&NHX:TOL=106048],calociasma nycteus[&&NHX:TOL=106049])calociasma[&&NHX:TOL=105818],(calospila antonii[&&NHX:TOL=105960],calospila asteria[&&NHX:TOL=105962],calospila byzeres[&&NHX:TOL=105963],calospila candace[&&NHX:TOL=105964],calospila cerealis[&&NHX:TOL=105965],calospila cilissa[&&NHX:TOL=105966],calospila cuprea[&&NHX:TOL=105967],calospila emylius[&&NHX:TOL=105968],calospila eupolemia[&&NHX:TOL=105969],calospila fannia[&&NHX:TOL=105970],calospila gallardi[&&NHX:TOL=105971],calospila gyges[&&NHX:TOL=105972],calospila hemileuca[&&NHX:TOL=105973],calospila idmon[&&NHX:TOL=105974],calospila irene[&&NHX:TOL=105975],calospila latona[&&NHX:TOL=105976],calospila lucetia[&&NHX:TOL=105977],calospila lucianus[&&NHX:TOL=105978],calospila maeon[&&NHX:TOL=105979],calospila maeonides[&&NHX:TOL=105980],calospila martialis[&&NHX:TOL=105981],calospila napoensis[&&NHX:TOL=124684],calospila overali[&&NHX:TOL=124685],calospila parthaon[&&NHX:TOL=105982],calospila pelarge[&&NHX:TOL=105983],calospila pirene[&&NHX:TOL=105984],calospila rhesa[&&NHX:TOL=105985],calospila rhodope[&&NHX:TOL=105986],calospila satyroides[&&NHX:TOL=105987],calospila siaka[&&NHX:TOL=105988],calospila simplaris[&&NHX:TOL=105989],calospila thara[&&NHX:TOL=105990],calospila urichi[&&NHX:TOL=105991],calospila zeanger[&&NHX:TOL=105992])calospila[&&NHX:TOL=105819],(catocyclotus adelina[&&NHX:TOL=106085],catocyclotus aemulius[&&NHX:TOL=106086],catocyclotus elpinice[&&NHX:TOL=106087])catocyclotis[&&NHX:TOL=105820],(dysmathia cindra[&&NHX:TOL=105946],dysmathia costalis[&&NHX:TOL=105947],dysmathia glaucina[&&NHX:TOL=105948],dysmathia glaucoconia[&&NHX:TOL=105949],dysmathia grosneyi[&&NHX:TOL=105950],dysmathia juno[&&NHX:TOL=105951],dysmathia portia[&&NHX:TOL=105952])dysmathia[&&NHX:TOL=105821],(hallonympha eudocia[&&NHX:TOL=124681],hallonympha paucipuncta[&&NHX:TOL=124682])hallonympha[&&NHX:TOL=106006],(harveyope densemaculata[&&NHX:TOL=106004],harveyope glauca[&&NHX:TOL=106007],harveyope sejuncta[&&NHX:TOL=106017],harveyope tinea[&&NHX:TOL=106018],harveyope zerna[&&NHX:TOL=106021])harveyope[&&NHX:TOL=124683],(hypophylla argenissa[&&NHX:TOL=105953],hypophylla caldensis[&&NHX:TOL=105954],hypophylla florus[&&NHX:TOL=105955],hypophylla idae[&&NHX:TOL=105956],hypophylla martia[&&NHX:TOL=105957],hypophylla sudias[&&NHX:TOL=105958],hypophylla zeurippa[&&NHX:TOL=105959])hypophylla[&&NHX:TOL=105822],joiceya praeclarus[&&NHX:TOL=105823],(livendula amasis[&&NHX:TOL=105993],livendula aminias[&&NHX:TOL=105994],livendula aristus[&&NHX:TOL=105997],livendula balista[&&NHX:TOL=105999],livendula epixanthe[&&NHX:TOL=106005],livendula huebneri[&&NHX:TOL=106008],livendula jasonhalli[&&NHX:TOL=106009],livendula leucocyana[&&NHX:TOL=106011],livendula leucophaea[&&NHX:TOL=106012],livendula pauxilla[&&NHX:TOL=106015],livendula violacea[&&NHX:TOL=106020])livendula[&&NHX:TOL=124679],(menander aldasi[&&NHX:TOL=105927],menander apotheta[&&NHX:TOL=105961],menander cicuta[&&NHX:TOL=105928],menander clotho[&&NHX:TOL=105929],menander coruscans[&&NHX:TOL=105930],menander felsina[&&NHX:TOL=105931],menander hebrus[&&NHX:TOL=105932],menander laobotas[&&NHX:TOL=105933],menander menander[&&NHX:TOL=105934],menander pretus[&&NHX:TOL=105935],menander thalassicus[&&NHX:TOL=105936])menander[&&NHX:TOL=105824],(minotauros charessa[&&NHX:TOL=106002],minotauros lampros[&&NHX:TOL=106010])minotauros[&&NHX:TOL=124680],(mycastor leucarpis[&&NHX:TOL=106088],mycastor nealces[&&NHX:TOL=106089],mycastor scurrilis[&&NHX:TOL=106090])mycastor[&&NHX:TOL=105825],(nymphidium acherois[&&NHX:TOL=106050],nymphidium ariari[&&NHX:TOL=106051],nymphidium ascolia[&&NHX:TOL=106052],nymphidium aurum[&&NHX:TOL=106053],nymphidium azanoides[&&NHX:TOL=106054],nymphidium baeotia[&&NHX:TOL=106055],nymphidium balbinus[&&NHX:TOL=106056],nymphidium cachrus[&&NHX:TOL=106057],nymphidium callaghani[&&NHX:TOL=106058],nymphidium caricae[&&NHX:TOL=106059],nymphidium carmentis[&&NHX:TOL=106060],nymphidium chimborazium[&&NHX:TOL=106061],nymphidium chione[&&NHX:TOL=106062],nymphidium derufata[&&NHX:TOL=106063],nymphidium fulminans[&&NHX:TOL=106064],nymphidium guyanensis[&&NHX:TOL=106065],nymphidium haematostictum[&&NHX:TOL=106066],nymphidium hesperinum[&&NHX:TOL=106067],nymphidium latibrunis[&&NHX:TOL=106068],nymphidium lenocinium[&&NHX:TOL=106069],nymphidium leucosia[&&NHX:TOL=106070],nymphidium lisimon[&&NHX:TOL=106071],nymphidium manicorensis[&&NHX:TOL=106072],nymphidium mantus[&&NHX:TOL=106073],nymphidium menalcus[&&NHX:TOL=106074],nymphidium ninias[&&NHX:TOL=106075],nymphidium nivea[&&NHX:TOL=106076],nymphidium olinda[&&NHX:TOL=106077],nymphidium omois[&&NHX:TOL=106078],nymphidium onaeum[&&NHX:TOL=106079],nymphidium plinthobaphis[&&NHX:TOL=106080],nymphidium smalli[&&NHX:TOL=106081],nymphidium strati[&&NHX:TOL=106082],nymphidium trinidadi[&&NHX:TOL=106083],nymphidium undimargo[&&NHX:TOL=106084])nymphidium[&&NHX:TOL=105826],pandemos pasiphae[&&NHX:TOL=105827],periplacis glaucoma[&&NHX:TOL=105828],rodinia calphurnia[&&NHX:TOL=105829],(setabis alcmaeon[&&NHX:TOL=106022],setabis buckleyi[&&NHX:TOL=106023],setabis cleomedes[&&NHX:TOL=106024],setabis cruentata[&&NHX:TOL=106025],setabis disparilis[&&NHX:TOL=106026],setabis epitus[&&NHX:TOL=106027],setabis extensa[&&NHX:TOL=106028],setabis fassli[&&NHX:TOL=106029],setabis flammula[&&NHX:TOL=106030],setabis heliodora[&&NHX:TOL=106031],setabis hippocrate[&&NHX:TOL=106032],setabis lagus[&&NHX:TOL=106033],setabis luceres[&&NHX:TOL=106034],setabis megalia[&&NHX:TOL=106035],setabis myrtis[&&NHX:TOL=106036],setabis phaedon[&&NHX:TOL=106037],setabis plagiaria[&&NHX:TOL=106038],setabis preciosa[&&NHX:TOL=106039],setabis pythia[&&NHX:TOL=106040],setabis pythioides[&&NHX:TOL=106041],setabis rhodinosa[&&NHX:TOL=106042],setabis serica[&&NHX:TOL=106043],setabis staudingeri[&&NHX:TOL=106044],setabis tapaja[&&NHX:TOL=106045],setabis velutina[&&NHX:TOL=106046])setabis[&&NHX:TOL=105830],(zelotaea alba[&&NHX:TOL=105937],zelotaea lya[&&NHX:TOL=105940],zelotaea phasma[&&NHX:TOL=105942],zelotaea suffusca[&&NHX:TOL=105943],zelotaea n. sp.[&&NHX:TOL=105945])zelotaea[&&NHX:TOL=105831])nymphidiina[&&NHX:TOL=105839],(protonymphidia senta[&&NHX:TOL=105835],((archaeonympha smalli[&&NHX:TOL=106093],(archaeonympha drepana[&&NHX:TOL=106091],archaeonympha urichi[&&NHX:TOL=106092])[&&NHX:TOL=113044])archaeonympha[&&NHX:TOL=105832],(((calicosama lilina[&&NHX:TOL=106094],calicosama robbinsi[&&NHX:TOL=106095])calicosama[&&NHX:TOL=105834],behemothia godmanii[&&NHX:TOL=105833])[&&NHX:TOL=113046],(((((((theope nycteis[&&NHX:TOL=106137],theope brevignoni[&&NHX:TOL=106108])[&&NHX:TOL=113052],theope philotes[&&NHX:TOL=106143])[&&NHX:TOL=113051],(theope tetrastigma[&&NHX:TOL=106156],theope orphana[&&NHX:TOL=106138])[&&NHX:TOL=113053])[&&NHX:TOL=113050],(theope hypoleuca[&&NHX:TOL=106125],theope simplicia[&&NHX:TOL=106149],theope azurea[&&NHX:TOL=106103])[&&NHX:TOL=113054],(theope archimedes[&&NHX:TOL=106100],theope matuta[&&NHX:TOL=106132])[&&NHX:TOL=113055])[&&NHX:TOL=113049],theope eurygonina[&&NHX:TOL=106119])[&&NHX:TOL=113048],((theope speciosa[&&NHX:TOL=106152],(((theope pedias[&&NHX:TOL=106140],theope pseudopedias[&&NHX:TOL=106145])[&&NHX:TOL=113060],(theope devriesi[&&NHX:TOL=106115],theope pepo[&&NHX:TOL=106141])[&&NHX:TOL=113061])[&&NHX:TOL=113059],((theope acosma[&&NHX:TOL=106096],theope eudocia[&&NHX:TOL=106117])[&&NHX:TOL=113063],(((theope barea[&&NHX:TOL=106105],theope mundula[&&NHX:TOL=106134])[&&NHX:TOL=113066],theope excelsa[&&NHX:TOL=106120],theope kingi[&&NHX:TOL=106128])[&&NHX:TOL=113065],((theope aureonitens[&&NHX:TOL=106102],theope galionicus[&&NHX:TOL=106123])[&&NHX:TOL=113068],theope sericea[&&NHX:TOL=106148],theope lampropteryx[&&NHX:TOL=106129],theope dabrerae[&&NHX:TOL=106113])[&&NHX:TOL=113067])[&&NHX:TOL=113064])[&&NHX:TOL=113062])[&&NHX:TOL=113058])[&&NHX:TOL=113057],(theope pieridoides[&&NHX:TOL=106144],(theope cratylus[&&NHX:TOL=106112],(theope sisemina[&&NHX:TOL=106150],theope antanitis[&&NHX:TOL=106098])[&&NHX:TOL=113071])[&&NHX:TOL=113070])[&&NHX:TOL=113069])[&&NHX:TOL=113056])[&&NHX:TOL=113047],theope fayneli[&&NHX:TOL=106121],(((theope iani[&&NHX:TOL=106126],(theope villai[&&NHX:TOL=106161],(theope virgilius[&&NHX:TOL=106162],theope eupolis[&&NHX:TOL=106118])[&&NHX:TOL=113076])[&&NHX:TOL=113075])[&&NHX:TOL=113074],(theope nobilils[&&NHX:TOL=106135],((theope syngenes[&&NHX:TOL=106154],theope terambus[&&NHX:TOL=106155])[&&NHX:TOL=113079],theope publius[&&NHX:TOL=106146],theope sanjuani[&&NHX:TOL=106147],(theope bacenis[&&NHX:TOL=106104],theope basilea[&&NHX:TOL=106106])[&&NHX:TOL=113080])[&&NHX:TOL=113078])[&&NHX:TOL=113077])[&&NHX:TOL=113073],((theope comosa[&&NHX:TOL=106111],((theope zostera[&&NHX:TOL=106164],theope nodosus[&&NHX:TOL=106136])[&&NHX:TOL=113084],(theope phaeo[&&NHX:TOL=106142],(theope theritas[&&NHX:TOL=106157],(theope thootes[&&NHX:TOL=106159],(theope apheles[&&NHX:TOL=106099],theope sobrina[&&NHX:TOL=106151])[&&NHX:TOL=113088])[&&NHX:TOL=113087])[&&NHX:TOL=113086])[&&NHX:TOL=113085])[&&NHX:TOL=113083])[&&NHX:TOL=113082],((theope guillaumei[&&NHX:TOL=106124],theope janus[&&NHX:TOL=106127],(theope discus[&&NHX:TOL=106116],(theope decorata[&&NHX:TOL=106114],theope thestias[&&NHX:TOL=106158])[&&NHX:TOL=113092])[&&NHX:TOL=113091])[&&NHX:TOL=113090],(theope lycaenina[&&NHX:TOL=106131],(theope leucanthe[&&NHX:TOL=106130],(theope busbyi[&&NHX:TOL=106109],theope amicitiae[&&NHX:TOL=106097],theope methemona[&&NHX:TOL=106133],theope sticheli[&&NHX:TOL=106153],theope christiani[&&NHX:TOL=106110],(theope turneri[&&NHX:TOL=106160],(theope batesi[&&NHX:TOL=106107],(theope atima[&&NHX:TOL=106101],(theope foliorum[&&NHX:TOL=106122],(theope pakitza[&&NHX:TOL=106139],theope wallacei[&&NHX:TOL=106163])[&&NHX:TOL=113100])[&&NHX:TOL=113099])[&&NHX:TOL=113098])[&&NHX:TOL=113097])[&&NHX:TOL=113096])[&&NHX:TOL=113095])[&&NHX:TOL=113094])[&&NHX:TOL=113093])[&&NHX:TOL=113089])[&&NHX:TOL=113081])[&&NHX:TOL=113072],theope minialba[&&NHX:TOL=124688])theope[&&NHX:TOL=105836])[&&NHX:TOL=113045])[&&NHX:TOL=113043])theopina[&&NHX:TOL=105840])[&&NHX:TOL=112153])[&&NHX:TOL=112111])nymphidiini[&&NHX:TOL=103513],(stalachtis calliope[&&NHX:TOL=104797],stalachtis euterpe[&&NHX:TOL=104798],stalachtis lineata[&&NHX:TOL=104799],stalachtis magdalena[&&NHX:TOL=104800],stalachtis phaedusa[&&NHX:TOL=104801],stalachtis phlegia[&&NHX:TOL=104802])stalachtis[&&NHX:TOL=103514],((apodemia castanea[&&NHX:TOL=105800],apodemia chisosensis[&&NHX:TOL=124692],apodemia duryi[&&NHX:TOL=124693],apodemia hepburni[&&NHX:TOL=105801],apodemia hypoglauca[&&NHX:TOL=105802],apodemia mejicanus[&&NHX:TOL=124694],apodemia mormo[&&NHX:TOL=105803],apodemia multiplaga[&&NHX:TOL=105804],apodemia murphyi[&&NHX:TOL=105805],apodemia nais[&&NHX:TOL=105806],apodemia palmerii[&&NHX:TOL=105807],apodemia phyciodoides[&&NHX:TOL=105809],apodemia virgulti[&&NHX:TOL=124695],apodemia walkeri[&&NHX:TOL=105810])apodemia[&&NHX:TOL=105605],(argyrogrammana alstonii[&&NHX:TOL=105703],argyrogrammana amalfreda[&&NHX:TOL=105704],argyrogrammana aparamilla[&&NHX:TOL=105705],argyrogrammana barine[&&NHX:TOL=105706],argyrogrammana bonita[&&NHX:TOL=105707],argyrogrammana caelestina[&&NHX:TOL=105708],argyrogrammana caesarion[&&NHX:TOL=105709],argyrogrammana celata[&&NHX:TOL=105710],argyrogrammana chicomendesi[&&NHX:TOL=105711],argyrogrammana crocea[&&NHX:TOL=105712],argyrogrammana danieli[&&NHX:TOL=124696],argyrogrammana denisi[&&NHX:TOL=105713],argyrogrammana glaucopis[&&NHX:TOL=105714],argyrogrammana johannismarci[&&NHX:TOL=105715],argyrogrammana leptographia[&&NHX:TOL=105716],argyrogrammana natalita[&&NHX:TOL=105717],argyrogrammana nurtia[&&NHX:TOL=105718],argyrogrammana occidentalis[&&NHX:TOL=105719],argyrogrammana pacsa[&&NHX:TOL=105720],argyrogrammana pastaza[&&NHX:TOL=105721],argyrogrammana physis[&&NHX:TOL=105722],argyrogrammana placibilis[&&NHX:TOL=105723],argyrogrammana praestigiosa[&&NHX:TOL=105724],argyrogrammana pulchra[&&NHX:TOL=105725],argyrogrammana rameli[&&NHX:TOL=105726],argyrogrammana saphirina[&&NHX:TOL=105727],argyrogrammana sebastiani[&&NHX:TOL=105728],argyrogrammana sonazul[&&NHX:TOL=124697],argyrogrammana sticheli[&&NHX:TOL=105729],argyrogrammana stilbe[&&NHX:TOL=105730],argyrogrammana subimis[&&NHX:TOL=105731],argyrogrammana subota[&&NHX:TOL=105732],argyrogrammana talboti[&&NHX:TOL=105733],argyrogrammana trochilia[&&NHX:TOL=105734],argyrogrammana venilia[&&NHX:TOL=105735])argyrogrammana[&&NHX:TOL=105606],astraeodes areuta[&&NHX:TOL=105607],(callistium cleadas[&&NHX:TOL=105627],callistium maculosa[&&NHX:TOL=105628])callistium[&&NHX:TOL=105608],(echenais thelephus[&&NHX:TOL=105612],((echydna chaseba[&&NHX:TOL=105636],echydna punctata[&&NHX:TOL=105637])echydna[&&NHX:TOL=105613],((calydna calamisa[&&NHX:TOL=105687],(calydna caieta[&&NHX:TOL=105686],calydna charila[&&NHX:TOL=105692])[&&NHX:TOL=113104])calydna caieta group[&&NHX:TOL=113103],((calydna venusta[&&NHX:TOL=105702],calydna stolata[&&NHX:TOL=105699],calydna lusca[&&NHX:TOL=105696],calydna fissilisima[&&NHX:TOL=105693],calydna thersander[&&NHX:TOL=105701],calydna jeannea[&&NHX:TOL=105695],calydna nicolayi[&&NHX:TOL=105698])calydna thersander group[&&NHX:TOL=113106],((calydna cea[&&NHX:TOL=105691],calydna pichita[&&NHX:TOL=124699])[&&NHX:TOL=124698],(calydna sturnula[&&NHX:TOL=105700],(calydna micra[&&NHX:TOL=105697],((calydna candace[&&NHX:TOL=105688],calydna hiria[&&NHX:TOL=105694])[&&NHX:TOL=113111],(calydna carneia[&&NHX:TOL=105689],(calydna catana[&&NHX:TOL=105690],calydna cabira[&&NHX:TOL=105685])[&&NHX:TOL=113112])[&&NHX:TOL=124700])[&&NHX:TOL=113110])[&&NHX:TOL=113109])[&&NHX:TOL=113108])calydna hiria group[&&NHX:TOL=113107])[&&NHX:TOL=113105])calydna[&&NHX:TOL=105609])[&&NHX:TOL=113102])[&&NHX:TOL=113101],(comphotis apachita[&&NHX:TOL=105629],comphotis clarissa[&&NHX:TOL=105630],comphotis debilis[&&NHX:TOL=105631],comphotis eanes[&&NHX:TOL=105632],comphotis ignicauda[&&NHX:TOL=105633],comphotis irroratum[&&NHX:TOL=105634],comphotis sophistes[&&NHX:TOL=105635])comphotis[&&NHX:TOL=105610],dianesia carteri[&&NHX:TOL=105611],(emesis adelpha[&&NHX:TOL=105643],emesis aerigera[&&NHX:TOL=105644],emesis angularis[&&NHX:TOL=105645],emesis ares[&&NHX:TOL=124701],emesis arnacis[&&NHX:TOL=105646],emesis aurimna[&&NHX:TOL=105647],emesis brimo[&&NHX:TOL=105648],emesis castigata[&&NHX:TOL=105649],emesis cereus[&&NHX:TOL=105650],emesis condigna[&&NHX:TOL=105651],emesis cypria[&&NHX:TOL=105652],emesis diogenia[&&NHX:TOL=105653],emesis elegia[&&NHX:TOL=105654],emesis emesia[&&NHX:TOL=105655],emesis eurydice[&&NHX:TOL=105656],emesis fastidiosa[&&NHX:TOL=105657],emesis fatimella[&&NHX:TOL=105658],emesis glaucescens[&&NHX:TOL=105659],emesis guttata[&&NHX:TOL=105660],emesis heterochroa[&&NHX:TOL=105661],emesis heteroclita[&&NHX:TOL=105662],emesis lacrines[&&NHX:TOL=105663],emesis liodes[&&NHX:TOL=105664],emesis lucinda[&&NHX:TOL=105665],emesis lupina[&&NHX:TOL=105666],emesis mandana[&&NHX:TOL=105667],emesis neemias[&&NHX:TOL=105668],emesis ocypore[&&NHX:TOL=105669],emesis orichalceus[&&NHX:TOL=105670],emesis poeas[&&NHX:TOL=105671],emesis russula[&&NHX:TOL=105672],emesis satema[&&NHX:TOL=105673],emesis saturata[&&NHX:TOL=105674],emesis sinuatus[&&NHX:TOL=105675],emesis spreta[&&NHX:TOL=105676],emesis tegula[&&NHX:TOL=105677],emesis temesa[&&NHX:TOL=105678],emesis tenedia[&&NHX:TOL=105679],emesis toltec[&&NHX:TOL=105680],emesis vimena[&&NHX:TOL=105681],emesis vulpina[&&NHX:TOL=105682],emesis xanthosa[&&NHX:TOL=105683],emesis zela[&&NHX:TOL=105684])emesis[&&NHX:TOL=105614],(imelda aenetus[&&NHX:TOL=105625],imelda mycea[&&NHX:TOL=105626])imelda[&&NHX:TOL=105615],lamphiotes velazquezi[&&NHX:TOL=105616],(((pachythone analuciae[&&NHX:TOL=105779],pachythone conspersa[&&NHX:TOL=105780],pachythone distigma[&&NHX:TOL=105781],pachythone erebia[&&NHX:TOL=105782],pachythone gigas[&&NHX:TOL=105783],pachythone lateritia[&&NHX:TOL=105784],pachythone mimula[&&NHX:TOL=105785],pachythone palades[&&NHX:TOL=105786],pachythone pasicles[&&NHX:TOL=105787],pachythone philonis[&&NHX:TOL=105788],pachythone robusta[&&NHX:TOL=105789],pachythone rubigo[&&NHX:TOL=105790],pachythone sumare[&&NHX:TOL=105791],pachythone thaumaria[&&NHX:TOL=105792],pachythone xanthe[&&NHX:TOL=105793])pachythone[&&NHX:TOL=105618],(machaya obstinata[&&NHX:TOL=124686],machaya watkinsi[&&NHX:TOL=124687])machaya[&&NHX:TOL=105617])[&&NHX:TOL=112496],((pseudonymphidia agave[&&NHX:TOL=105794],pseudonymphidia clearista[&&NHX:TOL=105795])pseudonymphidia[&&NHX:TOL=105621],(minstrellus grandis[&&NHX:TOL=105938],(minstrellus nivosa[&&NHX:TOL=105941],(minstrellus leucotopus[&&NHX:TOL=105939],minstrellus emphatica[&&NHX:TOL=112494])[&&NHX:TOL=112493])[&&NHX:TOL=112492])minstrellus[&&NHX:TOL=112491])[&&NHX:TOL=112490])[&&NHX:TOL=112495],petrocerus catiena[&&NHX:TOL=105619],pixus corculum[&&NHX:TOL=105620],(pseudotinea caprina[&&NHX:TOL=105638],pseudotinea eiseli[&&NHX:TOL=105639],pseudotinea gagarini[&&NHX:TOL=105640],pseudotinea hemis[&&NHX:TOL=105641],pseudotinea volcanicus[&&NHX:TOL=105642])pseudotinea[&&NHX:TOL=105622],(roeberella calvus[&&NHX:TOL=105796],roeberella flocculus[&&NHX:TOL=105797],roeberella gerres[&&NHX:TOL=105798],roeberella heberti[&&NHX:TOL=124702],roeberella lencates[&&NHX:TOL=105799],roeberella marajoara[&&NHX:TOL=124703])roeberella[&&NHX:TOL=105623],zabuella tenellus[&&NHX:TOL=105624])riodininae  incertae sedis[&&NHX:TOL=105604])[&&NHX:TOL=113114])[&&NHX:TOL=113113])riodininae[&&NHX:TOL=12221],(hamearis lucina[&&NHX:TOL=106198],(dodona adonira[&&NHX:TOL=106254],dodona binghami[&&NHX:TOL=124567],dodona chrysapha[&&NHX:TOL=106256],dodona deodata[&&NHX:TOL=106257],dodona dipoea[&&NHX:TOL=106258],dodona dracon[&&NHX:TOL=106259],dodona durga[&&NHX:TOL=106260],dodona egeon[&&NHX:TOL=106261],dodona elvira[&&NHX:TOL=106262],dodona eugenes[&&NHX:TOL=106263],dodona fruhstorferi[&&NHX:TOL=124568],dodona henrici[&&NHX:TOL=106264],dodona hoenei[&&NHX:TOL=124569],dodona kaolinkon[&&NHX:TOL=106265],dodona katerina[&&NHX:TOL=106266],dodona mizunumai[&&NHX:TOL=124570],dodona moritai[&&NHX:TOL=124571],dodona ouida[&&NHX:TOL=106268],dodona speciosa[&&NHX:TOL=106270],dodona windu[&&NHX:TOL=124572])dodona[&&NHX:TOL=106199],(zemeros emesoides[&&NHX:TOL=106252],zemeros flegyas[&&NHX:TOL=106253])zemeros[&&NHX:TOL=106200],((abisara barnsi[&&NHX:TOL=124560],abisara caeca[&&NHX:TOL=124561],abisara cameroonensis[&&NHX:TOL=124562],abisara delicata[&&NHX:TOL=106223],abisara dewitzi[&&NHX:TOL=106224],abisara gerontes[&&NHX:TOL=106225],abisara neavei[&&NHX:TOL=106227],abisara rogersi[&&NHX:TOL=106228],abisara rutherfordii[&&NHX:TOL=106229],abisara talantus[&&NHX:TOL=106231],abisara tantalus[&&NHX:TOL=106232])afrotropical abisara[&&NHX:TOL=124559],(abisara abnormis[&&NHX:TOL=106234],abisara aita[&&NHX:TOL=106235],abisara bifasciata[&&NHX:TOL=106236],abisara burnii[&&NHX:TOL=106237],abisara chela[&&NHX:TOL=106238],abisara chelina[&&NHX:TOL=124564],abisara echerius[&&NHX:TOL=106239],abisara freda[&&NHX:TOL=106240],abisara fylla[&&NHX:TOL=106241],abisara fylloides[&&NHX:TOL=106242],abisara geza[&&NHX:TOL=106243],abisara kausambi[&&NHX:TOL=106244],abisara miyazakii[&&NHX:TOL=124565],abisara neophron[&&NHX:TOL=106245],abisara saturata[&&NHX:TOL=106246],abisara savitri[&&NHX:TOL=106247],abisara sobrina[&&NHX:TOL=124566])oriental abisara[&&NHX:TOL=124563])abisara[&&NHX:TOL=106201],(laxita teneta[&&NHX:TOL=106303],laxita thuisto[&&NHX:TOL=106304])laxita[&&NHX:TOL=106202],(paralaxita damajanti[&&NHX:TOL=106299],paralaxita hewitsoni[&&NHX:TOL=124579],paralaxita orphna[&&NHX:TOL=106301],paralaxita telesia[&&NHX:TOL=106302])paralaxita[&&NHX:TOL=106203],(stiboges lushanica[&&NHX:TOL=124582],stiboges nymphidia[&&NHX:TOL=124583])stiboges[&&NHX:TOL=106204],(polycaena carmelita[&&NHX:TOL=106215],polycaena chauchowensis[&&NHX:TOL=106216],polycaena lama[&&NHX:TOL=106217],polycaena lua[&&NHX:TOL=106218],polycaena matuta[&&NHX:TOL=106219],polycaena princeps[&&NHX:TOL=106220],polycaena tamerlana[&&NHX:TOL=106221],polycaena timur[&&NHX:TOL=124580],polycaena yunnana[&&NHX:TOL=124581])polycaena[&&NHX:TOL=106205],takashia nana[&&NHX:TOL=106206],(dicallaneura albosignata[&&NHX:TOL=106272],dicallaneura amabilis[&&NHX:TOL=106273],dicallaneura angustifasciata[&&NHX:TOL=124573],dicallaneura cyanea[&&NHX:TOL=124574],dicallaneura decorata[&&NHX:TOL=106274],dicallaneura dilectissima[&&NHX:TOL=124575],dicallaneura ekeikei[&&NHX:TOL=106275],dicallaneura exiguus[&&NHX:TOL=106276],dicallaneura fulvofasciata[&&NHX:TOL=106277],dicallaneura hyacinthus[&&NHX:TOL=106278],dicallaneura kirschi[&&NHX:TOL=106280],dicallaneura leucomelas[&&NHX:TOL=106281],dicallaneura longifascia[&&NHX:TOL=124576],dicallaneura ostrina[&&NHX:TOL=124577],dicallaneura pulchra[&&NHX:TOL=106284],dicallaneura ribbei[&&NHX:TOL=106285],dicallaneura semirufa[&&NHX:TOL=124578],dicallaneura virgo[&&NHX:TOL=106286])dicallaneura[&&NHX:TOL=106207],(praetaxila albiplaga[&&NHX:TOL=106287],praetaxila heterisa[&&NHX:TOL=106288],praetaxila huntei[&&NHX:TOL=106289],praetaxila eromena[&&NHX:TOL=106290],praetaxila poultoni[&&NHX:TOL=106291],praetaxila satraps[&&NHX:TOL=106292],praetaxila segecia[&&NHX:TOL=106293],praetaxila statira[&&NHX:TOL=106294],praetaxila tyrannus[&&NHX:TOL=106296],praetaxila wallacei[&&NHX:TOL=106297],praetaxila weiskei[&&NHX:TOL=106298])praetaxila[&&NHX:TOL=106208],(saribia decaryi[&&NHX:TOL=106248],saribia ochracea[&&NHX:TOL=106249],saribia perroti[&&NHX:TOL=106250],saribia tepahi[&&NHX:TOL=106251])saribia[&&NHX:TOL=106209],(taxila dora[&&NHX:TOL=124584],taxila haquinus[&&NHX:TOL=124585])taxila[&&NHX:TOL=106210])nemeobiinae[&&NHX:TOL=103515])riodinidae[&&NHX:TOL=12174],((curetis acuta[&&NHX:TOL=106351],curetis barsine[&&NHX:TOL=106352],curetis brunnea[&&NHX:TOL=106353],curetis bulis[&&NHX:TOL=106354],curetis dentata[&&NHX:TOL=106355],curetis felderi[&&NHX:TOL=106356],curetis freda[&&NHX:TOL=106357],curetis insularis[&&NHX:TOL=106358],curetis neosphila[&&NHX:TOL=106359],curetis regula[&&NHX:TOL=106360],curetis santana[&&NHX:TOL=106361],curetis saronis[&&NHX:TOL=106362],curetis siva[&&NHX:TOL=106363],curetis sperthis[&&NHX:TOL=106364],curetis tagalica[&&NHX:TOL=106365],curetis thetis[&&NHX:TOL=106366],curetis tonkina[&&NHX:TOL=106367],curetis venata[&&NHX:TOL=106368])curetis[&&NHX:TOL=12182],(((((((alaena amazoula[&&NHX:TOL=106896],alaena bicolora[&&NHX:TOL=106897],alaena brainei[&&NHX:TOL=106898],alaena caissa[&&NHX:TOL=106899],alaena dodomaensis[&&NHX:TOL=106900],alaena ferrulineata[&&NHX:TOL=106901],alaena interposita[&&NHX:TOL=106902],alaena johanna[&&NHX:TOL=106903],alaena kiellandi[&&NHX:TOL=106904],alaena lamborni[&&NHX:TOL=106905],alaena maculata[&&NHX:TOL=106906],alaena madibirensis[&&NHX:TOL=106907],alaena margaritacea[&&NHX:TOL=106908],alaena ngonga[&&NHX:TOL=106909],alaena nyassa[&&NHX:TOL=106910],alaena oberthuri[&&NHX:TOL=106911],alaena ochracea[&&NHX:TOL=106912],alaena picata[&&NHX:TOL=106913],alaena reticulata[&&NHX:TOL=106914],alaena rosei[&&NHX:TOL=106915],alaena subruba[&&NHX:TOL=106916],alaena unimaculosa[&&NHX:TOL=106917],alaena bjornstadti[&&NHX:TOL=107018],alaena exotica[&&NHX:TOL=111629])alaena[&&NHX:TOL=106842],(ptelina carnuta[&&NHX:TOL=106918],ptelina subhyalina[&&NHX:TOL=106919])ptelina[&&NHX:TOL=106843])alaena section[&&NHX:TOL=106841],((pentila abraxas[&&NHX:TOL=106920],pentila alba[&&NHX:TOL=106921],pentila amenaida[&&NHX:TOL=106922],pentila amenaidoides[&&NHX:TOL=106923],pentila auga[&&NHX:TOL=106924],pentila bitje[&&NHX:TOL=106925],pentila camerunica[&&NHX:TOL=106926],pentila carcassoni[&&NHX:TOL=106927],pentila christina[&&NHX:TOL=106928],pentila cloetensi[&&NHX:TOL=106929],pentila condamini[&&NHX:TOL=106930],pentila fallax[&&NHX:TOL=106931],pentila fidonioides[&&NHX:TOL=106932],pentila glagoessa[&&NHX:TOL=106933],pentila hewitsoni[&&NHX:TOL=106934],pentila inconspicua[&&NHX:TOL=106935],pentila landbecki[&&NHX:TOL=106936],pentila mesia[&&NHX:TOL=106937],pentila nero[&&NHX:TOL=106938],pentila nigeriana[&&NHX:TOL=106939],pentila occidentalium[&&NHX:TOL=106940],pentila pauli[&&NHX:TOL=106941],pentila petreia[&&NHX:TOL=106942],pentila petreoides[&&NHX:TOL=106943],pentila phidia[&&NHX:TOL=106944],pentila picena[&&NHX:TOL=106945],pentila preussi[&&NHX:TOL=106946],pentila pseudorotha[&&NHX:TOL=106947],pentila rogersi[&&NHX:TOL=106948],pentila rondo[&&NHX:TOL=106949],pentila rotha[&&NHX:TOL=106950],pentila subfuscata[&&NHX:TOL=106951],pentila swynnertoni[&&NHX:TOL=106952],pentila tachyroides[&&NHX:TOL=106953],pentila torrida[&&NHX:TOL=106954],pentila tropicalis[&&NHX:TOL=106955],pentila umangiana[&&NHX:TOL=106956],pentila umbra[&&NHX:TOL=106957],pentila bennetti[&&NHX:TOL=111631],pentila maculata[&&NHX:TOL=111633])pentila[&&NHX:TOL=106845],(liptenara batesi[&&NHX:TOL=106958],liptenara hiendlmayeri[&&NHX:TOL=106959],liptenara schoutedeni[&&NHX:TOL=106960])liptenara[&&NHX:TOL=106846])pentila section[&&NHX:TOL=106844],((ornipholidotos bakotae[&&NHX:TOL=106988],ornipholidotos bitjeensis[&&NHX:TOL=106989],ornipholidotos camerunensis[&&NHX:TOL=106990],ornipholidotos congoensis[&&NHX:TOL=106991],ornipholidotos emarginata[&&NHX:TOL=106992],ornipholidotos etoumbi[&&NHX:TOL=106993],ornipholidotos gabonensis[&&NHX:TOL=106994],ornipholidotos irwini[&&NHX:TOL=111635],ornipholidotos issia[&&NHX:TOL=106995],ornipholidotos jacksoni[&&NHX:TOL=106996],ornipholidotos jax[&&NHX:TOL=111636],ornipholidotos katangae[&&NHX:TOL=106997],ornipholidotos kelle[&&NHX:TOL=106998],ornipholidotos kirbyi[&&NHX:TOL=106999],ornipholidotos latimargo[&&NHX:TOL=107001],ornipholidotos likouala[&&NHX:TOL=107002],ornipholidotos muhata[&&NHX:TOL=107003],ornipholidotos nguru[&&NHX:TOL=107004],ornipholidotos nigeriae[&&NHX:TOL=107005],ornipholidotos ntebi[&&NHX:TOL=107006],ornipholidotos nympha[&&NHX:TOL=111637],ornipholidotos onitshae[&&NHX:TOL=107007],ornipholidotos overlaeti[&&NHX:TOL=107008],ornipholidotos paradoxa[&&NHX:TOL=107009],ornipholidotos perfragilis[&&NHX:TOL=107010],ornipholidotos peucetia[&&NHX:TOL=107011],ornipholidotos sylpha[&&NHX:TOL=107012],ornipholidotos sylphida[&&NHX:TOL=111638],ornipholidotos tanganyikae[&&NHX:TOL=107013],ornipholidotos teroensis[&&NHX:TOL=107014],ornipholidotos tiassale[&&NHX:TOL=107015],ornipholidotos tirza[&&NHX:TOL=107016],ornipholidotos ugandae[&&NHX:TOL=107017],ornipholidotos mathildae[&&NHX:TOL=111643],ornipholidotos abriana[&&NHX:TOL=111645],ornipholidotos ackeryi[&&NHX:TOL=111646],ornipholidotos amieti[&&NHX:TOL=111647],ornipholidotos annae[&&NHX:TOL=111648],ornipholidotos aureliae[&&NHX:TOL=111649],ornipholidotos ayissii[&&NHX:TOL=111650],ornipholidotos boormani[&&NHX:TOL=111651],ornipholidotos carolinae[&&NHX:TOL=111652],ornipholidotos dargei[&&NHX:TOL=111653],ornipholidotos dowsetti[&&NHX:TOL=111654],ornipholidotos ducarmei[&&NHX:TOL=111655],ornipholidotos evoei[&&NHX:TOL=111656],ornipholidotos francisci[&&NHX:TOL=111657],ornipholidotos gemina[&&NHX:TOL=111658],ornipholidotos ghesquieri[&&NHX:TOL=111659],ornipholidotos ginettae[&&NHX:TOL=111660],ornipholidotos henrii[&&NHX:TOL=111661],ornipholidotos ivoiriensis[&&NHX:TOL=111662],ornipholidotos jolyana[&&NHX:TOL=111663],ornipholidotos josianae[&&NHX:TOL=111664],ornipholidotos kennedyi[&&NHX:TOL=111665],ornipholidotos kivu[&&NHX:TOL=111666],ornipholidotos maesseni[&&NHX:TOL=111667],ornipholidotos michaelae[&&NHX:TOL=111668],ornipholidotos nancy[&&NHX:TOL=111669],ornipholidotos nbeti[&&NHX:TOL=111670],ornipholidotos oremansi[&&NHX:TOL=111671],ornipholidotos sylviae[&&NHX:TOL=111672],ornipholidotos tessmani[&&NHX:TOL=111673],ornipholidotos goodgerae[&&NHX:TOL=111674])ornipholidotos[&&NHX:TOL=106848],(telipna acraea[&&NHX:TOL=106961],telipna acraeoides[&&NHX:TOL=106962],telipna albofasciata[&&NHX:TOL=106963],telipna atrinervis[&&NHX:TOL=106964],telipna aurivillii[&&NHX:TOL=106965],telipna cameroonensis[&&NHX:TOL=106966],telipna citrimaculata[&&NHX:TOL=106967],telipna consanguinea[&&NHX:TOL=106968],telipna erica[&&NHX:TOL=106969],telipna exsuperia[&&NHX:TOL=106970],telipna hollandi[&&NHX:TOL=106971],telipna kayonza[&&NHX:TOL=106972],telipna lotti[&&NHX:TOL=106973],telipna maesseni[&&NHX:TOL=106974],telipna medjensis[&&NHX:TOL=106975],telipna nyanza[&&NHX:TOL=106976],telipna plagiata[&&NHX:TOL=106977],telipna rothi[&&NHX:TOL=106978],telipna rufilla[&&NHX:TOL=106979],telipna ruspinoides[&&NHX:TOL=106980],telipna sanguinea[&&NHX:TOL=106981],telipna semirufa[&&NHX:TOL=106982],telipna sheffieldi[&&NHX:TOL=106983],telipna sulpitia[&&NHX:TOL=106984],telipna transverstigna[&&NHX:TOL=106985],telipna villiersi[&&NHX:TOL=106986])telipna[&&NHX:TOL=106849],(torbenia aurivilliusi[&&NHX:TOL=106987],torbenia larseni[&&NHX:TOL=107000],torbenia persimilis[&&NHX:TOL=111640],torbenia stempfferi[&&NHX:TOL=111641],torbenia wojtusiaki[&&NHX:TOL=111642])torbenia[&&NHX:TOL=111639])telipna section[&&NHX:TOL=106847])pentilini[&&NHX:TOL=106344],(((cooksonia aliciae[&&NHX:TOL=107020],cooksonia neavei[&&NHX:TOL=107021],cooksonia trimeni[&&NHX:TOL=107022])cooksonia[&&NHX:TOL=106851],(durbania amakosa[&&NHX:TOL=107023],durbania limbata[&&NHX:TOL=107024])durbania[&&NHX:TOL=106852],durbaniella clarki[&&NHX:TOL=106853],durbaniopsis saga[&&NHX:TOL=106854])durbania section[&&NHX:TOL=106850],((argyrocheila bitje[&&NHX:TOL=107139],argyrocheila inundifera[&&NHX:TOL=107140],argyrocheila undifera[&&NHX:TOL=107141])argyrocheila[&&NHX:TOL=107138],(baliochila amanica[&&NHX:TOL=107094],baliochila aslanga[&&NHX:TOL=107095],baliochila barnesi[&&NHX:TOL=107096],baliochila congdoni[&&NHX:TOL=107097],baliochila dubiosa[&&NHX:TOL=107098],baliochila fragilis[&&NHX:TOL=107099],baliochila hildegarda[&&NHX:TOL=107100],baliochila latimarginata[&&NHX:TOL=107101],baliochila lipara[&&NHX:TOL=107102],baliochila minima[&&NHX:TOL=107103],baliochila neavei[&&NHX:TOL=107104],baliochila nguru[&&NHX:TOL=107105],baliochila nyasae[&&NHX:TOL=107106],baliochila pringlei[&&NHX:TOL=107108],baliochila pseudofragilis[&&NHX:TOL=107109],baliochila singularis[&&NHX:TOL=107110],baliochila stygia[&&NHX:TOL=107111],baliochila woodi[&&NHX:TOL=107112])baliochila[&&NHX:TOL=106858],(citrinophila bennetti[&&NHX:TOL=107087],citrinophila erastus[&&NHX:TOL=107088],citrinophila marginalis[&&NHX:TOL=107089],citrinophila similis[&&NHX:TOL=107090],citrinophila tenera[&&NHX:TOL=107091],citrinophila terias[&&NHX:TOL=107092],citrinophila unipunctata[&&NHX:TOL=107093])citrinophila[&&NHX:TOL=106859],(cnodontes pallida[&&NHX:TOL=107113],cnodontes penningtoni[&&NHX:TOL=107114],cnodontes vansomereni[&&NHX:TOL=107115])cnodontes[&&NHX:TOL=106860],(eresina bergeri[&&NHX:TOL=107116],eresina bilineata[&&NHX:TOL=107117],eresina conradti[&&NHX:TOL=107118],eresina corynetes[&&NHX:TOL=107119],eresina crola[&&NHX:TOL=107120],eresina fontainei[&&NHX:TOL=107121],eresina fusca[&&NHX:TOL=107122],eresina jacksoni[&&NHX:TOL=107123],eresina katangana[&&NHX:TOL=107124],eresina katera[&&NHX:TOL=107125],eresina likouala[&&NHX:TOL=107126],eresina maesseni[&&NHX:TOL=107127],eresina masaka[&&NHX:TOL=107128],eresina pseudofusca[&&NHX:TOL=107129],eresina rougeoti[&&NHX:TOL=107130],eresina saundersi[&&NHX:TOL=107131],eresina theodori[&&NHX:TOL=107132],eresina toroensis[&&NHX:TOL=107133],eresina schmitti[&&NHX:TOL=111686])eresina[&&NHX:TOL=106861],(mimeresia cellularis[&&NHX:TOL=107048],mimeresia cornucopiae[&&NHX:TOL=107061],mimeresia debora[&&NHX:TOL=107049],mimeresia dinora[&&NHX:TOL=107050],mimeresia drucei[&&NHX:TOL=107051],mimeresia favillacea[&&NHX:TOL=107052],mimeresia issia[&&NHX:TOL=107053],mimeresia libentina[&&NHX:TOL=107054],mimeresia mapongwa[&&NHX:TOL=107063],mimeresia moreelsi[&&NHX:TOL=107055],mimeresia moyambina[&&NHX:TOL=107056],mimeresia neavei[&&NHX:TOL=107057],mimeresia pseudocellularis[&&NHX:TOL=107058],mimeresia russulus[&&NHX:TOL=107059],mimeresia semirufa[&&NHX:TOL=107060])mimeresia[&&NHX:TOL=106862],eresinopsides bichroma[&&NHX:TOL=106863],(eresiomera beni[&&NHX:TOL=107065],eresiomera bicolor[&&NHX:TOL=107066],eresiomera clenchi[&&NHX:TOL=107067],eresiomera cornesi[&&NHX:TOL=107068],eresiomera cornucopiae[&&NHX:TOL=107069],eresiomera isca[&&NHX:TOL=107070],eresiomera issia[&&NHX:TOL=107071],eresiomera jacksoni[&&NHX:TOL=107072],eresiomera mapongwa[&&NHX:TOL=107073],eresiomera nigeriana[&&NHX:TOL=107074],eresiomera osheba[&&NHX:TOL=107075],eresiomera ouesso[&&NHX:TOL=107076],eresiomera paradoxa[&&NHX:TOL=107077],eresiomera phaeochiton[&&NHX:TOL=107078],eresiomera rougeoti[&&NHX:TOL=107079],eresiomera rutilo[&&NHX:TOL=107080],eresiomera campbelli[&&NHX:TOL=111681],eresiomera kiellandi[&&NHX:TOL=111682],eresiomera nancy[&&NHX:TOL=111683],eresiomera petersi[&&NHX:TOL=111684],eresiomera phillipi[&&NHX:TOL=111685])eresiomera[&&NHX:TOL=106864],euthecta cooksoni[&&NHX:TOL=106865],(mimacraea angustata[&&NHX:TOL=107025],mimacraea charmian[&&NHX:TOL=107026],mimacraea costleyi[&&NHX:TOL=107027],mimacraea darwinia[&&NHX:TOL=107028],mimacraea eltringhami[&&NHX:TOL=107029],mimacraea flavofasciata[&&NHX:TOL=107030],mimacraea gelinia[&&NHX:TOL=107031],mimacraea graeseri[&&NHX:TOL=107032],mimacraea krausei[&&NHX:TOL=107033],mimacraea laeta[&&NHX:TOL=107034],mimacraea landbecki[&&NHX:TOL=107035],mimacraea mariae[&&NHX:TOL=107036],mimacraea marshalli[&&NHX:TOL=107037],mimacraea neavei[&&NHX:TOL=107038],mimacraea neokoton[&&NHX:TOL=107039],mimacraea neurata[&&NHX:TOL=107040],mimacraea paragora[&&NHX:TOL=107041],mimacraea pseudepaea[&&NHX:TOL=107042],mimacraea pulverulenta[&&NHX:TOL=107043],mimacraea schmidti[&&NHX:TOL=107044],mimacraea schubotzi[&&NHX:TOL=107045],mimacraea skoptoles[&&NHX:TOL=107046],mimacraea telloides[&&NHX:TOL=107047],mimacraea abriana[&&NHX:TOL=111676],mimacraea apicalis[&&NHX:TOL=111677],mimacraea febe[&&NHX:TOL=111678],mimacraea maesseni[&&NHX:TOL=111679],mimacraea marginata[&&NHX:TOL=111680])mimacraea[&&NHX:TOL=106866],(pseuderesia eleaza[&&NHX:TOL=107062],pseuderesia vidua[&&NHX:TOL=107064])pseuderesia[&&NHX:TOL=106867],(teriomima micra[&&NHX:TOL=107081],teriomima parva[&&NHX:TOL=107082],teriomima puella[&&NHX:TOL=107083],teriomima puellaris[&&NHX:TOL=107084],teriomima subpunctata[&&NHX:TOL=107085],teriomima zuluana[&&NHX:TOL=107086])teriomima[&&NHX:TOL=106868],(toxochitona ankole[&&NHX:TOL=107134],toxochitona gerda[&&NHX:TOL=107135],toxochitona sankuru[&&NHX:TOL=107136],toxochitona vansommereni[&&NHX:TOL=107137])toxochitona[&&NHX:TOL=106869])mimacraea section[&&NHX:TOL=106856],((falcuna campimus[&&NHX:TOL=107227],falcuna dorotheae[&&NHX:TOL=107228],falcuna gitte[&&NHX:TOL=107229],falcuna hollandi[&&NHX:TOL=107230],falcuna iturina[&&NHX:TOL=107231],falcuna kasai[&&NHX:TOL=107232],falcuna lacteata[&&NHX:TOL=107233],falcuna leonensis[&&NHX:TOL=107234],falcuna libyssa[&&NHX:TOL=107235],falcuna lybia[&&NHX:TOL=107236],falcuna margarita[&&NHX:TOL=107237],falcuna melandeta[&&NHX:TOL=107238],falcuna orientalis[&&NHX:TOL=107239],falcuna overlaeti[&&NHX:TOL=107240],falcuna reducta[&&NHX:TOL=107241],falcuna semliki[&&NHX:TOL=107242],falcuna synesia[&&NHX:TOL=107243])falcuna[&&NHX:TOL=106871],(larinopoda aspidos[&&NHX:TOL=107295],larinopoda batesi[&&NHX:TOL=107296],larinopoda eurema[&&NHX:TOL=107297],larinopoda lagyra[&&NHX:TOL=107298],larinopoda lircaea[&&NHX:TOL=107299],larinopoda tera[&&NHX:TOL=107300],larinopoda spuma[&&NHX:TOL=111695])larinopoda[&&NHX:TOL=106872],(kakumia ferruginea[&&NHX:TOL=107165],kakumia ideoides[&&NHX:TOL=107175],kakumia otlauga[&&NHX:TOL=107188])kakumia[&&NHX:TOL=111691],(liptena albicans[&&NHX:TOL=107142],liptena albomacuta[&&NHX:TOL=107143],liptena alluaudi[&&NHX:TOL=107144],liptena amabilis[&&NHX:TOL=107145],liptena augusta[&&NHX:TOL=107146],liptena bassae[&&NHX:TOL=107147],liptena batesana[&&NHX:TOL=107148],liptena bergeri[&&NHX:TOL=107149],liptena boei[&&NHX:TOL=107150],liptena bolivari[&&NHX:TOL=107151],liptena catalina[&&NHX:TOL=107152],liptena confusa[&&NHX:TOL=107153],liptena congoana[&&NHX:TOL=107154],liptena decempunctata[&&NHX:TOL=107155],liptena decipiens[&&NHX:TOL=107156],liptena despecta[&&NHX:TOL=107157],liptena durbania[&&NHX:TOL=107158],liptena eketi[&&NHX:TOL=107159],liptena eukrinaria[&&NHX:TOL=107160],liptena eukrines[&&NHX:TOL=107161],liptena eukrinoides[&&NHX:TOL=107162],liptena evanescens[&&NHX:TOL=107163],liptena fatima[&&NHX:TOL=107164],liptena ferrymani[&&NHX:TOL=107166],liptena flavicans[&&NHX:TOL=107167],liptena fontainei[&&NHX:TOL=107168],liptena fulvicans[&&NHX:TOL=107169],liptena griveaudi[&&NHX:TOL=107171],liptena hapale[&&NHX:TOL=107172],liptena helena[&&NHX:TOL=107173],liptena homeyeri[&&NHX:TOL=107174],liptena ilaro[&&NHX:TOL=107176],liptena inframacula[&&NHX:TOL=107178],liptena intermedia[&&NHX:TOL=107179],liptena lualaba[&&NHX:TOL=107180],liptena modesta[&&NHX:TOL=107181],liptena mwagensis[&&NHX:TOL=107182],liptena nigromarginata[&&NHX:TOL=107183],liptena occidentalis[&&NHX:TOL=107184],liptena ochrea[&&NHX:TOL=107185],liptena opaca[&&NHX:TOL=107186],liptena orubrum[&&NHX:TOL=107187],liptena ouesso[&&NHX:TOL=107189],liptena overlaeti[&&NHX:TOL=107190],liptena pearmani[&&NHX:TOL=107191],liptena perobscura[&&NHX:TOL=107192],liptena praestans[&&NHX:TOL=107193],liptena rochei[&&NHX:TOL=107194],liptena rubromacula[&&NHX:TOL=107195],liptena sauberi[&&NHX:TOL=107196],liptena septistrigata[&&NHX:TOL=107197],liptena similis[&&NHX:TOL=107198],liptena simplicia[&&NHX:TOL=107199],liptena submacula[&&NHX:TOL=107200],liptena subsuffusa[&&NHX:TOL=107201],liptena subundularis[&&NHX:TOL=107202],liptena tiassale[&&NHX:TOL=107204],liptena titei[&&NHX:TOL=107205],liptena tricolora[&&NHX:TOL=107206],liptena turbata[&&NHX:TOL=107209],liptena undina[&&NHX:TOL=107210],liptena undularis[&&NHX:TOL=107211],liptena xanthostola[&&NHX:TOL=107212],liptena yakadumae[&&NHX:TOL=107213],liptena kiellandi[&&NHX:TOL=111688],liptena priscilla[&&NHX:TOL=111689],liptena seyboui[&&NHX:TOL=111690])liptena[&&NHX:TOL=106874],(obania subvariegata[&&NHX:TOL=107203],obania tullia[&&NHX:TOL=107207],obania tulliana[&&NHX:TOL=107208])obania[&&NHX:TOL=111692],(micropentila adelgitha[&&NHX:TOL=107301],micropentila adelgunda[&&NHX:TOL=107302],micropentila alberta[&&NHX:TOL=107303],micropentila bakotae[&&NHX:TOL=107304],micropentila bitjeana[&&NHX:TOL=107305],micropentila brunnea[&&NHX:TOL=107306],micropentila bunyoro[&&NHX:TOL=107307],micropentila catocala[&&NHX:TOL=107308],micropentila cherereti[&&NHX:TOL=107309],micropentila cingulum[&&NHX:TOL=107310],micropentila dorothea[&&NHX:TOL=107311],micropentila flavopunctata[&&NHX:TOL=107312],micropentila fontainei[&&NHX:TOL=107313],micropentila fulvula[&&NHX:TOL=107314],micropentila fuscula[&&NHX:TOL=107315],micropentila gabunica[&&NHX:TOL=107316],micropentila galenides[&&NHX:TOL=107317],micropentila jacksoni[&&NHX:TOL=107318],micropentila katangana[&&NHX:TOL=107319],micropentila katerae[&&NHX:TOL=107320],micropentila kelleana[&&NHX:TOL=107321],micropentila mabangi[&&NHX:TOL=107322],micropentila mamfe[&&NHX:TOL=107323],micropentila mpigi[&&NHX:TOL=107324],micropentila nigeriana[&&NHX:TOL=107325],micropentila ogojae[&&NHX:TOL=107326],micropentila sankuru[&&NHX:TOL=107327],micropentila souanke[&&NHX:TOL=107328],micropentila subplagata[&&NHX:TOL=107329],micropentila triangularis[&&NHX:TOL=107330],micropentila ugandae[&&NHX:TOL=107331],micropentila victoriae[&&NHX:TOL=107332],micropentila villiersi[&&NHX:TOL=107333])micropentila[&&NHX:TOL=106875],(tetrarhanis diversa[&&NHX:TOL=107214],tetrarhanis etoumbi[&&NHX:TOL=107215],tetrarhanis ilma[&&NHX:TOL=107216],tetrarhanis laminifer[&&NHX:TOL=107217],tetrarhanis nubifera[&&NHX:TOL=107218],tetrarhanis ogojae[&&NHX:TOL=107219],tetrarhanis onitshae[&&NHX:TOL=107220],tetrarhanis rougeoti[&&NHX:TOL=107221],tetrarhanis schoutedeni[&&NHX:TOL=107222],tetrarhanis simplex[&&NHX:TOL=107223],tetrarhanis souanke[&&NHX:TOL=107224],tetrarhanis stempfferi[&&NHX:TOL=107225],tetrarhanis symplocus[&&NHX:TOL=107226],tetrarhanis baralingam[&&NHX:TOL=111693],tetrarhanis okwangwo[&&NHX:TOL=111694])tetrarhanis[&&NHX:TOL=106876])liptena section[&&NHX:TOL=106870],((iridana bwamba[&&NHX:TOL=107334],iridana euprepes[&&NHX:TOL=107335],iridana exquisita[&&NHX:TOL=107336],iridana gabunica[&&NHX:TOL=107337],iridana ghanana[&&NHX:TOL=107338],iridana hypocala[&&NHX:TOL=107339],iridana incredibilis[&&NHX:TOL=107340],iridana jacksoni[&&NHX:TOL=107341],iridana katera[&&NHX:TOL=107342],iridana marina[&&NHX:TOL=107343],iridana nigeriana[&&NHX:TOL=107344],iridana obscura[&&NHX:TOL=107345],iridana perdita[&&NHX:TOL=107346],iridana rougeoti[&&NHX:TOL=107347],iridana tororo[&&NHX:TOL=107348],iridana unyoro[&&NHX:TOL=107349])iridana[&&NHX:TOL=106877],(teratoneura congoensis[&&NHX:TOL=111698],teratoneura isabellae[&&NHX:TOL=106879])teratoneura[&&NHX:TOL=111697])iridana section[&&NHX:TOL=107350],(aethiopana honorius[&&NHX:TOL=106881],batelusia zebra[&&NHX:TOL=106882],(deloneura barca[&&NHX:TOL=111956],deloneura immaculata[&&NHX:TOL=111957],deloneura millari[&&NHX:TOL=111958],deloneura ochrascens[&&NHX:TOL=111959],deloneura sheppardi[&&NHX:TOL=111960],deloneura subfusca[&&NHX:TOL=111961])deloneura[&&NHX:TOL=106883],(epitola posthumus[&&NHX:TOL=111794],epitola urania[&&NHX:TOL=111795],epitola uranoides[&&NHX:TOL=111796])epitola[&&NHX:TOL=106885],((epitolina catori[&&NHX:TOL=111949],epitolina larseni[&&NHX:TOL=111952])[&&NHX:TOL=111954],(epitolina dispar[&&NHX:TOL=111951],epitolina collinsi[&&NHX:TOL=111950],epitolina melissa[&&NHX:TOL=111953])[&&NHX:TOL=111955])epitolina[&&NHX:TOL=106886],(hewitsonia amieti[&&NHX:TOL=111699],hewitsonia beryllina[&&NHX:TOL=111700],hewitsonia bitjeana[&&NHX:TOL=111701],hewitsonia boisduvalii[&&NHX:TOL=111702],hewitsonia congoensis[&&NHX:TOL=111703],hewitsonia danane[&&NHX:TOL=111705],hewitsonia dennisangwina[&&NHX:TOL=111706],hewitsonia gomensis[&&NHX:TOL=111707],hewitsonia inexpectata[&&NHX:TOL=111708],hewitsonia intermedia[&&NHX:TOL=111709],hewitsonia kirbyi[&&NHX:TOL=111710],hewitsonia magdalenae[&&NHX:TOL=111711],hewitsonia mittonae[&&NHX:TOL=111712],hewitsonia occidentalis[&&NHX:TOL=111713],hewitsonia prouvosti[&&NHX:TOL=111714],hewitsonia similis[&&NHX:TOL=111715],hewitsonia ugandae[&&NHX:TOL=111716])hewitsonia[&&NHX:TOL=106887],(hypophytala benitensis[&&NHX:TOL=111860],hypophytala henleyi[&&NHX:TOL=111861],hypophytala hyetta[&&NHX:TOL=111862],hypophytala hyettina[&&NHX:TOL=111863],hypophytala hyettoides[&&NHX:TOL=111864],hypophytala nigrescens[&&NHX:TOL=111865],hypophytala obscura[&&NHX:TOL=111866],hypophytala reducta[&&NHX:TOL=111867],hypophytala ultramarina[&&NHX:TOL=111868],hypophytala vansomereni[&&NHX:TOL=111869])hypophytala[&&NHX:TOL=106888],neaveia lamborni[&&NHX:TOL=106889],neoepitola barombiensis[&&NHX:TOL=106890],phytala elais[&&NHX:TOL=106891],powellana cottoni[&&NHX:TOL=106892],pseudoneaveia jacksoni[&&NHX:TOL=106893],((stempfferia abri[&&NHX:TOL=111894],stempfferia carcassoni[&&NHX:TOL=111895])subgenus stempfferia[&&NHX:TOL=111717],(stempfferia alba[&&NHX:TOL=111896],stempfferia badura[&&NHX:TOL=111898],((stempfferia baoule[&&NHX:TOL=111899],stempfferia cercene[&&NHX:TOL=111904],stempfferia moyambina[&&NHX:TOL=111928])[&&NHX:TOL=111940],(stempfferia cercenoides[&&NHX:TOL=111905],stempfferia dorothea[&&NHX:TOL=111910],stempfferia katherinae[&&NHX:TOL=111920])[&&NHX:TOL=111941],stempfferia subtumescens[&&NHX:TOL=111933])[&&NHX:TOL=111939],stempfferia bouyeri[&&NHX:TOL=111901],((stempfferia carcina[&&NHX:TOL=111902],stempfferia ife[&&NHX:TOL=111916],stempfferia michelae[&&NHX:TOL=111927])[&&NHX:TOL=111943],(stempfferia kholifa[&&NHX:TOL=111921],stempfferia tumentia[&&NHX:TOL=111936])[&&NHX:TOL=111944])[&&NHX:TOL=111942],stempfferia carilla[&&NHX:TOL=111903],stempfferia cinerea[&&NHX:TOL=111907],stempfferia coerulea[&&NHX:TOL=111908],stempfferia flavoantennata[&&NHX:TOL=111912],stempfferia francisci[&&NHX:TOL=111913],stempfferia ginettae[&&NHX:TOL=111914],(stempfferia gordoni[&&NHX:TOL=111915],stempfferia staudingeri[&&NHX:TOL=111932])[&&NHX:TOL=111945],stempfferia insulana[&&NHX:TOL=111917],stempfferia iturina[&&NHX:TOL=111918],stempfferia jolyana[&&NHX:TOL=111919],((stempfferia annae[&&NHX:TOL=111897],stempfferia boormani[&&NHX:TOL=111900],stempfferia elissa[&&NHX:TOL=111911],stempfferia leonina[&&NHX:TOL=111922],stempfferia marginata[&&NHX:TOL=111926])[&&NHX:TOL=111947],stempfferia ciconia[&&NHX:TOL=111906])[&&NHX:TOL=111946],stempfferia liberti[&&NHX:TOL=111923],stempfferia magnifica[&&NHX:TOL=111924],stempfferia mara[&&NHX:TOL=111925],stempfferia piersoni[&&NHX:TOL=111929],stempfferia schultzei[&&NHX:TOL=111930],stempfferia similis[&&NHX:TOL=111931],stempfferia suzannae[&&NHX:TOL=111934],stempfferia sylviae[&&NHX:TOL=111935],(stempfferia congoana[&&NHX:TOL=111909],stempfferia uniformis[&&NHX:TOL=111937],stempfferia zelza[&&NHX:TOL=111938])[&&NHX:TOL=111948])subgenus cercenia[&&NHX:TOL=111718])stempfferia[&&NHX:TOL=106894],tumerepedes flava[&&NHX:TOL=106895],((cerautola adolphifrederici[&&NHX:TOL=111721],cerautola ceraunia[&&NHX:TOL=111722],cerautola crippsi[&&NHX:TOL=111723],cerautola crowleyi[&&NHX:TOL=111724],cerautola fisheri[&&NHX:TOL=111725],cerautola legeri[&&NHX:TOL=111726],cerautola miranda[&&NHX:TOL=111727],cerautola semibrunnea[&&NHX:TOL=111728])subgenus cerautola[&&NHX:TOL=111720],(cerautola decellei[&&NHX:TOL=111730],cerautola hewitsoni[&&NHX:TOL=111731],cerautola hewitsonioides[&&NHX:TOL=111732],cerautola stempfferi[&&NHX:TOL=111733])subgenus hewitola[&&NHX:TOL=111729])cerautola[&&NHX:TOL=111719],(cephetola aureliae[&&NHX:TOL=111813],cephetola australis[&&NHX:TOL=111814],cephetola barnsi[&&NHX:TOL=111815],cephetola bwamba[&&NHX:TOL=111816],cephetola catuna[&&NHX:TOL=111817],cephetola cephena[&&NHX:TOL=111818],cephetola chari[&&NHX:TOL=111819],cephetola collinsi[&&NHX:TOL=111820],cephetola dolorosa[&&NHX:TOL=111821],cephetola ducarmei[&&NHX:TOL=111822],cephetola eliasis[&&NHX:TOL=111823],cephetola epitolina[&&NHX:TOL=111824],cephetola gerdae[&&NHX:TOL=111825],cephetola ghesquierei[&&NHX:TOL=111826],cephetola godarti[&&NHX:TOL=111827],cephetola izidori[&&NHX:TOL=111828],cephetola kakamegae[&&NHX:TOL=111829],cephetola kamengensis[&&NHX:TOL=111830],cephetola karinae[&&NHX:TOL=111831],cephetola katerae[&&NHX:TOL=111832],cephetola kiellandi[&&NHX:TOL=111833],cephetola maculata[&&NHX:TOL=111834],cephetola maesseni[&&NHX:TOL=111835],cephetola marci[&&NHX:TOL=111836],cephetola mariae[&&NHX:TOL=111837],cephetola martini[&&NHX:TOL=111838],cephetola mengoensis[&&NHX:TOL=111839],cephetola mercedes[&&NHX:TOL=111840],cephetola mpangensis[&&NHX:TOL=111841],cephetola nigeriae[&&NHX:TOL=111842],cephetola nigra[&&NHX:TOL=111843],cephetola obscura[&&NHX:TOL=111844],cephetola orientalis[&&NHX:TOL=111845],cephetola oubanguiensis[&&NHX:TOL=111846],cephetola oueso[&&NHX:TOL=111847],cephetola overlaeti[&&NHX:TOL=111848],cephetola peteri[&&NHX:TOL=111849],cephetola pinodes[&&NHX:TOL=111850],cephetola quentini[&&NHX:TOL=111851],cephetola rileyi[&&NHX:TOL=111852],cephetola subcoerulea[&&NHX:TOL=111853],cephetola subgriseata[&&NHX:TOL=111854],cephetola sublustris[&&NHX:TOL=111855],cephetola tanzaniensis[&&NHX:TOL=111856],cephetola vinalli[&&NHX:TOL=111857],cephetola viridana[&&NHX:TOL=111858])cephetola[&&NHX:TOL=111734],((geritola albomaculata[&&NHX:TOL=111872],geritola amieti[&&NHX:TOL=111873],geritola concepcion[&&NHX:TOL=111874],geritola cyanea[&&NHX:TOL=111875],geritola daveyi[&&NHX:TOL=111876],geritola dubia[&&NHX:TOL=111877],geritola frankdaveyi[&&NHX:TOL=111878],geritola gerina[&&NHX:TOL=111879],geritola goodi[&&NHX:TOL=111880],geritola jackiana[&&NHX:TOL=111881],geritola larae[&&NHX:TOL=111882],geritola liana[&&NHX:TOL=111883],geritola mirifica[&&NHX:TOL=111892],geritola nitide[&&NHX:TOL=111884],geritola nitidica[&&NHX:TOL=111885],geritola prouvosti[&&NHX:TOL=111886],geritola virginea[&&NHX:TOL=111890],geritola zelica[&&NHX:TOL=111891])subgenus geritola[&&NHX:TOL=111889],geritola subargentea[&&NHX:TOL=111737])geritola[&&NHX:TOL=111735])epitola section[&&NHX:TOL=106880])liptenini[&&NHX:TOL=106345])[&&NHX:TOL=106840],((cyaniriodes libna[&&NHX:TOL=106783],cyaniriodes siraspiorum[&&NHX:TOL=106784])cyaniriodes[&&NHX:TOL=106777],(deramas alixae[&&NHX:TOL=106812],deramas antynax[&&NHX:TOL=106813],deramas anyx[&&NHX:TOL=106814],deramas arshadorum[&&NHX:TOL=106815],deramas basrii[&&NHX:TOL=106816],deramas cham[&&NHX:TOL=106817],deramas bidotata[&&NHX:TOL=106818],deramas evelynae[&&NHX:TOL=106819],deramas ikedai[&&NHX:TOL=106820],deramas jasoda[&&NHX:TOL=106821],deramas kawazoei[&&NHX:TOL=106822],deramas livens[&&NHX:TOL=106823],deramas manobo[&&NHX:TOL=106824],deramas masae[&&NHX:TOL=106825],deramas montana[&&NHX:TOL=106826],deramas nanae[&&NHX:TOL=106827],deramas nelvis[&&NHX:TOL=106828],deramas nigriscens[&&NHX:TOL=106829],deramas nolens[&&NHX:TOL=106830],deramas osamui[&&NHX:TOL=106831],deramas philippensis[&&NHX:TOL=106832],deramas sumikat[&&NHX:TOL=106833],deramas suwartinae[&&NHX:TOL=106834],deramas talophi[&&NHX:TOL=106835],deramas tomokoae[&&NHX:TOL=106836],deramas toshikoae[&&NHX:TOL=106837],deramas treadawayi[&&NHX:TOL=106838],deramas woolletti[&&NHX:TOL=106839],deramas mindanensis[&&NHX:TOL=120591])deramas[&&NHX:TOL=106778],(poritia erycinoides[&&NHX:TOL=106785],poritia fruhstorferi[&&NHX:TOL=106786],poritia hewitsoni[&&NHX:TOL=106787],poritia karennia[&&NHX:TOL=106788],poritia kinoshitai[&&NHX:TOL=106789],poritia languana[&&NHX:TOL=106790],poritia manilia[&&NHX:TOL=106791],poritia palos[&&NHX:TOL=106792],poritia personata[&&NHX:TOL=106793],poritia phama[&&NHX:TOL=106794],poritia philota[&&NHX:TOL=106795],poritia phormedon[&&NHX:TOL=106796],poritia plateni[&&NHX:TOL=106797],poritia pleurata[&&NHX:TOL=106798],poritia promula[&&NHX:TOL=106799],poritia solitaria[&&NHX:TOL=106800],poritia sumatrae[&&NHX:TOL=106801])poritia[&&NHX:TOL=106779],poriskina phakos[&&NHX:TOL=106780],(simiskina pasira[&&NHX:TOL=106802],simiskina pavonica[&&NHX:TOL=106803],simiskina pediada[&&NHX:TOL=106804],simiskina phalena[&&NHX:TOL=106805],simiskina phalia[&&NHX:TOL=106806],simiskina pharyge[&&NHX:TOL=106807],simiskina pheretia[&&NHX:TOL=106808],simiskina philura[&&NHX:TOL=106809],simiskina proxima[&&NHX:TOL=106810],simiskina sibatika[&&NHX:TOL=106811])simiskina[&&NHX:TOL=106781])poritiini[&&NHX:TOL=106346])poritiinae[&&NHX:TOL=12180],(((lachnocnema abyssinica[&&NHX:TOL=111555],lachnocnema albimacula[&&NHX:TOL=111556],lachnocnema angolanus[&&NHX:TOL=111557],lachnocnema bamptoni[&&NHX:TOL=111558],lachnocnema bibulus[&&NHX:TOL=111559],lachnocnema brimoides[&&NHX:TOL=111560],lachnocnema brunea[&&NHX:TOL=111561],lachnocnema busoga[&&NHX:TOL=111562],lachnocnema camerunica[&&NHX:TOL=111563],lachnocnema congoensis[&&NHX:TOL=111564],lachnocnema disrupta[&&NHX:TOL=111565],lachnocnema divergens[&&NHX:TOL=111566],lachnocnema dohertyi[&&NHX:TOL=111567],lachnocnema ducarmei[&&NHX:TOL=111568],lachnocnema durbani[&&NHX:TOL=111569],lachnocnema emperamus[&&NHX:TOL=111570],lachnocnema exiguus[&&NHX:TOL=111571],lachnocnema inexpectata[&&NHX:TOL=111572],lachnocnema intermedia[&&NHX:TOL=111573],lachnocnema jacksoni[&&NHX:TOL=111574],lachnocnema jolyana[&&NHX:TOL=111575],lachnocnema katangae[&&NHX:TOL=111576],lachnocnema kiellandi[&&NHX:TOL=111577],lachnocnema laches[&&NHX:TOL=111578],lachnocnema luna[&&NHX:TOL=111579],lachnocnema magna[&&NHX:TOL=111580],lachnocnema makakensis[&&NHX:TOL=111581],lachnocnema nigrocellularis[&&NHX:TOL=111582],lachnocnema obscura[&&NHX:TOL=111583],lachnocnema overlaeti[&&NHX:TOL=111584],lachnocnema pseudobibulus[&&NHX:TOL=111585],lachnocnema regularis[&&NHX:TOL=111586],lachnocnema reutlingeri[&&NHX:TOL=111587],lachnocnema riftensis[&&NHX:TOL=111588],lachnocnema sosia[&&NHX:TOL=111589],lachnocnema tanzaniensis[&&NHX:TOL=111590],lachnocnema trianglaris[&&NHX:TOL=111591],lachnocnema unicolor[&&NHX:TOL=111592],lachnocnema vuattouxi[&&NHX:TOL=111593])lachnocnema[&&NHX:TOL=111547],(thestor basuta[&&NHX:TOL=111595],(thestor barbatus[&&NHX:TOL=111594],thestor brachycera[&&NHX:TOL=111596],thestor claasensi[&&NHX:TOL=111600],thestor holmesi[&&NHX:TOL=111605],thestor overbergensis[&&NHX:TOL=111609],thestor penningtoni[&&NHX:TOL=111610],thestor petra[&&NHX:TOL=111611],thestor rileyi[&&NHX:TOL=111615],thestor stepheni[&&NHX:TOL=111618],thestor yildizae[&&NHX:TOL=111623])[&&NHX:TOL=111624],(thestor braunsi[&&NHX:TOL=111597],thestor dicksoni[&&NHX:TOL=111602],thestor calviniae[&&NHX:TOL=111598])[&&NHX:TOL=111625],(thestor compassbergae[&&NHX:TOL=111601],thestor camdeboo[&&NHX:TOL=111599],thestor kaplani[&&NHX:TOL=111606],thestor pringlei[&&NHX:TOL=111613])[&&NHX:TOL=111626],(thestor dryburghi[&&NHX:TOL=111603],thestor protumnus[&&NHX:TOL=111614])[&&NHX:TOL=111627],(thestor montanus[&&NHX:TOL=111607],thestor pictus[&&NHX:TOL=111612],thestor rooibergensis[&&NHX:TOL=111616],thestor strutti[&&NHX:TOL=111619],thestor vansoni[&&NHX:TOL=111622])[&&NHX:TOL=111628],thestor murrayi[&&NHX:TOL=111608],thestor rossouwi[&&NHX:TOL=111617])thestor[&&NHX:TOL=111548])lachnocnemini[&&NHX:TOL=106347],((euliphyra hewitsoni[&&NHX:TOL=107800],euliphyra leucyania[&&NHX:TOL=107801],euliphyra mirifica[&&NHX:TOL=107802])euliphyra[&&NHX:TOL=107795],(liphyra brassolis[&&NHX:TOL=107866],liphyra grandis[&&NHX:TOL=107867])liphyra[&&NHX:TOL=107796],(aslauga aura[&&NHX:TOL=107846],aslauga australis[&&NHX:TOL=107847],aslauga bella[&&NHX:TOL=107848],aslauga bitjensis[&&NHX:TOL=107849],aslauga camerunica[&&NHX:TOL=107850],aslauga ernesti[&&NHX:TOL=107799],aslauga febe[&&NHX:TOL=107851],aslauga karamoja[&&NHX:TOL=107854],aslauga kallimoides[&&NHX:TOL=107798],aslauga katangana[&&NHX:TOL=107855],((aslauga abri[&&NHX:TOL=128885],aslauga lamborni[&&NHX:TOL=107856],aslauga modesta[&&NHX:TOL=107860],aslauga prouvosti[&&NHX:TOL=107863])[&&NHX:TOL=128884],(aslauga bouyeri[&&NHX:TOL=128887],aslauga confusa[&&NHX:TOL=128888])[&&NHX:TOL=128886],aslauga guineensis[&&NHX:TOL=107852],aslauga imitans[&&NHX:TOL=107853])aslauga lamborni group[&&NHX:TOL=128883],aslauga latifurca[&&NHX:TOL=107857],aslauga marginalis[&&NHX:TOL=107858],aslauga marshalli[&&NHX:TOL=107859],(aslauga orientalis[&&NHX:TOL=107861],aslauga purpurescens[&&NHX:TOL=107864],aslauga tanga[&&NHX:TOL=128890])[&&NHX:TOL=128889],aslauga pandora[&&NHX:TOL=107862],aslauga vininga[&&NHX:TOL=107865],aslauga atrophifurca[&&NHX:TOL=128891],aslauga satyroides[&&NHX:TOL=128892])aslauga[&&NHX:TOL=107797])liphyrini[&&NHX:TOL=106348],(((logania distanti[&&NHX:TOL=107911],logania drucei[&&NHX:TOL=107912],logania dumoga[&&NHX:TOL=107913],logania hampsoni[&&NHX:TOL=107914],logania malayica[&&NHX:TOL=107915],logania marmorata[&&NHX:TOL=107916],logania nehalemia[&&NHX:TOL=107917],logania obscura[&&NHX:TOL=107918],logania paluana[&&NHX:TOL=107919],logania regina[&&NHX:TOL=107920],logania waldtraudae[&&NHX:TOL=120587],logania watsoniana[&&NHX:TOL=107921])logania[&&NHX:TOL=107870],(miletus ancon[&&NHX:TOL=107922],miletus archilocus[&&NHX:TOL=107923],miletus bannanus[&&NHX:TOL=107924],miletus biggsi[&&NHX:TOL=107925],miletus boisduvali[&&NHX:TOL=107926],miletus celinus[&&NHX:TOL=107927],miletus cellarius[&&NHX:TOL=107928],miletus chinensis[&&NHX:TOL=107929],miletus croton[&&NHX:TOL=107930],miletus drucei[&&NHX:TOL=107931],miletus gaesa[&&NHX:TOL=107932],miletus gaetulus[&&NHX:TOL=107933],miletus gallus[&&NHX:TOL=107934],miletus gigantes[&&NHX:TOL=107935],miletus gopara[&&NHX:TOL=107936],miletus heracleion[&&NHX:TOL=107937],miletus leos[&&NHX:TOL=107938],miletus longeana[&&NHX:TOL=107939],miletus mallus[&&NHX:TOL=107940],miletus melanion[&&NHX:TOL=107941],miletus nymphis[&&NHX:TOL=107942],miletus petronius[&&NHX:TOL=107943],miletus rosei[&&NHX:TOL=107944],miletus symethus[&&NHX:TOL=107945],miletus valeus[&&NHX:TOL=107946],miletus zinckenii[&&NHX:TOL=107947],miletus takanamii[&&NHX:TOL=120580],miletus atimonicus[&&NHX:TOL=120581],miletus bazilanus[&&NHX:TOL=120582])miletus[&&NHX:TOL=107872],((allotinus agnolia[&&NHX:TOL=107875],allotinus albifasciatus[&&NHX:TOL=107876],allotinus fallax[&&NHX:TOL=107877],allotinus major[&&NHX:TOL=107878],allotinus maximus[&&NHX:TOL=107879],allotinus nicholsi[&&NHX:TOL=107880],allotinus subviolaceus[&&NHX:TOL=107881])allotinus allotinus[&&NHX:TOL=107908],(allotinus albatus[&&NHX:TOL=107882],allotinus apries[&&NHX:TOL=107883],allotinus corbeti[&&NHX:TOL=107884],allotinus davidis[&&NHX:TOL=107885],allotinus drumila[&&NHX:TOL=107886],allotinus horsfieldi[&&NHX:TOL=107887],allotinus leogoron[&&NHX:TOL=107888],allotinus luzonensis[&&NHX:TOL=120583],allotinus macassarensis[&&NHX:TOL=107889],allotinus melos[&&NHX:TOL=120584],allotinus nivalis[&&NHX:TOL=107890],allotinus parapus[&&NHX:TOL=107891],allotinus samarensis[&&NHX:TOL=107892],allotinus substrigosus[&&NHX:TOL=107893],allotinus unicolor[&&NHX:TOL=107894])allotinus paragerydus[&&NHX:TOL=107909],(allotinus bidiensis[&&NHX:TOL=107895],allotinus borneensis[&&NHX:TOL=107896],allotinus brooksi[&&NHX:TOL=107897],allotinus fabius[&&NHX:TOL=107898],allotinus kudaratus[&&NHX:TOL=120585],allotinus nigritus[&&NHX:TOL=107903],allotinus punctatus[&&NHX:TOL=120586],allotinus portunus[&&NHX:TOL=107899],allotinus sarrastes[&&NHX:TOL=107900],allotinus strigatus[&&NHX:TOL=107901],allotinus taras[&&NHX:TOL=107902])allotinus fabitaras[&&NHX:TOL=107910],allotinus paetus[&&NHX:TOL=107904],allotinus panormis[&&NHX:TOL=107905],allotinus posidion[&&NHX:TOL=107906],allotinus thalebanus[&&NHX:TOL=107907])allotinus[&&NHX:TOL=107868])[&&NHX:TOL=107955],(megalopalpus angulosus[&&NHX:TOL=107951],megalopalpus metaleucus[&&NHX:TOL=107952],megalopalpus simplex[&&NHX:TOL=107953],megalopalpus zymna[&&NHX:TOL=107954])megalopalpus[&&NHX:TOL=107871],lontalius eltus[&&NHX:TOL=120589],[&&NHX:TOL=120590])miletini[&&NHX:TOL=106349],((spalgis epius[&&NHX:TOL=111551],spalgis jacksoni[&&NHX:TOL=111552],spalgis lemolea[&&NHX:TOL=111553],spalgis tintinga[&&NHX:TOL=111554],spalgis asmus[&&NHX:TOL=117840],spalgis takanamii[&&NHX:TOL=117841],spalgis sp.[&&NHX:TOL=117842])spalgis[&&NHX:TOL=111549],feniseca tarquinius[&&NHX:TOL=111550],(taraka hamada[&&NHX:TOL=111964],taraka mahanetra[&&NHX:TOL=111965],taraka shiloi[&&NHX:TOL=111966])taraka[&&NHX:TOL=111962])spalgini[&&NHX:TOL=106350])miletinae[&&NHX:TOL=12181])[&&NHX:TOL=103504],(((aleoides almeida[&&NHX:TOL=121814],aleoides angolensis[&&NHX:TOL=121815],aleoides apicalis[&&NHX:TOL=121816],aleoides aranda[&&NHX:TOL=121817],aleoides argenteus[&&NHX:TOL=121818],aleoides arida[&&NHX:TOL=121819],aleoides bamptoni[&&NHX:TOL=121820],aleoides barbarae[&&NHX:TOL=121821],aleoides barklyi[&&NHX:TOL=121822],aleoides braueri[&&NHX:TOL=121823],aleoides caffrariae[&&NHX:TOL=121824],aleoides caledoni[&&NHX:TOL=121825],aleoides carolynnae[&&NHX:TOL=121826],aleoides clarki[&&NHX:TOL=121827],aleoides conradsi[&&NHX:TOL=121828],aleoides damarensis[&&NHX:TOL=121829],aleoides dentatis[&&NHX:TOL=121830],aleoides depicta[&&NHX:TOL=121831],aleoides dicksoni[&&NHX:TOL=121832],aleoides dryas[&&NHX:TOL=121833],aleoides egerides[&&NHX:TOL=121834],aleoides gowani[&&NHX:TOL=121835],aleoides griseus[&&NHX:TOL=121836],aleoides henningi[&&NHX:TOL=121837],aleoides juana[&&NHX:TOL=121838],aleoides kaplani[&&NHX:TOL=121839],aleoides lutescens[&&NHX:TOL=121840],aleoides macmasteri[&&NHX:TOL=121841],aleoides maluti[&&NHX:TOL=121842],aleoides margaretae[&&NHX:TOL=121843],aleoides mbuluensis[&&NHX:TOL=121844],aleoides merces[&&NHX:TOL=121845],aleoides molomo[&&NHX:TOL=121846],aleoides monticola[&&NHX:TOL=121847],aleoides mullini[&&NHX:TOL=121848],aleoides namibiensis[&&NHX:TOL=121849],aleoides natalensis[&&NHX:TOL=121850],aleoides nollothi[&&NHX:TOL=121851],aleoides nubilus[&&NHX:TOL=121852],aleoides oreas[&&NHX:TOL=121853],aleoides pallida[&&NHX:TOL=121854],aleoides penningtoni[&&NHX:TOL=121855],aleoides pierus[&&NHX:TOL=121856],aleoides plowesi[&&NHX:TOL=121857],aleoides pringlei[&&NHX:TOL=121858],aleoides quickelbergei[&&NHX:TOL=121859],aleoides rileyi[&&NHX:TOL=121860],aleoides rossouwi[&&NHX:TOL=121861],aleoides simplex[&&NHX:TOL=121862],aleoides stevensoni[&&NHX:TOL=121863],aleoides susanae[&&NHX:TOL=121864],aleoides swanepoeli[&&NHX:TOL=121865],aleoides taikosama[&&NHX:TOL=121866],aleoides taylori[&&NHX:TOL=121867],aleoides tearei[&&NHX:TOL=121868],aleoides thyra[&&NHX:TOL=121869],aleoides titei[&&NHX:TOL=121870],aleoides trimeni[&&NHX:TOL=121871],aleoides vansoni[&&NHX:TOL=121872])aloeides[&&NHX:TOL=106373],(((aphnaeus adamsi[&&NHX:TOL=121562],aphnaeus affinis[&&NHX:TOL=121563],aphnaeus argyrocyclus[&&NHX:TOL=121564],aphnaeus asterius[&&NHX:TOL=121565],aphnaeus brahami[&&NHX:TOL=121566],aphnaeus carcassoni[&&NHX:TOL=121567],aphnaeus chapini[&&NHX:TOL=121568],aphnaeus charboneli[&&NHX:TOL=121569],aphnaeus coronae[&&NHX:TOL=121570],aphnaeus erikssoni[&&NHX:TOL=121571],aphnaeus flavescens[&&NHX:TOL=121572],aphnaeus gilloni[&&NHX:TOL=121573],aphnaeus herbuloti[&&NHX:TOL=121574],aphnaeus jacksoni[&&NHX:TOL=121575],aphnaeus jefferyi[&&NHX:TOL=121576],aphnaeus liberti[&&NHX:TOL=121585],aphnaeus marshalli[&&NHX:TOL=121577],aphnaeus neavei[&&NHX:TOL=121578],aphnaeus nyanzae[&&NHX:TOL=121579],aphnaeus orcas[&&NHX:TOL=121580],aphnaeus questiauxi[&&NHX:TOL=121581])subgenus aphnaeus[&&NHX:TOL=121583],aphnaeus paraphnaeus hutchinsonii[&&NHX:TOL=121582])aphnaeus[&&NHX:TOL=106375],((apharitis acamas[&&NHX:TOL=121589],apharitis buchanani[&&NHX:TOL=121590],apharitis cilissa[&&NHX:TOL=121591],apharitis epargyros[&&NHX:TOL=121592],apharitis gilletti[&&NHX:TOL=121593],apharitis maxima[&&NHX:TOL=121594],apharitis mymecophila[&&NHX:TOL=121595],apharitis nilus[&&NHX:TOL=121596])apharitis[&&NHX:TOL=106374],(cigaritis allardi[&&NHX:TOL=121597],cigaritis siphax[&&NHX:TOL=121598],cigaritis zohra[&&NHX:TOL=121599])cigaritis[&&NHX:TOL=106379],cesa waggae[&&NHX:TOL=121634],((spindasis apelles[&&NHX:TOL=121601],spindasis apuleia[&&NHX:TOL=121602],spindasis avriko[&&NHX:TOL=121603],spindasis baghirmii[&&NHX:TOL=121604],spindasis bergeri[&&NHX:TOL=121605],spindasis brunnea[&&NHX:TOL=121606],spindasis collinsi[&&NHX:TOL=121607],spindasis crustaria[&&NHX:TOL=121608],spindasis cynica[&&NHX:TOL=121609],spindasis dufranei[&&NHX:TOL=121610],spindasis ella[&&NHX:TOL=121611],spindasis hassoni[&&NHX:TOL=121612],spindasis homeyeri[&&NHX:TOL=121613],spindasis iza[&&NHX:TOL=121614],spindasis lutosus[&&NHX:TOL=121615],spindasis shaba[&&NHX:TOL=121616],spindasis menelas[&&NHX:TOL=121617],spindasis modestus[&&NHX:TOL=121618],spindasis montana[&&NHX:TOL=121619],spindasis mozambica[&&NHX:TOL=121620],spindasis nairobiensis[&&NHX:TOL=121621],spindasis namaquus[&&NHX:TOL=121622],spindasis natalensis[&&NHX:TOL=121623],spindasis nyassae[&&NHX:TOL=121624],spindasis overlaeti[&&NHX:TOL=121625],spindasis phanes[&&NHX:TOL=121626],spindasis pinheyi[&&NHX:TOL=121627],spindasis scotti[&&NHX:TOL=121628],spindasis somalina[&&NHX:TOL=121629],spindasis tanganyikae[&&NHX:TOL=121630],spindasis tavetensis[&&NHX:TOL=121631],spindasis trimeni[&&NHX:TOL=121632],spindasis victoriae[&&NHX:TOL=121633])african spindasis species[&&NHX:TOL=121600],(spindasis abnormis[&&NHX:TOL=121636],spindasis arooni[&&NHX:TOL=121637],spindasis elima[&&NHX:TOL=121638],spindasis elwesi[&&NHX:TOL=121639],spindasis evansii[&&NHX:TOL=121640],spindasis greeni[&&NHX:TOL=121641],spindasis ictis[&&NHX:TOL=121642],spindasis kutu[&&NHX:TOL=121643],spindasis learmondi[&&NHX:TOL=121644],spindasis leechi[&&NHX:TOL=121645],spindasis lilacinus[&&NHX:TOL=121646],spindasis lohita[&&NHX:TOL=121647],spindasis lunulifera[&&NHX:TOL=121648],spindasis maximus[&&NHX:TOL=121660],spindasis nipalicus[&&NHX:TOL=121649],spindasis nubilus[&&NHX:TOL=121650],spindasis rukma[&&NHX:TOL=121651],spindasis rukmini[&&NHX:TOL=121652],spindasis schistacea[&&NHX:TOL=121653],spindasis seliga[&&NHX:TOL=121654],spindasis syama[&&NHX:TOL=121655],spindasis takanonis[&&NHX:TOL=121656],spindasis trifurcata[&&NHX:TOL=121657],spindasis vixinga[&&NHX:TOL=121658],spindasis vulcanus[&&NHX:TOL=121659])oriental spindasis species[&&NHX:TOL=121635])spindasis[&&NHX:TOL=106387])[&&NHX:TOL=121586])[&&NHX:TOL=121584],((axiocerses amanga[&&NHX:TOL=121680],axiocerses argeneomaculata[&&NHX:TOL=121681],axiocerses bambana[&&NHX:TOL=121682],axiocerses bamptoni[&&NHX:TOL=121697],axiocerses baumi[&&NHX:TOL=121683],axiocerses callaghani[&&NHX:TOL=121684],axiocerses coalescens[&&NHX:TOL=121698],axiocerses collinsi[&&NHX:TOL=121699],axiocerses croesus[&&NHX:TOL=121700],axiocerses harpax[&&NHX:TOL=121685],axiocerses heathi[&&NHX:TOL=121701],axiocerses jacksoni[&&NHX:TOL=121686],axiocerses karinae[&&NHX:TOL=121702],axiocerses kiellandi[&&NHX:TOL=121703],axiocerses maureli[&&NHX:TOL=121687],axiocerses melanica[&&NHX:TOL=121704],axiocerses nyika[&&NHX:TOL=121688],axiocerses punicea[&&NHX:TOL=121689],axiocerses styx[&&NHX:TOL=121690],axiocerses susanae[&&NHX:TOL=121705],axiocerses tjoane[&&NHX:TOL=121706])axiocerses[&&NHX:TOL=106376],(zeritis aurivillii[&&NHX:TOL=121691],zeritis fontainei[&&NHX:TOL=121692],zeritis krystyna[&&NHX:TOL=121693],zeritis nereine[&&NHX:TOL=121694],zeritis pulcherrima[&&NHX:TOL=121695],zeritis sorhagenii[&&NHX:TOL=121696])zeritis[&&NHX:TOL=106388])[&&NHX:TOL=121587],(((chloroselas argentea[&&NHX:TOL=121665],chloroselas azurea[&&NHX:TOL=121666],chloroselas esmeralda[&&NHX:TOL=121667],chloroselas minima[&&NHX:TOL=121668],chloroselas ogadenensis[&&NHX:TOL=121669],chloroselas overlaeti[&&NHX:TOL=121670],chloroselas pseudozeritis[&&NHX:TOL=121671],chloroselas tamaniba[&&NHX:TOL=121672],chloroselas taposana[&&NHX:TOL=121673],chloroselas trembathi[&&NHX:TOL=121674],chloroselas vansomereni[&&NHX:TOL=121675])chloroselas[&&NHX:TOL=106377],(desmolycaena arabica[&&NHX:TOL=121677],desmolycaena mazoensis[&&NHX:TOL=121678])desmolycaena[&&NHX:TOL=106381],vansomerenia rogersi[&&NHX:TOL=121679])[&&NHX:TOL=121676],(lipaphnaeus aderna[&&NHX:TOL=121661],lipaphnaeus eustorgia[&&NHX:TOL=121662],lipaphnaeus leonina[&&NHX:TOL=121663],lipaphnaeus loxura[&&NHX:TOL=121664])lipaphnaeus[&&NHX:TOL=106383])[&&NHX:TOL=121588],(((chrysoritis dicksoni[&&NHX:TOL=121724],chrysoritis oreas[&&NHX:TOL=121720])[&&NHX:TOL=121723],((((chrysoritis zeuxo[&&NHX:TOL=121721],chrysoritis cottrelli[&&NHX:TOL=131139])[&&NHX:TOL=131138],chrysoritis zonarius[&&NHX:TOL=121722])[&&NHX:TOL=131137],chrysoritis coetzeri[&&NHX:TOL=121726])[&&NHX:TOL=121725],chrysoritis pyroeis[&&NHX:TOL=121738],chrysoritis felthami[&&NHX:TOL=121737])[&&NHX:TOL=131136])chrysoritis oreas group[&&NHX:TOL=131135],(chrysoritis aethon[&&NHX:TOL=121728],chrysoritis aureus[&&NHX:TOL=121729],chrysoritis chrysaor[&&NHX:TOL=121730],chrysoritis lycegenes[&&NHX:TOL=121731],chrysoritis lyncurium[&&NHX:TOL=121732],chrysoritis midas[&&NHX:TOL=121733],chrysoritis natalensis[&&NHX:TOL=121734],chrysoritis phosphor[&&NHX:TOL=121735])chrysoritis chrysaor group[&&NHX:TOL=121727],(chrysoritis aridus[&&NHX:TOL=121740],chrysoritis endymion[&&NHX:TOL=121741],chrysoritis adonis[&&NHX:TOL=121742],chrysoritis azurius[&&NHX:TOL=121743],chrysoritis balli[&&NHX:TOL=131140],chrysoritis beaufortius[&&NHX:TOL=121744],chrysoritis beulah[&&NHX:TOL=121745],chrysoritis blencathrae[&&NHX:TOL=121746],chrysoritis braueri[&&NHX:TOL=121747],chrysoritis brooksi[&&NHX:TOL=121748],chrysoritis daphne[&&NHX:TOL=121749],chrysoritis irene[&&NHX:TOL=121750],chrysoritis nigricans[&&NHX:TOL=121751],chrysoritis orientalis[&&NHX:TOL=121752],chrysoritis palmus[&&NHX:TOL=121771],chrysoritis pan[&&NHX:TOL=121753],chrysoritis pelion[&&NHX:TOL=121754],chrysoritis penningtoni[&&NHX:TOL=121755],chrysoritis perseus[&&NHX:TOL=121756],chrysoritis plutus[&&NHX:TOL=121757],chrysoritis pyramus[&&NHX:TOL=121758],chrysoritis rileyi[&&NHX:TOL=121759],chrysoritis swanepoeli[&&NHX:TOL=121760],chrysoritis thysbe[&&NHX:TOL=121761],chrysoritis trimeni[&&NHX:TOL=121762],chrysoritis turneri[&&NHX:TOL=121763],chrysoritis uranus[&&NHX:TOL=121764],chrysoritis violescens[&&NHX:TOL=121765])chrysoritis thysbe group[&&NHX:TOL=121739])chrysoritis[&&NHX:TOL=106378],(crudaria capensis[&&NHX:TOL=121777],crudaria leroma[&&NHX:TOL=121778],crudaria wykehami[&&NHX:TOL=121779])crudaria[&&NHX:TOL=106380],(erikssonia acraeina[&&NHX:TOL=121811],erikssonia alaponoxa[&&NHX:TOL=121812],erikssonia cooksoni[&&NHX:TOL=121813])erikssonia[&&NHX:TOL=106382],(phasis braueri[&&NHX:TOL=121707],phasis clavum[&&NHX:TOL=121708],phasis pringlei[&&NHX:TOL=121709],phasis thero[&&NHX:TOL=121710])phasis[&&NHX:TOL=106385],(pseudaletis abriana[&&NHX:TOL=121780],pseudaletis agrippina[&&NHX:TOL=121781],pseudaletis angustimargo[&&NHX:TOL=121782],pseudaletis antimachus[&&NHX:TOL=121783],pseudaletis arrhon[&&NHX:TOL=121784],pseudaletis batesi[&&NHX:TOL=121785],pseudaletis bouyeri[&&NHX:TOL=121786],pseudaletis busoga[&&NHX:TOL=121787],pseudaletis camarensis[&&NHX:TOL=121788],pseudaletis catori[&&NHX:TOL=121789],pseudaletis clymenus[&&NHX:TOL=121790],pseudaletis cornesi[&&NHX:TOL=121791],pseudaletis dolieri[&&NHX:TOL=121792],pseudaletis ducarmei[&&NHX:TOL=121793],pseudaletis dardanella[&&NHX:TOL=121794],pseudaletis jolyana[&&NHX:TOL=121795],pseudaletis leonis[&&NHX:TOL=121796],pseudaletis lusambo[&&NHX:TOL=121797],pseudaletis malangi[&&NHX:TOL=121798],pseudaletis mazanguli[&&NHX:TOL=121799],pseudaletis melissae[&&NHX:TOL=121800],pseudaletis michelae[&&NHX:TOL=121801],pseudaletis nigra[&&NHX:TOL=121802],pseudaletis richardi[&&NHX:TOL=121803],pseudaletis rileyi[&&NHX:TOL=121804],pseudaletis spolia[&&NHX:TOL=121805],pseudaletis taeniata[&&NHX:TOL=121806],pseudaletis ugandae[&&NHX:TOL=121807],pseudaletis zebra[&&NHX:TOL=121808],pseudaletis subangulata[&&NHX:TOL=121809])pseudaletis[&&NHX:TOL=106389],tylopaedia sardonyx[&&NHX:TOL=121712],argyraspodes argyraspis[&&NHX:TOL=121713],(trimenai argyroplaga[&&NHX:TOL=121772],trimenia macmasteri[&&NHX:TOL=121773],trimenia malagrida[&&NHX:TOL=121774],trimenia wallengreni[&&NHX:TOL=121775],trimenia wykehami[&&NHX:TOL=121776])trimenia[&&NHX:TOL=121714])aphnaeinae[&&NHX:TOL=106369],((((anthene abruptus[&&NHX:TOL=122219],anthene afra[&&NHX:TOL=122220],anthene alberta[&&NHX:TOL=122221],anthene amarah[&&NHX:TOL=122222],anthene arnoldi[&&NHX:TOL=122223],anthene arora[&&NHX:TOL=122224],anthene atewa[&&NHX:TOL=122225],anthene aurobrunnea[&&NHX:TOL=122226],anthene bakeri[&&NHX:TOL=122227],anthene barnesi[&&NHX:TOL=122228],anthene bipuncta[&&NHX:TOL=122229],anthene bjoernstadi[&&NHX:TOL=122230],anthene buchholzi[&&NHX:TOL=122231],anthene butleri[&&NHX:TOL=122232],anthene chirinda[&&NHX:TOL=122233],anthene collinsi[&&NHX:TOL=122234],anthene contrastata[&&NHX:TOL=122235],anthene crawshayi[&&NHX:TOL=122236],anthene definita[&&NHX:TOL=122237],anthene discimacula[&&NHX:TOL=122238],anthene emkopoti[&&NHX:TOL=122239],anthene erythropoecilus[&&NHX:TOL=122240],anthene flavomaculatus[&&NHX:TOL=122241],anthene helpsi[&&NHX:TOL=122242],anthene hobleyi[&&NHX:TOL=122243],anthene hodsoni[&&NHX:TOL=122244],anthene indefinita[&&NHX:TOL=122245],anthene irumu[&&NHX:TOL=122246],anthene ituria[&&NHX:TOL=122247],anthene janna[&&NHX:TOL=122248],anthene juba[&&NHX:TOL=122249],anthene kampala[&&NHX:TOL=122250],anthene katera[&&NHX:TOL=122251],anthene kersteni[&&NHX:TOL=122252],anthene kikuyu[&&NHX:TOL=122253],anthene lachares[&&NHX:TOL=122254],anthene larydas[&&NHX:TOL=122255],anthene lasti[&&NHX:TOL=122256],anthene lemnos[&&NHX:TOL=122257],anthene leptala[&&NHX:TOL=122258],anthene leptines[&&NHX:TOL=122259],anthene levis[&&NHX:TOL=122260],anthene ligures[&&NHX:TOL=122261],anthene liodes[&&NHX:TOL=122262],anthene locuples[&&NHX:TOL=122263],anthene lunulata[&&NHX:TOL=122264],anthene lychnaptes[&&NHX:TOL=122265],anthene lychnides[&&NHX:TOL=122266],anthene lysicles[&&NHX:TOL=122267],anthene madibirensis[&&NHX:TOL=122268],anthene mahota[&&NHX:TOL=122269],anthene makala[&&NHX:TOL=122270],anthene melambrotus[&&NHX:TOL=122271],anthene millari[&&NHX:TOL=122272],anthene minima[&&NHX:TOL=122273],anthene montana[&&NHX:TOL=122274],anthene mpanda[&&NHX:TOL=122275],anthene ngoko[&&NHX:TOL=122276],anthene nigropunctata[&&NHX:TOL=122277],anthene onias[&&NHX:TOL=122278],anthene opalina[&&NHX:TOL=122279],anthene otacilia[&&NHX:TOL=122280],anthene pitmani[&&NHX:TOL=122281],anthene princeps[&&NHX:TOL=122282],anthene pyroptera[&&NHX:TOL=122283],anthene radiata[&&NHX:TOL=122284],anthene ramnika[&&NHX:TOL=122285],anthene rhodesiana[&&NHX:TOL=122286],anthene rothschildi[&&NHX:TOL=122287],anthene rubricinctus[&&NHX:TOL=122288],anthene rubrimaculata[&&NHX:TOL=122289],anthene rufomarginata[&&NHX:TOL=122290],anthene ruwenzoricus[&&NHX:TOL=122291],anthene saddacus[&&NHX:TOL=122292],anthene schoutedeni[&&NHX:TOL=122293],anthene scintillula[&&NHX:TOL=122294],anthene sheppardi[&&NHX:TOL=122295],anthene starki[&&NHX:TOL=122296],anthene suquala[&&NHX:TOL=122297],anthene sylvanus[&&NHX:TOL=122298],anthene talboti[&&NHX:TOL=122299],anthene ukerewensis[&&NHX:TOL=122300],anthene uzungwae[&&NHX:TOL=122301],anthene versatilis[&&NHX:TOL=122302],anthene wilsoni[&&NHX:TOL=122303],anthene xanthopoecilus[&&NHX:TOL=122304],anthene zenkeri[&&NHX:TOL=122305],(anthene emolus[&&NHX:TOL=122307],anthene licates[&&NHX:TOL=122308],anthene lycaenina[&&NHX:TOL=122309],anthene lycaenoides[&&NHX:TOL=122310],anthene lycaenolus[&&NHX:TOL=122311],anthene paraffinis[&&NHX:TOL=122312],anthene philo[&&NHX:TOL=122313],anthene seltuttus[&&NHX:TOL=122314],anthene villosa[&&NHX:TOL=122315])indoaustralian anthene[&&NHX:TOL=122306])anthene[&&NHX:TOL=111538],(cupidesthes albida[&&NHX:TOL=122350],cupidesthes arescopa[&&NHX:TOL=122351],cupidesthes caerulea[&&NHX:TOL=122352],cupidesthes cuprifascia[&&NHX:TOL=122353],cupidesthes eliasi[&&NHX:TOL=122354],cupidesthes jacksoni[&&NHX:TOL=122355],cupidesthes leonina[&&NHX:TOL=122356],cupidesthes lithas[&&NHX:TOL=122357],cupidesthes mimetica[&&NHX:TOL=122358],cupidesthes minor[&&NHX:TOL=122359],cupidesthes paludicola[&&NHX:TOL=122360],cupidesthes paralithas[&&NHX:TOL=122361],cupidesthes pungusei[&&NHX:TOL=122362],cupidesthes robusta[&&NHX:TOL=122363],cupidesthes salvatoris[&&NHX:TOL=122364],cupidesthes thyrsis[&&NHX:TOL=122365],cupidesthes vidua[&&NHX:TOL=122366],cupidesthes ysobelae[&&NHX:TOL=122367])cupidesthes[&&NHX:TOL=111539],(neurellipes aequatorialis[&&NHX:TOL=122320],neurellipes chryseostictus[&&NHX:TOL=122321],neurellipes fulvus[&&NHX:TOL=122322],neurellipes gemmifera[&&NHX:TOL=122323],neurellipes likouala[&&NHX:TOL=122324],neurellipes lusones[&&NHX:TOL=122325],neurellipes meander[&&NHX:TOL=122326],neurellipes staudingeri[&&NHX:TOL=122327])neurellipes[&&NHX:TOL=111540],(neurypexina kalinzu[&&NHX:TOL=122316],neurypexina lamprocles[&&NHX:TOL=122317],neurypexina lyzanius[&&NHX:TOL=122318],neurypexina quadricaudata[&&NHX:TOL=122319])neurypexina[&&NHX:TOL=111541],(triclema coerulea[&&NHX:TOL=122330],triclema fasciatus[&&NHX:TOL=122331],triclema hades[&&NHX:TOL=122332],triclema inconspicua[&&NHX:TOL=122333],triclema inferna[&&NHX:TOL=122334],triclema kamilila[&&NHX:TOL=122335],triclema kimboza[&&NHX:TOL=122336],triclema krokosua[&&NHX:TOL=122337],triclema lacides[&&NHX:TOL=122338],triclema lamias[&&NHX:TOL=122339],triclema lucretilis[&&NHX:TOL=122340],triclema lutzi[&&NHX:TOL=122341],triclema maesseni[&&NHX:TOL=122342],triclema marshalli[&&NHX:TOL=122343],triclema nigeriae[&&NHX:TOL=122344],triclema obscura[&&NHX:TOL=122345],triclema oculatus[&&NHX:TOL=122346],triclema phoenicis[&&NHX:TOL=122347],triclema rufoplagata[&&NHX:TOL=122348],triclema tisamenus[&&NHX:TOL=122349])triclema[&&NHX:TOL=111542])lycaenesthini[&&NHX:TOL=111534],((candaides absimilis[&&NHX:TOL=122371],candalides acasta[&&NHX:TOL=122372],candalides afretta[&&NHX:TOL=122373],candalides ardosiacea[&&NHX:TOL=122374],candalides coeruleus[&&NHX:TOL=122375],candalides consimilis[&&NHX:TOL=122376],candalides cupreus[&&NHX:TOL=122377],candalides cyprotus[&&NHX:TOL=122378],candalides erinus[&&NHX:TOL=122379],candalides geminus[&&NHX:TOL=122380],candalides gilberti[&&NHX:TOL=122381],candalides grandissima[&&NHX:TOL=122382],candalides heathi[&&NHX:TOL=122383],candalides helenita[&&NHX:TOL=122384],candalides hyacinthina[&&NHX:TOL=122385],candalides lamia[&&NHX:TOL=122386],candalides limbata[&&NHX:TOL=122387],candalides margarita[&&NHX:TOL=122388],candalides meforensis[&&NHX:TOL=122389],candalides neurapacuna[&&NHX:TOL=122390],candalides pruina[&&NHX:TOL=122391],candalides riuensis[&&NHX:TOL=122392],candalides silicea[&&NHX:TOL=122393],candalides tringa[&&NHX:TOL=122394],candalides viriditincta[&&NHX:TOL=122395],candalides xanthospilos[&&NHX:TOL=122396],2 undescribed species[&&NHX:TOL=122561])candalides[&&NHX:TOL=111544],(nesolycaena albosericea[&&NHX:TOL=122368],nesolycaena caesia[&&NHX:TOL=122369],nesolycaena urumelia[&&NHX:TOL=122370])nesolycaena[&&NHX:TOL=111545],zetona delospila[&&NHX:TOL=111546])candalidini[&&NHX:TOL=111535],(niphanda asialis[&&NHX:TOL=111967],niphanda cymbia[&&NHX:TOL=111968],niphanda fusca[&&NHX:TOL=111969],niphanda stubbsi[&&NHX:TOL=111970],niphanda tessellata[&&NHX:TOL=111971])niphanda[&&NHX:TOL=111536],((cupidopsis cissus[&&NHX:TOL=122565],cupidopsis jobates[&&NHX:TOL=122566])cupidopsis[&&NHX:TOL=112154],((una philippensis[&&NHX:TOL=122573],una usta[&&NHX:TOL=122574])una[&&NHX:TOL=112156],(orthomiella pontis[&&NHX:TOL=122575],orthomiella rantaizana[&&NHX:TOL=122576])orthomiella[&&NHX:TOL=112157])una section[&&NHX:TOL=112155],((petrelaea dana[&&NHX:TOL=122568],petrelaea tombugensis[&&NHX:TOL=122569])petrelaea[&&NHX:TOL=112158],(pseudonacaduba aethiops[&&NHX:TOL=122571],pseudonacaduba sichela[&&NHX:TOL=122572])pseudonacaduba[&&NHX:TOL=122570])petrelaea section[&&NHX:TOL=122567],((nacaduba angelae[&&NHX:TOL=123352],nacaduba angusta[&&NHX:TOL=123353],nacaduba asaga[&&NHX:TOL=123354],nacaduba berenice[&&NHX:TOL=123356],nacaduba beroe[&&NHX:TOL=123357],nacaduba biocellata[&&NHX:TOL=123358],nacaduba cajetani[&&NHX:TOL=123359],nacaduba calauria[&&NHX:TOL=123360],nacaduba cladara[&&NHX:TOL=123361],nacaduba cyanea[&&NHX:TOL=123362],nacaduba deliana[&&NHX:TOL=123363],nacaduba deplorans[&&NHX:TOL=123364],nacaduba dyopa[&&NHX:TOL=123365],nacaduba glauconia[&&NHX:TOL=123395],nacaduba hermus[&&NHX:TOL=123366],nacaduba kirtoni[&&NHX:TOL=123367],nacaduba kurava[&&NHX:TOL=123368],nacaduba limbura[&&NHX:TOL=123369],nacaduba lucana[&&NHX:TOL=123370],nacaduba major[&&NHX:TOL=123371],nacaduba mallicolo[&&NHX:TOL=123372],nacaduba metallica[&&NHX:TOL=123373],nacaduba mioswara[&&NHX:TOL=123374],nacaduba neaira[&&NHX:TOL=123375],nacaduba nerine[&&NHX:TOL=123377],nacaduba normani[&&NHX:TOL=123378],nacaduba novaehebridensis[&&NHX:TOL=123379],nacaduba ollyetti[&&NHX:TOL=123380],nacaduba pactolus[&&NHX:TOL=123381],nacaduba pavana[&&NHX:TOL=123382],nacaduba pendleburyi[&&NHX:TOL=123383],nacaduba ruficirca[&&NHX:TOL=123384],nacaduba russelli[&&NHX:TOL=123385],nacaduba sanaya[&&NHX:TOL=123386],nacaduba schneideri[&&NHX:TOL=123387],nacaduba sericina[&&NHX:TOL=123388],nacaduba sinhala[&&NHX:TOL=123396],nacaduba solta[&&NHX:TOL=123389],nacaduba subperusia[&&NHX:TOL=123390],nacaduba sumbawa[&&NHX:TOL=123391],nacaduba tristis[&&NHX:TOL=123392],nacaduba vulcana[&&NHX:TOL=123393],nacaduba zaron[&&NHX:TOL=123394])nacaduba[&&NHX:TOL=112160],(tartesa astarte[&&NHX:TOL=123398],tartesa ugiensis[&&NHX:TOL=123399])tartesa[&&NHX:TOL=123397],(prosotas aluta[&&NHX:TOL=123403],prosotas atra[&&NHX:TOL=123404],prosotas bhutea[&&NHX:TOL=123405],prosotas datarica[&&NHX:TOL=123406],prosotas dubiosa[&&NHX:TOL=123407],prosotas ella[&&NHX:TOL=123408],prosotas elsa[&&NHX:TOL=123409],prosotas felderi[&&NHX:TOL=123410],prosotas gracilis[&&NHX:TOL=123411],prosotas lutea[&&NHX:TOL=123412],prosotas maputi[&&NHX:TOL=123413],prosotas nelides[&&NHX:TOL=123414],prosotas nora[&&NHX:TOL=123415],prosotas noreia[&&NHX:TOL=123416],prosotas norina[&&NHX:TOL=123417],prosotas papuana[&&NHX:TOL=123418],prosotas pia[&&NHX:TOL=123419],prosotas talasea[&&NHX:TOL=123420])prosotas[&&NHX:TOL=112161],(ionolyce brunnescens[&&NHX:TOL=122976],ionolyce helicon[&&NHX:TOL=122977],ionolyce selkon[&&NHX:TOL=122978])ionolyce[&&NHX:TOL=112162],(catopyrops ancyra[&&NHX:TOL=123421],catopyrops florinda[&&NHX:TOL=123422],catopyrops holtra[&&NHX:TOL=123423],catopyrops keiria[&&NHX:TOL=123424],catopyrops kokopona[&&NHX:TOL=123425],catopyrops nebulosa[&&NHX:TOL=123426],catopyrops rita[&&NHX:TOL=123427],catopyrops zyx[&&NHX:TOL=123428])catopyrops[&&NHX:TOL=112163],(erysichton albiplaga[&&NHX:TOL=123400],erysichton lineata[&&NHX:TOL=123401],erysichton palmyra[&&NHX:TOL=123402])erysichton[&&NHX:TOL=112164],(paraduba metroides[&&NHX:TOL=122973],paraduba owgarra[&&NHX:TOL=122974],paraduba siwiensis[&&NHX:TOL=122975])paraduba[&&NHX:TOL=112165],(neolucia agricola[&&NHX:TOL=123429],neolucia hobartensis[&&NHX:TOL=123430],neolucia mathewi[&&NHX:TOL=123431])neolucia[&&NHX:TOL=112166])nacaduba section[&&NHX:TOL=112159],((theclinesthes albocincta[&&NHX:TOL=123432],theclinesthes hesperia[&&NHX:TOL=123433],theclinesthes miskini[&&NHX:TOL=123434],theclinesthes onycha[&&NHX:TOL=123435],theclinesthes serpentata[&&NHX:TOL=123436],theclinesthes sulpitius[&&NHX:TOL=123437])theclinesthes[&&NHX:TOL=112169],thaumaina uranothauma[&&NHX:TOL=112170],sahulana scintillata[&&NHX:TOL=123438])theclinesthes section[&&NHX:TOL=112168],((upolampes evena[&&NHX:TOL=123439],undescribed upolampes species[&&NHX:TOL=123440])upolampes[&&NHX:TOL=112172],(caleta argola[&&NHX:TOL=123441],caleta caleta[&&NHX:TOL=123442],caleta celebensis[&&NHX:TOL=123443],caleta decidia[&&NHX:TOL=123444],caleta elna[&&NHX:TOL=123445],caleta mindarus[&&NHX:TOL=123446],caleta rhode[&&NHX:TOL=123447],caleta roxus[&&NHX:TOL=123448])caleta[&&NHX:TOL=112173],(discolampa albula[&&NHX:TOL=123449],discolampa ethion[&&NHX:TOL=123450],discolampa ilissus[&&NHX:TOL=123451])discolampa[&&NHX:TOL=112174],pistoria nigropunctata[&&NHX:TOL=112175])upolampes section[&&NHX:TOL=112171],((danis concolor[&&NHX:TOL=123895],danis danis[&&NHX:TOL=123896],danis drucei[&&NHX:TOL=123897],danis glaucopis[&&NHX:TOL=123898],danis hengis[&&NHX:TOL=123899],danis melimnos[&&NHX:TOL=123900],danis metrophanes[&&NHX:TOL=123901],danis phroso[&&NHX:TOL=123902],danis regalis[&&NHX:TOL=123903],danis wallacei[&&NHX:TOL=123904],1 undescribed danis species[&&NHX:TOL=123905])danis[&&NHX:TOL=112177],perpheres perpheres[&&NHX:TOL=123906],(psychonotis brownii[&&NHX:TOL=123887],psychonotis caelius[&&NHX:TOL=123888],psychonotis hebes[&&NHX:TOL=123889],psychonotis hymetus[&&NHX:TOL=123890],psychonotis kruera[&&NHX:TOL=123891],psychonotis melanae[&&NHX:TOL=123892],psychonotis piepersii[&&NHX:TOL=123893],psychonotis purpurea[&&NHX:TOL=123894])psychonotis[&&NHX:TOL=112178],nothodanis schaeffera[&&NHX:TOL=122979])danis section[&&NHX:TOL=112176],(((jamides amarauge[&&NHX:TOL=123458],jamides bochus[&&NHX:TOL=123464],jamides candrenus[&&NHX:TOL=123469],jamides carissima[&&NHX:TOL=123470],jamides cephion[&&NHX:TOL=123473],jamides goodenovii[&&NHX:TOL=123485],jamides morphoides[&&NHX:TOL=123494],jamides phaseli[&&NHX:TOL=123499],jamides pulcherrima[&&NHX:TOL=123503],jamides seminiger[&&NHX:TOL=123510],jamides soemias[&&NHX:TOL=123512],jamides walkeri[&&NHX:TOL=123520])jamides bochus group[&&NHX:TOL=130770],((jamides areas[&&NHX:TOL=123461],jamides cyta[&&NHX:TOL=123477],jamides limes[&&NHX:TOL=123490],jamides lugine[&&NHX:TOL=123492],jamides nitens[&&NHX:TOL=123496],jamides puloensis[&&NHX:TOL=123504],jamides snelleni[&&NHX:TOL=123511])jamides cyta subgroup[&&NHX:TOL=130772],(jamides celeno[&&NHX:TOL=123472],jamides fractilinea[&&NHX:TOL=123484],jamides pura[&&NHX:TOL=123505],jamides tsukudai[&&NHX:TOL=123517])jamides celeno subgroup[&&NHX:TOL=130773],(jamides aetherialis[&&NHX:TOL=123453],jamides aratus[&&NHX:TOL=123460],jamides cleodus[&&NHX:TOL=123474],jamides zebra[&&NHX:TOL=123521])jamides aratus subgroup[&&NHX:TOL=130774],(jamides aleuas[&&NHX:TOL=123455],jamides allectus[&&NHX:TOL=123456],jamides anops[&&NHX:TOL=123459],jamides festivus[&&NHX:TOL=123483],jamides malaccanus[&&NHX:TOL=123493],jamides parasaturatus[&&NHX:TOL=123497],jamides philatus[&&NHX:TOL=123500],jamides suidas[&&NHX:TOL=123514])jamides aleuas subgroup[&&NHX:TOL=130775],(jamides abdul[&&NHX:TOL=123452],jamides alecto[&&NHX:TOL=123454],jamides alsietus[&&NHX:TOL=123457],jamides caeruleus[&&NHX:TOL=123466],jamides callistus[&&NHX:TOL=123467],jamides coruscans[&&NHX:TOL=123522],jamides cunilda[&&NHX:TOL=123476],jamides elpis[&&NHX:TOL=123479],jamides ferrari[&&NHX:TOL=123482],jamides halus[&&NHX:TOL=123486],jamides kankena[&&NHX:TOL=123487],jamides lacteata[&&NHX:TOL=123489],jamides latimargus[&&NHX:TOL=130777],jamides lucide[&&NHX:TOL=123491],jamides pseudosias[&&NHX:TOL=123502],jamides reverdini[&&NHX:TOL=123506],jamides rothschildi[&&NHX:TOL=123507],jamides schatzi[&&NHX:TOL=123508],jamides talinga[&&NHX:TOL=123515],jamides virgulatus[&&NHX:TOL=123519])jamides elpis subgroup[&&NHX:TOL=130776],(jamides aruensis[&&NHX:TOL=123462],jamides coritus[&&NHX:TOL=123475],jamides euchylas[&&NHX:TOL=123481],jamides nemophilus[&&NHX:TOL=123495])jamides euchylas subgroup[&&NHX:TOL=130778],jamides celebica[&&NHX:TOL=123471])jamides celeno group[&&NHX:TOL=130771],(jamides biru[&&NHX:TOL=123463],jamides elioti[&&NHX:TOL=123478],jamides petunia[&&NHX:TOL=123498],jamides uniformis[&&NHX:TOL=123518])jamides incertae sedis[&&NHX:TOL=130779])jamides[&&NHX:TOL=112181],(epimastidia arienis[&&NHX:TOL=123908],epimastidia inops[&&NHX:TOL=123909],1 undescribed epimastidia species[&&NHX:TOL=123910])epimastidia[&&NHX:TOL=112179])jamides section[&&NHX:TOL=123907],((catochrysops amasea[&&NHX:TOL=123872],catochrysops binna[&&NHX:TOL=123873],catochrysops nubila[&&NHX:TOL=123874],catochrysops panormus[&&NHX:TOL=123875],catochrysops strabo[&&NHX:TOL=123876],catochrysops strabobinna[&&NHX:TOL=123877])catochrysops[&&NHX:TOL=112184],rysops scintilla[&&NHX:TOL=112185])catochrysops section[&&NHX:TOL=112183],lampides boeticus[&&NHX:TOL=112186],(callictita albiplaga[&&NHX:TOL=123878],callictita arfakiana[&&NHX:TOL=123879],callictita cyara[&&NHX:TOL=123880],callictita felgara[&&NHX:TOL=123881],callictita jola[&&NHX:TOL=123882],callictita lara[&&NHX:TOL=123883],callictita mala[&&NHX:TOL=123884],callictita tifala[&&NHX:TOL=123885],callictita upola[&&NHX:TOL=123886])callictita[&&NHX:TOL=112187],(uranothauma antinorii[&&NHX:TOL=122577],uranothauma artemenes[&&NHX:TOL=122578],uranothauma belcastroi[&&NHX:TOL=122579],uranothauma confusa[&&NHX:TOL=122580],uranothauma cordatus[&&NHX:TOL=122581],uranothauma crawshayi[&&NHX:TOL=122582],uranothauma cuneatum[&&NHX:TOL=122583],uranothauma delatorum[&&NHX:TOL=122584],uranothauma falkensteini[&&NHX:TOL=122585],uranothauma frederikkae[&&NHX:TOL=122586],uranothauma heritsia[&&NHX:TOL=122587],uranothauma kilimensis[&&NHX:TOL=122588],uranothauma lukwangule[&&NHX:TOL=122589],uranothauma lunifer[&&NHX:TOL=122590],uranothauma nguru[&&NHX:TOL=122591],uranothauma nubifer[&&NHX:TOL=122592],uranothauma poggei[&&NHX:TOL=122593],uranothauma uganda[&&NHX:TOL=122594],uranothauma usambarae[&&NHX:TOL=122595],uranothauma vansomereni[&&NHX:TOL=122596],uranothauma williamsi[&&NHX:TOL=122597])uranothauma[&&NHX:TOL=112188],phylaria cyara[&&NHX:TOL=112189],(((cacyreus audeoudi[&&NHX:TOL=122598],cacyreus lingeus[&&NHX:TOL=122602],cacyreus virilis[&&NHX:TOL=122607])cacyreus lingeus group[&&NHX:TOL=122608],(cacyreus darius[&&NHX:TOL=122599],cacyreus dicksoni[&&NHX:TOL=122600],cacyreus ethiopicus[&&NHX:TOL=122601],cacyreus marshalli[&&NHX:TOL=122603],cacyreus niebuhri[&&NHX:TOL=122604],cacyreus palemon[&&NHX:TOL=122605])cacyreus palemon roup[&&NHX:TOL=122609])cacyreus[&&NHX:TOL=112191],(harpendyreus aequatorialis[&&NHX:TOL=122610],harpendyreus argenteostriata[&&NHX:TOL=122611],harpendyreus berger[&&NHX:TOL=122612],harpendyreus boma[&&NHX:TOL=122613],harpendyreus hazelae[&&NHX:TOL=122614],harpendyreus juno[&&NHX:TOL=122615],harpendyreus kisaba[&&NHX:TOL=122616],harpendyreus major[&&NHX:TOL=122617],harpendyreus marlieri[&&NHX:TOL=122618],harpendyreus marungensis[&&NHX:TOL=122619],harpendyreus meruana[&&NHX:TOL=122620],harpendyreus noquasa[&&NHX:TOL=122621],harpendyreus notoba[&&NHX:TOL=122622],harpendyreus reginaldi[&&NHX:TOL=122623],harpendyreus tsomo[&&NHX:TOL=122624])harpendyreus[&&NHX:TOL=112192])cacyreus section[&&NHX:TOL=112190],(((leptotes adamsoni[&&NHX:TOL=122625],leptotes babaulti[&&NHX:TOL=122626],leptotes brevidentatus[&&NHX:TOL=122627],leptotes casca[&&NHX:TOL=122628],leptotes cassioides[&&NHX:TOL=122629],leptotes jeanneli[&&NHX:TOL=122630],leptotes marginalis[&&NHX:TOL=122631],leptotes mayottensis[&&NHX:TOL=122632],leptotes pirithous[&&NHX:TOL=122633],leptotes pulchra[&&NHX:TOL=122634],leptotes rabefaner[&&NHX:TOL=122635],leptotes socotranus[&&NHX:TOL=122636],leptotes terrenus[&&NHX:TOL=122637])afrotropical leptotes group[&&NHX:TOL=122649],leptotes plinius[&&NHX:TOL=122638],(leptotes andicola[&&NHX:TOL=122639],leptotes bathyllos[&&NHX:TOL=122640],leptotes callanga[&&NHX:TOL=122641],leptotes cassius[&&NHX:TOL=122642],leptotes delalande[&&NHX:TOL=122643],leptotes lamasi[&&NHX:TOL=122644],leptotes marina[&&NHX:TOL=122645],leptotes parrhasioides[&&NHX:TOL=122646],leptotes perkinsae[&&NHX:TOL=122647],leptotes trigemmatus[&&NHX:TOL=122648])neotropical leptotes group[&&NHX:TOL=122650])leptotes[&&NHX:TOL=112194],(cyclyrius mandersi[&&NHX:TOL=122651],cyclyrius webbianus[&&NHX:TOL=122652])cyclyrius[&&NHX:TOL=112195])leptotes section[&&NHX:TOL=112193],((castalius clathratus[&&NHX:TOL=122683],castalius fasciatus[&&NHX:TOL=122684],castalius fluvialis[&&NHX:TOL=122685],castalius rosimon[&&NHX:TOL=122686])castalius[&&NHX:TOL=112197],((tarucus balkanica[&&NHX:TOL=122663],tarucus bowkeri[&&NHX:TOL=122664],tarucus grammicus[&&NHX:TOL=122665],tarucus kiki[&&NHX:TOL=122666],tarucus kulala[&&NHX:TOL=122667],tarucus legrasi[&&NHX:TOL=122668],tarucus quadratus[&&NHX:TOL=122669],tarucus rosacea[&&NHX:TOL=122670],tarucus sybaris[&&NHX:TOL=122671],tarucus theophrastus[&&NHX:TOL=122672],tarucus thespis[&&NHX:TOL=122673],tarucus ungemachi[&&NHX:TOL=122674])afrotropical tarucus group[&&NHX:TOL=122675],(tarucus ananda[&&NHX:TOL=122677],tarucus callinara[&&NHX:TOL=122678],tarucus indica[&&NHX:TOL=122679],tarucus nara[&&NHX:TOL=122680],tarucus venosus[&&NHX:TOL=122681],tarucus waterstradti[&&NHX:TOL=122682])south asian tarucus group[&&NHX:TOL=122676])tarucus[&&NHX:TOL=112198],(tuxentius calice[&&NHX:TOL=122653],tuxentius carana[&&NHX:TOL=122654],tuxentius cretosus[&&NHX:TOL=122655],tuxentius ertli[&&NHX:TOL=122656],tuxentius hesperis[&&NHX:TOL=122657],tuxentius interruptus[&&NHX:TOL=122658],tuxentius kaffana[&&NHX:TOL=122659],tuxentius margaritaceus[&&NHX:TOL=122660],tuxentius melaena[&&NHX:TOL=122661],tuxentius stempfferi[&&NHX:TOL=122662])tuxentius[&&NHX:TOL=112199])castalius section[&&NHX:TOL=112196],zintha hintza[&&NHX:TOL=112200],((zizeeria karsandra[&&NHX:TOL=122687],zizeeria knysna[&&NHX:TOL=122688])zizeeria[&&NHX:TOL=112202],(zizina antanossa[&&NHX:TOL=122709],zizina labradus[&&NHX:TOL=122710],zizina otis[&&NHX:TOL=122711])zizina[&&NHX:TOL=112203],pseudozizeeria maha[&&NHX:TOL=112204])zizeeria section[&&NHX:TOL=112201],famegana alsulus[&&NHX:TOL=112205],(actizera atrigemmata[&&NHX:TOL=122714],actizera lucida[&&NHX:TOL=122715],actizera stellata[&&NHX:TOL=122716],actizera drucei[&&NHX:TOL=122730])actizera[&&NHX:TOL=112206],(zizula cyna[&&NHX:TOL=122712],zizula hylax[&&NHX:TOL=122713])zizula[&&NHX:TOL=112207],((brephidium exilis[&&NHX:TOL=122717],brephidium metophis[&&NHX:TOL=122718],brephidium pseudofea[&&NHX:TOL=122719])brephidium[&&NHX:TOL=112209],oraidium barberae[&&NHX:TOL=112210])brephidium section[&&NHX:TOL=112208],(((cupido alcetas[&&NHX:TOL=123176],cupido amyntula[&&NHX:TOL=123168],cupido argiades[&&NHX:TOL=123177],cupido comyntas[&&NHX:TOL=123169],cupido decolor[&&NHX:TOL=123178],cupido decoloratus[&&NHX:TOL=123179],cupido lacturnus[&&NHX:TOL=123180],cupido sebrus[&&NHX:TOL=123181])everes group[&&NHX:TOL=123175],(cupido alaina[&&NHX:TOL=123183],cupido buddhista[&&NHX:TOL=123184],cupido carswelli[&&NHX:TOL=123185],cupido lorquini[&&NHX:TOL=123186],cupido minimus[&&NHX:TOL=123171],cupido osiris[&&NHX:TOL=123187],cupido peri[&&NHX:TOL=123188],cupido prosecusa[&&NHX:TOL=123189],cupido staudingeri[&&NHX:TOL=123190],cupido tusovi[&&NHX:TOL=123191])cupido group[&&NHX:TOL=123182])cupido[&&NHX:TOL=112213],bothrinia chennellii[&&NHX:TOL=112214],(tongeia amplifascia[&&NHX:TOL=123911],tongeia bella[&&NHX:TOL=123912],tongeia confusa[&&NHX:TOL=123913],tongeia davidi[&&NHX:TOL=123914],tongeia filicaudis[&&NHX:TOL=123915],tongeia fischeri[&&NHX:TOL=123916],tongeia hainani[&&NHX:TOL=123917],tongeia ion[&&NHX:TOL=123918],tongeia kala[&&NHX:TOL=123919],tongeia menpae[&&NHX:TOL=123920],tongeia potanini[&&NHX:TOL=123921],tongeia pseudozuthus[&&NHX:TOL=123922],tongeia zuthus[&&NHX:TOL=123923])tongeia[&&NHX:TOL=112215],shijimia moorei[&&NHX:TOL=112216],(talicada metana[&&NHX:TOL=123348],talicada nyseus[&&NHX:TOL=123349])talicada[&&NHX:TOL=112217])cupido section[&&NHX:TOL=112211],(pithecops corvus[&&NHX:TOL=123343],pithecops dionisius[&&NHX:TOL=123344],pithecops fulgens[&&NHX:TOL=123345],pithecops hylax[&&NHX:TOL=123346],pithecops phoenix[&&NHX:TOL=123347])pithecops[&&NHX:TOL=112219],(azanus isis[&&NHX:TOL=122720],azanus jesous[&&NHX:TOL=122721],azanus mirza[&&NHX:TOL=122722],azanus moriqua[&&NHX:TOL=122723],azanus natalensis[&&NHX:TOL=122724],azanus sitalces[&&NHX:TOL=122725],azanus soalalicus[&&NHX:TOL=122726],azanus ubaldus[&&NHX:TOL=122727],azanus uranus[&&NHX:TOL=122728],azanus urios[&&NHX:TOL=122729])azanus[&&NHX:TOL=112221],(eicochrysops antoto[&&NHX:TOL=122732],eicochrysops damiri[&&NHX:TOL=122733],eicochrysops distractus[&&NHX:TOL=122734],eicochrysops dudgeoni[&&NHX:TOL=122735],eicochrysops eicotrochilus[&&NHX:TOL=122736],eicochrysops fontainei[&&NHX:TOL=122737],eicochrysops hippocrates[&&NHX:TOL=122738],eicochrysops masai[&&NHX:TOL=122739],eicochrysops meryamae[&&NHX:TOL=122740],eicochrysops messapus[&&NHX:TOL=122741],eicochrysops pauliani[&&NHX:TOL=122742],eicochrysops pinheyi[&&NHX:TOL=122743],eicochrysops pusillus[&&NHX:TOL=122744],eicochrysops rogersi[&&NHX:TOL=122745],eicochrysops sanguigutta[&&NHX:TOL=122746],eicochrysops sanyere[&&NHX:TOL=122747])eicochrysops[&&NHX:TOL=112222],(lycaenopsis haraldus[&&NHX:TOL=112224],(neopithecops iolanthe[&&NHX:TOL=123328],neopithecops lucifer[&&NHX:TOL=123329],neopithecops sumbanus[&&NHX:TOL=123330],neopithecops umbretta[&&NHX:TOL=123331],neopithecops zalmora[&&NHX:TOL=123332])neopithecops[&&NHX:TOL=112225],(megisba malaya[&&NHX:TOL=123319],megisba strongyle[&&NHX:TOL=123320])megisba[&&NHX:TOL=112226],(celastrina acesina[&&NHX:TOL=123211],celastrina algernoni[&&NHX:TOL=123212],celastrina argiolus[&&NHX:TOL=123213],celastrina ebenina[&&NHX:TOL=130783],celastrina echo[&&NHX:TOL=123214],celastrina fedoseevi[&&NHX:TOL=123215],celastrina filipjevi[&&NHX:TOL=123216],celastrina gigas[&&NHX:TOL=123217],celastrina gozora[&&NHX:TOL=123218],celastrina hersilia[&&NHX:TOL=123219],celastrina huegelii[&&NHX:TOL=123220],celastrina humulus[&&NHX:TOL=123221],celastrina idella[&&NHX:TOL=123222],celastrina ladon[&&NHX:TOL=123223],celastrina lavendularis[&&NHX:TOL=123224],celastrina lucia[&&NHX:TOL=123225],celastrina morsheadi[&&NHX:TOL=123226],celastrina neglecta[&&NHX:TOL=123227],celastrina neglectamajor[&&NHX:TOL=123228],celastrina nigra[&&NHX:TOL=123229],celastrina ogasawaraensis[&&NHX:TOL=123230],celastrina oreas[&&NHX:TOL=123231],celastrina perplexa[&&NHX:TOL=123232],celastrina phellodendroni[&&NHX:TOL=123233],celastrina philippina[&&NHX:TOL=123234],celastrina serotina[&&NHX:TOL=123235],celastrina sugitanii[&&NHX:TOL=123236],celastrina tenella[&&NHX:TOL=123237])celastrina[&&NHX:TOL=112227],notarthrinus binghami[&&NHX:TOL=112228],(acytolepis lilacea[&&NHX:TOL=123238],acytolepis najara[&&NHX:TOL=123239],acytolepis puspa[&&NHX:TOL=123240],acytolepis ripte[&&NHX:TOL=123241],acytolepis samanga[&&NHX:TOL=123242])acytolepis[&&NHX:TOL=112229],(oreolyce archena[&&NHX:TOL=123313],oreolyce boulti[&&NHX:TOL=123314],oreolyce dohertyi[&&NHX:TOL=123315],oreolyce nearcha[&&NHX:TOL=123316],oreolyce quadriplaga[&&NHX:TOL=123317],oreolyce arletta vardhana[&&NHX:TOL=123318])oreolyce[&&NHX:TOL=112230],((monodontides apona[&&NHX:TOL=123250],monodontides argioloides[&&NHX:TOL=123251],monodontides hondai[&&NHX:TOL=123253],monodontides kolari[&&NHX:TOL=123254],monodontides luzonensis[&&NHX:TOL=123255],monodontides musina[&&NHX:TOL=123256],monodontides ternatensis[&&NHX:TOL=123257])subgenus monodontides[&&NHX:TOL=123258],monodontides buakraengius cara[&&NHX:TOL=123252])monodontides[&&NHX:TOL=112231],(ptox catreus[&&NHX:TOL=123321],ptox corythus[&&NHX:TOL=123322])ptox[&&NHX:TOL=112232],((udara akasa[&&NHX:TOL=123264],udara aristinus[&&NHX:TOL=123267],udara aristius[&&NHX:TOL=123268],udara camenae[&&NHX:TOL=123270],udara cardia[&&NHX:TOL=123271],udara coalita[&&NHX:TOL=123273],udara cyma[&&NHX:TOL=123275],udara dilectissima[&&NHX:TOL=123278],udara dilectus[&&NHX:TOL=123277],udara drucei[&&NHX:TOL=123279],udara etsuzoi[&&NHX:TOL=123280],udara lanka[&&NHX:TOL=123283],udara masinissa[&&NHX:TOL=123285],udara placidula[&&NHX:TOL=123290],udara rona[&&NHX:TOL=123292],udara serangana[&&NHX:TOL=123295],udara singalensis[&&NHX:TOL=123297],udara tenella[&&NHX:TOL=130782],udara toxopeusi[&&NHX:TOL=123298])subgenus udara[&&NHX:TOL=123302],(udara aemulus[&&NHX:TOL=123263],udara ceyx[&&NHX:TOL=123272],udara nishiyamai[&&NHX:TOL=123287],udara santotomasana[&&NHX:TOL=123293],udara selma[&&NHX:TOL=123294],udara wilemani[&&NHX:TOL=123300])subgenus selmanix[&&NHX:TOL=123303],(udara albocaerulea[&&NHX:TOL=123265],udara oviana[&&NHX:TOL=123288],udara tyotaroi[&&NHX:TOL=123299])subgenus penudara[&&NHX:TOL=123304],(udara antonia[&&NHX:TOL=123266],udara cybele[&&NHX:TOL=123274],udara davenporti[&&NHX:TOL=123276],udara kodama[&&NHX:TOL=123281],udara laetitia[&&NHX:TOL=123282],udara manokwariensis[&&NHX:TOL=123284],udara meeki[&&NHX:TOL=123286],udara owgarra[&&NHX:TOL=123289],udara pullus[&&NHX:TOL=123291],udara sibatanii[&&NHX:TOL=123296],udara n. sp.[&&NHX:TOL=123301])subgenus perivaga[&&NHX:TOL=123305],udara vaga blackburnii[&&NHX:TOL=123269])udara[&&NHX:TOL=112233],(rhinelephas arrhina[&&NHX:TOL=123333],rhinelephas cyanicornis[&&NHX:TOL=123334])rhinelephas[&&NHX:TOL=112234],(uranobothria celebica[&&NHX:TOL=123326],uranobothria tsukudai[&&NHX:TOL=123327])uranobothria[&&NHX:TOL=112235],parelodina aroa[&&NHX:TOL=112236],(callenya kaguya[&&NHX:TOL=123243],callenya lenya[&&NHX:TOL=123244],callenya melaena[&&NHX:TOL=123245])callenya[&&NHX:TOL=112281],((cebrela lingga[&&NHX:TOL=123308],cebrella matanga[&&NHX:TOL=123309],cebrella nigerrima[&&NHX:TOL=123310])subgenus chelakina[&&NHX:TOL=123311],(cebrella pellecebra[&&NHX:TOL=123306],cebrella penelope[&&NHX:TOL=123307])subgenus cebrella[&&NHX:TOL=123312])cebrella[&&NHX:TOL=112282],(celarchos archagnathos[&&NHX:TOL=123335],celarchus hermarchus[&&NHX:TOL=123336],celarchus armentulus shelfordii[&&NHX:TOL=123337])celarchus[&&NHX:TOL=112283],(celatoxia albidisca[&&NHX:TOL=123323],celatoxia carna[&&NHX:TOL=123324],celatoxia marginata[&&NHX:TOL=123325])celatoxia[&&NHX:TOL=112284],(lestranicus transpectus[&&NHX:TOL=123338],lestranicus yoshidai[&&NHX:TOL=123339])lestranicus[&&NHX:TOL=112285],plautella cossaea[&&NHX:TOL=112286],(sancterila deliciosa[&&NHX:TOL=123246],sancterila drakei[&&NHX:TOL=123247],sancterila prattorum[&&NHX:TOL=123248],sancterila russelli[&&NHX:TOL=123249],sancterila sohmai[&&NHX:TOL=130780])sancterila[&&NHX:TOL=112287],(sidima amarylde[&&NHX:TOL=123259],sidima idamis[&&NHX:TOL=123260],sidima murayamai[&&NHX:TOL=123261],sidima sulawesiana[&&NHX:TOL=123262])sidima[&&NHX:TOL=112288])lycaenopsis section[&&NHX:TOL=112223],((glaucopsyche alexis[&&NHX:TOL=123939],glaucopsyche argali[&&NHX:TOL=123940],glaucopsyche astraea[&&NHX:TOL=123941],glaucopsyche charybdis[&&NHX:TOL=123942],glaucopsyche kurnakovi[&&NHX:TOL=123943],glaucopsyche laetifica[&&NHX:TOL=123944],glaucopsyche lycormas[&&NHX:TOL=123945],glaucopsyche lygdamus[&&NHX:TOL=123946],glaucopsyche melanops[&&NHX:TOL=123947],glaucopsyche piasus[&&NHX:TOL=123948],glaucopsyche seminigra[&&NHX:TOL=123949])glaucopsyche[&&NHX:TOL=112238],scolitantides orion[&&NHX:TOL=112239],philotes sonorensis[&&NHX:TOL=112241],otnjukovia tatjana[&&NHX:TOL=123924],(turanana anisophtalma[&&NHX:TOL=123925],turanana cytis[&&NHX:TOL=123926],turanana dushak[&&NHX:TOL=123927],turanana endymion[&&NHX:TOL=123928],turanana grumi[&&NHX:TOL=123929],turanana jurileontyi[&&NHX:TOL=123930],turanana kugitangi[&&NHX:TOL=123931],turanana laspura[&&NHX:TOL=123932],turanana panageides[&&NHX:TOL=123933])turanana[&&NHX:TOL=112242],palaeophilotes triphysina[&&NHX:TOL=112243],praephilotes anthracias[&&NHX:TOL=112244],(euphilotes ancilla[&&NHX:TOL=123954],euphilotes battoides[&&NHX:TOL=123955],euphilotes baueri[&&NHX:TOL=123956],euphilotes bernardino[&&NHX:TOL=123957],euphilotes centralis[&&NHX:TOL=123958],euphilotes columbiae[&&NHX:TOL=123959],euphilotes ellisii[&&NHX:TOL=123960],euphilotes enoptes[&&NHX:TOL=123961],euphilotes glaucon[&&NHX:TOL=123962],euphilotes mojave[&&NHX:TOL=123963],euphilotes pallescens[&&NHX:TOL=123964],euphilotes rita[&&NHX:TOL=123965],euphilotes spaldingi[&&NHX:TOL=123966],4 undescribed euphilotes species[&&NHX:TOL=123967])euphilotes[&&NHX:TOL=123953],(pseudophilotes abencerragus[&&NHX:TOL=122748],pseudophilotes barbagiae[&&NHX:TOL=122749],pseudophilotes baton[&&NHX:TOL=122750],pseudophilotes bavius[&&NHX:TOL=122751],pseudophilotes panope[&&NHX:TOL=122752],pseudophilotes sinaicus[&&NHX:TOL=122753],pseudophilotes vicrama[&&NHX:TOL=122754])pseudophilotes[&&NHX:TOL=112245],(sinia divina[&&NHX:TOL=123934],sinia lanty[&&NHX:TOL=123935],sinia leechi[&&NHX:TOL=123936])sinia[&&NHX:TOL=112247],(iolana andreasi[&&NHX:TOL=123340],iolana gigantea[&&NHX:TOL=123341],iolana iolas[&&NHX:TOL=123342])iolana[&&NHX:TOL=112248],(caerulea coelestis[&&NHX:TOL=123937],caerulea coeligena[&&NHX:TOL=123938])caerulea[&&NHX:TOL=112249],(phengaris alcon[&&NHX:TOL=113130],((phengaris daitozana[&&NHX:TOL=113131],(phengaris albida[&&NHX:TOL=113132],phengaris atroguttata[&&NHX:TOL=113133])[&&NHX:TOL=113143])[&&NHX:TOL=113142],((phengaris kurentzovi[&&NHX:TOL=113134],(phengaris nausithous[&&NHX:TOL=113135],phengaris teleius[&&NHX:TOL=113136])[&&NHX:TOL=113146])[&&NHX:TOL=113145],(phengaris cyanecula[&&NHX:TOL=113137],(phengaris arion[&&NHX:TOL=113138],(phengaris takamukui[&&NHX:TOL=113140],phengaris arionides[&&NHX:TOL=113139])[&&NHX:TOL=113149])[&&NHX:TOL=113148])[&&NHX:TOL=113147])[&&NHX:TOL=113144])[&&NHX:TOL=113141])phengaris[&&NHX:TOL=112250],micropsyche ariana[&&NHX:TOL=112289],(philotiella leona[&&NHX:TOL=122980],philotiella speciosa[&&NHX:TOL=122981])philotiella[&&NHX:TOL=112290])glaucopsyche section[&&NHX:TOL=112237],((euchrysops abyssinica[&&NHX:TOL=122755],euchrysops alberta[&&NHX:TOL=122756],euchrysops albistriata[&&NHX:TOL=122757],euchrysops banyo[&&NHX:TOL=122758],euchrysops barkeri[&&NHX:TOL=122759],euchrysops brunneus[&&NHX:TOL=122760],euchrysops cnejus[&&NHX:TOL=122761],euchrysops crawshayi[&&NHX:TOL=122762],euchrysops cyclopteris[&&NHX:TOL=122763],euchrysops decaryi[&&NHX:TOL=122764],euchrysops dolorosa[&&NHX:TOL=122765],euchrysops horus[&&NHX:TOL=122766],euchrysops jacksoni[&&NHX:TOL=122767],euchrysops kabrosae[&&NHX:TOL=122768],euchrysops katangae[&&NHX:TOL=122769],euchrysops latrunculata[&&NHX:TOL=122770],euchrysops lois[&&NHX:TOL=122771],euchrysops malathana[&&NHX:TOL=122772],euchrysops mauensis[&&NHX:TOL=122773],euchrysops migiurtiniensis[&&NHX:TOL=122774],euchrysops nandensis[&&NHX:TOL=122775],euchrysops nilotica[&&NHX:TOL=122776],euchrysops osiris[&&NHX:TOL=122777],euchrysops philbyi[&&NHX:TOL=122778],euchrysops reducta[&&NHX:TOL=122779],euchrysops sagba[&&NHX:TOL=122780],euchrysops sahelianus[&&NHX:TOL=122781],euchrysops severini[&&NHX:TOL=122782],euchrysops subpallida[&&NHX:TOL=122783],euchrysops unigemmata[&&NHX:TOL=122784])euchrysops[&&NHX:TOL=112252],(lepidochrysops abri[&&NHX:TOL=122785],lepidochrysops aethiopia[&&NHX:TOL=122786],lepidochrysops albilinea[&&NHX:TOL=122787],lepidochrysops anerius[&&NHX:TOL=122788],lepidochrysops ansorgei[&&NHX:TOL=122789],lepidochrysops arabicus[&&NHX:TOL=122790],lepidochrysops asteris[&&NHX:TOL=122791],lepidochrysops auratus[&&NHX:TOL=122792],lepidochrysops australis[&&NHX:TOL=122793],lepidochrysops azureus[&&NHX:TOL=122794],lepidochrysops bacchus[&&NHX:TOL=122795],lepidochrysops badhami[&&NHX:TOL=122796],lepidochrysops balli[&&NHX:TOL=122797],lepidochrysops barnesi[&&NHX:TOL=122798],lepidochrysops braueri[&&NHX:TOL=122799],lepidochrysops budama[&&NHX:TOL=122800],lepidochrysops caerulea[&&NHX:TOL=122801],lepidochrysops carsoni[&&NHX:TOL=122802],lepidochrysops chala[&&NHX:TOL=122803],lepidochrysops chalceus[&&NHX:TOL=122804],lepidochrysops chittyi[&&NHX:TOL=122805],lepidochrysops chloauges[&&NHX:TOL=122806],lepidochrysops cinerea[&&NHX:TOL=122807],lepidochrysops coxii[&&NHX:TOL=122808],lepidochrysops cupreus[&&NHX:TOL=122809],lepidochrysops delicata[&&NHX:TOL=122810],lepidochrysops desmondi[&&NHX:TOL=122811],lepidochrysops dollmani[&&NHX:TOL=122812],lepidochrysops dukei[&&NHX:TOL=122813],lepidochrysops dunni[&&NHX:TOL=122814],lepidochrysops elgonae[&&NHX:TOL=122815],lepidochrysops erici[&&NHX:TOL=122816],lepidochrysops evae[&&NHX:TOL=122817],lepidochrysops flavisquamosa[&&NHX:TOL=122818],lepidochrysops forsskali[&&NHX:TOL=122819],lepidochrysops fulvescens[&&NHX:TOL=122820],lepidochrysops fumosa[&&NHX:TOL=122821],lepidochrysops gigantea[&&NHX:TOL=122822],lepidochrysops glauca[&&NHX:TOL=122823],lepidochrysops grahami[&&NHX:TOL=122824],lepidochrysops grandis[&&NHX:TOL=122825],lepidochrysops guichardi[&&NHX:TOL=122826],lepidochrysops gydoae[&&NHX:TOL=122827],lepidochrysops handmanni[&&NHX:TOL=122828],lepidochrysops hawkeri[&&NHX:TOL=122829],lepidochrysops haveni[&&NHX:TOL=122921],lepidochrysops heathi[&&NHX:TOL=122830],lepidochrysops hypopolia[&&NHX:TOL=122831],lepidochrysops ignota[&&NHX:TOL=122832],lepidochrysops intermedia[&&NHX:TOL=122833],lepidochrysops inyangae[&&NHX:TOL=122834],lepidochrysops irvingi[&&NHX:TOL=122835],lepidochrysops jacksoni[&&NHX:TOL=122836],lepidochrysops jamesi[&&NHX:TOL=122837],lepidochrysops jansei[&&NHX:TOL=122838],lepidochrysops jefferyi[&&NHX:TOL=122839],lepidochrysops kennethi[&&NHX:TOL=122840],lepidochrysops ketsi[&&NHX:TOL=122841],lepidochrysops kilimanjarensis[&&NHX:TOL=122842],lepidochrysops kitale[&&NHX:TOL=122843],lepidochrysops koaena[&&NHX:TOL=122844],lepidochrysops kocak[&&NHX:TOL=122845],lepidochrysops labeensis[&&NHX:TOL=122846],lepidochrysops labwor[&&NHX:TOL=122847],lepidochrysops lerothodi[&&NHX:TOL=122848],lepidochrysops letsea[&&NHX:TOL=122849],lepidochrysops leucon[&&NHX:TOL=122850],lepidochrysops littoralis[&&NHX:TOL=122851],lepidochrysops loewensteini[&&NHX:TOL=122852],lepidochrysops longifalces[&&NHX:TOL=122853],lepidochrysops lotana[&&NHX:TOL=122854],lepidochrysops loveni[&&NHX:TOL=122855],lepidochrysops lukenia[&&NHX:TOL=122856],lepidochrysops lunulifer[&&NHX:TOL=122857],lepidochrysops mashuna[&&NHX:TOL=122858],lepidochrysops mcgregori[&&NHX:TOL=122859],lepidochrysops methymna[&&NHX:TOL=122860],lepidochrysops michaeli[&&NHX:TOL=122861],lepidochrysops michellae[&&NHX:TOL=122862],lepidochrysops miniata[&&NHX:TOL=122863],lepidochrysops mpanda[&&NHX:TOL=122864],lepidochrysops nacrescens[&&NHX:TOL=122865],lepidochrysops neavei[&&NHX:TOL=122867],lepidochrysops negus[&&NHX:TOL=122868],lepidochrysops neonegus[&&NHX:TOL=122869],lepidochrysops nevillei[&&NHX:TOL=122870],lepidochrysops nigrita[&&NHX:TOL=122871],lepidochrysops nyika[&&NHX:TOL=122872],lepidochrysops oosthuizeni[&&NHX:TOL=122873],lepidochrysops oreas[&&NHX:TOL=122874],lepidochrysops ortygia[&&NHX:TOL=122875],lepidochrysops outeniqua[&&NHX:TOL=122876],lepidochrysops pampolis[&&NHX:TOL=122877],lepidochrysops parsimon[&&NHX:TOL=122878],lepidochrysops patricia[&&NHX:TOL=122879],lepidochrysops peculiaris[&&NHX:TOL=122880],lepidochrysops penningtoni[&&NHX:TOL=122881],lepidochrysops pephredo[&&NHX:TOL=122882],lepidochrysops phoebe[&&NHX:TOL=122883],lepidochrysops pittawayi[&&NHX:TOL=122884],lepidochrysops plebeia[&&NHX:TOL=122885],lepidochrysops polydialecta[&&NHX:TOL=122886],lepidochrysops poseidon[&&NHX:TOL=122887],lepidochrysops praeterita[&&NHX:TOL=122888],lepidochrysops pringlei[&&NHX:TOL=122889],lepidochrysops procera[&&NHX:TOL=122890],lepidochrysops pterou[&&NHX:TOL=122891],lepidochrysops puncticilia[&&NHX:TOL=122892],lepidochrysops quassi[&&NHX:TOL=122893],lepidochrysops quickelbergei[&&NHX:TOL=122894],lepidochrysops reichenowi[&&NHX:TOL=122895],lepidochrysops rhodesensae[&&NHX:TOL=122896],lepidochrysops ringa[&&NHX:TOL=122897],lepidochrysops robertsoni[&&NHX:TOL=122898],lepidochrysops rossouwi[&&NHX:TOL=122899],lepidochrysops ruthica[&&NHX:TOL=122900],lepidochrysops skotios[&&NHX:TOL=122901],lepidochrysops solwezii[&&NHX:TOL=122902],lepidochrysops southeyae[&&NHX:TOL=122903],lepidochrysops stormsi[&&NHX:TOL=122904],lepidochrysops subvariegata[&&NHX:TOL=122905],lepidochrysops swanepoeli[&&NHX:TOL=122906],lepidochrysops swarthbergensis[&&NHX:TOL=122907],lepidochrysops synchrematiza[&&NHX:TOL=122908],lepidochrysops tantalus[&&NHX:TOL=122909],lepidochrysops titei[&&NHX:TOL=122910],lepidochrysops trimeni[&&NHX:TOL=122911],lepidochrysops turlini[&&NHX:TOL=122912],lepidochrysops vansoni[&&NHX:TOL=122913],lepidochrysops variabilis[&&NHX:TOL=122914],lepidochrysops vera[&&NHX:TOL=122915],lepidochrysops victori[&&NHX:TOL=122916],lepidochrysops victoriae[&&NHX:TOL=122917],lepidochrysops violetta[&&NHX:TOL=122918],lepidochrysops wykehami[&&NHX:TOL=122919],lepidochrysops yvonnae[&&NHX:TOL=122920])lepidochrysops[&&NHX:TOL=112253],(orachrysops ariadne[&&NHX:TOL=122923],orachrysops brinkmani[&&NHX:TOL=122924],orachrysops lacrimosa[&&NHX:TOL=122925],orachrysops major[&&NHX:TOL=122926],orachrysops mijburghi[&&NHX:TOL=122927],orachrysops montanus[&&NHX:TOL=122928],orachrysops nasutus[&&NHX:TOL=122929],orachrysops niobe[&&NHX:TOL=122930],orachrysops regalis[&&NHX:TOL=122931],orachrysops subravus[&&NHX:TOL=122932],orachrysops violescens[&&NHX:TOL=122933],orachrysops warreni[&&NHX:TOL=122934])orachrysops[&&NHX:TOL=122922],(thermoniphas alberici[&&NHX:TOL=122935],thermoniphas albocaerulea[&&NHX:TOL=122936],thermoniphas bibundana[&&NHX:TOL=122937],thermoniphas caerulea[&&NHX:TOL=122938],thermoniphas colorata[&&NHX:TOL=122939],thermoniphas distincta[&&NHX:TOL=122940],thermoniphas fontainei[&&NHX:TOL=122941],thermoniphas fumosa[&&NHX:TOL=122942],thermoniphas kamitugensis[&&NHX:TOL=122943],thermoniphas kigezi[&&NHX:TOL=122944],thermoniphas leucocyanea[&&NHX:TOL=122945],thermoniphas micylus[&&NHX:TOL=122946],thermoniphas plurilimbata[&&NHX:TOL=122947],thermoniphas stempfferi[&&NHX:TOL=122948],thermoniphas togara[&&NHX:TOL=122949])thermoniphas[&&NHX:TOL=112254],(oboronia albicosta[&&NHX:TOL=122966],oboronia bueronica[&&NHX:TOL=122967],oboronia guessfeldti[&&NHX:TOL=122968],oboronia liberiana[&&NHX:TOL=122969],oboronia ornata[&&NHX:TOL=122970],oboronia pseudopunctatus[&&NHX:TOL=122971],oboronia punctatus[&&NHX:TOL=122972])oboronia[&&NHX:TOL=112255])euchrysops section[&&NHX:TOL=112251],(((polyommatus aloisi[&&NHX:TOL=124060],polyommatus amor[&&NHX:TOL=124061],polyommatus boisduvalii[&&NHX:TOL=124062],polyommatus chitralensis[&&NHX:TOL=124063],polyommatus eroides[&&NHX:TOL=124064],polyommatus eros[&&NHX:TOL=124065],polyommatus erotides[&&NHX:TOL=124066],polyommatus erotulus[&&NHX:TOL=124067],polyommatus forresti[&&NHX:TOL=124068],polyommatus forsteri[&&NHX:TOL=124069],polyommatus icadius[&&NHX:TOL=124070],polyommatus icarus[&&NHX:TOL=124071],polyommatus kamtshadalis[&&NHX:TOL=124072],polyommatus kashgharensis[&&NHX:TOL=124073],polyommatus juno[&&NHX:TOL=124074],polyommatus menelaos[&&NHX:TOL=124075],polyommatus meoticus[&&NHX:TOL=124076],polyommatus pseuderos[&&NHX:TOL=124077],polyommatus stigmatifera[&&NHX:TOL=124078],polyommatus tshetverikovi[&&NHX:TOL=124079],polyommatus tsvetaevi[&&NHX:TOL=124080],polyommatus venus[&&NHX:TOL=124081])subgenus polyommatus[&&NHX:TOL=112258],(((((((((((polyommatus damocles[&&NHX:TOL=124116],polyommatus altivagans[&&NHX:TOL=124099])[&&NHX:TOL=138088],(polyommatus ciscaucasicus[&&NHX:TOL=138090],polyommatus cyaneus[&&NHX:TOL=124114])[&&NHX:TOL=138089])[&&NHX:TOL=138087],polyommatus merhaba[&&NHX:TOL=124157])[&&NHX:TOL=138086],polyommatus mithridates[&&NHX:TOL=124158])[&&NHX:TOL=138085],(((polyommatus haigi[&&NHX:TOL=124139],polyommatus bilgini[&&NHX:TOL=124108],polyommatus pseudactis[&&NHX:TOL=124172])[&&NHX:TOL=138093],polyommatus firdussii[&&NHX:TOL=124135])[&&NHX:TOL=138092],((polyommatus poseidon[&&NHX:TOL=124169],polyommatus putnami[&&NHX:TOL=124174])[&&NHX:TOL=138095],polyommatus hopfferi[&&NHX:TOL=124141])[&&NHX:TOL=138094])[&&NHX:TOL=138091])[&&NHX:TOL=138084],(((polyommatus phyllis[&&NHX:TOL=124166],polyommatus posthumus[&&NHX:TOL=124171])[&&NHX:TOL=138098],polyommatus darius[&&NHX:TOL=124259])[&&NHX:TOL=138097],((polyommatus vanensis[&&NHX:TOL=124190],polyommatus erschoffi[&&NHX:TOL=124198])[&&NHX:TOL=138100],polyommatus glaucias[&&NHX:TOL=124200])[&&NHX:TOL=138099])[&&NHX:TOL=138096])[&&NHX:TOL=138083],((((polyommatus ninae[&&NHX:TOL=124163],polyommatus aserbeidschanus[&&NHX:TOL=124105])[&&NHX:TOL=138104],(polyommatus elbursicus[&&NHX:TOL=124126],polyommatus huberti[&&NHX:TOL=124202])[&&NHX:TOL=138105],polyommatus turcicolus[&&NHX:TOL=138106])[&&NHX:TOL=138103],((polyommatus surakovi[&&NHX:TOL=124183],polyommatus eurypilos[&&NHX:TOL=124129])[&&NHX:TOL=138108],((polyommatus kendevani[&&NHX:TOL=124150],polyommatus arasbarani[&&NHX:TOL=138112])[&&NHX:TOL=138111],polyommatus pierceae[&&NHX:TOL=124167])[&&NHX:TOL=138110])[&&NHX:TOL=138107])[&&NHX:TOL=138102],(polyommatus kurdistanicus[&&NHX:TOL=124152],polyommatus antidolus[&&NHX:TOL=124101])[&&NHX:TOL=138113])[&&NHX:TOL=138101])[&&NHX:TOL=138082],((((polyommatus phyllides[&&NHX:TOL=124165],polyommatus iphigenides[&&NHX:TOL=124147])[&&NHX:TOL=138117],polyommatus damone[&&NHX:TOL=124118],polyommatus karatavicus[&&NHX:TOL=138118],polyommatus juldusa[&&NHX:TOL=124149])[&&NHX:TOL=138116],polyommatus pljushtchi[&&NHX:TOL=138119])[&&NHX:TOL=138115],((((polyommatus baytopi[&&NHX:TOL=124107],polyommatus rovshani[&&NHX:TOL=124177])[&&NHX:TOL=138123],polyommatus tankeri[&&NHX:TOL=124184])[&&NHX:TOL=138122],polyommatus turcicus[&&NHX:TOL=124188])[&&NHX:TOL=138121],polyommatus iphigenia[&&NHX:TOL=124146])[&&NHX:TOL=138120])[&&NHX:TOL=138114])[&&NHX:TOL=138081],((polyommatus admetus[&&NHX:TOL=124094],(polyommatus demavendi[&&NHX:TOL=124122],polyommatus ripartii[&&NHX:TOL=124175])[&&NHX:TOL=138126])[&&NHX:TOL=138125],((((polyommatus ainsae[&&NHX:TOL=124097],polyommatus fulgens[&&NHX:TOL=124136])[&&NHX:TOL=138130],polyommatus fabressei[&&NHX:TOL=124133])[&&NHX:TOL=138129],polyommatus dolus[&&NHX:TOL=124124])[&&NHX:TOL=138128],((polyommatus eriwanensis[&&NHX:TOL=124127],polyommatus dantchenkoi[&&NHX:TOL=138133])[&&NHX:TOL=138132],polyommatus menalcas[&&NHX:TOL=124156])[&&NHX:TOL=138131])[&&NHX:TOL=138127])[&&NHX:TOL=138124])[&&NHX:TOL=138080],polyommatus damon[&&NHX:TOL=124117])[&&NHX:TOL=138079],polyommatus actinides[&&NHX:TOL=124092],polyommatus actis[&&NHX:TOL=124093],polyommatus afghanicus[&&NHX:TOL=124095],polyommatus afghanistana[&&NHX:TOL=124096],polyommatus alcestis[&&NHX:TOL=124098],polyommatus anticarmon[&&NHX:TOL=124100],polyommatus ardschira[&&NHX:TOL=124102],polyommatus aroaniensis[&&NHX:TOL=124103],polyommatus artvinensis[&&NHX:TOL=124104],polyommatus avinovi[&&NHX:TOL=124195],polyommatus baltazardi[&&NHX:TOL=124106],polyommatus biton[&&NHX:TOL=124109],polyommatus bogra[&&NHX:TOL=124196],polyommatus caeruleus[&&NHX:TOL=124110],polyommatus carmonides[&&NHX:TOL=124111],polyommatus charmeuxi[&&NHX:TOL=124112],polyommatus cilicius[&&NHX:TOL=124113],polyommatus csomai[&&NHX:TOL=124055],polyommatus dagmara[&&NHX:TOL=124197],polyommatus dama[&&NHX:TOL=124115],polyommatus damonides[&&NHX:TOL=124119],polyommatus deebi[&&NHX:TOL=124120],polyommatus delessei[&&NHX:TOL=124121],polyommatus dizinensis[&&NHX:TOL=124123],polyommatus ectabanensis[&&NHX:TOL=124125],polyommatus erzindjanensis[&&NHX:TOL=124128],polyommatus evansi[&&NHX:TOL=124130],polyommatus exuberans[&&NHX:TOL=124131],polyommatus fabiani[&&NHX:TOL=124132],polyommatus feminionides[&&NHX:TOL=124134],polyommatus frauvartianae[&&NHX:TOL=124199],polyommatus galloi[&&NHX:TOL=124137],polyommatus gorbunovi[&&NHX:TOL=124138],polyommatus guezelmavi[&&NHX:TOL=124201],polyommatus hamadanensis[&&NHX:TOL=124140],polyommatus humedasae[&&NHX:TOL=124142],polyommatus igisizilim[&&NHX:TOL=124143],polyommatus iphicarmon[&&NHX:TOL=124144],polyommatus iphidamon[&&NHX:TOL=124145],polyommatus ischkaschimicus[&&NHX:TOL=124148],polyommatus khoshyeilagi[&&NHX:TOL=124151],polyommatus larseni[&&NHX:TOL=124153],polyommatus lycius[&&NHX:TOL=124154],polyommatus magnifica[&&NHX:TOL=124203],polyommatus melanius[&&NHX:TOL=124155],polyommatus mofidi[&&NHX:TOL=124159],polyommatus morgani[&&NHX:TOL=124160],polyommatus nadira[&&NHX:TOL=124161],polyommatus nephohiptamenos[&&NHX:TOL=124162],polyommatus peilei[&&NHX:TOL=124164],polyommatus pfeifferi[&&NHX:TOL=124168],polyommatus poseidonides[&&NHX:TOL=124170],polyommatus pseudoxerxes[&&NHX:TOL=124173],polyommatus psylorita[&&NHX:TOL=124057],polyommatus pulchella[&&NHX:TOL=124204],polyommatus rjabovi[&&NHX:TOL=124176],polyommatus schuriani[&&NHX:TOL=124178],polyommatus sennanensis[&&NHX:TOL=124179],polyommatus sertavulensis[&&NHX:TOL=124180],polyommatus shamil[&&NHX:TOL=124181],polyommatus sigberti[&&NHX:TOL=124182],polyommatus theresiae[&&NHX:TOL=124185],polyommatus thersites[&&NHX:TOL=124186],polyommatus transcaspica[&&NHX:TOL=124187],polyommatus valiabadi[&&NHX:TOL=124189],polyommatus vittatus[&&NHX:TOL=124191],polyommatus yurinekrutenko[&&NHX:TOL=124192],polyommatus wagneri[&&NHX:TOL=124193],polyommatusus zamotajlovi[&&NHX:TOL=124058],polyommatus zarathustra[&&NHX:TOL=124194])subgenus agrodiaetus[&&NHX:TOL=124091],(polyommatus bellis[&&NHX:TOL=124205],polyommatus semiargus[&&NHX:TOL=124206])subgenus cyaniris[&&NHX:TOL=112261],(polyommatus coelestina[&&NHX:TOL=124208],polyommatus corona[&&NHX:TOL=124209],polyommatus diana[&&NHX:TOL=124210],polyommatus ellisoni[&&NHX:TOL=124211],polyommatus fatima[&&NHX:TOL=124212])subgenus neolysandra[&&NHX:TOL=124207],(polyommatus albicans[&&NHX:TOL=124213],polyommatus apennina[&&NHX:TOL=124214],polyommatus bellargus[&&NHX:TOL=124215],polyommatus caelestissima[&&NHX:TOL=124216],polyommatus coridon[&&NHX:TOL=124217],polyommatus corydonius[&&NHX:TOL=124218],polyommatus dezinus[&&NHX:TOL=124219],polyommatus hispana[&&NHX:TOL=124220],polyommatus melamarina[&&NHX:TOL=124221],polyommatus nufrellensis[&&NHX:TOL=124222],polyommatus ossmar[&&NHX:TOL=124223],polyommatus polonus[&&NHX:TOL=124224],polyommatus punctifera[&&NHX:TOL=124225],polyommatus sheikh[&&NHX:TOL=124226])subgenus lysandra[&&NHX:TOL=112264],(polyommatus aedon[&&NHX:TOL=124083],polyommatus bilucha[&&NHX:TOL=124084],polyommatus cornelia[&&NHX:TOL=124085],polyommatus isauricoides[&&NHX:TOL=124086],polyommatus muetingi[&&NHX:TOL=124087],polyommatus myrrha[&&NHX:TOL=124088],polyommatus myrrhinus[&&NHX:TOL=124089],polyommatus nuksani[&&NHX:TOL=124090])subgenus sublysandra[&&NHX:TOL=124082],polyommatus rimisia miris[&&NHX:TOL=124227],(polyommatus cyane[&&NHX:TOL=124229],polyommatus elvira[&&NHX:TOL=124230])subgenus elviria[&&NHX:TOL=124228],(polyommatus buzulmavi[&&NHX:TOL=124231],polyommatus daphnis[&&NHX:TOL=124232],polyommatus marcida[&&NHX:TOL=124233],polyommatus olympica[&&NHX:TOL=124234],polyommatus phillipi[&&NHX:TOL=124235])subgenus meleageria[&&NHX:TOL=112268],(polyommatus amandus[&&NHX:TOL=124236],polyommatus anthea[&&NHX:TOL=124237],polyommatus atlantica[&&NHX:TOL=124238],polyommatus dorylas[&&NHX:TOL=124239],polyommatus escheri[&&NHX:TOL=124240],polyommatus golgus[&&NHX:TOL=124241],polyommatus nivescens[&&NHX:TOL=124242])subgenus plebicula[&&NHX:TOL=112270],(polyommatus annamaria[&&NHX:TOL=124244],polyommatus ariana[&&NHX:TOL=124245],polyommatus ciloicus[&&NHX:TOL=124246],polyommatus dux[&&NHX:TOL=124247],polyommatus erigone[&&NHX:TOL=124248],polyommatus everesti[&&NHX:TOL=124249],polyommatus fraterluci[&&NHX:TOL=124250],polyommatus hunza[&&NHX:TOL=124251],polyommatus pierinoi[&&NHX:TOL=124252],polyommatus stoliczkanus[&&NHX:TOL=124253],polyommatus sutleja[&&NHX:TOL=124254])subgenus bryna[&&NHX:TOL=124243],(polyommatus andronicus[&&NHX:TOL=124256],polyommatus abdon[&&NHX:TOL=124257],polyommatus bollandi[&&NHX:TOL=124258],polyommatus elena[&&NHX:TOL=124260])polyommatus incertae sedis[&&NHX:TOL=124255])polyommatus[&&NHX:TOL=124059],((plebejus aegidon[&&NHX:TOL=123979],plebejus argus[&&NHX:TOL=123980],plebejus baroghila[&&NHX:TOL=123981],plebejus corsicus[&&NHX:TOL=123982],plebejus eversmanni[&&NHX:TOL=123983],plebejus firuskuhi[&&NHX:TOL=123984],plebejus hypochiona[&&NHX:TOL=123985],plebejus kwaja[&&NHX:TOL=123986],plebejus saepiolus[&&NHX:TOL=123987])subgenus plebejus[&&NHX:TOL=112259],(plebejus agnata[&&NHX:TOL=123988],plebejus anna[&&NHX:TOL=123989],plebejus argyrognomon[&&NHX:TOL=123990],plebejus baldur[&&NHX:TOL=123991],plebejus bellieri[&&NHX:TOL=123992],plebejus bergi[&&NHX:TOL=123993],plebejus callaghani[&&NHX:TOL=123994],plebejus calliopis[&&NHX:TOL=123995],plebejus christophi[&&NHX:TOL=123996],plebejus cleobis[&&NHX:TOL=123997],plebejus dzhizaki[&&NHX:TOL=123998],plebejus fridayi[&&NHX:TOL=123999],plebejus ganssuensis[&&NHX:TOL=124000],plebejus hishikawai[&&NHX:TOL=124001],plebejus iburiensis[&&NHX:TOL=124002],plebejus idas[&&NHX:TOL=124003],plebejus lepidus[&&NHX:TOL=124004],plebejus maracandicus[&&NHX:TOL=124005],plebejus melissa[&&NHX:TOL=124006],plebejus mongolicus[&&NHX:TOL=124007],plebejus nevadensis[&&NHX:TOL=124008],plebejus noah[&&NHX:TOL=124009],plebejus nushibi[&&NHX:TOL=124010],plebejus pseudoaegon[&&NHX:TOL=124011],plebejus roxane[&&NHX:TOL=124012],plebejus samudra[&&NHX:TOL=124013],plebejus shuroabadicus[&&NHX:TOL=124014],plebejus subsolanus[&&NHX:TOL=124015],plebejus uiguricus[&&NHX:TOL=124016])subgenus lycaeides[&&NHX:TOL=112260],plebejus plebulina emigdionis[&&NHX:TOL=124017],(plebejus annulata[&&NHX:TOL=124402],plebejus astorica[&&NHX:TOL=124403],plebejus berezowskii[&&NHX:TOL=124404],plebejus eudemon[&&NHX:TOL=124405],plebejus kogistana[&&NHX:TOL=124406],plebejus lamasem[&&NHX:TOL=124407],plebejus persephatta[&&NHX:TOL=124408],plebejus privata[&&NHX:TOL=124409])subgenus eudemonia[&&NHX:TOL=124401],(plebejus agestis[&&NHX:TOL=124383],plebejus artaxerxes[&&NHX:TOL=124384],plebejus cramera[&&NHX:TOL=124385],plebejus issekutzi[&&NHX:TOL=124386])subgenus aricia[&&NHX:TOL=124382],(plebejus anteros[&&NHX:TOL=124388],plebejus bassoni[&&NHX:TOL=124389],plebejus crassipuncta[&&NHX:TOL=124390],plebejus morronensis[&&NHX:TOL=124391],plebejus vandarbani[&&NHX:TOL=124392])subgenus ultraaricia[&&NHX:TOL=124387],(plebejus dorsumstellae[&&NHX:TOL=124394],plebejus hyacinthus[&&NHX:TOL=124395],plebejus isaurica[&&NHX:TOL=124396],plebejus nicais[&&NHX:TOL=124397],plebejus teberdina[&&NHX:TOL=124398],plebejus torulensis[&&NHX:TOL=124399])subgenus pseudoaricia[&&NHX:TOL=124393],(plebejus acmon[&&NHX:TOL=124019],plebejus icarioides[&&NHX:TOL=124020],plebejus lupini[&&NHX:TOL=124021],plebejus neurona[&&NHX:TOL=124022],plebejus shasta[&&NHX:TOL=124023])subgenus icaricia[&&NHX:TOL=124018],(plebejus aegargus[&&NHX:TOL=124262],plebejus aquilo[&&NHX:TOL=124263],plebejus diodorus[&&NHX:TOL=124264],plebejus dis[&&NHX:TOL=124265],plebejus ellisi[&&NHX:TOL=124266],plebejus errans[&&NHX:TOL=124267],plebejus forsteri[&&NHX:TOL=124268],plebejus glandon[&&NHX:TOL=124029],plebejus jaloka[&&NHX:TOL=124269],plebejus janigena[&&NHX:TOL=124270],plebejus kurtjohnsoni[&&NHX:TOL=124271],plebejus morsheadi[&&NHX:TOL=124272],plebejus pheretiades[&&NHX:TOL=124273],plebejus podarce[&&NHX:TOL=124030],plebejus pyrenaicus[&&NHX:TOL=124274],plebejus sikkima[&&NHX:TOL=124275],plebejus zullichi[&&NHX:TOL=124276])subgenus agriades[&&NHX:TOL=124028],(plebejus allardi[&&NHX:TOL=124035],plebejus beani[&&NHX:TOL=124036],plebejus hespericus[&&NHX:TOL=124037],plebejus klausrosei[&&NHX:TOL=124038],plebejus martini[&&NHX:TOL=124039],plebejus pylaon[&&NHX:TOL=124040],plebejus nichollae[&&NHX:TOL=124041],plebejus patriarcha[&&NHX:TOL=124042],plebejus philbyi[&&NHX:TOL=124043],plebejus sephirus[&&NHX:TOL=124044],plebejus trappi[&&NHX:TOL=124045],plebejus vogelii[&&NHX:TOL=124046],plebejus zephyrinus[&&NHX:TOL=124047])subgenus plebejides[&&NHX:TOL=124034],((plebejus lehanus[&&NHX:TOL=123968],plebejus orbitulus[&&NHX:TOL=123969],plebejus amphirrhoe[&&NHX:TOL=124414],plebejus artenita[&&NHX:TOL=124415],plebejus arcaseia[&&NHX:TOL=124416],plebejus asiatica[&&NHX:TOL=124417],plebejus pharis[&&NHX:TOL=124418],plebejus shahidulla[&&NHX:TOL=124419],plebejus armathea[&&NHX:TOL=124420])albulina group[&&NHX:TOL=123970],(plebejus chrysopis[&&NHX:TOL=123972],plebejus galathea[&&NHX:TOL=123973],plebejus issa[&&NHX:TOL=123974],plebejus metallica[&&NHX:TOL=123975],plebejus omphisa[&&NHX:TOL=123976],plebejus selma[&&NHX:TOL=123977])pamiria group[&&NHX:TOL=123971],(plebejus felicis[&&NHX:TOL=124421],plebejus gaborronkayi[&&NHX:TOL=124422],plebejus lucifera[&&NHX:TOL=124032],plebejus themis[&&NHX:TOL=124033],plebejus younghusbandi[&&NHX:TOL=124423])patricius group[&&NHX:TOL=124031],(plebejus chamanica[&&NHX:TOL=124425],plebejus fergana[&&NHX:TOL=124426],plebejus kumukuleensis[&&NHX:TOL=124427],plebejus loewii[&&NHX:TOL=124428],plebejus rosei[&&NHX:TOL=124429],plebejus sanoga[&&NHX:TOL=124430])plebejidea group[&&NHX:TOL=124424],(plebejus antoninae[&&NHX:TOL=124432],plebejus hanna[&&NHX:TOL=124433],plebejus jurii[&&NHX:TOL=124434],plebejus iris[&&NHX:TOL=124435],plebejus morgiana[&&NHX:TOL=124436],plebejus omotoi[&&NHX:TOL=124437],plebejus rutilans[&&NHX:TOL=124438],plebejus sieversii[&&NHX:TOL=124439])farsia group[&&NHX:TOL=124431],(plebejus alcedo[&&NHX:TOL=124025],plebejus optilete[&&NHX:TOL=124026])vaciniina group[&&NHX:TOL=124024],(plebejus lucifuga[&&NHX:TOL=124441],plebejus lucina[&&NHX:TOL=124442],plebejus orbona[&&NHX:TOL=124443])albulina incertae sedis[&&NHX:TOL=124440])subgenus albulina[&&NHX:TOL=112267],(plebejus devanica[&&NHX:TOL=124049],plebejus pilgram[&&NHX:TOL=124050],plebejus sarta[&&NHX:TOL=124051],plebejus sartoides[&&NHX:TOL=124052])subgenus alpherakya[&&NHX:TOL=124048],plebejus umpria chinensis[&&NHX:TOL=124400])plebejus[&&NHX:TOL=123978],((chilades eleusis[&&NHX:TOL=123145],chilades elicola[&&NHX:TOL=123146],chilades kedonga[&&NHX:TOL=123148],chilades minuscula[&&NHX:TOL=123149],chilades naidina[&&NHX:TOL=123150],chilades sanctithomae[&&NHX:TOL=123151],chilades serrula[&&NHX:TOL=123152],chilades trochylus[&&NHX:TOL=123153])african chilades species[&&NHX:TOL=123164],(chilades boopis[&&NHX:TOL=123154],chilades buruana[&&NHX:TOL=123155],chilades cleotas[&&NHX:TOL=123156],chilades contracta[&&NHX:TOL=123157],chilades ella[&&NHX:TOL=123166],chilades galba[&&NHX:TOL=123147],chilades lajus[&&NHX:TOL=123159],chilades mindora[&&NHX:TOL=123160],chilades pandava[&&NHX:TOL=123161],chilades parrhasius[&&NHX:TOL=123162],chilades putli[&&NHX:TOL=123163])orientalaustralasian chilades species[&&NHX:TOL=123165])chilades[&&NHX:TOL=112272],(hemiargus ceraunus[&&NHX:TOL=124296],hemiargus hanno[&&NHX:TOL=124297],hemiargus ramon[&&NHX:TOL=124298])hemiargus[&&NHX:TOL=112274],(itylos fumosus[&&NHX:TOL=124299],itylos mashenka[&&NHX:TOL=124300],itylos mira[&&NHX:TOL=124301],itylos pasco[&&NHX:TOL=124302],itylos pnin[&&NHX:TOL=124303],itylos titicaca[&&NHX:TOL=124304])itylos[&&NHX:TOL=112275],pseudochrysops bornoi[&&NHX:TOL=112276],(pseudolucia andina[&&NHX:TOL=124325],pseudolucia annamaria[&&NHX:TOL=124326],pseudolucia arauco[&&NHX:TOL=124327],pseudolucia argentina[&&NHX:TOL=124328],pseudolucia asafi[&&NHX:TOL=124329],pseudolucia aureliana[&&NHX:TOL=124330],pseudolucia avishai[&&NHX:TOL=124331],pseudolucia benyamini[&&NHX:TOL=124362],pseudolucia charlotte[&&NHX:TOL=124332],pseudolucia chilensis[&&NHX:TOL=124333],pseudolucia clarea[&&NHX:TOL=124334],pseudolucia collina[&&NHX:TOL=124335],pseudolucia dubi[&&NHX:TOL=124336],pseudolucia grata[&&NHX:TOL=124337],pseudolucia hazearum[&&NHX:TOL=124338],pseudolucia henyah[&&NHX:TOL=124339],pseudolucia humbert[&&NHX:TOL=124340],pseudolucia jujuyensis[&&NHX:TOL=124341],pseudolucia kechico[&&NHX:TOL=124342],pseudolucia kinbote[&&NHX:TOL=124343],pseudolucia lanin[&&NHX:TOL=124344],pseudolucia magellana[&&NHX:TOL=124345],pseudolucia neuqueniensis[&&NHX:TOL=124346],pseudolucia oligocyanea[&&NHX:TOL=124347],pseudolucia oraria[&&NHX:TOL=124348],pseudolucia parana[&&NHX:TOL=124349],pseudolucia patago[&&NHX:TOL=124350],pseudolucia penai[&&NHX:TOL=124351],pseudolucia plumbea[&&NHX:TOL=124352],pseudolucia scintilla[&&NHX:TOL=124353],pseudolucia shapiroi[&&NHX:TOL=124354],pseudolucia sibylla[&&NHX:TOL=124355],pseudolucia talia[&&NHX:TOL=124356],pseudolucia tamara[&&NHX:TOL=124357],pseudolucia ugartei[&&NHX:TOL=124358],pseudolucia vera[&&NHX:TOL=124359],pseudolucia whitakeri[&&NHX:TOL=124360],pseudolucia zina[&&NHX:TOL=124361])pseudolucia[&&NHX:TOL=112277],(paralycaeides inconspicua[&&NHX:TOL=124410],paralycaeides shade[&&NHX:TOL=124411],paralycaeides vapa[&&NHX:TOL=124412])paralycaeides[&&NHX:TOL=112278],(nabokovia ada[&&NHX:TOL=124305],nabokovia cuzquenha[&&NHX:TOL=124306],nabokovia faga[&&NHX:TOL=124307])nabokovia[&&NHX:TOL=112279],elkalyce cogina[&&NHX:TOL=123210],(cyclargus ammon[&&NHX:TOL=124309],cyclargus dominica[&&NHX:TOL=124310],cyclargus kathleena[&&NHX:TOL=124311],cyclargus oualiri[&&NHX:TOL=124312],cyclargus shuturn[&&NHX:TOL=124313],cyclargus sorpresus[&&NHX:TOL=124314],cyclargus thomasi[&&NHX:TOL=124315])cyclargus[&&NHX:TOL=124308],(eldoradina cyanea[&&NHX:TOL=124317],eldoradina sylphis[&&NHX:TOL=124318])eldoradina[&&NHX:TOL=124316],(echinargus huntingtoni[&&NHX:TOL=124320],echinargus isola[&&NHX:TOL=124321],echinargus martha[&&NHX:TOL=124322],1 undescribed echinargus species[&&NHX:TOL=124323])echinargus[&&NHX:TOL=124319],(madeleinea ardisensis[&&NHX:TOL=124363],madeleinea bella[&&NHX:TOL=124364],madeleinea cobaltana[&&NHX:TOL=124365],madeleinea colca[&&NHX:TOL=124366],madeleinea gradoslamasi[&&NHX:TOL=124367],madeleinea huascarana[&&NHX:TOL=124368],madeleinea koa[&&NHX:TOL=124369],madeleinea lea[&&NHX:TOL=124370],madeleinea lolita[&&NHX:TOL=124371],madeleinea ludicra[&&NHX:TOL=124372],madeleinea malvasa[&&NHX:TOL=124373],madeleinea moza[&&NHX:TOL=124374],madeleinea nodo[&&NHX:TOL=124375],madeleinea pacis[&&NHX:TOL=124376],madeleinea pelorias[&&NHX:TOL=124377],madeleinea sigal[&&NHX:TOL=124378],madeleinea tintarrona[&&NHX:TOL=124379],madeleinea vokoban[&&NHX:TOL=124380],1 undescribed madeleinea species[&&NHX:TOL=124381])madeleinea[&&NHX:TOL=124324],subsolanoides nagata[&&NHX:TOL=124413])polyommatus section[&&NHX:TOL=112257])polyommatini[&&NHX:TOL=111537])polyommatinae[&&NHX:TOL=106371],(((athamanthia alexandra[&&NHX:TOL=121995],athamanthia athamantis[&&NHX:TOL=121996],athamanthia balucha[&&NHX:TOL=121997],athamanthia churkini[&&NHX:TOL=121998],athamanthia dilutior[&&NHX:TOL=121999],athamanthia dimorpha[&&NHX:TOL=122000],athamanthia eitschbergeri[&&NHX:TOL=122001],athamanthia infera[&&NHX:TOL=122002],athamanthia issykkuli[&&NHX:TOL=122003],athamanthia japhetica[&&NHX:TOL=122004],athamanthia namanganica[&&NHX:TOL=122005],athamanthia phoenicura[&&NHX:TOL=122006],athamanthia rushanica[&&NHX:TOL=122007],athamanthia sogdiana[&&NHX:TOL=122008])athamanthia[&&NHX:TOL=111509],(hyrcanana caspia[&&NHX:TOL=121987],hyrcanana evansii[&&NHX:TOL=121988],hyrcanana pamira[&&NHX:TOL=121989],hyrcanana sartha[&&NHX:TOL=121990],hyrcanana sultan[&&NHX:TOL=121991],hyrcanana transiens[&&NHX:TOL=121992])hyrcanana[&&NHX:TOL=111510],((lycaena cupreus[&&NHX:TOL=121909],lycaena kiyokoae[&&NHX:TOL=121901],lycaena phlaeas[&&NHX:TOL=121902],lycaena sichuanica[&&NHX:TOL=121903])lycaena phlaeas group[&&NHX:TOL=121908],(lycaena aeolus[&&NHX:TOL=121911],lycaena dabrerai[&&NHX:TOL=121912],lycaena dispar[&&NHX:TOL=121904],lycaena kasyapa[&&NHX:TOL=121913],lycaena pavana[&&NHX:TOL=121905],lycaena splendens[&&NHX:TOL=121906],lycaena standfussi[&&NHX:TOL=121914],lycaena violacea[&&NHX:TOL=121907])lycaena dispar group[&&NHX:TOL=121910],(lycaena helle[&&NHX:TOL=121916],lycaena irmae[&&NHX:TOL=121917],lycaena li[&&NHX:TOL=121918],lycaena ouang[&&NHX:TOL=121919],lycaena pang[&&NHX:TOL=121920],lycaena svenhedini[&&NHX:TOL=121921],lycaena tseng[&&NHX:TOL=121922])lycaena helle group[&&NHX:TOL=121915],(lycaena alciphron[&&NHX:TOL=121924],lycaena bleusei[&&NHX:TOL=121925],lycaena ottomanus[&&NHX:TOL=121926],lycaena tityrus[&&NHX:TOL=121927],lycaena virgaureae[&&NHX:TOL=121928])lycaena virgaureae group[&&NHX:TOL=121923],(lycaena candens[&&NHX:TOL=121930],lycaena hippothoe[&&NHX:TOL=121931])lycaena hippothoe group[&&NHX:TOL=121929],(lycaena aditya[&&NHX:TOL=121933],lycaena alaica[&&NHX:TOL=121934],lycaena alpherakii[&&NHX:TOL=121935],lycaena asabinus[&&NHX:TOL=121936],lycaena eberti[&&NHX:TOL=121937],lycaena lampon[&&NHX:TOL=121938],lycaena lamponides[&&NHX:TOL=121939],lycaena ochimus[&&NHX:TOL=121940],lycaena phoebus[&&NHX:TOL=121941],lycaena solskyi[&&NHX:TOL=121942],lycaena thersamon[&&NHX:TOL=121943],lycaena thetis[&&NHX:TOL=121944])lycaena thersamon group[&&NHX:TOL=121932],(lycaena clarki[&&NHX:TOL=121946],lycaena orus[&&NHX:TOL=121947])lycaena orus group[&&NHX:TOL=121945],(lycaena dione[&&NHX:TOL=121949],lycaena editha[&&NHX:TOL=121950],lycaena gorgon[&&NHX:TOL=121951],lycaena xanthoides[&&NHX:TOL=121952])lycaena dione group[&&NHX:TOL=121948],lycaena arota[&&NHX:TOL=121953],lycaena hermes[&&NHX:TOL=121954],(lycaena rubidus[&&NHX:TOL=121956],lycaena heteronea[&&NHX:TOL=121957])lycaena rubidus group[&&NHX:TOL=121955],lycaena hyllus[&&NHX:TOL=121958],(lycaena epixanthe[&&NHX:TOL=121960],lycaena dorcas[&&NHX:TOL=121961],lycaena dospassosi[&&NHX:TOL=121962],lycaena helloides[&&NHX:TOL=121963],lycaena nivalis[&&NHX:TOL=121964],lycaena mariposa[&&NHX:TOL=121965])lycaena epixanthe group[&&NHX:TOL=121959],(lycaena boldenarum[&&NHX:TOL=121967],lycaena feredayi[&&NHX:TOL=121968],lycaena rauparaha[&&NHX:TOL=121969],lycaena salustius[&&NHX:TOL=121970])new zealand lycaena group[&&NHX:TOL=121966])lycaena[&&NHX:TOL=111507],(phoenicurusia euphratica[&&NHX:TOL=121993],phoenicurusia margelanica[&&NHX:TOL=121994])phoenicurusia[&&NHX:TOL=111513])lycaenini[&&NHX:TOL=111532],((heliophorus androcles[&&NHX:TOL=121875],heliophorus bakeri[&&NHX:TOL=121876],heliophorus brahma[&&NHX:TOL=121877],heliophorus brilliantinus[&&NHX:TOL=121878],heliophorus cantliei[&&NHX:TOL=121879],heliophorus epicles[&&NHX:TOL=121880],heliophorus eventa[&&NHX:TOL=121881],heliophorus gloria[&&NHX:TOL=121882],heliophorus hybrida[&&NHX:TOL=121883],heliophorus kiana[&&NHX:TOL=121884],heliophorus kohimensis[&&NHX:TOL=121885],heliophorus ila[&&NHX:TOL=121886],heliophorus indicus[&&NHX:TOL=121887],heliophorus moorei[&&NHX:TOL=121888],heliophorus oda[&&NHX:TOL=121889],heliophorus pulcher[&&NHX:TOL=121890],heliophorus saphir[&&NHX:TOL=121891],heliophorus saphiroides[&&NHX:TOL=121892],heliophorus sena[&&NHX:TOL=121893],heliophorus tamu[&&NHX:TOL=121894],heliophorus yunnani[&&NHX:TOL=121895],heliophorus forficatus[&&NHX:TOL=121899],[&&NHX:TOL=121900])heliophorus[&&NHX:TOL=111517],iophanus pyrrhias[&&NHX:TOL=111518],(melanolycaena altimontana[&&NHX:TOL=121897],melanolycaena thecloides[&&NHX:TOL=121898])melanolycaena[&&NHX:TOL=121896])heliophorini[&&NHX:TOL=111533])lycaeninae[&&NHX:TOL=106370],(((lucia limbaria[&&NHX:TOL=112294],(paralucia aurifera[&&NHX:TOL=120292],paralucia pyrodiscus[&&NHX:TOL=120293],paralucia spinifera[&&NHX:TOL=120294])paralucia[&&NHX:TOL=112295],(pseudodipsas aurea[&&NHX:TOL=117843],pseudodipsas eone[&&NHX:TOL=117844],pseudodipsas una[&&NHX:TOL=117845],pseudodipsas cephenes[&&NHX:TOL=117846],pseudodipsas sp. a[&&NHX:TOL=117847],pseudodipsas sp. b[&&NHX:TOL=117848])pseudodipsas[&&NHX:TOL=112296],(((((((acrodipsas arcana[&&NHX:TOL=120295],acrodipsas illidgei[&&NHX:TOL=120299])[&&NHX:TOL=124459],acrodipsas melania[&&NHX:TOL=120300])[&&NHX:TOL=124458],acrodipsas hirtipes[&&NHX:TOL=120298])[&&NHX:TOL=124457],acrodipsas mortoni[&&NHX:TOL=124460])[&&NHX:TOL=124456],(acrodipsas cuprea[&&NHX:TOL=120297],acrodipsas aurata[&&NHX:TOL=124462])[&&NHX:TOL=124461])[&&NHX:TOL=124455],acrodipsas brisbanensis[&&NHX:TOL=120296])[&&NHX:TOL=124454],acrodipsas myrmecophila[&&NHX:TOL=120301])acrodipsas[&&NHX:TOL=112297])lucia section[&&NHX:TOL=112293],(((hypochrysops digglesii[&&NHX:TOL=120202],hypochrysops rufimargo[&&NHX:TOL=120230])hypochrysops digglesi group[&&NHX:TOL=120277],(hypochrysops apollo[&&NHX:TOL=120184],hypochrysops chrysanthis[&&NHX:TOL=120193],hypochrysops coelisparsus[&&NHX:TOL=120197])hypochrysops chrysanthis group[&&NHX:TOL=120278],hypochrysops elgneri[&&NHX:TOL=120206],hypochrysops chrysargyra[&&NHX:TOL=120194],(hypochrysops arronica[&&NHX:TOL=120188],hypochrysops felderi[&&NHX:TOL=120208])hypochrysops arronica group[&&NHX:TOL=120279],(hypochrysops hypates[&&NHX:TOL=120216],hypochrysops luteus[&&NHX:TOL=120218],hypochrysops narcissus[&&NHX:TOL=120224],hypochrysops plotinus[&&NHX:TOL=120226])hypochrysops narcissus group[&&NHX:TOL=120280],(hypochrysops anacletus[&&NHX:TOL=120181],hypochrysops architas[&&NHX:TOL=120185],hypochrysops scintillans[&&NHX:TOL=120231],hypochrysops siren[&&NHX:TOL=120232],hypochrysops taeniata[&&NHX:TOL=120233])hypochrysops anacletus group[&&NHX:TOL=120281],(hypochrysops cyane[&&NHX:TOL=120199],hypochrysops epicurus[&&NHX:TOL=120207],hypochrysops halyaetus[&&NHX:TOL=120211],hypochrysops ignitus[&&NHX:TOL=120217],hypochrysops piceata[&&NHX:TOL=120225])hypochrysops ignitus group[&&NHX:TOL=120282],hypochrysops delicia[&&NHX:TOL=120200],(hypochrysops argyriorufus[&&NHX:TOL=120186],hypochrysops castaneus[&&NHX:TOL=120192],hypochrysops hermogenes[&&NHX:TOL=120213])hypochrysops hermogenes group[&&NHX:TOL=120283],(hypochrysops cleon[&&NHX:TOL=120195],hypochrysops cleonides[&&NHX:TOL=120196],hypochrysops miskini[&&NHX:TOL=120223],hypochrysops protogenes[&&NHX:TOL=120228],hypochrysops thesaurus[&&NHX:TOL=120235])hypochrysops protogenes group[&&NHX:TOL=120284],hypochrysops aristobul[&&NHX:TOL=120187],hypochrysops apelles[&&NHX:TOL=120183],(hypochrysops dicomas[&&NHX:TOL=120201],hypochrysops ferrugineus[&&NHX:TOL=120209],hypochrysops meeki[&&NHX:TOL=120220])hypochrysops dicomas group[&&NHX:TOL=120285],(hypochrysops byzos[&&NHX:TOL=120190],hypochrysops geminatus[&&NHX:TOL=120210],hypochrysops polycletus[&&NHX:TOL=120227],hypochrysops pythias[&&NHX:TOL=120229])hypochrysops byzos group[&&NHX:TOL=120286],(hypochrysops antiphon[&&NHX:TOL=120182],hypochrysops calliphon[&&NHX:TOL=120191],hypochrysops mioswara[&&NHX:TOL=120221])hypochrysops mioswara group[&&NHX:TOL=120287],(hypochrysops alyattes[&&NHX:TOL=120180],hypochrysops bakeri[&&NHX:TOL=120189],hypochrysops hippuris[&&NHX:TOL=120215])hypochrysops hippuris group[&&NHX:TOL=120288],(hypochrysops dohertyi[&&NHX:TOL=120204],hypochrysops doleschallii[&&NHX:TOL=120205],hypochrysops herdonius[&&NHX:TOL=120212],hypochrysops heros[&&NHX:TOL=120214],hypochrysops theon[&&NHX:TOL=120234])hypochrysops theon group[&&NHX:TOL=120289],(hypochrysops coruscans[&&NHX:TOL=120198],hypochrysops dinawa[&&NHX:TOL=120203],hypochrysops makrikii[&&NHX:TOL=120219],hypochrysops miraculum[&&NHX:TOL=120222],hypochrysops ribbei[&&NHX:TOL=120291])hypochrysops ribbei group[&&NHX:TOL=120290])hypochrysops[&&NHX:TOL=112299],(((philiris diana[&&NHX:TOL=120316],philiris gloriosa[&&NHX:TOL=120321],philiris montigena[&&NHX:TOL=120342],philiris praeclara[&&NHX:TOL=120349],philiris siassi[&&NHX:TOL=120354],philiris violetta[&&NHX:TOL=120362])philiris diana group[&&NHX:TOL=120468],(philiris albiplaga[&&NHX:TOL=120305],philiris bicolor[&&NHX:TOL=120312],philiris harterti[&&NHX:TOL=120322])philiris harterti group[&&NHX:TOL=120469])[&&NHX:TOL=120467],(philiris hemileuca[&&NHX:TOL=120324],philiris hypoxantha[&&NHX:TOL=120325])philiris hypoxantha group[&&NHX:TOL=120470],((philiris marginata[&&NHX:TOL=120336],philiris vicina[&&NHX:TOL=120361])philiris marginata group[&&NHX:TOL=120472],(philiris fulgens[&&NHX:TOL=120320],philiris remissa[&&NHX:TOL=120352])philiris fulgens group[&&NHX:TOL=120473])[&&NHX:TOL=120471],(philiris cadmica[&&NHX:TOL=120314],philiris misimensis[&&NHX:TOL=120339])philiris misimensis group[&&NHX:TOL=120474],((philiris agatha[&&NHX:TOL=120302],philiris ianthina[&&NHX:TOL=120326])[&&NHX:TOL=120476],philiris apicalis[&&NHX:TOL=120308],philiris elegans[&&NHX:TOL=120319],philiris helena[&&NHX:TOL=120323],philiris lavendula[&&NHX:TOL=120333],philiris moluccana[&&NHX:TOL=120341],philiris philotas[&&NHX:TOL=120347],philiris philotoides[&&NHX:TOL=120348])philiris helena group[&&NHX:TOL=120475],(philiris aquamarina[&&NHX:TOL=120309],philiris argentea[&&NHX:TOL=120310],philiris kumusiensis[&&NHX:TOL=120332],philiris nitens[&&NHX:TOL=120343],philiris scintillata[&&NHX:TOL=120356])philiris nitens group?[&&NHX:TOL=120477],(philiris oreas[&&NHX:TOL=120344],philiris tapini[&&NHX:TOL=120358])philiris oreas group[&&NHX:TOL=120478],(philiris azula[&&NHX:TOL=120311],philiris melanacra[&&NHX:TOL=120338],philiris ziska[&&NHX:TOL=120364])philiris ziska group[&&NHX:TOL=120479],(philiris ignobilis[&&NHX:TOL=120327],philiris mayri[&&NHX:TOL=120337],philiris putih[&&NHX:TOL=120350])philiris ignobilis group[&&NHX:TOL=120480],philiris albihumerata[&&NHX:TOL=120304],philiris tombara[&&NHX:TOL=120359],philiris sibatanii[&&NHX:TOL=120355],(philiris luscescens[&&NHX:TOL=120334],philiris zadne[&&NHX:TOL=120363])philiris zadne group[&&NHX:TOL=120481],(philiris doreia[&&NHX:TOL=120318],philiris ilias[&&NHX:TOL=120328],philiris intensa[&&NHX:TOL=120330],philiris subovata[&&NHX:TOL=120357])philiris ilias group[&&NHX:TOL=120482],(philiris dinawa[&&NHX:TOL=120317],philiris innotata[&&NHX:TOL=120329],philiris kapuara[&&NHX:TOL=120331],philiris moira[&&NHX:TOL=120340],philiris phengotes[&&NHX:TOL=120346])philiris innotata group[&&NHX:TOL=120483],(philiris albicostalis[&&NHX:TOL=120303],philiris satis[&&NHX:TOL=120353])philiris albicostalis group[&&NHX:TOL=120484],(philiris amethysta[&&NHX:TOL=120306],philiris angabunga[&&NHX:TOL=120307],philiris biplaga[&&NHX:TOL=120313],philiris caelestis[&&NHX:TOL=120315],philiris maculata[&&NHX:TOL=120335],philiris pagwi[&&NHX:TOL=120345],philiris refusa[&&NHX:TOL=120351],philiris unipunctata[&&NHX:TOL=120360])philiris refusa group[&&NHX:TOL=120485],3 undescribed species[&&NHX:TOL=120365])philiris[&&NHX:TOL=112301],(titea caerulea[&&NHX:TOL=117849],titea sublutea[&&NHX:TOL=117850])titea[&&NHX:TOL=112302])hypochrysops section[&&NHX:TOL=112298])luciini[&&NHX:TOL=111486],(((((arhopala acron[&&NHX:TOL=119850],arhopala adherbal[&&NHX:TOL=119852],arhopala admete[&&NHX:TOL=119853],arhopala aexone[&&NHX:TOL=119856],arhopala alkisthenes[&&NHX:TOL=119866],arhopala amantes[&&NHX:TOL=119868],arhopala ander[&&NHX:TOL=119873],arhopala araxes[&&NHX:TOL=119879],arhopala azenia[&&NHX:TOL=119899],arhopala centaurus[&&NHX:TOL=119911],arhopala eurisus[&&NHX:TOL=119930],arhopala kirwinii[&&NHX:TOL=119948],arhopala leander[&&NHX:TOL=119951],arhopala madytus[&&NHX:TOL=119954],arhopala meander[&&NHX:TOL=119956],arhopala micale[&&NHX:TOL=119958],arhopala philander[&&NHX:TOL=119976],arhopala pseudocentaurus[&&NHX:TOL=120008],arhopala sophrosyne[&&NHX:TOL=119988],arhopala styx[&&NHX:TOL=119992],arhopala wanda[&&NHX:TOL=120002])arhopala centaurus group[&&NHX:TOL=120007],(arhopala agesias[&&NHX:TOL=119859],arhopala kinabala[&&NHX:TOL=119947],arhopala similis[&&NHX:TOL=119985])arhopala agesias group[&&NHX:TOL=120009],arhopala ijanensis[&&NHX:TOL=119942],(arhopala achelous[&&NHX:TOL=119849],arhopala anthelus[&&NHX:TOL=119877],arhopala auxesia[&&NHX:TOL=119894],arhopala antharita[&&NHX:TOL=119876])arhopala anthelus group[&&NHX:TOL=120010],arhopala aedias[&&NHX:TOL=119854],arhopala hypomuta[&&NHX:TOL=119941],((arhopala anarte[&&NHX:TOL=119872],arhopala belphoebe[&&NHX:TOL=119905],arhopala camdana[&&NHX:TOL=119909],arhopala camdeo[&&NHX:TOL=120013],arhopala dispar[&&NHX:TOL=119920],arhopala hellada[&&NHX:TOL=119936],arhopala johoreana[&&NHX:TOL=119946],arhopala opalina[&&NHX:TOL=119968],arhopala semperi[&&NHX:TOL=119983],arhopala varro[&&NHX:TOL=120000])arhopala camdeo subgroup[&&NHX:TOL=120012],(arhopala bazaloides[&&NHX:TOL=119903],(arhopala myrzalina[&&NHX:TOL=119964],arhopala myrzala[&&NHX:TOL=119963])[&&NHX:TOL=120015])arhopala myrzala subgroup[&&NHX:TOL=120014])arhopala camdeo group[&&NHX:TOL=120011],(arhopala allata[&&NHX:TOL=119867],arhopala khamti[&&NHX:TOL=120017],arhopala oenea[&&NHX:TOL=120018])arhopala oenea group[&&NHX:TOL=120016],(arhopala atosia[&&NHX:TOL=119891],arhopala epimuta[&&NHX:TOL=119927],arhopala lurida[&&NHX:TOL=119953])arhopala epimuta group[&&NHX:TOL=120019],((arhopala alica[&&NHX:TOL=119864],arhopala amphimuta[&&NHX:TOL=119871],arhopala avathina[&&NHX:TOL=119896],arhopala baluensis[&&NHX:TOL=119901],arhopala dajagaka[&&NHX:TOL=119916],arhopala delta[&&NHX:TOL=119917],arhopala major[&&NHX:TOL=119955],arhopala moolaiana[&&NHX:TOL=119960],arhopala norda[&&NHX:TOL=119966],arhopala sceva[&&NHX:TOL=119982],arhopala stubbsi[&&NHX:TOL=119991],arhopala zylda[&&NHX:TOL=120006])arhopala amphimuta subgroup[&&NHX:TOL=120021],arhopala inornata[&&NHX:TOL=119943],arhopala kurzi[&&NHX:TOL=119949],(arhopala moorei[&&NHX:TOL=119961],arhopala muta[&&NHX:TOL=119962],arhopala tropaea[&&NHX:TOL=119998])arhopala muta subgroup[&&NHX:TOL=120022],(arhopala antimuta[&&NHX:TOL=119878],arhopala metamuta[&&NHX:TOL=119957],arhopala perimuta[&&NHX:TOL=119973])arhopala perimuta subgroup[&&NHX:TOL=120023])arhopala amphimuta group[&&NHX:TOL=120020],(arhopala agesilaus[&&NHX:TOL=119860],arhopala avatha[&&NHX:TOL=119895])arhopala agesilaus group[&&NHX:TOL=120024],arhopala democritus[&&NHX:TOL=119918],(arhopala aida[&&NHX:TOL=119862],arhopala alitaeus[&&NHX:TOL=119865],arhopala ariana[&&NHX:TOL=119881],arhopala arianaga[&&NHX:TOL=119882],arhopala denta[&&NHX:TOL=119919],arhopala elopura[&&NHX:TOL=119925],arhopala havilandi[&&NHX:TOL=119934],arhopala pseudomuta[&&NHX:TOL=119978],arhopala sintanga[&&NHX:TOL=119986])arhopala alitaeus group[&&NHX:TOL=120025],((arhopala ace[&&NHX:TOL=119847],arhopala azinis[&&NHX:TOL=119900])[&&NHX:TOL=120027],arhopala agrata[&&NHX:TOL=119861])arhopala agrata group[&&NHX:TOL=120026],((arhopala aruana[&&NHX:TOL=119886],arhopala ate[&&NHX:TOL=119889],arhopala athada[&&NHX:TOL=119890],arhopala cleander[&&NHX:TOL=119913],arhopala silhetensis[&&NHX:TOL=119984],arhopala zambra[&&NHX:TOL=120005])arhopala cleander subgroup[&&NHX:TOL=120029],(arhopala aenigma[&&NHX:TOL=119855],arhopala alea[&&NHX:TOL=120031],arhopala aroa[&&NHX:TOL=119884],arhopala aurelia[&&NHX:TOL=119893],arhopala evansi[&&NHX:TOL=119931],arhopala milleri[&&NHX:TOL=119959],arhopala normani[&&NHX:TOL=119967],arhopala phaenops[&&NHX:TOL=119974],arhopala phanda[&&NHX:TOL=119975],arhopala ralanda[&&NHX:TOL=120032],arhopala selta[&&NHX:TOL=119981],arhopala sublustris[&&NHX:TOL=119993])arhopala alea subgroup[&&NHX:TOL=120030],arhopala agaba[&&NHX:TOL=119857])arhopala cleander group[&&NHX:TOL=120028],arhopala vihara[&&NHX:TOL=120001],(arhopala acta[&&NHX:TOL=119851],arhopala asma[&&NHX:TOL=119888],arhopala bazalus[&&NHX:TOL=119904],arhopala chamaeleona[&&NHX:TOL=119912],arhopala corinda[&&NHX:TOL=119914],arhopala critala[&&NHX:TOL=119915],arhopala eumolphus[&&NHX:TOL=119929],arhopala florinda[&&NHX:TOL=119932],arhopala hellenore[&&NHX:TOL=119937],arhopala horsfieldi[&&NHX:TOL=119940],arhopala irma[&&NHX:TOL=119944],arhopala nobilis[&&NHX:TOL=119965],arhopala overdijkinki[&&NHX:TOL=119969],arhopala pagenstecheri[&&NHX:TOL=119970],arhopala tameanga[&&NHX:TOL=119994],arhopala wildei[&&NHX:TOL=120003])arhopala eumolphus group[&&NHX:TOL=120033],(arhopala arvina[&&NHX:TOL=119887],arhopala buddha[&&NHX:TOL=119907],arhopala paralea[&&NHX:TOL=119972],arhopala rama[&&NHX:TOL=120035])arhopala rama group[&&NHX:TOL=120034],((arhopala agelastus[&&NHX:TOL=119858],arhopala alesia[&&NHX:TOL=120038],arhopala barami[&&NHX:TOL=119902],arhopala labuana[&&NHX:TOL=119950],arhopala wildeyana[&&NHX:TOL=120004])[&&NHX:TOL=120037],arhopala alaconia[&&NHX:TOL=119863],arhopala cardoni[&&NHX:TOL=119910],arhopala epimete[&&NHX:TOL=119926])arhopala agelastus group[&&NHX:TOL=120036],(arhopala disparilis[&&NHX:TOL=119921],arhopala fulla[&&NHX:TOL=119933])arhopala fulla group[&&NHX:TOL=120039],(arhopala aurea[&&NHX:TOL=119892],arhopala borneensis[&&NHX:TOL=119906],arhopala caeca[&&NHX:TOL=119908],arhopala stinga[&&NHX:TOL=119989],arhopala trogon[&&NHX:TOL=119997])arhopala aurea group[&&NHX:TOL=120040],(arhopala ammon[&&NHX:TOL=119869],arhopala ammonides[&&NHX:TOL=119870],arhopala ariel[&&NHX:TOL=119883],arhopala elizabethae[&&NHX:TOL=119924],arhopala ganesa[&&NHX:TOL=120042],arhopala paraganesa[&&NHX:TOL=119971])arhopala ganesa group[&&NHX:TOL=120041],(arhopala abseus[&&NHX:TOL=119846],arhopala anella[&&NHX:TOL=119874])arhopala abseus group[&&NHX:TOL=120043],(arhopala arta[&&NHX:TOL=119885],arhopala axina[&&NHX:TOL=119897],arhopala axiothea[&&NHX:TOL=119898],arhopala doreena[&&NHX:TOL=119923],arhopala helianthes[&&NHX:TOL=119935],arhopala thamyras[&&NHX:TOL=119996])arhopala thamyras group[&&NHX:TOL=120044],(arhopala hercules[&&NHX:TOL=119938],arhopala herculina[&&NHX:TOL=119939],arhopala leo[&&NHX:TOL=119952],arhopala sophilus[&&NHX:TOL=119987],arhopala tyrannus[&&NHX:TOL=119999])arhopala hercules group[&&NHX:TOL=120045],arhopala aberrans[&&NHX:TOL=120046],arhopala acetes[&&NHX:TOL=119848],arhopala aeeta[&&NHX:TOL=120047],arhopala alax[&&NHX:TOL=120048],arhopala alexandrae[&&NHX:TOL=120049],arhopala anamuta[&&NHX:TOL=120050],arhopala annulata[&&NHX:TOL=120051],arhopala argentea[&&NHX:TOL=119880],arhopala aronya[&&NHX:TOL=120052],arhopala arsenius[&&NHX:TOL=120053],arhopala asinarus[&&NHX:TOL=120054],arhopala asopia[&&NHX:TOL=120055],arhopala atrax[&&NHX:TOL=120056],arhopala bella[&&NHX:TOL=120057],arhopala birmana[&&NHX:TOL=120058],arhopala comica[&&NHX:TOL=120059],arhopala curiosa[&&NHX:TOL=120060],arhopala davaona[&&NHX:TOL=120061],arhopala dodonaea[&&NHX:TOL=120062],arhopala dohertyi[&&NHX:TOL=119922],arhopala eridanus[&&NHX:TOL=119928],arhopala grandimuta[&&NHX:TOL=120594],arhopala halma[&&NHX:TOL=120063],arhopala halmaheira[&&NHX:TOL=120064],arhopala hellenoroides[&&NHX:TOL=120065],arhopala hesba[&&NHX:TOL=120066],arhopala hinigugma[&&NHX:TOL=120595],arhopala hylander[&&NHX:TOL=120067],arhopala ilocana[&&NHX:TOL=120596],arhopala irregularis[&&NHX:TOL=119945],arhopala japonica[&&NHX:TOL=120068],arhopala lata[&&NHX:TOL=120069],arhopala luzonensis[&&NHX:TOL=120597],arhopala matsutaroi[&&NHX:TOL=120598],arhopala mindanensis[&&NHX:TOL=120070],arhopala mizunumai[&&NHX:TOL=120071],arhopala myrtha[&&NHX:TOL=120072],arhopala nakamotoi[&&NHX:TOL=120073],arhopala nicevillei[&&NHX:TOL=120074],arhopala ocrida[&&NHX:TOL=120075],arhopala ormistoni[&&NHX:TOL=120076],arhopala pabihira[&&NHX:TOL=120077],arhopala paramuta[&&NHX:TOL=120078],arhopala phryxus[&&NHX:TOL=119977],arhopala pseudovihara[&&NHX:TOL=120599],arhopala qiongdaoensis[&&NHX:TOL=120079],arhopala quercoides[&&NHX:TOL=119979],arhopala rudepoema[&&NHX:TOL=120604],arhopala sakaguchii[&&NHX:TOL=120600],arhopala sangira[&&NHX:TOL=119980],arhopala schroederi[&&NHX:TOL=120080],arhopala siabra[&&NHX:TOL=120081],arhopala simoni[&&NHX:TOL=120601],arhopala singla[&&NHX:TOL=120082],arhopala staudingeri[&&NHX:TOL=120083],arhopala straatmani[&&NHX:TOL=119990],arhopala tephlis[&&NHX:TOL=119995],arhopala theba[&&NHX:TOL=120084],arhopala tindongani[&&NHX:TOL=120602],arhopala trionaea[&&NHX:TOL=120603],arhopala weelii[&&NHX:TOL=120085],arhopala zeta[&&NHX:TOL=120086])arhopala[&&NHX:TOL=112304],thaduka multicaudata[&&NHX:TOL=112306],apporasa atkinsoni[&&NHX:TOL=112307],(mahathala ameria[&&NHX:TOL=119837],mahathala ariadeva[&&NHX:TOL=119838])mahathala[&&NHX:TOL=112308],(flos adriana[&&NHX:TOL=119816],flos anniella[&&NHX:TOL=119817],flos apidanus[&&NHX:TOL=119818],flos arca[&&NHX:TOL=119819],flos areste[&&NHX:TOL=119820],flos asoka[&&NHX:TOL=119821],flos bungo[&&NHX:TOL=119822],flos chinensis[&&NHX:TOL=119823],flos diardi[&&NHX:TOL=119824],flos fulgida[&&NHX:TOL=119825],flos iriya[&&NHX:TOL=119826],flos kuehni[&&NHX:TOL=119827],flos morphina[&&NHX:TOL=119828],flos setsuroi[&&NHX:TOL=119829])flos[&&NHX:TOL=112309])arhopala section[&&NHX:TOL=112303],((semanga helena[&&NHX:TOL=119802],semanga superba[&&NHX:TOL=119803])semanga[&&NHX:TOL=112311],mota massyla[&&NHX:TOL=112312])semanga section[&&NHX:TOL=112310],((surendra florimel[&&NHX:TOL=119830],surendra manilana[&&NHX:TOL=119831],surendra quercetorum[&&NHX:TOL=119832],surendra vivarna[&&NHX:TOL=119833])surendra[&&NHX:TOL=112314],(zinaspa todara[&&NHX:TOL=119834],zinaspa youngi[&&NHX:TOL=119835],zinaspa zana[&&NHX:TOL=119836])zinaspa[&&NHX:TOL=112315])surendra section[&&NHX:TOL=112313])arhopalini[&&NHX:TOL=111488],((((artopoetes pryeri[&&NHX:TOL=112318],artopoetes praetextatus[&&NHX:TOL=138033])artopoetes[&&NHX:TOL=138032],laeosopis roboris[&&NHX:TOL=112319],(thecla betulae[&&NHX:TOL=121342],thecla betulina[&&NHX:TOL=121343])thecla[&&NHX:TOL=112320],(shirozua jonasi[&&NHX:TOL=121344],shirozua melpomene[&&NHX:TOL=121345])shirozua[&&NHX:TOL=112321],(cordelia comes[&&NHX:TOL=121346],cordelia kitawakii[&&NHX:TOL=121347],cordelia minerva[&&NHX:TOL=121348])cordelia[&&NHX:TOL=112322],(gonerilia budda[&&NHX:TOL=121349],gonerilia seraphim[&&NHX:TOL=121350],gonerilia thespis[&&NHX:TOL=121351])gonerilia[&&NHX:TOL=112323],coreana raphaelis[&&NHX:TOL=112324],(ussuriana michaelis[&&NHX:TOL=121363],ussuriana stygiana[&&NHX:TOL=121364],ussuriana takarana[&&NHX:TOL=121365])ussuriana[&&NHX:TOL=112325],shaanxiana takashimai[&&NHX:TOL=121366])[&&NHX:TOL=112317],((chaetoprocta baileyi[&&NHX:TOL=121407],chaetoprocta kurumi[&&NHX:TOL=121408],chaetoprocta odata[&&NHX:TOL=121409])chaetoprocta[&&NHX:TOL=112327],protantigius superans[&&NHX:TOL=112328],leucantigius atayalica[&&NHX:TOL=112329],(ravenna nivea[&&NHX:TOL=112330],goldia pacifica[&&NHX:TOL=121375])[&&NHX:TOL=121374],(antigius attilia[&&NHX:TOL=121369],antigius butleri[&&NHX:TOL=121370],antigius cheni[&&NHX:TOL=121371],antigius shizuyai[&&NHX:TOL=121372])antigius[&&NHX:TOL=112331],(wagimo abei[&&NHX:TOL=121376],wagimo asanoi[&&NHX:TOL=121377],wagimo insularis[&&NHX:TOL=121378],wagimo signata[&&NHX:TOL=121379],wagimo sulgeri[&&NHX:TOL=121380],wagimo tateishii[&&NHX:TOL=121381])wagimo[&&NHX:TOL=112332],(araragi enthea[&&NHX:TOL=121410],araragi panda[&&NHX:TOL=121411],araragi sugiyamai[&&NHX:TOL=121412])araragi[&&NHX:TOL=112333])[&&NHX:TOL=112326],((euaspa forsteri[&&NHX:TOL=121425],euaspa hishikawai[&&NHX:TOL=121426],euaspa mikamii[&&NHX:TOL=121427],euaspa milionia[&&NHX:TOL=121428],euaspa minaei[&&NHX:TOL=121429],euaspa miyashitai[&&NHX:TOL=121430],euaspa motokii[&&NHX:TOL=121431],euaspa nishimurai[&&NHX:TOL=121432],euaspa nosei[&&NHX:TOL=121433],euaspa pavo[&&NHX:TOL=121434],euaspa tayal[&&NHX:TOL=121435],euaspa ziha[&&NHX:TOL=121436])euaspa[&&NHX:TOL=112338],hypaurotis crysalus[&&NHX:TOL=112336],(habrodais grunus[&&NHX:TOL=119660],habrodais poodiae[&&NHX:TOL=119661])habrodais[&&NHX:TOL=112337],(howarthia caelestis[&&NHX:TOL=121509],howarthia cheni[&&NHX:TOL=121510],howarthia courvoisieri[&&NHX:TOL=121511],howarthia hishikawai[&&NHX:TOL=121512],howarthia kimurai[&&NHX:TOL=121513],howarthia melli[&&NHX:TOL=121514],howarthia nigricans[&&NHX:TOL=121515],howarthia sakakibarai[&&NHX:TOL=121516],howarthia sugiyamai[&&NHX:TOL=121517],howarthia ueharai[&&NHX:TOL=121518],howarthia wakaharai[&&NHX:TOL=121519],howarthia watanabei[&&NHX:TOL=121520],howarthia yukinobui[&&NHX:TOL=121521])howarthia[&&NHX:TOL=112339],iratsume orsedice[&&NHX:TOL=112344],(japonica bella[&&NHX:TOL=121413],japonica lutea[&&NHX:TOL=121414],japonica onoi[&&NHX:TOL=121415],japonica saepestriata[&&NHX:TOL=121416])japonica[&&NHX:TOL=112335],proteuaspa akikoae[&&NHX:TOL=121549],saigusaozephyrus atabyrius[&&NHX:TOL=121550],(teratozephyrus arisanus[&&NHX:TOL=121522],teratozephyrus chibahieyukii[&&NHX:TOL=121523],teratozephyrus elatus[&&NHX:TOL=121524],teratozephyrus florianii[&&NHX:TOL=121525],teratozephyrus hecale[&&NHX:TOL=121526],teratozephyrus hinomaru[&&NHX:TOL=121527],teratozephyrus kimurai[&&NHX:TOL=121528],teratozephyrus muroyai[&&NHX:TOL=121529],teratozephyrus nuwai[&&NHX:TOL=121530],teratozephyrus tsukiyamahiroshii[&&NHX:TOL=121531],teratozephyrus yugaii[&&NHX:TOL=121532])teratozephyrus[&&NHX:TOL=112340],((esakiozephyrus camurius[&&NHX:TOL=121533],esakiozephyrus icana[&&NHX:TOL=121534],esakiozephyrus longicaudatus[&&NHX:TOL=121535],esakiozephyrus neis[&&NHX:TOL=121536],esakiozephyrus tsankie[&&NHX:TOL=121537],esakiozephyrus vallonia[&&NHX:TOL=121538],esakiozephyrus zotelistes[&&NHX:TOL=121539])subgenus esakiozephyrus[&&NHX:TOL=121540],(esakiozephyrus ackeryi[&&NHX:TOL=121542],esakiozephyrus bieti[&&NHX:TOL=121543],esakiozephyrus mandara[&&NHX:TOL=121544],esakiozephyrus zhengi[&&NHX:TOL=121545])subgenus iwaseozephyrus[&&NHX:TOL=121541])esakiozephyrus[&&NHX:TOL=112341],yamamotozephyrus kwangtungensis[&&NHX:TOL=121367],(quercusia quercus[&&NHX:TOL=112346],((sibataniozephyrus fujisanus[&&NHX:TOL=121360],sibataniozephyrus kuafui[&&NHX:TOL=121361],sibataniozephyrus lijinae[&&NHX:TOL=121362])sibataniozephyrus[&&NHX:TOL=121354],((favonius cognatus[&&NHX:TOL=121390],favonius jezoensis[&&NHX:TOL=121391],favonius korshunovi[&&NHX:TOL=121392],favonius latimarginata[&&NHX:TOL=121393],favonius leechi[&&NHX:TOL=121394],favonius orientalis[&&NHX:TOL=121395],favonius saphirinus[&&NHX:TOL=121396],favonius taxila[&&NHX:TOL=121397],favonius ultramarinus[&&NHX:TOL=121398],favonius unoi[&&NHX:TOL=121399],favonius watanabei[&&NHX:TOL=121400],favonius yuasai[&&NHX:TOL=121401])favonius[&&NHX:TOL=112345],((austrozephyrus absolon[&&NHX:TOL=121546],austrozephyrus borneanus[&&NHX:TOL=121547],austrozephyrus reginae[&&NHX:TOL=121548])austrozephyrus[&&NHX:TOL=112347],((neozephyrus asahii[&&NHX:TOL=121382],neozephyrus coruscans[&&NHX:TOL=121383],neozephyrus dubernardi[&&NHX:TOL=121384],neozephyrus helenae[&&NHX:TOL=121385],neozephyrus japonicus[&&NHX:TOL=121386],neozephyrus taiwanus[&&NHX:TOL=121387],neozephyrus uedai[&&NHX:TOL=121388])neozephyrus[&&NHX:TOL=112342],((chrysozephyrus assamicus[&&NHX:TOL=121437],chrysozephyrus bhutanensis[&&NHX:TOL=121438],chrysozephyrus birupa[&&NHX:TOL=121439],chrysozephyrus brilliantinus[&&NHX:TOL=121440],chrysozephyrus chinensis[&&NHX:TOL=121441],chrysozephyrus disparatus[&&NHX:TOL=121442],chrysozephyrus duma[&&NHX:TOL=121443],chrysozephyrus dumoides[&&NHX:TOL=121444],chrysozephyrus fujiokai[&&NHX:TOL=121445],chrysozephyrus garmanitus[&&NHX:TOL=121447],chrysozephyrus giganteus[&&NHX:TOL=121448],chrysozephyrus hamadai[&&NHX:TOL=121449],chrysozephyrus haradai[&&NHX:TOL=121450],chrysozephyrus hatoyamai[&&NHX:TOL=121451],chrysozephyrus hayashii[&&NHX:TOL=121452],chrysozephyrus hisamatsusanus[&&NHX:TOL=121453],chrysozephyrus intermedius[&&NHX:TOL=121454],chrysozephyrus inthanonensis[&&NHX:TOL=121455],chrysozephyrus ioi[&&NHX:TOL=121456],chrysozephyrus jakamensis[&&NHX:TOL=121457],chrysozephyrus jiroi[&&NHX:TOL=121458],chrysozephyrus kabrua[&&NHX:TOL=121459],chrysozephyrus khasia[&&NHX:TOL=121460],chrysozephyrus kimurai[&&NHX:TOL=121461],chrysozephyrus kirbariensis[&&NHX:TOL=121462],chrysozephyrus koizumii[&&NHX:TOL=121463],chrysozephyrus leigongshanensis[&&NHX:TOL=121464],chrysozephyrus letha[&&NHX:TOL=121465],chrysozephyrus marginatus[&&NHX:TOL=121467],chrysozephyrus masatoshii[&&NHX:TOL=121468],chrysozephyrus mikamii[&&NHX:TOL=121470],chrysozephyrus mushaellus[&&NHX:TOL=121471],chrysozephyrus nansarae[&&NHX:TOL=121472],chrysozephyrus nigroapicalis[&&NHX:TOL=121473],chrysozephyrus nishikaze[&&NHX:TOL=121474],chrysozephyrus nosei[&&NHX:TOL=121475],chrysozephyrus nyishwini[&&NHX:TOL=121476],chrysozephyrus okamurai[&&NHX:TOL=121477],chrysozephyrus paona[&&NHX:TOL=121478],chrysozephyrus parakuromon[&&NHX:TOL=121479],chrysozephyrus rarasanus[&&NHX:TOL=121480],chrysozephyrus sakura[&&NHX:TOL=121481],chrysozephyrus sandersi[&&NHX:TOL=121482],chrysozephyrus scintillans[&&NHX:TOL=121483],chrysozephyrus setohi[&&NHX:TOL=121484],chrysozephyrus shakunage[&&NHX:TOL=121485],chrysozephyrus shimizui[&&NHX:TOL=121486],chrysozephyrus sikkimensis[&&NHX:TOL=121487],chrysozephyrus smaragdinus[&&NHX:TOL=121488],chrysozephyrus souleana[&&NHX:TOL=121489],chrysozephyrus syla[&&NHX:TOL=121490],chrysozephyrus tatsienluensis[&&NHX:TOL=121491],chrysozephyrus teisoi[&&NHX:TOL=121492],chrysozephyrus tienmushanus[&&NHX:TOL=121493],chrysozephyrus triloka[&&NHX:TOL=121494],chrysozephyrus tytleri[&&NHX:TOL=121495],chrysozephyrus uedai[&&NHX:TOL=121496],chrysozephyrus vietnamicus[&&NHX:TOL=121497],chrysozephyrus vittatus[&&NHX:TOL=121498],chrysozephyrus wakaharai[&&NHX:TOL=121499],chrysozephyrus watsoni[&&NHX:TOL=121500],chrysozephyrus yoshikoae[&&NHX:TOL=121501],chrysozephyrus yuani[&&NHX:TOL=121502],chrysozephyrus yuchingkinus[&&NHX:TOL=121503],chrysozephyrus zoa[&&NHX:TOL=121505])chrysozephyrus[&&NHX:TOL=112343],thermozephyrus ataxus[&&NHX:TOL=121359])[&&NHX:TOL=121358])[&&NHX:TOL=121357])[&&NHX:TOL=121356])[&&NHX:TOL=121355])[&&NHX:TOL=121353])[&&NHX:TOL=121352])[&&NHX:TOL=112334])thecla section[&&NHX:TOL=112316],amblopala avidiena[&&NHX:TOL=112348])theclini[&&NHX:TOL=111487],(ogyris abrota[&&NHX:TOL=119702],ogyris aenone[&&NHX:TOL=119703],ogyris amaryllis[&&NHX:TOL=119704],ogyris barnardi[&&NHX:TOL=119705],ogyris genoveva[&&NHX:TOL=119706],ogyris ianthis[&&NHX:TOL=119707],ogyris idmo[&&NHX:TOL=119708],ogyris iphis[&&NHX:TOL=119709],ogyris meeki[&&NHX:TOL=119710],ogyris olane[&&NHX:TOL=119711],ogyris oroetes[&&NHX:TOL=119712],ogyris otanes[&&NHX:TOL=119713],ogyris zosine[&&NHX:TOL=119714],ogyris subterrestris[&&NHX:TOL=119715])ogyris[&&NHX:TOL=111489])[&&NHX:TOL=111520],(zesius chrysomallus[&&NHX:TOL=112349],((jalmenus evagoras[&&NHX:TOL=117871],jalmenus eichhorni[&&NHX:TOL=117872],jalmenus ictinus[&&NHX:TOL=117873],jalmenus pseudictinus[&&NHX:TOL=117874],jalmenus daemeli[&&NHX:TOL=117875],jalmenus lithochroa[&&NHX:TOL=117876],jalmenus inous[&&NHX:TOL=117877],jalmenus icilius[&&NHX:TOL=117878],jalmenus clementi[&&NHX:TOL=117879],jalmenus aridus[&&NHX:TOL=117880],jalmenus notocrucifer[&&NHX:TOL=117881])jalmenus[&&NHX:TOL=112351],pseudalmenus chlorinda[&&NHX:TOL=112352])[&&NHX:TOL=112350])zesiini[&&NHX:TOL=111490],(((amblypodia anita[&&NHX:TOL=117864],amblypodia annetta[&&NHX:TOL=117865],amblypodia narada[&&NHX:TOL=117866])amblypodia[&&NHX:TOL=112353],(iraota abnormis[&&NHX:TOL=117867],iraota distantii[&&NHX:TOL=117868],iraota rochana[&&NHX:TOL=117869],iraota timoleon[&&NHX:TOL=117870])iraota[&&NHX:TOL=112354],(myrina dermaptera[&&NHX:TOL=117859],myrina silenus[&&NHX:TOL=117860],myrina subornata[&&NHX:TOL=117861],myrina sharpei[&&NHX:TOL=117862])myrina[&&NHX:TOL=112355])amblypodiini[&&NHX:TOL=111491],(((((((iolaus bilineata[&&NHX:TOL=120682],iolaus bolissus[&&NHX:TOL=120683],iolaus carina[&&NHX:TOL=120684],iolaus eurisus[&&NHX:TOL=120685],iolaus vexillarius[&&NHX:TOL=120686])subgenus iolaus[&&NHX:TOL=120720],iolaus tanuetheira timon[&&NHX:TOL=120721],(((iolaus alexanderi[&&NHX:TOL=120687],iolaus carolinae[&&NHX:TOL=120688],iolaus menas[&&NHX:TOL=120693],iolaus schultzei[&&NHX:TOL=120694],iolaus trimeni[&&NHX:TOL=120695])iolaus trimeni group[&&NHX:TOL=120724],iolaus gabunica[&&NHX:TOL=120689],iolaus henryi[&&NHX:TOL=120690],iolaus icipe[&&NHX:TOL=121013],iolaus iulus[&&NHX:TOL=120691],iolaus jamesoni[&&NHX:TOL=120692],iolaus shaba[&&NHX:TOL=121014])subgenus iolaphilus[&&NHX:TOL=120723],(iolaus aequatorialis[&&NHX:TOL=120696],iolaus bergeri[&&NHX:TOL=120698],iolaus caesareus[&&NHX:TOL=120699],iolaus cottrelli[&&NHX:TOL=120726],iolaus crawshayi[&&NHX:TOL=120727],iolaus dianae[&&NHX:TOL=120728],iolaus iturensis[&&NHX:TOL=120729],iolaus kayonza[&&NHX:TOL=120730],iolaus lalos[&&NHX:TOL=120731],(iolaus laonides[&&NHX:TOL=120733],iolaus poecilaon[&&NHX:TOL=120734])[&&NHX:TOL=120732],iolaus manasei[&&NHX:TOL=121015],iolaus maritimus[&&NHX:TOL=120735],iolaus montana[&&NHX:TOL=120736],iolaus ndolae[&&NHX:TOL=120737],iolaus pamae[&&NHX:TOL=120738],iolaus silarus[&&NHX:TOL=120739],iolaus silas[&&NHX:TOL=120740],iolaus stewarti[&&NHX:TOL=120741])subgenus argiolaus[&&NHX:TOL=120725],(iolaus alcibiades[&&NHX:TOL=120697],iolaus calisto[&&NHX:TOL=120700],iolaus christofferi[&&NHX:TOL=120743],iolaus ismenias[&&NHX:TOL=120744],(iolaus lukabas[&&NHX:TOL=120746],iolaus theodori[&&NHX:TOL=120747],iolaus mane[&&NHX:TOL=120748])[&&NHX:TOL=120745],iolaus newporti[&&NHX:TOL=120749],(iolaus parasilanus[&&NHX:TOL=120751],iolaus paneperata[&&NHX:TOL=120752])[&&NHX:TOL=120750],iolaus vansomereni[&&NHX:TOL=120753],iolaus likpe[&&NHX:TOL=120754])subgenus philiolaus[&&NHX:TOL=120742])[&&NHX:TOL=120722],(iolaus aemulus[&&NHX:TOL=120756],iolaus aethes[&&NHX:TOL=121016],(iolaus aethria[&&NHX:TOL=120758],iolaus farquharsoni[&&NHX:TOL=120759],iolaus frater[&&NHX:TOL=120760])[&&NHX:TOL=120757],iolaus agnes[&&NHX:TOL=120761],iolaus alienus[&&NHX:TOL=120762],iolaus apatosa[&&NHX:TOL=121017],iolaus aphnaeoides[&&NHX:TOL=120763],iolaus arborifera[&&NHX:TOL=120764],iolaus aurivillii[&&NHX:TOL=120765],iolaus australis[&&NHX:TOL=120766],iolaus bakeri[&&NHX:TOL=120767],iolaus bamptoni[&&NHX:TOL=121018],(iolaus banco[&&NHX:TOL=120769],iolaus coelestis[&&NHX:TOL=120770],iolaus laon[&&NHX:TOL=120771],iolaus moyambina[&&NHX:TOL=120772])[&&NHX:TOL=120768],iolaus bansana[&&NHX:TOL=120773],(iolaus bellina[&&NHX:TOL=120775],iolaus gemmarius[&&NHX:TOL=120776],iolaus sappirus[&&NHX:TOL=120777],iolaus sciophilus[&&NHX:TOL=120778])iolaus bellina group[&&NHX:TOL=120774],iolaus congdoni[&&NHX:TOL=120779],iolaus creta[&&NHX:TOL=120780],(iolaus cytaeis[&&NHX:TOL=120782],iolaus djaloni[&&NHX:TOL=120783],iolaus leonis[&&NHX:TOL=120784],iolaus pollux[&&NHX:TOL=120785])[&&NHX:TOL=120781],iolaus diametra[&&NHX:TOL=120786],iolaus dubiosa[&&NHX:TOL=120787],iolaus flavilinea[&&NHX:TOL=120788],iolaus fontainei[&&NHX:TOL=120789],iolaus glaucus[&&NHX:TOL=120790],iolaus handmani[&&NHX:TOL=120791],iolaus helenae[&&NHX:TOL=120792],iolaus hemicyanus[&&NHX:TOL=120793],iolaus iasis[&&NHX:TOL=120794],iolaus jacksoni[&&NHX:TOL=120795],iolaus kelle[&&NHX:TOL=120796],(iolaus longicauda[&&NHX:TOL=120798],iolaus neavei[&&NHX:TOL=120799],iolaus normani[&&NHX:TOL=120800])[&&NHX:TOL=120797],iolaus maesa[&&NHX:TOL=120801],iolaus mafugae[&&NHX:TOL=121019],iolaus mermis[&&NHX:TOL=120802],iolaus mimosae[&&NHX:TOL=120803],iolaus mongiro[&&NHX:TOL=120804],iolaus nasisii[&&NHX:TOL=120805],iolaus nolaensis[&&NHX:TOL=120806],iolaus nursei[&&NHX:TOL=120807],iolaus obscura[&&NHX:TOL=120808],iolaus penningtoni[&&NHX:TOL=120809],iolaus pseudofrater[&&NHX:TOL=120810],iolaus pseudopollux[&&NHX:TOL=120811],iolaus scintillans[&&NHX:TOL=120812],iolaus sibella[&&NHX:TOL=120813],iolaus sidus[&&NHX:TOL=120814],iolaus silanus[&&NHX:TOL=120815],iolaus stenogrammica[&&NHX:TOL=120816],iolaus sudanicus[&&NHX:TOL=120817],iolaus tajoraca[&&NHX:TOL=120818],iolaus umbrosa[&&NHX:TOL=120819],iolaus violacea[&&NHX:TOL=120820])subgenus epamera[&&NHX:TOL=120755],(iolaus argentarius[&&NHX:TOL=120822],iolaus mermeros[&&NHX:TOL=120823])subgenus trichiolaus[&&NHX:TOL=120821],iolaus aphniolaus pallene[&&NHX:TOL=120824],(iolaus lulua[&&NHX:TOL=120826],iolaus poultoni[&&NHX:TOL=120827])subgenus pseudiolaus[&&NHX:TOL=120825])iolaus s. s.[&&NHX:TOL=120719],(etesiolaus catori[&&NHX:TOL=120829],etesiolaus kyabobo[&&NHX:TOL=120830],etesiolaus pinheyi[&&NHX:TOL=120831])etesiolaus[&&NHX:TOL=120828],(stugeta bowkeri[&&NHX:TOL=120833],stugeta carpenteri[&&NHX:TOL=120834],stugeta marmoreus[&&NHX:TOL=120835],stugeta mimetica[&&NHX:TOL=120836],stugeta occidentalis[&&NHX:TOL=120837],stugeta somalina[&&NHX:TOL=120838],stugeta subinfuscata[&&NHX:TOL=120839])stugeta[&&NHX:TOL=120832])iolaus s. l.[&&NHX:TOL=112357],(pratapa deva[&&NHX:TOL=119840],pratapa icetas[&&NHX:TOL=119841],pratapa icetoides[&&NHX:TOL=119842],pratapa ismaeli[&&NHX:TOL=119843],pratapa tyotaroi[&&NHX:TOL=119844],pratapa cameria[&&NHX:TOL=120655])pratapa[&&NHX:TOL=112358],(tajuria alangani[&&NHX:TOL=120626],tajuria albiplaga[&&NHX:TOL=120627],tajuria berensis[&&NHX:TOL=120628],tajuria cippus[&&NHX:TOL=120629],tajuria culta[&&NHX:TOL=120630],tajuria cyrillus[&&NHX:TOL=120631],tajuria deudorix[&&NHX:TOL=120632],tajuria diaeus[&&NHX:TOL=120633],tajuria dominus[&&NHX:TOL=120634],tajuria floresica[&&NHX:TOL=120635],tajuria gui[&&NHX:TOL=120636],tajuria iapyx[&&NHX:TOL=120637],tajuria igolotiana[&&NHX:TOL=120638],tajuria illurgis[&&NHX:TOL=120639],tajuria illurgoides[&&NHX:TOL=120640],tajuria inexpectata[&&NHX:TOL=120641],tajuria isaeus[&&NHX:TOL=120642],tajuria ister[&&NHX:TOL=120643],tajuria jalajala[&&NHX:TOL=120644],tajuria jehana[&&NHX:TOL=120645],tajuria luculentus[&&NHX:TOL=120646],tajuria lucullus[&&NHX:TOL=120647],tajuria maculata[&&NHX:TOL=120648],tajuria mantra[&&NHX:TOL=120649],tajuria matsutaroi[&&NHX:TOL=120650],tajuria megistia[&&NHX:TOL=120651],tajuria melastigma[&&NHX:TOL=120652],tajuria sunia[&&NHX:TOL=120653],tajuria yajna[&&NHX:TOL=120654])tajuria[&&NHX:TOL=112359],(dacalana akayamai[&&NHX:TOL=120657],dacalana anysides[&&NHX:TOL=120658],dacalana anysis[&&NHX:TOL=120659],dacalana aristarchus[&&NHX:TOL=120660],dacalana burmana[&&NHX:TOL=120661],dacalana cotys[&&NHX:TOL=120662],dacalana cremera[&&NHX:TOL=120663],dacalana halconensis[&&NHX:TOL=120664],dacalana irmae[&&NHX:TOL=120665],dacalana kurosawai[&&NHX:TOL=120666],dacalana liaoi[&&NHX:TOL=120667],dacalana lowii[&&NHX:TOL=120668],dacalana lucillae[&&NHX:TOL=120669],dacalana mio[&&NHX:TOL=120670],dacalana monsapona[&&NHX:TOL=120671],dacalana penicilligera[&&NHX:TOL=120672],dacalana polyorketes[&&NHX:TOL=120673],dacalana sangirica[&&NHX:TOL=120674],dacalana sannio[&&NHX:TOL=120675],dacalana sinhara[&&NHX:TOL=120676],dacalana treadawayi[&&NHX:TOL=120677],dacalana vidura[&&NHX:TOL=120678])dacalana[&&NHX:TOL=112360],maneca bhotea[&&NHX:TOL=112361],creon cleobis[&&NHX:TOL=112362],(bullis buto[&&NHX:TOL=120679],bullis elioti[&&NHX:TOL=120680],bullis stigmata[&&NHX:TOL=120681])bullis[&&NHX:TOL=112363],sukidion inores[&&NHX:TOL=112364],purlisa giganteus[&&NHX:TOL=112365],jacoona anasuja[&&NHX:TOL=112366],(neocheritra amrita[&&NHX:TOL=120572],neocheritra fabronia[&&NHX:TOL=120573],neocheritra manata[&&NHX:TOL=120574],neocheritra namoa[&&NHX:TOL=120575])neocheritra[&&NHX:TOL=112367],manto hypoleuca[&&NHX:TOL=112368],mantoides gamma[&&NHX:TOL=112369],thrix scopula[&&NHX:TOL=112370],(charana mandarinus[&&NHX:TOL=120570],charana cepheis[&&NHX:TOL=120571])charana[&&NHX:TOL=112371],suasa lisides[&&NHX:TOL=112372],(paruparo annie[&&NHX:TOL=120612],paruparo cebuensis[&&NHX:TOL=120613],paruparo kuehni[&&NHX:TOL=120614],paruparo lumawigi[&&NHX:TOL=120615],paruparo mamertina[&&NHX:TOL=120616],paruparo mio[&&NHX:TOL=120617],paruparo rosemarie[&&NHX:TOL=120618],pratuparo violacea[&&NHX:TOL=120619])paruparo[&&NHX:TOL=120578],(rachana circumdata[&&NHX:TOL=120620],rachana jalindra[&&NHX:TOL=120621],rachana mariaba[&&NHX:TOL=120622],rachana mioae[&&NHX:TOL=120623],rachana plateni[&&NHX:TOL=120624])rachana[&&NHX:TOL=120579],matsutaroa iljai[&&NHX:TOL=120625])iolaus section[&&NHX:TOL=112356],(britomartis cleoboides[&&NHX:TOL=120576],britomartis igarashii[&&NHX:TOL=120577])britomartis[&&NHX:TOL=112373])iolaini[&&NHX:TOL=111493],(((((hypolycaena buxtoni[&&NHX:TOL=120492],hypolycaena kadiskos[&&NHX:TOL=120504],hypolycaena liara[&&NHX:TOL=120507],hypolycaena naara[&&NHX:TOL=120510],hypolycaena pachalica[&&NHX:TOL=120514],hypolycaena philippus[&&NHX:TOL=120517])[&&NHX:TOL=120531],((hypolycaena clenchi[&&NHX:TOL=120493],hypolycaena coerulea[&&NHX:TOL=120494],hypolycaena lebona[&&NHX:TOL=120506],hypolycaena scintillans[&&NHX:TOL=120521])[&&NHX:TOL=120533],(hypolycaena dubia[&&NHX:TOL=120498],hypolycaena kakumi[&&NHX:TOL=120505])[&&NHX:TOL=120534])[&&NHX:TOL=120532],(hypolycaena anara[&&NHX:TOL=120489],hypolycaena antifaunus[&&NHX:TOL=120490],hypolycaena hatita[&&NHX:TOL=120500],hypolycaena nigra[&&NHX:TOL=120511])[&&NHX:TOL=120535],hypolycaena amanica[&&NHX:TOL=120488],hypolycaena auricostalis[&&NHX:TOL=120491],hypolycaena condamini[&&NHX:TOL=120495],hypolycaena jacksoni[&&NHX:TOL=120503],hypolycaena lochmophila[&&NHX:TOL=120508],hypolycaena ogadenensis[&&NHX:TOL=120513],hypolycaena schubotzi[&&NHX:TOL=120519],hypolycaena similis[&&NHX:TOL=120523])african hypolycaena species[&&NHX:TOL=120530],((hypolycaena dictaea[&&NHX:TOL=120497],hypolycaena erylus[&&NHX:TOL=120499],hypolycaena periphorbas[&&NHX:TOL=120515],hypolycaena phorbas[&&NHX:TOL=120518])[&&NHX:TOL=120537],(hypolycaena alcestis[&&NHX:TOL=120486],hypolycaena danis[&&NHX:TOL=120496])[&&NHX:TOL=120538],hypolycaena amabilis[&&NHX:TOL=120487],hypolycaena irawana[&&NHX:TOL=120501],hypolycaena ithna[&&NHX:TOL=120502],hypolycaena merguia[&&NHX:TOL=120509],hypolycaena nilgirica[&&NHX:TOL=120512],hypolycaena phemis[&&NHX:TOL=120516],hypolycaena schroederi[&&NHX:TOL=120520],hypolycaena shirozui[&&NHX:TOL=120522],hypolycaena sipylus[&&NHX:TOL=120524],hypolycaena thecloides[&&NHX:TOL=120525],hypolycaena toshikoae[&&NHX:TOL=120526],hypolycaena umbrata[&&NHX:TOL=120527],hypolycaena vanavasa[&&NHX:TOL=120528],hypolycaena xenia[&&NHX:TOL=120529])indoaustralian hypolycaena species[&&NHX:TOL=120536])hypolycaena[&&NHX:TOL=112375],(chliaria balua[&&NHX:TOL=120543],chliaria kina[&&NHX:TOL=120544],chliaria othona[&&NHX:TOL=120545],chliaria pahanga[&&NHX:TOL=120546],chliaria tora[&&NHX:TOL=120547])chliaria[&&NHX:TOL=112376],zeltus amasa[&&NHX:TOL=112377],((leptomyrina boschi[&&NHX:TOL=120548],leptomyrina hirundo[&&NHX:TOL=120549],leptomyrina makala[&&NHX:TOL=120550],leptomyrina phidias[&&NHX:TOL=120551],leptomyrina sudanica[&&NHX:TOL=120552])subgenus leptomyrina[&&NHX:TOL=120557],(leptomyrina gorgias[&&NHX:TOL=120553],leptomyrina handmani[&&NHX:TOL=120554],leptomyrina henningi[&&NHX:TOL=120555],leptomyrina lara[&&NHX:TOL=120556])subgenus gonatomyrina[&&NHX:TOL=120558])leptomyrina[&&NHX:TOL=112378],(hemiolaus caeculus[&&NHX:TOL=120559],hemiolaus ceres[&&NHX:TOL=120560],hemiolaus cobaltina[&&NHX:TOL=120561],hemiolaus margites[&&NHX:TOL=120562],hemiolaus maryra[&&NHX:TOL=120563],hemiolaus varnieri[&&NHX:TOL=120564])hemiolaus[&&NHX:TOL=112374])hypolycaenini[&&NHX:TOL=111495],((remelana davisi[&&NHX:TOL=120566],remelana jangala[&&NHX:TOL=120567])remelana[&&NHX:TOL=112380],(ancema blanka[&&NHX:TOL=120568],ancema ctesia[&&NHX:TOL=120569])ancema[&&NHX:TOL=112381],pseudotajuria donatana[&&NHX:TOL=112382])remelanini[&&NHX:TOL=111494])[&&NHX:TOL=111524])[&&NHX:TOL=111523],(((((loxura atymnus[&&NHX:TOL=117926],loxura cassiopeia[&&NHX:TOL=117927])loxura[&&NHX:TOL=112384],(yasoda androconifera[&&NHX:TOL=117928],yasoda pita[&&NHX:TOL=117929],yasoda pitane[&&NHX:TOL=117930],yasoda robinsoni[&&NHX:TOL=117931],yasoda tripunctata[&&NHX:TOL=117932])yasoda[&&NHX:TOL=112385],(eooxylides tharis[&&NHX:TOL=117933],eooxylides etias[&&NHX:TOL=117934],eooxylides meduana[&&NHX:TOL=117935])eooxylides[&&NHX:TOL=112386],(thamala marciana[&&NHX:TOL=117936],thamala moultoni[&&NHX:TOL=117937])thamala[&&NHX:TOL=112387])loxura section[&&NHX:TOL=112383],neomyrina nivea[&&NHX:TOL=112388],(drina cowani[&&NHX:TOL=117938],drina discophora[&&NHX:TOL=117939],drina donina[&&NHX:TOL=117940],drina maneia[&&NHX:TOL=117941],drina mariae[&&NHX:TOL=117942],drina mavortia[&&NHX:TOL=117943])drina[&&NHX:TOL=112389])loxurini[&&NHX:TOL=111497],(((horaga araotina[&&NHX:TOL=120166],horaga albimacula[&&NHX:TOL=120167],horaga amethystus[&&NHX:TOL=120168],horaga bilineata[&&NHX:TOL=120610],horaga chalcedonyx[&&NHX:TOL=120169],horaga lefebvrei[&&NHX:TOL=120170],horaga natsumiae[&&NHX:TOL=120171],horaga onyx[&&NHX:TOL=120172],horaga rarasana[&&NHX:TOL=120173],horaga selina[&&NHX:TOL=120174],horaga sohmai[&&NHX:TOL=120175],horaga syrinx[&&NHX:TOL=120176])horaga[&&NHX:TOL=112390],rathinda amor[&&NHX:TOL=112391])horagini[&&NHX:TOL=111498],(((cheritra aenigma[&&NHX:TOL=117975],cheritra freja[&&NHX:TOL=117976],cheritra orpheus[&&NHX:TOL=117977],cheritra pallida[&&NHX:TOL=117978],cheritra aenea[&&NHX:TOL=117979])cheritra[&&NHX:TOL=112393],ritra aurea[&&NHX:TOL=112394],cheritrella truncipennis[&&NHX:TOL=112395],ticherra acte[&&NHX:TOL=112396],(drupadia cinderella[&&NHX:TOL=117980],drupadia cindi[&&NHX:TOL=117981],drupadia cineas[&&NHX:TOL=117982],drupadia cinesia[&&NHX:TOL=117983],drupadia cinesoides[&&NHX:TOL=117984],drupadia estella[&&NHX:TOL=117985],drupadia johorensis[&&NHX:TOL=117986],drupadia niasica[&&NHX:TOL=117987],drupadia ravindra[&&NHX:TOL=117988],drupadia rufotaenia[&&NHX:TOL=117989],drupadia scaeva[&&NHX:TOL=117990],drupadia theda[&&NHX:TOL=117991])drupadia[&&NHX:TOL=112397],cowania achaja[&&NHX:TOL=112398])cheritra section[&&NHX:TOL=112392],(dapidodigma demeter[&&NHX:TOL=117992],dapidodigma hymen[&&NHX:TOL=117993])dapidodigma[&&NHX:TOL=112399])cheritrini[&&NHX:TOL=111499])[&&NHX:TOL=111527])[&&NHX:TOL=111526],(((catapaecilma elegans[&&NHX:TOL=119692],catapaecilma evansi[&&NHX:TOL=119693],catapaecilma gracilis[&&NHX:TOL=119694],catapaecilma lila[&&NHX:TOL=119695],catapaecilma major[&&NHX:TOL=119696],catapaecilma nakamotoi[&&NHX:TOL=120606],catapaecilma nuydai[&&NHX:TOL=120607],catapaecilma subochrea[&&NHX:TOL=119697])catapaecilma[&&NHX:TOL=112400],(acupicta bubases[&&NHX:TOL=119698],acupicta delicatum[&&NHX:TOL=119699],acupicta flemingi[&&NHX:TOL=119700],acupicta meeki[&&NHX:TOL=119701],acupicta inopinatum[&&NHX:TOL=120608])acupicta[&&NHX:TOL=112401])catapaecilmatini[&&NHX:TOL=111496],(((hypothecla astyla[&&NHX:TOL=117882],hypothecla honos[&&NHX:TOL=117883])hypothecla[&&NHX:TOL=112402],(hypochlorosis ancharia[&&NHX:TOL=117884],hypochlorosis antipha[&&NHX:TOL=117885],hypochlorosis lorquinii[&&NHX:TOL=117886],hypochlorosis obiana[&&NHX:TOL=117887])hypochlorosis[&&NHX:TOL=112403])hypotheclini[&&NHX:TOL=111505],((oxylides albata[&&NHX:TOL=119681],oxylides bella[&&NHX:TOL=119682],oxylides binza[&&NHX:TOL=119683],oxylides faunus[&&NHX:TOL=119684],oxylides gloveri[&&NHX:TOL=119685],oxylides stempfferi[&&NHX:TOL=119686])oxylides[&&NHX:TOL=112404],(syrmoptera amasa[&&NHX:TOL=119687],(syrmoptera caritas[&&NHX:TOL=128894],syrmoptera homeyerii[&&NHX:TOL=119689],syrmoptera mixtura[&&NHX:TOL=119691])[&&NHX:TOL=128893],(syrmoptera bonifacei[&&NHX:TOL=119688],syrmoptera melanomitra[&&NHX:TOL=119690])[&&NHX:TOL=128895])syrmoptera[&&NHX:TOL=112405])oxylidini[&&NHX:TOL=111503])[&&NHX:TOL=111529])[&&NHX:TOL=111528])[&&NHX:TOL=111525])[&&NHX:TOL=111522])[&&NHX:TOL=111521],((((eumaeus atala[&&NHX:TOL=117952],eumaeus childrenae[&&NHX:TOL=117953],eumaeus godartii[&&NHX:TOL=117954],eumaeus minyas[&&NHX:TOL=117955],eumaeus toxea[&&NHX:TOL=117956],eumaeus toxana[&&NHX:TOL=117957])eumaeus[&&NHX:TOL=112453],(theorema dysmenia[&&NHX:TOL=117958],theorema eumenia[&&NHX:TOL=117959],theorema sapho[&&NHX:TOL=117960])theorema[&&NHX:TOL=112452],(paiwarria antinous[&&NHX:TOL=117961],paiwarria aphaca[&&NHX:TOL=117962],paiwarria episcopalis[&&NHX:TOL=117963],paiwarria telemus[&&NHX:TOL=117964],paiwarria umbratus[&&NHX:TOL=117965],paiwarria venulius[&&NHX:TOL=117966],paiwarria n. sp.[&&NHX:TOL=117967])paiwarria[&&NHX:TOL=112448],(mithras colombiensis[&&NHX:TOL=117968],mithras elis[&&NHX:TOL=117969],mithras nautes[&&NHX:TOL=117970],mithras oroanna[&&NHX:TOL=117971],mithras orobia[&&NHX:TOL=117972],mithras vossoroca[&&NHX:TOL=117973],mithras orobiana[&&NHX:TOL=118312],mithras orocana[&&NHX:TOL=118313],mithras catrea[&&NHX:TOL=118314],5 undescribed mithras species[&&NHX:TOL=117974])mithras[&&NHX:TOL=112441])eumaeus section[&&NHX:TOL=112953],((brangas caranus[&&NHX:TOL=118343],brangas carthaea[&&NHX:TOL=118344],brangas coccineifrons[&&NHX:TOL=118345],brangas dydimaon[&&NHX:TOL=118346],brangas felderi[&&NHX:TOL=118347],brangas getus[&&NHX:TOL=118348],brangas neora[&&NHX:TOL=118349],brangas rita[&&NHX:TOL=118350],brangas silumena[&&NHX:TOL=118351],brangas teucria[&&NHX:TOL=118352],brangas torfrida[&&NHX:TOL=118353],7 undescribed brangas species[&&NHX:TOL=118354])brangas[&&NHX:TOL=112451],(thaeides goleta[&&NHX:TOL=118355],thaeides muela[&&NHX:TOL=118356],thaeides pyrczi[&&NHX:TOL=118357],thaeides theia[&&NHX:TOL=118358],thaeides xavieri[&&NHX:TOL=118359])thaeides[&&NHX:TOL=112955],(enos falerina[&&NHX:TOL=118360],enos maculata[&&NHX:TOL=118361],enos mazurka[&&NHX:TOL=118362],enos myrtea[&&NHX:TOL=118363],enos thara[&&NHX:TOL=118364])enos[&&NHX:TOL=112956],(evenus batesii[&&NHX:TOL=118369],evenus candidus[&&NHX:TOL=118370],evenus coronata[&&NHX:TOL=118371],evenus floralia[&&NHX:TOL=118372],evenus gabriela[&&NHX:TOL=118373],evenus latreillii[&&NHX:TOL=118374],evenus regalis[&&NHX:TOL=118375],evenus satyroides[&&NHX:TOL=118376],evenus sponsa[&&NHX:TOL=118377],evenus sumptuosa[&&NHX:TOL=118378],evenus tagyra[&&NHX:TOL=118379],evenus temathea[&&NHX:TOL=118380])evenus[&&NHX:TOL=112957],(lamasina draudti[&&NHX:TOL=118365],lamasina ganimedes[&&NHX:TOL=118366],lamasina rhaptissima[&&NHX:TOL=118367],lamasina saphonota[&&NHX:TOL=118368])lamasina[&&NHX:TOL=112958])brangas section[&&NHX:TOL=112954],((lamprospilus albolineata[&&NHX:TOL=119187],lamprospilus argentiniensis[&&NHX:TOL=119188],lamprospilus arza[&&NHX:TOL=119189],lamprospilus aunus[&&NHX:TOL=119190],lamprospilus badaca[&&NHX:TOL=119191],lamprospilus calatia[&&NHX:TOL=119192],lamprospilus canacha[&&NHX:TOL=119193],lamprospilus clarissa[&&NHX:TOL=119194],lamprospilus coelicolor[&&NHX:TOL=119195],lamprospilus collucia[&&NHX:TOL=119196],lamprospilus decorata[&&NHX:TOL=119197],lamprospilus draudti[&&NHX:TOL=119198],lamprospilus genius[&&NHX:TOL=119199],lamprospilus japola[&&NHX:TOL=119200],lamprospilus lanckena[&&NHX:TOL=119201],lamprospilus? netesca[&&NHX:TOL=119202],lamprospilus nicetus[&&NHX:TOL=119203],lamprospilus nubilum[&&NHX:TOL=119204],lamprospilus orcidia[&&NHX:TOL=119205],lamprospilus paralus[&&NHX:TOL=119206],lamprospilus picentia[&&NHX:TOL=119207],lamprospilus quadrimacula[&&NHX:TOL=119208],lamprospilus sethon[&&NHX:TOL=119209],lamprospilus taminella[&&NHX:TOL=119210],lamprospilus tarpa[&&NHX:TOL=119211],lamprospilus tucumanensis[&&NHX:TOL=119212],15 undescribed species[&&NHX:TOL=119213])lamprospilus[&&NHX:TOL=112445],(electrostrymon angelia[&&NHX:TOL=119241],electrostrymon angerona[&&NHX:TOL=119242],electrostrymon constantinoi[&&NHX:TOL=119243],electrostrymon dominicana[&&NHX:TOL=119244],electrostrymon ecbatana[&&NHX:TOL=119245],electrostrymon endymion[&&NHX:TOL=119246],electrostrymon joya[&&NHX:TOL=119247],electrostrymon mathewi[&&NHX:TOL=119248],electrostrymon pan[&&NHX:TOL=119249],electrostrymon sangala[&&NHX:TOL=119250])electrostrymon[&&NHX:TOL=112417],(calycopis anastasia[&&NHX:TOL=119251],calycopis anfracta[&&NHX:TOL=119252],calycopis anthora[&&NHX:TOL=119253],calycopis atnius[&&NHX:TOL=119254],calycopis bactra[&&NHX:TOL=119255],calycopis barza[&&NHX:TOL=119256],calycopis bellera[&&NHX:TOL=119257],calycopis blora[&&NHX:TOL=119258],calycopis boliviensis[&&NHX:TOL=119259],calycopis buphonia[&&NHX:TOL=119260],calycopis caesaries[&&NHX:TOL=119261],calycopis calor[&&NHX:TOL=119262],calycopis calus[&&NHX:TOL=119263],calycopis caulonia[&&NHX:TOL=119264],calycopis cecrops[&&NHX:TOL=119328],calycopis centoripa[&&NHX:TOL=119265],calycopis cerata[&&NHX:TOL=119266],calycopis cinniana[&&NHX:TOL=119267],calycopis cissusa[&&NHX:TOL=119268],calycopis clarina[&&NHX:TOL=119269],calycopis cos[&&NHX:TOL=119270],calycopis cyanus[&&NHX:TOL=119271],calycopis demonassa[&&NHX:TOL=119272],calycopis drusilla[&&NHX:TOL=119273],calycopis fractunda[&&NHX:TOL=119274],calycopis gentilla[&&NHX:TOL=119275],calycopis gizela[&&NHX:TOL=119276],calycopis hosmeri[&&NHX:TOL=119277],calycopis indigo[&&NHX:TOL=119278],calycopis isobeon[&&NHX:TOL=119279],calycopis janeirica[&&NHX:TOL=119280],calycopis johnsoni[&&NHX:TOL=119281],calycopis lerbela[&&NHX:TOL=119282],calycopis malta[&&NHX:TOL=119283],calycopis matho[&&NHX:TOL=119284],calycopis meleager[&&NHX:TOL=119285],calycopis mimas[&&NHX:TOL=119286],calycopis mirna[&&NHX:TOL=119287],calycopis naka[&&NHX:TOL=119288],calycopis nicolayi[&&NHX:TOL=119289],calycopis orcilla[&&NHX:TOL=119290],calycopis orcillula[&&NHX:TOL=119291],calycopis origo[&&NHX:TOL=119292],calycopis partunda[&&NHX:TOL=119293],calycopis petaurister[&&NHX:TOL=119294],calycopis pisis[&&NHX:TOL=119295],calycopis plumans[&&NHX:TOL=119296],calycopis puppius[&&NHX:TOL=119297],calycopis spadectis[&&NHX:TOL=119298],calycopis suda[&&NHX:TOL=119299],calycopis talama[&&NHX:TOL=119300],calycopis tamos[&&NHX:TOL=119301],calycopis thama[&&NHX:TOL=119302],calycopis tifla[&&NHX:TOL=119303],calycopis torqueor[&&NHX:TOL=119304],calycopis trebula[&&NHX:TOL=119305],calycopis vesulus[&&NHX:TOL=119306],calycopis vibulina[&&NHX:TOL=119307],calycopis vidulus[&&NHX:TOL=119308],calycopis vitruvia[&&NHX:TOL=119309],calycopis wolfii[&&NHX:TOL=119310],calycopis xeneta[&&NHX:TOL=119311],(calycopis auria[&&NHX:TOL=119313],calycopis duida[&&NHX:TOL=119314],calycopis extensa[&&NHX:TOL=119315],calycopis fornoi[&&NHX:TOL=119316],calycopis itaituba[&&NHX:TOL=119317],calycopis macphersoni[&&NHX:TOL=119318],calycopis megana[&&NHX:TOL=119319],calycopis neorcillata[&&NHX:TOL=119320],calycopis panornata[&&NHX:TOL=119321],calycopis phryne[&&NHX:TOL=119322],calycopis spenceri[&&NHX:TOL=119323],calycopis splendida[&&NHX:TOL=119324],calycopis srandrea[&&NHX:TOL=119325],calycopis stacya[&&NHX:TOL=119326],calycopis strobilata[&&NHX:TOL=119327])calycopis nomina dubia[&&NHX:TOL=119312],12 undescribed calycopis species[&&NHX:TOL=119329])calycopis[&&NHX:TOL=112422],(arumecla aruma[&&NHX:TOL=119214],arumecla galliena[&&NHX:TOL=119215],arumecla nisaee[&&NHX:TOL=119216],4 undescribed species two of which may belong elsewhere[&&NHX:TOL=119217])arumecla[&&NHX:TOL=112960],(camissecla camissa[&&NHX:TOL=119218],camissecla charichlorus[&&NHX:TOL=119219],camissecla cleocha[&&NHX:TOL=119220],camissecla? gedrosia[&&NHX:TOL=119221],camissecla ledaea[&&NHX:TOL=119222],camissecla melma[&&NHX:TOL=119223],camissecla pactya[&&NHX:TOL=119224],camissecla saphronotis[&&NHX:TOL=119225],camissecla simasca[&&NHX:TOL=119226],camissecla verbenacea[&&NHX:TOL=119227],camissecla vespasianus[&&NHX:TOL=119228],camissecla vesper[&&NHX:TOL=119229],4 camissecla undescribed species[&&NHX:TOL=119230])camissecla[&&NHX:TOL=112961],(ziegleria ceromia[&&NHX:TOL=119231],ziegleria denarius[&&NHX:TOL=119232],ziegleria guzanta[&&NHX:TOL=119233],ziegleria? hernandezi[&&NHX:TOL=119234],ziegleria hesperitis[&&NHX:TOL=119235],ziegleria hoffmani[&&NHX:TOL=119236],ziegleria micandriana[&&NHX:TOL=119237],ziegleria perisus[&&NHX:TOL=119238],ziegleria syllis[&&NHX:TOL=119239],2 undescribed ziegleria species[&&NHX:TOL=119240])ziegleria[&&NHX:TOL=112962])lamprospilus section[&&NHX:TOL=112959],((thereus caltha[&&NHX:TOL=118622],thereus cithonius[&&NHX:TOL=118623],thereus columbicola[&&NHX:TOL=118624],thereus endera[&&NHX:TOL=118625],thereus ? enenia[&&NHX:TOL=118626],thereus eryssus[&&NHX:TOL=118627],thereus gabathana[&&NHX:TOL=118628],thereus genena[&&NHX:TOL=118629],thereus guianivaga[&&NHX:TOL=118630],thereus illex[&&NHX:TOL=118631],thereus ismarus[&&NHX:TOL=118632],thereus lausus[&&NHX:TOL=118633],thereus lutzi[&&NHX:TOL=118634],thereus molena[&&NHX:TOL=118635],thereus oppia[&&NHX:TOL=118636],thereus orasus[&&NHX:TOL=118637],thereus ortalus[&&NHX:TOL=118638],thereus pedusa[&&NHX:TOL=118639],thereus praxis[&&NHX:TOL=118640],thereus pseudarcula[&&NHX:TOL=118641],thereus tiasa[&&NHX:TOL=118642],thereus timoclea[&&NHX:TOL=118643],9 undescribed thereus species[&&NHX:TOL=118644])thereus[&&NHX:TOL=112443],(rekoa bourkei[&&NHX:TOL=118645],rekoa malina[&&NHX:TOL=118646],rekoa marius[&&NHX:TOL=118647],rekoa meton[&&NHX:TOL=118648],rekoa palegon[&&NHX:TOL=118649],rekoa stagira[&&NHX:TOL=118650],rekoa zebina[&&NHX:TOL=118651])rekoa[&&NHX:TOL=112449],(arawacus aethesa[&&NHX:TOL=118652],arawacus aetolus[&&NHX:TOL=118653],arawacus binangula[&&NHX:TOL=118654],arawacus dolylas[&&NHX:TOL=118655],arawacus dumenilii[&&NHX:TOL=118656],arawacus ellida[&&NHX:TOL=118657],arawacus euptychia[&&NHX:TOL=118658],arawacus hypocrita[&&NHX:TOL=118659],arawacus jada[&&NHX:TOL=118660],arawacus leucogyna[&&NHX:TOL=118661],arawacus lincoides[&&NHX:TOL=118662],arawacus meliboeus[&&NHX:TOL=118663],arawacus sito[&&NHX:TOL=118664],arawacus tadita[&&NHX:TOL=118665],arawacus tarania[&&NHX:TOL=118666],arawacus togarna[&&NHX:TOL=118667],arawacus separata[&&NHX:TOL=118669],1 undescribed species[&&NHX:TOL=118668])arawacus[&&NHX:TOL=112433],(contrafacia ahola[&&NHX:TOL=118945],contrafacia bassania[&&NHX:TOL=118946],contrafacia francis[&&NHX:TOL=118947],contrafacia imma[&&NHX:TOL=118948],contrafacia marmoris[&&NHX:TOL=118949],contrafacia muattina[&&NHX:TOL=118950],1 undescribed species[&&NHX:TOL=118951])contrafacia[&&NHX:TOL=112964],(kolana buccina[&&NHX:TOL=118671],kolana chlamys[&&NHX:TOL=118672],kolana ergina[&&NHX:TOL=118673],kolana ligurina[&&NHX:TOL=118674],kolana lyde[&&NHX:TOL=118675],1 undescribed species[&&NHX:TOL=118676])kolana[&&NHX:TOL=112965])thereus section[&&NHX:TOL=112963],((atlides atys[&&NHX:TOL=118381],atlides bacis[&&NHX:TOL=118382],atlides browni[&&NHX:TOL=118383],atlides carpasia[&&NHX:TOL=118384],atlides cosa[&&NHX:TOL=118385],atlides gaumeri[&&NHX:TOL=118386],atlides halesus[&&NHX:TOL=118387],atlides havila[&&NHX:TOL=118388],atlides inachus[&&NHX:TOL=118389],atlides misma[&&NHX:TOL=118390],atlides polama[&&NHX:TOL=118391],atlides polybe[&&NHX:TOL=118392],atlides rustan[&&NHX:TOL=118393],atlides thargelia[&&NHX:TOL=118394],atlides zava[&&NHX:TOL=118395],5 undescribed species[&&NHX:TOL=118396])atlides[&&NHX:TOL=112442],(arcas cypria[&&NHX:TOL=118329],arcas delphia[&&NHX:TOL=118330],arcas ducalis[&&NHX:TOL=118331],arcas imperialis[&&NHX:TOL=118332],arcas jivaro[&&NHX:TOL=118333],arcas nicolayi[&&NHX:TOL=118334],arcas splendor[&&NHX:TOL=118335],arcas tuneta[&&NHX:TOL=118336])arcas[&&NHX:TOL=112444],(pseudolycaena marsyas[&&NHX:TOL=112939],pseudolycaena nellyae[&&NHX:TOL=112940],pseudolycaena cybele[&&NHX:TOL=112941],(pseudolycaena damo[&&NHX:TOL=112942],pseudolycaena dorcas[&&NHX:TOL=112943])[&&NHX:TOL=112944])pseudolycaena[&&NHX:TOL=112446],(theritas acontius[&&NHX:TOL=118397],theritas adamsi[&&NHX:TOL=118398],theritas anna[&&NHX:TOL=118399],theritas arene[&&NHX:TOL=118400],theritas augustinula[&&NHX:TOL=118401],theritas augustula[&&NHX:TOL=118402],theritas chalumna[&&NHX:TOL=118403],theritas crines[&&NHX:TOL=118404],theritas curitibaensis[&&NHX:TOL=118405],theritas danaus[&&NHX:TOL=118406],theritas deniva[&&NHX:TOL=118407],theritas drucei[&&NHX:TOL=118408],theritas harrietta[&&NHX:TOL=118409],theritas hemon[&&NHX:TOL=118410],theritas lisus[&&NHX:TOL=118411],theritas margaritacea[&&NHX:TOL=118412],theritas mavors[&&NHX:TOL=118413],theritas monica[&&NHX:TOL=118414],theritas paupera[&&NHX:TOL=118415],theritas phegeus[&&NHX:TOL=118416],theritas theocritus[&&NHX:TOL=118417],theritas triquetra[&&NHX:TOL=118418],theritas viresco[&&NHX:TOL=118419],3 undescribed theritas species[&&NHX:TOL=118420])theritas[&&NHX:TOL=112440])atlides section[&&NHX:TOL=112966],((allosmaitia coelebs[&&NHX:TOL=119163],allosmaitia fidena[&&NHX:TOL=119164],allosmaitia mytrusa[&&NHX:TOL=119165],allosmaitia piplea[&&NHX:TOL=119166],allosmaitia strophius[&&NHX:TOL=119167])allosmaitia[&&NHX:TOL=112436],(laothus barajo[&&NHX:TOL=119168],laothus cockaynei[&&NHX:TOL=119169],laothus erybathis[&&NHX:TOL=119170],laothus gibberosa[&&NHX:TOL=119171],laothus numen[&&NHX:TOL=119172],laothus oceia[&&NHX:TOL=119173],laothus phydela[&&NHX:TOL=119174],laothus viridicans[&&NHX:TOL=119175])laothus[&&NHX:TOL=112968],(janthecla rocena[&&NHX:TOL=119184],(janthecla adrienne[&&NHX:TOL=138181],(janthecla malvina[&&NHX:TOL=119183],(janthecla sista[&&NHX:TOL=119185],(janthecla armilla[&&NHX:TOL=119176],(janthecla aurora[&&NHX:TOL=119177],janthecla flosculus[&&NHX:TOL=119179])[&&NHX:TOL=138185])[&&NHX:TOL=138184],(janthecla janthina[&&NHX:TOL=119180],janthecla janthodonia[&&NHX:TOL=119181],janthecla cydonia[&&NHX:TOL=119178],janthecla leea[&&NHX:TOL=119182],janthecla halli[&&NHX:TOL=119186])[&&NHX:TOL=138186])[&&NHX:TOL=138183])[&&NHX:TOL=138182])[&&NHX:TOL=138180])janthecla[&&NHX:TOL=112969])allosmaitia section[&&NHX:TOL=112967],((thestius azaria[&&NHX:TOL=119154],thestius epopea[&&NHX:TOL=119155],thestius lycabas[&&NHX:TOL=119156],thestius meridionalis[&&NHX:TOL=119157],thestius pholeus[&&NHX:TOL=119158],thestius selina[&&NHX:TOL=119159],4 undescribed thestius species[&&NHX:TOL=119160])thestius[&&NHX:TOL=112429],(bistonina bactriana[&&NHX:TOL=119145],bistonina biston[&&NHX:TOL=119146],bistonina erema[&&NHX:TOL=119147],bistonina feretria[&&NHX:TOL=119148],bistonina mantica[&&NHX:TOL=119149],bistonina olbia[&&NHX:TOL=119150],3 undescribed species[&&NHX:TOL=119151])bistonina[&&NHX:TOL=112971],(megathecla cupentus[&&NHX:TOL=119152],megathecla gigantea[&&NHX:TOL=119153])megathecla[&&NHX:TOL=112972],(lathecla latagus[&&NHX:TOL=119161],5 undescribed species[&&NHX:TOL=119162])lathecla[&&NHX:TOL=112973])thestius section[&&NHX:TOL=112970],((tmolus crolinus[&&NHX:TOL=119382],tmolus cydrara[&&NHX:TOL=119383],tmolus echion[&&NHX:TOL=119384],tmolus mutina[&&NHX:TOL=119385],tmolus ufentina[&&NHX:TOL=119386],tmolus venustus[&&NHX:TOL=119387],9 undescribed tmolus species[&&NHX:TOL=119388])tmolus[&&NHX:TOL=112425],(ministrymon albimimicus[&&NHX:TOL=119416],ministrymon arola[&&NHX:TOL=119417],ministrymon arthuri[&&NHX:TOL=119418],ministrymon azia[&&NHX:TOL=119419],ministrymon cleon[&&NHX:TOL=119420],ministrymon clytie[&&NHX:TOL=119421],ministrymon coronta[&&NHX:TOL=119422],ministrymon cruenta[&&NHX:TOL=119423],ministrymon fostera[&&NHX:TOL=119424],ministrymon gamma[&&NHX:TOL=119425],ministrymon inoa[&&NHX:TOL=119426],ministrymon leda[&&NHX:TOL=119427],ministrymon ligia[&&NHX:TOL=119428],ministrymon megacles[&&NHX:TOL=119429],ministrymon? ollantaitamba[&&NHX:TOL=119430],ministrymon phrutus[&&NHX:TOL=119431],ministrymon sanguinalis[&&NHX:TOL=119432],ministrymon una[&&NHX:TOL=119433],ministrymon zilda[&&NHX:TOL=119434],3 undescribed ministrymon species[&&NHX:TOL=119435])ministrymon[&&NHX:TOL=112419],(nicolaea bagrada[&&NHX:TOL=119389],nicolaea besidia[&&NHX:TOL=119390],nicolaea castinotus[&&NHX:TOL=119391],nicolaea cauter[&&NHX:TOL=119392],nicolaea? ceglusa[&&NHX:TOL=119393],nicolaea cupa[&&NHX:TOL=119394],nicolaea demilineata[&&NHX:TOL=119395],nicolaea? dolium[&&NHX:TOL=119396],nicolaea fabulla[&&NHX:TOL=119397],nicolaea heraldica[&&NHX:TOL=119398],nicolaea laconia[&&NHX:TOL=119399],nicolaea lemuria[&&NHX:TOL=119400],nicolaea munditia[&&NHX:TOL=119401],nicolaea obelus[&&NHX:TOL=119402],nicolaea opalia[&&NHX:TOL=119403],nicolaea opaliana[&&NHX:TOL=119404],nicolaea ophia[&&NHX:TOL=119405],nicolaea petilla[&&NHX:TOL=119406],nicolaea pyxis[&&NHX:TOL=119407],nicolaea schausa[&&NHX:TOL=119408],nicolaea socia[&&NHX:TOL=119409],nicolaea torris[&&NHX:TOL=119410],nicolaea umuarama[&&NHX:TOL=119411],nicolaea velina[&&NHX:TOL=119412],nicolaea viceta[&&NHX:TOL=119413],nicolaea xorema[&&NHX:TOL=119414],13 undescribed nicolaea species[&&NHX:TOL=119415])nicolaea[&&NHX:TOL=112975],(exorbaetta metanira[&&NHX:TOL=119436],undescribed exorbaetta species[&&NHX:TOL=119437])exorbaetta[&&NHX:TOL=112976],(gargina caninius[&&NHX:TOL=119438],gargina emessa[&&NHX:TOL=119439],gargina gargophia[&&NHX:TOL=119440],gargina gnosia[&&NHX:TOL=119441],gargina humber[&&NHX:TOL=119442],gargina? panchaea[&&NHX:TOL=119443],gargina? thoria[&&NHX:TOL=119444],gargina thyesta[&&NHX:TOL=119445],1 undescribed species[&&NHX:TOL=119446])gargina[&&NHX:TOL=112977],(siderus athymbra[&&NHX:TOL=119447],siderus bouvieri[&&NHX:TOL=119448],siderus eliatha[&&NHX:TOL=119449],siderus giapor[&&NHX:TOL=119450],siderus guapila[&&NHX:TOL=119451],siderus leucophaeus[&&NHX:TOL=119452],siderus parvinotus[&&NHX:TOL=119453],siderus philinna[&&NHX:TOL=119454],14 undescribed siderus species[&&NHX:TOL=119455])siderus[&&NHX:TOL=112432],(theclopsis aurina[&&NHX:TOL=119457],theclopsis demea[&&NHX:TOL=119458],theclopsis epidius[&&NHX:TOL=119459],theclopsis gargara[&&NHX:TOL=119460],theclopsis leos[&&NHX:TOL=119461],theclopsis lydus[&&NHX:TOL=119462],theclopsis murex[&&NHX:TOL=119463],theclopsis mycon[&&NHX:TOL=119464],2 undescribed theclopsis species[&&NHX:TOL=119465])theclopsis[&&NHX:TOL=112434],(ostrinotes empusa[&&NHX:TOL=119466],ostrinotes gentiana[&&NHX:TOL=119467],ostrinotes halciones[&&NHX:TOL=119468],ostrinotes keila[&&NHX:TOL=119469],ostrinotes purpuriticus[&&NHX:TOL=119470],ostrinotes sophocles[&&NHX:TOL=119471],ostrinotes sospes[&&NHX:TOL=119472],ostrinotes tarena[&&NHX:TOL=119473],ostrinotes tympania[&&NHX:TOL=119474],8 undescribed ostrinotes species[&&NHX:TOL=119475])ostrinotes[&&NHX:TOL=112978],(strephonota acameda[&&NHX:TOL=119476],strephonota adela[&&NHX:TOL=119477],strephonota agrippa[&&NHX:TOL=119478],strephonota ambrax[&&NHX:TOL=119479],strephonota azurinus[&&NHX:TOL=119480],strephonota bicolorata[&&NHX:TOL=119481],strephonota carteia[&&NHX:TOL=119482],strephonota cyllarissus[&&NHX:TOL=119483],strephonota elika[&&NHX:TOL=119484],strephonota ericeta[&&NHX:TOL=119485],strephonota falsistrephon[&&NHX:TOL=119486],strephonota foyi[&&NHX:TOL=119487],strephonota jactator[&&NHX:TOL=119488],strephonota malvania[&&NHX:TOL=119489],strephonota parvipuncta[&&NHX:TOL=119490],strephonota perola[&&NHX:TOL=119491],strephonota porphyritis[&&NHX:TOL=119492],strephonota pulchritudo[&&NHX:TOL=119493],strephonota purpurantes[&&NHX:TOL=119494],strephonota sphinx[&&NHX:TOL=119495],strephonota strephon[&&NHX:TOL=119496],strephonota syedra[&&NHX:TOL=119497],strephonota tephraeus[&&NHX:TOL=119498],strephonota trebonia[&&NHX:TOL=119499],strephonota tyriam[&&NHX:TOL=119500],19 undescribed strephonota species[&&NHX:TOL=119501])strephonota[&&NHX:TOL=112979])tmolus section[&&NHX:TOL=112974],((panthiades aeolus[&&NHX:TOL=119502],panthiades bathildis[&&NHX:TOL=119503],panthiades bitias[&&NHX:TOL=119504],panthiades boreas[&&NHX:TOL=119505],panthiades hebraeus[&&NHX:TOL=119506],panthiades ochus[&&NHX:TOL=119507],panthiades paphlagon[&&NHX:TOL=119508],panthiades phaleros[&&NHX:TOL=119509])panthiades[&&NHX:TOL=112423],(oenomaus atena[&&NHX:TOL=119523],oenomaus atesa[&&NHX:TOL=119524],oenomaus cortica[&&NHX:TOL=119525],oenomaus cyanovenata[&&NHX:TOL=119526],oenomaus geba[&&NHX:TOL=119527],oenomaus ortygnus[&&NHX:TOL=119528],16 undescribed oenomaus species[&&NHX:TOL=119529])oenomaus[&&NHX:TOL=112427],(porthecla barba[&&NHX:TOL=119510],porthecla dinus[&&NHX:TOL=119511],porthecla gemma[&&NHX:TOL=119512],porthecla melleus[&&NHX:TOL=119513],porthecla minyia[&&NHX:TOL=119514],porthecla porthura[&&NHX:TOL=119515],porthecla ravus[&&NHX:TOL=119516],2 undescribed porthecla species[&&NHX:TOL=119517])porthecla[&&NHX:TOL=112981],(thepytus arindela[&&NHX:TOL=119518],thepytus echelta[&&NHX:TOL=119519],thepytus epytus[&&NHX:TOL=119520],thepytus thyrea[&&NHX:TOL=119521],3 undescribed thepytus species[&&NHX:TOL=119522])thepytus[&&NHX:TOL=112982],(ignata brasiliensis[&&NHX:TOL=119542],ignata elana[&&NHX:TOL=119543],ignata gadira[&&NHX:TOL=119544],ignata levis[&&NHX:TOL=119545],ignata mulsus[&&NHX:TOL=119546],ignata norax[&&NHX:TOL=119547],1 undescribed species[&&NHX:TOL=119548])ignata[&&NHX:TOL=112983],(parrhasius malbum[&&NHX:TOL=119530],parrhasius moctezuma[&&NHX:TOL=119531],parrhasius orgia[&&NHX:TOL=119532],parrhasius polibetes[&&NHX:TOL=119533],parrhasius selika[&&NHX:TOL=119534],parrhasius urraca[&&NHX:TOL=119535])parrhasius[&&NHX:TOL=112424],(michaelus hecate[&&NHX:TOL=119536],michaelus ira[&&NHX:TOL=119537],michaelus jebus[&&NHX:TOL=119538],michaelus phoenissa[&&NHX:TOL=119539],michaelus thordesa[&&NHX:TOL=119540],1 undescribed species[&&NHX:TOL=119541])michaelus[&&NHX:TOL=112457],(olynthus avoca[&&NHX:TOL=119549],olynthus essus[&&NHX:TOL=119550],olynthus fancia[&&NHX:TOL=119551],olynthus fulvoventris[&&NHX:TOL=119552],olynthus hypsea[&&NHX:TOL=119553],olynthus lorea[&&NHX:TOL=119554],olynthus narbal[&&NHX:TOL=119555],olynthus negrus[&&NHX:TOL=119556],olynthus nitor[&&NHX:TOL=119557],olynthus obsoleta[&&NHX:TOL=119558],olynthus ophelia[&&NHX:TOL=119559],olynthus ostia[&&NHX:TOL=119560],olynthus porphyreticus[&&NHX:TOL=119561],olynthus punctum[&&NHX:TOL=119562],6 undescribed olynthus species[&&NHX:TOL=119563])olynthus[&&NHX:TOL=112428])panthiades section[&&NHX:TOL=112980],(strymon acis[&&NHX:TOL=119331],strymon albata[&&NHX:TOL=119332],strymon alea[&&NHX:TOL=119333],strymon astiocha[&&NHX:TOL=119334],strymon avalona[&&NHX:TOL=119335],strymon azuba[&&NHX:TOL=119336],strymon bazochii[&&NHX:TOL=119337],strymon bebrycia[&&NHX:TOL=119338],strymon bicolor[&&NHX:TOL=119339],strymon bubastus[&&NHX:TOL=119340],strymon cardus[&&NHX:TOL=119341],strymon cestri[&&NHX:TOL=119342],strymon christophei[&&NHX:TOL=119343],strymon colombiana[&&NHX:TOL=119344],strymon columella[&&NHX:TOL=119345],strymon crambusa[&&NHX:TOL=119346],strymon cyanofusca[&&NHX:TOL=119347],strymon daraba[&&NHX:TOL=119348],strymon davara[&&NHX:TOL=119349],strymon dindus[&&NHX:TOL=119350],strymon eremica[&&NHX:TOL=119351],strymon eurytulus[&&NHX:TOL=119352],strymon flavaria[&&NHX:TOL=119353],strymon gabatha[&&NHX:TOL=119354],strymon glorissima[&&NHX:TOL=119355],strymon heodes[&&NHX:TOL=119356],strymon istapa[&&NHX:TOL=119357],strymon limenia[&&NHX:TOL=119358],strymon lucena[&&NHX:TOL=119359],strymon martialis[&&NHX:TOL=119360],strymon megarus[&&NHX:TOL=119361],strymon melinus[&&NHX:TOL=119362],strymon monopeteinus[&&NHX:TOL=119363],strymon mulucha[&&NHX:TOL=119364],strymon nivea[&&NHX:TOL=119365],strymon ohausi[&&NHX:TOL=119366],strymon oreala[&&NHX:TOL=119367],strymon oribata[&&NHX:TOL=119368],strymon rana[&&NHX:TOL=119369],strymon rufofusca[&&NHX:TOL=119370],strymon sabinus[&&NHX:TOL=119371],strymon serapio[&&NHX:TOL=119372],strymon sylea[&&NHX:TOL=119373],strymon tegaea[&&NHX:TOL=119374],strymon toussainti[&&NHX:TOL=119375],strymon veterator[&&NHX:TOL=119376],strymon wagenknechti[&&NHX:TOL=119377],strymon yojoa[&&NHX:TOL=119378],strymon ziba[&&NHX:TOL=119379],7 undescribed strymon species[&&NHX:TOL=119380])strymon[&&NHX:TOL=112421],((hypostrymon aepona[&&NHX:TOL=119564],hypostrymon asa[&&NHX:TOL=119565],hypostrymon critola[&&NHX:TOL=119566],hypostrymon renidens[&&NHX:TOL=119567],5 undescribed species[&&NHX:TOL=119568])hypostrymon[&&NHX:TOL=112418],(nesiostrymon calchinia[&&NHX:TOL=119576],nesiostrymon celida[&&NHX:TOL=119577],nesiostrymon celona[&&NHX:TOL=119578],nesiostrymon dodava[&&NHX:TOL=119579],nesiostrymon endela[&&NHX:TOL=119580],nesiostrymon hyccara[&&NHX:TOL=119581],nesiostrymon shoumatoffi[&&NHX:TOL=119582],nesiostrymon tristis[&&NHX:TOL=119583])nesiostrymon[&&NHX:TOL=112435],(marachina fidelia[&&NHX:TOL=119569],marachina maraches[&&NHX:TOL=119570],marachina peonida[&&NHX:TOL=119571],2 undescribed species[&&NHX:TOL=119572])marachina[&&NHX:TOL=112985],(apuecla maeonis[&&NHX:TOL=119573],apuecla picus[&&NHX:TOL=119574],apuecla upupa[&&NHX:TOL=119575])apuecla[&&NHX:TOL=112986],balintus tityrus[&&NHX:TOL=112987],(aubergina alda[&&NHX:TOL=119584],aubergina hesychia[&&NHX:TOL=119585],aubergina hicetas[&&NHX:TOL=119586],aubergina paetus[&&NHX:TOL=119587],aubergina vanessoides[&&NHX:TOL=119588],2 undescribed species[&&NHX:TOL=119589])aubergina[&&NHX:TOL=112988],(terenthina bradyae[&&NHX:TOL=119590],terenthina terentia[&&NHX:TOL=119591])terenthina[&&NHX:TOL=112989],(celmia anastomosis[&&NHX:TOL=119603],celmia celmus[&&NHX:TOL=119604],celmia color[&&NHX:TOL=119605],celmia conoveria[&&NHX:TOL=119606],celmia mecrida[&&NHX:TOL=119607],celmia uzza[&&NHX:TOL=119608],1 undescribed celmia species[&&NHX:TOL=119609])celmia[&&NHX:TOL=112990],(dicya carnica[&&NHX:TOL=119610],dicya dicaea[&&NHX:TOL=119611],dicya eumorpha[&&NHX:TOL=119612],dicya iambe[&&NHX:TOL=119613],dicya lollia[&&NHX:TOL=119614],dicya lucagus[&&NHX:TOL=119615])dicya[&&NHX:TOL=112991],(iaspis beera[&&NHX:TOL=119592],iaspis castimonia[&&NHX:TOL=119593],iaspis castitas[&&NHX:TOL=119594],iaspis exiguus[&&NHX:TOL=119595],iaspis grandis[&&NHX:TOL=119596],iaspis ornata[&&NHX:TOL=119597],iaspis talayra[&&NHX:TOL=119598],iaspis temesa[&&NHX:TOL=119599],iaspis thabena[&&NHX:TOL=119600],iaspis verania[&&NHX:TOL=119601],1 undescribed species[&&NHX:TOL=119602])iaspis[&&NHX:TOL=112431],(trichonis hyacinthus[&&NHX:TOL=119616],trichonis immaculata[&&NHX:TOL=119617])trichonis[&&NHX:TOL=112463])hypostrymon section[&&NHX:TOL=112984],(((satyrium acadica[&&NHX:TOL=118984],satyrium auretorum[&&NHX:TOL=118977],satyrium behrii[&&NHX:TOL=118985],satyrium calanus[&&NHX:TOL=118986],satyrium californica[&&NHX:TOL=118978],satyrium caryaevorus[&&NHX:TOL=118987],satyrium edwardsii[&&NHX:TOL=118988],satyrium favonius[&&NHX:TOL=118979],satyrium fuliginosa[&&NHX:TOL=118989],satyrium ilavia[&&NHX:TOL=118980],satyrium kingi[&&NHX:TOL=118990],satyrium liparops[&&NHX:TOL=118991],satyrium polingi[&&NHX:TOL=118981],satyrium saepium[&&NHX:TOL=118982],satyrium sylvinus[&&NHX:TOL=119009],satyrium tetra[&&NHX:TOL=118983],satyrium titus[&&NHX:TOL=118992])nearctic satyrium[&&NHX:TOL=119017],((satyrium hyrcanica[&&NHX:TOL=119003],satyrium ledereri[&&NHX:TOL=119004])armenia[&&NHX:TOL=119019],(satyrium aeto[&&NHX:TOL=119021],satyrium baidula[&&NHX:TOL=119022],satyrium carbonaria[&&NHX:TOL=119023],satyrium davidi[&&NHX:TOL=119024],satyrium eckweileri[&&NHX:TOL=119025],satyrium falkovitshi[&&NHX:TOL=119026],satyrium iliensis[&&NHX:TOL=119027],satyrium irkuta[&&NHX:TOL=119028],satyrium lunara[&&NHX:TOL=119029],satyrium medea[&&NHX:TOL=119030],satyrium olga[&&NHX:TOL=119031],satyrium pretiosa[&&NHX:TOL=119032],satyrium rhymnus[&&NHX:TOL=119033],satyrium sajana[&&NHX:TOL=119034],satyrium sinensis[&&NHX:TOL=119035],satyrium submontana[&&NHX:TOL=119036],satyrium tengstroemi[&&NHX:TOL=119037])neolycaena[&&NHX:TOL=119020],(satyrium abdomnalis[&&NHX:TOL=118993],satyrium acaciae[&&NHX:TOL=118994],satyrium eximia[&&NHX:TOL=118995],satyrium herzi[&&NHX:TOL=118996],satyrium ilicis[&&NHX:TOL=118997],satyrium latior[&&NHX:TOL=118998],satyrium pruni[&&NHX:TOL=118999],satyrium prunoides[&&NHX:TOL=119000],satyrium spini[&&NHX:TOL=119001],satyrium walbum[&&NHX:TOL=119002])nordmannia[&&NHX:TOL=119038],(satyrium acaudata[&&NHX:TOL=119005],satyrium goniopterum[&&NHX:TOL=119006],satyrium sassanides[&&NHX:TOL=119008],satyrium lunulata[&&NHX:TOL=119007])superflua[&&NHX:TOL=119039],satyrium esculi[&&NHX:TOL=119011],satyrium grandis[&&NHX:TOL=119012],satyrium jebelia[&&NHX:TOL=119013],satyrium iyonis[&&NHX:TOL=119014],satyrium mackwoodi[&&NHX:TOL=119015],satyrium oenone[&&NHX:TOL=119016])palaearcticoriental satyrium[&&NHX:TOL=119018])satyrium[&&NHX:TOL=112413],phaeostrymon alcestis[&&NHX:TOL=112420],(ocaria aholiba[&&NHX:TOL=119050],ocaria arcula[&&NHX:TOL=119051],ocaria arpoxais[&&NHX:TOL=119052],ocaria calesia[&&NHX:TOL=119053],ocaria cinerea[&&NHX:TOL=119054],ocaria clenchi[&&NHX:TOL=119063],ocaria clepsydra[&&NHX:TOL=119055],ocaria elongata[&&NHX:TOL=119056],ocaria elvira[&&NHX:TOL=119057],ocaria ocrisia[&&NHX:TOL=119058],ocaria petelina[&&NHX:TOL=119059],ocaria sadiei[&&NHX:TOL=119060],ocaria thales[&&NHX:TOL=119061],3 undescribed ocaria species[&&NHX:TOL=119062])ocaria[&&NHX:TOL=112459],(chlorostrymon clenchi[&&NHX:TOL=118955],chlorostrymon kuscheli[&&NHX:TOL=118956],chlorostrymon maesites[&&NHX:TOL=118957],chlorostrymon orbis[&&NHX:TOL=118958],chlorostrymon simaethis[&&NHX:TOL=118959],chlorostrymon telea[&&NHX:TOL=118960])chlorostrymon[&&NHX:TOL=112416],(magnastigma elsa[&&NHX:TOL=118952],magnastigma hirsuta[&&NHX:TOL=118953],magnastigma julia[&&NHX:TOL=118954])magnastigma[&&NHX:TOL=112456])satyrium section[&&NHX:TOL=112992],((erora aura[&&NHX:TOL=119618],erora badeta[&&NHX:TOL=119619],erora biblia[&&NHX:TOL=119620],erora caespes[&&NHX:TOL=119621],erora campa[&&NHX:TOL=119622],erora carla[&&NHX:TOL=119623],erora facuna[&&NHX:TOL=119624],erora gabina[&&NHX:TOL=119625],erora laeta[&&NHX:TOL=119626],erora lampetia[&&NHX:TOL=119627],erora lorina[&&NHX:TOL=119628],erora melba[&&NHX:TOL=119629],erora muridosca[&&NHX:TOL=119630],erora nana[&&NHX:TOL=119631],erora nitetis[&&NHX:TOL=119632],erora opisena[&&NHX:TOL=119633],erora phrosine[&&NHX:TOL=119634],erora quaderna[&&NHX:TOL=119635],erora senta[&&NHX:TOL=119636],erora subflorens[&&NHX:TOL=119637],erora tella[&&NHX:TOL=119638],13 undescribed species[&&NHX:TOL=119639])erora[&&NHX:TOL=112410],(semonina ares[&&NHX:TOL=119640],semonina semones[&&NHX:TOL=119641],2 undescribed semonina species[&&NHX:TOL=119642])semonina[&&NHX:TOL=112994],(chalybs chloris[&&NHX:TOL=119643],chalybs hassan[&&NHX:TOL=119644],chalybs janias[&&NHX:TOL=119645],chalybs lineata[&&NHX:TOL=119646])chalybs[&&NHX:TOL=112995],(symbiopsis aprica[&&NHX:TOL=119647],symbiopsis lenitas[&&NHX:TOL=119648],symbiopsis? nivepunctata[&&NHX:TOL=119649],symbiopsis morpho[&&NHX:TOL=119650],symbiopsis panamensis[&&NHX:TOL=119651],symbiopsis pencilatus[&&NHX:TOL=119652],symbiopsis pentas[&&NHX:TOL=119653],symbiopsis perulera[&&NHX:TOL=119654],symbiopsis pupilla[&&NHX:TOL=119655],symbiopsis rickmani[&&NHX:TOL=119656],symbiopsis strenua[&&NHX:TOL=119657],symbiopsis tanais[&&NHX:TOL=119658],5 undescribed symbiopsis species[&&NHX:TOL=119659])symbiopsis[&&NHX:TOL=112438])erora section[&&NHX:TOL=112993],(((callophrys dospassosi[&&NHX:TOL=119082],callophrys estela[&&NHX:TOL=119085],callophrys gryneus[&&NHX:TOL=119087],callophrys guatemalena[&&NHX:TOL=119088],callophrys hesseli[&&NHX:TOL=119090],callophrys johnsoni[&&NHX:TOL=119092],callophrys muiri[&&NHX:TOL=119096],callophrys nelsoni[&&NHX:TOL=119097],callophrys spinetorum[&&NHX:TOL=119103],callophrys thornei[&&NHX:TOL=119104])nearctic mitoura[&&NHX:TOL=119116],(callophrys augustinus[&&NHX:TOL=119081],callophrys eryphon[&&NHX:TOL=119084],callophrys fotis[&&NHX:TOL=119086],callophrys henrici[&&NHX:TOL=119089],callophrys irus[&&NHX:TOL=119091],callophrys lanoraieensis[&&NHX:TOL=119093],callophrys mossii[&&NHX:TOL=119095],callophrys niphon[&&NHX:TOL=119098],callophrys polios[&&NHX:TOL=119100])nearctic incisalia[&&NHX:TOL=119117],(callophrys affinis[&&NHX:TOL=119080],callophrys dumetorum[&&NHX:TOL=119083],callophrys perplexa[&&NHX:TOL=119099],callophrys mcfarlandi[&&NHX:TOL=119094],callophrys scaphia[&&NHX:TOL=119101],callophrys sheridanii[&&NHX:TOL=119102],callophrys xami[&&NHX:TOL=119105])nearctic callophrys[&&NHX:TOL=119118],(callophrys armeniaca[&&NHX:TOL=119106],callophrys avis[&&NHX:TOL=119107],callophrys butlerovi[&&NHX:TOL=119108],callophrys chalybeitincta[&&NHX:TOL=119109],callophrys danchenkoi[&&NHX:TOL=119110],callophrys hatuma[&&NHX:TOL=119111],callophrys paulae[&&NHX:TOL=119112],callophrys rubi[&&NHX:TOL=119113],callophrys suaveola[&&NHX:TOL=119114],callophrys titanus[&&NHX:TOL=119115])palearctic callophrys[&&NHX:TOL=119119],(callophrys aleucopuncta[&&NHX:TOL=119121],callophrys arquata[&&NHX:TOL=119122],callophrys bimaculata[&&NHX:TOL=119123],callophrys caerulea[&&NHX:TOL=119124],callophrys caesius[&&NHX:TOL=119125],callophrys chalcidis[&&NHX:TOL=119126],callophrys chalybeia[&&NHX:TOL=119127],callophrys circe[&&NHX:TOL=119128],callophrys clarofacia[&&NHX:TOL=119129],callophrys distincta[&&NHX:TOL=119130],callophrys ferrea[&&NHX:TOL=119131],callophrys frivaldszkyi[&&NHX:TOL=119132],callophrys haradai[&&NHX:TOL=119133],callophrys hsui[&&NHX:TOL=119134],callophrys korea[&&NHX:TOL=119135],callophrys leechii[&&NHX:TOL=119136],callophrys leei[&&NHX:TOL=119137],callophrys lynda[&&NHX:TOL=119138],callophrys nicevillei[&&NHX:TOL=119139],callophrys pictila[&&NHX:TOL=119140],callophrys pluto[&&NHX:TOL=119141],callophrys prodiga[&&NHX:TOL=119142],callophrys unicolora[&&NHX:TOL=119143],callophrys zhujianhuai[&&NHX:TOL=119144])palearcticoriental ahlbergia[&&NHX:TOL=119120])callophrys[&&NHX:TOL=112407],(cyanophrys acaste[&&NHX:TOL=119064],cyanophrys agricolor[&&NHX:TOL=119065],cyanophrys amyntor[&&NHX:TOL=119066],cyanophrys argentinensis[&&NHX:TOL=119067],cyanophrys bertha[&&NHX:TOL=119068],cyanophrys banosensis[&&NHX:TOL=119069],cyanophrys crethona[&&NHX:TOL=119070],cyanophrys fusius[&&NHX:TOL=119071],cyanophrys goodsoni[&&NHX:TOL=119072],cyanophrys herodotus[&&NHX:TOL=119073],cyanophrys longula[&&NHX:TOL=119074],cyanophrys miserabilis[&&NHX:TOL=119075],cyanophrys pseudolongula[&&NHX:TOL=119076],cyanophrys remus[&&NHX:TOL=119077],cyanophrys roraimiensis[&&NHX:TOL=119078],cyanophrys velezi[&&NHX:TOL=119079])cyanophrys[&&NHX:TOL=112415])callophrys section[&&NHX:TOL=112996],((micandra aegides[&&NHX:TOL=118532],micandra comae[&&NHX:TOL=118533],micandra cyda[&&NHX:TOL=118534],micandra dignota[&&NHX:TOL=118535],micandra extrema[&&NHX:TOL=118536],micandra ion[&&NHX:TOL=118537],micandra platyptera[&&NHX:TOL=118538],micandra sylvana[&&NHX:TOL=118539],micandra tongida[&&NHX:TOL=118540],sp. n.?[&&NHX:TOL=118541])micandra[&&NHX:TOL=112462],(ipidecla crepundia[&&NHX:TOL=118529],ipidecla miadora[&&NHX:TOL=118530],ipidecla schausi[&&NHX:TOL=118531])ipidecla[&&NHX:TOL=112439],(johnsonita assula[&&NHX:TOL=118514],johnsonita auda[&&NHX:TOL=118515],johnsonita catadupa[&&NHX:TOL=118516],johnsonita chlamydem[&&NHX:TOL=118517],johnsonita johnsoni[&&NHX:TOL=118518],johnsonita pardoa[&&NHX:TOL=118519],9 undescribed species[&&NHX:TOL=118520])johnsonita[&&NHX:TOL=112998],(brevianta busa[&&NHX:TOL=118521],brevianta celelata[&&NHX:TOL=118522],brevianta ematheon[&&NHX:TOL=118523],brevianta hyas[&&NHX:TOL=118524],brevianta perpenna[&&NHX:TOL=118525],brevianta tolmides[&&NHX:TOL=118526],brevianta undulata[&&NHX:TOL=118527],brevianta undulella[&&NHX:TOL=118528])brevianta[&&NHX:TOL=112999],(timaeta aepea[&&NHX:TOL=118542],timaeta balzapampa[&&NHX:TOL=118543],timaeta eronos[&&NHX:TOL=118544],timaeta molinopampa[&&NHX:TOL=118545],timaeta timaeus[&&NHX:TOL=118546],timaeta trochus[&&NHX:TOL=118547],timaeta werneri[&&NHX:TOL=118548],7 undescribed timaeta species[&&NHX:TOL=118549])timaeta[&&NHX:TOL=113000],(rhamma adriana[&&NHX:TOL=118562],rhamma adunca[&&NHX:TOL=118563],rhamma amethystina[&&NHX:TOL=118564],rhamma ? anosma[&&NHX:TOL=118565],rhamma arria[&&NHX:TOL=118566],rhamma aurugo[&&NHX:TOL=118567],rhamma bilix[&&NHX:TOL=118568],rhamma brunea[&&NHX:TOL=118569],rhamma catamarca[&&NHX:TOL=118570],rhamma commodus[&&NHX:TOL=118571],rhamma comstocki[&&NHX:TOL=118572],rhamma confusa[&&NHX:TOL=118573],rhamma coquimbiensis[&&NHX:TOL=118574],rhamma familiaris[&&NHX:TOL=118575],rhamma hybla[&&NHX:TOL=118576],rhamma inexpectata[&&NHX:TOL=118577],rhamma lapazensis[&&NHX:TOL=118578],rhamma livida[&&NHX:TOL=118579],rhamma ? magenta[&&NHX:TOL=118580],rhamma mishma[&&NHX:TOL=118581],rhamma nigrasarotina[&&NHX:TOL=118582],rhamma oxida[&&NHX:TOL=118583],rhamma shapiroi[&&NHX:TOL=118584],rhamma tarma[&&NHX:TOL=118585],rhamma ? tolimensis[&&NHX:TOL=118586],rhamma tyrrius[&&NHX:TOL=118587],1 undescribed rhamma species[&&NHX:TOL=118588])rhamma[&&NHX:TOL=113001],(phothecla photismos[&&NHX:TOL=118550],phothecla thespia[&&NHX:TOL=118551])phothecla[&&NHX:TOL=113002],(salazaria elizabetha[&&NHX:TOL=118552],salazaria sala[&&NHX:TOL=118553],5 undescribed salazaria species[&&NHX:TOL=118554])salazaria[&&NHX:TOL=113003],(temecla bennetti[&&NHX:TOL=118555],temecla heraclides[&&NHX:TOL=118556],temecla paron[&&NHX:TOL=118557],temecla peona[&&NHX:TOL=118558],temecla sergius[&&NHX:TOL=118559],temecla tema[&&NHX:TOL=118560],3 undescribed species[&&NHX:TOL=118561])temecla[&&NHX:TOL=113004],(penaincisalia alatus[&&NHX:TOL=118589],penaincisalia albalineata[&&NHX:TOL=118590],penaincisalia amatista[&&NHX:TOL=118591],penaincisalia atymna[&&NHX:TOL=118592],penaincisalia atymnides[&&NHX:TOL=118593],penaincisalia aurulenta[&&NHX:TOL=118594],penaincisalia balzapampa[&&NHX:TOL=118595],penaincisalia bimediana[&&NHX:TOL=118596],penaincisalia browni[&&NHX:TOL=118597],penaincisalia caudata[&&NHX:TOL=118598],penaincisalia cillutincarae[&&NHX:TOL=118599],penaincisalia culminicola[&&NHX:TOL=118600],penaincisalia descimoni[&&NHX:TOL=118601],penaincisalia downeyi[&&NHX:TOL=118602],penaincisalia lamasi[&&NHX:TOL=118603],penaincisalia loxurina[&&NHX:TOL=118604],penaincisalia magnifica[&&NHX:TOL=118605],penaincisalia penai[&&NHX:TOL=118606],penaincisalia perezi[&&NHX:TOL=118607],penaincisalia purpurea[&&NHX:TOL=118608],penaincisalia rawlinsi[&&NHX:TOL=118609],penaincisalia saraha[&&NHX:TOL=118610],penaincisalia swarthea[&&NHX:TOL=118611],penaincisalia vittata[&&NHX:TOL=118612],18 undescribed species[&&NHX:TOL=118613])penaincisalia[&&NHX:TOL=113005],(podanotum ? andrewneildi[&&NHX:TOL=118614],podanotum clarissimus[&&NHX:TOL=118615],podanotum glorissimum[&&NHX:TOL=118616],podanotum metallicus[&&NHX:TOL=118617],podanotum ? paramosa[&&NHX:TOL=118618],podanotum salaeides[&&NHX:TOL=118619],podanotum vanewrighti[&&NHX:TOL=118620],4 undescribed species[&&NHX:TOL=118621])podanotum[&&NHX:TOL=113006],busbiina bosora[&&NHX:TOL=113007])micandra section[&&NHX:TOL=112997])eumaeini[&&NHX:TOL=111502],((((((deudorix ceramensis[&&NHX:TOL=121100],deudorix epirus[&&NHX:TOL=121101],deudorix maudei[&&NHX:TOL=121102],deudorix niepelti[&&NHX:TOL=121103])deudorix epirus group[&&NHX:TOL=121099],deudorix apayao[&&NHX:TOL=121020],deudorix cleora[&&NHX:TOL=121104],deudorix diara[&&NHX:TOL=121105],deudorix diovis[&&NHX:TOL=121106],deudorix elioti[&&NHX:TOL=121021],deudorix epijarbas[&&NHX:TOL=121022],deudorix gaetulia[&&NHX:TOL=121107],deudorix hainana[&&NHX:TOL=121108],deudorix hypargyria[&&NHX:TOL=121023],deudorix isocrates[&&NHX:TOL=121109],deudorix littoralis[&&NHX:TOL=121110],deudorix loxius[&&NHX:TOL=121111],deudorix mulleri[&&NHX:TOL=121112],deudorix novellus[&&NHX:TOL=121113],deudorix philippinensis[&&NHX:TOL=121024],deudorix rapaloides[&&NHX:TOL=121114],deudorix sumatrensis[&&NHX:TOL=121025],deudorix staudingeri[&&NHX:TOL=121026],deudorix viridens[&&NHX:TOL=121115],deudorix woodfordi[&&NHX:TOL=121116])subgenus deudorix[&&NHX:TOL=121098],((deudorix democles[&&NHX:TOL=121119],deudorix dohertyi[&&NHX:TOL=121120],deudorix kessuma[&&NHX:TOL=121121],deudorix masamichii[&&NHX:TOL=121122],deudorix perse[&&NHX:TOL=121123],deudorix smilis[&&NHX:TOL=121124],deudorix subguttata[&&NHX:TOL=121125])orientalaustralasian virachola[&&NHX:TOL=121118],(deudorix antalus[&&NHX:TOL=121127],deudorix badhami[&&NHX:TOL=121128],deudorix baronica[&&NHX:TOL=121129],deudorix batikeli[&&NHX:TOL=121130],deudorix batikelides[&&NHX:TOL=121131],deudorix caliginosa[&&NHX:TOL=121132],deudorix chalybeata[&&NHX:TOL=121133],deudorix dariaves[&&NHX:TOL=121134],deudorix dinochares[&&NHX:TOL=121135],deudorix dinomenes[&&NHX:TOL=121136],deudorix diocles[&&NHX:TOL=121137],deudorix ecaudata[&&NHX:TOL=121138],deudorix edwardsi[&&NHX:TOL=121139],deudorix galathea[&&NHX:TOL=121140],deudorix jacksoni[&&NHX:TOL=121141],deudorix kayonza[&&NHX:TOL=121142],deudorix livia[&&NHX:TOL=121143],deudorix lorisona[&&NHX:TOL=121144],deudorix magda[&&NHX:TOL=121145],deudorix montana[&&NHX:TOL=121146],deudorix mpanda[&&NHX:TOL=121147],deudorix nicephora[&&NHX:TOL=121148],deudorix odana[&&NHX:TOL=121149],deudorix penningtoni[&&NHX:TOL=121150],deudorix renidens[&&NHX:TOL=121151],deudorix suk[&&NHX:TOL=121152],deudorix ufipa[&&NHX:TOL=121153],deudorix vansomereni[&&NHX:TOL=121154],deudorix vansoni[&&NHX:TOL=121155],deudorix wardi[&&NHX:TOL=121156])afrotropical virachola[&&NHX:TOL=121126])subgenus virachola[&&NHX:TOL=121117])deudorix[&&NHX:TOL=112465],(artipe anna[&&NHX:TOL=121027],artipe dohertyi[&&NHX:TOL=121028],artipe eryx[&&NHX:TOL=121029],artipe grandis[&&NHX:TOL=121030])artipe[&&NHX:TOL=112466],(hypomyrina fournierae[&&NHX:TOL=121031],hypomyrina mimetica[&&NHX:TOL=121032],hypomyrina nomenia[&&NHX:TOL=121033],hypomyrina nomion[&&NHX:TOL=121034])hypomyrina[&&NHX:TOL=112467],((paradeudorix boormani[&&NHX:TOL=121036],paradeudorix ituri[&&NHX:TOL=121037],paradeudorix marginata[&&NHX:TOL=121038],paradeudorix michelae[&&NHX:TOL=121039])paradeudorix ituri group[&&NHX:TOL=121035],(paradeudorix cobaltina[&&NHX:TOL=121041],paradeudorix eleala[&&NHX:TOL=121042],paradeudorix elealodes[&&NHX:TOL=121043],paradeudorix petersi[&&NHX:TOL=121044])paradeudorix eleala group[&&NHX:TOL=121040],paradeudorix moyambina[&&NHX:TOL=121045],paradeudorix infuscata[&&NHX:TOL=121048],paradeudorix kafuensis[&&NHX:TOL=121049],paradeudorix kallipygos[&&NHX:TOL=121050],paradeudorix ugandae[&&NHX:TOL=121157])paradeudorix[&&NHX:TOL=112471],(sithon micea[&&NHX:TOL=121277],sithon nedymond[&&NHX:TOL=121278])sithon[&&NHX:TOL=112472],(sinthusa aspra[&&NHX:TOL=121325],sinthusa chandrana[&&NHX:TOL=121326],sinthusa indrasari[&&NHX:TOL=121327],sinthusa malika[&&NHX:TOL=121328],sinthusa menglaensis[&&NHX:TOL=121329],sinthusa mindanensis[&&NHX:TOL=121330],sinthusa nasaka[&&NHX:TOL=121331],sinthusa natsumiae[&&NHX:TOL=121332],sinthusa peregrinus[&&NHX:TOL=121333],sinthusa privata[&&NHX:TOL=121334],sinthusa rayata[&&NHX:TOL=121335],sinthusa tomokoae[&&NHX:TOL=121336],sinthusa verriculata[&&NHX:TOL=121337],sinthusa virgo[&&NHX:TOL=121338],sinthusa zhejiangensis[&&NHX:TOL=121339])sinthusa[&&NHX:TOL=112473],(araotes lapithis[&&NHX:TOL=121340],araotes perrhaebis[&&NHX:TOL=121341])araotes[&&NHX:TOL=112475],(bindahara meeki[&&NHX:TOL=121279],bindahara phocides[&&NHX:TOL=121280])bindahara[&&NHX:TOL=112476],(rapala abnormis[&&NHX:TOL=121281],rapala arata[&&NHX:TOL=121282],rapala buxaria[&&NHX:TOL=121283],rapala caerulea[&&NHX:TOL=121284],rapala caerulescens[&&NHX:TOL=121285],rapala cassidyi[&&NHX:TOL=121286],rapala cowani[&&NHX:TOL=121287],rapala damona[&&NHX:TOL=121288],rapala dieneces[&&NHX:TOL=121289],rapala dioetas[&&NHX:TOL=121290],rapala diopites[&&NHX:TOL=121291],rapala domitia[&&NHX:TOL=121292],rapala elcia[&&NHX:TOL=121293],rapala enipeus[&&NHX:TOL=121294],rapala extensa[&&NHX:TOL=121295],rapala hades[&&NHX:TOL=121296],rapala hinomaru[&&NHX:TOL=121297],rapala iarbus[&&NHX:TOL=121298],rapala lankana[&&NHX:TOL=121299],rapala manea[&&NHX:TOL=121300],rapala masara[&&NHX:TOL=121301],rapala melida[&&NHX:TOL=121302],rapala micans[&&NHX:TOL=121303],rapala nemorensis[&&NHX:TOL=121304],rapala nissa[&&NHX:TOL=121305],rapala pheretima[&&NHX:TOL=121306],rapala refulgens[&&NHX:TOL=121307],rapala renata[&&NHX:TOL=121308],rapala rhoda[&&NHX:TOL=121309],rapala rhoecus[&&NHX:TOL=121310],rapala rhodopis[&&NHX:TOL=121311],rapala ribbei[&&NHX:TOL=121312],rapala rosacea[&&NHX:TOL=121313],rapala rubida[&&NHX:TOL=121314],rapala scintilla[&&NHX:TOL=121315],rapala selira[&&NHX:TOL=121316],rapala sphinx[&&NHX:TOL=121317],rapala subpurpurea[&&NHX:TOL=121318],rapala suffusa[&&NHX:TOL=121319],rapala takasagonis[&&NHX:TOL=121320],rapala tara[&&NHX:TOL=121321],rapala tomokoae[&&NHX:TOL=121322],rapala varuna[&&NHX:TOL=121323],rapala zamona[&&NHX:TOL=121324])rapala[&&NHX:TOL=112477],(pilodeudorix ankoleensis[&&NHX:TOL=121053],pilodeudorix aruma[&&NHX:TOL=121079],pilodeudorix azurea[&&NHX:TOL=121046],pilodeudorix bemba[&&NHX:TOL=121054],pilodeudorix camerona[&&NHX:TOL=121055],pilodeudorix canescens[&&NHX:TOL=121047],((pilodeudorix aucta[&&NHX:TOL=121082],pilodeudorix aurivilliusi[&&NHX:TOL=121083],pilodeudorix curruscans[&&NHX:TOL=121084],pilodeudorix deritas[&&NHX:TOL=121085],pilodeudorix hugoi[&&NHX:TOL=121086],pilodeudorix kiellandi[&&NHX:TOL=121087],pilodeudorix laticlavia[&&NHX:TOL=121088],pilodeudorix pseudoderitas[&&NHX:TOL=121089])[&&NHX:TOL=121081],(pilodeudorix catalla[&&NHX:TOL=121091],pilodeudorix violetta[&&NHX:TOL=121092])[&&NHX:TOL=121090],pilodeudorix fumata[&&NHX:TOL=121093],pilodeudorix kedassa[&&NHX:TOL=121094],pilodeudorix nirmo[&&NHX:TOL=121095],pilodeudorix pasteon[&&NHX:TOL=121096],pilodeudorix sadeska[&&NHX:TOL=121097])pilodeudorix deritas group[&&NHX:TOL=121080],(pilodeudorix caerulea[&&NHX:TOL=121057],pilodeudorix congoana[&&NHX:TOL=121058],pilodeudorix diyllus[&&NHX:TOL=121059],pilodeudorix obscurata[&&NHX:TOL=121158])pilodeudorix diyllus group[&&NHX:TOL=121056],pilodeudorix ducarmei[&&NHX:TOL=121159],pilodeudorix kohli[&&NHX:TOL=121060],(pilodeudorix angelita[&&NHX:TOL=121072],pilodeudorix mera[&&NHX:TOL=121073])pilodeudorix mera group[&&NHX:TOL=121071],(pilodeudorix baginei[&&NHX:TOL=121161],pilodeudorix mimeta[&&NHX:TOL=121162])pilodeudorix mimeta group[&&NHX:TOL=121160],pilodeudorix nyanzana[&&NHX:TOL=121051],(pilodeudorix leonina[&&NHX:TOL=121075],pilodeudorix otraeda[&&NHX:TOL=121076])pilodeudorix otraeda group[&&NHX:TOL=121074],pilodeudorix rodgersi[&&NHX:TOL=121061],pilodeudorix tenuivittata[&&NHX:TOL=121163],pilodeudorix ula[&&NHX:TOL=121078],pilodeudorix ultramarina[&&NHX:TOL=121164],pilodeudorix virgata[&&NHX:TOL=121077],((pilodeudorix anetia[&&NHX:TOL=121064],pilodeudorix catori[&&NHX:TOL=121065],pilodeudorix hamidou[&&NHX:TOL=121066])[&&NHX:TOL=121063],(pilodeudorix zela[&&NHX:TOL=121068],pilodeudorix zeloides[&&NHX:TOL=121069])[&&NHX:TOL=121067])pilodeudorix zela group[&&NHX:TOL=121062],pilodeudorix zelomina[&&NHX:TOL=121070])pilodeudorix[&&NHX:TOL=121052])deudorix section[&&NHX:TOL=112464],((capys alphaeus[&&NHX:TOL=121259],capys bamendanus[&&NHX:TOL=121260],capys bamptoni[&&NHX:TOL=121261],capys brunneus[&&NHX:TOL=121262],capys calpurnia[&&NHX:TOL=121263],capys catharus[&&NHX:TOL=121264],capys collinsi[&&NHX:TOL=121265],capys connexivus[&&NHX:TOL=121266],capys cupreus[&&NHX:TOL=121267],capys disjunctus[&&NHX:TOL=121268],capys hermes[&&NHX:TOL=121269],capys juliae[&&NHX:TOL=121270],capys meruensis[&&NHX:TOL=121271],capys penningtoni[&&NHX:TOL=121272],capys stuarti[&&NHX:TOL=121273],capys vorgasi[&&NHX:TOL=121274],capys usambarae[&&NHX:TOL=121275],[&&NHX:TOL=121276])capys[&&NHX:TOL=112479],pamela dudgeoni[&&NHX:TOL=112480])capys section[&&NHX:TOL=112478])deudorigini[&&NHX:TOL=111500],(tomares ballus[&&NHX:TOL=117944],tomares callimachus[&&NHX:TOL=117945],tomares desinens[&&NHX:TOL=117946],tomares fedtshenkoi[&&NHX:TOL=117947],tomares mauretanicus[&&NHX:TOL=117948],tomares nogelii[&&NHX:TOL=117949],tomares romanovi[&&NHX:TOL=117950],tomares telemachus[&&NHX:TOL=117951])tomares[&&NHX:TOL=111501])[&&NHX:TOL=111531])[&&NHX:TOL=111530])theclinae[&&NHX:TOL=106372])[&&NHX:TOL=12179])[&&NHX:TOL=121717])[&&NHX:TOL=103503])lycaenidae[&&NHX:TOL=12175])[&&NHX:TOL=12173],((((((((parthenos tigrina[&&NHX:TOL=70347],parthenos sylvia[&&NHX:TOL=70348],parthenos aspila[&&NHX:TOL=70349])parthenos[&&NHX:TOL=70346],bhagadatta austenia[&&NHX:TOL=70350],lebadea martha[&&NHX:TOL=88084])parthenini[&&NHX:TOL=70194],((pseudacraea acholica[&&NHX:TOL=86791],pseudacraea annakae[&&NHX:TOL=86792],pseudacraea boisduvalii[&&NHX:TOL=86793],pseudacraea clarkii[&&NHX:TOL=86794],pseudacraea deludens[&&NHX:TOL=86795],pseudacraea dolomena[&&NHX:TOL=86796],pseudacraea eurytus[&&NHX:TOL=86797],pseudacraea imerina[&&NHX:TOL=86798],pseudacraea hostilia[&&NHX:TOL=86799],pseudacraea kuenowii[&&NHX:TOL=86800],pseudacraea lucretia[&&NHX:TOL=86801],pseudacraea poggei[&&NHX:TOL=86802],pseudacraea semire[&&NHX:TOL=86803],pseudacraea warburgi[&&NHX:TOL=86804],pseudacraea peyrierasi[&&NHX:TOL=93867])pseudacraea[&&NHX:TOL=70196],(((cymothoe oemilius[&&NHX:TOL=87243],((cymothoe beckeri[&&NHX:TOL=87198],cymothoe fumana[&&NHX:TOL=87217],cymothoe heliada[&&NHX:TOL=87222],cymothoe owassae[&&NHX:TOL=87246])[&&NHX:TOL=118754],(cymothoe egesta[&&NHX:TOL=87212],cymothoe hyarbita[&&NHX:TOL=87228],cymothoe lucasii[&&NHX:TOL=87235],cymothoe orphnina[&&NHX:TOL=87245],cymothoe reinholdi[&&NHX:TOL=87251])[&&NHX:TOL=118755])cymothoe egesta group[&&NHX:TOL=118753],(cymothoe hesiodina[&&NHX:TOL=87224],cymothoe hesiodotus[&&NHX:TOL=87225],cymothoe hypatha[&&NHX:TOL=87229],cymothoe lurida[&&NHX:TOL=87236])cymothoe lurida group[&&NHX:TOL=118756],(cymothoe adela[&&NHX:TOL=87186],cymothoe aubergeri[&&NHX:TOL=87196],cymothoe capella[&&NHX:TOL=87200])cymothoe capella group[&&NHX:TOL=118757],(cymothoe althea[&&NHX:TOL=87188],cymothoe alticola[&&NHX:TOL=118759],cymothoe caenis[&&NHX:TOL=87199],cymothoe consanguis[&&NHX:TOL=87206],cymothoe herminia[&&NHX:TOL=87223],cymothoe indamora[&&NHX:TOL=87230],cymothoe weymeri[&&NHX:TOL=87256],cymothoe zenkeri[&&NHX:TOL=87257])cymothoe althea group[&&NHX:TOL=118758],cymothoe jodutta[&&NHX:TOL=87232],cymothoe alcimeda[&&NHX:TOL=87187],cymothoe altisidora[&&NHX:TOL=87189],cymothoe amaniensis[&&NHX:TOL=87190],cymothoe amenides[&&NHX:TOL=87191],cymothoe angulifasciata[&&NHX:TOL=87192],((cymothoe anitorgis[&&NHX:TOL=87193],cymothoe haimodia[&&NHX:TOL=87218],cymothoe hartigi[&&NHX:TOL=87220])[&&NHX:TOL=118761],(cymothoe aramis[&&NHX:TOL=87194],cymothoe coccinata[&&NHX:TOL=87202],cymothoe excelsa[&&NHX:TOL=87215],cymothoe mabillei[&&NHX:TOL=87237],cymothoe ogova[&&NHX:TOL=87244],cymothoe preussi[&&NHX:TOL=87247])[&&NHX:TOL=118762],(cymothoe euthalioides[&&NHX:TOL=87214],cymothoe hobarthi[&&NHX:TOL=87226],cymothoe magnus[&&NHX:TOL=87239],cymothoe sangaris[&&NHX:TOL=87252])[&&NHX:TOL=118763])cymothoe sangaris group[&&NHX:TOL=118760],cymothoe arcuata[&&NHX:TOL=87195],cymothoe aurivillii[&&NHX:TOL=87197],cymothoe caprina[&&NHX:TOL=87201],cymothoe collarti[&&NHX:TOL=87203],cymothoe collinsi[&&NHX:TOL=87204],cymothoe colmanti[&&NHX:TOL=87205],cymothoe coranus[&&NHX:TOL=87207],cymothoe cottrelli[&&NHX:TOL=87208],cymothoe crocea[&&NHX:TOL=87209],cymothoe cyclades[&&NHX:TOL=87210],cymothoe dujardini[&&NHX:TOL=93866],cymothoe distincta[&&NHX:TOL=87211],cymothoe eris[&&NHX:TOL=87213],cymothoe fontainei[&&NHX:TOL=87216],cymothoe harmilla[&&NHX:TOL=87219],cymothoe haynae[&&NHX:TOL=87221],cymothoe howarthi[&&NHX:TOL=87227],cymothoe isiro[&&NHX:TOL=87231],cymothoe kraepelini[&&NHX:TOL=87233],cymothoe lambertoni[&&NHX:TOL=87234],cymothoe magambae[&&NHX:TOL=87238],cymothoe melanjae[&&NHX:TOL=87240],cymothoe meridionalis[&&NHX:TOL=87241],cymothoe ochreata[&&NHX:TOL=87242],cymothoe radialis[&&NHX:TOL=87248],cymothoe rebeli[&&NHX:TOL=87249],cymothoe reginaelisabethae[&&NHX:TOL=87250],cymothoe sassiana[&&NHX:TOL=87253],cymothoe teita[&&NHX:TOL=87254],cymothoe vumbui[&&NHX:TOL=87255],cymothoe zombana[&&NHX:TOL=87258])cymothoe[&&NHX:TOL=70386],harma theobene[&&NHX:TOL=70387])[&&NHX:TOL=70385],((alania deliquata[&&NHX:TOL=88184],aldania ilos[&&NHX:TOL=88185],aldania imitans[&&NHX:TOL=88186],aldania raddei[&&NHX:TOL=88187],aldania themis[&&NHX:TOL=88188],aldania thisbe[&&NHX:TOL=88189],aldania yunnana[&&NHX:TOL=88190])aldania[&&NHX:TOL=70389],(pantoporia antara[&&NHX:TOL=88191],panoporia assamica[&&NHX:TOL=88192],pantoporia aurelia[&&NHX:TOL=88193],pantoporia bieti[&&NHX:TOL=88194],pantoporia consimilis[&&NHX:TOL=88195],pantoporia cyrilla[&&NHX:TOL=88196],pantoporia dama[&&NHX:TOL=88197],pantoporia dindinga[&&NHX:TOL=88198],pantoporia epira[&&NHX:TOL=88199],pantoporia hordonia[&&NHX:TOL=88200],pantoporia mysia[&&NHX:TOL=88201],pantoporia paraka[&&NHX:TOL=88202],pantoporia sandaka[&&NHX:TOL=88203],pantoporia venilia[&&NHX:TOL=88204])pantoporia[&&NHX:TOL=70390],(phaedyma amphion[&&NHX:TOL=88174],phaedyma ampliata[&&NHX:TOL=88175],phaedyma aspasia[&&NHX:TOL=88176],phaedyma chinga[&&NHX:TOL=88177],phaedyma columella[&&NHX:TOL=88178],phaedyma daria[&&NHX:TOL=88179],phaedyma fissizonata[&&NHX:TOL=88180],phaedyma heliopolis[&&NHX:TOL=88181],phaedyma mimetica[&&NHX:TOL=88182],phaedyma shepherdi[&&NHX:TOL=88183])phaedyma[&&NHX:TOL=70391],((neptis agouale[&&NHX:TOL=87123],neptis alta[&&NHX:TOL=87124],neptis aurivillii[&&NHX:TOL=87125],neptis biafra[&&NHX:TOL=87126],neptis camarensis[&&NHX:TOL=87127],neptis carpenteri[&&NHX:TOL=87128],neptis clarei[&&NHX:TOL=87129],neptis comorarum[&&NHX:TOL=87130],neptis conspicua[&&NHX:TOL=87131],neptis constantiae[&&NHX:TOL=87132],neptis continuata[&&NHX:TOL=87133],neptis declaryi[&&NHX:TOL=87134],neptis dentifera[&&NHX:TOL=87135],neptis dumetorum[&&NHX:TOL=87136],neptis eltringhami[&&NHX:TOL=87137],neptis exaleuca[&&NHX:TOL=87138],neptis frobenia[&&NHX:TOL=87139],neptis goochi[&&NHX:TOL=87140],neptis gratiosa[&&NHX:TOL=87141],neptis incongrua[&&NHX:TOL=87142],neptis infusa[&&NHX:TOL=87143],neptis jamesoni[&&NHX:TOL=87144],neptis jordani[&&NHX:TOL=87145],neptis katama[&&NHX:TOL=87146],neptis kikideli[&&NHX:TOL=87147],neptis kikuyuensis[&&NHX:TOL=87148],neptis kiriakoffi[&&NHX:TOL=87149],neptis laeta[&&NHX:TOL=87150],neptis lermanni[&&NHX:TOL=87151],neptis livingstonei[&&NHX:TOL=87152],neptis lugubris[&&NHX:TOL=87153],neptis mayottensis[&&NHX:TOL=87154],neptis melicerta[&&NHX:TOL=87155],neptis metanira[&&NHX:TOL=87156],neptis metella[&&NHX:TOL=87157],neptis mixophyes[&&NHX:TOL=87158],neptis morosa[&&NHX:TOL=87159],neptis nebrodes[&&NHX:TOL=87160],neptis nemetes[&&NHX:TOL=87161],neptis nicobule[&&NHX:TOL=87162],neptis nicomedes[&&NHX:TOL=87163],neptis nicoteles[&&NHX:TOL=87164],neptis nina[&&NHX:TOL=87165],neptis nysiades[&&NHX:TOL=87166],neptis occidentalis[&&NHX:TOL=87167],neptis ochracea[&&NHX:TOL=87168],neptis paula[&&NHX:TOL=87169],neptis penningtoni[&&NHX:TOL=87170],neptis poultoni[&&NHX:TOL=87171],neptis puella[&&NHX:TOL=87172],neptis roberti[&&NHX:TOL=87173],neptis rogersi[&&NHX:TOL=87174],neptis rothschildi[&&NHX:TOL=87175],neptis saclava[&&NHX:TOL=87176],neptis seeldrayersi[&&NHX:TOL=87177],neptis serena[&&NHX:TOL=87178],neptis sextilla[&&NHX:TOL=87179],neptis strigata[&&NHX:TOL=87180],neptis swynnertoni[&&NHX:TOL=87181],neptis trigonophora[&&NHX:TOL=87182],neptis troundi[&&NHX:TOL=87183],neptis vindo[&&NHX:TOL=87184],neptis woodwardi[&&NHX:TOL=87185])[&&NHX:TOL=88161],(neptis alwina[&&NHX:TOL=88086],neptis ananta[&&NHX:TOL=88087],neptis anjana[&&NHX:TOL=88088],neptis antilope[&&NHX:TOL=88089],neptis arachne[&&NHX:TOL=88090],neptis armandia[&&NHX:TOL=88091],neptis beroe[&&NHX:TOL=88092],neptis brebissonii[&&NHX:TOL=88093],neptis cartica[&&NHX:TOL=88094],neptis celebica[&&NHX:TOL=88095],neptis choui[&&NHX:TOL=88096],neptis clinia[&&NHX:TOL=88097],neptis clinioides[&&NHX:TOL=88098],neptis cydippe[&&NHX:TOL=88100],neptis cymela[&&NHX:TOL=88101],neptis dejeani[&&NHX:TOL=88102],neptis divisa[&&NHX:TOL=88103],neptis duryodana[&&NHX:TOL=88104],neptis felisimilis[&&NHX:TOL=88105],neptis gracilis[&&NHX:TOL=88106],neptis guia[&&NHX:TOL=88107],neptis harita[&&NHX:TOL=88108],neptis hesione[&&NHX:TOL=88109],neptis hylas[&&NHX:TOL=88110],neptis ida[&&NHX:TOL=88111],neptis ilira[&&NHX:TOL=88112],neptis leucoporos[&&NHX:TOL=88113],neptis magadha[&&NHX:TOL=88114],neptis mahendra[&&NHX:TOL=88115],neptis manasa[&&NHX:TOL=88116],neptis meloria[&&NHX:TOL=88117],neptis miah[&&NHX:TOL=88118],neptis mindorana[&&NHX:TOL=88119],neptis namba[&&NHX:TOL=88120],neptis narayana[&&NHX:TOL=88121],neptis nashona[&&NHX:TOL=88122],neptis nata[&&NHX:TOL=88123],neptis nausicaa[&&NHX:TOL=88124],neptis nemorosa[&&NHX:TOL=88125],neptis nemorum[&&NHX:TOL=88126],neptis nisaea[&&NHX:TOL=88127],neptis nitetis[&&NHX:TOL=88128],neptis noyala[&&NHX:TOL=88129],neptis nycteus[&&NHX:TOL=88130],neptis omeroda[&&NHX:TOL=88131],neptis pampanga[&&NHX:TOL=88132],neptis philyra[&&NHX:TOL=88133],neptis philyroides[&&NHX:TOL=88134],neptis praslini[&&NHX:TOL=88135],neptis pryeri[&&NHX:TOL=88136],neptis pseudovikasi[&&NHX:TOL=88137],neptis pseudonamba[&&NHX:TOL=88138],neptis radha[&&NHX:TOL=88139],neptis reducta[&&NHX:TOL=88140],neptis rivularis[&&NHX:TOL=88141],neptis sangangi[&&NHX:TOL=88142],neptis sankara[&&NHX:TOL=88143],neptis sappho[&&NHX:TOL=88144],neptis satina[&&NHX:TOL=88145],neptis sedata[&&NHX:TOL=88146],neptis sinocartica[&&NHX:TOL=88147],neptis soma[&&NHX:TOL=88148],neptis speyeri[&&NHX:TOL=88149],neptis sunica[&&NHX:TOL=88150],neptis sylvana[&&NHX:TOL=88151],neptis theodora[&&NHX:TOL=88152],neptis thestias[&&NHX:TOL=88153],neptis thetis[&&NHX:TOL=88154],neptis vibusa[&&NHX:TOL=88155],neptis vikasi[&&NHX:TOL=88156],neptis yerburii[&&NHX:TOL=88157],neptis zaida[&&NHX:TOL=88158],neptis jumbah[&&NHX:TOL=88159])[&&NHX:TOL=88162],neptis cormilloti[&&NHX:TOL=94063],neptis loma[&&NHX:TOL=118764],neptis angusta[&&NHX:TOL=118766],neptis najo[&&NHX:TOL=118768],neptis quintilla[&&NHX:TOL=118770],neptis carlsbergi[&&NHX:TOL=118772],neptis liberti[&&NHX:TOL=118774],neptis claude[&&NHX:TOL=118776])neptis[&&NHX:TOL=70392],(lasippa bella[&&NHX:TOL=88163],lasippa ebusa[&&NHX:TOL=88164],lasippa heliodore[&&NHX:TOL=88165],lasippa illigera[&&NHX:TOL=88166],lasippa illigerella[&&NHX:TOL=88167],lasippa monata[&&NHX:TOL=88168],lasippa neriphus[&&NHX:TOL=88169],lasippa nirvana[&&NHX:TOL=88170],lasippa pata[&&NHX:TOL=88171],lasippa tiga[&&NHX:TOL=88172],lasippa viraja[&&NHX:TOL=88173])lasippa[&&NHX:TOL=70393])[&&NHX:TOL=70388])neptini[&&NHX:TOL=70202],kumothales inexpectata[&&NHX:TOL=70198],pseudoneptis bugandensis[&&NHX:TOL=70199],(((bassarona dunya[&&NHX:TOL=87961],bassarona durga[&&NHX:TOL=87962],bassarona iva[&&NHX:TOL=87963],bassarona labotas[&&NHX:TOL=87964],bassarona piratica[&&NHX:TOL=87965],bassarona recta[&&NHX:TOL=87966],bassarona teuta[&&NHX:TOL=87967])bassarona[&&NHX:TOL=70352],((euthalia aconthea[&&NHX:TOL=88005],euthalia adonia[&&NHX:TOL=88006],euthalia agnis[&&NHX:TOL=88007],euthalia alpheda[&&NHX:TOL=88008],euthalia alpherakyi[&&NHX:TOL=88009],euthalia amanda[&&NHX:TOL=88010],euthalia anosia[&&NHX:TOL=88011],euthalia aristedes[&&NHX:TOL=88012],euthalia confucius[&&NHX:TOL=88013],euthalia djata[&&NHX:TOL=88014],euthalia duda[&&NHX:TOL=88015],euthalia eriphylae[&&NHX:TOL=88016],euthalia formosana[&&NHX:TOL=88017],euthalia franciae[&&NHX:TOL=88018],euthalia ipona[&&NHX:TOL=88019],euthalia irrubescens[&&NHX:TOL=88020],euthalia kameii[&&NHX:TOL=88022],euthalia kanda[&&NHX:TOL=88023],euthalia khama[&&NHX:TOL=88025],euthalia lubentina[&&NHX:TOL=88026],euthalia lusiada[&&NHX:TOL=88027],euthalia mahadeva[&&NHX:TOL=88028],euthalia malaccana[&&NHX:TOL=88029],euthalia merta[&&NHX:TOL=88030],euthalia monina[&&NHX:TOL=88031],euthalia nara[&&NHX:TOL=88032],euthalia nais[&&NHX:TOL=88033],euthalia amabilis[&&NHX:TOL=93921],euthalia patala[&&NHX:TOL=88034],euthalia phemius[&&NHX:TOL=88035],euthalia sahadeva[&&NHX:TOL=88036],euthalia strephon[&&NHX:TOL=88037],euthalia telchinia[&&NHX:TOL=88038],euthalia teuta[&&NHX:TOL=137728],euthalia thibetana[&&NHX:TOL=88039],euthalia tsangpoi[&&NHX:TOL=88040],euthalia undosa[&&NHX:TOL=88041],euthalia whiteheadi[&&NHX:TOL=88042],euthalia yasuyukii[&&NHX:TOL=118302])euthalia[&&NHX:TOL=70353],euthaliopsis aetion[&&NHX:TOL=88004])[&&NHX:TOL=88003],(tanaecia amisa[&&NHX:TOL=137726],tanaecia aruna[&&NHX:TOL=87981],tanaecia borromeoi[&&NHX:TOL=87982],tanaecia calliphorus[&&NHX:TOL=87983],tanaecia cibaritis[&&NHX:TOL=87984],tanaecia clathrata[&&NHX:TOL=87985],tanaecia coyctus[&&NHX:TOL=87986],tanaecia coelebs[&&NHX:TOL=87987],tanaecia dodong[&&NHX:TOL=87988],tanaecia elone[&&NHX:TOL=137727],tanaecia flora[&&NHX:TOL=87989],tanaecia godartii[&&NHX:TOL=87990],tanaecia howarthi[&&NHX:TOL=87991],tanaecia iapis[&&NHX:TOL=87992],tanaecia jahnu[&&NHX:TOL=87993],tanaecia julii[&&NHX:TOL=87994],tanaecia lepidea[&&NHX:TOL=87995],tanaecia leucotaenia[&&NHX:TOL=87996],tanaecia munda[&&NHX:TOL=87997],tanaecia orphne[&&NHX:TOL=87998],tanaecia palguna[&&NHX:TOL=87999],tanaecia pelea[&&NHX:TOL=88000],tanaecia susoni[&&NHX:TOL=88001],tanaecia trigerta[&&NHX:TOL=88002])tanaecia[&&NHX:TOL=70358],((lexias dirtea[&&NHX:TOL=87974],lexias pardalis[&&NHX:TOL=87976],lexias perdix[&&NHX:TOL=87977],lexias cyanipardus[&&NHX:TOL=87972],lexias damalis[&&NHX:TOL=87973],lexias canescens[&&NHX:TOL=87971],lexias aegle[&&NHX:TOL=87969],lexias aeetes[&&NHX:TOL=87968])[&&NHX:TOL=87979],(lexias aeropa[&&NHX:TOL=87970],lexias panopus[&&NHX:TOL=87975])[&&NHX:TOL=87980])lexias[&&NHX:TOL=70354],dophla evelina[&&NHX:TOL=70355],abrota ganga[&&NHX:TOL=70356],neurosigma siva[&&NHX:TOL=70357])adoliadina[&&NHX:TOL=70351],((euptera crowleyi[&&NHX:TOL=86805],(euptera dorothea[&&NHX:TOL=118871],euptera elabontas[&&NHX:TOL=86806])[&&NHX:TOL=118870],(euptera knoopi[&&NHX:TOL=118873],euptera plantroui[&&NHX:TOL=118874],euptera pluto[&&NHX:TOL=86810],euptera zowa[&&NHX:TOL=118875])[&&NHX:TOL=118872],(euptera mimetica[&&NHX:TOL=118877],euptera neptunus[&&NHX:TOL=118878])[&&NHX:TOL=118876],euptera aurantiaca[&&NHX:TOL=118879],(euptera amieti[&&NHX:TOL=118881],euptera hirundo[&&NHX:TOL=86808],euptera nigeriensis[&&NHX:TOL=118882])[&&NHX:TOL=118880],euptera freyja[&&NHX:TOL=86807],euptera liberti[&&NHX:TOL=86809],euptera richelmanni[&&NHX:TOL=86811],euptera semirufa[&&NHX:TOL=86812],euptera kinugnana[&&NHX:TOL=93868],euptera collinsi[&&NHX:TOL=118883],euptera choveti[&&NHX:TOL=118884],euptera debruynei[&&NHX:TOL=118885],euptera ducarmei[&&NHX:TOL=118886],euptera falcata[&&NHX:TOL=118887],euptera falsathyma[&&NHX:TOL=118888],euptera ginettae[&&NHX:TOL=118889],euptera intricata[&&NHX:TOL=118890],euptera ituriensis[&&NHX:TOL=118891],euptera mirabilis[&&NHX:TOL=118892],euptera mirifica[&&NHX:TOL=118893],euptera mocquerysi[&&NHX:TOL=118894],euptera schultzei[&&NHX:TOL=118895])euptera[&&NHX:TOL=70367],cynandra opis[&&NHX:TOL=70360],(evena angustatum[&&NHX:TOL=87118],evena crithea[&&NHX:TOL=87119],evena niji[&&NHX:TOL=87120],evena oberthueri[&&NHX:TOL=87121],evena sikorana[&&NHX:TOL=87122])evena[&&NHX:TOL=70361],pseudargynnis hegemone[&&NHX:TOL=70362],(((euriphene goniogramma[&&NHX:TOL=86846],euriphene mundula[&&NHX:TOL=86863],euriphene obtusangula[&&NHX:TOL=86864])euriphene goniogramma group[&&NHX:TOL=118780],(euriphene duseni adumbrata[&&NHX:TOL=86824],euriphene duseni duseni[&&NHX:TOL=86841],euriphene duseni canui[&&NHX:TOL=86837],euriphene duseni romi[&&NHX:TOL=86870])[&&NHX:TOL=103059],(((euriphene barombina[&&NHX:TOL=86834],euriphene grosesmithi[&&NHX:TOL=86847],euriphene incerta[&&NHX:TOL=86848],euriphene milnei[&&NHX:TOL=86862],euriphene pavo[&&NHX:TOL=86865],euriphene plagiata[&&NHX:TOL=86867],euriphene schultzei[&&NHX:TOL=86873],euriphene tadema[&&NHX:TOL=86875],euriphene veronica[&&NHX:TOL=86876])[&&NHX:TOL=118783],(euriphene bernaudi[&&NHX:TOL=118785],euriphene regula[&&NHX:TOL=118786],euriphene simplex[&&NHX:TOL=86874])[&&NHX:TOL=118784],(euriphene abasa[&&NHX:TOL=86823],euriphene kiki[&&NHX:TOL=86856])[&&NHX:TOL=118787],euriphene larseni[&&NHX:TOL=118788],euriphene amicia[&&NHX:TOL=86827])euriphene barombina subgroup[&&NHX:TOL=118782],(euriphene aridatha[&&NHX:TOL=86829],euriphene atrovirens[&&NHX:TOL=86832],euriphene coerulea[&&NHX:TOL=86838],euriphene glaucopis[&&NHX:TOL=86845],euriphene obani[&&NHX:TOL=118790])euriphene niepelti subgroup[&&NHX:TOL=118789],(euriphene amaranta[&&NHX:TOL=86826],euriphene anaxibia[&&NHX:TOL=118792],euriphene atropurpurea[&&NHX:TOL=86831],euriphene conjugens[&&NHX:TOL=86839],euriphene ernestibaumanni[&&NHX:TOL=86842],euriphene karschi[&&NHX:TOL=86855],euriphene lomaensis[&&NHX:TOL=86858])euriphene amaranta subgroup[&&NHX:TOL=118791])euriphene barombina group[&&NHX:TOL=118781],euriphene gambiae[&&NHX:TOL=86844],(euriphene ampedusa[&&NHX:TOL=86828],euriphene atossa[&&NHX:TOL=86830],euriphene leonis[&&NHX:TOL=86857])euriphene atossa group[&&NHX:TOL=118793],euriphene alberici[&&NHX:TOL=86825],euriphene aurivillii[&&NHX:TOL=86833],euriphene batesana[&&NHX:TOL=103058],euriphene butleri[&&NHX:TOL=86835],euriphene camarensis[&&NHX:TOL=86836],(euriphene doriclea[&&NHX:TOL=86840],euriphene lysandra[&&NHX:TOL=86860],euriphene paralysandra[&&NHX:TOL=118795])doricleana[&&NHX:TOL=118794],euriphene excelsior[&&NHX:TOL=86843],euriphene intermixta[&&NHX:TOL=86849],euriphene iris[&&NHX:TOL=86850],euriphene ituriensis[&&NHX:TOL=86851],euriphene jacksoni[&&NHX:TOL=86852],euriphene jolyana[&&NHX:TOL=86853],euriphene kahli[&&NHX:TOL=86854],euriphene luteostriata[&&NHX:TOL=86859],euriphene melanops[&&NHX:TOL=86861],euriphene pinkieana[&&NHX:TOL=86866],euriphene rectangula[&&NHX:TOL=86868],euriphene ribensis[&&NHX:TOL=86869],euriphene rotundata[&&NHX:TOL=86871],euriphene saphirina[&&NHX:TOL=86872])euriphene[&&NHX:TOL=70363],(euryphura achlys[&&NHX:TOL=86877],euryphura chalcis[&&NHX:TOL=86878],euryphura ducarmei[&&NHX:TOL=86879],euryphura fontainei[&&NHX:TOL=86880],euryphura hecqui[&&NHX:TOL=86881],euryphura kiellandi[&&NHX:TOL=86882],euryphura plautilla[&&NHX:TOL=86884],euryphura porphyrion[&&NHX:TOL=86885],euryphura isuka[&&NHX:TOL=118778],euryphura togoensis[&&NHX:TOL=118779])euryphura[&&NHX:TOL=70368],euryphurana nobilis[&&NHX:TOL=86883])[&&NHX:TOL=86888],euryphaedra thauma[&&NHX:TOL=70364],((euphaedra aubergeri[&&NHX:TOL=86900],euphaedra imperialis[&&NHX:TOL=86958],(euphaedra luperca[&&NHX:TOL=86973],(euphaedra luteofasciata[&&NHX:TOL=86975],euphaedra fucora[&&NHX:TOL=118829])[&&NHX:TOL=118828])[&&NHX:TOL=118827])euphaedra subgenus proteuphaedra[&&NHX:TOL=118826],euphaedra medoniana medon[&&NHX:TOL=86980],(euphaedra athena[&&NHX:TOL=118831],euphaedra calliope[&&NHX:TOL=86908],euphaedra extensa[&&NHX:TOL=118832],euphaedra gausape[&&NHX:TOL=86945],euphaedra hastiri[&&NHX:TOL=86950],euphaedra judith[&&NHX:TOL=86964],euphaedra mariaechristinae[&&NHX:TOL=118833],euphaedra melpomene[&&NHX:TOL=86981],euphaedra ombrophila[&&NHX:TOL=118834],euphaedra plantroui[&&NHX:TOL=87008],euphaedra vulnerata[&&NHX:TOL=87045],euphaedra zaddachii[&&NHX:TOL=87049])euphaedra subgenus gausapia[&&NHX:TOL=118830],(euphaedra acuta[&&NHX:TOL=86891],euphaedra ansorgei[&&NHX:TOL=86898],euphaedra crockeri[&&NHX:TOL=86923],euphaedra crossei[&&NHX:TOL=86924],euphaedra diffusa[&&NHX:TOL=118836],euphaedra hebes[&&NHX:TOL=86951],euphaedra hewitsoni[&&NHX:TOL=86953],euphaedra hollandi[&&NHX:TOL=86954],euphaedra pervaga[&&NHX:TOL=118837],euphaedra xypete[&&NHX:TOL=87048])euphaedra subgenus xypetana[&&NHX:TOL=118835],(euphaedra eusemoides[&&NHX:TOL=86938],euphaedra imitans[&&NHX:TOL=86957])euphaedra subgenus radia[&&NHX:TOL=118838],(euphaedra cyparissa[&&NHX:TOL=86926],euphaedra sarcoptera[&&NHX:TOL=87021])euphaedra subgenus euphaedra[&&NHX:TOL=118839],(((euphaedra laboureana[&&NHX:TOL=86934],euphaedra permixtum[&&NHX:TOL=87002],euphaedra themis[&&NHX:TOL=87035])euphaedra themis subgroup[&&NHX:TOL=118842],(euphaedra aureola[&&NHX:TOL=86901],euphaedra exerrata[&&NHX:TOL=86939],euphaedra laguerrei[&&NHX:TOL=86968],euphaedra minuta[&&NHX:TOL=86983],euphaedra modesta[&&NHX:TOL=86986])euphaedra aureola subgroup[&&NHX:TOL=118843],(euphaedra adonina[&&NHX:TOL=86893],euphaedra splendens[&&NHX:TOL=87026],euphaedra dubreka[&&NHX:TOL=118845],(euphaedra janetta[&&NHX:TOL=86962],euphaedra occulta[&&NHX:TOL=86994])[&&NHX:TOL=118846])euphaedra janetta subgroup[&&NHX:TOL=118844],(euphaedra aberrans[&&NHX:TOL=86890],euphaedra vetusta[&&NHX:TOL=87041])[&&NHX:TOL=118847],euphaedra justicia[&&NHX:TOL=86965],euphaedra piriformis[&&NHX:TOL=87006],euphaedra controversa[&&NHX:TOL=118848])euphaedra themis group[&&NHX:TOL=118841],((euphaedra afzelii[&&NHX:TOL=86894],euphaedra ceres[&&NHX:TOL=86914])euphaedra ceres subgroup[&&NHX:TOL=118850],(euphaedra delera[&&NHX:TOL=86929],euphaedra inanum[&&NHX:TOL=86959],(euphaedra phaethusa[&&NHX:TOL=87004],euphaedra dargeana[&&NHX:TOL=86927],euphaedra demeter[&&NHX:TOL=86930],euphaedra knoopiana[&&NHX:TOL=118853],euphaedra luteolucens[&&NHX:TOL=118854])[&&NHX:TOL=118852],euphaedra villiersi[&&NHX:TOL=87043],euphaedra viridicaerulea[&&NHX:TOL=87044])euphaedra inanum subgroup[&&NHX:TOL=118851],(euphaedra cottoni[&&NHX:TOL=86921],euphaedra margaritifera[&&NHX:TOL=86976],euphaedra preussiana[&&NHX:TOL=118856],euphaedra ravola[&&NHX:TOL=87014],euphaedra rezia[&&NHX:TOL=87017],euphaedra sarita[&&NHX:TOL=87023])euphaedra ravola subgroup[&&NHX:TOL=118855],euphaedra proserpina[&&NHX:TOL=87011],(euphaedra nigrocilia[&&NHX:TOL=86992],euphaedra ignota[&&NHX:TOL=118858],euphaedra tenebrosa[&&NHX:TOL=118859],euphaedra wojtusiaki[&&NHX:TOL=103066])[&&NHX:TOL=118857],euphaedra velutina[&&NHX:TOL=118860],(euphaedra densamacula[&&NHX:TOL=118862],euphaedra compacta[&&NHX:TOL=118863])[&&NHX:TOL=118861],euphaedra francina[&&NHX:TOL=86943])euphaedra ceres group[&&NHX:TOL=118849],(euphaedra preussi[&&NHX:TOL=87009],euphaedra vicina[&&NHX:TOL=87042])euphaedra preussi group[&&NHX:TOL=118864],((euphaedra castanoides[&&NHX:TOL=86912],euphaedra edwardsii[&&NHX:TOL=86935],euphaedra eleus[&&NHX:TOL=86936],euphaedra ferruginea[&&NHX:TOL=86941],euphaedra mambili[&&NHX:TOL=118867],euphaedra semipreussiana[&&NHX:TOL=103065],euphaedra simplex[&&NHX:TOL=87024],euphaedra zampa[&&NHX:TOL=87050])[&&NHX:TOL=118866],euphaedra perseis[&&NHX:TOL=87003],euphaedra ruspina[&&NHX:TOL=87020])euphaedra eleus group[&&NHX:TOL=118865],((euphaedra eupalus[&&NHX:TOL=86937],euphaedra harpalyce[&&NHX:TOL=86949])[&&NHX:TOL=118869],euphaedra losinga[&&NHX:TOL=86972])euphaedra harpalyce group[&&NHX:TOL=118868])euphaedra subgenus euphaedrana[&&NHX:TOL=118840],euphaedra adolfifrederici[&&NHX:TOL=86892],euphaedra alacris[&&NHX:TOL=86895],euphaedra albofasciata[&&NHX:TOL=86896],euphaedra alboides[&&NHX:TOL=86897],euphaedra amieti[&&NHX:TOL=103062],euphaedra apparata[&&NHX:TOL=86899],euphaedra asteria[&&NHX:TOL=103063],euphaedra aurivillii[&&NHX:TOL=86902],euphaedra barnsi[&&NHX:TOL=86903],euphaedra bergeri[&&NHX:TOL=86904],euphaedra bombeana[&&NHX:TOL=86905],euphaedra bouyeri[&&NHX:TOL=103064],euphaedra brevis[&&NHX:TOL=86906],euphaedra caerulescens[&&NHX:TOL=86907],euphaedra campaspe[&&NHX:TOL=86909],euphaedra canui[&&NHX:TOL=86910],euphaedra castanea[&&NHX:TOL=86911],euphaedra centralis[&&NHX:TOL=86913],euphaedra christyi[&&NHX:TOL=86915],euphaedra clio[&&NHX:TOL=86916],euphaedra confina[&&NHX:TOL=86917],euphaedra congo[&&NHX:TOL=86918],euphaedra cooksoni[&&NHX:TOL=86919],euphaedra coprates[&&NHX:TOL=86920],euphaedra crawshayi[&&NHX:TOL=86922],euphaedra cuprea[&&NHX:TOL=86925],euphaedra dargei[&&NHX:TOL=86928],euphaedra disjuncta[&&NHX:TOL=86931],euphaedra ducarmei[&&NHX:TOL=86932],euphaedra eberti[&&NHX:TOL=86933],euphaedra fascinata[&&NHX:TOL=86940],euphaedra fontainei[&&NHX:TOL=86942],euphaedra fulvofasciata[&&NHX:TOL=86944],euphaedra grandis[&&NHX:TOL=86946],euphaedra graueri[&&NHX:TOL=86947],euphaedra grilloti[&&NHX:TOL=86948],euphaedra herberti[&&NHX:TOL=86952],euphaedra hybrida[&&NHX:TOL=86955],euphaedra illustris[&&NHX:TOL=86956],euphaedra intermedia[&&NHX:TOL=86960],euphaedra jacksoni[&&NHX:TOL=86961],euphaedra jolyana[&&NHX:TOL=86963],euphaedra karschi[&&NHX:TOL=86966],euphaedra landbecki[&&NHX:TOL=86969],euphaedra lata[&&NHX:TOL=86970],euphaedra leloupi[&&NHX:TOL=86971],euphaedra lupercoides[&&NHX:TOL=86974],euphaedra margueriteae[&&NHX:TOL=86977],euphaedra maxima[&&NHX:TOL=86978],euphaedra mayumbensis[&&NHX:TOL=86979],euphaedra mendax[&&NHX:TOL=86982],euphaedra mirabilis[&&NHX:TOL=86984],euphaedra miranda[&&NHX:TOL=86985],euphaedra morini[&&NHX:TOL=86987],euphaedra murphyi[&&NHX:TOL=86988],euphaedra neophron[&&NHX:TOL=86989],euphaedra neumannii[&&NHX:TOL=86990],euphaedra nigrobasalis[&&NHX:TOL=86991],euphaedra niveovittata[&&NHX:TOL=86993],euphaedra ochracea[&&NHX:TOL=86995],euphaedra ochrovirens[&&NHX:TOL=86996],euphaedra olivacea[&&NHX:TOL=86997],euphaedra orientalis[&&NHX:TOL=86998],euphaedra overlaeti[&&NHX:TOL=86999],euphaedra paradoxa[&&NHX:TOL=87000],euphaedra phosphor[&&NHX:TOL=87005],euphaedra plagiara[&&NHX:TOL=87007],euphaedra procera[&&NHX:TOL=87010],euphaedra protea[&&NHX:TOL=87012],euphaedra rattrayi[&&NHX:TOL=87013],euphaedra regularis[&&NHX:TOL=87015],euphaedra rex[&&NHX:TOL=87016],euphaedra rubrocostata[&&NHX:TOL=87019],euphaedra sardetta[&&NHX:TOL=87022],euphaedra sinuosa[&&NHX:TOL=87025],euphaedra stellata[&&NHX:TOL=87027],euphaedra subferruginea[&&NHX:TOL=87028],euphaedra subprocera[&&NHX:TOL=87029],euphaedra subprotea[&&NHX:TOL=87030],euphaedra subrezia[&&NHX:TOL=87031],euphaedra subviridis[&&NHX:TOL=87032],euphaedra symphona[&&NHX:TOL=87033],euphaedra thalie[&&NHX:TOL=87034],euphaedra ubangi[&&NHX:TOL=87036],euphaedra ueleana[&&NHX:TOL=87037],euphaedra uganda[&&NHX:TOL=87038],euphaedra uniformis[&&NHX:TOL=87039],euphaedra variabilis[&&NHX:TOL=87040],euphaedra wissmanni[&&NHX:TOL=87046],euphaedra xerophila[&&NHX:TOL=87047])euphaedra[&&NHX:TOL=70365],hamanumida daedalus[&&NHX:TOL=70366],((pseudathyma callina[&&NHX:TOL=86813],pseudathyma cyrili[&&NHX:TOL=118897],pseudathyma falcata[&&NHX:TOL=86815],pseudathyma sibyllina[&&NHX:TOL=86821])[&&NHX:TOL=118896],(pseudathyma legeri[&&NHX:TOL=118899],pseudathyma uluguru[&&NHX:TOL=86822])[&&NHX:TOL=118898],(pseudathyma neptidina[&&NHX:TOL=86818],pseudathyma martini[&&NHX:TOL=118901])[&&NHX:TOL=118900],pseudathyma debruynei[&&NHX:TOL=86814],pseudathyma lucretioides[&&NHX:TOL=86817],pseudathyma nzoia[&&NHX:TOL=86819],pseudathyma plutonica[&&NHX:TOL=86820],pseudathyma endjami[&&NHX:TOL=118902],pseudathyma jacksoni[&&NHX:TOL=118903],pseudathyma michelae[&&NHX:TOL=118904])pseudathyma[&&NHX:TOL=70197],(aterica galene[&&NHX:TOL=87116],aterica rabena[&&NHX:TOL=87117])aterica[&&NHX:TOL=70369],crenidomimas concordia[&&NHX:TOL=86886],((((bebearia carshena[&&NHX:TOL=87062],bebearia dallastai[&&NHX:TOL=118799],bebearia osyris[&&NHX:TOL=118800],bebearia lucayensis[&&NHX:TOL=118801],bebearia subtentyris[&&NHX:TOL=103068],bebearia tentyris[&&NHX:TOL=87111])bebearia tentyris subgroup[&&NHX:TOL=118798],(bebearia abesa[&&NHX:TOL=87051],bebearia absolon[&&NHX:TOL=87052],bebearia mandinga[&&NHX:TOL=87090],bebearia micans[&&NHX:TOL=87093],bebearia oxione[&&NHX:TOL=87097],bebearia zonara[&&NHX:TOL=87115])bebearia zonara subgroup[&&NHX:TOL=118802],bebearia partita[&&NHX:TOL=87098])bebearia tentyris group[&&NHX:TOL=118797],bebearia barce[&&NHX:TOL=87058],bebearia comus[&&NHX:TOL=87068],(bebearia cocalia[&&NHX:TOL=118804],bebearia cocalioides[&&NHX:TOL=118805],bebearia guineensis[&&NHX:TOL=87080],bebearia mardania[&&NHX:TOL=87091],bebearia paludicola[&&NHX:TOL=118806],bebearia senegalensis[&&NHX:TOL=87107])bebearia mardania group[&&NHX:TOL=118803],bebearia sophus[&&NHX:TOL=87109],bebearia staudingeri[&&NHX:TOL=87110],(bebearia arcadius[&&NHX:TOL=87054],bebearia plistonax[&&NHX:TOL=87103])bebearia plistonax group[&&NHX:TOL=118807],bebearia elpinice[&&NHX:TOL=87076])bebearia subgenus apectenaria[&&NHX:TOL=118796],((bebearia brunhilda[&&NHX:TOL=87061],bebearia occitana[&&NHX:TOL=118810],bebearia congolensis[&&NHX:TOL=87069],bebearia laetitioides[&&NHX:TOL=118811])bebearia brunhilda group[&&NHX:TOL=118809],(bebearia laetitia[&&NHX:TOL=87086],bebearia phranza[&&NHX:TOL=87101],bebearia severini[&&NHX:TOL=87108])bebearia severini group[&&NHX:TOL=118812],(bebearia denticula[&&NHX:TOL=118814],bebearia flaminia[&&NHX:TOL=87077],bebearia maximiana[&&NHX:TOL=87092],bebearia omo[&&NHX:TOL=118815])bebearia flaminia group[&&NHX:TOL=118813],bebearia nivaria[&&NHX:TOL=87094],((bebearia phantasia[&&NHX:TOL=87099],bebearia phantasiella[&&NHX:TOL=87100],bebearia phantasina[&&NHX:TOL=118818])bebearia phantasia subgroup[&&NHX:TOL=118817],(bebearia demetra[&&NHX:TOL=87072],bebearia inepta[&&NHX:TOL=118820],bebearia maledicta[&&NHX:TOL=87089],bebearia warrengashi[&&NHX:TOL=118821])bebearia demetra subgroup[&&NHX:TOL=118819],bebearia vinula[&&NHX:TOL=118822])bebearia phantasia group[&&NHX:TOL=118816],bebearia ashantina[&&NHX:TOL=87055],((bebearia cutteri[&&NHX:TOL=87071],bebearia innocua[&&NHX:TOL=87083],bebearia eliensis[&&NHX:TOL=87075])[&&NHX:TOL=118824],bebearia tessmanni[&&NHX:TOL=87112],(bebearia barombina[&&NHX:TOL=87059],bebearia octogramma[&&NHX:TOL=87095])[&&NHX:TOL=118825])bebearia cutteri group[&&NHX:TOL=118823])bebearia subgenus bebearia[&&NHX:TOL=118808],bebearia allardi[&&NHX:TOL=87053],bebearia aurora[&&NHX:TOL=87056],bebearia badiana[&&NHX:TOL=87057],bebearia braytoni[&&NHX:TOL=87060],bebearia castanea[&&NHX:TOL=87063],bebearia chilonis[&&NHX:TOL=87064],bebearia chloeropis[&&NHX:TOL=87065],bebearia chriemhilda[&&NHX:TOL=87066],bebearia cinaethon[&&NHX:TOL=87067],bebearia cottoni[&&NHX:TOL=87070],bebearia ducalis[&&NHX:TOL=87073],bebearia ducarmei[&&NHX:TOL=87074],bebearia fontainei[&&NHX:TOL=87078],bebearia fulgurata[&&NHX:TOL=87079],bebearia hargreavesi[&&NHX:TOL=87081],bebearia ikelemba[&&NHX:TOL=87082],bebearia intermedia[&&NHX:TOL=87084],bebearia jolyana[&&NHX:TOL=87085],bebearia luteola[&&NHX:TOL=87087],bebearia makala[&&NHX:TOL=87088],bebearia orientis[&&NHX:TOL=87096],bebearia picturata[&&NHX:TOL=87102],bebearia raeveli[&&NHX:TOL=87104],bebearia schoutedeni[&&NHX:TOL=87105],bebearia scrutata[&&NHX:TOL=87106],bebearia theogonis[&&NHX:TOL=87113],bebearia unita[&&NHX:TOL=87114],bebearia kiellandi[&&NHX:TOL=103067])bebearia[&&NHX:TOL=70370],harmilla elegans[&&NHX:TOL=86889])bebearina[&&NHX:TOL=70359])adoliadini[&&NHX:TOL=70200],(((((((limenitis arthemis[&&NHX:TOL=87345],limenitis lorquini[&&NHX:TOL=87346])[&&NHX:TOL=88224],limenitis weidemeyerii[&&NHX:TOL=87347])[&&NHX:TOL=88223],limenitis archippus[&&NHX:TOL=87344])limenitis basilarchia[&&NHX:TOL=88222],(((((((limenitis helmanni[&&NHX:TOL=88211],limenitis doerriesi[&&NHX:TOL=88208])[&&NHX:TOL=88231],limenitis homeyeri[&&NHX:TOL=88212])[&&NHX:TOL=88230],limenitis glorifica[&&NHX:TOL=88232])[&&NHX:TOL=88229],limenitis camilla[&&NHX:TOL=88206])[&&NHX:TOL=88228],(limenitis moltrechti[&&NHX:TOL=88220],limenitis amphyssa[&&NHX:TOL=88205])[&&NHX:TOL=88233])[&&NHX:TOL=88227],limenitis reducta[&&NHX:TOL=88216])[&&NHX:TOL=88226],limenitis populi[&&NHX:TOL=88215],limenitis ciocolatina[&&NHX:TOL=88207],limenitis lepechini[&&NHX:TOL=88213],limenitis misuji[&&NHX:TOL=88214],limenitis rileyi[&&NHX:TOL=88217],limenitis sydyi[&&NHX:TOL=88218],limenitis trivena[&&NHX:TOL=88219],limenitis elwesi[&&NHX:TOL=88210],limenitis dubernardi[&&NHX:TOL=88209])[&&NHX:TOL=88225])limenitis[&&NHX:TOL=70371],(sumalia agneya[&&NHX:TOL=88297],sumalia chilo[&&NHX:TOL=88298],sumalia daraxa[&&NHX:TOL=88299],sumalia zulema[&&NHX:TOL=88300])sumalia[&&NHX:TOL=70373],(parasarpa albomaculata[&&NHX:TOL=88301],parasarpa dudu[&&NHX:TOL=88302],parasarpa hollandi[&&NHX:TOL=88303],parasarpa zayla[&&NHX:TOL=88304])parasarpa[&&NHX:TOL=70377],auzakia danava[&&NHX:TOL=70378],(litinga cottini[&&NHX:TOL=88310],litinga mimica[&&NHX:TOL=88311])litinga[&&NHX:TOL=70379],patsuia sinensium[&&NHX:TOL=70375],((moduza jumaloni[&&NHX:TOL=88246],tarattia lycone[&&NHX:TOL=88307],tarattia lymire[&&NHX:TOL=88308],moduza mata[&&NHX:TOL=88247],moduza nuydai[&&NHX:TOL=88248],moduza pintayana[&&NHX:TOL=88249],moduza procris[&&NHX:TOL=88250],moduza thespias[&&NHX:TOL=88251],moduza urdaneta[&&NHX:TOL=88252])moduza[&&NHX:TOL=70374],(tarattia libnites[&&NHX:TOL=88306],tarattia lysanias[&&NHX:TOL=88309],tarattia bruijni[&&NHX:TOL=93915])tarattia[&&NHX:TOL=88305],lamasia lyncides[&&NHX:TOL=70376])[&&NHX:TOL=93919])[&&NHX:TOL=88294],((adelpha pithys[&&NHX:TOL=87321],(adelpha donysa[&&NHX:TOL=87282],adelpha tracta[&&NHX:TOL=87339],(adelpha corcyra[&&NHX:TOL=87275],(adelpha alala[&&NHX:TOL=87261],adelpha aricia[&&NHX:TOL=87264])[&&NHX:TOL=128695])[&&NHX:TOL=128694])[&&NHX:TOL=128693])adelpha alala group[&&NHX:TOL=128692],((adelpha gelania[&&NHX:TOL=87293],((adelpha bredowii[&&NHX:TOL=87271],(adelpha eulalia[&&NHX:TOL=128701],adelpha californica[&&NHX:TOL=128702])[&&NHX:TOL=128700])[&&NHX:TOL=128699],(adelpha diocles[&&NHX:TOL=87281],(adelpha herbita[&&NHX:TOL=87295],(adelpha zea[&&NHX:TOL=87342],((adelpha paroeca[&&NHX:TOL=87319],adelpha nea[&&NHX:TOL=87316])[&&NHX:TOL=128707],(adelpha paraena[&&NHX:TOL=87318],(adelpha hyas[&&NHX:TOL=87297],adelpha serpa[&&NHX:TOL=87331],adelpha seriphia[&&NHX:TOL=87330],adelpha radiata[&&NHX:TOL=87325])[&&NHX:TOL=128709])[&&NHX:TOL=128708])[&&NHX:TOL=128706])[&&NHX:TOL=128705])[&&NHX:TOL=128704])[&&NHX:TOL=128703])[&&NHX:TOL=128698])adelpha serpa group[&&NHX:TOL=128697],(adelpha fessonia[&&NHX:TOL=87291],(adelpha gavina[&&NHX:TOL=87292],((adelpha thoasa[&&NHX:TOL=87338],(adelpha thessalia[&&NHX:TOL=87337],(adelpha iphiclus[&&NHX:TOL=87299],adelpha iphicleola[&&NHX:TOL=87298],adelpha abyla[&&NHX:TOL=87260])[&&NHX:TOL=128715])[&&NHX:TOL=128714])[&&NHX:TOL=128713],((adelpha basiloides[&&NHX:TOL=87268],adelpha plesaure[&&NHX:TOL=87322])[&&NHX:TOL=128717],(adelpha calliphane[&&NHX:TOL=87272],(adelpha falcipennis[&&NHX:TOL=87289],(adelpha poltius[&&NHX:TOL=87324],(adelpha mythra[&&NHX:TOL=87314],(adelpha demialba[&&NHX:TOL=87279],((((adelpha epizygis[&&NHX:TOL=87284],adelpha abia[&&NHX:TOL=87259])[&&NHX:TOL=128726],(adelpha syma[&&NHX:TOL=87335],(adelpha cytherea[&&NHX:TOL=87277],(adelpha salmoneus[&&NHX:TOL=87327],adelpha viola[&&NHX:TOL=87340])[&&NHX:TOL=128729])[&&NHX:TOL=128728])[&&NHX:TOL=128727])[&&NHX:TOL=128725],(adelpha malea[&&NHX:TOL=87309],(adelpha atlantica[&&NHX:TOL=87265],(adelpha heraclea[&&NHX:TOL=87294],adelpha naxia[&&NHX:TOL=87315])[&&NHX:TOL=128732])[&&NHX:TOL=128731],((adelpha zina[&&NHX:TOL=87343],(adelpha jordani[&&NHX:TOL=87301],adelpha milleri[&&NHX:TOL=87313])[&&NHX:TOL=128735])[&&NHX:TOL=128734],(adelpha hesterbergi[&&NHX:TOL=87296],((adelpha messana[&&NHX:TOL=87312],(adelpha erotia[&&NHX:TOL=87285],(adelpha pollina[&&NHX:TOL=87323],adelpha thesprotia[&&NHX:TOL=87336])[&&NHX:TOL=128740])[&&NHX:TOL=128739])[&&NHX:TOL=128738],(adelpha mesentina[&&NHX:TOL=87311],adelpha lycorias[&&NHX:TOL=87308])[&&NHX:TOL=128741],adelpha phylaca[&&NHX:TOL=87320])adelpha phylaca group[&&NHX:TOL=128737])[&&NHX:TOL=128736],adelpha fabricia[&&NHX:TOL=87288])[&&NHX:TOL=128733])[&&NHX:TOL=128730])[&&NHX:TOL=128724],(((adelpha capucinus[&&NHX:TOL=87273],(adelpha barnesia[&&NHX:TOL=87267],adelpha diazi[&&NHX:TOL=87280])[&&NHX:TOL=128745])[&&NHX:TOL=128744],(adelpha attica[&&NHX:TOL=87266],(adelpha melona[&&NHX:TOL=87310],(adelpha epione[&&NHX:TOL=87283],adelpha ethelda[&&NHX:TOL=87287])[&&NHX:TOL=128748])[&&NHX:TOL=128747])[&&NHX:TOL=128746])[&&NHX:TOL=128743],(adelpha ximena[&&NHX:TOL=87341],(adelpha sichaeus[&&NHX:TOL=87333],(((adelpha cocala[&&NHX:TOL=87274],(adelpha amazona[&&NHX:TOL=87262],adelpha boeotia[&&NHX:TOL=87269])[&&NHX:TOL=128754])[&&NHX:TOL=128753],(adelpha salus[&&NHX:TOL=87328],(adelpha shuara[&&NHX:TOL=87332],(adelpha argentea[&&NHX:TOL=87263],adelpha coryneta[&&NHX:TOL=87276])[&&NHX:TOL=128757])[&&NHX:TOL=128756])[&&NHX:TOL=128755])[&&NHX:TOL=128752],((adelpha boreas[&&NHX:TOL=87270],(adelpha rothschildi[&&NHX:TOL=87326],adelpha stilesiana[&&NHX:TOL=87334])[&&NHX:TOL=128760])[&&NHX:TOL=128759],(adelpha erymanthis[&&NHX:TOL=87286],(adelpha leuceria[&&NHX:TOL=87304],adelpha leucerioides[&&NHX:TOL=87305])[&&NHX:TOL=128762])[&&NHX:TOL=128761])[&&NHX:TOL=128758],(adelpha felderi[&&NHX:TOL=87290],((adelpha lamasi[&&NHX:TOL=87303],adelpha saundersii[&&NHX:TOL=87329])[&&NHX:TOL=128765],((adelpha irmina[&&NHX:TOL=87300],adelpha leucophthalma[&&NHX:TOL=87306])[&&NHX:TOL=128767],(adelpha levona[&&NHX:TOL=87307],adelpha olynthia[&&NHX:TOL=87317],adelpha justina[&&NHX:TOL=87302])[&&NHX:TOL=128768])[&&NHX:TOL=128766])[&&NHX:TOL=128764])[&&NHX:TOL=128763])[&&NHX:TOL=128751])[&&NHX:TOL=128750])[&&NHX:TOL=128749],adelpha delinita[&&NHX:TOL=87278])[&&NHX:TOL=128742])[&&NHX:TOL=128723])[&&NHX:TOL=128722])[&&NHX:TOL=128721])[&&NHX:TOL=128720])[&&NHX:TOL=128719])[&&NHX:TOL=128718])[&&NHX:TOL=128716])[&&NHX:TOL=128712])[&&NHX:TOL=128711])[&&NHX:TOL=128710])[&&NHX:TOL=128696])adelpha[&&NHX:TOL=70382])[&&NHX:TOL=88293],(((athyma abiasa[&&NHX:TOL=88255],athyma alcamene[&&NHX:TOL=88256],athyma arayata[&&NHX:TOL=88257],athyma asura[&&NHX:TOL=88258],athyma bruijni[&&NHX:TOL=88259],athyma cama[&&NHX:TOL=88260],athyma cosmia[&&NHX:TOL=88261],athyma disjuncta[&&NHX:TOL=88262],athyma epithemis[&&NHX:TOL=88263],athyma fortuna[&&NHX:TOL=88265],athyma godmani[&&NHX:TOL=88266],athyma gutama[&&NHX:TOL=88267],athyma inara[&&NHX:TOL=88268],athyma jina[&&NHX:TOL=88269],athyma kanwa[&&NHX:TOL=88270],athyma karita[&&NHX:TOL=88271],athyma kasa[&&NHX:TOL=88272],athyma maenas[&&NHX:TOL=88291],athyma marguritha[&&NHX:TOL=88275],athyma mindanica[&&NHX:TOL=88276],athyma minensis[&&NHX:TOL=118304],athyma nefte[&&NHX:TOL=88277],athyma opalina[&&NHX:TOL=88278],athyma perius[&&NHX:TOL=88279],athyma pravara[&&NHX:TOL=88280],athyma punctata[&&NHX:TOL=88281],athyma ranga[&&NHX:TOL=88282],athyma recurva[&&NHX:TOL=88283],athyma reta[&&NHX:TOL=88284],athyma rufula[&&NHX:TOL=88285],athyma libnites[&&NHX:TOL=93917],athyma selenophora[&&NHX:TOL=88286],athyma separata[&&NHX:TOL=88287],athyma speciosa[&&NHX:TOL=88288],athyma sulpitia[&&NHX:TOL=88289],athyma zeroca[&&NHX:TOL=88290])athyma[&&NHX:TOL=70381],pandita sinope[&&NHX:TOL=70380],(tacola eulimene[&&NHX:TOL=88264],tacola magindana[&&NHX:TOL=88274],tacola larymna[&&NHX:TOL=88273])tacola[&&NHX:TOL=94062])[&&NHX:TOL=88296],seokia pratti[&&NHX:TOL=88253])[&&NHX:TOL=88295])limenitidini[&&NHX:TOL=70201])[&&NHX:TOL=70195])limenitidinae[&&NHX:TOL=12196],((cethosia biblis[&&NHX:TOL=87644],cethosia cyane[&&NHX:TOL=87645],cethosia cydippe[&&NHX:TOL=87646],cethosia hypsea[&&NHX:TOL=87647],cethosia luzonica[&&NHX:TOL=87648],cethosia myrina[&&NHX:TOL=87649],cethosia nietneri[&&NHX:TOL=87650],cethosia obscura[&&NHX:TOL=87651],cethosia penthesilea[&&NHX:TOL=87652],cethosia tambora[&&NHX:TOL=93864],[&&NHX:TOL=93865])cethosia[&&NHX:TOL=70394],((((((neruda metharme[&&NHX:TOL=72876],neruda godmani[&&NHX:TOL=72878])[&&NHX:TOL=72886],neruda aoede[&&NHX:TOL=72877])neruda[&&NHX:TOL=72230],(((((((heliconius cydno[&&NHX:TOL=72251],heliconius heurippa[&&NHX:TOL=72255])[&&NHX:TOL=72890],(heliconius timareta[&&NHX:TOL=72253],heliconius pachinus[&&NHX:TOL=72254])[&&NHX:TOL=72891])[&&NHX:TOL=72250],heliconius tristero[&&NHX:TOL=72892])[&&NHX:TOL=72889],heliconius melpomene[&&NHX:TOL=72252])[&&NHX:TOL=72888],((heliconius numata[&&NHX:TOL=72894],heliconius ismenius[&&NHX:TOL=72895])[&&NHX:TOL=72893],heliconius besckei[&&NHX:TOL=72896],(((heliconius elevatus[&&NHX:TOL=72900],heliconius luciana[&&NHX:TOL=72901])[&&NHX:TOL=72899],heliconius pardalinus[&&NHX:TOL=72902])[&&NHX:TOL=72898],(heliconius hecale[&&NHX:TOL=72904],heliconius atthis[&&NHX:TOL=72905])[&&NHX:TOL=72903])[&&NHX:TOL=72897],(heliconius ethilla[&&NHX:TOL=72907],heliconius nattereri[&&NHX:TOL=72908])[&&NHX:TOL=72906])[&&NHX:TOL=72883])[&&NHX:TOL=72249],(((heliconius burneyi[&&NHX:TOL=72246],heliconius wallacei[&&NHX:TOL=72247])[&&NHX:TOL=72245],(heliconius egeria[&&NHX:TOL=72248],heliconius astraea[&&NHX:TOL=72912],heliconius lalitae[&&NHX:TOL=72913])[&&NHX:TOL=72911])[&&NHX:TOL=72910],(((heliconius hierax[&&NHX:TOL=72917],heliconius xanthocles[&&NHX:TOL=72244])[&&NHX:TOL=72916],heliconius doris[&&NHX:TOL=72918])[&&NHX:TOL=72915],heliconius hecuba[&&NHX:TOL=72919])[&&NHX:TOL=72914])[&&NHX:TOL=72909])[&&NHX:TOL=72887],(((((heliconius hermathena[&&NHX:TOL=72240],heliconius himera[&&NHX:TOL=72241])[&&NHX:TOL=72924],heliconius erato[&&NHX:TOL=72242])[&&NHX:TOL=72923],heliconius hecalesia[&&NHX:TOL=72925])[&&NHX:TOL=72922],((heliconius clysonymus[&&NHX:TOL=72928],heliconius telesiphe[&&NHX:TOL=72929])[&&NHX:TOL=72927],heliconius hortense[&&NHX:TOL=72233])[&&NHX:TOL=72926])[&&NHX:TOL=72921],((((((((heliconius eleuchia[&&NHX:TOL=72938],heliconius congener[&&NHX:TOL=72939])[&&NHX:TOL=72937],heliconius sapho[&&NHX:TOL=72940])[&&NHX:TOL=72936],heliconius hewitsoni[&&NHX:TOL=72941])[&&NHX:TOL=72935],(heliconius sara[&&NHX:TOL=72943],heliconius leucadia[&&NHX:TOL=72944])[&&NHX:TOL=72942])[&&NHX:TOL=72934],heliconius antiochus[&&NHX:TOL=72945])[&&NHX:TOL=72933],heliconius demeter[&&NHX:TOL=72946])[&&NHX:TOL=72932],heliconius ricini[&&NHX:TOL=72947])[&&NHX:TOL=72931],(heliconius charithonia[&&NHX:TOL=72949],heliconius peruvianus[&&NHX:TOL=72950])[&&NHX:TOL=72948])[&&NHX:TOL=72930])pupalmating clade[&&NHX:TOL=72920])heliconius[&&NHX:TOL=72231])[&&NHX:TOL=70439],((((((eueides vibilia[&&NHX:TOL=72956],eueides lampeto[&&NHX:TOL=72957])[&&NHX:TOL=72955],eueides pavana[&&NHX:TOL=72958])[&&NHX:TOL=72954],eueides procula[&&NHX:TOL=72959])[&&NHX:TOL=72953],((eueides lineata[&&NHX:TOL=72962],eueides emsleyi[&&NHX:TOL=72963])[&&NHX:TOL=72961],eueides libitina[&&NHX:TOL=72964],eueides isabella[&&NHX:TOL=72965])[&&NHX:TOL=72960])[&&NHX:TOL=72952],eueides heliconioides[&&NHX:TOL=72966])[&&NHX:TOL=72951],((eueides lybia[&&NHX:TOL=72969],eueides tales[&&NHX:TOL=72970])[&&NHX:TOL=72968],eueides aliphera[&&NHX:TOL=72971])[&&NHX:TOL=72967])eueides[&&NHX:TOL=70440])[&&NHX:TOL=70438],(agraulis vanillae[&&NHX:TOL=70429],(dione moneta[&&NHX:TOL=72862],(dione juno[&&NHX:TOL=72863],dione glycera[&&NHX:TOL=72864])[&&NHX:TOL=70430])dione[&&NHX:TOL=72861])[&&NHX:TOL=70428],(((dryas iulia[&&NHX:TOL=70435],dryadula phaetusa[&&NHX:TOL=70436])[&&NHX:TOL=70434],(podotricha judith[&&NHX:TOL=72868],podotricha telesiphe[&&NHX:TOL=72872])podotricha[&&NHX:TOL=70441])[&&NHX:TOL=72972],(philaethria dido[&&NHX:TOL=72873],philaethria diatonica[&&NHX:TOL=72874],philaethria constantinoi[&&NHX:TOL=72875],philaethria andrei[&&NHX:TOL=103420],philaethria ostara[&&NHX:TOL=103421],philaethria pygmalion[&&NHX:TOL=103422],philaethria wernickei[&&NHX:TOL=103423])philaethria[&&NHX:TOL=70437])[&&NHX:TOL=72865])heliconiini[&&NHX:TOL=70208],(((acraea rogersi[&&NHX:TOL=85283],((acraea cerasa[&&NHX:TOL=85202],acraea kraka[&&NHX:TOL=85236])acraea cerasa group[&&NHX:TOL=118493],(((acraea abdera[&&NHX:TOL=85178],acraea acrita[&&NHX:TOL=85179],acraea annonae[&&NHX:TOL=85186],acraea asema[&&NHX:TOL=85188],acraea atolmis[&&NHX:TOL=85190],acraea bailunduensis[&&NHX:TOL=85192],acraea bellona[&&NHX:TOL=85193],acraea buettneri[&&NHX:TOL=85197],acraea cepheus[&&NHX:TOL=85201],acraea chaeribula[&&NHX:TOL=85203],acraea chambezi[&&NHX:TOL=85204],acraea diogenes[&&NHX:TOL=85209],acraea egina[&&NHX:TOL=85211],acraea eltringhamiana[&&NHX:TOL=85215],acraea guillemei[&&NHX:TOL=85223],acraea guluensis[&&NHX:TOL=85224],acraea lapidorum[&&NHX:TOL=85237],acraea lofua[&&NHX:TOL=85241],acraea loranae[&&NHX:TOL=85242],acraea lualabae[&&NHX:TOL=85243],acraea manca[&&NHX:TOL=85249],acraea mansya[&&NHX:TOL=85250],acraea medea[&&NHX:TOL=85253],acraea niobe[&&NHX:TOL=85258],acraea nohara[&&NHX:TOL=85259],acraea omrora[&&NHX:TOL=85261],acraea onerata[&&NHX:TOL=85263],acraea overlaeti[&&NHX:TOL=85265],acraea peetersi[&&NHX:TOL=93863],acraea periphanes[&&NHX:TOL=85266],acraea petraea[&&NHX:TOL=85268],acraea pseudatolmis[&&NHX:TOL=85270],acraea pudorina[&&NHX:TOL=85275],acraea punctellata[&&NHX:TOL=85276],acraea rohlfsi[&&NHX:TOL=85284],acraea utengulensis[&&NHX:TOL=85295],acraea violarum[&&NHX:TOL=85297])acraea egina group[&&NHX:TOL=118496],(acraea aglaonice[&&NHX:TOL=85183],(acraea asboloplintha[&&NHX:TOL=85187],acraea atergatis[&&NHX:TOL=85189],acraea axina[&&NHX:TOL=85191],acraea braesia[&&NHX:TOL=85195],acraea caecilia[&&NHX:TOL=85198],acraea caldarena[&&NHX:TOL=85199],acraea doubledayi[&&NHX:TOL=85210],acraea ella[&&NHX:TOL=85212],acraea equatorialis[&&NHX:TOL=85219],acraea intermediodes[&&NHX:TOL=85232],acraea leucopyga[&&NHX:TOL=85240],acraea lygus[&&NHX:TOL=85244],acraea marnois[&&NHX:TOL=85251],acraea mirabilis[&&NHX:TOL=85254],acraea miranda[&&NHX:TOL=85255],acraea natalica[&&NHX:TOL=85256],acraea oncaea[&&NHX:TOL=85262],acraea pseudegina[&&NHX:TOL=85271],acraea pudorella[&&NHX:TOL=85274],acraea rhodesiana[&&NHX:TOL=85282],acraea stenobea[&&NHX:TOL=85288],acraea sykesi[&&NHX:TOL=85289])acraea natalica group[&&NHX:TOL=118498])[&&NHX:TOL=118497])[&&NHX:TOL=118495],(((acraea zonata[&&NHX:TOL=85299],(acraea rabbaiae[&&NHX:TOL=85280],(acraea satis[&&NHX:TOL=85285],(acraea acara[&&NHX:TOL=118505],acraea anemosa[&&NHX:TOL=85185],acraea chilo[&&NHX:TOL=85205],acraea hypoleuca[&&NHX:TOL=85228],acraea oscari[&&NHX:TOL=85264],acraea pseudolycia[&&NHX:TOL=85273],acraea turna[&&NHX:TOL=85293],acraea zetes[&&NHX:TOL=85298])[&&NHX:TOL=118504])[&&NHX:TOL=118503])[&&NHX:TOL=118502])acraea zetes group[&&NHX:TOL=118501],((acraea machequena[&&NHX:TOL=85247],acraea ranavalona[&&NHX:TOL=85281])[&&NHX:TOL=118507],((acraea admatha[&&NHX:TOL=85180],acraea boopis[&&NHX:TOL=85194],acraea endoscota[&&NHX:TOL=85216],acraea hova[&&NHX:TOL=85227],acraea kappa[&&NHX:TOL=85233],acraea kinduana[&&NHX:TOL=85235],acraea leucographa[&&NHX:TOL=85239])[&&NHX:TOL=118509],(acraea quirina[&&NHX:TOL=85279],(acraea brainei[&&NHX:TOL=85196],acraea camaena[&&NHX:TOL=85200],acraea cuva[&&NHX:TOL=85207],acraea dammii[&&NHX:TOL=85208],acraea eltringhami[&&NHX:TOL=85214],acraea eugenia[&&NHX:TOL=85220],acraea hamata[&&NHX:TOL=85225],acraea horta[&&NHX:TOL=85226],acraea igati[&&NHX:TOL=85229],acraea insignis[&&NHX:TOL=85231],acraea kia[&&NHX:TOL=85234],acraea mahela[&&NHX:TOL=85248],acraea matuapa[&&NHX:TOL=85252],acraea neobule[&&NHX:TOL=85257],acraea punctimarginea[&&NHX:TOL=85277],acraea terpsicore[&&NHX:TOL=85291],acraea turlini[&&NHX:TOL=85292],(acraea andromacha[&&NHX:TOL=87639],acraea meyeri[&&NHX:TOL=87641],acraea moluccana[&&NHX:TOL=87642],acraea violae[&&NHX:TOL=87643])indoaustralian taxa[&&NHX:TOL=128863])[&&NHX:TOL=118511])[&&NHX:TOL=118510])[&&NHX:TOL=118508])acraea neobule group[&&NHX:TOL=118506])[&&NHX:TOL=118500],(acraea adrasta[&&NHX:TOL=85181],acraea aganice[&&NHX:TOL=85182],acraea alcinoe[&&NHX:TOL=85184],acraea consanguinea[&&NHX:TOL=85206],acraea elongata[&&NHX:TOL=85213],acraea epaea[&&NHX:TOL=85217],acraea epiprotea[&&NHX:TOL=85218],acraea excisa[&&NHX:TOL=85221],acraea formosa[&&NHX:TOL=85222],acraea indentata[&&NHX:TOL=85230],acraea leopoldina[&&NHX:TOL=85238],acraea macaria[&&NHX:TOL=85245],acraea macarista[&&NHX:TOL=85246],acraea obliqua[&&NHX:TOL=85260],acraea persanguinea[&&NHX:TOL=85267],acraea poggei[&&NHX:TOL=85269],acraea pseuderyta[&&NHX:TOL=85272],acraea quadricolor[&&NHX:TOL=85278],acraea scalivittata[&&NHX:TOL=85286],acraea umbra[&&NHX:TOL=85294],acraea tellus[&&NHX:TOL=85290],acraea vestalis[&&NHX:TOL=85296])bematistes[&&NHX:TOL=118512])[&&NHX:TOL=118499])[&&NHX:TOL=118494])[&&NHX:TOL=118492])acraea[&&NHX:TOL=70403],(actinote perenna[&&NHX:TOL=85591],((actinote actinotina[&&NHX:TOL=85531],actinote aubyni[&&NHX:TOL=85540],actinote baxteri[&&NHX:TOL=85542],actinote cinerea[&&NHX:TOL=85548])[&&NHX:TOL=118427],(actinote buschbecki[&&NHX:TOL=85545],actinote circeis[&&NHX:TOL=85549],actinote grosvenori[&&NHX:TOL=85560],(actinote masamba[&&NHX:TOL=85574],actinote siliana[&&NHX:TOL=93859])[&&NHX:TOL=118429],actinote oreas[&&NHX:TOL=85582],actinote orina[&&NHX:TOL=85584],(actinote parrhasia[&&NHX:TOL=85586],actinote servona[&&NHX:TOL=85601])[&&NHX:TOL=118430],actinote pelopeia[&&NHX:TOL=85587],actinote peneleos[&&NHX:TOL=85588],actinote quirinalis[&&NHX:TOL=85594],actinote sambavae[&&NHX:TOL=85599],actinote semivitrea[&&NHX:TOL=85600],actinote strattipocles[&&NHX:TOL=85604])actinote parrhasia subgroup[&&NHX:TOL=118428],(actinote amicitiae[&&NHX:TOL=85537],actinote conradti[&&NHX:TOL=85550],actinote igola[&&NHX:TOL=85564],actinote melanoxantha[&&NHX:TOL=85575],actinote newtoni[&&NHX:TOL=85578],(actinote ntebiae[&&NHX:TOL=85579],actinote alticola[&&NHX:TOL=118433])[&&NHX:TOL=118432],actinote orinata[&&NHX:TOL=85585],(actinote penelope[&&NHX:TOL=85589],actinote translucida[&&NHX:TOL=118435])[&&NHX:TOL=118434],actinote safie[&&NHX:TOL=85598],actinote ungemachi[&&NHX:TOL=85605])actinote penelope subgroup[&&NHX:TOL=118431])actinote penelope group[&&NHX:TOL=118426],(((actinote humilis[&&NHX:TOL=85563],actinote iturina[&&NHX:TOL=85566],actinote kalinzu[&&NHX:TOL=85569],actinote rileyi[&&NHX:TOL=85597])actinote iturina group[&&NHX:TOL=118438],((actinote pharsalus[&&NHX:TOL=85592],actinote insularis[&&NHX:TOL=85565],actinote vuilloti[&&NHX:TOL=85610])actinote pharsalus group[&&NHX:TOL=118440],((actinote acuta[&&NHX:TOL=118701],actinote alciope[&&NHX:TOL=85533],actinote alciopoides[&&NHX:TOL=85534],actinote ansorgei[&&NHX:TOL=85539],actinote aurivillii[&&NHX:TOL=85541],actinote disjuncta[&&NHX:TOL=85551],actinote esebria[&&NHX:TOL=85556],actinote johnstoni[&&NHX:TOL=85568],actinote jodutta[&&NHX:TOL=85567],actinote lycoa[&&NHX:TOL=85573])actinote lycoa group[&&NHX:TOL=118442],(actinote encedana[&&NHX:TOL=85552],actinote encedon[&&NHX:TOL=85553],actinote encoda[&&NHX:TOL=85554],actinote necoda[&&NHX:TOL=85577])actinote encedon group[&&NHX:TOL=118443])[&&NHX:TOL=118441])[&&NHX:TOL=118439])[&&NHX:TOL=118437],(((actinote pierrei[&&NHX:TOL=85593],actinote rangatana[&&NHX:TOL=85596],actinote serena[&&NHX:TOL=85555],actinote ventura[&&NHX:TOL=85607])actinote serena group[&&NHX:TOL=118446],((actinote acerata[&&NHX:TOL=85530],(actinote althoffi[&&NHX:TOL=85536],actinote pseudepaea[&&NHX:TOL=118450])[&&NHX:TOL=118449],actinote fornax[&&NHX:TOL=85558],actinote oberthueri[&&NHX:TOL=85581])actinote acerata group[&&NHX:TOL=118448],(actinote alicia[&&NHX:TOL=85535],actinote bonasia[&&NHX:TOL=85544],actinote burgessi[&&NHX:TOL=85546],actinote cabira[&&NHX:TOL=85547],actinote excelsior[&&NHX:TOL=85557],actinote goetzei[&&NHX:TOL=85559],actinote lumiri[&&NHX:TOL=85572],actinote sotikensis[&&NHX:TOL=85603],actinote uvui[&&NHX:TOL=85606],(actinote viviana[&&NHX:TOL=85609],actinote karschi[&&NHX:TOL=118453])[&&NHX:TOL=118452])actinote bonasia group[&&NHX:TOL=118451])[&&NHX:TOL=118447])[&&NHX:TOL=118445],((actinote lia[&&NHX:TOL=85571],actinote obeira[&&NHX:TOL=85580],actinote orestia[&&NHX:TOL=85583],actinote pentapolis[&&NHX:TOL=85590],actinote polis[&&NHX:TOL=118456],actinote vesperalis[&&NHX:TOL=85608])actinote pentapolis group[&&NHX:TOL=118455],((actinote anacreon[&&NHX:TOL=85538],actinote calida[&&NHX:TOL=93861],actinote guichardi[&&NHX:TOL=85561],actinote kaduna[&&NHX:TOL=118459],actinote rahira[&&NHX:TOL=85595],actinote wigginsi[&&NHX:TOL=85611],actinote zitja[&&NHX:TOL=85612],actinote issoria[&&NHX:TOL=87640])actinote anacreon group[&&NHX:TOL=118458],(actinote mirifica[&&NHX:TOL=85576],(altinote eresia[&&NHX:TOL=85166],(((abananote erinome[&&NHX:TOL=85131],(altinote rubrocellulata[&&NHX:TOL=85173],(abananote radiata[&&NHX:TOL=85134],(altinote alcione[&&NHX:TOL=85162],altinote neleus[&&NHX:TOL=85171])[&&NHX:TOL=118466],(abananote abana[&&NHX:TOL=85130],abananote euryleuca[&&NHX:TOL=85132],abananote hylonome[&&NHX:TOL=85133])     abananote[&&NHX:TOL=118905])[&&NHX:TOL=118465])[&&NHX:TOL=118464])[&&NHX:TOL=118463],((altinote momina[&&NHX:TOL=85169],altinote tenebrosa[&&NHX:TOL=85175])[&&NHX:TOL=118468],((altinote negra[&&NHX:TOL=85170],altinote stratonice[&&NHX:TOL=85174])[&&NHX:TOL=118470],altinote dicaeus[&&NHX:TOL=85165])[&&NHX:TOL=118469])[&&NHX:TOL=118467],altinote anaxo[&&NHX:TOL=85163],altinote callianthe[&&NHX:TOL=85164],altinote griseata[&&NHX:TOL=85167],altinote hilaris[&&NHX:TOL=85168],altinote ozomene[&&NHX:TOL=85172],altinote trinacria[&&NHX:TOL=85176],2 undescribed species[&&NHX:TOL=85177])altinote[&&NHX:TOL=70401],((actinote genitrix[&&NHX:TOL=85145],actinote romeroi[&&NHX:TOL=138531])[&&NHX:TOL=138530],actinote anteas[&&NHX:TOL=85136],actinote catarina[&&NHX:TOL=85141],actinote latior[&&NHX:TOL=85148],actinote lapitha[&&NHX:TOL=85147],actinote melampeplos[&&NHX:TOL=85150],actinote rufina[&&NHX:TOL=85157],5 undescribed neotropical species[&&NHX:TOL=85161],((actinote quadra[&&NHX:TOL=85155],(actinote canutia[&&NHX:TOL=85139],actinote mamita[&&NHX:TOL=85149])[&&NHX:TOL=118474])[&&NHX:TOL=118473],((actinote bonita[&&NHX:TOL=85137],(actinote alalia[&&NHX:TOL=85135],actinote conspicua[&&NHX:TOL=85142])[&&NHX:TOL=118477])[&&NHX:TOL=118476],actinote dalmedai[&&NHX:TOL=85143],((actinote parapheles[&&NHX:TOL=85153],(actinote ballettae[&&NHX:TOL=138534],actinote alberti[&&NHX:TOL=138535])[&&NHX:TOL=138533])[&&NHX:TOL=138532],((actinote thalia[&&NHX:TOL=85159],actinote pratensis[&&NHX:TOL=118481])[&&NHX:TOL=118480],((actinote brylla[&&NHX:TOL=85138],actinote zikani[&&NHX:TOL=85160])[&&NHX:TOL=118483],(actinote rhodope[&&NHX:TOL=85156],(actinote surima[&&NHX:TOL=85158],((actinote guatemalena[&&NHX:TOL=85146],actinote discrepans[&&NHX:TOL=85144])[&&NHX:TOL=118487],((actinote morio[&&NHX:TOL=85152],actinote melanisans[&&NHX:TOL=85151])[&&NHX:TOL=118489],(actinote pellenea[&&NHX:TOL=85154],actinote carycina[&&NHX:TOL=85140])[&&NHX:TOL=118490])[&&NHX:TOL=118488])[&&NHX:TOL=118486])[&&NHX:TOL=118485])[&&NHX:TOL=118484])[&&NHX:TOL=118482])[&&NHX:TOL=118479])[&&NHX:TOL=118478])[&&NHX:TOL=118475])[&&NHX:TOL=118472])[&&NHX:TOL=118471])[&&NHX:TOL=118462])neotropical actinote clade[&&NHX:TOL=118461])[&&NHX:TOL=118460])[&&NHX:TOL=118457])[&&NHX:TOL=118454])[&&NHX:TOL=118444])[&&NHX:TOL=118436])actinote[&&NHX:TOL=70399])acraeini[&&NHX:TOL=70203],(((vindula arsinoe[&&NHX:TOL=87653],vindula dejone[&&NHX:TOL=87654],vindula erota[&&NHX:TOL=87655],vindula sapor[&&NHX:TOL=87656])vindula[&&NHX:TOL=70416],((algia fasciata[&&NHX:TOL=87678],algia felderi[&&NHX:TOL=87679],algia satyrina[&&NHX:TOL=87680])algia[&&NHX:TOL=70424],(((cirrochroa eremita[&&NHX:TOL=94070],cirrochroa recondita[&&NHX:TOL=94071],cirrochroa aoris[&&NHX:TOL=87681],cirrochroa clagia[&&NHX:TOL=87682],cirrochroa emalea[&&NHX:TOL=87683],cirrochroa malaya[&&NHX:TOL=87684],cirrochroa menones[&&NHX:TOL=87685],cirrochroa niassica[&&NHX:TOL=87686],cirrochroa nicobarica[&&NHX:TOL=87687],cirrochroa orissa[&&NHX:TOL=87688],cirrochroa regina[&&NHX:TOL=87689],cirrochroa satellita[&&NHX:TOL=87690],cirrochroa semiramis[&&NHX:TOL=87691],cirrochroa surya[&&NHX:TOL=87692],cirrochroa thais[&&NHX:TOL=87693],cirrochroa thule[&&NHX:TOL=87694],cirrochroa tyche[&&NHX:TOL=87695],cirrochroa imperatrix[&&NHX:TOL=87696])cirrochroa[&&NHX:TOL=70426],algiachroa woodfordi[&&NHX:TOL=70425])[&&NHX:TOL=70423],((terinos abisares[&&NHX:TOL=87657],terinos alurgis[&&NHX:TOL=87658],terinos atlita[&&NHX:TOL=87659],terinos clarissa[&&NHX:TOL=87660],terinos maddelena[&&NHX:TOL=87661],terinos taxiles[&&NHX:TOL=87662],terinos terpander[&&NHX:TOL=87663],terinos tethys[&&NHX:TOL=87664])terinos[&&NHX:TOL=70417],((lachnoptera anticlia[&&NHX:TOL=85304],lachnoptera ayresii[&&NHX:TOL=85305])lachnoptera[&&NHX:TOL=70427],(((phalanta eurytis[&&NHX:TOL=85306],phalanta madagascariensis[&&NHX:TOL=85307],phalanta phalantha[&&NHX:TOL=85308],phalanta philiberti[&&NHX:TOL=85309],phalanta alcippe[&&NHX:TOL=94074],[&&NHX:TOL=94075])phalanta[&&NHX:TOL=70422],(vagrans egista[&&NHX:TOL=94072],vagrans sinha[&&NHX:TOL=94073])vagrans[&&NHX:TOL=70420])[&&NHX:TOL=87676],((cupha arias[&&NHX:TOL=87665],cupha crameri[&&NHX:TOL=87666],cupha erymanthis[&&NHX:TOL=87667],cupha lampetia[&&NHX:TOL=87668],cupha maeonides[&&NHX:TOL=87669],cupha melichrysos[&&NHX:TOL=87670],cupha prosope[&&NHX:TOL=87671])cupha[&&NHX:TOL=70421],smerina manoro[&&NHX:TOL=70415])[&&NHX:TOL=87677])[&&NHX:TOL=70418])[&&NHX:TOL=87675])[&&NHX:TOL=87674])[&&NHX:TOL=87673])[&&NHX:TOL=87672])vagrantini[&&NHX:TOL=70207],((euptoieta thekla[&&NHX:TOL=76545],euptoieta sunides[&&NHX:TOL=76544],euptoieta poasina[&&NHX:TOL=76543],euptoieta perdistincta[&&NHX:TOL=76542],euptoieta hortensia[&&NHX:TOL=76541],euptoieta hegesia[&&NHX:TOL=76540],euptoieta claudia[&&NHX:TOL=76539],euptoieta bogotana[&&NHX:TOL=87348],[&&NHX:TOL=87349],euptoieta n. sp.[&&NHX:TOL=87350],[&&NHX:TOL=87351])euptoieta[&&NHX:TOL=70405],(pardopsis punctatissima[&&NHX:TOL=70404],((yramea cytheris[&&NHX:TOL=76668],yramea inca[&&NHX:TOL=76669],yramea lathonioides[&&NHX:TOL=76670],yramea modesta[&&NHX:TOL=76671],yramea sobrina[&&NHX:TOL=76672],yramea lynx[&&NHX:TOL=76673])yramea[&&NHX:TOL=70414],((((((boloria selenis[&&NHX:TOL=76632],boloria oscarus[&&NHX:TOL=76633])[&&NHX:TOL=76631],boloria angarensis[&&NHX:TOL=76635],(boloria chariclea[&&NHX:TOL=76636],boloria butleri[&&NHX:TOL=76647],boloria titania[&&NHX:TOL=76634])[&&NHX:TOL=79158],boloria kriemhild[&&NHX:TOL=76637])[&&NHX:TOL=76630],boloria euphrosyne[&&NHX:TOL=76638],boloria polaris[&&NHX:TOL=76640],boloria erda[&&NHX:TOL=76639])[&&NHX:TOL=76628],boloria jerdoni[&&NHX:TOL=76641],boloria matveevi[&&NHX:TOL=76645],(boloria freija[&&NHX:TOL=76642],boloria natazhati[&&NHX:TOL=76644])[&&NHX:TOL=79159],boloria iphigenia[&&NHX:TOL=76624],boloria bellona[&&NHX:TOL=76654],boloria epithore[&&NHX:TOL=76656],boloria gong[&&NHX:TOL=76657],boloria improba[&&NHX:TOL=76658],boloria frigga[&&NHX:TOL=76659],boloria hegemone[&&NHX:TOL=76660],boloria thore[&&NHX:TOL=76661],(boloria astarte[&&NHX:TOL=76664],boloria distincta[&&NHX:TOL=76646])[&&NHX:TOL=79160],boloria dia[&&NHX:TOL=76665],boloria alberta[&&NHX:TOL=76666],boloria selene[&&NHX:TOL=76667],boloria perryi[&&NHX:TOL=76623],boloria tritonia[&&NHX:TOL=76643])boloria clossiana[&&NHX:TOL=76625],((boloria alaskensis[&&NHX:TOL=76610],boloria frigidalis[&&NHX:TOL=76611],boloria purpurea[&&NHX:TOL=76612],boloria altaica[&&NHX:TOL=76613],boloria sipora[&&NHX:TOL=76614],boloria banghaasi[&&NHX:TOL=76615],boloria caucasica[&&NHX:TOL=76616],boloria graeca[&&NHX:TOL=76617],boloria aquilonaris[&&NHX:TOL=76618],boloria napaea[&&NHX:TOL=76619],boloria pales[&&NHX:TOL=76620])boloria boloria[&&NHX:TOL=76609],boloria proclossiana eunomia[&&NHX:TOL=76621])[&&NHX:TOL=79161])boloria[&&NHX:TOL=70413],(((issoria eugenia[&&NHX:TOL=76599],issoria gemmata[&&NHX:TOL=76600],issoria altissima[&&NHX:TOL=76601])[&&NHX:TOL=76598],(((issoria hanningtoni[&&NHX:TOL=76605],issoria baumanni[&&NHX:TOL=76606])[&&NHX:TOL=76604],issoria smaragdifera[&&NHX:TOL=76607])[&&NHX:TOL=76603],issoria lathonia[&&NHX:TOL=76608])[&&NHX:TOL=76602])issoria[&&NHX:TOL=70412],((((argynnis paphia[&&NHX:TOL=76547],argynnis sagana[&&NHX:TOL=76548])[&&NHX:TOL=76546],argynnis pandora[&&NHX:TOL=76554])[&&NHX:TOL=79153],((argynnis childreni[&&NHX:TOL=76551],argynnis zenobia[&&NHX:TOL=76552])[&&NHX:TOL=76550],argynnis hyperbius[&&NHX:TOL=76553])[&&NHX:TOL=76549],((argynnis ruslana[&&NHX:TOL=76556],argynnis laodice[&&NHX:TOL=76557])[&&NHX:TOL=76555],argynnis anadyomene[&&NHX:TOL=76570])[&&NHX:TOL=79154],((argynnis niobe[&&NHX:TOL=76563],argynnis auresiana[&&NHX:TOL=76560],argynnis adippe[&&NHX:TOL=76564],argynnis coredippe[&&NHX:TOL=76566],argynnis nerippe[&&NHX:TOL=76567],argynnis xipe[&&NHX:TOL=76568],argynnis elisa[&&NHX:TOL=76571],argynnis vorax[&&NHX:TOL=76573],argynnis argyrospilata[&&NHX:TOL=76572],argynnis jainadeva[&&NHX:TOL=76569])[&&NHX:TOL=76562],argynnis kamala[&&NHX:TOL=76565])[&&NHX:TOL=79155],((argynnis diana[&&NHX:TOL=76576],argynnis cybele[&&NHX:TOL=76577],argynnis aphrodite[&&NHX:TOL=76578],argynnis idalia[&&NHX:TOL=76579],argynnis nokomis[&&NHX:TOL=76580],argynnis edwardsii[&&NHX:TOL=76581],argynnis coronis[&&NHX:TOL=76582],argynnis zerene[&&NHX:TOL=76583],argynnis carolae[&&NHX:TOL=76584],argynnis callippe[&&NHX:TOL=76585],argynnis egleis[&&NHX:TOL=76586],argynnis adiaste[&&NHX:TOL=76587],argynnis atlantis[&&NHX:TOL=76588],argynnis hesperis[&&NHX:TOL=76589],argynnis hydaspe[&&NHX:TOL=76590],argynnis mormonia[&&NHX:TOL=76591])[&&NHX:TOL=76575],argynnis clara[&&NHX:TOL=76559],(argynnis aglaja[&&NHX:TOL=76592],argynnis alexandra[&&NHX:TOL=76558])[&&NHX:TOL=79156])[&&NHX:TOL=76574])argynnis[&&NHX:TOL=70410],((brenthis daphne[&&NHX:TOL=76594],brenthis ino[&&NHX:TOL=76595])[&&NHX:TOL=76593],(brenthis mofidii[&&NHX:TOL=76597],brenthis hecate[&&NHX:TOL=76596])[&&NHX:TOL=93891])brenthis[&&NHX:TOL=70411])[&&NHX:TOL=70409])argynnina[&&NHX:TOL=70408])[&&NHX:TOL=70407])[&&NHX:TOL=70406])[&&NHX:TOL=118423])argynnini[&&NHX:TOL=70206])[&&NHX:TOL=70205])[&&NHX:TOL=118422])[&&NHX:TOL=118421])heliconiinae[&&NHX:TOL=12194])[&&NHX:TOL=69945],(((((apatura ambica[&&NHX:TOL=87881],apatura ilia[&&NHX:TOL=87883],apatura iris[&&NHX:TOL=87884],apatura laverna[&&NHX:TOL=87885],apatura metis[&&NHX:TOL=87886],apatura nycteis[&&NHX:TOL=87887])apatura[&&NHX:TOL=70223],(mimathyma schrenckii[&&NHX:TOL=87889],mimathyma chevana[&&NHX:TOL=87882],mimathyma ambica[&&NHX:TOL=138036],mimathyma nycteis[&&NHX:TOL=138037])mimathyma[&&NHX:TOL=70224],(chitoria sordida[&&NHX:TOL=87890],chitoria ulupi[&&NHX:TOL=87891])chitoria[&&NHX:TOL=70225],(dilipa fenestra[&&NHX:TOL=87892],dilipa morgiana[&&NHX:TOL=87893],dilipa limenitoides[&&NHX:TOL=70372])dilipa[&&NHX:TOL=70226],euapatura mirza[&&NHX:TOL=70227],eulaceura osteria[&&NHX:TOL=70228],(rohana macar[&&NHX:TOL=87876],rohana nakula[&&NHX:TOL=87877],rohana parisatis[&&NHX:TOL=87878],rohana parvata[&&NHX:TOL=87879],rohana rhea[&&NHX:TOL=87880])rohana[&&NHX:TOL=70229],(euripus consimilis[&&NHX:TOL=87897],euripus nyctelius[&&NHX:TOL=87898],euripus robustus[&&NHX:TOL=87899])euripus[&&NHX:TOL=70230],(helcyra chionippe[&&NHX:TOL=87900],helcyra hemina[&&NHX:TOL=87901],helcyra subalba[&&NHX:TOL=87902],helcyra superba[&&NHX:TOL=87903],helcyra celebensis[&&NHX:TOL=93923],helcyra miyamotoi[&&NHX:TOL=118315])helcyra[&&NHX:TOL=70231],(herona marathus[&&NHX:TOL=87904],herona sumatrana[&&NHX:TOL=87905])herona[&&NHX:TOL=70232],((hestina assimilis[&&NHX:TOL=87906],hestina dissimilis[&&NHX:TOL=87907],hestina japonica[&&NHX:TOL=87909],hestina persimilis[&&NHX:TOL=87912],hestina waterstradti[&&NHX:TOL=87913],hestina nama[&&NHX:TOL=137730],[&&NHX:TOL=137731])hestina[&&NHX:TOL=70233],(hestinalis divona[&&NHX:TOL=87908],hestinalis mimetica[&&NHX:TOL=87910],hestinalis nama[&&NHX:TOL=87911])hestinalis[&&NHX:TOL=70234])[&&NHX:TOL=93925],(sasakia charonda[&&NHX:TOL=87914],sasakia funebris[&&NHX:TOL=87915])sasakia[&&NHX:TOL=70235],(sephisa chandra[&&NHX:TOL=87916],sephisa daimio[&&NHX:TOL=87917],sephisa dichroa[&&NHX:TOL=87918],sephisa princeps[&&NHX:TOL=87919])sephisa[&&NHX:TOL=70236],apaturina erminea[&&NHX:TOL=70237],(apaturopsis cleochares[&&NHX:TOL=86788],apaturopsis kilusa[&&NHX:TOL=86789],apaturopsis paulianii[&&NHX:TOL=86790])apaturopsis[&&NHX:TOL=70238],(timelaea aformis[&&NHX:TOL=87920],timelaea albescens[&&NHX:TOL=87921],timelaea maculata[&&NHX:TOL=87922],timelaea nana[&&NHX:TOL=87923],timelaea radiata[&&NHX:TOL=87924])timelaea[&&NHX:TOL=70239],thaleropis ionia[&&NHX:TOL=70240],(asterocampa celtis[&&NHX:TOL=86769],asterocampa clyton[&&NHX:TOL=86770],asterocampa idyja[&&NHX:TOL=86771],asterocampa leilia[&&NHX:TOL=86772])asterocampa[&&NHX:TOL=70241],(doxocopa agathina[&&NHX:TOL=86773],doxocopa callianira[&&NHX:TOL=86774],doxocopa clothilda[&&NHX:TOL=86775],doxocopa cyane[&&NHX:TOL=86776],doxocopa elis[&&NHX:TOL=86777],doxocopa excelsa[&&NHX:TOL=86778],doxocopa kallina[&&NHX:TOL=86779],doxocopa laure[&&NHX:TOL=86780],doxocopa laurentia[&&NHX:TOL=86781],doxocopa lavinia[&&NHX:TOL=86782],doxocopa linda[&&NHX:TOL=86783],doxocopa pavon[&&NHX:TOL=86784],doxocopa thoe[&&NHX:TOL=86785],doxocopa zalmunna[&&NHX:TOL=86786],doxocopa zunilda[&&NHX:TOL=86787])doxocopa[&&NHX:TOL=70242])apaturinae[&&NHX:TOL=12191],((biblis hyperia[&&NHX:TOL=70442],(ariadne actisanes[&&NHX:TOL=86613],ariadne albifascia[&&NHX:TOL=86614],ariadne enotrea[&&NHX:TOL=86615],ariadne pagenstecheri[&&NHX:TOL=86616],ariadne personata[&&NHX:TOL=86617],ariadne ariadne[&&NHX:TOL=87716],ariadne merione[&&NHX:TOL=87717],ariadne specularia[&&NHX:TOL=87718],ariadne isaeus[&&NHX:TOL=87719],ariadne celebensis[&&NHX:TOL=93913],ariadne merionoides[&&NHX:TOL=93914])ariadne[&&NHX:TOL=70443],(laringa castelnaui[&&NHX:TOL=87720],laringa horsfieldii[&&NHX:TOL=87721])laringa[&&NHX:TOL=70444],(eurytela alinda[&&NHX:TOL=86620],eurytela dryope[&&NHX:TOL=86621],eurytela hiarbas[&&NHX:TOL=86622],eurytela narinda[&&NHX:TOL=86623])eurytela[&&NHX:TOL=70445],(neptidopsis fulgurata[&&NHX:TOL=86618],neptidopsis ophione[&&NHX:TOL=86619])neptidopsis[&&NHX:TOL=70446],mesoxantha ethosea[&&NHX:TOL=70447],(byblia anavatara[&&NHX:TOL=86611],byblia ilithyia[&&NHX:TOL=86612])byblia[&&NHX:TOL=70448],mestra dorcas[&&NHX:TOL=70449],archimestra teleboas[&&NHX:TOL=70450],(vila azeca[&&NHX:TOL=76736],vila emilia[&&NHX:TOL=76737],vila eueidiformis[&&NHX:TOL=76738])vila[&&NHX:TOL=70451])biblidini[&&NHX:TOL=70243],((catonephele acontius[&&NHX:TOL=76739],catonephele antinoe[&&NHX:TOL=76740],catonephele chromis[&&NHX:TOL=76741],catonephele cortesi[&&NHX:TOL=76742],catonephele mexicana[&&NHX:TOL=76743],catonephele numilia[&&NHX:TOL=76744],catonephele nyctimus[&&NHX:TOL=76745],catonephele orites[&&NHX:TOL=76746],catonephele sabrina[&&NHX:TOL=76747],catonephele salacia[&&NHX:TOL=76748],catonephele salambria[&&NHX:TOL=76749])catonephele[&&NHX:TOL=70452],(nessaea aglaura[&&NHX:TOL=76750],nessaea batesii[&&NHX:TOL=76751],nessaea hewitsonii[&&NHX:TOL=76752],nessaea obrinus[&&NHX:TOL=76753])nessaea[&&NHX:TOL=70453],(myscelia aracynthia[&&NHX:TOL=76765],myscelia capenas[&&NHX:TOL=76766],myscelia cyananthe[&&NHX:TOL=76767],myscelia cyaniris[&&NHX:TOL=76768],myscelia ethusa[&&NHX:TOL=76769],myscelia hypatia[&&NHX:TOL=76770],myscelia leucocyana[&&NHX:TOL=76771],myscelia milloi[&&NHX:TOL=76772],myscelia orsis[&&NHX:TOL=76773])myscelia[&&NHX:TOL=70454],sea sophronia[&&NHX:TOL=70455],(((eunica bechina[&&NHX:TOL=76782],eunica cuvierii[&&NHX:TOL=76790],eunica tatila[&&NHX:TOL=76812])[&&NHX:TOL=77735],(eunica evelide[&&NHX:TOL=76793],eunica caelina[&&NHX:TOL=76784])[&&NHX:TOL=77736],(((((eunica orphise[&&NHX:TOL=76806],eunica violetta[&&NHX:TOL=76815],eunica veronica[&&NHX:TOL=76813],(eunica viola[&&NHX:TOL=76814],eunica clytia[&&NHX:TOL=76788])[&&NHX:TOL=77742])[&&NHX:TOL=77741],(eunica pusilla[&&NHX:TOL=76809],eunica monima[&&NHX:TOL=76803])[&&NHX:TOL=77743],(eunica incognita[&&NHX:TOL=76795],eunica amelia[&&NHX:TOL=76779])[&&NHX:TOL=77744],eunica marsolia[&&NHX:TOL=76802])[&&NHX:TOL=77740],(eunica maja[&&NHX:TOL=76799],eunica anna[&&NHX:TOL=76781])[&&NHX:TOL=77745],(((((eunica pomona[&&NHX:TOL=76808],eunica alcmena[&&NHX:TOL=76777],eunica eurota[&&NHX:TOL=76792])[&&NHX:TOL=77750],eunica alpais[&&NHX:TOL=76778])[&&NHX:TOL=77749],(eunica volumna[&&NHX:TOL=76816],eunica brunnea[&&NHX:TOL=76783])[&&NHX:TOL=77751])[&&NHX:TOL=77748],eunica carias[&&NHX:TOL=76786],((eunica sophonisba[&&NHX:TOL=76810],eunica chlororhoa[&&NHX:TOL=76787])[&&NHX:TOL=77753],eunica norica[&&NHX:TOL=76805])[&&NHX:TOL=77752])[&&NHX:TOL=77747],eunica sydonia[&&NHX:TOL=76811])[&&NHX:TOL=77746],eunica malvina[&&NHX:TOL=76800],eunica concordia[&&NHX:TOL=76789])[&&NHX:TOL=77739],(eunica mygdonia[&&NHX:TOL=76804],eunica amycla[&&NHX:TOL=76780],eunica caralis[&&NHX:TOL=76785])[&&NHX:TOL=77754])[&&NHX:TOL=77738],((eunica macris[&&NHX:TOL=76798],eunica heraclitus[&&NHX:TOL=76794],eunica phasis[&&NHX:TOL=76807])[&&NHX:TOL=77756],eunica interphasis[&&NHX:TOL=76797])[&&NHX:TOL=77755],((eunica ingens[&&NHX:TOL=76796],eunica eburnea[&&NHX:TOL=76791])[&&NHX:TOL=77758],eunica margarita[&&NHX:TOL=76801])[&&NHX:TOL=77757])[&&NHX:TOL=77737])eunica[&&NHX:TOL=70457],(sevenia amazoula[&&NHX:TOL=86625],sevenia amulia[&&NHX:TOL=86626],sevenia benguelae[&&NHX:TOL=86627],sevenia boisduvali[&&NHX:TOL=86628],sevenia consors[&&NHX:TOL=86629],sevenia garega[&&NHX:TOL=86630],sevenia howensis[&&NHX:TOL=86631],sevenia madagascariensis[&&NHX:TOL=86632],sevenia moranti[&&NHX:TOL=86633],sevenia natalensis[&&NHX:TOL=86634],sevenia occidentalium[&&NHX:TOL=86635],sevenia pechueli[&&NHX:TOL=86636],sevenia pseudotrimeni[&&NHX:TOL=86637],sevenia silvicola[&&NHX:TOL=86638],sevenia trimeni[&&NHX:TOL=86639],sevenia umbrina[&&NHX:TOL=86640])sevenia[&&NHX:TOL=86624])[&&NHX:TOL=70456],(cybdelis boliviana[&&NHX:TOL=76774],cybdelis mnasylus[&&NHX:TOL=76775],cybdelis phaesyla[&&NHX:TOL=76776])cybdelis[&&NHX:TOL=70459])epicaliini[&&NHX:TOL=70244],((hamadryas albicornis[&&NHX:TOL=86641],hamadryas alicia[&&NHX:TOL=86642],hamadryas amphichloe[&&NHX:TOL=86643],hamadryas amphinome[&&NHX:TOL=86644],hamadryas arete[&&NHX:TOL=86645],hamadryas arinome[&&NHX:TOL=86646],hamadryas atlantis[&&NHX:TOL=86647],hamadryas belladonna[&&NHX:TOL=86648],hamadryas chloe[&&NHX:TOL=86649],hamadryas epinome[&&NHX:TOL=86650],hamadryas februa[&&NHX:TOL=86651],hamadryas feronia[&&NHX:TOL=86652],hamadryas fornax[&&NHX:TOL=86653],hamadryas glauconome[&&NHX:TOL=86654],hamadryas guatemalena[&&NHX:TOL=86655],hamadryas iphthime[&&NHX:TOL=86656],hamadryas julitta[&&NHX:TOL=86657],hamadryas laodamia[&&NHX:TOL=86658],hamadryas rosandra[&&NHX:TOL=86659],hamadryas velutina[&&NHX:TOL=86660])hamadryas[&&NHX:TOL=70460],(ectima erycinoides[&&NHX:TOL=86664],ectima iona[&&NHX:TOL=86665],ectima lirides[&&NHX:TOL=86666],ectima thecla[&&NHX:TOL=86667])ectima[&&NHX:TOL=70461],((panacea procilla[&&NHX:TOL=86661],panacea prola[&&NHX:TOL=86662],panacea regina[&&NHX:TOL=86663])panacea[&&NHX:TOL=70463],batesia hypochlora[&&NHX:TOL=70464])[&&NHX:TOL=70462])ageroniini[&&NHX:TOL=70245],(((asterope batesii[&&NHX:TOL=86668],asterope markii[&&NHX:TOL=86672])[&&NHX:TOL=111385],((((asterope leprieuri[&&NHX:TOL=86671],asterope sapphira[&&NHX:TOL=86673])[&&NHX:TOL=111389],asterope buckleyi[&&NHX:TOL=86669])[&&NHX:TOL=111388],asterope whitelyi[&&NHX:TOL=86674])[&&NHX:TOL=111387],asterope degandii[&&NHX:TOL=86670])[&&NHX:TOL=111386])asterope[&&NHX:TOL=70465],(pyrrhogyra amphiro[&&NHX:TOL=86690],pyrrhogyra crameri[&&NHX:TOL=86691],pyrrhogyra edocla[&&NHX:TOL=86692],pyrrhogyra neaerea[&&NHX:TOL=86693],pyrrhogyra otolais[&&NHX:TOL=86694],pyrrhogyra stratonicus[&&NHX:TOL=86695])pyrrhogyra[&&NHX:TOL=70466],(epiphile adrasta[&&NHX:TOL=86675],epiphile boliviana[&&NHX:TOL=86676],epiphile chrysites[&&NHX:TOL=86677],epiphile dilecta[&&NHX:TOL=86678],epiphile epicaste[&&NHX:TOL=86679],epiphile epimenes[&&NHX:TOL=86680],epiphile eriopis[&&NHX:TOL=86681],epiphile grandis[&&NHX:TOL=86682],epiphile hermosa[&&NHX:TOL=86683],epiphile hubneri[&&NHX:TOL=86684],epiphile iblis[&&NHX:TOL=86685],epiphile lampethusa[&&NHX:TOL=86686],epiphile latifasciata[&&NHX:TOL=86687],epiphile orea[&&NHX:TOL=86688],epiphile n. sp.[&&NHX:TOL=86689])epiphile[&&NHX:TOL=70467],lucinia cadma[&&NHX:TOL=70468],bolboneura sylphis[&&NHX:TOL=70469],(temenis huebneri[&&NHX:TOL=86696],temenis laothoe[&&NHX:TOL=86697],temenis pulchra[&&NHX:TOL=86698])temenis[&&NHX:TOL=70470],nica flavilla[&&NHX:TOL=70471],peria lamis[&&NHX:TOL=70472])epiphilini[&&NHX:TOL=70246],(dynamine aerata[&&NHX:TOL=70473],dynamine agacles[&&NHX:TOL=70474],dynamine agatha[&&NHX:TOL=70475],dynamine amplias[&&NHX:TOL=70476],dynamine anubis[&&NHX:TOL=70477],dynamine arene[&&NHX:TOL=70478],dynamine artemisia[&&NHX:TOL=70479],dynamine ate[&&NHX:TOL=70480],dynamine athemon[&&NHX:TOL=70481],dynamine chryseis[&&NHX:TOL=70482],dynamine coenus[&&NHX:TOL=70483],dynamine colombiana[&&NHX:TOL=70484],dynamine dyonis[&&NHX:TOL=70485],dynamine erchia[&&NHX:TOL=70486],dynamine gisella[&&NHX:TOL=70487],dynamine haenschi[&&NHX:TOL=70488],dynamine hecuba[&&NHX:TOL=70489],dynamine ines[&&NHX:TOL=70490],dynamine intermedia[&&NHX:TOL=70491],dynamine laugieri[&&NHX:TOL=70492],dynamine meridionalis[&&NHX:TOL=70493],dynamine myrrhina[&&NHX:TOL=70494],dynamine myrson[&&NHX:TOL=70495],dynamine neoris[&&NHX:TOL=70496],dynamine onias[&&NHX:TOL=70497],dynamine paulina[&&NHX:TOL=70498],dynamine pebana[&&NHX:TOL=70499],dynamine perpetua[&&NHX:TOL=70500],dynamine persis[&&NHX:TOL=70501],dynamine postverta[&&NHX:TOL=70502],dynamine racidula[&&NHX:TOL=70503],dynamine sara[&&NHX:TOL=70504],dynamine serina[&&NHX:TOL=70505],dynamine setabis[&&NHX:TOL=70506],dynamine sosthenes[&&NHX:TOL=70507],dynamine theseus[&&NHX:TOL=70508],dynamine tithia[&&NHX:TOL=70509],dynamine vicaria[&&NHX:TOL=70510],dynamine zenobia[&&NHX:TOL=70511],dynamine n. sp.[&&NHX:TOL=86699],dynamine alexae[&&NHX:EXT=Y:TOL=110617])dynamine[&&NHX:TOL=70247],((diaethria anna[&&NHX:TOL=86721],diaethria astala[&&NHX:TOL=86722],diaethria bacchis[&&NHX:TOL=86723],diaethria candrena[&&NHX:TOL=86724],diaethria ceryx[&&NHX:TOL=86725],diaethria clymena[&&NHX:TOL=86726],diaethria eluina[&&NHX:TOL=86727],diaethria euclides[&&NHX:TOL=86728],diaethria gabaza[&&NHX:TOL=86729],diaethria neglecta[&&NHX:TOL=86730],diaethria nystographa[&&NHX:TOL=86731],diaethria pandama[&&NHX:TOL=86732])diaethria[&&NHX:TOL=70512],(callicore astarte[&&NHX:TOL=86701],callicore atacama[&&NHX:TOL=86702],callicore brome[&&NHX:TOL=86703],callicore cyclops[&&NHX:TOL=86704],callicore cynosura[&&NHX:TOL=86705],callicore eunomia[&&NHX:TOL=86706],callicore excelsior[&&NHX:TOL=86707],callicore felderi[&&NHX:TOL=86708],callicore hesperis[&&NHX:TOL=86709],callicore hydarnis[&&NHX:TOL=86710],callicore hydaspes[&&NHX:TOL=86711],callicore hystaspes[&&NHX:TOL=86712],callicore ines[&&NHX:TOL=86713],callicore lyca[&&NHX:TOL=86714],callicore maronensis[&&NHX:TOL=86715],callicore pitheas[&&NHX:TOL=86716],callicore pygas[&&NHX:TOL=86717],callicore sorana[&&NHX:TOL=86718],callicore texa[&&NHX:TOL=86719],callicore tolima[&&NHX:TOL=86720])callicore[&&NHX:TOL=70513],(perisama alicia[&&NHX:TOL=86737],perisama antioquia[&&NHX:TOL=86738],perisama bomplandii[&&NHX:TOL=86739],perisama cabirnia[&&NHX:TOL=86740],perisama calamis[&&NHX:TOL=86741],perisama camelita[&&NHX:TOL=86742],perisama canoma[&&NHX:TOL=86743],perisama clisithera[&&NHX:TOL=86744],perisama cloelia[&&NHX:TOL=86745],perisama comnena[&&NHX:TOL=86746],perisama dorbignyi[&&NHX:TOL=86747],perisama euriclea[&&NHX:TOL=86748],perisama gisco[&&NHX:TOL=86749],perisama goeringi[&&NHX:TOL=86750],perisama hazarma[&&NHX:TOL=86751],perisama humboldtii[&&NHX:TOL=86752],perisama lanice[&&NHX:TOL=86753],perisama lebasii[&&NHX:TOL=86754],perisama morona[&&NHX:TOL=86755],perisama nevada[&&NHX:TOL=86756],perisama oppelii[&&NHX:TOL=86757],perisama ouma[&&NHX:TOL=86758],perisama paralicia[&&NHX:TOL=86759],perisama patara[&&NHX:TOL=86760],perisama philinus[&&NHX:TOL=86761],perisama satanas[&&NHX:TOL=86762],perisama tristrigosa[&&NHX:TOL=86763],perisama tryphena[&&NHX:TOL=86764],perisama typhania[&&NHX:TOL=86765],perisama vitringa[&&NHX:TOL=86766],perisama yeba[&&NHX:TOL=86767],perisama n. sp.[&&NHX:TOL=86768])perisama[&&NHX:TOL=70514],(orophila cardases[&&NHX:TOL=86735],orophila diotima[&&NHX:TOL=86736])orophila[&&NHX:TOL=70515],(mesotaenia barnesi[&&NHX:TOL=86733],mesotaenia vaninka[&&NHX:TOL=86734])mesotaenia[&&NHX:TOL=70516],antigonis pharsalia[&&NHX:TOL=70517],haematera pyrame[&&NHX:TOL=70518],paulogramma pyracmon[&&NHX:TOL=70519],catacore kolyma[&&NHX:TOL=70520])callicorini[&&NHX:TOL=70248])biblidinae[&&NHX:TOL=69947])[&&NHX:TOL=139173],((((cyrestis achates[&&NHX:TOL=87813],cyrestis acilia[&&NHX:TOL=87814],cyrestis adaemon[&&NHX:TOL=87815],cyrestis camillus[&&NHX:TOL=87816],cyrestis cocles[&&NHX:TOL=87817],cyrestis eximia[&&NHX:TOL=93910],cyrestis heracles[&&NHX:TOL=93911],cyrestis lutea[&&NHX:TOL=87818],cyrestis maenalis[&&NHX:TOL=87819],cyrestis nais[&&NHX:TOL=87820],cyrestis nivea[&&NHX:TOL=87821],cyrestis paulinus[&&NHX:TOL=87822],cyrestis strigata[&&NHX:TOL=93912],cyrestis tabula[&&NHX:TOL=137732],cyrestis telamon[&&NHX:TOL=87823],cyrestis themire[&&NHX:TOL=87824],cyrestis theresae[&&NHX:TOL=137734],cyrestis thyodamas[&&NHX:TOL=87825],cyrestis thyonneus[&&NHX:TOL=87826])cyrestis[&&NHX:TOL=69958],(chersonesia intermedia[&&NHX:TOL=87808],chersonesia nicevillei[&&NHX:TOL=87809],chersonesia peraka[&&NHX:TOL=87810],chersonesia rahria[&&NHX:TOL=87811],chersonesia risa[&&NHX:TOL=87812])chersonesia[&&NHX:TOL=69961])[&&NHX:TOL=87807],(marpesia berania[&&NHX:TOL=87790],marpesia chiron[&&NHX:TOL=87791],marpesia corinna[&&NHX:TOL=87792],marpesia corita[&&NHX:TOL=87793],marpesia crethon[&&NHX:TOL=87794],marpesia egina[&&NHX:TOL=87795],marpesia eleuchea[&&NHX:TOL=87796],marpesia furcula[&&NHX:TOL=87797],marpesia harmonia[&&NHX:TOL=87798],marpesia livius[&&NHX:TOL=87799],marpesia marcella[&&NHX:TOL=87800],marpesia merops[&&NHX:TOL=87801],marpesia orsilochus[&&NHX:TOL=87802],marpesia petreus[&&NHX:TOL=87803],marpesia themistocles[&&NHX:TOL=87804],marpesia tutelina[&&NHX:TOL=87805],marpesia zerynthia[&&NHX:TOL=87806])marpesia[&&NHX:TOL=69960])cyrestinae[&&NHX:TOL=69949],(((historis odius[&&NHX:TOL=77175],historis acheronta[&&NHX:TOL=77176])historis[&&NHX:TOL=70297],(((baeotus aeilus[&&NHX:TOL=77179],baeotus beotus[&&NHX:TOL=77180])[&&NHX:TOL=77178],baeotus deucalion[&&NHX:TOL=77181])[&&NHX:TOL=77177],baeotus japetus[&&NHX:TOL=77182])baeotus[&&NHX:TOL=70298])coeini[&&NHX:TOL=70209],(((((precis coelestina[&&NHX:TOL=93953],precis eurodoce[&&NHX:TOL=93955],precis frobeniusi[&&NHX:TOL=93956],precis limnoria[&&NHX:TOL=93960],precis milonia[&&NHX:TOL=93961],precis pelarga[&&NHX:TOL=93963],precis rauana[&&NHX:TOL=93964],precis silvicola[&&NHX:TOL=93967],(precis ceryne[&&NHX:TOL=93952],((precis sinuata[&&NHX:TOL=93968],((precis andremiaja[&&NHX:TOL=93949],precis antilope[&&NHX:TOL=93950])[&&NHX:TOL=94002],(precis cuama[&&NHX:TOL=93954],precis tugela[&&NHX:TOL=93969])[&&NHX:TOL=94003])[&&NHX:TOL=94001])[&&NHX:TOL=94000],(precis octavia[&&NHX:TOL=93962],precis archesia[&&NHX:TOL=93951])[&&NHX:TOL=94004])[&&NHX:TOL=93999])[&&NHX:TOL=93998],precis actia[&&NHX:TOL=93947])precis[&&NHX:TOL=70314],(hypolimnas alimena[&&NHX:TOL=94026],hypolimnas anomala[&&NHX:TOL=94027],hypolimnas antevorta[&&NHX:TOL=94028],hypolimnas anthedon[&&NHX:TOL=94029],hypolimnas antilope[&&NHX:TOL=94030],hypolimnas aubergeri[&&NHX:TOL=94031],hypolimnas bartelotti[&&NHX:TOL=94032],hypolimnas bolina[&&NHX:TOL=94033],hypolimnas chapmani[&&NHX:TOL=94034],hypolimnas deceptor[&&NHX:TOL=94035],hypolimnas deois[&&NHX:TOL=94036],hypolimnas dexithea[&&NHX:TOL=94037],hypolimnas dimona[&&NHX:TOL=94038],hypolimnas dinarcha[&&NHX:TOL=94039],hypolimnas diomea[&&NHX:TOL=94040],hypolimnas euploeoides[&&NHX:TOL=94041],hypolimnas macarthuri[&&NHX:TOL=94042],hypolimnas mechowi[&&NHX:TOL=94043],hypolimnas misippus[&&NHX:TOL=94044],hypolimnas monteironis[&&NHX:TOL=94045],hypolimnas octocula[&&NHX:TOL=94046],hypolimnas pandarus[&&NHX:TOL=94047],hypolimnas pithoeka[&&NHX:TOL=94048],hypolimnas salmacis[&&NHX:TOL=94049],hypolimnas usambara[&&NHX:TOL=94050])hypolimnas[&&NHX:TOL=70315])[&&NHX:TOL=70313],(((protogoniomorpha anacardii[&&NHX:TOL=94017],protogoniomorpha parhassus[&&NHX:TOL=94018],protogoniomorpha duprei[&&NHX:TOL=118702])protogoniomorpha[&&NHX:TOL=70318],(yoma algina[&&NHX:TOL=94024],yoma sabina[&&NHX:TOL=94025])yoma[&&NHX:TOL=70319])[&&NHX:TOL=70317],(junonia goudoti[&&NHX:TOL=93957],junonia hadrope[&&NHX:TOL=93958],junonia rhadama[&&NHX:TOL=93965],junonia schmiedeli[&&NHX:TOL=93966],junonia adulatrix[&&NHX:TOL=93972],junonia timorensis[&&NHX:TOL=93994],junonia chorimene[&&NHX:TOL=94016],junonia africana[&&NHX:TOL=93948],junonia erigone[&&NHX:TOL=93980],(junonia cymodoce[&&NHX:TOL=93978],junonia ansorgei[&&NHX:TOL=93974])[&&NHX:TOL=118704],((junonia cytora[&&NHX:TOL=93979],junonia ? temora[&&NHX:TOL=94023])[&&NHX:TOL=118703],(junonia artaxia[&&NHX:TOL=93975],junonia touhilimasa[&&NHX:TOL=93995])[&&NHX:TOL=94014])[&&NHX:TOL=94013],(junonia gregorii[&&NHX:TOL=118706],(junonia natalica[&&NHX:TOL=93988],junonia terea[&&NHX:TOL=93993])[&&NHX:TOL=94012],junonia stygia[&&NHX:TOL=93992])[&&NHX:TOL=118705],((junonia hedonia[&&NHX:TOL=93983],(junonia iphita[&&NHX:TOL=93986],junonia atlites[&&NHX:TOL=93976])[&&NHX:TOL=118709])[&&NHX:TOL=118708],(junonia almana[&&NHX:TOL=93973],(junonia lemonias[&&NHX:TOL=93987],(((junonia oenone[&&NHX:TOL=93989],junonia hierta[&&NHX:TOL=93984])[&&NHX:TOL=118712],(junonia sophia[&&NHX:TOL=93991],junonia westermanni[&&NHX:TOL=93997])[&&NHX:TOL=118713],junonia villida[&&NHX:TOL=118714],junonia orithya[&&NHX:TOL=93990])[&&NHX:TOL=94011],(junonia vestina[&&NHX:TOL=93996],(junonia evarete[&&NHX:TOL=93981],(junonia coenia[&&NHX:TOL=93977],junonia genoveva[&&NHX:TOL=93982])[&&NHX:TOL=118716])[&&NHX:TOL=118715])[&&NHX:TOL=94010])[&&NHX:TOL=94009])[&&NHX:TOL=118711])[&&NHX:TOL=118710])[&&NHX:TOL=118707])junonia[&&NHX:TOL=70320],(salamis anteva[&&NHX:TOL=94019],salamis augustina[&&NHX:TOL=94020],salamis cacta[&&NHX:TOL=94021],salamis humbloti[&&NHX:TOL=103060])salamis[&&NHX:TOL=70321])[&&NHX:TOL=70316])junoniini[&&NHX:TOL=70215],((((((euphydryas anicia[&&NHX:TOL=70551],euphydryas colon[&&NHX:TOL=70552],euphydryas chalcedona[&&NHX:TOL=70553])[&&NHX:TOL=70550],euphydryas phaeton[&&NHX:TOL=70554])[&&NHX:TOL=70549],euphydryas editha[&&NHX:TOL=70555])[&&NHX:TOL=70548],(((((euphydryas maturna[&&NHX:TOL=70561],euphydryas intermedia[&&NHX:TOL=70562])[&&NHX:TOL=70560],euphydryas iduna[&&NHX:TOL=70563])[&&NHX:TOL=70559],euphydryas gillettii[&&NHX:TOL=70564])[&&NHX:TOL=70558],euphydryas cynthia[&&NHX:TOL=70565])[&&NHX:TOL=70557],(euphydryas desfontainii[&&NHX:TOL=70567],euphydryas aurinia[&&NHX:TOL=70568],euphydryas merope[&&NHX:TOL=70569],euphydryas orientalis[&&NHX:TOL=70570],euphydryas asiatica[&&NHX:TOL=70571])[&&NHX:TOL=70566])[&&NHX:TOL=70556])euphydryas[&&NHX:TOL=70299],(((((atlantea cryptadea[&&NHX:TOL=103095],atlantea pantoni[&&NHX:TOL=103096],atlantea perezi[&&NHX:TOL=103097],atlantea tulita[&&NHX:TOL=103098])atlantea[&&NHX:TOL=70572],((antillea pelops[&&NHX:TOL=103077],antillea proclea[&&NHX:TOL=103078])antillea[&&NHX:TOL=70595],((phystis simois[&&NHX:TOL=70594],telenassa fontus[&&NHX:TOL=103175])[&&NHX:TOL=117483],((mazia amazonica[&&NHX:TOL=70593],(ortilia gentina[&&NHX:TOL=103139],ortilia liriope[&&NHX:TOL=103141],ortilia polinella[&&NHX:TOL=103144],ortilia sejona[&&NHX:TOL=103145])ortilia[&&NHX:TOL=70592])[&&NHX:TOL=70591],((ortilia dicoma[&&NHX:TOL=103138],(ortilia velica[&&NHX:TOL=103146],(ortilia orthia[&&NHX:TOL=103142],ortilia orticas[&&NHX:TOL=103143])[&&NHX:TOL=117485])[&&NHX:TOL=117484])new phyciodina genus[&&NHX:TOL=70590],((tisona saladillensis[&&NHX:TOL=70588],(((tegosa etia[&&NHX:TOL=103160],tegosa selene[&&NHX:TOL=103169])[&&NHX:TOL=117488],(tegosa anieta[&&NHX:TOL=103158],tegosa tissoides[&&NHX:TOL=103171])[&&NHX:TOL=117489])[&&NHX:TOL=117487],((tegosa infrequens[&&NHX:TOL=103164],tegosa orobia[&&NHX:TOL=103167])[&&NHX:TOL=117491],(tegosa similis[&&NHX:TOL=117493],tegosa claudina[&&NHX:TOL=103159])[&&NHX:TOL=117492])[&&NHX:TOL=117490],tegosa flavida[&&NHX:TOL=103161],tegosa fragilis[&&NHX:TOL=103162],tegosa guatemalena[&&NHX:TOL=103163],tegosa nazaria[&&NHX:TOL=103165],tegosa nigrella[&&NHX:TOL=103166],tegosa pastazena[&&NHX:TOL=103168],tegosa serpia[&&NHX:TOL=103170])tegosa[&&NHX:TOL=70587])[&&NHX:TOL=70586],(phyciodes graphica[&&NHX:TOL=103149],((phyciodes pallescens[&&NHX:TOL=103152],phyciodes picta[&&NHX:TOL=103155])[&&NHX:TOL=117495],(phyciodes orseis[&&NHX:TOL=103151],(phyciodes mylitta[&&NHX:TOL=103150],phyciodes pallida[&&NHX:TOL=103153])[&&NHX:TOL=117497])[&&NHX:TOL=117496],phyciodes phaon[&&NHX:TOL=103154],(phyciodes cocyta[&&NHX:TOL=103148],phyciodes batesii[&&NHX:TOL=103147],phyciodes tharos[&&NHX:TOL=103157],phyciodes pulchella[&&NHX:TOL=103156])[&&NHX:TOL=117498])[&&NHX:TOL=117494])phyciodes[&&NHX:TOL=70589])[&&NHX:TOL=117486],((anthanassa acesas[&&NHX:TOL=103079],anthanassa annulata[&&NHX:TOL=103080],(anthanassa frisia[&&NHX:TOL=103088],(anthanassa texana[&&NHX:TOL=103094],(anthanassa otanes[&&NHX:TOL=103090],(anthanassa ardys[&&NHX:TOL=103081],anthanassa drusilla[&&NHX:TOL=103086])[&&NHX:TOL=117502])[&&NHX:TOL=117501])[&&NHX:TOL=117500])[&&NHX:TOL=117499],anthanassa argentea[&&NHX:TOL=103082],anthanassa atronia[&&NHX:TOL=103083],anthanassa crithona[&&NHX:TOL=103084],anthanassa dracaena[&&NHX:TOL=103085],anthanassa drymaea[&&NHX:TOL=103087],anthanassa nebulosa[&&NHX:TOL=103089],anthanassa ptolyca[&&NHX:TOL=103091],anthanassa sitalces[&&NHX:TOL=103092],anthanassa sosis[&&NHX:TOL=103093])anthanassa[&&NHX:TOL=70585],(((telenassa abas[&&NHX:TOL=103172],(telenassa delphia[&&NHX:TOL=103174],(telenassa berenice[&&NHX:TOL=103173],telenassa teletusa[&&NHX:TOL=103179])[&&NHX:TOL=117504])[&&NHX:TOL=117503],telenassa jana[&&NHX:TOL=103176],telenassa notus[&&NHX:TOL=103177],telenassa sepultus[&&NHX:TOL=103178])telenassa[&&NHX:TOL=70580],(castilia angusta[&&NHX:TOL=103099],((castilia castilla[&&NHX:TOL=103100],castilia perilla[&&NHX:TOL=103111])[&&NHX:TOL=117506],(castilia eranites[&&NHX:TOL=103103],(castilia ofella[&&NHX:TOL=103110],castilia myia[&&NHX:TOL=103107])[&&NHX:TOL=117508])[&&NHX:TOL=117507])[&&NHX:TOL=117505],castilia chiapaensis[&&NHX:TOL=103101],castilia chinantlensis[&&NHX:TOL=103102],castilia fulgora[&&NHX:TOL=103104],castilia griseobasalis[&&NHX:TOL=103105],castilia guaya[&&NHX:TOL=103106],castilia neria[&&NHX:TOL=103108],castilia nortbrundii[&&NHX:TOL=103109])castilia[&&NHX:TOL=70581])[&&NHX:TOL=70579],((janatella fellula[&&NHX:TOL=103135],(janatella leucodesma[&&NHX:TOL=103137],janatella hera[&&NHX:TOL=103136])[&&NHX:TOL=117510])janatella[&&NHX:TOL=70582],(eresia lansdorfi[&&NHX:TOL=103125],ortilia ithra[&&NHX:TOL=103140])[&&NHX:TOL=117511])[&&NHX:TOL=117509],(dagon catula[&&NHX:TOL=103112],dagon morena[&&NHX:TOL=103113],dagon pusilla[&&NHX:TOL=103114],eresia levina[&&NHX:TOL=103127])dagon[&&NHX:TOL=70583],(eresia actinote[&&NHX:TOL=103115],((eresia eunice[&&NHX:TOL=103123],eresia nauplius[&&NHX:TOL=103128])[&&NHX:TOL=117513],((eresia emerantia[&&NHX:TOL=103120],(eresia carme[&&NHX:TOL=103116],eresia polina[&&NHX:TOL=103133])[&&NHX:TOL=117516])[&&NHX:TOL=117515],((eresia letitia[&&NHX:TOL=103126],(eresia clio[&&NHX:TOL=103118],eresia perna[&&NHX:TOL=103131])[&&NHX:TOL=117519])[&&NHX:TOL=117518],(eresia phillyra[&&NHX:TOL=103132],(eresia pelonia[&&NHX:TOL=103130],(eresia ithomioides[&&NHX:TOL=103124],(eresia datis[&&NHX:TOL=103119],(eresia casiphia[&&NHX:TOL=103117],eresia sticta[&&NHX:TOL=103134])[&&NHX:TOL=117524])[&&NHX:TOL=117523])[&&NHX:TOL=117522])[&&NHX:TOL=117521])[&&NHX:TOL=117520])[&&NHX:TOL=117517])[&&NHX:TOL=117514])[&&NHX:TOL=117512],eresia erysice[&&NHX:TOL=103121],eresia estebana[&&NHX:TOL=103122],eresia olivencia[&&NHX:TOL=103129])eresia[&&NHX:TOL=70584])eresia s. l.[&&NHX:TOL=70578])[&&NHX:TOL=70577])[&&NHX:TOL=70576])[&&NHX:TOL=70575])[&&NHX:TOL=70574])[&&NHX:TOL=70573])phyciodina[&&NHX:TOL=70303],((gnathotriche mundina[&&NHX:TOL=70597],gnathotriche exclamationis[&&NHX:TOL=70598])gnathotriche[&&NHX:TOL=70304],(higginsius fasciata[&&NHX:TOL=70600],higginsius miriam[&&NHX:TOL=70601])higginsius[&&NHX:TOL=70599])[&&NHX:TOL=103180])[&&NHX:TOL=70302],(((melitaea mimetica[&&NHX:TOL=70621],melitaea cinxia[&&NHX:TOL=70638],melitaea agar[&&NHX:TOL=70637])melitaea cinxiagroup[&&NHX:TOL=77442],(((melitaea leechi[&&NHX:TOL=70641],((melitaea arcesia[&&NHX:TOL=70642],melitaea chuana[&&NHX:TOL=138222])[&&NHX:TOL=138221],(melitaea amoenula[&&NHX:TOL=70640],melitaea bellona[&&NHX:TOL=138224])[&&NHX:TOL=138223])[&&NHX:TOL=138220])melitaea arcesiagroup[&&NHX:TOL=138219],(melitaea diamina[&&NHX:TOL=70653],melitaea protomedia[&&NHX:TOL=70652])melitaea diaminagroup[&&NHX:TOL=70651])[&&NHX:TOL=138218],((melitaea elisabethae[&&NHX:TOL=138227],(melitaea solona[&&NHX:TOL=70643],(melitaea ludmilla[&&NHX:TOL=70644],(melitaea sultanensis[&&NHX:TOL=70648],(melitaea minerva[&&NHX:TOL=70650],melitaea pallas[&&NHX:TOL=70647])[&&NHX:TOL=138231])[&&NHX:TOL=138230])[&&NHX:TOL=138229])[&&NHX:TOL=138228])melitaea minervagroup[&&NHX:TOL=138226],(melitaea alatauica[&&NHX:TOL=70668],melitaea westsibirica[&&NHX:TOL=70671],melitaea rebeli[&&NHX:TOL=70672],((melitaea varia[&&NHX:TOL=70675],(melitaea parthenoides[&&NHX:TOL=70676],((melitaea centralasiae[&&NHX:TOL=70670],melitaea menetriesi[&&NHX:TOL=70673])[&&NHX:TOL=138236],(melitaea asteria[&&NHX:TOL=70674],melitaea aurelia[&&NHX:TOL=70677])[&&NHX:TOL=138237])[&&NHX:TOL=138235])[&&NHX:TOL=138234])[&&NHX:TOL=138233],(melitaea plotina[&&NHX:TOL=70669],(melitaea celadussa[&&NHX:TOL=70683],((melitaea britomartis[&&NHX:TOL=70679],melitaea deione[&&NHX:TOL=70678])[&&NHX:TOL=138241],(melitaea ambigua[&&NHX:TOL=70680],(melitaea athalia[&&NHX:TOL=70682],melitaea caucasogenita[&&NHX:TOL=70681])[&&NHX:TOL=138243])[&&NHX:TOL=138242])[&&NHX:TOL=138240])[&&NHX:TOL=138239])[&&NHX:TOL=138238])[&&NHX:TOL=138232])melitaea athaliagroup[&&NHX:TOL=70667])[&&NHX:TOL=138225],melitaea asteroida[&&NHX:TOL=70645],melitaea balba[&&NHX:TOL=70649],melitaea turanica[&&NHX:TOL=70646])[&&NHX:TOL=138217])melitaea clade[&&NHX:TOL=77439],((((melitaea collina[&&NHX:TOL=70663],melitaea consulis[&&NHX:TOL=70665])[&&NHX:TOL=138246],(melitaea romanovi[&&NHX:TOL=70634],melitaea trivia[&&NHX:TOL=70632])[&&NHX:TOL=138247])[&&NHX:TOL=138245],melitaea turkmanica[&&NHX:TOL=70664])melitaea collinagroup[&&NHX:TOL=77438],(melitaea pseudosibina[&&NHX:TOL=70655],melitaea sarvistana[&&NHX:TOL=70658],((melitaea arduinna[&&NHX:TOL=70635],melitaea avinovi[&&NHX:TOL=70636])[&&NHX:TOL=138249],(melitaea aetherie[&&NHX:TOL=70657],(melitaea telona[&&NHX:TOL=70660],(melitaea punica[&&NHX:TOL=70659],(melitaea sibina[&&NHX:TOL=70656],(melitaea phoebe[&&NHX:TOL=70662],melitaea scotosia[&&NHX:TOL=70661])[&&NHX:TOL=138254])[&&NHX:TOL=138253])[&&NHX:TOL=138252])[&&NHX:TOL=138251])[&&NHX:TOL=138250])[&&NHX:TOL=138248])melitaea phoebegroup[&&NHX:TOL=70654],(melitaea lutko[&&NHX:TOL=70620],(((melitaea athene[&&NHX:TOL=70631],((melitaea infernalis[&&NHX:TOL=70627],melitaea shandura[&&NHX:TOL=70630])[&&NHX:TOL=138258],(melitaea ambrisia[&&NHX:TOL=70628],((melitaea fergana[&&NHX:TOL=70626],melitaea macarandica[&&NHX:TOL=138262])[&&NHX:TOL=138261],(melitaea cassandra[&&NHX:TOL=70625],melitaea lunulata[&&NHX:TOL=70624])[&&NHX:TOL=138263])[&&NHX:TOL=138260])[&&NHX:TOL=138259])[&&NHX:TOL=138257])[&&NHX:TOL=138256],melitaea alraschid[&&NHX:TOL=70629])melitaea ferganagroup[&&NHX:TOL=70623],(((melitaea casta[&&NHX:TOL=70612],(melitaea persea[&&NHX:TOL=70616],melitaea wiltshirei[&&NHX:TOL=138267])[&&NHX:TOL=138266])[&&NHX:TOL=138265],((melitaea acreina[&&NHX:TOL=70622],(melitaea permuta[&&NHX:TOL=70605],melitaea ala[&&NHX:TOL=70609])[&&NHX:TOL=138270])[&&NHX:TOL=138269],((melitaea gina[&&NHX:TOL=70666],melitaea deserticola[&&NHX:TOL=70614])[&&NHX:TOL=138272],(((melitaea didymoides[&&NHX:TOL=70610],melitaea sutschana[&&NHX:TOL=70604])[&&NHX:TOL=138275],melitaea saxatilis[&&NHX:TOL=70615],melitaea interrupta[&&NHX:TOL=70617])[&&NHX:TOL=138274],(melitaea latonigena[&&NHX:TOL=70618],(melitaea ninae[&&NHX:TOL=70607],(melitaea chitralensis[&&NHX:TOL=70606],melitaea enarea[&&NHX:TOL=70603])[&&NHX:TOL=138278])[&&NHX:TOL=138277])[&&NHX:TOL=138276],melitaea didyma[&&NHX:TOL=70619])[&&NHX:TOL=138273])[&&NHX:TOL=138271])[&&NHX:TOL=138268])[&&NHX:TOL=138264],melitaea kotshubeji[&&NHX:TOL=70608],melitaea didymina[&&NHX:TOL=70611],melitaea abyssinica[&&NHX:TOL=70613],melitaea yuenty[&&NHX:TOL=70633])melitaea didymagroup[&&NHX:TOL=70602])[&&NHX:TOL=77437])[&&NHX:TOL=138255])didymaeformia clade[&&NHX:TOL=138244])melitaea[&&NHX:TOL=70305])[&&NHX:TOL=70301],(poladryas minuta[&&NHX:TOL=70684],((chlosyne acastus[&&NHX:TOL=103190],chlosyne californica[&&NHX:TOL=103191],chlosyne cyneas[&&NHX:TOL=103192],chlosyne definita[&&NHX:TOL=103193],chlosyne ehrenbergii[&&NHX:TOL=103194],chlosyne endeis[&&NHX:TOL=103195],chlosyne erodyle[&&NHX:TOL=103196],chlosyne fulvia[&&NHX:TOL=103197],chlosyne gabbii[&&NHX:TOL=103198],chlosyne gaudialis[&&NHX:TOL=103199],chlosyne gorgone[&&NHX:TOL=103200],chlosyne hippodrome[&&NHX:TOL=103201],chlosyne janais[&&NHX:TOL=103202],chlosyne kendallorum[&&NHX:TOL=103203],chlosyne lacinia[&&NHX:TOL=103204],chlosyne leanira[&&NHX:TOL=103205],chlosyne marina[&&NHX:TOL=103206],chlosyne melanarge[&&NHX:TOL=103207],chlosyne narva[&&NHX:TOL=103208],chlosyne nycteis[&&NHX:TOL=103209],chlosyne rosita[&&NHX:TOL=103210],chlosyne theona[&&NHX:TOL=103211],chlosyne harrisii[&&NHX:TOL=103212],chlosyne palla[&&NHX:TOL=103213],chlosyne whitneyi[&&NHX:TOL=103214],chlosyne hoffmanni[&&NHX:TOL=103215])chlosyne[&&NHX:TOL=70686],(((texola anomalus[&&NHX:TOL=103184],texola elada[&&NHX:TOL=103185])texola[&&NHX:TOL=103183],dymasia dymas[&&NHX:TOL=103186])[&&NHX:TOL=103182],microtia elva[&&NHX:TOL=70687])[&&NHX:TOL=103181])[&&NHX:TOL=70685])chlosynegroup[&&NHX:TOL=70306])[&&NHX:TOL=70300])melitaeini[&&NHX:TOL=70213],((doleschallia bisaltide[&&NHX:TOL=93928],doleschallia browni[&&NHX:TOL=93929],doleschallia dascon[&&NHX:TOL=93930],doleschallia hexophthalmos[&&NHX:TOL=93931],doleschallia melana[&&NHX:TOL=93932],doleschallia nacar[&&NHX:TOL=93933],doleschallia noorna[&&NHX:TOL=93934],doleschallia polibete[&&NHX:TOL=94067],doleschallia rickardi[&&NHX:TOL=93935],doleschallia tongana[&&NHX:TOL=93936])doleschallia[&&NHX:TOL=70307],((kallima paralekta[&&NHX:TOL=93937],kallima albofasciata[&&NHX:TOL=93938],kallima alompra[&&NHX:TOL=93939],kallima buxtoni[&&NHX:TOL=93940],kallima horsfieldi[&&NHX:TOL=93941],kallima inachus[&&NHX:TOL=93942],kallima knyvetti[&&NHX:TOL=93943],kallima limborgii[&&NHX:TOL=93944],kallima philarchus[&&NHX:TOL=93945],kallima spiridiva[&&NHX:TOL=93946])kallima[&&NHX:TOL=70312],(mallika jacksoni[&&NHX:TOL=70310],catacroptera cloanthe[&&NHX:TOL=70311])[&&NHX:TOL=70309])[&&NHX:TOL=70308])kallimini[&&NHX:TOL=70214])[&&NHX:TOL=70212],(kallimoides rumia[&&NHX:TOL=70217],(metamorpha elissa[&&NHX:TOL=70322],(((anartia amathea[&&NHX:TOL=94054],anartia fatima[&&NHX:TOL=94056])[&&NHX:TOL=94060],anartia jatrophae[&&NHX:TOL=94057])[&&NHX:TOL=94059],(anartia lytrea[&&NHX:TOL=94058],anartia chrysopelea[&&NHX:TOL=94055])[&&NHX:TOL=94061])anartia[&&NHX:TOL=70323],((siproeta epaphus[&&NHX:TOL=94051],siproeta stelenes[&&NHX:TOL=94052],siproeta superba[&&NHX:TOL=94053])siproeta[&&NHX:TOL=70325],napeocles jucunda[&&NHX:TOL=70326])[&&NHX:TOL=70324])victorinini[&&NHX:TOL=70218])[&&NHX:TOL=70216],(vanessula milca[&&NHX:TOL=70220],rhinopalpa polynice[&&NHX:TOL=70221])[&&NHX:TOL=70219])[&&NHX:TOL=70211],((smyrna blomfildia[&&NHX:TOL=77083],smyrna karwinskii[&&NHX:TOL=77084])smyrna[&&NHX:TOL=70327],pycina zamba[&&NHX:TOL=70328],((antanartia borbonica[&&NHX:TOL=77089],antanartia delius[&&NHX:TOL=77085],antanartia dimorphica[&&NHX:TOL=77086],antanartia hippomene[&&NHX:TOL=77087],antanartia schaenia[&&NHX:TOL=77088])antanartia[&&NHX:TOL=70330],((vanessa annabella[&&NHX:TOL=77091],vanessa carye[&&NHX:TOL=77092])[&&NHX:TOL=77090],((vanessa terpsichore[&&NHX:TOL=77095],(vanessa kershawi[&&NHX:TOL=77097],vanessa cardui[&&NHX:TOL=77098])[&&NHX:TOL=77096],(vanessa virginiensis[&&NHX:TOL=77100],(vanessa myrinna[&&NHX:TOL=77102],vanessa braziliensis[&&NHX:TOL=77103])[&&NHX:TOL=77101])[&&NHX:TOL=77099],vanessa altissima[&&NHX:TOL=77104])[&&NHX:TOL=77094],((vanessa indica[&&NHX:TOL=77107],vanessa dejeani[&&NHX:TOL=77108],vanessa samani[&&NHX:TOL=77109],vanessa vulcania[&&NHX:TOL=77110])[&&NHX:TOL=77106],(vanessa abyssinica[&&NHX:TOL=77112],vanessa atalanta[&&NHX:TOL=77113])[&&NHX:TOL=77111],vanessa tameamea[&&NHX:TOL=77114],vanessa buana[&&NHX:TOL=93926])[&&NHX:TOL=77105],(vanessa gonerilla[&&NHX:TOL=77116],vanessa itea[&&NHX:TOL=77117])[&&NHX:TOL=77115])[&&NHX:TOL=77093])vanessa[&&NHX:TOL=70331],((((hypanartia godmanii[&&NHX:TOL=76677],hypanartia lethe[&&NHX:TOL=76678])[&&NHX:TOL=76676],hypanartia bella[&&NHX:TOL=76679])[&&NHX:TOL=76675],hypanartia paullus[&&NHX:TOL=76680])[&&NHX:TOL=76674],((((((hypanartia kefersteini[&&NHX:TOL=76687],hypanartia cinderella[&&NHX:TOL=76688])[&&NHX:TOL=76686],hypanartia trimaculata[&&NHX:TOL=76689])[&&NHX:TOL=76685],((hypanartia christophori[&&NHX:TOL=76692],hypanartia lindigii[&&NHX:TOL=76693])[&&NHX:TOL=76691],hypanartia fassli[&&NHX:TOL=76694])[&&NHX:TOL=76690])[&&NHX:TOL=76684],hypanartia splendida[&&NHX:TOL=76695])[&&NHX:TOL=76683],(hypanartia dione[&&NHX:TOL=76697],hypanartia celestia[&&NHX:TOL=76698])[&&NHX:TOL=76696])[&&NHX:TOL=76682],hypanartia charon[&&NHX:TOL=76699])[&&NHX:TOL=76681])hypanartia[&&NHX:TOL=70332],(((symbrenthia intricata[&&NHX:TOL=77130],(symbrenthia hypatia[&&NHX:TOL=77135],(symbrenthia lilaea[&&NHX:TOL=77136],(symbrenthia hippoclus[&&NHX:TOL=77133],(symbrenthia hylaeus[&&NHX:TOL=143288],(symbrenthia platena[&&NHX:TOL=77134],(symbrenthia hippalus[&&NHX:TOL=77118],(symbrenthia hypselis[&&NHX:TOL=77127],((symbrenthia brabira[&&NHX:TOL=77125],symbrenthia dalailama[&&NHX:TOL=77126],symbrenthia leoparda[&&NHX:TOL=143291],symbrenthia viridilunulata[&&NHX:TOL=143292])[&&NHX:TOL=77124],(symbrenthia niphanda[&&NHX:TOL=77122],symbrenthia sinoides[&&NHX:TOL=77123])[&&NHX:TOL=77121])[&&NHX:TOL=77120])[&&NHX:TOL=77119])[&&NHX:TOL=143290])[&&NHX:TOL=143289])[&&NHX:TOL=143287])[&&NHX:TOL=143286])[&&NHX:TOL=143285])[&&NHX:TOL=143284])[&&NHX:TOL=143283],symbrenthia silana[&&NHX:TOL=77128],symbrenthia hysudra[&&NHX:TOL=77129],symbrenthia anna[&&NHX:TOL=77131],symbrenthia javanus[&&NHX:TOL=77132])symbrenthia[&&NHX:TOL=70334],((mynes woodfordi[&&NHX:TOL=77138],mynes katharina[&&NHX:TOL=77139])[&&NHX:TOL=77137],mynes anemone[&&NHX:TOL=77140],(mynes aroensis[&&NHX:TOL=77142],mynes websteri[&&NHX:TOL=77143])[&&NHX:TOL=77141],((((mynes plateni[&&NHX:TOL=77148],mynes eucosmetos[&&NHX:TOL=77149])[&&NHX:TOL=77147],mynes doubledayi[&&NHX:TOL=77150])[&&NHX:TOL=77146],mynes talboti[&&NHX:TOL=77151])[&&NHX:TOL=77145],mynes geoffroyi[&&NHX:TOL=77152])[&&NHX:TOL=77144],mynes obiana[&&NHX:TOL=143281])mynes[&&NHX:TOL=70335],(((((araschnia burejana[&&NHX:TOL=77157],araschnia levana[&&NHX:TOL=77158])[&&NHX:TOL=77156],araschnia dohertyi[&&NHX:TOL=77159])[&&NHX:TOL=77155],(araschnia zhangi[&&NHX:TOL=77161],araschnia doris[&&NHX:TOL=77162])[&&NHX:TOL=77160])[&&NHX:TOL=77154],araschnia prorsoides[&&NHX:TOL=77163])[&&NHX:TOL=77153],araschnia davidis[&&NHX:TOL=77164],araschnia oreas[&&NHX:TOL=77165])araschnia[&&NHX:TOL=70336])[&&NHX:TOL=70333],((aglais io[&&NHX:TOL=77172],(aglais milberti[&&NHX:TOL=77171],(aglais caschmirensis[&&NHX:TOL=77170],aglais ladakensis[&&NHX:TOL=77169],(aglais urticae[&&NHX:TOL=77168],aglais ichnusa[&&NHX:TOL=138010])[&&NHX:TOL=138009])[&&NHX:TOL=77167])[&&NHX:TOL=77166])aglais[&&NHX:TOL=70338],((kaniska canace[&&NHX:TOL=70341],(nymphalis lalbum[&&NHX:TOL=76726],(nymphalis polychloros[&&NHX:TOL=76735],((nymphalis antiopa[&&NHX:TOL=76732],nymphalis cyanomelas[&&NHX:TOL=76731])[&&NHX:TOL=138281],(nymphalis xanthomelas[&&NHX:TOL=76734],nymphalis californica[&&NHX:TOL=76733])[&&NHX:TOL=76729])[&&NHX:TOL=138280])[&&NHX:TOL=76728])nymphalis[&&NHX:TOL=70342])[&&NHX:TOL=138279],(polygonia caureum[&&NHX:TOL=76700],((polygonia giganteum[&&NHX:TOL=76724],(polygonia egea[&&NHX:TOL=76718],polygonia undina[&&NHX:TOL=138285])[&&NHX:TOL=138284])[&&NHX:TOL=138283],((polygonia faunus[&&NHX:TOL=76720],(polygonia calbum[&&NHX:TOL=76722],polygonia interposita[&&NHX:TOL=76723])[&&NHX:TOL=76721])[&&NHX:TOL=76719],(polygonia interrogationis[&&NHX:TOL=76716],((polygonia comma[&&NHX:TOL=76715],polygonia gargenteum[&&NHX:TOL=76714])[&&NHX:TOL=138286],(polygonia satyrus[&&NHX:TOL=76713],((polygonia progne[&&NHX:TOL=76710],polygonia haroldii[&&NHX:TOL=76711])[&&NHX:TOL=76709],(polygonia oreas[&&NHX:TOL=76707],(polygonia gracilis[&&NHX:TOL=76708],polygonia zephyrus[&&NHX:TOL=138288])[&&NHX:TOL=138287])[&&NHX:TOL=76706])[&&NHX:TOL=76705])[&&NHX:TOL=76704])[&&NHX:TOL=76703])[&&NHX:TOL=76702])[&&NHX:TOL=76701])[&&NHX:TOL=138282])polygonia[&&NHX:TOL=70340])[&&NHX:TOL=70339])[&&NHX:TOL=70337])[&&NHX:TOL=70329],((colobura dirce[&&NHX:TOL=77173],colobura annulata[&&NHX:TOL=77174])colobura[&&NHX:TOL=70344],tigridia acesta[&&NHX:TOL=70345])[&&NHX:TOL=70343])nymphalini[&&NHX:TOL=70222])[&&NHX:TOL=70210])nymphalinae[&&NHX:TOL=12195])[&&NHX:TOL=139174])[&&NHX:TOL=69946],((amnosia decora[&&NHX:TOL=69953],(pseudergolis wedah[&&NHX:TOL=69964],pseudergolis avesta[&&NHX:TOL=69965])pseudergolis[&&NHX:TOL=69954])[&&NHX:TOL=69952],((stibochiona nicea[&&NHX:TOL=69966],(stibochiona coresia[&&NHX:TOL=69967],stibochiona schoenbergi[&&NHX:TOL=88081])[&&NHX:TOL=88083])stibochiona[&&NHX:TOL=69956],(dichorragia nesimachus[&&NHX:TOL=69968],dichorragia ninus[&&NHX:TOL=69969])dichorragia[&&NHX:TOL=69957])[&&NHX:TOL=69955])pseudergolinae[&&NHX:TOL=69948])[&&NHX:TOL=139172])[&&NHX:TOL=69944],((((((charaxes boueti[&&NHX:TOL=85648],charaxes cynthia[&&NHX:TOL=85666],charaxes protoclea[&&NHX:TOL=85757])charaxes cynthia group[&&NHX:TOL=118680],((charaxes anticlea[&&NHX:TOL=85634],charaxes hilderandti[&&NHX:TOL=85696])[&&NHX:TOL=118682],(charaxes angelae[&&NHX:TOL=85631],charaxes bocqueti[&&NHX:TOL=85646],charaxes catachrous[&&NHX:TOL=85655],charaxes cedreatis[&&NHX:TOL=85656],charaxes chevroti[&&NHX:TOL=111797],charaxes dreuxi[&&NHX:TOL=85673],charaxes etheocles[&&NHX:TOL=85679],charaxes petersi[&&NHX:TOL=85747],charaxes plantroui[&&NHX:TOL=85751],charaxes viola[&&NHX:TOL=85779],charaxes virilis[&&NHX:TOL=85782])[&&NHX:TOL=118683],charaxes northcotti[&&NHX:TOL=85734])charaxes etheocles group[&&NHX:TOL=118681],(charaxes achaemenes[&&NHX:TOL=85621],charaxes etesipe[&&NHX:TOL=85677])charaxes etesipe group[&&NHX:TOL=118684],(charaxes dilutus[&&NHX:TOL=85669],charaxes eupale[&&NHX:TOL=85681],charaxes subornatus[&&NHX:TOL=85765])charaxes eupale group[&&NHX:TOL=118685],((charaxes hadrianus[&&NHX:TOL=85694],charaxes lecerfi[&&NHX:TOL=85709])charaxes hadrianus group[&&NHX:TOL=118687],(charaxes nobilis[&&NHX:TOL=85733],charaxes superbus[&&NHX:TOL=85767])charaxes nobilis group[&&NHX:TOL=118688])[&&NHX:TOL=118686],(charaxes brutus[&&NHX:TOL=85650],charaxes castor[&&NHX:TOL=85654],charaxes epijasius[&&NHX:TOL=118690],charaxes jasius[&&NHX:TOL=85700],charaxes legeri[&&NHX:TOL=85710])charaxes jasius group[&&NHX:TOL=118689],(charaxes lactetinctus[&&NHX:TOL=85706],charaxes lucretius[&&NHX:TOL=85714])charaxes lucretuis group[&&NHX:TOL=118691],((charaxes lycurgus[&&NHX:TOL=85715],charaxes porthos[&&NHX:TOL=85755],charaxes zelica[&&NHX:TOL=85784])[&&NHX:TOL=118693],(charaxes mycerina[&&NHX:TOL=85730],charaxes doubledayi[&&NHX:TOL=85671])[&&NHX:TOL=118694])charaxes lycurgus group[&&NHX:TOL=118692],(charaxes paphianus[&&NHX:TOL=85742],charaxes pleione[&&NHX:TOL=85752])charaxes pleione group[&&NHX:TOL=118695],(charaxes eudoxus[&&NHX:TOL=85680],charaxes pollux[&&NHX:TOL=85753],charaxes druceanus[&&NHX:TOL=85674],charaxes tectonis[&&NHX:TOL=118697])charaxes pollux group[&&NHX:TOL=118696],(charaxes ameliae[&&NHX:TOL=85627],charaxes bipunctatus[&&NHX:TOL=85644],charaxes imperialis[&&NHX:TOL=85698],charaxes numenes[&&NHX:TOL=85735],charaxes pythodoris[&&NHX:TOL=85758],charaxes smaragdalis[&&NHX:TOL=85763],charaxes tiridates[&&NHX:TOL=85772])charaxes tiridates group[&&NHX:TOL=118698],(charaxes varanes[&&NHX:TOL=85776],charaxes fulvescens[&&NHX:TOL=85686],charaxes obudoensis[&&NHX:TOL=85737])charaxes varanes group[&&NHX:TOL=118699],charaxes saperanus[&&NHX:TOL=85760],charaxes schiltzei[&&NHX:TOL=85761],charaxes sidamo[&&NHX:TOL=85762],charaxes smilesi[&&NHX:TOL=85764],charaxes subrubidus[&&NHX:TOL=85766],charaxes taverniersi[&&NHX:TOL=85768],charaxes tessieri[&&NHX:TOL=85769],charaxes thysi[&&NHX:TOL=85770],charaxes thomasius[&&NHX:TOL=85771],charaxes turlini[&&NHX:TOL=85773],charaxes usumbarae[&&NHX:TOL=85774],charaxes vansoni[&&NHX:TOL=85775],charaxes variata[&&NHX:TOL=85777],charaxes velox[&&NHX:TOL=85778],charaxes violetta[&&NHX:TOL=85780],charaxes virescens[&&NHX:TOL=85781],charaxes xiphares[&&NHX:TOL=85783],charaxes zingha[&&NHX:TOL=85785],charaxes affinis[&&NHX:TOL=87833],charaxes zoolina[&&NHX:TOL=85786],charaxes acraeoides[&&NHX:TOL=85622],charaxes acuminatus[&&NHX:TOL=85623],charaxes alpinus[&&NHX:TOL=85624],charaxes alticola[&&NHX:TOL=85625],charaxes amandae[&&NHX:TOL=85626],charaxes analava[&&NHX:TOL=85628],charaxes andara[&&NHX:TOL=85629],charaxes andranodorus[&&NHX:TOL=85630],charaxes ansorgei[&&NHX:TOL=85632],charaxes antamboulou[&&NHX:TOL=85633],charaxes antiquus[&&NHX:TOL=85635],charaxes aubyni[&&NHX:TOL=85636],charaxes baileyi[&&NHX:TOL=85637],charaxes balfouri[&&NHX:TOL=85638],charaxes barnsi[&&NHX:TOL=85639],charaxes baumanni[&&NHX:TOL=85640],charaxes berkeleyi[&&NHX:TOL=85641],charaxes bernardii[&&NHX:TOL=85642],charaxes bernsdorffi[&&NHX:TOL=85643],charaxes blanda[&&NHX:TOL=85645],charaxes bohemani[&&NHX:TOL=85647],charaxes brainei[&&NHX:TOL=85649],charaxes cacuthis[&&NHX:TOL=85651],charaxes candiope[&&NHX:TOL=85652],charaxes carteri[&&NHX:TOL=85653],charaxes chanleri[&&NHX:TOL=85657],charaxes chepalungu[&&NHX:TOL=85658],charaxes chintechi[&&NHX:TOL=85659],charaxes chittyi[&&NHX:TOL=85660],charaxes chunguensis[&&NHX:TOL=85661],charaxes cithaeron[&&NHX:TOL=85662],charaxes congdoni[&&NHX:TOL=85663],charaxes contrarius[&&NHX:TOL=85664],charaxes cowani[&&NHX:TOL=85665],charaxes daria[&&NHX:TOL=85667],charaxes defulvata[&&NHX:TOL=85668],charaxes diversiforma[&&NHX:TOL=85670],charaxes dowsetti[&&NHX:TOL=85672],charaxes dubiosus[&&NHX:TOL=85675],charaxes ephyra[&&NHX:TOL=85676],charaxes ethalion[&&NHX:TOL=85678],charaxes figini[&&NHX:TOL=85682],charaxes fionae[&&NHX:TOL=85683],charaxes fournierae[&&NHX:TOL=85684],charaxes fulgurata[&&NHX:TOL=85685],charaxes fuscus[&&NHX:TOL=85687],charaxes galawadiwosi[&&NHX:TOL=85688],charaxes gallagheri[&&NHX:TOL=85689],charaxes galleyanus[&&NHX:TOL=85690],charaxes gerdae[&&NHX:TOL=85691],charaxes grahamei[&&NHX:TOL=85692],charaxes guderiana[&&NHX:TOL=85693],charaxes hansali[&&NHX:TOL=85695],charaxes howarthi[&&NHX:TOL=85697],charaxes jahlusa[&&NHX:TOL=85699],charaxes junius[&&NHX:TOL=85701],charaxes kahldeni[&&NHX:TOL=85702],charaxes karkloof[&&NHX:TOL=85703],charaxes kheili[&&NHX:TOL=85704],charaxes kirki[&&NHX:TOL=85705],charaxes larseni[&&NHX:TOL=85707],charaxes lasti[&&NHX:TOL=85708],charaxes lemosi[&&NHX:TOL=85711],charaxes loandae[&&NHX:TOL=85712],charaxes lucyae[&&NHX:TOL=85713],charaxes musashi[&&NHX:TOL=93905],charaxes setan[&&NHX:TOL=93906],charaxes lydiae[&&NHX:TOL=85716],charaxes macclouni[&&NHX:TOL=85717],charaxes mafuga[&&NHX:TOL=85718],charaxes manica[&&NHX:TOL=85719],charaxes margaretae[&&NHX:TOL=85720],charaxes marieps[&&NHX:TOL=85721],charaxes martini[&&NHX:TOL=85722],charaxes matakall[&&NHX:TOL=85723],charaxes mccleeryi[&&NHX:TOL=85724],charaxes mixtus[&&NHX:TOL=85725],charaxes monteiri[&&NHX:TOL=85726],charaxes montis[&&NHX:TOL=85727],charaxes murphyi[&&NHX:TOL=85728],charaxes musakensis[&&NHX:TOL=85729],charaxes nandina[&&NHX:TOL=85731],charaxes nichetes[&&NHX:TOL=85732],charaxes nyikensis[&&NHX:TOL=85736],charaxes octavus[&&NHX:TOL=85738],charaxes odysseus[&&NHX:TOL=85739],charaxes opinatus[&&NHX:TOL=85740],charaxes overlaeti[&&NHX:TOL=85741],charaxes paradoxa[&&NHX:TOL=85743],charaxes pelias[&&NHX:TOL=85744],charaxes pembanus[&&NHX:TOL=85745],charaxes penricei[&&NHX:TOL=85746],charaxes phaeus[&&NHX:TOL=85748],charaxes phoebus[&&NHX:TOL=85749],charaxes phraortes[&&NHX:TOL=85750],charaxes pondoensis[&&NHX:TOL=85754],charaxes prettejohni[&&NHX:TOL=85756],charaxes richelmanni[&&NHX:TOL=85759],charaxes phenix[&&NHX:TOL=94065],charaxes amycus[&&NHX:TOL=87834],charaxes antonius[&&NHX:TOL=87835],charaxes aristogiton[&&NHX:TOL=87836],charaxes bernardus[&&NHX:TOL=87837],charaxes borneensis[&&NHX:TOL=87838],charaxes distanti[&&NHX:TOL=87839],charaxes durnfordi[&&NHX:TOL=87840],charaxes elwesi[&&NHX:TOL=87841],charaxes harmodius[&&NHX:TOL=87842],charaxes kahruba[&&NHX:TOL=87843],charaxes latona[&&NHX:TOL=87844],charaxes marmax[&&NHX:TOL=87845],charaxes mars[&&NHX:TOL=87846],charaxes nitebis[&&NHX:TOL=87847],charaxes ocellatus[&&NHX:TOL=87848],charaxes orilus[&&NHX:TOL=87849],charaxes plateni[&&NHX:TOL=87850],charaxes psaphon[&&NHX:TOL=87851],charaxes solon[&&NHX:TOL=87852])charaxes[&&NHX:TOL=70521],((polyura andrewsi[&&NHX:TOL=87855],polyura arja[&&NHX:TOL=87856],polyura athamas[&&NHX:TOL=87857],polyura caphontis[&&NHX:TOL=87858],polyura clitarchus[&&NHX:TOL=87859],polyura cognata[&&NHX:TOL=87860],polyura dehanii[&&NHX:TOL=87861],polyura delphis[&&NHX:TOL=87862],polyura dolon[&&NHX:TOL=87863],polyura epigenes[&&NHX:TOL=87864],polyura eudamippus[&&NHX:TOL=87865],polyura gamma[&&NHX:TOL=87866],polyura hebe[&&NHX:TOL=87867],polyura jalysus[&&NHX:TOL=87868],polyura jupiter[&&NHX:TOL=87869],polyura nepenthes[&&NHX:TOL=87870],polyura moorei[&&NHX:TOL=87871],polyura narcaeus[&&NHX:TOL=87872],polyura posidonius[&&NHX:TOL=87873],polyura pyrrhus[&&NHX:TOL=87874],polyura schreiber[&&NHX:TOL=87875],polyura alphius[&&NHX:TOL=93907],polyura galaxia[&&NHX:TOL=93908],polyura inopinatus[&&NHX:TOL=93909])polyura[&&NHX:TOL=70523],((euxanthe crossleyi[&&NHX:TOL=85615],euxanthe wakefieldi[&&NHX:TOL=85618],euxanthe madagascariensis[&&NHX:TOL=85617])subgenus euxanthe[&&NHX:TOL=111799],(euxanthe eurinome[&&NHX:TOL=85616],euxanthe tiberius[&&NHX:TOL=85619],euxanthe trajanus[&&NHX:TOL=85620])subgenus hypomelaena[&&NHX:TOL=111800])euxanthe[&&NHX:TOL=70524])[&&NHX:TOL=70522])charaxini[&&NHX:TOL=70250],(((palla decius[&&NHX:TOL=70525],palla violinitens[&&NHX:TOL=70526],palla ussheri[&&NHX:TOL=70527],palla publius[&&NHX:TOL=70528])palla[&&NHX:TOL=70254],((prothoe ribbei[&&NHX:TOL=70530],prothoe franck[&&NHX:TOL=70531],(prothoe australis[&&NHX:TOL=70532],prothoe layardi[&&NHX:TOL=87827])[&&NHX:TOL=87829])prothoe[&&NHX:TOL=70529],agatasa calydonia[&&NHX:TOL=70533])prothoini[&&NHX:TOL=70255])[&&NHX:TOL=70253],((anaea troglodyta[&&NHX:TOL=70534],coenophlebia archidona[&&NHX:TOL=70535],(zaretis callidryas[&&NHX:TOL=86536],zaretis ellops[&&NHX:TOL=86537],zaretis isidora[&&NHX:TOL=86538],zaretis itys[&&NHX:TOL=86539],zaretis syene[&&NHX:TOL=86540],zaretis n. sp.[&&NHX:TOL=86541])zaretis[&&NHX:TOL=70536],(siderone galanthis[&&NHX:TOL=86534],siderone syntyche[&&NHX:TOL=86535])siderone[&&NHX:TOL=70537],hypna clytemnestra[&&NHX:TOL=70538],(polygrapha cyanea[&&NHX:TOL=86530],polygrapha suprema[&&NHX:TOL=86531],polygrapha tyrianthina[&&NHX:TOL=86532],polygrapha xenocrates[&&NHX:TOL=86533])polygrapha[&&NHX:TOL=70539],(consul electra[&&NHX:TOL=86526],consul excellens[&&NHX:TOL=86527],consul fabius[&&NHX:TOL=86528],consul panariste[&&NHX:TOL=86529])consul[&&NHX:TOL=70540],(memphis acaudata[&&NHX:TOL=86550],memphis acidalia[&&NHX:TOL=86551],memphis alberta[&&NHX:TOL=86552],memphis ambrosia[&&NHX:TOL=86553],memphis anassa[&&NHX:TOL=86554],memphis anna[&&NHX:TOL=86555],memphis appias[&&NHX:TOL=86556],memphis arginussa[&&NHX:TOL=86557],memphis artacaena[&&NHX:TOL=86558],memphis aulica[&&NHX:TOL=86559],memphis aureola[&&NHX:TOL=86560],memphis basilia[&&NHX:TOL=86561],memphis beatrix[&&NHX:TOL=86562],memphis boliviana[&&NHX:TOL=86563],memphis catinka[&&NHX:TOL=86564],memphis cerealia[&&NHX:TOL=86565],memphis cleomestra[&&NHX:TOL=86566],memphis cluvia[&&NHX:TOL=86567],memphis dia[&&NHX:TOL=86568],memphis falcata[&&NHX:TOL=86569],memphis forreri[&&NHX:TOL=86570],memphis glauce[&&NHX:TOL=86571],memphis grandis[&&NHX:TOL=86572],memphis hedemanni[&&NHX:TOL=86573],memphis herbacea[&&NHX:TOL=86574],memphis hirta[&&NHX:TOL=86575],memphis iphis[&&NHX:TOL=86576],memphis juliani[&&NHX:TOL=86577],memphis laertes[&&NHX:TOL=86578],memphis laura[&&NHX:TOL=86579],memphis lemnos[&&NHX:TOL=86580],memphis leonida[&&NHX:TOL=86581],memphis lineata[&&NHX:TOL=86582],memphis lorna[&&NHX:TOL=86583],memphis lyceus[&&NHX:TOL=86584],memphis maria[&&NHX:TOL=86585],memphis moeris[&&NHX:TOL=86586],memphis montesino[&&NHX:TOL=86587],memphis mora[&&NHX:TOL=86588],memphis moruus[&&NHX:TOL=86589],memphis neidhoeferi[&&NHX:TOL=86590],memphis nenia[&&NHX:TOL=86591],memphis oenomais[&&NHX:TOL=86592],memphis offa[&&NHX:TOL=86593],memphis otrere[&&NHX:TOL=86594],memphis pasibula[&&NHX:TOL=86595],memphis perenna[&&NHX:TOL=86596],memphis phantes[&&NHX:TOL=86597],memphis philumena[&&NHX:TOL=86598],memphis pithyusa[&&NHX:TOL=86599],memphis polycarmes[&&NHX:TOL=86600],memphis polyxo[&&NHX:TOL=86601],memphis praxias[&&NHX:TOL=86602],memphis proserpina[&&NHX:TOL=86603],memphis pseudiphis[&&NHX:TOL=86604],memphis salinasi[&&NHX:TOL=86605],memphis verticordia[&&NHX:TOL=86606],memphis viloriae[&&NHX:TOL=86607],memphis wellingi[&&NHX:TOL=86608],memphis xenippa[&&NHX:TOL=86609],memphis xenocles[&&NHX:TOL=86610])memphis[&&NHX:TOL=70541],(fountainea centaurus[&&NHX:TOL=86542],fountainea eurypyle[&&NHX:TOL=86543],fountainea glycerium[&&NHX:TOL=86544],fountainea halice[&&NHX:TOL=86545],fountainea nessus[&&NHX:TOL=86546],fountainea nobilis[&&NHX:TOL=86547],fountainea ryphea[&&NHX:TOL=86548],fountainea sosippus[&&NHX:TOL=86549])fountainea[&&NHX:TOL=70542],anaeomorpha splendida[&&NHX:TOL=70543])anaeini[&&NHX:TOL=70257],((prepona deiphile[&&NHX:TOL=86519],prepona dexamenus[&&NHX:TOL=86520],(prepona laertes laertes[&&NHX:TOL=138162],prepona laertes demodice[&&NHX:TOL=138163],prepona laertes louisa[&&NHX:TOL=138164],prepona laertes octavia[&&NHX:TOL=138165])prepona laertes[&&NHX:TOL=86521],prepona pheridamas[&&NHX:TOL=86522],prepona praeneste[&&NHX:TOL=86523],prepona pylene[&&NHX:TOL=86524],prepona werneri[&&NHX:TOL=86525])prepona[&&NHX:TOL=70544],(archaeoprepona amphimachus[&&NHX:TOL=86511],archaeoprepona camilla[&&NHX:TOL=86512],archaeoprepona chalciope[&&NHX:TOL=86513],archaeoprepona demophon[&&NHX:TOL=86514],archaeoprepona demophoon[&&NHX:TOL=86515],archaeoprepona licomedes[&&NHX:TOL=86516],archaeoprepona meander[&&NHX:TOL=86517],archaeoprepona phaedra[&&NHX:TOL=86518])archaeoprepona[&&NHX:TOL=70545],(agrias aedon[&&NHX:TOL=86506],agrias amydon[&&NHX:TOL=86507],agrias claudina[&&NHX:TOL=86508],agrias hewitsonius[&&NHX:TOL=86509],agrias narcissus[&&NHX:TOL=86510])agrias[&&NHX:TOL=70546],noreppa chromus[&&NHX:TOL=70547])preponini[&&NHX:TOL=70258])[&&NHX:TOL=70256])[&&NHX:TOL=70252])charaxinae[&&NHX:TOL=12192],((((elymnias agondas[&&NHX:TOL=87602],elymnias beza[&&NHX:TOL=87603],elymnias casiphone[&&NHX:TOL=87604],elymnias casiphonides[&&NHX:TOL=87605],elymnias ceryx[&&NHX:TOL=87606],elymnias congruens[&&NHX:TOL=87607],elymnias cottonis[&&NHX:TOL=87608],elymnias cumaea[&&NHX:TOL=87609],elymnias cybele[&&NHX:TOL=87610],elymnias dara[&&NHX:TOL=87611],elymnias esaca[&&NHX:TOL=87612],elymnias harteri[&&NHX:TOL=87613],elymnias hewitsoni[&&NHX:TOL=87614],elymnias hicetas[&&NHX:TOL=87615],elymnias holofernes[&&NHX:TOL=87616],elymnias hypermnestra[&&NHX:TOL=87617],elymnias kamara[&&NHX:TOL=87618],elymnias kanekoi[&&NHX:TOL=87619],elymnias kuenstleri[&&NHX:TOL=87620],elymnias luteofasciata[&&NHX:TOL=87621],elymnias malelas[&&NHX:TOL=87622],elymnias melias[&&NHX:TOL=87623],elymnias mimalon[&&NHX:TOL=87624],elymnias nelsoni[&&NHX:TOL=87625],elymnias nesaea[&&NHX:TOL=87626],elymnias panthera[&&NHX:TOL=87627],elymnias papua[&&NHX:TOL=87628],elymnias paradoxa[&&NHX:TOL=87629],elymnias patna[&&NHX:TOL=87630],elymnias pealii[&&NHX:TOL=87631],elymnias penanga[&&NHX:TOL=87632],elymnias vasudeva[&&NHX:TOL=87633],elymnias vitellia[&&NHX:TOL=87634],elymnias sangira[&&NHX:TOL=93887],[&&NHX:TOL=93888])elymnias[&&NHX:TOL=70785],elymniopsis bamakoo[&&NHX:TOL=70786])[&&NHX:TOL=87601],(hyantis hodeva[&&NHX:TOL=87531],(morphopsis albertisi[&&NHX:TOL=87539],morphopsis biakensis[&&NHX:TOL=87540],morphopsis ula[&&NHX:TOL=87541],morphopsis phippsi[&&NHX:TOL=87542],morphopsis meeki[&&NHX:TOL=87543])morphopsis[&&NHX:TOL=87532])[&&NHX:TOL=87538])elymniini[&&NHX:TOL=70274],(((xanthotaenia busiris[&&NHX:TOL=70716],((((neorina crishna[&&NHX:TOL=87925],neorina hilda[&&NHX:TOL=87926],neorina lowii[&&NHX:TOL=87927],neorina neosinica[&&NHX:TOL=87928],neorina patria[&&NHX:TOL=87929])neorina[&&NHX:TOL=70720],(penthema adelma[&&NHX:TOL=87930],penthema darlisa[&&NHX:TOL=87931],penthema formosanum[&&NHX:TOL=87932],penthema lisarda[&&NHX:TOL=87933])penthema[&&NHX:TOL=70721])[&&NHX:TOL=70719],((zethera hestioides[&&NHX:TOL=87934],zethera incerta[&&NHX:TOL=87935],zethera musa[&&NHX:TOL=87936],zethera musides[&&NHX:TOL=87937],zethera pimplea[&&NHX:TOL=87938],zethera thermaea[&&NHX:TOL=87939])zethera[&&NHX:TOL=70723],(ethope diademoides[&&NHX:TOL=87940],ethope henrici[&&NHX:TOL=87941],ethope himachala[&&NHX:TOL=87942],ethope noirei[&&NHX:TOL=87943])ethope[&&NHX:TOL=70724])[&&NHX:TOL=70722])[&&NHX:TOL=70718],(callarge occidentalis[&&NHX:TOL=87944],callarge sagitta[&&NHX:TOL=87945])callarge[&&NHX:TOL=70725])[&&NHX:TOL=70717])zetherini[&&NHX:TOL=70259],((((faunis aerope[&&NHX:TOL=87518],faunis arcesilaus[&&NHX:TOL=87519],faunis eumeus[&&NHX:TOL=87520],faunis kirata[&&NHX:TOL=87521],faunis gracilis[&&NHX:TOL=87522],faunis menado[&&NHX:TOL=87523],faunis phaon[&&NHX:TOL=87524],faunis sappho[&&NHX:TOL=87525],faunis stomphax[&&NHX:TOL=87526])faunis[&&NHX:TOL=70772],melanocyma faunula[&&NHX:TOL=70774],(taenaris horsfieldii[&&NHX:TOL=87544],taenaris schoenbergi[&&NHX:TOL=87545],(taenaris phorcas[&&NHX:TOL=87547],taenaris catops[&&NHX:TOL=87546],taenaris scylla[&&NHX:TOL=87548],taenaris selene[&&NHX:TOL=87550],taenaris macrops[&&NHX:TOL=87549])[&&NHX:TOL=87570],(taenaris gorgo[&&NHX:TOL=87552],taenaris bioculatus[&&NHX:TOL=87551],taenaris dina[&&NHX:TOL=87553])[&&NHX:TOL=87571],((taenaris domitilla[&&NHX:TOL=87554],taenaris onolaus[&&NHX:TOL=87573],taenaris honrathi[&&NHX:TOL=87556])[&&NHX:TOL=87555],(taenaris hyperbolus[&&NHX:TOL=87558],taenaris montana[&&NHX:TOL=87557],taenaris myops[&&NHX:TOL=87560],taenaris dioptrica[&&NHX:TOL=87559])[&&NHX:TOL=87574],(taenaris alocus[&&NHX:TOL=87564],taenaris chionides[&&NHX:TOL=87563])[&&NHX:TOL=87575],(taenaris cyclops[&&NHX:TOL=87562],taenaris mailua[&&NHX:TOL=87561])[&&NHX:TOL=87576])[&&NHX:TOL=87572],taenaris butleri[&&NHX:TOL=87565],taenaris dimona[&&NHX:TOL=87566],(taenaris urania[&&NHX:TOL=87568],taenaris artemis[&&NHX:TOL=87569],taenaris diana[&&NHX:TOL=87567])[&&NHX:TOL=87577])taenaris[&&NHX:TOL=87529])[&&NHX:TOL=87527],(aemona amathusia[&&NHX:TOL=87488],aemona lena[&&NHX:TOL=87489])aemona[&&NHX:TOL=70773])[&&NHX:TOL=87534],(enispe cycnus[&&NHX:TOL=87513],enispe euthymius[&&NHX:TOL=87514],enispe intermedia[&&NHX:TOL=87515],enispe lunatus[&&NHX:TOL=87516],enispe milvus[&&NHX:TOL=87517])enispe[&&NHX:TOL=70775],(((amathusia andamanensis[&&NHX:TOL=87490],amathusia binghami[&&NHX:TOL=87491],amathusia friderici[&&NHX:TOL=87492],amathusia masina[&&NHX:TOL=87493],amathusia ochraceofusca[&&NHX:TOL=87494],amathusia perakana[&&NHX:TOL=87495],amathusia phidippus[&&NHX:TOL=87496],amathusia schoenbergi[&&NHX:TOL=87497],amathusia taenia[&&NHX:TOL=87498],amathusia virgata[&&NHX:TOL=87499])amathusia[&&NHX:TOL=70777],(zeuxidia amethystus[&&NHX:TOL=87589],zeuxidia doubledayi[&&NHX:TOL=87590],zeuxidia aurelius[&&NHX:TOL=87591],zeuxidia luxerii[&&NHX:TOL=87592],zeuxidia mesilauensis[&&NHX:TOL=87593],zeuxidia semperi[&&NHX:TOL=87594],zeuxidia sibulana[&&NHX:TOL=87595],zeuxidia dohrni[&&NHX:TOL=138449],[&&NHX:TOL=138450])zeuxidia[&&NHX:TOL=87537],(amathuxidia amythaon[&&NHX:TOL=87500],amathuxidia plateni[&&NHX:TOL=87501],amathuxidia morishitai[&&NHX:TOL=87502])amathuxidia[&&NHX:TOL=70779])[&&NHX:TOL=87536],(thaumantis odana[&&NHX:TOL=87585],thaumantis noureddin[&&NHX:TOL=87586],thaumantis klugius[&&NHX:TOL=87587],thaumantis diores[&&NHX:TOL=87588])thaumantis[&&NHX:TOL=70780],thauria aliris[&&NHX:TOL=70781],(discophora bambusae[&&NHX:TOL=87503],discophora celinde[&&NHX:TOL=87504],discophora deo[&&NHX:TOL=87505],discophora dodong[&&NHX:TOL=87506],discophora lepida[&&NHX:TOL=87507],discophora necho[&&NHX:TOL=87508],discophora ogina[&&NHX:TOL=87509],discophora simplex[&&NHX:TOL=87510],discophora sondaica[&&NHX:TOL=87511],discophora timora[&&NHX:TOL=87512])discophora[&&NHX:TOL=70776])[&&NHX:TOL=87535],(stichophthalma camadeva[&&NHX:TOL=87578],stichophthalma howqua[&&NHX:TOL=87579],stichophthalma louisa[&&NHX:TOL=87580],stichophthalma neumogeni[&&NHX:TOL=87581],stichophthalma nourmahal[&&NHX:TOL=87582],stichophthalma sparta[&&NHX:TOL=87583],stichophthalma uemurai[&&NHX:TOL=87584],stichophthalma godfreyi[&&NHX:TOL=138447],[&&NHX:TOL=138448])stichophthalma[&&NHX:TOL=70782])amathusiini[&&NHX:TOL=70273])[&&NHX:TOL=87596],(((((bia actorion[&&NHX:TOL=82967],bia peruana[&&NHX:TOL=82968])bia[&&NHX:TOL=70748],((aponarope sutor[&&NHX:TOL=70764],(narope albopunctum[&&NHX:TOL=83552],narope cyllabarus[&&NHX:TOL=83553],narope cyllarus[&&NHX:TOL=83554],narope cyllastros[&&NHX:TOL=83555],narope cyllene[&&NHX:TOL=83556],narope denticulatus[&&NHX:TOL=83557],narope guilhermei[&&NHX:TOL=83558],narope marmorata[&&NHX:TOL=83559],narope minor[&&NHX:TOL=83560],narope nesope[&&NHX:TOL=83561],narope obidos[&&NHX:TOL=83562],narope panniculus[&&NHX:TOL=83563],narope syllabus[&&NHX:TOL=83564],narope testacea[&&NHX:TOL=83565],narope ybyra[&&NHX:TOL=83566],narope anartes[&&NHX:TOL=83567],narope cauca[&&NHX:TOL=83568])narope[&&NHX:TOL=70765])naropina[&&NHX:TOL=70763],(((brassolis astyra[&&NHX:TOL=83485],brassolis haenschi[&&NHX:TOL=83486],brassolis isthmia[&&NHX:TOL=83487],brassolis sophorae[&&NHX:TOL=83488])brassolis[&&NHX:TOL=70751],(dynastor darius[&&NHX:TOL=83524],dynastor macrosiris[&&NHX:TOL=83525],dynastor napoleon[&&NHX:TOL=83526])dynastor[&&NHX:TOL=70756])[&&NHX:TOL=117722],((((dasyophthalma creusa[&&NHX:TOL=83520],dasyophthalma vertebralis[&&NHX:TOL=83523])[&&NHX:TOL=137739],(dasyophthalma rusina[&&NHX:TOL=83522],dasyophthalma geraensis[&&NHX:TOL=83521])[&&NHX:TOL=137740])dasyophthalma[&&NHX:TOL=70755],(((opoptera syme[&&NHX:TOL=83536],opoptera sulcius[&&NHX:TOL=83535])[&&NHX:TOL=134294],opoptera fruhstorferi[&&NHX:TOL=83534])[&&NHX:TOL=134293],(opoptera staudingeri[&&NHX:TOL=70759],((opoptera aorsa[&&NHX:TOL=83532],opoptera hilaris[&&NHX:TOL=134297])[&&NHX:TOL=134296],(opoptera arsippe[&&NHX:TOL=83533],opoptera bracteolata[&&NHX:TOL=134299])[&&NHX:TOL=134298])[&&NHX:TOL=117712])[&&NHX:TOL=134295],opoptera n. sp.[&&NHX:TOL=83537])opoptera[&&NHX:TOL=70760])[&&NHX:TOL=117708],((((caligopsis seleucida[&&NHX:TOL=83510],caligopsis n. sp.[&&NHX:TOL=83511])caligopsis[&&NHX:TOL=70753],(((((eryphanis automedon[&&NHX:TOL=83528],eryphanis lycomedon[&&NHX:TOL=125319])[&&NHX:TOL=125318],(eryphanis aesacus[&&NHX:TOL=83527],eryphanis bubocula[&&NHX:TOL=125321])[&&NHX:TOL=125320])[&&NHX:TOL=125317],eryphanis gerhardi[&&NHX:TOL=83529])[&&NHX:TOL=125316],eryphanis reevesii[&&NHX:TOL=83530])[&&NHX:TOL=125315],(eryphanis zolvizora[&&NHX:TOL=83531],(eryphanis opimus[&&NHX:TOL=125324],eryphanis greeneyi[&&NHX:TOL=125325])[&&NHX:TOL=125323])[&&NHX:TOL=125322])eryphanis[&&NHX:TOL=70757])[&&NHX:TOL=117715],(caligo arisbe[&&NHX:TOL=83489],caligo atreus[&&NHX:TOL=83490],caligo bellerophon[&&NHX:TOL=83491],caligo beltrao[&&NHX:TOL=83492],caligo brasiliensis[&&NHX:TOL=83493],caligo euphorbus[&&NHX:TOL=83494],caligo eurilochus[&&NHX:TOL=83495],caligo idomeneus[&&NHX:TOL=83496],caligo illioneus[&&NHX:TOL=83497],caligo martia[&&NHX:TOL=83498],caligo oberthurii[&&NHX:TOL=83499],caligo oedipus[&&NHX:TOL=83500],caligo oileus[&&NHX:TOL=83501],caligo placidianus[&&NHX:TOL=83502],caligo prometheus[&&NHX:TOL=83503],caligo superbus[&&NHX:TOL=83504],caligo suzanna[&&NHX:TOL=83505],caligo telamonius[&&NHX:TOL=83506],caligo teucer[&&NHX:TOL=83507],caligo uranus[&&NHX:TOL=83508],caligo zeuxippus[&&NHX:TOL=83509])caligo[&&NHX:TOL=70752])[&&NHX:TOL=117714],((selenophanes cassiope[&&NHX:TOL=83549],selenophanes josephus[&&NHX:TOL=83550],selenophanes supremus[&&NHX:TOL=83551])selenophanes[&&NHX:TOL=70766],(penetes pamphanis[&&NHX:TOL=70767],((catoblepia amphirhoe[&&NHX:TOL=83512],catoblepia berecynthia[&&NHX:TOL=83513],catoblepia generosa[&&NHX:TOL=83514],catoblepia orgetorix[&&NHX:TOL=83515],catoblepia soranus[&&NHX:TOL=83516],catoblepia versitincta[&&NHX:TOL=83517],catoblepia xanthicles[&&NHX:TOL=83518],catoblepia xanthus[&&NHX:TOL=83519])catoblepia[&&NHX:TOL=70754],(mielkella singularis[&&NHX:TOL=70758],(orobrassolis ornamentalis[&&NHX:TOL=70762],((blepolenis bassus[&&NHX:TOL=83482],blepolenis batea[&&NHX:TOL=83483],blepolenis catharinae[&&NHX:TOL=83484])blepolenis[&&NHX:TOL=70750],(opsiphanes bogotanus[&&NHX:TOL=83538],(opsiphanes boisduvalii[&&NHX:TOL=83539],opsiphanes blythekitzmillerae[&&NHX:TOL=112938])[&&NHX:TOL=112937],opsiphanes camena[&&NHX:TOL=83540],opsiphanes cassiae[&&NHX:TOL=83541],opsiphanes cassina[&&NHX:TOL=83542],opsiphanes invirae[&&NHX:TOL=83543],opsiphanes mutatus[&&NHX:TOL=83544],opsiphanes quiteria[&&NHX:TOL=83545],opsiphanes sallei[&&NHX:TOL=83546],opsiphanes tamarindi[&&NHX:TOL=83547],opsiphanes zelotes[&&NHX:TOL=83548])opsiphanes[&&NHX:TOL=70761])[&&NHX:TOL=117721])[&&NHX:TOL=117720])[&&NHX:TOL=117719])[&&NHX:TOL=117718])[&&NHX:TOL=117717])[&&NHX:TOL=117716])[&&NHX:TOL=117713])[&&NHX:TOL=117707])brassolina[&&NHX:TOL=117706])[&&NHX:TOL=70749])brassolini[&&NHX:TOL=70271],((antirrhea adoptiva[&&NHX:TOL=82989],antirrhea archaea[&&NHX:TOL=82990],antirrhea geryon[&&NHX:TOL=82991],antirrhea hela[&&NHX:TOL=82992],antirrhea ornata[&&NHX:TOL=82993],antirrhea phasiana[&&NHX:TOL=82994],antirrhea philoctetes[&&NHX:TOL=82995],antirrhea pterocopha[&&NHX:TOL=82996],antirrhea taygetina[&&NHX:TOL=82997],antirrhea undulata[&&NHX:TOL=82998],antirrhea watkinsi[&&NHX:TOL=82999])antirrhea[&&NHX:TOL=70768],((morpho absoloni[&&NHX:TOL=83002],morpho athena[&&NHX:TOL=83007],morpho rhodopteron[&&NHX:TOL=83024],(((morpho aega[&&NHX:TOL=83004],morpho portis[&&NHX:TOL=83022])[&&NHX:TOL=83033],((morpho sulkowskyi[&&NHX:TOL=83026],morpho lympharis[&&NHX:TOL=83017])[&&NHX:TOL=83035],(morpho aurora[&&NHX:TOL=83008],(((((((morpho theseus[&&NHX:TOL=83028],morpho telemachus[&&NHX:TOL=83027],morpho niepelti[&&NHX:TOL=83020])[&&NHX:TOL=83043],morpho amphitryton[&&NHX:TOL=83005])[&&NHX:TOL=83042],morpho hercules[&&NHX:TOL=83016])morpho iphimedeia[&&NHX:TOL=83041],(morpho hecuba[&&NHX:TOL=83014],morpho cisseis[&&NHX:TOL=83009])morpho schwartzia[&&NHX:TOL=83044])[&&NHX:TOL=83040],(morpho anaxibia[&&NHX:TOL=83006],morpho richardus[&&NHX:TOL=83025])morpho iphixibia[&&NHX:TOL=83045])[&&NHX:TOL=83039],(morpho cypris[&&NHX:TOL=83010],morpho rhetenor[&&NHX:TOL=83023])morpho cypritis[&&NHX:TOL=83046])[&&NHX:TOL=83038],(morpho menelaus[&&NHX:TOL=83019],((morpho deidamia[&&NHX:TOL=83011],(morpho polyphemus[&&NHX:TOL=83021],morpho epistrophus[&&NHX:TOL=83012])[&&NHX:TOL=83050])[&&NHX:TOL=83049],(morpho achilles[&&NHX:TOL=83003],morpho helenor[&&NHX:TOL=83015])[&&NHX:TOL=83051])[&&NHX:TOL=83048])[&&NHX:TOL=83047])[&&NHX:TOL=83037])[&&NHX:TOL=83036])[&&NHX:TOL=83034])[&&NHX:TOL=83032],(morpho eugenia[&&NHX:TOL=83013],morpho marcus[&&NHX:TOL=83018])[&&NHX:TOL=83052])[&&NHX:TOL=83031],morpho uraneis[&&NHX:TOL=83029],morpho zephyritis[&&NHX:TOL=83030])morpho[&&NHX:TOL=70770],(caerois chorinaeus[&&NHX:TOL=83000],caerois gertrudtus[&&NHX:TOL=83001])caerois[&&NHX:TOL=70771])[&&NHX:TOL=70769])morphini[&&NHX:TOL=70272])[&&NHX:TOL=70270],(((manataria hercyna[&&NHX:TOL=70742],(parantirrhoea marshalli[&&NHX:TOL=70744],(gnophodes bestimena[&&NHX:TOL=85310],gnophodes chelys[&&NHX:TOL=85311],gnophodes grogani[&&NHX:TOL=85312])gnophodes[&&NHX:TOL=70745],(melanitis amabilis[&&NHX:TOL=87949],melanitis ansorgei[&&NHX:TOL=87950],melanitis atrax[&&NHX:TOL=87951],melanitis belinda[&&NHX:TOL=87952],melanitis boisduvalia[&&NHX:TOL=87953],melanitis constantia[&&NHX:TOL=87954],melanitis leda[&&NHX:TOL=87955],melanitis libya[&&NHX:TOL=87956],melanitis phedima[&&NHX:TOL=87957],melanitis pyrrha[&&NHX:TOL=87958],melanitis velutina[&&NHX:TOL=87959],melanitis zitenius[&&NHX:TOL=87960])melanitis[&&NHX:TOL=70746],(cyllogenes janetae[&&NHX:TOL=87946],cyllogenes suradeva[&&NHX:TOL=87947],cyllogenes woolletti[&&NHX:TOL=87948])cyllogenes[&&NHX:TOL=70747],(bletogona mycalesis[&&NHX:TOL=93885],bletogona inexspectata[&&NHX:TOL=93886])bletogona[&&NHX:TOL=89839])[&&NHX:TOL=70743])melanitini[&&NHX:TOL=70268],(((torynesis hawequas[&&NHX:TOL=84885],torynesis magna[&&NHX:TOL=84886],torynesis mintha[&&NHX:TOL=84887],torynesis orangica[&&NHX:TOL=84888],torynesis pringlei[&&NHX:TOL=84889])torynesis[&&NHX:TOL=70735],(tarsocera cassina[&&NHX:TOL=84890],tarsocera cassus[&&NHX:TOL=84891],tarsocera dicksoni[&&NHX:TOL=84892],tarsocera fulvina[&&NHX:TOL=84893],tarsocera imitator[&&NHX:TOL=84894],tarsocera namaquensis[&&NHX:TOL=84895],tarsocera southeyae[&&NHX:TOL=84896])tarsocera[&&NHX:TOL=70736],(dingana alaedus[&&NHX:TOL=84882],dingana bowkeri[&&NHX:TOL=84883],dingana dingana[&&NHX:TOL=84884])dingana[&&NHX:TOL=70737],(dira clytus[&&NHX:TOL=84878],dira jansei[&&NHX:TOL=84879],dira oxylus[&&NHX:TOL=84880],dira swanepoeli[&&NHX:TOL=84881])dira[&&NHX:TOL=70738])[&&NHX:TOL=70734],(paralethe dendrophilus[&&NHX:TOL=70740],aeropetes tulbaghia[&&NHX:TOL=70741])[&&NHX:TOL=70739])dirini[&&NHX:TOL=70267])[&&NHX:TOL=87600],((pierella amalia[&&NHX:TOL=82976],pierella astyoche[&&NHX:TOL=82977],pierella helvina[&&NHX:TOL=82978],pierella hortona[&&NHX:TOL=82979],pierella hyalinus[&&NHX:TOL=82980],pierella hyceta[&&NHX:TOL=82981],pierella lamia[&&NHX:TOL=82982],pierella lena[&&NHX:TOL=82983],pierella lucia[&&NHX:TOL=82984],pierella luna[&&NHX:TOL=82985],pierella nereis[&&NHX:TOL=82986])pierella[&&NHX:TOL=70726],((((haetera macleannania[&&NHX:TOL=82974],haetera piera[&&NHX:TOL=82975])haetera[&&NHX:TOL=70730],(cithaerias andromeda[&&NHX:TOL=82969],cithaerias phantoma[&&NHX:TOL=82970],cithaerias pireta[&&NHX:TOL=82971],cithaerias pyritosa[&&NHX:TOL=82972],cithaerias pyropina[&&NHX:TOL=82973])cithaerias[&&NHX:TOL=70731])[&&NHX:TOL=70729],(pseudohaetera hypaesia[&&NHX:TOL=82987],pseudohaetera mimica[&&NHX:TOL=82988])pseudohaetera[&&NHX:TOL=70732])[&&NHX:TOL=70728],dulcedo polita[&&NHX:TOL=70733])[&&NHX:TOL=70727])haeterini[&&NHX:TOL=70265])[&&NHX:TOL=87599])[&&NHX:TOL=87598],(((erites angularis[&&NHX:TOL=88327],erites argentina[&&NHX:TOL=88328],erites elegans[&&NHX:TOL=88329],erites falcipennis[&&NHX:TOL=88330],erites medura[&&NHX:TOL=88331])erites[&&NHX:TOL=88324],(orsotriaena medus[&&NHX:TOL=93889],orsotriaena jopas[&&NHX:TOL=93890])orsotriaena[&&NHX:TOL=88325],(zipaetis saitis[&&NHX:TOL=88332],zipaetis scylax[&&NHX:TOL=88333],zipaetis unipupillata[&&NHX:TOL=88334])zipaetis[&&NHX:TOL=88326])eritina[&&NHX:TOL=70790],(archeuptychia cluena[&&NHX:TOL=83569],caenoptychia boulleti[&&NHX:TOL=83570],(caeruleuptychia aegrota[&&NHX:TOL=83609],caeruleuptychia brixius[&&NHX:TOL=83610],caeruleuptychia caerulea[&&NHX:TOL=83611],caeruleuptychia coelestis[&&NHX:TOL=83612],caeruleuptychia coelica[&&NHX:TOL=83613],caeruleuptychia cyanites[&&NHX:TOL=83614],caeruleuptychia divina[&&NHX:TOL=83615],caeruleuptychia glauca[&&NHX:TOL=83616],caeruleuptychia helena[&&NHX:TOL=83617],caeruleuptychia helios[&&NHX:TOL=83618],caeruleuptychia lobelia[&&NHX:TOL=83619],caeruleuptychia mare[&&NHX:TOL=83620],caeruleuptychia penicillata[&&NHX:TOL=83621],caeruleuptychia pilata[&&NHX:TOL=83622],caeruleuptychia scopulata[&&NHX:TOL=83623],caeruleuptychia tenera[&&NHX:TOL=83624],caeruleuptychia umbrosa[&&NHX:TOL=83625],caeruleuptychia urania[&&NHX:TOL=83626],caeruleuptychia ziza[&&NHX:TOL=83627],6 undescribed species[&&NHX:TOL=83628])caeruleuptychia[&&NHX:TOL=83571],capronnieria galesus[&&NHX:TOL=83572],(cepheuptychia angelica[&&NHX:TOL=83629],cepheuptychia cephus[&&NHX:TOL=83630],cepheuptychia glaucina[&&NHX:TOL=83631],cepheuptychia romani[&&NHX:TOL=83632],cepheuptychia n. sp.[&&NHX:TOL=83633])cepheuptychia[&&NHX:TOL=83573],cercyeuptychia luederwaldti[&&NHX:TOL=83574],(chloreuptychia agatha[&&NHX:TOL=83634],chloreuptychia arnaca[&&NHX:TOL=83635],chloreuptychia callichloris[&&NHX:TOL=83636],chloreuptychia catharina[&&NHX:TOL=83637],chloreuptychia chlorimene[&&NHX:TOL=83638],chloreuptychia herseis[&&NHX:TOL=83639],chloreuptychia hewitsonii[&&NHX:TOL=83640],chloreuptychia marica[&&NHX:TOL=83641],chloreuptychia sericeella[&&NHX:TOL=83642],chloreuptychia tolumnia[&&NHX:TOL=83643],chloreuptychia n. sp. 1[&&NHX:TOL=83644],chloreuptychia n. sp. 2[&&NHX:TOL=83645])chloreuptychia[&&NHX:TOL=83575],coeruleotaygetis peribaea[&&NHX:TOL=83576],(cyllopsis argentella[&&NHX:TOL=83663],cyllopsis caballeroi[&&NHX:TOL=83664],cyllopsis clinas[&&NHX:TOL=83665],cyllopsis diazi[&&NHX:TOL=83666],cyllopsis dospassosi[&&NHX:TOL=83667],cyllopsis emilia[&&NHX:TOL=83668],cyllopsis gemma[&&NHX:TOL=83669],cyllopsis guatemalena[&&NHX:TOL=83670],cyllopsis hedemanni[&&NHX:TOL=83671],cyllopsis hilaria[&&NHX:TOL=83672],cyllopsis jacquelineae[&&NHX:TOL=83673],cyllopsis nayarit[&&NHX:TOL=83674],cyllopsis nelsoni[&&NHX:TOL=83675],cyllopsis pallens[&&NHX:TOL=83676],cyllopsis parvimaculata[&&NHX:TOL=83677],cyllopsis pephredo[&&NHX:TOL=83678],cyllopsis perplexa[&&NHX:TOL=83679],cyllopsis pertepida[&&NHX:TOL=83680],cyllopsis philodice[&&NHX:TOL=83681],cyllopsis pseudopephredo[&&NHX:TOL=83682],cyllopsis pyracmon[&&NHX:TOL=83683],cyllopsis rogersi[&&NHX:TOL=83684],cyllopsis schausi[&&NHX:TOL=83685],cyllopsis steinhauserorum[&&NHX:TOL=83686],cyllopsis suivalenoides[&&NHX:TOL=83687],cyllopsis suivalens[&&NHX:TOL=83688],cyllopsis whiteorum[&&NHX:TOL=83689],cyllopsis windi[&&NHX:TOL=83690])cyllopsis[&&NHX:TOL=83577],(erichthodes antonina[&&NHX:TOL=83691],erichthodes arius[&&NHX:TOL=83692],erichthodes jovita[&&NHX:TOL=83693],erichthodes julia[&&NHX:TOL=83694],erichthodes narapa[&&NHX:TOL=83695])erichthodes[&&NHX:TOL=83578],(euptychia enyo[&&NHX:TOL=83696],euptychia ernestina[&&NHX:TOL=83697],euptychia fetna[&&NHX:TOL=83698],euptychia hannemanni[&&NHX:TOL=83699],euptychia hilara[&&NHX:TOL=83700],euptychia insolata[&&NHX:TOL=83701],euptychia jesia[&&NHX:TOL=83702],euptychia meta[&&NHX:TOL=83703],euptychia mollina[&&NHX:TOL=83704],euptychia picea[&&NHX:TOL=83705],euptychia rubrofasciata[&&NHX:TOL=83706],euptychia rufocincta[&&NHX:TOL=83707],euptychia westwoodi[&&NHX:TOL=83708],16 undescribed species[&&NHX:TOL=83709])euptychia[&&NHX:TOL=83579],((euptychioides albofasciata[&&NHX:TOL=83710],euptychioides eugenia[&&NHX:TOL=83711],euptychioides fida[&&NHX:TOL=83712],euptychioides griphe[&&NHX:TOL=83713],euptychioides hotchkissi[&&NHX:TOL=83714],euptychioides laccine[&&NHX:TOL=83715],euptychioides nossis[&&NHX:TOL=83716],euptychioides pseudosaturnus[&&NHX:TOL=83717],euptychioides saturnus[&&NHX:TOL=83718],euptychioides n. sp.[&&NHX:TOL=83719],euptychioides castrensis[&&NHX:TOL=83720])euptychioides[&&NHX:TOL=83580],(moneuptychia melchiades[&&NHX:TOL=83788],moneuptychia soter[&&NHX:TOL=83790],moneuptychia itapeva[&&NHX:TOL=113125])moneuptychia[&&NHX:TOL=83588])[&&NHX:TOL=113124],(godartiana byses[&&NHX:TOL=83736],godartiana muscosa[&&NHX:TOL=83737])godartiana[&&NHX:TOL=83582],((harjesia blanda[&&NHX:TOL=83738],harjesia griseola[&&NHX:TOL=83739],harjesia obscura[&&NHX:TOL=83740],harjesia oreba[&&NHX:TOL=83741],harjesia vrazi[&&NHX:TOL=83742],4 undescribed species[&&NHX:TOL=83743])harjesia[&&NHX:TOL=83583],(((forsterinaria boliviana[&&NHX:TOL=83723],forsterinaria inornata[&&NHX:TOL=83725],forsterinaria pallida[&&NHX:TOL=109983],forsterinaria coipa[&&NHX:TOL=109978])[&&NHX:TOL=110204],(forsterinaria neonympha[&&NHX:TOL=83727],forsterinaria stella[&&NHX:TOL=83733],forsterinaria pyrczi[&&NHX:TOL=109987],forsterinaria proxima[&&NHX:TOL=83728])[&&NHX:TOL=110205],((forsterinaria enjuerma[&&NHX:TOL=109979],forsterinaria pseudinornata[&&NHX:TOL=83729],forsterinaria anophthalma[&&NHX:TOL=83722])[&&NHX:TOL=110207],forsterinaria punctata[&&NHX:TOL=109986])[&&NHX:TOL=110206],(forsterinaria quantius[&&NHX:TOL=83731],(forsterinaria itatiaia[&&NHX:TOL=109982],forsterinaria necys[&&NHX:TOL=83726])[&&NHX:TOL=110209])[&&NHX:TOL=110208],(forsterinaria pilosa[&&NHX:TOL=109985],forsterinaria pichita[&&NHX:TOL=109984],forsterinaria guaniloi[&&NHX:TOL=109981],forsterinaria falcata[&&NHX:TOL=109980],forsterinaria rotunda[&&NHX:TOL=109988],forsterinaria difficilis[&&NHX:TOL=83724],forsterinaria rustica[&&NHX:TOL=83732],forsterinaria antje[&&NHX:TOL=109977])[&&NHX:TOL=110210])forsterinaria[&&NHX:TOL=83581],guaianaza pronophila[&&NHX:TOL=83936])[&&NHX:TOL=110616],(taygetomorpha celia[&&NHX:TOL=83897],taygetomorpha puritana[&&NHX:TOL=83898],taygetomorpha n. sp.[&&NHX:TOL=83899])taygetomorpha[&&NHX:TOL=83606])[&&NHX:TOL=110211],(hermeuptychia atalanta[&&NHX:TOL=83744],hermeuptychia cucullina[&&NHX:TOL=83745],hermeuptychia fallax[&&NHX:TOL=83746],hermeuptychia harmonia[&&NHX:TOL=83747],hermeuptychia hermes[&&NHX:TOL=83748],hermeuptychia maimoune[&&NHX:TOL=83749],hermeuptychia pimpla[&&NHX:TOL=83750],hermeuptychia sosybius[&&NHX:TOL=83751],4 undescribed species[&&NHX:TOL=83752])hermeuptychia[&&NHX:TOL=83584],(magneuptychia agnata[&&NHX:TOL=83753],magneuptychia alcinoe[&&NHX:TOL=83754],magneuptychia analis[&&NHX:TOL=83755],magneuptychia divergens[&&NHX:TOL=83756],magneuptychia drymo[&&NHX:TOL=83757],magneuptychia francisca[&&NHX:TOL=83758],magneuptychia fugitiva[&&NHX:TOL=83759],magneuptychia gera[&&NHX:TOL=83760],magneuptychia gomezi[&&NHX:TOL=83761],magneuptychia harpyia[&&NHX:TOL=83762],magneuptychia inani[&&NHX:TOL=83763],magneuptychia iris[&&NHX:TOL=83764],magneuptychia lea[&&NHX:TOL=83765],magneuptychia libye[&&NHX:TOL=83766],magneuptychia metagera[&&NHX:TOL=83767],magneuptychia mimas[&&NHX:TOL=83768],magneuptychia moderata[&&NHX:TOL=83769],magneuptychia modesta[&&NHX:TOL=83770],magneuptychia mycalesis[&&NHX:TOL=83771],magneuptychia nebulosa[&&NHX:TOL=83772],magneuptychia newtoni[&&NHX:TOL=83773],magneuptychia ocnus[&&NHX:TOL=83774],magneuptychia ocypete[&&NHX:TOL=83775],magneuptychia opima[&&NHX:TOL=83776],magneuptychia pallema[&&NHX:TOL=83777],magneuptychia probata[&&NHX:TOL=83778],magneuptychia segesta[&&NHX:TOL=83779],magneuptychia tiessa[&&NHX:TOL=83780],magneuptychia tricolor[&&NHX:TOL=83781],11 undescribed species[&&NHX:TOL=83782])magneuptychia[&&NHX:TOL=83585],(megeuptychia antonoe[&&NHX:TOL=83783],megeuptychia monopunctata[&&NHX:TOL=83784])megeuptychia[&&NHX:TOL=83586],(megisto cymela[&&NHX:TOL=83785],megisto rubricata[&&NHX:TOL=83786])megisto[&&NHX:TOL=83587],(neonympha areolatus[&&NHX:TOL=93262],neonympha mitchellii[&&NHX:TOL=93263])neonympha[&&NHX:TOL=93260],palaeonympha opalina[&&NHX:TOL=90381],(paramacera allyni[&&NHX:TOL=83794],paramacera chinanteca[&&NHX:TOL=83795],paramacera copiosa[&&NHX:TOL=83796],paramacera xicaque[&&NHX:TOL=83797])paramacera[&&NHX:TOL=83590],(parataygetis albinotata[&&NHX:TOL=83798],parataygetis lineata[&&NHX:TOL=83799])parataygetis[&&NHX:TOL=83591],(pareuptychia binocula[&&NHX:TOL=83800],pareuptychia difficilis[&&NHX:TOL=83801],pareuptychia hesionides[&&NHX:TOL=83802],pareuptychia lydia[&&NHX:TOL=83803],pareuptychia metaleuca[&&NHX:TOL=83804],pareuptychia ocirrhoe[&&NHX:TOL=83805],pareuptychia summandosa[&&NHX:TOL=83806],pareuptychia n. sp.[&&NHX:TOL=83807])pareuptychia[&&NHX:TOL=83592],((paryphthimoides argulus[&&NHX:TOL=83808],paryphthimoides difficilis[&&NHX:TOL=83809],paryphthimoides eous[&&NHX:TOL=83810],paryphthimoides grimon[&&NHX:TOL=83811],paryphthimoides melobosis[&&NHX:TOL=83812],paryphthimoides numeria[&&NHX:TOL=83813],paryphthimoides numilia[&&NHX:TOL=83814],paryphthimoides phronius[&&NHX:TOL=83815],paryphthimoides poltys[&&NHX:TOL=83816],paryphthimoides sylvina[&&NHX:TOL=83817],paryphthimoides undulata[&&NHX:TOL=83818],paryphthimoides vestigiata[&&NHX:TOL=83819],paryphthimoides zeredatha[&&NHX:TOL=83820])paryphthimoides[&&NHX:TOL=83593],(carminda umuarama[&&NHX:TOL=83791],carminda paeon[&&NHX:TOL=83789],carminda griseldis[&&NHX:TOL=83787])carminda[&&NHX:TOL=113127])[&&NHX:TOL=113126],(pharneuptychia boliviana[&&NHX:TOL=83821],pharneuptychia innocentia[&&NHX:TOL=83822],pharneuptychia phares[&&NHX:TOL=83823],pharneuptychia pharnabazos[&&NHX:TOL=83824],pharneuptychia pharnaces[&&NHX:TOL=83825],pharneuptychia romanina[&&NHX:TOL=83826])pharneuptychia[&&NHX:TOL=83594],pindis squamistriga[&&NHX:TOL=83595],posttaygetis penelea[&&NHX:TOL=83596],(praefaunula armilla[&&NHX:TOL=83827],praefaunula liturata[&&NHX:TOL=83828],praefaunula vesper[&&NHX:TOL=83829],praefaunula n. sp.[&&NHX:TOL=83830])praefaunula[&&NHX:TOL=83597],(pseudeuptychia hemileuca[&&NHX:TOL=83831],pseudeuptychia languida[&&NHX:TOL=83832],pseudeuptychia n. sp. 1[&&NHX:TOL=83833],pseudeuptychia n. sp. 2[&&NHX:TOL=83834])pseudeuptychia[&&NHX:TOL=83598],(pseudodebis dubiosa[&&NHX:TOL=83840],pseudodebis euptychidia[&&NHX:TOL=83841],pseudodebis marpessa[&&NHX:TOL=83842],pseudodebis valentina[&&NHX:TOL=83843],pseudodebis zimri[&&NHX:TOL=83844])pseudodebis[&&NHX:TOL=83599],rareuptychia clio[&&NHX:TOL=83600],satyrotaygetis satyrina[&&NHX:TOL=83601],(splendeuptychia ambra[&&NHX:TOL=83845],splendeuptychia ashna[&&NHX:TOL=83846],splendeuptychia aurigera[&&NHX:TOL=83847],splendeuptychia boliviensis[&&NHX:TOL=83848],splendeuptychia clementia[&&NHX:TOL=83849],splendeuptychia clorimena[&&NHX:TOL=83850],splendeuptychia cosmophila[&&NHX:TOL=83851],splendeuptychia doxes[&&NHX:TOL=83852],splendeuptychia furina[&&NHX:TOL=83853],splendeuptychia hygina[&&NHX:TOL=83854],splendeuptychia itonis[&&NHX:TOL=83855],splendeuptychia junonia[&&NHX:TOL=83856],splendeuptychia kendalli[&&NHX:TOL=83857],splendeuptychia latia[&&NHX:TOL=83858],splendeuptychia libitina[&&NHX:TOL=83859],splendeuptychia pagyris[&&NHX:TOL=83860],splendeuptychia purusana[&&NHX:TOL=83861],splendeuptychia quadrina[&&NHX:TOL=83862],splendeuptychia salvini[&&NHX:TOL=83863],splendeuptychia telesphora[&&NHX:TOL=83864],splendeuptychia toynei[&&NHX:TOL=83865],splendeuptychia triangula[&&NHX:TOL=83866],splendeuptychia zischkai[&&NHX:TOL=83867],23 undescribed species[&&NHX:TOL=83868])splendeuptychia[&&NHX:TOL=83602],taydebis peculiaris[&&NHX:TOL=83603],taygetina banghaasi[&&NHX:TOL=83604],(taygetis acuta[&&NHX:TOL=83869],taygetis angulosa[&&NHX:TOL=83870],taygetis asterie[&&NHX:TOL=83871],taygetis chiquitana[&&NHX:TOL=83872],taygetis chrysogone[&&NHX:TOL=83873],taygetis cleopatra[&&NHX:TOL=83874],taygetis echo[&&NHX:TOL=83875],taygetis elegia[&&NHX:TOL=83876],taygetis n. sp. 1[&&NHX:TOL=83877],taygetis inambari[&&NHX:TOL=83878],taygetis inconspicua[&&NHX:TOL=83879],taygetis kerea[&&NHX:TOL=83880],taygetis laches[&&NHX:TOL=83881],taygetis n. sp. 2[&&NHX:TOL=83882],taygetis larua[&&NHX:TOL=83883],taygetis leuctra[&&NHX:TOL=83884],taygetis mermeria[&&NHX:TOL=83885],taygetis rectifascia[&&NHX:TOL=83886],taygetis sosis[&&NHX:TOL=83887],taygetis sylvia[&&NHX:TOL=83888],taygetis thamyra[&&NHX:TOL=83889],taygetis tripunctata[&&NHX:TOL=83890],taygetis uncinata[&&NHX:TOL=83891],taygetis uzza[&&NHX:TOL=83892],taygetis virgilia[&&NHX:TOL=83893],taygetis weymeri[&&NHX:TOL=83894],taygetis ypthima[&&NHX:TOL=83895],taygetis zippora[&&NHX:TOL=83896])taygetis[&&NHX:TOL=83605],(yphthimoides acmenis[&&NHX:TOL=83900],yphthimoides affinis[&&NHX:TOL=83901],yphthimoides angularis[&&NHX:TOL=83902],yphthimoides argyrospila[&&NHX:TOL=83903],yphthimoides austera[&&NHX:TOL=83904],yphthimoides borasta[&&NHX:TOL=83905],yphthimoides celmis[&&NHX:TOL=83906],yphthimoides eriphule[&&NHX:TOL=83907],yphthimoides leguialimai[&&NHX:TOL=83908],yphthimoides maepius[&&NHX:TOL=83909],yphthimoides manasses[&&NHX:TOL=83910],yphthimoides mimula[&&NHX:TOL=83911],yphthimoides mythra[&&NHX:TOL=83912],yphthimoides neomaenas[&&NHX:TOL=83913],yphthimoides ochracea[&&NHX:TOL=83914],yphthimoides pacta[&&NHX:TOL=83915],yphthimoides patricia[&&NHX:TOL=83916],yphthimoides punctata[&&NHX:TOL=83917],yphthimoides renata[&&NHX:TOL=83918],yphthimoides straminea[&&NHX:TOL=83919],yphthimoides viviana[&&NHX:TOL=83920],yphthimoides yphthima[&&NHX:TOL=83921],yphthimoides cipoensis[&&NHX:TOL=83922],yphthimoides n. sp.[&&NHX:TOL=83923])yphthimoides[&&NHX:TOL=83607],(zischkaia amalda[&&NHX:TOL=83924],zischkaia mima[&&NHX:TOL=83925],zischkaia pacarus[&&NHX:TOL=83926],zischkaia saundersii[&&NHX:TOL=83927],zischkaia n. sp.[&&NHX:TOL=83928])zischkaia[&&NHX:TOL=83608],(cissia cleophes[&&NHX:TOL=83648],cissia confusa[&&NHX:TOL=83649],cissia joyceae[&&NHX:TOL=83650],cissia labe[&&NHX:TOL=83651],cissia lesbia[&&NHX:TOL=83652],cissia moneta[&&NHX:TOL=83653],cissia myncea[&&NHX:TOL=83654],cissia palladia[&&NHX:TOL=83655],cissia penelope[&&NHX:TOL=83656],cissia pompilia[&&NHX:TOL=83657],cissia proba[&&NHX:TOL=83658],cissia pseudoconfusa[&&NHX:TOL=83659],cissia similis[&&NHX:TOL=83660],cissia terrestris[&&NHX:TOL=83661],cissia themis[&&NHX:TOL=83662])cissia[&&NHX:TOL=83646],(euptychia insignis[&&NHX:TOL=83931],neonympha lupita[&&NHX:TOL=83932],euptychia ordinata[&&NHX:TOL=83934],euptychia pellonia[&&NHX:TOL=83935])euptychiina incertae sedis[&&NHX:TOL=83929])euptychiina[&&NHX:TOL=70791],(acropolis thalia[&&NHX:TOL=88312],(acrophtalmia artemis[&&NHX:TOL=88315],acrophtalmia leuce[&&NHX:TOL=88316],acrophthalmia windorum[&&NHX:TOL=93903])acrophtalmia[&&NHX:TOL=88313],(ragadia annulata[&&NHX:TOL=88317],ragadia crisilda[&&NHX:TOL=88318],ragadia critias[&&NHX:TOL=88319],ragadia luzonia[&&NHX:TOL=88320],ragadia maganda[&&NHX:TOL=88321],ragadia makuta[&&NHX:TOL=88322],ragadia melindena[&&NHX:TOL=88323])ragadia[&&NHX:TOL=88314])ragadiina[&&NHX:TOL=70792],((argynnina cyrila[&&NHX:TOL=88335],argynnina hobartia[&&NHX:TOL=88336])argynnina[&&NHX:TOL=87453],(erycinidia ducis[&&NHX:TOL=88356],erycinidia gracilis[&&NHX:TOL=88357],erycinidia hemileuca[&&NHX:TOL=88358],erycinidia maudei[&&NHX:TOL=88359],erycinidia tenera[&&NHX:TOL=88360],erycinidia virgo[&&NHX:TOL=88361])erycinidia[&&NHX:TOL=87458],(harsiesis hecaerge[&&NHX:TOL=88374],harsiesis hygea[&&NHX:TOL=88375],harsiesis yolanthe[&&NHX:TOL=88376])harsiesis[&&NHX:TOL=87460],hyalodia tenuisquamosa[&&NHX:TOL=87462],paratisiphone lyrnessa[&&NHX:TOL=87466],(platypthima antapa[&&NHX:TOL=88348],platypthima dispar[&&NHX:TOL=88349],platypthima homochroa[&&NHX:TOL=88350],platypthima leucomelas[&&NHX:TOL=88351],platypthima ornata[&&NHX:TOL=88352],platypthima placiva[&&NHX:TOL=88353],platypthima septentrionalis[&&NHX:TOL=88354],platypthima simplex[&&NHX:TOL=88355])platypthima[&&NHX:TOL=87468],((((dodonidia helmsi[&&NHX:TOL=87456],(tisiphone abeona[&&NHX:TOL=88396],tisiphone helena[&&NHX:TOL=88397])tisiphone[&&NHX:TOL=87469])[&&NHX:TOL=87477],(argyrophenga antipodum[&&NHX:TOL=87455],(percnodaimon merula[&&NHX:TOL=87467],erebiola butleri[&&NHX:TOL=87457])[&&NHX:TOL=87479])[&&NHX:TOL=87478])[&&NHX:TOL=87476],(((((oreixenica correae[&&NHX:TOL=88390],oreixenica kershawi[&&NHX:TOL=88391],oreixenica lathoniella[&&NHX:TOL=88392],oreixenica latialis[&&NHX:TOL=88393],oreixenica orichora[&&NHX:TOL=88394],oreixenica ptunarra[&&NHX:TOL=88395])oreixenica[&&NHX:TOL=87465],(hypocysta adiante[&&NHX:TOL=88362],hypocysta angustata[&&NHX:TOL=88363],hypocysta aroa[&&NHX:TOL=88364],hypocysta calypso[&&NHX:TOL=88365],hypocysta euphemia[&&NHX:TOL=88366],hypocysta haemonia[&&NHX:TOL=88367],hypocysta irius[&&NHX:TOL=88368],hypocysta isis[&&NHX:TOL=88369],hypocysta metirius[&&NHX:TOL=88370],hypocysta osyris[&&NHX:TOL=88371],hypocysta pseudirius[&&NHX:TOL=88372],hypocysta serapis[&&NHX:TOL=88373])hypocysta[&&NHX:TOL=87463])[&&NHX:TOL=87483],lamprolenis nitida[&&NHX:TOL=87484])[&&NHX:TOL=87482],nesoxenica leprea[&&NHX:TOL=87464])[&&NHX:TOL=87481],(((geitoneura acantha[&&NHX:TOL=88380],geitoneura klugii[&&NHX:TOL=88381],geitoneura minyas[&&NHX:TOL=88382])geitoneura[&&NHX:TOL=87459],(heteronympha banksii[&&NHX:TOL=88383],heteronympha cordace[&&NHX:TOL=88384],heteronympha merope[&&NHX:TOL=88385],heteronympha mirifica[&&NHX:TOL=88386],heteronympha paradelpha[&&NHX:TOL=88387],heteronympha penelope[&&NHX:TOL=88388],heteronympha solandri[&&NHX:TOL=88389])heteronympha[&&NHX:TOL=87461])[&&NHX:TOL=87486],((oressinoma sorata[&&NHX:TOL=83792],oressinoma typhla[&&NHX:TOL=83793])oressinoma[&&NHX:TOL=83589],((((coenonympha nolckeni[&&NHX:TOL=88417],(coenonympha myops[&&NHX:TOL=88379],coenonympha amirica[&&NHX:TOL=88377],coenonympha mcmahoni[&&NHX:TOL=87471])[&&NHX:TOL=137791])[&&NHX:TOL=137790],(coenonympha saadi[&&NHX:TOL=88421],(((coenonympha austauti[&&NHX:TOL=137767],coenonympha dorus[&&NHX:TOL=88406])[&&NHX:TOL=137766],((coenonympha pamphilus[&&NHX:TOL=88419],coenonympha thyrsis[&&NHX:TOL=88426])[&&NHX:TOL=137769],(coenonympha tullia north america[&&NHX:TOL=137771],(coenonympha amaryllis[&&NHX:TOL=88401],(coenonympha rhodopensis[&&NHX:TOL=88427],coenonympha tullia[&&NHX:TOL=88428])[&&NHX:TOL=137773])[&&NHX:TOL=137772])[&&NHX:TOL=137770])[&&NHX:TOL=137768])[&&NHX:TOL=137765],((coenonympha sunbecca[&&NHX:TOL=88424],(coenonympha iphioides[&&NHX:TOL=88410],(coenonympha glycerion[&&NHX:TOL=88408],coenonympha mahometana[&&NHX:TOL=88413])[&&NHX:TOL=137777])[&&NHX:TOL=137776])[&&NHX:TOL=137775],((coenonympha corinna[&&NHX:TOL=88405],coenonympha elbana[&&NHX:TOL=137780])[&&NHX:TOL=137779],((coenonympha arcanioides[&&NHX:TOL=88403],coenonympha vaucheri[&&NHX:TOL=88430])[&&NHX:TOL=137782],((coenonympha semenovi[&&NHX:TOL=88422],(coenonympha hero[&&NHX:TOL=88411],coenonympha leander[&&NHX:TOL=88412])[&&NHX:TOL=137785])[&&NHX:TOL=137784],(coenonympha gardetta[&&NHX:TOL=137787],coenonympha arcania[&&NHX:TOL=88402])[&&NHX:TOL=137786])[&&NHX:TOL=137783])[&&NHX:TOL=137781])[&&NHX:TOL=137778])[&&NHX:TOL=137774])[&&NHX:TOL=137764])[&&NHX:TOL=137763])[&&NHX:TOL=137789],(coenonympha oedippus[&&NHX:TOL=88418],(coenonympha phryne[&&NHX:TOL=88400],coenonympha dohrnii[&&NHX:TOL=88398],coenonympha nervosa[&&NHX:TOL=88399])[&&NHX:TOL=137793])[&&NHX:TOL=137792])[&&NHX:TOL=137788],coenonympha caeca[&&NHX:TOL=88404],coenonympha darwiniana[&&NHX:TOL=128138],coenonympha fettigii[&&NHX:TOL=88407],coenonympha haydenii[&&NHX:TOL=88409],coenonympha mangeri[&&NHX:TOL=88414],coenonympha mongolica[&&NHX:TOL=88415],coenonympha nipisiquit[&&NHX:TOL=88416],coenonympha pavonina[&&NHX:TOL=88420],coenonympha sinica[&&NHX:TOL=88423],coenonympha symphita[&&NHX:TOL=88425],coenonympha tydeus[&&NHX:TOL=88429],coenonympha xinjiangensis[&&NHX:TOL=88431])coenonympha[&&NHX:TOL=87470])[&&NHX:TOL=87487])[&&NHX:TOL=87485])[&&NHX:TOL=87480])[&&NHX:TOL=87475],(argyronympha gracilipes[&&NHX:TOL=88337],argyronympha pulchra[&&NHX:TOL=88338],argyronympha rubianensis[&&NHX:TOL=88339],argyronympha ugiensis[&&NHX:TOL=88340],argyronympha ulava[&&NHX:TOL=88341])argyronympha[&&NHX:TOL=87454])[&&NHX:TOL=87474],(altiapa colorata[&&NHX:TOL=88344],altiapa decolor[&&NHX:TOL=88345],altiapa klossi[&&NHX:TOL=88346],altiapa pandora[&&NHX:TOL=88347])altiapa[&&NHX:TOL=88342],sinonympha amoena[&&NHX:TOL=93269])coenonymphina[&&NHX:TOL=70794],(((pararge aegeria[&&NHX:TOL=89101],pararge xiphioides[&&NHX:TOL=89102],pararge xiphia[&&NHX:TOL=89103])pararge[&&NHX:TOL=89070],(lasiommata megera[&&NHX:TOL=89086],lasiommata adrastoides[&&NHX:TOL=89087],lasiommata felix[&&NHX:TOL=89088],lasiommata hindukushica[&&NHX:TOL=89089],lasiommata maderakal[&&NHX:TOL=89090],lasiommata maera[&&NHX:TOL=89091],lasiommata maeroides[&&NHX:TOL=89092],lasiommata maerula[&&NHX:TOL=89093],lasiommata majuscula[&&NHX:TOL=89094],lasiommata meadewaldoi[&&NHX:TOL=89095],lasiommata menava[&&NHX:TOL=89096],lasiommata minuscla[&&NHX:TOL=89097],lasiommata paramegaera[&&NHX:TOL=89098],lasiommata petropolitana[&&NHX:TOL=89099],lasiommata schakra[&&NHX:TOL=89100])lasiommata[&&NHX:TOL=89071],(lopinga dumetorum[&&NHX:TOL=89104],lopinga achine[&&NHX:TOL=89105],lopinga catena[&&NHX:TOL=89106],lopinga deidamia[&&NHX:TOL=89107],lopinga eckweileri[&&NHX:TOL=89108],lopinga fulvescens[&&NHX:TOL=89109],lopinga gerdae[&&NHX:TOL=89110],lopinga lehmanni[&&NHX:TOL=89111],lopinga nemorum[&&NHX:TOL=89112])lopinga[&&NHX:TOL=89072],(kirinia epimenides[&&NHX:TOL=89081],kirinia epaminondas[&&NHX:TOL=89082],kirinia roxelana[&&NHX:TOL=89083],kirinia climene[&&NHX:TOL=89084],kirinia eversmanni[&&NHX:TOL=89085])kirinia[&&NHX:TOL=89073],(chonala masoni[&&NHX:TOL=89078],chonala episcopalis[&&NHX:TOL=89079],chonala praeusta[&&NHX:TOL=89080],chonala laurae[&&NHX:TOL=89113],chonala miyatai[&&NHX:TOL=89114])chonala[&&NHX:TOL=89074],(orinoma damaris[&&NHX:TOL=89120],orinoma alba[&&NHX:TOL=89121])orinoma[&&NHX:TOL=89075],(rhaphicera satricus[&&NHX:TOL=89115],rhaphicera dumicola[&&NHX:TOL=89116],rhaphicera moorei[&&NHX:TOL=89117])rhaphicera[&&NHX:TOL=89076],tatinga thibetana[&&NHX:TOL=89077],nosea hainanensis[&&NHX:TOL=89118])parargina[&&NHX:TOL=70797],(((bicyclus abnormis[&&NHX:TOL=85322],bicyclus albocincta[&&NHX:TOL=85323],bicyclus aurivillii[&&NHX:TOL=85330],bicyclus campina[&&NHX:TOL=85332],bicyclus condamini[&&NHX:TOL=85334],bicyclus cooksoni[&&NHX:TOL=85335],bicyclus danckelmani[&&NHX:TOL=85337],bicyclus dekeyseri[&&NHX:TOL=85338],bicyclus ephorus[&&NHX:TOL=85343],bicyclus feae[&&NHX:TOL=85345],bicyclus howarthi[&&NHX:TOL=85350],bicyclus kiellandi[&&NHX:TOL=85358],bicyclus lamani[&&NHX:TOL=85359],bicyclus maesseni[&&NHX:TOL=85361],bicyclus milyas[&&NHX:TOL=85366],((bicyclus evadne[&&NHX:TOL=85344],(bicyclus xeneas[&&NHX:TOL=85400],(bicyclus xeneoides[&&NHX:TOL=85401],bicyclus alboplaga[&&NHX:TOL=85324])[&&NHX:TOL=85406])[&&NHX:TOL=85405])[&&NHX:TOL=85404],((((bicyclus analis[&&NHX:TOL=85325],bicyclus uniformis[&&NHX:TOL=85396])[&&NHX:TOL=85410],(bicyclus procora[&&NHX:TOL=85374],(bicyclus hyperanthus[&&NHX:TOL=85351],bicyclus sciathis[&&NHX:TOL=85383])[&&NHX:TOL=85412])[&&NHX:TOL=85411])[&&NHX:TOL=85409],(bicyclus hewitsoni[&&NHX:TOL=85349],(bicyclus medontias[&&NHX:TOL=85364],(bicyclus sweadneri[&&NHX:TOL=85390],(bicyclus iccius[&&NHX:TOL=85352],((bicyclus graueri[&&NHX:TOL=85348],bicyclus sebetus[&&NHX:TOL=85384])[&&NHX:TOL=85418],(bicyclus italus[&&NHX:TOL=85355],bicyclus zinebi[&&NHX:TOL=85402])[&&NHX:TOL=85419])[&&NHX:TOL=85417])[&&NHX:TOL=85416])[&&NHX:TOL=85415])[&&NHX:TOL=85414])[&&NHX:TOL=85413])[&&NHX:TOL=85408],((bicyclus trilophus[&&NHX:TOL=85395],(bicyclus pavonis[&&NHX:TOL=85372],bicyclus ignobilis[&&NHX:TOL=85353])[&&NHX:TOL=85422])[&&NHX:TOL=85421],((bicyclus taenias[&&NHX:TOL=85392],(bicyclus anisops[&&NHX:TOL=85327],bicyclus dentata[&&NHX:TOL=85339])[&&NHX:TOL=85425])[&&NHX:TOL=85424],((((bicyclus technatis[&&NHX:TOL=85394],bicyclus vansoni[&&NHX:TOL=85398])[&&NHX:TOL=85429],(bicyclus ena[&&NHX:TOL=85342],(bicyclus sandace[&&NHX:TOL=85380],(bicyclus vulgaris[&&NHX:TOL=85399],(bicyclus jeffreyi[&&NHX:TOL=85356],(bicyclus moyses[&&NHX:TOL=85368],bicyclus dorothea[&&NHX:TOL=85340])[&&NHX:TOL=85434])[&&NHX:TOL=85433])[&&NHX:TOL=85432])[&&NHX:TOL=85431])[&&NHX:TOL=85430])[&&NHX:TOL=85428],((bicyclus sambulos[&&NHX:TOL=85378],(bicyclus sangmelinae[&&NHX:TOL=85381],bicyclus mesogena[&&NHX:TOL=85365])[&&NHX:TOL=85437])[&&NHX:TOL=85436],((bicyclus auricruda[&&NHX:TOL=85329],(bicyclus mandanes[&&NHX:TOL=85362],bicyclus kenia[&&NHX:TOL=85357])[&&NHX:TOL=85440])[&&NHX:TOL=85439],(bicyclus mollitia[&&NHX:TOL=85367],(bicyclus anynana[&&NHX:TOL=85328],(bicyclus campus[&&NHX:TOL=85333],bicyclus angulosa[&&NHX:TOL=85326])[&&NHX:TOL=85443])[&&NHX:TOL=85442])[&&NHX:TOL=85441])[&&NHX:TOL=85438])[&&NHX:TOL=85435])[&&NHX:TOL=85427],((bicyclus cottrelli[&&NHX:TOL=85336],bicyclus safitza[&&NHX:TOL=85377])[&&NHX:TOL=85445],((bicyclus funebris[&&NHX:TOL=85346],bicyclus dubia[&&NHX:TOL=85341])[&&NHX:TOL=85447],(bicyclus matuta[&&NHX:TOL=85363],(((bicyclus sophrosyne[&&NHX:TOL=85388],bicyclus istaris[&&NHX:TOL=85354])[&&NHX:TOL=85451],(bicyclus madetes[&&NHX:TOL=85360],(bicyclus smithi[&&NHX:TOL=85387],bicyclus golo[&&NHX:TOL=85347])[&&NHX:TOL=85453])[&&NHX:TOL=85452])[&&NHX:TOL=85450],(bicyclus persimilis[&&NHX:TOL=85373],(bicyclus sanaos[&&NHX:TOL=85379],bicyclus buea[&&NHX:TOL=85331])[&&NHX:TOL=85455])[&&NHX:TOL=85454])[&&NHX:TOL=85449])[&&NHX:TOL=85448])[&&NHX:TOL=85446])[&&NHX:TOL=85444])[&&NHX:TOL=85426])[&&NHX:TOL=85423])[&&NHX:TOL=85420])[&&NHX:TOL=85407])[&&NHX:TOL=85403],bicyclus nachtetis[&&NHX:TOL=85369],bicyclus neustetteri[&&NHX:TOL=85370],bicyclus nobilis[&&NHX:TOL=85371],bicyclus rhacotis[&&NHX:TOL=85375],bicyclus rileyi[&&NHX:TOL=85376],bicyclus saussurei[&&NHX:TOL=85382],bicyclus similis[&&NHX:TOL=85385],bicyclus simulacris[&&NHX:TOL=85386],bicyclus suffusa[&&NHX:TOL=85389],bicyclus sylvicolus[&&NHX:TOL=85391],bicyclus tanzanicus[&&NHX:TOL=85393],bicyclus uzungwensis[&&NHX:TOL=85397])bicyclus[&&NHX:TOL=85314],(hallelesis asochis[&&NHX:TOL=85456],hallelesis halyma[&&NHX:TOL=85457])hallelesis[&&NHX:TOL=85315],((heteropsis centralis[&&NHX:TOL=85470],heteropsis decira[&&NHX:TOL=128897],heteropsis eliasis[&&NHX:TOL=85475],heteropsis elisi[&&NHX:TOL=85476],heteropsis nigrescens[&&NHX:TOL=128896],heteropsis ochracea[&&NHX:TOL=85490],heteropsis peitho[&&NHX:TOL=85496],heteropsis perspicua[&&NHX:TOL=85497],heteropsis phaea[&&NHX:TOL=85498],heteropsis simonsii[&&NHX:TOL=85500],heteropsis teratia[&&NHX:TOL=85504],heteropsis ubenica[&&NHX:TOL=85507])heteropsis african[&&NHX:TOL=85316],heteropsis comorensis[&&NHX:TOL=85472],(heteropsis fuliginosa[&&NHX:TOL=85479],heteropsis exocellata[&&NHX:TOL=85478],heteropsis cowani[&&NHX:TOL=85473],heteropsis ankaratra[&&NHX:TOL=85462],heteropsis narcissus[&&NHX:TOL=85488])heteropsis subgenus 1[&&NHX:TOL=93761],heteropsis heteropsis drepana[&&NHX:TOL=85317],(heteropsis telinga vola[&&NHX:TOL=85512],heteropsis telinga adolphei[&&NHX:TOL=93763],heteropsis telinga sp. 2[&&NHX:TOL=93764])heteropsis telinga[&&NHX:TOL=93762],heteropsis admiratio paradoxa[&&NHX:TOL=85313],(heteropsis masoura alaokola[&&NHX:TOL=85525],heteropsis masoura ankoma[&&NHX:TOL=85526],heteropsis masoura antahala[&&NHX:TOL=85527],heteropsis masoura mabillei[&&NHX:TOL=85528],heteropsis masoura masoura[&&NHX:TOL=85529])heteropsis masoura[&&NHX:TOL=85319],(heteropsis henotesia viettei[&&NHX:TOL=93765],heteropsis henotesia andravahana[&&NHX:TOL=93766],heteropsis henotesia strato[&&NHX:TOL=85501],heteropsis henotesia obscura[&&NHX:TOL=85489],heteropsis henotesia passandava[&&NHX:TOL=85522],heteropsis henotesia difficilis[&&NHX:TOL=85510],heteropsis henotesia erebina[&&NHX:TOL=85477],heteropsis henotesia narova[&&NHX:TOL=85521],heteropsis henotesia anganavo[&&NHX:TOL=85460],heteropsis henotesia wardii[&&NHX:TOL=85524],heteropsis henotesia erebennis[&&NHX:TOL=85519])heteropsis henotesia[&&NHX:TOL=85318],(heteropsis anceps[&&NHX:TOL=85459],heteropsis andasibe[&&NHX:TOL=93768],heteropsis angulifasciata[&&NHX:TOL=85461],heteropsis ankova[&&NHX:TOL=85463],heteropsis avelona[&&NHX:TOL=85466],heteropsis bicristata[&&NHX:TOL=85468],heteropsis iboina[&&NHX:TOL=85482],heteropsis laeta[&&NHX:TOL=85483],heteropsis laetifica[&&NHX:TOL=85484],heteropsis maeva[&&NHX:TOL=85485],heteropsis pallida[&&NHX:TOL=85492],heteropsis parva[&&NHX:TOL=85493],heteropsis parvidens[&&NHX:TOL=85494],heteropsis pauper[&&NHX:TOL=85495],heteropsis sabas[&&NHX:TOL=85499],heteropsis strigula[&&NHX:TOL=85502],heteropsis subsimilis[&&NHX:TOL=85503],heteropsis turbans[&&NHX:TOL=85505],heteropsis turbata[&&NHX:TOL=85506],heteropsis undulans[&&NHX:TOL=85508],heteropsis uniformis[&&NHX:TOL=85511])heteropsis subgenus 2[&&NHX:TOL=93767],numerous undescribed species[&&NHX:TOL=85514])heteropsis[&&NHX:TOL=93760],((((lohora anna[&&NHX:TOL=93895],lohora dexamenus[&&NHX:TOL=90309],lohora dinon[&&NHX:TOL=90312],lohora haasei[&&NHX:TOL=90318],lohora ophthalmicus[&&NHX:TOL=90342],lohora tilmara[&&NHX:TOL=90357],lohora transiens[&&NHX:TOL=90358],lohora unipupillata[&&NHX:TOL=93896])lohora lohora[&&NHX:TOL=93894],(lohora decipiens[&&NHX:TOL=93898],lohora deianira[&&NHX:TOL=90310],lohora deianirina[&&NHX:TOL=90311],lohora erna[&&NHX:TOL=90314],lohora imitatrix[&&NHX:TOL=93899],lohora inga[&&NHX:TOL=90323],lohora pandaea[&&NHX:TOL=90343],lohora umbrosa[&&NHX:TOL=93900])lohora physcon[&&NHX:TOL=93897],lohora pseudomycalesis tanuki[&&NHX:TOL=89841])lohora[&&NHX:TOL=93893],nirvanopsis hypnus[&&NHX:TOL=89840])[&&NHX:TOL=93902],(mycalesis adamsoni[&&NHX:TOL=90304],mycalesis aethiops[&&NHX:TOL=89793],mycalesis anapita[&&NHX:TOL=89794],mycalesis anaxias[&&NHX:TOL=89795],mycalesis anaxioides[&&NHX:TOL=89796],mycalesis annamitica[&&NHX:TOL=90305],mycalesis arabella[&&NHX:TOL=90306],mycalesis aramis[&&NHX:TOL=90307],mycalesis asophis[&&NHX:TOL=89797],mycalesis barbara[&&NHX:TOL=89798],mycalesis bazochii[&&NHX:TOL=89799],mycalesis biformis[&&NHX:TOL=89800],mycalesis bilineata[&&NHX:TOL=89801],mycalesis bisaya[&&NHX:TOL=90308],mycalesis cacodaemon[&&NHX:TOL=89802],mycalesis comes[&&NHX:TOL=89803],mycalesis discobolus[&&NHX:TOL=89804],mycalesis drusillodes[&&NHX:TOL=89806],mycalesis duponchelii[&&NHX:TOL=89807],mycalesis durga[&&NHX:TOL=89808],mycalesis elia[&&NHX:TOL=89809],mycalesis evansii[&&NHX:TOL=90315],mycalesis felderi[&&NHX:TOL=90316],mycalesis francisca[&&NHX:TOL=89792],mycalesis fulvianetta[&&NHX:TOL=89810],mycalesis fuscum[&&NHX:TOL=89811],mycalesis giamana[&&NHX:TOL=89812],mycalesis gotama[&&NHX:TOL=90317],mycalesis heri[&&NHX:TOL=90319],mycalesis horsfieldi[&&NHX:TOL=89813],mycalesis igilia[&&NHX:TOL=90320],mycalesis igoleta[&&NHX:TOL=90321],mycalesis inayoshii[&&NHX:TOL=90322],mycalesis inopia[&&NHX:TOL=90324],mycalesis intermedia[&&NHX:TOL=89814],mycalesis ita[&&NHX:TOL=90325],mycalesis itys[&&NHX:TOL=90326],mycalesis janardana[&&NHX:TOL=89815],mycalesis lepcha[&&NHX:TOL=90327],mycalesis maianeas[&&NHX:TOL=89816],mycalesis malsara[&&NHX:TOL=90328],mycalesis malsarida[&&NHX:TOL=90329],mycalesis mamerta[&&NHX:TOL=90330],mycalesis manii[&&NHX:TOL=90331],mycalesis marginata[&&NHX:TOL=89817],mycalesis mehadeva[&&NHX:TOL=89818],mycalesis messene[&&NHX:TOL=90332],mycalesis mestra[&&NHX:TOL=90333],mycalesis mineus[&&NHX:TOL=89819],mycalesis misenus[&&NHX:TOL=90334],mycalesis mnasicles[&&NHX:TOL=89820],mycalesis moorei[&&NHX:TOL=90335],mycalesis mucia[&&NHX:TOL=89821],mycalesis mulleri[&&NHX:TOL=90336],mycalesis mynois[&&NHX:TOL=90337],mycalesis mystes[&&NHX:TOL=90338],mycalesis nala[&&NHX:TOL=90339],mycalesis nerida[&&NHX:TOL=89822],mycalesis nicotia[&&NHX:TOL=90340],mycalesis oculus[&&NHX:TOL=90341],mycalesis oroatis[&&NHX:TOL=89823],mycalesis orseis[&&NHX:TOL=89824],mycalesis panthaka[&&NHX:TOL=90344],mycalesis patiana[&&NHX:TOL=89825],mycalesis patnia[&&NHX:TOL=90345],mycalesis pernotata[&&NHX:TOL=89826],mycalesis perseoides[&&NHX:TOL=89827],mycalesis perseus[&&NHX:TOL=89828],mycalesis phidon[&&NHX:TOL=89829],mycalesis pitana[&&NHX:TOL=90346],mycalesis radza[&&NHX:TOL=90347],mycalesis rama[&&NHX:TOL=90348],mycalesis sangaica[&&NHX:TOL=90350],mycalesis sara[&&NHX:TOL=89830],mycalesis shiva[&&NHX:TOL=89831],mycalesis siamica[&&NHX:TOL=90351],mycalesis sirius[&&NHX:TOL=89832],mycalesis splendens[&&NHX:TOL=89833],mycalesis suaveolens[&&NHX:TOL=90352],mycalesis sudra[&&NHX:TOL=90353],mycalesis tagala[&&NHX:TOL=90354],mycalesis terminus[&&NHX:TOL=89834],mycalesis thailandica[&&NHX:TOL=90355],mycalesis thyateira[&&NHX:TOL=90356],mycalesis treadawayi[&&NHX:TOL=90359],mycalesis valeria[&&NHX:TOL=89835],mycalesis visala[&&NHX:TOL=89836],mycalesis wayewa[&&NHX:TOL=90360],mycalesis sp. a[&&NHX:TOL=89837],mycalesis sp. b[&&NHX:TOL=89838])mycalesis[&&NHX:TOL=85320])[&&NHX:TOL=93892])mycalesina[&&NHX:TOL=70799],((lethe europa[&&NHX:TOL=89689],lethe albolineata[&&NHX:TOL=89690],lethe andersoni[&&NHX:TOL=89691],lethe arete[&&NHX:TOL=89692],lethe argentata[&&NHX:TOL=89693],lethe armandina[&&NHX:TOL=89694],lethe atkinsonia[&&NHX:TOL=89695],lethe baileyi[&&NHX:TOL=89696],lethe baladeva[&&NHX:TOL=89697],lethe bhairava[&&NHX:TOL=89698],lethe bitaensis[&&NHX:TOL=118317],lethe brisanda[&&NHX:TOL=89699],lethe butleri[&&NHX:TOL=89700],lethe callipteris[&&NHX:TOL=89701],lethe camilla[&&NHX:TOL=89702],lethe chandica[&&NHX:TOL=89703],lethe christophi[&&NHX:TOL=89704],lethe confusa[&&NHX:TOL=89705],lethe cybele[&&NHX:TOL=89706],lethe cyrene[&&NHX:TOL=89707],lethe dakwania[&&NHX:TOL=89708],lethe darena[&&NHX:TOL=89709],lethe daretis[&&NHX:TOL=89710],lethe dataensis[&&NHX:TOL=89711],lethe deliades[&&NHX:TOL=89712],lethe delila[&&NHX:TOL=89713],lethe diana[&&NHX:TOL=89714],lethe dinarbas[&&NHX:TOL=89715],lethe distans[&&NHX:TOL=89716],lethe dora[&&NHX:TOL=89717],lethe drypetis[&&NHX:TOL=89718],lethe dura[&&NHX:TOL=89719],lethe dynsate[&&NHX:TOL=89720],lethe gemina[&&NHX:TOL=89721],lethe goalpara[&&NHX:TOL=89722],lethe gracilis[&&NHX:TOL=89723],lethe gulnihal[&&NHX:TOL=89724],lethe hayashii[&&NHX:TOL=89725],lethe hecate[&&NHX:TOL=89790],lethe helena[&&NHX:TOL=89726],lethe helle[&&NHX:TOL=89727],lethe hyrania[&&NHX:TOL=89728],lethe inomatai[&&NHX:TOL=89729],lethe insana[&&NHX:TOL=89730],lethe insularis[&&NHX:TOL=89731],lethe jalaurida[&&NHX:TOL=89732],lethe kabrua[&&NHX:TOL=89733],lethe kanjupkula[&&NHX:TOL=89734],lethe kansa[&&NHX:TOL=89735],lethe kazuichiroi[&&NHX:TOL=118325],lethe kouleikouzana[&&NHX:TOL=118326],lethe labyrinthea[&&NHX:TOL=89736],lethe lanaris[&&NHX:TOL=89737],lethe laodamia[&&NHX:TOL=89738],lethe latiaris[&&NHX:TOL=89739],lethe luteofasciata[&&NHX:TOL=89740],lethe maitrya[&&NHX:TOL=89741],lethe manthara[&&NHX:TOL=89742],lethe manzorum[&&NHX:TOL=89743],lethe margaritae[&&NHX:TOL=89744],lethe marginalis[&&NHX:TOL=89745],lethe mataja[&&NHX:TOL=89746],lethe mekara[&&NHX:TOL=89747],lethe minerva[&&NHX:TOL=89748],lethe moelleri[&&NHX:TOL=89749],lethe monilifera[&&NHX:TOL=89750],lethe naga[&&NHX:TOL=89751],lethe neelgherriensis[&&NHX:TOL=89752],lethe nicetas[&&NHX:TOL=89753],lethe nicetella[&&NHX:TOL=89754],lethe nigrifascia[&&NHX:TOL=89755],lethe nujiangensis[&&NHX:TOL=118327],lethe ocellata[&&NHX:TOL=89756],lethe oculatissima[&&NHX:TOL=89757],lethe perimede[&&NHX:TOL=89758],lethe procne[&&NHX:TOL=89759],lethe proxima[&&NHX:TOL=89760],lethe ramadeva[&&NHX:TOL=89761],lethe rohria[&&NHX:TOL=89762],lethe sadona[&&NHX:TOL=89763],lethe samio[&&NHX:TOL=89764],lethe satyavati[&&NHX:TOL=89765],lethe satyrina[&&NHX:TOL=89766],lethe scanda[&&NHX:TOL=89767],lethe serbonis[&&NHX:TOL=89768],lethe shirozui[&&NHX:TOL=89769],lethe sicelides[&&NHX:TOL=89770],lethe sicelis[&&NHX:TOL=89771],lethe siderea[&&NHX:TOL=89772],lethe sidonis[&&NHX:TOL=89773],lethe sinorix[&&NHX:TOL=89774],lethe sura[&&NHX:TOL=89775],lethe syrcis[&&NHX:TOL=89776],lethe titania[&&NHX:TOL=89777],lethe todara[&&NHX:TOL=89778],lethe trimacula[&&NHX:TOL=89779],lethe tristigmata[&&NHX:TOL=89780],lethe uemurai[&&NHX:TOL=89781],lethe vaivarta[&&NHX:TOL=89782],lethe verma[&&NHX:TOL=89783],lethe vindhya[&&NHX:TOL=89784],lethe violaceopicta[&&NHX:TOL=89785],lethe violae[&&NHX:TOL=89786],lethe visrava[&&NHX:TOL=89787],lethe yantra[&&NHX:TOL=89788],lethe yunnana[&&NHX:TOL=89789])lethe[&&NHX:TOL=89501],(aphysoneura pigmentaria[&&NHX:TOL=89521],aphysoneura scapulifascia[&&NHX:TOL=89522])aphysoneura[&&NHX:TOL=89502],(enodia creola[&&NHX:TOL=89520],(enodia portlandia[&&NHX:TOL=89518],enodia anthedon[&&NHX:TOL=89519])[&&NHX:TOL=124449])enodia[&&NHX:TOL=89503],(neope bhadra[&&NHX:TOL=89523],neope agrestis[&&NHX:TOL=89524],neope armandii[&&NHX:TOL=89525],neope bremeri[&&NHX:TOL=89526],neope christi[&&NHX:TOL=89527],neope dejeani[&&NHX:TOL=89528],neope goschkevitschii[&&NHX:TOL=89529],neope lacticolora[&&NHX:TOL=89530],neope muirheadii[&&NHX:TOL=89531],neope niphonica[&&NHX:TOL=89532],neope oberthueri[&&NHX:TOL=89533],neope pulaha[&&NHX:TOL=89534],neope pulahina[&&NHX:TOL=89535],neope pulahoides[&&NHX:TOL=89536],neope sagittata[&&NHX:TOL=89537],neope shirozui[&&NHX:TOL=89538],neope simulans[&&NHX:TOL=89539],neope watanabei[&&NHX:TOL=89540],neope yama[&&NHX:TOL=89541])neope[&&NHX:TOL=89504],ninguta schrenkii[&&NHX:TOL=89506],(ptychandra lorquinii[&&NHX:TOL=89511],ptychandra leucogyne[&&NHX:TOL=89512],ptychandra leytensis[&&NHX:TOL=89513],ptychandra schadenbergi[&&NHX:TOL=89514],ptychandra talboti[&&NHX:TOL=89515])ptychandra[&&NHX:TOL=89507],(satyrodes eurydice[&&NHX:TOL=89516],satyrodes appalachia[&&NHX:TOL=89517])satyrodes[&&NHX:TOL=89508],mandarinia regalis[&&NHX:TOL=89509])lethina[&&NHX:TOL=70800])[&&NHX:TOL=70798])[&&NHX:TOL=70796],(((maniola jurtina[&&NHX:TOL=92935],maniola chia[&&NHX:TOL=92936],maniola halicarnassus[&&NHX:TOL=92937],maniola megala[&&NHX:TOL=92938],maniola nurag[&&NHX:TOL=92939],maniola telmessia[&&NHX:TOL=92940])maniola[&&NHX:TOL=92919],(pyronia tithonus[&&NHX:TOL=92941],pyronia bathseba[&&NHX:TOL=92942],pyronia cecilia[&&NHX:TOL=92943],pyronia coenonympha[&&NHX:TOL=92944],pyronia janiroides[&&NHX:TOL=92945])pyronia[&&NHX:TOL=92920],aphantopus hyperantus[&&NHX:TOL=89068],gyrocheilus patrobas[&&NHX:TOL=93271],[&&NHX:TOL=93272])maniolina[&&NHX:TOL=70802],(melanargia galathea[&&NHX:TOL=92948],melanargia arge[&&NHX:TOL=92949],melanargia asiatica[&&NHX:TOL=92950],melanargia epimede[&&NHX:TOL=92951],melanargia evartianae[&&NHX:TOL=92952],melanargia ganymedes[&&NHX:TOL=92953],melanargia halimede[&&NHX:TOL=92954],melanargia hylata[&&NHX:TOL=92955],melanargia ines[&&NHX:TOL=92956],melanargia lachesis[&&NHX:TOL=92957],melanargia larissa[&&NHX:TOL=92958],melanargia leda[&&NHX:TOL=92959],melanargia lugens[&&NHX:TOL=92960],melanargia meridionalis[&&NHX:TOL=92961],melanargia occitanica[&&NHX:TOL=92962],melanargia parce[&&NHX:TOL=92963],melanargia pherusa[&&NHX:TOL=92964],melanargia russiae[&&NHX:TOL=92965],melanargia teneates[&&NHX:TOL=92966])melanargia[&&NHX:TOL=70803],(((((((pseudomaniola asuba[&&NHX:TOL=83465],pseudomaniola clethra[&&NHX:TOL=83466],pseudomaniola gerlinda[&&NHX:TOL=83467],pseudomaniola gigas[&&NHX:TOL=83468],pseudomaniola helche[&&NHX:TOL=83469],pseudomaniola ilsa[&&NHX:TOL=83470],pseudomaniola loxo[&&NHX:TOL=83471],pseudomaniola mena[&&NHX:TOL=83472],pseudomaniola mirabilis[&&NHX:TOL=83473],pseudomaniola phaselis[&&NHX:TOL=83474],pseudomaniola n. sp.[&&NHX:TOL=83475])pseudomaniola[&&NHX:TOL=82841],(apexacuta astoreth[&&NHX:TOL=83106],apexacuta orsedice[&&NHX:TOL=83107],apexacuta improvisa[&&NHX:TOL=83108],apexacuta superior[&&NHX:TOL=83109])apexacuta[&&NHX:TOL=82811])[&&NHX:TOL=82879],((lasiophila circe[&&NHX:TOL=83150],lasiophila cirta[&&NHX:TOL=83152],lasiophila hewitsonia[&&NHX:TOL=83153],lasiophila piscina[&&NHX:TOL=83158],lasiophila n. sp.[&&NHX:TOL=83162],lasiophila palades[&&NHX:TOL=83155])[&&NHX:TOL=125187],(lasiophila ciris[&&NHX:TOL=83151],lasiophila orbifera[&&NHX:TOL=83154],lasiophila zapatoza[&&NHX:TOL=83161])[&&NHX:TOL=125188],(lasiophila phalaesia[&&NHX:TOL=83157],((lasiophila regia[&&NHX:TOL=83160],lasiophila luna[&&NHX:TOL=125192])[&&NHX:TOL=125191],(lasiophila prosymna[&&NHX:TOL=83159],lasiophila parthyene[&&NHX:TOL=83156],lasiophila alkaios[&&NHX:TOL=83149])[&&NHX:TOL=125193])[&&NHX:TOL=125190])[&&NHX:TOL=125189])lasiophila[&&NHX:TOL=82825])[&&NHX:TOL=82878],(((proboscis pomarancia[&&NHX:TOL=94904],proboscis propylea[&&NHX:TOL=94905])proboscis[&&NHX:TOL=82838],(mygona irmina[&&NHX:TOL=83257],mygona prochyta[&&NHX:TOL=83258])mygona[&&NHX:TOL=82827])[&&NHX:TOL=82881],(oxeoschistus cothon[&&NHX:TOL=83454],oxeoschistus cothonides[&&NHX:TOL=83455],oxeoschistus hilara[&&NHX:TOL=83456],oxeoschistus leucospilos[&&NHX:TOL=83457],oxeoschistus pronax[&&NHX:TOL=83458],oxeoschistus puerta[&&NHX:TOL=83459],oxeoschistus tauropolis[&&NHX:TOL=83460],oxeoschistus iphigenia[&&NHX:TOL=83461])oxeoschistus[&&NHX:TOL=82829],cheimas opalinus[&&NHX:TOL=82814])[&&NHX:TOL=82880],((pronophila attali[&&NHX:TOL=83439],pronophila cordillera[&&NHX:TOL=83440],pronophila cuchillaensis[&&NHX:TOL=83441],pronophila epidipnis[&&NHX:TOL=83442],pronophila intercidona[&&NHX:TOL=83443],pronophila isobelae[&&NHX:TOL=83444],pronophila juliani[&&NHX:TOL=83445],pronophila margarita[&&NHX:TOL=83446],pronophila obscura[&&NHX:TOL=83447],pronophila orcus[&&NHX:TOL=83448],pronophila rosenbergi[&&NHX:TOL=83449],pronophila thelebe[&&NHX:TOL=83450],pronophila timanthes[&&NHX:TOL=83451],pronophila unifasciata[&&NHX:TOL=83452],pronophila tremocrata[&&NHX:TOL=83453],pronophila bernardi[&&NHX:TOL=94906])pronophila[&&NHX:TOL=82839],(arhuaco dryadina[&&NHX:TOL=83110],arhuaco ica[&&NHX:TOL=83111])arhuaco[&&NHX:TOL=82812])[&&NHX:TOL=125183],(corades anfortas[&&NHX:TOL=83112],corades argentata[&&NHX:TOL=83113],corades callipolis[&&NHX:TOL=83114],corades chelonis[&&NHX:TOL=83115],corades chirone[&&NHX:TOL=83116],corades cistene[&&NHX:TOL=83117],corades cybele[&&NHX:TOL=83118],corades dymantis[&&NHX:TOL=83119],corades enyo[&&NHX:TOL=83120],corades iduna[&&NHX:TOL=83121],corades lactefusa[&&NHX:TOL=83122],corades medeba[&&NHX:TOL=83123],corades melania[&&NHX:TOL=83124],corades pannonia[&&NHX:TOL=83125],corades pax[&&NHX:TOL=83126],corades sareba[&&NHX:TOL=83127],corades tricordatus[&&NHX:TOL=83128],corades tripunctata[&&NHX:TOL=83129],corades ulema[&&NHX:TOL=83130],corades n. sp. 1[&&NHX:TOL=83131],corades n. sp. 2[&&NHX:TOL=83132],corades n. sp. 3[&&NHX:TOL=83133],corades liliaceus[&&NHX:TOL=83134])corades[&&NHX:TOL=82815],(daedalma dinias[&&NHX:TOL=83138],daedalma drusilla[&&NHX:TOL=83139],daedalma inconspicua[&&NHX:TOL=83140],daedalma palacio[&&NHX:TOL=83141],daedalma parvomaculata[&&NHX:TOL=83142],daedalma fraudata[&&NHX:TOL=83143],daedalma vertex[&&NHX:TOL=83144])daedalma[&&NHX:TOL=82817],(junea doraete[&&NHX:TOL=83147],junea dorinda[&&NHX:TOL=83148])junea[&&NHX:TOL=82824],druphila venerata[&&NHX:TOL=82820])[&&NHX:TOL=82877],(foetterleia schreineri[&&NHX:TOL=82823],eteona tisiphone[&&NHX:TOL=82822])[&&NHX:TOL=82882],(praepronophila emma[&&NHX:TOL=83436],(praepronophila perperna[&&NHX:TOL=83437],praepronophila petronius[&&NHX:TOL=83438])[&&NHX:TOL=125198])praepronophila[&&NHX:TOL=82837],thiemeia phoronea[&&NHX:TOL=82847],(drucina championi[&&NHX:TOL=83145],drucina leonata[&&NHX:TOL=83146])drucina[&&NHX:TOL=82819],dangond dangondi[&&NHX:TOL=82818])pronophila clade[&&NHX:TOL=82876],((((praepedaliodes amussis[&&NHX:TOL=83430],praepedaliodes exul[&&NHX:TOL=83431],praepedaliodes granulata[&&NHX:TOL=83432],praepedaliodes phanias[&&NHX:TOL=83433],praepedaliodes n. sp. 1[&&NHX:TOL=83434],praepedaliodes n. sp. 2[&&NHX:TOL=83435])praepedaliodes[&&NHX:TOL=82836],(parapedaliodes parepa[&&NHX:TOL=82832],(punapedaliodes albopunctata[&&NHX:TOL=83476],punapedaliodes flavopunctata[&&NHX:TOL=83477])punapedaliodes[&&NHX:TOL=82842])[&&NHX:TOL=82886])[&&NHX:TOL=82885],(pedaliodes adamsi[&&NHX:TOL=83284],pedaliodes albicilia[&&NHX:TOL=94908],pedaliodes albutia[&&NHX:TOL=83285],pedaliodes alusana[&&NHX:TOL=83286],pedaliodes amafania[&&NHX:TOL=83287],pedaliodes anchiphilonis[&&NHX:TOL=83288],pedaliodes antigua[&&NHX:TOL=83289],pedaliodes antulla[&&NHX:TOL=83290],pedaliodes arnotti[&&NHX:TOL=83291],pedaliodes arturi[&&NHX:TOL=83292],pedaliodes asconia[&&NHX:TOL=83293],pedaliodes auraria[&&NHX:TOL=83294],pedaliodes aureola[&&NHX:TOL=94909],pedaliodes auristriga[&&NHX:TOL=83295],pedaliodes baccara[&&NHX:TOL=83296],pedaliodes balnearia[&&NHX:TOL=83297],pedaliodes bernardi[&&NHX:TOL=83298],pedaliodes boettgeri[&&NHX:TOL=94910],pedaliodes caeca[&&NHX:TOL=83299],pedaliodes canela[&&NHX:TOL=83300],pedaliodes cebolleta[&&NHX:TOL=83301],pedaliodes cesarense[&&NHX:TOL=83302],pedaliodes chaconi[&&NHX:TOL=83303],pedaliodes chrysotaenia[&&NHX:TOL=83304],pedaliodes circumducta[&&NHX:TOL=83305],pedaliodes cledonia[&&NHX:TOL=83306],pedaliodes coca[&&NHX:TOL=83307],pedaliodes costipunctata[&&NHX:TOL=83308],pedaliodes cremera[&&NHX:TOL=83309],pedaliodes croizatorum[&&NHX:TOL=83310],pedaliodes daulis[&&NHX:TOL=83311],pedaliodes dejecta[&&NHX:TOL=83312],pedaliodes demarmelsi[&&NHX:TOL=83313],pedaliodes demathani[&&NHX:TOL=94911],pedaliodes dracula[&&NHX:TOL=83314],pedaliodes empusa[&&NHX:TOL=83315],pedaliodes ereiba[&&NHX:TOL=83316],pedaliodes erschoffi[&&NHX:TOL=94912],pedaliodes exanima[&&NHX:TOL=83317],pedaliodes fassli[&&NHX:TOL=83318],pedaliodes ferratilis[&&NHX:TOL=83319],pedaliodes fuscata[&&NHX:TOL=83320],pedaliodes guicana[&&NHX:TOL=83321],pedaliodes gustavi[&&NHX:TOL=83322],pedaliodes hardyi[&&NHX:TOL=83323],pedaliodes hebena[&&NHX:TOL=83324],pedaliodes hewitsoni[&&NHX:TOL=83325],pedaliodes hopfferi[&&NHX:TOL=83326],pedaliodes japhleta[&&NHX:TOL=83327],pedaliodes jelskii[&&NHX:TOL=94913],pedaliodes leucocheilus[&&NHX:TOL=83328],pedaliodes luperca[&&NHX:TOL=83329],pedaliodes manis[&&NHX:TOL=83330],pedaliodes manneja[&&NHX:TOL=83331],pedaliodes maruda[&&NHX:TOL=94914],pedaliodes melaleuca[&&NHX:TOL=83332],pedaliodes minabilis[&&NHX:TOL=125185],pedaliodes montagna[&&NHX:TOL=83333],pedaliodes morenoi[&&NHX:TOL=83334],pedaliodes napaea[&&NHX:TOL=83335],pedaliodes negreti[&&NHX:TOL=83336],pedaliodes niveonota[&&NHX:TOL=83337],pedaliodes obscura[&&NHX:TOL=83338],pedaliodes obstructa[&&NHX:TOL=83339],pedaliodes occulta[&&NHX:TOL=83340],pedaliodes ochrotaenia[&&NHX:TOL=83341],pedaliodes ornata[&&NHX:TOL=83342],pedaliodes pacifica[&&NHX:TOL=83343],pedaliodes pactyes[&&NHX:TOL=83344],pedaliodes paeonides[&&NHX:TOL=83345],pedaliodes palaepolis[&&NHX:TOL=83346],pedaliodes pallantis[&&NHX:TOL=83347],pedaliodes palpita[&&NHX:TOL=83348],pedaliodes pammenes[&&NHX:TOL=83349],pedaliodes paneis[&&NHX:TOL=83350],pedaliodes panthides[&&NHX:TOL=83351],pedaliodes parma[&&NHX:TOL=83352],pedaliodes parranda[&&NHX:TOL=83353],pedaliodes patizathes[&&NHX:TOL=83354],pedaliodes pausia[&&NHX:TOL=83355],pedaliodes pedacia[&&NHX:TOL=83356],pedaliodes pelinaea[&&NHX:TOL=83357],pedaliodes pelinna[&&NHX:TOL=83358],pedaliodes perisades[&&NHX:TOL=83359],pedaliodes peruda[&&NHX:TOL=83360],pedaliodes peruviana[&&NHX:TOL=83361],pedaliodes petri[&&NHX:TOL=83362],pedaliodes peucestas[&&NHX:TOL=83363],pedaliodes phaea[&&NHX:TOL=83364],pedaliodes phaedra[&&NHX:TOL=83365],pedaliodes phaeina[&&NHX:TOL=83366],pedaliodes phanoclea[&&NHX:TOL=83367],pedaliodes phazania[&&NHX:TOL=83368],pedaliodes pheres[&&NHX:TOL=83369],pedaliodes pheretias[&&NHX:TOL=83370],pedaliodes philonis[&&NHX:TOL=83371],pedaliodes phoenissa[&&NHX:TOL=83372],pedaliodes phoenix[&&NHX:TOL=83373],pedaliodes phrasa[&&NHX:TOL=83374],pedaliodes phrasicla[&&NHX:TOL=83375],pedaliodes phrasiclea[&&NHX:TOL=83376],pedaliodes phrasis[&&NHX:TOL=83377],pedaliodes phthiotis[&&NHX:TOL=83378],pedaliodes piletha[&&NHX:TOL=83379],pedaliodes pimienta[&&NHX:TOL=83380],pedaliodes piscolabis[&&NHX:TOL=83381],pedaliodes pisonia[&&NHX:TOL=83382],pedaliodes plotina[&&NHX:TOL=83383],pedaliodes poema[&&NHX:TOL=83384],pedaliodes poesia[&&NHX:TOL=83385],pedaliodes polla[&&NHX:TOL=83386],pedaliodes pollonia[&&NHX:TOL=83387],pedaliodes polusca[&&NHX:TOL=83388],pedaliodes pomponia[&&NHX:TOL=83389],pedaliodes porcia[&&NHX:TOL=83390],pedaliodes porima[&&NHX:TOL=83391],pedaliodes porina[&&NHX:TOL=83392],pedaliodes praemontagna[&&NHX:TOL=108353],pedaliodes praxia[&&NHX:TOL=83393],pedaliodes praxithea[&&NHX:TOL=83394],pedaliodes proerna[&&NHX:TOL=83396],pedaliodes prosa[&&NHX:TOL=83397],pedaliodes prytanis[&&NHX:TOL=83398],pedaliodes puciula[&&NHX:TOL=94915],pedaliodes puma[&&NHX:TOL=83276],pedaliodes puracana[&&NHX:TOL=83399],pedaliodes pylas[&&NHX:TOL=83400],pedaliodes ralphi[&&NHX:TOL=83401],pedaliodes reyi[&&NHX:TOL=108354],pedaliodes roraimae[&&NHX:TOL=83402],pedaliodes rudnyi[&&NHX:TOL=83403],pedaliodes rumba[&&NHX:TOL=83404],pedaliodes scydmaena[&&NHX:TOL=83405],pedaliodes simmias[&&NHX:TOL=83406],pedaliodes simpla[&&NHX:TOL=83407],pedaliodes simplissima[&&NHX:TOL=94916],pedaliodes socorrae[&&NHX:TOL=83408],pedaliodes sonata[&&NHX:TOL=83409],pedaliodes sophismata[&&NHX:TOL=94917],pedaliodes spina[&&NHX:TOL=83410],pedaliodes stuebeli[&&NHX:TOL=94918],pedaliodes suspiro[&&NHX:TOL=83411],pedaliodes syleus[&&NHX:TOL=83412],pedaliodes sztolcmani[&&NHX:TOL=94919],pedaliodes tabaconas[&&NHX:TOL=83413],pedaliodes terramaris[&&NHX:TOL=83414],pedaliodes thiemei[&&NHX:TOL=83415],pedaliodes transmontana[&&NHX:TOL=83416],pedaliodes triaria[&&NHX:TOL=83417],pedaliodes tucca[&&NHX:TOL=83418],pedaliodes tyro[&&NHX:TOL=83419],pedaliodes tyrrheoides[&&NHX:TOL=83420],pedaliodes tyrrheus[&&NHX:TOL=83421],pedaliodes uniformis[&&NHX:TOL=83422],pedaliodes uniplaga[&&NHX:TOL=83423],pedaliodes uaniuna[&&NHX:TOL=94920],pedaliodes valencia[&&NHX:TOL=108355],pedaliodes vallenata[&&NHX:TOL=83424],pedaliodes wilhelmi[&&NHX:TOL=83425],pedaliodes woytkowskii[&&NHX:TOL=94921],pedaliodes xanthosphenisca[&&NHX:TOL=83426],pedaliodes yutajeana[&&NHX:TOL=83427],pedaliodes zuleta[&&NHX:TOL=83428],81 undescribed pedaliodes species[&&NHX:TOL=83429])pedaliodes[&&NHX:TOL=82833])[&&NHX:TOL=82884],(panyapedaliodes drymaea[&&NHX:TOL=83270],panyapedaliodes jephtha[&&NHX:TOL=83271],panyapedaliodes mara[&&NHX:TOL=83272],panyapedaliodes muscosa[&&NHX:TOL=83273],panyapedaliodes panyasis[&&NHX:TOL=83274],panyapedaliodes phila[&&NHX:TOL=83275],panyapedaliodes rahab[&&NHX:TOL=83277],panyapedaliodes silpa[&&NHX:TOL=83278],panyapedaliodes tomentosa[&&NHX:TOL=83279],panyapedaliodes tracyannae[&&NHX:TOL=83280],panyapedaliodes monticola[&&NHX:TOL=83282],panyapedaliodes stellata[&&NHX:TOL=94922],panyapedaliodes cocorna[&&NHX:TOL=94980],panyapedialodes sp. 1[&&NHX:TOL=83281])panyapedaliodes[&&NHX:TOL=82830],(corderopedaliodes corderoi[&&NHX:TOL=83135],corderopedaliodes pandates[&&NHX:TOL=83136],corderopedaliodes symmachus[&&NHX:TOL=83137])corderopedaliodes[&&NHX:TOL=82816],(altopedaliodes cocytia[&&NHX:TOL=83096],altopedaliodes halli[&&NHX:TOL=125186],altopedaliodes kruegeri[&&NHX:TOL=83097],altopedaliodes kurti[&&NHX:TOL=83098],altopedaliodes nebris[&&NHX:TOL=83099],altopedaliodes perita[&&NHX:TOL=83101],altopedaliodes reissi[&&NHX:TOL=83102],altopedaliodes tamaensis[&&NHX:TOL=83105],altopedaliodes tena[&&NHX:TOL=83103],altopedaliodes zsolti[&&NHX:TOL=83104])altopedaliodes[&&NHX:TOL=82809],antopedaliodes antonia[&&NHX:TOL=82810],(steromapedaliodes albarregas[&&NHX:TOL=83478],steromapedaliodes albonotata[&&NHX:TOL=83479],steromapedaliodes sanchezi[&&NHX:TOL=83480],steromapedaliodes schuberti[&&NHX:TOL=83481])steromapedaliodes[&&NHX:TOL=82846],(protopedaliodes kukenani[&&NHX:TOL=83462],protopedaliodes profauna[&&NHX:TOL=83463],protopedaliodes ridouti[&&NHX:TOL=83464])protopedaliodes[&&NHX:TOL=82840],(pherepedaliodes angela[&&NHX:TOL=125184],pherepedaliodes naevia[&&NHX:TOL=83242],pherepedaliodes nubilia[&&NHX:TOL=83243],phepedaliodes pheretiades[&&NHX:TOL=83244])pherepedaliodes[&&NHX:TOL=82834],physcopedaliodes physcoa[&&NHX:TOL=82835],paramo oculata[&&NHX:TOL=82831],(neopedaliodes chingazaensis[&&NHX:TOL=83259],neopedaliodes entella[&&NHX:TOL=83260],neopedaliodes juba[&&NHX:TOL=83261],neopedaliodes lafebreae[&&NHX:TOL=124546],neopedaliodes margaretha[&&NHX:TOL=83262],neopedaliodes michaeli[&&NHX:TOL=124547],neopedaliodes nora[&&NHX:TOL=83263],neopedaliodes parrhoebia[&&NHX:TOL=83264],neopedaliodes philotera[&&NHX:TOL=83265],neopedaliodes phoenicusa[&&NHX:TOL=83266],neopedaliodes proculeja[&&NHX:TOL=83395],neopedaliodes yeyo[&&NHX:TOL=124548],neopedaliodes zipa[&&NHX:TOL=83268])neopedaliodes[&&NHX:TOL=82828],(redonda bordoni[&&NHX:TOL=124446],redonda empetrus[&&NHX:TOL=124447],1 undescribed redonda species[&&NHX:TOL=124448])redonda[&&NHX:TOL=124445])pedaliodes s. l. clade[&&NHX:TOL=82883])[&&NHX:TOL=82875],(calisto chrysoaros[&&NHX:TOL=83060],calisto zangis[&&NHX:TOL=83094],calisto woodsi[&&NHX:TOL=83093],calisto wetherbeei[&&NHX:TOL=83092],calisto tragius[&&NHX:TOL=83091],calisto thomasi[&&NHX:TOL=83090],calisto tasajera[&&NHX:TOL=83089],calisto sommeri[&&NHX:TOL=83088],calisto sibylla[&&NHX:TOL=83087],calisto schwartzi[&&NHX:TOL=83086],calisto raburni[&&NHX:TOL=83085],calisto pulchella[&&NHX:TOL=83084],calisto phoinix[&&NHX:TOL=83083],calisto pauli[&&NHX:TOL=83082],calisto obscura[&&NHX:TOL=83081],calisto nubila[&&NHX:TOL=83080],calisto neochma[&&NHX:TOL=83079],calisto neiba[&&NHX:TOL=83078],calisto montana[&&NHX:TOL=83077],calisto micrommata[&&NHX:TOL=83076],calisto micheneri[&&NHX:TOL=83075],calisto lyceius[&&NHX:TOL=83074],calisto loxias[&&NHX:TOL=83073],calisto hysius[&&NHX:TOL=83072],calisto herophile[&&NHX:TOL=83071],calisto grannus[&&NHX:TOL=83070],calisto gonzalezi[&&NHX:TOL=83069],calisto galii[&&NHX:TOL=83068],calisto franciscoi[&&NHX:TOL=83067],calisto eleleus[&&NHX:TOL=83066],calisto dystacta[&&NHX:TOL=83065],calisto crypta[&&NHX:TOL=83064],calisto confusa[&&NHX:TOL=83063],calisto clydoniata[&&NHX:TOL=83062],calisto clenchi[&&NHX:TOL=83061],calisto batesi[&&NHX:TOL=83059],calisto archebates[&&NHX:TOL=83058],calisto arcas[&&NHX:TOL=83057],calisto anegadensis[&&NHX:TOL=83056],calisto amazona[&&NHX:TOL=83055],calisto ainigma[&&NHX:TOL=83053],calisto aleucosticha[&&NHX:TOL=83054])calisto[&&NHX:TOL=83095],((((((elina montroli[&&NHX:TOL=82906],elina vanessoides[&&NHX:TOL=82907])elina[&&NHX:TOL=82860],(quilaphoetosus janiroides[&&NHX:TOL=82950],quilaphoetosus monachus[&&NHX:TOL=82951])quilaphoetosus[&&NHX:TOL=82872])[&&NHX:TOL=82891],((auca barrosi[&&NHX:TOL=82922],auca coctei[&&NHX:TOL=82923],auca nycteropus[&&NHX:TOL=82924],auca pales[&&NHX:TOL=82925])auca[&&NHX:TOL=82857],(chillanella stelligera[&&NHX:TOL=82858],cosmosatyrus leptoneuroides[&&NHX:TOL=82859])[&&NHX:TOL=82893])[&&NHX:TOL=82892])[&&NHX:TOL=82890],((etcheverrius chiliensis[&&NHX:TOL=82908],etcheverrius tandilensis[&&NHX:TOL=82909])etcheverrius[&&NHX:TOL=82861],(pampasatyrus glaucope[&&NHX:TOL=82938],pampasatyrus gyrtone[&&NHX:TOL=82939],pampasatyrus imbrialis[&&NHX:TOL=82940],pampasatyrus nilesi[&&NHX:TOL=82941],pampasatyrus ocelloides[&&NHX:TOL=82942],pampasatyrus periphas[&&NHX:TOL=82943],pampasatyrus quies[&&NHX:TOL=82944],pampasatyrus reticulata[&&NHX:TOL=82945],pampasatyrus yacantoensis[&&NHX:TOL=82946],pampasatyrus n. sp.[&&NHX:TOL=82947])pampasatyrus[&&NHX:TOL=82869])[&&NHX:TOL=82894],(argyrophorus argenteus[&&NHX:TOL=82918],argyrophorus n. sp. 1[&&NHX:TOL=82919],argyrophorus n. sp. 2[&&NHX:TOL=82920],argyrophorus n. sp. 3[&&NHX:TOL=82921])argyrophorus[&&NHX:TOL=82856],(punargentus angusta[&&NHX:TOL=82948],punargentus lamna[&&NHX:TOL=82949])punargentus[&&NHX:TOL=82871])[&&NHX:TOL=82889],((((neosatyrus ambiorix[&&NHX:TOL=82867],(homeonympha boisduvalii[&&NHX:TOL=82912],homeonympha humilis[&&NHX:TOL=82913],homeonympha schajovskoii[&&NHX:TOL=82914],homeonympha vesagus[&&NHX:TOL=82915])homeonympha[&&NHX:TOL=82864])[&&NHX:TOL=82898],(nelia calvertii[&&NHX:TOL=82916],nelia nemyroides[&&NHX:TOL=82917])nelia[&&NHX:TOL=82865])[&&NHX:TOL=82897],(faunula leucoglene[&&NHX:TOL=82910],faunula patagonica[&&NHX:TOL=82911])faunula[&&NHX:TOL=82862])[&&NHX:TOL=82896],(eretris apuleja[&&NHX:TOL=82952],eretris calisto[&&NHX:TOL=82953],eretris centralis[&&NHX:TOL=82954],eretris depresissima[&&NHX:TOL=82955],eretris encycla[&&NHX:TOL=82956],eretris porphyria[&&NHX:TOL=82957],eretris subpunctata[&&NHX:TOL=82958],eretris subrufescens[&&NHX:TOL=82959],eretris suzannae[&&NHX:TOL=82960],eretris maria[&&NHX:TOL=82962],eretris oculata[&&NHX:TOL=82963],eretris hulda[&&NHX:TOL=82964],eretris lecromi[&&NHX:TOL=82965],eretris ocellifera[&&NHX:TOL=82966],eretris apuleina[&&NHX:TOL=94885],eretris mendoza[&&NHX:TOL=94886],eretris truncatina[&&NHX:TOL=94887],12 unnamed species[&&NHX:TOL=82961])eretris[&&NHX:TOL=82821])[&&NHX:TOL=82895],haywardella edmondsii[&&NHX:TOL=82863],(neomaenas coenonymphina[&&NHX:TOL=82926],neomaenas edmondsii[&&NHX:TOL=82927],neomaenas fractifascia[&&NHX:TOL=82928],neomaenas inornata[&&NHX:TOL=82929],neomaenas poliozona[&&NHX:TOL=82930],neomaenas servilia[&&NHX:TOL=82931],neomaenas simplex[&&NHX:TOL=82932],neomaenas wallengrenii[&&NHX:TOL=82933])neomaenas[&&NHX:TOL=82866],(palmaris antarcticus[&&NHX:TOL=82934],palmaris gustavi[&&NHX:TOL=82935],palmaris monticolens[&&NHX:TOL=82936],palmaris penai[&&NHX:TOL=82937])palmaris[&&NHX:TOL=82868],pamperis poaoeneis[&&NHX:TOL=82870],spinantenna tristis[&&NHX:TOL=82873],tetraphlebia germainii[&&NHX:TOL=82874])south temperate pronophilina clade[&&NHX:TOL=82888],(((((idioneurula erebioides[&&NHX:TOL=83216],idioneurula donegani[&&NHX:TOL=125180],(idioneurula eremita[&&NHX:TOL=83217],idioneurula jacquelinae[&&NHX:TOL=125182])[&&NHX:TOL=125181])idioneurula[&&NHX:TOL=82850],ianussiusa maso[&&NHX:TOL=82849])[&&NHX:TOL=82902],(lymanopoda acraeida[&&NHX:TOL=83163],lymanopoda affineola[&&NHX:TOL=83164],lymanopoda albocincta[&&NHX:TOL=83165],lymanopoda albomaculata[&&NHX:TOL=83166],lymanopoda altaselva[&&NHX:TOL=83167],lymanopoda altis[&&NHX:TOL=83168],lymanopoda apulia[&&NHX:TOL=83169],lymanopoda caeruleata[&&NHX:TOL=83170],lymanopoda caracara[&&NHX:TOL=83171],lymanopoda caucana[&&NHX:TOL=83172],lymanopoda caudalis[&&NHX:TOL=83173],lymanopoda cinna[&&NHX:TOL=83174],lymanopoda confusa[&&NHX:TOL=83175],lymanopoda dietzi[&&NHX:TOL=83176],lymanopoda eubagioides[&&NHX:TOL=83177],lymanopoda euopis[&&NHX:TOL=83178],lymanopoda ferruginosa[&&NHX:TOL=83179],lymanopoda galactea[&&NHX:TOL=83180],lymanopoda hazelana[&&NHX:TOL=83181],lymanopoda huilana[&&NHX:TOL=83182],lymanopoda hyagnis[&&NHX:TOL=83183],lymanopoda ichu[&&NHX:TOL=83184],lymanopoda ionius[&&NHX:TOL=83185],lymanopoda labda[&&NHX:TOL=83186],lymanopoda labineta[&&NHX:TOL=83187],lymanopoda lactea[&&NHX:TOL=83188],lymanopoda lebbaea[&&NHX:TOL=83189],lymanopoda malatera[&&NHX:TOL=83190],lymanopoda marianna[&&NHX:TOL=83191],lymanopoda melendeza[&&NHX:TOL=83192],lymanopoda melia[&&NHX:TOL=83193],lymanopoda nadia[&&NHX:TOL=83194],lymanopoda nevada[&&NHX:TOL=83195],lymanopoda nivea[&&NHX:TOL=83196],lymanopoda obsoleta[&&NHX:TOL=83197],lymanopoda orientalis[&&NHX:TOL=83198],lymanopoda panacea[&&NHX:TOL=83199],lymanopoda paramera[&&NHX:TOL=83200],lymanopoda pieridina[&&NHX:TOL=83201],lymanopoda prusia[&&NHX:TOL=83202],lymanopoda rana[&&NHX:TOL=83203],lymanopoda samius[&&NHX:TOL=83204],lymanopoda schmidti[&&NHX:TOL=83205],lymanopoda shefteli[&&NHX:TOL=83206],lymanopoda tolima[&&NHX:TOL=83207],lymanopoda translucida[&&NHX:TOL=83208],lymanopoda venosa[&&NHX:TOL=83209],lymanopoda viventieni[&&NHX:TOL=83210],lymanopoda araneola[&&NHX:TOL=94879],lymanopoda dyari[&&NHX:TOL=94880],lymanopoda inde[&&NHX:TOL=94881],lymanopoda ingasayana[&&NHX:TOL=94882],lymanopoda magna[&&NHX:TOL=94883],lymanopoda paisa[&&NHX:TOL=94884],lymanopoda lecromi[&&NHX:TOL=108351],2 undescribed lymanopoda species[&&NHX:TOL=83211])lymanopoda[&&NHX:TOL=82826])[&&NHX:TOL=82901],(manerebia apiculata[&&NHX:TOL=83218],manerebia cyclopella[&&NHX:TOL=83219],manerebia cyclopina[&&NHX:TOL=83220],manerebia cyclops[&&NHX:TOL=83221],manerebia franciscae[&&NHX:TOL=83222],manerebia ignilineata[&&NHX:TOL=83223],manerebia indirena[&&NHX:TOL=83224],manerebia insulsa[&&NHX:TOL=83225],manerebia interrupta[&&NHX:TOL=83226],manerebia leaena[&&NHX:TOL=83227],manerebia levana[&&NHX:TOL=83228],manerebia lisa[&&NHX:TOL=83229],manerebia mycalesoides[&&NHX:TOL=83230],manerebia navarrae[&&NHX:TOL=83231],manerebia nevadensis[&&NHX:TOL=83232],manerebia quinterae[&&NHX:TOL=83233],manerebia reducta[&&NHX:TOL=83234],manerebia rubescens[&&NHX:TOL=83235],manerebia satura[&&NHX:TOL=83236],manerebia staudingeri[&&NHX:TOL=83237],manerebia trimaculata[&&NHX:TOL=83238],manerebia typhlops[&&NHX:TOL=83239],manerebia zoippus[&&NHX:TOL=83240],manerebia benigni[&&NHX:TOL=94890],manerebia diffusa[&&NHX:TOL=94891],manerebia germaniae[&&NHX:TOL=94892],manerebia golondrina[&&NHX:TOL=94893],manerebia haywardi[&&NHX:TOL=94894],manerebia magnifica[&&NHX:TOL=94895],manerebia mammuthus[&&NHX:TOL=94896],manerebia pervaga[&&NHX:TOL=94897],manerebia pluviosa[&&NHX:TOL=94898],manerebia prattorum[&&NHX:TOL=94899],manerebia rufanalis[&&NHX:TOL=94900],manerebia seducta[&&NHX:TOL=94901],manerebia trirufa[&&NHX:TOL=94902],manerebia undulata[&&NHX:TOL=94903],8 undescribed manerebia species[&&NHX:TOL=83241])manerebia[&&NHX:TOL=82851])[&&NHX:TOL=82900],((steroma bega[&&NHX:TOL=83252],steroma modesta[&&NHX:TOL=83253],steroma superba[&&NHX:TOL=83254],steroma n. sp. 1[&&NHX:TOL=83255],steroma n. sp. 2[&&NHX:TOL=83256])steroma[&&NHX:TOL=82845],(steremnia agraulis[&&NHX:TOL=83245],steremnia monachella[&&NHX:TOL=83246],steremnia pronophila[&&NHX:TOL=83247],steremnia rugilas[&&NHX:TOL=83248],steremnia selva[&&NHX:TOL=83249],steremnia umbracina[&&NHX:TOL=83250],steremnia lucillae[&&NHX:TOL=94888],4 undescribed steremnia species[&&NHX:TOL=83251])steremnia[&&NHX:TOL=82844],sierrasteroma polyxo[&&NHX:TOL=82843])[&&NHX:TOL=82905],stuardosatyrus williamsianus[&&NHX:TOL=82854],sabatoga mirabilis[&&NHX:TOL=82853],(diaphanos curvignathos[&&NHX:TOL=83212],diaphanos fuscus[&&NHX:TOL=83213],diaphanos huberi[&&NHX:TOL=83214],diaphanos n. sp.[&&NHX:TOL=83215])diaphanos[&&NHX:TOL=82848],neomaniola euripides[&&NHX:TOL=82852])erebiine clade[&&NHX:TOL=82899])[&&NHX:TOL=82887],(amphidecta calliomma[&&NHX:TOL=93266],amphidecta pignerator[&&NHX:TOL=93267],amphidecta reynoldsi[&&NHX:TOL=93268])amphidecta[&&NHX:TOL=93264])pronophilina[&&NHX:TOL=70804],(aulocera[&&NHX:TOL=92969],(davidina armandi[&&NHX:TOL=93189],davidina alticola[&&NHX:TOL=93190])davidina[&&NHX:TOL=92973],(((((neominois carmen[&&NHX:TOL=132633],neominois ridingsii[&&NHX:TOL=132634])neominois[&&NHX:TOL=92978],(oeneis norna[&&NHX:TOL=93024],oeneis actaeoides[&&NHX:TOL=93025],oeneis aktashi[&&NHX:TOL=93026],oeneis alberta[&&NHX:TOL=93027],oeneis alpina[&&NHX:TOL=93028],oeneis ammon[&&NHX:TOL=93029],oeneis bore[&&NHX:TOL=93030],oeneis buddha[&&NHX:TOL=93032],oeneis chryxus[&&NHX:TOL=93033],oeneis diluta[&&NHX:TOL=93034],oeneis elwesi[&&NHX:TOL=93035],oeneis fulla[&&NHX:TOL=93036],oeneis glacialis[&&NHX:TOL=93037],oeneis hora[&&NHX:TOL=93038],oeneis jutta[&&NHX:TOL=93040],oeneis lederi[&&NHX:TOL=93041],oeneis macounii[&&NHX:TOL=93042],oeneis magna[&&NHX:TOL=93043],oeneis melissa[&&NHX:TOL=93044],oeneis mulla[&&NHX:TOL=93045],oeneis nanna[&&NHX:TOL=93046],oeneis nevadensis[&&NHX:TOL=93047],oeneis pansa[&&NHX:TOL=93049],oeneis polixenes[&&NHX:TOL=93050],oeneis sculda[&&NHX:TOL=93052],oeneis tarpeia[&&NHX:TOL=93053],oeneis taygete[&&NHX:TOL=93054],oeneis uhleri[&&NHX:TOL=93055],oeneis urda[&&NHX:TOL=93056])oeneis[&&NHX:TOL=92979],(paroeneis pumilus[&&NHX:TOL=93065],paroeneis palaearcticus[&&NHX:TOL=93066],paroeneis parapumilus[&&NHX:TOL=93067],paroeneis sikkimensis[&&NHX:TOL=93068])paroeneis[&&NHX:TOL=92980])[&&NHX:TOL=93009],(karanasa huebneri[&&NHX:TOL=93071],karanasa abramovi[&&NHX:TOL=93072],karanasa alpherakyi[&&NHX:TOL=93073],karanasa astorica[&&NHX:TOL=93074],karanasa bolorica[&&NHX:TOL=93075],karanasa cadesia[&&NHX:TOL=93076],karanasa decolorata[&&NHX:TOL=93077],karanasa eburnea[&&NHX:TOL=93078],karanasa goergneri[&&NHX:TOL=93079],karanasa haslundi[&&NHX:TOL=93080],karanasa hoffmanni[&&NHX:TOL=93081],karanasa incerta[&&NHX:TOL=93082],karanasa josephi[&&NHX:TOL=93083],karanasa kasakstana[&&NHX:TOL=93084],karanasa kirgizorum[&&NHX:TOL=93085],karanasa latifasciata[&&NHX:TOL=93086],karanasa leechi[&&NHX:TOL=93087],karanasa maureri[&&NHX:TOL=93088],karanasa mohsenii[&&NHX:TOL=93089],karanasa modesta[&&NHX:TOL=93090],karanasa moorei[&&NHX:TOL=93091],karanasa pamira[&&NHX:TOL=93092],karanasa praestans[&&NHX:TOL=93093],karanasa puengeleri[&&NHX:TOL=93094],karanasa pupilata[&&NHX:TOL=93095],karanasa regeli[&&NHX:TOL=93096],karanasa rohtanga[&&NHX:TOL=93097],karanasa safeda[&&NHX:TOL=93098],karanasa straminea[&&NHX:TOL=93099],karanasa talastauana[&&NHX:TOL=93100],karanasa tancrei[&&NHX:TOL=93101],karanasa voigti[&&NHX:TOL=93102],karanasa wilkinsi[&&NHX:TOL=93103])karanasa[&&NHX:TOL=92976])[&&NHX:TOL=93008],(brintesia circe[&&NHX:TOL=92971],arethusana arethusa[&&NHX:TOL=92968])[&&NHX:TOL=93010])[&&NHX:TOL=93007],(((chazara briseis[&&NHX:TOL=93014],chazara bischoffi[&&NHX:TOL=93015],chazara eitschbergeri[&&NHX:TOL=93016],chazara enervata[&&NHX:TOL=93017],chazara heydenreichi[&&NHX:TOL=93018],chazara kaufmanni[&&NHX:TOL=93019],chazara persephone[&&NHX:TOL=93020],chazara prieuri[&&NHX:TOL=93021],chazara rangontavica[&&NHX:TOL=93022],chazara staudingeri[&&NHX:TOL=93023])chazara[&&NHX:TOL=92972],(pseudochazara pelopea[&&NHX:TOL=93138],pseudochazara alpina[&&NHX:TOL=93139],pseudochazara anthelea[&&NHX:TOL=93140],pseudochazara atlantis[&&NHX:TOL=93141],pseudochazara baldiva[&&NHX:TOL=93142],pseudochazara beroe[&&NHX:TOL=93143],pseudochazara cingovskii[&&NHX:TOL=93144],pseudochazara daghestana[&&NHX:TOL=93145],pseudochazara droshica[&&NHX:TOL=93146],pseudochazara euxina[&&NHX:TOL=93147],pseudochazara geyeri[&&NHX:TOL=93148],pseudochazara graeca[&&NHX:TOL=93149],pseudochazara guriensis[&&NHX:TOL=93150],pseudochazara hippolyte[&&NHX:TOL=93151],pseudochazara kanishka[&&NHX:TOL=93152],pseudochazara lehana[&&NHX:TOL=93153],pseudochazara lydia[&&NHX:TOL=93154],pseudochazara mamurra[&&NHX:TOL=93155],pseudochazara mniszechii[&&NHX:TOL=93156],pseudochazara nukatli[&&NHX:TOL=93157],pseudochazara pakistana[&&NHX:TOL=93158],pseudochazara pallida[&&NHX:TOL=93159],pseudochazara panjshira[&&NHX:TOL=93160],pseudochazara schahrudensis[&&NHX:TOL=93161],pseudochazara schakuhensis[&&NHX:TOL=93162],pseudochazara thelephassa[&&NHX:TOL=93163],pseudochazara turkestana[&&NHX:TOL=93164],pseudochazara watsoni[&&NHX:TOL=93165])pseudochazara[&&NHX:TOL=92981])[&&NHX:TOL=93012],satyrus[&&NHX:TOL=92967],(minois aurata[&&NHX:TOL=93069],minois paupera[&&NHX:TOL=93070],minois dryas[&&NHX:TOL=92985])minois[&&NHX:TOL=92977])[&&NHX:TOL=93011])[&&NHX:TOL=93006],((berberia abdelkader[&&NHX:TOL=93004],berberia lambessanus[&&NHX:TOL=93005])berberia[&&NHX:TOL=92970],(hipparchia fagi[&&NHX:TOL=93166],hipparchia alcyone[&&NHX:TOL=93167],hipparchia aristaeus[&&NHX:TOL=93168],hipparchia autonoe[&&NHX:TOL=93169],hipparchia azorina[&&NHX:TOL=93170],hipparchia cretica[&&NHX:TOL=93171],hipparchia cypriensis[&&NHX:TOL=93172],hipparchia ellena[&&NHX:TOL=93173],hipparchia fatua[&&NHX:TOL=93174],hipparchia fidia[&&NHX:TOL=93175],hipparchia hansii[&&NHX:TOL=93176],hipparchia mersina[&&NHX:TOL=93177],hipparchia neomiris[&&NHX:TOL=93178],hipparchia parisatis[&&NHX:TOL=93179],hipparchia pellucida[&&NHX:TOL=93180],hipparchia pisidice[&&NHX:TOL=93181],hipparchia semele[&&NHX:TOL=93182],hipparchia statilinus[&&NHX:TOL=93183],hipparchia stulta[&&NHX:TOL=93184],hipparchia syriaca[&&NHX:TOL=93185],hipparchia wyssii[&&NHX:TOL=93186],hipparchia tewfiki[&&NHX:TOL=93187])hipparchia[&&NHX:TOL=92974],kanetisa digna[&&NHX:TOL=92975])[&&NHX:TOL=93013])satyrina[&&NHX:TOL=70805],((argestina waltoni[&&NHX:TOL=90383],argestina inconstans[&&NHX:TOL=90384],argestina karta[&&NHX:TOL=90385],argestina pomena[&&NHX:TOL=90386])argestina[&&NHX:TOL=90361],austroypthima petersi[&&NHX:TOL=90362],boeberia parmenio[&&NHX:TOL=90363],(callerebia scanda[&&NHX:TOL=90387],callerebia annada[&&NHX:TOL=90388],callerebia baileyi[&&NHX:TOL=90389],callerebia caeca[&&NHX:TOL=90390],callerebia hybrida[&&NHX:TOL=90391],callerebia kalinda[&&NHX:TOL=90392],callerebia nirmala[&&NHX:TOL=90393],callerebia orixa[&&NHX:TOL=90394],callerebia polyphemus[&&NHX:TOL=90395],callerebia shallada[&&NHX:TOL=90396],callerebia suroia[&&NHX:TOL=90397],callerebia ulfi[&&NHX:TOL=90398],callerebia tsirava[&&NHX:TOL=90399],callerebia watsoni[&&NHX:TOL=90400])callerebia[&&NHX:TOL=90364],cassionympha cassius[&&NHX:TOL=90365],(coenyra hebe[&&NHX:TOL=90409],coenyra aurantiaca[&&NHX:TOL=90410],coenyra rufiplaga[&&NHX:TOL=90411])coenyra[&&NHX:TOL=90366],(coenyropsis natalii[&&NHX:TOL=90412],coenyropsis bera[&&NHX:TOL=90413],coenyropsis carcassoni[&&NHX:TOL=90414])coenyropsis[&&NHX:TOL=90367],(loxerebia pratorum[&&NHX:TOL=91391],loxerebia albipuncta[&&NHX:TOL=91392],loxerebia bocki[&&NHX:TOL=91393],loxerebia carola[&&NHX:TOL=91394],loxerebia delavayi[&&NHX:TOL=91395],loxerebia innupta[&&NHX:TOL=91396],loxerebia loczyi[&&NHX:TOL=91397],loxerebia martyr[&&NHX:TOL=91398],loxerebia megalops[&&NHX:TOL=91399],loxerebia narasingha[&&NHX:TOL=91400],loxerebia phyllis[&&NHX:TOL=91401],loxerebia pieli[&&NHX:TOL=91402],loxerebia ruricola[&&NHX:TOL=91403],loxerebia rurigena[&&NHX:TOL=91404],loxerebia saxicola[&&NHX:TOL=91405],loxerebia seitzi[&&NHX:TOL=91406],loxerebia sylvicola[&&NHX:TOL=91407],loxerebia ypthimoides[&&NHX:TOL=91408])loxerebia[&&NHX:TOL=90368],(mashuna mashuna[&&NHX:TOL=90407],mashuna upemba[&&NHX:TOL=90408])mashuna[&&NHX:TOL=90369],melampias huebneri[&&NHX:TOL=90370],(neita neita[&&NHX:TOL=90401],neita durbani[&&NHX:TOL=90402],neita extensa[&&NHX:TOL=90403],neita lotenia[&&NHX:TOL=90404],neita orbipalus[&&NHX:TOL=90405],neita victoriae[&&NHX:TOL=90406])neita[&&NHX:TOL=90371],(neocoenyra duplex[&&NHX:TOL=90420],neocoenyra bioculata[&&NHX:TOL=90421],neocoenyra cooksoni[&&NHX:TOL=90422],neocoenyra fuligo[&&NHX:TOL=90423],neocoenyra fulleborni[&&NHX:TOL=90424],neocoenyra gregorii[&&NHX:TOL=90425],neocoenyra heckmanni[&&NHX:TOL=90426],neocoenyra jordani[&&NHX:TOL=90427],neocoenyra kivuensis[&&NHX:TOL=90428],neocoenyra masaica[&&NHX:TOL=90429],neocoenyra parallelopupillata[&&NHX:TOL=90430],neocoenyra petersi[&&NHX:TOL=90431],neocoenyra pinheyi[&&NHX:TOL=90432],neocoenyra rufilineata[&&NHX:TOL=90433],neocoenyra ypthimoides[&&NHX:TOL=90434])neocoenyra[&&NHX:TOL=90372],(paralasa kalinda[&&NHX:TOL=91409],paralasa afghana[&&NHX:TOL=91410],paralasa ali[&&NHX:TOL=91411],paralasa asura[&&NHX:TOL=91412],paralasa batanga[&&NHX:TOL=91413],paralasa chitralica[&&NHX:TOL=91414],paralasa danorum[&&NHX:TOL=91415],paralasa hades[&&NHX:TOL=91416],paralasa herse[&&NHX:TOL=91417],paralasa horaki[&&NHX:TOL=91418],paralasa howarthi[&&NHX:TOL=91419],paralasa icelos[&&NHX:TOL=91420],paralasa ida[&&NHX:TOL=91421],paralasa jordana[&&NHX:TOL=91422],paralasa kotzscheae[&&NHX:TOL=91423],paralasa kuszenovi[&&NHX:TOL=91424],paralasa langara[&&NHX:TOL=91425],paralasa mani[&&NHX:TOL=91426],paralasa maracandica[&&NHX:TOL=91427],paralasa mohabbati[&&NHX:TOL=91428],paralasa nero[&&NHX:TOL=91429],paralasa paghmanni[&&NHX:TOL=91430],paralasa panjshira[&&NHX:TOL=91431],paralasa semenovi[&&NHX:TOL=91432],paralasa shakti[&&NHX:TOL=91433],paralasa styx[&&NHX:TOL=91434])paralasa[&&NHX:TOL=90373],(physcaneura panda[&&NHX:TOL=90415],physcaneura jacksoni[&&NHX:TOL=90416],physcaneura leda[&&NHX:TOL=90417],physcaneura pione[&&NHX:TOL=90418],physcaneura robertsi[&&NHX:TOL=90419])physcaneura[&&NHX:TOL=90374],(pseudonympha hippia[&&NHX:TOL=91199],pseudonympha arnoldi[&&NHX:TOL=91200],pseudonympha camdeboo[&&NHX:TOL=91201],pseudonympha cyclops[&&NHX:TOL=91202],pseudonympha detecta[&&NHX:TOL=91203],pseudonympha gaika[&&NHX:TOL=91204],pseudonympha machacha[&&NHX:TOL=91205],pseudonympha magoides[&&NHX:TOL=91206],pseudonympha magus[&&NHX:TOL=91207],pseudonympha narcyia[&&NHX:TOL=91208],pseudonympha paludis[&&NHX:TOL=91209],pseudonympha paragaika[&&NHX:TOL=91210],pseudonympha penningtoni[&&NHX:TOL=91211],pseudonympha poetula[&&NHX:TOL=91212],pseudonympha southeyi[&&NHX:TOL=91213],pseudonympha swanepoeli[&&NHX:TOL=91214],pseudonympha trimenii[&&NHX:TOL=91215],pseudonympha varii[&&NHX:TOL=91216])pseudonympha[&&NHX:TOL=90375],(strabena smithii[&&NHX:TOL=91225],strabena affinis[&&NHX:TOL=91226],strabena albivittula[&&NHX:TOL=91228],strabena andilabe[&&NHX:TOL=91229],strabena argyrina[&&NHX:TOL=91231],strabena mabillei[&&NHX:TOL=91232],strabena batesii[&&NHX:TOL=91233],strabena consobrina[&&NHX:TOL=91234],strabena consors[&&NHX:TOL=91235],strabena daphne[&&NHX:TOL=91237],strabena dyscola[&&NHX:TOL=91238],strabena eros[&&NHX:TOL=91239],strabena germanus[&&NHX:TOL=91241],strabena ibitina[&&NHX:TOL=91243],strabena impar[&&NHX:TOL=91244],strabena mandraka[&&NHX:TOL=91247],strabena modesta[&&NHX:TOL=91249],strabena modestissima[&&NHX:TOL=91250],strabena mopsus[&&NHX:TOL=91251],strabena niveata[&&NHX:TOL=91252],strabena perrieri[&&NHX:TOL=91254],(strabena andriana[&&NHX:TOL=91230],strabena vicina[&&NHX:TOL=91263])[&&NHX:TOL=93814],strabena perroti[&&NHX:TOL=91255],strabena excellens[&&NHX:TOL=93815],(strabena goudoti[&&NHX:TOL=91242],strabena isoalensis[&&NHX:TOL=91246],strabena martini[&&NHX:TOL=91248])[&&NHX:TOL=93816],strabena rakoto[&&NHX:TOL=91257],strabena nepos[&&NHX:TOL=93817],strabena soror[&&NHX:TOL=91258],strabena sufferti[&&NHX:TOL=91259],strabena tamatave[&&NHX:TOL=91260],strabena triophthalma[&&NHX:TOL=91261],strabena tsaratananae[&&NHX:TOL=91262],strabena vinsoni[&&NHX:TOL=91264],strabena zanjuka[&&NHX:TOL=91265],strabena cachani[&&NHX:TOL=91266])strabena[&&NHX:TOL=90376],(stygionympha vigilans[&&NHX:TOL=91217],stygionympha dicksoni[&&NHX:TOL=91218],stygionympha geraldi[&&NHX:TOL=91219],stygionympha irrorata[&&NHX:TOL=91220],stygionympha robertsoni[&&NHX:TOL=91221],stygionympha scotina[&&NHX:TOL=91222],stygionympha vansoni[&&NHX:TOL=91223],stygionympha wichgrafi[&&NHX:TOL=91224])stygionympha[&&NHX:TOL=90377],(ypthima albida[&&NHX:TOL=91269],ypthima antennata[&&NHX:TOL=91270],ypthima asterope[&&NHX:TOL=91271],ypthima bolanica[&&NHX:TOL=91272],ypthima condamini[&&NHX:TOL=91273],ypthima congoana[&&NHX:TOL=91274],ypthima diplommata[&&NHX:TOL=91275],ypthima doleta[&&NHX:TOL=91276],ypthima granulosa[&&NHX:TOL=91277],ypthima impura[&&NHX:TOL=91278],ypthima jacksoni[&&NHX:TOL=91279],ypthima lamto[&&NHX:TOL=91280],ypthima praestans[&&NHX:TOL=91281],ypthima pulchra[&&NHX:TOL=91282],ypthima pupillaris[&&NHX:TOL=91283],ypthima recta[&&NHX:TOL=91284],ypthima rhodesiana[&&NHX:TOL=91285],ypthima simplicia[&&NHX:TOL=91286],ypthima vuattauxi[&&NHX:TOL=91287],ypthima yatta[&&NHX:TOL=91288],ypthima affectata[&&NHX:TOL=91289],ypthima akbar[&&NHX:TOL=91290],ypthima albipuncta[&&NHX:TOL=91291],ypthima ancus[&&NHX:TOL=93820],ypthima aphnius[&&NHX:TOL=91292],ypthima arctoa[&&NHX:TOL=91293],ypthima atra[&&NHX:TOL=91380],ypthima avanta[&&NHX:TOL=91294],ypthima baileyi[&&NHX:TOL=91295],ypthima baldus[&&NHX:TOL=91296],ypthima beautei[&&NHX:TOL=91297],ypthima cantlei[&&NHX:TOL=91298],ypthima cerealis[&&NHX:TOL=91299],ypthima ceylonica[&&NHX:TOL=91300],ypthima chenui[&&NHX:TOL=91301],ypthima chinensis[&&NHX:TOL=91302],ypthima ciris[&&NHX:TOL=91303],ypthima confusa[&&NHX:TOL=91304],ypthima conjuncta[&&NHX:TOL=91305],ypthima daclaca[&&NHX:TOL=91389],ypthima dengae[&&NHX:TOL=91306],ypthima dohertyi[&&NHX:TOL=91307],ypthima esakii[&&NHX:TOL=91308],ypthima evansi[&&NHX:TOL=91309],ypthima fasciata[&&NHX:TOL=91310],ypthima frontierii[&&NHX:TOL=91311],ypthima fulvida[&&NHX:TOL=91312],ypthima gavalisi[&&NHX:TOL=91313],ypthima hanburyi[&&NHX:TOL=91314],ypthima hannyngtoni[&&NHX:TOL=91315],ypthima horsfieldii[&&NHX:TOL=91316],ypthima huebneri[&&NHX:TOL=91268],ypthima hyagriva[&&NHX:TOL=91317],ypthima iarba[&&NHX:TOL=91318],ypthima imitans[&&NHX:TOL=91387],ypthima indecora[&&NHX:TOL=91319],ypthima inica[&&NHX:TOL=91320],ypthima insolita[&&NHX:TOL=91321],ypthima iris[&&NHX:TOL=91322],ypthima junkoae[&&NHX:TOL=93821],ypthima kalelonda[&&NHX:TOL=91323],ypthima lihongxingi[&&NHX:TOL=91324],ypthima lisandra[&&NHX:TOL=91325],ypthima loryma[&&NHX:TOL=91326],ypthima lycus[&&NHX:TOL=91327],ypthima masakii[&&NHX:TOL=91328],ypthima megalomma[&&NHX:TOL=91329],ypthima methora[&&NHX:TOL=91330],ypthima methorina[&&NHX:TOL=91331],ypthima microphthalma[&&NHX:TOL=91332],ypthima motscholskyi[&&NHX:TOL=91333],ypthima multistriata[&&NHX:TOL=91334],ypthima muotuoensis[&&NHX:TOL=91335],ypthima nareda[&&NHX:TOL=91336],ypthima nebulosa[&&NHX:TOL=91337],ypthima newara[&&NHX:TOL=91338],ypthima nigricans[&&NHX:TOL=91339],ypthima nikaea[&&NHX:TOL=91340],ypthima norma[&&NHX:TOL=91383],ypthima nynias[&&NHX:TOL=93818],ypthima pandocus[&&NHX:TOL=91341],ypthima parasakra[&&NHX:TOL=91342],ypthima pemakoi[&&NHX:TOL=91343],ypthima perfecta[&&NHX:TOL=91344],ypthima persimilis[&&NHX:TOL=91345],ypthima philomela[&&NHX:TOL=91346],ypthima praenubila[&&NHX:TOL=91347],ypthima pseudodromon[&&NHX:TOL=91348],ypthima putamdui[&&NHX:TOL=91349],ypthima risompae[&&NHX:TOL=93822],ypthima riukiuana[&&NHX:TOL=91350],ypthima sakra[&&NHX:TOL=91351],ypthima sarcaposa[&&NHX:TOL=91385],ypthima savara[&&NHX:TOL=91352],ypthima sensilis[&&NHX:TOL=91353],ypthima sesara[&&NHX:TOL=91354],ypthima similis[&&NHX:TOL=91355],ypthima singala[&&NHX:TOL=91356],ypthima singorensis[&&NHX:TOL=91381],ypthima sinica[&&NHX:TOL=91357],ypthima sobrina[&&NHX:TOL=91358],ypthima sordida[&&NHX:TOL=91359],ypthima stellera[&&NHX:TOL=91360],ypthima striata[&&NHX:TOL=91361],ypthima tappana[&&NHX:TOL=91362],ypthima tiani[&&NHX:TOL=91363],ypthima watsoni[&&NHX:TOL=91364],ypthima yangjiahei[&&NHX:TOL=91365],ypthima yoshinobui[&&NHX:TOL=91366],ypthima yunosukei[&&NHX:TOL=91367],ypthima ypthimoides[&&NHX:TOL=91368],ypthima zyzzomacula[&&NHX:TOL=91369])ypthima[&&NHX:TOL=90378],ypthimomorpha itonia[&&NHX:TOL=90379])ypthimina[&&NHX:TOL=70806],((((erebia callias[&&NHX:TOL=92833],erebia hispania[&&NHX:TOL=92857],erebia rondoui[&&NHX:TOL=131131],(erebia nivalis[&&NHX:TOL=92882],erebia calcaria[&&NHX:TOL=92832],erebia cassioides[&&NHX:TOL=92834],erebia tyndarus[&&NHX:TOL=92911])[&&NHX:TOL=131132])[&&NHX:TOL=131130],(erebia iranica[&&NHX:TOL=92858],(erebia graucasica[&&NHX:TOL=92854],erebia ottomana[&&NHX:TOL=92887])[&&NHX:TOL=131134])[&&NHX:TOL=131133])erebia tyndarus group[&&NHX:TOL=131129],erebia ligea[&&NHX:TOL=92824],erebia aethiopella[&&NHX:TOL=92825],erebia aethiops[&&NHX:TOL=92826],erebia ajanensis[&&NHX:TOL=93057],erebia alberganus[&&NHX:TOL=92827],erebia alcmena[&&NHX:TOL=92828],erebia anyuica[&&NHX:TOL=92829],erebia arctica[&&NHX:TOL=92830],erebia atramentaria[&&NHX:TOL=92831],erebia christi[&&NHX:TOL=92835],erebia claudina[&&NHX:TOL=92836],erebia cyclopius[&&NHX:TOL=92837],erebia dabanensis[&&NHX:TOL=92838],erebia disa[&&NHX:TOL=92839],erebia discoidalis[&&NHX:TOL=92840],erebia dromulus[&&NHX:TOL=92841],erebia edda[&&NHX:TOL=92842],erebia embla[&&NHX:TOL=92843],erebia epiphron[&&NHX:TOL=92844],erebia epipsodea[&&NHX:TOL=92845],erebia epistygne[&&NHX:TOL=92846],erebia erinnyn[&&NHX:TOL=93059],erebia eugenia[&&NHX:TOL=92847],erebia euryale[&&NHX:TOL=92848],erebia fasciata[&&NHX:TOL=92849],erebia flavofasciata[&&NHX:TOL=92850],erebia fletcheri[&&NHX:TOL=92851],erebia gorge[&&NHX:TOL=92852],erebia gorgone[&&NHX:TOL=92853],erebia haberhaueri[&&NHX:TOL=92855],erebia hewitsoni[&&NHX:TOL=92856],erebia jeniseiensis[&&NHX:TOL=92859],erebia kalmuka[&&NHX:TOL=92860],erebia kefersteini[&&NHX:TOL=92861],erebia kindermanni[&&NHX:TOL=92862],erebia kozhantshikovi[&&NHX:TOL=92863],erebia lafontainei[&&NHX:TOL=92864],erebia lefebvrei[&&NHX:TOL=92865],erebia mackinleyensis[&&NHX:TOL=92866],erebia magdalena[&&NHX:TOL=92867],erebia mancinus[&&NHX:TOL=92868],erebia manto[&&NHX:TOL=92869],erebia maurisius[&&NHX:TOL=92870],erebia medusa[&&NHX:TOL=92871],erebia melampus[&&NHX:TOL=92872],erebia melancholica[&&NHX:TOL=92873],erebia melas[&&NHX:TOL=92874],erebia meolans[&&NHX:TOL=92875],erebia meta[&&NHX:TOL=92876],erebia mnestra[&&NHX:TOL=92877],erebia montana[&&NHX:TOL=92878],erebia neoridas[&&NHX:TOL=92879],erebia neriene[&&NHX:TOL=92880],erebia niphonica[&&NHX:TOL=92881],erebia occulta[&&NHX:TOL=92883],erebia ocnus[&&NHX:TOL=92884],erebia oeme[&&NHX:TOL=92885],erebia orientalis[&&NHX:TOL=92886],erebia palarica[&&NHX:TOL=92888],erebia pandrose[&&NHX:TOL=92889],erebia pawlowskii[&&NHX:TOL=92890],erebia pharte[&&NHX:TOL=92891],erebia pluto[&&NHX:TOL=92892],erebia polaris[&&NHX:TOL=92893],erebia progne[&&NHX:TOL=92894],erebia pronoe[&&NHX:TOL=92895],erebia radians[&&NHX:TOL=92896],erebia rhodopensis[&&NHX:TOL=92897],erebia rossii[&&NHX:TOL=92898],erebia sachaensis[&&NHX:TOL=93061],erebia scipio[&&NHX:TOL=92899],erebia serotina[&&NHX:TOL=92900],erebia sibo[&&NHX:TOL=92901],erebia sokolovi[&&NHX:TOL=93062],erebia sthennyo[&&NHX:TOL=92902],erebia stirius[&&NHX:TOL=92903],erebia stubbendorfii[&&NHX:TOL=93063],erebia styx[&&NHX:TOL=92904],erebia sudetica[&&NHX:TOL=92905],erebia theano[&&NHX:TOL=92906],erebia tianschanica[&&NHX:TOL=92907],erebia triarius[&&NHX:TOL=92908],erebia troubridgei[&&NHX:TOL=92909],erebia turanica[&&NHX:TOL=92910],erebia usgentensis[&&NHX:TOL=92912],erebia vidleri[&&NHX:TOL=92913],erebia wanga[&&NHX:TOL=92914],erebia youngi[&&NHX:TOL=92915],erebia zapateri[&&NHX:TOL=92916],erebia eriphyle[&&NHX:TOL=92917])erebia[&&NHX:TOL=91435],proterebia afra[&&NHX:TOL=91436])erebiina[&&NHX:TOL=70807],((hyponephele lycaon[&&NHX:TOL=93200],hyponephele amardaea[&&NHX:TOL=93201],hyponephele argyrostigma[&&NHX:TOL=93202],hyponephele astorica[&&NHX:TOL=93203],hyponephele bala[&&NHX:TOL=93204],hyponephele baroghila[&&NHX:TOL=93205],hyponephele brevistigma[&&NHX:TOL=93206],hyponephele cadusia[&&NHX:TOL=93207],hyponephele cadusina[&&NHX:TOL=93208],hyponephele capella[&&NHX:TOL=93209],hyponephele carbonelli[&&NHX:TOL=93210],hyponephele comara[&&NHX:TOL=93211],hyponephele davendra[&&NHX:TOL=93212],hyponephele difficilis[&&NHX:TOL=93213],hyponephele dysdora[&&NHX:TOL=93214],hyponephele dzhungarica[&&NHX:TOL=93215],hyponephele fortambeka[&&NHX:TOL=93216],hyponephele fusca[&&NHX:TOL=93217],hyponephele galtscha[&&NHX:TOL=93218],hyponephele germana[&&NHX:TOL=93219],hyponephele glasunovi[&&NHX:TOL=93220],hyponephele haberhaueri[&&NHX:TOL=93221],hyponephele hilaris[&&NHX:TOL=93222],hyponephele huebneri[&&NHX:TOL=93223],hyponephele interposita[&&NHX:TOL=93224],hyponephele issykkuli[&&NHX:TOL=93225],hyponephele jasavi[&&NHX:TOL=93226],hyponephele kaschmirensis[&&NHX:TOL=93227],hyponephele kirghisa[&&NHX:TOL=93228],hyponephele kocaki[&&NHX:TOL=93229],hyponephele korshunovi[&&NHX:TOL=93230],hyponephele laeta[&&NHX:TOL=93231],hyponephele lupina[&&NHX:TOL=93232],hyponephele lycaonoides[&&NHX:TOL=93233],hyponephele mandane[&&NHX:TOL=93234],hyponephele maroccana[&&NHX:TOL=93235],hyponephele maureri[&&NHX:TOL=93236],hyponephele murzini[&&NHX:TOL=93237],hyponephele mussitans[&&NHX:TOL=93238],hyponephele narica[&&NHX:TOL=93239],hyponephele naricina[&&NHX:TOL=93240],hyponephele naricoides[&&NHX:TOL=93241],hyponephele naubidensis[&&NHX:TOL=93242],hyponephele neoza[&&NHX:TOL=93243],hyponephele pamira[&&NHX:TOL=93244],hyponephele pasimelas[&&NHX:TOL=93245],hyponephele perplexa[&&NHX:TOL=93246],hyponephele prasolovi[&&NHX:TOL=93247],hyponephele przhewalskyi[&&NHX:TOL=93248],hyponephele pseudokirgisa[&&NHX:TOL=93249],hyponephele pseudomussitans[&&NHX:TOL=93250],hyponephele pulchella[&&NHX:TOL=93251],hyponephele pulchra[&&NHX:TOL=93252],hyponephele rubriceps[&&NHX:TOL=93253],hyponephele rueckbeili[&&NHX:TOL=93254],hyponephele sheljuzhkoi[&&NHX:TOL=93255],hyponephele sylvia[&&NHX:TOL=93256],hyponephele susurrans[&&NHX:TOL=93257],hyponephele tenuistigma[&&NHX:TOL=93258],hyponephele tristis[&&NHX:TOL=93259])hyponephele[&&NHX:TOL=93194],(cercyonis meadii[&&NHX:TOL=93196],cercyonis oetus[&&NHX:TOL=93197],cercyonis pegala[&&NHX:TOL=93198],cercyonis sthenele[&&NHX:TOL=93199])cercyonis[&&NHX:TOL=93193])[&&NHX:TOL=93191])[&&NHX:TOL=70801])satyrini[&&NHX:TOL=70264])[&&NHX:TOL=87597])[&&NHX:TOL=70261])satyrinae[&&NHX:TOL=12189])[&&NHX:TOL=69951],(calinaga lhatso[&&NHX:TOL=70275],calinaga buddha[&&NHX:TOL=70276],calinaga cercyon[&&NHX:TOL=70277],calinaga davidis[&&NHX:TOL=70278],calinaga gautama[&&NHX:TOL=70279],calinaga aborica[&&NHX:TOL=70280],calinaga sudassana[&&NHX:TOL=70281])calinaga[&&NHX:TOL=12188])[&&NHX:TOL=69950])[&&NHX:TOL=69943],(((((melinaea ethra[&&NHX:TOL=72260],melinaea idae[&&NHX:TOL=72261],melinaea isocomma[&&NHX:TOL=72262],melinaea lilis[&&NHX:TOL=72263],melinaea ludovica[&&NHX:TOL=72264],melinaea marsaeus[&&NHX:TOL=72265],melinaea menophilus[&&NHX:TOL=72266],melinaea mnasias[&&NHX:TOL=72267],melinaea mneme[&&NHX:TOL=72268],melinaea mnemopsis[&&NHX:TOL=72269],melinaea satevis[&&NHX:TOL=72270])melinaea[&&NHX:TOL=27591],athyrtis mechanitis[&&NHX:TOL=27587])[&&NHX:TOL=69970],(paititia neglecta[&&NHX:TOL=27588],(olyras crathis[&&NHX:TOL=72283],olyras insignis[&&NHX:TOL=72284],olyras theon[&&NHX:TOL=72285])olyras[&&NHX:TOL=27589])[&&NHX:TOL=69971])melinaeina[&&NHX:TOL=27574],((((aeria elara[&&NHX:TOL=72275],aeria eurimedia[&&NHX:TOL=72276],aeria olena[&&NHX:TOL=72277])aeria[&&NHX:TOL=27579],((elzunia humboldt[&&NHX:TOL=72273],elzunia pavonii[&&NHX:TOL=72274])elzunia[&&NHX:TOL=27577],(tithorea harmonia[&&NHX:TOL=72271],tithorea tarricina[&&NHX:TOL=72272])tithorea[&&NHX:TOL=27578])[&&NHX:TOL=70001])tithoreina[&&NHX:TOL=27573],(thyridia psidii[&&NHX:TOL=27594],(((mechanitis lysimnia[&&NHX:TOL=72305],mechanitis mazaeus[&&NHX:TOL=72306],mechanitis menapis[&&NHX:TOL=72307],mechanitis polymnia[&&NHX:TOL=72308])mechanitis[&&NHX:TOL=27598],(forbestra equicola[&&NHX:TOL=72303],forbestra olivencia[&&NHX:TOL=72304])forbestra[&&NHX:TOL=27597])[&&NHX:TOL=70003],((sais browni[&&NHX:TOL=72301],sais rosalia[&&NHX:TOL=72302])sais[&&NHX:TOL=27596],(scada karschina[&&NHX:TOL=72296],scada kusa[&&NHX:TOL=72297],scada reckia[&&NHX:TOL=72298],scada zemira[&&NHX:TOL=72299],scada zibia[&&NHX:TOL=72300])scada[&&NHX:TOL=27595])[&&NHX:TOL=70004])[&&NHX:TOL=70002])mechanitina[&&NHX:TOL=27575],(methona confusa[&&NHX:TOL=72289],methona curvifascia[&&NHX:TOL=72290],methona grandior[&&NHX:TOL=72291],methona maxima[&&NHX:TOL=72292],methona megisto[&&NHX:TOL=72293],methona singularis[&&NHX:TOL=72294],methona themisto[&&NHX:TOL=72295])methona[&&NHX:TOL=27592])[&&NHX:TOL=70000],(((eutresis dilucida[&&NHX:TOL=72281],eutresis hypereia[&&NHX:TOL=72282])eutresis[&&NHX:TOL=27586],((athesis acrisione[&&NHX:TOL=72278],athesis clearista[&&NHX:TOL=72279],athesis vitrala[&&NHX:TOL=72280])athesis[&&NHX:TOL=27585],(patricia demylus[&&NHX:TOL=72286],patricia dercyllidas[&&NHX:TOL=72287],patricia oligyrtis[&&NHX:TOL=72288])patricia[&&NHX:TOL=27590])[&&NHX:TOL=69999])new tribe[&&NHX:TOL=69998],((((((((ithomia amarilla[&&NHX:TOL=27626],ithomia arduinna[&&NHX:TOL=27627])[&&NHX:TOL=27649],ithomia jucunda[&&NHX:TOL=27637])[&&NHX:TOL=27648],(ithomia agnosia[&&NHX:TOL=27625],ithomia drymo[&&NHX:TOL=27632],ithomia lichyi[&&NHX:TOL=27640],ithomia pseudoagalla[&&NHX:TOL=27642])[&&NHX:TOL=27652])[&&NHX:TOL=27651],ithomia terra[&&NHX:TOL=27644])[&&NHX:TOL=27650],((((((((ithomia iphianassa[&&NHX:TOL=27636],ithomia salapia[&&NHX:TOL=27643])[&&NHX:TOL=27660],ithomia cleora[&&NHX:TOL=27630])[&&NHX:TOL=27659],ithomia diasia[&&NHX:TOL=27631])[&&NHX:TOL=27661],ithomia patilla[&&NHX:TOL=27641])[&&NHX:TOL=27662],(ithomia celemia[&&NHX:TOL=27629],ithomia heraldica[&&NHX:TOL=27657])[&&NHX:TOL=27658])[&&NHX:TOL=27666],ithomia hyala[&&NHX:TOL=27635])[&&NHX:TOL=27663],((((ithomia eleonora[&&NHX:TOL=27633],ithomia ellara[&&NHX:TOL=27634])[&&NHX:TOL=27653],ithomia praeithomia[&&NHX:TOL=27647])[&&NHX:TOL=27654],ithomia hymettia[&&NHX:TOL=27646])[&&NHX:TOL=27655],ithomia avella[&&NHX:TOL=27628])[&&NHX:TOL=27656])[&&NHX:TOL=27667],(ithomia xenos[&&NHX:TOL=27645],ithomia lagusa[&&NHX:TOL=27638])[&&NHX:TOL=27664])[&&NHX:TOL=27665],ithomia leila[&&NHX:TOL=27639])ithomia[&&NHX:TOL=27607],((pagyris cymothoe[&&NHX:TOL=72363],pagyris priscilla[&&NHX:TOL=72364],pagyris ulla[&&NHX:TOL=72365],pagyris n. sp.[&&NHX:TOL=72366])pagyris[&&NHX:TOL=27606],placidina euryanassa[&&NHX:TOL=27593])[&&NHX:TOL=69997])ithomiina[&&NHX:TOL=27581],((napeogenes achaea[&&NHX:TOL=72322],(napeogenes larilla[&&NHX:TOL=72332],(((napeogenes cranto[&&NHX:TOL=72324],napeogenes flossina[&&NHX:TOL=72326])[&&NHX:TOL=138137],((napeogenes lycora[&&NHX:TOL=72334],napeogenes harbona[&&NHX:TOL=72329])[&&NHX:TOL=138139],(napeogenes sulphureophila[&&NHX:TOL=72341],(napeogenes sodalis[&&NHX:TOL=72339],napeogenes benigna[&&NHX:TOL=138142])[&&NHX:TOL=138141])[&&NHX:TOL=138140])[&&NHX:TOL=138138])[&&NHX:TOL=138136],((napeogenes verticilla[&&NHX:TOL=72344],((napeogenes rhezia[&&NHX:TOL=72338],(napeogenes peridia[&&NHX:TOL=72335],napeogenes pharo[&&NHX:TOL=72336])[&&NHX:TOL=138147])[&&NHX:TOL=138146],((napeogenes aethra[&&NHX:TOL=138150],napeogenes larina[&&NHX:TOL=72333])[&&NHX:TOL=138149],(napeogenes glycera[&&NHX:TOL=72327],napeogenes n. sp. 1[&&NHX:TOL=138152])[&&NHX:TOL=138151])[&&NHX:TOL=138148])[&&NHX:TOL=138145])[&&NHX:TOL=138144],(napeogenes tolosa[&&NHX:TOL=72343],((napeogenes duessa[&&NHX:TOL=72325],napeogenes stella[&&NHX:TOL=72340])[&&NHX:TOL=138155],(napeogenes sylphis[&&NHX:TOL=72342],(napeogenes apulia[&&NHX:TOL=72323],napeogenes inachia[&&NHX:TOL=72330],napeogenes gracilis[&&NHX:TOL=72328],napeogenes n. sp. 2[&&NHX:TOL=138158])[&&NHX:TOL=138157])[&&NHX:TOL=138156])[&&NHX:TOL=138154])[&&NHX:TOL=138153])[&&NHX:TOL=138143])[&&NHX:TOL=138135])[&&NHX:TOL=138134])napeogenes[&&NHX:TOL=27604],(((hyalyris antea[&&NHX:TOL=72309],hyalyris coeno[&&NHX:TOL=72310],hyalyris excelsa[&&NHX:TOL=72311],hyalyris fiammetta[&&NHX:TOL=72312],hyalyris juninensis[&&NHX:TOL=72313],hyalyris latitimbata[&&NHX:TOL=72314],hyalyris leptalina[&&NHX:TOL=72315],hyalyris mestra[&&NHX:TOL=72316],hyalyris ocna[&&NHX:TOL=72317],hyalyris oulita[&&NHX:TOL=72318],hyalyris praxilla[&&NHX:TOL=72319],hyalyris schlingeri[&&NHX:TOL=72320],hyalyris n. sp.[&&NHX:TOL=72321])hyalyris[&&NHX:TOL=27603],(hypothyris anastasia[&&NHX:TOL=72345],hypothyris cantobrica[&&NHX:TOL=72346],hypothyris connexa[&&NHX:TOL=72347],hypothyris daphnis[&&NHX:TOL=72348],hypothyris euclea[&&NHX:TOL=72349],hypothyris fluonia[&&NHX:TOL=72350],hypothyris gemella[&&NHX:TOL=72351],hypothyris leprieuri[&&NHX:TOL=72352],hypothyris lycaste[&&NHX:TOL=72353],hypothyris mamercus[&&NHX:TOL=72354],hypothyris mansuetus[&&NHX:TOL=72355],hypothyris moebiusi[&&NHX:TOL=72356],hypothyris ninonia[&&NHX:TOL=72357],hypothyris semifulva[&&NHX:TOL=72358],hypothyris thea[&&NHX:TOL=72359],hypothyris vallonia[&&NHX:TOL=72360],hypothyris xanthostola[&&NHX:TOL=72361],hypothyris n. sp.[&&NHX:TOL=72362])hypothyris[&&NHX:TOL=27605])[&&NHX:TOL=69995],(epityches eupompe[&&NHX:TOL=27602],aremfoxia ferra[&&NHX:TOL=27601])[&&NHX:TOL=69996])[&&NHX:TOL=69994])napeogenina[&&NHX:TOL=27580])[&&NHX:TOL=69993],(((hyposcada anchialia[&&NHX:TOL=72369],hyposcada attilodes[&&NHX:TOL=72370],hyposcada n. sp.[&&NHX:TOL=72371],hyposcada illinissa[&&NHX:TOL=72372],hyposcada schausi[&&NHX:TOL=72373],hyposcada taliata[&&NHX:TOL=72374],hyposcada virginiana[&&NHX:TOL=72375],hyposcada zarepha[&&NHX:TOL=72376],hyposcada dujardini[&&NHX:TOL=138536],[&&NHX:TOL=138537])hyposcada[&&NHX:TOL=27610],(megoleria orestilla[&&NHX:TOL=72367],megoleria susiana[&&NHX:TOL=72368])megoleria[&&NHX:TOL=27609],(oleria n. sp. 1[&&NHX:TOL=72377],oleria aegineta[&&NHX:TOL=72378],oleria aegle[&&NHX:TOL=72379],oleria agarista[&&NHX:TOL=72380],oleria alexina[&&NHX:TOL=72381],oleria amalda[&&NHX:TOL=72382],oleria antaxis[&&NHX:TOL=72383],oleria aquata[&&NHX:TOL=72384],oleria assimilis[&&NHX:TOL=72385],oleria astrea[&&NHX:TOL=72386],oleria athalina[&&NHX:TOL=72387],oleria attalia[&&NHX:TOL=72388],oleria baizana[&&NHX:TOL=72389],oleria n. sp. 2[&&NHX:TOL=72390],oleria bioculata[&&NHX:TOL=72391],oleria n. sp. 3[&&NHX:TOL=72392],oleria canilla[&&NHX:TOL=72393],oleria n. sp. 4[&&NHX:TOL=72394],oleria cyrene[&&NHX:TOL=72395],oleria deronda[&&NHX:TOL=72396],oleria derondina[&&NHX:TOL=72397],oleria enania[&&NHX:TOL=72398],oleria estella[&&NHX:TOL=72399],oleria fasciata[&&NHX:TOL=72400],oleria flora[&&NHX:TOL=72401],oleria fumata[&&NHX:TOL=72402],oleria gunilla[&&NHX:TOL=72403],oleria ilerdina[&&NHX:TOL=72404],oleria n. sp. 5[&&NHX:TOL=72405],oleria makrena[&&NHX:TOL=72406],oleria olerioides[&&NHX:TOL=72407],oleria onega[&&NHX:TOL=72408],oleria padilla[&&NHX:TOL=72409],oleria paula[&&NHX:TOL=72410],oleria phenomoe[&&NHX:TOL=72411],oleria quadrata[&&NHX:TOL=72412],oleria quintina[&&NHX:TOL=72413],oleria radina[&&NHX:TOL=72414],oleria rubescens[&&NHX:TOL=72415],oleria santineza[&&NHX:TOL=72416],oleria sexmaculata[&&NHX:TOL=72417],oleria similigena[&&NHX:TOL=72418],oleria synnova[&&NHX:TOL=72419],oleria tigilla[&&NHX:TOL=72420],oleria tremona[&&NHX:TOL=72421],oleria vicina[&&NHX:TOL=72422],oleria victorine[&&NHX:TOL=72423],oleria boyeri[&&NHX:TOL=72424],oleria zea[&&NHX:TOL=72425],oleria zelica[&&NHX:TOL=72426])oleria[&&NHX:TOL=27611])oleriina[&&NHX:TOL=27582],(((callithomia alexirrhoe[&&NHX:TOL=72431],callithomia hezia[&&NHX:TOL=72432],callithomia lenea[&&NHX:TOL=72433])callithomia[&&NHX:TOL=69991],((((ceratinia cayana[&&NHX:TOL=72427],ceratinia iolaia[&&NHX:TOL=72428],ceratinia neso[&&NHX:TOL=72429],ceratinia tutia[&&NHX:TOL=72430])ceratinia[&&NHX:TOL=27613],(episcada apuleia[&&NHX:TOL=72453],episcada carcinia[&&NHX:TOL=72454],episcada clausina[&&NHX:TOL=72455],episcada doto[&&NHX:TOL=72456],episcada hemixanthe[&&NHX:TOL=72457],episcada hymen[&&NHX:TOL=72458],episcada hymenaea[&&NHX:TOL=72459],episcada n. sp. 1[&&NHX:TOL=72460],episcada mira[&&NHX:TOL=72461],episcada philoclea[&&NHX:TOL=72462],episcada n. sp. 2[&&NHX:TOL=72463],episcada polita[&&NHX:TOL=72464],episcada n. sp. 3[&&NHX:TOL=72465],episcada n. sp. 4[&&NHX:TOL=72466],episcada salvinia[&&NHX:TOL=72467],episcada suphurea[&&NHX:TOL=72468],episcada sylpha[&&NHX:TOL=72469],episcada ticidella[&&NHX:TOL=72470],episcada vitrea[&&NHX:TOL=72471],episcada n. sp. 5[&&NHX:TOL=72472])episcada[&&NHX:TOL=27616])[&&NHX:TOL=69987],((pteronymia alcmena[&&NHX:TOL=72477],pteronymia aletta[&&NHX:TOL=72478],pteronymia n. sp. 1[&&NHX:TOL=72479],pteronymia alida[&&NHX:TOL=72480],pteronymia alissa[&&NHX:TOL=72481],pteronymia artena[&&NHX:TOL=72482],pteronymia calgiria[&&NHX:TOL=72483],pteronymia n. sp. 2[&&NHX:TOL=72484],pteronymia cotytto[&&NHX:TOL=72485],pteronymia n. sp. 3[&&NHX:TOL=72486],pteronymia dispaena[&&NHX:TOL=72487],pteronymia donella[&&NHX:TOL=72488],pteronymia euritea[&&NHX:TOL=72489],pteronymia n. sp. 4[&&NHX:TOL=72490],pteronymia forsteri[&&NHX:TOL=72491],pteronymia fulvimargo[&&NHX:TOL=72492],pteronymia fumida[&&NHX:TOL=72493],pteronymia gertschi[&&NHX:TOL=72494],pteronymia glauca[&&NHX:TOL=72495],pteronymia granica[&&NHX:TOL=72496],pteronymia n. sp. 5[&&NHX:TOL=72497],pteronymia hara[&&NHX:TOL=72498],pteronymia latilla[&&NHX:TOL=72499],pteronymia laura[&&NHX:TOL=72500],pteronymia lonera[&&NHX:TOL=72501],pteronymia medellina[&&NHX:TOL=72502],pteronymia obscuratus[&&NHX:TOL=72503],pteronymia olimba[&&NHX:TOL=72504],pteronymia oneida[&&NHX:TOL=72505],pteronymia ozia[&&NHX:TOL=72506],pteronymia parva[&&NHX:TOL=72507],pteronymia n. sp. 6[&&NHX:TOL=72508],pteronymia picta[&&NHX:TOL=72509],pteronymia primula[&&NHX:TOL=72510],pteronymia rufocincta[&&NHX:TOL=72511],pteronymia sao[&&NHX:TOL=72512],pteronymia serrata[&&NHX:TOL=72513],pteronymia simplex[&&NHX:TOL=72514],pteronymia sylvo[&&NHX:TOL=72515],pteronymia tamina[&&NHX:TOL=72516],pteronymia teresita[&&NHX:TOL=72517],pteronymia ticida[&&NHX:TOL=72518],pteronymia tucuna[&&NHX:TOL=72519],pteronymia veia[&&NHX:TOL=72520],pteronymia vestilla[&&NHX:TOL=72521],pteronymia zerlina[&&NHX:TOL=72522])pteronymia[&&NHX:TOL=27617],(haenschia derama[&&NHX:TOL=72473],haenschia sidonia[&&NHX:TOL=72474],haenschia n. sp. 1[&&NHX:TOL=72475],haenschia n. sp. 2[&&NHX:TOL=72476])haenschia[&&NHX:TOL=69989])[&&NHX:TOL=69988])[&&NHX:TOL=69986],((dircenna adina[&&NHX:TOL=72434],(dircenna dero[&&NHX:TOL=72436],dircenna loreta[&&NHX:TOL=72437])[&&NHX:TOL=72435],dircenna jemima[&&NHX:TOL=72438],dircenna klugii[&&NHX:TOL=72439],dircenna olyras[&&NHX:TOL=72440])dircenna[&&NHX:TOL=27614],(((hyalenna paradoxa[&&NHX:TOL=72443],hyalenna hugia[&&NHX:TOL=72444])[&&NHX:TOL=72442],hyalenna perasippa[&&NHX:TOL=72445])[&&NHX:TOL=72441],(hyalenna buckleyi[&&NHX:TOL=72447],(hyalenna sulmona[&&NHX:TOL=72449],hyalenna pascua[&&NHX:TOL=72450],hyalenna alidella[&&NHX:TOL=72451])[&&NHX:TOL=72448])[&&NHX:TOL=72446])hyalenna[&&NHX:TOL=27615])[&&NHX:TOL=69990])[&&NHX:TOL=69985])dircennina[&&NHX:TOL=27583],(((veladyris pardalis[&&NHX:TOL=72540],veladyris n. sp.[&&NHX:TOL=72541])veladyris[&&NHX:TOL=27619],(velamysta peninna[&&NHX:TOL=72523],velamysta phengites[&&NHX:TOL=72524],velamysta pupilla[&&NHX:TOL=72525])velamysta[&&NHX:TOL=69978])[&&NHX:TOL=69977],(((greta alphesiboea[&&NHX:TOL=72555],greta andromica[&&NHX:TOL=72556],greta annette[&&NHX:TOL=72557],greta n. sp. 1[&&NHX:TOL=72558],greta n. sp. 2[&&NHX:TOL=72559],greta n. sp. 3[&&NHX:TOL=72560],greta cubana[&&NHX:TOL=72561],greta n. sp. 4[&&NHX:TOL=72562],greta depauperata[&&NHX:TOL=72563],greta dercetis[&&NHX:TOL=72564],greta diaphanus[&&NHX:TOL=72565],greta enigma[&&NHX:TOL=72566],greta n. sp. 5[&&NHX:TOL=72567],greta esula[&&NHX:TOL=72568],greta n. sp. 6[&&NHX:TOL=72569],greta n. sp. 7[&&NHX:TOL=72570],greta gardneri[&&NHX:TOL=72571],greta hermana[&&NHX:TOL=72572],greta libethris[&&NHX:TOL=72573],greta lojana[&&NHX:TOL=72574],greta lydia[&&NHX:TOL=72575],greta morgane[&&NHX:TOL=72576],greta n. sp. 8[&&NHX:TOL=72577],greta ochretis[&&NHX:TOL=72578],greta oneidodes[&&NHX:TOL=72579],greta ortygia[&&NHX:TOL=72580],greta n. sp. 9[&&NHX:TOL=72581],greta polissena[&&NHX:TOL=72582],greta theudelinda[&&NHX:TOL=72583],greta n. sp. 10[&&NHX:TOL=72584])greta[&&NHX:TOL=27622],(pseudoscada acilla[&&NHX:TOL=72587],pseudoscada erruca[&&NHX:TOL=72588],pseudoscada florula[&&NHX:TOL=72589],pseudoscada timna[&&NHX:TOL=72590])pseudoscada[&&NHX:TOL=27624])[&&NHX:TOL=69984],((godyris crinippa[&&NHX:TOL=72527],godyris dircenna[&&NHX:TOL=72528],godyris duillia[&&NHX:TOL=72529],godyris kedema[&&NHX:TOL=72531],godyris lauta[&&NHX:TOL=72532],godyris nepos[&&NHX:TOL=72534],godyris nero[&&NHX:TOL=72535],godyris panthyale[&&NHX:TOL=72536],godyris sappho[&&NHX:TOL=72537],godyris zavaleta[&&NHX:TOL=72538])godyris[&&NHX:TOL=27618],((heterosais edessa[&&NHX:TOL=72585],heterosais giulia[&&NHX:TOL=72586])heterosais[&&NHX:TOL=27623],(((hypoleria adasa[&&NHX:TOL=72542],hypoleria alema[&&NHX:TOL=72543],hypoleria aureliana[&&NHX:TOL=72544],hypoleria jaruensis[&&NHX:TOL=72545],hypoleria lavinia[&&NHX:TOL=72546],hypoleria ocalea[&&NHX:TOL=72547],hypoleria sarepta[&&NHX:TOL=72548],hypoleria xenophis[&&NHX:TOL=72549])hypoleria[&&NHX:TOL=27620],mcclungia cymo[&&NHX:TOL=27621],(brevioleria aelia[&&NHX:TOL=72550],brevioleria arzalia[&&NHX:TOL=72551],brevioleria coenina[&&NHX:TOL=72552],brevioleria seba[&&NHX:TOL=72553],brevioleria n. sp.[&&NHX:TOL=72554])brevioleria[&&NHX:TOL=69983])[&&NHX:TOL=69982],(((pachacutia cleomella[&&NHX:TOL=72526],pachacutia germaini[&&NHX:TOL=72530])[&&NHX:TOL=108252],pachacutia mantura[&&NHX:TOL=72533])[&&NHX:TOL=108251],pachacutia baroni[&&NHX:TOL=72539])pachacutia[&&NHX:TOL=108250])[&&NHX:TOL=108253])[&&NHX:TOL=69981])[&&NHX:TOL=69980])[&&NHX:TOL=69979])godyridina[&&NHX:TOL=27584])[&&NHX:TOL=69976])[&&NHX:TOL=69975])[&&NHX:TOL=69974])[&&NHX:TOL=69973])[&&NHX:TOL=69972])ithomiini[&&NHX:TOL=27570],(((((anetia thirza[&&NHX:TOL=77042],(anetia jaegeri[&&NHX:TOL=77047],anetia cubana[&&NHX:TOL=77043])[&&NHX:TOL=77046])[&&NHX:TOL=77045],(anetia pantheratus[&&NHX:TOL=77049],anetia briarea[&&NHX:TOL=77044])[&&NHX:TOL=77048])anetia[&&NHX:TOL=70699],((lycorea paisinuntia[&&NHX:TOL=77038],lycorea cleobaea[&&NHX:TOL=77039])[&&NHX:TOL=77041],lycorea ilione[&&NHX:TOL=77040])lycorea[&&NHX:TOL=70700],archaeolycorea ferreirai[&&NHX:EXT=Y:TOL=138008])[&&NHX:TOL=70698],((((idea durvillei[&&NHX:TOL=77026],idea blanchardii[&&NHX:TOL=77035],idea idea[&&NHX:TOL=77025])[&&NHX:TOL=77034],idea electra[&&NHX:TOL=77024],(idea hypermnestra[&&NHX:TOL=77022],idea leuconoe[&&NHX:TOL=77023])[&&NHX:TOL=77036],idea tambusisiana[&&NHX:TOL=77027])[&&NHX:TOL=77033],(idea iasonia[&&NHX:TOL=77029],idea lynceus[&&NHX:TOL=77028],idea stolli[&&NHX:TOL=77030],idea malabarica[&&NHX:TOL=77031],idea agamarschana[&&NHX:TOL=77032])[&&NHX:TOL=77037])idea[&&NHX:TOL=70702],protoploea apatela[&&NHX:TOL=70703],(euploea magou[&&NHX:TOL=76948],(euploea euphon[&&NHX:TOL=76949],(((euploea tripunctata[&&NHX:TOL=76952],euploea lacon[&&NHX:TOL=76951])[&&NHX:TOL=77002],euploea sylvester[&&NHX:TOL=76950])[&&NHX:TOL=77001],(euploea mulciber[&&NHX:TOL=77004],(euploea phaenareta[&&NHX:TOL=76954],euploea midamus[&&NHX:TOL=76955],euploea configurata[&&NHX:TOL=76956],euploea eupator[&&NHX:TOL=76957],((euploea martinii[&&NHX:TOL=76967],euploea gamelia[&&NHX:TOL=77008],euploea blossomae[&&NHX:TOL=76968])[&&NHX:TOL=77007],euploea cordelia[&&NHX:TOL=76969],euploea hewitsonii[&&NHX:TOL=76971],euploea tulliolus[&&NHX:TOL=76970],euploea stephensii[&&NHX:TOL=76972],euploea darchia[&&NHX:TOL=76973])[&&NHX:TOL=77006],((euploea eleusina[&&NHX:TOL=76958],euploea caespes[&&NHX:TOL=76959])[&&NHX:TOL=77010],euploea eunice[&&NHX:TOL=76960],euploea klugii[&&NHX:TOL=76961],euploea radamanthus[&&NHX:TOL=76962],((euploea leucostictos[&&NHX:TOL=76964],euploea usipetes[&&NHX:TOL=76965],euploea asyllus[&&NHX:TOL=76966])[&&NHX:TOL=77012],euploea westwoodii[&&NHX:TOL=76963])[&&NHX:TOL=77011])[&&NHX:TOL=77009])[&&NHX:TOL=77005])[&&NHX:TOL=77003])[&&NHX:TOL=77000])[&&NHX:TOL=76999],(((euploea eyndhovii[&&NHX:TOL=76975],euploea doubledayi[&&NHX:TOL=76974])[&&NHX:TOL=77015],euploea dentiplaga[&&NHX:TOL=76976],euploea boisduvalii[&&NHX:TOL=76977],euploea morosa[&&NHX:TOL=76978],euploea algea[&&NHX:TOL=76979],(euploea core[&&NHX:TOL=76980],euploea andamanensis[&&NHX:TOL=118307],euploea scherzeri[&&NHX:TOL=118308],euploea charox[&&NHX:TOL=118309],euploea corinna[&&NHX:TOL=118310])[&&NHX:TOL=118306],(euploea eurianassa[&&NHX:TOL=76981],euploea netscheri[&&NHX:TOL=77017])[&&NHX:TOL=77016],euploea swainson[&&NHX:TOL=77018],(euploea climena[&&NHX:TOL=76983],euploea alcathoe[&&NHX:TOL=76982])[&&NHX:TOL=77019])[&&NHX:TOL=77014],((euploea modesta[&&NHX:TOL=76985],euploea treitschkei[&&NHX:TOL=76984],(euploea crameri[&&NHX:TOL=76986],euploea orontobates[&&NHX:TOL=108210])[&&NHX:TOL=118311],euploea camaralzeman[&&NHX:TOL=76987])[&&NHX:TOL=77021],euploea wallacei[&&NHX:TOL=76988],euploea doretta[&&NHX:TOL=76989],euploea batesii[&&NHX:TOL=76990],euploea latifasciata[&&NHX:TOL=76991],euploea eboraci[&&NHX:TOL=76992],euploea redtenbacheri[&&NHX:TOL=76993],euploea albicosta[&&NHX:TOL=76994],euploea lewinii[&&NHX:TOL=76995])[&&NHX:TOL=77020],euploea nechos[&&NHX:TOL=76996],euploea mitra[&&NHX:TOL=76997],euploea tobleri[&&NHX:TOL=76998])[&&NHX:TOL=77013])euploea[&&NHX:TOL=70704])[&&NHX:TOL=70701])euploeina[&&NHX:TOL=70697],((((miriamica weiskei[&&NHX:TOL=85302],miriamica thalassina[&&NHX:TOL=85303])miriamica[&&NHX:TOL=70708],((ideopsis oberthurii[&&NHX:TOL=76877],(ideopsis similis[&&NHX:TOL=76879],ideopsis vulgaris[&&NHX:TOL=76880],ideopsis juventa[&&NHX:TOL=76878])[&&NHX:TOL=76886])[&&NHX:TOL=76885],(ideopsis vitrea[&&NHX:TOL=76882],ideopsis gaura[&&NHX:TOL=76881],ideopsis klassika[&&NHX:TOL=76883],ideopsis hewitsonii[&&NHX:TOL=76884])[&&NHX:TOL=76887])ideopsis[&&NHX:TOL=70709],((parantica aglea[&&NHX:TOL=76817],(parantica agleoides[&&NHX:TOL=76818],(((parantica schenkii[&&NHX:TOL=76819],parantica kirbyi[&&NHX:TOL=76820])[&&NHX:TOL=76857],parantica clinias[&&NHX:TOL=76821])[&&NHX:TOL=76856],(parantica aspasia[&&NHX:TOL=76822],parantica cleona[&&NHX:TOL=76823])[&&NHX:TOL=76858],parantica vitrina[&&NHX:TOL=76859])[&&NHX:TOL=76855])[&&NHX:TOL=76854])[&&NHX:TOL=76853],(((((((parantica kuekenthali[&&NHX:TOL=76843],parantica toxopei[&&NHX:TOL=76842])[&&NHX:TOL=76866],parantica dabrerai[&&NHX:TOL=76844],parantica hypowattan[&&NHX:TOL=76845],parantica sp. n.[&&NHX:TOL=94069])[&&NHX:TOL=76865],parantica timorica[&&NHX:TOL=76846],parantica albata[&&NHX:TOL=76841])[&&NHX:TOL=76864],parantica pseudomelaneus[&&NHX:TOL=76840],parantica tityoides[&&NHX:TOL=76839])[&&NHX:TOL=76863],(((((parantica pedonga[&&NHX:TOL=76826],parantica sita[&&NHX:TOL=76824])[&&NHX:TOL=76871],(parantica melaneus[&&NHX:TOL=76827],parantica swinhoei[&&NHX:TOL=124464])[&&NHX:TOL=124463],parantica luzonensis[&&NHX:TOL=76828])[&&NHX:TOL=76870],parantica taprobana[&&NHX:TOL=76829],parantica nilgiriensis[&&NHX:TOL=76830],parantica schoenigi[&&NHX:TOL=76831])[&&NHX:TOL=76869],(parantica philo[&&NHX:TOL=76837],parantica sulewattan[&&NHX:TOL=76836],parantica wegneri[&&NHX:TOL=76838])[&&NHX:TOL=76872],(parantica dannatti[&&NHX:TOL=76832],parantica phyle[&&NHX:TOL=76833],parantica davidi[&&NHX:TOL=76834],parantica milagros[&&NHX:TOL=76835],parantica noeli[&&NHX:TOL=124465])[&&NHX:TOL=76873])[&&NHX:TOL=76868],parantica crowleyi[&&NHX:TOL=76825])[&&NHX:TOL=76867])[&&NHX:TOL=76862],parantica menadensis[&&NHX:TOL=76847])[&&NHX:TOL=76861],(((parantica melusine[&&NHX:TOL=76849],(parantica marcia[&&NHX:TOL=76848],parantica fuscela[&&NHX:TOL=124467])[&&NHX:TOL=124466],parantica rotundata[&&NHX:TOL=76850])[&&NHX:TOL=76876],parantica garamantis[&&NHX:TOL=76851])[&&NHX:TOL=76875],parantica pumila[&&NHX:TOL=76852])[&&NHX:TOL=76874])[&&NHX:TOL=76860])parantica[&&NHX:TOL=70710])[&&NHX:TOL=70707],((amauris niavius[&&NHX:TOL=76888],amauris tartarea[&&NHX:TOL=76889])[&&NHX:TOL=76903],(amauris ellioti[&&NHX:TOL=76890],(amauris comorana[&&NHX:TOL=76892],(amauris phoedon[&&NHX:TOL=76891],(amauris echeria[&&NHX:TOL=76893],(amauris vashti[&&NHX:TOL=76894],(amauris crawshayi[&&NHX:TOL=76895],(amauris hecate[&&NHX:TOL=76902],((amauris inferna[&&NHX:TOL=76901],amauris dannfelti[&&NHX:TOL=76900])[&&NHX:TOL=76912],(amauris albimaculata[&&NHX:TOL=76897],(amauris damocles[&&NHX:TOL=76896],(amauris ochlea[&&NHX:TOL=76899],amauris nossima[&&NHX:TOL=76898])[&&NHX:TOL=76911])[&&NHX:TOL=76915])[&&NHX:TOL=76910])[&&NHX:TOL=76914])[&&NHX:TOL=76909])[&&NHX:TOL=76908])[&&NHX:TOL=76907])[&&NHX:TOL=76906])[&&NHX:TOL=76913])[&&NHX:TOL=76905])[&&NHX:TOL=76904])amauris[&&NHX:TOL=70711])[&&NHX:TOL=70706],(tiradelphe schneideri[&&NHX:TOL=70713],(((danaus plexippus[&&NHX:TOL=76926],danaus erippus[&&NHX:TOL=76928])[&&NHX:TOL=76937],danaus cleophile[&&NHX:TOL=76927])danaus danaus[&&NHX:TOL=111220],((danaus ismare[&&NHX:TOL=76930],(danaus genutia[&&NHX:TOL=76929],(danaus melanippus[&&NHX:TOL=76932],danaus affinis[&&NHX:TOL=76931])[&&NHX:TOL=76942])[&&NHX:TOL=76941])danaus salatura[&&NHX:TOL=76940],((danaus eresimus[&&NHX:TOL=76933],danaus plexaure[&&NHX:TOL=76934])[&&NHX:TOL=76944],(danaus gilippus[&&NHX:TOL=76935],(danaus petilia[&&NHX:TOL=76947],danaus chrysippus[&&NHX:TOL=76936])[&&NHX:TOL=76946])[&&NHX:TOL=76945])danaus anosia[&&NHX:TOL=76943])[&&NHX:TOL=76939])danaus[&&NHX:TOL=70714],(tirumala formosa[&&NHX:TOL=76916],(tirumala gautama[&&NHX:TOL=76918],tirumala petiverana[&&NHX:TOL=76917],tirumala euploeomorpha[&&NHX:TOL=76919],tirumala limniace[&&NHX:TOL=76921],tirumala choaspes[&&NHX:TOL=76920],tirumala septentrionis[&&NHX:TOL=76922],tirumala hamata[&&NHX:TOL=76923],tirumala ishmoides[&&NHX:TOL=76924])[&&NHX:TOL=76925])tirumala[&&NHX:TOL=70715])[&&NHX:TOL=70712])danaina[&&NHX:TOL=70705])danaini[&&NHX:TOL=27571],(tellervo juriaansei[&&NHX:TOL=70688],(((tellervo assarica[&&NHX:TOL=70692],tellervo zoilus[&&NHX:TOL=70693])[&&NHX:TOL=70691],tellervo parvipuncta[&&NHX:TOL=70694],tellervo hiero[&&NHX:TOL=70695])[&&NHX:TOL=70690],tellervo nedusia[&&NHX:TOL=70696])[&&NHX:TOL=70689])tellervo[&&NHX:TOL=27572])danainae[&&NHX:TOL=12187])[&&NHX:TOL=69942],((libythea collenettei[&&NHX:TOL=70282],(((libythea geoffroy[&&NHX:TOL=70286],libythea narina[&&NHX:TOL=70287])[&&NHX:TOL=70285],libythea myrrha[&&NHX:TOL=70288],(libythea celtis[&&NHX:TOL=70289],libythea lepita[&&NHX:TOL=76306])[&&NHX:TOL=76305])[&&NHX:TOL=70284],(libythea laius[&&NHX:TOL=70291],libythea labdaca[&&NHX:TOL=70292])[&&NHX:TOL=70290])[&&NHX:TOL=70283],libythea cinyras[&&NHX:TOL=76307])libythea[&&NHX:TOL=12184],(libytheana carinenta[&&NHX:TOL=70293],libytheana fulvescens[&&NHX:TOL=70294],libytheana motya[&&NHX:TOL=70295],libytheana terena[&&NHX:TOL=70296])libytheana[&&NHX:TOL=12185])libytheinae[&&NHX:TOL=12193])nymphalidae[&&NHX:TOL=12172])[&&NHX:TOL=12171])[&&NHX:TOL=103505])papilionoidea[&&NHX:TOL=12027],(((((((choaspes adhara[&&NHX:TOL=124785],choaspes benjaminii[&&NHX:TOL=94486],choaspes estrella[&&NHX:TOL=124786],choaspes furcatus[&&NHX:TOL=94487],choaspes hemixanthus[&&NHX:TOL=94488],choaspes illuensis[&&NHX:TOL=94489],choaspes plateni[&&NHX:TOL=94490],choaspes stigmata[&&NHX:TOL=124787],choaspes subcaudata[&&NHX:TOL=94491],choaspes xanthopogon[&&NHX:TOL=94492])choaspes[&&NHX:TOL=94261],(coeliades aeschylus[&&NHX:TOL=94511],coeliades anchises[&&NHX:TOL=94512],coeliades bixana[&&NHX:TOL=94513],coeliades bocagii[&&NHX:TOL=94514],coeliades chalybe[&&NHX:TOL=94515],coeliades ernesti[&&NHX:TOL=94516],coeliades fervida[&&NHX:TOL=94517],coeliades fidia[&&NHX:TOL=94518],coeliades forestan[&&NHX:TOL=94519],coeliades hanno[&&NHX:TOL=94520],coeliades keithloa[&&NHX:TOL=94521],coeliades libeon[&&NHX:TOL=94522],coeliades pisistratus[&&NHX:TOL=94523],coeliades rama[&&NHX:TOL=94524],coeliades ramanatek[&&NHX:TOL=94525],coeliades sejuncta[&&NHX:TOL=94526])coeliades[&&NHX:TOL=94262])[&&NHX:TOL=138292],(hasora anura[&&NHX:TOL=94527],hasora badra[&&NHX:TOL=94528],hasora borneensis[&&NHX:TOL=94529],hasora buina[&&NHX:TOL=94530],hasora celaenus[&&NHX:TOL=94531],hasora chromus[&&NHX:TOL=94532],hasora danda[&&NHX:TOL=94533],hasora discolor[&&NHX:TOL=94534],hasora hurama[&&NHX:TOL=94535],hasora khoda[&&NHX:TOL=94536],hasora lavella[&&NHX:TOL=94537],hasora leucospila[&&NHX:TOL=94538],hasora lizetta[&&NHX:TOL=94539],hasora mavis[&&NHX:TOL=94540],hasora mixta[&&NHX:TOL=94541],(hasora moestissima[&&NHX:TOL=94542],hasora caeruleostriata[&&NHX:TOL=124784])[&&NHX:TOL=124783],hasora mus[&&NHX:TOL=94543],hasora myra[&&NHX:TOL=94544],hasora proxissima[&&NHX:TOL=94545],hasora quadripunctata[&&NHX:TOL=94546],hasora sakit[&&NHX:TOL=94547],hasora salanga[&&NHX:TOL=94548],hasora schoenherr[&&NHX:TOL=94549],hasora subcaelestis[&&NHX:TOL=94550],hasora takwa[&&NHX:TOL=94551],hasora taminatus[&&NHX:TOL=94552],hasora thridas[&&NHX:TOL=94553],hasora umbrina[&&NHX:TOL=94554],hasora vitta[&&NHX:TOL=94555],hasora wilcocksi[&&NHX:TOL=94556],hasora zoma[&&NHX:TOL=94557])hasora[&&NHX:TOL=94263])[&&NHX:TOL=138291],((bibasis aquilina[&&NHX:TOL=94508],bibasis iluska[&&NHX:TOL=94509],bibasis sena[&&NHX:TOL=94510])bibasis[&&NHX:TOL=94259],(burara amara[&&NHX:TOL=94493],burara anadi[&&NHX:TOL=94494],burara aphrodite[&&NHX:TOL=94495],burara etelka[&&NHX:TOL=94497],burara gomata[&&NHX:TOL=94498],burara harisa[&&NHX:TOL=94499],burara imperialis[&&NHX:TOL=94500],burara jaina[&&NHX:TOL=94501],burara oedipodea[&&NHX:TOL=94502],burara owstoni[&&NHX:TOL=94503],burara phul[&&NHX:TOL=94504],burara striata[&&NHX:TOL=94505],burara tuckeri[&&NHX:TOL=94506],burara vasutana[&&NHX:TOL=94507])burara[&&NHX:TOL=94260])[&&NHX:TOL=124782])[&&NHX:TOL=138290],(badamia atrox[&&NHX:TOL=94484],badamia exclamationis[&&NHX:TOL=94485])badamia[&&NHX:TOL=94258])[&&NHX:TOL=138289],(allora doleschallii[&&NHX:TOL=94482],allora major[&&NHX:TOL=94483])allora[&&NHX:TOL=94257],pyrrhiades lucagus[&&NHX:TOL=94264],pyrrhochalcia iphis[&&NHX:TOL=94265])coeliadinae[&&NHX:TOL=12150],(euschemon rafflesia[&&NHX:TOL=95273],(((((((((((chioides albofasciatus[&&NHX:TOL=96709],chioides catillus[&&NHX:TOL=96710],chioides churchi[&&NHX:TOL=96711],chioides cinereus[&&NHX:TOL=96712],chioides concinnus[&&NHX:TOL=96713],chioides iverna[&&NHX:TOL=96714],chioides ixion[&&NHX:TOL=96715],chioides marmorosa[&&NHX:TOL=96716],chioides vintra[&&NHX:TOL=96717],chioides zilpa[&&NHX:TOL=96718])chioides[&&NHX:TOL=95285],(proteides maysi[&&NHX:TOL=96918],proteides mercurius[&&NHX:TOL=96919])proteides[&&NHX:TOL=95312])[&&NHX:TOL=138294],spathilepia clonius[&&NHX:TOL=95316])[&&NHX:TOL=138293],((thorybes bathyllus[&&NHX:TOL=100497],thorybes diversus[&&NHX:TOL=100498],thorybes drusius[&&NHX:TOL=100499],thorybes mexicana[&&NHX:TOL=100500],thorybes pylades[&&NHX:TOL=100501],thorybes confusis[&&NHX:TOL=100502])thorybes[&&NHX:TOL=95320],(achalarus albociliatus[&&NHX:TOL=96608],achalarus casica[&&NHX:TOL=96609],achalarus lyciades[&&NHX:TOL=96610],achalarus tehuanaca[&&NHX:TOL=96611],achalarus toxeus[&&NHX:TOL=96612])achalarus[&&NHX:TOL=95274],(autochton bipunctatus[&&NHX:TOL=96670],autochton cellus[&&NHX:TOL=96671],autochton cincta[&&NHX:TOL=96672],autochton integrifascia[&&NHX:TOL=96673],autochton itylus[&&NHX:TOL=96674],autochton longipennis[&&NHX:TOL=96675],autochton neis[&&NHX:TOL=96676],autochton pseudocellus[&&NHX:TOL=96677],autochton reflexus[&&NHX:TOL=96678],autochton siermadror[&&NHX:TOL=96679],autochton sulfureolus[&&NHX:TOL=96680],autochton vectilucis[&&NHX:TOL=96681],autochton zarex[&&NHX:TOL=96682])autochton[&&NHX:TOL=95279],(urbanus albimargo[&&NHX:TOL=100518],urbanus ambiguus[&&NHX:TOL=100519],urbanus belli[&&NHX:TOL=100520],urbanus carmelita[&&NHX:TOL=100521],urbanus chalco[&&NHX:TOL=100522],urbanus chales[&&NHX:TOL=100523],urbanus cindra[&&NHX:TOL=100524],urbanus dorantes[&&NHX:TOL=100525],urbanus doryssus[&&NHX:TOL=100526],urbanus dubius[&&NHX:TOL=100527],urbanus elmina[&&NHX:TOL=100528],urbanus esma[&&NHX:TOL=100529],urbanus esmeraldus[&&NHX:TOL=100530],urbanus esta[&&NHX:TOL=100531],urbanus evenus[&&NHX:TOL=100532],urbanus evona[&&NHX:TOL=100533],urbanus huancavillcas[&&NHX:TOL=100534],urbanus longicaudus[&&NHX:TOL=100535],urbanus magnus[&&NHX:TOL=100536],urbanus parvus[&&NHX:TOL=100537],urbanus procne[&&NHX:TOL=100538],urbanus prodicus[&&NHX:TOL=100539],urbanus pronta[&&NHX:TOL=100540],urbanus pronus[&&NHX:TOL=100541],urbanus proteus[&&NHX:TOL=100542],urbanus reductus[&&NHX:TOL=100543],urbanus simplicius[&&NHX:TOL=100544],urbanus tanna[&&NHX:TOL=100545],urbanus teleus[&&NHX:TOL=100546],urbanus velinus[&&NHX:TOL=100547],urbanus villus[&&NHX:TOL=100548],urbanus virescens[&&NHX:TOL=100549],urbanus viridis[&&NHX:TOL=100550],urbanus viterboana[&&NHX:TOL=100551],urbanus zagorus[&&NHX:TOL=100552])urbanus[&&NHX:TOL=95323])[&&NHX:TOL=138303])[&&NHX:TOL=138306],((astraptes alardus[&&NHX:TOL=96639],astraptes alector[&&NHX:TOL=96640],astraptes anaphus[&&NHX:TOL=96641],astraptes apastus[&&NHX:TOL=96642],astraptes aulus[&&NHX:TOL=96643],astraptes brevicauda[&&NHX:TOL=96644],astraptes cassander[&&NHX:TOL=96645],astraptes chiriquensis[&&NHX:TOL=96646],astraptes cretatus[&&NHX:TOL=96647],astraptes creteus[&&NHX:TOL=96648],astraptes egregius[&&NHX:TOL=96649],astraptes elorus[&&NHX:TOL=96650],astraptes enotrus[&&NHX:TOL=96651],astraptes erycina[&&NHX:TOL=96652],astraptes fulgerator[&&NHX:TOL=96653],astraptes fulgor[&&NHX:TOL=96654],astraptes galesus[&&NHX:TOL=96655],astraptes halesius[&&NHX:TOL=96656],astraptes jaira[&&NHX:TOL=96657],astraptes janeira[&&NHX:TOL=96658],astraptes latimargo[&&NHX:TOL=96659],astraptes mabillei[&&NHX:TOL=96660],astraptes megalurus[&&NHX:TOL=96661],astraptes naxos[&&NHX:TOL=96662],astraptes palliolum[&&NHX:TOL=96663],astraptes phalaecus[&&NHX:TOL=96664],astraptes talus[&&NHX:TOL=96665],astraptes tucuti[&&NHX:TOL=96666],astraptes xagua[&&NHX:TOL=96667])astraptes[&&NHX:TOL=95276],(narcosius aulina[&&NHX:TOL=96837],narcosius colossus[&&NHX:TOL=96838],narcosius dosula[&&NHX:TOL=96839],narcosius hercules[&&NHX:TOL=96840],narcosius mura[&&NHX:TOL=96841],narcosius narcosius[&&NHX:TOL=96842],narcosius nazaraeus[&&NHX:TOL=96843],narcosius odysseus[&&NHX:TOL=96844],narcosius parisi[&&NHX:TOL=96845],narcosius pseudomura[&&NHX:TOL=96846],narcosius samson[&&NHX:TOL=96847],narcosius steinhauseri[&&NHX:TOL=96848])narcosius[&&NHX:TOL=95299])[&&NHX:TOL=138307])[&&NHX:TOL=138305],(cabares potrillo[&&NHX:TOL=96693],cabares rinta[&&NHX:TOL=96694])cabares[&&NHX:TOL=95281])[&&NHX:TOL=138304],(aguna albistria[&&NHX:TOL=96613],aguna asander[&&NHX:TOL=96614],aguna aurunce[&&NHX:TOL=96615],aguna camagura[&&NHX:TOL=96616],aguna cirrus[&&NHX:TOL=96617],aguna claxon[&&NHX:TOL=96618],aguna clina[&&NHX:TOL=96619],aguna coeloides[&&NHX:TOL=96620],aguna coelus[&&NHX:TOL=96621],aguna ganna[&&NHX:TOL=96622],aguna glaphyrus[&&NHX:TOL=96623],aguna latifascia[&&NHX:TOL=96624],aguna latimacula[&&NHX:TOL=96625],aguna longicauda[&&NHX:TOL=96626],aguna megaeles[&&NHX:TOL=96627],aguna mesodentata[&&NHX:TOL=96628],aguna metophis[&&NHX:TOL=96629],aguna nicolayi[&&NHX:TOL=96630],aguna panama[&&NHX:TOL=96631],aguna parva[&&NHX:TOL=96632],aguna penicillata[&&NHX:TOL=96633],aguna similis[&&NHX:TOL=96634],aguna spatulata[&&NHX:TOL=96635],aguna spicata[&&NHX:TOL=96636],aguna squamalba[&&NHX:TOL=96637],aguna venezuelae[&&NHX:TOL=96638])aguna[&&NHX:TOL=95275],((codatractus alcaeus[&&NHX:TOL=96729],codatractus aminias[&&NHX:TOL=96730],codatractus arizonensis[&&NHX:TOL=96731],codatractus bryaxis[&&NHX:TOL=96732],codatractus carlos[&&NHX:TOL=96733],codatractus cyda[&&NHX:TOL=96734],codatractus cyledis[&&NHX:TOL=96735],codatractus hyster[&&NHX:TOL=96736],codatractus imalena[&&NHX:TOL=96737],codatractus melon[&&NHX:TOL=96738],codatractus sallyae[&&NHX:TOL=96739],codatractus uvydixa[&&NHX:TOL=96740],codatractus valeriana[&&NHX:TOL=96741],codatractus yucatanus[&&NHX:TOL=96742])codatractus[&&NHX:TOL=95287],(typhedanus ampyx[&&NHX:TOL=100503],typhedanus aziris[&&NHX:TOL=100504],typhedanus crameri[&&NHX:TOL=100505],typhedanus cursinoi[&&NHX:TOL=100506],typhedanus eliasi[&&NHX:TOL=100507],typhedanus galbula[&&NHX:TOL=100508],typhedanus optica[&&NHX:TOL=100509],typhedanus salas[&&NHX:TOL=100510],typhedanus stylites[&&NHX:TOL=100511],typhedanus umber[&&NHX:TOL=100512],typhedanus undulatus[&&NHX:TOL=100513])typhedanus[&&NHX:TOL=95321])[&&NHX:TOL=138308],((lobocla bifasciata[&&NHX:TOL=96830],lobocla germana[&&NHX:TOL=96831],lobocla iliana[&&NHX:TOL=96832],lobocla proximus[&&NHX:TOL=96833],lobocla simplex[&&NHX:TOL=96834])lobocla[&&NHX:TOL=95297],(zestusa dorus[&&NHX:TOL=100558],zestusa elwesi[&&NHX:TOL=100559],zestusa levona[&&NHX:TOL=100560],zestusa staudingeri[&&NHX:TOL=100561])zestusa[&&NHX:TOL=95325])[&&NHX:TOL=138315],(calliades oryx[&&NHX:TOL=96695],calliades zeutus[&&NHX:TOL=96696])calliades[&&NHX:TOL=95283])[&&NHX:TOL=138314],((((((drephalys eous[&&NHX:TOL=96759],(drephalys helixus[&&NHX:TOL=96760],drephalys kidonoi[&&NHX:TOL=96762])[&&NHX:TOL=96777],drephalys alcmon[&&NHX:TOL=96758],drephalys heraclides[&&NHX:TOL=96761],drephalys miersi[&&NHX:TOL=96763],drephalys mourei[&&NHX:TOL=96764],drephalys olva[&&NHX:TOL=96765],drephalys olvina[&&NHX:TOL=96766],drephalys opifex[&&NHX:TOL=96767],drephalys phoenice[&&NHX:TOL=96768],drephalys phoenicoides[&&NHX:TOL=96769])subgenus drephalys[&&NHX:TOL=96776],(drephalys dumeril[&&NHX:TOL=96771],drephalys croceus[&&NHX:TOL=96770],drephalys oria[&&NHX:TOL=96772],drephalys oriander[&&NHX:TOL=96773],drephalys talboti[&&NHX:TOL=96774],drephalys tortus[&&NHX:TOL=96775])subgenus paradrephalys[&&NHX:TOL=96778])drephalys[&&NHX:TOL=95289],(udranomia eurus[&&NHX:TOL=100514],udranomia kikkawai[&&NHX:TOL=100515],udranomia orcinus[&&NHX:TOL=100516],udranomia spitzi[&&NHX:TOL=100517])udranomia[&&NHX:TOL=95322])[&&NHX:TOL=138298],(hyalothyrus infernalis[&&NHX:TOL=96825],hyalothyrus leucomelas[&&NHX:TOL=96826],hyalothyrus mimicus[&&NHX:TOL=96827],hyalothyrus neleus[&&NHX:TOL=96828],hyalothyrus nitocris[&&NHX:TOL=96829])hyalothyrus[&&NHX:TOL=95295],(augiades crinsius[&&NHX:TOL=96668],augiades epimethea[&&NHX:TOL=96669])augiades[&&NHX:TOL=95277],cabirus procas[&&NHX:TOL=95282],(entheus crux[&&NHX:TOL=96791],(entheus eumelus[&&NHX:TOL=96793],entheus ninyas[&&NHX:TOL=96799],entheus eunyas[&&NHX:TOL=96794])[&&NHX:TOL=96802],(entheus gentius[&&NHX:TOL=96795],entheus bombus[&&NHX:TOL=96790],entheus aureolus[&&NHX:TOL=96789])[&&NHX:TOL=96803],entheus lemna[&&NHX:TOL=96797],entheus matho[&&NHX:TOL=96798],((entheus priassus[&&NHX:TOL=96800],entheus curvus[&&NHX:TOL=96792])[&&NHX:TOL=96805],(entheus telemus[&&NHX:TOL=96801],entheus latebrosus[&&NHX:TOL=96796])[&&NHX:TOL=96806],entheus aureanota[&&NHX:TOL=96788])[&&NHX:TOL=96804])entheus[&&NHX:TOL=95292],(phanus albiapicalis[&&NHX:TOL=96861],phanus australis[&&NHX:TOL=96862],phanus confusis[&&NHX:TOL=96863],phanus ecitonorum[&&NHX:TOL=96864],phanus grandis[&&NHX:TOL=96865],phanus marshalli[&&NHX:TOL=96866],phanus obscurior[&&NHX:TOL=96867],phanus rilma[&&NHX:TOL=96868],phanus vitreus[&&NHX:TOL=96869])phanus[&&NHX:TOL=95306],phareas coeleste[&&NHX:TOL=95307],(tarsoctenus corytus[&&NHX:TOL=96955],tarsoctenus papias[&&NHX:TOL=96956],tarsoctenus praecia[&&NHX:TOL=96957])tarsoctenus[&&NHX:TOL=95317])[&&NHX:TOL=138297],((((bungalotis astylos[&&NHX:TOL=96683],bungalotis aureus[&&NHX:TOL=138320],bungalotis milleri[&&NHX:TOL=96690],bungalotis midas[&&NHX:TOL=96689])bungalotis midas group[&&NHX:TOL=138319],(bungalotis borax[&&NHX:TOL=96684],bungalotis lactos[&&NHX:TOL=138322])[&&NHX:TOL=138321],bungalotis clusia[&&NHX:TOL=96685],bungalotis diophorus[&&NHX:TOL=96686],bungalotis erythus[&&NHX:TOL=96687],bungalotis gagarini[&&NHX:TOL=96688],bungalotis quadratum[&&NHX:TOL=96691],bungalotis sipa[&&NHX:TOL=96692])bungalotis[&&NHX:TOL=95280],nicephellus nicephorus[&&NHX:TOL=96783],(salatis canalis[&&NHX:TOL=96940],salatis cebrenus[&&NHX:TOL=96941],salatis flavomarginatus[&&NHX:TOL=96942],salatis fulvius[&&NHX:TOL=96943],salatis salatis[&&NHX:TOL=96944],salatis sapucayae[&&NHX:TOL=96945],salatis scyrus[&&NHX:TOL=96946])salatis[&&NHX:TOL=95314])[&&NHX:TOL=138327],((ocyba calathana[&&NHX:TOL=95302],(porphyrogenes boliva[&&NHX:TOL=96904],porphyrogenes convexus[&&NHX:TOL=130784],porphyrogenes despecta[&&NHX:TOL=96905],porphyrogenes ferruginea[&&NHX:TOL=130785],porphyrogenes glavia[&&NHX:TOL=96906],porphyrogenes omphale[&&NHX:TOL=130786],porphyrogenes passalus[&&NHX:TOL=96907],porphyrogenes pausias[&&NHX:TOL=96908],porphyrogenes probus[&&NHX:TOL=96909],porphyrogenes simulator[&&NHX:TOL=130787],porphyrogenes sororcula[&&NHX:TOL=96910],porphyrogenes spadix[&&NHX:TOL=130788],porphyrogenes spanda[&&NHX:TOL=96911],porphyrogenes sparta[&&NHX:TOL=96912],porphyrogenes sparus[&&NHX:TOL=130789],porphyrogenes speciosus[&&NHX:TOL=130790],porphyrogenes specularis[&&NHX:TOL=130791],porphyrogenes spina[&&NHX:TOL=130792],porphyrogenes splendidus[&&NHX:TOL=130793],porphyrogenes spoda[&&NHX:TOL=96913],porphyrogenes sporta[&&NHX:TOL=130794],porphyrogenes stresa[&&NHX:TOL=130795],porphyrogenes stupa[&&NHX:TOL=96914],porphyrogenes sula[&&NHX:TOL=130796],porphyrogenes vulpecula[&&NHX:TOL=96916],porphyrogenes zohra[&&NHX:TOL=96917],porphyrogenes n. sp.[&&NHX:TOL=130797])porphyrogenes[&&NHX:TOL=95311])[&&NHX:TOL=138309],((oileides amazonensis[&&NHX:TOL=96857],oileides azines[&&NHX:TOL=96858],oileides fenestratus[&&NHX:TOL=96859],oileides vulpinus[&&NHX:TOL=96860])oileides[&&NHX:TOL=95304],aurina dida[&&NHX:TOL=95278])[&&NHX:TOL=138316])[&&NHX:TOL=138311],(sarmientoia almeidai[&&NHX:TOL=96947],sarmientoia browni[&&NHX:TOL=96948],sarmientoia dinka[&&NHX:TOL=96949],sarmientoia eriopis[&&NHX:TOL=96950],sarmientoia faustinus[&&NHX:TOL=96951],sarmientoia haywardi[&&NHX:TOL=96952],sarmientoia phaselis[&&NHX:TOL=96953],sarmientoia similis[&&NHX:TOL=96954])sarmientoia[&&NHX:TOL=95315])[&&NHX:TOL=138299])[&&NHX:TOL=138296],((polygonus leo[&&NHX:TOL=96888],polygonus savigny[&&NHX:TOL=96889])polygonus[&&NHX:TOL=95309],(telemiades amphion[&&NHX:TOL=100479],telemiades antiope[&&NHX:TOL=100480],telemiades avitus[&&NHX:TOL=100481],telemiades centrites[&&NHX:TOL=100482],telemiades choricus[&&NHX:TOL=100483],telemiades delalande[&&NHX:TOL=100484],telemiades epicalus[&&NHX:TOL=100485],telemiades laogonus[&&NHX:TOL=100486],telemiades litanicus[&&NHX:TOL=100487],telemiades megallus[&&NHX:TOL=100488],telemiades meris[&&NHX:TOL=100489],telemiades nicomedes[&&NHX:TOL=100490],telemiades penidas[&&NHX:TOL=100491],telemiades sila[&&NHX:TOL=100492],telemiades squanda[&&NHX:TOL=100493],telemiades trenda[&&NHX:TOL=100494],telemiades vansa[&&NHX:TOL=100495],telemiades vespasius[&&NHX:TOL=100496],telemiades corbulo[&&NHX:TOL=101560],telemiades oiclus[&&NHX:TOL=101561],telemiades gallius[&&NHX:TOL=101562],telemiades chrysorrhoea[&&NHX:TOL=101563])telemiades[&&NHX:TOL=95318])[&&NHX:TOL=138300])[&&NHX:TOL=138295],(((phocides belus[&&NHX:TOL=96870],phocides charon[&&NHX:TOL=96871],phocides distans[&&NHX:TOL=96872],phocides johnsoni[&&NHX:TOL=96873],phocides lincea[&&NHX:TOL=96874],phocides metrodorus[&&NHX:TOL=96875],phocides novalis[&&NHX:TOL=96876],phocides oreides[&&NHX:TOL=96877],phocides padrona[&&NHX:TOL=96878],phocides partia[&&NHX:TOL=96879],phocides perillus[&&NHX:TOL=96880],phocides pialia[&&NHX:TOL=96881],phocides pigmalion[&&NHX:TOL=96882],phocides polybius[&&NHX:TOL=96883],phocides thermus[&&NHX:TOL=96884],phocides urania[&&NHX:TOL=96885],phocides vulcanides[&&NHX:TOL=96886],phocides yokhara[&&NHX:TOL=96887])phocides[&&NHX:TOL=95308],hypocryptothrix teutas[&&NHX:TOL=95296])[&&NHX:TOL=138310],((nascus broteas[&&NHX:TOL=96849],nascus phintias[&&NHX:TOL=96851],nascus phocus[&&NHX:TOL=96852],nascus prax[&&NHX:TOL=96853],nascus solon[&&NHX:TOL=96854])nascus[&&NHX:TOL=95300],pseudonascus paulliniae[&&NHX:TOL=96850])[&&NHX:TOL=138328])[&&NHX:TOL=138302])[&&NHX:TOL=138313],(((dyscophellus diaphorus[&&NHX:TOL=96779],dyscophellus erythras[&&NHX:TOL=96780],dyscophellus marian[&&NHX:TOL=96782],dyscophellus mielkei[&&NHX:TOL=138324],dyscophellus phraxanor[&&NHX:TOL=96784],dyscophellus porcius[&&NHX:TOL=96785],dyscophellus porsena[&&NHX:TOL=138325],dyscophellus ramon[&&NHX:TOL=138326],dyscophellus ramusis[&&NHX:TOL=96786],dyscophellus sebaldus[&&NHX:TOL=96787])dyscophellus[&&NHX:TOL=95290],euriphellus euribates[&&NHX:TOL=96781])[&&NHX:TOL=138323],(((cogia abdul[&&NHX:TOL=96743],cogia aventinus[&&NHX:TOL=96744],cogia azila[&&NHX:TOL=96745],cogia caicus[&&NHX:TOL=96746],cogia cajeta[&&NHX:TOL=96747],cogia calchas[&&NHX:TOL=96748],cogia cerradicola[&&NHX:TOL=96749],cogia elaites[&&NHX:TOL=96750],cogia grandis[&&NHX:TOL=96751],cogia hassan[&&NHX:TOL=96752],cogia hippalus[&&NHX:TOL=96753],cogia mala[&&NHX:TOL=96754],cogia outis[&&NHX:TOL=96755],cogia punctilia[&&NHX:TOL=96756],cogia troilus[&&NHX:TOL=96757])cogia[&&NHX:TOL=95288],paracogia acanthopoda[&&NHX:TOL=95305])[&&NHX:TOL=138318],(marela tamyris[&&NHX:TOL=96835],marela tamyroides[&&NHX:TOL=96836])marela[&&NHX:TOL=95298],oechydrus chersis[&&NHX:TOL=95303],(nerula fibrena[&&NHX:TOL=96855],nerula tuba[&&NHX:TOL=96856])nerula[&&NHX:TOL=95301])[&&NHX:TOL=138317])[&&NHX:TOL=138301])[&&NHX:TOL=138312],(cephise aelius[&&NHX:TOL=96697],cephise burnsi[&&NHX:TOL=96698],cephise callias[&&NHX:TOL=96699],cephise cephise[&&NHX:TOL=96700],cephise glarus[&&NHX:TOL=96701],cephise guatemalensis[&&NHX:TOL=96702],cephise impunctus[&&NHX:TOL=96703],cephise maculatus[&&NHX:TOL=96704],cephise malesedis[&&NHX:TOL=96705],cephise mexicanus[&&NHX:TOL=96706],cephise nuspesez[&&NHX:TOL=96707],cephise procerus[&&NHX:TOL=96708])cephise[&&NHX:TOL=95284],(chrysoplectrum albovenae[&&NHX:TOL=96719],chrysoplectrum bahiana[&&NHX:TOL=96720],chrysoplectrum cuminaensis[&&NHX:TOL=96721],chrysoplectrum epicincea[&&NHX:TOL=96722],chrysoplectrum orpheus[&&NHX:TOL=96723],chrysoplectrum orphne[&&NHX:TOL=96724],chrysoplectrum otriades[&&NHX:TOL=96725],chrysoplectrum perna[&&NHX:TOL=96726],chrysoplectrum perniciosus[&&NHX:TOL=96727],chrysoplectrum pervivax[&&NHX:TOL=96728])chrysoplectrum[&&NHX:TOL=95286],ectomis cythna[&&NHX:TOL=95291],(epargyreus antaeus[&&NHX:TOL=96807],epargyreus aspina[&&NHX:TOL=96808],epargyreus barisses[&&NHX:TOL=96809],epargyreus brodkorbi[&&NHX:TOL=96810],epargyreus clarus[&&NHX:TOL=96811],epargyreus clavicornis[&&NHX:TOL=96812],epargyreus deleoni[&&NHX:TOL=96813],epargyreus enispe[&&NHX:TOL=96814],epargyreus exadeus[&&NHX:TOL=96815],epargyreus nutra[&&NHX:TOL=96816],epargyreus socus[&&NHX:TOL=96817],epargyreus spanna[&&NHX:TOL=96818],epargyreus spina[&&NHX:TOL=96819],epargyreus spinosa[&&NHX:TOL=96820],epargyreus spinta[&&NHX:TOL=96821],epargyreus tmolis[&&NHX:TOL=96822],epargyreus windi[&&NHX:TOL=96823],epargyreus zestos[&&NHX:TOL=96824])epargyreus[&&NHX:TOL=95293],heronia labriaris[&&NHX:TOL=95294],(polythrix asine[&&NHX:TOL=96890],polythrix auginus[&&NHX:TOL=96891],polythrix caunus[&&NHX:TOL=96892],polythrix ceculus[&&NHX:TOL=96893],polythrix eudoxus[&&NHX:TOL=96894],polythrix gyges[&&NHX:TOL=96895],polythrix hirtius[&&NHX:TOL=96896],polythrix kanshul[&&NHX:TOL=96897],polythrix maizae[&&NHX:TOL=96898],polythrix metallescens[&&NHX:TOL=96899],polythrix mexicanus[&&NHX:TOL=96900],polythrix minvanes[&&NHX:TOL=96901],polythrix octomaculata[&&NHX:TOL=96902],polythrix roma[&&NHX:TOL=96903])polythrix[&&NHX:TOL=95310],(ridens allyni[&&NHX:TOL=96920],ridens bidens[&&NHX:TOL=96921],ridens biolleyi[&&NHX:TOL=96922],ridens bridgmani[&&NHX:TOL=96923],ridens crison[&&NHX:TOL=96924],ridens fieldi[&&NHX:TOL=96925],ridens fulima[&&NHX:TOL=96926],ridens fulminans[&&NHX:TOL=96927],ridens harpagus[&&NHX:TOL=96928],ridens mephitis[&&NHX:TOL=96929],ridens mercedes[&&NHX:TOL=96930],ridens miltas[&&NHX:TOL=96931],ridens nora[&&NHX:TOL=96932],ridens pacasa[&&NHX:TOL=96933],ridens panche[&&NHX:TOL=96934],ridens philistus[&&NHX:TOL=96935],ridens ridens[&&NHX:TOL=96936],ridens telegonoides[&&NHX:TOL=96937],ridens toddi[&&NHX:TOL=96938],ridens tristis[&&NHX:TOL=96939])ridens[&&NHX:TOL=95313],(thessia athesis[&&NHX:TOL=96958],thessia jalapus[&&NHX:TOL=96959])thessia[&&NHX:TOL=95319],(venada advena[&&NHX:TOL=100553],venada cacao[&&NHX:TOL=100554],venada daneva[&&NHX:TOL=100555],venada naranja[&&NHX:TOL=100556],venada nevada[&&NHX:TOL=100557])venada[&&NHX:TOL=95324])eudaminae[&&NHX:TOL=95266],((((((cyclopyge roscius[&&NHX:TOL=94270],(oxynetra confusa[&&NHX:TOL=94333],oxynetra hopfferi[&&NHX:TOL=94334],oxynetra semihyalina[&&NHX:TOL=94335])oxynetra[&&NHX:TOL=94271])oxynetrina[&&NHX:TOL=94266],((aspitha agenoria[&&NHX:TOL=94336],aspitha aspitha[&&NHX:TOL=94337],aspitha bassleri[&&NHX:TOL=94338],aspitha leander[&&NHX:TOL=94339])aspitha[&&NHX:TOL=94272],azonax typhaon[&&NHX:TOL=94273],granila paseas[&&NHX:TOL=94274],(myscelus amystis[&&NHX:TOL=94340],myscelus assaricus[&&NHX:TOL=94341],myscelus belti[&&NHX:TOL=94342],myscelus draudti[&&NHX:TOL=94343],myscelus epimachia[&&NHX:TOL=94344],myscelus nobilis[&&NHX:TOL=94345],myscelus pardalina[&&NHX:TOL=94346],myscelus pegasus[&&NHX:TOL=94347],myscelus perissodora[&&NHX:TOL=94348],myscelus phoronis[&&NHX:TOL=94349],myscelus santhilarius[&&NHX:TOL=94350])myscelus[&&NHX:TOL=94275],(passova ganymedes[&&NHX:TOL=94351],passova gazera[&&NHX:TOL=94352],passova gellias[&&NHX:TOL=94353],passova glacia[&&NHX:TOL=94354],passova greta[&&NHX:TOL=94355],passova nigrocephala[&&NHX:TOL=94356],passova passova[&&NHX:TOL=94357],passova polemon[&&NHX:TOL=94358],passova vilna[&&NHX:TOL=94359])passova[&&NHX:TOL=94276])passovina[&&NHX:TOL=94267],(amenis pionia[&&NHX:TOL=94277],amysoria galgala[&&NHX:TOL=94278],((apyrrothrix araxes[&&NHX:TOL=94360],apyrrothrix arizonae[&&NHX:TOL=94361])apyrrhothrix[&&NHX:TOL=94279],creonpyge creon[&&NHX:TOL=94282])[&&NHX:TOL=138329],ardaris eximia[&&NHX:TOL=94280],(chalypyge chalybea[&&NHX:TOL=94362],chalypyge zereda[&&NHX:TOL=94363])chalypyge[&&NHX:TOL=94281],croniades pieria[&&NHX:TOL=94283],cyanopyge sangaris[&&NHX:TOL=94284],((elbella adonis[&&NHX:TOL=94364],elbella azeta[&&NHX:TOL=94365],elbella bicuspis[&&NHX:TOL=94366],elbella blanda[&&NHX:TOL=94367],elbella dulcinea[&&NHX:TOL=94368],elbella etna[&&NHX:TOL=94369],elbella hegesippe[&&NHX:TOL=94370],elbella intersecta[&&NHX:TOL=94371],elbella iphinous[&&NHX:TOL=94372],elbella lamprus[&&NHX:TOL=94373],elbella lustra[&&NHX:TOL=94374],elbella luteizona[&&NHX:TOL=94375],elbella madeira[&&NHX:TOL=94376],elbella mariae[&&NHX:TOL=94377],elbella merops[&&NHX:TOL=94378],elbella miodesmiata[&&NHX:TOL=94379],elbella patrobas[&&NHX:TOL=94380],elbella patroclus[&&NHX:TOL=94381],elbella rondonia[&&NHX:TOL=94382],elbella scylla[&&NHX:TOL=94383],elbella theseus[&&NHX:TOL=94384],elbella viriditas[&&NHX:TOL=94385])elbella[&&NHX:TOL=94285],(parelbella ahira[&&NHX:TOL=94426],parelbella macleannani[&&NHX:TOL=94427],parelbella peruana[&&NHX:TOL=94428],parelbella polyzona[&&NHX:TOL=94429],parelbella nigra[&&NHX:TOL=120465])parelbella[&&NHX:TOL=94298])[&&NHX:TOL=138330],(gunayan rhacia[&&NHX:TOL=94388],gunayan rubricollis[&&NHX:TOL=94389],gunayan timaeus[&&NHX:TOL=94390])gunayan[&&NHX:TOL=94286],(jemadia brevipennis[&&NHX:TOL=94391],jemadia fallax[&&NHX:TOL=94392],jemadia gnetus[&&NHX:TOL=94393],jemadia hewitsonii[&&NHX:TOL=94394],jemadia hospita[&&NHX:TOL=94395],jemadia menechmus[&&NHX:TOL=94396],jemadia pater[&&NHX:TOL=94397],jemadia pseudognetus[&&NHX:TOL=94398],jemadia scomber[&&NHX:TOL=94399],jemadia sosia[&&NHX:TOL=94400])jemadia[&&NHX:TOL=94287],(jonaspyge aesculapus[&&NHX:TOL=94401],jonaspyge jonas[&&NHX:TOL=94402],jonaspyge tzotzili[&&NHX:TOL=94403])jonaspyge[&&NHX:TOL=94288],(melanopyge cossea[&&NHX:TOL=94404],melanopyge erythrosticta[&&NHX:TOL=94405],melanopyge hoffmanni[&&NHX:TOL=94406],melanopyge maculosa[&&NHX:TOL=94407],melanopyge mulleri[&&NHX:TOL=94408])melanopyge[&&NHX:TOL=94289],metardaris cosinga[&&NHX:TOL=94290],microceris variicolor[&&NHX:TOL=94291],(mimardaris aerata[&&NHX:TOL=94409],mimardaris lomax[&&NHX:TOL=94410],mimardaris minthe[&&NHX:TOL=94411],mimardaris pityusa[&&NHX:TOL=94412],mimardaris porus[&&NHX:TOL=94413],mimardaris sela[&&NHX:TOL=94414],mimardaris montra[&&NHX:TOL=94415])mimardaris[&&NHX:TOL=94292],(mimoniades baroni[&&NHX:TOL=94417],mimoniades montana[&&NHX:TOL=94418],mimoniades nurscia[&&NHX:TOL=94419],mimoniades ocyalus[&&NHX:TOL=94420],mimoniades versicolor[&&NHX:TOL=94421])mimoniades[&&NHX:TOL=94293],mysarbia sejanus[&&NHX:TOL=94294],((mysoria affinis[&&NHX:TOL=94422],mysoria amra[&&NHX:TOL=94423],mysoria barcastus[&&NHX:TOL=94424],mysoria wilsoni[&&NHX:TOL=94425])mysoria[&&NHX:TOL=94295],(sarbia antias[&&NHX:TOL=94468],sarbia catomelaena[&&NHX:TOL=94469],sarbia curitiba[&&NHX:TOL=94470],sarbia damippe[&&NHX:TOL=94471],sarbia oneka[&&NHX:TOL=94472],sarbia pertyi[&&NHX:TOL=94473],sarbia soza[&&NHX:TOL=94474],sarbia xanthippe[&&NHX:TOL=94475])sarbia[&&NHX:TOL=94302])[&&NHX:TOL=138331],nosphistia zonara[&&NHX:TOL=94296],ochropyge ruficauda[&&NHX:TOL=94297],pseudocroniades machaon[&&NHX:TOL=94299],protelbella alburna[&&NHX:TOL=94300],(pyrrhopyge amyclas[&&NHX:TOL=94430],pyrrhopyge amythaon[&&NHX:TOL=94431],pyrrhopyge arax[&&NHX:TOL=94432],pyrrhopyge arinas[&&NHX:TOL=94433],pyrrhopyge aziza[&&NHX:TOL=94434],pyrrhopyge boulleti[&&NHX:TOL=94435],pyrrhopyge charybdis[&&NHX:TOL=94436],pyrrhopyge creona[&&NHX:TOL=94437],pyrrhopyge cressoni[&&NHX:TOL=94438],pyrrhopyge creusae[&&NHX:TOL=94439],pyrrhopyge crida[&&NHX:TOL=94440],pyrrhopyge crista[&&NHX:TOL=94441],pyrrhopyge decipiens[&&NHX:TOL=94442],pyrrhopyge frona[&&NHX:TOL=94443],pyrrhopyge hadassa[&&NHX:TOL=94444],pyrrhopyge haemon[&&NHX:TOL=94445],pyrrhopyge infantilis[&&NHX:TOL=94446],pyrrhopyge kelita[&&NHX:TOL=94447],pyrrhopyge martena[&&NHX:TOL=94448],pyrrhopyge melanomerus[&&NHX:TOL=94449],pyrrhopyge mopsus[&&NHX:TOL=94450],pyrrhopyge papius[&&NHX:TOL=94451],pyrrhopyge pelota[&&NHX:TOL=94452],pyrrhopyge phidias[&&NHX:TOL=94453],pyrrhopyge phylleia[&&NHX:TOL=94454],pyrrhopyge placeta[&&NHX:TOL=94455],pyrrhopyge proculus[&&NHX:TOL=94456],pyrrhopyge punctata[&&NHX:TOL=94457],pyrrhopyge pusca[&&NHX:TOL=94458],pyrrhopyge sadia[&&NHX:TOL=94459],pyrrhopyge sarpedon[&&NHX:TOL=94460],pyrrhopyge schausi[&&NHX:TOL=94461],pyrrhopyge sergius[&&NHX:TOL=94462],pyrrhopyge tatei[&&NHX:TOL=94463],pyrrhopyge telassa[&&NHX:TOL=94464],pyrrhopyge telassina[&&NHX:TOL=94465],pyrrhopyge terra[&&NHX:TOL=94466],pyrrhopyge thericles[&&NHX:TOL=94467])pyrrhopyge[&&NHX:TOL=94301],(yanguna cometes[&&NHX:TOL=94476],yanguna cosyra[&&NHX:TOL=94477],yanguna erebus[&&NHX:TOL=94478],yanguna spatiosa[&&NHX:TOL=94479],yanguna tetricus[&&NHX:TOL=94480],yanguna thelersa[&&NHX:TOL=94481])yanguna[&&NHX:TOL=94303])pyrrhopygina[&&NHX:TOL=94268],zonia zonia[&&NHX:TOL=94269])pyrrhopygini[&&NHX:TOL=12151],((abraximorpha davidii[&&NHX:TOL=103050],abraximorpha esta[&&NHX:TOL=103051],abraximorpha heringi[&&NHX:TOL=103052],abraximorpha pieridoides[&&NHX:TOL=103053])abraximorpha[&&NHX:TOL=95327],(calleagris hollandi[&&NHX:TOL=102120],calleagris jamesoni[&&NHX:TOL=102121],calleagris kobela[&&NHX:TOL=102122],calleagris kroomi[&&NHX:TOL=102123],calleagris lacteus[&&NHX:TOL=102124],calleagris landbecki[&&NHX:TOL=102125])calleagris[&&NHX:TOL=95328],(capila hainana[&&NHX:TOL=102996],capila jayadeva[&&NHX:TOL=102997],capila lidderdali[&&NHX:TOL=102998],capila lineata[&&NHX:TOL=102999],capila nigrilima[&&NHX:TOL=103000],capila omeia[&&NHX:TOL=103001],capila pauripunetana[&&NHX:TOL=103002],capila pennicillatum[&&NHX:TOL=103003],capila phanaeus[&&NHX:TOL=103004],capila pieridoides[&&NHX:TOL=103005],capila translucida[&&NHX:TOL=103006],capila zennara[&&NHX:TOL=103007])capila[&&NHX:TOL=95329],(chaetocneme antipodes[&&NHX:TOL=102459],chaetocneme beata[&&NHX:TOL=102460],chaetocneme callixenus[&&NHX:TOL=102461],chaetocneme caristus[&&NHX:TOL=102462],chaetocneme critomedia[&&NHX:TOL=102463],chaetocneme denitza[&&NHX:TOL=102464],chaetocneme editus[&&NHX:TOL=102465],chaetocneme helirius[&&NHX:TOL=102466],chaetocneme lunula[&&NHX:TOL=102467],chaetocneme morea[&&NHX:TOL=102468],chaetocneme naevifera[&&NHX:TOL=102469],chaetocneme porphyropis[&&NHX:TOL=102470],chaetocneme sphintifera[&&NHX:TOL=102471],chaetocneme sombra[&&NHX:TOL=102472],chaetocneme tenuis[&&NHX:TOL=102473],chaetocneme trifenestrata[&&NHX:TOL=102474],chaetocneme triton[&&NHX:TOL=102475],3 undescribed species[&&NHX:TOL=102476])chaetocneme[&&NHX:TOL=95331],chamunda chamunda[&&NHX:TOL=95332],((coladenia agni[&&NHX:TOL=103029],coladenia agnioides[&&NHX:TOL=103030],coladenia buchananii[&&NHX:TOL=103031],coladenia hoenei[&&NHX:TOL=103032],coladenia indrani[&&NHX:TOL=103034],coladenia laxmi[&&NHX:TOL=103036],coladenia maeniata[&&NHX:TOL=103037],coladenia nankoshana[&&NHX:TOL=103039],coladenia sheila[&&NHX:TOL=103043],coladenia tanya[&&NHX:TOL=103045],coladenia uemurai[&&NHX:TOL=103046],coladenia vitrea[&&NHX:TOL=103047],(coladenia igna[&&NHX:TOL=103033],coladenia ochracea[&&NHX:TOL=103040])[&&NHX:TOL=124853])[&&NHX:TOL=124852],((coladenia minor[&&NHX:TOL=103038],coladenia similis[&&NHX:TOL=103044])[&&NHX:TOL=124855],(coladenia kehelatha[&&NHX:TOL=103035],coladenia palawana[&&NHX:TOL=103041],coladenia semperi[&&NHX:TOL=103042])[&&NHX:TOL=124856])[&&NHX:TOL=124854])coladenia[&&NHX:TOL=95333],((abantis bamptoni[&&NHX:TOL=102135],abantis bicolor[&&NHX:TOL=102136],abantis bismarcki[&&NHX:TOL=102137],abantis contigua[&&NHX:TOL=102138],abantis efulensis[&&NHX:TOL=102139],abantis elegantula[&&NHX:TOL=102140],abantis eltringhami[&&NHX:TOL=102141],abantis ja[&&NHX:TOL=102142],abantis leucogaster[&&NHX:TOL=102143],abantis lucretia[&&NHX:TOL=102144],abantis maesseni[&&NHX:TOL=102145],abantis meneliki[&&NHX:TOL=102146],abantis meru[&&NHX:TOL=102147],abantis nigeriana[&&NHX:TOL=102148],abantis paradisea[&&NHX:TOL=102149],abantis pseudonigeriana[&&NHX:TOL=102150],abantis rubra[&&NHX:TOL=102151],abantis tettensis[&&NHX:TOL=102152],abantis venosa[&&NHX:TOL=102153],abantis vidua[&&NHX:TOL=102154],abantis zambesiaca[&&NHX:TOL=102155],abantis tanobia[&&NHX:TOL=118914])abantis[&&NHX:TOL=95326],(caprona adelica[&&NHX:TOL=102126],caprona agama[&&NHX:TOL=102127],caprona alida[&&NHX:TOL=102128],caprona cassualalla[&&NHX:TOL=102129],caprona pillaana[&&NHX:TOL=102130],caprona ransonnetii[&&NHX:TOL=102131])caprona[&&NHX:TOL=95330],(ctenoptilum multiguttata[&&NHX:TOL=103048],ctenoptilum vasava[&&NHX:TOL=103049])ctenoptilum[&&NHX:TOL=95334],(leucochitonea amneris[&&NHX:TOL=102132],leucochitonea hindei[&&NHX:TOL=102133],leucochitonea levubu[&&NHX:TOL=102134])leucochitonea[&&NHX:TOL=95340],netrobalane canopus[&&NHX:TOL=95342],((odontoptilum angulata[&&NHX:TOL=102991],(odontoptilum abbreviata[&&NHX:TOL=107292],odontoptilum corria[&&NHX:TOL=107293],odontoptilum helias[&&NHX:TOL=102992])[&&NHX:TOL=107291])[&&NHX:TOL=107290],odontoptilum pygela[&&NHX:TOL=102993])odontoptilum[&&NHX:TOL=95345],semperium leptogramma[&&NHX:TOL=107294],(tagiades calligana[&&NHX:TOL=102092],tagiades cohaerens[&&NHX:TOL=102093],tagiades distans[&&NHX:TOL=102094],tagiades flesus[&&NHX:TOL=102095],tagiades gana[&&NHX:TOL=102096],tagiades hybridus[&&NHX:TOL=102097],tagiades insularis[&&NHX:TOL=102098],tagiades japetus[&&NHX:TOL=102099],tagiades lavata[&&NHX:TOL=102100],tagiades litigiosus[&&NHX:TOL=102101],tagiades menaka[&&NHX:TOL=102102],tagiades nestus[&&NHX:TOL=102103],tagiades obscurus[&&NHX:TOL=102104],tagiades parra[&&NHX:TOL=102105],tagiades saborana[&&NHX:TOL=102106],tagiades toba[&&NHX:TOL=102107],tagiades trebellius[&&NHX:TOL=102108],tagiades ultra[&&NHX:TOL=102109],tagiades waterstradti[&&NHX:TOL=102110])tagiades[&&NHX:TOL=95350])tagiades group[&&NHX:TOL=107289],daimio tethys[&&NHX:TOL=95335],(darpa hanria[&&NHX:TOL=103022],darpa inopinata[&&NHX:TOL=103023],darpa pteria[&&NHX:TOL=103024],darpa striata[&&NHX:TOL=103025])darpa[&&NHX:TOL=95336],(eagris decastigma[&&NHX:TOL=102111],eagris denuba[&&NHX:TOL=102112],eagris hereus[&&NHX:TOL=102113],eagris lucetia[&&NHX:TOL=102114],eagris nottoana[&&NHX:TOL=102115],eagris sabadius[&&NHX:TOL=102116],eagris subalbida[&&NHX:TOL=102117],eagris tetrastigma[&&NHX:TOL=102118],eagris tigris[&&NHX:TOL=102119])eagris[&&NHX:TOL=95337],exometoeca nycteris[&&NHX:TOL=95338],(gerosis bhagava[&&NHX:TOL=102983],gerosis celebica[&&NHX:TOL=102984],gerosis corona[&&NHX:TOL=102985],gerosis limax[&&NHX:TOL=102986],gerosis phisara[&&NHX:TOL=102987],gerosis sinica[&&NHX:TOL=102988],gerosis tristis[&&NHX:TOL=102989],gerosis yuani[&&NHX:TOL=102990])gerosis[&&NHX:TOL=95339],(mooreana princeps[&&NHX:TOL=102994],mooreana trichoneura[&&NHX:TOL=102995])mooreana[&&NHX:TOL=95341],(netrocoryne repanda[&&NHX:TOL=102477],netrocoryne thaddeus[&&NHX:TOL=102478])netrocoryne[&&NHX:TOL=95343],((odina chrysomelaena[&&NHX:TOL=103026],odina cuneiformis[&&NHX:TOL=124851],odina hieroglyphica[&&NHX:TOL=103028])[&&NHX:TOL=124850],odina decoratus[&&NHX:TOL=103027])odina[&&NHX:TOL=95344],(pintara bowringi[&&NHX:TOL=103018],pintara capiloides[&&NHX:TOL=103019],pintara pinwilli[&&NHX:TOL=103020],pintara tabrica[&&NHX:TOL=103021])pintara[&&NHX:TOL=95346],procampta rara[&&NHX:TOL=95347],(satarupa formosibia[&&NHX:TOL=103008],satarupa gopala[&&NHX:TOL=103009],satarupa monbeigi[&&NHX:TOL=103010],satarupa nymphalis[&&NHX:TOL=103011],satarupa splendens[&&NHX:TOL=103012])satarupa[&&NHX:TOL=95348],(seseria affinis[&&NHX:TOL=103013],seseria dohertyi[&&NHX:TOL=103014],seseria formosana[&&NHX:TOL=103015],seseria sambara[&&NHX:TOL=103016],seseria strigata[&&NHX:TOL=103017])seseria[&&NHX:TOL=95349],tapena thwaitesi[&&NHX:TOL=95351])tagiadini[&&NHX:TOL=95264])[&&NHX:TOL=95269],((alenia namaqua[&&NHX:TOL=101276],alenia sandaster[&&NHX:TOL=101277])alenia[&&NHX:TOL=95352],(((celaenorrhinus ambra[&&NHX:TOL=101317],celaenorrhinus ankasa[&&NHX:TOL=118906],celaenorrhinus bakolo[&&NHX:TOL=101318],celaenorrhinus beni[&&NHX:TOL=101319],celaenorrhinus bettoni[&&NHX:TOL=101320],celaenorrhinus bitjena[&&NHX:TOL=101321],celaenorrhinus boadicea[&&NHX:TOL=101322],celaenorrhinus chrysoglossa[&&NHX:TOL=101323],celaenorrhinus dargei[&&NHX:TOL=101324],celaenorrhinus galenus[&&NHX:TOL=101325],celaenorrhinus hecqui[&&NHX:TOL=101326],celaenorrhinus homeyeri[&&NHX:TOL=101327],celaenorrhinus humbloti[&&NHX:TOL=101328],(celaenorrhinus illustris[&&NHX:TOL=101329],celaenorrhinus perlustris[&&NHX:TOL=101342])[&&NHX:TOL=118907],celaenorrhinus intermixtus[&&NHX:TOL=101331],celaenorrhinus kasai[&&NHX:TOL=101332],celaenorrhinus kimboza[&&NHX:TOL=101333],celaenorrhinus kivuensis[&&NHX:TOL=101334],celaenorrhinus leona[&&NHX:TOL=101335],celaenorrhinus lourentis[&&NHX:TOL=101336],celaenorrhinus macrostictus[&&NHX:TOL=101337],(celaenorrhinus meditrina[&&NHX:TOL=101338],celaenorrhinus ovalis[&&NHX:TOL=101341])[&&NHX:TOL=118908],celaenorrhinus milleri[&&NHX:TOL=118909],celaenorrhinus mokeezi[&&NHX:TOL=101339],celaenorrhinus nigropunctata[&&NHX:TOL=101340],celaenorrhinus nimba[&&NHX:TOL=118910],celaenorrhinus opalinus[&&NHX:TOL=118911],celaenorrhinus plagiatus[&&NHX:TOL=101343],celaenorrhinus pooanus[&&NHX:TOL=118912],celaenorrhinus proxima[&&NHX:TOL=101344],celaenorrhinus rubeho[&&NHX:TOL=101345],celaenorrhinus rutilans[&&NHX:TOL=101346],celaenorrhinus sagamase[&&NHX:TOL=118913],celaenorrhinus sanjeensis[&&NHX:TOL=101347],celaenorrhinus selysi[&&NHX:TOL=101348],celaenorrhinus suzannae[&&NHX:TOL=101349],celaenorrhinus uluguru[&&NHX:TOL=101350],celaenorrhinus zanqua[&&NHX:TOL=101351])afrotropical taxa[&&NHX:TOL=124788],(celaenorrhinus ambareesa[&&NHX:TOL=101352],celaenorrhinus asmara[&&NHX:TOL=101353],celaenorrhinus aspersa[&&NHX:TOL=101354],celaenorrhinus aurivittata[&&NHX:TOL=101355],celaenorrhinus bazilanus[&&NHX:TOL=124790],celaenorrhinus choui[&&NHX:TOL=101356],celaenorrhinus consanguinea[&&NHX:TOL=101357],celaenorrhinus dhanada[&&NHX:TOL=101358],celaenorrhinus ficulnea[&&NHX:TOL=101359],celaenorrhinus halconis[&&NHX:TOL=124791],celaenorrhinus horishanus[&&NHX:TOL=101360],celaenorrhinus inaequalis[&&NHX:TOL=101361],celaenorrhinus incestus[&&NHX:TOL=101362],celaenorrhinus inexspectus[&&NHX:TOL=101363],celaenorrhinus kuzsenovi[&&NHX:TOL=101364],celaenorrhinus ladana[&&NHX:TOL=101365],celaenorrhinus leucocera[&&NHX:TOL=101366],celaenorrhinus maculosa[&&NHX:TOL=101367],celaenorrhinus major[&&NHX:TOL=101368],celaenorrhinus munda[&&NHX:TOL=101369],celaenorrhinus nigricans[&&NHX:TOL=101370],celaenorrhinus oscula[&&NHX:TOL=101371],celaenorrhinus pahangensis[&&NHX:TOL=101372],celaenorrhinus patula[&&NHX:TOL=101373],celaenorrhinus pero[&&NHX:TOL=101374],celaenorrhinus phuongi[&&NHX:TOL=101375],celaenorrhinus pulomaya[&&NHX:TOL=101376],celaenorrhinus putra[&&NHX:TOL=101377],celaenorrhinus pyrrha[&&NHX:TOL=101378],celaenorrhinus ratna[&&NHX:TOL=101379],celaenorrhinus ruficornis[&&NHX:TOL=101380],celaenorrhinus spilothyrus[&&NHX:TOL=101381],celaenorrhinus sumitra[&&NHX:TOL=101382],celaenorrhinus tibetana[&&NHX:TOL=101383],celaenorrhinus treadawayi[&&NHX:TOL=124792],celaenorrhinus vietnamicus[&&NHX:TOL=101384],celaenorrhinus yaojiani[&&NHX:TOL=101385])tropical asian taxa[&&NHX:TOL=124789],(celaenorrhinus aegiochus[&&NHX:TOL=101386],celaenorrhinus anchialus[&&NHX:TOL=101387],celaenorrhinus approximatus[&&NHX:TOL=101388],celaenorrhinus astrigera[&&NHX:TOL=101389],celaenorrhinus autochton[&&NHX:TOL=101390],celaenorrhinus badia[&&NHX:TOL=101410],celaenorrhinus bifurcus[&&NHX:TOL=101391],celaenorrhinus cordeironis[&&NHX:TOL=102748],celaenorrhinus cynapes[&&NHX:TOL=101392],celaenorrhinus disjunctus[&&NHX:TOL=101393],celaenorrhinus eligius[&&NHX:TOL=101394],celaenorrhinus fritzgaertneri[&&NHX:TOL=101395],celaenorrhinus jao[&&NHX:TOL=101396],celaenorrhinus monartus[&&NHX:TOL=101397],celaenorrhinus morena[&&NHX:TOL=101411],celaenorrhinus orneates[&&NHX:TOL=101398],celaenorrhinus par[&&NHX:TOL=101399],celaenorrhinus savia[&&NHX:TOL=101400],celaenorrhinus shema[&&NHX:TOL=101401],celaenorrhinus similis[&&NHX:TOL=101402],celaenorrhinus songoensis[&&NHX:TOL=101403],celaenorrhinus stallingsi[&&NHX:TOL=101404],celaenorrhinus stola[&&NHX:TOL=101405],celaenorrhinus suthina[&&NHX:TOL=101406],celaenorrhinus syllius[&&NHX:TOL=101407],celaenorrhinus tritonae[&&NHX:TOL=101408],celaenorrhinus vagra[&&NHX:TOL=101409])neotropical taxa[&&NHX:TOL=124793])celaenorrhinus[&&NHX:TOL=95353],katreus johnstonii[&&NHX:TOL=95355])[&&NHX:TOL=102091],(((eretis buamba[&&NHX:TOL=101278],eretis camerona[&&NHX:TOL=101279],eretis djaelaelae[&&NHX:TOL=101280],eretis herewardi[&&NHX:TOL=101281],eretis lugens[&&NHX:TOL=101282],eretis melania[&&NHX:TOL=101283],eretis mitiana[&&NHX:TOL=101284],eretis mixta[&&NHX:TOL=101285],eretis plistonicus[&&NHX:TOL=101286],eretis umbra[&&NHX:TOL=101287],eretis vaga[&&NHX:TOL=101288])eretis[&&NHX:TOL=95354],(sarangesa astrigera[&&NHX:TOL=101289],sarangesa aza[&&NHX:TOL=101290],sarangesa bouvieri[&&NHX:TOL=101291],sarangesa brigida[&&NHX:TOL=101292],sarangesa dasahara[&&NHX:TOL=101293],sarangesa gaerdesi[&&NHX:TOL=101294],sarangesa haplopa[&&NHX:TOL=101295],sarangesa laelius[&&NHX:TOL=101296],sarangesa lucidella[&&NHX:TOL=101297],sarangesa lunula[&&NHX:TOL=101298],sarangesa maculata[&&NHX:TOL=101299],sarangesa majorella[&&NHX:TOL=101300],sarangesa maxima[&&NHX:TOL=101301],sarangesa motozi[&&NHX:TOL=101302],sarangesa motozioides[&&NHX:TOL=101303],sarangesa pandaensis[&&NHX:TOL=101304],sarangesa penningtoni[&&NHX:TOL=101305],sarangesa phidyle[&&NHX:TOL=101306],sarangesa princei[&&NHX:TOL=101307],sarangesa purendra[&&NHX:TOL=101308],sarangesa ruona[&&NHX:TOL=101309],sarangesa seineri[&&NHX:TOL=101310],sarangesa tertullianus[&&NHX:TOL=101311],sarangesa thecla[&&NHX:TOL=101312],sarangesa tricerata[&&NHX:TOL=101313])sarangesa[&&NHX:TOL=95358])[&&NHX:TOL=138333],(pseudocoladenia dan[&&NHX:TOL=101412],pseudocoladenia dea[&&NHX:TOL=101413],pseudocoladenia fatua[&&NHX:TOL=101414],pseudocoladenia festa[&&NHX:TOL=101415])pseudocoladenia[&&NHX:TOL=95357])[&&NHX:TOL=138332],(ortholexis hollandi[&&NHX:TOL=102089],ortholexis holocausta[&&NHX:TOL=101315],ortholexis dimidia[&&NHX:TOL=101314])ortholexis[&&NHX:TOL=95356])celaenorrhinini[&&NHX:TOL=95261])[&&NHX:TOL=95268],((((((antigonus corrosus[&&NHX:TOL=101116],antigonus decens[&&NHX:TOL=101117],antigonus emorsa[&&NHX:TOL=101118],antigonus erosus[&&NHX:TOL=101119],antigonus funebris[&&NHX:TOL=101120],antigonus liborius[&&NHX:TOL=101121],antigonus minor[&&NHX:TOL=101122],antigonus mutilatus[&&NHX:TOL=101123],antigonus nearchus[&&NHX:TOL=101124])antigonus[&&NHX:TOL=95420],(((systasea microsticta[&&NHX:TOL=101214],systasea pulverulenta[&&NHX:TOL=101215],systasea zampa[&&NHX:TOL=101216])systasea[&&NHX:TOL=95435],(zopyrion evenor[&&NHX:TOL=101222],zopyrion reticulata[&&NHX:TOL=101223],zopyrion sandace[&&NHX:TOL=101224],zopyrion satyrina[&&NHX:TOL=101225],zopyrion subvariegata[&&NHX:TOL=101226])zopyrion[&&NHX:TOL=95440])[&&NHX:TOL=138368],((((heliopetes alana[&&NHX:TOL=101140],heliopetes arsalte[&&NHX:TOL=101141],heliopetes chimbo[&&NHX:TOL=101142],heliopetes ericetorum[&&NHX:TOL=101143],heliopetes laviana[&&NHX:TOL=101144],heliopetes leucola[&&NHX:TOL=101145],heliopetes libra[&&NHX:TOL=101146],heliopetes macaira[&&NHX:TOL=101147],heliopetes marginata[&&NHX:TOL=101148],heliopetes nivella[&&NHX:TOL=101149],heliopetes ochroleuca[&&NHX:TOL=101150],heliopetes omrina[&&NHX:TOL=101151],heliopetes petrus[&&NHX:TOL=101152],heliopetes purgia[&&NHX:TOL=101153])heliopetes[&&NHX:TOL=95427],(heliopyrgus americanus[&&NHX:TOL=101154],heliopyrgus domicella[&&NHX:TOL=101155],heliopyrgus sublinea[&&NHX:TOL=101156])heliopyrgus[&&NHX:TOL=95428])[&&NHX:TOL=138372],(pyrgus albescens[&&NHX:TOL=101171],pyrgus alpinus[&&NHX:TOL=101172],pyrgus alveus[&&NHX:TOL=101173],pyrgus andromedae[&&NHX:TOL=101174],pyrgus armoricanus[&&NHX:TOL=101175],pyrgus barrosi[&&NHX:TOL=101176],pyrgus bellieri[&&NHX:TOL=101177],pyrgus bocchoris[&&NHX:TOL=101178],pyrgus brenda[&&NHX:TOL=101179],pyrgus cacaliae[&&NHX:TOL=101180],pyrgus carlinae[&&NHX:TOL=101181],pyrgus carthami[&&NHX:TOL=101182],pyrgus cashmirensis[&&NHX:TOL=101183],pyrgus centaureae[&&NHX:TOL=101184],pyrgus cinarae[&&NHX:TOL=101185],pyrgus cirsii[&&NHX:TOL=101186],pyrgus communis[&&NHX:TOL=101187],pyrgus crisia[&&NHX:TOL=101188],pyrgus darwazicus[&&NHX:TOL=101189],pyrgus fides[&&NHX:TOL=101190],pyrgus jupei[&&NHX:TOL=101191],pyrgus limbata[&&NHX:TOL=101192],pyrgus maculatus[&&NHX:TOL=101193],pyrgus malvae[&&NHX:TOL=101194],pyrgus malvoides[&&NHX:TOL=101195],pyrgus melotis[&&NHX:TOL=101196],pyrgus notatus[&&NHX:TOL=101197],pyrgus oileus[&&NHX:TOL=101198],pyrgus onopordi[&&NHX:TOL=101199],pyrgus orcus[&&NHX:TOL=101200],pyrgus orcynoides[&&NHX:TOL=101201],pyrgus philetas[&&NHX:TOL=101202],pyrgus ruralis[&&NHX:TOL=101203],pyrgus scriptura[&&NHX:TOL=101204],pyrgus serratulae[&&NHX:TOL=101205],pyrgus siberica[&&NHX:TOL=101206],pyrgus sidae[&&NHX:TOL=101207],pyrgus speyeri[&&NHX:TOL=101208],pyrgus veturius[&&NHX:TOL=101209],pyrgus xanthus[&&NHX:TOL=101210])pyrgus[&&NHX:TOL=95433])[&&NHX:TOL=138370],(celotes limpia[&&NHX:TOL=101125],celotes nessus[&&NHX:TOL=101126],celotes spurcus[&&NHX:TOL=133634],[&&NHX:TOL=133635])celotes[&&NHX:TOL=95422])[&&NHX:TOL=138369])[&&NHX:TOL=138367],(anisochoria albida[&&NHX:TOL=101106],anisochoria bacchus[&&NHX:TOL=101107],anisochoria minorella[&&NHX:TOL=101108],anisochoria nadia[&&NHX:TOL=101109],anisochoria pedaliodina[&&NHX:TOL=101110],anisochoria quadrifenestrata[&&NHX:TOL=101111],anisochoria sublimbata[&&NHX:TOL=101112],anisochoria subpicta[&&NHX:TOL=101113],anisochoria superior[&&NHX:TOL=101114],anisochoria vianna[&&NHX:TOL=101115])anisochoria[&&NHX:TOL=95419],((carrhenes canescens[&&NHX:TOL=101061],carrhenes leada[&&NHX:TOL=101065],carrhenes lilloi[&&NHX:TOL=101066],carrhenes recurva[&&NHX:TOL=101068],carrhenes callipetes[&&NHX:TOL=101060],carrhenes santes[&&NHX:TOL=101069])[&&NHX:TOL=101071],(carrhenes fuscescens[&&NHX:TOL=101063],carrhenes chaeremon[&&NHX:TOL=101062],carrhenes bamba[&&NHX:TOL=101058],carrhenes calidius[&&NHX:TOL=101059],carrhenes sinesinus[&&NHX:TOL=101070],carrhenes infuscescens[&&NHX:TOL=101064])[&&NHX:TOL=101072],carrhenes meridensis[&&NHX:TOL=101067])carrhenes[&&NHX:TOL=95421],(diaeus ambata[&&NHX:TOL=101130],diaeus lacaena[&&NHX:TOL=101131],diaeus variegata[&&NHX:TOL=101132],diaeus varna[&&NHX:TOL=101133])diaeus[&&NHX:TOL=95425],(onenses hyalophora[&&NHX:TOL=101157],onenses kelso[&&NHX:TOL=101158])onenses[&&NHX:TOL=95429],(paches era[&&NHX:TOL=101159],paches exosa[&&NHX:TOL=101160],paches gladiatus[&&NHX:TOL=101161],paches loxus[&&NHX:TOL=101162],paches polla[&&NHX:TOL=101163],paches trifasciatus[&&NHX:TOL=101164])paches[&&NHX:TOL=95430],(plumbago plumbago[&&NHX:TOL=101165],plumbago pulverea[&&NHX:TOL=101166],plumbago serapion[&&NHX:TOL=101167])plumbago[&&NHX:TOL=95431],(timochreon doria[&&NHX:TOL=101217],timochreon satyrus[&&NHX:TOL=101218])timochreon[&&NHX:TOL=95436],trina geometrina[&&NHX:TOL=95437],(zobera albopunctata[&&NHX:TOL=101219],zobera marginata[&&NHX:TOL=101220],zobera oaxaquena[&&NHX:TOL=101221])zobera[&&NHX:TOL=95439])[&&NHX:TOL=138366],((clito aberrans[&&NHX:TOL=101073],clito bibulus[&&NHX:TOL=101074],clito clada[&&NHX:TOL=101075],clito jonkersi[&&NHX:TOL=101076],clito littera[&&NHX:TOL=101077],clito sompa[&&NHX:TOL=101078],clito trinidadensis[&&NHX:TOL=101079],clito tuva[&&NHX:TOL=101080],clito zelotes[&&NHX:TOL=101081],clito zenda[&&NHX:TOL=101082])clito[&&NHX:TOL=95423],((eracon asymmetrica[&&NHX:TOL=101134],eracon biternata[&&NHX:TOL=101135],eracon clinias[&&NHX:TOL=101136],eracon mnemon[&&NHX:TOL=101137],eracon paulinus[&&NHX:TOL=101138],eracon pebana[&&NHX:TOL=101139],eracon lachesis[&&NHX:TOL=101564])eracon[&&NHX:TOL=95426],(cornuphallus albifascia[&&NHX:TOL=101127],cornuphallus onoribo[&&NHX:TOL=101128],cornuphallus problematica[&&NHX:TOL=101129])cornuphallus[&&NHX:TOL=95424],(spioniades abbreviata[&&NHX:TOL=101211],spioniades artemides[&&NHX:TOL=101212],spioniades libethra[&&NHX:TOL=101213])spioniades[&&NHX:TOL=95434])[&&NHX:TOL=138373],(pseudodrephalys atinas[&&NHX:TOL=101168],pseudodrephalys hypargus[&&NHX:TOL=101169],pseudodrephalys sohni[&&NHX:TOL=101170])pseudodrephalys[&&NHX:TOL=95432])[&&NHX:TOL=138371],xenophanes tryxus[&&NHX:TOL=95438])pyrgini[&&NHX:TOL=95263],(((achylodes busirus[&&NHX:TOL=100562],achylodes pallida[&&NHX:TOL=100566])achylodes[&&NHX:TOL=95405],(aethilla chiapa[&&NHX:TOL=100567],aethilla echina[&&NHX:TOL=100568],aethilla eleusina[&&NHX:TOL=100569],aethilla epicra[&&NHX:TOL=100570],aethilla gigas[&&NHX:TOL=100571],aethilla haber[&&NHX:TOL=100572],aethilla later[&&NHX:TOL=100573],aethilla lavochrea[&&NHX:TOL=100574],aethilla melas[&&NHX:TOL=100575],aethilla memmius[&&NHX:TOL=100576])aethilla[&&NHX:TOL=95406],(doberes anticus[&&NHX:TOL=100581],doberes hewitsonius[&&NHX:TOL=100582])doberes[&&NHX:TOL=95409],(eantis minna[&&NHX:TOL=100563],eantis mithridates[&&NHX:TOL=100564],eantis munroei[&&NHX:TOL=100565])eantis[&&NHX:TOL=95410])[&&NHX:TOL=138360],((((atarnes hierax[&&NHX:TOL=100577],atarnes sallei[&&NHX:TOL=100578])atarnes[&&NHX:TOL=95407],(charidia empolaeus[&&NHX:TOL=100579],charidia lucaria[&&NHX:TOL=100580])charidia[&&NHX:TOL=95408],(paramimus scurra[&&NHX:TOL=100607],paramimus stigma[&&NHX:TOL=100608])paramimus[&&NHX:TOL=95415])[&&NHX:TOL=138363],(milanion alaricus[&&NHX:TOL=100589],milanion clito[&&NHX:TOL=100590],milanion cramba[&&NHX:TOL=100591],milanion hemes[&&NHX:TOL=100592],milanion leucaspis[&&NHX:TOL=100593],milanion marciana[&&NHX:TOL=100594],milanion pilumnus[&&NHX:TOL=100595])milanion[&&NHX:TOL=95413],(haemactis albamarita[&&NHX:TOL=100586],haemactis pyrrhosphenus[&&NHX:TOL=100587],haemactis sanguinalis[&&NHX:TOL=100588])haemactis[&&NHX:TOL=95412])[&&NHX:TOL=138362],((pythonides braga[&&NHX:TOL=100609],pythonides eminus[&&NHX:TOL=100610],pythonides grandis[&&NHX:TOL=100611],pythonides hampa[&&NHX:TOL=100612],pythonides herennius[&&NHX:TOL=100613],pythonides homer[&&NHX:TOL=100614],pythonides jovianus[&&NHX:TOL=100615],pythonides lancea[&&NHX:TOL=100616],pythonides lerina[&&NHX:TOL=100617],pythonides limaea[&&NHX:TOL=100618],pythonides maraca[&&NHX:TOL=100619],pythonides mundo[&&NHX:TOL=100620],pythonides neivai[&&NHX:TOL=100621],pythonides nides[&&NHX:TOL=100622],pythonides parallelus[&&NHX:TOL=100623],pythonides pescada[&&NHX:TOL=100624],pythonides proxenus[&&NHX:TOL=100625],pythonides pteras[&&NHX:TOL=100626],pythonides rosa[&&NHX:TOL=100627],pythonides tullia[&&NHX:TOL=100628])pythonides[&&NHX:TOL=95416],(quadrus cerealis[&&NHX:TOL=100629],quadrus contubernalis[&&NHX:TOL=100630],quadrus deyrollei[&&NHX:TOL=100631],quadrus fanda[&&NHX:TOL=100632],quadrus francesius[&&NHX:TOL=100633],quadrus ineptus[&&NHX:TOL=100634],quadrus jacobus[&&NHX:TOL=100635],quadrus lugubris[&&NHX:TOL=100636],quadrus tros[&&NHX:TOL=100637],quadrus truncata[&&NHX:TOL=100638],quadrus ulucida[&&NHX:TOL=100639])quadrus[&&NHX:TOL=95417],(gindanes bora[&&NHX:TOL=100583],gindanes brebisson[&&NHX:TOL=100584],gindanes brontinus[&&NHX:TOL=100585])gindanes[&&NHX:TOL=95411])[&&NHX:TOL=138364],(ouleus accedens[&&NHX:TOL=100596],ouleus bubaris[&&NHX:TOL=100597],ouleus calavius[&&NHX:TOL=100598],ouleus candidus[&&NHX:TOL=100599],ouleus cyrna[&&NHX:TOL=100600],ouleus dilla[&&NHX:TOL=100601],ouleus fatinitza[&&NHX:TOL=100602],ouleus fridericus[&&NHX:TOL=100603],ouleus juxta[&&NHX:TOL=100604],ouleus narycus[&&NHX:TOL=100605],ouleus negrus[&&NHX:TOL=100606])ouleus[&&NHX:TOL=95414],(zera belti[&&NHX:TOL=100640],zera eboneus[&&NHX:TOL=100641],zera hyacinthinus[&&NHX:TOL=100642],zera nolckeni[&&NHX:TOL=100643],zera phila[&&NHX:TOL=100644],zera teresa[&&NHX:TOL=100645],zera tetrastigma[&&NHX:TOL=100646],zera zera[&&NHX:TOL=100647])zera[&&NHX:TOL=95418])[&&NHX:TOL=138361])achylodidini[&&NHX:TOL=95259])[&&NHX:TOL=95272],((((((theagenes aegides[&&NHX:TOL=101093],theagenes albiplaga[&&NHX:TOL=101094],theagenes dichrous[&&NHX:TOL=101095])theagenes[&&NHX:TOL=95402],(gorgythion alcandra[&&NHX:TOL=100788],gorgythion begga[&&NHX:TOL=100789],gorgythion beggina[&&NHX:TOL=100790],gorgythion canda[&&NHX:TOL=100791],gorgythion plautia[&&NHX:TOL=100792],gorgythion vox[&&NHX:TOL=100793])gorgythion[&&NHX:TOL=95396])[&&NHX:TOL=138347],((((camptopleura auxo[&&NHX:TOL=100659],camptopleura impressus[&&NHX:TOL=100660],camptopleura janthinus[&&NHX:TOL=100661],camptopleura oaxaca[&&NHX:TOL=100662],camptopleura termon[&&NHX:TOL=100663],camptopleura theramenes[&&NHX:TOL=100664])camptopleura[&&NHX:TOL=95389],(cycloglypha caeruleonigra[&&NHX:TOL=100670],cycloglypha enega[&&NHX:TOL=100671],cycloglypha polax[&&NHX:TOL=100672],cycloglypha stellita[&&NHX:TOL=100673],cycloglypha thrasibulus[&&NHX:TOL=100674],cycloglypha tisias[&&NHX:TOL=100675])cycloglypha[&&NHX:TOL=95391])[&&NHX:TOL=138350],(timochares runia[&&NHX:TOL=101096],timochares ruptifasciata[&&NHX:TOL=101097],timochares trifasciata[&&NHX:TOL=101098])timochares[&&NHX:TOL=95403])[&&NHX:TOL=138349],((ebrietas anacreon[&&NHX:TOL=100676],ebrietas badia[&&NHX:TOL=100677],ebrietas elaudia[&&NHX:TOL=100678],ebrietas evanidus[&&NHX:TOL=100679],ebrietas infanda[&&NHX:TOL=100680],ebrietas osyris[&&NHX:TOL=100681],ebrietas sappho[&&NHX:TOL=100682])ebrietas[&&NHX:TOL=95392],(helias cama[&&NHX:TOL=100794],helias godmani[&&NHX:TOL=100795],helias phalaenoides[&&NHX:TOL=100796])helias[&&NHX:TOL=95398])[&&NHX:TOL=138351])[&&NHX:TOL=138348])[&&NHX:TOL=138346],((((mylon cajus[&&NHX:TOL=100799],mylon maimon[&&NHX:TOL=100805])[&&NHX:TOL=101055],(mylon jason[&&NHX:TOL=100803],mylon pelopidas[&&NHX:TOL=100808],mylon exstincta[&&NHX:TOL=100801],mylon simplex[&&NHX:TOL=100810],mylon argonautarum[&&NHX:TOL=100798],mylon cristata[&&NHX:TOL=100800])[&&NHX:TOL=101056],(mylon salvia[&&NHX:TOL=100809],mylon zephus[&&NHX:TOL=100811],mylon lassia[&&NHX:TOL=100804],mylon illineatus[&&NHX:TOL=100802],mylon orsa[&&NHX:TOL=100807],mylon mestor[&&NHX:TOL=100806],mylon ander[&&NHX:TOL=100797])[&&NHX:TOL=101057])mylon[&&NHX:TOL=95399],(potamanaxas andraemon[&&NHX:TOL=100812],potamanaxas bana[&&NHX:TOL=100813],potamanaxas effusa[&&NHX:TOL=100814],potamanaxas flavofasciata[&&NHX:TOL=100815],potamanaxas frenda[&&NHX:TOL=100816],potamanaxas hirta[&&NHX:TOL=100817],potamanaxas laoma[&&NHX:TOL=100818],potamanaxas latrea[&&NHX:TOL=100819],potamanaxas melicertes[&&NHX:TOL=100820],potamanaxas paralus[&&NHX:TOL=100821],potamanaxas quira[&&NHX:TOL=100822],potamanaxas thestia[&&NHX:TOL=100823],potamanaxas thoria[&&NHX:TOL=100824],potamanaxas tunga[&&NHX:TOL=100825],potamanaxas unifasciata[&&NHX:TOL=100826],potamanaxas xantholeuce[&&NHX:TOL=100827])potamanaxas[&&NHX:TOL=95400])[&&NHX:TOL=138353],(sostrata adamantinus[&&NHX:TOL=101085],sostrata bifasciata[&&NHX:TOL=101086],sostrata caerulans[&&NHX:TOL=101087],sostrata cronion[&&NHX:TOL=101088],sostrata festiva[&&NHX:TOL=101089],sostrata grippa[&&NHX:TOL=101090],sostrata jinna[&&NHX:TOL=101091],sostrata pusilla[&&NHX:TOL=101092])sostrata[&&NHX:TOL=95401])[&&NHX:TOL=138352])[&&NHX:TOL=138345],(((erynnis brizo[&&NHX:TOL=100687],erynnis icelus[&&NHX:TOL=100688],erynnis mercurius[&&NHX:TOL=100690])erynnis erynnis[&&NHX:TOL=101083],erynnis marloyi[&&NHX:TOL=100689],erynnis montanus[&&NHX:TOL=100691],erynnis pathan[&&NHX:TOL=100692],erynnis pelias[&&NHX:TOL=100693],erynnis popoviana[&&NHX:TOL=100694],erynnis tages[&&NHX:TOL=100695],((erynnis afrianus[&&NHX:TOL=100696],erynnis baptisiae[&&NHX:TOL=100708],erynnis lucilius[&&NHX:TOL=100709],erynnis persius[&&NHX:TOL=100710])erynnis persius group[&&NHX:TOL=138357],(erynnis horatius[&&NHX:TOL=100698],erynnis juvenalis[&&NHX:TOL=100699],erynnis meridianus[&&NHX:TOL=100701],erynnis scudderi[&&NHX:TOL=100704],erynnis telemachus[&&NHX:TOL=100705],erynnis tristis[&&NHX:TOL=100706])erynnis juvenalis group[&&NHX:TOL=138358],(erynnis funeralis[&&NHX:TOL=100697],erynnis martialis[&&NHX:TOL=100700],erynnis pacuvius[&&NHX:TOL=100702],erynnis zarucco[&&NHX:TOL=100707])erynnis martialis group[&&NHX:TOL=138359],erynnis propertius[&&NHX:TOL=100703])erynnis erynnides[&&NHX:TOL=101084])erynnis[&&NHX:TOL=95394],(gesta austerus[&&NHX:TOL=100783],gesta gesta[&&NHX:TOL=100784],gesta heteropterus[&&NHX:TOL=100785],gesta inga[&&NHX:TOL=100786],gesta invisus[&&NHX:TOL=100787])gesta[&&NHX:TOL=95395])[&&NHX:TOL=138354])[&&NHX:TOL=138344],(anastrus chaqua[&&NHX:TOL=100648],anastrus meliboea[&&NHX:TOL=100649],anastrus neaeris[&&NHX:TOL=100650],anastrus obliqua[&&NHX:TOL=100651],anastrus obscurus[&&NHX:TOL=100652],anastrus peruvianus[&&NHX:TOL=100653],anastrus petius[&&NHX:TOL=100654],anastrus sempiternus[&&NHX:TOL=100655],anastrus tolimus[&&NHX:TOL=100656],anastrus ulpianus[&&NHX:TOL=100657],anastrus virens[&&NHX:TOL=100658])anastrus[&&NHX:TOL=95388],(chiomara asychis[&&NHX:TOL=100665],chiomara basigutta[&&NHX:TOL=100666],chiomara crenda[&&NHX:TOL=100667],chiomara khalili[&&NHX:TOL=100668],chiomara mithrax[&&NHX:TOL=100669],chiomara georgina[&&NHX:TOL=138355],[&&NHX:TOL=138356])chiomara[&&NHX:TOL=95390],(ephyriades arcas[&&NHX:TOL=100683],ephyriades brunnea[&&NHX:TOL=100684],ephyriades eugramma[&&NHX:TOL=100685],ephyriades zephodes[&&NHX:TOL=100686])ephyriades[&&NHX:TOL=95393],grais stigmaticus[&&NHX:TOL=95397],(tosta capra[&&NHX:TOL=101099],tosta gorgus[&&NHX:TOL=101100],tosta niger[&&NHX:TOL=101101],tosta platypterus[&&NHX:TOL=101102],(tosta sapasoa[&&NHX:TOL=101103],tosta saltarana[&&NHX:TOL=112951])[&&NHX:TOL=112950],tosta taurus[&&NHX:TOL=101104],tosta tosta[&&NHX:TOL=101105])tosta[&&NHX:TOL=95404],speculum speculum[&&NHX:TOL=131127])erynnini[&&NHX:TOL=95262])[&&NHX:TOL=95271],(arteurotia tractipennis[&&NHX:TOL=95359],conognathus platon[&&NHX:TOL=95363],windia windi[&&NHX:TOL=95386],((cyclosemia anastomosis[&&NHX:TOL=101267],cyclosemia caerulea[&&NHX:TOL=101268],cyclosemia earina[&&NHX:TOL=101269],cyclosemia elelea[&&NHX:TOL=101270],cyclosemia herennius[&&NHX:TOL=101271],cyclosemia lathaea[&&NHX:TOL=101272],cyclosemia leppa[&&NHX:TOL=101273],cyclosemia lyrcaea[&&NHX:TOL=101274],cyclosemia pedro[&&NHX:TOL=101275])cyclosemia[&&NHX:TOL=95364],fuscocimex caecus[&&NHX:TOL=134182],(morvina falisca[&&NHX:TOL=101430],morvina fissimacula[&&NHX:TOL=101431],morvina morvus[&&NHX:TOL=101432])morvina[&&NHX:TOL=95372],(myrinia binoculus[&&NHX:TOL=101477],myrinia catua[&&NHX:TOL=101478],myrinia laddeyi[&&NHX:TOL=101479],myrinia myris[&&NHX:TOL=101480],myrinia raymundo[&&NHX:TOL=101481],myrinia santa[&&NHX:TOL=101482])myrinia[&&NHX:TOL=95374],(ocella albata[&&NHX:TOL=101522],ocella diophthalma[&&NHX:TOL=101523],ocella monophthalma[&&NHX:TOL=101524])ocella[&&NHX:TOL=95377],(xispia quadrata[&&NHX:TOL=101725],xispia satyrus[&&NHX:TOL=101726])xispia[&&NHX:TOL=95387])[&&NHX:TOL=138343],((((burca braco[&&NHX:TOL=101255],burca concolor[&&NHX:TOL=101256],burca cubensis[&&NHX:TOL=101257],burca hispaniolae[&&NHX:TOL=101258],burca stillmanni[&&NHX:TOL=101259])burca[&&NHX:TOL=95361],jera tricuspidata[&&NHX:TOL=95369],(iliana heros[&&NHX:TOL=101424],iliana purpurascens[&&NHX:TOL=101425],iliana remus[&&NHX:TOL=101426],iliana romulus[&&NHX:TOL=101427])iliana[&&NHX:TOL=95368],mictris crispus[&&NHX:TOL=95370],(mimia chiapaensis[&&NHX:TOL=101428],mimia phydile[&&NHX:TOL=101429])mimia[&&NHX:TOL=95371],(noctuana brunneofusca[&&NHX:TOL=101516],noctuana diurna[&&NHX:TOL=101517],noctuana hematospila[&&NHX:TOL=101518],noctuana lactifera[&&NHX:TOL=101519],noctuana noctua[&&NHX:TOL=101520],noctuana stator[&&NHX:TOL=101521])noctuana[&&NHX:TOL=95376],((nisoniades benda[&&NHX:TOL=101483],nisoniades bessus[&&NHX:TOL=101484],nisoniades bipuncta[&&NHX:TOL=101485],nisoniades borra[&&NHX:TOL=101486],nisoniades brazia[&&NHX:TOL=101487],nisoniades brunneata[&&NHX:TOL=101488],nisoniades castolus[&&NHX:TOL=101489],nisoniades cauca[&&NHX:TOL=101490],nisoniades coca[&&NHX:TOL=101491],nisoniades criton[&&NHX:TOL=101492],nisoniades ephora[&&NHX:TOL=101493],nisoniades evansi[&&NHX:TOL=101494],nisoniades godma[&&NHX:TOL=101495],nisoniades guianae[&&NHX:TOL=101496],nisoniades haywardi[&&NHX:TOL=101497],nisoniades hecale[&&NHX:TOL=101498],nisoniades hesperia[&&NHX:TOL=101499],nisoniades hora[&&NHX:TOL=101500],nisoniades indistincta[&&NHX:TOL=101501],nisoniades lata[&&NHX:TOL=101502],nisoniades laurentina[&&NHX:TOL=101503],nisoniades macarius[&&NHX:TOL=101504],nisoniades maura[&&NHX:TOL=101505],nisoniades mimas[&&NHX:TOL=101506],nisoniades montana[&&NHX:TOL=101507],nisoniades nyctineme[&&NHX:TOL=101508],nisoniades panama[&&NHX:TOL=101509],nisoniades remo[&&NHX:TOL=101510],nisoniades rimana[&&NHX:TOL=101511],nisoniades rubescens[&&NHX:TOL=101512],nisoniades supra[&&NHX:TOL=101513],nisoniades suprapanama[&&NHX:TOL=101514],nisoniades torta[&&NHX:TOL=101515])nisoniades[&&NHX:TOL=95375],(pachyneuria damon[&&NHX:TOL=101525],pachyneuria duidae[&&NHX:TOL=101526],pachyneuria helena[&&NHX:TOL=101527],pachyneuria herophile[&&NHX:TOL=101528],pachyneuria inops[&&NHX:TOL=101529],pachyneuria jaguar[&&NHX:TOL=101530],pachyneuria licisca[&&NHX:TOL=101531],pachyneuria lineatopunctata[&&NHX:TOL=101532],pachyneuria lista[&&NHX:TOL=101533],pachyneuria milleri[&&NHX:TOL=101534],pachyneuria obscura[&&NHX:TOL=101535])pachyneuria[&&NHX:TOL=95378],(pellicia angra[&&NHX:TOL=101536],pellicia arina[&&NHX:TOL=101537],pellicia costimacula[&&NHX:TOL=101538],pellicia demetrius[&&NHX:TOL=101539],pellicia dimidiata[&&NHX:TOL=101540],pellicia hersilia[&&NHX:TOL=101541],pellicia klugi[&&NHX:TOL=101542],pellicia najodes[&&NHX:TOL=101543],pellicia ranta[&&NHX:TOL=101544],pellicia santana[&&NHX:TOL=101545],pellicia simulator[&&NHX:TOL=101546],pellicia theon[&&NHX:TOL=101547],pellicia tonga[&&NHX:TOL=101548],pellicia trax[&&NHX:TOL=101549],pellicia tyana[&&NHX:TOL=101550],pellicia vecina[&&NHX:TOL=101551],pellicia alta[&&NHX:TOL=112952])pellicia[&&NHX:TOL=95379],(polyctor cleta[&&NHX:TOL=101554],polyctor enops[&&NHX:TOL=101555],polyctor extensa[&&NHX:TOL=101556],polyctor fera[&&NHX:TOL=101557],polyctor polyctor[&&NHX:TOL=101558],polyctor tensa[&&NHX:TOL=101559])polyctor[&&NHX:TOL=95381],(viola alicus[&&NHX:TOL=101719],viola dagamba[&&NHX:TOL=101720],viola egra[&&NHX:TOL=101721],viola minor[&&NHX:TOL=101722],viola olla[&&NHX:TOL=101723],viola violella[&&NHX:TOL=101724])viola[&&NHX:TOL=95385])[&&NHX:TOL=138342],(sophista aristoteles[&&NHX:TOL=101566],sophista latifasciata[&&NHX:TOL=101567])sophista[&&NHX:TOL=95382])[&&NHX:TOL=138337],(((staphylus ascalaphus[&&NHX:TOL=101595],staphylus ascalon[&&NHX:TOL=101596],staphylus astra[&&NHX:TOL=101597],staphylus azteca[&&NHX:TOL=101598],staphylus balsa[&&NHX:TOL=101599],staphylus buena[&&NHX:TOL=101600],staphylus caribbea[&&NHX:TOL=101601],staphylus cartagoa[&&NHX:TOL=101602],staphylus ceos[&&NHX:TOL=101603],staphylus chlora[&&NHX:TOL=101604],staphylus chlorocephala[&&NHX:TOL=101605],staphylus coecatus[&&NHX:TOL=101606],staphylus cordillerae[&&NHX:TOL=101607],staphylus corumba[&&NHX:TOL=101608],staphylus eryx[&&NHX:TOL=101609],staphylus esmeraldus[&&NHX:TOL=101610],staphylus evemerus[&&NHX:TOL=101611],staphylus fasciatus[&&NHX:TOL=101612],staphylus hayhurstii[&&NHX:TOL=101613],staphylus huigra[&&NHX:TOL=101614],staphylus iguala[&&NHX:TOL=101615],staphylus imperspicua[&&NHX:TOL=101616],staphylus incanus[&&NHX:TOL=101617],staphylus incisus[&&NHX:TOL=101618],staphylus insignis[&&NHX:TOL=101619],staphylus kayei[&&NHX:TOL=101620],staphylus lenis[&&NHX:TOL=101621],staphylus lizeri[&&NHX:TOL=101622],staphylus mazans[&&NHX:TOL=101623],staphylus melaina[&&NHX:TOL=101624],staphylus melangon[&&NHX:TOL=101625],staphylus melius[&&NHX:TOL=101626],staphylus menuda[&&NHX:TOL=101627],staphylus minor[&&NHX:TOL=101628],staphylus mossi[&&NHX:TOL=101629],staphylus musculus[&&NHX:TOL=101630],staphylus oeta[&&NHX:TOL=101631],staphylus parvus[&&NHX:TOL=101632],staphylus perforata[&&NHX:TOL=101633],staphylus perna[&&NHX:TOL=101634],staphylus punctiseparatus[&&NHX:TOL=101635],staphylus putumayo[&&NHX:TOL=101636],staphylus sambo[&&NHX:TOL=101637],staphylus saxos[&&NHX:TOL=101638],staphylus shola[&&NHX:TOL=101639],staphylus tepeca[&&NHX:TOL=101640],staphylus tierra[&&NHX:TOL=101641],staphylus tingo[&&NHX:TOL=101642],staphylus tridentis[&&NHX:TOL=101643],staphylus tucumanus[&&NHX:TOL=101644],staphylus tyro[&&NHX:TOL=101645],staphylus unicornis[&&NHX:TOL=101646],staphylus veytius[&&NHX:TOL=101647],staphylus vincula[&&NHX:TOL=101648],staphylus vulgata[&&NHX:TOL=101649])staphylus[&&NHX:TOL=95384],(gorgopas agylla[&&NHX:TOL=101416],gorgopas chlorocephala[&&NHX:TOL=101417],gorgopas gutta[&&NHX:TOL=101418],gorgopas petale[&&NHX:TOL=101419],gorgopas trochilus[&&NHX:TOL=101420])gorgopas[&&NHX:TOL=95366],(bolla antha[&&NHX:TOL=101227],bolla atahuallpai[&&NHX:TOL=101228],bolla boliviensis[&&NHX:TOL=101229],bolla brennus[&&NHX:TOL=101230],bolla catharina[&&NHX:TOL=101231],bolla clytius[&&NHX:TOL=101232],bolla cupreiceps[&&NHX:TOL=101233],bolla cybele[&&NHX:TOL=101234],bolla cyclops[&&NHX:TOL=101235],bolla cylindus[&&NHX:TOL=101236],bolla dorsolaciniae[&&NHX:TOL=101237],bolla eusebius[&&NHX:TOL=101238],bolla evippe[&&NHX:TOL=101239],bolla fenestra[&&NHX:TOL=101240],bolla giselus[&&NHX:TOL=101241],bolla litus[&&NHX:TOL=101242],bolla mancoi[&&NHX:TOL=101243],bolla morona[&&NHX:TOL=101244],bolla nigerrima[&&NHX:TOL=101245],bolla orsines[&&NHX:TOL=101247],bolla phylo[&&NHX:TOL=101248],bolla saletas[&&NHX:TOL=101249],bolla solitaria[&&NHX:TOL=101250],bolla sonda[&&NHX:TOL=101251],bolla subapicatus[&&NHX:TOL=101252],bolla zora[&&NHX:TOL=101253],bolla zorilla[&&NHX:TOL=101254])bolla[&&NHX:TOL=95360])[&&NHX:TOL=138339],((pholisora catullus[&&NHX:TOL=101552],pholisora mejicanus[&&NHX:TOL=101553])pholisora[&&NHX:TOL=95380],(hesperopsis alpheus[&&NHX:TOL=101421],hesperopsis gracielae[&&NHX:TOL=101422],hesperopsis libya[&&NHX:TOL=101423])hesperopsis[&&NHX:TOL=95367])[&&NHX:TOL=138341])[&&NHX:TOL=138338])[&&NHX:TOL=138336],((carcharodus alceae[&&NHX:TOL=101260],carcharodus baeticus[&&NHX:TOL=101261],carcharodus dravira[&&NHX:TOL=101262],carcharodus flocciferus[&&NHX:TOL=101263],carcharodus lavatherae[&&NHX:TOL=101264],carcharodus orientalis[&&NHX:TOL=101265],carcharodus stauderi[&&NHX:TOL=101266])carcharodus[&&NHX:TOL=95362],(spialia agylla[&&NHX:TOL=101449],spialia asterodia[&&NHX:TOL=101450],spialia colotes[&&NHX:TOL=101451],spialia confusa[&&NHX:TOL=101452],spialia delagoae[&&NHX:TOL=101453],spialia depauperata[&&NHX:TOL=101454],spialia diomus[&&NHX:TOL=101455],spialia doris[&&NHX:TOL=101456],spialia dromus[&&NHX:TOL=101457],spialia galba[&&NHX:TOL=101458],spialia geron[&&NHX:TOL=101459],spialia kituina[&&NHX:TOL=101460],spialia mafa[&&NHX:TOL=101461],spialia mangana[&&NHX:TOL=101462],spialia nanus[&&NHX:TOL=101463],spialia orbifer[&&NHX:TOL=101464],spialia osthelderi[&&NHX:TOL=101465],spialia paula[&&NHX:TOL=101466],spialia phlomidis[&&NHX:TOL=101467],spialia ploetzi[&&NHX:TOL=101468],spialia sataspes[&&NHX:TOL=101469],spialia secessus[&&NHX:TOL=101470],spialia sertorius[&&NHX:TOL=101471],spialia spio[&&NHX:TOL=101472],spialia struvei[&&NHX:TOL=101473],spialia therapne[&&NHX:TOL=101474],spialia wrefordi[&&NHX:TOL=101475],spialia zebra[&&NHX:TOL=101476])spialia[&&NHX:TOL=95383],gomalia elma[&&NHX:TOL=95365],(muschampia antonia[&&NHX:TOL=101433],muschampia cribrellum[&&NHX:TOL=101434],muschampia gigas[&&NHX:TOL=101435],muschampia kuenlunus[&&NHX:TOL=101436],muschampia leuzeae[&&NHX:TOL=101437],muschampia lutulenta[&&NHX:TOL=101438],muschampia mohammed[&&NHX:TOL=101439],muschampia nobilis[&&NHX:TOL=101440],muschampia poggei[&&NHX:TOL=101441],muschampia prometheus[&&NHX:TOL=101442],muschampia proteus[&&NHX:TOL=101443],muschampia protheon[&&NHX:TOL=101444],muschampia proto[&&NHX:TOL=101445],muschampia staudingeri[&&NHX:TOL=101446],muschampia tersa[&&NHX:TOL=101447],muschampia tessellum[&&NHX:TOL=101448])muschampia[&&NHX:TOL=95373])[&&NHX:TOL=138340])[&&NHX:TOL=138335])carcharodini[&&NHX:TOL=95260])[&&NHX:TOL=95270])pyrginae[&&NHX:TOL=12152],(((((carterocephalus abax[&&NHX:TOL=94747],carterocephalus alcinoides[&&NHX:TOL=94748],carterocephalus argyrostigma[&&NHX:TOL=94749],carterocephalus avanti[&&NHX:TOL=94750],carterocephalus christophi[&&NHX:TOL=94751],carterocephalus dieckmanni[&&NHX:TOL=94752],carterocephalus flavomaculatus[&&NHX:TOL=94753],carterocephalus habaensis[&&NHX:TOL=94754],carterocephalus houangty[&&NHX:TOL=94755],carterocephalus micio[&&NHX:TOL=94756],carterocephalus niveomaculatus[&&NHX:TOL=94757],carterocephalus palaemon[&&NHX:TOL=94758],carterocephalus pulchra[&&NHX:TOL=94759],carterocephalus silvicola[&&NHX:TOL=94760])carterocephalus[&&NHX:TOL=94306],leptalina unicolor[&&NHX:TOL=94312],((metisella aegipan[&&NHX:TOL=94766],metisella alticola[&&NHX:TOL=94767],metisella angolana[&&NHX:TOL=94768],metisella carsoni[&&NHX:TOL=94769],metisella congdoni[&&NHX:TOL=94770],metisella decipiens[&&NHX:TOL=94771],metisella formosus[&&NHX:TOL=94772],metisella kakamega[&&NHX:TOL=94773],metisella kambove[&&NHX:TOL=94774],metisella kumbona[&&NHX:TOL=94775],metisella malgacha[&&NHX:TOL=94776],metisella medea[&&NHX:TOL=94777],metisella meninx[&&NHX:TOL=94778],metisella metis[&&NHX:TOL=94779],metisella midas[&&NHX:TOL=94780],metisella orientalis[&&NHX:TOL=94781],metisella perexcellens[&&NHX:TOL=94782],metisella quadrisignatus[&&NHX:TOL=94783],metisella syrinx[&&NHX:TOL=94784],metisella trisignatus[&&NHX:TOL=94785],metisella tsadicus[&&NHX:TOL=94786],metisella willemi[&&NHX:TOL=94787])metisella[&&NHX:TOL=94313],(hovala amena[&&NHX:TOL=94761],hovala arota[&&NHX:TOL=94762],hovala dispar[&&NHX:TOL=94763],hovala pardalina[&&NHX:TOL=94764],hovala saclavus[&&NHX:TOL=94765])hovala[&&NHX:TOL=94311])[&&NHX:TOL=138377])[&&NHX:TOL=138376],((dardarina amadryas[&&NHX:TOL=94715],dardarina aspila[&&NHX:TOL=94716],dardarina castra[&&NHX:TOL=94717],dardarina dardaris[&&NHX:TOL=94718],dardarina daridaeus[&&NHX:TOL=94719],dardarina gaucha[&&NHX:TOL=94720],dardarina jonesi[&&NHX:TOL=94721],dardarina para[&&NHX:TOL=94722],dardarina rana[&&NHX:TOL=94723],dardarina salta[&&NHX:TOL=94724],dardarina tessellatus[&&NHX:TOL=94725],dardarina umuarama[&&NHX:TOL=94726])dardarina[&&NHX:TOL=94308],((piruna aea[&&NHX:TOL=94727],piruna ajijiciensis[&&NHX:TOL=94728],piruna brunnea[&&NHX:TOL=94729],piruna ceracates[&&NHX:TOL=94730],piruna cyclosticta[&&NHX:TOL=94731],piruna dampfi[&&NHX:TOL=94732],piruna gyrans[&&NHX:TOL=94733],piruna haferniki[&&NHX:TOL=94734],piruna jonka[&&NHX:TOL=94735],piruna kemneri[&&NHX:TOL=94736],piruna maculata[&&NHX:TOL=94737],piruna microsticta[&&NHX:TOL=94738],piruna millerorum[&&NHX:TOL=94739],piruna mullinsi[&&NHX:TOL=94740],piruna penaea[&&NHX:TOL=94741],piruna pirus[&&NHX:TOL=94742],piruna polingii[&&NHX:TOL=94743],piruna purepecha[&&NHX:TOL=94744],piruna roeveri[&&NHX:TOL=94745],piruna sina[&&NHX:TOL=94746])piruna[&&NHX:TOL=94314],(dalla agathocles[&&NHX:TOL=94620],dalla bos[&&NHX:TOL=94621],dalla bubobon[&&NHX:TOL=94622],dalla caenides[&&NHX:TOL=94623],dalla caicus[&&NHX:TOL=94624],dalla calaon[&&NHX:TOL=94625],dalla calima[&&NHX:TOL=94626],dalla carnis[&&NHX:TOL=94627],dalla celsus[&&NHX:TOL=94628],dalla cocha[&&NHX:TOL=94629],dalla cola[&&NHX:TOL=94630],dalla connexa[&&NHX:TOL=94631],dalla costala[&&NHX:TOL=94632],dalla crithote[&&NHX:TOL=94633],dalla cuadrada[&&NHX:TOL=94634],dalla cupavia[&&NHX:TOL=94635],dalla curia[&&NHX:TOL=94636],dalla cyprius[&&NHX:TOL=94637],dalla cypselus[&&NHX:TOL=94638],dalla decca[&&NHX:TOL=94639],dalla dimidiatus[&&NHX:TOL=94640],dalla diraspes[&&NHX:TOL=94641],dalla disconnexa[&&NHX:TOL=94642],dalla dividuum[&&NHX:TOL=94643],dalla dognini[&&NHX:TOL=94644],dalla dora[&&NHX:TOL=94645],dalla eburones[&&NHX:TOL=94646],dalla epiphaneus[&&NHX:TOL=94647],dalla eryonas[&&NHX:TOL=94648],dalla faula[&&NHX:TOL=94649],dalla frater[&&NHX:TOL=94650],dalla freemani[&&NHX:TOL=94651],dalla frontinia[&&NHX:TOL=94652],dalla gelus[&&NHX:TOL=94653],dalla genes[&&NHX:TOL=94654],dalla geon[&&NHX:TOL=94655],dalla granites[&&NHX:TOL=94656],dalla grovius[&&NHX:TOL=94657],dalla hesperioides[&&NHX:TOL=94658],dalla hilina[&&NHX:TOL=94659],dalla huanca[&&NHX:TOL=94660],dalla ibhara[&&NHX:TOL=94661],dalla jelskyi[&&NHX:TOL=94662],dalla kemneri[&&NHX:TOL=94663],dalla lalage[&&NHX:TOL=94664],dalla lenda[&&NHX:TOL=94665],dalla lethaea[&&NHX:TOL=94666],dalla ligilla[&&NHX:TOL=94667],dalla lorda[&&NHX:TOL=94668],dalla mars[&&NHX:TOL=94669],dalla mentor[&&NHX:TOL=94670],dalla merida[&&NHX:TOL=94671],dalla mesoxantha[&&NHX:TOL=94672],dalla miser[&&NHX:TOL=94673],dalla monospila[&&NHX:TOL=94674],dalla mora[&&NHX:TOL=94675],dalla morva[&&NHX:TOL=94676],dalla nubes[&&NHX:TOL=94677],dalla ochrolimbata[&&NHX:TOL=94678],dalla octomaculata[&&NHX:TOL=94679],dalla orsines[&&NHX:TOL=94680],dalla oxaites[&&NHX:TOL=94681],dalla pantha[&&NHX:TOL=94682],dalla parma[&&NHX:TOL=94683],dalla pedro[&&NHX:TOL=94684],dalla pincha[&&NHX:TOL=94685],dalla plancus[&&NHX:TOL=94686],dalla polycrates[&&NHX:TOL=94687],dalla pota[&&NHX:TOL=94688],dalla pulchra[&&NHX:TOL=94689],dalla pura[&&NHX:TOL=94690],dalla puracensis[&&NHX:TOL=94691],dalla quadristriga[&&NHX:TOL=94692],dalla quasca[&&NHX:TOL=94693],dalla ramirezi[&&NHX:TOL=94694],dalla riza[&&NHX:TOL=94695],dalla rosea[&&NHX:TOL=94696],dalla rubia[&&NHX:TOL=94697],dalla scylla[&&NHX:TOL=94698],dalla seirocastnia[&&NHX:TOL=94699],dalla semiargentea[&&NHX:TOL=94700],dalla sepia[&&NHX:TOL=94701],dalla simplicis[&&NHX:TOL=94702],dalla spica[&&NHX:TOL=94703],dalla steinhauseri[&&NHX:TOL=94704],dalla superior[&&NHX:TOL=94705],dalla taza[&&NHX:TOL=94706],dalla thalia[&&NHX:TOL=94707],dalla ticidas[&&NHX:TOL=94708],dalla tona[&&NHX:TOL=94709],dalla vinca[&&NHX:TOL=94710],dalla vista[&&NHX:TOL=94711],dalla wardi[&&NHX:TOL=94712],dalla xantha[&&NHX:TOL=94713],dalla xicca[&&NHX:TOL=94714])dalla[&&NHX:TOL=94307],freemaniana rawlinsi[&&NHX:TOL=94309])[&&NHX:TOL=138379])[&&NHX:TOL=138378])[&&NHX:TOL=138375],heteroperus morpheus[&&NHX:TOL=94310],((butleria flavomaculatus[&&NHX:TOL=94610],(butleria fruticolens[&&NHX:TOL=94611],butleria bissexgutatus[&&NHX:TOL=94612],butleria philippii[&&NHX:TOL=94613],butleria sotoi[&&NHX:TOL=94614])subgenus marthae[&&NHX:TOL=94618],(butleria paniscoides[&&NHX:TOL=94615],butleria elwesi[&&NHX:TOL=94616],butleria quilla[&&NHX:TOL=94617])subgenus nivis[&&NHX:TOL=94619])butleria[&&NHX:TOL=94305],(argopteron aureipennis[&&NHX:TOL=94607],argopteron aureum[&&NHX:TOL=94608],argopteron puelmae[&&NHX:TOL=94609])argopteron[&&NHX:TOL=94304])[&&NHX:TOL=138380])heteropterinae[&&NHX:TOL=12153],((((((((antipodia chaostola[&&NHX:TOL=94828],antipodia atralba[&&NHX:TOL=94853])antipodia[&&NHX:TOL=94316],(mesodina aeluropis[&&NHX:TOL=94846],mesodina gracillima[&&NHX:TOL=94847],mesodina halyzia[&&NHX:TOL=94848],mesodina hayi[&&NHX:TOL=94849])mesodina[&&NHX:TOL=94323])[&&NHX:TOL=138389],dispar compacta[&&NHX:TOL=94318])[&&NHX:TOL=138388],(((oreisplanus munionga[&&NHX:TOL=94842],oreisplanus perornata[&&NHX:TOL=94843])oreisplanus[&&NHX:TOL=94326],(hesperilla chrysotricha[&&NHX:TOL=94829],hesperilla crypsargyra[&&NHX:TOL=94830],hesperilla crypsigramma[&&NHX:TOL=94831],hesperilla donnysa[&&NHX:TOL=94832],hesperilla flavescens[&&NHX:TOL=94833],hesperilla furva[&&NHX:TOL=94834],hesperilla idothea[&&NHX:TOL=94835],hesperilla malindeva[&&NHX:TOL=94836],hesperilla mastersi[&&NHX:TOL=94837],hesperilla ornata[&&NHX:TOL=94838],hesperilla picta[&&NHX:TOL=94839],hesperilla sarnia[&&NHX:TOL=94840],hesperilla sexguttata[&&NHX:TOL=94841])hesperilla[&&NHX:TOL=94321])[&&NHX:TOL=138391],(motasingha dirphia[&&NHX:TOL=94844],motasingha trimaculata[&&NHX:TOL=94845])motasingha[&&NHX:TOL=94324])[&&NHX:TOL=138390])[&&NHX:TOL=138387],((signeta flammeata[&&NHX:TOL=94799],signeta tymbophora[&&NHX:TOL=94800])signeta[&&NHX:TOL=94330],(toxidia andersoni[&&NHX:TOL=94790],toxidia arfakensis[&&NHX:TOL=94791],toxidia doubledayi[&&NHX:TOL=94792],toxidia inornata[&&NHX:TOL=94793],toxidia melania[&&NHX:TOL=94794],toxidia parvula[&&NHX:TOL=94795],toxidia peron[&&NHX:TOL=94796],toxidia rietmanni[&&NHX:TOL=94797],toxidia thyrrhus[&&NHX:TOL=94798])toxidia[&&NHX:TOL=94331])[&&NHX:TOL=138392])[&&NHX:TOL=138386],(trapezites eliena[&&NHX:TOL=94811],trapezites heteromacula[&&NHX:TOL=94812],trapezites iacchoides[&&NHX:TOL=94813],trapezites iacchus[&&NHX:TOL=94814],trapezites luteus[&&NHX:TOL=94815],trapezites macqueeni[&&NHX:TOL=94816],trapezites maheta[&&NHX:TOL=94817],trapezites petalia[&&NHX:TOL=94818],trapezites phigalia[&&NHX:TOL=94819],trapezites phigalioides[&&NHX:TOL=94820],trapezites sciron[&&NHX:TOL=94821],trapezites symmomus[&&NHX:TOL=94822],trapezites argenteoornatus[&&NHX:TOL=94823],trapezites praxedes[&&NHX:TOL=94824],trapezites waterhousei[&&NHX:TOL=94825])trapezites[&&NHX:TOL=94332],(anisynta cynone[&&NHX:TOL=94806],anisynta dominula[&&NHX:TOL=94807],anisynta monticolae[&&NHX:TOL=94808],anisynta sphenosema[&&NHX:TOL=94809],anisynta tillyardi[&&NHX:TOL=94810])anisynta[&&NHX:TOL=94315],(croitana aestiva[&&NHX:TOL=94850],croitana arenaria[&&NHX:TOL=94851],croitana croites[&&NHX:TOL=94852])croitana[&&NHX:TOL=94317],(felicena dirpha[&&NHX:TOL=94826],felicena dora[&&NHX:TOL=94827])felicena[&&NHX:TOL=94319],herimosa albovenata[&&NHX:TOL=94805],hewitsoniella migonitis[&&NHX:TOL=94322],(neohesperilla crocea[&&NHX:TOL=94801],neohesperilla senta[&&NHX:TOL=94802],neohesperilla xanthomera[&&NHX:TOL=94803],neohesperilla xiphophora[&&NHX:TOL=94804])neohesperilla[&&NHX:TOL=94325],pasma tasmanica[&&NHX:TOL=94327],proeidosa polysema[&&NHX:TOL=94328])[&&NHX:TOL=138385],(rachelia extrusa[&&NHX:TOL=94788],rachelia icosia[&&NHX:TOL=94789])rachelia[&&NHX:TOL=94329])trapezitinae[&&NHX:TOL=12154],(((((ampittia capenas[&&NHX:TOL=102173],ampittia dalailama[&&NHX:TOL=102174],ampittia dioscorides[&&NHX:TOL=102175],ampittia maro[&&NHX:TOL=102176],ampittia maroides[&&NHX:TOL=102177],ampittia parva[&&NHX:TOL=102178],ampittia trimacula[&&NHX:TOL=102179],ampittia virgata[&&NHX:TOL=102180])ampittia[&&NHX:TOL=94933],(sovia albipectus[&&NHX:TOL=102976],sovia fangi[&&NHX:TOL=102977],sovia grahami[&&NHX:TOL=102978],sovia hyrtacus[&&NHX:TOL=102979],sovia lucasii[&&NHX:TOL=102980],sovia separata[&&NHX:TOL=102981],sovia subflava[&&NHX:TOL=102982])sovia[&&NHX:TOL=94942])[&&NHX:TOL=138394],((halpe albicilia[&&NHX:TOL=102917],halpe arcuata[&&NHX:TOL=102918],halpe aucma[&&NHX:TOL=102919],halpe aurifera[&&NHX:TOL=102920],halpe beturia[&&NHX:TOL=102921],halpe burmana[&&NHX:TOL=102922],halpe clara[&&NHX:TOL=102923],halpe cristata[&&NHX:TOL=124861],halpe damar[&&NHX:TOL=102924],halpe dante[&&NHX:TOL=124862],halpe dizangpusa[&&NHX:TOL=102925],halpe egena[&&NHX:TOL=102926],halpe elana[&&NHX:TOL=102927],halpe falcata[&&NHX:TOL=124863],halpe filda[&&NHX:TOL=102963],halpe flava[&&NHX:TOL=102928],halpe frontieri[&&NHX:TOL=102929],halpe gamma[&&NHX:TOL=102930],halpe handa[&&NHX:TOL=102931],halpe hauxwelli[&&NHX:TOL=102932],halpe hermaphrodite[&&NHX:TOL=102933],halpe hieron[&&NHX:TOL=102934],halpe homolea[&&NHX:TOL=102935],halpe honorei[&&NHX:TOL=102936],halpe inconspicua[&&NHX:TOL=124864],halpe insignis[&&NHX:TOL=102937],halpe knyvetti[&&NHX:TOL=102938],halpe kumara[&&NHX:TOL=102939],halpe kusala[&&NHX:TOL=102940],halpe latipinna[&&NHX:TOL=102941],halpe luteisquama[&&NHX:TOL=124865],halpe mahapara[&&NHX:TOL=124866],halpe major[&&NHX:TOL=124867],halpe mixta[&&NHX:TOL=102943],halpe molta[&&NHX:TOL=102944],halpe muoi[&&NHX:TOL=102945],halpe nephele[&&NHX:TOL=102946],halpe ormenes[&&NHX:TOL=102947],halpe palawea[&&NHX:TOL=124868],halpe parakuamara[&&NHX:TOL=102948],halpe paupera[&&NHX:TOL=102949],halpe pelethronix[&&NHX:TOL=102950],halpe purpurascens[&&NHX:TOL=102951],halpe porus[&&NHX:TOL=102952],halpe scissa[&&NHX:TOL=102953],halpe sikkima[&&NHX:TOL=102954],halpe sulphurifera[&&NHX:TOL=102955],halpe toxopea[&&NHX:TOL=102957],halpe veluvana[&&NHX:TOL=102958],halpe wantona[&&NHX:TOL=102959],halpe zema[&&NHX:TOL=102960],halpe zinda[&&NHX:TOL=102961],halpe zola[&&NHX:TOL=102962])halpe[&&NHX:TOL=94935],(thoressa aina[&&NHX:TOL=103436],thoressa bivitta[&&NHX:TOL=103437],thoressa cerata[&&NHX:TOL=103438],thoressa decorata[&&NHX:TOL=103439],thoressa fusca[&&NHX:TOL=103440],thoressa gupta[&&NHX:TOL=103441],thoressa horishama[&&NHX:TOL=124859],thoressa horshana[&&NHX:TOL=103442],thoressa hyrie[&&NHX:TOL=103443],thoressa justini[&&NHX:TOL=124860],thoressa latris[&&NHX:TOL=103444],thoressa masoni[&&NHX:TOL=103445],thoressa monastyrskyi[&&NHX:TOL=103446],thoressa nakai[&&NHX:TOL=118319],thoressa similissima[&&NHX:TOL=103447],thoressa submacula[&&NHX:TOL=103448],thoressa varia[&&NHX:TOL=103449],thoressa xiaoqingae[&&NHX:TOL=103450])thoressa[&&NHX:TOL=94943])[&&NHX:TOL=138395])[&&NHX:TOL=138393],(aeromachus catocyanea[&&NHX:TOL=102904],aeromachus cognatus[&&NHX:TOL=102905],aeromachus dubius[&&NHX:TOL=102906],aeromachus inachus[&&NHX:TOL=102907],aeromachus jhora[&&NHX:TOL=102908],aeromachus kali[&&NHX:TOL=102909],aeromachus monstrabilus[&&NHX:TOL=102910],aeromachus musca[&&NHX:TOL=124857],aeromachus piceus[&&NHX:TOL=102911],aeromachus plumbeola[&&NHX:TOL=102912],aeromachus propinquus[&&NHX:TOL=102913],aeromachus pseudojhora[&&NHX:TOL=102914],aeromachus pygmaeus[&&NHX:TOL=102915],aeromachus stigmata[&&NHX:TOL=102916])aeromachus[&&NHX:TOL=94932],baracus vittatus[&&NHX:TOL=94934],ochus vittatus[&&NHX:TOL=94936],(onryza maga[&&NHX:TOL=102965],onryza meiktila[&&NHX:TOL=102966],onryza siamica[&&NHX:TOL=102967])onryza[&&NHX:TOL=94937],parasovia perbella[&&NHX:TOL=94938],(pedesta baileyi[&&NHX:TOL=103424],pedesta blanchardii[&&NHX:TOL=103425],pedesta cuneomaculata[&&NHX:TOL=103426],pedesta hishikawai[&&NHX:TOL=103427],pedesta luanchuanensis[&&NHX:TOL=103428],pedesta masuriensis[&&NHX:TOL=103429],pedesta nanshaona[&&NHX:TOL=103430],pedesta naumanni[&&NHX:TOL=103431],pedesta panda[&&NHX:TOL=103432],pedesta pandita[&&NHX:TOL=103433],pedesta serena[&&NHX:TOL=103434],pedesta viridis[&&NHX:TOL=103435])pedesta[&&NHX:TOL=94939],(pithauria linus[&&NHX:TOL=102968],pithauria marsena[&&NHX:TOL=102969],pithauria murdava[&&NHX:TOL=102970],pithauria stramineipennis[&&NHX:TOL=102971])pithauria[&&NHX:TOL=94940],(sebastonyma dolopia[&&NHX:TOL=102972],sebastonyma medoensis[&&NHX:TOL=102973],sebastonyma pudens[&&NHX:TOL=102974],sebastonyma suthepiana[&&NHX:TOL=102975])sebastonyma[&&NHX:TOL=94941])aeromachini[&&NHX:TOL=94924],(((acada annulifer[&&NHX:TOL=102269],acada biseriata[&&NHX:TOL=102270])acada[&&NHX:TOL=95158],(acerbas anthea[&&NHX:TOL=102784],acerbas azona[&&NHX:TOL=102785],acerbas duris[&&NHX:TOL=124880],acerbas latefascia[&&NHX:TOL=102786],acerbas martini[&&NHX:TOL=102787],acerbas suttoni[&&NHX:TOL=102788])acerbas[&&NHX:TOL=95159],(acleros bibundica[&&NHX:TOL=102295],acleros leucopyga[&&NHX:TOL=102296],acleros mackenii[&&NHX:TOL=102297],acleros neavei[&&NHX:TOL=102298],acleros nigrapex[&&NHX:TOL=102299],acleros ploetzi[&&NHX:TOL=102300],acleros sparsum[&&NHX:TOL=102301])acleros[&&NHX:TOL=95160],actinor radians[&&NHX:TOL=95161],aegiale hesperiaris[&&NHX:TOL=95162],(agathymus alliae[&&NHX:TOL=96115],agathymus aryxna[&&NHX:TOL=96116],agathymus baueri[&&NHX:TOL=96117],agathymus belli[&&NHX:TOL=96118],agathymus carlsbadensis[&&NHX:TOL=96119],agathymus chisosensis[&&NHX:TOL=96120],agathymus comstocki[&&NHX:TOL=96121],agathymus dawsoni[&&NHX:TOL=96122],agathymus diabloensis[&&NHX:TOL=96123],agathymus escalantei[&&NHX:TOL=96124],agathymus estelleae[&&NHX:TOL=96125],agathymus evansi[&&NHX:TOL=96126],agathymus fieldi[&&NHX:TOL=96127],agathymus florenceae[&&NHX:TOL=96128],agathymus gentryi[&&NHX:TOL=96129],agathymus gilberti[&&NHX:TOL=96130],agathymus hoffmanni[&&NHX:TOL=96131],agathymus indecisa[&&NHX:TOL=96132],agathymus juliae[&&NHX:TOL=96133],agathymus mariae[&&NHX:TOL=96134],agathymus micheneri[&&NHX:TOL=96135],agathymus neumoegeni[&&NHX:TOL=96136],agathymus polingi[&&NHX:TOL=96137],agathymus remingtoni[&&NHX:TOL=96138],agathymus rethon[&&NHX:TOL=96139],agathymus ricei[&&NHX:TOL=96140],agathymus rindgei[&&NHX:TOL=96141],agathymus stephensi[&&NHX:TOL=96142])agathymus[&&NHX:TOL=95163],(alera furcata[&&NHX:TOL=96090],alera haworthiana[&&NHX:TOL=96091],alera manu[&&NHX:TOL=96092],alera metallica[&&NHX:TOL=96093],alera romeroi[&&NHX:TOL=96094],alera vulpina[&&NHX:TOL=96095])alera[&&NHX:TOL=95164],(ancistroides armatus[&&NHX:TOL=102885],ancistroides gemmifer[&&NHX:TOL=102886],ancistroides longicornis[&&NHX:TOL=102887],ancistroides nigrita[&&NHX:TOL=102888])ancistroides[&&NHX:TOL=95165],(andronymus caesar[&&NHX:TOL=102331],andronymus evander[&&NHX:TOL=102332],andronymus fenestrella[&&NHX:TOL=102333],andronymus gander[&&NHX:TOL=102334],andronymus helles[&&NHX:TOL=102335],andronymus hero[&&NHX:TOL=102336],andronymus marcus[&&NHX:TOL=102337],andronymus marina[&&NHX:TOL=102338],andronymus neander[&&NHX:TOL=102339])andronymus[&&NHX:TOL=95166],ankola fan[&&NHX:TOL=95167],apostictopterus fuliginosus[&&NHX:TOL=95168],(arnetta atkinsoni[&&NHX:TOL=102878],arnetta verones[&&NHX:TOL=102879],arnetta vindhiana[&&NHX:TOL=102880],arnetta mercara[&&NHX:TOL=102881])arnetta[&&NHX:TOL=95169],(artitropa alaotrana[&&NHX:TOL=102372],artitropa boseae[&&NHX:TOL=102373],artitropa cama[&&NHX:TOL=102374],artitropa comus[&&NHX:TOL=102375],artitropa erinnys[&&NHX:TOL=102376],artitropa hollandi[&&NHX:TOL=102377],artitropa milleri[&&NHX:TOL=102378],artitropa reducta[&&NHX:TOL=102379])artitropa[&&NHX:TOL=95170],(astictopterus abjecta[&&NHX:TOL=102162],astictopterus anomoeus[&&NHX:TOL=102163],astictopterus bruno[&&NHX:TOL=102164],astictopterus inornatus[&&NHX:TOL=102165],astictopterus jama[&&NHX:TOL=102166],astictopterus punctulata[&&NHX:TOL=102167],astictopterus stellata[&&NHX:TOL=102168],astictopterus tura[&&NHX:TOL=102169])astictopterus[&&NHX:TOL=95171],barca bicolor[&&NHX:TOL=95172],(caenides benga[&&NHX:TOL=102396],caenides dacela[&&NHX:TOL=102398],caenides dacena[&&NHX:TOL=102399],caenides dacenilla[&&NHX:TOL=102400],caenides hidaroides[&&NHX:TOL=102402],caenides kangvensis[&&NHX:TOL=102403],caenides otilia[&&NHX:TOL=102412],caenides soritia[&&NHX:TOL=102413],caenides volta[&&NHX:TOL=102415],caenides xychus[&&NHX:TOL=102416])caenides[&&NHX:TOL=95173],(ceratrichia argyrosticta[&&NHX:TOL=102243],ceratrichia aurea[&&NHX:TOL=102244],ceratrichia bonga[&&NHX:TOL=102245],ceratrichia brunnea[&&NHX:TOL=102246],ceratrichia clara[&&NHX:TOL=118916],ceratrichia crowleyi[&&NHX:TOL=102247],ceratrichia flandria[&&NHX:TOL=102248],ceratrichia flava[&&NHX:TOL=102249],ceratrichia hollandi[&&NHX:TOL=102250],ceratrichia lewisi[&&NHX:TOL=118917],ceratrichia mabirensis[&&NHX:TOL=102251],ceratrichia maesseni[&&NHX:TOL=102252],ceratrichia nothus[&&NHX:TOL=102253],ceratrichia phocion[&&NHX:TOL=102254],ceratrichia punctata[&&NHX:TOL=102255],ceratrichia semilutea[&&NHX:TOL=102256],ceratrichia weberi[&&NHX:TOL=102257],ceratrichia wollastoni[&&NHX:TOL=102258])ceratrichia[&&NHX:TOL=95174],(chondrolepis cynthia[&&NHX:TOL=102358],chondrolepis leggei[&&NHX:TOL=102359],chondrolepis nero[&&NHX:TOL=102360],chondrolepis niveicornis[&&NHX:TOL=102361],chondrolepis obscurior[&&NHX:TOL=102362],chondrolepis similis[&&NHX:TOL=102363],chondrolepis telisignata[&&NHX:TOL=102364])chondrolepis[&&NHX:TOL=95175],creteus cyrina[&&NHX:TOL=95176],cupitha purreea[&&NHX:TOL=95177],eetion elia[&&NHX:TOL=95178],(eogenes alcides[&&NHX:TOL=102902],eogenes lesliei[&&NHX:TOL=102903])eogenes[&&NHX:TOL=95179],(erionota grandis[&&NHX:TOL=102231],erionota harmachis[&&NHX:TOL=102232],erionota hiraca[&&NHX:TOL=102233],erionota hislopi[&&NHX:TOL=102234],erionota surprisa[&&NHX:TOL=124878],erionota sybirita[&&NHX:TOL=102235],erionota thrax[&&NHX:TOL=102236],erionota torus[&&NHX:TOL=102237],erionota tribus[&&NHX:TOL=102238])erionota[&&NHX:TOL=95180],(fresna carlo[&&NHX:TOL=102431],fresna cojo[&&NHX:TOL=102432],fresna maesseni[&&NHX:TOL=102433],fresna netopha[&&NHX:TOL=102434],fresna nyassae[&&NHX:TOL=102435],fresna jacquelinae[&&NHX:TOL=118941])fresna[&&NHX:TOL=95181],(fulda bernieri[&&NHX:TOL=102204],fulda coroller[&&NHX:TOL=102205],fulda imorina[&&NHX:TOL=102206],fulda rhadama[&&NHX:TOL=102207],fulda australis[&&NHX:TOL=103054],fulda gatiana[&&NHX:TOL=103055],fulda lucida[&&NHX:TOL=103056],fulda pauliani[&&NHX:TOL=103057])fulda[&&NHX:TOL=95182],(galerga ellipsis[&&NHX:TOL=102208],galerga fito[&&NHX:TOL=102209],galerga hyposticta[&&NHX:TOL=102210])galerga[&&NHX:TOL=95183],(gamia abri[&&NHX:TOL=118931],gamia buchholtzi[&&NHX:TOL=102370],gamia shelleyi[&&NHX:TOL=102371])gamia[&&NHX:TOL=95184],(gangara lebadea[&&NHX:TOL=102789],gangara sanguinocculus[&&NHX:TOL=102790],gangara thyrsis[&&NHX:TOL=102791],gangara tumpa[&&NHX:TOL=102792])gangara[&&NHX:TOL=95185],ge geta[&&NHX:TOL=95186],(gorgyra aburae[&&NHX:TOL=102211],gorgyra afikpo[&&NHX:TOL=102212],gorgyra aretina[&&NHX:TOL=102213],gorgyra bibulus[&&NHX:TOL=102214],gorgyra bina[&&NHX:TOL=102215],gorgyra bule[&&NHX:TOL=102216],gorgyra diva[&&NHX:TOL=102217],gorgyra diversata[&&NHX:TOL=102218],gorgyra heterochrus[&&NHX:TOL=102219],gorgyra johnstoni[&&NHX:TOL=102220],gorgyra kalinzu[&&NHX:TOL=102221],gorgyra minima[&&NHX:TOL=102222],gorgyra mocquerysii[&&NHX:TOL=102223],gorgyra pali[&&NHX:TOL=102224],gorgyra rubescens[&&NHX:TOL=102225],gorgyra sara[&&NHX:TOL=102226],gorgyra sola[&&NHX:TOL=102227],gorgyra subfacatus[&&NHX:TOL=102228],gorgyra subflavidus[&&NHX:TOL=102229])gorgyra[&&NHX:TOL=95187],(gretna balenge[&&NHX:TOL=102380],gretna bugoma[&&NHX:TOL=102386],gretna carmen[&&NHX:TOL=102381],gretna cylinda[&&NHX:TOL=102382],gretna lacida[&&NHX:TOL=102383],gretna leakeyi[&&NHX:TOL=118933],gretna waga[&&NHX:TOL=102384],gretna zaremba[&&NHX:TOL=102385])gretna[&&NHX:TOL=95188],gyrogra subnotata[&&NHX:TOL=95189],(hidari bhawani[&&NHX:TOL=102798],hidari doesoena[&&NHX:TOL=102799],hidari irava[&&NHX:TOL=102800])hidari[&&NHX:TOL=95190],(hyarotis adrastus[&&NHX:TOL=102858],hyarotis iadera[&&NHX:TOL=102859],hyarotis microsticta[&&NHX:TOL=102860],hyarotis stubbsi[&&NHX:TOL=102861])hyarotis[&&NHX:TOL=95191],(hypoleucis ophiusa[&&NHX:TOL=102308],hypoleucis sophia[&&NHX:TOL=102309],hypoleucis tripunctata[&&NHX:TOL=102310])hypoleucis[&&NHX:TOL=95192],(iambrix salsala[&&NHX:TOL=102898],iambrix stellifer[&&NHX:TOL=102899])iambrix[&&NHX:TOL=95193],(idmon bicolora[&&NHX:TOL=110610],idmon distanti[&&NHX:TOL=102895],idmon flavata[&&NHX:TOL=110611],idmon latifascia[&&NHX:TOL=102896],idmon obliquans[&&NHX:TOL=102897],idmon fujianana[&&NHX:TOL=96598],idmon sinica[&&NHX:TOL=96599])idmon[&&NHX:TOL=95194],ilma irvina[&&NHX:TOL=95195],(isma binotatus[&&NHX:TOL=102843],isma bononia[&&NHX:TOL=102844],isma bononoides[&&NHX:TOL=102845],isma cinnamomea[&&NHX:TOL=102846],isma cronus[&&NHX:TOL=102847],isma damocles[&&NHX:TOL=102848],isma dawna[&&NHX:TOL=102849],isma elioti[&&NHX:TOL=124875],isma feralia[&&NHX:TOL=102850],isma flemingi[&&NHX:TOL=102851],isma guttulifera[&&NHX:TOL=102852],isma hislopi[&&NHX:TOL=102853],isma iapis[&&NHX:TOL=102854],isma miosticta[&&NHX:TOL=102855],isma protoclea[&&NHX:TOL=102856],isma umbrosa[&&NHX:TOL=102857])isma[&&NHX:TOL=95196],isoteinon lamprospilus[&&NHX:TOL=95197],(kedestes barberae[&&NHX:TOL=102181],kedestes brunneostriga[&&NHX:TOL=102182],kedestes callicles[&&NHX:TOL=102183],kedestes chaca[&&NHX:TOL=102184],kedestes heathi[&&NHX:TOL=102185],kedestes lema[&&NHX:TOL=102186],kedestes lenis[&&NHX:TOL=102187],kedestes lepenula[&&NHX:TOL=102188],kedestes macomo[&&NHX:TOL=102189],kedestes malua[&&NHX:TOL=102190],kedestes marshalli[&&NHX:TOL=102191],kedestes michaeli[&&NHX:TOL=102192],kedestes mohozutza[&&NHX:TOL=102193],kedestes monostichus[&&NHX:TOL=102194],kedestes nancy[&&NHX:TOL=102195],kedestes nerva[&&NHX:TOL=102196],kedestes niveostriga[&&NHX:TOL=102197],kedestes protensa[&&NHX:TOL=102198],kedestes pinheyi[&&NHX:TOL=102199],kedestes rogersi[&&NHX:TOL=102200],kedestes straeleni[&&NHX:TOL=102201],kedestes sublineata[&&NHX:TOL=102202],kedestes wallengrenii[&&NHX:TOL=102203])kedestes[&&NHX:TOL=95198],(koruthaialos butleri[&&NHX:TOL=102891],koruthaialos focula[&&NHX:TOL=102892],koruthaialos rubecula[&&NHX:TOL=102893],koruthaialos sindu[&&NHX:TOL=102894])koruthaialos[&&NHX:TOL=95199],(leona stoehri[&&NHX:TOL=102414],leona na[&&NHX:TOL=102411],leona meloui[&&NHX:TOL=102410],leona maracanda[&&NHX:TOL=102409],leona luehderi[&&NHX:TOL=102408],leona lota[&&NHX:TOL=102407],leona lissa[&&NHX:TOL=102406],leona leonora[&&NHX:TOL=102405],leona lena[&&NHX:TOL=102404],leona halma[&&NHX:TOL=102401],leona binoevatus[&&NHX:TOL=102397],leona allyni[&&NHX:TOL=102395])leona[&&NHX:TOL=118938],lepella lepeletier[&&NHX:TOL=95201],(lotongus avesta[&&NHX:TOL=102793],lotongus calathus[&&NHX:TOL=102794],lotongus saralus[&&NHX:TOL=102795])lotongus[&&NHX:TOL=95202],(lycas argentea[&&NHX:TOL=102900],lycas godart[&&NHX:TOL=102901])lycas[&&NHX:TOL=95203],(malaza carmides[&&NHX:TOL=102340],malaza empyreus[&&NHX:TOL=102341],malaza fastuosus[&&NHX:TOL=102342])malaza[&&NHX:TOL=95204],(matapa aria[&&NHX:TOL=102772],matapa celsina[&&NHX:TOL=102773],matapa cresta[&&NHX:TOL=102774],matapa deprivata[&&NHX:TOL=102775],matapa druna[&&NHX:TOL=102776],matapa intermedia[&&NHX:TOL=102777],matapa purpurascens[&&NHX:TOL=102778],matapa sasivarna[&&NHX:TOL=102779])matapa[&&NHX:TOL=95205],(megathymus beulahae[&&NHX:TOL=96143],megathymus cofaqui[&&NHX:TOL=96144],megathymus streckeri[&&NHX:TOL=96145],megathymus texanus[&&NHX:TOL=96146],megathymus ursus[&&NHX:TOL=96147],megathymus violae[&&NHX:TOL=96148],megathymus yuccae[&&NHX:TOL=96149])megathymus[&&NHX:TOL=95206],(melphina argyrodes[&&NHX:TOL=102420],melphina evansi[&&NHX:TOL=102421],melphina flavina[&&NHX:TOL=102422],melphina hulstaerti[&&NHX:TOL=102423],melphina malthina[&&NHX:TOL=102424],melphina melphis[&&NHX:TOL=102425],melphina noctula[&&NHX:TOL=102426],melphina statira[&&NHX:TOL=102427],melphina statirides[&&NHX:TOL=102428],melphina tarace[&&NHX:TOL=102429],melphina unistriga[&&NHX:TOL=102430],melphina maximiliani[&&NHX:TOL=118939])melphina[&&NHX:TOL=95207],(meza banda[&&NHX:TOL=102317],meza cybeutes[&&NHX:TOL=102319],meza elba[&&NHX:TOL=102320],meza indusiata[&&NHX:TOL=102321],meza larea[&&NHX:TOL=102322],meza leucophaea[&&NHX:TOL=102323],meza mabea[&&NHX:TOL=102324],meza mabillei[&&NHX:TOL=102325],meza meza[&&NHX:TOL=102326])meza[&&NHX:TOL=95208],(miraja flora[&&NHX:TOL=102343],miraja howa[&&NHX:TOL=102344],miraja ismael[&&NHX:TOL=102345],miraja ochracea[&&NHX:TOL=102346],miraja paroechus[&&NHX:TOL=102347],miraja sida[&&NHX:TOL=102348],miraja silvestralis[&&NHX:TOL=102349],miraja sylvia[&&NHX:TOL=102350],miraja varians[&&NHX:TOL=102351])miraja[&&NHX:TOL=95209],moltena fiara[&&NHX:TOL=95210],(monza alberti[&&NHX:TOL=102417],monza cretacea[&&NHX:TOL=102418],monza punctata[&&NHX:TOL=102419])monza[&&NHX:TOL=95211],mopala orma[&&NHX:TOL=95212],(notocrypta aluensis[&&NHX:TOL=102482],notocrypta caerulea[&&NHX:TOL=102483],notocrypta clavata[&&NHX:TOL=102484],notocrypta curvifascia[&&NHX:TOL=102485],notocrypta feisthamelii[&&NHX:TOL=102486],notocrypta flavipes[&&NHX:TOL=102487],notocrypta maria[&&NHX:TOL=102488],notocrypta paralysos[&&NHX:TOL=102489],notocrypta pria[&&NHX:TOL=102490],notocrypta quadrata[&&NHX:TOL=102491],notocrypta renardi[&&NHX:TOL=102492],notocrypta waigensis[&&NHX:TOL=102493])notocrypta[&&NHX:TOL=95213],oerane microthyrus[&&NHX:TOL=95214],(orses cynisca[&&NHX:TOL=96096],orses itea[&&NHX:TOL=96097])orses[&&NHX:TOL=95215],((osmodes adon[&&NHX:TOL=102273],osmodes adonia[&&NHX:TOL=102274])[&&NHX:TOL=118920],osmodes adonides[&&NHX:TOL=102275],(osmodes adosus[&&NHX:TOL=102276],osmodes lindseyi[&&NHX:TOL=102282])[&&NHX:TOL=118921],(osmodes banghaasii[&&NHX:TOL=102277],osmodes costatus[&&NHX:TOL=102278])[&&NHX:TOL=118922],(osmodes distincta[&&NHX:TOL=102279],osmodes hollandi[&&NHX:TOL=102280],osmodes thora[&&NHX:TOL=102287])[&&NHX:TOL=118923],osmodes laronia[&&NHX:TOL=102281],(osmodes lux[&&NHX:TOL=102283],osmodes omar[&&NHX:TOL=102286])[&&NHX:TOL=118924],osmodes minchini[&&NHX:TOL=102285])osmodes[&&NHX:TOL=95216],osphantes ogowena[&&NHX:TOL=95217],(paracleros biguttulus[&&NHX:TOL=102291],paracleros maesseni[&&NHX:TOL=102292],paracleros placidus[&&NHX:TOL=102294],paracleros sangoanus[&&NHX:TOL=118925],paracleros staudei[&&NHX:TOL=118926],paracleros substrigata[&&NHX:TOL=118927])paracleros[&&NHX:TOL=95218],(parosmodes lentiginosa[&&NHX:TOL=102288],parosmodes morantii[&&NHX:TOL=102289],parosmodes onza[&&NHX:TOL=102290])parosmodes[&&NHX:TOL=95219],(pardaleodes bule[&&NHX:TOL=102259],pardaleodes edipus[&&NHX:TOL=102260],pardaleodes incerta[&&NHX:TOL=102261],pardaleodes sator[&&NHX:TOL=102262],pardaleodes tibullus[&&NHX:TOL=102263],pardaleodes xanthopeplus[&&NHX:TOL=102264])pardaleodes[&&NHX:TOL=95220],(paronymus budonga[&&NHX:TOL=102318],paronymus ligora[&&NHX:TOL=102327],paronymus nevea[&&NHX:TOL=102328],paronymus xanthias[&&NHX:TOL=102329],paronymus xanthioides[&&NHX:TOL=102330])paronymus[&&NHX:TOL=95221],pemara pugnans[&&NHX:TOL=95222],(perichares butus[&&NHX:TOL=96098],perichares chima[&&NHX:TOL=96099],perichares colenda[&&NHX:TOL=96100],perichares deceptus[&&NHX:TOL=96101],perichares forbesi[&&NHX:TOL=96102],perichares lotus[&&NHX:TOL=96103],perichares matha[&&NHX:TOL=96104],perichares philetes[&&NHX:TOL=96105],perichares seneca[&&NHX:TOL=96106])perichares[&&NHX:TOL=95223],(perrotia albiplaga[&&NHX:TOL=102352],perrotia eximia[&&NHX:TOL=102353],perrotia gala[&&NHX:TOL=102354],perrotia gillias[&&NHX:TOL=102355],perrotia kingdoni[&&NHX:TOL=102356],perrotia malchus[&&NHX:TOL=102357])perrotia[&&NHX:TOL=95224],(pirdana disanti[&&NHX:TOL=102781],pirdana fusca[&&NHX:TOL=124883],pirdana hyela[&&NHX:TOL=102782],pirdana ismene[&&NHX:TOL=102783])pirdana[&&NHX:TOL=95225],(plastingia flavescens[&&NHX:TOL=102809],plastingia mangola[&&NHX:TOL=102810],plastingia naga[&&NHX:TOL=102811],plastingia pellonia[&&NHX:TOL=102812],plastingia tessellata[&&NHX:TOL=102813],plastingia viburnia[&&NHX:TOL=124876])plastingia[&&NHX:TOL=95226],(platylesches affinissima[&&NHX:TOL=102436],platylesches ayresii[&&NHX:TOL=102437],platylesches batangae[&&NHX:TOL=102438],platylesches chamaeleon[&&NHX:TOL=102439],platylesches fosta[&&NHX:TOL=102440],platylesches galesa[&&NHX:TOL=102441],platylesches iva[&&NHX:TOL=102442],platylesches lamba[&&NHX:TOL=102443],platylesches langa[&&NHX:TOL=102444],platylesches moritili[&&NHX:TOL=102445],platylesches neba[&&NHX:TOL=102446],platylesches panga[&&NHX:TOL=102447],platylesches picanini[&&NHX:TOL=102448],platylesches rasta[&&NHX:TOL=102449],platylesches robustus[&&NHX:TOL=102450],platylesches rossii[&&NHX:TOL=102451],platylesches shona[&&NHX:TOL=102452],platylesches tina[&&NHX:TOL=102453],platylesches larseni[&&NHX:TOL=102750])platylesches[&&NHX:TOL=95227],ploetzia amygdalis[&&NHX:TOL=95228],(prada maria[&&NHX:TOL=102479],prada papua[&&NHX:TOL=102480],prada rothschildi[&&NHX:TOL=102481])prada[&&NHX:TOL=95229],praescobura chrysomaculata[&&NHX:TOL=95230],(prosopalpus debilis[&&NHX:TOL=102170],prosopalpus saga[&&NHX:TOL=102171],prosopalpus styla[&&NHX:TOL=102172])prosopalpus[&&NHX:TOL=95231],pseudokerana fulgur[&&NHX:TOL=95232],pseudopirdana albicornis[&&NHX:TOL=102780],(pseudosarbia flavofasciata[&&NHX:TOL=96107],pseudosarbia phoenicicola[&&NHX:TOL=96108])pseudosarbia[&&NHX:TOL=95234],psolos fuligo[&&NHX:TOL=95235],(pteroteinon caenira[&&NHX:TOL=102388],pteroteinon capronnieri[&&NHX:TOL=102389],pteroteinon ceucaenira[&&NHX:TOL=102390],pteroteinon concaenira[&&NHX:TOL=118935],pteroteinon iricolor[&&NHX:TOL=102391],pteroteinon laterculus[&&NHX:TOL=102392],pteroteinon laufella[&&NHX:TOL=102393],pteroteinon pruna[&&NHX:TOL=102394])pteroteinon[&&NHX:TOL=95236],pudicitia pholus[&&NHX:TOL=95237],(pyroneura agnesia[&&NHX:TOL=102819],pyroneura aurantiaca[&&NHX:TOL=102820],pyroneura callineura[&&NHX:TOL=102821],pyroneura derna[&&NHX:TOL=102822],pyroneura flavia[&&NHX:TOL=102823],pyroneura helena[&&NHX:TOL=102824],pyroneura klanga[&&NHX:TOL=102825],pyroneura latoia[&&NHX:TOL=102826],pyroneura liburnia[&&NHX:TOL=124881],pyroneura margherita[&&NHX:TOL=102827],pyroneura natuna[&&NHX:TOL=102828],pyroneura niasana[&&NHX:TOL=102829],pyroneura perakana[&&NHX:TOL=102830],pyroneura toshikoae[&&NHX:TOL=124882],pyroneura vermiculata[&&NHX:TOL=102831])pyroneura[&&NHX:TOL=95238],(pyrrhopygopsis agaricon[&&NHX:TOL=96109],pyrrhopygopsis quispica[&&NHX:TOL=96110],pyrrhopygopsis romula[&&NHX:TOL=96111],pyrrhopygopsis socrates[&&NHX:TOL=96112])pyrrhopygopsis[&&NHX:TOL=95239],(quedara albifascia[&&NHX:TOL=102832],quedara flavens[&&NHX:TOL=102833],quedara monteithi[&&NHX:TOL=102834],quedra singularis[&&NHX:TOL=102835])quedara[&&NHX:TOL=95240],(rhabdomantis galatia[&&NHX:TOL=102271],rhabdomantis sosia[&&NHX:TOL=102272])rhabdomantis[&&NHX:TOL=95241],(salanoemia fuscicornis[&&NHX:TOL=102814],salanoemia noemi[&&NHX:TOL=102815],salanoemia sala[&&NHX:TOL=102816],salanoemia similis[&&NHX:TOL=102817],salanoemia tavoyana[&&NHX:TOL=102818])salanoemia[&&NHX:TOL=95242],(scobura cephala[&&NHX:TOL=102866],scobura cephaloides[&&NHX:TOL=102867],scobura coniata[&&NHX:TOL=102868],scobura eximia[&&NHX:TOL=102869],scobura isota[&&NHX:TOL=102870],scobura phiditia[&&NHX:TOL=102871],scobura tytleri[&&NHX:TOL=102872],scobura woollettii[&&NHX:TOL=102873])scobura[&&NHX:TOL=95243],(semalea arela[&&NHX:TOL=102302],semalea atrio[&&NHX:TOL=102303],semalea kola[&&NHX:TOL=102304],semalea proxima[&&NHX:TOL=102305],semalea pulvina[&&NHX:TOL=102306],semalea sextilis[&&NHX:TOL=102307])semalea[&&NHX:TOL=95244],(stallingsia jacki[&&NHX:TOL=96150],stallingsia maculosus[&&NHX:TOL=96151],stallingsia smithi[&&NHX:TOL=96152])stallingsia[&&NHX:TOL=95245],stimula swinhoei[&&NHX:TOL=95246],(suada albinus[&&NHX:TOL=102874],suada albolineata[&&NHX:TOL=102875],suada cataleucos[&&NHX:TOL=102876],suada swerga[&&NHX:TOL=102877])suada[&&NHX:TOL=95247],(suastus everyx[&&NHX:TOL=102862],suastus gremius[&&NHX:TOL=102863],suastus migreus[&&NHX:TOL=102864],suastus minutus[&&NHX:TOL=102865])suastus[&&NHX:TOL=95248],(teniorhinus harona[&&NHX:TOL=102239],teniorhinus herilus[&&NHX:TOL=102240],teniorhinus ignita[&&NHX:TOL=102241],teniorhinus watsoni[&&NHX:TOL=102242],teniorhinus niger[&&NHX:TOL=118918])teniorhinus[&&NHX:TOL=95249],tiacellia tiacellia[&&NHX:TOL=95250],(tsitana dicksoni[&&NHX:TOL=102158],tsitana tsita[&&NHX:TOL=102159],tsitana tulbagha[&&NHX:TOL=102160],tsitana wallacei[&&NHX:TOL=102161])tsitana[&&NHX:TOL=102156],(turnerina hazelae[&&NHX:TOL=96113],turnerina mejicanus[&&NHX:TOL=96114])turnerina[&&NHX:TOL=95251],(udaspes folus[&&NHX:TOL=102883],udaspes stellata[&&NHX:TOL=102884])udaspes[&&NHX:TOL=95252],(unkana ambasa[&&NHX:TOL=102796],unkana flava[&&NHX:TOL=124879],unkana mytheca[&&NHX:TOL=102797])unkana[&&NHX:TOL=95253],(xanthodisca ariel[&&NHX:TOL=102265],xanthodisca astrape[&&NHX:TOL=102266],xanthodisca rega[&&NHX:TOL=102267],xanthodisca vibius[&&NHX:TOL=102268])xanthodisca[&&NHX:TOL=95254],(xanthoneura corissa[&&NHX:TOL=124871],xanthoneura kazuhisai[&&NHX:TOL=124872],xanthoneura obscurior[&&NHX:TOL=124873],xanthoneura telesinus[&&NHX:TOL=124874])xanthoneura[&&NHX:TOL=95255],(((zela onara[&&NHX:TOL=102804],zela excellens[&&NHX:TOL=102803])[&&NHX:TOL=124885],zela zeus[&&NHX:TOL=102808])subgenus zela[&&NHX:TOL=124884],zela matapoides smaragdinus[&&NHX:TOL=102805],((zela zenon[&&NHX:TOL=102806],zela cowani[&&NHX:TOL=102801])[&&NHX:TOL=124887],zela zero[&&NHX:TOL=102807],zela storeyi[&&NHX:TOL=124888])subgenus zampa[&&NHX:TOL=124886],zela elioti[&&NHX:TOL=102802])zela[&&NHX:TOL=95256],(zographetus abima[&&NHX:TOL=102836],zographetus doxus[&&NHX:TOL=102837],zographetus durga[&&NHX:TOL=124869],zographetus kutu[&&NHX:TOL=102838],zographetus ogygia[&&NHX:TOL=102839],zographetus ogygioides[&&NHX:TOL=102840],zographetus pallens[&&NHX:TOL=124870],zographetus rama[&&NHX:TOL=102841],zographetus satwa[&&NHX:TOL=102842])zographetus[&&NHX:TOL=95257],(zophopetes cerymica[&&NHX:TOL=102365],zophopetes dysmephila[&&NHX:TOL=102366],zophopetes ganda[&&NHX:TOL=102367],zophopetes haifa[&&NHX:TOL=102368],zophopetes nobilior[&&NHX:TOL=102369],zophopetes quaternata[&&NHX:TOL=118929])zophopetes[&&NHX:TOL=95258])hesperiinae incertae sedis[&&NHX:TOL=95156],(((baoris chapmani[&&NHX:TOL=102731],baoris farri[&&NHX:TOL=102732],baoris leechii[&&NHX:TOL=102733],baoris oceia[&&NHX:TOL=102734],baoris pagana[&&NHX:TOL=102735],baoris penicillata[&&NHX:TOL=102736],baoris unicolor[&&NHX:TOL=102737])baoris[&&NHX:TOL=94962],(borbo bevani[&&NHX:TOL=102664],borbo binga[&&NHX:TOL=102665],borbo borbonica[&&NHX:TOL=102666],borbo chagwa[&&NHX:TOL=102667],borbo cinnara[&&NHX:TOL=102668],borbo detecta[&&NHX:TOL=102669],borbo fallax[&&NHX:TOL=102670],borbo fanta[&&NHX:TOL=102671],borbo fatuellus[&&NHX:TOL=102672],borbo ferruginea[&&NHX:TOL=102673],borbo gemella[&&NHX:TOL=102674],borbo havei[&&NHX:TOL=102675],borbo holtzi[&&NHX:TOL=102676],borbo impar[&&NHX:TOL=102677],borbo kaka[&&NHX:TOL=102678],borbo liana[&&NHX:TOL=102679],borbo lugens[&&NHX:TOL=102680],borbo micans[&&NHX:TOL=102681],borbo perobscura[&&NHX:TOL=102682],borbo ratek[&&NHX:TOL=102683],borbo sirena[&&NHX:TOL=102684])borbo[&&NHX:TOL=94963],(brusa allardi[&&NHX:TOL=102454],brusa saxicola[&&NHX:TOL=102455])brusa[&&NHX:TOL=94964],(caltoris aurociliata[&&NHX:TOL=102711],caltoris beraka[&&NHX:TOL=102712],caltoris boisduvalii[&&NHX:TOL=102713],caltoris bromus[&&NHX:TOL=102714],caltoris brunnea[&&NHX:TOL=102715],caltoris cahira[&&NHX:TOL=102716],caltoris confusa[&&NHX:TOL=102717],caltoris cormasa[&&NHX:TOL=102718],caltoris kumara[&&NHX:TOL=102719],caltoris malaya[&&NHX:TOL=102720],caltoris mehavagga[&&NHX:TOL=102721],caltoris nirwana[&&NHX:TOL=102722],caltoris plebeia[&&NHX:TOL=102723],caltoris philippina[&&NHX:TOL=102724],caltoris sirius[&&NHX:TOL=102725],caltoris tenuis[&&NHX:TOL=102726],caltoris tulsi[&&NHX:TOL=102727])caltoris[&&NHX:TOL=94965],(gegenes hottentota[&&NHX:TOL=102744],gegenes niso[&&NHX:TOL=102745],gegenes nostrodamus[&&NHX:TOL=102746],gegenes pumilio[&&NHX:TOL=102747])gegenes[&&NHX:TOL=94966],(iton semamora[&&NHX:TOL=102742],iton watsonii[&&NHX:TOL=102743])iton[&&NHX:TOL=94967],(parnara amalia[&&NHX:TOL=102685],parnara apostata[&&NHX:TOL=102686],parnara bada[&&NHX:TOL=102687],parnara batta[&&NHX:TOL=102688],parnara ganga[&&NHX:TOL=102689],parnara guttatus[&&NHX:TOL=102690],parnara kawazoei[&&NHX:TOL=102691],parnara monasi[&&NHX:TOL=118943],parnara naso[&&NHX:TOL=102692])parnara[&&NHX:TOL=94968],(pelopidas agna[&&NHX:TOL=102654],pelopidas assamensis[&&NHX:TOL=102655],pelopidas conjuncta[&&NHX:TOL=102656],pelopidas flava[&&NHX:TOL=102657],pelopidas jansonis[&&NHX:TOL=102658],pelopidas lyelli[&&NHX:TOL=102659],pelopidas mathias[&&NHX:TOL=102660],pelopidas sinensis[&&NHX:TOL=102661],pelopidas subochracea[&&NHX:TOL=102662],pelopidas thrax[&&NHX:TOL=102663])pelopidas[&&NHX:TOL=94969],(polytremis caerulescens[&&NHX:TOL=102693],polytremis choui[&&NHX:TOL=102694],polytremis discreta[&&NHX:TOL=102695],polytremis eltola[&&NHX:TOL=102696],polytremis flaivinerva[&&NHX:TOL=102697],polytremis gigantea[&&NHX:TOL=102698],polytremis gotama[&&NHX:TOL=102699],polytremis kiraizana[&&NHX:TOL=102700],polytremis lubricans[&&NHX:TOL=102701],polytremis matsuii[&&NHX:TOL=102702],polytremis mencia[&&NHX:TOL=102703],polytremis micropunctata[&&NHX:TOL=102704],polytremis minuta[&&NHX:TOL=102705],polytremis nascens[&&NHX:TOL=102706],polytremis pellucida[&&NHX:TOL=102707],polytremis suprema[&&NHX:TOL=102708],polytremis theca[&&NHX:TOL=102709],polytremis zina[&&NHX:TOL=102710])polytremis[&&NHX:TOL=94970],(prusiana hercules[&&NHX:TOL=102728],prusiana kuehni[&&NHX:TOL=102729],prusiana prusias[&&NHX:TOL=102730])prusiana[&&NHX:TOL=94971],(zenonia anax[&&NHX:TOL=102456],zenonia crasta[&&NHX:TOL=102457],zenonia zeno[&&NHX:TOL=102458])zenonia[&&NHX:TOL=94972])baorini[&&NHX:TOL=94926],((((((telicota ancilla[&&NHX:TOL=102571],telicota angiana[&&NHX:TOL=102572],telicota anisodesma[&&NHX:TOL=102573],telicota argeus[&&NHX:TOL=102574],telicota aroa[&&NHX:TOL=102575],telicota augias[&&NHX:TOL=102576],telicota bambusae[&&NHX:TOL=102577],telicota besta[&&NHX:TOL=102578],telicota brachydesma[&&NHX:TOL=102579],telicota brandti[&&NHX:TOL=102580],telicota bulwa[&&NHX:TOL=102581],telicota colon[&&NHX:TOL=102582],telicota doba[&&NHX:TOL=102583],telicota elsa[&&NHX:TOL=102584],telicota eurotas[&&NHX:TOL=102585],telicota fenia[&&NHX:TOL=102586],telicota gervasa[&&NHX:TOL=102587],telicota hilda[&&NHX:TOL=102588],telicota ixion[&&NHX:TOL=102589],telicota kaimana[&&NHX:TOL=102590],telicota kezia[&&NHX:TOL=102591],telicota linna[&&NHX:TOL=102592],telicota melanion[&&NHX:TOL=102593],telicota mesoptis[&&NHX:TOL=102594],telicota mimena[&&NHX:TOL=102595],telicota ohara[&&NHX:TOL=102596],telicota paceka[&&NHX:TOL=102597],telicota pythias[&&NHX:TOL=102598],telicota sadra[&&NHX:TOL=102599],telicota sadrella[&&NHX:TOL=102600],telicota solva[&&NHX:TOL=102601],telicota subha[&&NHX:TOL=102602],telicota ternatensis[&&NHX:TOL=102603],telicota vinta[&&NHX:TOL=102604])telicota[&&NHX:TOL=94961],(arrhenes dschilus[&&NHX:TOL=102605],arrhenes elena[&&NHX:TOL=102606],arrhenes germana[&&NHX:TOL=102607],arrhenes marnas[&&NHX:TOL=102608],arrhenes martha[&&NHX:TOL=102609],arrhenes tranquilla[&&NHX:TOL=102610])arrhenes[&&NHX:TOL=94949])[&&NHX:TOL=138397],(cephrenes acalle[&&NHX:TOL=102561],cephrenes augiades[&&NHX:TOL=102562],cephrenes augiana[&&NHX:TOL=102563],cephrenes augusta[&&NHX:TOL=102564],cephrenes carna[&&NHX:TOL=102565],cephrenes moseleyi[&&NHX:TOL=102567],cephrenes shortlandica[&&NHX:TOL=102568],cephrenes trichopepla[&&NHX:TOL=102569],cephrenes sp.[&&NHX:TOL=102570])cephrenes[&&NHX:TOL=94951])[&&NHX:TOL=138396],((banta anna[&&NHX:TOL=102497],banta banta[&&NHX:TOL=102498],banta fulvomargo[&&NHX:TOL=102499],banta linnei[&&NHX:TOL=124773])banta[&&NHX:TOL=94950],(kobrona croma[&&NHX:TOL=102542],kobrona denva[&&NHX:TOL=102543],kobrona edfina[&&NHX:TOL=102544],kobrona eva[&&NHX:TOL=102545],kobrona idea[&&NHX:TOL=102546],kobrona infralutea[&&NHX:TOL=102547],kobrona kobros[&&NHX:TOL=102548],kobrona lexa[&&NHX:TOL=102549],kobrona mirza[&&NHX:TOL=102550],kobrona pansa[&&NHX:TOL=102551],kobrona rasta[&&NHX:TOL=102552],kobrona sebana[&&NHX:TOL=102553],kobrona sota[&&NHX:TOL=102554],kobrona tabella[&&NHX:TOL=102555],kobrona vanda[&&NHX:TOL=102556],kobrona vasna[&&NHX:TOL=102557],kobrona wama[&&NHX:TOL=102558],kobrona zadma[&&NHX:TOL=102559],kobrona species a[&&NHX:TOL=102560])kobrona[&&NHX:TOL=94952],((mimene miltias[&&NHX:TOL=102518],mimene basalis[&&NHX:TOL=102519],mimene verda[&&NHX:TOL=102520],mimene lysima[&&NHX:TOL=102521])[&&NHX:TOL=102517],(mimene celia[&&NHX:TOL=102522],mimene celiaba[&&NHX:TOL=102523],mimene biakensis[&&NHX:TOL=102524],mimene waigeuensis[&&NHX:TOL=102525],mimene caesar[&&NHX:TOL=102526],mimene sariba[&&NHX:TOL=102527],mimene saribana[&&NHX:TOL=102528],mimene albiclavata[&&NHX:TOL=102529],mimene toxopei[&&NHX:TOL=124774])[&&NHX:TOL=94953],mimene kolbei[&&NHX:TOL=102530],mimene melie[&&NHX:TOL=102531],(mimene atropatene[&&NHX:TOL=102533],mimene cyanea[&&NHX:TOL=102534],mimene albidiscus[&&NHX:TOL=102535])[&&NHX:TOL=102532],(mimene ozada[&&NHX:TOL=102537],mimene orida[&&NHX:TOL=102538],mimene milnea[&&NHX:TOL=102539],mimene wandammenensis[&&NHX:TOL=102540],mimene wara[&&NHX:TOL=102541])[&&NHX:TOL=102536])mimene[&&NHX:TOL=102516],((sabera aruana[&&NHX:TOL=102500],sabera dobboe[&&NHX:TOL=102503],sabera dorena[&&NHX:TOL=102504],sabera expansa[&&NHX:TOL=102505],sabera madrella[&&NHX:TOL=102510],sabera tabla[&&NHX:TOL=102512])[&&NHX:TOL=102514],(sabera biaga[&&NHX:TOL=102501],sabera fuliginosa[&&NHX:TOL=102506],sabera fusca[&&NHX:TOL=102507],sabera iloda[&&NHX:TOL=102508],sabera kumpia[&&NHX:TOL=102509],sabera misola[&&NHX:TOL=102511],sabera metallica[&&NHX:TOL=124775])[&&NHX:TOL=102515],sabera caesina[&&NHX:TOL=102502])sabera[&&NHX:TOL=94958])[&&NHX:TOL=102513])[&&NHX:TOL=124772],((((ocybadistes ardea[&&NHX:TOL=102766],ocybadistes flavovittatus[&&NHX:TOL=102767],ocybadistes hypomeloma[&&NHX:TOL=102768],ocybadistes papua[&&NHX:TOL=102769],ocybadistes walkeri[&&NHX:TOL=102770],ocybadistes zelda[&&NHX:TOL=102771])ocybadistes[&&NHX:TOL=94954],(potanthus chloe[&&NHX:TOL=102611],potanthus confucius[&&NHX:TOL=102612],potanthus dara[&&NHX:TOL=102613],potanthus fettingi[&&NHX:TOL=102614],potanthus flava[&&NHX:TOL=102615],potanthus floresia[&&NHX:TOL=102616],potanthus ganda[&&NHX:TOL=102617],potanthus hetaerus[&&NHX:TOL=102618],potanthus hyugai[&&NHX:TOL=124779],potanthus juno[&&NHX:TOL=102619],potanthus lydia[&&NHX:TOL=102620],potanthus mara[&&NHX:TOL=102621],potanthus mingo[&&NHX:TOL=102622],potanthus motzui[&&NHX:TOL=102623],potanthus nesta[&&NHX:TOL=102624],potanthus niobe[&&NHX:TOL=124780],potanthus omaha[&&NHX:TOL=102625],potanthus pallidus[&&NHX:TOL=102626],potanthus palnia[&&NHX:TOL=102627],potanthus pamela[&&NHX:TOL=102628],potanthus pava[&&NHX:TOL=102629],potanthus pseudomaesa[&&NHX:TOL=102630],potanthus rectifasciata[&&NHX:TOL=102631],potanthus riefenstahli[&&NHX:TOL=102632],potanthus serina[&&NHX:TOL=124781],potanthus sita[&&NHX:TOL=102633],potanthus taqini[&&NHX:TOL=102634],potanthus tibetana[&&NHX:TOL=102635],potanthus trachala[&&NHX:TOL=102636],potanthus yani[&&NHX:TOL=102637])potanthus[&&NHX:TOL=94957])[&&NHX:TOL=138399],(suniana lascivia[&&NHX:TOL=102651],suniana subfasciata[&&NHX:TOL=102652],suniana sunias[&&NHX:TOL=102653])suniana[&&NHX:TOL=94959])[&&NHX:TOL=138398],(oriens alfurus[&&NHX:TOL=102645],oriens augustulus[&&NHX:TOL=102646],oriens californica[&&NHX:TOL=124777],oriens concinna[&&NHX:TOL=102647],oriens fons[&&NHX:TOL=124778],oriens gola[&&NHX:TOL=102648],oriens goloides[&&NHX:TOL=102649],oriens paragola[&&NHX:TOL=102650])oriens[&&NHX:TOL=94955],(taractrocera anisomorpha[&&NHX:TOL=102752],taractrocera archias[&&NHX:TOL=102753],taractrocera ardonia[&&NHX:TOL=102754],taractrocera ceramas[&&NHX:TOL=102755],taractrocera danna[&&NHX:TOL=102756],taractrocera dolon[&&NHX:TOL=102757],taractrocera flavoides[&&NHX:TOL=102758],taractrocera ilia[&&NHX:TOL=102759],taractrocera ina[&&NHX:TOL=102760],taractrocera luzonensis[&&NHX:TOL=102761],taractrocera maevius[&&NHX:TOL=102762],taractrocera nigrolimbata[&&NHX:TOL=102763],taractrocera papyria[&&NHX:TOL=102764],taractrocera sp. n.[&&NHX:TOL=102765])taractrocera[&&NHX:TOL=94960])[&&NHX:TOL=124776],(pastria albimedia[&&NHX:TOL=102494],pastria grinpela[&&NHX:TOL=102495],pastria pastria[&&NHX:TOL=102496])pastria[&&NHX:TOL=94956])taractrocerini[&&NHX:TOL=94930],(((adopaeoides bistriata[&&NHX:TOL=95921],adopaeoides prittwitzi[&&NHX:TOL=95922])adopaeoides[&&NHX:TOL=94944],(ancyloxypha arene[&&NHX:TOL=95923],ancyloxypha aurea[&&NHX:TOL=95924],ancyloxypha dryas[&&NHX:TOL=95925],ancyloxypha melanoneura[&&NHX:TOL=95926],ancyloxypha nitedula[&&NHX:TOL=95927],ancyloxypha numitor[&&NHX:TOL=95928],ancyloxypha ramba[&&NHX:TOL=95929])ancyloxypha[&&NHX:TOL=94945],(((copaeodes aurantiaca[&&NHX:TOL=95930],copaeodes castanea[&&NHX:TOL=95931],copaeodes eoa[&&NHX:TOL=95932],copaeodes jean[&&NHX:TOL=95933],copaeodes minima[&&NHX:TOL=95934],copaeodes stillmani[&&NHX:TOL=95935])copaeodes[&&NHX:TOL=94946],(oarisma boeta[&&NHX:TOL=95936],oarisma bruneri[&&NHX:TOL=95937],oarisma edwardsii[&&NHX:TOL=95938],oarisma era[&&NHX:TOL=95939],oarisma garita[&&NHX:TOL=95940],oarisma nanus[&&NHX:TOL=95941],oarisma poweshiek[&&NHX:TOL=95942])oarisma[&&NHX:TOL=94947])[&&NHX:TOL=138401],(thymelicus acteon[&&NHX:TOL=95943],thymelicus alaica[&&NHX:TOL=95944],thymelicus hamza[&&NHX:TOL=95945],thymelicus hyrax[&&NHX:TOL=95946],thymelicus leonina[&&NHX:TOL=95947],thymelicus lineola[&&NHX:TOL=95948],thymelicus sylvatica[&&NHX:TOL=95949],thymelicus sylvestris[&&NHX:TOL=95950],thymelicus stigma[&&NHX:TOL=95951])thymelicus[&&NHX:TOL=94948])[&&NHX:TOL=138400])thymelicini[&&NHX:TOL=94931],(((aides aegita[&&NHX:TOL=95952],aides aestria[&&NHX:TOL=95953],aides brilla[&&NHX:TOL=95954],aides brino[&&NHX:TOL=95955],aides duma[&&NHX:TOL=95956],aides dysoni[&&NHX:TOL=95957],aides ocrinus[&&NHX:TOL=95958])aides[&&NHX:TOL=94982],argon lota[&&NHX:TOL=94983],(aroma aroma[&&NHX:TOL=95959],aroma henricus[&&NHX:TOL=95960])aroma[&&NHX:TOL=94984],calpodes ethlius[&&NHX:TOL=94985],(carystina aurifer[&&NHX:TOL=95961],carystina lysiteles[&&NHX:TOL=95962],carystina pieris[&&NHX:TOL=95963])carystina[&&NHX:TOL=94986],(carystoides abrahami[&&NHX:TOL=95964],carystoides alda[&&NHX:TOL=95965],carystoides balza[&&NHX:TOL=95966],carystoides basoches[&&NHX:TOL=95967],carystoides cathaea[&&NHX:TOL=95968],carystoides certima[&&NHX:TOL=95969],carystoides escalantei[&&NHX:TOL=95970],carystoides floresi[&&NHX:TOL=95971],carystoides hondura[&&NHX:TOL=95972],carystoides lebbaeus[&&NHX:TOL=95973],carystoides lila[&&NHX:TOL=95974],carystoides manta[&&NHX:TOL=95975],carystoides maroma[&&NHX:TOL=95976],carystoides mexicana[&&NHX:TOL=95977],carystoides noseda[&&NHX:TOL=95978],carystoides siciana[&&NHX:TOL=95979],carystoides yenna[&&NHX:TOL=95980])carystoides[&&NHX:TOL=94987],(carystus diores[&&NHX:TOL=95981],carystus elvira[&&NHX:TOL=95982],carystus hocus[&&NHX:TOL=95983],carystus jolus[&&NHX:TOL=95984],carystus junior[&&NHX:TOL=95985],carystus periphas[&&NHX:TOL=95986],carystus phorcus[&&NHX:TOL=95987],carystus ploetzi[&&NHX:TOL=95988],carystus superbiens[&&NHX:TOL=95989],carystus cacaulandia[&&NHX:TOL=112945],carystus rufoventris[&&NHX:TOL=112946])carystus[&&NHX:TOL=94988],chloeria psittacina[&&NHX:TOL=94989],cobaloides argus[&&NHX:TOL=94990],(cobalus calvina[&&NHX:TOL=95990],cobalus discors[&&NHX:TOL=95991],cobalus virbius[&&NHX:TOL=95992])cobalus[&&NHX:TOL=94991],(damas clavus[&&NHX:TOL=95993],damas horridus[&&NHX:TOL=95994],damas immacula[&&NHX:TOL=95995])damas[&&NHX:TOL=94992],(dubiella dubius[&&NHX:TOL=95996],dubiella fiscella[&&NHX:TOL=95997])dubiella[&&NHX:TOL=94993],ebusus ebusus[&&NHX:TOL=94994],evansiella cordela[&&NHX:TOL=94995],(lychnuchoides ozias[&&NHX:TOL=95998],lychnuchoides saptine[&&NHX:TOL=95999])lychnuchoides[&&NHX:TOL=94996],(lychnuchus brasta[&&NHX:TOL=96000],lychnuchus celsus[&&NHX:TOL=96001],lychnuchus pelta[&&NHX:TOL=96002],lychnuchus victa[&&NHX:TOL=96003])lychnuchus[&&NHX:TOL=94997],megaleas syrna[&&NHX:TOL=94998],moeros moeros[&&NHX:TOL=94999],(neoxeniades bajula[&&NHX:TOL=96004],neoxeniades braesia[&&NHX:TOL=96005],neoxeniades cincia[&&NHX:TOL=96006],neoxeniades irena[&&NHX:TOL=96007],neoxeniades molion[&&NHX:TOL=96008],neoxeniades myra[&&NHX:TOL=96010],neoxeniades seron[&&NHX:TOL=96012],(neoxeniades scipio[&&NHX:TOL=96011],neoxeniades anchicayensis[&&NHX:TOL=112948],neoxeniades tropa[&&NHX:TOL=96013],neoxeniades musarion[&&NHX:TOL=96009])scipio group[&&NHX:TOL=112947])neoxeniades[&&NHX:TOL=95000],(nyctus crinitus[&&NHX:TOL=96014],nyctus hiarbas[&&NHX:TOL=96015])nyctus[&&NHX:TOL=95001],(orphe gerasa[&&NHX:TOL=96016],orphe vatinius[&&NHX:TOL=96017])orphe[&&NHX:TOL=95002],(panoquina bola[&&NHX:TOL=96018],panoquina chapada[&&NHX:TOL=96019],panoquina corrupta[&&NHX:TOL=96020],panoquina errans[&&NHX:TOL=96021],panoquina evadnes[&&NHX:TOL=96022],panoquina evansi[&&NHX:TOL=96023],panoquina fusina[&&NHX:TOL=96024],panoquina hecebolus[&&NHX:TOL=96025],panoquina lucas[&&NHX:TOL=96026],panoquina luctuosa[&&NHX:TOL=96027],panoquina nero[&&NHX:TOL=96028],panoquina ocola[&&NHX:TOL=96029],panoquina panoquin[&&NHX:TOL=96030],panoquina panoquinoides[&&NHX:TOL=96031],panoquina pauper[&&NHX:TOL=96032],panoquina peraea[&&NHX:TOL=96033],panoquina trix[&&NHX:TOL=96034])panoquina[&&NHX:TOL=95003],(sacrator polites[&&NHX:TOL=96035],sacrator sacrator[&&NHX:TOL=96036])sacrator[&&NHX:TOL=95004],(saliana antoninus[&&NHX:TOL=96037],saliana chiomara[&&NHX:TOL=96038],saliana covancae[&&NHX:TOL=96039],saliana esperi[&&NHX:TOL=96040],saliana fischer[&&NHX:TOL=96041],saliana fusta[&&NHX:TOL=96042],saliana hewitsoni[&&NHX:TOL=96043],saliana longirostris[&&NHX:TOL=96044],saliana mamurra[&&NHX:TOL=96045],saliana mathiolus[&&NHX:TOL=96046],saliana morsa[&&NHX:TOL=96047],saliana nigel[&&NHX:TOL=96048],saliana placens[&&NHX:TOL=96049],saliana saladin[&&NHX:TOL=96050],saliana salius[&&NHX:TOL=96051],saliana salona[&&NHX:TOL=96052],saliana salva[&&NHX:TOL=96053],saliana severus[&&NHX:TOL=96054],saliana triangularis[&&NHX:TOL=96055],saliana vixen[&&NHX:TOL=96056])saliana[&&NHX:TOL=95005],(synale cynaxa[&&NHX:TOL=96059],synale elana[&&NHX:TOL=96060],synale hylaspes[&&NHX:TOL=96061],synale metella[&&NHX:TOL=96062],synale sylvanus[&&NHX:TOL=96063])synale[&&NHX:TOL=95006],(talides alternata[&&NHX:TOL=96064],talides cantra[&&NHX:TOL=96065],talides hispa[&&NHX:TOL=96066],talides riosa[&&NHX:TOL=96067],talides sergestus[&&NHX:TOL=96068],talides sinois[&&NHX:TOL=96069])talides[&&NHX:TOL=95007],(telles arcalaus[&&NHX:TOL=96070],telles pyrex[&&NHX:TOL=96071])telles[&&NHX:TOL=95008],tellona variegata[&&NHX:TOL=95009],(thracides cilissa[&&NHX:TOL=96072],thracides cleanthes[&&NHX:TOL=96073],thracides joannisii[&&NHX:TOL=96074],thracides nanea[&&NHX:TOL=96075],thracides panimeron[&&NHX:TOL=96076],thracides phidon[&&NHX:TOL=96077],thracides thrasea[&&NHX:TOL=96078])thracides[&&NHX:TOL=95010],(tisias caesena[&&NHX:TOL=96602],tisias carystoides[&&NHX:TOL=96603],tisias lesueur[&&NHX:TOL=96604],tisias myna[&&NHX:TOL=96605],tisias quadrata[&&NHX:TOL=96606],tisias rinda[&&NHX:TOL=96607])tisias[&&NHX:TOL=96600],(tromba tromba[&&NHX:TOL=96079],tromba xanthura[&&NHX:TOL=96080])tromba[&&NHX:TOL=95011],(turesis basta[&&NHX:TOL=96081],turesis complanula[&&NHX:TOL=96082],turesis osibius[&&NHX:TOL=96083],turesis tabascoensis[&&NHX:TOL=96084],turesis theste[&&NHX:TOL=96085])turesis[&&NHX:TOL=95012],(turmada camposa[&&NHX:TOL=96086],turmada turmada[&&NHX:TOL=96087])turmada[&&NHX:TOL=95013],(zenis jebus[&&NHX:TOL=96088],zenis minos[&&NHX:TOL=96089])zenis[&&NHX:TOL=95014])calpodini[&&NHX:TOL=94927],(((((anthoptus epictetus[&&NHX:TOL=96541],anthoptus inculta[&&NHX:TOL=96542],anthoptus insignis[&&NHX:TOL=96543],anthoptus macalpinei[&&NHX:TOL=96544],anthoptus maracanae[&&NHX:TOL=96545])anthoptus[&&NHX:TOL=94973],(corticea aidae[&&NHX:TOL=96546],corticea bella[&&NHX:TOL=96547],corticea corticea[&&NHX:TOL=96548],corticea diamantina[&&NHX:TOL=96549],corticea graziellae[&&NHX:TOL=96550],corticea immocerinus[&&NHX:TOL=96551],corticea lysias[&&NHX:TOL=96552],corticea mendica[&&NHX:TOL=96553],corticea noctis[&&NHX:TOL=96554],corticea oblinita[&&NHX:TOL=96555],corticea obscura[&&NHX:TOL=96556],corticea rivula[&&NHX:TOL=96557],corticea similea[&&NHX:TOL=110608])corticea[&&NHX:TOL=94974])[&&NHX:TOL=138404],(synapte lutulenta[&&NHX:TOL=96570],synapte malitiosa[&&NHX:TOL=96571],synapte puma[&&NHX:TOL=96572],synapte salenus[&&NHX:TOL=96573],synapte shiva[&&NHX:TOL=96574],synapte silius[&&NHX:TOL=96575],synapte syraces[&&NHX:TOL=96576])synapte[&&NHX:TOL=94977])[&&NHX:TOL=138403],(falga farina[&&NHX:TOL=96564],falga jeconia[&&NHX:TOL=96565],falga sciras[&&NHX:TOL=96566],falga theoclea[&&NHX:TOL=96567])falga[&&NHX:TOL=94975],(mnaseas bias[&&NHX:TOL=96568],mnseas bicolor[&&NHX:TOL=96569])mnaseas[&&NHX:TOL=94976],(wahydra bella[&&NHX:TOL=96577],wahydra dores[&&NHX:TOL=96578],wahydra kenava[&&NHX:TOL=96579],wahydra nieblensis[&&NHX:TOL=96580],wahydra obscura[&&NHX:TOL=96581],wahydra subhebetis[&&NHX:TOL=96582],wahydra tassa[&&NHX:TOL=96583],wahydra thisbe[&&NHX:TOL=96584],wahydra vola[&&NHX:TOL=96585])wahydra[&&NHX:TOL=94978],(zalomes allynorum[&&NHX:TOL=96586],zalomes banco[&&NHX:TOL=96587],zalomes biforis[&&NHX:TOL=96588],zalomes conspicua[&&NHX:TOL=96589],zalomes cordillera[&&NHX:TOL=96590],zalomes coto[&&NHX:TOL=96591],zalomes illimanensis[&&NHX:TOL=96592],zalomes merida[&&NHX:TOL=96593],zalomes naco[&&NHX:TOL=96594],zalomes wanda[&&NHX:TOL=96595])zalomes[&&NHX:TOL=94979])anthoptini[&&NHX:TOL=94929],(((((cumbre belli[&&NHX:TOL=95524],cumbre cumbre[&&NHX:TOL=95525],cumbre triumviralis[&&NHX:TOL=95526])cumbre[&&NHX:TOL=95024],(lucida bocus[&&NHX:TOL=95638],lucida lucia[&&NHX:TOL=95639],lucida ranesus[&&NHX:TOL=95640],lucida rogan[&&NHX:TOL=95641],lucida schmithi[&&NHX:TOL=95642])lucida[&&NHX:TOL=95043])[&&NHX:TOL=138405],(eutychide asema[&&NHX:TOL=95577],eutychide complana[&&NHX:TOL=95578],eutychide olympia[&&NHX:TOL=95579],eutychide paria[&&NHX:TOL=95580],eutychide physcella[&&NHX:TOL=95581],eutychide rastaca[&&NHX:TOL=95582],eutychide subcordata[&&NHX:TOL=95583],eutychide subpunctata[&&NHX:TOL=95584])eutychide[&&NHX:TOL=95030],(((lento apta[&&NHX:TOL=95601],lento ferrago[&&NHX:TOL=95602],lento flavocostata[&&NHX:TOL=95603],lento genta[&&NHX:TOL=95604],lento grosso[&&NHX:TOL=95605],lento hermione[&&NHX:TOL=95606],lento imerius[&&NHX:TOL=95607],lento kadeni[&&NHX:TOL=95608],lento krexoides[&&NHX:TOL=95609],lento lento[&&NHX:TOL=95610],lento listo[&&NHX:TOL=95611],lento longa[&&NHX:TOL=95612],lento lora[&&NHX:TOL=95613],lento lotus[&&NHX:TOL=95614],lento lucto[&&NHX:TOL=95615],lento ludo[&&NHX:TOL=95616],lento pyra[&&NHX:TOL=95617],lento vicinus[&&NHX:TOL=95618],lento xanthina[&&NHX:TOL=95619])lento[&&NHX:TOL=95039],(virga austrinus[&&NHX:TOL=95902],virga clenchi[&&NHX:TOL=95903],virga hygrophila[&&NHX:TOL=95904],virga paraiba[&&NHX:TOL=95905],virga riparia[&&NHX:TOL=95906],virga silvanus[&&NHX:TOL=95907],virga virginius[&&NHX:TOL=95908],virga xantho[&&NHX:TOL=95909])virga[&&NHX:TOL=95094])[&&NHX:TOL=138415],(callimormus alsimo[&&NHX:TOL=95493],callimormus corades[&&NHX:TOL=95494],callimormus corus[&&NHX:TOL=95495],callimormus interpunctata[&&NHX:TOL=95496],callimormus juventus[&&NHX:TOL=95497],callimormus radiola[&&NHX:TOL=95498],callimormus rivera[&&NHX:TOL=95499],callimormus saturnus[&&NHX:TOL=95500],callimormus simplicius[&&NHX:TOL=95501])callimormus[&&NHX:TOL=95021])[&&NHX:TOL=138414],(((mnasicles geta[&&NHX:TOL=95650],mnasicles hicetaon[&&NHX:TOL=95651],mnasicles thymoetes[&&NHX:TOL=95652])mnasicles[&&NHX:TOL=95048],(remella cusillunia[&&NHX:TOL=95795],remella duena[&&NHX:TOL=95796],remella remus[&&NHX:TOL=95797],remella rita[&&NHX:TOL=95799],remella vopiscus[&&NHX:TOL=95800])remella[&&NHX:TOL=95076])[&&NHX:TOL=138407],((amblyscirtes aesculapius[&&NHX:TOL=95446],amblyscirtes carolina[&&NHX:TOL=95451],amblyscirtes elissa[&&NHX:TOL=95454],amblyscirtes hegon[&&NHX:TOL=95461],amblyscirtes reversa[&&NHX:TOL=95470],amblyscirtes texanae[&&NHX:TOL=95472])amblyscirtes aesculapius group[&&NHX:TOL=138408],(amblyscirtes aenus[&&NHX:TOL=95445],amblyscirtes cassus[&&NHX:TOL=95452],amblyscirtes exoteria[&&NHX:TOL=95456],amblyscirtes linda[&&NHX:TOL=95462],amblyscirtes oslari[&&NHX:TOL=95466])amblyscirtes exoteria group[&&NHX:TOL=138409],(amblyscirtes fimbriata[&&NHX:TOL=95457],amblyscirtes phylace[&&NHX:TOL=95468])amblyscirtes phylace group[&&NHX:TOL=138410],(amblyscirtes celia[&&NHX:TOL=95453],amblyscirtes tolteca[&&NHX:TOL=95473],amblyscirtes belli[&&NHX:TOL=95449])amblyscirtes tolteca group[&&NHX:TOL=138411],(amblyscirtes alternata[&&NHX:TOL=95447],amblyscirtes eos[&&NHX:TOL=95455],amblyscirtes nereus[&&NHX:TOL=95463],amblyscirtes nysa[&&NHX:TOL=95465],amblyscirtes vialis[&&NHX:TOL=95474])amblyscirtes vialis group[&&NHX:TOL=138412],amblyscirtes anubis[&&NHX:TOL=95448],amblyscirtes brocki[&&NHX:TOL=95450],amblyscirtes florus[&&NHX:TOL=95458],amblyscirtes fluonia[&&NHX:TOL=95459],amblyscirtes folia[&&NHX:TOL=95460],amblyscirtes novimmaculatus[&&NHX:TOL=95464],amblyscirtes patriciae[&&NHX:TOL=95467],amblyscirtes raphaeli[&&NHX:TOL=95469])amblyscirtes[&&NHX:TOL=95016])[&&NHX:TOL=138406],(((saturnus harpe[&&NHX:TOL=124555],saturnus metonidia[&&NHX:TOL=95803],saturnus reticulata[&&NHX:TOL=95804],saturnus saturnus[&&NHX:TOL=95805],saturnus steinbachi[&&NHX:TOL=95806])saturnus[&&NHX:TOL=95080],(vettius argentus[&&NHX:TOL=95858],vettius artona[&&NHX:TOL=95859],vettius arva[&&NHX:TOL=95860],vettius chagres[&&NHX:TOL=95861],vettius coryna[&&NHX:TOL=95862],vettius crispa[&&NHX:TOL=95863],vettius diana[&&NHX:TOL=95864],vettius diversa[&&NHX:TOL=95865],vettius drova[&&NHX:TOL=95866],vettius fantasos[&&NHX:TOL=95867],vettius fuldai[&&NHX:TOL=95868],vettius jabesa[&&NHX:TOL=95869],vettius klugi[&&NHX:TOL=95870],vettius lafrenaye[&&NHX:TOL=95871],vettius lucretius[&&NHX:TOL=95872],vettius marcus[&&NHX:TOL=95873],vettius monacha[&&NHX:TOL=95874],vettius onaca[&&NHX:TOL=95875],vettius phyllus[&&NHX:TOL=95876],vettius ploetzii[&&NHX:TOL=95877],vettius richardi[&&NHX:TOL=95878],vettius tertianus[&&NHX:TOL=95879],vettius triangularis[&&NHX:TOL=95880],vettius umbrata[&&NHX:TOL=95881])vettius[&&NHX:TOL=95090])[&&NHX:TOL=138417],(((cymaenes albiventris[&&NHX:TOL=95527],cymaenes alumna[&&NHX:TOL=95528],cymaenes campestris[&&NHX:TOL=95529],cymaenes cavalla[&&NHX:TOL=95530],cymaenes chapa[&&NHX:TOL=95531],cymaenes chela[&&NHX:TOL=95532],cymaenes distigma[&&NHX:TOL=95533],cymaenes finca[&&NHX:TOL=95534],cymaenes fraus[&&NHX:TOL=95535],cymaenes gisca[&&NHX:TOL=95536],cymaenes idria[&&NHX:TOL=95537],cymaenes jamba[&&NHX:TOL=95538],cymaenes laurelolus[&&NHX:TOL=95539],cymaenes laza[&&NHX:TOL=95540],cymaenes lepta[&&NHX:TOL=95541],cymaenes limae[&&NHX:TOL=95542],cymaenes mabillei[&&NHX:TOL=95543],cymaenes modestus[&&NHX:TOL=95544],cymaenes odilia[&&NHX:TOL=95545],cymaenes perloides[&&NHX:TOL=95546],cymaenes psyllus[&&NHX:TOL=95547],cymaenes riba[&&NHX:TOL=95548],cymaenes tripunctata[&&NHX:TOL=95549],cymaenes tripunctus[&&NHX:TOL=95550],cymaenes uruba[&&NHX:TOL=95551],cymaenes warreni[&&NHX:TOL=95552],cymaenes zama[&&NHX:TOL=95553])cymaenes[&&NHX:TOL=95025],(vidius anna[&&NHX:TOL=95882],vidius catarinae[&&NHX:TOL=95883],vidius felus[&&NHX:TOL=95884],vidius fido[&&NHX:TOL=95885],vidius laska[&&NHX:TOL=95886],vidius mictra[&&NHX:TOL=95887],vidius nappa[&&NHX:TOL=95888],vidius nostra[&&NHX:TOL=95889],vidius ochraceus[&&NHX:TOL=95890],vidius perigenes[&&NHX:TOL=95891],vidius similis[&&NHX:TOL=95892],vidius spitzi[&&NHX:TOL=95893],vidius tinta[&&NHX:TOL=95894],vidius vidius[&&NHX:TOL=95895],vidius xanthus[&&NHX:TOL=95896])vidius[&&NHX:TOL=95091])[&&NHX:TOL=138419],((papias cascatona[&&NHX:TOL=95720],papias dictys[&&NHX:TOL=95721],papias ignarus[&&NHX:TOL=95722],papias phaeomelas[&&NHX:TOL=95723],papias phainis[&&NHX:TOL=95724],papias projectus[&&NHX:TOL=95725],papias quigua[&&NHX:TOL=95726],papias subcostulata[&&NHX:TOL=95727],papias trimacula[&&NHX:TOL=95728],papias tristissimus[&&NHX:TOL=95729])papias[&&NHX:TOL=95064],(vehilius barrosi[&&NHX:TOL=95840],vehilius celeus[&&NHX:TOL=95841],vehilius clavicula[&&NHX:TOL=95842],vehilius gorta[&&NHX:TOL=95843],vehilius inca[&&NHX:TOL=95844],vehilius lugubris[&&NHX:TOL=95845],vehilius madius[&&NHX:TOL=95846],vehilius major[&&NHX:TOL=95847],vehilius putus[&&NHX:TOL=95848],vehilius seriatus[&&NHX:TOL=95849],vehilius stictomenes[&&NHX:TOL=95850],vehilius vetula[&&NHX:TOL=95851])vehilius[&&NHX:TOL=95087])[&&NHX:TOL=138420],((mnasilus allubita[&&NHX:TOL=95049],(monca branca[&&NHX:TOL=95671],monca jera[&&NHX:TOL=95672],monca ornata[&&NHX:TOL=95673],monca telata[&&NHX:TOL=95674])monca[&&NHX:TOL=95055])[&&NHX:TOL=138422],(morys compta[&&NHX:TOL=95675],morys geisa[&&NHX:TOL=95676],morys sinta[&&NHX:TOL=95677],morys sobra[&&NHX:TOL=95678],morys subgrisea[&&NHX:TOL=95679],morys subviridis[&&NHX:TOL=95680],morys valerius[&&NHX:TOL=95681],morys yahua[&&NHX:TOL=95682])morys[&&NHX:TOL=95056])[&&NHX:TOL=138421])[&&NHX:TOL=138418],(adlerodea lemba[&&NHX:TOL=95441],adlerodea mineira[&&NHX:TOL=95442],adlerodea modesta[&&NHX:TOL=95443],adlerodea petrovna[&&NHX:TOL=95444])adlerodea[&&NHX:TOL=95015],(arita arita[&&NHX:TOL=95478],arita mubevensis[&&NHX:TOL=95479],arita polistion[&&NHX:TOL=95480],arita serra[&&NHX:TOL=95481])arita[&&NHX:TOL=95018],(artines acroleuca[&&NHX:TOL=95482],artines aepitus[&&NHX:TOL=95483],artines aquilina[&&NHX:TOL=95484],artines bipunctata[&&NHX:TOL=95485],artines focus[&&NHX:TOL=95486],artines fosca[&&NHX:TOL=95487],artines satyr[&&NHX:TOL=95488],artines tobiasi[&&NHX:TOL=95489],artines trogon[&&NHX:TOL=95490],artines rica[&&NHX:TOL=95491])artines[&&NHX:TOL=95019],(apaustus gracilis[&&NHX:TOL=95475],apaustus menes[&&NHX:TOL=95476],apaustus radiatus[&&NHX:TOL=95477])apaustus[&&NHX:TOL=95017],(cobalopsis autumna[&&NHX:TOL=95508],cobalopsis brema[&&NHX:TOL=95509],cobalopsis catocala[&&NHX:TOL=95510],cobalopsis cocalus[&&NHX:TOL=95511],cobalopsis dagon[&&NHX:TOL=95512],cobalopsis dorpa[&&NHX:TOL=95513],cobalopsis hazarma[&&NHX:TOL=95514],cobalopsis latonia[&&NHX:TOL=95515],cobalopsis miaba[&&NHX:TOL=95516],cobalopsis monotona[&&NHX:TOL=95517],cobalopsis nero[&&NHX:TOL=95518],cobalopsis obscurior[&&NHX:TOL=95519],cobalopsis similis[&&NHX:TOL=95520],cobalopsis tanna[&&NHX:TOL=95521],cobalopsis venias[&&NHX:TOL=95522],cobalopsis vorgia[&&NHX:TOL=95523])cobalopsis[&&NHX:TOL=95023],crinifemur viridans[&&NHX:TOL=124551],(eutocus arabupuana[&&NHX:TOL=95569],eutocus fabulinus[&&NHX:TOL=95570],eutocus facilis[&&NHX:TOL=95571],eutocus minimus[&&NHX:TOL=95572],eutocus minor[&&NHX:TOL=95573],eutocus paulo[&&NHX:TOL=95574],eutocus quichua[&&NHX:TOL=95575],eutocus vetulus[&&NHX:TOL=95576])eutocus[&&NHX:TOL=95029],eprius veleda[&&NHX:TOL=95028],flaccilla aecas[&&NHX:TOL=95031],gallio carasta[&&NHX:TOL=95032],igapophilus rufus[&&NHX:TOL=95034],inglorius mediocris[&&NHX:TOL=95035],(justinia gava[&&NHX:TOL=95590],justinia gertschi[&&NHX:TOL=95591],justinia justinianus[&&NHX:TOL=95592],justinia kora[&&NHX:TOL=95593],justinia maculata[&&NHX:TOL=95594],justinia papaea[&&NHX:TOL=95595],justinia phaetusa[&&NHX:TOL=95596],justinia septa[&&NHX:TOL=95597])justinia[&&NHX:TOL=95037],(lamponia elegantula[&&NHX:TOL=95598],lamponia lamponia[&&NHX:TOL=95599],lamponia travassosi[&&NHX:TOL=95600])lamponia[&&NHX:TOL=95038],(lerema accius[&&NHX:TOL=95620],lerema ancillaris[&&NHX:TOL=95621],lerema caraca[&&NHX:TOL=95622],lerema duroca[&&NHX:TOL=95623],lerema lineosa[&&NHX:TOL=95624],lerema lumina[&&NHX:TOL=95625],lerema veadeira[&&NHX:TOL=95626],lerema viridis[&&NHX:TOL=95627])lerema[&&NHX:TOL=95040],(ludens ludens[&&NHX:TOL=95643],ludens petrovna[&&NHX:TOL=95644],ludens silvaticus[&&NHX:TOL=95645])ludens[&&NHX:TOL=95044],methion melas[&&NHX:TOL=95045],(methionopsis dolor[&&NHX:TOL=95646],methionopsis ina[&&NHX:TOL=95647],methionopsis purus[&&NHX:TOL=95648],methionopsis typhon[&&NHX:TOL=95649])methionopsis[&&NHX:TOL=95046],mnasinous patage[&&NHX:TOL=95050],(mnasitheus cephoides[&&NHX:TOL=95653],mnasitheus chrysophrys[&&NHX:TOL=95654],mnasitheus continua[&&NHX:TOL=95655],mnasitheus forma[&&NHX:TOL=95656],mnasitheus gemignanii[&&NHX:TOL=95657],mnasitheus nella[&&NHX:TOL=95658],mnasitheus nitra[&&NHX:TOL=95659],mnasitheus ritans[&&NHX:TOL=95660],mnasitheus simplicissima[&&NHX:TOL=95661],mnasitheus spangla[&&NHX:TOL=95662],mnasitheus strandi[&&NHX:TOL=95663])mnasitheus[&&NHX:TOL=95051],(mnestheus damma[&&NHX:TOL=95664],mnestheus ittona[&&NHX:TOL=95665])mnestheus[&&NHX:TOL=95052],(moeris ekka[&&NHX:TOL=95666],moeris hyagnis[&&NHX:TOL=95667],moeris padus[&&NHX:TOL=95668],moeris striga[&&NHX:TOL=95669],moeris submetallescens[&&NHX:TOL=95670])moeris[&&NHX:TOL=95053],molla molla[&&NHX:TOL=95054],naevolus orius[&&NHX:TOL=95058],(nastra chao[&&NHX:TOL=95687],nastra dryas[&&NHX:TOL=95688],nastra ethologus[&&NHX:TOL=95689],nastra guianae[&&NHX:TOL=95690],nastra incomptus[&&NHX:TOL=95691],nastra julia[&&NHX:TOL=95692],nastra leucone[&&NHX:TOL=95693],nastra lherminier[&&NHX:TOL=95694],nastra lurida[&&NHX:TOL=95695],nastra neamathla[&&NHX:TOL=95696],nastra tanta[&&NHX:TOL=95697])nastra[&&NHX:TOL=95059],(onophas chlorocephala[&&NHX:TOL=95715],onophas columbaria[&&NHX:TOL=95716],onophas watsoni[&&NHX:TOL=95717])onophas[&&NHX:TOL=95061],(pamba boyaca[&&NHX:TOL=95718],pamba pamba[&&NHX:TOL=95719])pamba[&&NHX:TOL=95062],panca subpunctuli[&&NHX:TOL=95063],(paracarystus evansi[&&NHX:TOL=95730],paracarystus hypagyra[&&NHX:TOL=95731],paracarystus menestries[&&NHX:TOL=95732])paracarystus[&&NHX:TOL=95065],peba verames[&&NHX:TOL=95067],(phanes abaris[&&NHX:TOL=95754],phanes aletes[&&NHX:TOL=95755],phanes almoda[&&NHX:TOL=95756],phanes espa[&&NHX:TOL=95757],phanes monastica[&&NHX:TOL=95758],phanes rezia[&&NHX:TOL=95759],phanes tavola[&&NHX:TOL=95760])phanes[&&NHX:TOL=95069],(psoralis brunnescens[&&NHX:TOL=95784],psoralis chittara[&&NHX:TOL=95785],psoralis concolor[&&NHX:TOL=95786],psoralis coyana[&&NHX:TOL=95787],psoralis degener[&&NHX:TOL=95788],psoralis exclamationis[&&NHX:TOL=95789],psoralis gota[&&NHX:TOL=95790],psoralis idee[&&NHX:TOL=95791],psoralis rusta[&&NHX:TOL=95792],psoralis stacara[&&NHX:TOL=95793],psoralis venta[&&NHX:TOL=95794])psoralis[&&NHX:TOL=95073],radiatus radiatus[&&NHX:TOL=95075],repens repens[&&NHX:TOL=95077],saniba sabina[&&NHX:TOL=95079],sucova sucova[&&NHX:TOL=95083],(thargella caura[&&NHX:TOL=95818],thargella evansi[&&NHX:TOL=95819])thargella[&&NHX:TOL=95084],(thoon aethus[&&NHX:TOL=95820],thoon canta[&&NHX:TOL=95821],thoon circellata[&&NHX:TOL=95822],thoon dubia[&&NHX:TOL=95823],thoon maritza[&&NHX:TOL=95824],thoon modius[&&NHX:TOL=95825],thoon opus[&&NHX:TOL=124553],thoon ponka[&&NHX:TOL=95826],thoon ranka[&&NHX:TOL=95827],thoon slopa[&&NHX:TOL=95828],thoon taxes[&&NHX:TOL=95829],thoon yesta[&&NHX:TOL=95830])thoon[&&NHX:TOL=95085],(tigasis coda[&&NHX:TOL=95831],tigasis colomus[&&NHX:TOL=95832],tigasis fusca[&&NHX:TOL=95833],tigasis garima[&&NHX:TOL=95834],tigasis nausiphanes[&&NHX:TOL=95835],tigasis physcoa[&&NHX:TOL=95836],tigasis simplex[&&NHX:TOL=95837],tigasis viridenex[&&NHX:TOL=95838],tigasis zalates[&&NHX:TOL=95839])tigasis[&&NHX:TOL=95086],(venas caerulans[&&NHX:TOL=95852],venas evans[&&NHX:TOL=95853])venas[&&NHX:TOL=95088])apaustus group[&&NHX:TOL=138416],((niconiades bifurcus[&&NHX:TOL=134180],niconiades caeso[&&NHX:TOL=95698],niconiades centralis[&&NHX:TOL=95699],niconiades comitana[&&NHX:TOL=95700],niconiades cydia[&&NHX:TOL=95701],niconiades gladys[&&NHX:TOL=95702],niconiades incomptus[&&NHX:TOL=95703],niconiades linga[&&NHX:TOL=95704],niconiades loda[&&NHX:TOL=95705],niconiades merenda[&&NHX:TOL=95706],niconiades nabona[&&NHX:TOL=95707],niconiades nikko[&&NHX:TOL=95708],niconiades pares[&&NHX:TOL=95709],niconiades parna[&&NHX:TOL=95710],niconiades tina[&&NHX:TOL=95711],niconiades viridis[&&NHX:TOL=95712],niconiades xanthaphes[&&NHX:TOL=95713],niconiades yoka[&&NHX:TOL=95714])niconiades[&&NHX:TOL=95060],(penicula advena[&&NHX:TOL=95747],penicula bryanti[&&NHX:TOL=95748],penicula crista[&&NHX:TOL=95749],penicula cristatus[&&NHX:TOL=95750],penicula cristina[&&NHX:TOL=95751],penicula roppai[&&NHX:TOL=95752],penicula subviridis[&&NHX:TOL=95753])penicula[&&NHX:TOL=95068])[&&NHX:TOL=138423],(sodalia coler[&&NHX:TOL=95807],sodalia dimassa[&&NHX:TOL=95808],sodalia sodalis[&&NHX:TOL=95809])sodalia[&&NHX:TOL=95081],(vinius exilis[&&NHX:TOL=95897],vinius letis[&&NHX:TOL=95898],vinius pulcherrimus[&&NHX:TOL=95899],vinius sagitta[&&NHX:TOL=95900],vinius tryhana[&&NHX:TOL=95901])vinius[&&NHX:TOL=95092])[&&NHX:TOL=138413],((dion carmenta[&&NHX:TOL=95554],dion gemmatus[&&NHX:TOL=95555],dion meda[&&NHX:TOL=95556])dion[&&NHX:TOL=95026],(enosis achelous[&&NHX:TOL=95557],enosis angularis[&&NHX:TOL=95558],enosis aphilos[&&NHX:TOL=95559],enosis blenda[&&NHX:TOL=95560],enosis blotta[&&NHX:TOL=95561],enosis dognini[&&NHX:TOL=95562],enosis iccius[&&NHX:TOL=95563],enosis immaculata[&&NHX:TOL=95564],enosis matheri[&&NHX:TOL=95565],enosis schausi[&&NHX:TOL=95566],enosis topo[&&NHX:TOL=95567],enosis uza[&&NHX:TOL=95568])enosis[&&NHX:TOL=95027],miltomiges cinnamomea[&&NHX:TOL=95047],(styriodes badius[&&NHX:TOL=95810],styriodes dedecora[&&NHX:TOL=95811],styriodes lyco[&&NHX:TOL=95812],styriodes penna[&&NHX:TOL=95813],styriodes planus[&&NHX:TOL=95814],styriodes quadrinotata[&&NHX:TOL=95815],styriodes quota[&&NHX:TOL=95816],styriodes zeteki[&&NHX:TOL=95817])styriodes[&&NHX:TOL=95082],(vertica ibis[&&NHX:TOL=95854],vertica pudor[&&NHX:TOL=95855],vertica umber[&&NHX:TOL=95856],vertica verticalis[&&NHX:TOL=95857])vertica[&&NHX:TOL=95089])[&&NHX:TOL=138424],bruna bruna[&&NHX:TOL=95020],(cantha calva[&&NHX:TOL=95502],cantha honor[&&NHX:TOL=95503],cantha ivea[&&NHX:TOL=95504],cantha matuta[&&NHX:TOL=95505],cantha roraimae[&&NHX:TOL=95506],cantha zara[&&NHX:TOL=95507])cantha[&&NHX:TOL=95022],(halotus angellus[&&NHX:TOL=95585],halotus jonaveriorum[&&NHX:TOL=95586],halotus rica[&&NHX:TOL=95587])halotus[&&NHX:TOL=95033],(joanna boxi[&&NHX:TOL=95588],joanna joanna[&&NHX:TOL=95589],joanna clara[&&NHX:TOL=112949])joanna[&&NHX:TOL=95036],(lerodea arabus[&&NHX:TOL=95628],lerodea casta[&&NHX:TOL=95629],lerodea emba[&&NHX:TOL=95631],lerodea erythrostictus[&&NHX:TOL=95632],lerodea eufala[&&NHX:TOL=95633],lerodea gracia[&&NHX:TOL=95634],lerodea williamsi[&&NHX:TOL=95636],lerodea xenos[&&NHX:TOL=95637])lerodea[&&NHX:TOL=95041],levina levina[&&NHX:TOL=95042],(mucia gulala[&&NHX:TOL=95683],mucia immaculatus[&&NHX:TOL=95684],mucia scitula[&&NHX:TOL=95685],mucia zygia[&&NHX:TOL=95686])mucia[&&NHX:TOL=95057],(parphorus auristriga[&&NHX:TOL=95733],parphorus decora[&&NHX:TOL=95734],parphorus fartuga[&&NHX:TOL=95735],parphorus felta[&&NHX:TOL=95736],parphorus granta[&&NHX:TOL=95737],parphorus hesia[&&NHX:TOL=95738],parphorus ira[&&NHX:TOL=95739],parphorus jaguar[&&NHX:TOL=124549],parphorus oca[&&NHX:TOL=95740],parphorus oeagrus[&&NHX:TOL=95741],parphorus paramus[&&NHX:TOL=95742],parphorus prosper[&&NHX:TOL=95743],parphorus pseudecorus[&&NHX:TOL=95744],parphorus sapala[&&NHX:TOL=95745],parphorus storax[&&NHX:TOL=95746])parphorus[&&NHX:TOL=95066],(pheraeus argynnis[&&NHX:TOL=95761],pheraeus covadonga[&&NHX:TOL=95762],pheraeus fastus[&&NHX:TOL=95763],pheraeus honta[&&NHX:TOL=95764],pheraeus jaruensis[&&NHX:TOL=95765],pheraeus maria[&&NHX:TOL=95766],pheraeus montes[&&NHX:TOL=95767],pheraeus odilia[&&NHX:TOL=95768],pheraeus perpulcher[&&NHX:TOL=95769],pheraeus rumba[&&NHX:TOL=95770],pheraeus unia[&&NHX:TOL=95771])pheraeus[&&NHX:TOL=95070],(phlebodes buriti[&&NHX:TOL=95772],phlebodes campo[&&NHX:TOL=95773],phlebodes confixa[&&NHX:TOL=95774],phlebodes eteocla[&&NHX:TOL=95775],phlebodes meesi[&&NHX:TOL=95776],phlebodes notex[&&NHX:TOL=95777],phlebodes pertinax[&&NHX:TOL=95778],phlebodes sameda[&&NHX:TOL=95779],phlebodes torax[&&NHX:TOL=95780],phlebodes vira[&&NHX:TOL=95781],phlebodes virgo[&&NHX:TOL=95782],phlebodes xanthobasis[&&NHX:TOL=95783])phlebodes[&&NHX:TOL=95071],propapias sipariana[&&NHX:TOL=95072],punta punta[&&NHX:TOL=95074],(rhinthon bushi[&&NHX:TOL=95801],rhinthon cubana[&&NHX:TOL=95802])rhinthon[&&NHX:TOL=95078],vinpeius tinga[&&NHX:TOL=95093],(zariaspes mys[&&NHX:TOL=95910],zariaspes mythecus[&&NHX:TOL=95911])zariaspes[&&NHX:TOL=95095])moncini[&&NHX:TOL=94925],(((((caligulana caligula[&&NHX:TOL=95106],(hansa cotundo[&&NHX:TOL=96255],hansa devergens[&&NHX:TOL=96256],hansa hyboma[&&NHX:TOL=96257])hansa[&&NHX:TOL=95115],(libra aligula[&&NHX:TOL=96306],libra anatolica[&&NHX:TOL=96307])libra[&&NHX:TOL=95120],(lindra boliviana[&&NHX:TOL=96310],lindra brasus[&&NHX:TOL=96311],lindra procax[&&NHX:TOL=96312],lindra simulina[&&NHX:TOL=96313],lindra vanewrighti[&&NHX:TOL=96314])lindra[&&NHX:TOL=95122])[&&NHX:TOL=138428],((((euphyes arpa[&&NHX:TOL=96236],euphyes bimacula[&&NHX:TOL=96239],euphyes vestris[&&NHX:TOL=96254])euphyes vestris group[&&NHX:TOL=138444],(euphyes bayensis[&&NHX:TOL=96237],euphyes berryi[&&NHX:TOL=96238],euphyes conspicuus[&&NHX:TOL=96243],euphyes dion[&&NHX:TOL=96245],euphyes dukesi[&&NHX:TOL=96246],euphyes pilatka[&&NHX:TOL=96251])euphyes dion group[&&NHX:TOL=138445],euphyes ampa[&&NHX:TOL=96234],euphyes antra[&&NHX:TOL=96235],euphyes canda[&&NHX:TOL=96240],euphyes chamuli[&&NHX:TOL=96241],euphyes cherra[&&NHX:TOL=96242],euphyes cornelius[&&NHX:TOL=96244],euphyes eberti[&&NHX:TOL=96247],euphyes fumata[&&NHX:TOL=96248],euphyes leptosema[&&NHX:TOL=96249],euphyes peneia[&&NHX:TOL=96250],euphyes singularis[&&NHX:TOL=96252],euphyes subferrugineus[&&NHX:TOL=96253])euphyes[&&NHX:TOL=95114],notamblyscirtes simius[&&NHX:TOL=95471])[&&NHX:TOL=138430],(thespieus abatira[&&NHX:TOL=96488],thespieus abauna[&&NHX:TOL=96489],thespieus argentina[&&NHX:TOL=96490],thespieus aspernatus[&&NHX:TOL=96491],thespieus caraca[&&NHX:TOL=96492],thespieus castor[&&NHX:TOL=96493],thespieus catochra[&&NHX:TOL=96494],thespieus dalman[&&NHX:TOL=96495],thespieus duidensis[&&NHX:TOL=96496],thespieus ethemides[&&NHX:TOL=96497],thespieus fassli[&&NHX:TOL=96498],thespieus fulvangula[&&NHX:TOL=96499],thespieus haywardi[&&NHX:TOL=96500],thespieus hieroglyphica[&&NHX:TOL=96501],thespieus himella[&&NHX:TOL=96502],thespieus homochromus[&&NHX:TOL=96503],thespieus inez[&&NHX:TOL=96504],thespieus jora[&&NHX:TOL=96505],thespieus lutetia[&&NHX:TOL=96506],thespieus macareus[&&NHX:TOL=96507],thespieus matucanae[&&NHX:TOL=96508],thespieus opigena[&&NHX:TOL=96509],thespieus othna[&&NHX:TOL=96510],thespieus peruviae[&&NHX:TOL=96511],thespieus pinda[&&NHX:TOL=96512],thespieus tapayuna[&&NHX:TOL=96513],thespieus thona[&&NHX:TOL=96514],thespieus tihoneta[&&NHX:TOL=96515],thespieus vividus[&&NHX:TOL=96516],thespieus xarina[&&NHX:TOL=96517],thespieus zikani[&&NHX:TOL=96518],thespieus xarippe[&&NHX:TOL=96519])thespieus[&&NHX:TOL=95150])[&&NHX:TOL=138429])[&&NHX:TOL=138427],(((((conga chydaea[&&NHX:TOL=96198],conga iheringii[&&NHX:TOL=96199],conga immaculata[&&NHX:TOL=96200],conga urqua[&&NHX:TOL=96201],conga zela[&&NHX:TOL=96202])conga[&&NHX:TOL=95109],nyctelius nyctelius[&&NHX:TOL=95128])[&&NHX:TOL=138434],((atalopedes bahiensis[&&NHX:TOL=96168],atalopedes campestris[&&NHX:TOL=96169],atalopedes carteri[&&NHX:TOL=96170],atalopedes flaveola[&&NHX:TOL=96171],atalopedes mesogramma[&&NHX:TOL=96172])atalopedes[&&NHX:TOL=95102],pseudocopaeodes eunus[&&NHX:TOL=95143])[&&NHX:TOL=138435],((hesperia attalus[&&NHX:TOL=96259],hesperia metea[&&NHX:TOL=96269],hesperia viridis[&&NHX:TOL=96277])hesperia metea group[&&NHX:TOL=138439],(hesperia assiniboia[&&NHX:TOL=96258],hesperia colorado[&&NHX:TOL=96260],hesperia comma[&&NHX:TOL=96262],hesperia juba[&&NHX:TOL=96265],hesperia uncas[&&NHX:TOL=96276],hesperia woodgatei[&&NHX:TOL=96278])hesperia comma group[&&NHX:TOL=138440],(hesperia columbia[&&NHX:TOL=96261],hesperia leonardus[&&NHX:TOL=96266],hesperia ottoe[&&NHX:TOL=96273],hesperia pahaska[&&NHX:TOL=96274])hesperia leonardus group[&&NHX:TOL=138441],hesperia dacotae[&&NHX:TOL=96263],hesperia florinda[&&NHX:TOL=96264],hesperia lindseyi[&&NHX:TOL=96267],hesperia meskei[&&NHX:TOL=96268],hesperia miriamae[&&NHX:TOL=96270],hesperia nabokovi[&&NHX:TOL=96271],hesperia nevada[&&NHX:TOL=96272],hesperia sassacus[&&NHX:TOL=96275])hesperia[&&NHX:TOL=95116])[&&NHX:TOL=138433],((hylephila adriennae[&&NHX:TOL=96279],hylephila ignorans[&&NHX:TOL=96286])[&&NHX:TOL=96300],(hylephila ancora[&&NHX:TOL=96280],hylephila fasciolata[&&NHX:TOL=96283],hylephila isonira[&&NHX:TOL=96287],hylephila signata[&&NHX:TOL=96296],hylephila phyleus[&&NHX:TOL=96292],hylephila zapala[&&NHX:TOL=96299])[&&NHX:TOL=96301],((hylephila herrerai[&&NHX:TOL=96285],hylephila pseudoherrerai[&&NHX:TOL=96293],hylephila pallisteri[&&NHX:TOL=96290],hylephila blancasi[&&NHX:TOL=96281],hylephila tentativa[&&NHX:TOL=96297])[&&NHX:TOL=96303],(hylephila shapiroi[&&NHX:TOL=96295],hylephila galera[&&NHX:TOL=96284],hylephila boulleti[&&NHX:TOL=96282],hylephila rossi[&&NHX:TOL=96294],hylephila peruana[&&NHX:TOL=96291])[&&NHX:TOL=96304])[&&NHX:TOL=96302],(hylephila venustus[&&NHX:TOL=96298],hylephila lamasi[&&NHX:TOL=96289],hylephila kenhaywardi[&&NHX:TOL=96288])[&&NHX:TOL=96305])hylephila[&&NHX:TOL=95118],(appia appia[&&NHX:TOL=95099],(pompeius amblyspila[&&NHX:TOL=96403],pompeius dares[&&NHX:TOL=96404],pompeius darina[&&NHX:TOL=96405],pompeius pompeius[&&NHX:TOL=96406],pompeius postpuncta[&&NHX:TOL=96407],pompeius verna[&&NHX:TOL=96408])pompeius[&&NHX:TOL=95140])[&&NHX:TOL=138436],((polites mystic[&&NHX:TOL=96391],polites origenes[&&NHX:TOL=96393],polites sonora[&&NHX:TOL=96398])origenes group[&&NHX:TOL=138442],(polites draco[&&NHX:TOL=96389],polites mardon[&&NHX:TOL=96390],polites peckius[&&NHX:TOL=96388],polites sabuleti[&&NHX:TOL=96397],polites themistocles[&&NHX:TOL=96400])polites themistocles group[&&NHX:TOL=138443],polites baracoa[&&NHX:TOL=96385],polites bittiae[&&NHX:TOL=96386],polites carus[&&NHX:TOL=96387],polites norae[&&NHX:TOL=96392],polites pupillus[&&NHX:TOL=96394],polites puxillius[&&NHX:TOL=96395],polites rhesus[&&NHX:TOL=96396],polites subreticulata[&&NHX:TOL=96399],polites vibex[&&NHX:TOL=96401],polites vibicoides[&&NHX:TOL=96402])polites[&&NHX:TOL=95139])[&&NHX:TOL=138432],((ochlodes agricola[&&NHX:TOL=96325],ochlodes batesi[&&NHX:TOL=96326],ochlodes ochracea[&&NHX:TOL=96328],ochlodes samenta[&&NHX:TOL=96329],ochlodes siva[&&NHX:TOL=96330],ochlodes subhyalina[&&NHX:TOL=96331],ochlodes sylvanoides[&&NHX:TOL=96332],ochlodes thibetana[&&NHX:TOL=96333],ochlodes venata[&&NHX:TOL=96334],ochlodes yuma[&&NHX:TOL=96335])ochlodes[&&NHX:TOL=95129],(poanes aaroni[&&NHX:TOL=96369],poanes azin[&&NHX:TOL=96370],poanes hobomok[&&NHX:TOL=96372],poanes inimica[&&NHX:TOL=96373],poanes macneilli[&&NHX:TOL=96374],poanes massasoit[&&NHX:TOL=96375],poanes melane[&&NHX:TOL=96376],poanes monticola[&&NHX:TOL=96377],poanes niveolimbus[&&NHX:TOL=96378],poanes taxiles[&&NHX:TOL=96379],poanes ulphila[&&NHX:TOL=96380],poanes viator[&&NHX:TOL=96381],poanes yehl[&&NHX:TOL=96382],poanes zabulon[&&NHX:TOL=96383],poanes zachaeus[&&NHX:TOL=96384])poanes[&&NHX:TOL=95138],(stinga morrisoni[&&NHX:TOL=138820],stinga kendamulaza[&&NHX:TOL=138821])stinga[&&NHX:TOL=95149])[&&NHX:TOL=138437])[&&NHX:TOL=138431])[&&NHX:TOL=138426],((((anatrytone logan[&&NHX:TOL=96155],anatrytone mazai[&&NHX:TOL=96156])[&&NHX:TOL=96474],(anatrytone barbara[&&NHX:TOL=96153],anatrytone flavens[&&NHX:TOL=96154])[&&NHX:TOL=96475])[&&NHX:TOL=96473],((anatrytone mella[&&NHX:TOL=96157],anatrytone sarah[&&NHX:TOL=96160])[&&NHX:TOL=96477],anatrytone potosiensis[&&NHX:TOL=96159],anatrytone perfida[&&NHX:TOL=96158])[&&NHX:TOL=96476])anatrytone[&&NHX:TOL=95098],(decinea dama[&&NHX:TOL=96224],decinea decinea[&&NHX:TOL=96225],decinea lucifer[&&NHX:TOL=96226],decinea mammaea[&&NHX:TOL=96227],decinea milesi[&&NHX:TOL=96228],decinea mustea[&&NHX:TOL=96229],decinea neroides[&&NHX:TOL=96230],decinea percosius[&&NHX:TOL=96231],decinea rindgei[&&NHX:TOL=96232],decinea zapota[&&NHX:TOL=96233])decinea[&&NHX:TOL=95113])[&&NHX:TOL=138438])[&&NHX:TOL=138425],(arotis bryna[&&NHX:TOL=96161],arotis derasa[&&NHX:TOL=96162],arotis evansi[&&NHX:TOL=96163],arotis kayei[&&NHX:TOL=96164],arotis mapirica[&&NHX:TOL=96165],arotis pandora[&&NHX:TOL=96166],arotis sirene[&&NHX:TOL=96167])arotis[&&NHX:TOL=95100],asbolis capucinus[&&NHX:TOL=95101],atrytone arogos[&&NHX:TOL=95103],(atrytonopsis cestus[&&NHX:TOL=96173],atrytonopsis deva[&&NHX:TOL=96174],(atrytonopsis edwardsi[&&NHX:TOL=96175],atrytonopsis ovinia[&&NHX:TOL=96180])[&&NHX:TOL=138075],atrytonopsis hianna[&&NHX:TOL=96177],atrytonopsis loammi[&&NHX:TOL=96178],((atrytonopsis frappenda[&&NHX:TOL=96176],atrytonopsis lunus[&&NHX:TOL=96179],atrytonopsis zweifeli[&&NHX:TOL=96184])atrytonopsis lunus group[&&NHX:TOL=138077],atrytonopsis llorentei[&&NHX:TOL=138078])[&&NHX:TOL=138076],atrytonopsis pittacus[&&NHX:TOL=96181],atrytonopsis python[&&NHX:TOL=96182],atrytonopsis vierecki[&&NHX:TOL=96183])atrytonopsis[&&NHX:TOL=95104],((buzyges benito[&&NHX:TOL=96371],buzyges idothea[&&NHX:TOL=138812],buzyges mellanaformis[&&NHX:TOL=138813],buzyges rolla[&&NHX:TOL=138814])buzyges[&&NHX:TOL=95105],librita librita[&&NHX:TOL=95121],(neposa armandoi[&&NHX:TOL=138816],neposa heras[&&NHX:TOL=138817],neposa hestia[&&NHX:TOL=138818],neposa isabelae[&&NHX:TOL=138819])neposa[&&NHX:TOL=138815],(onespa brockorum[&&NHX:TOL=138550],onespa nakamura[&&NHX:TOL=138551],onespa gala[&&NHX:TOL=96351],onespa nubis[&&NHX:TOL=138549])onespa[&&NHX:TOL=95132])[&&NHX:TOL=138811],(chalcone briquenydan[&&NHX:TOL=96185],chalcone santarus[&&NHX:TOL=96186],chalcone tania[&&NHX:TOL=96187],chalcone zisa[&&NHX:TOL=96188])chalcone[&&NHX:TOL=95107],(choranthus borincona[&&NHX:TOL=96189],choranthus haitensis[&&NHX:TOL=96190],choranthus lilliae[&&NHX:TOL=96191],choranthus maria[&&NHX:TOL=96192],choranthus melissa[&&NHX:TOL=96193],choranthus radians[&&NHX:TOL=96194],choranthus richmondi[&&NHX:TOL=96195],choranthus schwartzi[&&NHX:TOL=96196],choranthus vitellius[&&NHX:TOL=96197])choranthus[&&NHX:TOL=95108],(cravera laureatus[&&NHX:TOL=96203],cravera rara[&&NHX:TOL=96204])cravera[&&NHX:TOL=95110],(cyclosma abdonides[&&NHX:TOL=96205],cyclosma altama[&&NHX:TOL=96206],cyclosma glamis[&&NHX:TOL=96207])cyclosma[&&NHX:TOL=95111],(cynea anthracinus[&&NHX:TOL=96208],cynea bistrigula[&&NHX:TOL=96209],cynea corisana[&&NHX:TOL=96210],cynea corope[&&NHX:TOL=96211],cynea cynea[&&NHX:TOL=96212],cynea cyrus[&&NHX:TOL=96213],cynea diluta[&&NHX:TOL=96214],cynea hycsos[&&NHX:TOL=96215],cynea iquita[&&NHX:TOL=96216],cynea irma[&&NHX:TOL=96217],cynea megalops[&&NHX:TOL=96218],cynea melius[&&NHX:TOL=96219],cynea nigricola[&&NHX:TOL=96220],cynea popla[&&NHX:TOL=96221],cynea robba[&&NHX:TOL=96222],cynea trimaculata[&&NHX:TOL=96223])cynea[&&NHX:TOL=95112],holguinia holguin[&&NHX:TOL=95117],jongiana unica[&&NHX:TOL=95119],linka lina[&&NHX:TOL=95123],(metron chrysogastra[&&NHX:TOL=96315],metron leucogaster[&&NHX:TOL=96316],metron noctis[&&NHX:TOL=96317],metron oropa[&&NHX:TOL=96318],metron schrottkyi[&&NHX:TOL=96319],metron zimra[&&NHX:TOL=96320])metron[&&NHX:TOL=95124],misius misius[&&NHX:TOL=95125],(molo calcarea[&&NHX:TOL=96321],molo mango[&&NHX:TOL=96322],molo muzo[&&NHX:TOL=96323],molo visendus[&&NHX:TOL=96324])molo[&&NHX:TOL=95126],neochlodes maculosus[&&NHX:TOL=95127],(oeonus edlichi[&&NHX:TOL=96336],oeonus egma[&&NHX:TOL=96337],oeonus pyste[&&NHX:TOL=96338])oeonus[&&NHX:TOL=95130],oligoria maculata[&&NHX:TOL=95131],(orthos gabina[&&NHX:TOL=96339],orthos lycortas[&&NHX:TOL=96340],orthos orthos[&&NHX:TOL=96341],orthos potesta[&&NHX:TOL=96342],orthos trinka[&&NHX:TOL=96343])orthos[&&NHX:TOL=95133],(oxynthes corusca[&&NHX:TOL=96344],oxynthes viricuculla[&&NHX:TOL=96345])oxynthes[&&NHX:TOL=95134],parachoranthus magdalia[&&NHX:TOL=95135],(paratrytone aphractoia[&&NHX:TOL=96346],paratrytone argentea[&&NHX:TOL=96347],paratrytone barroni[&&NHX:TOL=96348],paratrytone browni[&&NHX:TOL=96349],paratrytone decepta[&&NHX:TOL=96350],paratrytone kemneri[&&NHX:TOL=96352],paratrytone omiltemensis[&&NHX:TOL=96353],paratrytone pilza[&&NHX:TOL=96354],paratrytone polyclea[&&NHX:TOL=96355],paratrytone raspa[&&NHX:TOL=96356],paratrytone rhexenor[&&NHX:TOL=96357],paratrytone snowi[&&NHX:TOL=96358])paratrytone[&&NHX:TOL=95136],(phemiades milvius[&&NHX:TOL=96364],phemiades pohli[&&NHX:TOL=96365],phemiades pseudophineus[&&NHX:TOL=96366],phemiades rufescens[&&NHX:TOL=96367],phemiades vergens[&&NHX:TOL=96368])phemiades[&&NHX:TOL=95137],(problema bulenta[&&NHX:TOL=96409],problema byssus[&&NHX:TOL=96410])problema[&&NHX:TOL=95141],(propertius dejongi[&&NHX:TOL=124557],propertius phineus[&&NHX:TOL=96411],propertius propertius[&&NHX:TOL=96412])propertius[&&NHX:TOL=95142],(pyrrhocalles antiqua[&&NHX:TOL=96413],pyrrhocalles jamaicensis[&&NHX:TOL=96414])pyrrhocalles[&&NHX:TOL=95144],(((quasimellana aurora[&&NHX:TOL=96420],quasimellana nayana[&&NHX:TOL=96431])[&&NHX:TOL=96466],quasimellana noka[&&NHX:TOL=96433],(quasimellana antipazina[&&NHX:TOL=96419],quasimellana pazina[&&NHX:TOL=96435])[&&NHX:TOL=96467],quasimellana sista[&&NHX:TOL=96439],quasimellana andersoni[&&NHX:TOL=96417],quasimellana sethos[&&NHX:TOL=96437],(quasimellana servilius[&&NHX:TOL=96436],quasimellana myron[&&NHX:TOL=96430],quasimellana inconspicua[&&NHX:TOL=96425],quasimellana angra[&&NHX:TOL=96418])[&&NHX:TOL=96468])[&&NHX:TOL=96465],(((quasimellana eulogius[&&NHX:TOL=96422],quasimellana agnesae[&&NHX:TOL=96415])[&&NHX:TOL=96471],quasimellana balsa[&&NHX:TOL=96421],quasimellana siblinga[&&NHX:TOL=96438],quasimellana mulleri[&&NHX:TOL=96429])[&&NHX:TOL=96470],quasimellana mexicana[&&NHX:TOL=96427])[&&NHX:TOL=96469],(quasimellana nicomedes[&&NHX:TOL=96432],quasimellana amicus[&&NHX:TOL=96416],quasimellana fieldi[&&NHX:TOL=96423],quasimellana imperfida[&&NHX:TOL=96424],quasimellana mielkei[&&NHX:TOL=96428],quasimellana meridiani[&&NHX:TOL=96426],quasimellana pandora[&&NHX:TOL=96434])[&&NHX:TOL=96472])quasimellana[&&NHX:TOL=95145],(quinta cannae[&&NHX:TOL=96478],quinta locutia[&&NHX:TOL=96479])quinta[&&NHX:TOL=95146],(racta apella[&&NHX:TOL=96480],racta chiria[&&NHX:TOL=96481],racta dalla[&&NHX:TOL=96482],racta plasma[&&NHX:TOL=96483],racta racta[&&NHX:TOL=96484])racta[&&NHX:TOL=95147],(serdis statius[&&NHX:TOL=96485],serdis venezuelae[&&NHX:TOL=96486],serdis viridicans[&&NHX:TOL=96487])serdis[&&NHX:TOL=95148],(tirynthia cinica[&&NHX:TOL=96521],tirynthia conda[&&NHX:TOL=96522],tirynthia conflua[&&NHX:TOL=96523])tirynthia[&&NHX:TOL=95151],(tirynthioides lotana[&&NHX:TOL=96524],tirynthioides virilis[&&NHX:TOL=96525])tirynthoides[&&NHX:TOL=95152],(vacerra bonfilius[&&NHX:TOL=96526],vacerra caniola[&&NHX:TOL=96527],vacerra cervara[&&NHX:TOL=96528],vacerra egla[&&NHX:TOL=96529],vacerra evansi[&&NHX:TOL=96530],vacerra hermesia[&&NHX:TOL=96531],vacerra lachares[&&NHX:TOL=96532],vacerra molla[&&NHX:TOL=96533])vacerra[&&NHX:TOL=95153],(wallengrenia egeremet[&&NHX:TOL=96534],wallengrenia otho[&&NHX:TOL=96535],wallengrenia premnas[&&NHX:TOL=96536])wallengrenia[&&NHX:TOL=95154],(xeniades chalestra[&&NHX:TOL=96537],xeniades ethoda[&&NHX:TOL=96538],xeniades orchamus[&&NHX:TOL=96539],xeniades victoria[&&NHX:TOL=96540])xeniades[&&NHX:TOL=95155])hesperiini[&&NHX:TOL=94928])[&&NHX:TOL=96563])[&&NHX:TOL=138402])[&&NHX:TOL=96562])[&&NHX:TOL=96561])[&&NHX:TOL=96560])[&&NHX:TOL=96559])[&&NHX:TOL=96558],pamphilites[&&NHX:EXT=Y:TOL=95096],thanatites[&&NHX:EXT=Y:TOL=95097])hesperiinae[&&NHX:TOL=12155])[&&NHX:TOL=94256])[&&NHX:TOL=94255])[&&NHX:TOL=94253])[&&NHX:TOL=95265])[&&NHX:TOL=103804])hesperiidae[&&NHX:TOL=12028],hedylidae[&&NHX:TOL=12029])rhopalocera[&&NHX:TOL=12026],(((sematurinae[&&NHX:TOL=122012],apoprogones[&&NHX:TOL=122013])sematuridae[&&NHX:TOL=12122],(microniinae[&&NHX:TOL=122009],epipleminae[&&NHX:TOL=122010],uraniinae[&&NHX:TOL=122011])uraniidae[&&NHX:TOL=12123],(archiearinae[&&NHX:TOL=122014],(macariini[&&NHX:TOL=122081],abraxini[&&NHX:TOL=122082],bistonini[&&NHX:TOL=122083],boarmiini[&&NHX:TOL=122084],melanolophini[&&NHX:TOL=122085],ennomini[&&NHX:TOL=122086],baptini[&&NHX:TOL=122087],azelinini[&&NHX:TOL=122088],campaeini[&&NHX:TOL=122089],nacophorini[&&NHX:TOL=122090],epirranthini[&&NHX:TOL=122091],angeronini[&&NHX:TOL=122092],lithinini[&&NHX:TOL=122093],hypochrosini[&&NHX:TOL=122094],ourapterygini[&&NHX:TOL=122095],gonodontini[&&NHX:TOL=122096],sphacelodini[&&NHX:TOL=122097],caberini[&&NHX:TOL=122098])ennominae[&&NHX:TOL=122015],(oenochromini[&&NHX:TOL=122062],ametridini[&&NHX:TOL=122063])oenochrominae[&&NHX:TOL=122016],alsophila[&&NHX:TOL=122017],(desmobathrini[&&NHX:TOL=122060],eumeleini[&&NHX:TOL=122061])desmobathrinae[&&NHX:TOL=122018],(nemoriini[&&NHX:TOL=122064],dichordophorini[&&NHX:TOL=122065],synchlorini[&&NHX:TOL=122066],lophochoristini[&&NHX:TOL=122067],hemitheini[&&NHX:TOL=122068],terpnini[&&NHX:TOL=122069],aracimini[&&NHX:TOL=122070],timandromorphini[&&NHX:TOL=122071],geometrini[&&NHX:TOL=122072],neohipparchini[&&NHX:TOL=122073],ochrognesiini[&&NHX:TOL=122074],thalassodini[&&NHX:TOL=122075],jodiini[&&NHX:TOL=122076],rhomboristini[&&NHX:TOL=122077],comibaenini[&&NHX:TOL=122078],hemistolini[&&NHX:TOL=122079],comostolini[&&NHX:TOL=122080])geometrinae[&&NHX:TOL=122019],(scopulini[&&NHX:TOL=122100],cyclophorini[&&NHX:TOL=122101],sterrhini[&&NHX:TOL=122102],timandrini[&&NHX:TOL=122103],rhodometrini[&&NHX:TOL=122104],cyclopodini[&&NHX:TOL=122105],rhodostrophini[&&NHX:TOL=122106])sterrhinae[&&NHX:TOL=122020],(hydriomenini[&&NHX:TOL=122107],stamnodini[&&NHX:TOL=122108],xanthorhoini[&&NHX:TOL=122109],asthenini[&&NHX:TOL=122110],operophterini[&&NHX:TOL=122111],eudulini[&&NHX:TOL=122112],eupithecini[&&NHX:TOL=122113],trichopterygini[&&NHX:TOL=122114])larentiinae[&&NHX:TOL=122021])geometridae[&&NHX:TOL=12124])geometroidea[&&NHX:TOL=12031],(epicopeiidae[&&NHX:TOL=12101],((drepanini[&&NHX:TOL=122115],oretini[&&NHX:TOL=122116],nidarini[&&NHX:TOL=122117])drepaninae[&&NHX:TOL=122022],cyclidiinae[&&NHX:TOL=122023],thyatirinae[&&NHX:TOL=122024])drepanidae[&&NHX:TOL=12102])drepanoidea[&&NHX:TOL=12032])[&&NHX:TOL=12030],cimeliidae[&&NHX:TOL=12033],((tetragonus[&&NHX:TOL=12078],comella[&&NHX:TOL=12079],pterodecta[&&NHX:TOL=12080],callidula[&&NHX:TOL=12081],cleis[&&NHX:TOL=12082])callidulinae[&&NHX:TOL=12077],(griveaudia[&&NHX:TOL=12084],(helicomitra[&&NHX:TOL=12086],pterothysanus[&&NHX:TOL=12087])pterothysaninae[&&NHX:TOL=12085])[&&NHX:TOL=12083])callidulidae[&&NHX:TOL=12034])[&&NHX:TOL=12025],(oenosandridae[&&NHX:TOL=12160],(doidae[&&NHX:TOL=12162],(thaumetopoeninae[&&NHX:TOL=138552],(pygaerinae[&&NHX:TOL=138554],(platychasmatinae[&&NHX:TOL=138556],(lirimiris[&&NHX:TOL=138558],(notodontinae[&&NHX:TOL=138560],(phalerinae[&&NHX:TOL=138562],(dudusinae[&&NHX:TOL=138564],(hemiceras[&&NHX:TOL=138566],(heterocampinae[&&NHX:TOL=138568],(nystaleinae[&&NHX:TOL=138570],(((proutiella esoterica[&&NHX:TOL=138650],proutiella ilaire[&&NHX:TOL=138767],proutiella infans[&&NHX:TOL=138651],proutiella jordani[&&NHX:TOL=138652],proutiella latifascia[&&NHX:TOL=138653],proutiella repetita[&&NHX:TOL=138654],proutiella simplex[&&NHX:TOL=138655],proutiella tegyra[&&NHX:TOL=138656],proutiella vittula[&&NHX:TOL=138657])proutiella[&&NHX:TOL=138573],(((getta ennia[&&NHX:TOL=138659],(getta unicolor[&&NHX:TOL=138663],getta niveifascia[&&NHX:TOL=138660],(getta baetifica[&&NHX:TOL=138658],getta tica[&&NHX:TOL=138661],getta turrenti[&&NHX:TOL=138662])[&&NHX:TOL=138769])[&&NHX:TOL=138768])getta[&&NHX:TOL=138576],((polyptychia fasciculosa[&&NHX:TOL=138664],polyptychia hermieri[&&NHX:TOL=138665])polyptychia[&&NHX:TOL=138578],(phavaraea dilatata[&&NHX:TOL=138666],phavaraea poliana[&&NHX:TOL=138667],phavaraea rectangularis[&&NHX:TOL=138668],phavaraea rejecta[&&NHX:TOL=138669])phavaraea[&&NHX:TOL=138579])[&&NHX:TOL=138577])[&&NHX:TOL=138575],((((ephialtias abrupta[&&NHX:TOL=138671],ephialtias pseudena[&&NHX:TOL=138676])[&&NHX:TOL=138770],ephialtias choba[&&NHX:TOL=138672],ephialtias consueta[&&NHX:TOL=138673],(ephialtias dorsispilota[&&NHX:TOL=138674],ephialtias monilis[&&NHX:TOL=138675])[&&NHX:TOL=138771],ephialtias velutinum[&&NHX:TOL=138677])ephialtias abrupta group[&&NHX:TOL=138670],(ephialtias bryce[&&NHX:TOL=138679],ephialtias draconis[&&NHX:TOL=138680],ephialtias tenuifascia[&&NHX:TOL=138681])ephialtias bryce group[&&NHX:TOL=138678])ephialtias[&&NHX:TOL=138581],(((lyces eterusialis[&&NHX:TOL=138683],lyces flavissima[&&NHX:TOL=138684])lyces eterusialis group[&&NHX:TOL=138682],((lyces angulosa[&&NHX:TOL=138687],lyces constricta[&&NHX:TOL=138688])[&&NHX:TOL=138686],((lyces ariaca[&&NHX:TOL=138690],lyces latistriga[&&NHX:TOL=138695])[&&NHX:TOL=139052],lyces banana[&&NHX:TOL=138691],(lyces ignorata[&&NHX:TOL=138694],(lyces ena[&&NHX:TOL=138692],lyces enoides[&&NHX:TOL=138693])[&&NHX:TOL=139054])[&&NHX:TOL=139053])[&&NHX:TOL=139051])lyces angulosa group[&&NHX:TOL=138685],((lyces annulata[&&NHX:TOL=138698],lyces aurimutua[&&NHX:TOL=138699],lyces cruciata[&&NHX:TOL=138700],lyces minuta[&&NHX:TOL=138701],lyces tamara[&&NHX:TOL=138702])[&&NHX:TOL=138697],((lyces andosa[&&NHX:TOL=138704],(lyces attenuata[&&NHX:TOL=138705],lyces striata[&&NHX:TOL=138709])[&&NHX:TOL=138891])[&&NHX:TOL=138890],((lyces gopala[&&NHX:TOL=138706],lyces patula[&&NHX:TOL=138708])[&&NHX:TOL=138893],lyces longistria[&&NHX:TOL=138707])[&&NHX:TOL=138892])[&&NHX:TOL=138703],lyces fluonia[&&NHX:TOL=138710],(lyces fornax[&&NHX:TOL=138712],lyces solaris[&&NHX:TOL=138713],lyces vulturata[&&NHX:TOL=138714])[&&NHX:TOL=138711])lyces patula group[&&NHX:TOL=138696])lyces[&&NHX:TOL=138583],(caribojosia youngi[&&NHX:TOL=138585],((phintia broweri[&&NHX:TOL=138715],phintia podarce[&&NHX:TOL=138716])phintia[&&NHX:TOL=138587],((notascea brevispinula[&&NHX:TOL=138717],notascea loxa[&&NHX:TOL=138718],notascea nudata[&&NHX:TOL=138719],notascea obliquaria[&&NHX:TOL=138720])notascea[&&NHX:TOL=138589],(((josia infausta[&&NHX:TOL=138723],josia interrupta[&&NHX:TOL=138725],((josia lativitta[&&NHX:TOL=138726],josia ligula[&&NHX:TOL=138727])[&&NHX:TOL=139111],josia oribia[&&NHX:TOL=138730])[&&NHX:TOL=139108],(josia insincera[&&NHX:TOL=138724],(josia mononeura[&&NHX:TOL=138728],josia similis[&&NHX:TOL=138731])[&&NHX:TOL=139110])[&&NHX:TOL=139109])josia ligula group[&&NHX:TOL=138722],(josia frigida[&&NHX:TOL=138733],josia fusigera[&&NHX:TOL=138734],josia fustula[&&NHX:TOL=138735],josia gigantea[&&NHX:TOL=138736],(josia ligata[&&NHX:TOL=138737],josia radians[&&NHX:TOL=138739])[&&NHX:TOL=139122],josia neblina[&&NHX:TOL=138738])josia ligata group[&&NHX:TOL=138732],(josia auriflua[&&NHX:TOL=138741],josia aurifusa[&&NHX:TOL=138742],josia subcuneifera[&&NHX:TOL=138743],josia turgida[&&NHX:TOL=138744])josia aurifusa group[&&NHX:TOL=138740],(josia integra[&&NHX:TOL=138746],josia megaera[&&NHX:TOL=138747])josia megaera group[&&NHX:TOL=138745])josia[&&NHX:TOL=138591],((scea angustimargo[&&NHX:TOL=138748],scea torrida[&&NHX:TOL=138766])[&&NHX:TOL=140570],scea auriflamma[&&NHX:TOL=138749],(scea bellona[&&NHX:TOL=138750],scea necyria[&&NHX:TOL=138760])cyanotricha[&&NHX:TOL=140571],scea bryki[&&NHX:TOL=138751],((scea cleonica[&&NHX:TOL=138753],scea curvilimes[&&NHX:TOL=138754])[&&NHX:TOL=140573],scea erasa[&&NHX:TOL=138757])[&&NHX:TOL=140572],(scea circumscripta[&&NHX:TOL=138752],(scea dimidiata[&&NHX:TOL=138755],scea discinota[&&NHX:TOL=138756])[&&NHX:TOL=140575],scea grandis[&&NHX:TOL=138759],scea superba[&&NHX:TOL=138765])thirmida[&&NHX:TOL=140574],(scea gigantea[&&NHX:TOL=138758],scea subcyanea[&&NHX:TOL=138764])[&&NHX:TOL=140576],scea semifulva[&&NHX:TOL=138761],scea servula[&&NHX:TOL=138762],scea steinbachi[&&NHX:TOL=138763])scea[&&NHX:TOL=138592])[&&NHX:TOL=138590])[&&NHX:TOL=138588])[&&NHX:TOL=138586])[&&NHX:TOL=138584])[&&NHX:TOL=138582])[&&NHX:TOL=138580])[&&NHX:TOL=138574])josiini[&&NHX:TOL=138572],dioptini[&&NHX:TOL=138593])dioptinae[&&NHX:TOL=138571])[&&NHX:TOL=138569])[&&NHX:TOL=138567])[&&NHX:TOL=138565])[&&NHX:TOL=138563])[&&NHX:TOL=138561])[&&NHX:TOL=138559])[&&NHX:TOL=138557])[&&NHX:TOL=138555])[&&NHX:TOL=138553])notodontidae[&&NHX:TOL=12163])[&&NHX:TOL=12161],(pantheidae[&&NHX:TOL=12165],nolidae[&&NHX:TOL=12166],lymantriidae[&&NHX:TOL=12167],((arctiini[&&NHX:TOL=121552],callimorphini[&&NHX:TOL=121553],phaegoterini[&&NHX:TOL=121554],pericopini[&&NHX:TOL=121555],euchromiini[&&NHX:TOL=121556],ctenuchini[&&NHX:TOL=121557])arctiinae[&&NHX:TOL=121551],lithosiinae[&&NHX:TOL=121558],(syntomini[&&NHX:TOL=121560],thyretini[&&NHX:TOL=121561])syntominae[&&NHX:TOL=121559])arctiidae[&&NHX:TOL=12168],noctuidae[&&NHX:TOL=12169])quadrifid noctuoidea[&&NHX:TOL=12164],micronoctuidae[&&NHX:TOL=138166])noctuoidea[&&NHX:TOL=12035],((((homoeopteryx[&&NHX:TOL=29580],oxytenis[&&NHX:TOL=29581],ashtenidia[&&NHX:TOL=29582])oxyteninae[&&NHX:TOL=29571],(janiodes[&&NHX:TOL=29583],microdulia[&&NHX:TOL=29584],neocercophana[&&NHX:TOL=29585],cercophana[&&NHX:TOL=29586])cercophaninae[&&NHX:TOL=29572],(almeidaia[&&NHX:TOL=29595],grammopelta[&&NHX:TOL=29594],copiopteryx[&&NHX:TOL=29593],paradaemonia[&&NHX:TOL=29592],rhescyntis[&&NHX:TOL=29591],titaea[&&NHX:TOL=29590],dysdaemonia[&&NHX:TOL=29589],caio[&&NHX:TOL=29588],arsenura[&&NHX:TOL=29587])arsenurinae[&&NHX:TOL=29573],ceratocampinae[&&NHX:TOL=29574],hemileucinae[&&NHX:TOL=29575],aglia[&&NHX:TOL=29576],salassa[&&NHX:TOL=29577],ludiinae[&&NHX:TOL=29578],saturniinae[&&NHX:TOL=29579])saturniidae[&&NHX:TOL=12075],((smerinthinae[&&NHX:TOL=29605],sphinginae[&&NHX:TOL=29606],macroglossinae[&&NHX:TOL=29607])sphingidae[&&NHX:TOL=12074],(lemonia[&&NHX:TOL=29598],sabalia[&&NHX:TOL=29599])lemoniidae[&&NHX:TOL=29597],(spiramiopsis comma[&&NHX:TOL=29600],dactyloceras[&&NHX:TOL=29601],calliprogonos miraculosa[&&NHX:TOL=29602],acanthobrahmaea europaea[&&NHX:TOL=29603],brahmaea[&&NHX:TOL=29604])brahmaeidae[&&NHX:TOL=12072])[&&NHX:TOL=29596],(apatelodinae[&&NHX:TOL=29560],(phiditia[&&NHX:TOL=29562],rolepa[&&NHX:TOL=29563],sorocaba[&&NHX:TOL=29564],tepilia[&&NHX:TOL=29565])phiditiinae[&&NHX:TOL=29561],prismostictinae[&&NHX:TOL=29566],bombycinae[&&NHX:TOL=29567])bombycidae[&&NHX:TOL=12071],(tissanga pretoriae[&&NHX:TOL=29555],hibrildes norax[&&NHX:TOL=29556],janinae[&&NHX:TOL=29557],panacelinae[&&NHX:TOL=29558],eupterotinae[&&NHX:TOL=29559])eupterotidae[&&NHX:TOL=12069],(mirina christophi[&&NHX:TOL=29568],mirina confucius[&&NHX:TOL=29569],mirina fenzeli[&&NHX:TOL=138528],[&&NHX:TOL=138529])mirina[&&NHX:TOL=12068],carthaea saturnioides[&&NHX:TOL=12073],dalailama bifurca[&&NHX:TOL=29570],endromis vericolora[&&NHX:TOL=12067])bombycoidea[&&NHX:TOL=12037],(anthelidae[&&NHX:TOL=12157],lasiocampidae[&&NHX:TOL=12158])lasiocampoidea[&&NHX:TOL=12038],mimallonidae[&&NHX:TOL=12039])[&&NHX:TOL=12036])macrolepidoptera[&&NHX:TOL=12024],(striglininae[&&NHX:TOL=122032],thyridinae[&&NHX:TOL=122033],siculodinae[&&NHX:TOL=122034],charideinae[&&NHX:TOL=122035])thyrididae[&&NHX:TOL=12040],hyblaeidae[&&NHX:TOL=12042],(copromorphidae[&&NHX:TOL=12089],carposinidae[&&NHX:TOL=12090])copromorphoidea[&&NHX:TOL=12043],((scopariinae[&&NHX:TOL=12238],crambiinae[&&NHX:TOL=12237],schoenobiinae[&&NHX:TOL=12236],cybalomiinae[&&NHX:TOL=12235],linostinae[&&NHX:TOL=12234],midilinae[&&NHX:TOL=12233],musotiminae[&&NHX:TOL=12232],nymphulinae[&&NHX:TOL=12231],noorda[&&NHX:TOL=12230],(odontiini[&&NHX:TOL=133867],eurrhypini[&&NHX:TOL=133868])odontiinae[&&NHX:TOL=12229],wurthiinae[&&NHX:TOL=12228],evergestinae[&&NHX:TOL=12227],glaphyriinae[&&NHX:TOL=12226],cathariinae[&&NHX:TOL=12225],pyraustinae[&&NHX:TOL=12224])crambidae[&&NHX:TOL=12223],(galleriinae[&&NHX:TOL=12240],chrysauginae[&&NHX:TOL=12241],pyralinae[&&NHX:TOL=12242],epipaschiinae[&&NHX:TOL=12243],phycitinae[&&NHX:TOL=12244])pyralidae[&&NHX:TOL=12239])pyraloidea[&&NHX:TOL=12041],immidae[&&NHX:TOL=12044],whalleyana[&&NHX:TOL=12045])obtectomera[&&NHX:TOL=12023],((phricanthini[&&NHX:TOL=12258],tortricini[&&NHX:TOL=12259],schoenotenini[&&NHX:TOL=12260],cochylini[&&NHX:TOL=12261],cnephasiini[&&NHX:TOL=12262],archipini[&&NHX:TOL=12263],epitymbiini[&&NHX:TOL=12264],sparganothini[&&NHX:TOL=12265],atteriini[&&NHX:TOL=12266],ceracini[&&NHX:TOL=12267],euliini[&&NHX:TOL=12268])tortricinae[&&NHX:TOL=12257],((chlidanotini[&&NHX:TOL=12271],polyorthini[&&NHX:TOL=12272],hilarographini[&&NHX:TOL=12273])chlidanotinae[&&NHX:TOL=12270],(olethreutini[&&NHX:TOL=12275],microcorsini[&&NHX:TOL=12276],gatesclarkeanini[&&NHX:TOL=12277],bactrini[&&NHX:TOL=12278],enarmoniini[&&NHX:TOL=12279],eucosmini[&&NHX:TOL=12280],grapholitini[&&NHX:TOL=12281])olethreutinae[&&NHX:TOL=12274])[&&NHX:TOL=12269])tortricidae[&&NHX:TOL=12046],(((chalcosiinae[&&NHX:TOL=68782],procridinae[&&NHX:TOL=68783],callizygaeninae[&&NHX:TOL=68784])[&&NHX:TOL=68781],zygaeninae[&&NHX:TOL=68785])zygaenidae[&&NHX:TOL=12290],(((acraga goes[&&NHX:TOL=29633],acraga ingenescens[&&NHX:TOL=29634],acraga luteola[&&NHX:TOL=29635],acraga hamata[&&NHX:TOL=29636],acraga andina[&&NHX:TOL=29637],acraga flava[&&NHX:TOL=29638],acraga obscura[&&NHX:TOL=29639],acraga ria[&&NHX:TOL=29640],acraga neblina[&&NHX:TOL=29641],acraga serrata[&&NHX:TOL=29642],acraga infusa[&&NHX:TOL=29643],acraga philetera[&&NHX:TOL=29644],acraga conda[&&NHX:TOL=29645],acraga ciliata[&&NHX:TOL=29646],acraga moorei[&&NHX:TOL=29647],acraga coa[&&NHX:TOL=29648],acraga chicana[&&NHX:TOL=29649],acraga concolor[&&NHX:TOL=29650],acraga citrinopsis[&&NHX:TOL=29651],acraga beebei[&&NHX:TOL=29652],acraga melinda[&&NHX:TOL=29653],acraga amazonica[&&NHX:TOL=29654],acraga meridensis[&&NHX:TOL=29655],acraga mariala[&&NHX:TOL=29656],acraga perbrunnea[&&NHX:TOL=29657],acraga citrina[&&NHX:TOL=29658],acraga hoppiana[&&NHX:TOL=29659],acraga ferruginea[&&NHX:TOL=29660],acraga brunnea[&&NHX:TOL=29661],acraga ampela[&&NHX:TOL=29662],acraga puno[&&NHX:TOL=29663],acraga boliviana[&&NHX:TOL=29664],acraga angulifera[&&NHX:TOL=29665],acraga isothea[&&NHX:TOL=29666],acraga leberna[&&NHX:TOL=29667],acraga umbrifera[&&NHX:TOL=29668],acraga ochracea[&&NHX:TOL=29669],acraga victoria[&&NHX:TOL=29670],acraga sexquicentenaria[&&NHX:TOL=29671],acraga parana[&&NHX:TOL=29672])acraga[&&NHX:TOL=29609],(dalcerides flavetta[&&NHX:TOL=29701],dalcerides rebella[&&NHX:TOL=29702],dalcerides chirma[&&NHX:TOL=29703],dalcerides radians[&&NHX:TOL=29704],dalcerides dulciola[&&NHX:TOL=29705],dalcerides mesoa[&&NHX:TOL=29706],dalcerides nana[&&NHX:TOL=29707],dalcerides sofia[&&NHX:TOL=29708],dalcerides ingenita[&&NHX:TOL=29709],dalcerides bicolor[&&NHX:TOL=29710],dalcerides alba[&&NHX:TOL=29711])dalcerides[&&NHX:TOL=29610],(zikanyrops dubiosa[&&NHX:TOL=29712],zikanyrops sparsa[&&NHX:TOL=29713])zikanyrops[&&NHX:TOL=29611])acraginae[&&NHX:TOL=29608],(((((minacraga disconitens[&&NHX:TOL=29865],minacraga plata[&&NHX:TOL=29866],minacraga similis[&&NHX:TOL=29867],minacraga indiscata[&&NHX:TOL=29868],minacraga argentata[&&NHX:TOL=29869],minacraga itatiaia[&&NHX:TOL=29870],minacraga aenea[&&NHX:TOL=29871],minacraga hyalina[&&NHX:TOL=29872])minacraga[&&NHX:TOL=29614],(dalcerina tijucana[&&NHX:TOL=29873],dalcerina fumata[&&NHX:TOL=29874],dalcerina arhathodota[&&NHX:TOL=29875],dalcerina muncia[&&NHX:TOL=29876],dalcerina dierrhyeoa[&&NHX:TOL=29877])dalcerina[&&NHX:TOL=29616])[&&NHX:TOL=29626],(dalcera abrasa[&&NHX:TOL=29878],dalcera haywardi[&&NHX:TOL=29879],dalcera canescens[&&NHX:TOL=29880],dalcera semirufa[&&NHX:TOL=29881])dalcera[&&NHX:TOL=29613])[&&NHX:TOL=29625],oroya aurora[&&NHX:TOL=29620])[&&NHX:TOL=29624],(((minacragides arnacis[&&NHX:TOL=29618],ca anastigma[&&NHX:TOL=29615])[&&NHX:TOL=29629],(paracraga innocens[&&NHX:TOL=29882],paracraga amianta[&&NHX:TOL=29883],paracraga argentea[&&NHX:TOL=29884],paracraga canalicula[&&NHX:TOL=29885],paracraga halophora[&&NHX:TOL=29886],paracraga necoda[&&NHX:TOL=29887],paracraga pulverina[&&NHX:TOL=29888])paracraga[&&NHX:TOL=29617])[&&NHX:TOL=29628],(minonoa elvira[&&NHX:TOL=29889],minonoa pachitea[&&NHX:TOL=29890],minonoa perbella[&&NHX:TOL=29891])minonoa[&&NHX:TOL=29619])[&&NHX:TOL=29627])dalcerinae[&&NHX:TOL=29612])dalceridae[&&NHX:TOL=12299],lacturidae[&&NHX:TOL=12291],(heterogynis[&&NHX:TOL=138073],janseola[&&NHX:TOL=138074])heterogynidae[&&NHX:TOL=12292],himantopteridae[&&NHX:TOL=12293],anomoeotidae[&&NHX:TOL=12294],aididae[&&NHX:TOL=12295],(megalopyginae[&&NHX:TOL=122185],trosiinae[&&NHX:TOL=122186])megalopygidae[&&NHX:TOL=12296],(somabrachys[&&NHX:TOL=29621],psycharium[&&NHX:TOL=29622],parapsycharium[&&NHX:TOL=29623])somabrachyidae[&&NHX:TOL=12297],(limacodinae[&&NHX:TOL=122187],chrysopolominae[&&NHX:TOL=122188])limacodidae[&&NHX:TOL=12298],epipyropidae[&&NHX:TOL=12300],cyclotornidae[&&NHX:TOL=12301],phaudidae[&&NHX:TOL=68786])zygaenoidea[&&NHX:TOL=12056],(macropiratinae[&&NHX:TOL=122036],agdistinae[&&NHX:TOL=122037],ochyroticinae[&&NHX:TOL=122038],deuterocopinae[&&NHX:TOL=122039],pterophorinae[&&NHX:TOL=122040])pterophoridae[&&NHX:TOL=12047],(tineodidae[&&NHX:TOL=12064],alucitidae[&&NHX:TOL=12065])alucitoidea[&&NHX:TOL=12048],epermeniidae[&&NHX:TOL=12049],schreckensteiniidae[&&NHX:TOL=12050],choreutidae[&&NHX:TOL=12051],urodidae[&&NHX:TOL=12052],((brachodidae[&&NHX:TOL=12246],sesiidae[&&NHX:TOL=12247],castniidae[&&NHX:TOL=12248])sesioidea[&&NHX:TOL=12054],(dudgeonea[&&NHX:TOL=12092],(hypoptinae[&&NHX:TOL=12094],ratardinae[&&NHX:TOL=12095],metarbelinae[&&NHX:TOL=12096],cossulinae[&&NHX:TOL=12097],zeuzerinae[&&NHX:TOL=12098],cossinae[&&NHX:TOL=12099])cossidae[&&NHX:TOL=12093])cossoidea[&&NHX:TOL=12055])[&&NHX:TOL=12053])apoditrysia[&&NHX:TOL=12022],((oecophorinae[&&NHX:TOL=122193],stathmopodinae[&&NHX:TOL=122194])oecophoridae[&&NHX:TOL=12104],(batrachedrinae[&&NHX:TOL=122183],epimarptis[&&NHX:TOL=122184])batrachedridae[&&NHX:TOL=12105],glyphidoceridae[&&NHX:TOL=12106],(xyloryctinae[&&NHX:TOL=122205],scythridinae[&&NHX:TOL=122206])xyloryctidae[&&NHX:TOL=12107],(coleophorinae[&&NHX:TOL=122189],momphinae[&&NHX:TOL=122190],blastobasinae[&&NHX:TOL=122191],pterolonchinae[&&NHX:TOL=122192])coleophoridae[&&NHX:TOL=12108],(stenomatinae[&&NHX:TOL=122175],ethmiinae[&&NHX:TOL=122176],depressariinae[&&NHX:TOL=122177],elachistinae[&&NHX:TOL=122178],ogonoxeninae[&&NHX:TOL=122179],hypertrophinae[&&NHX:TOL=122180],deuterogoniinae[&&NHX:TOL=122181],aeolanthes[&&NHX:TOL=122182])elachistidae[&&NHX:TOL=12109],amphisbatidae[&&NHX:TOL=12110],(acria[&&NHX:TOL=137608],antoloea[&&NHX:TOL=137609],durrantia[&&NHX:TOL=137610],leptogenes[&&NHX:TOL=137611],peleopoda[&&NHX:TOL=137612],pseuderotis[&&NHX:TOL=137613])peleopodidae[&&NHX:TOL=12111],(oecia[&&NHX:TOL=122217],schistonoeinae[&&NHX:TOL=122218])schistonoeidae[&&NHX:TOL=12113],(deocloninae[&&NHX:TOL=122207],syringopainae[&&NHX:TOL=122208])deoclonidae[&&NHX:TOL=12114],(chrysopeleinae[&&NHX:TOL=122199],cosmopteriginae[&&NHX:TOL=122200],antequerinae[&&NHX:TOL=122201])cosmopterigidae[&&NHX:TOL=12115],(gelechiinae[&&NHX:TOL=122195],physoptila[&&NHX:TOL=122196],dichomeridinae[&&NHX:TOL=122197],pexicopiinae[&&NHX:TOL=122198])gelechiidae[&&NHX:TOL=12116],(autostichinae[&&NHX:TOL=122203],holcopogoninae[&&NHX:TOL=122202],symmocinae[&&NHX:TOL=122204])autostichidae[&&NHX:TOL=12117],chimabachidae[&&NHX:TOL=12118],lecithoceridae[&&NHX:TOL=12119])gelechioidea[&&NHX:TOL=12057],(yponomeutidae[&&NHX:TOL=12283],ypsolophidae[&&NHX:TOL=12284],plutellidae[&&NHX:TOL=12285],glyphipterigidae[&&NHX:TOL=12286],heliodinidae[&&NHX:TOL=12287],lyonetiidae[&&NHX:TOL=12288],(bedellia annuligera[&&NHX:TOL=138168],bedellia autoconis[&&NHX:TOL=138517],bedellia boehmeriella[&&NHX:TOL=138518],bedellia enthrypta[&&NHX:TOL=138519],bedellia minor[&&NHX:TOL=138520],bedellia oplismeniella[&&NHX:TOL=138521],bedellia orchilella[&&NHX:TOL=138522],bedellia psamminella[&&NHX:TOL=138523],bedellia somnulentella[&&NHX:TOL=138524],bedellia struthionella[&&NHX:TOL=138525],bedellia terenodes[&&NHX:TOL=138526])bedellia[&&NHX:TOL=122171],acrolepiidae[&&NHX:TOL=138042])yponomeutoidea[&&NHX:TOL=12058],((phyllocnistinae[&&NHX:TOL=12127],lithocolletinae[&&NHX:TOL=12128],gracillariinae[&&NHX:TOL=12129])gracillariidae[&&NHX:TOL=12126],((bucculatrix[&&NHX:TOL=12132],leucoedemia ingens[&&NHX:TOL=12133])bucculatricidae[&&NHX:TOL=12131],((tinagma[&&NHX:TOL=12136],klimeschia[&&NHX:TOL=12137])douglasiidae[&&NHX:TOL=12135],(roeslerstammia[&&NHX:TOL=12139],thereutis[&&NHX:TOL=12140],macarangela[&&NHX:TOL=12141],dasycera[&&NHX:TOL=12142],telethera[&&NHX:TOL=12143],sphenograptis[&&NHX:TOL=12144],enchoptila[&&NHX:TOL=12145],chalcoteuches[&&NHX:TOL=12146],amphithera[&&NHX:TOL=12147],agriothera[&&NHX:TOL=12148])roeslerstammiidae[&&NHX:TOL=12138])[&&NHX:TOL=12134])[&&NHX:TOL=12130])gracillarioidea[&&NHX:TOL=12059],(tineidae[&&NHX:TOL=12250],eriocottidae[&&NHX:TOL=12251],(acrolophus[&&NHX:TOL=139671],amydria[&&NHX:TOL=139672],apreta[&&NHX:TOL=139673],drastea[&&NHX:TOL=139674],exoncotis[&&NHX:TOL=139675],ptilopsaltis[&&NHX:TOL=139676])acrolophidae[&&NHX:TOL=12252],(lypusa maurella[&&NHX:TOL=139664],lypusa tokari[&&NHX:TOL=139665])lypusa[&&NHX:TOL=12253],(palaeophanes[&&NHX:TOL=139666],notiophanes[&&NHX:TOL=139667],arrhenophanes[&&NHX:TOL=139668],cnissostages[&&NHX:TOL=139669],dysoptus[&&NHX:TOL=139670])arrhenophanidae[&&NHX:TOL=12254],psychidae[&&NHX:TOL=12255])tineoidea[&&NHX:TOL=12060])[&&NHX:TOL=12021],(metaprotus[&&NHX:TOL=138453],simaethistis[&&NHX:TOL=138454])simaethistidae[&&NHX:TOL=12061],galacticidae[&&NHX:TOL=12062])ditrysia[&&NHX:TOL=11868],(tischeria[&&NHX:TOL=87830],coptotriche[&&NHX:TOL=87831],astrotischeria[&&NHX:TOL=87832])tischeriidae[&&NHX:TOL=11869],(sesommata[&&NHX:TOL=11924],metaphatus[&&NHX:TOL=11925],plesiophatus inarmigerus[&&NHX:TOL=11926],palaephatus[&&NHX:TOL=11927],apophatus[&&NHX:TOL=11928],azaleodes[&&NHX:TOL=11929],ptyssoptera[&&NHX:TOL=11930])palaephatidae[&&NHX:TOL=11870],((prodoxoides asymmetra[&&NHX:TOL=12409],((lampronia aeneella[&&NHX:TOL=12352],lampronia tanysaccus aenescens[&&NHX:TOL=12353],lampronia aereipennella[&&NHX:TOL=12354],lampronia altaica[&&NHX:TOL=12355],lampronia argillella[&&NHX:TOL=12356],lampronia capitella[&&NHX:TOL=12357],lampronia corticella[&&NHX:TOL=12358],lampronia flavifrontella[&&NHX:TOL=12359],lampronia flavimitrella[&&NHX:TOL=12360],lampronia fuscatella[&&NHX:TOL=12361],lampronia tanysaccus humilis[&&NHX:TOL=12362],lampronia intermediella[&&NHX:TOL=12363],lampronia luzella[&&NHX:TOL=12364],lampronia morosa[&&NHX:TOL=12365],lampronia novempunctata[&&NHX:TOL=12366],lampronia oregonella[&&NHX:TOL=12367],lampronia provectella[&&NHX:TOL=12368],lampronia quinquepunctata[&&NHX:TOL=12369],lampronia redimitella[&&NHX:TOL=12370],lampronia rupella[&&NHX:TOL=12371],lampronia russatella[&&NHX:TOL=12372],lampronia sakhalinella[&&NHX:TOL=12373],lampronia splendidella[&&NHX:TOL=12374],lampronia standfussiella[&&NHX:TOL=12375],lampronia tanysaccus sublustris[&&NHX:TOL=12376],lampronia taylorella[&&NHX:TOL=12377],lampronia triangulifera[&&NHX:TOL=12378])lampronia[&&NHX:TOL=12411],tetragma gei[&&NHX:TOL=12412])[&&NHX:TOL=12410],(((greya variata[&&NHX:TOL=12304],(greya variabilis[&&NHX:TOL=12306],(greya pectinifera[&&NHX:TOL=12308],((greya politella[&&NHX:TOL=12311],greya enchrysa[&&NHX:TOL=12312])politella group[&&NHX:TOL=12310],((((greya mitellae[&&NHX:TOL=12317],greya piperella[&&NHX:TOL=12318])[&&NHX:TOL=12316],greya punctiferella[&&NHX:TOL=12319])[&&NHX:TOL=12315],greya obscura[&&NHX:TOL=12320])punctiferella group[&&NHX:TOL=12314],greya obscuromaculata[&&NHX:TOL=12321],(greya powelli[&&NHX:TOL=12323],(greya solenobiella[&&NHX:TOL=12325],greya suffusca[&&NHX:TOL=12326])[&&NHX:TOL=12324],(greya reticulata[&&NHX:TOL=12328],greya subalba[&&NHX:TOL=12329])[&&NHX:TOL=12327])solenobiella group[&&NHX:TOL=12322])[&&NHX:TOL=12313])[&&NHX:TOL=12309])[&&NHX:TOL=12307])[&&NHX:TOL=12305])[&&NHX:TOL=12303],greya sparsipunctella[&&NHX:TOL=12330],greya kononenkoi[&&NHX:TOL=12331],greya marginimaculata[&&NHX:TOL=12332])greya[&&NHX:TOL=12414],(mesepiola specca[&&NHX:TOL=12416],(((tegeticula maculata[&&NHX:TOL=12450],(tegeticula synthetica[&&NHX:TOL=12452],((tegeticula treculeanella[&&NHX:TOL=12455],tegeticula carnerosanella[&&NHX:TOL=12456])[&&NHX:TOL=12454],(tegeticula maderae[&&NHX:TOL=12458],(tegeticula mojavella[&&NHX:TOL=12460],(((tegeticula altiplanella[&&NHX:TOL=12464],tegeticula baccatella[&&NHX:TOL=12465])[&&NHX:TOL=12463],tegeticula rostratella[&&NHX:TOL=12466])[&&NHX:TOL=12462],(tegeticula superficiella[&&NHX:TOL=12468],tegeticula elatella[&&NHX:TOL=12469])[&&NHX:TOL=12467],tegeticula corruptrix[&&NHX:TOL=12470],((tegeticula cassandra[&&NHX:TOL=12473],tegeticula intermedia[&&NHX:TOL=12474])[&&NHX:TOL=12472],tegeticula yuccasella[&&NHX:TOL=12475])[&&NHX:TOL=12471])[&&NHX:TOL=12461])[&&NHX:TOL=12459])[&&NHX:TOL=12457])tegeticula yuccasella complex[&&NHX:TOL=12453])[&&NHX:TOL=12451])tegeticula[&&NHX:TOL=12419],parategeticula pollenifera[&&NHX:TOL=12420])[&&NHX:TOL=12418],(((prodoxus coloradensis[&&NHX:TOL=12426],prodoxus yinversus[&&NHX:TOL=12427],prodoxus quinquepunctellus[&&NHX:TOL=12428],(prodoxus ochrocarus[&&NHX:TOL=12430],prodoxus intricatus[&&NHX:TOL=12431])[&&NHX:TOL=12429],prodoxus sordidus[&&NHX:TOL=12432],(prodoxus marginatus[&&NHX:TOL=12434],(prodoxus cinereus[&&NHX:TOL=12436],prodoxus aenescens[&&NHX:TOL=12437])[&&NHX:TOL=12435])[&&NHX:TOL=12433])[&&NHX:TOL=12425],prodoxus phylloryctus[&&NHX:TOL=12438])prodoxus[&&NHX:TOL=12422],agavenema sp.[&&NHX:TOL=12423])[&&NHX:TOL=12421])[&&NHX:TOL=12417])[&&NHX:TOL=12415])[&&NHX:TOL=12413])prodoxidae[&&NHX:TOL=11872],(cecidoses eremita[&&NHX:TOL=11760],dicranoses capsulifex[&&NHX:TOL=11761],dicranoses congregatella[&&NHX:TOL=11762],eucecidoses minutanus[&&NHX:TOL=11763],oliera argentinana[&&NHX:TOL=11764],ptisanora trivialis[&&NHX:TOL=11765],scyrothis athleta[&&NHX:TOL=11766],scyrothis diplosamma[&&NHX:TOL=11767],scyrothis granosa[&&NHX:TOL=11768],xanadoses nielseni[&&NHX:TOL=11769])cecidosidae[&&NHX:TOL=11873],(perthida[&&NHX:TOL=11846],alloclemensia[&&NHX:TOL=11847],excurvaria[&&NHX:TOL=11848],incurvaria[&&NHX:TOL=11849],paraclemensia[&&NHX:TOL=11850],procacitas[&&NHX:TOL=11851],subclemensia[&&NHX:TOL=11852],protaephagus capensis[&&NHX:TOL=11853],basileura[&&NHX:TOL=11854],simacauda[&&NHX:TOL=11855],vespina quercivora[&&NHX:TOL=11856])incurvariidae[&&NHX:TOL=11874],crinopteryx familiella[&&NHX:TOL=11875],(adela[&&NHX:TOL=11751],cauchas[&&NHX:TOL=11752],nemophora[&&NHX:TOL=11753],ceromitia[&&NHX:TOL=11754],nematopogon[&&NHX:TOL=11755],tridentaforma[&&NHX:TOL=11756])adelidae[&&NHX:TOL=11876],(lamprozela[&&NHX:TOL=11773],plesiozela[&&NHX:TOL=11774],hoplophanes[&&NHX:TOL=11775],holocacista[&&NHX:TOL=11776],antispilina[&&NHX:TOL=11777],phanerozela[&&NHX:TOL=11778],monachozela[&&NHX:TOL=11779],heliozela[&&NHX:TOL=11780],antispila[&&NHX:TOL=11781],coptodisca[&&NHX:TOL=11782])heliozelidae[&&NHX:TOL=11877])incurvarioidea[&&NHX:TOL=11871],(((roscidotoga[&&NHX:TOL=11893],pectinivalva[&&NHX:TOL=11894])pectinivalvinae[&&NHX:TOL=11892],(acalyptris[&&NHX:TOL=11896],areticulata[&&NHX:TOL=11897],bohemannia[&&NHX:TOL=11898],ectoedemia[&&NHX:TOL=11899],enteucha[&&NHX:TOL=11900],parafomaria[&&NHX:TOL=11901],simplimorpha[&&NHX:TOL=11902],stigmella[&&NHX:TOL=11903],trifurcula[&&NHX:TOL=11904],varius[&&NHX:TOL=11905])nepticulinae[&&NHX:TOL=11895])nepticulidae[&&NHX:TOL=11879],((notiopostega[&&NHX:TOL=11908],eosopostega[&&NHX:TOL=11909],opostegoides[&&NHX:TOL=11910],paralopostega[&&NHX:TOL=11911])opostegoidinae[&&NHX:TOL=11907],(opostega[&&NHX:TOL=11913],pseudopostega[&&NHX:TOL=11914])oposteginae[&&NHX:TOL=11912])opostegidae[&&NHX:TOL=11880])nepticuloidea[&&NHX:TOL=11878],andesiana[&&NHX:TOL=122133])heteroneura[&&NHX:TOL=11867],((mnesarchaea acuta[&&NHX:TOL=11858],mnesarchaea fallax[&&NHX:TOL=11859],mnesarchaea fusca[&&NHX:TOL=11860],mnesarchaea fusilella[&&NHX:TOL=11861],mnesarchaea loxoscia[&&NHX:TOL=11862],mnesarchaea hamadelpha[&&NHX:TOL=11863],mnesarchaea paracosma[&&NHX:TOL=11864],mnesarchaea similis[&&NHX:TOL=11865])mnesarchaea[&&NHX:TOL=11882],((((fraus basicornis[&&NHX:TOL=28072],fraus basidispina[&&NHX:TOL=28073],fraus bilineata[&&NHX:TOL=28074],fraus biloba[&&NHX:TOL=28075],fraus crocea[&&NHX:TOL=28076],fraus distispina[&&NHX:TOL=28077],fraus furcata[&&NHX:TOL=28078],fraus fusca[&&NHX:TOL=28079],fraus griseomaculata[&&NHX:TOL=28080],fraus latistria[&&NHX:TOL=28081],fraus linogyna[&&NHX:TOL=28082],fraus marginispina[&&NHX:TOL=28083],fraus mediaspina[&&NHX:TOL=28084],fraus megacornis[&&NHX:TOL=28085],fraus minima[&&NHX:TOL=28086],fraus nanus[&&NHX:TOL=28087],fraus orientalis[&&NHX:TOL=28088],fraus pelagia[&&NHX:TOL=28089],fraus pilosa[&&NHX:TOL=28090],fraus polyspila[&&NHX:TOL=28091],fraus pteromela[&&NHX:TOL=28092],fraus quadrangular[&&NHX:TOL=28093],fraus serrata[&&NHX:TOL=28094],fraus simulans[&&NHX:TOL=28095],fraus tedi[&&NHX:TOL=28096])fraus[&&NHX:TOL=11785],(gazoryctra chishimana[&&NHX:TOL=28097],gazoryctra confusus[&&NHX:TOL=28098],gazoryctra fuscoargenteus[&&NHX:TOL=28099],gazoryctra ganna[&&NHX:TOL=28100],gazoryctra hyperboreus[&&NHX:TOL=28101],gazoryctra lembertii[&&NHX:TOL=28102],gazoryctra macilentus[&&NHX:TOL=28103],gazoryctra mathewi[&&NHX:TOL=28104],gazoryctra mcglshani[&&NHX:TOL=28105],gazoryctra novigannus[&&NHX:TOL=28106],gazoryctra pulcher[&&NHX:TOL=28107],gazoryctra roseicaput[&&NHX:TOL=28108],gazoryctra sciophanes[&&NHX:TOL=28109],gazoryctra wielgusi[&&NHX:TOL=28110])gazoryctra[&&NHX:TOL=11786],(afrotheora argentimaculata[&&NHX:TOL=28111],afrotheora brevivalva[&&NHX:TOL=28112],afrotheora flavimaculata[&&NHX:TOL=28113],afrotheora jordani[&&NHX:TOL=28114],afrotheora minirhodaula[&&NHX:TOL=28115],afrotheora rhodaula[&&NHX:TOL=28116],afrotheora thermodes[&&NHX:TOL=28117])afrotheora[&&NHX:TOL=11787],(antihepialus antarcticus[&&NHX:TOL=28118],antihepialus capeneri[&&NHX:TOL=28119],antihepialus keiniae[&&NHX:TOL=28120],antihepialus vansoni[&&NHX:TOL=28121])antihepialus[&&NHX:TOL=11788])[&&NHX:TOL=11784],((bipectilus gracilirami[&&NHX:TOL=28122],bipectilus latirami[&&NHX:TOL=28123],bipectilus omaiensis[&&NHX:TOL=28124],bipectilus paraunimacula[&&NHX:TOL=28125],bipectilus perfuscus[&&NHX:TOL=28126],bipectilus tindalei[&&NHX:TOL=28127],bipectilus unimacula[&&NHX:TOL=28128],bipectilus yunnanensis[&&NHX:TOL=28129])bipectilus[&&NHX:TOL=11790],(abantiades albofasciatus[&&NHX:TOL=28546],abantiades aphenges[&&NHX:TOL=28547],abantiades aurilegulus[&&NHX:TOL=28548],abantiades barcas[&&NHX:TOL=28549],abantiades fulvomarginatus[&&NHX:TOL=28550],abantiades hyalinatus[&&NHX:TOL=28551],abantiades hydrographus[&&NHX:TOL=28552],abantiades labyrinthicus[&&NHX:TOL=28553],abantiades latipennis[&&NHX:TOL=28554],abantiades leucochiton[&&NHX:TOL=28555],abantiades magnificus[&&NHX:TOL=28556],abantiades marcidus[&&NHX:TOL=28557],abantiades ocellatus[&&NHX:TOL=28558],abantiades sericatuas[&&NHX:TOL=28559])abantiades[&&NHX:TOL=11842],(palpifer falkneri[&&NHX:TOL=28130],palpifer hopponis[&&NHX:TOL=28131],palpifer madurensis[&&NHX:TOL=28132],palpifer murinus[&&NHX:TOL=28133],palpifer pellicia[&&NHX:TOL=28134],palpifer sexnotatus[&&NHX:TOL=28135],palpifer sordida[&&NHX:TOL=28136],palpifer taprobanus[&&NHX:TOL=28137],palpifer tavoyanus[&&NHX:TOL=28138],palpifer umbrinus[&&NHX:TOL=28139])palpifer[&&NHX:TOL=11791],(eudalaca aequifascia[&&NHX:TOL=28140],eudalaca albiplumis[&&NHX:TOL=28141],eudalaca albistriata[&&NHX:TOL=28142],eudalaca ammon[&&NHX:TOL=28143],eudalaca amphiarma[&&NHX:TOL=28144],eudalaca aurifuscalis[&&NHX:TOL=28145],eudalaca bacotii[&&NHX:TOL=28146],eudalaca cretata[&&NHX:TOL=28147],eudalaca crossosema[&&NHX:TOL=28148],eudalaca crudeni[&&NHX:TOL=28149],eudalaca eriogastra[&&NHX:TOL=28150],eudalaca exul[&&NHX:TOL=28151],eudalaca gutterata[&&NHX:TOL=28152],eudalaca hololecuca[&&NHX:TOL=28153],eudalaca holophaea[&&NHX:TOL=28154],eudalaca homoterma[&&NHX:TOL=28155],eudalaca ibex[&&NHX:TOL=28156],eudalaca infumata[&&NHX:TOL=28157],eudalaca isorrhoa[&&NHX:TOL=28158],eudalaca laeucophaea[&&NHX:TOL=28159],eudalaca leniflua[&&NHX:TOL=28160],eudalaca leucocyma[&&NHX:TOL=28161],eudalaca limbopuncta[&&NHX:TOL=28162],eudalaca miniscula[&&NHX:TOL=28163],eudalaca nomaqua[&&NHX:TOL=28164],eudalaca orthocosma[&&NHX:TOL=28165],eudalaca rivula[&&NHX:TOL=28166],eudalaca rufescens[&&NHX:TOL=28167],eudalaca sanctahelena[&&NHX:TOL=28168],eudalaca semicanus[&&NHX:TOL=28169],eudalaca strictigrapha[&&NHX:TOL=28170],eudalaca troglodytis[&&NHX:TOL=28171],eudalaca vaporalis[&&NHX:TOL=28172],eudalaca vindex[&&NHX:TOL=28173],eudalaca zernyi[&&NHX:TOL=28174])eudalaca[&&NHX:TOL=11792],(gorgopis alticola[&&NHX:TOL=28175],gorgopis annulosa[&&NHX:TOL=28176],gorgopis armillata[&&NHX:TOL=28177],gorgopis auratilis[&&NHX:TOL=28178],gorgopis aurifuscata[&&NHX:TOL=28179],gorgopis butlerii[&&NHX:TOL=28180],gorgopis caffra[&&NHX:TOL=28181],gorgopis centaurica[&&NHX:TOL=28182],gorgopis cochlias[&&NHX:TOL=28183],gorgopis crudeni[&&NHX:TOL=28184],gorgopis furcata[&&NHX:TOL=28185],gorgopis fuscalis[&&NHX:TOL=28186],gorgopis grisescens[&&NHX:TOL=28187],gorgopis hunti[&&NHX:TOL=28188],gorgopis inornata[&&NHX:TOL=28189],gorgopis intervallata[&&NHX:TOL=28190],gorgopis leucopetala[&&NHX:TOL=28191],gorgopis libania[&&NHX:TOL=28192],gorgopis lobata[&&NHX:TOL=28193],gorgopis olivaceonotata[&&NHX:TOL=28194],gorgopis pallidiflava[&&NHX:TOL=28195],gorgopis pholidota[&&NHX:TOL=28196],gorgopis ptiloscelis[&&NHX:TOL=28197],gorgopis salti[&&NHX:TOL=28198],gorgopis serangota[&&NHX:TOL=28199],gorgopis subrimosa[&&NHX:TOL=28200],gorgopis tanganyikaensis[&&NHX:TOL=28201],gorgopis zellerii[&&NHX:TOL=28202])gorgopis[&&NHX:TOL=11793],(metahepialus anguistiptera[&&NHX:TOL=28203],metahepialus plurimaculata[&&NHX:TOL=28204],metahepialus xenoctenis[&&NHX:TOL=28205])matahepialus[&&NHX:TOL=11794],(dalaca chilensis[&&NHX:TOL=28206],dalaca crocatus[&&NHX:TOL=28207],dalaca laminata[&&NHX:TOL=28208],dalaca nigricornis[&&NHX:TOL=28209],dalaca pallens[&&NHX:TOL=28210],dalaca patriciae[&&NHX:TOL=28211],dalaca postvariabilis[&&NHX:TOL=28212],dalaca quadricornis[&&NHX:TOL=28213],dalaca variabilis[&&NHX:TOL=28214])dalaca[&&NHX:TOL=11795],(callipielus arenosus[&&NHX:TOL=28215],callipielus argentata[&&NHX:TOL=28216],callipielus digitata[&&NHX:TOL=28217],callipielus fumosa[&&NHX:TOL=28218],callipielus gentillii[&&NHX:TOL=28219],callipielus izquierdoi[&&NHX:TOL=28220],callipielus krahmeri[&&NHX:TOL=28221],callipielus perforata[&&NHX:TOL=28222],callipielus salasi[&&NHX:TOL=28223],callipielus vulgaris[&&NHX:TOL=28224])callipielus[&&NHX:TOL=11796],blanchardinella venosus[&&NHX:TOL=11797],(calada fuegensis[&&NHX:TOL=28225],calada migueli[&&NHX:TOL=28226])calada[&&NHX:TOL=11798],puermytrans chilensis[&&NHX:TOL=11799],(parapielus heimlichi[&&NHX:TOL=28227],parapielus luteicornis[&&NHX:TOL=28228],parapielus oberthuri[&&NHX:TOL=28229],parapielus reeedi[&&NHX:TOL=28230])parapielus[&&NHX:TOL=11800],andeabatis  chilensis[&&NHX:TOL=11801],(druceiella amzonensis[&&NHX:TOL=28231],druceiellabasirubra[&&NHX:TOL=28232],druceiella metellus[&&NHX:TOL=28233],druceiella momus[&&NHX:TOL=28234])druceiella[&&NHX:TOL=11802],trichophassus giganteus[&&NHX:TOL=11803],(phassus absyrtus[&&NHX:TOL=28235],phassus agrionides[&&NHX:TOL=28236],phassus aurigenus[&&NHX:TOL=28237],phassus basirei[&&NHX:TOL=28238],phassus championi[&&NHX:TOL=28239],phassus costaricensis[&&NHX:TOL=28240],phassus chrysodidyma[&&NHX:TOL=28241],phassus eldorado[&&NHX:TOL=28242],phassus exclamationis[&&NHX:TOL=28243],phassus guianensis[&&NHX:TOL=28244],phassus huebneri[&&NHX:TOL=28245],phassus marcisu[&&NHX:TOL=28246],phassus nsignatus[&&NHX:TOL=28247],phassus phalerus[&&NHX:TOL=28248],phassus pharus[&&NHX:TOL=28249],phassus pretiosus[&&NHX:TOL=28250],phassus rosulentus[&&NHX:TOL=28251],phassus smithi[&&NHX:TOL=28252],phassus tesselatus[&&NHX:TOL=28253],phassus transversus[&&NHX:TOL=28254],phassus triangularis[&&NHX:TOL=28255])phassus[&&NHX:TOL=11804],schausiana trojesa[&&NHX:TOL=11805],(aplatissa michaelis[&&NHX:TOL=28256],aplatissa strangoides[&&NHX:TOL=28257])aplatissa[&&NHX:TOL=11806],(pfitzneriana allura[&&NHX:TOL=28258],pfitzneriana olivescens[&&NHX:TOL=28259],pfitzneriana prosopus[&&NHX:TOL=28260],pfitzneriana volgi[&&NHX:TOL=28261])pfitzneriana[&&NHX:TOL=11807],(cibyra aepytus biedermanni[&&NHX:TOL=28262],cibyra aepytus danieli[&&NHX:TOL=28263],cibyra aepytus exclamans[&&NHX:TOL=28264],cibyra aepytus forsteri[&&NHX:TOL=28265],cibyra aepytus helga[&&NHX:TOL=28266],cibyra aepytus jeanneli[&&NHX:TOL=28267],cibyra aepytus munona[&&NHX:TOL=28268],cibyra aepytus petropolisiensis[&&NHX:TOL=28269],cibyra aepytus zischkai[&&NHX:TOL=28270],cibyra alloaepytus tesselloides[&&NHX:TOL=28271],cibyra cibyra poltrona[&&NHX:TOL=28272],cibyra gymelloxes paropus[&&NHX:TOL=28273],cibyra gymelloxes tera[&&NHX:TOL=28274],cibyra gymelloxes trilinearis[&&NHX:TOL=28275],cibyra hampsoniella assa[&&NHX:TOL=28276],cibyra hampsoniella equatorialis[&&NHX:TOL=28277],cibyra hampsoniella serta[&&NHX:TOL=28278],cibyra lamelliformia prytanes[&&NHX:TOL=28279],cibyra lamelliformia sladeni[&&NHX:TOL=28280],cibyra paragorgopis jordani[&&NHX:TOL=28281],cibyra paragorgopis nigrovenosalis[&&NHX:TOL=28282],cibyra paragorgopis oreas[&&NHX:TOL=28283],cibyra paragorgopis pittionii[&&NHX:TOL=28284],cibyra paragorgopis schausi[&&NHX:TOL=28285],cibyra paragorgopis spitzii[&&NHX:TOL=28286],cibyra philoenia brasiliensis[&&NHX:TOL=28287],cibyra philoenia fasslii[&&NHX:TOL=28288],cibyra philoenia guyanensis[&&NHX:TOL=28289],cibyra philoenia indicata[&&NHX:TOL=28290],cibyra philoenia lagopus[&&NHX:TOL=28291],cibyra philoenia saguanmachica[&&NHX:TOL=28292],cibyra philoenia thisbe[&&NHX:TOL=28293],cibyra pseudodalaca gugelmanni[&&NHX:TOL=28294],cibyra pseudodalaca mexicanensis[&&NHX:TOL=28295],cibyra schaefferiana epigramma[&&NHX:TOL=28296],cibyra schaefferiana simplex[&&NHX:TOL=28297],cibyra tricladia mahagoniatus[&&NHX:TOL=28298],cibyra tricladia philiponi[&&NHX:TOL=28299],cibyra tricladia umbrifera[&&NHX:TOL=28300],cibyra xytrops dorita[&&NHX:TOL=28301],cibyra xytrops monoargenteus[&&NHX:TOL=28302],cibyra xytrops pluriargenteus[&&NHX:TOL=28303],cibyra xytrops verresi[&&NHX:TOL=28304],cibyra xytrops yungas[&&NHX:TOL=28305],cibyra yleuxas brunea[&&NHX:TOL=28306])cibyra[&&NHX:TOL=11808],phialuse palmar[&&NHX:TOL=11809],roseala bourgognei[&&NHX:TOL=11810],(dalaca chiriquensis[&&NHX:TOL=28307],dalaca cocama[&&NHX:TOL=28308],dalaca cupifera[&&NHX:TOL=28309],dalaca guarani[&&NHX:TOL=28310],dalaca katharinae[&&NHX:TOL=28311],dalaca manoa[&&NHX:TOL=28312],dalaca mummia[&&NHX:TOL=28313],dalaca niepelti[&&NHX:TOL=28314],dalaca obliquestrigata[&&NHX:TOL=28315],dalaca perkeo[&&NHX:TOL=28316],dalaca stigmatica[&&NHX:TOL=28317],dalaca tapuja[&&NHX:TOL=28318],dalaca usaque[&&NHX:TOL=28319],dalaca vibicata[&&NHX:TOL=28320])dalaca auctt. nec walker 1856[&&NHX:TOL=11811],(pfitzneriella lucicola[&&NHX:TOL=28321],pfitzneriella monticola[&&NHX:TOL=28322],pfitzneriella remota[&&NHX:TOL=28323],pfitzneriella similis[&&NHX:TOL=28324])pfitzneriella[&&NHX:TOL=11812],(aoraia aspina[&&NHX:TOL=28325],aoraia aurimaculata[&&NHX:TOL=28326],aoraia dinodes[&&NHX:TOL=28327],aoraia flavida[&&NHX:TOL=28328],aoraia hespera[&&NHX:TOL=28329],aoraia insularis[&&NHX:TOL=28330],aoraia lenis[&&NHX:TOL=28331],aoraia macropis[&&NHX:TOL=28332],aoraia oreobolae[&&NHX:TOL=28333],aoraia orientalis[&&NHX:TOL=28334],aoraia rufivena[&&NHX:TOL=28335],aoraia senex[&&NHX:TOL=28336])aoraia[&&NHX:TOL=11813],(triodia adriaticus[&&NHX:TOL=28337],triodia froitzheimi[&&NHX:TOL=28338],triodia amasinus[&&NHX:TOL=28339],triodia laetus[&&NHX:TOL=28340],triodia mlokossevitschi[&&NHX:TOL=28341],triodia nubifer[&&NHX:TOL=28342],triodia sylvina[&&NHX:TOL=28343])triodia[&&NHX:TOL=11814],(korscheltellus gracilis[&&NHX:TOL=28344],korscheltellus lupulina[&&NHX:TOL=28345])korscheltellus[&&NHX:TOL=11815],(pharmacis aemilianus[&&NHX:TOL=28346],pharmacis aneslminae[&&NHX:TOL=28347],pharmacis bertrandi[&&NHX:TOL=28348],pharmacis carna[&&NHX:TOL=28349],pharmacis castillanus[&&NHX:TOL=28350],pharmacis claudiae[&&NHX:TOL=28351],pharmacis fusconebulosa[&&NHX:TOL=28352],pharmacis pyrenaicus[&&NHX:TOL=28353])pharmacis[&&NHX:TOL=11816],(thitarodes albipictus[&&NHX:TOL=28354],thitarodes anomopterus[&&NHX:TOL=28355],thitarodes arizanus[&&NHX:TOL=28356],thitarodes armoricanus[&&NHX:TOL=28357],thitarodes baimaensis[&&NHX:TOL=28358],thitarodes baqingensis[&&NHX:TOL=28359],thitarodes callinivalis[&&NHX:TOL=28360],thitarodes cingulatus[&&NHX:TOL=28361],thitarodes damxungensis[&&NHX:TOL=28362],thitarodes danieli[&&NHX:TOL=28363],thitarodes dierli[&&NHX:TOL=28364],thitarodes dongyuensis[&&NHX:TOL=28365],thitarodes eberti[&&NHX:TOL=28366],thitarodes ferrugineus[&&NHX:TOL=28367],thitarodes gonggaensis[&&NHX:TOL=28368],thitarodes jialangensis[&&NHX:TOL=28369],thitarodes jianchuanensis[&&NHX:TOL=28370],thitarodes jinshanensis[&&NHX:TOL=28371],thitarodes kangdingensis[&&NHX:TOL=28372],thitarodes kangdingroides[&&NHX:TOL=28373],thitarodes lijiangensis[&&NHX:TOL=28374],thitarodes litangensis[&&NHX:TOL=28375],thitarodes luquensis[&&NHX:TOL=28376],thitarodes luteus[&&NHX:TOL=28377],thitarodes malaisei[&&NHX:TOL=28378],thitarodes markamensis[&&NHX:TOL=28379],thitarodes meiliensis[&&NHX:TOL=28380],thitarodes menyuanicus[&&NHX:TOL=28381],thitarodes nebulosus[&&NHX:TOL=28382],thitarodes nipponennsis[&&NHX:TOL=28383],thitarodes oblifurcus[&&NHX:TOL=28384],thitarodes pratensis[&&NHX:TOL=28385],thitarodes renzhiensis[&&NHX:TOL=28386],thitarodes richthofeni[&&NHX:TOL=28387],thitarodes sichuanus[&&NHX:TOL=28388],thitarodes sinarabesca[&&NHX:TOL=28389],thitarodes varians[&&NHX:TOL=28390],thitarodes variabilis[&&NHX:TOL=28391],thitarodes varius[&&NHX:TOL=28392],thitarodes xizangensis[&&NHX:TOL=28393],thitarodes xunhuaensis[&&NHX:TOL=28394],thitarodes yeriensis[&&NHX:TOL=28395],thitarodes yulongensis[&&NHX:TOL=28396],thitarodes yunglongensis[&&NHX:TOL=28397],thitarodes yunnanensis[&&NHX:TOL=28398],thitarodes zaliensis[&&NHX:TOL=28399],thitarodes zhangmoensis[&&NHX:TOL=28400],thitarodes zhayuensis[&&NHX:TOL=28401],thitarodes zhongzhiensis[&&NHX:TOL=28402])thitarodes[&&NHX:TOL=11817],(phymatopus hecta[&&NHX:TOL=28403],phymatopus hectica[&&NHX:TOL=28404],phymatopus japonicus[&&NHX:TOL=28408])phymatopus[&&NHX:TOL=11818],(phymatopus behrensii[&&NHX:TOL=28405],phymatopus californicus[&&NHX:TOL=28406],phymatopus hectoides[&&NHX:TOL=28407])phymatopus auctt. nec wallengren 1869[&&NHX:TOL=11819],hepialus humuli[&&NHX:TOL=11820],zenophassus schamyl[&&NHX:TOL=11821],(sthenopis argenteomaculatus[&&NHX:TOL=28409],sthenopis auratus[&&NHX:TOL=28410],sthenopis purpurascens[&&NHX:TOL=28411],sthenopis thule[&&NHX:TOL=28412])sthenopis[&&NHX:TOL=11822],(sthenopis bouvieri[&&NHX:TOL=28414],sthenopis dirschi[&&NHX:TOL=28415],sthenopis regius[&&NHX:TOL=28416],sthenopis roseus[&&NHX:TOL=28417])sthenopis auctt. nec packard 1865[&&NHX:TOL=28413],(endoclita aboe[&&NHX:TOL=28418],endoclita absurdus[&&NHX:TOL=28419],endoclita actinidae[&&NHX:TOL=28420],endoclita aikasama[&&NHX:TOL=28421],endoclita albofasciatus[&&NHX:TOL=28422],endoclita albosignata[&&NHX:TOL=28423],endoclita anhuiensis[&&NHX:TOL=28424],endoclita annae[&&NHX:TOL=28425],endoclita aroura[&&NHX:TOL=28426],endoclita auratus[&&NHX:TOL=28427],endoclita aurifer[&&NHX:TOL=28428],endoclita broma[&&NHX:TOL=28429],endoclita buettneria[&&NHX:TOL=28430],endoclita chalybeatus[&&NHX:TOL=28431],endoclita coomani[&&NHX:TOL=28432],endoclita crinilimbata[&&NHX:TOL=28433],endoclita chrysoptera[&&NHX:TOL=28434],endoclita damor[&&NHX:TOL=28435],endoclita davidi[&&NHX:TOL=28436],endoclita excrescens[&&NHX:TOL=28437],endoclita fijianodus[&&NHX:TOL=28438],endoclita gmelina[&&NHX:TOL=28439],endoclita hoenei[&&NHX:TOL=28440],endoclita hosei[&&NHX:TOL=28441],endoclita ijereja[&&NHX:TOL=28442],endoclita inouei[&&NHX:TOL=28443],endoclita javaensis[&&NHX:TOL=28444],endoclita jianglingensis[&&NHX:TOL=28445],endoclita jingdongensis[&&NHX:TOL=28446],endoclita kara[&&NHX:TOL=28447],endoclita magnus[&&NHX:TOL=28448],endoclita malabaricus[&&NHX:TOL=28449],endoclita marginenotatus[&&NHX:TOL=28450],endoclita metallica[&&NHX:TOL=28451],endoclita microscripta[&&NHX:TOL=28452],endoclita minanus[&&NHX:TOL=28453],endoclita mingiganteus[&&NHX:TOL=28454],endoclita niger[&&NHX:TOL=28455],endoclita nodus[&&NHX:TOL=28456],endoclita paraja[&&NHX:TOL=28457],endoclita punctimargo[&&NHX:TOL=28458],endoclita purpurescens[&&NHX:TOL=28459],endoclita raapi[&&NHX:TOL=28460],endoclita rustica[&&NHX:TOL=28461],endoclita salsettensis[&&NHX:TOL=28462],endoclita salvazi[&&NHX:TOL=28463],endoclita sericeus[&&NHX:TOL=28464],endoclita sibelae[&&NHX:TOL=28465],endoclita signifer[&&NHX:TOL=28466],endoclita sinensis[&&NHX:TOL=28467],endoclita strobilanthes[&&NHX:TOL=28468],endoclita taranu[&&NHX:TOL=28469],endoclita topeza[&&NHX:TOL=28470],endoclita tosa[&&NHX:TOL=28471],endoclita undulifer[&&NHX:TOL=28472],endoclita viridis[&&NHX:TOL=28473],endoclita warawita[&&NHX:TOL=28474],endoclita williamsi[&&NHX:TOL=28475],endoclita xizangensis[&&NHX:TOL=28476],endoclita yunnanensis[&&NHX:TOL=28477])endoclita[&&NHX:TOL=11823],neohepialiscus algeriensis[&&NHX:TOL=11824],(elhamma australasiae[&&NHX:TOL=28478],elhamma diakonoffi[&&NHX:TOL=28479],elhamma roepkei[&&NHX:TOL=28480],elhamma toxopeusi[&&NHX:TOL=28481])elhamma[&&NHX:TOL=11825],(jeana delicatula[&&NHX:TOL=28482],jeana robiginosa[&&NHX:TOL=28483])jeana[&&NHX:TOL=11826],cladoxycanus minos[&&NHX:TOL=11827],(wiseana cervinata[&&NHX:TOL=28484],wiseana copularis[&&NHX:TOL=28485],wiseana fuliginea[&&NHX:TOL=28486],wiseana jocosa[&&NHX:TOL=28487],wiseana mimica[&&NHX:TOL=28488],wiseana signata[&&NHX:TOL=28489],wiseana umbraculatus[&&NHX:TOL=28490])wiseana[&&NHX:TOL=11828],heloxycanus patricki[&&NHX:TOL=11829],(dumbletonius characterifer[&&NHX:TOL=28491],dumbletonius unimaculata[&&NHX:TOL=28492])dumbletonius[&&NHX:TOL=11830],(dioxycanus fusca[&&NHX:TOL=28493],dioxycanus oreas[&&NHX:TOL=28494])dioxycanus[&&NHX:TOL=11831],(napialus hunanensis[&&NHX:TOL=28495],napialus kulingi[&&NHX:TOL=28496],napialus chongquingensis[&&NHX:TOL=28497])napialus[&&NHX:TOL=11832],(hepialiscus monticola[&&NHX:TOL=28498],hepialiscus nepalensis[&&NHX:TOL=28499],hepialiscus robinsoni[&&NHX:TOL=28500],hepialiscus taiwanus[&&NHX:TOL=28501])hepialiscus[&&NHX:TOL=11833],parahepialiscus borneensis[&&NHX:TOL=11834],xhoaphryx lemeei[&&NHX:TOL=11835],(aenetus arfaki[&&NHX:TOL=28502],aenetus astathes[&&NHX:TOL=28503],aenetus blackburnii[&&NHX:TOL=28504],aenetus cohici[&&NHX:TOL=28505],aenetus crameri[&&NHX:TOL=28506],aenetus dulcis[&&NHX:TOL=28507],aenetus eugyna[&&NHX:TOL=28508],aenetus eximia[&&NHX:TOL=28509],aenetus hampsoni[&&NHX:TOL=28510],aenetus lewinii[&&NHX:TOL=28511],aenetus ligniveren[&&NHX:TOL=28512],aenetus marginatus[&&NHX:TOL=28513],aenetus mirabilis[&&NHX:TOL=28514],aenetus montanus[&&NHX:TOL=28515],aenetus ombraloma[&&NHX:TOL=28516],aenetus ramsayi[&&NHX:TOL=28517],aenetus scotti[&&NHX:TOL=28518],aenetus scripta[&&NHX:TOL=28519],aenetus sordida[&&NHX:TOL=28520],aenetus splendens[&&NHX:TOL=28521],aenetus tegulatus[&&NHX:TOL=28522],aenetus tephroptilus[&&NHX:TOL=28523],aenetus toxopeusi[&&NHX:TOL=28524],aenetus virescens[&&NHX:TOL=28525])aenetus[&&NHX:TOL=11836],leto venus[&&NHX:TOL=11837],zelotypia stacyi[&&NHX:TOL=11838],(oncopera alboguttata[&&NHX:TOL=28526],oncopera alpina[&&NHX:TOL=28527],oncopera brachyphylla[&&NHX:TOL=28528],oncopera brunneata[&&NHX:TOL=28529],oncopera epargyra[&&NHX:TOL=28530],oncopera fasciculatus[&&NHX:TOL=28531],oncopera intricata[&&NHX:TOL=28532],oncopera intricoides[&&NHX:TOL=28533],oncopera mitocera[&&NHX:TOL=28534],oncopera parva[&&NHX:TOL=28535],oncopera rufobrunnea[&&NHX:TOL=28536],oncopera tindalei[&&NHX:TOL=28537])oncopera[&&NHX:TOL=11839],(trictena argyrosticha[&&NHX:TOL=28538],trictena atripalpis[&&NHX:TOL=28539],trictena barnardi[&&NHX:TOL=28540])trictena[&&NHX:TOL=11840],(bordaia furva[&&NHX:TOL=28541],bordaia karnka[&&NHX:TOL=28542],bordaia moesta[&&NHX:TOL=28543],bordaia paradoxa[&&NHX:TOL=28544],bordaia pica[&&NHX:TOL=28545])bordaia[&&NHX:TOL=11841],(oxycanus aedesima[&&NHX:TOL=28560],oxycanus aegrus[&&NHX:TOL=28561],oxycanus albostrigata[&&NHX:TOL=28562],oxycanus altenai[&&NHX:TOL=28563],oxycanus antipoda[&&NHX:TOL=28564],oxycanus armatus[&&NHX:TOL=28565],oxycanus atrox[&&NHX:TOL=28566],oxycanus aurifex[&&NHX:TOL=28567],oxycanus australis[&&NHX:TOL=28568],oxycanus ballux[&&NHX:TOL=28569],oxycanus barnardi[&&NHX:TOL=28570],oxycanus beltista[&&NHX:TOL=28571],oxycanus buluwandji[&&NHX:TOL=28572],oxycanus byrsa[&&NHX:TOL=28573],oxycanus carus[&&NHX:TOL=28574],oxycanus determinate[&&NHX:TOL=28575],oxycanus diakonoffi[&&NHX:TOL=28576],oxycanus dirempta[&&NHX:TOL=28577],oxycanus discipennis[&&NHX:TOL=28578],oxycanus dives[&&NHX:TOL=28579],oxycanus eos[&&NHX:TOL=28580],oxycanus fuliginosa[&&NHX:TOL=28581],oxycanus gelidus[&&NHX:TOL=28582],oxycanus glauerti[&&NHX:TOL=28583],oxycanus goldfinchi[&&NHX:TOL=28584],oxycanus goodingi[&&NHX:TOL=28585],oxycanus hamatus[&&NHX:TOL=28586],oxycanus hebe[&&NHX:TOL=28587],oxycanus hecabe[&&NHX:TOL=28588],oxycanus herbuloti[&&NHX:TOL=28589],oxycanus herdus[&&NHX:TOL=28590],oxycanus hildae[&&NHX:TOL=28591],oxycanus incanus[&&NHX:TOL=28592],oxycanus janeus[&&NHX:TOL=28593],oxycanus kochi[&&NHX:TOL=28594],oxycanus loesus[&&NHX:TOL=28595],oxycanus lyelli[&&NHX:TOL=28596],oxycanus maculosus[&&NHX:TOL=28597],oxycanus mayri[&&NHX:TOL=28598],oxycanus meeki[&&NHX:TOL=28599],oxycanus naias[&&NHX:TOL=28600],oxycanus nigra[&&NHX:TOL=28601],oxycanus nigripuncta[&&NHX:TOL=28602],oxycanus niphadias[&&NHX:TOL=28603],oxycanus novaguineensis[&&NHX:TOL=28604],oxycanus nuptialis[&&NHX:TOL=28605],oxycanus oxidentalis[&&NHX:TOL=28606],oxycanus perditus[&&NHX:TOL=28607],oxycanus perplexus[&&NHX:TOL=28608],oxycanus postflavida[&&NHX:TOL=28609],oxycanus postxois[&&NHX:TOL=28610],oxycanus promiscuus[&&NHX:TOL=28611],oxycanus rileyi[&&NHX:TOL=28612],oxycanus rosaceus[&&NHX:TOL=28613],oxycanus rufescens[&&NHX:TOL=28614],oxycanus salmonacea[&&NHX:TOL=28615],oxycanus sirpus[&&NHX:TOL=28616],oxycanus spadix[&&NHX:TOL=28617],oxycanus sphragidias[&&NHX:TOL=28618],oxycanus stellans[&&NHX:TOL=28619],oxycanus serratus[&&NHX:TOL=28620],oxycanus snelleni[&&NHX:TOL=28621],oxycanus subochracea[&&NHX:TOL=28622],oxycanus subvaria[&&NHX:TOL=28623],oxycanus sylvanus[&&NHX:TOL=28624],oxycanus tamsi[&&NHX:TOL=28625],oxycanus thasus[&&NHX:TOL=28626],oxycanus toxopeusi[&&NHX:TOL=28627],oxycanus tyres[&&NHX:TOL=28628],oxycanus xois[&&NHX:TOL=28629],oxycanus waterhousei[&&NHX:TOL=28630])oxycanus[&&NHX:TOL=11843],phassodes vitienis[&&NHX:TOL=11844])hepialidae s. str.[&&NHX:TOL=11789])hepialidae[&&NHX:TOL=11884],(osrhoes coronta[&&NHX:TOL=11916],palaeoses scholastica[&&NHX:TOL=11917],genustes lutata[&&NHX:TOL=11918],ogygioses caliginosa[&&NHX:TOL=11919],ogygioses eurata[&&NHX:TOL=11920],ogygioses issikii[&&NHX:TOL=11921],ogygioses luangensis[&&NHX:TOL=11922])palaeosetidae[&&NHX:TOL=11885],neotheora chiloides[&&NHX:TOL=11886],anomoses hylecoetes[&&NHX:TOL=11887],(prototheora parachlora[&&NHX:TOL=11932],(prototheora petrosema[&&NHX:TOL=11934],(prototheora corvifera[&&NHX:TOL=11936],(prototheora merga[&&NHX:TOL=11938],(((prototheora serruligera[&&NHX:TOL=11942],prototheora biserrata[&&NHX:TOL=11943])[&&NHX:TOL=11941],prototheora quadricornis[&&NHX:TOL=11944])[&&NHX:TOL=11940],(prototheora cooperi[&&NHX:TOL=11946],(prototheora geniculata[&&NHX:TOL=11948],(prototheora drackensbergae[&&NHX:TOL=11950],prototheora angolae[&&NHX:TOL=11951])[&&NHX:TOL=11949])[&&NHX:TOL=11947])[&&NHX:TOL=11945])[&&NHX:TOL=11939])[&&NHX:TOL=11937])[&&NHX:TOL=11935])[&&NHX:TOL=11933])prototheora[&&NHX:TOL=11888])hepialoidea[&&NHX:TOL=11883])exoporia[&&NHX:TOL=11881])neolepidoptera[&&NHX:TOL=11719],(nematocentropus[&&NHX:TOL=11746],neopseustis[&&NHX:TOL=11747],synempora andesae[&&NHX:TOL=11748],apoplania[&&NHX:TOL=11749])neopseustidae[&&NHX:TOL=11720],(lophocorona pediasia[&&NHX:TOL=11728],lophocorona astiptica[&&NHX:TOL=11729],lophocorona melanora[&&NHX:TOL=11730],lophocorona commoni[&&NHX:TOL=11731],lophocorona robinsoni[&&NHX:TOL=11732],lophocorona flavicosta[&&NHX:TOL=11733])lophocorona[&&NHX:TOL=11721])[&&NHX:TOL=11718],(dyseriocrania[&&NHX:TOL=11704],eriocraniella[&&NHX:TOL=11705],eriocrania[&&NHX:TOL=11706],heringocrania[&&NHX:TOL=11707],issikiocrania[&&NHX:TOL=11708],neocrania[&&NHX:TOL=11709])eriocraniidae[&&NHX:TOL=11722],(acanthopteroctetes aurulenta[&&NHX:TOL=11695],acanthopteroctetes bimaculata[&&NHX:TOL=11696],acanthopteroctetes tripunctata[&&NHX:TOL=11697],acanthopteroctetes unifascia[&&NHX:TOL=11698],catapterix crimaea[&&NHX:TOL=11699])acanthopteroctetidae[&&NHX:TOL=11723])glossata[&&NHX:TOL=11717],(heterobathmia valvifer[&&NHX:TOL=11711],heterobathmia pseuderiocrania[&&NHX:TOL=11712],heterobathmia diffusa[&&NHX:TOL=11713])heterobathmia[&&NHX:TOL=11724])[&&NHX:TOL=11716],(agathiphaga queenslandensis[&&NHX:TOL=11701],agathiphaga vitiensis[&&NHX:TOL=11702])agathiphaga[&&NHX:TOL=11725])[&&NHX:TOL=11715],(micropterix[&&NHX:TOL=11735],(epimartyria[&&NHX:TOL=11737],paramartyria[&&NHX:TOL=11738],palaeomicroides[&&NHX:TOL=11739],neomicropteryx[&&NHX:TOL=11740],sabatinca[&&NHX:TOL=11741],agrionympha[&&NHX:TOL=11742],hypomartyria micropteroides[&&NHX:TOL=11743],squamicornia aequatoriella[&&NHX:TOL=11744])sabatinca group[&&NHX:TOL=11736])micropterigidae[&&NHX:TOL=11726])lepidoptera[&&NHX:TOL=8231])[&&NHX:TOL=8229])[&&NHX:TOL=8224],(xyelinae[&&NHX:TOL=22012],macroxyelinae[&&NHX:TOL=22013],(tenthredinoidea[&&NHX:TOL=22015],(pamphilioidea[&&NHX:TOL=22017],(cephoidea[&&NHX:TOL=22019],((anaxyelidae[&&NHX:TOL=11152],gigasiricidae[&&NHX:EXT=Y:TOL=11153])[&&NHX:TOL=11151],(siricidae[&&NHX:TOL=11155],(xiphydrioidea[&&NHX:TOL=22022],(orussoidea[&&NHX:TOL=22024],((((ibaliidae[&&NHX:TOL=11304],liopteridae[&&NHX:TOL=11305],figitidae[&&NHX:TOL=11306],cynipidae[&&NHX:TOL=11307],charipidae[&&NHX:TOL=11308],eucoilidae[&&NHX:TOL=11309])cynipoidea[&&NHX:TOL=11182],(heloridae[&&NHX:TOL=11313],(vanhorniidae[&&NHX:TOL=11317],pelecinidae[&&NHX:TOL=11318],proctotrupidae[&&NHX:TOL=11316])[&&NHX:TOL=22041])[&&NHX:TOL=22040])[&&NHX:TOL=22039],((mymarommatidae[&&NHX:TOL=22044],(chalcididae[&&NHX:TOL=11284],leucospidae[&&NHX:TOL=11285],eurytomidae[&&NHX:TOL=11286],ormyridae[&&NHX:TOL=11287],agaonidae[&&NHX:TOL=11288],pteromalidae[&&NHX:TOL=11289],perilampidae[&&NHX:TOL=11290],eucharitidae[&&NHX:TOL=11291],eupelmidae[&&NHX:TOL=11292],tanaostigmatidae[&&NHX:TOL=11293],encyrtidae[&&NHX:TOL=11294],aphelinidae[&&NHX:TOL=11295],signiphoridae[&&NHX:TOL=11296],tetracampidae[&&NHX:TOL=11297],rotoitidae[&&NHX:TOL=11298],eulophidae[&&NHX:TOL=11299],elasmidae[&&NHX:TOL=11300],trichogrammatidae[&&NHX:TOL=11301],mymaridae[&&NHX:TOL=11302])chalcidoidea[&&NHX:TOL=11183])[&&NHX:TOL=22043],(scelionidae[&&NHX:TOL=27421],platygastridae[&&NHX:TOL=27422])platygastroidea[&&NHX:TOL=11179])[&&NHX:TOL=22042])[&&NHX:TOL=22038],roproniidae[&&NHX:TOL=11319],(maamingidae[&&NHX:TOL=22036],((ambositrinae[&&NHX:TOL=29008],belytinae[&&NHX:TOL=29009],(diapriinae[&&NHX:TOL=29011],peckidium enigmaticum[&&NHX:TOL=29012])[&&NHX:TOL=29010],ismarinae[&&NHX:TOL=29013])diapriidae[&&NHX:TOL=11312],austroniidae[&&NHX:TOL=11315],monomachidae[&&NHX:TOL=11311])[&&NHX:TOL=22037])[&&NHX:TOL=22035],(trigonaloidea[&&NHX:TOL=22032],(rigel chiliensis[&&NHX:TOL=28840],(((((((((megalyra fasciipennis[&&NHX:TOL=28887],megalyra caudata[&&NHX:TOL=28889])[&&NHX:TOL=29075],megalyra australia[&&NHX:TOL=28888])megalyra fasciipennis group[&&NHX:TOL=28865],((megalyra longiseta[&&NHX:TOL=28885],megalyra spectabilis[&&NHX:TOL=28886])megalyra longiseta group[&&NHX:TOL=28864],megalyra shuckardi[&&NHX:TOL=28863])[&&NHX:TOL=28907])[&&NHX:TOL=28906],(((megalyra rufipes[&&NHX:TOL=28881],megalyra viridescens[&&NHX:TOL=28883])[&&NHX:TOL=29076],megalyra transversistriata[&&NHX:TOL=28884])[&&NHX:TOL=29077],megalyra rufiventris[&&NHX:TOL=28882])megalyra rufipes group[&&NHX:TOL=28861])[&&NHX:TOL=29078],megalyra caledonica[&&NHX:TOL=28862])[&&NHX:TOL=28908],(((megalyra minuta[&&NHX:TOL=28870],megalyra lilliputiana[&&NHX:TOL=28871])[&&NHX:TOL=29085],(megalyra exigua[&&NHX:TOL=28877],megalyra nanella[&&NHX:TOL=28878])[&&NHX:TOL=29084],(megalyra troglodytes[&&NHX:TOL=28873],megalyra aquilonia[&&NHX:TOL=28874])[&&NHX:TOL=29083],((megalyra brevicauda[&&NHX:TOL=28875],megalyra rieki[&&NHX:TOL=28880])[&&NHX:TOL=29082],megalyra testaceipies[&&NHX:TOL=28872])[&&NHX:TOL=29086],megalyra gnoma[&&NHX:TOL=28876],megalyra pygmaea[&&NHX:TOL=28879])megalyra minuta group[&&NHX:TOL=28860],((megalyra wagneri[&&NHX:TOL=28866],megalyra globula[&&NHX:TOL=28867])[&&NHX:TOL=29080],(megalyra plana[&&NHX:TOL=28868],megalyra sedlaceki[&&NHX:TOL=28869])[&&NHX:TOL=29081])megalyra wagneri group[&&NHX:TOL=28859])[&&NHX:TOL=28909])[&&NHX:TOL=29079],megalyra tawiensis[&&NHX:TOL=28858])megalyra[&&NHX:TOL=28842],(((prodinapsis succinalis[&&NHX:EXT=Y:TOL=28904],prodinapsis minor[&&NHX:EXT=Y:TOL=28905])prodinapsis[&&NHX:EXT=Y:TOL=28849],cretodinapsis caucasica[&&NHX:EXT=Y:TOL=28850])[&&NHX:TOL=29087],(neodinapsis peckorum[&&NHX:TOL=28848],(((((((dinapsis albicoxa[&&NHX:TOL=28897],dinapsis seyrigi[&&NHX:TOL=28901])[&&NHX:TOL=29070],dinapsis nubilus[&&NHX:TOL=28899])[&&NHX:TOL=29072],dinapsis hirtipes[&&NHX:TOL=28898])[&&NHX:TOL=29069],dinapsis oculohirta[&&NHX:TOL=28900])[&&NHX:TOL=29071],dinapsis turneri[&&NHX:TOL=28896])dinapsis[&&NHX:TOL=28845],(ettchellsia piliceps[&&NHX:TOL=28902],ettchellsia philippinensis[&&NHX:TOL=28903])ettchellsia[&&NHX:TOL=28846])[&&NHX:TOL=28851],maimetsha arctica[&&NHX:EXT=Y:TOL=28847])[&&NHX:TOL=28852])dinapsini[&&NHX:TOL=28853],(((cryptalyra plaumanni[&&NHX:TOL=28891],cryptalyra depressa[&&NHX:TOL=96058])[&&NHX:TOL=96057],cryptalyra colombia[&&NHX:TOL=28890])cryptalyra[&&NHX:TOL=28843],(((carminator affinis[&&NHX:TOL=28892],carminator ater[&&NHX:TOL=28893])[&&NHX:TOL=29073],carminator cavus[&&NHX:TOL=28894])[&&NHX:TOL=29074],carminator nooni[&&NHX:TOL=28895])carminator[&&NHX:TOL=28844])cryptalyrini[&&NHX:TOL=28855])[&&NHX:TOL=28854])[&&NHX:TOL=28856],megalyridia capensis[&&NHX:TOL=28841])[&&NHX:TOL=28857])megalyridae[&&NHX:TOL=22033],((((((gasteruption[&&NHX:TOL=25832],(hyptiogaster[&&NHX:TOL=30283],pseudofoenus[&&NHX:TOL=30284])hyptiogastrinae[&&NHX:TOL=25833],kotujellitinae[&&NHX:EXT=Y:TOL=66367])gasteruptiidae[&&NHX:TOL=23535],((aulacus[&&NHX:TOL=25825],panaulix[&&NHX:TOL=25826],pristaulacus[&&NHX:TOL=25827])[&&NHX:TOL=25829],hyptiogastrites electrinus[&&NHX:EXT=Y:TOL=25828],electrofoenus gracilipes[&&NHX:EXT=Y:TOL=66371],protofoenus swinhoei[&&NHX:EXT=Y:TOL=66372],vectevania vetula[&&NHX:EXT=Y:TOL=66373])aulacidae[&&NHX:TOL=23534])[&&NHX:TOL=66353],baissinae[&&NHX:EXT=Y:TOL=66354])[&&NHX:TOL=66352],(((((((brachygaster[&&NHX:TOL=25808],semaeomyia[&&NHX:TOL=25800],(decevania[&&NHX:TOL=25812],hyptia[&&NHX:TOL=25802],rothevania valdiviana[&&NHX:TOL=25814],evaniscus[&&NHX:TOL=25811])[&&NHX:TOL=29273])[&&NHX:TOL=29276],(micrevania[&&NHX:TOL=25805],thaumatevania ensifera[&&NHX:TOL=25798])[&&NHX:TOL=29272],((szepligetella[&&NHX:TOL=25810],acanthinevania[&&NHX:TOL=25809],evaniella[&&NHX:TOL=25799])[&&NHX:TOL=29274],(alobevania gattiae[&&NHX:TOL=120540],alobevania longisaeta[&&NHX:TOL=120541],alobevania tavaresi[&&NHX:TOL=120542])alobevania[&&NHX:TOL=120177])[&&NHX:TOL=120179],(parevania[&&NHX:TOL=25797],papatuka[&&NHX:TOL=25804],zeuxevania[&&NHX:TOL=25813])[&&NHX:TOL=29275],(prosevania[&&NHX:TOL=25796],(evania[&&NHX:TOL=25795],trissevania anemotis[&&NHX:TOL=25807])[&&NHX:TOL=29271])[&&NHX:TOL=29270],vernevania urbanusorum[&&NHX:TOL=25803],brachevania kristenseni[&&NHX:TOL=25801],afrevania leroyi[&&NHX:TOL=25806],eoevania magnifica[&&NHX:EXT=Y:TOL=25824],protoparevania lourothi[&&NHX:EXT=Y:TOL=25819])[&&NHX:TOL=66364],(procretevania pristina[&&NHX:EXT=Y:TOL=25821],cretevania[&&NHX:EXT=Y:TOL=25823])[&&NHX:TOL=66365],eovernevania cyrtocerca[&&NHX:EXT=Y:TOL=52757],grimaldivania ackermani[&&NHX:EXT=Y:TOL=25817],newjersevania[&&NHX:EXT=Y:TOL=25816])[&&NHX:TOL=66363],andrenelia pinnata[&&NHX:EXT=Y:TOL=66366])[&&NHX:TOL=66362],mesevania swinhoei[&&NHX:EXT=Y:TOL=25818])[&&NHX:TOL=66361],lebanevania azari[&&NHX:EXT=Y:TOL=25815])[&&NHX:TOL=66360],praevania sculpturata[&&NHX:EXT=Y:TOL=25822],botsvania cretacea[&&NHX:EXT=Y:TOL=53064])evaniidae[&&NHX:TOL=23533])[&&NHX:TOL=66351],(evaniops rostratus[&&NHX:EXT=Y:TOL=66356],evanigaster petiolatus[&&NHX:EXT=Y:TOL=66357])[&&NHX:TOL=66355],cletocleistogastrinae[&&NHX:EXT=Y:TOL=66358],praeaulacinae[&&NHX:EXT=Y:TOL=66359],anomopterellinae[&&NHX:EXT=Y:TOL=66370])evanioidea[&&NHX:TOL=11170],ceraphronoidea[&&NHX:TOL=11167])[&&NHX:TOL=22034])[&&NHX:TOL=22031],((archaeostephanus[&&NHX:EXT=Y:TOL=51192],electrostephanus[&&NHX:EXT=Y:TOL=51193],denaeostephanus[&&NHX:EXT=Y:TOL=51194],megischus basalis[&&NHX:TOL=51195],schlettererius[&&NHX:TOL=51196])[&&NHX:TOL=51191],(protostephanus[&&NHX:EXT=Y:TOL=51198],stephanus[&&NHX:TOL=51199],(megischus[&&NHX:TOL=51201],afromegischus[&&NHX:TOL=51202],madegafoenus[&&NHX:TOL=51203],(hemistephanus[&&NHX:TOL=51205],(parastephanellus[&&NHX:TOL=51206],(comnatopus[&&NHX:TOL=51208],(profoenatopus[&&NHX:TOL=51210],foenatopus[&&NHX:TOL=51213])[&&NHX:TOL=51209])[&&NHX:TOL=51207])[&&NHX:TOL=51215])[&&NHX:TOL=51204])[&&NHX:TOL=51200])[&&NHX:TOL=51197])stephanidae[&&NHX:TOL=22029],((ichneumonidae[&&NHX:TOL=23445],tanychora[&&NHX:EXT=Y:TOL=23446],(eoichneumonidae[&&NHX:EXT=Y:TOL=23448],(((adeliinae[&&NHX:TOL=23450],cheloninae[&&NHX:TOL=23451])[&&NHX:TOL=23495],((microgastrinae[&&NHX:TOL=23452],(mirax brasiliensis[&&NHX:TOL=105557],mirax ectoedemiae[&&NHX:TOL=105558])mirax[&&NHX:TOL=23453],cardiochilinae[&&NHX:TOL=23454],khoikhoiiinae[&&NHX:TOL=23455])[&&NHX:TOL=23496],((epsilogaster panama[&&NHX:TOL=95913],epsilogaster tico[&&NHX:TOL=95914],epsilogaster durero[&&NHX:TOL=95915],epsilogaster braziliensis[&&NHX:TOL=95916],epsilogaster fabiolae[&&NHX:TOL=94861],epsilogaster antoniae[&&NHX:TOL=94860],epsilogaster palenque[&&NHX:TOL=94859],epsilogaster bicolor[&&NHX:TOL=94858])epsilogaster[&&NHX:TOL=95912],(mendesella magna[&&NHX:TOL=95918],mendesella braziliensis[&&NHX:TOL=95919],mendesella amazonica[&&NHX:TOL=95920],mendesella orianae[&&NHX:TOL=94862])mendesella[&&NHX:TOL=95917])mendesellinae[&&NHX:TOL=23456])[&&NHX:TOL=23497])[&&NHX:TOL=23498],masoninae[&&NHX:TOL=23457],dirrhopinae[&&NHX:TOL=23458],neoneurinae[&&NHX:TOL=23459],ichneutinae[&&NHX:TOL=23460],(trachypetinae[&&NHX:TOL=23461],(((pselaphaninae[&&NHX:TOL=23463],agathidinae[&&NHX:TOL=23462])[&&NHX:TOL=23499],sigalphinae[&&NHX:TOL=23464])[&&NHX:TOL=23500],cenocoeliinae[&&NHX:TOL=23465])[&&NHX:TOL=23501],(((homolobinae[&&NHX:TOL=23466],xiphozelinae[&&NHX:TOL=23467])[&&NHX:TOL=23506],(amicrocentrinae[&&NHX:TOL=23468],macrocentrinae[&&NHX:TOL=23469])[&&NHX:TOL=23507],orgilinae[&&NHX:TOL=23470],helconinae[&&NHX:TOL=23471],ecnomiinae[&&NHX:TOL=23472],blacinae[&&NHX:TOL=23473],microtypinae[&&NHX:TOL=23474])[&&NHX:TOL=23505],meteorideinae[&&NHX:TOL=23475],(meteorinae[&&NHX:TOL=23476],euphorinae[&&NHX:TOL=23477])[&&NHX:TOL=23503])[&&NHX:TOL=23504])[&&NHX:TOL=23502],((((((alysiinae[&&NHX:TOL=23478],opiinae[&&NHX:TOL=23479])[&&NHX:TOL=23508],exothecinae[&&NHX:TOL=23480],gnamptodontinae[&&NHX:TOL=23481])[&&NHX:TOL=23509],mesostoinae[&&NHX:TOL=23482],vaepellinae[&&NHX:TOL=23483],braconinae[&&NHX:TOL=23484])[&&NHX:TOL=23510],betylobraconinae[&&NHX:TOL=23485],rogadinae[&&NHX:TOL=23486],(ypsistocerinae[&&NHX:TOL=23487],doryctinae[&&NHX:TOL=23488])[&&NHX:TOL=23512],hormiinae[&&NHX:TOL=23489],telengaiinae[&&NHX:TOL=23490])[&&NHX:TOL=23511],histeromerinae[&&NHX:TOL=23491])[&&NHX:TOL=23513],rhyssalinae[&&NHX:TOL=23492],aphidiinae[&&NHX:TOL=23493],apozyginae[&&NHX:TOL=23494])[&&NHX:TOL=23514])braconidae[&&NHX:TOL=23447])[&&NHX:TOL=23449])ichneumonoidea[&&NHX:TOL=11174],((plumariidae[&&NHX:TOL=11215],(scolebythidae[&&NHX:TOL=11214],((bethylidae[&&NHX:TOL=11212],chrysididae[&&NHX:TOL=11213])[&&NHX:TOL=11211],(sclerogibbidae[&&NHX:TOL=11207],(embolemidae[&&NHX:TOL=11209],dryinidae[&&NHX:TOL=11210])[&&NHX:TOL=11208])[&&NHX:TOL=11206])[&&NHX:TOL=11205])[&&NHX:TOL=11204])chrysidoidea[&&NHX:TOL=11186],((heterogynaidae[&&NHX:TOL=22061],(ampulicidae[&&NHX:TOL=11217],(sphecidae[&&NHX:TOL=11218],((crabroninae[&&NHX:TOL=22086],(astatinae[&&NHX:TOL=22087],pemphredoninae[&&NHX:TOL=22088],(bembicinae[&&NHX:TOL=22089],philanthinae[&&NHX:TOL=22090])[&&NHX:TOL=22092])[&&NHX:TOL=22091])crabronidae[&&NHX:TOL=11223],(stenotritidae[&&NHX:TOL=22093],(rophitinae[&&NHX:TOL=22111],(nomiinae[&&NHX:TOL=22112],(nomioidini[&&NHX:TOL=22127],(augochlorini[&&NHX:TOL=22128],halictini[&&NHX:TOL=22129])[&&NHX:TOL=22130])halictinae[&&NHX:TOL=22113])[&&NHX:TOL=22114])halictidae[&&NHX:TOL=22094],((andreninae[&&NHX:TOL=22115],(oxaeinae[&&NHX:TOL=22116],panurginae[&&NHX:TOL=22117])[&&NHX:TOL=22118])andrenidae[&&NHX:TOL=22096],(euryglossinae[&&NHX:TOL=22119],((hylaeinae[&&NHX:TOL=22120],xeromelissinae[&&NHX:TOL=22121])[&&NHX:TOL=22124],(colletinae[&&NHX:TOL=22122],diphaglossinae[&&NHX:TOL=22123])[&&NHX:TOL=22125])[&&NHX:TOL=22126])colletidae[&&NHX:TOL=22095])[&&NHX:TOL=22102],(melittidae[&&NHX:TOL=22097],dasypodidae[&&NHX:TOL=22098],meganomiidae[&&NHX:TOL=22099],((fideliinae[&&NHX:TOL=22109],megachilinae[&&NHX:TOL=22110])megachilidae[&&NHX:TOL=22100],((allodapini[&&NHX:TOL=22131],ceratinini[&&NHX:TOL=22132],manueliini[&&NHX:TOL=22133],xylocopini[&&NHX:TOL=22134])xylocopinae[&&NHX:TOL=22105],((ammobatini[&&NHX:TOL=22135],ammobatoidini[&&NHX:TOL=22136],biastini[&&NHX:TOL=22137],brachynomadini[&&NHX:TOL=22138],caenoprosopidini[&&NHX:TOL=22139],epeolini[&&NHX:TOL=22140],hexepeolini[&&NHX:TOL=22141],neolarrini[&&NHX:TOL=22142],nomadini[&&NHX:TOL=22143],townsendiellini[&&NHX:TOL=22144])nomadinae[&&NHX:TOL=22106],(ancylini[&&NHX:TOL=22145],anthophorini[&&NHX:TOL=22146],apini[&&NHX:TOL=22147],bombini[&&NHX:TOL=22148],centridini[&&NHX:TOL=22149],ctenoplectrini[&&NHX:TOL=22150],emphorini[&&NHX:TOL=22151],ericrocidini[&&NHX:TOL=22152],eucerini[&&NHX:TOL=22153],euglossini[&&NHX:TOL=22154],exomalopsini[&&NHX:TOL=22155],isepeolini[&&NHX:TOL=22156],melectini[&&NHX:TOL=22157],meliponini[&&NHX:TOL=22163],osirini[&&NHX:TOL=22158],protepeolini[&&NHX:TOL=22159],rhathymini[&&NHX:TOL=22160],tapinotaspidini[&&NHX:TOL=22161],tetrapediini[&&NHX:TOL=22162])apinae[&&NHX:TOL=22107])[&&NHX:TOL=22108])apidae[&&NHX:TOL=22101])[&&NHX:TOL=22104])[&&NHX:TOL=22103])apidae sensu lato[&&NHX:TOL=11193])[&&NHX:TOL=22064])[&&NHX:TOL=22063])[&&NHX:TOL=22062])apoidea[&&NHX:TOL=11190],(sierolomorphidae[&&NHX:TOL=11229],(((anthoboscinae[&&NHX:TOL=22164],(diamminae[&&NHX:TOL=22165],(thynninae[&&NHX:TOL=22166],((tiphiinae[&&NHX:TOL=22167],brachycistidinae[&&NHX:TOL=22168])[&&NHX:TOL=22173],(myzininae[&&NHX:TOL=22169],methochinae[&&NHX:TOL=22170])[&&NHX:TOL=22175])[&&NHX:TOL=22174])[&&NHX:TOL=22172])[&&NHX:TOL=22171])tiphiidae[&&NHX:TOL=11235],((fedtschenkiinae[&&NHX:TOL=22178],sapyginae[&&NHX:TOL=22179])sapygidae[&&NHX:TOL=11233],(myrmosinae[&&NHX:TOL=22180],(pseudophotopsidinae[&&NHX:TOL=22181],(ticoplinae[&&NHX:TOL=22182],(rhopalomutillinae[&&NHX:TOL=22183],(sphaerophthalminae[&&NHX:TOL=22184],(myrmillinae[&&NHX:TOL=22185],mutillinae[&&NHX:TOL=22186])[&&NHX:TOL=22191])[&&NHX:TOL=22190])[&&NHX:TOL=22189])[&&NHX:TOL=22188])[&&NHX:TOL=22187])mutillidae[&&NHX:TOL=11234])[&&NHX:TOL=11232])[&&NHX:TOL=11231],((pompilidae[&&NHX:TOL=11238],rhopalosomatidae[&&NHX:TOL=11237])[&&NHX:TOL=11236],((typhoctinae[&&NHX:TOL=22192],(chyphotinae[&&NHX:TOL=22193],(apterogyninae[&&NHX:TOL=22194],bradynobaeninae[&&NHX:TOL=22195])[&&NHX:TOL=22197])[&&NHX:TOL=22196])bradynobaenidae[&&NHX:TOL=11240],((((archaeopone kzylzharica[&&NHX:EXT=Y:TOL=22968],archaeopone taylori[&&NHX:EXT=Y:TOL=22969])archaeopone[&&NHX:EXT=Y:TOL=22234],(armania capitata[&&NHX:EXT=Y:TOL=22970],armania curiosa[&&NHX:EXT=Y:TOL=22971],armania pristina[&&NHX:EXT=Y:TOL=22972],armania robusta[&&NHX:EXT=Y:TOL=22973])armania[&&NHX:EXT=Y:TOL=22235],(dolichomyrma latipes[&&NHX:EXT=Y:TOL=22974],dolichomyrma longiceps[&&NHX:EXT=Y:TOL=22975])dolichomyrma[&&NHX:EXT=Y:TOL=22236],khetania mandibulata[&&NHX:EXT=Y:TOL=22237],poneropterus sphecoides[&&NHX:EXT=Y:TOL=22238],(pseudarmania aberrans[&&NHX:EXT=Y:TOL=22976],pseudarmania rasnitsyni[&&NHX:EXT=Y:TOL=22977])pseudarmania[&&NHX:EXT=Y:TOL=22239])armaniinae[&&NHX:EXT=Y:TOL=11246],((((baikuris casei[&&NHX:EXT=Y:TOL=22978],baikuris mandibularis[&&NHX:EXT=Y:TOL=22979],baikuris mirabilis[&&NHX:EXT=Y:TOL=22980])baikuris[&&NHX:EXT=Y:TOL=22242],(sphecomyrma canadensis[&&NHX:EXT=Y:TOL=22983],sphecomyrma freyi[&&NHX:EXT=Y:TOL=22984])sphecomyrma[&&NHX:EXT=Y:TOL=22245],(cretomyrma arnoldii[&&NHX:EXT=Y:TOL=22981],cretomyrma unicornis[&&NHX:EXT=Y:TOL=22982])cretomyrma[&&NHX:EXT=Y:TOL=22243],dlusskyidris zherichini[&&NHX:EXT=Y:TOL=22244])sphecomyrmini[&&NHX:EXT=Y:TOL=22240],haidomyrmex cerberus[&&NHX:EXT=Y:TOL=22241])sphecomyrminae[&&NHX:EXT=Y:TOL=22198],((((amblyopone oregonensis[&&NHX:TOL=24042],amblyopone pallipes[&&NHX:TOL=24041])amblyopone[&&NHX:TOL=22247],(myopopone castanea[&&NHX:TOL=23035],myopopone sinensis[&&NHX:TOL=23036])myopopone[&&NHX:TOL=22251],adetomyrma venatrix[&&NHX:TOL=22246],((mystrium camillae[&&NHX:TOL=24043],mystrium fallax[&&NHX:TOL=24044],mystrium mysticum[&&NHX:TOL=24045],mystrium oberthueri[&&NHX:TOL=24046],mystrium oculatum[&&NHX:TOL=24047],mystrium rogeri[&&NHX:TOL=24048],mystrium silvestrii[&&NHX:TOL=24049],mystrium stadelmanni[&&NHX:TOL=24050],mystrium voeltzkowi[&&NHX:TOL=24051])mystrium[&&NHX:TOL=22252],apomyrma stygia[&&NHX:TOL=22212])[&&NHX:TOL=24037])[&&NHX:TOL=24040],((onychomyrmex doddi[&&NHX:TOL=23037],onychomyrmex hedleyi[&&NHX:TOL=23038],onychomyrmex mjobergi[&&NHX:TOL=23039])onychomyrmex[&&NHX:TOL=22253],((prionopelta aethiopica[&&NHX:TOL=24052],prionopelta amabilis[&&NHX:TOL=24053],prionopelta amieti[&&NHX:TOL=24054],prionopelta antillana[&&NHX:TOL=24055],prionopelta brocha[&&NHX:TOL=24056],prionopelta descarpentriesi[&&NHX:TOL=24057],prionopelta humicola[&&NHX:TOL=24058],prionopelta kraepelini[&&NHX:TOL=24059],prionopelta majuscula[&&NHX:TOL=24060],prionopelta marthae[&&NHX:TOL=24061],prionopelta modesta[&&NHX:TOL=24062],prionopelta opaca[&&NHX:TOL=24063],prionopelta punctulata[&&NHX:TOL=24064])prionopelta[&&NHX:TOL=22254],concoctio concenta[&&NHX:TOL=22250])[&&NHX:TOL=24039])[&&NHX:TOL=24038],bannapone mulanae[&&NHX:TOL=22248],casaleia inversa[&&NHX:EXT=Y:TOL=22249],paraprionopelta minima[&&NHX:TOL=22255])amblyoponinae[&&NHX:TOL=22214],brownimecia clavata[&&NHX:EXT=Y:TOL=22199],(formicium berryi[&&NHX:EXT=Y:TOL=23040],formicium brodiei[&&NHX:EXT=Y:TOL=23041],formicium giganteum[&&NHX:EXT=Y:TOL=23042],formicium mirabile[&&NHX:EXT=Y:TOL=23043],formicium simillimum[&&NHX:EXT=Y:TOL=23044])formicium[&&NHX:EXT=Y:TOL=22200],(aneuretellus deformis[&&NHX:EXT=Y:TOL=22256],aneuretus simoni[&&NHX:TOL=22257],mianeuretus mirabilis[&&NHX:EXT=Y:TOL=22258],(paraneuretus longicornis[&&NHX:EXT=Y:TOL=23045],paraneuretus tornquisti[&&NHX:EXT=Y:TOL=23046])paraneuretus[&&NHX:EXT=Y:TOL=22259],protaneuretus succineus[&&NHX:EXT=Y:TOL=22260],burmomyrma rossi[&&NHX:EXT=Y:TOL=22261])aneuretinae[&&NHX:TOL=22201],(amyrmex golbachi[&&NHX:TOL=22263],anillidris bruchi[&&NHX:TOL=22264],(anonychomyrma anguliceps[&&NHX:TOL=24103],anonychomyrma angusta[&&NHX:TOL=24104],anonychomyrma arcadia[&&NHX:TOL=24105],anonychomyrma biconvexa[&&NHX:TOL=24106],anonychomyrma constricta[&&NHX:TOL=24107],anonychomyrma dimorpha[&&NHX:TOL=24108],anonychomyrma fornicata[&&NHX:TOL=24109],anonychomyrma froggatti[&&NHX:TOL=24110],anonychomyrma gigantea[&&NHX:TOL=24111],anonychomyrma gilberti[&&NHX:TOL=24112],anonychomyrma glabrata[&&NHX:TOL=24113],anonychomyrma incisa[&&NHX:TOL=24114],anonychomyrma itinerans[&&NHX:TOL=24115],anonychomyrma longicapitata[&&NHX:TOL=24116],anonychomyrma longiceps[&&NHX:TOL=24117],anonychomyrma malandana[&&NHX:TOL=24118],anonychomyrma minuta[&&NHX:TOL=24119],anonychomyrma murina[&&NHX:TOL=24120],anonychomyrma myrmex[&&NHX:TOL=24121],anonychomyrma nitidiceps[&&NHX:TOL=24122],anonychomyrma polita[&&NHX:TOL=24123],anonychomyrma procidua[&&NHX:TOL=24124],anonychomyrma purpurescens[&&NHX:TOL=24125],anonychomyrma samlandica[&&NHX:TOL=24126],anonychomyrma scrutator[&&NHX:TOL=24127],anonychomyrma sellata[&&NHX:TOL=24128],anonychomyrma tigris[&&NHX:TOL=24129])anonychomyrma[&&NHX:TOL=22265],azteca[&&NHX:TOL=22268],bothriomyrmex[&&NHX:TOL=22269],dolichoderus[&&NHX:TOL=22272],ecphorella wellmani[&&NHX:TOL=22274],(leptomyrmex contractus[&&NHX:TOL=24136],leptomyrmex darlingtoni[&&NHX:TOL=24137],leptomyrmex erythrocephalus[&&NHX:TOL=24138],leptomyrmex flavitarsus[&&NHX:TOL=24139],leptomyrmex fragilis[&&NHX:TOL=24140],leptomyrmex froggatti[&&NHX:TOL=24141],leptomyrmex lugubris[&&NHX:TOL=24142],leptomyrmex mjobergi[&&NHX:TOL=24143],leptomyrmex neotropicus[&&NHX:TOL=24144],leptomyrmex niger[&&NHX:TOL=24145],leptomyrmex nigriventris[&&NHX:TOL=24146],leptomyrmex pallens[&&NHX:TOL=24147],leptomyrmex puberulus[&&NHX:TOL=24148],leptomyrmex unicolor[&&NHX:TOL=24149],leptomyrmex varians[&&NHX:TOL=24150],leptomyrmex wheeleri[&&NHX:TOL=24151],leptomyrmex wiburdi[&&NHX:TOL=24152])leptomyrmex[&&NHX:TOL=22284],((axinidris acholli[&&NHX:TOL=24153],axinidris bidens[&&NHX:TOL=24154],axinidris denticulata[&&NHX:TOL=24155],axinidris ghanensis[&&NHX:TOL=24156],axinidris hylekoites[&&NHX:TOL=24157],axinidris kakamegensis[&&NHX:TOL=24158],axinidris kinoin[&&NHX:TOL=24159],axinidris murielae[&&NHX:TOL=24160],axinidris nigripes[&&NHX:TOL=24161],axinidris occidentalis[&&NHX:TOL=24162],axinidris palligastrion[&&NHX:TOL=24163],axinidris parvus[&&NHX:TOL=24164])axinidris[&&NHX:TOL=22267],(liometopum antiquum[&&NHX:TOL=24165],liometopum apiculatum[&&NHX:TOL=24166],liometopum eremicum[&&NHX:TOL=24167],liometopum goepperti[&&NHX:TOL=24168],liometopum imhoffii[&&NHX:TOL=24169],liometopum lindgreeni[&&NHX:TOL=24170],liometopum lubricum[&&NHX:TOL=24171],liometopum luctuosum[&&NHX:TOL=24172],liometopum masonium[&&NHX:TOL=24173],liometopum microcephalum[&&NHX:TOL=24174],liometopum minimum[&&NHX:TOL=24175],liometopum miocenicum[&&NHX:TOL=24176],liometopum occidentale[&&NHX:TOL=24177],liometopum oligocenicum[&&NHX:TOL=24178],liometopum orientale[&&NHX:TOL=24179],liometopum potamophilum[&&NHX:TOL=24180],liometopum scudderi[&&NHX:TOL=24181],liometopum sinense[&&NHX:TOL=24182])liometopum[&&NHX:TOL=22287],tapinoma[&&NHX:TOL=22296],technomyrmex[&&NHX:TOL=22297])[&&NHX:TOL=22674],(doleromyrma darwiniana[&&NHX:TOL=22271],dorymyrmex[&&NHX:TOL=22273],(forelius albiventris[&&NHX:TOL=24189],forelius analis[&&NHX:TOL=24190],forelius andinus[&&NHX:TOL=24191],forelius bahianus[&&NHX:TOL=24192],forelius brasiliensis[&&NHX:TOL=24193],forelius breviscapus[&&NHX:TOL=24194],forelius chalybaeus[&&NHX:TOL=24195],forelius grandis[&&NHX:TOL=24196],forelius kieferi[&&NHX:TOL=24197],forelius lilloi[&&NHX:TOL=24198],forelius macrops[&&NHX:TOL=24199],forelius maranhaoensis[&&NHX:TOL=24200],forelius mccooki[&&NHX:TOL=24201],forelius minor[&&NHX:TOL=24202],forelius nigriventris[&&NHX:TOL=24203],forelius pruinosus[&&NHX:TOL=24204],forelius pusillus[&&NHX:TOL=24205],forelius rubriceps[&&NHX:TOL=24206],forelius rufus[&&NHX:TOL=24207])forelius[&&NHX:TOL=22280],(linepithema aspidocoptum[&&NHX:TOL=24208],linepithema dispertitum[&&NHX:TOL=24209],linepithema fuscum[&&NHX:TOL=24210],linepithema hispaniolae[&&NHX:TOL=24211],linepithema humile[&&NHX:TOL=24212],linepithema humiloides[&&NHX:TOL=24213],linepithema impotens[&&NHX:TOL=24214],linepithema inacatum[&&NHX:TOL=24215],linepithema iniquum[&&NHX:TOL=24216],linepithema keiteli[&&NHX:TOL=24217],linepithema leucomelas[&&NHX:TOL=24218],linepithema melleum[&&NHX:TOL=24219],linepithema oblongum[&&NHX:TOL=24220],linepithema piliferum[&&NHX:TOL=24221],linepithema pordescens[&&NHX:TOL=24222],linepithema riograndense[&&NHX:TOL=24223])linepithema[&&NHX:TOL=22286],loweriella boltoni[&&NHX:TOL=22288],(iridomyrmex[&&NHX:TOL=22282],(ochetellus epinotalis[&&NHX:TOL=24226],ochetellus flavipes[&&NHX:TOL=24227],ochetellus glaber[&&NHX:TOL=24228],ochetellus itoi[&&NHX:TOL=24229],ochetellus punctatissimus[&&NHX:TOL=24230],ochetellus sororis[&&NHX:TOL=24231],ochetellus vinsoni[&&NHX:TOL=24232])ochetellus[&&NHX:TOL=22290],(papyrius flavus[&&NHX:TOL=24233],papyrius nitidus[&&NHX:TOL=24234])papyrius[&&NHX:TOL=22291],((philidris brunnea[&&NHX:TOL=24235],philidris cordata[&&NHX:TOL=24236],philidris cruda[&&NHX:TOL=24237],philidris laevigata[&&NHX:TOL=24238],philidris myrmecodiae[&&NHX:TOL=24239],philidris nagasau[&&NHX:TOL=24240],philidris notiola[&&NHX:TOL=24241],philidris pubescens[&&NHX:TOL=24242])philidris[&&NHX:TOL=22293],((froggattella kirbii[&&NHX:TOL=24243],froggattella latispina[&&NHX:TOL=24244])froggattella[&&NHX:TOL=22281],(turneria arbusta[&&NHX:TOL=24245],turneria bidentata[&&NHX:TOL=24246],turneria collina[&&NHX:TOL=24247],turneria dahlii[&&NHX:TOL=24248],turneria frenchi[&&NHX:TOL=24249],turneria pacifica[&&NHX:TOL=24250],turneria postomma[&&NHX:TOL=24251])turneria[&&NHX:TOL=22298])[&&NHX:TOL=22675])[&&NHX:TOL=22676])[&&NHX:TOL=22678])[&&NHX:TOL=22679],alloiomma changweiensis[&&NHX:EXT=Y:TOL=22262],asymphylomyrmex balticus[&&NHX:EXT=Y:TOL=22266],ctenobethylus succinalis[&&NHX:EXT=Y:TOL=22270],(elaeomyrmex coloradensis[&&NHX:EXT=Y:TOL=24252],elaeomyrmex gracilis[&&NHX:EXT=Y:TOL=24253])elaeomyrmex[&&NHX:EXT=Y:TOL=22275],(elaphrodites mutatus[&&NHX:EXT=Y:TOL=24254],elaphrodites scutulatus[&&NHX:EXT=Y:TOL=24255])elaphrodites[&&NHX:EXT=Y:TOL=22276],emplastus emeryi[&&NHX:EXT=Y:TOL=22277],(eotapinoma compacta[&&NHX:EXT=Y:TOL=24256],eotapinoma gracilis[&&NHX:EXT=Y:TOL=24257],eotapinoma macalpini[&&NHX:EXT=Y:TOL=24258])eotapinoma[&&NHX:EXT=Y:TOL=22278],eurymyrmex geologicus[&&NHX:EXT=Y:TOL=22279],kotshkorkia laticeps[&&NHX:EXT=Y:TOL=22283],leptomyrmula maravignae[&&NHX:EXT=Y:TOL=22285],(miomyrmex impactus[&&NHX:EXT=Y:TOL=24259],miomyrmex striatus[&&NHX:EXT=Y:TOL=24260])miomyrmex[&&NHX:EXT=Y:TOL=22289],petraeomyrmex minimus[&&NHX:EXT=Y:TOL=22292],pityomyrmex tornquisti[&&NHX:EXT=Y:TOL=22294],(protazteca capitata[&&NHX:EXT=Y:TOL=24261],protazteca elongata[&&NHX:EXT=Y:TOL=24262],protazteca hendersoni[&&NHX:EXT=Y:TOL=24263],protazteca quadrata[&&NHX:EXT=Y:TOL=24264])protazteca[&&NHX:EXT=Y:TOL=22295],(zherichinius horribilis[&&NHX:EXT=Y:TOL=24265],zherichinius rapax[&&NHX:EXT=Y:TOL=24266])zherichinius[&&NHX:EXT=Y:TOL=22299])dolichoderinae[&&NHX:TOL=22202],((((calomyrmex albertisi[&&NHX:TOL=24274],calomyrmex albopilosus[&&NHX:TOL=24275],calomyrmex glauerti[&&NHX:TOL=24276],calomyrmex impavidus[&&NHX:TOL=24277],calomyrmex laevissimus[&&NHX:TOL=24278],calomyrmex purpureus[&&NHX:TOL=24279],calomyrmex similis[&&NHX:TOL=24280],calomyrmex splendidus[&&NHX:TOL=24281],calomyrmex tropicus[&&NHX:TOL=24282])calomyrmex[&&NHX:TOL=22314],camponotites macropterus[&&NHX:EXT=Y:TOL=22315],(camponotus camponotus[&&NHX:TOL=24283],camponotus colobopsis[&&NHX:TOL=24284],camponotus mayria[&&NHX:TOL=24285],camponotus rhinomyrmex[&&NHX:TOL=24286],camponotus dendromyrmex[&&NHX:TOL=24287],camponotus dinomyrmex[&&NHX:TOL=24288],camponotus tanaemyrmex[&&NHX:TOL=24289],camponotus orthonotomyrmex[&&NHX:TOL=24290],camponotus myrmamblys[&&NHX:TOL=24291],camponotus myrmothrix[&&NHX:TOL=24292],camponotus myrmosericus[&&NHX:TOL=24293],camponotus myrmophyma[&&NHX:TOL=24294],camponotus myrmotrema[&&NHX:TOL=24295],camponotus myrmobrachys[&&NHX:TOL=24296],camponotus myrmentoma[&&NHX:TOL=24297],camponotus myrmosphincta[&&NHX:TOL=24298],camponotus myrmotarsus[&&NHX:TOL=24299],camponotus myrmepomis[&&NHX:TOL=24300],camponotus myrmogonia[&&NHX:TOL=24301],camponotus myrmeurynota[&&NHX:TOL=24302],camponotus myrmopsamma[&&NHX:TOL=24303],camponotus myrmomalis[&&NHX:TOL=24304],camponotus myrmoplatys[&&NHX:TOL=24305],camponotus myrmaphaenus[&&NHX:TOL=24306],camponotus myrmonesites[&&NHX:TOL=24307],camponotus myrmopytia[&&NHX:TOL=24308],camponotus myrmotemnus[&&NHX:TOL=24309],camponotus pseudocolobopsis[&&NHX:TOL=24310],camponotus myrmostenus[&&NHX:TOL=24311],camponotus hypercolobopsis[&&NHX:TOL=24312],camponotus myrmopiromis[&&NHX:TOL=24313],camponotus myrmosaulus[&&NHX:TOL=24314],camponotus myrmocladoecus[&&NHX:TOL=24315],camponotus manniella[&&NHX:TOL=24316],camponotus myrmisolepis[&&NHX:TOL=24317],camponotus myrmopelta[&&NHX:TOL=24318],camponotus myrmoplatypus[&&NHX:TOL=24319],camponotus myrmepinotus[&&NHX:TOL=24320],camponotus myrmoxygenys[&&NHX:TOL=24321],camponotus karavaievia[&&NHX:TOL=24322],camponotus myrmodirachis[&&NHX:TOL=24323],camponotus myrmespera[&&NHX:TOL=24324],camponotus paramyrmamblys[&&NHX:TOL=24325],camponotus myrmacrhaphe[&&NHX:TOL=24326],camponotus thlipsepinotus[&&NHX:TOL=24327],camponotus myrmopalpella[&&NHX:TOL=24328])camponotus[&&NHX:TOL=22316],chimaeromyrma brachycephala[&&NHX:EXT=Y:TOL=22317],(echinopla arfaki[&&NHX:TOL=24351],echinopla australis[&&NHX:TOL=24352],echinopla crenulata[&&NHX:TOL=24353],echinopla deceptor[&&NHX:TOL=24354],echinopla densistriata[&&NHX:TOL=24355],echinopla dubitata[&&NHX:TOL=24356],echinopla lineata[&&NHX:TOL=24357],echinopla maeandrina[&&NHX:TOL=24358],echinopla melanarctos[&&NHX:TOL=24359],echinopla mistura[&&NHX:TOL=24360],echinopla nitida[&&NHX:TOL=24361],echinopla octodentata[&&NHX:TOL=24362],echinopla pallipes[&&NHX:TOL=24363],echinopla praetexta[&&NHX:TOL=24364],echinopla pseudostriata[&&NHX:TOL=24365],echinopla rugosa[&&NHX:TOL=24366],echinopla serrata[&&NHX:TOL=24367],echinopla silvestrii[&&NHX:TOL=24368],echinopla striata[&&NHX:TOL=24369],echinopla tritschleri[&&NHX:TOL=24370],echinopla turneri[&&NHX:TOL=24371],echinopla vermiculata[&&NHX:TOL=24372])echinopla[&&NHX:TOL=22318],forelophilus overbecki[&&NHX:TOL=22319],(opisthopsis diadematus[&&NHX:TOL=24373],opisthopsis haddoni[&&NHX:TOL=24374],opisthopsis halmaherae[&&NHX:TOL=24375],opisthopsis jocosus[&&NHX:TOL=24376],opisthopsis lienosus[&&NHX:TOL=24377],opisthopsis linnaei[&&NHX:TOL=24378],opisthopsis major[&&NHX:TOL=24379],opisthopsis manni[&&NHX:TOL=24380],opisthopsis maurus[&&NHX:TOL=24381],opisthopsis panops[&&NHX:TOL=24382],opisthopsis pictus[&&NHX:TOL=24383],opisthopsis respiciens[&&NHX:TOL=24384],opisthopsis rufithorax[&&NHX:TOL=24385])opisthopsis[&&NHX:TOL=22320],overbeckia subclavata[&&NHX:TOL=22321],(phasmomyrmex aberrans[&&NHX:TOL=24386],phasmomyrmex buchneri[&&NHX:TOL=24387],phasmomyrmex paradoxus[&&NHX:TOL=24388],phasmomyrmex wolfi[&&NHX:TOL=24389])phasmomyrmex[&&NHX:TOL=22322],(polyrhachis polyrhachis[&&NHX:TOL=24390],polyrhachis myrma[&&NHX:TOL=24391],polyrhachis hemioptica[&&NHX:TOL=24392],polyrhachis campomyrma[&&NHX:TOL=24393],polyrhachis hagiomyrma[&&NHX:TOL=24394],polyrhachis myrmothrinax[&&NHX:TOL=24395],polyrhachis cyrtomyrma[&&NHX:TOL=24396],polyrhachis myrmhopla[&&NHX:TOL=24397],polyrhachis chariomyrma[&&NHX:TOL=24398],polyrhachis hedomyrma[&&NHX:TOL=24399],polyrhachis myrmatopa[&&NHX:TOL=24400],polyrhachis aulacomyrma[&&NHX:TOL=24401])polyrhachis[&&NHX:TOL=22323],pseudocamponotus elkoanus[&&NHX:EXT=Y:TOL=22324])camponotini[&&NHX:TOL=22300],((alloformica aberrans[&&NHX:TOL=24402],alloformica flavicornis[&&NHX:TOL=24403],alloformica nitidior[&&NHX:TOL=24404],alloformica obscurior[&&NHX:TOL=24405])alloformica[&&NHX:TOL=22325],(bajcaridris kraussii[&&NHX:TOL=24406],bajcaridris menozzii[&&NHX:TOL=24407],bajcaridris theryi[&&NHX:TOL=24408])bajcaridris[&&NHX:TOL=22326],cataglyphis[&&NHX:TOL=22327],formica[&&NHX:TOL=22328],(polyergus breviceps[&&NHX:TOL=24413],polyergus lucidus[&&NHX:TOL=24414],polyergus nigerrimus[&&NHX:TOL=24415],polyergus rugescens[&&NHX:TOL=24416],polyergus samurai[&&NHX:TOL=24417],polyergus texana[&&NHX:TOL=24418])polyergus[&&NHX:TOL=22330],glaphyromyrmex oligocenicus[&&NHX:EXT=Y:TOL=22329],(proformica alaica[&&NHX:TOL=24419],proformica buddhaensis[&&NHX:TOL=24420],proformica caucasea[&&NHX:TOL=24421],proformica coriacea[&&NHX:TOL=24422],proformica dolichocephala[&&NHX:TOL=24423],proformica epinotalis[&&NHX:TOL=24424],proformica ferreri[&&NHX:TOL=24425],proformica flavosetosa[&&NHX:TOL=24426],proformica jacoti[&&NHX:TOL=24427],proformica kaszabi[&&NHX:TOL=24428],proformica kobachidzei[&&NHX:TOL=24429],proformica korbi[&&NHX:TOL=24430],proformica kosswigi[&&NHX:TOL=24431],proformica kusnezowi[&&NHX:TOL=24432],proformica longiseta[&&NHX:TOL=24433],proformica mongolica[&&NHX:TOL=24434],proformica nasuta[&&NHX:TOL=24435],proformica nitida[&&NHX:TOL=24436],proformica oculatissima[&&NHX:TOL=24437],proformica pilosiscapa[&&NHX:TOL=24438],proformica seraphimi[&&NHX:TOL=24439],proformica similis[&&NHX:TOL=24440],proformica splendida[&&NHX:TOL=24441],proformica striaticeps[&&NHX:TOL=24442])proformica[&&NHX:TOL=22331],protoformica proformicoides[&&NHX:EXT=Y:TOL=22332],(rossomyrmex minuchae[&&NHX:TOL=24443],rossomyrmex proformicarum[&&NHX:TOL=24444],rossomyrmex quandratinodum[&&NHX:TOL=24445])rossomyrmex[&&NHX:TOL=22333])formicini[&&NHX:TOL=22301],gigantiops destructor[&&NHX:TOL=22303],(melophorus aeneovirens[&&NHX:TOL=24446],melophorus anderseni[&&NHX:TOL=24447],melophorus bagoti[&&NHX:TOL=24448],melophorus biroi[&&NHX:TOL=24449],melophorus bruneus[&&NHX:TOL=24450],melophorus constans[&&NHX:TOL=24451],melophorus curtus[&&NHX:TOL=24452],melophorus fieldi[&&NHX:TOL=24453],melophorus fulvohirtus[&&NHX:TOL=24454],melophorus hirsutus[&&NHX:TOL=24455],melophorus insularis[&&NHX:TOL=24456],melophorus iridescens[&&NHX:TOL=24457],melophorus laticeps[&&NHX:TOL=24458],melophorus ludius[&&NHX:TOL=24459],melophorus majeri[&&NHX:TOL=24460],melophorus marius[&&NHX:TOL=24461],melophorus mjobergi[&&NHX:TOL=24462],melophorus omniparens[&&NHX:TOL=24463],melophorus pillipes[&&NHX:TOL=24464],melophorus potteri[&&NHX:TOL=24465],melophorus scipio[&&NHX:TOL=24466],melophorus turneri[&&NHX:TOL=24467],melophorus wheeleri[&&NHX:TOL=24468])melophorus[&&NHX:TOL=22313],(notostigma carazzii[&&NHX:TOL=24469],notostigma foreli[&&NHX:TOL=24470])notostigma[&&NHX:TOL=22307],(oecophylla atavina[&&NHX:EXT=Y:TOL=24471],oecophylla bartoniana[&&NHX:EXT=Y:TOL=24472],oecophylla brischkei[&&NHX:EXT=Y:TOL=24473],oecophylla crassinoda[&&NHX:EXT=Y:TOL=24474],oecophylla leakeyi[&&NHX:EXT=Y:TOL=24475],oecophylla longinoda[&&NHX:TOL=24476],oecophylla megarche[&&NHX:EXT=Y:TOL=24477],oecophylla obesa[&&NHX:EXT=Y:TOL=24478],oecophylla perdita[&&NHX:EXT=Y:TOL=24479],oecophylla praeclara[&&NHX:EXT=Y:TOL=24480],oecophylla sicula[&&NHX:EXT=Y:TOL=24481],oecophylla smaragdina[&&NHX:TOL=24482],oecophylla superba[&&NHX:EXT=Y:TOL=24483])oecophylla[&&NHX:TOL=22308])formicine tribe group[&&NHX:TOL=22312],((gesomyrmex chaperi[&&NHX:TOL=24484],gesomyrmex expectans[&&NHX:TOL=24485],gesomyrmex hoernesi[&&NHX:TOL=24486],gesomyrmex howardi[&&NHX:TOL=24487],gesomyrmex kalshoveni[&&NHX:TOL=24488],gesomyrmex luzonensis[&&NHX:TOL=24489],gesomyrmex miegi[&&NHX:TOL=24490],gesomyrmex spatulatus[&&NHX:TOL=24491])gesomyrmex[&&NHX:TOL=22339],santschiella kohli[&&NHX:TOL=22340],sicilomyrmex corniger[&&NHX:EXT=Y:TOL=22341],prodimorphomyrmex primigenius[&&NHX:EXT=Y:TOL=22342])gesomyrmecini[&&NHX:TOL=22302],(((((acanthomyops arizonicus[&&NHX:TOL=24492],acanthomyops bureni[&&NHX:TOL=24493],acanthomyops californicus[&&NHX:TOL=24494],acanthomyops claviger[&&NHX:TOL=24495],acanthomyops colei[&&NHX:TOL=24496],acanthomyops coloradensis[&&NHX:TOL=24497],acanthomyops creightoni[&&NHX:TOL=24498],acanthomyops interjectus[&&NHX:TOL=24499],acanthomyops latipes[&&NHX:TOL=24500],acanthomyops mexicanus[&&NHX:TOL=24501],acanthomyops murphyi[&&NHX:TOL=24502],acanthomyops occidentalis[&&NHX:TOL=24503],acanthomyops plumopilosus[&&NHX:TOL=24504],acanthomyops pogonogynus[&&NHX:TOL=24505],acanthomyops pubescens[&&NHX:TOL=24506],acanthomyops subglaber[&&NHX:TOL=24507])acanthomyops[&&NHX:TOL=22343],(lasius lasius[&&NHX:TOL=24508],lasius dendrolasius[&&NHX:TOL=24509],lasius chthonolasius[&&NHX:TOL=24510],lasius cautolasius[&&NHX:TOL=24511],lasius austrolasius[&&NHX:TOL=24512])lasius[&&NHX:TOL=22348])[&&NHX:TOL=22370],(acropyga acropyga[&&NHX:TOL=24513],acropyga rhizomyrma[&&NHX:TOL=24514],acropyga atopodon[&&NHX:TOL=24515],acropyga malacomyrma[&&NHX:TOL=24516])acropyga[&&NHX:TOL=22344],(anoplolepis carinata[&&NHX:TOL=24517],anoplolepis custodiens[&&NHX:TOL=24518],anoplolepis fallax[&&NHX:TOL=24519],anoplolepis gracilipes[&&NHX:TOL=24520],anoplolepis nuptialis[&&NHX:TOL=24521],anoplolepis opaciventris[&&NHX:TOL=24522],anoplolepis rufescens[&&NHX:TOL=24523],anoplolepis steingroeveri[&&NHX:TOL=24524],anoplolepis tenella[&&NHX:TOL=24525])anoplolepis[&&NHX:TOL=22345],(cladomyrma andrei[&&NHX:TOL=24526],cladomyrma aurochaetae[&&NHX:TOL=24527],cladomyrma crypteroniae[&&NHX:TOL=24528],cladomyrma dianeae[&&NHX:TOL=24529],cladomyrma hewitti[&&NHX:TOL=24530],cladomyrma hobbyi[&&NHX:TOL=24531],cladomyrma maryatiae[&&NHX:TOL=24532],cladomyrma maschwitzi[&&NHX:TOL=24533],cladomyrma nudidorsalis[&&NHX:TOL=24534],cladomyrma petalae[&&NHX:TOL=24535])cladomyrma[&&NHX:TOL=22346],(lasiophanes atriventris[&&NHX:TOL=24536],lasiophanes hoffmanni[&&NHX:TOL=24537],lasiophanes perplexus[&&NHX:TOL=24538],lasiophanes picinus[&&NHX:TOL=24539],lasiophanes valdiviensis[&&NHX:TOL=24540])lasiophanes[&&NHX:TOL=22347],(myrmecocystus testaceus[&&NHX:TOL=24568],((myrmecocystus perimeces[&&NHX:TOL=24561],myrmecocystus creightoni[&&NHX:TOL=24543])[&&NHX:TOL=26488],myrmecocystus mexicanus[&&NHX:TOL=24557],(myrmecocystus wheeleri[&&NHX:TOL=24569],(myrmecocystus flaviceps[&&NHX:TOL=24546],((myrmecocystus mendax[&&NHX:TOL=24556],myrmecocystus placodops[&&NHX:TOL=24562])[&&NHX:TOL=26491],(myrmecocystus yuma[&&NHX:TOL=24570],((myrmecocystus kennedyi[&&NHX:TOL=24550],myrmecocystus romainei[&&NHX:TOL=24564])[&&NHX:TOL=26494],(myrmecocystus nequatzcatl[&&NHX:TOL=24560],(myrmecocystus depilis[&&NHX:TOL=24544],myrmecocystus mimicus[&&NHX:TOL=24558])[&&NHX:TOL=26497])[&&NHX:TOL=26496])[&&NHX:TOL=26495])[&&NHX:TOL=26493])[&&NHX:TOL=26492])[&&NHX:TOL=26490])[&&NHX:TOL=26489])[&&NHX:TOL=26487],myrmecocystus christineae[&&NHX:TOL=24541],myrmecocystus colei[&&NHX:TOL=24542],myrmecocystus ewarti[&&NHX:TOL=24545],myrmecocystus hammettensis[&&NHX:TOL=24547],myrmecocystus intonsus[&&NHX:TOL=24548],myrmecocystus kathjuli[&&NHX:TOL=24549],myrmecocystus koso[&&NHX:TOL=24551],myrmecocystus lugubris[&&NHX:TOL=24552],myrmecocystus melanoticus[&&NHX:TOL=24553],myrmecocystus melliger forel[&&NHX:TOL=24554],myrmecocystus melliger llave[&&NHX:TOL=24555],myrmecocystus navajo[&&NHX:TOL=24559],myrmecocystus pyramicus[&&NHX:TOL=24563],myrmecocystus semirufus[&&NHX:TOL=24565],myrmecocystus snellingi[&&NHX:TOL=24566],myrmecocystus tenuinodis[&&NHX:TOL=24567])myrmecocystus[&&NHX:TOL=22349],(prolasius abruptus[&&NHX:TOL=24571],prolasius advenus[&&NHX:TOL=24572],prolasius antennatus[&&NHX:TOL=24573],prolasius bruneus[&&NHX:TOL=24574],prolasius clarki[&&NHX:TOL=24575],prolasius convexus[&&NHX:TOL=24576],prolasius depressiceps[&&NHX:TOL=24577],prolasius flavicornis[&&NHX:TOL=24578],prolasius formicoides[&&NHX:TOL=24579],prolasius hellenae[&&NHX:TOL=24580],prolasius hemiflavus[&&NHX:TOL=24581],prolasius mjoebergella[&&NHX:TOL=24582],prolasius nitidissimus[&&NHX:TOL=24583],prolasius pallidus[&&NHX:TOL=24584],prolasius quadratus[&&NHX:TOL=24585],prolasius reticulatus[&&NHX:TOL=24586],prolasius robustus[&&NHX:TOL=24587],prolasius wheeleri[&&NHX:TOL=24588],prolasius wilsoni[&&NHX:TOL=24589])prolasius[&&NHX:TOL=22350],stigmacros[&&NHX:TOL=22351],teratomyrmex greavesi[&&NHX:TOL=22352])lasiini[&&NHX:TOL=22304],((agraulomyrmex meridionalis[&&NHX:TOL=24592],agraulomyrmex wilsoni[&&NHX:TOL=24593])agraulomyrmex[&&NHX:TOL=22353],aphomomyrmex afer[&&NHX:TOL=22354],brachymyrmex[&&NHX:TOL=22355],bregmatomyrma carnosa[&&NHX:TOL=22356],(euprenolepis antespectans[&&NHX:TOL=24596],euprenolepis helleri[&&NHX:TOL=24597],euprenolepis negrosensis[&&NHX:TOL=24598],euprenolepis procera[&&NHX:TOL=24599],euprenolepis steeli[&&NHX:TOL=24600],euprenolepis stigmatica[&&NHX:TOL=24601])euprenolepis[&&NHX:TOL=22357],lepisiota[&&NHX:TOL=22358],myrmelachista[&&NHX:TOL=22359],paratrechina[&&NHX:TOL=22360],petalomyrmex phylax[&&NHX:TOL=22361],plagiolepis[&&NHX:TOL=22362],(prenolepis acuminata[&&NHX:TOL=24610],prenolepis albimaculata[&&NHX:TOL=24611],prenolepis angularis[&&NHX:TOL=24612],prenolepis emmae[&&NHX:TOL=24613],prenolepis gibberosa[&&NHX:TOL=24614],prenolepis henschei[&&NHX:TOL=24615],prenolepis imparis[&&NHX:TOL=24616],prenolepis jacobsoni[&&NHX:TOL=24617],prenolepis jerdoni[&&NHX:TOL=24618],prenolepis karstica[&&NHX:TOL=24619],prenolepis longiventris[&&NHX:TOL=24620],prenolepis magnocula[&&NHX:TOL=24621],prenolepis melanogaster[&&NHX:TOL=24622],prenolepis naoroji[&&NHX:TOL=24623],prenolepis nigriflagella[&&NHX:TOL=24624],prenolepis nitens[&&NHX:TOL=24625],prenolepis pygmaea[&&NHX:TOL=24626],prenolepis sphingthorax[&&NHX:TOL=24627],prenolepis umbra[&&NHX:TOL=24628])prenolepis[&&NHX:TOL=22363],pseudaphomomyrmex emeryi[&&NHX:TOL=22365],pseudolasius[&&NHX:TOL=22364],(tapinolepis bothae[&&NHX:TOL=24631],tapinolepis candida[&&NHX:TOL=24632],tapinolepis deceptor[&&NHX:TOL=24633],tapinolepis decolor[&&NHX:TOL=24634],tapinolepis litoralis[&&NHX:TOL=24635],tapinolepis longitarsis[&&NHX:TOL=24636],tapinolepis macgregori[&&NHX:TOL=24637],tapinolepis macrophthalma[&&NHX:TOL=24638],tapinolepis mediterranea[&&NHX:TOL=24639],tapinolepis melanaria[&&NHX:TOL=24640],tapinolepis pernix[&&NHX:TOL=24641],tapinolepis simulans[&&NHX:TOL=24642],tapinolepis trimenii[&&NHX:TOL=24643],tapinolepis tumidula[&&NHX:TOL=24644])tapinolepis[&&NHX:TOL=22366])plagiolepidini[&&NHX:TOL=22309])[&&NHX:TOL=22311],myrmoteras[&&NHX:TOL=22306])lasiine tribe group[&&NHX:TOL=22310],((myrmecorhynchus carteri[&&NHX:TOL=24647],myrmecorhynchus emeryi[&&NHX:TOL=24648],myrmecorhynchus musgravei[&&NHX:TOL=24649],myrmecorhynchus nitidus[&&NHX:TOL=24650],myrmecorhynchus rufithorax[&&NHX:TOL=24651])myrmecorhynchus[&&NHX:TOL=22367],(notoncus capitatus[&&NHX:TOL=24652],notoncus ectatommoides[&&NHX:TOL=24653],notoncus enormis[&&NHX:TOL=24654],notoncus gilberti[&&NHX:TOL=24655],notoncus hickmani[&&NHX:TOL=24656],notoncus spinisquamis[&&NHX:TOL=24657])notoncus[&&NHX:TOL=22368],(pseudonotoncus hirsutus[&&NHX:TOL=24658],pseudonotoncus turneri[&&NHX:TOL=24659])pseudonotoncus[&&NHX:TOL=22369])myrmecorhynchini[&&NHX:TOL=22305],(imhoffia nigra[&&NHX:EXT=Y:TOL=24660],imhoffia pallida[&&NHX:EXT=Y:TOL=24661])imhoffia[&&NHX:EXT=Y:TOL=22334],kyromyrma neffi[&&NHX:EXT=Y:TOL=22335],(leucotaphus cockerelli[&&NHX:EXT=Y:TOL=24662],leucotaphus gurnetensis[&&NHX:EXT=Y:TOL=24663],leucotaphus permancus[&&NHX:EXT=Y:TOL=24664])leucotaphus[&&NHX:EXT=Y:TOL=22336],protrechina carpenteri[&&NHX:EXT=Y:TOL=22337],tylolasius inflatus[&&NHX:EXT=Y:TOL=22338])formicinae[&&NHX:TOL=22203],((myrmecia aberrans[&&NHX:TOL=24671],myrmecia simillima[&&NHX:TOL=24665])myrmecia[&&NHX:TOL=24666],(nothomyrmecia macrops[&&NHX:TOL=24673],(prionomyrmex janzeni[&&NHX:EXT=Y:TOL=24675],prionomyrmex longiceps[&&NHX:EXT=Y:TOL=24676])prionomyrmex[&&NHX:EXT=Y:TOL=24674])prionomyrmecini[&&NHX:TOL=24670],(archimyrmex piatnitzkyi[&&NHX:EXT=Y:TOL=24677],archimyrmex rostratus[&&NHX:EXT=Y:TOL=24678],archimyrmex smekali[&&NHX:EXT=Y:TOL=24679])archimyrmex[&&NHX:EXT=Y:TOL=24672])myrmeciinae[&&NHX:TOL=22204],((pseudomyrmex[&&NHX:TOL=22386],myrcidris epicharis[&&NHX:TOL=22385])[&&NHX:TOL=22932],tetraponera[&&NHX:TOL=22387])pseudomyrmecinae[&&NHX:TOL=22205],((((basiceros conjugans[&&NHX:TOL=24684],basiceros convexiceps[&&NHX:TOL=24685],basiceros disciger[&&NHX:TOL=24686],basiceros manni[&&NHX:TOL=24687],basiceros militaris[&&NHX:TOL=24688],basiceros redux[&&NHX:TOL=24689],basiceros singularis[&&NHX:TOL=24690])basiceros[&&NHX:TOL=22697],creightonidris scambognatha[&&NHX:TOL=22698],(eurhopalothrix alopeciosa[&&NHX:TOL=24691],34 additional described species[&&NHX:TOL=24692])eurhopalothrix[&&NHX:TOL=22699],(octostruma balzani[&&NHX:TOL=24693],octostruma batesi[&&NHX:TOL=24694],octostruma betschi[&&NHX:TOL=24695],octostruma iheringi[&&NHX:TOL=24696],octostruma impressa[&&NHX:TOL=24697],octostruma inca[&&NHX:TOL=24698],octostruma petiolata[&&NHX:TOL=24699],octostruma rugifera[&&NHX:TOL=24700],octostruma rugiferoides[&&NHX:TOL=24701],octostruma stenognatha[&&NHX:TOL=24702],octostruma stenoscapa[&&NHX:TOL=24703],octostruma wheeleri[&&NHX:TOL=24704])octostruma[&&NHX:TOL=22700],protalaridris armata[&&NHX:TOL=22701],(rhopalothrix acutipilis[&&NHX:TOL=24705],rhopalothrix ciliata[&&NHX:TOL=24706],rhopalothrix diadema[&&NHX:TOL=24707],rhopalothrix inopinata[&&NHX:TOL=24708],rhopalothrix isthmica[&&NHX:TOL=24709],rhopalothrix kusnezovi[&&NHX:TOL=24710],rhopalothrix orbis[&&NHX:TOL=24711],rhopalothrix plaumanni[&&NHX:TOL=24712],rhopalothrix stannardi[&&NHX:TOL=24713],rhopalothrix weberi[&&NHX:TOL=24714])rhopalothrix[&&NHX:TOL=22702],talaridris mandibularis[&&NHX:TOL=22703])basicerotini[&&NHX:TOL=22430],((acanthognathus brevicornis[&&NHX:TOL=24715],acanthognathus lentus[&&NHX:TOL=24716],acanthognathus ocellatus[&&NHX:TOL=24717],acanthognathus poinari[&&NHX:TOL=24718],acanthognathus rudis[&&NHX:TOL=24719],acanthognathus stipulosus[&&NHX:TOL=24720],acanthognathus teledectus[&&NHX:TOL=24721])acanthognathus[&&NHX:TOL=22475],(colobostruma allinodis[&&NHX:TOL=24722],colobostruma australis[&&NHX:TOL=24723],colobostruma binconcava[&&NHX:TOL=24724],colobostruma biconvexa[&&NHX:TOL=24725],colobostruma bicorna[&&NHX:TOL=24726],colobostruma cerornata[&&NHX:TOL=24727],colobostruma elliotti[&&NHX:TOL=24728],colobostruma foliacea[&&NHX:TOL=24729],colobostruma froggatti[&&NHX:TOL=24730],colobostruma lacuna[&&NHX:TOL=24731],colobostruma leae[&&NHX:TOL=24732],colobostruma mellea[&&NHX:TOL=24733],colobostruma nancyae[&&NHX:TOL=24734],colobostruma papulata[&&NHX:TOL=24735],colobostruma sisypha[&&NHX:TOL=24736],colobostruma unicorna[&&NHX:TOL=24737])colobostruma[&&NHX:TOL=22476],daceton armigerum[&&NHX:TOL=22477],(epopostruma alata[&&NHX:TOL=24738],epopostruma angela[&&NHX:TOL=24739],epopostruma angulata[&&NHX:TOL=24740],epopostruma avicula[&&NHX:TOL=24741],epopostruma curiosa[&&NHX:TOL=24742],epopostruma frosti[&&NHX:TOL=24743],epopostruma infuscocephala[&&NHX:TOL=24744],epopostruma kangarooensis[&&NHX:TOL=24745],epopostruma lattini[&&NHX:TOL=24746],epopostruma mercurii[&&NHX:TOL=24747],epopostruma monstrosa[&&NHX:TOL=24748],epopostruma natalae[&&NHX:TOL=24749],epopostruma quadrispinosa[&&NHX:TOL=24750],epopostruma sowestensis[&&NHX:TOL=24751],epopostruma terrula[&&NHX:TOL=24752],epopostruma vita[&&NHX:TOL=24753],epopostruma vitta[&&NHX:TOL=24754],epopostruma wardi[&&NHX:TOL=24755])epopostruma[&&NHX:TOL=22478],(mesostruma bella[&&NHX:TOL=24756],mesostruma browni[&&NHX:TOL=24757],mesostruma eccentrica[&&NHX:TOL=24758],mesostruma exolympica[&&NHX:TOL=24759],mesostruma inornata[&&NHX:TOL=24760],mesostruma laevigata[&&NHX:TOL=24761],mesostruma loweryi[&&NHX:TOL=24762],mesostruma turneri[&&NHX:TOL=24763])mesostruma[&&NHX:TOL=22479],(microdaceton exornatum[&&NHX:TOL=24764],microdaceton tanyspinosum[&&NHX:TOL=24765],microdaceton tibialis[&&NHX:TOL=24766],microdaceton viriosum[&&NHX:TOL=24767])microdaceton[&&NHX:TOL=22480],(orectognathus alligator[&&NHX:TOL=24768],28 additional described species[&&NHX:TOL=24769])orectognathus[&&NHX:TOL=22481],(pyramica abdita[&&NHX:TOL=24770],a few hundred additional described species[&&NHX:TOL=24771])pyramica[&&NHX:TOL=22482],(strumigenys abdera[&&NHX:TOL=24772],several hundred additional described species[&&NHX:TOL=24773])strumigenys[&&NHX:TOL=22483])dacetini[&&NHX:TOL=22431],(ishakidris ascitaspis[&&NHX:TOL=22704],phalacromyrmex fugax[&&NHX:TOL=22705],pilotrochus besmerus[&&NHX:TOL=22706])phalacromyrmecini[&&NHX:TOL=22432])dacetine tribe group[&&NHX:TOL=22462],((cataulacus adpressus[&&NHX:TOL=25498],67 additional described species[&&NHX:TOL=25499])cataulacus[&&NHX:TOL=22433],((cephalotes abdominalis[&&NHX:TOL=25500],133 additional described species[&&NHX:TOL=25501])cephalotes[&&NHX:TOL=22707],(procryptocerus adlerzi[&&NHX:TOL=25502],43 additional described species[&&NHX:TOL=25503])procryptocerus[&&NHX:TOL=22708])cephalotini[&&NHX:TOL=22434])cephalotine tribe group[&&NHX:TOL=22463],(((apterostigma acre[&&NHX:TOL=25504],43 additional described species[&&NHX:TOL=25505])apterostigma[&&NHX:TOL=22501],(mycetagroicus cerradensis[&&NHX:TOL=25506],mycetagroicus triangularis[&&NHX:TOL=25507],mycetagroicus urbanus[&&NHX:TOL=25508])mycetagroicus[&&NHX:TOL=22492],(mycetarotes acutus[&&NHX:TOL=25509],mycetarotes carinatus[&&NHX:TOL=25510],mycetarotes parallelus[&&NHX:TOL=25511],mycetarotes senticosus[&&NHX:TOL=25512])mycetarotes[&&NHX:TOL=22493],(mycetophylax bruchi[&&NHX:TOL=25513],mycetophylax conformis[&&NHX:TOL=25514],mycetophylax cristulatus[&&NHX:TOL=25515],mycetophylax emeryi[&&NHX:TOL=25516],mycetophylax glaber[&&NHX:TOL=25517],mycetophylax simplex[&&NHX:TOL=25518])mycetophylax[&&NHX:TOL=22494],(mycetosoritis aspera[&&NHX:TOL=25519],mycetosoritis clorindae[&&NHX:TOL=25520],mycetosoritis explicata[&&NHX:TOL=25521],mycetosoritis hartmanni[&&NHX:TOL=25522],mycetosoritis vinsoni[&&NHX:TOL=25523])mycetosoritis[&&NHX:TOL=22495],(mycocepurus curvispinosus[&&NHX:TOL=25524],mycocepurus goeldii[&&NHX:TOL=25525],mycocepurus obsoletus[&&NHX:TOL=25526],mycocepurus smithii[&&NHX:TOL=25527],mycocepurus tardus[&&NHX:TOL=25528])mycocepurus[&&NHX:TOL=22496],(myrmicocrypta boliviana[&&NHX:TOL=25529],myrmicocrypta bruchi[&&NHX:TOL=25530],myrmicocrypta buenzlii[&&NHX:TOL=25531],myrmicocrypta collaris[&&NHX:TOL=25532],myrmicocrypta dilacerata[&&NHX:TOL=25533],myrmicocrypta ednaella[&&NHX:TOL=25534],myrmicocrypta elisabethae[&&NHX:TOL=25535],myrmicocrypta foreli[&&NHX:TOL=25536],myrmicocrypta godmani[&&NHX:TOL=25537],myrmicocrypta guianensis[&&NHX:TOL=25538],myrmicocrypta infuscata[&&NHX:TOL=25539],myrmicocrypta longinoda[&&NHX:TOL=25540],myrmicocrypta microphthalma[&&NHX:TOL=25541],myrmicocrypta occipitalis[&&NHX:TOL=25542],myrmicocrypta ogloblini[&&NHX:TOL=25543],myrmicocrypta rudiscapa[&&NHX:TOL=25544],myrmicocrypta spinosa[&&NHX:TOL=25545],myrmicocrypta squamosa[&&NHX:TOL=25546],myrmicocrypta subnitida[&&NHX:TOL=25547],myrmicocrypta triangulata[&&NHX:TOL=25548],myrmicocrypta tuberculata[&&NHX:TOL=25549],myrmicocrypta unidentata[&&NHX:TOL=25550],myrmicocrypta urichi[&&NHX:TOL=25551],myrmicocrypta weyrauchi[&&NHX:TOL=25552])myrmicocrypta[&&NHX:TOL=22497],pseudoatta argentina[&&NHX:TOL=22498],((cyphomyrmex auritus[&&NHX:TOL=25553],36 additional described species[&&NHX:TOL=25554])cyphomyrmex[&&NHX:TOL=22491],((sericomyrmex amabilis[&&NHX:TOL=25555],sericomyrmex aztecus[&&NHX:TOL=25556],sericomyrmex beniensis[&&NHX:TOL=25557],sericomyrmex bondari[&&NHX:TOL=25558],sericomyrmex burchelli[&&NHX:TOL=25559],sericomyrmex diego[&&NHX:TOL=25560],sericomyrmex harekulli[&&NHX:TOL=25561],sericomyrmex impexus[&&NHX:TOL=25562],sericomyrmex luederwaldti[&&NHX:TOL=25563],sericomyrmex lutzi[&&NHX:TOL=25564],sericomyrmex mayri[&&NHX:TOL=25565],sericomyrmex moreirai[&&NHX:TOL=25566],sericomyrmex myersi[&&NHX:TOL=25567],sericomyrmex opacus[&&NHX:TOL=25568],sericomyrmex parvulus[&&NHX:TOL=25569],sericomyrmex saussurei[&&NHX:TOL=25570],sericomyrmex scrobifer[&&NHX:TOL=25571],sericomyrmex urichi[&&NHX:TOL=25572],sericomyrmex zacapanus[&&NHX:TOL=25573])sericomyrmex[&&NHX:TOL=22499],(trachymyrmex agudensis[&&NHX:TOL=25574],42 additional described species[&&NHX:TOL=25575])trachymyrmex[&&NHX:TOL=22500],((acromyrmex ambiguus[&&NHX:TOL=25576],26 additional described species[&&NHX:TOL=25577])acromyrmex[&&NHX:TOL=22489],(atta bisphaerica[&&NHX:TOL=25578],atta capiguara[&&NHX:TOL=25579],atta cephalotes[&&NHX:TOL=25580],atta columbica[&&NHX:TOL=25581],atta cubana[&&NHX:TOL=25582],atta dissimilis[&&NHX:TOL=25583],atta domicola[&&NHX:TOL=25584],atta goiana[&&NHX:TOL=25585],atta insularis[&&NHX:TOL=25586],atta laevigata[&&NHX:TOL=25587],atta mexicana[&&NHX:TOL=25588],atta opaciceps[&&NHX:TOL=25589],atta pilosa[&&NHX:TOL=25590],atta robusta[&&NHX:TOL=25591],atta saltensis[&&NHX:TOL=25592],atta sexdens[&&NHX:TOL=25593],atta silvae[&&NHX:TOL=25594],atta tardigrada[&&NHX:TOL=25595],atta texana[&&NHX:TOL=25596],atta vollenweideri[&&NHX:TOL=25597])atta[&&NHX:TOL=22490])leafcutter ants[&&NHX:TOL=22502])[&&NHX:TOL=22695])[&&NHX:TOL=22696])attini[&&NHX:TOL=22435],((blepharidatta brasiliensis[&&NHX:TOL=23057],blepharidatta conops[&&NHX:TOL=23058])blepharidatta[&&NHX:TOL=22709],(wasmannia affinis[&&NHX:TOL=25598],wasmannia auropunctata[&&NHX:TOL=25599],wasmannia iheringi[&&NHX:TOL=25600],wasmannia lutzi[&&NHX:TOL=25601],wasmannia rochai[&&NHX:TOL=25602],wasmannia scrobifera[&&NHX:TOL=25603],wasmannia sigmoidea[&&NHX:TOL=25604],wasmannia sulcaticeps[&&NHX:TOL=25605],wasmannia villosa[&&NHX:TOL=25606],wasmannia williamsoni[&&NHX:TOL=25607])wasmannia[&&NHX:TOL=22710])blepharidattini[&&NHX:TOL=22436])attine tribe group[&&NHX:TOL=22464],(((ancyridris polyrhachioides[&&NHX:TOL=25608],ancyridris rupicapra[&&NHX:TOL=25609])ancyridris[&&NHX:TOL=22711],bariamyrma hispidula[&&NHX:TOL=22712],(calyptomyrmex arnoldi[&&NHX:TOL=25610],calyptomyrmex barak[&&NHX:TOL=25611],calyptomyrmex beccarii[&&NHX:TOL=25612],calyptomyrmex brevis[&&NHX:TOL=25613],calyptomyrmex brunneus[&&NHX:TOL=25614],calyptomyrmex clavatus[&&NHX:TOL=25615],calyptomyrmex claviseta[&&NHX:TOL=25616],calyptomyrmex duhun[&&NHX:TOL=25617],calyptomyrmex emeryi[&&NHX:TOL=25618],calyptomyrmex foreli[&&NHX:TOL=25619],calyptomyrmex friederikae[&&NHX:TOL=25620],calyptomyrmex glabratus[&&NHX:TOL=25621],calyptomyrmex kaurus[&&NHX:TOL=25622],calyptomyrmex nedjem[&&NHX:TOL=25623],calyptomyrmex nummuliticus[&&NHX:TOL=25624],calyptomyrmex piripilis[&&NHX:TOL=25625],calyptomyrmex rennefer[&&NHX:TOL=25626],calyptomyrmex shasu[&&NHX:TOL=25627],calyptomyrmex singalensis[&&NHX:TOL=25628],calyptomyrmex stellatus[&&NHX:TOL=25629],calyptomyrmex tamil[&&NHX:TOL=25630],calyptomyrmex tensus[&&NHX:TOL=25631],calyptomyrmex vedda[&&NHX:TOL=25632],calyptomyrmex wittmeri[&&NHX:TOL=25633])calyptomyrmex[&&NHX:TOL=22713],(cyphoidris exalta[&&NHX:TOL=25634],cyphoidris parissa[&&NHX:TOL=25635],cyphoidris spinosa[&&NHX:TOL=25636],cyphoidris werneri[&&NHX:TOL=25637])cyphoidris[&&NHX:TOL=22714],dacatria templaris[&&NHX:TOL=22715],(dacetinops cibdelus[&&NHX:TOL=25638],dacetinops cirrosus[&&NHX:TOL=25639],dacetinops concinnus[&&NHX:TOL=25640],dacetinops darlingtoni[&&NHX:TOL=25641],dacetinops ignotus[&&NHX:TOL=25642],dacetinops solivagus[&&NHX:TOL=25643],dacetinops wilsoni[&&NHX:TOL=25644])dacetinops[&&NHX:TOL=22716],(dicroaspis cryptocera[&&NHX:TOL=25645],dicroaspis laevidens[&&NHX:TOL=25646])dicroaspis[&&NHX:TOL=22717],indomyrma dasypyx[&&NHX:TOL=22718],(lachnomyrmex grandis[&&NHX:TOL=25647],lachnomyrmex haskinsi[&&NHX:TOL=25648],lachnomyrmex longinodus[&&NHX:TOL=25649],lachnomyrmex pilosus[&&NHX:TOL=25650],lachnomyrmex plaumanni[&&NHX:TOL=25651],lachnomyrmex scrobiculatus[&&NHX:TOL=25652])lachnomyrmex[&&NHX:TOL=22719],(lasiomyrma gedensis[&&NHX:TOL=25653],lasiomyrma gracilinoda[&&NHX:TOL=25654],lasiomyrma maryatiae[&&NHX:TOL=25655])lasiomyrma[&&NHX:TOL=22720],(lordomyrma azumai[&&NHX:TOL=25656],lordomyrma bensoni[&&NHX:TOL=25657],lordomyrma caledonica[&&NHX:TOL=25658],lordomyrma crawleyi[&&NHX:TOL=25659],lordomyrma cryptocera[&&NHX:TOL=25660],lordomyrma epinotalis[&&NHX:TOL=25661],lordomyrma furcifera[&&NHX:TOL=25662],lordomyrma infundibuli[&&NHX:TOL=25663],lordomyrma leae[&&NHX:TOL=25664],lordomyrma nigra[&&NHX:TOL=25665],lordomyrma punctiventris[&&NHX:TOL=25666],lordomyrma rouxi[&&NHX:TOL=25667],lordomyrma rugosa[&&NHX:TOL=25668],lordomyrma sarasini[&&NHX:TOL=25669],lordomyrma striatella[&&NHX:TOL=25670],lordomyrma tortuosa[&&NHX:TOL=25671])lordomyrma[&&NHX:TOL=22721],proatta butteli[&&NHX:TOL=22722],(rogeria alzatei[&&NHX:TOL=25672],45 additional described species[&&NHX:TOL=25673])rogeria[&&NHX:TOL=22723],rostromyrmex pasohensis[&&NHX:TOL=22724],(stenamma africanum[&&NHX:TOL=25674],46 additional described species[&&NHX:TOL=25675])stenamma[&&NHX:TOL=22725],tetheamyrma subspongia[&&NHX:TOL=22726],(vollenhovia ambitiosa[&&NHX:TOL=25676],47 additional described species[&&NHX:TOL=25677])vollenhovia[&&NHX:TOL=22727],(adelomyrmex betoi[&&NHX:TOL=25678],adelomyrmex biroi[&&NHX:TOL=25679],adelomyrmex boltoni[&&NHX:TOL=25680],adelomyrmex brevispinosus[&&NHX:TOL=25681],adelomyrmex costatus[&&NHX:TOL=25682],adelomyrmex cristiani[&&NHX:TOL=25683],adelomyrmex foveolatus[&&NHX:TOL=25684],adelomyrmex grandis[&&NHX:TOL=25685],adelomyrmex hirsutus[&&NHX:TOL=25686],adelomyrmex laevigatus[&&NHX:TOL=25687],adelomyrmex longinodus[&&NHX:TOL=25688],adelomyrmex longinoi[&&NHX:TOL=25689],adelomyrmex mackayi[&&NHX:TOL=25690],adelomyrmex micans[&&NHX:TOL=25691],adelomyrmex microps[&&NHX:TOL=25692],adelomyrmex minimus[&&NHX:TOL=25693],adelomyrmex myops[&&NHX:TOL=25694],adelomyrmex robustus[&&NHX:TOL=25695],adelomyrmex samoanus[&&NHX:TOL=25696],adelomyrmex silvestrii[&&NHX:TOL=25697],adelomyrmex striatus[&&NHX:TOL=25698],adelomyrmex tristani[&&NHX:TOL=25699],adelomyrmex vaderi[&&NHX:TOL=25700])adelomyrmex[&&NHX:TOL=22728],(baracidris meketra[&&NHX:TOL=25701],baracidris pilosa[&&NHX:TOL=25702],baracidris sitra[&&NHX:TOL=25703])baracidris[&&NHX:TOL=22729],ilemomyrmex caecus[&&NHX:EXT=Y:TOL=22730])stenammini[&&NHX:TOL=22437],(adlerzia froggatti[&&NHX:TOL=22525],afroxyidris crigensis[&&NHX:TOL=22526],(allomerus decemarticulatus[&&NHX:TOL=25704],allomerus octoarticulatus[&&NHX:TOL=25705],allomerus vogeli[&&NHX:TOL=25706])allomerus[&&NHX:TOL=22527],(anillomyrma decamera[&&NHX:TOL=25707],anillomyrma tridens[&&NHX:TOL=25708])anillomyrma[&&NHX:TOL=22528],(bondroitia lujae[&&NHX:TOL=25709],bondroitia saharensis[&&NHX:TOL=25710])bondroitia[&&NHX:TOL=22529],(carebara ampla[&&NHX:TOL=25716],carebara anophthalma[&&NHX:TOL=25717],carebara arnoldi[&&NHX:TOL=25718],carebara bartrumi[&&NHX:TOL=25719],carebara bicarinata[&&NHX:TOL=25720],carebara castanea[&&NHX:TOL=25721],carebara incerta[&&NHX:TOL=25722],carebara junodi[&&NHX:TOL=25723],carebara langi[&&NHX:TOL=25724],carebara lignata[&&NHX:TOL=25725],carebara mayri[&&NHX:TOL=25726],carebara osborni[&&NHX:TOL=25727],carebara patrizii[&&NHX:TOL=25728],carebara sicheli[&&NHX:TOL=25729],carebara silvestrii[&&NHX:TOL=25730],carebara sudanica[&&NHX:TOL=25731],carebara vidua[&&NHX:TOL=25732],carebara winifredae[&&NHX:TOL=25733])carebara[&&NHX:TOL=22530],(carebarella alvarengai[&&NHX:TOL=25734],carebarella bicolor[&&NHX:TOL=25735],carebarella condei[&&NHX:TOL=25736])carebarella[&&NHX:TOL=22531],diplomorium longipenne[&&NHX:TOL=22532],epelysidris brocha[&&NHX:TOL=22533],machomyrma dispar[&&NHX:TOL=22534],(mayriella abstinens[&&NHX:TOL=25711],mayriella hackeri[&&NHX:TOL=25712],mayriella spinosior[&&NHX:TOL=25713],mayriella transfuga[&&NHX:TOL=25714],mayriella venustula[&&NHX:TOL=25715])mayriella[&&NHX:TOL=22535],(megalomyrmex acauna[&&NHX:TOL=25737],33 additional described species[&&NHX:TOL=25738])megalomyrmex[&&NHX:TOL=22536],(monomorium abeillei[&&NHX:TOL=25739],a few hundred additional described species[&&NHX:TOL=25740])monomorium[&&NHX:TOL=22537],(nothidris bicolor[&&NHX:TOL=25741],nothidris cekalovici[&&NHX:TOL=25742],nothidris latastei[&&NHX:TOL=25743])nothidris[&&NHX:TOL=22538],(oligomyrmex aborensis[&&NHX:TOL=25744],105 additional described species[&&NHX:TOL=25745])oligomyrmex[&&NHX:TOL=22539],(oxyepoecus browni[&&NHX:TOL=25746],oxyepoecus bruchi[&&NHX:TOL=25747],oxyepoecus crassinodus[&&NHX:TOL=25748],oxyepoecus daguerrei[&&NHX:TOL=25749],oxyepoecus ephippiatus[&&NHX:TOL=25750],oxyepoecus inquilinus[&&NHX:TOL=25751],oxyepoecus kempfi[&&NHX:TOL=25752],oxyepoecus longicephalus[&&NHX:TOL=25753],oxyepoecus mandibularis[&&NHX:TOL=25754],oxyepoecus plaumanni[&&NHX:TOL=25755],oxyepoecus punctifrons[&&NHX:TOL=25756],oxyepoecus quadratus[&&NHX:TOL=25757],oxyepoecus rastratus[&&NHX:TOL=25758],oxyepoecus reticulatus[&&NHX:TOL=25759],oxyepoecus vezenyii[&&NHX:TOL=25760],oxyepoecus vivax[&&NHX:TOL=25761])oxyepoecus[&&NHX:TOL=22540],(paedalgus distinctus[&&NHX:TOL=25762],paedalgus escherichi[&&NHX:TOL=25763],paedalgus infimus[&&NHX:TOL=25764],paedalgus octatus[&&NHX:TOL=25765],paedalgus pisinnus[&&NHX:TOL=25766],paedalgus rarus[&&NHX:TOL=25767],paedalgus robertsoni[&&NHX:TOL=25768],paedalgus saritus[&&NHX:TOL=25769],paedalgus sudanensis[&&NHX:TOL=25770],paedalgus termitolestes[&&NHX:TOL=25771])paedalgus[&&NHX:TOL=22541],phacota sichelii[&&NHX:TOL=22542],(pheidologeton aberrans[&&NHX:TOL=25772],30 additional described species[&&NHX:TOL=25773])pheidologeton[&&NHX:TOL=22543],(solenopsis abdita[&&NHX:TOL=25774],199 additional described species[&&NHX:TOL=25775])solenopsis[&&NHX:TOL=22544],(tranopelta gilva[&&NHX:TOL=25776],tranopelta subterranea[&&NHX:TOL=25777])tranopelta[&&NHX:TOL=22545],hypopomyrmex bombiccii[&&NHX:EXT=Y:TOL=22546],oxyidris antillana[&&NHX:EXT=Y:TOL=22547])solenopsidini[&&NHX:TOL=22438])solenopsidine tribe group[&&NHX:TOL=22465],(((eutetramorium mocquerysi[&&NHX:TOL=23059],eutetramorium monticellii[&&NHX:TOL=23060])eutetramorium[&&NHX:TOL=22548],(huberia brounii[&&NHX:TOL=23061],huberia striata[&&NHX:TOL=23062])huberia[&&NHX:TOL=22549],(hylomyrma balzani[&&NHX:TOL=25834],hylomyrma blandiens[&&NHX:TOL=25835],hylomyrma columbica[&&NHX:TOL=25836],hylomyrma dentiloba[&&NHX:TOL=25837],hylomyrma dolichops[&&NHX:TOL=25838],hylomyrma immanis[&&NHX:TOL=25839],hylomyrma longiscapa[&&NHX:TOL=25840],hylomyrma praepotens[&&NHX:TOL=25841],hylomyrma reginae[&&NHX:TOL=25842],hylomyrma reitteri[&&NHX:TOL=25843],hylomyrma sagax[&&NHX:TOL=25844],hylomyrma transversa[&&NHX:TOL=25845],hylomyrma versuta[&&NHX:TOL=25846])hylomyrma[&&NHX:TOL=22550],(manica bradleyi[&&NHX:TOL=25847],manica hunteri[&&NHX:TOL=25848],manica invidia[&&NHX:TOL=25849],manica parasitica[&&NHX:TOL=25850],manica rubida[&&NHX:TOL=25851],manica yessensis[&&NHX:TOL=25852])manica[&&NHX:TOL=22551],(myrmica ademonia[&&NHX:TOL=25853],165 additional described species[&&NHX:TOL=25854])myrmica[&&NHX:TOL=22552],(pogonomyrmex abdominalis[&&NHX:TOL=25855],61 additional described species[&&NHX:TOL=25856])pogonomyrmex[&&NHX:TOL=22553],secostruma lethifera[&&NHX:TOL=22554],(nothomyrmica intermedia[&&NHX:EXT=Y:TOL=25857],nothomyrmica petiolata[&&NHX:EXT=Y:TOL=25858],nothomyrmica rudis[&&NHX:EXT=Y:TOL=25859],nothomyrmica rugosostriata[&&NHX:EXT=Y:TOL=25860])nothomyrmica[&&NHX:EXT=Y:TOL=22555])myrmicini[&&NHX:TOL=22439],(anergates atratulus[&&NHX:TOL=22731],(decamorium decem[&&NHX:TOL=23063],decamorium uelense[&&NHX:TOL=23064])decamorium[&&NHX:TOL=22732],(rhoptromyrmex caritus[&&NHX:TOL=25861],rhoptromyrmex critchleyi[&&NHX:TOL=25862],rhoptromyrmex globulinodis[&&NHX:TOL=25863],rhoptromyrmex mayri[&&NHX:TOL=25864],rhoptromyrmex melleus[&&NHX:TOL=25865],rhoptromyrmex opacus[&&NHX:TOL=25866],rhoptromyrmex rawlinsoni[&&NHX:TOL=25867],rhoptromyrmex schmitzi[&&NHX:TOL=25868],rhoptromyrmex transversinodis[&&NHX:TOL=25869],rhoptromyrmex wroughtonii[&&NHX:TOL=25870])rhoptromyrmex[&&NHX:TOL=22733],(strongylognathus afer[&&NHX:TOL=25871],strongylognathus alboini[&&NHX:TOL=25872],strongylognathus alpinus[&&NHX:TOL=25873],strongylognathus arnoldii[&&NHX:TOL=25874],strongylognathus caeciliae[&&NHX:TOL=25875],strongylognathus chelifer[&&NHX:TOL=25876],strongylognathus christophi[&&NHX:TOL=25877],strongylognathus dalmaticus[&&NHX:TOL=25878],strongylognathus destefanii[&&NHX:TOL=25879],strongylognathus huberi[&&NHX:TOL=25880],strongylognathus insularis[&&NHX:TOL=25881],strongylognathus italicus[&&NHX:TOL=25882],strongylognathus karawajewi[&&NHX:TOL=25883],strongylognathus kervillei[&&NHX:TOL=25884],strongylognathus koreanus[&&NHX:TOL=25885],strongylognathus kratochvili[&&NHX:TOL=25886],strongylognathus minutus[&&NHX:TOL=25887],strongylognathus palaestinensis[&&NHX:TOL=25888],strongylognathus pisarskii[&&NHX:TOL=25889],strongylognathus rehbinderi[&&NHX:TOL=25890],strongylognathus ruzskyi[&&NHX:TOL=25891],strongylognathus silvestrii[&&NHX:TOL=25892],strongylognathus testaceus[&&NHX:TOL=25893])strongylognathus[&&NHX:TOL=22734],(teleutomyrmex kutteri[&&NHX:TOL=23065],teleutomyrmex schneideri[&&NHX:TOL=23066])teleutomyrmex[&&NHX:TOL=22735],(tetramorium aculeatum[&&NHX:TOL=25894],several hundred additional described species[&&NHX:TOL=25895])tetramorium[&&NHX:TOL=22736])tetramoriini[&&NHX:TOL=22440],(anisopheidole antipodum[&&NHX:TOL=22737],(aphaenogaster albisetosa[&&NHX:TOL=25896],168 additional described species[&&NHX:TOL=25897])aphaenogaster[&&NHX:TOL=22738],(chimaeridris boltoni[&&NHX:TOL=25898],chimaeridris burckhardti[&&NHX:TOL=25899])chimaeridris[&&NHX:TOL=22739],(goniomma baeticum[&&NHX:TOL=25900],goniomma blanci[&&NHX:TOL=25901],goniomma collingwoodi[&&NHX:TOL=25902],goniomma decipiens[&&NHX:TOL=25903],goniomma hispanicum[&&NHX:TOL=25904],goniomma kugleri[&&NHX:TOL=25905],goniomma punicum[&&NHX:TOL=25906])goniomma[&&NHX:TOL=22740],(kartidris ashima[&&NHX:TOL=25907],kartidris fujianensis[&&NHX:TOL=25908],kartidris galos[&&NHX:TOL=25909],kartidris matertera[&&NHX:TOL=25910],kartidris nyos[&&NHX:TOL=25911],kartidris sparsipila[&&NHX:TOL=25912])kartidris[&&NHX:TOL=22741],(lophomyrmex ambiguus[&&NHX:TOL=25913],lophomyrmex bedoti[&&NHX:TOL=25914],lophomyrmex birmanus[&&NHX:TOL=25915],lophomyrmex kali[&&NHX:TOL=25916],lophomyrmex longicornis[&&NHX:TOL=25917],lophomyrmex lucidus[&&NHX:TOL=25918],lophomyrmex opaciceps[&&NHX:TOL=25919],lophomyrmex quadrispinosus[&&NHX:TOL=25920],lophomyrmex striatulus[&&NHX:TOL=25921],lophomyrmex taivanae[&&NHX:TOL=25922])lophomyrmex[&&NHX:TOL=22742],(messor abdelazizi[&&NHX:TOL=25923],111 additional described species[&&NHX:TOL=25924])messor[&&NHX:TOL=22743],(ocymyrmex afradu[&&NHX:TOL=25925],36 additional described species[&&NHX:TOL=25926])ocymyrmex[&&NHX:TOL=22744],(oxyopomyrmex emeryi[&&NHX:TOL=25927],oxyopomyrmex gaetulus[&&NHX:TOL=25928],oxyopomyrmex insularis[&&NHX:TOL=25929],oxyopomyrmex krueperi[&&NHX:TOL=25930],oxyopomyrmex lagoi[&&NHX:TOL=25931],oxyopomyrmex oculatus[&&NHX:TOL=25932],oxyopomyrmex sabulonis[&&NHX:TOL=25933],oxyopomyrmex santschii[&&NHX:TOL=25934],oxyopomyrmex saulcyi[&&NHX:TOL=25935])oxyopomyrmex[&&NHX:TOL=22745],(pheidole rhea[&&NHX:TOL=25936],pheidole rugulosa[&&NHX:TOL=25937])pheidole[&&NHX:TOL=22746],(lonchomyrmex freyeri[&&NHX:EXT=Y:TOL=25938],lonchomyrmex nigritus[&&NHX:EXT=Y:TOL=25939])lonchomyrmex[&&NHX:EXT=Y:TOL=22747],(paraphaenogaster microphthalma[&&NHX:EXT=Y:TOL=25940],paraphaenogaster shanwangensis[&&NHX:EXT=Y:TOL=25941])paraphaenogaster[&&NHX:EXT=Y:TOL=22748])pheidolini[&&NHX:TOL=22441],(lenomyrmex costatus[&&NHX:TOL=25942],lenomyrmex foveolatus[&&NHX:TOL=25943],lenomyrmex inusitatus[&&NHX:TOL=25944],lenomyrmex mandibularis[&&NHX:TOL=25945],lenomyrmex wardi[&&NHX:TOL=25946])lenomyrmex[&&NHX:TOL=22442],(paratopula andamanensis[&&NHX:TOL=25947],paratopula ankistra[&&NHX:TOL=25948],paratopula catocha[&&NHX:TOL=25949],paratopula ceylonica[&&NHX:TOL=25950],paratopula demeta[&&NHX:TOL=25951],paratopula longispina[&&NHX:TOL=25952],paratopula macta[&&NHX:TOL=25953],paratopula oculata[&&NHX:TOL=25954],paratopula sumatrensis[&&NHX:TOL=25955])paratopula[&&NHX:TOL=22443])myrmicine tribe group[&&NHX:TOL=22466],(((crematogaster abdominalis[&&NHX:TOL=25956],several hundred additional described species[&&NHX:TOL=25957])crematogaster[&&NHX:TOL=22749],(recurvidris browni[&&NHX:TOL=25958],recurvidris glabriceps[&&NHX:TOL=25959],recurvidris hebe[&&NHX:TOL=25960],recurvidris kemneri[&&NHX:TOL=25961],recurvidris nuwa[&&NHX:TOL=25962],recurvidris pickburni[&&NHX:TOL=25963],recurvidris proles[&&NHX:TOL=25964],recurvidris recurvispinosa[&&NHX:TOL=25965],recurvidris williami[&&NHX:TOL=25966])recurvidris[&&NHX:TOL=22750])crematogastrini[&&NHX:TOL=22444],ankylomyrma coronacantha[&&NHX:TOL=22445],(liomyrmex aurianus[&&NHX:TOL=25967],liomyrmex carinatus[&&NHX:TOL=25968],liomyrmex froggatti[&&NHX:TOL=25969],liomyrmex gestroi[&&NHX:TOL=25970],liomyrmex reneae[&&NHX:TOL=25971],liomyrmex tagalanus[&&NHX:TOL=25972],liomyrmex taylori[&&NHX:TOL=25973])liomyrmex[&&NHX:TOL=22446],((meranoplus ajax[&&NHX:TOL=25974],61 additional described species[&&NHX:TOL=25975])meranoplus[&&NHX:TOL=22751],parameranoplus primaevus[&&NHX:EXT=Y:TOL=22752])meranoplini[&&NHX:TOL=22447],(myrmicaria anomala[&&NHX:TOL=25976],31 additional described species[&&NHX:TOL=25977])myrmicaria[&&NHX:TOL=22448],((atopomyrmex calpocalycola[&&NHX:TOL=25978],atopomyrmex cryptoceroides[&&NHX:TOL=25979],atopomyrmex mocquerysi[&&NHX:TOL=25980])atopomyrmex[&&NHX:TOL=22753],(cardiocondyla batesii[&&NHX:TOL=25981],40 additional described species[&&NHX:TOL=25982])cardiocondyla[&&NHX:TOL=22754],(chalepoxenus brunneus[&&NHX:TOL=25983],chalepoxenus kutteri[&&NHX:TOL=25984],chalepoxenus muellerianus[&&NHX:TOL=25985],chalepoxenus spinosus[&&NHX:TOL=25986],chalepoxenus tarbinskii[&&NHX:TOL=25987],chalepoxenus tauricus[&&NHX:TOL=25988],chalepoxenus tramieri[&&NHX:TOL=25989],chalepoxenus zabelini[&&NHX:TOL=25990])chalepoxenus[&&NHX:TOL=22755],(dilobocondyla borneensis[&&NHX:TOL=25991],dilobocondyla cataulacoidea[&&NHX:TOL=25992],dilobocondyla chapmani[&&NHX:TOL=25993],dilobocondyla didita[&&NHX:TOL=25994],dilobocondyla fouqueti[&&NHX:TOL=25995],dilobocondyla fulva[&&NHX:TOL=25996],dilobocondyla karnyi[&&NHX:TOL=25997],dilobocondyla sebesiana[&&NHX:TOL=25998],dilobocondyla selebensis[&&NHX:TOL=25999])dilobocondyla[&&NHX:TOL=22756],(formicoxenus chamberlini[&&NHX:TOL=26000],formicoxenus diversipilosus[&&NHX:TOL=26001],formicoxenus hirticornis[&&NHX:TOL=26002],formicoxenus nitidulus[&&NHX:TOL=26003],formicoxenus provancheri[&&NHX:TOL=26004],formicoxenus quebecensis[&&NHX:TOL=26005],formicoxenus sibiricus[&&NHX:TOL=26006])formicoxenus[&&NHX:TOL=22757],(gauromyrmex acanthinus[&&NHX:TOL=26007],gauromyrmex bengakalisi[&&NHX:TOL=26008])gauromyrmex[&&NHX:TOL=22758],(harpagoxenus canadensis[&&NHX:TOL=26009],harpagoxenus sublaevis[&&NHX:TOL=26010],harpagoxenus zaisanicus[&&NHX:TOL=26011])harpagoxenus[&&NHX:TOL=22759],(leptothorax acervorum[&&NHX:TOL=26012],leptothorax aguayoi[&&NHX:TOL=26013],leptothorax anemicus[&&NHX:TOL=26014],leptothorax buschingeri[&&NHX:TOL=26015],leptothorax caparica[&&NHX:TOL=26016],leptothorax crassipilis[&&NHX:TOL=26017],leptothorax faberi[&&NHX:TOL=26018],leptothorax goesswaldi[&&NHX:TOL=26019],leptothorax gredleri[&&NHX:TOL=26020],leptothorax kutteri[&&NHX:TOL=26021],leptothorax muscorum[&&NHX:TOL=26022],leptothorax oceanicus[&&NHX:TOL=26023],leptothorax opalinus[&&NHX:TOL=26024],leptothorax pacis[&&NHX:TOL=26025],leptothorax paraxenus[&&NHX:TOL=26026],leptothorax pastoris[&&NHX:TOL=26027],leptothorax pocahontas[&&NHX:TOL=26028],leptothorax retractus[&&NHX:TOL=26029],leptothorax rugiceps[&&NHX:TOL=26030],leptothorax scabripes[&&NHX:TOL=26031],leptothorax scamni[&&NHX:TOL=26032],leptothorax sphagnicola[&&NHX:TOL=26033],leptothorax stipaceus[&&NHX:TOL=26034],leptothorax umbratipes[&&NHX:TOL=26035],leptothorax wilsoni[&&NHX:TOL=26036])leptothorax[&&NHX:TOL=22760],(myrmoxenus adlerzi[&&NHX:TOL=26037],myrmoxenus africanus[&&NHX:TOL=26038],myrmoxenus algerianus[&&NHX:TOL=26039],myrmoxenus bernardi[&&NHX:TOL=26040],myrmoxenus birgitae[&&NHX:TOL=26041],myrmoxenus corsicus[&&NHX:TOL=26042],myrmoxenus gordiagini[&&NHX:TOL=26043],myrmoxenus kraussei[&&NHX:TOL=26044],myrmoxenus ravouxi[&&NHX:TOL=26045],myrmoxenus stumperi[&&NHX:TOL=26046],myrmoxenus tamarae[&&NHX:TOL=26047],myrmoxenus zaleskyi[&&NHX:TOL=26048])myrmoxenus[&&NHX:TOL=22761],(nesomyrmex anduzei[&&NHX:TOL=26049],36 additional described species[&&NHX:TOL=26050])nesomyrmex[&&NHX:TOL=22762],(ochetomyrmex neopolitus[&&NHX:TOL=26051],ochetomyrmex semipolitus[&&NHX:TOL=26052])ochetomyrmex[&&NHX:TOL=22763],(peronomyrmex bartoni[&&NHX:TOL=26053],peronomyrmex overbecki[&&NHX:TOL=26054])peronomyrmex[&&NHX:TOL=22764],(podomyrma abdominalis[&&NHX:TOL=26055],53 additional described species[&&NHX:TOL=26056])podomyrma[&&NHX:TOL=22765],poecilomyrma senirewae[&&NHX:TOL=22766],protomognathus americanus[&&NHX:TOL=22767],(romblonella elysii[&&NHX:TOL=26057],romblonella heatwolei[&&NHX:TOL=26058],romblonella opaca[&&NHX:TOL=26059],romblonella palauensis[&&NHX:TOL=26060],romblonella scrobifera[&&NHX:TOL=26061],romblonella townesi[&&NHX:TOL=26062],romblonella vitiensis[&&NHX:TOL=26063],romblonella yapensis[&&NHX:TOL=26064])romblonella[&&NHX:TOL=22768],(rotastruma recava[&&NHX:TOL=26065],rotastruma stenoceps[&&NHX:TOL=26066])rotastruma[&&NHX:TOL=22769],(stereomyrmex anderseni[&&NHX:TOL=26067],stereomyrmex dispar[&&NHX:TOL=26068],stereomyrmex horni[&&NHX:TOL=26069])stereomyrmex[&&NHX:TOL=22770],(temnothorax abeli[&&NHX:TOL=26070],several hundred additional described species[&&NHX:TOL=26071])temnothorax[&&NHX:TOL=22771],(terataner alluaudi[&&NHX:TOL=26072],terataner bottegoi[&&NHX:TOL=26073],terataner elegans[&&NHX:TOL=26074],terataner foreli[&&NHX:TOL=26075],terataner luteus[&&NHX:TOL=26076],terataner piceus[&&NHX:TOL=26077],terataner rufipes[&&NHX:TOL=26078],terataner scotti[&&NHX:TOL=26079],terataner steinheili[&&NHX:TOL=26080],terataner transvaalensis[&&NHX:TOL=26081],terataner velatus[&&NHX:TOL=26082],terataner xaltus[&&NHX:TOL=26083])terataner[&&NHX:TOL=22772],(vombisidris acherdos[&&NHX:TOL=26084],vombisidris australis[&&NHX:TOL=26085],vombisidris bilongrudi[&&NHX:TOL=26086],vombisidris dryas[&&NHX:TOL=26087],vombisidris harpeza[&&NHX:TOL=26088],vombisidris jacobsoni[&&NHX:TOL=26089],vombisidris lochme[&&NHX:TOL=26090],vombisidris nahet[&&NHX:TOL=26091],vombisidris occidua[&&NHX:TOL=26092],vombisidris philax[&&NHX:TOL=26093],vombisidris regina[&&NHX:TOL=26094],vombisidris renateae[&&NHX:TOL=26095],vombisidris xylochos[&&NHX:TOL=26096])vombisidris[&&NHX:TOL=22773],(xenomyrmex floridanus[&&NHX:TOL=26097],xenomyrmex panamanus[&&NHX:TOL=26098],xenomyrmex stollii[&&NHX:TOL=26099])xenomyrmex[&&NHX:TOL=22774],stigmomyrmex venustus[&&NHX:EXT=Y:TOL=22775],tricytarus parviumgulatus[&&NHX:TOL=22776])formicoxenini[&&NHX:TOL=22449])formicoxenine tribe group[&&NHX:TOL=22467],(stegomyrmex connectens[&&NHX:TOL=26100],stegomyrmex manni[&&NHX:TOL=26101],stegomyrmex vizottoi[&&NHX:TOL=26102])stegomyrmex[&&NHX:TOL=22450],((acanthomyrmex basispinosus[&&NHX:TOL=26103],acanthomyrmex careoscrobis[&&NHX:TOL=26104],acanthomyrmex concavus[&&NHX:TOL=26105],acanthomyrmex crassispinus[&&NHX:TOL=26106],acanthomyrmex dusun[&&NHX:TOL=26107],acanthomyrmex ferox[&&NHX:TOL=26108],acanthomyrmex foveolatus[&&NHX:TOL=26109],acanthomyrmex glabfemoralis[&&NHX:TOL=26110],acanthomyrmex laevis[&&NHX:TOL=26111],acanthomyrmex luciolae[&&NHX:TOL=26112],acanthomyrmex mindanao[&&NHX:TOL=26113],acanthomyrmex notabilis[&&NHX:TOL=26114],acanthomyrmex thailandensis[&&NHX:TOL=26115])acanthomyrmex[&&NHX:TOL=22777],(myrmecina amamiana[&&NHX:TOL=26116],31 additional described species[&&NHX:TOL=26117])myrmecina[&&NHX:TOL=22778],(perissomyrmex monticola[&&NHX:TOL=23068],perissomyrmex snyderi[&&NHX:TOL=23069])perissomyrmex[&&NHX:TOL=22779],(pristomyrmex africanus[&&NHX:TOL=26118],39 additional described species[&&NHX:TOL=26119])pristomyrmex[&&NHX:TOL=22780],enneamerus reticulatus[&&NHX:EXT=Y:TOL=22781],stiphromyrmex robustus[&&NHX:EXT=Y:TOL=22782])myrmecinini[&&NHX:TOL=22451],(metapone bakeri[&&NHX:TOL=26464],metapone emersoni[&&NHX:TOL=26465],metapone gracilis[&&NHX:TOL=26466],metapone greeni[&&NHX:TOL=26467],metapone hewitti[&&NHX:TOL=26468],metapone jacobsoni[&&NHX:TOL=26469],metapone johni[&&NHX:TOL=26470],metapone krombeini[&&NHX:TOL=26471],metapone leae[&&NHX:TOL=26472],metapone madagascarica[&&NHX:TOL=26473],metapone mjobergi[&&NHX:TOL=26474],metapone nicobarensis[&&NHX:TOL=26475],metapone quadridentata[&&NHX:TOL=26476],metapone sauteri[&&NHX:TOL=26477],metapone tillyardi[&&NHX:TOL=26478],metapone tricolor[&&NHX:TOL=26479],metapone truki[&&NHX:TOL=26480])metapone[&&NHX:TOL=22452],((melissotarsus beccarii[&&NHX:TOL=23070],melissotarsus emeryi[&&NHX:TOL=23071],melissotarsus insularis[&&NHX:TOL=23072],melissotarsus weissi[&&NHX:TOL=23073])melissotarsus[&&NHX:TOL=22783],(rhopalomastix escherichi[&&NHX:TOL=23074],rhopalomastix janeti[&&NHX:TOL=23075],rhopalomastix omotoensis[&&NHX:TOL=23076],rhopalomastix rohneyi[&&NHX:TOL=23077],rhopalomastix umbracapita[&&NHX:TOL=23078])rhopalomastix[&&NHX:TOL=22784])melissotarsini[&&NHX:TOL=22453],tyrranomyrmex rex[&&NHX:TOL=23067],(attopsis longipennis[&&NHX:EXT=Y:TOL=26481],attopsis longipes[&&NHX:EXT=Y:TOL=26482])attopsis[&&NHX:EXT=Y:TOL=22454],cephalomyrmex rotundatus[&&NHX:EXT=Y:TOL=22455],electromyrmex klebsi[&&NHX:EXT=Y:TOL=22456],eocenidris crassa[&&NHX:EXT=Y:TOL=22457],eoformica pinguis[&&NHX:EXT=Y:TOL=22458],eomyrmex guchengziensis[&&NHX:EXT=Y:TOL=22459],miosolenopsis fossilis[&&NHX:EXT=Y:TOL=22460],zhangidris atopogaster[&&NHX:EXT=Y:TOL=22461])myrmicinae[&&NHX:TOL=22221],(tatuidris tatusia[&&NHX:TOL=22612],agroecomyrmex duisburgi[&&NHX:EXT=Y:TOL=22610],(eulithomyrmex rugosus[&&NHX:EXT=Y:TOL=23079],eulithomyrmex striatus[&&NHX:EXT=Y:TOL=23080])eulithomyrmex[&&NHX:EXT=Y:TOL=22611])agroecomyrmecinae[&&NHX:TOL=22220],(((ectatomma brunneum[&&NHX:TOL=26498],ectatomma confine[&&NHX:TOL=26499],ectatomma edentatum[&&NHX:TOL=26500],ectatomma gibbum[&&NHX:TOL=26501],ectatomma goninion[&&NHX:TOL=26502],ectatomma gracile[&&NHX:TOL=26503],ectatomma lugens[&&NHX:TOL=26504],ectatomma muticum[&&NHX:TOL=26505],ectatomma opaciventre[&&NHX:TOL=26506],ectatomma permagnum[&&NHX:TOL=26507],ectatomma planidens[&&NHX:TOL=26508],ectatomma ruidum[&&NHX:TOL=26509],ectatomma suzanae[&&NHX:TOL=26510],ectatomma tuberculatum[&&NHX:TOL=26511],ectatomma vizottoi[&&NHX:TOL=26512])ectatomma[&&NHX:TOL=22616],(gnamptogenys aculeaticoxae[&&NHX:TOL=26513],132 additional described species[&&NHX:TOL=26514])gnamptogenys[&&NHX:TOL=22617],(rhytidoponera abdominalis[&&NHX:TOL=26515],104 additional described species[&&NHX:TOL=26516])rhytidoponera[&&NHX:TOL=22618],electroponera dubia[&&NHX:EXT=Y:TOL=22619])ectatommini[&&NHX:TOL=22613],(typhlomyrmex clavicornis[&&NHX:TOL=26517],typhlomyrmex foreli[&&NHX:TOL=26518],typhlomyrmex major[&&NHX:TOL=26519],typhlomyrmex prolatus[&&NHX:TOL=26520],typhlomyrmex pusillus[&&NHX:TOL=26521],typhlomyrmex rogenhoferi[&&NHX:TOL=26522])typhlomyrmex[&&NHX:TOL=22614],canapone dentata[&&NHX:EXT=Y:TOL=22615])ectatomminae[&&NHX:TOL=22216],((acanthoponera goeldii[&&NHX:TOL=26523],acanthoponera minor[&&NHX:TOL=26524],acanthoponera mucronata[&&NHX:TOL=26525],acanthoponera peruviana[&&NHX:TOL=26526])acanthoponera[&&NHX:TOL=22388],(heteroponera angulata[&&NHX:TOL=26527],heteroponera brounii[&&NHX:TOL=26528],heteroponera carinifrons[&&NHX:TOL=26529],heteroponera dentinodis[&&NHX:TOL=26530],heteroponera dolo[&&NHX:TOL=26531],heteroponera flava[&&NHX:TOL=26532],heteroponera georgesi[&&NHX:TOL=26533],heteroponera imbellis[&&NHX:TOL=26534],heteroponera inca[&&NHX:TOL=26535],heteroponera inermis[&&NHX:TOL=26536],heteroponera leae[&&NHX:TOL=26537],heteroponera mayri[&&NHX:TOL=26538],heteroponera microps[&&NHX:TOL=26539],heteroponera monticola[&&NHX:TOL=26540],heteroponera panamensis[&&NHX:TOL=26541],heteroponera relicta[&&NHX:TOL=26542],heteroponera robusta[&&NHX:TOL=26543])heteroponera[&&NHX:TOL=22389],aulacopone relicta[&&NHX:TOL=22390])heteroponerinae[&&NHX:TOL=22217],(paraponera clavata[&&NHX:TOL=22933],paraponera dieteri[&&NHX:EXT=Y:TOL=22934])paraponera[&&NHX:TOL=22218],(((discothyrea antarctica[&&NHX:TOL=26560],27 additional described species[&&NHX:TOL=26561])discothyrea[&&NHX:TOL=22394],(proceratium silaceum[&&NHX:TOL=26562],76 additional described species[&&NHX:TOL=26563])proceratium[&&NHX:TOL=22395],bradoponera meieri[&&NHX:EXT=Y:TOL=22393])proceratiini[&&NHX:TOL=22391],(probolomyrmex bidens[&&NHX:TOL=26544],probolomyrmex boliviensis[&&NHX:TOL=26545],probolomyrmex brevirostris[&&NHX:TOL=26546],probolomyrmex brujitae[&&NHX:TOL=26547],probolomyrmex dammermani[&&NHX:TOL=26548],probolomyrmex filiformis[&&NHX:TOL=26549],probolomyrmex greavesi[&&NHX:TOL=26550],probolomyrmex guanacastensis[&&NHX:TOL=26551],probolomyrmex guineensis[&&NHX:TOL=26552],probolomyrmex longinodus[&&NHX:TOL=26553],probolomyrmex longiscapus[&&NHX:TOL=26554],probolomyrmex okinawensis[&&NHX:TOL=26555],probolomyrmex petiolatus[&&NHX:TOL=26556],probolomyrmex procne[&&NHX:TOL=26557],probolomyrmex salomonis[&&NHX:TOL=26558],probolomyrmex watanabei[&&NHX:TOL=26559])probolomyrmex[&&NHX:TOL=22392])proceratiinae[&&NHX:TOL=22219],((platythyrea punctata[&&NHX:TOL=26566],platythyrea strenua[&&NHX:TOL=26891],40 additional described species[&&NHX:TOL=26567])platythyrea[&&NHX:TOL=22396],((thaumatomyrmex atrox[&&NHX:TOL=26568],thaumatomyrmex bariay[&&NHX:TOL=26569],thaumatomyrmex cochlearis[&&NHX:TOL=26570],thaumatomyrmex contumax[&&NHX:TOL=26571],thaumatomyrmex ferox[&&NHX:TOL=26572],thaumatomyrmex mandibularis[&&NHX:TOL=26573],thaumatomyrmex mutilatus[&&NHX:TOL=26574],thaumatomyrmex nageli[&&NHX:TOL=26575])thaumatomyrmex[&&NHX:TOL=22397],((anochetus bequaerti[&&NHX:TOL=26881],anochetus emarginatus[&&NHX:TOL=26882],anochetus madagascarensis[&&NHX:TOL=26883],anochetus mayri[&&NHX:TOL=26884],anochetus neglectus[&&NHX:TOL=26885],91 additional described species[&&NHX:TOL=26577])anochetus[&&NHX:TOL=22399],(odontomachus chelifer[&&NHX:TOL=26578],63 additional described species[&&NHX:TOL=26579])odontomachus[&&NHX:TOL=22413],(asphinctopone lamottei[&&NHX:TOL=26580],asphinctopone lucida[&&NHX:TOL=26581],asphinctopone silvestrii[&&NHX:TOL=26582])asphinctopone[&&NHX:TOL=22400],(belonopelta attenuata[&&NHX:TOL=26583],belonopelta deletrix[&&NHX:TOL=26584])belonopelta[&&NHX:TOL=22401],(centromyrmex alfaroi[&&NHX:TOL=26585],centromyrmex bequaerti[&&NHX:TOL=26586],centromyrmex brachycola[&&NHX:TOL=26587],centromyrmex congolensis[&&NHX:TOL=26588],centromyrmex constanciae[&&NHX:TOL=26589],centromyrmex feae[&&NHX:TOL=26590],centromyrmex gigas[&&NHX:TOL=26591],centromyrmex hamulatus[&&NHX:TOL=26592],centromyrmex sellaris[&&NHX:TOL=26593],centromyrmex silvestrii[&&NHX:TOL=26594])centromyrmex[&&NHX:TOL=22402],(cryptopone arabica[&&NHX:TOL=26595],cryptopone butteli[&&NHX:TOL=26596],cryptopone crassicornis[&&NHX:TOL=26597],cryptopone fusciceps[&&NHX:TOL=26598],cryptopone gigas[&&NHX:TOL=26599],cryptopone gilva[&&NHX:TOL=26600],cryptopone guatemalensis[&&NHX:TOL=26601],cryptopone hartwigi[&&NHX:TOL=26602],cryptopone jinxiuensis[&&NHX:TOL=26603],cryptopone motschulskyi[&&NHX:TOL=26604],cryptopone nicobarensis[&&NHX:TOL=26605],cryptopone ochracea[&&NHX:TOL=26606],cryptopone pseudogigas[&&NHX:TOL=26607],cryptopone recticlypea[&&NHX:TOL=26608],cryptopone rotundiceps[&&NHX:TOL=26609],cryptopone sauteri[&&NHX:TOL=26610],cryptopone taivanae[&&NHX:TOL=26611],cryptopone takahashii[&&NHX:TOL=26612],cryptopone testacea[&&NHX:TOL=26613],cryptopone typhlos[&&NHX:TOL=26614])cryptopone[&&NHX:TOL=22403],(diacamma assamense[&&NHX:TOL=26615],diacamma australe[&&NHX:TOL=26616],diacamma baguiense[&&NHX:TOL=26617],diacamma bispinosum[&&NHX:TOL=26618],diacamma ceylonense[&&NHX:TOL=26619],diacamma cupreum[&&NHX:TOL=26620],diacamma cyaneiventre[&&NHX:TOL=26621],diacamma holosericeum[&&NHX:TOL=26622],diacamma intricatum[&&NHX:TOL=26623],diacamma jacobsoni[&&NHX:TOL=26624],diacamma longitudinale[&&NHX:TOL=26625],diacamma palawanicum[&&NHX:TOL=26626],diacamma panayense[&&NHX:TOL=26627],diacamma purpureum[&&NHX:TOL=26628],diacamma rugivertex[&&NHX:TOL=26629],diacamma rugosum[&&NHX:TOL=26630],diacamma scalpratum[&&NHX:TOL=26631],diacamma sericeiventre[&&NHX:TOL=26632],diacamma tritschleri[&&NHX:TOL=26633])diacamma[&&NHX:TOL=22404],(dinoponera australis[&&NHX:TOL=26634],dinoponera gigantea[&&NHX:TOL=26635],dinoponera longipes[&&NHX:TOL=26636],dinoponera lucida[&&NHX:TOL=26637],dinoponera mutica[&&NHX:TOL=26638],dinoponera quadriceps[&&NHX:TOL=26639])dinoponera[&&NHX:TOL=22405],dolioponera fustigera[&&NHX:TOL=22406],(emeryopone buttelreepeni[&&NHX:TOL=26640],emeryopone franzi[&&NHX:TOL=26641],emeryopone loebli[&&NHX:TOL=26642],emeryopone melaina[&&NHX:TOL=26643])emeryopone[&&NHX:TOL=22407],(harpegnathos empesoi[&&NHX:TOL=26644],harpegnathos hobbyi[&&NHX:TOL=26645],harpegnathos macgregori[&&NHX:TOL=26646],harpegnathos medioniger[&&NHX:TOL=26647],harpegnathos pallipes[&&NHX:TOL=26648],harpegnathos saltator[&&NHX:TOL=26649],harpegnathos venator[&&NHX:TOL=26650])harpegnathos[&&NHX:TOL=22408],(hypoponera inexorata[&&NHX:TOL=26651],131 additional described species[&&NHX:TOL=26652])hypoponera[&&NHX:TOL=22409],(ponera affinis[&&NHX:TOL=26653],53 additional described species[&&NHX:TOL=26654])ponera[&&NHX:TOL=22418],(leptogenys attenuata[&&NHX:TOL=26655],213 additional described species[&&NHX:TOL=26656])leptogenys[&&NHX:TOL=22410],(myopias chapmani[&&NHX:TOL=26657],33 described species[&&NHX:TOL=26658])myopias[&&NHX:TOL=22412],(loboponera basalis[&&NHX:TOL=26659],loboponera edentula[&&NHX:TOL=26660],loboponera nasica[&&NHX:TOL=26661],loboponera obeliscata[&&NHX:TOL=26662],loboponera politula[&&NHX:TOL=26663],loboponera subatra[&&NHX:TOL=26664],loboponera trica[&&NHX:TOL=26665],loboponera vigilans[&&NHX:TOL=26666])loboponera[&&NHX:TOL=22411],(plectroctena anops[&&NHX:TOL=26667],plectroctena cristata[&&NHX:TOL=26668],plectroctena cryptica[&&NHX:TOL=26669],plectroctena dentata[&&NHX:TOL=26670],plectroctena gestroi[&&NHX:TOL=26671],plectroctena hastifera[&&NHX:TOL=26672],plectroctena laevior[&&NHX:TOL=26673],plectroctena latinodis[&&NHX:TOL=26674],plectroctena lygaria[&&NHX:TOL=26675],plectroctena macgeei[&&NHX:TOL=26676],plectroctena mandibularis[&&NHX:TOL=26677],plectroctena minor[&&NHX:TOL=26678],plectroctena strigosa[&&NHX:TOL=26679],plectroctena subterranea[&&NHX:TOL=26680],plectroctena ugandensis[&&NHX:TOL=26681])plectroctena[&&NHX:TOL=22417],(psalidomyrmex feae[&&NHX:TOL=26682],psalidomyrmex foveolatus[&&NHX:TOL=26683],psalidomyrmex procerus[&&NHX:TOL=26684],psalidomyrmex reichenspergeri[&&NHX:TOL=26685],psalidomyrmex sallyae[&&NHX:TOL=26686],psalidomyrmex wheeleri[&&NHX:TOL=26687])psalidomyrmex[&&NHX:TOL=22419],odontoponera transversa[&&NHX:TOL=22414],(bothroponera rufipes[&&NHX:TOL=26892],brachyponera chinensis[&&NHX:TOL=26893],hagensia havilandi[&&NHX:TOL=26886],neoponera villosa[&&NHX:TOL=26887],ophthalmopone berthoudi[&&NHX:TOL=26888],pachycondyla harpax[&&NHX:TOL=26688],paltothyreus tarsatus[&&NHX:TOL=26889],termitopone marginata[&&NHX:TOL=26890],203 additional described species[&&NHX:TOL=26689])pachycondyla[&&NHX:TOL=22415],(phrynoponera armata[&&NHX:TOL=26690],phrynoponera bequaerti[&&NHX:TOL=26691],phrynoponera gabonensis[&&NHX:TOL=26692],phrynoponera heteroda[&&NHX:TOL=26693],phrynoponera sveni[&&NHX:TOL=26694])phrynoponera[&&NHX:TOL=22416],(simopelta bicolor[&&NHX:TOL=26695],simopelta curvata[&&NHX:TOL=26696],simopelta jeckylli[&&NHX:TOL=26697],simopelta laticeps[&&NHX:TOL=26698],simopelta manni[&&NHX:TOL=26699],simopelta minima[&&NHX:TOL=26700],simopelta oculata[&&NHX:TOL=26701],simopelta paeminosa[&&NHX:TOL=26702],simopelta pergandei[&&NHX:TOL=26703],simopelta williamsi[&&NHX:TOL=26704])simopelta[&&NHX:TOL=22420],(streblognathus aethiopicus[&&NHX:TOL=26705],streblognathus peetersi[&&NHX:TOL=26706])streblognathus[&&NHX:TOL=22421],archiponera wheeleri[&&NHX:EXT=Y:TOL=22422],(poneropsis affinis[&&NHX:EXT=Y:TOL=26707],18 additional described species[&&NHX:EXT=Y:TOL=26708])poneropsis[&&NHX:EXT=Y:TOL=22423],protopone primigena[&&NHX:EXT=Y:TOL=22424])ponerini[&&NHX:TOL=22398])[&&NHX:TOL=22425])ponerinae[&&NHX:TOL=22215],((anomalomyrma taylori[&&NHX:TOL=22622],(protanilla bicolor[&&NHX:TOL=26748],protanilla concolor[&&NHX:TOL=26749],protanilla furcomandibula[&&NHX:TOL=26750],protanilla rafflesi[&&NHX:TOL=26751])protanilla[&&NHX:TOL=22623])anomalomyrmini[&&NHX:TOL=22620],((leptanilla africana[&&NHX:TOL=26752],41 additional described species[&&NHX:TOL=26753])leptanilla[&&NHX:TOL=22624],phaulomyrma javana[&&NHX:TOL=22625],(yavnella argamani[&&NHX:TOL=23082],yavnella indica[&&NHX:TOL=23083])yavnella[&&NHX:TOL=22626])leptanillini[&&NHX:TOL=22621])leptanillinae[&&NHX:TOL=22213],(((asphinctanilloides anae[&&NHX:TOL=22687],(asphinctanilloides manauara[&&NHX:TOL=22688],asphinctanilloides amazona[&&NHX:TOL=22686])[&&NHX:TOL=22694])asphinctanilloides[&&NHX:TOL=22627],(leptanilloides biconstricta[&&NHX:TOL=22689],leptanilloides improvisa[&&NHX:TOL=22690],leptanilloides legionaria[&&NHX:TOL=22691],leptanilloides mckennae[&&NHX:TOL=22692],leptanilloides sculpturata[&&NHX:TOL=22693])leptanilloides[&&NHX:TOL=22628])leptanilloidinae[&&NHX:TOL=22208],(aenictogiton attenuatus[&&NHX:TOL=26754],aenictogiton bequaerti[&&NHX:TOL=26755],aenictogiton elongatus[&&NHX:TOL=26756],aenictogiton emeryi[&&NHX:TOL=26757],aenictogiton fossiceps[&&NHX:TOL=26758],aenictogiton schoutedeni[&&NHX:TOL=26759],aenictogiton sulcatus[&&NHX:TOL=26760])aenictogiton[&&NHX:TOL=22211],((acanthostichus arizonensis[&&NHX:TOL=26761],acanthostichus bentoni[&&NHX:TOL=26762],acanthostichus brevicornis[&&NHX:TOL=26763],acanthostichus brevinodis[&&NHX:TOL=26764],acanthostichus concavinodis[&&NHX:TOL=26765],acanthostichus emmae[&&NHX:TOL=26766],acanthostichus femoralis[&&NHX:TOL=26767],acanthostichus flexuosus[&&NHX:TOL=26768],acanthostichus fuscipennis[&&NHX:TOL=26769],acanthostichus hispaniolicus[&&NHX:TOL=26770],acanthostichus kirbyi[&&NHX:TOL=26771],acanthostichus laevigatus[&&NHX:TOL=26772],acanthostichus laticornis[&&NHX:TOL=26773],acanthostichus lattkei[&&NHX:TOL=26774],acanthostichus longinodis[&&NHX:TOL=26775],acanthostichus punctiscapus[&&NHX:TOL=26776],acanthostichus quadratus[&&NHX:TOL=26777],acanthostichus quirozi[&&NHX:TOL=26778],acanthostichus sanchezorum[&&NHX:TOL=26779],acanthostichus serratulus[&&NHX:TOL=26780],acanthostichus skwarrae[&&NHX:TOL=26781],acanthostichus texanus[&&NHX:TOL=26782],acanthostichus truncatus[&&NHX:TOL=26783])acanthostichus[&&NHX:TOL=22629],(cylindromyrmex antillanus[&&NHX:TOL=26784],cylindromyrmex boliviae[&&NHX:TOL=26785],cylindromyrmex brasiliensis[&&NHX:TOL=26786],cylindromyrmex brevitarsus[&&NHX:TOL=26787],cylindromyrmex darlingtoni[&&NHX:TOL=26788],cylindromyrmex electrinus[&&NHX:TOL=26789],cylindromyrmex escobari[&&NHX:TOL=26790],cylindromyrmex godmani[&&NHX:TOL=26791],cylindromyrmex inopinatus[&&NHX:TOL=26792],cylindromyrmex longiceps[&&NHX:TOL=26793],cylindromyrmex meinerti[&&NHX:TOL=26794],cylindromyrmex schmidti[&&NHX:TOL=26795],cylindromyrmex striatus[&&NHX:TOL=26796])cylindromyrmex[&&NHX:TOL=22936],((cerapachys aberrans[&&NHX:TOL=26797],143 additional described species[&&NHX:TOL=26798])cerapachys[&&NHX:TOL=22632],(simopone annettae[&&NHX:TOL=26799],simopone bakeri[&&NHX:TOL=26800],simopone chapmani[&&NHX:TOL=26801],simopone conciliatrix[&&NHX:TOL=26802],simopone conradti[&&NHX:TOL=26803],simopone emeryi[&&NHX:TOL=26804],simopone fulvinodis[&&NHX:TOL=26805],simopone grandidieri[&&NHX:TOL=26806],simopone grandis[&&NHX:TOL=26807],simopone gressitti[&&NHX:TOL=26808],simopone laevissima[&&NHX:TOL=26809],simopone marleyi[&&NHX:TOL=26810],simopone matthiasi[&&NHX:TOL=26811],simopone oculata[&&NHX:TOL=26812],simopone satagia[&&NHX:TOL=26813],simopone schoutedeni[&&NHX:TOL=26814])simopone[&&NHX:TOL=22633],(sphinctomyrmex asper[&&NHX:TOL=26815],sphinctomyrmex caledonicus[&&NHX:TOL=26816],sphinctomyrmex cedaris[&&NHX:TOL=26817],sphinctomyrmex chariensis[&&NHX:TOL=26818],sphinctomyrmex clarus[&&NHX:TOL=26819],sphinctomyrmex cribratus[&&NHX:TOL=26820],sphinctomyrmex duchaussoyi[&&NHX:TOL=26821],sphinctomyrmex emeryi[&&NHX:TOL=26822],sphinctomyrmex froggatti[&&NHX:TOL=26823],sphinctomyrmex furcatus[&&NHX:TOL=26824],sphinctomyrmex imbecilis[&&NHX:TOL=26825],sphinctomyrmex mjobergi[&&NHX:TOL=26826],sphinctomyrmex myops[&&NHX:TOL=26827],sphinctomyrmex nigricans[&&NHX:TOL=26828],sphinctomyrmex occidentalis[&&NHX:TOL=26829],sphinctomyrmex rufiventris[&&NHX:TOL=26830],sphinctomyrmex septentrionalis[&&NHX:TOL=26831],sphinctomyrmex stali[&&NHX:TOL=26832],sphinctomyrmex steinheili[&&NHX:TOL=26833],sphinctomyrmex taylori[&&NHX:TOL=26834],sphinctomyrmex trux[&&NHX:TOL=26835],sphinctomyrmex turneri[&&NHX:TOL=26836])sphinctomyrmex[&&NHX:TOL=22634])cerapachyini[&&NHX:TOL=22631])cerapachyinae[&&NHX:TOL=22935],(((cheliomyrmex andicola[&&NHX:TOL=26837],cheliomyrmex audax[&&NHX:TOL=26838],cheliomyrmex megalonyx[&&NHX:TOL=26839],cheliomyrmex morosus[&&NHX:TOL=26840])cheliomyrmex[&&NHX:TOL=22635],((neivamyrmex adnepos[&&NHX:TOL=26841],126 additional described species[&&NHX:TOL=26842])neivamyrmex[&&NHX:TOL=22639],((nomamyrmex esenbeckii[&&NHX:TOL=26843],nomamyrmex hartigii[&&NHX:TOL=26844])nomamyrmex[&&NHX:TOL=22640],((labidus auropubens[&&NHX:TOL=26845],labidus coecus[&&NHX:TOL=26846],labidus curvipes[&&NHX:TOL=26847],labidus mars[&&NHX:TOL=26848],labidus nero[&&NHX:TOL=26849],labidus praedator[&&NHX:TOL=26850],labidus spininodis[&&NHX:TOL=26851],labidus truncatidens[&&NHX:TOL=26852])labidus[&&NHX:TOL=22638],(eciton burchellii[&&NHX:TOL=26853],eciton drepanophorum[&&NHX:TOL=26854],eciton dulcium[&&NHX:TOL=26855],eciton hamatum[&&NHX:TOL=26856],eciton jansoni[&&NHX:TOL=26857],eciton lucanoides[&&NHX:TOL=26858],eciton mexicanum[&&NHX:TOL=26859],eciton quadrigiume[&&NHX:TOL=26860],eciton rapax[&&NHX:TOL=26861],eciton setigaster[&&NHX:TOL=26862],eciton uncinatum[&&NHX:TOL=26863],eciton vagans[&&NHX:TOL=26864])eciton[&&NHX:TOL=22637])[&&NHX:TOL=22682])[&&NHX:TOL=22683])ecitonini[&&NHX:TOL=22684])ecitoninae[&&NHX:TOL=22207],((aenictus abeillei[&&NHX:TOL=26865],109 additional described species[&&NHX:TOL=26866])aenictus[&&NHX:TOL=22209],(dorylus acutus[&&NHX:TOL=26867],60 additional described species[&&NHX:TOL=26868])dorylus[&&NHX:TOL=22210])[&&NHX:TOL=22229])[&&NHX:TOL=22228])dorylomorphs[&&NHX:TOL=22227])[&&NHX:TOL=22231])[&&NHX:TOL=22223],calyptites antediluvianum[&&NHX:EXT=Y:TOL=22371],cariridris bipetiolata[&&NHX:EXT=Y:TOL=22372],condylodon audouini[&&NHX:TOL=22373],hypochira subspinosa[&&NHX:TOL=22374],noonilla copiosa[&&NHX:TOL=22375],paleosminthurus juliae[&&NHX:EXT=Y:TOL=22376],syntaphus wheeleri[&&NHX:EXT=Y:TOL=22377])formicidae[&&NHX:TOL=11247],(vespidae[&&NHX:TOL=11244],(scoliinae[&&NHX:TOL=22176],proscoliinae[&&NHX:TOL=22177])scoliidae[&&NHX:TOL=11243])[&&NHX:TOL=11242])[&&NHX:TOL=11241])[&&NHX:TOL=11239])[&&NHX:TOL=22065])[&&NHX:TOL=11230])vespoidea[&&NHX:TOL=11191])[&&NHX:TOL=11187])aculeata[&&NHX:TOL=11184])[&&NHX:TOL=22030])apocrita[&&NHX:TOL=11162])[&&NHX:TOL=22023])[&&NHX:TOL=22021])[&&NHX:TOL=22020])[&&NHX:TOL=11150])[&&NHX:TOL=22018])[&&NHX:TOL=22016])[&&NHX:TOL=22014])hymenoptera[&&NHX:TOL=8232])[&&NHX:TOL=8223])[&&NHX:TOL=8215],(metropator[&&NHX:EXT=Y:TOL=13120],(archaemioptera[&&NHX:EXT=Y:TOL=13122],eodelopterum[&&NHX:EXT=Y:TOL=13123],saaromioptera[&&NHX:EXT=Y:TOL=13124],tychtodelopterum[&&NHX:EXT=Y:TOL=13125])archaemiopteridae[&&NHX:TOL=13121],(palaeomantis[&&NHX:EXT=Y:TOL=13127],delopterum[&&NHX:EXT=Y:TOL=13128],miomatoneura[&&NHX:EXT=Y:TOL=13129],miomatoneurella[&&NHX:EXT=Y:TOL=13130],permodelopterum[&&NHX:EXT=Y:TOL=13131],perunopterum[&&NHX:EXT=Y:TOL=13132])palaeomanteidae[&&NHX:TOL=13126])miomoptera[&&NHX:EXT=Y:TOL=8233])endopterygota[&&NHX:TOL=8243])[&&NHX:TOL=8241],paraplecoptera[&&NHX:EXT=Y:TOL=8244],((eustheniidae[&&NHX:TOL=13928],diamphipnoidae[&&NHX:TOL=13929])[&&NHX:TOL=13927],((austroperlidae[&&NHX:TOL=13932],gripopterygidae[&&NHX:TOL=13933])[&&NHX:TOL=13931],(scopuridae[&&NHX:TOL=13935],((taeniopteryx[&&NHX:TOL=14389],(strophopteryx[&&NHX:TOL=14391],(((taenionema grinnelli[&&NHX:TOL=14366],(taenionema pallidum[&&NHX:TOL=14368],taenionema jewetti[&&NHX:TOL=14369])[&&NHX:TOL=14367])[&&NHX:TOL=14365],(((taenionema californicum[&&NHX:TOL=14373],taenionema raynorium[&&NHX:TOL=14374])[&&NHX:TOL=14372],(taenionema oregonense[&&NHX:TOL=14376],(taenionema umatilla[&&NHX:TOL=14378],(((taenionema atlanticum[&&NHX:TOL=14382],taenionema pacificum[&&NHX:TOL=14383])[&&NHX:TOL=14381],taenionema uinta[&&NHX:TOL=14384])[&&NHX:TOL=14380],taenionema jacobii[&&NHX:TOL=14385])[&&NHX:TOL=14379])[&&NHX:TOL=14377])[&&NHX:TOL=14375])[&&NHX:TOL=14371],taenionema japonicum[&&NHX:TOL=14386])[&&NHX:TOL=14370])[&&NHX:TOL=14364],taenionema kincaidi[&&NHX:TOL=14387])taenionema[&&NHX:TOL=14392],obipteryx[&&NHX:TOL=14393],doddsia[&&NHX:TOL=14394],kyphopteryx[&&NHX:TOL=14395],brachyptera[&&NHX:TOL=14396],oemopteryx[&&NHX:TOL=14397],rhabdiopteryx[&&NHX:TOL=14398])brachypterinae[&&NHX:TOL=14390])taeniopterygidae[&&NHX:TOL=13937],((notonemouridae[&&NHX:TOL=13940],((amphinemura[&&NHX:TOL=14169],malenka[&&NHX:TOL=14170])amphinemurinae[&&NHX:TOL=14168],((protonemura[&&NHX:TOL=14173],(mesonemoura[&&NHX:TOL=14175],indonemoura[&&NHX:TOL=14176])[&&NHX:TOL=14174])[&&NHX:TOL=14172],(((soyedina[&&NHX:TOL=14180],nemoura[&&NHX:TOL=14181])[&&NHX:TOL=14179],(illiesonemoura[&&NHX:TOL=14183],zapada[&&NHX:TOL=14184])[&&NHX:TOL=14182])[&&NHX:TOL=14178],(((nemurella[&&NHX:TOL=14188],ostrocerca[&&NHX:TOL=14189])[&&NHX:TOL=14187],(podmosta[&&NHX:TOL=14191],shipsa[&&NHX:TOL=14192])[&&NHX:TOL=14190])[&&NHX:TOL=14186],((visoka[&&NHX:TOL=14195],lednia[&&NHX:TOL=14196])[&&NHX:TOL=14194],(paranemoura[&&NHX:TOL=14198],prostoia[&&NHX:TOL=14199])[&&NHX:TOL=14197])[&&NHX:TOL=14193])[&&NHX:TOL=14185])[&&NHX:TOL=14177])nemourinae[&&NHX:TOL=14171])nemouridae[&&NHX:TOL=13941])[&&NHX:TOL=13939],((isocapnia[&&NHX:TOL=14083],(paracapnia[&&NHX:TOL=14085],(((nemocapnia[&&NHX:TOL=14089],capnioneura[&&NHX:TOL=14090])[&&NHX:TOL=14088],eucapnopsis[&&NHX:TOL=14091])[&&NHX:TOL=14087],(allocapniella[&&NHX:TOL=14093],(bolshecapnia[&&NHX:TOL=14095],capnia in part 2[&&NHX:TOL=14096])[&&NHX:TOL=14094],(((capnura manitoba[&&NHX:TOL=14113],((capnura fibula[&&NHX:TOL=14116],(capnura wanica[&&NHX:TOL=14118],capnura intermontana[&&NHX:TOL=14119])[&&NHX:TOL=14117])[&&NHX:TOL=14115],((capnura venosa[&&NHX:TOL=14122],capnura anas[&&NHX:TOL=14123])[&&NHX:TOL=14121],capnura elevata[&&NHX:TOL=14124])[&&NHX:TOL=14120])[&&NHX:TOL=14114])capnura[&&NHX:TOL=14099],capnia nigra type[&&NHX:TOL=14100])[&&NHX:TOL=14098],baikaloperla[&&NHX:TOL=14101],(allocapnia simmonsi[&&NHX:TOL=13956],(allocapnia harperi[&&NHX:TOL=13958],(allocapnia frumi[&&NHX:TOL=13960],(((allocapnia vivipara[&&NHX:TOL=13964],allocapnia tennessa[&&NHX:TOL=13965])[&&NHX:TOL=13963],allocapnia brooksi[&&NHX:TOL=13966])[&&NHX:TOL=13962],(((((allocapnia loshada[&&NHX:TOL=13972],(allocapnia polemistis[&&NHX:TOL=13974],allocapnia recta[&&NHX:TOL=13975])[&&NHX:TOL=13973])[&&NHX:TOL=13971],allocapnia mohri[&&NHX:TOL=13976])[&&NHX:TOL=13970],allocapnia malverna[&&NHX:TOL=13977])[&&NHX:TOL=13969],allocapnia oribata[&&NHX:TOL=13978])[&&NHX:TOL=13968],((allocapnia virginiana[&&NHX:TOL=13981],(allocapnia fumosa[&&NHX:TOL=13983],((allocapnia warreni[&&NHX:TOL=13986],allocapnia unzickeri[&&NHX:TOL=13987])[&&NHX:TOL=13985],allocapnia granulata[&&NHX:TOL=13988],(allocapnia frisoni[&&NHX:TOL=13990],allocapnia peltoides[&&NHX:TOL=13991])[&&NHX:TOL=13989])[&&NHX:TOL=13984])[&&NHX:TOL=13982])[&&NHX:TOL=13980],((allocapnia zekia[&&NHX:TOL=13994],allocapnia wrayi[&&NHX:TOL=13995],allocapnia mystica[&&NHX:TOL=13996])[&&NHX:TOL=13993],((allocapnia illinoensis[&&NHX:TOL=13999],((allocapnia forbesi[&&NHX:TOL=14002],allocapnia ozarkana[&&NHX:TOL=14003])[&&NHX:TOL=14001],(allocapnia curiosa[&&NHX:TOL=14005],(allocapnia pechumani[&&NHX:TOL=14007],(allocapnia maria[&&NHX:TOL=14009],allocapnia minima[&&NHX:TOL=14010])[&&NHX:TOL=14008])[&&NHX:TOL=14006])[&&NHX:TOL=14004])[&&NHX:TOL=14000])[&&NHX:TOL=13998],((allocapnia jeanae[&&NHX:TOL=14013],(((allocapnia stannardi[&&NHX:TOL=14017],allocapnia rickeri[&&NHX:TOL=14018])[&&NHX:TOL=14016],allocapnia sandersoni[&&NHX:TOL=14019])[&&NHX:TOL=14015],allocapnia zola[&&NHX:TOL=14020],allocapnia cunninghami[&&NHX:TOL=14021],allocapnia perplexa[&&NHX:TOL=14022])[&&NHX:TOL=14014])[&&NHX:TOL=14012],(allocapnia pygmaea[&&NHX:TOL=14024],(allocapnia aurora[&&NHX:TOL=14026],(allocapnia ohioensis[&&NHX:TOL=14028],allocapnia indianae[&&NHX:TOL=14029],(allocapnia smithi[&&NHX:TOL=14031],allocapnia nivicola[&&NHX:TOL=14032])[&&NHX:TOL=14030])[&&NHX:TOL=14027])[&&NHX:TOL=14025])[&&NHX:TOL=14023])[&&NHX:TOL=14011])[&&NHX:TOL=13997])[&&NHX:TOL=13992])[&&NHX:TOL=13979])[&&NHX:TOL=13967])[&&NHX:TOL=13961])[&&NHX:TOL=13959])[&&NHX:TOL=13957])allocapnia[&&NHX:TOL=14102],utacapnia[&&NHX:TOL=14103])[&&NHX:TOL=14097],capnia in part 3[&&NHX:TOL=14104],((((((((capnia quadrituberosa[&&NHX:TOL=14040],capnia californica[&&NHX:TOL=14041])[&&NHX:TOL=14039],capnia ophiona[&&NHX:TOL=14042])[&&NHX:TOL=14038],capnia jewetti[&&NHX:TOL=14043])[&&NHX:TOL=14037],capnia regilla[&&NHX:TOL=14044])[&&NHX:TOL=14036],(capnia saratoga[&&NHX:TOL=14046],capnia ventura[&&NHX:TOL=14047])[&&NHX:TOL=14045])[&&NHX:TOL=14035],capnia umpqua[&&NHX:TOL=14048])californica group[&&NHX:TOL=14034],(((capnia giulianii[&&NHX:TOL=14052],capnia mariposa[&&NHX:TOL=14053])[&&NHX:TOL=14051],capnia inyo[&&NHX:TOL=14054])mariposa group[&&NHX:TOL=14050],(((((capnia yosemite[&&NHX:TOL=14060],capnia barberi[&&NHX:TOL=14061])[&&NHX:TOL=14059],capnia hornigi[&&NHX:TOL=14062])[&&NHX:TOL=14058],capnia mono[&&NHX:TOL=14063])[&&NHX:TOL=14057],capnia shepardi[&&NHX:TOL=14064])barberi group[&&NHX:TOL=14056],(((capnia palomar[&&NHX:TOL=14068],capnia arapahoe[&&NHX:TOL=14069])[&&NHX:TOL=14067],((capnia coyote[&&NHX:TOL=14072],capnia decepta[&&NHX:TOL=14073])[&&NHX:TOL=14071],capnia pileata[&&NHX:TOL=14074])[&&NHX:TOL=14070])[&&NHX:TOL=14066],(((capnia sequoia[&&NHX:TOL=14078],capnia tumida[&&NHX:TOL=14079])[&&NHX:TOL=14077],capnia utahensis[&&NHX:TOL=14080])[&&NHX:TOL=14076],capnia teresa[&&NHX:TOL=14081])[&&NHX:TOL=14075])decepta group[&&NHX:TOL=14065])[&&NHX:TOL=14055])[&&NHX:TOL=14049])capnia in part 1[&&NHX:TOL=14106],mesocapnia[&&NHX:TOL=14107])[&&NHX:TOL=14105],capniella[&&NHX:TOL=14108],capnopsis[&&NHX:TOL=14109],eocapnia[&&NHX:TOL=14110],takagripopteryx[&&NHX:TOL=14111])[&&NHX:TOL=14092])[&&NHX:TOL=14086])[&&NHX:TOL=14084])capniidae[&&NHX:TOL=13943],(megaleuctra[&&NHX:TOL=14147],(tyrrhenoluectra[&&NHX:TOL=14149],((((((((pachyleuctra[&&NHX:TOL=14158],leuctra[&&NHX:TOL=14159])[&&NHX:TOL=14157],despaxia[&&NHX:TOL=14160])[&&NHX:TOL=14156],moselia[&&NHX:TOL=14161])[&&NHX:TOL=14155],paraleuctra[&&NHX:TOL=14162])[&&NHX:TOL=14154],zealeuctra[&&NHX:TOL=14163])[&&NHX:TOL=14153],rhopalosole[&&NHX:TOL=14164])[&&NHX:TOL=14152],perlomyia[&&NHX:TOL=14165])[&&NHX:TOL=14151],calileuctra[&&NHX:TOL=14166])[&&NHX:TOL=14150])[&&NHX:TOL=14148])leuctridae[&&NHX:TOL=13944])[&&NHX:TOL=13942])[&&NHX:TOL=13938])[&&NHX:TOL=13936],(((pteronarcella regularis[&&NHX:TOL=14339],pteronarcella badia[&&NHX:TOL=14340])[&&NHX:TOL=14338],((pteronarcys sachalina[&&NHX:TOL=14343],pteronarcys reticulata[&&NHX:TOL=14344])[&&NHX:TOL=14342],((pteronarcys biloba[&&NHX:TOL=14347],pteronarcys scotti[&&NHX:TOL=14348])[&&NHX:TOL=14346],(pteronarcys comstocki[&&NHX:TOL=14350],(pteronarcys proteus[&&NHX:TOL=14352],((pteronarcys pictetii[&&NHX:TOL=14355],pteronarcys dorsata[&&NHX:TOL=14356])[&&NHX:TOL=14354],(pteronarcys californica[&&NHX:TOL=14358],pteronarcys princeps[&&NHX:TOL=14359])[&&NHX:TOL=14357])[&&NHX:TOL=14353])[&&NHX:TOL=14351])[&&NHX:TOL=14349])[&&NHX:TOL=14345])[&&NHX:TOL=14341])pteronarcyidae[&&NHX:TOL=13946],(((styloperla[&&NHX:TOL=14361],cerconychia[&&NHX:TOL=14362])styloperlidae[&&NHX:TOL=13949],(microperla[&&NHX:TOL=14201],(peltoperlopsis[&&NHX:TOL=14203],peltoperlodes[&&NHX:TOL=14204],cryptoperla[&&NHX:TOL=14205],(((peltoperla[&&NHX:TOL=14209],tallaperla[&&NHX:TOL=14210])[&&NHX:TOL=14208],viehoperla[&&NHX:TOL=14211])[&&NHX:TOL=14207],((((soliperla campanula[&&NHX:TOL=14220],soliperla sierra[&&NHX:TOL=14221])[&&NHX:TOL=14219],(soliperla quadrispinula[&&NHX:TOL=14223],soliperla thyra[&&NHX:TOL=14224])[&&NHX:TOL=14222])[&&NHX:TOL=14218],soliperla fenderi[&&NHX:TOL=14225],soliperla tilamook[&&NHX:TOL=14226])soliperla[&&NHX:TOL=14213],((((yoraperla han[&&NHX:TOL=14230],yoraperla uchidai[&&NHX:TOL=14231])[&&NHX:TOL=14229],yoraperla uenoi[&&NHX:TOL=14232])[&&NHX:TOL=14228],((yoraperla brevis[&&NHX:TOL=14235],yoraperla mariana[&&NHX:TOL=14236])[&&NHX:TOL=14234],(yoraperla nigrisoma[&&NHX:TOL=14238],yoraperla siletz[&&NHX:TOL=14239])[&&NHX:TOL=14237])[&&NHX:TOL=14233])yoraperla[&&NHX:TOL=14215],sierraperla[&&NHX:TOL=14216])[&&NHX:TOL=14214])[&&NHX:TOL=14212])[&&NHX:TOL=14206])peltoperlinae[&&NHX:TOL=14202])peltoperlidae[&&NHX:TOL=13950])[&&NHX:TOL=13948],((isoperlinae[&&NHX:TOL=14331],((((((skwala[&&NHX:TOL=14314],neofilchneria[&&NHX:TOL=14315])[&&NHX:TOL=14313],arcynopteryx[&&NHX:TOL=14316])[&&NHX:TOL=14312],((perlinodes[&&NHX:TOL=14319],frisonia[&&NHX:TOL=14320])[&&NHX:TOL=14318],(salmoperla[&&NHX:TOL=14322],oroperla[&&NHX:TOL=14323])[&&NHX:TOL=14321])[&&NHX:TOL=14317])[&&NHX:TOL=14311],(megarcys[&&NHX:TOL=14325],sopkalia[&&NHX:TOL=14326])[&&NHX:TOL=14324])[&&NHX:TOL=14310],(setvena[&&NHX:TOL=14328],pseudomegarcys[&&NHX:TOL=14329])[&&NHX:TOL=14327])arcynopterygini[&&NHX:TOL=14333],(diploperlini[&&NHX:TOL=14335],perlodini[&&NHX:TOL=14336])[&&NHX:TOL=14334])perlodinae[&&NHX:TOL=14332])perlodidae[&&NHX:TOL=13952],(claassenia[&&NHX:TOL=14241],((((((tyloperla[&&NHX:TOL=14248],((paragnetina[&&NHX:TOL=14251],togoperla[&&NHX:TOL=14252])[&&NHX:TOL=14250],(oyamia[&&NHX:TOL=14254],(marthamea[&&NHX:TOL=14256],agnetina[&&NHX:TOL=14257])[&&NHX:TOL=14255])[&&NHX:TOL=14253])[&&NHX:TOL=14249])[&&NHX:TOL=14247],(kamimuria[&&NHX:TOL=14259],(etrocorema[&&NHX:TOL=14261],(tetropina[&&NHX:TOL=14263],neoperlops[&&NHX:TOL=14264])[&&NHX:TOL=14262])[&&NHX:TOL=14260])[&&NHX:TOL=14258])[&&NHX:TOL=14246],miniperla[&&NHX:TOL=14265])[&&NHX:TOL=14245],(perla[&&NHX:TOL=14267],(eoperla[&&NHX:TOL=14269],dinocras[&&NHX:TOL=14270])[&&NHX:TOL=14268])[&&NHX:TOL=14266])perlini[&&NHX:TOL=14244],(furcaperla[&&NHX:TOL=14272],(neoperla[&&NHX:TOL=14274],(chinoperla[&&NHX:TOL=14276],phanoperla[&&NHX:TOL=14277])[&&NHX:TOL=14275])[&&NHX:TOL=14273])neoperlini[&&NHX:TOL=14271])perlinae[&&NHX:TOL=14243],((nigroperla[&&NHX:TOL=14280],inconeuria[&&NHX:TOL=14281],kempynia[&&NHX:TOL=14282],kempnyella[&&NHX:TOL=14283],macrogynoplax[&&NHX:TOL=14284],onychoplax[&&NHX:TOL=14285],klapalekia[&&NHX:TOL=14286],pictetoperla[&&NHX:TOL=14287],anacroneuria[&&NHX:TOL=14288],enderleina[&&NHX:TOL=14289])anacroneuriini[&&NHX:TOL=14279],(acroneuria[&&NHX:TOL=14291],attaneuria[&&NHX:TOL=14292],beloneuria[&&NHX:TOL=14293],brahmana[&&NHX:TOL=14294],calineuria[&&NHX:TOL=57908],caroperla[&&NHX:TOL=14295],doroneuria[&&NHX:TOL=14296],eccoptura[&&NHX:TOL=14297],gibosia[&&NHX:TOL=14298],hesperoperla[&&NHX:TOL=14299],kalidasia[&&NHX:TOL=14300],kiotina[&&NHX:TOL=14301],mesoperla[&&NHX:TOL=14302],neoeuryplax[&&NHX:TOL=14303],niponiella[&&NHX:TOL=14304],nirvania[&&NHX:TOL=14305],perlesta[&&NHX:TOL=14306],perlinella[&&NHX:TOL=14307],schistoperla[&&NHX:TOL=14308])acroneuriini[&&NHX:TOL=14290])acroneuriinae[&&NHX:TOL=14278])[&&NHX:TOL=14242])perlidae[&&NHX:TOL=13953],((paraperla[&&NHX:TOL=14127],kathroperla[&&NHX:TOL=14128],utaperla[&&NHX:TOL=14129])paraperlinae[&&NHX:TOL=14126],(((sweltsa[&&NHX:TOL=14133],alloperla[&&NHX:TOL=14134])[&&NHX:TOL=14132],bisancora[&&NHX:TOL=14135])alloperlini[&&NHX:TOL=14131],((suwallia[&&NHX:TOL=14138],neaviperla[&&NHX:TOL=14139])suwalliini[&&NHX:TOL=14137],((plumiperla[&&NHX:TOL=14142],triznaka[&&NHX:TOL=14143])[&&NHX:TOL=14141],chloroperla[&&NHX:TOL=14144],seven other genera[&&NHX:TOL=14145])chloroperlini[&&NHX:TOL=14140])[&&NHX:TOL=14136])chloroperlinae[&&NHX:TOL=14130])chloroperlidae[&&NHX:TOL=13954])[&&NHX:TOL=13951])[&&NHX:TOL=13947])[&&NHX:TOL=13945])[&&NHX:TOL=13934])[&&NHX:TOL=13930])plecoptera[&&NHX:TOL=8245],protoperlaria[&&NHX:EXT=Y:TOL=8246],(caloneura[&&NHX:EXT=Y:TOL=8841],anomalogramma[&&NHX:EXT=Y:TOL=8842],(apsidoneura[&&NHX:EXT=Y:TOL=8844],homaloptila[&&NHX:EXT=Y:TOL=8845])aspidoneuridae[&&NHX:TOL=8843],euthygramma[&&NHX:EXT=Y:TOL=8846],(paleuthygramma[&&NHX:EXT=Y:TOL=8848],paleuthygrammella[&&NHX:EXT=Y:TOL=8849],vilvia[&&NHX:EXT=Y:TOL=8850],vilviopsis[&&NHX:EXT=Y:TOL=8851])paleuthygrammatidae[&&NHX:TOL=8847],(permobiella[&&NHX:EXT=Y:TOL=8853],pseudobiella[&&NHX:EXT=Y:TOL=8854])permobiellidae[&&NHX:TOL=8852],amboneura[&&NHX:EXT=Y:TOL=8855],pleisiogramma[&&NHX:EXT=Y:TOL=8856],synomaloptila[&&NHX:EXT=Y:TOL=8857],caloneurella[&&NHX:EXT=Y:TOL=8858],pruvostiella[&&NHX:EXT=Y:TOL=8859])caloneurodea[&&NHX:EXT=Y:TOL=8247],(((antipaluria[&&NHX:TOL=10701],chromatoclothoda[&&NHX:TOL=10702],clothoda[&&NHX:TOL=10703],cryptoclothoda spinula[&&NHX:TOL=10704])clothodidae[&&NHX:TOL=10734],(((((chelicerca[&&NHX:TOL=10692],dactylocerca[&&NHX:TOL=10693],pelorembia tumidiceps[&&NHX:TOL=10694])[&&NHX:TOL=10691],bulbocerca[&&NHX:TOL=10695])[&&NHX:TOL=10690],anisembia[&&NHX:TOL=10696],mesembia[&&NHX:TOL=10697])[&&NHX:TOL=10689],stenembia[&&NHX:TOL=10698])[&&NHX:TOL=10688],saussurembia[&&NHX:TOL=10699])anisembiidae[&&NHX:TOL=10735],(((metoligotoma[&&NHX:TOL=10739],australembia[&&NHX:TOL=10740])australembiidae[&&NHX:TOL=10738],(microembia rugosifrons[&&NHX:TOL=10742],ptilocerembia[&&NHX:TOL=10743])[&&NHX:TOL=10741],notoligotoma[&&NHX:TOL=10744])[&&NHX:TOL=10737],(((diradius[&&NHX:TOL=10759],paroligembia angolica[&&NHX:TOL=10760],oligembia[&&NHX:TOL=10761],teratembia[&&NHX:TOL=10762])teratembiidae[&&NHX:TOL=10747],(oligotoma[&&NHX:TOL=10749],aposthonia[&&NHX:TOL=10750])[&&NHX:TOL=10748])[&&NHX:TOL=10746],haploembia[&&NHX:TOL=10751])[&&NHX:TOL=10745],(apterembia cercocyrta[&&NHX:TOL=10706],arabembia biarmata[&&NHX:TOL=10707],berlandiella errans[&&NHX:TOL=10708],calamoclostes[&&NHX:TOL=10709],cleomia guareschi[&&NHX:TOL=10710],dihybocercus[&&NHX:TOL=10711],parachirembia brunnea[&&NHX:TOL=10712],parthenembia reclusa[&&NHX:TOL=10713],(embia[&&NHX:TOL=10715],machadoembia[&&NHX:TOL=10716],pseudembia[&&NHX:TOL=10717],dinembia ferruginea[&&NHX:TOL=10718],metembia[&&NHX:TOL=10719],donaconethis[&&NHX:TOL=10720],parembia persica[&&NHX:TOL=10721])[&&NHX:TOL=10714],(embolyntha[&&NHX:TOL=10723],conicercembia tepicensis[&&NHX:TOL=10724],brachypterembia moreliensis[&&NHX:TOL=10725],neorhagadochir[&&NHX:TOL=10726],archembia[&&NHX:TOL=10727],pachylembia[&&NHX:TOL=10728],pararhagadochir[&&NHX:TOL=10729],scelembia[&&NHX:TOL=10730],biguembia[&&NHX:TOL=10731],gibocercus[&&NHX:TOL=10732])[&&NHX:TOL=10722])embiidae[&&NHX:TOL=10752])[&&NHX:TOL=10736])[&&NHX:TOL=10733],embonycha interrupta[&&NHX:TOL=10753],enveja bequaerti[&&NHX:TOL=10754],burmitembia venosa[&&NHX:EXT=Y:TOL=10755],electroembia antiqua[&&NHX:EXT=Y:TOL=10756],lithembia florissantensis[&&NHX:EXT=Y:TOL=10757])embiidina[&&NHX:TOL=8248],(timema[&&NHX:TOL=13635],(aschiphasmatinae[&&NHX:TOL=13626],(agathemera[&&NHX:TOL=13633],(all other euphasmida[&&NHX:TOL=91440],pseudoperla lineata[&&NHX:EXT=Y:TOL=13630],pseudoperla gracilipes[&&NHX:EXT=Y:TOL=13631],electrobaculum gracilis[&&NHX:EXT=Y:TOL=13632])[&&NHX:TOL=91439])[&&NHX:TOL=13628])euphasmida[&&NHX:TOL=13636])phasmida[&&NHX:TOL=8249],((((((((((cyphoderris strepitans[&&NHX:TOL=13309],cyphoderris buckelli[&&NHX:TOL=13310],cyphoderris monstrosa[&&NHX:TOL=13311])[&&NHX:TOL=13308],paracyphoderris erebeus[&&NHX:TOL=13312])haglinae[&&NHX:TOL=13307],prophalangopsis obscura[&&NHX:TOL=13313])haglidae[&&NHX:TOL=13297],((phaneropterinae[&&NHX:TOL=13319],((mecopodinae[&&NHX:TOL=13322],phyllophorinae[&&NHX:TOL=13323])[&&NHX:TOL=13321],pseudophyllinae[&&NHX:TOL=13324])[&&NHX:TOL=13320])[&&NHX:TOL=13318],((((((conocephalinae[&&NHX:TOL=13331],hetrodinae[&&NHX:TOL=13332])[&&NHX:TOL=13330],(tettigoniinae[&&NHX:TOL=13334],bradyporinae[&&NHX:TOL=13335])[&&NHX:TOL=13333])[&&NHX:TOL=13329],saginae[&&NHX:TOL=13336])[&&NHX:TOL=13328],tympanophorinae[&&NHX:TOL=13337])[&&NHX:TOL=13327],(austrosaginae[&&NHX:TOL=13339],listroscelidinae[&&NHX:TOL=13340])[&&NHX:TOL=13338])[&&NHX:TOL=13326],((meconematinae[&&NHX:TOL=13343],lipotactinae[&&NHX:TOL=13344],microtettigoniidae[&&NHX:TOL=13345])[&&NHX:TOL=13342],(zaprochilinae[&&NHX:TOL=13347],phasmodinae[&&NHX:TOL=13348])[&&NHX:TOL=13346])[&&NHX:TOL=13341])[&&NHX:TOL=13325])tettigoniidae[&&NHX:TOL=13298])[&&NHX:TOL=13296],stenopelmatidae[&&NHX:TOL=13299])[&&NHX:TOL=13295],cooloolidae[&&NHX:TOL=13300])[&&NHX:TOL=13294],gryllacrididae[&&NHX:TOL=13301])[&&NHX:TOL=13293],rhaphidophoridae[&&NHX:TOL=13302])tettigonioids[&&NHX:TOL=13292],(schizodactylidae[&&NHX:TOL=13304],true crickets and allies[&&NHX:TOL=13305])[&&NHX:TOL=13303])ensifera[&&NHX:TOL=13315],(((tridactylinae[&&NHX:TOL=13456],dentridactylinae[&&NHX:TOL=13457])tridactylidae[&&NHX:TOL=13455],rhipipterygidae[&&NHX:TOL=13458],cylindrachetidae[&&NHX:TOL=13459])tridactyloidea[&&NHX:TOL=13278],(((sceleminiae[&&NHX:TOL=13446],tetriginae[&&NHX:TOL=13447],amorphopinae[&&NHX:TOL=13448],cladonotinae[&&NHX:TOL=13449],discotettiginae[&&NHX:TOL=13450],tripetalocerinae[&&NHX:TOL=13451],cleostratinae[&&NHX:TOL=13452])tetrigidae[&&NHX:TOL=13445],batrachideidae[&&NHX:TOL=13453])tetrigoidea[&&NHX:TOL=13280],((proscopiidae[&&NHX:TOL=13419],(mastacideidae[&&NHX:TOL=13421],((mnesicleinae[&&NHX:TOL=13397],chininae[&&NHX:TOL=13398],eruciinae[&&NHX:TOL=13399],erianthinae[&&NHX:TOL=13400],prionacanthinae[&&NHX:TOL=13401],chorotypinae[&&NHX:TOL=13402])chorotypidae[&&NHX:TOL=13396],(espagnolinae[&&NHX:TOL=13404],episactinae[&&NHX:TOL=13405])episactidae[&&NHX:TOL=13403])cryptophalli[&&NHX:TOL=13422],((stenoschmidtiinae[&&NHX:TOL=13408],pseudoschmidtiinae[&&NHX:TOL=13409],euschmidtiinae[&&NHX:TOL=13410])euschmidtiidae[&&NHX:TOL=13407],(thericleinae[&&NHX:TOL=13412],chromothericleinae[&&NHX:TOL=13413],loxicephalinae[&&NHX:TOL=13414],afromastacinae[&&NHX:TOL=13415],plagiotryptinae[&&NHX:TOL=13416],bathythericleinae[&&NHX:TOL=13417])thericleidae[&&NHX:TOL=13411])disclerophalli[&&NHX:TOL=13423],((eumastacopinae[&&NHX:TOL=13433],temnomastacinae[&&NHX:TOL=13434],paramastacinae[&&NHX:TOL=13435],pseudomastacinae[&&NHX:TOL=13436],eumastacinae[&&NHX:TOL=13437],parepisactinae[&&NHX:TOL=13438],masynteinae[&&NHX:TOL=13439],morseinae[&&NHX:TOL=13440])eumastacidae[&&NHX:TOL=13432],(biroellinae[&&NHX:TOL=13442],morabinae[&&NHX:TOL=13443])morabidae[&&NHX:TOL=13441])stenophalli[&&NHX:TOL=13424],(heteromastacinae[&&NHX:TOL=13426],malagassinae[&&NHX:TOL=13427],miraculinae[&&NHX:TOL=13428])miraculidae[&&NHX:TOL=13425],teicophryinae[&&NHX:TOL=13429],gomphomastacinae[&&NHX:TOL=13430])eumastacoidea s.s.[&&NHX:TOL=13420])eumastacoidea[&&NHX:TOL=13282],(tanaeoceroidea[&&NHX:TOL=13284],(xyronotidae[&&NHX:TOL=13461],(borneacridinae[&&NHX:TOL=13463],trigonopteryginae[&&NHX:TOL=13464])trigonopterygidae[&&NHX:TOL=13462])trigonopterygoidea[&&NHX:TOL=13285],(pneumoroidea[&&NHX:TOL=13287],(pyrgomorphoidea[&&NHX:TOL=13289],((copiocerinae[&&NHX:TOL=13350],leptysminae[&&NHX:TOL=13351],proctolabinae[&&NHX:TOL=13352],ommatolampinae[&&NHX:TOL=13353],rhytidochrotinae[&&NHX:TOL=13354],pauliniinae[&&NHX:TOL=13355],marellia[&&NHX:TOL=13356],acridinae[&&NHX:TOL=13357],apoboleinae[&&NHX:TOL=13358],calliptaminae[&&NHX:TOL=13359],caryandinae[&&NHX:TOL=13360],catantopinae[&&NHX:TOL=13361],conophyminae[&&NHX:TOL=13362],coptacridinae[&&NHX:TOL=13363],cyrtacanthacridinae[&&NHX:TOL=13364],diexinae[&&NHX:TOL=13365],dericorythinae[&&NHX:TOL=13366],egnatiinae[&&NHX:TOL=13367],eremogryllinae[&&NHX:TOL=13368],euryphyminae[&&NHX:TOL=13369],eyprepocnemidinae[&&NHX:TOL=13370],gomphocerinae[&&NHX:TOL=13371],hemiacridinae[&&NHX:TOL=13372],lithidiinae[&&NHX:TOL=13373],melanoplinae[&&NHX:TOL=13374],oedipodinae[&&NHX:TOL=13375],oxyinae[&&NHX:TOL=13376],spathosterninae[&&NHX:TOL=13377],teratodinae[&&NHX:TOL=13378],tropidopolinae[&&NHX:TOL=13379])acrididae[&&NHX:TOL=13381],(akicerinae[&&NHX:TOL=13391],echinotropinae[&&NHX:TOL=13392],porthetinae[&&NHX:TOL=13393],pamphaginae[&&NHX:TOL=13394])pamphagidae[&&NHX:TOL=13382],lathiceridae[&&NHX:TOL=13383],charilaidae[&&NHX:TOL=13384],romaleidae[&&NHX:TOL=13385],ommexechidae[&&NHX:TOL=13386],tristiridae[&&NHX:TOL=13387],lentulidae[&&NHX:TOL=13388],pyrgacrididae[&&NHX:TOL=13389])acridoidea[&&NHX:TOL=13290])[&&NHX:TOL=13288])[&&NHX:TOL=13286])[&&NHX:TOL=13283])[&&NHX:TOL=13281])[&&NHX:TOL=13279])caelifera[&&NHX:TOL=13316])orthoptera[&&NHX:TOL=8250],(tanzaniophasma subsolana[&&NHX:TOL=25778],(mantophasma zephyra[&&NHX:TOL=12958],sclerophasma paresisensis[&&NHX:TOL=25779])mantophasmatidae[&&NHX:TOL=25787],((((austrophasma caledonensis[&&NHX:TOL=25780],austrophasma gansbaaiensis[&&NHX:TOL=25781])[&&NHX:TOL=25793],austrophasma rawsonvillensis[&&NHX:TOL=25782])[&&NHX:TOL=25790],lobophasma redelinghuysensis[&&NHX:TOL=25783])[&&NHX:TOL=25794],hemilobophasma montaguensis[&&NHX:TOL=25784],(karoophasma botterkloofensis[&&NHX:TOL=25786],karoophasma biedouwensis[&&NHX:TOL=25785])[&&NHX:TOL=25792],namaquaphasma ookiepensis[&&NHX:TOL=25788])austrophasmatidae[&&NHX:TOL=25791],raptophasma kerneggeri[&&NHX:EXT=Y:TOL=12962],praedatophasma maraisi[&&NHX:TOL=12961],tyrannophasma gladiator[&&NHX:TOL=25789],adicophasma spinosa[&&NHX:EXT=Y:TOL=26120])mantophasmatodea[&&NHX:TOL=8251],(xenozorotypus burmiticus[&&NHX:EXT=Y:TOL=14687],((zorotypus zimmermani[&&NHX:TOL=14686],zorotypus vinsoni[&&NHX:TOL=14685],zorotypus barberi[&&NHX:TOL=14651],zorotypus brasiliensis[&&NHX:TOL=14652],zorotypus buxtoni[&&NHX:TOL=14653],zorotypus caudelli[&&NHX:TOL=14654],(zorotypus ceylonicus[&&NHX:TOL=14655],zorotypus gurneyi[&&NHX:TOL=14662],zorotypus hamiltoni[&&NHX:TOL=14663],zorotypus palaeus[&&NHX:EXT=Y:TOL=14677],zorotypus weidneri[&&NHX:TOL=14684],zorotypus hubbardi[&&NHX:TOL=14664],zorotypus javanicus[&&NHX:TOL=14666])[&&NHX:TOL=27789],zorotypus snyderi[&&NHX:TOL=14682],zorotypus sinensis[&&NHX:TOL=14681],zorotypus swezeyi[&&NHX:TOL=14683],zorotypus silvestrii[&&NHX:TOL=14680],zorotypus shannoni[&&NHX:TOL=14679],zorotypus philippinensis[&&NHX:TOL=14678],zorotypus mexicanus[&&NHX:TOL=14673],zorotypus neotropicus[&&NHX:TOL=14675],zorotypus manni[&&NHX:TOL=14671],zorotypus medoensis[&&NHX:TOL=14672],(zorotypus longicercatus[&&NHX:TOL=14670],zorotypus newi[&&NHX:TOL=14676])[&&NHX:TOL=27788],zorotypus leleupi[&&NHX:TOL=14669],zorotypus lawrencei[&&NHX:TOL=14668],zorotypus juninensis[&&NHX:TOL=14667],zorotypus huxleyi[&&NHX:TOL=14665],zorotypus guineensis[&&NHX:TOL=14661],zorotypus goeleti[&&NHX:EXT=Y:TOL=14660],zorotypus delamarei[&&NHX:TOL=14659],zorotypus cramptoni[&&NHX:TOL=14657],zorotypus congensis[&&NHX:TOL=14656])zorotypus zorotypus[&&NHX:TOL=27787],(zorotypus acanthothorax[&&NHX:EXT=Y:TOL=14650],zorotypus nascimbenei[&&NHX:EXT=Y:TOL=14674])zorotypus octozoros[&&NHX:EXT=Y:TOL=27786],zorotypus cretatus[&&NHX:EXT=Y:TOL=14658])zorotypus s.l.[&&NHX:TOL=27785])zoraptera[&&NHX:TOL=8252],((((((acroporoblatta[&&NHX:TOL=8587],anisolampra[&&NHX:TOL=8588],apsidopis[&&NHX:TOL=8589],ataxigamia[&&NHX:TOL=8590],audreia[&&NHX:TOL=8591],calolamprodes[&&NHX:TOL=8592],colapteroblatta[&&NHX:TOL=8593],compsolampra[&&NHX:TOL=8594],cyrtonotula[&&NHX:TOL=8595],derocardia[&&NHX:TOL=8596],dryadoblatta[&&NHX:TOL=8597],elfridaia[&&NHX:TOL=8598],epilampra[&&NHX:TOL=8599],galiblatta[&&NHX:TOL=8600],haanina[&&NHX:TOL=8601],homalopteryx[&&NHX:TOL=8602],litopeltis[&&NHX:TOL=8603],molytria[&&NHX:TOL=8604],morphna[&&NHX:TOL=8605],nauclidas[&&NHX:TOL=8606],notolampra[&&NHX:TOL=8607],opisthoplatia[&&NHX:TOL=8608],phlebonotus[&&NHX:TOL=8609],phoraspis[&&NHX:TOL=8610],pinaconota[&&NHX:TOL=8611],placoblatta[&&NHX:TOL=8612],poroblatta[&&NHX:TOL=8613],pseudophoraspis[&&NHX:TOL=8614],pseudoplatia[&&NHX:TOL=8615],rhabdoblatta[&&NHX:TOL=8616],rhicnoda[&&NHX:TOL=8617],stictolampra[&&NHX:TOL=8618],stictomorphna[&&NHX:TOL=8619],thorax[&&NHX:TOL=8620],(aptera[&&NHX:TOL=8622],blepharodera[&&NHX:TOL=8623],miroblatta[&&NHX:TOL=8624],ylangella[&&NHX:TOL=8625])[&&NHX:TOL=8621])epilamprinae[&&NHX:TOL=8303],(aeluropoda[&&NHX:TOL=8658],ateloblatta[&&NHX:TOL=8659],coleoblatta[&&NHX:TOL=8660],elliptorhina[&&NHX:TOL=57754],griffiniella[&&NHX:TOL=8661],gromphadorhina[&&NHX:TOL=8662],heminauphoeta[&&NHX:TOL=8663],henschoutedenia[&&NHX:TOL=8664],jagrehnia[&&NHX:TOL=8665],nauphoeta[&&NHX:TOL=8667],oxyhaloa[&&NHX:TOL=8668],pelloblatta[&&NHX:TOL=8669],princisia[&&NHX:TOL=57755],pronauphoeta[&&NHX:TOL=8670],rhypharobia[&&NHX:TOL=8666],simandoa[&&NHX:TOL=57756])oxyhaloinae[&&NHX:TOL=8304],(panchlora[&&NHX:TOL=8672],phortioecoides[&&NHX:TOL=8673],proscratea[&&NHX:TOL=8674])panchlorinae[&&NHX:TOL=8305],(ancaudellia[&&NHX:TOL=8676],caeparia[&&NHX:TOL=8677],dicellonotus[&&NHX:TOL=8678],dolichosphaeria[&&NHX:TOL=8679],hemipanesthia[&&NHX:TOL=8680],heteroblatta[&&NHX:TOL=8681],geoscapheus[&&NHX:TOL=8682],macropanesthia[&&NHX:TOL=8683],microdina[&&NHX:TOL=8684],miopanesthia[&&NHX:TOL=8685],mylacrina[&&NHX:TOL=8686],neogeoscaphus[&&NHX:TOL=8687],panesthia[&&NHX:TOL=8688],parapanesthia[&&NHX:TOL=8689],salganea[&&NHX:TOL=8690])panesthiinae[&&NHX:TOL=8306],(bantua[&&NHX:TOL=8692],compsagis[&&NHX:TOL=8693],cyrtotria[&&NHX:TOL=8694],derocalymma[&&NHX:TOL=8695],ellipsica[&&NHX:TOL=8696],elliptoblatta[&&NHX:TOL=8697],gymnonyx[&&NHX:TOL=8698],hostilia[&&NHX:TOL=8699],laxta[&&NHX:TOL=8700],neolaxta[&&NHX:TOL=8701],paranauphoeta[&&NHX:TOL=8702],perisphaeria[&&NHX:TOL=8703],perisphaerus[&&NHX:TOL=8704],pilema[&&NHX:TOL=8705],platysilpha[&&NHX:TOL=8706],poeciloblatta[&&NHX:TOL=8707],pronaonota[&&NHX:TOL=8708],pseudoglomeris[&&NHX:TOL=8709],trichoblatta[&&NHX:TOL=8710],zuluia[&&NHX:TOL=8711])perisphaeriinae[&&NHX:TOL=8307],(pycnoscelus[&&NHX:TOL=8819],stilpnoblatta[&&NHX:TOL=8820])pycnoscelinae[&&NHX:TOL=8308],(((archimandrita[&&NHX:TOL=8318],aspiduchus[&&NHX:TOL=8319],bionoblatta[&&NHX:TOL=8320],blaberus[&&NHX:TOL=8321],blaptica[&&NHX:TOL=8322],brachycola[&&NHX:TOL=8323],byrsotria[&&NHX:TOL=8324],eublaberus[&&NHX:TOL=8325],hemiblabera[&&NHX:TOL=8326],hiereoblatta[&&NHX:TOL=8327],hormetica[&&NHX:TOL=8328],hyporhicnoda[&&NHX:TOL=8329],mioblatta[&&NHX:TOL=8330],monachoda[&&NHX:TOL=8331],monastria[&&NHX:TOL=8332],neorhicnoda[&&NHX:TOL=8333],paradicta[&&NHX:TOL=8334],parahormetica[&&NHX:TOL=8335],petasodes[&&NHX:TOL=8336],phoetalia[&&NHX:TOL=8337],(achroblatta[&&NHX:TOL=8339],anchoblatta[&&NHX:TOL=8340],antioquita[&&NHX:TOL=8341],cacoblatta[&&NHX:TOL=8342],capucinella[&&NHX:TOL=8343],cariacasia[&&NHX:TOL=8344],glomerexis[&&NHX:TOL=8345],glyptopeltis[&&NHX:TOL=8346],kemneria[&&NHX:TOL=8347],mesoblaberus[&&NHX:TOL=8348],minablatta[&&NHX:TOL=8349],oxycercus[&&NHX:TOL=8350],pseudogyna[&&NHX:TOL=8351],sibylloblatta[&&NHX:TOL=8352],styphon[&&NHX:TOL=8353])[&&NHX:TOL=8338])blaberinae[&&NHX:TOL=8298],((thanatophyllum[&&NHX:TOL=8836],(parasphaeria[&&NHX:TOL=8839],schultesia[&&NHX:TOL=8838])[&&NHX:TOL=8837])[&&NHX:TOL=8835],((tribonium[&&NHX:TOL=8824],(zetobora[&&NHX:TOL=8826],zetoborella[&&NHX:TOL=8827])[&&NHX:TOL=8825])[&&NHX:TOL=8823],(phortioeca[&&NHX:TOL=8829],(schizopilia[&&NHX:TOL=8831],(capucina[&&NHX:TOL=8833],lanxoblatta[&&NHX:TOL=8834])[&&NHX:TOL=8832])[&&NHX:TOL=8830])[&&NHX:TOL=8828])[&&NHX:TOL=8822])zetoborinae[&&NHX:TOL=8299])[&&NHX:TOL=8297],((calolampra[&&NHX:TOL=8573],diploptera[&&NHX:TOL=8574])diplopterinae[&&NHX:TOL=8302],((pseudocalolampra[&&NHX:TOL=8634],((alloblatta[&&NHX:TOL=8630],gyna[&&NHX:TOL=8629])[&&NHX:TOL=8628],(paraprincisaria[&&NHX:TOL=8632],princisaria[&&NHX:TOL=8633])[&&NHX:TOL=8631])[&&NHX:TOL=8627])[&&NHX:TOL=8626],evea[&&NHX:TOL=8635],paraplecta[&&NHX:TOL=8636],progonogamia[&&NHX:TOL=8637],thliptoblatta[&&NHX:TOL=8638])gyninae[&&NHX:TOL=8301])[&&NHX:TOL=8300])[&&NHX:TOL=8296])[&&NHX:TOL=8295],apotrogia[&&NHX:TOL=8309],diplopoterina[&&NHX:TOL=8310],eustegasta[&&NHX:TOL=8311],gynopeltis[&&NHX:TOL=8312],hedaia[&&NHX:TOL=8313],isoniscus[&&NHX:TOL=8314],phenacisma[&&NHX:TOL=8315],africalolampra[&&NHX:TOL=8316])blaberidae[&&NHX:TOL=8288],((anaplecta[&&NHX:TOL=8290],anaplectella[&&NHX:TOL=8291],anaplectoidea[&&NHX:TOL=8292],malaccina[&&NHX:TOL=8293],maraca[&&NHX:TOL=8294])anaplectinae[&&NHX:TOL=8355],(agmoblatta[&&NHX:TOL=8361],akaniblatta[&&NHX:TOL=8362],alsteinia[&&NHX:TOL=8363],anallacta[&&NHX:TOL=8364],aneurinita[&&NHX:TOL=8365],anisopygia[&&NHX:TOL=8366],antitheton[&&NHX:TOL=8367],aphlebiella[&&NHX:TOL=8368],arublatta[&&NHX:TOL=8369],aruistra[&&NHX:TOL=8370],aseucina[&&NHX:TOL=8371],astylella[&&NHX:TOL=8372],astyloblatta[&&NHX:TOL=8373],beybienkoa[&&NHX:TOL=8374],blattella[&&NHX:TOL=8375],blattellina[&&NHX:TOL=8376],caboverdea[&&NHX:TOL=8377],caffroblatta[&&NHX:TOL=8378],cahita[&&NHX:TOL=8379],calhypnorna[&&NHX:TOL=8380],caloblatta[&&NHX:TOL=8381],carbrunneria[&&NHX:TOL=8382],ceratinoptera[&&NHX:TOL=8383],ceuthobia[&&NHX:TOL=8384],ceuthobiella[&&NHX:TOL=8385],chorisia[&&NHX:TOL=8386],chrastoblatta[&&NHX:TOL=8387],chromatonotus[&&NHX:TOL=8388],compsosilpha[&&NHX:TOL=8389],dasyblatta[&&NHX:TOL=8390],dendroblatta[&&NHX:TOL=8391],desmosia[&&NHX:TOL=8392],dewittea[&&NHX:TOL=8393],dictyoblattella[&&NHX:TOL=8394],dipteretrum[&&NHX:TOL=8395],distichopis[&&NHX:TOL=8396],disymploce[&&NHX:TOL=8397],dyakina[&&NHX:TOL=8398],dyakinodes[&&NHX:TOL=8399],eowilsonia[&&NHX:TOL=8400],episymploce[&&NHX:TOL=8401],escala[&&NHX:TOL=8402],euandroblatta[&&NHX:TOL=8403],eublattella[&&NHX:TOL=8404],eudromiella[&&NHX:TOL=8405],euhanitschia[&&NHX:TOL=8406],euhebardula[&&NHX:TOL=8407],euhypnorna[&&NHX:TOL=8408],eulissosoma[&&NHX:TOL=8409],euloboptera[&&NHX:TOL=8410],eurylestes[&&NHX:TOL=8411],franwalkeria[&&NHX:TOL=8412],gislenia[&&NHX:TOL=8413],hanitschella[&&NHX:TOL=8414],hanitschia[&&NHX:TOL=8415],haplosymploce[&&NHX:TOL=8416],helgaia[&&NHX:TOL=8417],hemipterisca[&&NHX:TOL=8418],hemithyrsocera[&&NHX:TOL=8419],hensaussurea[&&NHX:TOL=8420],hololeptoblatta[&&NHX:TOL=8421],hoplophoropyga[&&NHX:TOL=8422],hypnorna[&&NHX:TOL=8423],hypnornoides[&&NHX:TOL=8424],ignabolivaria[&&NHX:TOL=8425],incoblatta[&&NHX:TOL=8426],ischnoptera[&&NHX:TOL=8427],isoldaia[&&NHX:TOL=8428],jacobsonina[&&NHX:TOL=8429],johnrehnia[&&NHX:TOL=8430],jotepperia[&&NHX:TOL=8431],lanta[&&NHX:TOL=8432],leptothyrsocera[&&NHX:TOL=8433],litoblatta[&&NHX:TOL=8434],lobodromia[&&NHX:TOL=8435],loboptera[&&NHX:TOL=8436],lobopterella[&&NHX:TOL=8437],lobopteromorpha[&&NHX:TOL=8438],lophometopum[&&NHX:TOL=8439],macrophyllodromia[&&NHX:TOL=8440],mallotoblatta[&&NHX:TOL=8441],maretina[&&NHX:TOL=8442],maretiola[&&NHX:TOL=8443],mayottella[&&NHX:TOL=8444],microblatta[&&NHX:TOL=8445],miriamrothschildia[&&NHX:TOL=8446],molestella[&&NHX:TOL=8447],moluchia[&&NHX:TOL=8448],namablatta[&&NHX:TOL=8449],nelipophygus[&&NHX:TOL=8450],neoleptoblatta[&&NHX:TOL=8451],neoloboptera[&&NHX:TOL=8452],neotemnopteryx[&&NHX:TOL=8453],nesomylachris[&&NHX:TOL=8454],nicuesa[&&NHX:TOL=8455],nimbablatta[&&NHX:TOL=8456],nondewittea[&&NHX:TOL=8457],nothoblatta[&&NHX:TOL=8458],nymphodromia[&&NHX:TOL=8459],onycholobus[&&NHX:TOL=8460],operculea[&&NHX:TOL=8461],ornatiblatta[&&NHX:TOL=8462],pachneblatta[&&NHX:TOL=8463],papuablatta[&&NHX:TOL=8464],parajacobsonina[&&NHX:TOL=8465],paraloboptera[&&NHX:TOL=8466],parascalida[&&NHX:TOL=8467],parasigmoidella[&&NHX:TOL=8468],parasymploce[&&NHX:TOL=8469],paratemnopteryx[&&NHX:TOL=8470],parcoblatta[&&NHX:TOL=8471],parellipsidion[&&NHX:TOL=8472],pholeosilpha[&&NHX:TOL=8473],phymatosilpha[&&NHX:TOL=8474],pseudoanaplectinia[&&NHX:TOL=8475],pseudoceratinoptera[&&NHX:TOL=8476],pseudectobia[&&NHX:TOL=8477],pseudomops[&&NHX:TOL=8478],pseudosigmella[&&NHX:TOL=8479],pseudosymploce[&&NHX:TOL=8480],pseudothyrsocera[&&NHX:TOL=8481],rhytidometopum[&&NHX:TOL=8482],richanitschia[&&NHX:TOL=8483],robshelfordia[&&NHX:TOL=8484],rudebeckia[&&NHX:TOL=8485],scalida[&&NHX:TOL=8486],sciablatta[&&NHX:TOL=8487],shawella[&&NHX:TOL=8488],sigmella[&&NHX:TOL=8489],sinablatta[&&NHX:TOL=8490],sliferia[&&NHX:TOL=8491],squamoptera[&&NHX:TOL=8492],stayella[&&NHX:TOL=8493],symploce[&&NHX:TOL=8494],symplocodes[&&NHX:TOL=8495],tairella[&&NHX:TOL=8496],tartaroblatta[&&NHX:TOL=8497],temnopteryx[&&NHX:TOL=8498],termitoblatta[&&NHX:TOL=8499],trogloblattella[&&NHX:TOL=8500],xestoblatta[&&NHX:TOL=8501],xosablatta[&&NHX:TOL=8502],xosaia[&&NHX:TOL=8503])blattellinae[&&NHX:TOL=8356],(africablatta[&&NHX:TOL=8576],aristiger[&&NHX:TOL=8577],burchellia[&&NHX:TOL=8578],choristima[&&NHX:TOL=8579],ectobius[&&NHX:TOL=8580],eutheganopteryx[&&NHX:TOL=8581],miothyrsocera[&&NHX:TOL=8582],phyllodromica[&&NHX:TOL=8583],piroblatta[&&NHX:TOL=8584],theganopteryx[&&NHX:TOL=8585])ectobiinae[&&NHX:TOL=8357],(eunyctibora[&&NHX:TOL=8649],eushelfordia[&&NHX:TOL=8650],megaloblatta[&&NHX:TOL=8651],muzoa[&&NHX:TOL=8652],nyctibora[&&NHX:TOL=8653],paramuzoa[&&NHX:TOL=8654],paratropes[&&NHX:TOL=8655],pseudischnoptera[&&NHX:TOL=8656])nyctiborinae[&&NHX:TOL=8358],(afrobalta[&&NHX:TOL=8760],afroneura[&&NHX:TOL=8761],allacta[&&NHX:TOL=8762],amazonina[&&NHX:TOL=8763],anareolaria[&&NHX:TOL=8764],apteroblatta[&&NHX:TOL=8765],arawakina[&&NHX:TOL=8766],areolaria[&&NHX:TOL=8767],asemoblattana[&&NHX:TOL=8768],balta[&&NHX:TOL=8769],cariblatta[&&NHX:TOL=8770],cariblattoides[&&NHX:TOL=8771],chorisoblatta[&&NHX:TOL=8772],chorisoneura[&&NHX:TOL=8773],chorisoneurodes[&&NHX:TOL=8774],chorisoserrata[&&NHX:TOL=8775],choristimodes[&&NHX:TOL=8776],delosia[&&NHX:TOL=8777],doradoblatta[&&NHX:TOL=8778],duryodana[&&NHX:TOL=8779],ectoneura[&&NHX:TOL=8780],ellipsidion[&&NHX:TOL=8781],euphyllodromia[&&NHX:TOL=8782],euthlastoblatta[&&NHX:TOL=8783],hemipterota[&&NHX:TOL=8784],imblattella[&&NHX:TOL=8785],latiblattella[&&NHX:TOL=8786],leuropeltis[&&NHX:TOL=8787],liosilpha[&&NHX:TOL=8788],liosilphoidea[&&NHX:TOL=8789],lophoblatta[&&NHX:TOL=8790],lupparia[&&NHX:TOL=8791],margattea[&&NHX:TOL=8792],margatteoidea[&&NHX:TOL=8793],margattina[&&NHX:TOL=8794],matabelina[&&NHX:TOL=8795],mediastinia[&&NHX:TOL=8796],megamareta[&&NHX:TOL=8797],melyroidea[&&NHX:TOL=8798],nahublattella[&&NHX:TOL=8799],neoblattella[&&NHX:TOL=8800],nisibis[&&NHX:TOL=8801],oulopteryx[&&NHX:TOL=8802],pachnepteryx[&&NHX:TOL=8803],phidon[&&NHX:TOL=8804],plectoptera[&&NHX:TOL=8805],prosoplecta[&&NHX:TOL=8806],pseudobalta[&&NHX:TOL=8807],pseudophyllodromia[&&NHX:TOL=8808],riatia[&&NHX:TOL=8809],shelfordina[&&NHX:TOL=8810],sorineuchora[&&NHX:TOL=8811],stenectoneura[&&NHX:TOL=8812],sundablatta[&&NHX:TOL=8813],supella[&&NHX:TOL=8814],sutteriana[&&NHX:TOL=8815],tomeisneria[&&NHX:TOL=8816],trioblattella[&&NHX:TOL=8817])pseudophyllodromiinae[&&NHX:TOL=8359])blattellidae[&&NHX:TOL=8287],(alluaudellina[&&NHX:TOL=8640],cardacus[&&NHX:TOL=8641],cardacopsis[&&NHX:TOL=8642],metanocticola[&&NHX:TOL=8643],nocticola[&&NHX:TOL=8644],spelaeoblatta[&&NHX:TOL=8645],typhloblatta[&&NHX:TOL=8646],typhloblattodes[&&NHX:TOL=8647])nocticolidae[&&NHX:TOL=8286])[&&NHX:TOL=8285],((anamesia[&&NHX:TOL=8505],angustonicus[&&NHX:TOL=8506],apterisca[&&NHX:TOL=8507],archiblatta[&&NHX:TOL=8508],blatta[&&NHX:TOL=8509],brinckella[&&NHX:TOL=8510],cartoblatta[&&NHX:TOL=8511],catara[&&NHX:TOL=8512],celatoblatta[&&NHX:TOL=8513],celeriblattina[&&NHX:TOL=8514],cosmozosteria[&&NHX:TOL=8515],cutilia[&&NHX:TOL=8516],deropeltis[&&NHX:TOL=8517],desmozosteria[&&NHX:TOL=8518],distylopyga[&&NHX:TOL=8519],dorylaea[&&NHX:TOL=8520],drymaplaneta[&&NHX:TOL=8521],duchailluia[&&NHX:TOL=8522],eppertia[&&NHX:TOL=8523],eroblatta[&&NHX:TOL=8524],eumethana[&&NHX:TOL=8525],eurycotis[&&NHX:TOL=8526],euzosteria[&&NHX:TOL=8527],hebardina[&&NHX:TOL=8528],henicotyle[&&NHX:TOL=8529],homalosilpha[&&NHX:TOL=8530],lamproblatta[&&NHX:TOL=8531],lamproglandifera[&&NHX:TOL=57761],lauraesilpha[&&NHX:TOL=8532],macrocerca[&&NHX:TOL=8533],maoriblatta[&&NHX:TOL=8534],melanozosteria[&&NHX:TOL=8535],methana[&&NHX:TOL=8536],mimosilpha[&&NHX:TOL=8537],miostylopyga[&&NHX:TOL=8538],neostylopyga[&&NHX:TOL=8539],pallidionicus[&&NHX:TOL=8540],paramethana[&&NHX:TOL=8541],pellucidonicus[&&NHX:TOL=8542],pelmatosilpha[&&NHX:TOL=8543],periplaneta[&&NHX:TOL=8544],platyzosteria[&&NHX:TOL=8545],polyzosteria[&&NHX:TOL=8546],protagonista[&&NHX:TOL=8547],pseudoderopeltis[&&NHX:TOL=8548],pseudozosteria[&&NHX:TOL=8549],punctulonicus[&&NHX:TOL=8550],rothisilpha[&&NHX:TOL=8551],scabina[&&NHX:TOL=8552],shelfordella[&&NHX:TOL=8553],temnelytra[&&NHX:TOL=8554],thyrsocera[&&NHX:TOL=8555],tryonicus[&&NHX:TOL=8556],zonioploca[&&NHX:TOL=8557])blattidae[&&NHX:TOL=8282],(cryptocercus kyebangensis[&&NHX:TOL=8571],cryptocercus matilei[&&NHX:TOL=8569],cryptocercus primarius[&&NHX:TOL=8570],cryptocercus relictus[&&NHX:TOL=8568],(cryptocercus clevelandi[&&NHX:TOL=8567],(cryptocercus punctulatus[&&NHX:TOL=8561],(cryptocercus wrighti[&&NHX:TOL=8563],(cryptocercus darwini[&&NHX:TOL=8565],cryptocercus garciai[&&NHX:TOL=8566])[&&NHX:TOL=8564])[&&NHX:TOL=8562])[&&NHX:TOL=8560])[&&NHX:TOL=8559])cryptocercus[&&NHX:TOL=8283],(anacompsa[&&NHX:TOL=8713],anisogamia[&&NHX:TOL=8714],arenivaga[&&NHX:TOL=8715],attaphila[&&NHX:TOL=8716],atticola[&&NHX:TOL=8717],austropolyphaga[&&NHX:TOL=8718],biolleya[&&NHX:TOL=8719],buboblatta[&&NHX:TOL=8720],bucolion[&&NHX:TOL=8721],compsodes[&&NHX:TOL=8722],ctenoneura[&&NHX:TOL=8723],eremoblatta[&&NHX:TOL=8724],ergaula[&&NHX:TOL=8725],eucorydia[&&NHX:TOL=8726],eupolyphaga[&&NHX:TOL=8727],euthyrrhapha[&&NHX:TOL=8728],hemelytroblatta[&&NHX:TOL=8729],heterogamia[&&NHX:TOL=8730],heterogamisca[&&NHX:TOL=8731],heterogamodes[&&NHX:TOL=8732],holocompsa[&&NHX:TOL=8733],homeogamia[&&NHX:TOL=8734],homopteroidea[&&NHX:TOL=8735],hypercompsa[&&NHX:TOL=8736],ipisoma[&&NHX:TOL=8737],ipolatta[&&NHX:TOL=8738],latindia[&&NHX:TOL=8739],leiopteroblatta[&&NHX:TOL=8740],melestora[&&NHX:TOL=8741],mononychoblatta[&&NHX:TOL=8742],myrmeblattina[&&NHX:TOL=8743],myrmecoblatta[&&NHX:TOL=8744],nymphrytria[&&NHX:TOL=8745],paralatindia[&&NHX:TOL=8746],pholadoblatta[&&NHX:TOL=8747],phorticolea[&&NHX:TOL=8748],polyphaga[&&NHX:TOL=8749],polyphagina[&&NHX:TOL=8750],polyphagoides[&&NHX:TOL=8751],psammoblatta[&&NHX:TOL=8752],simblerastes[&&NHX:TOL=8753],sphecophila[&&NHX:TOL=8754],stenoblatta[&&NHX:TOL=8755],therea[&&NHX:TOL=8756],tivia[&&NHX:TOL=8757],zetha[&&NHX:TOL=8758])polyphagidae[&&NHX:TOL=8284])[&&NHX:TOL=8281],(cameloblatta[&&NHX:EXT=Y:TOL=57758],raphidiomima[&&NHX:EXT=Y:TOL=57759],raphidiomimula burmitica[&&NHX:EXT=Y:TOL=57760])raphidiomimidae[&&NHX:EXT=Y:TOL=57757])blattaria[&&NHX:TOL=8214],(((mastotermes darwiniensis[&&NHX:TOL=11429],mastotermes anglicus[&&NHX:EXT=Y:TOL=11437],mastotermes bournemouthensis[&&NHX:EXT=Y:TOL=11439],mastotermes croaticus[&&NHX:EXT=Y:TOL=11432],mastotermes electrodominicus[&&NHX:EXT=Y:TOL=11433],mastotermes electromexicus[&&NHX:EXT=Y:TOL=11434],mastotermes gallica[&&NHX:EXT=Y:TOL=11438],mastotermes haidingeri[&&NHX:EXT=Y:TOL=11431],mastotermes heerii[&&NHX:EXT=Y:TOL=11436],mastotermes minor[&&NHX:EXT=Y:TOL=11430],mastotermes picardi[&&NHX:EXT=Y:TOL=11435],aff. mastotermes sarthensis[&&NHX:EXT=Y:TOL=11440])mastotermes[&&NHX:TOL=52741],(blattotermes massiliensis[&&NHX:EXT=Y:TOL=11446],blattotermes neoxenus[&&NHX:EXT=Y:TOL=11447],blattotermes wheeleri[&&NHX:EXT=Y:TOL=11448])blattotermes[&&NHX:EXT=Y:TOL=52742],mastotermites stuttgartensis[&&NHX:EXT=Y:TOL=11441],(miotermes insignis[&&NHX:EXT=Y:TOL=11442],miotermes procerus[&&NHX:EXT=Y:TOL=11445],miotermes randeckensis[&&NHX:EXT=Y:TOL=11444],miotermes spectabilis[&&NHX:EXT=Y:TOL=11443])miotermes[&&NHX:EXT=Y:TOL=52743],spargotermes costalimai[&&NHX:EXT=Y:TOL=11449])mastotermitidae[&&NHX:TOL=11383],((anacanthotermes[&&NHX:TOL=11366],hodotermes[&&NHX:TOL=11364],microhodotermes[&&NHX:TOL=11365],carinatermes nascimbeni[&&NHX:EXT=Y:TOL=52745],jitermes[&&NHX:EXT=Y:TOL=11369],luteitermes prisca[&&NHX:EXT=Y:TOL=52746],(meiatermes araripena[&&NHX:EXT=Y:TOL=11368],meiatermes bertrani[&&NHX:EXT=Y:TOL=11367])meiatermes[&&NHX:EXT=Y:TOL=52744],yanjingatermes[&&NHX:EXT=Y:TOL=11370],yongdingia[&&NHX:EXT=Y:TOL=11371])hodotermitidae[&&NHX:TOL=11382],(allotermes[&&NHX:TOL=11385],bicornitermes[&&NHX:TOL=11386],bifiditermes[&&NHX:TOL=11387],calcaritermes[&&NHX:TOL=11388],ceratokalotermes[&&NHX:TOL=11389],comatermes[&&NHX:TOL=11390],cryptotermes[&&NHX:TOL=11391],epicalotermes[&&NHX:TOL=11392],eucryptotermes[&&NHX:TOL=11393],glyptotermes[&&NHX:TOL=11394],incisitermes[&&NHX:TOL=11395],kalotermes[&&NHX:TOL=11396],marginitermes[&&NHX:TOL=11397],neotermes[&&NHX:TOL=11398],paraneotermes[&&NHX:TOL=11399],postelectrotermes[&&NHX:TOL=11400],procryptotermes[&&NHX:TOL=11401],proneotermes[&&NHX:TOL=11402],pterotermes[&&NHX:TOL=11403],rugitermes[&&NHX:TOL=11404],tauritermes[&&NHX:TOL=11405],electrotermes affinis[&&NHX:EXT=Y:TOL=11411],eotermes grandeava[&&NHX:EXT=Y:TOL=11406],(proelectrotermes berendti[&&NHX:EXT=Y:TOL=11408],proelectrotermes fodinae[&&NHX:EXT=Y:TOL=11409],proelectrotermes roseni[&&NHX:EXT=Y:TOL=11410])proelectrotermes[&&NHX:EXT=Y:TOL=52747],prokalotermes hageni[&&NHX:EXT=Y:TOL=11407],oligokalotermes fischeri[&&NHX:EXT=Y:TOL=11412])kalotermitidae[&&NHX:TOL=11379],(archotermopsis[&&NHX:TOL=11667],hodotermopsis[&&NHX:TOL=11668],porotermes[&&NHX:TOL=11669],stolotermes[&&NHX:TOL=11670],zootermopsis[&&NHX:TOL=11671],asiatermes[&&NHX:EXT=Y:TOL=11679],cretatermes carpenteri[&&NHX:EXT=Y:TOL=11674],huaxiatermes[&&NHX:EXT=Y:TOL=11680],lutetiatermes prisca[&&NHX:EXT=Y:TOL=11676],mesotermopsis[&&NHX:EXT=Y:TOL=11681],paleotermopsis oligocenicus[&&NHX:EXT=Y:TOL=11672],parotermes insignis[&&NHX:EXT=Y:TOL=11673],(valditermes acutipennis[&&NHX:EXT=Y:TOL=11677],valditermes brenanae[&&NHX:EXT=Y:TOL=11678])valditermes[&&NHX:EXT=Y:TOL=52748])termopsidae[&&NHX:TOL=11380],(ulmeriella aquisextana[&&NHX:EXT=Y:TOL=11692],ulmeriella bauckhorni[&&NHX:EXT=Y:TOL=11691],ulmeriella cockerelli[&&NHX:EXT=Y:TOL=11690],ulmeriella latahensis[&&NHX:EXT=Y:TOL=11686],ulmeriella martynovi[&&NHX:EXT=Y:TOL=11689],ulmeriella pliocenica[&&NHX:EXT=Y:TOL=11685],ulmeriella rubiensis[&&NHX:EXT=Y:TOL=11693],ulmeriella shizukuishiensis[&&NHX:EXT=Y:TOL=11688],ulmeriella straussi[&&NHX:EXT=Y:TOL=11683],ulmeriella uemurai[&&NHX:EXT=Y:TOL=11687],ulmeriella willershausensis[&&NHX:EXT=Y:TOL=11684])ulmeriella[&&NHX:EXT=Y:TOL=11381],(gnathamitermes magnoculus[&&NHX:EXT=Y:TOL=11376],(acorhinotermes[&&NHX:TOL=11548],coptotermes[&&NHX:TOL=11542],dolichorhinotermes[&&NHX:TOL=11549],heterotermes[&&NHX:TOL=11543],macrorhinotermes[&&NHX:TOL=11550],parrhinotermes[&&NHX:TOL=11551],prorhinotermes[&&NHX:TOL=11552],psammotermes[&&NHX:TOL=11547],reticulitermes[&&NHX:TOL=11544],rhinotermes[&&NHX:TOL=11553],schedorhinotermes[&&NHX:TOL=11554],stylotermes[&&NHX:TOL=11555],termitogeton[&&NHX:TOL=11557],tsaitermes[&&NHX:TOL=11545],archeorhinotermes rossi[&&NHX:EXT=Y:TOL=11558],parastylotermes[&&NHX:EXT=Y:TOL=11556])rhinotermitidae[&&NHX:TOL=11377],(glossotermes[&&NHX:TOL=11546],serritermes serrifer[&&NHX:TOL=11378])serritermitidae[&&NHX:TOL=57745],((acholotermes[&&NHX:TOL=11321],acidnotermes[&&NHX:TOL=11322],acutidentitermes[&&NHX:TOL=11323],adaiphrotermes[&&NHX:TOL=11324],aderitotermes[&&NHX:TOL=11325],adynatotermes[&&NHX:TOL=11326],aganotermes[&&NHX:TOL=11327],allognathotermes[&&NHX:TOL=11328],alyscotermes[&&NHX:TOL=11329],amalotermes[&&NHX:TOL=11330],amicotermes[&&NHX:TOL=11331],anaorotermes[&&NHX:TOL=11332],anenteotermes[&&NHX:TOL=11333],anoplotermes[&&NHX:TOL=11334],apagotermes[&&NHX:TOL=11335],aparatermes[&&NHX:TOL=11336],apicotermes[&&NHX:TOL=11337],asagarotermes[&&NHX:TOL=11338],astalotermes[&&NHX:TOL=11339],astratotermes[&&NHX:TOL=11340],ateuchotermes[&&NHX:TOL=11341],coxotermes[&&NHX:TOL=11342],doonitermes[&&NHX:TOL=11343],duplidentitermes[&&NHX:TOL=11344],eburnitermes[&&NHX:TOL=11345],euhamitermes[&&NHX:TOL=11346],eurytermes[&&NHX:TOL=11347],firmitermes[&&NHX:TOL=11348],grigiotermes[&&NHX:TOL=11349],heimitermes[&&NHX:TOL=11350],hoplognathotermes[&&NHX:TOL=11351],indotermes[&&NHX:TOL=11352],jugositermes[&&NHX:TOL=11353],labidotermes[&&NHX:TOL=11354],machadotermes[&&NHX:TOL=11355],phoxotermes[&&NHX:TOL=11356],rostrotermes[&&NHX:TOL=11357],ruptitermes[&&NHX:TOL=11358],skatitermes[&&NHX:TOL=11359],speculitermes[&&NHX:TOL=11360],tetimatermes[&&NHX:TOL=11361],trichotermes[&&NHX:TOL=11362])apicotermitinae[&&NHX:TOL=11562],((acanthotermes[&&NHX:TOL=11414],pseudacanthotermes[&&NHX:TOL=11425])[&&NHX:TOL=52749],((protermes[&&NHX:TOL=11424],(hypotermes[&&NHX:TOL=11418],odontotermes[&&NHX:TOL=11422])[&&NHX:TOL=52752])[&&NHX:TOL=52751],((ancistrotermes[&&NHX:TOL=11416],microtermes[&&NHX:TOL=11421])[&&NHX:TOL=52754],(macrotermes[&&NHX:TOL=11419],synacanthotermes[&&NHX:TOL=11427])[&&NHX:TOL=52755])[&&NHX:TOL=52753])[&&NHX:TOL=52750],allodontermes[&&NHX:TOL=11415],euscaiotermes[&&NHX:TOL=11417],megaprotermes[&&NHX:TOL=11420],parahypotermes[&&NHX:TOL=11423])macrotermitinae[&&NHX:TOL=11563],(aciculioiditermes[&&NHX:TOL=11451],aciculitermes[&&NHX:TOL=11452],afrosubulitermes[&&NHX:TOL=11453],agnathotermes[&&NHX:TOL=11454],ahmaditermes[&&NHX:TOL=11455],alstonitermes[&&NHX:TOL=11456],ampoulitermes[&&NHX:TOL=11457],angularitermes[&&NHX:TOL=11458],anhangatermes[&&NHX:TOL=11459],antillitermes[&&NHX:TOL=11460],araujotermes[&&NHX:TOL=11461],arcotermes[&&NHX:TOL=11462],armitermes[&&NHX:TOL=11463],atlantitermes[&&NHX:TOL=11464],australitermes[&&NHX:TOL=11465],baucaliotermes[&&NHX:TOL=11466],bulbitermes[&&NHX:TOL=11467],caetetermes[&&NHX:TOL=11468],cahuallitermes[&&NHX:TOL=11469],caribitermes[&&NHX:TOL=11470],ceylonitermellus[&&NHX:TOL=11471],ceylonitermes[&&NHX:TOL=11472],coarctotermes[&&NHX:TOL=11473],coatitermes[&&NHX:TOL=11474],coendutermes[&&NHX:TOL=11475],constrictotermes[&&NHX:TOL=11476],(convexitermes convexifrons[&&NHX:TOL=57746],convexitermes manni[&&NHX:TOL=57747])convexitermes[&&NHX:TOL=11477],cornitermes[&&NHX:TOL=11478],cortaritermes[&&NHX:TOL=11479],cucurbitermes[&&NHX:TOL=11480],curvitermes[&&NHX:TOL=11481],cyranotermes[&&NHX:TOL=11482],cyrilliotermes[&&NHX:TOL=11483],diversitermes[&&NHX:TOL=11484],diwaitermes[&&NHX:TOL=11485],eleanoritermes[&&NHX:TOL=11486],embiratermes[&&NHX:TOL=11487],emersonitermes[&&NHX:TOL=11488],enetotermes[&&NHX:TOL=11489],ereymatermes[&&NHX:TOL=11490],eutermellus[&&NHX:TOL=11491],fulleritermes[&&NHX:TOL=11492],grallatotermes[&&NHX:TOL=11493],havilanditermes[&&NHX:TOL=11494],hirtitermes[&&NHX:TOL=11495],hospitalitermes[&&NHX:TOL=11496],ibitermes[&&NHX:TOL=11497],kaudernitermes[&&NHX:TOL=11498],labiotermes[&&NHX:TOL=11499],lacessititermes[&&NHX:TOL=11500],leptomyxotermes[&&NHX:TOL=11501],leucopsitermes[&&NHX:TOL=11502],longipeditermes[&&NHX:TOL=11503],macrosubulitermes[&&NHX:TOL=11504],macuxitermes[&&NHX:TOL=11505],malagasitermes[&&NHX:TOL=11506],malaysiotermes[&&NHX:TOL=11507],mimeutermes[&&NHX:TOL=11508],mironasutitermes[&&NHX:TOL=11509],mycterotermes[&&NHX:TOL=11510],nasopilotermes[&&NHX:TOL=11511],nasutitermes[&&NHX:TOL=11512],niuginitermes[&&NHX:TOL=11513],noirotitermes[&&NHX:TOL=11514],obtusitermes[&&NHX:TOL=11515],occasitermes[&&NHX:TOL=11516],oriensubulitermes[&&NHX:TOL=11517],(paraconvexitermes acangapua[&&NHX:TOL=57749],paraconvexitermes junceus[&&NHX:TOL=57750],paraconvexitermes nigricornis[&&NHX:TOL=57751])paraconvexitermes[&&NHX:TOL=57748],paracornitermes[&&NHX:TOL=11518],parvitermes[&&NHX:TOL=11519],periaciculitermes[&&NHX:TOL=11520],peribulbitermes[&&NHX:TOL=11521],postsubulitermes[&&NHX:TOL=11522],proaciculitermes[&&NHX:TOL=11523],procornitermes[&&NHX:TOL=11524],rhadinotermes[&&NHX:TOL=11525],rhynchotermes[&&NHX:TOL=11526],rotunditermes[&&NHX:TOL=11527],sinonasutitermes[&&NHX:TOL=11528],spatulitermes[&&NHX:TOL=11529],subulioiditermes[&&NHX:TOL=11530],subulitermes[&&NHX:TOL=11531],syntermes[&&NHX:TOL=11532],tarditermes[&&NHX:TOL=11533],tenuirostritermes[&&NHX:TOL=11534],triangularitermes[&&NHX:TOL=11535],trinervitermes[&&NHX:TOL=11536],tumulitermes[&&NHX:TOL=11537],velocitermes[&&NHX:TOL=11538],verrucositermes[&&NHX:TOL=11539],xiaitermes[&&NHX:TOL=11540])nasutitermitinae[&&NHX:TOL=11564],sphaerotermes[&&NHX:TOL=52756],((foraminitermes[&&NHX:TOL=11569],labritermes[&&NHX:TOL=11568])foraminitermes group[&&NHX:TOL=11567],((ahamitermes[&&NHX:TOL=11572],amitermes[&&NHX:TOL=11573],amphidotermes[&&NHX:TOL=11574],cephalotermes[&&NHX:TOL=11575],cylindrotermes[&&NHX:TOL=11576],dentispicotermes[&&NHX:TOL=11577],drepanotermes[&&NHX:TOL=11578],eremotermes[&&NHX:TOL=11579],genuotermes[&&NHX:TOL=11580],globitermes[&&NHX:TOL=11581],gnathamitermes[&&NHX:TOL=11582],hoplotermes[&&NHX:TOL=11583],incolitermes[&&NHX:TOL=11584],invasitermes[&&NHX:TOL=11585],microcerotermes[&&NHX:TOL=11586],onkotermes[&&NHX:TOL=11587],orientotermes[&&NHX:TOL=11588],orthognathotermes[&&NHX:TOL=11589],prohamitermes[&&NHX:TOL=11590],protohamitermes[&&NHX:TOL=11591],pseudhamitermes[&&NHX:TOL=11592],pseudomicrotermes[&&NHX:TOL=11593],spinitermes[&&NHX:TOL=11594],synhamitermes[&&NHX:TOL=11595])amitermes group[&&NHX:TOL=11571],((apilitermes[&&NHX:TOL=11598],basidentitermes[&&NHX:TOL=11599],batillitermes[&&NHX:TOL=11600],crenetermes[&&NHX:TOL=11601],cubitermes[&&NHX:TOL=11602],euchilotermes[&&NHX:TOL=11603],fastigitermes[&&NHX:TOL=11604],forficulitermes[&&NHX:TOL=11605],furculitermes[&&NHX:TOL=11606],gibbotermes[&&NHX:TOL=11607],lepidotermes[&&NHX:TOL=11608],megagnathotermes[&&NHX:TOL=11609],mucrotermes[&&NHX:TOL=11610],nitiditermes[&&NHX:TOL=11611],noditermes[&&NHX:TOL=11612],okavangotermes[&&NHX:TOL=11613],ophiotermes[&&NHX:TOL=11614],orthotermes[&&NHX:TOL=11615],ovambotermes[&&NHX:TOL=11616],pilotermes[&&NHX:TOL=11617],proboscitermes[&&NHX:TOL=11618],procubitermes[&&NHX:TOL=11619],profastigitermes[&&NHX:TOL=11620],thoracotermes[&&NHX:TOL=11621],trapellitermes[&&NHX:TOL=11622],unguitermes[&&NHX:TOL=11623],unicornitermes[&&NHX:TOL=11624])cubitermes group[&&NHX:TOL=11597],(angulitermes[&&NHX:TOL=11626],apsenterotermes[&&NHX:TOL=11627],capritermes[&&NHX:TOL=11628],cavitermes[&&NHX:TOL=11629],cornicapritermes[&&NHX:TOL=11630],coxocapritermes[&&NHX:TOL=11631],crepititermes[&&NHX:TOL=11632],cristatitermes[&&NHX:TOL=11633],dicuspiditermes[&&NHX:TOL=11634],dihoplotermes[&&NHX:TOL=11635],ekphysotermes[&&NHX:TOL=11636],ephelotermes[&&NHX:TOL=11637],hapsidotermes[&&NHX:TOL=11638],hesperotermes[&&NHX:TOL=11639],homallotermes[&&NHX:TOL=11640],indocapritermes[&&NHX:TOL=11641],inquilinitermes[&&NHX:TOL=11642],kemneritermes[&&NHX:TOL=11643],krishnacapritermes[&&NHX:TOL=11644],labiocapritermes[&&NHX:TOL=11645],lophotermes[&&NHX:TOL=11646],macrognathotermes[&&NHX:TOL=11647],malaysiocapritermes[&&NHX:TOL=11648],mirocapritermes[&&NHX:TOL=11649],neocapritermes[&&NHX:TOL=11650],oriencapritermes[&&NHX:TOL=11651],paracapritermes[&&NHX:TOL=11652],pericapritermes[&&NHX:TOL=11653],planicapritermes[&&NHX:TOL=11654],procapritermes[&&NHX:TOL=11655],promirotermes[&&NHX:TOL=11656],protocapritermes[&&NHX:TOL=11657],pseudocapritermes[&&NHX:TOL=11658],quasitermes[&&NHX:TOL=11659],saxatilitermes[&&NHX:TOL=11660],sinocapritermes[&&NHX:TOL=11661],syncapritermes[&&NHX:TOL=11662],termes[&&NHX:TOL=11663],tuberculitermes[&&NHX:TOL=11664],xylochomitermes[&&NHX:TOL=11665])termes group[&&NHX:TOL=11625])[&&NHX:TOL=11596])[&&NHX:TOL=11570])termitinae[&&NHX:TOL=11565])termitidae[&&NHX:TOL=11375])[&&NHX:TOL=11374])[&&NHX:TOL=11373])isoptera[&&NHX:TOL=8212],((baissomantis maculata[&&NHX:EXT=Y:TOL=12617],baissomantis picta[&&NHX:EXT=Y:TOL=12618])baissomantis[&&NHX:EXT=Y:TOL=52653],((archaeophlebia enigmatica[&&NHX:EXT=Y:TOL=12609],arvernineura insignis[&&NHX:EXT=Y:TOL=12608],(burmantis asiatica[&&NHX:EXT=Y:TOL=52661],burmantis lebanensis[&&NHX:EXT=Y:TOL=52662])burmantis[&&NHX:EXT=Y:TOL=52660],chaeteessites minutissimus[&&NHX:EXT=Y:TOL=12610],cretomantis larvalis[&&NHX:EXT=Y:TOL=12619],(cretophotina mongolica[&&NHX:EXT=Y:TOL=12615],cretophotina selenginensis[&&NHX:EXT=Y:TOL=52949],cretophotina serotina[&&NHX:EXT=Y:TOL=12614],cretophotina tristriata[&&NHX:EXT=Y:TOL=12616])cretophotina[&&NHX:EXT=Y:TOL=52663],electromantis sukatshevae[&&NHX:EXT=Y:TOL=12611],(jersimantis burmiticus[&&NHX:EXT=Y:TOL=52665],jersimantis luzzii[&&NHX:EXT=Y:TOL=12612])jersimantis[&&NHX:EXT=Y:TOL=52664],kazakhophotina corrupta[&&NHX:EXT=Y:TOL=12613],megaphotina sichotensis[&&NHX:EXT=Y:TOL=12606],santanmantis axelrodi[&&NHX:EXT=Y:TOL=52666],vitimiphotina corrugata[&&NHX:EXT=Y:TOL=12620])miscellaneous fossil mantodea[&&NHX:EXT=Y:TOL=12502],(ambermantis wozniaki[&&NHX:EXT=Y:TOL=52658],(((chaeteessa caudata[&&NHX:TOL=12573],chaeteessa filata[&&NHX:TOL=12574],chaeteessa nana[&&NHX:TOL=52667],chaeteessa valida[&&NHX:TOL=12575])chaeteessa[&&NHX:TOL=52736],lithophotina floccosa[&&NHX:EXT=Y:TOL=12607])chaeteessidae[&&NHX:TOL=12501],(mantoida argentinae[&&NHX:TOL=52668],mantoida brunneriana[&&NHX:TOL=12803],mantoida fulgidipennis[&&NHX:TOL=12804],mantoida luteola[&&NHX:TOL=12802],mantoida maya[&&NHX:TOL=12801],mantoida nitida[&&NHX:TOL=12800],mantoida ronderosi[&&NHX:TOL=52669],mantoida schraderi[&&NHX:TOL=12799],mantoida tenuis[&&NHX:TOL=12798])mantoida[&&NHX:TOL=12499],(metallyticus fallax[&&NHX:TOL=12806],metallyticus pallipes[&&NHX:TOL=12807],metallyticus semiaeneus[&&NHX:TOL=12810],metallyticus splendidus[&&NHX:TOL=12809],metallyticus violaceus[&&NHX:TOL=12808])metallyticus[&&NHX:TOL=12500],(((((acanthops royi[&&NHX:TOL=52920],(acanthops centralis[&&NHX:TOL=52922],(acanthops falcata[&&NHX:TOL=52924],acanthops parafalcata[&&NHX:TOL=52925])[&&NHX:TOL=52923])[&&NHX:TOL=52921])acanthops falcata group[&&NHX:TOL=52919],((acanthops onorei[&&NHX:TOL=52928],(acanthops godmani[&&NHX:TOL=52930],(acanthops bidens[&&NHX:TOL=52932],acanthops elegans[&&NHX:TOL=52933])[&&NHX:TOL=52931])[&&NHX:TOL=52929])[&&NHX:TOL=52927],((acanthops fuscifolia[&&NHX:TOL=52936],(acanthops erosa[&&NHX:TOL=52938],acanthops falcatoria[&&NHX:TOL=52939])[&&NHX:TOL=52937])[&&NHX:TOL=52935],(acanthops erosula[&&NHX:TOL=52941],(acanthops parva[&&NHX:TOL=52943],(acanthops occidentalis[&&NHX:TOL=52945],acanthops tuberculata[&&NHX:TOL=52946])[&&NHX:TOL=52944])[&&NHX:TOL=52942])[&&NHX:TOL=52940])[&&NHX:TOL=52934])acanthops falcataria group[&&NHX:TOL=52926],acanthops contorta[&&NHX:TOL=52947],acanthops soukana[&&NHX:TOL=52948])acanthops[&&NHX:TOL=12639],astollia chloris[&&NHX:TOL=52961],(decimiana bolivari[&&NHX:TOL=53108],decimiana clavata[&&NHX:TOL=57000],decimiana hebardi[&&NHX:TOL=53109],decimiana rehni[&&NHX:TOL=53110],decimiana tessellata[&&NHX:TOL=53111])decimiana[&&NHX:TOL=12650],(lagrecacanthops brasiliensis[&&NHX:TOL=56990],lagrecacanthops guyanensis[&&NHX:TOL=56991])lagrecacanthops[&&NHX:TOL=56989],(metilia boliviana[&&NHX:TOL=53112],metilia brunnerii[&&NHX:TOL=53113])metilia[&&NHX:TOL=52962],(miracanthops lombardoi[&&NHX:TOL=56993],miracanthops poulaini[&&NHX:TOL=56994])miracanthops[&&NHX:TOL=56992],(pseudacanthops angulata[&&NHX:TOL=53114],pseudacanthops caelebs[&&NHX:TOL=53115],pseudacanthops lobipes[&&NHX:TOL=53116],pseudacanthops spinulosa[&&NHX:TOL=53117])pseudacanthops[&&NHX:TOL=12661])acanthopinae[&&NHX:TOL=52960],((acontista amazonica[&&NHX:TOL=53118],acontista amoenula[&&NHX:TOL=53119],acontista brevipennis[&&NHX:TOL=53120],acontista cayennensis[&&NHX:TOL=53121],acontista championi[&&NHX:TOL=53122],acontista chopardi[&&NHX:TOL=53123],acontista concinna[&&NHX:TOL=53124],acontista cordillerae[&&NHX:TOL=53125],acontista cubana[&&NHX:TOL=53126],acontista ecuadorica[&&NHX:TOL=53127],acontista eximia[&&NHX:TOL=53128],acontista festae[&&NHX:TOL=53129],acontista fraterna[&&NHX:TOL=53130],acontista inquinata[&&NHX:TOL=53131],acontista iriodes[&&NHX:TOL=53132],acontista maroniensis[&&NHX:TOL=53133],acontista mexicana[&&NHX:TOL=53134],acontista minima[&&NHX:TOL=53135],acontista multicolor[&&NHX:TOL=53136],acontista piracicabensis[&&NHX:TOL=53137],acontista quadrimaculata[&&NHX:TOL=53138],acontista rehni[&&NHX:TOL=53139],acontista semirufa[&&NHX:TOL=53140],acontista travassosi[&&NHX:TOL=53141],acontista vitrea[&&NHX:TOL=53142])acontista[&&NHX:TOL=52964],callibia diana[&&NHX:TOL=12624],paratithrone royi[&&NHX:TOL=52965],(raptrix fusca[&&NHX:TOL=53143],raptrix fuscata[&&NHX:TOL=53144],raptrix intermedia[&&NHX:TOL=56995],raptrix occidentalis[&&NHX:TOL=53145],raptrix perspicua[&&NHX:TOL=56996])raptrix[&&NHX:TOL=52966],(tithrone catharinensis[&&NHX:TOL=53146],tithrone clauseni[&&NHX:TOL=53147],tithrone corseuili[&&NHX:TOL=53148],tithrone laeta[&&NHX:TOL=53149],tithrone latipennis[&&NHX:TOL=53150],tithrone major[&&NHX:TOL=53151],tithrone roseipennis[&&NHX:TOL=53152])tithrone[&&NHX:TOL=12664])acontiothespinae[&&NHX:TOL=52963],(stenophylla cornigera[&&NHX:TOL=53153],stenophylla lobivertex[&&NHX:TOL=53154])stenophylla[&&NHX:TOL=12917])acanthopidae[&&NHX:TOL=52959],(((amorphoscelis abyssinica[&&NHX:TOL=53155],amorphoscelis angolica[&&NHX:TOL=53156],amorphoscelis annulicornis[&&NHX:TOL=53157],amorphoscelis austrogermanica[&&NHX:TOL=53158],amorphoscelis borneana[&&NHX:TOL=53159],amorphoscelis brunneipennis[&&NHX:TOL=53160],amorphoscelis ceylonica[&&NHX:TOL=53161],amorphoscelis chinensis[&&NHX:TOL=53162],amorphoscelis chopardi[&&NHX:TOL=53163],amorphoscelis elegans[&&NHX:TOL=53164],amorphoscelis griffini[&&NHX:TOL=53165],amorphoscelis grisea[&&NHX:TOL=53166],amorphoscelis javana[&&NHX:TOL=53167],amorphoscelis lamottei[&&NHX:TOL=53168],amorphoscelis laxeretis[&&NHX:TOL=53169],amorphoscelis machadoi[&&NHX:TOL=53170],amorphoscelis naumanni[&&NHX:TOL=53171],amorphoscelis nigriventer[&&NHX:TOL=53172],amorphoscelis nubeculosa[&&NHX:TOL=53173],amorphoscelis opaca[&&NHX:TOL=53174],amorphoscelis orientalis[&&NHX:TOL=53175],amorphoscelis pallida[&&NHX:TOL=53176],amorphoscelis pantherina[&&NHX:TOL=53177],amorphoscelis papua[&&NHX:TOL=53178],amorphoscelis parva[&&NHX:TOL=53179],amorphoscelis pellucida[&&NHX:TOL=53180],amorphoscelis philippina[&&NHX:TOL=53181],amorphoscelis pulchella[&&NHX:TOL=53182],amorphoscelis pulchra[&&NHX:TOL=53183],amorphoscelis punctata[&&NHX:TOL=53184],amorphoscelis reticulata[&&NHX:TOL=53185],amorphoscelis rufula[&&NHX:TOL=53186],amorphoscelis siebersi[&&NHX:TOL=53187],amorphoscelis singaporana[&&NHX:TOL=53188],amorphoscelis spinosa[&&NHX:TOL=53189],amorphoscelis subnigra[&&NHX:TOL=53190],amorphoscelis tigrina[&&NHX:TOL=53191],amorphoscelis tuberculata[&&NHX:TOL=53192],amorphoscelis villiersi[&&NHX:TOL=53193])amorphoscelis[&&NHX:TOL=12540],(bolivaroscelis bolivarii[&&NHX:TOL=53194],bolivaroscelis carinata[&&NHX:TOL=53195],bolivaroscelis werneri[&&NHX:TOL=53196])bolivaroscelis[&&NHX:TOL=52951],(caudatoscelis annulipes[&&NHX:TOL=53197],caudatoscelis caudata[&&NHX:TOL=53198],caudatoscelis collarti[&&NHX:TOL=53199],caudatoscelis lagrecai[&&NHX:TOL=53200],caudatoscelis marmorata[&&NHX:TOL=53201])caudatoscelis[&&NHX:TOL=52952],gigliotoscelis simulans[&&NHX:TOL=52953],(maculatoscelis ascalaphoides[&&NHX:TOL=53202],maculatoscelis gilloni[&&NHX:TOL=53203],maculatoscelis maculata[&&NHX:TOL=53204])maculatoscelis[&&NHX:TOL=52954])amorphoscelinae[&&NHX:TOL=12539],((cliomantis cornuta[&&NHX:TOL=53205],cliomantis dispar[&&NHX:TOL=53206],cliomantis lateralis[&&NHX:TOL=53207],cliomantis obscura[&&NHX:TOL=53208])cliomantis[&&NHX:TOL=52955],exparoxypilus africanus[&&NHX:TOL=52956],(gyromantis kraussii[&&NHX:TOL=53209],gyromantis occidentalis[&&NHX:TOL=53210])gyromantis[&&NHX:TOL=12545],(metoxypilus costalis[&&NHX:TOL=53211],metoxypilus lobifrons[&&NHX:TOL=53212],metoxypilus werneri[&&NHX:TOL=53213])metoxypilus[&&NHX:TOL=12546],myrmecomantis atra[&&NHX:TOL=12547],(nesoxypilus albomaculatus[&&NHX:TOL=53214],nesoxypilus pseudomyrmex[&&NHX:TOL=53215])nesoxypilus[&&NHX:TOL=52957],(paraoxypilus armatus[&&NHX:TOL=53216],paraoxypilus distinctus[&&NHX:TOL=53217],paraoxypilus flavifemur[&&NHX:TOL=53218],paraoxypilus insularis[&&NHX:TOL=53219],paraoxypilus kimberleyensis[&&NHX:TOL=53220],paraoxypilus laticollis[&&NHX:TOL=53221],paraoxypilus tasmaniensis[&&NHX:TOL=53222],paraoxypilus verreauxii[&&NHX:TOL=53223])paraoxypilus[&&NHX:TOL=12548],(phthersigena centralis[&&NHX:TOL=53224],phthersigena conspersa[&&NHX:TOL=53225],phthersigena insularis[&&NHX:TOL=53226],phthersigena melania[&&NHX:TOL=53227],phthersigena minor[&&NHX:TOL=53228],phthersigena nebulosa[&&NHX:TOL=53229],phthersigena timorensis[&&NHX:TOL=53230],phthersigena unicornis[&&NHX:TOL=53231])phthersigena[&&NHX:TOL=12549])paraoxypilinae[&&NHX:TOL=12543],(paramorphoscelis gondokorensis[&&NHX:TOL=12541],(perlamantis algerica[&&NHX:TOL=53232],perlamantis allibertii[&&NHX:TOL=53233])perlamantis[&&NHX:TOL=12542])perlamantinae[&&NHX:TOL=52958],amorphoscelites sharovi[&&NHX:EXT=Y:TOL=12538])amorphoscelidae[&&NHX:TOL=12498],(((blepharodes candelarius[&&NHX:TOL=53234],blepharodes cornutus[&&NHX:TOL=53235],blepharodes parumspinosus[&&NHX:TOL=53236],blepharodes sudanensis[&&NHX:TOL=53237])blepharodes[&&NHX:TOL=12599],(blepharopsis mendica[&&NHX:TOL=12600],idolomantis diabolica[&&NHX:TOL=12601])[&&NHX:TOL=56953])blepharodinae[&&NHX:TOL=12598],((chopardempusa neglecta[&&NHX:TOL=56936],(hemiempusa capensis[&&NHX:TOL=12595],(idolomorpha dentifrons[&&NHX:TOL=53240],idolomorpha lateralis[&&NHX:TOL=53241],idolomorpha madagascariensis[&&NHX:TOL=53242],idolomorpha sagitta[&&NHX:TOL=53243])idolomorpha[&&NHX:TOL=12597])[&&NHX:TOL=56937])idolomorphini[&&NHX:TOL=53107],((gongylus gongylodes[&&NHX:TOL=53238],gongylus trachelophyllus[&&NHX:TOL=53239])gongylus[&&NHX:TOL=12594],(hypsicorypha gracilis[&&NHX:TOL=12596],(dilatempusa aegyptiaca[&&NHX:TOL=56940],(empusa binotata[&&NHX:TOL=56941],empusa fasciata[&&NHX:TOL=56942],empusa guttula[&&NHX:TOL=56943],empusa hedenborgii[&&NHX:TOL=56944],empusa longicollis[&&NHX:TOL=56945],empusa pauperata[&&NHX:TOL=56946],empusa pennata[&&NHX:TOL=56947],empusa pennicornis[&&NHX:TOL=56948],empusa romboidae[&&NHX:TOL=56949],empusa spinosa[&&NHX:TOL=56950],empusa simonyi[&&NHX:TOL=56951],empusa uvarovi[&&NHX:TOL=56952])empusa[&&NHX:TOL=12593])[&&NHX:TOL=56939])[&&NHX:TOL=56938])empusini[&&NHX:TOL=53106])empusinae[&&NHX:TOL=12592])empusidae[&&NHX:TOL=12495],((eremiaphila ammonita[&&NHX:TOL=53245],eremiaphila andresi[&&NHX:TOL=53246],eremiaphila anubis[&&NHX:TOL=53247],eremiaphila arabica[&&NHX:TOL=53248],eremiaphila aristidis[&&NHX:TOL=53249],eremiaphila audouini[&&NHX:TOL=53250],eremiaphila barbara[&&NHX:TOL=53251],eremiaphila berndstiewi[&&NHX:TOL=56998],eremiaphila bifasciata[&&NHX:TOL=53252],eremiaphila bovei[&&NHX:TOL=53253],eremiaphila braueri[&&NHX:TOL=53254],eremiaphila brevipennis[&&NHX:TOL=53255],eremiaphila brunneri[&&NHX:TOL=53256],eremiaphila cairina[&&NHX:TOL=53257],eremiaphila cerisyi[&&NHX:TOL=53258],eremiaphila collenettei[&&NHX:TOL=53259],eremiaphila cordofan[&&NHX:TOL=53260],eremiaphila cycloptera[&&NHX:TOL=53261],eremiaphila dentata[&&NHX:TOL=53262],eremiaphila denticollis[&&NHX:TOL=53263],eremiaphila foureaui[&&NHX:TOL=53264],eremiaphila fraseri[&&NHX:TOL=53265],eremiaphila genei[&&NHX:TOL=53266],eremiaphila gigas[&&NHX:TOL=53267],eremiaphila hebraica[&&NHX:TOL=53268],eremiaphila hedenborgii[&&NHX:TOL=53269],eremiaphila heluanensis[&&NHX:TOL=53270],eremiaphila hralili[&&NHX:TOL=53271],eremiaphila irridipennis[&&NHX:TOL=53272],eremiaphila khamsin[&&NHX:TOL=53273],eremiaphila kheych[&&NHX:TOL=53274],eremiaphila klunzingeri[&&NHX:TOL=53275],eremiaphila laeviceps[&&NHX:TOL=53276],eremiaphila lefebvrii[&&NHX:TOL=53277],eremiaphila luxor[&&NHX:TOL=53278],eremiaphila maculipennis[&&NHX:TOL=53279],eremiaphila monodi[&&NHX:TOL=53280],eremiaphila moreti[&&NHX:TOL=53281],eremiaphila murati[&&NHX:TOL=53282],eremiaphila mzabi[&&NHX:TOL=53283],eremiaphila nilotica[&&NHX:TOL=53284],eremiaphila nova[&&NHX:TOL=53285],eremiaphila numida[&&NHX:TOL=53286],eremiaphila persica[&&NHX:TOL=53287],eremiaphila petiti[&&NHX:TOL=53288],eremiaphila pierrei[&&NHX:TOL=53289],eremiaphila pyramidum[&&NHX:TOL=53290],eremiaphila rectangulata[&&NHX:TOL=53291],eremiaphila reticulata[&&NHX:TOL=53292],eremiaphila rohlfsi[&&NHX:TOL=53293],eremiaphila rotundipennis[&&NHX:TOL=53294],eremiaphila rufipennis[&&NHX:TOL=53295],eremiaphila rufula[&&NHX:TOL=53296],eremiaphila savignyi[&&NHX:TOL=53297],eremiaphila somalica[&&NHX:TOL=53298],eremiaphila spinulosa[&&NHX:TOL=53299],eremiaphila tuberculifera[&&NHX:TOL=53300],eremiaphila turica[&&NHX:TOL=53301],eremiaphila typhon[&&NHX:TOL=53302],eremiaphila uvarovi[&&NHX:TOL=53303],eremiaphila voltaensis[&&NHX:TOL=53304],eremiaphila werneri[&&NHX:TOL=53305],eremiaphila wettsteini[&&NHX:TOL=53306],eremiaphila yemenita[&&NHX:TOL=53307],eremiaphila zetterstedti[&&NHX:TOL=53308],eremiaphila zolotarevskyi[&&NHX:TOL=53309])eremiaphila[&&NHX:TOL=12603],(heteronutarsus aegyptiacus[&&NHX:TOL=53310],heteronutarsus albipennis[&&NHX:TOL=53311])heteronutarsus[&&NHX:TOL=12604])eremiaphilidae[&&NHX:TOL=12497],(((acromantis australis[&&NHX:TOL=53312],acromantis dyaka[&&NHX:TOL=53313],acromantis elegans[&&NHX:TOL=53314],acromantis formosana[&&NHX:TOL=53315],acromantis gestri[&&NHX:TOL=53316],acromantis grandis[&&NHX:TOL=53317],acromantis hesione[&&NHX:TOL=53318],acromantis indica[&&NHX:TOL=53319],acromantis insularis[&&NHX:TOL=53320],acromantis japonica[&&NHX:TOL=53321],acromantis lilii[&&NHX:TOL=53322],acromantis luzonica[&&NHX:TOL=53323],acromantis montana[&&NHX:TOL=53324],acromantis moultoni[&&NHX:TOL=53325],acromantis nicobarica[&&NHX:TOL=53326],acromantis oligoneura[&&NHX:TOL=53327],acromantis palauana[&&NHX:TOL=53328],acromantis philippina[&&NHX:TOL=53329],acromantis satsumensis[&&NHX:TOL=53330],acromantis siporana[&&NHX:TOL=53331])acromantis[&&NHX:TOL=12642],(anasigerpes amieti[&&NHX:TOL=53332],anasigerpes bifasciata[&&NHX:TOL=53333],anasigerpes centralis[&&NHX:TOL=53334],anasigerpes grilloti[&&NHX:TOL=53335],anasigerpes heydeni[&&NHX:TOL=53336],anasigerpes nigripes[&&NHX:TOL=53337],anasigerpes unifasciata[&&NHX:TOL=53338])anasigerpes[&&NHX:TOL=12643],(anaxarcha acuta[&&NHX:TOL=53339],anaxarcha graminea[&&NHX:TOL=53340],anaxarcha hyalina[&&NHX:TOL=53341],anaxarcha intermedia[&&NHX:TOL=53342],anaxarcha limbata[&&NHX:TOL=53343],anaxarcha sinensis[&&NHX:TOL=53344],anaxarcha tianmushanensis[&&NHX:TOL=53345])anaxarcha[&&NHX:TOL=12644],anoplosigerpes tessmanni[&&NHX:TOL=12645],(catasigerpes acuminatus[&&NHX:TOL=53346],catasigerpes brunnerianus[&&NHX:TOL=53347],catasigerpes camerunensis[&&NHX:TOL=53348],catasigerpes congicus[&&NHX:TOL=53349],catasigerpes erlangeri[&&NHX:TOL=53350],catasigerpes granulatus[&&NHX:TOL=53351],catasigerpes jeanneli[&&NHX:TOL=53352],catasigerpes margarethae[&&NHX:TOL=53353],catasigerpes mortuifolia[&&NHX:TOL=53354],catasigerpes nigericus[&&NHX:TOL=53355],catasigerpes occidentalis[&&NHX:TOL=53356],catasigerpes toganus[&&NHX:TOL=53357],catasigerpes zernyi[&&NHX:TOL=53358])catasigerpes[&&NHX:TOL=12647],(chrysomantis cachani[&&NHX:TOL=53359],chrysomantis centralis[&&NHX:TOL=53360],chrysomantis cervoides[&&NHX:TOL=53361],chrysomantis congica[&&NHX:TOL=53362],chrysomantis girardi[&&NHX:TOL=53363],chrysomantis royi[&&NHX:TOL=53364],chrysomantis speciosa[&&NHX:TOL=53365],chrysomantis tristis[&&NHX:TOL=53366])chrysomantis[&&NHX:TOL=12648],citharomantis falcata[&&NHX:TOL=12649],(ephestiasula amoena[&&NHX:TOL=53367],ephestiasula intermedia[&&NHX:TOL=53368],ephestiasula pictipes[&&NHX:TOL=53369])ephestiasula[&&NHX:TOL=52971],ephippiomantis ophirensis[&&NHX:TOL=12652],(euantissa ornata[&&NHX:TOL=53370],euantissa pulchra[&&NHX:TOL=53371],euantissa sinensis[&&NHX:TOL=53372])euantissa[&&NHX:TOL=52972],(heliomantis elegans[&&NHX:TOL=53373],heliomantis latipennis[&&NHX:TOL=53374])heliomantis[&&NHX:TOL=12653],(hestiasula basinigra[&&NHX:TOL=53375],hestiasula brunneriana[&&NHX:TOL=53376],hestiasula castetsi[&&NHX:TOL=53377],hestiasula ceylonica[&&NHX:TOL=53378],hestiasula gyldenstolpei[&&NHX:TOL=53379],hestiasula hoffmanni[&&NHX:TOL=53380],hestiasula inermis[&&NHX:TOL=53381],hestiasula javana[&&NHX:TOL=53382],hestiasula kaestneri[&&NHX:TOL=53383],hestiasula major[&&NHX:TOL=53384],hestiasula masoni[&&NHX:TOL=53385],hestiasula moultoni[&&NHX:TOL=53386],hestiasula nigrofemorata[&&NHX:TOL=53387],hestiasula nitida[&&NHX:TOL=53388],hestiasula phyllopus[&&NHX:TOL=53389],hestiasula rogenhoferi[&&NHX:TOL=53390],hestiasula seminigra[&&NHX:TOL=53391],hestiasula woodi[&&NHX:TOL=53392],hestiasula zhejiangensis[&&NHX:TOL=53393])hestiasula[&&NHX:TOL=12654],metacromantis oxyops[&&NHX:TOL=12655],(odontomantis brachyptera[&&NHX:TOL=53394],odontomantis buehleri[&&NHX:TOL=53395],odontomantis chayuensis[&&NHX:TOL=53396],odontomantis euphrosyne[&&NHX:TOL=53397],odontomantis foveafrons[&&NHX:TOL=53398],odontomantis hainana[&&NHX:TOL=53399],odontomantis laticollis[&&NHX:TOL=53400],odontomantis longipennis[&&NHX:TOL=53401],odontomantis micans[&&NHX:TOL=53402],odontomantis montana[&&NHX:TOL=53403],odontomantis monticola[&&NHX:TOL=53404],odontomantis nigrimarginalis[&&NHX:TOL=53405],odontomantis parva[&&NHX:TOL=53406],odontomantis planiceps[&&NHX:TOL=53407],odontomantis rhyssa[&&NHX:TOL=53408],odontomantis xizangensis[&&NHX:TOL=53409])odontomantis[&&NHX:TOL=12657],(oligomantis hyalina[&&NHX:TOL=53410],oligomantis mentaweiana[&&NHX:TOL=53411],oligomantis orientalis[&&NHX:TOL=53412])oligomantis[&&NHX:TOL=12658],(otomantis aurita[&&NHX:TOL=53413],otomantis capirica[&&NHX:TOL=53414],otomantis casaica[&&NHX:TOL=53415],otomantis rendalli[&&NHX:TOL=53416],otomantis scutigera[&&NHX:TOL=53417])otomantis[&&NHX:TOL=12659],(oxypiloidea subcornuta[&&NHX:TOL=53418],oxypiloidea tridens[&&NHX:TOL=53419])oxypiloidea[&&NHX:TOL=52973],parahestiasula obscura[&&NHX:TOL=52974],(psychomantis borneensis[&&NHX:TOL=53420],psychomantis malayensis[&&NHX:TOL=53421])psychomantis[&&NHX:TOL=12662],rhomantis moultoni[&&NHX:TOL=12663])acromantinae[&&NHX:TOL=12638],(amphecostephanus rex[&&NHX:TOL=52970],(epaphrodita lobivertex[&&NHX:TOL=57002],epaphrodita musarum[&&NHX:TOL=53423],epaphrodita undulata[&&NHX:TOL=56982])epaphrodita[&&NHX:TOL=12651],parablepharis kuhlii[&&NHX:TOL=12590],phyllocrania paradoxa[&&NHX:TOL=12660])epaphroditinae[&&NHX:TOL=52969],(attalia philbyi[&&NHX:TOL=52975],(chlidonoptera chopardi[&&NHX:TOL=53424],chlidonoptera lestoni[&&NHX:TOL=53425],chlidonoptera vexillum[&&NHX:TOL=53426],chlidonoptera werneri[&&NHX:TOL=53427])chlidonoptera[&&NHX:TOL=12625],chloroharpax modesta[&&NHX:TOL=12626],(congoharpax aberrans[&&NHX:TOL=53428],congoharpax boulardi[&&NHX:TOL=53429],congoharpax coiffaiti[&&NHX:TOL=53430],congoharpax judithae[&&NHX:TOL=53431])congoharpax[&&NHX:TOL=52976],(creobroter apicalis[&&NHX:TOL=53432],creobroter celebensis[&&NHX:TOL=53433],creobroter disciferus[&&NHX:TOL=53434],creobroter elongatus[&&NHX:TOL=53435],creobroter episcopalis[&&NHX:TOL=53436],creobroter fasciatus[&&NHX:TOL=53437],creobroter fuscoareatus[&&NHX:TOL=53438],creobroter gemmatus[&&NHX:TOL=53439],creobroter granulicollis[&&NHX:TOL=53440],creobroter insolitus[&&NHX:TOL=53441],creobroter jiangxiensis[&&NHX:TOL=53442],creobroter labuanae[&&NHX:TOL=53443],creobroter laevicollis[&&NHX:TOL=53444],creobroter medanus[&&NHX:TOL=53445],creobroter meleagris[&&NHX:TOL=53446],creobroter nebulosus[&&NHX:TOL=53447],creobroter pictipennis[&&NHX:TOL=53448],creobroter signifer[&&NHX:TOL=53449],creobroter sumatranus[&&NHX:TOL=53450],creobroter urbanus[&&NHX:TOL=53451],creobroter vitripennis[&&NHX:TOL=53452])creobroter[&&NHX:TOL=12627],(galinthias amoena[&&NHX:TOL=53453],galinthias meruensis[&&NHX:TOL=53454],galinthias occidentalis[&&NHX:TOL=53455])galinthias[&&NHX:TOL=12628],harpagomantis tricolor[&&NHX:TOL=12629],helvia cardinalis[&&NHX:TOL=12630],(hymenopus coronatoides[&&NHX:TOL=53456],hymenopus coronatus[&&NHX:TOL=53457])hymenopus[&&NHX:TOL=12631],(panurgica basilewskyi[&&NHX:TOL=53458],panurgica compressicollis[&&NHX:TOL=53459],panurgica duplex[&&NHX:TOL=53460],panurgica feae[&&NHX:TOL=53461],panurgica fratercula[&&NHX:TOL=53462],panurgica fusca[&&NHX:TOL=53463],panurgica langi[&&NHX:TOL=53464],panurgica liberiana[&&NHX:TOL=53465],panurgica mende[&&NHX:TOL=53466],panurgica rehni[&&NHX:TOL=53467])panurgica[&&NHX:TOL=12632],parhymenopus davisoni[&&NHX:TOL=12633],(pseudocreobotra amarae[&&NHX:TOL=53468],pseudocreobotra ocellata[&&NHX:TOL=53469],pseudocreobotra wahlbergii[&&NHX:TOL=53470])pseudocreobotra[&&NHX:TOL=12635],(pseudoharpax abyssinicus[&&NHX:TOL=53471],pseudoharpax beieri[&&NHX:TOL=53472],pseudoharpax crenaticollis[&&NHX:TOL=53473],pseudoharpax dubius[&&NHX:TOL=53474],pseudoharpax erythraeus[&&NHX:TOL=53475],pseudoharpax francoisi[&&NHX:TOL=53476],pseudoharpax parallelus[&&NHX:TOL=53477],pseudoharpax ugandanus[&&NHX:TOL=53478],pseudoharpax virescens[&&NHX:TOL=53479])pseudoharpax[&&NHX:TOL=12636],(theopropus borneensis[&&NHX:TOL=53480],theopropus cattulus[&&NHX:TOL=53481],theopropus elegans[&&NHX:TOL=53482])theopropus[&&NHX:TOL=12637])hymenopodinae[&&NHX:TOL=12622],((ceratomantis saussurii[&&NHX:TOL=53507],ceratomantis yunnanensis[&&NHX:TOL=53508])ceratomantis[&&NHX:TOL=12667],(junodia amoena[&&NHX:TOL=53509],junodia beieri[&&NHX:TOL=53510],junodia congicus[&&NHX:TOL=53511],junodia hararensis[&&NHX:TOL=53512],junodia lameyi[&&NHX:TOL=53513],junodia maculata[&&NHX:TOL=53514],junodia spinosa[&&NHX:TOL=53515],junodia strigipennis[&&NHX:TOL=53516],junodia vansomereni[&&NHX:TOL=53517])junodia[&&NHX:TOL=12668],((oxypilus oxypilus annulatus[&&NHX:TOL=53484],oxypilus oxypilus cherlonneixi[&&NHX:TOL=53485],oxypilus oxypilus descampsi[&&NHX:TOL=53486],oxypilus oxypilus distinctus[&&NHX:TOL=53487],oxypilus oxypilus enei[&&NHX:TOL=53488],oxypilus oxypilus falcatus[&&NHX:TOL=53489],oxypilus oxypilus flavicoxa[&&NHX:TOL=53490],oxypilus oxypilus gillonae[&&NHX:TOL=53491],oxypilus oxypilus guentheri[&&NHX:TOL=53492],oxypilus oxypilus hamatus[&&NHX:TOL=53493],oxypilus oxypilus lamottei[&&NHX:TOL=53494],oxypilus oxypilus montanus[&&NHX:TOL=53495],oxypilus oxypilus pallidus[&&NHX:TOL=53496],oxypilus oxypilus polyacanthus[&&NHX:TOL=53497],oxypilus oxypilus raggei[&&NHX:TOL=53498],oxypilus oxypilus tanzanicus[&&NHX:TOL=53499],oxypilus oxypilus villiersi[&&NHX:TOL=53500])oxypilus oxypilus[&&NHX:TOL=53483],(oxypilus setoxypilus basilewskyi[&&NHX:TOL=53502],oxypilus setoxypilus burri[&&NHX:TOL=53503],oxypilus setoxypilus nasutus[&&NHX:TOL=53504],oxypilus setoxypilus nigericus[&&NHX:TOL=53505],oxypilus setoxypilus transvalensis[&&NHX:TOL=53506])oxypilus setoxypilus[&&NHX:TOL=53501])oxypilus[&&NHX:TOL=12671],(pachymantis bicingulata[&&NHX:TOL=53518],pachymantis dohertii[&&NHX:TOL=53519])pachymantis[&&NHX:TOL=12669],pseudoxypilus hemerobius[&&NHX:TOL=12670])oxypilinae[&&NHX:TOL=12665])hymenopodidae[&&NHX:TOL=12496],(((bolbe lowi[&&NHX:TOL=53520],bolbe maia[&&NHX:TOL=53521],bolbe nigra[&&NHX:TOL=53522],bolbe pallida[&&NHX:TOL=53523],bolbe pygmea[&&NHX:TOL=53524])bolbe[&&NHX:TOL=12709],((bolbena bolbena assimilis[&&NHX:TOL=53526],bolbena bolbena hottentotta[&&NHX:TOL=53527],bolbena bolbena maraisi[&&NHX:TOL=53528],bolbena bolbena minor[&&NHX:TOL=53529],bolbena bolbena orientalis[&&NHX:TOL=53530])bolbena bolbena[&&NHX:TOL=53525],bolbena bolboda minutissima[&&NHX:TOL=53531])bolbena[&&NHX:TOL=12711],(bolbula debilis[&&NHX:TOL=53532],bolbula exigua[&&NHX:TOL=53533],bolbula widenmanni[&&NHX:TOL=53534])bolbula[&&NHX:TOL=12710],hapalogymnes gymnes[&&NHX:TOL=53000],((hapalomantis bolbira congica[&&NHX:TOL=53540],hapalomantis bolbira lacualis[&&NHX:TOL=53541],hapalomantis bolbira minima[&&NHX:TOL=53542])hapalomantis bolbira[&&NHX:TOL=53539],(hapalomantis hapalomantis abyssinica[&&NHX:TOL=53536],hapalomantis hapalomantis orba[&&NHX:TOL=53537],hapalomantis hapalomantis rhombochir[&&NHX:TOL=53538])hapalomantis hapalomantis[&&NHX:TOL=53535])hapalomantis[&&NHX:TOL=12708],(papubolbe curvidens[&&NHX:TOL=53543],papubolbe eximia[&&NHX:TOL=53544],papubolbe flava[&&NHX:TOL=53545],papubolbe gressitti[&&NHX:TOL=53546],papubolbe longipennis[&&NHX:TOL=53547],papubolbe picea[&&NHX:TOL=53548])papubolbe[&&NHX:TOL=12712],(tarachina brevipennis[&&NHX:TOL=53549],tarachina congica[&&NHX:TOL=53550],tarachina constricta[&&NHX:TOL=53551],tarachina occidentalis[&&NHX:TOL=53552],tarachina rammei[&&NHX:TOL=53553],tarachina raphidioides[&&NHX:TOL=53554],tarachina schultzei[&&NHX:TOL=53555],tarachina seriepunctata[&&NHX:TOL=53556],tarachina transvaalensis[&&NHX:TOL=53557],tarachina werneri[&&NHX:TOL=53558],tarachina zernyi[&&NHX:TOL=53559])tarachina[&&NHX:TOL=12707],microbolbella[&&NHX:TOL=12713])hapalomantinae[&&NHX:TOL=12706],(((hapalopeza hapalopeza fulmeki[&&NHX:TOL=53561],hapalopeza hapalopeza nigricornis[&&NHX:TOL=53562],hapalopeza hapalopeza nilgirica[&&NHX:TOL=53563],hapalopeza hapalopeza nitens[&&NHX:TOL=53564],hapalopeza hapalopeza periyara[&&NHX:TOL=53565],hapalopeza hapalopeza tigrina[&&NHX:TOL=53566])hapalopeza hapalopeza[&&NHX:TOL=53560],hapalopeza spilomantis occipitalis[&&NHX:TOL=53567])hapalopeza[&&NHX:TOL=12700],hapalopezella maculata[&&NHX:TOL=53001],iridopteryx iridipennis[&&NHX:TOL=12701],micromantis glauca[&&NHX:TOL=12702],muscimantis montana[&&NHX:TOL=53002],(nemotha coomani[&&NHX:TOL=53568],nemotha metallica[&&NHX:TOL=53569],nemotha mirabilis[&&NHX:TOL=53570])nemotha[&&NHX:TOL=12704],pezomantis henryi[&&NHX:TOL=53003],rawarena[&&NHX:TOL=12697],shirakia[&&NHX:TOL=12699])iridopteryginae[&&NHX:TOL=12687],(((calofulcinia australis[&&NHX:TOL=53720],calofulcinia elegans[&&NHX:TOL=53721],calofulcinia integra[&&NHX:TOL=53722],calofulcinia oxynata[&&NHX:TOL=53723],calofulcinia paraoxypila[&&NHX:TOL=53724],calofulcinia viridula[&&NHX:TOL=53725])calofulcinia[&&NHX:TOL=12698],(fulcinia alaris[&&NHX:TOL=53726],fulcinia exilis[&&NHX:TOL=53727],fulcinia punctipes[&&NHX:TOL=53728],fulcinia uxor[&&NHX:TOL=53729])fulcinia[&&NHX:TOL=12691],(fulciniella infumata[&&NHX:TOL=53730],fulciniella loriae[&&NHX:TOL=53731],fulciniella verticalis[&&NHX:TOL=53732])fulciniella[&&NHX:TOL=12688],fulciniola snelleni[&&NHX:TOL=53006],hedigerella fasciatella[&&NHX:TOL=53007],nannofulinia pulchra[&&NHX:TOL=53008],pilomantis fusca[&&NHX:TOL=12690],(tylomantis armillata[&&NHX:TOL=53733],tylomantis fuliginosa[&&NHX:TOL=53734])tylomantis[&&NHX:TOL=12689])fulcinini[&&NHX:TOL=53005],(ima fusca[&&NHX:TOL=12696],machairima papua[&&NHX:TOL=53010],(nanomantis australis[&&NHX:TOL=53735],nanomantis gilolae[&&NHX:TOL=53736],nanomantis lactea[&&NHX:TOL=53737],nanomantis yunnanensis[&&NHX:TOL=53738])nanomantis[&&NHX:TOL=12693],parananomantis brevis[&&NHX:TOL=53011],(sceptuchus baehri[&&NHX:TOL=53739],sceptuchus simplex[&&NHX:TOL=53740])sceptuchus[&&NHX:TOL=12694],sinomantis denticulata[&&NHX:TOL=12692])nanomantini[&&NHX:TOL=53009])nanomantinae[&&NHX:TOL=53004],(epsomantis tortricoides[&&NHX:TOL=12705],ilomantis thalassina[&&NHX:TOL=53013],mimomantis milloti[&&NHX:TOL=53014],(nilomantis edmundsi[&&NHX:TOL=53571],nilomantis floweri[&&NHX:TOL=53572])nilomantis[&&NHX:TOL=12685],(papugalepsus alatus[&&NHX:TOL=53573],papugalepsus elongatus[&&NHX:TOL=53574])papugalepsus[&&NHX:TOL=12695])nilomantinae[&&NHX:TOL=53012],((chloromantis impunctata[&&NHX:TOL=53575],chloromantis rhombica[&&NHX:TOL=53576])chloromantis[&&NHX:TOL=12680],(enicophlebia hilara[&&NHX:TOL=53577],enicophlebia pallida[&&NHX:TOL=53578])enicophlebia[&&NHX:TOL=12677],(hyalomantis madagascariensis[&&NHX:TOL=53579],hyalomantis punctata[&&NHX:TOL=53580])hyalomantis[&&NHX:TOL=12678],(ichromantis befascia[&&NHX:TOL=53581],ichromantis dichroica[&&NHX:TOL=53582])ichromantis[&&NHX:TOL=53015],(kongobatha diademata[&&NHX:TOL=53583],kongobatha papua[&&NHX:TOL=53584])kongobatha[&&NHX:TOL=12684],(melomantis africana[&&NHX:TOL=53585],melomantis asema[&&NHX:TOL=53586])melomantis[&&NHX:TOL=12679],miromantis mirandula[&&NHX:TOL=12683],(negromantis gracilis[&&NHX:TOL=53587],negromantis gracillima[&&NHX:TOL=53588],negromantis lutescens[&&NHX:TOL=53589],negromantis modesta[&&NHX:TOL=53590])negromantis[&&NHX:TOL=12681],(neomantis australis[&&NHX:TOL=53591],neomantis hyalina[&&NHX:TOL=53592],neomantis robusta[&&NHX:TOL=53593])neomantis[&&NHX:TOL=12674],(ormomantis indica[&&NHX:TOL=53594],ormomantis yunnanensis[&&NHX:TOL=53595])ormomantis[&&NHX:TOL=53016],oxymantis punctillata[&&NHX:TOL=12703],platycalymma latipennis[&&NHX:TOL=12676],((tropidomantis eomantis guttatipennis[&&NHX:TOL=53600],tropidomantis eomantis iridipennis[&&NHX:TOL=53601],tropidomantis eomantis yunnanensis[&&NHX:TOL=53602])tropidomantis eomantis[&&NHX:TOL=53599],(tropidomantis tropidomantis gressitti[&&NHX:TOL=53597],tropidomantis tropidomantis tenera[&&NHX:TOL=53598])tropidomantis tropidomantis[&&NHX:TOL=53596])tropidomantis[&&NHX:TOL=12675],(xanthomantis oligocanthopus ornata[&&NHX:TOL=53607],xanthomantis pliacanthopus mantispoides[&&NHX:TOL=53608],(xanthomantis xanthomantis bimaculata[&&NHX:TOL=53604],xanthomantis xanthomantis flava[&&NHX:TOL=53605],xanthomantis xanthomantis malayana[&&NHX:TOL=53606])xanthomantis xanthomantis[&&NHX:TOL=53603])xanthomantis[&&NHX:TOL=12682])tropidomantinae[&&NHX:TOL=12673])iridopterygidae[&&NHX:TOL=12742],((ciulfina biseriata[&&NHX:TOL=53741],ciulfina liturgusa[&&NHX:TOL=53742])ciulfina[&&NHX:TOL=12715],(dactylopteryx flexuosa[&&NHX:TOL=53743],dactylopteryx intermedia[&&NHX:TOL=53744],dactylopteryx orientalis[&&NHX:TOL=53745])dactylopteryx[&&NHX:TOL=12716],(gonatista grisea[&&NHX:TOL=53746],gonatista jaiba[&&NHX:TOL=57003],gonatista major[&&NHX:TOL=53747],gonatista phryganoides[&&NHX:TOL=53748],gonatista reticulata[&&NHX:TOL=53749])gonatista[&&NHX:TOL=12719],(gonatistella gongylodes[&&NHX:TOL=53750],gonatistella trachelophyllus[&&NHX:TOL=53751])gonatistella[&&NHX:TOL=12718],(hagiomantis fluminensis[&&NHX:TOL=53752],hagiomantis ornata[&&NHX:TOL=53753],hagiomantis pallida[&&NHX:TOL=53754],hagiomantis parva[&&NHX:TOL=53755],hagiomantis superba[&&NHX:TOL=53756],hagiomantis surinamensis[&&NHX:TOL=53757])hagiomantis[&&NHX:TOL=12720],(humbertiella affinis[&&NHX:TOL=53758],humbertiella ceylonica[&&NHX:TOL=53759],humbertiella indica[&&NHX:TOL=53760],humbertiella laosana[&&NHX:TOL=53761],humbertiella nada[&&NHX:TOL=53762],humbertiella nigrospinosa[&&NHX:TOL=53763],humbertiella ocularis[&&NHX:TOL=53764],humbertiella similis[&&NHX:TOL=53765],humbertiella taprobanarum[&&NHX:TOL=53766],humbertiella yunnanensis[&&NHX:TOL=53767])humbertiella[&&NHX:TOL=12721],(liturgusa actuosa[&&NHX:TOL=53768],liturgusa annulipes[&&NHX:TOL=53769],liturgusa atricoxata[&&NHX:TOL=53770],liturgusa cayennensis[&&NHX:TOL=53771],liturgusa charpentieri[&&NHX:TOL=53772],liturgusa cursor[&&NHX:TOL=53773],liturgusa guyanensis[&&NHX:TOL=53774],liturgusa lichenalis[&&NHX:TOL=53775],liturgusa maya[&&NHX:TOL=53776],liturgusa mesopoda[&&NHX:TOL=53777],liturgusa nubeculosa[&&NHX:TOL=53778],liturgusa parva[&&NHX:TOL=53779],liturgusa peruviana[&&NHX:TOL=53780],liturgusa sinvalnetoi[&&NHX:TOL=53781])liturgusa[&&NHX:TOL=12722],liturgusella malagassa[&&NHX:TOL=12723],(majanga basilaris[&&NHX:TOL=53782],majanga spinosa[&&NHX:TOL=53783],majanga tricolor[&&NHX:TOL=53784])majanga[&&NHX:TOL=12724],(majangella carli[&&NHX:TOL=53785],majangella moultoni[&&NHX:TOL=53786])majangella[&&NHX:TOL=12725],mellierella biroi[&&NHX:TOL=12727],pseudogousa sinensis[&&NHX:TOL=52977],scolodera pardalotus[&&NHX:TOL=52978],stenomantis novaeguineae[&&NHX:TOL=12728],(theopompa borneana[&&NHX:TOL=53787],theopompa burmeisteri[&&NHX:TOL=53788],theopompa ophthalmica[&&NHX:TOL=53789],theopompa servillei[&&NHX:TOL=53790],theopompa tosta[&&NHX:TOL=53791])theopompa[&&NHX:TOL=12729],(theopompella aurivillii[&&NHX:TOL=53792],theopompella chopardi[&&NHX:TOL=53793],theopompella congica[&&NHX:TOL=53794],theopompella elegans[&&NHX:TOL=53795],theopompella fusca[&&NHX:TOL=53796],theopompella heterochroa[&&NHX:TOL=53797],theopompella orientalis[&&NHX:TOL=53798],theopompella pallida[&&NHX:TOL=53799],theopompella westwoodi[&&NHX:TOL=53800])theopompella[&&NHX:TOL=12730],zouza radiosa[&&NHX:TOL=12731])liturgusidae[&&NHX:TOL=12743],(((amantis aeta[&&NHX:TOL=53801],amantis aliena[&&NHX:TOL=53802],amantis basilana[&&NHX:TOL=53803],amantis biroi[&&NHX:TOL=53804],amantis bolivarii[&&NHX:TOL=53805],amantis fuliginosa[&&NHX:TOL=53806],amantis fumosa[&&NHX:TOL=53807],amantis gestri[&&NHX:TOL=53808],amantis hainanensis[&&NHX:TOL=53809],amantis indica[&&NHX:TOL=53810],amantis irina[&&NHX:TOL=53811],amantis lofaoshanensis[&&NHX:TOL=53812],amantis longipennis[&&NHX:TOL=53813],amantis malabarensis[&&NHX:TOL=56985],amantis malayana[&&NHX:TOL=53814],amantis nawai[&&NHX:TOL=53815],amantis philippina[&&NHX:TOL=53816],amantis reticulata[&&NHX:TOL=53817],amantis saussurei[&&NHX:TOL=53818],amantis subirina[&&NHX:TOL=53819],amantis testacea[&&NHX:TOL=53820],amantis tristis[&&NHX:TOL=53821],amantis vitalisi[&&NHX:TOL=53822])amantis[&&NHX:TOL=12515],(ameles aegyptiaca[&&NHX:TOL=53823],ameles africana[&&NHX:TOL=53824],ameles arabica[&&NHX:TOL=53825],ameles assoi[&&NHX:TOL=53826],ameles crassinervis[&&NHX:TOL=53827],ameles cyprica[&&NHX:TOL=53828],ameles decolor[&&NHX:TOL=53829],ameles dumonti[&&NHX:TOL=53830],ameles fasciipennis[&&NHX:TOL=53831],ameles gracilis[&&NHX:TOL=53832],ameles heldreichi[&&NHX:TOL=53833],ameles kervillei[&&NHX:TOL=53834],ameles limbata[&&NHX:TOL=53835],ameles maroccana[&&NHX:TOL=53836],ameles modesta[&&NHX:TOL=53837],ameles moralesi[&&NHX:TOL=53838],ameles persa[&&NHX:TOL=53839],ameles picteti[&&NHX:TOL=53840],ameles poggii[&&NHX:TOL=53841],ameles spallanzania[&&NHX:TOL=53842],ameles syriensis[&&NHX:TOL=53843],ameles taurica[&&NHX:TOL=53844],ameles wadisirhani[&&NHX:TOL=53845])ameles[&&NHX:TOL=12516],apterameles rammei[&&NHX:TOL=53036],(apteromantis aptera[&&NHX:TOL=53846],apteromantis bolivari[&&NHX:TOL=53847])apteromantis[&&NHX:TOL=12517],armeniola laevis[&&NHX:TOL=12519],bimantis malaccana[&&NHX:TOL=12520],(bolbella affinis[&&NHX:TOL=53848],bolbella brevis[&&NHX:TOL=53849],bolbella punctigera[&&NHX:TOL=53850],bolbella rhodesiaca[&&NHX:TOL=53851])bolbella[&&NHX:TOL=53037],(compsomantis ceylonica[&&NHX:TOL=53852],compsomantis crassiceps[&&NHX:TOL=53853],compsomantis mindoroensis[&&NHX:TOL=53854],compsomantis robusta[&&NHX:TOL=53855],compsomantis semirufula[&&NHX:TOL=53856],compsomantis tumidiceps[&&NHX:TOL=53857])compsomantis[&&NHX:TOL=12522],congomantis femoralis[&&NHX:TOL=12521],dimantis haani[&&NHX:TOL=12523],dystactula grisea[&&NHX:TOL=12524],(elaea gestroi[&&NHX:TOL=53858],elaea infumata[&&NHX:TOL=53859],elaea marchali[&&NHX:TOL=53860],elaea richteri[&&NHX:TOL=53861])elaea[&&NHX:TOL=53038],(elmantis lata[&&NHX:TOL=53862],elmantis nira[&&NHX:TOL=53863],elmantis trincomaliae[&&NHX:TOL=53864])elmantis[&&NHX:TOL=12525],(gimantis assamica[&&NHX:TOL=53865],gimantis authaemon[&&NHX:TOL=53866],gimantis insularis[&&NHX:TOL=53867])gimantis[&&NHX:TOL=12526],(gonypeta borneana[&&NHX:TOL=53868],gonypeta brigittae[&&NHX:TOL=53869],gonypeta brunneri[&&NHX:TOL=53870],gonypeta punctata[&&NHX:TOL=53871],gonypeta rotundata[&&NHX:TOL=53872],gonypeta simplex[&&NHX:TOL=53873])gonypeta[&&NHX:TOL=12527],(gonypetella atra[&&NHX:TOL=53874],gonypetella atrocephala[&&NHX:TOL=53875],gonypetella australis[&&NHX:TOL=53876],gonypetella carinata[&&NHX:TOL=53877],gonypetella deletrix[&&NHX:TOL=53878],gonypetella flavicornis[&&NHX:TOL=53879],gonypetella fusca[&&NHX:TOL=53880],gonypetella fuscipes[&&NHX:TOL=53881],gonypetella infumata[&&NHX:TOL=53882],gonypetella ivoirensis[&&NHX:TOL=53883],gonypetella kilimandjarica[&&NHX:TOL=53884],gonypetella punctata[&&NHX:TOL=53885])gonypetella[&&NHX:TOL=12528],gonypetoides brevipennis[&&NHX:TOL=53039],gonypetyllis semuncialis[&&NHX:TOL=53040],holaptilon pusillulum[&&NHX:TOL=53041],(litaneutria borealis[&&NHX:TOL=53886],litaneutria longipennis[&&NHX:TOL=53887],litaneutria minor[&&NHX:TOL=53888],litaneutria obscura[&&NHX:TOL=53889],litaneutria ocularis[&&NHX:TOL=53890],litaneutria pacifica[&&NHX:TOL=53891],litaneutria skinneri[&&NHX:TOL=53892])litaneutria[&&NHX:TOL=12530],(memantis anomala[&&NHX:TOL=53893],memantis fuliginosa[&&NHX:TOL=53894],memantis gardeneri[&&NHX:TOL=53895],memantis minor[&&NHX:TOL=53896])memantis[&&NHX:TOL=12531],(myrcinus aspera[&&NHX:TOL=53897],myrcinus octispinus[&&NHX:TOL=53898],myrcinus tuberosus[&&NHX:TOL=53899])myrcinus[&&NHX:TOL=12532],(pseudoyersinia betancuriae[&&NHX:TOL=53900],pseudoyersinia brevipennis[&&NHX:TOL=53901],pseudoyersinia canariensis[&&NHX:TOL=53902],pseudoyersinia inaspectata[&&NHX:TOL=53903],pseudoyersinia kabilica[&&NHX:TOL=53904],pseudoyersinia lagrecai[&&NHX:TOL=53905],pseudoyersinia occidentalis[&&NHX:TOL=53906],pseudoyersinia paui[&&NHX:TOL=53907],pseudoyersinia pilipes[&&NHX:TOL=53908],pseudoyersinia salvinae[&&NHX:TOL=53909],pseudoyersinia subaptera[&&NHX:TOL=53910],pseudoyersinia teydeana[&&NHX:TOL=53911])pseudoyersinia[&&NHX:TOL=12533],(telomantis lamperti[&&NHX:TOL=53912],telomantis robusta[&&NHX:TOL=53913])telomantis[&&NHX:TOL=12534],yersinia mexicana[&&NHX:TOL=12535],(yersiniops newboldi[&&NHX:TOL=53914],yersiniops solitaria[&&NHX:TOL=53915],yersiniops sophronica[&&NHX:TOL=53916])yersiniops[&&NHX:TOL=12536])amelinae[&&NHX:TOL=12733],((agrionopsis brachyptera[&&NHX:TOL=53917],agrionopsis congica[&&NHX:TOL=53918],agrionopsis distanti[&&NHX:TOL=53919],agrionopsis modesta[&&NHX:TOL=53920])agrionopsis[&&NHX:TOL=12552],(angela armata[&&NHX:TOL=53921],angela championi[&&NHX:TOL=53922],angela decolor[&&NHX:TOL=53923],angela guianensis[&&NHX:TOL=53924],angela inermis[&&NHX:TOL=53925],angela lemoulti[&&NHX:TOL=53926],angela maxima[&&NHX:TOL=53927],angela minor[&&NHX:TOL=53928],angela miranda[&&NHX:TOL=53929],angela perpulchra[&&NHX:TOL=53930],angela peruviana[&&NHX:TOL=53931],angela purpurascens[&&NHX:TOL=53932],angela quinquemaculata[&&NHX:TOL=53933],angela saussurii[&&NHX:TOL=53934],angela subhyalina[&&NHX:TOL=53935],angela trifasciata[&&NHX:TOL=53936],angela werneri[&&NHX:TOL=53937])angela[&&NHX:TOL=12553],(euchomenella apicalis[&&NHX:TOL=53938],euchomenella heteroptera[&&NHX:TOL=53940],euchomenella indica[&&NHX:TOL=56999],euchomenella macrops[&&NHX:TOL=53941],euchomenella matilei[&&NHX:TOL=53942],euchomenella moluccarum[&&NHX:TOL=53943],euchomenella pallida[&&NHX:TOL=53944],euchomenella thoracica[&&NHX:TOL=53945])euchomenella[&&NHX:TOL=12554],(leptocola fragilis[&&NHX:TOL=53946],leptocola gracilis[&&NHX:TOL=53947],leptocola gracillima[&&NHX:TOL=53948],leptocola phthisica[&&NHX:TOL=53949],leptocola seriepunctata[&&NHX:TOL=53950],leptocola stanleyana[&&NHX:TOL=53951])leptocola[&&NHX:TOL=12555],(mythomantis confusa[&&NHX:TOL=53952],mythomantis gracilis[&&NHX:TOL=53953])mythomantis[&&NHX:TOL=12556],(stenopyga agriomantis casta[&&NHX:TOL=53954],(stenopyga stenopyga belinga[&&NHX:TOL=53956],stenopyga stenopyga extera[&&NHX:TOL=53957],stenopyga stenopyga ipassa[&&NHX:TOL=53958],stenopyga stenopyga rhodesiaca[&&NHX:TOL=53959],stenopyga stenopyga tenera[&&NHX:TOL=53960],stenopyga stenopyga ziela[&&NHX:TOL=53961])stenopyga stenopyga[&&NHX:TOL=53955],(stenopyga stenopygella orientalis[&&NHX:TOL=53963],stenopyga stenopygella reticulata[&&NHX:TOL=53964],stenopyga stenopygella usambarica[&&NHX:TOL=53965])stenopyga stenopygella[&&NHX:TOL=53962])stenopyga[&&NHX:TOL=12558],(tagalomantis brevis[&&NHX:TOL=53966],tagalomantis manillensis[&&NHX:TOL=53967])tagalomantis[&&NHX:TOL=53023],thespoides bolivari[&&NHX:TOL=12559])angelinae[&&NHX:TOL=12734],antemna rapax[&&NHX:TOL=53096],((asiadodis squilla[&&NHX:TOL=12583],asiadodis yunnanensis[&&NHX:TOL=56934])asiadodis[&&NHX:TOL=56933],(choeradodis columbica[&&NHX:TOL=56935],choeradodis rhombicollis[&&NHX:TOL=12580],choeradodis rhomboidea[&&NHX:TOL=12581],choeradodis stalii[&&NHX:TOL=12584],choeradodis strumaria[&&NHX:TOL=12585])choeradodis[&&NHX:TOL=52737],prochoeradodis enigmaticus[&&NHX:EXT=Y:TOL=12586])choeradodinae[&&NHX:TOL=12736],((betamantis aliena[&&NHX:TOL=53968],betamantis marginella[&&NHX:TOL=53969])betamantis[&&NHX:TOL=12507],(chopardentella backlundi[&&NHX:TOL=53970],chopardentella royi[&&NHX:TOL=53971])chopardentella[&&NHX:TOL=53025],(chroicoptera longa[&&NHX:TOL=53972],chroicoptera saussurei[&&NHX:TOL=53973],chroicoptera vidua[&&NHX:TOL=53974])chroicoptera[&&NHX:TOL=12508],((entella entella angolensis[&&NHX:TOL=53976],entella entella angolica[&&NHX:TOL=53977],entella entella brunni[&&NHX:TOL=53978],entella entella congica[&&NHX:TOL=53979],entella entella delalandi[&&NHX:TOL=53980],entella entella exilis[&&NHX:TOL=53981],entella entella femina[&&NHX:TOL=53982],entella entella grandis[&&NHX:TOL=53983],entella entella machadoi[&&NHX:TOL=53984],entella entella maesta[&&NHX:TOL=53985],entella entella meruensis[&&NHX:TOL=53986],entella entella minor[&&NHX:TOL=53987],entella entella natalica[&&NHX:TOL=53988],entella entella nebulosa[&&NHX:TOL=53989],entella entella obscura[&&NHX:TOL=53990],entella entella orientalis[&&NHX:TOL=53991],entella entella personata[&&NHX:TOL=53992],entella entella pusilla[&&NHX:TOL=53993],entella entella reussi[&&NHX:TOL=53994],entella entella rudebecki[&&NHX:TOL=53995],entella entella rukwaensis[&&NHX:TOL=53996],entella entella stegmanni[&&NHX:TOL=53997],entella entella taborana[&&NHX:TOL=53998],entella entella transvaalica[&&NHX:TOL=53999],entella entella vitticeps[&&NHX:TOL=54000])entella entella[&&NHX:TOL=53975],entella euentella gaerdesi[&&NHX:TOL=54001])entella[&&NHX:TOL=12510],entelloptera rogenhoferi[&&NHX:TOL=53026],(ligaria aberrans[&&NHX:TOL=54002],ligaria affinis[&&NHX:TOL=54003],ligaria brevicollis[&&NHX:TOL=54004],ligaria brevis[&&NHX:TOL=54005],ligaria chopardi[&&NHX:TOL=54006],ligaria clara[&&NHX:TOL=54007],ligaria culicivora[&&NHX:TOL=54008],ligaria dentata[&&NHX:TOL=54009],ligaria denticollis[&&NHX:TOL=54010],ligaria inexpectata[&&NHX:TOL=54011],ligaria quadrinotata[&&NHX:TOL=54012])ligaria[&&NHX:TOL=12511],(ligariella bicornuta[&&NHX:TOL=54013],ligariella diabolica[&&NHX:TOL=54014],ligariella gracilis[&&NHX:TOL=54015],ligariella trigonalis[&&NHX:TOL=54016])ligariella[&&NHX:TOL=53028],(ligentella beieri[&&NHX:TOL=54017],ligentella lacualis[&&NHX:TOL=54018],ligentella zairensis[&&NHX:TOL=54019])ligentella[&&NHX:TOL=53027],(macracanthopus costalis[&&NHX:TOL=54020],macracanthopus schoutedeni[&&NHX:TOL=54021],macracanthopus seydeli[&&NHX:TOL=54022])macracanthopus[&&NHX:TOL=53029],(namamantis cruciata[&&NHX:TOL=54023],namamantis nigropunctata[&&NHX:TOL=54024])namamantis[&&NHX:TOL=53030],(parentella benguelae[&&NHX:TOL=54025],parentella laticollis[&&NHX:TOL=54026],parentella major[&&NHX:TOL=54027],parentella parva[&&NHX:TOL=54028],parentella producta[&&NHX:TOL=54029])parentella[&&NHX:TOL=12512],rhachimantis carinata[&&NHX:TOL=12513],(rogermantis natalensis[&&NHX:TOL=54030],rogermantis royi[&&NHX:TOL=54031])rogermantis[&&NHX:TOL=53031])chroicopterinae[&&NHX:TOL=53024],(compsothespis abyssinica[&&NHX:TOL=54032],compsothespis anomala[&&NHX:TOL=54033],compsothespis australiensis[&&NHX:TOL=54034],compsothespis brevipennis[&&NHX:TOL=54035],compsothespis cinnabarina[&&NHX:TOL=54036],compsothespis ebneri[&&NHX:TOL=54037],compsothespis falcifera[&&NHX:TOL=54038],compsothespis hispida[&&NHX:TOL=54039],compsothespis kilwana[&&NHX:TOL=54040],compsothespis marginipennis[&&NHX:TOL=54041],compsothespis michaelseni[&&NHX:TOL=54042],compsothespis natalica[&&NHX:TOL=54043],compsothespis occidentalis[&&NHX:TOL=54044],compsothespis zavattarii[&&NHX:TOL=54045])compsothespis[&&NHX:TOL=12737],((brancsikia aeroplana[&&NHX:TOL=54046],brancsikia freyi[&&NHX:TOL=54047],brancsikia simplex[&&NHX:TOL=54048])brancsikia[&&NHX:TOL=12589],(deroplatys angustata[&&NHX:TOL=54049],deroplatys desiccata[&&NHX:TOL=54050],deroplatys gorochovi[&&NHX:TOL=54051],deroplatys lobata[&&NHX:TOL=54052],deroplatys moultoni[&&NHX:TOL=54053],deroplatys philippinica[&&NHX:TOL=54054],deroplatys rhombica[&&NHX:TOL=54055],deroplatys sarawaca[&&NHX:TOL=54056],deroplatys shelfordi[&&NHX:TOL=54057],deroplatys trigonodera[&&NHX:TOL=54058],deroplatys truncata[&&NHX:TOL=54059])deroplatys[&&NHX:TOL=12588])deroplatyinae[&&NHX:TOL=12738],(achlaena grandis[&&NHX:TOL=12505],achlaenella adolphifrederici[&&NHX:TOL=12506],(armene breviptera[&&NHX:TOL=54097],armene fanica[&&NHX:TOL=54098],armene griseoalata[&&NHX:TOL=54099],armene hissarica[&&NHX:TOL=54100],armene macroalata[&&NHX:TOL=54101],armene pusilla[&&NHX:TOL=54102],armene robusta[&&NHX:TOL=54103],armene silvicola[&&NHX:TOL=54104])armene[&&NHX:TOL=12518],beesonula pallida[&&NHX:TOL=53032],dystacta alticeps[&&NHX:TOL=12509],(paraligaria jeanneli[&&NHX:TOL=54105],paraligaria malawica[&&NHX:TOL=54106])paraligaria[&&NHX:TOL=53033],pseudodystacta braueri[&&NHX:TOL=53034],(sphaeromantis spinicollis[&&NHX:TOL=54107],sphaeromantis spinulosa[&&NHX:TOL=54108])sphaeromantis[&&NHX:TOL=53035])dystactinae[&&NHX:TOL=12504],(((archimantis armata[&&NHX:TOL=54370],archimantis brunneriana[&&NHX:TOL=54371],archimantis gracilis[&&NHX:TOL=54372],archimantis latistyla[&&NHX:TOL=54373],archimantis monstrosa[&&NHX:TOL=54374],archimantis quinquelobata[&&NHX:TOL=54375],archimantis sobrina[&&NHX:TOL=54376],archimantis straminea[&&NHX:TOL=54377],archimantis vittata[&&NHX:TOL=54378])archimantis[&&NHX:TOL=12565],austromantis albomarginata[&&NHX:TOL=53076],(austrovates papua[&&NHX:TOL=54379],austrovates variegata[&&NHX:TOL=54380])austrovates[&&NHX:TOL=12564],coenomantis kraussiana[&&NHX:TOL=12563],corthylomantis baldersoni[&&NHX:TOL=53077],nullabora flavoguttata[&&NHX:TOL=12566])archimantini[&&NHX:TOL=12764],(mantilia ehrmanni[&&NHX:TOL=53078],(mantis beieri[&&NHX:TOL=54381],mantis indica[&&NHX:TOL=54382],mantis insignis[&&NHX:TOL=54383],mantis macrocephala[&&NHX:TOL=54384],mantis octospilota[&&NHX:TOL=54385],mantis religiosa[&&NHX:TOL=54386])mantis[&&NHX:TOL=12778],(mesopteryx alata[&&NHX:TOL=54387],mesopteryx platycephala[&&NHX:TOL=54388],mesopteryx robusta[&&NHX:TOL=54389])mesopteryx[&&NHX:TOL=12781],(omomantis sigma[&&NHX:TOL=54390],omomantis tigrina[&&NHX:TOL=54391],omomantis zebrata[&&NHX:TOL=54392])omomantis[&&NHX:TOL=12796],(pseudomantis albofimbriata[&&NHX:TOL=54393],pseudomantis dimorpha[&&NHX:TOL=54394],pseudomantis hartmeyeri[&&NHX:TOL=54395],pseudomantis victorina[&&NHX:TOL=54396])pseudomantis[&&NHX:TOL=12561],(rhodomantis carinicollis[&&NHX:TOL=54397],rhodomantis gracilis[&&NHX:TOL=54398],rhodomantis pulchella[&&NHX:TOL=54399],rhodomantis queenslandica[&&NHX:TOL=54400])rhodomantis[&&NHX:TOL=12562],(statilia agresta[&&NHX:TOL=54401],statilia apicalis[&&NHX:TOL=54402],statilia chayuensis[&&NHX:TOL=54403],statilia flavobrunnea[&&NHX:TOL=54404],statilia maculata[&&NHX:TOL=54405],statilia nemoralis[&&NHX:TOL=54406],statilia ocellata[&&NHX:TOL=54407],statilia pallida[&&NHX:TOL=54408],statilia spanis[&&NHX:TOL=54409],statilia viridibrunnea[&&NHX:TOL=54410])statilia[&&NHX:TOL=12780])mantini[&&NHX:TOL=12763],((alalomantis coxalis[&&NHX:TOL=54411],alalomantis muta[&&NHX:TOL=54412])alalomantis[&&NHX:TOL=12772],(bisanthe lagrecai[&&NHX:TOL=54413],bisanthe menyharthi[&&NHX:TOL=54414],bisanthe pulchripennis[&&NHX:TOL=54415])bisanthe[&&NHX:TOL=12775],(camelomantis giraffa[&&NHX:TOL=54416],camelomantis gracillima[&&NHX:TOL=54417],camelomantis moultoni[&&NHX:TOL=54418],camelomantis parva[&&NHX:TOL=54419],camelomantis penangica[&&NHX:TOL=54420],camelomantis sondaica[&&NHX:TOL=54421],camelomantis sumatrana[&&NHX:TOL=54422])camelomantis[&&NHX:TOL=12776],(epitenodera brevipennis[&&NHX:TOL=54423],epitenodera capitata[&&NHX:TOL=54424],epitenodera equatoriana[&&NHX:TOL=54425],epitenodera herbacea[&&NHX:TOL=54426],epitenodera houyi[&&NHX:TOL=54427],epitenodera nimbana[&&NHX:TOL=54428])epitenodera[&&NHX:TOL=53071],(hierodula ansusana[&&NHX:TOL=54429],hierodula aruana[&&NHX:TOL=54430],hierodula assamensis[&&NHX:TOL=54431],hierodula atrocoxata[&&NHX:TOL=54432],hierodula beieri[&&NHX:TOL=54433],hierodula bhamoana[&&NHX:TOL=54434],hierodula biaka[&&NHX:TOL=54435],hierodula borneana[&&NHX:TOL=54436],hierodula brunnea[&&NHX:TOL=54437],hierodula chinensis[&&NHX:TOL=54438],hierodula coarctata[&&NHX:TOL=54439],hierodula cuchingina[&&NHX:TOL=54440],hierodula daqingshanensis[&&NHX:TOL=54441],hierodula dolichoptera[&&NHX:TOL=54442],hierodula doveri[&&NHX:TOL=54443],hierodula dubia[&&NHX:TOL=54444],hierodula dyaka[&&NHX:TOL=54445],hierodula everetti[&&NHX:TOL=54446],hierodula excellens[&&NHX:TOL=54447],hierodula formosana[&&NHX:TOL=54448],hierodula fruhstorferi[&&NHX:TOL=54449],hierodula fumipennis[&&NHX:TOL=54450],hierodula fuscescens[&&NHX:TOL=54451],hierodula gigliotosi[&&NHX:TOL=54452],hierodula gracilicollis[&&NHX:TOL=54453],hierodula grandis[&&NHX:TOL=54454],hierodula harpyia[&&NHX:TOL=54455],hierodula heinrichi[&&NHX:TOL=54456],hierodula heteroptera[&&NHX:TOL=54457],hierodula immaculifemorata[&&NHX:TOL=54458],hierodula inconspicua[&&NHX:TOL=54459],hierodula ingens[&&NHX:TOL=54460],hierodula jobina[&&NHX:TOL=54461],hierodula kapaurana[&&NHX:TOL=54462],hierodula keralensis[&&NHX:TOL=57001],hierodula laevicollis[&&NHX:TOL=54463],hierodula lamasonga[&&NHX:TOL=54464],hierodula latipennis[&&NHX:TOL=54465],hierodula longedentata[&&NHX:TOL=54466],hierodula macrosticmata[&&NHX:TOL=54467],hierodula maculisternum[&&NHX:TOL=54468],hierodula majuscula[&&NHX:TOL=54469],hierodula malaya[&&NHX:TOL=54470],hierodula membranacea[&&NHX:TOL=54471],hierodula microdon[&&NHX:TOL=54472],hierodula mindanensis[&&NHX:TOL=54473],hierodula modesta[&&NHX:TOL=54474],hierodula monochroa[&&NHX:TOL=54475],hierodula multispina[&&NHX:TOL=54476],hierodula multispinulosa[&&NHX:TOL=54477],hierodula nicobarica[&&NHX:TOL=54478],hierodula obiensis[&&NHX:TOL=54479],hierodula obtusata[&&NHX:TOL=54480],hierodula oraea[&&NHX:TOL=54481],hierodula papua[&&NHX:TOL=54482],hierodula parviceps[&&NHX:TOL=54483],hierodula patellifera[&&NHX:TOL=54484],hierodula perakana[&&NHX:TOL=54485],hierodula philippina[&&NHX:TOL=54486],hierodula prosternalis[&&NHX:TOL=54487],hierodula pulchra[&&NHX:TOL=54488],hierodula pulchripes[&&NHX:TOL=54489],hierodula purpurescens[&&NHX:TOL=54490],hierodula pustulifera[&&NHX:TOL=54491],hierodula pygmaea[&&NHX:TOL=54492],hierodula quadridens[&&NHX:TOL=54493],hierodula quadripunctata[&&NHX:TOL=54494],hierodula quinquepatellata[&&NHX:TOL=54495],hierodula rajah[&&NHX:TOL=54496],hierodula ralumina[&&NHX:TOL=54497],hierodula rufomaculata[&&NHX:TOL=54498],hierodula rufopatellata[&&NHX:TOL=54499],hierodula salomonis[&&NHX:TOL=54500],hierodula sarsinorum[&&NHX:TOL=54501],hierodula schultzei[&&NHX:TOL=54502],hierodula simbangana[&&NHX:TOL=54503],hierodula similis[&&NHX:TOL=54504],hierodula siporana[&&NHX:TOL=54505],hierodula sorongana[&&NHX:TOL=54506],hierodula sternosticta[&&NHX:TOL=54507],hierodula striata[&&NHX:TOL=54508],hierodula striatipes[&&NHX:TOL=54509],hierodula szentivanyi[&&NHX:TOL=54510],hierodula tenuidentata[&&NHX:TOL=54511],hierodula tenuis[&&NHX:TOL=54512],hierodula timorensis[&&NHX:TOL=54513],hierodula togiana[&&NHX:TOL=54514],hierodula tonkinensis[&&NHX:TOL=54515],hierodula tornica[&&NHX:TOL=54516],hierodula transcaucasica[&&NHX:TOL=54517],hierodula trimaculata[&&NHX:TOL=54518],hierodula unimaculata[&&NHX:TOL=54519],hierodula venosa[&&NHX:TOL=54520],hierodula ventralis[&&NHX:TOL=54521],hierodula versicolor[&&NHX:TOL=54522],hierodula vitreoides[&&NHX:TOL=54523],hierodula werneri[&&NHX:TOL=54524],hierodula xishaensis[&&NHX:TOL=54525],hierodula yunnanensis[&&NHX:TOL=54526])hierodula[&&NHX:TOL=12768],(hierodulella albomaculata[&&NHX:TOL=54527],hierodulella celebensis[&&NHX:TOL=54528],hierodulella reticulata[&&NHX:TOL=54529],hierodulella soror[&&NHX:TOL=54530])hierodulella[&&NHX:TOL=12771],(mantasoa lebbei[&&NHX:TOL=56984],mantasoa macula[&&NHX:TOL=54628])mantasoa[&&NHX:TOL=56983],(notomantis brunneriana[&&NHX:TOL=54531],notomantis chlorophana[&&NHX:TOL=54532])notomantis[&&NHX:TOL=12774],(paramantis natalensis[&&NHX:TOL=54533],paramantis nyassana[&&NHX:TOL=54534],paramantis prasina[&&NHX:TOL=54535],paramantis sacra[&&NHX:TOL=54536],paramantis togana[&&NHX:TOL=54537],paramantis victoriana[&&NHX:TOL=54538],paramantis viridis[&&NHX:TOL=54539])paramantis[&&NHX:TOL=12777],pnigomantis medioconstricta[&&NHX:TOL=12770],pseudostagmatoptera infuscata[&&NHX:TOL=53072],(rhombodera basalis[&&NHX:TOL=54540],rhombodera boschmai[&&NHX:TOL=54541],rhombodera brachynota[&&NHX:TOL=54542],rhombodera butleri[&&NHX:TOL=54543],rhombodera crassa[&&NHX:TOL=54544],rhombodera doriana[&&NHX:TOL=54545],rhombodera extensicollis[&&NHX:TOL=54546],rhombodera extraordinaria[&&NHX:TOL=54547],rhombodera flava[&&NHX:TOL=54548],rhombodera fratricida[&&NHX:TOL=54549],rhombodera fusca[&&NHX:TOL=54550],rhombodera handschini[&&NHX:TOL=54551],rhombodera javana[&&NHX:TOL=54552],rhombodera keiana[&&NHX:TOL=54553],rhombodera kirbyi[&&NHX:TOL=54554],rhombodera laticollis[&&NHX:TOL=54555],rhombodera latipronotum[&&NHX:TOL=54556],rhombodera lingulata[&&NHX:TOL=54557],rhombodera megaera[&&NHX:TOL=54558],rhombodera mjoebergi[&&NHX:TOL=54559],rhombodera morokana[&&NHX:TOL=54560],rhombodera ornatipes[&&NHX:TOL=54561],rhombodera palawanensis[&&NHX:TOL=54562],rhombodera papuana[&&NHX:TOL=54563],rhombodera rennellana[&&NHX:TOL=54564],rhombodera rollei[&&NHX:TOL=54565],rhombodera sjoestedti[&&NHX:TOL=54566],rhombodera stalii[&&NHX:TOL=54567],rhombodera taprobana[&&NHX:TOL=54568],rhombodera tectiformis[&&NHX:TOL=54569],rhombodera titania[&&NHX:TOL=54570],rhombodera valida[&&NHX:TOL=54571],rhombodera woodmasoni[&&NHX:TOL=54572],rhombodera zhangi[&&NHX:TOL=54573])rhombodera[&&NHX:TOL=12792],(rhomboderella gabonica[&&NHX:TOL=54574],rhomboderella parmata[&&NHX:TOL=54575],rhomboderella scutata[&&NHX:TOL=54576],rhomboderella thorectes[&&NHX:TOL=54577])rhomboderella[&&NHX:TOL=53073],(sphodromantis abessinica[&&NHX:TOL=54578],sphodromantis aethiopica[&&NHX:TOL=54579],sphodromantis annobonensis[&&NHX:TOL=54580],sphodromantis aurea[&&NHX:TOL=54581],sphodromantis baccettii[&&NHX:TOL=54582],sphodromantis balachowskyi[&&NHX:TOL=54583],sphodromantis biocellata[&&NHX:TOL=54584],sphodromantis centralis[&&NHX:TOL=54585],sphodromantis citernii[&&NHX:TOL=54586],sphodromantis congica[&&NHX:TOL=54587],sphodromantis conspicua[&&NHX:TOL=54588],sphodromantis elegans[&&NHX:TOL=54589],sphodromantis elongata[&&NHX:TOL=54590],sphodromantis fenestrata[&&NHX:TOL=54591],sphodromantis gastrica[&&NHX:TOL=54592],sphodromantis gestri[&&NHX:TOL=54593],sphodromantis giubana[&&NHX:TOL=54594],sphodromantis gracilicollis[&&NHX:TOL=54595],sphodromantis gracilis[&&NHX:TOL=54596],sphodromantis hyalina[&&NHX:TOL=54597],sphodromantis kersteni[&&NHX:TOL=54598],sphodromantis lagrecai[&&NHX:TOL=54599],sphodromantis lineola[&&NHX:TOL=54600],sphodromantis obscura[&&NHX:TOL=54601],sphodromantis pachinota[&&NHX:TOL=54602],sphodromantis pardii[&&NHX:TOL=54603],sphodromantis pavonina[&&NHX:TOL=54604],sphodromantis quinquecallosa[&&NHX:TOL=54605],sphodromantis royi[&&NHX:TOL=54606],sphodromantis rubrostigma[&&NHX:TOL=54607],sphodromantis rudolfae[&&NHX:TOL=54608],sphodromantis tenuidentata[&&NHX:TOL=54609],sphodromantis trimacula[&&NHX:TOL=54610],sphodromantis viridis[&&NHX:TOL=54611])sphodromantis[&&NHX:TOL=12787],stictomantis cinctipes[&&NHX:TOL=53074],(tamolanica andaina[&&NHX:TOL=54612],tamolanica atricoxis[&&NHX:TOL=54613],tamolanica denticulata[&&NHX:TOL=54614],tamolanica dilena[&&NHX:TOL=54615],tamolanica katauana[&&NHX:TOL=54616],tamolanica leopoldi[&&NHX:TOL=54617],tamolanica pectoralis[&&NHX:TOL=54618],tamolanica phryne[&&NHX:TOL=54619],tamolanica splendida[&&NHX:TOL=54620],tamolanica tamolana[&&NHX:TOL=54621])tamolanica[&&NHX:TOL=12791],(tarachomantis alaotrana[&&NHX:TOL=54622],tarachomantis betanimena[&&NHX:TOL=54623],tarachomantis betsilea[&&NHX:TOL=54624],tarachomantis caldwellii[&&NHX:TOL=54625],tarachomantis confusa[&&NHX:TOL=54626],tarachomantis hova[&&NHX:TOL=54627],tarachomantis rubiginosa[&&NHX:TOL=54629],tarachomantis sakalava[&&NHX:TOL=54630])tarachomantis[&&NHX:TOL=12769],(tisma acutipennis[&&NHX:TOL=54631],tisma chopardi[&&NHX:TOL=56979],tisma freyi[&&NHX:TOL=54632],tisma grandidieri[&&NHX:TOL=54633],tisma pauliani[&&NHX:TOL=56980],tisma peyrierasi[&&NHX:TOL=56981])tisma[&&NHX:TOL=12767],(tismomorpha cherlonneixi[&&NHX:TOL=54634],tismomorpha inexpectata[&&NHX:TOL=54635],tismomorpha vitripennis[&&NHX:TOL=54636])tismomorpha[&&NHX:TOL=53075])paramantini[&&NHX:TOL=53070],((calospilota armicollis[&&NHX:TOL=54109],calospilota calabarica[&&NHX:TOL=54110],calospilota duchaillui[&&NHX:TOL=54111],calospilota guineensis[&&NHX:TOL=54112],calospilota lolodorfana[&&NHX:TOL=54113],calospilota misana[&&NHX:TOL=54114],calospilota pulchra[&&NHX:TOL=54115],calospilota tristis[&&NHX:TOL=54116])calospilota[&&NHX:TOL=12790],(plistospilota camerunensis[&&NHX:TOL=54117],plistospilota congica[&&NHX:TOL=54118],plistospilota gasconi[&&NHX:TOL=54119],plistospilota guineensis[&&NHX:TOL=54120],plistospilota insignis[&&NHX:TOL=54121],plistospilota mabirica[&&NHX:TOL=54122],plistospilota maxima[&&NHX:TOL=54123],plistospilota nigerica[&&NHX:TOL=54124],plistospilota nova[&&NHX:TOL=54125],plistospilota validissima[&&NHX:TOL=54126])plistospilota[&&NHX:TOL=12795],(polyspilota aeruginosa[&&NHX:TOL=54127],polyspilota caffra[&&NHX:TOL=54128],polyspilota comorana[&&NHX:TOL=54129],polyspilota griffinii[&&NHX:TOL=54130],polyspilota magna[&&NHX:TOL=54131],polyspilota montana[&&NHX:TOL=54132],polyspilota pavani[&&NHX:TOL=54133],polyspilota robusta[&&NHX:TOL=54134],polyspilota seychelliana[&&NHX:TOL=54135],polyspilota voelzkowiana[&&NHX:TOL=54136])polyspilota[&&NHX:TOL=12794],(prohierodula brunnea[&&NHX:TOL=54137],prohierodula congica[&&NHX:TOL=54138],prohierodula enghoffii[&&NHX:TOL=54139],prohierodula flavipennis[&&NHX:TOL=54140],prohierodula grassei[&&NHX:TOL=54141],prohierodula laticollis[&&NHX:TOL=54142],prohierodula lineata[&&NHX:TOL=54143],prohierodula mundamensis[&&NHX:TOL=54144],prohierodula nigrispinis[&&NHX:TOL=54145],prohierodula ornatipennis[&&NHX:TOL=54146],prohierodula picta[&&NHX:TOL=54147],prohierodula viridimarginata[&&NHX:TOL=54148])prohierodula[&&NHX:TOL=12793],(tenodera angustipennis[&&NHX:TOL=54149],tenodera aridifolia[&&NHX:TOL=54150],tenodera australasiae[&&NHX:TOL=54151],tenodera blanchardi[&&NHX:TOL=54152],tenodera brevicollis[&&NHX:TOL=54153],tenodera caudafissilis[&&NHX:TOL=54154],tenodera costalis[&&NHX:TOL=54155],tenodera fasciata[&&NHX:TOL=54156],tenodera phillippina[&&NHX:TOL=54157],tenodera rungsi[&&NHX:TOL=54158],tenodera sinensis[&&NHX:TOL=54159],tenodera stoetzneri[&&NHX:TOL=54160],tenodera superstitiosa[&&NHX:TOL=54161])tenodera[&&NHX:TOL=12779])polyspilotini[&&NHX:TOL=57154])mantinae[&&NHX:TOL=12744],((melliera brevipes[&&NHX:TOL=54162],melliera chorotega[&&NHX:TOL=54163],melliera major[&&NHX:TOL=54164],melliera mordax[&&NHX:TOL=54165])melliera[&&NHX:TOL=53087],(xystropeltis lankesteri[&&NHX:TOL=54166],xystropeltis meridionalis[&&NHX:TOL=54167],xystropeltis quadrilobata[&&NHX:TOL=54168])xystropeltis[&&NHX:TOL=53088])mellierinae[&&NHX:TOL=53086],((arria cinctipes[&&NHX:TOL=12821],(cilnia chopardi[&&NHX:TOL=54169],cilnia humeralis[&&NHX:TOL=54170])cilnia[&&NHX:TOL=12831],(miomantis abyssinica[&&NHX:TOL=54171],miomantis acutipes[&&NHX:TOL=54172],miomantis affinis[&&NHX:TOL=54173],miomantis alata[&&NHX:TOL=54174],miomantis amanica[&&NHX:TOL=54175],miomantis andreinii[&&NHX:TOL=54176],miomantis annulipes[&&NHX:TOL=54177],miomantis arabica[&&NHX:TOL=54178],miomantis aurantiaca[&&NHX:TOL=54179],miomantis aurea[&&NHX:TOL=54180],miomantis binotata[&&NHX:TOL=54181],miomantis bintumanensis[&&NHX:TOL=54182],miomantis brachyptera[&&NHX:TOL=54183],miomantis brevipennis[&&NHX:TOL=54184],miomantis brunni[&&NHX:TOL=54185],miomantis buettneri[&&NHX:TOL=54186],miomantis caffra[&&NHX:TOL=54187],miomantis cinnabarina[&&NHX:TOL=54188],miomantis ciprianii[&&NHX:TOL=54189],miomantis coxalis[&&NHX:TOL=54190],miomantis devylderi[&&NHX:TOL=54191],miomantis diademata[&&NHX:TOL=54192],miomantis ehrenbergi[&&NHX:TOL=54193],miomantis equalis[&&NHX:TOL=54194],miomantis exilis[&&NHX:TOL=54195],miomantis fallax[&&NHX:TOL=54196],miomantis feminina[&&NHX:TOL=54197],miomantis fenestrata[&&NHX:TOL=54198],miomantis griffinii[&&NHX:TOL=54199],miomantis gyldenstolpei[&&NHX:TOL=54200],miomantis helenae[&&NHX:TOL=54201],miomantis kibweziana[&&NHX:TOL=54202],miomantis kilimandjarica[&&NHX:TOL=54203],miomantis lacualis[&&NHX:TOL=54204],miomantis lamtoensis[&&NHX:TOL=54205],miomantis longicollis[&&NHX:TOL=54206],miomantis menelikii[&&NHX:TOL=54207],miomantis milmilena[&&NHX:TOL=54208],miomantis minuta[&&NHX:TOL=54209],miomantis misana[&&NHX:TOL=54210],miomantis mombasica[&&NHX:TOL=54211],miomantis monacha[&&NHX:TOL=54212],miomantis montana[&&NHX:TOL=54213],miomantis multipunctata[&&NHX:TOL=54214],miomantis nairobiensis[&&NHX:TOL=54215],miomantis natalica[&&NHX:TOL=54216],miomantis ornata[&&NHX:TOL=54217],miomantis paykullii[&&NHX:TOL=54218],miomantis pellucida[&&NHX:TOL=54219],miomantis planivertex[&&NHX:TOL=54220],miomantis prasina[&&NHX:TOL=54221],miomantis preussi[&&NHX:TOL=54222],miomantis pygmaea[&&NHX:TOL=54223],miomantis quadripunctata[&&NHX:TOL=54224],miomantis rebeli[&&NHX:TOL=54225],miomantis rehni[&&NHX:TOL=54226],miomantis rouxi[&&NHX:TOL=54227],miomantis rubra[&&NHX:TOL=54228],miomantis sangarana[&&NHX:TOL=54229],miomantis saussurei[&&NHX:TOL=54230],miomantis scabricollis[&&NHX:TOL=54231],miomantis semialata[&&NHX:TOL=54232],miomantis sjoestedti[&&NHX:TOL=54233],miomantis steelae[&&NHX:TOL=54234],miomantis tangana[&&NHX:TOL=54235],miomantis tenuis[&&NHX:TOL=54236],miomantis togana[&&NHX:TOL=54237],miomantis usambarica[&&NHX:TOL=54238],miomantis vitrea[&&NHX:TOL=54239],miomantis wittei[&&NHX:TOL=54240])miomantis[&&NHX:TOL=12825],neocilnia gracilis[&&NHX:TOL=12820],paracilnia neavei[&&NHX:TOL=12823],(parasphendale affinis[&&NHX:TOL=54241],parasphendale africana[&&NHX:TOL=54242],parasphendale agrionina[&&NHX:TOL=54243],parasphendale albicosta[&&NHX:TOL=54244],parasphendale costalis[&&NHX:TOL=54245],parasphendale ghindana[&&NHX:TOL=54246],parasphendale minor[&&NHX:TOL=54247],parasphendale scioana[&&NHX:TOL=54248],parasphendale stali[&&NHX:TOL=54249])parasphendale[&&NHX:TOL=12832],(sphodropoda lepida[&&NHX:TOL=56972],sphodropoda loripes[&&NHX:TOL=54251],sphodropoda quinquedens[&&NHX:TOL=54255],sphodropoda tristis[&&NHX:TOL=54256],sphodropoda viridis[&&NHX:TOL=54257])sphodropoda[&&NHX:TOL=12833],(taumantis cephalotes[&&NHX:TOL=54258],taumantis globiceps[&&NHX:TOL=54259],taumantis sigiana[&&NHX:TOL=54260])taumantis[&&NHX:TOL=12822],(trachymantis dentifrons[&&NHX:TOL=54250],trachymantis obesa[&&NHX:TOL=12834])trachymantis[&&NHX:TOL=56973])miomantini[&&NHX:TOL=53079],((bolivaria amnicola[&&NHX:TOL=54261],bolivaria brachyptera[&&NHX:TOL=54262],bolivaria kurda[&&NHX:TOL=54263],bolivaria xanthoptera[&&NHX:TOL=54264])bolivaria[&&NHX:TOL=12818],(carvilia gracilis[&&NHX:TOL=54265],carvilia obscura[&&NHX:TOL=54266],carvilia saussurii[&&NHX:TOL=54267])carvilia[&&NHX:TOL=12819],(deiphobe australiana[&&NHX:TOL=54268],deiphobe brevipennis[&&NHX:TOL=54269],deiphobe brunneri[&&NHX:TOL=54270],deiphobe incisa[&&NHX:TOL=54271],deiphobe indica[&&NHX:TOL=54272],deiphobe infuscata[&&NHX:TOL=54273],deiphobe longipes[&&NHX:TOL=54274],deiphobe mesomelas[&&NHX:TOL=54275],deiphobe yunnanensis[&&NHX:TOL=54276])deiphobe[&&NHX:TOL=12814],(deiphobella gardeneri[&&NHX:TOL=54277],deiphobella laticeps[&&NHX:TOL=54278])deiphobella[&&NHX:TOL=53081],eremoplana infelix[&&NHX:TOL=12830],euchomena madecassa[&&NHX:TOL=12828],geomantis larvoides[&&NHX:TOL=12827],geothespis australis[&&NHX:TOL=12826],gretella gracilis[&&NHX:TOL=53082],indothespis assamensis[&&NHX:TOL=53083],(ischnomantis aethiopica[&&NHX:TOL=54279],ischnomantis fasciata[&&NHX:TOL=54280],ischnomantis fatiloqua[&&NHX:TOL=54281],ischnomantis flavescens[&&NHX:TOL=54282],ischnomantis gigas[&&NHX:TOL=54283],ischnomantis gracilis[&&NHX:TOL=54284],ischnomantis media[&&NHX:TOL=54285],ischnomantis perfida[&&NHX:TOL=54286],ischnomantis spinigera[&&NHX:TOL=54287],ischnomantis usambarica[&&NHX:TOL=54288],ischnomantis werneri[&&NHX:TOL=54289])ischnomantis[&&NHX:TOL=12835],(microthespis dmitriewi[&&NHX:TOL=54290],microthespis evansi[&&NHX:TOL=54291])microthespis[&&NHX:TOL=12813],pararivetina fraseri[&&NHX:TOL=12817],(pseudempusa pavonina[&&NHX:TOL=54292],pseudempusa pinnapavonis[&&NHX:TOL=54293])pseudempusa[&&NHX:TOL=12816],(rivetina asiatica[&&NHX:TOL=54294],rivetina baetica[&&NHX:TOL=54295],rivetina balcanica[&&NHX:TOL=54296],rivetina beybienkoi[&&NHX:TOL=54297],rivetina buettikeri[&&NHX:TOL=54298],rivetina byblica[&&NHX:TOL=54299],rivetina caucasica[&&NHX:TOL=54300],rivetina compacta[&&NHX:TOL=54301],rivetina crassa[&&NHX:TOL=54302],rivetina dentata[&&NHX:TOL=54303],rivetina deserta[&&NHX:TOL=54304],rivetina dolichoptera[&&NHX:TOL=54305],rivetina elegans[&&NHX:TOL=54306],rivetina excellens[&&NHX:TOL=54307],rivetina gigantea[&&NHX:TOL=54308],rivetina inermis[&&NHX:TOL=54309],rivetina karadumi[&&NHX:TOL=54310],rivetina karateginica[&&NHX:TOL=54311],rivetina laticollis[&&NHX:TOL=54312],rivetina monticola[&&NHX:TOL=54313],rivetina nana[&&NHX:TOL=54314],rivetina pallida[&&NHX:TOL=54315],rivetina parva[&&NHX:TOL=54316],rivetina pulisangini[&&NHX:TOL=54317],rivetina rhombicollis[&&NHX:TOL=54318],rivetina similis[&&NHX:TOL=54319],rivetina syriaca[&&NHX:TOL=54320],rivetina tarda[&&NHX:TOL=54321],rivetina varsobica[&&NHX:TOL=54322])rivetina[&&NHX:TOL=12815],rivetinula fraterna[&&NHX:TOL=53084],solygia sulcatifrons[&&NHX:TOL=12829],teddia dioscoris[&&NHX:TOL=12812])rivetinini[&&NHX:TOL=53080])miomantinae[&&NHX:TOL=12762],((orthodera australiana[&&NHX:TOL=54323],orthodera burmeisteri[&&NHX:TOL=54324],orthodera gracilis[&&NHX:TOL=54325],orthodera gunnii[&&NHX:TOL=54326],orthodera insularis[&&NHX:TOL=54327],orthodera ministralis[&&NHX:TOL=54328],orthodera novaezealandiae[&&NHX:TOL=54329],orthodera rubrocoxata[&&NHX:TOL=54330])orthodera[&&NHX:TOL=12851],(orthoderina fergusoniana[&&NHX:TOL=54331],orthoderina straminea[&&NHX:TOL=54332])orthoderina[&&NHX:TOL=12852])orthoderinae[&&NHX:TOL=12746],((acithespis gigas[&&NHX:TOL=12749],(heterochaetula fissispinis[&&NHX:TOL=54333],heterochaetula tricolor[&&NHX:TOL=54334])heterochaetula[&&NHX:TOL=12750],(oxyothespis acuticeps[&&NHX:TOL=54335],oxyothespis alata[&&NHX:TOL=54336],oxyothespis apostata[&&NHX:TOL=54337],oxyothespis bifurcata[&&NHX:TOL=54338],oxyothespis brevicollis[&&NHX:TOL=54339],oxyothespis brevipennis[&&NHX:TOL=54340],oxyothespis dumonti[&&NHX:TOL=54341],oxyothespis flavipennis[&&NHX:TOL=54342],oxyothespis longicollis[&&NHX:TOL=54343],oxyothespis longipennis[&&NHX:TOL=54344],oxyothespis mammillata[&&NHX:TOL=54345],oxyothespis maroccana[&&NHX:TOL=54346],oxyothespis meridionalis[&&NHX:TOL=54347],oxyothespis nilotica[&&NHX:TOL=54348],oxyothespis noctivaga[&&NHX:TOL=54349],oxyothespis parva[&&NHX:TOL=54350],oxyothespis pellucida[&&NHX:TOL=54351],oxyothespis persica[&&NHX:TOL=54352],oxyothespis philbyi[&&NHX:TOL=54353],oxyothespis senegalensis[&&NHX:TOL=54354],oxyothespis sudanensis[&&NHX:TOL=54355],oxyothespis tricolor[&&NHX:TOL=54356],oxyothespis villiersi[&&NHX:TOL=54357],oxyothespis wagneri[&&NHX:TOL=54358])oxyothespis[&&NHX:TOL=12748],(severinia granulata[&&NHX:TOL=54359],severinia lemoroi[&&NHX:TOL=54360],severinia mistshenkoi[&&NHX:TOL=54361],severinia nigrofasciata[&&NHX:TOL=54362],severinia obscurus[&&NHX:TOL=54363],severinia popovi[&&NHX:TOL=54364],severinia turcomaniae[&&NHX:TOL=54365],severinia ullrichi[&&NHX:TOL=54366])severinia[&&NHX:TOL=53018],(sinaiella nebulosa[&&NHX:TOL=54367],sinaiella raggei[&&NHX:TOL=54368],sinaiella sabulosa[&&NHX:TOL=54369])sinaiella[&&NHX:TOL=12557],somalithespis minor[&&NHX:TOL=53019])oxyothespini[&&NHX:TOL=53017],(lobothespis vignai[&&NHX:TOL=53021],paraseverinia finoti[&&NHX:TOL=53022])paraseveriniini[&&NHX:TOL=53020])oxyothespinae[&&NHX:TOL=12747],(((brunneria borealis[&&NHX:TOL=56080],brunneria brasiliensis[&&NHX:TOL=56081],brunneria gracilis[&&NHX:TOL=56082],brunneria longa[&&NHX:TOL=56083],brunneria subaptera[&&NHX:TOL=56084])brunneria[&&NHX:TOL=12855],(coptopteryx argentina[&&NHX:TOL=56085],coptopteryx bonariensis[&&NHX:TOL=56086],coptopteryx brevipennis[&&NHX:TOL=56087],coptopteryx claraziana[&&NHX:TOL=56088],coptopteryx constricta[&&NHX:TOL=56089],coptopteryx ermannoi[&&NHX:TOL=56090],coptopteryx fallax[&&NHX:TOL=56091],coptopteryx gayi[&&NHX:TOL=56092],coptopteryx gigliotosi[&&NHX:TOL=56093],coptopteryx gracilis[&&NHX:TOL=56094],coptopteryx inermis[&&NHX:TOL=56095],coptopteryx magna[&&NHX:TOL=56096],coptopteryx parva[&&NHX:TOL=56097],coptopteryx platana[&&NHX:TOL=56098],coptopteryx precaria[&&NHX:TOL=56099],coptopteryx pusilla[&&NHX:TOL=56100],coptopteryx spinosa[&&NHX:TOL=56101],coptopteryx thoracica[&&NHX:TOL=56102],coptopteryx thoracoides[&&NHX:TOL=56103],coptopteryx viridis[&&NHX:TOL=56104])coptopteryx[&&NHX:TOL=12857])coptopterygini[&&NHX:TOL=12854],((cardioptera brachyptera[&&NHX:TOL=56105],cardioptera minor[&&NHX:TOL=56106],cardioptera nigridens[&&NHX:TOL=56107],cardioptera parva[&&NHX:TOL=56108],cardioptera squalodon[&&NHX:TOL=56109],cardioptera viridipennis[&&NHX:TOL=56110])cardioptera[&&NHX:TOL=12856],(hicetia breviceps[&&NHX:TOL=56111],hicetia goeldiana[&&NHX:TOL=56112])hicetia[&&NHX:TOL=12861],(macromantis hyalina[&&NHX:TOL=56113],macromantis nicaraguae[&&NHX:TOL=56114],macromantis ovalifolia[&&NHX:TOL=56115],macromantis saussurei[&&NHX:TOL=56116])macromantis[&&NHX:TOL=12862],(metriomantis boliviana[&&NHX:TOL=56117],metriomantis cupido[&&NHX:TOL=56118],metriomantis occidentalis[&&NHX:TOL=56119],metriomantis ovata[&&NHX:TOL=56120],metriomantis paraensis[&&NHX:TOL=56121],metriomantis pilosella[&&NHX:TOL=56122])metriomantis[&&NHX:TOL=53097],microphotina[&&NHX:TOL=12863],(orthoderella deluchii[&&NHX:TOL=56987],orthoderella ornata[&&NHX:TOL=12858])orthoderella[&&NHX:TOL=56986],(paraphotina insolita[&&NHX:TOL=56123],paraphotina occidentalis[&&NHX:TOL=56124],paraphotina reticulata[&&NHX:TOL=56125])paraphotina[&&NHX:TOL=12859],(photina amplipennis[&&NHX:TOL=56126],photina gracilis[&&NHX:TOL=56127],photina laevis[&&NHX:TOL=56128],photina reticulata[&&NHX:TOL=56129],photina vitrea[&&NHX:TOL=56130])photina[&&NHX:TOL=12864],(photinella biramosa[&&NHX:TOL=56131],photinella brevis[&&NHX:TOL=56132],photinella magna[&&NHX:TOL=56133],photinella media[&&NHX:TOL=56134],photinella silvai[&&NHX:TOL=56135])photinella[&&NHX:TOL=12865],rehniella planicephala[&&NHX:TOL=53098])photinini[&&NHX:TOL=12860])photininae[&&NHX:TOL=12751],(ceratocrania macra[&&NHX:TOL=12753],(phyllothelys bakeri[&&NHX:TOL=56136],phyllothelys decipiens[&&NHX:TOL=56137],phyllothelys mitratum[&&NHX:TOL=56138],phyllothelys paradoxum[&&NHX:TOL=56139],phyllothelys werneri[&&NHX:TOL=56140],phyllothelys westwoodi[&&NHX:TOL=56141])phyllothelys[&&NHX:TOL=12754])phyllotheliinae[&&NHX:TOL=12752],schizocephala bicornis[&&NHX:TOL=12755],(catoxyopsis dubiosa[&&NHX:TOL=12947],(lobocneme colombiae[&&NHX:TOL=56142],lobocneme lobipes[&&NHX:TOL=56143])lobocneme[&&NHX:TOL=12944],(oxyopsis acutipennis[&&NHX:TOL=56144],oxyopsis festae[&&NHX:TOL=56145],oxyopsis gracilis[&&NHX:TOL=56146],oxyopsis lobeter[&&NHX:TOL=56147],oxyopsis media[&&NHX:TOL=56148],oxyopsis obtusa[&&NHX:TOL=56149],oxyopsis oculea[&&NHX:TOL=56150],oxyopsis peruviana[&&NHX:TOL=56151],oxyopsis rubicunda[&&NHX:TOL=56152],oxyopsis saussurei[&&NHX:TOL=56153],oxyopsis stali[&&NHX:TOL=56154])oxyopsis[&&NHX:TOL=12943],(parastagmatoptera abnormis[&&NHX:TOL=56155],parastagmatoptera amazonica[&&NHX:TOL=56156],parastagmatoptera concolor[&&NHX:TOL=56157],parastagmatoptera confusa[&&NHX:TOL=56158],parastagmatoptera flavoguttata[&&NHX:TOL=56159],parastagmatoptera glauca[&&NHX:TOL=56160],parastagmatoptera hoorie[&&NHX:TOL=56161],parastagmatoptera pellucida[&&NHX:TOL=56162],parastagmatoptera serricornis[&&NHX:TOL=56163],parastagmatoptera tessellata[&&NHX:TOL=56164],parastagmatoptera unipunctata[&&NHX:TOL=56165],parastagmatoptera vitrepennis[&&NHX:TOL=56166],parastagmatoptera zernyi[&&NHX:TOL=56167])parastagmatoptera[&&NHX:TOL=12942],paroxyopsis icterica[&&NHX:TOL=12941],(pseudoxyops boliviana[&&NHX:TOL=56168],pseudoxyops borelli[&&NHX:TOL=56169],pseudoxyops diluta[&&NHX:TOL=56170],pseudoxyops minuta[&&NHX:TOL=56171],pseudoxyops perpulchra[&&NHX:TOL=56172])pseudoxyops[&&NHX:TOL=12940],(stagmatoptera abdominalis[&&NHX:TOL=56173],stagmatoptera binotata[&&NHX:TOL=56174],stagmatoptera biocellata[&&NHX:TOL=56175],stagmatoptera femoralis[&&NHX:TOL=56176],stagmatoptera flavipennis[&&NHX:TOL=56177],stagmatoptera hyaloptera[&&NHX:TOL=56178],stagmatoptera ignota[&&NHX:TOL=56179],stagmatoptera indicator[&&NHX:TOL=56180],stagmatoptera nova[&&NHX:TOL=56181],stagmatoptera pia[&&NHX:TOL=56182],stagmatoptera precaria[&&NHX:TOL=56183],stagmatoptera pumila[&&NHX:TOL=56184],stagmatoptera reimoseri[&&NHX:TOL=56185],stagmatoptera septentrionalis[&&NHX:TOL=56186],stagmatoptera supplicaria[&&NHX:TOL=56187])stagmatoptera[&&NHX:TOL=12939])stagmatopterinae[&&NHX:TOL=12938],(callimantis antillarum[&&NHX:TOL=12824],(phasmomantis championi[&&NHX:TOL=56188],phasmomantis sumichrasti[&&NHX:TOL=56189])phasmomantis[&&NHX:TOL=12782],(stagmomantis amazonica[&&NHX:TOL=56190],stagmomantis californica[&&NHX:TOL=56191],stagmomantis carolina[&&NHX:TOL=56192],stagmomantis centralis[&&NHX:TOL=56193],stagmomantis colorata[&&NHX:TOL=56194],stagmomantis domingensis[&&NHX:TOL=56195],stagmomantis floridensis[&&NHX:TOL=56196],stagmomantis fraterna[&&NHX:TOL=56197],stagmomantis gracilipes[&&NHX:TOL=56198],stagmomantis hebardi[&&NHX:TOL=56199],stagmomantis heterogamia[&&NHX:TOL=56200],stagmomantis limbata[&&NHX:TOL=56201],stagmomantis montana[&&NHX:TOL=56202],stagmomantis nahua[&&NHX:TOL=56203],stagmomantis paraensis[&&NHX:TOL=56204],stagmomantis parvidentata[&&NHX:TOL=56205],stagmomantis theophila[&&NHX:TOL=56206],stagmomantis venusta[&&NHX:TOL=56207],stagmomantis vicina[&&NHX:TOL=56208])stagmomantis[&&NHX:TOL=12786])stagmomantinae[&&NHX:TOL=53085],(((ambivia parapopa[&&NHX:TOL=56209],ambivia undata[&&NHX:TOL=56210])ambivia[&&NHX:TOL=53089],((danuria danuria angusticollis[&&NHX:TOL=56212],danuria danuria buchholzi[&&NHX:TOL=56213],danuria danuria contorta[&&NHX:TOL=56214],danuria danuria gracilis[&&NHX:TOL=56215],danuria danuria impannosa[&&NHX:TOL=56216],danuria danuria obscuripennis[&&NHX:TOL=56217],danuria danuria sublineata[&&NHX:TOL=56218],danuria danuria thunbergi[&&NHX:TOL=56219])danuria danuria[&&NHX:TOL=56211],(danuria danuriodes affinis[&&NHX:TOL=56221],danuria danuriodes barbozae[&&NHX:TOL=56222],danuria danuriodes congica[&&NHX:TOL=56223],danuria danuriodes kilimandjarica[&&NHX:TOL=56224])danuria danuriodes[&&NHX:TOL=56220])danuria[&&NHX:TOL=12949],(danuriella irregularis[&&NHX:TOL=56225],danuriella madagascariensis[&&NHX:TOL=56226],danuriella marojejyensis[&&NHX:TOL=56227])danuriella[&&NHX:TOL=53090],(kishinouyeum breve[&&NHX:TOL=56228],kishinouyeum cornuta[&&NHX:TOL=56229],kishinouyeum hepatica[&&NHX:TOL=56230],kishinouyeum jianfenglingensis[&&NHX:TOL=56231],kishinouyeum parvula[&&NHX:TOL=56997],kishinouyeum robusta[&&NHX:TOL=56232],kishinouyeum sinensis[&&NHX:TOL=56233],kishinouyeum stigmosus[&&NHX:TOL=56988])kishinouyeum[&&NHX:TOL=53091],macrodanuria elongata[&&NHX:TOL=12950],macropopa lobata[&&NHX:TOL=53092],(neodanuria bolauana[&&NHX:TOL=56234],neodanuria simonettai[&&NHX:TOL=56235])neodanuria[&&NHX:TOL=12951],popa spurca[&&NHX:TOL=12952],(toxodanuria orientalis[&&NHX:TOL=56236],toxodanuria parvula[&&NHX:TOL=56237])toxodanuria[&&NHX:TOL=53093])danuriini[&&NHX:TOL=12948],(heterochaeta bernardii[&&NHX:TOL=56238],heterochaeta girardi[&&NHX:TOL=56239],heterochaeta kumari[&&NHX:TOL=56240],heterochaeta lamellosa[&&NHX:TOL=56241],heterochaeta occidentalis[&&NHX:TOL=56242],heterochaeta orientalis[&&NHX:TOL=56243],heterochaeta pantherina[&&NHX:TOL=56244],heterochaeta reticulata[&&NHX:TOL=56245],heterochaeta strachani[&&NHX:TOL=56246],heterochaeta tenuipes[&&NHX:TOL=56247],heterochaeta zavattarii[&&NHX:TOL=56248])heterochaeta[&&NHX:TOL=12954],(chopardiella latipennis[&&NHX:TOL=53094],hagiotata hofmanni[&&NHX:TOL=12937],heterovates pardalina[&&NHX:TOL=12946],lobovates chopardi[&&NHX:TOL=53095],(phyllovates brasiliensis[&&NHX:TOL=56249],phyllovates brevicornis[&&NHX:TOL=56250],phyllovates chlorophaea[&&NHX:TOL=56251],phyllovates cingulata[&&NHX:TOL=56252],phyllovates cornuta[&&NHX:TOL=56253],phyllovates iheringi[&&NHX:TOL=56254],phyllovates maya[&&NHX:TOL=56255],phyllovates minor[&&NHX:TOL=56256],phyllovates parallela[&&NHX:TOL=56257],phyllovates parvula[&&NHX:TOL=56258],phyllovates spinicollis[&&NHX:TOL=56259],phyllovates tripunctata[&&NHX:TOL=56260])phyllovates[&&NHX:TOL=12936],(pseudovates arizonae[&&NHX:TOL=56261],pseudovates bidens[&&NHX:TOL=56262],pseudovates denticulata[&&NHX:TOL=56263],pseudovates hyalostigma[&&NHX:TOL=56264],pseudovates longicollis[&&NHX:TOL=56265],pseudovates paraensis[&&NHX:TOL=56266],pseudovates tolteca[&&NHX:TOL=56267],pseudovates townsendi[&&NHX:TOL=56268])pseudovates[&&NHX:TOL=52738],(vates amazonica[&&NHX:TOL=56269],vates biplagiata[&&NHX:TOL=56270],vates boliviana[&&NHX:TOL=56271],vates festae[&&NHX:TOL=56272],vates foliata[&&NHX:TOL=56273],vates lobata[&&NHX:TOL=56274],vates luxuriosa[&&NHX:TOL=56275],vates multilobata[&&NHX:TOL=56276],vates obscura[&&NHX:TOL=56277],vates pectinata[&&NHX:TOL=56278],vates pectinicornis[&&NHX:TOL=56279],vates peruviana[&&NHX:TOL=56280],vates serraticornis[&&NHX:TOL=56281],vates weyrauchi[&&NHX:TOL=56282])vates[&&NHX:TOL=12935],(zoolea borellii[&&NHX:TOL=56283],zoolea gigas[&&NHX:TOL=56284],zoolea guerinii[&&NHX:TOL=56285],zoolea lobipes[&&NHX:TOL=56286],zoolea major[&&NHX:TOL=56287],zoolea minor[&&NHX:TOL=56288],zoolea orba[&&NHX:TOL=56289])zoolea[&&NHX:TOL=12934])vatini[&&NHX:TOL=12933],callivates stephanei[&&NHX:TOL=57005])vatinae[&&NHX:TOL=12760])mantidae[&&NHX:TOL=12494],(leptosibylla gracilis[&&NHX:TOL=53104],(presibylla elegans[&&NHX:TOL=56290],presibylla speciosa[&&NHX:TOL=56291])presibylla[&&NHX:TOL=12868],((sibylla sibylla dives[&&NHX:TOL=56293],sibylla sibylla dolosa[&&NHX:TOL=56294],sibylla sibylla limbata[&&NHX:TOL=56295],sibylla sibylla maculosa[&&NHX:TOL=56296],sibylla sibylla marmorata[&&NHX:TOL=56297],sibylla sibylla pretiosa[&&NHX:TOL=56298])sibylla sibylla[&&NHX:TOL=56292],(sibylla sibyllopsis griffinii[&&NHX:TOL=56300],sibylla sibyllopsis operosa[&&NHX:TOL=56301],sibylla sibyllopsis pannulata[&&NHX:TOL=56302],sibylla sibyllopsis punctata[&&NHX:TOL=56303],sibylla sibyllopsis vanderplaetseni[&&NHX:TOL=56304])sibylla sibyllopsis[&&NHX:TOL=56299])sibylla[&&NHX:TOL=12867])sibyllidae[&&NHX:TOL=12756],(((caliris elegans[&&NHX:TOL=56305],caliris masoni[&&NHX:TOL=56306],caliris melli[&&NHX:TOL=56307],caliris pallens[&&NHX:TOL=56308])caliris[&&NHX:TOL=12568],deromantis limbalicollis[&&NHX:TOL=12571],gildella suavis[&&NHX:TOL=12569],hebardia pellucida[&&NHX:TOL=52979],(hebardiella karnyi[&&NHX:TOL=56309],hebardiella rehni[&&NHX:TOL=56310])hebardiella[&&NHX:TOL=52980],((leptomantella aetaella bakeri[&&NHX:TOL=56323],leptomantella aetaella pluvisilvae[&&NHX:TOL=56324])leptomantella aetaella[&&NHX:TOL=56322],(leptomantella leptomantella albella[&&NHX:TOL=56312],leptomantella leptomantella ceylonica[&&NHX:TOL=56313],leptomantella leptomantella fragilis[&&NHX:TOL=56314],leptomantella leptomantella indica[&&NHX:TOL=56315],leptomantella leptomantella lactea[&&NHX:TOL=56316],leptomantella leptomantella montana[&&NHX:TOL=56317],leptomantella leptomantella nigrocoxata[&&NHX:TOL=56318],leptomantella leptomantella parva[&&NHX:TOL=56319],leptomantella leptomantella tonkinae[&&NHX:TOL=56320],leptomantella leptomantella xizangensis[&&NHX:TOL=56321])leptomantella leptomantella[&&NHX:TOL=56311])leptomantella[&&NHX:TOL=12570])caliridinae[&&NHX:TOL=12735],((antistia maculipennis[&&NHX:TOL=56325],antistia parva[&&NHX:TOL=56326],antistia robusta[&&NHX:TOL=56327],antistia vicina[&&NHX:TOL=56328])antistia[&&NHX:TOL=12870],ariusia conspersa[&&NHX:TOL=12871],charieis peeli[&&NHX:TOL=12872],didymocorypha lanceolata[&&NHX:TOL=12873],(dysaules himalayanus[&&NHX:TOL=56329],dysaules longicollis[&&NHX:TOL=56330],dysaules uvana[&&NHX:TOL=56331])dysaules[&&NHX:TOL=12874],(episcopomantis chalybea[&&NHX:TOL=56332],episcopomantis congica[&&NHX:TOL=56333])episcopomantis[&&NHX:TOL=12875],((galepsus galepsus affinis[&&NHX:TOL=56335],galepsus galepsus binotatus[&&NHX:TOL=56336],galepsus galepsus buettneri[&&NHX:TOL=56337],galepsus galepsus coronatus[&&NHX:TOL=56338],galepsus galepsus feae[&&NHX:TOL=56339],galepsus galepsus globiceps[&&NHX:TOL=56340],galepsus galepsus konakrynus[&&NHX:TOL=56341],galepsus galepsus laticeps[&&NHX:TOL=56342],galepsus galepsus montanus[&&NHX:TOL=56343],galepsus galepsus nyassensis[&&NHX:TOL=56344],galepsus galepsus tenuis[&&NHX:TOL=56345])galepsus galepsus[&&NHX:TOL=56334],(galepsus lygdamia brincki[&&NHX:TOL=56347],galepsus lygdamia cacuminatus[&&NHX:TOL=56348],galepsus lygdamia culminans[&&NHX:TOL=56349],galepsus lygdamia lenticularis[&&NHX:TOL=56350],galepsus lygdamia nimulensis[&&NHX:TOL=56351],galepsus lygdamia oxycephalus[&&NHX:TOL=56352],galepsus lygdamia scorteccii[&&NHX:TOL=56353],galepsus lygdamia signatus[&&NHX:TOL=56354],galepsus lygdamia trilobus[&&NHX:TOL=56355])galepsus lygdamia[&&NHX:TOL=56346],(galepsus onychogalepsus aberrans[&&NHX:TOL=56357],galepsus onychogalepsus angolensis[&&NHX:TOL=56358],galepsus onychogalepsus bioculatus[&&NHX:TOL=56359],galepsus onychogalepsus bispinosus[&&NHX:TOL=56360],galepsus onychogalepsus capensis[&&NHX:TOL=56361],galepsus onychogalepsus capitatus[&&NHX:TOL=56362],galepsus onychogalepsus centralis[&&NHX:TOL=56363],galepsus onychogalepsus damaranus[&&NHX:TOL=56364],galepsus onychogalepsus decipiens[&&NHX:TOL=56365],galepsus onychogalepsus diversus[&&NHX:TOL=56366],galepsus onychogalepsus erythraeus[&&NHX:TOL=56367],galepsus onychogalepsus fallaciosus[&&NHX:TOL=56368],galepsus onychogalepsus fallax[&&NHX:TOL=56369],galepsus onychogalepsus femoratus[&&NHX:TOL=56370],galepsus onychogalepsus focki[&&NHX:TOL=56371],galepsus onychogalepsus fumipennis[&&NHX:TOL=56372],galepsus onychogalepsus gracilis[&&NHX:TOL=56373],galepsus onychogalepsus intermedius[&&NHX:TOL=56374],galepsus onychogalepsus letabaensis[&&NHX:TOL=56375],galepsus onychogalepsus machadoi[&&NHX:TOL=56376],galepsus onychogalepsus malawiensis[&&NHX:TOL=56377],galepsus onychogalepsus meridionalis[&&NHX:TOL=56378],galepsus onychogalepsus minimus[&&NHX:TOL=56379],galepsus onychogalepsus minutus[&&NHX:TOL=56380],galepsus onychogalepsus pentheri[&&NHX:TOL=56381],galepsus onychogalepsus rhodesicus[&&NHX:TOL=56382],galepsus onychogalepsus rouxi[&&NHX:TOL=56383],galepsus onychogalepsus schwetzi[&&NHX:TOL=56384],galepsus onychogalepsus sudanensis[&&NHX:TOL=56385],galepsus onychogalepsus supervacaneus[&&NHX:TOL=56386],galepsus onychogalepsus transvaalensis[&&NHX:TOL=56387],galepsus onychogalepsus ulricae[&&NHX:TOL=56388],galepsus onychogalepsus wittei[&&NHX:TOL=56389],galepsus onychogalepsus zambesicus[&&NHX:TOL=56390])galepsus onychogalepsus[&&NHX:TOL=56356],(galepsus syngalepsus beieri[&&NHX:TOL=56392],galepsus syngalepsus bikenmeierae[&&NHX:TOL=56393],galepsus syngalepsus bipunctatus[&&NHX:TOL=56394],galepsus syngalepsus denigratus[&&NHX:TOL=56395])galepsus syngalepsus[&&NHX:TOL=56391])galepsus[&&NHX:TOL=12877],(iris coeca[&&NHX:TOL=56396],iris deserti[&&NHX:TOL=56397],iris fasciata[&&NHX:TOL=56398],iris insolita[&&NHX:TOL=56399],iris minima[&&NHX:TOL=56400],iris nana[&&NHX:TOL=56401],iris narzykulovi[&&NHX:TOL=56402],iris oratoria[&&NHX:TOL=56403],iris orientalis[&&NHX:TOL=56404],iris persa[&&NHX:TOL=56405],iris pitcheri[&&NHX:TOL=56406],iris polystictica[&&NHX:TOL=56407],iris senegalensis[&&NHX:TOL=56408],iris splendida[&&NHX:TOL=56409])iris[&&NHX:TOL=12766],(metagalepsus occidentalis[&&NHX:TOL=56410],metagalepsus stramineus[&&NHX:TOL=56411])metagalepsus[&&NHX:TOL=52983],(nesogalepsus andriai[&&NHX:TOL=56412],nesogalepsus beieri[&&NHX:TOL=56413],nesogalepsus conspersus[&&NHX:TOL=56414],nesogalepsus hova[&&NHX:TOL=56415],nesogalepsus madagascariensis[&&NHX:TOL=56416],nesogalepsus sikorai[&&NHX:TOL=56417],nesogalepsus tuberculatus[&&NHX:TOL=56418])nesogalepsus[&&NHX:TOL=52984],nothogalepsus planivertex[&&NHX:TOL=52985],(oxyelaea elegans[&&NHX:TOL=56419],oxyelaea heteromorpha[&&NHX:TOL=56420],oxyelaea stefaniae[&&NHX:TOL=56421])oxyelaea[&&NHX:TOL=52982],(oxyophthalma engaea[&&NHX:TOL=56422],oxyophthalma giraffa[&&NHX:TOL=56423],oxyophthalma gracilis[&&NHX:TOL=56424])oxyophthalma[&&NHX:TOL=12878],(oxyophthalmellus rehni[&&NHX:TOL=56425],oxyophthalmellus somalicus[&&NHX:TOL=56426])oxyophthalmellus[&&NHX:TOL=12879],(paragalepsus bassari[&&NHX:TOL=56427],paragalepsus gestri[&&NHX:TOL=56428],paragalepsus nigericus[&&NHX:TOL=56429],paragalepsus toganus[&&NHX:TOL=56430])paragalepsus[&&NHX:TOL=52986],paralygdamia madecassa[&&NHX:TOL=12880],(paroxyophthalmus collaris[&&NHX:TOL=56431],paroxyophthalmus nigericus[&&NHX:TOL=56432],paroxyophthalmus ornatus[&&NHX:TOL=56433],paroxyophthalmus savatieri[&&NHX:TOL=56434])paroxyophthalmus[&&NHX:TOL=12882],(pseudogalepsus dispar[&&NHX:TOL=56435],pseudogalepsus inermis[&&NHX:TOL=56436],pseudogalepsus modestior[&&NHX:TOL=56437],pseudogalepsus modestus[&&NHX:TOL=56438],pseudogalepsus nigricoxa[&&NHX:TOL=56439])pseudogalepsus[&&NHX:TOL=12883],(pyrgomantis bisignata[&&NHX:TOL=56440],pyrgomantis congica[&&NHX:TOL=56441],pyrgomantis fasciata[&&NHX:TOL=56442],pyrgomantis jonesi[&&NHX:TOL=56443],pyrgomantis mabuia[&&NHX:TOL=56444],pyrgomantis mitrata[&&NHX:TOL=56445],pyrgomantis nana[&&NHX:TOL=56446],pyrgomantis nasuta[&&NHX:TOL=56447],pyrgomantis ornatipes[&&NHX:TOL=56448],pyrgomantis pallida[&&NHX:TOL=56449],pyrgomantis rhodesica[&&NHX:TOL=56450],pyrgomantis runifera[&&NHX:TOL=56451],pyrgomantis signatifrons[&&NHX:TOL=56452],pyrgomantis simillima[&&NHX:TOL=56453],pyrgomantis singularis[&&NHX:TOL=56454],pyrgomantis wellmanni[&&NHX:TOL=56455])pyrgomantis[&&NHX:TOL=12884],tarachodella monticola[&&NHX:TOL=12885],((tarachodes tarachodes abyssinicus[&&NHX:TOL=56459],tarachodes tarachodes alluaudi[&&NHX:TOL=56460],tarachodes tarachodes beieri[&&NHX:TOL=56461],tarachodes tarachodes bicornis[&&NHX:TOL=56462],tarachodes tarachodes brevipennis[&&NHX:TOL=56463],tarachodes tarachodes chopardii[&&NHX:TOL=56464],tarachodes tarachodes circulifer[&&NHX:TOL=56465],tarachodes tarachodes circuliferoides[&&NHX:TOL=56466],tarachodes tarachodes davidi[&&NHX:TOL=56467],tarachodes tarachodes feae[&&NHX:TOL=56468],tarachodes tarachodes fraterculus[&&NHX:TOL=56469],tarachodes tarachodes fuscipennis[&&NHX:TOL=56470],tarachodes tarachodes gibber[&&NHX:TOL=56471],tarachodes tarachodes gigas[&&NHX:TOL=56472],tarachodes tarachodes griseus[&&NHX:TOL=56473],tarachodes tarachodes haedus[&&NHX:TOL=56474],tarachodes tarachodes insidiator[&&NHX:TOL=56475],tarachodes tarachodes karschii[&&NHX:TOL=56476],tarachodes tarachodes lucubrans[&&NHX:TOL=56477],tarachodes tarachodes maurus[&&NHX:TOL=56478],tarachodes tarachodes monstrosus[&&NHX:TOL=56479],tarachodes tarachodes namibiensis[&&NHX:TOL=56480],tarachodes tarachodes nubifer[&&NHX:TOL=56481],tarachodes tarachodes obscuripennis[&&NHX:TOL=56482],tarachodes tarachodes okahandyanus[&&NHX:TOL=56483],tarachodes tarachodes oxynotus[&&NHX:TOL=56484],tarachodes tarachodes rhodesicus[&&NHX:TOL=56485],tarachodes tarachodes robustus[&&NHX:TOL=56486],tarachodes tarachodes rotundiceps[&&NHX:TOL=56487],tarachodes tarachodes sanctus[&&NHX:TOL=56488],tarachodes tarachodes severini[&&NHX:TOL=56489],tarachodes tarachodes taboranus[&&NHX:TOL=56490],tarachodes tarachodes tananus[&&NHX:TOL=56491],tarachodes tarachodes thomseni[&&NHX:TOL=56492],tarachodes tarachodes usambarica[&&NHX:TOL=56493],tarachodes tarachodes vitreus[&&NHX:TOL=56494])tarachodes tarachodes[&&NHX:TOL=56458],tarachodes barbachodes afzelii[&&NHX:TOL=56495],(tarachodes chiropacha aestuans[&&NHX:TOL=56497],tarachodes chiropacha arabicus[&&NHX:TOL=56498],tarachodes chiropacha gilvus[&&NHX:TOL=56499],tarachodes chiropacha obtusiceps[&&NHX:TOL=56500],tarachodes chiropacha saussurei[&&NHX:TOL=56501],tarachodes chiropacha smithi[&&NHX:TOL=56502])tarachodes chiropacha[&&NHX:TOL=56496],(tarachodes chiropus bispinosus[&&NHX:TOL=56504],tarachodes chiropus dives[&&NHX:TOL=56505],tarachodes chiropus sjoestedti[&&NHX:TOL=56506])tarachodes chiropus[&&NHX:TOL=56503],(tarachodes tarachodina basinotatus[&&NHX:TOL=56508],tarachodes tarachodina dissimulator[&&NHX:TOL=56509],tarachodes tarachodina gerstaeckeri[&&NHX:TOL=56510],tarachodes tarachodina maculisternum[&&NHX:TOL=56511],tarachodes tarachodina natalensis[&&NHX:TOL=56512],tarachodes tarachodina similis[&&NHX:TOL=56513])tarachodes tarachodina[&&NHX:TOL=56507])tarachodes[&&NHX:TOL=12886],(tarachodula ornata[&&NHX:TOL=56456],tarachodula pantherina[&&NHX:TOL=56457])tarachodula[&&NHX:TOL=12887])tarachodinae[&&NHX:TOL=52981],alfredistia reticulata[&&NHX:TOL=57004],episcopus[&&NHX:TOL=12876],parepiscopus[&&NHX:TOL=12881])tarachodidae[&&NHX:TOL=12757],((astape denticollis[&&NHX:TOL=52995],(haania aspera[&&NHX:TOL=56514],haania borneana[&&NHX:TOL=56515],haania confusa[&&NHX:TOL=56516],haania doroshenkoi[&&NHX:TOL=56978],haania lobiceps[&&NHX:TOL=56517],haania philippina[&&NHX:TOL=56518],haania simplex[&&NHX:TOL=56519],haania vitalisi[&&NHX:TOL=56520])haania[&&NHX:TOL=52996])haaniinae[&&NHX:TOL=12906],((apterocorypha atra[&&NHX:TOL=56521],apterocorypha aurita[&&NHX:TOL=56522],apterocorypha bispina[&&NHX:TOL=56523],apterocorypha somalica[&&NHX:TOL=56524])apterocorypha[&&NHX:TOL=52997],(hoplocorypha acuta[&&NHX:TOL=56525],hoplocorypha bicornis[&&NHX:TOL=56526],hoplocorypha boromensis[&&NHX:TOL=56527],hoplocorypha bottegi[&&NHX:TOL=56528],hoplocorypha boviformis[&&NHX:TOL=56529],hoplocorypha brevicollis[&&NHX:TOL=56530],hoplocorypha cacomana[&&NHX:TOL=56531],hoplocorypha carli[&&NHX:TOL=56532],hoplocorypha congica[&&NHX:TOL=56533],hoplocorypha dentata[&&NHX:TOL=56534],hoplocorypha distinguenda[&&NHX:TOL=56535],hoplocorypha foliata[&&NHX:TOL=56536],hoplocorypha fumosa[&&NHX:TOL=56537],hoplocorypha galeata[&&NHX:TOL=56538],hoplocorypha garuana[&&NHX:TOL=56539],hoplocorypha hamulifera[&&NHX:TOL=56540],hoplocorypha lacualis[&&NHX:TOL=56541],hoplocorypha lobata[&&NHX:TOL=56542],hoplocorypha macra[&&NHX:TOL=56543],hoplocorypha mellea[&&NHX:TOL=56544],hoplocorypha nana[&&NHX:TOL=56545],hoplocorypha narocana[&&NHX:TOL=56546],hoplocorypha nigerica[&&NHX:TOL=56547],hoplocorypha nigra[&&NHX:TOL=56548],hoplocorypha perplexa[&&NHX:TOL=56549],hoplocorypha picea[&&NHX:TOL=56550],hoplocorypha punctata[&&NHX:TOL=56551],hoplocorypha rapax[&&NHX:TOL=56552],hoplocorypha salfii[&&NHX:TOL=56553],hoplocorypha saussurii[&&NHX:TOL=56554],hoplocorypha striata[&&NHX:TOL=56555],hoplocorypha turneri[&&NHX:TOL=56556],hoplocorypha ugandana[&&NHX:TOL=56557],hoplocorypha vittata[&&NHX:TOL=56558],hoplocorypha wittei[&&NHX:TOL=56559])hoplocorypha[&&NHX:TOL=12890],hoplocoryphella grandis[&&NHX:TOL=12891])hoplocoryphinae[&&NHX:TOL=12889],((calopteromantis hebardi[&&NHX:TOL=56560],calopteromantis otongica[&&NHX:TOL=56561],calopteromantis terrai[&&NHX:TOL=56562])calopteromantis[&&NHX:TOL=52991],chloromiopteryx thalassina[&&NHX:TOL=12908],emboicy mirim[&&NHX:TOL=52992],(miobantia aptera[&&NHX:TOL=56563],miobantia ciliata[&&NHX:TOL=56564],miobantia fuscata[&&NHX:TOL=56565],miobantia nebulosa[&&NHX:TOL=56566],miobantia phryganea[&&NHX:TOL=56567],miobantia rustica[&&NHX:TOL=56568])miobantia[&&NHX:TOL=12913],(promiopteryx fallax[&&NHX:TOL=56569],promiopteryx granadensis[&&NHX:TOL=56570],promiopteryx punctata[&&NHX:TOL=56571],promiopteryx simplex[&&NHX:TOL=56572],promiopteryx stigmatica[&&NHX:TOL=56573])promiopteryx[&&NHX:TOL=12914])miopteryginae[&&NHX:TOL=52990],(((bactromantis mexicana[&&NHX:TOL=56574],bactromantis parvula[&&NHX:TOL=56575],bactromantis tolteca[&&NHX:TOL=56576],bactromantis virga[&&NHX:TOL=56577])bactromantis[&&NHX:TOL=12838],(bantia chopardi[&&NHX:TOL=56578],bantia fusca[&&NHX:TOL=56579],bantia marmorata[&&NHX:TOL=56580],bantia metzi[&&NHX:TOL=56581],bantia michaelisi[&&NHX:TOL=56582],bantia nana[&&NHX:TOL=56583],bantia pygmea[&&NHX:TOL=56584],bantia simoni[&&NHX:TOL=56585],bantia werneri[&&NHX:TOL=56586])bantia[&&NHX:TOL=12839],(bantiella columbina[&&NHX:TOL=56587],bantiella fusca[&&NHX:TOL=56588],bantiella hyalina[&&NHX:TOL=56589],bantiella pallida[&&NHX:TOL=56590],bantiella trinitatis[&&NHX:TOL=56591])bantiella[&&NHX:TOL=12907],(diabantia minima[&&NHX:TOL=56592],diabantia perparva[&&NHX:TOL=56593])diabantia[&&NHX:TOL=12909],(oligonicella bolliana[&&NHX:TOL=56594],oligonicella brunneri[&&NHX:TOL=56595],oligonicella punctulata[&&NHX:TOL=56596],oligonicella scudderi[&&NHX:TOL=56597],oligonicella striolata[&&NHX:TOL=56598],oligonicella tessellata[&&NHX:TOL=56599])oligonicella[&&NHX:TOL=12841],(oligonyx bicornis[&&NHX:TOL=56600],oligonyx bidens[&&NHX:TOL=56601],oligonyx dohrnianus[&&NHX:TOL=56602],oligonyx insularis[&&NHX:TOL=56603],oligonyx maya[&&NHX:TOL=56604])oligonyx[&&NHX:TOL=12842],(pseudomusonia fera[&&NHX:TOL=56605],pseudomusonia lineativentris[&&NHX:TOL=56606],pseudomusonia maculosa[&&NHX:TOL=56607],pseudomusonia rapax[&&NHX:TOL=56608])pseudomusonia[&&NHX:TOL=12843],(thesprotiella bicorniculata[&&NHX:TOL=56609],thesprotiella festae[&&NHX:TOL=56610],thesprotiella fronticornis[&&NHX:TOL=56611],thesprotiella peruana[&&NHX:TOL=56612],thesprotiella similis[&&NHX:TOL=56613])thesprotiella[&&NHX:TOL=12845],(thrinaconyx fumosa[&&NHX:TOL=56614],thrinaconyx kirschianus[&&NHX:TOL=56615])thrinaconyx[&&NHX:TOL=12846])oligonicini[&&NHX:TOL=12837],((carrikerella ceratophora[&&NHX:TOL=56616],carrikerella empusa[&&NHX:TOL=56617])carrikerella[&&NHX:TOL=12848],liguanea pediodromia[&&NHX:TOL=52998],mantellias pubicornis[&&NHX:TOL=12911],(mantillica beieri[&&NHX:TOL=56618],mantillica nigricans[&&NHX:TOL=56619],mantillica sialidea[&&NHX:TOL=56620])mantillica[&&NHX:TOL=12912],(pogonogaster latens[&&NHX:TOL=56621],pogonogaster tristani[&&NHX:TOL=56622])pogonogaster[&&NHX:TOL=12849],pseudopogonogaster mirabilis[&&NHX:TOL=52999],(thesprotia brasiliensis[&&NHX:TOL=56623],thesprotia brevis[&&NHX:TOL=56624],thesprotia caribea[&&NHX:TOL=56625],thesprotia filum[&&NHX:TOL=56626],thesprotia fuscipennis[&&NHX:TOL=56627],thesprotia gigas[&&NHX:TOL=56628],thesprotia graminis[&&NHX:TOL=56629],thesprotia infumata[&&NHX:TOL=56630],thesprotia insolita[&&NHX:TOL=56631],thesprotia macilenta[&&NHX:TOL=56632],thesprotia maculata[&&NHX:TOL=56633],thesprotia pellucida[&&NHX:TOL=56634],thesprotia simplex[&&NHX:TOL=56635],thesprotia subhyalina[&&NHX:TOL=56636])thesprotia[&&NHX:TOL=12844])pogonogasterini[&&NHX:TOL=12847])oligonicinae[&&NHX:TOL=12745],((anamiopteryx borellii[&&NHX:TOL=56637],anamiopteryx grandis[&&NHX:TOL=56638],anamiopteryx tuberculata[&&NHX:TOL=56639])anamiopteryx[&&NHX:TOL=12905],(eumiopteryx bicentenaria[&&NHX:TOL=56640],eumiopteryx laticollis[&&NHX:TOL=56641],eumiopteryx magna[&&NHX:TOL=56642])eumiopteryx[&&NHX:TOL=12910],(leptomiopteryx argentina[&&NHX:TOL=56643],leptomiopteryx dispar[&&NHX:TOL=56644])leptomiopteryx[&&NHX:TOL=12897],(palaeothespis oreophilus[&&NHX:TOL=56645],palaeothespis pallidus[&&NHX:TOL=56646],palaeothespis stictus[&&NHX:TOL=56647])palaeothespis[&&NHX:TOL=52987],pizaia seabrai[&&NHX:TOL=52988],(pseudomiopteryx amazonensis[&&NHX:TOL=56648],pseudomiopteryx bogotensis[&&NHX:TOL=56649],pseudomiopteryx columbica[&&NHX:TOL=56650],pseudomiopteryx decipiens[&&NHX:TOL=56651],pseudomiopteryx festae[&&NHX:TOL=56652],pseudomiopteryx guyanensis[&&NHX:TOL=56653],pseudomiopteryx infuscata[&&NHX:TOL=56654],pseudomiopteryx maculata[&&NHX:TOL=56655],pseudomiopteryx meridana[&&NHX:TOL=56656],pseudomiopteryx spinifrons[&&NHX:TOL=56657])pseudomiopteryx[&&NHX:TOL=12915],(sinomiopteryx brevifrons[&&NHX:TOL=56658],sinomiopteryx grahami[&&NHX:TOL=56659],sinomiopteryx guangxiensis[&&NHX:TOL=56660])sinomiopteryx[&&NHX:TOL=52989])pseudomiopteryginae[&&NHX:TOL=12904],(parathespsis humbertiana[&&NHX:TOL=12892],aconthiothespis[&&NHX:TOL=12894],((eumusonia intermedia[&&NHX:TOL=56661],eumusonia livida[&&NHX:TOL=56662],eumusonia viridis[&&NHX:TOL=56663])eumusonia[&&NHX:TOL=12895],(galapagia amazonica[&&NHX:TOL=56664],galapagia peruana[&&NHX:TOL=56665],galapagia solitaria[&&NHX:TOL=56666])galapagia[&&NHX:TOL=12896],(macromusonia conspersa[&&NHX:TOL=56667],macromusonia major[&&NHX:TOL=56668])macromusonia[&&NHX:TOL=12898],(musonia boliviana[&&NHX:TOL=56669],musonia costalis[&&NHX:TOL=56670],musonia lineata[&&NHX:TOL=56671],musonia maculata[&&NHX:TOL=56672],musonia seclusa[&&NHX:TOL=56673],musonia sexdentata[&&NHX:TOL=56674],musonia surinama[&&NHX:TOL=56675])musonia[&&NHX:TOL=12899],(musoniella affinis[&&NHX:TOL=56676],musoniella argentina[&&NHX:TOL=56677],musoniella brasiliensis[&&NHX:TOL=56678],musoniella chopardi[&&NHX:TOL=56679],musoniella fragilis[&&NHX:TOL=56680],musoniella ipiranga[&&NHX:TOL=56681],musoniella laevithorax[&&NHX:TOL=56682],musoniella longicauda[&&NHX:TOL=56683],musoniella parva[&&NHX:TOL=56684])musoniella[&&NHX:TOL=12900],(musoniola conservatrix[&&NHX:TOL=56685],musoniola dohrniana[&&NHX:TOL=56686],musoniola plurilobata[&&NHX:TOL=56687],musoniola venezuelana[&&NHX:TOL=56688],musoniola vicina[&&NHX:TOL=56689])musoniola[&&NHX:TOL=12901],paramusonia cubensis[&&NHX:TOL=12902],pseudothespis meghalayensis[&&NHX:TOL=52994],(thespis disparilis[&&NHX:TOL=56690],thespis dissimilis[&&NHX:TOL=56691],thespis exposita[&&NHX:TOL=56692],thespis major[&&NHX:TOL=56693],thespis media[&&NHX:TOL=56694],thespis metae[&&NHX:TOL=56695],thespis parva[&&NHX:TOL=56696])thespis[&&NHX:TOL=12903])thespini[&&NHX:TOL=52993])thespinae[&&NHX:TOL=12893])thespidae[&&NHX:TOL=12758],(((aethalochroa affinis[&&NHX:TOL=56697],aethalochroa ashmoliana[&&NHX:TOL=56698],aethalochroa insignis[&&NHX:TOL=56699],aethalochroa simplicipes[&&NHX:TOL=56700],aethalochroa spinipes[&&NHX:TOL=56701])aethalochroa[&&NHX:TOL=12919],belomantis helenae[&&NHX:TOL=12920])aethalochroaini[&&NHX:TOL=53099],(cheddikulama straminea[&&NHX:TOL=53101],oestomantis bacillaris[&&NHX:TOL=12925],(paratoxodera borneana[&&NHX:TOL=56702],paratoxodera cornicollis[&&NHX:TOL=56703],paratoxodera meggitti[&&NHX:TOL=56704],paratoxodera pluto[&&NHX:TOL=56705])paratoxodera[&&NHX:TOL=12927],(pareuthyphlebs arabica[&&NHX:TOL=56706],pareuthyphlebs occidentalis[&&NHX:TOL=56707],pareuthyphlebs palmonii[&&NHX:TOL=56708],pareuthyphlebs popovi[&&NHX:TOL=56709],pareuthyphlebs scorteccii[&&NHX:TOL=56710],pareuthyphlebs somalica[&&NHX:TOL=56711],pareuthyphlebs uvarovi[&&NHX:TOL=56712])pareuthyphlebs[&&NHX:TOL=53102],(toxodera denticulata[&&NHX:TOL=56713],toxodera fimbriata[&&NHX:TOL=56714],toxodera integrifolia[&&NHX:TOL=56715],toxodera maculata[&&NHX:TOL=56716],toxodera monstrosa[&&NHX:TOL=56717])toxodera[&&NHX:TOL=12928],toxoderella fortnumi[&&NHX:TOL=12929],(toxomantis sinensis[&&NHX:TOL=56718],toxomantis westwoodi[&&NHX:TOL=56719])toxomantis[&&NHX:TOL=12931])toxoderini[&&NHX:TOL=53100],((calamothespis adusta[&&NHX:TOL=56720],calamothespis condamini[&&NHX:TOL=56721],calamothespis lineatipennis[&&NHX:TOL=56722],calamothespis oxyops[&&NHX:TOL=56723],calamothespis rourei[&&NHX:TOL=56724],calamothespis subcornuta[&&NHX:TOL=56725],calamothespis taylori[&&NHX:TOL=56726],calamothespis vuattouxi[&&NHX:TOL=56727])calamothespis[&&NHX:TOL=12921],dorymantis congica[&&NHX:TOL=12922],(euthyphleps curtipes[&&NHX:TOL=56728],euthyphleps rectivenis[&&NHX:TOL=56729],euthyphleps tectiformis[&&NHX:TOL=56730])euthyphleps[&&NHX:TOL=12923],loxomantis indica[&&NHX:TOL=12924],(toxoderopsis spinigera[&&NHX:TOL=56731],toxoderopsis taurus[&&NHX:TOL=56732])toxoderopsis[&&NHX:TOL=12930])toxoderopsini[&&NHX:TOL=53103])toxoderidae[&&NHX:TOL=12759])[&&NHX:TOL=52655])[&&NHX:TOL=52659])[&&NHX:TOL=52657])[&&NHX:TOL=52654])mantodea[&&NHX:TOL=8213])dictyoptera[&&NHX:TOL=8253],(((asiodiplatys[&&NHX:EXT=Y:TOL=10369],protodiplatys[&&NHX:EXT=Y:TOL=10370],archidermapteron[&&NHX:EXT=Y:TOL=10371],microdiplatys[&&NHX:EXT=Y:TOL=10372])[&&NHX:TOL=10368],(turanovia[&&NHX:EXT=Y:TOL=10374],dermapteron[&&NHX:EXT=Y:TOL=10376])[&&NHX:TOL=10373])archidermaptera[&&NHX:EXT=Y:TOL=10379],(hemimerina[&&NHX:TOL=10381],(arixenina[&&NHX:TOL=10383],forficulina[&&NHX:TOL=10384])[&&NHX:TOL=10382])[&&NHX:TOL=10380])dermaptera[&&NHX:TOL=8254],(elytroneura[&&NHX:EXT=Y:TOL=14400],(archelytron[&&NHX:EXT=Y:TOL=14402],ortelytron[&&NHX:EXT=Y:TOL=14403])archelytridae[&&NHX:TOL=14401],apachelytron[&&NHX:EXT=Y:TOL=14404],(protocoleus[&&NHX:EXT=Y:TOL=14406],austrelytron[&&NHX:TOL=14407],phyllelytron[&&NHX:TOL=14408])protocoleidae[&&NHX:TOL=14405],(protelytron[&&NHX:EXT=Y:TOL=14410],permelytropsis[&&NHX:EXT=Y:TOL=14411],uralelytron[&&NHX:EXT=Y:TOL=14412])protelytridae[&&NHX:TOL=14409],megelytron[&&NHX:EXT=Y:TOL=14413],planelytron[&&NHX:EXT=Y:TOL=14414],(permelytron[&&NHX:EXT=Y:TOL=14416],blattelytron[&&NHX:EXT=Y:TOL=14417],parablattelytron[&&NHX:EXT=Y:TOL=14418])permelytridae[&&NHX:TOL=14415],(permophilus[&&NHX:EXT=Y:TOL=14420],elytrathrix[&&NHX:EXT=Y:TOL=14421])permophilidae[&&NHX:TOL=14419],(labidelytron[&&NHX:EXT=Y:TOL=14423],xenelytron[&&NHX:EXT=Y:TOL=14424])labidelytridae[&&NHX:TOL=14422],(dermelytron[&&NHX:EXT=Y:TOL=14426],chanoselytron[&&NHX:EXT=Y:TOL=14427],psychelytron[&&NHX:EXT=Y:TOL=14428])dermelytridae[&&NHX:TOL=14425],umenocoleus[&&NHX:EXT=Y:TOL=14429],artocoleus[&&NHX:EXT=Y:TOL=14430],crasselytron[&&NHX:EXT=Y:TOL=14431],glabelytron[&&NHX:EXT=Y:TOL=14432],protelytropsis[&&NHX:EXT=Y:TOL=14433],rugelytron[&&NHX:EXT=Y:TOL=14434],venelytron[&&NHX:EXT=Y:TOL=14435])protelytroptera[&&NHX:EXT=Y:TOL=8255],((galloisiana chujoi[&&NHX:TOL=69098],galloisiana kiyosawai[&&NHX:TOL=69097],galloisiana kosuensis[&&NHX:TOL=69100],galloisiana magnus[&&NHX:TOL=69101],galloisiana nipponensis[&&NHX:TOL=69095],galloisiana notabilis[&&NHX:TOL=69099],galloisiana olgae[&&NHX:TOL=69102],galloisiana sinensis[&&NHX:TOL=69103],galloisiana sofiae[&&NHX:TOL=69104],galloisiana ussuriensis[&&NHX:TOL=69105],galloisiana yezoensis[&&NHX:TOL=69094],galloisiana yuasai[&&NHX:TOL=69096])galloisiana[&&NHX:TOL=10795],((grylloblatta barberi[&&NHX:TOL=69108],grylloblatta bifratrilecta[&&NHX:TOL=69107],(grylloblatta campodeiformis campodeiformis[&&NHX:TOL=69117],grylloblatta campodeiformis athapaska[&&NHX:TOL=69118],grylloblatta campodeiformis nahanni[&&NHX:TOL=69119])grylloblatta campodeiformis[&&NHX:TOL=69116],grylloblatta chandleri[&&NHX:TOL=69109],grylloblatta chirurgica[&&NHX:TOL=69113],grylloblatta gurneyi[&&NHX:TOL=69110],grylloblatta occidentalis[&&NHX:TOL=69114],grylloblatta rothi[&&NHX:TOL=69111],grylloblatta scudderi[&&NHX:TOL=69115],grylloblatta sculleni[&&NHX:TOL=69112],grylloblatta washoa[&&NHX:TOL=69106])grylloblatta[&&NHX:TOL=10796],grylloblattina djakonovi[&&NHX:TOL=10797])[&&NHX:TOL=69122],(grylloblattella pravdini[&&NHX:TOL=69120],grylloblattella sayanensis[&&NHX:TOL=69121])grylloblattella[&&NHX:TOL=10798],namkungia biryongensis[&&NHX:TOL=69092])grylloblattidae[&&NHX:TOL=8256],((mesotitan[&&NHX:EXT=Y:TOL=14537],mesotitanodes[&&NHX:EXT=Y:TOL=14538],prototitan[&&NHX:EXT=Y:TOL=14539],ultratitan[&&NHX:EXT=Y:TOL=14540])mesotitanidae[&&NHX:TOL=14536],paratitan[&&NHX:EXT=Y:TOL=14541],(gigatitan[&&NHX:EXT=Y:TOL=14543],nanotitan[&&NHX:EXT=Y:TOL=14544],ootitan[&&NHX:EXT=Y:TOL=14545])gigatitanidae[&&NHX:TOL=14542])titanoptera[&&NHX:EXT=Y:TOL=8257])neoptera[&&NHX:TOL=8267])pterygota[&&NHX:TOL=8210])[&&NHX:TOL=8208])insecta[&&NHX:TOL=8205])hexapoda[&&NHX:TOL=2528],((((polyartemiidae[&&NHX:TOL=6381],chirocephalidae[&&NHX:TOL=6382],branchinectidae[&&NHX:TOL=6383],streptocephalidae[&&NHX:TOL=6384],thamnocephalidae[&&NHX:TOL=6385])[&&NHX:TOL=6380],(artemiidae[&&NHX:TOL=6387],branchipodidae[&&NHX:TOL=6388])[&&NHX:TOL=6386])anostraca[&&NHX:TOL=6390],(notostraca[&&NHX:TOL=6392],spinicaudata[&&NHX:TOL=6394],laevicaudata[&&NHX:TOL=6395],(cyclestheria hislopi[&&NHX:TOL=6397],cladocera[&&NHX:TOL=6398])[&&NHX:TOL=6396])phyllopoda[&&NHX:TOL=6391])branchiopoda[&&NHX:TOL=6243],(((godzillius robustus[&&NHX:TOL=6325],godzilliognomus frondosus[&&NHX:TOL=6326],pleomothra aplectocheles[&&NHX:TOL=6327])godzilliidae[&&NHX:TOL=6324],(cryptocorynectes haptodiscus[&&NHX:TOL=6329],(lasionectes exleyi[&&NHX:TOL=6331],lasionectes entrichoma[&&NHX:TOL=6332])[&&NHX:TOL=6330],(speleonectes tulumensis[&&NHX:TOL=6334],speleonectes ondinae[&&NHX:TOL=6335],speleonectes lucayensis[&&NHX:TOL=6336],speleonectes gironensis[&&NHX:TOL=6337],speleonectes epilimnius[&&NHX:TOL=6338],speleonectes benjamini[&&NHX:TOL=6339])[&&NHX:TOL=6333])speleonectidae[&&NHX:TOL=6328])nectiopoda[&&NHX:TOL=6323],tesnusocaris goldichi[&&NHX:EXT=Y:TOL=6340])remipedia[&&NHX:TOL=6244],(hutchinsoniella[&&NHX:TOL=6237],lightiella[&&NHX:TOL=6238],chiltonella[&&NHX:TOL=6239],sandersiella[&&NHX:TOL=6240],hampsonellus[&&NHX:TOL=6241])cephalocarida[&&NHX:TOL=6245],((platycopia[&&NHX:TOL=6539],nanocopia[&&NHX:TOL=6540],sarsicopia[&&NHX:TOL=6541],antrisocopia[&&NHX:TOL=6542])platycopioida[&&NHX:TOL=6451],(acartiidae[&&NHX:TOL=6407],aetideidae[&&NHX:TOL=6408],arietellidae[&&NHX:TOL=6409],augaptilidae[&&NHX:TOL=6410],bathypontiidae[&&NHX:TOL=6411],boholinidae[&&NHX:TOL=6412],calanidae[&&NHX:TOL=6413],candaciidae[&&NHX:TOL=6414],centropagidae[&&NHX:TOL=6415],clausocalanidae[&&NHX:TOL=6416],diaixidae[&&NHX:TOL=6417],diaptomidae[&&NHX:TOL=6418],discoidae[&&NHX:TOL=6419],epacteriscidae[&&NHX:TOL=6420],eucalanidae[&&NHX:TOL=6421],euchaetidae[&&NHX:TOL=6422],fosshageniidae[&&NHX:TOL=6423],heterorhabdidae[&&NHX:TOL=6424],hyperbionychidae[&&NHX:TOL=6425],lucicutiidae[&&NHX:TOL=6426],mecynoceridae[&&NHX:TOL=6427],megacalanidae[&&NHX:TOL=6428],mesaiokeratidae[&&NHX:TOL=6429],metridinidae[&&NHX:TOL=6430],nullosetigeridae[&&NHX:TOL=6431],paracalanidae[&&NHX:TOL=6432],parapontellidae[&&NHX:TOL=6433],parkiidae[&&NHX:TOL=6434],phaennidae[&&NHX:TOL=6435],pontellidae[&&NHX:TOL=6436],pseudocyclopidae[&&NHX:TOL=6437],pseudocyclopiidae[&&NHX:TOL=6438],pseudodiaptomidae[&&NHX:TOL=6439],rhincalanidae[&&NHX:TOL=6440],ridgewayiidae[&&NHX:TOL=6441],ryocalanidae[&&NHX:TOL=6442],scolecithricidae[&&NHX:TOL=6443],spinocalanidae[&&NHX:TOL=6444],stephidae[&&NHX:TOL=6445],sulcanidae[&&NHX:TOL=6446],temoridae[&&NHX:TOL=6447],tharybidae[&&NHX:TOL=6448],tortanidae[&&NHX:TOL=6449])calanoida[&&NHX:TOL=6452],((speleophriidae[&&NHX:TOL=6534],(palpophriidae[&&NHX:TOL=6536],misophriidae[&&NHX:TOL=6537])[&&NHX:TOL=6535])misophrioida[&&NHX:TOL=6454],gelyelloida[&&NHX:TOL=6455],(archinotodelphyidae[&&NHX:TOL=6463],ascidicolidae[&&NHX:TOL=6464],buproridae[&&NHX:TOL=6465],chordeumiidae[&&NHX:TOL=6466],cucumaricolidae[&&NHX:TOL=6467],cyclopidae[&&NHX:TOL=6468],cyclopinidae[&&NHX:TOL=6469],fratiidae[&&NHX:TOL=6470],lernaeidae[&&NHX:TOL=6471],mantridae[&&NHX:TOL=6472],notodelphyidae[&&NHX:TOL=6473],oithonidae[&&NHX:TOL=6474],ozmanidae[&&NHX:TOL=6475],speleoithonidae[&&NHX:TOL=6476],thaumatopsyllidae[&&NHX:TOL=6477])cyclopoida[&&NHX:TOL=6456],mormonilloida[&&NHX:TOL=6457],(adenopleurellidae[&&NHX:TOL=6479],aegisthidae[&&NHX:TOL=6480],ambunguipedidae[&&NHX:TOL=6481],ameiridae[&&NHX:TOL=6482],ancorabolidae[&&NHX:TOL=6483],argestidae[&&NHX:TOL=6484],balaenophilidae[&&NHX:TOL=6485],cancrincolidae[&&NHX:TOL=6486],canthocamptidae[&&NHX:TOL=6487],canuellidae[&&NHX:TOL=6488],cerviniidae[&&NHX:TOL=6489],chappuisiidae[&&NHX:TOL=6490],cletodidae[&&NHX:TOL=6491],cletopsyllidae[&&NHX:TOL=6492],clytemnestridae[&&NHX:TOL=6493],cristacoxidae[&&NHX:TOL=6494],cylindropsyllidae[&&NHX:TOL=6495],darcythompsoniidae[&&NHX:TOL=6496],diosaccidae[&&NHX:TOL=6497],ectinosomatidae[&&NHX:TOL=6498],euterpinidae[&&NHX:TOL=6499],hamondiidae[&&NHX:TOL=6500],harpacticidae[&&NHX:TOL=6501],huntemanniidae[&&NHX:TOL=6502],laophontidae[&&NHX:TOL=6503],laophontopsidae[&&NHX:TOL=6504],latiremidae[&&NHX:TOL=6505],leptastacidae[&&NHX:TOL=6506],leptopontiidae[&&NHX:TOL=6507],longipediidae[&&NHX:TOL=6508],louriniidae[&&NHX:TOL=6509],metidae[&&NHX:TOL=6510],miraciidae[&&NHX:TOL=6511],neobradyidae[&&NHX:TOL=6512],normanellidae[&&NHX:TOL=6513],novocriniidae[&&NHX:TOL=6514],orthopsyllidae[&&NHX:TOL=6515],paramesochridae[&&NHX:TOL=6516],parastenheliidae[&&NHX:TOL=6517],parastenocarididae[&&NHX:TOL=6518],peltidiidae[&&NHX:TOL=6519],phyllognathopodidae[&&NHX:TOL=6520],porcellidiidae[&&NHX:TOL=6521],pseudotachidiidae[&&NHX:TOL=6522],rhizothricidae[&&NHX:TOL=6523],rotundiclipeidae[&&NHX:TOL=6524],styracothoracidae[&&NHX:TOL=6525],superornatiremidae[&&NHX:TOL=6526],tachidiidae[&&NHX:TOL=6527],tegastidae[&&NHX:TOL=6528],tetragonicipitidae[&&NHX:TOL=6529],thalestridae[&&NHX:TOL=6530],thompsonulidae[&&NHX:TOL=6531],tisbidae[&&NHX:TOL=6532])harpacticoida[&&NHX:TOL=6458],(anchimolgidae[&&NHX:TOL=6544],anomoclausiidae[&&NHX:TOL=6545],antheacherida[&&NHX:TOL=6546],anthessiidae[&&NHX:TOL=6547],bomolochidae[&&NHX:TOL=6548],catiniidae[&&NHX:TOL=6549],chitonophilidae[&&NHX:TOL=6550],chondracanthidae[&&NHX:TOL=6551],clausidiidae[&&NHX:TOL=6552],clausiidae[&&NHX:TOL=6553],corallovexiidae[&&NHX:TOL=6554],corycaeidae[&&NHX:TOL=6555],echiurophilidae[&&NHX:TOL=6556],entobiidae[&&NHX:TOL=6557],erebonasteridae[&&NHX:TOL=6558],ergasilidae[&&NHX:TOL=6559],eunicicolidae[&&NHX:TOL=6560],gastrodelphyidae[&&NHX:TOL=6561],herpyllobiidae[&&NHX:TOL=6562],intramolgidae[&&NHX:TOL=6563],kelleriidae[&&NHX:TOL=6564],lampippidae[&&NHX:TOL=6565],lernaeosoleidae[&&NHX:TOL=6566],lichomolgidae[&&NHX:TOL=6567],lubbockiidae[&&NHX:TOL=6568],macrochironidae[&&NHX:TOL=6569],mesoglicolidae[&&NHX:TOL=6570],micrallectidae[&&NHX:TOL=6571],myicolidae[&&NHX:TOL=6572],mytilicolidae[&&NHX:TOL=6573],nereicolidae[&&NHX:TOL=6574],nucellicolidae[&&NHX:TOL=6575],octopicolidae[&&NHX:TOL=6576],oncaeidae[&&NHX:TOL=6577],paralubbockiidae[&&NHX:TOL=6578],pharodidae[&&NHX:TOL=6579],philichthyidae[&&NHX:TOL=6580],philoblennidae[&&NHX:TOL=6581],phyllodicolidae[&&NHX:TOL=6582],polyankylidae[&&NHX:TOL=6583],pseudanthessiidae[&&NHX:TOL=6584],rhynchomolgidae[&&NHX:TOL=6585],sabelliphilidae[&&NHX:TOL=6586],saccopsidae[&&NHX:TOL=6587],sapphirinidae[&&NHX:TOL=6588],serpulidicolidae[&&NHX:TOL=6589],shiinoidae[&&NHX:TOL=6590],spiophanicolidae[&&NHX:TOL=6591],splanchnotrophidae[&&NHX:TOL=6592],synapticolidae[&&NHX:TOL=6593],synaptiphilidae[&&NHX:TOL=6594],taeniacanthidae[&&NHX:TOL=6595],tegobomolochidae[&&NHX:TOL=6596],telsidae[&&NHX:TOL=6597],thamnomolgidae[&&NHX:TOL=6598],tuccidae[&&NHX:TOL=6599],urocopiidae[&&NHX:TOL=6600],vahiniidae[&&NHX:TOL=6601],ventriculinidae[&&NHX:TOL=6602],xarifiidae[&&NHX:TOL=6603],xenocoelomatidae[&&NHX:TOL=6604])poecilostomatoida[&&NHX:TOL=6459],monstrilloida[&&NHX:TOL=6460],(archidactylinidae[&&NHX:TOL=6606],artotrogidae[&&NHX:TOL=6607],asterocheridae[&&NHX:TOL=6608],brychiopontiidae[&&NHX:TOL=6609],caligidae[&&NHX:TOL=6610],calverocheridae[&&NHX:TOL=6611],cancerillidae[&&NHX:TOL=6612],cecropidae[&&NHX:TOL=6613],codobidae[&&NHX:TOL=6614],coralliomyzontidae[&&NHX:TOL=6615],dichelinidae[&&NHX:TOL=6616],dichelesthiidae[&&NHX:TOL=6617],dinopontiidae[&&NHX:TOL=6618],dirivultidae[&&NHX:TOL=6619],dissonidae[&&NHX:TOL=6620],ecbathyriontidae[&&NHX:TOL=6621],entomolepididae[&&NHX:TOL=6622],eudactylinidae[&&NHX:TOL=6623],euryphoridae[&&NHX:TOL=6624],hatschekiidae[&&NHX:TOL=6625],hyponeoidae[&&NHX:TOL=6626],kroyeriidae[&&NHX:TOL=6627],lernaeopodidae[&&NHX:TOL=6628],lernanthropidae[&&NHX:TOL=6629],megapontiidae[&&NHX:TOL=6630],micropontiidae[&&NHX:TOL=6631],nanaspididae[&&NHX:TOL=6632],nicothoidae[&&NHX:TOL=6633],pandaridae[&&NHX:TOL=6634],pennellidae[&&NHX:TOL=6635],pontoeciellidae[&&NHX:TOL=6636],pseudocycnidae[&&NHX:TOL=6637],rataniidae[&&NHX:TOL=6638],scottomyzontidae[&&NHX:TOL=6639],sphyriidae[&&NHX:TOL=6640],sponginticolidae[&&NHX:TOL=6641],spongiocnizontidae[&&NHX:TOL=6642],stellicomitidae[&&NHX:TOL=6643],tanypleuridae[&&NHX:TOL=6644],trebiidae[&&NHX:TOL=6645])siphonostomatoida[&&NHX:TOL=6461])[&&NHX:TOL=6453])copepoda[&&NHX:TOL=6246],(((cypridinidae[&&NHX:TOL=8028],cylindroleberididae[&&NHX:TOL=8029],philomedidae[&&NHX:TOL=8030],rutidermatidae[&&NHX:TOL=8031],sarsiellidae[&&NHX:TOL=8032])myodocopina[&&NHX:TOL=8027],(thaumatocyprididae[&&NHX:TOL=8034],halocyprididae[&&NHX:TOL=8035],polycopidae[&&NHX:TOL=8036])halocyprida[&&NHX:TOL=8033])myodocopa[&&NHX:TOL=8026],((punciidae[&&NHX:TOL=8039],cytherellidae[&&NHX:TOL=8040])platycopida[&&NHX:TOL=8038],((bairdiidae[&&NHX:TOL=8043],bythocyprididae[&&NHX:TOL=8044])[&&NHX:TOL=8042],(bythocytheridae[&&NHX:TOL=8046],cytheridae[&&NHX:TOL=8047],cytherideidae[&&NHX:TOL=8048],cytheromatidae[&&NHX:TOL=8049],cytheruridae[&&NHX:TOL=8050],entocytheridae[&&NHX:TOL=8051],eucytheridae[&&NHX:TOL=8052],hemicytheridae[&&NHX:TOL=8053],kliellidae[&&NHX:TOL=8054],krithidae[&&NHX:TOL=8055],loxoconchidae[&&NHX:TOL=8056],leptocytheridae[&&NHX:TOL=8057],microcytheridae[&&NHX:TOL=8058],neocytherideidae[&&NHX:TOL=8059],paradoxostomatidae[&&NHX:TOL=8060],pectocytheridae[&&NHX:TOL=8061],protocytheridae[&&NHX:TOL=8062],psammocytheridae[&&NHX:TOL=8063],schizocytheridae[&&NHX:TOL=8064],terrestricytheridae[&&NHX:TOL=8065],thaerocytheridae[&&NHX:TOL=8066],trachyleberididae[&&NHX:TOL=8067],xestoleberididae[&&NHX:TOL=8068])[&&NHX:TOL=8045],sigiliidae[&&NHX:TOL=8069],pontocyprididae[&&NHX:TOL=8070],macrocyprididae[&&NHX:TOL=8071],(candonidae[&&NHX:TOL=8073],cyprididae[&&NHX:TOL=8074],ilyocyprididae[&&NHX:TOL=8075],notodromadidae[&&NHX:TOL=8076])[&&NHX:TOL=8072],darwinulidae[&&NHX:TOL=8077])podocopida[&&NHX:TOL=8041])podocopa[&&NHX:TOL=8037])ostracoda[&&NHX:TOL=6247],((argulus[&&NHX:TOL=6401],chonopeltis[&&NHX:TOL=6402],dipteropeltis[&&NHX:TOL=6403],dolops[&&NHX:TOL=6404])argulidae[&&NHX:TOL=6400],pentastomida[&&NHX:TOL=6405])branchiura[&&NHX:TOL=6248],(tantulocarida[&&NHX:TOL=6250],((((cryptophyalidae[&&NHX:TOL=8081],lithoglyptidae[&&NHX:TOL=8082])pygophora[&&NHX:TOL=8080],trypetesidae[&&NHX:TOL=8083])acrothoracica[&&NHX:TOL=8079],((peltogastridae[&&NHX:TOL=8086],lernaeodiscidae[&&NHX:TOL=8087],sacculinidae[&&NHX:TOL=8088])kentrogonida[&&NHX:TOL=8085],(chthamalophilidae[&&NHX:TOL=8090],clistosaccidae[&&NHX:TOL=8091],duplorbidae[&&NHX:TOL=8092],mycetomorphidae[&&NHX:TOL=8093],polysaccidae[&&NHX:TOL=8094],thompsoniidae[&&NHX:TOL=8095])akentrogonida[&&NHX:TOL=8089])rhizocephala[&&NHX:TOL=8084],(((anelasmatidae[&&NHX:TOL=139858],heteralepadidae[&&NHX:TOL=139859],koleolepadidae[&&NHX:TOL=139860],malacolepadidae[&&NHX:TOL=139861],microlepadidae[&&NHX:TOL=139862],rhizolepadidae[&&NHX:TOL=139863])heteralepadomorpha[&&NHX:TOL=139857],iblidae[&&NHX:TOL=139864],(lepadidae[&&NHX:TOL=139868],oxynaspididae[&&NHX:TOL=139869],poecilasmatidae[&&NHX:TOL=139870])lepadomorpha[&&NHX:TOL=139867],(calanticidae[&&NHX:TOL=139872],lithotryidae[&&NHX:TOL=139873],pollicipedidae[&&NHX:TOL=139874],scalpellidae[&&NHX:TOL=139875])scalpellomorpha[&&NHX:TOL=139871])pedunculata[&&NHX:TOL=8097],(neobrachylepadidae[&&NHX:TOL=139876],(neoverrucidae[&&NHX:TOL=139880],verrucidae[&&NHX:TOL=139881])verrucomorpha[&&NHX:TOL=139879],(chinoelasmatidae[&&NHX:TOL=139883],pachylasmatidae[&&NHX:TOL=139886],(catophragmidae[&&NHX:TOL=139890],chthamalidae[&&NHX:TOL=139891])chthamaloidea[&&NHX:TOL=139889],(chelonibiidae[&&NHX:TOL=139893],coronulidae[&&NHX:TOL=139894],platylepadidae[&&NHX:TOL=139895])coronuloidea[&&NHX:TOL=139892],(bathylasmatidae[&&NHX:TOL=139897],tetraclitidae[&&NHX:TOL=139898])tetraclitoidea[&&NHX:TOL=139896],(archaeobalanidae[&&NHX:TOL=139900],balanidae[&&NHX:TOL=139901],pyrgomatidae[&&NHX:TOL=139902])balanoidea[&&NHX:TOL=139899])balanomorpha[&&NHX:TOL=139882])sessilia[&&NHX:TOL=8112])thoracica[&&NHX:TOL=8096])cirripedia[&&NHX:TOL=8127],hansenocaris[&&NHX:TOL=8128],((lauridae[&&NHX:TOL=8131],petrarcidae[&&NHX:TOL=8132],synagogidae[&&NHX:TOL=8133])laurida[&&NHX:TOL=8130],(ascothoracidae[&&NHX:TOL=8135],ctenosculidae[&&NHX:TOL=8136],dendrogastridae[&&NHX:TOL=8137])dendrogastrida[&&NHX:TOL=8134])ascothoracida[&&NHX:TOL=8129])thecostraca[&&NHX:TOL=6251])[&&NHX:TOL=6249],mystacocarida[&&NHX:TOL=6252],((nebaliopsis typica[&&NHX:TOL=6255],(paranebalia longipes[&&NHX:TOL=6257],paranebalia belizensis[&&NHX:TOL=6258])[&&NHX:TOL=6256],(nebalia antarctica[&&NHX:TOL=6260],nebalia bipes[&&NHX:TOL=6261],nebalia borealis[&&NHX:TOL=6262],nebalia brucei[&&NHX:TOL=6263],nebalia cannoni[&&NHX:TOL=6264],nebalia capensis[&&NHX:TOL=6265],nebalia chilensis[&&NHX:TOL=6266],nebalia clausi[&&NHX:TOL=6267],nebalia dahli[&&NHX:TOL=6268],nebalia daytoni[&&NHX:TOL=6269],nebalia falklandensis[&&NHX:TOL=6270],nebalia gerkenae[&&NHX:TOL=6271],nebalia herbstii[&&NHX:TOL=6272],nebalia hessleri[&&NHX:TOL=6273],nebalia ilheoensis[&&NHX:TOL=6274],nebalia japanensis[&&NHX:TOL=6275],nebalia lagartensis[&&NHX:TOL=6276],nebalia longicornis[&&NHX:TOL=6277],nebalia marerubri[&&NHX:TOL=6278],nebalia patagonica[&&NHX:TOL=6279],nebalia pugettensis[&&NHX:TOL=6280],nebalia schizophthalma[&&NHX:TOL=6281],nebalia strausi[&&NHX:TOL=6282])[&&NHX:TOL=6259],sarsinebalia typhlops[&&NHX:TOL=6283],dahlella caldariensis[&&NHX:TOL=6284],(nebaliella antarctica[&&NHX:TOL=6286],nebaliella brevicarinata[&&NHX:TOL=6287],nebaliella caboti[&&NHX:TOL=6288],nebaliella declivatas[&&NHX:TOL=6289],nebaliella extrema[&&NHX:TOL=6290])[&&NHX:TOL=6285],speonebalia cannoni[&&NHX:TOL=6291],(levinebalia maria[&&NHX:TOL=6293],levinebalia fortunata[&&NHX:TOL=6294])[&&NHX:TOL=6292])leptostraca[&&NHX:TOL=6296],(((((((((((gonodactylidae[&&NHX:TOL=6350],takuidae[&&NHX:TOL=6351])[&&NHX:TOL=6349],protosquillidae[&&NHX:TOL=6352])[&&NHX:TOL=6348],odontodactylidae[&&NHX:TOL=6353])[&&NHX:TOL=6347],alainosquillidae[&&NHX:TOL=6354])[&&NHX:TOL=6346],pseudosquillidae[&&NHX:TOL=6355])[&&NHX:TOL=6345],hemisquillidae[&&NHX:TOL=6356])[&&NHX:TOL=6344],((((coronididae[&&NHX:TOL=6361],(nannosquillidae[&&NHX:TOL=6363],tetrasquillidae[&&NHX:TOL=6364])[&&NHX:TOL=6362])[&&NHX:TOL=6360],lysiosquillidae[&&NHX:TOL=6365])[&&NHX:TOL=6359],erythrosquillidae[&&NHX:TOL=6366])[&&NHX:TOL=6358],((bathysquillidae[&&NHX:TOL=6369],indosquillidae[&&NHX:TOL=6370])[&&NHX:TOL=6368],((eurysquillidae[&&NHX:TOL=6373],parasquillidae[&&NHX:TOL=6374])[&&NHX:TOL=6372],squillidae[&&NHX:TOL=6375])[&&NHX:TOL=6371])[&&NHX:TOL=6367])[&&NHX:TOL=6357])[&&NHX:TOL=6343],sculdidae[&&NHX:EXT=Y:TOL=6376],pseudosculdidae[&&NHX:EXT=Y:TOL=6377])unipeltata[&&NHX:TOL=6342],archaestomatopodea[&&NHX:EXT=Y:TOL=6378])stomatopoda[&&NHX:TOL=6299],aeschronectida[&&NHX:EXT=Y:TOL=6300],palaeostomatopoda[&&NHX:EXT=Y:TOL=6301])hoplocarida[&&NHX:TOL=6298],((bathynellacea[&&NHX:TOL=6304],anaspidacea[&&NHX:TOL=6305])syncarida[&&NHX:TOL=6303],(amphionides[&&NHX:TOL=6307],((penaeoidea[&&NHX:TOL=6648],sergestoidea[&&NHX:TOL=6649])dendrobranchiata[&&NHX:TOL=6647],(stenopodidea[&&NHX:TOL=6653],((((((((((((((((aegla leptochela[&&NHX:TOL=76244],aegla marginata[&&NHX:TOL=76269])[&&NHX:TOL=94216],(aegla inconspicua[&&NHX:TOL=76271],(aegla serrana[&&NHX:TOL=76259],(aegla ligulata[&&NHX:TOL=76270],aegla franciscana[&&NHX:TOL=76253])[&&NHX:TOL=94219])[&&NHX:TOL=94218])[&&NHX:TOL=94217])[&&NHX:TOL=94215],(aegla obstipa[&&NHX:TOL=76252],aegla itacolomiensis[&&NHX:TOL=76272],(aegla plana[&&NHX:TOL=76257],(aegla grisella[&&NHX:TOL=76248],(aegla inermis[&&NHX:TOL=76268],aegla longirostri[&&NHX:TOL=76246])[&&NHX:TOL=94223])[&&NHX:TOL=94222])[&&NHX:TOL=94221])[&&NHX:TOL=94220])[&&NHX:TOL=94214],(((aegla humahuaca[&&NHX:TOL=76286],(aegla septentrionalis[&&NHX:TOL=76277],(aegla sanlorenzo[&&NHX:TOL=76282],aegla jujuyana[&&NHX:TOL=76284])[&&NHX:TOL=94228])[&&NHX:TOL=94227])[&&NHX:TOL=94226],(aegla intercalata[&&NHX:TOL=76285],(aegla violacea[&&NHX:TOL=76273],aegla prado[&&NHX:TOL=76258])[&&NHX:TOL=94230])[&&NHX:TOL=94229])[&&NHX:TOL=94225],(aegla platensis[&&NHX:TOL=76279],(aegla singularis[&&NHX:TOL=76255],(aegla rossiana[&&NHX:TOL=76274],aegla uruguayana[&&NHX:TOL=76281])[&&NHX:TOL=94233])[&&NHX:TOL=94232])[&&NHX:TOL=94231])[&&NHX:TOL=94224])[&&NHX:TOL=94213],(aegla spinipalma[&&NHX:TOL=76250],(aegla camargoi[&&NHX:TOL=76265],((aegla leptodactyla[&&NHX:TOL=76251],(aegla spinosa[&&NHX:TOL=76266],(aegla odebrechtii[&&NHX:TOL=76267],aegla jarai[&&NHX:TOL=76263])[&&NHX:TOL=94239])[&&NHX:TOL=94238])[&&NHX:TOL=94237],(aegla paulensis[&&NHX:TOL=76254],(aegla perobae[&&NHX:TOL=76249],(((aegla cavernicola[&&NHX:TOL=76243],aegla strinatii[&&NHX:TOL=76260])[&&NHX:TOL=94244],(aegla schmitti[&&NHX:TOL=76262],aegla parana[&&NHX:TOL=76247])[&&NHX:TOL=94245])[&&NHX:TOL=94243],(aegla castro[&&NHX:TOL=76261],aegla parva[&&NHX:TOL=76245])[&&NHX:TOL=94246])[&&NHX:TOL=94242])[&&NHX:TOL=94241])[&&NHX:TOL=94240])[&&NHX:TOL=94236])[&&NHX:TOL=94235])[&&NHX:TOL=94234])[&&NHX:TOL=94212],((aegla abtao riolimayana[&&NHX:TOL=76288],aegla abtao abtao[&&NHX:TOL=76289])[&&NHX:TOL=76354],(aegla spectabilis[&&NHX:TOL=76287],(aegla araucaniensis[&&NHX:TOL=76295],(aegla pewenchae[&&NHX:TOL=76294],(aegla laevis laevis[&&NHX:TOL=76290],((aegla cholchol[&&NHX:TOL=76293],aegla rostrata[&&NHX:TOL=76292])[&&NHX:TOL=76352],aegla laevis talcahuano[&&NHX:TOL=76291])[&&NHX:TOL=76351])[&&NHX:TOL=76350])[&&NHX:TOL=76349])[&&NHX:TOL=76348])[&&NHX:TOL=94247])[&&NHX:TOL=76353])[&&NHX:TOL=94211],(((aegla bahamondei[&&NHX:TOL=76301],(aegla neuquensis[&&NHX:TOL=76278],aegla affinis[&&NHX:TOL=76303])[&&NHX:TOL=94249])[&&NHX:TOL=94248],aegla sp.[&&NHX:TOL=76302])[&&NHX:TOL=76357],(aegla alacalufi[&&NHX:TOL=76299],(aegla manni[&&NHX:TOL=76298],(aegla hueicollensis[&&NHX:TOL=76300],(aegla denticulata lacustris[&&NHX:TOL=76297],aegla denticulata denticulata[&&NHX:TOL=76296])[&&NHX:TOL=76361])[&&NHX:TOL=94251])[&&NHX:TOL=94250])[&&NHX:TOL=76359])[&&NHX:TOL=76355])[&&NHX:TOL=94210],aegla scamosa[&&NHX:TOL=76280])[&&NHX:TOL=94209],aegla ringueleti[&&NHX:TOL=76283])[&&NHX:TOL=94208],aegla papudo[&&NHX:TOL=76304])[&&NHX:TOL=94207],aegla microphthalma[&&NHX:TOL=76242],aegla franca[&&NHX:TOL=76256],aegla lata[&&NHX:TOL=76264],aegla intermedia[&&NHX:TOL=76275],aegla concepcionensis[&&NHX:TOL=76276])aegla[&&NHX:TOL=72690],((galatheidae[&&NHX:TOL=72692],(chirostylidae[&&NHX:TOL=72691],porcellanidae[&&NHX:TOL=72693])[&&NHX:TOL=88565])[&&NHX:TOL=88564],(coenobitidae[&&NHX:TOL=72698],diogenidae[&&NHX:TOL=72699],lithodidae[&&NHX:TOL=72700],paguridae[&&NHX:TOL=72701],parapaguridae[&&NHX:TOL=72702],pylochelidae[&&NHX:TOL=72703])paguroidea[&&NHX:TOL=72697])[&&NHX:TOL=88563])galatheoidea[&&NHX:TOL=72689],(albuneidae[&&NHX:TOL=72695],hippidae[&&NHX:TOL=72696])hippoidea[&&NHX:TOL=72694],lomisidae[&&NHX:TOL=72687])anomura[&&NHX:TOL=6658],((polychelidae[&&NHX:TOL=72680],(((palinustus[&&NHX:TOL=111753],justitia[&&NHX:TOL=111744],palinurus[&&NHX:TOL=111751],panulirus[&&NHX:TOL=111773],(puerulus[&&NHX:TOL=111775],linuparus[&&NHX:TOL=111778])[&&NHX:TOL=111811],palibythus[&&NHX:TOL=111749])[&&NHX:TOL=111805],(projasus[&&NHX:TOL=111774],jasus[&&NHX:TOL=111743])[&&NHX:TOL=111812])palinuridae[&&NHX:TOL=72683],scyllaridae[&&NHX:TOL=72684],synaxidae[&&NHX:TOL=72685])palinuroidea[&&NHX:TOL=72682])achelata[&&NHX:TOL=6657],(((thaumastochelidae[&&NHX:TOL=6662],nephropidae[&&NHX:TOL=6663])nephropoidea[&&NHX:TOL=6661],(((((((astacoides granulimanus[&&NHX:TOL=7690],((astacoides betsileoensis[&&NHX:TOL=7693],astacoides caldwelli[&&NHX:TOL=7694])[&&NHX:TOL=7692],astacoides madagascarensis[&&NHX:TOL=7695])[&&NHX:TOL=7691])[&&NHX:TOL=7689],(astacoides crosnieri[&&NHX:TOL=7697],astacoides petiti[&&NHX:TOL=7698])[&&NHX:TOL=7696])astacoides[&&NHX:TOL=7703],(astacopsis franklinii[&&NHX:TOL=7730],astacopsis tricornius[&&NHX:TOL=7731],astacopsis gouldi[&&NHX:TOL=7732])astacopsis[&&NHX:TOL=7704])[&&NHX:TOL=7702],(euastacus armatus[&&NHX:TOL=7904],euastacus australasiensis[&&NHX:TOL=7905],euastacus balanensis[&&NHX:TOL=7906],euastacus bidawalus[&&NHX:TOL=7907],euastacus bindal[&&NHX:TOL=7908],euastacus bispinosus[&&NHX:TOL=7909],euastacus brachythorax[&&NHX:TOL=7910],euastacus clarkae[&&NHX:TOL=7911],euastacus claytoni[&&NHX:TOL=7912],euastacus crassus[&&NHX:TOL=7913],euastacus dangadi[&&NHX:TOL=7914],euastacus dharawalus[&&NHX:TOL=7915],euastacus diversus[&&NHX:TOL=7916],euastacus eungella[&&NHX:TOL=7917],euastacus fleckeri[&&NHX:TOL=7918],euastacus gamilaroi[&&NHX:TOL=7919],euastacus gumar[&&NHX:TOL=7920],euastacus guwinus[&&NHX:TOL=7921],euastacus hirsutus[&&NHX:TOL=7922],euastacus hystricosus[&&NHX:TOL=7923],euastacus jagara[&&NHX:TOL=7924],euastacus kershawi[&&NHX:TOL=7925],euastacus maidae[&&NHX:TOL=7926],euastacus monteithorum[&&NHX:TOL=7927],euastacus neodiversus[&&NHX:TOL=7928],euastacus neohirsutus[&&NHX:TOL=7929],euastacus polysetosus[&&NHX:TOL=7930],euastacus reductus[&&NHX:TOL=7931],euastacus rieki[&&NHX:TOL=7932],euastacus robertsi[&&NHX:TOL=7933],euastacus setosus[&&NHX:TOL=7934],euastacus simplex[&&NHX:TOL=7935],euastacus spinichelatus[&&NHX:TOL=7936],euastacus spinifer[&&NHX:TOL=7937],euastacus sulcatus[&&NHX:TOL=7938],euastacus suttoni[&&NHX:TOL=7939],euastacus urospinosus[&&NHX:TOL=7940],euastacus valentulus[&&NHX:TOL=7941],euastacus woiwuru[&&NHX:TOL=7942],euastacus yanga[&&NHX:TOL=7943],euastacus yarraensis[&&NHX:TOL=7944],euastacus yigara[&&NHX:TOL=7945])euastacus[&&NHX:TOL=7705])[&&NHX:TOL=7701],(((gramastacus insolitus[&&NHX:TOL=7709],geocharax falcata[&&NHX:TOL=7710])[&&NHX:TOL=7708],(virilastacus araucanius[&&NHX:TOL=7712],(samastacus araucanius[&&NHX:TOL=7977],samastacus spinifrons[&&NHX:TOL=7978])samastacus[&&NHX:TOL=7713])[&&NHX:TOL=7711])[&&NHX:TOL=7707],((cherax setosus[&&NHX:TOL=7747],((cherax albidus[&&NHX:TOL=7750],cherax destructor[&&NHX:TOL=7751])destructor group[&&NHX:TOL=7749],(cherax neopunctatus[&&NHX:TOL=7753],cherax depressus[&&NHX:TOL=7754],cherax cairnsensis[&&NHX:TOL=7755],cherax wasselli[&&NHX:TOL=7756],cherax gladstonensis[&&NHX:TOL=7757],cherax glaber[&&NHX:TOL=7758],cherax urospinosus[&&NHX:TOL=7759],cherax robustus[&&NHX:TOL=7760],cherax cartalacoolah[&&NHX:TOL=7761],cherax punctatus[&&NHX:TOL=7762],cherax rotundus[&&NHX:TOL=7763])punctatus group[&&NHX:TOL=7752],(cherax cuspidatus[&&NHX:TOL=7765],cherax dispar[&&NHX:TOL=7766])dispar group[&&NHX:TOL=7764],(cherax preissii[&&NHX:TOL=7768],cherax plebejus[&&NHX:TOL=7769],cherax glabrimanus[&&NHX:TOL=7770],cherax neocarinatus[&&NHX:TOL=7771],cherax quinquecarinatus[&&NHX:TOL=7772],cherax crassimanus[&&NHX:TOL=7773])quinquecarinatus group[&&NHX:TOL=7767],(cherax divergens[&&NHX:TOL=7775],cherax lorentzi[&&NHX:TOL=7776],cherax quadricarinatus[&&NHX:TOL=7777],cherax tenuimanus[&&NHX:TOL=7778],cherax rhynchotus[&&NHX:TOL=7779],cherax monticola[&&NHX:TOL=7780],cherax barretti[&&NHX:TOL=7781],cherax nucifraga[&&NHX:TOL=7782],cherax parvus[&&NHX:TOL=7783])quadricarinatus group[&&NHX:TOL=7774])[&&NHX:TOL=7748])cherax[&&NHX:TOL=7715],(paranephrops planifrons[&&NHX:TOL=7717],(parastacoides insignis[&&NHX:TOL=7955],parastacoides pulcher[&&NHX:TOL=7956])parastacoides[&&NHX:TOL=7718])[&&NHX:TOL=7716])[&&NHX:TOL=7714])[&&NHX:TOL=7706])[&&NHX:TOL=7700],(tennuibranchiurus glypt[&&NHX:TOL=7720],((engaewa subcoerulea[&&NHX:TOL=7858],engaewa reducta[&&NHX:TOL=7859],engaewa similis[&&NHX:TOL=7860])engaewa[&&NHX:TOL=7722],((engaeus affinis[&&NHX:TOL=7820],engaeus australis[&&NHX:TOL=7821],engaeus cisternarius[&&NHX:TOL=7822],engaeus cunicularius[&&NHX:TOL=7823],engaeus curvisuturus[&&NHX:TOL=7824],engaeus cymus[&&NHX:TOL=7825],engaeus disjuncticus[&&NHX:TOL=7826],engaeus fossor[&&NHX:TOL=7827],engaeus fultoni[&&NHX:TOL=7828],engaeus granulatus[&&NHX:TOL=7829],engaeus hemicirratulus[&&NHX:TOL=7830],engaeus karnanga[&&NHX:TOL=7831],engaeus laevis[&&NHX:TOL=7832],engaeus lengana[&&NHX:TOL=7833],engaeus leptorhynchus[&&NHX:TOL=7834],engaeus lyelli[&&NHX:TOL=7835],engaeus mairener[&&NHX:TOL=7836],engaeus mallacoota[&&NHX:TOL=7837],engaeus martigener[&&NHX:TOL=7838],engaeus merosetosus[&&NHX:TOL=7839],engaeus nulloporius[&&NHX:TOL=7840],engaeus orientalis[&&NHX:TOL=7841],engaeus orramakunna[&&NHX:TOL=7842],engaeus phyllocercus[&&NHX:TOL=7843],engaeus quadrimanus[&&NHX:TOL=7844],engaeus rostrogaleatus[&&NHX:TOL=7845],engaeus sericatus[&&NHX:TOL=7846],engaeus spinicaudatus[&&NHX:TOL=7847],engaeus strictifrons[&&NHX:TOL=7848],engaeus sternalis[&&NHX:TOL=7849],engaeus tayatea[&&NHX:TOL=7850],engaeus tuberculatus[&&NHX:TOL=7851],engaeus urostrictus[&&NHX:TOL=7852],engaeus victoriensis[&&NHX:TOL=7853],engaeus yabbimunna[&&NHX:TOL=7854])engaeus[&&NHX:TOL=7724],(parastacus brasiliensis[&&NHX:TOL=7966],parastacus defossus[&&NHX:TOL=7967],parastacus laevigatus[&&NHX:TOL=7968],parastacus nicoleti[&&NHX:TOL=7969],parastacus pilimanus[&&NHX:TOL=7970],parastacus pugnax[&&NHX:TOL=7971],parastacus saffordi[&&NHX:TOL=7972],parastacus varicosus[&&NHX:TOL=7973])parastacus[&&NHX:TOL=7725])[&&NHX:TOL=7723])[&&NHX:TOL=7721])[&&NHX:TOL=7719])parastacidae[&&NHX:TOL=6665],((((pacifastacus hobbsastacus chenoderma[&&NHX:TOL=6679],pacifastacus hobbsastacus connectens[&&NHX:TOL=6680],pacifastacus hobbsastacus fortis[&&NHX:TOL=6681],pacifastacus hobbsastacus gambelii[&&NHX:TOL=6682],pacifastacus hobbsastacus nigrescens[&&NHX:TOL=6683])pacifastacus hobbsastacus[&&NHX:TOL=6690],(pacifastacus pacifastacus leniusculus klamathensis[&&NHX:TOL=6685],pacifastacus pacifastacus leniusculus leniusculus[&&NHX:TOL=6686],pacifastacus pacifastacus leniusculus trowbridgii[&&NHX:TOL=6687])pacifastacus pacifastacus[&&NHX:TOL=6691])pacifastacus[&&NHX:TOL=6670],((astacus astacus[&&NHX:TOL=6675],astacus leptodactylus[&&NHX:TOL=6676],astacus pachypus[&&NHX:TOL=6677])astacus[&&NHX:TOL=6672],austropotamobius[&&NHX:TOL=6673])[&&NHX:TOL=6671])astacidae[&&NHX:TOL=6667],(((cambarellus dirigicambarus shufeldtii[&&NHX:TOL=6733],((((((cambarellus pandicambarus schmitti[&&NHX:TOL=6775],cambarellus pandicambarus blacki[&&NHX:TOL=6776])[&&NHX:TOL=6774],cambarellus pandicambarus lesliei[&&NHX:TOL=6777])[&&NHX:TOL=6773],(cambarellus pandicambarus texanus[&&NHX:TOL=6779],cambarellus pandicambarus ninae[&&NHX:TOL=6780])[&&NHX:TOL=6778])[&&NHX:TOL=6772],cambarellus pandicambarus puer[&&NHX:TOL=6781])[&&NHX:TOL=6771],cambarellus pandicambarus diminutus[&&NHX:TOL=6782])cambarellus pandicambarus[&&NHX:TOL=6735],((cambarellus cambarellus prolixus[&&NHX:TOL=6748],(cambarellus cambarellus chapalanus[&&NHX:TOL=6750],cambarellus cambarellus montezumae[&&NHX:TOL=6751])[&&NHX:TOL=6749])[&&NHX:TOL=6747],((cambarellus cambarellus chihuahuae[&&NHX:TOL=6754],cambarellus cambarellus alvarezi[&&NHX:TOL=6755],cambarellus cambarellus occidentalis[&&NHX:TOL=6756])[&&NHX:TOL=6753],(cambarellus cambarellus zempoalensis[&&NHX:TOL=6758],cambarellus cambarellus patzcuarensis[&&NHX:TOL=6759])[&&NHX:TOL=6757],cambarellus cambarellus areolatus[&&NHX:TOL=6760])[&&NHX:TOL=6752])cambarellus cambarellus[&&NHX:TOL=6736])[&&NHX:TOL=6734])cambarellinae[&&NHX:TOL=6701],(((((((fallicambarus creaserinus byersi[&&NHX:TOL=7064],fallicambarus creaserinus oryktes[&&NHX:TOL=7065])[&&NHX:TOL=7063],(fallicambarus creaserinus hortoni[&&NHX:TOL=7067],(fallicambarus creaserinus uhleri[&&NHX:TOL=7069],(fallicambarus creaserinus fodiens[&&NHX:TOL=7071],fallicambarus creaserinus hedgpethi[&&NHX:TOL=7072])[&&NHX:TOL=7070])[&&NHX:TOL=7068])[&&NHX:TOL=7066])[&&NHX:TOL=7062],fallicambarus creaserinus gilpini[&&NHX:TOL=7073],fallicambarus creaserinus gordoni[&&NHX:TOL=7074],fallicambarus creaserinus danielae[&&NHX:TOL=7075],fallicambarus creaserinus caesius[&&NHX:TOL=7076],fallicambarus creaserinus burrisi[&&NHX:TOL=7077])fallicambarus creaserinus[&&NHX:TOL=7051],(fallicambarus fallicambarus petilicarpus[&&NHX:TOL=7085],fallicambarus fallicambarus harpi[&&NHX:TOL=7086],fallicambarus fallicambarus devastator[&&NHX:TOL=7087],((fallicambarus fallicambarus macneesei[&&NHX:TOL=7090],fallicambarus fallicambarus dissitus[&&NHX:TOL=7091])[&&NHX:TOL=7089],(fallicambarus fallicambarus strawni[&&NHX:TOL=7093],fallicambarus fallicambarus jeanae[&&NHX:TOL=7094])[&&NHX:TOL=7092])[&&NHX:TOL=7088])fallicambarus fallicambarus[&&NHX:TOL=7052])fallicambarus[&&NHX:TOL=6707],(barbicambarus cornutus[&&NHX:TOL=6709],(cambarus exilicambarus cracens[&&NHX:TOL=6784],(((((cambarus jugicambarus gentryi[&&NHX:TOL=6931],cambarus jugicambarus dubius[&&NHX:TOL=6932],cambarus jugicambarus crinipes[&&NHX:TOL=6933],cambarus jugicambarus bouchardi[&&NHX:TOL=6934],cambarus jugicambarus batchi[&&NHX:TOL=6935],(((((cambarus jugicambarus conasaugaensis[&&NHX:TOL=6941],cambarus jugicambarus asperimanus[&&NHX:TOL=6942])[&&NHX:TOL=6940],cambarus jugicambarus nodosus[&&NHX:TOL=6943])[&&NHX:TOL=6939],((cambarus jugicambarus carolinus[&&NHX:TOL=6946],cambarus jugicambarus monongalensis[&&NHX:TOL=6947])[&&NHX:TOL=6945],(((cambarus jugicambarus unestami[&&NHX:TOL=6951],cambarus jugicambarus parvoculus[&&NHX:TOL=6952])[&&NHX:TOL=6950],cambarus jugicambarus cryptodytes[&&NHX:TOL=6953])[&&NHX:TOL=6949],cambarus jugicambarus distans[&&NHX:TOL=6954])[&&NHX:TOL=6948])[&&NHX:TOL=6944])[&&NHX:TOL=6938],((((cambarus jugicambarus subterraneus[&&NHX:TOL=6959],cambarus jugicambarus aculabrum[&&NHX:TOL=6960])[&&NHX:TOL=6958],(cambarus jugicambarus zophonastes[&&NHX:TOL=6962],(cambarus jugicambarus tartarus[&&NHX:TOL=6964],cambarus jugicambarus setosus[&&NHX:TOL=6965])[&&NHX:TOL=6963])[&&NHX:TOL=6961])[&&NHX:TOL=6957],cambarus jugicambarus causeyi[&&NHX:TOL=6966])[&&NHX:TOL=6956],(cambarus jugicambarus brachydactylus[&&NHX:TOL=6968],(cambarus jugicambarus williami[&&NHX:TOL=6970],cambarus jugicambarus friaufi[&&NHX:TOL=6971])[&&NHX:TOL=6969])[&&NHX:TOL=6967])[&&NHX:TOL=6955])[&&NHX:TOL=6937],cambarus jugicambarus obeyensis[&&NHX:TOL=6972])[&&NHX:TOL=6936])cambarus jugicambarus[&&NHX:TOL=6789],(cambarus glareocola brachydactylus[&&NHX:TOL=7023],(cambarus glareocola friaufi[&&NHX:TOL=7025],cambarus glareocola williami[&&NHX:TOL=7026])[&&NHX:TOL=7024])cambarus glareocola[&&NHX:TOL=6790])[&&NHX:TOL=6788],((cambarus cambarus bartonii bartonii[&&NHX:TOL=6821],cambarus cambarus bartonii cavatus[&&NHX:TOL=6822],cambarus cambarus bartonii carinirostris[&&NHX:TOL=6823])[&&NHX:TOL=6820],cambarus cambarus howardi[&&NHX:TOL=6824],cambarus cambarus ortmanni[&&NHX:TOL=6825],cambarus cambarus sciotensis[&&NHX:TOL=6826])cambarus cambarus[&&NHX:TOL=6791])[&&NHX:TOL=6787],((cambarus lacunicambarus acanthura[&&NHX:TOL=6978],cambarus lacunicambarus diogenes[&&NHX:TOL=6979],cambarus lacunicambarus ludovicianus[&&NHX:TOL=6980],cambarus lacunicambarus miltus[&&NHX:TOL=6981])cambarus lacunicambarus[&&NHX:TOL=6793],(cambarus tubericambarus acanthura[&&NHX:TOL=7031],cambarus tubericambarus thomai[&&NHX:TOL=7032],cambarus tubericambarus sp. a[&&NHX:TOL=7033])cambarus tubericambarus[&&NHX:TOL=6794])[&&NHX:TOL=6792])[&&NHX:TOL=6786],(cambarus veticambarus pristinus[&&NHX:TOL=6796],(((((((((cambarus puncticambarus extraneus[&&NHX:TOL=7002],cambarus puncticambarus georgiae[&&NHX:TOL=7003])[&&NHX:TOL=7001],cambarus puncticambarus chaugaensis[&&NHX:TOL=7004])[&&NHX:TOL=7000],(cambarus puncticambarus hiwasseensis[&&NHX:TOL=7006],cambarus puncticambarus parrishi[&&NHX:TOL=7007])[&&NHX:TOL=7005])[&&NHX:TOL=6999],(cambarus puncticambarus scotti[&&NHX:TOL=7009],cambarus puncticambarus coosae[&&NHX:TOL=7010])[&&NHX:TOL=7008])georgia representatives[&&NHX:TOL=6998],cambarus puncticambarus acuminatus[&&NHX:TOL=7011],cambarus puncticambarus buntingi[&&NHX:TOL=7012],cambarus puncticambarus cumberlandensis[&&NHX:TOL=7013],cambarus puncticambarus nerterius[&&NHX:TOL=7014],cambarus puncticambarus reburrus[&&NHX:TOL=7015],cambarus puncticambarus robustus[&&NHX:TOL=7016],cambarus puncticambarus spicatus[&&NHX:TOL=7017],cambarus puncticambarus veteranus[&&NHX:TOL=7018])cambarus puncticambarus[&&NHX:TOL=6801],(cambarus depressicambarus sphenoides[&&NHX:TOL=6844],cambarus depressicambarus reduncus[&&NHX:TOL=6845],cambarus depressicambarus pyronotus[&&NHX:TOL=6846],cambarus depressicambarus obstipus[&&NHX:TOL=6847],cambarus depressicambarus graysoni[&&NHX:TOL=6848],cambarus depressicambarus deweesae[&&NHX:TOL=6849],cambarus depressicambarus catagius[&&NHX:TOL=6850],(((((((cambarus depressicambarus latimanus[&&NHX:TOL=6858],cambarus depressicambarus striatus[&&NHX:TOL=6859])[&&NHX:TOL=6857],cambarus depressicambarus harti[&&NHX:TOL=6860])[&&NHX:TOL=6856],cambarus depressicambarus strigosus[&&NHX:TOL=6861])[&&NHX:TOL=6855],cambarus depressicambarus reflexus[&&NHX:TOL=6862])[&&NHX:TOL=6854],cambarus depressicambarus truncatus[&&NHX:TOL=6863])[&&NHX:TOL=6853],cambarus depressicambarus cymatilis[&&NHX:TOL=6864])[&&NHX:TOL=6852],(cambarus depressicambarus englishi[&&NHX:TOL=6866],cambarus depressicambarus halli[&&NHX:TOL=6867])[&&NHX:TOL=6865])georgia representatives[&&NHX:TOL=6851])cambarus depressicambarus[&&NHX:TOL=6802])[&&NHX:TOL=6800],(cambarus aviticambarus hamulatus[&&NHX:TOL=6810],cambarus aviticambarus jonesi[&&NHX:TOL=6811],cambarus aviticambarus veitchorum[&&NHX:TOL=6812])cambarus aviticambarus[&&NHX:TOL=6803])[&&NHX:TOL=6799],(cambarus hiaticambarus longulus[&&NHX:TOL=6894],(cambarus hiaticambarus coosawattae[&&NHX:TOL=6896],(cambarus hiaticambarus manningi[&&NHX:TOL=6898],cambarus hiaticambarus longirostris[&&NHX:TOL=6899])[&&NHX:TOL=6897])[&&NHX:TOL=6895],(cambarus hiaticambarus chasmodactylus[&&NHX:TOL=6901],cambarus hiaticambarus elkensis[&&NHX:TOL=6902])[&&NHX:TOL=6900],((cambarus hiaticambarus speciosus[&&NHX:TOL=6905],cambarus hiaticambarus girardianus[&&NHX:TOL=6906])[&&NHX:TOL=6904],cambarus hiaticambarus fasciatus[&&NHX:TOL=6907])[&&NHX:TOL=6903])cambarus hiaticambarus[&&NHX:TOL=6804])[&&NHX:TOL=6798],(cambarus erebicambarus hubbsi[&&NHX:TOL=6878],cambarus erebicambarus hubrichti[&&NHX:TOL=6879],cambarus erebicambarus maculatus[&&NHX:TOL=6880],cambarus erebicambarus laevis[&&NHX:TOL=6881],cambarus erebicambarus ornatus[&&NHX:TOL=6882],cambarus erebicambarus rusticiformis[&&NHX:TOL=6883],cambarus erebicambarus tenebrosus[&&NHX:TOL=6884])cambarus erebicambarus[&&NHX:TOL=6805])[&&NHX:TOL=6797])[&&NHX:TOL=6795])[&&NHX:TOL=6785])cambarus[&&NHX:TOL=6710])[&&NHX:TOL=6708])[&&NHX:TOL=6706],(((hobbseus attenuatus[&&NHX:TOL=7105],hobbseus cristatus[&&NHX:TOL=7106],hobbseus orconectoides[&&NHX:TOL=7107],hobbseus petilus[&&NHX:TOL=7108],hobbseus prominens[&&NHX:TOL=7109],hobbseus valleculus[&&NHX:TOL=7110])hobbseus[&&NHX:TOL=6713],bouchardina robisoni[&&NHX:TOL=6714])[&&NHX:TOL=6712],((faxonella beyeri[&&NHX:TOL=7096],faxonella blairi[&&NHX:TOL=7097],faxonella clypeata[&&NHX:TOL=7098],faxonella creaseri[&&NHX:TOL=7099])faxonella[&&NHX:TOL=6716],((orconectes orconectes australis australis[&&NHX:TOL=7247],orconectes orconectes australis packardi[&&NHX:TOL=7248],orconectes orconectes incomptus[&&NHX:TOL=7249],orconectes orconectes inermis inermis[&&NHX:TOL=7250],orconectes orconectes inermis testii[&&NHX:TOL=7251],orconectes orconectes pellucidus[&&NHX:TOL=7252],orconectes orconectes pagei[&&NHX:TOL=7253],orconectes orconectes sheltae[&&NHX:TOL=7254])orconectes orconectes[&&NHX:TOL=7128],((((orconectes crockerinus bisectus[&&NHX:TOL=7178],orconectes crockerinus erichsonianus[&&NHX:TOL=7179],orconectes crockerinus eupunctus[&&NHX:TOL=7180],orconectes crockerinus illinoiensis[&&NHX:TOL=7181],orconectes crockerinus jeffersoni[&&NHX:TOL=7182],orconectes crockerinus marchandi[&&NHX:TOL=7183],orconectes crockerinus obscurus[&&NHX:TOL=7184],orconectes crockerinus propinquus[&&NHX:TOL=7185],orconectes crockerinus rafinesquei[&&NHX:TOL=7186],orconectes crockerinus sanbornii erismophorous[&&NHX:TOL=7187],orconectes crockerinus sanbornii sanbornii[&&NHX:TOL=7188],orconectes crockerinus shoupi[&&NHX:TOL=7189],orconectes crockerinus stannardi[&&NHX:TOL=7190],orconectes crockerinus tricuspis[&&NHX:TOL=7191],orconectes crockerinus virginiensis[&&NHX:TOL=7192])orconectes crockerinus[&&NHX:TOL=7132],(((((((((((orconectes procericambarus medius[&&NHX:TOL=7290],orconectes procericambarus luteus[&&NHX:TOL=7291])[&&NHX:TOL=7289],(orconectes procericambarus durelli[&&NHX:TOL=7293],orconectes procericambarus neglectus neglectus[&&NHX:TOL=7294],orconectes procericambarus neglectus chaenodactylus[&&NHX:TOL=7295])[&&NHX:TOL=7292])[&&NHX:TOL=7288],(orconectes procericambarus quadruncus[&&NHX:TOL=7297],(orconectes procericambarus leptogonopodus[&&NHX:TOL=7299],orconectes procericambarus transfuga[&&NHX:TOL=7300])[&&NHX:TOL=7298])[&&NHX:TOL=7296])[&&NHX:TOL=7287],orconectes procericambarus punctimanus[&&NHX:TOL=7301])[&&NHX:TOL=7286],(orconectes procericambarus saxatilis[&&NHX:TOL=7303],orconectes procericambarus longidigitus[&&NHX:TOL=7304])[&&NHX:TOL=7302])[&&NHX:TOL=7285],(orconectes procericambarus hylas[&&NHX:TOL=7306],orconectes procericambarus peruncus[&&NHX:TOL=7307])[&&NHX:TOL=7305])[&&NHX:TOL=7284],orconectes procericambarus ozarkae[&&NHX:TOL=7308])[&&NHX:TOL=7283],((((orconectes procericambarus spinosus[&&NHX:TOL=7313],orconectes procericambarus placidus[&&NHX:TOL=7314])[&&NHX:TOL=7312],orconectes procericambarus putnami[&&NHX:TOL=7315])[&&NHX:TOL=7311],(orconectes procericambarus barrenensis[&&NHX:TOL=7317],orconectes procericambarus forceps[&&NHX:TOL=7318])[&&NHX:TOL=7316])[&&NHX:TOL=7310],orconectes procericambarus rusticus[&&NHX:TOL=7319])[&&NHX:TOL=7309])[&&NHX:TOL=7282],(orconectes procericambarus macrus[&&NHX:TOL=7321],orconectes procericambarus nana[&&NHX:TOL=7322])[&&NHX:TOL=7320])[&&NHX:TOL=7281],orconectes procericambarus acares[&&NHX:TOL=7323],(orconectes procericambarus mirus[&&NHX:TOL=7325],orconectes procericambarus menae[&&NHX:TOL=7326])[&&NHX:TOL=7324])[&&NHX:TOL=7280],orconectes procericambarus williamsi[&&NHX:TOL=7327])orconectes procericambarus[&&NHX:TOL=7133])[&&NHX:TOL=7131],(orconectes faxonius indianensis[&&NHX:TOL=7197],orconectes faxonius limosus[&&NHX:TOL=7198],orconectes faxonius wrighti[&&NHX:TOL=7199])orconectes faxonius[&&NHX:TOL=7134])[&&NHX:TOL=7130],(((((orconectes gremicambarus alabamensis[&&NHX:TOL=7214],orconectes gremicambarus causeyi[&&NHX:TOL=7215],orconectes gremicambarus chickasawae[&&NHX:TOL=7216],orconectes gremicambarus compressus[&&NHX:TOL=7217],orconectes gremicambarus cooperi[&&NHX:TOL=7218],orconectes gremicambarus etnieri[&&NHX:TOL=7219],orconectes gremicambarus holti[&&NHX:TOL=7220],orconectes gremicambarus immunis[&&NHX:TOL=7221],orconectes gremicambarus mississippiensis[&&NHX:TOL=7222],orconectes gremicambarus nais[&&NHX:TOL=7223],orconectes gremicambarus rhoadesi[&&NHX:TOL=7224],orconectes gremicambarus validus[&&NHX:TOL=7225],orconectes gremicambarus virilis[&&NHX:TOL=7226])orconectes gremicambarus[&&NHX:TOL=7139],(orconectes alabamensis[&&NHX:TOL=7118],orconectes chickasawae[&&NHX:TOL=7119],orconectes cooperi[&&NHX:TOL=7120],orconectes etnieri[&&NHX:TOL=7121],orconectes holti[&&NHX:TOL=7122],orconectes immunis[&&NHX:TOL=7123],orconectes mississippiensis[&&NHX:TOL=7124],orconectes rhoadesi[&&NHX:TOL=7125],orconectes validus[&&NHX:TOL=7126])orconectes trisellescens[&&NHX:TOL=7140])[&&NHX:TOL=7138],(orconectes buannulifictus hobbsi[&&NHX:TOL=7156],orconectes buannulifictus meeki brevis[&&NHX:TOL=7157],orconectes buannulifictus meeki meeki[&&NHX:TOL=7158],orconectes buannulifictus palmeri creolanus[&&NHX:TOL=7159],orconectes buannulifictus palmeri longimanus[&&NHX:TOL=7160],orconectes buannulifictus palmeri palmeri[&&NHX:TOL=7161])orconectes buannulifictus[&&NHX:TOL=7141])[&&NHX:TOL=7137],(orconectes hespericambarus blacki[&&NHX:TOL=7234],orconectes hespericambarus deanae[&&NHX:TOL=7235],orconectes hespericambarus difficilis[&&NHX:TOL=7236],orconectes hespericambarus hathawayi[&&NHX:TOL=7237],orconectes hespericambarus maletae[&&NHX:TOL=7238],orconectes hespericambarus perfectus[&&NHX:TOL=7239])orconectes hespericambarus[&&NHX:TOL=7142])[&&NHX:TOL=7136],((orconectes rhoadesius kentuckiensis[&&NHX:TOL=7331],orconectes rhoadesius sloanii[&&NHX:TOL=7332])orconectes rhoadesius[&&NHX:TOL=7144],orconectes billecambarus harrisonii[&&NHX:TOL=7145])[&&NHX:TOL=7143])[&&NHX:TOL=7135],orconectes tragulicambarus lancifer[&&NHX:TOL=7146])[&&NHX:TOL=7129])orconectes[&&NHX:TOL=6717])[&&NHX:TOL=6715])[&&NHX:TOL=6711])[&&NHX:TOL=6705],(((procambarus acucauda fitzpatricki[&&NHX:TOL=7338],(procambarus austrocambarus acanthophorus[&&NHX:TOL=7376],procambarus austrocambarus atkinsoni[&&NHX:TOL=7377],procambarus austrocambarus cubensis cubensis[&&NHX:TOL=7378],procambarus austrocambarus cubensis rivalis[&&NHX:TOL=7379],procambarus austrocambarus llamasi[&&NHX:TOL=7380],procambarus austrocambarus mexicanus[&&NHX:TOL=7381],procambarus austrocambarus mirandai[&&NHX:TOL=7382],procambarus austrocambarus niveus[&&NHX:TOL=7383],procambarus austrocambarus oaxacae oaxacae[&&NHX:TOL=7384],procambarus austrocambarus oaxacae reddelli[&&NHX:TOL=7385],procambarus austrocambarus pilosimanus[&&NHX:TOL=7386],procambarus austrocambarus primaevus[&&NHX:EXT=Y:TOL=7387],procambarus austrocambarus rodriguezi[&&NHX:TOL=7388],procambarus austrocambarus ruthveni[&&NHX:TOL=7389],procambarus austrocambarus sbordonii[&&NHX:TOL=7390],procambarus austrocambarus vazquezae[&&NHX:TOL=7391],procambarus austrocambarus veracruzanus[&&NHX:TOL=7392],procambarus austrocambarus williamsoni[&&NHX:TOL=7393],procambarus austrocambarus zapoapensis[&&NHX:TOL=7394],procambarus austrocambarus citlaltepetl[&&NHX:TOL=7395],procambarus austrocambarus olmecorum[&&NHX:TOL=7396])procambarus austrocambarus[&&NHX:TOL=7339],(procambarus capillicambarus brazoriensis[&&NHX:TOL=7401],procambarus capillicambarus hinei[&&NHX:TOL=7402],procambarus capillicambarus incilis[&&NHX:TOL=7403])procambarus capillicambarus[&&NHX:TOL=7340],(((((procambarus girardiella connus[&&NHX:TOL=7424],procambarus girardiella hagenianus vesticeps[&&NHX:TOL=7425],procambarus girardiella hagenianus hagenianus[&&NHX:TOL=7426])[&&NHX:TOL=7423],procambarus girardiella barbiger[&&NHX:TOL=7427])[&&NHX:TOL=7422],(procambarus girardiella pogum[&&NHX:TOL=7429],procambarus girardiella cometes[&&NHX:TOL=7430])[&&NHX:TOL=7428])[&&NHX:TOL=7421],procambarus girardiella tulanei[&&NHX:TOL=7431])hagenianus group[&&NHX:TOL=7420],procambarus girardiella ceruleus[&&NHX:TOL=7432],procambarus girardiella regalis[&&NHX:TOL=7433],procambarus girardiella ferrugineus[&&NHX:TOL=7434],procambarus girardiella curdi[&&NHX:TOL=7435],procambarus girardiella gracilis[&&NHX:TOL=7436],procambarus girardiella liberorum[&&NHX:TOL=7437],procambarus girardiella parasimulans[&&NHX:TOL=7438],procambarus girardiella regiomontanus[&&NHX:TOL=7439],procambarus girardiella reimeri[&&NHX:TOL=7440],procambarus girardiella simulans[&&NHX:TOL=7441])procambarus girardiella[&&NHX:TOL=7341],(procambarus hagenides advena[&&NHX:TOL=7453],procambarus hagenides caritus[&&NHX:TOL=7454],procambarus hagenides geodytes[&&NHX:TOL=7455],procambarus hagenides pygmaeus[&&NHX:TOL=7456],procambarus hagenides rogersi campestris[&&NHX:TOL=7457],procambarus hagenides rogersi expletus[&&NHX:TOL=7458],procambarus hagenides rogersi ochlocknensis[&&NHX:TOL=7459],procambarus hagenides rogersi rogersi[&&NHX:TOL=7460],procambarus hagenides talpoides[&&NHX:TOL=7461],procambarus hagenides truculentus[&&NHX:TOL=7462])procambarus hagenides[&&NHX:TOL=7342],(procambarus leconticambarus alleni[&&NHX:TOL=7480],procambarus leconticambarus apalachicolae[&&NHX:TOL=7481],procambarus leconticambarus barbatus[&&NHX:TOL=7482],procambarus leconticambarus capillatus[&&NHX:TOL=7483],procambarus leconticambarus econfinae[&&NHX:TOL=7484],procambarus leconticambarus escambiensis[&&NHX:TOL=7485],procambarus leconticambarus hubbelli[&&NHX:TOL=7486],procambarus leconticambarus kilbyi[&&NHX:TOL=7487],procambarus leconticambarus latipleurum[&&NHX:TOL=7488],procambarus leconticambarus milleri[&&NHX:TOL=7489],procambarus leconticambarus pubischelae deficiens[&&NHX:TOL=7490],procambarus leconticambarus pubischelae pubischelae[&&NHX:TOL=7491],procambarus leconticambarus rathbunae[&&NHX:TOL=7492],procambarus leconticambarus shermani[&&NHX:TOL=7493])procambarus leconticambarus[&&NHX:TOL=7343],procambarus lonnbergius acherontis[&&NHX:TOL=7344],procambarus mexicambarus bouvieri[&&NHX:TOL=7345],(procambarus ortmannicus acutissimus[&&NHX:TOL=7548],procambarus ortmannicus acutus acutus[&&NHX:TOL=7549],procambarus ortmannicus acutus cuevachicae[&&NHX:TOL=7550],procambarus ortmannicus ancylus[&&NHX:TOL=7551],procambarus ortmannicus angustatus[&&NHX:TOL=7552],procambarus ortmannicus bivittatus[&&NHX:TOL=7553],procambarus ortmannicus blandingii[&&NHX:TOL=7554],procambarus ortmannicus caballeroi[&&NHX:TOL=7555],procambarus ortmannicus chacei[&&NHX:TOL=7556],procambarus ortmannicus delicatus[&&NHX:TOL=7557],procambarus ortmannicus enoplosternum[&&NHX:TOL=7558],procambarus ortmannicus epicyrtus[&&NHX:TOL=7559],procambarus ortmannicus erythrops[&&NHX:TOL=7560],procambarus ortmannicus evermanni[&&NHX:TOL=7561],procambarus ortmannicus fallax[&&NHX:TOL=7562],procambarus ortmannicus franzi[&&NHX:TOL=7563],procambarus ortmannicus geminus[&&NHX:TOL=7564],procambarus ortmannicus gonopodocristatus[&&NHX:TOL=7565],procambarus ortmannicus hayi[&&NHX:TOL=7566],procambarus ortmannicus hirsutus[&&NHX:TOL=7567],procambarus ortmannicus horsti[&&NHX:TOL=7568],procambarus ortmannicus hybus[&&NHX:TOL=7569],procambarus ortmannicus jaculus[&&NHX:TOL=7570],procambarus ortmannicus lecontei[&&NHX:TOL=7571],procambarus ortmannicus leitheuseri[&&NHX:TOL=7572],procambarus ortmannicus leonensis[&&NHX:TOL=7573],procambarus ortmannicus lepidodactylus[&&NHX:TOL=7574],procambarus ortmannicus lewisi[&&NHX:TOL=7575],procambarus ortmannicus litosternum[&&NHX:TOL=7576],procambarus ortmannicus lophotus[&&NHX:TOL=7577],procambarus ortmannicus lucifugus alachua[&&NHX:TOL=7578],procambarus ortmannicus lucifugus lucifugus[&&NHX:TOL=7579],procambarus ortmannicus lunzi[&&NHX:TOL=7580],procambarus ortmannicus mancus[&&NHX:TOL=7581],procambarus ortmannicus marthae[&&NHX:TOL=7582],procambarus ortmannicus medialis[&&NHX:TOL=7583],procambarus ortmannicus orcinus[&&NHX:TOL=7584],procambarus ortmannicus pallidus[&&NHX:TOL=7585],procambarus ortmannicus pearsei[&&NHX:TOL=7586],procambarus ortmannicus pictus[&&NHX:TOL=7587],procambarus ortmannicus planirostris[&&NHX:TOL=7588],procambarus ortmannicus plumimanus[&&NHX:TOL=7589],procambarus ortmannicus pubescens[&&NHX:TOL=7590],procambarus ortmannicus pycnogonopodus[&&NHX:TOL=7591],procambarus ortmannicus seminolae[&&NHX:TOL=7592],procambarus ortmannicus texanus[&&NHX:TOL=7593],procambarus ortmannicus toltecae[&&NHX:TOL=7594],procambarus ortmannicus verrucosus[&&NHX:TOL=7595],procambarus ortmannicus viaeviridis[&&NHX:TOL=7596],procambarus ortmannicus villalobosi[&&NHX:TOL=7597],procambarus ortmannicus xilitlae[&&NHX:TOL=7598],procambarus ortmannicus youngi[&&NHX:TOL=7599],procambarus ortmannicus braswelli[&&NHX:TOL=7600],procambarus ortmannicus nueces[&&NHX:TOL=7601])procambarus ortmannicus[&&NHX:TOL=7346],(procambarus paracambarus ortmannii[&&NHX:TOL=7625],procambarus paracambarus paradoxus[&&NHX:TOL=7626])procambarus paracambarus[&&NHX:TOL=7347],(procambarus pennides ablusus[&&NHX:TOL=7628],procambarus pennides clemmeri[&&NHX:TOL=7629],procambarus pennides dupratzi[&&NHX:TOL=7630],procambarus pennides echinatus[&&NHX:TOL=7631],procambarus pennides elegans[&&NHX:TOL=7632],procambarus pennides gibbus[&&NHX:TOL=7633],procambarus pennides lagniappe[&&NHX:TOL=7634],procambarus pennides lylei[&&NHX:TOL=7635],procambarus pennides natchitochae[&&NHX:TOL=7636],procambarus pennides ouachitae[&&NHX:TOL=7637],procambarus pennides penni[&&NHX:TOL=7638],procambarus pennides petersi[&&NHX:TOL=7639],procambarus pennides raneyi[&&NHX:TOL=7640],procambarus pennides roberti[&&NHX:TOL=7641],procambarus pennides spiculifer[&&NHX:TOL=7642],procambarus pennides suttkusi[&&NHX:TOL=7643],procambarus pennides versutus[&&NHX:TOL=7644],procambarus pennides vioscai[&&NHX:TOL=7645])procambarus pennides[&&NHX:TOL=7348],procambarus procambarus digueti[&&NHX:TOL=7349],procambarus remoticambarus pecki[&&NHX:TOL=7350],(procambarus scapulicambarus clarkii[&&NHX:TOL=7655],procambarus scapulicambarus howellae[&&NHX:TOL=7656],procambarus scapulicambarus okaloosae[&&NHX:TOL=7657],procambarus scapulicambarus paeninsulanus[&&NHX:TOL=7658],procambarus scapulicambarus strenthi[&&NHX:TOL=7659],procambarus scapulicambarus troglodytes[&&NHX:TOL=7660])procambarus scapulicambarus[&&NHX:TOL=7351],procambarus tenuicambarus tenuis[&&NHX:TOL=7352],(procambarus villalobosus contrerasi[&&NHX:TOL=7674],procambarus villalobosus cuetzalanae[&&NHX:TOL=7675],procambarus villalobosus erichsoni[&&NHX:TOL=7676],procambarus villalobosus hoffmanni[&&NHX:TOL=7677],procambarus villalobosus hortonhobbsi[&&NHX:TOL=7678],procambarus villalobosus riojai[&&NHX:TOL=7679],procambarus villalobosus teziutlanensis[&&NHX:TOL=7680],procambarus villalobosus tlapacoyanensis[&&NHX:TOL=7681],procambarus villalobosus xochitlanae[&&NHX:TOL=7682],procambarus villalobosus zihuateutlensis[&&NHX:TOL=7683])procambarus villalobosus[&&NHX:TOL=7353])procambarus[&&NHX:TOL=6720],troglocambarus maclanei[&&NHX:TOL=6721])[&&NHX:TOL=6719],((distocambarus distocambarus crockeri[&&NHX:TOL=7041],distocambarus distocambarus devexus[&&NHX:TOL=7042])distocambarus distocambarus[&&NHX:TOL=7036],(distocambarus fitzcambarus carlsoni[&&NHX:TOL=7046],distocambarus fitzcambarus youngineri[&&NHX:TOL=7047],distocambarus fitzcambarus hunteri[&&NHX:TOL=7048])distocambarus fitzcambarus[&&NHX:TOL=7037])distocambarus[&&NHX:TOL=6722])[&&NHX:TOL=6718])cambarinae[&&NHX:TOL=6702])[&&NHX:TOL=6700],(cambaroides dauricus[&&NHX:TOL=6724],cambaroides japonicus[&&NHX:TOL=6725],cambaroides schrenckii[&&NHX:TOL=6726],cambaroides similis[&&NHX:TOL=6727])cambaroides[&&NHX:TOL=6703])cambaridae[&&NHX:TOL=6668])astacoidea[&&NHX:TOL=6666])[&&NHX:TOL=6664])astacidea[&&NHX:TOL=6655],thalassinidea[&&NHX:TOL=6656])[&&NHX:TOL=79173])[&&NHX:TOL=78699])[&&NHX:TOL=78590],((homolodromiidae[&&NHX:TOL=72706],(homolidae[&&NHX:TOL=72709],latreilliidae[&&NHX:TOL=72710],poupiniidae[&&NHX:TOL=72711])homoloidea[&&NHX:TOL=72708],(dromiidae[&&NHX:TOL=77256],dynomenidae[&&NHX:TOL=77257])dromioidea[&&NHX:TOL=77255])dromiacea[&&NHX:TOL=72704],(((raninidae[&&NHX:TOL=72718],symethidae[&&NHX:TOL=72719])raninoidea[&&NHX:TOL=72717],(cyclodorippidae[&&NHX:TOL=72721],cymonomidae[&&NHX:TOL=72722],phyllotymolinidae[&&NHX:TOL=72723])cyclodorippoidea[&&NHX:TOL=72720])raninoida[&&NHX:TOL=72716],(cryptochiridae[&&NHX:TOL=72726],(gecarcinucidae[&&NHX:TOL=72729],parathelphusidae[&&NHX:TOL=72730])gecarcinucoidea[&&NHX:TOL=72728],pseudothelphusidae[&&NHX:TOL=72732],(deckeniidae[&&NHX:TOL=72735],platythelphusidae[&&NHX:TOL=72736],potamidae[&&NHX:TOL=72737],potamonautidae[&&NHX:TOL=72738])potamoidea[&&NHX:TOL=72734],belliidae[&&NHX:TOL=72740],(carpiliidae[&&NHX:TOL=72743],eumedonidae[&&NHX:TOL=72744],goneplacidae[&&NHX:TOL=72745],hexapodidae[&&NHX:TOL=72746],menippidae[&&NHX:TOL=72747],panopeidae[&&NHX:TOL=72748],pilumnidae[&&NHX:TOL=72749],platyxanthidae[&&NHX:TOL=72750],pseudorhombilidae[&&NHX:TOL=72751],trapeziidae[&&NHX:TOL=72752],xanthidae[&&NHX:TOL=72753])xanthoidea[&&NHX:TOL=72742],bythograeidae[&&NHX:TOL=72755],(geryonidae[&&NHX:TOL=72758],portunidae[&&NHX:TOL=72759],trichodactylidae[&&NHX:TOL=72760])portunoidea[&&NHX:TOL=72757],(atelecyclidae[&&NHX:TOL=72762],cancridae[&&NHX:TOL=72763],cheiragonidae[&&NHX:TOL=72764],corystidae[&&NHX:TOL=72765],pirimelidae[&&NHX:TOL=72766],thiidae[&&NHX:TOL=72767])cancroidea[&&NHX:TOL=72761],retroplumidae[&&NHX:TOL=72769],(aethridae[&&NHX:TOL=72772],dairidae[&&NHX:TOL=72773],daldorfiidae[&&NHX:TOL=72774],parthenopidae[&&NHX:TOL=72775])parthenopoidea[&&NHX:TOL=72771],hymenosomatidae[&&NHX:TOL=72777],(epialtidae[&&NHX:TOL=72780],inachidae[&&NHX:TOL=72781],inachoididae[&&NHX:TOL=72782],majidae[&&NHX:TOL=72783],mithracidae[&&NHX:TOL=72784],pisidae[&&NHX:TOL=72785],tychidae[&&NHX:TOL=72786])majoidea[&&NHX:TOL=72779],(leucosiidae[&&NHX:TOL=72788],matutidae[&&NHX:TOL=72789])leucosioidea[&&NHX:TOL=72787],(calappidae[&&NHX:TOL=72791],hepatidae[&&NHX:TOL=72792])calappoidea[&&NHX:TOL=72790],(dorippidae[&&NHX:TOL=72794],orithyiidae[&&NHX:TOL=72795])dorippoidea[&&NHX:TOL=72793])heterotremata[&&NHX:TOL=72724],(pinnotheridae[&&NHX:TOL=72798],(camptandriidae[&&NHX:TOL=72801],mictyridae[&&NHX:TOL=72802],ocypodidae[&&NHX:TOL=72803],palicidae[&&NHX:TOL=72804])ocypodoidea[&&NHX:TOL=72800],(gecarcinidae[&&NHX:TOL=72806],glyptograpsidae[&&NHX:TOL=72807],grapsidae[&&NHX:TOL=72808],plagusiidae[&&NHX:TOL=72809],sesarmidae[&&NHX:TOL=72810],varunidae[&&NHX:TOL=72811])grapsoidea[&&NHX:TOL=72805])thoracotremata[&&NHX:TOL=72796])eubrachyura[&&NHX:TOL=72715])brachyura[&&NHX:TOL=6659])reptantia[&&NHX:TOL=6654],caridea[&&NHX:TOL=6651])[&&NHX:TOL=78698])pleocyemata[&&NHX:TOL=6650])decapoda[&&NHX:TOL=6308])[&&NHX:TOL=6306],euphausiacea[&&NHX:TOL=6309],(mysida[&&NHX:TOL=6312],lophogastrida[&&NHX:TOL=6313],thermosbaenacea[&&NHX:TOL=6314],(cumacea[&&NHX:TOL=6316],tanaidacea[&&NHX:TOL=6317],mictacea[&&NHX:TOL=6318],spelaeogriphacea[&&NHX:TOL=6319],(phreatoicidea[&&NHX:TOL=7984],((asellota[&&NHX:TOL=7987],microcerberidea[&&NHX:TOL=7988])[&&NHX:TOL=7986],((calabozoidea[&&NHX:TOL=7991],oniscidea[&&NHX:TOL=7992])[&&NHX:TOL=7990],(valvifera[&&NHX:TOL=7994],(sphaeromatidae[&&NHX:TOL=7996],((bathynataliidae[&&NHX:TOL=7999],(keuphyliidae[&&NHX:TOL=8001],(plakarthriidae[&&NHX:TOL=8003],serolidae[&&NHX:TOL=8004])[&&NHX:TOL=8002])[&&NHX:TOL=8000])[&&NHX:TOL=7998],(epicaridea[&&NHX:TOL=8006],gnathiidea[&&NHX:TOL=8007])[&&NHX:TOL=8005],(limnoriidae[&&NHX:TOL=8009],lynseiidae[&&NHX:TOL=8010])[&&NHX:TOL=8008],(cirolanidae[&&NHX:TOL=8012],phoratopodidae[&&NHX:TOL=8013],(anthuridea[&&NHX:TOL=8015],(anuropidae[&&NHX:TOL=8017],protognathiidae[&&NHX:TOL=8018],(corallanidae[&&NHX:TOL=8020],tridentellidae[&&NHX:TOL=8021],(aegidae[&&NHX:TOL=8023],cymothoidae[&&NHX:TOL=8024])[&&NHX:TOL=8022])[&&NHX:TOL=8019])[&&NHX:TOL=8016])[&&NHX:TOL=8014])[&&NHX:TOL=8011])[&&NHX:TOL=7997])[&&NHX:TOL=7995])[&&NHX:TOL=7993])[&&NHX:TOL=7989])[&&NHX:TOL=7985])isopoda[&&NHX:TOL=6320],amphipoda[&&NHX:TOL=6321])[&&NHX:TOL=6315])peracarida[&&NHX:TOL=6310])caridoida[&&NHX:TOL=6302])eumalacostraca[&&NHX:TOL=6297])malacostraca[&&NHX:TOL=6253])crustacea[&&NHX:TOL=2529])[&&NHX:TOL=2527],(((millotauropus[&&NHX:TOL=52705],rosettauropus[&&NHX:TOL=52706])millotauropodidae[&&NHX:TOL=14689],(allopauropus[&&NHX:TOL=52676],asphaeridiopus[&&NHX:TOL=52677],australopauropus[&&NHX:TOL=52678],cauvetauropus[&&NHX:TOL=52679],decapauropus[&&NHX:TOL=52680],donzelotauropus[&&NHX:TOL=52681],fagepauropus[&&NHX:TOL=52682],hemipauropus[&&NHX:TOL=52683],neopauropus[&&NHX:TOL=52684],nesopauropus[&&NHX:TOL=52685],pauropus[&&NHX:TOL=52686],perissopauropus[&&NHX:TOL=52687],polypauropoides[&&NHX:TOL=52688],polypauropus[&&NHX:TOL=52689],rabaudauropus[&&NHX:TOL=52690],remypus[&&NHX:TOL=52691],scleropauropus[&&NHX:TOL=52692],stylopauropoides[&&NHX:TOL=52693],stylopauropus[&&NHX:TOL=52694])pauropodidae[&&NHX:TOL=14690],(brachypauropoides[&&NHX:TOL=52695],brachypauropus[&&NHX:TOL=52696])brachypauropodidae[&&NHX:TOL=14691],afrauropus occiduus[&&NHX:TOL=14692],(acopauropus[&&NHX:TOL=52697],eurypauropus[&&NHX:TOL=52698],gravieripus[&&NHX:TOL=52699],latzelipus[&&NHX:TOL=52700],samarangopus[&&NHX:TOL=52701],sphaeropauropus[&&NHX:TOL=52702],thaumatopauropus[&&NHX:TOL=52703],trachypauropus[&&NHX:TOL=52704])eurypauropodidae[&&NHX:TOL=14693])pauropoda[&&NHX:TOL=2531],((hypogexenidae[&&NHX:TOL=52758],lophoproctidae[&&NHX:TOL=52759],polyxenidae[&&NHX:TOL=52760],synxenidae[&&NHX:TOL=52761])polyxenida[&&NHX:TOL=8139],(((glomeridesmus adjuntas[&&NHX:TOL=52762],glomeridesmus albiceps[&&NHX:TOL=52763],glomeridesmus angulosus[&&NHX:TOL=52764],glomeridesmus barricolens[&&NHX:TOL=52765],glomeridesmus bicolor[&&NHX:TOL=52766],glomeridesmus centralis[&&NHX:TOL=52767],glomeridesmus circularis[&&NHX:TOL=52768],glomeridesmus concolor[&&NHX:TOL=52769],glomeridesmus grenadanus[&&NHX:TOL=52770],glomeridesmus jenkinsi[&&NHX:TOL=52771],glomeridesmus latus[&&NHX:TOL=52772],glomeridesmus marmoreus[&&NHX:TOL=52773],glomeridesmus parvior[&&NHX:TOL=52774],glomeridesmus pectinatus[&&NHX:TOL=52775],glomeridesmus riveroi[&&NHX:TOL=52776],glomeridesmus rotundatus[&&NHX:TOL=52777],glomeridesmus sbordoni[&&NHX:TOL=52778])glomeridesmus[&&NHX:TOL=8142],(sphaeropoeidae[&&NHX:TOL=52779],sphaerotheriidae[&&NHX:TOL=52780])sphaerotheriida[&&NHX:TOL=8143],(glomeridae[&&NHX:TOL=52781],glomeridellidae[&&NHX:TOL=52782],trachysphaeridae[&&NHX:TOL=52783])glomerida[&&NHX:TOL=8144])pentazonia[&&NHX:TOL=8141],(siphoniulus neotropicus[&&NHX:TOL=8146],((andrognathidae[&&NHX:TOL=52784],platydesmidae[&&NHX:TOL=52785])platydesmida[&&NHX:TOL=8148],(siphonophoridae[&&NHX:TOL=52786],siphonorhinidae[&&NHX:TOL=52787])siphonophorida[&&NHX:TOL=8149],(hirudisomatidae[&&NHX:TOL=52788],polyzoniidae[&&NHX:TOL=52789],siphonotidae[&&NHX:TOL=52790],siphonocryptidae[&&NHX:TOL=52791])polyzoniida[&&NHX:TOL=8150])colobognatha[&&NHX:TOL=8147],(((prostemmiulus[&&NHX:TOL=52915],scoliogmus[&&NHX:TOL=52916],stemmiulus[&&NHX:TOL=52917])stemmiulida[&&NHX:TOL=8153],(abacionidae[&&NHX:TOL=52792],callipodidae[&&NHX:TOL=52793],caspiopetalidae[&&NHX:TOL=52794],dorypetalidae[&&NHX:TOL=52795],schizopetalidae[&&NHX:TOL=52796],sinocallipodidae[&&NHX:TOL=52797])callipodida[&&NHX:TOL=8154],(adritylidae[&&NHX:TOL=52798],altajellidae[&&NHX:TOL=52799],anthroleucosomatidae[&&NHX:TOL=52800],apterouridae[&&NHX:TOL=52801],attemsiidae[&&NHX:TOL=52802],biokoviellidae[&&NHX:TOL=52803],brachychaeteumatidae[&&NHX:TOL=52804],branneriidae[&&NHX:TOL=52805],caseyidae[&&NHX:TOL=52806],chaemosomatidae[&&NHX:TOL=52807],chordeumatidae[&&NHX:TOL=52808],cleidogonidae[&&NHX:TOL=52809],conotylidae[&&NHX:TOL=52810],craspedosomatidae[&&NHX:TOL=52811],diplomaragnidae[&&NHX:TOL=52812],entomobielziidae[&&NHX:TOL=52813],eudigonidae[&&NHX:TOL=52814],faginidae[&&NHX:TOL=52815],golovatchiidae[&&NHX:TOL=52816],haaseidae[&&NHX:TOL=52817],haasiidae[&&NHX:TOL=52818],haplobainosomatidae[&&NHX:TOL=52819],heterochordeumatidae[&&NHX:TOL=52820],heterolatzeliidae[&&NHX:TOL=52821],hoffmaneumatidae[&&NHX:TOL=52822],kashmireumatidae[&&NHX:TOL=52823],lankasomatidae[&&NHX:TOL=52824],lusitaniosomatidae[&&NHX:TOL=52825],macrochaeteumatidae[&&NHX:TOL=52826],mastigophorophyllidae[&&NHX:TOL=52827],megalotylidae[&&NHX:TOL=52828],metopidiotrichidae[&&NHX:TOL=52829],neoatractosomatidae[&&NHX:TOL=52830],niponiosomatidae[&&NHX:TOL=52831],opisthocheiridae[&&NHX:TOL=52832],origmatogonidae[&&NHX:TOL=52833],peterjohionsiidae[&&NHX:TOL=52834],pygmaeosomatidae[&&NHX:TOL=52835],rhiscosomididae[&&NHX:TOL=52836],speophilosomatidae[&&NHX:TOL=52837],striariidae[&&NHX:TOL=52838],tingupidae[&&NHX:TOL=52839],trachygonidae[&&NHX:TOL=52840],trichopetalidae[&&NHX:TOL=52841],urochordeumatidae[&&NHX:TOL=52842],vandeleumatidae[&&NHX:TOL=52843],verhoeffiidae[&&NHX:TOL=52844])chordeumatida[&&NHX:TOL=8155])nematophora[&&NHX:TOL=8152],((aprosphylosomatidae[&&NHX:TOL=52845],blaniulidae[&&NHX:TOL=52846],chelojulidae[&&NHX:TOL=52847],galliobatidae[&&NHX:TOL=52848],julidae[&&NHX:TOL=52849],mongoliulidae[&&NHX:TOL=52850],nemasomatidae[&&NHX:TOL=52851],nematozoniidae[&&NHX:TOL=52852],okeanobatidae[&&NHX:TOL=52853],paeromopodidae[&&NHX:TOL=52854],parajulidae[&&NHX:TOL=52855],pseudonemasomatidae[&&NHX:TOL=52856],rhopaloiulidae[&&NHX:TOL=52857],telsonemasomatidae[&&NHX:TOL=52858],trichoblaniulidae[&&NHX:TOL=52859],trichonemasomatidae[&&NHX:TOL=52860],zosteractinidae[&&NHX:TOL=52861])julida[&&NHX:TOL=8157],(allopocockiidae[&&NHX:TOL=52862],atopetholidae[&&NHX:TOL=52863],floridobolidae[&&NHX:TOL=52864],messicobolidae[&&NHX:TOL=52865],pachybolidae[&&NHX:TOL=52866],pseudospirobolellidae[&&NHX:TOL=52867],rhinocricidae[&&NHX:TOL=52868],spirobolellidae[&&NHX:TOL=52869],spirobolidae[&&NHX:TOL=52870],trigoniulidae[&&NHX:TOL=52871],typhlobolellidae[&&NHX:TOL=52872])spirobolida[&&NHX:TOL=8158],(adiaphorostreptidae[&&NHX:TOL=52873],cambalidae[&&NHX:TOL=52874],cambalospidae[&&NHX:TOL=52875],choctellidae[&&NHX:TOL=52876],glyphiulidae[&&NHX:TOL=52877],harpagophoridae[&&NHX:TOL=52878],iulomorphidae[&&NHX:TOL=52879],odontopygidae[&&NHX:TOL=52880],pericambalidae[&&NHX:TOL=52881],physiostreptidae[&&NHX:TOL=52882],pseudonannolenidae[&&NHX:TOL=52883],spirostreptidae[&&NHX:TOL=52884])spirostreptida[&&NHX:TOL=8159])juliformia[&&NHX:TOL=8156],(ammodesmidae[&&NHX:TOL=52885],aphelidesmidae[&&NHX:TOL=52886],campodesmidae[&&NHX:TOL=52887],chelodesmidae[&&NHX:TOL=52888],cryptodesmidae[&&NHX:TOL=52889],cyrtodesmidae[&&NHX:TOL=52890],dalodesmidae[&&NHX:TOL=52891],doratodesmidae[&&NHX:TOL=52892],dorsoporidae[&&NHX:TOL=52893],eurymerodesmidae[&&NHX:TOL=52894],euryuridae[&&NHX:TOL=52895],fuhrmannodesmidae[&&NHX:TOL=52896],gomphodesmidae[&&NHX:TOL=52897],haplodesmidae[&&NHX:TOL=52898],holistophallidae[&&NHX:TOL=52899],macrosternodesmidae[&&NHX:TOL=52900],nearctodesmidae[&&NHX:TOL=52901],oniscodesmidae[&&NHX:TOL=52902],opisotretidae[&&NHX:TOL=52903],oxydesmidae[&&NHX:TOL=52904],paradoxosomatidae[&&NHX:TOL=52905],platyrhacidae[&&NHX:TOL=52906],polydesmidae[&&NHX:TOL=52907],pygrodesmidae[&&NHX:TOL=52908],rhachodesmidae[&&NHX:TOL=52909],sphaeriodesmidae[&&NHX:TOL=52910],trichopolydesmidae[&&NHX:TOL=52911],tridontomidae[&&NHX:TOL=52912],vaalogonopodidae[&&NHX:TOL=52913],xystodesmidae[&&NHX:TOL=52914])polydesmida[&&NHX:TOL=8160])eugnatha[&&NHX:TOL=8151])helminthomorpha[&&NHX:TOL=8145])chilognatha[&&NHX:TOL=8140])diplopoda[&&NHX:TOL=2532],(((scutigerina[&&NHX:TOL=23173],madagassophora[&&NHX:TOL=23174])scutigerininae[&&NHX:TOL=23145],(scutigerinae[&&NHX:TOL=23147],thereuoneminae[&&NHX:TOL=23148])[&&NHX:TOL=23146])scutigeromorpha[&&NHX:TOL=6228],((lithobiidae[&&NHX:TOL=23149],(anopsobiinae[&&NHX:TOL=23151],henicopinae[&&NHX:TOL=23152])[&&NHX:TOL=23150])lithobiomorpha[&&NHX:TOL=6230],(devonobius delta[&&NHX:EXT=Y:TOL=23153],craterostigmus tasmanianus[&&NHX:TOL=6232],((mecistocephalidae[&&NHX:TOL=23154],(himantariidae[&&NHX:TOL=23155],(schendylidae[&&NHX:TOL=23156],ballophilidae[&&NHX:TOL=23167])[&&NHX:TOL=23166],(dignathodontidae[&&NHX:TOL=23170],linotaeniidae[&&NHX:TOL=23171])[&&NHX:TOL=23168],geophilidae[&&NHX:TOL=23169],aphilodontidae[&&NHX:TOL=23172])adesmata[&&NHX:TOL=23165])geophilomorpha[&&NHX:TOL=6235],((scolopendrinae[&&NHX:TOL=23159],otostigminae[&&NHX:TOL=23158])[&&NHX:TOL=23160],(scolopocryptopinae[&&NHX:TOL=23161],(plutoniuminae[&&NHX:TOL=23163],cryptopinae[&&NHX:TOL=23164])[&&NHX:TOL=23162])[&&NHX:TOL=23157])scolopendromorpha[&&NHX:TOL=6234])epimorpha[&&NHX:TOL=23175])phylactometria[&&NHX:TOL=6231])pleurostigmophora[&&NHX:TOL=6229])chilopoda[&&NHX:TOL=2533],((scutigerella[&&NHX:TOL=14710],neoscutigerella[&&NHX:TOL=14711],scopoliella[&&NHX:TOL=14712],scolopendrelloides[&&NHX:TOL=14713],hanseniella[&&NHX:TOL=14714],millotellina[&&NHX:TOL=14715],tasmaniella[&&NHX:TOL=14716])scutigerellidae[&&NHX:TOL=14709],(scolopendrella[&&NHX:TOL=14718],scolopendrellopsis[&&NHX:TOL=14719],symphylella[&&NHX:TOL=14720],symphylellina[&&NHX:TOL=14721],geophilella[&&NHX:TOL=14722],remysymphyla[&&NHX:TOL=14723],symphylellopsis[&&NHX:TOL=14724],ribautiella[&&NHX:TOL=14725])scolopendrellidae[&&NHX:TOL=14717])symphyla[&&NHX:TOL=2534])myriapoda[&&NHX:TOL=2530],((((palpigradi[&&NHX:TOL=2544],((mesothelae[&&NHX:TOL=93104],(((((cyrtaucheniidae[&&NHX:TOL=2775],(bothriocyrtum[&&NHX:TOL=129912],conothele[&&NHX:TOL=129913],cteniza[&&NHX:TOL=129914],cyclocosmia[&&NHX:TOL=129915],cyrtocarenum[&&NHX:TOL=129916],hebestatis[&&NHX:TOL=129917],latouchia[&&NHX:TOL=129918],stasimopus[&&NHX:TOL=129919],ummidia[&&NHX:TOL=129920])ctenizidae[&&NHX:TOL=2779],((blakistonia[&&NHX:TOL=129934],cataxia[&&NHX:TOL=129936],arbanitis[&&NHX:TOL=129933],euoplos[&&NHX:TOL=129939],idiosoma[&&NHX:TOL=129946],aganippe[&&NHX:TOL=129931],eucyrtops[&&NHX:TOL=129938],anidiops[&&NHX:TOL=129932],misgolas[&&NHX:TOL=129947],cantuaria[&&NHX:TOL=129935])arbanitinae[&&NHX:TOL=129993],((heligmomerus[&&NHX:TOL=129943],gorgyrella[&&NHX:TOL=129942])[&&NHX:TOL=129995],(ctenolophus[&&NHX:TOL=129937],galeosoma[&&NHX:TOL=129940],idiops[&&NHX:TOL=129945])[&&NHX:TOL=129996],titanidiops[&&NHX:TOL=129952],segregara[&&NHX:TOL=129951])idiopinae[&&NHX:TOL=129994],((hiboka[&&NHX:TOL=129944],scalidognathus[&&NHX:TOL=129950],genysa[&&NHX:TOL=129941],prothemenops[&&NHX:TOL=129949])[&&NHX:TOL=129998],neocteniza[&&NHX:TOL=129948])genysinae[&&NHX:TOL=129997])idiopidae[&&NHX:TOL=2777],(actinopus[&&NHX:TOL=129953],missulena[&&NHX:TOL=129954],plesiolena[&&NHX:TOL=129955])actinopodidae[&&NHX:TOL=2781],(heteromigas[&&NHX:TOL=129923],((thyropoeus[&&NHX:TOL=129930],(micromesomma cowani[&&NHX:TOL=129925],paramigas[&&NHX:TOL=129928])[&&NHX:TOL=129964])[&&NHX:TOL=129963],((moggridgea[&&NHX:TOL=129927],(migas[&&NHX:TOL=129926],poecilomigas[&&NHX:TOL=129929])[&&NHX:TOL=129967])[&&NHX:TOL=129966],(mallecomigas schlingeri[&&NHX:TOL=129924],(calathotarsus[&&NHX:TOL=129921],goloboffia vellardi[&&NHX:TOL=129922])[&&NHX:TOL=129969])[&&NHX:TOL=129968])[&&NHX:TOL=129965])[&&NHX:TOL=129962])migidae[&&NHX:TOL=2782])[&&NHX:TOL=2774],((envia[&&NHX:TOL=130353],micromygale[&&NHX:TOL=130354],microstigmata[&&NHX:TOL=130355],ministigmata[&&NHX:TOL=130356],pseudonemesia[&&NHX:TOL=130357],spelocteniza[&&NHX:TOL=130358],xenonemesia[&&NHX:TOL=130359])microstigmatidae[&&NHX:TOL=2757],nemesiidae[&&NHX:TOL=2764],(barychelidae[&&NHX:TOL=2766],theraphosidae[&&NHX:TOL=2769])[&&NHX:TOL=93107])[&&NHX:TOL=2755])bipectina[&&NHX:TOL=129908],(anisaspis[&&NHX:TOL=129989],anisaspoides[&&NHX:TOL=129990],melloina[&&NHX:TOL=129991],paratropis[&&NHX:TOL=129992])paratropidae[&&NHX:TOL=2768],(atrax[&&NHX:TOL=129970],bymainiella[&&NHX:TOL=129971],hadronyche[&&NHX:TOL=129972],hexathele[&&NHX:TOL=129973],macrothele[&&NHX:TOL=129974],paraembolides[&&NHX:TOL=129975],plesiothele[&&NHX:TOL=129976],porrhothele[&&NHX:TOL=129977],scotinoecus[&&NHX:TOL=129978],teranodes[&&NHX:TOL=129979])hexathelidae[&&NHX:TOL=2760],(allothele [&&NHX:TOL=130329],andethele [&&NHX:TOL=130330],australothele [&&NHX:TOL=130331],caledothele [&&NHX:TOL=130332],carrai [&&NHX:TOL=130333],cethegus [&&NHX:TOL=130334],chilehexops [&&NHX:TOL=130335],diplura [&&NHX:TOL=130336],euagrus [&&NHX:TOL=130337],harmonicon [&&NHX:TOL=130338],indothele [&&NHX:TOL=130339],ischnothele [&&NHX:TOL=130340],lathrothele [&&NHX:TOL=130341],leptothele [&&NHX:TOL=130342],linothele [&&NHX:TOL=130343],masteria [&&NHX:TOL=130344],microhexura [&&NHX:TOL=130345],namirea [&&NHX:TOL=130346],phyxioschema [&&NHX:TOL=130347],stenygrocercus [&&NHX:TOL=130348],striamea [&&NHX:TOL=130349],thelechoris [&&NHX:TOL=130350],trechona [&&NHX:TOL=130351],troglodiplura [&&NHX:TOL=130352])dipluridae[&&NHX:TOL=2762])[&&NHX:TOL=129907],(((((((aliatypus californicus[&&NHX:TOL=130199],aliatypus gnomus[&&NHX:TOL=130201])[&&NHX:TOL=130212],(aliatypus aquilonius[&&NHX:TOL=130198],(aliatypus janus[&&NHX:TOL=130204],aliatypus isolatus[&&NHX:TOL=130203])[&&NHX:TOL=130214])[&&NHX:TOL=130213])aliatypus californicus group[&&NHX:TOL=130211],aliatypus thompsoni[&&NHX:TOL=130206])[&&NHX:TOL=130210],((aliatypus trophonius[&&NHX:TOL=130208],aliatypus erebus[&&NHX:TOL=130200])[&&NHX:TOL=130216],(aliatypus plutonis[&&NHX:TOL=130205],aliatypus torridus[&&NHX:TOL=130207])[&&NHX:TOL=130217])aliatypus erebus group[&&NHX:TOL=130215])[&&NHX:TOL=130209],aliatypus gulosus[&&NHX:TOL=130202])aliatypus[&&NHX:TOL=129987],antrodiaetus[&&NHX:TOL=129988])antrodiaetidae[&&NHX:TOL=2772],(atypus[&&NHX:TOL=129984],calommata[&&NHX:TOL=129985],sphodros[&&NHX:TOL=129986])atypidae[&&NHX:TOL=2773],(hexura[&&NHX:TOL=129980],hexurella[&&NHX:TOL=129981],mecicobothrium[&&NHX:TOL=129982],megahexura[&&NHX:TOL=129983])mecicobothriidae[&&NHX:TOL=2758])atypoidea[&&NHX:TOL=129909])mygalomorphae[&&NHX:TOL=2641],(hypochilidae[&&NHX:TOL=2644],((gradungulidae[&&NHX:TOL=2647],austrochilidae[&&NHX:TOL=2648])[&&NHX:TOL=2646],((((caponiidae[&&NHX:TOL=2708],(tetrablemmidae[&&NHX:TOL=2710],((oonopidae[&&NHX:TOL=2713],orsolobidae[&&NHX:TOL=2714])[&&NHX:TOL=2712],dysderidae[&&NHX:TOL=2715],segestriidae[&&NHX:TOL=2716])dysderoidea[&&NHX:TOL=2711])[&&NHX:TOL=2709])[&&NHX:TOL=2707],((((((psilochorus[&&NHX:TOL=135150],(anopsicus[&&NHX:TOL=135784],modisimus[&&NHX:TOL=135785])[&&NHX:TOL=135783])[&&NHX:TOL=135782],(ciboneia[&&NHX:TOL=135152],mesabolivar[&&NHX:TOL=135153])[&&NHX:TOL=135151],coryssocnemis[&&NHX:TOL=135154],(carapoia[&&NHX:TOL=135155],chibchea[&&NHX:TOL=135787])[&&NHX:TOL=135786],priscula[&&NHX:TOL=135156],(systenita[&&NHX:TOL=135158],mecolaesthus[&&NHX:TOL=135159],stenosfemuraria[&&NHX:TOL=135160])[&&NHX:TOL=135157],otavaloa[&&NHX:TOL=135788],ixchela[&&NHX:TOL=135789],aymaria[&&NHX:TOL=135790],(canaima[&&NHX:TOL=135792],(blancoa[&&NHX:TOL=135794],tupigea[&&NHX:TOL=135795])[&&NHX:TOL=135793])[&&NHX:TOL=135791],(waunana[&&NHX:TOL=135797],pisaboa[&&NHX:TOL=135798])[&&NHX:TOL=135796],(pomboa[&&NHX:TOL=135800],litoporus[&&NHX:TOL=135801])[&&NHX:TOL=135799],bryantina[&&NHX:TOL=135803],tainonia[&&NHX:TOL=135804],teuia[&&NHX:TOL=135805])new world clade[&&NHX:TOL=135149],(trichocyclus[&&NHX:TOL=135162],artema[&&NHX:TOL=135163],physocyclus[&&NHX:TOL=135164])[&&NHX:TOL=135161],((smeringopus[&&NHX:TOL=135167],(holocnemus[&&NHX:TOL=135169],crossopriza[&&NHX:TOL=135170])[&&NHX:TOL=135168],ceratopholcus[&&NHX:TOL=135816],hoplopholcus[&&NHX:TOL=135817])holocnemines[&&NHX:TOL=135166],(quamtana[&&NHX:TOL=135173],((((pholcus[&&NHX:TOL=135175],leptopholcus[&&NHX:TOL=135826])[&&NHX:TOL=135832],micropholcus[&&NHX:TOL=135176],ossinissa[&&NHX:TOL=135818])[&&NHX:TOL=135174],micromerys[&&NHX:TOL=135820])[&&NHX:TOL=135831],panjange[&&NHX:TOL=135821])[&&NHX:TOL=135830],(zatavua[&&NHX:TOL=135180],nyikoa[&&NHX:TOL=135834])[&&NHX:TOL=135833],spermophora[&&NHX:TOL=135178],metagonia[&&NHX:TOL=135177],belisana[&&NHX:TOL=135181],paramicromerys[&&NHX:TOL=135182],spermophorides[&&NHX:TOL=135183],calapnita[&&NHX:TOL=135819],smeringopina[&&NHX:TOL=135822],uthina[&&NHX:TOL=135823],wanniyala[&&NHX:TOL=135827],savarna[&&NHX:TOL=135828],khorata[&&NHX:TOL=135829],aetana[&&NHX:TOL=135835],anansus[&&NHX:TOL=135836],buitinga[&&NHX:TOL=135837])pholcines[&&NHX:TOL=135172])[&&NHX:TOL=135165],holocneminus[&&NHX:TOL=135824],carupania[&&NHX:TOL=135838],cenemus[&&NHX:TOL=135839],mariguitaia[&&NHX:TOL=135840],pehrforsskalia[&&NHX:TOL=135841],pholciella[&&NHX:TOL=135842],pholcoides[&&NHX:TOL=135843],queliceria[&&NHX:TOL=135844],sanluisi[&&NHX:TOL=135845],stygopholcus[&&NHX:TOL=135846],tibetia[&&NHX:TOL=135847],tibiosa[&&NHX:TOL=135848],venezuela[&&NHX:TOL=135849],wugigarra[&&NHX:TOL=135850])[&&NHX:TOL=135148],(ibotyporanga[&&NHX:TOL=135852],(papiamenta[&&NHX:TOL=135853],pholcophora[&&NHX:TOL=135854],galapa[&&NHX:TOL=135814],(aucana[&&NHX:TOL=135811],chisosa[&&NHX:TOL=135813],nita[&&NHX:TOL=135851])[&&NHX:TOL=135856],(ninetis[&&NHX:TOL=135809],tolteca[&&NHX:TOL=135810])[&&NHX:TOL=135857],kambiwa[&&NHX:TOL=135806],mystes[&&NHX:TOL=135825],guaranita[&&NHX:TOL=135815],enetea[&&NHX:TOL=135812],gertschiola[&&NHX:TOL=135808],nerudia[&&NHX:TOL=135807])[&&NHX:TOL=135855])ninetines[&&NHX:TOL=135179])pholcidae[&&NHX:TOL=2719],(diguetidae[&&NHX:TOL=2721],plectruridae[&&NHX:TOL=2722])[&&NHX:TOL=2720])[&&NHX:TOL=2718],((ochyroceratidae[&&NHX:TOL=2725],((appaleptoneta[&&NHX:TOL=108336],archoleptoneta[&&NHX:TOL=108337],barusia[&&NHX:TOL=108338],calileptoneta[&&NHX:TOL=108339],cataleptoneta[&&NHX:TOL=108340],falcileptoneta[&&NHX:TOL=108341],leptoneta[&&NHX:TOL=108342],leptonetela[&&NHX:TOL=108343],masirana[&&NHX:TOL=108344],neoleptoneta[&&NHX:TOL=108345],paraleptoneta[&&NHX:TOL=108346],protoleptoneta[&&NHX:TOL=108347],rhyssoleptoneta[&&NHX:TOL=108348],sulcia[&&NHX:TOL=108349],teloleptoneta[&&NHX:TOL=108350])leptonetidae[&&NHX:TOL=2727],telemidae[&&NHX:TOL=2728])[&&NHX:TOL=2726])[&&NHX:TOL=2724],(((((((loxosceles apachea[&&NHX:TOL=135896],loxosceles alamosa[&&NHX:TOL=135897],loxosceles aranea[&&NHX:TOL=135898],loxosceles arizonica[&&NHX:TOL=135899],loxosceles aurea[&&NHX:TOL=135900],loxosceles baja[&&NHX:TOL=135901],loxosceles barbara[&&NHX:TOL=135902],loxosceles belli[&&NHX:TOL=135903],loxosceles blanda[&&NHX:TOL=135904],loxosceles boneti[&&NHX:TOL=135905],loxosceles candela[&&NHX:TOL=135906],loxosceles caribbaea[&&NHX:TOL=135907],loxosceles carmena[&&NHX:TOL=135908],loxosceles chinateca[&&NHX:TOL=135909],loxosceles colima[&&NHX:TOL=135910],loxosceles coyote[&&NHX:TOL=135911],loxosceles cubana[&&NHX:TOL=135912],loxosceles deserta[&&NHX:TOL=135913],loxosceles devia[&&NHX:TOL=135914],loxosceles francisca[&&NHX:TOL=135915],loxosceles guatemala[&&NHX:TOL=135916],loxosceles huasteca[&&NHX:TOL=135917],loxosceles insula[&&NHX:TOL=135918],loxosceles jaca[&&NHX:TOL=135919],loxosceles jamaica[&&NHX:TOL=135920],loxosceles jarmila[&&NHX:TOL=135921],loxosceles kaiba[&&NHX:TOL=135922],loxosceles luteola[&&NHX:TOL=135923],loxosceles martha[&&NHX:TOL=135924],loxosceles manuela[&&NHX:TOL=135925],loxosceles misteca[&&NHX:TOL=135926],loxosceles mulege[&&NHX:TOL=135927],loxosceles nahuana[&&NHX:TOL=135928],loxosceles palma[&&NHX:TOL=135929],loxosceles reclusa[&&NHX:TOL=135930],loxosceles rica[&&NHX:TOL=135931],loxosceles rothi[&&NHX:TOL=135932],loxosceles russelli[&&NHX:TOL=135933],loxosceles sabina[&&NHX:TOL=135934],loxosceles seri[&&NHX:TOL=135935],loxosceles sonora[&&NHX:TOL=135936],loxosceles taino[&&NHX:TOL=135937],loxosceles tehuana[&&NHX:TOL=135938],loxosceles tenango[&&NHX:TOL=135939],loxosceles teresa[&&NHX:TOL=135940],loxosceles tlacolula[&&NHX:TOL=135941],loxosceles valdosa[&&NHX:TOL=135942],loxosceles virgo[&&NHX:TOL=135943],loxosceles yucatana[&&NHX:TOL=135944],loxosceles zapoteca[&&NHX:TOL=135945])loxosceles reclusa species group[&&NHX:TOL=129551],(loxosceles accepta[&&NHX:TOL=135946],loxosceles alicea[&&NHX:TOL=135947],loxosceles bettyae[&&NHX:TOL=135948],loxosceles blancasi[&&NHX:TOL=135949],loxosceles conococha[&&NHX:TOL=135950],loxosceles coquimbo[&&NHX:TOL=135951],loxosceles frizzelli[&&NHX:TOL=135952],loxosceles gloria[&&NHX:TOL=135953],loxosceles julia[&&NHX:TOL=135954],loxosceles harrietae[&&NHX:TOL=135955],loxosceles herreri[&&NHX:TOL=135956],loxosceles laeta[&&NHX:TOL=135957],loxosceles lawrencei[&&NHX:TOL=135958],loxosceles lutea[&&NHX:TOL=135959],loxosceles olmea[&&NHX:TOL=135960],loxosceles panama[&&NHX:TOL=135961],loxosceles piura[&&NHX:TOL=135962],loxosceles pucara[&&NHX:TOL=135963],loxosceles rosana[&&NHX:TOL=135964],loxosceles rufipes[&&NHX:TOL=135965],loxosceles surca[&&NHX:TOL=135966],loxosceles weyrauchi[&&NHX:TOL=135967])loxosceles laeta species group[&&NHX:TOL=129552])[&&NHX:TOL=129550],((((loxosceles rufescens[&&NHX:TOL=135968],loxosceles lacta[&&NHX:TOL=135969])loxosceles rufescens species group[&&NHX:TOL=129556],loxosceles amazonica[&&NHX:TOL=129557])[&&NHX:TOL=129555],(loxosceles gaucho[&&NHX:TOL=135970],loxosceles variegata[&&NHX:TOL=135971],loxosceles similis[&&NHX:TOL=135972],loxosceles adelaida[&&NHX:TOL=135973])loxosceles gaucho species group[&&NHX:TOL=129558])[&&NHX:TOL=129554],(loxosceles spadecia[&&NHX:TOL=135974],loxosceles hirsuta[&&NHX:TOL=135975],loxosceles intermedia[&&NHX:TOL=135976])loxosceles spadecia species group[&&NHX:TOL=129559])[&&NHX:TOL=129553])[&&NHX:TOL=129549],(loxosceles vonwredei[&&NHX:TOL=135977],loxosceles sp. nov.[&&NHX:TOL=135978])loxosceles vonwredei species group[&&NHX:TOL=129560])[&&NHX:TOL=129568],(loxosceles spinulosa[&&NHX:TOL=135979],loxosceles parrami[&&NHX:TOL=135980],loxosceles speluncarum[&&NHX:TOL=135981])loxosceles spinulosa species group[&&NHX:TOL=129563],loxosceles anomala[&&NHX:TOL=136008],loxosceles aphrasta[&&NHX:TOL=136009],loxosceles fontainei[&&NHX:TOL=136010],loxosceles foutadjalloni[&&NHX:TOL=136011],loxosceles immodesta[&&NHX:TOL=136012],loxosceles lacroixi[&&NHX:TOL=136013],loxosceles meruensis[&&NHX:TOL=136014],loxosceles neuvillei[&&NHX:TOL=136015],loxosceles pallidecolorata[&&NHX:TOL=136016],loxosceles puortoi[&&NHX:TOL=136017],loxosceles smithi[&&NHX:TOL=136018])loxosceles[&&NHX:TOL=129537],((sicarius albospinosus[&&NHX:TOL=135982],sicarius damarensis[&&NHX:TOL=135983],sicarius dolichocephalus[&&NHX:TOL=135984],sicarius hahni[&&NHX:TOL=135985],sicarius testaceus[&&NHX:TOL=135986],sicarius spatulatus[&&NHX:TOL=135987])african sicarius[&&NHX:TOL=129567],(sicarius crustosus[&&NHX:TOL=135988],sicarius deformis[&&NHX:TOL=135989],sicarius fumosus[&&NHX:TOL=135990],sicarius gracilis[&&NHX:TOL=135991],sicarius lanuginosus[&&NHX:TOL=135992],sicarius minoratus[&&NHX:TOL=135993],sicarius nicoleti[&&NHX:TOL=135994],sicarius patagonicus[&&NHX:TOL=135995],sicarius peruensis[&&NHX:TOL=135996],sicarius rubripes[&&NHX:TOL=135997],sicarius rugosus[&&NHX:TOL=135998],sicarius rupestris[&&NHX:TOL=135999],sicarius terrosus[&&NHX:TOL=136000],sicarius tropicus[&&NHX:TOL=136002],sicarius utriformis[&&NHX:TOL=136003])central and south american sicarius[&&NHX:TOL=135893])sicarius[&&NHX:TOL=129538])sicariidae[&&NHX:TOL=2731],(drymusidae[&&NHX:TOL=2735],(scytodidae[&&NHX:TOL=2734],periegopidae[&&NHX:TOL=2732])[&&NHX:TOL=93110])[&&NHX:TOL=2733])[&&NHX:TOL=2729])[&&NHX:TOL=2723])[&&NHX:TOL=2717])[&&NHX:TOL=2706],filistatidae[&&NHX:TOL=2705])haplogynae[&&NHX:TOL=2650],(((oecobiidae[&&NHX:TOL=2701],hersiliidae[&&NHX:TOL=2702])[&&NHX:TOL=2700],eresidae[&&NHX:TOL=2703])eresoidea[&&NHX:TOL=2684],(nicodamidae[&&NHX:TOL=2812],cryptothelidae[&&NHX:TOL=2813],cycloctenidae[&&NHX:TOL=2814],zodariidae[&&NHX:TOL=2815],miturgidae[&&NHX:TOL=2816])other entelegynes[&&NHX:TOL=2686],((mimetidae[&&NHX:TOL=2819],malkaridae[&&NHX:TOL=2820])[&&NHX:TOL=2818],((huttoniidae[&&NHX:TOL=2823],palpimanidae[&&NHX:TOL=2824])[&&NHX:TOL=2822],(micropholocommatidae[&&NHX:TOL=2826],(holarchaeidae[&&NHX:TOL=2828],(pararchaeidae[&&NHX:TOL=2830],(archaeidae[&&NHX:TOL=2832],mecysmaucheniidae[&&NHX:TOL=2833])[&&NHX:TOL=2831])[&&NHX:TOL=2829])[&&NHX:TOL=2827])[&&NHX:TOL=2825])[&&NHX:TOL=2821])palpimanoidea[&&NHX:TOL=2688],(((deinopidae[&&NHX:TOL=2785],uloboridae[&&NHX:TOL=2786])deinopoidea[&&NHX:TOL=2784],(araneidae[&&NHX:TOL=2788],((nephilidae[&&NHX:TOL=93920],((((((cyrtognatha paradoxa[&&NHX:TOL=134584],cyrtognatha lepida[&&NHX:TOL=134619],cyrtognatha pathetica[&&NHX:TOL=134620],((cyrtognatha quichua[&&NHX:TOL=134587],(cyrtognatha catia[&&NHX:TOL=134589],cyrtognatha pachygnathoides[&&NHX:TOL=134590])[&&NHX:TOL=134588])cyrtognatha quichua clade[&&NHX:TOL=134586],(cyrtognatha leviorum[&&NHX:TOL=134592],(cyrtognatha waorani[&&NHX:TOL=134594],((cyrtognatha morona[&&NHX:TOL=134597],(cyrtognatha atopica[&&NHX:TOL=134599],cyrtognatha eberhardi[&&NHX:TOL=134600])[&&NHX:TOL=134598])cyrtognatha morona clade[&&NHX:TOL=134596],((cyrtognatha orphana[&&NHX:TOL=134603],(cyrtognatha nigrovittata[&&NHX:TOL=134605],(cyrtognatha insolita[&&NHX:TOL=134607],cyrtognatha petila[&&NHX:TOL=134608])[&&NHX:TOL=134606])[&&NHX:TOL=134604])cyrtognatha orphana clade[&&NHX:TOL=134602],(cyrtognatha bella[&&NHX:TOL=134610],(((cyrtognatha rucilla[&&NHX:TOL=134614],cyrtognatha serrata[&&NHX:TOL=134615])[&&NHX:TOL=134613],cyrtognatha espanola[&&NHX:TOL=134616],cyrtognatha simoni[&&NHX:TOL=134617])[&&NHX:TOL=134612],cyrtognatha bryantae[&&NHX:TOL=134618])[&&NHX:TOL=134611])cyrtognatha bella clade[&&NHX:TOL=134609])[&&NHX:TOL=134601])[&&NHX:TOL=134595])[&&NHX:TOL=134593])[&&NHX:TOL=134591])[&&NHX:TOL=134585])cyrtognatha[&&NHX:TOL=134582],(tetragnatha[&&NHX:TOL=134622],doryonychus raptor [&&NHX:TOL=135743],(glenognatha[&&NHX:TOL=134624],pachygnatha[&&NHX:TOL=134625])[&&NHX:TOL=134623],antillognatha[&&NHX:TOL=135742],dyschiriognatha[&&NHX:TOL=135744],hispanognatha[&&NHX:TOL=135745])[&&NHX:TOL=134621])tetragnathinae[&&NHX:TOL=134581],allende[&&NHX:TOL=134655])[&&NHX:TOL=134669],mollemeta[&&NHX:TOL=134654])[&&NHX:TOL=134668],((meta[&&NHX:TOL=134628],(metellina[&&NHX:TOL=134630],(dolichognatha[&&NHX:TOL=134632],(chrysometa[&&NHX:TOL=134634],diphya[&&NHX:TOL=134635])[&&NHX:TOL=134633])[&&NHX:TOL=134631])[&&NHX:TOL=134629])metainae[&&NHX:TOL=134627],((nanometa[&&NHX:TOL=134638],orsinome sarasini[&&NHX:TOL=134639])nanometa clade[&&NHX:TOL=134637],(metleucauge[&&NHX:TOL=134641],((metabus[&&NHX:TOL=134647],(tylorida[&&NHX:TOL=134646],orsinome[&&NHX:TOL=134645])[&&NHX:TOL=136005])[&&NHX:TOL=134643],(mesida[&&NHX:TOL=134649],(opadometa[&&NHX:TOL=134651],leucauge[&&NHX:TOL=134652])[&&NHX:TOL=134650])[&&NHX:TOL=136006],alcimosphenus[&&NHX:TOL=135760],atelidea[&&NHX:TOL=135761],mecynometa[&&NHX:TOL=135762],okileucauge[&&NHX:TOL=135763],pickardinella[&&NHX:TOL=135764],opas[&&NHX:TOL=135765])[&&NHX:TOL=134642])leucaugines[&&NHX:TOL=134640])[&&NHX:TOL=134636])[&&NHX:TOL=134626],dianleucauge[&&NHX:TOL=135766],eryciniolia[&&NHX:TOL=135767],guizygiella[&&NHX:TOL=135768],homalometa[&&NHX:TOL=135769],menosira[&&NHX:TOL=135770],mitoscelis[&&NHX:TOL=135771],nanningia[&&NHX:TOL=135772],neoprolochus[&&NHX:TOL=135773],parameta[&&NHX:TOL=135774],parazilia[&&NHX:TOL=135775],pholcipes[&&NHX:TOL=135776],sancus[&&NHX:TOL=135777],schenkeliella[&&NHX:TOL=135778],timonoe[&&NHX:TOL=135779],wolongia[&&NHX:TOL=135780],zygiometella[&&NHX:TOL=135781])[&&NHX:TOL=134580],azilia[&&NHX:TOL=134653])tetragnathidae[&&NHX:TOL=2799])[&&NHX:TOL=134292],(((stemonyphantinae[&&NHX:TOL=25489],(mynogleninae[&&NHX:TOL=25490],(erigoninae[&&NHX:TOL=25491],(linyphiini[&&NHX:TOL=25493],micronetini[&&NHX:TOL=25492])linyphiinae[&&NHX:TOL=25494])[&&NHX:TOL=25495])[&&NHX:TOL=25496])linyphiidae[&&NHX:TOL=25497],pimoidae[&&NHX:TOL=25488])linyphioids[&&NHX:TOL=25487],((nesticidae[&&NHX:TOL=2796],((((latrodectus geometricus[&&NHX:TOL=93770],latrodectus rhodesiensis[&&NHX:TOL=93771])latrodectus geometricus clade[&&NHX:TOL=93769],((((((((latrodectus diaguita[&&NHX:TOL=93780],latrodectus corallinus[&&NHX:TOL=93781])[&&NHX:TOL=93779],latrodectus antheratus[&&NHX:TOL=93782])[&&NHX:TOL=93778],latrodectus mirabilis[&&NHX:TOL=93783],latrodectus variegatus[&&NHX:TOL=93784])[&&NHX:TOL=93777],((latrodectus hesperus[&&NHX:TOL=93787],latrodectus mactans[&&NHX:TOL=93788])[&&NHX:TOL=93786],(latrodectus variolus[&&NHX:TOL=93790],latrodectus bishopi[&&NHX:TOL=93791])[&&NHX:TOL=93789])[&&NHX:TOL=93785])[&&NHX:TOL=93776],(latrodectus revivensis[&&NHX:TOL=93793],latrodectus pallidus[&&NHX:TOL=93794])[&&NHX:TOL=93792])[&&NHX:TOL=93775],latrodectus menavodi[&&NHX:TOL=93795])[&&NHX:TOL=93774],(latrodectus hasselti[&&NHX:TOL=93797],latrodectus katipo[&&NHX:TOL=93798])[&&NHX:TOL=93796])[&&NHX:TOL=93773],latrodectus renivulvatus[&&NHX:TOL=93799],latrodectus tredecimguttatus[&&NHX:TOL=93800])latrodectus mactans clade[&&NHX:TOL=93772],latrodectus apicalis[&&NHX:TOL=93801],latrodectus atritus[&&NHX:TOL=93802],latrodectus cinctus[&&NHX:TOL=93803],latrodectus curacaviensis[&&NHX:TOL=93804],latrodectus dahli[&&NHX:TOL=93805],latrodectus elegans[&&NHX:TOL=93806],latrodectus erythromelas[&&NHX:TOL=93807],latrodectus hystrix[&&NHX:TOL=93808],latrodectus indistinctus[&&NHX:TOL=93809],latrodectus karrooensis[&&NHX:TOL=93810],latrodectus lilianae[&&NHX:TOL=93811],latrodectus obscurior[&&NHX:TOL=93812],latrodectus quartus[&&NHX:TOL=93813])latrodectus[&&NHX:TOL=93274],(steatoda[&&NHX:TOL=93276],crustulina[&&NHX:TOL=93277])[&&NHX:TOL=93275])latrodectinae[&&NHX:TOL=93273],(pholcommatinae[&&NHX:TOL=93279],(argyrodinae[&&NHX:TOL=93281],((hadrotarsinae[&&NHX:TOL=93283],spintharinae[&&NHX:TOL=93285])[&&NHX:TOL=93869],(anelosimus[&&NHX:TOL=93287],theridiinae[&&NHX:TOL=93288])[&&NHX:TOL=93286])[&&NHX:TOL=93282])[&&NHX:TOL=93280])[&&NHX:TOL=93278])theridiidae[&&NHX:TOL=2797])theridioids[&&NHX:TOL=2795],(synotaxidae[&&NHX:TOL=93137],(((africepheia madagascariensis[&&NHX:TOL=137001],cepheia longiseta[&&NHX:TOL=137002],(synaphris agaetensis[&&NHX:TOL=137359],synaphris calerensis[&&NHX:TOL=137360],synaphris dalmatensis[&&NHX:TOL=137361],synaphris franzi[&&NHX:TOL=137362],synaphris lehtineni[&&NHX:TOL=137363],synaphris letourneuxi[&&NHX:TOL=137364],synaphris orientalis[&&NHX:TOL=137365],synaphris saphrynis[&&NHX:TOL=137366],synaphris schlingeri[&&NHX:TOL=137367],synaphris toliara[&&NHX:TOL=137368])synaphris[&&NHX:TOL=137003])synaphridae[&&NHX:TOL=134291],cyatholipidae[&&NHX:TOL=2792])[&&NHX:TOL=134290],(((naatlo[&&NHX:TOL=93121],epeirotypus[&&NHX:TOL=93122])[&&NHX:TOL=93120],(plato[&&NHX:TOL=93124],chthonos[&&NHX:TOL=93125])[&&NHX:TOL=93123],(ogulnius[&&NHX:TOL=93127],(theridiosoma[&&NHX:TOL=93129],(baalzebub[&&NHX:TOL=93131],(wendilgarda[&&NHX:TOL=93133],epilineutes[&&NHX:TOL=93134])[&&NHX:TOL=93132])[&&NHX:TOL=93130])[&&NHX:TOL=93128])[&&NHX:TOL=93126])theridiosomatidae[&&NHX:TOL=2801],((anjouanella[&&NHX:TOL=136980],brasilionata[&&NHX:TOL=136981],calodipoena[&&NHX:TOL=136982],calomyspoena[&&NHX:TOL=136983],crassignatha[&&NHX:TOL=136984],iardinis[&&NHX:TOL=136985],isela[&&NHX:TOL=136986],itapua[&&NHX:TOL=136987],kekenboschiella[&&NHX:TOL=136988],kilifina[&&NHX:TOL=136989],leviola[&&NHX:TOL=136990],maymena[&&NHX:TOL=136991],microdipoena[&&NHX:TOL=136992],mysmena[&&NHX:TOL=136993],mysmenella[&&NHX:TOL=136994],mysmeniola[&&NHX:TOL=136995],mysmenopsis[&&NHX:TOL=136996],phricotelus[&&NHX:TOL=136997],tamasesia[&&NHX:TOL=136998],taphiassa[&&NHX:TOL=136999],trogloneta[&&NHX:TOL=137000])mysmenidae[&&NHX:TOL=2803],(anapidae[&&NHX:TOL=2805],symphytognathidae[&&NHX:TOL=2806])[&&NHX:TOL=2804])[&&NHX:TOL=2802])symphytognathoids[&&NHX:TOL=2800])clawless female clade[&&NHX:TOL=134289])[&&NHX:TOL=134288])[&&NHX:TOL=134287])reduced piriform clade[&&NHX:TOL=2789])derived araneoids[&&NHX:TOL=93119])araneoidea[&&NHX:TOL=2787])orbiculariae[&&NHX:TOL=2698],((dictynidae[&&NHX:TOL=2653],neolanidae[&&NHX:TOL=2654],hahniidae[&&NHX:TOL=2655],argyronetidae[&&NHX:TOL=2656],cybaeidae[&&NHX:TOL=2657],desidae[&&NHX:TOL=2658])dictynoidea[&&NHX:TOL=2691],((((corinnidae[&&NHX:TOL=2663],liocranidae[&&NHX:TOL=2664])[&&NHX:TOL=2662],(gallieniellidae[&&NHX:TOL=2666],lamponidae[&&NHX:TOL=2667],trochanteriidae[&&NHX:TOL=2668],cithaeronidae[&&NHX:TOL=2669],ammoxenidae[&&NHX:TOL=2670],(gnaphosidae[&&NHX:TOL=2672],prodidomidae[&&NHX:TOL=2673])[&&NHX:TOL=2671])gnaphosoidea[&&NHX:TOL=2665])[&&NHX:TOL=2661],((alloclubionoides[&&NHX:TOL=60565],carteroniella[&&NHX:TOL=60566],carteronius[&&NHX:TOL=60567],clubiona[&&NHX:TOL=60568],clubionina[&&NHX:TOL=60569],dorymetaecus[&&NHX:TOL=60570],elaver[&&NHX:TOL=60571],malamatidia[&&NHX:TOL=60572],matidia[&&NHX:TOL=60573],nusatidia[&&NHX:TOL=60574],pristidia[&&NHX:TOL=60575],pteroneta[&&NHX:TOL=60576],scopalio[&&NHX:TOL=60577],simalio[&&NHX:TOL=60578],tixcocoba[&&NHX:TOL=60579])clubionidae[&&NHX:TOL=2675],anyphaenidae[&&NHX:TOL=2676],((((lyssomanes amazonicus[&&NHX:TOL=4426],lyssomanes anchicaya[&&NHX:TOL=4427],lyssomanes antillanus[&&NHX:TOL=4428],lyssomanes austerus[&&NHX:TOL=4429],lyssomanes belgranoi[&&NHX:TOL=4430],lyssomanes bitaeniatus[&&NHX:TOL=4431],lyssomanes blandus[&&NHX:TOL=4432],lyssomanes boraceia[&&NHX:TOL=4433],lyssomanes bryantae[&&NHX:TOL=4434],lyssomanes camacanensis[&&NHX:TOL=4435],lyssomanes ceplaci[&&NHX:TOL=4436],lyssomanes consimilis[&&NHX:TOL=4437],lyssomanes convexus[&&NHX:TOL=4438],lyssomanes deinognathus[&&NHX:TOL=4439],lyssomanes devotoi[&&NHX:TOL=4440],lyssomanes dissimilis[&&NHX:TOL=4441],lyssomanes diversus[&&NHX:TOL=4442],lyssomanes eatoni[&&NHX:TOL=4443],lyssomanes elegans[&&NHX:TOL=4444],lyssomanes elongatus[&&NHX:TOL=4445],lyssomanes flagellum[&&NHX:TOL=4446],lyssomanes hieroglyphicus[&&NHX:TOL=4447],lyssomanes ipanamae[&&NHX:TOL=4448],lyssomanes jemineus[&&NHX:TOL=4449],lyssomanes jucari[&&NHX:TOL=4450],lyssomanes lancetillae[&&NHX:TOL=4451],lyssomanes leucomelas[&&NHX:TOL=4452],lyssomanes limpidus[&&NHX:TOL=4453],lyssomanes longipes[&&NHX:TOL=4454],lyssomanes malinche[&&NHX:TOL=4455],lyssomanes mandibulatus[&&NHX:TOL=4456],lyssomanes michae[&&NHX:TOL=4457],lyssomanes miniaceus[&&NHX:TOL=4458],lyssomanes minor[&&NHX:TOL=4459],lyssomanes nigrofimbriatus[&&NHX:TOL=4460],lyssomanes nigropictus[&&NHX:TOL=4461],lyssomanes parallelus[&&NHX:TOL=4462],lyssomanes parki[&&NHX:TOL=4463],lyssomanes patens[&&NHX:TOL=4464],lyssomanes pauper[&&NHX:TOL=4465],lyssomanes penicillatus[&&NHX:TOL=4466],lyssomanes pichilingue[&&NHX:TOL=4467],lyssomanes placidus[&&NHX:TOL=4468],lyssomanes portoricensis[&&NHX:TOL=4469],lyssomanes protarsalis[&&NHX:TOL=4470],lyssomanes quadrinotatus[&&NHX:TOL=4471],lyssomanes reductus[&&NHX:TOL=4472],lyssomanes remotus[&&NHX:TOL=4473],lyssomanes robustus[&&NHX:TOL=4474],lyssomanes santarem[&&NHX:TOL=4475],lyssomanes spinifer[&&NHX:TOL=4476],lyssomanes spiralis[&&NHX:TOL=4477],lyssomanes sylvicola[&&NHX:TOL=4478],lyssomanes taczanowskii[&&NHX:TOL=4479],lyssomanes tapuiramae[&&NHX:TOL=4480],lyssomanes tarmae[&&NHX:TOL=4481],lyssomanes temperatus[&&NHX:TOL=4482],lyssomanes tenuis[&&NHX:TOL=4483],lyssomanes trifurcatus[&&NHX:TOL=4484],lyssomanes tristis[&&NHX:TOL=4485],lyssomanes unicolor[&&NHX:TOL=4486],lyssomanes velox[&&NHX:TOL=4487],lyssomanes viridis[&&NHX:TOL=4488],lyssomanes yacui[&&NHX:TOL=4489])lyssomanes[&&NHX:TOL=3008],chinoscopus[&&NHX:TOL=3009])new world[&&NHX:TOL=3007],(asemonea[&&NHX:TOL=3011],goleba[&&NHX:TOL=3012],pandisus[&&NHX:TOL=3013],onomastus[&&NHX:TOL=3014])old world[&&NHX:TOL=3010])lyssomaninae[&&NHX:TOL=2835],(allococalodes[&&NHX:TOL=3093],brettus[&&NHX:TOL=3094],cocalodes[&&NHX:TOL=3095],cocalus[&&NHX:TOL=3096],cyrba[&&NHX:TOL=3097],eolinus[&&NHX:EXT=Y:TOL=3098],gelotia[&&NHX:TOL=3099],meleon[&&NHX:TOL=3100],mintonia[&&NHX:TOL=3101],neobrettus[&&NHX:TOL=3102],(portia africana[&&NHX:TOL=5432],portia albimana[&&NHX:TOL=5433],portia anchorum[&&NHX:TOL=5434],portia assamensis[&&NHX:TOL=5435],portia crassipalpis[&&NHX:TOL=5436],portia deciliata[&&NHX:TOL=5437],portia fimbriata[&&NHX:TOL=5438],portia heteroidea[&&NHX:TOL=5439],portia hoggi[&&NHX:TOL=5440],portia labiata[&&NHX:TOL=5441],portia orientalis[&&NHX:TOL=5442],portia quei[&&NHX:TOL=5443],portia schultzi[&&NHX:TOL=5444],portia semifimbriata[&&NHX:TOL=5445],portia strandi[&&NHX:TOL=5446])portia[&&NHX:TOL=3103],taraxella[&&NHX:TOL=3104],veissella[&&NHX:TOL=3105],yaginumanis[&&NHX:TOL=3106],spartaeus[&&NHX:TOL=3107])spartaeinae[&&NHX:TOL=2836],((((amycus annulatus[&&NHX:TOL=3173],amycus delicatus[&&NHX:TOL=3174],amycus ectypus[&&NHX:TOL=3175],amycus effeminatus[&&NHX:TOL=3176],amycus equulus[&&NHX:TOL=3177],amycus flavicomis[&&NHX:TOL=3178],amycus flavolineatus[&&NHX:TOL=3179],amycus igneus[&&NHX:TOL=3180],amycus lechugalensis[&&NHX:TOL=3181],amycus lycosiformis[&&NHX:TOL=3182],amycus palpinalis[&&NHX:TOL=3183],amycus patellaris[&&NHX:TOL=3184],amycus pertyi[&&NHX:TOL=3185],amycus rufifrons[&&NHX:TOL=3186],amycus spectabilis[&&NHX:TOL=3187],amycus thoracicus[&&NHX:TOL=3188],amycus tristis[&&NHX:TOL=3189])amycus[&&NHX:TOL=2860],(acragas carinatus[&&NHX:TOL=3134],acragas castaneiceps[&&NHX:TOL=3135],acragas erythraeus[&&NHX:TOL=3136],acragas fallax[&&NHX:TOL=3137],acragas flavescens[&&NHX:TOL=3138],acragas hieroglyphicus[&&NHX:TOL=3139],acragas humilis[&&NHX:TOL=3140],acragas humaites[&&NHX:TOL=3141],acragas leucaspis[&&NHX:TOL=3142],acragas longimanus[&&NHX:TOL=3143],acragas longipalpus[&&NHX:TOL=3144],acragas mendax[&&NHX:TOL=3145],acragas miniaceus[&&NHX:TOL=3146],acragas nigromaculatus[&&NHX:TOL=3147],acragas pacatus[&&NHX:TOL=3148],acragas peckhami[&&NHX:TOL=3149],acragas phasianius[&&NHX:TOL=3150],acragas procalvus[&&NHX:TOL=3151],acragas rosenbergi[&&NHX:TOL=3152],acragas quadriguttatus[&&NHX:TOL=3153],acragas trimaculatus[&&NHX:TOL=3154],acragas zeteki[&&NHX:TOL=3155])acragas[&&NHX:TOL=2861],(encolpius albobarbatus[&&NHX:TOL=3571],encolpius fimbriatus[&&NHX:TOL=3572],encolpius guaraniticus[&&NHX:TOL=3573])encolpius[&&NHX:TOL=2862],(hypaeus annulifer[&&NHX:TOL=4352],hypaeus barromachadoi[&&NHX:TOL=4353],hypaeus benignus[&&NHX:TOL=4354],hypaeus bivittatus[&&NHX:TOL=4355],hypaeus concinnus[&&NHX:TOL=4356],hypaeus cucullatus[&&NHX:TOL=4357],hypaeus duodentatus[&&NHX:TOL=4358],hypaeus estebanensis[&&NHX:TOL=4359],hypaeus flavipes[&&NHX:TOL=4360],hypaeus flemingi[&&NHX:TOL=4361],hypaeus frontosus[&&NHX:TOL=4362],hypaeus furcifer[&&NHX:TOL=4363],hypaeus ignicomis[&&NHX:TOL=4364],hypaeus luridomaculatus[&&NHX:TOL=4365],hypaeus miles[&&NHX:TOL=4366],hypaeus mystacalis[&&NHX:TOL=4367],hypaeus nigrocomosus[&&NHX:TOL=4368],hypaeus porcatus[&&NHX:TOL=4369],hypaeus quadrinotatus[&&NHX:TOL=4370],hypaeus taczanowskii[&&NHX:TOL=4371],hypaeus tenuimanus[&&NHX:TOL=4372],hypaeus triplagiatus[&&NHX:TOL=4373],hypaeus venezuelanus[&&NHX:TOL=4374])hypaeus[&&NHX:TOL=2863],(mago acutidens[&&NHX:TOL=4537],mago angustichelis[&&NHX:TOL=4538],mago australis[&&NHX:TOL=4539],mago barbatus[&&NHX:TOL=4540],mago dentichelis[&&NHX:TOL=4541],mago fasciatus[&&NHX:TOL=4542],mago fonsecai[&&NHX:TOL=4543],mago fulvitorax[&&NHX:TOL=4544],mago intentus[&&NHX:TOL=4545],mago longidens[&&NHX:TOL=4546],mago opiparis[&&NHX:TOL=4547],mago procax[&&NHX:TOL=4548],mago saperda[&&NHX:TOL=4549],mago silvae[&&NHX:TOL=4550],mago steindachneri[&&NHX:TOL=4551],mago vicanus[&&NHX:TOL=4552])mago[&&NHX:TOL=2864],(noegus actionosus[&&NHX:TOL=4952],noegus arator[&&NHX:TOL=4953],noegus argenteopunctatus[&&NHX:TOL=4954],noegus australis[&&NHX:TOL=4955],noegus bidens[&&NHX:TOL=4956],noegus coccineus[&&NHX:TOL=4957],noegus comatulus[&&NHX:TOL=4958],noegus difficilis[&&NHX:TOL=4959],noegus franganilloi[&&NHX:TOL=4960],noegus fulvocristatus[&&NHX:TOL=4961],noegus fuscimanus[&&NHX:TOL=4962],noegus fuscomanus[&&NHX:TOL=4963],noegus mantovani[&&NHX:TOL=4964],noegus niveogularis[&&NHX:TOL=4965],noegus niveomarginatus[&&NHX:TOL=4966],noegus pallidus[&&NHX:TOL=4967],noegus rufus[&&NHX:TOL=4968],noegus spiralifer[&&NHX:TOL=4969],noegus transversalis[&&NHX:TOL=4970],noegus trilineatus[&&NHX:TOL=4971],noegus uncatus[&&NHX:TOL=4972],noegus vulpio[&&NHX:TOL=4973])noegus[&&NHX:TOL=2865])amycinae[&&NHX:TOL=2839],((thiodina candida[&&NHX:TOL=5899],thiodina crucifera[&&NHX:TOL=5900],thiodina germaini[&&NHX:TOL=5901],thiodina inerma[&&NHX:TOL=5902],thiodina melanogaster[&&NHX:TOL=5903],thiodina nicoleti[&&NHX:TOL=5904],thiodina pallida[&&NHX:TOL=5905],thiodina puerpera[&&NHX:TOL=5906],thiodina punctulata[&&NHX:TOL=5907],thiodina pseustes[&&NHX:TOL=5908],thiodina robusta[&&NHX:TOL=5909],thiodina setosa[&&NHX:TOL=5910],thiodina sylvana[&&NHX:TOL=5911],thiodina vaccula[&&NHX:TOL=5912],thiodina vellardi[&&NHX:TOL=5913])thiodina[&&NHX:TOL=3126],(cotinusa adelae[&&NHX:TOL=3463],cotinusa albescens[&&NHX:TOL=3464],cotinusa bisetosa[&&NHX:TOL=3465],cotinusa bryantae[&&NHX:TOL=3466],cotinusa cancellata[&&NHX:TOL=3467],cotinusa deserta[&&NHX:TOL=3468],cotinusa dimidiata[&&NHX:TOL=3469],cotinusa distincta[&&NHX:TOL=3470],cotinusa fenestrata[&&NHX:TOL=3471],cotinusa gemmea[&&NHX:TOL=3472],cotinusa gertschi[&&NHX:TOL=3473],cotinusa horatia[&&NHX:TOL=3474],cotinusa irregularis[&&NHX:TOL=3475],cotinusa leucoprocta[&&NHX:TOL=3476],cotinusa magna[&&NHX:TOL=3477],cotinusa mathematica[&&NHX:TOL=3478],cotinusa melanura[&&NHX:TOL=3479],cotinusa puella[&&NHX:TOL=3480],cotinusa pulchra[&&NHX:TOL=3481],cotinusa rosascostai[&&NHX:TOL=3482],cotinusa septempunctata[&&NHX:TOL=3483],cotinusa simoni[&&NHX:TOL=3484],cotinusa stolzmanni[&&NHX:TOL=3485],cotinusa trifasciata[&&NHX:TOL=3486],cotinusa trimaculata[&&NHX:TOL=3487],cotinusa vittata[&&NHX:TOL=3488])cotinusa[&&NHX:TOL=3127],banksetosa[&&NHX:TOL=3128],carabella[&&NHX:TOL=3129])thiodininae[&&NHX:TOL=2840])[&&NHX:TOL=2838],(hispo[&&NHX:TOL=2991],gorgopsina[&&NHX:EXT=Y:TOL=2992],prolinus[&&NHX:EXT=Y:TOL=2993],tomocyrba[&&NHX:TOL=2994])hisponinae[&&NHX:TOL=2841],((bocus[&&NHX:TOL=3116],corcovetella[&&NHX:TOL=3117],(fluda angulosa[&&NHX:TOL=3795],fluda araguae[&&NHX:TOL=3796],fluda elata[&&NHX:TOL=3797],fluda goianiae[&&NHX:TOL=3798],fluda inpae[&&NHX:TOL=3799],fluda minuta[&&NHX:TOL=3800],fluda narcissa[&&NHX:TOL=3801],fluda nigritarsis[&&NHX:TOL=3802],fluda opica[&&NHX:TOL=3803],fluda perdita[&&NHX:TOL=3804],fluda princeps[&&NHX:TOL=3805],fluda ruficeps[&&NHX:TOL=3806],fluda usta[&&NHX:TOL=3807])fluda[&&NHX:TOL=3118],martella[&&NHX:TOL=3119],(myrmarachne aenescens[&&NHX:TOL=4723],myrmarachne albicrurata[&&NHX:TOL=4724],myrmarachne albosetosa[&&NHX:TOL=4725],myrmarachne alticeps[&&NHX:TOL=4726],myrmarachne andrewi[&&NHX:TOL=4727],myrmarachne andringintra[&&NHX:TOL=4728],myrmarachne angusta[&&NHX:TOL=4729],myrmarachne annamita[&&NHX:TOL=4730],myrmarachne annandalei[&&NHX:TOL=4731],myrmarachne assimilis[&&NHX:TOL=4732],myrmarachne attenuata[&&NHX:TOL=4733],myrmarachne augusta[&&NHX:TOL=4734],myrmarachne bakeri[&&NHX:TOL=4735],myrmarachne bamakoi[&&NHX:TOL=4736],myrmarachne bengalensis[&&NHX:TOL=4737],myrmarachne bicolor[&&NHX:TOL=4738],myrmarachne bicurvata[&&NHX:TOL=4739],myrmarachne bidentata[&&NHX:TOL=4740],myrmarachne biseratensis[&&NHX:TOL=4741],myrmarachne borneensis[&&NHX:TOL=4742],myrmarachne brasiliensis[&&NHX:TOL=4743],myrmarachne calcuttaensis[&&NHX:TOL=4744],myrmarachne capito[&&NHX:TOL=4745],myrmarachne centralis[&&NHX:TOL=4746],myrmarachne chapmani[&&NHX:TOL=4747],myrmarachne chickeringi[&&NHX:TOL=4748],myrmarachne clavigera[&&NHX:TOL=4749],myrmarachne cognata[&&NHX:TOL=4750],myrmarachne collarti[&&NHX:TOL=4751],myrmarachne confusa[&&NHX:TOL=4752],myrmarachne consobrina[&&NHX:TOL=4753],myrmarachne constricta[&&NHX:TOL=4754],myrmarachne contracta[&&NHX:TOL=4755],myrmarachne cornuta[&&NHX:TOL=4756],myrmarachne corpuzrarosae[&&NHX:TOL=4757],myrmarachne cowani[&&NHX:TOL=4758],myrmarachne cuneata[&&NHX:TOL=4759],myrmarachne cuprea[&&NHX:TOL=4760],myrmarachne daitarensis[&&NHX:TOL=4761],myrmarachne debilis[&&NHX:TOL=4762],myrmarachne decorata[&&NHX:TOL=4763],myrmarachne denticulata[&&NHX:TOL=4764],myrmarachne diegoensis[&&NHX:TOL=4765],myrmarachne dilatata[&&NHX:TOL=4766],myrmarachne dubia[&&NHX:TOL=4767],myrmarachne dundoensis[&&NHX:TOL=4768],myrmarachne edentula[&&NHX:TOL=4769],myrmarachne eidmanni[&&NHX:TOL=4770],myrmarachne electrica[&&NHX:TOL=4771],myrmarachne elongata[&&NHX:TOL=4772],myrmarachne erythrocephala[&&NHX:TOL=4773],myrmarachne eugenei[&&NHX:TOL=4774],myrmarachne eumenes[&&NHX:TOL=4775],myrmarachne evidens[&&NHX:TOL=4776],myrmarachne exasperans[&&NHX:TOL=4777],myrmarachne exultans[&&NHX:TOL=4778],myrmarachne foenisex[&&NHX:TOL=4779],myrmarachne foreli[&&NHX:TOL=4780],myrmarachne formica[&&NHX:TOL=4781],myrmarachne formicaria[&&NHX:TOL=4782],myrmarachne formosa[&&NHX:TOL=4783],myrmarachne formosana[&&NHX:TOL=4784],myrmarachne formosicola[&&NHX:TOL=4785],myrmarachne furcata[&&NHX:TOL=4786],myrmarachne galianoae[&&NHX:TOL=4787],myrmarachne gedongensis[&&NHX:TOL=4788],myrmarachne gigantea[&&NHX:TOL=4789],myrmarachne giltayi[&&NHX:TOL=4790],myrmarachne gisti[&&NHX:TOL=4791],myrmarachne globosa[&&NHX:TOL=4792],myrmarachne guaranitica[&&NHX:TOL=4793],myrmarachne hanoii[&&NHX:TOL=4794],myrmarachne hesperia[&&NHX:TOL=4795],myrmarachne hidaspis[&&NHX:TOL=4796],myrmarachne himalayensis[&&NHX:TOL=4797],myrmarachne hoffmanni[&&NHX:TOL=4798],myrmarachne ichneumon[&&NHX:TOL=4799],myrmarachne imbellis[&&NHX:TOL=4800],myrmarachne incerta[&&NHX:TOL=4801],myrmarachne inermichelis[&&NHX:TOL=4802],myrmarachne inflatipalpis[&&NHX:TOL=4803],myrmarachne insulana[&&NHX:TOL=4804],myrmarachne iridescens[&&NHX:TOL=4805],myrmarachne isolata[&&NHX:TOL=4806],myrmarachne jacobsoni[&&NHX:TOL=4807],myrmarachne jajpurensis[&&NHX:TOL=4808],myrmarachne japonica[&&NHX:TOL=4809],myrmarachne jugularis[&&NHX:TOL=4810],myrmarachne kiboschensis[&&NHX:TOL=4811],myrmarachne kilifi[&&NHX:TOL=4812],myrmarachne kitale[&&NHX:TOL=4813],myrmarachne kochi[&&NHX:TOL=4814],myrmarachne kuroiwana[&&NHX:TOL=4815],myrmarachne kuwagata[&&NHX:TOL=4816],myrmarachne laeta[&&NHX:TOL=4817],myrmarachne laurentina[&&NHX:TOL=4818],myrmarachne lawrencei[&&NHX:TOL=4819],myrmarachne lateralis[&&NHX:TOL=4820],myrmarachne legon[&&NHX:TOL=4821],myrmarachne leleupi[&&NHX:TOL=4822],myrmarachne leptognatha[&&NHX:TOL=4823],myrmarachne lesserti[&&NHX:TOL=4824],myrmarachne longiventris[&&NHX:TOL=4825],myrmarachne luachimo[&&NHX:TOL=4826],myrmarachne luctuosa[&&NHX:TOL=4827],myrmarachne lugens[&&NHX:TOL=4828],myrmarachne lugubris[&&NHX:TOL=4829],myrmarachne lulengana[&&NHX:TOL=4830],myrmarachne lulengensis[&&NHX:TOL=4831],myrmarachne lupata[&&NHX:TOL=4832],myrmarachne lurida[&&NHX:TOL=4833],myrmarachne macgregori[&&NHX:TOL=4834],myrmarachne macleayana[&&NHX:TOL=4835],myrmarachne macrognatha[&&NHX:TOL=4836],myrmarachne magna[&&NHX:TOL=4837],myrmarachne mahasoa[&&NHX:TOL=4838],myrmarachne mandibularis[&&NHX:TOL=4839],myrmarachne manducator[&&NHX:TOL=4840],myrmarachne maratha[&&NHX:TOL=4841],myrmarachne marshalli[&&NHX:TOL=4842],myrmarachne matsumurana[&&NHX:TOL=4843],myrmarachne maxillosa[&&NHX:TOL=4844],myrmarachne melanocephala[&&NHX:TOL=4845],myrmarachne militaris[&&NHX:TOL=4846],myrmarachne mocamboensis[&&NHX:TOL=4847],myrmarachne moesta[&&NHX:TOL=4848],myrmarachne mussungue[&&NHX:TOL=4849],myrmarachne myrmicaeformis[&&NHX:TOL=4850],myrmarachne naro[&&NHX:TOL=4851],myrmarachne natalica[&&NHX:TOL=4852],myrmarachne nemorensis[&&NHX:TOL=4853],myrmarachne nigella[&&NHX:TOL=4854],myrmarachne nigeriensis[&&NHX:TOL=4855],myrmarachne nigra[&&NHX:TOL=4856],myrmarachne nitidissima[&&NHX:TOL=4857],myrmarachne nubilis[&&NHX:TOL=4858],myrmarachne obscura[&&NHX:TOL=4859],myrmarachne opaca[&&NHX:TOL=4860],myrmarachne orientalis[&&NHX:TOL=4861],myrmarachne paivai[&&NHX:TOL=4862],myrmarachne palladia[&&NHX:TOL=4863],myrmarachne panamensis[&&NHX:TOL=4864],myrmarachne parallela[&&NHX:TOL=4865],myrmarachne patellata[&&NHX:TOL=4866],myrmarachne paviei[&&NHX:TOL=4867],myrmarachne peckhami[&&NHX:TOL=4868],myrmarachne pectorosa[&&NHX:TOL=4869],myrmarachne penicillata[&&NHX:TOL=4870],myrmarachne piercei[&&NHX:TOL=4871],myrmarachne plataleoides[&&NHX:TOL=4872],myrmarachne platypalpus[&&NHX:TOL=4873],myrmarachne poonaensis[&&NHX:TOL=4874],myrmarachne prava[&&NHX:TOL=4875],myrmarachne prognatha[&&NHX:TOL=4876],myrmarachne providens[&&NHX:TOL=4877],myrmarachne pumilio[&&NHX:TOL=4878],myrmarachne pygmaea[&&NHX:TOL=4879],myrmarachne radiata[&&NHX:TOL=4880],myrmarachne ramosa[&&NHX:TOL=4881],myrmarachne ramunni[&&NHX:TOL=4882],myrmarachne ransoni[&&NHX:TOL=4883],myrmarachne rhopalota[&&NHX:TOL=4884],myrmarachne richardsi[&&NHX:TOL=4885],myrmarachne robusta[&&NHX:TOL=4886],myrmarachne roeweri[&&NHX:TOL=4887],myrmarachne rufescens[&&NHX:TOL=4888],myrmarachne rufisquei[&&NHX:TOL=4889],myrmarachne russellsmithi[&&NHX:TOL=4890],myrmarachne sakisimana[&&NHX:TOL=4891],myrmarachne sanibarica[&&NHX:TOL=4892],myrmarachne satarensis[&&NHX:TOL=4893],myrmarachne seriatis[&&NHX:TOL=4894],myrmarachne shelfordi[&&NHX:TOL=4895],myrmarachne simoni[&&NHX:TOL=4896],myrmarachne simonis[&&NHX:TOL=4897],myrmarachne simplexella[&&NHX:TOL=4898],myrmarachne solitaria[&&NHX:TOL=4899],myrmarachne spissa[&&NHX:TOL=4900],myrmarachne striatipes[&&NHX:TOL=4901],myrmarachne sumana[&&NHX:TOL=4902],myrmarachne tagalica[&&NHX:TOL=4903],myrmarachne tayabasana[&&NHX:TOL=4904],myrmarachne thaii[&&NHX:TOL=4905],myrmarachne topali[&&NHX:TOL=4906],myrmarachne transversa[&&NHX:TOL=4907],myrmarachne tristis[&&NHX:TOL=4908],myrmarachne turriformis[&&NHX:TOL=4909],myrmarachne uelensis[&&NHX:TOL=4910],myrmarachne uniseriata[&&NHX:TOL=4911],myrmarachne uvira[&&NHX:TOL=4912],myrmarachne vanessae[&&NHX:TOL=4913],myrmarachne vehemens[&&NHX:TOL=4914],myrmarachne vestita[&&NHX:TOL=4915],myrmarachne volatilis[&&NHX:TOL=4916])myrmarachne[&&NHX:TOL=3120],(sarinda armata[&&NHX:TOL=5682],sarinda atrata[&&NHX:TOL=5683],sarinda camba[&&NHX:TOL=5684],sarinda capibarae[&&NHX:TOL=5685],sarinda cayennensis[&&NHX:TOL=5686],sarinda cutleri[&&NHX:TOL=5687],sarinda exilis[&&NHX:TOL=5688],sarinda glabra[&&NHX:TOL=5689],sarinda hentzi[&&NHX:TOL=5690],sarinda imitans[&&NHX:TOL=5691],sarinda longula[&&NHX:TOL=5692],sarinda marcosi[&&NHX:TOL=5693],sarinda nigra[&&NHX:TOL=5694],sarinda panamae[&&NHX:TOL=5695],sarinda pretiosa[&&NHX:TOL=5696],sarinda ruficeps[&&NHX:TOL=5697],sarinda silvatica[&&NHX:TOL=5698],sarinda utingae[&&NHX:TOL=5699])sarinda[&&NHX:TOL=3121],(simprulla nigricolor[&&NHX:TOL=24809],simprulla argentina[&&NHX:TOL=24810])simprulla[&&NHX:TOL=3122],(synemosyna americana[&&NHX:TOL=5858],synemosyna ankeli[&&NHX:TOL=5859],synemosyna aurantiaca[&&NHX:TOL=5860],synemosyna bimaculata[&&NHX:TOL=5861],synemosyna decipiens[&&NHX:TOL=5862],synemosyna edwardsi[&&NHX:TOL=5863],synemosyna fasciata[&&NHX:TOL=5864],synemosyna fissidentata[&&NHX:TOL=5865],synemosyna formica[&&NHX:TOL=5866],synemosyna hentzi[&&NHX:TOL=5867],synemosyna invemar[&&NHX:TOL=5868],synemosyna lauretta[&&NHX:TOL=5869],synemosyna lucasi[&&NHX:TOL=5870],synemosyna maddisoni[&&NHX:TOL=5871],synemosyna magniscuti[&&NHX:TOL=5872],synemosyna melanura[&&NHX:TOL=5873],synemosyna myrmeciaeformis[&&NHX:TOL=5874],synemosyna paraensis[&&NHX:TOL=5875],synemosyna petrunkevitchi[&&NHX:TOL=5876],synemosyna scutata[&&NHX:TOL=5877],synemosyna smithi[&&NHX:TOL=5878],synemosyna subtilis[&&NHX:TOL=5879],synemosyna taperae[&&NHX:TOL=5880],synemosyna ubicki[&&NHX:TOL=5881])synemosyna[&&NHX:TOL=3123],zuniga[&&NHX:TOL=3124])synemosyninae[&&NHX:TOL=2843],((agelista[&&NHX:TOL=2997],arachnomura[&&NHX:TOL=2998],atomosphyrus[&&NHX:TOL=2999],(bredana alternata[&&NHX:TOL=24795],bredana complicata[&&NHX:TOL=24796])bredana[&&NHX:TOL=3000],(cyllodania bicruciata[&&NHX:TOL=3498],cyllodania fasciata[&&NHX:TOL=3499],cyllodania minuta[&&NHX:TOL=3500],cyllodania sp. arizona[&&NHX:TOL=3501])cyllodania[&&NHX:TOL=3001],(hyetussa aguilari[&&NHX:TOL=4345],hyetussa andalgalaensis[&&NHX:TOL=4346],hyetussa cribrata[&&NHX:TOL=4347],hyetussa mesopotamica[&&NHX:TOL=4348],hyetussa secta[&&NHX:TOL=4349],hyetussa simoni[&&NHX:TOL=4350])hyetussa[&&NHX:TOL=3002],(scopocira atypica[&&NHX:TOL=5723],scopocira carinata[&&NHX:TOL=5724],scopocira dentichelis[&&NHX:TOL=5725],scopocira fuscimana[&&NHX:TOL=5726],scopocira histrio[&&NHX:TOL=5727],scopocira melanops[&&NHX:TOL=5728],scopocira panamena[&&NHX:TOL=5729],scopocira sexspinosa[&&NHX:TOL=5730],scopocira tenella[&&NHX:TOL=5731],scopocira vivida[&&NHX:TOL=5732])scopocira[&&NHX:TOL=3003],(titanattus cretatus[&&NHX:TOL=5917],titanattus juduliani[&&NHX:TOL=5918],titanattus notabilis[&&NHX:TOL=5919],titanattus novarai[&&NHX:TOL=5920],titanattus paganus[&&NHX:TOL=5921],titanattus pallidus[&&NHX:TOL=5922],titanattus pegaseus[&&NHX:TOL=5923],titanattus saevus[&&NHX:TOL=5924])titanattus[&&NHX:TOL=3004])[&&NHX:TOL=2996],unidentified hyetussinae[&&NHX:TOL=3005])hyetussinae[&&NHX:TOL=2844])[&&NHX:TOL=2842],(((sitticus dorsatus[&&NHX:TOL=5757],sitticus albolineatus[&&NHX:TOL=5758],sitticus ammophilus[&&NHX:TOL=5759],sitticus ansobicus[&&NHX:TOL=5760],sitticus auricomus[&&NHX:TOL=5761],sitticus avocator[&&NHX:TOL=5762],sitticus basalis[&&NHX:TOL=5763],sitticus cabellensis[&&NHX:TOL=5764],sitticus canus[&&NHX:TOL=5765],sitticus caricis[&&NHX:TOL=5766],sitticus cautus[&&NHX:TOL=5767],sitticus cellulanus[&&NHX:TOL=5768],sitticus clavator[&&NHX:TOL=5769],sitticus concolor[&&NHX:TOL=5770],sitticus cutleri[&&NHX:TOL=5771],sitticus damini[&&NHX:TOL=5772],sitticus designatus[&&NHX:TOL=5773],sitticus diductus[&&NHX:TOL=5774],sitticus distinguendus[&&NHX:TOL=5775],sitticus dzieduszycki[&&NHX:TOL=5776],sitticus fasciger[&&NHX:TOL=5777],sitticus finschi[&&NHX:TOL=5778],sitticus flabellatus[&&NHX:TOL=5779],sitticus floricola[&&NHX:TOL=5780],sitticus palustris[&&NHX:TOL=5781],sitticus goricus[&&NHX:TOL=5782],sitticus inopinabilis[&&NHX:TOL=5783],sitticus juniperi[&&NHX:TOL=5784],sitticus karakumensis[&&NHX:TOL=5785],sitticus leucoproctus[&&NHX:TOL=5786],sitticus longipes[&&NHX:TOL=5787],sitticus sylvestris[&&NHX:TOL=5788],sitticus mazorcanus[&&NHX:TOL=5789],sitticus monstrabilis[&&NHX:TOL=5790],sitticus nenilini[&&NHX:TOL=5791],sitticus niveosignatus[&&NHX:TOL=5792],sitticus palpalis[&&NHX:TOL=5793],sitticus penicillatus[&&NHX:TOL=5794],sitticus penicilloides[&&NHX:TOL=5795],sitticus peninsulanus[&&NHX:TOL=5796],sitticus phaleratus[&&NHX:TOL=5797],sitticus pubescens[&&NHX:TOL=5798],sitticus pulchellus[&&NHX:TOL=5799],sitticus ranieri[&&NHX:TOL=5800],sitticus rupicola[&&NHX:TOL=5801],sitticus saltator[&&NHX:TOL=5802],sitticus saxicola[&&NHX:TOL=5803],sitticus sexsignatus[&&NHX:TOL=5804],sitticus sinensis[&&NHX:TOL=5805],sitticus striatus[&&NHX:TOL=5806],sitticus talgarensis[&&NHX:TOL=5807],sitticus tannuolana[&&NHX:TOL=5808],sitticus tenebricus[&&NHX:TOL=5809],sitticus terebratus[&&NHX:TOL=5810],sitticus uber[&&NHX:TOL=5811],sitticus uphami[&&NHX:TOL=5812],sitticus vilis[&&NHX:TOL=5813],sitticus welchi[&&NHX:TOL=5814],sitticus zimmermanni[&&NHX:TOL=5815],sitticus dyali[&&NHX:TOL=5816],sitticus exiguus[&&NHX:TOL=5817],sitticus japonicus[&&NHX:TOL=5818],sitticus manni[&&NHX:TOL=5819],sitticus saevus[&&NHX:TOL=5820],sitticus saganus[&&NHX:TOL=5821],sitticus walckenaeri[&&NHX:TOL=5822])sitticus[&&NHX:TOL=3089],(jollas amazonicus[&&NHX:TOL=4412],jollas geniculatus[&&NHX:TOL=4413],jollas manantiales[&&NHX:TOL=4414],jollas paranacito[&&NHX:TOL=4415],jollas pompatus[&&NHX:TOL=4416],jollas puntalara[&&NHX:TOL=4417])jollas[&&NHX:TOL=3090],(aillutticus brutus[&&NHX:TOL=3164],aillutticus nitens[&&NHX:TOL=3165],aillutticus pinquidor[&&NHX:TOL=3166],aillutticus rotundatus[&&NHX:TOL=3167])aillutticus[&&NHX:TOL=3091])sitticinae[&&NHX:TOL=2846],((bianor aemulus[&&NHX:TOL=3259],bianor aeneiceps[&&NHX:TOL=3260],bianor aeneus[&&NHX:TOL=3261],bianor albobimaculatus[&&NHX:TOL=3262],bianor angulosus[&&NHX:TOL=3263],bianor aurocinctus[&&NHX:TOL=3264],bianor balius[&&NHX:TOL=3265],bianor biocellosus[&&NHX:TOL=3266],bianor carli[&&NHX:TOL=3267],bianor compactus[&&NHX:TOL=3268],bianor concolor[&&NHX:TOL=3269],bianor diversipes[&&NHX:TOL=3270],bianor fasciatus[&&NHX:TOL=3271],bianor fimbriatus[&&NHX:TOL=3272],bianor hotingchiehi[&&NHX:TOL=3273],bianor inexploratus[&&NHX:TOL=3274],bianor insignis[&&NHX:TOL=3275],bianor latens[&&NHX:TOL=3276],bianor maculatus[&&NHX:TOL=3277],bianor monster[&&NHX:TOL=3278],bianor pulchellus[&&NHX:TOL=3279],bianor rusticulus[&&NHX:TOL=3280],bianor scutatus[&&NHX:TOL=3281],bianor simoni[&&NHX:TOL=3282],bianor simplex[&&NHX:TOL=3283],bianor staintoni[&&NHX:TOL=3284],bianor stepposus[&&NHX:TOL=3285],bianor trepidans[&&NHX:TOL=3286])bianor[&&NHX:TOL=3073],brancus[&&NHX:TOL=3074],dexippus[&&NHX:TOL=3075],(evarcha albaria[&&NHX:TOL=3752],evarcha amabilis[&&NHX:TOL=3753],evarcha arcuata[&&NHX:TOL=3754],evarcha bicoronata[&&NHX:TOL=3755],evarcha brevis[&&NHX:TOL=3756],evarcha bulbosa[&&NHX:TOL=3757],evarcha cancellata[&&NHX:TOL=3758],evarcha cara[&&NHX:TOL=3759],evarcha chappuisi[&&NHX:TOL=3760],evarcha chubbi[&&NHX:TOL=3761],evarcha coreana[&&NHX:TOL=3762],evarcha crassipes[&&NHX:TOL=3763],evarcha dubia[&&NHX:TOL=3764],evarcha eriki[&&NHX:TOL=3765],evarcha falcata[&&NHX:TOL=3766],evarcha hoyi[&&NHX:TOL=3767],evarcha fasciata[&&NHX:TOL=3768],evarcha flammata[&&NHX:TOL=3769],evarcha flavocincta[&&NHX:TOL=3770],evarcha gausapata[&&NHX:TOL=3771],evarcha hyllinella[&&NHX:TOL=3772],evarcha infrastriata[&&NHX:TOL=3773],evarcha jucunda[&&NHX:TOL=3774],evarcha kochi[&&NHX:TOL=3775],evarcha laetabunda[&&NHX:TOL=3776],evarcha madagascariensis[&&NHX:TOL=3777],evarcha michailovi[&&NHX:TOL=3778],evarcha natalica[&&NHX:TOL=3779],evarcha nepos[&&NHX:TOL=3780],evarcha obscura[&&NHX:TOL=3781],evarcha optabilis[&&NHX:TOL=3782],evarcha paralbaria[&&NHX:TOL=3783],evarcha patagiata[&&NHX:TOL=3784],evarcha petrae[&&NHX:TOL=3785],evarcha pococki[&&NHX:TOL=3786],evarcha praecincta[&&NHX:TOL=3787],evarcha pulchella[&&NHX:TOL=3788],evarcha similis[&&NHX:TOL=3789],evarcha syriaca[&&NHX:TOL=3790],evarcha venezuelica[&&NHX:TOL=3791],evarcha vitosa[&&NHX:TOL=3792])evarcha[&&NHX:TOL=3076],harmochirus[&&NHX:TOL=3077],hyllus[&&NHX:TOL=3078],mogrus[&&NHX:TOL=3079],paramodunda[&&NHX:TOL=3080],plexippoides[&&NHX:TOL=3081],(plexippus andamanensis[&&NHX:TOL=5375],plexippus aper[&&NHX:TOL=5376],plexippus auberti[&&NHX:TOL=5377],plexippus bhutani[&&NHX:TOL=5378],plexippus brachypus[&&NHX:TOL=5379],plexippus brocchus[&&NHX:TOL=5380],plexippus caeruleus[&&NHX:TOL=5381],plexippus calcutaensis[&&NHX:TOL=5382],plexippus catellus[&&NHX:TOL=5383],plexippus clemens[&&NHX:TOL=5384],plexippus coccinatus[&&NHX:TOL=5385],plexippus devorans[&&NHX:TOL=5386],plexippus elaphus[&&NHX:TOL=5387],plexippus fannae[&&NHX:TOL=5388],plexippus felis[&&NHX:TOL=5389],plexippus frendens[&&NHX:TOL=5390],plexippus furtivus[&&NHX:TOL=5391],plexippus gulosus[&&NHX:TOL=5392],plexippus hepaticus[&&NHX:TOL=5393],plexippus incanus[&&NHX:TOL=5394],plexippus incognitus[&&NHX:TOL=5395],plexippus insulanus[&&NHX:TOL=5396],plexippus intermedius[&&NHX:TOL=5397],plexippus kondarensis[&&NHX:TOL=5398],plexippus lividus[&&NHX:TOL=5399],plexippus luteus[&&NHX:TOL=5400],plexippus malayensis[&&NHX:TOL=5401],plexippus marginellus[&&NHX:TOL=5402],plexippus mutillarius[&&NHX:TOL=5403],plexippus niccensis[&&NHX:TOL=5404],plexippus nigrifrons[&&NHX:TOL=5405],plexippus obesus[&&NHX:TOL=5406],plexippus ochropsis[&&NHX:TOL=5407],plexippus paykulli[&&NHX:TOL=5408],plexippus perfidus[&&NHX:TOL=5409],plexippus petersi[&&NHX:TOL=5410],plexippus phyllus[&&NHX:TOL=5411],plexippus planiceps[&&NHX:TOL=5412],plexippus pokharae[&&NHX:TOL=5413],plexippus pupulus[&&NHX:TOL=5414],plexippus redimitus[&&NHX:TOL=5415],plexippus robustus[&&NHX:TOL=5416],plexippus rubrigularis[&&NHX:TOL=5417],plexippus seladonicus[&&NHX:TOL=5418],plexippus semiater[&&NHX:TOL=5419],plexippus setipes[&&NHX:TOL=5420],plexippus severus[&&NHX:TOL=5421],plexippus similis[&&NHX:TOL=5422],plexippus simplicissimus[&&NHX:TOL=5423],plexippus stridulator[&&NHX:TOL=5424],plexippus taeniatus[&&NHX:TOL=5425],plexippus tortilis[&&NHX:TOL=5426],plexippus unicolor[&&NHX:TOL=5427],plexippus validus[&&NHX:TOL=5428],plexippus veles[&&NHX:TOL=5429],plexippus wallacei[&&NHX:TOL=5430])plexippus[&&NHX:TOL=3082],telamonia[&&NHX:TOL=3083],thyene[&&NHX:TOL=3084],yaginumella[&&NHX:TOL=3085])plexippinae[&&NHX:TOL=2847],(((((((habronattus tuberculatus[&&NHX:TOL=3928],((habronattus bulbipes[&&NHX:TOL=3931],(habronattus waughi[&&NHX:TOL=3933],habronattus americanus[&&NHX:TOL=3934])[&&NHX:TOL=3932],habronattus sansoni[&&NHX:TOL=3935])[&&NHX:TOL=3930],(habronattus ophrys[&&NHX:TOL=3937],(habronattus kawini[&&NHX:TOL=3939],(habronattus mustaciata[&&NHX:TOL=3941],habronattus tarsalis[&&NHX:TOL=3942])[&&NHX:TOL=3940],habronattus gigas[&&NHX:TOL=3943])[&&NHX:TOL=3938])[&&NHX:TOL=3936])[&&NHX:TOL=3929])habronattus americanus group[&&NHX:TOL=3998],(habronattus moratus[&&NHX:TOL=4000],(habronattus captiosus[&&NHX:TOL=3945],habronattus ciboneyanus[&&NHX:TOL=3946],(habronattus cuspidatus[&&NHX:TOL=3948],habronattus coecatus[&&NHX:TOL=3949])[&&NHX:TOL=3947],habronattus borealis[&&NHX:TOL=3950],habronattus abditus[&&NHX:TOL=3951],(habronattus virgulatus[&&NHX:TOL=3953],habronattus zebranus[&&NHX:TOL=3954])[&&NHX:TOL=3952],habronattus brunneus[&&NHX:TOL=3955],(((habronattus mexicanus[&&NHX:TOL=3959],habronattus anepsius[&&NHX:TOL=3960],(habronattus pyrrithrix[&&NHX:TOL=3962],habronattus carpus[&&NHX:TOL=3963])[&&NHX:TOL=3961])[&&NHX:TOL=3958],(habronattus festus[&&NHX:TOL=3965],habronattus klauserii[&&NHX:TOL=3966])[&&NHX:TOL=3964])[&&NHX:TOL=3957],habronattus encantadas[&&NHX:TOL=3967],habronattus ammophilus[&&NHX:TOL=3968],(habronattus tlaxcalanus[&&NHX:TOL=3970],habronattus schlingeri[&&NHX:TOL=3971],habronattus ballatoris[&&NHX:TOL=3972])[&&NHX:TOL=3969])[&&NHX:TOL=3956])habronattus coecatus group[&&NHX:TOL=4001],((((habronattus velivolus[&&NHX:TOL=3976],habronattus forticulus[&&NHX:TOL=3977])[&&NHX:TOL=3975],((habronattus notialis[&&NHX:TOL=3980],habronattus viridipes[&&NHX:TOL=3981])[&&NHX:TOL=3979],(habronattus calcaratus calcaratus[&&NHX:TOL=65333],habronattus calcaratus maddisoni[&&NHX:TOL=65334],habronattus calcaratus agricola[&&NHX:TOL=65335])habronattus calcaratus[&&NHX:TOL=3982],habronattus jucundus[&&NHX:TOL=3983])[&&NHX:TOL=3978],habronattus dossenus[&&NHX:TOL=3984])[&&NHX:TOL=3974],(habronattus aztecanus[&&NHX:TOL=3986],((habronattus californicus[&&NHX:TOL=3989],habronattus divaricatus[&&NHX:TOL=3990])[&&NHX:TOL=3988],(habronattus formosus[&&NHX:TOL=3992],habronattus clypeatus[&&NHX:TOL=3993])[&&NHX:TOL=3991])[&&NHX:TOL=3987])[&&NHX:TOL=3985])habronattus viridipes group[&&NHX:TOL=4003],habronattus orbus[&&NHX:TOL=4004],habronattus trimaculatus[&&NHX:TOL=4005])[&&NHX:TOL=4002])[&&NHX:TOL=3999])[&&NHX:TOL=3997],(habronattus decorus[&&NHX:TOL=4007],habronattus cockerelli[&&NHX:TOL=4008],(habronattus banksi[&&NHX:TOL=4010],habronattus nahuatlanus[&&NHX:TOL=4011],habronattus sugillatus[&&NHX:TOL=4012])[&&NHX:TOL=4009])habronattus decorus group[&&NHX:TOL=4006],((habronattus pretiosus[&&NHX:TOL=4020],(habronattus zapotecanus[&&NHX:TOL=4022],habronattus pochtecanus[&&NHX:TOL=4023])[&&NHX:TOL=4021])[&&NHX:TOL=4019],(((habronattus texanus[&&NHX:TOL=4027],habronattus altanus[&&NHX:TOL=4028])[&&NHX:TOL=4026],(habronattus delectus[&&NHX:TOL=4046],habronattus icenoglei[&&NHX:TOL=4033])[&&NHX:TOL=22055],habronattus renidens[&&NHX:TOL=4030],(habronattus fallax[&&NHX:TOL=4031],habronattus cambridgei[&&NHX:TOL=4045])[&&NHX:TOL=22056],habronattus hallani[&&NHX:TOL=4032],habronattus pugillis[&&NHX:TOL=4034],((habronattus ocala[&&NHX:TOL=4037],habronattus nesiotus[&&NHX:TOL=4038])[&&NHX:TOL=4036],(habronattus carolinensis[&&NHX:TOL=4040],habronattus venatoris[&&NHX:TOL=4041])[&&NHX:TOL=4039])[&&NHX:TOL=4035],habronattus iviei[&&NHX:TOL=4029])[&&NHX:TOL=4025],habronattus tarascanus[&&NHX:TOL=4042],[&&NHX:TOL=4043],habronattus oregonensis[&&NHX:TOL=4044])[&&NHX:TOL=4024])[&&NHX:TOL=4018])[&&NHX:TOL=3996],(habronattus dorotheae[&&NHX:TOL=4014],(habronattus huastecanus[&&NHX:TOL=4016],habronattus geronimoi[&&NHX:TOL=4017])[&&NHX:TOL=4015])habronattus dorotheae group[&&NHX:TOL=4013])[&&NHX:TOL=22054],habronattus paratus[&&NHX:TOL=3995])[&&NHX:TOL=22053],(((habronattus tranquillus[&&NHX:TOL=4055],habronattus hirsutus[&&NHX:TOL=4056])habronattus tranquillus group[&&NHX:TOL=4054],(habronattus signatus[&&NHX:TOL=4050],(habronattus ustulatus[&&NHX:TOL=4052],habronattus amicus[&&NHX:TOL=4053])[&&NHX:TOL=4051])habronattus amicus group[&&NHX:TOL=4049])[&&NHX:TOL=22057],(habronattus contingens[&&NHX:TOL=3915],(habronattus conjunctus[&&NHX:TOL=3917],(habronattus agilis[&&NHX:TOL=3919],habronattus georgiensis[&&NHX:TOL=3920],habronattus elegans[&&NHX:TOL=3921],habronattus peckhami[&&NHX:TOL=3922],(habronattus cognatus[&&NHX:TOL=3924],habronattus mataxus[&&NHX:TOL=3925])[&&NHX:TOL=3923],habronattus alachua[&&NHX:TOL=3926])[&&NHX:TOL=3918])[&&NHX:TOL=3916])habronattus agilis group[&&NHX:TOL=4047])[&&NHX:TOL=4048])habronattus[&&NHX:TOL=3069],neaetha[&&NHX:TOL=3070],(pellenes aethiopicus[&&NHX:TOL=5097],pellenes allegri[&&NHX:TOL=5098],pellenes apacheus[&&NHX:TOL=5099],pellenes arcigerus[&&NHX:TOL=5100],pellenes beani[&&NHX:TOL=5101],pellenes brevis[&&NHX:TOL=5102],pellenes campylophorus[&&NHX:TOL=5103],pellenes canosus[&&NHX:TOL=5104],pellenes cinctipes[&&NHX:TOL=5105],pellenes corticolens[&&NHX:TOL=5106],pellenes crandalli[&&NHX:TOL=5107],pellenes dahli[&&NHX:TOL=5108],pellenes denisi[&&NHX:TOL=5109],pellenes dorsalis[&&NHX:TOL=5110],pellenes dubitatus[&&NHX:TOL=5111],pellenes durieui[&&NHX:TOL=5112],pellenes dyali[&&NHX:TOL=5113],pellenes epularis[&&NHX:TOL=5114],pellenes flavipalpis[&&NHX:TOL=5115],pellenes frischii[&&NHX:TOL=5116],pellenes geniculatus[&&NHX:TOL=5117],pellenes gobiensis[&&NHX:TOL=5118],pellenes grammaticus[&&NHX:TOL=5119],pellenes hadaensis[&&NHX:TOL=5120],pellenes hedjazensis[&&NHX:TOL=5121],pellenes iforhasorum[&&NHX:TOL=5122],pellenes ignifrons[&&NHX:TOL=5123],pellenes inexcultus[&&NHX:TOL=5124],pellenes kulabicus[&&NHX:TOL=5125],pellenes lapponicus[&&NHX:TOL=5126],pellenes levaillanti[&&NHX:TOL=5127],pellenes levii[&&NHX:TOL=5128],pellenes limatus[&&NHX:TOL=5129],pellenes limbatus[&&NHX:TOL=5130],pellenes longimanus[&&NHX:TOL=5131],pellenes luteus[&&NHX:TOL=5132],pellenes maderianus[&&NHX:TOL=5133],pellenes mimicus[&&NHX:TOL=5134],pellenes minimus[&&NHX:TOL=5135],pellenes nigrociliatus[&&NHX:TOL=5136],pellenes obliquostriatus[&&NHX:TOL=5137],pellenes ostrinus[&&NHX:TOL=5138],pellenes peninsularis[&&NHX:TOL=5139],pellenes peregrinus[&&NHX:TOL=5140],pellenes perexcultus[&&NHX:TOL=5141],pellenes placidus[&&NHX:TOL=5142],pellenes purcelli[&&NHX:TOL=5143],pellenes ravoisiaei[&&NHX:TOL=5144],pellenes rufoclypeatus[&&NHX:TOL=5145],pellenes seriatus[&&NHX:TOL=5146],pellenes shoshonensis[&&NHX:TOL=5147],pellenes simoni[&&NHX:TOL=5148],pellenes tocharistanus[&&NHX:TOL=5149],pellenes tripunctatus[&&NHX:TOL=5150],pellenes unipunctus[&&NHX:TOL=5151],pellenes univittatus[&&NHX:TOL=5152],pellenes washonus[&&NHX:TOL=5153],pellenes wrighti[&&NHX:TOL=5154])pellenes[&&NHX:TOL=3071])pelleninae[&&NHX:TOL=2848],(((heliophanus abditus[&&NHX:TOL=4156],heliophanus aberdarensis[&&NHX:TOL=4157],heliophanus activus[&&NHX:TOL=4158],heliophanus acutissimus[&&NHX:TOL=4159],heliophanus aeneus[&&NHX:TOL=4160],heliophanus africanus[&&NHX:TOL=4161],heliophanus agricola[&&NHX:TOL=4162],heliophanus agricoloides[&&NHX:TOL=4163],heliophanus alienus[&&NHX:TOL=4164],heliophanus anomalus[&&NHX:TOL=4165],heliophanus apiatus[&&NHX:TOL=4166],heliophanus auratus[&&NHX:TOL=4167],heliophanus aviculus[&&NHX:TOL=4168],heliophanus baikalensis[&&NHX:TOL=4169],heliophanus bellus[&&NHX:TOL=4170],heliophanus berlandi[&&NHX:TOL=4171],heliophanus bisulcus[&&NHX:TOL=4172],heliophanus butemboensis[&&NHX:TOL=4173],heliophanus camtschadalicus[&&NHX:TOL=4174],heliophanus canariensis[&&NHX:TOL=4175],heliophanus capensis[&&NHX:TOL=4176],heliophanus capicola[&&NHX:TOL=4177],heliophanus cassinicola[&&NHX:TOL=4178],heliophanus chicangawanus[&&NHX:TOL=4179],heliophanus chovdensis[&&NHX:TOL=4180],heliophanus clarus[&&NHX:TOL=4181],heliophanus claviger[&&NHX:TOL=4182],heliophanus cognatus[&&NHX:TOL=4183],heliophanus congolensis[&&NHX:TOL=4184],heliophanus conspicuus[&&NHX:TOL=4185],heliophanus creticus[&&NHX:TOL=4186],heliophanus crudeni[&&NHX:TOL=4187],heliophanus cupreus[&&NHX:TOL=4188],heliophanus curvidens[&&NHX:TOL=4189],heliophanus dampfi[&&NHX:TOL=4190],heliophanus deamatus[&&NHX:TOL=4191],heliophanus debilis[&&NHX:TOL=4192],heliophanus decempunctatus[&&NHX:TOL=4193],heliophanus decoratus[&&NHX:TOL=4194],heliophanus deformis[&&NHX:TOL=4195],heliophanus demonstrativus[&&NHX:TOL=4196],heliophanus deserticola[&&NHX:TOL=4197],heliophanus didieri[&&NHX:TOL=4198],heliophanus difficilis[&&NHX:TOL=4199],heliophanus dilutus[&&NHX:TOL=4200],heliophanus dubius[&&NHX:TOL=4201],heliophanus dubourgi[&&NHX:TOL=4202],heliophanus dux[&&NHX:TOL=4203],heliophanus edentulus[&&NHX:TOL=4204],heliophanus encifer[&&NHX:TOL=4205],heliophanus equester[&&NHX:TOL=4206],heliophanus erythropleurus[&&NHX:TOL=4207],heliophanus eucharis[&&NHX:TOL=4208],heliophanus extinctus[&&NHX:TOL=4209],heliophanus falcatus[&&NHX:TOL=4210],heliophanus fascinatus[&&NHX:TOL=4211],heliophanus filiolus[&&NHX:TOL=4212],heliophanus flavimaxillis[&&NHX:TOL=4213],heliophanus flavipes[&&NHX:TOL=4214],heliophanus flavocinctus[&&NHX:TOL=4215],heliophanus forcipifer[&&NHX:TOL=4216],heliophanus furcillatus[&&NHX:TOL=4217],heliophanus giltayi[&&NHX:TOL=4218],heliophanus gladiator[&&NHX:TOL=4219],heliophanus glaucus[&&NHX:TOL=4220],heliophanus gloriosus[&&NHX:TOL=4221],heliophanus hamifer[&&NHX:TOL=4222],heliophanus harpago[&&NHX:TOL=4223],heliophanus hastatus[&&NHX:TOL=4224],heliophanus horrifer[&&NHX:TOL=4225],heliophanus ibericus[&&NHX:TOL=4226],heliophanus ignorabilis[&&NHX:TOL=4227],heliophanus imerinensis[&&NHX:TOL=4228],heliophanus imperator[&&NHX:TOL=4229],heliophanus improcerus[&&NHX:TOL=4230],heliophanus innominatus[&&NHX:TOL=4231],heliophanus inornatus[&&NHX:TOL=4232],heliophanus insperatus[&&NHX:TOL=4233],heliophanus iranus[&&NHX:TOL=4234],heliophanus japonicus[&&NHX:TOL=4235],heliophanus kankanensis[&&NHX:TOL=4236],heliophanus kashmiricus[&&NHX:TOL=4237],heliophanus kenyaensis[&&NHX:TOL=4238],heliophanus kilimanjaroensis[&&NHX:TOL=4239],heliophanus kochi[&&NHX:TOL=4240],heliophanus lawrencei[&&NHX:TOL=4241],heliophanus lesserti[&&NHX:TOL=4242],heliophanus lineiventris[&&NHX:TOL=4243],heliophanus macentensis[&&NHX:TOL=4244],heliophanus machaerodus[&&NHX:TOL=4245],heliophanus maculatus[&&NHX:TOL=4246],heliophanus malus[&&NHX:TOL=4247],heliophanus maestus[&&NHX:TOL=4248],heliophanus marshalli[&&NHX:TOL=4249],heliophanus mauricianus[&&NHX:TOL=4250],heliophanus melinus[&&NHX:TOL=4251],heliophanus menemeriformis[&&NHX:TOL=4252],heliophanus micans[&&NHX:TOL=4253],heliophanus minutissimus[&&NHX:TOL=4254],heliophanus mirabilis[&&NHX:TOL=4255],heliophanus modicus[&&NHX:TOL=4256],heliophanus moestus[&&NHX:TOL=4257],heliophanus mongolicus[&&NHX:TOL=4258],heliophanus mordax[&&NHX:TOL=4259],heliophanus mucronatus[&&NHX:TOL=4260],heliophanus nitens[&&NHX:TOL=4261],heliophanus nitidus[&&NHX:TOL=4262],heliophanus niveivestis[&&NHX:TOL=4263],heliophanus nivosus[&&NHX:TOL=4264],heliophanus nobilis[&&NHX:TOL=4265],heliophanus nossibeensis[&&NHX:TOL=4266],heliophanus ochrichelis[&&NHX:TOL=4267],heliophanus okinawensis[&&NHX:TOL=4268],heliophanus orchesta[&&NHX:TOL=4269],heliophanus orchestioides[&&NHX:TOL=4270],heliophanus parvus[&&NHX:TOL=4271],heliophanus patagiatus[&&NHX:TOL=4272],heliophanus patellaris[&&NHX:TOL=4273],heliophanus paulus[&&NHX:TOL=4274],heliophanus pauper[&&NHX:TOL=4275],heliophanus peckhami[&&NHX:TOL=4276],heliophanus portentosus[&&NHX:TOL=4277],heliophanus potanini[&&NHX:TOL=4278],heliophanus pratti[&&NHX:TOL=4279],heliophanus pulverulentus[&&NHX:TOL=4280],heliophanus ramosus[&&NHX:TOL=4281],heliophanus recurvus[&&NHX:TOL=4282],heliophanus redimitus[&&NHX:TOL=4283],heliophanus riedeli[&&NHX:TOL=4284],heliophanus robustus[&&NHX:TOL=4285],heliophanus rufithorax[&&NHX:TOL=4286],heliophanus saudis[&&NHX:TOL=4287],heliophanus semirasus[&&NHX:TOL=4288],heliophanus simplex[&&NHX:TOL=4289],heliophanus soudanicus[&&NHX:TOL=4290],heliophanus stylifer[&&NHX:TOL=4291],heliophanus tessalensis[&&NHX:TOL=4292],heliophanus transvaalicus[&&NHX:TOL=4293],heliophanus trepidus[&&NHX:TOL=4294],heliophanus tribulosus[&&NHX:TOL=4295],heliophanus tricinctus[&&NHX:TOL=4296],heliophanus turanicus[&&NHX:TOL=4297],heliophanus uncinatus[&&NHX:TOL=4298],heliophanus undecimmaculatus[&&NHX:TOL=4299],heliophanus ussuricus[&&NHX:TOL=4300],heliophanus uvirensis[&&NHX:TOL=4301],heliophanus validus[&&NHX:TOL=4302],heliophanus verus[&&NHX:TOL=4303],heliophanus villosus[&&NHX:TOL=4304],heliophanus viridimanus[&&NHX:TOL=4305],heliophanus vittatus[&&NHX:TOL=4306])heliophanus[&&NHX:TOL=2982],(icius abnormis[&&NHX:TOL=4376],icius afolius[&&NHX:TOL=4377],icius angustatus[&&NHX:TOL=4378],icius boryi[&&NHX:TOL=4379],icius brunelli[&&NHX:TOL=4380],icius cervinus[&&NHX:TOL=4381],icius congener[&&NHX:TOL=4382],icius crassipes[&&NHX:TOL=4383],icius daisetsuzanus[&&NHX:TOL=4384],icius delectus[&&NHX:TOL=4385],icius dendryphantoides[&&NHX:TOL=4386],icius desertorum[&&NHX:TOL=4387],icius discatus[&&NHX:TOL=4388],icius erraticus[&&NHX:TOL=4389],icius eximius[&&NHX:TOL=4390],icius foliosus[&&NHX:TOL=4391],icius guyoni[&&NHX:TOL=4392],icius hamatus[&&NHX:TOL=4393],icius ildefonsus[&&NHX:TOL=4394],icius inhonestus[&&NHX:TOL=4395],icius miniamus[&&NHX:TOL=4396],icius niger[&&NHX:TOL=4397],icius ocellatus[&&NHX:TOL=4398],icius pallidulus[&&NHX:TOL=4399],icius pseudocellatus[&&NHX:TOL=4400],icius separatus[&&NHX:TOL=4401],icius striatus[&&NHX:TOL=4402],icius subinermis[&&NHX:TOL=4403],icius testaceolineatus[&&NHX:TOL=4404])icius[&&NHX:TOL=2983],((pseudicius afghanicus[&&NHX:TOL=5465],pseudicius africanus[&&NHX:TOL=5466],pseudicius andamanius[&&NHX:TOL=5467],pseudicius arabicus[&&NHX:TOL=5468],pseudicius asoroticus[&&NHX:TOL=5469],pseudicius badius[&&NHX:TOL=5470],pseudicius bamakoi[&&NHX:TOL=5471],pseudicius bipunctatus[&&NHX:TOL=5472],pseudicius braunsi[&&NHX:TOL=5473],pseudicius cambridgei[&&NHX:TOL=5474],pseudicius cinctus[&&NHX:TOL=5475],pseudicius cognatus[&&NHX:TOL=5476],pseudicius courtauldi[&&NHX:TOL=5477],pseudicius courti[&&NHX:TOL=5478],pseudicius cultrifer[&&NHX:TOL=5479],pseudicius daitaricus[&&NHX:TOL=5480],pseudicius decemnotatus[&&NHX:TOL=5481],pseudicius delesserti[&&NHX:TOL=5482],pseudicius deletus[&&NHX:TOL=5483],pseudicius elmenteitae[&&NHX:TOL=5484],pseudicius encarpatus[&&NHX:TOL=5485],pseudicius epiblemmoides[&&NHX:TOL=5486],pseudicius espereyi[&&NHX:TOL=5487],pseudicius flavipes[&&NHX:TOL=5488],pseudicius frigidus[&&NHX:TOL=5489],pseudicius ghesquierei[&&NHX:TOL=5490],pseudicius grayorum[&&NHX:TOL=5491],pseudicius himeshimensis[&&NHX:TOL=5492],pseudicius histrionicus[&&NHX:TOL=5493],pseudicius huntorum[&&NHX:TOL=5494],pseudicius kaszabi[&&NHX:TOL=5495],pseudicius koreanus[&&NHX:TOL=5496],pseudicius kulczynskii[&&NHX:TOL=5497],pseudicius ludhianaensis[&&NHX:TOL=5498],pseudicius manillaensis[&&NHX:TOL=5499],pseudicius maureri[&&NHX:TOL=5500],pseudicius marshi[&&NHX:TOL=5501],pseudicius modestus[&&NHX:TOL=5502],pseudicius musculus[&&NHX:TOL=5503],pseudicius nepalicus[&&NHX:TOL=5504],pseudicius nuclearis[&&NHX:TOL=5505],pseudicius okinawaensis[&&NHX:TOL=5506],pseudicius originalis[&&NHX:TOL=5507],pseudicius palaestinensis[&&NHX:TOL=5508],pseudicius picaceus[&&NHX:TOL=5509],pseudicius philippinensis[&&NHX:TOL=5510],pseudicius punctatus[&&NHX:TOL=5511],pseudicius pseudicioides[&&NHX:TOL=5512],pseudicius reiskindi[&&NHX:TOL=5513],pseudicius risbeci[&&NHX:TOL=5514],pseudicius rudakii[&&NHX:TOL=5515],pseudicius samoaensis[&&NHX:TOL=5516],pseudicius seychellensis[&&NHX:TOL=5517],pseudicius sheherezadae[&&NHX:TOL=5518],pseudicius shirinae[&&NHX:TOL=5519],pseudicius similis[&&NHX:TOL=5520],pseudicius sindbadi[&&NHX:TOL=5521],pseudicius solomonensis[&&NHX:TOL=5522],pseudicius spasskyi[&&NHX:TOL=5523],pseudicius spiniger[&&NHX:TOL=5524],pseudicius stridulator[&&NHX:TOL=5525],pseudicius tamaricis[&&NHX:TOL=5526],pseudicius tokaraensis[&&NHX:TOL=5527],pseudicius tripunctatus[&&NHX:TOL=5528],pseudicius unicus[&&NHX:TOL=5529],pseudicius vesporum[&&NHX:TOL=5530],pseudicius vestjensi[&&NHX:TOL=5531],pseudicius vulpes[&&NHX:TOL=5532],pseudicius wadis[&&NHX:TOL=5533],pseudicius yeni[&&NHX:TOL=5534],pseudicius zebra[&&NHX:TOL=5535])old world[&&NHX:TOL=5464],(pseudicius oblongus[&&NHX:TOL=5537],pseudicius siticulosus[&&NHX:TOL=5538])new world[&&NHX:TOL=5536])pseudicius[&&NHX:TOL=2984],festucula[&&NHX:TOL=2985],marchena minuta[&&NHX:TOL=2986],(helvetia albovittata[&&NHX:TOL=4308],helvetia cancrimana[&&NHX:TOL=4309],helvetia insularis[&&NHX:TOL=4310],helvetia riojanensis[&&NHX:TOL=4311],helvetia santaremica[&&NHX:TOL=4312],helvetia zebrina[&&NHX:TOL=4313],helvetia zonata[&&NHX:TOL=4314])helvetia[&&NHX:TOL=2987],(yepoella crassistyli[&&NHX:TOL=24827],yepoella tenuistyli[&&NHX:TOL=24828])yepoella[&&NHX:TOL=2988],(phintella abnormis[&&NHX:TOL=5287],phintella accentifera[&&NHX:TOL=5288],phintella aequipeiformis[&&NHX:TOL=5289],phintella aequipes[&&NHX:TOL=5290],phintella arenicolor[&&NHX:TOL=5291],phintella argenteola[&&NHX:TOL=5292],phintella assamica[&&NHX:TOL=5293],phintella bifurcata[&&NHX:TOL=5294],phintella bifurcilinea[&&NHX:TOL=5295],phintella castriesiana[&&NHX:TOL=5296],phintella cavaleriei[&&NHX:TOL=5297],phintella clathrata[&&NHX:TOL=5298],phintella coonooriensis[&&NHX:TOL=5299],phintella debilis[&&NHX:TOL=5300],phintella dives[&&NHX:TOL=5301],phintella hainani[&&NHX:TOL=5302],phintella indica[&&NHX:TOL=5303],phintella leucaspis[&&NHX:TOL=5304],phintella linea[&&NHX:TOL=5305],phintella lucai[&&NHX:TOL=5306],phintella macrops[&&NHX:TOL=5307],phintella melloteei[&&NHX:TOL=5308],phintella multimaculata[&&NHX:TOL=5309],phintella mussooriensis[&&NHX:TOL=5310],phintella nilgirica[&&NHX:TOL=5311],phintella parva[&&NHX:TOL=5312],phintella popovi[&&NHX:TOL=5313],phintella reinhardti[&&NHX:TOL=5314],phintella suavis[&&NHX:TOL=5315],phintella suknana[&&NHX:TOL=5316],phintella tibialis[&&NHX:TOL=5317],phintella versicolor[&&NHX:TOL=5318],phintella vittata[&&NHX:TOL=5319],phintella volupe[&&NHX:TOL=5320])phintella[&&NHX:TOL=2989])heliophaninae[&&NHX:TOL=2850],(salticus albipalpis[&&NHX:TOL=5596],salticus albobarbatus[&&NHX:TOL=5597],salticus albovittatus[&&NHX:TOL=5598],salticus alpinus[&&NHX:TOL=5599],salticus ambiguus[&&NHX:TOL=5600],salticus apressus[&&NHX:TOL=5601],salticus arenarius[&&NHX:TOL=5602],salticus atratus[&&NHX:TOL=5603],salticus attenuatus[&&NHX:TOL=5604],salticus aubryi[&&NHX:TOL=5605],salticus austinensis[&&NHX:TOL=5606],salticus berbruggeri[&&NHX:TOL=5607],salticus biguttatus[&&NHX:TOL=5608],salticus bonaeriensis[&&NHX:TOL=5609],salticus brasiliensis[&&NHX:TOL=5610],salticus canariensis[&&NHX:TOL=5611],salticus candidus[&&NHX:TOL=5612],salticus cephalicus[&&NHX:TOL=5613],salticus cingulatus[&&NHX:TOL=5614],salticus confusus[&&NHX:TOL=5615],salticus conjunctus[&&NHX:TOL=5616],salticus curvus[&&NHX:TOL=5617],salticus dzhungaricus[&&NHX:TOL=5618],salticus exilis[&&NHX:TOL=5619],salticus festivus[&&NHX:TOL=5620],salticus flavicruris[&&NHX:TOL=5621],salticus flavipalpis[&&NHX:TOL=5622],salticus fulvounilineatus[&&NHX:TOL=5623],salticus fumosus[&&NHX:TOL=5624],salticus furvus[&&NHX:TOL=5625],salticus gomerensis[&&NHX:TOL=5626],salticus gracilis[&&NHX:TOL=5627],salticus guerini[&&NHX:TOL=5628],salticus guichenoti[&&NHX:TOL=5629],salticus jenynsi[&&NHX:TOL=5630],salticus koreanus[&&NHX:TOL=5631],salticus latidentatus[&&NHX:TOL=5632],salticus lilliputanus[&&NHX:TOL=5633],salticus limbatus[&&NHX:TOL=5634],salticus major[&&NHX:TOL=5635],salticus mandibularis[&&NHX:TOL=5636],salticus marenzelleri[&&NHX:TOL=5637],salticus meticulosus[&&NHX:TOL=5638],salticus minax[&&NHX:TOL=5639],salticus modicus[&&NHX:TOL=5640],salticus mustillinus[&&NHX:TOL=5641],salticus mutabilis[&&NHX:TOL=5642],salticus myrmecinus[&&NHX:TOL=5643],salticus myrmecoides[&&NHX:TOL=5644],salticus nigrifrons[&&NHX:TOL=5645],salticus notatus[&&NHX:TOL=5646],salticus olivaceus[&&NHX:TOL=5647],salticus oranensis[&&NHX:TOL=5648],salticus oseryi[&&NHX:TOL=5649],salticus palpalis[&&NHX:TOL=5650],salticus paludivagus[&&NHX:TOL=5651],salticus peckhamae[&&NHX:TOL=5652],salticus placidus[&&NHX:TOL=5653],salticus potanini[&&NHX:TOL=5654],salticus propinquus[&&NHX:TOL=5655],salticus proruptus[&&NHX:TOL=5656],salticus prosper[&&NHX:TOL=5657],salticus proszynskii[&&NHX:TOL=5658],salticus ravus[&&NHX:TOL=5659],salticus rufifrons[&&NHX:TOL=5660],salticus rufolineatus[&&NHX:TOL=5661],salticus quagga[&&NHX:TOL=5662],salticus scenicus[&&NHX:TOL=5663],salticus scitulus[&&NHX:TOL=5664],salticus sedulus[&&NHX:TOL=5665],salticus splendens[&&NHX:TOL=5666],salticus tabinus[&&NHX:TOL=5667],salticus tenebricus[&&NHX:TOL=5668],salticus testaceolineatus[&&NHX:TOL=5669],salticus tricinctus[&&NHX:TOL=5670],salticus trunctatus[&&NHX:TOL=5671],salticus unciger[&&NHX:TOL=5672],salticus unicolor[&&NHX:TOL=5673],salticus unispina[&&NHX:TOL=5674],salticus vnotatus[&&NHX:TOL=5675],salticus xantofrontalis[&&NHX:TOL=5676],salticus zebraneus[&&NHX:TOL=5677])salticus[&&NHX:TOL=2851])[&&NHX:TOL=2849],(((hasarius adansoni[&&NHX:TOL=4117],hasarius albocircumdatus[&&NHX:TOL=4118],hasarius arciger[&&NHX:TOL=4119],hasarius bellicosus[&&NHX:TOL=4120],hasarius berlandi[&&NHX:TOL=4121],hasarius biprocessiger[&&NHX:TOL=4122],hasarius coelestis[&&NHX:TOL=4123],hasarius egaenus[&&NHX:TOL=4124],hasarius elisabethae[&&NHX:TOL=4125],hasarius glaucus[&&NHX:TOL=4126],hasarius inhebes[&&NHX:TOL=4127],hasarius inhonestus[&&NHX:TOL=4128],hasarius insignis[&&NHX:TOL=4129],hasarius kjellerupi[&&NHX:TOL=4130],hasarius kulczynskii[&&NHX:TOL=4131],hasarius lisei[&&NHX:TOL=4132],hasarius mahensis[&&NHX:TOL=4133],hasarius mccooki[&&NHX:TOL=4134],hasarius mulciber[&&NHX:TOL=4135],hasarius neocaledonicus[&&NHX:TOL=4136],hasarius obscurus[&&NHX:TOL=4137],hasarius pauciaculeis[&&NHX:TOL=4138],hasarius peckhami[&&NHX:TOL=4139],hasarius roeweri[&&NHX:TOL=4140],hasarius rufociliatus[&&NHX:TOL=4141],hasarius rusticus[&&NHX:TOL=4142],hasarius scylax[&&NHX:TOL=4143],hasarius sobarus[&&NHX:TOL=4144],hasarius sulfuratus[&&NHX:TOL=4145],hasarius testaceus[&&NHX:TOL=4146],hasarius trivialis[&&NHX:TOL=4147],hasarius validus[&&NHX:TOL=4148],hasarius varicans[&&NHX:TOL=4149],hasarius villosus[&&NHX:TOL=4150],hasarius vittatus[&&NHX:TOL=4151],hasarius workmani[&&NHX:TOL=4152],hasarius xanthopus[&&NHX:TOL=4153])hasarius[&&NHX:TOL=3017],((marpissa agricola[&&NHX:TOL=4556],marpissa anusuae[&&NHX:TOL=4557],marpissa arenaria[&&NHX:TOL=4558],marpissa armifera[&&NHX:TOL=4559],marpissa bina[&&NHX:TOL=4560],marpissa broadwayi[&&NHX:TOL=4561],marpissa bryantae[&&NHX:TOL=4562],marpissa canestrini[&&NHX:TOL=4563],marpissa capensis[&&NHX:TOL=4564],marpissa cineracca[&&NHX:TOL=4565],marpissa civilis[&&NHX:TOL=4566],marpissa decorata[&&NHX:TOL=4567],marpissa dentoides[&&NHX:TOL=4568],marpissa dybowskii[&&NHX:TOL=4569],marpissa elata[&&NHX:TOL=4570],marpissa elongata[&&NHX:TOL=4571],marpissa formosa[&&NHX:TOL=4572],marpissa grata[&&NHX:TOL=4573],marpissa hieroglyphica[&&NHX:TOL=4574],marpissa hiroseae[&&NHX:TOL=4575],marpissa ibarakiensis[&&NHX:TOL=4576],marpissa kalapani[&&NHX:TOL=4577],marpissa leptochira[&&NHX:TOL=4578],marpissa leuocphaea[&&NHX:TOL=4579],marpissa lineata[&&NHX:TOL=4580],marpissa longiuscula[&&NHX:TOL=4581],marpissa magister[&&NHX:TOL=4582],marpissa magna pkm[&&NHX:TOL=4583],marpissa magna kishida[&&NHX:TOL=4584],marpissa marina[&&NHX:TOL=4585],marpissa memorabilis[&&NHX:TOL=4586],marpissa milleri[&&NHX:TOL=4587],marpissa minor[&&NHX:TOL=4588],marpissa muscosa[&&NHX:TOL=4589],marpissa mystacina[&&NHX:TOL=4590],marpissa nanodes[&&NHX:TOL=4591],marpissa nemoralis[&&NHX:TOL=4592],marpissa nivoyi[&&NHX:TOL=4593],marpissa nobilis[&&NHX:TOL=4594],marpissa nutanae[&&NHX:TOL=4595],marpissa obscura[&&NHX:TOL=4596],marpissa obtusa[&&NHX:TOL=4597],marpissa pikei[&&NHX:TOL=4598],marpissa pomatia[&&NHX:TOL=4599],marpissa prathamae[&&NHX:TOL=4600],marpissa pulchra[&&NHX:TOL=4601],marpissa pulla[&&NHX:TOL=4602],marpissa radiata[&&NHX:TOL=4603],marpissa raimondii[&&NHX:TOL=4604],marpissa ridens[&&NHX:TOL=4605],marpissa robusta[&&NHX:TOL=4606],marpissa rubriceps[&&NHX:TOL=4607],marpissa singhi[&&NHX:TOL=4608],marpissa soricina[&&NHX:TOL=4609],marpissa stuhlmanni[&&NHX:TOL=4610],marpissa tikaderi[&&NHX:TOL=4611],marpissa tigrina[&&NHX:TOL=4612],marpissa wallacei[&&NHX:TOL=4613])marpissa[&&NHX:TOL=3019],(menemerus acuminatus[&&NHX:TOL=4620],menemerus albocinctus[&&NHX:TOL=4621],menemerus animatus[&&NHX:TOL=4622],menemerus banksi[&&NHX:TOL=4623],menemerus bicolor[&&NHX:TOL=4624],menemerus bivittatus[&&NHX:TOL=4625],menemerus bracteatus[&&NHX:TOL=4626],menemerus brevibulbus[&&NHX:TOL=4627],menemerus congoensis[&&NHX:TOL=4628],menemerus delus[&&NHX:TOL=4629],menemerus depressus[&&NHX:TOL=4630],menemerus dimidius[&&NHX:TOL=4631],menemerus diversus[&&NHX:TOL=4632],menemerus dubius[&&NHX:TOL=4633],menemerus duvali[&&NHX:TOL=4634],menemerus eburnensis[&&NHX:TOL=4635],menemerus fagei[&&NHX:TOL=4636],menemerus falconensis[&&NHX:TOL=4637],menemerus falsificus[&&NHX:TOL=4638],menemerus fasciculatus[&&NHX:TOL=4639],menemerus felix[&&NHX:TOL=4640],menemerus fraternus[&&NHX:TOL=4641],menemerus fulvus[&&NHX:TOL=4642],menemerus galapagoensis[&&NHX:TOL=4643],menemerus gesneri[&&NHX:TOL=4644],menemerus hottentotus[&&NHX:TOL=4645],menemerus hunteri[&&NHX:TOL=4646],menemerus hypenetes[&&NHX:TOL=4647],menemerus illigeri[&&NHX:TOL=4648],menemerus kochi[&&NHX:TOL=4649],menemerus legalli[&&NHX:TOL=4650],menemerus legendrei[&&NHX:TOL=4651],menemerus lesnei[&&NHX:TOL=4652],menemerus lesserti[&&NHX:TOL=4653],menemerus marginatus[&&NHX:TOL=4654],menemerus milloti[&&NHX:TOL=4655],menemerus niger[&&NHX:TOL=4656],menemerus ochraceus[&&NHX:TOL=4657],menemerus paradoxus[&&NHX:TOL=4658],menemerus plenus[&&NHX:TOL=4659],menemerus proximus[&&NHX:TOL=4660],menemerus raji[&&NHX:TOL=4661],menemerus rabudi[&&NHX:TOL=4662],menemerus rubicundus[&&NHX:TOL=4663],menemerus schutzae[&&NHX:TOL=4664],menemerus semilimbatus[&&NHX:TOL=4665],menemerus soldanii[&&NHX:TOL=4666],menemerus taeniatus[&&NHX:TOL=4667],menemerus vernei[&&NHX:TOL=4668],menemerus vittatus[&&NHX:TOL=4669],menemerus wuchangensis[&&NHX:TOL=4670],menemerus yunnanensis[&&NHX:TOL=4671])menemerus[&&NHX:TOL=3020])[&&NHX:TOL=3018])world wide[&&NHX:TOL=3016],((ligurra latidens[&&NHX:TOL=3023],(trite albopilosa[&&NHX:TOL=5926],trite auricoma[&&NHX:TOL=5927],trite bimaculosa[&&NHX:TOL=5928],trite concinna[&&NHX:TOL=5929],trite daemeli[&&NHX:TOL=5930],trite gracilipalipis[&&NHX:TOL=5931],trite herbigrada[&&NHX:TOL=5932],trite ignipilosa[&&NHX:TOL=5933],trite lineata[&&NHX:TOL=5934],trite longipalpis[&&NHX:TOL=5935],trite longula[&&NHX:TOL=5936],trite ornata[&&NHX:TOL=5937],trite pennata[&&NHX:TOL=5938],trite planiceps[&&NHX:TOL=5939],trite rapaensis[&&NHX:TOL=5940],trite rubriceps[&&NHX:TOL=5941],trite urvillei[&&NHX:TOL=5942],trite vulpecula[&&NHX:TOL=5943])trite[&&NHX:TOL=3024])old world[&&NHX:TOL=3022],(((((cylistella adjacens[&&NHX:TOL=3490],cylistella castaneaa[&&NHX:TOL=3491],cylistella coccineloides[&&NHX:TOL=3492],cylistella cuprea[&&NHX:TOL=3493],cylistella fulva[&&NHX:TOL=3494],cylistella sanctipauli[&&NHX:TOL=3495],cylistella scarabaeoides[&&NHX:TOL=3496])cylistella[&&NHX:TOL=3029],(hurius aeneus[&&NHX:TOL=4340],hurius petrohue[&&NHX:TOL=4341],hurius pisac[&&NHX:TOL=4342],hurius vulpinus[&&NHX:TOL=4343])hurius[&&NHX:TOL=3030])[&&NHX:TOL=3028],(((maevia inclemens[&&NHX:TOL=4496],maevia intermedia[&&NHX:TOL=4497],maevia expansa[&&NHX:TOL=4498])subgenus maevia[&&NHX:TOL=4495],((maevia hobbsae[&&NHX:TOL=4501],maevia michelsoni[&&NHX:TOL=4502])[&&NHX:TOL=4500],maevia poultoni[&&NHX:TOL=4503])subgenus paramaevia[&&NHX:TOL=4499])north american maevia[&&NHX:TOL=4494],(maevia agapeta[&&NHX:TOL=4505],maevia albizonata[&&NHX:TOL=4506],maevia atricapilla[&&NHX:TOL=4507],maevia auricapilla[&&NHX:TOL=4508],maevia coeruleostriata[&&NHX:TOL=4509],maevia debilis[&&NHX:TOL=4510],maevia gemmans[&&NHX:TOL=4511],maevia gracilipes[&&NHX:TOL=4512],maevia latrunculata[&&NHX:TOL=4513],maevia luteocincta[&&NHX:TOL=4514],maevia luzonica[&&NHX:TOL=4515],maevia margaritacea[&&NHX:TOL=4516],maevia metallica[&&NHX:TOL=4517],maevia micans[&&NHX:TOL=4518],maevia monacha[&&NHX:TOL=4519],maevia nigrifrontis[&&NHX:TOL=4520],maevia nuda[&&NHX:TOL=4521],maevia paula[&&NHX:TOL=4522],maevia pavo[&&NHX:TOL=4523],maevia persecta[&&NHX:TOL=4524],maevia psittacina[&&NHX:TOL=4525],maevia quadrilineata[&&NHX:TOL=4526],maevia rhinoceros[&&NHX:TOL=4527],maevia roseolimbata[&&NHX:TOL=4528],maevia scalaris[&&NHX:TOL=4529],maevia simoni[&&NHX:TOL=4530],maevia susiformis[&&NHX:TOL=4531],maevia trilineata[&&NHX:TOL=4532])other maevia[&&NHX:TOL=4504])maevia[&&NHX:TOL=3031])[&&NHX:TOL=3027],(paramarpissa piratica[&&NHX:TOL=4990],paramarpissa tibialis[&&NHX:TOL=4991])paramarpissa[&&NHX:TOL=3032])[&&NHX:TOL=3026],((balmaceda[&&NHX:TOL=3035],((breda apicalis[&&NHX:TOL=3289],breda bicruciata[&&NHX:TOL=3290],breda bistriata[&&NHX:TOL=3291],breda flavostriata[&&NHX:TOL=3292],breda furcifera[&&NHX:TOL=3293],breda jovialis[&&NHX:TOL=3294],breda leucoprocta[&&NHX:TOL=3295],breda lubomirskii[&&NHX:TOL=3296],breda milvina[&&NHX:TOL=3297],breda nigrotaeniata[&&NHX:TOL=3298],breda notata[&&NHX:TOL=3299],breda oserictops[&&NHX:TOL=3300],breda quinquedentata[&&NHX:TOL=3301],breda spinimana[&&NHX:TOL=3302],breda tristis[&&NHX:TOL=3303],breda variolosa[&&NHX:TOL=3304])breda[&&NHX:TOL=3037],(fuentes[&&NHX:TOL=3039],((metacyrba floridana[&&NHX:TOL=4693],metacyrba insularis[&&NHX:TOL=4694],metacyrba nigrosecta[&&NHX:TOL=4695],metacyrba pictipes[&&NHX:TOL=4696],metacyrba punctata[&&NHX:TOL=4697],metacyrba taeniola[&&NHX:TOL=4698])metacyrba[&&NHX:TOL=3041],(platycryptus californicus[&&NHX:TOL=5368],platycryptus undatus[&&NHX:TOL=5369],platycryptus arizonensis[&&NHX:TOL=5370])platycryptus[&&NHX:TOL=3042])[&&NHX:TOL=3040])[&&NHX:TOL=3038])[&&NHX:TOL=3036])metacyrbalike bark dwellers[&&NHX:TOL=3034],((freya albosignata[&&NHX:TOL=3809],freya ambigua[&&NHX:TOL=3810],freya arraijanica[&&NHX:TOL=3811],freya bicava[&&NHX:TOL=3812],freya bicavata[&&NHX:TOL=3813],freya bifida[&&NHX:TOL=3814],freya bifurcata[&&NHX:TOL=3815],freya chinopogn[&&NHX:TOL=3816],freya decorata[&&NHX:TOL=3817],freya demarcata[&&NHX:TOL=3818],freya disparipes[&&NHX:TOL=3819],freya distincta[&&NHX:TOL=3820],freya dyali[&&NHX:TOL=3821],freya emarginata[&&NHX:TOL=3822],freya exculta[&&NHX:TOL=3823],freya frontalis[&&NHX:TOL=3824],freya grisea[&&NHX:TOL=3825],freya guianensis[&&NHX:TOL=3826],freya infuscata[&&NHX:TOL=3827],freya justina[&&NHX:TOL=3828],freya longispina[&&NHX:TOL=3829],freya maculatipes[&&NHX:TOL=3830],freya minuta[&&NHX:TOL=3831],freya nannispina[&&NHX:TOL=3832],freya perelegans[&&NHX:TOL=3833],freya petrunkevitchi[&&NHX:TOL=3834],freya prominens[&&NHX:TOL=3835],freya regia[&&NHX:TOL=3836],freya rufohirta[&&NHX:TOL=3837],freya rustica[&&NHX:TOL=3838],freya sagittifera[&&NHX:TOL=3839],freya simplicicava[&&NHX:TOL=3840],freya strandi[&&NHX:TOL=3841])freya[&&NHX:TOL=3044],((phiale albovittata[&&NHX:TOL=5194],phiale alicea[&&NHX:TOL=5195],phiale bicuspidata[&&NHX:TOL=5196],phiale bilobata[&&NHX:TOL=5197],phiale bipunctata[&&NHX:TOL=5198],phiale bisignata[&&NHX:TOL=5199],phiale bryante[&&NHX:TOL=5200],phiale bulbosa[&&NHX:TOL=5201],phiale crocea[&&NHX:TOL=5202],phiale cruentata[&&NHX:TOL=5203],phiale cubana[&&NHX:TOL=5204],phiale duplocellata[&&NHX:TOL=5205],phiale dybowskii[&&NHX:TOL=5206],phiale elegans[&&NHX:TOL=5207],phiale flammea[&&NHX:TOL=5208],phiale flavescens[&&NHX:TOL=5209],phiale formosa[&&NHX:TOL=5210],phiale geminata[&&NHX:TOL=5211],phiale gratiosa[&&NHX:TOL=5212],phiale guttata[&&NHX:TOL=5213],phiale hieroglyphica[&&NHX:TOL=5214],phiale huadquinina[&&NHX:TOL=5215],phiale laticava[&&NHX:TOL=5216],phiale lehmanni[&&NHX:TOL=5217],phiale maculosa[&&NHX:TOL=5218],phiale mediocava[&&NHX:TOL=5219],phiale mimica[&&NHX:TOL=5220],phiale ministerialis[&&NHX:TOL=5221],phiale modestissima[&&NHX:TOL=5222],phiale nigrotaeniata[&&NHX:TOL=5223],phiale niveoguttata[&&NHX:TOL=5224],phiale ortrudae[&&NHX:TOL=5225],phiale pallida[&&NHX:TOL=5226],phiale pantherina[&&NHX:TOL=5227],phiale quadrimaculata[&&NHX:TOL=5228],phiale radians[&&NHX:TOL=5229],phiale roburifoliata[&&NHX:TOL=5230],phiale septemguttata[&&NHX:TOL=5231],phiale similis[&&NHX:TOL=5232],phiale simplicicava[&&NHX:TOL=5233],phiale tristis[&&NHX:TOL=5234],phiale virgo[&&NHX:TOL=5235])phiale[&&NHX:TOL=3046],((eustiromastix bahiensis[&&NHX:TOL=3738],eustiromastix chaperi[&&NHX:TOL=3739],eustiromastix efferatus[&&NHX:TOL=3740],eustiromastix falcatus[&&NHX:TOL=3741],eustiromastix guianae[&&NHX:TOL=3742],eustiromastix intermedius[&&NHX:TOL=3743],eustiromastix keyserlingi[&&NHX:TOL=3744],eustiromastix macropalpus[&&NHX:TOL=3745],eustiromastix major[&&NHX:TOL=3746],eustiromastix moraballi[&&NHX:TOL=3747],eustiromastix obscurus[&&NHX:TOL=3748],eustiromastix pusilla[&&NHX:TOL=3749],eustiromastix vincenti[&&NHX:TOL=3750])eustiromastix[&&NHX:TOL=3048],(tullgrenella[&&NHX:TOL=3050],(aphirape[&&NHX:TOL=3052],((nycerella albomaculata[&&NHX:TOL=4975],nycerella aprica[&&NHX:TOL=4976],nycerella decorata[&&NHX:TOL=4977],nycerella delecta[&&NHX:TOL=4978],nycerella donaldi[&&NHX:TOL=4979],nycerella melanopygia[&&NHX:TOL=4980],nycerella neglecta[&&NHX:TOL=4981],nycerella sanguinea[&&NHX:TOL=4982],nycerella volucripes[&&NHX:TOL=4983])nycerella[&&NHX:TOL=3054],((frigga coronigera[&&NHX:TOL=3843],frigga crocuta[&&NHX:TOL=3844],frigga finitima[&&NHX:TOL=3845],frigga flava[&&NHX:TOL=3846],frigga kessleri[&&NHX:TOL=3847],frigga opulenta[&&NHX:TOL=3848],frigga pratensis[&&NHX:TOL=3849],frigga quintensis[&&NHX:TOL=3850],frigga rufa[&&NHX:TOL=3851],frigga simoni[&&NHX:TOL=3852])frigga[&&NHX:TOL=3056],(chira distincta[&&NHX:TOL=3338],chira fagei[&&NHX:TOL=3339],chira flavescens[&&NHX:TOL=3340],chira gounellei[&&NHX:TOL=3341],chira guianensis[&&NHX:TOL=3342],chira lanei[&&NHX:TOL=3343],chira lucina[&&NHX:TOL=3344],chira micans[&&NHX:TOL=3345],chira simoni[&&NHX:TOL=3346],chira spinipes[&&NHX:TOL=3347],chira spinosa[&&NHX:TOL=3348],chira superba[&&NHX:TOL=3349],chira thysbe[&&NHX:TOL=3350],chira trivittata[&&NHX:TOL=3351],chira typica[&&NHX:TOL=3352])chira[&&NHX:TOL=3057])[&&NHX:TOL=3055])[&&NHX:TOL=3053])[&&NHX:TOL=3051])[&&NHX:TOL=3049])[&&NHX:TOL=3047])[&&NHX:TOL=3045])neotropical freyalike[&&NHX:TOL=3043])[&&NHX:TOL=3033])new world[&&NHX:TOL=3025])[&&NHX:TOL=3021])miscellaneous salticids with a fixed embolus[&&NHX:TOL=2852],(((admirala[&&NHX:TOL=2875],agassa cyanea[&&NHX:TOL=2876],anamosa[&&NHX:TOL=2877],anicius dolius[&&NHX:TOL=2878],(ashtabula bicristata[&&NHX:TOL=3192],ashtabula cuprea[&&NHX:TOL=3193],ashtabula dentata[&&NHX:TOL=3194],ashtabula dentichelis[&&NHX:TOL=3195],ashtabula furcillata[&&NHX:TOL=3196],ashtabula glauca[&&NHX:TOL=3197],ashtabula montana[&&NHX:TOL=3198],ashtabula sexguttata[&&NHX:TOL=3199],ashtabula zonura[&&NHX:TOL=3200])ashtabula[&&NHX:TOL=2879],avitus[&&NHX:TOL=2880],(bagheera prosper[&&NHX:TOL=3202],bagheera kiplingi[&&NHX:TOL=3203])bagheera[&&NHX:TOL=2881],((beata magna[&&NHX:TOL=3226],beata hispida[&&NHX:TOL=3227],beata inconcinna[&&NHX:TOL=3228],beata maccunii[&&NHX:TOL=3229],beata rustica[&&NHX:TOL=3230],beata longipes[&&NHX:TOL=3231])beata species[&&NHX:TOL=3225],(beata striata[&&NHX:TOL=3233],beata lineaga[&&NHX:TOL=3234],beata germaini[&&NHX:TOL=3235],beata cinereonitida[&&NHX:TOL=3236])may belong in beata[&&NHX:TOL=3232],(beata wickhami[&&NHX:TOL=3238],beata pernix[&&NHX:TOL=3239],beata munda[&&NHX:TOL=3240],beata jubata[&&NHX:TOL=3241],beata cephalica[&&NHX:TOL=3242],beata venusta[&&NHX:TOL=3243])do not belong in beata[&&NHX:TOL=3237])beata[&&NHX:TOL=2882],(bellota fascialis[&&NHX:TOL=3246],bellota formicina[&&NHX:TOL=3247],bellota fusca[&&NHX:TOL=3248],(bellota livida[&&NHX:TOL=3250],bellota longimanus[&&NHX:TOL=3251])[&&NHX:TOL=3249],bellota micans[&&NHX:TOL=3252],bellota modesta[&&NHX:TOL=3253],bellota peckhami[&&NHX:TOL=3254],bellota violacea[&&NHX:TOL=3255],bellota wheelerii[&&NHX:TOL=3256],bellota yacui[&&NHX:TOL=3257])bellota[&&NHX:TOL=2883],(bryantella smaragdus[&&NHX:TOL=24829],bryantella speciosa[&&NHX:TOL=24830])bryantella[&&NHX:TOL=2884],cerionesta[&&NHX:TOL=2885],(chirothecia amazonica[&&NHX:TOL=3354],chirothecia botucatuensis[&&NHX:TOL=3355],chirothecia clavimana[&&NHX:TOL=3356],chirothecia crassipes[&&NHX:TOL=3357],chirothecia cruciata[&&NHX:TOL=3358],chirothecia daguerrei[&&NHX:TOL=3359],chirothecia euchira[&&NHX:TOL=3360],chirothecia minima[&&NHX:TOL=3361],chirothecia rosea[&&NHX:TOL=3362],chirothecia semiornata[&&NHX:TOL=3363],chirothecia soaresi[&&NHX:TOL=3364],chirothecia uncata[&&NHX:TOL=3365],chirothecia wrzesniowskii[&&NHX:TOL=3366])chirothecia[&&NHX:TOL=2886],(dendryphantes amphibolus[&&NHX:TOL=3504],dendryphantes andinus[&&NHX:TOL=3505],dendryphantes balteatus[&&NHX:TOL=3506],dendryphantes barrosmachadoi[&&NHX:TOL=3507],dendryphantes biankii[&&NHX:TOL=3508],dendryphantes bimaculatus[&&NHX:TOL=3509],dendryphantes bisquinquepunctatus[&&NHX:TOL=3510],dendryphantes calus[&&NHX:TOL=3511],dendryphantes canariensis[&&NHX:TOL=3512],dendryphantes capensis[&&NHX:TOL=3513],dendryphantes caporiaccoi[&&NHX:TOL=3514],dendryphantes carmenensis[&&NHX:TOL=3515],dendryphantes catus[&&NHX:TOL=3516],dendryphantes centromaculatus[&&NHX:TOL=3517],dendryphantes chera[&&NHX:TOL=3518],dendryphantes chuldensis[&&NHX:TOL=3519],dendryphantes coccineocinctus[&&NHX:TOL=3520],dendryphantes comatus[&&NHX:TOL=3521],dendryphantes czekanowskii[&&NHX:TOL=3522],dendryphantes duodecempunctatus[&&NHX:TOL=3523],dendryphantes flavicomis[&&NHX:TOL=3524],dendryphantes foveolatus[&&NHX:TOL=3525],dendryphantes franganilloi[&&NHX:TOL=3526],dendryphantes fulvipes[&&NHX:TOL=3527],dendryphantes fusconotatus[&&NHX:TOL=3528],dendryphantes gertschi[&&NHX:TOL=3529],dendryphantes granti[&&NHX:TOL=3530],dendryphantes hastatus[&&NHX:TOL=3531],dendryphantes hewitti[&&NHX:TOL=3532],dendryphantes honestus[&&NHX:TOL=3533],dendryphantes huberi[&&NHX:TOL=3534],dendryphantes incertus[&&NHX:TOL=3535],dendryphantes insolitus[&&NHX:TOL=3536],dendryphantes lanipes[&&NHX:TOL=3537],dendryphantes lepidus[&&NHX:TOL=3538],dendryphantes madrynensis[&&NHX:TOL=3539],dendryphantes melanomerus[&&NHX:TOL=3540],dendryphantes mendicus[&&NHX:TOL=3541],dendryphantes modestus[&&NHX:TOL=3542],dendryphantes moebi[&&NHX:TOL=3543],dendryphantes mordax[&&NHX:TOL=3544],dendryphantes musae[&&NHX:TOL=3545],dendryphantes nicator[&&NHX:TOL=3546],(dendryphantes nigromaculatus[&&NHX:TOL=3548],dendryphantes nidicolides[&&NHX:TOL=3549])[&&NHX:TOL=3547],dendryphantes niveornatus[&&NHX:TOL=3550],dendryphantes nobilis[&&NHX:TOL=3551],dendryphantes noxiosus[&&NHX:TOL=3552],dendryphantes pallidus[&&NHX:TOL=3553],dendryphantes palmensis[&&NHX:TOL=3554],dendryphantes patagonicus[&&NHX:TOL=3555],dendryphantes praeposterus[&&NHX:TOL=3556],dendryphantes pugnax[&&NHX:TOL=3557],dendryphantes purcelli[&&NHX:TOL=3558],dendryphantes quesitus[&&NHX:TOL=3559],dendryphantes reimoseri[&&NHX:TOL=3560],dendryphantes rudis[&&NHX:TOL=3561],dendryphantes sacci[&&NHX:TOL=3562],dendryphantes schultzei[&&NHX:TOL=3563],dendryphantes seriatus[&&NHX:TOL=3564],dendryphantes sexguttatus[&&NHX:TOL=3565],dendryphantes spinosissimus[&&NHX:TOL=3566],dendryphantes strenuus[&&NHX:TOL=3567],dendryphantes tuvinensis[&&NHX:TOL=3568],dendryphantes zygoballoides[&&NHX:TOL=3569])dendryphantes[&&NHX:TOL=2887],donaldius[&&NHX:TOL=2888],(eris aurantia[&&NHX:TOL=3575],eris bella[&&NHX:TOL=3576],eris disjunctus[&&NHX:TOL=3577],eris fartilis[&&NHX:TOL=3578],eris flava[&&NHX:TOL=3579],eris floridana[&&NHX:TOL=3580],eris funebris[&&NHX:TOL=3581],eris illustris[&&NHX:TOL=3582],eris inermis[&&NHX:TOL=3583],eris lanipes[&&NHX:TOL=3584],eris lutea[&&NHX:TOL=3585],eris mexicana[&&NHX:TOL=3586],eris militaris[&&NHX:TOL=3587],eris nidicolens[&&NHX:TOL=3588],eris nigropilosus[&&NHX:TOL=3589],eris pinea[&&NHX:TOL=3590],eris riedeli[&&NHX:TOL=3591])eris[&&NHX:TOL=2889],(gastromicans albopilosa[&&NHX:TOL=3854],gastromicans hondurensis[&&NHX:TOL=3855],gastromicans levispina[&&NHX:TOL=3856],gastromicans noxiosa[&&NHX:TOL=3857],gastromicans vigens[&&NHX:TOL=3858])gastromicans[&&NHX:TOL=2890],(ghelna castaneus[&&NHX:TOL=3860],ghelna barrowsi[&&NHX:TOL=3861],(ghelna canadensis[&&NHX:TOL=3863],ghelna sexmaculatus[&&NHX:TOL=3864])[&&NHX:TOL=3862])ghelna[&&NHX:TOL=2891],(hentzia antillana[&&NHX:TOL=4316],hentzia audax[&&NHX:TOL=4317],hentzia calypso[&&NHX:TOL=4318],hentzia chekika[&&NHX:TOL=4319],hentzia cubana[&&NHX:TOL=4320],hentzia fimbriata[&&NHX:TOL=4321],hentzia footei[&&NHX:TOL=4322],hentzia grenada[&&NHX:TOL=4323],hentzia mandibularis[&&NHX:TOL=4324],hentzia mitrata[&&NHX:TOL=4325],hentzia palmarum[&&NHX:TOL=4326],hentzia parallela[&&NHX:TOL=4327],hentzia pima[&&NHX:TOL=4328],hentzia poenitens[&&NHX:TOL=4329],hentzia squamata[&&NHX:TOL=4330],hentzia tibialis[&&NHX:TOL=4331],hentzia vernalis[&&NHX:TOL=4332],hentzia vittata[&&NHX:TOL=4333],hentzia whitcombi[&&NHX:TOL=4334],hentzia zombia[&&NHX:TOL=4335])hentzia[&&NHX:TOL=2892],homalattus[&&NHX:TOL=2893],(lurio conspicuus[&&NHX:TOL=4420],lurio crassichelis[&&NHX:TOL=4421],lurio lethierryi[&&NHX:TOL=4422],lurio splendidissimus[&&NHX:TOL=4423],lurio solennis[&&NHX:TOL=4424])lurio[&&NHX:TOL=2894],mabellina prescotti[&&NHX:TOL=2895],((((((((messua desidiosa[&&NHX:TOL=4681],messua centralis[&&NHX:TOL=4682],messua dentiger[&&NHX:TOL=4683])[&&NHX:TOL=4680],messua donalda[&&NHX:TOL=4684])[&&NHX:TOL=4679],messua lata[&&NHX:TOL=4685])[&&NHX:TOL=4678],messua laxa[&&NHX:TOL=4686])[&&NHX:TOL=4677],messua limbata[&&NHX:TOL=4687])[&&NHX:TOL=4676],messua moma[&&NHX:TOL=4688])[&&NHX:TOL=4675],messua octonotata[&&NHX:TOL=4689])[&&NHX:TOL=4674],messua pura[&&NHX:TOL=4690])messua[&&NHX:TOL=2896],(metaphidippus mandibulatus[&&NHX:TOL=4701],((metaphidippus carmenensis[&&NHX:TOL=4704],metaphidippus chera[&&NHX:TOL=4705],metaphidippus diplacis[&&NHX:TOL=4706],metaphidippus emmiltus[&&NHX:TOL=4707],metaphidippus mannii[&&NHX:TOL=4708],metaphidippus tricolor[&&NHX:TOL=4709])mannii group[&&NHX:TOL=4703],(metaphidippus vitis[&&NHX:TOL=4711],metaphidippus mathetes[&&NHX:TOL=4712],metaphidippus texanus[&&NHX:TOL=4713],metaphidippus melanomerus[&&NHX:TOL=4714])vitis group[&&NHX:TOL=4710])[&&NHX:TOL=4702])metaphidippus[&&NHX:TOL=2897],(nagaina berlandi[&&NHX:TOL=4918],nagaina diademata[&&NHX:TOL=4919],nagaina incunda[&&NHX:TOL=4920],nagaina modesta[&&NHX:TOL=4921],nagaina olivacea[&&NHX:TOL=4922],nagaina tricincta[&&NHX:TOL=4923])nagaina[&&NHX:TOL=2898],osericta[&&NHX:TOL=2899],(paradamoetas cara[&&NHX:TOL=4985],paradamoetas changuinola[&&NHX:TOL=4986],paradamoetas fontana[&&NHX:TOL=4987],paradamoetas formicina[&&NHX:TOL=4988])paradamoetas[&&NHX:TOL=2900],(parnaenus crassidens[&&NHX:TOL=4995],parnaenus cuspidatus[&&NHX:TOL=4996],parnaenus cyanidens[&&NHX:TOL=4997],parnaenus fimbriatus[&&NHX:TOL=4998],parnaenus recurvus[&&NHX:TOL=4999])parnaenus[&&NHX:TOL=2901],(pelegrina bunites[&&NHX:TOL=5009],pelegrina orestes[&&NHX:TOL=5010],(pelegrina yucatecana[&&NHX:TOL=5012],pelegrina variegata[&&NHX:TOL=5013],pelegrina sandaracina[&&NHX:TOL=5014],pelegrina pallidata[&&NHX:TOL=5015],pelegrina clavator[&&NHX:TOL=5016],pelegrina tillandsiae[&&NHX:TOL=5017],pelegrina verecunda[&&NHX:TOL=5018],pelegrina clemata[&&NHX:TOL=5019],pelegrina aeneola[&&NHX:TOL=5020],pelegrina balia[&&NHX:TOL=5021],pelegrina chalceola[&&NHX:TOL=5022],(pelegrina montana[&&NHX:TOL=5024],pelegrina insignis[&&NHX:TOL=5025],pelegrina chaimona[&&NHX:TOL=5026])montana group[&&NHX:TOL=5023],(pelegrina arizonensis[&&NHX:TOL=5028],pelegrina helenae[&&NHX:TOL=5029])arizonensis group[&&NHX:TOL=5027],(pelegrina furcata[&&NHX:TOL=5031],pelegrina morelos[&&NHX:TOL=5032],pelegrina bicuspidata[&&NHX:TOL=5033],pelegrina ochracea[&&NHX:TOL=5034],pelegrina huachuca[&&NHX:TOL=5035],pelegrina volcana[&&NHX:TOL=5036])furcatus group[&&NHX:TOL=5030],(pelegrina dithalea[&&NHX:TOL=5038],pelegrina proxima[&&NHX:TOL=5039],pelegrina peckhamorum[&&NHX:TOL=5040],(pelegrina edrilana[&&NHX:TOL=5042],pelegrina proterva[&&NHX:TOL=5043],pelegrina galathea[&&NHX:TOL=5044],((pelegrina tristis[&&NHX:TOL=5047],pelegrina neoleonis[&&NHX:TOL=5048])[&&NHX:TOL=5046],((pelegrina pervaga[&&NHX:TOL=5051],pelegrina sabinema[&&NHX:TOL=5052],pelegrina kastoni[&&NHX:TOL=5053])pervaga group[&&NHX:TOL=5050],(pelegrina flaviceps[&&NHX:TOL=5055],pelegrina exigua[&&NHX:TOL=5056],pelegrina flavipedes[&&NHX:TOL=5057])flavipedes group[&&NHX:TOL=5054])[&&NHX:TOL=5049])[&&NHX:TOL=5045])[&&NHX:TOL=5041])[&&NHX:TOL=5037])[&&NHX:TOL=5011])pelegrina[&&NHX:TOL=2902],(phanias albeolus[&&NHX:TOL=5178],phanias concoloratus[&&NHX:TOL=5179],phanias dominatus[&&NHX:TOL=5180],phanias furcifer[&&NHX:TOL=5181],phanias furcillatus[&&NHX:TOL=5182],phanias harfordii[&&NHX:TOL=5183],phanias monticola[&&NHX:TOL=5184],phanias neomexicanus[&&NHX:TOL=5185])phanias[&&NHX:TOL=2903],(phidippus albulatus[&&NHX:TOL=5237],phidippus apacheanus[&&NHX:TOL=5238],phidippus ardens[&&NHX:TOL=5239],phidippus arizonensis[&&NHX:TOL=5240],phidippus asotus[&&NHX:TOL=5241],phidippus audax[&&NHX:TOL=5242],phidippus borealis[&&NHX:TOL=5243],phidippus californicus[&&NHX:TOL=5244],phidippus cardinalis[&&NHX:TOL=5245],phidippus carneus[&&NHX:TOL=5246],phidippus carolinensis[&&NHX:TOL=5247],phidippus clarus[&&NHX:TOL=5248],phidippus coccineus[&&NHX:TOL=5249],phidippus comatus[&&NHX:TOL=5250],phidippus concinnus[&&NHX:TOL=5251],phidippus cruentus[&&NHX:TOL=5252],phidippus georgii[&&NHX:TOL=5253],phidippus insignarius[&&NHX:TOL=5254],phidippus johnsoni[&&NHX:TOL=5255],phidippus mystaceus[&&NHX:TOL=5256],phidippus nikites[&&NHX:TOL=5257],phidippus octopunctatus[&&NHX:TOL=5258],phidippus otiosus[&&NHX:TOL=5259],phidippus pius[&&NHX:TOL=5260],phidippus princeps[&&NHX:TOL=5261],phidippus pruinosus[&&NHX:TOL=5262],phidippus pulcherrimus[&&NHX:TOL=5263],phidippus purpuratus[&&NHX:TOL=5264],phidippus putnami[&&NHX:TOL=5265],phidippus regius[&&NHX:TOL=5266],phidippus texanus[&&NHX:TOL=5267],phidippus toro[&&NHX:TOL=5268],phidippus tux[&&NHX:TOL=5269],phidippus tyrrelli[&&NHX:TOL=5270],phidippus whitmani[&&NHX:TOL=5271])phidippus[&&NHX:TOL=2904],(poultonella alboimmaculata[&&NHX:TOL=24831],poultonella nuecensensis[&&NHX:TOL=24832])poultonella[&&NHX:TOL=2905],ramboia[&&NHX:TOL=2906],(rhene albigera[&&NHX:TOL=5542],rhene atrata[&&NHX:TOL=5543],rhene aurata[&&NHX:TOL=5544],rhene banksii[&&NHX:TOL=5545],rhene biembolusa[&&NHX:TOL=5546],rhene biguttata[&&NHX:TOL=5547],rhene brevipes[&&NHX:TOL=5548],rhene bufo[&&NHX:TOL=5549],rhene callida[&&NHX:TOL=5550],rhene callosa[&&NHX:TOL=5551],rhene candida[&&NHX:TOL=5552],rhene capensis[&&NHX:TOL=5553],rhene cooperi[&&NHX:TOL=5554],rhene daitarensis[&&NHX:TOL=5555],rhene danieli[&&NHX:TOL=5556],rhene darjeelingiana[&&NHX:TOL=5557],rhene decorata[&&NHX:TOL=5558],rhene flavicomans[&&NHX:TOL=5559],rhene flavigera[&&NHX:TOL=5560],rhene foai[&&NHX:TOL=5561],rhene gambeyi[&&NHX:TOL=5562],rhene hirsuta[&&NHX:TOL=5563],rhene inconcinna[&&NHX:TOL=5564],rhene indica[&&NHX:TOL=5565],rhene ipis[&&NHX:TOL=5566],rhene jelskii[&&NHX:TOL=5567],rhene khandalaensis[&&NHX:TOL=5568],rhene lesserti[&&NHX:TOL=5569],rhene machadoi[&&NHX:TOL=5570],rhene margarops[&&NHX:TOL=5571],rhene mordax[&&NHX:TOL=5572],rhene mus[&&NHX:TOL=5573],rhene nigrita[&&NHX:TOL=5574],rhene parvula[&&NHX:TOL=5575],rhene rubrigera[&&NHX:TOL=5576],rhene saeva[&&NHX:TOL=5577],rhene setipes[&&NHX:TOL=5578],rhene sulfurea[&&NHX:TOL=5579],rhene tamula[&&NHX:TOL=5580],rhene tricolor[&&NHX:TOL=5581],rhene vaga[&&NHX:TOL=5582])rhene[&&NHX:TOL=2907],(rhetenor diversipes[&&NHX:TOL=24833],rhetenor texanus[&&NHX:TOL=24834])rhetenor[&&NHX:TOL=2908],(rudra baurensis[&&NHX:TOL=5585],rudra geniculata[&&NHX:TOL=5586],rudra humilis[&&NHX:TOL=5587],rudra minensis[&&NHX:TOL=5588],rudra multispina[&&NHX:TOL=5589],rudra oriximina[&&NHX:TOL=5590],rudra polita[&&NHX:TOL=5591],rudra proxima[&&NHX:TOL=5592],rudra tenera[&&NHX:TOL=5593],rudra wagae[&&NHX:TOL=5594])rudra[&&NHX:TOL=2909],(sassacus alboguttatus[&&NHX:TOL=5703],sassacus arcuatus[&&NHX:TOL=5704],sassacus aurantiacus[&&NHX:TOL=5705],sassacus barbipes[&&NHX:TOL=5706],sassacus biaccentuatus[&&NHX:TOL=5707],sassacus bicinctus[&&NHX:TOL=5708],sassacus dissimilis[&&NHX:TOL=5709],sassacus flavicinctus[&&NHX:TOL=5710],sassacus helenicus[&&NHX:TOL=5711],sassacus glyphochela[&&NHX:TOL=5712],sassacus marginellus[&&NHX:TOL=5713],sassacus ocellatus[&&NHX:TOL=5714],sassacus papenhoei[&&NHX:TOL=5715],sassacus poecilopus[&&NHX:TOL=5716],sassacus resplendens[&&NHX:TOL=5717],sassacus trochilus[&&NHX:TOL=5718],sassacus vanduzei[&&NHX:TOL=5719])sassacus[&&NHX:TOL=2910],sebastira[&&NHX:TOL=2911],selimus[&&NHX:TOL=2912],semora[&&NHX:TOL=2913],tacuna[&&NHX:TOL=2914],(terralonus mylothrus[&&NHX:TOL=5889],terralonus californicus[&&NHX:TOL=5890],terralonus shaferi[&&NHX:TOL=5891],terralonus unicus[&&NHX:TOL=5892],terralonus fraternus[&&NHX:TOL=5893],terralonus vittatus[&&NHX:TOL=5894],terralonus versicolor[&&NHX:TOL=5895])terralonus[&&NHX:TOL=2915],thammaca[&&NHX:TOL=2916],(tulpius gauchus[&&NHX:TOL=24835],tulpius hilarus[&&NHX:TOL=24836])tulpius[&&NHX:TOL=2917],(tutelina elegans[&&NHX:TOL=5946],tutelina formicaria[&&NHX:TOL=5947],tutelina hartii[&&NHX:TOL=5948],tutelina similis[&&NHX:TOL=5949])tutelina[&&NHX:TOL=2918],uluella[&&NHX:TOL=2919],(zygoballus citri[&&NHX:TOL=5974],zygoballus concolor[&&NHX:TOL=5975],zygoballus desidiosus[&&NHX:TOL=5976],zygoballus electus[&&NHX:TOL=5977],zygoballus gracilipes[&&NHX:TOL=5978],zygoballus incertus[&&NHX:TOL=5979],zygoballus iridescens[&&NHX:TOL=5980],zygoballus lineatus[&&NHX:TOL=5981],zygoballus maculatipes[&&NHX:TOL=5982],zygoballus maculatus[&&NHX:TOL=5983],zygoballus melloleitaoi[&&NHX:TOL=5984],zygoballus minutus[&&NHX:TOL=5985],zygoballus mundus[&&NHX:TOL=5986],zygoballus narmadaensis[&&NHX:TOL=5987],zygoballus nervosus[&&NHX:TOL=5988],zygoballus optatus[&&NHX:TOL=5989],zygoballus pashanensis[&&NHX:TOL=5990],zygoballus remotus[&&NHX:TOL=5991],zygoballus rufipes[&&NHX:TOL=5992],zygoballus sexpunctatus[&&NHX:TOL=5993],zygoballus suavis[&&NHX:TOL=5994],zygoballus tibialis[&&NHX:TOL=5995])zygoballus[&&NHX:TOL=2920])[&&NHX:TOL=2874],unidentified dendryphantinae[&&NHX:TOL=2921])dendryphantinae[&&NHX:TOL=2854],((anasaitis[&&NHX:TOL=2924],(amphidraus auriga[&&NHX:TOL=3169],amphidraus duckei[&&NHX:TOL=3170],amphidraus santanae[&&NHX:TOL=3171])amphidraus[&&NHX:TOL=2925],asaphobelis[&&NHX:TOL=2926],ascyltus[&&NHX:TOL=2927],athamas[&&NHX:TOL=2928],bathippus[&&NHX:TOL=2929],belliena[&&NHX:TOL=2930],bindax[&&NHX:TOL=2931],canama[&&NHX:TOL=2932],(chalcoscirtus alpicola[&&NHX:TOL=3308],chalcoscirtus ansobicus[&&NHX:TOL=3309],chalcoscirtus asiatica[&&NHX:TOL=3310],chalcoscirtus atratus[&&NHX:TOL=3311],chalcoscirtus carbonarius[&&NHX:TOL=3312],chalcoscirtus flavipes[&&NHX:TOL=3313],chalcoscirtus fulvus[&&NHX:TOL=3314],chalcoscirtus glacialis[&&NHX:TOL=3315],chalcoscirtus grishkanae[&&NHX:TOL=3316],chalcoscirtus hyperboreus[&&NHX:TOL=3317],chalcoscirtus infimus[&&NHX:TOL=3318],chalcoscirtus insularis[&&NHX:TOL=3319],chalcoscirtus janetscheki[&&NHX:TOL=3320],chalcoscirtus kamchik[&&NHX:TOL=3321],chalcoscirtus karakurt[&&NHX:TOL=3322],chalcoscirtus khirghisicus[&&NHX:TOL=3323],chalcoscirtus martensi[&&NHX:TOL=3324],chalcoscirtus minutus[&&NHX:TOL=3325],chalcoscirtus molo[&&NHX:TOL=3326],chalcoscirtus nenilini[&&NHX:TOL=3327],chalcoscirtus paransobicus[&&NHX:TOL=3328],chalcoscirtus pavuk[&&NHX:TOL=3329],chalcoscirtus pseudoinfimus[&&NHX:TOL=3330],chalcoscirtus rehoboticus[&&NHX:TOL=3331],chalcoscirtus sublestus[&&NHX:TOL=3332],chalcoscirtus tanasevichi[&&NHX:TOL=3333],chalcoscirtus vietnamensis[&&NHX:TOL=3334],chalcoscirtus zyuzini[&&NHX:TOL=3335])chalcoscirtus[&&NHX:TOL=2933],chalcotropis[&&NHX:TOL=2934],chloridusa[&&NHX:TOL=2935],(cobanus beebei[&&NHX:TOL=3368],cobanus bifurcatus[&&NHX:TOL=3369],cobanus cambridgei[&&NHX:TOL=3370],cobanus electus[&&NHX:TOL=3371],cobanus erythrocras[&&NHX:TOL=3372],cobanus exstensus[&&NHX:TOL=3373],cobanus flavens[&&NHX:TOL=3374],cobanus incurvus[&&NHX:TOL=3375],cobanus mandibularis[&&NHX:TOL=3376],cobanus obscurus[&&NHX:TOL=3377],cobanus perditus[&&NHX:TOL=3378],cobanus scintillans[&&NHX:TOL=3379],cobanus seclusus[&&NHX:TOL=3380],cobanus subfuscus[&&NHX:TOL=3381],cobanus unicolor[&&NHX:TOL=3382])cobanus[&&NHX:TOL=2936],colyttus[&&NHX:TOL=2937],commoris[&&NHX:TOL=2938],coryphasia[&&NHX:TOL=2939],(corythalia alacris[&&NHX:TOL=3384],corythalia albocincta[&&NHX:TOL=3385],corythalia arcuata[&&NHX:TOL=3386],corythalia argyrochrysos[&&NHX:TOL=3387],corythalia argentinensis[&&NHX:TOL=3388],corythalia banksi[&&NHX:TOL=3389],corythalia barbipes[&&NHX:TOL=3390],corythalia bicincta[&&NHX:TOL=3391],corythalia binotata[&&NHX:TOL=3392],corythalia blanda[&&NHX:TOL=3393],corythalia brevispina[&&NHX:TOL=3394],corythalia bryantae[&&NHX:TOL=3395],corythalia canalis[&&NHX:TOL=3396],corythalia canosa[&&NHX:TOL=3397],corythalia chalcea[&&NHX:TOL=3398],corythalia chickeringi[&&NHX:TOL=3399],corythalia cincta[&&NHX:TOL=3400],corythalia circumcincta[&&NHX:TOL=3401],corythalia circumflexa[&&NHX:TOL=3402],corythalia clara[&&NHX:TOL=3403],corythalia conformans[&&NHX:TOL=3404],corythalia conspecta[&&NHX:TOL=3405],corythalia cristata[&&NHX:TOL=3406],corythalia cubana[&&NHX:TOL=3407],corythalia diminuta[&&NHX:TOL=3408],corythalia diffusa[&&NHX:TOL=3409],corythalia dimidiata[&&NHX:TOL=3410],corythalia electa[&&NHX:TOL=3411],corythalia elegantissima[&&NHX:TOL=3412],corythalia emertoni[&&NHX:TOL=3413],corythalia endigma[&&NHX:TOL=3414],corythalia excavata[&&NHX:TOL=3415],corythalia fimbriata[&&NHX:TOL=3416],corythalia flavida[&&NHX:TOL=3417],corythalia gloriae[&&NHX:TOL=3418],corythalia grata[&&NHX:TOL=3419],corythalia hadzii[&&NHX:TOL=3420],corythalia heliophanina[&&NHX:TOL=3421],corythalia iridescens[&&NHX:TOL=3422],corythalia latipes[&&NHX:TOL=3423],corythalia locuples[&&NHX:TOL=3424],corythalia luctuosa[&&NHX:TOL=3425],corythalia lutea[&&NHX:TOL=3426],corythalia metallica[&&NHX:TOL=3427],corythalia modesta[&&NHX:TOL=3428],corythalia murcida[&&NHX:TOL=3429],corythalia neglecta[&&NHX:TOL=3430],corythalia nigriventer[&&NHX:TOL=3431],corythalia nigropicta[&&NHX:TOL=3432],corythalia noda[&&NHX:TOL=3433],corythalia obsoleta[&&NHX:TOL=3434],corythalia opima[&&NHX:TOL=3435],corythalia panamana[&&NHX:TOL=3436],corythalia parva[&&NHX:TOL=3437],corythalia parvula[&&NHX:TOL=3438],corythalia peckhami[&&NHX:TOL=3439],corythalia penicillata[&&NHX:TOL=3440],corythalia placata[&&NHX:TOL=3441],corythalia pulchra[&&NHX:TOL=3442],corythalia quadriguttata[&&NHX:TOL=3443],corythalia roweri[&&NHX:TOL=3444],corythalia rugosa[&&NHX:TOL=3445],corythalia sellata[&&NHX:TOL=3446],corythalia serrapophysis[&&NHX:TOL=3447],corythalia spiralis[&&NHX:TOL=3448],corythalia spirorbis[&&NHX:TOL=3449],corythalia squamata[&&NHX:TOL=3450],corythalia sulfurea[&&NHX:TOL=3451],corythalia tristriata[&&NHX:TOL=3452],corythalia tropica[&&NHX:TOL=3453],corythalia ursina[&&NHX:TOL=3454],corythalia valida[&&NHX:TOL=3455],corythalia vervloeti[&&NHX:TOL=3456],corythalia variegata[&&NHX:TOL=3457],corythalia voluta[&&NHX:TOL=3458],corythalia waleckii[&&NHX:TOL=3459],corythalia xanthopa[&&NHX:TOL=3460])corythalia[&&NHX:TOL=2940],cynapes[&&NHX:TOL=2941],cytaea[&&NHX:TOL=2942],donoessus[&&NHX:TOL=2943],emathis[&&NHX:TOL=2944],ergane[&&NHX:TOL=2945],(euophrys acripes[&&NHX:TOL=3597],euophrys aequipes[&&NHX:TOL=3598],euophrys albimana[&&NHX:TOL=3599],euophrys albipalpis[&&NHX:TOL=3600],euophrys albopatella[&&NHX:TOL=3601],euophrys alticola[&&NHX:TOL=3602],euophrys anotata[&&NHX:TOL=3603],euophrys aperta[&&NHX:TOL=3604],euophrys astuta[&&NHX:TOL=3605],euophrys auricolor[&&NHX:TOL=3606],euophrys aurifrons[&&NHX:TOL=3607],euophrys baliola[&&NHX:TOL=3608],euophrys banksi[&&NHX:TOL=3609],euophrys bifoveolata[&&NHX:TOL=3610],euophrys browningi[&&NHX:TOL=3611],euophrys brunnescens[&&NHX:TOL=3612],euophrys canariensis[&&NHX:TOL=3613],euophrys capicola[&&NHX:TOL=3614],euophrys chiriatapuensis[&&NHX:TOL=3615],euophrys concolorata[&&NHX:TOL=3616],euophrys convergentis[&&NHX:TOL=3617],euophrys cooki[&&NHX:TOL=3618],euophrys crux[&&NHX:TOL=3619],euophrys declivis[&&NHX:TOL=3620],euophrys dhaulagirica[&&NHX:TOL=3621],(euophrys difficilis[&&NHX:TOL=3623],euophrys diminuta[&&NHX:TOL=3624])[&&NHX:TOL=3622],euophrys elongata[&&NHX:TOL=3625],euophrys erratica[&&NHX:TOL=3626],euophrys evae[&&NHX:TOL=3627],euophrys everestensis[&&NHX:TOL=3628],euophrys ferrequinum[&&NHX:TOL=3629],euophrys flavoatra[&&NHX:TOL=3630],euophrys frontalis[&&NHX:TOL=3631],euophrys fucata[&&NHX:TOL=3632],euophrys gambosa[&&NHX:TOL=3633],euophrys gibberula[&&NHX:TOL=3634],euophrys giebeli[&&NHX:TOL=3635],euophrys graeca[&&NHX:TOL=3636],euophrys granulata[&&NHX:TOL=3637],euophrys hamata[&&NHX:TOL=3638],euophrys heliophaniformis[&&NHX:TOL=3639],euophrys herbigrada[&&NHX:TOL=3640],euophrys imitata[&&NHX:TOL=3641],euophrys incompta[&&NHX:TOL=3642],euophrys infausta[&&NHX:TOL=3643],euophrys innotata[&&NHX:TOL=3644],euophrys iwatensis[&&NHX:TOL=3645],euophrys jirica[&&NHX:TOL=3646],euophrys kulczynskii[&&NHX:TOL=3647],euophrys kittenbergeri[&&NHX:TOL=3648],euophrys laetata[&&NHX:TOL=3649],euophrys lanigera[&&NHX:TOL=3650],euophrys larvata[&&NHX:TOL=3651],euophrys leipoldti[&&NHX:TOL=3652],euophrys leucodon[&&NHX:TOL=3653],euophrys leucopalpis[&&NHX:TOL=3654],euophrys leucostigma[&&NHX:TOL=3655],euophrys littoralis[&&NHX:TOL=3656],euophrys lunata[&&NHX:TOL=3657],euophrys luteolineata[&&NHX:TOL=3658],euophrys manicata[&&NHX:TOL=3659],euophrys mapuche[&&NHX:TOL=3660],euophrys marmarica[&&NHX:TOL=3661],euophrys maura[&&NHX:TOL=3662],euophrys melanoleucus[&&NHX:TOL=3663],euophrys menemerellus[&&NHX:TOL=3664],euophrys milleri[&&NHX:TOL=3665],euophrys minutus[&&NHX:TOL=3666],euophrys molesta[&&NHX:TOL=3667],euophrys monadnock[&&NHX:TOL=3668],euophrys monticola[&&NHX:TOL=3669],euophrys mottli[&&NHX:TOL=3670],euophrys nanchonensis[&&NHX:TOL=3671],euophrys nearctica[&&NHX:TOL=3672],euophrys nepalica[&&NHX:TOL=3673],euophrys newtoni[&&NHX:TOL=3674],euophrys nigripalpis[&&NHX:TOL=3675],euophrys nigrita[&&NHX:TOL=3676],euophrys nigritarsis[&&NHX:TOL=3677],euophrys nigromaculata[&&NHX:TOL=3678],euophrys obsoleta[&&NHX:TOL=3679],euophrys omnisupertes[&&NHX:TOL=3680],euophrys parvula[&&NHX:TOL=3681],euophrys pascualis[&&NHX:TOL=3682],euophrys patagonica[&&NHX:TOL=3683],euophrys patellaris[&&NHX:TOL=3684],euophrys pehuenche[&&NHX:TOL=3685],euophrys pelzelni[&&NHX:TOL=3686],euophrys peruviana[&&NHX:TOL=3687],euophrys petrensis[&&NHX:TOL=3688],euophrys pexa[&&NHX:TOL=3689],euophrys pictilis[&&NHX:TOL=3690],euophrys poloi[&&NHX:TOL=3691],euophrys prinkipona[&&NHX:TOL=3692],euophrys proszynski[&&NHX:TOL=3693],euophrys pseudogambosa[&&NHX:TOL=3694],euophrys pulchella[&&NHX:TOL=3695],euophrys purcelli[&&NHX:TOL=3696],euophrys pygmaea[&&NHX:TOL=3697],euophrys quadricolor[&&NHX:TOL=3698],euophrys quadripunctata[&&NHX:TOL=3699],euophrys quadrispinosa[&&NHX:TOL=3700],euophrys quilpuensis[&&NHX:TOL=3701],euophrys quinquenotata[&&NHX:TOL=3702],euophrys rapida[&&NHX:TOL=3703],euophrys rosenhaueri[&&NHX:TOL=3704],euophrys rubiginosa[&&NHX:TOL=3705],euophrys rubroclypea[&&NHX:TOL=3706],euophrys rufa[&&NHX:TOL=3707],euophrys rufibarbis[&&NHX:TOL=3708],euophrys rufimana[&&NHX:TOL=3709],euophrys saitiformis[&&NHX:TOL=3710],euophrys salomonis[&&NHX:TOL=3711],euophrys sanctimatei[&&NHX:TOL=3712],euophrys sedula[&&NHX:TOL=3713],euophrys semiglabrata[&&NHX:TOL=3714],euophrys semirufa[&&NHX:TOL=3715],euophrys sima[&&NHX:TOL=3716],euophrys sinapicolor[&&NHX:TOL=3717],euophrys striolata[&&NHX:TOL=3718],euophrys sulfurea[&&NHX:TOL=3719],euophrys sutrix[&&NHX:TOL=3720],euophrys tehuelche[&&NHX:TOL=3721],euophrys terrestris[&&NHX:TOL=3722],euophrys testaceozonata[&&NHX:TOL=3723],euophrys thorelli[&&NHX:TOL=3724],euophrys trivittata[&&NHX:TOL=3725],euophrys uralensis[&&NHX:TOL=3726],euophrys vafra[&&NHX:TOL=3727],euophrys valens[&&NHX:TOL=3728],euophrys vestita[&&NHX:TOL=3729],euophrys vetusta[&&NHX:TOL=3730],euophrys vittata[&&NHX:TOL=3731],euophrys westringi[&&NHX:TOL=3732],euophrys yulungensis[&&NHX:TOL=3733],euophrys yzabalensis[&&NHX:TOL=3734])euophrys[&&NHX:TOL=2946],euryattus[&&NHX:TOL=2947],eustirognathus[&&NHX:TOL=2948],(((((habrocestum acerbum[&&NHX:TOL=3870],habrocestum bufoides[&&NHX:TOL=3871])[&&NHX:TOL=3869],habrocestum pulex[&&NHX:TOL=3872])[&&NHX:TOL=3868],habrocestum xerophilum[&&NHX:TOL=3873])[&&NHX:TOL=3867],habrocestum parvulum[&&NHX:TOL=3874])north american[&&NHX:TOL=3866],(habrocestum albimanum[&&NHX:TOL=3876],habrocestum algericum[&&NHX:TOL=3877],habrocestum annae[&&NHX:TOL=3878],habrocestum arabicum[&&NHX:TOL=3879],habrocestum bitaeniatum[&&NHX:TOL=3880],habrocestum bovaei[&&NHX:TOL=3881],habrocestum diversipes[&&NHX:TOL=3882],habrocestum dotatum[&&NHX:TOL=3883],habrocestum flavimanum[&&NHX:TOL=3884],habrocestum flavipes[&&NHX:TOL=3885],habrocestum graecum[&&NHX:TOL=3886],habrocestum hongkongiensis[&&NHX:TOL=3887],habrocestum ibericum[&&NHX:TOL=3888],habrocestum insignipalpe[&&NHX:TOL=3889],habrocestum kweilinensis[&&NHX:TOL=3890],habrocestum latifasciatum[&&NHX:TOL=3891],habrocestum laurae[&&NHX:TOL=3892],habrocestum lepidum[&&NHX:TOL=3893],habrocestum luculentum[&&NHX:TOL=3894],habrocestum nigricans[&&NHX:TOL=3895],habrocestum nigristernum[&&NHX:TOL=3896],habrocestum orientale[&&NHX:TOL=3897],habrocestum ornaticeps[&&NHX:TOL=3898],habrocestum papilionaceum[&&NHX:TOL=3899],habrocestum peckhami[&&NHX:TOL=3900],habrocestum pullatum[&&NHX:TOL=3901],habrocestum punctiventre[&&NHX:TOL=3902],habrocestum rubroclypeatum[&&NHX:TOL=3903],habrocestum schinzi[&&NHX:TOL=3904],habrocestum simoni[&&NHX:TOL=3905],habrocestum speciosum[&&NHX:TOL=3906],habrocestum subdotatum[&&NHX:TOL=3907],habrocestum subpenicillatum[&&NHX:TOL=3908],habrocestum verattii[&&NHX:TOL=3909])old world[&&NHX:TOL=3875])habrocestum[&&NHX:TOL=2949],ilargus[&&NHX:TOL=2950],klamathia[&&NHX:TOL=2951],laufeia[&&NHX:TOL=2952],lepidemathis[&&NHX:TOL=2953],maeota dichrura[&&NHX:TOL=2954],maratus[&&NHX:TOL=2955],margaromma[&&NHX:TOL=2956],mopiopia[&&NHX:TOL=2957],(neon avalonus[&&NHX:TOL=4925],neon convolutus[&&NHX:TOL=4926],neon ellamae[&&NHX:TOL=4927],neon laevis[&&NHX:TOL=4928],neon minutus[&&NHX:TOL=4929],neon muticus[&&NHX:TOL=4930],neon nelli[&&NHX:TOL=4931],neon nigriceps[&&NHX:TOL=4932],neon pictus[&&NHX:TOL=4933],neon pixii[&&NHX:TOL=4934],neon plutonus[&&NHX:TOL=4935],neon punctulatus[&&NHX:TOL=4936],neon pusio[&&NHX:TOL=4937],neon rayi[&&NHX:TOL=4938],neon reticulatus[&&NHX:TOL=4939],neon robustus[&&NHX:TOL=4940],neon valentulus[&&NHX:TOL=4941])neon[&&NHX:TOL=2958],(neonella antillana[&&NHX:TOL=4945],neonella lubrica[&&NHX:TOL=4946],neonella minuta[&&NHX:TOL=4947],neonella montana[&&NHX:TOL=4948],neonella nana[&&NHX:TOL=4949],neonella vinnula[&&NHX:TOL=4950])neonella[&&NHX:TOL=2959],ocnotelus[&&NHX:TOL=2960],(pensacola castanea[&&NHX:TOL=5162],pensacola cyaneochirus[&&NHX:TOL=5163],pensacola darlingtoni[&&NHX:TOL=5164],pensacola electa[&&NHX:TOL=5165],pensacola gaujoni[&&NHX:TOL=5166],pensacola maxillosa[&&NHX:TOL=5167],pensacola montana[&&NHX:TOL=5168],pensacola murina[&&NHX:TOL=5169],pensacola ornata[&&NHX:TOL=5170],pensacola poecilocilia[&&NHX:TOL=5171],pensacola peckhami[&&NHX:TOL=5172],pensacola radians[&&NHX:TOL=5173],pensacola signata[&&NHX:TOL=5174],pensacola silvestris[&&NHX:TOL=5175],pensacola tubercolotibiata[&&NHX:TOL=5176])pensacola[&&NHX:TOL=2961],plotius[&&NHX:TOL=2962],pristobaeus[&&NHX:TOL=2963],pystira[&&NHX:TOL=2964],saitis[&&NHX:TOL=2965],semnolius[&&NHX:TOL=2966],servaea[&&NHX:TOL=2967],(sidusa angulitarsis[&&NHX:TOL=5734],sidusa borealis[&&NHX:TOL=5735],sidusa carinata[&&NHX:TOL=5736],sidusa dominicana[&&NHX:TOL=5737],sidusa femoralis[&&NHX:TOL=5738],sidusa gratiosa[&&NHX:TOL=5739],sidusa inconspicua[&&NHX:TOL=5740],sidusa marmorea[&&NHX:TOL=5741],sidusa mona[&&NHX:TOL=5742],sidusa nigrina[&&NHX:TOL=5743],sidusa olivacea[&&NHX:TOL=5744],sidusa pallida[&&NHX:TOL=5745],sidusa pavida[&&NHX:TOL=5746],sidusa recondita[&&NHX:TOL=5747],sidusa stoneri[&&NHX:TOL=5748],sidusa tarsalis[&&NHX:TOL=5749],sidusa turquinensis[&&NHX:TOL=5750],sidusa unica[&&NHX:TOL=5751],sidusa variegata[&&NHX:TOL=5752],sidusa sp. arizona[&&NHX:TOL=5753])sidusa[&&NHX:TOL=2968],siloca[&&NHX:TOL=2969],spilargis[&&NHX:TOL=2970],stoides[&&NHX:TOL=2971],(talavera aequipes[&&NHX:TOL=5884],talavera inopinata[&&NHX:TOL=5885],talavera minuta[&&NHX:TOL=5886])talavera[&&NHX:TOL=2972],tariona[&&NHX:TOL=2973],thiania[&&NHX:TOL=2974],thorelliola[&&NHX:TOL=2975],thyenula[&&NHX:TOL=2976],((tylogonus auricapillus[&&NHX:TOL=5955],tylogonus craneae[&&NHX:TOL=5956],tylogonus dentichelis[&&NHX:TOL=5957],tylogonus miles[&&NHX:TOL=5958],tylogonus parabolicus[&&NHX:TOL=5959],tylogonus pichincha[&&NHX:TOL=5960],tylogonus prasinus[&&NHX:TOL=5961],tylogonus putumayo[&&NHX:TOL=5962],tylogonus vachoni[&&NHX:TOL=5963],tylogonus viridimicans[&&NHX:TOL=5964])neotropical[&&NHX:TOL=5954],(tylogonus arizonensis[&&NHX:TOL=5966],(tylogonus minutus[&&NHX:TOL=5968],tylogonus morosus[&&NHX:TOL=5969])[&&NHX:TOL=5967])nearctic[&&NHX:TOL=5965])tylogonus[&&NHX:TOL=2977],udvardya[&&NHX:TOL=2978],zenodorus[&&NHX:TOL=2979])[&&NHX:TOL=2923],unidentified euophryinae[&&NHX:TOL=2980])euophryinae[&&NHX:TOL=2855],((synageles albotrimaculatus[&&NHX:TOL=5836],synageles bishopi[&&NHX:TOL=5837],synageles canadensis[&&NHX:TOL=5838],synageles charitonovi[&&NHX:TOL=5839],synageles dalmaticus[&&NHX:TOL=5840],synageles hilarulus[&&NHX:TOL=5841],synageles idahoanus[&&NHX:TOL=5842],synageles leechi[&&NHX:TOL=5843],synageles lepidus[&&NHX:TOL=5844],synageles mexicanus[&&NHX:TOL=5845],synageles noxiosus[&&NHX:TOL=5846],synageles occidentalis[&&NHX:TOL=5847],synageles ovatus[&&NHX:TOL=5848],synageles pulcher[&&NHX:TOL=5849],synageles ramitus[&&NHX:TOL=5850],synageles repudiatus[&&NHX:TOL=5851],synageles scutiger[&&NHX:TOL=5852],synageles subcingulatus[&&NHX:TOL=5853],synageles venator[&&NHX:TOL=5854])synageles[&&NHX:TOL=3109],(peckhamia americana[&&NHX:TOL=5001],peckhamia argentinensis[&&NHX:TOL=5002],peckhamia picata[&&NHX:TOL=5003],peckhamia prescoti[&&NHX:TOL=5004],peckhamia scorpionia[&&NHX:TOL=5005],peckhamia seminola[&&NHX:TOL=5006],peckhamia variegata[&&NHX:TOL=5007])peckhamia[&&NHX:TOL=3110],consingis[&&NHX:TOL=3111],descanso[&&NHX:TOL=3112],(cheliferoides segmentatus[&&NHX:TOL=24837],cheliferoides planus[&&NHX:TOL=24838])cheliferoides[&&NHX:TOL=3113],leptorchestes[&&NHX:TOL=3114])synagelinae[&&NHX:TOL=2856],((ballus armadillo[&&NHX:TOL=3205],ballus chalybeius[&&NHX:TOL=3206],ballus cinctipes[&&NHX:TOL=3207],ballus clathratus[&&NHX:TOL=3208],ballus immaculatus[&&NHX:TOL=3209],ballus japonicus[&&NHX:TOL=3210],ballus lendli[&&NHX:TOL=3211],ballus obscuroides[&&NHX:TOL=3212],ballus piger[&&NHX:TOL=3213],ballus planus[&&NHX:TOL=3214],ballus rufipes[&&NHX:TOL=3215],ballus sellatus[&&NHX:TOL=3216],ballus segmentatus[&&NHX:TOL=3217],ballus sociabilis[&&NHX:TOL=3218],ballus tabupumensis[&&NHX:TOL=3219],ballus variegatus[&&NHX:TOL=3220],ballus vulpinus[&&NHX:TOL=3221],ballus youngi[&&NHX:TOL=3222])ballus[&&NHX:TOL=2867],colaxes[&&NHX:TOL=2868],padilla[&&NHX:TOL=2869],pachyballus[&&NHX:TOL=2870],marengo[&&NHX:TOL=2871],(admestina wheeleri[&&NHX:TOL=3157],admestina tibialis[&&NHX:TOL=3158],admestina archboldi[&&NHX:TOL=3159])admestina[&&NHX:TOL=2872])ballinae[&&NHX:TOL=2857],((phlegra albostriata[&&NHX:TOL=5322],phlegra abyssinica[&&NHX:TOL=5323],phlegra bairstowi[&&NHX:TOL=5324],phlegra bresnieri[&&NHX:TOL=5325],phlegra chrysops[&&NHX:TOL=5326],phlegra cinereofasciata[&&NHX:TOL=5327],phlegra desquamata[&&NHX:TOL=5328],phlegra dhakuriensis[&&NHX:TOL=5329],phlegra fasciata[&&NHX:TOL=5330],phlegra festiva[&&NHX:TOL=5331],phlegra flavipes[&&NHX:TOL=5332],phlegra fulvastra[&&NHX:TOL=5333],phlegra fulviventris[&&NHX:TOL=5334],phlegra fulvotrilineata[&&NHX:TOL=5335],phlegra fuscipes[&&NHX:TOL=5336],phlegra imperiosa[&&NHX:TOL=5337],phlegra lineata[&&NHX:TOL=5338],phlegra lippiens[&&NHX:TOL=5339],phlegra loripes[&&NHX:TOL=5340],phlegra lugubris[&&NHX:TOL=5341],phlegra mayeti[&&NHX:TOL=5342],phlegra memoralis[&&NHX:TOL=5343],phlegra micans[&&NHX:TOL=5344],phlegra moesta[&&NHX:TOL=5345],phlegra nitidiventris[&&NHX:TOL=5346],phlegra particeps[&&NHX:TOL=5347],phlegra pisarskii[&&NHX:TOL=5348],phlegra potanini[&&NHX:TOL=5349],phlegra proxima[&&NHX:TOL=5350],phlegra pusilla[&&NHX:TOL=5351],phlegra rogenhoferi[&&NHX:TOL=5352],phlegra ruficapilla[&&NHX:TOL=5353],phlegra sapphirina[&&NHX:TOL=5354],phlegra semipullata[&&NHX:TOL=5355],phlegra sierrana[&&NHX:TOL=5356],phlegra samchiensis[&&NHX:TOL=5357],phlegra simoni[&&NHX:TOL=5358],phlegra sogdiana[&&NHX:TOL=5359],phlegra soudanica[&&NHX:TOL=5360],phlegra suaverubens[&&NHX:TOL=5361],phlegra thibetana[&&NHX:TOL=5362],phlegra trifovelata[&&NHX:TOL=5363],phlegra tristis[&&NHX:TOL=5364],phlegra tuzetae[&&NHX:TOL=5365])phlegra[&&NHX:TOL=3059],(((psecas bacelarae[&&NHX:TOL=5449],psecas barbaricus[&&NHX:TOL=5450],psecas bubo[&&NHX:TOL=5451],psecas chapoda[&&NHX:TOL=5452],psecas chrysogrammus[&&NHX:TOL=5453],psecas cyaneus[&&NHX:TOL=5454],psecas euoplus[&&NHX:TOL=5455],psecas jaguaritica[&&NHX:TOL=5456],psecas pulcher[&&NHX:TOL=5457],psecas rubrostriatus[&&NHX:TOL=5458],psecas sumptuosus[&&NHX:TOL=5459],psecas vellutinus[&&NHX:TOL=5460],psecas viridipurpureus[&&NHX:TOL=5461],psecas zonatus[&&NHX:TOL=5462])psecas[&&NHX:TOL=3062],(itata completa[&&NHX:TOL=4406],itata isabellina[&&NHX:TOL=4407],itata partita[&&NHX:TOL=4408],itata tipuloides[&&NHX:TOL=4409],itata vadia[&&NHX:TOL=4410])itata[&&NHX:TOL=3063])[&&NHX:TOL=3061],((mantisatta longicauda[&&NHX:TOL=24839],mantisatta trucidans[&&NHX:TOL=24840])mantisatta[&&NHX:TOL=3065],mopsus[&&NHX:TOL=3066],sandalodes[&&NHX:TOL=3067])[&&NHX:TOL=3064])[&&NHX:TOL=3060])miscellaneous salticids with a free embolus[&&NHX:TOL=2858])freeembolus group[&&NHX:TOL=2853])unidentates[&&NHX:TOL=2845])salticinae division[&&NHX:TOL=2837])salticidae[&&NHX:TOL=2677])[&&NHX:TOL=2674])[&&NHX:TOL=2660],(acentroscelus[&&NHX:TOL=60395],acracanthostoma[&&NHX:TOL=60396],alcimochthes[&&NHX:TOL=60397],amyciaea[&&NHX:TOL=60398],angaeus[&&NHX:TOL=60399],ansiea[&&NHX:TOL=60400],aphantochilus[&&NHX:TOL=60401],apyretina[&&NHX:TOL=60402],ascurisoma[&&NHX:TOL=60403],avelis[&&NHX:TOL=60404],bassaniana[&&NHX:TOL=60405],bassaniodes[&&NHX:TOL=60406],boliscodes[&&NHX:TOL=60407],boliscus[&&NHX:TOL=60408],bomis[&&NHX:TOL=60409],bonapruncinia[&&NHX:TOL=60410],borboropactus[&&NHX:TOL=60411],bucranium[&&NHX:TOL=60412],camaricus[&&NHX:TOL=60413],carcinarachne[&&NHX:TOL=60414],cebrenninus[&&NHX:TOL=60415],ceraarachne[&&NHX:TOL=60416],cetratus[&&NHX:TOL=60417],coenypha[&&NHX:TOL=60418],coriarachne[&&NHX:TOL=60419],corynethrix[&&NHX:TOL=60420],cozyptila[&&NHX:TOL=60421],cupa[&&NHX:TOL=60422],cymbacha[&&NHX:TOL=60423],cymbachina[&&NHX:TOL=60424],cynathea[&&NHX:TOL=60425],cyriogonus[&&NHX:TOL=60426],deltoclita[&&NHX:TOL=60427],demogenes[&&NHX:TOL=60428],diaea[&&NHX:TOL=60429],dietopsa[&&NHX:TOL=60430],dimizonops[&&NHX:TOL=60431],diplotychus[&&NHX:TOL=60432],domatha[&&NHX:TOL=60433],ebelingia[&&NHX:TOL=60434],ebrechtella[&&NHX:TOL=60435],emplesiogonus[&&NHX:TOL=60436],epicadinus[&&NHX:TOL=60437],epicadus[&&NHX:TOL=60438],epidius[&&NHX:TOL=60439],erissoides[&&NHX:TOL=60440],erissus[&&NHX:TOL=60441],felsina[&&NHX:TOL=60442],firmicus[&&NHX:TOL=60443],geraesta[&&NHX:TOL=60444],gnoerichia[&&NHX:TOL=60445],haedanula[&&NHX:TOL=60446],haplotmarus[&&NHX:TOL=60447],hedana[&&NHX:TOL=60448],henriksenia[&&NHX:TOL=60449],herbessus[&&NHX:TOL=60450],heriaesynaema[&&NHX:TOL=60451],heriaeus[&&NHX:TOL=60452],heterogriffus[&&NHX:TOL=60453],hewittia[&&NHX:TOL=60454],hexommulocymus[&&NHX:TOL=60455],holopelus[&&NHX:TOL=60456],iphoctesis[&&NHX:TOL=60457],isala[&&NHX:TOL=60458],isaloides[&&NHX:TOL=60459],lampertia[&&NHX:TOL=60460],latifrons[&&NHX:TOL=60461],ledouxia[&&NHX:TOL=60462],loxobates[&&NHX:TOL=60463],loxoporetes[&&NHX:TOL=60464],lycopus[&&NHX:TOL=60465],lysiteles[&&NHX:TOL=60466],majellula[&&NHX:TOL=60467],martus[&&NHX:TOL=60468],massuria[&&NHX:TOL=60469],mastira[&&NHX:TOL=60470],mecaphesa[&&NHX:TOL=60471],megapyge[&&NHX:TOL=60472],metadiaea[&&NHX:TOL=60473],misumena[&&NHX:TOL=60474],misumenoides[&&NHX:TOL=60475],misumenops[&&NHX:TOL=60476],modysticus[&&NHX:TOL=60477],monaeses[&&NHX:TOL=60478],musaeus[&&NHX:TOL=60479],mystaria[&&NHX:TOL=60480],narcaeus[&&NHX:TOL=60481],nyctimus[&&NHX:TOL=60482],ocyllus[&&NHX:TOL=60483],onocolus[&&NHX:TOL=60484],ostanes[&&NHX:TOL=60485],oxytate[&&NHX:TOL=60486],ozyptila[&&NHX:TOL=60487],pactactes[&&NHX:TOL=60488],pagida[&&NHX:TOL=60489],parabomis[&&NHX:TOL=60490],paramystaria[&&NHX:TOL=60491],parasmodix[&&NHX:TOL=60492],parastephanops[&&NHX:TOL=60493],parastrophius[&&NHX:TOL=60494],parasynema[&&NHX:TOL=60495],pasias[&&NHX:TOL=60496],pasiasula[&&NHX:TOL=60497],peritraeus[&&NHX:TOL=60498],phaenopoma[&&NHX:TOL=60499],pharta[&&NHX:TOL=60500],pherecydes[&&NHX:TOL=60501],philodamia[&&NHX:TOL=60502],philogaeus[&&NHX:TOL=60503],phireza[&&NHX:TOL=60504],phrynarachne[&&NHX:TOL=60505],physoplatys[&&NHX:TOL=60506],pistius[&&NHX:TOL=60507],plancinus[&&NHX:TOL=60508],plastonomus[&&NHX:TOL=60509],platyarachne[&&NHX:TOL=60510],platythomisus[&&NHX:TOL=60511],poecilothomisus[&&NHX:TOL=60512],porropis[&&NHX:TOL=60513],pothaeus[&&NHX:TOL=60514],prepotelus[&&NHX:TOL=60515],pseudamyciaea[&&NHX:TOL=60516],pseudoporrhopis[&&NHX:TOL=60517],pycnaxis[&&NHX:TOL=60518],pyresthesis[&&NHX:TOL=60519],rejanellus[&&NHX:TOL=60520],reinickella[&&NHX:TOL=60521],rhaebobates[&&NHX:TOL=60522],runcinia[&&NHX:TOL=60523],saccodomus[&&NHX:TOL=60524],sanmenia[&&NHX:TOL=60525],scopticus[&&NHX:TOL=60526],sidymella[&&NHX:TOL=60527],simorcus[&&NHX:TOL=60528],smodicinodes[&&NHX:TOL=60529],smodicinus[&&NHX:TOL=60530],soelteria[&&NHX:TOL=60531],stephanopis[&&NHX:TOL=60532],stephanopoides[&&NHX:TOL=60533],stiphropella[&&NHX:TOL=60534],stiphropus[&&NHX:TOL=60535],strigoplus[&&NHX:TOL=60536],strophius[&&NHX:TOL=60537],sylligma[&&NHX:TOL=60538],synaemops[&&NHX:TOL=60539],synalus[&&NHX:TOL=60540],synema[&&NHX:TOL=60541],synstrophius[&&NHX:TOL=60542],tagulinus[&&NHX:TOL=60543],tagulis[&&NHX:TOL=60544],takachihoa[&&NHX:TOL=60545],talaus[&&NHX:TOL=60546],tarrocanus[&&NHX:TOL=60547],taypaliito[&&NHX:TOL=60548],tharpyna[&&NHX:TOL=60549],tharrhalea[&&NHX:TOL=60550],thomisops[&&NHX:TOL=60551],thomisus[&&NHX:TOL=60552],titidiops[&&NHX:TOL=60553],titidius[&&NHX:TOL=60554],tmarus[&&NHX:TOL=60555],tobias[&&NHX:TOL=60556],trichopagis[&&NHX:TOL=60557],ulocymus[&&NHX:TOL=60558],uraarachne[&&NHX:TOL=60559],wechselia[&&NHX:TOL=60560],xysticus[&&NHX:TOL=60561],zametopias[&&NHX:TOL=60562],zametopina[&&NHX:TOL=60563],zygometis[&&NHX:TOL=60564])thomisidae[&&NHX:TOL=2678],philodromidae[&&NHX:TOL=2679],sparassidae[&&NHX:TOL=2680],selenopidae[&&NHX:TOL=2681],zoridae[&&NHX:TOL=2682])dionycha[&&NHX:TOL=2692],(altellopsis[&&NHX:TOL=60589],amaurobius[&&NHX:TOL=60590],ambanus[&&NHX:TOL=60591],anisacate[&&NHX:TOL=60592],arctobius[&&NHX:TOL=60593],asiacoelotes[&&NHX:TOL=60594],auhunga[&&NHX:TOL=60595],auximella[&&NHX:TOL=60596],bakala[&&NHX:TOL=60597],bifidocoelotes[&&NHX:TOL=60598],callevopsis[&&NHX:TOL=60599],callobius[&&NHX:TOL=60600],cavernocymbium[&&NHX:TOL=60601],chresiona[&&NHX:TOL=60602],ciniflella[&&NHX:TOL=60603],coelotes[&&NHX:TOL=60604],coras[&&NHX:TOL=60605],coronilla[&&NHX:TOL=60606],cybaeopsis[&&NHX:TOL=60607],dardurus[&&NHX:TOL=60608],draconarius[&&NHX:TOL=60609],emmenomma[&&NHX:TOL=60610],eurocoelotes[&&NHX:TOL=60611],femoracoelotes[&&NHX:TOL=60612],hicanodon[&&NHX:TOL=60613],himalcoelotes[&&NHX:TOL=60614],jamara[&&NHX:TOL=60615],leptocoelotes[&&NHX:TOL=60616],livius[&&NHX:TOL=60617],longicoelotes[&&NHX:TOL=60618],macrobunus[&&NHX:TOL=60619],malala[&&NHX:TOL=60620],maloides[&&NHX:TOL=60621],manjala[&&NHX:TOL=60622],midgee[&&NHX:TOL=60623],muritaia[&&NHX:TOL=60624],naevius[&&NHX:TOL=60625],neoporteria[&&NHX:TOL=60626],neowadotes[&&NHX:TOL=60627],neuquenia[&&NHX:TOL=60628],obatala[&&NHX:TOL=60629],otira[&&NHX:TOL=60630],pakeha[&&NHX:TOL=60631],paracoelotes[&&NHX:TOL=60632],paravoca[&&NHX:TOL=60633],parazanomys[&&NHX:TOL=60634],pimus[&&NHX:TOL=60635],platocoelotes[&&NHX:TOL=60636],poaka[&&NHX:TOL=60637],pseudauximus[&&NHX:TOL=60638],retiro[&&NHX:TOL=60639],rhoicinaria[&&NHX:TOL=60640],robusticoelotes[&&NHX:TOL=60641],rubrius[&&NHX:TOL=60642],spiricoelotes[&&NHX:TOL=60643],storenosoma[&&NHX:TOL=60644],taira[&&NHX:TOL=60645],tamgrinia[&&NHX:TOL=60646],tegecoelotes[&&NHX:TOL=60647],tonsilla[&&NHX:TOL=60648],tugana[&&NHX:TOL=60649],tymbira[&&NHX:TOL=60650],urepus[&&NHX:TOL=60651],urocoras[&&NHX:TOL=60652],virgilus[&&NHX:TOL=60653],wabarra[&&NHX:TOL=60654],wadotes[&&NHX:TOL=60655],waitetola[&&NHX:TOL=60656],yacolla[&&NHX:TOL=60657],yupanquia[&&NHX:TOL=60658],zanomys[&&NHX:TOL=60659])amaurobiidae[&&NHX:TOL=2693],(agelenidae[&&NHX:TOL=2808],amphinectidae[&&NHX:TOL=2809],titanoecidae[&&NHX:TOL=2810])other amaurobioids[&&NHX:TOL=2694],(tengellidae[&&NHX:TOL=2696],((acanthoctenidae[&&NHX:TOL=2738],zoropsidae[&&NHX:TOL=2739])[&&NHX:TOL=2737],ctenidae[&&NHX:TOL=2740],((pisauridae[&&NHX:TOL=2743],(trechaleidae[&&NHX:TOL=2745],(acantholycosa[&&NHX:TOL=59447],adelocosa[&&NHX:TOL=59448],agalenocosa[&&NHX:TOL=59449],aglaoctenus[&&NHX:TOL=59450],algidus[&&NHX:TOL=59451],allocosa[&&NHX:TOL=59452],allotrochosina[&&NHX:TOL=59453],alopecosa[&&NHX:TOL=59454],alopecosella[&&NHX:TOL=59455],amblyothele[&&NHX:TOL=59456],anomalomma[&&NHX:TOL=59457],anomalosa[&&NHX:TOL=59458],anoteropsis[&&NHX:TOL=59459],arctosa[&&NHX:TOL=59460],arctosippa[&&NHX:TOL=59461],arctosomma[&&NHX:TOL=59462],artoria[&&NHX:TOL=59463],artoriellula[&&NHX:TOL=59464],aulonia[&&NHX:TOL=59465],auloniella[&&NHX:TOL=59466],brevilabus[&&NHX:TOL=59467],bristowiella[&&NHX:TOL=59468],camptocosa[&&NHX:TOL=59469],caporiaccosa[&&NHX:TOL=59470],crocodilosa[&&NHX:TOL=59471],cynosa[&&NHX:TOL=59472],dejerosa[&&NHX:TOL=59473],diapontia[&&NHX:TOL=59474],dingosa[&&NHX:TOL=59475],dolocosa[&&NHX:TOL=59476],donacosa[&&NHX:TOL=59477],dorjulopirata[&&NHX:TOL=59478],edenticosa[&&NHX:TOL=59479],evippa[&&NHX:TOL=59480],evippomma[&&NHX:TOL=59481],geolycosa[&&NHX:TOL=59482],gladicosa[&&NHX:TOL=59483],gnatholycosa[&&NHX:TOL=59484],hesperocosa[&&NHX:TOL=59485],hippasa[&&NHX:TOL=59486],hippasella[&&NHX:TOL=59487],hippasosa[&&NHX:TOL=59488],hogna[&&NHX:TOL=59489],hognoides[&&NHX:TOL=59490],hyaenosa[&&NHX:TOL=59491],hygrolycosa[&&NHX:TOL=59492],loculla[&&NHX:TOL=59493],lycosa[&&NHX:TOL=59494],lycosella[&&NHX:TOL=59495],lycosula[&&NHX:TOL=59496],lysania[&&NHX:TOL=59497],malimbosa[&&NHX:TOL=59498],margonia[&&NHX:TOL=59499],megarctosa[&&NHX:TOL=59500],melloicosa[&&NHX:TOL=59501],melocosa[&&NHX:TOL=59502],molitorosa[&&NHX:TOL=59503],mongolicosa[&&NHX:TOL=59504],mustelicosa[&&NHX:TOL=59505],notocosa[&&NHX:TOL=59506],oculicosa[&&NHX:TOL=59507],ocyale[&&NHX:TOL=59508],orinocosa[&&NHX:TOL=59509],orthocosa[&&NHX:TOL=59510],paratrochosina[&&NHX:TOL=59511],pardosa[&&NHX:TOL=59512],pardosella[&&NHX:TOL=59513],passiena[&&NHX:TOL=59514],pavocosa[&&NHX:TOL=59515],phonophilus[&&NHX:TOL=59516],pirata[&&NHX:TOL=59517],piratosa[&&NHX:TOL=59518],proevippa[&&NHX:TOL=59519],prolycosides[&&NHX:TOL=59520],pseudevippa[&&NHX:TOL=59521],pterartoria[&&NHX:TOL=59522],pterartoriola[&&NHX:TOL=59523],pyrenecosa[&&NHX:TOL=59524],rabidosa[&&NHX:TOL=59525],satta[&&NHX:TOL=59526],schizocosa[&&NHX:TOL=59527],shapna[&&NHX:TOL=59528],sibirocosa[&&NHX:TOL=59529],sosippus[&&NHX:TOL=59530],syroloma[&&NHX:TOL=59531],tasmanicosa[&&NHX:TOL=59532],trabea[&&NHX:TOL=59533],trabeops[&&NHX:TOL=59534],trebacosa[&&NHX:TOL=59535],tricassa[&&NHX:TOL=59536],trochosa[&&NHX:TOL=59537],trochosippa[&&NHX:TOL=59538],trochosula[&&NHX:TOL=59539],varacosa[&&NHX:TOL=59540],venator[&&NHX:TOL=59541],venatrix[&&NHX:TOL=59542],venonia[&&NHX:TOL=59543],vesubia[&&NHX:TOL=59544],wadicosa[&&NHX:TOL=59545],xerolycosa[&&NHX:TOL=59546],zantheres[&&NHX:TOL=59547],zenonina[&&NHX:TOL=59548],zoica[&&NHX:TOL=59549])lycosidae[&&NHX:TOL=2746])[&&NHX:TOL=2744])[&&NHX:TOL=2742],(psechridae[&&NHX:TOL=2748],(stiphidiidae[&&NHX:TOL=2750],(senoculidae[&&NHX:TOL=2752],(hamataliwa[&&NHX:TOL=60580],hostus[&&NHX:TOL=60581],megullia[&&NHX:TOL=60582],oxyopes[&&NHX:TOL=60583],peucetia[&&NHX:TOL=60584],pseudohostus[&&NHX:TOL=60585],schaenicoscelis[&&NHX:TOL=60586],tapinillus[&&NHX:TOL=60587],tapponia[&&NHX:TOL=60588])oxyopidae[&&NHX:TOL=2753])[&&NHX:TOL=2751])[&&NHX:TOL=2749])[&&NHX:TOL=2747])[&&NHX:TOL=2741])lycosoidea[&&NHX:TOL=2697])[&&NHX:TOL=2695])rta clade[&&NHX:TOL=2690])[&&NHX:TOL=2689])entelegynae[&&NHX:TOL=2651])[&&NHX:TOL=2649])[&&NHX:TOL=2645])araneomorphae[&&NHX:TOL=2642])opisthothelae[&&NHX:TOL=2640])araneae[&&NHX:TOL=2546],(amblypygi[&&NHX:TOL=2548],(thelyphonida[&&NHX:TOL=2550],schizomida[&&NHX:TOL=2551])[&&NHX:TOL=2549])[&&NHX:TOL=2547])[&&NHX:TOL=2545])[&&NHX:TOL=2543],(ricinulei[&&NHX:TOL=2553],(((sphaerolichida[&&NHX:TOL=2577],(((((erythraeoidea[&&NHX:TOL=2603],calyptostomatoidea[&&NHX:TOL=2604])[&&NHX:TOL=2602],((stygothrombioidea[&&NHX:TOL=2615],(hydrovolzioidea[&&NHX:TOL=2617],(hydryphantoidea[&&NHX:TOL=2619],(eylaoidea[&&NHX:TOL=2621],(hydrachnoidea[&&NHX:TOL=2623],(sperchontoidea[&&NHX:TOL=2625],arrenuroidea[&&NHX:TOL=2626],lebertioidea[&&NHX:TOL=2627],hygrobatoidea[&&NHX:TOL=2628])[&&NHX:TOL=2624])[&&NHX:TOL=2622])[&&NHX:TOL=2620])[&&NHX:TOL=2618])[&&NHX:TOL=2616])hydracarina[&&NHX:TOL=2606],(tanaupodoidea[&&NHX:TOL=2608],(chyzerioidea[&&NHX:TOL=2610],(trombiculoidea[&&NHX:TOL=2612],trombidioidea[&&NHX:TOL=2613])[&&NHX:TOL=2611])[&&NHX:TOL=2609])[&&NHX:TOL=2607])[&&NHX:TOL=2605])parasitengona[&&NHX:TOL=2581],anystae[&&NHX:TOL=2582])[&&NHX:TOL=2580],(((tetranychoidea[&&NHX:TOL=2586],cheyletoidea[&&NHX:TOL=2587])[&&NHX:TOL=2585],raphignathoidea[&&NHX:TOL=2588])[&&NHX:TOL=2584],heterostigmata[&&NHX:TOL=2589])eleutherengona[&&NHX:TOL=2583])anystina[&&NHX:TOL=2579],((labidostommatoidea[&&NHX:TOL=2592],(halacaroidea[&&NHX:TOL=2594],bdelloidea[&&NHX:TOL=2595])[&&NHX:TOL=2593])[&&NHX:TOL=2591],(eupodoidea[&&NHX:TOL=2597],(tydeoidea[&&NHX:TOL=2599],eriophyoidea[&&NHX:TOL=2600])[&&NHX:TOL=2598])[&&NHX:TOL=2596])eupodina[&&NHX:TOL=2590])prostigmata[&&NHX:TOL=2578])trombidiformes[&&NHX:TOL=2568],(endeostigmata in part[&&NHX:TOL=2570],(oribatida part a[&&NHX:TOL=2572],(astigmata[&&NHX:TOL=2574],oribatida part b[&&NHX:TOL=2575])[&&NHX:TOL=2573])[&&NHX:TOL=2571])sarcoptiformes[&&NHX:TOL=2569])acariformes[&&NHX:TOL=2563],(opilioacariformes[&&NHX:TOL=2565],((holothyrida[&&NHX:TOL=2631],(ixodidae[&&NHX:TOL=2635],argasidae[&&NHX:TOL=2636],nuttalliellidae[&&NHX:TOL=2637])ixodida[&&NHX:TOL=2632])[&&NHX:TOL=2630],mesostigmata[&&NHX:TOL=2633])parasitiformes[&&NHX:TOL=2566])[&&NHX:TOL=2564])acari[&&NHX:TOL=2554])[&&NHX:TOL=2552])[&&NHX:TOL=2542],(opiliones[&&NHX:TOL=2556],(((allopalaeophonidae[&&NHX:EXT=Y:TOL=6003],palaeoscorpiidae[&&NHX:EXT=Y:TOL=6004])protoscorpiones[&&NHX:EXT=Y:TOL=6006],((proscorpiidae[&&NHX:EXT=Y:TOL=6000],archaeoctonidae[&&NHX:EXT=Y:TOL=6001])palaeoscorpiones[&&NHX:EXT=Y:TOL=6008],(mesoscorpionina[&&NHX:EXT=Y:TOL=6147],(paleosterni[&&NHX:EXT=Y:TOL=6149],(((akentrobuthus[&&NHX:TOL=6031],alayotityus[&&NHX:TOL=6032],ananteris[&&NHX:TOL=6033],androctonus[&&NHX:TOL=6034],anomalobuthus[&&NHX:TOL=6035],apistobuthus[&&NHX:TOL=6036],babycurus[&&NHX:TOL=6037],birulatus[&&NHX:TOL=6038],buthacus[&&NHX:TOL=6039],butheolus[&&NHX:TOL=6040],butheoloides[&&NHX:TOL=6041],buthiscus[&&NHX:TOL=6042],buthus[&&NHX:TOL=6043],centruroides[&&NHX:TOL=6044],charmus[&&NHX:TOL=6045],cicielus[&&NHX:TOL=6046],compsobuthus[&&NHX:TOL=6047],darchenia[&&NHX:TOL=6048],grosphus[&&NHX:TOL=6049],hemibuthus[&&NHX:TOL=6050],hoplocystis[&&NHX:TOL=6051],hottentotta[&&NHX:TOL=6052],isometrus[&&NHX:TOL=6053],isometroides[&&NHX:TOL=6054],karasbergia[&&NHX:TOL=6055],kraepelinia[&&NHX:TOL=6056],leiurus[&&NHX:TOL=6057],liobuthus[&&NHX:TOL=6058],lissothus[&&NHX:TOL=6059],lychas[&&NHX:TOL=6060],lychasoides[&&NHX:TOL=6061],mesobuthus[&&NHX:TOL=6062],mesotityus[&&NHX:TOL=6063],microbuthus[&&NHX:TOL=6064],microtityus[&&NHX:TOL=6065],odontobuthus[&&NHX:TOL=6066],odonturus[&&NHX:TOL=6067],orthochirus[&&NHX:TOL=6068],parabuthus[&&NHX:TOL=6069],pocockius[&&NHX:TOL=6070],pseudolychas[&&NHX:TOL=6071],psammobuthus[&&NHX:TOL=6072],rhopalurus[&&NHX:TOL=6073],tityobuthus[&&NHX:TOL=6074],tityopsis[&&NHX:TOL=6075],tityus[&&NHX:TOL=6076],uroplectes[&&NHX:TOL=6077],vachoniolus[&&NHX:TOL=6078],vachonus[&&NHX:TOL=6079],zabius[&&NHX:TOL=6080])buthidae[&&NHX:TOL=6082],chaerilus[&&NHX:TOL=6083])buthoidea[&&NHX:TOL=6151],((((chactopsis[&&NHX:TOL=6086],broteochactas[&&NHX:TOL=6087],brotheas[&&NHX:TOL=6088])[&&NHX:TOL=6085],vachoniochactas[&&NHX:TOL=6089],nullibrotheas[&&NHX:TOL=6090],teuthraustes[&&NHX:TOL=6091],chactas[&&NHX:TOL=6092])chactidae[&&NHX:TOL=6094],((troglocormus[&&NHX:TOL=6114],(plesiochactas[&&NHX:TOL=6116],megacormus[&&NHX:TOL=6117],euscorpius[&&NHX:TOL=6118])[&&NHX:TOL=6115])euscorpiidae[&&NHX:TOL=6096],(scorpiops scorpiops[&&NHX:TOL=6174],parascorpiops[&&NHX:TOL=6175],(scorpiops alloscorpiops[&&NHX:TOL=6177],scorpiops euscorpiops[&&NHX:TOL=6178],(scorpiops neoscorpiops[&&NHX:TOL=6180],dasyscorpiops[&&NHX:TOL=6181])[&&NHX:TOL=6179])[&&NHX:TOL=6176])scorpiopsidae[&&NHX:TOL=6097])[&&NHX:TOL=6095])chactoidea[&&NHX:TOL=6153],((((scorpio[&&NHX:TOL=6158],(opisthophthalmus[&&NHX:TOL=6160],(heterometrus[&&NHX:TOL=6162],pandinus[&&NHX:TOL=6163])[&&NHX:TOL=6161])[&&NHX:TOL=6159])scorpionidae[&&NHX:TOL=6166],(nebo[&&NHX:TOL=6101],(heteronebo[&&NHX:TOL=6103],(((diplocentrus[&&NHX:TOL=6107],didymocentrus[&&NHX:TOL=6108])[&&NHX:TOL=6106],bioculus[&&NHX:TOL=6109])[&&NHX:TOL=6105],cazierius[&&NHX:TOL=6110],oiclus[&&NHX:TOL=6111],tarsoporosus[&&NHX:TOL=6112])[&&NHX:TOL=6104])diplocentrinae[&&NHX:TOL=6102])diplocentridae[&&NHX:TOL=6167])[&&NHX:TOL=6165],(urodacidae[&&NHX:TOL=6169],((heteroscorpion[&&NHX:TOL=6120],((hemiscorpius[&&NHX:TOL=6123],habibiella[&&NHX:TOL=6124])hemiscorpiinae[&&NHX:TOL=6122],(((iomachus[&&NHX:TOL=6128],liocheles[&&NHX:TOL=6129])[&&NHX:TOL=6127],chiromachus[&&NHX:TOL=6130])[&&NHX:TOL=6126],opisthacanthus[&&NHX:TOL=6131],hadogenes[&&NHX:TOL=6132],chiromachetes[&&NHX:TOL=6133],cheloctonus[&&NHX:TOL=6134])ischnurinae[&&NHX:TOL=6125])[&&NHX:TOL=6121])ischnuridae[&&NHX:TOL=6171],(lisposoma[&&NHX:TOL=6011],(thestylus[&&NHX:TOL=6013],(phoniocercus[&&NHX:TOL=6015],(((bothriurus[&&NHX:TOL=6019],(timogenes[&&NHX:TOL=6021],vachonia[&&NHX:TOL=6022])[&&NHX:TOL=6020])[&&NHX:TOL=6018],(urophonius[&&NHX:TOL=6024],centromachetes[&&NHX:TOL=6025],cercophonius[&&NHX:TOL=6026])[&&NHX:TOL=6023])[&&NHX:TOL=6017],brachistosternus[&&NHX:TOL=6027],orobothriurus[&&NHX:TOL=6028],tehuankea[&&NHX:TOL=6029])[&&NHX:TOL=6016])[&&NHX:TOL=6014])bothriurinae[&&NHX:TOL=6012])bothriuridae[&&NHX:TOL=6172])[&&NHX:TOL=6170])[&&NHX:TOL=6168])scorpionoidea[&&NHX:TOL=6155],((((vaejovis mexicanus group[&&NHX:TOL=6195],(vaejovis nitidulus group[&&NHX:TOL=6197],(pseudouroctonus reddelli[&&NHX:TOL=6199],( pseudouroctonus bogerti group[&&NHX:TOL=6201], pseudouroctonus minimus group[&&NHX:TOL=6202])[&&NHX:TOL=6200])[&&NHX:TOL=6198],(((vaejovis eusthenura group[&&NHX:TOL=6206],vaejovis punctipalpi group[&&NHX:TOL=6207])[&&NHX:TOL=6205],syntropis[&&NHX:TOL=6208])[&&NHX:TOL=6204],serradigitus[&&NHX:TOL=6209])[&&NHX:TOL=6203],(((vejovoidus[&&NHX:TOL=6213],smeringurus[&&NHX:TOL=6214])[&&NHX:TOL=6212],paruroctonus[&&NHX:TOL=6215])[&&NHX:TOL=6211],paravaejovis[&&NHX:TOL=6216])[&&NHX:TOL=6210])[&&NHX:TOL=6196])[&&NHX:TOL=6194],(uroctonus[&&NHX:TOL=6218],(uroctonites[&&NHX:TOL=6220],vaejovis lindsayi[&&NHX:TOL=6221])[&&NHX:TOL=6219])[&&NHX:TOL=6217])vaejovidae[&&NHX:TOL=6224],(((anuroctonus[&&NHX:TOL=6138],hadrurus[&&NHX:TOL=6139])[&&NHX:TOL=6137],(caraboctonus[&&NHX:TOL=6141],hadruroides[&&NHX:TOL=6142])[&&NHX:TOL=6140])[&&NHX:TOL=6136],(calchas[&&NHX:TOL=6144],irurus[&&NHX:TOL=6145])[&&NHX:TOL=6143])iuridae[&&NHX:TOL=6225])[&&NHX:TOL=6223],(((((typhlochactas[&&NHX:TOL=6187],sotanochactas[&&NHX:TOL=6188])[&&NHX:TOL=6186],alacran[&&NHX:TOL=6189])typhlochactinae[&&NHX:TOL=6185],belisarius[&&NHX:TOL=6190])[&&NHX:TOL=6184],troglotayosicus[&&NHX:TOL=6191])[&&NHX:TOL=6183],superstitionia[&&NHX:TOL=6192])superstitionidae[&&NHX:TOL=6226])vaejovoidea[&&NHX:TOL=6156])[&&NHX:TOL=6154])[&&NHX:TOL=6152])orthosterni[&&NHX:TOL=6150])neoscorpionina[&&NHX:TOL=6148])scorpiones[&&NHX:TOL=6009])[&&NHX:TOL=6007])scorpionida[&&NHX:TOL=2558],(pseudoscorpiones[&&NHX:TOL=2560],(((ammotrecha[&&NHX:TOL=67204],ammotrechella[&&NHX:TOL=67205],ammotrechesta[&&NHX:TOL=67206],ammotrechinus[&&NHX:TOL=67207],ammotrechona[&&NHX:TOL=67208],ammotrechula[&&NHX:TOL=67209],antillotrecha[&&NHX:TOL=67210],campostrecha[&&NHX:TOL=67211],dasycleobis[&&NHX:TOL=67212],neocleobis[&&NHX:TOL=67213],pseudocleobis[&&NHX:TOL=67214])ammotrechinae[&&NHX:TOL=67203],mortola mortola[&&NHX:TOL=67215],nothopuga[&&NHX:TOL=67216],oltacola[&&NHX:TOL=67217],saronominae[&&NHX:TOL=67218],chileotrecha atacamensis[&&NHX:TOL=67219],eutrecha longirostris[&&NHX:TOL=67220],xenotrecha huebneri[&&NHX:TOL=67221],happlodontus proterus[&&NHX:EXT=Y:TOL=67222])ammotrechidae[&&NHX:TOL=29277],ceromidae[&&NHX:TOL=29278],daesiidae[&&NHX:TOL=29279],eremobatidae[&&NHX:TOL=29280],galeodidae[&&NHX:TOL=29281],gylippidae[&&NHX:TOL=29282],hexisopodidae[&&NHX:TOL=29283],karschiidae[&&NHX:TOL=29284],melanoblossidae[&&NHX:TOL=29285],mummuciidae[&&NHX:TOL=29286],rhagodidae[&&NHX:TOL=29287],solpugidae[&&NHX:TOL=29288])solifugae[&&NHX:TOL=2561])[&&NHX:TOL=2559])[&&NHX:TOL=2557])[&&NHX:TOL=2555])arachnida[&&NHX:TOL=2536],(((slimoniidae[&&NHX:EXT=Y:TOL=8164],(hughmilleriidae[&&NHX:EXT=Y:TOL=8166],carcinosomatidae[&&NHX:EXT=Y:TOL=8167],adelophthalmidae[&&NHX:EXT=Y:TOL=8168])hughmillerioidea[&&NHX:EXT=Y:TOL=8165],(mixopteridae[&&NHX:EXT=Y:TOL=8170],lanarkopteridae[&&NHX:EXT=Y:TOL=8171])mixopteroidea[&&NHX:EXT=Y:TOL=8169],megalograptidae[&&NHX:EXT=Y:TOL=8172],(eurypteridae[&&NHX:EXT=Y:TOL=8174],dolichopteridae[&&NHX:EXT=Y:TOL=8175],erieopteridae[&&NHX:EXT=Y:TOL=8176])eurypteroidea[&&NHX:EXT=Y:TOL=8173],(stylonuridae[&&NHX:EXT=Y:TOL=8178],drepanopteridae[&&NHX:EXT=Y:TOL=8179],parastylonuridae[&&NHX:EXT=Y:TOL=8180],laurieipteridae[&&NHX:EXT=Y:TOL=8181])stylonuroidea[&&NHX:EXT=Y:TOL=8177],(kokomopteridae[&&NHX:EXT=Y:TOL=8183],hardieopteridae[&&NHX:EXT=Y:TOL=8184])kokomopteroidea[&&NHX:EXT=Y:TOL=8182],brachyopterellidae[&&NHX:EXT=Y:TOL=8185],rhenopteridae[&&NHX:EXT=Y:TOL=8186],(mycteropidae[&&NHX:EXT=Y:TOL=8188],woodwardopteridae[&&NHX:EXT=Y:TOL=8189])mycopteropoidea[&&NHX:EXT=Y:TOL=8187])[&&NHX:EXT=Y:TOL=8163],(jaekelopteridae[&&NHX:EXT=Y:TOL=8191],pterygotidae[&&NHX:EXT=Y:TOL=8192])pterygotoidea[&&NHX:EXT=Y:TOL=8190])[&&NHX:EXT=Y:TOL=8162],willwerathia[&&NHX:EXT=Y:TOL=8193],tylopterella[&&NHX:EXT=Y:TOL=8194],tarsopterella[&&NHX:EXT=Y:TOL=8195],pittsfordipterus[&&NHX:EXT=Y:TOL=8196],hastimima[&&NHX:EXT=Y:TOL=8197],dorfopterus[&&NHX:EXT=Y:TOL=8198],melbournopterus[&&NHX:EXT=Y:TOL=8199])eurypterida[&&NHX:EXT=Y:TOL=2537],(((((((((((limulus polyphemus[&&NHX:TOL=14737],limulus coffini[&&NHX:EXT=Y:TOL=14738],limulus woodwardi[&&NHX:EXT=Y:TOL=14739],limulus henkeli[&&NHX:EXT=Y:TOL=14740],limulus priscus[&&NHX:EXT=Y:TOL=14741],limulus sandbergeri[&&NHX:EXT=Y:TOL=14742])limulus[&&NHX:TOL=14736],carcinoscorpius rotundicauda[&&NHX:TOL=14743],(tachypleus tridentatus[&&NHX:TOL=14745],tachypleus gigas[&&NHX:TOL=14746],tachypleus decheni[&&NHX:EXT=Y:TOL=14747])tachypleus[&&NHX:TOL=14744],casterolimulus kletti[&&NHX:EXT=Y:TOL=14748],(mesolimulus sibiricus[&&NHX:EXT=Y:TOL=14750],mesolimulus crespelli[&&NHX:EXT=Y:TOL=14751],mesolimulus walchi[&&NHX:EXT=Y:TOL=14752],mesolimulus syriacus[&&NHX:EXT=Y:TOL=14753])mesolimulus[&&NHX:EXT=Y:TOL=14749],victalimulus mcqueeni[&&NHX:EXT=Y:TOL=14754],(limulitella bronni[&&NHX:EXT=Y:TOL=14756],limulitella volgensis[&&NHX:EXT=Y:TOL=14757],limulitella vicensis[&&NHX:EXT=Y:TOL=14758],limulitella liasokeuperinus[&&NHX:EXT=Y:TOL=14759])limulitella[&&NHX:EXT=Y:TOL=14755],tarracolimulus crespelli[&&NHX:EXT=Y:TOL=14760],heterolimulus gadeai[&&NHX:EXT=Y:TOL=14761],austrolimulus fletcheri[&&NHX:EXT=Y:TOL=14762],psammolimulus gottingensis[&&NHX:EXT=Y:TOL=14763],valloisella  lievensis[&&NHX:EXT=Y:TOL=14764])limuloidea[&&NHX:TOL=14774],(paleolimulus[&&NHX:EXT=Y:TOL=14776],xaniopyramis[&&NHX:EXT=Y:TOL=14777])paleolimulidae[&&NHX:EXT=Y:TOL=14775])limulina[&&NHX:TOL=14773],rolfeia[&&NHX:EXT=Y:TOL=14778])[&&NHX:TOL=14772],bellinuroopsis[&&NHX:EXT=Y:TOL=14779])[&&NHX:TOL=14771],((liomesaspis[&&NHX:EXT=Y:TOL=14782],euproops[&&NHX:EXT=Y:TOL=14783])[&&NHX:EXT=Y:TOL=14781],bellinurus[&&NHX:EXT=Y:TOL=14784])bellinurina[&&NHX:EXT=Y:TOL=14780])xiphosurida[&&NHX:TOL=14770],kasibelinurus[&&NHX:EXT=Y:TOL=14785])[&&NHX:TOL=14769],cyamocephalus[&&NHX:EXT=Y:TOL=14786],pseudoniscus[&&NHX:EXT=Y:TOL=14787])[&&NHX:TOL=14768],pasternakevia[&&NHX:EXT=Y:TOL=14788])[&&NHX:TOL=14767],bunodes[&&NHX:EXT=Y:TOL=14789],limuloides[&&NHX:EXT=Y:TOL=14790])[&&NHX:TOL=14766],weinbergina[&&NHX:EXT=Y:TOL=14791],legrandella[&&NHX:EXT=Y:TOL=14792])xiphosura[&&NHX:TOL=2538],((pallenopsis[&&NHX:TOL=14696],callipallenidae[&&NHX:TOL=14697],phoxichilidiidae[&&NHX:TOL=14698],nymphonidae[&&NHX:TOL=14699],pycnogonidae[&&NHX:TOL=14700],endeis[&&NHX:TOL=14701])[&&NHX:TOL=14695],palaeoisopus problematicus[&&NHX:EXT=Y:TOL=26743],palaeopantopus maucheri[&&NHX:EXT=Y:TOL=26744],palaeothea devonica[&&NHX:EXT=Y:TOL=26745],haliestes dasos[&&NHX:EXT=Y:TOL=26747],cambropycnogon klausmuelleri[&&NHX:EXT=Y:TOL=26746],(ammotheidae[&&NHX:TOL=14703],colossendeidae[&&NHX:TOL=14704],rhynchothorax[&&NHX:TOL=14705],tanystylum[&&NHX:TOL=14706],austrodecus[&&NHX:TOL=14707])[&&NHX:TOL=14702])pycnogonida[&&NHX:TOL=2539])chelicerata[&&NHX:TOL=2535],(agnostida[&&NHX:EXT=Y:TOL=14727],redlichiida[&&NHX:EXT=Y:TOL=14728],corynexochida[&&NHX:EXT=Y:TOL=14729],ptychopariida[&&NHX:EXT=Y:TOL=14730],phacopida[&&NHX:EXT=Y:TOL=14731],proetida[&&NHX:EXT=Y:TOL=14732],lichida[&&NHX:EXT=Y:TOL=14733],asaphida[&&NHX:EXT=Y:TOL=14734])trilobites[&&NHX:EXT=Y:TOL=2540])arthropoda[&&NHX:TOL=2469],(peripatidae[&&NHX:TOL=20356],peripatopsidae[&&NHX:TOL=20357])onychophora[&&NHX:TOL=2470],((apochela[&&NHX:TOL=26485],parachela[&&NHX:TOL=26486])eutardigrada[&&NHX:TOL=20482],thermozodium esakii[&&NHX:TOL=20481],(arthrotardigrada[&&NHX:TOL=26483],echiniscoidea[&&NHX:TOL=26484])heterotardigrada[&&NHX:TOL=20480])tardigrada[&&NHX:TOL=2471])[&&NHX:TOL=2468],((trichocephalida[&&NHX:TOL=20296],mermithida[&&NHX:TOL=20297],dorylaimida[&&NHX:TOL=20298],mononchida[&&NHX:TOL=20299])[&&NHX:TOL=20295],(triplonchida[&&NHX:TOL=20301],enoplida[&&NHX:TOL=20302])[&&NHX:TOL=20300],monhysterida[&&NHX:TOL=20303],(chromadorida[&&NHX:TOL=20305],((rhigonematida[&&NHX:TOL=20308],oxyurida[&&NHX:TOL=20309],ascaridida[&&NHX:TOL=20310],spirurida[&&NHX:TOL=20311])[&&NHX:TOL=20307],((tylenchida[&&NHX:TOL=20314],aphelenchida[&&NHX:TOL=20315],cephalobidae[&&NHX:TOL=20316])[&&NHX:TOL=20313],(strongyloididae[&&NHX:TOL=20318],steinernematidae[&&NHX:TOL=20319],panagrolaimidae[&&NHX:TOL=20320])[&&NHX:TOL=20317])[&&NHX:TOL=20312],(strongylida[&&NHX:TOL=20322],rhabditina[&&NHX:TOL=20323],diplogasterida[&&NHX:TOL=20324])[&&NHX:TOL=20321])secernentea[&&NHX:TOL=20306])[&&NHX:TOL=20304])nematoda[&&NHX:TOL=2472],(nectonema[&&NHX:TOL=20326],((gordius[&&NHX:TOL=20329],acutogordius[&&NHX:TOL=20330])[&&NHX:TOL=20328],chordodes[&&NHX:TOL=20331],paragordius[&&NHX:TOL=20332],parachordodes[&&NHX:TOL=20333],gordonius[&&NHX:TOL=20334],beatogordius[&&NHX:TOL=20335],euchordodes[&&NHX:TOL=20336],neochordodes[&&NHX:TOL=20337],pseudochordodes[&&NHX:TOL=20338],digordius[&&NHX:TOL=20339],progordius maculosus[&&NHX:TOL=20340],noteochordodes[&&NHX:TOL=20341],semigordionus circumannulatus[&&NHX:TOL=20342],pseudogordius tanganyikae[&&NHX:TOL=20343],(spinochordodes[&&NHX:TOL=20345],dacochordodes bacescui[&&NHX:TOL=20346],lanochordodes zeravshanicus[&&NHX:TOL=20347],pantachordodes europaeus[&&NHX:TOL=20348])[&&NHX:TOL=20344])gordiida[&&NHX:TOL=20327])nematomorpha[&&NHX:TOL=2473],(((((echinoderidae[&&NHX:TOL=19353],dracoderidae[&&NHX:TOL=19354])[&&NHX:TOL=19352],zelinkaderidae[&&NHX:TOL=19355])[&&NHX:TOL=19351],centroderidae[&&NHX:TOL=19356])[&&NHX:TOL=19350],(semnoderidae[&&NHX:TOL=19358],cateridae[&&NHX:TOL=19359])[&&NHX:TOL=19357])cyclorhagida[&&NHX:TOL=19349],(neocentrophyidae[&&NHX:TOL=19361],pycnophyidae[&&NHX:TOL=19362])homalorhagida[&&NHX:TOL=19360])kinorhyncha[&&NHX:TOL=2474],(nanaloricus[&&NHX:TOL=19364],pliciloricus[&&NHX:TOL=19365],rugiloricus[&&NHX:TOL=19366])loricifera[&&NHX:TOL=2475],(priapulidae[&&NHX:TOL=20444],tubiluchidae[&&NHX:TOL=20445],maccabaeidae[&&NHX:TOL=20446])priapulida[&&NHX:TOL=2476])ecdysozoa[&&NHX:TOL=2467],(((spadella cephaloptera[&&NHX:TOL=68975],spadella angulata[&&NHX:TOL=68976],spadella antarctica[&&NHX:TOL=68977],spadella birostrata[&&NHX:TOL=68978],spadella boucheri[&&NHX:TOL=68979],spadella bradshawi[&&NHX:TOL=68980],spadella equidentata[&&NHX:TOL=68981],spadella gaetanoi[&&NHX:TOL=68982],spadella japonica[&&NHX:TOL=68983],spadella ledoyeri[&&NHX:TOL=68984],spadella moretonensis[&&NHX:TOL=68985])spadella[&&NHX:TOL=14810],(paraspadella schizoptera[&&NHX:TOL=68986],paraspadella anops[&&NHX:TOL=68987],paraspadella caecafea[&&NHX:TOL=68988],paraspadella gotoi[&&NHX:TOL=68989],paraspadella johnstoni[&&NHX:TOL=68990],paraspadella legazpichessi[&&NHX:TOL=68991],paraspadella nana[&&NHX:TOL=68992],paraspadella pimukatharos[&&NHX:TOL=68993],paraspadella pulchella[&&NHX:TOL=68994],paraspadella sheardi[&&NHX:TOL=68995])paraspadella[&&NHX:TOL=59551])spadellidae[&&NHX:TOL=59550],pterosagitta draco[&&NHX:TOL=14816],(krohnitta subtilis[&&NHX:TOL=68996],krohnitta pacifica[&&NHX:TOL=68997])krohnitta[&&NHX:TOL=14813],((sagitta bipunctata[&&NHX:TOL=69030],sagitta bombayensis[&&NHX:TOL=69031],sagitta helenae[&&NHX:TOL=69032])sagitta[&&NHX:TOL=14817],(serratosagitta serratodentata[&&NHX:TOL=69033],serratosagitta bierii[&&NHX:TOL=69034],serratosagitta pacifica[&&NHX:TOL=69035],serratosagitta pseudoserratodentata[&&NHX:TOL=69036],serratosagitta tasmanica[&&NHX:TOL=69037])serratosagitta[&&NHX:TOL=59556],(parasagitta elegans[&&NHX:TOL=69038],parasagitta euneritica[&&NHX:TOL=69039],parasagitta friderici[&&NHX:TOL=69040],parasagitta megalophthalma[&&NHX:TOL=69041],parasagitta peruviana[&&NHX:TOL=69042],parasagitta popovicii[&&NHX:TOL=69043],parasagitta setosa[&&NHX:TOL=69044],parasagitta tenuis[&&NHX:TOL=69045])parasagitta[&&NHX:TOL=59557],(aidanosagitta neglecta[&&NHX:TOL=69046],aidanosagitta alvarinoae[&&NHX:TOL=69047],aidanosagitta bedfordi[&&NHX:TOL=69048],aidanosagitta crassa[&&NHX:TOL=69049],aidanosagitta delicata[&&NHX:TOL=69050],aidanosagitta demipenna[&&NHX:TOL=69051],aidanosagitta erythraea[&&NHX:TOL=69052],aidanosagitta guileri[&&NHX:TOL=69053],aidanosagitta johorensis[&&NHX:TOL=69054],aidanosagitta oceania[&&NHX:TOL=69055],aidanosagitta ophicephala[&&NHX:TOL=69056],aidanosagitta regularis[&&NHX:TOL=69057],aidanosagitta septata[&&NHX:TOL=69058],aidanosagitta tropica[&&NHX:TOL=69059])aidanosagitta[&&NHX:TOL=59558],mesosagitta minima[&&NHX:TOL=59559],(flaccisagitta hexaptera[&&NHX:TOL=69060],flaccisagitta adenensis[&&NHX:TOL=69061],flaccisagitta enflata[&&NHX:TOL=69062])flaccisagitta[&&NHX:TOL=59560],caecosagitta macrocephala[&&NHX:TOL=59567],(decipisagitta decipiens[&&NHX:TOL=69063],decipisagitta sibogae[&&NHX:TOL=69064])decipisagitta[&&NHX:TOL=59568],(ferosagitta robusta[&&NHX:TOL=69065],ferosagitta tokiokai[&&NHX:TOL=69066],ferosagitta americana[&&NHX:TOL=69067],ferosagitta ferox[&&NHX:TOL=69068],ferosagitta hispida[&&NHX:TOL=69069],ferosagitta galerita[&&NHX:TOL=69070],ferosagitta madhupratapi[&&NHX:TOL=69071],ferosagitta siamensis[&&NHX:TOL=69072])ferosagitta[&&NHX:TOL=59569],(pseudosagitta lyra[&&NHX:TOL=69073],pseudosagitta gazellae[&&NHX:TOL=69074],pseudosagitta maxima[&&NHX:TOL=69075])pseudosagitta[&&NHX:TOL=59570],(solidosagitta planctonis[&&NHX:TOL=69076],solidosagitta marri[&&NHX:TOL=69077])solidosagitta[&&NHX:TOL=59571],(zonosagitta bedoti[&&NHX:TOL=69078],zonosagitta izuensis[&&NHX:TOL=69079],zonosagitta littoralis[&&NHX:TOL=69080],zonosagitta lucida[&&NHX:TOL=69081],zonosagitta pulchra[&&NHX:TOL=69082])zonosagitta[&&NHX:TOL=59572],adhesisagitta hispida[&&NHX:TOL=69083])sagittidae[&&NHX:TOL=59555],((eukrohnia hamata[&&NHX:TOL=68998],eukrohnia bathyantarctica[&&NHX:TOL=68999],eukrohnia bathypelagica[&&NHX:TOL=69000],eukrohnia calliops[&&NHX:TOL=69001],eukrohnia flaccicoeca[&&NHX:TOL=69002],eukrohnia fowleri[&&NHX:TOL=69003],eukrohnia kitoui[&&NHX:TOL=69004],eukrohnia macroneura[&&NHX:TOL=69005],eukrohnia minuta[&&NHX:TOL=69006],eukrohnia proboscidea[&&NHX:TOL=69007],eukrohnia sinica[&&NHX:TOL=69008])eukrohnia[&&NHX:TOL=14811],(heterokrohnia mirabilis[&&NHX:TOL=69009],heterokrohnia alvinae[&&NHX:TOL=69010],heterokrohnia angeli[&&NHX:TOL=69011],heterokrohnia bathybia[&&NHX:TOL=69012],heterokrohnia biscayensis[&&NHX:TOL=69013],heterokrohnia curvichaeta[&&NHX:TOL=69014],heterokrohnia davidi[&&NHX:TOL=69015],heterokrohnia discoveryi[&&NHX:TOL=69016],heterokrohnia fragilis[&&NHX:TOL=69017],heterokrohnia furnestinae[&&NHX:TOL=69018],heterokrohnia heterodonta[&&NHX:TOL=69019],heterokrohnia involucrum[&&NHX:TOL=69020],heterokrohnia longidentata[&&NHX:TOL=69021],heterokrohnia mirabiloides[&&NHX:TOL=69022],heterokrohnia murina[&&NHX:TOL=69023],heterokrohnia wishernae[&&NHX:TOL=69024])heterokrohnia[&&NHX:TOL=59554],bathyspadella edentata[&&NHX:TOL=59553],xenokrohnia sorbei[&&NHX:TOL=59564],(archeterokrohnia rubra[&&NHX:TOL=69025],archeterokrohnia longicaudata[&&NHX:TOL=69026],archeterokrohnia palpifera[&&NHX:TOL=69027])archeterokrohnia[&&NHX:TOL=59563])eukrohniidaeheterokrohniidae[&&NHX:TOL=59552],calispadella alata[&&NHX:TOL=59561],hemispadella dauvini[&&NHX:TOL=59562],(krohnittella boureei[&&NHX:TOL=69028],krohnittella tokiokai[&&NHX:TOL=69029])krohnittella[&&NHX:TOL=59565],bathybelos typhlops[&&NHX:TOL=59566],pterokrohnia arabica[&&NHX:TOL=59573],paucijaculum samamithion[&&NHX:EXT=Y:TOL=69086],eoserratosagitta serrata[&&NHX:EXT=Y:TOL=69090],titerina rokycanensis[&&NHX:EXT=Y:TOL=69089],oesia disjuncta[&&NHX:EXT=Y:TOL=69088],eognathacantha ercainella[&&NHX:EXT=Y:TOL=69087])chaetognatha[&&NHX:TOL=2478],((planodasyidae[&&NHX:TOL=19275],lepidodasyidae[&&NHX:TOL=19276],thaumastodermatidae[&&NHX:TOL=19277],macrodasyidae[&&NHX:TOL=19278],turbanellidae[&&NHX:TOL=19279],dactylopodolidae[&&NHX:TOL=19280])macrodasyida[&&NHX:TOL=19274],(neodasyidae[&&NHX:TOL=19282],(chaetonotidae[&&NHX:TOL=19284],xenotrichulidae[&&NHX:TOL=19285],dichaeturidae[&&NHX:TOL=19286],proichthydidae[&&NHX:TOL=19287],neogosseidae[&&NHX:TOL=19288],dasydytidae[&&NHX:TOL=19289])paucitubulatina[&&NHX:TOL=19283])chaetonotida[&&NHX:TOL=19281])gastrotricha[&&NHX:TOL=2479],((archiacanthocephala[&&NHX:TOL=20449],((polyacanthorhynchus caballeroi[&&NHX:TOL=68547],polyacanthorhynchus kenyensis[&&NHX:TOL=68548],polyacanthorhynchus macrorhynchus[&&NHX:TOL=68549],polyacanthorhynchus rhopalorhynchus[&&NHX:TOL=68550])polyacanthorhynchus[&&NHX:TOL=68546],eoacanthecephala[&&NHX:TOL=20450],palaeacanthocephala[&&NHX:TOL=20448])[&&NHX:TOL=68545])acanthocephala[&&NHX:TOL=20452],(seison annulatus[&&NHX:TOL=68362],(seison nebaliae[&&NHX:TOL=68363],seison africanus[&&NHX:TOL=68513])[&&NHX:TOL=68512])seisonidea[&&NHX:TOL=20453],((habrotrocha[&&NHX:TOL=68365],otostephanos[&&NHX:TOL=68366],scepanotrocha[&&NHX:TOL=68367])habrotrochidae[&&NHX:TOL=68364],(abrochtha[&&NHX:TOL=68369],henoceros[&&NHX:TOL=68370],philodinavus[&&NHX:TOL=68371])philodinavidae[&&NHX:TOL=68368],(anomopus[&&NHX:TOL=68373],ceratotrocha[&&NHX:TOL=68374],didymodactylus[&&NHX:TOL=68375],dissotrocha[&&NHX:TOL=68376],embata[&&NHX:TOL=68377],macrotrachela[&&NHX:TOL=68378],mniobia[&&NHX:TOL=68379],philodina[&&NHX:TOL=68380],pleuretra[&&NHX:TOL=68381],rotaria[&&NHX:TOL=68382],zelinkiella[&&NHX:TOL=68383])philodinidae[&&NHX:TOL=68372],(adineta[&&NHX:TOL=68385],bradyscela[&&NHX:TOL=68386])adinetidae[&&NHX:TOL=68384])bdelloidea[&&NHX:TOL=20454],(((asplanchna[&&NHX:TOL=68391],asplanchnopus[&&NHX:TOL=68392],harringia[&&NHX:TOL=68393])asplanchnidae[&&NHX:TOL=68390],birgea[&&NHX:TOL=68394],(anuraeopsis[&&NHX:TOL=68396],brachionus[&&NHX:TOL=68397],kellicottia[&&NHX:TOL=68398],keratella[&&NHX:TOL=68399],notholca[&&NHX:TOL=68400],plationus[&&NHX:TOL=68401],platyias[&&NHX:TOL=68402])brachionidae[&&NHX:TOL=68395],claria[&&NHX:TOL=68403],(albertia[&&NHX:TOL=68405],aspelta[&&NHX:TOL=68406],balatro[&&NHX:TOL=68407],dicranophoroides[&&NHX:TOL=68408],dicranophorus[&&NHX:TOL=68409],dorria[&&NHX:TOL=68410],encentrum[&&NHX:TOL=68411],erignatha[&&NHX:TOL=68412],glaciera[&&NHX:TOL=68413],inflatana[&&NHX:TOL=68414],kostea[&&NHX:TOL=68415],myersinella[&&NHX:TOL=68416],paradicranophorus[&&NHX:TOL=68417],parencentrum[&&NHX:TOL=68418],pedipartia[&&NHX:TOL=68419],streptognatha[&&NHX:TOL=68420],wierzejskiella[&&NHX:TOL=68421],wigrella[&&NHX:TOL=68422])dicranophoridae[&&NHX:TOL=68404],(cyrtonia[&&NHX:TOL=68424],epiphanes[&&NHX:TOL=68425],mikrocodides[&&NHX:TOL=68426],proalides[&&NHX:TOL=68427],rhinoglena[&&NHX:TOL=68428])epiphanidae[&&NHX:TOL=68423],(beauchampiella[&&NHX:TOL=68430],dipleuchlanis[&&NHX:TOL=68431],diplois[&&NHX:TOL=68432],euchlanis[&&NHX:TOL=68433],tripleuchlanis[&&NHX:TOL=68434])euchlanidae[&&NHX:TOL=68429],(ascomorpha[&&NHX:TOL=68436],gastropus[&&NHX:TOL=68437])gastropodidae[&&NHX:TOL=68435],itura[&&NHX:TOL=68438],lecane[&&NHX:TOL=68439],(colurella[&&NHX:TOL=68441],lepadella[&&NHX:TOL=68442],paracolurella[&&NHX:TOL=68443],squatinella[&&NHX:TOL=68444])lepadellidae[&&NHX:TOL=68440],lindia[&&NHX:TOL=68445],microcodon[&&NHX:TOL=68446],(lophocharis[&&NHX:TOL=68448],mytilina[&&NHX:TOL=68449])mytilinidae[&&NHX:TOL=68447],(cephalodella[&&NHX:TOL=68451],dorystoma[&&NHX:TOL=68452],drilophaga[&&NHX:TOL=68453],enteroplea[&&NHX:TOL=68454],eosphora[&&NHX:TOL=68455],eothinia[&&NHX:TOL=68456],monommata[&&NHX:TOL=68457],notommata[&&NHX:TOL=68458],pleurata[&&NHX:TOL=68459],pleurotrocha[&&NHX:TOL=68460],pleurotrochopsis[&&NHX:TOL=68461],pseudoharringia[&&NHX:TOL=68462],resticula[&&NHX:TOL=68463],rousseletia[&&NHX:TOL=68464],sphyrias[&&NHX:TOL=68465],taphrocampa[&&NHX:TOL=68466],tylotrocha[&&NHX:TOL=68467])notommatidae[&&NHX:TOL=68450],(bryceella[&&NHX:TOL=68469],proales[&&NHX:TOL=68470],proalinopsis[&&NHX:TOL=68471],wulfertia[&&NHX:TOL=68472])proalidae[&&NHX:TOL=68468],scaridium[&&NHX:TOL=68473],(ploesoma[&&NHX:TOL=68475],polyarthra[&&NHX:TOL=68476],pseudoploesoma[&&NHX:TOL=68477],synchaeta[&&NHX:TOL=68478])synchaetidae[&&NHX:TOL=68474],tetrasiphon[&&NHX:TOL=68479],(ascomorphella[&&NHX:TOL=68481],elosa[&&NHX:TOL=68482],trichocerca[&&NHX:TOL=68483])trichocercidae[&&NHX:TOL=68480],(macrochaetus[&&NHX:TOL=68485],trichotria[&&NHX:TOL=68486],wolga[&&NHX:TOL=68487])trichotriidae[&&NHX:TOL=68484])ploima[&&NHX:TOL=68387],((conochilopsis[&&NHX:TOL=68489],conochilus[&&NHX:TOL=68490])conochilidae[&&NHX:TOL=68488],filinia[&&NHX:TOL=68491],(beauchampia[&&NHX:TOL=68493],floscularia[&&NHX:TOL=68494],lacinularia[&&NHX:TOL=68495],limnias[&&NHX:TOL=68496],octotrocha[&&NHX:TOL=68497],ptygura[&&NHX:TOL=68498],sinantherina[&&NHX:TOL=68499])flosculariidae[&&NHX:TOL=68492],hexarthra[&&NHX:TOL=68500],(anchitestudinella[&&NHX:TOL=68502],pompholyx[&&NHX:TOL=68503],testudinella[&&NHX:TOL=68504])testudinellidae[&&NHX:TOL=68501])flosculariacea[&&NHX:TOL=68388],((acyclus[&&NHX:TOL=68506],atrochus[&&NHX:TOL=68507],cupelopagis[&&NHX:TOL=68508])atrochidae[&&NHX:TOL=68505],(collotheca[&&NHX:TOL=68510],stephanoceros[&&NHX:TOL=68511])collothecidae[&&NHX:TOL=68509])collothecacea[&&NHX:TOL=68389])monogononta[&&NHX:TOL=20455])rotifera[&&NHX:TOL=2480],((haplognathia[&&NHX:TOL=19292],(pterognathia[&&NHX:TOL=19294],cosmognathia[&&NHX:TOL=19295])[&&NHX:TOL=19293])filospermoidea[&&NHX:TOL=19291],((nanognathia[&&NHX:TOL=19298],(vampyrognathia[&&NHX:TOL=19300],(onychognathia[&&NHX:TOL=19302],(valvognathia[&&NHX:TOL=19304],rastrognathia[&&NHX:TOL=19305])[&&NHX:TOL=19303])[&&NHX:TOL=19301])[&&NHX:TOL=19299])[&&NHX:TOL=19297],paucidentula[&&NHX:TOL=19306],((gnathostomaria[&&NHX:TOL=19309],(goannagnathia[&&NHX:TOL=19311],((clausognathia[&&NHX:TOL=19314],(agnathiella[&&NHX:TOL=19316],paragnathiella[&&NHX:TOL=19317])[&&NHX:TOL=19315])[&&NHX:TOL=19313],((labidognathia[&&NHX:TOL=19320],mesognatharia[&&NHX:TOL=19321])[&&NHX:TOL=19319],tenuignathia[&&NHX:TOL=19322])[&&NHX:TOL=19318])[&&NHX:TOL=19312])[&&NHX:TOL=19310])[&&NHX:TOL=19308],(problognathia[&&NHX:TOL=19324],((corculognathia[&&NHX:TOL=19327],gnathostomula[&&NHX:TOL=19328],semaeognathia[&&NHX:TOL=19329],ratugnathia[&&NHX:TOL=19330])[&&NHX:TOL=19326],((austrognathia[&&NHX:TOL=19333],austrognatharia[&&NHX:TOL=19334])[&&NHX:TOL=19332],triplignathia[&&NHX:TOL=19335])[&&NHX:TOL=19331])[&&NHX:TOL=19325])[&&NHX:TOL=19323])[&&NHX:TOL=19307])bursovaginoidea[&&NHX:TOL=19296])gnathostomulida[&&NHX:TOL=2481],limnognathia maerski[&&NHX:TOL=2482],(symbion pandora[&&NHX:TOL=68758],symbion americanus[&&NHX:TOL=68759])cycliophora[&&NHX:TOL=2483],((conocyemidae[&&NHX:TOL=19369],dicyemidae[&&NHX:TOL=19370],kantharellidae[&&NHX:TOL=19371])rhombozoa[&&NHX:TOL=19368],(pelmatosphaeridae[&&NHX:TOL=19373],rhopaluridae[&&NHX:TOL=19374])orthonectida[&&NHX:TOL=19372])mesozoa[&&NHX:TOL=2484],((nemertodermatida[&&NHX:TOL=20382],acoela[&&NHX:TOL=20383],catenulida[&&NHX:TOL=20384],macrostomida[&&NHX:TOL=20385],lecithoepitheliata[&&NHX:TOL=20386],rhabdocoela[&&NHX:TOL=20387],prolecithophora[&&NHX:TOL=20388],proseriata[&&NHX:TOL=20389],tricladida[&&NHX:TOL=20390],polycladida[&&NHX:TOL=20391])turbellaria[&&NHX:TOL=20381],(((monopisthocotylea[&&NHX:TOL=20395],polyopishtocotylea[&&NHX:TOL=20396])monogenea[&&NHX:TOL=20394],(digenea[&&NHX:TOL=20398],(aspidogastridae[&&NHX:TOL=20427],(stichocotylidae[&&NHX:TOL=20429],multicalycidae[&&NHX:TOL=20430],rugogastridae[&&NHX:TOL=20431])[&&NHX:TOL=20428])aspidogastrea[&&NHX:TOL=20399])trematoda[&&NHX:TOL=20397])[&&NHX:TOL=20393],((gyrocotylidea[&&NHX:TOL=20378],((amphilina foliacea[&&NHX:TOL=20407],amphilina japonica[&&NHX:TOL=20408])[&&NHX:TOL=20406],((gigantolina elongata[&&NHX:TOL=20411],gigantolina magna[&&NHX:TOL=20412])[&&NHX:TOL=20410],(((schizochoerus janickii[&&NHX:TOL=20418],schizochoerus africanus[&&NHX:TOL=20419])[&&NHX:TOL=20417],schizochoerus liguloideus[&&NHX:TOL=20416])[&&NHX:TOL=20415],schizochoerus paragonopora[&&NHX:TOL=20414])[&&NHX:TOL=20413])[&&NHX:TOL=20409])amphilinidea[&&NHX:TOL=20379])cestodaria[&&NHX:TOL=20401],eucestoda[&&NHX:TOL=20402])cestoda[&&NHX:TOL=20400])[&&NHX:TOL=20392])platyhelminthes[&&NHX:TOL=2477],((((scolecida[&&NHX:TOL=2502],(((eunicida[&&NHX:TOL=2506],amphinomida[&&NHX:TOL=2507],((sigalionidae[&&NHX:TOL=22787],pholoidae[&&NHX:TOL=22786],aphroditoidea[&&NHX:TOL=22785])aphroditiformia[&&NHX:TOL=22809],pisionidae[&&NHX:TOL=22788],((((((((amphiduros[&&NHX:TOL=22820],amphiduropsis[&&NHX:TOL=22821])[&&NHX:TOL=22844],gyptis[&&NHX:TOL=22843])[&&NHX:TOL=22845],capricornia[&&NHX:TOL=22822],(hesiodeira[&&NHX:TOL=22823],parahesione[&&NHX:TOL=22824])[&&NHX:TOL=22846])gyptini[&&NHX:TOL=22847],(mahesia[&&NHX:TOL=22825],(((heteropodarke[&&NHX:TOL=22826],parasyllidea[&&NHX:TOL=22827])[&&NHX:TOL=22848],ophiodromus[&&NHX:TOL=22828])[&&NHX:TOL=22849],sinohesione[&&NHX:TOL=22829])[&&NHX:TOL=22850],podarkeopsis[&&NHX:TOL=22830])ophiodromini[&&NHX:TOL=22851])ophiodrominae[&&NHX:TOL=22852],(((((((bonuania parva[&&NHX:TOL=22831],nereimyra[&&NHX:TOL=22832])[&&NHX:TOL=22853],syllidia[&&NHX:TOL=22833])[&&NHX:TOL=22854],sirsoe[&&NHX:TOL=22834])[&&NHX:TOL=22855],micropodarke[&&NHX:TOL=22835])[&&NHX:TOL=22856],hesiospina[&&NHX:TOL=22836])[&&NHX:TOL=22857],psamathe[&&NHX:TOL=22837])psamathini[&&NHX:TOL=22858],((hesione[&&NHX:TOL=22838],wesenbergia[&&NHX:TOL=22839])[&&NHX:TOL=22859],(leocrates[&&NHX:TOL=22840],leocratides[&&NHX:TOL=22841])[&&NHX:TOL=22860])hesionini[&&NHX:TOL=22861])hesioninae[&&NHX:TOL=22862])[&&NHX:TOL=22863],hesiolyra bergi[&&NHX:TOL=22842])hesionidae[&&NHX:TOL=22789],nereididae[&&NHX:TOL=22790],chrysopetalidae[&&NHX:TOL=22791])[&&NHX:TOL=22810],nautiliniellidae[&&NHX:TOL=22792],pilargidae[&&NHX:TOL=22793],syllidae[&&NHX:TOL=22794],microphthalmus[&&NHX:TOL=22795],hesionides[&&NHX:TOL=22814])nereidiformia[&&NHX:TOL=22811],(glyceridae[&&NHX:TOL=22796],gonididae[&&NHX:TOL=22797])glyceriformia[&&NHX:TOL=22812],ichthyotomus[&&NHX:TOL=22798],lopadorhynchidae[&&NHX:TOL=22799],(iospilidae[&&NHX:TOL=22816],pontodora[&&NHX:TOL=22815],typhloscolecidae[&&NHX:TOL=22800])minor holopelagic phyllodocida[&&NHX:TOL=22819],myzostomida[&&NHX:TOL=22801],nephtyidae[&&NHX:TOL=22802],paralacydonia[&&NHX:TOL=22803],(phyllodocidae[&&NHX:TOL=22804],lacydonia[&&NHX:TOL=22805])[&&NHX:TOL=22813],sphaerodoridae[&&NHX:TOL=22806],tomopteridae[&&NHX:TOL=22807],antonbruunia[&&NHX:TOL=22808],struwela[&&NHX:TOL=22817],yndolacia[&&NHX:TOL=22818])phyllodocida[&&NHX:TOL=2508])[&&NHX:TOL=2505],spinther[&&NHX:TOL=2509],nerillidae[&&NHX:TOL=2510],aberranta[&&NHX:TOL=2511])aciculata[&&NHX:TOL=2504],((spionida[&&NHX:TOL=2514],sabellida[&&NHX:TOL=2515],(terebelliformia[&&NHX:TOL=2517],cirratuliformia[&&NHX:TOL=2518])terebellida[&&NHX:TOL=2516])[&&NHX:TOL=2513],protodrilida[&&NHX:TOL=2519],polygordiidae[&&NHX:TOL=2520])canalipalpata[&&NHX:TOL=2512])palpata[&&NHX:TOL=2503])[&&NHX:TOL=2501],aeolosomatidae  potamodrilus[&&NHX:TOL=2521],parergodrilidae  hrabeiella[&&NHX:TOL=2522],psammodrilidae[&&NHX:TOL=2523])polychaetes[&&NHX:TOL=2500],echiura[&&NHX:TOL=2524],clitellata[&&NHX:TOL=2525])annelida[&&NHX:TOL=2486],((cyclostomata[&&NHX:TOL=14799],fenestrata[&&NHX:TOL=14800],cryptostomata[&&NHX:TOL=14801],cystoporata[&&NHX:TOL=14802],trepostomata[&&NHX:TOL=14803])stenolaemata[&&NHX:TOL=14798],(ctenostomata[&&NHX:TOL=14805],cheilostomata[&&NHX:TOL=14806])gymnolaemata[&&NHX:TOL=14804],phylactolaemata[&&NHX:TOL=14807])bryozoa[&&NHX:TOL=2490],(siphonomecus multicinctus[&&NHX:TOL=20477],(sipunculus[&&NHX:TOL=20457],xenosiphon[&&NHX:TOL=20478])[&&NHX:TOL=114135],siphonosoma[&&NHX:TOL=20471],((themiste[&&NHX:TOL=20460],lagenopsis[&&NHX:TOL=20461],golfingia[&&NHX:TOL=20462],phascolopsis gouldii[&&NHX:TOL=20463],phascolion[&&NHX:TOL=20464],onchnesoma[&&NHX:TOL=20465],nephasoma[&&NHX:TOL=20466],thysanocardia[&&NHX:TOL=20467],phascolosoma turnerae[&&NHX:TOL=114136],apionsoma murinae[&&NHX:TOL=114137])golfingiiformes[&&NHX:TOL=20459],(phascolosoma[&&NHX:TOL=20469],apionsoma[&&NHX:TOL=20470],(aspidosiphon[&&NHX:TOL=20473],lithacrosiphon[&&NHX:TOL=20474],antillesoma antillarum[&&NHX:TOL=20475],cloeosiphon aspergillus[&&NHX:TOL=20476])[&&NHX:TOL=20472])phascolosomatidea[&&NHX:TOL=20468])[&&NHX:TOL=20458])sipuncula[&&NHX:TOL=2487],(solenogastres[&&NHX:TOL=19378],caudofoveata[&&NHX:TOL=19379],(lepidopleurina[&&NHX:TOL=20282],ischnochitonina[&&NHX:TOL=20283],acanthochitonina[&&NHX:TOL=20284],choriplacina[&&NHX:TOL=20285])polyplacophora[&&NHX:TOL=19380],(monoplacophora[&&NHX:TOL=19382],(protobranchia[&&NHX:TOL=19388],anomalodesmata[&&NHX:TOL=19389],pteriomorphia[&&NHX:TOL=19390],palaeoheterodonta[&&NHX:TOL=19391],heterodonta[&&NHX:TOL=19392])bivalvia[&&NHX:TOL=19383],scaphopoda[&&NHX:TOL=19384],(eogastropoda[&&NHX:TOL=20274],(vetigastropoda & relatives[&&NHX:TOL=20276],cocculinoidea[&&NHX:TOL=27793],neritopsina[&&NHX:TOL=20277],(((cyclophoroidea[&&NHX:TOL=27794],ampullarioidea[&&NHX:TOL=27795])architaenioglossa[&&NHX:TOL=27790],(campanilidae[&&NHX:TOL=27817],cerithioidea[&&NHX:TOL=27818],(((((atlanta brunnea[&&NHX:TOL=28759],atlanta turriculata[&&NHX:TOL=28773])atlanta brunnea species group[&&NHX:TOL=107970],(atlanta inflata[&&NHX:TOL=28764],atlanta helicinoidea[&&NHX:TOL=28762],atlanta californiensis[&&NHX:TOL=28755],atlanta selvagensis[&&NHX:TOL=103522])atlanta inflata species group[&&NHX:TOL=107969],(atlanta lesueurii[&&NHX:TOL=28765],atlanta oligogyra[&&NHX:TOL=28767])atlanta lesueuri species group[&&NHX:TOL=107971],(atlanta peronii[&&NHX:TOL=28769],atlanta fragilis[&&NHX:TOL=28757],atlanta rosea[&&NHX:TOL=28771],atlanta frontieri[&&NHX:TOL=28758])atlanta peroni species group[&&NHX:TOL=107972],(atlanta gaudichaudi[&&NHX:TOL=28760],atlanta plana[&&NHX:TOL=28770],atlanta echinogyra[&&NHX:TOL=28756])atlanta gaudichaudi species group[&&NHX:TOL=107973],(atlanta inclinata[&&NHX:TOL=28763],atlanta tokiokai[&&NHX:TOL=28772])atlanta inclinata species group[&&NHX:TOL=107974],(atlanta gibbosa[&&NHX:TOL=28761],atlanta meteori[&&NHX:TOL=28766])atlanta gibbosa species group[&&NHX:TOL=107975],atlanta peresi[&&NHX:TOL=28768])atlanta[&&NHX:TOL=28752],protatlanta souleyeti[&&NHX:TOL=28754],oxygyrus keraudreni[&&NHX:TOL=28753])atlantidae[&&NHX:TOL=28732],((carinaria challengeri[&&NHX:TOL=28746],carinaria cithara[&&NHX:TOL=28747],carinaria cristata[&&NHX:TOL=28748],carinaria galea[&&NHX:TOL=28749],carinaria japonica[&&NHX:TOL=28750],carinaria lamarcki[&&NHX:TOL=28751])carinaria[&&NHX:TOL=28741],(cardiapoda placenta[&&NHX:TOL=28744],cardiapoda richardi[&&NHX:TOL=28745])cardiapoda[&&NHX:TOL=28742],pterosoma planum[&&NHX:TOL=28743])carinariidae[&&NHX:TOL=28733],(firoloida demarestia[&&NHX:TOL=28736],(pterotrachea coronata[&&NHX:TOL=28738],pterotrachea hippocampus[&&NHX:TOL=28739],pterotrachea scutata[&&NHX:TOL=28740])pterotrachea[&&NHX:TOL=28737])pterotracheidae[&&NHX:TOL=28734])pterotracheoidea[&&NHX:TOL=27801],(muricoidea[&&NHX:TOL=27823],volutoidea[&&NHX:TOL=27824],buccinoidea[&&NHX:TOL=27825],cancellarioidea[&&NHX:TOL=27826],conoidea[&&NHX:TOL=27827])neogastropoda[&&NHX:TOL=27822],calyptraeidae[&&NHX:TOL=27802],capuloidea[&&NHX:TOL=27803],cingulopsoidea[&&NHX:TOL=27807],cypraeoidea[&&NHX:TOL=27804],eulimoidea[&&NHX:TOL=27821],ficoidea[&&NHX:TOL=27811],janthinoidea[&&NHX:TOL=27820],laubierinoidea[&&NHX:TOL=27813],littorinoidea[&&NHX:TOL=27806],naticoidea[&&NHX:TOL=27808],rissooidea[&&NHX:TOL=27809],stromboidea[&&NHX:TOL=27810],tonnoidea[&&NHX:TOL=27812],triphoroidea[&&NHX:TOL=27819],vanikoroidea[&&NHX:TOL=27814],velutinoidea[&&NHX:TOL=27805],vermetidae[&&NHX:TOL=27815],xenophoroidea[&&NHX:TOL=27816])hypsogastropoda[&&NHX:TOL=27800])sorbeoconcha[&&NHX:TOL=27791])caenogastropoda[&&NHX:TOL=20279],((opisthobranchia[&&NHX:TOL=117889],pulmonata[&&NHX:TOL=117890])euthyneura[&&NHX:TOL=117888],heterostropha[&&NHX:TOL=117891])heterobranchia[&&NHX:TOL=20280])apogastropoda[&&NHX:TOL=20278])orthogastropoda[&&NHX:TOL=20275])gastropoda[&&NHX:TOL=19385],(endoceratoidea[&&NHX:EXT=Y:TOL=19394],actinoceratoidea[&&NHX:EXT=Y:TOL=19395],((nautilus belauensis[&&NHX:TOL=20267],nautilus macromphalus[&&NHX:TOL=20268],nautilus pompilius[&&NHX:TOL=20269],nautilus repertus ?[&&NHX:TOL=20270],nautilus stenomphalus[&&NHX:TOL=20271],allonautilus scrobiculatus[&&NHX:TOL=20272])nautilidae[&&NHX:TOL=19397],(ammonoidea[&&NHX:EXT=Y:TOL=19399],(belemnoidea[&&NHX:EXT=Y:TOL=19402],((((bathyteuthis abyssicola[&&NHX:TOL=19432],bathyteuthis bacidifera[&&NHX:TOL=19433],bathyteuthis berryi[&&NHX:TOL=19434])bathyteuthis[&&NHX:TOL=19429],(chtenopteryx canariensis[&&NHX:TOL=19439],chtenopteryx sepioloides[&&NHX:TOL=19440],chtenopteryx sicula[&&NHX:TOL=19441])chtenopteryx[&&NHX:TOL=19430])bathyteuthoidea[&&NHX:TOL=19421],(idiosepius biserialis[&&NHX:TOL=19991],idiosepius macrocheir[&&NHX:TOL=19992],idiosepius mimus ?[&&NHX:TOL=23874],idiosepius notoides[&&NHX:TOL=19993],idiosepius picteti[&&NHX:TOL=19994],idiosepius paradoxus[&&NHX:TOL=19995],idiosepius pygmaeus[&&NHX:TOL=19996],idiosepius thailandicus[&&NHX:TOL=23873])idiosepiidae[&&NHX:TOL=19985],(australiteuthis aldrichi[&&NHX:TOL=52671],((loligo forbesii[&&NHX:TOL=52918],(loligo reynaudii[&&NHX:TOL=19869],loligo vulgaris[&&NHX:TOL=19866])[&&NHX:TOL=57905])loligo[&&NHX:TOL=19858],afrololigo mercatoris[&&NHX:TOL=23875],(alloteuthis africanus[&&NHX:TOL=52719],alloteuthis media[&&NHX:TOL=52720],alloteuthis subulata[&&NHX:TOL=52721])alloteuthis[&&NHX:TOL=23876],((doryteuthis gahi[&&NHX:TOL=52724],doryteuthis ocula[&&NHX:TOL=52725],doryteuthis opalescens[&&NHX:TOL=52726],doryteuthis pealeii[&&NHX:TOL=52727],doryteuthis surinamensis[&&NHX:TOL=52730])doryteuthis amerigo[&&NHX:TOL=52732],(doryteuthis roperi[&&NHX:TOL=52729],doryteuthis plei[&&NHX:TOL=52728])doryteuthis doryteuthis[&&NHX:TOL=52733],doryteuthis subgenus undescribed sanpaulensis[&&NHX:TOL=53068])doryteuthis[&&NHX:TOL=23877],heterololigo bleekeri[&&NHX:TOL=23878],((loliolus  affinis[&&NHX:TOL=19884],loliolus  hardwickei[&&NHX:TOL=19885])loliolus loliolus[&&NHX:TOL=19883],(loliolus  beka[&&NHX:TOL=19887],loliolus  japonica[&&NHX:TOL=19888],loliolus  sumatrensis[&&NHX:TOL=19889],loliolus  uyii[&&NHX:TOL=19890])loliolus nipponololigo[&&NHX:TOL=19886])loliolus[&&NHX:TOL=19859],((lolliguncula argus[&&NHX:TOL=19894],(lolliguncula brevis[&&NHX:TOL=19893],lolliguncula panamensis[&&NHX:TOL=19895])[&&NHX:TOL=57906])lolliguncula lolliguncula[&&NHX:TOL=19892],lolliguncula loliolopsis diomedeae     [&&NHX:TOL=19896])lolliguncula[&&NHX:TOL=19860],(pickfordiateuthis bayeri[&&NHX:TOL=52734],pickfordiateuthis pulchella[&&NHX:TOL=19898],pickfordiateuthis vossi[&&NHX:TOL=19899],pickfordiateuthis species a[&&NHX:TOL=19900])pickfordiateuthis[&&NHX:TOL=19861],(sepioteuthis australis[&&NHX:TOL=19903],sepioteuthis lessoniana[&&NHX:TOL=19904],sepioteuthis sepioidea[&&NHX:TOL=19902])sepioteuthis[&&NHX:TOL=19862],(uroteuthis uroteuthis bartschi[&&NHX:TOL=19911],uroteuthis aestuariolus nocticula[&&NHX:TOL=52735],(uroteuthis  abulati[&&NHX:TOL=19913],uroteuthis  arabica[&&NHX:TOL=19914],uroteuthis  bengalensis[&&NHX:TOL=19915],uroteuthis  chinensis[&&NHX:TOL=19916],uroteuthis  duvaucelii[&&NHX:TOL=19917],uroteuthis  edulis[&&NHX:TOL=19918],uroteuthis  robsoni[&&NHX:TOL=19921],uroteuthis sibogae[&&NHX:TOL=57907],uroteuthis  singhalensis[&&NHX:TOL=19922],uroteuthis  vossi[&&NHX:TOL=19923])uroteuthis photololigo[&&NHX:TOL=19912],uroteuthis  subgenus uncertain pickfordi[&&NHX:TOL=19919],uroteuthis  subgenus uncertain reesi[&&NHX:TOL=19920])uroteuthis[&&NHX:TOL=19863])loliginidae[&&NHX:TOL=19422])myopsida[&&NHX:TOL=52670],((architeuthis dux[&&NHX:TOL=19425],architeuthis martensi[&&NHX:TOL=19426],architeuthis sanctipauli[&&NHX:TOL=19427])architeuthis[&&NHX:TOL=19408],(brachioteuthis[&&NHX:TOL=24101],slosarczykovia circumantarctica[&&NHX:TOL=24102])brachioteuthidae[&&NHX:TOL=19409],(batoteuthis skolops[&&NHX:TOL=19452],((asperoteuthis acanthoderma[&&NHX:TOL=19466],asperoteuthis mangoldae[&&NHX:TOL=19467],asperoteuthis sp. b[&&NHX:TOL=19468],asperoteuthis lui[&&NHX:TOL=112030])asperoteuthis[&&NHX:TOL=19461],(chiroteuthis sp. b2[&&NHX:TOL=19473],chiroteuthis calyx[&&NHX:TOL=19474],chiroteuthis joubini[&&NHX:TOL=19475],chiroteuthis mega[&&NHX:TOL=19476],chiroteuthis picteti[&&NHX:TOL=19477],chiroteuthis spoeli[&&NHX:TOL=19478],chiroteuthis veranyi[&&NHX:TOL=19479])chiroteuthis[&&NHX:TOL=19462],grimalditeuthis bonplandi[&&NHX:TOL=19463],(planctoteuthis danae[&&NHX:TOL=19492],planctoteuthis exopthalmica[&&NHX:TOL=19493],planctoteuthis levimana[&&NHX:TOL=19494],planctoteuthis lippula[&&NHX:TOL=19495],planctoteuthis oligobessa[&&NHX:TOL=19496])planctoteuthis[&&NHX:TOL=19464],new genus b[&&NHX:TOL=19460],new genus c[&&NHX:TOL=19459])chiroteuthidae[&&NHX:TOL=19451],joubiniteuthis portieri[&&NHX:TOL=19450],(magnapinna atlantica[&&NHX:TOL=52204],magnapinna sp. b[&&NHX:TOL=52210],magnapinna sp. c[&&NHX:TOL=52211],magnapinna pacifica[&&NHX:TOL=19449],magnapinna talismani[&&NHX:TOL=52212])magnapinna[&&NHX:TOL=52203],((mastigoteuthis agassizii[&&NHX:TOL=19508],mastigoteuthis dentata[&&NHX:TOL=19512],mastigoteuthis psychrophila[&&NHX:TOL=19522])mastigoteuthis agassizii group[&&NHX:TOL=65306],mastigoteuthis cordiformis[&&NHX:TOL=19510],mastigoteuthis danae[&&NHX:TOL=19511],(mastigoteuthis atlantica[&&NHX:TOL=19509],mastigoteuthis famelica[&&NHX:TOL=19513],mastigoteuthis glaukopis[&&NHX:TOL=52637])mastigoteuthis glaukopis group[&&NHX:TOL=65305],mastigoteuthis hjorti[&&NHX:TOL=19517],(mastigoteuthis magna[&&NHX:TOL=19520],mastigoteuthis microlucens[&&NHX:TOL=65304],mastigoteuthis type beta[&&NHX:TOL=65357])mastigoteuthis magna group[&&NHX:TOL=65303],mastigoteuthis pyrodes[&&NHX:TOL=19523],mastigoteuthis tyroi[&&NHX:TOL=19526])mastigoteuthis[&&NHX:TOL=19453],(promachoteuthis megaptera[&&NHX:TOL=19528],promachoteuthis sloani[&&NHX:TOL=19529],promachoteuthis sp. b[&&NHX:TOL=19530],promachoteuthis sulcus[&&NHX:TOL=19531],promachoteuthis sp. d[&&NHX:TOL=19532])promachoteuthis[&&NHX:TOL=19454])chiroteuthid families[&&NHX:TOL=19410],((((liocranchia reinhardti[&&NHX:TOL=19596],liocranchia valdiviae[&&NHX:TOL=19597])liocranchia[&&NHX:TOL=19543],cranchia scabra[&&NHX:TOL=19542])[&&NHX:TOL=19541],(leachia atlantica[&&NHX:TOL=19585],leachia cyclura[&&NHX:TOL=19586],leachia danae[&&NHX:TOL=19587],leachia dislocata[&&NHX:TOL=19588],leachia lemur[&&NHX:TOL=19589],leachia pacifica[&&NHX:TOL=19590],leachia sp. a[&&NHX:TOL=19591])leachia[&&NHX:TOL=19544])cranchiinae[&&NHX:TOL=19540],((((bathothauma lyromma[&&NHX:TOL=19549],(helicocranchia pfefferi[&&NHX:TOL=19580],helicocranchia papillata[&&NHX:TOL=19581],helicocranchia joubini[&&NHX:TOL=19582])helicocranchia[&&NHX:TOL=19550])[&&NHX:TOL=19548],sandalops melancholicus[&&NHX:TOL=19551])[&&NHX:TOL=19547],liguriella podophtalma[&&NHX:TOL=19552])[&&NHX:TOL=19546],(((mesonychoteuthis hamiltoni[&&NHX:TOL=19556],(galiteuthis armata[&&NHX:TOL=19571],galiteuthis glacialis[&&NHX:TOL=19572],galiteuthis pacifica[&&NHX:TOL=19573],galiteuthis phyllura[&&NHX:TOL=19574],galiteuthis suhmi[&&NHX:TOL=19575])galiteuthis[&&NHX:TOL=19557])[&&NHX:TOL=19555],(taonius borealis[&&NHX:TOL=19610],taonius pavo[&&NHX:TOL=19611],taonius belone[&&NHX:TOL=120159],[&&NHX:TOL=120160])taonius[&&NHX:TOL=19558])[&&NHX:TOL=19554],((teuthowenia megalops[&&NHX:TOL=19613],teuthowenia maculata[&&NHX:TOL=19614],teuthowenia pellucida[&&NHX:TOL=19615])teuthowenia[&&NHX:TOL=19560],((megalocranchia sp. a[&&NHX:TOL=19601],megalocranchia fisheri[&&NHX:TOL=19602],megalocranchia maxima[&&NHX:TOL=19603],megalocranchia oceanica[&&NHX:TOL=19604])megalocranchia[&&NHX:TOL=19562],egea inermis[&&NHX:TOL=19563])[&&NHX:TOL=19561])[&&NHX:TOL=19559])[&&NHX:TOL=19553])taoniinae[&&NHX:TOL=19545])cranchiidae[&&NHX:TOL=19411],(cycloteuthis sirventyi[&&NHX:TOL=19620],(discoteuthis discus[&&NHX:TOL=19625],discoteuthis laciniosa[&&NHX:TOL=19626],discoteuthis sp. a[&&NHX:TOL=19627],discoteuthis sp. b[&&NHX:TOL=57150])discoteuthis[&&NHX:TOL=19621])cycloteuthidae[&&NHX:TOL=19412],(ancistrocheirus lesueurii[&&NHX:TOL=19632],((((enoploteuthis leptura[&&NHX:TOL=19722],enoploteuthis magnoceani[&&NHX:TOL=19710],enoploteuthis obliqua[&&NHX:TOL=19711],enoploteuthis octolineata[&&NHX:TOL=19712],enoploteuthis reticulata[&&NHX:TOL=19713])enoploteuthis[&&NHX:TOL=138170],(enoploteuthis anapsis[&&NHX:TOL=19705],enoploteuthis chuni[&&NHX:TOL=19706],enoploteuthis galaxias[&&NHX:TOL=19707],enoploteuthis higginsi[&&NHX:TOL=19708],enoploteuthis jonesi[&&NHX:TOL=19709],enoploteuthis semilineata[&&NHX:TOL=19714])paraenoploteuthis[&&NHX:TOL=138171])enoploteuthis[&&NHX:TOL=19641],((abralia armata[&&NHX:TOL=19647],abralia multihamata[&&NHX:TOL=19658],abralia renschi[&&NHX:TOL=19649],abralia spaercki[&&NHX:TOL=19650],abralia steindachneri[&&NHX:TOL=19648])abralia[&&NHX:TOL=138172],abralia veranyi[&&NHX:TOL=19654],(abralia astrosticta[&&NHX:TOL=19652],abralia astrolineata[&&NHX:TOL=19651])astrabralia[&&NHX:TOL=138173],(abralia grimpei[&&NHX:TOL=19659],abralia omiae[&&NHX:TOL=138446],abralia redfieldi[&&NHX:TOL=19661],abralia similis[&&NHX:TOL=19662])pygmabralia[&&NHX:TOL=138174],(abralia andamanica[&&NHX:TOL=19655],abralia heminuchalis[&&NHX:TOL=19665],abralia robsoni[&&NHX:TOL=19660],abralia siedleckyi[&&NHX:TOL=19656],abralia trigonura[&&NHX:TOL=19657])heterabralia[&&NHX:TOL=138175],(abralia dubia[&&NHX:TOL=19663],abralia fasciolata[&&NHX:TOL=19664],abralia marisarabica[&&NHX:TOL=19653])enigmoteuthis[&&NHX:TOL=138176])abralia[&&NHX:TOL=19642],(((abraliopsis felis[&&NHX:TOL=19686],abraliopsis hoylei[&&NHX:TOL=19688],abraliopsis morisii[&&NHX:TOL=19691],abraliopsis pacificus[&&NHX:TOL=19690],abraliopsis tui[&&NHX:TOL=19692])abraliopsis[&&NHX:TOL=138177],(abraliopsis lineata[&&NHX:TOL=19689],abraliopsis gilchristi[&&NHX:TOL=19687])micrabralia[&&NHX:TOL=138178],(abraliopsis affinis[&&NHX:TOL=19682],abraliopsis atlantica[&&NHX:TOL=19683],abraliopsis chuni[&&NHX:TOL=19684],abraliopsis falco[&&NHX:TOL=19685])pfefferiteuthis[&&NHX:TOL=138179])abraliopsis[&&NHX:TOL=19644],watasenia scintillans[&&NHX:TOL=19645])[&&NHX:TOL=19643])enoploteuthidae[&&NHX:TOL=19634],((lampadioteuthis megaleia[&&NHX:TOL=19730],((lycoteuthis lorigera[&&NHX:TOL=19738],lycoteuthis springeri[&&NHX:TOL=19739])lycoteuthis[&&NHX:TOL=19732],(nematolampas regalis[&&NHX:TOL=19733],nematolampas venezuelensis[&&NHX:TOL=29248])nematolampas[&&NHX:TOL=29247],selenoteuthis scintillans[&&NHX:TOL=19734])lycoteuthinae[&&NHX:TOL=19731])lycoteuthidae[&&NHX:TOL=19636],((pterygioteuthis gemmata[&&NHX:TOL=19750],pterygioteuthis giardi[&&NHX:TOL=19751],pterygioteuthis microlampas[&&NHX:TOL=19752])pterygioteuthis[&&NHX:TOL=19747],(pyroteuthis addolux[&&NHX:TOL=19757],pyroteuthis margaritifera[&&NHX:TOL=19758],pyroteuthis serrata[&&NHX:TOL=19759],pyroteuthis sp. a[&&NHX:TOL=138538])pyroteuthis[&&NHX:TOL=19748])pyroteuthidae[&&NHX:TOL=19637])[&&NHX:TOL=19635])[&&NHX:TOL=19633])enoploteuthid families[&&NHX:TOL=19413],((berryteuthis anonychus[&&NHX:TOL=26874],(berryteuthis magister nipponensis[&&NHX:TOL=66578],berryteuthis magister shevtsovi[&&NHX:TOL=66579],berryteuthis magister magister[&&NHX:TOL=67069])berryteuthis magister[&&NHX:TOL=26875])berryteuthis[&&NHX:TOL=19765],eogonatus tinro[&&NHX:TOL=19766],(gonatopsis borealis[&&NHX:TOL=26876],gonatopsis japonicus[&&NHX:TOL=26877],gonatopsis makko[&&NHX:TOL=26878],(gonatopsis octopedatus[&&NHX:TOL=26879],gonatopsis sp. a[&&NHX:TOL=66369])[&&NHX:TOL=66368],gonatopsis okutanii[&&NHX:TOL=26880])gonatopsis[&&NHX:TOL=19764],(gonatus antarcticus[&&NHX:TOL=19778],gonatus berryi[&&NHX:TOL=19773],gonatus californiensis[&&NHX:TOL=19779],gonatus fabricii[&&NHX:TOL=19777],gonatus kamtschaticus[&&NHX:TOL=66512],gonatus madokai[&&NHX:TOL=19770],gonatus middendorffi[&&NHX:TOL=19771],gonatus onyx[&&NHX:TOL=19769],gonatus oregonensis[&&NHX:TOL=19775],gonatus pyros[&&NHX:TOL=19774],gonatus steenstrupi[&&NHX:TOL=19780],gonatus ursabrunae[&&NHX:TOL=19776])gonatus[&&NHX:TOL=19767])gonatidae[&&NHX:TOL=19414],(((histioteuthis bonnellii[&&NHX:TOL=19786],histioteuthis macrohista[&&NHX:TOL=19787])histioteuthis bonnelliigroup[&&NHX:TOL=19785],(histioteuthis atlantica[&&NHX:TOL=19789],histioteuthis eltaninae[&&NHX:TOL=19790],histioteuthis reversa[&&NHX:TOL=19791])histioteuthis reversagroup[&&NHX:TOL=19788],(stigmatoteuthis arcturi[&&NHX:TOL=19793],stigmatoteuthis dofleini[&&NHX:TOL=19794],stigmatoteuthis hoylei[&&NHX:TOL=19795])stigmatoteuthis[&&NHX:TOL=19792],(histioteuthis sp. a[&&NHX:TOL=19797],histioteuthis celetaria[&&NHX:TOL=19798],histioteuthis inermis[&&NHX:TOL=19799],histioteuthis pacifica[&&NHX:TOL=19800])histioteuthis celetariagroup[&&NHX:TOL=19796],(histioteuthis berryi[&&NHX:TOL=19802],histioteuthis cerasina[&&NHX:TOL=19803],histioteuthis corona[&&NHX:TOL=19804])histioteuthis coronagroup[&&NHX:TOL=19801],(histioteuthis miranda[&&NHX:TOL=19806],histioteuthis oceani[&&NHX:TOL=19807])histioteuthis mirandagroup[&&NHX:TOL=19805],(histioteuthis heteropsis[&&NHX:TOL=19809],histioteuthis meleagroteuthis[&&NHX:TOL=19810])histioteuthis meleagroteuthisgroup[&&NHX:TOL=19808])histioteuthidae[&&NHX:TOL=19782],psychroteuthis glacialis[&&NHX:TOL=19783])histioteuthid families[&&NHX:TOL=19415],(lepidoteuthis grimaldii[&&NHX:TOL=19833],((octopoteuthis danae[&&NHX:TOL=19842],octopoteuthis deletron[&&NHX:TOL=19843],octopoteuthis indica[&&NHX:TOL=19844],octopoteuthis neilseni[&&NHX:TOL=19845],octopoteuthis megaptera[&&NHX:TOL=19846],octopoteuthis rugosa[&&NHX:TOL=19847],octopoteuthis sicula[&&NHX:TOL=19848])octopoteuthis[&&NHX:TOL=19839],taningia danae[&&NHX:TOL=19840])octopoteuthidae[&&NHX:TOL=19834],(pholidoteuthis adami[&&NHX:TOL=19853],pholidoteuthis massyae[&&NHX:TOL=19854])pholidoteuthis[&&NHX:TOL=19835])lepidoteuthid families[&&NHX:TOL=19416],(alluroteuthis antarcticus[&&NHX:TOL=19925],neoteuthis thielei[&&NHX:TOL=19926],nototeuthis dimegacotyle[&&NHX:TOL=19927],narrowteuthis nesisi[&&NHX:TOL=19928])neoteuthidae[&&NHX:TOL=19417],((illex argentinus[&&NHX:TOL=77443],illex coindetii[&&NHX:TOL=77444],illex illecebrosus[&&NHX:TOL=77445],illex oxygonius[&&NHX:TOL=77446])illex[&&NHX:TOL=19940],((ornithoteuthis antillarum[&&NHX:TOL=77433],ornithoteuthis volatilis[&&NHX:TOL=77434])ornithoteuthis[&&NHX:TOL=19942],((dosidicus gigas[&&NHX:TOL=19945],(sthenoteuthis oualaniensis[&&NHX:TOL=77447],sthenoteuthis pteropus[&&NHX:TOL=77448],sthenoteuthis  pacific dwarf form[&&NHX:TOL=137794])sthenoteuthis[&&NHX:TOL=19946])[&&NHX:TOL=19944],ommastrephes bartramii[&&NHX:TOL=19947],(eucleoteuthis luminosa[&&NHX:TOL=19949],hyaloteuthis pelagica[&&NHX:TOL=19950])[&&NHX:TOL=19948])[&&NHX:TOL=19943])ommastrephinae[&&NHX:TOL=19941],(martialia hyadesi[&&NHX:TOL=19936],todaropsis[&&NHX:TOL=19939],((nototodarus gouldi[&&NHX:TOL=77449],nototodarus hawaiiensis[&&NHX:TOL=77450],nototodarus sloanii[&&NHX:TOL=77451])nototodarus[&&NHX:TOL=19938],todarodes[&&NHX:TOL=19935])[&&NHX:TOL=19937])todarodinae[&&NHX:TOL=19934])ommastrephidae[&&NHX:TOL=19418],(ancistroteuthis lichtensteinii[&&NHX:TOL=19952],kondakovia longimana[&&NHX:TOL=19953],(onychoteuthis banksii[&&NHX:TOL=19962],onychoteuthis borealijaponicus[&&NHX:TOL=19963],onychoteuthis compacta[&&NHX:TOL=19964],onychoteuthis meridiopacifica[&&NHX:TOL=19965],onychoteuthis sp. b[&&NHX:TOL=108201],onychoteuthis sp. d[&&NHX:TOL=108202])onychoteuthis[&&NHX:TOL=19955],(onykia carriboea[&&NHX:TOL=19971],onykia ingens[&&NHX:TOL=19972],onykia knipovitchi[&&NHX:TOL=19973],onykia loennbergii[&&NHX:TOL=19974],onykia robsoni[&&NHX:TOL=19975],onykia robusta[&&NHX:TOL=19976],onykia aequatorialis[&&NHX:TOL=108190],onykia sp. a[&&NHX:TOL=137607])onykia[&&NHX:TOL=19956],walvisteuthis rancureli[&&NHX:TOL=19957],(notonykia nesisi[&&NHX:TOL=108189],notonykia africanae[&&NHX:TOL=19954])notonykia[&&NHX:TOL=108188])onychoteuthidae[&&NHX:TOL=19419],thysanoteuthis rhombus[&&NHX:TOL=19420])oegopsida[&&NHX:TOL=19407],(((metasepia pfefferi[&&NHX:TOL=20012],metasepia tullbergi[&&NHX:TOL=20013])metasepia[&&NHX:TOL=20008],sepia[&&NHX:TOL=20009],(sepiella ornata[&&NHX:TOL=20016],sepiella cyanea[&&NHX:TOL=20017],sepiella inermis[&&NHX:TOL=20018],sepiella japonica[&&NHX:TOL=20019],sepiella ocellata[&&NHX:TOL=20020],sepiella weberi[&&NHX:TOL=20021])sepiella[&&NHX:TOL=20010])sepiidae[&&NHX:TOL=19987],((((austrorossia australis[&&NHX:TOL=23978],austrorossia antillensis[&&NHX:TOL=23979],austrorossia bipapillata[&&NHX:TOL=23980],austrorossia enigmatica?[&&NHX:TOL=23981],austrorossia mastigophora[&&NHX:TOL=23982])austrorossia[&&NHX:TOL=23977],(neorossia caroli[&&NHX:TOL=23983],neorossia leptodons[&&NHX:TOL=23984])neorossia[&&NHX:TOL=20026],(rossia brachyura[&&NHX:TOL=20064],rossia bullisi[&&NHX:TOL=20065],rossia enigmatica[&&NHX:TOL=20066],rossia macrosoma[&&NHX:TOL=20067],rossia megaptera[&&NHX:TOL=20069],rossia moelleri[&&NHX:TOL=20070],rossia mollicella[&&NHX:TOL=20071],(rossia pacifica diegensis[&&NHX:TOL=20072],rossia pacifica pacifica[&&NHX:TOL=20073])rossia pacifica[&&NHX:TOL=107950],rossia palpebrosa[&&NHX:TOL=20074],rossia tortugaensis[&&NHX:TOL=20075])rossia[&&NHX:TOL=20024],(semirossia equalis[&&NHX:TOL=23985],semirossia patagonica[&&NHX:TOL=23986],semirossia tenera[&&NHX:TOL=23987])semirossia[&&NHX:TOL=20025])rossiinae[&&NHX:TOL=20023],((((euprymna albatrossae[&&NHX:TOL=20044],euprymna berryi[&&NHX:TOL=20045],euprymna hoylei[&&NHX:TOL=20046],euprymna hyllebergi[&&NHX:TOL=23988],euprymna morsei[&&NHX:TOL=20047],euprymna penares?[&&NHX:TOL=23989],euprymna phenax[&&NHX:TOL=20048],euprymna scolopes[&&NHX:TOL=20049],euprymna stenodactyla[&&NHX:TOL=20050],euprymna tasmanica[&&NHX:TOL=20051])euprymna[&&NHX:TOL=20036],((inioteuthis japonica[&&NHX:TOL=23990],inioteuthis maculosa[&&NHX:TOL=23991])inioteuthis[&&NHX:TOL=20042],((rondeletiola capensis[&&NHX:TOL=23992],rondeletiola minor[&&NHX:TOL=23993])rondeletiola[&&NHX:TOL=20040],(sepietta neglecta[&&NHX:TOL=24032],sepietta oweniana[&&NHX:TOL=24033],sepietta petersi[&&NHX:TOL=24034])sepietta[&&NHX:TOL=20041])[&&NHX:TOL=20039],(sepiola affinis[&&NHX:TOL=24018],sepiola atlantica[&&NHX:TOL=24019],sepiola aurantiaca[&&NHX:TOL=24020],sepiola birostrata[&&NHX:TOL=24021],sepiola intermedia[&&NHX:TOL=24022],sepiola knudseni[&&NHX:TOL=24023],sepiola ligulata[&&NHX:TOL=24024],sepiola parva[&&NHX:TOL=24025],sepiola pfefferi?[&&NHX:TOL=24026],sepiola robusta[&&NHX:TOL=24027],sepiola rondeleti[&&NHX:TOL=24028],sepiola rossiaeformis?[&&NHX:TOL=24029],sepiola steenstrupiana[&&NHX:TOL=24030],sepiola trirostrata[&&NHX:TOL=24031])sepiola[&&NHX:TOL=20038])[&&NHX:TOL=20037])sepiolinae[&&NHX:TOL=20035],(new genus new species a[&&NHX:TOL=77761],new genus new species b[&&NHX:TOL=77762])new genus[&&NHX:TOL=77759])[&&NHX:TOL=112500],((((heteroteuthis dispar[&&NHX:TOL=20054],heteroteuthis hawaiiensis[&&NHX:TOL=20055],heteroteuthis dagamensis[&&NHX:TOL=20053],heteroteuthis sp. a[&&NHX:TOL=91437])heteroteuthis[&&NHX:TOL=20030],nectoteuthis pourtalesi[&&NHX:TOL=20031],(stoloteuthis leucoptera[&&NHX:TOL=27774],stoloteuthis maoria[&&NHX:TOL=27775],stoloteuthis weberi[&&NHX:TOL=27776])stoloteuthis[&&NHX:TOL=20033],(iridoteuthis iris[&&NHX:TOL=111801],iridoteuthis sp. a[&&NHX:TOL=111802])iridoteuthis[&&NHX:TOL=20032],amphorateuthis alveatus[&&NHX:TOL=52334])[&&NHX:TOL=20029],sepiolina nipponensis[&&NHX:TOL=20034])heteroteuthinae[&&NHX:TOL=20027],choneteuthis tongaensis[&&NHX:TOL=91865])[&&NHX:TOL=112499])[&&NHX:TOL=112498])sepiolidae[&&NHX:TOL=19988],((sepioloidea pacifica[&&NHX:TOL=19999],sepioloidea lineolata[&&NHX:TOL=20000])[&&NHX:TOL=19998],(sepiadarium nipponianum[&&NHX:TOL=20002],sepiadarium kochi[&&NHX:TOL=20003],sepiadarium auritum[&&NHX:TOL=20004],sepiadarium gracilis[&&NHX:TOL=20005],sepiadarium austrinum[&&NHX:TOL=20006])[&&NHX:TOL=20001])sepiadariidae[&&NHX:TOL=19986])sepiolida[&&NHX:TOL=23872])sepioidea[&&NHX:TOL=23870],spirula spirula[&&NHX:TOL=19989])decapodiformes[&&NHX:TOL=19404],(((((cirroctopus antarctica[&&NHX:TOL=20108],cirroctopus glacialis[&&NHX:TOL=20109],cirroctopus hochbergi[&&NHX:TOL=20110],cirroctopus mawsoni[&&NHX:TOL=20111])cirroctopus[&&NHX:TOL=20103],(grimpoteuthis abyssicola[&&NHX:TOL=20117],grimpoteuthis bathynectes[&&NHX:TOL=20118],grimpoteuthis boylei[&&NHX:TOL=20119],grimpoteuthis challengeri[&&NHX:TOL=20120],grimpoteuthis discoveryi[&&NHX:TOL=20121],grimpoteuthis hippocrepium[&&NHX:TOL=20122],grimpoteuthis innominata[&&NHX:TOL=20123],grimpoteuthis meangensis[&&NHX:TOL=20124],grimpoteuthis megaptera[&&NHX:TOL=20125],grimpoteuthis pacifica[&&NHX:TOL=20126],grimpoteuthis plena[&&NHX:TOL=20127],grimpoteuthis tuftsi[&&NHX:TOL=20128],grimpoteuthis umbellata[&&NHX:TOL=20129],grimpoteuthis wuelkeri[&&NHX:TOL=20130])grimpoteuthis[&&NHX:TOL=20104],(luteuthis dentatus[&&NHX:TOL=20146],luteuthis shuishi[&&NHX:TOL=20147])luteuthis[&&NHX:TOL=20105],(opisthoteuthis agassizii[&&NHX:TOL=20151],opisthoteuthis albatrossi[&&NHX:TOL=20152],opisthoteuthis bruuni[&&NHX:TOL=20153],opisthoteuthis californiana[&&NHX:TOL=20155],opisthoteuthis calypso[&&NHX:TOL=20154],opisthoteuthis chathamensis[&&NHX:TOL=20156],opisthoteuthis depressa[&&NHX:TOL=20157],opisthoteuthis extensa[&&NHX:TOL=20158],opisthoteuthis grimaldii[&&NHX:TOL=20159],opisthoteuthis hardyi[&&NHX:TOL=20160],opisthoteuthis massyae[&&NHX:TOL=20161],opisthoteuthis medusoides[&&NHX:TOL=20162],opisthoteuthis mero[&&NHX:TOL=20163],opisthoteuthis persephone[&&NHX:TOL=20164],opisthoteuthis philipii[&&NHX:TOL=20165],opisthoteuthis pluto[&&NHX:TOL=20166],opisthoteuthis robsoni[&&NHX:TOL=20167],opisthoteuthis borealis[&&NHX:TOL=68278],opisthoteuthis japonica[&&NHX:TOL=68279])opisthoteuthis[&&NHX:TOL=20106],cryptoteuthis brevibracchiata[&&NHX:TOL=121985])opisthoteuthidae[&&NHX:TOL=20089],((cirroteuthis muelleri[&&NHX:TOL=20094],(cirrothauma magna[&&NHX:TOL=20098],cirrothauma murrayi[&&NHX:TOL=20099])cirrothauma[&&NHX:TOL=20095])cirroteuthidae[&&NHX:TOL=20091],(stauroteuthis gilchristi[&&NHX:TOL=20186],stauroteuthis syrtensis[&&NHX:TOL=20187])stauroteuthis[&&NHX:TOL=20092])[&&NHX:TOL=22060])cirrata[&&NHX:TOL=20086],((amphitretus pelagicus[&&NHX:TOL=20197],amphitretus thielei[&&NHX:TOL=20198])amphitretidae[&&NHX:TOL=20191],(abdopus[&&NHX:TOL=29360],adelieledone[&&NHX:TOL=29361],ameloctopus litoralis[&&NHX:TOL=20230],amphioctopus[&&NHX:TOL=29362],aphrodoctopus[&&NHX:TOL=20231],bathypolypus[&&NHX:TOL=20232],benthoctopus[&&NHX:TOL=20234],callistoctopus[&&NHX:TOL=20235],cistopus[&&NHX:TOL=20236],eledone[&&NHX:TOL=20237],enteroctopus[&&NHX:TOL=20238],euaxoctopus[&&NHX:TOL=20239],galeoctopus[&&NHX:TOL=29363],graneledone[&&NHX:TOL=20240],grimpella[&&NHX:TOL=20241],hapalochlaena[&&NHX:TOL=20242],megaleledone[&&NHX:TOL=20243],microeledone[&&NHX:TOL=29364],octopus sensu strictu[&&NHX:TOL=20244],(pareledone turqueti[&&NHX:TOL=20257],pareledone harrissoni[&&NHX:TOL=20258],pareledone charcoti[&&NHX:TOL=20259],pareledone framensis[&&NHX:TOL=20260],pareledone prydzensis[&&NHX:TOL=20261])pareledone[&&NHX:TOL=20245],praealtus[&&NHX:TOL=20233],pteroctopus[&&NHX:TOL=20246],scaeurgus[&&NHX:TOL=20247],tetracheledone[&&NHX:TOL=20249],thaumeledone[&&NHX:TOL=20250],velodona[&&NHX:TOL=20251],vosseledone[&&NHX:TOL=20252],vulcanoctopus[&&NHX:TOL=20253])octopodidae[&&NHX:TOL=20194],(haliphron atlanticus[&&NHX:TOL=20200],((tremoctopus violaceus[&&NHX:TOL=20216],tremoctopus gelatus[&&NHX:TOL=20218],tremoctopus gracilis[&&NHX:TOL=20220],tremoctopus robsoni[&&NHX:TOL=20221])tremoctopus[&&NHX:TOL=20202],((argonauta argo[&&NHX:TOL=20209],argonauta hians[&&NHX:TOL=20210],argonauta boettgeri[&&NHX:TOL=20211],argonauta nodosa[&&NHX:TOL=20212])argonauta[&&NHX:TOL=20204],ocythoe tuberculata[&&NHX:TOL=20205])[&&NHX:TOL=20203])[&&NHX:TOL=20201])argonautoidea[&&NHX:TOL=20192],(japetella diaphana[&&NHX:TOL=20224],bolitaena pygmaea[&&NHX:TOL=20223])bolitaenidae[&&NHX:TOL=20193],vitreledonella richardi[&&NHX:TOL=20195])incirrata[&&NHX:TOL=20087])octopoda[&&NHX:TOL=20083],vampyroteuthis infernalis[&&NHX:TOL=20084])octopodiformes[&&NHX:TOL=19405])neocoleoidea[&&NHX:TOL=19403])coleoidea[&&NHX:TOL=19400])[&&NHX:TOL=19398])orthoceratoidea[&&NHX:TOL=19396])cephalopoda[&&NHX:TOL=19386])conchifera[&&NHX:TOL=19381])mollusca[&&NHX:TOL=2488],(((((amphiporidae[&&NHX:TOL=22656],malacobdellidae[&&NHX:TOL=20354],prosorhochmidae[&&NHX:TOL=22651],tetrastemmatidae[&&NHX:TOL=22652],carcinonemertidae[&&NHX:TOL=22657],ototyphlonemertidae[&&NHX:TOL=22658],emplectonematidae[&&NHX:TOL=22659])distromatonemertea[&&NHX:TOL=22653],cratenemertidae[&&NHX:TOL=22645])monostilifera[&&NHX:TOL=22641],(pelagica[&&NHX:TOL=22655],reptantia[&&NHX:TOL=22654])polystilifera[&&NHX:TOL=22642])hoplonemertea[&&NHX:TOL=20353],((lineiformes[&&NHX:TOL=22660],baseodiscidae[&&NHX:TOL=22661],valencinidae[&&NHX:TOL=22662])heteronemertea[&&NHX:TOL=22646],hubrechtella[&&NHX:TOL=22647])pilidiophora[&&NHX:TOL=20351])neonemertea[&&NHX:TOL=22644],hubrechtidae[&&NHX:TOL=22663],carinomidae[&&NHX:TOL=22650],(cephalothricidae[&&NHX:TOL=22648],tubulanidae[&&NHX:TOL=22649])[&&NHX:TOL=20350])nemertea[&&NHX:TOL=2489],(loxosomatidae[&&NHX:TOL=19267],(loxokalypodidae[&&NHX:TOL=19269],(pedicellinidae[&&NHX:TOL=19271],barentsiidae[&&NHX:TOL=19272])stolonata[&&NHX:TOL=19270])coloniales[&&NHX:TOL=19268])entoprocta[&&NHX:TOL=2491],(((phoronis ovalis[&&NHX:TOL=20359],phoronis hippocrepia[&&NHX:TOL=20360],phoronis ijimai[&&NHX:TOL=20361],phoronis australis[&&NHX:TOL=20362],phoronis muelleri[&&NHX:TOL=20363],phoronis psammophila[&&NHX:TOL=20364],phoronis pallida[&&NHX:TOL=20365],phoronis svetlanae[&&NHX:TOL=20366],phoronis vancouverensis[&&NHX:TOL=20367],phoronis architecta[&&NHX:TOL=20368])phoronis[&&NHX:TOL=114126],(phoronopsis albomaculata[&&NHX:TOL=20369],phoronopsis harmeri[&&NHX:TOL=20370],phoronopsis californica[&&NHX:TOL=20371],phoronopsis viridis[&&NHX:TOL=20372],phoronopsis malakhovi[&&NHX:TOL=20373])phoronopsis[&&NHX:TOL=114127])phoronida[&&NHX:TOL=2493],((chileata[&&NHX:TOL=114128],obolellata[&&NHX:TOL=114129],kutorginata[&&NHX:TOL=114130],strophomenata[&&NHX:TOL=114131],rhynchonellata[&&NHX:TOL=114132])rhynchonelliformea[&&NHX:TOL=14794],(lingulata[&&NHX:TOL=114133],paterinata[&&NHX:TOL=114134])linguliformea[&&NHX:TOL=14795],craniata[&&NHX:TOL=14796])brachiopoda[&&NHX:TOL=2494])[&&NHX:TOL=2492])lophotrochozoa[&&NHX:TOL=2485])bilateria[&&NHX:TOL=2459],(((((((((((((((((((myxobolus siddalli[&&NHX:TOL=125412],myxobolus alonquinensis[&&NHX:TOL=125206],myxobolus martini[&&NHX:TOL=125413])[&&NHX:TOL=125411],myxobolus smithi[&&NHX:TOL=125414])[&&NHX:TOL=125410],(myxobolus impressus[&&NHX:TOL=125416],myxobolus parviformis[&&NHX:TOL=125417])[&&NHX:TOL=125415])[&&NHX:TOL=125409],myxobolus macrocapsularis[&&NHX:TOL=125418])[&&NHX:TOL=125408],henneguya cutanea[&&NHX:TOL=125419])[&&NHX:TOL=125407],(myxobolus dispar[&&NHX:TOL=125421],myxobolus pavlovskii[&&NHX:TOL=125422])[&&NHX:TOL=125420])[&&NHX:TOL=125406],myxobolus basilamellaris[&&NHX:TOL=125423])[&&NHX:TOL=125405],(thelohannelus hovorkai[&&NHX:TOL=125207],thelohanellus wuhanensis[&&NHX:TOL=125425])[&&NHX:TOL=125424])[&&NHX:TOL=125404],((sphaerospora renicola[&&NHX:TOL=125208],sphaerospora molnari[&&NHX:TOL=125428])[&&NHX:TOL=125427],(myxobolus rotundus[&&NHX:TOL=125430],myxobolus rotundatus[&&NHX:TOL=125431])[&&NHX:TOL=125429])[&&NHX:TOL=125426])[&&NHX:TOL=125403],((((((myxobolus intimus[&&NHX:TOL=125438],myxobolus obesus[&&NHX:TOL=125439],myxobolus hungaricus[&&NHX:TOL=125440])[&&NHX:TOL=125437],myxobolus pseudokoi[&&NHX:TOL=125441])[&&NHX:TOL=125436],((myxobolus pellicides[&&NHX:TOL=125444],myxobolus pendula[&&NHX:TOL=125445])[&&NHX:TOL=125443],myxobolus longisporus[&&NHX:TOL=125446])[&&NHX:TOL=125442])[&&NHX:TOL=125435],(((myxobolus musculi[&&NHX:TOL=125450],myxobolus cyprini[&&NHX:TOL=125209])[&&NHX:TOL=125449],myxobolus pseudodispar[&&NHX:TOL=125451])[&&NHX:TOL=125448],myxobolus bartai[&&NHX:TOL=125452])[&&NHX:TOL=125447])[&&NHX:TOL=125434],myxobolus bibullatus[&&NHX:TOL=125453])[&&NHX:TOL=125433],myxobolus elegans[&&NHX:TOL=125454])[&&NHX:TOL=125432])[&&NHX:TOL=125402],((myxobolus bononiense[&&NHX:TOL=125457],myxobolus xiaoi[&&NHX:TOL=125458],myxobolus cultus[&&NHX:TOL=125459],myxobolus lentisuturalis[&&NHX:TOL=125460],myxobolus kubanicum[&&NHX:TOL=125461])[&&NHX:TOL=125456],myxobolus portucalensis[&&NHX:TOL=125462])[&&NHX:TOL=125455])[&&NHX:TOL=125401],(((henneguya zschokkei[&&NHX:TOL=125466],henneguya salminicola[&&NHX:TOL=125212],henneguya nuesslini[&&NHX:TOL=125467])[&&NHX:TOL=125465],(myxobolus sandrae[&&NHX:TOL=125469],myxobolus cerebralis[&&NHX:TOL=125211],myxobolus neurobius[&&NHX:TOL=125470],myxobolus drjagini[&&NHX:TOL=125471],myxobolus elipsoides[&&NHX:TOL=125472],myxobolus bramae[&&NHX:TOL=125473],myxobolus arcticus[&&NHX:TOL=125474],myxobolus insidiosus[&&NHX:TOL=125475])[&&NHX:TOL=125468])[&&NHX:TOL=125464],myxobolus squamalis[&&NHX:TOL=125476])[&&NHX:TOL=125463])[&&NHX:TOL=125400],((((((((myxobolus ichkeulensis[&&NHX:TOL=125485],myxobolus spinacurvatura[&&NHX:TOL=125486])[&&NHX:TOL=125484],myxobolus bizerti[&&NHX:TOL=125487])[&&NHX:TOL=125483],myxobolus episquamalis[&&NHX:TOL=125488])[&&NHX:TOL=125482],(myxobolus muelleri[&&NHX:TOL=125490],myxobolus exiguus[&&NHX:TOL=125491])[&&NHX:TOL=125489])[&&NHX:TOL=125481],(henneguya lesteri[&&NHX:TOL=125493],myxobolus procerus[&&NHX:TOL=125494])[&&NHX:TOL=125492])[&&NHX:TOL=125480],(((henneguya exilis[&&NHX:TOL=125498],henneguya ictaluri[&&NHX:TOL=125214])[&&NHX:TOL=125497],henneguya weishanensis[&&NHX:TOL=125499])[&&NHX:TOL=125496],henneguya doori[&&NHX:TOL=125500])[&&NHX:TOL=125495])[&&NHX:TOL=125479],myxobolus osburni[&&NHX:TOL=125215])[&&NHX:TOL=125478],myxobolus acanthogobii[&&NHX:TOL=125501])[&&NHX:TOL=125477])myxobolidae[&&NHX:TOL=125202],((chloromyxum schurovi[&&NHX:TOL=125218],myxidium giardi[&&NHX:TOL=125219])[&&NHX:TOL=125217],(hoferellus gilsoni[&&NHX:TOL=125221],myxobilatus gasterostei[&&NHX:TOL=125222])[&&NHX:TOL=125220])[&&NHX:TOL=125216])[&&NHX:TOL=125201],(myxidium lieberkuehni[&&NHX:TOL=125223],sphaerospora oncorhynchi[&&NHX:TOL=125224],chloromyxum legeri[&&NHX:TOL=125225])[&&NHX:TOL=20291])[&&NHX:TOL=125200],((((sphaeromyxa longa[&&NHX:TOL=125229],sphaeromyxa zaharoni[&&NHX:TOL=125230],sphaeromyxa hellandi[&&NHX:TOL=125231])sphaeromyxa[&&NHX:TOL=125228],(soricimyxum fegati[&&NHX:TOL=125233],myxidium coryphaenoideum[&&NHX:TOL=125234])[&&NHX:TOL=125232])[&&NHX:TOL=125227],(chloromyxum trijugum[&&NHX:TOL=125236],(((zschokkella nova[&&NHX:TOL=125240],myxidium truttae[&&NHX:TOL=125241])[&&NHX:TOL=125239],(zschokkella icterica[&&NHX:TOL=125243],myxidium cuneiforme[&&NHX:TOL=125244])[&&NHX:TOL=125242])[&&NHX:TOL=125238],myxidium scripta[&&NHX:TOL=125245])[&&NHX:TOL=125237])[&&NHX:TOL=125235])[&&NHX:TOL=125226],chloromyxum[&&NHX:TOL=125246])[&&NHX:TOL=20292])[&&NHX:TOL=125199],chloromyxum leydigi[&&NHX:TOL=20293])freshwater myxosporea clade[&&NHX:TOL=20290],(((((((((((kudoa yasanugai[&&NHX:TOL=125508],kudoa neurophila[&&NHX:TOL=125254])[&&NHX:TOL=125507],kudoa thalassomi[&&NHX:TOL=125509])[&&NHX:TOL=125506],((kudoa permulticapsula[&&NHX:TOL=125256],kudoa scomberomori[&&NHX:TOL=125512])[&&NHX:TOL=125511],kudoa grammatorcyni[&&NHX:TOL=125513])[&&NHX:TOL=125510])[&&NHX:TOL=125505],((kudoa minithyrsites[&&NHX:TOL=125516],kudoa thyrsites[&&NHX:TOL=125253])[&&NHX:TOL=125515],kudoa lateolabracis[&&NHX:TOL=125517])[&&NHX:TOL=125514])[&&NHX:TOL=125504],((kudoa unicapsula[&&NHX:TOL=125520],kudoa trifolia[&&NHX:TOL=125521])[&&NHX:TOL=125519],kudoa quadricornis[&&NHX:TOL=125522])[&&NHX:TOL=125518])[&&NHX:TOL=125503],(((((kudoa funduli[&&NHX:TOL=125528],kudoa clupeidae[&&NHX:TOL=125529])[&&NHX:TOL=125527],kudoa rosenbuschi[&&NHX:TOL=125530])[&&NHX:TOL=125526],kudoa aminiauriculata[&&NHX:TOL=125531])[&&NHX:TOL=125525],kudoa dianae[&&NHX:TOL=125532])[&&NHX:TOL=125524],kudoa paniformis[&&NHX:TOL=125255])[&&NHX:TOL=125523])[&&NHX:TOL=125502],kudoa ovivora[&&NHX:TOL=125533])kudoa[&&NHX:TOL=125252],sphaerospora dicentrarchi[&&NHX:TOL=125257],kudoa iwatai[&&NHX:TOL=125534])[&&NHX:TOL=125251],((kudoa amamiensis[&&NHX:TOL=125258],kudoa crumena[&&NHX:TOL=125537])[&&NHX:TOL=125536],(kudoa hypoepicardialis[&&NHX:TOL=125539],kudoa shiomitsui[&&NHX:TOL=125540])[&&NHX:TOL=125538])[&&NHX:TOL=125535])[&&NHX:TOL=124929],unicapsula pflugfelderi[&&NHX:TOL=124930])[&&NHX:TOL=125250],(enteromyxum leei[&&NHX:TOL=125260],(enteromyxum scophthalmi[&&NHX:TOL=125262],enteromyxum fugu[&&NHX:TOL=125263])[&&NHX:TOL=125261])enteromyxum[&&NHX:TOL=125259],(((((parvicapsula limandae[&&NHX:TOL=125393],parvicapsula asymmetrica[&&NHX:TOL=125267])[&&NHX:TOL=125392],parvicapsula pseudobranchicola[&&NHX:TOL=125266])[&&NHX:TOL=125391],parvicapsula unicornis[&&NHX:TOL=125394])[&&NHX:TOL=125390],(parvicapsula kabatai[&&NHX:TOL=125396],parvicapsula spinaciae[&&NHX:TOL=125397])[&&NHX:TOL=125395])[&&NHX:TOL=125389],(parvicapsula bicornis[&&NHX:TOL=125399],parvicapsula minibicornis[&&NHX:TOL=125265])[&&NHX:TOL=125398])parvicapsula[&&NHX:TOL=125264],(ceratomyxa anco[&&NHX:TOL=125270],(ceratomyxa sparusaurati[&&NHX:TOL=125271],ceratomyxa labracis[&&NHX:TOL=125269])[&&NHX:TOL=125383],(ceratomyxa cheilinae[&&NHX:TOL=125385],ceratomyxa oxycheilinae[&&NHX:TOL=125386])[&&NHX:TOL=125384],ceratomyxa thalassonae[&&NHX:TOL=125387],ceratomyxa choerodonae[&&NHX:TOL=125388],palliatus indecorus[&&NHX:TOL=125541])ceratomyxa[&&NHX:TOL=125268],zschokkella lophii[&&NHX:TOL=125272],ceratomyxa shasta[&&NHX:TOL=125273],((ellipsomyxa gobii[&&NHX:TOL=125276],zschokkella mugilis[&&NHX:TOL=125277])[&&NHX:TOL=125275],((((myxidium bergense[&&NHX:TOL=125282],myxidium gadi[&&NHX:TOL=125283])[&&NHX:TOL=125281],(myxidium incurvatum[&&NHX:TOL=125285],sinuolinea phyllopteryxa[&&NHX:TOL=125286])[&&NHX:TOL=125284])[&&NHX:TOL=125280],zschokkella neopomacentri[&&NHX:TOL=125287])[&&NHX:TOL=125279],(coccomyxa jirilomi[&&NHX:TOL=125289],auerbachia pulchra[&&NHX:TOL=125290])[&&NHX:TOL=125288])[&&NHX:TOL=125278])[&&NHX:TOL=125274])marine myxosporea clade[&&NHX:TOL=20289],sphaerospora[&&NHX:TOL=125291],(ortholinea[&&NHX:TOL=125543],neomyxobolus[&&NHX:TOL=125544],cardimyxobolus[&&NHX:TOL=125545],triangula[&&NHX:TOL=125546],kentmoseria[&&NHX:TOL=125547],davisia[&&NHX:TOL=125548],myxoproteus[&&NHX:TOL=125549],bipteria[&&NHX:TOL=125550],paramyxoproteus[&&NHX:TOL=125551],neobipteria[&&NHX:TOL=125552],schulmania[&&NHX:TOL=125553],noblea[&&NHX:TOL=125554],fabespora[&&NHX:TOL=125555],meglitschia[&&NHX:TOL=125556],polysporoplasma[&&NHX:TOL=125557],wardia[&&NHX:TOL=125558],caudomyxum[&&NHX:TOL=125559],agarella[&&NHX:TOL=125560],globospora[&&NHX:TOL=125561],alatospora[&&NHX:TOL=125562],pseudoalatospora[&&NHX:TOL=125563],renispora[&&NHX:TOL=125564],neoparvicapsula[&&NHX:TOL=125565],spirosuturia[&&NHX:TOL=125566],unicauda[&&NHX:TOL=125567],dicauda[&&NHX:TOL=125568],phlogospora[&&NHX:TOL=125569],laterocaudata[&&NHX:TOL=125570],hennegoides[&&NHX:TOL=125571],tetrauronema[&&NHX:TOL=125572],neothelohanellus[&&NHX:TOL=125573],neohenneguya[&&NHX:TOL=125574],trigonosporus[&&NHX:TOL=125575],trilospora[&&NHX:TOL=125576],trilosporoides[&&NHX:TOL=125577])unplaced myxosporea genera[&&NHX:TOL=125542])myxosporea[&&NHX:TOL=20288],((buddenbrockia plumatellae[&&NHX:TOL=27418],buddenbrockia allmani[&&NHX:TOL=126561])[&&NHX:TOL=126740],tetracapsuloides bryosalmonae[&&NHX:TOL=27419])malacosporea[&&NHX:TOL=20287])myxozoa[&&NHX:TOL=2460],(((alcyonacea[&&NHX:TOL=120149],gorgonacea[&&NHX:TOL=120151],(epiphaxum[&&NHX:TOL=120157],heliopora[&&NHX:TOL=120158])helioporacea[&&NHX:TOL=120152],(anthoptilidae[&&NHX:TOL=139124],funiculinidae[&&NHX:TOL=139125],halipteridae[&&NHX:TOL=139126],kophobelemnidae[&&NHX:TOL=139127],protoptilidae[&&NHX:TOL=139128],renillidae[&&NHX:TOL=139129],umbellulidae[&&NHX:TOL=139130],pennatulidae[&&NHX:TOL=139132],veretillidae[&&NHX:TOL=139133],virgulariidae[&&NHX:TOL=139134])pennatulacea[&&NHX:TOL=120153],(haimea[&&NHX:TOL=120161],hartea[&&NHX:TOL=120162],monoxenia[&&NHX:TOL=120163],psuchastes[&&NHX:TOL=120164],taiaroa[&&NHX:TOL=120165])protoalcyonaria[&&NHX:TOL=120154],stolonifera[&&NHX:TOL=120155],telestacea[&&NHX:TOL=120156],pseudogorgia godeffroyi[&&NHX:TOL=120150])alcyonaria[&&NHX:TOL=17642],(((ceriantharia[&&NHX:TOL=17647],(((actinia prolifera[&&NHX:TOL=18912],protanthea simplex[&&NHX:TOL=18913])protantheae[&&NHX:TOL=17671],(((halcurias carlgreni[&&NHX:TOL=17691],halcurias endocoelactis[&&NHX:TOL=17692],halcurias capensis[&&NHX:TOL=17693],halcurias minimus[&&NHX:TOL=17694],halcurias pilatus[&&NHX:TOL=17695])halcurias[&&NHX:TOL=17697],carlgrenia desiderata[&&NHX:TOL=17698])halcuriidae[&&NHX:TOL=17688],(ilyanthopsis elegans[&&NHX:TOL=17675],isactinernus 4lobatus[&&NHX:TOL=17676],synactinernus flavus[&&NHX:TOL=17677],(actinernus nobilis[&&NHX:TOL=17680],actinernus michaelsarsi[&&NHX:TOL=17681],porponia antarcticus[&&NHX:TOL=17682],porponia elongatus[&&NHX:TOL=17683],porponia robustus[&&NHX:TOL=17684])actinernus[&&NHX:TOL=17678])actinernidae[&&NHX:TOL=17689])endocoelantheae[&&NHX:TOL=17672],((((edwardsia beautempsi[&&NHX:TOL=17734],edwardsia arctica[&&NHX:TOL=17735],edwardsia vegae[&&NHX:TOL=17736],edwardioides vitrea[&&NHX:TOL=17737],edwardsia fusca[&&NHX:TOL=17738],edwardsia finmarchica[&&NHX:TOL=17739],edwardsia islandica[&&NHX:TOL=17740],edwardsia andresi[&&NHX:TOL=17741],edwardsia costata[&&NHX:TOL=17742],edwardsia incerta[&&NHX:TOL=17743],edwardsia tuberculata[&&NHX:TOL=17744],edwardsia norvegica[&&NHX:TOL=17745],edwardsia longicorais[&&NHX:TOL=17746],edwardsia pallida[&&NHX:TOL=17747],edwardsia danica[&&NHX:TOL=17748],scolanthus callimorpha[&&NHX:TOL=17749],edwardsia delapii[&&NHX:TOL=17750],edwardsia callianthus[&&NHX:TOL=17751],edwardsia tecta[&&NHX:TOL=17752],edwardsia allmanni[&&NHX:TOL=17753],edwardsia goodsiri[&&NHX:TOL=17754],edwardsia harassei[&&NHX:TOL=17755],edwardsia timida[&&NHX:TOL=17756],edwardsia fischeri[&&NHX:TOL=17757],edwardsia janthina[&&NHX:TOL=17758],edwardsia. maroccana[&&NHX:TOL=17759],actinia sipunculoides[&&NHX:TOL=17760],halcampa sulcata[&&NHX:TOL=17761],edwardsia elegans[&&NHX:TOL=17762],edwardsia sp.[&&NHX:TOL=17763],edwardsia horstii[&&NHX:TOL=17764],edwardsia kameruniensis[&&NHX:TOL=17765],edwardsia sanctae helenae[&&NHX:TOL=17766],edwardsia capensis[&&NHX:TOL=17767],edwardsia intermedia[&&NHX:TOL=17768],edwardsia pudica[&&NHX:TOL=17769],edwardsia tinctrix[&&NHX:TOL=17770],edwardsia annamensis[&&NHX:TOL=17771],edwardsia japonica[&&NHX:TOL=17772],edwardsia octoradiata[&&NHX:TOL=17773],edwardsia mamillata[&&NHX:TOL=17774],edwardsia rugosa[&&NHX:TOL=17775],edwardsia vermiformis[&&NHX:TOL=17776],edwardsia rekaiyae[&&NHX:TOL=17777],edwardsia willeyana[&&NHX:TOL=17778],edwardsia gilbertensis[&&NHX:TOL=17779],edwardsia stephensoni[&&NHX:TOL=17780],edwardsia bocki[&&NHX:TOL=17781],edwardsia 12tentaculata[&&NHX:TOL=17782],edwardsia armata[&&NHX:TOL=17783],edwardsia tricolor[&&NHX:TOL=17784],edwardsia neozelanica[&&NHX:TOL=17785],edwardsia ignota[&&NHX:TOL=17786],edwardsia carneola[&&NHX:TOL=17787],edwardsia californica[&&NHX:TOL=17788])edwardsia[&&NHX:TOL=17790],(isoedwardsia ingolfi[&&NHX:TOL=17807],isoedwardsia nidarosiensis[&&NHX:TOL=17808],isoedwardsia mediterranea[&&NHX:TOL=17809],edwardsia lucifuga[&&NHX:TOL=17810],isoedwardsia curacaoensis[&&NHX:TOL=17811],isoedwardsia ignota[&&NHX:TOL=17812])isoedwardsia[&&NHX:TOL=17791],(halcampogeton papillosus[&&NHX:TOL=17805])halcampogeton[&&NHX:TOL=17792],(paraedwardsia arenaria[&&NHX:TOL=17821],edwardsia sarsii[&&NHX:TOL=17822],edwardsia cretata[&&NHX:TOL=17823])paraedwardsia[&&NHX:TOL=17793],(halcampa oustromovi[&&NHX:TOL=17825])synhalcampella[&&NHX:TOL=17794],(milneedwardsia loveni[&&NHX:TOL=17800],edwardsia carnea[&&NHX:TOL=17801],milneedwardsia dixoni[&&NHX:TOL=17802],edwardsia lineata[&&NHX:TOL=17803])fagesia[&&NHX:TOL=17795],(nematostella vectensis[&&NHX:TOL=17816],milneedwardsia polaris[&&NHX:TOL=17817],milneedwardsia nathorsti[&&NHX:TOL=17818],nematostella pellucida[&&NHX:TOL=17819])nematostella[&&NHX:TOL=17796],(edwardsia pallida[&&NHX:TOL=17732])drillactis[&&NHX:TOL=17797],(milneedwardsia akkeshi[&&NHX:TOL=17814])metedwardsia[&&NHX:TOL=17798])edwardsiidae[&&NHX:TOL=17710],((halcampa purpurea[&&NHX:TOL=17866],halcampoides abyssorum[&&NHX:TOL=17867])halcampoides[&&NHX:TOL=17869],calamactis praelongus[&&NHX:TOL=17870],siphonactinopsis laevis[&&NHX:TOL=17871],(scytophorus striatus[&&NHX:TOL=17880],peachia antarcticus[&&NHX:TOL=17881])scytophorus[&&NHX:TOL=17872],calamactinia goughiensis[&&NHX:TOL=17873],actinia intestinalis[&&NHX:TOL=17874],(halcampa endromitata[&&NHX:TOL=17862],halcampella maxima[&&NHX:TOL=17863],halcampella robusta[&&NHX:TOL=17864])halcampella[&&NHX:TOL=17875],pentactinia californica[&&NHX:TOL=17876])halcampoididae[&&NHX:TOL=17711],(halcampella minuta[&&NHX:TOL=17912],(ilyanthus mazelii[&&NHX:TOL=17906],actinia clavus[&&NHX:TOL=17907],eloactis australis[&&NHX:TOL=17908])anemonactis[&&NHX:TOL=17913],peachia tropica[&&NHX:TOL=17914],ilyanthus mitchelli[&&NHX:TOL=17915],harenactis attenuata[&&NHX:TOL=17916],(peachia hastata[&&NHX:TOL=17928],siphonactinia boekii[&&NHX:TOL=17929],peachia koreni[&&NHX:TOL=17930],bicidium parasitica[&&NHX:TOL=17931],peachia quinquecapitata[&&NHX:TOL=17932],peachia mira[&&NHX:TOL=17933],peachia hilli[&&NHX:TOL=17934],peachia neozelanica[&&NHX:TOL=17935],peachia carnea[&&NHX:TOL=17936],peachia chilensis[&&NHX:TOL=17937])peachia[&&NHX:TOL=17917],oractis diomedeae[&&NHX:TOL=17918])haloclavidae[&&NHX:TOL=17712],ilyanthus parthenopea[&&NHX:TOL=17713],((actinia crysanthellum[&&NHX:TOL=17832],edwardsia duodecimcirrata[&&NHX:TOL=17833],halcampa arctica[&&NHX:TOL=17834],halcampa vegae[&&NHX:TOL=17835],halcampa octocirrata[&&NHX:TOL=17836],halcampa capensis[&&NHX:TOL=17837])halcampa[&&NHX:TOL=17841],(cactosoma abyssorum[&&NHX:TOL=17827],cactosoma arenaria[&&NHX:TOL=17828],halianthus chilensis[&&NHX:TOL=17829],halcampoides aspera[&&NHX:TOL=17830])cactosoma[&&NHX:TOL=17842],parahalcampa antarctica[&&NHX:TOL=17843],halcampaster teres[&&NHX:TOL=17844],(phytocoetes chilkaea[&&NHX:TOL=17851],halianthus limnicola[&&NHX:TOL=17852])mena[&&NHX:TOL=17845],(edwardsia kerguelensisa[&&NHX:TOL=17848],halianthella annularis[&&NHX:TOL=17849])halianthella[&&NHX:TOL=17846])halcampidae[&&NHX:TOL=17714],(limnactinia laevis[&&NHX:TOL=17939],limnactinia nuda[&&NHX:TOL=17940])limnactiniidae[&&NHX:TOL=17715],(haliactis arctica[&&NHX:TOL=17888],(halcampactis mirabilis[&&NHX:TOL=17885],halcampactis dubia[&&NHX:TOL=17886])halcampactis[&&NHX:TOL=17889],(pelocoetes exul[&&NHX:TOL=17897],pelocoetes minima[&&NHX:TOL=17898])pelocoetes[&&NHX:TOL=17890],stephensonactis ornata[&&NHX:TOL=17891],phytocoetes gangeticus[&&NHX:TOL=17892],phytocoetopsis ramunni[&&NHX:TOL=17893])haliactiidae[&&NHX:TOL=17716],(octineon lindahli[&&NHX:TOL=17942],octineon suecicum[&&NHX:TOL=17943])octineonidae[&&NHX:TOL=17717],((andwakia mirabilis[&&NHX:TOL=17722],andwakia parva[&&NHX:TOL=17723],andwakia boniensis[&&NHX:TOL=17724],andwakia insignis[&&NHX:TOL=17725])andwakia[&&NHX:TOL=17727],andwakia hozawai[&&NHX:TOL=17728])andwakiidae[&&NHX:TOL=17718])athenaria[&&NHX:TOL=17706],(((bolocera mc murrichi[&&NHX:TOL=17950],nectothela liliae[&&NHX:TOL=17951])boloceroides[&&NHX:TOL=17953],(boloceractis gopalayi[&&NHX:TOL=17945])boloceractis[&&NHX:TOL=17954],(bunodeopsis strumosa[&&NHX:TOL=17957],bunodeopsis antilliensis[&&NHX:TOL=17958],viatrix globulifera[&&NHX:TOL=17959],bunodeopsis sp.[&&NHX:TOL=17960],bunodeopsis sp.[&&NHX:TOL=17961],bunodeopsis australis[&&NHX:TOL=17962])bunodeopsis[&&NHX:TOL=17955])boloceroididae[&&NHX:TOL=17947],(gyrostoma glauca[&&NHX:TOL=17964])nevadneidae[&&NHX:TOL=17948])boloceroidaria[&&NHX:TOL=17707],((((alicia mirabilis[&&NHX:TOL=18657],cladactis costae[&&NHX:TOL=18658],alicia uruguayensis[&&NHX:TOL=18659],alicia sansibarensis[&&NHX:TOL=18660],alicia rhadina[&&NHX:TOL=18661],actinia pretiosa[&&NHX:TOL=18662],thaumactis medusoides[&&NHX:TOL=18663],alicia beebei[&&NHX:TOL=18664])alicia[&&NHX:TOL=18666],phyllodiscus semoni[&&NHX:TOL=18667],(triactis producta[&&NHX:TOL=18676],viatarix cincta[&&NHX:TOL=18677])triactis[&&NHX:TOL=18668],(oulactis danae[&&NHX:TOL=18671],hoplophoria coralligens[&&NHX:TOL=18672])lebrunia[&&NHX:TOL=18669])aliciidae[&&NHX:TOL=18322],((condylanthus magellanicus[&&NHX:TOL=18701],condylanthus aucklandicus[&&NHX:TOL=18702])condylanthus[&&NHX:TOL=18695],pseudhormathia bocki[&&NHX:TOL=18696],macrocnema nicobarica[&&NHX:TOL=18697],charisea saxicola[&&NHX:TOL=18698],charisella elongata[&&NHX:TOL=18699])condylanthidae[&&NHX:TOL=18323],((actinia equina[&&NHX:TOL=18333],actinia cari[&&NHX:TOL=18334],diplactis bermudensis[&&NHX:TOL=18335],actinia grobbeni[&&NHX:TOL=18336],actinia melanaster[&&NHX:TOL=18337],actinia infecunda[&&NHX:TOL=18338],actinia kraemeri[&&NHX:TOL=18339],actinia tenebrosa[&&NHX:TOL=18340])actinia[&&NHX:TOL=18342],(actinia sulcata[&&NHX:TOL=18393],anemonia sargassiensis[&&NHX:TOL=18394],anemonia elegans[&&NHX:TOL=18395],anemonia antilliensis[&&NHX:TOL=18396],paractis hemprichi[&&NHX:TOL=18397],entacmaea erythrea[&&NHX:TOL=18398],anemonia manjano[&&NHX:TOL=18399],anemonia natalensis[&&NHX:TOL=18400])anemonia[&&NHX:TOL=18343],(anthostella stephensoni[&&NHX:TOL=18432],isactinia badia[&&NHX:TOL=18433])anthostella[&&NHX:TOL=18344],(actinia clematis[&&NHX:TOL=18624],rivetia papillosa[&&NHX:TOL=18625],actinia sanctae helenae[&&NHX:TOL=18626],actinia pustulata[&&NHX:TOL=18627])phymactis[&&NHX:TOL=18345],(actinia granulifera[&&NHX:TOL=18484],actinia cavernata[&&NHX:TOL=18485],bunodosoma spherulata[&&NHX:TOL=18486],bunodosoma kuekenthali[&&NHX:TOL=18487],actinia diadema[&&NHX:TOL=18488],actinia capensis[&&NHX:TOL=18489],bunodactis fallax[&&NHX:TOL=18490],cladactis grandis[&&NHX:TOL=18491],bunodosoma californica[&&NHX:TOL=18492])bunodosoma[&&NHX:TOL=18346],(comactis flagellifera[&&NHX:TOL=18629],pseudactinia varia[&&NHX:TOL=18630],actinia infecunda[&&NHX:TOL=18631])pseudactinia[&&NHX:TOL=18347],(metridium muscosa[&&NHX:TOL=18581],oulactis plicata[&&NHX:TOL=18582],saccactis macmurrichi[&&NHX:TOL=18583],saccactis australis[&&NHX:TOL=18584],saccactis musculosa[&&NHX:TOL=18585],tealidium cinctum[&&NHX:TOL=18586])oulactis[&&NHX:TOL=18348],(anthopleura krebsi[&&NHX:TOL=18402],anthopleura varioarmata[&&NHX:TOL=18403],anthopleura pallida[&&NHX:TOL=18404],bunodes thallia[&&NHX:TOL=18405],actinia ballii[&&NHX:TOL=18406],bunodes crassa[&&NHX:TOL=18407],bunodes listeri[&&NHX:TOL=18408],anthopleura mortenseni[&&NHX:TOL=18409],anthopleura sanctae helenae[&&NHX:TOL=18410],bunodactis michaelseni[&&NHX:TOL=18411],anthopleura anneae[&&NHX:TOL=18412],anthopleura insignis[&&NHX:TOL=18413],actinia stellula[&&NHX:TOL=18414],anthopleura fuxi[&&NHX:TOL=18415],actinioides africana[&&NHX:TOL=18416],gyractis pallida[&&NHX:TOL=18417],gyractis excavata[&&NHX:TOL=18418],anthopleura japonica[&&NHX:TOL=18419],anthopleura pacifica[&&NHX:TOL=18420],actinia xanthogrammica[&&NHX:TOL=18421],anthopleura fuscoviridis[&&NHX:TOL=18422],actinoides haddoni[&&NHX:TOL=18423],actinioides dixoniana[&&NHX:TOL=18424],condylactis gelam[&&NHX:TOL=18425],bunodes aureoradiata[&&NHX:TOL=18426],anthopleura kohli[&&NHX:TOL=18427],phymactis inconspicua[&&NHX:TOL=18428],anthopleura dowii[&&NHX:TOL=18429],bunodes hermafroditica[&&NHX:TOL=18430])anthopleura[&&NHX:TOL=18349],(actinia tuediae[&&NHX:TOL=18435],bolocera maxima[&&NHX:TOL=18436],bolocera occidua[&&NHX:TOL=18437],bolocera capensis[&&NHX:TOL=18438],bolocera kerguelensis[&&NHX:TOL=18439],bolocera somaliensis[&&NHX:TOL=18440],bolocera pannosa[&&NHX:TOL=18441],polystomidium patens[&&NHX:TOL=18442])bolocera[&&NHX:TOL=18350],(liponema multipora[&&NHX:TOL=18571],bolocera multicornis[&&NHX:TOL=18572],liponema brevicirrata[&&NHX:TOL=18573],bolocera brevicornis[&&NHX:TOL=18574])liponema[&&NHX:TOL=18351],(bolocera pollens[&&NHX:TOL=18568],leipsiceras valens[&&NHX:TOL=18569])leipsiceras[&&NHX:TOL=18352],(condylactis hertwigi[&&NHX:TOL=18590],paracondylactis sinensis[&&NHX:TOL=18591],paracondylactis davydoffi[&&NHX:TOL=18592])paracondylactis[&&NHX:TOL=18353],(anemonia citrina[&&NHX:TOL=18553],isactinia ignota[&&NHX:TOL=18554],isactinia lobata[&&NHX:TOL=18555])isactinia[&&NHX:TOL=18354],isotealia pachyderma[&&NHX:TOL=18355],(isotealia antarctica[&&NHX:TOL=18565],isotealia dubia[&&NHX:TOL=18566])isotealia[&&NHX:TOL=18356],(myonanthus ambiguus[&&NHX:TOL=18578],myonanthus bankamensis[&&NHX:TOL=18579])myonanthus[&&NHX:TOL=18357],paractis alba[&&NHX:TOL=18358],actinopsis rosea[&&NHX:TOL=18359],dofleinia armata[&&NHX:TOL=18360],boloceropsis platei[&&NHX:TOL=18361],(epiactis prolifera[&&NHX:TOL=18509],epiactis marsupialis[&&NHX:TOL=18510],epiactis incerta[&&NHX:TOL=18511],phellia arctica[&&NHX:TOL=18512],epiactis nordmanni[&&NHX:TOL=18513],epigonactis fecunda[&&NHX:TOL=18514],epiactis vincentina[&&NHX:TOL=18515],epiactis georgiana[&&NHX:TOL=18516],epiactis brucei[&&NHX:TOL=18517],epiactis crateriformis[&&NHX:TOL=18518],epiactis adeliana[&&NHX:TOL=18519],epiactis lewisi[&&NHX:TOL=18520],bunodactis japonica[&&NHX:TOL=18521],epiactis novazealandica[&&NHX:TOL=18522],actinia thomsoni[&&NHX:TOL=18523],epiactis irregularis[&&NHX:TOL=18524])epiactis[&&NHX:TOL=18362],(gyrostoma hertwigi[&&NHX:TOL=18532],gyrostoma sanctithomae[&&NHX:TOL=18533],gyrostoma monodi[&&NHX:TOL=18534],actinia erythrosoma[&&NHX:TOL=18535],actinia quadricolor[&&NHX:TOL=18536],actinia helianthus[&&NHX:TOL=18537],actinia adherens[&&NHX:TOL=18538],isacmaea euchlora[&&NHX:TOL=18539],gyrostoma tristis[&&NHX:TOL=18540],gyrostoma dubia[&&NHX:TOL=18541],gyrostoma stuhlmanni[&&NHX:TOL=18542],gyrostoma dysancritum[&&NHX:TOL=18543],gyrostoma tulearense[&&NHX:TOL=18544],anemonia kwoiam[&&NHX:TOL=18545],gyrostoma haddoni[&&NHX:TOL=18546],gyrostoma sulcatum[&&NHX:TOL=18547],gyrostoma selkirkei[&&NHX:TOL=18548],gyrostoma incertum[&&NHX:TOL=18549],anemonia inequale[&&NHX:TOL=18550],anemonia stimpsoni[&&NHX:TOL=18551])gyrostoma[&&NHX:TOL=18363],anemonia cinerea[&&NHX:TOL=18364],phialoba steinbecki[&&NHX:TOL=18365],glyphoperidium bursa[&&NHX:TOL=18366],glyphostylum calyx[&&NHX:TOL=18367],(urticina antarctica[&&NHX:TOL=18638],urticinopsis crassa[&&NHX:TOL=18639])urticinopsis[&&NHX:TOL=18368],isadamsia cancrisocia[&&NHX:TOL=18369],(actinia tuberculosa[&&NHX:TOL=18603],phlyctenactis retifera[&&NHX:TOL=18604],phlyctenactis morrisoni[&&NHX:TOL=18605])phlyctenactis[&&NHX:TOL=18370],(bunodactis manni[&&NHX:TOL=18494],cladactella obscura[&&NHX:TOL=18495])cladactella[&&NHX:TOL=18371],phlyctenanthus australis[&&NHX:TOL=18372],epiactis ritteri[&&NHX:TOL=18373],(actinioides sultana[&&NHX:TOL=18386],actinioides rapanuiensis[&&NHX:TOL=18387],actinioides sesere[&&NHX:TOL=18388],actinioides spenceri[&&NHX:TOL=18389],actinioides papuensis[&&NHX:TOL=18390],actinioides ambonensis[&&NHX:TOL=18391])actiniogeton[&&NHX:TOL=18374],(actinia cruentata[&&NHX:TOL=18596],bunodella georgiana[&&NHX:TOL=18597],actinia ocellata[&&NHX:TOL=18598],bunodactis vanhoeffeni[&&NHX:TOL=18599])parantheopsis[&&NHX:TOL=18375],(actinia aurantiaca[&&NHX:TOL=18499],anthea gigantea[&&NHX:TOL=18500],condylactis natalensis[&&NHX:TOL=18501],condylactis parvicornis[&&NHX:TOL=18502])condylactis[&&NHX:TOL=18376],condylactis aspera[&&NHX:TOL=18377],(actinia felina[&&NHX:TOL=18633],urticina columbiana[&&NHX:TOL=18634])tealia[&&NHX:TOL=18378],actinia artemisia[&&NHX:TOL=18379],(cribrinopsis similis[&&NHX:TOL=18504],cribrinopsis williamsi[&&NHX:TOL=18505])cribrinopsis[&&NHX:TOL=18380],(actinia verrucosa[&&NHX:TOL=18446],bunodes stella[&&NHX:TOL=18447],cribrina spetsbergensis[&&NHX:TOL=18448],bunodes biscayensis[&&NHX:TOL=18449],bunodes duregnei[&&NHX:TOL=18450],bunodes rigidus[&&NHX:TOL=18451],bunodes sabelloides[&&NHX:TOL=18452],bunodactis steinitze[&&NHX:TOL=18453],aulactinia capitata[&&NHX:TOL=18454],aulactinia stelloides[&&NHX:TOL=18455],bunodactis curacaoensis[&&NHX:TOL=18456],tealia bunodiformis[&&NHX:TOL=18457],bunodes patagoniensis[&&NHX:TOL=18458],bunodes octoradiata[&&NHX:TOL=18459],cystiactis reynaudi[&&NHX:TOL=18460],bunodactis vanhoeffeni[&&NHX:TOL=18461],urticina sulcata[&&NHX:TOL=18462],urticina carlgreni[&&NHX:TOL=18463],bunodes varidi[&&NHX:TOL=18464],bunodactis nicobarica[&&NHX:TOL=18465],actinia inornata[&&NHX:TOL=18466],anthopleura stimpsoni[&&NHX:TOL=18467],bunodes japonica[&&NHX:TOL=18468],tealiopsis nigrescens[&&NHX:TOL=18469],cribrina verruculata[&&NHX:TOL=18470],cribrina altifossa[&&NHX:TOL=18471],bunodactis rubrofusca[&&NHX:TOL=18472],bunodes rosea[&&NHX:TOL=18473],bunodes minima[&&NHX:TOL=18474],epiactis mortenseni[&&NHX:TOL=18475],bunodactis aucklandica[&&NHX:TOL=18476],taractostephanus elegantissima[&&NHX:TOL=18477],bunodactis mexicana[&&NHX:TOL=18478],bunodes papillosa[&&NHX:TOL=18479],bunodes pluvia[&&NHX:TOL=18480],cribrina elongata[&&NHX:TOL=18481],cribrina conica[&&NHX:TOL=18482])bunodactis[&&NHX:TOL=18381],cradactis magna[&&NHX:TOL=18382],bunodactis inflexibilis[&&NHX:TOL=18383],(metridium praetexta[&&NHX:TOL=18609],actinia flosculifera[&&NHX:TOL=18610],oulactis conquilega[&&NHX:TOL=18611],actinostella formosa[&&NHX:TOL=18612],oulactis radiata[&&NHX:TOL=18613],cradactis digitata[&&NHX:TOL=18614],oulactis californica[&&NHX:TOL=18615],asteractis bradleyi[&&NHX:TOL=18616],metridium concinnata[&&NHX:TOL=18617],lophactis ornata[&&NHX:TOL=18618],phyllactis cichoracea[&&NHX:TOL=18619],oulactis plicata[&&NHX:TOL=18620],cradactis striata[&&NHX:TOL=18621],cradactis excelsa[&&NHX:TOL=18622])phyllactis[&&NHX:TOL=18384])actiniidae[&&NHX:TOL=18324],((actinia arboreum[&&NHX:TOL=18641],actinia alcyonidium[&&NHX:TOL=18642],acremodactyla ambonense[&&NHX:TOL=18643],actinodendron plumosum[&&NHX:TOL=18644],actinodendron  glomeratum[&&NHX:TOL=18645],actinodendron hansingorum[&&NHX:TOL=18646])actinodendron[&&NHX:TOL=18648],(megalactis hemprichii[&&NHX:TOL=18654],megalactis griffithsii[&&NHX:TOL=18655])megalactis[&&NHX:TOL=18649],actinostephanus haeckeli[&&NHX:TOL=18650])actinodendronidae[&&NHX:TOL=18325],((thalassianthus aster[&&NHX:TOL=18779],thalassianthus kraepelini[&&NHX:TOL=18780],thalassianthus senckenbergianus[&&NHX:TOL=18781])thalassianthus[&&NHX:TOL=18774],(actinia villosa[&&NHX:TOL=18765],actineria dendrophora[&&NHX:TOL=18766])actineria[&&NHX:TOL=18775],(heterodactyla hemprichii[&&NHX:TOL=18770],heterodactyla hypnoides[&&NHX:TOL=18771],heterodactyla sp.[&&NHX:TOL=18772])heterodactyla[&&NHX:TOL=18776],cryptodendrum adhaesivum[&&NHX:TOL=18777])thalassianthidae[&&NHX:TOL=18326],((corynactis heterocera[&&NHX:TOL=18682],aureliana georgiana[&&NHX:TOL=18683],leiotealia nymphaea[&&NHX:TOL=18684],aureliana japonica[&&NHX:TOL=18685],stephanactis indica[&&NHX:TOL=18686])aureliana[&&NHX:TOL=18688],(actinoporus elegans[&&NHX:TOL=18679],actinoporus elongatus[&&NHX:TOL=18680])actinoporus[&&NHX:TOL=18689])aurelianidae[&&NHX:TOL=18327],(actinia ultramarina[&&NHX:TOL=18710],minyas coerulea[&&NHX:TOL=18711],minyas torpedo[&&NHX:TOL=18712],actinia olivacea[&&NHX:TOL=18713],stichophora cyanea[&&NHX:TOL=18714])minyadidae[&&NHX:TOL=18328],homostichanthus duerdeni[&&NHX:TOL=18329],((stoichactis kenti[&&NHX:TOL=18754],priapus giganteum[&&NHX:TOL=18755],actinia tapetum[&&NHX:TOL=18756],homactis rupicola[&&NHX:TOL=18757],discosoma ambonensis[&&NHX:TOL=18758],stoichactis haddoni[&&NHX:TOL=18759],actinia helianthus[&&NHX:TOL=18760],stoichactis laevis[&&NHX:TOL=18761],stoichactis intermedia[&&NHX:TOL=18762],stoichactis australis[&&NHX:TOL=18763])stoichactis[&&NHX:TOL=18751],(radianthus kuekenthali[&&NHX:TOL=18735],bunodes koseiriensis[&&NHX:TOL=18736],actinia crispus[&&NHX:TOL=18737],helianthopsis mabrucki[&&NHX:TOL=18738],helianthopsis ritteri[&&NHX:TOL=18739],radianthus lobatus[&&NHX:TOL=18740],stichodactis papillosa[&&NHX:TOL=18741],actinia parvitentaculata[&&NHX:TOL=18742],discosoma macrodactylus[&&NHX:TOL=18743],discosoma malu[&&NHX:TOL=18744],stichodactis glandulosa[&&NHX:TOL=18745],stichodactis kwietniewskii[&&NHX:TOL=18746],antheopsis carlgreni[&&NHX:TOL=18747],antheopsis concinnata[&&NHX:TOL=18748],myriactis tubicola[&&NHX:TOL=18749])radianthus[&&NHX:TOL=18752])stoichactiidae[&&NHX:TOL=18330],((actinodendron loligo[&&NHX:TOL=18722],actinia crucifer[&&NHX:TOL=18723],phymanthus sansibaricus[&&NHX:TOL=18724],phymanthus strandesi[&&NHX:TOL=18725],phymanthus pinnulatum[&&NHX:TOL=18726],thelaceros rhizophoreae[&&NHX:TOL=18727],phymanthus laevis[&&NHX:TOL=18728],phymanthus buitendijki[&&NHX:TOL=18729],phymanthus muscosus[&&NHX:TOL=18730],actinia coeruleus[&&NHX:TOL=18731],phymanthus simplex[&&NHX:TOL=18732],ragactis pulcra[&&NHX:TOL=18733])phymanthus[&&NHX:TOL=18719],(heteranthus verruculatus[&&NHX:TOL=18716],heteranthus insignis[&&NHX:TOL=18717])heteranthus[&&NHX:TOL=18720])phymanthidae[&&NHX:TOL=18331])endomyaria[&&NHX:TOL=17966],((isanthus capensis[&&NHX:TOL=18786],neophellia mutsuensis[&&NHX:TOL=18787])isanthidae[&&NHX:TOL=18791],((urticina callosa[&&NHX:TOL=18802],actinostola spetsbergensis[&&NHX:TOL=18803],bunodes abyssorum[&&NHX:TOL=18804],actinostola  groenlandica[&&NHX:TOL=18805],actinostola pergamentacea[&&NHX:TOL=18806],dysactis crassicornis[&&NHX:TOL=18807],actinostola intermedia[&&NHX:TOL=18808],actinostola excelsa[&&NHX:TOL=18809],actinostola georgiana[&&NHX:TOL=18810],actinostola clubbi[&&NHX:TOL=18811],actinostola kerguelensis[&&NHX:TOL=18812],actinostola carlgreni[&&NHX:TOL=18813])actinostola[&&NHX:TOL=18815],(paractinostola bulbosa[&&NHX:TOL=18861],paractinostola capensis[&&NHX:TOL=18862],cymbactis faeculenta[&&NHX:TOL=18863])paractinostola[&&NHX:TOL=18816],(actinia coccinea[&&NHX:TOL=18897],tealiopsis polaris[&&NHX:TOL=18898],cymbactis selaginella[&&NHX:TOL=18899],stomphia japonica[&&NHX:TOL=18900],paractis vinosa[&&NHX:TOL=18901])stomphia[&&NHX:TOL=18817],(ophiodiscus annulatus[&&NHX:TOL=18858],ophiodiscus sulcatus[&&NHX:TOL=18859])ophiodiscus[&&NHX:TOL=18818],(parasicyonis sarsii[&&NHX:TOL=18871],parasicyonis  ingolfi[&&NHX:TOL=18872],parasicyonis groenlandica[&&NHX:TOL=18873],parasicyonis antarctica[&&NHX:TOL=18874],cymbactis actinostoloides[&&NHX:TOL=18875],cymbactis maxima[&&NHX:TOL=18876])parasicyonis[&&NHX:TOL=18819],(sicyonis crassa[&&NHX:TOL=18884],sicyonis tuberculata[&&NHX:TOL=18885],sicyonis ingolfi[&&NHX:TOL=18886],sicyonis variabilis[&&NHX:TOL=18887],cymbactis gossei[&&NHX:TOL=18888],sicyonis hemisphaerica[&&NHX:TOL=18889],actinernus obesa[&&NHX:TOL=18890],sicyonis antarctica[&&NHX:TOL=18891],cymbactis erythrocephala[&&NHX:TOL=18892],sicyonis sumatriensis[&&NHX:TOL=18893],sicyonis aurora[&&NHX:TOL=18894],paractis tubulifera[&&NHX:TOL=18895])sicyonis[&&NHX:TOL=18820],synsicyonis elongata[&&NHX:TOL=18821],(tealidium cingulatum[&&NHX:TOL=18905],tealidium jungerseni[&&NHX:TOL=18906])tealidium[&&NHX:TOL=18822],(anthosactis jan mayeni[&&NHX:TOL=18839],anthosactis ingolfi[&&NHX:TOL=18840],paractis excavata[&&NHX:TOL=18841],anthosactis capensis[&&NHX:TOL=18842],antholoba epizoica[&&NHX:TOL=18843],anthosactis georgiana[&&NHX:TOL=18844])anthosactis[&&NHX:TOL=18823],hormosoma scotti[&&NHX:TOL=18824],cnidanthus polaris[&&NHX:TOL=18825],(actinia rapiformis[&&NHX:TOL=18865],parantheoides crassus[&&NHX:TOL=18866],actinia niveus[&&NHX:TOL=18867],paractis ignotus[&&NHX:TOL=18868],dysactis rhodorus[&&NHX:TOL=18869])paranthus[&&NHX:TOL=18826],bathydactylus valdiviae[&&NHX:TOL=18827],paractis ferax[&&NHX:TOL=18828],(actinernus saginata[&&NHX:TOL=18797],actinernus plebeia[&&NHX:TOL=18798],actinernus aurelia[&&NHX:TOL=18799],actinernus verrilli[&&NHX:TOL=18800])actinoscyphia[&&NHX:TOL=18829],epiparactis dubia[&&NHX:TOL=18830],paractis lineolatus[&&NHX:TOL=18831],paractis tenuicollis[&&NHX:TOL=18832],(pycnanthus maliformis[&&NHX:TOL=18880],pycnanthus laevis[&&NHX:TOL=18881],pycnanthus densus[&&NHX:TOL=18882])pycnanthus[&&NHX:TOL=18833],(actinia achates[&&NHX:TOL=18836],urticina perdix[&&NHX:TOL=18837])antholoba[&&NHX:TOL=18834])actinostolidae[&&NHX:TOL=18792],(polysiphonia tuberosa[&&NHX:TOL=18783],exocoelactis valdiviae[&&NHX:TOL=18784])exocoelactiidae[&&NHX:TOL=18793])mesomyaria[&&NHX:TOL=17967],((acontiophorum mortenseni[&&NHX:TOL=17982],acontiophorum niveum[&&NHX:TOL=126390])acontiophoridae[&&NHX:TOL=17970],(phellia margaritacea[&&NHX:TOL=18020],sagartiogeton praelonga[&&NHX:TOL=18021],(phelliogeton falklandicus[&&NHX:TOL=18027],phelliogeton kerguelensis[&&NHX:TOL=18028])phelliogeton[&&NHX:TOL=18022],acraspedanthus elongatus[&&NHX:TOL=18023])bathyphelliidae[&&NHX:TOL=17971],((isophellia sabulosa[&&NHX:TOL=18181],isophellia algonensis[&&NHX:TOL=18182])isophellia[&&NHX:TOL=18184],flosmaris phellioides[&&NHX:TOL=18185],decaphellia psammomitra[&&NHX:TOL=18186],(epiphellia anneae[&&NHX:TOL=18171],epiphellia elongata[&&NHX:TOL=18172],epiphellia australis[&&NHX:TOL=18173],phellia browni[&&NHX:TOL=18174],phellia capitata[&&NHX:TOL=18175])epiphellia[&&NHX:TOL=18187],(telmatactis valle flori[&&NHX:TOL=18194],actinia elongata[&&NHX:TOL=18195],phellia limicola[&&NHX:TOL=18196],entacmaea forskalii[&&NHX:TOL=18197],phellia rufa[&&NHX:TOL=18198],phellia roseni[&&NHX:TOL=18199],phellia pseudoroseni[&&NHX:TOL=18200],phellia simplex[&&NHX:TOL=18201],paractis americana[&&NHX:TOL=18202],paractis vestita[&&NHX:TOL=18203],actinia decora[&&NHX:TOL=18204],telmatactis natalensis[&&NHX:TOL=18205],edwardsia clavata[&&NHX:TOL=18206],phellia inequalis[&&NHX:TOL=18207],edwardsia collaris[&&NHX:TOL=18208],phellia castanea[&&NHX:TOL=18209],phellia phassonesiotes[&&NHX:TOL=18210],phellia allanatoides[&&NHX:TOL=18211],phellia cylicodes[&&NHX:TOL=18212],phellia ambonensis[&&NHX:TOL=18213],phellia ternatana[&&NHX:TOL=18214],phellia vermiformis[&&NHX:TOL=18215],phellia sipunculoides[&&NHX:TOL=18216],phellia devisi[&&NHX:TOL=18217],telmatactis stephensoni[&&NHX:TOL=18218],telmatactis insignis[&&NHX:TOL=18219],telmatactis australiensis[&&NHX:TOL=18220],phellia humilis[&&NHX:TOL=18221],phellia sollasi[&&NHX:TOL=18222],phellia rapanuiensis[&&NHX:TOL=18223],phellia panamensis[&&NHX:TOL=18224])telmatactis[&&NHX:TOL=18188],euphellia cinclidifera[&&NHX:TOL=18189],litophellia octoradiata[&&NHX:TOL=18190])isophelliidae[&&NHX:TOL=17972],((actinia digitata[&&NHX:TOL=18101],actinia nodosa[&&NHX:TOL=18102],chitonanthus incubans[&&NHX:TOL=18103],bunodes coronata[&&NHX:TOL=18104],chitonactis marioni[&&NHX:TOL=18105],hormathia mediterranea[&&NHX:TOL=18106],phellia pectinata[&&NHX:TOL=18107],hormathia georgiana[&&NHX:TOL=18108],paranthus erythrosoma[&&NHX:TOL=18109],parantheoides rhododactyla[&&NHX:TOL=18110],leptoteichus insignis[&&NHX:TOL=18111],liliella lacunifera[&&NHX:TOL=18112],hormathia andersoni[&&NHX:TOL=18113],cereus spinosa[&&NHX:TOL=18114],chitonanthus castanea[&&NHX:TOL=18115])hormathia[&&NHX:TOL=18119],(chitonactis richardi[&&NHX:TOL=18036],actinauge verrillii[&&NHX:TOL=18037],actinauge abyssorum[&&NHX:TOL=18038],actinauge granulata[&&NHX:TOL=18039],actinauge bocki[&&NHX:TOL=18040])actinauge[&&NHX:TOL=18120],(paraphelliactis spinosa[&&NHX:TOL=18145],paraphelliactis michaelsarsi[&&NHX:TOL=18146])paraphelliactis[&&NHX:TOL=18121],(paracalliactis valdiviae[&&NHX:TOL=18135],paracalliactis stephensoni[&&NHX:TOL=18136],paracalliactis michaelsarsi[&&NHX:TOL=18137],adamsia involvens[&&NHX:TOL=18138])paracalliactis[&&NHX:TOL=18122],phellia brodricii[&&NHX:TOL=18123],allantactis parasitica[&&NHX:TOL=18124],sagartia nutrix[&&NHX:TOL=18125],(chitonactis expansa[&&NHX:TOL=18140],paraphellia sanzoi[&&NHX:TOL=18141],paraphellia lineata[&&NHX:TOL=18142],paraphellia hunti[&&NHX:TOL=18143])paraphellia[&&NHX:TOL=18126],(phelliactis hertwigi[&&NHX:TOL=18148],chondrodactis coccinea[&&NHX:TOL=18149],chondrodactis pulchra[&&NHX:TOL=18150],phelliactis robusta[&&NHX:TOL=18151],phelliactis incerta[&&NHX:TOL=18152],phelliactis capensis[&&NHX:TOL=18153],phelliactis algoaensis[&&NHX:TOL=18154],phelliactis somaliensis[&&NHX:TOL=18155],phelliactis siberutiensis[&&NHX:TOL=18156],chondrodactis japonica[&&NHX:TOL=18157],chondrodactis magna[&&NHX:TOL=18158],chondrodactis crassa[&&NHX:TOL=18159])phelliactis[&&NHX:TOL=18127],hormathianthus tuberculatus[&&NHX:TOL=18128],(actinia decorata[&&NHX:TOL=18078],actinia parasitica[&&NHX:TOL=18079],actinia tricolor[&&NHX:TOL=18080],calliactis vincentina[&&NHX:TOL=18081],cereus brevicornis[&&NHX:TOL=18082],calliactis reticulata[&&NHX:TOL=18083],calliactis algoaënsis[&&NHX:TOL=18084],priapus polypus[&&NHX:TOL=18085],calliactis valdiviae[&&NHX:TOL=18086],adamsia fusca[&&NHX:TOL=18087],cereus sinensis[&&NHX:TOL=18088],calliactis japonica[&&NHX:TOL=18089],calliactis miriam[&&NHX:TOL=18090],calliactis armillatus[&&NHX:TOL=18091],calliactis variegata[&&NHX:TOL=18092])calliactis[&&NHX:TOL=18129],(medusa palliata[&&NHX:TOL=18042],sagartia paguri[&&NHX:TOL=18043],adamsia sociabilis[&&NHX:TOL=18044])adamsia[&&NHX:TOL=18130],(actinauge nodosa var. coronata[&&NHX:TOL=18096],chondrophellia africana[&&NHX:TOL=18097])chondrophellia[&&NHX:TOL=18131],(amphianthus bathybium[&&NHX:TOL=18048],korenia margaritaceus[&&NHX:TOL=18049],amphianthus norvegicus[&&NHX:TOL=18050],stelidiactis mopsiae[&&NHX:TOL=18051],stephanactis inornata[&&NHX:TOL=18052],amphianthus islandicus[&&NHX:TOL=18053],amphianthus ingolfi[&&NHX:TOL=18054],amphianthus vermiculatus[&&NHX:TOL=18055],gephyra dohrni[&&NHX:TOL=18056],raphactis nitidus[&&NHX:TOL=18057],gliatactis crassus[&&NHX:TOL=18058],synanthus mirabilis[&&NHX:TOL=18059],raphactis caribea[&&NHX:TOL=18060],amphianthus michaelsarsi[&&NHX:TOL=18061],stephanactis impeditus[&&NHX:TOL=18062],amphianthus radiatus[&&NHX:TOL=18063],amphianthus sanctae helenae[&&NHX:TOL=18064],stephanauge giganteus[&&NHX:TOL=18065],amphianthus laevis[&&NHX:TOL=18066],amphianthus capensis[&&NHX:TOL=18067],amphianthus natalensis[&&NHX:TOL=18068],bunodes minutus[&&NHX:TOL=18069],amphianthus valdiviae[&&NHX:TOL=18070],amphianthus armatus[&&NHX:TOL=18071],gephyra brunneus[&&NHX:TOL=18072],amphianthus rosaceus[&&NHX:TOL=18073],amphianthus ornatus[&&NHX:TOL=18074],amphianthus californicus[&&NHX:TOL=18075],sagartia lacteus[&&NHX:TOL=18076])amphianthus[&&NHX:TOL=18132],(actinauge nexilis[&&NHX:TOL=18161],sagartia acanellae[&&NHX:TOL=18162],sagartia spongicola[&&NHX:TOL=18163],stephanauge bulbosa[&&NHX:TOL=18164],stephanactis tuberculata[&&NHX:TOL=18165],stephanauge annularis[&&NHX:TOL=18166],stephanactis hyalonematis[&&NHX:TOL=18167])stephanauge[&&NHX:TOL=18133])hormathiidae[&&NHX:TOL=17973],(sagartiomorphe carlgreni[&&NHX:TOL=18320])sagartiomorphidae[&&NHX:TOL=17974],((actinia elegans[&&NHX:TOL=18291],actinia troglodytes[&&NHX:TOL=18292],sagartia herpetodes[&&NHX:TOL=18293])sagartia[&&NHX:TOL=18297],actinia pedunculatus[&&NHX:TOL=18298],sagartianthus indosinensis[&&NHX:TOL=18299],artemidactis victrix[&&NHX:TOL=18300],(sagartia sphyrodeta[&&NHX:TOL=18239],sagartia ignea[&&NHX:TOL=18240],sagartia modesta[&&NHX:TOL=18241],sagartia gracillima[&&NHX:TOL=18242],sagartia pustulata[&&NHX:TOL=18243],sagartia georgiana[&&NHX:TOL=18244],sagartia patagonica[&&NHX:TOL=18245],sagartia paradoxa[&&NHX:TOL=18246],sagartia sancti matthaei[&&NHX:TOL=18247],sagartia kerguelensis[&&NHX:TOL=18248],sagartia pugnax[&&NHX:TOL=18249],sagartia longa[&&NHX:TOL=18250],sagartia pusilla[&&NHX:TOL=18251],sagartia plebeia[&&NHX:TOL=18252],actinothoe milmani[&&NHX:TOL=18253],sagartia carlgreni[&&NHX:TOL=18254],gregoria albocincta[&&NHX:TOL=18255],thoe neozealandica[&&NHX:TOL=18256],thoe albens[&&NHX:TOL=18257],actinothoe californica[&&NHX:TOL=18258],sagartia bradley[&&NHX:TOL=18259],sagartia gravieri[&&NHX:TOL=18260],actinia chilensis[&&NHX:TOL=18261],sagartia lobata[&&NHX:TOL=18262])actinothoe[&&NHX:TOL=18301],(cereus stimpsoni[&&NHX:TOL=18264],calliactis vincentina[&&NHX:TOL=18265],entacmaea olivacea[&&NHX:TOL=18266],mitactis australiae[&&NHX:TOL=18267],mitactis similis[&&NHX:TOL=18268],anthothoe australiensis[&&NHX:TOL=18269],sagartia vagrans[&&NHX:TOL=18270],anthothoe panamensis[&&NHX:TOL=18271])anthothoe[&&NHX:TOL=18302],(actinia impatiens[&&NHX:TOL=18277],choriactis subantarctica[&&NHX:TOL=18278])choriactis[&&NHX:TOL=18303],(phellia gausapata[&&NHX:TOL=18286],hormathia exlex[&&NHX:TOL=18287],synphellia aucklandica[&&NHX:TOL=18288],synphellia dubia[&&NHX:TOL=18289])phellia[&&NHX:TOL=18304],(kadosactis  rosea[&&NHX:TOL=18280],phellia abyssicola[&&NHX:TOL=18281],phellia spitzbergensis[&&NHX:TOL=18282],kadosanthus sulcatus[&&NHX:TOL=18283],sicyopus commensalis[&&NHX:TOL=18284])kadosactis[&&NHX:TOL=18305],(sagartiogeton robustus[&&NHX:TOL=18308],phellia tubicolus[&&NHX:TOL=18309],phellia flexibilis[&&NHX:TOL=18310],actinia undatus[&&NHX:TOL=18311],actinia viduatus[&&NHX:TOL=18312],actinia laceratus[&&NHX:TOL=18313],sagartiogeton abyssorum[&&NHX:TOL=18314],sagartiogeton ingolfi[&&NHX:TOL=18315],sagartiogeton verrilli[&&NHX:TOL=18316],sagartiogeton antarcticus[&&NHX:TOL=18317],actinothoe californicus[&&NHX:TOL=18318])sagartiogeton[&&NHX:TOL=18306])sagartiidae[&&NHX:TOL=17975],((actinia senile[&&NHX:TOL=18231],metridium parvulum[&&NHX:TOL=18232],metridium canum[&&NHX:TOL=18233])metridium[&&NHX:TOL=18228],isometrdium  richettsi sic[&&NHX:TOL=18229])metridiidae[&&NHX:TOL=17976],((anthea couchii[&&NHX:TOL=17984],actinia diaphana[&&NHX:TOL=17985],aiptasia saxicola[&&NHX:TOL=17986],aiptasia carnea[&&NHX:TOL=17987],aiptasia leiodactyla[&&NHX:TOL=17988],dysactis pallida[&&NHX:TOL=17989],bartholomea tagetes[&&NHX:TOL=17990],aiptasioides prima[&&NHX:TOL=17991],aiptasia insignis[&&NHX:TOL=17992],aiptasia parva[&&NHX:TOL=17993],aiptasia pulchella[&&NHX:TOL=17994],aiptasia californica[&&NHX:TOL=17995])aiptasia[&&NHX:TOL=17997],(actinia annulata[&&NHX:TOL=18001],bartholomea werneri[&&NHX:TOL=18002],aiptasia sp.? tagetes[&&NHX:TOL=18003],aiptasia lucida[&&NHX:TOL=18004],aiptasia peruviana[&&NHX:TOL=18005])bartholomea[&&NHX:TOL=17998],(actinia aurora[&&NHX:TOL=18007],capnea lucida[&&NHX:TOL=18008])heteractis[&&NHX:TOL=17999])aiptasiidae[&&NHX:TOL=17977],(aiptasia minima[&&NHX:TOL=18010],sagartia luciae[&&NHX:TOL=18011],actinia mutabilis[&&NHX:TOL=18012],aiptasiomorpha paxi[&&NHX:TOL=18013],aiptasiomorpha elongata[&&NHX:TOL=18014])aiptasiomorphidae[&&NHX:TOL=17978],(sagartia schilleriana[&&NHX:TOL=18030],diadumene cincta[&&NHX:TOL=18031],sagartia leucolena[&&NHX:TOL=18032],diadumene kameruniensis[&&NHX:TOL=18033],diadumene neozelandica[&&NHX:TOL=18034])diadumenidae[&&NHX:TOL=17979],(sagartia nitidus[&&NHX:TOL=18235],nemanthus annamensis[&&NHX:TOL=18236],nemanthus californicus[&&NHX:TOL=18237])nemanthidae[&&NHX:TOL=17980])acontiaria[&&NHX:TOL=17968])thenaria[&&NHX:TOL=17708])nynantheae[&&NHX:TOL=17673])actiniaria[&&NHX:TOL=17649],corallimorpharia[&&NHX:TOL=17650],(numidiaphyllida[&&NHX:EXT=Y:TOL=17652],(stylophylliina[&&NHX:EXT=Y:TOL=19153],pachythecalina[&&NHX:EXT=Y:TOL=19154],archaeocoeniina[&&NHX:TOL=19155],archaeofungiina[&&NHX:EXT=Y:TOL=19156],stylina[&&NHX:EXT=Y:TOL=19157],((fungiidae[&&NHX:TOL=19112],synastreidae[&&NHX:EXT=Y:TOL=19113],cyclolitidae[&&NHX:EXT=Y:TOL=19114],haplaraeidae[&&NHX:EXT=Y:TOL=19115],(micrabacia[&&NHX:EXT=Y:TOL=19121],leptopenus[&&NHX:TOL=19122],letepsammia[&&NHX:TOL=19123],stephanophyllia[&&NHX:TOL=19124],rhombopsammia[&&NHX:TOL=19125])micrabaciidae[&&NHX:TOL=19116],(fungiacyathus fungiacyathus[&&NHX:TOL=19106],fungiacyathus bathyactis[&&NHX:TOL=19107])fungiacyathus[&&NHX:TOL=19117])fungioidea[&&NHX:TOL=19109],agaricioidea[&&NHX:TOL=19110])fungiina[&&NHX:TOL=19158],astraeoina[&&NHX:TOL=19159],((faviidae[&&NHX:TOL=19081],montlivaltiidae[&&NHX:EXT=Y:TOL=19082],(rhizangia[&&NHX:EXT=Y:TOL=19142],culicia[&&NHX:TOL=19143],astrangia[&&NHX:TOL=19144],oulangia[&&NHX:TOL=19145],cladangia[&&NHX:TOL=19146],arctangia[&&NHX:EXT=Y:TOL=19147],reussangia[&&NHX:EXT=Y:TOL=19148],hindeastraea[&&NHX:EXT=Y:TOL=19149],septastraea[&&NHX:EXT=Y:TOL=19150],platyhelia[&&NHX:EXT=Y:TOL=19151])rhizangiidae[&&NHX:TOL=19083],((oculina[&&NHX:TOL=19130],schizoculina[&&NHX:TOL=19131],petrophyllia[&&NHX:TOL=19132],sclerhelia[&&NHX:TOL=19133],bathelia[&&NHX:TOL=19134],cyathelia[&&NHX:TOL=19135],madrepora[&&NHX:TOL=19136],haplohelia[&&NHX:EXT=Y:TOL=19137],astrhelia[&&NHX:EXT=Y:TOL=19138],diplhelia[&&NHX:EXT=Y:TOL=19139],diblasus[&&NHX:EXT=Y:TOL=19140])oculininae[&&NHX:TOL=19127],galaxeinae[&&NHX:TOL=19128])oculinidae[&&NHX:TOL=19084],merulinidae[&&NHX:TOL=19085],mussidae[&&NHX:TOL=19086],pectinidae[&&NHX:TOL=19087],(anthemiphyllia spinifera[&&NHX:TOL=18915],anthemiphyllia multidentata[&&NHX:TOL=18916],anthemiphyllia macrolobata[&&NHX:TOL=18917],anthemiphyllia patera[&&NHX:TOL=18918],anthemiphyllia dentata[&&NHX:TOL=18919],anthemiphyllia pacifica[&&NHX:TOL=18920],anthemiphyllia frustum[&&NHX:TOL=18921],anthemiphyllia catinata[&&NHX:EXT=Y:TOL=18922],anthemiphyllia verbeeki[&&NHX:EXT=Y:TOL=18923])anthemiphyllia[&&NHX:TOL=19088])favioidea[&&NHX:TOL=19078],stylopyllioidea[&&NHX:EXT=Y:TOL=19079])faviina[&&NHX:TOL=19160],(((((caryophyllia[&&NHX:TOL=18927],premocyathus[&&NHX:TOL=18928],antillocyathus[&&NHX:EXT=Y:TOL=18929],coenocyathus[&&NHX:TOL=18930],dendrocyathus[&&NHX:EXT=Y:TOL=18931],crispatotrochus[&&NHX:TOL=18932],labyrinthocyathus[&&NHX:TOL=18933],oxysmilia[&&NHX:TOL=18934],concentrotheca[&&NHX:TOL=18935],lophosmilia[&&NHX:EXT=Y:TOL=18936],bathycyathus[&&NHX:TOL=18937],frescocyathus[&&NHX:EXT=Y:TOL=18938],nomlandia[&&NHX:TOL=18939],protrochocyathus[&&NHX:EXT=Y:TOL=18940],prototrochocyathus[&&NHX:EXT=Y:TOL=18941],trochocyathus[&&NHX:TOL=18942],cryptocyathus[&&NHX:EXT=Y:TOL=18943],tethocyathus[&&NHX:TOL=18944],stylocyathus[&&NHX:EXT=Y:TOL=18945],axocyathus[&&NHX:EXT=Y:TOL=18946],deltocyathus[&&NHX:TOL=18947],bourneotrochus[&&NHX:TOL=18948],paracyathus[&&NHX:TOL=18949],polycyathus[&&NHX:TOL=18950],phyllangia[&&NHX:TOL=18951],colangia[&&NHX:TOL=18952],sympodangia[&&NHX:TOL=18953],leptocyathus[&&NHX:EXT=Y:TOL=18954],heterocyathus[&&NHX:TOL=18955],ceratotrochus[&&NHX:TOL=18956],ghirobocyathus[&&NHX:EXT=Y:TOL=18957],lochmaeotrochus[&&NHX:TOL=18959],paraconotrochus[&&NHX:TOL=18960],stephanosmilia[&&NHX:EXT=Y:TOL=18961],stephanocyathus[&&NHX:TOL=18962],vaughanella[&&NHX:TOL=18963],ericiocyathus[&&NHX:TOL=18964],aulocyathus[&&NHX:TOL=18965],stylotrochus[&&NHX:EXT=Y:TOL=18966],kangiliacyathus[&&NHX:EXT=Y:TOL=18967],wellsia[&&NHX:EXT=Y:TOL=18968])caryophylliidae genus group 1[&&NHX:TOL=18926],(desmophyllum[&&NHX:TOL=18970],thalamophyllia[&&NHX:TOL=18971],dactylotrochus[&&NHX:TOL=18972],hoplangia[&&NHX:TOL=18973],lophelia[&&NHX:TOL=18974],tiarasmilia[&&NHX:EXT=Y:TOL=18975],stelloria[&&NHX:EXT=Y:TOL=18976],conicosmilotrochus[&&NHX:EXT=Y:TOL=18977],metasmilia[&&NHX:EXT=Y:TOL=18978])caryophylliidae genus group 2[&&NHX:TOL=18969],(dasmia[&&NHX:EXT=Y:TOL=18980],dasmiopsis[&&NHX:EXT=Y:TOL=18981])caryophylliidae genus group 3[&&NHX:EXT=Y:TOL=18979],(parasmilia[&&NHX:EXT=Y:TOL=18983],edwardsosmilia[&&NHX:EXT=Y:TOL=18984],smilotrochus[&&NHX:EXT=Y:TOL=18985],rennenismilia[&&NHX:EXT=Y:TOL=18986],meandrosmilia[&&NHX:EXT=Y:TOL=18987],coenosmilia[&&NHX:TOL=18988],anomocora[&&NHX:TOL=18989],pourtalosmilia[&&NHX:TOL=18990],phacelocyathus[&&NHX:TOL=18991],rhizosmilia[&&NHX:TOL=18992],dungulia[&&NHX:EXT=Y:TOL=18993],caryosmilia[&&NHX:EXT=Y:TOL=18994],solenosmilia[&&NHX:TOL=18995],dendrosmilia[&&NHX:EXT=Y:TOL=18996],asterosmilia[&&NHX:TOL=18997],dasmosmilia[&&NHX:TOL=18998],goniocorella[&&NHX:TOL=18999],confluphyllia[&&NHX:TOL=19000],faksephyllia[&&NHX:EXT=Y:TOL=19001],sagittastrea[&&NHX:EXT=Y:TOL=19002],brachiatusmilia[&&NHX:EXT=Y:TOL=19003],montanarophyllia[&&NHX:EXT=Y:TOL=19004],clavismilia[&&NHX:EXT=Y:TOL=19005])caryophylliidae genus group 4[&&NHX:TOL=18982])[&&NHX:TOL=18925],(eusmilia[&&NHX:TOL=19007],euphyllia[&&NHX:TOL=19008],cladocora[&&NHX:TOL=19009],plerogyra[&&NHX:TOL=19010],physogyra[&&NHX:TOL=19011],gyrosmilia[&&NHX:TOL=19012],progyrosmilia[&&NHX:EXT=Y:TOL=19013],placophyllia[&&NHX:EXT=Y:TOL=19014],catalaphyllia[&&NHX:TOL=19015],montigyra[&&NHX:TOL=19016],nemenzophyllia[&&NHX:TOL=19017])caryophylliidae genus group 5[&&NHX:TOL=19006])caryophylliidae[&&NHX:TOL=19023],((alatotrochus[&&NHX:TOL=19168],pleotrochus[&&NHX:TOL=19169])[&&NHX:TOL=19167],(australocyathus[&&NHX:TOL=19171],(tropidocyathus[&&NHX:TOL=19173],((cyathotrochus[&&NHX:TOL=19176],deltocyathoides[&&NHX:TOL=19177])[&&NHX:TOL=19175],(notocyathus[&&NHX:TOL=19179],(palocyathus[&&NHX:EXT=Y:TOL=19181],bothrophoria[&&NHX:EXT=Y:TOL=19182])[&&NHX:TOL=19180],(levicyathus[&&NHX:EXT=Y:TOL=19184],thrypticotrochus[&&NHX:TOL=19185])[&&NHX:TOL=19183],(cryptotrochus[&&NHX:TOL=19187],(laminocyathus[&&NHX:EXT=Y:TOL=19189],alveolocyathus[&&NHX:EXT=Y:TOL=19190])[&&NHX:TOL=19188])[&&NHX:TOL=19186])[&&NHX:TOL=19178])[&&NHX:TOL=19174])[&&NHX:TOL=19172])[&&NHX:TOL=19170],(pseudocyathoceras[&&NHX:TOL=19192],((idiotrochus[&&NHX:TOL=19195],dunocyathus[&&NHX:TOL=19196])[&&NHX:TOL=19194],(wellsotrochus[&&NHX:EXT=Y:TOL=19198],(holcotrochus[&&NHX:TOL=19200],(conotrochus[&&NHX:TOL=19202],(turbinolia[&&NHX:TOL=19204],sphenotrochus[&&NHX:TOL=19205])[&&NHX:TOL=19203])[&&NHX:TOL=19201])[&&NHX:TOL=19199])[&&NHX:TOL=19197],(foveolocyathus[&&NHX:TOL=19207],endocyathopora[&&NHX:TOL=19208],(trematotrochus[&&NHX:TOL=19210],kionotrochus[&&NHX:TOL=19211])[&&NHX:TOL=19209],(platytrochus[&&NHX:TOL=19213],peponocyathus[&&NHX:TOL=19214])[&&NHX:TOL=19212])[&&NHX:TOL=19206])[&&NHX:TOL=19193])[&&NHX:TOL=19191],platytrochopsis[&&NHX:EXT=Y:TOL=19215])turbinoliidae[&&NHX:TOL=19024],thecocyathidae[&&NHX:EXT=Y:TOL=19025],stenocyathidae[&&NHX:TOL=19026])caryophyllioidea[&&NHX:TOL=19019],((flabellum[&&NHX:TOL=19090],truncatoflabellum[&&NHX:TOL=19091],blastotrochus[&&NHX:TOL=19092],placotrochus[&&NHX:TOL=19093],javania[&&NHX:TOL=19094],placotrochides[&&NHX:TOL=19095],falcatoflabellum[&&NHX:TOL=19096],monomyces[&&NHX:TOL=19097],rhizotrochus[&&NHX:TOL=19098],polymyces[&&NHX:TOL=19099],conosmilia[&&NHX:EXT=Y:TOL=19100],adkinsella[&&NHX:EXT=Y:TOL=19101])flabellidae[&&NHX:TOL=19103],guynia annulata[&&NHX:TOL=19104])flabelloidea[&&NHX:TOL=19020],volzeioidea[&&NHX:EXT=Y:TOL=19021])caryophylliina[&&NHX:TOL=19161],distichophylliina[&&NHX:EXT=Y:TOL=19162],meandriina[&&NHX:TOL=19163],poritiina[&&NHX:TOL=19164],(areopsammia[&&NHX:EXT=Y:TOL=19028],(palaeopsammia[&&NHX:EXT=Y:TOL=19030],(balanophyllia[&&NHX:TOL=19032],(calostylopsis[&&NHX:EXT=Y:TOL=19034],wadeopsammia[&&NHX:EXT=Y:TOL=19035],heteropsammia[&&NHX:TOL=19036],lamellophyllia[&&NHX:EXT=Y:TOL=19037])[&&NHX:TOL=19033])[&&NHX:TOL=19031],(bathypsammia[&&NHX:TOL=19039],(pourtalopsammia[&&NHX:TOL=19041],trochopsammia[&&NHX:TOL=19042])[&&NHX:TOL=19040],(endopsammia[&&NHX:TOL=19044],(leptopsammia[&&NHX:TOL=19046],((thecopsammia[&&NHX:TOL=19049],(endopachys[&&NHX:TOL=19051],notophyllia[&&NHX:TOL=19052])[&&NHX:TOL=19050])[&&NHX:TOL=19048],(eguchipsammia[&&NHX:TOL=19054],(rhizopsammia[&&NHX:TOL=19056],cladopsammia[&&NHX:TOL=19057],(paleoastreoides[&&NHX:EXT=Y:TOL=19059],(astroides[&&NHX:TOL=19061],(tubastraea[&&NHX:TOL=19063],turbinaria[&&NHX:TOL=19064])[&&NHX:TOL=19062])[&&NHX:TOL=19060])[&&NHX:TOL=19058])[&&NHX:TOL=19055],(dendrophyllia[&&NHX:TOL=19066],(enallopsammia[&&NHX:TOL=19068],(duncanopsammia[&&NHX:TOL=19070],(lobopsammia[&&NHX:EXT=Y:TOL=19072],dichopsammia[&&NHX:TOL=19073],(reussopsammia[&&NHX:EXT=Y:TOL=19075],stichopsammia[&&NHX:EXT=Y:TOL=19076])[&&NHX:TOL=19074])[&&NHX:TOL=19071])[&&NHX:TOL=19069])[&&NHX:TOL=19067])[&&NHX:TOL=19065])[&&NHX:TOL=19053])[&&NHX:TOL=19047])[&&NHX:TOL=19045])[&&NHX:TOL=19043])[&&NHX:TOL=19038])[&&NHX:TOL=19029])dendrophylliidae[&&NHX:TOL=19165])scleractinia[&&NHX:TOL=17653])[&&NHX:TOL=17651])[&&NHX:TOL=17648])[&&NHX:TOL=17646],kilbuchophyllida[&&NHX:EXT=Y:TOL=17654])[&&NHX:TOL=17645],(((((antipatharia[&&NHX:TOL=17660],zoanthidea[&&NHX:TOL=17661])[&&NHX:TOL=17659],(heterocorallia[&&NHX:EXT=Y:TOL=17663],rugosa[&&NHX:EXT=Y:TOL=17664])[&&NHX:TOL=17662])[&&NHX:TOL=17658],(heliolitida[&&NHX:EXT=Y:TOL=17666],tabulata[&&NHX:EXT=Y:TOL=17667])[&&NHX:TOL=17665])[&&NHX:TOL=17657],cothoniida[&&NHX:EXT=Y:TOL=17668])[&&NHX:TOL=17656],tabuloconida[&&NHX:EXT=Y:TOL=17669])[&&NHX:TOL=17655])zoantharia[&&NHX:TOL=17643])anthozoa[&&NHX:TOL=17634],(conulata[&&NHX:EXT=Y:TOL=17636],(cubozoa[&&NHX:TOL=17638],scyphozoa[&&NHX:TOL=17639],hydrozoa[&&NHX:TOL=17640])[&&NHX:TOL=17637])[&&NHX:TOL=17635])cnidaria[&&NHX:TOL=2461],(cydippida[&&NHX:TOL=19217],platyctenida[&&NHX:TOL=19218],beroida[&&NHX:TOL=19219],(thalassocalycida[&&NHX:TOL=19221],cestida[&&NHX:TOL=19222],lobata[&&NHX:TOL=19223])[&&NHX:TOL=19220])ctenophora[&&NHX:TOL=2462],(trichoplax adhaerens[&&NHX:TOL=20375],treptoplax reptans[&&NHX:TOL=20376])placozoa[&&NHX:TOL=2463])[&&NHX:TOL=2458],((calcinea[&&NHX:TOL=20434],calcaronea[&&NHX:TOL=20435])calcarea[&&NHX:TOL=20433],(amphidiscophora[&&NHX:TOL=20437],hexasterophora[&&NHX:TOL=20438])hexactinellida[&&NHX:TOL=20436],(homoscleromorpha[&&NHX:TOL=20440],tetractinomorpha[&&NHX:TOL=20441],ceractinomorpha[&&NHX:TOL=20442])demospongiae[&&NHX:TOL=20439])porifera[&&NHX:TOL=2464])animals[&&NHX:TOL=2374],(codosigidae[&&NHX:TOL=58009],salpingoecidae[&&NHX:TOL=58010],acanthoecidae[&&NHX:TOL=58011])choanoflagellates[&&NHX:TOL=2375])[&&NHX:TOL=124794],(ministeria[&&NHX:TOL=130436],capsaspora[&&NHX:TOL=130437])filasterea[&&NHX:TOL=121171],ichthyosporea[&&NHX:TOL=121172])[&&NHX:TOL=2373],((((((((((((((((inocybaceae[&&NHX:TOL=103941],crepidotaceae[&&NHX:TOL=103942])[&&NHX:TOL=103940],tubarieae[&&NHX:TOL=103943],panaeoleae[&&NHX:TOL=103944],(strophariaceae s. str.[&&NHX:TOL=103946],hymenogasteraceae[&&NHX:TOL=103947])[&&NHX:TOL=103945],gymnopileae[&&NHX:TOL=103948])[&&NHX:TOL=103939],cortinariaceae s. str.[&&NHX:TOL=103949],bolbitiaceae[&&NHX:TOL=103950],psathyrellaceae[&&NHX:TOL=103951],agaricaceae[&&NHX:TOL=103952],nidulariaceae[&&NHX:TOL=103953],cystodermateae s. str.[&&NHX:TOL=103954],hydnangiaceae[&&NHX:TOL=103955])agaricoid[&&NHX:TOL=103938],((lyophyllaceae[&&NHX:TOL=103958],entolomataceae[&&NHX:TOL=103959],clitocybe p. p.[&&NHX:TOL=103960])[&&NHX:TOL=103957],tricholomataceae s. str.[&&NHX:TOL=103961],clitocybeae[&&NHX:TOL=103962],dendrocollybia[&&NHX:TOL=103963],neohygrophorus[&&NHX:TOL=103964],catathelasma clade[&&NHX:TOL=103965],mycenaceae[&&NHX:TOL=103966],infundibulicybe[&&NHX:TOL=103967],pseudoclitocybe[&&NHX:TOL=103968])tricholomatoid[&&NHX:TOL=103956])[&&NHX:TOL=103937],(((hemimycena[&&NHX:TOL=103972],pleurotopsis[&&NHX:TOL=103973])[&&NHX:TOL=103971],cyphellaceae s. str.[&&NHX:TOL=103974],hydropoid clade[&&NHX:TOL=103975])[&&NHX:TOL=103970],(lachnellaceae[&&NHX:TOL=103977],schizophyllaceae[&&NHX:TOL=103978])[&&NHX:TOL=103976],(marasmiaceae[&&NHX:TOL=103980],omphalotaceae[&&NHX:TOL=103981])[&&NHX:TOL=103979],physalacriaceae[&&NHX:TOL=103982])marasmioid[&&NHX:TOL=103969],pleurotaceae[&&NHX:TOL=103983],amanitaceae[&&NHX:TOL=103984],((pluteaceae[&&NHX:TOL=103987],limnoperdonaceae[&&NHX:TOL=103988])[&&NHX:TOL=103986],macrocystidiaceae[&&NHX:TOL=103989])pluteoid[&&NHX:TOL=103985],(((pterulaceae[&&NHX:TOL=103993],typhulaceae[&&NHX:TOL=103994])[&&NHX:TOL=103992],sarcomyxa[&&NHX:TOL=103995],xeromphalina[&&NHX:TOL=103996],stephanospora[&&NHX:TOL=103997],coronicium[&&NHX:TOL=103998],phlebiella[&&NHX:TOL=103999],radulomyces[&&NHX:TOL=104000])[&&NHX:TOL=103991],hygrophoraceae s. lat.[&&NHX:TOL=104001])hygrophoroid[&&NHX:TOL=103990])[&&NHX:TOL=103936],(((hypochniciellum[&&NHX:TOL=104005],podoserpula[&&NHX:TOL=104006])[&&NHX:TOL=104004],athelia p. p.[&&NHX:TOL=104007],plicaturopsis[&&NHX:TOL=104008],anomoporia[&&NHX:TOL=104009],ceraceomyces s. str.[&&NHX:TOL=104010],amylocorticium[&&NHX:TOL=104011])[&&NHX:TOL=104003],(clavariaceae s. str.[&&NHX:TOL=104013],camarophyllopsis[&&NHX:TOL=104014])[&&NHX:TOL=104012])plicaturopsidoid[&&NHX:TOL=104002],agaricales incertae sedis[&&NHX:TOL=104015])agaricales[&&NHX:TOL=20551],(tapinellaceae[&&NHX:TOL=100828],serpulaceae[&&NHX:TOL=100829],coniophoraceae[&&NHX:TOL=100830],boletales incertae sedis[&&NHX:TOL=100831],(hygrophoropsidaceae[&&NHX:TOL=100833],(rhizopogonaceae[&&NHX:TOL=100835],gomphidiaceae[&&NHX:TOL=100836],truncocolumellaceae[&&NHX:TOL=100837],suillaceae[&&NHX:TOL=100838])[&&NHX:TOL=100834])[&&NHX:TOL=100832],(((pisolithaceae[&&NHX:TOL=100842],diplocystaceae[&&NHX:TOL=100843],calostomataceae[&&NHX:TOL=100844],gyroporaceae[&&NHX:TOL=100845],sclerodermataceae[&&NHX:TOL=100846])[&&NHX:TOL=100841],boletinellaceae[&&NHX:TOL=100847])[&&NHX:TOL=100840],(paxillaceae[&&NHX:TOL=100849],boletaceae[&&NHX:TOL=100850])[&&NHX:TOL=100848])[&&NHX:TOL=100839])boletales[&&NHX:TOL=20550],atheliales[&&NHX:TOL=20554])agaricomycetidae[&&NHX:TOL=20549],russulales[&&NHX:TOL=20559],(polyporales[&&NHX:TOL=20558],thelephorales[&&NHX:TOL=20560])[&&NHX:TOL=20553],gloeophyllales[&&NHX:TOL=20557],corticiales[&&NHX:TOL=20556],((inonotus s. str.[&&NHX:TOL=23837],fomitiporella[&&NHX:TOL=23838],inocutis[&&NHX:TOL=23839],phylloporia[&&NHX:TOL=23840],fulvifomes[&&NHX:TOL=23841],aurificaria[&&NHX:TOL=23842],mensularia[&&NHX:TOL=23843],phellinus s. str.[&&NHX:TOL=23844],pseudoinonotus[&&NHX:TOL=23845],fomitiporia[&&NHX:TOL=23846],porodaedalea[&&NHX:TOL=23847],onnia[&&NHX:TOL=23848],pseudochaete[&&NHX:TOL=23851])hymenochaetales sensu oberwinkler 1977 pro parte[&&NHX:TOL=23113],coltricia[&&NHX:TOL=23853],coltriciella[&&NHX:TOL=23854],pyrrhoderma[&&NHX:TOL=23855],hyphodontia[&&NHX:TOL=23856],schizoporia[&&NHX:TOL=23857],bridgeoporus[&&NHX:TOL=28712],hymenochaete[&&NHX:TOL=23869],asterodon[&&NHX:TOL=23858],inonotopsis[&&NHX:TOL=23861],phellinidium[&&NHX:TOL=23862],fuscoporia[&&NHX:TOL=23863],phellopilus[&&NHX:TOL=23867],basidioradulum[&&NHX:TOL=23868],oxyporus[&&NHX:TOL=23865],trichaptum[&&NHX:TOL=23864],cotylidia[&&NHX:TOL=28713],rickenella[&&NHX:TOL=28714],loreleia[&&NHX:TOL=51146],contumyces[&&NHX:TOL=51147],gyroflexus[&&NHX:TOL=51148])hymenochaetoid clade[&&NHX:TOL=20547])[&&NHX:TOL=20548],(geastrales[&&NHX:TOL=103619],gomphales[&&NHX:TOL=103620],hysterangiales[&&NHX:TOL=103621],phallales[&&NHX:TOL=103622])phallomycetidae[&&NHX:TOL=20546],trechisporales[&&NHX:TOL=20555],cantharellales[&&NHX:TOL=20545],sebacinales[&&NHX:TOL=103623],auriculariales[&&NHX:TOL=20536])agaricomycetes[&&NHX:TOL=20535],dacrymycetales[&&NHX:TOL=20537])[&&NHX:TOL=103618],(tremellales[&&NHX:TOL=20540],filobasidiales[&&NHX:TOL=20541],cystofilobasidiales[&&NHX:TOL=20542])tremellomycetes[&&NHX:TOL=20538])agaricomycotina[&&NHX:TOL=20531],(malasseziales[&&NHX:TOL=104022],(urocystales[&&NHX:TOL=112650],ustilaginales[&&NHX:TOL=112649])ustilaginomycetes[&&NHX:TOL=20564],(doassansiales[&&NHX:TOL=104016],entylomatales[&&NHX:TOL=104017],exobasidiales[&&NHX:TOL=104018],georgefischeriales[&&NHX:TOL=104019],microstromatales[&&NHX:TOL=104020],tilletiales[&&NHX:TOL=104021])exobasidiomycetes[&&NHX:TOL=20565])ustilaginomycotina[&&NHX:TOL=20530],(((septobasidium[&&NHX:TOL=54064],coccidiodictyon[&&NHX:TOL=54070],auriculoscypha[&&NHX:TOL=54071],uredinella[&&NHX:TOL=54072],ordonia[&&NHX:TOL=54073])septobasidiaceae[&&NHX:TOL=51247],(platygloeales[&&NHX:TOL=51278],pucciniales[&&NHX:TOL=51277])[&&NHX:TOL=51276],((tuberculina sbrozzii[&&NHX:TOL=58092],(helicobasidium purpureum i[&&NHX:TOL=60318],helicobasidium purpureum ii[&&NHX:TOL=60319],helicobasidium purpureum iii[&&NHX:TOL=60320])helicobasidium purpureum[&&NHX:TOL=58093],(tuberculina maxima i[&&NHX:TOL=60323],tuberculina maxima ii[&&NHX:TOL=60324])tuberculina maxima[&&NHX:TOL=58094])[&&NHX:TOL=58090],((helicobasidium longisporum i[&&NHX:TOL=60321],helicobasidium longisporum ii[&&NHX:TOL=60322])helicobasidium longisporum[&&NHX:TOL=58098],helicobasidium mompa[&&NHX:TOL=58100])[&&NHX:TOL=58096])helicobasidiales[&&NHX:TOL=51250],pachnocybales[&&NHX:TOL=118301],pucciniomycetes incertae sedis[&&NHX:TOL=51251])pucciniomycetes[&&NHX:TOL=51246],atractiellales[&&NHX:TOL=51252],(spiculogloeales[&&NHX:TOL=108141],agaricostilbales[&&NHX:TOL=51268],agaricostilbomycetes incertae sedis[&&NHX:TOL=51269])agaricostilbomycetes[&&NHX:TOL=51253],(heterogastridiales[&&NHX:TOL=51255],microbotryales[&&NHX:TOL=51256],sporidiobolales[&&NHX:TOL=51257],leucosporidiales[&&NHX:TOL=51258],microbotryomycetes incertae sedis[&&NHX:TOL=51267])microbotryomycetes[&&NHX:TOL=51254],(cystobasidiales[&&NHX:TOL=59443],erythrobasidiales[&&NHX:TOL=59444],naohideales[&&NHX:TOL=108137],cystobasidiomycetes incertae sedis[&&NHX:TOL=59445])cystobasidiomycetes[&&NHX:TOL=51262],mixia osmundae[&&NHX:TOL=51266],cryptomycocolax[&&NHX:TOL=51270],classicula[&&NHX:TOL=52262],pucciniomycotina incertae sedis[&&NHX:TOL=59446])pucciniomycotina[&&NHX:TOL=20528],entorrhizales[&&NHX:TOL=103624],wallemiales[&&NHX:TOL=103625])basidiomycota[&&NHX:TOL=20520],(((orbiliales[&&NHX:TOL=29046],pezizales[&&NHX:TOL=29045],((((lecanorales[&&NHX:TOL=29366],peltigerales[&&NHX:TOL=29367],teloschistales[&&NHX:TOL=29368])lecanoromycetidae[&&NHX:TOL=29065],(agyriales[&&NHX:TOL=29369],ostropales[&&NHX:TOL=29371],pertusariales[&&NHX:TOL=29372],baeomycetales[&&NHX:TOL=29373])ostropomycetidae[&&NHX:TOL=29066])[&&NHX:TOL=29063],acarosporales          [&&NHX:TOL=29064],candelariales[&&NHX:TOL=112647],umbilicariales[&&NHX:TOL=112648])lecanoromycetes[&&NHX:TOL=29057],(mycocaliciales[&&NHX:TOL=103367],((eurotiales[&&NHX:TOL=29309],onygenales[&&NHX:TOL=29310])[&&NHX:TOL=29060],coryneliales[&&NHX:TOL=65361])eurotiomycetidae[&&NHX:TOL=65360],(((chaetothyriaceae[&&NHX:TOL=117667],herpotrichiellaceae[&&NHX:TOL=117668])chaetothyriales[&&NHX:TOL=29305],((((bagliettoa[&&NHX:TOL=110536],(placidium[&&NHX:TOL=117695],clavascidium[&&NHX:TOL=117696])placidium clavascidium[&&NHX:TOL=110537],(heteroplacidium contumescens[&&NHX:TOL=110560],(heteroplacidium fusculum[&&NHX:TOL=110563],heteroplacidium imbricatum[&&NHX:TOL=110562])[&&NHX:TOL=110561])heteroplacidium[&&NHX:TOL=110538],dermatocarpon[&&NHX:TOL=110539],((((endocarpon adscendens[&&NHX:TOL=110553],endocarpon psorodeum[&&NHX:TOL=110554])[&&NHX:TOL=110552],endocarpon petrolepideum[&&NHX:TOL=110555])[&&NHX:TOL=110551],(endocarpon pallidulum[&&NHX:TOL=110557],endocarpon pusillum[&&NHX:TOL=110558])[&&NHX:TOL=110556])[&&NHX:TOL=110550],endocarpon diffractellum[&&NHX:TOL=110559])endocarpon[&&NHX:TOL=110540],neocatapyrenium[&&NHX:TOL=110541],polyblastia[&&NHX:TOL=110542],thelidium[&&NHX:TOL=110543],verrucaria[&&NHX:TOL=110544],placopyrenium[&&NHX:TOL=110545],henrica[&&NHX:TOL=117697],involucropyrenium[&&NHX:TOL=117698],trimmatothele[&&NHX:TOL=117699])[&&NHX:TOL=110578],(((catapyrenium cinereum[&&NHX:TOL=110564],catapyrenium daedaleum[&&NHX:TOL=110565])catapyrenium[&&NHX:TOL=110546],(placidiopsis cinerascens[&&NHX:TOL=110566],placidiopsis cartilaginea[&&NHX:TOL=110567])placidiopsis[&&NHX:TOL=110547])[&&NHX:TOL=110568],(((staurothele frustulenta[&&NHX:TOL=110571],staurothele drummondii[&&NHX:TOL=110572])[&&NHX:TOL=110570],staurothele areolata[&&NHX:TOL=110573])[&&NHX:TOL=110569],(staurothele fissa[&&NHX:TOL=110575],staurothele clopima[&&NHX:TOL=110576])[&&NHX:TOL=110574])staurothele[&&NHX:TOL=110548])[&&NHX:TOL=110579])[&&NHX:TOL=110577],(verrucula[&&NHX:TOL=110581],placocarpus schaereri[&&NHX:TOL=110549],norrlinia[&&NHX:TOL=117700])[&&NHX:TOL=110580],agonimia[&&NHX:TOL=117669],anthracocarpon[&&NHX:TOL=117670],awasthiella[&&NHX:TOL=117671],bellemerella[&&NHX:TOL=117672],bogoriella[&&NHX:TOL=117673],clauzadella[&&NHX:TOL=117674],dermatocarpella[&&NHX:TOL=117675],diederimyces[&&NHX:TOL=117676],glomerilla[&&NHX:TOL=117677],haleomyces[&&NHX:TOL=117678],heterocarpon[&&NHX:TOL=117679],lauderlindsaya[&&NHX:TOL=117680],leucocarpia[&&NHX:TOL=117681],merismatium[&&NHX:TOL=117682],muellerella[&&NHX:TOL=117683],mycophycias[&&NHX:TOL=117684],phaeospora[&&NHX:TOL=117685],placothelium[&&NHX:TOL=117686],plurisperma[&&NHX:TOL=117687],psoroglaena[&&NHX:TOL=117688],rhabdospora[&&NHX:TOL=117689],scleropyrenium[&&NHX:TOL=117690],spheconisca[&&NHX:TOL=117691],telogalla[&&NHX:TOL=117692],thelidiopsis[&&NHX:TOL=117693],trimmatothelopsis[&&NHX:TOL=117694])verrucariaceae[&&NHX:TOL=110534],(adelococcus[&&NHX:TOL=110582],sagediopsis[&&NHX:TOL=110583])adelococcaceae[&&NHX:TOL=110535])verrucariales[&&NHX:TOL=29307])[&&NHX:TOL=110533],(monoblastaceae[&&NHX:TOL=117701],pyrenulaceae[&&NHX:TOL=117702],requienellaceae[&&NHX:TOL=117703])pyrenulales[&&NHX:TOL=29306])chaetothyriomycetidae[&&NHX:TOL=29062])eurotiomycetes[&&NHX:TOL=29058],lichinales[&&NHX:TOL=29056],(geoglossum[&&NHX:TOL=29311],trichoglossum[&&NHX:TOL=29312],sarcoleotia[&&NHX:TOL=77435])geoglossaceae[&&NHX:TOL=29055],((cyttariales[&&NHX:TOL=29313],erysiphales[&&NHX:TOL=29314],helotiales 1[&&NHX:TOL=29315],helotiales 2[&&NHX:TOL=108991],helotiales 3[&&NHX:TOL=108992],rhytismatales[&&NHX:TOL=29316],thelebolales[&&NHX:TOL=29317],myxotrichaceae[&&NHX:TOL=108993],pseudeurotiaceae[&&NHX:TOL=110641])leotiomycetes[&&NHX:TOL=29048],((coronophorales[&&NHX:TOL=29374],((([&&NHX:TOL=118338],(cordyceps s.s.[&&NHX:TOL=119044],cordyceps s.l.[&&NHX:TOL=119045],torrubiella s.s.[&&NHX:TOL=119046])cordycipitaceae[&&NHX:TOL=119041])[&&NHX:TOL=118337],(clavicipitaceae[&&NHX:TOL=118341],(cordyceps s.l.[&&NHX:TOL=119047],elaphocordyceps[&&NHX:TOL=119048],ophiocordyceps[&&NHX:TOL=119049])ophiocordycipitaceae[&&NHX:TOL=119042])[&&NHX:TOL=118339])[&&NHX:TOL=119040],nectriaceae[&&NHX:TOL=118340],bionectriaceae[&&NHX:TOL=118342],stachybotrysclade[&&NHX:TOL=119043])hypocreales[&&NHX:TOL=29328],melanosporales[&&NHX:TOL=57149],microascales[&&NHX:TOL=29329],glomerellaceae[&&NHX:TOL=58015])hypocreomycetidae[&&NHX:TOL=29301],(boliniales[&&NHX:TOL=29330],chaetosphaeriales[&&NHX:TOL=29375],coniochaetales[&&NHX:TOL=29376],diaporthales[&&NHX:TOL=29331],ophiostomatales[&&NHX:TOL=29332],sordariales[&&NHX:TOL=29333],magnaporthe[&&NHX:TOL=58017],papulosa[&&NHX:TOL=58018],annulusmagnus[&&NHX:TOL=58019])sordariomycetidae[&&NHX:TOL=29302],xylariomycetidae[&&NHX:TOL=29303],lulworthiales[&&NHX:TOL=58014],calosphaeriales[&&NHX:TOL=103451],meliolales[&&NHX:TOL=103452],phyllachorales[&&NHX:TOL=103453],trichosphaeriales[&&NHX:TOL=103454])sordariomycetes[&&NHX:TOL=29050])[&&NHX:TOL=65362],(laboulbeniales[&&NHX:TOL=29318],pyxidiophorales[&&NHX:TOL=29319])laboulbeniomycetes[&&NHX:TOL=29049],((((myriangiaceae[&&NHX:TOL=60133],elsinoaceae[&&NHX:TOL=60134])myriangiales[&&NHX:TOL=29324],(dothideaceae[&&NHX:TOL=60143],dothioraceae[&&NHX:TOL=60144])dothideales[&&NHX:TOL=29321],(davidiellaceae[&&NHX:TOL=60135],mycosphaerellaceae[&&NHX:TOL=60136],capnodiaceae[&&NHX:TOL=60137])capnodiales[&&NHX:TOL=29320])dothideomycetidae[&&NHX:TOL=60123],((pleosporaceae[&&NHX:TOL=60138],phaeosphaeriaceae[&&NHX:TOL=60139],leptosphaeriaceae[&&NHX:TOL=60140],(chaetopreussia[&&NHX:TOL=67574],pleophragmia[&&NHX:TOL=67575],preussia[&&NHX:TOL=67576],pycnidiophora[&&NHX:TOL=67577],sporormia[&&NHX:TOL=67578],sporormiella[&&NHX:TOL=67579],spororminula[&&NHX:TOL=67580],westerdykella[&&NHX:TOL=67581])sporormiaceae[&&NHX:TOL=60141],(delitschia[&&NHX:TOL=65358],ohleriella[&&NHX:TOL=67572],semidelitschia[&&NHX:TOL=67573])delitschiaceae[&&NHX:TOL=60142])pleosporales[&&NHX:TOL=60124],(hysterium[&&NHX:TOL=124940],hysterographium[&&NHX:TOL=124941],glonium[&&NHX:TOL=125328],gloniopsis[&&NHX:TOL=124942],gloniella[&&NHX:TOL=124943],actidiographium[&&NHX:TOL=124947],hysterocarina[&&NHX:TOL=124946],farlowiella[&&NHX:TOL=125329])hysteriaceae[&&NHX:TOL=29322],mytilinidaceae[&&NHX:TOL=60231])pleosporomycetidae[&&NHX:TOL=60230],((thaxteriella[&&NHX:TOL=66508],tubeufia[&&NHX:TOL=66509],acanthostigma[&&NHX:TOL=66510],uncertainly placed genera[&&NHX:TOL=66511])tubeufiaceae[&&NHX:TOL=60229],trypetheliales[&&NHX:TOL=60228],botryosphaeriales[&&NHX:TOL=60125],aliquandostipitaceae[&&NHX:TOL=29323],patellariales[&&NHX:TOL=29325],hysteroglonium[&&NHX:TOL=125330],hysteropatella[&&NHX:TOL=125331],pseudoscypha[&&NHX:TOL=125332])uncertainly placed groups of dothideomycetes[&&NHX:TOL=60232])dothideomycetes[&&NHX:TOL=29051],arthoniales[&&NHX:TOL=29052])[&&NHX:TOL=65363])leotiomyceta[&&NHX:TOL=29044],lahmiales[&&NHX:TOL=112644],medeolariales[&&NHX:TOL=112645],triblidiales[&&NHX:TOL=112646])pezizomycotina[&&NHX:TOL=29296],(trichomonascus clade[&&NHX:TOL=134184],zygozyma oligophaga clade[&&NHX:TOL=134185],(pichia membranifaciens clade[&&NHX:TOL=134187],dipodascus albidus clade[&&NHX:TOL=134188],metschnikowia bicuspidata clade[&&NHX:TOL=134189])[&&NHX:TOL=134186],(candida albicans clade[&&NHX:TOL=134191],candida tanzawaensis clade[&&NHX:TOL=134192],scheffersomyces stipitis clade[&&NHX:TOL=134193],saccharomycopsis clade[&&NHX:TOL=134194],wickerhamomyces anomalus clade[&&NHX:TOL=134195],candida ovalis clade[&&NHX:TOL=134196],saccharomyces cerevisiae clade[&&NHX:TOL=134197])[&&NHX:TOL=134190])saccharomycetales[&&NHX:TOL=29043])[&&NHX:TOL=29295],(schizosaccharomycetales[&&NHX:TOL=77429],pneumocystidales[&&NHX:TOL=77430],neolectales[&&NHX:TOL=77431],taphrinales[&&NHX:TOL=77432])taphrinomycotina[&&NHX:TOL=29068])ascomycota[&&NHX:TOL=20521])dikarya[&&NHX:TOL=20519],(((glomerales[&&NHX:TOL=51218],(((acaulospora[&&NHX:TOL=51222],entrophospora[&&NHX:TOL=51223])acaulosporaceae[&&NHX:TOL=51221],glomus group c diversispora[&&NHX:TOL=51224])[&&NHX:TOL=51220],(pacispora[&&NHX:TOL=51226],(gigaspora[&&NHX:TOL=51228],scutellospora[&&NHX:TOL=51229])gigasporaceae[&&NHX:TOL=51227])[&&NHX:TOL=51225])diversisporales[&&NHX:TOL=51219])[&&NHX:TOL=51217],(archaeospora[&&NHX:TOL=51231],geosiphon[&&NHX:TOL=51232])archaeosporales[&&NHX:TOL=51230])[&&NHX:TOL=51216],paraglomus[&&NHX:TOL=51233])glomeromycota[&&NHX:TOL=28715])[&&NHX:TOL=28716],((endogonales[&&NHX:TOL=103791],mucorales[&&NHX:TOL=103792],mortierellales[&&NHX:TOL=26981])mucoromycotina[&&NHX:TOL=26979],entomophthorales         [&&NHX:TOL=26978],(asellariales[&&NHX:TOL=103787],kickxellales[&&NHX:TOL=103788],dimargaritales[&&NHX:TOL=103789],harpellales[&&NHX:TOL=26982])kickxellomycotina[&&NHX:TOL=26976],zoopagales[&&NHX:TOL=26977])zygomycota[&&NHX:TOL=20518],olpidium brassicae[&&NHX:TOL=103934],blastocladiales[&&NHX:TOL=103790],(((chytridiales[&&NHX:TOL=103602],spizellomycetales[&&NHX:TOL=103603],rhizophydiales[&&NHX:TOL=103604])chytridiomycetes[&&NHX:TOL=103601],monoblepharidales         [&&NHX:TOL=103600])chytridiomycota[&&NHX:TOL=20517],neocallimastigales[&&NHX:TOL=103786])[&&NHX:TOL=103785],microsporidia[&&NHX:TOL=2378],rozella spp.[&&NHX:TOL=103935])fungi[&&NHX:TOL=2377],nucleariidae[&&NHX:TOL=2419])[&&NHX:TOL=121173])opisthokonts[&&NHX:TOL=2372],(eumycetozoa[&&NHX:TOL=121176],((tubulinida[&&NHX:TOL=129716],(((microcorycia[&&NHX:TOL=124474],amphizonella violacea[&&NHX:TOL=124475],diplochlamys[&&NHX:TOL=124476],parmulina[&&NHX:TOL=124477],penardochlamys[&&NHX:TOL=124478],zonomyxa[&&NHX:TOL=124479])microcoryciidae[&&NHX:TOL=124473],(arcella[&&NHX:TOL=124482],pyxidicula[&&NHX:TOL=124483],antarcella[&&NHX:TOL=124484])arcellidae[&&NHX:TOL=124481],(spumochlamys[&&NHX:TOL=128379],(microchlamys patella[&&NHX:TOL=129407],microchlamys sylvatica[&&NHX:TOL=129408])microchlamys[&&NHX:TOL=124480])microchlamyiidae[&&NHX:TOL=128377])arcellina[&&NHX:TOL=124472],((zivkovicia[&&NHX:TOL=124496],suiadifflugia[&&NHX:TOL=124495],sexangularia[&&NHX:TOL=124494],schwabia[&&NHX:TOL=124493],pontigulasia[&&NHX:TOL=124492],pentagonia[&&NHX:TOL=124491],maghrebia[&&NHX:TOL=124490],lagenodifflugia[&&NHX:TOL=124489],cucurbitella[&&NHX:TOL=124488],difflugia[&&NHX:TOL=124487])difflugiidae[&&NHX:TOL=124486],(centropyxis[&&NHX:TOL=124498],centropyxiella[&&NHX:TOL=124499],proplagiopyxis[&&NHX:TOL=124500])centropyxidae[&&NHX:TOL=124497],(trigonopyxis[&&NHX:TOL=124502],cornuapyxis[&&NHX:TOL=124503],cyclopyxis[&&NHX:TOL=124504],geopyxella[&&NHX:TOL=124505],ellipsopyxis[&&NHX:TOL=124506],ellipsopyxella[&&NHX:TOL=124507])trigonopyxidae[&&NHX:TOL=124501],lamtopyxidae[&&NHX:TOL=124508],distomatopyxidae[&&NHX:TOL=124509],(plagiopyxis[&&NHX:TOL=124511],bullinularia[&&NHX:TOL=124512],geoplagiopyxis[&&NHX:TOL=124513],hoogenraadia[&&NHX:TOL=124514],paracentropyxis[&&NHX:TOL=124515],planhoogenraadia[&&NHX:TOL=124516],protoplagiopyxis[&&NHX:TOL=124517])plagiopyxidae[&&NHX:TOL=124510],(paraquadrula[&&NHX:TOL=124519],lamtoquadrula[&&NHX:TOL=124520])paraquadrulidae[&&NHX:TOL=124518],(lesquereusia[&&NHX:TOL=124522],microquadrula[&&NHX:TOL=124523],netzelia[&&NHX:TOL=124524],pomoriella[&&NHX:TOL=124525],quadrulella[&&NHX:TOL=124526])lesquereusidae[&&NHX:TOL=124521],(hyalosphenia[&&NHX:TOL=124528],leptochlamys[&&NHX:TOL=124529],nebela[&&NHX:TOL=124530],alocodera[&&NHX:TOL=124531],apodera[&&NHX:TOL=124532],certesella[&&NHX:TOL=124533],physochila[&&NHX:TOL=124534],porosia[&&NHX:TOL=124535],schoenbornia[&&NHX:TOL=124536])hyalospheniidae[&&NHX:TOL=124527],(heleopera[&&NHX:TOL=124538],awerintzewia[&&NHX:TOL=124539])heleoperidae[&&NHX:TOL=124537],argynnia[&&NHX:TOL=124540])difflugina[&&NHX:TOL=124485],(phryganellidae[&&NHX:TOL=124542],(cryptodifflugia[&&NHX:TOL=124544],wailesella[&&NHX:TOL=124545])cryptodifflugiidae[&&NHX:TOL=124543])phryganellina[&&NHX:TOL=124541])arcellinida[&&NHX:TOL=124471],leptomyxida[&&NHX:TOL=124470])tubulinea[&&NHX:TOL=129715],((dactylopodida[&&NHX:TOL=129742],vannellidae[&&NHX:TOL=129750],cochliopodium[&&NHX:TOL=129756],stygamoeba[&&NHX:TOL=129757],trichosphaerium[&&NHX:TOL=129758])flabellinia[&&NHX:TOL=129741],(dermamoebida[&&NHX:TOL=129760],thecamoebidae[&&NHX:TOL=129765],centramoebida[&&NHX:TOL=129770])longamoebia[&&NHX:TOL=129759])discosea[&&NHX:TOL=129740],(varipodida[&&NHX:TOL=129776],phalansteriida[&&NHX:TOL=129781],holomastigida[&&NHX:TOL=129782])variosea[&&NHX:TOL=129775],pseudothecamoeba[&&NHX:TOL=129783],thecochaos[&&NHX:TOL=129784],janickina[&&NHX:TOL=129785],gocevia[&&NHX:TOL=129786],paragocevia[&&NHX:TOL=129787],stereomyxa[&&NHX:TOL=129789],corallomyxa[&&NHX:TOL=129788])lobosea[&&NHX:TOL=121174],archamoebae[&&NHX:TOL=121175])amoebozoa[&&NHX:TOL=121165])unikonts[&&NHX:TOL=121170],((((((((((((((euglyphida[&&NHX:TOL=124588],(thaumatomonads[&&NHX:TOL=2437],spongomonads[&&NHX:TOL=2433])[&&NHX:TOL=135146],(pseudopirsonia mucosa[&&NHX:TOL=136814],auranticordis quadriverberis[&&NHX:TOL=136815])novel clade 1 pseudopirsonia auranticordis[&&NHX:TOL=126325])[&&NHX:TOL=126324],novel clade 2[&&NHX:TOL=126326],novel clade 3[&&NHX:TOL=126327],((cryothecomonas[&&NHX:TOL=2395],((ammodochium[&&NHX:EXT=Y:TOL=97331],proebria[&&NHX:EXT=Y:TOL=97332])ammodochiidae[&&NHX:TOL=97330],(dicladia[&&NHX:EXT=Y:TOL=97334],ditripodium[&&NHX:EXT=Y:TOL=97335],parathranium[&&NHX:EXT=Y:TOL=97336],thranium[&&NHX:EXT=Y:TOL=97337])ditripodiidae[&&NHX:TOL=97333],(ebria tripartita[&&NHX:TOL=97339],ebriella[&&NHX:EXT=Y:TOL=97340],ebrinula[&&NHX:EXT=Y:TOL=97341])ebriidae[&&NHX:TOL=97338],(bosporella[&&NHX:EXT=Y:TOL=97343],craniopsis[&&NHX:EXT=Y:TOL=97344],ebriopsis[&&NHX:EXT=Y:TOL=97345],falsebria[&&NHX:EXT=Y:TOL=97346],hermesinella[&&NHX:EXT=Y:TOL=97347],hermesinopsis[&&NHX:EXT=Y:TOL=97348],hermesinum adriaticum[&&NHX:TOL=97349],hovassebria[&&NHX:EXT=Y:TOL=97350],micromarsupium[&&NHX:EXT=Y:TOL=97351],parebriopsis[&&NHX:EXT=Y:TOL=97352],podamphora[&&NHX:EXT=Y:TOL=97353],podamphoropsis[&&NHX:EXT=Y:TOL=97354],polyebriopsis[&&NHX:EXT=Y:TOL=97355],pseudammodochium[&&NHX:EXT=Y:TOL=97356],semantebria[&&NHX:EXT=Y:TOL=97357],spongebria[&&NHX:EXT=Y:TOL=97358],spyrebria[&&NHX:EXT=Y:TOL=97359])hermisinidae[&&NHX:TOL=97342])ebriida[&&NHX:TOL=2401])[&&NHX:TOL=124281],phaeodarea[&&NHX:TOL=2424],((chlamydophryidae[&&NHX:TOL=124632],(micramphora[&&NHX:TOL=124623],ogdeniella[&&NHX:TOL=124624],nadinella[&&NHX:TOL=124625],micropsammella[&&NHX:TOL=124626],chardezia[&&NHX:TOL=124627],alepiella[&&NHX:TOL=124628],propsammonobiotus[&&NHX:TOL=124629],psammonobiotus[&&NHX:TOL=124630],edaphonobiotus[&&NHX:TOL=124631])psammonobiotidae[&&NHX:TOL=124622])[&&NHX:TOL=126330],pseudodifflugiidae[&&NHX:TOL=124621],(amphitrema[&&NHX:TOL=124618],archerella[&&NHX:TOL=124619],paramphitrema[&&NHX:TOL=124620])amphitrematidae[&&NHX:TOL=124617])tectofilosida[&&NHX:TOL=126490])thecofilosea[&&NHX:TOL=124280])[&&NHX:TOL=126323],(glissomonadida[&&NHX:TOL=126391],katabia gromovi[&&NHX:TOL=124291],novel clade 7 including pansomonadida[&&NHX:TOL=126333],(dimorphids[&&NHX:TOL=2398],sainouroidea[&&NHX:TOL=124292])[&&NHX:TOL=136100])[&&NHX:TOL=97201])[&&NHX:TOL=126322],cercomonads[&&NHX:TOL=2390])[&&NHX:TOL=126321],metopiida & novel clade 6[&&NHX:TOL=126334])[&&NHX:TOL=126320],granofilosea[&&NHX:TOL=124293])[&&NHX:TOL=126319],metromonadida[&&NHX:TOL=126337])[&&NHX:TOL=126318],((lotharella globosa[&&NHX:TOL=20507],lotharella amoeboformis[&&NHX:TOL=20508],gymnochlora stellata[&&NHX:TOL=20509],(chlorarachnion reptans[&&NHX:TOL=20511],(strain bc52[&&NHX:TOL=20513],flagellated strains[&&NHX:TOL=20514])[&&NHX:TOL=20512])[&&NHX:TOL=20510])[&&NHX:TOL=20506],cryptochlora perforans[&&NHX:TOL=20515])chlorarachniophytes[&&NHX:TOL=2391],chlorarachnean sister lineages[&&NHX:TOL=126338])[&&NHX:TOL=126317],novel clades 10 11 12[&&NHX:TOL=126339],gymnosphaerida[&&NHX:TOL=2410])filosa[&&NHX:TOL=126316],(((((phagomyxida[&&NHX:TOL=98637],plasmodiophorida[&&NHX:TOL=121506])phytomyxea[&&NHX:TOL=126344],novel clade endo1[&&NHX:TOL=126349])[&&NHX:TOL=126343],novel clade 9[&&NHX:TOL=126350])[&&NHX:TOL=126342],aconchulinida[&&NHX:TOL=126351])[&&NHX:TOL=126341],pseudospora[&&NHX:TOL=2429],((((((ascetosporea[&&NHX:TOL=126358],novel clade endo2[&&NHX:TOL=126359])[&&NHX:TOL=126357],novel clade endo3 paradinium[&&NHX:TOL=126360])[&&NHX:TOL=126356],gromiidea[&&NHX:TOL=126361])[&&NHX:TOL=126355],reticulosida[&&NHX:TOL=126362])[&&NHX:TOL=126354],novel clade endo4[&&NHX:TOL=126363])[&&NHX:TOL=126353],novel clade endo5[&&NHX:TOL=126364])[&&NHX:TOL=126352])endomyxa[&&NHX:TOL=126340])cercozoa[&&NHX:TOL=121187],foraminifera[&&NHX:TOL=98077])[&&NHX:TOL=121184],(((acanthodesmiidae[&&NHX:TOL=98842],arachnocalpis[&&NHX:TOL=98843],artostrobiidae[&&NHX:TOL=98844],cannobotryidae[&&NHX:TOL=98851],carpocaniidae[&&NHX:TOL=98858],hexapylocapsa[&&NHX:TOL=98862],plagiacanthidae[&&NHX:TOL=98901],pterocorythidae[&&NHX:TOL=98922],sethophormididae[&&NHX:TOL=98928],theoperidae[&&NHX:TOL=98939],nassellarid genera of uncertain affinities[&&NHX:TOL=98863])nassellaria[&&NHX:TOL=98841],(actinommidae[&&NHX:TOL=98983],artiscinae[&&NHX:TOL=99063],collosphaeridae[&&NHX:TOL=99071],collozoidae[&&NHX:TOL=99107],ethmosphaeridae[&&NHX:TOL=99136],larnacalpis[&&NHX:TOL=99149],litheliidae[&&NHX:TOL=99150],myelastrum[&&NHX:TOL=99158],heliodiscus[&&NHX:TOL=99161],porodiscidae[&&NHX:TOL=99164],pyloniidae[&&NHX:TOL=99182],sphaerozoidae[&&NHX:TOL=99204],spongodiscidae[&&NHX:TOL=99221],thalassicollidae[&&NHX:TOL=99283],tholoniidae[&&NHX:TOL=99307],spumellarid genera of uncertain affinities[&&NHX:TOL=99233])spumellaria[&&NHX:TOL=98982],polycistine genera of uncertain affinities[&&NHX:TOL=99331])polycystine radiolarians[&&NHX:TOL=121189],acantharea[&&NHX:TOL=2385])radiolaria[&&NHX:TOL=139596])rhizaria[&&NHX:TOL=121166],(((((((haemoproteus[&&NHX:TOL=68066],garniidae[&&NHX:TOL=124977],leucocytozoon[&&NHX:TOL=68068],(billbraya[&&NHX:TOL=68064],dionisia[&&NHX:TOL=68065],haemocystidium[&&NHX:TOL=125094],hepatocystis[&&NHX:TOL=68067],mesnilium[&&NHX:TOL=68069],nycteria[&&NHX:TOL=68070],(((plasmodium reichenowi[&&NHX:TOL=68103],plasmodium falciparum[&&NHX:TOL=68104])[&&NHX:TOL=68102],((((((plasmodium fieldi[&&NHX:TOL=68107],plasmodium simiovale[&&NHX:TOL=68108])[&&NHX:TOL=68106],(plasmodium hylobati[&&NHX:TOL=68110],plasmodium inui[&&NHX:TOL=68111])[&&NHX:TOL=68109],(plasmodium knowlesi[&&NHX:TOL=68113],plasmodium coatneyi[&&NHX:TOL=68114])[&&NHX:TOL=68112],(plasmodium simium[&&NHX:TOL=68116],plasmodium vivax[&&NHX:TOL=68117])[&&NHX:TOL=68115],plasmodium cynomolgi[&&NHX:TOL=68118])[&&NHX:TOL=68105],plasmodium gonderi[&&NHX:TOL=68119])[&&NHX:TOL=68139],(plasmodium malariae[&&NHX:TOL=68121],plasmodium brasilianum[&&NHX:TOL=68120])[&&NHX:TOL=68140])[&&NHX:TOL=68138],plasmodium ovale[&&NHX:TOL=68122],hepatocystis sp.[&&NHX:TOL=68123])[&&NHX:TOL=68137],(((plasmodium atheruri[&&NHX:TOL=111222],plasmodium vinkei[&&NHX:TOL=111223])[&&NHX:TOL=111221],plasmodium chabaudi[&&NHX:TOL=111224])[&&NHX:TOL=68124],(plasmodium berghei[&&NHX:TOL=68143],plasmodium yoelii[&&NHX:TOL=68126])[&&NHX:TOL=68142])[&&NHX:TOL=68127])[&&NHX:TOL=68136])[&&NHX:TOL=68135],(((plasmodium mexicanum[&&NHX:TOL=68145],plasmodium chiricahuae[&&NHX:TOL=68146])[&&NHX:TOL=68130],(plasmodium elongatum[&&NHX:TOL=68132],plasmodium gallinaceum[&&NHX:TOL=68147])[&&NHX:TOL=68133],plasmodium relictum[&&NHX:TOL=68129],plasmodium floridense[&&NHX:TOL=111225],(plasmodium azurophilum[&&NHX:TOL=111227],plasmodium faircihildi[&&NHX:TOL=111228])[&&NHX:TOL=111226],(plasmodium agamae[&&NHX:TOL=111230],plasmodium giganteum[&&NHX:TOL=111231])[&&NHX:TOL=111229])[&&NHX:TOL=68131],plasmodium mackerassae[&&NHX:TOL=68134])[&&NHX:TOL=68144],(plasmodium achiotense[&&NHX:TOL=110831],plasmodium achromaticum[&&NHX:TOL=110832],plasmodium acuminatum[&&NHX:TOL=110833],plasmodium aegyptensis[&&NHX:TOL=110834],plasmodium anasum[&&NHX:TOL=110835],plasmodium anomaluri[&&NHX:TOL=110836],plasmodium attenuatum[&&NHX:TOL=110837],plasmodium audaciosum[&&NHX:TOL=110838],plasmodium aurulentum[&&NHX:TOL=110839],plasmodium balli[&&NHX:TOL=110840],plasmodium basilisci[&&NHX:TOL=110841],plasmodium beebei[&&NHX:TOL=110842],plasmodium beltrami[&&NHX:TOL=110843],plasmodium bertii[&&NHX:TOL=110844],plasmodium bitis[&&NHX:TOL=110845],plasmodium booliati[&&NHX:TOL=110846],plasmodium brodeni[&&NHX:TOL=110847],plasmodium brucei[&&NHX:TOL=110848],plasmodium brumpti[&&NHX:TOL=110849],plasmodium bubalis[&&NHX:TOL=110850],plasmodium bufoni[&&NHX:TOL=110851],plasmodium caprea[&&NHX:TOL=110852],plasmodium carinii[&&NHX:TOL=110853],plasmodium cathemerium[&&NHX:TOL=110854],plasmodium causi[&&NHX:TOL=110855],plasmodium cephalophi[&&NHX:TOL=110856],plasmodium clelandi[&&NHX:TOL=110857],plasmodium cnemaspi[&&NHX:TOL=110858],plasmodium cnemidophori[&&NHX:TOL=110859],plasmodium colombiense[&&NHX:TOL=110860],plasmodium columbae[&&NHX:TOL=110861],plasmodium coturnixae[&&NHX:TOL=110862],plasmodium cyclopsi[&&NHX:TOL=110863],plasmodium diminutivum[&&NHX:TOL=110864],plasmodium dissanaikei[&&NHX:TOL=110865],plasmodium durae[&&NHX:TOL=110866],plasmodium effusum[&&NHX:TOL=110867],plasmodium egerniae[&&NHX:TOL=110868],plasmodium eyelesi[&&NHX:TOL=110869],plasmodium fallax[&&NHX:TOL=110870],plasmodium fischeri[&&NHX:TOL=110871],plasmodium foleyi[&&NHX:TOL=110873],plasmodium formosanum[&&NHX:TOL=110874],plasmodium fragile[&&NHX:TOL=110875],plasmodium garnhami[&&NHX:TOL=110876],plasmodium giganteumaustralis[&&NHX:TOL=110877],plasmodium giovannolai[&&NHX:TOL=110878],plasmodium girardi[&&NHX:TOL=110879],plasmodium gonatodi[&&NHX:TOL=110880],plasmodium griffithsi[&&NHX:TOL=110881],plasmodium gundersi[&&NHX:TOL=110882],plasmodium guyannese[&&NHX:TOL=110883],plasmodium hegneri[&&NHX:TOL=110884],plasmodium heischi[&&NHX:TOL=110885],plasmodium hermani[&&NHX:TOL=110886],plasmodium herodiadis[&&NHX:TOL=110887],plasmodium hexamerium[&&NHX:TOL=110888],plasmodium holti[&&NHX:TOL=110889],plasmodium huffi[&&NHX:TOL=110890],plasmodium iguanae[&&NHX:TOL=110891],plasmodium jefferyi[&&NHX:TOL=110892],plasmodium josephinae[&&NHX:TOL=110893],plasmodium juxtanucleare[&&NHX:TOL=110894],plasmodium kempi[&&NHX:TOL=110895],plasmodium lacertiliae[&&NHX:TOL=110896],plasmodium lagopi[&&NHX:TOL=110897],plasmodium lainsoni[&&NHX:TOL=110898],plasmodium landauae[&&NHX:TOL=110899],plasmodium limnotragi[&&NHX:TOL=110900],plasmodium lionatum[&&NHX:TOL=110901],plasmodium loveridgei[&&NHX:TOL=110902],plasmodium lutzi[&&NHX:TOL=110903],plasmodium lygosomae[&&NHX:TOL=110904],plasmodium mabuiae[&&NHX:TOL=110905],plasmodium mackiei[&&NHX:TOL=110906],plasmodium maculilabre[&&NHX:TOL=110907],plasmodium marginatum[&&NHX:TOL=110908],plasmodium matutinum[&&NHX:TOL=110909],plasmodium melanoleuca[&&NHX:TOL=110910],plasmodium minasense[&&NHX:TOL=110911],plasmodium modestum[&&NHX:TOL=110912],plasmodium morulum[&&NHX:TOL=110913],plasmodium multiformis[&&NHX:TOL=110914],plasmodium narayani[&&NHX:TOL=110915],plasmodium neotropicalis[&&NHX:TOL=110916],plasmodium nucleophilum[&&NHX:TOL=110917],plasmodium octamerium[&&NHX:TOL=110918],plasmodium odocoilei[&&NHX:TOL=110919],plasmodium paranucleophilum[&&NHX:TOL=110920],plasmodium pediocetti[&&NHX:TOL=110921],plasmodium pessoai[&&NHX:TOL=110922],plasmodium pifanoi[&&NHX:TOL=110923],plasmodium pinottii[&&NHX:TOL=110924],plasmodium pitheci[&&NHX:TOL=110925],plasmodium pitmani[&&NHX:TOL=110926],plasmodium polare[&&NHX:TOL=110927],plasmodium pulmophilum[&&NHX:TOL=110928],plasmodium pythonias[&&NHX:TOL=110929],plasmodium quelea[&&NHX:TOL=110930],plasmodium rhadinurum[&&NHX:TOL=110931],plasmodium robinsoni[&&NHX:TOL=110932],plasmodium rousseloti[&&NHX:TOL=110933],plasmodium rousetti[&&NHX:TOL=110934],plasmodium rouxi[&&NHX:TOL=110935],plasmodium sandoshami[&&NHX:TOL=110936],plasmodium sasai[&&NHX:TOL=110937],plasmodium scelopori[&&NHX:TOL=110938],plasmodium schweitzi[&&NHX:TOL=110939],plasmodium scorzai[&&NHX:TOL=110940],plasmodium silvaticum[&&NHX:TOL=110941],plasmodium simplex[&&NHX:TOL=110942],plasmodium smirnovi[&&NHX:TOL=110943],plasmodium stuthionis[&&NHX:TOL=110944],plasmodium subpraecox[&&NHX:TOL=110945],plasmodium teijerai[&&NHX:TOL=110946],plasmodium telfordi[&&NHX:TOL=110947],plasmodium tenue[&&NHX:TOL=110948],plasmodium tomodoni[&&NHX:TOL=110949],plasmodium  torrealbai[&&NHX:TOL=110950],plasmodium toucani[&&NHX:TOL=110951],plasmodium traguli[&&NHX:TOL=110952],plasmodium tropiduri[&&NHX:TOL=110953],plasmodium tyrio[&&NHX:TOL=110954],plasmodium uluguruense[&&NHX:TOL=110955],plasmodium uncinatum[&&NHX:TOL=110956],plasmodium uranoscodoni[&&NHX:TOL=110957],plasmodium utingensis[&&NHX:TOL=110958],plasmodium vacuolatum[&&NHX:TOL=110959],plasmodium vastator[&&NHX:TOL=110960],plasmodium vaughani[&&NHX:TOL=110961],plasmodium vautieri[&&NHX:TOL=110962],plasmodium venkataramiahii[&&NHX:TOL=110963],plasmodium voltaicum[&&NHX:TOL=110964],plasmodium watteni[&&NHX:TOL=110965],plasmodium wenyoni[&&NHX:TOL=110966],plasmodium youngi[&&NHX:TOL=110967],plasmodium zonuriae[&&NHX:TOL=110968],plasmodium saurocaudatum[&&NHX:TOL=110969],plasmodium holaspi[&&NHX:TOL=110970],plasmodium siamense[&&NHX:TOL=110971],plasmodium brygooi[&&NHX:TOL=110972],plasmodium cordyli[&&NHX:TOL=110973],plasmodium arachniformis[&&NHX:TOL=110974],plasmodium gologoloense[&&NHX:TOL=110975],plasmodium michikoa[&&NHX:TOL=110976],plasmodium tanzaniae[&&NHX:TOL=110977],plasmodium uzungwiense[&&NHX:TOL=110978],plasmodium pelaezi[&&NHX:TOL=110979],plasmodium parajuxtanucleare[&&NHX:TOL=110980],plasmodium bucki[&&NHX:TOL=110981],plasmodium coulangesi[&&NHX:TOL=110982],plasmodium percygarnhami[&&NHX:TOL=110983],plasmodium georgesi[&&NHX:TOL=110984],plasmodium petersi[&&NHX:TOL=110985],plasmodium draconis[&&NHX:TOL=110986],plasmodium volans[&&NHX:TOL=110987],plasmodium neusticuri[&&NHX:TOL=110988],plasmodium forresteri[&&NHX:TOL=110989],plasmodium circularis[&&NHX:TOL=110990],plasmodium kentropyxi[&&NHX:TOL=110991],plasmodium bigueti[&&NHX:TOL=110992],plasmodium parvulum[&&NHX:TOL=110993],plasmodium tribolonti[&&NHX:TOL=110994],plasmodium gracilis[&&NHX:TOL=110995])plasmodia of uncertain phylogenetic placement[&&NHX:TOL=110830])plasmodium[&&NHX:TOL=68071],polychromophilus[&&NHX:TOL=68072],rayella[&&NHX:TOL=68073],saurocytozoon[&&NHX:TOL=68074])plasmodiidae[&&NHX:TOL=68059])haemospororida[&&NHX:TOL=124976],(anthemosoma[&&NHX:TOL=68075],(babesia[&&NHX:TOL=68087],echinozoon[&&NHX:TOL=68088])babesiidae[&&NHX:TOL=68076],(cristalloidophora[&&NHX:TOL=68089],dobellia[&&NHX:TOL=68090],echinococcidium[&&NHX:TOL=68091],globidiellum[&&NHX:TOL=68092],haemohormidium[&&NHX:TOL=68093],joyeuxella[&&NHX:TOL=68094],rhabdospora[&&NHX:TOL=68095],sauroplasma[&&NHX:TOL=68096],spermatobium[&&NHX:TOL=68097],toxocytis[&&NHX:TOL=68098],trophosphaera[&&NHX:TOL=68099])haemohormidiidae[&&NHX:TOL=68077],theileria[&&NHX:TOL=68078])piroplasmorida[&&NHX:TOL=68060])hematozoa  aconoidasida[&&NHX:TOL=68058],cryptosporidium[&&NHX:TOL=124803],protococcidia[&&NHX:TOL=124804],agamococcidia[&&NHX:TOL=124805],(selenidium and relatives[&&NHX:TOL=126365],(lecudinidae[&&NHX:TOL=126367],urosporidae[&&NHX:TOL=126368],lankesteria[&&NHX:TOL=126369],(monocystids[&&NHX:TOL=126371],neogregarinida[&&NHX:TOL=126372])[&&NHX:TOL=126370],septate eugregarines[&&NHX:TOL=126373])eugregarinida[&&NHX:TOL=126366])gregarina[&&NHX:TOL=124806],((heteroxenic coccidia[&&NHX:TOL=124809],monoxenic coccidia[&&NHX:TOL=124810])[&&NHX:TOL=124808],adeleorina[&&NHX:TOL=124811])coccidia[&&NHX:TOL=124807])apicomplexans[&&NHX:TOL=2446],colpodellids[&&NHX:TOL=2447],chromera[&&NHX:TOL=68086])[&&NHX:TOL=124799],((perkinsus[&&NHX:TOL=126515],parvilucifera[&&NHX:TOL=126516],rastrimonas[&&NHX:TOL=126517])perkinsids[&&NHX:TOL=126468],(((duboscquella[&&NHX:TOL=126513],ichthyodinium[&&NHX:TOL=126514])marine alveolate group i[&&NHX:TOL=126470],((syndinium[&&NHX:TOL=126524],hematodinium[&&NHX:TOL=126525],merodinium[&&NHX:TOL=126526],solenodinium[&&NHX:TOL=126527],trypanodinium[&&NHX:TOL=126528])syndiniaceae[&&NHX:TOL=126523],amoebophrya[&&NHX:TOL=126529],(sphaeripara[&&NHX:TOL=126533],atlanticellodinium[&&NHX:TOL=126534])sphaeriparaceae[&&NHX:TOL=126532],(coccidinium[&&NHX:TOL=126743],atelodinium[&&NHX:TOL=126742])syndinians incertae sedis[&&NHX:TOL=126741])syndiniales[&&NHX:TOL=126471])syndinians[&&NHX:TOL=128862],oxyrrhis marina[&&NHX:TOL=126473],((((((gymnodinium sensu stricto[&&NHX:TOL=126747],dissodinium[&&NHX:TOL=126748],lepidodinium[&&NHX:TOL=126749],pheopolykrikos[&&NHX:TOL=126750])gymnodiniaceae[&&NHX:TOL=126746],(polykrikos[&&NHX:TOL=126752],pheopolykrikos hartmannii[&&NHX:TOL=126753])polykrikaceae[&&NHX:TOL=126751],(warnowia[&&NHX:TOL=126755],erythropsidinium[&&NHX:TOL=126756],greuetodinium[&&NHX:TOL=126757],nematodinium[&&NHX:TOL=126758],nematopsides[&&NHX:TOL=126759],proterythropsis[&&NHX:TOL=126760],protopsis[&&NHX:TOL=126761])warnowiaceae[&&NHX:TOL=126754],(actiniscus[&&NHX:TOL=126763],diaster[&&NHX:TOL=126764],dicroerisma[&&NHX:TOL=126765])actiniscaceae[&&NHX:TOL=126762],(noctiluca[&&NHX:TOL=126767],(kofoidinium[&&NHX:TOL=126769],pomatodinium[&&NHX:TOL=126770],spatulodinium[&&NHX:TOL=126771])kofoidiniaceae[&&NHX:TOL=126768],(leptodiscus[&&NHX:TOL=126773],abedinium[&&NHX:TOL=126774],cachonodinium[&&NHX:TOL=126775],craspedotella[&&NHX:TOL=126776],cymbodinium[&&NHX:TOL=126777],petalodinium[&&NHX:TOL=126778],scaphodinium[&&NHX:TOL=126779])leptodiscaceae[&&NHX:TOL=126772])noctilucoids[&&NHX:TOL=126766])[&&NHX:TOL=127779],gyrodinium sensu stricto[&&NHX:TOL=126780])gymnodinineae[&&NHX:TOL=126745],((ptychodiscus[&&NHX:TOL=126783],balechina[&&NHX:TOL=126784],berghiella[&&NHX:TOL=126785],ceratoperidinium[&&NHX:TOL=126786],kolkwitziella[&&NHX:TOL=126787],lissaiella[&&NHX:TOL=126788],lophodinium[&&NHX:TOL=126789],sclerodinium[&&NHX:TOL=126790],woloszynskia[&&NHX:TOL=126791])ptychodiscaceae[&&NHX:TOL=126782],(amphitholus[&&NHX:TOL=126793],achradina[&&NHX:TOL=126794],monaster[&&NHX:TOL=126795])amphitholaceae[&&NHX:TOL=126792],(brachidinium[&&NHX:TOL=126797],asterodinium[&&NHX:TOL=126798],microceratium[&&NHX:TOL=126799])brachidiniaceae[&&NHX:TOL=126796])ptychodiscoids[&&NHX:TOL=126781],(karlodinium[&&NHX:TOL=126801],karenia[&&NHX:TOL=126802],takayama[&&NHX:TOL=126803])haptophores[&&NHX:TOL=126800],(tovellia[&&NHX:TOL=126805],jadwigia[&&NHX:TOL=126806],esoptrodinium[&&NHX:TOL=126807])tovelliaceae[&&NHX:TOL=126804],(borghiella[&&NHX:TOL=126809],baldinia[&&NHX:TOL=126810],woloszynskia pesheri[&&NHX:TOL=126811])the borghiella clade[&&NHX:TOL=126808],(akashiwo[&&NHX:TOL=126813],amphidinium sensu stricto[&&NHX:TOL=126814],apicoporus[&&NHX:TOL=126815],haplozoon[&&NHX:TOL=126816],togula[&&NHX:TOL=126817],the cochlodinium polykrikoides | cochlodinium fulvescens clade[&&NHX:TOL=126818],the cochlodinium convolutum | gyrodinium falcatum clade[&&NHX:TOL=126819],the gyrodinium dorsum | gyrodinium instriatum|gyrodinium uncatenum clade[&&NHX:TOL=126820],cochlodinium[&&NHX:TOL=126821],katodinium[&&NHX:TOL=126822],bernardinium[&&NHX:TOL=126823],crepidoodinium[&&NHX:TOL=126824],filodinium[&&NHX:TOL=126825],herdmania[&&NHX:TOL=126826],pavillardia[&&NHX:TOL=126827],piscinoodinium[&&NHX:TOL=126828],schizochytriodinium[&&NHX:TOL=126829],spiniferodinium[&&NHX:TOL=126830],syltodinium[&&NHX:TOL=126831],torodinium[&&NHX:TOL=126832])gymnodinoids incertae sedis[&&NHX:TOL=126812])gymnodinoids[&&NHX:TOL=126475],(symbiodinium[&&NHX:TOL=126705],polarella[&&NHX:TOL=126706],protodinium[&&NHX:TOL=126707],prosoaulax[&&NHX:TOL=126708],woloszynskia pseudopalustris[&&NHX:TOL=126709],woloszynskia halophila[&&NHX:TOL=126710],gymnodinium natalense[&&NHX:TOL=126711],gymnodinium linucheae[&&NHX:TOL=126712],katodinium fungiforme[&&NHX:TOL=126713])suessioids[&&NHX:TOL=126476])[&&NHX:TOL=126474],((heterocapsa[&&NHX:TOL=126611],((glenodinium[&&NHX:TOL=126615],glenodiniopsis[&&NHX:TOL=126616],gymnodinium impatiens[&&NHX:TOL=126617])glenodinioids[&&NHX:TOL=126614],((peridinium[&&NHX:TOL=126620],(kryptoperidinium[&&NHX:TOL=126624],durinskia[&&NHX:TOL=126625],dinothrix[&&NHX:TOL=126626],galeidinium[&&NHX:TOL=126627],peridinium quinquecorne[&&NHX:TOL=126628],gymnodinium quatrilobatum[&&NHX:TOL=126629],peridiniopsis penardii[&&NHX:TOL=126630],peridiniopsis cf. kevei[&&NHX:TOL=126631])diatomophores[&&NHX:TOL=126623],((pentapharsodinium[&&NHX:TOL=126633],ensiculifera[&&NHX:TOL=126634],pernambugia[&&NHX:TOL=126635],scrippsiella[&&NHX:TOL=126636],calciodinellum[&&NHX:TOL=126637],calcigonellum[&&NHX:TOL=126638],leonella[&&NHX:TOL=126639],thoracosphaera[&&NHX:TOL=126640],bysmatrum[&&NHX:TOL=126641],peridinium polonicum[&&NHX:TOL=126642],peridinium wierzejskii[&&NHX:TOL=126643],peridinium aciculiferumscrippsiella hangoei[&&NHX:TOL=126644])calciodinellids[&&NHX:TOL=126632],(pfiesteria[&&NHX:TOL=126646],stoeckeria[&&NHX:TOL=126647],cryptoperidiniopsis[&&NHX:TOL=126648],luciella[&&NHX:TOL=126649],paulsenella[&&NHX:TOL=126650],amyloodinium[&&NHX:TOL=126651])the pfiesteria clade[&&NHX:TOL=126645])[&&NHX:TOL=127778],blastodinium[&&NHX:TOL=126652],(peridiniopsis[&&NHX:TOL=126656],peridinium umbonatum[&&NHX:TOL=126657],peridinium inconspicuum[&&NHX:TOL=126658],peridinium centenniale[&&NHX:TOL=126659],peridinium palatinum[&&NHX:TOL=126660],peridinium pseudolaeve[&&NHX:TOL=126661])peridiniopsideae[&&NHX:TOL=126655],(amphidiniella[&&NHX:TOL=126663],amphidiniopsis[&&NHX:TOL=126664],kansodinium[&&NHX:TOL=126665],pileidinium[&&NHX:TOL=126666])peridiniaceae incertae sedis[&&NHX:TOL=126662])peridiniaceae[&&NHX:TOL=126619],((protoperidinium[&&NHX:TOL=126669],congruentidium[&&NHX:TOL=126670],archaeperidinium[&&NHX:TOL=126671],glochidinium[&&NHX:TOL=126672])protoperidinioideae[&&NHX:TOL=126668],(diplopsalis[&&NHX:TOL=126674],apsteinia[&&NHX:TOL=126675],boreadinium[&&NHX:TOL=126676],diplopelta[&&NHX:TOL=126677],diplopsalopsis[&&NHX:TOL=126678],dissodium[&&NHX:TOL=126679],gotoius[&&NHX:TOL=126680],oblea[&&NHX:TOL=126681],preperidinium[&&NHX:TOL=126682],zygabikodinium[&&NHX:TOL=126683])diplopsaloideae[&&NHX:TOL=126673],(lessardia[&&NHX:TOL=126685],roscoffia[&&NHX:TOL=126686],cabra[&&NHX:TOL=126687],rhinodinium[&&NHX:TOL=126688])lessardioideae[&&NHX:TOL=126684])protoperidiniaceae[&&NHX:TOL=126667],(podolampas[&&NHX:TOL=126690],blepharocysta[&&NHX:TOL=126691],gaarderia[&&NHX:TOL=126692],heterobractum[&&NHX:TOL=126693],lissodinium[&&NHX:TOL=126694],mysticella[&&NHX:TOL=126695])podolampaceae[&&NHX:TOL=126689])peridiniineans[&&NHX:TOL=126618])[&&NHX:TOL=127777],(chalubinskia[&&NHX:TOL=126697],hemidinium[&&NHX:TOL=126698],oodinium[&&NHX:TOL=126699],plagiodinium[&&NHX:TOL=126700],protoodinium[&&NHX:TOL=126701],sabulodinium[&&NHX:TOL=126702],staszicella[&&NHX:TOL=126703],thaurilens[&&NHX:TOL=126704])peridinioids incertae sedis[&&NHX:TOL=126696])peridinioids[&&NHX:TOL=126478],((cladopyxis[&&NHX:TOL=126564],acanthodinium[&&NHX:TOL=126565],amphidoma[&&NHX:TOL=126566],palaeophalacroma[&&NHX:TOL=126567],sinodinium[&&NHX:TOL=126568])cladopyxineans[&&NHX:TOL=126563],((protoceratium[&&NHX:TOL=126571],lingulodinium[&&NHX:TOL=126572],gonyaulax[&&NHX:TOL=126573],acanthogonyaulax[&&NHX:TOL=126574],spiraulax[&&NHX:TOL=126575],halostylodinium[&&NHX:TOL=126576])gonyaulacaceae[&&NHX:TOL=126570],ceratocorys[&&NHX:TOL=126577],(ceratium[&&NHX:TOL=126580],((goniodoma[&&NHX:TOL=126585],pachydinium[&&NHX:TOL=126586])goniodomoideae[&&NHX:TOL=127681],(gambierdiscus[&&NHX:TOL=126587],coolia[&&NHX:TOL=126588],ostreopsis[&&NHX:TOL=126589])gambierdiscoideae[&&NHX:TOL=127682],(pyrodinium[&&NHX:TOL=126594],(helgolandinium[&&NHX:TOL=126590],alexandrium[&&NHX:TOL=126591],fragilidium[&&NHX:TOL=126592],pyrophacus[&&NHX:TOL=126593])helgolandinioideae[&&NHX:TOL=127683],pyrocystis[&&NHX:TOL=126595])[&&NHX:TOL=126584])[&&NHX:TOL=127686])[&&NHX:TOL=127685])[&&NHX:TOL=127684],(adenoides[&&NHX:TOL=126599],heterodinium[&&NHX:TOL=126600],crypthecodinium[&&NHX:TOL=126601],centrodinium[&&NHX:TOL=126602],dolichodinium[&&NHX:TOL=126603],goniodinium[&&NHX:TOL=126604],peridiniella[&&NHX:TOL=126605],planodinium[&&NHX:TOL=126606],thecadiniopsis[&&NHX:TOL=126607],thecadinium[&&NHX:TOL=126608],pseudothecadinium[&&NHX:TOL=126609],stylodinium[&&NHX:TOL=126610])gonyaulacoids incertae sedis[&&NHX:TOL=126598])gonyaulacoids[&&NHX:TOL=126479],((prorocentrum[&&NHX:TOL=126511],mesoporus[&&NHX:TOL=126512],haplodinium[&&NHX:TOL=126557])prorocentroids[&&NHX:TOL=126481],((dinophysis[&&NHX:TOL=126536],citharistes[&&NHX:TOL=126537],dinofurcula[&&NHX:TOL=126538],heteroschisma[&&NHX:TOL=126539],histioneis[&&NHX:TOL=126540],histiophysis[&&NHX:TOL=126541],metadinophysis[&&NHX:TOL=126542],metaphalacroma[&&NHX:TOL=126543],ornithocercus[&&NHX:TOL=126544],pseudophalacroma[&&NHX:TOL=126545],sinophysis[&&NHX:TOL=126546],thaumatodinium[&&NHX:TOL=126547])dinophysiaceae[&&NHX:TOL=126535],(amphisolenia[&&NHX:TOL=126549],triposolenia[&&NHX:TOL=126550])amphisoleniaceae[&&NHX:TOL=126548],oxyphysis[&&NHX:TOL=126551],dinophysoids incertae sedis[&&NHX:TOL=126559])dinophysoids[&&NHX:TOL=126480])[&&NHX:TOL=126556])[&&NHX:TOL=126477],(actinodinium[&&NHX:TOL=126715],adinimonas[&&NHX:TOL=126716],apodinium[&&NHX:TOL=126717],cachonella[&&NHX:TOL=126718],caryotoma[&&NHX:TOL=126719],chytriodinium[&&NHX:TOL=126720],cystodinedria[&&NHX:TOL=126721],cystodinium[&&NHX:TOL=126722],desmocapsa[&&NHX:TOL=126723],desmomastix[&&NHX:TOL=126724],dinamoeba[&&NHX:TOL=126725],dinastridium[&&NHX:TOL=126726],dinoclonium[&&NHX:TOL=126727],gloeodinium[&&NHX:TOL=126728],hypnodinium[&&NHX:TOL=126729],manchudinium[&&NHX:TOL=126730],myxodinium[&&NHX:TOL=126731],oodinioides[&&NHX:TOL=126732],phytodinium[&&NHX:TOL=126733],pleromonas[&&NHX:TOL=126734],rhizodinium[&&NHX:TOL=126735],rufusiella[&&NHX:TOL=126736],schizodinium[&&NHX:TOL=126737],tetradinium[&&NHX:TOL=126738])dinokaryotes incertae sedis[&&NHX:TOL=126714])dinokaryotes[&&NHX:TOL=126472])dinoflagellates[&&NHX:TOL=2445],(ellobiopsis[&&NHX:TOL=126518],thalassomyces[&&NHX:TOL=126519],parallobiopsis[&&NHX:TOL=126520],ellobiocystis[&&NHX:TOL=126521],rhizellobiopsis[&&NHX:TOL=126522])ellobiopsids[&&NHX:TOL=126469])[&&NHX:TOL=129910])myzozoa[&&NHX:TOL=2444],colponema[&&NHX:TOL=129911],ciliates[&&NHX:TOL=2441])alveolates[&&NHX:TOL=2379],(((((((((((bolidophytes[&&NHX:TOL=142186],((ellerbeckia[&&NHX:TOL=125669],leptocylindrus[&&NHX:TOL=125670],pseudoguinardia[&&NHX:TOL=129364],((melosira[&&NHX:TOL=129320],aulacoseira[&&NHX:TOL=129321],druridgea[&&NHX:TOL=129393],miosira[&&NHX:EXT=Y:TOL=129335])[&&NHX:TOL=129319],podosira[&&NHX:TOL=129322],hyalodiscus[&&NHX:TOL=129323],paralia[&&NHX:TOL=129324],stephanopyxis[&&NHX:TOL=129325],endictya[&&NHX:TOL=129394])melosirids[&&NHX:TOL=125671],((hemidiscus[&&NHX:TOL=129343],roperia[&&NHX:TOL=129344],actinocyclus[&&NHX:TOL=129345],azpeitia[&&NHX:TOL=129346])hemidiscaceae[&&NHX:TOL=129326],(coscinodiscus[&&NHX:TOL=129347],palmeria[&&NHX:TOL=129348],brightwellia[&&NHX:EXT=Y:TOL=129349],craspedodiscus[&&NHX:EXT=Y:TOL=129350],rocella[&&NHX:EXT=Y:TOL=129351])coscinodiscaceae[&&NHX:TOL=129327],(asterolampra[&&NHX:TOL=129336],asteromphalus[&&NHX:TOL=129337],discodiscus[&&NHX:EXT=Y:TOL=129338],rylandsia[&&NHX:EXT=Y:TOL=129339],bergonia[&&NHX:EXT=Y:TOL=129340])asterolampraceae[&&NHX:TOL=129328],(actinoptychus[&&NHX:TOL=129361],glorioptychus[&&NHX:EXT=Y:TOL=129362],lepidodiscus[&&NHX:EXT=Y:TOL=129363])heliopeltaceae[&&NHX:TOL=129329],(fenestrella[&&NHX:EXT=Y:TOL=129356],stellarima[&&NHX:TOL=129352])stellarimaceae[&&NHX:TOL=129357],(benetorus[&&NHX:EXT=Y:TOL=129359],azpeitiopsis[&&NHX:EXT=Y:TOL=129360])benetoraceae[&&NHX:EXT=Y:TOL=129358],(aulacodiscus[&&NHX:TOL=129341],moisseevia[&&NHX:EXT=Y:TOL=129342])aulacodiscaceae[&&NHX:TOL=129330],(annellus[&&NHX:EXT=Y:TOL=129354],porodiscus[&&NHX:EXT=Y:TOL=129355])[&&NHX:EXT=Y:TOL=129353])coscinodiscids[&&NHX:TOL=125672],arachnoidiscus[&&NHX:TOL=125673],(rhizosolenia[&&NHX:TOL=129331],guinardia[&&NHX:TOL=129332],dactyliosolen[&&NHX:TOL=129333])rhizosolenids[&&NHX:TOL=125674],corethron[&&NHX:TOL=125675],gossleriella[&&NHX:TOL=129334],proboscia[&&NHX:TOL=125676],chrysanthemodiscus[&&NHX:TOL=125678],ethmodiscus[&&NHX:TOL=125679],stictocyclus[&&NHX:TOL=125680],orthoseira[&&NHX:TOL=125681])radial centric diatoms[&&NHX:TOL=125295],(((hemiaulus[&&NHX:TOL=129280],eucampia[&&NHX:TOL=129282],cerataulina[&&NHX:TOL=129283],trinacria[&&NHX:EXT=Y:TOL=129285],ailuretta[&&NHX:EXT=Y:TOL=129290],sphynctolethus[&&NHX:EXT=Y:TOL=129291],pseudaulacodiscus[&&NHX:EXT=Y:TOL=129292],(keratophora[&&NHX:EXT=Y:TOL=129293],thaumatonema[&&NHX:EXT=Y:TOL=129294],strelnikovia[&&NHX:EXT=Y:TOL=129295],bonea[&&NHX:EXT=Y:TOL=129296],dicladiopsis[&&NHX:EXT=Y:TOL=129297],briggera[&&NHX:EXT=Y:TOL=129287])[&&NHX:TOL=129281],(pseudorutilaria[&&NHX:EXT=Y:TOL=129288],solium[&&NHX:EXT=Y:TOL=129299],monile[&&NHX:EXT=Y:TOL=129300])[&&NHX:TOL=129298],(abas[&&NHX:EXT=Y:TOL=129286],dextradonator[&&NHX:EXT=Y:TOL=129302])[&&NHX:TOL=129301],kittonia[&&NHX:EXT=Y:TOL=129289],climacodium[&&NHX:TOL=129284])hemiaulaceae[&&NHX:TOL=126195],(chaetoceros[&&NHX:TOL=129189],bacteriastrum[&&NHX:TOL=129190])chaetocerotaceae[&&NHX:TOL=126196])[&&NHX:TOL=126194],(lampriscus[&&NHX:TOL=126204],(toxarium[&&NHX:TOL=128945],(ardissonea[&&NHX:TOL=128947],climacosphenia[&&NHX:TOL=128948],synedrosphenia[&&NHX:TOL=128949])[&&NHX:TOL=128946])ardissoneales[&&NHX:TOL=126205])[&&NHX:TOL=126203],biddulphiopsis[&&NHX:TOL=129313],(pleurosira[&&NHX:TOL=129315],odontella[&&NHX:TOL=129316],cerataulus 1[&&NHX:TOL=129317])pleurosiraceae[&&NHX:TOL=129314],(eupodiscus[&&NHX:TOL=129792],actinodiscus[&&NHX:TOL=129793],craspedoporus[&&NHX:EXT=Y:TOL=129794],corona[&&NHX:EXT=Y:TOL=129795],sextiputeus[&&NHX:EXT=Y:TOL=129796],cerataulus 2[&&NHX:TOL=128944],fryxelliella[&&NHX:TOL=129797],auliscus[&&NHX:TOL=129409],rattrayella[&&NHX:EXT=Y:TOL=129798],neohuttonia[&&NHX:TOL=129799],glyphodiscus[&&NHX:TOL=129800])eupodiscaceae[&&NHX:TOL=129791],(triceratium[&&NHX:TOL=128943],praetriceratium[&&NHX:EXT=Y:TOL=129790])triceratiaceae[&&NHX:TOL=125297],(biddulphia[&&NHX:TOL=129306],hydrosera[&&NHX:TOL=129307],stoermeria[&&NHX:TOL=129318],terpsino?[&&NHX:TOL=129308],euodiella[&&NHX:TOL=129309],trigonium[&&NHX:TOL=129310],isthmia[&&NHX:TOL=129311],pseudotriceratium[&&NHX:TOL=129312])biddulphiaceae[&&NHX:TOL=126202],(anaulus[&&NHX:TOL=129303],eunotogramma[&&NHX:TOL=129304],porpeia[&&NHX:TOL=129305])anaulaceae[&&NHX:TOL=126201],((cymatosira[&&NHX:TOL=128951],campylosira[&&NHX:TOL=128952],plagiogrammopsis[&&NHX:TOL=128953],papiliocellulus[&&NHX:TOL=128954],minutocellus[&&NHX:TOL=128955],brockmanniella[&&NHX:TOL=128956],leyanella[&&NHX:TOL=128957],arcocellulus[&&NHX:TOL=128958],extubocellulus[&&NHX:TOL=128959])[&&NHX:TOL=128950],(rutilaria[&&NHX:EXT=Y:TOL=128961],syndetocystis[&&NHX:EXT=Y:TOL=128962])[&&NHX:TOL=128960])cymatosirales[&&NHX:TOL=126197],(((lithodesmium undulatum[&&NHX:TOL=129199],lithodesmium duckerae[&&NHX:TOL=129200],lithodesmium variabile[&&NHX:TOL=129201])lithodesmium[&&NHX:TOL=129191],(ditylum sol[&&NHX:TOL=129204],ditylum brightwellii[&&NHX:TOL=129205],ditylum buchananii[&&NHX:TOL=129206],ditylum pernodii[&&NHX:TOL=129207])ditylum[&&NHX:TOL=129192],(bellerochea malleus[&&NHX:TOL=129208],bellerochea horologicalis[&&NHX:TOL=129209],bellerochea yucatanensis[&&NHX:TOL=129210])bellerochea[&&NHX:TOL=129195],helicotheca tamesis[&&NHX:TOL=129196],(neostreptotheca subindica[&&NHX:TOL=129211],neostreptotheca torta[&&NHX:TOL=129212])neostreptotheca[&&NHX:TOL=129197],(lithodesmioides minutum[&&NHX:TOL=129202],lithodesmioides polymorphum[&&NHX:TOL=129203])lithodesmioides[&&NHX:TOL=129198])lithodesmiales[&&NHX:TOL=126199],((porosira[&&NHX:TOL=129169],lauderia[&&NHX:TOL=129170])[&&NHX:TOL=129168],(thalassiosira group i[&&NHX:TOL=129172],cyclotella[&&NHX:TOL=129173],(skeletonema[&&NHX:TOL=129175],(thalassiosira group ii[&&NHX:TOL=129177],(shionodiscus group[&&NHX:TOL=129179],thalassiosira group iii[&&NHX:TOL=129180],bacterosira[&&NHX:TOL=129181],(discostella[&&NHX:TOL=129183],(cyclotella bodanica group[&&NHX:TOL=129185],(stephanodiscus[&&NHX:TOL=129187],cyclostephanos[&&NHX:TOL=129188])[&&NHX:TOL=129186])[&&NHX:TOL=129184])[&&NHX:TOL=129182])[&&NHX:TOL=129178])[&&NHX:TOL=129176])[&&NHX:TOL=129174])[&&NHX:TOL=129171])thalassiosirales[&&NHX:TOL=126200])[&&NHX:TOL=126198],attheya[&&NHX:TOL=126207],(((plagiogramma[&&NHX:TOL=129367],talaroneis[&&NHX:TOL=129368],dimeregramma[&&NHX:TOL=129369],glyphodesmis[&&NHX:TOL=129370])plagiogrammaceae[&&NHX:TOL=125311],(rhaphoneis[&&NHX:TOL=129371],delphineis[&&NHX:TOL=129372],perissono?[&&NHX:TOL=129373],diplomenora[&&NHX:TOL=129374],dickensoniaforma[&&NHX:EXT=Y:TOL=129375],sceptroneis[&&NHX:TOL=129376],detonia[&&NHX:TOL=129377],adoneis[&&NHX:TOL=129378])rhaphoneidaceae[&&NHX:TOL=125310],(asteroplanus[&&NHX:TOL=125312],asterionellopsis[&&NHX:TOL=125313])[&&NHX:TOL=125309])clade i araphid pennate diatoms[&&NHX:TOL=125304],((rhabdonema[&&NHX:TOL=126273],(grammatophora[&&NHX:TOL=126275],hyalosira[&&NHX:TOL=126276])[&&NHX:TOL=126274],(tabularia[&&NHX:TOL=126278],catacombas[&&NHX:TOL=126279],hyalosynedra[&&NHX:TOL=126280],pteroncola[&&NHX:TOL=126281])[&&NHX:TOL=126277],(thalassionema[&&NHX:TOL=129379],thalassiothrix[&&NHX:TOL=129380],trichotoxon[&&NHX:TOL=129381],lioloma[&&NHX:TOL=129382])thalassionemataceae[&&NHX:TOL=126282],(licmophora[&&NHX:TOL=129383],licmosphenia[&&NHX:TOL=129384])licmophoraceae[&&NHX:TOL=126283],(diatoma[&&NHX:TOL=129385],odontidium[&&NHX:TOL=129386],meridion[&&NHX:TOL=129387],asterionella[&&NHX:TOL=129388],tabellaria[&&NHX:TOL=129389],tetracyclus[&&NHX:TOL=129390])diatomaceae[&&NHX:TOL=126284],(fragilaria[&&NHX:TOL=129391],synedra[&&NHX:TOL=129392])fragilariaceae[&&NHX:TOL=126285],(nanofrustulum[&&NHX:TOL=126287],staurosira[&&NHX:TOL=126288],punctastriata[&&NHX:TOL=126289])[&&NHX:TOL=126286],(cyclophora[&&NHX:TOL=126291],neosynedra[&&NHX:TOL=126292])[&&NHX:TOL=126290],falcula[&&NHX:TOL=126293],opephora[&&NHX:TOL=126294],thalassioneis[&&NHX:TOL=126295],(protoraphis[&&NHX:TOL=126297],pseudohimantidium[&&NHX:TOL=126298])[&&NHX:TOL=126296],podocystis[&&NHX:TOL=126299],entopyla[&&NHX:TOL=126300],gephyria[&&NHX:TOL=126301])clade ii araphid pennate diatoms[&&NHX:TOL=125306],(((eunotia[&&NHX:TOL=125739],desmogonium[&&NHX:TOL=125740],semiorbis[&&NHX:TOL=125741],actinella[&&NHX:TOL=125742],eunophora[&&NHX:TOL=125743],amphorotia[&&NHX:TOL=125744])eunotiaceae[&&NHX:TOL=125737],peronia[&&NHX:TOL=125738])eunotiophycidae[&&NHX:TOL=125326],((mastogloia[&&NHX:TOL=126271],aneumastus[&&NHX:TOL=126272])mastogloiaceae[&&NHX:TOL=125682],dictyoneis[&&NHX:TOL=125683],(bacillaria[&&NHX:TOL=125758],nitzschia[&&NHX:TOL=125749],(fragilariopsis[&&NHX:TOL=125746],pseudonitzschia[&&NHX:TOL=125747],denticulopsis[&&NHX:TOL=125748])[&&NHX:TOL=125745],cylindrotheca[&&NHX:TOL=125757],denticula[&&NHX:TOL=125751],tryblionella[&&NHX:TOL=125753],psammodictyon[&&NHX:TOL=125754],simonsenia[&&NHX:TOL=125759],cymbellonitzschia[&&NHX:TOL=125752],hantzschia[&&NHX:TOL=125750],gomphonitzschia[&&NHX:TOL=125756],gomphotheca[&&NHX:TOL=125755],perrya[&&NHX:TOL=125760],cymatonitzschia[&&NHX:TOL=129412])bacillariaceae[&&NHX:TOL=125684],achnanthes[&&NHX:TOL=125685],((navicula[&&NHX:TOL=125761],hippodonta[&&NHX:TOL=125762],seminavis[&&NHX:TOL=125763],pseudogomphonema[&&NHX:TOL=125764],rhoikoneis[&&NHX:TOL=125765],trachyneis[&&NHX:TOL=125768],cymatoneis[&&NHX:TOL=125766],haslea[&&NHX:TOL=125767])naviculaceae[&&NHX:TOL=125687],((pleurosigma[&&NHX:TOL=125783],toxonidea[&&NHX:TOL=125784],rhoicosigma[&&NHX:TOL=125785])[&&NHX:TOL=125782],(gyrosigma[&&NHX:TOL=125787],donkinia[&&NHX:TOL=125788])[&&NHX:TOL=125786])pleurosigmataceae[&&NHX:TOL=125688],(plagiotropis[&&NHX:TOL=125789],ephemera[&&NHX:TOL=125790],banquisia[&&NHX:TOL=125791],mannsia[&&NHX:TOL=125792],manguinea[&&NHX:TOL=125793],membraneis[&&NHX:TOL=125794],pachyneis[&&NHX:TOL=125795],stauropsis[&&NHX:TOL=125796])plagiotropidaceae[&&NHX:TOL=125689])naviculineae[&&NHX:TOL=125686],proschkinia[&&NHX:TOL=125690],(stauroneis[&&NHX:TOL=125797],craticula[&&NHX:TOL=125798],prestauroneis[&&NHX:TOL=126302],parlibellus[&&NHX:TOL=126374])stauroneidaceae[&&NHX:TOL=125691],(berkeleya[&&NHX:TOL=125799],climaconeis[&&NHX:TOL=125800],stenoneis[&&NHX:TOL=125801])berkeleyaceae[&&NHX:TOL=125692],((neidium[&&NHX:TOL=125803],neidiopsis[&&NHX:TOL=125804])neidiaceae[&&NHX:TOL=125694],(biremis[&&NHX:TOL=125805],(scoliotropis[&&NHX:TOL=125807],scoliopleura[&&NHX:TOL=125808])[&&NHX:TOL=125806],progonoia[&&NHX:TOL=125809],diademoides[&&NHX:TOL=125810],muelleria[&&NHX:TOL=125811])scoliotropidaceae[&&NHX:TOL=125695])neidiineae[&&NHX:TOL=125693],(diploneis[&&NHX:TOL=126208],raphidodiscus[&&NHX:TOL=126209])diploneidaceae[&&NHX:TOL=125696],(cavinula[&&NHX:TOL=125697],cocconeiopsis[&&NHX:TOL=126260],decussata[&&NHX:TOL=126304])cavinulaceae[&&NHX:TOL=126259],(cosmioneis[&&NHX:TOL=125699],scolioneis[&&NHX:TOL=125700])cosmioneidaceae[&&NHX:TOL=125698],((amphipleura[&&NHX:TOL=126210],frustulia[&&NHX:TOL=126211],frickea[&&NHX:TOL=126212],cistula[&&NHX:TOL=126213])amphipleuraceae[&&NHX:TOL=125702],(brachysira[&&NHX:TOL=126214],gomphosphenia[&&NHX:TOL=126215])brachysiraceae[&&NHX:TOL=125703])hyalines[&&NHX:TOL=125701],((((sellaphora blackfordensis[&&NHX:TOL=129681],sellaphora capitata[&&NHX:TOL=129682])[&&NHX:TOL=129680],sellaphora pupula[&&NHX:TOL=129683],(sellaphora bacillum[&&NHX:TOL=129685],sellaphora lanceolata[&&NHX:TOL=129686])[&&NHX:TOL=129684],sellaphora obesa[&&NHX:TOL=129687],sellaphora auldreekie[&&NHX:TOL=129688])sellaphora[&&NHX:TOL=125733],fallacia[&&NHX:TOL=125734],rossia[&&NHX:TOL=125735],caponea[&&NHX:TOL=125736])sellaphoraceae[&&NHX:TOL=125705],(pinnularia[&&NHX:TOL=126216],caloneis[&&NHX:TOL=126217],pinnunavis[&&NHX:TOL=126218],lecohuia[&&NHX:TOL=126311],oestrupia[&&NHX:TOL=126219],dimidiata[&&NHX:TOL=126220],chamaepinnularia[&&NHX:TOL=126221],diatomella[&&NHX:TOL=126222])pinnulariaceae[&&NHX:TOL=125706])sellaphorineae[&&NHX:TOL=125704],veigaludwigia[&&NHX:TOL=126309],adlafia[&&NHX:TOL=126305],kobayasiella[&&NHX:TOL=126306],frankophila[&&NHX:TOL=126307],(diadesmis[&&NHX:TOL=126223],luticola[&&NHX:TOL=126224],nupela[&&NHX:TOL=126312],germainiella[&&NHX:TOL=126315])diadesmidaceae[&&NHX:TOL=125707],((rhoicosphenia[&&NHX:TOL=126225],campylopyxis[&&NHX:TOL=126226],cuneolus[&&NHX:TOL=126227],gomphoseptatum[&&NHX:TOL=126228],gomphonemopsis[&&NHX:TOL=126229])rhoicospheniaceae[&&NHX:TOL=125709],(anomoeoneis[&&NHX:TOL=126230],staurophora[&&NHX:TOL=126231],dickieia[&&NHX:TOL=126232])anomoeoneidaceae[&&NHX:TOL=125710],(lyrella[&&NHX:TOL=126233],petroneis[&&NHX:TOL=126234])lyrellaceae[&&NHX:TOL=125711],((cymbella[&&NHX:TOL=126235],encyonema[&&NHX:TOL=126236],brebissonia[&&NHX:TOL=126237])cymbellaceae[&&NHX:TOL=125713],(gomphonema[&&NHX:TOL=126238],gomphoneis[&&NHX:TOL=126239])gomphonemataceae[&&NHX:TOL=125714],placoneis[&&NHX:TOL=125715],didymosphenia[&&NHX:TOL=126240],gomphopleura[&&NHX:TOL=126241],reimeria[&&NHX:TOL=126242],geissleria[&&NHX:TOL=126308])gomphocymbelloids[&&NHX:TOL=125712],((cocconeis[&&NHX:TOL=126243],campyloneis[&&NHX:TOL=126244],anorthoneis[&&NHX:TOL=126245],bennettella[&&NHX:TOL=126246],epipellis[&&NHX:TOL=126247])cocconeidaceae[&&NHX:TOL=125717],(achnanthidium[&&NHX:TOL=126248],planothidium[&&NHX:TOL=126249],eucocconeis[&&NHX:TOL=126250],karayevia[&&NHX:TOL=126251],kolbesia[&&NHX:TOL=126252],lemnicola[&&NHX:TOL=126253],pauliella[&&NHX:TOL=126254],psammothidium[&&NHX:TOL=126255],rossithidium[&&NHX:TOL=126256],astartiella[&&NHX:TOL=126257],vikingea[&&NHX:TOL=126258])achnanthidiaceae[&&NHX:TOL=125718])nondisplacing monoraphids[&&NHX:TOL=125716])pyrenoplacatae[&&NHX:TOL=125708],phaeodactylum[&&NHX:TOL=125719],(amphora[&&NHX:TOL=125721],undatella[&&NHX:TOL=125728],thalassiophysa[&&NHX:TOL=125724],((entomoneis[&&NHX:TOL=125723],auricula[&&NHX:TOL=125726],(hydrosilicon[&&NHX:TOL=126261],petrodictyon[&&NHX:TOL=126262],plagiodiscus[&&NHX:TOL=126263],surirella[&&NHX:TOL=126264],campylodiscus[&&NHX:TOL=126265],cymatopleura[&&NHX:TOL=126266],stenopterobia[&&NHX:TOL=126267])surirellaceae[&&NHX:TOL=125727])surirellales[&&NHX:TOL=125722],(epithemia[&&NHX:TOL=126268],rhopalodia[&&NHX:TOL=126269],protokeelia[&&NHX:TOL=126270])rhopalodiaceae[&&NHX:TOL=125725])[&&NHX:TOL=125732])mutabilis clade[&&NHX:TOL=125720],mayamaea[&&NHX:TOL=125729],fistulifera[&&NHX:TOL=125730],krasskella[&&NHX:TOL=126310],rouxia[&&NHX:TOL=125731])bacillariophycidae[&&NHX:TOL=125327],nanoneis[&&NHX:TOL=129411])raphid diatoms[&&NHX:TOL=125307])[&&NHX:TOL=125305],(striatella[&&NHX:TOL=129365],pseudostriatella[&&NHX:TOL=129366])striatellaceae[&&NHX:TOL=125382],subsilicea[&&NHX:TOL=129410])bacillariophyceae[&&NHX:TOL=125298])bacillariophytina[&&NHX:TOL=125296])diatoms[&&NHX:TOL=21810])[&&NHX:TOL=142184],pelagophytes[&&NHX:TOL=142187])[&&NHX:TOL=142183],dictyophytes[&&NHX:TOL=142188])[&&NHX:TOL=142182],pinguiophytes[&&NHX:TOL=142189])[&&NHX:TOL=142181],((chrysomerophytes[&&NHX:TOL=142192],phaeophyceae[&&NHX:TOL=129402],(phaeothamnion[&&NHX:TOL=141579],(stichogloea[&&NHX:TOL=141581],phaeoschizochlamys[&&NHX:TOL=141582])[&&NHX:TOL=141580],chrysapion[&&NHX:TOL=141583],chrysoclonium[&&NHX:TOL=141584],chrysodictyon[&&NHX:TOL=141585],phaeobotrys[&&NHX:TOL=141586],phaeogloea[&&NHX:TOL=141587],sphaeridiothrix[&&NHX:TOL=141588],selenophaea[&&NHX:TOL=141589],tetrachrysis[&&NHX:TOL=141590],tetrapion[&&NHX:TOL=141591],tetrasporopsis[&&NHX:TOL=141592])phaeothamniophyceae[&&NHX:TOL=141578],xanthophytes[&&NHX:TOL=142194])[&&NHX:TOL=142191],raphidophytes[&&NHX:TOL=142195])[&&NHX:TOL=142190])[&&NHX:TOL=142180],(chrysophytes[&&NHX:TOL=142197],synurophytes[&&NHX:TOL=142198])[&&NHX:TOL=142196])[&&NHX:TOL=142179],eustigmatophytes[&&NHX:TOL=142199])[&&NHX:TOL=142178],oomycetes[&&NHX:TOL=21800])[&&NHX:TOL=142177],hypochytridiomycetes[&&NHX:TOL=21801])[&&NHX:TOL=142176],developayella[&&NHX:TOL=142200])[&&NHX:TOL=142175],((diplophrys[&&NHX:TOL=21793],((labyrinthula vitellina[&&NHX:TOL=130247],labyrinthula macrocystis[&&NHX:TOL=130248],labyrinthula cienkowskii[&&NHX:TOL=130249],labyrinthula valkanovii[&&NHX:TOL=130250],labyrinthula algeriensis[&&NHX:TOL=130251],labyrinthula roscoffensis[&&NHX:TOL=130252],labyrinthula coenocystis[&&NHX:TOL=130253],labyrinthula magnifica[&&NHX:TOL=130254],labyrinthula zosterae[&&NHX:TOL=130255])labyrinthula[&&NHX:TOL=103495],(aplanochytrium kerguelensis[&&NHX:TOL=130244],aplanochytrium yorkensis[&&NHX:TOL=130245],aplanochytrium minutum[&&NHX:TOL=130246])aplanochytrium[&&NHX:TOL=103496])labyrinthulids[&&NHX:TOL=21794])[&&NHX:TOL=21792],thraustochytrids[&&NHX:TOL=21795])labyrinthulomycetes[&&NHX:TOL=21791],opalinids[&&NHX:TOL=142201],blastocystis[&&NHX:TOL=142202],bicosoecids[&&NHX:TOL=142203])stramenopiles[&&NHX:TOL=2380])[&&NHX:TOL=136822])[&&NHX:TOL=136821],(haptophyta[&&NHX:TOL=2412],biliphytes[&&NHX:TOL=121508],telonema[&&NHX:TOL=2436],((((cryptomonas marssonii[&&NHX:TOL=97224],cryptomonas ovata[&&NHX:TOL=97228],((cryptomonas paramaecium[&&NHX:TOL=97229],cryptomonas borealis[&&NHX:TOL=97218])[&&NHX:TOL=128793],cryptomonas gyropyrenoidosa[&&NHX:TOL=97222],cryptomonas lundii[&&NHX:TOL=97223])[&&NHX:TOL=128792],(cryptomonas tetrapyrenoidosa[&&NHX:TOL=97234],cryptomonas pyrenoidifera[&&NHX:TOL=97231],cryptomonas curvata[&&NHX:TOL=97219])[&&NHX:TOL=128794],cryptomonas phaseolus[&&NHX:TOL=128795],((cryptomonas commutata[&&NHX:TOL=128798],(cryptomonas loricata[&&NHX:TOL=128800],photosynthetic cryptomonas strain m2504[&&NHX:TOL=128801],photosynthetic cryptomonas strain m2807[&&NHX:TOL=128802],colorless cryptomonas strain sag9772f[&&NHX:TOL=128803])[&&NHX:TOL=128799])[&&NHX:TOL=128797],cryptomonas obovoidea[&&NHX:TOL=128804],cryptomonas erosa[&&NHX:TOL=128805],photosynthetic cryptomonas strain m2089[&&NHX:TOL=128806],colorless cryptomonas strain m1634[&&NHX:TOL=128807])[&&NHX:TOL=128796])cryptomonas[&&NHX:TOL=97214],((hemiselmis cryptochromatica[&&NHX:TOL=128769],(hemiselmis virescens[&&NHX:TOL=128777],hemiselmis pacifica[&&NHX:TOL=128778])[&&NHX:TOL=128790],(hemiselmis andersenii[&&NHX:TOL=128779],hemiselmis rufescens[&&NHX:TOL=128780],hemiselmis tepida[&&NHX:TOL=128788],nameless strain utex2000[&&NHX:TOL=128782])[&&NHX:TOL=128791])hemiselmis[&&NHX:TOL=97239],(chroomonas[&&NHX:TOL=97212],komma[&&NHX:TOL=97240])chroomonas | komma[&&NHX:TOL=128542])[&&NHX:TOL=128539],((rhodomonas baltica[&&NHX:TOL=97245],rhodomonas lacustris[&&NHX:TOL=97246],rhodomonas maculata[&&NHX:TOL=97247],rhodomonas minuta[&&NHX:TOL=97248],rhodomonas ovalis[&&NHX:TOL=97249],rhodomonas rubra[&&NHX:TOL=97250],rhodomonas salina[&&NHX:TOL=97251],rhodomonas stigmatica[&&NHX:TOL=97252])rhodomonas[&&NHX:TOL=97244],rhinomonas[&&NHX:TOL=97243],storeatula[&&NHX:TOL=97253])rhodomonas | rhinomonas | storeatula[&&NHX:TOL=128540],(geminigera cryophila[&&NHX:TOL=97237],plagioselmis prolonga[&&NHX:TOL=97241],(teleaulax acuta[&&NHX:TOL=97255],teleaulax merimbula[&&NHX:TOL=97256])teleaulax[&&NHX:TOL=97254])geminigera | plagioselmis | teleaulax[&&NHX:TOL=128541],falcomonas daucoides[&&NHX:TOL=97236],proteomonas sulcata[&&NHX:TOL=128543],guillardia theta | hanusia phi[&&NHX:TOL=128688])cryptophytes plastidcontaining[&&NHX:TOL=128538],(goniomonas amphinema[&&NHX:TOL=97258],goniomonas pacifica[&&NHX:TOL=97259],goniomonas truncata[&&NHX:TOL=97260])goniomonas[&&NHX:TOL=97257],cryptomonads of uncertain placement[&&NHX:TOL=121368])cryptomonads[&&NHX:TOL=2396],((katablepharis[&&NHX:TOL=117724],(leucocryptos marina[&&NHX:TOL=117725],hatena arenicola[&&NHX:TOL=117723],platychilomonas psammobia[&&NHX:TOL=117726])[&&NHX:TOL=139617])[&&NHX:TOL=139616],roombia truncata[&&NHX:TOL=139612])katablepharids[&&NHX:TOL=2413])[&&NHX:TOL=124798],centroheliozoa[&&NHX:TOL=2389])hacrobia[&&NHX:TOL=124797])chromalveolates[&&NHX:TOL=121167],((malawimonas californiana[&&NHX:TOL=97417],malawimonas jakobiformis[&&NHX:TOL=97418])malawimonas[&&NHX:TOL=97416],((((((bodonida[&&NHX:TOL=98014],(blastocrithidia[&&NHX:TOL=98016],(crithidia fasciculata[&&NHX:TOL=98018],crithidia luciliae[&&NHX:TOL=98019])crithidia[&&NHX:TOL=98017],endotrypanum[&&NHX:TOL=98020],herpetomonas[&&NHX:TOL=98021],(leishmania donovani[&&NHX:TOL=98023],leishmania infantum[&&NHX:TOL=98024],leishmania major[&&NHX:TOL=98027],leishmania tropica[&&NHX:TOL=98028],leishmania mexicana[&&NHX:TOL=133920],leishmania tarentolae[&&NHX:TOL=125349],leishmania braziliensis[&&NHX:TOL=133921])leishmania[&&NHX:TOL=98022],(leptomonas[&&NHX:TOL=98029],wallaceina[&&NHX:TOL=98050])[&&NHX:TOL=125347],paleoleishmania proterus[&&NHX:TOL=98030],phytomonas[&&NHX:TOL=98031],sergeia[&&NHX:TOL=125350],rhynchoidomonas[&&NHX:TOL=98032],sauroleishmania[&&NHX:TOL=98033],(trypanosoma congolense[&&NHX:TOL=98036],trypanosoma cruzi[&&NHX:TOL=98037],trypanosoma devei[&&NHX:TOL=98038],trypanosoma minasense[&&NHX:TOL=98039],trypanosoma rangeli[&&NHX:TOL=98040],(trypanosoma brucei equiperdum[&&NHX:TOL=124921],trypanosoma brucei evansi[&&NHX:TOL=125351],trypanosoma brucei brucei[&&NHX:TOL=125352],trypanosoma brucei rhodesiense[&&NHX:TOL=125353],trypanosoma brucei gambiense[&&NHX:TOL=125354])trypanosoma brucei[&&NHX:TOL=124922],trypanosoma carassii[&&NHX:TOL=125355],trypanosoma rotatorium[&&NHX:TOL=125356],trypanosoma theileri[&&NHX:TOL=133922],trypanosoma melophagium[&&NHX:TOL=133923])trypanosoma[&&NHX:TOL=98034],agamomonas[&&NHX:TOL=98043],cercoplasma[&&NHX:TOL=98044],cystotrypanosoma[&&NHX:TOL=98045],lamellasoma[&&NHX:TOL=98046],pyramidomonas[&&NHX:TOL=98047],strigomonas[&&NHX:TOL=98048],trypanopsis[&&NHX:TOL=98049])trypanosomatida[&&NHX:TOL=98015])[&&NHX:TOL=125664],((perkinsiella amoebae[&&NHX:TOL=98011],ichthyobodo necator[&&NHX:TOL=125348])[&&NHX:TOL=125665],bordnamonas tropicana[&&NHX:TOL=98010],trypanoplasmoides[&&NHX:TOL=98053],cryptoicus[&&NHX:TOL=98052])prokinetoplastina[&&NHX:TOL=125663])kinetoplastida[&&NHX:TOL=98013],diplonemida[&&NHX:TOL=97450])[&&NHX:TOL=124814],(((petalomonas abscissa[&&NHX:TOL=126833],petalomonas acuminata[&&NHX:TOL=126834],petalomonas alata[&&NHX:TOL=126835],petalomonas aliformis[&&NHX:TOL=126836],petalomonas angusta[&&NHX:TOL=126837],petalomonas applanata[&&NHX:TOL=126838],petalomonas arcuata[&&NHX:TOL=126839],petalomonas asymmetrica[&&NHX:TOL=126840],petalomonas bicarinata[&&NHX:TOL=126841],petalomonas boadicea[&&NHX:TOL=126842],petalomonas brevicauda[&&NHX:TOL=126843],petalomonas cantuscygni[&&NHX:TOL=126844],petalomonas carinata[&&NHX:TOL=126845],petalomonas coxydensis[&&NHX:TOL=126846],petalomonas curvata[&&NHX:TOL=126847],petalomonas disomata[&&NHX:TOL=126848],petalomonas dorsalis[&&NHX:TOL=126849],petalomonas dubosqui[&&NHX:TOL=126850],petalomonas excavata[&&NHX:TOL=126851],petalomonas gigas[&&NHX:TOL=126852],petalomonas hubei[&&NHX:TOL=126853],petalomonas inflexa[&&NHX:TOL=126854],petalomonas intortus[&&NHX:TOL=126855],petalomonas involuta[&&NHX:TOL=126856],petalomonas irregularis[&&NHX:TOL=126857],petalomonas iugosus[&&NHX:TOL=126858],petalomonas klinostoma[&&NHX:TOL=126859],petalomonas labrum[&&NHX:TOL=126860],petalomonas marginalis[&&NHX:TOL=126861],petalomonas marina[&&NHX:TOL=126862],petalomonas mediocanellata[&&NHX:TOL=126863],petalomonas micra[&&NHX:TOL=126864],petalomonas minor[&&NHX:TOL=126865],petalomonas minuta[&&NHX:TOL=126866],petalomonas minutula[&&NHX:TOL=126867],petalomonas minutus[&&NHX:TOL=126868],petalomonas mira[&&NHX:TOL=126869],petalomonas obliquisulcus[&&NHX:TOL=126870],petalomonas oranata[&&NHX:TOL=126871],petalomonas ornata[&&NHX:TOL=126872],petalomonas phacoides[&&NHX:TOL=126873],petalomonas planus[&&NHX:TOL=126874],petalomonas platyrhyncha[&&NHX:TOL=126875],petalomonas pleurosigma[&&NHX:TOL=126876],petalomonas poosilla[&&NHX:TOL=126877],petalomonas praegnans[&&NHX:TOL=126878],petalomonas prototheca[&&NHX:TOL=126879],petalomonas punctatostriata[&&NHX:TOL=126880],petalomonas pusilla[&&NHX:TOL=126881],petalomonas quadrilineata[&&NHX:TOL=126882],petalomonas quinquecarinata[&&NHX:TOL=126883],petalomonas quinquemarginata[&&NHX:TOL=126884],petalomonas raiula[&&NHX:TOL=126885],petalomonas septemcarinata[&&NHX:TOL=126886],petalomonas sexlobata[&&NHX:TOL=126887],petalomonas sinica[&&NHX:TOL=126888],petalomonas sinuata[&&NHX:TOL=126889],petalomonas spinifera[&&NHX:TOL=126890],petalomonas splendens[&&NHX:TOL=126891],petalomonas steinii[&&NHX:TOL=126892],petalomonas sulcata[&&NHX:TOL=126893],petalomonas tibetica[&&NHX:TOL=126894],petalomonas triangula[&&NHX:TOL=126895],petalomonas tricarinata[&&NHX:TOL=126896],petalomonas triquetra[&&NHX:TOL=126897],petalomonas ventritracta[&&NHX:TOL=126898],petalomonas virgatus[&&NHX:TOL=126899],petalomonas vulgaris[&&NHX:TOL=126900],petalomonas wuhanica[&&NHX:TOL=126901])petalomonas[&&NHX:TOL=126396],(notosolenus adamas[&&NHX:TOL=97950],notosolenus adamus[&&NHX:TOL=97951],notosolenus alatellus[&&NHX:TOL=97952],notosolenus amadas[&&NHX:TOL=97953],notosolenus apocamptus[&&NHX:TOL=97954],notosolenus brothernis[&&NHX:TOL=97955],notosolenus canellatus[&&NHX:TOL=97956],notosolenus cashew[&&NHX:TOL=97957],notosolenus chelonides[&&NHX:TOL=97958],notosolenus esulcis[&&NHX:TOL=97959],notosolenus hemicircularis[&&NHX:TOL=97960],notosolenus lagenos[&&NHX:TOL=97961],notosolenus lashue[&&NHX:TOL=97962],notosolenus mediocanellata[&&NHX:TOL=97963],notosolenus navicula[&&NHX:TOL=97964],notosolenus nitidus[&&NHX:TOL=97965],notosolenus obliquus[&&NHX:TOL=97966],notosolenus orbicularis[&&NHX:TOL=97967],notosolenus ostium[&&NHX:TOL=97968],notosolenus papilio[&&NHX:TOL=97969],notosolenus pentagonus[&&NHX:TOL=97970],notosolenus pyriforme[&&NHX:TOL=97971],notosolenus rhombicus[&&NHX:TOL=97972],notosolenus scutulum[&&NHX:TOL=97973],notosolenus similis[&&NHX:TOL=97974],notosolenus skujai[&&NHX:TOL=97975],notosolenus steinii[&&NHX:TOL=97976],notosolenus stenoschismus[&&NHX:TOL=97977],notosolenus tamanduensis[&&NHX:TOL=97978],notosolenus triangularis[&&NHX:TOL=97979],notosolenus urceolatus[&&NHX:TOL=97980])notosolenus[&&NHX:TOL=97949])[&&NHX:TOL=126392],calycimonas physaloides[&&NHX:TOL=97936],(dylakosoma pelophilum[&&NHX:TOL=97939],dylakosoma symbionticum[&&NHX:TOL=97940])dylakosoma[&&NHX:TOL=97938],((entosiphon caudata[&&NHX:TOL=97808],entosiphon cuneatiformis[&&NHX:TOL=97809],entosiphon cuneatum[&&NHX:TOL=97810],entosiphon limenites[&&NHX:TOL=97811],entosiphon liminites[&&NHX:TOL=97812],entosiphon ovatus[&&NHX:TOL=97813],entosiphon sulcatum[&&NHX:TOL=97814])entosiphon[&&NHX:TOL=97807],((ploeotia adhaerens[&&NHX:TOL=97853],ploeotia azurina[&&NHX:TOL=97854],ploeotia corrugata[&&NHX:TOL=97855],ploeotia costata[&&NHX:TOL=97856],ploeotia decipiens[&&NHX:TOL=97857],ploeotia discoides[&&NHX:TOL=97858],ploeotia heracleum[&&NHX:TOL=97859],ploeotia laminae[&&NHX:TOL=97860],ploeotia longifilum[&&NHX:TOL=97861],ploeotia obliquum[&&NHX:TOL=97862],ploeotia oblonga[&&NHX:TOL=97863],ploeotia planum[&&NHX:TOL=97864],ploeotia plumosa[&&NHX:TOL=97865],ploeotia pseudanisonema[&&NHX:TOL=97866],ploeotia punctata[&&NHX:TOL=97867],ploeotia robusta[&&NHX:TOL=97868],ploeotia scrobiculata[&&NHX:TOL=97869],ploeotia tasmanica[&&NHX:TOL=97870],ploeotia tenuis[&&NHX:TOL=97871],ploeotia vitrea[&&NHX:TOL=97872])ploeotia[&&NHX:TOL=97852],lentomonas applanatum[&&NHX:TOL=97842])[&&NHX:TOL=126463],((dinema australiense[&&NHX:TOL=97793],dinema dimorphum[&&NHX:TOL=97794],dinema griseolum[&&NHX:TOL=97795],dinema inaequale[&&NHX:TOL=97796],dinema litorale[&&NHX:TOL=97797],dinema maculata[&&NHX:TOL=97798],dinema maculatum[&&NHX:TOL=97799],dinema picta[&&NHX:TOL=97800],dinema platysomum[&&NHX:TOL=97801],dinema rostratum[&&NHX:TOL=97802],dinema rotundum[&&NHX:TOL=97803],dinema valida[&&NHX:TOL=97804],dinema validum[&&NHX:TOL=97805],dinema zabra[&&NHX:TOL=97806])dinema[&&NHX:TOL=97792],(metanema mia[&&NHX:TOL=97945],metanema sedatum[&&NHX:TOL=97946],metanema strenuum[&&NHX:TOL=97947],metanema variabile[&&NHX:TOL=97948])metanema[&&NHX:TOL=97944],(anisonema acinus[&&NHX:TOL=97914],anisonema decacista[&&NHX:TOL=97915],anisonema decacostata[&&NHX:TOL=97916],anisonema dexiotaxum[&&NHX:TOL=97917],anisonema elliptica[&&NHX:TOL=97918],anisonema emarginatum[&&NHX:TOL=97919],anisonema glaciale[&&NHX:TOL=97920],anisonema grande[&&NHX:TOL=97921],anisonema hexagonum[&&NHX:TOL=97922],anisonema intermedium[&&NHX:TOL=97923],anisonema lineata[&&NHX:TOL=97924],anisonema marinus[&&NHX:TOL=97925],anisonema multicostatum[&&NHX:TOL=97926],anisonema orbiculatum[&&NHX:TOL=97927],anisonema ovale[&&NHX:TOL=97928],anisonema picta[&&NHX:TOL=97929],anisonema prosgeobium[&&NHX:TOL=97930],anisonema pusillum[&&NHX:TOL=97931],anisonema quadricostatum[&&NHX:TOL=97932],anisonema striata[&&NHX:TOL=97933],anisonema trepidum[&&NHX:TOL=97934])anisonema[&&NHX:TOL=97913],((distigma curvatum[&&NHX:TOL=97464],distigma gracilis[&&NHX:TOL=97465],distigma proteus[&&NHX:TOL=97466],distigma senni[&&NHX:TOL=97467],distigma sennii[&&NHX:TOL=97468],distigma urceolaris[&&NHX:TOL=97469])distigma[&&NHX:TOL=97463],distigmopsis[&&NHX:TOL=126410],((astasia bodo[&&NHX:TOL=97477],astasia contorta[&&NHX:TOL=97478],astasia curta[&&NHX:TOL=97479],astasia curvata[&&NHX:TOL=97480],astasia gomphonema[&&NHX:TOL=97481],astasia granulata[&&NHX:TOL=97482],astasia guttula[&&NHX:TOL=97483],astasia harrisii[&&NHX:TOL=97484],astasia klebsii[&&NHX:TOL=97485],astasia lagenula[&&NHX:TOL=97486],astasia maragaritifera[&&NHX:TOL=97488],astasia ocellata[&&NHX:TOL=97489],astasia parvula[&&NHX:TOL=97490],astasia sagittifera[&&NHX:TOL=97491],astasia tenax[&&NHX:TOL=97492])astasia[&&NHX:TOL=97476],((rhabdomonas costata[&&NHX:TOL=97905],rhabdomonas incurva[&&NHX:TOL=97906],rhabdomonas intermedia[&&NHX:TOL=97907],rhabdomonas minima[&&NHX:TOL=97908],rhabdomonas mirabilis[&&NHX:TOL=97909],rhabdomonas spiralis[&&NHX:TOL=97910])rhabdomonas[&&NHX:TOL=97904],rhabdospira[&&NHX:TOL=126415],(menoidium acutissimum[&&NHX:TOL=97887],menoidium astasia[&&NHX:TOL=97888],menoidium bibacillatum[&&NHX:TOL=97889],menoidium cultellus[&&NHX:TOL=97890],menoidium falcatum[&&NHX:TOL=97891],menoidium gladius[&&NHX:TOL=97892],menoidium gracile[&&NHX:TOL=97893],menoidium incurvum[&&NHX:TOL=97894],menoidium inflatum[&&NHX:TOL=97895],menoidium intermedium[&&NHX:TOL=97896],menoidium minimum[&&NHX:TOL=97897],menoidium obtusum[&&NHX:TOL=97898],menoidium pellucidum[&&NHX:TOL=97899],menoidium tortuosum[&&NHX:TOL=97903])menoidium[&&NHX:TOL=97886],parmidium circulare[&&NHX:TOL=98003],(gyropaigne kosmos[&&NHX:TOL=126902],gyropaigne lefevrei[&&NHX:TOL=126903],gyropaigne spiralis[&&NHX:TOL=126904])gyropaigne[&&NHX:TOL=97885],helikotropsis[&&NHX:TOL=126419])rhabdomonadidae[&&NHX:TOL=126413])[&&NHX:TOL=126411])[&&NHX:TOL=126408],dinematomonas[&&NHX:TOL=126420],(heteronema acus[&&NHX:TOL=97816],heteronema acutissimum[&&NHX:TOL=97817],heteronema cryptocercum[&&NHX:TOL=97818],heteronema discomorphum[&&NHX:TOL=97819],heteronema exaratum[&&NHX:TOL=97820],heteronema globuliferum[&&NHX:TOL=97821],heteronema hexagonum[&&NHX:TOL=97822],heteronema larseni[&&NHX:TOL=97823],heteronema leptosomum[&&NHX:TOL=97824],heteronema marina[&&NHX:TOL=97825],heteronema ovale[&&NHX:TOL=97826],heteronema polymorphum[&&NHX:TOL=97827],heteronema pterbica[&&NHX:TOL=97828],heteronema scaphurum[&&NHX:TOL=97829],heteronema splendens[&&NHX:TOL=97830],heteronema tortum[&&NHX:TOL=97831],heteronema trotum[&&NHX:TOL=97832],heteronema variabile[&&NHX:TOL=97833],heteronema vittatum[&&NHX:TOL=97834])heteronema[&&NHX:TOL=97815],((peranema anorexia[&&NHX:TOL=97844],peranema asperum[&&NHX:TOL=97845],peranema cuneatum[&&NHX:TOL=97846],peranema deflexum[&&NHX:TOL=97847],peranema dolichonema[&&NHX:TOL=97848],peranema inflexum[&&NHX:TOL=97849],peranema pleururum[&&NHX:TOL=97850],peranema trichophorum[&&NHX:TOL=97851])peranema[&&NHX:TOL=97843],(jenningsia deflexum[&&NHX:TOL=97836],jenningsia fusiforme[&&NHX:TOL=97837],jenningsia granulifera[&&NHX:TOL=97838],jenningsia kupfferi[&&NHX:TOL=97839],jenningsia macrostoma[&&NHX:TOL=97840],jenningsia striata[&&NHX:TOL=97841])jenningsia[&&NHX:TOL=97835],chasmostoma nieuportense[&&NHX:TOL=97791],(urceolus alenizini[&&NHX:TOL=97874],urceolus cornutus[&&NHX:TOL=97875],urceolus costata[&&NHX:TOL=97876],urceolus costatus[&&NHX:TOL=97877],urceolus cristatus[&&NHX:TOL=97878],urceolus cyclostomus[&&NHX:TOL=97879],urceolus macromastix[&&NHX:TOL=97880],urceolus pascheri[&&NHX:TOL=97881],urceolus sabulosa[&&NHX:TOL=97882],urceolus sabulosus[&&NHX:TOL=97883])urceolus[&&NHX:TOL=97873],(((eutreptia pertyi[&&NHX:TOL=97782],eutreptia viridis[&&NHX:TOL=97783])eutreptia[&&NHX:TOL=97781],(eutreptiella eupharyngia[&&NHX:TOL=97785],eutreptiella marina[&&NHX:TOL=97786],eutreptiella pomquetensis[&&NHX:TOL=97787],eutreptiella viridis[&&NHX:TOL=97788])eutreptiella[&&NHX:TOL=97784])eutreptiales[&&NHX:TOL=126428],tetreutreptia[&&NHX:TOL=126431],(euglenomorpha[&&NHX:TOL=126433],hegneria[&&NHX:TOL=126457])[&&NHX:TOL=126432],((euglena spadix[&&NHX:TOL=97506],euglena acutata[&&NHX:TOL=97507],euglena acutissima[&&NHX:TOL=97508],euglena adhaerens[&&NHX:TOL=97512],euglena agilis[&&NHX:TOL=97513],euglena alata[&&NHX:TOL=97514],euglena allorgei[&&NHX:TOL=97515],euglena ambylophis[&&NHX:TOL=97518],euglena americana[&&NHX:TOL=97519],euglena amphipyrenica[&&NHX:TOL=97520],euglena anabaena[&&NHX:TOL=97521],euglena angusta[&&NHX:TOL=97524],euglena antefossa[&&NHX:TOL=97525],euglena archaeoplastidata[&&NHX:TOL=97526],euglena archaeoviridis[&&NHX:TOL=97527],euglena aumuelleri[&&NHX:TOL=97528],euglena australica[&&NHX:TOL=97529],euglena bacillaris[&&NHX:TOL=97532],euglena bacilliformis[&&NHX:TOL=97533],euglena bellovacensis[&&NHX:TOL=97534],euglena bichloris[&&NHX:TOL=97535],euglena bivittata[&&NHX:TOL=97536],euglena breviflagellum[&&NHX:TOL=97537],euglena bucharica[&&NHX:TOL=97538],euglena carteriae[&&NHX:TOL=97539],euglena caudata[&&NHX:TOL=97540],euglena ceniculata[&&NHX:TOL=97541],euglena centralis[&&NHX:TOL=97542],euglena chadefaudii[&&NHX:TOL=97544],euglena chamberlini[&&NHX:TOL=97545],euglena charkowiensis[&&NHX:TOL=97546],euglena chlamydophora[&&NHX:TOL=97547],euglena chloropheonicea[&&NHX:TOL=97548],euglena choretes[&&NHX:TOL=97549],euglena cingula[&&NHX:TOL=97550],euglena clara[&&NHX:TOL=97551],euglena clavata[&&NHX:TOL=97552],euglena convoluta[&&NHX:TOL=97553],euglena copula[&&NHX:TOL=97554],euglena curta[&&NHX:TOL=97555],euglena cyclopicola[&&NHX:TOL=97556],euglena cylindrica[&&NHX:TOL=97557],euglena deses[&&NHX:TOL=97558],euglena detonii[&&NHX:TOL=97562],euglena diagrana[&&NHX:TOL=97563],euglena dicentra[&&NHX:TOL=97564],euglena ehrenbergii[&&NHX:TOL=97565],euglena elastica[&&NHX:TOL=97566],euglena elenkinii[&&NHX:TOL=97567],euglena elongata[&&NHX:TOL=97568],euglena ettlii[&&NHX:TOL=97569],euglena excavata[&&NHX:TOL=97570],euglena exilis[&&NHX:TOL=97571],euglena fenestrata[&&NHX:TOL=97572],euglena flava[&&NHX:TOL=97573],euglena fronsundulata[&&NHX:TOL=97574],euglena fundoversata[&&NHX:TOL=97575],euglena fusiformis[&&NHX:TOL=97577],euglena gasterosteus[&&NHX:TOL=97578],euglena gaumei[&&NHX:TOL=97579],euglena geniculata[&&NHX:TOL=97580],euglena gibbosa[&&NHX:TOL=97583],euglena gracilis[&&NHX:TOL=97585],euglena granulata[&&NHX:TOL=97586],euglena grisoli[&&NHX:TOL=97587],euglena guttula[&&NHX:TOL=97588],euglena gymnodinioides[&&NHX:TOL=97591],euglena haematodes[&&NHX:TOL=97592],euglena heimii[&&NHX:TOL=97593],euglena heliorubescens[&&NHX:TOL=97595],euglena hemichromata[&&NHX:TOL=97596],euglena hemipellucida[&&NHX:TOL=97597],euglena hiemalis[&&NHX:TOL=97598],euglena hirudo[&&NHX:TOL=97599],euglena ignobilis[&&NHX:TOL=97600],euglena incisa[&&NHX:TOL=97601],euglena incurva[&&NHX:TOL=97602],euglena intermedia[&&NHX:TOL=97603],euglena interrupta[&&NHX:TOL=97607],euglena jirovecii[&&NHX:TOL=97608],euglena laciniata[&&NHX:TOL=97609],euglena lata[&&NHX:TOL=97610],euglena longa[&&NHX:TOL=97615],euglena longicaudata[&&NHX:TOL=97616],euglena lucens[&&NHX:TOL=97617],euglena mainxii[&&NHX:TOL=97618],euglena mangini[&&NHX:TOL=97619],euglena megalithus[&&NHX:TOL=97620],euglena mesnili[&&NHX:TOL=97621],euglena minima[&&NHX:TOL=97622],euglena minor[&&NHX:TOL=97623],euglena minuta[&&NHX:TOL=97624],euglena mucifera[&&NHX:TOL=97625],euglena multiformis[&&NHX:TOL=97626],euglena mutabilis[&&NHX:TOL=97627],euglena nana[&&NHX:TOL=97630],euglena navicula[&&NHX:TOL=97631],euglena neustonica[&&NHX:TOL=97632],euglena oblonga[&&NHX:TOL=97633],euglena obtusa[&&NHX:TOL=97634],euglena obtusocaudata[&&NHX:TOL=97635],euglena olivacea[&&NHX:TOL=97636],euglena orientalis[&&NHX:TOL=97637],euglena oxyuropsis[&&NHX:TOL=97644],euglena paludosa[&&NHX:TOL=97645],euglena pascheri[&&NHX:TOL=97646],euglena phacoides[&&NHX:TOL=97647],euglena pisciformis[&&NHX:TOL=97648],euglena platydesma[&&NHX:TOL=97653],euglena polymorpha[&&NHX:TOL=97654],euglena pringsheimii[&&NHX:TOL=97655],euglena proxima[&&NHX:TOL=97656],euglena pseudocentralis[&&NHX:TOL=97657],euglena pseudoehrenbergii[&&NHX:TOL=97658],euglena pseudospirogyra[&&NHX:TOL=97659],euglena pseudospiroides[&&NHX:TOL=97660],euglena pseudotuba[&&NHX:TOL=97661],euglena pseudoviridis[&&NHX:TOL=97662],euglena pseudoxyuris[&&NHX:TOL=97663],euglena purpurea[&&NHX:TOL=97664],euglena pusilla[&&NHX:TOL=97665],euglena quartana[&&NHX:TOL=97666],euglena refringens[&&NHX:TOL=97667],euglena repulsans[&&NHX:TOL=97668],euglena retronata[&&NHX:TOL=97669],euglena ribra[&&NHX:TOL=97670],euglena rostrata[&&NHX:TOL=97671],euglena rostrifera[&&NHX:TOL=97672],euglena rubida[&&NHX:TOL=97673],euglena rubra[&&NHX:TOL=97674],euglena rustica[&&NHX:TOL=97675],euglena sacculiformis[&&NHX:TOL=97676],euglena salina[&&NHX:TOL=97677],euglena sanguinea[&&NHX:TOL=97678],euglena satelles[&&NHX:TOL=97679],euglena schmitzii[&&NHX:TOL=97680],euglena sciotensis[&&NHX:TOL=97681],euglena sima[&&NHX:TOL=97682],euglena simulacra[&&NHX:TOL=97683],euglena smulkowskiana[&&NHX:TOL=97684],euglena sociabilis[&&NHX:TOL=97685],euglena spiroides[&&NHX:TOL=97698],euglena splendens[&&NHX:TOL=97699],euglena srinagari[&&NHX:TOL=97700],euglena stellata[&&NHX:TOL=97701],euglena subehrenbergii[&&NHX:TOL=97702],euglena subthinophila[&&NHX:TOL=97703],euglena swirenkoi[&&NHX:TOL=97704],euglena synchlora[&&NHX:TOL=97705],euglena szorgiensis[&&NHX:TOL=97706],euglena tatrica[&&NHX:TOL=97707],euglena tentans[&&NHX:TOL=97708],euglena terricola[&&NHX:TOL=97709],euglena texta[&&NHX:TOL=97710],euglena thinophila[&&NHX:TOL=97714],euglena tiszae[&&NHX:TOL=97715],euglena torta[&&NHX:TOL=97716],euglena tortilis[&&NHX:TOL=97717],euglena tristella[&&NHX:TOL=97722],euglena trisulcata[&&NHX:TOL=97723],euglena truncata[&&NHX:TOL=97724],euglena tuba[&&NHX:TOL=97725],euglena tuberculata[&&NHX:TOL=97726],euglena univittata[&&NHX:TOL=97727],euglena vagans[&&NHX:TOL=97728],euglena vaginicola[&&NHX:TOL=97729],euglena vangoori[&&NHX:TOL=97730],euglena variabilis[&&NHX:TOL=97731],euglena velata[&&NHX:TOL=97732],euglena vermicularis[&&NHX:TOL=97733],euglena vermiformis[&&NHX:TOL=97734],euglena viridis[&&NHX:TOL=97735],euglena vivida[&&NHX:TOL=97745],euglena walnei[&&NHX:TOL=97746],euglena wangi[&&NHX:TOL=97747],euglena acutecaudata[&&NHX:TOL=97751],euglena breviflagellata[&&NHX:TOL=97752])euglena[&&NHX:TOL=97505],((colacium arbuscula[&&NHX:TOL=97494],colacium arcuatum[&&NHX:TOL=97495],colacium elongatum[&&NHX:TOL=97496],colacium ovale[&&NHX:TOL=97497],colacium vesiculosum[&&NHX:TOL=97498])colacium[&&NHX:TOL=97493],(ascoglena amphoroides[&&NHX:TOL=126905],ascoglena vaginicola[&&NHX:TOL=126906])ascoglena[&&NHX:TOL=126442],klebsiella[&&NHX:TOL=126443],((trachelomonas abrupta[&&NHX:TOL=126907],trachelomonas acanthophora[&&NHX:TOL=126908],trachelomonas acanthostoma[&&NHX:TOL=126909],trachelomonas aculeata[&&NHX:TOL=126910],trachelomonas acuminata[&&NHX:TOL=126911],trachelomonas acuta[&&NHX:TOL=126912],trachelomonas aegyptiaca[&&NHX:TOL=126913],trachelomonas affinis[&&NHX:TOL=126914],trachelomonas africana[&&NHX:TOL=126915],trachelomonas alata[&&NHX:TOL=126916],trachelomonas alisoviana[&&NHX:TOL=126917],trachelomonas allia[&&NHX:TOL=126918],trachelomonas allorgei[&&NHX:TOL=126919],trachelomonas amazonensis[&&NHX:TOL=126920],trachelomonas americana[&&NHX:TOL=126921],trachelomonas amphora[&&NHX:TOL=126922],trachelomonas amphoriformis[&&NHX:TOL=126923],trachelomonas ampulliformis[&&NHX:TOL=126924],trachelomonas ampullula[&&NHX:TOL=126925],trachelomonas angustata[&&NHX:TOL=126926],trachelomonas angusteovata[&&NHX:TOL=126927],trachelomonas angustispina[&&NHX:TOL=126928],trachelomonas anulifera[&&NHX:TOL=126929],trachelomonas apiata[&&NHX:TOL=126930],trachelomonas argentinensis[&&NHX:TOL=126931],trachelomonas armata[&&NHX:TOL=126932],trachelomonas arnoldiana[&&NHX:TOL=126933],trachelomonas adiatica[&&NHX:TOL=126934],trachelomonas aspera[&&NHX:TOL=126935],trachelomonas atomaria[&&NHX:TOL=126936],trachelomonas australica[&&NHX:TOL=126937],trachelomonas australis[&&NHX:TOL=126938],trachelomonas avinata[&&NHX:TOL=126939],trachelomonas bacillifera[&&NHX:TOL=126940],trachelomonas baikovii[&&NHX:TOL=126941],trachelomonas balechii[&&NHX:TOL=126942],trachelomonas banatica[&&NHX:TOL=126943],trachelomonas bernardi[&&NHX:TOL=126944],trachelomonas bernardinensis[&&NHX:TOL=126945],trachelomonas bidentata[&&NHX:TOL=126946],trachelomonas bituricensis[&&NHX:TOL=126947],trachelomonas bonariensis[&&NHX:TOL=126948],trachelomonas bonnieri[&&NHX:TOL=126949],trachelomonas borodiniana[&&NHX:TOL=126950],trachelomonas borystheniensis[&&NHX:TOL=126951],trachelomonas botanica[&&NHX:TOL=126952],trachelomonas boyeri[&&NHX:TOL=126953],trachelomonas bucharica[&&NHX:TOL=126954],trachelomonas bulla[&&NHX:TOL=126955],trachelomonas cactacea[&&NHX:TOL=126956],trachelomonas calva[&&NHX:TOL=126957],trachelomonas castrensis[&&NHX:TOL=126958],trachelomonas caudata[&&NHX:TOL=126959],trachelomonas cervicula[&&NHX:TOL=126960],trachelomonas charkowiensis[&&NHX:TOL=126961],trachelomonas chinensis[&&NHX:TOL=126962],trachelomonas chlamydophora[&&NHX:TOL=126963],trachelomonas chodati[&&NHX:TOL=126964],trachelomonas cingulata[&&NHX:TOL=126965],trachelomonas cinkotaensis[&&NHX:TOL=126966],trachelomonas circulifera[&&NHX:TOL=126967],trachelomonas citifromis[&&NHX:TOL=126968],trachelomonas clavata[&&NHX:TOL=126969],trachelomonas cliffordii[&&NHX:TOL=126970],trachelomonas columba[&&NHX:TOL=126971],trachelomonas compacta[&&NHX:TOL=126972],trachelomonas congolense[&&NHX:TOL=126973],trachelomonas conica[&&NHX:TOL=126974],trachelomonas conkataensis[&&NHX:TOL=126975],trachelomonas conradi[&&NHX:TOL=126976],trachelomonas conradiana[&&NHX:TOL=126977],trachelomonas conspersa[&&NHX:TOL=126978],trachelomonas cordata[&&NHX:TOL=126979],trachelomonas coronata[&&NHX:TOL=126980],trachelomonas coronetta[&&NHX:TOL=126981],trachelomonas coroniformis[&&NHX:TOL=126982],trachelomonas crassata[&&NHX:TOL=126983],trachelomonas crassitheca[&&NHX:TOL=126984],trachelomonas crebea[&&NHX:TOL=126985],trachelomonas crenulatocollis[&&NHX:TOL=126986],trachelomonas cribrum[&&NHX:TOL=126987],trachelomonas crispa[&&NHX:TOL=126988],trachelomonas cucurbita[&&NHX:TOL=126989],trachelomonas cuneata[&&NHX:TOL=126990],trachelomonas cupula[&&NHX:TOL=126991],trachelomonas curta[&&NHX:TOL=126992],trachelomonas cylindrica[&&NHX:TOL=126993],trachelomonas dangeardi[&&NHX:TOL=126994],trachelomonas dangeardiana[&&NHX:TOL=126995],trachelomonas dastuguei[&&NHX:TOL=126996],trachelomonas debruyneii[&&NHX:TOL=126997],trachelomonas decora[&&NHX:TOL=126998],trachelomonas decorate[&&NHX:TOL=126999],trachelomonas deflandrei[&&NHX:TOL=127000],trachelomonas denisii[&&NHX:TOL=127001],trachelomonas depressa[&&NHX:TOL=127002],trachelomonas derephora[&&NHX:TOL=127003],trachelomonas dewildemanii[&&NHX:TOL=127004],trachelomonas dictyophora[&&NHX:TOL=127005],trachelomonas diploperlata[&&NHX:TOL=127006],trachelomonas drangeardiana[&&NHX:TOL=127007],trachelomonas drezepolski[&&NHX:TOL=127008],trachelomonas drezepolskiana[&&NHX:TOL=127009],trachelomonas dubia[&&NHX:TOL=127010],trachelomonas duplex[&&NHX:TOL=127011],trachelomonas dybowskii[&&NHX:TOL=127012],trachelomonas echinata[&&NHX:TOL=127013],trachelomonas echinoides[&&NHX:TOL=127014],trachelomonas elegans[&&NHX:TOL=127015],trachelomonas elegantissima[&&NHX:TOL=127016],trachelomonas ellipsoidalis[&&NHX:TOL=127017],trachelomonas elliptica[&&NHX:TOL=127018],trachelomonas elongata[&&NHX:TOL=127019],trachelomonas ensifera[&&NHX:TOL=127020],trachelomoas erinacea[&&NHX:TOL=127021],trachelomonas euchlora[&&NHX:TOL=127022],trachelomonas eurystoma[&&NHX:TOL=127023],trachelomonas felix[&&NHX:TOL=127024],trachelomonas flava[&&NHX:TOL=127025],trachelomonas flexicollis[&&NHX:TOL=127026],trachelomonas fluviatile[&&NHX:TOL=127027],trachelomonas flubiatilis[&&NHX:TOL=127028],trachelomonas foliolata[&&NHX:TOL=127029],trachelomonas formosa[&&NHX:TOL=127030],trachelomonas fortii[&&NHX:TOL=127031],trachelomonas fossa[&&NHX:TOL=127032],trachelomonas fragaria[&&NHX:TOL=127033],trachelomonas fukiensis[&&NHX:TOL=127034],trachelomonas furcata[&&NHX:TOL=127035],trachelomonas fusiformis[&&NHX:TOL=127036],trachelomonas gibberosa[&&NHX:TOL=127037],trachelomonas gicklhorni[&&NHX:TOL=127038],trachelomonas gilingensis[&&NHX:TOL=127039],trachelomonas girardiana[&&NHX:TOL=127040],trachelomonas glabra[&&NHX:TOL=127041],trachelomonas globularis[&&NHX:TOL=127042],trachelomonas goossensii[&&NHX:TOL=127043],trachelomonas gracilicostata[&&NHX:TOL=127044],trachelomonas gracilis[&&NHX:TOL=127045],trachelomonas gracillima[&&NHX:TOL=127046],trachelomonas grandis[&&NHX:TOL=127047],trachelomonas granulata[&&NHX:TOL=127048],trachelomonas granulatopsis[&&NHX:TOL=127049],trachelomonas granulosa[&&NHX:TOL=127050],trachelomonas gregussii[&&NHX:TOL=127051],trachelomonas guttata[&&NHX:TOL=127052],trachelomonas hamelii[&&NHX:TOL=127053],trachelomonas heduma[&&NHX:TOL=127054],trachelomonas helix[&&NHX:TOL=127055],trachelomonas helvetica[&&NHX:TOL=127056],trachelomonas hemisphaerica[&&NHX:TOL=127057],trachelomonas hesperia[&&NHX:TOL=127058],trachelomonas heterospina[&&NHX:TOL=127059],trachelomonas hexagona[&&NHX:TOL=127060],trachelomonas hexangulata[&&NHX:TOL=127061],trachelomonas hirta[&&NHX:TOL=127062],trachelomonas hispida[&&NHX:TOL=127063],trachelomonas hohuensis[&&NHX:TOL=127064],trachelomonas horrida[&&NHX:TOL=127065],trachelomonas hungarica[&&NHX:TOL=127066],trachelomonas hyalina[&&NHX:TOL=127067],trachelomonas hystrix[&&NHX:TOL=127068],trachelomonas incerta[&&NHX:TOL=127069],trachelomonas incertissima[&&NHX:TOL=127070],trachelomonas inconstans[&&NHX:TOL=127071],trachelomonas indica[&&NHX:TOL=127072],trachelomonas inflata[&&NHX:TOL=127073],trachelomonsa infundibularis[&&NHX:TOL=127074],trachelomonas infundibulum[&&NHX:TOL=127075],trachelomonas intermedia[&&NHX:TOL=127076],trachelomonas irregularis[&&NHX:TOL=127077],trachelomonas jaculata[&&NHX:TOL=127078],trachelomonas janczowskii[&&NHX:TOL=127079],trachelomonas kalotrachelos[&&NHX:TOL=127080],trachelomonas kashmiri[&&NHX:TOL=127081],trachelomonas kelloggii[&&NHX:TOL=127082],trachelomonas klebsii[&&NHX:TOL=127083],trachelomonas koliana[&&NHX:TOL=127084],trachelomonas kolkoilsii[&&NHX:TOL=127085],trachelomonas komarovii[&&NHX:TOL=127086],trachelomonas kozlovi[&&NHX:TOL=127087],trachelomonas kufferathi[&&NHX:TOL=127088],trachelomonas labiata[&&NHX:TOL=127089],trachelomonas lacustris[&&NHX:TOL=127090],trachelomonas laevis[&&NHX:TOL=127091],trachelomonas lagenella[&&NHX:TOL=127092],trachelomonas lanceolata[&&NHX:TOL=127093],trachelomonas latviensis[&&NHX:TOL=127094],trachelomonas legatovii[&&NHX:TOL=127095],trachelomonas lemmermannii[&&NHX:TOL=127096],trachelomonas lepida[&&NHX:TOL=127097],trachelomonas levefrei[&&NHX:TOL=127098],trachelomonas lilloensis[&&NHX:TOL=127099],trachelomonas lineata[&&NHX:TOL=127100],trachelomonas lismorensis[&&NHX:TOL=127101],trachelomonas lomnickii[&&NHX:TOL=127102],trachelomonas longa[&&NHX:TOL=127103],trachelomonas longicauda[&&NHX:TOL=127104],trachelomonas longicollis[&&NHX:TOL=127105],trachelomonas longispina[&&NHX:TOL=127106],trachelomonas longissima[&&NHX:TOL=127107],trachelomonas lotharingiae[&&NHX:TOL=127108],trachelomonas lucidula[&&NHX:TOL=127109],trachelomonas lukoviensis[&&NHX:TOL=127110],trachelomonas lychenensis[&&NHX:TOL=127111],trachelomonas maculata[&&NHX:TOL=127112],travhelomonas macropunctata[&&NHX:TOL=127113],trachelomonas magdaleniana[&&NHX:TOL=127114],trachelomonas magnigranulata[&&NHX:TOL=127115],trachelomonas malum[&&NHX:TOL=127116],trachelomonas mammillosa[&&NHX:TOL=127117],trachelomonas manchurica[&&NHX:TOL=127118],trachelomonas manginii[&&NHX:TOL=127119],trachelomonas margaritifera[&&NHX:TOL=127120],trachelomonas marginella[&&NHX:TOL=127121],trachelomonas maskellii[&&NHX:TOL=127122],trachelomonas maxima[&&NHX:TOL=127123],trachelomonas mediospinosa[&&NHX:TOL=127124],trachelomonas megalacantha[&&NHX:TOL=127125],trachelomonas meisteri[&&NHX:TOL=127126],trachelomonas minima[&&NHX:TOL=127127],trachelomonas minor[&&NHX:TOL=127128],trachelomonas minuscula[&&NHX:TOL=127129],trachelomonas minuta[&&NHX:TOL=127130],trachelomonas mirabilis[&&NHX:TOL=127131],trachelomonas molesta[&&NHX:TOL=127132],trachelomonas mucosa[&&NHX:TOL=127133],trachelomonas multifacies[&&NHX:TOL=127134],trachelomonas myersii[&&NHX:TOL=127135],trachelomonas nadsonii[&&NHX:TOL=127136],trachelomonas napiformis[&&NHX:TOL=127137],trachelomonas naviculiformis[&&NHX:TOL=127138],trachelomonas neotropica[&&NHX:TOL=127139],trachelomonas nexilis[&&NHX:TOL=127140],trachelomonas nigra[&&NHX:TOL=127141],trachelomonas niklewskii[&&NHX:TOL=127142],trachelomonas nobilis[&&NHX:TOL=127143],trachelomonas nodsonii[&&NHX:TOL=127144],trachelomonas nova[&&NHX:TOL=127145],trachelomonas obesa[&&NHX:TOL=127146],trachelomonas oblonga[&&NHX:TOL=127147],trachelomonas obovata[&&NHX:TOL=127148],trachelomonas obtusa[&&NHX:TOL=127149],trachelomonas olla[&&NHX:TOL=127150],trachelomonas omphalon[&&NHX:TOL=127151],trachelomonas orenburgica[&&NHX:TOL=127152],trachelomonas orientalis[&&NHX:TOL=127153],trachelomonas ornata[&&NHX:TOL=127154],trachelomonas ovalis[&&NHX:TOL=127155],trachelomonas ovata[&&NHX:TOL=127156],trachelomonas oviformis[&&NHX:TOL=127157],trachelomonas ovoides[&&NHX:TOL=127158],trachelomonas palmeri[&&NHX:TOL=127159],trachelomonas paludosa[&&NHX:TOL=127160],trachelomonas papillatopunctata[&&NHX:TOL=127161],trachelomonas parafusiformis[&&NHX:TOL=127162],trachelomonas parvicollis[&&NHX:TOL=127163],trachelomonas pascheri[&&NHX:TOL=127164],trachelomonas pascherana[&&NHX:TOL=127165],trachelomonas paucispinosa[&&NHX:TOL=127166],trachelomonas pelegrina[&&NHX:TOL=127167],trachelomonas pepo[&&NHX:TOL=127168],trachelomonas perforata[&&NHX:TOL=127169],trachelomonas peridiniformis[&&NHX:TOL=127170],trachelomonas perlata[&&NHX:TOL=127171],trachelomonas pisciformis[&&NHX:TOL=127172],trachelomonas piscatoris[&&NHX:TOL=127173],trachelomonas planctonica[&&NHX:TOL=127174],trachelomonas playfairii[&&NHX:TOL=127175],trachelomonas polonica[&&NHX:TOL=127176],trachelomonas polymoprha[&&NHX:TOL=127177],trachelomonas praeliaris[&&NHX:TOL=127178],trachelomonas prismatica[&&NHX:TOL=127179],trachelomonas proxima[&&NHX:TOL=127180],trachelomonas pruniformis[&&NHX:TOL=127181],trachelomonas pseudoarmata[&&NHX:TOL=127182],trachelomonas pseudobulla[&&NHX:TOL=127183],trachelomonas pseudocaudata[&&NHX:TOL=127184],trachelomonas pseudofelix[&&NHX:TOL=127185],trachelomonas pulchella[&&NHX:TOL=127186],trachelomonas pulcherrima[&&NHX:TOL=127187],trachelomonas pulchra[&&NHX:TOL=127188],trachelomonas pumila[&&NHX:TOL=127189],trachelomonas punctata[&&NHX:TOL=127190],trachelomonas pungens[&&NHX:TOL=127191],trachelomonas pusilla[&&NHX:TOL=127192],trachelomonas pustulosa[&&NHX:TOL=127193],trachelomonas pyramidata[&&NHX:TOL=127194],trachelomonas quadriformis[&&NHX:TOL=127195],trachelomonas raciborskii[&&NHX:TOL=127196],trachelomonas radiosa[&&NHX:TOL=127197],trachelomonas rapacea[&&NHX:TOL=127198],trachelomonas rara[&&NHX:TOL=127199],trachelomonas rasumowskoensis[&&NHX:TOL=127200],trachelomonas recticollis[&&NHX:TOL=127201],trachelomonas reeuwijkiana[&&NHX:TOL=127202],trachelomonas regularis[&&NHX:TOL=127203],trachelomonas reinhradi[&&NHX:TOL=127204],trachelomonas reticulata[&&NHX:TOL=127205],trachelomonas rhodopensis[&&NHX:TOL=127206],trachelomonas rhombica[&&NHX:TOL=127207],trachelomonas richmondiae[&&NHX:TOL=127208],trachelomonas rivularis[&&NHX:TOL=127209],trachelomonas robusta[&&NHX:TOL=127210],trachelomonas rolli[&&NHX:TOL=127211],trachelomonas rostafinskii[&&NHX:TOL=127212],trachelomonas rotunda[&&NHX:TOL=127213],trachelomonas rotundata[&&NHX:TOL=127214],trachelomonas rugulosa[&&NHX:TOL=127215],trachelomonas saccata[&&NHX:TOL=127216],trachelomonas sarmatica[&&NHX:TOL=127217],trachelomonas scabra[&&NHX:TOL=127218],trachelomonas scabratula[&&NHX:TOL=127219],trachelomonas schauinslandii[&&NHX:TOL=127220],trachelomonas schewiakoffi[&&NHX:TOL=127221],trachelomonas sculpta[&&NHX:TOL=127222],trachelomonas selecta[&&NHX:TOL=127223],trachelomonas sessilis[&&NHX:TOL=127224],trachelomonas setosa[&&NHX:TOL=127225],trachelomonas silvatica[&&NHX:TOL=127226],trachelomonas similis[&&NHX:TOL=127227],trachelomonas sinica[&&NHX:TOL=127228],trachelomonas skujae[&&NHX:TOL=127229],trachelomonas skvortzowiana[&&NHX:TOL=127230],trachelomonas sowerbii[&&NHX:TOL=127231],trachelomonas sparsesetulosa[&&NHX:TOL=127232],trachelomonas speciosa[&&NHX:TOL=127233],trachelomonas spectabilis[&&NHX:TOL=127234],trachelomonas sphagnicola[&&NHX:TOL=127235],trachelomonas spiculifera[&&NHX:TOL=127236],trachelomonas spinigera[&&NHX:TOL=127237],trachelomonas spinosa[&&NHX:TOL=127238],trachelomonas spinulosa[&&NHX:TOL=127239],trachelomonas spiragyra[&&NHX:TOL=127240],trachelomonas spiralis[&&NHX:TOL=127241],trachelomonas spiricostatum[&&NHX:TOL=127242],trachelomonas spirogyra[&&NHX:TOL=127243],trachelomonas splendida[&&NHX:TOL=127244],trachelomonas splendidissima[&&NHX:TOL=127245],trachelomonas stagnalis[&&NHX:TOL=127246],trachelomonas stanleyi[&&NHX:TOL=127247],trachelomonas staszicii[&&NHX:TOL=127248],trachelomonas steinii[&&NHX:TOL=127249],trachelomonas stokesi[&&NHX:TOL=127250],trachelomonas stokesiana[&&NHX:TOL=127251],trachelomonas striata[&&NHX:TOL=127252],trachelomonas subcurvata[&&NHX:TOL=127253],trachelomonas subcaudata[&&NHX:TOL=127254],trachelomonas subcoronetta[&&NHX:TOL=127255],trachelomonas subdenticulata[&&NHX:TOL=127256],trachelomonas subflava[&&NHX:TOL=127257],trachelomonas subglobosa[&&NHX:TOL=127258],trachelomonas sublonga[&&NHX:TOL=127259],trachelomonas suboblonga[&&NHX:TOL=127260],trachelomonas subolonga[&&NHX:TOL=127261],trachelomonas subulata[&&NHX:TOL=127262],trachelomonas sueverrucosa[&&NHX:TOL=127263],trachelomonas superba[&&NHX:TOL=127264],trachelomonas swirenko[&&NHX:TOL=127265],trachelomonas sydneyensis[&&NHX:TOL=127266],trachelomonas szabadosiana[&&NHX:TOL=127267],trachelomonas tambowika[&&NHX:TOL=127268],trachelomonas taxandriae[&&NHX:TOL=127269],trachelomonas teres[&&NHX:TOL=127270],trachelomonas terminus[&&NHX:TOL=127271],trachelomonas torleyi[&&NHX:TOL=127272],trachelomonas torquata[&&NHX:TOL=127273],trachelomonas torta[&&NHX:TOL=127274],trachelomonas treubii[&&NHX:TOL=127275],trachelomonas triangularis[&&NHX:TOL=127276],trachelomonas triquetra[&&NHX:TOL=127277],trachelomonas troitzkajae[&&NHX:TOL=127278],trachelomonas tshopoensid[&&NHX:TOL=127279],trachelomonas tubantia[&&NHX:TOL=127280],trachelomonas tuberculata[&&NHX:TOL=127281],trachelomonas tuberosa[&&NHX:TOL=127282],trachelomonas tulerosa[&&NHX:TOL=127283],trachelomonas tumida[&&NHX:TOL=127284],trachelomonas tympanum[&&NHX:TOL=127285],trachelomonas umbilicorphora[&&NHX:TOL=127286],trachelomomas undulata[&&NHX:TOL=127287],trachelomonas undulaticollum[&&NHX:TOL=127288],trachelomonas unicoronata[&&NHX:TOL=127289],trachelomonas unifromis[&&NHX:TOL=127290],trachelomonas urceolata[&&NHX:TOL=127291],trachelomonas urdulata[&&NHX:TOL=127292],trachelomonas urnigera[&&NHX:TOL=127293],trachelomonas variabilis[&&NHX:TOL=127294],trachelomonas varians[&&NHX:TOL=127295],trachelomonas vas[&&NHX:TOL=127296],trachelomonas venusta[&&NHX:TOL=127297],trachelomonas vermiculosa[&&NHX:TOL=127298],trachelomonas vermoesenii[&&NHX:TOL=127299],trachelomonas vermonti[&&NHX:TOL=127300],trachelomonas verrucosa[&&NHX:TOL=127301],trachelomonas vestita[&&NHX:TOL=127302],trachelomonas volgensis[&&NHX:TOL=127303],trachelomonas volvocina[&&NHX:TOL=127304],trachelomonas volvocinopsis[&&NHX:TOL=127305],trachelomonas volzii[&&NHX:TOL=127306],trachelomonas wermelii[&&NHX:TOL=127307],trachelomonas werneri[&&NHX:TOL=127308],trachelomonas westii[&&NHX:TOL=127309],trachelomonas wislouchii[&&NHX:TOL=127310],trachelomonas woloszynskii[&&NHX:TOL=127311],trachelomonas woycickii[&&NHX:TOL=127312],trachelomonas zingeri[&&NHX:TOL=127313],trachelomonas zmiewika[&&NHX:TOL=127314],trachelomonas zorensis[&&NHX:TOL=127315],trachelomonas zuberi[&&NHX:TOL=127316])trachelomonas[&&NHX:TOL=126439],(strombomonas acuminata[&&NHX:TOL=127317],strombomonas affinis[&&NHX:TOL=127318],strombomonas alata[&&NHX:TOL=127319],strombomonas amphoraeformis[&&NHX:TOL=127320],strombomonas angusta[&&NHX:TOL=127321],strombomonas annulata[&&NHX:TOL=127322],strombomonas aspera[&&NHX:TOL=127323],strombomonas australica[&&NHX:TOL=127324],strombomonas bonariensis[&&NHX:TOL=127325],strombomonas borystheniensis[&&NHX:TOL=127326],strombomonas chinensis[&&NHX:TOL=127327],strombomonas chodati[&&NHX:TOL=127328],strombomonas clavata[&&NHX:TOL=127329],strombomonas costata[&&NHX:TOL=127330],strombomonas cuneata[&&NHX:TOL=127331],strombomonas deflandrei[&&NHX:TOL=127332],strombomonas dissimilis[&&NHX:TOL=127333],strombomonas elegans[&&NHX:TOL=127334],strombomonas ensifera[&&NHX:TOL=127335],strombomonas eurystoma[&&NHX:TOL=127336],strombomonas fluviatilis[&&NHX:TOL=127337],strombomonas fusiformis[&&NHX:TOL=127338],strombomonas gibberosa[&&NHX:TOL=127339],strombomonas ginlingensis[&&NHX:TOL=127340],strombomonas girardiana[&&NHX:TOL=127341],strombomonas glabra[&&NHX:TOL=127342],strombomonas gonitrachela[&&NHX:TOL=127343],strombomonas helicaudata[&&NHX:TOL=127344],strombomonas inconstans[&&NHX:TOL=127345],strombomonas jaculata[&&NHX:TOL=127346],strombomonas kalotrachelos[&&NHX:TOL=127347],strombomonas kozlovii[&&NHX:TOL=127348],strombomonas lagenaeformis[&&NHX:TOL=127349],strombomonas lanceolata[&&NHX:TOL=127350],strombomonas longicauda[&&NHX:TOL=127351],strombomonas massartii[&&NHX:TOL=127352],strombomonas maxima[&&NHX:TOL=127353],strombomonas morenensis[&&NHX:TOL=127354],strombomonas napiformis[&&NHX:TOL=127355],strombomonas ovalis[&&NHX:TOL=127356],strombomonas ovata[&&NHX:TOL=127357],strombomonas praeliaris[&&NHX:TOL=127358],strombomonas prismatica[&&NHX:TOL=127359],strombomonas pungens[&&NHX:TOL=127360],strombomonas rapacea[&&NHX:TOL=127361],strombomonas rotunda[&&NHX:TOL=127362],strombomonas schauninslandii[&&NHX:TOL=127363],strombomonas spiralis[&&NHX:TOL=127364],strombomonas subarmata[&&NHX:TOL=127365],strombomonas subcurvata[&&NHX:TOL=127366],strombomonas suborbicularis[&&NHX:TOL=127367],strombomonas tambowika[&&NHX:TOL=127368],strombomonas tetraptera[&&NHX:TOL=127369],strombomonas treubii[&&NHX:TOL=127370],strombomonas triquetra[&&NHX:TOL=127371],strombomonas tuberculata[&&NHX:TOL=127372],strombomonas tuberosa[&&NHX:TOL=127373],strombomonas undulata[&&NHX:TOL=127374],strombomonas urceolata[&&NHX:TOL=127375],strombomonas vermonti[&&NHX:TOL=127376],strombomonas verrucosa[&&NHX:TOL=127377],strombomonas volgensis[&&NHX:TOL=127378])strombomonas[&&NHX:TOL=97759])loricates[&&NHX:TOL=126438])mucilagenous clade[&&NHX:TOL=126437],((monomorphina arnoldi[&&NHX:TOL=127379],monomorphina atraktoides[&&NHX:TOL=127380],monomorphina capito[&&NHX:TOL=127381],monomorphina cochleata[&&NHX:TOL=127382],monomorphina costata[&&NHX:TOL=127383],monomorphina filicauda[&&NHX:TOL=127384],monomorphina lepocincloides[&&NHX:TOL=127385],monomorphina minuscula[&&NHX:TOL=127386],monomorphina monochloron[&&NHX:TOL=127387],monomorphina ovata[&&NHX:TOL=127388],monomorphina pseudonordstedti[&&NHX:TOL=127389],monomorphina pulcherrima[&&NHX:TOL=127390],monomorphina pyriformis[&&NHX:TOL=127391],monomorphina pyrum[&&NHX:TOL=127392],monomorphina reeuwykiana[&&NHX:TOL=127393],monomorphina rudicula[&&NHX:TOL=127394],monomorphina striata[&&NHX:TOL=127395],monomorphina strongyla[&&NHX:TOL=127396],monomorphina trypanon[&&NHX:TOL=127397],monomorphina turgidula[&&NHX:TOL=127398])monomorphina[&&NHX:TOL=126445],(cryptoglena australis[&&NHX:TOL=97500],cryptoglena phacoidea[&&NHX:TOL=97501],cryptoglena pigra[&&NHX:TOL=97502],cryptoglena skujai[&&NHX:TOL=97503])cryptoglena[&&NHX:TOL=97499])[&&NHX:TOL=126444],(discoplastis spathirhyncha[&&NHX:TOL=97686],discoplastis adunca[&&NHX:TOL=126465],discoplastis limnophila[&&NHX:TOL=97612])discoplastis[&&NHX:TOL=126447],((phacus abruptus[&&NHX:TOL=127399],phacus acuminatus[&&NHX:TOL=127400],phacus acuticaudata[&&NHX:TOL=127401],phacus acutissima[&&NHX:TOL=127402],phacus acutus[&&NHX:TOL=127403],phacus aenigmaticus[&&NHX:TOL=127404],phacus agilis[&&NHX:TOL=127405],phacus alata[&&NHX:TOL=127406],phacus anacoelus[&&NHX:TOL=127407],phacus angulatus[&&NHX:TOL=127408],phacus angustatus[&&NHX:TOL=127409],phacus ankylonoton[&&NHX:TOL=127410],phacus anomalus[&&NHX:TOL=127411],phacus applanatus[&&NHX:TOL=127412],phacus argentiniensis[&&NHX:TOL=127413],phacus arnoldi[&&NHX:TOL=127414],phacus aspidion[&&NHX:TOL=127415],phacus asymmetricus[&&NHX:TOL=127416],phacus atraktoides[&&NHX:TOL=127417],phacus bacillifer[&&NHX:TOL=127418],phacus bacilliformis[&&NHX:TOL=127419],phacus balatonicus[&&NHX:TOL=127420],phacus balechii[&&NHX:TOL=127421],phacus bicarinatus[&&NHX:TOL=127422],phacus birgei[&&NHX:TOL=127423],phacus bonettoi[&&NHX:TOL=127424],phacus brachykentron[&&NHX:TOL=127425],phacus brevicaudata[&&NHX:TOL=127426],phacus carinatus[&&NHX:TOL=127427],phacus caudatus[&&NHX:TOL=127428],phacus chloroplastes[&&NHX:TOL=127429],phacus circulatus[&&NHX:TOL=127430],phacus circumflexus[&&NHX:TOL=127431],phacus clavatus[&&NHX:TOL=127432],phacus cochleatus[&&NHX:TOL=127433],phacus concavus[&&NHX:TOL=127434],phacus contortus[&&NHX:TOL=127435],phacus contractus[&&NHX:TOL=127436],phacus corculum[&&NHX:TOL=127437],phacus costatus[&&NHX:TOL=127438],phacus crenulata[&&NHX:TOL=127439],phacus cuneatus[&&NHX:TOL=127440],phacus curvicauda[&&NHX:TOL=127441],phacus cylindrus[&&NHX:TOL=127442],phacus dangeardii[&&NHX:TOL=127443],phacus denisii[&&NHX:TOL=127444],phacus dihistion[&&NHX:TOL=127445],phacus discifera[&&NHX:TOL=127446],phacus elegans[&&NHX:TOL=127447],phacus elongatus[&&NHX:TOL=127448],phacus ephippion[&&NHX:TOL=127449],phacus fernii[&&NHX:TOL=127450],phacus filicaudus[&&NHX:TOL=127451],phacus florii[&&NHX:TOL=127452],phacus formosus[&&NHX:TOL=127453],phacus gibbosus[&&NHX:TOL=127454],phacus gigas[&&NHX:TOL=127455],phacus glaber[&&NHX:TOL=127456],phacus globosus[&&NHX:TOL=127457],phacus gracilis[&&NHX:TOL=127458],phacus granulata[&&NHX:TOL=127459],phacus granum[&&NHX:TOL=127460],phacus gregussii[&&NHX:TOL=127461],phacus hamatus[&&NHX:TOL=127462],phacus hameli[&&NHX:TOL=127463],phacus heimii[&&NHX:TOL=127464],phacus helicoides[&&NHX:TOL=127465],phacus hispidulus[&&NHX:TOL=127466],phacus horridus[&&NHX:TOL=127467],phacus hystrix[&&NHX:TOL=127468],phacus ichthydion[&&NHX:TOL=127469],phacus incisus[&&NHX:TOL=127470],phacus inconspicuus[&&NHX:TOL=127471],phacus incrassatus[&&NHX:TOL=127472],phacus indicus[&&NHX:TOL=127473],phacus inflatus[&&NHX:TOL=127474],phacus inflexus[&&NHX:TOL=127475],phacus insecta[&&NHX:TOL=127476],phacus intortus[&&NHX:TOL=127477],phacus kemenesii[&&NHX:TOL=127478],phacus latus[&&NHX:TOL=127479],phacus lefevrei[&&NHX:TOL=127480],phacus lemmermannii[&&NHX:TOL=127481],phacus lepocincloides[&&NHX:TOL=127482],phacus lismorensis[&&NHX:TOL=127483],phacus longicauda[&&NHX:TOL=127484],phacus longicaudus[&&NHX:TOL=127485],phacus makrostigma[&&NHX:TOL=127486],phacus manginii[&&NHX:TOL=127487],phacus marconii[&&NHX:TOL=127488],phacus margaritatus[&&NHX:TOL=127489],phacus mariae[&&NHX:TOL=127490],phacus mariana[&&NHX:TOL=127491],phacus matanzae[&&NHX:TOL=127492],phacus megalopsis[&&NHX:TOL=127493],phacus megaparamylica[&&NHX:TOL=127494],phacus megapyrenoidea[&&NHX:TOL=127495],phacus mentaweiensis[&&NHX:TOL=127496],phacus meson[&&NHX:TOL=127497],phacus miniscula[&&NHX:TOL=127498],phacus minor[&&NHX:TOL=127499],phacus minutus[&&NHX:TOL=127500],phacus mirabilis[&&NHX:TOL=127501],phacus monilata[&&NHX:TOL=127502],phacus monilatus[&&NHX:TOL=127503],phacus monilicostatus[&&NHX:TOL=127504],phacus moraviensis[&&NHX:TOL=127505],phacus morii[&&NHX:TOL=127506],phacus multiannulatus[&&NHX:TOL=127507],phacus multifidis[&&NHX:TOL=127508],phacus musculus[&&NHX:TOL=127509],phacus myersi[&&NHX:TOL=127510],phacus nannos[&&NHX:TOL=127511],phacus neosulcatus[&&NHX:TOL=127512],phacus niloticus[&&NHX:TOL=127513],phacus nordstedtii[&&NHX:TOL=127514],phacus novus[&&NHX:TOL=127515],phacus oblongus[&&NHX:TOL=127516],phacus obolus[&&NHX:TOL=127517],phacus ocellatus[&&NHX:TOL=127518],phacus onyx[&&NHX:TOL=127519],phacus orbicularis[&&NHX:TOL=127520],phacus orbiculata[&&NHX:TOL=127521],phacus oscillans[&&NHX:TOL=127522],phacus ostreatus[&&NHX:TOL=127523],phacus ovalis[&&NHX:TOL=127524],phacus ovoidea[&&NHX:TOL=127525],phacus parvulus[&&NHX:TOL=127526],phacus pekinensis[&&NHX:TOL=127527],phacus pentacaudus[&&NHX:TOL=127528],phacus persikon[&&NHX:TOL=127529],phacus peteloti[&&NHX:TOL=127530],phacus pisiformis[&&NHX:TOL=127531],phacus platalea[&&NHX:TOL=127532],phacus platyaulax[&&NHX:TOL=127533],phacus pleuronectes[&&NHX:TOL=127534],phacus plicatus[&&NHX:TOL=127535],phacus polytrophus[&&NHX:TOL=127536],phacus pomiformis[&&NHX:TOL=127537],phacus poulae[&&NHX:TOL=127538],phacus prescotti[&&NHX:TOL=127539],phacus prunoideus[&&NHX:TOL=127540],phacus pseudonordstedtii[&&NHX:TOL=127541],phacus pseudoplatalea[&&NHX:TOL=127542],phacus pseudoswirenkoi[&&NHX:TOL=127543],phacus pulcher[&&NHX:TOL=127544],phacus pulcherrimus[&&NHX:TOL=127545],phacus pusillus[&&NHX:TOL=127546],phacus pygmaeus[&&NHX:TOL=127547],phacus pyrum[&&NHX:TOL=127548],phacus pyrus[&&NHX:TOL=127549],phacus quinquemarginatus[&&NHX:TOL=127550],phacus raciborskii[&&NHX:TOL=127551],phacus ranula[&&NHX:TOL=127552],phacus ridicula[&&NHX:TOL=127553],phacus rodriguesiae[&&NHX:TOL=127554],phacus rostafinskii[&&NHX:TOL=127555],phacus rotundus[&&NHX:TOL=127556],phacus rudicula[&&NHX:TOL=127557],phacus schroeteri[&&NHX:TOL=127558],phacus segretti[&&NHX:TOL=127559],phacus sesquitortus[&&NHX:TOL=127560],phacus setosus[&&NHX:TOL=127561],phacus skujai[&&NHX:TOL=127562],phacus spiralis[&&NHX:TOL=127563],phacus splendens[&&NHX:TOL=127564],phacus staurastroides[&&NHX:TOL=127565],phacus stokesi[&&NHX:TOL=127566],phacus stokesii[&&NHX:TOL=127567],phacus striatus[&&NHX:TOL=127568],phacus strombiliformis[&&NHX:TOL=127569],phacus strongylus[&&NHX:TOL=127570],phacus subspiralis[&&NHX:TOL=127571],phacus suecicus[&&NHX:TOL=127572],phacus swirenkoanus[&&NHX:TOL=127573],phacus swirenkoi[&&NHX:TOL=127574],phacus tabodyanus[&&NHX:TOL=127575],phacus teres[&&NHX:TOL=127576],phacus textus[&&NHX:TOL=127577],phacus thombus[&&NHX:TOL=127578],phacus thompsoni[&&NHX:TOL=127579],phacus thrombus[&&NHX:TOL=127580],phacus tortifolius[&&NHX:TOL=127581],phacus tortuosus[&&NHX:TOL=127582],phacus tortus[&&NHX:TOL=127583],phacus trapezialis[&&NHX:TOL=127584],phacus trapezoides[&&NHX:TOL=127585],phacus triangularis[&&NHX:TOL=127586],phacus triangulus[&&NHX:TOL=127587],phacus tricarinatus[&&NHX:TOL=127588],phacus tricostatus[&&NHX:TOL=127589],phacus trifacialis[&&NHX:TOL=127590],phacus trimarginatus[&&NHX:TOL=127591],phacus tripteris[&&NHX:TOL=127592],phacus triqueter[&&NHX:TOL=127593],phacus tropicalis[&&NHX:TOL=127594],phacus tropidonotus[&&NHX:TOL=127595],phacus truncatus[&&NHX:TOL=127596],phacus trypanon[&&NHX:TOL=127597],phacus turgidulus[&&NHX:TOL=127598],phacus ulula[&&NHX:TOL=127599],phacus undulatus[&&NHX:TOL=127600],phacus unguis[&&NHX:TOL=127601],phacus unidentatus[&&NHX:TOL=127602],phacus variabilis[&&NHX:TOL=127603],phacus ventricosus[&&NHX:TOL=127604],phacus venustus[&&NHX:TOL=127605],phacus viguieri[&&NHX:TOL=127606],phacus warszewiczii[&&NHX:TOL=127607],phacus wettsteini[&&NHX:TOL=127608],phacus zingeri[&&NHX:TOL=127609])phacus[&&NHX:TOL=126449],(lepocinclis acus[&&NHX:TOL=126466],lepocinclis helicoideus[&&NHX:TOL=97594],lepocinclis gigas[&&NHX:TOL=97584],lepocinclis fusca[&&NHX:TOL=97576],lepocinclis lepocincloides[&&NHX:TOL=97611],(lepocinclis oxyuris estonica[&&NHX:TOL=97639],lepocinclis oxyuris gracillima[&&NHX:TOL=97640],lepocinclis oxyuris minina[&&NHX:TOL=97641],lepocinclis oxyuris minor[&&NHX:TOL=97642],lepocinclis oxyuris playfairii[&&NHX:TOL=97643])lepocinclis oxyuris[&&NHX:TOL=97638],(lepocinclis spirogyra abrupteacuminata[&&NHX:TOL=97688],lepocinclis spirogyra compressa[&&NHX:TOL=97689],lepocinclis spirogyra elegans[&&NHX:TOL=97690],lepocinclis spirogyra fusca[&&NHX:TOL=97691],lepocinclisspirogyra fusiformis[&&NHX:TOL=97692],lepocinclis spirogyra laticlavius[&&NHX:TOL=97693],lepocinclis spirogyra marchica[&&NHX:TOL=97694],lepocinclis spirogyra minor[&&NHX:TOL=97695],lepocinclis spirogyra suprema[&&NHX:TOL=97696],lepocinclis spirogyra torta[&&NHX:TOL=97697])lepocinclis spirogyra[&&NHX:TOL=97687],(lepocinclis tripteris crassa[&&NHX:TOL=97719],lepocinclis tripteris klebsii[&&NHX:TOL=97720],lepocinclis tripteris major[&&NHX:TOL=97721])euglena tripteris[&&NHX:TOL=97718],lepocinclis acicularis[&&NHX:TOL=127610],lepocinclis acuminata[&&NHX:TOL=127611],lepocinclis acuta[&&NHX:TOL=127612],lepocinclis aegyptiaca[&&NHX:TOL=127613],lepocinclis agilis[&&NHX:TOL=127614],lepocinclis australica[&&NHX:TOL=127615],lepocinclis autumnalis[&&NHX:TOL=127616],lepocinclis boseensis[&&NHX:TOL=127617],leopcinclis butschlii[&&NHX:TOL=127618],lepocinclis capitata[&&NHX:TOL=127619],lepocinclis caudata[&&NHX:TOL=127620],lepocinclis colligera[&&NHX:TOL=127621],lepocinclis constricta[&&NHX:TOL=127622],lepocinclis costata[&&NHX:TOL=127623],lepocinclis crassicollis[&&NHX:TOL=127624],lepocinclis cylindrica[&&NHX:TOL=127625],lepocinclis cymbiformis[&&NHX:TOL=127626],lepocinclis czeydapommersheimii[&&NHX:TOL=127627],lepocinclis difficilis[&&NHX:TOL=127628],lepocinclis deflandriana[&&NHX:TOL=127629],lepocinclis elongata[&&NHX:TOL=127630],lepocinclis fusiformis[&&NHX:TOL=127631],lepocinclis glabra[&&NHX:TOL=127632],lepocinclis globulus[&&NHX:TOL=127633],lepocinclis gracilicauda[&&NHX:TOL=127634],lepocinclis gracillima[&&NHX:TOL=127635],lepocinclis griffithi[&&NHX:TOL=127636],lepocinclis heterochila[&&NHX:TOL=127637],lepocinclis hispidula[&&NHX:TOL=127638],lepocinclis horrida[&&NHX:TOL=127639],lepocinclis huangpanchiaoensis[&&NHX:TOL=127640],lepocinclis indica[&&NHX:TOL=127641],lepocinclis khannae[&&NHX:TOL=127642],lepocinclis kufferathi[&&NHX:TOL=127643],lepocinclis lefevrei[&&NHX:TOL=127644],lepocinclis lobata[&&NHX:TOL=127645],lepocinclis longistriata[&&NHX:TOL=127646],lepocinclis mammillata[&&NHX:TOL=127647],lepocinclis marssonii[&&NHX:TOL=127648],lepocinclis mespiliformis[&&NHX:TOL=127649],lepocinclis nankingensis[&&NHX:TOL=127650],lepocinclis nayali[&&NHX:TOL=127651],lepocinclis obtusa[&&NHX:TOL=127652],lepocinclis ovum[&&NHX:TOL=127653],lepocinclis paxilliformis[&&NHX:TOL=127654],lepocinclis perlaria[&&NHX:TOL=127655],lepocinclis physalis[&&NHX:TOL=127656],lepocinclis piriformis[&&NHX:TOL=127657],lepocinclis plana[&&NHX:TOL=127658],lepocinclis platydesma[&&NHX:TOL=127659],lepocinclis playfairiana[&&NHX:TOL=127660],lepocinclis pseudoovum[&&NHX:TOL=127661],lepocinclis pseudotexta[&&NHX:TOL=127662],lepocinclis quadrata[&&NHX:TOL=127663],lepocinclis radiata[&&NHX:TOL=127664],lepocinclis redekei[&&NHX:TOL=127665],lepocinclis reeuwykiana[&&NHX:TOL=127666],lepocinclis rugulosa[&&NHX:TOL=127667],lepocinclis salina[&&NHX:TOL=127668],lepocinclis sphagnophila[&&NHX:TOL=127669],lepocinclis spirogyroides[&&NHX:TOL=127670],lepocinclis spiroides[&&NHX:TOL=127671],lepocinclis steinii[&&NHX:TOL=127672],lepocinclis taeda[&&NHX:TOL=127673],lepocinclis teres[&&NHX:TOL=127674],lepocinclis texta[&&NHX:TOL=127675],lepocinclis truncate[&&NHX:TOL=127676],lepocinclis turbiniformis[&&NHX:TOL=127677],lepocinclis wangii[&&NHX:TOL=127678])lepocinclis[&&NHX:TOL=126450])[&&NHX:TOL=126448])euglenales[&&NHX:TOL=126435])euglenophytes[&&NHX:TOL=126427])[&&NHX:TOL=126422])[&&NHX:TOL=126404])[&&NHX:TOL=126393],scytomonas[&&NHX:TOL=126452],(sphenomonas alburiae[&&NHX:TOL=97983],sphenomonas angusta[&&NHX:TOL=97984],sphenomonas australis[&&NHX:TOL=97985],sphenomonas elongata[&&NHX:TOL=97988],sphenomonas excavata[&&NHX:TOL=97989],sphenomonas mirabilis[&&NHX:TOL=97990],sphenomonas octocostatus[&&NHX:TOL=97991],sphenomonas quadrangularis[&&NHX:TOL=97992],sphenomonas rhomboidea[&&NHX:TOL=97993],sphenomonas spiralis[&&NHX:TOL=97994],sphenomonas teres[&&NHX:TOL=97995],sphenomonas triquetra[&&NHX:TOL=97996],sphenomonas tristriata[&&NHX:TOL=97997])sphenomonas[&&NHX:TOL=97982],atraktomonas laevis[&&NHX:TOL=98000],dolium sedentarium[&&NHX:TOL=97937],(euglenopsis vorax[&&NHX:TOL=97942],euglenopsis zabra[&&NHX:TOL=97943])euglenopsis[&&NHX:TOL=97941],marsupiogaster[&&NHX:TOL=126458],pentamonas[&&NHX:TOL=126459],triangulomonas[&&NHX:TOL=126460],(tropidoscyphus octocostatus[&&NHX:TOL=127679],tropidoscyphus richiae[&&NHX:TOL=127680])tropidoscyphus[&&NHX:TOL=97998],moyeria[&&NHX:EXT=Y:TOL=126461])euglenida[&&NHX:TOL=97461],postgaardi mariagerensis[&&NHX:TOL=98012],calkinsia aureus[&&NHX:TOL=97935])euglenozoa[&&NHX:TOL=2405],(((((((((stephanopogon apogon[&&NHX:TOL=129958],((stephanopogon mobiliensis[&&NHX:TOL=129959],stephanopogon minuta[&&NHX:TOL=129961])[&&NHX:TOL=130433],((stephanopogon paramesnili[&&NHX:TOL=129960],stephanopogon colpoda[&&NHX:TOL=129956])[&&NHX:TOL=130435],stephanopogon mesnili[&&NHX:TOL=129957])[&&NHX:TOL=130434])[&&NHX:TOL=130432])stephanopogon[&&NHX:TOL=124646],percolomonas cosmopolitus[&&NHX:TOL=124647])[&&NHX:TOL=124645],((vahlkampfia avara[&&NHX:TOL=130218],vahlkampfia ciguana[&&NHX:TOL=130220],vahlkampfia inornata[&&NHX:TOL=130224],vahlkampfia orchilla[&&NHX:TOL=130225],vahlkampfia signyensis[&&NHX:TOL=130226])vahlkampfia[&&NHX:TOL=124649],(tetramitus aberdonicus[&&NHX:TOL=129437],tetramitus anasazii[&&NHX:TOL=130228],tetramitus angularis[&&NHX:TOL=129438],tetramitus entericus[&&NHX:TOL=129439],tetramitus hohokami[&&NHX:TOL=130227],tetramitus horticolus[&&NHX:TOL=129440],tetramitus jugosus[&&NHX:TOL=129441],tetramitus lobospinosus[&&NHX:TOL=129442],tetramitus ovis[&&NHX:TOL=129443],tetramitus parangularis[&&NHX:TOL=129444],tetramitus pararusselli[&&NHX:TOL=129445],tetramitus rostratus[&&NHX:TOL=129446],tetramitus russelli[&&NHX:TOL=129447],tetramitus thermacidophilus[&&NHX:TOL=129822],tetramitus thorntoni[&&NHX:TOL=129448],tetramitus vestfoldii[&&NHX:TOL=129449],tetramitus waccamawensis[&&NHX:TOL=129450])tetramitus[&&NHX:TOL=124650])[&&NHX:TOL=124648])[&&NHX:TOL=124644],(((((((((((((naegleria endoi[&&NHX:TOL=129829],naegleria gruberi[&&NHX:TOL=129413],naegleria pringsheimi[&&NHX:TOL=129434],naegleria dunnebackei[&&NHX:TOL=129834],naegleria gallica[&&NHX:TOL=129823],naegleria canariensis[&&NHX:TOL=129837],naegleria philippinensis[&&NHX:TOL=129436],naegleria tenerifensis[&&NHX:TOL=129836],naegleria italica[&&NHX:TOL=129418],naegleria clarki[&&NHX:TOL=129421],naegleria schusteri[&&NHX:TOL=129826],naegleria laresi[&&NHX:TOL=129830],naegleria mexicana[&&NHX:TOL=129825],naegleria tihangensis[&&NHX:TOL=129433],naegleria australiensis[&&NHX:TOL=129417])[&&NHX:TOL=130309],naegleria pagei[&&NHX:TOL=129435])[&&NHX:TOL=130308],naegleria byersi[&&NHX:TOL=129828])[&&NHX:TOL=130307],(((naegleria galeacystis[&&NHX:TOL=129422],naegleria americana[&&NHX:TOL=129824])[&&NHX:TOL=130312],(naegleria indonesiensis[&&NHX:TOL=129432],naegleria fultoni[&&NHX:TOL=129430])[&&NHX:TOL=130313])[&&NHX:TOL=130311],naegleria robinsoni[&&NHX:TOL=129429])subcluster5[&&NHX:TOL=130310])cluster5[&&NHX:TOL=130306],((naegleria dobsoni[&&NHX:TOL=129827],naegleria neodobsoni[&&NHX:TOL=129842])[&&NHX:TOL=130298],naegleria paradobsoni[&&NHX:TOL=130291])cluster8[&&NHX:TOL=130297])[&&NHX:TOL=130314],(naegleria minor[&&NHX:TOL=129423],naegleria carteri[&&NHX:TOL=129425])cluster3[&&NHX:TOL=130304])[&&NHX:TOL=130320],(((((naegleria antarctica[&&NHX:TOL=129833],naegleria neoantarcitica[&&NHX:TOL=129843])[&&NHX:TOL=130301],naegleria arctica[&&NHX:TOL=129840])[&&NHX:TOL=130300],(naegleria polaris[&&NHX:TOL=129838],naegleria neopolaris[&&NHX:TOL=129839])[&&NHX:TOL=130302])cluster7[&&NHX:TOL=130299],(((naegleria morganensis[&&NHX:TOL=129426],naegleria sturti[&&NHX:TOL=129428])[&&NHX:TOL=130293],naegleria niuginensis[&&NHX:TOL=129427])cluster2[&&NHX:TOL=130292],naegleria psitzbergensis[&&NHX:TOL=129841])[&&NHX:TOL=130322])[&&NHX:TOL=130316],(naegleria andersoni[&&NHX:TOL=129419],naegleria jamiesoni[&&NHX:TOL=129420])cluster4[&&NHX:TOL=130303])[&&NHX:TOL=130321])[&&NHX:TOL=130319],naegleria jadini[&&NHX:TOL=129415])[&&NHX:TOL=130361],(naegleria fowleri[&&NHX:TOL=129414],(naegleria lovaniensis[&&NHX:TOL=129416],naegleria johanseni[&&NHX:TOL=129832],naegleria martinezi[&&NHX:TOL=129831])[&&NHX:TOL=130289])cluster1[&&NHX:TOL=130288])[&&NHX:TOL=130318],((naegleria angularis[&&NHX:TOL=129835],naegleria pussardi[&&NHX:TOL=129424])[&&NHX:TOL=130295],(naegleria chilensis[&&NHX:TOL=129431],naegleria neochilensis[&&NHX:TOL=129844])[&&NHX:TOL=130296])cluster6[&&NHX:TOL=130294])naegleria[&&NHX:TOL=124653],willaertia magna[&&NHX:TOL=124654])[&&NHX:TOL=124652],ev10a[&&NHX:TOL=126376])[&&NHX:TOL=124651],pleurostomum flabellatum[&&NHX:TOL=124655])[&&NHX:TOL=126375])[&&NHX:TOL=124643],(acrasis rosea[&&NHX:TOL=126377],and 12[&&NHX:TOL=126378],pocheina[&&NHX:TOL=128549],guttulinopsis[&&NHX:TOL=128550],rosculus ithacus[&&NHX:TOL=128551])acrasida[&&NHX:TOL=124656])[&&NHX:TOL=124642],(neovahlkampfia damariscottae[&&NHX:TOL=126379],and 9[&&NHX:TOL=126380])[&&NHX:TOL=124657])[&&NHX:TOL=124641],(paravahlkampfia ustiana[&&NHX:TOL=124658],paravahlkampfia lenta[&&NHX:TOL=129906])paravahlkampfia[&&NHX:TOL=129905])[&&NHX:TOL=124640],((((monopylocystis visvesvarai[&&NHX:TOL=126386],undetermined atcc 50575[&&NHX:TOL=126387])[&&NHX:TOL=124662],(sawyeria marylandensis[&&NHX:TOL=124664],psalteriomonas lanterna[&&NHX:TOL=124665])[&&NHX:TOL=124663])[&&NHX:TOL=124661],(san2[&&NHX:TOL=126381],stachyamoeba sp.[&&NHX:TOL=126382],65f[&&NHX:TOL=126383],stachyamoeba lipophora[&&NHX:TOL=129498],gruberella flavescens[&&NHX:TOL=128553])gruberellidae[&&NHX:TOL=124666])[&&NHX:TOL=124660],(heteramoeba clara[&&NHX:TOL=124668],plaesiobystra hypersalinica[&&NHX:TOL=124669],pernina chaumonti[&&NHX:TOL=128552])[&&NHX:TOL=124667])[&&NHX:TOL=124659])[&&NHX:TOL=126384],macropharyngomonas halophila[&&NHX:TOL=126385])heterolobosea[&&NHX:TOL=96360])discicristates[&&NHX:TOL=124813],(((histiona[&&NHX:TOL=97409],reclinomonas americana[&&NHX:TOL=97410],stenocodon[&&NHX:TOL=97411],stomatochone[&&NHX:TOL=97412])histionidae[&&NHX:TOL=97408],jakoba libera[&&NHX:TOL=97415],seculamonas ecuadoriensis[&&NHX:TOL=97449],jakoba bahamensis[&&NHX:TOL=129570])[&&NHX:TOL=129569],(andalucia godoyi[&&NHX:TOL=125099],andalucia incarcerata[&&NHX:TOL=125100])andalucia[&&NHX:TOL=125098])jakobida[&&NHX:TOL=97407])[&&NHX:TOL=121180],(parabasalids[&&NHX:TOL=2421],(((((spironucleus anguillae[&&NHX:TOL=126313],spironucleus barkhanus[&&NHX:TOL=97387],spironucleus columbae[&&NHX:TOL=125132],spironucleus elegans[&&NHX:TOL=128380],spironucleus meleagridis[&&NHX:TOL=125131],spironucleus mobilis[&&NHX:TOL=126314],spironucleus muris[&&NHX:TOL=124840],spironucleus phycidis[&&NHX:TOL=128381],spironucleus salmonicida[&&NHX:TOL=124891],spironucleus salpae[&&NHX:TOL=128382],spironucleus torosa[&&NHX:TOL=124847],spironucleus vortens[&&NHX:TOL=124892])spironucleus[&&NHX:TOL=124844],((gyromonas ambulans[&&NHX:TOL=97381],gyromonas salinus[&&NHX:TOL=97382])gyromonas[&&NHX:TOL=97380],(hexamita axostyles[&&NHX:TOL=125144],hexamita capsulapris[&&NHX:TOL=125145],hexamita copelani[&&NHX:TOL=125314],hexamita cryptocerci[&&NHX:TOL=125123],hexamita giganti[&&NHX:TOL=125146],hexamita globulus[&&NHX:TOL=125147],hexamita guanqiaoensis[&&NHX:TOL=125148],hexamita honghuensis[&&NHX:TOL=125149],hexamita inflata[&&NHX:TOL=97384],hexamita intestinalis[&&NHX:TOL=125124],hexamita lateralis[&&NHX:TOL=124925],hexamita liangzihuensis[&&NHX:TOL=125150],hexamita longiformis[&&NHX:TOL=125151],hexamita mugilis[&&NHX:TOL=125125],hexamita nelsoni[&&NHX:TOL=125122],hexamita nobilis[&&NHX:TOL=125152],hexamita oviformis[&&NHX:TOL=125153],hexamita parva[&&NHX:TOL=125126],hexamita periplanetae[&&NHX:TOL=125127],hexamita pitheci[&&NHX:TOL=125128],hexamita polymorphola[&&NHX:TOL=125154],hexamita pusilla[&&NHX:TOL=97385],hexamita rodiformis[&&NHX:TOL=125155],hexamita salmonis[&&NHX:TOL=125129],hexamita teres[&&NHX:TOL=125130],hexamita transparenta[&&NHX:TOL=125156],hexamita variformis[&&NHX:TOL=125157],hexamita vesiformis[&&NHX:TOL=125158],hexamita wuchangensis[&&NHX:TOL=125159],hexamita xenocyprii[&&NHX:TOL=125160])hexamita[&&NHX:TOL=97383],(trepomonas agilis[&&NHX:TOL=97390],trepomonas angulatus[&&NHX:TOL=125120],trepomonas rotans[&&NHX:TOL=97391],trepomonas simplex[&&NHX:TOL=125121],trepomonas steini[&&NHX:TOL=97392])trepomonas[&&NHX:TOL=97389],((enteromonas caviae[&&NHX:TOL=124833],enteromonas hominis[&&NHX:TOL=124832],enteromonas intestinalis[&&NHX:TOL=125139],enteromonas lagostomi[&&NHX:TOL=125140],enteromonas ratti[&&NHX:TOL=125141],enteromonas suis[&&NHX:TOL=125142],enteromonas wenyoni[&&NHX:TOL=125143])enteromonas[&&NHX:TOL=97365],(trimitus motellae[&&NHX:TOL=124834],trimitus ranae[&&NHX:TOL=124835],trimitus trionici[&&NHX:TOL=128383])trimitus[&&NHX:TOL=97366],(caviomonas frugivori[&&NHX:TOL=124837],caviomonas mobilis[&&NHX:TOL=124836])caviomonas[&&NHX:TOL=124827])enteromonadidae[&&NHX:TOL=97363])[&&NHX:TOL=97379],trigonomonas[&&NHX:TOL=97393])hexamitinae[&&NHX:TOL=97386],(brugerolleia algonquinensis[&&NHX:TOL=97369],(giardia agilis[&&NHX:TOL=97371],giardia ardeae[&&NHX:TOL=97372],giardia beckeri[&&NHX:TOL=128384],giardia beltrani[&&NHX:TOL=128385],giardia botauri[&&NHX:TOL=128386],giardia bovis[&&NHX:TOL=128387],giardia bradypi[&&NHX:TOL=128388],giardia canis[&&NHX:TOL=128389],giardia caprae[&&NHX:TOL=128390],giardia cati[&&NHX:TOL=128391],giardia caviae[&&NHX:TOL=124927],giardia chinchillae[&&NHX:TOL=128392],giardia dasi[&&NHX:TOL=128393],giardia equii[&&NHX:TOL=128395],giardia floridae[&&NHX:TOL=128396],giardia hegneri[&&NHX:TOL=128397],giardia herodiadis[&&NHX:TOL=128398],giarida hyderabadensis[&&NHX:TOL=128399],giardia intestinalis[&&NHX:TOL=124841],giardia irarae[&&NHX:TOL=128400],giardia marginalis[&&NHX:TOL=128401],giardia melospizae[&&NHX:TOL=128402],giardia microti[&&NHX:TOL=124849],giardia muris[&&NHX:TOL=97376],giardia nycticori[&&NHX:TOL=128403],girdia ondatrae[&&NHX:TOL=128404],giardia otomyis[&&NHX:TOL=128405],giardia pitymysi[&&NHX:TOL=128406],giardia pseudoardeae[&&NHX:TOL=128407],giardia psittaci[&&NHX:TOL=124842],giardia recurvirostrae[&&NHX:TOL=128408],giardia sanguinis[&&NHX:TOL=128409],giardia serpentis[&&NHX:TOL=128410],giardia simoni[&&NHX:TOL=128411],giardia sturnellae[&&NHX:TOL=128412],giardia suricatae[&&NHX:TOL=128413],giardia tucani[&&NHX:TOL=128414],giardia varani[&&NHX:TOL=124843],giardia viscaciae[&&NHX:TOL=128415],giardia wenyoni[&&NHX:TOL=128416])giardia[&&NHX:TOL=97370],(octomitus intestinalis[&&NHX:TOL=124828],octomitus neglectus[&&NHX:TOL=124829])octomitus[&&NHX:TOL=97378])giardiinae[&&NHX:TOL=97368])diplomonadida[&&NHX:TOL=97367],((chilomastix aulastomi[&&NHX:TOL=124918],chilomastix bandicooti[&&NHX:TOL=124897],chilomastix bettencourti[&&NHX:TOL=124896],chilomastix bocis[&&NHX:TOL=124898],chilomastix bursa[&&NHX:TOL=124825],chilomastix caprae[&&NHX:TOL=124899],chilomastix caulleryi[&&NHX:TOL=97422],chilomastix cuniculi[&&NHX:TOL=124900],chilomastix cuspidata[&&NHX:TOL=97423],chilomastix equi[&&NHX:TOL=124901],chilomastix gallinarum[&&NHX:TOL=124902],chilomastix gigantea[&&NHX:TOL=124903],chilomastix hemidactyli[&&NHX:TOL=125133],chilomastix hyderabadensis[&&NHX:TOL=124904],chilomastix indica[&&NHX:TOL=124905],chilomastix instabilis[&&NHX:TOL=124906],chilomastix intestinalis[&&NHX:TOL=124907],chilomastix kudoi[&&NHX:TOL=125134],chilomastix magna[&&NHX:TOL=124908],chilomastix mediterraneus[&&NHX:TOL=124909],chilomastix megamorpha[&&NHX:TOL=124910],chilomastix mesnili[&&NHX:TOL=124824],chilomastix motellae[&&NHX:TOL=124911],chilomastix muris[&&NHX:TOL=125135],chilomastix nigricollisi[&&NHX:TOL=124912],chilomastix oblonga[&&NHX:TOL=124913],chilomastix palmari[&&NHX:TOL=124914],chilomastix quadrii[&&NHX:TOL=124915],chilomastix rosenbuchi[&&NHX:TOL=124916],chilomastix wenrichi[&&NHX:TOL=97424],chilomastix undulata[&&NHX:TOL=125136])chilomastix[&&NHX:TOL=97421],(retortamonas agilis[&&NHX:TOL=125108],retortamonas alexeieffi[&&NHX:TOL=124924],retortamonas arae[&&NHX:TOL=125137],retortamonas belostomae[&&NHX:TOL=125110],retortamonas blattae[&&NHX:TOL=97427],retortamonas boae[&&NHX:TOL=124920],retortamonas bradypi[&&NHX:TOL=125111],retortamonas caudatus[&&NHX:TOL=124893],retortamonas caviae[&&NHX:TOL=124926],retortamonas cheloni[&&NHX:TOL=125117],retortamonas cuniculi[&&NHX:TOL=125112],retortamonas dobelli[&&NHX:TOL=125113],retortamonas gryllotalpae[&&NHX:TOL=125104],retortamonas hodotermitis[&&NHX:TOL=97428],retortamonas intestinalis[&&NHX:TOL=124894],retortamonas kirbii[&&NHX:TOL=125116],retortamonas masoodi[&&NHX:TOL=125138],retortamonas mitrula[&&NHX:TOL=125118],retortamonas ovis[&&NHX:TOL=125114],retortamonas pericopti[&&NHX:TOL=125106],retortamonas phyllophagae[&&NHX:TOL=125107],retortamonas saurarum[&&NHX:TOL=124895],retortamonas sinensis[&&NHX:TOL=125115],retortamonas termitis[&&NHX:TOL=124919],retortamonas testudae[&&NHX:TOL=125119],retortamonas wenrichi[&&NHX:TOL=125109])retortamonas[&&NHX:TOL=97425])retortamonadida[&&NHX:TOL=97419])eopharyngia[&&NHX:TOL=126303],dysnectes brevis[&&NHX:TOL=121406],(carpediemonas bialata[&&NHX:TOL=124839],carpediemonas membranifera[&&NHX:TOL=124838])carpediemonas[&&NHX:TOL=124830])fornicata[&&NHX:TOL=121182])[&&NHX:TOL=124815],(oxymonads[&&NHX:TOL=2420],(trimastix inaequalis[&&NHX:TOL=97438],trimastix marina[&&NHX:TOL=97439],trimastix pyriformis[&&NHX:TOL=97440])trimastix[&&NHX:TOL=97437])preaxostyla[&&NHX:TOL=124889])excavates[&&NHX:TOL=2404],(((apusomonas proboscidea[&&NHX:TOL=20502],apusomonas australiensis[&&NHX:TOL=20503])apusomonas[&&NHX:TOL=20484],(amastigomonas bermudensis[&&NHX:TOL=20487],amastigomonas debruynei[&&NHX:TOL=20488],amastigomonas filosa[&&NHX:TOL=20489],amastigomonas mutabilis[&&NHX:TOL=20490],amastigomonas terricola[&&NHX:TOL=20491],amastigomonas klosteria[&&NHX:TOL=20492],amastigomonas gigantea[&&NHX:TOL=20493],amastigomonas griebensis[&&NHX:TOL=20494],amastigomonas marina[&&NHX:TOL=20495],amastigomonas muscula[&&NHX:TOL=20496])amastigomonas[&&NHX:TOL=20485])apusomonads[&&NHX:TOL=2387],(ancyromonas contorta[&&NHX:TOL=2452],ancyromonas sigmoides[&&NHX:TOL=2453],ancyromonas melba[&&NHX:TOL=2454])ancyromonas[&&NHX:TOL=2386],hemimastigotes[&&NHX:TOL=124817],biomyxa[&&NHX:TOL=2388],breviata anathema[&&NHX:TOL=124818],collodictyon[&&NHX:TOL=2393],anehmia exotica[&&NHX:TOL=98009],coelosporidium[&&NHX:TOL=2392],diphylleia[&&NHX:TOL=2399],discocelis[&&NHX:TOL=2400],komokiacea[&&NHX:TOL=2414],(luffisphaera bulbochaete[&&NHX:TOL=56954],luffisphaera cucumiformis[&&NHX:TOL=56955],luffisphaera hamatus[&&NHX:TOL=56956],luffisphaera longihastis[&&NHX:TOL=56957],luffisphaera myosurus[&&NHX:TOL=56958],luffisphaera perforata[&&NHX:TOL=56959],luffisphaera poculifera[&&NHX:TOL=56960],luffisphaera turriformis[&&NHX:TOL=56961])luffisphaera[&&NHX:TOL=2415],nephridiophagids[&&NHX:TOL=2418],desmothoracids[&&NHX:TOL=2397],schizocladus[&&NHX:TOL=96363],sticholonche[&&NHX:TOL=2435])protists of uncertain placement[&&NHX:TOL=2383])eukaryotes[&&NHX:TOL=3],(korarchaeota[&&NHX:TOL=7],(((thermofilum[&&NHX:TOL=13],(pyrobaculum[&&NHX:TOL=15],thermoproteus[&&NHX:TOL=16])[&&NHX:TOL=14])[&&NHX:TOL=12],((sulfolobus[&&NHX:TOL=19],(metallosphaera[&&NHX:TOL=21],acidianus[&&NHX:TOL=22])[&&NHX:TOL=20])[&&NHX:TOL=18],(((thermodiscus[&&NHX:TOL=26],igneococcus[&&NHX:TOL=27])[&&NHX:TOL=25],((thermosphaera[&&NHX:TOL=30],desulfurococcus[&&NHX:TOL=31])[&&NHX:TOL=29],staphylothermus[&&NHX:TOL=32])[&&NHX:TOL=28])[&&NHX:TOL=24],(pyrolobus[&&NHX:TOL=34],(hyperthermus[&&NHX:TOL=36],pyrodictium[&&NHX:TOL=37])[&&NHX:TOL=35])[&&NHX:TOL=33])[&&NHX:TOL=23])[&&NHX:TOL=17])crenarchaeota[&&NHX:TOL=9],((halobacteriales[&&NHX:TOL=40],methanomicrobiales[&&NHX:TOL=41])[&&NHX:TOL=39],methanobacteriales[&&NHX:TOL=42],methanococcales[&&NHX:TOL=43],methanopyrales[&&NHX:TOL=44],archeoglobales[&&NHX:TOL=45],thermoplasmales[&&NHX:TOL=46],thermococcales[&&NHX:TOL=47])euryarchaeota[&&NHX:TOL=10])[&&NHX:TOL=8])archaea[&&NHX:TOL=4],((cystoviridae[&&NHX:TOL=57917],(orthoreovirus[&&NHX:TOL=57919],orbivirus[&&NHX:TOL=57920],rotavirus[&&NHX:TOL=57921],coltivirus[&&NHX:TOL=57922],seadornavirus[&&NHX:TOL=57923],aquareovirus[&&NHX:TOL=57924],idnoreovirus[&&NHX:TOL=57925],cypovirus[&&NHX:TOL=57926],fijivirus[&&NHX:TOL=57927],phytoreovirus[&&NHX:TOL=57928],oryzavirus[&&NHX:TOL=57929],mycoreovirus[&&NHX:TOL=57930])reoviridae[&&NHX:TOL=57918],(aquabirnavirus[&&NHX:TOL=57932],avibirnavirus[&&NHX:TOL=57933],entomobirnavirus[&&NHX:TOL=57934])birnaviridae[&&NHX:TOL=57931],(totivirus[&&NHX:TOL=57936],giardiavirus[&&NHX:TOL=57937],leishmaniavirus[&&NHX:TOL=57938])totiviridae[&&NHX:TOL=57935],(partitivirus[&&NHX:TOL=57940],alphacryptovirus[&&NHX:TOL=57941],betacryptovirus[&&NHX:TOL=57942])partitiviridae[&&NHX:TOL=57939],chrysoviridae[&&NHX:TOL=57943],endornavirus[&&NHX:TOL=57944])doublestranded rna viruses[&&NHX:TOL=21833],((bornaviridae[&&NHX:TOL=57946],rhabdoviridae[&&NHX:TOL=57947],filoviridae[&&NHX:TOL=57948],paramyxoviridae[&&NHX:TOL=57949])mononegavirales[&&NHX:TOL=57945],orthomyxoviridae[&&NHX:TOL=57950],bunyaviridae[&&NHX:TOL=57951],arenaviridae[&&NHX:TOL=57952],tenuivirus[&&NHX:TOL=57953],varicosavirus[&&NHX:TOL=57954],ophiovirus[&&NHX:TOL=57955],deltavirus[&&NHX:TOL=57956])singlestranded negative sense rna viruses[&&NHX:TOL=21834],(leviviridae[&&NHX:TOL=57957],narnaviridae[&&NHX:TOL=57958],picornaviridae[&&NHX:TOL=57959],iflavirus[&&NHX:TOL=57960],dicistroviridae[&&NHX:TOL=57961],marnaviridae[&&NHX:TOL=57962],sequiviridae[&&NHX:TOL=57963],sadwavirus[&&NHX:TOL=57964],cheravirus[&&NHX:TOL=57965],comoviridae[&&NHX:TOL=57966],potyviridae[&&NHX:TOL=57967],caliciviridae[&&NHX:TOL=57968],hepevirus[&&NHX:TOL=57969],astroviridae[&&NHX:TOL=57970],nodaviridae[&&NHX:TOL=57971],tetraviridae[&&NHX:TOL=57972],sobemovirus[&&NHX:TOL=57973],luteoviridae[&&NHX:TOL=57974],umbravirus[&&NHX:TOL=57975],tombusviridae[&&NHX:TOL=57976],(coronaviridae[&&NHX:TOL=57978],arteriviridae[&&NHX:TOL=57979],roniviridae[&&NHX:TOL=57980])nidovirales[&&NHX:TOL=57977],flaviviridae[&&NHX:TOL=57981],togaviridae[&&NHX:TOL=57982],tobamovirus[&&NHX:TOL=57983],tobravirus[&&NHX:TOL=57984],hordeivirus[&&NHX:TOL=57985],furovirus[&&NHX:TOL=57986],pomovirus[&&NHX:TOL=57987],pecluvirus[&&NHX:TOL=57988],benyvirus[&&NHX:TOL=57989],bromoviridae[&&NHX:TOL=57990],ourmiavirus[&&NHX:TOL=57991],idaeovirus[&&NHX:TOL=57992],tymoviridae[&&NHX:TOL=57993],closteroviridae[&&NHX:TOL=57994],flexiviridae[&&NHX:TOL=57995],barnaviridae[&&NHX:TOL=57996])singlestranded positive sense rna viruses[&&NHX:TOL=21835],((inovirus[&&NHX:TOL=57257],plectrovirus[&&NHX:TOL=57258])inoviridae[&&NHX:TOL=57256],(microvirus[&&NHX:TOL=57260],chlamydiamicrovirus[&&NHX:TOL=57261],bdellomicrovirus[&&NHX:TOL=57262],spiromicrovirus[&&NHX:TOL=57263])microviridae[&&NHX:TOL=57259],(mastrevirus[&&NHX:TOL=57265],curtovirus[&&NHX:TOL=57266],topocuvirus[&&NHX:TOL=57267],begomovirus[&&NHX:TOL=57268])geminiviridae[&&NHX:TOL=57264],(circovirus[&&NHX:TOL=57270],gyrovirus[&&NHX:TOL=57271])circoviridae[&&NHX:TOL=57269],(nanovirus[&&NHX:TOL=57273],babuvirus[&&NHX:TOL=57274])nanoviridae[&&NHX:TOL=57272],((parvovirus[&&NHX:TOL=57277],erythrovirus[&&NHX:TOL=57278],dependovirus[&&NHX:TOL=57279],amdovirus[&&NHX:TOL=57280],bocavirus[&&NHX:TOL=57281])parvovirinae[&&NHX:TOL=57276],(densovirus[&&NHX:TOL=57283],iteravirus[&&NHX:TOL=57284],brevidensovirus[&&NHX:TOL=57285],pefudensovirus[&&NHX:TOL=57286])densovirinae[&&NHX:TOL=57282])parvoviridae[&&NHX:TOL=57275],anellovirus[&&NHX:TOL=57997])singlestranded dna viruses[&&NHX:TOL=21829],((siphoviridae[&&NHX:TOL=57289],myoviridae[&&NHX:TOL=57288],podoviridae[&&NHX:TOL=57999])caudovirales[&&NHX:TOL=57998],tectiviridae[&&NHX:TOL=57292],corticoviridae[&&NHX:TOL=57293],plasmaviridae[&&NHX:TOL=57294],(alphalipothrixvirus[&&NHX:TOL=57296],betalipothrixvirus[&&NHX:TOL=57297],gammalipothrixvirus[&&NHX:TOL=57298])lipothrixviridae[&&NHX:TOL=57295],rudiviridae[&&NHX:TOL=57299],fuselloviridae[&&NHX:TOL=57300],guttaviridae[&&NHX:TOL=57301],((orthopoxvirus[&&NHX:TOL=57304],parapoxvirus[&&NHX:TOL=57305],avipoxvirus[&&NHX:TOL=57306],capripoxvirus[&&NHX:TOL=57307],leporipoxvirus[&&NHX:TOL=57308],suipoxvirus[&&NHX:TOL=57309],molluscipoxvirus[&&NHX:TOL=57310],yatapoxvirus[&&NHX:TOL=57311])chordopoxvirinae[&&NHX:TOL=57303],(alphaentomopoxvirus[&&NHX:TOL=57313],betaentomopoxvirus[&&NHX:TOL=57314],gammaentomopoxvirus[&&NHX:TOL=57315])entomopoxvirinae[&&NHX:TOL=57312])poxviridae[&&NHX:TOL=57302],asfarviridae[&&NHX:TOL=57316],(iridovirus[&&NHX:TOL=57318],chloriridovirus[&&NHX:TOL=57319],ranavirus[&&NHX:TOL=57320],lymphocystivirus[&&NHX:TOL=57321],megalocytivirus[&&NHX:TOL=57322])iridoviridae[&&NHX:TOL=57317],(chlorovirus[&&NHX:TOL=57324],coccolithovirus[&&NHX:TOL=57325],prasinovirus[&&NHX:TOL=57326],prymnesiovirus[&&NHX:TOL=57327],phaeovirus[&&NHX:TOL=57328],raphidovirus[&&NHX:TOL=57329])phycodnaviridae[&&NHX:TOL=57323],(nucleopolyhedrovirus[&&NHX:TOL=57331],granulovirus[&&NHX:TOL=57332])baculoviridae[&&NHX:TOL=57330],nimaviridae[&&NHX:TOL=57333],((simplexvirus[&&NHX:TOL=57336],varicellovirus[&&NHX:TOL=57337],mardivirus[&&NHX:TOL=57338],iltovirus[&&NHX:TOL=57339])alphaherpesvirinae[&&NHX:TOL=57335],(cytomegalovirus[&&NHX:TOL=57341],muromegalovirus[&&NHX:TOL=57342],roseolovirus[&&NHX:TOL=57343])betaherpesvirinae[&&NHX:TOL=57340],(lymphocryptovirus[&&NHX:TOL=57345],rhadinovirus[&&NHX:TOL=57346])gammaherpesvirinae[&&NHX:TOL=57344],ictalurivirus[&&NHX:TOL=57347])herpesviridae[&&NHX:TOL=57334],(mastadenovirus[&&NHX:TOL=57349],aviadenovirus[&&NHX:TOL=57350],atadenovirus[&&NHX:TOL=57351],siadenovirus[&&NHX:TOL=57352])adenoviridae[&&NHX:TOL=57348],polyomaviridae[&&NHX:TOL=57353],(alphapapillomavirus[&&NHX:TOL=57355],betapapillomavirus[&&NHX:TOL=57356],gammapapillomavirus[&&NHX:TOL=57357],deltapapillomavirus[&&NHX:TOL=57358],epsilonpapillomavirus[&&NHX:TOL=57359],zetapapillomavirus[&&NHX:TOL=57360],etapapillomavirus[&&NHX:TOL=57361],thetapapillomavirus[&&NHX:TOL=57362],iotapapillomavirus[&&NHX:TOL=57363],kappapapillomavirus[&&NHX:TOL=57364],lambdapapillomavirus[&&NHX:TOL=57365],mupapillomavirus[&&NHX:TOL=57366],nupapillomavirus[&&NHX:TOL=57367],xipapillomavirus[&&NHX:TOL=57368],omikronpapillomavirus[&&NHX:TOL=57369],pipapillomavirus[&&NHX:TOL=57370])papillomaviridae[&&NHX:TOL=57354],(bracovirus[&&NHX:TOL=57372],ichnovirus[&&NHX:TOL=57373])polydnaviridae[&&NHX:TOL=57371],ascoviridae[&&NHX:TOL=57374],salterprovirus[&&NHX:TOL=58000],rhizidiovirus[&&NHX:TOL=58001],mimivirus[&&NHX:TOL=57375])doublestranded dna viruses[&&NHX:TOL=21830],(hepadnaviridae[&&NHX:TOL=57376],caulimoviridae[&&NHX:TOL=57377],pseudoviridae[&&NHX:TOL=57378],metaviridae[&&NHX:TOL=57379],(alpharetrovirus[&&NHX:TOL=57381],betaretrovirus[&&NHX:TOL=57382],gammaretrovirus[&&NHX:TOL=57383],deltaretrovirus[&&NHX:TOL=57384],epsilonretrovirus[&&NHX:TOL=57385],lentivirus[&&NHX:TOL=57386],spumavirus[&&NHX:TOL=57387])retroviridae[&&NHX:TOL=57380])dnarna reverse transcribing viruses[&&NHX:TOL=21831])viruses[&&NHX:TOL=5])life on earth[&&NHX:TOL=1]BioPerl-1.007002/t/data/traits.tab000444000766000024        56113155576322 16651 0ustar00cjfieldsstaff000000000000"id"	"assoc"	disp	"intermediate"
0	"blue"	blue	"red"
1	"blue"	blue	"red"
2	"blue"		"blue"
3	"blue"	blue	"blue"
4	"blue"	red	"blue"
5	"blue"	blue	"red"
6	"blue"	red	"blue"
7	"blue"	blue	"blue"
8	"blue"	red	"blue"
9	"red"	blue	"red"
10	"red"	red	"red"
11	"red"	blue	"blue"
12	"red"	red	"blue"
13	"red"	blue	"red"
14	"red"	red	"red"
15	"red"	blue	"red"
16	"red"	red	"red"
BioPerl-1.007002/t/data/traittree.nexus000444000766000024        32413155576322 17737 0ustar00cjfieldsstaff000000000000#NEXUS 

Begin trees;

tree PAUP_1 = [&U] ((((1:1,2:1)N1:1,(3:1,4:1)N2:1)N3:1,((5:1,6:1)N4:1,(7:1,8:1)N5:1)N6:1)N7:1,(((9:1,10:1)N8:1,(11:1,12:1)N9:1)N10:1,((13:1,14:1)N11:1,(15:1,16:1)N12:1)N13:1)N14:1);


end;
BioPerl-1.007002/t/data/transfac.dat000444000766000024       454313155576322 17172 0ustar00cjfieldsstaff000000000000VV  TRANSFAC MATRIX TABLE, Release 6.4 - licensed - 2002-12-02, (C) Biobase GmbH
XX
//
AC  M00001
XX
ID  V$MYOD_01
XX
DT  19.10.1992 (created); ewi.
DT  22.10.1997 (updated); dbo.
CO  Copyright (C), Biobase GmbH.
XX
NA  MyoD
XX
DE  myoblast determination gene product
XX
BF  T00526; MyoD; Species: mouse, Mus musculus.
XX
P0      A      C      G      T
01      1      2      2      0      S
02      2      1      2      0      R
03      3      0      1      1      A
04      0      5      0      0      C
05      5      0      0      0      A
06      0      0      4      1      G
07      0      1      4      0      G
08      0      0      0      5      T
09      0      0      5      0      G
10      0      1      2      2      K
11      0      2      0      3      Y
12      1      0      3      1      G
XX
BA  5 functional elements in 3 genes
XX
CC  no comment
XX
//
AC  M00002
XX
ID  V$E47_01
XX
DT  19.10.1992 (created); ewi.
DT  18.07.2000 (updated); ewi.
CO  Copyright (C), Biobase GmbH.
XX
NA  E47
XX
DE  E47
XX
BF  T00207; E47; Species: human, Homo sapiens.
XX
P0      A      C      G      T
01      4      4      3      0      V
02      2      5      4      0      S
03      3      2      4      2      N
04      2      0      9      0      G
05      0     11      0      0      C
06     11      0      0      0      A
07      0      0     11      0      G
08      1      2      8      0      G
09      0      0      0     11      T
10      0      0     11      0      G
11      0      0      4      7      K
12      1      4      3      3      N
13      1      6      2      2      C
14      1      4      4      2      N
15      1      4      2      3      N
XX
BA  11 selected strong binding sites for E47, E47-MyoD, E12+MyoD and (weak) for
BA  E12
XX
BS  R05108; Start: 3; Length: 15; Gaps: 17; Orientation: p.
BS  R05109; Start: 1; Length: 15; Gaps:; Orientation: p.
BS  R05110; Start: 5; Length: 15; Gaps:; Orientation: p.
BS  R05111; Start: 5; Length: 15; Gaps:; Orientation: p.
BS  R05112; Start: 8; Length: 15; Gaps:; Orientation: p.
BS  R05113; Start: 9; Length: 15; Gaps:; Orientation: p.
BS  R05114; Start: 8; Length: 15; Gaps:; Orientation: p.
BS  R05115; Start: 7; Length: 15; Gaps:; Orientation: p.
BS  R05116; Start: 11; Length: 15; Gaps:; Orientation: p.
BS  R05117; Start: 5; Length: 15; Gaps:; Orientation: p.
BS  R05118; Start: 5; Length: 15; Gaps:; Orientation: p.
XX

BioPerl-1.007002/t/data/tree_nonewline.nexus000444000766000024        43713155576322 20756 0ustar00cjfieldsstaff000000000000#NEXUS 

Begin trees;  [Treefile saved Wed Jul 26 19:40:41 2000]

[output from your data run]

Translate 1 TRXEcoli, 2 TRXHomo, 3 TRXSacch, 4 erCaelA, 5 erCaelB, 6 erCaelC, 7 erHomoA, 8 erHomoB, 9 erHomoC, 10 erpCaelC ; 

tree PAUP_1 = [&U] (1,((2,3),((((4,10),(5,8)),(6,9)),7))); End; 
BioPerl-1.007002/t/data/trees.nexml.old.xml000444000766000024      1071013155576322 20453 0ustar00cjfieldsstaff000000000000


	
		
		
		
		
		
	
	
	
		
		
			
			
			
			
				
					true
				
			
			
			
			
			
			
						
			
			
			
			
			
			
			
		
		
		
			
			
			
			
				
					true
				
			
			
			
			
			
			
						
			
			
			
			
			
			
			
			
		
		
			
			
			
			
			
			
			
			
			
						
			
			
			
			
			
			 
			
			
						
	

BioPerl-1.007002/t/data/tricky.wublast000444000766000024       573213155576322 17610 0ustar00cjfieldsstaff000000000000Reference:  Gish, W. (1996-2004) http://blast.wustl.edu

Query=  AT1G70100.2 | Symbol: None | expressed protein | chr1:26406799-26409760
    FORWARD | Aliases: None
        (483 letters; record 9)

Database:  AraRicMaiMedVir
           151,652 sequences; 63,865,049 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done

                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

AT5G55660.1 | Symbol: None | expressed protein, similar t...   104  0.019     1




>AT5G55660.1 | Symbol: None | expressed protein, similar to unknown protein
            (pir::T08929) | chr5:22556601-22560700 FORWARD | Aliases: MDF20.10,
            MDF20_10
        Length = 779

 Score = 104 (41.7 bits), Expect = 0.019, P = 0.019
 Identities = 58/240 (24%), Positives = 106/240 (44%)

Query: 115 - 350
Sbjct: 159 - 380

 Score = 93 (37.8 bits), Expect = 0.29, P = 0.26
 Identities = 45/211 (21%), Positives = 82/211 (38%)

Query: 182 - 389
Sbjct: 527 - 730

 Score = 88 (36.0 bits), Expect = 1.0, P = 0.64
 Identities = 54/229 (23%), Positives = 91/229 (39%)

Query: 175 - 398
Sbjct: 444 - 642

 Score = 83 (34.3 bits), Expect = 3.6, P = 0.97
 Identities = 85/386 (22%), Positives = 150/386 (38%)

Query: 115 - 473
Sbjct: 159 - 534

 Score = 78 (32.5 bits), Expect = 0.43, Sum P(2) = 0.35
 Identities = 50/253 (19%), Positives = 112/253 (44%)

Query: 36 - 280
Sbjct: 24 - 261

 Score = 59 (25.8 bits), Expect = 0.43, Sum P(2) = 0.35
 Identities = 45/225 (20%), Positives = 83/225 (36%)

Query: 267 - 478
Sbjct: 445 - 662

 Score = 57 (25.1 bits), Expect = 0.68, Sum P(2) = 0.50
 Identities = 43/212 (20%), Positives = 89/212 (41%)

Query: 276 - 481
Sbjct: 479 - 678



Parameters:
  gi
  noseqs
  stats
  wordmask=seg+xnu
  qrecmin=1
  qrecmax=10110
  E=10
  V=10000
  B=10000
  postsw

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.306   0.122   0.320    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E    S W   T  X   E2     S2
   +0      0      483       483       10.  78 3  10 23  0.19    35
                                                    35  0.22    37


Statistics:
  Query          Expected          Observed           HSPs
  Frame  MatID  High Score        High Score       Reportable
   +0      0    71 (31.4 bits)  2415 (1066.8 bits)   1089

  Query         Neighborhd  Word      Excluded    Failed   Successful  Overlaps
  Frame  MatID   Words      Hits        Hits    Extensions Extensions  Excluded
   +0      0     14620    91959369    23132921    68703395   123053      3666

BioPerl-1.007002/t/data/trna.strict.rnamotif000444000766000024      4676113155576322 20743 0ustar00cjfieldsstaff000000000000#RM scored
#RM descr h5 ss h5 ss h3 ss h5 ss h3 ss h5 ss h3 h3 ss
#RM dfile trna.strict.descr
>gi|173683|gb|M10671|ACSTRW Avian oncornavirus Trp-tRNA
gi|173683|gb|M10671|ACSTRW    0.000 0       1   75 gacctcg tg gcg caacggtag cgc g tctga ctccaga tcaga aggctgc gtgt tcgaatc acgt cggggtc acca
>gi|173683|gb|M10671|ACSTRW Avian oncornavirus Trp-tRNA
gi|173683|gb|M10671|ACSTRW    0.000 0       1   75 gacctcg tg gcg caacggtag cgc g tctga ctccaga tcaga aggct gcgtg ttcgaat cacgt cggggtc acca
>gi|173683|gb|M10671|ACSTRW Avian oncornavirus Trp-tRNA
gi|173683|gb|M10671|ACSTRW    0.000 0       1   75 gacctcg tg gcgc aacggta gcgc g tctga ctccaga tcaga aggctgc gtgt tcgaatc acgt cggggtc acca
>gi|173683|gb|M10671|ACSTRW Avian oncornavirus Trp-tRNA
gi|173683|gb|M10671|ACSTRW    0.000 0       1   75 gacctcg tg gcgc aacggta gcgc g tctga ctccaga tcaga aggct gcgtg ttcgaat cacgt cggggtc acca
>gi|173683|gb|M10671|ACSTRW Avian oncornavirus Trp-tRNA
gi|173683|gb|M10671|ACSTRW    0.000 0       2   73 acctcg tg gcg caacggtag cgc g tctga ctccaga tcaga aggctgc gtgt tcgaatc acgt cggggt cacc
>gi|173683|gb|M10671|ACSTRW Avian oncornavirus Trp-tRNA
gi|173683|gb|M10671|ACSTRW    0.000 0       2   73 acctcg tg gcg caacggtag cgc g tctga ctccaga tcaga aggct gcgtg ttcgaat cacgt cggggt cacc
>gi|173683|gb|M10671|ACSTRW Avian oncornavirus Trp-tRNA
gi|173683|gb|M10671|ACSTRW    0.000 0       2   73 acctcg tg gcgc aacggta gcgc g tctga ctccaga tcaga aggctgc gtgt tcgaatc acgt cggggt cacc
>gi|173683|gb|M10671|ACSTRW Avian oncornavirus Trp-tRNA
gi|173683|gb|M10671|ACSTRW    0.000 0       2   73 acctcg tg gcgc aacggta gcgc g tctga ctccaga tcaga aggct gcgtg ttcgaat cacgt cggggt cacc
>gi|173684|gb|M29552|ACYRR16S A.pyogenes 16S ribosomal RNA
gi|173684|gb|M29552|ACYRR16S    0.000 0     510   76 cgcggta at acg tagggcnctag cgt t gtccg gaattat tgggc gtaaag agct cgtaggc ggtt tgttgcg cctg
>gi|173684|gb|M29552|ACYRR16S A.pyogenes 16S ribosomal RNA
gi|173684|gb|M29552|ACYRR16S    0.000 0     510   76 cgcggta at acgt agggcncta gcgt t gtccg gaattat tgggc gtaaag agct cgtaggc ggtt tgttgcg cctg
>gi|173684|gb|M29552|ACYRR16S A.pyogenes 16S ribosomal RNA
gi|173684|gb|M29552|ACYRR16S    0.000 0     511   74 gcggta at acg tagggcnctag cgt t gtccg gaattat tgggc gtaaag agct cgtaggc ggtt tgttgc gcct
>gi|173684|gb|M29552|ACYRR16S A.pyogenes 16S ribosomal RNA
gi|173684|gb|M29552|ACYRR16S    0.000 0     511   74 gcggta at acgt agggcncta gcgt t gtccg gaattat tgggc gtaaag agct cgtaggc ggtt tgttgc gcct
>gi|173689|gb|M33910|ACYRRNAO A.odontolyticus 16S ribosomal RNA
gi|173689|gb|M33910|ACYRRNAO    0.000 0      92   77 gggttg gt gga aaggttttt tct g gtggg ggatggg ctcgc ggcctatcagc ttgt tggtggg gtga tggcct acca
>gi|173689|gb|M33910|ACYRRNAO A.odontolyticus 16S ribosomal RNA
gi|173689|gb|M33910|ACYRRNAO    0.000 0      92   77 gggttg gt ggaa aggtttt ttct g gtggg ggatggg ctcgc ggcctatcagc ttgt tggtggg gtga tggcct acca
>gi|173725|gb|K00230|ANITRLCAA Anacystis nidulans Leu-tRNA-CAA
gi|173725|gb|K00230|ANITRLCAA    0.000 0       1   87 gggcaag tg gcg gaattggtaga cgc a gcaga ctcaaaa tctgc cgctagcgatagtgt gtggg ttcgagt cccac cttgccc acca
>gi|173725|gb|K00230|ANITRLCAA Anacystis nidulans Leu-tRNA-CAA
gi|173725|gb|K00230|ANITRLCAA    0.000 0       2   85 ggcaag tg gcg gaattggtaga cgc a gcaga ctcaaaa tctgc cgctagcgatagtgt gtggg ttcgagt cccac cttgcc cacc
>gi|173726|gb|K00231|ANITRLCAG Anacystis nidulans Leu-tRNA-CAG
gi|173726|gb|K00231|ANITRLCAG    0.000 0       1   87 gcggaac tg gcg aaattggtaga cgc g ctaga ttcaggt tctag tggtttcacgactgt ccggg ttcaagt cccgg gttccgc acca
>gi|173726|gb|K00231|ANITRLCAG Anacystis nidulans Leu-tRNA-CAG
gi|173726|gb|K00231|ANITRLCAG    0.000 0       2   85 cggaac tg gcg aaattggtaga cgc g ctaga ttcaggt tctag tggtttcacgactgt ccggg ttcaagt cccgg gttccg cacc
>gi|173727|gb|K00311|ANITRMF Anacystis nidulans initiator Met-tRNA-f
gi|173727|gb|K00311|ANITRMF    0.000 0       2   75 gcgggg ta gag cagcctggtag ctc g tcggg ctcataa cccga aggtc agagg ttcaaat cctct ccccgc cacc
>gi|173727|gb|K00311|ANITRMF Anacystis nidulans initiator Met-tRNA-f
gi|173727|gb|K00311|ANITRMF    0.000 0       2   75 gcgggg ta gagc agcctggta gctc g tcggg ctcataa cccga aggtc agagg ttcaaat cctct ccccgc cacc
>gi|1236163|gb|L41047|ANNRRO Actinoplanes sp. ribosomal RNA (rRNA)
gi|1236163|gb|L41047|ANNRRO    0.000 0     464   85 cgcggt aa gacg tagggcgcgag cgtt g tccg gatttat tggg cgtaaagagctcgtagg cggc ttgttgc gtcg gctgtg aaaa
>gi|1236163|gb|L41047|ANNRRO Actinoplanes sp. ribosomal RNA (rRNA)
gi|1236163|gb|L41047|ANNRRO    0.000 0     464   76 cgcggt aa gacg tagggcgcgag cgtt g tccg gatttat tggg cgtaaa gagct cgtaggc ggctt gttgcg tcgg
>gi|1236163|gb|L41047|ANNRRO Actinoplanes sp. ribosomal RNA (rRNA)
gi|1236163|gb|L41047|ANNRRO    0.000 0     464   76 cgcggta ag acg tagggcgcgag cgt t gtccg gatttat tgggc gtaaag agct cgtaggc ggct tgttgcg tcgg
>gi|1236163|gb|L41047|ANNRRO Actinoplanes sp. ribosomal RNA (rRNA)
gi|1236163|gb|L41047|ANNRRO    0.000 0     464   76 cgcggta ag acgt agggcgcga gcgt t gtccg gatttat tgggc gtaaag agct cgtaggc ggct tgttgcg tcgg
>gi|1236163|gb|L41047|ANNRRO Actinoplanes sp. ribosomal RNA (rRNA)
gi|1236163|gb|L41047|ANNRRO    0.000 0     465   74 gcggta ag acg tagggcgcgag cgt t gtccg gatttat tgggc gtaaag agct cgtaggc ggct tgttgc gtcg
>gi|1236163|gb|L41047|ANNRRO Actinoplanes sp. ribosomal RNA (rRNA)
gi|1236163|gb|L41047|ANNRRO    0.000 0     465   74 gcggta ag acgt agggcgcga gcgt t gtccg gatttat tgggc gtaaag agct cgtaggc ggct tgttgc gtcg
>gi|173750|gb|M37693|ARGRRNASS Arthobacter simplex small subunit ribosomal RNA
gi|173750|gb|M37693|ARGRRNASS    0.000 0     502   76 cgcggta at acg tagggtccnag cgt t gtccg gaattat tgggc gtaaag ggct cgtaggc ggtt tgtcgcg tcgg
>gi|173750|gb|M37693|ARGRRNASS Arthobacter simplex small subunit ribosomal RNA
gi|173750|gb|M37693|ARGRRNASS    0.000 0     502   76 cgcggta at acgt agggtccna gcgt t gtccg gaattat tgggc gtaaag ggct cgtaggc ggtt tgtcgcg tcgg
>gi|173750|gb|M37693|ARGRRNASS Arthobacter simplex small subunit ribosomal RNA
gi|173750|gb|M37693|ARGRRNASS    0.000 0     503   74 gcggta at acg tagggtccnag cgt t gtccg gaattat tgggc gtaaag ggct cgtaggc ggtt tgtcgc gtcg
>gi|173750|gb|M37693|ARGRRNASS Arthobacter simplex small subunit ribosomal RNA
gi|173750|gb|M37693|ARGRRNASS    0.000 0     503   74 gcggta at acgt agggtccna gcgt t gtccg gaattat tgggc gtaaag ggct cgtaggc ggtt tgtcgc gtcg
>gi|173764|gb|K00326|ASRTRMI Asterias amurensis initiator Met-tRNA-i
gi|173764|gb|K00326|ASRTRMI    0.000 0       1   75 agcagag tg gcg cagtggaag cgt g ctggg cccataa cccag aggtc cgagg atcgaaa cctcg ctctgct acca
>gi|173764|gb|K00326|ASRTRMI Asterias amurensis initiator Met-tRNA-i
gi|173764|gb|K00326|ASRTRMI    0.000 0       1   75 agcagag tg gcgc agtggaa gcgt g ctggg cccataa cccag aggtc cgagg atcgaaa cctcg ctctgct acca
>gi|173764|gb|K00326|ASRTRMI Asterias amurensis initiator Met-tRNA-i
gi|173764|gb|K00326|ASRTRMI    0.000 0       2   73 gcagag tg gcg cagtggaag cgt g ctggg cccataa cccag aggtc cgagg atcgaaa cctcg ctctgc tacc
>gi|173764|gb|K00326|ASRTRMI Asterias amurensis initiator Met-tRNA-i
gi|173764|gb|K00326|ASRTRMI    0.000 0       2   73 gcagag tg gcgc agtggaa gcgt g ctggg cccataa cccag aggtc cgagg atcgaaa cctcg ctctgc tacc
>gi|173764|gb|K00326|ASRTRMI Asterias amurensis initiator Met-tRNA-i
gi|173764|gb|K00326|ASRTRMI    0.000 0       2   73 gcagagt gg cgc agtggaagc gtg c tggg cccataa ccca gaggtcc gagg atcgaaa cctc gctctgc tacc
>gi|173764|gb|K00326|ASRTRMI Asterias amurensis initiator Met-tRNA-i
gi|173764|gb|K00326|ASRTRMI    0.000 0       3   71 cagagt gg cgc agtggaagc gtg c tggg cccataa ccca gaggtcc gagg atcgaaa cctc gctctg ctac
>gi|173793|gb|K00141|BACTRA B.subtilis Ala-tRNA
gi|173793|gb|K00141|BACTRA    0.000 0       1   76 ggagcct ta gct cagctgggag agc g cctgc tttgcac gcagg aggtc agcgg ttcgatc ccgct aggctcc acca
>gi|173793|gb|K00141|BACTRA B.subtilis Ala-tRNA
gi|173793|gb|K00141|BACTRA    0.000 0       1   76 ggagcct ta gctc agctggga gagc g cctgc tttgcac gcagg aggtc agcgg ttcgatc ccgct aggctcc acca
>gi|173793|gb|K00141|BACTRA B.subtilis Ala-tRNA
gi|173793|gb|K00141|BACTRA    0.000 0       2   74 gagcct ta gct cagctgggag agc g cctgc tttgcac gcagg aggtc agcgg ttcgatc ccgct aggctc cacc
>gi|173793|gb|K00141|BACTRA B.subtilis Ala-tRNA
gi|173793|gb|K00141|BACTRA    0.000 0       2   74 gagcct ta gctc agctggga gagc g cctgc tttgcac gcagg aggtc agcgg ttcgatc ccgct aggctc cacc
>gi|304176|gb|L18939|BACTRCYSA Bacillus subtilis transfer RNA-Cys
gi|304176|gb|L18939|BACTRCYSA    0.000 0       1   74 ggcggca ta gcc aagtggtaa ggc a gaggt cttcaaa acctt tatc cccgg ttcgaat ccggg tgccgcc tcca
>gi|304176|gb|L18939|BACTRCYSA Bacillus subtilis transfer RNA-Cys
gi|304176|gb|L18939|BACTRCYSA    0.000 0       2   72 gcggca ta gcc aagtggtaa ggc a gaggt cttcaaa acctt tatc cccgg ttcgaat ccggg tgccgc ctcc
>gi|173794|gb|K00332|BACTRF B.stearothermophilus Phe-tRNA
gi|173794|gb|K00332|BACTRF    0.000 0       1   76 ggctcgg ta gct cagtcggtag agc a aagga ctgaaaa tcctt gtgtc ggcgg ttcgatt ccgtc ccgagcc acca
>gi|173794|gb|K00332|BACTRF B.stearothermophilus Phe-tRNA
gi|173794|gb|K00332|BACTRF    0.000 0       1   76 ggctcgg ta gctc agtcggta gagc a aagga ctgaaaa tcctt gtgtc ggcgg ttcgatt ccgtc ccgagcc acca
>gi|173794|gb|K00332|BACTRF B.stearothermophilus Phe-tRNA
gi|173794|gb|K00332|BACTRF    0.000 0       2   74 gctcgg ta gct cagtcggtag agc a aagga ctgaaaa tcctt gtgtc ggcgg ttcgatt ccgtc ccgagc cacc
>gi|173794|gb|K00332|BACTRF B.stearothermophilus Phe-tRNA
gi|173794|gb|K00332|BACTRF    0.000 0       2   74 gctcgg ta gctc agtcggta gagc a aagga ctgaaaa tcctt gtgtc ggcgg ttcgatt ccgtc ccgagc cacc
>gi|173795|gb|K00333|BACTRFA B.subtilis Phe-tRNA
gi|173795|gb|K00333|BACTRFA    0.000 0       1   76 ggctcgg ta gct cagttggtag agc a acgga ctgaaaa tccgt gtgtc ggcgg ttcgatt ccgtc ccgagcc acca
>gi|173795|gb|K00333|BACTRFA B.subtilis Phe-tRNA
gi|173795|gb|K00333|BACTRFA    0.000 0       1   76 ggctcgg ta gctc agttggta gagc a acgga ctgaaaa tccgt gtgtc ggcgg ttcgatt ccgtc ccgagcc acca
>gi|173795|gb|K00333|BACTRFA B.subtilis Phe-tRNA
gi|173795|gb|K00333|BACTRFA    0.000 0       2   74 gctcgg ta gct cagttggtag agc a acgga ctgaaaa tccgt gtgtc ggcgg ttcgatt ccgtc ccgagc cacc
>gi|173795|gb|K00333|BACTRFA B.subtilis Phe-tRNA
gi|173795|gb|K00333|BACTRFA    0.000 0       2   74 gctcgg ta gctc agttggta gagc a acgga ctgaaaa tccgt gtgtc ggcgg ttcgatt ccgtc ccgagc cacc
>gi|173796|gb|M24863|BACTRFAA B.stearothermophilus Phe-tRNA
gi|173796|gb|M24863|BACTRFAA    0.000 0       1   76 gctcgtg ta gct cagtcggtag agc a aagga ctgaaya tcctt gtgtc ggcgg ttcgatt ccgtc cgcgagc acca
>gi|173796|gb|M24863|BACTRFAA B.stearothermophilus Phe-tRNA
gi|173796|gb|M24863|BACTRFAA    0.000 0       1   76 gctcgtg ta gctc agtcggta gagc a aagga ctgaaya tcctt gtgtc ggcgg ttcgatt ccgtc cgcgagc acca
>gi|173796|gb|M24863|BACTRFAA B.stearothermophilus Phe-tRNA
gi|173796|gb|M24863|BACTRFAA    0.000 0       2   74 ctcgtg ta gct cagtcggtag agc a aagga ctgaaya tcctt gtgtc ggcgg ttcgatt ccgtc cgcgag cacc
>gi|173796|gb|M24863|BACTRFAA B.stearothermophilus Phe-tRNA
gi|173796|gb|M24863|BACTRFAA    0.000 0       2   74 ctcgtg ta gctc agtcggta gagc a aagga ctgaaya tcctt gtgtc ggcgg ttcgatt ccgtc cgcgag cacc
>gi|173797|gb|K00201|BACTRG1 B.subtilis Gly-tRNA-1
gi|173797|gb|K00201|BACTRG1    0.000 0       1   74 gcgggtg ta gtt tagtggtaa aac c tcagc cttccaa gctga tgtc gtgag ttcgatt ctcat cacccgc tcca
>gi|173797|gb|K00201|BACTRG1 B.subtilis Gly-tRNA-1
gi|173797|gb|K00201|BACTRG1    0.000 0       1   74 gcgggtg ta gttt agtggta aaac c tcagc cttccaa gctga tgtc gtgag ttcgatt ctcat cacccgc tcca
>gi|173797|gb|K00201|BACTRG1 B.subtilis Gly-tRNA-1
gi|173797|gb|K00201|BACTRG1    0.000 0       2   72 cgggtg ta gtt tagtggtaa aac c tcagc cttccaa gctga tgtc gtgag ttcgatt ctcat cacccg ctcc
>gi|173797|gb|K00201|BACTRG1 B.subtilis Gly-tRNA-1
gi|173797|gb|K00201|BACTRG1    0.000 0       2   72 cgggtg ta gttt agtggta aaac c tcagc cttccaa gctga tgtc gtgag ttcgatt ctcat cacccg ctcc
>gi|173800|gb|M26875|BACTRLC B.stearothermophilus Leu-tRNA-CAA
gi|173800|gb|M26875|BACTRLC    0.000 0       1   86 gccgatg tg gcg gaattggcaga cgc g cacga ctcaaaa tcgtg tgggctttgcccgt gtggg ttcgact cccac catcggc acca
>gi|173800|gb|M26875|BACTRLC B.stearothermophilus Leu-tRNA-CAA
gi|173800|gb|M26875|BACTRLC    0.000 0       2   84 ccgatg tg gcg gaattggcaga cgc g cacga ctcaaaa tcgtg tgggctttgcccgt gtggg ttcgact cccac catcgg cacc
>gi|173801|gb|K00310|BACTRMF B.subtilis initiator Met-tRNA-f
gi|173801|gb|K00310|BACTRMF    0.000 0       2   75 gcgggg tg gag cagttcggtag ctc g tcggg ctcataa cccga aggtc gcagg ttcaaat cctgc ccccgc aacc
>gi|173801|gb|K00310|BACTRMF B.subtilis initiator Met-tRNA-f
gi|173801|gb|K00310|BACTRMF    0.000 0       2   75 gcgggg tg gagc agttcggta gctc g tcggg ctcataa cccga aggtc gcagg ttcaaat cctgc ccccgc aacc
>gi|173802|gb|K00297|BACTRMM Bacillus subtilis Met-tRNA-m
gi|173802|gb|K00297|BACTRMM    0.000 0       1   76 ggcggtg ta gct cagcggctag agc g tacgg ttcatac ccgtg aggtc ggggg ttcgatc ccctc cgccgct acca
>gi|173802|gb|K00297|BACTRMM Bacillus subtilis Met-tRNA-m
gi|173802|gb|K00297|BACTRMM    0.000 0       1   76 ggcggtg ta gctc agcggcta gagc g tacgg ttcatac ccgtg aggtc ggggg ttcgatc ccctc cgccgct acca
>gi|173802|gb|K00297|BACTRMM Bacillus subtilis Met-tRNA-m
gi|173802|gb|K00297|BACTRMM    0.000 0       2   74 gcggtg ta gct cagcggctag agc g tacgg ttcatac ccgtg aggtc ggggg ttcgatc ccctc cgccgc tacc
>gi|173802|gb|K00297|BACTRMM Bacillus subtilis Met-tRNA-m
gi|173802|gb|K00297|BACTRMM    0.000 0       2   74 gcggtg ta gctc agcggcta gagc g tacgg ttcatac ccgtg aggtc ggggg ttcgatc ccctc cgccgc tacc
>gi|173803|gb|M27310|BACTRPA B.subtilis Pro-tRNA
gi|173803|gb|M27310|BACTRPA    0.000 0       1   77 cgggaag ta gct cagcttggtag agc a catgg tttggga ccatg gggtc gcagg ttcgaat cctgt cttcccg acca
>gi|173803|gb|M27310|BACTRPA B.subtilis Pro-tRNA
gi|173803|gb|M27310|BACTRPA    0.000 0       1   77 cgggaag ta gctc agcttggta gagc a catgg tttggga ccatg gggtc gcagg ttcgaat cctgt cttcccg acca
>gi|173803|gb|M27310|BACTRPA B.subtilis Pro-tRNA
gi|173803|gb|M27310|BACTRPA    0.000 0       2   75 gggaag ta gct cagcttggtag agc a catgg tttggga ccatg gggtc gcagg ttcgaat cctgt cttccc gacc
>gi|173803|gb|M27310|BACTRPA B.subtilis Pro-tRNA
gi|173803|gb|M27310|BACTRPA    0.000 0       2   75 gggaag ta gctc agcttggta gagc a catgg tttggga ccatg gggtc gcagg ttcgaat cctgt cttccc gacc
>gi|173804|gb|K00156|BACTRR B.subtilis Arg-tRNA
gi|173804|gb|K00156|BACTRR    0.000 0       1   76 gcgcccg ta gct caatggatag agc g tttga ctgcgga tcaaa aggtt agggg ttcgact cccct cgggcgc gcca
>gi|173804|gb|K00156|BACTRR B.subtilis Arg-tRNA
gi|173804|gb|K00156|BACTRR    0.000 0       1   76 gcgcccg ta gctc aatggata gagc g tttga ctgcgga tcaaa aggtt agggg ttcgact cccct cgggcgc gcca
>gi|173804|gb|K00156|BACTRR B.subtilis Arg-tRNA
gi|173804|gb|K00156|BACTRR    0.000 0       2   74 cgcccg ta gct caatggatag agc g tttga ctgcgga tcaaa aggtt agggg ttcgact cccct cgggcg cgcc
>gi|173804|gb|K00156|BACTRR B.subtilis Arg-tRNA
gi|173804|gb|K00156|BACTRR    0.000 0       2   74 cgcccg ta gctc aatggata gagc g tttga ctgcgga tcaaa aggtt agggg ttcgact cccct cgggcg cgcc
>gi|173805|gb|K00276|BACTRT B.subtilis Thr-tRNA
gi|173805|gb|K00276|BACTRT    0.000 0       1   76 gccggtg ta gct caattggtag agc a actga cttgtaa tcagt aggtt ggggg ttcaagt cctct tgccggc acca
>gi|173805|gb|K00276|BACTRT B.subtilis Thr-tRNA
gi|173805|gb|K00276|BACTRT    0.000 0       1   76 gccggtg ta gctc aattggta gagc a actga cttgtaa tcagt aggtt ggggg ttcaagt cctct tgccggc acca
>gi|173805|gb|K00276|BACTRT B.subtilis Thr-tRNA
gi|173805|gb|K00276|BACTRT    0.000 0       2   74 ccggtg ta gct caattggtag agc a actga cttgtaa tcagt aggtt ggggg ttcaagt cctct tgccgg cacc
>gi|173805|gb|K00276|BACTRT B.subtilis Thr-tRNA
gi|173805|gb|K00276|BACTRT    0.000 0       2   74 ccggtg ta gctc aattggta gagc a actga cttgtaa tcagt aggtt ggggg ttcaagt cctct tgccgg cacc
>gi|173806|gb|K00246|BACTRV1 B.subtilis Val-tRNA-1
gi|173806|gb|K00246|BACTRV1    0.000 0       1   76 ggaggat ta gct cagctgggag agc a tctgc cttacaa gcaga gggtc ggcgg ttcgagc ccgtc atcctcc acca
>gi|173806|gb|K00246|BACTRV1 B.subtilis Val-tRNA-1
gi|173806|gb|K00246|BACTRV1    0.000 0       1   76 ggaggat ta gctc agctggga gagc a tctgc cttacaa gcaga gggtc ggcgg ttcgagc ccgtc atcctcc acca
>gi|173806|gb|K00246|BACTRV1 B.subtilis Val-tRNA-1
gi|173806|gb|K00246|BACTRV1    0.000 0       2   74 gaggat ta gct cagctgggag agc a tctgc cttacaa gcaga gggtc ggcgg ttcgagc ccgtc atcctc cacc
>gi|173806|gb|K00246|BACTRV1 B.subtilis Val-tRNA-1
gi|173806|gb|K00246|BACTRV1    0.000 0       2   74 gaggat ta gctc agctggga gagc a tctgc cttacaa gcaga gggtc ggcgg ttcgagc ccgtc atcctc cacc
>gi|173807|gb|K01065|BACTRV2 B.stearothermophilus Val-tRNA-2
gi|173807|gb|K01065|BACTRV2    0.000 0       1   76 gattccg ta gct cagctgggag agc g ccacc ttgacag ggtgg aggtc gctgg ttcgagc ccagt cggaatc acca
>gi|173807|gb|K01065|BACTRV2 B.stearothermophilus Val-tRNA-2
gi|173807|gb|K01065|BACTRV2    0.000 0       1   76 gattccg ta gctc agctggga gagc g ccacc ttgacag ggtgg aggtc gctgg ttcgagc ccagt cggaatc acca
>gi|173807|gb|K01065|BACTRV2 B.stearothermophilus Val-tRNA-2
gi|173807|gb|K01065|BACTRV2    0.000 0       2   74 attccg ta gct cagctgggag agc g ccacc ttgacag ggtgg aggtc gctgg ttcgagc ccagt cggaat cacc
>gi|173807|gb|K01065|BACTRV2 B.stearothermophilus Val-tRNA-2
gi|173807|gb|K01065|BACTRV2    0.000 0       2   74 attccg ta gctc agctggga gagc g ccacc ttgacag ggtgg aggtc gctgg ttcgagc ccagt cggaat cacc
>gi|173809|gb|K00270|BACTRY B.stearothermophilus Tyr-tRNA
gi|173809|gb|K00270|BACTRY    0.000 0       1   85 ggagggg ta gcg aagtggctaaa cgc g gcgga ctgtaaa tccgc tccctttgggttc ggcgg ttcgaat ccgtc cccctcc acca
>gi|173809|gb|K00270|BACTRY B.stearothermophilus Tyr-tRNA
gi|173809|gb|K00270|BACTRY    0.000 0       2   83 gagggg ta gcg aagtggctaaa cgc g gcgga ctgtaaa tccgc tccctttgggttc ggcgg ttcgaat ccgtc cccctc cacc
>gi|173811|gb|K00269|BACTRYI B.subtilis Tyr-tRNA, species I and II
gi|173811|gb|K00269|BACTRYI    0.000 0       1   85 ggagggg ta gcg aagtggctaaa cgc g gcgga ctgtaaa tccgc tccctcagggttc ggcag ttcgaat ctgcc cccctcc acca
>gi|173811|gb|K00269|BACTRYI B.subtilis Tyr-tRNA, species I and II
gi|173811|gb|K00269|BACTRYI    0.000 0       2   83 gagggg ta gcg aagtggctaaa cgc g gcgga ctgtaaa tccgc tccctcagggttc ggcag ttcgaat ctgcc cccctc cacc
>gi|173880|gb|M38018|BIFRRDQ B.bifidum small subunit ribosomal RNA gene
gi|173880|gb|M38018|BIFRRDQ    0.000 0     538   82 cggatt ta ttg ggcg taa a gggct cgtaggc ggctc gtcgcgtccggtgtgaaagtc catc gcttaac ggtg gatctg cgcc
>gi|459692|gb|L29265|BLHRRNA Blastocrithidia culicis ribosomal RNA
gi|459692|gb|L29265|BLHRRNA    0.000 0    1657   77 gggtctg ta gct cagctggttag agc a ccgtc ttgataa ggcgg gggtc gttgg ttcaagt ccaac tagaccc acca
>gi|459692|gb|L29265|BLHRRNA Blastocrithidia culicis ribosomal RNA
gi|459692|gb|L29265|BLHRRNA    0.000 0    1657   77 gggtctg ta gctc agctggtta gagc a ccgtc ttgataa ggcgg gggtc gttgg ttcaagt ccaac tagaccc acca
>gi|459692|gb|L29265|BLHRRNA Blastocrithidia culicis ribosomal RNA
gi|459692|gb|L29265|BLHRRNA    0.000 0    1658   75 ggtctg ta gct cagctggttag agc a ccgtc ttgataa ggcgg gggtc gttgg ttcaagt ccaac tagacc cacc
>gi|459692|gb|L29265|BLHRRNA Blastocrithidia culicis ribosomal RNA
gi|459692|gb|L29265|BLHRRNA    0.000 0    1658   75 ggtctg ta gctc agctggtta gagc a ccgtc ttgataa ggcgg gggtc gttgg ttcaagt ccaac tagacc cacc
>gi|173898|gb|M22136|BLYCPTREA Hordeum vulgare chloroplast Glu-tRNA
gi|173898|gb|M22136|BLYCPTREA    0.000 0       1   76 tccgtcg ta gtc taggdggdtag gat a ctcgg ctttcac ccgag agac ccggg ttcaagt cccgg cgacgga acca
>gi|173898|gb|M22136|BLYCPTREA Hordeum vulgare chloroplast Glu-tRNA
gi|173898|gb|M22136|BLYCPTREA    0.000 0       1   76 tccgtcg ta gtct aggdggdta ggat a ctcgg ctttcac ccgag agac ccggg ttcaagt cccgg cgacgga acca
>gi|173898|gb|M22136|BLYCPTREA Hordeum vulgare chloroplast Glu-tRNA
gi|173898|gb|M22136|BLYCPTREA    0.000 0       2   74 ccgtcg ta gtc taggdggdtag gat a ctcgg ctttcac ccgag agac ccggg ttcaagt cccgg cgacgg aacc
BioPerl-1.007002/t/data/unigene.data000444000766000024      2056213155576322 17203 0ustar00cjfieldsstaff000000000000ID          Hs.2
TITLE       N-acetyltransferase 2 (arylamine N-acetyltransferase)
GENE        NAT2
CYTOBAND    8p22
LOCUSLINK   10
HOMOL       YES
EXPRESS     liver ; hepatocellular carcinoma ; adenocarcinoma ; corresponding non cancerous liver tissue ; Liver ; colon ; Cell lines 
RESTR_EXPR   liver
GNM_TERMINUS      S
CHROMOSOME  8
STS         ACC=G59899 UNISTS=137181
STS         ACC=GDB:386004 UNISTS= 157141
STS         ACC=WIAF-2120 UNISTS= 44576
STS         ACC=G06461 UNISTS= 17088
STS         ACC=GDB:310612 UNISTS= 156422
STS         ACC=PMC310725P3 UNISTS= 272646
STS         ACC=GDB:310613 UNISTS= 156423
STS         ACC=GDB:187676 UNISTS= 155563
PROTSIM     ORG=Escherischia coli; PROTGI=16129422; PROTID=ref:NP_415980.1; PCT=24.81; ALN=255
PROTSIM     ORG=Homo sapiens; PROTGI=105377; PROTID=pir:B34585; PCT=100.00; ALN=290
PROTSIM     ORG=Mus musculus; PROTGI=1703436; PROTID=sp:P50295; PCT=74.83; ALN=290
PROTSIM     ORG=Rattus norvegicus; PROTGI=16758720; PROTID=ref:NP_446306.1; PCT=73.79; ALN=290
SCOUNT      26
SEQUENCE    ACC=BX095770.1; NID=g27827877; CLONE=IMAGp998I184581_,_IMAGE:1870937; LID=1079; SEQTYPE=EST; PERIPHERAL=1
SEQUENCE    ACC=AI262683.1; NID=g3870886; CLONE=IMAGE:1870937; END=3'; LID=1079; SEQTYPE=EST
SEQUENCE    ACC=CB161982.1; NID=g28148108; CLONE=L17N670205n1-15-F12; END=5'; LID=12542; SEQTYPE=EST; PERIPHERAL=1
SEQUENCE    ACC=CB161860.1; NID=g28147986; CLONE=L17N670205n1-41-A04; END=5'; LID=12542; SEQTYPE=EST
SEQUENCE    ACC=AI460128.1; NID=g4313009; CLONE=IMAGE:2151449; END=3'; LID=1556; SEQTYPE=EST
SEQUENCE    ACC=AI733799.1; NID=g5054912; CLONE=IMAGE:1870937; END=3'; LID=1079; SEQTYPE=EST
SEQUENCE    ACC=AI792606.1; NID=g5340322; CLONE=IMAGE:1870937; END=5'; LID=1079; SEQTYPE=EST
SEQUENCE    ACC=NM_000015.1; NID=g4557782; PID=g4557783; SEQTYPE=mRNA
SEQUENCE    ACC=BC067218.1; NID=g45501306; PID=g45501307; SEQTYPE=mRNA
SEQUENCE    ACC=CR407631.1; NID=g47115198; PID=g47115199; SEQTYPE=mRNA
SEQUENCE    ACC=AV658623.1; NID=g9879637; CLONE=GLCFOD10; END=3'; LID=5601; SEQTYPE=EST
SEQUENCE    ACC=AV658656.1; NID=g9879670; CLONE=GLCFOG07; END=3'; LID=5601; SEQTYPE=EST
SEQUENCE    ACC=AV684197.1; NID=g10286060; CLONE=GKCFZH06; END=5'; LID=6533; SEQTYPE=EST
SEQUENCE    ACC=D90040.1; NID=g219411; PID=g219412; SEQTYPE=mRNA
SEQUENCE    ACC=AU099534.1; NID=g13550663; CLONE=HSI08034; LID=8800; SEQTYPE=EST
SEQUENCE    ACC=BG533459.1; NID=g13524999; CLONE=IMAGE:4072143; END=5'; LID=6989; MGC=4557782; SEQTYPE=EST; TRACE=44404609
SEQUENCE    ACC=BG563731.1; NID=g13571383; CLONE=IMAGE:4712210; END=5'; LID=6989; MGC=4557782; SEQTYPE=EST; TRACE=44153506
SEQUENCE    ACC=BG568400.1; NID=g13576053; CLONE=IMAGE:4716802; END=5'; LID=6989; MGC=4557782; SEQTYPE=EST; TRACE=44156561
SEQUENCE    ACC=BG569272.1; NID=g13576925; CLONE=IMAGE:4722638; END=5'; LID=6989; SEQTYPE=EST; TRACE=44157191
SEQUENCE    ACC=BG569293.1; NID=g13576946; CLONE=IMAGE:4722596; END=5'; LID=6989; MGC=4557782; SEQTYPE=EST; TRACE=44157214
SEQUENCE    ACC=BG617259.1; NID=g13668630; CLONE=IMAGE:4734378; END=5'; LID=6989; SEQTYPE=EST; TRACE=44229423
SEQUENCE    ACC=BG618195.1; NID=g13669566; CLONE=IMAGE:4767316; END=5'; LID=6989; MGC=4557782; SEQTYPE=EST; TRACE=45338366
SEQUENCE    ACC=BG204539.1; NID=g13726226; LID=8655; SEQTYPE=EST
SEQUENCE    ACC=BC015878.1; NID=g16198419; PID=g16198420; SEQTYPE=mRNA
SEQUENCE    ACC=D90042.1; NID=g219415; PID=g219416; SEQTYPE=mRNA
SEQUENCE    ACC=BU624903.1; NID=g23291118; CLONE=UI-H-FG1-bgl-g-02-0-UI; END=3'; LID=11914; SEQTYPE=EST; TRACE=159705553
//
ID          Rn.1
TITLE       Transcribed sequences
EXPRESS     Mixed tissues 
STS         ACC=RH128068 UNISTS=211376
SCOUNT      9
SEQUENCE    ACC=AA859577.1; NID=g4230123; CLONE=UI-R-E0-bv-c-09-0-UI; END=3'; LID=1127; SEQTYPE=EST; TRACE=154346471
SEQUENCE    ACC=AW251121.1; NID=g6594732; CLONE=UI-R-BJ0-adi-f-04-0-UI; END=3'; LID=2759; SEQTYPE=EST; TRACE=154371414
SEQUENCE    ACC=AW252428.1; NID=g6596019; CLONE=UI-R-BJ0-adx-d-05-0-UI; END=3'; LID=2759; SEQTYPE=EST; TRACE=154373036
SEQUENCE    ACC=BQ194853.1; NID=g20370404; CLONE=UI-R-CN1-cmb-f-16-0-UI; END=3'; LID=10150; SEQTYPE=EST; TRACE=154334854
SEQUENCE    ACC=BU758764.1; NID=g23721624; CLONE=UI-R-FF0-cow-c-07-0-UI; END=3'; LID=11044; SEQTYPE=EST; TRACE=154339445
SEQUENCE    ACC=CA510294.1; NID=g25001248; CLONE=UI-R-FS0-cqr-l-23-0-UI; END=3'; LID=12129; SEQTYPE=EST; TRACE=159666883
SEQUENCE    ACC=CB613849.1; NID=g29573737; CLONE=urrg1-00170-g2; END=5'; LID=12874; SEQTYPE=EST
SEQUENCE    ACC=CB763094.1; NID=g29851485; CLONE=urrg1-00038-c12; END=5'; LID=12874; SEQTYPE=EST
SEQUENCE    ACC=CK838684.1; NID=g45188969; CLONE=UI-R-AC1-xo-a-03-0-UI; END=3'; LID=1719; SEQTYPE=EST
//
ID          Mm.340763
TITLE       Transcribed locus, strongly similar to NP_003008.1 splicing factor, arginine/serine-rich 3; splicing factor, arginine//serine-rich, 20-kD [Homo sapiens]
HOMOL       YES
EXPRESS     other ; brain ; liver ; eye ; kidney ; testis ; pituitary gland ; whole body ; colon ; muscle ; thymus 
CHROMOSOME  11
STS         ACC=- UNISTS=3193
PROTSIM     ORG=Arabidopsis thaliana; PROTGI=15236000; PROTID=ref:NP_194886.1; PCT=37.25; ALN=95
PROTSIM     ORG=Caenorhabditis elegans; PROTGI=7496951; PROTID=pir:T34145; PCT=50.33; ALN=131
PROTSIM     ORG=Drosophila melanogaster; PROTGI=384217; PROTID=prf:1905314A; PCT=67.29; ALN=106
PROTSIM     ORG=Homo sapiens; PROTGI=139781; PROTID=sp:P23152; PCT=99.26; ALN=136
PROTSIM     ORG=Mus musculus; PROTGI=111257; PROTID=pir:S14016; PCT=99.26; ALN=136
PROTSIM     ORG=Rattus norvegicus; PROTGI=1168968; PROTID=sp:Q09167; PCT=48.84; ALN=83
SCOUNT      31
SEQUENCE    ACC=BY050916.1; NID=g26156364; CLONE=I730062L23; END=5'; LID=12235; SEQTYPE=EST
SEQUENCE    ACC=BY066798.1; NID=g26170395; CLONE=I920050M24; END=5'; LID=12249; SEQTYPE=EST
SEQUENCE    ACC=BY297944.1; NID=g26488281; CLONE=K530357B20; END=5'; LID=12286; SEQTYPE=EST
SEQUENCE    ACC=BY403069.1; NID=g26632637; CLONE=I730043J07; END=3'; LID=12253; SEQTYPE=EST
SEQUENCE    ACC=BY417621.1; NID=g26684533; CLONE=I920028M23; END=3'; LID=4141; SEQTYPE=EST
SEQUENCE    ACC=BY426591.1; NID=g26701831; CLONE=I920085O07; END=3'; LID=12250; SEQTYPE=EST
SEQUENCE    ACC=BY448670.1; NID=g26740448; CLONE=K630031D11; END=3'; LID=2601; SEQTYPE=EST
SEQUENCE    ACC=BY677654.1; NID=g27066665; CLONE=K920015D15; END=3'; LID=12304; SEQTYPE=EST
SEQUENCE    ACC=CB947876.1; NID=g30199635; CLONE=IMAGE:30309766; END=5'; LID=12883; SEQTYPE=EST
SEQUENCE    ACC=CD775546.1; NID=g32434048; CLONE=UI-M-AQ0-ciz-j-19-0-UI; END=3'; LID=1947; SEQTYPE=EST
SEQUENCE    ACC=BX630904.1; NID=g33610776; CLONE=LIONp462B02438; END=3'; LID=14219; SEQTYPE=EST
SEQUENCE    ACC=CF748683.1; NID=g37645028; CLONE=IMAGE:30629174; END=5'; LID=14478; SEQTYPE=EST
SEQUENCE    ACC=CF750995.1; NID=g37647341; CLONE=IMAGE:30623151; END=5'; LID=14479; SEQTYPE=EST; TRACE=302787286
SEQUENCE    ACC=CA587449.1; NID=g40792709; LID=12138; SEQTYPE=EST
SEQUENCE    ACC=CO044451.1; NID=g48584991; CLONE=IMAGE:30657728; END=3'; LID=15581; SEQTYPE=EST
SEQUENCE    ACC=D28619.1; NID=g618936; CLONE=86F09; LID=240; SEQTYPE=EST
SEQUENCE    ACC=AA474597.1; NID=g2202752; CLONE=IMAGE:805477; END=5'; LID=850; SEQTYPE=EST
SEQUENCE    ACC=AA498526.1; NID=g2233549; CLONE=IMAGE:889465; END=5'; LID=609; SEQTYPE=EST
SEQUENCE    ACC=AA638070.1; NID=g2561658; CLONE=IMAGE:1121421; END=5'; LID=916; SEQTYPE=EST; TRACE=216759053
SEQUENCE    ACC=AV101859.1; NID=g5249407; CLONE=2410079M03; LID=1882; SEQTYPE=EST
SEQUENCE    ACC=AV113236.1; NID=g5267316; CLONE=2610020C14; LID=1884; SEQTYPE=EST
SEQUENCE    ACC=AI840089.1; NID=g5474302; CLONE=UI-M-AL0-abt-e-09-0-UI; END=3'; LID=1937; SEQTYPE=EST; TRACE=158440126
SEQUENCE    ACC=AI843632.1; NID=g5477845; CLONE=UI-M-AO1-aen-f-09-0-UI; END=3'; LID=1944; SEQTYPE=EST; TRACE=158502493
SEQUENCE    ACC=AV259282.1; NID=g6246741; CLONE=4930404D15; END=3'; LID=2547; SEQTYPE=EST
SEQUENCE    ACC=AV290384.1; NID=g6304415; CLONE=5133400P08; END=3'; LID=2560; SEQTYPE=EST
SEQUENCE    ACC=AW111788.1; NID=g6824501; CLONE=MT1455; END=3'; LID=2483; SEQTYPE=EST
SEQUENCE    ACC=BE333113.1; NID=g9206889; CLONE=IMAGE:3326433; END=5'; LID=544; SEQTYPE=EST; TRACE=114452409
SEQUENCE    ACC=BE951610.1; NID=g10591137; CLONE=UI-M-CC0-ayc-f-08-0-UI; END=3'; LID=6769; SEQTYPE=EST; TRACE=158466712
SEQUENCE    ACC=BE984495.1; NID=g10656785; CLONE=UI-M-CG0p-bgf-c-02-0-UI; END=3'; LID=6780; SEQTYPE=EST; TRACE=158541808
SEQUENCE    ACC=BU525661.1; NID=g22836102; CLONE=IMAGE:6534145; END=5'; LID=11268; SEQTYPE=EST
SEQUENCE    ACC=BU554412.1; NID=g22904684; CLONE=IMAGE:6581716; END=5'; LID=11140; SEQTYPE=EST
//
BioPerl-1.007002/t/data/urease.tre.nexus000444000766000024       205313155576322 20032 0ustar00cjfieldsstaff000000000000#NEXUS 

Begin trees;  [Treefile saved Thu Jun 24 10:15:07 2004]
[!
>Data file = /home/jes12/possel/urease/urease.cdna.nex
>Heuristic search settings:
>  Optimality criterion = distance (minimum evolution)
>    Negative branch lengths allowed, but set to zero for tree-score calculation
>    Distance measure = uncorrected ("p")
>  Starting tree(s) obtained via neighbor-joining
>  Branch-swapping algorithm: tree-bisection-reconnection (TBR)
>  Steepest descent option not in effect
>  Initial 'MaxTrees' setting = 100
>  Zero-length branches not collapsed
>  'MulTrees' option in effect
>  Topological constraints not enforced
>  Trees are unrooted
>
>Heuristic search completed
>   Total number of rearrangements tried = 34
>   Score of best tree(s) found = 1.13334
>   Number of trees retained = 1
>   Time used = <1 sec (CPU time = 0.00 sec)
]
	Translate
		1 Anidulans,
		2 CneoA,
		3 Cimmitis,
		4 Mgrisea,
		5 Ncrassa,
		6 Spombe
		;
tree PAUP_1 = [&U] (((1:0.188380,(4:0.147551,5:0.134318):0.027742):0.012293,3:0.175935):0.012799,2:0.212917,6:0.221404);
End;
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					GATGATTCCGGCTTCGGACGACTCTAGAGGATCCCCATTTTTATAGTTTTTATCTTGTAATAGATGTTTAGATTTTTCGTTGTAATTATTTTCTTTATTGTTGAAATTAGTATCTCTGGGTAATTTATCATATTCTCTGGAAAATGATTTACTATCACTAGATACTTCATAAGATTTATAATCTTTATTATGAAAATCATCTCTATTTTTCAAATTATTATTATATCTATCAAAGTTTCTGTCTTCATTATATCTATTAGCATATCTATCTTTATCTTTATCCCTATCACTATATCTATCATATGGTTCATCTTGTTCAACCGATCAGACTCGATTCGCCATCGCCTCTAACGGATGGCCGCTCCCCCTCTCATACCTCGCTCCCCTCGACATCCCCCGTCTCGCCACCCTATCCGCCCCCTTCATCACCCCCCCTTATCCACACCCTCACCCCCCGCATCGCGCACCCACGACCACCCGAAGAACCGCCCTTACTCCCAAGTACGCCCCGACCTCCATCACCCTATGCGGTACCACTCCCACCACACCCAGTCCTACTTTCGCCCGCACATCGGCCCCGCTTCAGACAGCTCCCAACTACGCAACCCACGCTTGTTCTTGTTCACACTCGAATACTCGAATCTCTCATTACTCCGCGGACTCCGCCGCACCTGTGCACCATTAACTGTGTAGCGCCTGAACCGGCACCTCTGATTACCACTTCCTCCACCAGCACAGTCCTATTACCGCATGTCGCTCTGCTAAGACAGTGCAAGACTCTGCGGTCGCTCTGACCCGCATCCGCCAGGGCACCTCTCACCCTCGCTGGCCACCCCGCCCCCCTCTCCCTGCCCCTTCATTCCCCCAAACCGCTTTCAACGGGACACACCCCTCCGCGGCGGACCACAACTCGCCGTCGGCCACCACTCACACCTTCCCTCCTCCTTCCCCCACATCACGCCAACCCCGTGGGACGGCTCTCCCGCGGCTACGACGCGCAACCCCCCCTCGCCGCTTCCCCCCCAACTTCCCACGGGCTCCCCTCCGCCCCTTACCCGCGAGGAGCTTCACCCGCGAACCACCTCCCCCCTTTCCCAACAGCACCGSIGN=A=42,C=41,G=25,T=111
SPAC= 12.74
PRIM=1523
MACH=377-96 
DYEP=DT {BD Set Any-Primer}
NAME=IIABP1D4373
LANE=50
GELN=Gel File
PROC=
RTRK=
CONV=phred version=0.990722.h
COMM=

SRCE=ABI 373A or 377BioPerl-1.007002/t/data/wellcome_tol.nhx000444000766000024      1503213155576322 20116 0ustar00cjfieldsstaff000000000000((((((((((((((((((((((((((((((Antelope:25.38857142856932[&&NHX:id=51129:tol=Y],Sheep:25.38857142856932[&&NHX:id=51093:tol=Y]):4.231428571428751[&&NHX:id=51154],Cow:29.619999999998072[&&N
HX:id=51150])Bovidae:33.26333333333336[&&NHX:id=50878:tol=Y],Pig:62.883333333331485[&&NHX:id=51287:tol=Y]):0.978333333333334,Hippopotamus:63.86166666666491[&&NHX:id=30366]):2.445833333333335,Camel:66.307
49999999811[&&NHX:id=30350:tol=Y])Artiodactyla:7.337500000000006[&&NHX:id=15976:tol=Y],Humpback_whale:73.64499999999816[&&NHX:id=16054]):9.663854166666676[&&NHX:id=15975],(((Horse:72.14374999999836[&&NHX
:id=16255],Rhino:72.14374999999836[&&NHX:id=16262])Perissodactyla:5.153125000000017[&&NHX:id=15980:tol=Y],Elephant:77.29687499999827[&&NHX:id=22667:tol=Y]):4.294270833333347[&&NHX:id=15979],Aardvark:81.5
9114583333152[&&NHX:id=16881]):1.717708333333339):15.761701388888907[&&NHX:id=15974],((((Brown_bear:40.2599999999984[&&NHX:id=123666:tol=Y],Polar_bear:40.2599999999984[&&NHX:id=123667:tol=Y])Ursidae:11.1
8333333333332[&&NHX:id=16015:tol=Y],Seal:51.443333333331715[&&NHX:id=16020]):4.473333333333327,Dog:55.91666666666514[&&NHX:id=16013])Caniformia:11.18333333333332[&&NHX:id=16011],(Cat:40.259999999998215[&
&NHX:id=123531:tol=Y],Lion:40.259999999998215[&&NHX:id=123566:tol=Y])Felidae:26.839999999999964[&&NHX:id=16006:tol=Y])Carnivora:31.9705555555556[&&NHX:id=15971:tol=Y]):0.15222222222222132,((Mole:86.06453
703703531[&&NHX:id=16213],Shrew:86.06453703703531[&&NHX:id=16223]):3.759497354497354,Hedgehog:89.82403439153265[&&NHX:id=16211])Insectivora:9.398743386243385[&&NHX:id=15968:tol=Y]):0.3805555555555533,(((
Chimpanzee:9.143333333331611[&&NHX:id=26565],Human:9.143333333331611[&&NHX:id=16421:tol=Y]):82.69666666666664[&&NHX:id=16412],Tree_shrew:91.83999999999833[&&NHX:id=50808]):4.1099999999999755[&&NHX:id=159
62],Fruit_bat:95.94999999999834[&&NHX:id=16076]):3.6533333333333116[&&NHX:id=15961]):1.14166666666666,((Hamster:56.967999999998256[&&NHX:id=16546],Rat:56.96799999999821[&&NHX:id=50732])Eumuroida:33.21199
9999999804[&&NHX:id=16528],Rabbit:90.17999999999788[&&NHX:id=16227])Glires:10.565000000000104[&&NHX:id=15957]):16.484999999999623[&&NHX:id=15955],Kangaroo:117.22999999999797[&&NHX:id=16248]):31.384999999
99999[&&NHX:id=15993],Platypus:148.61499999999816[&&NHX:id=16253:tol=Y]):39.50999999999999[&&NHX:id=15990],Megazostrodon:4.0625[&&NHX:ext=Y:id=15032:ncol=red:nsz=2])Cynodontia:32.5[&&NHX:id=15030],Dimetr
odon:4.0625[&&NHX:ext=Y:id=14972:ncol=red:nsz=2])Sphenacodontoidea:73.125[&&NHX:id=14971],(((((((((((((Flamingo:106.30859375000043[&&NHX:id=89474:tol=Y],Toucan:106.3085937500002[&&NHX:id=93330:tol=Y]):1.
4296874999999905,Penguin:107.73828125000037[&&NHX:id=57223:tol=Y])Neoaves:3.5742187499999765[&&NHX:id=26305:tol=Y],Duck:111.31250000000024[&&NHX:id=89298:tol=Y])Neognathae:4.289062499999972[&&NHX:id=2629
1],Ostrich:115.60156250000016[&&NHX:id=26289:tol=Y])Neornithes:4.289062499999972[&&NHX:id=15834:tol=Y],Ichthyornis:4.386242378048764[&&NHX:ext=Y:id=15833:ncol=red:nsz=2])Euornithes_true_birds:12.86718749
9999915[&&NHX:id=15829],Archaeopteryx:2.144531249999986[&&NHX:ext=Y:id=15824:ncol=red:nsz=2])Aves:12.867187499999915[&&NHX:id=15721:tol=Y],Tyrannosaurus_Rex:79.47061157226744[&&NHX:ext=Y:id=15889:ncol=re
d:nsz=2]):74.99999999999773[&&NHX:id=15713],Diplodocus:157.62263488769486[&&NHX:ext=Y:id=15756:ncol=red:nsz=2])Saurischia:9.374999999999716[&&NHX:id=15724],Iguanadon:165.44959259033112[&&NHX:ext=Y:id=157
40:ncol=red:nsz=2])Dinosauria:20.400000000000002[&&NHX:id=14883:tol=Y],Crocodile:250.39999999999782[&&NHX:id=14868])Archosauria:22.950000000000003[&&NHX:id=14900:tol=Y],Snake:273.34999999999803[&&NHX:id=
17563])Sauria:12.75[&&NHX:id=14913],Brouffia:1.275[&&NHX:ext=Y:id=14865:ncol=red:nsz=2]):5.1[&&NHX:id=14864],Tortoise:291.1999999999979[&&NHX:id=17631])Reptilia:2.55[&&NHX:id=14846])Amniota:56.2500000000
0091[&&NHX:id=14990:tol=Y],(Amphibians:317.3333333333312[&&NHX:id=14940],Newt:317.3333333333311[&&NHX:id=82771])Living_amphibians:32.66666666666758[&&NHX:id=14997:tol=Y])Tetrapoda:9.00000000000009[&&NHX:
id=14987],Seymouriamorpha:14.610465116279109[&&NHX:ext=Y:id=17554:ncol=red:nsz=2]):40.87500000000041[&&NHX:id=14985],(Acanthostega:1.8750000000000189[&&NHX:ext=Y:id=15016:ncol=red:nsz=2:tol=Y],Icthyosteg
a:1.8750000000000189[&&NHX:ext=Y:id=15015:ncol=red:nsz=2:tol=Y]):0.7500000000000075):13.125000000000131[&&NHX:id=14976],Panderichthys:2.2500000000000226[&&NHX:ext=Y:id=14951:ncol=red:nsz=2]):4.500000000000045[&&NHX:id=14950],Eusthenopteron:2.2500000000000226[&&NHX:ext=Y:id=14949:ncol=red:nsz=2]):9.00000000000009[&&NHX:id=14948],((Paddle_fish:363.6363636363626[&&NHX:id=68750],Sturgeon:363.6363636363626[&&NHX:id=68749])Acipenseriformes:24.242424242424242[&&NHX:id=68726:tol=Y],Clown_fish:387.8787878787866[&&NHX:id=52149]):38.621212121213034[&&NHX:id=68709])Osteichthyes:9.00000000000009[&&NHX:id=14921],Shark:435.5[&&NHX:id=14925])Node_1:13.944444444444489[&&NHX:id=14919],Cephalaspidida:19.261904761904795[&&NHX:ext=Y:id=16894:ncol=red:nsz=2])Node_3:28.333333333333336[&&NHX:id=14840],Pteraspis:46.45061728395067[&&NHX:ext=Y:id=16929:ncol=red:nsz=2])Node_1:9.444444444444445[&&NHX:id=14833],Lamprey:487.22222222222223[&&NHX:id=15919])Vertebrata:18.88888888888889[&&NHX:id=14829:tol=Y],Pikaia:506.1111111111113[&&NHX:id=14824]):158.00000000000003[&&NHX:id=14822],((((((((Fruit_fly:339.4285714285717[&&NHX:id=10610],Peacock_butterfly:339.42857142857144[&&NHX:id=94054]):7.071428571428555[&&NHX:id=8224],Wasp:346.5000000000002[&&NHX:id=11244]):28.28571428571422[&&NHX:id=8223],Cockroach:374.7857142857142[&&NHX:id=8544])Neoptera:7.071428571428555[&&NHX:id=8267:tol=Y],Giant_dragonfly:10.607142857142833[&&NHX:ext=Y:id=13265:ncol=red:nsz=2])Pterygota:98.80952380952378[&&NHX:id=8210:tol=Y],Brine_shrimp:480.6666666666665[&&NHX:id=6387]):43.81073446327684[&&NHX:id=2527],((((Harevest_mite:496.40677966101725[&&NHX:id=2612],Spider:496.4067796610171[&&NHX:id=2788:tol=Y]):8.864406779661008[&&NHX:id=2542],Harvestman:505.27118644067804[&&NHX:id=2556])Arachnida:8.864406779661008[&&NHX:id=2536:tol=Y],Sea_Scorpion:39.88983050847454[&&NHX:ext=Y:id=8174:ncol=red:nsz=2])Chelicerata:7.387005649717507[&&NHX:id=2535],Millipede:521.5225988700563[&&NHX:id=52849]):2.954802259887003)Arthropoda:40.855932203389834[&&NHX:id=2469:tol=Y],(Opabinia:555.9111111111108[&&NHX:id=20357],Velvet_worm:555.9111111111108[&&NHX:id=20356])Onychophora:9.422222222222217[&&NHX:id=2470:tol=Y]):70.55555555555556[&&NHX:id=2468],Acoel:635.8888888888889[&&NHX:id=20383]):28.222222222222225)Bilateria:85.88888888888889[&&NHX:id=2459:tol=Y],Sponge:750.0[&&NHX:id=20438])Animals:2250.0[&&NHX:id=2374:tol=Y],E._coli:3000.0[&&NHX:id=2306])Life_on_earth;BioPerl-1.007002/t/data/withrefm.906000555000766000024   1131070113155576322 17065 0ustar00cjfieldsstaff000000000000 
REBASE version 906                                              withrefm.906
 
    =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
    REBASE, The Restriction Enzyme Database   http://rebase.neb.com
    Copyright (c)  Dr. Richard J. Roberts, 2009.   All rights reserved.
    =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
 
Rich Roberts                                                    May 29 2009
 

   Restriction enzyme name.
 Other enzymes with this specificity.
 
                These are written from 5' to 3', only one strand being given.
                If the point of cleavage has been determined, the precise site
                is marked with ^.  For enzymes such as HgaI, MboII etc., which
                cleave away from their recognition sequence the cleavage sites
                are indicated in parentheses.  

                For example HgaI GACGC (5/10) indicates cleavage as follows:
                                5' GACGCNNNNN^      3'
                                3' CTGCGNNNNNNNNNN^ 5'

                In all cases the recognition sequences are oriented so that
                the cleavage sites lie on their 3' side.

                REBASE Recognition sequences representations use the standard 
                abbreviations (Eur. J. Biochem. 150: 1-5, 1985) to represent 
                ambiguity.
                                R = G or A
                                Y = C or T
                                M = A or C
                                K = G or T
                                S = G or C
                                W = A or T
                                B = not A (C or G or T)
                                D = not C (A or G or T)
                                H = not G (A or C or T)
                                V = not T (A or C or G)
                                N = A or C or G or T



                ENZYMES WITH UNUSUAL CLEAVAGE PROPERTIES:  

                Enzymes that cut on both sides of their recognition sequences,
                such as BcgI, Bsp24I, CjeI and CjePI, have 4 cleavage sites
                each instead of 2.

                Bsp24I
                          5'      ^NNNNNNNNGACNNNNNNTGGNNNNNNNNNNNN^   3'
                          3' ^NNNNNNNNNNNNNCTGNNNNNNACCNNNNNNN^        5'


                This will be described in some REBASE reports as:

                             Bsp24I (8/13)GACNNNNNNTGG(12/7)


                The site of methylation by the cognate methylase when known
                is indicated X(Y) or X,X2(Y,Y2), where X is the base within
                the recognition sequence that is modified.  A negative number
                indicates the complementary strand, numbered from the 5' base 
                of that strand, and Y is the specific type of methylation 
                involved:
                               (6) = N6-methyladenosine 
                               (5) = 5-methylcytosine 
                               (4) = N4-methylcytosine

                If the methylation information is different for the 3' strand,
                X2 and Y2 are given as well.

 Organism from which this enzyme had been isolated.
        Either an individual or a National Culture Collection.

                Each commercial source of restriction enzymes and/or methylases
                listed in REBASE is assigned a single character abbreviation 
                code.  For example:

                K        Takara (1/98)
                M        Boehringer Mannheim (10/97)
                N        New England Biolabs (4/98)
 
                The date in parentheses indicates the most recent update of 
                that organization's listings in REBASE.

only the primary references for the isolation and/or purification
of the restriction enzyme or methylase, the determination of the recognition
sequence and cleavage site or the methylation specificity are given.


REBASE codes for commercial sources of enzymes

                B        Invitrogen Corporation (5/09)
                C        Minotech Biotechnology (5/09)
                E        Stratagene (5/09)
                F        Fermentas International Inc. (5/09)
                H        American Allied Biochemical, Inc. (5/09)
                I        SibEnzyme Ltd. (5/09)
                J        Nippon Gene Co., Ltd. (5/09)
                K        Takara Bio Inc. (5/09)
                M        Roche Applied Science (5/09)
                N        New England Biolabs (5/09)
                O        Toyobo Biochemicals (12/08)
                Q        Molecular Biology Resources - CHIMERx (5/09)
                R        Promega Corporation (5/09)
                S        Sigma Chemical Corporation (5/09)
                U        Bangalore Genei (5/09)
                V        Vivantis Technologies (4/09)
                W        MP Biomedicals (5/09)
                X        EURx Ltd. (5/09)
                Y        CinnaGen Inc. (5/09)

<1>AaaI
<2>XmaIII,BseX3I,BsoDI,BstZI,EagI,EclXI,Eco52I,SenPT16I,TauII,Tsp504I
<3>C^GGCCG
<4>
<5>Acetobacter aceti ss aceti
<6>M. Fukaya
<7>
<8>Tagami, H., Tayama, K., Tohyama, T., Fukaya, M., Okumura, H., Kawamura, Y., Horinouchi, S., Beppu, T., (1988) FEMS Microbiol. Lett., vol. 56, pp. 161-166.

<1>AacLI
<2>BamHI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Acetobacter aceti sub. liquefaciens
<6>IFO 12388
<7>
<8>Seurinck, J., van Montagu, M., Unpublished observations.

<1>AaeI
<2>BamHI,AacLI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Acetobacter aceti sub. liquefaciens
<6>M. Van Montagu
<7>
<8>Seurinck, J., van Montagu, M., Unpublished observations.

<1>AagI
<2>ClaI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Achromobacter agile
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Maneliene, Z.P., Butkus, V.V., Fitzner, A.B., Khoroshutina, E.B., Kalugin, A.A., Janulaitis, A., (1990) Bioorg. Khim., vol. 16, pp. 1040-1044.

<1>AamI
<2>
<3>?
<4>
<5>Azospirillum amazonense
<6>G. Schwabe
<7>
<8>Schwabe, G., Posseckert, G., Klingmuller, W., (1985) Gene, vol. 39, pp. 113-116.

<1>AanI
<2>PsiI
<3>TTA^TAA
<4>
<5>Arthrobacter aurescens RFL2
<6>Fermentas G324
<7>F
<8>Vitkute, J., Lapcinskaja, S., Capskaja, L., Zakareviciene, L., Janulaitis, A., Unpublished observations.

<1>AaqI
<2>ApaLI,Alw44I,AmeI,Bsp146I,DaqI,Pfl23I,Pfr12I,PliI,ScoNI,SnoI,Uba1203I,Uba1387I,VneI
<3>GTGCAC
<4>
<5>Alcaligenes aquamarinus 559
<6>V.E. Repin
<7>
<8>Repin, V.E., Unpublished observations.

<1>AarI
<2>
<3>CACCTGC(4/8)
<4>
<5>Arthrobacter aurescens SS2-322
<6>A. Janulaitis
<7>F
<8>Grigaite, R., Maneliene, Z., Janulaitis, A., (2002) Nucleic Acids Res., vol. 30.
Maneliene, Z., Zakareviciene, L., Unpublished observations.

<1>AasI
<2>DrdI,DseDI,TrsSII
<3>GACNNNN^NNGTC
<4>
<5>Arthrobacter aurescens RFL3
<6>V. Butkus
<7>F
<8>Kazlauskiene, R., Vaitkevicius, D., Maneliene, Z., Trinkunaite, L., Kiuduliene, L., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>AatI
<2>StuI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGG^CCT
<4>
<5>Acetobacter aceti
<6>IFO 3281
<7>O
<8>Sato, H., Yamada, Y., (1990) J. Gen. Appl. Microbiol., vol. 36, pp. 273-277.
Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Nucleic Acids Res., vol. 10, pp. 5747-5752.

<1>AatII
<2>AspJI,Ppu1253I,Ssp5230I,ZraI
<3>GACGT^C
<4>
<5>Acetobacter aceti
<6>IFO 3281
<7>FIKMNORV
<8>Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Nucleic Acids Res., vol. 10, pp. 5747-5752.
Xu, S.-Y., Nwankwo, D.O., European Patent Office, 1992.

<1>AauI
<2>Bsp1407I,BsmGI,BsmRI,BsrGI,Bst170I,BstAUI,Ssp4800I,SspBI
<3>T^GTACA
<4>
<5>Arthrobacter aurescens
<6>S.K. Degtyarev
<7>
<8>Shinkarenko, N.M., Schevchenko, A.V., Dedkov, V.S., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>AbaI
<2>BclI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>T^GATCA
<4>
<5>Azospirillum brasilense UQ 1796
<6>N.I. Matvienko
<7>
<8>Zabaznaya, E.V., Nikiforev, V.V., Zheleznaya, L.A., Matvienko, N.I., (1997) Biokhimiia, vol. 62, pp. 403-410.

<1>AbeI
<2>BbvCI,PmdI
<3>CCTCAGC(-5/-2)
<4>
<5>Azotobacter beijerinckii Slo 54-028
<6>V. Butkus
<7>
<8>Vitkute, J., Maneliene, Z., Janulaitis, A., (1998) Nucleic Acids Res., vol. 26, pp. 4917-4918.

<1>AbrI
<2>XhoI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Azospirillum brasilense
<6>ATCC 29711
<7>
<8>Schwabe, G., Helke, A., Klinkmueller, W., Unpublished observations.
Schwabe, G., Posseckert, G., Klingmuller, W., (1985) Gene, vol. 39, pp. 113-116.

<1>AbsI
<2>
<3>CC^TCGAGG
<4>
<5>Arthrobacter species 7M06
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Kashirina, Y.G., Tomilova, J.E., Gonchar, D.A., Dedkov, V.S., Mikhnenkova, N.A., Degtyarev, S.K., (2006) Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol., vol. 2, pp. 29-34.

<1>AcaI
<2>AsuII,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Anabaena catenula
<6>CCAP 1403/1
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.
Hughes, S.G., Bruce, T., Murray, K., Unpublished observations.

<1>AcaII
<2>BamHI,AacLI,AaeI,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Anabaena catenula
<6>CCAP 1403/1
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>AcaIII
<2>MstI,Acc16I,AosI,ApcTR183I,AviII,Bco6I,BsaTI,ClcII,CliII,FdiII,FspI,GspAII,NsbI,NspHIII,NspLI,NspMI,PamI,Pun14627I
<3>TGCGCA
<4>
<5>Anabaena catenula
<6>CCAP 1403/1
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>AcaIV
<2>HaeIII,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Anabaena catenula
<6>CCAP 1403/1
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>AccI
<2>DsaVI,FblI,OmiBII,XmiI
<3>GT^MKAC
<4>5(6)
<5>Acinetobacter calcoaceticus
<6>ATCC 49823
<7>BJKMNORSUWX
<8>Kawakami, B., Hilzheber, C., Nagatomo, M., Oka, M., (1991) Agric. Biol. Chem., vol. 55, pp. 1553-1559.
Kawakami, B., Maekawa, Y., Japanese Patent Office, 1991.
Lunnen, K.D., Barsomian, J.M., Camp, R.R., Card, C.O., Chen, S.-Z., Croft, R., Looney, M.C., Meda, M.M., Moran, L.S., Nwankwo, D.O., Slatko, B.E., Van Cott, E.M., Wilson, G.G., (1988) Gene, vol. 74, pp. 25-32.
Zabeau, M., Roberts, R.J., Unpublished observations.

<1>AccII
<2>FnuDII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>
<5>Acinetobacter calcoaceticus
<6>ATCC 49823
<7>JK
<8>Kita, K., Hiraoka, N., Kimizuka, F., Obayashi, A., (1984) Agric. Biol. Chem., vol. 48, pp. 531-532.
Zabeau, M., Roberts, R.J., Unpublished observations.

<1>AccIII
<2>BspMII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>
<5>Acinetobacter calcoaceticus
<6>ATCC 49823
<7>JKRW
<8>Kita, K., Hiraoka, N., Oshima, A., Kadonishi, S., Obayashi, A., (1985) Nucleic Acids Res., vol. 13, pp. 8685-8694.
Myers, P.A., Roberts, R.J., Unpublished observations.
Sagawa, H., Ueno, H., Oshima, A., Kato, I., International Patent Office, 1997.

<1>Acc16I
<2>MstI,AcaIII,AosI,ApcTR183I,AviII,Bco6I,BsaTI,ClcII,CliII,FdiII,FspI,GspAII,NsbI,NspHIII,NspLI,NspMI,PamI,Pun14627I
<3>TGC^GCA
<4>
<5>Acinetobacter calcoaceticus 16
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.K., Unpublished observations.

<1>Acc36I
<2>BspMI,BfuAI,BveI
<3>ACCTGC(4/8)
<4>
<5>Acinetobacter calcoaceticus 36
<6>S.K. Degtyarev
<7>I
<8>Gonchar, D.A., Shinkarenko, N.M., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>Acc38I
<2>EcoRII,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Acinetobacter calcoaceticus 38
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>Acc65I
<2>KpnI,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>G^GTACC
<4>
<5>Acinetobacter calcoaceticus 65
<6>S.K. Degtyarev
<7>FINRVW
<8>Lunnen, K.D., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Prichodko, G.G., Rechnukova, N.I., Repin, V.E., Degtyarev, S.K., (1991) Sib. Biol. J., vol. 1, pp. 59-60.

<1>Acc113I
<2>ScaI,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGT^ACT
<4>
<5>Acinetobacter calcoaceticus 113
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Shevchenko, A.V., Kileva, E.V., Degtyarev, S.K., Unpublished observations.

<1>AccB1I
<2>HgiCI,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>G^GYRCC
<4>
<5>Acinetobacter calcoaceticus B1
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.K., Unpublished observations.

<1>AccB2I
<2>HaeII,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGC^Y
<4>
<5>Acinetobacter calcoaceticus B2
<6>S.K. Degtyarev
<7>
<8>Zhilkina, O.A., Dedkov, V.S., Shevchenko, A.V., Kileva, E.V., Degtyarev, S.K., Unpublished observations.

<1>AccB7I
<2>PflMI,AcpII,Asp10HII,BasI,Esp1396I,PflBI,Van91I
<3>CCANNNN^NTGG
<4>
<5>Acinetobacter calcoaceticus B7
<6>S.K. Degtyarev
<7>IRV
<8>Dedkov, V.S., Repin, V.E., Rechkunova, N.I., Degtyarev, S.K., Verhosina, V.A., Vinogradova, T.P., (1990) Izv. Sib. Otd. Akad. Nauk SSSR, vol. 1, pp. 35-37.

<1>AccBSI
<2>BsrBI,BstD102I,Bst31NI,MbiI
<3>CCGCTC(-3/-3)
<4>
<5>Acinetobacter calcoaceticus BS
<6>S.K. Degtyarev
<7>IV
<8>Abdurashitov, M.A., Kileva, E.V., Myakisheva, T.V., Dedkov, V.S., Shevchenko, A.V., Degtyarev, S.K., (1997) Prikl. Biokhim. Mikrobiol., vol. 33, pp. 556-558.

<1>AccEBI
<2>BamHI,AacLI,AaeI,AcaII,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Acinetobacter calcoaceticus EBF 65/65
<6>A. Vivian
<7>
<8>Walker, J.N.B., Vivian, A., Saunders, J.R., Unpublished observations.

<1>AceI
<2>TseI,ApeKI,SuiI,Taq52I,TneI,TseBI
<3>G^CWGC
<4>
<5>Anabaena cedrorum
<6>M.M. Wijdenbosch
<7>
<8>Rahman, H., Affram, C., Unpublished observations.

<1>AceII
<2>NheI,AsuNHI,BmtI,BspOI,LlaG2I,PstNHI
<3>GCTAG^C
<4>
<5>Anabaena cedrorum
<6>M.M. Wijdenbosch
<7>
<8>Affram, C., Rahman, H., Unpublished observations.

<1>AceIII
<2>
<3>CAGCTC(7/11)
<4>
<5>Anabaena cedrorum
<6>M.M. Wijdenbosch
<7>
<8>Affram, C., Rahman, H., Unpublished observations.

<1>AciI
<2>BspACI,SsiI
<3>CCGC(-3/-1)
<4>1(5),-2(5)
<5>Arthrobacter citreus
<6>NEB 577
<7>N
<8>Lunnen, K.D., Heiter, D., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Polisson, C., Morgan, R.D., (1990) Nucleic Acids Res., vol. 18, pp. 5911.
Samuelson, J., Unpublished observations.

<1>AclI
<2>Psp1406I,UbaN9I
<3>AA^CGTT
<4>3(5)
<5>Acinetobacter calcoaceticus M4
<6>S.K. Degtyarev
<7>INV
<8>Degtyarev, S.K., Abdurashitov, M.A., Kolyhalov, A.A., Rechkunova, N.I., (1992) Nucleic Acids Res., vol. 20, pp. 3787.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>AclNI
<2>SpeI,AhlI,BcuI
<3>A^CTAGT
<4>
<5>Acinetobacter calcoaceticus N20
<6>S.K. Degtyarev
<7>
<8>Rechkunova, N.I., Shevchenko, A.V., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>AclWI
<2>BinI,AlwI,BpuFI,BspPI,BsrWI,BstH9I,Bst31TI,BthII,Bth617I,EacI,Ral8I
<3>GGATC(4/5)
<4>
<5>Acinetobacter calcoaceticus W2131
<6>S.K. Degtyarev
<7>I
<8>Abdurashitov, M.A., Belichenko, O.A., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>AcoI
<2>CfrI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>Y^GGCCR
<4>
<5>Acinetobacter calcoaceticus
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Belichenko, O.A., Doroganov, A.O., Tomilova, J.E., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>AcpI
<2>AsuII,AcaI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Acidiphilium cryptum 25H
<6>K. Inagaki
<7>
<8>Inagaki, K., Ito, T., Sagawa, H., Kotani, H., Kishimoto, N., Sugio, T., Tano, T., Tanaka, H., (1991) Nucleic Acids Res., vol. 19, pp. 6335.

<1>AcpII
<2>PflMI,AccB7I,Asp10HII,BasI,Esp1396I,PflBI,Van91I
<3>CCANNNN^NTGG
<4>
<5>Acidiphilium cryptum 25H
<6>K. Inagaki
<7>
<8>Inagaki, K., Ito, T., Kotani, H., Kishimoto, N., Tano, T., Unpublished observations.

<1>AcrI
<2>AvaI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Anabaenopsis circularis
<6>ATCC 27895
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>AcrII
<2>BstEII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Anabaenopsis circularis
<6>ATCC 27895
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>AcsI
<2>ApoI,CfaI,FsiI,XapI
<3>R^AATTY
<4>
<5>Arthrobacter citreus 310
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.K., Kolyhalov, A.A., Rechkunova, N.I., Abdurashitov, M.A., (1992) Nucleic Acids Res., vol. 20, pp. 3789.

<1>Acs1371I
<2>SalI,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Acidobacterium capsulatum 1371
<6>K. Inagaki
<7>
<8>Inagaki, K., Hamafuku, H., Kotani, H., Kishimoto, N., Tano, T., Unpublished observations.

<1>Acs1372I
<2>SalI,Acs1371I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Acidobacterium capsulatum 1372
<6>K. Inagaki
<7>
<8>Inagaki, K., Hamafuku, H., Kotani, H., Kishimoto, N., Tano, T., Unpublished observations.

<1>Acs1373I
<2>SalI,Acs1371I,Acs1372I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Acidobacterium capsulatum 1373
<6>K. Inagaki
<7>
<8>Inagaki, K., Hamafuku, H., Kotani, H., Kishimoto, N., Tano, T., Unpublished observations.

<1>Acs1421I
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Acidobacterium capsulatum 1421
<6>K. Inagaki
<7>
<8>Inagaki, K., Hamafuku, H., Kotani, H., Kishimoto, N., Tano, T., Unpublished observations.

<1>Acs1422I
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Acidobacterium capsulatum 1422
<6>K. Inagaki
<7>
<8>Inagaki, K., Hamafuku, H., Kotani, H., Kishimoto, N., Tano, T., Unpublished observations.

<1>AcuI
<2>Eco57I,Bsp6II,BspD6II,BspKT5I,Eco112I,Eco125I,FsfI
<3>CTGAAG(16/14)
<4>
<5>Acinetobacter calcoaceticus SRW4
<6>S.K. Degtyarev
<7>IN
<8>Degtyarev, S.K., Kileva, E.V., Dedkov, V.S., Unpublished observations.
Samuelson, J., Xu, S.-Y., Unpublished observations.

<1>AcuII
<2>EcoRII,Acc38I,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Acinetobacter calcoaceticus SRW4
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Kileva, E.V., Dedkov, V.S., Unpublished observations.

<1>AcvI
<2>PmaCI,BbrPI,BcoAI,Bsp87I,Eco72I,Pgl34I,PmlI,PshCI,PshDI,Psp38I,PspBI,PspCI,VpaK3AI,VpaK3BI
<3>CAC^GTG
<4>
<5>Aeromonas caviae
<6>P.M. Skowron
<7>QX
<8>Skowron, P.M., Unpublished observations.

<1>AcyI
<2>AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>
<5>Anabaena cylindrica
<6>CCAP 1403/2a
<7>JM
<8>de Waard, A., Korsuize, J., van Beveren, C.P., Maat, J., (1978) FEBS Lett., vol. 96, pp. 106-110.

<1>AcyII
<2>
<3>?
<4>
<5>Anabaena cylindrica
<6>CCAP 1403/2a
<7>
<8>de Waard, A., Korsuize, J., van Beveren, C.P., Maat, J., (1978) FEBS Lett., vol. 96, pp. 106-110.

<1>AdeI
<2>DraIII,BstIZ316I
<3>CACNNN^GTG
<4>
<5>Alcaligenes denitrificans Ss 3-028
<6>A. Janulaitis
<7>F
<8>Maneliene, Z., Butkus, V., Unpublished observations.
Vitkute, J., Zutautiene, D., Capskaja, L., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>AerAI
<2>XhoI,AbrI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Aeromonas hydrophila AH63
<6>K. Mise
<7>
<8>Miyahara, M., Kimizuka, F., Kita, A., Matsushita, S., Kudo, Y., Shimada, T., Mise, K., (1996) Biol. Pharm. Bull., vol. 19, pp. 1506-1507.

<1>AeuI
<2>EcoRII,Acc38I,AcuII,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Achromobacter eurydice
<6>ATCC 39312
<7>
<8>Polisson, C., Morgan, R., Unpublished observations.

<1>AfaI
<2>RsaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GT^AC
<4>
<5>Acidiphilium facilis 28H
<6>D. Dou
<7>K
<8>Dou, D., Inagaki, K., Kita, K., Ohshima, A., Hiraoka, N., Kishimoto, N., Sugio, T., Tano, T., (1989) Biochim. Biophys. Acta, vol. 1009, pp. 83-86.

<1>Afa22MI
<2>PvuI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGAT^CG
<4>?(5)
<5>Acidocella facilis
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kita, K., Hiraoka, N., Kishimoto, N., Sugio, T., Tano, T., (1990) J. Ferment. Bioeng., vol. 69, pp. 60-62.
Yamaoka, S., Tamura, T., Takenobu, H., Kojo, T., Tanaka, H., Inagaki, K., (2003) Sci. Reports. Fac. Agric. Okayama Univ., vol. 92, pp. 9-15.

<1>Afa16RI
<2>PvuI,Afa22MI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGAT^CG
<4>
<5>Acidiphilium species 16R
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kita, K., Hiraoka, N., Kishimoto, N., Sugio, T., Tano, T., (1990) J. Ferment. Bioeng., vol. 69, pp. 60-62.

<1>Afa24RI
<2>NaeI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Acidiphilium facilis 24R
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>AfeI
<2>Eco47III,AitI,Aor51HI,FunI
<3>AGC^GCT
<4>
<5>Alcaligenes faecalis T2774
<6>NEB 1775
<7>IN
<8>Abdurashitov, M.A., Kileva, E.V., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.
Lunnen, K., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>AfiI
<2>BsiYI,BflI,Bsc4I,Bsc107I,Bse23I,BseLI,BslI,BsmYI,Bst22I
<3>CCNNNNN^NNGG
<4>
<5>Anoxybacillus flavithermus
<6>Vivantis 24
<7>V
<8>Chee, H.Y., Unpublished observations.

<1>AflI
<2>AvaII,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Anabaena flos-aquae
<6>CCAP 1403/13f
<7>
<8>Whitehead, P.R., Brown, N.L., (1985) J. Gen. Microbiol., vol. 131, pp. 951-958.

<1>AflII
<2>BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>C^TTAAG
<4>
<5>Anabaena flos-aquae
<6>CCAP 1403/13f
<7>JKN
<8>Lunnen, K.D., Wilson, G.G., US Patent Office, 1991.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Whitehead, P.R., Brown, N.L., (1985) J. Gen. Microbiol., vol. 131, pp. 951-958.

<1>AflIII
<2>Asp90I
<3>A^CRYGT
<4>2(4)
<5>Anabaena flos-aquae
<6>CCAP 1403/13f
<7>MNW
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Stickel, S.K., Roberts, R.J., Unpublished observations.
Whitehead, P.R., Brown, N.L., (1985) J. Gen. Microbiol., vol. 131, pp. 951-958.

<1>AflIV
<2>ScaI,Acc113I,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGTACT
<4>
<5>Anabaena flos-aquae
<6>CCAP 1403/13f
<7>
<8>Groot, E., Schouten, J.P., Unpublished observations.

<1>Afl83I
<2>AsuII,AcaI,AcpI,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Anabaena flos-aquae NIVA-CYA83
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Afl83II
<2>HaeIII,AcaIV,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Anabaena flos-aquae NIVA-CYA83
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>AgeI
<2>AsiAI,AsiGI,BshTI,CsiAI,CspAI,PinAI
<3>A^CCGGT
<4>?(5)
<5>Agrobacterium gelatinovorum
<6>IAM 12617
<7>JNR
<8>Suzuki, T., Sugimoto, E., Tahara, Y., Yamada, Y., (1996) Biosci. Biotechnol. Biochem., vol. 60, pp. 444-447.
Xu, S.-Y., Maunus, R.E., Lunnen, K.D., Allen, R., US Patent Office, 1999.
Yamada, Y., Mizuno, H., Sato, H., Akagawa, M., Yamasato, K., (1989) Agric. Biol. Chem., vol. 53, pp. 1747-1749.

<1>AglI
<2>EcoRII,Acc38I,AcuII,AeuI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Arthrobacter globiformis
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., (1995) Vestn. Akad. Med. Nauk SSSR, vol. 2, pp. 47-51.

<1>AgsI
<2>
<3>TTS^AA
<4>
<5>Agrococcus species 25
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Kileva, E.V., Tarasova, G.V., Dedkov, V.S., Mikhnenkova, N.A., Degtyarev, S.K., Unpublished observations.

<1>AhaI
<2>CauII,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CC^SGG
<4>
<5>Aphanothece halophytica
<6>ATCC 29534
<7>
<8>Whitehead, P.R., Brown, N.L., (1985) Arch. Microbiol., vol. 141, pp. 70-74.

<1>AhaII
<2>AcyI,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>
<5>Aphanothece halophytica
<6>ATCC 29534
<7>
<8>Whitehead, P.R., Brown, N.L., (1985) Arch. Microbiol., vol. 141, pp. 70-74.

<1>AhaIII
<2>DraI,PauAII,Srl19I,Srl61DI,Srl76DI,SruI
<3>TTT^AAA
<4>
<5>Aphanothece halophytica
<6>ATCC 29534
<7>
<8>Whitehead, P.R., Brown, N.L., (1982) FEBS Lett., vol. 143, pp. 296-300.

<1>AhaB1I
<2>AsuI,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Alteromonas haloplanktis B1
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Zernov, Y.P., Rechkunova, N.I., Degtyarev, S.Kh., (1990) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 17-18.

<1>AhaB8I
<2>KpnI,Acc65I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>G^GTACC
<4>
<5>Alteromonas haloplanktis B8
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Zernov, Y.P., Rechkunova, N.I., Degtyarev, S.Kh., (1990) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 17-18.

<1>AhdI
<2>Eam1105I,AspEI,BmeRI,BspOVI,BstZ2I,DriI,EclHKI,NruGI,Uba1190I,Uba1191I
<3>GACNNN^NNGTC
<4>
<5>Aeromonas hydrophila
<6>NEB 724
<7>N
<8>Chang, Z., Morgan, R., Unpublished observations.
Lunnen, K.L., Tao, C., Wilson, G.G., Unpublished observations.
Polisson, C., Unpublished observations.

<1>AhlI
<2>SpeI,AclNI,BcuI
<3>A^CTAGT
<4>
<5>Alteromonas haloplanktis SP
<6>S.K. Degtyarev
<7>IV
<8>Myakisheva, T.V., Belichenko, O.A., Popichenko, D.V., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>AhyI
<2>SmaI,Cfr9I,CfrJ4I,EaeAI,EclRI,KteAI,Pac25I,PaeBI,PspAI,PspALI,TspMI,Uba1220I,Uba1393I,XcyI,XmaI,XmaCI
<3>C^CCGGG
<4>
<5>Aeromonas hydrophila
<6>NEB 503
<7>
<8>Tenkanen, T., Unpublished observations.

<1>Ahy45I
<2>
<3>?
<4>
<5>Aeromonas hydrophila
<6>A.M. Kulba
<7>
<8>Kulba, A.M., Elgammudi, A.A., (1997) Vestn. Beloruss. Gos. Univ., vol. 2, pp. 47-49.

<1>AhyAI
<2>XhoI,AbrI,AerAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Aeromonas hydrophila AH63
<6>T. Shimada
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>AimI
<2>
<3>?
<4>
<5>Achromobacter immobilis
<6>ATCC 15934
<7>
<8>Endow, S.A., Roberts, R.J., Unpublished observations.

<1>M.AimAI
<2>
<3>?
<4>?(5)
<5>Ascobolus immersus
<6>J. Walter
<7>
<8>Malagnac, F., Wendel, B., Goyon, C., Faugeron, G., Zickler, D., Rossignol, J.-L., Noyer-Weidner, M., Vollmayr, P., Trautner, T.A., Walter, J., (1997) Cell, vol. 91, pp. 281-290.

<1>M.AimAII
<2>
<3>?
<4>?(5)
<5>Ascobolus immersus
<6>J. Walter
<7>
<8>Chernov, A.V., Vollmayr, P., Walter, J., Trautner, T.A., (1997) Biol. Chem., vol. 378, pp. 1467-1473.

<1>AinI
<2>PstI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Anabaena inequalis
<6>CCAP 1446/1a
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>AinII
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Anabaena inequalis
<6>CCAP 1446/1a
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>AitI
<2>Eco47III,AfeI,Aor51HI,FunI
<3>AGC^GCT
<4>
<5>Aquaspirillum itersonii
<6>NEB 443
<7>
<8>Polisson, C., McMahon, M., Unpublished observations.

<1>AitII
<2>XhoII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>RGATCY
<4>
<5>Aquaspirillum itersonii
<6>NEB 443
<7>
<8>Polisson, C., McMahon, M., Unpublished observations.

<1>AitAI
<2>XhoII,AitII,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>RGATCY
<4>
<5>Aquaspirillum itersonii
<6>ATCC 12639
<7>
<8>Polisson, C., Unpublished observations.

<1>AjiI
<2>BtrI,BmgBI
<3>CACGTC(-3/-3)
<4>
<5>Acinetobacter johnsonii RFL47
<6>Fermentas G303
<7>F
<8>Lauciuniene, N., Capskaja, L., Kiuduliene, L., Vitkute, J., Janulaitis, A., Unpublished observations.
Maneliene, Z., Zakareviciene, L., Lubys, A., Unpublished observations.

<1>AjnI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>^CCWGG
<4>
<5>Acinetobacter johnsonii R2
<6>S.K. Degtyarev
<7>I
<8>Dedkov, V.S., Mikhnenkova, N.A., Vlasenko, L.P., Tomilova, J.E., Kashirina, J.G., Gonchar, D.A., Degtyarev, S.K., Unpublished observations.

<1>AjoI
<2>PstI,AinI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Acinetobacter johnsonii 350
<6>E. Gospodarek
<7>
<8>Nowak, A., Kur, J., Gospodarek, E., Bielawski, K., (1994) FEMS Microbiol. Lett., vol. 117, pp. 97-102.

<1>AjuI
<2>
<3>(7/12)GAANNNNNNNTTGG(11/6)
<4>
<5>Acinetobacter junii RFL46
<6>A. Janulaitis
<7>F
<8>Maneliene, Z., Zakareviciene, L., Lubys, A., Unpublished observations.
Nekrasiene, D., Lapcinskaja, S., Capskaja, L., Kiuduliene, L., Vitkute, J., Janulaitis, A., Unpublished observations.

<1>AleI
<2>OliI
<3>CACNN^NNGTG
<4>
<5>Aureobacterium liquefaciens
<6>NEB 1374
<7>N
<8>Degtyarev, S.K., Unpublished observations.
Wilson, G.G., Lunnen, K.D., Unpublished observations.

<1>AlfI
<2>
<3>(10/12)GCANNNNNNTGC(12/10)
<4>
<5>Acinetobacter lwoffi BH 32.
<6>A. Janulaitis
<7>F
<8>Maneliene, Z., Zakareviciene, L., Unpublished observations.
Vitkute, J., Giedriene, J., Timinskas, A., Capskaja, L., Kiuduliene, L., Markauskas, A., Butkus, V., Janulaitis, A., Unpublished observations.

<1>AliI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Acetobacter liquefaciens
<6>IFO 12388
<7>
<8>Yamada, Y., Yoshioka, H., Sasaki, J., Tahara, Y., (1983) J. Gen. Appl. Microbiol., vol. 29, pp. 157-166.

<1>Ali2882I
<2>PstI,AinI,AjoI,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Acetobacter liquefaciens
<6>K. Komagata
<7>
<8>Yamada, Y., Sasaki, J., (1984) J. Gen. Appl. Microbiol., vol. 30, pp. 309-312.

<1>Ali12257I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Acetobacter liquefaciens
<6>IFO 12257
<7>
<8>Yamada, Y., Sasaki, J., (1984) J. Gen. Appl. Microbiol., vol. 30, pp. 309-312.

<1>Ali12258I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Acetobacter liquefaciens
<6>IFO 12258
<7>
<8>Yamada, Y., Sasaki, J., (1984) J. Gen. Appl. Microbiol., vol. 30, pp. 309-312.

<1>AliAJI
<2>PstI,AinI,AjoI,Ali2882I,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Acetobacter liquefaciens AJ 2881
<6>K. Komagata
<7>
<8>Sasaki, J., Yamada, Y., (1984) Agric. Biol. Chem., vol. 48, pp. 3027-3034.

<1>AloI
<2>
<3>(7/12)GAACNNNNNNTCC(12/7)
<4>3(6),-3(6)
<5>Acinetobacter lwoffi Ks 4-8
<6>V. Butkus
<7>F
<8>Cesnaviciene, E.E., Petrusyte, M.M., Kazlauskiene, R.R., Maneliene, Z., Timinskas, A., Lubys, A., Janulaitis, A., (2001) J. Mol. Biol., vol. 314, pp. 205-216.
Savelskiene, A., Petrusyte, M., Padegimiene, E., Vonseviciene, E., Kiuduliene, E., Butkus, V., Janulaitis, A., Unpublished observations.

<1>AluI
<2>AluBI,BsaLI,MarI,Mho2111I,MltI,OtuI,OtuNI,OxaI,Uba1433I,Uba1441I
<3>AG^CT
<4>3(5)
<5>Arthrobacter luteus
<6>ATCC 21606
<7>BCFHIJKMNOQRSUVWXY
<8>Kramarov, V.M., Smolyaninov, V.V., (1981) Biokhimiia, vol. 46, pp. 1526-1529.
Labeots, L.A., (1993) Diss. Abstr., vol. 53, pp. 2842.
Roberts, R.J., Myers, P.A., Morrison, A., Murray, K., (1976) J. Mol. Biol., vol. 102, pp. 157-165.
Smith, M.D., Schmidt, B.J., Longo, M.C., Chatterjee, D.K., US Patent Office, 1994.
Ware, J., Zhang, B.-H., Slatko, B.S., Wilson, G.G., Unpublished observations.
Yoon, H., Suh, H., Han, M.H., Yoo, O.J., (1985) Korean Biochem. J., vol. 18, pp. 82-87.
Yoon, H., Suh, H., Kim, K., Han, M.H., Yoo, O.J., (1985) Korean Biochem. J., vol. 18, pp. 88-93.

<1>AluBI
<2>AluI,BsaLI,MarI,Mho2111I,MltI,OtuI,OtuNI,OxaI,Uba1433I,Uba1441I
<3>AG^CT
<4>
<5>Arthrobacter luteus B
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Boltengagen, A.A., Tarasova, G.V., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.
Chernukhin, V.A., Boltengagen, A.A., Tarasova, G.V., Dedkov, V.S., Degtyarev, S.K., (2007) Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol., vol. 3, pp. 21-27.

<1>AlwI
<2>BinI,AclWI,BpuFI,BspPI,BsrWI,BstH9I,Bst31TI,BthII,Bth617I,EacI,Ral8I
<3>GGATC(4/5)
<4>3(6),-2(6)
<5>Acinetobacter lwoffi
<6>NEB 402
<7>N
<8>Lunnen, K.D., Wilson, G.G., Unpublished observations.
Morgan, R., Bonventre, J., Unpublished observations.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>Alw21I
<2>HgiAI,AspHI,Bbv12I,Bfu1570I,BsaGI,Bsh45I,BsiHKAI,Bsm6I,BsmPI,Hpy8III,HpyF7II,HpyF46II,MspV281I,Pph3215I
<3>GWGCW^C
<4>
<5>Acinetobacter lwoffi RFL21
<6>A. Janulaitis
<7>F
<8>Jagelavicius, M., Bitinaite, J., Maneliene, Z., Butkus, V., Janulaitis, A., Unpublished observations.

<1>Alw26I
<2>BsmAI,BcoDI,BscQII,BsoMAI,BstMAI
<3>GTCTC(1/5)
<4>3(5),-4(6)
<5>Acinetobacter lwoffi RFL26
<6>A. Janulaitis
<7>F
<8>Bitinaite, J., Maneliene, Z., Menkevicius, S., Klimasauskas, S., Butkus, V., Janulaitis, A., (1992) Nucleic Acids Res., vol. 20, pp. 4981-4985.
Bitinaite, J., Mitkaite, G., Dauksaite, V., Jakubauskas, A., Timinskas, A., Vaisvila, R., Lubys, A., Janulaitis, A., (2002) Mol. Genet. Genomics, vol. 267, pp. 664-672.
Gilvonauskaite, R., Bitinaite, J., Petrusyte, M., Butkus, V., Maneliene, Z., Janulaitis, A., Unpublished observations.

<1>Alw44I
<2>ApaLI,AaqI,AmeI,Bsp146I,DaqI,Pfl23I,Pfr12I,PliI,ScoNI,SnoI,Uba1203I,Uba1387I,VneI
<3>G^TGCAC
<4>
<5>Acinetobacter lwoffi RFL44
<6>A. Janulaitis
<7>FJOR
<8>Jagelavicius, M., Bitinaite, J., Maneliene, Z., Butkus, V., Janulaitis, A., Unpublished observations.

<1>AlwFI
<2>
<3>GAAAYNNNNNRTG
<4>
<5>Acinetobacter lwoffii RFL45
<6>A. Janulaitis
<7>
<8>Nekrasiene, D., Lapcinskaja, S., Kiuduliene, L., Vitkute, J., Janulaitis, A., Unpublished observations.

<1>AlwFII
<2>XhoI,AbrI,AerAI,AhyAI,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Acinetobacter lwoffii RFL45
<6>A. Janulaitis
<7>
<8>Nekrasiene, D., Lapcinskaja, S., Kiuduliene, L., Vitkute, J., Janulaitis, A., Unpublished observations.

<1>AlwNI
<2>CaiI
<3>CAGNNN^CTG
<4>
<5>Acinetobacter lwoffi
<6>NEB 419
<7>N
<8>Morgan, R.D., Dalton, M., Stote, R., (1987) Nucleic Acids Res., vol. 15, pp. 7201.
Zhu, Z., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>AlwXI
<2>BbvI,BchI,BsaUI,BseKI,BseXI,Bsp423I,BsrVI,Bst12I,Bst71I,BstV1I,LfeI,Lsp1109I
<3>GCAGC(8/12)
<4>
<5>Acinetobacter lwoffi X
<6>NEB 413
<7>
<8>Morgan, R., Ingalls, D., Unpublished observations.

<1>Ama87I
<2>AvaI,AcrI,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>
<5>Alteromonas macleodii 87
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.K., Unpublished observations.

<1>AmaSI
<2>NruI,Bsp68I,BtuMI,Mlu9273I,MluB2I,PspDI,RruI,SalDI,Sbo13I,Sna3286I,SpoI,Uba1117I,Uba1386I,VchO70I
<3>TCGCGA
<4>
<5>Actinomadura madurae
<6>ATCC 15904
<7>
<8>Hurlin, P., Schildkraut, I., Unpublished observations.

<1>AmeI
<2>ApaLI,AaqI,Alw44I,Bsp146I,DaqI,Pfl23I,Pfr12I,PliI,ScoNI,SnoI,Uba1203I,Uba1387I,VneI
<3>GTGCAC
<4>
<5>Aquaspirillum metamorphum
<6>ATCC 15280
<7>
<8>Polisson, C., Unpublished observations.

<1>AmeII
<2>NaeI,Afa24RI,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Aquaspirillum metamorphum
<6>ATCC 15280
<7>
<8>Polisson, C., Unpublished observations.

<1>AniAI
<2>
<3>?
<4>
<5>Anacystis nidulans
<6>PCC 6301
<7>
<8>Szekeres, M., (1981) Virology, vol. 111, pp. 1-10.

<1>AniMI
<2>NaeI,Afa24RI,AmeII,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Arthrobacter nicotianae
<6>ATCC 15236
<7>
<8>Morgan, R.D., Unpublished observations.

<1>AniRI
<2>
<3>?
<4>
<5>Anacystis nidulans R2
<6>L. Sherman
<7>
<8>Gallagher, M.L., Burke, W.F., (1985) FEMS Microbiol. Lett., vol. 26, pp. 317-321.

<1>AocI
<2>SauI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CC^TNAGG
<4>
<5>Anabaena species
<6>CCAP 1403/9
<7>
<8>de Waard, A., Unpublished observations.

<1>AocII
<2>SduI,Bka1125I,BmyI,BsoCI,Bsp1286I,BspLS2I,BstZ15I,HpyF36IV,HpyF47I,MhlI,Mlu40I,NspII,TseAI,Uba1362I
<3>GDGCH^C
<4>
<5>Anabaena species
<6>CCAP 1403/9
<7>
<8>de Waard, A., Unpublished observations.

<1>AorI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Acetobacter aceti sub. orleanensis
<6>NCIB 8622
<7>
<8>Seurinck, J., van Montagu, M., Unpublished observations.

<1>Aor13HI
<2>BspMII,AccIII,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>
<5>Acidiphilium organovorum 13H
<6>K. Inagaki
<7>K
<8>Inagaki, K., Hikita, T., Yanagidani, S., Nomura, Y., Kishimoto, N., Tano, T., Tanaka, H., (1993) Biosci. Biotechnol. Biochem., vol. 57, pp. 1716-1721.

<1>Aor51HI
<2>Eco47III,AfeI,AitI,FunI
<3>AGC^GCT
<4>
<5>Acidiphilium organovorum 51H
<6>Takara
<7>K
<8>Sagawa, H., Takagi, M., Nomura, Y., Inagaki, K., Tano, T., Kishimato, N., Kotani, H., Nakajima, K., (1992) Nucleic Acids Res., vol. 20, pp. 365.

<1>AosI
<2>MstI,AcaIII,Acc16I,ApcTR183I,AviII,Bco6I,BsaTI,ClcII,CliII,FdiII,FspI,GspAII,NsbI,NspHIII,NspLI,NspMI,PamI,Pun14627I
<3>TGC^GCA
<4>
<5>Anabaena oscillarioides
<6>CCAP 1403/11
<7>
<8>de Waard, A., van Beveren, C.P., Duyvesteyn, M., van Ormondt, H., (1979) FEBS Lett., vol. 101, pp. 71-76.

<1>AosII
<2>AcyI,AhaII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>
<5>Anabaena oscillarioides
<6>CCAP 1403/11
<7>
<8>de Waard, A., van Beveren, C.P., Duyvesteyn, M., van Ormondt, H., (1979) FEBS Lett., vol. 101, pp. 71-76.

<1>AosIII
<2>SacII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Anabaena oscillarioides
<6>CCAP 1403/11
<7>
<8>de Waard, A., Unpublished observations.

<1>ApaI
<2>Bsp120I,EciEI,PpeI,Psp30I,PspOMI,Uba1156I,Uba1157I,Uba1165I,Uba1202I,Uba1241I,Uba1368I
<3>GGGCC^C
<4>4(5)
<5>Acetobacter pasteurianus sub. pasteurianus
<6>NCIB 7215
<7>BFIJKMNOQRSUVWX
<8>Gunthert, U., Trautner, T.A., (1984) Curr. Top. Microbiol. Immunol., vol. 108, pp. 11-22.
Kong, H., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Seurinck, J., Van de Voorde, A., Van Montagu, M., (1983) Nucleic Acids Res., vol. 11, pp. 4409-4415.
Trautner, T.A., Unpublished observations.
Yamada, Y., Murakami, M., (1985) Agric. Biol. Chem., vol. 49, pp. 3627-3629.

<1>ApaBI
<2>BstAPI
<3>GCANNNNN^TGC
<4>
<5>Acetobacter pasteurianus B
<6>J. Grones
<7>
<8>Grones, J., Turna, J., (1991) Biologia (Bratisl), vol. 46, pp. 1103-1108.

<1>ApaCI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Acetobacter pasteurianus C
<6>J. Grones
<7>
<8>Grones, J., Turna, J., (1992) Nucleic Acids Res., vol. 20, pp. 3513.

<1>ApaDI
<2>
<3>?
<4>
<5>Acetobacter pasteurianus D
<6>J. Grones
<7>
<8>Grones, J., Turna, J., (1991) Biologia (Bratisl), vol. 46, pp. 1103-1108.

<1>ApaLI
<2>AaqI,Alw44I,AmeI,Bsp146I,DaqI,Pfl23I,Pfr12I,PliI,ScoNI,SnoI,Uba1203I,Uba1387I,VneI
<3>G^TGCAC
<4>?(5)
<5>Acetobacter pasteurianus
<6>IFO 13753
<7>CKNU
<8>Murakami, M., Yamada, Y., (1990) Agric. Biol. Chem., vol. 54, pp. 1791-1796.
Suzuki, T., Sugimoto, E., Tahara, Y., Yamada, Y., (1996) Biosci. Biotechnol. Biochem., vol. 60, pp. 1401-1405.
Xia, Y., Van Etten, J.L., Dobos, P., Ling, Y.Y., Krell, P.J., (1993) Virology, vol. 196, pp. 817-824.
Xu, S.-Y., Xiao, J.-P., Ettwiller, L., Holden, M., Aliotta, J., Poh, C.L., Dalton, M., Robinson, D.P., Petronzio, T.R., Moran, L., Ganatra, M., Ware, J., Slatko, B., Benner, J., (1998) Mol. Gen. Genet., vol. 260, pp. 226-231.
Yamada, Y., Murakami, M., (1985) Agric. Biol. Chem., vol. 49, pp. 3627-3629.

<1>ApaORI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Acetobacter pasteurianus
<6>IFO 13752
<7>
<8>Ishikawa, T., Yamada, Y., (1990) J. Gen. Appl. Microbiol., vol. 36, pp. 127-135.

<1>Apc202I
<2>
<3>?
<4>
<5>Aphanizomenon species 202
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>ApcTR183I
<2>MstI,AcaIII,Acc16I,AosI,AviII,Bco6I,BsaTI,ClcII,CliII,FdiII,FspI,GspAII,NsbI,NspHIII,NspLI,NspMI,PamI,Pun14627I
<3>TGCGCA
<4>
<5>Aphanizomenon species TR183
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>ApeI
<2>MluI,Bbi24I,BstZ9I,Uba6I
<3>ACGCGT
<4>
<5>Achromobacter pestifer
<6>ATCC 15445
<7>
<8>Hall, D., Morgan, R., Unpublished observations.

<1>ApeAI
<2>NaeI,Afa24RI,AmeII,AniMI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Aquaspirillum peregrinum
<6>ATCC 15387
<7>
<8>Polisson, C., Unpublished observations.

<1>ApeKI
<2>TseI,AceI,SuiI,Taq52I,TneI,TseBI
<3>G^CWGC
<4>?(5)
<5>Aeropyrum pernix K1
<6>ATCC 700893
<7>N
<8>Kawarabayasi, Y. et al., (1999) DNA Res., vol. 6, pp. 83-101.
Opitz, L., Xu, S.-Y., Unpublished observations.
Xu, S.-Y., Opitz, L., Unpublished observations.

<1>ApiI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Arthrobacter picolinophilus
<6>CAMB 2604
<7>
<8>Choudhry, S., (1999) Proc. Pakistan Acad. Sci., vol. 36, pp. 165-171.

<1>ApoI
<2>AcsI,CfaI,FsiI,XapI
<3>R^AATTY
<4>?(6)
<5>Arthrobacter protophormiae
<6>NEB 723
<7>N
<8>Lunnen, K.D., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Polisson, C., Robinson, D., (1992) Nucleic Acids Res., vol. 20, pp. 2888.

<1>AprI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Actinosynnema pretiosum
<6>ATCC 31281
<7>
<8>Wickberg, L., Schildkraut, I., Unpublished observations.

<1>ApuI
<2>AsuI,AhaB1I,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Alteromonas putrefaciens
<6>M. Sargent
<7>
<8>Walker, J.N.B., Dean, P.G., Saunders, J.R., Unpublished observations.

<1>Apu16I
<2>ClaI,AagI,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Aeromonas punctata 16
<6>S.K. Degtyarev
<7>
<8>Repin, V.E., Prichodko, E.A., Degtyarev, S.K., (1988) Izv. Sib. Otd. Akad. Nauk SSSR, vol. 14, pp. 110-113.

<1>ApyI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Arthrobacter pyridinolis
<6>ATCC 49829
<7>
<8>DiLauro, R., Unpublished observations.

<1>ApyPI
<2>
<3>ATCGAC(20/18)
<4>
<5>Arcanobacterium pyogenes
<6>S.J. Billington
<7>
<8>Jost, B.H., Field, A.C., Trinh, H.T., Songer, J.G., Billington, S.J., (2003) Antimicrob. Agents Chemother., vol. 47, pp. 3519-3524.
Morgan, R.D., Unpublished observations.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>AquI
<2>AvaI,AcrI,Ama87I,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>1(5)
<5>Agmenellum quadruplicatum PR-6
<6>PCC 7002
<7>
<8>Karreman, C., Tandeau de Marsac, N., de Waard, A., (1986) Nucleic Acids Res., vol. 14, pp. 5199-5205.
Lau, R.H., Doolittle, W.F., (1980) FEBS Lett., vol. 121, pp. 200-202.
Li, T., Zhao, J., Zhao, C., Liu, Z., Zhao, F., Marquardt, J., Nomura, C.T., Persson, S., Detter, J.C., Richardson, P.M., Lanz, C., Schuster, S.C., Wang, J., Li, S., Huang, X., Cai, T., Yu, Z., Luo, J., Zhao, J., Bryant, D.A., Unpublished observations.

<1>ArsI
<2>
<3>(8/13)GACNNNNNNTTYG(11/6)
<4>
<5>Arthrobacter species NTS
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Kileva, E.V., Tomilova, J.E., Dedkov, V.S., Mikhnenkova, N.A., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>AscI
<2>PalAI,SgsI
<3>GG^CGCGCC
<4>?(5)
<5>Arthrobacter species
<6>NEB 688
<7>NW
<8>Lunnen, K.D., Wilson, G.G., Unpublished observations.
Morgan, R., European Patent Office, 1992.
Morgan, R.D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>AseI
<2>VspI,AsnI,BpoAI,CprJK722I,PbuMZI,PshBI,Srl8DI,Srl55DII,Srl65DI,Srr17I,Sru4DI
<3>AT^TAAT
<4>?(6)
<5>Aquaspirillum serpens
<6>NEB 448
<7>JNO
<8>Morgan, R.D., US Patent Office, 1992.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Polisson, C., Morgan, R.D., (1988) Nucleic Acids Res., vol. 16, pp. 10365.
Stewart, F., Morgan, R.D., Unpublished observations.

<1>AseII
<2>CauII,AhaI,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CC^SGG
<4>
<5>Aquaspirillum serpens
<6>NEB 448
<7>
<8>Polisson, C., Morgan, R.D., (1988) Nucleic Acids Res., vol. 16, pp. 10365.

<1>AsiI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Azotobacter species
<6>N.N. Sokolov
<7>
<8>Korolev, S.V., Sokolov, N.N., Rina, M., Eldarov, M.A., Omelyanyuk, N.M., Markaki, M., Skryabin, K.G., Bouriotis, V., (1998) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 32-35.

<1>Asi256I
<2>MboI,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>G^ATC
<4>
<5>Arthrobacter species strain Ck256
<6>V.E. Repin
<7>
<8>Ushakova, T.A., Puchkova, L.I., Gutorov, V.V., Totmenina, O.D., Repin, V.E., (2008) Prikl. Biokhim. Mikrobiol., vol. 44, pp. 28-31.

<1>Asi372I
<2>AvaIII,BfrBI,BfrCI,Csp68KIII,EcoT22I,Mph1103I,NsiI,PinBI,Ppu10I,PxyJKI,SepI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>ATGCA^T
<4>
<5>Arthrobacter species Mn372
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Totmenina, O.D., Afonina, V.S., Polushkina, A.F., Repin, V.E., Russian Patent Office, 2007.

<1>AsiAI
<2>AgeI,AsiGI,BshTI,CsiAI,CspAI,PinAI
<3>A^CCGGT
<4>
<5>Arthrobacter species A7359
<6>S.K. Degtyarev
<7>
<8>Abdurashitov, M.A., Bondar, T.S., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>AsiGI
<2>AgeI,AsiAI,BshTI,CsiAI,CspAI,PinAI
<3>A^CCGGT
<4>
<5>Arthrobacter species G
<6>S.K. Degtyarev
<7>IV
<8>Chmuzh, E.V., Mikhnenkova, N.A., Nayakshina, T.N., Mezentseva, N.V., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>AsiSI
<2>SgfI,RgaI,SfaAI
<3>GCGAT^CGC
<4>?(5)
<5>Arthrobacter species S
<6>S.K. Degtyarev
<7>N
<8>Abdurashitov, M.A., Shinkarenko, N.M., Shevchenko, A.V., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.
Zhu, Z., Xu, S.-Y., Unpublished observations.
Zhu, Z., Xu, S.-Y., US Patent Office, 2003.

<1>AsnI
<2>VspI,AseI,BpoAI,CprJK722I,PbuMZI,PshBI,Srl8DI,Srl55DII,Srl65DI,Srr17I,Sru4DI
<3>AT^TAAT
<4>
<5>Arthrobacter species strain N-CM
<6>C. Kessler
<7>
<8>Rexer, B.U., Jarsch, M., Sagmeister, C., Gluck, B., Berger, G., Kessler, C., (1988) FEBS Lett., vol. 235, pp. 241-246.

<1>AspI
<2>Tth111I,AtsI,BgiI,FsuI,NtaI,PflFI,PsyI,SmaAII,SpaPI,SplII,SplAII,TelI,TrsKTII,TspI,TteI,TtrI
<3>GACN^NNGTC
<4>
<5>Achromobacter species 699
<6>U. Mayr
<7>M
<8>Bolton, B.J., Schmitz, G.G., Jarsch, M., Kessler, C., (1990) Nucleic Acids Res., vol. 18, pp. 3422.

<1>Asp1I
<2>CauII,AhaI,AseII,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Arthrobacter species RFL1
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Asp10I
<2>
<3>?
<4>
<5>Aeromonas species
<6>A.M. Kulba
<7>
<8>Kulba, A.M., Elgammudi, A.A., (1997) Vestn. Beloruss. Gos. Univ., vol. 2, pp. 47-49.

<1>Asp14I
<2>ClaI,AagI,Apu16I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Anabaena species 14
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Asp15I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Acidiphilium species 15
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp17I
<2>XhoII,AitII,AitAI,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>RGATCY
<4>
<5>Acidiphilium species 17
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp22I
<2>XhoII,AitII,AitAI,Asp17I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>RGATCY
<4>
<5>Acidiphilium species 22
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp28I
<2>
<3>?
<4>
<5>Aeromonas species
<6>A.M. Kulba
<7>
<8>Kulba, A.M., Elgammudi, A.A., (1997) Vestn. Beloruss. Gos. Univ., vol. 2, pp. 47-49.

<1>Asp36I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Alcaligenes species RFL36
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Unpublished observations.

<1>Asp37I
<2>ClaI,AagI,Apu16I,Asp14I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Anabaena species 37
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Asp47I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Alcaligenes species 47
<6>C. Kessler
<7>
<8>Bolton, B.J., Comer, M.J., Kessler, C., Unpublished observations.

<1>Asp52I
<2>HindIII,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Alcaligenes species 52
<6>C. Kessler
<7>
<8>Bolton, B.J., Comer, M.J., Kessler, C., Unpublished observations.

<1>Asp54I
<2>
<3>?
<4>
<5>Anabaena species 54
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Asp78I
<2>StuI,AatI,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGGCCT
<4>
<5>Alcaligenes species 78
<6>C. Kessler
<7>
<8>Bolton, B.J., Comer, M.J., Kessler, C., Unpublished observations.

<1>Asp86I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Anabaena species 86
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Asp86II
<2>
<3>?
<4>
<5>Anabaena species 86
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Asp90I
<2>AflIII
<3>ACRYGT
<4>
<5>Anabaena species 90
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Asp90II
<2>
<3>?
<4>
<5>Anabaena species 90
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Asp123I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Anabaena species 123
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Asp123II
<2>
<3>?
<4>
<5>Anabaena species 123
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Asp130I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Anabaena species 130
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Asp697I
<2>AvaII,AflI,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Achromobacter species 697
<6>C. Kessler
<7>
<8>Kessler, C., Neumaier, P.S., Wolf, W., (1985) Gene, vol. 33, pp. 1-102.

<1>Asp700I
<2>XmnI,BbvAI,MroXI,PdmI,Psc2I,SynII
<3>GAANN^NNTTC
<4>
<5>Achromobacter species 700
<6>C. Kessler
<7>M
<8>Bolton, B.J., Comer, M., Kessler, C., (1989) Nucleic Acids Res., vol. 17, pp. 8879.

<1>Asp703I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Achromobacter species 703
<6>C. Kessler
<7>
<8>Kessler, C., Neumaier, P.S., Wolf, W., (1985) Gene, vol. 33, pp. 1-102.

<1>Asp707I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Achromobacter species 707
<6>C. Kessler
<7>
<8>Kessler, C., Neumaier, P.S., Wolf, W., (1985) Gene, vol. 33, pp. 1-102.

<1>Asp708I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Achromobacter species 708
<6>C. Kessler
<7>
<8>Kessler, C., Neumaier, P.S., Wolf, W., (1985) Gene, vol. 33, pp. 1-102.

<1>Asp713I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Achromobacter species 713
<6>U. Mayr
<7>
<8>Wersig, U., Bolton, B., Frey, B., Jarsch, M., Kessler, C., Unpublished observations.

<1>Asp718I
<2>KpnI,Acc65I,AhaB8I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>G^GTACC
<4>
<5>Achromobacter species 718
<6>DSM 2969
<7>M
<8>Bolton, B.J., Nesch, G., Comer, M.J., Wolf, W., Kessler, C., (1985) FEBS Lett., vol. 182, pp. 130-134.

<1>Asp742I
<2>HaeIII,AcaIV,Afl83II,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Achromobacter species 742
<6>C. Kessler
<7>
<8>Bolton, B.J., Comer, M.J., Kessler, C., Unpublished observations.

<1>Asp745I
<2>AvaII,AflI,Asp697I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Achromobacter species 745
<6>U. Mayr
<7>
<8>Wersig, U., Bolton, B., Frey, B., Jarsch, M., Kessler, C., Unpublished observations.

<1>Asp748I
<2>HpaII,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Achromobacter species 748
<6>C. Kessler
<7>
<8>Bolton, B.J., Comer, M.J., Kessler, C., Unpublished observations.

<1>Asp763I
<2>ScaI,Acc113I,AflIV,AssI,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGTACT
<4>
<5>Achromobacter species 763
<6>C. Kessler
<7>
<8>Bolton, B.J., Comer, M.J., Kessler, C., Unpublished observations.

<1>Asp3065I
<2>HindIII,Asp52I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Alcaligenes species 3065
<6>U. Mayr
<7>
<8>Bolton, B.J., Schmitz, G., Jarsch, M., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>AspAI
<2>BstEII,AcrII,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Alcaligenes species
<6>N.L. Brown
<7>
<8>Whitehead, P.R., Brown, N.L., (1981) Biochem. Soc. Trans., vol. 9, pp. 272P.

<1>AspA2I
<2>AvrII,AvrBII,BlnI,BspA2I,XmaJI
<3>C^CTAGG
<4>
<5>Arthrobacter species A2
<6>S.K. Degtyarev
<7>IV
<8>Abdurashitov, M.A., Dedkov, V.S., Shinkarenko, N.M., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>Asp202A1I
<2>
<3>?
<4>
<5>Anabaena species 202A1
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Asp202A135I
<2>
<3>?
<4>
<5>Anabaena species 202A135I
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>AspBI
<2>AvaI,AcrI,Ama87I,AquI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Anabaena species
<6>ATCC 29151
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., Vonshak, A., Wolk, C.P., (1983) Arch. Microbiol., vol. 134, pp. 276-281.

<1>AspBII
<2>AvaII,AflI,Asp697I,Asp745I,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Anabaena species
<6>ATCC 29151
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., Vonshak, A., Wolk, C.P., (1983) Arch. Microbiol., vol. 134, pp. 276-281.

<1>AspCNI
<2>
<3>GCCGC
<4>?(5)
<5>Acinetobacter species 1690
<6>NEB 1318
<7>
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Nkenfou, C., Morgan, R.D., Unpublished observations.
Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.
Rausch, C., Nkenfou, C., Morgan, R.D., Unpublished observations.

<1>AspDI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Anabaena species
<6>ATCC 27898
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., Vonshak, A., Wolk, C.P., (1983) Arch. Microbiol., vol. 134, pp. 276-281.

<1>AspDII
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Anabaena species
<6>ATCC 27898
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., Vonshak, A., Wolk, C.P., (1983) Arch. Microbiol., vol. 134, pp. 276-281.

<1>AspEI
<2>Eam1105I,AhdI,BmeRI,BspOVI,BstZ2I,DriI,EclHKI,NruGI,Uba1190I,Uba1191I
<3>GACNNN^NNGTC
<4>
<5>Aureobacterium species
<6>K. Kaluza
<7>M
<8>Frey, B., Kaluza, K., Auer, J., Stratidakis, I., Rina, M., Bouriotis, V., Schmitz, G., (1992) Nucleic Acids Res., vol. 20, pp. 3782.

<1>AspHI
<2>HgiAI,Alw21I,Bbv12I,Bfu1570I,BsaGI,Bsh45I,BsiHKAI,Bsm6I,BsmPI,Hpy8III,HpyF7II,HpyF46II,MspV281I,Pph3215I
<3>GWGCW^C
<4>
<5>Achromobacter species H
<6>U. Mayr
<7>
<8>Bolton, B.J., Holtke, H.-J., Schmitz, G.G., Jarsch, M., Kessler, C., (1989) Nucleic Acids Res., vol. 17, pp. 9500.

<1>Asp1HI
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>RGATCY
<4>
<5>Acidiphilium species 1H
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp2HI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Acidiphilium species 2H
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp5HI
<2>SphI,BbuI,BscOI,Bsp121I,BtgAII,CglAI,PaeI,PaeCI,PfaAIII,RspLKI,SpaHI,SpaXI,Uba1162I,Uba1226I,VchO68I
<3>GCATGC
<4>
<5>Acidiphilium species 5H
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp6HI
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>RGATCY
<4>
<5>Acidiphilium species 6H
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp8HI
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>RGATCY
<4>
<5>Acidiphilium species 8H
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp10HI
<2>AsuII,AcaI,AcpI,Afl83I,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Acidiphilium species 10H
<6>K. Inagaki
<7>
<8>Inagaki, K., Ito, T., Kotani, H., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp10HII
<2>PflMI,AccB7I,AcpII,BasI,Esp1396I,PflBI,Van91I
<3>CCANNNN^NTGG
<4>
<5>Acidiphilium species 10H
<6>K. Inagaki
<7>
<8>Inagaki, K., Ito, T., Kotani, H., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp14HI
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>RGATCY
<4>
<5>Acidiphilium species 14H
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp16HI
<2>RsaI,AfaI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Acidiphilium species 16H
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp17HI
<2>RsaI,AfaI,Asp16HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Acidiphilium species 17H
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp18HI
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Acidiphilium species 18H
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp21HI
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>RGATCY
<4>
<5>Acidiphilium species 21H
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp26HI
<2>BsmI,Asp27HI,Asp35HI,Asp36HI,Asp40HI,Asp50HI,BmaHI,BsaMI,BscCI,Mva1269I,PctI,Uba1382I,Uba1415I
<3>GAATGC(1/-1)
<4>
<5>Acidiphilium species 26H
<6>K. Inagaki
<7>
<8>Inagaki, K., Kobayashi, F., Dou, D., Nomura, Y., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp27HI
<2>BsmI,Asp26HI,Asp35HI,Asp36HI,Asp40HI,Asp50HI,BmaHI,BsaMI,BscCI,Mva1269I,PctI,Uba1382I,Uba1415I
<3>GAATGC(1/-1)
<4>
<5>Acidiphilium species 27H
<6>K. Inagaki
<7>
<8>Inagaki, K., Kobayashi, F., Dou, D., Nomura, Y., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp29HI
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Acidiphilium species 29H
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp32HI
<2>SacII,AosIII,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Acidiphilium species 32H
<6>K. Inagaki
<7>
<8>Inagaki, K., Dou, D., Kobayashi, F., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp35HI
<2>BsmI,Asp26HI,Asp27HI,Asp36HI,Asp40HI,Asp50HI,BmaHI,BsaMI,BscCI,Mva1269I,PctI,Uba1382I,Uba1415I
<3>GAATGC(1/-1)
<4>
<5>Acidiphilium species 35H
<6>K. Inagaki
<7>
<8>Inagaki, K., Kobayashi, F., Dou, D., Nomura, Y., Kotani, H., Kishimoto, N., Sugio, T., Tano, T., (1990) Nucleic Acids Res., vol. 18, pp. 6155.

<1>Asp36HI
<2>BsmI,Asp26HI,Asp27HI,Asp35HI,Asp40HI,Asp50HI,BmaHI,BsaMI,BscCI,Mva1269I,PctI,Uba1382I,Uba1415I
<3>GAATGC(1/-1)
<4>
<5>Acidiphilium species 36H
<6>K. Inagaki
<7>
<8>Inagaki, K., Kobayashi, F., Dou, D., Nomura, Y., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp40HI
<2>BsmI,Asp26HI,Asp27HI,Asp35HI,Asp36HI,Asp50HI,BmaHI,BsaMI,BscCI,Mva1269I,PctI,Uba1382I,Uba1415I
<3>GAATGC(1/-1)
<4>
<5>Acidiphilium species 40H
<6>K. Inagaki
<7>
<8>Inagaki, K., Kobayashi, F., Dou, D., Nomura, Y., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>Asp50HI
<2>BsmI,Asp26HI,Asp27HI,Asp35HI,Asp36HI,Asp40HI,BmaHI,BsaMI,BscCI,Mva1269I,PctI,Uba1382I,Uba1415I
<3>GAATGC(1/-1)
<4>
<5>Acidiphilium species 50H
<6>K. Inagaki
<7>
<8>Inagaki, K., Kobayashi, F., Dou, D., Nomura, Y., Hiraoka, N., Kishimoto, N., Tano, T., Unpublished observations.

<1>AspJI
<2>AatII,Ppu1253I,Ssp5230I,ZraI
<3>GACGTC
<4>
<5>Alcaligenes species J-482
<6>J.-T. Lee
<7>
<8>Lee, J.-T., Cho, T.-J., Lim, J.-Y., (1994) Korean J. Microbiol., vol. 32, pp. 285-290.

<1>AspLEI
<2>HhaI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCG^C
<4>
<5>Arthrobacter species LE3860
<6>S.K. Degtyarev
<7>IV
<8>Vysotskaya, E.M., Gonchar, D.A., Shevchenko, A.V., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>AspMI
<2>StuI,AatI,Asp78I,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGG^CCT
<4>
<5>Acinetobacter species M
<6>N.I. Matvienko
<7>
<8>Zelinskaya, N.V., Kovalevskaya, N.P., Matvienko, N.N., Zheleznaya, L.A., Matvienko, N.I., (1996) Biokhimiia, vol. 61, pp. 1471-1482.

<1>AspMDI
<2>MboI,Asi256I,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Alcaligenes species MD1
<6>H.X. Chiura
<7>
<8>Chiura, H.X., Kamiyama, T., Hirano, H., Futagami, M., Watahiki, M., Kobayashi, K., Simidu, U., Takagi, J., (1992) Nucleic Acids Res., vol. 20, pp. 1996.

<1>AspNI
<2>NlaIV,BcrI,BmiI,BsaEI,BscBI,Bsp29I,BspLI,BssI,HpyF44II,HpyF73I,NgoBV,NgoGV,PspN4I,Rlu3I,Uba1305I,Uba1445I
<3>GGN^NCC
<4>
<5>Anabaena species J3
<6>U. Mayr
<7>
<8>Frey, B., Unpublished observations.

<1>AspS9I
<2>AsuI,AhaB1I,ApuI,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Arthrobacter species S9
<6>S.K. Degtyarev
<7>IV
<8>Dedkov, V.S., Kileva, E.V., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>AspTI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Anabaena species TA 1
<6>C.P. Wolk
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>AspTII
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Anabaena species TA 1
<6>C.P. Wolk
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>AspTIII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Anabaena species TA 1
<6>C.P. Wolk
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>AssI
<2>ScaI,Acc113I,AflIV,Asp763I,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGT^ACT
<4>
<5>Arthrobacter species
<6>P. Babu
<7>U
<8>Suma, M.A., Chandrashekaran, S., Babu, J., Unpublished observations.

<1>AstWI
<2>AcyI,AhaII,AosII,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>
<5>Anabaena species
<6>ATCC 29208
<7>
<8>de Waard, A., Duyvesteyn, M., (1980) Arch. Microbiol., vol. 128, pp. 242-247.

<1>AsuI
<2>AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Anabaena subcylindrica
<6>CCAP 1403/4b
<7>
<8>de Waard, A., Duyvesteyn, M., (1980) Arch. Microbiol., vol. 128, pp. 242-247.
Hughes, S.G., Bruce, T., Murray, K., (1980) Biochem. J., vol. 185, pp. 59-63.

<1>AsuII
<2>AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Anabaena subcylindrica
<6>CCAP 1403/4b
<7>C
<8>de Waard, A., Duyvesteyn, M., (1980) Arch. Microbiol., vol. 128, pp. 242-247.

<1>AsuIII
<2>AcyI,AhaII,AosII,AstWI,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>
<5>Anabaena subcylindrica
<6>CCAP 1403/4b
<7>
<8>de Waard, A., Duyvesteyn, M., (1980) Arch. Microbiol., vol. 128, pp. 242-247.

<1>AsuC2I
<2>CauII,AhaI,AseII,Asp1I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CC^SGG
<4>
<5>Actinobacillus suis C2
<6>S.K. Degtyarev
<7>I
<8>Kileva, E.V., Dedkov, V.S., Abdurashitov, M.A., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>AsuHPI
<2>HphI,NgoBVIII,NgoDVIII,NgoJVIII,NgoMVIII,SspD5I
<3>GGTGA(8/7)
<4>
<5>Actinobacillus suis HP
<6>S.K. Degtyarev
<7>IV
<8>Dedkov, V.S., Degtyarev, S.Kh., (1998) Biol. Chem., vol. 379, pp. 573-574.

<1>AsuMBI
<2>MboI,Asi256I,AspMDI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Actinobacillus suis MB
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Degtyarev, S.Kh., (1998) Biol. Chem., vol. 379, pp. 573-574.

<1>AsuNHI
<2>NheI,AceII,BmtI,BspOI,LlaG2I,PstNHI
<3>G^CTAGC
<4>
<5>Actinobacillus suis NH
<6>S.K. Degtyarev
<7>IV
<8>Dedkov, V.S., Degtyarev, S.Kh., (1998) Biol. Chem., vol. 379, pp. 573-574.

<1>AsuSAI
<2>SauI,AocI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Actinobacillus suis SA
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Degtyarev, S.Kh., (1998) Biol. Chem., vol. 379, pp. 573-574.

<1>AteI
<2>NcoI,Bse19I,Bsp19I,NspSAIII
<3>CCATGG
<4>
<5>Actinoplanes teochomyceticus
<6>Glaxo 2523C
<7>
<8>Earle-Hughes, J., Roberts, R.J., Unpublished observations.

<1>M.AthIII
<2>
<3>?
<4>?(5)
<5>Arabidopsis thaliana
<6>A. Graessmann
<7>
<8>Arabidopsis, E.U., Unpublished observations.
Bevan, M. et al., (1998) Nature, vol. 391, pp. 485-488.
GenBank, D.B., Unpublished observations.

<1>M.AthDRM1
<2>
<3>?
<4>?(5)
<5>Arabidopsis thaliana
<6>A. Graessmann
<7>
<8>GenBank, D.B., Unpublished observations.

<1>M.AthDRM2
<2>
<3>?
<4>?(5)
<5>Arabidopsis thaliana
<6>A. Graessmann
<7>
<8>Arabidopsis, E.U., Unpublished observations.
Bevan, M., Murphy, G., Ridley, P., Hudson, S., Bancroft, I., Mewes, H.W., Rudd, S., Lemcke, K., Mayer, K.F.X., Unpublished observations.
Cao, X., Springer, N.M., Muszynski, M.G., Phillips, R.L., Kaeppler, S., Jacobsen, S.E., (2000) Proc. Natl. Acad. Sci. U. S. A., vol. 97, pp. 4979-4984.
Comai, L., Young, K., Till, B.J., Reynolds, S., Greene, E.A., Codomo, C.A., Enns, L., Johnson, J.E., Burtner, C., Odden, A., Henikoff, S., (2004) Plant J., vol. 37, pp. 778-786.
GenBank, D.B., Unpublished observations.

<1>M.AthDnmt1A
<2>
<3>?
<4>?(5)
<5>Arabidopsis thaliana
<6>A. Graessmann
<7>
<8>Arabidopsis, E.U., Unpublished observations.
Asamizu, E., Sato, S., Kaneko, T., Nakamura, Y., Kotani, H., Miyajima, N., Tabata, S., (1998) DNA Res., vol. 5, pp. 379-391.
Finnegan, E.J., Dennis, E.S., (1993) Nucleic Acids Res., vol. 21, pp. 2383-2388.
GenBank, D.B., Unpublished observations.
Plesch, G., Blau, A., Daeschner, K., International Patent Office, 2004.
Scheidt, G., Graessmann, A., Weber, H., (1991) Biol. Chem. Hoppe Seyler, vol. 372, pp. 742.

<1>M.AthDnmt1B
<2>
<3>?
<4>?(5)
<5>Arabidopsis thaliana
<6>A. Graessmann
<7>
<8>Bevan, M. et al., Unpublished observations.
Chang, S., Pikaard, C.S., Unpublished observations.
Finnegan, E.J., Dennis, E.S., (1993) Nucleic Acids Res., vol. 21, pp. 2383-2388.
Genger, R.K., Kovac, K.A., Dennis, E.S., Peacock, W.J., Finnegan, E.J., (1999) Plant Mol. Biol., vol. 41, pp. 269-278.
Nakamura, Y., Unpublished observations.

<1>AtsI
<2>Tth111I,AspI,BgiI,FsuI,NtaI,PflFI,PsyI,SmaAII,SpaPI,SplII,SplAII,TelI,TrsKTII,TspI,TteI,TtrI
<3>GACN^NNGTC
<4>
<5>Aureobacterium testaceum 4842
<6>S.K. Degtyarev
<7>
<8>Abdurashitov, M.A., Kileva, E.V., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>AtuII
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Agrobacterium tumefaciens ID 135
<6>C.I. Kado
<7>
<8>LeBon, J.M., Kado, C.I., Rosenthal, L.J., Chirikjian, J.G., (1978) Proc. Natl. Acad. Sci. U. S. A., vol. 75, pp. 4097-4101.

<1>Atu1I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Agrobacterium tumefaciens RFL1
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.

<1>Atu1II
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Agrobacterium tumefaciens RFL1
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.

<1>AtuAI
<2>
<3>?
<4>
<5>Agrobacterium tumefaciens
<6>ATCC 15955
<7>
<8>Sciaky, D., Roberts, R.J., Unpublished observations.

<1>AtuBI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Agrobacterium tumefaciens B6806
<6>E. Nester
<7>
<8>Roizes, G., Patillon, M., Kovoor, A., (1977) FEBS Lett., vol. 82, pp. 69-70.

<1>AtuBVI
<2>
<3>?
<4>
<5>Agrobacterium tumefaciens IIBV7
<6>G. Roizes
<7>
<8>Roizes, G., Pages, M., Lecou, C., Patillon, M., Kovoor, A., (1979) Gene, vol. 6, pp. 43-50.

<1>M.AtuCI
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>2(6)
<5>Agrobacterium tumefaciens C58 (Cereon)
<6>E. Nester
<7>
<8>Goodner, B. et al., (2001) Science, vol. 294, pp. 2323-2328.
Kahng, L.S., Shapiro, L., (2001) J. Bacteriol., vol. 183, pp. 3065-3075.

<1>AtuIAMI
<2>
<3>?
<4>
<5>Agrobacterium tumefaciens
<6>IAM B-26-1
<7>
<8>Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Bull. Inst. Chem. Res. Kyoto Univ., vol. 60, pp. 328-335.

<1>AtuSI
<2>BclI,AbaI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Agrobacterium tumefaciens C58 (Cereon)
<6>E. Nester
<7>
<8>Sciaky, D., Roberts, R.J., Unpublished observations.

<1>AvaI
<2>AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>?(4)
<5>Anabaena variabilis
<6>ATCC 27893
<7>BJMNOQRSUWX
<8>Hughes, S.G., Murray, K., (1980) Biochem. J., vol. 185, pp. 65-75.
Kaneko, T. et al., (2001) DNA Res., vol. 8, pp. 205-213.
Lunnen, K.D., Barsomian, J.M., Camp, R.R., Card, C.O., Chen, S.-Z., Croft, R., Looney, M.C., Meda, M.M., Moran, L.S., Nwankwo, D.O., Slatko, B.E., Van Cott, E.M., Wilson, G.G., (1988) Gene, vol. 74, pp. 25-32.
Murray, K., Hughes, S.G., Brown, J.S., Bruce, S.A., (1976) Biochem. J., vol. 159, pp. 317-322.
Ruan, H., Lunnen, K.D., Scott, M.E., Moran, L.S., Slatko, B.E., Pelletier, J.J., Hess, E.J., Benner, J., Wilson, G.G., Xu, S.-Y., (1996) Mol. Gen. Genet., vol. 252, pp. 695-699.

<1>AvaII
<2>AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>?(5)
<5>Anabaena variabilis
<6>ATCC 27893
<7>JKMNRSWY
<8>Fuchs, C., Rosenvold, E.C., Honigman, A., Szybalski, W., (1978) Gene, vol. 4, pp. 1-23.
Hughes, S.G., Murray, K., (1980) Biochem. J., vol. 185, pp. 65-75.
Kaneko, T. et al., (2001) DNA Res., vol. 8, pp. 205-213.
Lunnen, K.D., Barsomian, J.M., Camp, R.R., Card, C.O., Chen, S.-Z., Croft, R., Looney, M.C., Meda, M.M., Moran, L.S., Nwankwo, D.O., Slatko, B.E., Van Cott, E.M., Wilson, G.G., (1988) Gene, vol. 74, pp. 25-32.
Lunnen, K.D., Wilson, G.G., Kroeger, M., Unpublished observations.
Murray, K., Hughes, S.G., Brown, J.S., Bruce, S.A., (1976) Biochem. J., vol. 159, pp. 317-322.
Sutcliffe, J.G., Church, G.M., (1978) Nucleic Acids Res., vol. 5, pp. 2313-2319.

<1>AvaIII
<2>Asi372I,BfrBI,BfrCI,Csp68KIII,EcoT22I,Mph1103I,NsiI,PinBI,Ppu10I,PxyJKI,SepI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>ATGCAT
<4>
<5>Anabaena variabilis
<6>ATCC 27893
<7>
<8>Elhai, J., Unpublished observations.
Roizes, G., Nardeux, P.C., Monier, R., (1979) FEBS Lett., vol. 104, pp. 39-44.
Shimatake, H., Rosenberg, M., Unpublished observations.

<1>Ava458I
<2>CfrI,AcoI,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Anabaena variabilis CALU 458
<6>M.I. Mendzhul
<7>
<8>Mendzhul, M.I., Moshinsky, I.D., Syrchin, S.A., (1999) Mikrobiol. Zh., vol. 61, pp. 10-14.

<1>AvcI
<2>AsuI,AhaB1I,ApuI,AspS9I,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Actinomyces violaceoniger cristalomycini
<6>A.J. Podhajska
<7>
<8>Rutkowska, S.M., Skowron, P.M., Podhajska, A.J., (1995) Gene, vol. 157, pp. 317-318.

<1>AviI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Anabaena variabilis (halle)
<6>CCAP 1403/12
<7>
<8>de Waard, A., Unpublished observations.

<1>AviII
<2>MstI,AcaIII,Acc16I,AosI,ApcTR183I,Bco6I,BsaTI,ClcII,CliII,FdiII,FspI,GspAII,NsbI,NspHIII,NspLI,NspMI,PamI,Pun14627I
<3>TGC^GCA
<4>
<5>Anabaena variabilis (halle)
<6>CCAP 1403/12
<7>M
<8>de Waard, A., Unpublished observations.

<1>AvoI
<2>NspI,BstNSI,Lsp1270I,NspHI,PauAI,PunAII,XceI
<3>RCATG^Y
<4>
<5>Anoxybacillus voinovskiensi
<6>Vivantis 224
<7>
<8>Chee, H.Y., Unpublished observations.

<1>AvrI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Anabaena variabilis uw
<6>E.C. Rosenvold
<7>
<8>Rosenvold, E.C., Szybalski, W., Unpublished observations.

<1>AvrII
<2>AspA2I,AvrBII,BlnI,BspA2I,XmaJI
<3>C^CTAGG
<4>
<5>Anabaena variabilis uw
<6>E.C. Rosenvold
<7>N
<8>Lunnen, K.D., Moran, L.S., Slatko, B.E., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Rosenvold, E.C., Szybalski, W., Unpublished observations.

<1>AvrBI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Arthrobacter variabilis
<6>M.M. Wijdenbosch
<7>
<8>Calmero, J., Unpublished observations.

<1>AvrBII
<2>AvrII,AspA2I,BlnI,BspA2I,XmaJI
<3>C^CTAGG
<4>
<5>Arthrobacter variabilis
<6>M.M. Wijdenbosch
<7>
<8>Calmero, J., Unpublished observations.

<1>AxyI
<2>SauI,AocI,AsuSAI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CC^TNAGG
<4>
<5>Acetobacter xylinus
<6>IFO 3288
<7>J
<8>Yoshioka, H., Nakamura, H., Sasaki, J., Tahara, Y., Yamada, Y., (1983) Agric. Biol. Chem., vol. 47, pp. 2871-2879.

<1>M.BabI
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>2(6)
<5>Brucella abortus
<6>L. Shapiro
<7>
<8>Paulsen, I. et al., (2002) Proc. Natl. Acad. Sci. U. S. A., vol. 99, pp. 13148-13153.
Robertson, G.T., Reisenauer, A., Wright, R., Jensen, R.B., Jensen, A., Shapiro, L., Roop, R.M., (2000) J. Bacteriol., vol. 182, pp. 3482-3489.
Wright, R., Stephens, C., Shapiro, L., (1997) J. Bacteriol., vol. 179, pp. 5869-5877.

<1>BacI
<2>SacII,AosIII,Asp32HI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Bacillus acidocaldarius
<6>ATCC 27009
<7>
<8>Mayer, H., Schutte, H., Unpublished observations.
Myers, P.A., Roberts, R.J., Unpublished observations.

<1>Bac36I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Bacillus alcalophilus 36
<6>M.V. Jones
<7>
<8>Walker, J.N.B., Dean, P.G., Saunders, J.R., Unpublished observations.

<1>Bac465I
<2>SacII,AosIII,Asp32HI,BacI,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Bacillus acidocaldarius 465
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>BadI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Bifidobacterium adolescentis LVA1
<6>G.N. Gabrichevsky
<7>
<8>Skrypina, N.A., Kramarov, V.M., Lyannaya, A.M., Smolyaninov, V.V., Goncharova, G.I., (1988) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 15-16.

<1>BaeI
<2>
<3>(10/15)ACNNNNGTAYC(12/7)
<4>
<5>Bacillus sphaericus
<6>NEB 659
<7>N
<8>Sears, L.E., Zhou, B., Aliotta, J.M., Morgan, R.D., Kong, H., (1996) Nucleic Acids Res., vol. 24, pp. 3590-3592.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BaeGI
<2>BseSI,Bme1580I,BmgAI,BstSLI
<3>GKGCM^C
<4>
<5>Bacillus aestuarii GG790
<6>NEB 1902
<7>N
<8>Pan, X.S., Morgan, R., Unpublished observations.

<1>BalI
<2>MlsI,Mlu31I,MluNI,MscI,Msp16I,Msp20I
<3>TGG^CCA
<4>?(4)
<5>Brevibacterium albidum
<6>ATCC 15831
<7>JKRX
<8>Forrow, S., Lee, M., Souhami, R.L., Hartley, J.A., (1994) ACS Abstracts, vol. 208, pp. 97.
Gelinas, R.E., Myers, P.A., Weiss, G.H., Roberts, R.J., Murray, K., (1977) J. Mol. Biol., vol. 114, pp. 433-440.
Trautner, T.A., Unpublished observations.
Ueno, H., Kato, I., Ishino, Y., (1996) Nucleic Acids Res., vol. 24, pp. 2268-2270.

<1>Bal228I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Bacillus alcalophilus 228
<6>U. Mayr
<7>
<8>Wersig, U., Bolton, B., Frey, B., Jarsch, M., Kessler, C., Unpublished observations.

<1>Bal475I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus alvei 475
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>Bal3006I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus alvei 3006
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>BamFI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus amyloliquefaciens F
<6>ATCC 23350
<7>
<8>Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>BamGI
<2>PvuII,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>
<5>B.acetylicum KSG
<6>Vivantis 52
<7>
<8>Chee, H.Y., Unpublished observations.

<1>BamHI
<2>AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>5(4)
<5>Bacillus amyloliquefaciens H
<6>ATCC 49763
<7>BCFHIJKMNOQRSUVWXY
<8>Brooks, J.E., Nathan, P.D., Landry, D., Sznyter, L.A., Waite-Rees, P., Ives, C.L., Moran, L.S., Slatko, B.E., Benner, J.S., (1991) Nucleic Acids Res., vol. 19, pp. 841-850.
Endo, M., Majima, T., Japanese Patent Office, 2003.
Hattman, S., Keister, T., Gottehrer, A., (1978) J. Mol. Biol., vol. 124, pp. 701-711.
Majima, T., Endo, M., Japanese Patent Office, 2006.
Roberts, R.J., Wilson, G.A., Young, F.E., (1977) Nature, vol. 265, pp. 82-84.
Usami, S., Kurimura, H., Kino, K., Kamigaki, K., Kirimura, K., Japanese Patent Office, 2003.
Wilson, G.A., Young, F.E., (1975) J. Mol. Biol., vol. 97, pp. 123-125.

<1>M.BamHII
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus amyloliquefaciens H
<6>ATCC 49763
<7>
<8>Connaughton, J.E., Vanek, P.G., Chirikjian, J.G., (1988) J. Cell Biol., vol. 107, pp. 535a.

<1>BamKI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus amyloliquefaciens K
<6>T. Kaneko
<7>
<8>Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>BamNI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus amyloliquefaciens N
<6>T. Ando
<7>
<8>Shibata, T., Ando, T., (1976) Biochim. Biophys. Acta, vol. 442, pp. 184-196.

<1>BamNxI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Bacillus amyloliquefaciens N
<6>T. Ando
<7>
<8>Ikawa, S., Shibata, T., Ando, T., (1979) Agric. Biol. Chem., vol. 43, pp. 873-875.
Shibata, T., Ando, T., (1975) Mol. Gen. Genet., vol. 138, pp. 269-279.

<1>BanI
<2>HgiCI,AccB1I,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>G^GYRCC
<4>?(5)
<5>Bacillus aneurinolyticus
<6>IAM 1077
<7>NORU
<8>Kawakami, B., Maekawa, Y., Japanese Patent Office, 1989.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
Maekawa, Y., Kawakami, F., Yasukawa, H., Japanese Patent Office, 1991.
Maekawa, Y., Yasukawa, H., Kawakami, B., (1990) J. Biochem. (Tokyo), vol. 107, pp. 645-649.
Schildkraut, I., Lynch, J., Morgan, R., (1987) Nucleic Acids Res., vol. 15, pp. 5492.
Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Nucleic Acids Res., vol. 10, pp. 5747-5752.

<1>BanII
<2>HgiJII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCY^C
<4>4(5)
<5>Bacillus aneurinolyticus
<6>IAM 1077
<7>KNOQRWX
<8>Forrow, S., Lee, M., Souhami, R.L., Hartley, J.A., (1994) ACS Abstracts, vol. 208, pp. 97.
Kilz, S., Kroeger, M., Lunnen, K.D., Wilson, G.G., Unpublished observations.
Lunnen, K.D., Barsomian, J.M., Camp, R.R., Card, C.O., Chen, S.-Z., Croft, R., Looney, M.C., Meda, M.M., Moran, L.S., Nwankwo, D.O., Slatko, B.E., Van Cott, E.M., Wilson, G.G., (1988) Gene, vol. 74, pp. 25-32.
Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Nucleic Acids Res., vol. 10, pp. 5747-5752.
Wilson, G.G., Unpublished observations.

<1>BanIII
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus aneurinolyticus
<6>IAM 1077
<7>O
<8>Kawakami, B., Sasaki, A., Oka, M., Maekawa, Y., (1990) Agric. Biol. Chem., vol. 54, pp. 3227-3233.
Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., Unpublished observations.
Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Nucleic Acids Res., vol. 10, pp. 5747-5752.

<1>BanAI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Bacillus anthracis
<6>J.M. Chies
<7>
<8>Chies, J.M., de O-Dias, A.C., Maia, H.M.M., Astolfi-Filho, S., Unpublished observations.

<1>BarI
<2>
<3>(7/12)GAAGNNNNNNTAC(12/7)
<4>
<5>Bacillus sphaericus
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Abdurashitov, M.A., Kileva, E.V., Tomilova, J.E., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>BasI
<2>PflMI,AccB7I,AcpII,Asp10HII,Esp1396I,PflBI,Van91I
<3>CCANNNN^NTGG
<4>
<5>Bacillus species
<6>V. Nagaraja
<7>U
<8>Chandrashekaran, S., Babu, P., Nagaraja, V., (1999) J. Biochem. Mol. Biol. Biophys., vol. 3, pp. 225-229.

<1>BauI
<2>BsiI,BssSI,Bst2BI
<3>CACGAG(-5/-1)
<4>
<5>Bacillus aquaemaris RFL1
<6>Fermentas G268
<7>F
<8>Maneliene, Z., Zakareviciene, L., Unpublished observations.
Vitkute, J., Nekrasiene, D., Lapcinskaja, L., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BavI
<2>PvuII,BamGI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>
<5>Bacillus alvei
<6>ATCC 6348
<7>
<8>McEvoy, S., Roberts, R.J., Unpublished observations.

<1>BavAI
<2>PvuII,BamGI,BavI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>
<5>Bacillus alvei A
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Fitzner, A.B., Eldarov, M.A., Anikeicheva, N.B., Kalugin, A.A., Samko, O.T., Khoroshoutina, E.B., Fodor, I., (1992) Nucleic Acids Res., vol. 20, pp. 2897.

<1>BavAII
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Bacillus alvei A
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Fitsner, A.B., Anikeitcheva, N.V., Kalugin, A.A., Choroshoutina, E.B., Plutalov, O.V., Berlin, Y.A., Unpublished observations.

<1>BavBI
<2>PvuII,BamGI,BavI,BavAI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>
<5>Bacillus alvei B
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Fitsner, A.B., Anikeitcheva, N.V., Samko, O.T., Kalugin, A.A., Unpublished observations.

<1>BavBII
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Bacillus alvei B
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Anikeitcheva, N.V., Fitsner, A.B., Samko, O.T., Choroshoutina, E.B., Kalugin, A.A., Lidrik, G.I., Soviet Patent Office, 1992.

<1>BavCI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus alvei C
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., (1995) Vestn. Akad. Med. Nauk SSSR, vol. 2, pp. 47-51.
Sokolov, N.N., Fitsner, A.B., Anikeitcheva, N.V., Kalugin, A.A., Unpublished observations.

<1>BazI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus azotoformans
<6>ATCC 29788
<7>
<8>Waaijer, R.J.A., Unpublished observations.

<1>BbaI
<2>
<3>?
<4>
<5>Bacillus badius 1458
<6>MTCC 1458
<7>
<8>Jutur, P.P., Reddy, A.R., (2007) Microbiol. Res., vol. 162, pp. 378-383.

<1>Bba179I
<2>BetI,Bca77I,BsaWI,Bst1473I,UbaN10I
<3>WCCGGW
<4>
<5>Bacillus badius BKPM B-6616
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Repin, V.E., Rechkunova, N.I., Shevchenko, A.V., Abdurashitov, M.A., Russian Patent Office, 1996.

<1>BbeI
<2>NarI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GGCGC^C
<4>
<5>Bifidobacterium breve YIT4006
<6>H. Takahashi
<7>K
<8>Khosaka, T., Sakurai, T., Takahashi, H., Saito, H., (1982) Gene, vol. 17, pp. 117-122.

<1>BbeII
<2>
<3>?
<4>
<5>Bifidobacterium breve YIT4006
<6>H. Takahashi
<7>
<8>Sakurai, T., Kosaka, T., Japanese Patent Office, 1983.
Sakurai, T., Kosaka, T., US Patent Office, 1983.

<1>BbeAI
<2>NarI,BbeI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GGCGCC
<4>
<5>Bifidobacterium breve S50
<6>ATCC 15698
<7>
<8>Khosaka, T., Unpublished observations.

<1>BbeAII
<2>
<3>?
<4>
<5>Bifidobacterium breve S50
<6>ATCC 15698
<7>
<8>Khosaka, T., Unpublished observations.

<1>BbeSI
<2>
<3>?
<4>
<5>Bifidobacterium breve S1
<6>ATCC 15700
<7>
<8>Sakurai, T., Kosaka, T., Japanese Patent Office, 1983.
Sakurai, T., Kosaka, T., US Patent Office, 1983.

<1>BbfI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Bifidobacterium bifidum LVA3
<6>G.N. Gabrichevsky
<7>
<8>Skrypina, N.A., Kramarov, V.M., Lyannaya, A.M., Smolyaninov, V.V., Goncharova, G.I., (1988) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 15-16.

<1>Bbf7411I
<2>BspMII,AccIII,Aor13HI,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Bifidobacterium bifidum 7411
<6>G.N. Gabrichevsky
<7>
<8>Skrypina, N.A., Kramarov, V.M., Lyannaya, A.M., Smolyaninov, V.V., Goncharova, G.I., (1988) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 15-16.

<1>BbiI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bifidobacterium bifidum YIT4007
<6>T. Khosaka
<7>
<8>Khosaka, T., Kiwaki, M., (1984) FEBS Lett., vol. 177, pp. 57-60.

<1>BbiII
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>
<5>Bifidobacterium bifidum YIT4007
<6>T. Khosaka
<7>
<8>Khosaka, T., Kiwaki, M., (1984) FEBS Lett., vol. 177, pp. 57-60.

<1>BbiIII
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Bifidobacterium bifidum YIT4007
<6>T. Khosaka
<7>
<8>Khosaka, T., Kiwaki, M., (1984) FEBS Lett., vol. 177, pp. 57-60.

<1>BbiIV
<2>
<3>?
<4>
<5>Bifidobacterium bifidum YIT4007
<6>T. Khosaka
<7>
<8>Khosaka, T., Unpublished observations.

<1>Bbi24I
<2>MluI,ApeI,BstZ9I,Uba6I
<3>A^CGCGT
<4>
<5>Bifidobacterium bifidum S-24
<6>T. Kanematsu
<7>
<8>Kanematsu, T., Ozawa, O., Murakami, M., Japanese Patent Office, 1991.

<1>BboI
<2>
<3>?
<4>
<5>Brevibacillus borstelensis
<6>NEB 1047
<7>
<8>Ge, L., Unpublished observations.

<1>BbrI
<2>HindIII,Asp52I,Asp3065I,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>A^AGCTT
<4>
<5>Bordetella bronchiseptica 4994
<6>T.I. Tikchonenko
<7>
<8>Kalinin, V.N., Lapaeva, I.A., Lunin, V.G., Skripkin, E.A., Smirnov, V.D., Tikchonenko, T.I., (1986) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 16-19.

<1>Bbr7I
<2>BbvII,BbsI,Bbv16II,Bco102II,BpiI,BpuAI,BsaVI,Bsc91I,BscKI,BspBS31I,BspIS4I,BspTS514I,BspVI,BstBS32I,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC(7/11)
<4>
<5>Bacillus brevis 7
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>BbrAI
<2>HindIII,Asp52I,Asp3065I,BbrI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Bordetella bronchiseptica
<6>ATCC 19395
<7>
<8>Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BbrPI
<2>PmaCI,AcvI,BcoAI,Bsp87I,Eco72I,Pgl34I,PmlI,PshCI,PshDI,Psp38I,PspBI,PspCI,VpaK3AI,VpaK3BI
<3>CAC^GTG
<4>
<5>Bacillus brevis
<6>U. Mayr
<7>MO
<8>Vesely, Z., Schmitz, G.G., Jarsch, M., Kessler, C., (1990) Nucleic Acids Res., vol. 18, pp. 3423.

<1>BbsI
<2>BbvII,Bbr7I,Bbv16II,Bco102II,BpiI,BpuAI,BsaVI,Bsc91I,BscKI,BspBS31I,BspIS4I,BspTS514I,BspVI,BstBS32I,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC(2/6)
<4>
<5>Bacillus brevis
<6>NEB 573
<7>N
<8>Story, C.M., Morgan, R., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BbtI
<2>HhaI,AspLEI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>G^CGC
<4>
<5>Bacillus bataviensis
<6>Vivantis 384
<7>
<8>Chee, H.Y., Unpublished observations.

<1>BbuI
<2>SphI,Asp5HI,BscOI,Bsp121I,BtgAII,CglAI,PaeI,PaeCI,PfaAIII,RspLKI,SpaHI,SpaXI,Uba1162I,Uba1226I,VchO68I
<3>GCATG^C
<4>
<5>Bacillus circulans
<6>J. Davies
<7>R
<8>Aubert, E., Spurgeon, S., Ray, W., Davies, J., (1990) Nucleic Acids Res., vol. 18, pp. 6152.

<1>M.Bbu297I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>?(5)
<5>Borrelia burgdorferi 297
<6>R.C. Johnson
<7>
<8>Norton Hughes, C.A., Johnson, R.C., (1994) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 94, pp. 125.

<1>BbvI
<2>AlwXI,BchI,BsaUI,BseKI,BseXI,Bsp423I,BsrVI,Bst12I,Bst71I,BstV1I,LfeI,Lsp1109I
<3>GCAGC(8/12)
<4>2(5),-2(5)
<5>Bacillus brevis
<6>ATCC 9999
<7>N
<8>Gingeras, T.R., Milazzo, J.P., Roberts, R.J., (1978) Nucleic Acids Res., vol. 5, pp. 4105-4127.
Hattman, S., Keister, T., Gottehrer, A., (1978) J. Mol. Biol., vol. 124, pp. 701-711.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Schildkraut, I., Unpublished observations.

<1>BbvII
<2>Bbr7I,BbsI,Bbv16II,Bco102II,BpiI,BpuAI,BsaVI,Bsc91I,BscKI,BspBS31I,BspIS4I,BspTS514I,BspVI,BstBS32I,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC(2/6)
<4>
<5>Bacillus brevis 80
<6>V.M. Kramarov
<7>
<8>Bunina, Z.F., Kramarov, V.M., Mazanov, A.L., Pachkunov, D.M., Smolianinov, V.V., Matvienko, N.N., (1983) Bioorg. Khim., vol. 9, pp. 1578-1580.
Matvienko, N.I., Pachkunov, D.M., Kramarov, V.M., (1984) FEBS Lett., vol. 177, pp. 23-26.

<1>Bbv12I
<2>HgiAI,Alw21I,AspHI,Bfu1570I,BsaGI,Bsh45I,BsiHKAI,Bsm6I,BsmPI,Hpy8III,HpyF7II,HpyF46II,MspV281I,Pph3215I
<3>GWGCW^C
<4>
<5>Bacillus brevis 12
<6>S.K. Degtyarev
<7>IV
<8>Repin, V.E., Rechkunova, N.I., Degtyarev, S.K., Hachaturyan, A.A., Afrikyan, E.K., (1989) Biol. J. Armenia, vol. 42, pp. 969-972.

<1>Bbv16II
<2>BbvII,Bbr7I,BbsI,Bco102II,BpiI,BpuAI,BsaVI,Bsc91I,BscKI,BspBS31I,BspIS4I,BspTS514I,BspVI,BstBS32I,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC(2/6)
<4>
<5>Bacillus brevis 16
<6>S.K. Degtyarev
<7>
<8>Repin, V.E., Shilyayeva, O.H., (1989) Microbiological investigations in Western Siberia, ed. Klevenskaya, I.L. (Nauka Siberian Division, Novosibirsk), vol. 0, pp. 14-17.

<1>BbvAI
<2>XmnI,Asp700I,MroXI,PdmI,Psc2I,SynII
<3>GAANN^NNTTC
<4>
<5>Bacillus brevis A
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Butkus, V., Vaitkevicius, D., Anikeitcheva, N.V., Fitsner, A.B., Kalugin, A.A., Janulaitis, A., Unpublished observations.
Sokolov, N.N., Samko, O.T., Anikeitcheva, N.V., Kalugin, A.A., Khoroshutina, E.B., Plutalov, O.V., Birikh, K.R., Berlin, Y.A., (1994) Bioorg. Khim., vol. 20, pp. 1334-1341.

<1>BbvAII
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus brevis A
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Anikeitcheva, N.V., Samko, O.T., Choroshoutina, E.B., Kalugin, A.A., Fitsner, A.B., Unpublished observations.
Sokolov, N.N., Samko, O.T., Anikeitcheva, N.V., Kalugin, A.A., Khoroshutina, E.B., Plutalov, O.V., Birikh, K.R., Berlin, Y.A., (1994) Bioorg. Khim., vol. 20, pp. 1334-1341.

<1>BbvAIII
<2>BspMII,AccIII,Aor13HI,Bbf7411I,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>
<5>Bacillus brevis A
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Samko, O.T., Anikeitcheva, N.V., Kalugin, A.A., Khoroshutina, E.B., Plutalov, O.V., Birikh, K.R., Berlin, Y.A., (1994) Bioorg. Khim., vol. 20, pp. 1334-1341.

<1>BbvBI
<2>HgiCI,AccB1I,BanI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>G^GYRCC
<4>
<5>Bacillus brevis B
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Eldarov, M.A., Anikeitcheva, N.V., Karpychev, I.V., Samko, O.T., Fitzner, A.B., Kalugin, A.A., Choroshoutina, E.B., Skryabin, K.G., (1992) Bioorg. Khim., vol. 18, pp. 47-51.

<1>BbvCI
<2>AbeI,PmdI
<3>CCTCAGC(-5/-2)
<4>?(5)
<5>Bacillus brevis
<6>NEB 1030
<7>N
<8>Ge, L., Unpublished observations.
Heiter, D.F., Lunnen, K.D., Wilson, G.G., (2005) J. Mol. Biol., vol. 348, pp. 631-640.
Krotee, S., Ganatra, M., Grandoni, R., Unpublished observations.
Lunnen, K.D., Heiter, D., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>M.BbvSI
<2>TseI,AceI,ApeKI,SuiI,Taq52I,TneI,TseBI
<3>GCWGC
<4>2(5)
<5>Bacillus brevis S
<6>A.P. Zarubina
<7>
<8>Vanyushin, B.F., Dobritsa, A.P., (1975) Biochim. Biophys. Acta, vol. 407, pp. 61-72.

<1>BcaI
<2>HhaI,AspLEI,BbtI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCGC
<4>
<5>Branhamella catarrhalis
<6>ATCC 25240
<7>
<8>Hall, D., Unpublished observations.

<1>Bca77I
<2>BetI,Bba179I,BsaWI,Bst1473I,UbaN10I
<3>W^CCGGW
<4>
<5>Bacillus caldolyticus
<6>Promega 77
<7>
<8>Schoenfeld, T., King, K.B., Schink, M., (1992) Gene, vol. 117, pp. 99-101.

<1>Bca1259I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus caldotenax 1259
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>BccI
<2>HpyC1I
<3>CCATC(4/5)
<4>
<5>Bacteroides caccae
<6>NEB 669
<7>N
<8>Morgan, R., Reinecke, S., Unpublished observations.
Morgan, R.D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>Bce4I
<2>MwoI,Bce1247I,BceCI,BspWI,BstMWI,HpyF10VI
<3>GCNNNNN^NNGC
<4>
<5>Bacillus cereus B4
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Kashirina, J.G., Tomilova, J.E., Degtyarev, S.K., Unpublished observations.

<1>Bce22I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Bacillus cereus 22
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>Bce71I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus cereus 71
<6>S.Y. Ye
<7>
<8>Yan, P.-F., Ye, S.-Y., Wang, P.-Z., Li, Q.-L., Lu, Y.-Y., Zhou, B., (1982) Acta Biochim. Biophys. Sin., vol. 14, pp. 151-158.

<1>Bce83I
<2>BpuEI
<3>CTTGAG(16/14)
<4>
<5>Bacillus cereus 83
<6>N.I. Matvienko
<7>
<8>Matvienko, N.N., Kramarov, V.M., Ivanov, L.Y., Matvienko, N.I., (1992) Nucleic Acids Res., vol. 20, pp. 1803.
Matvienko, N.N., Kramarov, V.M., Zheleznaya, L.A., Matvienko, N.I., (1993) Biokhimiia, vol. 58, pp. 1845-1860.

<1>Bce170I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus cereus
<6>T. Ando
<7>
<8>Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>Bce243I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus cereus
<6>IOC 243
<7>
<8>Cruz, A.K., Kidane, G., Pires, M.Q., Rabinovitch, L., Guaycurus, T.V., Morel, C.M., (1984) FEBS Lett., vol. 173, pp. 99-102.

<1>Bce751I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Bacillus cereus 751
<6>N.I. Matvienko
<7>
<8>Kramarov, V.M., Skrypina, N.A., Smolyaninov, V.V., Smirnov, V.V., Resnik, S.R., Sorokulova, I.B., Matvienko, N.I., (1989) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 42-45.

<1>Bce1229I
<2>
<3>?
<4>
<5>Bacillus cereus
<6>IAM 1229
<7>
<8>Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>Bce1247I
<2>MwoI,Bce4I,BceCI,BspWI,BstMWI,HpyF10VI
<3>GCNNNNNNNGC
<4>
<5>Bacillus cereus RFL1247
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.
Slesaraviciute, Z., Vaisvila, R., Janulaitis, A., Unpublished observations.

<1>Bce14579I
<2>
<3>?
<4>
<5>Bacillus cereus
<6>ATCC 14579
<7>
<8>Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>Bce31293I
<2>FnuDII,AccII,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Bacillus cereus
<6>ATCC 31293
<7>
<8>Parker, P., Schildkraut, I., Unpublished observations.

<1>BceAI
<2>BcefI,BceSIII,BctI
<3>ACGGC(12/14)
<4>?(4)
<5>Bacillus cereus 1315
<6>NEB 1288
<7>N
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Nkenfou, C., Unpublished observations.
Nkenfou, C., (2002) Ph.D. Thesis, University of Yaounde I, Cameroon (Yaounde), pp. 1-226.
Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>BceBI
<2>FnuDII,AccII,Bce31293I,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>
<5>Bacillus cereus 1323
<6>NEB 1289
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>BceCI
<2>MwoI,Bce4I,Bce1247I,BspWI,BstMWI,HpyF10VI
<3>GCNNNNN^NNGC
<4>
<5>Bacillus cereus 1195
<6>NEB 1290
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>BceDI
<2>BclI,AbaI,AtuSI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Bacillus cereus 2323
<6>NEB 1401
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>BceRI
<2>FnuDII,AccII,Bce31293I,BceBI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Bacillus cereus Rf sm st
<6>T. Ando
<7>
<8>Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>BceSI
<2>
<3>SSAAGCG(27/27)
<4>
<5>Bacillus cereus
<6>ATCC 10987
<7>
<8>Hegna, I.K., Bratland, H., Kolsto, A., (2001) FEMS Microbiol. Lett., vol. 202, pp. 189-193.
Xu, S.-Y., Unpublished observations.

<1>BceSII
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>?(5)
<5>Bacillus cereus
<6>ATCC 10987
<7>
<8>Rasko, D.A., Ravel, J., Okstad, O.A., Helgason, E., Cer, R.Z., Jiang, L., Shores, K.A., Fouts, D.E., Tourasse, N.J., Angiuoli, S.V., Kolonay, J., Nelson, W.C., Kolsto, A.-B., Fraser, C.M., Read, T.D., (2004) Nucleic Acids Res., vol. 32, pp. 977-988.
Zheng, Y., Roberts, R.J., Unpublished observations.

<1>BceSIII
<2>BcefI,BceAI,BctI
<3>ACGGC(12/14)
<4>
<5>Bacillus cereus
<6>ATCC 10987
<7>
<8>Fomenkov, A., Xu, S.-Y., Unpublished observations.
Rasko, D.A., Ravel, J., Okstad, O.A., Helgason, E., Cer, R.Z., Jiang, L., Shores, K.A., Fouts, D.E., Tourasse, N.J., Angiuoli, S.V., Kolonay, J., Nelson, W.C., Kolsto, A.-B., Fraser, C.M., Read, T.D., (2004) Nucleic Acids Res., vol. 32, pp. 977-988.

<1>BcefI
<2>BceAI,BceSIII,BctI
<3>ACGGC(12/13)
<4>
<5>Bacillus cereus sub. fluorescens
<6>P. Venetianer
<7>
<8>Venetianer, P., Orosz, A., (1988) Nucleic Acids Res., vol. 16, pp. 3053-3060.

<1>BcgI
<2>
<3>(10/12)CGANNNNNNTGC(12/10)
<4>3(6),-3(6)
<5>Bacillus coagulans
<6>NEB 566
<7>N
<8>Kong, H., Unpublished observations.
Kong, H., Morgan, R.D., Maunus, R.E., Schildkraut, I., (1993) Nucleic Acids Res., vol. 21, pp. 987-991.
Kong, H., Roemer, S.E., Waite-Rees, P.A., Benner, J.S., Wilson, G.G., Nwankwo, D.O., (1994) J. Biol. Chem., vol. 269, pp. 683-690.
Kong, H., Schildkraut, I., European Patent Office, 1994.

<1>BchI
<2>BbvI,AlwXI,BsaUI,BseKI,BseXI,Bsp423I,BsrVI,Bst12I,Bst71I,BstV1I,LfeI,Lsp1109I
<3>GCAGC
<4>?(5)
<5>Bacillus chitinosporus
<6>NEB 955
<7>
<8>Morgan, R.D., Unpublished observations.

<1>Bci29I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus circulans 29
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bci528I
<2>
<3>?
<4>
<5>Bacillus circulans strain 528
<6>R.S. Ra
<7>
<8>Kim, U.Y., Jon, S.C., Ra, S.R., (2008) Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo, vol. 97, pp. 42-43.

<1>BciAI
<2>
<3>?
<4>
<5>Bacillus circulans A
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Eldarov, M.A., Anikeitcheva, N.V., Karpichev, I.V., Samko, O.T., Fitsner, A.B., Kalugin, A.A., Unpublished observations.

<1>BciBI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus circulans B
<6>N.N. Sokolov
<7>
<8>Samko, O.T., Kalugin, A.A., Eldarov, M.A., Karpychev, I.V., Anikeitcheva, N.V., Khoroshutina, E.B., Skryabin, K.G., Librik, G.I., Sokolov, N.N., (1994) Bioorg. Khim., vol. 20, pp. 1327-1333.

<1>BciBII
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus circulans B
<6>N.N. Sokolov
<7>
<8>Eldarov, M.A., Karpichev, I.V., Samko, O.T., Anikeitcheva, N.V., Kalugin, A.A., Khoroshoutina, E.B., Sokolov, N.N., (1992) Nucleic Acids Res., vol. 20, pp. 2896.

<1>BciVI
<2>BfuI
<3>GTATCC(6/5)
<4>
<5>Bacillus circulans
<6>NEB 1000
<7>N
<8>Le, T.K.T., Vu, T.K.L., Vu, H.N., Polisson, C., Morgan, R., Unpublished observations.
Wei, H., Unpublished observations.

<1>BclI
<2>AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>T^GATCA
<4>3(6)
<5>Bacillus caldolyticus
<6>A. Atkinson
<7>CFJMNORSUWY
<8>Bingham, A.H.A., Atkinson, T., Sciaky, D., Roberts, R.J., (1978) Nucleic Acids Res., vol. 5, pp. 3457-3467.
Mersha, F., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Strimpel, D., Stickel, S., Roberts, R.J., Unpublished observations.

<1>BcmI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus species
<6>N.V. Tsvetkova
<7>
<8>Tsvetkova, N.V., Mileikovskaya, M.M., Gruber, I.M., Polyachenko, V.M., Butkus, V.V., Janulaitis, A., Sudzhyuvene, O.F., Tarasov, A.P., (1987) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 19-22.

<1>BcnI
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CC^SGG
<4>2(4)
<5>Bacillus centrosporus RFL1
<6>A. Janulaitis
<7>FK
<8>Janulaitis, A., Klimasauskas, S., Petrusyte, M., Butkus, V., (1983) FEBS Lett., vol. 161, pp. 131-134.
Janulaitis, A., Petrusyte, M.A., Jaskeleviciene, B.P., Krayev, A.S., Skryabin, K.G., Bayev, A.A., (1982) FEBS Lett., vol. 137, pp. 178-180.
Janulaitis, A., Petrusyte, M.P., Jaskeleviciene, B.P., Krayev, A.S., Skryabin, K.G., Bayev, A.A., (1981) Dokl. Akad. Nauk., vol. 257, pp. 749-750.
Klimasauskas, S., Butkus, V., Janulaitis, A., (1987) Mol. Biol. (Mosk), vol. 21, pp. 87-92.
Petrusyte, M.P., Janulaitis, A., (1981) Bioorg. Khim., vol. 7, pp. 1885-1887.

<1>BcoI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>
<5>Bacillus coagulans SM 1
<6>P.C. Shaw
<7>
<8>Leung, S.M., Kam, K.M., Chan, K.Y., Shaw, P.C., (1990) FEMS Microbiol. Lett., vol. 66, pp. 153-156.

<1>Bco5I
<2>Ksp632I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC(1/4)
<4>
<5>Bacillus coagulans 5
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bco6I
<2>MstI,AcaIII,Acc16I,AosI,ApcTR183I,AviII,BsaTI,ClcII,CliII,FdiII,FspI,GspAII,NsbI,NspHIII,NspLI,NspMI,PamI,Pun14627I
<3>TGCGCA
<4>
<5>Bacillus coagulans 6
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bco27I
<2>HpaII,Asp748I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>C^CGG
<4>
<5>Bacillus coagulans 27
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bco33I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus coagulans RFL33
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bco35I
<2>GsuI,BpmI,Bsp22I,Bsp28I,BspJ74I,Bth1795I,Uba1437I,Uba1444I
<3>CTGGAG
<4>
<5>Bacillus coagulans RFL35
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Bco63I
<2>BsaBI,Bco631I,Bse8I,Bse631I,BseJI,Bsh1365I,BsiBI,BsrBRI,MamI,UbaN6I
<3>GATNNNNATC
<4>
<5>Bacillus coagulans 63
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Puchkova, L., Serov, G.D., Tereschenko, T., Chizikov, V.E., Andreeva, I., (1995) Gene, vol. 157, pp. 321-322.
Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bco79I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus coagulans 79
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Bco102I
<2>BclI,AbaI,AtuSI,BceDI,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Bacillus coagulans 102
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bco102II
<2>BbvII,Bbr7I,BbsI,Bbv16II,BpiI,BpuAI,BsaVI,Bsc91I,BscKI,BspBS31I,BspIS4I,BspTS514I,BspVI,BstBS32I,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC
<4>
<5>Bacillus coagulans 102
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bco116I
<2>Ksp632I,Bco5I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC(1/4)
<4>
<5>Bacillus coagulans 116
<6>V.E. Repin
<7>
<8>Repin, V.E., Chizhikov, V.E., Tereshchenko, T.A., Lebedev, L.R., (1993) Bioorg. Khim., vol. 4, pp. 410-413.
Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bco118I
<2>Cfr10I,BscRI,Bse118I,Bse634I,Bsp21I,BsrFI,BssAI,BstB7SI,NmeDI,TseDI
<3>R^CCGGY
<4>
<5>Bacillus coagulans 118
<6>V.E. Repin
<7>
<8>Repin, V.E., Unpublished observations.

<1>Bco163I
<2>SfeI,BdiSI,BfmI,BpcI,BstSFI,BthP35I,HpyF2I,LlaBI,SfcI,Srl56DI
<3>CTRYAG
<4>
<5>Bacillus coagulans 163
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bco631I
<2>BsaBI,Bco63I,Bse8I,Bse631I,BseJI,Bsh1365I,BsiBI,BsrBRI,MamI,UbaN6I
<3>GATNNNNATC
<4>
<5>Bacillus coagulans 631
<6>V.E. Repin
<7>
<8>Repin, V.E., Tereshchenko, T.A., Lebedev, L.R., Russian Patent Office, 1996.

<1>Bco10278I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus coagulans
<6>NCIB 10278
<7>
<8>Leung, S.M., Chan, K.Y., Suen, Y.K., Shaw, P.C., (1989) Nucleic Acids Res., vol. 17, pp. 10133.

<1>BcoAI
<2>PmaCI,AcvI,BbrPI,Bsp87I,Eco72I,Pgl34I,PmlI,PshCI,PshDI,Psp38I,PspBI,PspCI,VpaK3AI,VpaK3BI
<3>CAC^GTG
<4>
<5>Bacillus coagulans AUCM B-732
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Eldarov, M.A., Anikeitcheva, N.V., Karpychev, I.V., Samko, O.T., Fitzner, A.B., Kalugin, A.A., Choroshoutina, E.B., Skryabin, K.G., (1991) Bioorg. Khim., vol. 17, pp. 1188-1192.

<1>BcoDI
<2>BsmAI,Alw26I,BscQII,BsoMAI,BstMAI
<3>GTCTC(1/5)
<4>
<5>Bacteroides coprocola DSM 17136
<6>DSM 17136
<7>
<8>Chan, S.H., Xu, S.Y., Unpublished observations.
Fulton, L., Clifton, S., Fulton, B., Xu, J., Minx, P., Mardis, E.R., Wilson, R.K., Unpublished observations.
Fulton, L., Clifton, S., Fulton, B., Xu, J., Minx, P., Pepin, K.H., Johnson, M., Thiruvilangam, P., Bhonagiri, V., Nash, W.E., Mardis, E.R., Wilson, R.K., Unpublished observations.

<1>BcoKI
<2>Ksp632I,Bco5I,Bco116I,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC(1/4)
<4>1(4)
<5>Bacillus coagulans
<6>N.I. Matvienko
<7>
<8>Kovalevskaya, N.P., Zhelenznaya, L.A., Zelinskaya, N.V., Matvienko, N.I., (1994) Mikrobiologiia, vol. 63, pp. 235-238.
Svadbina, I.V., Matvienko, N.N., Zheleznaya, L.A., Matvienko, N.I., (2005) Biochemistry, vol. 70, pp. 1363-1366.
Svadbina, I.V., Zelinskaya, N.V., Kovalevskaya, N.P., Zheleznaya, L.A., Matvienko, N.I., (2004) Biokhimiia, vol. 69, pp. 372-379.

<1>BcoSI
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC
<4>
<5>Bacillus coagulans S
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>BcrI
<2>NlaIV,AspNI,BmiI,BsaEI,BscBI,Bsp29I,BspLI,BssI,HpyF44II,HpyF73I,NgoBV,NgoGV,PspN4I,Rlu3I,Uba1305I,Uba1445I
<3>GGNNCC
<4>
<5>Bacillus cereus
<6>NEB 442
<7>
<8>Polisson, C., McMahon, M., Unpublished observations.

<1>BcrAI
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC
<4>
<5>Bacillus cremoris
<6>A. Piekarowicz
<7>
<8>Piekarowicz, A., Skowronek, K., (1995) Acta Microbiol. Pol., vol. 44, pp. 315-316.

<1>BctI
<2>BcefI,BceAI,BceSIII
<3>ACGGC
<4>
<5>Bacillus cereus
<6>FZ 852
<7>
<8>Torsti, A.-M., Unpublished observations.

<1>BcuI
<2>SpeI,AclNI,AhlI
<3>A^CTAGT
<4>
<5>Bacillus coagulans Vs 29-022
<6>A. Janulaitis
<7>F
<8>Maneliene, Z., Butkus, V., Unpublished observations.
Vitkute, J., Zutautiene, D., Valickiene, D., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BcuAI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Bacillus cereus BKM B-814
<6>N.N. Sokolov
<7>
<8>Eldarov, M.A., Karpichev, I.V., Samko, O.T., Anikeitcheva, N.V., Kalugin, A.A., Khoroshoutina, E.B., Sokolov, N.N., (1992) Nucleic Acids Res., vol. 20, pp. 2898.
Korolev, S.V., Samko, O.T., Eldarov, M.A., Kalugin, A.A., Khoroshutina, E.B., Omelyanyuk, N.M., Sokolov, N.N., Skryabin, K.G., (1996) Bioorg. Khim., vol. 22, pp. 528-531.

<1>BdaI
<2>
<3>(10/12)TGANNNNNNTCA(12/10)
<4>
<5>Brevundimonas diminuta RFL2
<6>A. Janulaitis
<7>F
<8>Maneliene, Z., Zakareviciene, L., Lubys, A., Unpublished observations.
Nekrasiene, D., Vitkute, J., Lapcinskaja, S., Capskaja, L., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BdiI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Brevibacterium divaricatum
<6>H.M. Rho
<7>
<8>Jun, H.S., Kim, Y.S., Choi, K.R., Rho, H.M., (1987) Korean J. Microbiol., vol. 25, pp. 40-45.
Kanematsu, T., Ozawa, O., Japanese Patent Office, 1990.
Kim, Y.S., Rho, H.M., (1986) Korean J. Microbiol., vol. 24, pp. 18-23.

<1>BdiSI
<2>SfeI,Bco163I,BfmI,BpcI,BstSFI,BthP35I,HpyF2I,LlaBI,SfcI,Srl56DI
<3>C^TRYAG
<4>
<5>Bacteroides distasonis
<6>T. Kanematsu
<7>
<8>Murakami, M., Ozawa, O., Kanematsu, T., Yamada, Y., (1990) Agric. Biol. Chem., vol. 54, pp. 275-277.

<1>BecAI
<2>
<3>?
<4>
<5>Brevibacterium species A
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Korolev, S.V., Rina, M., Eldarov, M.A., Gervaziev, Y.V., Skryabin, K.G., Bouriotis, V., (1998) Mol. Gen. Mikrobiol. Virusol., vol. 9, pp. 35-38.

<1>BecAII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Brevibacterium species A
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Korolev, S.V., Rina, M., Eldarov, M.A., Gervaziev, Y.V., Skryabin, K.G., Bouriotis, V., (1998) Mol. Gen. Mikrobiol. Virusol., vol. 9, pp. 35-38.

<1>BepI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>1(5)
<5>Brevibacterium epidermidis
<6>P. Venetianer
<7>
<8>Kupper, D., Zhou, J.-G., Kiss, A., Venetianer, P., (1988) Gene, vol. 74, pp. 33.
Kupper, D., Zhou, J.-G., Venetianer, P., Kiss, A., (1989) Nucleic Acids Res., vol. 17, pp. 1077-1088.
Venetianer, P., Komocsin, M., Orosz, A., Hungarian Patent Office, 1990.
Venetianer, P., Orosz, A., (1988) Nucleic Acids Res., vol. 16, pp. 350.

<1>BetI
<2>Bba179I,Bca77I,BsaWI,Bst1473I,UbaN10I
<3>W^CCGGW
<4>
<5>Brevibacterium acetyliticum
<6>NEB 678
<7>
<8>Zhou, B., Morgan, R., Unpublished observations.

<1>BfaI
<2>MaeI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>C^TAG
<4>
<5>Bacteroides fragilis
<6>NEB 1140
<7>N
<8>Lunnen, K.D., Wilson, G.G., Unpublished observations.
McLeod, B., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Reinecke, S.N., Morgan, R.D., (1991) Nucleic Acids Res., vol. 19, pp. 1152.

<1>BfiI
<2>BmrI,BmuI,BsxI
<3>ACTGGG(5/4)
<4>-2(4)
<5>Bacillus firmus S8120
<6>A. Janulaitis
<7>F
<8>Maneliene, Z., Butkus, V., Unpublished observations.
Sapranauskas, R., Sasnauskas, G., Lagunavicius, A., Vilkaitis, G., Lubys, A., Siksnys, V., (2000) J. Biol. Chem., vol. 275, pp. 30878-30885.

<1>Bfi57I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Butyrivibrio fibrisolvens OB157
<6>R.M. Teather
<7>
<8>Mohn, W.W., Teather, R.M., (1995) Gene, vol. 155, pp. 131-132.

<1>Bfi89I
<2>CfrI,AcoI,Ava458I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>Y^GGCCR
<4>
<5>Butyrivibrio fibrisolvens OB189
<6>R.M. Teather
<7>
<8>Mohn, W.W., Teather, R.M., (1995) Gene, vol. 155, pp. 131-132.

<1>Bfi105I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Bacillus firmus 105
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Bfi458I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus firmus 458
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>Bfi2411I
<2>
<3>?
<4>
<5>Bacillus firmus 2411
<6>A.R. Reddy
<7>
<8>Jutur, P.P., Hoti, S.L., Reddy, A.R., (2004) Mol. Biol. Rep., vol. 31, pp. 139-142.

<1>BfiSHI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Butyrivibrio fibrisolvens SH-1
<6>P. Pristas
<7>
<8>Piknova, M., Pristas, P., Javorsky, P., (2004) Folia Microbiol. (Praha), vol. 49, pp. 191-193.

<1>BflI
<2>BsiYI,AfiI,Bsc4I,Bsc107I,Bse23I,BseLI,BslI,BsmYI,Bst22I
<3>CCNNNNN^NNGG
<4>
<5>Bacillus flavothermus
<6>P. Sharma
<7>
<8>D'Souza, D.R., Morgan, R.D., Parashar, V., Capalash, N., Sharma, P., (2004) World J. Microbiol. Biotechnol., vol. 20, pp. 593-598.

<1>BfmI
<2>SfeI,Bco163I,BdiSI,BpcI,BstSFI,BthP35I,HpyF2I,LlaBI,SfcI,Srl56DI
<3>C^TRYAG
<4>
<5>Bacillus firmus S8-336
<6>V. Butkus
<7>F
<8>Maneliene, Z., Butkus, V., Unpublished observations.
Vitkute, J., Capskaja, L., Markauskiene, J., Kiuduliene, L., Butkus, V., Janulaitis, J., Unpublished observations.

<1>BfoI
<2>HaeII,AccB2I,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGC^Y
<4>
<5>Bacillus fusiformis RFL1
<6>Fermentas G345
<7>F
<8>Vitkute, J., Lauciuniene, N., Lapcinskaja, S., Trinkunaite, L., Zakareviciene, L., Lubys, A., Janulaitis, A., Unpublished observations.

<1>BfrI
<2>AflII,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>C^TTAAG
<4>
<5>Bacteroides fragilis
<6>U. Mayr
<7>MO
<8>Prinz, B., Hardt, A., Schmitz, G., Jarsch, M., Kessler, C., Unpublished observations.

<1>BfrAI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacteroides fragilis
<6>NCTC 11155
<7>
<8>Clark, D., Unpublished observations.

<1>BfrBI
<2>AvaIII,Asi372I,BfrCI,Csp68KIII,EcoT22I,Mph1103I,NsiI,PinBI,Ppu10I,PxyJKI,SepI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>ATGCA^T
<4>
<5>Bacteroides fragilis BE3
<6>H. Azeddoug
<7>
<8>Azeddoug, H., Reysset, G., Sebald, M., (1992) FEMS Microbiol. Lett., vol. 95, pp. 133-136.
Morgan, R.D., Unpublished observations.

<1>BfrCI
<2>AvaIII,Asi372I,BfrBI,Csp68KIII,EcoT22I,Mph1103I,NsiI,PinBI,Ppu10I,PxyJKI,SepI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>ATGCAT
<4>
<5>Bacteroides fragilis AIP10006
<6>NCTC 9383
<7>
<8>Azeddoug, H., Reysset, G., Sebald, M., (1992) FEMS Microbiol. Lett., vol. 95, pp. 133-136.

<1>BfuI
<2>BciVI
<3>GTATCC(6/5)
<4>
<5>Bacillus firmus Auk 22-m21
<6>V. Butkus
<7>F
<8>Vitkute, J., Lazareviciute, L., Luksiene, A., Maneliene, Z., Capskaja, L., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>Bfu1570I
<2>HgiAI,Alw21I,AspHI,Bbv12I,BsaGI,Bsh45I,BsiHKAI,Bsm6I,BsmPI,Hpy8III,HpyF7II,HpyF46II,MspV281I,Pph3215I
<3>GWGCWC
<4>
<5>Bacillus fusiformis 1570
<6>NEB 1301
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>BfuAI
<2>BspMI,Acc36I,BveI
<3>ACCTGC(4/8)
<4>?(5)
<5>Bacillus fusiformis 1083
<6>NEB 1292
<7>N
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>BfuCI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus fusiformis 1226
<6>NEB 1441
<7>N
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.
Samuelson, J.C., Luo, J., International Patent Office, 2009.
Zhu, Z., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BgiI
<2>Tth111I,AspI,AtsI,FsuI,NtaI,PflFI,PsyI,SmaAII,SpaPI,SplII,SplAII,TelI,TrsKTII,TspI,TteI,TtrI
<3>GACN^NNGTC
<4>
<5>Brevibacillus agri
<6>Vivantis 187
<7>
<8>Chee, H.Y., Unpublished observations.

<1>BglI
<2>Bpu86I,BseB631I,BsoJI,Psp1009I,Tsp219I,Tsp8EI,VanI
<3>GCCNNNN^NGGC
<4>?(4)
<5>Bacillus globigii
<6>ATCC 49760
<7>CFHIJKMNOQRSUVWXY
<8>Bickle, T.A., Ineichen, K., (1980) Gene, vol. 9, pp. 205-212.
Duncan, C.H., Wilson, G.A., Young, F.E., (1978) J. Bacteriol., vol. 134, pp. 338-344.
Lautenberger, J.A., White, C.T., Haigwood, N.L., Edgell, M.H., Hutchison, C.A., (1980) Gene, vol. 9, pp. 213-231.
Lunnen, K.D., Barsomian, J.M., Camp, R.R., Card, C.O., Chen, S.-Z., Croft, R., Looney, M.C., Meda, M.M., Moran, L.S., Nwankwo, D.O., Slatko, B.E., Van Cott, E.M., Wilson, G.G., (1988) Gene, vol. 74, pp. 25-32.
Lunnen, K.D., Wilson, G.G., US Patent Office, 1994.
Van Heuverswyn, H., Fiers, W., (1980) Gene, vol. 9, pp. 195-203.

<1>BglII
<2>BseB631II,NcrI,NspMACI,Pae2kI,Pae18kI
<3>A^GATCT
<4>5(4)
<5>Bacillus globigii
<6>ATCC 49760
<7>BCFHIJKMNOQRSUVWXY
<8>Anton, B.P., Brooks, J.E., Unpublished observations.
Anton, B.P., Heiter, D.F., Benner, J.S., Hess, E.J., Greenough, L., Moran, L.S., Slatko, B.E., Brooks, J.E., (1997) Gene, vol. 187, pp. 19-27.
Duncan, C.H., Wilson, G.A., Young, F.E., (1978) J. Bacteriol., vol. 134, pp. 338-344.
Pirrotta, V., (1976) Nucleic Acids Res., vol. 3, pp. 1747-1760.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>BhaI
<2>SfaNI,BmsI,BscAI,BscUI,BsmNI,BspST5I,Bst19I,CjeP338II,LweI,PhaI
<3>GCATC
<4>
<5>Bacillus halodurans C-125
<6>JCM 9153
<7>
<8>Morgan, R.D., Unpublished observations.
Takami, H., Nakasone, K., Takaki, Y., Maeno, G., Sasaki, R., Masui, N., Fuji, F., Hirama, C., Nakamura, Y., Ogasawara, N., Kuhara, S., Horikoshi, K., (2000) Nucleic Acids Res., vol. 28, pp. 4317-4331.

<1>BhaII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>?(5)
<5>Bacillus halodurans C-125
<6>JCM 9153
<7>
<8>Morgan, R.D., Unpublished observations.
Roberts, R.J., Unpublished observations.
Takami, H., Nakasone, K., Takaki, Y., Maeno, G., Sasaki, R., Masui, N., Fuji, F., Hirama, C., Nakamura, Y., Ogasawara, N., Kuhara, S., Horikoshi, K., (2000) Nucleic Acids Res., vol. 28, pp. 4317-4331.

<1>BheI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Brevibacterium helvolum
<6>ATCC 11822
<7>
<8>Mattila, P., Pitkanen, K., Unpublished observations.

<1>BimI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Brevibacterium immotum
<6>G.G. Prikhodko
<7>
<8>Morgan, R.D., Unpublished observations.
Prihodko, G.G., Degtyarev, S.K., Rechkunova, N.I., Sosnovsev, S.V., Tchigikov, V.E., (1990) Biotekhnologiya, vol. 1, pp. 12-16.

<1>Bim19I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Brevibacterium immotum 19
<6>S.K. Degtyarev
<7>
<8>Prihodko, G.G., Degtyarev, S.K., Rechkunova, N.I., Sosnovsev, S.V., Tchigikov, V.E., (1990) Biotekhnologiya, vol. 1, pp. 12-16.

<1>Bim19II
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Brevibacterium immotum 19
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>BinI
<2>AclWI,AlwI,BpuFI,BspPI,BsrWI,BstH9I,Bst31TI,BthII,Bth617I,EacI,Ral8I
<3>GGATC(4/5)
<4>
<5>Bifidobacterium infantis 659
<6>ATCC 25962
<7>
<8>Khosaka, T., Kiwaki, M., (1984) Gene, vol. 31, pp. 251-255.

<1>BinSI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Bifidobacterium infantis S76e
<6>ATCC 15702
<7>
<8>Khosaka, T., Kiwaki, M., Rak, B., (1983) FEBS Lett., vol. 163, pp. 170-174.

<1>BinSII
<2>NarI,BbeI,BbeAI,DinI,Eco78I,EgeI,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GGCGC^C
<4>
<5>Bifidobacterium infantis S76e
<6>ATCC 15702
<7>
<8>Khosaka, T., Kiwaki, M., Rak, B., (1983) FEBS Lett., vol. 163, pp. 170-174.
Khosaka, T., Sakurai, T., Mutai, M., European Patent Office, 1981.

<1>BisI
<2>BlsI,GluI
<3>GC^NGC
<4>
<5>Bacillus subtilis T30
<6>S.K. Degtyarev
<7>I
<8>Chmuzh, E.V., Kashirina, J.G., Tomilova, J.E., Mezentzeva, N.V., Dedkov, V.S., Gonchar, D.A., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>Bka1125I
<2>SduI,AocII,BmyI,BsoCI,Bsp1286I,BspLS2I,BstZ15I,HpyF36IV,HpyF47I,MhlI,Mlu40I,NspII,TseAI,Uba1362I
<3>GDGCHC
<4>
<5>Bacillus kaustophilus 1125
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>Bla7920I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Bifidobacterium lactentis 7920
<6>G.N. Gabrichevsky
<7>
<8>Skrypina, N.A., Kramarov, V.M., Lyannaya, A.M., Smolyaninov, V.V., Goncharova, G.I., (1988) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 15-16.

<1>BleI
<2>
<3>?
<4>
<5>Bacillus lentus 1689
<6>MTCC 1689
<7>
<8>Jutur, P.P., Reddy, A.R., (2007) Microbiol. Res., vol. 162, pp. 378-383.

<1>BlfI
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>
<5>Bacillus licheniformis
<6>P. Babu
<7>
<8>Suma, M.A., Janaki, B., Babu, P., Unpublished observations.

<1>BliI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus licheniformis
<6>P.L. Manachini
<7>
<8>Manachini, P.L., Parini, C., Fortina, M.G., Benazzi, L., (1987) FEBS Lett., vol. 214, pp. 305-307.

<1>Bli41I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus licheniformis 41
<6>S.K. Degtyarev
<7>
<8>Repin, V.E., Rechkunova, N.I., Degtyarev, S.K., Hachaturyan, A.A., Afrikyan, E.K., (1989) Biol. J. Armenia, vol. 42, pp. 969-972.

<1>Bli49I
<2>Eco31I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Bacillus licheniformis 49
<6>N.I. Matvienko
<7>
<8>Kramarov, V.M., Skrypina, N.A., Smolyaninov, V.V., Smirnov, V.V., Resnik, S.R., Sorokulova, I.B., Matvienko, N.I., (1989) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 42-45.

<1>Bli86I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus licheniformis 86
<6>N.I. Matvienko
<7>
<8>Kramarov, V.M., Skrypina, N.A., Smolyaninov, V.V., Smirnov, V.V., Resnik, S.R., Sorokulova, I.B., Matvienko, N.I., (1989) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 42-45.

<1>Bli161I
<2>Eco31I,Bli49I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Bacillus licheniformis 16.1
<6>C. Parini
<7>
<8>Parini, C., Fortina, M.G., (1995) FEMS Microbiol. Lett., vol. 132, pp. 285-289.

<1>Bli576I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus licheniformis 576
<6>C. Parini
<7>
<8>Parini, C., Fortina, M.G., (1995) FEMS Microbiol. Lett., vol. 132, pp. 285-289.

<1>Bli576II
<2>Eco31I,Bli49I,Bli161I,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Bacillus licheniformis 576
<6>C. Parini
<7>
<8>Parini, C., Fortina, M.G., (1995) FEMS Microbiol. Lett., vol. 132, pp. 285-289.

<1>Bli585I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus licheniformis 58.5
<6>C. Parini
<7>
<8>Parini, C., Fortina, M.G., (1995) FEMS Microbiol. Lett., vol. 132, pp. 285-289.

<1>Bli643I
<2>SauI,AocI,AsuSAI,AxyI,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Bacillus licheniformis 64.3
<6>C. Parini
<7>
<8>Parini, C., Fortina, M.G., (1995) FEMS Microbiol. Lett., vol. 132, pp. 285-289.

<1>Bli736I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC(1/5)
<4>
<5>Bacillus licheniformis 736
<6>N.I. Matvienko
<7>
<8>Matvienko, N.N., Kramarov, V.M., Zheleznaya, L.A., Matvienko, N.I., (1993) Biokhimiia, vol. 58, pp. 1139-1153.

<1>Bli1904II
<2>Fnu4HI,Bpu1811I,BsoFI,Bsp6I,BssFI,BssXI,BthCI,Cac824I,CcoP215I,CcoP216I,FbrI,Fsp4HI,ItaI,LlaDII,SatI,Uur960I
<3>GCNGC
<4>?(5)
<5>Bacillus licheniformis SJ1904
<6>M. Rey
<7>
<8>Thomas, M., Rey, M., International Patent Office, 2008.

<1>Bli5508I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Bacillus licheniformis B-5508
<6>V.V. Lukyanchuk
<7>
<8>Lukyanchuk, V.V., Reva, O.M., Polishchuk, L.V., (1999) Mikrobiol. Zh., vol. 61, pp. 28-30.

<1>Bli11054I
<2>
<3>?
<4>
<5>Bacillus licheniformis
<6>IAM 11054
<7>
<8>Ando, T., Shibata, T., (1977) Tanpakushitsu Kakusan Koso, vol. 22, pp. 1012-1019.

<1>BliAI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus licheniformis
<6>J.M. Chies
<7>
<8>Chies, J.M., Dias, A.C.D.O., Maia, H.M.M., Braga, L.P.D.S., Astolfi-Filho, S., (2006) Braz. J. Microbiol., vol. 37, pp. 551-555.

<1>BliDI
<2>
<3>?
<4>
<5>Bacillus licheniformis DSM 13
<6>DSM 13
<7>
<8>Waschkau, B., Waldeck, J., Wieland, S., Eichstadt, R., Meinhardt, F., (2008) Appl. Microbiol. Biotechnol., vol. 78, pp. 181-188.

<1>BliDII
<2>
<3>?
<4>
<5>Bacillus licheniformis DSM 13
<6>DSM 13
<7>
<8>Waschkau, B., Waldeck, J., Wieland, S., Eichstadt, R., Meinhardt, F., (2008) Appl. Microbiol. Biotechnol., vol. 78, pp. 181-188.

<1>BliHKI
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CC^TNAGG
<4>
<5>Bacillus licheniformis HK
<6>P.C. Shaw
<7>
<8>Wu, S.Y., Lee, K.F., Kam, K.M., Shaw, P.C., (1993) Biosci. Biotechnol. Biochem., vol. 57, pp. 1193-1194.

<1>BliRI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus licheniformis
<6>ATCC 6634
<7>
<8>Mushtaq, R., Naeem, S., Riazuddin, S., Unpublished observations.

<1>BlnI
<2>AvrII,AspA2I,AvrBII,BspA2I,XmaJI
<3>C^CTAGG
<4>
<5>Brevibacterium linens
<6>IAM 1902
<7>KMS
<8>Yamamoto, K., Sagawa, H., Kotani, H., Hiraoka, N., Nakamura, T., US Patent Office, 1995.

<1>BloI
<2>
<3>?
<4>
<5>Bifidobacterium longum E194b
<6>ATCC 15707
<7>
<8>Sakurai, T., Kosaka, T., Japanese Patent Office, 1983.
Sakurai, T., Kosaka, T., US Patent Office, 1983.

<1>BloHI
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>R^GATCY
<4>
<5>Bifidobacterium longum E194b
<6>ATCC 15707
<7>
<8>Hartke, A., Benachour, A., Boutibonnes, P., Auffray, Y., (1996) Appl. Microbiol. Biotechnol., vol. 45, pp. 132-136.

<1>BloHII
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Bifidobacterium longum E194b
<6>ATCC 15707
<7>
<8>Hartke, A., Benachour, A., Boutibonnes, P., Auffray, Y., (1996) Appl. Microbiol. Biotechnol., vol. 45, pp. 132-136.

<1>BloHIII
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bifidobacterium longum E194b
<6>ATCC 15707
<7>
<8>Hartke, A., Benachour, A., Boutibonnes, P., Auffray, Y., (1996) Appl. Microbiol. Biotechnol., vol. 45, pp. 132-136.

<1>BlpI
<2>EspI,Bpu1102I,BpuGCI,Bsp1720I,CelII,Uba1221I,Uba1222I,Uba1284I,Uba1320I
<3>GC^TNAGC
<4>?(5)
<5>Bacillus species lp
<6>NEB 819
<7>N
<8>Chang, Z., Morgan, R., Unpublished observations.
Heiter, D., Lunnen, K., Wilson, G.G., US Patent Office, 2006.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Polisson, C., Unpublished observations.

<1>BlsI
<2>BisI,GluI
<3>GCN^GC
<4>
<5>Bacillus simplex 23
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Tomilova, J.E., Chmuzh, E.V., Sokolova, O.O., Dedkov, V.S., Degtyarev, S.K., (2007) Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol., vol. 3, pp. 28-33.
Chernukhin, V.A., Tomilova, J.E., Chmuzh, E.V., Sokolova, O.O., Dedkov, V.S., Degtyarev, S.K., Russian Patent Office, 2008.

<1>BluI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Brevibacterium luteum
<6>ATCC 15830
<7>
<8>Gingeras, T.R., Myers, P.A., Olson, J.A., Hanberg, F.A., Roberts, R.J., (1978) J. Mol. Biol., vol. 118, pp. 113-122.

<1>BluII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Brevibacterium luteum
<6>ATCC 15830
<7>
<8>Van Montagu, M., Unpublished observations.

<1>BmaI
<2>PvuI,Afa22MI,Afa16RI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Bacillus macerans
<6>ATCC 8244
<7>
<8>Kwon, Y.T., Jun, H.S., Rho, H.M., (1988) Korean J. Microbiol., vol. 26, pp. 1-5.
Kwon, Y.T., Jun, H.S., Rho, H.M., (1988) Korean J. Microbiol., vol. 26, pp. 88-92.
Polisson, C., Unpublished observations.

<1>BmaAI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Bacillus macerans
<6>ATCC 8513
<7>
<8>Hall, D., Unpublished observations.

<1>BmaBI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Bacillus macerans
<6>ATCC 8510
<7>
<8>Polisson, C., Unpublished observations.

<1>BmaCI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Bacillus macerans
<6>ATCC 7069
<7>
<8>Polisson, C., Unpublished observations.

<1>BmaDI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Bacillus macerans
<6>ATCC 8509
<7>
<8>Polisson, C., Unpublished observations.

<1>BmaHI
<2>BsmI,Asp26HI,Asp27HI,Asp35HI,Asp36HI,Asp40HI,Asp50HI,BsaMI,BscCI,Mva1269I,PctI,Uba1382I,Uba1415I
<3>GAATGC(1/-1)
<4>
<5>Bacillus megaterium
<6>Vivantis 12
<7>
<8>Chee, H.Y., Unpublished observations.

<1>BmcAI
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGT^ACT
<4>
<5>Bacillus macroides
<6>Vivantis 181
<7>V
<8>Chee, H.Y., Unpublished observations.

<1>BmeI
<2>
<3>?
<4>
<5>Bacillus megaterium
<6>J. Upcroft
<7>
<8>Gelinas, R.E., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>Bme05I
<2>HgiCI,AccB1I,BanI,BbvBI,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Bacillus megaterium 5
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Bme12I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus megaterium 12
<6>S.K. Degtyarev
<7>
<8>Akulinin, G.E., Getko, G.A., Repin, V.E., Degtyarev, S.K., (1988) Izv. Sib. Otd. Akad. Nauk SSSR, vol. 14, pp. 105-108.

<1>Bme18I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Bacillus megaterium 18
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.K., Rechkunova, N.I., Grinev, A.A., Dedkov, V.S., (1989) Izv. Sib. Otd. Akad. Nauk SSSR, vol. 15, pp. 25-26.

<1>Bme46I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus megaterium 46
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Bme74I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus megaterium 74
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Bme142I
<2>HaeII,AccB2I,BfoI,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGC^GCY
<4>
<5>Bacillus megaterium 142
<6>N.I. Matvienko
<7>
<8>Fomenkov, A.I., Kramarov, V.M., Andreev, L.V., Mochalov, V.V., Smolyaninov, V.V., Matvienko, N.I., (1988) Nucleic Acids Res., vol. 16, pp. 10399.

<1>Bme205I
<2>
<3>?
<4>
<5>Bacillus megaterium B205-3
<6>T. Kaneko
<7>
<8>Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>Bme216I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Bacillus megaterium 216
<6>V.M. Kramarov
<7>
<8>Kramarov, V.M., Pachkunov, D.M., Matvienko, N.I., (1983) Nek. Aspekty Fiziol. Mikroorg. Akad. Nauk. SSR., ed. Gaziev, A.I. (Nauchn. Tsentr Biol. Issled., Pushchino, USSR.), vol. 0, pp. 22-26.
Matvienko, N.I., Kramarov, V.M., Pachkunov, D.M., (1987) Eur. J. Biochem., vol. 165, pp. 565-570.

<1>Bme361I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Bacillus megaterium 361
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Bme585I
<2>FauI,BstFZ438I,SmuI
<3>CCCGC(4/6)
<4>
<5>Bacillus mesentericus 585
<6>J. Ziberovski
<7>
<8>Davalieva, K., Ziberovski, J., Efremov, G.D., (2004) Microbiol. Res., vol. 159, pp. 129-133.

<1>Bme899I
<2>
<3>?
<4>
<5>Bacillus megaterium 899
<6>IPP 899
<7>
<8>Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>Bme1390I
<2>ScrFI,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CC^NGG
<4>
<5>Bacillus megaterium RFL1390
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Kazlauskiene, R., Trinkunaite, L., Kiuduliene, L., Maneliene, Z., Petrusyte, M., Butkus, V., Unpublished observations.

<1>Bme1580I
<2>BseSI,BaeGI,BmgAI,BstSLI
<3>GKGCM^C
<4>?(5)
<5>Bacillus megaterium 1580
<6>NEB 1302
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.
Wei, H., Unpublished observations.

<1>Bme2095I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Bacillus megaterium 2095
<6>NEB 1361
<7>
<8>Nkenfou, C.N., Nkenfou, J., Unpublished observations.

<1>Bme2494I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus megaterium 2494
<6>NEB 1399
<7>
<8>Nkenfou, C.N., Nkenfou, J., Unpublished observations.

<1>BmeBI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus megaterium B78
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BmeRI
<2>Eam1105I,AhdI,AspEI,BspOVI,BstZ2I,DriI,EclHKI,NruGI,Uba1190I,Uba1191I
<3>GACNNN^NNGTC
<4>
<5>Bacillus megaterium
<6>Vivantis 32
<7>V
<8>Chee, H.Y., Unpublished observations.

<1>BmeTI
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>3(6)
<5>Bacillus methanolicus
<6>ATCC 53907
<7>
<8>Cue, D., Hong, L., Hanson, R.S., Flickinger, M.C., (1996) Appl. Environ. Microbiol., vol. 62, pp. 1107-1111.

<1>BmeT110I
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>
<5>Bacillus megaterium T110
<6>Takara T110
<7>K
<8>Sawaragi, H., Unpublished observations.

<1>BmeU1594I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus megaterium
<6>NEB 1594
<7>
<8>Abila, P., Nanyonjo, H., Egwang, T.G., Unpublished observations.

<1>BmgI
<2>
<3>GKGCCC
<4>
<5>Bacillus megaterium E11-132
<6>A. Janulaitis
<7>
<8>Vitkute, J., Markauskiene, J., Valickiene, D., Trinkunaite, L., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BmgAI
<2>BseSI,BaeGI,Bme1580I,BstSLI
<3>GKGCMC
<4>
<5>Bacillus megaterium
<6>NEB 1355
<7>
<8>Le, T.K.T., Vu, H.N., Vu, T.K.L., Polisson, C., Morgan, R., Unpublished observations.

<1>BmgBI
<2>BtrI,AjiI
<3>CACGTC(-3/-3)
<4>?(5)
<5>Bacillus thermoglucosidasius
<6>NEB 1353
<7>N
<8>Le, T.K.T., Vu, H.N., Vu, T.K.L., Polisson, C., Morgan, R., Unpublished observations.
Nkenfou, C., Morgan, R.D., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BmgT120I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GG^NCC
<4>
<5>Bacillus megalosporus T120
<6>Takara T120
<7>K
<8>Sawaragi, H., Unpublished observations.

<1>BmiI
<2>NlaIV,AspNI,BcrI,BsaEI,BscBI,Bsp29I,BspLI,BssI,HpyF44II,HpyF73I,NgoBV,NgoGV,PspN4I,Rlu3I,Uba1305I,Uba1445I
<3>GGN^NCC
<4>
<5>Bacillus megaterium
<6>Vivantis 62
<7>V
<8>Chee, H.Y., Unpublished observations.

<1>BmpI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Bacillus megaterium
<6>Vivantis 42
<7>
<8>Chee, H.Y., Unpublished observations.

<1>BmrI
<2>BfiI,BmuI,BsxI
<3>ACTGGG(5/4)
<4>
<5>Bacillus megaterium GC subgroup A
<6>NEB 1067
<7>N
<8>Bao, Y., Higgins, L., Zhang, P., Chan, S.H., Laget, S., Sweeney, S., Lunnen, K., Xu, S.Y., (2008) Protein Expr. Purif., vol. 58, pp. 42-52.
Krotee, S., Ganatra, M., Unpublished observations.
Le, T.K.T., Morgan, R., Unpublished observations.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>BmrFI
<2>ScrFI,Bme1390I,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CC^NGG
<4>
<5>Bacillus megaterium F
<6>Vivantis 91
<7>V
<8>Chee, H.Y., Unpublished observations.

<1>BmsI
<2>SfaNI,BhaI,BscAI,BscUI,BsmNI,BspST5I,Bst19I,CjeP338II,LweI,PhaI
<3>GCATC(5/9)
<4>
<5>Bacillus massiliensis RFL101
<6>Fermentas G358
<7>F
<8>Vitkute, J., Lauciuniene, N., Lapcinskaja, S., Trinkunaite, L., Zakareviciene, L., Lubys, A., Janulaitis, A., Unpublished observations.

<1>BmtI
<2>NheI,AceII,AsuNHI,BspOI,LlaG2I,PstNHI
<3>GCTAG^C
<4>?(5)
<5>Bacillus megaterium S2
<6>NEB 1776
<7>INV
<8>Dedkov, V.S., Nayakshina, T.N., Popichenko, D.V., Degtyarev, S.K., (2003) Biotekhnologiya, vol. 1, pp. 11-15.
Zhu, Z., Unpublished observations.

<1>BmuI
<2>BfiI,BmrI,BsxI
<3>ACTGGG(5/4)
<4>
<5>Bacillus megaterium S87
<6>S.K. Degtyarev
<7>I
<8>Dedkov, V.S., Nayakshina, T.N., Mezentseva, N.V., Degtyarev, S.K., Unpublished observations.

<1>BmyI
<2>SduI,AocII,Bka1125I,BsoCI,Bsp1286I,BspLS2I,BstZ15I,HpyF36IV,HpyF47I,MhlI,Mlu40I,NspII,TseAI,Uba1362I
<3>GDGCH^C
<4>
<5>Bacillus mycoides
<6>U. Mayr
<7>
<8>Wagner, E., Schmitz, G.G., Kaluza, K., Jarsch, M., Gotz, F., Kessler, C., (1990) Nucleic Acids Res., vol. 18, pp. 3088.

<1>BnaI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>5(5)
<5>Bacillus natto B3364
<6>E.L. Kim
<7>
<8>Kim, E.L., Maliuta, S.S., (1989) FEBS Lett., vol. 255, pp. 361-364.
Kim, E.L., Maliuta, S.S., (1989) Gene, vol. 80, pp. 363-368.

<1>BniI
<2>Cac8I,BstC8I
<3>GCNNGC
<4>
<5>Bacillus niacini RFL102
<6>Fermentas G361
<7>
<8>Vitkute, J., Spiliauskaite, K., Trinkunaite, L., Vitkute, J., Janulaitis, A., Unpublished observations.

<1>BoxI
<2>PshAI,BstPAI
<3>GACNN^NNGTC
<4>
<5>Brevibacterium oxydans Iti 12-025
<6>V. Butkus
<7>F
<8>Maneliene, Z., Butkus, V., Unpublished observations.
Vitkute, J., Lazareviciute, L., Kvietkiene, E., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BpaI
<2>
<3>?
<4>
<5>Bacillus pasteurii strain 1761
<6>A.R. Reddy
<7>
<8>Jutur, P.P., Reddy, A.R., (2004) Biotechnol. Lett., vol. 26, pp. 929-932.

<1>Bpa34I
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,BmcAI,BshHI,BsoSI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGT^ACT
<4>
<5>Bacillus pallidus
<6>NEB 1562
<7>
<8>Pan, X.S., Morgan, R., Unpublished observations.

<1>Bpa36I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus pallidus
<6>NEB 1564
<7>
<8>Pan, X.S., Morgan, R., Unpublished observations.

<1>Bpa36II
<2>DdeI,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Bacillus pallidus
<6>NEB 1564
<7>
<8>Pan, X.S., Morgan, R., Unpublished observations.

<1>BpcI
<2>SfeI,Bco163I,BdiSI,BfmI,BstSFI,BthP35I,HpyF2I,LlaBI,SfcI,Srl56DI
<3>C^TRYAG
<4>
<5>Bacillus sphaericus
<6>P. Babu
<7>
<8>Suma, M.A., Janaki, B., Babu, P., Unpublished observations.

<1>BpeI
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Bordetella pertussis
<6>P. Novotny
<7>
<8>Greenaway, P.J., (1980) Biochem. Biophys. Res. Commun., vol. 95, pp. 1282-1287.
Kazennova, E.V., Tarasov, A.P., Mileikovskaya, M.M., Semina, I.E., Tsvetkova, N.V., (1982) Zh. Mikrobiol. Epidemiol. Immunobiol., vol. 0, pp. 56-57.

<1>BpiI
<2>BbvII,Bbr7I,BbsI,Bbv16II,Bco102II,BpuAI,BsaVI,Bsc91I,BscKI,BspBS31I,BspIS4I,BspTS514I,BspVI,BstBS32I,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC(2/6)
<4>
<5>Bacillus pumilus sw 4-3
<6>A. Janulaitis
<7>F
<8>Jurgelyte, R., Maniusyte, V., Lazareviciute, L., Maneliene, Z., Kiuduliene, E., Norgeliene, D., Kvietkiene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BplI
<2>
<3>(8/13)GAGNNNNNCTC(13/8)
<4>
<5>Bacillus pumilus
<6>V. Butkus
<7>F
<8>Maneliene, Z., Butkus, V., Unpublished observations.
Vitkute, J., Maneliene, Z., Petrusyte, M., Janulaitis, A., (1997) Nucleic Acids Res., vol. 25, pp. 4444-4446.

<1>BpmI
<2>GsuI,Bco35I,Bsp22I,Bsp28I,BspJ74I,Bth1795I,Uba1437I,Uba1444I
<3>CTGGAG(16/14)
<4>
<5>Bacillus pumilus
<6>NEB 711
<7>IN
<8>Degtyarev, S.K., Morgan, R., Unpublished observations.
Zhou, J., Zhu, Z., Xu, S.Y., US Patent Office, 2002.

<1>BpnI
<2>
<3>?
<4>
<5>Bacillus pantothenticus strain 1639
<6>A.R. Reddy
<7>
<8>Jutur, P.P., Reddy, A.R., (2004) Biotechnol. Lett., vol. 26, pp. 929-932.

<1>BpoAI
<2>VspI,AseI,AsnI,CprJK722I,PbuMZI,PshBI,Srl8DI,Srl55DII,Srl65DI,Srr17I,Sru4DI
<3>AT^TAAT
<4>
<5>Bacillus polymyxa
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Eldarov, M.A., Samko, O.T., Karpichev, I.V., Kalugin, A.A., Anikeitcheva, N.V., Scryabin, K.G., Unpublished observations.
Sokolov, N.N., Kalugin, A.A., Samko, O.T., Omeljanuk, N.M., Unpublished observations.

<1>BprI
<2>
<3>?
<4>
<5>Brevibacterium protophormiae
<6>IFO 12128
<7>
<8>Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Bull. Inst. Chem. Res. Kyoto Univ., vol. 60, pp. 328-335.

<1>BpsI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Bacillus species
<6>P. Babu
<7>
<8>Shroff, D., Damodaran, B., Bulla, S., Ramesh, S., Suma, M.A., Kumar, M., Hegde, V., Babu, P., Unpublished observations.

<1>BptI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus pantothenticus
<6>P. Babu
<7>
<8>Suma, M.A., Janaki, B., Babu, P., Unpublished observations.

<1>BpuI
<2>HgiJII,BanII,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCY^C
<4>
<5>Bacillus pumilus AHU1387A
<6>T. Ando
<7>
<8>Ikawa, S., Shibata, T., Ando, T., (1976) J. Biochem. (Tokyo), vol. 80, pp. 1457-1460.
Iwabuchi, M., Tajima, S., Inoue, T., Shibata, T., Ando, T., (1992) Nucleic Acids Res., vol. 20, pp. 5850.
Kong, H., Unpublished observations.

<1>Bpu10I
<2>BpuDI
<3>CCTNAGC(-5/-2)
<4>?(5)
<5>Bacillus pumilus 10
<6>NEB 1777
<7>FINV
<8>Degtyarev, S.K., Zilkin, P.A., Prihodko, G.G., Repin, V.E., Rechkunova, N.I., (1989) Mol. Biol. (Mosk), vol. 23, pp. 1051-1056.
Stankevicius, K., Lubys, A., Timinskas, A., Vaitkevicius, D., Janulaitis, A., (1998) Nucleic Acids Res., vol. 26, pp. 1084-1091.

<1>Bpu14I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Bacillus pumilus 14
<6>S.K. Degtyarev
<7>IV
<8>Semenchenko, G.V., Rechkunova, N.I., Degtyarev, S.K., Unpublished observations.

<1>Bpu86I
<2>BglI,BseB631I,BsoJI,Psp1009I,Tsp219I,Tsp8EI,VanI
<3>GCCNNNNNGGC
<4>
<5>Bacillus pumilis 86
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Bpu95I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>
<5>Bacillus pumilus 95
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>Bpu1102I
<2>EspI,BlpI,BpuGCI,Bsp1720I,CelII,Uba1221I,Uba1222I,Uba1284I,Uba1320I
<3>GC^TNAGC
<4>
<5>Bacillus pumilus RFL1102
<6>A. Janulaitis
<7>FK
<8>Janulaitis, A., Steponaviciene, D., Trinkunaite, L., Maneliene, Z., Kiuduliene, L., Petrusyte, M., Butkus, V., Unpublished observations.

<1>Bpu1268I
<2>EcoNI,BsoEI,BstENI,BstWI,Uba1289I,Uba1290I,Uba1308I,Uba1309I,Uba1310I,XagI
<3>CCTNNNNNAGG
<4>
<5>Bacillus pumilus RFL1268
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Krikstulyte, V., Trinkunaite, L., Maneliene, Z., Kiuduliene, L., Petrusyte, M., Butkus, V., Unpublished observations.

<1>Bpu1811I
<2>Fnu4HI,Bli1904II,BsoFI,Bsp6I,BssFI,BssXI,BthCI,Cac824I,CcoP215I,CcoP216I,FbrI,Fsp4HI,ItaI,LlaDII,SatI,Uur960I
<3>GCNGC
<4>
<5>Bacillus pumilus 1811
<6>NEB 1325
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>Bpu1831I
<2>SnaBI,BstSNI,EciAI,Eco105I,Eco158II,SspJI,SspM1I,SspM2I,Uba1240I
<3>TACGTA
<4>
<5>Bacillus pumilus 1831
<6>NEB 1357
<7>
<8>Nkenfou, C.N., Nkenfou, J., Unpublished observations.

<1>BpuAI
<2>BbvII,Bbr7I,BbsI,Bbv16II,Bco102II,BpiI,BsaVI,Bsc91I,BscKI,BspBS31I,BspIS4I,BspTS514I,BspVI,BstBS32I,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC(2/6)
<4>
<5>Bacillus pumilus
<6>G. Schmitz
<7>M
<8>Pogge von Strandmann, R., Stadtler, R., Walter, T., Frey, B., Kaluza, K., Hengstenberg, W., Schmitz, G., (1992) Nucleic Acids Res., vol. 20, pp. 4664.

<1>BpuAmI
<2>SacI,Ecl136II,Ecl137I,EcoICRI,Eco53kI,MxaI,NasSI,Pfl18I,Psp124BI,ScoI,Ssm4I,Ssm5I,SstI
<3>GAG^CTC
<4>
<5>Bacillus pumilus
<6>J.M. Chies
<7>
<8>Chies, J.M., de O-Dias, A.C., Maia, H.M.M., Astolfi-Filho, S., Unpublished observations.

<1>BpuB5I
<2>SplI,BsiWI,BsmWI,BvuBI,MaeK81I,Pfl23II,PfuNI,PpuAI,PspLI,SmaAI,SplAI,SspKI,SunI
<3>C^GTACG
<4>
<5>Bacillus pumilus
<6>P.C. Shaw
<7>
<8>Zhao, Z.-H., Yung, M.-H., Cui, T., Wang, Y.-Z., Shaw, P.C., (1992) Nucleic Acids Res., vol. 20, pp. 1156.

<1>BpuCI
<2>EciI
<3>GGCGGA
<4>
<5>Bacillus pumilus
<6>NEB 1220
<7>
<8>Nkenfou, C., Polisson, C., Morgan, R.D., Unpublished observations.

<1>BpuDI
<2>Bpu10I
<3>CCTNAGC(-5/-2)
<4>
<5>Bacillus pumilus 1117
<6>NEB 1287
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>BpuEI
<2>Bce83I
<3>CTTGAG(16/14)
<4>
<5>Bacillus pumilus 2187a
<6>NEB 1378
<7>N
<8>Murray, I.A., Wei, H., Unpublished observations.
Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>BpuFI
<2>BinI,AclWI,AlwI,BspPI,BsrWI,BstH9I,Bst31TI,BthII,Bth617I,EacI,Ral8I
<3>GGATC
<4>
<5>Bacillus pumilus 1567
<6>NEB 1358
<7>
<8>Nkenfou, C.N., Nkenfou, J., Unpublished observations.

<1>BpuGI
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BscSI,BstX2I,BstYI,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>RGATCY
<4>
<5>Bacillus pumilus 980
<6>NEB 1359
<7>
<8>Nkenfou, C.N., Nkenfou, J., Unpublished observations.

<1>BpuGCI
<2>EspI,BlpI,Bpu1102I,Bsp1720I,CelII,Uba1221I,Uba1222I,Uba1284I,Uba1320I
<3>GCTNAGC
<4>
<5>Bacillus pumilis GC subgroup 8
<6>NEB 1034
<7>
<8>Osterfield, T., Unpublished observations.

<1>BpuHI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Bacillus pumilus 1520
<6>NEB 1360
<7>
<8>Nkenfou, C.N., Nkenfou, J., Unpublished observations.

<1>BpuJI
<2>BscGI,BstDZ247I
<3>CCCGT
<4>
<5>Bacillus pumilus RFL1458
<6>A. Janulaitis
<7>
<8>Sukackaite, R., Lagunavicius, A., Stankevicius, K., Urbanke, C., Venclovas, C., Siksnys, V., (2007) Nucleic Acids Res., vol. 35, pp. 2377-2389.
Vitkute, J., Trinkunaite, L., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BpuMI
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CC^SGG
<4>
<5>Bacillus pumilus
<6>Vivantis 371
<7>V
<8>Chee, H.Y., Unpublished observations.

<1>BpuNI
<2>FinI,BpuSI,BscWI,BslFI,BsmFI,BspLU11III,BstOZ616I,FaqI
<3>GGGAC
<4>
<5>Bacillus pumilus 1703
<6>NEB 1316
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>BpuSI
<2>FinI,BpuNI,BscWI,BslFI,BsmFI,BspLU11III,BstOZ616I,FaqI
<3>GGGAC(10/14)
<4>
<5>Bacillus pumilus
<6>NEB 1539
<7>
<8>Xu, D., Zhu, Z., Xu, S.-Y., Unpublished observations.
Zhu, Z., Unpublished observations.

<1>BpvUI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGAT^CG
<4>
<5>Bacillus pumilus VU
<6>Vivantis 14
<7>V
<8>Chee, H.Y., Unpublished observations.

<1>BsaI
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC(1/5)
<4>?(5)
<5>Bacillus stearothermophilus 6-55
<6>Z. Chen
<7>N
<8>Kong, H., Chen, Z., Unpublished observations.
Morgan, R.D., Unpublished observations.
Zhou, J., Xu, S., Unpublished observations.
Zhu, Z., Xu, S.-Y., Unpublished observations.
Zhu, Z., Xu, S.-Y., US Patent Office, 2003.

<1>Bsa29I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus species 29
<6>S.K. Degtyarev
<7>I
<8>Repin, V.E., Degtyarev, S.K., Unpublished observations.

<1>BsaAI
<2>BstBAI,MspYI,Ppu6I,Ppu11I,Ppu21I,PsuAI
<3>YAC^GTR
<4>3(5)
<5>Bacillus stearothermophilus G668
<6>Z. Chen
<7>N
<8>Kong, H., Unpublished observations.
Kong, H., Morgan, R.D., Chen, Z., (1990) Nucleic Acids Res., vol. 18, pp. 2832.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Zhu, Z., Unpublished observations.

<1>BsaBI
<2>Bco63I,Bco631I,Bse8I,Bse631I,BseJI,Bsh1365I,BsiBI,BsrBRI,MamI,UbaN6I
<3>GATNN^NNATC
<4>
<5>Bacillus stearothermophilus B674
<6>NEB 537
<7>N
<8>Chen, Z., Kong, H., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BsaCI
<2>ScrFI,Bme1390I,BmrFI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>
<5>Bacillus stearothermophilus C34
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsaDI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus stearothermophilus D144
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsaEI
<2>NlaIV,AspNI,BcrI,BmiI,BscBI,Bsp29I,BspLI,BssI,HpyF44II,HpyF73I,NgoBV,NgoGV,PspN4I,Rlu3I,Uba1305I,Uba1445I
<3>GGNNCC
<4>
<5>Bacillus stearothermophilus EJ04
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsaFI
<2>AflII,BfrI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>CTTAAG
<4>
<5>Bacillus stearothermophilus F272
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsaGI
<2>HgiAI,Alw21I,AspHI,Bbv12I,Bfu1570I,Bsh45I,BsiHKAI,Bsm6I,BsmPI,Hpy8III,HpyF7II,HpyF46II,MspV281I,Pph3215I
<3>GWGCWC
<4>
<5>Bacillus stearothermophilus G426
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsaHI
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>?(5)
<5>Bacillus stearothermophilus CPW11
<6>Z. Chen
<7>N
<8>Chen, W., Pan, X., Chen, Z., Unpublished observations.
Morgan, R.D., Unpublished observations.
Neely, R.K., Roberts, R.J., (2008) BMC Mol. Biol., vol. 9, pp. 48.

<1>BsaJI
<2>SecI,BseDI,BsoKI,BssECI,BstZ10I,Hpy99IV,HpyF10III,HpyF61II,HpyF67IV,Uba1442I
<3>C^CNNGG
<4>?(4)
<5>Bacillus stearothermophilus J695
<6>Z. Chen
<7>N
<8>Kong, H., Chen, Z., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Xu, S.-Y., Unpublished observations.

<1>BsaKI
<2>HpaI,BseII,BstEZ359I,BstHPI,KspAI,MwhI,SsrI,Uba1408II
<3>GTTAAC
<4>
<5>Bacillus stearothermophilus K524
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsaLI
<2>AluI,AluBI,MarI,Mho2111I,MltI,OtuI,OtuNI,OxaI,Uba1433I,Uba1441I
<3>AGCT
<4>
<5>Bacillus stearothermophilus L170
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsaMI
<2>BsmI,Asp26HI,Asp27HI,Asp35HI,Asp36HI,Asp40HI,Asp50HI,BmaHI,BscCI,Mva1269I,PctI,Uba1382I,Uba1415I
<3>GAATGC(1/-1)
<4>
<5>Bacillus stearothermophilus M293
<6>Z. Chen
<7>R
<8>Chen, Z., Unpublished observations.

<1>BsaNI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Bacillus stearothermophilus CPW1
<6>Z. Chen
<7>
<8>Chen, W., Pan, X., Chen, Z., Unpublished observations.

<1>BsaNII
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus stearothermophilus CPW1
<6>Z. Chen
<7>
<8>Chen, W., Pan, X., Chen, Z., Unpublished observations.

<1>BsaOI
<2>McrI,BscNI,Bsh1285I,BsiEI,BstMCI,BstZ5I,Uba1303I
<3>CGRY^CG
<4>
<5>Bacillus stearothermophilus O-122
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z.F., (1991) Chinese Sci. Bull., vol. 36, pp. 1231-1232.

<1>BsaPI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus stearothermophilus P8
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BsaQI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus stearothermophilus CPW59
<6>Z. Chen
<7>
<8>Chen, W., Pan, X., Chen, Z., Unpublished observations.

<1>BsaRI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus stearothermophilus CPW8
<6>Z. Chen
<7>
<8>Chen, W., Pan, X., Chen, Z., Unpublished observations.

<1>BsaRII
<2>
<3>?
<4>
<5>Bacillus stearothermophilus CPW8
<6>Z. Chen
<7>
<8>Chen, W., Pan, X., Chen, Z., Unpublished observations.

<1>BsaSI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Bacillus stearothermophilus D47
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsaTI
<2>MstI,AcaIII,Acc16I,AosI,ApcTR183I,AviII,Bco6I,ClcII,CliII,FdiII,FspI,GspAII,NsbI,NspHIII,NspLI,NspMI,PamI,Pun14627I
<3>TGCGCA
<4>
<5>Bacillus stearothermophilus T1544
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsaUI
<2>BbvI,AlwXI,BchI,BseKI,BseXI,Bsp423I,BsrVI,Bst12I,Bst71I,BstV1I,LfeI,Lsp1109I
<3>GCAGC
<4>
<5>Bacillus stearothermophilus SR65
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsaVI
<2>BbvII,Bbr7I,BbsI,Bbv16II,Bco102II,BpiI,BpuAI,Bsc91I,BscKI,BspBS31I,BspIS4I,BspTS514I,BspVI,BstBS32I,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC
<4>
<5>Bacillus stearothermophilus V018
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsaWI
<2>BetI,Bba179I,Bca77I,Bst1473I,UbaN10I
<3>W^CCGGW
<4>?(5)
<5>Bacillus stearothermophilus W1718
<6>Z. Chen
<7>N
<8>Chen, W., Pan, X., Chen, Z., Unpublished observations.
Morgan, R.D., Unpublished observations.
Xu, S.-Y., Unpublished observations.

<1>BsaXI
<2>BsmCI,BsmDI,BsmXI
<3>(9/12)ACNNNNNCTCC(10/7)
<4>
<5>Bacillus stearothermophilus Cpw230
<6>Z. Chen
<7>N
<8>Chen, Z., Unpublished observations.
Morgan, R.D., Unpublished observations.
Polisson, C., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BsaZI
<2>HpaII,Asp748I,Bco27I,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Bacillus stearothermophilus Cpw514
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsbI
<2>
<3>CAACAC(21/19)
<4>
<5>Bacillus species
<6>NEB 686
<7>
<8>Morgan, R.D., Unpublished observations.
Zhou, B., Morgan, R., Unpublished observations.

<1>BscI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus species
<6>P. Eastlake
<7>
<8>Brown, N.L., Unpublished observations.
Gordon, R., Unpublished observations.

<1>Bsc4I
<2>BsiYI,AfiI,BflI,Bsc107I,Bse23I,BseLI,BslI,BsmYI,Bst22I
<3>CCNNNNN^NNGG
<4>
<5>Bacillus schlegelii 4
<6>V.E. Repin
<7>I
<8>Degtyarev, S.K., Unpublished observations.
Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bsc91I
<2>BbvII,Bbr7I,BbsI,Bbv16II,Bco102II,BpiI,BpuAI,BsaVI,BscKI,BspBS31I,BspIS4I,BspTS514I,BspVI,BstBS32I,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC(2/6)
<4>
<5>Bacillus species
<6>T. Schoenfeld
<7>
<8>Schoenfeld, T., Unpublished observations.

<1>Bsc107I
<2>BsiYI,AfiI,BflI,Bsc4I,Bse23I,BseLI,BslI,BsmYI,Bst22I
<3>CCNNNNN^NNGG
<4>
<5>Bacillus schlegelii 107
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.
Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bsc217I
<2>EcoRV,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Bacillus species HK217
<6>D. Clark
<7>
<8>Lam, P., Clark, D.R., Unpublished observations.

<1>BscAI
<2>SfaNI,BhaI,BmsI,BscUI,BsmNI,BspST5I,Bst19I,CjeP338II,LweI,PhaI
<3>GCATC(4/6)
<4>
<5>Bacillus schlegelii S3
<6>CAMB 2585
<7>
<8>Choudhry, S., Sohail, A., Malik, K., Riazuddin, S., Unpublished observations.
Zhu, Z., Unpublished observations.

<1>BscBI
<2>NlaIV,AspNI,BcrI,BmiI,BsaEI,Bsp29I,BspLI,BssI,HpyF44II,HpyF73I,NgoBV,NgoGV,PspN4I,Rlu3I,Uba1305I,Uba1445I
<3>GGN^NCC
<4>
<5>Bacillus species A11
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BscCI
<2>BsmI,Asp26HI,Asp27HI,Asp35HI,Asp36HI,Asp40HI,Asp50HI,BmaHI,BsaMI,Mva1269I,PctI,Uba1382I,Uba1415I
<3>GAATGC(1/-1)
<4>
<5>Bacillus species 2G
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BscDI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus species E13
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BscEI
<2>BsePI,BsoPI,BsrHI,BssBI,BssHII,BstBZ153I,CfrJ5I,Eco143I,Eco152I,Esp7I,Esp8I,Kpn30I,McaTI,PauI,PteI,TtmII,Uba69I
<3>GCGCGC
<4>
<5>Bacillus species APR91
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BscFI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus species JY391
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BscGI
<2>BpuJI,BstDZ247I
<3>CCCGT
<4>?(5)
<5>Bacillus smithii
<6>NEB 771
<7>
<8>Higgins, L.S., Chang, Z., Morgan, R.D., Kong, H., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Polisson, C., Unpublished observations.

<1>BscHI
<2>BsrI,Bse1I,BseNI,BsoHI,BsrSI,Bst11I,Tsp1I
<3>ACTGG
<4>
<5>Bacillus species A
<6>D. Clark
<7>
<8>Polisson, C., Unpublished observations.

<1>BscJI
<2>BstXI,BssGI,BstHZ55I,BstTI
<3>CCANNNNNNTGG
<4>
<5>Bacillus species 9A
<6>D. Clark
<7>
<8>Polisson, C., Unpublished observations.

<1>BscKI
<2>BbvII,Bbr7I,BbsI,Bbv16II,Bco102II,BpiI,BpuAI,BsaVI,Bsc91I,BspBS31I,BspIS4I,BspTS514I,BspVI,BstBS32I,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC
<4>
<5>Bacillus species 217
<6>D. Clark
<7>
<8>Lam, P., Clark, D.R., Unpublished observations.

<1>BscLI
<2>AflII,BfrI,BsaFI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>CTTAAG
<4>
<5>Bacillus species 1302
<6>D. Clark
<7>
<8>Lam, P., Clark, D.R., Unpublished observations.

<1>BscMI
<2>HgiJII,BanII,BpuI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Bacillus species 4231
<6>D. Clark
<7>
<8>Lam, P., Clark, D.R., Unpublished observations.

<1>BscNI
<2>McrI,BsaOI,Bsh1285I,BsiEI,BstMCI,BstZ5I,Uba1303I
<3>CGRYCG
<4>
<5>Bacillus species 4515
<6>D. Clark
<7>
<8>Lam, P., Clark, D.R., Unpublished observations.

<1>BscOI
<2>SphI,Asp5HI,BbuI,Bsp121I,BtgAII,CglAI,PaeI,PaeCI,PfaAIII,RspLKI,SpaHI,SpaXI,Uba1162I,Uba1226I,VchO68I
<3>GCATGC
<4>
<5>Bacillus species 4319
<6>D. Clark
<7>
<8>Lam, P., Clark, D.R., Unpublished observations.

<1>BscPI
<2>DdeI,Bpa36II,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Bacillus species 9006
<6>D. Clark
<7>
<8>Lam, P., Clark, D.R., Unpublished observations.

<1>BscQI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus species 4304
<6>D. Clark
<7>
<8>Lam, P., Clark, D.R., Unpublished observations.

<1>BscQII
<2>BsmAI,Alw26I,BcoDI,BsoMAI,BstMAI
<3>GTCTC
<4>
<5>Bacillus species 4304
<6>D. Clark
<7>
<8>Lam, P., Clark, D.R., Unpublished observations.

<1>BscRI
<2>Cfr10I,Bco118I,Bse118I,Bse634I,Bsp21I,BsrFI,BssAI,BstB7SI,NmeDI,TseDI
<3>RCCGGY
<4>
<5>Bacillus species 4709
<6>D. Clark
<7>
<8>Lam, P., Clark, D.R., Unpublished observations.

<1>BscSI
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BstX2I,BstYI,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>RGATCY
<4>
<5>Bacillus species 508
<6>D. Clark
<7>
<8>Lam, P., Clark, D.R., Unpublished observations.

<1>BscTI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Bacillus species 106
<6>D. Clark
<7>
<8>Lam, P., Clark, D.R., Unpublished observations.

<1>BscUI
<2>SfaNI,BhaI,BmsI,BscAI,BsmNI,BspST5I,Bst19I,CjeP338II,LweI,PhaI
<3>GCATC
<4>
<5>Bacillus species SA506a
<6>D. Clark
<7>
<8>Lam, P., Clark, D.R., Unpublished observations.

<1>BscVI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus species
<6>P. Babu
<7>
<8>Shroff, D., Damodaran, B., Bulla, S., Ramesh, S., Suma, M.A., Kumar, M., Hegde, V., Babu, P., Unpublished observations.

<1>BscWI
<2>FinI,BpuNI,BpuSI,BslFI,BsmFI,BspLU11III,BstOZ616I,FaqI
<3>GGGAC
<4>
<5>Bacillus species 2142
<6>NEB 1395
<7>
<8>Nkenfou, C.N., Nkenfou, J., Unpublished observations.

<1>BseI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus stearothermophilus strain 822
<6>T. Oshima
<7>
<8>Shinomiya, T., Unpublished observations.

<1>BseII
<2>HpaI,BsaKI,BstEZ359I,BstHPI,KspAI,MwhI,SsrI,Uba1408II
<3>GTTAAC
<4>
<5>Bacillus stearothermophilus strain 822
<6>T. Oshima
<7>
<8>Shinomiya, T., Unpublished observations.

<1>Bse1I
<2>BsrI,BscHI,BseNI,BsoHI,BsrSI,Bst11I,Tsp1I
<3>ACTGG(1/-1)
<4>
<5>Bacillus stearothermophilus 1
<6>S.K. Degtyarev
<7>IV
<8>Repin, V.E., Degtyarev, S.K., Unpublished observations.

<1>Bse8I
<2>BsaBI,Bco63I,Bco631I,Bse631I,BseJI,Bsh1365I,BsiBI,BsrBRI,MamI,UbaN6I
<3>GATNN^NNATC
<4>
<5>Bacillus species 8
<6>V.E. Repin
<7>IV
<8>Degtyarev, S.K., Unpublished observations.
Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bse9I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus species 9
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Bse15I
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>
<5>Bacillus species 15
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Puchkova, L., Serov, G.D., Tereschenko, T., Chizikov, V.E., Andreeva, I., (1995) Gene, vol. 157, pp. 321-322.

<1>Bse16I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus species 16
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bse17I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus species 17
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bse19I
<2>NcoI,AteI,Bsp19I,NspSAIII
<3>CCATGG
<4>
<5>bacillus species 19
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Bse21I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CC^TNAGG
<4>
<5>Bacillus species 21
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.Kh., Rechkunova, N.I., Repin, V.E., Kolyhalov, A.A., Netesov, S.V., (1990) Izv. Sib. Otd. Akad. Nauk SSSR, vol. 1, pp. 138-139.
Repin, V.E., Polshina, S.V., Bozhko, N.A., Degtyarev, S.Kh., (1989) Izv. Sib. Otd. Akad. Nauk SSSR, vol. 15, pp. 108-111.

<1>Bse23I
<2>BsiYI,AfiI,BflI,Bsc4I,Bsc107I,BseLI,BslI,BsmYI,Bst22I
<3>CCNNNNNNNGG
<4>
<5>Bacillus species 23
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Puchkova, L., Serov, G.D., Tereschenko, T., Chizikov, V.E., Andreeva, I., (1995) Gene, vol. 157, pp. 321-322.
Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bse24I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus species 24
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bse54I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Bacillus species 54
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Bse59I
<2>BstEII,AcrII,AspAI,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>GGTNACC
<4>
<5>Bacillus species 59
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Puchkova, L., Serov, G.D., Tereschenko, T., Chizikov, V.E., Andreeva, I., (1995) Gene, vol. 157, pp. 321-322.
Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bse64I
<2>BstEII,AcrII,AspAI,Bse59I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Bacillus species 64
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.
Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bse118I
<2>Cfr10I,Bco118I,BscRI,Bse634I,Bsp21I,BsrFI,BssAI,BstB7SI,NmeDI,TseDI
<3>R^CCGGY
<4>
<5>Bacillus species 118
<6>V.E. Repin
<7>IV
<8>Repin, V.E., Babkin, I.V., Tereshchenko, T.A., (1993) Bioorg. Khim., vol. 19, pp. 406-409.

<1>Bse126I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus species 12-6
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Bse631I
<2>BsaBI,Bco63I,Bco631I,Bse8I,BseJI,Bsh1365I,BsiBI,BsrBRI,MamI,UbaN6I
<3>GATNNNNATC
<4>
<5>Bacillus species 631
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Puchkova, L., Serov, G.D., Tereschenko, T., Chizikov, V.E., Andreeva, I., (1995) Gene, vol. 157, pp. 321-322.

<1>Bse634I
<2>Cfr10I,Bco118I,BscRI,Bse118I,Bsp21I,BsrFI,BssAI,BstB7SI,NmeDI,TseDI
<3>R^CCGGY
<4>?(5)
<5>Bacillus species 634
<6>V.E. Repin
<7>
<8>Grazulis, S., Deibert, M., Rimseliene, R., Skirgaila, R., Sasnauskas, G., Lagunavicius, A., Repin, V., Urbanke, C., Huber, R., Siksnys, V., (2002) Nucleic Acids Res., vol. 30, pp. 876-885.
Repin, V.E., Lebedev, L.R., Puchkova, L., Serov, G.D., Tereschenko, T., Chizikov, V.E., Andreeva, I., (1995) Gene, vol. 157, pp. 321-322.

<1>BseAI
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>
<5>Bacillus sphaericus
<6>V. Bouriotis
<7>CM
<8>Thanos, D., Scarpelis, G., Papamatheakis, J., Bouriotis, V., (1989) Nucleic Acids Res., vol. 17, pp. 8881.

<1>BseBI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus stearothermophilus
<6>V. Bouriotis
<7>C
<8>Rina, M., Tsigos, I., Karagouni, A., Pagomenou, M., Bouriotis, V., (1991) Nucleic Acids Res., vol. 19, pp. 4776.

<1>BseB631I
<2>BglI,Bpu86I,BsoJI,Psp1009I,Tsp219I,Tsp8EI,VanI
<3>GCCNNNNNGGC
<4>
<5>Bacillus species 6-3-1
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>BseB631II
<2>BglII,NcrI,NspMACI,Pae2kI,Pae18kI
<3>AGATCT
<4>
<5>Bacillus species 6-3-1
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>BseCI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>5(6)
<5>Bacillus species
<6>V. Bouriotis
<7>C
<8>Rina, M., Bouriotis, V., (1993) Gene, vol. 133, pp. 91-94.
Rina, M., Dialektakis, D., Clark, D., Pagomenou, M., Bouriotis, V., (1992) Nucleic Acids Res., vol. 20, pp. 1807.

<1>BseDI
<2>SecI,BsaJI,BsoKI,BssECI,BstZ10I,Hpy99IV,HpyF10III,HpyF61II,HpyF67IV,Uba1442I
<3>C^CNNGG
<4>
<5>Bacillus stearothermophilus RFL1434
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Unpublished observations.
Vilkaitis, G., Janulaitis, A., Unpublished observations.

<1>Bse3DI
<2>BsrDI,BseMI
<3>GCAATG(2/0)
<4>
<5>Bacillus stearothermophilus 3D
<6>S.K. Degtyarev
<7>IV
<8>Abdurashitov, M.A., Bondar, T.S., Shevchenko, A.V., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>BseEI
<2>
<3>?
<4>
<5>Bacillus stearothermophilus D88
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BseFI
<2>
<3>?
<4>
<5>Bacillus stearothermophilus F245
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BseGI
<2>FokI,BstF5I,BtsCI,HinGUII,Hpy178VI,HpyF6I,HpyF67III,PbuJKI,StsI
<3>GGATG(2/0)
<4>
<5>Bacillus stearothermophilus Vs 34-031
<6>A. Janulaitis
<7>F
<8>Vitkute, J., Lazareviciute, L., Maneliene, Z., Kvietkiene, E., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BseG73I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Bacillus species G-7-3
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>BseHI
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Bacillus stearothermophilus CPW5
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BseJI
<2>BsaBI,Bco63I,Bco631I,Bse8I,Bse631I,Bsh1365I,BsiBI,BsrBRI,MamI,UbaN6I
<3>GATNN^NNATC
<4>
<5>Bacillus stearothermophilus Tsp5
<6>V. Butkus
<7>F
<8>Vitkute, J., Lazareviciute, L., Maneliene, Z., Capskaja, L., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BseKI
<2>BbvI,AlwXI,BchI,BsaUI,BseXI,Bsp423I,BsrVI,Bst12I,Bst71I,BstV1I,LfeI,Lsp1109I
<3>GCAGC(8/12)
<4>
<5>Bacillus stearothermophilus Ra3-212
<6>V. Butkus
<7>
<8>Vitkute, J., Grigaite, R., Maneliene, Z., Capskaja, L., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BseLI
<2>BsiYI,AfiI,BflI,Bsc4I,Bsc107I,Bse23I,BslI,BsmYI,Bst22I
<3>CCNNNNN^NNGG
<4>
<5>Bacillus stearothermophilus LK3-551
<6>A. Janulaitis
<7>F
<8>Vitkute, J., Kazlauskiene, R., Maneliene, Z., Capskaja, L., Vonseviciene, E., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BseMI
<2>BsrDI,Bse3DI
<3>GCAATG(2/0)
<4>
<5>Bacillus stearothermophilus Isl 15-111
<6>A. Janulaitis
<7>F
<8>Maneliene, Z., Butkus, V., Unpublished observations.
Vitkute, J., Kazlauskiene, R., Capskaja, L., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BseMII
<2>BspCNI
<3>CTCAG(10/8)
<4>
<5>Bacillus stearothermophilus Isl 15-111
<6>A. Janulaitis
<7>F
<8>Jurenaite-Urbanaviciene, S., Kazlauskiene, R., Urbelyte, V., Maneliene, Z., Petrusyte, M., Lubys, A., Janulaitis, A., (2001) Nucleic Acids Res., vol. 29, pp. 895-903.
Maneliene, Z., Butkus, V., Unpublished observations.

<1>BseNI
<2>BsrI,BscHI,Bse1I,BsoHI,BsrSI,Bst11I,Tsp1I
<3>ACTGG(1/-1)
<4>
<5>Bacillus species N
<6>A. Janulaitis
<7>F
<8>Kolesnikov, V.A., Kovalenko, S.P., Repin, V.E., Protopopov, M.O., Karginov, V.A., Unpublished observations.

<1>BsePI
<2>BscEI,BsoPI,BsrHI,BssBI,BssHII,BstBZ153I,CfrJ5I,Eco143I,Eco152I,Esp7I,Esp8I,Kpn30I,McaTI,PauI,PteI,TtmII,Uba69I
<3>G^CGCGC
<4>
<5>Bacillus stearothermophilus P6
<6>N. Welker
<7>IV
<8>Degtyarev, S.K., Unpublished observations.
Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BseQI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Bacillus species Q
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>BseRI
<2>SasI
<3>GAGGAG(10/8)
<4>
<5>Bacillus species R
<6>CAMB 2669
<7>N
<8>Mushtaq, R., Naeem, S., Sohail, A., Riazuddin, S., (1993) Nucleic Acids Res., vol. 21, pp. 3585.

<1>BseSI
<2>BaeGI,Bme1580I,BmgAI,BstSLI
<3>GKGCM^C
<4>
<5>Bacillus stearothermophilus Jo-553
<6>V. Butkus
<7>F
<8>Steponaviciene, D., Maneliene, Z., Petrusyte, M., Janulaitis, A., (1999) Nucleic Acids Res., vol. 27, pp. 2644-2645.

<1>BseTI
<2>
<3>?
<4>
<5>Bacillus stearothermophilus T889
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BseT9I
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Bacillus species T9
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Puchkova, L., Serov, G.D., Tereschenko, T., Chizikov, V.E., Andreeva, I., (1995) Gene, vol. 157, pp. 321-322.

<1>BseT10I
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Bacillus species T10
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Puchkova, L., Serov, G.D., Tereschenko, T., Chizikov, V.E., Andreeva, I., (1995) Gene, vol. 157, pp. 321-322.

<1>BseWI
<2>
<3>?
<4>
<5>Bacillus stearothermophilus 30T
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BseXI
<2>BbvI,AlwXI,BchI,BsaUI,BseKI,Bsp423I,BsrVI,Bst12I,Bst71I,BstV1I,LfeI,Lsp1109I
<3>GCAGC(8/12)
<4>
<5>Bacillus stearothermophilus Ra 3-212
<6>V. Butkus
<7>F
<8>Vitkute, J., Grigaite, R., Maneliene, Z., Capskaja, L., Kiuduliene, E., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BseX3I
<2>XmaIII,AaaI,BsoDI,BstZI,EagI,EclXI,Eco52I,SenPT16I,TauII,Tsp504I
<3>C^GGCCG
<4>
<5>Bacillus stearothermophilus X3
<6>S.K. Degtyarev
<7>IV
<8>Kileva, E.V., Dedkov, V.S., Shevchenko, A.V., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>BseYI
<2>GsaI,PspFI
<3>CCCAGC(-5/-1)
<4>
<5>Bacillus species 2521
<6>NEB 1396
<7>N
<8>Bhatia, T., Morgan, R.D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Nkenfou, C., Morgan, R.D., Unpublished observations.

<1>BseZI
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC(1/4)
<4>
<5>Bacillus species Z
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>BsgI
<2>
<3>GTGCAG(16/14)
<4>
<5>Bacillus sphaericus GC subgroup
<6>NEB 581
<7>N
<8>Kong, H., Sears, L., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>BshI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Bacillus sphaericus
<6>WHO/CCBC 1593
<7>
<8>Clark, D., Unpublished observations.

<1>Bsh45I
<2>HgiAI,Alw21I,AspHI,Bbv12I,Bfu1570I,BsaGI,BsiHKAI,Bsm6I,BsmPI,Hpy8III,HpyF7II,HpyF46II,MspV281I,Pph3215I
<3>GWGCW^C
<4>
<5>Bacillus sphaericus 45
<6>V.E. Repin
<7>
<8>Serov, G.D., Repin, V.E., Puchkova, L.E., Kolesnikov, V.A., Russian Patent Office, 1994.

<1>Bsh1236I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>
<5>Bacillus sphaericus RFL1236
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Bitinaite, J., Jagelavicius, M., Naureckiene, S., Vaitkevicius, D., Maneliene, Z., Kiuduliene, L., Butkus, V., Unpublished observations.

<1>Bsh1285I
<2>McrI,BsaOI,BscNI,BsiEI,BstMCI,BstZ5I,Uba1303I
<3>CGRY^CG
<4>
<5>Bacillus sphaericus RFL1285
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Petrusyte, M., Maneliene, Z., Capskaya, L., Kiuduliene, L., Butkus, V., Unpublished observations.

<1>Bsh1365I
<2>BsaBI,Bco63I,Bco631I,Bse8I,Bse631I,BseJI,BsiBI,BsrBRI,MamI,UbaN6I
<3>GATNN^NNATC
<4>
<5>Bacillus sphaericus RFL1365
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Bitinaite, J., Maneliene, Z., Kiuduliene, L., Butkus, V., Unpublished observations.

<1>BshAI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus
<6>WHO/CCBC 1691
<7>
<8>Clark, D., Unpublished observations.

<1>Bsh108AI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus sphaericus 108A
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>BshBI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus
<6>WHO/CCBC 1881
<7>
<8>Clark, D., Unpublished observations.

<1>BshCI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus
<6>WHO/CCBC 2013-6
<7>
<8>Clark, D., Unpublished observations.

<1>BshDI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus
<6>WHO/CCBC 2117-2
<7>
<8>Clark, D., Unpublished observations.

<1>BshEI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus
<6>WHO/CCBC 2362
<7>
<8>Clark, D., Unpublished observations.

<1>BshFI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Bacillus sphaericus
<6>WHO/CCBC 2500
<7>C
<8>Vlatakis, G., Clark, D., Bouriotis, V., (1989) Nucleic Acids Res., vol. 17, pp. 8882.

<1>BshGI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus sphaericus
<6>V. Bouriotis
<7>
<8>Scarpelis, G., Moissidou, A., Rina, M., Bouriotis, V., (1989) Nucleic Acids Res., vol. 17, pp. 8883.

<1>BshHI
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BsoSI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGTACT
<4>
<5>Bacillus sphaericus DC1
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BshKI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Bacillus sphaericus
<6>V. Bouriotis
<7>
<8>Moissidou, A., Rina, M., Bouriotis, V., (1989) Nucleic Acids Res., vol. 17, pp. 8884.

<1>BshLI
<2>EcoRV,Bsc217I,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Bacillus sphaericus DC2
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BshMI
<2>HpaII,Asp748I,Bco27I,BsaZI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Bacillus sphaericus DC3
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BshNI
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>G^GYRCC
<4>
<5>Bacillus sphaericus TK-45
<6>A. Janulaitis
<7>F
<8>Maniusyte, V., Lazareviciute, L., Jurgelyte, R., Maneliene, Z., Velickiene, Z., Norgeliene, D., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BshTI
<2>AgeI,AsiAI,AsiGI,CsiAI,CspAI,PinAI
<3>A^CCGGT
<4>
<5>Bacillus sphaericus Jo22-024
<6>V. Butkus
<7>F
<8>Rudokas, K., Petrusyte, M., Maneliene, Z., Trinkunaite, L., Kiuduliene, E., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BshVI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus sphaericus CKJ18
<6>Vivantis 182
<7>V
<8>Chee, H.Y., Unpublished observations.

<1>BsiI
<2>BauI,BssSI,Bst2BI
<3>CACGAG(-5/-1)
<4>
<5>Bacillus sphaericus
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.Kh., Kolykhalov, A.A., Rechkunova, N.I., Dedkov, V.S., Zhilkin, P.A., (1990) Mol. Biol. (Mosk), vol. 24, pp. 244-247.

<1>BsiAI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiBI
<2>BsaBI,Bco63I,Bco631I,Bse8I,Bse631I,BseJI,Bsh1365I,BsrBRI,MamI,UbaN6I
<3>GATNN^NNATC
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Mok, Y.K., Clark, D.R., Kam, K.M., Shaw, P.C., (1990) Nucleic Acids Res., vol. 18, pp. 6740.

<1>BsiCI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiDI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiEI
<2>McrI,BsaOI,BscNI,Bsh1285I,BstMCI,BstZ5I,Uba1303I
<3>CGRY^CG
<4>
<5>Bacillus species
<6>D. Clark
<7>N
<8>Mok, Y.K., Clark, D.R., Kam, K.M., Shaw, P.C., (1990) Nucleic Acids Res., vol. 18, pp. 4954.
Zhu, Z., Unpublished observations.

<1>BsiFI
<2>
<3>?
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiGI
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Shaw, P.C., Clark, D.R., Kam, K.M., Mok, Y.K., (1991) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 91, pp. 199.

<1>BsiHI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiHKAI
<2>HgiAI,Alw21I,AspHI,Bbv12I,Bfu1570I,BsaGI,Bsh45I,Bsm6I,BsmPI,Hpy8III,HpyF7II,HpyF46II,MspV281I,Pph3215I
<3>GWGCW^C
<4>?(5)
<5>Bacillus stearothermophilus
<6>P.C. Shaw
<7>N
<8>Lee, K.-F., Shi, S.-D., Kam, K.-M., Shaw, P.-C., (1992) Nucleic Acids Res., vol. 20, pp. 921.
Zhu, Z., Unpublished observations.

<1>BsiHKCI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>
<5>Bacillus species HKC
<6>P.M. Skowron
<7>QX
<8>Skowron, P.M., Unpublished observations.

<1>BsiJI
<2>
<3>?
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiKI
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Rina, M., Clark, D., Bouriotis, V., (1990) Nucleic Acids Res., vol. 18, pp. 1655.

<1>BsiLI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiMI
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiNI
<2>
<3>?
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiOI
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiPI
<2>
<3>?
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiQI
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>T^GATCA
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiRI
<2>
<3>?
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiSI
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>C^CGG
<4>
<5>Bacillus species
<6>D. Clark
<7>C
<8>Rina, M., Bouriotis, V., (1990) Nucleic Acids Res., vol. 18, pp. 1654.

<1>BsiTI
<2>
<3>?
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiUI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Shaw, P.C., Clark, D.R., Kam, K.M., Mok, Y.K., (1991) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 91, pp. 199.

<1>BsiVI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiWI
<2>SplI,BpuB5I,BsmWI,BvuBI,MaeK81I,Pfl23II,PfuNI,PpuAI,PspLI,SmaAI,SplAI,SspKI,SunI
<3>C^GTACG
<4>
<5>Bacillus species
<6>D. Clark
<7>MNO
<8>Clark, D.R., Klein, S., Roberts, R.J., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Zhu, Z., Unpublished observations.

<1>BsiXI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus species X
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsiYI
<2>AfiI,BflI,Bsc4I,Bsc107I,Bse23I,BseLI,BslI,BsmYI,Bst22I
<3>CCNNNNN^NNGG
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Mok, Y.K., Clark, D.R., Kam, K.M., Shaw, P.C., (1991) Nucleic Acids Res., vol. 19, pp. 2321-2323.

<1>BsiZI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Bacillus species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BslI
<2>BsiYI,AfiI,BflI,Bsc4I,Bsc107I,Bse23I,BseLI,BsmYI,Bst22I
<3>CCNNNNN^NNGG
<4>?(4)
<5>Bacillus species
<6>NEB 606
<7>NW
<8>Cowan, D., Ward, J., Pelletier, J.J., Morgan, R., Unpublished observations.
Hsieh, P.-C., Xiao, J.-P., O'Loane, D., Xu, S.-Y., (2000) J. Bacteriol., vol. 182, pp. 949-955.

<1>BslFI
<2>FinI,BpuNI,BpuSI,BscWI,BsmFI,BspLU11III,BstOZ616I,FaqI
<3>GGGAC(10/14)
<4>
<5>Bacillus stearothermophilus FI
<6>S.K. Degtyarev
<7>I
<8>Nadeev, A.N., Kashirina, J.G., Nayakshina, T.N., Dedkov, V.S., Mezentseva, N.V., Tomilova, J.E., Degtyarev, S.K., Unpublished observations.

<1>BsmI
<2>Asp26HI,Asp27HI,Asp35HI,Asp36HI,Asp40HI,Asp50HI,BmaHI,BsaMI,BscCI,Mva1269I,PctI,Uba1382I,Uba1415I
<3>GAATGC(1/-1)
<4>
<5>Bacillus stearothermophilus NUB36
<6>N. Welker
<7>JMNOSW
<8>Christ, C., Ingalls, D., Unpublished observations.
Myers, P.A., Roberts, R.J., Unpublished observations.
Zhou, J., Zhu, Z., Xu, S.Y., US Patent Office, 2002.

<1>Bsm6I
<2>HgiAI,Alw21I,AspHI,Bbv12I,Bfu1570I,BsaGI,Bsh45I,BsiHKAI,BsmPI,Hpy8III,HpyF7II,HpyF46II,MspV281I,Pph3215I
<3>GWGCW^C
<4>
<5>Bacillus sp
<6>Vivantis 61
<7>
<8>Chee, H.Y., Unpublished observations.

<1>BsmAI
<2>Alw26I,BcoDI,BscQII,BsoMAI,BstMAI
<3>GTCTC(1/5)
<4>?(5)
<5>Bacillus stearothermophilus A664
<6>Z. Chen
<7>N
<8>Kong, H., Morgan, R.D., Chen, Z., (1990) Nucleic Acids Res., vol. 18, pp. 686.
Zhou, J., Xu, S., Unpublished observations.

<1>BsmBI
<2>Esp3I,BstGZ53I,Esp16I,Esp23I
<3>CGTCTC(1/5)
<4>?(5),?(4)
<5>Bacillus stearothermophilus B61
<6>NEB 857
<7>N
<8>Chen, Z., Morgan, R., Unpublished observations.
Xu, S.-Y., Unpublished observations.
Xu, S.-Y., Dore, A., Hume, A., Pelletier, J., Zhou, J., European Patent Office, 2003.
Xu, S.-Y., Dore, A., Hume, A., Pelletier, J., Zhou, J., US Patent Office, 2004.

<1>BsmCI
<2>BsaXI,BsmDI,BsmXI
<3>ACNNNNNCTCC
<4>
<5>Bacillus stearothermophilus 21P
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsmDI
<2>BsaXI,BsmCI,BsmXI
<3>ACNNNNNCTCC
<4>
<5>Bacillus stearothermophilus 25B
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsmEI
<2>PleI,BspD6I,MlyI,PpsI,SchI
<3>GAGTC
<4>
<5>Bacillus stearothermophilus E505
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsmFI
<2>FinI,BpuNI,BpuSI,BscWI,BslFI,BspLU11III,BstOZ616I,FaqI
<3>GGGAC(10/14)
<4>
<5>Bacillus stearothermophilus F
<6>Z. Chen
<7>N
<8>Chen, Z., Morgan, R., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Zhu, Z., Unpublished observations.

<1>BsmGI
<2>Bsp1407I,AauI,BsmRI,BsrGI,Bst170I,BstAUI,Ssp4800I,SspBI
<3>TGTACA
<4>
<5>Bacillus stearothermophilus G170
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsmGII
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Bacillus stearothermophilus G170
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsmHI
<2>HaeII,AccB2I,BfoI,Bme142I,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGCY
<4>
<5>Bacillus stearothermophilus H426
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsmNI
<2>SfaNI,BhaI,BmsI,BscAI,BscUI,BspST5I,Bst19I,CjeP338II,LweI,PhaI
<3>GCATC
<4>
<5>Bacillus stearothermophilus N365
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsmPI
<2>HgiAI,Alw21I,AspHI,Bbv12I,Bfu1570I,BsaGI,Bsh45I,BsiHKAI,Bsm6I,Hpy8III,HpyF7II,HpyF46II,MspV281I,Pph3215I
<3>GWGCWC
<4>
<5>Bacillus stearothermophilus CPW548
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsmRI
<2>Bsp1407I,AauI,BsmGI,BsrGI,Bst170I,BstAUI,Ssp4800I,SspBI
<3>T^GTACA
<4>
<5>Bacillus species FRIM
<6>Vivantis 224
<7>
<8>Chee, H.Y., Unpublished observations.

<1>BsmSI
<2>StyI,BssT1I,Bst224I,CfrBI,Eco130I,Eco208II,EcoT14I,EcoT104I,ErhI,ErhB9II,SblAI,SblBI,SblCI,Uba1311I
<3>C^CWWGG
<4>
<5>Bacillus stearothermophilus CP114
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.
Wright, D.J., Unpublished observations.

<1>BsmWI
<2>SplI,BpuB5I,BsiWI,BvuBI,MaeK81I,Pfl23II,PfuNI,PpuAI,PspLI,SmaAI,SplAI,SspKI,SunI
<3>CGTACG
<4>
<5>Bacillus stearothermophilus N658
<6>X.S. Pan
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BsmXI
<2>BsaXI,BsmCI,BsmDI
<3>ACNNNNNCTCC
<4>
<5>Bacillus stearothermophilus GY
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BsmXII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus stearothermophilus GY
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BsmYI
<2>BsiYI,AfiI,BflI,Bsc4I,Bsc107I,Bse23I,BseLI,BslI,Bst22I
<3>CCNNNNNNNGG
<4>
<5>Bacillus stearothermophilus Y36
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsnI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Bacillus sp. SJN7
<6>Vivantis 78
<7>V
<8>Chee, H.Y., Unpublished observations.

<1>BsoI
<2>ScrFI,Bme1390I,BmrFI,BsaCI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>
<5>Bacillus stearothermophilus JN791
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>Bso31I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC(1/5)
<4>
<5>Bacillus stearothermophilus E31
<6>S.K. Degtyarev
<7>IV
<8>Shinkarenko, N.M., Lebedeva, N.A., Dedkov, V.S., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>BsoAI
<2>EcoRV,Bsc217I,BshLI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Bacillus stearothermophilus JN1891
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsoBI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>?(4)
<5>Bacillus stearothermophilus JN2091
<6>D. Clark
<7>N
<8>Clark, D., Unpublished observations.
Fomenkov, A., Dila, D.K., Raleigh, E.A., Xu, S.-Y., European Patent Office, 2004.
Ruan, H., Lunnen, K.D., Scott, M.E., Moran, L.S., Slatko, B.E., Pelletier, J.J., Hess, E.J., Benner, J., Wilson, G.G., Xu, S.-Y., (1996) Mol. Gen. Genet., vol. 252, pp. 695-699.
Spargo, C.A., Unpublished observations.

<1>BsoCI
<2>SduI,AocII,Bka1125I,BmyI,Bsp1286I,BspLS2I,BstZ15I,HpyF36IV,HpyF47I,MhlI,Mlu40I,NspII,TseAI,Uba1362I
<3>GDGCH^C
<4>
<5>Bacillus stearothermophilus AU891
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.
Wright, D.J., Unpublished observations.

<1>BsoDI
<2>XmaIII,AaaI,BseX3I,BstZI,EagI,EclXI,Eco52I,SenPT16I,TauII,Tsp504I
<3>CGGCCG
<4>
<5>Bacillus stearothermophilus SE2091
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsoEI
<2>EcoNI,Bpu1268I,BstENI,BstWI,Uba1289I,Uba1290I,Uba1308I,Uba1309I,Uba1310I,XagI
<3>CCTNNNNNAGG
<4>
<5>Bacillus stearothermophilus OC391
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsoFI
<2>Fnu4HI,Bli1904II,Bpu1811I,Bsp6I,BssFI,BssXI,BthCI,Cac824I,CcoP215I,CcoP216I,FbrI,Fsp4HI,ItaI,LlaDII,SatI,Uur960I
<3>GC^NGC
<4>
<5>Bacillus stearothermophilus F66
<6>Z. Chen
<7>
<8>Chen, Z., Morgan, R., Unpublished observations.

<1>BsoGI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Bacillus stearothermophilus Lipari 29
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsoGII
<2>
<3>?
<4>
<5>Bacillus stearothermophilus Lipari 29
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsoHI
<2>BsrI,BscHI,Bse1I,BseNI,BsrSI,Bst11I,Tsp1I
<3>ACTGG
<4>
<5>Bacillus stearothermophilus Lipari 28
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>BsoJI
<2>BglI,Bpu86I,BseB631I,Psp1009I,Tsp219I,Tsp8EI,VanI
<3>GCCNNNNNGGC
<4>
<5>Bacillus stearothermophilus Azores9582A
<6>D. Clark
<7>
<8>Jones, S., Hill, V.J., Vincent, S., Clark, D.R., Unpublished observations.

<1>BsoKI
<2>SecI,BsaJI,BseDI,BssECI,BstZ10I,Hpy99IV,HpyF10III,HpyF61II,HpyF67IV,Uba1442I
<3>CCNNGG
<4>
<5>Bacillus stearothermophilus SA124-20
<6>D. Clark
<7>
<8>Lam, P., Clark, D.R., Unpublished observations.

<1>BsoMAI
<2>BsmAI,Alw26I,BcoDI,BscQII,BstMAI
<3>GTCTC(1/5)
<4>
<5>Bacillus stearothermophilus MA
<6>S.K. Degtyarev
<7>
<8>Shinkarenko, N.M., Dedkov, V.S., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>BsoPI
<2>BsePI,BscEI,BsrHI,BssBI,BssHII,BstBZ153I,CfrJ5I,Eco143I,Eco152I,Esp7I,Esp8I,Kpn30I,McaTI,PauI,PteI,TtmII,Uba69I
<3>GCGCGC
<4>
<5>Bacillus stearothermophilus P9
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BsoSI
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGTACT
<4>
<5>Bacillus stearothermophilus SR65
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BspI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus sphaericus
<6>P.C. Shaw
<7>
<8>Leung, S.M., Kam, K.M., Shaw, P.C., Unpublished observations.

<1>Bsp2I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus species RFL2
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp4I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus species RFL4
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp5I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Bacillus species RFL5
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp6I
<2>Fnu4HI,Bli1904II,Bpu1811I,BsoFI,BssFI,BssXI,BthCI,Cac824I,CcoP215I,CcoP216I,FbrI,Fsp4HI,ItaI,LlaDII,SatI,Uur960I
<3>GC^NGC
<4>?(5)
<5>Bacillus species RFL6
<6>A. Janulaitis
<7>
<8>Lubys, A., Janulaitis, A., (1995) Gene, vol. 157, pp. 25-29.

<1>Bsp6II
<2>Eco57I,AcuI,BspD6II,BspKT5I,Eco112I,Eco125I,FsfI
<3>CTGAAG
<4>
<5>Bacillus species RFL6
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.

<1>Bsp7I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Bacillus species RFL7
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp8I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Bacillus species RFL8
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp9I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL9
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp12I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Bacillus species RFL12
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp12II
<2>
<3>?
<4>
<5>Bacillus species RFL12
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp13I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>
<5>Bacillus species 13
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.K., Unpublished observations.

<1>Bsp16I
<2>EcoRV,Bsc217I,BshLI,BsoAI,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Bacillus species RFL16
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp17I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus species RFL17
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp18I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL18
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp19I
<2>NcoI,AteI,Bse19I,NspSAIII
<3>C^CATGG
<4>
<5>Bacillus species 19
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.K., Unpublished observations.

<1>Bsp21I
<2>Cfr10I,Bco118I,BscRI,Bse118I,Bse634I,BsrFI,BssAI,BstB7SI,NmeDI,TseDI
<3>RCCGGY
<4>
<5>Bacillus species RFL21
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.

<1>Bsp22I
<2>GsuI,Bco35I,BpmI,Bsp28I,BspJ74I,Bth1795I,Uba1437I,Uba1444I
<3>CTGGAG
<4>
<5>Bacillus species RFL22
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.

<1>Bsp23I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus species
<6>ITI 23
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Bsp24I
<2>
<3>(8/13)GACNNNNNNTGG(12/7)
<4>
<5>Bacillus species 24
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Rechkunova, N.I., Zernov, Y.P., Dedkov, V.S., Chizikov, V.E., Van Calligan, M., Williams, R., Murray, E., (1993) Gene, vol. 131, pp. 93-95.

<1>Bsp28I
<2>GsuI,Bco35I,BpmI,Bsp22I,BspJ74I,Bth1795I,Uba1437I,Uba1444I
<3>CTGGAG
<4>
<5>Bacillus species RFL28
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp29I
<2>NlaIV,AspNI,BcrI,BmiI,BsaEI,BscBI,BspLI,BssI,HpyF44II,HpyF73I,NgoBV,NgoGV,PspN4I,Rlu3I,Uba1305I,Uba1445I
<3>GGNNCC
<4>
<5>Bacillus species RFL29
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp30I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus species RFL30
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp42I
<2>
<3>?
<4>
<5>Bacillus sphaericus SL42
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>Bsp43I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus species RFL43
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Bsp44I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Bacillus species
<6>ITI 44
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Bsp44II
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus species
<6>ITI 44
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Bsp46I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus species RFL46
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp47I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Bacillus species RFL47
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp48I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Bacillus species RFL48
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp49I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL49
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp50I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>
<5>Bacillus species RFL50
<6>A. Janulaitis
<7>
<8>Davenis, A., Lubys, A., Janulaitis, A., Unpublished observations.
Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.
Janulaitis, A., Maneliene, Z., Butkus, V., Unpublished observations.

<1>Bsp51I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL51
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp52I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL52
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp53I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>
<5>Bacillus species RFL53
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp54I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL54
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp55I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Bacillus species RFL55
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp56I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Bacillus species RFL56
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp57I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL57
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp58I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL58
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp59I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL59
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp60I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL60
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp61I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL61
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp63I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Bacillus sphaericus 63
<6>S.Y. Ye
<7>
<8>Yan, P.-F., Ye, S.-Y., Wang, P.-Z., Li, Q.-L., Lu, Y.-Y., Zhou, B., (1982) Acta Biochim. Biophys. Sin., vol. 14, pp. 151-158.

<1>Bsp64I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus sphaericus 64
<6>S.Y. Ye
<7>
<8>Yan, P.-F., Ye, S.-Y., Wang, P.-Z., Li, Q.-L., Lu, Y.-Y., Zhou, B., (1982) Acta Biochim. Biophys. Sin., vol. 14, pp. 151-158.

<1>Bsp65I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL65
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp66I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL66
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp67I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus sphaericus 67
<6>S.Y. Ye
<7>
<8>Yan, P.-F., Ye, S.-Y., Wang, P.-Z., Li, Q.-L., Lu, Y.-Y., Zhou, B., (1982) Acta Biochim. Biophys. Sin., vol. 14, pp. 151-158.

<1>Bsp68I
<2>NruI,AmaSI,BtuMI,Mlu9273I,MluB2I,PspDI,RruI,SalDI,Sbo13I,Sna3286I,SpoI,Uba1117I,Uba1386I,VchO70I
<3>TCG^CGA
<4>
<5>Bacillus species RFL68
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.
Janulaitis, A., Maneliene, Z., Butkus, V., Unpublished observations.

<1>Bsp70I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Bacillus species RFL70
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp71I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Bacillus species RFL71
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp72I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL72
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp73I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>
<5>Bacillus species RFL73
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp74I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus sphaericus 74
<6>S.Y. Ye
<7>
<8>Yan, P.-F., Ye, S.-Y., Wang, P.-Z., Li, Q.-L., Lu, Y.-Y., Zhou, B., (1982) Acta Biochim. Biophys. Sin., vol. 14, pp. 151-158.

<1>Bsp76I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus sphaericus 76
<6>S.Y. Ye
<7>
<8>Yan, P.-F., Ye, S.-Y., Wang, P.-Z., Li, Q.-L., Lu, Y.-Y., Zhou, B., (1982) Acta Biochim. Biophys. Sin., vol. 14, pp. 151-158.

<1>Bsp78I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus sphaericus 78
<6>S.Y. Ye
<7>
<8>Yan, P.-F., Ye, S.-Y., Wang, P.-Z., Li, Q.-L., Lu, Y.-Y., Zhou, B., (1982) Acta Biochim. Biophys. Sin., vol. 14, pp. 151-158.

<1>Bsp81I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus species RFL81
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp82I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Bacillus species RFL82
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp84I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus species RFL84
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp87I
<2>PmaCI,AcvI,BbrPI,BcoAI,Eco72I,Pgl34I,PmlI,PshCI,PshDI,Psp38I,PspBI,PspCI,VpaK3AI,VpaK3BI
<3>CACGTG
<4>
<5>Bacillus species RFL87
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp90I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Bacillus species
<6>ITI 90
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Bsp90II
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus species
<6>ITI 90
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Bsp91I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL91
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp92I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Bacillus species RFL92
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp93I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus species RFL93
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp98I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>?(4)
<5>Bacillus species RFL98
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.
Kriukiene, E., Lubys, A., (1998) Biologija, vol. 1, pp. 55-59.

<1>Bsp100I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Bacillus species RFL100
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp101I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Bacillus species
<6>ITI 101
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Bsp102I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Bacillus species
<6>ITI 102
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Bsp103I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Bacillus species RFL103
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp104I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Bacillus species
<6>ITI 104
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Bsp105I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus sphaericus 105
<6>Q.-L. Li
<7>
<8>Yan, P.-F., Ye, S.-Y., Wang, P.-Z., Li, Q.-L., Lu, Y.-Y., Zhou, B., (1982) Acta Biochim. Biophys. Sin., vol. 14, pp. 151-158.

<1>Bsp106I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>5(6)
<5>Bacillus sphaericus 106
<6>B. Zhou
<7>
<8>Nelson, M., McClelland, M., Unpublished observations.
Yan, P.F., Zhou, B., Unpublished observations.

<1>Bsp107I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus species RFL107
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp108I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus species RFL108
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp116I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Bacillus species RFL116
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp117I
<2>HgiJII,BanII,BpuI,BscMI,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Bacillus species RFL117
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp119I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Bacillus species RFL119
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Maneliene, Z., Butkus, V., Unpublished observations.
Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Bsp120I
<2>ApaI,EciEI,PpeI,Psp30I,PspOMI,Uba1156I,Uba1157I,Uba1165I,Uba1202I,Uba1241I,Uba1368I
<3>G^GGCCC
<4>
<5>Bacillus species RFL120
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.
Janulaitis, A., Maneliene, Z., Butkus, V., Unpublished observations.

<1>Bsp121I
<2>SphI,Asp5HI,BbuI,BscOI,BtgAII,CglAI,PaeI,PaeCI,PfaAIII,RspLKI,SpaHI,SpaXI,Uba1162I,Uba1226I,VchO68I
<3>GCATGC
<4>
<5>Bacillus species RFL121
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Bsp122I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL122
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Bsp123I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>
<5>Bacillus species 123
<6>N.I. Matvienko
<7>
<8>Alzhanova, D.V., Alzhanov, D.T., Zheleznaya, L.A., Matvienko, N.I., (1998) Biokhimiia, vol. 63, pp. 207-211.

<1>Bsp125I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus species RFL125
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp126I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus species RFL126
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp127I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus species RFL127
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp128I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Bacillus species RFL128
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp129I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Bacillus species RFL129
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp130I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus species RFL130
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp131I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus species RFL131
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp132I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Bacillus species RFL132
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp133I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Bacillus species RFL133
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp135I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL135
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp136I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL136
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp137I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus species RFL137
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp138I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL138
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp139I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Bacillus species RFL139
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp140I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Bacillus species RFL140
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp141I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Bacillus species RFL141
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp142I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Bacillus species RFL142
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp143I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus species RFL143
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Unpublished observations.

<1>Bsp143II
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGC^Y
<4>
<5>Bacillus species RFL143
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.
Lubiene, J., Lubys, A., Janulaitis, A., Unpublished observations.

<1>Bsp144I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus species RFL144
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp145I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus species cy145
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>Bsp146I
<2>ApaLI,AaqI,Alw44I,AmeI,DaqI,Pfl23I,Pfr12I,PliI,ScoNI,SnoI,Uba1203I,Uba1387I,VneI
<3>GTGCAC
<4>
<5>Bacillus species RFL146
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp147I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL147
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp148I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Bacillus species RFL148
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp151I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Bacillus species
<6>ITI 151
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Bsp211I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Bacillus sphaericus 211
<6>P.F. Yan
<7>
<8>Yan, P.-F., Ye, S.-Y., Wang, P.-Z., Li, Q.-L., Lu, Y.-Y., Zhou, B., (1982) Acta Biochim. Biophys. Sin., vol. 14, pp. 151-158.

<1>Bsp226I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus 226
<6>P.F. Yan
<7>
<8>Yan, P.-F., Ye, S.-Y., Wang, P.-Z., Li, Q.-L., Lu, Y.-Y., Zhou, B., (1982) Acta Biochim. Biophys. Sin., vol. 14, pp. 151-158.

<1>Bsp228I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Bacillus species
<6>ITI 228
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Bsp233I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Bacillus species
<6>ITI 233
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Bsp241I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Bacillus species
<6>ITI 241
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Bsp268I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus species cy268
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>Bsp317I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Bacillus species cy317
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>Bsp423I
<2>BbvI,AlwXI,BchI,BsaUI,BseKI,BseXI,BsrVI,Bst12I,Bst71I,BstV1I,LfeI,Lsp1109I
<3>GCAGC(8/12)
<4>
<5>Bacillus species 423
<6>P. Westermann
<7>
<8>Sellmann, E., Knoblich, I.-M., Kaluza, K., Frey, B., Schmitz, G.G., Westermann, P., (1992) Nucleic Acids Res., vol. 20, pp. 2377.

<1>Bsp508I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Bacillus species
<6>ITI 225
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Bsp519I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCY^C
<4>
<5>Bacillus species 519
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>Bsp548I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>
<5>Bacillus species
<6>ITI 439
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Bsp774I
<2>
<3>?
<4>
<5>Bacillus sphaericus IAB 774
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>Bsp881I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus IAB 881
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>Bsp1260I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Bacillus sphaericus RFL1260
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp1261I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus RFL1261
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Bsp1286I
<2>SduI,AocII,Bka1125I,BmyI,BsoCI,BspLS2I,BstZ15I,HpyF36IV,HpyF47I,MhlI,Mlu40I,NspII,TseAI,Uba1362I
<3>GDGCH^C
<4>?(5)
<5>Bacillus sphaericus
<6>IAM 1286
<7>JKNR
<8>Myers, P.A., Roberts, R.J., Unpublished observations.
Schildkraut, I., Christ, C., Unpublished observations.
Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.
Zhu, Z., Unpublished observations.

<1>Bsp1407I
<2>AauI,BsmGI,BsmRI,BsrGI,Bst170I,BstAUI,Ssp4800I,SspBI
<3>T^GTACA
<4>
<5>Bacillus stearothermophilus RFL1407
<6>A. Janulaitis
<7>FK
<8>Petrusyte, M., Rudokas, K., Maneliene, Z., Kiuduliene, E., Butkus, V., Janulaitis, A., (1993) Nucleic Acids Res., vol. 21, pp. 2514.

<1>Bsp1566I
<2>
<3>?
<4>
<5>Bacillus sphaericus IAB 1566
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>Bsp1591I
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>GGTNACC
<4>
<5>Bacillus sphaericus 1591
<6>NEB 1300
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>Bsp1591II
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Bacillus sphaericus 1591
<6>NEB 1300
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>Bsp1593I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus 1593
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>Bsp1720I
<2>EspI,BlpI,Bpu1102I,BpuGCI,CelII,Uba1221I,Uba1222I,Uba1284I,Uba1320I
<3>GC^TNAGC
<4>
<5>Bacillus species 1720
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.Kh., Kolyhalov, A.A., Rechkunova, N.T., Tepavicharova, I.I., Mechandjiska, L.I., Builieva, E.I., (1991) Nucleic Acids Res., vol. 19, pp. 2504.

<1>Bsp1883I
<2>
<3>?
<4>
<5>Bacillus sphaericus 1883
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>Bsp1894I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Bacillus sphaericus 1894
<6>KCTC 1188
<7>
<8>Ryu, C.J., Lee, C.H., Yoo, O.J., (1989) Korean Biochem. J., vol. 22, pp. 444-447.

<1>Bsp2013I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus 2013.6
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>Bsp2095I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus sphaericus 2095
<6>S.K. Degtyarev
<7>
<8>Repin, V.E., Rechkunova, N.I., Degtyarev, S.K., Hachaturyan, A.A., Afrikyan, E.K., (1989) Biol. J. Armenia, vol. 42, pp. 969-972.

<1>Bsp2362I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus 2362
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>Bsp2500I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus 2500
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>Bsp4009I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Bacillus species 4009
<6>N.N. Sokolov
<7>
<8>Korolev, S.V., Sokolov, N.N., Rina, M., Eldarov, M.A., Omelyanyuk, N.M., Markaki, M., Skryabin, K.G., Bouriotis, V., (1998) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 32-35.

<1>Bsp9002I
<2>
<3>?
<4>
<5>Bacillus sphaericus 9002
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>BspAI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus sphaericus JL4B
<6>R. Mullings
<7>
<8>Mullings, R., Evans, L.R., Brown, N.L., (1986) FEMS Microbiol. Lett., vol. 37, pp. 237-240.

<1>BspA2I
<2>AvrII,AspA2I,AvrBII,BlnI,XmaJI
<3>C^CTAGG
<4>
<5>Bacillus species A2
<6>S.K. Degtyarev
<7>
<8>Abdurashitov, M.A., Shinkarenko, N.M., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>Bsp153AI
<2>PvuII,BamGI,BavI,BavAI,BavBI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>
<5>Bacillus species 153A
<6>V. Bouriotis
<7>
<8>Kalugin, A.A., Rina, M., Eldarov, M.A., Markaki, M., Korolev, S.V., Samko, O.T., Khoroshutina, E.B., Sikolov, N.N., Bouriotis, V., (1996) Bioorg. Khim., vol. 22, pp. 108-110.

<1>BspAAI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Bacillus species AA
<6>N.I. Matvienko
<7>
<8>Alzhanov, D.T., Alzhanova, D.V., Zheleznaya, L.A., Matvienko, N.I., (1998) Biokhimiia, vol. 63, pp. 636-645.

<1>BspAAII
<2>XbaI,BspLU11II,BsrXI,Msp23I
<3>T^CTAGA
<4>
<5>Bacillus species AA
<6>N.I. Matvienko
<7>
<8>Alzhanov, D.T., Alzhanova, D.V., Zheleznaya, L.A., Matvienko, N.I., (1998) Biokhimiia, vol. 63, pp. 636-645.

<1>BspAAIII
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Bacillus species AA
<6>N.I. Matvienko
<7>
<8>Alzhanov, D.T., Alzhanova, D.V., Zheleznaya, L.A., Matvienko, N.I., (1998) Biokhimiia, vol. 63, pp. 636-645.

<1>BspACI
<2>AciI,SsiI
<3>CCGC(-3/-1)
<4>
<5>Bacillus species AC
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Janobilova, Z., Tomilova, J.E., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>BspANI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Bacillus sp. AN
<6>P.M. Skowron
<7>
<8>Skowron, P.M., Unpublished observations.

<1>BspBI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Bacillus sphaericus JL14
<6>R. Mullings
<7>
<8>Mullings, R., Evans, L.R., Brown, N.L., (1986) FEMS Microbiol. Lett., vol. 37, pp. 237-240.

<1>BspBII
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Bacillus sphaericus JL14
<6>R. Mullings
<7>
<8>Mullings, R., Evans, L.R., Brown, N.L., (1986) FEMS Microbiol. Lett., vol. 37, pp. 237-240.

<1>BspB2I
<2>
<3>?
<4>
<5>Bacillus species B2I
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Zernov, Y.P., Rechkunova, N.I., Degtyarev, S.Kh., (1990) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 17-18.

<1>BspBDG2I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus BDG2
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>BspBRI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Bacillus species
<6>C.M. Morel
<7>
<8>Cruz, A.K., Pires, M.Q., Lima, V.G., Morel, C.M., (1989) Braz. J. Med. Biol. Res., vol. 22, pp. 1321-1328.

<1>BspBS31I
<2>BbvII,Bbr7I,BbsI,Bbv16II,Bco102II,BpiI,BpuAI,BsaVI,Bsc91I,BscKI,BspIS4I,BspTS514I,BspVI,BstBS32I,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC(2/6)
<4>
<5>Bacillus species BS31
<6>N.I. Matvienko
<7>
<8>Kovalevskaya, N.P., Zelinskaya, N.V., Zheleznaya, L.A., Matvienko, N.I., (1993) Bioorg. Khim., vol. 19, pp. 1073-1076.

<1>BspBSE18I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus BSE18
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>BspBake1I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus Bake 1
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>BspCI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGAT^CG
<4>
<5>Bacillus species C1
<6>T.G. Simcox
<7>
<8>Nelson, M., McClelland, M., Unpublished observations.

<1>BspCHE15I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus CHE 15S
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>BspCNI
<2>BseMII
<3>CTCAG(9/7)
<4>?(6)
<5>Bacillus species 1310
<6>NEB 1303
<7>N
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Nkenfou, C., Unpublished observations.
Nkenfou, C., (2002) Ph.D. Thesis, University of Yaounde I, Cameroon (Yaounde), pp. 1-226.
Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.
Rausch, C., Nkenfou, C., Morgan, R.D., Unpublished observations.

<1>BspDI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus species
<6>NEB 595
<7>N
<8>Kong, H., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BspD6I
<2>PleI,BsmEI,MlyI,PpsI,SchI
<3>GACTC(4/6)
<4>
<5>Bacillus species D6
<6>N.I. Matvienko
<7>
<8>Perevyazova, T.A., Rogulin, E.A., Zheleznaya, L.A., Matvienko, N.I., (2003) Biokhimiia, vol. 68, pp. 1203-1207.
Yunusova, A.K., Rogulin, E.A., Artyukh, R.I., Zheleznaya, L.A., Matvienko, N.I., (2006) Biokhimiia, vol. 71, pp. 1002-1008.

<1>BspD6II
<2>Eco57I,AcuI,Bsp6II,BspKT5I,Eco112I,Eco125I,FsfI
<3>CTGAAG
<4>
<5>Bacillus species D6
<6>N.I. Matvienko
<7>
<8>Zheleznaya, L.A., Perevyazova, T.A., Alzhanova, D.V., Matvienko, N.I., (2001) Biokhimiia, vol. 66, pp. 1215-1220.

<1>BspD6III
<2>
<3>?
<4>
<5>Bacillus species D6
<6>N.I. Matvienko
<7>
<8>Zheleznaya, L.A., Perevyazova, T.A., Alzhanova, D.V., Matvienko, N.I., (2001) Biokhimiia, vol. 66, pp. 1215-1220.

<1>BspEI
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>
<5>Bacillus species
<6>NEB 553
<7>N
<8>Kong, H., Hoffman, L., Unpublished observations.
Lunnen, K., Nwankwo, D., Wilson, G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Nwankwo, D.O., (1995) Gene, vol. 157, pp. 31-35.

<1>BspFI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus species
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Samko, O.T., Anikeitcheva, N.V., Kalugin, A.A., Khoroshutina, E.B., Plutalov, O.V., Birikh, K.R., Berlin, Y.A., (1994) Bioorg. Khim., vol. 20, pp. 1334-1341.

<1>BspF4I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Bacillus species F4
<6>N.I. Matvienko
<7>
<8>Zharmukhamedova, T.Y., Privezencova, N.G., Shishova, O.V., Shiryaev, S.A., Zheleznaya, L.A., Matvienko, N.I., (1999) Biokhimiia, vol. 64, pp. 697-702.

<1>BspF53I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Bacillus species cy53
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BspF105I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Bacillus species cy105
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BspFNI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>
<5>Bacillus stearothermophilus FN
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Nayakshina, T.N., Tomilova, J.E., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>BspGI
<2>
<3>CTGGAC
<4>
<5>Bacillus species 5802
<6>U. Mayr
<7>
<8>Kaluza, K., Unpublished observations.

<1>BspGHA1I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus sphaericus GHA 1
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>BspHI
<2>CciI,PagI,RcaI,RhcI,RspXI
<3>T^CATGA
<4>?(6)
<5>Bacillus species H
<6>NEB 394
<7>N
<8>Hall, D., Camp, R., Morgan, R., Hoffman, L., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>BspH22I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Bacillus species
<6>ITI 22
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>BspH43I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Bacillus species
<6>ITI 43
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>BspH103I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Bacillus species
<6>ITI 103
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>BspH106I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Bacillus species
<6>ITI 106
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>BspH106II
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus species
<6>ITI 106
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>BspH226I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Bacillus species
<6>ITI 226
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>BspIAB59I
<2>
<3>?
<4>
<5>Bacillus sphaericus IAB 59
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>BspIS4I
<2>BbvII,Bbr7I,BbsI,Bbv16II,Bco102II,BpiI,BpuAI,BsaVI,Bsc91I,BscKI,BspBS31I,BspTS514I,BspVI,BstBS32I,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC(2/6)
<4>?(6)
<5>Bacillus species IS4
<6>N.I. Matvienko
<7>
<8>Kovalevskaya, N.P., Zelinskaya, N.V., Zheleznaya, L.A., Matvienko, N.I., (1993) Bioorg. Khim., vol. 19, pp. 1073-1076.
Zelinskaya, N.V., Kovalevskaya, N.P., Matvienko, N.N., Zheleznaya, L.A., Matvienko, N.I., (1995) Biokhimiia, vol. 60, pp. 1435-1448.

<1>BspJI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus species
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Fitsner, A.B., Anikeitcheva, N.V., Kalugin, A.A., Samko, O.T., Unpublished observations.

<1>BspJII
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus species
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Anikeitcheva, N.V., Samko, O.T., Kalugin, A.A., Fitsner, A.B., Unpublished observations.

<1>BspJ64I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus species RFL64
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>BspJ67I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Bacillus species RFL67
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>BspJ74I
<2>GsuI,Bco35I,BpmI,Bsp22I,Bsp28I,Bth1795I,Uba1437I,Uba1444I
<3>CTGGAG
<4>
<5>Bacillus species RFL74
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>BspJ76I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Bacillus species RFL76
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>BspJ105I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Bacillus species RFL105
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>BspJ106I
<2>KpnI,Acc65I,AhaB8I,Asp718I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Bacillus species RFL106
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>BspKI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Bacillus species K
<6>V.M. Kramarov
<7>
<8>Kramarov, V.M., Unpublished observations.

<1>BspKMI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus species
<6>CAMB 2843
<7>
<8>Malik, K., Riazuddin, S., Unpublished observations.

<1>BspKT5I
<2>Eco57I,AcuI,Bsp6II,BspD6II,Eco112I,Eco125I,FsfI
<3>CTGAAG(16/14)
<4>
<5>Bacillus species
<6>N.I. Matvienko
<7>
<8>Shapovalova, N.I., Zheleznaya, L.A., Matvienko, N.N., Matvienko, N.I., (1994) Biokhimiia, vol. 59, pp. 485-493.

<1>BspKT6I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GAT^C
<4>2(6)
<5>Bacillus species KT6
<6>N.I. Matvienko
<7>
<8>Shapovalova, N.I., Zheleznaja, L.A., Matvienko, N.I., (1993) Nucleic Acids Res., vol. 21, pp. 5794.
Shapovalova, N.I., Zheleznaya, L.A., Matvienko, N.I., (1994) Biokhimiia, vol. 59, pp. 1730-1738.
Zhu, Z., Unpublished observations.

<1>BspKT8I
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>A^AGCTT
<4>
<5>Bacillus species KT8
<6>N.I. Matvienko
<7>
<8>Chernov, A.V., Zheleznaya, L.A., Matvienko, N.I., (1995) Biokhimiia, vol. 60, pp. 1318-1325.

<1>BspK1aI
<2>
<3>?
<4>
<5>Bacillus sphaericus K
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>BspLI
<2>NlaIV,AspNI,BcrI,BmiI,BsaEI,BscBI,Bsp29I,BssI,HpyF44II,HpyF73I,NgoBV,NgoGV,PspN4I,Rlu3I,Uba1305I,Uba1445I
<3>GGN^NCC
<4>
<5>Bacillus species RJ3-212
<6>V. Butkus
<7>F
<8>Lazareviciute, L., Petrusyte, M., Maneliene, Z., Trinkunaite, L., Capskaja, L., Kiuduliene, E., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BspLAI
<2>HhaI,AspLEI,BbtI,BcaI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCG^C
<4>
<5>Bacillus species LA
<6>N.I. Matvienko
<7>
<8>Shiryaev, S.A., Zheleznaya, L.A., Matvienko, N.I., (1997) Biokhimiia, vol. 62, pp. 280-290.

<1>BspLAII
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Bacillus species LA
<6>N.I. Matvienko
<7>
<8>Shiryaev, S.A., Zheleznaya, L.A., Matvienko, N.I., (1997) Biokhimiia, vol. 62, pp. 280-290.

<1>BspLAIII
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>A^AGCTT
<4>
<5>Bacillus species LA
<6>N.I. Matvienko
<7>
<8>Shiryaev, S.A., Zheleznaya, L.A., Matvienko, N.I., (1997) Biokhimiia, vol. 62, pp. 280-290.

<1>BspLRI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus species L
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>BspLS2I
<2>SduI,AocII,Bka1125I,BmyI,BsoCI,Bsp1286I,BstZ15I,HpyF36IV,HpyF47I,MhlI,Mlu40I,NspII,TseAI,Uba1362I
<3>GDGCH^C
<4>
<5>Bacillus species LS2
<6>N.I. Matvienko
<7>
<8>Kovalevskaya, N.P., Zheleznaya, L.A., Matvienko, N.I., (1992) Bioorg. Khim., vol. 18, pp. 1473-1477.

<1>BspLU4I
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>
<5>Bacillus species LU4
<6>N.I. Matvienko
<7>
<8>Svadbina, I.V., Zheleznyakova, E.N., Zheleznaya, L.A., Matvienko, N.I., (2003) Biokhimiia, vol. 68, pp. 429-435.

<1>BspLU11I
<2>PciI,PscI
<3>A^CATGT
<4>
<5>Bacillus species LU11
<6>N.I. Matvienko
<7>
<8>Matvienko, N.N., Zeleznaja, L.A., Matvienko, N.I., (1993) Nucleic Acids Res., vol. 21, pp. 1495.

<1>BspLU11II
<2>XbaI,BspAAII,BsrXI,Msp23I
<3>TCTAGA
<4>
<5>Bacillus species LU11
<6>N.I. Matvienko
<7>
<8>Matvienko, N.N., Zeleznaja, L.A., Matvienko, N.I., (1993) Nucleic Acids Res., vol. 21, pp. 1495.

<1>BspLU11III
<2>FinI,BpuNI,BpuSI,BscWI,BslFI,BsmFI,BstOZ616I,FaqI
<3>GGGAC(10/14)
<4>4(6)
<5>Bacillus species LU11
<6>N.I. Matvienko
<7>
<8>Chernov, A.V., Matvienko, N.N., Zheleznaya, L.A., Matvienko, N.I., (1994) Biokhimiia, vol. 59, pp. 1714-1729.
Lepikhov, K., Tchernov, A., Zheleznaja, L., Matvienko, N., Walter, J., Trautner, T.A., (2001) Nucleic Acids Res., vol. 29, pp. 4691-4698.

<1>BspMI
<2>Acc36I,BfuAI,BveI
<3>ACCTGC(4/8)
<4>?(5)
<5>Bacillus species M
<6>NEB 356
<7>N
<8>Morgan, R., Hoffman, L., Unpublished observations.
Morgan, R.D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>BspMII
<2>AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>
<5>Bacillus species M
<6>NEB 356
<7>
<8>Morgan, R., Hoffman, L., Unpublished observations.
Nwankwo, D.O., (1995) Gene, vol. 157, pp. 31-35.

<1>BspM39I
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>
<5>Bacillus species M39
<6>V. Bouriotis
<7>
<8>Kalugin, A.A., Rina, M., Eldarov, M.A., Markaki, M., Korolev, S.V., Samko, O.T., Khoroshutina, E.B., Sikolov, N.N., Bouriotis, V., (1996) Bioorg. Khim., vol. 22, pp. 108-110.

<1>BspM90I
<2>SnaI,BssNAI,Bst1107I,BstBSI,BstZ17I,VchO25I,XcaI
<3>GTA^TAC
<4>
<5>Bacillus species M90
<6>V.M. Kramarov
<7>
<8>Kramarov, V.M., Unpublished observations.

<1>BspMAI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Bacillus stearothermophilus MA
<6>P.M. Skowron
<7>
<8>Skowron, P.M., Unpublished observations.

<1>BspMKI
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>G^TCGAC
<4>
<5>Bacillus species MKI
<6>N.I. Matvienko
<7>
<8>Kerzhner, M.A., Shiryaev, S.A., Zheleznaya, L.A., Matvienko, N.I., (1997) Biokhimiia, vol. 62, pp. 1029-1036.

<1>BspNI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus species N
<6>CAMB 2677
<7>
<8>Saboohi, N., Malik, K., Sohail, A., Unpublished observations.

<1>BspNCI
<2>
<3>CCAGA
<4>
<5>Bacillus species
<6>NEB 1304
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BspOI
<2>NheI,AceII,AsuNHI,BmtI,LlaG2I,PstNHI
<3>GCTAG^C
<4>
<5>Bacillus sphaericus RFL3
<6>Fermentas G337
<7>F
<8>Vitkute, J., Lapcinskaja, S., Trinkunaite, L., Capskaja, L., Zakareviciene, L., Janulaitis, A., Unpublished observations.

<1>BspO4I
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>
<5>Bacillus species O-4
<6>ATCC 21536
<7>
<8>Moriya, S., Yanagawa, S., Aoki, N., Iwabuchi, M., Inoue, T., Ando, T., (1992) Nucleic Acids Res., vol. 20, pp. 3781.

<1>BspOVI
<2>Eam1105I,AhdI,AspEI,BmeRI,BstZ2I,DriI,EclHKI,NruGI,Uba1190I,Uba1191I
<3>GACNNN^NNGTC
<4>
<5>Bacillus species OV
<6>N.I. Matvienko
<7>
<8>Chernov, A.V., Lepikhov, K.A., Zheleznaya, L.A., Matvienko, N.I., (1996) Biokhimiia, vol. 61, pp. 1837-1847.

<1>BspOVII
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus species OV
<6>N.I. Matvienko
<7>
<8>Chernov, A.V., Lepikhov, K.A., Zheleznaya, L.A., Matvienko, N.I., (1996) Biokhimiia, vol. 61, pp. 1837-1847.

<1>BspPI
<2>BinI,AclWI,AlwI,BpuFI,BsrWI,BstH9I,Bst31TI,BthII,Bth617I,EacI,Ral8I
<3>GGATC(4/5)
<4>
<5>Bacillus species d 1-34
<6>A. Janulaitis
<7>F
<8>Padegimiene, E., Maneliene, Z., Norgeliene, D., Vonseviciene, E., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BspPR1I
<2>
<3>?
<4>
<5>Bacillus sphaericus Pr-1
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>BspQI
<2>SapI,LguI,PciSI,VpaK32I
<3>GCTCTTC(1/4)
<4>
<5>Bacillus sphaericus
<6>NEB 1214
<7>N
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.
Zhu, Z., Blanchard, A., Xu, S.-Y., Guan, S., Wei, H., Zhang, P., Sun, D., Chan, S.-h., International Patent Office, 2009.
Zhu, Z., Blanchard, A., Xu, S.-Y., Guan, S., Wei, H., Zhang, P., Sun, D., Chang, S.-H., International Patent Office, 2009.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BspRI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>3(5)
<5>Bacillus sphaericus R
<6>P. Venetianer
<7>
<8>Kim, S.C., Posfai, G., Szybalski, W., (1991) Gene, vol. 100, pp. 45-50.
Kiss, A., Sain, B., Csordas-Toth, E., Venetianer, P., (1977) Gene, vol. 1, pp. 323-329.
Koncz, C., Kiss, A., Venetianer, P., (1978) Eur. J. Biochem., vol. 89, pp. 523-529.
Posfai, G., Kiss, A., Erdei, S., Posfai, J., Venetianer, P., (1983) J. Mol. Biol., vol. 170, pp. 597-610.
Posfai, G., Szybalski, W., (1988) Gene, vol. 74, pp. 179-181.
Szilak, L., Finta, C., Patthy, A., Venetianer, P., Kiss, A., (1994) Nucleic Acids Res., vol. 22, pp. 2876-2881.

<1>BspR7I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CC^TNAGG
<4>
<5>Bacillus species R7
<6>N.I. Matvienko
<7>
<8>Vasiljeva, L.Yu., Zheleznaya, L.A., Matvienko, N.I., (1996) Biokhimiia, vol. 61, pp. 2147-2157.

<1>BspSI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Bacillus species S
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>BspS122I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus species 122
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>BspSSI
<2>
<3>?
<4>
<5>Bacillus sphaericus SSII-1
<6>F.G. Priest
<7>
<8>Zahner, V., Priest, F.G., (1997) Lett. Appl. Microbiol., vol. 24, pp. 483-487.

<1>BspST5I
<2>SfaNI,BhaI,BmsI,BscAI,BscUI,BsmNI,Bst19I,CjeP338II,LweI,PhaI
<3>GCATC(5/9)
<4>3(6)
<5>Bacillus species ST5
<6>N.I. Matvienko
<7>
<8>Matvienko, N.N., Zheleznaya, L.A., Zelinskaya, N.V., Matvienko, N.I., (1997) Biokhimiia, vol. 62, pp. 304-306.
Zelinskaya, N.V., Matvienko, N.N., Zheleznaya, L.A., Matvienko, N.I., (1995) Biokhimiia, vol. 60, pp. 1999-2010.
Zelinskaya, N.V., Matvienko, N.N., Zheleznaya, L.A., Matvienko, N.I., (1996) Biokhimiia, vol. 61, pp. 1006-1014.

<1>BspTI
<2>AflII,BfrI,BsaFI,BscLI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>C^TTAAG
<4>
<5>Bacillus species RFL1265
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Unpublished observations.

<1>BspT104I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Bacillus species T104
<6>Takara T104
<7>K
<8>Sawaragi, H., Unpublished observations.

<1>BspT107I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>G^GYRCC
<4>
<5>Bacillus species T107
<6>Takara T107
<7>K
<8>Sawaragi, H., Unpublished observations.

<1>BspTNI
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC(1/5)
<4>
<5>Bacillus sp. TN
<6>P.M. Skowron
<7>QX
<8>Skowron, P.M., Unpublished observations.

<1>BspTS514I
<2>BbvII,Bbr7I,BbsI,Bbv16II,Bco102II,BpiI,BpuAI,BsaVI,Bsc91I,BscKI,BspBS31I,BspIS4I,BspVI,BstBS32I,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC(2/6)
<4>
<5>Bacillus species TS514
<6>N.I. Matvienko
<7>
<8>Kovalevskaya, N.P., Zelinskaya, N.V., Zheleznaya, L.A., Matvienko, N.I., (1993) Bioorg. Khim., vol. 19, pp. 1073-1076.

<1>BspUI
<2>TauI,CglI,NgoFVII
<3>GCSG^C
<4>
<5>Bacillus species
<6>NEB 1593
<7>
<8>Abila, P., Nanyonjo, H., Egwang, T.G., Unpublished observations.
Morgan, R.D., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BspVI
<2>BbvII,Bbr7I,BbsI,Bbv16II,Bco102II,BpiI,BpuAI,BsaVI,Bsc91I,BscKI,BspBS31I,BspIS4I,BspTS514I,BstBS32I,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC
<4>
<5>Bacillus species 6801
<6>U. Mayr
<7>
<8>Kaluza, K., Unpublished observations.

<1>BspWI
<2>MwoI,Bce4I,Bce1247I,BceCI,BstMWI,HpyF10VI
<3>GCNNNNN^NNGC
<4>
<5>Bacillus species 3456
<6>U. Mayr
<7>
<8>Kaluza, K., Unpublished observations.

<1>BspXI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus sphaericus X
<6>D. Dupret
<7>W
<8>Zieger, M., Patillon, M., Roizes, G., Lerouge, T., Dupret, D., Jeltsch, J.M., (1987) Nucleic Acids Res., vol. 15, pp. 3919.

<1>BspXII
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>T^GATCA
<4>
<5>Bacillus sphaericus X
<6>D. Dupret
<7>
<8>Zieger, M., Patillon, M., Roizes, G., Lerouge, T., Dupret, D., Jeltsch, J.M., (1987) Nucleic Acids Res., vol. 15, pp. 3919.

<1>BspZEI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus species ZE
<6>N.I. Matvienko
<7>
<8>Zheleznyakova, E.N., Zheleznaya, L.A., Svadbina, I.V., Matvienko, N.I., (1998) Biokhimiia, vol. 63, pp. 1675-1681.

<1>BsrI
<2>BscHI,Bse1I,BseNI,BsoHI,BsrSI,Bst11I,Tsp1I
<3>ACTGG(1/-1)
<4>?(4)
<5>Bacillus stearothermophilus
<6>NEB 447
<7>N
<8>Lunnen, K.D., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Polisson, C., Morgan, R.D., (1988) Nucleic Acids Res., vol. 16, pp. 5205.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>BsrAI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Bacillus stearothermophilus CPW7
<6>Z. Chen
<7>
<8>Chen, W., Pan, X., Chen, Z., Unpublished observations.
Wright, D.J., Unpublished observations.

<1>BsrBI
<2>AccBSI,BstD102I,Bst31NI,MbiI
<3>CCGCTC(-3/-3)
<4>?(4)
<5>Bacillus stearothermophilus CPW193
<6>Z. Chen
<7>N
<8>Chen, Z., Unpublished observations.
Heiter, D., Nwankwo, D.O., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>BsrBRI
<2>BsaBI,Bco63I,Bco631I,Bse8I,Bse631I,BseJI,Bsh1365I,BsiBI,MamI,UbaN6I
<3>GATNN^NNATC
<4>
<5>Bacillus stearothermophilus BR
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>BsrCI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus stearothermophilus C1825
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsrDI
<2>Bse3DI,BseMI
<3>GCAATG(2/0)
<4>
<5>Bacillus stearothermophilus D70
<6>Z. Chen
<7>N
<8>Chen, Z., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Xu, S.Y., Zhu, Z., Zhang, P., Chan, S.H., Samuelson, J.C., Xiao, J., Ingalls, D., Wilson, G.G., (2007) Nucleic Acids Res., vol. 35, pp. 4608-4618.

<1>BsrEI
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC
<4>
<5>Bacillus stearothermophilus CPW9
<6>Z. Chen
<7>
<8>Chen, W., Pan, X., Chen, Z., Unpublished observations.

<1>BsrFI
<2>Cfr10I,Bco118I,BscRI,Bse118I,Bse634I,Bsp21I,BssAI,BstB7SI,NmeDI,TseDI
<3>R^CCGGY
<4>?(5)
<5>Bacillus stearothermophilus CPW16
<6>Z. Chen
<7>N
<8>Chen, W., Pan, X., Chen, Z., Unpublished observations.
Xu, S.-Y., Xiao, J.-P., US Patent Office, 2000.

<1>BsrGI
<2>Bsp1407I,AauI,BsmGI,BsmRI,Bst170I,BstAUI,Ssp4800I,SspBI
<3>T^GTACA
<4>
<5>Bacillus stearothermophilus GR75
<6>Z. Chen
<7>N
<8>Chen, Z., Unpublished observations.
Chen, Z.F., Pan, X.S., (1994) Chinese Sci. Bull., vol. 39, pp. 526-528.
Fang, N., Xu, S.-Y., US Patent Office, 2005.
Xu, S.-Y., Fang, N., Unpublished observations.

<1>BsrGII
<2>
<3>?
<4>
<5>Bacillus stearothermophilus GR75
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsrHI
<2>BsePI,BscEI,BsoPI,BssBI,BssHII,BstBZ153I,CfrJ5I,Eco143I,Eco152I,Esp7I,Esp8I,Kpn30I,McaTI,PauI,PteI,TtmII,Uba69I
<3>GCGCGC
<4>
<5>Bacillus stearothermophilus H4
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BsrMI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus stearothermophilus CPW13
<6>Z. Chen
<7>
<8>Chen, W., Pan, X., Chen, Z., Unpublished observations.

<1>BsrPI
<2>
<3>?
<4>
<5>Bacillus stearothermophilus P5
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BsrPII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus stearothermophilus P5
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BsrSI
<2>BsrI,BscHI,Bse1I,BseNI,BsoHI,Bst11I,Tsp1I
<3>ACTGG(1/-1)
<4>
<5>Bacillus stearothermophilus CPW19
<6>Z. Chen
<7>R
<8>Chen, Z., Unpublished observations.

<1>BsrVI
<2>BbvI,AlwXI,BchI,BsaUI,BseKI,BseXI,Bsp423I,Bst12I,Bst71I,BstV1I,LfeI,Lsp1109I
<3>GCAGC
<4>
<5>Bacillus stearothermophilus V35
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsrWI
<2>BinI,AclWI,AlwI,BpuFI,BspPI,BstH9I,Bst31TI,BthII,Bth617I,EacI,Ral8I
<3>GGATC
<4>
<5>Bacillus stearothermophilus W493
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BsrXI
<2>XbaI,BspAAII,BspLU11II,Msp23I
<3>TCTAGA
<4>
<5>Bacillus stearothermophilus X173
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BssI
<2>NlaIV,AspNI,BcrI,BmiI,BsaEI,BscBI,Bsp29I,BspLI,HpyF44II,HpyF73I,NgoBV,NgoGV,PspN4I,Rlu3I,Uba1305I,Uba1445I
<3>GGNNCC
<4>
<5>Bacillus stearothermophilus 881
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BssAI
<2>Cfr10I,Bco118I,BscRI,Bse118I,Bse634I,Bsp21I,BsrFI,BstB7SI,NmeDI,TseDI
<3>R^CCGGY
<4>
<5>Bacillus species
<6>V. Bouriotis
<7>C
<8>Rina, M., Stratidakis, I., Bouriotis, V., (1990) Nucleic Acids Res., vol. 18, pp. 6161.

<1>BssBI
<2>BsePI,BscEI,BsoPI,BsrHI,BssHII,BstBZ153I,CfrJ5I,Eco143I,Eco152I,Esp7I,Esp8I,Kpn30I,McaTI,PauI,PteI,TtmII,Uba69I
<3>GCGCGC
<4>
<5>Bacillus stearothermophilus BZ153
<6>X.S. Pan
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BssCI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus stearothermophilus C11
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BssECI
<2>SecI,BsaJI,BseDI,BsoKI,BstZ10I,Hpy99IV,HpyF10III,HpyF61II,HpyF67IV,Uba1442I
<3>C^CNNGG
<4>
<5>Bacillus stearothermophilus EC
<6>S.K. Degtyarev
<7>I
<8>Abdurashitov, M.A., Dedkov, V.S., Kileva, E.V., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>BssFI
<2>Fnu4HI,Bli1904II,Bpu1811I,BsoFI,Bsp6I,BssXI,BthCI,Cac824I,CcoP215I,CcoP216I,FbrI,Fsp4HI,ItaI,LlaDII,SatI,Uur960I
<3>GCNGC
<4>
<5>Bacillus stearothermophilus F6
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BssGI
<2>BstXI,BscJI,BstHZ55I,BstTI
<3>CCANNNNNNTGG
<4>
<5>Bacillus stearothermophilus G6
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BssGII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus stearothermophilus G6
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BssHI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Bacillus stearothermophilus H3
<6>ATCC 49820
<7>
<8>Calmero, J., Unpublished observations.
Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.
Nwankwo, D.O., Moran, L.S., Perler, F.B., Slatko, B.E., Wilson, G.G., Benner, J.S., Unpublished observations.
Schumann, J., Willert, J., Wild, C., Waler, J., Trautner, T.A., (1995) Gene, vol. 157, pp. 103-104.

<1>BssHII
<2>BsePI,BscEI,BsoPI,BsrHI,BssBI,BstBZ153I,CfrJ5I,Eco143I,Eco152I,Esp7I,Esp8I,Kpn30I,McaTI,PauI,PteI,TtmII,Uba69I
<3>G^CGCGC
<4>?(5)
<5>Bacillus stearothermophilus H3
<6>ATCC 49820
<7>JKMNOQRSX
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.
Schildkraut, I., Greenough, L., Unpublished observations.
Schumann, J., Willert, J., Wild, C., Waler, J., Trautner, T.A., (1995) Gene, vol. 157, pp. 103-104.
Xu, S.-Y., Xiao, J.-P., Posfai, J., Maunus, R., Benner, J., (1997) Nucleic Acids Res., vol. 25, pp. 3991-3994.

<1>M.BssHIII
<2>MluI,ApeI,Bbi24I,BstZ9I,Uba6I
<3>ACGCGT,CCGCGG,RGCGCY,RCCGGY,GCGCGC
<4>2(5), 2(5), 3(5), 2(5), 2(5)
<5>Bacillus stearothermophilus H3
<6>ATCC 49820
<7>
<8>Schumann, J., Walter, J., Willert, J., Wild, C., Koch, D., Trautner, T.A., (1996) J. Mol. Biol., vol. 257, pp. 949-959.
Schumann, J., Willert, J., Wild, C., Waler, J., Trautner, T.A., (1995) Gene, vol. 157, pp. 103-104.

<1>BssIMI
<2>SimI,BtsPI,SaiI,ShaI
<3>GGGTC(-3/0)
<4>
<5>Bacillus stearothermophilus IM
<6>S.K. Degtyarev
<7>
<8>Abdurashitov, M.A., Belichenko, O.A., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.
Wilson, G.G., Lunnen, K.D., Heiter, D.F., Unpublished observations.

<1>BssKI
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>^CCNGG
<4>?(5)
<5>Bacillus stearothermophilus
<6>NEB 547
<7>N
<8>Kong, H., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BssMI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus sp.
<6>Vivantis 11
<7>V
<8>Benner, J.S., Unpublished observations.
Chee, H.Y., Unpublished observations.

<1>BssNI
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>
<5>Bacillus sphaericus KTN
<6>Vivantis 111
<7>V
<8>Chee, H.Y., Unpublished observations.

<1>BssNAI
<2>SnaI,BspM90I,Bst1107I,BstBSI,BstZ17I,VchO25I,XcaI
<3>GTA^TAC
<4>
<5>Bacillus stearothermophilus NA
<6>S.K. Degtyarev
<7>IV
<8>Shinkarenko, N.M., Dedkov, V.S., Shevchenko, A.V., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>BssPI
<2>
<3>?
<4>
<5>Bacillus stearothermophilus P1
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BssSI
<2>BsiI,BauI,Bst2BI
<3>CACGAG(-5/-1)
<4>?(4)
<5>Bacillus stearothermophilus 27S
<6>Z. Chen
<7>N
<8>Heiter, D.F., Wilson, G.G., Unpublished observations.
Pan, X.S., Chen, Z., Unpublished observations.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>BssT1I
<2>StyI,BsmSI,Bst224I,CfrBI,Eco130I,Eco208II,EcoT14I,EcoT104I,ErhI,ErhB9II,SblAI,SblBI,SblCI,Uba1311I
<3>C^CWWGG
<4>
<5>Bacillus stearothermophilus T1
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.K., Unpublished observations.

<1>BssXI
<2>Fnu4HI,Bli1904II,Bpu1811I,BsoFI,Bsp6I,BssFI,BthCI,Cac824I,CcoP215I,CcoP216I,FbrI,Fsp4HI,ItaI,LlaDII,SatI,Uur960I
<3>GCNGC
<4>
<5>Bacillus species
<6>G. Elgar
<7>
<8>Elgar, G., Unpublished observations.

<1>BstI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>3(6)
<5>Bacillus stearothermophilus 1503-4R
<6>N. Welker
<7>
<8>Catterall, J.F., Welker, N.E., (1977) J. Bacteriol., vol. 129, pp. 1110-1120.
Clarke, C.M., Hartley, B.S., (1979) Biochem. J., vol. 177, pp. 49-62.
Levy, W.P., Welker, N.E., (1981) Biochemistry, vol. 20, pp. 1120-1127.

<1>Bst1I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus stearothermophilus 1
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bst2I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus stearothermophilus 2
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bst6I
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC(1/4)
<4>
<5>Bacillus stearothermophilus 6
<6>S.K. Degtyarev
<7>IV
<8>Abdurashitov, M.A., Dedkov, V.S., Kileva, E.V., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>Bst11I
<2>BsrI,BscHI,Bse1I,BseNI,BsoHI,BsrSI,Tsp1I
<3>ACTGG(1/-1)
<4>
<5>Bacillus stearothermophilus 11
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bst12I
<2>BbvI,AlwXI,BchI,BsaUI,BseKI,BseXI,Bsp423I,BsrVI,Bst71I,BstV1I,LfeI,Lsp1109I
<3>GCAGC(8/12)
<4>
<5>Bacillus stearothermophilus 12
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.
Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bst16I
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGCY
<4>
<5>Bacillus stearothermophilus M16
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>Bst19I
<2>SfaNI,BhaI,BmsI,BscAI,BscUI,BsmNI,BspST5I,CjeP338II,LweI,PhaI
<3>GCATC(4/6)
<4>
<5>Bacillus stearothermophilus 19
<6>S.K. Degtyarev
<7>
<8>Tomilova, Y.E., Dedkov, V.S., Shinkarenko, N.M., Popichenko, D.V., Degtyarev, S.K., (2002) Biotekhnologiya, vol. 6, pp. 17-20.

<1>Bst19II
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus stearothermophilus 19
<6>S.K. Degtyarev
<7>
<8>Tomilova, J.E., Dedkov, V.S., Shinkarenko, N.M., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>Bst22I
<2>BsiYI,AfiI,BflI,Bsc4I,Bsc107I,Bse23I,BseLI,BslI,BsmYI
<3>CCNNNNN^NNGG
<4>
<5>Bacillus stearothermophilus 22
<6>V.E. Repin
<7>
<8>Ushakova, T.A., Puchkova, L.I., Radionenko, Y.V., Kuvshinov, V.N., Repin, V.E., (2003) Biotekhnologiya, vol. 0, pp. 11-15.

<1>Bst28I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus stearothermophilus 28
<6>S.K. Degtyarev
<7>
<8>Repin, V.E., Rechkunova, N.I., Degtyarev, S.K., Hachaturyan, A.A., Afrikyan, E.K., (1989) Biol. J. Armenia, vol. 42, pp. 969-972.

<1>Bst29I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Bacillus stearothermophilus 29
<6>V.E. Repin
<7>
<8>Serov, G.D., Tereschenko, T.A., Puchkova, L.I., Repin, V.E., Unpublished observations.

<1>Bst30I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Bacillus stearothermophilus 30
<6>V.E. Repin
<7>
<8>Serov, G.D., Tereschenko, T.A., Puchkova, L.I., Repin, V.E., Unpublished observations.

<1>Bst31I
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>GGTNACC
<4>
<5>Bacillus stearothermophilus NUB31
<6>N. Welker
<7>
<8>Hendrix, J.D., Welker, N.E., (1985) J. Bacteriol., vol. 162, pp. 682-692.

<1>Bst38I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus stearothermophilus 38
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bst40I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>C^CGG
<4>
<5>Bacillus stearothermophilus 40
<6>S.K. Degtyarev
<7>
<8>Repin, V.E., Rechkunova, N.I., Degtyarev, S.K., Hachaturyan, A.A., Afrikyan, E.K., (1989) Biol. J. Armenia, vol. 42, pp. 969-972.

<1>Bst44I
<2>
<3>?
<4>
<5>Bacillus stearothermophilus 4.4
<6>N.I. Matvienko
<7>
<8>Kramarov, V.M., Fomenkov, A.I., Matvienko, N.I., (1988) Bioorg. Khim., vol. 14, pp. 916-920.

<1>Bst71I
<2>BbvI,AlwXI,BchI,BsaUI,BseKI,BseXI,Bsp423I,BsrVI,Bst12I,BstV1I,LfeI,Lsp1109I
<3>GCAGC(8/12)
<4>
<5>Bacillus stearothermophilus 71
<6>Promega 71
<7>
<8>Schoenfeld, T., Fiandt, M., Schink, M., (1992) Gene, vol. 111, pp. 141-142.

<1>Bst77I
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Bacillus stearothermophilus 77
<6>V.E. Repin
<7>
<8>Repin, V.E., Andreeva, I.S., Sizov, A.A., Khomov, V.V., Unpublished observations.

<1>Bst98I
<2>AflII,BfrI,BsaFI,BscLI,BspTI,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>C^TTAAG
<4>
<5>Bacillus stearothermophilus C98
<6>Z. Chen
<7>R
<8>Chen, Z., Unpublished observations.

<1>Bst100I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus stearothermophilus 100
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Puchkova, L.I., Tereshenko, T.A., Lebedev, L.R., Chigikov, V.E., (1993) Bioorg. Khim., vol. 19, pp. 583-585.

<1>Bst158I
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC
<4>
<5>Bacillus stearothermophilus P158
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>Bst170I
<2>Bsp1407I,AauI,BsmGI,BsmRI,BsrGI,BstAUI,Ssp4800I,SspBI
<3>TGTACA
<4>
<5>Bacillus stearothermophilus D170
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>Bst170II
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Bacillus stearothermophilus D170
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>Bst224I
<2>StyI,BsmSI,BssT1I,CfrBI,Eco130I,Eco208II,EcoT14I,EcoT104I,ErhI,ErhB9II,SblAI,SblBI,SblCI,Uba1311I
<3>CCWWGG
<4>
<5>Bacillus stearothermophilus I224
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>Bst295I
<2>DdeI,Bpa36II,BscPI,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Bacillus stearothermophilus Z295
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>Bst1107I
<2>SnaI,BspM90I,BssNAI,BstBSI,BstZ17I,VchO25I,XcaI
<3>GTA^TAC
<4>
<5>Bacillus stearothermophilus RFL1107
<6>A. Janulaitis
<7>FKM
<8>Janulaitis, A., Kazlauskiene, R., Trinkunaite, L., Kiuduliene, L., Maneliene, Z., Petrusyte, M., Butkus, V., Unpublished observations.

<1>Bst1126I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus stearothermophilus 1126
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>Bst1274I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus stearothermophilus 1274
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>Bst1473I
<2>BetI,Bba179I,Bca77I,BsaWI,UbaN10I
<3>WCCGGW
<4>
<5>Bacillus stearothermophilus 1473
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>Bst1473II
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGCY
<4>
<5>Bacillus stearothermophilus 1473
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>Bst2464I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus stearothermophilus 2464
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>Bst2902I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus stearothermophilus 2902
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>BstAI
<2>
<3>?
<4>
<5>Bacillus stearothermophilus 240
<6>A. Atkinson
<7>
<8>Bingham, A.H.A., Sharp, R.J., Atkinson, T., Unpublished observations.

<1>BstACI
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>
<5>Bacillus stearothermophilus AC
<6>S.K. Degtyarev
<7>I
<8>Belichenko, O.A., Schevchenko, A.V., Dedkov, V.S., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>BstAFI
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>C^TTAAG
<4>
<5>Bacillus stearothermophilus AF
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Belichenko, O.A., Tarasova, G.V., Dedkov, V.S., Mikhnenkova, N.A., Degtyarev, S.K., Unpublished observations.

<1>BstAPI
<2>ApaBI
<3>GCANNNN^NTGC
<4>
<5>Bacillus stearothermophilus AP
<6>NEB 1778
<7>IN
<8>Abdurashitov, M.A., Belichenko, O.A., Shevchenko, A.V., Dedkov, V.S., Degtyarev, S.Kh., (1997) Nucleic Acids Res., vol. 25, pp. 2301-2302.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BstAUI
<2>Bsp1407I,AauI,BsmGI,BsmRI,BsrGI,Bst170I,Ssp4800I,SspBI
<3>T^GTACA
<4>
<5>Bacillus stearothermophilus AU
<6>S.K. Degtyarev
<7>IV
<8>Abdurashitov, M.A., Dedkov, V.S., Shinkarenko, N.M., Tomilova, J.E., Degtyarev, S.K., Unpublished observations.

<1>BstBI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Bacillus stearothermophilus B225
<6>Z. Chen
<7>N
<8>Chen, Z., Kong, H., Unpublished observations.
Morgan, R.D., Unpublished observations.
Wei, H., Unpublished observations.

<1>Bst2BI
<2>BsiI,BauI,BssSI
<3>CACGAG(-5/-1)
<4>
<5>Bacillus stearothermophilus 2B
<6>S.K. Degtyarev
<7>IV
<8>Abdurashitov, M.A., Belichenko, O.A., Degtyarev, S.K., Unpublished observations.

<1>BstBAI
<2>BsaAI,MspYI,Ppu6I,Ppu11I,Ppu21I,PsuAI
<3>YAC^GTR
<4>
<5>Bacillus stearothermophilus BA
<6>S.K. Degtyarev
<7>IV
<8>Abdurashitov, M.A., Shinkarenko, N.M., Dedkov, V.S., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>BstBAII
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Bacillus stearothermophilus BA
<6>S.K. Degtyarev
<7>
<8>Abdurashitov, M.A., Shinkarenko, N.M., Dedkov, V.S., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>BstBSI
<2>SnaI,BspM90I,BssNAI,Bst1107I,BstZ17I,VchO25I,XcaI
<3>GTA^TAC
<4>
<5>Bacillus stearothermophilus BS
<6>N.I. Matvienko
<7>
<8>Kovalevskaya, N.P., Ivanov, L.Yu., Zheleznaya, L.A., Matvienko, N.I., (1991) Nucleic Acids Res., vol. 19, pp. 4296.

<1>BstB7SI
<2>Cfr10I,Bco118I,BscRI,Bse118I,Bse634I,Bsp21I,BsrFI,BssAI,NmeDI,TseDI
<3>R^CCGGY
<4>
<5>Bacillus stearothermophilus B7S
<6>R.A.D. Williams
<7>
<8>Al-Awadhi, S., Welch, S.G., Smith, K.E., Williams, R.A.D., (1998) FEMS Microbiol. Lett., vol. 160, pp. 205-208.

<1>BstBS32I
<2>BbvII,Bbr7I,BbsI,Bbv16II,Bco102II,BpiI,BpuAI,BsaVI,Bsc91I,BscKI,BspBS31I,BspIS4I,BspTS514I,BspVI,BstTS5I,BstV2I,Rtr20I
<3>GAAGAC(2/6)
<4>
<5>Bacillus stearothermophilus BS32
<6>N.I. Matvienko
<7>
<8>Kovalevskaya, N.P., Zelinskaya, N.V., Zheleznaya, L.A., Matvienko, N.I., (1993) Bioorg. Khim., vol. 19, pp. 1073-1076.

<1>BstBZ153I
<2>BsePI,BscEI,BsoPI,BsrHI,BssBI,BssHII,CfrJ5I,Eco143I,Eco152I,Esp7I,Esp8I,Kpn30I,McaTI,PauI,PteI,TtmII,Uba69I
<3>G^CGCGC
<4>
<5>Bacillus stearothermophilus BZ153
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstCI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus stearothermophilus C1
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>Bst4CI
<2>Tsp4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACN^GT
<4>
<5>Bacillus stearothermophilus 4C
<6>S.K. Degtyarev
<7>IV
<8>Shinkarenko, N.M., Schevchenko, A.V., Dedkov, V.S., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>BstC8I
<2>Cac8I,BniI
<3>GCN^NGC
<4>
<5>Bacillus stearothermophilus C8
<6>S.K. Degtyarev
<7>I
<8>Abdurashitov, M.A., Dedkov, V.S., Mikhnenkova, N.A., Kileva, E.V., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>BstDI
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>GGTNACC
<4>
<5>Bacillus stearothermophilus D428
<6>Z. Chen
<7>
<8>Chen, Z., Kong, H., Unpublished observations.

<1>BstD102I
<2>BsrBI,AccBSI,Bst31NI,MbiI
<3>CCGCTC(-3/-3)
<4>
<5>Bacillus stearothermophilus D102
<6>L. Ge
<7>
<8>DiFrancesco, R., Ge, L., Unpublished observations.

<1>BstDEI
<2>DdeI,Bpa36II,BscPI,Bst295I,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>C^TNAG
<4>
<5>Bacillus stearothermophilus DE
<6>S.K. Degtyarev
<7>IV
<8>Shinkarenko, N.M., Shevchenko, A.V., Dedkov, V.S., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>BstDSI
<2>DsaI,BtgI,TspBI
<3>C^CRYGG
<4>
<5>Bacillus stearothermophilus DS
<6>S.K. Degtyarev
<7>IV
<8>Belichenko, O.A., Shevchenko, A.V., Dedkov, V.S., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>BstDZ247I
<2>BscGI,BpuJI
<3>CCCGT
<4>
<5>Bacillus stearothermophilus DZ247
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstEI
<2>
<3>?
<4>
<5>Bacillus stearothermophilus ET
<6>ATCC 49830
<7>
<8>Meagher, R.B., Unpublished observations.

<1>BstEII
<2>AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Bacillus stearothermophilus ET
<6>ATCC 49830
<7>CHJMNORSUW
<8>Chang, Z., Morgan, R., Unpublished observations.
Lautenberger, J.A., Edgell, M.H., Hutchison, C.A. III, (1980) Gene, vol. 12, pp. 171-174.
Meagher, R.B., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Ware, J., Morgan, R.D., Unpublished observations.

<1>BstEIII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus stearothermophilus ET
<6>ATCC 49830
<7>
<8>Grandoni, R.P., Comb, D., Unpublished observations.
Meagher, R.B., Unpublished observations.
Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BstENI
<2>EcoNI,Bpu1268I,BsoEI,BstWI,Uba1289I,Uba1290I,Uba1308I,Uba1309I,Uba1310I,XagI
<3>CCTNN^NNNAGG
<4>
<5>Bacillus stearothermophilus EN
<6>S.K. Degtyarev
<7>IV
<8>Abdurashitov, M.A., Dedkov, V.S., Kileva, E.V., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>BstENII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus stearothermophilus EN
<6>S.K. Degtyarev
<7>
<8>Abdurashitov, M.A., Dedkov, V.S., Kileva, E.V., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>BstEZ359I
<2>HpaI,BsaKI,BseII,BstHPI,KspAI,MwhI,SsrI,Uba1408II
<3>GTT^AAC
<4>
<5>Bacillus stearothermophilus EZ359
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstFI
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>A^AGCTT
<4>
<5>Bacillus stearothermophilus FH58
<6>Z. Chen
<7>
<8>Kong, H., Chen, Z., (1987) Nucleic Acids Res., vol. 15, pp. 7205.

<1>BstF5I
<2>FokI,BseGI,BtsCI,HinGUII,Hpy178VI,HpyF6I,HpyF67III,PbuJKI,StsI
<3>GGATG(2/0)
<4>3(6)
<5>Bacillus stearothermophilus F5
<6>S.K. Degtyarev
<7>IV
<8>Abdurashitov, M.A., Kileva, E.V., Shinkarenko, N.M., Shevchenko, A.V., Dedkov, V.S., Degtyarev, S.Kh., (1996) Gene, vol. 172, pp. 49-51.
Degtyarev, S.Kh., Netesova, N.A., Abdurashitov, M.A., Shevchenko, A.V., (1997) Gene, vol. 187, pp. 217-219.

<1>BstFNI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>
<5>Bacillus stearothermophilus
<6>S.K. Degtyarev
<7>IV
<8>Nayakshina, T.N., Lebedeva, N.A., Dedkov, V.S., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>BstFZ438I
<2>FauI,Bme585I,SmuI
<3>CCCGC(4/6)
<4>
<5>Bacillus stearothermophilus FZ438
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstGI
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Bacillus stearothermophilus G3
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BstGII
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Bacillus stearothermophilus G3
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BstGZ53I
<2>Esp3I,BsmBI,Esp16I,Esp23I
<3>CGTCTC(1/5)
<4>
<5>Bacillus stearothermophilus GZ53
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstHI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Bacillus stearothermophilus H1
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BstH2I
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGC^Y
<4>
<5>Bacillus stearothermophilus H2
<6>S.K. Degtyarev
<7>IV
<8>Abdurashitov, M.A., Kileva, E.V., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>BstH9I
<2>BinI,AclWI,AlwI,BpuFI,BspPI,BsrWI,Bst31TI,BthII,Bth617I,EacI,Ral8I
<3>GGATC(4/5)
<4>
<5>Bacillus stearothermophilus H9
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstHHI
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCG^C
<4>
<5>Bacillus stearothermophilus HH
<6>S.K. Degtyarev
<7>IV
<8>Shapovalova, M.A., Abdurashitov, M.A., Tumanova, I.Y., Dedkov, V.S., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>BstHPI
<2>HpaI,BsaKI,BseII,BstEZ359I,KspAI,MwhI,SsrI,Uba1408II
<3>GTT^AAC
<4>
<5>Bacillus stearothermophilus HP
<6>S.K. Degtyarev
<7>
<8>Abdurashitov, M.A., Kileva, E.V., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>BstHZ55I
<2>BstXI,BscJI,BssGI,BstTI
<3>CCANNNNN^NTGG
<4>
<5>Bacillus stearothermophilus HZ55
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstIZ316I
<2>DraIII,AdeI
<3>CACNNN^GTG
<4>
<5>Bacillus stearothermophilus IZ316
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstJI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus stearothermophilus J460
<6>Z. Chen
<7>
<8>Chen, Z., Kong, H., Unpublished observations.

<1>BstJZ301I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>C^TNAG
<4>
<5>Bacillus stearothermophilus JZ301
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstKI
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Bacillus stearothermophilus K554
<6>Z. Chen
<7>
<8>Chen, Z., Kong, H., Unpublished observations.

<1>BstKTI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GAT^C
<4>
<5>Bacillus stearothermophilus KT
<6>S.K. Degtyarev
<7>I
<8>Nadeev, A.N., Abdurashitov, M.A., Dedkov, V.S., Shinkarenko, N.M., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>BstKZ418I
<2>
<3>?
<4>
<5>Bacillus stearothermophilus KZ418
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstLI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Bacillus stearothermophilus L95
<6>Z. Chen
<7>
<8>Chen, Z., Kong, H., Unpublished observations.

<1>BstLVI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus stearothermophilus LV
<6>C. Vasquez
<7>
<8>Lobos, C., Vasquez, C., (1993) Biochim. Biophys. Acta, vol. 1171, pp. 295-298.

<1>BstMI
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BsoSI,DpaI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGTACT
<4>
<5>Bacillus stearothermophilus M571
<6>Z. Chen
<7>
<8>Chen, Z., Kong, H., Unpublished observations.

<1>BstM6I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus stearothermophilus M6
<6>N.I. Matvienko
<7>
<8>Shapovalova, N.I., Ivanov, L.Yu., Matvienko, N.I., (1992) Bioorg. Khim., vol. 18, pp. 1186-1189.

<1>BstMAI
<2>BsmAI,Alw26I,BcoDI,BscQII,BsoMAI
<3>GTCTC(1/5)
<4>
<5>Bacillus stearothermophilus MA
<6>S.K. Degtyarev
<7>IV
<8>Chernukhin, V.A., Mikhnenkova, N.A., Kileva, E.V., Mezentseva, N.V., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>BstMBI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus stearothermophilus MB
<6>S.K. Degtyarev
<7>IV
<8>Kovalenko, K., Kileva, E.V., Mezentseva, N.V., Mikhnenkova, N.A., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>BstMCI
<2>McrI,BsaOI,BscNI,Bsh1285I,BsiEI,BstZ5I,Uba1303I
<3>CGRY^CG
<4>
<5>Bacillus stearothermophilus MC
<6>S.K. Degtyarev
<7>IV
<8>Belichenko, O.A., Shevchenko, A.V., Dedkov, V.S., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>BstMWI
<2>MwoI,Bce4I,Bce1247I,BceCI,BspWI,HpyF10VI
<3>GCNNNNN^NNGC
<4>
<5>Bacillus stearothermophilus MW
<6>S.K. Degtyarev
<7>I
<8>Nadeev, A.N., Dedkov, V.S., Tomilova, J.T., Degtyarev, S.K., Unpublished observations.

<1>BstMZ611I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>^CCNGG
<4>
<5>Bacillus stearothermophilus MZ611
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstNI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>2(4)
<5>Bacillus stearothermophilus
<6>D.G. Comb
<7>N
<8>Baryshev, M.M., Buryanov, Y.I., Kosykh, V.G., Bayev, A.A., (1989) Biokhimiia, vol. 54, pp. 1894-1903.
Schildkraut, I., Greenough, L., Comb, D., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>Bst31NI
<2>BsrBI,AccBSI,BstD102I,MbiI
<3>CCGCTC(-3/-3)
<4>
<5>Bacillus stearothermophilus 31N
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>M.BstNBII
<2>
<3>?
<4>
<5>Bacillus stearothermophilus
<6>NEB 928
<7>
<8>Higgins, L.S., Holden, M., Kong, H., Unpublished observations.

<1>BstNSI
<2>NspI,AvoI,Lsp1270I,NspHI,PauAI,PunAII,XceI
<3>RCATG^Y
<4>
<5>Bacillus stearothermophilus 1161NS
<6>S.K. Degtyarev
<7>IV
<8>Abdurashitov, M.A., Bondar, T.S., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>BstNSII
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Bacillus stearothermophilus 1161NS
<6>S.K. Degtyarev
<7>
<8>Abdurashitov, M.A., Bondar, T.S., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>BstNZ169I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus stearothermophilus NZ169
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstOI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus stearothermophilus O22
<6>Z. Chen
<7>R
<8>Chen, Z., Kong, H., Unpublished observations.

<1>BstOZ616I
<2>FinI,BpuNI,BpuSI,BscWI,BslFI,BsmFI,BspLU11III,FaqI
<3>GGGAC(10/14)
<4>
<5>Bacillus stearothermophilus OZ616
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstPI
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Bacillus stearothermophilus
<6>ATCC 12980
<7>K
<8>Pugatsch, T., Weber, H., (1979) Nucleic Acids Res., vol. 7, pp. 1429-1444.

<1>BstPAI
<2>PshAI,BoxI
<3>GACNN^NNGTC
<4>
<5>Bacillus stearothermophilus PA
<6>S.K. Degtyarev
<7>IV
<8>Tomilova, J.E., Dedkov, V.S., Kileva, E.V., Popichenko, D.V., Degtyarev, S.Kh., Unpublished observations.

<1>BstPZ740I
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>C^TTAAG
<4>
<5>Bacillus stearothermophilus PZ740
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstQI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus stearothermophilus Q407
<6>Z. Chen
<7>
<8>Chen, Z., Kong, H., Unpublished observations.

<1>Bst4QI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Bacillus stearothermophilus 4Q
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>Bst7QI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Bacillus stearothermophilus 7Q
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>Bst7QII
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Bacillus stearothermophilus 7Q
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BstRI
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Bacillus stearothermophilus R463
<6>Z. Chen
<7>
<8>Chen, Z., Kong, H., Unpublished observations.

<1>BstRZ246I
<2>SwaI,BstSWI,MspSWI,SmiI
<3>ATTT^AAAT
<4>
<5>Bacillus stearothermophilus RZ246
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstRZ459I
<2>
<3>?
<4>
<5>Bacillus stearothermophilus RZ459
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstSI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>
<5>Bacillus stearothermophilus S183
<6>Z. Chen
<7>
<8>Chen, Z., Kong, H., Wang, L., (1989) J. Fudan Univ. (Natural Sci.), vol. 28, pp. 363-366.

<1>BstSCI
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>^CCNGG
<4>
<5>Bacillus stearothermophilus SC
<6>S.K. Degtyarev
<7>I
<8>Dedkov, V.S., Muradov, S.V., Kileva, E.V., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>BstSFI
<2>SfeI,Bco163I,BdiSI,BfmI,BpcI,BthP35I,HpyF2I,LlaBI,SfcI,Srl56DI
<3>C^TRYAG
<4>
<5>Bacillus stearothermophilus SF
<6>S.K. Degtyarev
<7>I
<8>Belichenko, O.A., Shevchenko, A.V., Dedkov, V.S., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>BstSLI
<2>BseSI,BaeGI,Bme1580I,BmgAI
<3>GKGCM^C
<4>
<5>Bacillus stearothermophilus SL
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Kileva, E.V., Tarasova, G.V., Degtyarev, S.K., Unpublished observations.

<1>BstSNI
<2>SnaBI,Bpu1831I,EciAI,Eco105I,Eco158II,SspJI,SspM1I,SspM2I,Uba1240I
<3>TAC^GTA
<4>
<5>Bacillus stearothermophilus SN
<6>S.K. Degtyarev
<7>IV
<8>Myakisheva, T.V., Dedkov, V.S., Kileva, E.V., Abdurashitov, M.A., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>BstSWI
<2>SwaI,BstRZ246I,MspSWI,SmiI
<3>ATTT^AAAT
<4>
<5>Bacillus stearothermophilus SW
<6>S.K. Degtyarev
<7>
<8>Abdurashitov, M.A., Dedkov, V.S., Bondar, T.S., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>BstTI
<2>BstXI,BscJI,BssGI,BstHZ55I
<3>CCANNNNNNTGG
<4>
<5>Bacillus stearothermophilus T12
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>BstT7I
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>T^GATCA
<4>
<5>Bacillus stearothermophilus T7
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>BstT9I
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Bacillus stearothermophilus T9
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>BstT10I
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Bacillus stearothermophilus T10
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Bst31TI
<2>BinI,AclWI,AlwI,BpuFI,BspPI,BsrWI,BstH9I,BthII,Bth617I,EacI,Ral8I
<3>GGATC(4/5)
<4>
<5>Bacillus stearothermophilus 31T
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstTS5I
<2>BbvII,Bbr7I,BbsI,Bbv16II,Bco102II,BpiI,BpuAI,BsaVI,Bsc91I,BscKI,BspBS31I,BspIS4I,BspTS514I,BspVI,BstBS32I,BstV2I,Rtr20I
<3>GAAGAC(2/6)
<4>
<5>Bacillus stearothermophilus TS5
<6>N.I. Matvienko
<7>
<8>Kovalevskaya, N.P., Zelinskaya, N.V., Zheleznaya, L.A., Matvienko, N.I., (1993) Bioorg. Khim., vol. 19, pp. 1073-1076.

<1>BstUI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>?(5)
<5>Bacillus stearothermophilus U458
<6>Z. Chen
<7>N
<8>Chen, Z., Kong, H., Unpublished observations.
Zheng, Y., Unpublished observations.

<1>Bst2UI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus stearothermophilus 2U
<6>S.K. Degtyarev
<7>IV
<8>Myakisheva, T.V., Degtyarev, S.K., Unpublished observations.

<1>BstVI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>5(6)
<5>Bacillus stearothermophilus V
<6>C. Vasquez
<7>
<8>Barra, R., Chiong, M., Gonzalez, E., Vasquez, C., (1988) Biochem. J., vol. 255, pp. 699-703.
Gonzalez, E., Padilla, C., Saavedra, C., Vasquez, C., (1994) Microbiology, vol. 140, pp. 1337-1340.
Vasquez, C., (1985) Biochem. Int., vol. 10, pp. 655-662.
Vasquez, C., (1988) Arch. Biol. Med. Exp. (Santiago), vol. 21.

<1>BstV1I
<2>BbvI,AlwXI,BchI,BsaUI,BseKI,BseXI,Bsp423I,BsrVI,Bst12I,Bst71I,LfeI,Lsp1109I
<3>GCAGC(8/12)
<4>
<5>Bacillus stearothermophilus V1
<6>S.K. Degtyarev
<7>I
<8>Dedkov, V.S., Muradov, S.V., Shinkarenko, N.M., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>BstV2I
<2>BbvII,Bbr7I,BbsI,Bbv16II,Bco102II,BpiI,BpuAI,BsaVI,Bsc91I,BscKI,BspBS31I,BspIS4I,BspTS514I,BspVI,BstBS32I,BstTS5I,Rtr20I
<3>GAAGAC(2/6)
<4>
<5>Bacillus stearothermophilus V2
<6>S.K. Degtyarev
<7>IV
<8>Sinichkina, S.A., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>BstWI
<2>EcoNI,Bpu1268I,BsoEI,BstENI,Uba1289I,Uba1290I,Uba1308I,Uba1309I,Uba1310I,XagI
<3>CCTNNNNNAGG
<4>
<5>Bacillus stearothermophilus W574
<6>Z. Chen
<7>
<8>Chen, Z., Unpublished observations.

<1>BstXI
<2>BscJI,BssGI,BstHZ55I,BstTI
<3>CCANNNNN^NTGG
<4>
<5>Bacillus stearothermophilus X1
<6>N. Welker
<7>FHIJKMNOQRVWX
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.
Skowron, P.M., Rutkowska, S.M., Harasimowicz-Slowinska, R.I., Unpublished observations.
Wise, R., Schildkraut, I., Unpublished observations.
Zhu, Z., Blanchard, A., Xu, S.-Y., Guan, S., Wei, H., Zhang, P., Sun, D., Chan, S.-h., International Patent Office, 2009.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BstXII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus stearothermophilus X1
<6>N. Welker
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BstX2I
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstYI,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>R^GATCY
<4>
<5>Bacillus stearothermophilus X2
<6>S.K. Degtyarev
<7>IV
<8>Belichenko, O.A., Shevchenko, A.V., Dedkov, V.S., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>BstYI
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>R^GATCY
<4>5(4)
<5>Bacillus stearothermophilus Y406
<6>Z. Chen
<7>N
<8>Chen, Z., Kong, H., (1988) FEBS Lett., vol. 234, pp. 169-171.
Strimpel, D., Stickel, S., Roberts, R.J., Unpublished observations.
Xu, S.-Y., Samuelson, J., Pelletier, J., Sibley, M., Wilson, G.G., US Patent Office, 2002.

<1>BstZI
<2>XmaIII,AaaI,BseX3I,BsoDI,EagI,EclXI,Eco52I,SenPT16I,TauII,Tsp504I
<3>C^GGCCG
<4>
<5>Bacillus stearothermophilus Z130
<6>Z. Chen
<7>R
<8>Chen, Z., Kong, H., Unpublished observations.
King, K., Unpublished observations.

<1>BstZ1I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Bacillus stearothermophilus 14P
<6>NEB 944
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.
Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstZ1II
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Bacillus stearothermophilus 14P
<6>NEB 944
<7>
<8>Mruk, I., Kaczorowski, T., (2007) Appl. Environ. Microbiol., vol. 73, pp. 4286-4293.
Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BstZ2I
<2>Eam1105I,AhdI,AspEI,BmeRI,BspOVI,DriI,EclHKI,NruGI,Uba1190I,Uba1191I
<3>GACNNNNNGTC
<4>
<5>Bacillus stearothermophilus 37T
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ3I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Bacillus stearothermophilus 31H
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ4I
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Bacillus stearothermophilus N136
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ5I
<2>McrI,BsaOI,BscNI,Bsh1285I,BsiEI,BstMCI,Uba1303I
<3>CGRYCG
<4>
<5>Bacillus stearothermophilus 15E
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ6I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Bacillus stearothermophilus 25Q
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ7I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Bacillus stearothermophilus 26W
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ8I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Bacillus stearothermophilus 29K
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ9I
<2>MluI,ApeI,Bbi24I,Uba6I
<3>ACGCGT
<4>
<5>Bacillus stearothermophilus 34G
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ10I
<2>SecI,BsaJI,BseDI,BsoKI,BssECI,Hpy99IV,HpyF10III,HpyF61II,HpyF67IV,Uba1442I
<3>CCNNGG
<4>
<5>Bacillus stearothermophilus 35L
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ10II
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Bacillus stearothermophilus 35L
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ12I
<2>
<3>?
<4>
<5>Bacillus stearothermophilus 35O
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ13I
<2>
<3>?
<4>
<5>Bacillus stearothermophilus 36A
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ14I
<2>
<3>?
<4>
<5>Bacillus stearothermophilus 36N
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ15I
<2>SduI,AocII,Bka1125I,BmyI,BsoCI,Bsp1286I,BspLS2I,HpyF36IV,HpyF47I,MhlI,Mlu40I,NspII,TseAI,Uba1362I
<3>GDGCHC
<4>
<5>Bacillus stearothermophilus BD102
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ16I
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Bacillus stearothermophilus 37Q
<6>Z. Chen
<7>
<8>Pan, X.S., Chen, Z., Unpublished observations.

<1>BstZ17I
<2>SnaI,BspM90I,BssNAI,Bst1107I,BstBSI,VchO25I,XcaI
<3>GTA^TAC
<4>
<5>Bacillus stearothermophilus 38M
<6>Z. Chen
<7>N
<8>Morgan, R.D., Unpublished observations.
Pan, X.S., Chen, Z., Unpublished observations.
Wei, H., Unpublished observations.

<1>Bsu6I
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC(1/4)
<4>
<5>Bacillus subtilis 6vl
<6>S.K. Degtyarev
<7>
<8>Abdurashitov, M.A., Kileva, E.V., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>Bsu15I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>5(6)
<5>Bacillus subtilis 15
<6>S.K. Degtyarev
<7>F
<8>Janulaitis, A., Lubys, A., Mitkaite, G., Bitinaite, J., Maneliene, Z., Butkus, V., Unpublished observations.
Prihodko, G.G., Petrov, N.A., Repin, V.E., Degtyarev, S.K., (1988) Izv. Sib. Otd. Akad. Nauk SSSR, vol. 14, pp. 108-109.

<1>Bsu22I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Bacillus subtilis 22
<6>N.I. Matvienko
<7>
<8>Kramarov, V.M., Skrypina, N.A., Smolyaninov, V.V., Smirnov, V.V., Resnik, S.R., Sorokulova, I.B., Matvienko, N.I., (1989) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 42-45.

<1>Bsu23I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>
<5>Bacillus subtilis 23
<6>V.M. Kramarov
<7>
<8>Kramarov, V.M., Unpublished observations.

<1>Bsu36I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CC^TNAGG
<4>
<5>Bacillus subtilis 36
<6>B. Zhou
<7>NR
<8>Heiter, D., Lunnen, K., Wilson, G.G., US Patent Office, 2006.
Lunnen, K.D., Heiter, D., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Zhou, B., Li, Q., (1987) Acta Biochim. Biophys. Sin., vol. 19, pp. 537-540.

<1>Bsu54I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Bacillus subtilis 54
<6>V.M. Kramarov
<7>
<8>Kramarov, V.M., Unpublished observations.

<1>Bsu90I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus subtilis 90
<6>N.I. Matvienko
<7>
<8>Kramarov, V.M., Skrypina, N.A., Smolyaninov, V.V., Smirnov, V.V., Resnik, S.R., Sorokulova, I.B., Matvienko, N.I., (1989) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 42-45.

<1>Bsu121I
<2>
<3>?
<4>
<5>Bacillus subtilis strain 121
<6>A.R. Reddy
<7>
<8>Jutur, P.P., Reddy, A.R., (2002) Mol. Biol. Rep., vol. 29, pp. 383-385.

<1>Bsu1076I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus subtilis
<6>IAM 1076
<7>
<8>Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>Bsu1114I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Bacillus subtilis
<6>IAM 1114
<7>
<8>Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>Bsu1145I
<2>
<3>?
<4>
<5>Bacillus subtilis
<6>ATCC 14593
<7>
<8>Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>Bsu1192I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Bacillus subtilis
<6>IAM 1192
<7>
<8>Qiang, B.-Q., Schildkraut, I., Unpublished observations.
Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>Bsu1192II
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Bacillus subtilis
<6>IAM 1192
<7>
<8>Qiang, B.-Q., Schildkraut, I., Unpublished observations.

<1>Bsu1193I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Bacillus subtilis
<6>IAM 1193
<7>
<8>Qiang, B.-Q., Schildkraut, I., Unpublished observations.
Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>Bsu1259I
<2>
<3>?
<4>
<5>Bacillus subtilis
<6>IAM 1259
<7>
<8>Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>Bsu1532I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>
<5>Bacillus subtilis 1532
<6>A.A. Prozorov
<7>
<8>Kholmina, G.V., Rebentish, B.A., Kozlovskii, Y.-E., Sorokin, A.V., Goldenberg, D.S., Prozorov, A.A., (1986) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 23-25.

<1>Bsu1854I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCY^C
<4>
<5>Bacillus subtilis 1854
<6>A.A. Prozorov
<7>
<8>Kholmina, G.V., Rebentish, B.A., Kozlovskii, Y.-E., Sorokin, A.V., Goldenberg, D.S., Prozorov, A.A., (1986) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 23-25.

<1>Bsu2413I
<2>
<3>?
<4>
<5>Bacillus subtilis 2413
<6>A.R. Reddy
<7>
<8>Jutur, P.P., Hoti, S.L., Reddy, A.R., (2004) Mol. Biol. Rep., vol. 31, pp. 139-142.

<1>Bsu5044I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Bacillus subtilis UCM B-5044
<6>O.M. Reva
<7>
<8>Reva, O.M., Lukyanchuk, V.V., Polishchuk, L.V., (2002) Mikrobiol. Zh., vol. 64, pp. 57-59.

<1>Bsu6633I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Bacillus subtilis
<6>ATCC 6633
<7>
<8>Ikawa, S., Shibata, T., Ando, T., Saito, H., (1980) Mol. Gen. Genet., vol. 177, pp. 359-368.
Oda, K., Marmur, J., (1966) Biochemistry, vol. 5, pp. 761-773.
Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>Bsu8565I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus subtilis
<6>NCIB 8565
<7>
<8>Leung, S.M., Chan, K.Y., Suen, Y.K., Shaw, P.C., (1989) Nucleic Acids Res., vol. 17, pp. 10133.

<1>Bsu8646I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus subtilis
<6>NCIB 88646
<7>
<8>Leung, S.M., Chan, K.Y., Suen, Y.K., Shaw, P.C., (1989) Nucleic Acids Res., vol. 17, pp. 10133.

<1>BsuBI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>5(6)
<5>Bacillus subtilis
<6>IAM 1247
<7>
<8>Hoshino, T., Uozumi, T., Horinouchi, S., Ozaki, A., Beppu, T., Arima, K., (1977) Biochim. Biophys. Acta, vol. 479, pp. 367-369.
Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.
Xu, G.L., Kapfer, W., Walter, J., Trautner, T.A., (1992) Nucleic Acids Res., vol. 20, pp. 6517-6523.

<1>BsuB519I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus subtilis B519
<6>Y.I. Buryanov
<7>
<8>Bogdarina, I.G., Nadirova, I.M., Buryanov, Y.I., (1986) Mikrobiologiia, vol. 55, pp. 699-700.

<1>BsuB763I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Bacillus subtilis B763
<6>Y.I. Buryanov
<7>
<8>Bogdarina, I.G., Nadirova, I.M., Buryanov, Y.I., (1986) Mikrobiologiia, vol. 55, pp. 699-700.

<1>BsuCI
<2>
<3>?
<4>?(6)
<5>Bacillus subtilis
<6>IAM 1247
<7>
<8>Xu, G., Willert, J., Kapfer, W., Trautner, T.A., (1995) Gene, vol. 157, pp. 59.

<1>BsuEII
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>1(5)
<5>Bacillus subtilis
<6>IAM 1231
<7>
<8>Gaido, M.L., Prostko, C.R., Strobl, J.S., (1988) J. Biol. Chem., vol. 263, pp. 4832-4836.
Qiang, B.-Q., Schildkraut, I., Unpublished observations.

<1>BsuFI
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>C^CGG
<4>1(5)
<5>Bacillus subtilis
<6>IAM 1231
<7>
<8>Jentsch, S., (1983) J. Bacteriol., vol. 156, pp. 800-808.
Kapfer, W., Walter, J., Trautner, T.A., (1991) Nucleic Acids Res., vol. 19, pp. 6457-6463.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Qiang, B.-Q., Schildkraut, I., Unpublished observations.
Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.
Walter, J., Noyer-Weidner, M., Trautner, T.A., (1990) EMBO J., vol. 9, pp. 1007-1013.

<1>BsuF2I
<2>
<3>?
<4>
<5>Bacillus subtilis F2
<6>N. Jamil
<7>
<8>Chaboki, K.M., (2001) Biophys. J., vol. 80, pp. 282A.

<1>BsuMI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>?(5)
<5>Bacillus subtilis 168
<6>A. Danchin
<7>
<8>Guha, S., (1985) J. Bacteriol., vol. 163, pp. 573-579.
Jentsch, S., (1983) J. Bacteriol., vol. 156, pp. 800-808.
Kunst, F. et al., (1997) Nature, vol. 390, pp. 249-256.
Sadaie, Y., Unpublished observations.
Shibata, T., Ikawa, S., Kim, C., Ando, T., (1976) J. Bacteriol., vol. 128, pp. 473-476.

<1>BsuRI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>3(5)
<5>Bacillus subtilis strain R
<6>T.A. Trautner
<7>FI
<8>Bron, S., Murray, K., (1975) Mol. Gen. Genet., vol. 143, pp. 25-33.
Bron, S., Murray, K., Trautner, T.A., (1975) Mol. Gen. Genet., vol. 143, pp. 13-23.
Gunthert, U., Storm, K., Bald, R., (1978) Eur. J. Biochem., vol. 90, pp. 581-583.
Heitman, J., Model, P., (1987) J. Bacteriol., vol. 169, pp. 3243-3250.
Kiss, A., Posfai, G., Keller, C.C., Venetianer, P., Roberts, R.J., (1985) Nucleic Acids Res., vol. 13, pp. 6403-6420.

<1>BsuTUI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Bacillus subtilis TU
<6>P.M. Skowron
<7>X
<8>Skowron, P.M., Unpublished observations.

<1>BsxI
<2>BfiI,BmrI,BmuI
<3>ACTGGG
<4>
<5>Bacillus simplex 2472
<6>NEB 1400
<7>
<8>Nkenfou, C.N., Nkenfou, J., Unpublished observations.

<1>BtcI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis var canadensis
<6>R.R. Azizbekyan
<7>
<8>Kuzin, A.I., Bolesnin, M.I., Smolyaninov, V.V., Azizbekyan, R.R., (1989) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 36-39.

<1>BteI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Brochothrix thermosphacter
<6>CAMB 2590
<7>
<8>Mushtaq, R., Sohail, A., Malik, K., Riazuddin, S., Unpublished observations.

<1>BtgI
<2>DsaI,BstDSI,TspBI
<3>C^CRYGG
<4>
<5>Bacillus thermoglucosidasius
<6>NEB 1165
<7>N
<8>Ganatra, M., Krotee, S., Unpublished observations.
Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BtgAI
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Brevibacterium thiogenitalis
<6>NEB 969
<7>
<8>Polisson, C., Unpublished observations.

<1>BtgAII
<2>SphI,Asp5HI,BbuI,BscOI,Bsp121I,CglAI,PaeI,PaeCI,PfaAIII,RspLKI,SpaHI,SpaXI,Uba1162I,Uba1226I,VchO68I
<3>GCATGC
<4>
<5>Brevibacterium thiogenitalis
<6>NEB 969
<7>
<8>Polisson, C., Unpublished observations.

<1>BtgZI
<2>
<3>GCGATG(10/14)
<4>
<5>Bacillus thermoglucosidasius
<6>NEB 1384
<7>N
<8>Morgan, R.D., Walsh, P., US Patent Office, 2006.
Pan, X.S., Morgan, R., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BthI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Bifidobacterium thermophilum RU326
<6>ATCC 25866
<7>
<8>Sakurai, T., Kosaka, T., Japanese Patent Office, 1983.
Sakurai, T., Kosaka, T., US Patent Office, 1983.

<1>BthII
<2>BinI,AclWI,AlwI,BpuFI,BspPI,BsrWI,BstH9I,Bst31TI,Bth617I,EacI,Ral8I
<3>GGATC
<4>
<5>Bifidobacterium thermophilum RU326
<6>ATCC 25866
<7>
<8>Khosaka, T., Unpublished observations.

<1>Bth84I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis ssp. amagiensis
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Kalmykova, G.V., Burtseva, L.I., Repin, V.E., (2002) Prikl. Biokhim. Mikrobiol., vol. 38, pp. 140-144.

<1>Bth211I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis ssp. tolworthi
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Kalmykova, G.V., Burtseva, L.I., Repin, V.E., (2002) Prikl. Biokhim. Mikrobiol., vol. 38, pp. 140-144.

<1>Bth213I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis strain 213
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Kalmykova, G.V., Burtseva, L.I., Repin, V.E., (2002) Prikl. Biokhim. Mikrobiol., vol. 38, pp. 140-144.

<1>Bth221I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis strain 221
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Kalmykova, G.V., Burtseva, L.I., Repin, V.E., (2002) Prikl. Biokhim. Mikrobiol., vol. 38, pp. 140-144.

<1>Bth617I
<2>BinI,AclWI,AlwI,BpuFI,BspPI,BsrWI,BstH9I,Bst31TI,BthII,EacI,Ral8I
<3>GGATC
<4>
<5>Bacillus thuringiensis ssp. sotto
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Kalmykova, G.V., Burtseva, L.I., Repin, V.E., (2002) Prikl. Biokhim. Mikrobiol., vol. 38, pp. 140-144.

<1>Bth945I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis ssp. tohokuensis
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Kalmykova, G.V., Burtseva, L.I., Repin, V.E., (2002) Prikl. Biokhim. Mikrobiol., vol. 38, pp. 140-144.

<1>Bth1140I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis ssp. yunnanensis
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Kalmykova, G.V., Burtseva, L.I., Repin, V.E., (2002) Prikl. Biokhim. Mikrobiol., vol. 38, pp. 140-144.

<1>Bth1141I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis ssp. pondicheriensis
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Kalmykova, G.V., Burtseva, L.I., Repin, V.E., (2002) Prikl. Biokhim. Mikrobiol., vol. 38, pp. 140-144.

<1>Bth1202I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus thuringiensis ssp. kumamotoensis
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Kalmykova, G.V., Burtseva, L.I., Repin, V.E., (2002) Prikl. Biokhim. Mikrobiol., vol. 38, pp. 140-144.

<1>Bth1786I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis 1786
<6>NEB 1422
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>Bth1795I
<2>GsuI,Bco35I,BpmI,Bsp22I,Bsp28I,BspJ74I,Uba1437I,Uba1444I
<3>CTGGAG
<4>
<5>Bacillus thuringiensis 1795
<6>NEB 1326
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>Bth1997I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis ssp. novosibirsk
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Kalmykova, G.V., Burtseva, L.I., Repin, V.E., (2002) Prikl. Biokhim. Mikrobiol., vol. 38, pp. 140-144.

<1>Bth2350I
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAGCTG
<4>
<5>Bacillus thuringiensis 2350
<6>NEB 1397
<7>
<8>Nkenfou, C.N., Nkenfou, J., Unpublished observations.

<1>Bth9411I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Bacillus thuringiensis ssp. neolensis
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Kalmykova, G.V., Burtseva, L.I., Repin, V.E., (2002) Prikl. Biokhim. Mikrobiol., vol. 38, pp. 140-144.

<1>Bth9415I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus thuringiensis ssp. monterrey
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Kalmykova, G.V., Burtseva, L.I., Repin, V.E., (2002) Prikl. Biokhim. Mikrobiol., vol. 38, pp. 140-144.

<1>BthAI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Bacillus thuringiensis AII
<6>CAMB 2661
<7>
<8>Arif, A., Ehsan, A., Sohail, A., Unpublished observations.

<1>BthCI
<2>Fnu4HI,Bli1904II,Bpu1811I,BsoFI,Bsp6I,BssFI,BssXI,Cac824I,CcoP215I,CcoP216I,FbrI,Fsp4HI,ItaI,LlaDII,SatI,Uur960I
<3>GCNG^C
<4>?(5)
<5>Bacillus thuringiensis 2294
<6>NEB 1402
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>BthCanI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis ssp. canadensis
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Kalmykova, G.V., Burtseva, L.I., Repin, V.E., (2002) Prikl. Biokhim. Mikrobiol., vol. 38, pp. 140-144.

<1>BthDI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus thuringiensis D4
<6>CAMB 2657
<7>
<8>Choudhry, S., Malik, K., Unpublished observations.

<1>BthEI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Bacillus thuringiensis E
<6>CAMB 2660
<7>
<8>Arif, A., Naeem, S., Malik, K., Unpublished observations.

<1>BthP35I
<2>SfeI,Bco163I,BdiSI,BfmI,BpcI,BstSFI,HpyF2I,LlaBI,SfcI,Srl56DI
<3>C^TRYAG
<4>
<5>Bacillus thermoglucosidasius
<6>NEB 1563
<7>
<8>Pan, X.S., Morgan, R., Unpublished observations.

<1>BtiI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Bacillus thuringiensis var israelensis
<6>R.R. Azizbekyan
<7>
<8>Azizbekyan, R.R., Rebentish, B.A., Stepanova, T.V., Netyksa, E.M., Bychkova, M.A., (1984) Dokl. Akad. Nauk., vol. 274, pp. 742-744.

<1>BtkI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>
<5>Bacillus thuringiensis var Kumantoensis
<6>R.R. Azizbekyan
<7>
<8>Azizbekyan, R.R., Rebentish, B.A., Netyksa, E.M., Bychkova, M.A., Bolotin, A.P., (1992) Mol. Gen. Mikrobiol. Virusol., vol. 1-2, pp. 13-15.

<1>BtkII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Bacillus thuringiensis var Kumantoensis
<6>R.R. Azizbekyan
<7>
<8>Azizbekyan, R.R., Rebentish, B.A., Netyksa, E.M., Bychkova, M.A., Bolotin, A.P., (1992) Mol. Gen. Mikrobiol. Virusol., vol. 1-2, pp. 13-15.

<1>BtrI
<2>AjiI,BmgBI
<3>CACGTC(-3/-3)
<4>
<5>Bacillus stearothermophilus SE-U62
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.Kh., Belichenko, O.A., Lebedeva, N.A., Dedkov, V.S., Abdurashitov, M.A., (2000) Nucleic Acids Res., vol. 28.

<1>BtsI
<2>
<3>GCAGTG(2/0)
<4>
<5>Bacillus thermoglucosidasius
<6>NEB 1137
<7>N
<8>Ganatra, M., Krotee, S., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Pan, X.S., Morgan, R., Unpublished observations.
Xu, S.Y., Zhu, Z., Zhang, P., Chan, S.H., Samuelson, J.C., Xiao, J., Ingalls, D., Wilson, G.G., (2007) Nucleic Acids Res., vol. 35, pp. 4608-4618.

<1>BtsCI
<2>FokI,BseGI,BstF5I,HinGUII,Hpy178VI,HpyF6I,HpyF67III,PbuJKI,StsI
<3>GGATG(2/0)
<4>
<5>Bacillus thermosphaericus
<6>NEB 1621
<7>N
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Pan, X.S., Morgan, R., Unpublished observations.
Zhu, Z., Xu, S.-Y., Unpublished observations.

<1>BtsPI
<2>SimI,BssIMI,SaiI,ShaI
<3>GGGTC
<4>
<5>Bacillus thermosphaericus
<6>NEB 1507
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>BtuI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Bacillus thuringiensis U44
<6>R.R. Azizbekyan
<7>
<8>Azizbekyan, R.R., Rebentish, B.A., Netyksa, E.M., (1988) Biotekhnologiya, vol. 4, pp. 197-198.

<1>Btu33I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis 33
<6>V.E. Repin
<7>
<8>Repin, V.E., Burtseva, L.I., Burlak, V.A., Trusova, S.I., (1991) Mol. Gen. Mikrobiol. Virusol., vol. 11, pp. 20-22.

<1>Btu34I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis 34
<6>V.E. Repin
<7>
<8>Repin, V.E., Burtseva, L.I., Burlak, V.A., Trusova, S.I., (1991) Mol. Gen. Mikrobiol. Virusol., vol. 11, pp. 20-22.

<1>Btu34II
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGCY
<4>
<5>Bacillus thuringiensis 34
<6>V.E. Repin
<7>
<8>Repin, V.E., Burtseva, L.I., Burlak, V.A., Trusova, S.I., Unpublished observations.

<1>Btu36I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis 36
<6>V.E. Repin
<7>
<8>Repin, V.E., Burtseva, L.I., Burlak, V.A., Trusova, S.I., (1991) Mol. Gen. Mikrobiol. Virusol., vol. 11, pp. 20-22.

<1>Btu37I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis 37
<6>V.E. Repin
<7>
<8>Repin, V.E., Burtseva, L.I., Burlak, V.A., Trusova, S.I., (1991) Mol. Gen. Mikrobiol. Virusol., vol. 11, pp. 20-22.

<1>Btu39I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis 39
<6>V.E. Repin
<7>
<8>Repin, V.E., Burtseva, L.I., Burlak, V.A., Trusova, S.I., (1991) Mol. Gen. Mikrobiol. Virusol., vol. 11, pp. 20-22.

<1>Btu41I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Bacillus thuringiensis 41
<6>V.E. Repin
<7>
<8>Repin, V.E., Burtseva, L.I., Burlak, V.A., Trusova, S.I., (1991) Mol. Gen. Mikrobiol. Virusol., vol. 11, pp. 20-22.

<1>BtuMI
<2>NruI,AmaSI,Bsp68I,Mlu9273I,MluB2I,PspDI,RruI,SalDI,Sbo13I,Sna3286I,SpoI,Uba1117I,Uba1386I,VchO70I
<3>TCG^CGA
<4>
<5>Brevibacillus thermoruber
<6>Vivantis 61
<7>V
<8>Chee, H.Y., Unpublished observations.

<1>BveI
<2>BspMI,Acc36I,BfuAI
<3>ACCTGC(4/8)
<4>
<5>Brevundimonas vesicularis RFL1
<6>V. Butkus
<7>F
<8>Mociskyte, S., Vaitkevicius, D., Maneliene, Z., Trinkunaite, L., Kiuduliene, L., Petrusyte, M., Markauskas, A., Butkus, V., Janulaitis, A., Unpublished observations.

<1>BvuI
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCY^C
<4>
<5>Bacillus vulgatis
<6>OSB 816
<7>
<8>Beaty, J.S., Mclean-Bowen, C.A., Brown, L.R., (1982) Gene, vol. 18, pp. 61-67.

<1>BvuBI
<2>SplI,BpuB5I,BsiWI,BsmWI,MaeK81I,Pfl23II,PfuNI,PpuAI,PspLI,SmaAI,SplAI,SspKI,SunI
<3>C^GTACG
<4>
<5>Bacteroides vulgatus
<6>T. Kanematsu
<7>
<8>Kanematsu, T., Ozawa, O., Murakami, M., Yoshida, N., Japanese Patent Office, 1991.

<1>CacI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Clostridium acetobutylicum N1-4081
<6>G. Reysett
<7>
<8>Azeddoug, H., Hubert, J., Reysset, G., (1989) FEMS Microbiol. Lett., vol. 65, pp. 323-326.

<1>Cac8I
<2>BniI,BstC8I
<3>GCN^NGC
<4>?(5)
<5>Clostridium acetobutylicum ABKn8
<6>G. Reysett
<7>N
<8>Azeddoug, H., Reysset, G., (1991) FEMS Microbiol. Lett., vol. 78, pp. 153-156.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>Cac824I
<2>Fnu4HI,Bli1904II,Bpu1811I,BsoFI,Bsp6I,BssFI,BssXI,BthCI,CcoP215I,CcoP216I,FbrI,Fsp4HI,ItaI,LlaDII,SatI,Uur960I
<3>GCNGC
<4>?(5)
<5>Clostridium acetobutylicum 824
<6>ATCC 824
<7>
<8>Mermelstein, L.D., Welker, N.E., Bennett, G.N., Papoutsakis, E.T., (1992) Biotechnology, vol. 10, pp. 190-195.
Nolling, J. et al., (2001) J. Bacteriol., vol. 183, pp. 4823-4838.

<1>CaiI
<2>AlwNI
<3>CAGNNN^CTG
<4>
<5>Comamonas acidovarans Iti19-021
<6>V. Butkus
<7>F
<8>Vitkute, J., Rudokas, K., Maneliene, Z., Trinkunaite, L., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>CalI
<2>
<3>?
<4>
<5>Caryophanon latum H7
<6>W.C. Trentini
<7>
<8>Mayer, H., Schutte, H., Unpublished observations.

<1>Cas2I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Caulobacter species RFL2
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>CatHI
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC(1/4)
<4>
<5>Croceibacter atlanticus HTCC2559
<6>S.J. Giovannoni
<7>
<8>Chan, S.H., Xu, S.Y., Unpublished observations.
Giovannoni, S.J., Cho, J.-C., Ferriera, S., Johnson, J., Kravitz, S., Halpern, A., Remington, K., Beeson, K., Tran, B., Rogers, Y.-H., Friedman, R., Venter, J.C., Unpublished observations.

<1>CauI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Chloroflexus aurantiacus
<6>A. Bingham
<7>
<8>Bennett, S.P., (1987) Ph.D. Thesis, University of Bristol, UK, pp. 1-196.
Bingham, A.H.A., Darbyshire, J., (1982) Gene, vol. 18, pp. 87-91.
Molemans, F., van Emmelo, J., Fiers, W., (1982) Gene, vol. 18, pp. 93-96.

<1>CauII
<2>AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CC^SGG
<4>
<5>Chloroflexus aurantiacus
<6>A. Bingham
<7>
<8>Bennett, S.P., (1987) Ph.D. Thesis, University of Bristol, UK, pp. 1-196.
Bingham, A.H.A., Darbyshire, J., (1982) Gene, vol. 18, pp. 87-91.
Levi, C., Bickle, T., Unpublished observations.
Molemans, F., van Emmelo, J., Fiers, W., (1982) Gene, vol. 18, pp. 93-96.

<1>CauIII
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Chloroflexus aurantiacus
<6>A. Bingham
<7>
<8>Bennett, S.P., Halford, S.E., (1987) DNA-ligand interactions: from drugs to proteins., ed. Guschlbauer, W., Saenger, W. (Plenum Press, New York), pp. 239-250.

<1>CauB3I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>
<5>Chloroflexus aurantiacus B3
<6>V.M. Kramarov
<7>
<8>Kramarov, V.M., Fomenkov, A.I., Matvienko, N.I., Ubieta, R.H., Smolianinov, V.V., Gorlenko, V.M., (1987) Bioorg. Khim., vol. 13, pp. 773-776.

<1>CbiI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Clostridium bifermentans B-4
<6>T. Mitsuoka
<7>
<8>Murakami, M., Ozawa, O., Kanematsu, T., Yamada, Y., (1991) Nucleic Acids Res., vol. 19, pp. 3458.

<1>CboI
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>C^CGG
<4>2(5)
<5>Clostridium botulinum
<6>ATCC 25765
<7>
<8>Davis, T.O., Henderson, I., Brehm, J.K., Minton, N.P., (2000) J. Mol. Microbiol. Biotechnol., vol. 2, pp. 59-69.

<1>CbrI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Citrobacter braakii 1146
<6>NEB 1293
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>CceI
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>?(5)
<5>Clostridium cellulolyticum
<6>ATCC 35319
<7>
<8>Jennert, K.C., Tardif, C., Young, D.I., Young, M., (2000) Microbiology, vol. 146, pp. 3071-3080.
Lucas, S. et al., Unpublished observations.

<1>CciI
<2>BspHI,PagI,RcaI,RhcI,RspXI
<3>T^CATGA
<4>
<5>Curtobacterium citreus
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Kashirina, Y.G., Tarasova, G.V., Dedkov, V.S., Mikhnenkova, N.A., Degtyarev, S.K., Unpublished observations.

<1>CciNI
<2>NotI,CsiBI,CspBI,MchAI
<3>GC^GGCCGC
<4>
<5>Curtobacterium citreum N
<6>S.K. Degtyarev
<7>IV
<8>Dedkov, V.S., Rechkunova, N.I., Prihodko, E.A., Kileva, E.V., Kusner, Y.S., Verchozina, V.A., Degtyarev, S.Kh., (1995) Gene, vol. 157, pp. 99-100.

<1>CcoI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCC^GGC
<4>
<5>Clostridium coccoides B-2
<6>T. Kanematsu
<7>
<8>Kanematsu, T., Ozawa, O., Japanese Patent Office, 1991.

<1>CcoP31I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Campylobacter coli P31
<6>J.M.B. Vitor
<7>
<8>Vitor, J.M.B., Polisson, C., Cabrita, J., Silva, R.V.C., (1993) Acta Gastroenterol. Belg., vol. 56, pp. 41.

<1>CcoP73I
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Campylobacter coli P73
<6>J.M.B. Vitor
<7>
<8>Vitor, J.M.B., Polisson, C., Cabrita, J., Silva, R.V.C., (1993) Acta Gastroenterol. Belg., vol. 56, pp. 41.

<1>CcoP76I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Campylobacter coli P76
<6>J.M.B. Vitor
<7>
<8>Vitor, J.M.B., Polisson, C., Cabrita, J., Silva, R.V.C., (1993) Acta Gastroenterol. Belg., vol. 56, pp. 41.

<1>CcoP84I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Campylobacter coli P84
<6>J.M.B. Vitor
<7>
<8>Vitor, J.M.B., Polisson, C., Cabrita, J., Silva, R.V.C., (1993) Acta Gastroenterol. Belg., vol. 56, pp. 41.

<1>CcoP95I
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCGC
<4>
<5>Campylobacter coli P95
<6>J.M.B. Vitor
<7>
<8>Vitor, J.M.B., Polisson, C., Cabrita, J., Silva, R.V.C., (1993) Acta Gastroenterol. Belg., vol. 56, pp. 41.

<1>CcoP95II
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Campylobacter coli P95
<6>J.M.B. Vitor
<7>
<8>Vitor, J.M.B., Polisson, C., Cabrita, J., Silva, R.V.C., (1993) Acta Gastroenterol. Belg., vol. 56, pp. 41.

<1>CcoP215I
<2>Fnu4HI,Bli1904II,Bpu1811I,BsoFI,Bsp6I,BssFI,BssXI,BthCI,Cac824I,CcoP216I,FbrI,Fsp4HI,ItaI,LlaDII,SatI,Uur960I
<3>GCNGC
<4>
<5>Campylobacter coli P215
<6>J.M.B. Vitor
<7>
<8>Vitor, J.M.B., Polisson, C., Cabrita, J., Silva, R.V.C., (1993) Acta Gastroenterol. Belg., vol. 56, pp. 41.

<1>CcoP216I
<2>Fnu4HI,Bli1904II,Bpu1811I,BsoFI,Bsp6I,BssFI,BssXI,BthCI,Cac824I,CcoP215I,FbrI,Fsp4HI,ItaI,LlaDII,SatI,Uur960I
<3>GCNGC
<4>
<5>Campylobacter coli P216
<6>J.M.B. Vitor
<7>
<8>Vitor, J.M.B., Polisson, C., Cabrita, J., Silva, R.V.C., (1993) Acta Gastroenterol. Belg., vol. 56, pp. 41.

<1>CcoP219I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Campylobacter coli P219
<6>J.M.B. Vitor
<7>
<8>Vitor, J.M.B., Polisson, C., Cabrita, J., Silva, R.V.C., (1993) Acta Gastroenterol. Belg., vol. 56, pp. 41.

<1>CcrI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Caulobacter crescentus CB-13
<6>J. Poindexter
<7>
<8>Syddall, R., Stachow, C., (1985) Biochim. Biophys. Acta, vol. 825, pp. 236-243.

<1>CcuI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Chroococcidiopsis cubana
<6>A.J. Podhajska
<7>
<8>Waleron, K., Piechula, S., Unpublished observations.

<1>CcyI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Clostridium cylindrosporum
<6>C.S. Chen
<7>
<8>Wen, T.N., Tung, P.H., Chen, C.S., (1989) Bot. Bull. Acad. Sinica, vol. 30, pp. 91-98.

<1>CdiI
<2>
<3>CATCG(-1/-1)
<4>
<5>Clostridium difficile CD3
<6>N.P. Minton
<7>
<8>Minton, N.P., Unpublished observations.
Minton, N.P., Purdy, D.A., Elmore, M.J., O'Keeffe, K.M.T., International Patent Office, 2001.
Purdy, D., O'Keeffe, T.A., Elmore, M., Herbert, M., McLeod, A., Bokori-Brown, M., Ostrowski, A., Minton, N.P., (2002) Mol. Microbiol., vol. 46, pp. 439-452.

<1>Cdi27I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter diversus RFL27
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Unpublished observations.

<1>Cdi630V
<2>
<3>?
<4>
<5>Clostridium difficile strain 630
<6>B. Wren
<7>
<8>Herbert, M., O'Keeffe, T.A., Purdy, D., Elmore, M., Minton, N.P., (2003) FEMS Microbiol. Lett., vol. 229, pp. 103-110.

<1>CdiAI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Citrobacter diversus
<6>ATCC 25408
<7>
<8>Polisson, C., Unpublished observations.

<1>CdiCD6I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>4(5)
<5>Clostridium difficile CD6
<6>N. Minton
<7>
<8>Minton, N.P., Purdy, D.A., Elmore, M.J., O'Keeffe, K.M.T., International Patent Office, 2001.
Purdy, D., O'Keeffe, T.A., Elmore, M., Herbert, M., McLeod, A., Bokori-Brown, M., Ostrowski, A., Minton, N.P., (2002) Mol. Microbiol., vol. 46, pp. 439-452.

<1>CdiCD6II
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Clostridium difficile CD6
<6>N. Minton
<7>
<8>Minton, N.P., Purdy, D.A., Elmore, M.J., O'Keeffe, K.M.T., International Patent Office, 2001.
Purdy, D., O'Keeffe, T.A., Elmore, M., Herbert, M., McLeod, A., Bokori-Brown, M., Ostrowski, A., Minton, N.P., (2002) Mol. Microbiol., vol. 46, pp. 439-452.

<1>CdpI
<2>
<3>GCGGAG(20/18)
<4>
<5>Corynebacterium diphtheriae
<6>NCTC 13129
<7>
<8>Cerdeno-Tarraga, A.M. et al., (2003) Nucleic Acids Res., vol. 31, pp. 6516-6523.
Morgan, R.D., Unpublished observations.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>CelI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Coccochloris elabens 17a
<6>ATCC 27265
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.
Waaijer, R.J.A., Unpublished observations.

<1>CelII
<2>EspI,BlpI,Bpu1102I,BpuGCI,Bsp1720I,Uba1221I,Uba1222I,Uba1284I,Uba1320I
<3>GC^TNAGC
<4>
<5>Coccochloris elabens 17a
<6>ATCC 27265
<7>M
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>CeqI
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GAT^ATC
<4>
<5>Corynebacterium equi
<6>E.G. Duda
<7>
<8>Duda, E.G., Izsvak, Z., Orosz, A., (1987) Nucleic Acids Res., vol. 15, pp. 1334.
Izsvak, Z., Jobbagy, Z., Takacs, I., Duda, E., (1997) Int. J. Biochem. Cell Biol., vol. 29, pp. 895-900.

<1>CfaI
<2>ApoI,AcsI,FsiI,XapI
<3>R^AATTY
<4>
<5>Curtobacterium flaccumfaciens
<6>Vivantis 216
<7>
<8>Chee, H.Y., Unpublished observations.

<1>CflI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Cellulomonas flavigena
<6>IFO 3753
<7>
<8>Hiraoka, N., Kita, K., Nakajima, H., Kimizuka, F., Obayashi, A., (1985) J. Ferment. Technol., vol. 63, pp. 151-157.

<1>CfoI
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCG^C
<4>
<5>Clostridium formicoaceticum
<6>ATCC 23439
<7>MRS
<8>Makula, R.A., Unpublished observations.

<1>CfrI
<2>AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>Y^GGCCR
<4>4(5)
<5>Citrobacter freundii RFL2
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Stakenas, P., Jaskeleviciene, B., Lebedenko, E.N., Berlin, Y.A., (1980) Bioorg. Khim., vol. 6, pp. 1746-1748.
Janulaitis, A., Stakenas, P.S., Lebedenko, E.N., Berlin, Y.A., (1982) Nucleic Acids Res., vol. 10, pp. 6521-6530.
Janulaitis, A., Stakenas, P.S., Petrusyte, M.P., Bitinaite, J.B., Klimasauskas, S.I., Butkus, V.V., (1983) Mol. Biol. (Mosk), vol. 18, pp. 115-129.
Klimasauskas, S., Butkus, V., Janulaitis, A., (1987) Mol. Biol. (Mosk), vol. 21, pp. 87-92.

<1>Cfr4I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Citrobacter freundii RFL4
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Stakenas, P.S., Bitinaite, J.B., Jaskeleviciene, B.P., (1983) Dokl. Akad. Nauk., vol. 271, pp. 483-485.

<1>Cfr5I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter freundii RFL5
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Stakenas, P.S., Bitinaite, J.B., Jaskeleviciene, B.P., (1983) Dokl. Akad. Nauk., vol. 271, pp. 483-485.

<1>Cfr6I
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>4(4)
<5>Citrobacter freundii RFL6
<6>A. Janulaitis
<7>
<8>Butkus, V., Klimasauskas, S., Petrauskiene, L., Maneliene, Z., Lebionka, A., Janulaitis, A., (1987) Biochim. Biophys. Acta, vol. 909, pp. 201-207.
Janulaitis, A., Stakenas, P.S., Bitinaite, J.B., Jaskeleviciene, B.P., (1983) Dokl. Akad. Nauk., vol. 271, pp. 483-485.
Janulaitis, A., Stakenas, P.S., Petrusyte, M.P., Bitinaite, J.B., Klimasauskas, S.I., Butkus, V.V., (1983) Mol. Biol. (Mosk), vol. 18, pp. 115-129.

<1>Cfr7I
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>GGTNACC
<4>
<5>Citrobacter freundii RFL7
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Stakenas, P.S., Bitinaite, J.B., Jaskeleviciene, B.P., (1983) Dokl. Akad. Nauk., vol. 271, pp. 483-485.

<1>Cfr8I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Citrobacter freundii RFL8
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Stakenas, P.S., Bitinaite, J.B., Jaskeleviciene, B.P., (1983) Dokl. Akad. Nauk., vol. 271, pp. 483-485.

<1>Cfr9I
<2>SmaI,AhyI,CfrJ4I,EaeAI,EclRI,KteAI,Pac25I,PaeBI,PspAI,PspALI,TspMI,Uba1220I,Uba1393I,XcyI,XmaI,XmaCI
<3>C^CCGGG
<4>2(4)
<5>Citrobacter freundii
<6>A. Janulaitis
<7>FO
<8>Butkus, V., Petrauskiene, L., Maneliene, Z., Klimasauskas, S., Laucys, V., Janulaitis, A., (1987) Nucleic Acids Res., vol. 15, pp. 7091-7102.
Janulaitis, A., Stakenas, P.S., Bitinaite, J.B., Jaskeleviciene, B.P., (1983) Dokl. Akad. Nauk., vol. 271, pp. 483-485.
Janulaitis, A., Stakenas, P.S., Petrusyte, M.P., Bitinaite, J.B., Klimasauskas, S.I., Butkus, V.V., (1983) Mol. Biol. (Mosk), vol. 18, pp. 115-129.
Lubys, A., Menkevicius, S., Timinskas, A., Butkus, V., Janulaitis, A., (1994) Gene, vol. 141, pp. 85-89.
Siksnys, V., Pleckaityte, M., (1993) Eur. J. Biochem., vol. 217, pp. 411-419.

<1>Cfr10I
<2>Bco118I,BscRI,Bse118I,Bse634I,Bsp21I,BsrFI,BssAI,BstB7SI,NmeDI,TseDI
<3>R^CCGGY
<4>2(5)
<5>Citrobacter freundii RFL10
<6>A. Janulaitis
<7>FKO
<8>Grazulis, S., Deibert, M., Rimseliene, R., Skirgaila, R., Sasnauskas, G., Lagunavicius, A., Repin, V., Urbanke, C., Huber, R., Siksnys, V., (2002) Nucleic Acids Res., vol. 30, pp. 876-885.
Janulaitis, A., Stakenas, P.S., Berlin, Y.A., (1983) FEBS Lett., vol. 161, pp. 210-212.
Janulaitis, A., Stakenas, P.S., Petrusyte, M.P., Bitinaite, J.B., Klimasauskas, S.I., Butkus, V.V., (1983) Mol. Biol. (Mosk), vol. 18, pp. 115-129.
Klimasauskas, S., Butkus, V., Janulaitis, A., (1987) Mol. Biol. (Mosk), vol. 21, pp. 87-92.

<1>Cfr11I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter freundii RFL11
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Stakenas, P.S., Bitinaite, J.B., Jaskeleviciene, B.P., (1983) Dokl. Akad. Nauk., vol. 271, pp. 483-485.

<1>Cfr13I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>4(5)
<5>Citrobacter freundii RFL13
<6>A. Janulaitis
<7>FO
<8>Bitinaite, J.B., Klimasauskas, S.J., Butkus, V.V., Janulaitis, A., (1985) FEBS Lett., vol. 182, pp. 509-513.
Janulaitis, A., Stakenas, P.S., Bitinaite, J.B., Jaskeleviciene, B.P., (1983) Dokl. Akad. Nauk., vol. 271, pp. 483-485.

<1>Cfr14I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Citrobacter freundii RFL14
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Stakenas, P.S., Bitinaite, J.B., Jaskeleviciene, B.P., (1983) Dokl. Akad. Nauk., vol. 271, pp. 483-485.

<1>Cfr19I
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>GGTNACC
<4>
<5>Citrobacter freundii RFL19
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr20I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter freundii RFL20
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr22I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter freundii RFL22
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr23I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Citrobacter freundii RFL23
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Lebionka, A., Unpublished observations.

<1>Cfr24I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter freundii RFL24
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr25I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter freundii RFL25
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr27I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter freundii RFL27
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr28I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter freundii RFL28
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr29I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter freundii RFL29
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr30I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter freundii RFL30
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr31I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter freundii RFL31
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr32I
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Citrobacter freundii RFL32
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr33I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Citrobacter freundii RFL33
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr35I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter freundii RFL35
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr37I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Citrobacter freundii RFL37
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Lebionka, A., Unpublished observations.

<1>Cfr38I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Citrobacter freundii RFL38
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Lebionka, A., Unpublished observations.

<1>Cfr39I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Citrobacter freundii RFL39
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr40I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Citrobacter freundii RFL40
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr41I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Citrobacter freundii RFL41
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Lebionka, A., Unpublished observations.

<1>Cfr42I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>?(5)
<5>Citrobacter freundii RFL42
<6>A. Janulaitis
<7>F
<8>Gasiunas, G., Sasnauskas, G., Tamulaitis, G., Urbanke, C., Razaniene, D., Siksnys, V., (2008) Nucleic Acids Res., vol. 36, pp. 938-949.
Lazareviciute, L., Laucys, V., Maneliene, Z., Poliachenko, V., Bitinaite, J., Butkus, V., Janulaitis, A., Unpublished observations.
Rimseliene, R., Vaisvila, R., Janulaitis, A., Unpublished observations.

<1>Cfr43I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Citrobacter freundii RFL43
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr45I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Citrobacter freundii RFL45
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr45II
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Citrobacter freundii RFL45
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr46I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Citrobacter freundii RFL46
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr47I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Citrobacter freundii RFL47
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr48I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Citrobacter freundii RFL48
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Lazareviciute, L., Unpublished observations.

<1>Cfr51I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Citrobacter freundii RFL51
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Cfr52I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Citrobacter freundii RFL52
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Cfr54I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Citrobacter freundii RFL54
<6>A. Janulaitis
<7>
<8>Jagelavicius, M., Bitinaite, J., Janulaitis, A., Unpublished observations.

<1>Cfr55I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Citrobacter freundii RFL55
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Cfr56I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Citrobacter freundii RFL56
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Cfr57I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Citrobacter freundii RFL57
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Cfr58I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter freundii RFL58
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Cfr59I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Citrobacter freundii RFL59
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Cfr92I
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>CTTAAG
<4>
<5>Citrobacter freundii RFL92
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Grigaite, R., Bitinaite, J., Maneliene, Z., Butkus, V., Kiuduliene, L., Unpublished observations.

<1>CfrAI
<2>
<3>GCANNNNNNNNGTGG
<4>
<5>Citrobacter freundii
<6>NCTC 9750
<7>
<8>Daniel, A.S., Fuller-Pace, F.V., Legge, D.M., Murray, N.E., (1988) J. Bacteriol., vol. 170, pp. 1775-1782.
Kannan, P., Cowan, G.M., Daniel, A.S., Gann, A.A.F., Murray, N.E., (1989) J. Mol. Biol., vol. 209, pp. 335-344.

<1>CfrA4I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Citrobacter freundii A4
<6>CAMB 2537
<7>
<8>Riazuddin, S., Sohail, A., Maqbool, T., Khan, E., Mushtaq, R., (1987) Pak. J. Sci. Ind. Res., vol. 30, pp. 819-824.
Sohail, A., Unpublished observations.

<1>CfrBI
<2>StyI,BsmSI,BssT1I,Bst224I,Eco130I,Eco208II,EcoT14I,EcoT104I,ErhI,ErhB9II,SblAI,SblBI,SblCI,Uba1311I
<3>C^CWWGG
<4>1(4)
<5>Citrobacter freundii 4111
<6>A.S. Solonin
<7>
<8>Beletskaya, I.V., Zakharova, M.V., Shlyapnikov, M.G., Semenova, L.M., Solonin, A.S., (2000) Nucleic Acids Res., vol. 28, pp. 3817-3822.
Zakharova, M.V., Kravetz, A.N., Beletzkaja, I.V., Repyk, A.V., Solonin, A.S., (1993) Gene, vol. 129, pp. 77-81.

<1>CfrJ4I
<2>SmaI,AhyI,Cfr9I,EaeAI,EclRI,KteAI,Pac25I,PaeBI,PspAI,PspALI,TspMI,Uba1220I,Uba1393I,XcyI,XmaI,XmaCI
<3>CCC^GGG
<4>
<5>Citrobacter freundii J4
<6>CAMB 2599
<7>
<8>Mushtaq, R., Riazuddin, S., Unpublished observations.

<1>CfrJ5I
<2>BsePI,BscEI,BsoPI,BsrHI,BssBI,BssHII,BstBZ153I,Eco143I,Eco152I,Esp7I,Esp8I,Kpn30I,McaTI,PauI,PteI,TtmII,Uba69I
<3>GCGCGC
<4>
<5>Citrobacter freundii
<6>CAMB 2600
<7>
<8>Mushtaq, R., Unpublished observations.

<1>CfrNI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Citrobacter freundii
<6>ATCC 11102
<7>
<8>Schneider, A., Unpublished observations.

<1>CfrS37I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Citrobacter freundii S39
<6>W. Piepersberg
<7>
<8>Bolton, B.J., Comer, M.J., Kessler, C., Unpublished observations.

<1>CfuI
<2>DpnI,FtnUIV,MalI,Mph1103II,NanII,NgoDXIV,NmeAII,NmeBL859I,NmuDI,NmuEI,NsuDI,TdeI
<3>GA^TC
<4>
<5>Caulobacter fusiformis BC-25
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Marcinkeviciene, L.Y., Petrusyte, M.P., (1982) Dokl. Akad. Nauk., vol. 262, pp. 241-244.

<1>CfuII
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Caulobacter fusiformis BC-25
<6>A. Janulaitis
<7>
<8>Lebenka, A.Yu., Chitavichyus, D.B., (1988) Biokhimiia, vol. 53, pp. 1895-1899.

<1>M.CfuIII
<2>
<3>?
<4>
<5>Caulobacter fusiformis BC-25
<6>A. Janulaitis
<7>
<8>Lebenka, A.Yu., Chitavichyus, D.B., (1988) Biokhimiia, vol. 53, pp. 1895-1899.

<1>CglI
<2>TauI,BspUI,NgoFVII
<3>GCSGC
<4>?(5)
<5>Corynebacterium glutamicum
<6>ATCC 13032
<7>
<8>Ikeda, M., Nakagawa, S., (2003) Appl. Microbiol. Biotechnol., vol. 62, pp. 99-109.
Kalinowski, J. et al., (2003) J. Biotechnol., vol. 104, pp. 5-25.
Nakagawa, S., Mizoguchi, H., Ando, S., Hayashi, M., Ochiai, K., Yokoi, H., Tateishi, N., Senoh, A., Ikeda, M., Ozaki, A., Korean Patent Office, 2000.
Nakagawa, S., Mizoguchi, H., Ando, S., Hayashi, M., Ochiai, K., Yokoi, H., Tateishi, N., Senoh, A., Ikeda, M., Ozaki, A., US Patent Office, 2008.
Nakagawa, S., Mizoguchi, H., Ando, S., Hayashi, M., Ochiai, K., Yokoi, H., Tateishi, N., Senoo, A., Ikeda, M., Ozaki, A., Japanese Patent Office, 2002.
Pompejus, M., Kroeger, B., Schroeder, H., Zelder, O., Haberhauer, G., Korean Patent Office, 2001.
Pompejus, M., Kroeger, B., Schroeder, H., Zelder, O., Haberhauer, G., Korean Patent Office, 2006.
Roberts, R.J., Unpublished observations.
Schaefer, A., Tauch, A., Droste, N., Kalinowski, J., Puehler, A., Unpublished observations.
Schafer, A., Schwarzer, A., Kalinowski, J., Puhler, A., (1994) J. Bacteriol., vol. 176, pp. 7309-7319.
Schafer, A., Tauch, A., Droste, N., Puhler, A., Kalinowski, J., (1997) Gene, vol. 203, pp. 95-101.
Zelder, O., Schroeder, H., Haberhauer, G., Kroeger, B., Pompejus, M., Japanese Patent Office, 2004.

<1>Cgl165I
<2>
<3>?
<4>
<5>Corynebacterium glutamicum 165
<6>D.C. Ri
<7>
<8>Ra, S.R., Ri, D.C., (2000) Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo, vol. 0, pp. 36-38.

<1>CglAI
<2>SphI,Asp5HI,BbuI,BscOI,Bsp121I,BtgAII,PaeI,PaeCI,PfaAIII,RspLKI,SpaHI,SpaXI,Uba1162I,Uba1226I,VchO68I
<3>GCATGC
<4>
<5>Corynebacterium glutamicum
<6>NEB 968
<7>
<8>Polisson, C., Unpublished observations.

<1>CglAII
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Corynebacterium glutamicum
<6>NEB 968
<7>
<8>Polisson, C., Unpublished observations.

<1>ChaI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC^
<4>
<5>Corynebacterium halofytica
<6>M.M. Wijdenbosch
<7>
<8>Afram, C., Unpublished observations.

<1>ChiI
<2>
<3>?
<4>
<5>Clostridium histolyticum
<6>R. Hansen
<7>
<8>Hansen, R., Unpublished observations.

<1>ChuEI
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Corynebacterium humiferum
<6>ATCC 21108
<7>
<8>Endow, S.A., Roberts, R.J., Unpublished observations.

<1>ChuEII
<2>HindII,Hin1160II,Hin1161II,HinJCI,HincII,MnnI
<3>GTYRAC
<4>
<5>Corynebacterium humiferum
<6>ATCC 21108
<7>
<8>Endow, S.A., Roberts, R.J., Unpublished observations.

<1>ChyI
<2>StuI,AatI,Asp78I,AspMI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGGCCT
<4>
<5>Corynebacterium hydrocarboclastum
<6>ATCC 21628
<7>
<8>Hall, D., Unpublished observations.

<1>Cin1467I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Clostridium indolis 1467
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>CjaI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Catenuloplanes japonicus
<6>ATCC 31637
<7>
<8>Hamablet, L., Meyertons, J.L., Roberts, R.J., Unpublished observations.

<1>CjeI
<2>
<3>(8/14)CCANNNNNNGT(15/9)
<4>
<5>Campylobacter jejuni P37
<6>J.M.B. Vitor
<7>
<8>Vitor, J.M.B., (1999) Ph.D. Thesis, University of Lisbon (Lisbon), pp. 1-220.
Vitor, J.M.B., Morgan, R.D., (1995) Gene, vol. 157, pp. 109-110.

<1>M.CjeEDam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Campylobacter jejuni subsp. jejuni 81116
<6>NCTC 11828
<7>
<8>Judge, N.A., Fields, J.A., Pajaniappan, M., Newell, D.G., Manning, J., Burns, C.M., Thompson, S.A., (2005) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 105, pp. 79.
Pearson, B.M., Gaskin, D.J., Segers, R.P., Wells, J.M., Nuijten, P.J., Mvan, V.A.H., (2007) J. Bacteriol., vol. 189, pp. 8402-8403.

<1>CjeNII
<2>
<3>GAGNNNNNGT
<4>
<5>Campylobacter jejuni 11168
<6>NCTC 11168
<7>
<8>Parkhill, J. et al., (2000) Nature, vol. 403, pp. 665-668.
Vitor, J., Vital, J., Morgan, R.D., Unpublished observations.

<1>M.CjeNIII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Campylobacter jejuni 11168
<6>NCTC 11168
<7>
<8>Judge, N.A., Fields, J.A., Pajaniappan, M., Newell, D.G., Manning, J., Burns, C.M., Thompson, S.A., (2005) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 105, pp. 79.
Parkhill, J. et al., (2000) Nature, vol. 403, pp. 665-668.

<1>CjePI
<2>
<3>(7/13)CCANNNNNNNTC(14/8)
<4>
<5>Campylobacter jejuni P116
<6>J.M.B. Vitor
<7>
<8>Vitor, J.M.B., Morgan, R.D., (1995) Gene, vol. 157, pp. 109-110.

<1>CjeP338I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Campylobacter jejuni P338
<6>J.M.B. Vitor
<7>
<8>Vitor, J.M.B., Unpublished observations.

<1>CjeP338II
<2>SfaNI,BhaI,BmsI,BscAI,BscUI,BsmNI,BspST5I,Bst19I,LweI,PhaI
<3>GCATC
<4>
<5>Campylobacter jejuni P338
<6>J.M.B. Vitor
<7>
<8>Vitor, J.M.B., Unpublished observations.

<1>CjuI
<2>
<3>CAYNNNNNRTG
<4>
<5>Campylobacter jejuni RFL1
<6>Fermentas G311
<7>
<8>Vitkute, J., Lauciuniene, N., Riauba, L., Capskaja, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>CjuII
<2>
<3>CAYNNNNNCTC
<4>
<5>Campylobacter jejuni RFL1
<6>Fermentas G311
<7>
<8>Vitkute, J., Lauciuniene, N., Riauba, L., Capskaja, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>ClaI
<2>AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>5(6)
<5>Caryophanon latum L
<6>ATCC 49862
<7>BHKMNRSU
<8>Longo, M.C., Smith, M.D., Chatterjee, D.K., US Patent Office, 1994.
Mayer, H., Grosschedl, R., Schutte, H., Hobom, G., (1981) Nucleic Acids Res., vol. 9, pp. 4833-4845.
McClelland, M., (1981) Nucleic Acids Res., vol. 9, pp. 6795-6804.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>ClcI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Cylindrospermum lichenforme
<6>ATCC 29412
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>ClcII
<2>MstI,AcaIII,Acc16I,AosI,ApcTR183I,AviII,Bco6I,BsaTI,CliII,FdiII,FspI,GspAII,NsbI,NspHIII,NspLI,NspMI,PamI,Pun14627I
<3>TGCGCA
<4>
<5>Cylindrospermum lichenforme
<6>ATCC 29412
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>CliI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Cylindrospermum lichenforme
<6>UTEX 2014
<7>
<8>Karreman, C., de Waard, A., Unpublished observations.

<1>CliII
<2>MstI,AcaIII,Acc16I,AosI,ApcTR183I,AviII,Bco6I,BsaTI,ClcII,FdiII,FspI,GspAII,NsbI,NspHIII,NspLI,NspMI,PamI,Pun14627I
<3>TGCGCA
<4>
<5>Cylindrospermum lichenforme
<6>UTEX 2014
<7>
<8>Karreman, C., de Waard, A., Unpublished observations.

<1>CliIII
<2>
<3>?
<4>
<5>Cylindrospermum lichenforme
<6>UTEX 2014
<7>
<8>Karreman, C., de Waard, A., Unpublished observations.

<1>ClmI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Caryophanon latum
<6>ATCC 15219
<7>
<8>Smith, J., Comb, D., Unpublished observations.

<1>ClmII
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Caryophanon latum
<6>ATCC 15219
<7>
<8>Smith, J., Comb, D., Unpublished observations.

<1>CltI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Caryophanon latum
<6>DSM 484
<7>
<8>Mayer, H., Schutte, H., Unpublished observations.

<1>CluI
<2>
<3>?
<4>
<5>Caryophanon latum RII
<6>H. Mayer
<7>
<8>Mayer, H., Schutte, H., Unpublished observations.

<1>Cpa1150I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Clostridium pasteurianum 1150
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>CpaAI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Clostridium pasteurianum
<6>ATCC 6013
<7>
<8>Richards, D.F., Linnett, P.E., Oultram, J.D., Young, M., (1988) J. Gen. Microbiol., vol. 134, pp. 3151-3157.

<1>CpaPI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Clostridium pasteurianum
<6>NRCC 33011
<7>
<8>Venetianer, P., Unpublished observations.

<1>CpeI
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Corynebacterium petrophilum
<6>ATCC 19080
<7>
<8>Fisherman, J., Gingeras, T.R., Roberts, R.J., Unpublished observations.

<1>CpfI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Clostridium perfringens
<6>R. Hansen
<7>
<8>Hansen, R., Unpublished observations.

<1>CpfAI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Clostridium perfringens
<6>H.P. Blaschek
<7>
<8>Tay, N.K., Blaschek, H.P., (1994) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 94, pp. 224.

<1>CpoI
<2>RsrII,CspI,Rsr2I
<3>CG^GWCCG
<4>
<5>Caseobacter polymorphus
<6>ATCC 33010
<7>FK
<8>Kotani, H., Sagawa, H., Nakajima, K., Unpublished observations.
Polisson, C., Unpublished observations.

<1>CprJK699I
<2>
<3>?
<4>
<5>Clostridium proteoclasticum JK 669
<6>P. Pristas
<7>
<8>Mrazek, J., Piknova, M., Pristas, P., Kopecny, J., (2005) Anaerobe, vol. 11, pp. 280-284.

<1>CprJK722I
<2>VspI,AseI,AsnI,BpoAI,PbuMZI,PshBI,Srl8DI,Srl55DII,Srl65DI,Srr17I,Sru4DI
<3>ATTAAT
<4>
<5>Clostridium proteoclasticum JK 722
<6>P. Pristas
<7>
<8>Mrazek, J., Piknova, M., Pristas, P., Kopecny, J., (2005) Anaerobe, vol. 11, pp. 280-284.

<1>M.CreDnmt1
<2>
<3>?
<4>?(5)
<5>Chlamydomonas reinhardtii
<6>J.-D. Rochaix
<7>
<8>Kobayashi, I., (2001) Tanpakushitsu Kakusan Koso, vol. 46, pp. 2393-2399.
Nishiyama, R., Ito, M., Yamaguchi, Y., Koizumi, N., Sano, H., (2002) Plant Cell Physiol., vol. 43.
Nishiyama, R., Wada, Y., Mibu, M., Yamaguchi, Y., Shimogawara, K., Sano, H., (2004) Genetics, vol. 168, pp. 809-816.

<1>CscI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Calothrix scopulorum
<6>CCAP 1410/5
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., (1981) Plant Mol. Biol., vol. 1, pp. 75-79.

<1>CseI
<2>HgaI,NmeBI
<3>GACGC(5/10)
<4>
<5>Chryseobacterium species RFL1
<6>Fermentas G281
<7>F
<8>Nekrasiene, D., Vitkute, J., Maneliene, Z., Capskaja, L., Trinkunaite, L., Janulaitis, A., Unpublished observations.

<1>CsiI
<2>SexAI,MabI
<3>A^CCWGGT
<4>
<5>Cellulomonas species RFL1
<6>Fermentas G356
<7>F
<8>Vitkute, J., Lapcinskaja, S., Capskaja, L., Trinkunaite, L., Zakareviciene, L., Lubys, A., Janulaitis, A., Unpublished observations.

<1>CsiAI
<2>AgeI,AsiAI,AsiGI,BshTI,CspAI,PinAI
<3>A^CCGGT
<4>
<5>Corynebacterium species A
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., (1995) Vestn. Akad. Med. Nauk SSSR, vol. 2, pp. 47-51.

<1>CsiBI
<2>NotI,CciNI,CspBI,MchAI
<3>GC^GGCCGC
<4>
<5>Corynebacterium species B
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., (1995) Vestn. Akad. Med. Nauk SSSR, vol. 2, pp. 47-51.

<1>CspI
<2>RsrII,CpoI,Rsr2I
<3>CG^GWCCG
<4>
<5>Corynebacterium species
<6>M. Nelson
<7>OR
<8>Nelson, M., McClelland, M., Unpublished observations.

<1>Csp2I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Corynebacterium species RFL2
<6>A. Janulaitis
<7>
<8>Jagelavicius, M., Bitinaite, J., Janulaitis, A., Unpublished observations.

<1>Csp4I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Corynebacterium species RFL4
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Csp5I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Corynebacterium species RFL5
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Csp6I
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>G^TAC
<4>
<5>Corynebacterium species RFL6
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.
Rimseliene, R., Janulaitis, A., Unpublished observations.

<1>Csp45I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Clostridium sporogenes
<6>T. Schoenfeld
<7>OR
<8>Schoenfeld, T., Mead, D.A., Fiandt, M., (1989) Nucleic Acids Res., vol. 17, pp. 4417.

<1>Csp231I
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Citrobacter sp. RFL231
<6>T. Kaczorowski
<7>
<8>Mruk, I., Kaczorowski, T., (2007) Appl. Environ. Microbiol., vol. 73, pp. 4286-4293.

<1>Csp1470I
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCGC
<4>
<5>Clostridium sporogenes 1470
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>CspAI
<2>AgeI,AsiAI,AsiGI,BshTI,CsiAI,PinAI
<3>A^CCGGT
<4>
<5>Corynebacterium species 301
<6>N.N. Sokolov
<7>C
<8>Rina, M., Markaki, M., Sokolov, N., Bouriotis, V., Unpublished observations.

<1>CspBI
<2>NotI,CciNI,CsiBI,MchAI
<3>GC^GGCCGC
<4>
<5>Corynebacterium species B
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Eldarov, M.A., Rina, M., Korolev, S.V., Markaki, M., Kalugin, A.A., Omelyanuk, N.M., Skryabin, K.G., Bouriotis, V., (1998) Biochem. Mol. Biol. Int., vol. 44, pp. 433-441.

<1>CspCI
<2>
<3>(11/13)CAANNNNNGTGG(12/10)
<4>
<5>Citrobacter species 2144
<6>NEB 1398
<7>N
<8>Lunnen, K.D., Heiter, D.F., Benner, J.S., Wilson, G.G., Unpublished observations.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
Morgan, R., Nkenfou, C.N., US Patent Office, 2005.
Morgan, R., Wilson, G., Lunnen, K., Heiter, D., Benner, J., Nkenfou, C.N., Picone, S., International Patent Office, 2005.

<1>Csp68KI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>?(5)
<5>Cyanothece species BH68K
<6>ATCC 51142
<7>
<8>Soper, B.W., Reddy, K.J., (1994) J. Bacteriol., vol. 176, pp. 5565-5570.
Welsh, E.A., Liberton, M., Stockel, J., Sato, H., Loh, T., Wang, C., Wollam, A., Fulton, R.S., Clifton, S.W., Jacobs, J.M., Aurora, R., Sherman, L.A., Smith, R.D., Wilson, R.K., Pakrasi, H.B., Unpublished observations.

<1>Csp68KII
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Cyanothece species BH68K
<6>ATCC 51142
<7>
<8>Soper, B.W., (1996) Diss. Abstr., vol. 56, pp. 3585B.
Welsh, E.A., Liberton, M., Stockel, J., Sato, H., Loh, T., Wang, C., Wollam, A., Fulton, R.S., Clifton, S.W., Jacobs, J.M., Aurora, R., Sherman, L.A., Smith, R.D., Wilson, R.K., Pakrasi, H.B., Unpublished observations.

<1>Csp68KIII
<2>AvaIII,Asi372I,BfrBI,BfrCI,EcoT22I,Mph1103I,NsiI,PinBI,Ppu10I,PxyJKI,SepI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>ATGCA^T
<4>
<5>Cyanothece species BH68K
<6>ATCC 51142
<7>
<8>Soper, B.W., (1996) Diss. Abstr., vol. 56, pp. 3585B.
Welsh, E.A., Liberton, M., Stockel, J., Sato, H., Loh, T., Wang, C., Wollam, A., Fulton, R.S., Clifton, S.W., Jacobs, J.M., Aurora, R., Sherman, L.A., Smith, R.D., Wilson, R.K., Pakrasi, H.B., Unpublished observations.

<1>M.Csp68KIV
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>?(5)
<5>Cyanothece species BH68K
<6>ATCC 51142
<7>
<8>Soper, B.W., Hollister, W.R., Reddy, K.J., (1998) J. Mar. Biotechnol., vol. 6, pp. 183-185.
Welsh, E.A., Liberton, M., Stockel, J., Sato, H., Loh, T., Wang, C., Wollam, A., Fulton, R.S., Clifton, S.W., Jacobs, J.M., Aurora, R., Sherman, L.A., Smith, R.D., Wilson, R.K., Pakrasi, H.B., Unpublished observations.

<1>M.Csp68KV
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Cyanothece species BH68K
<6>ATCC 51142
<7>
<8>Soper, B.W., Hollister, W.R., Reddy, K.J., (1998) J. Mar. Biotechnol., vol. 6, pp. 183-185.
Welsh, E.A., Liberton, M., Stockel, J., Sato, H., Loh, T., Wang, C., Wollam, A., Fulton, R.S., Clifton, S.W., Jacobs, J.M., Aurora, R., Sherman, L.A., Smith, R.D., Wilson, R.K., Pakrasi, H.B., Unpublished observations.

<1>Csp68KVI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>
<5>Cyanothece species BH68K
<6>ATCC 51142
<7>
<8>Soper, B.W., Hollister, W.R., Reddy, K.J., (1998) J. Mar. Biotechnol., vol. 6, pp. 183-185.

<1>CstI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Clostridium sticklandii
<6>C.S. Chen
<7>
<8>Jou, T.-W., Chen, C.-S., (1988) Bot. Bull. Acad. Sinica, vol. 29, pp. 201-208.

<1>CstMI
<2>
<3>AAGGAG(20/18)
<4>
<5>Corynebacterium striatum M82B
<6>A. Tauch
<7>
<8>Morgan, R.D., Bhatia, T., US Patent Office, 2007.
Morgan, R.D., Bhatia, T., US Patent Office, 2005.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>CsuI
<2>
<3>?
<4>
<5>Caulobacter subvibroides
<6>ATCC 15264
<7>
<8>Grandoni, R., Unpublished observations.

<1>Cte1I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Comamonas testosteroni RFL1
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Cte1179I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Clostridium tetanomorphum 1179
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>Cte1180I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Clostridium tetanomorphum 1180
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>CthI
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Clostridium thermocellum
<6>ATCC 27405
<7>
<8>Choi, K.D., Kim, K., Yoo, O.J., (1987) Sanop Misaengmul Hakhoe Chi, vol. 15, pp. 352-355.

<1>CthII
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Clostridium thermocellum
<6>ATCC 27405
<7>
<8>Choi, K.D., Yoo, O.J., (1990) Korean Biochem. J., vol. 23, pp. 418-421.

<1>CtyI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Clostridium thermohydrosulfuricum
<6>DSM 568
<7>
<8>Richards, D.F., Linnett, P.E., Oultram, J.D., Young, M., (1988) J. Gen. Microbiol., vol. 134, pp. 3151-3157.

<1>CveI
<2>
<3>?
<4>
<5>Cystobacter velatus Plv9
<6>H. Reichenbach
<7>
<8>Mayer, H., Schutte, H., Unpublished observations.

<1>CviI
<2>
<3>?
<4>
<5>Chromobacterium violaceum
<6>ATCC 12472
<7>
<8>Endow, S.A., Roberts, R.J., Unpublished observations.

<1>CviAI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>2(6)
<5>Chlorella strain NC64A (PBCV-1)
<6>J.L. Van Etten
<7>
<8>Xia, Y., Burbank, D.E., Uher, L., Rabussay, D., Van Etten, J.L., (1986) Mol. Cell. Biol., vol. 6, pp. 1430-1439.
Xia, Y., Van Etten, J.L., (1986) Mol. Cell. Biol., vol. 6, pp. 1440-1445.

<1>CviAII
<2>NlaIII,FaeI,FatI,FatII,Hin1II,Hin8II,HpyCH4I,Hsp92II
<3>C^ATG
<4>2(6)
<5>Chlorella strain NC64A (PBCV-1)
<6>J.L. Van Etten
<7>N
<8>Gurnon, J.R., Graves, M.V., Van Etten, J.L., Unpublished observations.
Zhang, Y., Nelson, M., Nietfeldt, J.W., Burbank, D.E., Van Etten, J.L., (1992) Nucleic Acids Res., vol. 20, pp. 5351-5356.

<1>M.CviAIV
<2>M.CviJI
<3>RGCB
<4>3(5)
<5>Chlorella strain NC64A (PBCV-1)
<6>J.L. Van Etten
<7>
<8>Kutish, G.F., Li, Y., Lu, Z., Furuta, M., Rock, D.L., Van Etten, J.L., (1996) Virology, vol. 223, pp. 303-317.
Zhang, Y., Nelson, M., Van Etten, J.L., (1992) Nucleic Acids Res., vol. 20, pp. 1637-1642.

<1>M.CviAV
<2>
<3>?
<4>?(5)
<5>Chlorella strain NC64A (PBCV-1)
<6>J.L. Van Etten
<7>
<8>Lu, Z., Li, Y., Que, Q., Kutish, G.F., Rock, D.L., Van Etten, J.L., (1996) Virology, vol. 216, pp. 102-123.
Nelson, M., Burbank, D.E., Van Etten, J.L., (1998) Biol. Chem., vol. 379, pp. 423-428.

<1>CviBI
<2>HinfI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>G^ANTC
<4>2(6)
<5>Chlorella strain NC64A (NC-1A)
<6>J.L. Van Etten
<7>
<8>Kan, T.N., Lin, L., Chandrasegaran, S., (1992) Gene, vol. 121, pp. 1-7.
Xia, Y., Burbank, D.E., Van Etten, J.L., (1986) Nucleic Acids Res., vol. 14, pp. 6017-6030.

<1>M.CviBII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Chlorella strain NC64A (NC-1A)
<6>J.L. Van Etten
<7>
<8>Narva, K.E., Wendell, D.L., Skrdla, M.P., Van Etten, J.L., (1987) Nucleic Acids Res., vol. 15, pp. 9807-9823.
Van Etten, J.L., Xia, Y., Burbank, D.E., (1989) J. Cell Biochem. Suppl., vol. 13D, pp. 199.

<1>M.CviBIII
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>4(6)
<5>Chlorella strain NC64A (NC-1A)
<6>J.L. Van Etten
<7>
<8>Narva, K.E., Wendell, D.L., Skrdla, M.P., Van Etten, J.L., (1987) Nucleic Acids Res., vol. 15, pp. 9807-9823.

<1>CviCI
<2>HinfI,CviBI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Chlorella strain NC64A (NE-8A)
<6>J.L. Van Etten
<7>
<8>Xia, Y., Burbank, D.E., Van Etten, J.L., (1986) Nucleic Acids Res., vol. 14, pp. 6017-6030.

<1>CviDI
<2>HinfI,CviBI,CviCI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Chlorella strain NC64A (Al-2C)
<6>J.L. Van Etten
<7>
<8>Xia, Y., Burbank, D.E., Van Etten, J.L., (1986) Nucleic Acids Res., vol. 14, pp. 6017-6030.

<1>CviEI
<2>HinfI,CviBI,CviCI,CviDI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Chlorella strain NC64A (MA-1E)
<6>J.L. Van Etten
<7>
<8>Xia, Y., Burbank, D.E., Van Etten, J.L., (1986) Nucleic Acids Res., vol. 14, pp. 6017-6030.

<1>CviFI
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Chlorella strain NC64A (NY-2F)
<6>J.L. Van Etten
<7>
<8>Xia, Y., Burbank, D.E., Van Etten, J.L., (1986) Nucleic Acids Res., vol. 14, pp. 6017-6030.

<1>CviGI
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Chlorella strain NC64A (CA-1D)
<6>J.L. Van Etten
<7>
<8>Xia, Y., Burbank, D.E., Van Etten, J.L., (1986) Nucleic Acids Res., vol. 14, pp. 6017-6030.

<1>CviHI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Chlorella strain NC64A (NC-1C)
<6>J.L. Van Etten
<7>
<8>Xia, Y., Burbank, D.E., Van Etten, J.L., Unpublished observations.

<1>CviJI
<2>CviKI,CviKI-I,CviLI,CviMI,CviNI,CviOI
<3>RG^CY
<4>3(5)
<5>Chlorella strain NC64A (IL-3A)
<6>J.L. Van Etten
<7>QX
<8>Shields, S.L., Burbank, D.E., Grabherr, R., Van Etten, J.L., (1990) Virology, vol. 176, pp. 16-24.
Swaminathan, N., Mead, D.A., McMaster, K., George, D., Van Etten, J.L., Skowron, P.M., (1996) Nucleic Acids Res., vol. 24, pp. 2463-2469.
Xia, Y., Burbank, D.E., Uher, L., Rabussay, D., Van Etten, J.L., (1987) Nucleic Acids Res., vol. 15, pp. 6075-6090.

<1>CviKI
<2>CviJI,CviKI-I,CviLI,CviMI,CviNI,CviOI
<3>RG^CY
<4>3(5)
<5>Chlorella strain NC64A (CA-1A)
<6>J.L. Van Etten
<7>
<8>Agarwal, K., Unpublished observations.
Nelson, M., Van Etten, J.L., Unpublished observations.
Xu, S.-Y., Unpublished observations.
Zhu, Z., Xu, S.-Y., Unpublished observations.

<1>CviKI-I
<2>CviJI,CviKI,CviLI,CviMI,CviNI,CviOI
<3>RG^CY
<4>
<5>Chlorella strain NC64A (CA-1A)
<6>NEB 1772
<7>N
<8>Xu, S.-Y., Unpublished observations.

<1>CviLI
<2>CviJI,CviKI,CviKI-I,CviMI,CviNI,CviOI
<3>RGCY
<4>
<5>Chlorella strain NC64A (CA-2A)
<6>J.L. Van Etten
<7>
<8>Agarwal, K., Unpublished observations.

<1>CviMI
<2>CviJI,CviKI,CviKI-I,CviLI,CviNI,CviOI
<3>RGCY
<4>
<5>Chlorella strain NC64A (IL-2A)
<6>J.L. Van Etten
<7>
<8>Agarwal, K., Unpublished observations.

<1>CviNI
<2>CviJI,CviKI,CviKI-I,CviLI,CviMI,CviOI
<3>RGCY
<4>
<5>Chlorella strain NC64A (IL-2B)
<6>J.L. Van Etten
<7>
<8>Agarwal, K., Unpublished observations.

<1>CviOI
<2>CviJI,CviKI,CviKI-I,CviLI,CviMI,CviNI
<3>RGCY
<4>
<5>Chlorella strain NC64A (IL-3D)
<6>J.L. Van Etten
<7>
<8>Agarwal, K., Unpublished observations.

<1>M.CviPI
<2>
<3>GC
<4>2(5)
<5>Chlorella strain NC64A (NYs-1)
<6>J.L. Van Etten
<7>
<8>Kladde, M.P., Simpson, R.T., Xu, M., US Patent Office, 2006.
Xu, M., Kladde, M.P., Van Etten, J.L., Simpson, R.T., (1998) Nucleic Acids Res., vol. 26, pp. 3961-3966.

<1>CviQI
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>G^TAC
<4>3(6)
<5>Chlorella strain NC64A (NY-2A)
<6>J.L. Van Etten
<7>N
<8>Van Etten, J.L., Unpublished observations.
Xia, Y., Narva, K.E., Van Etten, J.L., (1987) Nucleic Acids Res., vol. 15, pp. 10063.
Zhang, Y., Nelson, M., Nietfeldt, J., Xia, Y., Burbank, D., Ropp, S., Van Etten, J.L., Unpublished observations.
Zhang, Y., Nelson, M., Nietfeldt, J., Xia, Y., Burbank, D., Ropp, S., Van Etten, J.L., (1998) Virology, vol. 240, pp. 366-375.
Zhu, Z., Unpublished observations.

<1>CviRI
<2>Hpy26I,HpyCH4V,HpyF36III,HpyF38II,HpyF44III,HpyF45II,HpyF48III,HpyF49V,HpyF67II,HpyJP26I
<3>TG^CA
<4>4(6)
<5>Chlorella strain NC64A (XZ-6E)
<6>J.L. Van Etten
<7>
<8>Hickman, A.B., Li, Y., Mathew, S.V., May, E.W., Craig, N.L., Dyda, F., (2000) Mol. Cell, vol. 5, pp. 1025-1034.
Jin, A., Zhang, Y., Xia, Y., Traylor, E., Nelson, M., Van Etten, J.L., (1994) Nucleic Acids Res., vol. 22, pp. 3928-3929.
Stefan, C., Xia, Y., Van Etten, J.L., (1991) Nucleic Acids Res., vol. 19, pp. 307-311.
Xia, Y., Van Etten, J.L., Dobos, P., Ling, Y.Y., Krell, P.J., (1993) Virology, vol. 196, pp. 817-824.

<1>CviRII
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>G^TAC
<4>3(6)
<5>Chlorella strain NC64A (XZ-6E)
<6>J.L. Van Etten
<7>
<8>Nelson, M., Zhang, Y., Van Etten, J.L., (1993) DNA Methylation: Molecular Biology and Biological Significance, ed. Jost, J.P., Saluz, H.P. (Birkhauser Verlag, Basel, Switzerland), vol. 0, pp. 186-211.

<1>M.CviSI
<2>CviRI,Hpy26I,HpyCH4V,HpyF36III,HpyF38II,HpyF44III,HpyF45II,HpyF48III,HpyF49V,HpyF67II,HpyJP26I
<3>TGCA
<4>4(6)
<5>Chlorella strain NC64A (SC-1A)
<6>J.L. Van Etten
<7>
<8>Que, Q., Zhang, Y., Nelson, M., Ropp, S., Burbank, D.E., Van Etten, J.L., (1997) Gene, vol. 190, pp. 237-244.

<1>M.CviSII
<2>NlaIII,CviAII,FaeI,FatI,FatII,Hin1II,Hin8II,HpyCH4I,Hsp92II
<3>CATG
<4>2(6)
<5>Chlorella strain NC64A (SC-1A)
<6>J.L. Van Etten
<7>
<8>Que, Q., Zhang, Y., Nelson, M., Ropp, S., Burbank, D.E., Van Etten, J.L., (1997) Gene, vol. 190, pp. 237-244.

<1>CviSIII
<2>TaqI,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>4(6)
<5>Chlorella strain NC64A (SC-1A)
<6>J.L. Van Etten
<7>
<8>Nelson, M., Que, Q., Van Etten, J.L., Unpublished observations.
Que, Q., Zhang, Y., Nelson, M., Ropp, S., Burbank, D.E., Van Etten, J.L., (1997) Gene, vol. 190, pp. 237-244.

<1>CvnI
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CC^TNAGG
<4>
<5>Chromatium vinosum
<6>G.C. Grosveld
<7>
<8>Grosveld, G.C., Unpublished observations.

<1>DaqI
<2>ApaLI,AaqI,Alw44I,AmeI,Bsp146I,Pfl23I,Pfr12I,PliI,ScoNI,SnoI,Uba1203I,Uba1387I,VneI
<3>GTGCAC
<4>
<5>Deleya aquamana
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>M.DcaI
<2>
<3>?
<4>?(5)
<5>Daucus carota
<6>R. Cella
<7>
<8>Bernacchia, G., Primo, A., Giorgetti, L., Pitto, L., Cella, R., (1998) Plant J., vol. 13, pp. 317-329.

<1>M.DcaII
<2>
<3>?
<4>?(5)
<5>Daucus carota
<6>R. Cella
<7>
<8>Bernacchia, G., Primo, A., Giorgetti, L., Pitto, L., Cella, R., (1998) Plant J., vol. 13, pp. 317-329.

<1>DdeI
<2>Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>C^TNAG
<4>1(5)
<5>Desulfovibrio desulfuricans Norway strain
<6>NCIB 83120
<7>BMNORSW
<8>Brooks, J.E., Howard, K.A., US Patent Office, 1994.
Gelinas, R.E., Roberts, R.J., Unpublished observations.
Howard, K.A., Card, C., Benner, J.S., Callahan, H.L., Maunus, R., Silber, K., Wilson, G., Brooks, J.E., (1986) Nucleic Acids Res., vol. 14, pp. 7939-7951.
Makula, R.A., Meagher, R.B., (1980) Nucleic Acids Res., vol. 8, pp. 3125-3131.
Sznyter, L.A., Slatko, B., Moran, L., O'Donnell, K.H., Brooks, J.E., (1987) Nucleic Acids Res., vol. 15, pp. 8249-8266.

<1>DdeII
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Desulfovibrio desulfuricans Norway strain
<6>NCIB 83120
<7>
<8>Myers, P.A., Roberts, R.J., Unpublished observations.

<1>DdsI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Desulfovibrio desulfuricans
<6>ATCC 27774
<7>
<8>Lucas, S. et al., Unpublished observations.
Makula, R.A., Unpublished observations.

<1>DinI
<2>NarI,BbeI,BbeAI,BinSII,Eco78I,EgeI,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GGC^GCC
<4>
<5>Deinococcus indicus
<6>Vivantis 83
<7>V
<8>Chee, H.Y., Unpublished observations.

<1>DmaI
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>
<5>Deleya marina
<6>IAM 14114
<7>
<8>Mizuno, H., Suzuki, T., Yamada, Y., Akagawa, M., Yamasato, K., (1990) Agric. Biol. Chem., vol. 54, pp. 2863-2867.

<1>DmoAI
<2>
<3>?
<4>
<5>Desulfococcus mobilus
<6>W. Zillig
<7>
<8>McWilliam, P., Unpublished observations.

<1>DpaI
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGT^ACT
<4>
<5>Deleya pacifica
<6>IAM 14115
<7>
<8>Suzuki, T., Sato, Y., Yamada, Y., Akagawa-Matsushita, M., Yamasato, K., (1991) Agric. Biol. Chem., vol. 55, pp. 2647-2649.

<1>DpnI
<2>CfuI,FtnUIV,MalI,Mph1103II,NanII,NgoDXIV,NmeAII,NmeBL859I,NmuDI,NmuEI,NsuDI,TdeI
<3>GA^TC
<4>
<5>Diplococcus pneumoniae
<6>S. Lacks
<7>BEFMNORSWX
<8>Geier, G.E., Modrich, P., (1979) J. Biol. Chem., vol. 254, pp. 1408-1413.
Lacks, S., Greenberg, B., (1975) J. Biol. Chem., vol. 250, pp. 4060-4066.
Lacks, S., Greenberg, B., (1977) J. Mol. Biol., vol. 114, pp. 153-168.

<1>DpnII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>2(6)
<5>Diplococcus pneumoniae
<6>S. Lacks
<7>N
<8>Cerritelli, S., White, S.W., Springhorn, S.S., Lacks, S.A., (1990) FASEB J., vol. 4.
de la Campa, A.G., Kale, P., Springhorn, S.S., Lacks, S.A., (1987) J. Mol. Biol., vol. 196, pp. 457-469.
Lacks, S., Greenberg, B., (1975) J. Biol. Chem., vol. 250, pp. 4060-4066.
Lacks, S., Greenberg, B., (1977) J. Mol. Biol., vol. 114, pp. 153-168.
Lacks, S.A., Dunn, J.J., Greenberg, B., (1982) Cell, vol. 31, pp. 327-336.
Lacks, S.A., Springhorn, S.S., (1984) J. Bacteriol., vol. 157, pp. 934-936.

<1>DraI
<2>AhaIII,PauAII,Srl19I,Srl61DI,Srl76DI,SruI
<3>TTT^AAA
<4>6(6)
<5>Deinococcus radiophilus
<6>ATCC 27603
<7>BFIJKMNOQRSUVWXY
<8>Benner, J.S., Unpublished observations.
Kur, J., (1993) Acta Microbiol. Pol., vol. 42, pp. 145-150.
Morgan, R.D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Purvis, I.J., Moseley, B.E.B., (1983) Nucleic Acids Res., vol. 11, pp. 5467-5474.

<1>DraII
<2>EcoO109I,Kaz48kI,PssI,Uba1326I,VneAI
<3>RG^GNCCY
<4>
<5>Deinococcus radiophilus
<6>ATCC 27603
<7>MW
<8>Benner, J.S., Unpublished observations.
de Wit, C.M., Dekker, B.M.M., Neele, A.C., de Waard, A., (1985) FEBS Lett., vol. 180, pp. 219-223.
Grosskopf, R., Wolf, W., Kessler, C., (1985) Nucleic Acids Res., vol. 13, pp. 1517-1528.
Hansen, R., Unpublished observations.

<1>DraIII
<2>AdeI,BstIZ316I
<3>CACNNN^GTG
<4>2(6)
<5>Deinococcus radiophilus
<6>ATCC 27603
<7>IMNVW
<8>de Wit, C.M., Dekker, B.M.M., Neele, A.C., de Waard, A., (1985) FEBS Lett., vol. 180, pp. 219-223.
Grosskopf, R., Wolf, W., Kessler, C., (1985) Nucleic Acids Res., vol. 13, pp. 1517-1528.
Hansen, R., Unpublished observations.
Kong, H., Higgins, L.S., Dalton, M.A., US Patent Office, 2000.

<1>DraRI
<2>
<3>CAAGNAC(20/18)
<4>
<5>Deinococcus radiophilus R1
<6>ATCC BAA-816
<7>
<8>Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.
White, O. et al., (1999) Science, vol. 286, pp. 1571-1577.

<1>DrdI
<2>AasI,DseDI,TrsSII
<3>GACNNNN^NNGTC
<4>
<5>Deinococcus radiodurans
<6>NEB 479
<7>N
<8>Polisson, C., Morgan, R.D., (1989) Nucleic Acids Res., vol. 17, pp. 3316.

<1>DrdII
<2>
<3>GAACCA
<4>
<5>Deinococcus radiodurans
<6>NEB 479
<7>
<8>Polisson, C., Murray, R.G.E., Unpublished observations.

<1>DrdIII
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Deinococcus radiodurans
<6>NEB 479
<7>
<8>Polisson, C., Murray, R.G.E., Unpublished observations.

<1>DrdIV
<2>
<3>TACGAC(20/18)
<4>
<5>Deinococcus radiodurans
<6>NEB 479
<7>
<8>Dwinnel, E., Morgan, R.D., Unpublished observations.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>DrdAI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Deinococcus radiodurans 1048
<6>R.G.E. Murray
<7>
<8>Polisson, C., Murray, R.G.E., Unpublished observations.

<1>DrdBI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Deinococcus radiodurans 288
<6>R.G.E. Murray
<7>
<8>Polisson, C., Murray, R.G.E., Unpublished observations.

<1>DrdCI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Deinococcus radiodurans 1054
<6>R.G.E. Murray
<7>
<8>Polisson, C., Murray, R.G.E., Unpublished observations.

<1>DrdDI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Deinococcus radiodurans 1077
<6>R.G.E. Murray
<7>
<8>Croft, R., Murray, R.G.E., Unpublished observations.

<1>DrdEI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Deinococcus radiodurans 1050
<6>R.G.E. Murray
<7>
<8>Croft, R., Murray, R.G.E., Unpublished observations.

<1>DrdFI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Deinococcus radiodurans 1051
<6>R.G.E. Murray
<7>
<8>Polisson, C., Murray, R.G.E., Unpublished observations.

<1>M.DreLDnmt1
<2>
<3>?
<4>?(5)
<5>Danio rerio
<6>E. Li
<7>
<8>Martin, C.C., Laforest, L., Akimenko, M.-A., Ekker, M., Unpublished observations.
Mhanni, A.A., Yoder, J.A., Dubesky, C., McGowan, R.A., (2001) Genesis, vol. 30, pp. 213-219.

<1>M.DreLDnmt3
<2>
<3>?
<4>?(5)
<5>Danio rerio
<6>E. Li
<7>
<8>Mhanni, A.A., Yoder, J.A., Dubesky, C., McGowan, R.A., (2001) Genesis, vol. 30, pp. 213-219.
Shimoda, N., Unpublished observations.
Shimoda, N., Yamakoshi, K., Miyake, A., Takeda, H., (2005) Dev. Dyn., vol. 233, pp. 1509-1516.
Xie, S., Wang, Z., Okano, M., Nogami, M., Li, Y., He, W.-W., Okumura, K., Li, E., (1999) Gene, vol. 236, pp. 87-95.

<1>DriI
<2>Eam1105I,AhdI,AspEI,BmeRI,BspOVI,BstZ2I,EclHKI,NruGI,Uba1190I,Uba1191I
<3>GACNNN^NNGTC
<4>
<5>Deinococcus radiodurans EA
<6>S.K. Degtyarev
<7>I
<8>Abdurashitov, M.A., Nayakshina, T.N., Dedkov, V.S., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>DsaI
<2>BstDSI,BtgI,TspBI
<3>C^CRYGG
<4>
<5>Dactylococcopsis salina
<6>A.E. Walsby
<7>
<8>Laue, F., Evans, L.R., Jarsch, M., Brown, N.L., Kessler, C., (1991) Gene, vol. 97, pp. 87-95.

<1>DsaII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Dactylococcopsis salina
<6>A.E. Walsby
<7>
<8>Laue, F., Evans, L.R., Jarsch, M., Brown, N.L., Kessler, C., (1991) Gene, vol. 97, pp. 87-95.

<1>DsaIII
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,MflI,PsuI,Tru201I,Uba1432I
<3>R^GATCY
<4>
<5>Dactylococcopsis salina
<6>A.E. Walsby
<7>
<8>Laue, F., Evans, L.R., Jarsch, M., Brown, N.L., Kessler, C., (1991) Gene, vol. 97, pp. 87-95.

<1>DsaIV
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Dactylococcopsis salina
<6>A.E. Walsby
<7>
<8>Laue, F., Evans, L.R., Jarsch, M., Brown, N.L., Kessler, C., (1991) Gene, vol. 97, pp. 87-95.

<1>DsaV
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>^CCNGG
<4>2(5)
<5>Dactylococcopsis salina
<6>A.E. Walsby
<7>
<8>Gopal, J., Bhagwat, A.S., (1995) Nucleic Acids Res., vol. 23, pp. 29-35.
Gopal, J., Yebra, M.J., Bhagwat, A.S., (1994) Nucleic Acids Res., vol. 22, pp. 4482-4488.
Laue, F., Evans, L.R., Jarsch, M., Brown, N.L., Kessler, C., (1991) Gene, vol. 97, pp. 87-95.

<1>DsaVI
<2>AccI,FblI,OmiBII,XmiI
<3>GTMKAC
<4>
<5>Dactylococcopsis salina
<6>A.E. Walsby
<7>
<8>Laue, F., Evans, L.R., Jarsch, M., Brown, N.L., Kessler, C., (1991) Gene, vol. 97, pp. 87-95.

<1>DseDI
<2>DrdI,AasI,TrsSII
<3>GACNNNN^NNGTC
<4>
<5>Deinococcus species Dx
<6>S.K. Degtyarev
<7>IV
<8>Abdurashitov, M.A., Kileva, E.V., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>Dsp1I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Deinococcus species RFL1
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>EacI
<2>BinI,AclWI,AlwI,BpuFI,BspPI,BsrWI,BstH9I,Bst31TI,BthII,Bth617I,Ral8I
<3>GGATC(4/5)
<4>
<5>Eubacterium acidaminophilum
<6>DSM 3953
<7>
<8>Graentzdoerffer, A., Lindenstrauss, U., Pich, A., Andreesen, J.R., German Patent Office, 2002.
Graentzdoerffer, A., Lindenstrauss, U., Pich, A., Andreesen, J.R., German Patent Office, 2002.

<1>EaeI
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>Y^GGCCR
<4>4(5)
<5>Enterobacter aerogenes
<6>P.R. Whitehead
<7>KN
<8>Jacobs, D., Brown, N.L., (1986) Biochem. J., vol. 238, pp. 613-616.
Lee, K.-F., Shaw, P.-C., Picone, S.J., Wilson, G.G., Lunnen, K.D., (1998) Biol. Chem., vol. 379, pp. 437-441.
Whitehead, P.R., Brown, N.L., (1983) FEBS Lett., vol. 155, pp. 97-101.

<1>Eae2I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Enterobacter aerogenes RFL2
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Eae46I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Enterobacter aerogenes 46
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>EaeAI
<2>SmaI,AhyI,Cfr9I,CfrJ4I,EclRI,KteAI,Pac25I,PaeBI,PspAI,PspALI,TspMI,Uba1220I,Uba1393I,XcyI,XmaI,XmaCI
<3>C^CCGGG
<4>
<5>Enterobacter aerogenes
<6>CAMB 2670
<7>
<8>Arif, A., Malik, K., Sohail, A., Unpublished observations.

<1>EaePI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Enterobacter aerogenes
<6>ATCC 15038
<7>
<8>Parker, P., Schildkraut, I., Unpublished observations.

<1>EagI
<2>XmaIII,AaaI,BseX3I,BsoDI,BstZI,EclXI,Eco52I,SenPT16I,TauII,Tsp504I
<3>C^GGCCG
<4>4(5)
<5>Enterobacter agglomerans
<6>NEB 368
<7>NW
<8>Brooks, J.E., Sznyter, L.A., US Patent Office, 1991.
Morgan, R., Camp, R., Soltis, A., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Samuelson, J., Unpublished observations.

<1>EagBI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGAT^CG
<4>
<5>Enterobacter agglomerans CBNU45
<6>J. Yim
<7>
<8>Choi, Y.-J., Kim, S.-J., Hwang, H.-Y., Yim, J., Kim, J.-C., (1994) Korean J. Microbiol., vol. 32, pp. 91-95.

<1>EagKI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter agglomerans
<6>L. Kauc
<7>
<8>Kauc, L., Leszczynska, K., (1986) Acta Microbiol. Pol., vol. 35, pp. 317-320.

<1>EagMI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Enterobacter agglomerans M3
<6>CAMB 2541
<7>
<8>Sohail, A., Unpublished observations.
Sohail, A., Mushtaq, R., Khan, E., Maqbool, T., Riazuddin, S., (1987) Pak. J. Zool., vol. 19, pp. 371-391.

<1>Eam1104I
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC(1/4)
<4>
<5>Enterobacter amnigenus RFL1104
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Kazlauskiene, R., Trinkunaite, L., Kiuduliene, L., Maneliene, Z., Petrusyte, M., Butkus, V., Unpublished observations.

<1>Eam1105I
<2>AhdI,AspEI,BmeRI,BspOVI,BstZ2I,DriI,EclHKI,NruGI,Uba1190I,Uba1191I
<3>GACNNN^NNGTC
<4>
<5>Enterobacter amnigenus RFL1105
<6>A. Janulaitis
<7>FK
<8>Janulaitis, A., Krikstulyte, V., Trinkunaite, L., Maneliene, Z., Kiuduliene, L., Petrusyte, M., Butkus, V., Unpublished observations.

<1>EarI
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC(1/4)
<4>?(4)
<5>Enterobacter aerogenes
<6>NEB 450
<7>N
<8>Lunnen, K.D., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Polisson, C., Morgan, R.D., (1988) Nucleic Acids Res., vol. 16, pp. 9872.
Stickel, S.K., Roberts, R.J., Unpublished observations.
Zhu, Z., Blanchard, A., Xu, S.-Y., Guan, S., Wei, H., Zhang, P., Sun, D., Chan, S.-h., International Patent Office, 2009.

<1>EcaI
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>5(6)
<5>Enterobacter cloacae
<6>DSM 30056
<7>
<8>Brenner, V., Venetianer, P., Kiss, A., (1990) Nucleic Acids Res., vol. 18, pp. 355-359.
Hobom, G., Schwarz, E., Melzer, M., Mayer, H., (1981) Nucleic Acids Res., vol. 9, pp. 4823-4832.
Szilak, L., Venetianer, P., Kiss, A., (1992) Eur. J. Biochem., vol. 209, pp. 391-397.

<1>EcaII
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter cloacae
<6>DSM 30056
<7>
<8>Myers, P.A., Roberts, R.J., Unpublished observations.

<1>EccI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Enterobacter cloacae
<6>DSM 30060
<7>
<8>Mayer, H., Klaar, J., Unpublished observations.
Myers, P.A., Roberts, R.J., Unpublished observations.

<1>EciI
<2>BpuCI
<3>GGCGGA(11/9)
<4>
<5>Escherichia coli
<6>NEB 484
<7>N
<8>Croft, R., Levin, B., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>Eci125I
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Escherichia coli VKM-125
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Eldarov, M.A., Anikeitcheva, N.V., Karpichev, I.V., Samko, O.T., Kalugin, A.A., Fitsner, A.B., Choroshoutina, E.B., Scryabin, K.G., Unpublished observations.

<1>EciAI
<2>SnaBI,Bpu1831I,BstSNI,Eco105I,Eco158II,SspJI,SspM1I,SspM2I,Uba1240I
<3>TACGTA
<4>
<5>Escherichia coli T13
<6>B. Levin
<7>
<8>Croft, R., Levin, B., Unpublished observations.

<1>EciBI
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Escherichia coli T83
<6>B. Levin
<7>
<8>Croft, R., Levin, B., Unpublished observations.

<1>EciCI
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Escherichia coli T18
<6>B. Levin
<7>
<8>Croft, R., Levin, B., Unpublished observations.

<1>EciDI
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Escherichia coli T20
<6>B. Levin
<7>
<8>Croft, R., Levin, B., Unpublished observations.

<1>EciEI
<2>ApaI,Bsp120I,PpeI,Psp30I,PspOMI,Uba1156I,Uba1157I,Uba1165I,Uba1202I,Uba1241I,Uba1368I
<3>GGGCCC
<4>
<5>Escherichia coli T39
<6>B. Levin
<7>
<8>Croft, R., Levin, B., Unpublished observations.

<1>EclI
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>
<5>Enterobacter cloacae
<6>H. Hartmann
<7>
<8>Degtyarev, S.K., Unpublished observations.
Hartmann, H., Goebel, W., (1977) FEBS Lett., vol. 80, pp. 285-287.

<1>EclII
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter cloacae
<6>H. Hartmann
<7>
<8>Hartmann, H., Goebel, W., (1977) FEBS Lett., vol. 80, pp. 285-287.

<1>Ecl1I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Enterobacter cloacae RFL1
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Ecl28I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Enterobacter cloacae RFL28
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Unpublished observations.

<1>Ecl37I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Enterobacter cloacae RFL37
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Adomaviciute, L., Unpublished observations.

<1>Ecl66I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter cloacae RFL66
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Unpublished observations.

<1>Ecl77I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Enterobacter cloacae RFL77
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Unpublished observations.

<1>Ecl133I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Enterobacter cloacae RFL133
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Ecl136I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter cloacae RFL136
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Ecl136II
<2>SacI,BpuAmI,Ecl137I,EcoICRI,Eco53kI,MxaI,NasSI,Pfl18I,Psp124BI,ScoI,Ssm4I,Ssm5I,SstI
<3>GAG^CTC
<4>
<5>Enterobacter cloacae RFL136
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Steponaviciene, D., Butkus, V., Maneliene, Z., Petrusyte, M., Unpublished observations.

<1>Ecl137I
<2>SacI,BpuAmI,Ecl136II,EcoICRI,Eco53kI,MxaI,NasSI,Pfl18I,Psp124BI,ScoI,Ssm4I,Ssm5I,SstI
<3>GAGCTC
<4>
<5>Enterobacter cloacae RFL137
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Ecl137II
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter cloacae RFL137
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Ecl593I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Enterobacter cloacae 593
<6>C. Kessler
<7>
<8>Bolton, B.J., Comer, M.J., Kessler, C., Unpublished observations.

<1>EclHKI
<2>Eam1105I,AhdI,AspEI,BmeRI,BspOVI,BstZ2I,DriI,NruGI,Uba1190I,Uba1191I
<3>GACNNN^NNGTC
<4>
<5>Enterobacter cloacae
<6>P.C. Shaw
<7>
<8>Chan, H.-Y., Chan, Y.-C., Kam, K.-M., Shaw, P.-C., (1994) World J. Microbiol. Biotechnol., vol. 10, pp. 30-32.

<1>EclJI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Enterobacter cloacae J
<6>CAMB 2542
<7>
<8>Maqbool, T., Sohail, A., Choudhry, S., Riazuddin, S., Unpublished observations.

<1>EclRI
<2>SmaI,AhyI,Cfr9I,CfrJ4I,EaeAI,KteAI,Pac25I,PaeBI,PspAI,PspALI,TspMI,Uba1220I,Uba1393I,XcyI,XmaI,XmaCI
<3>C^CCGGG
<4>
<5>Enterobacter cloacae R
<6>CAMB 2596
<7>
<8>Mushtaq, R., Riazuddin, S., Unpublished observations.

<1>EclS39I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter cloacae
<6>W. Piepersberg
<7>
<8>Bolton, B.J., Comer, M.J., Kessler, C., Unpublished observations.

<1>EclXI
<2>XmaIII,AaaI,BseX3I,BsoDI,BstZI,EagI,Eco52I,SenPT16I,TauII,Tsp504I
<3>C^GGCCG
<4>
<5>Enterobacter cloacae 590
<6>U. Mayr
<7>MS
<8>Bolton, B.J., Reischl, U., Holtke, H.-J., Schmitz, G.G., Jarsch, M., Kessler, C., (1990) Nucleic Acids Res., vol. 18, pp. 381.

<1>Ecl18kI
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>^CCNGG
<4>2(5)
<5>Enterobacter cloaceae 18k
<6>A.S. Solonin
<7>
<8>Denjmukhametov, M.M., Brevnov, M.G., Zakharova, M.V., Repyk, A.V., Solonin, A.S., Petrauskene, O.V., Gromova, E.S., (1998) FEBS Lett., vol. 433, pp. 233-236.
Denjmukhametov, M.M., Zakharova, M.V., Kravets, A.N., Pertsev, A.V., Sineva, E.V., Repik, A.V., Beletskaya, I.V., Gromova, E.S., Solonin, A.S., (1997) Mol. Biol. (Mosk), vol. 31, pp. 831-838.

<1>Ecl37kI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Enterobacter cloacae 37k
<6>A.S. Solonin
<7>
<8>Sineva, E.V., Zakharova, G.G., Tarutina, Z.E., Kravetz, A.N., Solonin, A.S., (1993) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 10-13.

<1>Ecl37kII
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter cloacae 37k
<6>A.S. Solonin
<7>
<8>Sineva, E.V., Zakharova, G.G., Tarutina, Z.E., Kravetz, A.N., Solonin, A.S., (1993) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 10-13.

<1>Ecl54kI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter cloacae 54k
<6>A.S. Solonin
<7>
<8>Sineva, E.V., Zakharova, G.G., Tarutina, Z.E., Kravetz, A.N., Solonin, A.S., (1993) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 10-13.

<1>Ecl57kI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter cloacae 57k
<6>A.S. Solonin
<7>
<8>Sineva, E.V., Zakharova, G.G., Tarutina, Z.E., Kravetz, A.N., Solonin, A.S., (1993) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 10-13.

<1>Ecl699kI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Enterobacter cloacae 699k
<6>A.S. Solonin
<7>
<8>Sineva, E.V., Zakharova, G.G., Tarutina, Z.E., Kravetz, A.N., Solonin, A.S., (1993) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 10-13.

<1>Ecl1zI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Enterobacter cloacae 1z
<6>A.S. Solonin
<7>
<8>Sineva, E.V., Zakharova, G.G., Tarutina, Z.E., Kravetz, A.N., Solonin, A.S., (1993) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 10-13.

<1>Ecl1zII
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter cloacae 1z
<6>A.S. Solonin
<7>
<8>Sineva, E.V., Zakharova, G.G., Tarutina, Z.E., Kravetz, A.N., Solonin, A.S., (1993) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 10-13.

<1>Ecl2zI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Enterobacter cloacae 2z
<6>A.S. Solonin
<7>
<8>Sineva, E.V., Zakharova, G.G., Tarutina, Z.E., Kravetz, A.N., Solonin, A.S., (1993) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 10-13.

<1>Eco17I
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Escherichia coli 17
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Eco24I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCY^C
<4>
<5>Escherichia coli RFL24
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Bitinaite, J., Unpublished observations.
Naureckiene, S., Bitinaite, J., Vaitkevicius, D., Menkevicius, S., Butkus, V., Janulaitis, A., Unpublished observations.

<1>Eco25I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli RFL25
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Unpublished observations.

<1>Eco26I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli RFL26
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Stakenas, P.S., Petrusyte, M.P., Bitinaite, J.B., Klimasauskas, S.I., Butkus, V.V., (1983) Mol. Biol. (Mosk), vol. 18, pp. 115-129.

<1>Eco31I
<2>Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC(1/5)
<4>4(5)
<5>Escherichia coli RFL31
<6>A. Janulaitis
<7>F
<8>Bitinaite, J., Maneliene, Z., Menkevicius, S., Klimasauskas, S., Butkus, V., Janulaitis, A., (1992) Nucleic Acids Res., vol. 20, pp. 4981-4985.
Bitinaite, J., Mitkaite, G., Dauksaite, V., Jakubauskas, A., Timinskas, A., Vaisvila, R., Lubys, A., Janulaitis, A., (2002) Mol. Genet. Genomics, vol. 267, pp. 664-672.
Butkus, V., Bitinaite, J., Kersulyte, D., Janulaitis, A., (1985) Biochim. Biophys. Acta, vol. 826, pp. 208-212.

<1>Eco32I
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GAT^ATC
<4>
<5>Escherichia coli RFL32
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Stakenas, P.S., Petrusyte, M.P., Bitinaite, J.B., Klimasauskas, S.I., Butkus, V.V., (1983) Mol. Biol. (Mosk), vol. 18, pp. 115-129.
Maneliene, Z., Bitinaite, J., Butkus, V., Janulaitis, A., Unpublished observations.
Vaisvila, R., Janulaitis, A., Unpublished observations.

<1>Eco35I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli RFL35
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Unpublished observations.

<1>Eco37I
<2>Eco377I,Eco1323I,Eco1344II,Eco1386I,Eco1427I,Eco1430I,Eco1456I,Eco1476I
<3>GGANNNNNNNNATGC
<4>
<5>Escherichia coli ECL 37
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco38I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Escherichia coli RFL38
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Adomaviciute, L., Unpublished observations.

<1>Eco39I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Escherichia coli RFL39
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Adomaviciute, L., Unpublished observations.

<1>Eco40I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Escherichia coli RFL40
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Adomaviciute, L., Unpublished observations.

<1>Eco41I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Escherichia coli RFL41
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Adomaviciute, L., Unpublished observations.

<1>Eco42I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL42
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco43I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>
<5>Escherichia coli RFL43
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bagdonaviciute, V., Petrusyte, M., Unpublished observations.

<1>Eco47I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Escherichia coli RFL47
<6>A. Janulaitis
<7>FO
<8>Butkus, V.V., Petrusyte, M.P., Janulaitis, A., (1985) Bioorg. Khim., vol. 11, pp. 987-988.
Janulaitis, A., Petrusyte, M., Butkus, V., (1983) FEBS Lett., vol. 161, pp. 213-216.
Lubys, A., Pagarauskaite, K., Unpublished observations.

<1>Eco47II
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>?(5)
<5>Escherichia coli RFL47
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Butkus, V., (1983) FEBS Lett., vol. 161, pp. 213-216.
Stankevicius, K., Povilionis, P., Lubys, A., Menkevicius, S., Janulaitis, A., (1995) Gene, vol. 157, pp. 49-53.

<1>Eco47III
<2>AfeI,AitI,Aor51HI,FunI
<3>AGC^GCT
<4>
<5>Escherichia coli RFL47
<6>A. Janulaitis
<7>FMORW
<8>Janulaitis, A., Petrusyte, M., Butkus, V., (1983) FEBS Lett., vol. 161, pp. 213-216.

<1>Eco48I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Escherichia coli RFL48
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Eco49I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Escherichia coli RFL49
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Eco50I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Escherichia coli RFL50
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Eco51I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL51
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Eco51II
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>
<5>Escherichia coli RFL51
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Eco52I
<2>XmaIII,AaaI,BseX3I,BsoDI,BstZI,EagI,EclXI,SenPT16I,TauII,Tsp504I
<3>C^GGCCG
<4>
<5>Escherichia coli RFL52
<6>A. Janulaitis
<7>FKO
<8>Butkus, V.V., Petrusyte, M.P., Janulaitis, A., (1985) Bioorg. Khim., vol. 11, pp. 987-988.
Janulaitis, A., Stakenas, P.S., Petrusyte, M.P., Bitinaite, J.B., Klimasauskas, S.I., Butkus, V.V., (1983) Mol. Biol. (Mosk), vol. 18, pp. 115-129.

<1>Eco55I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Escherichia coli RFL55
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Eco56I
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>G^CCGGC
<4>?(5)
<5>Escherichia coli RFL56
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Stakenas, P.S., Petrusyte, M.P., Bitinaite, J.B., Klimasauskas, S.I., Butkus, V.V., (1983) Mol. Biol. (Mosk), vol. 18, pp. 115-129.
Lubys, A., Janulaitis, A., Unpublished observations.
Lubys, A., Lubiene, J., Janulaitis, A., Unpublished observations.
Petrusyte, M., Padegimiene, A., Butkus, V., Janulaitis, A., Unpublished observations.

<1>Eco57I
<2>AcuI,Bsp6II,BspD6II,BspKT5I,Eco112I,Eco125I,FsfI
<3>CTGAAG(16/14)
<4>5(6)
<5>Escherichia coli RFL57
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Petrusyte, M., Maneliene, Z., Klimasauskas, S., Butkus, V., (1992) Nucleic Acids Res., vol. 20, pp. 6043-6049.
Petrusyte, M.P., Bitinaite, J.B., Kersulyte, D.R., Menkevicius, S.J., Butkus, V.V., Janulaitis, A., (1987) Dokl. Akad. Nauk., vol. 295, pp. 1250-1253.

<1>Eco60I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Escherichia coli RFL60
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Stakenas, P.S., Petrusyte, M.P., Bitinaite, J.B., Klimasauskas, S.I., Butkus, V.V., (1983) Mol. Biol. (Mosk), vol. 18, pp. 115-129.

<1>Eco61I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Escherichia coli RFL61
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Stakenas, P.S., Petrusyte, M.P., Bitinaite, J.B., Klimasauskas, S.I., Butkus, V.V., (1983) Mol. Biol. (Mosk), vol. 18, pp. 115-129.

<1>Eco64I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>G^GYRCC
<4>
<5>Escherichia coli RFL64
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Gilvonauskaite, R., Unpublished observations.
Naureckiene, S., Kazlauskiene, R., Maneliene, Z., Vaitkevicius, D., Butkus, V., Janulaitis, A., Unpublished observations.
Vaisvila, R., Janulaitis, A., Unpublished observations.

<1>Eco65I
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Escherichia coli RFL65
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Unpublished observations.

<1>Eco67I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Escherichia coli RFL67
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Gilvonauskaite, R., Unpublished observations.

<1>Eco68I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli RFL68
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Unpublished observations.

<1>Eco70I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Escherichia coli RFL70
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Gilvonauskaite, R., Unpublished observations.

<1>Eco71I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Escherichia coli RFL71
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Steponaviciene, D., Unpublished observations.

<1>Eco72I
<2>PmaCI,AcvI,BbrPI,BcoAI,Bsp87I,Pgl34I,PmlI,PshCI,PshDI,Psp38I,PspBI,PspCI,VpaK3AI,VpaK3BI
<3>CAC^GTG
<4>
<5>Escherichia coli RFL72
<6>A. Janulaitis
<7>F
<8>Kazlauskiene, R., Maneliene, Z., Butkus, V., Petrusyte, M., Janulaitis, A., (1986) Bioorg. Khim., vol. 12, pp. 836-838.

<1>Eco76I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Escherichia coli RFL76
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Unpublished observations.

<1>Eco78I
<2>NarI,BbeI,BbeAI,BinSII,DinI,EgeI,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GGC^GCC
<4>
<5>Escherichia coli RFL78
<6>A. Janulaitis
<7>
<8>Butkus, V., Kazlauskiene, R., Gilvonauskaite, R., Petrusyte, M., Janulaitis, A., (1985) Bioorg. Khim., vol. 11, pp. 1572-1573.

<1>Eco80I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>
<5>Escherichia coli RFL80
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Unpublished observations.

<1>Eco81I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CC^TNAGG
<4>
<5>Escherichia coli RFL81
<6>A. Janulaitis
<7>FKO
<8>Janulaitis, A., Kazlauskiene, R., Butkus, V., Petrauskiene, L., Petrusyte, M., Unpublished observations.

<1>Eco82I
<2>EcoRI,Eco159I,Eco228I,Eco237I,Eco252I,FunII,HalI,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl32DII,Srl55DI,SsoI,Uba58I,Van91II,VchN100I,VchO2I
<3>GAATTC
<4>
<5>Escherichia coli RFL82
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Gilvonauskaite, R., Unpublished observations.

<1>Eco83I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Escherichia coli RFL83
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Unpublished observations.

<1>Eco85I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>
<5>Escherichia coli RFL85
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bagdonaviciute, V., Petrusyte, M., Unpublished observations.

<1>Eco88I
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>
<5>Escherichia coli RFL88
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Kazlauskiene, R., Bagdonaviciute, V., Unpublished observations.
Janulaitis, A., Maneliene, Z., Butkus, V., Unpublished observations.
Lubys, A., Janulaitis, A., Unpublished observations.

<1>Eco90I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Escherichia coli RFL90
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.

<1>Eco91I
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Escherichia coli RFL91
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.
Naureckiene, S., Kazlauskiene, R., Vaitkevicius, D., Butkus, V., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>Eco92I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Escherichia coli RFL92
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Unpublished observations.

<1>Eco93I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>
<5>Escherichia coli RFL93
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Unpublished observations.

<1>Eco95I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL95
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Gilvonauskaite, R., Unpublished observations.

<1>Eco96I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Escherichia coli RFL96
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Unpublished observations.

<1>Eco97I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL97
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Unpublished observations.

<1>Eco98I
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Escherichia coli RFL98
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Unpublished observations.

<1>Eco99I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Escherichia coli RFL99
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Unpublished observations.

<1>Eco100I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Escherichia coli RFL100
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco101I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL101
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco104I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Escherichia coli RFL104
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Steponaviciene, D., Unpublished observations.

<1>Eco105I
<2>SnaBI,Bpu1831I,BstSNI,EciAI,Eco158II,SspJI,SspM1I,SspM2I,Uba1240I
<3>TAC^GTA
<4>
<5>Escherichia coli RFL105
<6>A. Janulaitis
<7>FO
<8>Janulaitis, A., Steponaviciene, D., Butkus, V., Maneliene, Z., Petrusyte, M., Unpublished observations.

<1>Eco112I
<2>Eco57I,AcuI,Bsp6II,BspD6II,BspKT5I,Eco125I,FsfI
<3>CTGAAG
<4>
<5>Escherichia coli RFL112
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Eco113I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli RFL113
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco115I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Escherichia coli RFL115
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco118I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Escherichia coli RFL118
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco120I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL120
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco121I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Escherichia coli RFL121
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco125I
<2>Eco57I,AcuI,Bsp6II,BspD6II,BspKT5I,Eco112I,FsfI
<3>CTGAAG
<4>
<5>Escherichia coli RFL125
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco127I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL127
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco128I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>?(5)
<5>Escherichia coli RFL128
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.
Waleron, K., Waleron, M., Osipiuk, J., Podhajska, A.J., Lojkowska, E., (2006) J. Appl. Microbiol., vol. 100, pp. 343-351.

<1>Eco129I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL129
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco130I
<2>StyI,BsmSI,BssT1I,Bst224I,CfrBI,Eco208II,EcoT14I,EcoT104I,ErhI,ErhB9II,SblAI,SblBI,SblCI,Uba1311I
<3>C^CWWGG
<4>
<5>Escherichia coli RFL130
<6>A. Janulaitis
<7>F
<8>Gilvonauskaite, R., Padegimiene, A., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.
Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Eco134I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Escherichia coli RFL134
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco135I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Escherichia coli RFL135
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco143I
<2>BsePI,BscEI,BsoPI,BsrHI,BssBI,BssHII,BstBZ153I,CfrJ5I,Eco152I,Esp7I,Esp8I,Kpn30I,McaTI,PauI,PteI,TtmII,Uba69I
<3>GCGCGC
<4>
<5>Escherichia coli RFL143
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Eco147I
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGG^CCT
<4>
<5>Escherichia coli RFL147
<6>A. Janulaitis
<7>F
<8>Gilvonauskaite, R., Maneliene, Z., Padegimiene, A., Petrusyte, M., Janulaitis, A., Unpublished observations.
Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.
Stankevicius, K., Povilionis, P., Lubys, A., Menkevicius, S., Janulaitis, A., (1995) Gene, vol. 157, pp. 49-53.

<1>Eco149I
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Escherichia coli RFL149
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco151I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Escherichia coli RFL151
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Eco152I
<2>BsePI,BscEI,BsoPI,BsrHI,BssBI,BssHII,BstBZ153I,CfrJ5I,Eco143I,Esp7I,Esp8I,Kpn30I,McaTI,PauI,PteI,TtmII,Uba69I
<3>GCGCGC
<4>
<5>Escherichia coli RFL152
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Eco153I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>
<5>Escherichia coli RFL153
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco155I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL155
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco156I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL156
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco157I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL157
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco158I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Escherichia coli RFL158
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco158II
<2>SnaBI,Bpu1831I,BstSNI,EciAI,Eco105I,SspJI,SspM1I,SspM2I,Uba1240I
<3>TACGTA
<4>
<5>Escherichia coli RFL158
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco159I
<2>EcoRI,Eco82I,Eco228I,Eco237I,Eco252I,FunII,HalI,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl32DII,Srl55DI,SsoI,Uba58I,Van91II,VchN100I,VchO2I
<3>GAATTC
<4>
<5>Escherichia coli RFL159
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco161I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Escherichia coli RFL161
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco162I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL162
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco164I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Escherichia coli RFL164
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Eco167I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Escherichia coli RFL167
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco168I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Escherichia coli RFL168
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco169I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Escherichia coli RFL169
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Eco170I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Escherichia coli RFL170
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Eco171I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Escherichia coli RFL171
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco173I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Escherichia coli RFL173
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco178I
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Escherichia coli RFL178
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco179I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Escherichia coli RFL179
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco180I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli RFL180
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco182I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Escherichia coli RFL182
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco185I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL185
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco188I
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Escherichia coli RFL188
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco190I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Escherichia coli RFL190
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco191I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL191
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco193I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Escherichia coli RFL193
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco195I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Escherichia coli RFL195
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco196I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Escherichia coli RFL196
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco196II
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Escherichia coli RFL196
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco200I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>
<5>Escherichia coli RFL200
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco201I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Escherichia coli RFL201
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Eco203I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL203
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco204I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL204
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco205I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL205
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Eco206I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Escherichia coli RFL206
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Eco207I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Escherichia coli RFL207
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Eco208I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Escherichia coli RFL208
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Eco208II
<2>StyI,BsmSI,BssT1I,Bst224I,CfrBI,Eco130I,EcoT14I,EcoT104I,ErhI,ErhB9II,SblAI,SblBI,SblCI,Uba1311I
<3>CCWWGG
<4>
<5>Escherichia coli RFL208
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Eco211I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli RFL211
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Eco215I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli RFL215
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.

<1>Eco216I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli RFL216
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.

<1>Eco217I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL217
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Eco225I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL225
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Eco228I
<2>EcoRI,Eco82I,Eco159I,Eco237I,Eco252I,FunII,HalI,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl32DII,Srl55DI,SsoI,Uba58I,Van91II,VchN100I,VchO2I
<3>GAATTC
<4>
<5>Escherichia coli RFL228
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Eco231I
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Escherichia coli RFL231
<6>A. Janulaitis
<7>
<8>Kaczorowski, T., Unpublished observations.
Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Eco232I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli RFL232
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Eco233I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL233
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Eco237I
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco252I,FunII,HalI,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl32DII,Srl55DI,SsoI,Uba58I,Van91II,VchN100I,VchO2I
<3>GAATTC
<4>
<5>Escherichia coli RFL237
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Eco239I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL239
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Eco240I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL240
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Eco241I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL241
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Eco246I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL246
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Eco247I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL247
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Eco249I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli RFL249
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Eco252I
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco237I,FunII,HalI,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl32DII,Srl55DI,SsoI,Uba58I,Van91II,VchN100I,VchO2I
<3>GAATTC
<4>
<5>Escherichia coli RFL252
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Eco254I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Escherichia coli RFL254
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Eco255I
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,LlaDI,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGT^ACT
<4>
<5>Escherichia coli RFL255
<6>A. Janulaitis
<7>
<8>Dauksaite, V., Janulaitis, A., Unpublished observations.
Janulaitis, A., Bitinaite, J., Jagelavicius, M., Naureckiene, S., Vaitkevicius, D., Maneliene, Z., Kiuduliene, L., Butkus, V., Unpublished observations.

<1>Eco256I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Escherichia coli RFL256
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Eco260I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Escherichia coli RFL260
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Eco261I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Escherichia coli RFL261
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Eco262I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli RFL262
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Eco263I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli RFL263
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Eco377I
<2>Eco37I,Eco1323I,Eco1344II,Eco1386I,Eco1427I,Eco1430I,Eco1456I,Eco1476I
<3>GGANNNNNNNNATGC
<4>
<5>Escherichia coli EC377
<6>J.-I. Ryu
<7>
<8>Kasarjian, J.K.A., Iida, M., Ryu, J., (2003) Nucleic Acids Res., vol. 31.

<1>Eco394I
<2>
<3>GACNNNNNRTAAY
<4>
<5>Escherichia coli ECL 394
<6>J.-I. Ryu
<7>
<8>Kasarjian, J.K.A., Kodama, Y., Iida, M., Matsuda, K., Ryu, J., (2005) Nucleic Acids Res., vol. 33.

<1>Eco585I
<2>
<3>GCCNNNNNNTGCG
<4>
<5>Escherichia coli EC585
<6>J.-I. Ryu
<7>
<8>Kasarjian, J.K.A., Iida, M., Ryu, J., (2003) Nucleic Acids Res., vol. 31.

<1>Eco646I
<2>Eco1341I,Eco1383I,Eco1413I,Eco1422I,Eco1424I,Eco1432I
<3>CCANNNNNNNCTTC
<4>
<5>Escherichia coli EC646
<6>J.-I. Ryu
<7>
<8>Kasarjian, J.K.A., Iida, M., Ryu, J., (2003) Nucleic Acids Res., vol. 31.

<1>Eco777I
<2>Eco1348I,Eco1412I
<3>GGANNNNNNTATC
<4>
<5>Escherichia coli EC777
<6>J.-I. Ryu
<7>
<8>Kasarjian, J.K.A., Iida, M., Ryu, J., (2003) Nucleic Acids Res., vol. 31.

<1>Eco826I
<2>Eco1455I
<3>GCANNNNNNCTGA
<4>
<5>Escherichia coli ECL 826
<6>J.-I. Ryu
<7>
<8>Kasarjian, J.K.A., Kodama, Y., Iida, M., Matsuda, K., Ryu, J., (2005) Nucleic Acids Res., vol. 33.

<1>Eco851I
<2>
<3>GTCANNNNNNTGAY
<4>
<5>Escherichia coli ECL 851
<6>J.-I. Ryu
<7>
<8>Kasarjian, J.K.A., Kodama, Y., Iida, M., Matsuda, K., Ryu, J., (2005) Nucleic Acids Res., vol. 33.

<1>Eco912I
<2>
<3>CACNNNNNTGGC
<4>
<5>Escherichia coli ECL 912
<6>J.-I. Ryu
<7>
<8>Kasarjian, J.K.A., Kodama, Y., Iida, M., Matsuda, K., Ryu, J., (2005) Nucleic Acids Res., vol. 33.

<1>Eco1158I
<2>EcoBI,Eco1265I,Eco1441I,Eco1443I,Eco1447I,Eco14444I
<3>TGANNNNNNNNTGCT
<4>
<5>Escherichia coli EC1158
<6>J.-I. Ryu
<7>
<8>Kasarjian, J.K.A., Iida, M., Ryu, J., (2003) Nucleic Acids Res., vol. 31.

<1>Eco1265I
<2>EcoBI,Eco1158I,Eco1441I,Eco1443I,Eco1447I,Eco14444I
<3>TGANNNNNNNNTGCT
<4>
<5>Escherichia coli ECL 1265
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1323I
<2>Eco377I,Eco37I,Eco1344II,Eco1386I,Eco1427I,Eco1430I,Eco1456I,Eco1476I
<3>GGANNNNNNNNATGC
<4>
<5>Escherichia coli EC1323
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1341I
<2>Eco646I,Eco1383I,Eco1413I,Eco1422I,Eco1424I,Eco1432I
<3>CCANNNNNNNCTTC
<4>
<5>Escherichia coli EC1341
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1342I
<2>EcoKI,Eco1344I,Eco1394I
<3>AACNNNNNNGTGC
<4>
<5>Escherichia coli EC1342
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1344I
<2>EcoKI,Eco1342I,Eco1394I
<3>AACNNNNNNGTGC
<4>
<5>Escherichia coli EC1344
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1344II
<2>Eco377I,Eco37I,Eco1323I,Eco1386I,Eco1427I,Eco1430I,Eco1456I,Eco1476I
<3>GGANNNNNNNNATGC
<4>
<5>Escherichia coli EC1344
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1348I
<2>Eco777I,Eco1412I
<3>GGANNNNNNTATC
<4>
<5>Escherichia coli EC1348
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1383I
<2>Eco646I,Eco1341I,Eco1413I,Eco1422I,Eco1424I,Eco1432I
<3>CCANNNNNNNCTTC
<4>
<5>Escherichia coli EC1393
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1386I
<2>Eco377I,Eco37I,Eco1323I,Eco1344II,Eco1427I,Eco1430I,Eco1456I,Eco1476I
<3>GGANNNNNNNNATGC
<4>
<5>Escherichia coli EC1386
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1394I
<2>EcoKI,Eco1342I,Eco1344I
<3>AACNNNNNNGTGC
<4>
<5>Escherichia coli EC1394
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1412I
<2>Eco777I,Eco1348I
<3>GGANNNNNNTATC
<4>
<5>Escherichia coli EC1412
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1413I
<2>Eco646I,Eco1341I,Eco1383I,Eco1422I,Eco1424I,Eco1432I
<3>CCANNNNNNNCTTC
<4>
<5>Escherichia coli EC1413
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1422I
<2>Eco646I,Eco1341I,Eco1383I,Eco1413I,Eco1424I,Eco1432I
<3>CCANNNNNNNCTTC
<4>
<5>Escherichia coli EC1422
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1424I
<2>Eco646I,Eco1341I,Eco1383I,Eco1413I,Eco1422I,Eco1432I
<3>CCANNNNNNNCTTC
<4>
<5>Escherichia coli EC1424
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1427I
<2>Eco377I,Eco37I,Eco1323I,Eco1344II,Eco1386I,Eco1430I,Eco1456I,Eco1476I
<3>GGANNNNNNNNATGC
<4>
<5>Escherichia coli EC1427
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1430I
<2>Eco377I,Eco37I,Eco1323I,Eco1344II,Eco1386I,Eco1427I,Eco1456I,Eco1476I
<3>GGANNNNNNNNATGC
<4>
<5>Escherichia coli EC1430
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1432I
<2>Eco646I,Eco1341I,Eco1383I,Eco1413I,Eco1422I,Eco1424I
<3>CCANNNNNNNCTTC
<4>
<5>Escherichia coli EC1432
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1441I
<2>EcoBI,Eco1158I,Eco1265I,Eco1443I,Eco1447I,Eco14444I
<3>TGANNNNNNNNTGCT
<4>
<5>Escherichia coli EC1441
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1443I
<2>EcoBI,Eco1158I,Eco1265I,Eco1441I,Eco1447I,Eco14444I
<3>TGANNNNNNNNTGCT
<4>
<5>Escherichia coli EC1443
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1446I
<2>EcoAI
<3>GAGNNNNNNNGTCA
<4>
<5>Escherichia coli EC1446
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1447I
<2>EcoBI,Eco1158I,Eco1265I,Eco1441I,Eco1443I,Eco14444I
<3>TGANNNNNNNNTGCT
<4>
<5>Escherichia coli EC1447
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1455I
<2>Eco826I
<3>GCANNNNNNCTGA
<4>
<5>Escherichia coli EC1455
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1456I
<2>Eco377I,Eco37I,Eco1323I,Eco1344II,Eco1386I,Eco1427I,Eco1430I,Eco1476I
<3>GGANNNNNNNNATGC
<4>
<5>Escherichia coli EC1456
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1476I
<2>Eco377I,Eco37I,Eco1323I,Eco1344II,Eco1386I,Eco1427I,Eco1430I,Eco1456I
<3>GGANNNNNNNNATGC
<4>
<5>Escherichia coli EC1476
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>Eco1524I
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGG^CCT
<4>
<5>Escherichia coli 1524
<6>H. Lazim
<7>
<8>Lazim, H., Josephsen, J., Ben Hassen, A., Belhadj, O., Limam, R., (2005) Appl. Biochem. Biotechnol., vol. 125, pp. 189-199.
Lazim, H., Mankai, H., Limam, F., Unpublished observations.

<1>Eco1831I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>^CCSGG
<4>2(5)
<5>Escherichia coli 1831
<6>A.S. Solonin
<7>
<8>Kravetz, A.N., Zakharova, M.V., Beletskaya, I.V., Sineva, E.V., Denjmuchametov, M.M., Petrov, S.I., Glatman, L.I., Solonin, A.S., (1993) Gene, vol. 129, pp. 153-154.

<1>Eco14444I
<2>EcoBI,Eco1158I,Eco1265I,Eco1441I,Eco1443I,Eco1447I
<3>TGANNNNNNNNTGCT
<4>
<5>Escherichia coli EC1444
<6>J.-I. Ryu
<7>
<8>Ryu, J.-I., Unpublished observations.

<1>EcoAI
<2>Eco1446I
<3>GAGNNNNNNNGTCA
<4>2(6),-3(6)
<5>Escherichia coli 15T-
<6>T.A. Bickle
<7>
<8>Kroger, M., Hobom, G., (1984) Nucleic Acids Res., vol. 12, pp. 887-899.
Suri, B., Shepherd, J.C.W., Bickle, T.A., (1984) EMBO J., vol. 3, pp. 575-579.

<1>EcoA4I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC(1/5)
<4>
<5>Escherichia coli A4
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>EcoBI
<2>Eco1158I,Eco1265I,Eco1441I,Eco1443I,Eco1447I,Eco14444I
<3>TGANNNNNNNNTGCT
<4>3(6),-4(6)
<5>Escherichia coli B
<6>W. Arber
<7>
<8>Eskin, B., Linn, S., (1972) J. Biol. Chem., vol. 247, pp. 6183-6191.
Kuhnlein, U., Arber, W., (1972) J. Mol. Biol., vol. 63, pp. 9-19.
Kuhnlein, U., Linn, S., Arber, W., (1969) Proc. Natl. Acad. Sci. U. S. A., vol. 63, pp. 556-562.
Lautenberger, J.A., Edgell, M.H., Hutchison, C.A. III, (1979) J. Mol. Biol., vol. 131, pp. 871-875.
Lautenberger, J.A., Kan, N.C., Lackey, D., Linn, S., Edgell, M.H., Hutchison, C.A. III, (1978) Proc. Natl. Acad. Sci. U. S. A., vol. 75, pp. 2271-2275.
Lautenberger, J.A., Linn, S., (1972) J. Biol. Chem., vol. 247, pp. 6176-6182.
Ravetch, J.V., Horiuchi, K., Zinder, N.D., (1978) Proc. Natl. Acad. Sci. U. S. A., vol. 75, pp. 2266-2270.
Sommer, R., Schaller, H., (1979) Mol. Gen. Genet., vol. 168, pp. 331-335.
van Ormondt, H., Lautenberger, J.A., Linn, S., de Waard, A., (1973) FEBS Lett., vol. 33, pp. 177-180.

<1>EcoCKI
<2>
<3>?
<4>
<5>Escherichia coli CK
<6>S.S. Debov
<7>
<8>Uporova, T.M., Nikolskaya, I.I., Rubtsova, E.N., Debov, S.S., (1981) Vestn. Akad. Med. Nauk SSSR, vol. 2, pp. 21-26.

<1>EcoDI
<2>
<3>TTANNNNNNNGTCY
<4>
<5>Escherichia coli E166
<6>N.E. Murray
<7>
<8>Nagaraja, V., Stieger, M., Nager, C., Hadi, S.M., Bickle, T.A., (1985) Nucleic Acids Res., vol. 13, pp. 389-399.

<1>EcoDR2
<2>
<3>TCANNNNNNGTCG
<4>
<5>Artificial construct
<6>T.A. Bickle
<7>
<8>Gubler, M., Braguglia, D., Meyer, J., Piekarowicz, A., Bickle, T.A., (1992) EMBO J., vol. 11, pp. 233-240.

<1>EcoDR3
<2>
<3>TCANNNNNNNATCG
<4>
<5>Artificial construct
<6>T.A. Bickle
<7>
<8>Gubler, M., Braguglia, D., Meyer, J., Piekarowicz, A., Bickle, T.A., (1992) EMBO J., vol. 11, pp. 233-240.

<1>EcoDXXI
<2>
<3>TCANNNNNNNRTTC
<4>
<5>Escherichia coli pDXX1
<6>A. Piekarowicz
<7>
<8>Gubler, M., Braguglia, D., Meyer, J., Piekarowicz, A., Bickle, T.A., (1992) EMBO J., vol. 11, pp. 233-240.
Piekarowicz, A., Goguen, J.D., (1986) Eur. J. Biochem., vol. 154, pp. 295-298.
Piekarowicz, A., Goguen, J.D., Skrzypek, E., (1985) Eur. J. Biochem., vol. 152, pp. 387-393.

<1>EcoEI
<2>
<3>GAGNNNNNNNATGC
<4>
<5>Escherichia coli A58
<6>N.E. Murray
<7>
<8>Cowan, G.M., Gann, A.A.F., Murray, N.E., (1989) Cell, vol. 56, pp. 103-109.
Fuller-Pace, F.V., Cowan, G.M., Murray, N.E., (1985) J. Mol. Biol., vol. 186, pp. 65-75.
Murray, N.E., Daniel, A.S., Cowan, G.M., Sharp, P.M., (1993) Mol. Microbiol., vol. 9, pp. 133-143.

<1>M.EcoEc67Dam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Escherichia coli
<6>M. Inouye
<7>
<8>Hsu, M.-Y., Inouye, M., Inouye, S., (1990) Proc. Natl. Acad. Sci. U. S. A., vol. 87, pp. 9454-9458.

<1>EcoHI
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>^CCSGG
<4>2(5)
<5>Escherichia coli H1
<6>L.I. Glatman
<7>
<8>Glatman, L.I., Terekhov, A.A., Kalnin, K.V., Bolotin, A.P., Rebentish, B.A., (1990) Mol. Gen. Mikrobiol. Virusol., vol. 3, pp. 32.
Kravetz, A.N., Zakharova, M.V., Beletskaya, I.V., Sineva, E.V., Denjmuchametov, M.M., Petrov, S.I., Glatman, L.I., Solonin, A.S., (1993) Gene, vol. 129, pp. 153-154.

<1>EcoHAI
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Escherichia coli
<6>ATCC 26
<7>
<8>Hall, D., Unpublished observations.

<1>EcoHK31I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>Y^GGCCR
<4>4(5)
<5>Escherichia coli HK31
<6>P.C. Shaw
<7>
<8>Lee, K.-F., Kam, K.-M., Shaw, P.-C., (1995) Nucleic Acids Res., vol. 23, pp. 103-108.
Lee, K.-F., Liaw, Y.-C., Shaw, P.-C., (1996) Biochem. J., vol. 314, pp. 321-326.
Lee, K.-F., Shaw, P.-C., Picone, S.J., Wilson, G.G., Lunnen, K.D., (1998) Biol. Chem., vol. 379, pp. 437-441.

<1>EcoICRI
<2>SacI,BpuAmI,Ecl136II,Ecl137I,Eco53kI,MxaI,NasSI,Pfl18I,Psp124BI,ScoI,Ssm4I,Ssm5I,SstI
<3>GAG^CTC
<4>
<5>Escherichia coli 2bT
<6>ICR 0020
<7>IRV
<8>Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Bull. Inst. Chem. Res. Kyoto Univ., vol. 60, pp. 328-335.
Yankovsky, N.K., Fonstein, M.Yu., Lashina, S.Yu., Bukanov, N.O., Yakubovich, N.V., Ermakova, L.M., Rebentish, B.A., Janulaitis, A., Debabov, V.G., (1989) Gene, vol. 81, pp. 203-210.

<1>EcoKI
<2>Eco1342I,Eco1344I,Eco1394I
<3>AACNNNNNNGTGC
<4>2(6),-3(6)
<5>Escherichia coli K MG1655
<6>F.R. Blattner
<7>
<8>Blattner, F.R., Plunkett, G. III, Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., Gregor, J., Davis, N.W., Kirkpatrick, H.A., Goeden, M.A., Rose, D.J., Mau, B., Shao, Y., (1997) Science, vol. 277, pp. 1453-1462.
Gough, J.A., Murray, N.E., (1983) J. Mol. Biol., vol. 166, pp. 1-19.
Haberman, A., Heywood, J., Meselson, M., (1972) Proc. Natl. Acad. Sci. U. S. A., vol. 69, pp. 3138-3141.
Kan, N.C., Lautenberger, J.A., Edgell, M.H., Hutchison, C.A. III, (1979) J. Mol. Biol., vol. 130, pp. 191-209.
Loenen, W.A.M., Daniel, A.S., Braymer, H.D., Murray, N.E., (1987) J. Mol. Biol., vol. 198, pp. 159-170.
Meselson, M., Yuan, R., (1968) Nature, vol. 217, pp. 1110-1114.
Puzio, P., Ascenzi, R., Mittendorf, V., International Patent Office, 2009.
Willcock, D.F., Dryden, D.T.F., Murray, N.E., (1994) EMBO J., vol. 13, pp. 3902-3908.

<1>Eco71KI
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Escherichia coli VKM V-2006D
<6>A.S. Solonin
<7>
<8>Denjmukhametov, M.M., Kravets, A.N., Solonin, A.S., Russian Patent Office, 1996.

<1>Eco75KI
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCY^C
<4>
<5>Escherichia coli BKM B-2007D
<6>A.S. Solonin
<7>
<8>Pertsev, A.V., Kravets, A.N., Beletskaya, I.V., Zakharova, M.V., Solonin, A.S., Russian Patent Office, 1996.

<1>M.EcoKDam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Escherichia coli K MG1655
<6>F.R. Blattner
<7>
<8>Deschavanne, P., Radman, M., (1991) J. Mol. Evol., vol. 33, pp. 125-132.
Geier, G.E., Modrich, P., (1979) J. Biol. Chem., vol. 254, pp. 1408-1413.
Hattman, S., Brooks, J.E., Masurekar, M., (1978) J. Mol. Biol., vol. 126, pp. 367-380.
Hulsmann, K.-H., Quaas, R., Georgalis, Y., Saenger, W., Hahn, U., (1991) Gene, vol. 98, pp. 83-88.
Lacks, S., Greenberg, B., (1977) J. Mol. Biol., vol. 114, pp. 153-168.
Marinus, M.G., Morris, N.R., (1973) J. Bacteriol., vol. 114, pp. 1143-1150.

<1>M.EcoKDcm
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>2(5)
<5>Escherichia coli K MG1655
<6>F.R. Blattner
<7>
<8>Blattner, F.R., Plunkett, G. III, Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., Gregor, J., Davis, N.W., Kirkpatrick, H.A., Goeden, M.A., Rose, D.J., Mau, B., Shao, Y., (1997) Science, vol. 277, pp. 1453-1462.
Marinus, M.G., Morris, N.R., (1973) J. Bacteriol., vol. 114, pp. 1143-1150.
May, M.S., Hattman, S., (1975) J. Bacteriol., vol. 122, pp. 129-138.

<1>Eco57MI
<2>
<3>CTGRAG(16/14)
<4>
<5>Escherichia coli RFL57M
<6>A. Janulaitis
<7>F
<8>Rimseliene, R., Maneliene, Z., Lubys, A., Janulaitis, A., (2003) J. Mol. Biol., vol. 327, pp. 383-391.

<1>EcoNI
<2>Bpu1268I,BsoEI,BstENI,BstWI,Uba1289I,Uba1290I,Uba1308I,Uba1309I,Uba1310I,XagI
<3>CCTNN^NNNAGG
<4>
<5>Escherichia coli
<6>NEB 441
<7>N
<8>Hall, D., Morgan, R., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Zhu, Z., Unpublished observations.
Zhu, Z., Xu, S.-Y., Unpublished observations.

<1>EcoO34I
<2>
<3>?
<4>
<5>Escherichia coli H304
<6>K. Mise
<7>
<8>Yoshida, Y., Mise, K., (1986) J. Bacteriol., vol. 165, pp. 357-362.

<1>EcoO44I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC(1/5)
<4>
<5>Escherichia coli O44 Hiromi
<6>N. Shinohara
<7>
<8>Miyahara, M., Shinohara, N., Mise, K., (1996) Eisei Shikenjo Hokoku, vol. 114, pp. 13-15.

<1>EcoO65I
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO128I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Escherichia coli K11a
<6>K. Mise
<7>K
<8>Tsui, W.-C., Unpublished observations.

<1>EcoO109I
<2>DraII,Kaz48kI,PssI,Uba1326I,VneAI
<3>RG^GNCCY
<4>5(5)
<5>Escherichia coli H709c
<6>I. Orskov
<7>FJKN
<8>Kita, K., Tsuda, J., Kato, T., Okamoto, K., Yanase, H., Tanaka, M., (1999) J. Bacteriol., vol. 181, pp. 6822-6827.
Kita, K., Tsuda, J., Nishigaki, R., (2001) Biosci. Biotechnol. Biochem., vol. 65, pp. 2512-2518.
Mise, K., Nakajima, K., (1985) Gene, vol. 36, pp. 363-367.
Xu, S.-Y., Unpublished observations.

<1>EcoO128I
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,KoxI,NspSAII,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Escherichia coli O128Ly3
<6>H. Matsumoto
<7>
<8>Mise, K., Unpublished observations.
Miyahara, M., Mise, K., Kimizuka, F., Matsumoto, H., Terawaki, Y., (1992) Gene, vol. 113, pp. 135-136.

<1>EcoPI
<2>
<3>AGACC(25/27)
<4>3(6)
<5>Escherichia coli (PI)
<6>K. Murray
<7>
<8>Bachi, B., Reiser, J., Pirrotta, V., (1979) J. Mol. Biol., vol. 128, pp. 143-163.
Brockes, J.P., Brown, P.R., Murray, K., (1972) Biochem. J., vol. 127, pp. 1-10.
Haberman, A., (1974) J. Mol. Biol., vol. 89, pp. 545-563.
Haberman, A., Heywood, J., Meselson, M., (1972) Proc. Natl. Acad. Sci. U. S. A., vol. 69, pp. 3138-3141.
Hattman, S., Brooks, J.E., Masurekar, M., (1978) J. Mol. Biol., vol. 126, pp. 367-380.
Krishnamurthy, V., Rao, D.N., (1994) Biochem. Mol. Biol. Int., vol. 32, pp. 623-632.
Lobocka, M.B., Rose, D.J., Rusin, M., Plunkett, G. III, Samojedny, A., Lehnherr, H., Yarmolinsky, M.B., Blattner, F.R., (2004) J. Bacteriol., vol. 186, pp. 7032-7068.

<1>EcoP15I
<2>
<3>CAGCAG(25/27)
<4>5(6)
<5>Escherichia coli P15
<6>W. Arber
<7>N
<8>Ahmad, I., Rao, D.N., (1994) Gene, vol. 142, pp. 67-71.
Hadi, S.M., Bachi, B., Shepherd, J.C.W., Yuan, R., Ineichen, K., Bickle, T.A., (1979) J. Mol. Biol., vol. 134, pp. 655-666.
Meisel, A., Kruger, D.H., Bickle, T.A., (1991) Nucleic Acids Res., vol. 19, pp. 3997.
Moencke-Buchner, E., Mackeldanz, P., Krueger, D.H., Reuter, M., (2004) J. Biotechnol., vol. 114, pp. 99-106.
Reiser, J., Yuan, R., (1977) J. Biol. Chem., vol. 252, pp. 451-456.
Wagenfuhr, K., Pieper, S., Mackeldanz, P., Linscheid, M., Kruger, D.H., Reuter, M., (2007) J. Mol. Biol., vol. 366, pp. 93-102.

<1>M.EcoP1Dam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Escherichia coli phage P1
<6>N. Sternberg
<7>
<8>Coulby, J.N., Sternberg, N.L., (1988) Gene, vol. 74, pp. 191.

<1>EcoRI
<2>Eco82I,Eco159I,Eco228I,Eco237I,Eco252I,FunII,HalI,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl32DII,Srl55DI,SsoI,Uba58I,Van91II,VchN100I,VchO2I
<3>G^AATTC
<4>3(6)
<5>Escherichia coli RY13
<6>R.N. Yoshimori
<7>BCFHIJKMNOQRSUVWXY
<8>Albertsen, H.M., Le Paslier, D., Abderrahim, H., Dausset, J., Cann, H., Cohen, D., (1989) Nucleic Acids Res., vol. 17, pp. 808.
Dugaiczyk, A., Hedgpeth, J., Boyer, H.W., Goodman, H.M., (1974) Biochemistry, vol. 13, pp. 503-512.
Forrow, S., Lee, M., Souhami, R.L., Hartley, J.A., (1994) ACS Abstracts, vol. 208, pp. 97.
Greene, P.J., Betlach, M.C., Boyer, H.W., Goodman, H.M., (1974) Methods Mol. Biol., vol. 7, pp. 87-105.
Hedgpeth, J., Goodman, H.M., Boyer, H.W., (1972) Proc. Natl. Acad. Sci. U. S. A., vol. 69, pp. 3448-3452.
Pingoud, A., Alves, J., Fliess, A., Geiger, R., Rueter, T., Wolfes, H., (1987) Biol. Chem. Hoppe Seyler, vol. 368, pp. 1093.
Tanaka, M., Japanese Patent Office, 2002.
Winkler, F.K., (1994) J. Mol. Recognit., vol. 6, pp. 9.

<1>EcoRII
<2>Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>^CCWGG
<4>2(5)
<5>Escherichia coli R245
<6>R.N. Yoshimori
<7>FJMOS
<8>Bigger, C.H., Murray, K., Murray, N.E., (1973) Nature New Biol., vol. 244, pp. 7-10.
Boyer, H.W., Chow, L.T., Dugaiczyk, A., Hedgpeth, J., Goodman, H.M., (1973) Nature New Biol., vol. 244, pp. 40-43.
Buryanov, Y.I., Bogdarina, I.G., Bayev, A.A., (1978) FEBS Lett., vol. 88, pp. 251-254.
Reuter, M., Schneider-Mergener, J., Kupper, D., Meisel, A., Mackeldanz, P., Kruger, D.H., Schroeder, C., (1999) J. Biol. Chem., vol. 274, pp. 5213-5221.
Som, S., Bhagwat, A.S., Friedman, S., (1987) Nucleic Acids Res., vol. 15, pp. 313-332.
Som, S., Friedman, S., (1994) J. Biol. Chem., vol. 269, pp. 25986-25991.
Yoshimori, R.N., (1971) Ph.D. Thesis, University of California, San Francisco, USA, pp. 1-73.

<1>EcoRV
<2>Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GAT^ATC
<4>2(6)
<5>Escherichia coli J62 pLG74
<6>L.I. Glatman
<7>BCHIJKMNOQRSUVWXY
<8>Baldwin, G.S., Halford, S.E., (1994) Biochem. Soc. Trans., vol. 22, pp. 300S.
Erskine, S.G., Halford, S.E., (1994) Biochem. Soc. Trans., vol. 22, pp. 299s.
Forrow, S., Lee, M., Souhami, R.L., Hartley, J.A., (1994) ACS Abstracts, vol. 208, pp. 97.
Kholmina, G.V., Rebentish, B.A., Skoblov, Y.S., Mironov, A.A., Yankovskii, N.K., Kozlov, Y.I., Glatmann, L.I., Moroz, A.F., Debabov, V.G., (1980) Dokl. Akad. Nauk., vol. 253, pp. 495-497.
Nwosu, V.U., Connolly, B.A., Halford, S.E., Garnett, J., (1988) Nucleic Acids Res., vol. 16, pp. 3705-3720.
Schildkraut, I., Banner, C.D.B., Rhodes, C.S., Parekh, S., (1984) Gene, vol. 27, pp. 327-329.
Vipond, I.B., Moon, B.J., Halford, S.E., (1994) Biochem. Soc. Trans., vol. 22, pp. 301S.
Winkler, F.K., (1994) J. Mol. Recognit., vol. 6, pp. 9.
Zakharova, M.V., Unpublished observations.

<1>EcoR5I
<2>
<3>?
<4>
<5>Escherichia coli ECOR5
<6>ATCC 35324
<7>
<8>Barcus, V.A., Titheradge, A.J.B., Murray, N.E., (1995) Genetics, vol. 140, pp. 1187-1197.

<1>EcoR9I
<2>
<3>?
<4>
<5>Escherichia coli ECOR9
<6>ATCC 35328
<7>
<8>Campbell, A.J.B., Murray, N.E., Unpublished observations.
Titheradge, A.J.B., Unpublished observations.

<1>EcoR10I
<2>
<3>?
<4>
<5>Escherichia coli ECOR10
<6>ATCC 35329
<7>
<8>Barcus, V.A., Titheradge, A.J.B., Murray, N.E., (1995) Genetics, vol. 140, pp. 1187-1197.

<1>EcoR11I
<2>
<3>?
<4>
<5>Escherichia coli ECOR11
<6>ATCC 35330
<7>
<8>Barcus, V.A., Titheradge, A.J.B., Murray, N.E., (1995) Genetics, vol. 140, pp. 1187-1197.

<1>EcoR12I
<2>
<3>?
<4>
<5>Escherichia coli ECOR12
<6>ATCC 35331
<7>
<8>Barcus, V.A., Titheradge, A.J.B., Murray, N.E., (1995) Genetics, vol. 140, pp. 1187-1197.

<1>EcoR13I
<2>
<3>?
<4>
<5>Escherichia coli ECOR13
<6>ATCC 35332
<7>
<8>Barcus, V.A., Titheradge, A.J.B., Murray, N.E., (1995) Genetics, vol. 140, pp. 1187-1197.

<1>EcoR15I
<2>
<3>?
<4>
<5>Escherichia coli ECOR15
<6>ATCC 35334
<7>
<8>Barcus, V.A., Titheradge, A.J.B., Murray, N.E., (1995) Genetics, vol. 140, pp. 1187-1197.

<1>EcoR17I
<2>
<3>?
<4>
<5>Escherichia coli ECOR17
<6>ATCC 35334
<7>
<8>Barcus, V.A., Titheradge, A.J.B., Murray, N.E., (1995) Genetics, vol. 140, pp. 1187-1197.

<1>EcoR23I
<2>
<3>?
<4>
<5>Escherichia coli ECOR23
<6>ATCC 35342
<7>
<8>Barcus, V.A., Titheradge, A.J.B., Murray, N.E., (1995) Genetics, vol. 140, pp. 1187-1197.

<1>EcoR24I
<2>
<3>?
<4>
<5>Escherichia coli ECOR24
<6>ATCC 35343
<7>
<8>Barcus, V.A., Titheradge, A.J.B., Murray, N.E., (1995) Genetics, vol. 140, pp. 1187-1197.

<1>EcoR25I
<2>
<3>?
<4>
<5>Escherichia coli ECOR25
<6>ATCC 35344
<7>
<8>Barcus, V.A., Titheradge, A.J.B., Murray, N.E., (1995) Genetics, vol. 140, pp. 1187-1197.

<1>EcoR42I
<2>
<3>?
<4>
<5>Escherichia coli ECOR42
<6>ATCC 35361
<7>
<8>Barcus, V.A., Titheradge, A.J.B., Murray, N.E., (1995) Genetics, vol. 140, pp. 1187-1197.

<1>EcoR70I
<2>
<3>?
<4>
<5>Escherichia coli ECOR70
<6>ATCC 35389
<7>
<8>Barcus, V.A., Titheradge, A.J.B., Murray, N.E., (1995) Genetics, vol. 140, pp. 1187-1197.

<1>EcoR124I
<2>
<3>GAANNNNNNRTCG
<4>3(6),-3(6)
<5>Escherichia coli (R124)
<6>S. Glover
<7>
<8>Abadjieva, A., Webb, M., Patel, J., Zinkevich, V., Firman, K., (1994) J. Mol. Biol., vol. 241, pp. 35-43.
Hubacek, J., Weiserova, M., Janscak, P., Firman, K., (1994) Folia Microbiol. (Praha), vol. 39, pp. 162-165.
Patel, J., Taylor, I., Dutta, C.F., Kneale, G., Firman, K., (1992) Gene, vol. 112, pp. 21-27.
Price, C., Lingner, J., Bickle, T.A., Firman, K., Glover, S.W., (1989) J. Mol. Biol., vol. 205, pp. 115-125.
Price, C., Shepherd, J.C.W., Bickle, T.A., (1987) EMBO J., vol. 6, pp. 1493-1497.
Taylor, I., Watts, D., Kneale, G., (1993) Nucleic Acids Res., vol. 21, pp. 4929-4935.
Taylor, J.E.N., Kneale, G.G., Unpublished observations.

<1>EcoR124II
<2>
<3>GAANNNNNNNRTCG
<4>3(6),-3(6)
<5>Escherichia coli (R124/3)
<6>S. Glover
<7>
<8>Price, C., Lingner, J., Bickle, T.A., Firman, K., Glover, S.W., (1989) J. Mol. Biol., vol. 205, pp. 115-125.
Price, C., Pripfl, T., Bickle, T.A., (1987) Eur. J. Biochem., vol. 167, pp. 111-115.
Price, C., Shepherd, J.C.W., Bickle, T.A., (1987) EMBO J., vol. 6, pp. 1493-1497.
Taylor, I., Watts, D., Kneale, G., (1993) Nucleic Acids Res., vol. 21, pp. 4929-4935.
Taylor, J.E.N., Kneale, G.G., Unpublished observations.

<1>EcoRD2
<2>
<3>GAANNNNNNRTTC
<4>
<5>Artificial construct
<6>T.A. Bickle
<7>
<8>Gubler, M., Braguglia, D., Meyer, J., Piekarowicz, A., Bickle, T.A., (1992) EMBO J., vol. 11, pp. 233-240.

<1>EcoRD3
<2>
<3>GAANNNNNNNRTTC
<4>
<5>Artificial construct
<6>T.A. Bickle
<7>
<8>Gubler, M., Braguglia, D., Meyer, J., Piekarowicz, A., Bickle, T.A., (1992) EMBO J., vol. 11, pp. 233-240.

<1>EcoT14I
<2>StyI,BsmSI,BssT1I,Bst224I,CfrBI,Eco130I,Eco208II,EcoT104I,ErhI,ErhB9II,SblAI,SblBI,SblCI,Uba1311I
<3>C^CWWGG
<4>
<5>Escherichia coli TB14
<6>N. Terakado
<7>K
<8>Yoshida, Y., Mise, K., Unpublished observations.

<1>EcoT22I
<2>AvaIII,Asi372I,BfrBI,BfrCI,Csp68KIII,Mph1103I,NsiI,PinBI,Ppu10I,PxyJKI,SepI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>ATGCA^T
<4>
<5>Escherichia coli TB22
<6>N. Terakado
<7>KO
<8>Elhai, J., Cai, Y., Wolk, C.P., (1994) J. Bacteriol., vol. 176, pp. 5059-5067.
Mise, K., Nakajima, K., Terakado, N., Ishidate, M., (1986) Gene, vol. 44, pp. 165-169.

<1>EcoT38I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCY^C
<4>4(5)
<5>Escherichia coli TH38
<6>K. Mise
<7>J
<8>Kita, K., Kawakami, H., Tanaka, H., (2003) J. Bacteriol., vol. 185, pp. 2296-2305.
Mise, K., Nakajima, K., Terakado, N., Ishidate, M., (1986) Gene, vol. 44, pp. 165-169.
Ueda, Y., Unpublished observations.

<1>EcoT88I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli TH88
<6>N. Terakado
<7>
<8>Mise, K., Unpublished observations.

<1>EcoT93I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli TH93
<6>N. Terakado
<7>
<8>Mise, K., Unpublished observations.

<1>EcoT95I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Escherichia coli TH95
<6>N. Terakado
<7>
<8>Mise, K., Unpublished observations.

<1>EcoT104I
<2>StyI,BsmSI,BssT1I,Bst224I,CfrBI,Eco130I,Eco208II,EcoT14I,ErhI,ErhB9II,SblAI,SblBI,SblCI,Uba1311I
<3>CCWWGG
<4>
<5>Escherichia coli TB104
<6>N. Terakado
<7>
<8>Yoshida, Y., Mise, K., Unpublished observations.

<1>M.EcoT1Dam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Escherichia coli phage T1
<6>M. Schweiger
<7>
<8>Roberts, M.D., Martin, N.L., Kropinski, A.M., (2004) Virology, vol. 318, pp. 245-266.
Scherzer, E., Auer, B., Schweiger, M., (1987) J. Biol. Chem., vol. 262, pp. 15225-15231.
Schneider-Scherzer, E., Auer, B., de Groot, E.J., Schweiger, M., (1990) J. Biol. Chem., vol. 265, pp. 6086-6091.

<1>M.EcoT2Dam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Escherichia coli bacteriophage T2
<6>S. Hattman
<7>
<8>Revel, H.R., Hattman, S.M., (1971) Virology, vol. 45, pp. 484-495.
van Ormondt, H., Gorter, J., Havelaar, K.J., de Waard, A., (1975) Nucleic Acids Res., vol. 2, pp. 1391-1400.

<1>M.EcoT4Dam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Escherichia coli phage T4
<6>S. Hattman
<7>
<8>Schlagman, S.L., Hattman, S., (1983) Gene, vol. 22, pp. 139-156.

<1>EcoVIII
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>A^AGCTT
<4>1(6)
<5>Escherichia coli E1585-68
<6>M. Yoshikawa
<7>
<8>Mise, K., Nakajima, K., (1984) Gene, vol. 30, pp. 79-85.
Mruk, I., Kaczorowski, T., (2003) Appl. Environ. Microbiol., vol. 69, pp. 2638-2650.

<1>M.EcoVT2Dam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Escherichia coli prophage VT2-Sa
<6>H. Miyamoto
<7>
<8>Miyamoto, H., Nakai, W., Yajima, N., Fujibayashi, A., Higuchi, T., Sato, K., Matsushiro, A., (1999) DNA Res., vol. 6, pp. 235-240.

<1>Eco13kI
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>^CCNGG
<4>
<5>Escherichia coli 13k
<6>A.S. Solonin
<7>
<8>Denjmukhametov, M.M., Zakharova, M.V., Kravets, A.N., Pertsev, A.V., Sineva, E.V., Repik, A.V., Beletskaya, I.V., Gromova, E.S., Solonin, A.S., (1997) Mol. Biol. (Mosk), vol. 31, pp. 831-838.

<1>Eco21kI
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>^CCNGG
<4>
<5>Escherichia coli 21k
<6>A.S. Solonin
<7>
<8>Denjmukhametov, M.M., Zakharova, M.V., Kravets, A.N., Pertsev, A.V., Sineva, E.V., Repik, A.V., Beletskaya, I.V., Gromova, E.S., Solonin, A.S., (1997) Mol. Biol. (Mosk), vol. 31, pp. 831-838.

<1>Eco27kI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>
<5>Escherichia coli 27
<6>A.S. Solonin
<7>
<8>Denjmuchametov, M.M., Ruban, N.M., Zakharova, M.V., Beletzkaja, I.V., Kravetz, A.N., Solonin, A.S., (1992) Nucleic Acids Res., vol. 20, pp. 1992.

<1>Eco29kI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>2(5)
<5>Escherichia coli
<6>A.S. Solonin
<7>
<8>Nikitin, D., Mokrishcheva, M., Solonin, A., (2007) Biochim. Biophys. Acta, vol. 1774, pp. 1014-1019.
Pertzev, A.V., Kravetz, A.N., Mayorov, S.G., Zakharova, M.V., Solonin, A.S., (1997) Biokhimiia, vol. 62, pp. 858-867.
Pertzev, A.V., Ruban, N.M., Zakharova, M.V., Beletzkaja, I.V., Petrov, S.I., Kravetz, A.N., Solonin, A.S., (1992) Nucleic Acids Res., vol. 20, pp. 1991.
Zakharova, M.V., Beletskaya, I.V., Kravetz, A.N., Pertzev, A.V., Mayorov, S.G., Shlyapnikov, M.G., Solonin, A.S., (1998) Gene, vol. 208, pp. 177-182.

<1>Eco53kI
<2>SacI,BpuAmI,Ecl136II,Ecl137I,EcoICRI,MxaI,NasSI,Pfl18I,Psp124BI,ScoI,Ssm4I,Ssm5I,SstI
<3>GAG^CTC
<4>
<5>Escherichia coli 53k
<6>A.S. Solonin
<7>N
<8>Denjmukhametov, M.M., Zakharova, M.V., Kravets, A.N., Pertsev, A.V., Sineva, E.V., Repik, A.V., Beletskaya, I.V., Gromova, E.S., Solonin, A.S., (1997) Mol. Biol. (Mosk), vol. 31, pp. 831-838.

<1>Eco110kI
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Escherichia coli BKM B-2004
<6>A.N. Kravets
<7>
<8>Pertsev, A.V., Kravets, A.N., Russian Patent Office, 1995.

<1>Eco137kI
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>^CCNGG
<4>
<5>Escherichia coli 137k
<6>A.S. Solonin
<7>
<8>Denjmukhametov, M.M., Zakharova, M.V., Kravets, A.N., Pertsev, A.V., Sineva, E.V., Repik, A.V., Beletskaya, I.V., Gromova, E.S., Solonin, A.S., (1997) Mol. Biol. (Mosk), vol. 31, pp. 831-838.

<1>EcoprrI
<2>
<3>CCANNNNNNNRTGC
<4>
<5>Escherichia coli
<6>T.A. Bickle
<7>
<8>Levitz, R., Chapman, D., Amitsur, M., Green, R., Snyder, L., Kaufmann, G., (1990) EMBO J., vol. 9, pp. 1383-1389.
Tyndall, C., Meister, J., Bickle, T.A., (1994) J. Mol. Biol., vol. 237, pp. 266-274.

<1>EgeI
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GGC^GCC
<4>
<5>Enterobacter gergoviae NA
<6>S.K. Degtyarev
<7>I
<8>Dedkov, V.S., Myakisheva, T.V., Kileva, E.V., Degtyarev, S.K., Unpublished observations.

<1>EheI
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GGC^GCC
<4>
<5>Erwinia herbicola 9/5
<6>A. Janulaitis
<7>FO
<8>Kulba, A.M., Abdel-Sabur, M.S., Butkus, V.V., Janulaitis, A., Fomichev, Y.K., (1987) Mol. Biol. (Mosk), vol. 21, pp. 250-254.

<1>ErhI
<2>StyI,BsmSI,BssT1I,Bst224I,CfrBI,Eco130I,Eco208II,EcoT14I,EcoT104I,ErhB9II,SblAI,SblBI,SblCI,Uba1311I
<3>C^CWWGG
<4>
<5>Erwinia rhaponici B9
<6>S.K. Degtyarev
<7>IV
<8>Zhilkina, O.A., Rechkunova, N.I., Semenchenko, G.V., Degtyarev, S.K., Unpublished observations.

<1>ErhB9I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGAT^CG
<4>
<5>Erwinia rhaponici B9
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>ErhB9II
<2>StyI,BsmSI,BssT1I,Bst224I,CfrBI,Eco130I,Eco208II,EcoT14I,EcoT104I,ErhI,SblAI,SblBI,SblCI,Uba1311I
<3>C^CWWGG
<4>
<5>Erwinia rhaponici B9
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>ErpI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Erwinia rhaponici
<6>D. Jones
<7>
<8>Walker, J.N.B., Dean, P.G., Saunders, J.R., Unpublished observations.

<1>EsaBC3I
<2>TaqI,CviSIII,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TC^GA
<4>2(4)
<5>Environmental sample BC3
<6>R.D. Morgan
<7>
<8>Morgan, R.D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>EsaBC4I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>?(4)
<5>Environmental sample BC4
<6>R.D. Morgan
<7>
<8>Morgan, R.D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>EsaBS9I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>?(4)
<5>Environmental sample BS #9
<6>R.D. Morgan
<7>
<8>Morgan, R.D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>EsaLHCI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>4(4)
<5>Environmental sample LHC
<6>R.D. Morgan
<7>
<8>Morgan, R.D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>EsaSSI
<2>
<3>GACCAC
<4>
<5>Environmental sample Sargasso Sea
<6>J.C. Venter
<7>
<8>Morgan, R.D., Unpublished observations.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.
Venter, J.C. et al., (2004) Science, vol. 304, pp. 66-74.

<1>EsaWC1I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Environmental sample WC1
<6>R.D. Morgan
<7>
<8>Morgan, R.D., Unpublished observations.

<1>EscI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Exiguobacterium sp. strain SCF
<6>Vivantis 641
<7>
<8>Chee, H.Y., Unpublished observations.

<1>Ese3I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Enterobacter species RFL3
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Ese4I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Enterobacter species RFL4
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Ese6I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Enterobacter species RFL6
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Ese6II
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter species RFL6
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>EspI
<2>BlpI,Bpu1102I,BpuGCI,Bsp1720I,CelII,Uba1221I,Uba1222I,Uba1284I,Uba1320I
<3>GC^TNAGC
<4>
<5>Eucapsis species
<6>PCC 6906
<7>
<8>Calleja, F., Dekker, B.M.M., Coursin, T., de Waard, A., (1984) FEBS Lett., vol. 178, pp. 69-72.

<1>EspII
<2>
<3>?
<4>
<5>Eucapsis species
<6>PCC 6906
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>Esp1I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Erwinia species RFL1
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Esp2I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Erwinia species RFL2
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Esp3I
<2>BsmBI,BstGZ53I,Esp16I,Esp23I
<3>CGTCTC(1/5)
<4>4(5),-4(6)
<5>Erwinia species RFL3
<6>A. Janulaitis
<7>F
<8>Bitinaite, J., Grigaite, R., Maneliene, Z., Butkus, V., Janulaitis, A., (1991) Nucleic Acids Res., vol. 19, pp. 5076.
Bitinaite, J., Maneliene, Z., Menkevicius, S., Klimasauskas, S., Butkus, V., Janulaitis, A., (1992) Nucleic Acids Res., vol. 20, pp. 4981-4985.

<1>Esp4I
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>C^TTAAG
<4>
<5>Erwinia species RFL4
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Butkus, V., Maneliene, Z., Petrusyte, M., Unpublished observations.

<1>Esp5I
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Erwinia species RFL5
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.

<1>Esp5II
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Erwinia species RFL5
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.

<1>Esp6I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Erwinia species RFL6
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Esp7I
<2>BsePI,BscEI,BsoPI,BsrHI,BssBI,BssHII,BstBZ153I,CfrJ5I,Eco143I,Eco152I,Esp8I,Kpn30I,McaTI,PauI,PteI,TtmII,Uba69I
<3>GCGCGC
<4>
<5>Erwinia species RFL7
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Esp8I
<2>BsePI,BscEI,BsoPI,BsrHI,BssBI,BssHII,BstBZ153I,CfrJ5I,Eco143I,Eco152I,Esp7I,Kpn30I,McaTI,PauI,PteI,TtmII,Uba69I
<3>GCGCGC
<4>
<5>Erwinia species RFL8
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Esp9I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Erwinia species RFL9
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Esp10I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Erwinia species RFL10
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Esp11I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Erwinia species RFL11
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Esp12I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Erwinia species RFL12
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Esp13I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Erwinia species RFL13
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Esp14I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Erwinia species RFL14
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Grigaite, R., Jagelavicius, M., Unpublished observations.

<1>Esp15I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Erwinia species RFL15
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Esp16I
<2>Esp3I,BsmBI,BstGZ53I,Esp23I
<3>CGTCTC
<4>
<5>Erwinia species RFL16
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Esp19I
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Erwinia species RFL19
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Esp21I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Erwinia species RFL21
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Esp22I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Erwinia species RFL22
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Esp23I
<2>Esp3I,BsmBI,BstGZ53I,Esp16I
<3>CGTCTC
<4>
<5>Erwinia species RFL23
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Esp24I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Erwinia species RFL24
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Esp25I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Erwinia species RFL25
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Esp141I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Enterobacter species RFL141
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Esp1396I
<2>PflMI,AccB7I,AcpII,Asp10HII,BasI,PflBI,Van91I
<3>CCANNNN^NTGG
<4>3(6)
<5>Enterobacter species RFL1396
<6>A. Janulaitis
<7>
<8>Cesnaviciene, E., Mitkaite, G., Stankevicius, K., Janulaitis, A., Lubys, A., (2003) Nucleic Acids Res., vol. 31, pp. 743-749.
Janulaitis, A., Krikstulyte, V., Trinkunaite, L., Maneliene, Z., Kiuduliene, L., Petrusyte, M., Butkus, V., Unpublished observations.
Stankevicius, K., Janulaitis, A., Unpublished observations.

<1>EspHK7I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter species N7
<6>P.C. Shaw
<7>
<8>Chan, Y.C., Kam, K.M., Shaw, P.C., Unpublished observations.

<1>EspHK16I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK24I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Enterobacter species N16
<6>P.C. Shaw
<7>
<8>Chan, Y.C., Kam, K.M., Shaw, P.C., Unpublished observations.

<1>EspHK22I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter species N22
<6>P.C. Shaw
<7>
<8>Chan, Y.C., Kam, K.M., Shaw, P.C., Unpublished observations.

<1>EspHK24I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,KspHK15I,Uba36I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Enterobacter species 24I
<6>P.C. Shaw
<7>
<8>Chan, Y.C., Kam, K.M., Shaw, P.C., Unpublished observations.

<1>EspHK26I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Enterobacter species N26
<6>P.C. Shaw
<7>
<8>Chan, Y.C., Kam, K.M., Shaw, P.C., Unpublished observations.

<1>EspHK29I
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Enterobacter species N29
<6>P.C. Shaw
<7>
<8>Chan, Y.C., Kam, K.M., Shaw, P.C., Unpublished observations.

<1>EspHK30I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Enterobacter species N30
<6>P.C. Shaw
<7>
<8>Chan, Y.C., Kam, K.M., Shaw, P.C., Unpublished observations.

<1>FaeI
<2>NlaIII,CviAII,FatI,FatII,Hin1II,Hin8II,HpyCH4I,Hsp92II
<3>CATG^
<4>
<5>Flavobacterium aquatile N3
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Kileva, E.V., Tomilova, J.E., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>FaiI
<2>
<3>YA^TR
<4>
<5>Flavobacterium aquatile B15
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Dedkov, V.S., Mikhnenkova, N.A., Kileva, E.V., Tomilova, J.E., Degtyarev, S.K., Unpublished observations.

<1>FalI
<2>
<3>(8/13)AAGNNNNNCTT(13/8)
<4>
<5>Flavobacterium aquatile Ob10
<6>S.K. Degtyarev
<7>I
<8>Dedkov, V.S., Sinichkina, S.A., Abdurashitov, M.A., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>FalII
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>
<5>Flavobacterium aquatile Ob10
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Sinichkina, S.A., Abdurashitov, M.A., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>FaqI
<2>FinI,BpuNI,BpuSI,BscWI,BslFI,BsmFI,BspLU11III,BstOZ616I
<3>GGGAC(10/14)
<4>
<5>Flavobacterium aquatile RFL1
<6>Fermentas G263
<7>F
<8>Vitkute, J., Mociskyte, S., Maneliene, Z., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>FatI
<2>NlaIII,CviAII,FaeI,FatII,Hin1II,Hin8II,HpyCH4I,Hsp92II
<3>^CATG
<4>?(5)
<5>Flavobacterium aquatile NL3
<6>NEB 1779
<7>IN
<8>Dedkov, V.S., Kileva, E.V., Popichenko, D.V., Degtyarev, S.K., (2002) Biotekhnologiya, vol. 5, pp. 3-7.
Morgan, R.D., Unpublished observations.

<1>FatII
<2>NlaIII,CviAII,FaeI,FatI,Hin1II,Hin8II,HpyCH4I,Hsp92II
<3>CATG
<4>
<5>Flavobacterium aquatile NL3
<6>NEB 1779
<7>
<8>Morgan, R.D., Unpublished observations.

<1>FauI
<2>Bme585I,BstFZ438I,SmuI
<3>CCCGC(4/6)
<4>2(5)
<5>Flavobacterium aquatile
<6>NEB 1780
<7>IN
<8>Chernukhin, V.A., Kashirina, Y.G., Sukhanova, K.S., Abdurashitov, M.A., Gonchar, D.A., Degtyarev, S.K., (2005) Biokhimiia, vol. 70, pp. 829-837.
Degtyarev, S.K., Kolyhalov, A.A., Rechkunova, N.I., Dedkov, V.S., (1989) Bioorg. Khim., vol. 15, pp. 130-132.
Degtyarev, S.K., Netesova, N.A., Chizhikov, V.E., Abdurashitov, M.A., (1998) Biol. Chem., vol. 379, pp. 567-568.
Degtyarev, S.Kh., Unpublished observations.

<1>FauBI
<2>
<3>?
<4>
<5>Flavobacterium aureus B
<6>M.M. Wijdenbosch
<7>
<8>Rahman, H., Unpublished observations.

<1>FauBII
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>
<5>Flavobacterium aureus B
<6>M.M. Wijdenbosch
<7>
<8>Rahman, H., Unpublished observations.

<1>FauNDI
<2>NdeI,PfaAII,TrsKTIII
<3>CA^TATG
<4>
<5>Flavobacterium aquatile ND
<6>S.K. Degtyarev
<7>IV
<8>Shevchenko, A.V., Belichenko, O.A., Myakisheva, T.V., Dedkov, V.S., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>FbaI
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>T^GATCA
<4>
<5>Flavobacterium balustinum
<6>ATCC 33487
<7>K
<8>Stote, R., Schildkraut, I., Unpublished observations.
Yamamoto, K., Hiraoka, N., Unpublished observations.

<1>FblI
<2>AccI,DsaVI,OmiBII,XmiI
<3>GT^MKAC
<4>
<5>Flavobacterium balustinum
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.K., Unpublished observations.

<1>FbrI
<2>Fnu4HI,Bli1904II,Bpu1811I,BsoFI,Bsp6I,BssFI,BssXI,BthCI,Cac824I,CcoP215I,CcoP216I,Fsp4HI,ItaI,LlaDII,SatI,Uur960I
<3>GC^NGC
<4>
<5>Flavobacterium breve
<6>NEB 379
<7>
<8>Stote, R., Schildkraut, I., Unpublished observations.

<1>FdiI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Fremyella diplosiphon
<6>PCC 7601
<7>
<8>van den Hondel, C.A.M.J.J., van Leen, R.W., van Arkel, G.A., Duyvesteyn, M., de Waard, A., (1983) FEMS Microbiol. Lett., vol. 16, pp. 7-12.

<1>FdiII
<2>MstI,AcaIII,Acc16I,AosI,ApcTR183I,AviII,Bco6I,BsaTI,ClcII,CliII,FspI,GspAII,NsbI,NspHIII,NspLI,NspMI,PamI,Pun14627I
<3>TGC^GCA
<4>
<5>Fremyella diplosiphon
<6>PCC 7601
<7>
<8>Streips, U., Golemboski, B., Unpublished observations.
van den Hondel, C.A.M.J.J., van Leen, R.W., van Arkel, G.A., Duyvesteyn, M., de Waard, A., (1983) FEMS Microbiol. Lett., vol. 16, pp. 7-12.

<1>FgoI
<2>MaeI,BfaI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>C^TAG
<4>
<5>Fervidobacterium gondwanense AB39T
<6>B.K.C. Patel
<7>
<8>Andrews, K.T., Patel, B.K.C., Clarke, F.M., (1998) Anaerobe, vol. 4, pp. 227-232.

<1>FinI
<2>BpuNI,BpuSI,BscWI,BslFI,BsmFI,BspLU11III,BstOZ616I,FaqI
<3>GGGAC
<4>
<5>Flavobacterium indologenes
<6>NEB 382
<7>
<8>Morgan, R.D., Unpublished observations.

<1>FinII
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Flavobacterium indologenes
<6>NEB 382
<7>
<8>Morgan, R.D., Unpublished observations.

<1>FinSI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Flavobacterium indoltheticum
<6>ATCC 27950
<7>
<8>Stote, R., Schildkraut, I., Unpublished observations.

<1>FisI
<2>MaeI,BfaI,FgoI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Fervidobacterium islandicum H21
<6>DSM 5733
<7>
<8>Andrews, K.T., Patel, B.K.C., Clarke, F.M., (1998) Anaerobe, vol. 4, pp. 227-232.

<1>FmuI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNC^C
<4>
<5>Flavobacterium multivorum
<6>B.A. Rebentish
<7>
<8>Rebentish, B.A., Bolotin, A.P., Grachova, I.M., Ren, L.S., Uyan, J.M., (1994) Biotekhnologiya, vol. 3, pp. 15-16.

<1>Fnu48I
<2>
<3>?
<4>
<5>Fusobacterium nucleatum 48
<6>M. Smith
<7>
<8>Lui, A.C.P., McBride, B.C., Smith, M., Unpublished observations.

<1>FnuAI
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>G^ANTC
<4>
<5>Fusobacterium nucleatum A
<6>M. Smith
<7>
<8>Lui, A.C.P., McBride, B.C., Vovis, G.F., Smith, M., (1979) Nucleic Acids Res., vol. 6, pp. 1-15.

<1>FnuAII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Fusobacterium nucleatum A
<6>M. Smith
<7>
<8>Lui, A.C.P., McBride, B.C., Vovis, G.F., Smith, M., (1979) Nucleic Acids Res., vol. 6, pp. 1-15.
Myers, P.A., Roberts, R.J., Unpublished observations.

<1>FnuCI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Fusobacterium nucleatum C
<6>M. Smith
<7>
<8>Lui, A.C.P., McBride, B.C., Vovis, G.F., Smith, M., (1979) Nucleic Acids Res., vol. 6, pp. 1-15.

<1>FnuDI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>?(5)
<5>Fusobacterium nucleatum D
<6>M. Smith
<7>
<8>Lui, A.C.P., McBride, B.C., Vovis, G.F., Smith, M., (1979) Nucleic Acids Res., vol. 6, pp. 1-15.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
Van Cott, E., Wilson, G., European Patent Office, 1987.
Van Cott, E.M., Wilson, G.G., US Patent Office, 1991.

<1>FnuDII
<2>AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>1(5)
<5>Fusobacterium nucleatum D
<6>M. Smith
<7>
<8>Lui, A.C.P., McBride, B.C., Vovis, G.F., Smith, M., (1979) Nucleic Acids Res., vol. 6, pp. 1-15.
Murray, I.A., Unpublished observations.
Qiang, B.-Q., McClelland, M., Poddar, S., Spokauskas, A., Nelson, M., (1990) Gene, vol. 88, pp. 101-105.

<1>FnuDIII
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCG^C
<4>
<5>Fusobacterium nucleatum D
<6>M. Smith
<7>
<8>Lui, A.C.P., McBride, B.C., Vovis, G.F., Smith, M., (1979) Nucleic Acids Res., vol. 6, pp. 1-15.

<1>FnuEI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Fusobacterium nucleatum E
<6>M. Smith
<7>
<8>Lui, A.C.P., McBride, B.C., Vovis, G.F., Smith, M., (1979) Nucleic Acids Res., vol. 6, pp. 1-15.

<1>Fnu4HI
<2>Bli1904II,Bpu1811I,BsoFI,Bsp6I,BssFI,BssXI,BthCI,Cac824I,CcoP215I,CcoP216I,FbrI,Fsp4HI,ItaI,LlaDII,SatI,Uur960I
<3>GC^NGC
<4>?(5)
<5>Fusobacterium nucleatum 4H
<6>M. Smith
<7>N
<8>Forrow, S., Lee, M., Souhami, R.L., Hartley, J.A., (1994) ACS Abstracts, vol. 208, pp. 97.
Leung, D.W., Lui, A.C.P., Merilees, H., McBride, B.C., Smith, M., (1979) Nucleic Acids Res., vol. 6, pp. 17-25.
Morgan, R.D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Vaisvila, R., Unpublished observations.

<1>FokI
<2>BseGI,BstF5I,BtsCI,HinGUII,Hpy178VI,HpyF6I,HpyF67III,PbuJKI,StsI
<3>GGATG(9/13)
<4>3(6),-2(6)
<5>Flavobacterium okeanokoites
<6>IFO 12536
<7>IJKMNQRVWX
<8>Landry, D., Looney, M.C., Feehery, G.R., Slatko, B.E., Jack, W.E., Schildkraut, I., Wilson, G.G., (1989) Gene, vol. 77, pp. 1-10.
Li, L., Wu, L.P., Clarke, R., Chandrasegaran, S., (1993) Gene, vol. 133, pp. 79-84.
Matvienko, N.I., Kramarov, V.M., Irismetov, A.A., (1985) Bioorg. Khim., vol. 11, pp. 953-956.
Posfai, G., Szybalski, W., (1988) Gene, vol. 69, pp. 147-151.
Posfai, G., Szybalski, W., (1988) Gene, vol. 74, pp. 179-181.
Steenstrup, T.D., Norby, P.L., International Patent Office, 2007.
Sugisaki, H., Kanazawa, S., (1981) Gene, vol. 16, pp. 73-78.
Sugisaki, H., Kita, K., Takanami, M., (1989) J. Biol. Chem., vol. 264, pp. 5757-5761.

<1>FriOI
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCY^C
<4>
<5>Flavobacterium species O9
<6>S.K. Degtyarev
<7>IV
<8>Belichenko, O.A., Prikhodko, E.A., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>FscI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Frankia species 32.61
<6>M. Lechevalier
<7>
<8>Miceli, S., Meyertons, J.L., Roberts, R.J., Unpublished observations.

<1>FseI
<2>RigI
<3>GGCCGG^CC
<4>?(5)
<5>Frankia species Eul1b
<6>NRRL 18528
<7>N
<8>Morgan, R.D., US Patent Office, 1996.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Nelson, J.M., Miceli, S.M., Lechevalier, M.P., Roberts, R.J., (1990) Nucleic Acids Res., vol. 18, pp. 2061-2064.

<1>FsfI
<2>Eco57I,AcuI,Bsp6II,BspD6II,BspKT5I,Eco112I,Eco125I
<3>CTGAAG
<4>
<5>Flavobacterium sulfureum
<6>NEB 386
<7>
<8>Morgan, R., Stote, R., Schildkraut, I., Unpublished observations.

<1>FsiI
<2>ApoI,AcsI,CfaI,XapI
<3>R^AATTY
<4>
<5>Frankia species
<6>NEB 685
<7>
<8>Morgan, R.D., Unpublished observations.

<1>FspI
<2>MstI,AcaIII,Acc16I,AosI,ApcTR183I,AviII,Bco6I,BsaTI,ClcII,CliII,FdiII,GspAII,NsbI,NspHIII,NspLI,NspMI,PamI,Pun14627I
<3>TGC^GCA
<4>?(5)
<5>Fischerella species
<6>ATCC 29114
<7>JNO
<8>Christ, C., Ingalls, D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Szekeres, M., Unpublished observations.
Ware, J., Meda, M., Mazzola, L., Wilson, G.G., Unpublished observations.
Wilson, G.G., Meda, M.M., US Patent Office, 1993.

<1>FspII
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Fischerella species
<6>ATCC 29114
<7>
<8>Szekeres, M., Unpublished observations.

<1>Fsp1604I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Flavobacterium species I 16-04
<6>U. Simidu
<7>
<8>Chiura, H., Noro, Y., Kanayama, S., Ueda, Y., Simidu, U., Takagi, J., (1988) Agric. Biol. Chem., vol. 52, pp. 2107-2109.

<1>FspAI
<2>
<3>RTGC^GCAY
<4>
<5>Flexibacter species Tv-m21K
<6>V. Butkus
<7>F
<8>Kesminiene, A., Maneliene, Z., Vitkute, J., Petrusyte, M., Janulaitis, A., (2001) Nucleic Acids Res., vol. 29.

<1>FspBI
<2>MaeI,BfaI,FgoI,FisI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>C^TAG
<4>
<5>Flavobacterium species RFLI
<6>A. Janulaitis
<7>F
<8>Starkovska, E., Maneliene, Z., Steponaviciene, D., Trinkunaite, L., Kiuduliene, L., Petrusyte, M., Markauskas, A., Butkus, V., Janulaitis, A., Unpublished observations.

<1>Fsp4HI
<2>Fnu4HI,Bli1904II,Bpu1811I,BsoFI,Bsp6I,BssFI,BssXI,BthCI,Cac824I,CcoP215I,CcoP216I,FbrI,ItaI,LlaDII,SatI,Uur960I
<3>GC^NGC
<4>2(5)
<5>Flavobacterium species 4H
<6>S.K. Degtyarev
<7>I
<8>Chmuzh, E.V., Abdurashitov, M.A., Gonchar, D.A., Kashirina, J.G., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.
Chmuzh, E.V., Kashirina, Y.G., Tomilova, Y.E., Chernukhin, V.A., Okhapkina, S.S., Gonchar, D.A., Dedkov, V.S., Abdurashitov, M.A., Degtyarev, S.K., (2007) Mol. Biol. (Mosk), vol. 41, pp. 43-50.
Dedkov, V.S., Kileva, E.V., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>FspMI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Flavobacterium species
<6>NEB 380
<7>
<8>Morgan, R.D., Unpublished observations.

<1>FspMSI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Fischerella species
<6>M. Sargent
<7>
<8>Walker, J.N.B., Dean, P.G., Saunders, J.R., Unpublished observations.

<1>M.FspVDam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Feldmannia species virus
<6>T.J. Choi
<7>
<8>Park, Y., Kim, G.-Do., Choi, T.-Jin., (2007) Virus Genes, vol. 34, pp. 177-183.
Schroeder, D.C., Park, Y., Yoon, H.-M., Lee, Y.S., Kang, S.W., Meints, R.H., Choi, T.-J., Unpublished observations.

<1>FssI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Fibrobacter succinogenes S85
<6>A.M. Gibbins
<7>
<8>Lee, S.F., Forsberg, C.W., Gibbins, A.M., (1992) J. Bacteriol., vol. 174, pp. 5275-5283.

<1>FsuI
<2>Tth111I,AspI,AtsI,BgiI,NtaI,PflFI,PsyI,SmaAII,SpaPI,SplII,SplAII,TelI,TrsKTII,TspI,TteI,TtrI
<3>GACNNNGTC
<4>
<5>Flavobacterium suaveolens
<6>ATCC 13718
<7>
<8>Stote, R., Morgan, R., Unpublished observations.

<1>FtnUI
<2>
<3>?
<4>
<5>Francisella tularensis subsp. novicida U112
<6>F. Nano
<7>
<8>Gallagher, L.A., McKevitt, M., Ramage, E.R., Manoil, C., (2008) J. Bacteriol., vol. 190, pp. 7830-7837.

<1>FtnUII
<2>
<3>?
<4>
<5>Francisella tularensis subsp. novicida U112
<6>F. Nano
<7>
<8>Gallagher, L.A., McKevitt, M., Ramage, E.R., Manoil, C., (2008) J. Bacteriol., vol. 190, pp. 7830-7837.

<1>FtnUIII
<2>
<3>?
<4>
<5>Francisella tularensis subsp. novicida U112
<6>F. Nano
<7>
<8>Gallagher, L.A., McKevitt, M., Ramage, E.R., Manoil, C., (2008) J. Bacteriol., vol. 190, pp. 7830-7837.

<1>FtnUIV
<2>DpnI,CfuI,MalI,Mph1103II,NanII,NgoDXIV,NmeAII,NmeBL859I,NmuDI,NmuEI,NsuDI,TdeI
<3>GATC
<4>
<5>Francisella tularensis subsp. novicida U112
<6>F. Nano
<7>
<8>Brittnacher, M. et al., Unpublished observations.
Gallagher, L.A., McKevitt, M., Ramage, E.R., Manoil, C., (2008) J. Bacteriol., vol. 190, pp. 7830-7837.

<1>FunI
<2>Eco47III,AfeI,AitI,Aor51HI
<3>AGC^GCT
<4>
<5>Fischerella uniformis
<6>M.M. Wijdenbosch
<7>
<8>Affram, C., Unpublished observations.

<1>FunII
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco237I,Eco252I,HalI,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl32DII,Srl55DI,SsoI,Uba58I,Van91II,VchN100I,VchO2I
<3>G^AATTC
<4>
<5>Fischerella uniformis
<6>M.M. Wijdenbosch
<7>
<8>Waaijer, R.J.A., Unpublished observations.

<1>M.Fvi3I
<2>
<3>?
<4>?(5)
<5>Frog virus 3
<6>K. Kaur
<7>
<8>Willis, D.B., Goorha, R., Granoff, A., (1984) J. Virol., vol. 49, pp. 86-91.

<1>GalI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Gluconobacter albidus
<6>IFO 3251
<7>
<8>Hiraoka, N., Kita, K., Nakajima, H., Kimizuka, F., Obayashi, A., (1985) J. Ferment. Technol., vol. 63, pp. 151-157.

<1>GceI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Gluconobacter cerinus
<6>IFO 3262
<7>
<8>Hiraoka, N., Kita, K., Nakajima, H., Kimizuka, F., Obayashi, A., (1985) J. Ferment. Technol., vol. 63, pp. 151-157.

<1>GceGLI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Gluconobacter cerinus
<6>IFO 3285
<7>
<8>Sasaki, J., Murakami, M., Yamada, Y., (1985) Agric. Biol. Chem., vol. 49, pp. 3017-3022.

<1>GdiI
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGG^CCT
<4>
<5>Gluconobacter dioxyacetonicus
<6>IAM 1814
<7>
<8>Van Montagu, M., Unpublished observations.

<1>GdiII
<2>
<3>CGGCCR(-5/-1)
<4>
<5>Gluconobacter dioxyacetonicus
<6>IAM 1814
<7>
<8>Van Montagu, M., Unpublished observations.

<1>GdoI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Gluconobacter dioxyacetonicus
<6>IAM 1840
<7>
<8>Seurinck, J., van Montagu, M., Unpublished observations.

<1>M.GgaDnmt1
<2>
<3>?
<4>?(5)
<5>Gallus gallus
<6>S. Tajima
<7>
<8>Tajima, S., Tsuda, H., Wakabayashi, N., Asano, A., Mizuno, S., Nishimori, K., (1995) J. Biochem. (Tokyo), vol. 117, pp. 1050-1057.

<1>GglI
<2>
<3>?
<4>
<5>Gluconobacter gluconicus
<6>IFO 3285
<7>
<8>Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Bull. Inst. Chem. Res. Kyoto Univ., vol. 60, pp. 328-335.

<1>GinI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Gluconobacter industricus
<6>IFO 3260
<7>
<8>Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Bull. Inst. Chem. Res. Kyoto Univ., vol. 60, pp. 328-335.

<1>GlaI
<2>
<3>GC^GC
<4>
<5>Glacial ice bacterium GL29
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Nayakshina, T.N., Abdurashitov, M.A., Tomilova, Y.E., Mezentseva, N.V., Dedkov, V.S., Mikhnenkova, N.A., Gonchar, D.A., Degtyarev, S.K., (2006) Biotekhnologiya, vol. 0, pp. 26-30.

<1>GluI
<2>BisI,BlsI
<3>GC^NGC
<4>
<5>Glacial ice bacterium GL24
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Chmuzh, E.V., Tomilova, J.E., Nayakshina, T.N., Dedkov, V.S., Degtyarev, S.K., Russian Patent Office, 2008.
Chernukhin, V.A., Chmuzh, E.V., Tomilova, Y.E., Nayakshina, T.N., Gonchar, D.A., Dedkov, V.S., Degtyarev, S.K., (2007) Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol., vol. 3, pp. 13-17.

<1>GobAI
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGGCCT
<4>
<5>Geodermatophilus obscurus
<6>Glaxo 2323C
<7>
<8>Earle-Hughes, J., Roberts, R.J., Unpublished observations.

<1>GoxI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Gluconobacter oxydans sub. melonogenes
<6>IAM 1836
<7>
<8>Seurinck, J., van Montagu, M., Unpublished observations.

<1>GsaI
<2>BseYI,PspFI
<3>CCCAGC(-1/-5)
<4>
<5>Geobacillus stearothermophilus Y
<6>S.K. Degtyarev
<7>I
<8>Dedkov, V.S., Mikhnenkova, N.A., Kileva, E.V., Tarasova, G.V., Gonchar, D.A., Akishev, A.G., Okhapkina, S.S., Degtyarev, S.K., Unpublished observations.

<1>GseI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Gloeocapsa species
<6>ATCC 29159
<7>
<8>Brand, P., de Waard, A., Unpublished observations.

<1>GseII
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Gloeocapsa species
<6>ATCC 29159
<7>
<8>Brand, P., de Waard, A., Unpublished observations.

<1>GseIII
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Gloeocapsa species
<6>ATCC 29159
<7>
<8>Brand, P., de Waard, A., Unpublished observations.

<1>GspI
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAGCTG
<4>
<5>Gloeothece species
<6>ATCC 27152
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>GspAI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Gloeotricia species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>GspAII
<2>MstI,AcaIII,Acc16I,AosI,ApcTR183I,AviII,Bco6I,BsaTI,ClcII,CliII,FdiII,FspI,NsbI,NspHIII,NspLI,NspMI,PamI,Pun14627I
<3>TGCGCA
<4>
<5>Gloeotricia species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>GspAIII
<2>
<3>?
<4>
<5>Gloeotricia species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>GstI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Geobacillus stearothermophilus
<6>ATCC 7953
<7>
<8>Skowron, P.M., Unpublished observations.

<1>Gst1588I
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Geobacillus stearothermophilus
<6>NEB 1588
<7>
<8>Pan, X.S., Morgan, R., Unpublished observations.

<1>Gst1588II
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Geobacillus stearothermophilus
<6>NEB 1588
<7>
<8>Pan, X.S., Morgan, R., Unpublished observations.

<1>GsuI
<2>Bco35I,BpmI,Bsp22I,Bsp28I,BspJ74I,Bth1795I,Uba1437I,Uba1444I
<3>CTGGAG(16/14)
<4>
<5>Gluconobacter suboxydans H-15T
<6>M.S. Loytsianskaya
<7>F
<8>Janulaitis, A., Bitinaite, J., Jaskeleviciene, B., (1983) FEBS Lett., vol. 151, pp. 243-247.
Petrusyte, M.P., Bitinaite, J.B., Kersulyte, D.R., Menkevicius, S.J., Butkus, V.V., Janulaitis, A., (1987) Dokl. Akad. Nauk., vol. 295, pp. 1250-1253.
Vaisvila, R., Janulaitis, A., Unpublished observations.

<1>M.H2I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>?(5)
<5>Bacillus amyloliquefaciens phage H2
<6>T.A. Trautner
<7>
<8>Lange, C., Noyer-Weidner, M., Trautner, T.A., Weiner, M., Zahler, S.A., (1991) Gene, vol. 100, pp. 213-218.

<1>HacI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Halococcus acetoinfaciens
<6>IAM 12094
<7>
<8>Hiraoka, N., Kita, K., Nakajima, H., Kimizuka, F., Obayashi, A., (1985) J. Ferment. Technol., vol. 63, pp. 151-157.

<1>HaeI
<2>
<3>WGG^CCW
<4>
<5>Haemophilus aegyptius
<6>ATCC 11116
<7>
<8>Murray, K., Morrison, A., Cooke, H.W., Roberts, R.J., Unpublished observations.

<1>HaeII
<2>AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGC^Y
<4>?(5)
<5>Haemophilus aegyptius
<6>ATCC 11116
<7>JKNORW
<8>Lunnen, K.D., Barsomian, J.M., Camp, R.R., Card, C.O., Chen, S.-Z., Croft, R., Looney, M.C., Meda, M.M., Moran, L.S., Nwankwo, D.O., Slatko, B.E., Van Cott, E.M., Wilson, G.G., (1988) Gene, vol. 74, pp. 25-32.
Roberts, R.J., Breitmeyer, J.B., Tabachnik, N.F., Myers, P.A., (1975) J. Mol. Biol., vol. 91, pp. 121-123.
Stein, D.C., Gunn, J.S., Piekarowicz, A., (1998) Biol. Chem., vol. 379, pp. 575-578.
Tu, C.-P.D., Roychoudhury, R., Wu, R., (1976) Biochem. Biophys. Res. Commun., vol. 72, pp. 355-362.

<1>HaeIII
<2>AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>3(5)
<5>Haemophilus aegyptius
<6>ATCC 11116
<7>BHIJKMNOQRSUWXY
<8>Bron, S., Murray, K., (1975) Mol. Gen. Genet., vol. 143, pp. 25-33.
Mann, M.B., Smith, H.O., (1977) Nucleic Acids Res., vol. 4, pp. 4211-4221.
Middleton, J.H., Edgell, M.H., Hutchison, C.A. III, (1972) J. Virol., vol. 10, pp. 42-50.

<1>HaeIV
<2>
<3>(7/13)GAYNNNNNRTC(14/9)
<4>2(6)
<5>Haemophilus aegyptius
<6>ATCC 11116
<7>
<8>Piekarowicz, A., Golaszewska, M., Sunday, A.O., Siwinska, M., Stein, D.C., (1999) J. Mol. Biol., vol. 293, pp. 1055-1065.

<1>HagI
<2>
<3>?
<4>
<5>Halococcus agglomeratus
<6>ATCC 25862
<7>
<8>Qiang, B.-Q., Schildkraut, I., Unpublished observations.

<1>HalI
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco237I,Eco252I,FunII,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl32DII,Srl55DI,SsoI,Uba58I,Van91II,VchN100I,VchO2I
<3>G^AATTC
<4>
<5>Hafnia alvei B6
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Repin, V.E., Rechkunova, N.I., Degtyarev, S.K., Verhosina, V.A., Vinogradova, T.P., (1990) Izv. Sib. Otd. Akad. Nauk SSSR, vol. 1, pp. 35-37.

<1>HalII
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Hafnia alvei B6
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Repin, V.E., Rechkunova, N.I., Degtyarev, S.K., Verhosina, V.A., Vinogradova, T.P., (1990) Izv. Sib. Otd. Akad. Nauk SSSR, vol. 1, pp. 35-37.

<1>Hal22I
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco237I,Eco252I,FunII,HalI,Kpn49kI,Ppu111I,RsrI,Srl32DII,Srl55DI,SsoI,Uba58I,Van91II,VchN100I,VchO2I
<3>GAATTC
<4>
<5>Hafnia alvei 22
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>HapI
<2>
<3>?
<4>
<5>Haemophilus aphrophilus
<6>ATCC 19415
<7>
<8>Myers, P.A., Roberts, R.J., Unpublished observations.

<1>HapII
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>C^CGG
<4>2(5)
<5>Haemophilus aphrophilus
<6>ATCC 19415
<7>K
<8>Hiraoka, N., Kadonishi, S., Unpublished observations.
Sugisaki, H., Takanami, M., (1973) Nature New Biol., vol. 246, pp. 138-140.
Takanami, M., (1974) Methods Mol. Biol., vol. 7, pp. 113-133.

<1>HcuI
<2>
<3>?
<4>
<5>Halobacterium cutirubrum
<6>D. Oesterhelt
<7>
<8>Schinzel, R., Unpublished observations.

<1>HgaI
<2>CseI,NmeBI
<3>GACGC(5/10)
<4>-2(5)
<5>Haemophilus gallinarum
<6>ATCC 14385
<7>IN
<8>Brown, N.L., Smith, M., (1977) Proc. Natl. Acad. Sci. U. S. A., vol. 74, pp. 3213-3216.
Landry, D., Barsomian, J.M., Feehery, G.R., Wilson, G.G., (1992) Methods Enzymol., vol. 216, pp. 244-259.
Lunnen, K.D., Barsomian, J.M., Camp, R.R., Card, C.O., Chen, S.-Z., Croft, R., Looney, M.C., Meda, M.M., Moran, L.S., Nwankwo, D.O., Slatko, B.E., Van Cott, E.M., Wilson, G.G., (1988) Gene, vol. 74, pp. 25-32.
Moses, P., Horiuchi, K., (1979) J. Mol. Biol., vol. 135, pp. 517-524.
Sugisaki, H., (1978) Gene, vol. 3, pp. 17-28.
Sugisaki, H., Yamamoto, K., Takanami, M., (1991) J. Biol. Chem., vol. 266, pp. 13952-13957.
Takanami, M., (1974) Methods Mol. Biol., vol. 7, pp. 113-133.
Wilson, G.G., Murray, N.E., (1991) Annu. Rev. Genet., vol. 25, pp. 585-627.
Zinovev, V.V., Rechkunova, N.I., Gorbunov, Y.A., Buryanov, Y.I., Malygin, E.G., (1989) Biopol. Kletka, vol. 5, pp. 22-27.

<1>HgiI
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>
<5>Herpetosiphon giganteus 3303
<6>U. Mayr
<7>
<8>Wersig, U., Bolton, B., Frey, B., Jarsch, M., Kessler, C., Unpublished observations.

<1>HgiAI
<2>Alw21I,AspHI,Bbv12I,Bfu1570I,BsaGI,Bsh45I,BsiHKAI,Bsm6I,BsmPI,Hpy8III,HpyF7II,HpyF46II,MspV281I,Pph3215I
<3>GWGCW^C
<4>
<5>Herpetosiphon giganteus HP1023
<6>J.H. Parish
<7>
<8>Brown, N.L., McClelland, M., Whitehead, P.R., (1980) Gene, vol. 9, pp. 49-68.
Lunnen, K.D., Wilson, G.G., US Patent Office, 1991.

<1>HgiBI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>?(5)
<5>Herpetosiphon giganteus Hpg5
<6>H. Reichenbach
<7>
<8>Dusterhoft, A., Erdmann, D., Kroger, M., (1991) Nucleic Acids Res., vol. 19, pp. 3207-3211.
Kroger, M., Hobom, G., Schutte, H., Mayer, H., (1984) Nucleic Acids Res., vol. 12, pp. 3127-3141.

<1>HgiCI
<2>AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>G^GYRCC
<4>5(5)
<5>Herpetosiphon giganteus Hpg9
<6>H. Reichenbach
<7>
<8>Erdmann, D., Dusterhoft, A., Kroger, M., (1991) Eur. J. Biochem., vol. 202, pp. 1247-1256.
Kroger, M., Hobom, G., Schutte, H., Mayer, H., (1984) Nucleic Acids Res., vol. 12, pp. 3127-3141.
Schildkraut, I., Lynch, J., Morgan, R., (1987) Nucleic Acids Res., vol. 15, pp. 5492.

<1>HgiCII
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>?(5)
<5>Herpetosiphon giganteus Hpg9
<6>H. Reichenbach
<7>
<8>Erdmann, D., (1991) Ph.D. Thesis, Justus-Liebig University, Geissen, W. Germany, pp. 1-204.
Erdmann, D., Horst, G., Dusterhoft, A., Kroger, M., (1992) Gene, vol. 117, pp. 15-22.
Kroger, M., Hobom, G., Schutte, H., Mayer, H., (1984) Nucleic Acids Res., vol. 12, pp. 3127-3141.

<1>HgiCIII
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>G^TCGAC
<4>
<5>Herpetosiphon giganteus Hpg9
<6>H. Reichenbach
<7>
<8>Kroger, M., Hobom, G., Schutte, H., Mayer, H., (1984) Nucleic Acids Res., vol. 12, pp. 3127-3141.

<1>HgiDI
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>?(5)
<5>Herpetosiphon giganteus Hpa2
<6>H. Reichenbach
<7>
<8>Dusterhoft, A., Erdmann, D., Kroger, M., (1991) Nucleic Acids Res., vol. 19, pp. 1049-1056.
Kroger, M., Hobom, G., Schutte, H., Mayer, H., (1984) Nucleic Acids Res., vol. 12, pp. 3127-3141.

<1>HgiDII
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>G^TCGAC
<4>?(5)
<5>Herpetosiphon giganteus Hpa2
<6>H. Reichenbach
<7>
<8>Dusterhoft, A., (1990) Ph.D. Thesis, Justus-Liebig University, Geissen, W. Germany, pp. 1-160.
Dusterhoft, A., Kroger, M., (1991) Gene, vol. 106, pp. 87-92.
Kroger, M., Hobom, G., Schutte, H., Mayer, H., (1984) Nucleic Acids Res., vol. 12, pp. 3127-3141.

<1>HgiEI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>?(5)
<5>Herpetosiphon giganteus Hpg24
<6>H. Reichenbach
<7>
<8>Erdmann, D., (1991) Ph.D. Thesis, Justus-Liebig University, Geissen, W. Germany, pp. 1-204.
Kroger, M., Hobom, G., Schutte, H., Mayer, H., (1984) Nucleic Acids Res., vol. 12, pp. 3127-3141.

<1>HgiEII
<2>
<3>ACCNNNNNNGGT
<4>
<5>Herpetosiphon giganteus Hpg24
<6>H. Reichenbach
<7>
<8>Kroger, M., Hobom, G., Schutte, H., Mayer, H., (1984) Nucleic Acids Res., vol. 12, pp. 3127-3141.

<1>HgiFI
<2>
<3>?
<4>
<5>Herpetosiphon giganteus Hpg14
<6>H. Reichenbach
<7>
<8>Mayer, H., Schutte, H., Unpublished observations.

<1>HgiGI
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>?(5)
<5>Herpetosiphon giganteus Hpa1
<6>H. Reichenbach
<7>
<8>Dusterhoft, A., (1990) Ph.D. Thesis, Justus-Liebig University, Geissen, W. Germany, pp. 1-160.
Kroger, M., Hobom, G., Schutte, H., Mayer, H., (1984) Nucleic Acids Res., vol. 12, pp. 3127-3141.

<1>HgiHI
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>G^GYRCC
<4>
<5>Herpetosiphon giganteus HP1049
<6>J.H. Parish
<7>
<8>Whitehead, P.R., Jacobs, D., Brown, N.L., (1986) Nucleic Acids Res., vol. 14, pp. 7031-7045.

<1>HgiHII
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>
<5>Herpetosiphon giganteus HP1049
<6>J.H. Parish
<7>
<8>Whitehead, P.R., Jacobs, D., Brown, N.L., (1986) Nucleic Acids Res., vol. 14, pp. 7031-7045.

<1>HgiHIII
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Herpetosiphon giganteus HP1049
<6>J.H. Parish
<7>
<8>Whitehead, P.R., Jacobs, D., Brown, N.L., (1986) Nucleic Acids Res., vol. 14, pp. 7031-7045.

<1>HgiJI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Herpetosiphon giganteus HFS101
<6>H. Foster
<7>
<8>Whitehead, P.R., Jacobs, D., Brown, N.L., (1986) Nucleic Acids Res., vol. 14, pp. 7031-7045.

<1>HgiJII
<2>BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCY^C
<4>
<5>Herpetosiphon giganteus HFS101
<6>H. Foster
<7>
<8>Whitehead, P.R., Jacobs, D., Brown, N.L., (1986) Nucleic Acids Res., vol. 14, pp. 7031-7045.

<1>HgiKI
<2>
<3>?
<4>
<5>Herpetosiphon giganteus Hpg32
<6>H. Reichenbach
<7>
<8>Mayer, H., Schutte, H., Unpublished observations.

<1>HgiS21I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Herpetosiphon giganteus S21
<6>H. Foster
<7>
<8>Bolton, B.J., Comer, M.J., Kessler, C., Unpublished observations.

<1>HgiS22I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CC^SGG
<4>
<5>Herpetosiphon giganteus
<6>H. Foster
<7>
<8>Wersig, U., Bolton, B., Frey, B., Jarsch, M., Kessler, C., Unpublished observations.

<1>HhaI
<2>AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCG^C
<4>2(5)
<5>Haemophilus haemolyticus
<6>ATCC 10014
<7>BFJKNORUWY
<8>Mann, M.B., Smith, H.O., (1979) Proceedings of the Conference on Transmethylation, ed. Usdin, E., Borchardt, R.T., Creveling, C.R. (Elsevier North Holland, New York), vol. 0, pp. 483-492.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Roberts, R.J., (1994) Angew. Chem. Int. Ed. Engl., vol. 33, pp. 1222-1228.
Roberts, R.J., Myers, P.A., Morrison, A., Murray, K., (1976) J. Mol. Biol., vol. 103, pp. 199-208.
Som, S., Friedman, S., (1994) J. Biol. Chem., vol. 269, pp. 25986-25991.

<1>HhaII
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>G^ANTC
<4>2(6)
<5>Haemophilus haemolyticus
<6>ATCC 10014
<7>
<8>Kelly, S., Kaddurah-Daouk, R., Smith, H.O., (1985) J. Biol. Chem., vol. 260, pp. 15339-15344.
Kelly, S.V., Unpublished observations.
Mann, M.B., Rao, R.N., Smith, H.O., (1978) Gene, vol. 3, pp. 97-112.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>HhdI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Halomonas halodurans
<6>ATCC 29686
<7>
<8>Earle-Hughes, J., Roberts, R.J., Unpublished observations.

<1>HhgI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Haemophilus haemoglobinophilus
<6>ATCC 19416
<7>
<8>Myers, P.A., Roberts, R.J., Unpublished observations.

<1>HhlI
<2>
<3>?
<4>
<5>Halobacterium halobium NRC817
<6>D. Oesterhelt
<7>
<8>Schinzel, R., Unpublished observations.

<1>Hin1I
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>
<5>Haemophilus influenzae RFL1
<6>A. Janulaitis
<7>FKO
<8>Lazareviciute, L., Maneliene, Z., Padegimiene, A., Kiuduliene, L., Laucys, V., Bitinaite, J., Gruber, I.M., Polyachenko, V.M., Butkus, V., Janulaitus, A., (1990) Bioorg. Khim., vol. 16, pp. 889-897.

<1>Hin1II
<2>NlaIII,CviAII,FaeI,FatI,FatII,Hin8II,HpyCH4I,Hsp92II
<3>CATG^
<4>
<5>Haemophilus influenzae RFL1
<6>A. Janulaitis
<7>F
<8>Lazareviciute, L., Maneliene, Z., Padegimiene, A., Kiuduliene, L., Laucys, V., Bitinaite, J., Gruber, I.M., Polyachenko, V.M., Butkus, V., Janulaitus, A., (1990) Bioorg. Khim., vol. 16, pp. 889-897.

<1>Hin2I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>C^CGG
<4>
<5>Haemophilus influenzae RFL2
<6>A. Janulaitis
<7>
<8>Lazareviciute, L., Maneliene, Z., Padegimiene, A., Kiuduliene, L., Laucys, V., Bitinaite, J., Gruber, I.M., Polyachenko, V.M., Butkus, V., Janulaitus, A., (1990) Bioorg. Khim., vol. 16, pp. 889-897.

<1>Hin3I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Haemophilus influenzae RFL3
<6>A. Janulaitis
<7>
<8>Lazareviciute, L., Maneliene, Z., Padegimiene, A., Kiuduliene, L., Laucys, V., Bitinaite, J., Gruber, I.M., Polyachenko, V.M., Butkus, V., Janulaitus, A., (1990) Bioorg. Khim., vol. 16, pp. 889-897.

<1>Hin4I
<2>
<3>(8/13)GAYNNNNNVTC(13/8)
<4>
<5>Haemophilus influenzae RFL4
<6>A. Janulaitis
<7>F
<8>Lazareviciute, L., Bitinaite, J., Laucys, V., Kvietkiene, E., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.
Maneliene, Z., Zakareviciene, L., Unpublished observations.

<1>Hin4II
<2>HpyAV
<3>CCTTC(6/5)
<4>?(5)
<5>Haemophilus influenzae RFL4
<6>A. Janulaitis
<7>
<8>Azarinskas, A., Maneliene, Z., Jakubauskas, A., (2006) J. Biotechnol., vol. 123, pp. 288-296.

<1>Hin5I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Haemophilus influenzae RFL5
<6>A. Janulaitis
<7>
<8>Lazareviciute, L., Maneliene, Z., Padegimiene, A., Kiuduliene, L., Laucys, V., Bitinaite, J., Gruber, I.M., Polyachenko, V.M., Butkus, V., Janulaitus, A., (1990) Bioorg. Khim., vol. 16, pp. 889-897.

<1>Hin5II
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Haemophilus influenzae RFL5
<6>A. Janulaitis
<7>
<8>Lazareviciute, L., Maneliene, Z., Padegimiene, A., Kiuduliene, L., Laucys, V., Bitinaite, J., Gruber, I.M., Polyachenko, V.M., Butkus, V., Janulaitus, A., (1990) Bioorg. Khim., vol. 16, pp. 889-897.

<1>Hin5III
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Haemophilus influenzae RFL5
<6>A. Janulaitis
<7>
<8>Lazareviciute, L., Maneliene, Z., Padegimiene, A., Kiuduliene, L., Laucys, V., Bitinaite, J., Gruber, I.M., Polyachenko, V.M., Butkus, V., Janulaitus, A., (1990) Bioorg. Khim., vol. 16, pp. 889-897.

<1>Hin6I
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>G^CGC
<4>
<5>Haemophilus influenzae RFL6
<6>A. Janulaitis
<7>F
<8>Lazareviciute, L., Maneliene, Z., Padegimiene, A., Kiuduliene, L., Laucys, V., Bitinaite, J., Gruber, I.M., Polyachenko, V.M., Butkus, V., Janulaitus, A., (1990) Bioorg. Khim., vol. 16, pp. 889-897.

<1>Hin7I
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCGC
<4>
<5>Haemophilus influenzae RFL7
<6>A. Janulaitis
<7>
<8>Lazareviciute, L., Maneliene, Z., Padegimiene, A., Kiuduliene, L., Laucys, V., Bitinaite, J., Gruber, I.M., Polyachenko, V.M., Butkus, V., Janulaitus, A., (1990) Bioorg. Khim., vol. 16, pp. 889-897.

<1>Hin8I
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GRCGYC
<4>
<5>Haemophilus influenzae RFL8
<6>A. Janulaitis
<7>
<8>Lazareviciute, L., Maneliene, Z., Padegimiene, A., Kiuduliene, L., Laucys, V., Bitinaite, J., Gruber, I.M., Polyachenko, V.M., Butkus, V., Janulaitus, A., (1990) Bioorg. Khim., vol. 16, pp. 889-897.

<1>Hin8II
<2>NlaIII,CviAII,FaeI,FatI,FatII,Hin1II,HpyCH4I,Hsp92II
<3>CATG
<4>
<5>Haemophilus influenzae RFL8
<6>A. Janulaitis
<7>
<8>Lazareviciute, L., Maneliene, Z., Padegimiene, A., Kiuduliene, L., Laucys, V., Bitinaite, J., Gruber, I.M., Polyachenko, V.M., Butkus, V., Janulaitus, A., (1990) Bioorg. Khim., vol. 16, pp. 889-897.

<1>Hin173I
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Haemophilus influenzae 173
<6>J. Chirikjian
<7>
<8>Smith, L., Blakesley, R., Chirikjian, J., Unpublished observations.

<1>Hin1056I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Haemophilus influenzae 1056
<6>J. Stuy
<7>
<8>Olson, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>Hin1056II
<2>
<3>?
<4>
<5>Haemophilus influenzae 1056
<6>J. Stuy
<7>
<8>Olson, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>Hin1076III
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Haemophilus influenzae serotype b, 1076
<6>J. Stuy
<7>
<8>Olson, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>Hin1160II
<2>HindII,ChuEII,Hin1161II,HinJCI,HincII,MnnI
<3>GTYRAC
<4>
<5>Haemophilus influenzae serotype c, 1160
<6>J. Stuy
<7>
<8>Olson, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>Hin1161II
<2>HindII,ChuEII,Hin1160II,HinJCI,HincII,MnnI
<3>GTYRAC
<4>
<5>Haemophilus influenzae serotype c, 1161
<6>J. Stuy
<7>
<8>Olson, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>HinGUI
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCGC
<4>
<5>Haemophilus influenzae GU
<6>J. Chirikjian
<7>
<8>Chirikjian, J.G., George, A., Smith, L.A., (1978) Fed. Proc., vol. 37, pp. 1415.
Smith, L., Blakesley, R., Chirikjian, J., Unpublished observations.

<1>HinGUII
<2>FokI,BseGI,BstF5I,BtsCI,Hpy178VI,HpyF6I,HpyF67III,PbuJKI,StsI
<3>GGATG
<4>
<5>Haemophilus influenzae GU
<6>J. Chirikjian
<7>
<8>Nardone, G., Blakesley, R., (1981) Fed. Proc., vol. 40, pp. 1848.
Smith, L., Blakesley, R., Chirikjian, J., Unpublished observations.
Tolstoshev, C.M., Blakesley, R.W., (1982) Nucleic Acids Res., vol. 10, pp. 1-17.

<1>HinHI
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGCY
<4>
<5>Haemophilus influenzae H-1
<6>M. Takanami
<7>
<8>Takanami, M., (1974) Methods Mol. Biol., vol. 7, pp. 113-133.

<1>M.HinHP1Dam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Haemophilus influenza bacteriophage HP1
<6>J.J. Scocca
<7>
<8>Esposito, D., Fitzmaurice, W.P., Benjamin, R.C., Goodman, S.D., Waldman, A.S., Socca, J.J., (1996) Nucleic Acids Res., vol. 24, pp. 2360-2368.
Piekarowicz, A., Bujnicki, J., (1999) Acta Microbiol. Pol., vol. 48, pp. 123-129.

<1>M.HinHP2Dam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Haemophilus influenzae phage HP2
<6>A.L. Smith
<7>
<8>Williams, B.J., Golomb, M., Phillips, T., Brownlee, J., Olson, M.V., Smith, A.L., (2002) J. Bacteriol., vol. 184, pp. 6893-6905.

<1>HinJCI
<2>HindII,ChuEII,Hin1160II,Hin1161II,HincII,MnnI
<3>GTY^RAC
<4>
<5>Haemophilus influenzae JC9
<6>A. Piekarowicz
<7>
<8>Piekarowicz, A., Stasiak, A., Stanczak, J., (1980) Acta Microbiol. Pol., vol. 29, pp. 151-156.

<1>HinJCII
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Haemophilus influenzae JC9
<6>A. Piekarowicz
<7>
<8>Piekarowicz, A., Stasiak, A., Stanczak, J., (1980) Acta Microbiol. Pol., vol. 29, pp. 151-156.

<1>HinP1I
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>G^CGC
<4>2(5)
<5>Haemophilus influenzae P1
<6>S. Shen
<7>N
<8>Barsomian, J.M., Wilson, G.G., US Patent Office, 1991.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Shen, S., Li, Q., Yan, P., Zhou, B., Ye, S., Lu, Y., Wang, D., (1980) Sci. Sin., vol. 23, pp. 1435-1442.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>HinS1I
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCGC
<4>
<5>Haemophilus influenzae S1
<6>S. Shen
<7>
<8>Shen, S., Li, Q., Yan, P., Zhou, B., Ye, S., Lu, Y., Wang, D., (1980) Sci. Sin., vol. 23, pp. 1435-1442.

<1>HinS2I
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCGC
<4>
<5>Haemophilus influenzae S2
<6>S. Shen
<7>
<8>Shen, S., Li, Q., Yan, P., Zhou, B., Ye, S., Lu, Y., Wang, D., (1980) Sci. Sin., vol. 23, pp. 1435-1442.

<1>HinSAFI
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Haemophilus influenzae serotype b, SAF6
<6>A. Bakir
<7>
<8>Putrus, S.G., Al-Ani, F., Bakir, A., Unpublished observations.

<1>HinbIII
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Haemophilus influenzae Rb
<6>C.A. Hutchison
<7>
<8>Middleton, J.H., Stankus, P.V., Edgell, M.H., Hutchison, C.A. III, Unpublished observations.
Myers, P.A., Roberts, R.J., Unpublished observations.

<1>HincII
<2>HindII,ChuEII,Hin1160II,Hin1161II,HinJCI,MnnI
<3>GTY^RAC
<4>5(6)
<5>Haemophilus influenzae Rc
<6>ATCC 49699
<7>BFHJKNOQRUWXY
<8>Benner, J.S., Rees, P.A., European Patent Office, 1995.
Ito, H., Sadaoka, A., Japanese Patent Office, 1991.
Ito, H., Sadaoka, A., Kotani, H., Hiraoka, N., Nakamura, T., (1990) Nucleic Acids Res., vol. 18, pp. 3903-3911.
Landy, A., Ruedisueli, E., Robinson, L., Foeller, C., Ross, W., (1974) Biochemistry, vol. 13, pp. 2134-2142.

<1>HindI
<2>
<3>CAC
<4>2(6)
<5>Haemophilus influenzae Rd (exo-mutant)
<6>ATCC 51907
<7>
<8>Fleischmann, R.D. et al., (1995) Science, vol. 269, pp. 496-512.
Fleischmann, R.D., Adams, M.D., White, O., Smith, H.O., Venter, J.C., Japanese Patent Office, 2004.
Fleischmann, R.D., Adams, M.D., White, O., Smith, H.O., Venter, J.C., US Patent Office, 2003.
Gromkova, R., LaPorte, J., Goodgal, S.H., (1973) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 73, pp. 72.
Roy, P.H., Smith, H.O., (1973) J. Mol. Biol., vol. 81, pp. 427-444.
Roy, P.H., Smith, H.O., (1973) J. Mol. Biol., vol. 81, pp. 445-459.

<1>HindII
<2>ChuEII,Hin1160II,Hin1161II,HinJCI,HincII,MnnI
<3>GTY^RAC
<4>5(6)
<5>Haemophilus influenzae Rd (exo-mutant)
<6>ATCC 51907
<7>IMV
<8>Fleischmann, R.D. et al., (1995) Science, vol. 269, pp. 496-512.
Fleischmann, R.D., Adams, M.D., White, O., Smith, H.O., Venter, J.C., Japanese Patent Office, 2004.
Fleischmann, R.D., Adams, M.D., White, O., Smith, H.O., Venter, J.C., US Patent Office, 2005.
Kelly, T.J. Jr., Smith, H.O., (1970) J. Mol. Biol., vol. 51, pp. 393-409.
Roy, P.H., Smith, H.O., (1973) J. Mol. Biol., vol. 81, pp. 427-444.
Roy, P.H., Smith, H.O., (1973) J. Mol. Biol., vol. 81, pp. 445-459.
Smith, H.O., Wilcox, K.W., (1970) J. Mol. Biol., vol. 51, pp. 379-391.

<1>HindIII
<2>Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>A^AGCTT
<4>1(6)
<5>Haemophilus influenzae Rd (exo-mutant)
<6>ATCC 51907
<7>BCFHIJKMNOQRSUVWXY
<8>Fleischmann, R.D. et al., (1995) Science, vol. 269, pp. 496-512.
Fleischmann, R.D., Adams, M.D., White, O., Smith, H.O., Venter, J.C., Japanese Patent Office, 2004.
Fleischmann, R.D., Adams, M.D., White, O., Smith, H.O., Venter, J.C., US Patent Office, 2003.
Fleischmann, R.D., Adams, M.D., White, O., Smith, H.O., Venter, J.C., US Patent Office, 2005.
Old, R., Murray, K., Roizes, G., (1975) J. Mol. Biol., vol. 92, pp. 331-339.
Roy, P.H., Smith, H.O., (1973) J. Mol. Biol., vol. 81, pp. 427-444.
Roy, P.H., Smith, H.O., (1973) J. Mol. Biol., vol. 81, pp. 445-459.

<1>M.HindDam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Haemophilus influenzae Rd (exo-mutant)
<6>ATCC 51907
<7>
<8>Fleischmann, R.D. et al., (1995) Science, vol. 269, pp. 496-512.
Fleischmann, R.D., Adams, M.D., White, O., Smith, H.O., Venter, J.C., Japanese Patent Office, 2004.
Roy, P.H., Smith, H.O., (1973) J. Mol. Biol., vol. 81, pp. 427-444.
Roy, P.H., Smith, H.O., (1973) J. Mol. Biol., vol. 81, pp. 445-459.

<1>HineI
<2>HinfIII
<3>CGAAT
<4>
<5>Haemophilus influenzae serotype e
<6>A. Piekarowicz
<7>
<8>Piekarowicz, A., (1982) J. Mol. Biol., vol. 157, pp. 373-381.

<1>HinfI
<2>CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>G^ANTC
<4>2(6)
<5>Haemophilus influenzae Rf
<6>ATCC 17947
<7>BCFHIJKMNOQRUVWXY
<8>Bassing, C.H., Kim, Y.-G., Li, L., Chandrasegaran, S., (1992) Gene, vol. 113, pp. 83-88.
Chandrasegaran, S., Lunnen, K.D., Smith, H.O., Wilson, G.G., (1988) Gene, vol. 70, pp. 387-392.
Huang, L.-H., Farnet, C.M., Ehrlich, K.C., Ehrlich, M., (1982) Nucleic Acids Res., vol. 10, pp. 1579-1591.
Hutchison, C.A., Barrell, B.G., Unpublished observations.
Middleton, J.H., Stankus, P.V., Edgell, M.H., Hutchison, C.A. III, Unpublished observations.
Murray, K., Morrison, A., Unpublished observations.
Stickel, S.K., Roberts, R.J., Unpublished observations.
Treml, S., Draveling, C., Huang, C., Heaster, J., Walker, D., DiFrancesco, R., Jolly, J., (1994) Clin. Chem., vol. 40, pp. 1092.
Wilson, G.G., US Patent Office, 1993.

<1>HinfII
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Haemophilus influenzae Rf
<6>ATCC 17947
<7>
<8>Mann, M.B., Smith, H.O., Unpublished observations.

<1>HinfIII
<2>HineI
<3>CGAAT
<4>4(6)
<5>Haemophilus influenzae Rf
<6>ATCC 17947
<7>
<8>Fox, K.L., Dowideit, S.J., Erwin, A.L., Srikhanta, Y.N., Smith, A.L., Jennings, M.P., (2007) Nucleic Acids Res., vol. 35, pp. 5242-5252.
Kauc, L., Piekarowicz, A., (1978) Eur. J. Biochem., vol. 92, pp. 417-426.
Piekarowicz, A., Bickle, T.A., Shepherd, J.C.W., Ineichen, K., (1981) J. Mol. Biol., vol. 146, pp. 167-172.
Rao, D.N., Saha, S., Krishnamurthy, V., (2000) Prog. Nucleic Acid Res. Mol. Biol., vol. 64, pp. 1-63.

<1>HjaI
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GAT^ATC
<4>
<5>Hyphomonas jannaschiana
<6>R. Weiner
<7>
<8>Danaher, R., Stein, D.C., (1988) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 88, pp. 213.

<1>HpaI
<2>BsaKI,BseII,BstEZ359I,BstHPI,KspAI,MwhI,SsrI,Uba1408II
<3>GTT^AAC
<4>5(6)
<5>Haemophilus parainfluenzae
<6>ATCC 49669
<7>BCHIJKMNOQRSUVWX
<8>Benner, J.S., Rees, P., European Patent Office, 1995.
Benner, J.S., Rees, P., US Patent Office, 1994.
Garfin, D.E., Goodman, H.M., (1974) Biochem. Biophys. Res. Commun., vol. 59, pp. 108-116.
Ito, H., Shimado, H., Kimizuka, F., Kato, I., Japanese Patent Office, 1993.
Sharp, P.A., Sugden, B., Sambrook, J., (1973) Biochemistry, vol. 12, pp. 3055-3063.
Yoo, O.J., Dwyer-Hallquist, P., Agarwal, K.L., (1982) Nucleic Acids Res., vol. 10, pp. 6511-6519.

<1>HpaII
<2>Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>C^CGG
<4>2(5)
<5>Haemophilus parainfluenzae
<6>ATCC 49669
<7>BFIMNOQRSUVWX
<8>Butkus, V., Petrauskiene, L., Maneliene, Z., Klimasauskas, S., Laucys, V., Janulaitis, A., (1987) Nucleic Acids Res., vol. 15, pp. 7091-7102.
Chatterjee, D.K., US Patent Office, 1993.
Garfin, D.E., Goodman, H.M., (1974) Biochem. Biophys. Res. Commun., vol. 59, pp. 108-116.
Kulakauskas, S., Barsomian, J.M., Lubys, A., Roberts, R.J., Wilson, G.G., (1994) Gene, vol. 142, pp. 9-15.
Mann, M.B., Smith, H.O., (1977) Nucleic Acids Res., vol. 4, pp. 4211-4221.
Sharp, P.A., Sugden, B., Sambrook, J., (1973) Biochemistry, vol. 12, pp. 3055-3063.
Som, S., Friedman, S., (1994) J. Biol. Chem., vol. 269, pp. 25986-25991.

<1>HphI
<2>AsuHPI,NgoBVIII,NgoDVIII,NgoJVIII,NgoMVIII,SspD5I
<3>GGTGA(8/7)
<4>-2(5)
<5>Haemophilus parahaemolyticus
<6>ATCC 49700
<7>FN
<8>Daniels, J.S., Gates, K.S., (1994) ACS Abstracts, vol. 208, pp. 66.
Kleid, D., Humayun, Z., Jeffrey, A., Ptashne, M., (1976) Proc. Natl. Acad. Sci. U. S. A., vol. 73, pp. 293-297.
Lubys, A., Lubiene, J., Kulakauskas, S., Stankevicius, K., Timinskas, A., Janulaitis, A., (1996) Nucleic Acids Res., vol. 24, pp. 2760-2766.
Middleton, J.H., Stankus, P.V., Edgell, M.H., Hutchison, C.A. III, Unpublished observations.
Nelson, M., Unpublished observations.

<1>HpyII
<2>MboII,Hpy178II,HpyAII,NcuI,TceI
<3>GAAGA
<4>
<5>Helicobacter pylori 60190
<6>ATCC 49503
<7>
<8>Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>HpyIV
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Helicobacter pylori 60190
<6>ATCC 49503
<7>
<8>Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>HpyV
<2>TaqI,CviSIII,EsaBC3I,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori 60190
<6>ATCC 49503
<7>
<8>Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>HpyVIII
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Helicobacter pylori 60190
<6>ATCC 49503
<7>
<8>Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>Hpy8I
<2>MjaIV,Hpy166II,HpyBII,HpyF7III,HpyF14II,HpyF46III,HpyF49III,HpyF50I
<3>GTN^NAC
<4>5(6)
<5>Helicobacter pylori A 8-5
<6>A. Janulaitis
<7>F
<8>Lubys, A., Minkute, J., Janulaitis, A., Unpublished observations.
Maneliene, Z., Butkus, V., Unpublished observations.
Vitkute, J., Trinkunaite, L., Kiuduliene, E., Butkus, V., Janulaitis, A., Unpublished observations.

<1>Hpy8II
<2>Tsp45I,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori A 8-5
<6>A. Janulaitis
<7>
<8>Vitkute, J., Trinkunaite, L., Kiuduliene, E., Butkus, V., Janulaitis, A., Unpublished observations.

<1>Hpy8III
<2>HgiAI,Alw21I,AspHI,Bbv12I,Bfu1570I,BsaGI,Bsh45I,BsiHKAI,Bsm6I,BsmPI,HpyF7II,HpyF46II,MspV281I,Pph3215I
<3>GWGCWC
<4>
<5>Helicobacter pylori A 8-5
<6>A. Janulaitis
<7>
<8>Vitkute, J., Trinkunaite, L., Kiuduliene, E., Butkus, V., Janulaitis, A., Unpublished observations.

<1>Hpy26I
<2>CviRI,HpyCH4V,HpyF36III,HpyF38II,HpyF44III,HpyF45II,HpyF48III,HpyF49V,HpyF67II,HpyJP26I
<3>TGCA
<4>
<5>Helicobacter pylori J26
<6>M.J. Blaser
<7>
<8>Ando, T., Xu, Q., Torres, M., Kusugami, K., Israel, D.A., Blaser, M.J., (2000) Mol. Microbiol., vol. 37, pp. 1052-1065.

<1>Hpy26II
<2>TaqI,CviSIII,EsaBC3I,HpyV,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori J26
<6>M.J. Blaser
<7>
<8>Ando, T., Xu, Q., Torres, M., Kusugami, K., Israel, D.A., Blaser, M.J., (2000) Mol. Microbiol., vol. 37, pp. 1052-1065.

<1>Hpy51I
<2>Tsp45I,Hpy8II,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>^GTSAC
<4>
<5>Helicobacter pylori 51
<6>M.J. Cho
<7>
<8>Baik, S.C., Lee, W.K., Song, J.Y., Choi, Y.J., Rye, B.D., Choi, S.H., Cho, M.J., Rhee, K.H., (1998) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 0, pp. 120.

<1>Hpy99I
<2>HpyF61III
<3>CGWCG^
<4>?(4)
<5>Helicobacter pylori J99
<6>R.A. Alm
<7>N
<8>Lin, L., Porter, N., Kong, H., Unpublished observations.
Morgan, R.D., Xu, Q., International Patent Office, 2001.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>Hpy99II
<2>Tsp45I,Hpy8II,Hpy51I,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>4(6)
<5>Helicobacter pylori J99
<6>R.A. Alm
<7>
<8>Stickel, S.K., Roberts, R.J., Unpublished observations.
Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>Hpy99III
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCGC
<4>?(5)
<5>Helicobacter pylori J99
<6>R.A. Alm
<7>
<8>Alm, R.A., Ling, L.-S.L., Moir, D.T., King, B.L., Brown, E.D., Doig, P.C., Smith, D.R., Noonan, B., Guild, B.C., deJonge, B.L., Carmel, G., Tummino, P.J., Caruso, A., Uria-Nickelsen, M., Mills, D.M., Ives, C., Gibson, R., Merberg, D., Mills, S., (1999) Nature, vol. 397, pp. 176-180.
Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>Hpy99IV
<2>SecI,BsaJI,BseDI,BsoKI,BssECI,BstZ10I,HpyF10III,HpyF61II,HpyF67IV,Uba1442I
<3>CCNNGG
<4>?(4)
<5>Helicobacter pylori J99
<6>R.A. Alm
<7>
<8>Kong, H., Unpublished observations.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>Hpy166I
<2>Hpy188I,HpyF11II,HpyF12II,HpyF15II,HpyF17I,HpyF19II,HpyF27II,HpyF28I,HpyF33I,HpyF42III,HpyF46IV,HpyF50II,HpyF61I,HpyF64III
<3>TCNGA
<4>
<5>Helicobacter pylori J166
<6>M.J. Blaser
<7>
<8>Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>Hpy166II
<2>MjaIV,Hpy8I,HpyBII,HpyF7III,HpyF14II,HpyF46III,HpyF49III,HpyF50I
<3>GTN^NAC
<4>
<5>Helicobacter pylori J166
<6>M.J. Blaser
<7>N
<8>Slatko, B., Morgan, R.D., Unpublished observations.
Xu, Q., Morgan, R., Blaser, M., Unpublished observations.
Zhu, Z., Unpublished observations.
Zhu, Z., Blanchard, A., Xu, S.-Y., Guan, S., Wei, H., Zhang, P., Sun, D., Chan, S.-h., International Patent Office, 2009.

<1>Hpy166III
<2>MnlI
<3>CCTC
<4>
<5>Helicobacter pylori J166
<6>M.J. Blaser
<7>
<8>Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>Hpy178II
<2>MboII,HpyII,HpyAII,NcuI,TceI
<3>GAAGA
<4>
<5>Helicobacter pylori J178
<6>M.J. Blaser
<7>
<8>Xu, Q., Blaser, M., Unpublished observations.

<1>Hpy178III
<2>Hpy188III,HpyCH4VI,HpyF16II,HpyF19III,HpyF22III,HpyF44IV,HpyNSH57II
<3>TC^NNGA
<4>
<5>Helicobacter pylori J178
<6>M.J. Blaser
<7>
<8>Morgan, R.D., Unpublished observations.
Xu, Q., Blaser, M., Unpublished observations.

<1>Hpy178VI
<2>FokI,BseGI,BstF5I,BtsCI,HinGUII,HpyF6I,HpyF67III,PbuJKI,StsI
<3>GGATG
<4>
<5>Helicobacter pylori J178
<6>M.J. Blaser
<7>
<8>Xu, Q., Blaser, M., Unpublished observations.

<1>Hpy178VII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Helicobacter pylori J178
<6>M.J. Blaser
<7>
<8>Xu, Q., Blaser, M., Unpublished observations.

<1>Hpy188I
<2>Hpy166I,HpyF11II,HpyF12II,HpyF15II,HpyF17I,HpyF19II,HpyF27II,HpyF28I,HpyF33I,HpyF42III,HpyF46IV,HpyF50II,HpyF61I,HpyF64III
<3>TCN^GA
<4>5(6)
<5>Helicobacter pylori J188
<6>M.J. Blaser
<7>N
<8>Xu, Q., Stickel, S., Roberts, R.J., Blaser, M.J., Morgan, R.D., (2000) J. Biol. Chem., vol. 275, pp. 17086-17093.

<1>Hpy188III
<2>Hpy178III,HpyCH4VI,HpyF16II,HpyF19III,HpyF22III,HpyF44IV,HpyNSH57II
<3>TC^NNGA
<4>
<5>Helicobacter pylori J188
<6>M.J. Blaser
<7>N
<8>Morgan, R.D., Xu, Q., US Patent Office, 2001.
Xu, Q., Morgan, R.D., Unpublished observations.

<1>Hpy303I
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori 30-3
<6>N.R. Salama
<7>
<8>Humbert, O., Salama, N.R., (2008) Nucleic Acids Res., vol. 36, pp. 6893-6906.
Salama, N.R., Unpublished observations.

<1>Hpy312I
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori 31-2
<6>N.R. Salama
<7>
<8>Humbert, O., Salama, N.R., (2008) Nucleic Acids Res., vol. 36, pp. 6893-6906.
Salama, N.R., Unpublished observations.

<1>Hpy401I
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori 40-1
<6>N.R. Salama
<7>
<8>Humbert, O., Salama, N.R., (2008) Nucleic Acids Res., vol. 36, pp. 6893-6906.
Salama, N.R., Unpublished observations.

<1>Hpy421I
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori 42-1
<6>N.R. Salama
<7>
<8>Humbert, O., Salama, N.R., (2008) Nucleic Acids Res., vol. 36, pp. 6893-6906.
Salama, N.R., Unpublished observations.

<1>Hpy423I
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori 42-3
<6>N.R. Salama
<7>
<8>Humbert, O., Salama, N.R., (2008) Nucleic Acids Res., vol. 36, pp. 6893-6906.
Salama, N.R., Unpublished observations.

<1>Hpy471I
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori 47-1
<6>N.R. Salama
<7>
<8>Humbert, O., Salama, N.R., (2008) Nucleic Acids Res., vol. 36, pp. 6893-6906.
Salama, N.R., Unpublished observations.

<1>Hpy501I
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori 50-1
<6>N.R. Salama
<7>
<8>Humbert, O., Salama, N.R., (2008) Nucleic Acids Res., vol. 36, pp. 6893-6906.
Salama, N.R., Unpublished observations.

<1>HpyAII
<2>MboII,HpyII,Hpy178II,NcuI,TceI
<3>GAAGA
<4>5(6)
<5>Helicobacter pylori 26695
<6>D.E. Berg
<7>
<8>Lin, L.-F., Kong, H., Unpublished observations.
Stickel, S.K., Roberts, R.J., Unpublished observations.
Tomb, J.-F. et al., (1997) Nature, vol. 388, pp. 539-547.
Vitkute, J., Stankevicius, K., Tamulaitiene, G., Maneliene, Z., Timinskas, A., Berg, D.E., Janulaitis, A., (2001) J. Bacteriol., vol. 183, pp. 443-450.

<1>HpyAIII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Helicobacter pylori 26695
<6>D.E. Berg
<7>
<8>Kleanthous, H., Garawi, A.A., Miller, C., Tomb, J.F., Oomen, R.P., Japanese Patent Office, 2001.
Lin, L.-F., Kong, H., Unpublished observations.
Tomb, J.-F. et al., (1997) Nature, vol. 388, pp. 539-547.
Vitkute, J., Stankevicius, K., Tamulaitiene, G., Maneliene, Z., Timinskas, A., Berg, D.E., Janulaitis, A., (2001) J. Bacteriol., vol. 183, pp. 443-450.

<1>HpyAIV
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>2(6)
<5>Helicobacter pylori 26695
<6>D.E. Berg
<7>
<8>Lin, L.-F., Kong, H., Unpublished observations.
Tomb, J.-F. et al., (1997) Nature, vol. 388, pp. 539-547.
Vitkute, J., Stankevicius, K., Tamulaitiene, G., Maneliene, Z., Timinskas, A., Berg, D.E., Janulaitis, A., (2001) J. Bacteriol., vol. 183, pp. 443-450.

<1>HpyAV
<2>Hin4II
<3>CCTTC(6/5)
<4>?(5)
<5>Helicobacter pylori 26695
<6>D.E. Berg
<7>N
<8>Higgins, L., Morgan, R.D., Kong, H., Unpublished observations.
Kleanthous, H., Garawi, A.A., Miller, C., Tomb, J.F., Oomen, R.P., Japanese Patent Office, 2001.
Kong, H., Sears, L., Unpublished observations.
Lin, L.-F., Kong, H., Unpublished observations.
Tomb, J.-F. et al., (1997) Nature, vol. 388, pp. 539-547.

<1>Hpy87AI
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Helicobacter pylori strain 87A
<6>L. Shapiro
<7>
<8>Benkovic, S.J., Berdis, A., Lee, I., Shapiro, L., Wright, R., Stephens, C., Kahng, L.S., US Patent Office, 2002.

<1>HpyBI
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GT^AC
<4>
<5>Helicobacter pylori strain Roberts
<6>N.L. Brown
<7>
<8>Ivic, A., Jakeman, K.J., Penn, C.W., Brown, N.L., (1999) FEMS Microbiol. Lett., vol. 179, pp. 175-180.

<1>HpyBII
<2>MjaIV,Hpy8I,Hpy166II,HpyF7III,HpyF14II,HpyF46III,HpyF49III,HpyF50I
<3>GTN^NAC
<4>
<5>Helicobacter pylori strain Roberts
<6>N.L. Brown
<7>
<8>Ivic, A., Jakeman, K.J., Penn, C.W., Brown, N.L., (1999) FEMS Microbiol. Lett., vol. 179, pp. 175-180.

<1>HpyCI
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GAT^ATC
<4>
<5>Helicobacter pylori
<6>NCTC 11637
<7>
<8>Ivic, A., Jakeman, K.J., Penn, C.W., Brown, N.L., (1999) FEMS Microbiol. Lett., vol. 179, pp. 175-180.

<1>HpyCII
<2>
<3>?
<4>
<5>Helicobacter pylori
<6>NCTC 11637
<7>
<8>Ivic, A., Jakeman, K.J., Penn, C.W., Brown, N.L., (1999) FEMS Microbiol. Lett., vol. 179, pp. 175-180.

<1>HpyC1I
<2>BccI
<3>CCATC(4/5)
<4>
<5>Helicobacter pylori
<6>J.-T. Wang
<7>
<8>Lin, T.L., Shun, C.T., Chang, K.C., Wang, J.T., (2004) J. Biol. Chem., vol. 279, pp. 11156-11162.
Wang, J.-T., Lin, T.-L., US Patent Office, 2007.

<1>HpyCH4I
<2>NlaIII,CviAII,FaeI,FatI,FatII,Hin1II,Hin8II,Hsp92II
<3>CATG^
<4>
<5>Helicobacter pylori CH4
<6>M.J. Blaser
<7>
<8>Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>HpyCH4II
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori CH4
<6>M.J. Blaser
<7>
<8>Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>HpyCH4III
<2>Tsp4CI,Bst4CI,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACN^GT
<4>
<5>Helicobacter pylori CH4
<6>M.J. Blaser
<7>N
<8>Morgan, R.D., Xu, Q., International Patent Office, 2001.
Zhu, Z., Unpublished observations.

<1>HpyCH4IV
<2>MaeII,HpyF13III,HpyF35II,HpyF74II,TaiI,TscI,Tsp49I,TspIDSI,TspWAM8AI,TtmI
<3>A^CGT
<4>2(5)
<5>Helicobacter pylori CH4
<6>M.J. Blaser
<7>N
<8>Morgan, R.D., Xu, Q., US Patent Office, 2001.

<1>HpyCH4V
<2>CviRI,Hpy26I,HpyF36III,HpyF38II,HpyF44III,HpyF45II,HpyF48III,HpyF49V,HpyF67II,HpyJP26I
<3>TG^CA
<4>
<5>Helicobacter pylori CH4
<6>M.J. Blaser
<7>N
<8>Morgan, R.D., Xu, Q., US Patent Office, 2000.

<1>HpyCH4VI
<2>Hpy178III,Hpy188III,HpyF16II,HpyF19III,HpyF22III,HpyF44IV,HpyNSH57II
<3>TCNNGA
<4>
<5>Helicobacter pylori CH4
<6>M.J. Blaser
<7>
<8>Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>HpyF1I
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL1
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF2I
<2>SfeI,Bco163I,BdiSI,BfmI,BpcI,BstSFI,BthP35I,LlaBI,SfcI,Srl56DI
<3>CTRYAG
<4>
<5>Helicobacter pylori RFL2
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF2II
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Helicobacter pylori RFL2
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF3I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>C^TNAG
<4>
<5>Helicobacter pylori RFL3
<6>V. Butkus
<7>F
<8>Maneliene, Z., Unpublished observations.
Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF4I
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL4
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF4II
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL4
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF5I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL5
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF5II
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL5
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF6I
<2>FokI,BseGI,BstF5I,BtsCI,HinGUII,Hpy178VI,HpyF67III,PbuJKI,StsI
<3>GGATG
<4>
<5>Helicobacter pylori RFL6
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF6II
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL6
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF6III
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL6
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF7I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL7
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF7II
<2>HgiAI,Alw21I,AspHI,Bbv12I,Bfu1570I,BsaGI,Bsh45I,BsiHKAI,Bsm6I,BsmPI,Hpy8III,HpyF46II,MspV281I,Pph3215I
<3>GWGCWC
<4>
<5>Helicobacter pylori RFL7
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF7III
<2>MjaIV,Hpy8I,Hpy166II,HpyBII,HpyF14II,HpyF46III,HpyF49III,HpyF50I
<3>GTNNAC
<4>
<5>Helicobacter pylori RFL7
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF9I
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL9
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF9II
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL9
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF9III
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL9
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF10I
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HsoI,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>GCGC
<4>
<5>Helicobacter pylori RFL10
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF10II
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Helicobacter pylori RFL10
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF10III
<2>SecI,BsaJI,BseDI,BsoKI,BssECI,BstZ10I,Hpy99IV,HpyF61II,HpyF67IV,Uba1442I
<3>CCNNGG
<4>
<5>Helicobacter pylori RFL10
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF10IV
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori RFL10
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF10V
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Helicobacter pylori RFL10
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF10VI
<2>MwoI,Bce4I,Bce1247I,BceCI,BspWI,BstMWI
<3>GCNNNNN^NNGC
<4>
<5>Helicobacter pylori RFL10
<6>V. Butkus
<7>F
<8>Maneliene, Z., Butkus, V., Unpublished observations.
Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF11I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL11
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF11II
<2>Hpy188I,Hpy166I,HpyF12II,HpyF15II,HpyF17I,HpyF19II,HpyF27II,HpyF28I,HpyF33I,HpyF42III,HpyF46IV,HpyF50II,HpyF61I,HpyF64III
<3>TCNGA
<4>
<5>Helicobacter pylori RFL11
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF12I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL12
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF12II
<2>Hpy188I,Hpy166I,HpyF11II,HpyF15II,HpyF17I,HpyF19II,HpyF27II,HpyF28I,HpyF33I,HpyF42III,HpyF46IV,HpyF50II,HpyF61I,HpyF64III
<3>TCNGA
<4>
<5>Helicobacter pylori RFL12
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF13I
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL13
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF13II
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL13
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF13III
<2>MaeII,HpyCH4IV,HpyF35II,HpyF74II,TaiI,TscI,Tsp49I,TspIDSI,TspWAM8AI,TtmI
<3>ACGT
<4>
<5>Helicobacter pylori RFL13
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF13IV
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori RFL13
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF14I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Helicobacter pylori RFL14
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF14II
<2>MjaIV,Hpy8I,Hpy166II,HpyBII,HpyF7III,HpyF46III,HpyF49III,HpyF50I
<3>GTNNAC
<4>
<5>Helicobacter pylori RFL14
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF14III
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL14
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF15I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Helicobacter pylori RFL15
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF15II
<2>Hpy188I,Hpy166I,HpyF11II,HpyF12II,HpyF17I,HpyF19II,HpyF27II,HpyF28I,HpyF33I,HpyF42III,HpyF46IV,HpyF50II,HpyF61I,HpyF64III
<3>TCNGA
<4>
<5>Helicobacter pylori RFL15
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF16I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL16
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF16II
<2>Hpy178III,Hpy188III,HpyCH4VI,HpyF19III,HpyF22III,HpyF44IV,HpyNSH57II
<3>TCNNGA
<4>
<5>Helicobacter pylori RFL16
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF17I
<2>Hpy188I,Hpy166I,HpyF11II,HpyF12II,HpyF15II,HpyF19II,HpyF27II,HpyF28I,HpyF33I,HpyF42III,HpyF46IV,HpyF50II,HpyF61I,HpyF64III
<3>TCNGA
<4>
<5>Helicobacter pylori RFL17
<6>V. Butkus
<7>
<8>Sapranauskas, R., Lubys, A., Janulaitis, A., Unpublished observations.
Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF18I
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Helicobacter pylori RFL18
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF19I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL19
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF19II
<2>Hpy188I,Hpy166I,HpyF11II,HpyF12II,HpyF15II,HpyF17I,HpyF27II,HpyF28I,HpyF33I,HpyF42III,HpyF46IV,HpyF50II,HpyF61I,HpyF64III
<3>TCNGA
<4>
<5>Helicobacter pylori RFL19
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF19III
<2>Hpy178III,Hpy188III,HpyCH4VI,HpyF16II,HpyF22III,HpyF44IV,HpyNSH57II
<3>TCNNGA
<4>
<5>Helicobacter pylori RFL19
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF20I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL20
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF21I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL21
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF21II
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori RFL21
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF22I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL22
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF22II
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL22
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF22III
<2>Hpy178III,Hpy188III,HpyCH4VI,HpyF16II,HpyF19III,HpyF44IV,HpyNSH57II
<3>TCNNGA
<4>
<5>Helicobacter pylori RFL22
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF23I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL23
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF24I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL24
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF24II
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL24
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF25I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL25
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF25II
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL25
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF26I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Helicobacter pylori RFL26
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF26II
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Helicobacter pylori RFL26
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF26III
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL26
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF27I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL27
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF27II
<2>Hpy188I,Hpy166I,HpyF11II,HpyF12II,HpyF15II,HpyF17I,HpyF19II,HpyF28I,HpyF33I,HpyF42III,HpyF46IV,HpyF50II,HpyF61I,HpyF64III
<3>TCNGA
<4>
<5>Helicobacter pylori RFL27
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF28I
<2>Hpy188I,Hpy166I,HpyF11II,HpyF12II,HpyF15II,HpyF17I,HpyF19II,HpyF27II,HpyF33I,HpyF42III,HpyF46IV,HpyF50II,HpyF61I,HpyF64III
<3>TCNGA
<4>
<5>Helicobacter pylori RFL28
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF29I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Helicobacter pylori RFL29
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF30I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL30
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF30II
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL30
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF31I
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori RFL31
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF31II
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL31
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF32I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL32
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF33I
<2>Hpy188I,Hpy166I,HpyF11II,HpyF12II,HpyF15II,HpyF17I,HpyF19II,HpyF27II,HpyF28I,HpyF42III,HpyF46IV,HpyF50II,HpyF61I,HpyF64III
<3>TCNGA
<4>
<5>Helicobacter pylori RFL33
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF33II
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Helicobacter pylori RFL33
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF34I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL34
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF34II
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL34
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF35I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL35
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF35II
<2>MaeII,HpyCH4IV,HpyF13III,HpyF74II,TaiI,TscI,Tsp49I,TspIDSI,TspWAM8AI,TtmI
<3>ACGT
<4>
<5>Helicobacter pylori RFL35
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF35III
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL35
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF35IV
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL35
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF36I
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL36
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF36II
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori RFL36
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF36III
<2>CviRI,Hpy26I,HpyCH4V,HpyF38II,HpyF44III,HpyF45II,HpyF48III,HpyF49V,HpyF67II,HpyJP26I
<3>TGCA
<4>
<5>Helicobacter pylori RFL36
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF36IV
<2>SduI,AocII,Bka1125I,BmyI,BsoCI,Bsp1286I,BspLS2I,BstZ15I,HpyF47I,MhlI,Mlu40I,NspII,TseAI,Uba1362I
<3>GDGCHC
<4>
<5>Helicobacter pylori RFL36
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF37I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL37
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF38I
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Helicobacter pylori RFL38
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF38II
<2>CviRI,Hpy26I,HpyCH4V,HpyF36III,HpyF44III,HpyF45II,HpyF48III,HpyF49V,HpyF67II,HpyJP26I
<3>TGCA
<4>
<5>Helicobacter pylori RFL38
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF40I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL40
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF40II
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL40
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF40III
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL40
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF41I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL41
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF41II
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL41
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF42I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Helicobacter pylori RFL42
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF42II
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL42
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF42III
<2>Hpy188I,Hpy166I,HpyF11II,HpyF12II,HpyF15II,HpyF17I,HpyF19II,HpyF27II,HpyF28I,HpyF33I,HpyF46IV,HpyF50II,HpyF61I,HpyF64III
<3>TCNGA
<4>
<5>Helicobacter pylori RFL42
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF42IV
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL42
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF43I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Helicobacter pylori RFL43
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF44I
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Helicobacter pylori RFL44
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF44II
<2>NlaIV,AspNI,BcrI,BmiI,BsaEI,BscBI,Bsp29I,BspLI,BssI,HpyF73I,NgoBV,NgoGV,PspN4I,Rlu3I,Uba1305I,Uba1445I
<3>GGNNCC
<4>
<5>Helicobacter pylori RFL44
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF44III
<2>CviRI,Hpy26I,HpyCH4V,HpyF36III,HpyF38II,HpyF45II,HpyF48III,HpyF49V,HpyF67II,HpyJP26I
<3>TG^CA
<4>
<5>Helicobacter pylori RFL44
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF44IV
<2>Hpy178III,Hpy188III,HpyCH4VI,HpyF16II,HpyF19III,HpyF22III,HpyNSH57II
<3>TCNNGA
<4>
<5>Helicobacter pylori RFL44
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF44V
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori RFL44
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF45I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL45
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF45II
<2>CviRI,Hpy26I,HpyCH4V,HpyF36III,HpyF38II,HpyF44III,HpyF48III,HpyF49V,HpyF67II,HpyJP26I
<3>TGCA
<4>
<5>Helicobacter pylori RFL45
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF46I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL46
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF46II
<2>HgiAI,Alw21I,AspHI,Bbv12I,Bfu1570I,BsaGI,Bsh45I,BsiHKAI,Bsm6I,BsmPI,Hpy8III,HpyF7II,MspV281I,Pph3215I
<3>GWGCWC
<4>
<5>Helicobacter pylori RFL46
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF46III
<2>MjaIV,Hpy8I,Hpy166II,HpyBII,HpyF7III,HpyF14II,HpyF49III,HpyF50I
<3>GTNNAC
<4>
<5>Helicobacter pylori RFL46
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF46IV
<2>Hpy188I,Hpy166I,HpyF11II,HpyF12II,HpyF15II,HpyF17I,HpyF19II,HpyF27II,HpyF28I,HpyF33I,HpyF42III,HpyF50II,HpyF61I,HpyF64III
<3>TCNGA
<4>
<5>Helicobacter pylori RFL46
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF46V
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Helicobacter pylori RFL46
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF47I
<2>SduI,AocII,Bka1125I,BmyI,BsoCI,Bsp1286I,BspLS2I,BstZ15I,HpyF36IV,MhlI,Mlu40I,NspII,TseAI,Uba1362I
<3>GDGCHC
<4>
<5>Helicobacter pylori RFL47
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF48I
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL48
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF48II
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL48
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF48III
<2>CviRI,Hpy26I,HpyCH4V,HpyF36III,HpyF38II,HpyF44III,HpyF45II,HpyF49V,HpyF67II,HpyJP26I
<3>TGCA
<4>
<5>Helicobacter pylori RFL48
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF49I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL49
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF49II
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF51I,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL49
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF49III
<2>MjaIV,Hpy8I,Hpy166II,HpyBII,HpyF7III,HpyF14II,HpyF46III,HpyF50I
<3>GTNNAC
<4>
<5>Helicobacter pylori RFL49
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF49IV
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Helicobacter pylori RFL49
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF49V
<2>CviRI,Hpy26I,HpyCH4V,HpyF36III,HpyF38II,HpyF44III,HpyF45II,HpyF48III,HpyF67II,HpyJP26I
<3>TGCA
<4>
<5>Helicobacter pylori RFL49
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF50I
<2>MjaIV,Hpy8I,Hpy166II,HpyBII,HpyF7III,HpyF14II,HpyF46III,HpyF49III
<3>GTNNAC
<4>
<5>Helicobacter pylori RFL50
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF50II
<2>Hpy188I,Hpy166I,HpyF11II,HpyF12II,HpyF15II,HpyF17I,HpyF19II,HpyF27II,HpyF28I,HpyF33I,HpyF42III,HpyF46IV,HpyF61I,HpyF64III
<3>TCNGA
<4>
<5>Helicobacter pylori RFL50
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF51I
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF62III,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL51
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF51II
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL51
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF52I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL52
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF52II
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Helicobacter pylori RFL52
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF52III
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori RFL52
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF53I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Helicobacter pylori RFL53
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF53II
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori RFL53
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF54I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL54
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF55I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL55
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF55II
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Helicobacter pylori RFL55
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF56I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL56
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF57I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Helicobacter pylori RFL57
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF58I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL58
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF59I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL59
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF59II
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori RFL59
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF59III
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL59
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF60I
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Helicobacter pylori RFL60
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF60II
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL60
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF61I
<2>Hpy188I,Hpy166I,HpyF11II,HpyF12II,HpyF15II,HpyF17I,HpyF19II,HpyF27II,HpyF28I,HpyF33I,HpyF42III,HpyF46IV,HpyF50II,HpyF64III
<3>TCNGA
<4>
<5>Helicobacter pylori RFL61
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF61II
<2>SecI,BsaJI,BseDI,BsoKI,BssECI,BstZ10I,Hpy99IV,HpyF10III,HpyF67IV,Uba1442I
<3>CCNNGG
<4>
<5>Helicobacter pylori RFL61
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF61III
<2>Hpy99I
<3>CGWCG
<4>
<5>Helicobacter pylori RFL61
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF62I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL62
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF62II
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL62
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF62III
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,NmuCI
<3>GTSAC
<4>
<5>Helicobacter pylori RFL62
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF63I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Helicobacter pylori RFL63
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF64I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL64
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF64II
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL64
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF64III
<2>Hpy188I,Hpy166I,HpyF11II,HpyF12II,HpyF15II,HpyF17I,HpyF19II,HpyF27II,HpyF28I,HpyF33I,HpyF42III,HpyF46IV,HpyF50II,HpyF61I
<3>TCNGA
<4>
<5>Helicobacter pylori RFL64
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF64IV
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Helicobacter pylori RFL64
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF64V
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL64
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF65I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL65
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF65II
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL65
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF65III
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori RFL65
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF66I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Helicobacter pylori RFL66
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF66II
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL66
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF66III
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori RFL66
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF66IV
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL66
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF67I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF68II,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL67
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF67II
<2>CviRI,Hpy26I,HpyCH4V,HpyF36III,HpyF38II,HpyF44III,HpyF45II,HpyF48III,HpyF49V,HpyJP26I
<3>TGCA
<4>
<5>Helicobacter pylori RFL67
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF67III
<2>FokI,BseGI,BstF5I,BtsCI,HinGUII,Hpy178VI,HpyF6I,PbuJKI,StsI
<3>GGATG
<4>
<5>Helicobacter pylori RFL67
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF67IV
<2>SecI,BsaJI,BseDI,BsoKI,BssECI,BstZ10I,Hpy99IV,HpyF10III,HpyF61II,Uba1442I
<3>CCNNGG
<4>
<5>Helicobacter pylori RFL67
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF68I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF69I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL68
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF68II
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF70I,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL68
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF69I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF74I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL69
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF69II
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Helicobacter pylori RFL69
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF70I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF72II,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL70
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF71I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL71
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF71II
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Helicobacter pylori RFL71
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF71III
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Helicobacter pylori RFL71
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF72I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Helicobacter pylori RFL72
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF72II
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyHI,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori RFL72
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF72III
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Helicobacter pylori RFL72
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF73I
<2>NlaIV,AspNI,BcrI,BmiI,BsaEI,BscBI,Bsp29I,BspLI,BssI,HpyF44II,NgoBV,NgoGV,PspN4I,Rlu3I,Uba1305I,Uba1445I
<3>GGNNCC
<4>
<5>Helicobacter pylori RFL73
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF73II
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori RFL73
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF73III
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Helicobacter pylori RFL73
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF73IV
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Helicobacter pylori RFL73
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF74I
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,TaaI
<3>ACNGT
<4>
<5>Helicobacter pylori RFL74
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyF74II
<2>MaeII,HpyCH4IV,HpyF13III,HpyF35II,TaiI,TscI,Tsp49I,TspIDSI,TspWAM8AI,TtmI
<3>ACGT
<4>
<5>Helicobacter pylori RFL74
<6>V. Butkus
<7>
<8>Vitkute, J., Petrusyte, V., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>HpyHI
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHPK5I
<3>CTNAG
<4>
<5>Helicobacter pylori HPAG1
<6>J. Gordon
<7>
<8>Oh, J.D., Kling-Backhed, H., Giannakis, M., Xu, J., Fulton, R.S., Fulton, L.A., Cordum, H.S., Wang, C., Elliott, G., Edwards, J., Mardis, E.R., Engstrand, L.G., Gordon, J.I., (2006) Proc. Natl. Acad. Sci. U. S. A., vol. 103, pp. 9999-10004.
Zheng, Y., Unpublished observations.

<1>HpyHII
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori HPAG1
<6>J. Gordon
<7>
<8>Humbert, O., Salama, N.R., (2008) Nucleic Acids Res., vol. 36, pp. 6893-6906.
Oh, J.D., Kling-Backhed, H., Giannakis, M., Xu, J., Fulton, R.S., Fulton, L.A., Cordum, H.S., Wang, C., Elliott, G., Edwards, J., Mardis, E.R., Engstrand, L.G., Gordon, J.I., (2006) Proc. Natl. Acad. Sci. U. S. A., vol. 103, pp. 9999-10004.

<1>HpyHPK5I
<2>DdeI,Bpa36II,BscPI,Bst295I,BstDEI,BstJZ301I,HpyCH4II,HpyF3I,HpyF4II,HpyF5I,HpyF6III,HpyF7I,HpyF9II,HpyF11I,HpyF13II,HpyF19I,HpyF21I,HpyF22II,HpyF24II,HpyF25I,HpyF27I,HpyF30II,HpyF32I,HpyF34I,HpyF37I,HpyF41II,HpyF59I,HpyF60II,HpyF64V,HpyF66II,HpyF67I,HpyF68II,HpyF70I,HpyF72II,HpyHI
<3>CTNAG
<4>
<5>Helicobacter pylori HPK5
<6>M.J. Blaser
<7>
<8>Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>HpyHPK5II
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Helicobacter pylori HPK5
<6>M.J. Blaser
<7>
<8>Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>HpyJP26I
<2>CviRI,Hpy26I,HpyCH4V,HpyF36III,HpyF38II,HpyF44III,HpyF45II,HpyF48III,HpyF49V,HpyF67II
<3>TGCA
<4>
<5>Helicobacter pylori JP26
<6>T. Ando
<7>
<8>Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>HpyJP26II
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Helicobacter pylori JP26
<6>T. Ando
<7>
<8>Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

<1>HpyNI
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>
<5>Helicobacter pylori Novosibirsk N1
<6>V.E. Repin
<7>
<8>Repin, V.E., Puchkova, L.I., Ananko, G.G., Reshetnikov, O.V., Kurilovich, S.A., (1999) Gut, vol. 45.

<1>HpyNSH57I
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,MjaV,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Helicobacter pylori NSH57
<6>N.R. Salama
<7>
<8>Humbert, O., Salama, N.R., (2008) Nucleic Acids Res., vol. 36, pp. 6893-6906.

<1>HpyNSH57II
<2>Hpy178III,Hpy188III,HpyCH4VI,HpyF16II,HpyF19III,HpyF22III,HpyF44IV
<3>TCNNGA
<4>
<5>Helicobacter pylori NSH57
<6>N.R. Salama
<7>
<8>Humbert, O., Salama, N.R., (2008) Nucleic Acids Res., vol. 36, pp. 6893-6906.

<1>M.HsaDnmt1A
<2>
<3>?
<4>?(5)
<5>Homo sapiens
<6>S.B. Baylin
<7>
<8>Nagase, T., Yamakawa, H., Tadokoro, S., Nakajima, D., Inoue, S., Yamaguchi, K., Itokawa, Y., Kikuno, R.F., Koga, H., Ohara, O., Unpublished observations.
Robertson, K.D., Keyomarsi, K., Gonzales, F.A., Velicescu, M., Jones, P.A., (2000) Nucleic Acids Res., vol. 28, pp. 2108-2113.
Totoki, Y., Toyoda, A., Takeda, T., Sakaki, Y., Tanaka, A., Yokoyama, S., Ohara, O., Nagase, T., Kikuno, R., Unpublished observations.
Yen, R.-W.C., Vertino, P.M., Nelkin, B.D., Yu, J.J., El-Deiry, W., Cumaraswamy, A., Lennon, G.G., Trask, B.J., Celano, P., Baylin, S.B., (1992) Nucleic Acids Res., vol. 20, pp. 2287-2291.

<1>M.HsaDnmt1B
<2>
<3>?
<4>?(5)
<5>Homo sapiens
<6>S.B. Baylin
<7>
<8>DOE, J.G.I., Stanford, H.G.C., Unpublished observations.
Hsu, D.W., Lin, M.J., Lee, T.L., Wen, S.C., Chen, X., Shen, C.J., (1999) Proc. Natl. Acad. Sci. U. S. A., vol. 96, pp. 9751-9756.
Isogai, T., Yamamoto, J., Unpublished observations.
Kalos, M.D., Mannion, J., Elliott, M., Algate, P.A., Fling, S.P., Henderson, R.A., Benson, D.R., Indiriasu, C.J., Secrist, H., Mohamath, R., Lodes, M.J., Reed, S.G., Japanese Patent Office, 2004.
Li, L.C., Au, H., Chui, R., Dahiya, R., Unpublished observations.
Lodes, M.J., Mohamath, R., Henderson, R.A., Benson, D.R., Secrist, H., US Patent Office, 2004.

<1>M.HsaDnmt3A
<2>
<3>?
<4>?(5)
<5>Homo sapiens
<6>S.B. Baylin
<7>
<8>Bethel, G., Bye, J.M., Deane, N.L., Martin, P., Lawton, J.C., Sheridan, E.M., McLaren, S., Burton, J., Allouis, S., Prange, C., Beare, D.M., Collins, J.E., Dunham, I., Unpublished observations.
Chen, T., Ueda, Y., Xie, S., Li, E., (2002) J. Biol. Chem., vol. 277, pp. 38746-38754.
Dai, H., He, Y., Linsley, P.S., Mao, M., Roberts, C.J., Van't, V., L, J., Van de Vijver, M.J., Bernards, R., Hart, A.A.M., US Patent Office, 2007.
Li, E., Okano, M., Xie, S., US Patent Office, 2008.
Li, E., Okano, M., Xie, S., Chen, T., US Patent Office, 2008.
Ni, J., Pradhan, S., Roberts, R.J., Unpublished observations.
Robertson, K.D., Uzvolgyi, E., Liang, G., Talmadge, C., Sumegi, J., Gonzales, F.A., Jones, P.A., (1999) Nucleic Acids Res., vol. 27, pp. 2291-2298.
Strausberg, R.L. et al., (2002) Proc. Natl. Acad. Sci. U. S. A., vol. 99, pp. 16899-16903.
Totoki, Y., Toyoda, A., Takeda, T., Sakaki, Y., Tanaka, A., Yokoyama, S., Ohara, O., Nagase, T., Kikuno, R., Unpublished observations.
Xie, S., Wang, Z., Okano, M., Nogami, M., Li, Y., He, W.-W., Okumura, K., Li, E., (1999) Gene, vol. 236, pp. 87-95.

<1>M.HsaDnmt3B
<2>
<3>?
<4>?(5)
<5>Homo sapiens
<6>S.B. Baylin
<7>
<8>Ota, T., Isogai, T., Nishikawa, T., Hayashi, K., Saito, K., Yamamoto, J., Ishii, S., Sugiyama, T., Wakamatsu, A., Nagai, K., Otsuki, T., European Patent Office, 2001.
Phillimore, B., Unpublished observations.
Robertson, K.D., Keyomarsi, K., Gonzales, F.A., Velicescu, M., Jones, P.A., (2000) Nucleic Acids Res., vol. 28, pp. 2108-2113.
Robertson, K.D., Uzvolgyi, E., Liang, G., Talmadge, C., Sumegi, J., Gonzales, F.A., Jones, P.A., (1999) Nucleic Acids Res., vol. 27, pp. 2291-2298.
Strausberg, R.L. et al., (2002) Proc. Natl. Acad. Sci. U. S. A., vol. 99, pp. 16899-16903.
Totoki, Y., Toyoda, A., Takeda, T., Sakaki, Y., Tanaka, A., Yokoyama, S., Ohara, O., Nagase, T., Kikuno, R., Unpublished observations.
Xie, S., Wang, Z., Okano, M., Nogami, M., Li, Y., He, W.-W., Okumura, K., Li, E., (1999) Gene, vol. 236, pp. 87-95.
Xu, G.L., Bestor, T.H., Unpublished observations.

<1>M.HsaDnmt3L
<2>
<3>?
<4>
<5>Homo sapiens
<6>S.B. Baylin
<7>
<8>Aapola, U., Kawasaki, K., Scott, H.S., Ollila, J., Vihinen, M., Heino, M., Shintani, A., Kawasaki, K., Minoshima, S., Krohn, K., Antonarakis, S.E., Shimizu, N., Kudoh, J., Peterson, P., (2000) Genomics, vol. 65, pp. 293-298.

<1>HsoI
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HspAI,Mho2965I,MnnIV,NgoEII,SciNI
<3>G^CGC
<4>
<5>Haemophilus somnus 2336
<6>L.B. Corbeil
<7>
<8>Briggs, R.E., Tatum, F.M., (2005) Appl. Environ. Microbiol., vol. 71, pp. 7187-7195.
Briggs, R.E., Tatum, F.M., International Patent Office, 1997.

<1>Hsp2I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Hafnia species RFL2
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Hsp92I
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>
<5>Haemophilus species 92
<6>R. Williams
<7>R
<8>Allen, J., Unpublished observations.

<1>Hsp92II
<2>NlaIII,CviAII,FaeI,FatI,FatII,Hin1II,Hin8II,HpyCH4I
<3>CATG^
<4>
<5>Haemophilus species 92
<6>R. Williams
<7>R
<8>Allen, J., Unpublished observations.

<1>HspAI
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,Mho2965I,MnnIV,NgoEII,SciNI
<3>G^CGC
<4>2(5)
<5>Haemophilus species A
<6>S.K. Degtyarev
<7>IV
<8>Chernuhin, V.A., Gonchar, D.A., Kashirina, J.G., Suhanova, K.S., Degtyarev, S.K., Unpublished observations.
Rechkunova, N.I., Prikhodko, E.A., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>HsuI
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>A^AGCTT
<4>
<5>Haemophilus suis
<6>ATCC 19417
<7>
<8>Myers, P.A., Roberts, R.J., Unpublished observations.

<1>ItaI
<2>Fnu4HI,Bli1904II,Bpu1811I,BsoFI,Bsp6I,BssFI,BssXI,BthCI,Cac824I,CcoP215I,CcoP216I,FbrI,Fsp4HI,LlaDII,SatI,Uur960I
<3>GC^NGC
<4>
<5>Ilyobacter tartaricus
<6>U. Mayr
<7>M
<8>Stadtler, P., von Strandmann, R.P., Walter, T., Frey, B., Auer, H., Hengstenberg, W., Schmitz, G., (1993) Gene, vol. 137, pp. 347-348.

<1>KasI
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>G^GCGCC
<4>?(5)
<5>Kluyvera ascorbata
<6>NEB 593
<7>N
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Polisson, C., Barsomian, J.M., US Patent Office, 1992.
Vaisvila, R., Unpublished observations.

<1>Kaz48kI
<2>DraII,EcoO109I,PssI,Uba1326I,VneAI
<3>RGGNC^CY
<4>
<5>Klebsiella azeanae
<6>A.N. Kravets
<7>
<8>Pertsev, A.V., Kravets, A.N., Russian Patent Office, 1995.

<1>KflI
<2>SanDI,Sse1825I
<3>GG^GWCCC
<4>
<5>Kribbella flavida RFL1
<6>Fermentas G320
<7>F
<8>Lauciuniene, N., Norgeliene, D., Trinkunaite, L., Vitkute, J., Janulaitis, A., Unpublished observations.
Zakareviciene, L., Lubys, A., Unpublished observations.

<1>KoxI
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,NspSAII,PspEI,SciAI,Uba1291I
<3>GGTNACC
<4>
<5>Klebsiella oxytoca
<6>CAMB 2553
<7>
<8>Sohail, A., Khan, E., Mushtaq, R., Riazuddin, S., Unpublished observations.

<1>KoxII
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCY^C
<4>
<5>Klebsiella oxytoca
<6>CAMB 2553
<7>
<8>Sohail, A., Unpublished observations.

<1>Kox165I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Klebsiella oxytoca RFL165
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>KoyI
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Klebsiella oxytoca
<6>ATCC 13183
<7>
<8>Polisson, C., Unpublished observations.

<1>Kpl79I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Klebsiella planticola RFL79
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>KpnI
<2>Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTAC^C
<4>4(6)
<5>Klebsiella pneumoniae OK8
<6>ATCC 49790
<7>BCFHIJKMNOQRSUVWXY
<8>Chatterjee, D., Longo, M., Flynn, E., Oberfelder, R., US Patent Office, 2004.
Kiss, A., Finta, C., Venetianer, P., (1991) Nucleic Acids Res., vol. 19, pp. 3460.
Smith, D.I., Blattner, F.R., Davies, J., (1976) Nucleic Acids Res., vol. 3, pp. 343-353.
Tomassini, J., Roychoudhury, R., Wu, R., Roberts, R.J., (1978) Nucleic Acids Res., vol. 5, pp. 4055-4064.

<1>Kpn2I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>?(5)
<5>Klebsiella pneumoniae RFL2
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Unpublished observations.
Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.
Lubys, A., Jurenaite, S., Janulaitis, A., (1999) Nucleic Acids Res., vol. 27, pp. 4228-4234.

<1>Kpn10I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Klebsiella pneumoniae RFL10
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Kpn12I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Klebsiella pneumoniae RFL12
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Kpn13I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Klebsiella pneumoniae RFL13
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Kpn14I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Klebsiella pneumoniae RFL14
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Kpn16I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Klebsiella pneumoniae RFL16
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Unpublished observations.

<1>Kpn19I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Klebsiella pneumoniae RFL19
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Kpn30I
<2>BsePI,BscEI,BsoPI,BsrHI,BssBI,BssHII,BstBZ153I,CfrJ5I,Eco143I,Eco152I,Esp7I,Esp8I,McaTI,PauI,PteI,TtmII,Uba69I
<3>GCGCGC
<4>
<5>Klebsiella pneumoniae RFL30
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Bitinaite, J., Unpublished observations.

<1>Kpn378I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Klebsiella pneumoniae 378
<6>Y.P. Zernov
<7>
<8>Zernov, Y.P., Lebedev, L.R., Babkin, I.V., Chizhikov, V.E., (1990) Bioorg. Khim., vol. 16, pp. 603-604.

<1>KpnAI
<2>
<3>GAANNNNNNTGCC
<4>3(6),-4(6)
<5>Klebsiella pneumoniae M5a1
<6>J.-I. Ryu
<7>
<8>Kasarjian, J., Valinluck, V., Ryu, J., (2002) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 102, pp. 236.
Kasarjian, J.K.A., Burnett, A.S., Ryu, J., (2001) J. Invest. Med., vol. 49, pp. 12A.
Kasarjian, J.K.A., Burnett, A.S., Ryu, J., (2001) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 101, pp. 403.
Lee, N.S., Rutebuka, O., Arakawa, T., Bickle, T.A., Ryu, J., (1997) J. Mol. Biol., vol. 271, pp. 342-348.
Ryu, J.-I., Unpublished observations.
Valinluck, B., Reyno, M., Ryu, J., (1989) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 89, pp. 180.

<1>KpnBI
<2>
<3>CAAANNNNNNRTCA
<4>4(6),-3(6)
<5>Klebsiella pneumoniae GM236
<6>J.-I. Ryu
<7>
<8>Kasarjian, J., Valinluck, V., Ryu, J., (2002) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 102, pp. 236.
Ryu, J.-I., Unpublished observations.
Valinluck, B., Reyno, M., Ryu, J., (1989) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 89, pp. 180.

<1>M.Kpn43816Dam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Klebsiella pneumoniae strain 43816
<6>S. Clegg
<7>
<8>Mehling, J.S., Lavender, H., Clegg, S., (2007) FEMS Microbiol. Lett., vol. 268, pp. 187-193.

<1>KpnK14I
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Klebsiella pneumoniae mmK14
<6>W. Piepersberg
<7>
<8>Bolton, B.J., Comer, M.J., Kessler, C., Unpublished observations.

<1>Kpn2kI
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>^CCNGG
<4>?(5)
<5>Klebsiella pneumoniae 2k
<6>A.S. Solonin
<7>
<8>Denjmukhametov, M.M., Zakharova, M.V., Kravets, A.N., Pertsev, A.V., Sineva, E.V., Repik, A.V., Beletskaya, I.V., Gromova, E.S., Solonin, A.S., (1997) Mol. Biol. (Mosk), vol. 31, pp. 831-838.
Zakharova, M.V., Beletskaya, I.V., Denjmukhametov, M.M., Yurkova, T.V., Semenova, L.M., Shlyapnikov, M.G., Solonin, A.S., (2002) Mol. Genet. Genomics, vol. 267, pp. 171-178.

<1>Kpn49kI
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco237I,Eco252I,FunII,HalI,Hal22I,Ppu111I,RsrI,Srl32DII,Srl55DI,SsoI,Uba58I,Van91II,VchN100I,VchO2I
<3>G^AATTC
<4>
<5>Klebsiella pneumoniae 49k
<6>A.S. Solonin
<7>
<8>Kravetz, A.N., Zakharova, M.V., Beljetzkaja, I.V., Pertzev, A.V., Spivak, O.I., Solonin, A.S., (1993) Nucleic Acids Res., vol. 21, pp. 1501.

<1>Kpn49kII
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>^CCSGG
<4>
<5>Klebsiella pneumoniae 49k
<6>A.S. Solonin
<7>
<8>Kravetz, A.N., Zakharova, M.V., Beljetzkaja, I.V., Pertzev, A.V., Spivak, O.I., Solonin, A.S., (1993) Nucleic Acids Res., vol. 21, pp. 1501.

<1>KspI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Kluyvera species
<6>U. Mayr
<7>MS
<8>Bolton, B.J., Schmitz, G.G., Jarsch, M., Kessler, C., (1989) Nucleic Acids Res., vol. 17, pp. 9476.

<1>Ksp22I
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>T^GATCA
<4>
<5>Kurthia species 22
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.K., Unpublished observations.

<1>Ksp632I
<2>Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC(1/4)
<4>
<5>Kluyvera species 632
<6>DSM 4196
<7>
<8>Bolton, B.J., Schmitz, G.G., Jarsch, M., Comer, M.J., Kessler, C., (1988) Gene, vol. 66, pp. 31-43.
Tsukahara, S., Yamakawa, H., Takai, K., Takaku, H., (1994) Nucleosides and Nucleotides, vol. 13, pp. 1617-1626.

<1>KspAI
<2>HpaI,BsaKI,BseII,BstEZ359I,BstHPI,MwhI,SsrI,Uba1408II
<3>GTT^AAC
<4>
<5>Kurthia species N88
<6>A. Janulaitis
<7>F
<8>Vaitkevicius, D., Maneliene, Z., Norgeliene, D., Valickiene, D., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>KspHK12I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Klebsiella species N12
<6>P.C. Shaw
<7>
<8>Chan, Y.C., Kam, K.M., Shaw, P.C., Unpublished observations.

<1>KspHK14I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Klebsiella species N14
<6>P.C. Shaw
<7>
<8>Chan, Y.C., Kam, K.M., Shaw, P.C., Unpublished observations.

<1>KspHK15I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,Uba36I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Klebsiella species N15
<6>P.C. Shaw
<7>
<8>Chan, Y.C., Kam, K.M., Shaw, P.C., Unpublished observations.

<1>KteAI
<2>SmaI,AhyI,Cfr9I,CfrJ4I,EaeAI,EclRI,Pac25I,PaeBI,PspAI,PspALI,TspMI,Uba1220I,Uba1393I,XcyI,XmaI,XmaCI
<3>CCCGGG
<4>
<5>Klebsiella terrigena
<6>ATCC 33631
<7>
<8>Polisson, C., Unpublished observations.

<1>Kzo9I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Kurthia zopfii 9
<6>S.K. Degtyarev
<7>I
<8>Degtyarev, S.K., Rechkunova, N.I., Grinev, A.A., Dedkov, V.S., (1989) Izv. Sib. Otd. Akad. Nauk SSSR, vol. 15, pp. 25-26.

<1>Kzo49I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Kurthia zopfii 49
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>LcaI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Lactobacillus casei
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Anikeitcheva, N.V., Kalugin, A.A., Samko, O.T., Choroshoutina, E.B., Fitsner, A.B., Unpublished observations.

<1>LdeAb1I
<2>
<3>?
<4>
<5>Lactobacillus delbrueckii subs. lactis Ab1
<6>V.B. Suarez
<7>
<8>Suarez, V.B., Maciel, N., Guglielmotti, D., Zago, M., Giraffa, G., Reinheimer, J., (2008) Int. J. Food Microbiol., vol. 128, pp. 401-405.

<1>LfeI
<2>BbvI,AlwXI,BchI,BsaUI,BseKI,BseXI,Bsp423I,BsrVI,Bst12I,Bst71I,BstV1I,Lsp1109I
<3>GCAGC
<4>
<5>Lactobacillus fermentum CP-34
<6>N. Yamamoto
<7>
<8>Takano, T., Ochi, A., Yamamoto, N., (1990) FEMS Microbiol. Rev., vol. 7, pp. 64.

<1>LguI
<2>SapI,BspQI,PciSI,VpaK32I
<3>GCTCTTC(1/4)
<4>
<5>Lysobacter gummosus RFL1
<6>Fermentas G307
<7>F
<8>Vitkute, J., Lapcinskaja, S., Maneliene, Z., Capskaja, L., Trinkunaite, L., Janulaitis, A., Unpublished observations.

<1>LlaI
<2>
<3>?
<4>?(6)
<5>Lactococcus lactis subsp. lactis
<6>T.R. Klaenhammer
<7>
<8>Djordjevic, G.M., Klaenhammer, T.R., (1995) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 95, pp. 527.
Hill, C., Miller, L., Klaenhammer, T., (1990) Plasmid, vol. 23, pp. 167-168.
Klaenhammer, T.R., Romero, D., Sing, W., Hill, C., (1991) Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci, ed. Dunny, G.M., Cleary, P.P., McKay, L.L. (American Society for Microbiology, Washington), vol. 8, pp. 124-130.

<1>Lla82I
<2>
<3>?
<4>
<5>Lactococcus lactis plasmid pAH82
<6>D.D. O'Sullivan
<7>
<8>O'Sullivan, D., Twomey, D.P., Coffey, A., Hill, C., Fitzgerald, G.F., Ross, R.P., (2000) Mol. Microbiol., vol. 36, pp. 866-875.

<1>Lla497I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Lactococcus lactis ssp lactis NCDO 497
<6>B. Mayo
<7>
<8>Mayo, B., Hardisson, C., Brana, A.F., (1991) FEMS Microbiol. Lett., vol. 79, pp. 195-198.

<1>Lla1403I
<2>
<3>?
<4>
<5>Lactococcus lactis IL1403
<6>M. Chopin
<7>
<8>Schouler, C., Gautier, M., Ehrlich, S.D., Chopin, M.-C., (1998) Mol. Microbiol., vol. 28, pp. 169-178.

<1>Lla2614I
<2>
<3>?
<4>
<5>Lactococcus lactis pIL2614
<6>M. Chopin
<7>
<8>Schouler, C., Clier, F., Luisa, A., Lerayer, L., Ehrlich, S.D., Chopin, M.-C., (1998) J. Bacteriol., vol. 180, pp. 407-411.

<1>LlaAI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Lactococcus lactis subsp. cremoris W9
<6>J. Josephsen
<7>
<8>Josephsen, J., Nyengaard, N.R., Vogensen, F.K., Madsen, A., International Patent Office, 1996.
Nyengaard, N., Vogensen, F.K., Josephsen, J., (1993) Gene, vol. 136, pp. 371-372.

<1>LlaBI
<2>SfeI,Bco163I,BdiSI,BfmI,BpcI,BstSFI,BthP35I,HpyF2I,SfcI,Srl56DI
<3>C^TRYAG
<4>
<5>Lactococcus lactis subsp. cremoris W56
<6>J. Josephsen
<7>
<8>Nyengaard, N., Vogensen, F.K., Josephsen, J., (1993) Gene, vol. 136, pp. 371-372.
Nyengaard, N.R., Falkenberg-Klok, J., Josephsen, J., (1996) Appl. Environ. Microbiol., vol. 62, pp. 3494-3498.

<1>LlaBIII
<2>
<3>?
<4>
<5>Lactococcus lactis subsp. cremoris W56
<6>J. Josephsen
<7>
<8>Kong, J., Matvienko, N., Josephsen, J., Unpublished observations.

<1>LlaCI
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>A^AGCTT
<4>1(6)
<5>Lactococcus lactis W15
<6>J. Josephsen
<7>
<8>Josephsen, J., Jorgen-Jensen, B., Nyengaard, N.R., (1998) FEMS Microbiol. Lett., vol. 163, pp. 25-29.
Madsen, A., Josephsen, J., (1998) Biol. Chem., vol. 379, pp. 443-449.
Mruk, I., Cichowicz, M., Kaczorowski, T., (2003) Microbiology, vol. 149, pp. 3331-3341.
Nyengaard, N., Vogensen, F.K., Josephsen, J., (1995) Gene, vol. 157, pp. 13-18.

<1>LlaDI
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,Eco255I,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGTACT
<4>
<5>Lactococcus lactis W39
<6>J. Josephsen
<7>
<8>Evison, T.P., Aideh, B., Josephsen, J., Unpublished observations.
Nyengaard, N., Vogensen, F.K., Josephsen, J., (1995) Gene, vol. 157, pp. 13-18.

<1>LlaDII
<2>Fnu4HI,Bli1904II,Bpu1811I,BsoFI,Bsp6I,BssFI,BssXI,BthCI,Cac824I,CcoP215I,CcoP216I,FbrI,Fsp4HI,ItaI,SatI,Uur960I
<3>GCNGC
<4>?(5)
<5>Lactococcus lactis W39
<6>J. Josephsen
<7>
<8>Josephsen, J., Nyengaard, N.R., Vogensen, F.K., Madsen, A., International Patent Office, 1996.
Madsen, A., Josephsen, J., (1998) Appl. Environ. Microbiol., vol. 64, pp. 2424-2431.

<1>LlaDCHI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Lactococcus lactis subsp. cremoris DCH-4
<6>S. Moineau
<7>
<8>Moineau, S., Walker, S.A., Vedamuthu, E.R., Vandenbergh, P.A., (1995) Appl. Environ. Microbiol., vol. 61, pp. 2193-2202.

<1>LlaEI
<2>
<3>?
<4>
<5>Lactococcus lactis W12
<6>J. Josephsen
<7>
<8>Nyengaard, N., Vogensen, F.K., Josephsen, J., (1995) Gene, vol. 157, pp. 13-18.

<1>LlaFI
<2>
<3>?
<4>
<5>Lactococcus lactis LL42-1
<6>P. Su
<7>
<8>Su, P., Im, H., Hsieh, H., Kanga, S., Dunn, N.W., (1999) Appl. Environ. Microbiol., vol. 65, pp. 686-693.

<1>LlaGI
<2>
<3>?
<4>
<5>Lactococcus lactis
<6>J. Josephsen
<7>
<8>Madsen, A., Josephsen, J., (2001) FEMS Microbiol. Lett., vol. 200, pp. 91-96.

<1>LlaG2I
<2>NheI,AceII,AsuNHI,BmtI,BspOI,PstNHI
<3>G^CTAGC
<4>
<5>Lactococcus lactis ssp. cremoris
<6>B. Karska-Wysocki
<7>
<8>Karska-Wysocki, B., Szatmari, G., Barrette, B., Mamet-Bratley, M.D., (1996) Life Sc. Confer. Ottawa, vol. 0.
Karska-Wysocki, B., Szatmari, G., Beauregard, G., Mamet-Bratley, M.D., (1995) Life Sc. Confer. Ottawa (Ottawa), vol. 0.

<1>R1.LlaJI
<2>
<3>?
<4>3(5)
<5>Lactococcus lactis
<6>G.F. Fitzgerald
<7>
<8>O'Driscoll, J., Fitzgerald, G.F., van Sinderen, D., (2005) Mol. Microbiol., vol. 57, pp. 1532-1544.
O'Driscoll, J., Glynn, F., Cahalane, O., O'Connell-Motherway, M., Fitzgerald, G.F., van Sinderen, D., (2004) Appl. Environ. Microbiol., vol. 70, pp. 5546-5556.

<1>R2.LlaJI
<2>
<3>?
<4>3(5)
<5>Lactococcus lactis
<6>G.F. Fitzgerald
<7>
<8>O'Driscoll, J., Fitzgerald, G.F., van Sinderen, D., (2005) Mol. Microbiol., vol. 57, pp. 1532-1544.
O'Driscoll, J., Glynn, F., Cahalane, O., O'Connell-Motherway, M., Fitzgerald, G.F., van Sinderen, D., (2004) Appl. Environ. Microbiol., vol. 70, pp. 5546-5556.

<1>LlaKR2I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>4(5)
<5>Lactococcus lactis subsp. lactis KR2
<6>D.P. Twomey
<7>
<8>Twomey, D.P., McKay, L.L., O'Sullivan, D.J., (1997) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 97, pp. 426.

<1>LlaMI
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>
<5>Lactococcus lactis subs. cremoris M19
<6>B. Karska-Wysocki
<7>
<8>Karska-Wysocki, B., Hua, N.M., Vzdornov, D., Szatmari, G., Mamet-Bratley, M.D., (1999) Sixth Symposium on Lactic Acid Bacteria Genetics, Metabolism and Applications, ed. none (Fed. European Microbiol. Socs. and Netherlands Soc. for Microbiology, Veldhoven, The Netherlands), vol. 0.
Szatmari, G., Hua, N.M., Vzdornov, D., Daigle, F., Smoragiewicz, W., Mamet-Bratley, M.D., Karska-Wysocki, B., (2006) J. Biotechnol., vol. 121, pp. 144-153.

<1>LldI
<2>
<3>?
<4>
<5>Lactococcus lactis bv. diacetylactis
<6>N.W. Dunn
<7>
<8>Deng, Y.M., Liu, C.Q., Dunn, N.W., (2000) DNA Seq., vol. 11, pp. 239-245.

<1>Lmu60I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CC^TNAGG
<4>
<5>Listeria murrayi 60
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>LplI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Lactobacillus plantarum
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Maneliene, Z.P., Butkus, V.V., Fitzner, A.B., Khoroshutina, E.B., Kalugin, A.A., Janulaitis, A., (1990) Bioorg. Khim., vol. 16, pp. 1040-1044.

<1>LpnI
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGC^GCY
<4>
<5>Legionella pneumophila Philadelphia 1
<6>A. Brown
<7>
<8>Chen, G.C.C., Brown, A., Lema, M.W., (1986) Can. J. Microbiol., vol. 32, pp. 591-593.
Hamablet, L., Chen, G.C., Brown, A., Roberts, R.J., (1989) Nucleic Acids Res., vol. 17, pp. 6417.

<1>LpnII
<2>
<3>?
<4>
<5>Legionella pneumophila Philadelphia 1
<6>A. Brown
<7>
<8>Chen, G.C.C., Brown, A., Lema, M.W., (1986) Can. J. Microbiol., vol. 32, pp. 591-593.

<1>LspI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Lactobacillus species
<6>P. Eastlake
<7>
<8>Brown, N.L., Unpublished observations.
Eastlake, P., Unpublished observations.

<1>Lsp1109I
<2>BbvI,AlwXI,BchI,BsaUI,BseKI,BseXI,Bsp423I,BsrVI,Bst12I,Bst71I,BstV1I,LfeI
<3>GCAGC(8/12)
<4>?(5)
<5>Listeria species RFL1109
<6>A. Janulaitis
<7>F
<8>Jakubauskas, A., Kriukiene, E., Trinkunaite, L., Sapranauskas, R., Jurenaite-Urbanaviciene, S., Lubys, A., (2009) Plasmid, vol. 61, pp. 52-64.
Janulaitis, A., Grigaite, R., Trinkunaite, L., Maneliene, Z., Bitinaite, J., Kiuduliene, L., Butkus, V., Unpublished observations.
Lubys, A., Janulaitis, A., Unpublished observations.
Zakareviciene, L., Lubys, A., Unpublished observations.

<1>Lsp1109II
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Listeria species RFL1109
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Grigaite, R., Trinkunaite, L., Maneliene, Z., Bitinaite, J., Kiuduliene, L., Butkus, V., Unpublished observations.

<1>Lsp1270I
<2>NspI,AvoI,BstNSI,NspHI,PauAI,PunAII,XceI
<3>RCATGY
<4>
<5>Listeria species RFL1270
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Krikstulyte, V., Trinkunaite, L., Maneliene, Z., Kiuduliene, L., Petrusyte, M., Butkus, V., Unpublished observations.

<1>LweI
<2>SfaNI,BhaI,BmsI,BscAI,BscUI,BsmNI,BspST5I,Bst19I,CjeP338II,PhaI
<3>GCATC(5/9)
<4>
<5>Listeria welshimeri RFL 131
<6>V. Butkus
<7>F
<8>Vitkute, J., Zutautiene, D., Maneliene, Z., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>MabI
<2>SexAI,CsiI
<3>A^CCWGGT
<4>
<5>Microbacterium arborescens SE
<6>S.K. Degtyarev
<7>I
<8>Nadeev, A.N., Tsaplin, M.M., Abdurashitov, M.A., Dedkov, V.S., Kashirina, J.G., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>MaeI
<2>BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>C^TAG
<4>
<5>Methanococcus aeolicus PL-15/H
<6>K.O. Stetter
<7>M
<8>Schmid, K., Thomm, M., Laminet, A., Laue, F.G., Kessler, C., Stetter, K.O., Schmitt, R., (1984) Nucleic Acids Res., vol. 12, pp. 2619-2628.

<1>MaeII
<2>HpyCH4IV,HpyF13III,HpyF35II,HpyF74II,TaiI,TscI,Tsp49I,TspIDSI,TspWAM8AI,TtmI
<3>A^CGT
<4>
<5>Methanococcus aeolicus PL-15/H
<6>K.O. Stetter
<7>M
<8>Schmid, K., Thomm, M., Laminet, A., Laue, F.G., Kessler, C., Stetter, K.O., Schmitt, R., (1984) Nucleic Acids Res., vol. 12, pp. 2619-2628.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>MaeIII
<2>
<3>^GTNAC
<4>
<5>Methanococcus aeolicus PL-15/H
<6>K.O. Stetter
<7>M
<8>Schmid, K., Thomm, M., Laminet, A., Laue, F.G., Kessler, C., Stetter, K.O., Schmitt, R., (1984) Nucleic Acids Res., vol. 12, pp. 2619-2628.

<1>MaeK81I
<2>SplI,BpuB5I,BsiWI,BsmWI,BvuBI,Pfl23II,PfuNI,PpuAI,PspLI,SmaAI,SplAI,SspKI,SunI
<3>C^GTACG
<4>
<5>Microcystis aeruginosa K-81
<6>M. Shirai
<7>
<8>Takahashi, I., Hayano, D., Asayama, M., Masahiro, F., Watahiki, M., Shirai, M., (1996) FEMS Microbiol. Lett., vol. 145, pp. 107-111.

<1>MaeK81II
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Microcystis aeruginosa K-81
<6>M. Shirai
<7>
<8>Takahashi, I., Hayano, D., Asayama, M., Masahiro, F., Watahiki, M., Shirai, M., (1996) FEMS Microbiol. Lett., vol. 145, pp. 107-111.

<1>MalI
<2>DpnI,CfuI,FtnUIV,Mph1103II,NanII,NgoDXIV,NmeAII,NmeBL859I,NmuDI,NmuEI,NsuDI,TdeI
<3>GA^TC
<4>
<5>Marinococus albus I
<6>S.K. Degtyarev
<7>I
<8>Chernuhin, V.A., Nayakshina, T.N., Tomilova, J.E., Degtyarev, S.K., Unpublished observations.

<1>MamI
<2>BsaBI,Bco63I,Bco631I,Bse8I,Bse631I,BseJI,Bsh1365I,BsiBI,BsrBRI,UbaN6I
<3>GATNN^NNATC
<4>?(6)
<5>Microbacterium ammoniaphilum
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Kessler, C., US Patent Office, 1992.
Striebel, H.-M., Schmitz, G.G., Kaluza, K., Jarsch, M., Kessler, C., (1990) Gene, vol. 91, pp. 95-100.
Striebel, H.-M., Seeber, S., Jarsch, M., Kessler, C., (1996) Gene, vol. 172, pp. 41-46.

<1>MaqI
<2>
<3>CRTTGAC(21/19)
<4>
<5>Marinobacter aquaeolei VT8
<6>K. Edwards
<7>
<8>Copeland, A. et al., Unpublished observations.
Dwinnel, E., Morgan, R.D., Unpublished observations.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>MarI
<2>AluI,AluBI,BsaLI,Mho2111I,MltI,OtuI,OtuNI,OxaI,Uba1433I,Uba1441I
<3>AGCT
<4>
<5>Mycoplasma arthritidis 1581
<6>K. Dybvig
<7>
<8>Voelker, L.L., Dybvig, K., (1996) J. Bacteriol., vol. 178, pp. 6078-6081.

<1>MauI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Micrococcus aurantiacus
<6>IFO 12422
<7>
<8>Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Bull. Inst. Chem. Res. Kyoto Univ., vol. 60, pp. 328-335.

<1>MauAI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Micromonospora aurantiaca
<6>NRRL B16091
<7>
<8>Klein, S., Roberts, R.J., Unpublished observations.

<1>MauBI
<2>
<3>CG^CGCGCG
<4>
<5>Microbacterium aurum RFL2
<6>Fermentas G348
<7>F
<8>Vitkute, J., Lauciuniene, N., Capskaja, L., Trinkunaite, L., Janulaitis, A., Unpublished observations.
Zakareviciene, L., Lubys, A., Unpublished observations.

<1>MavI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Mycobacterium avium
<6>J.T. Crawford
<7>
<8>McDermott, P.F., Crawford, J.T., (1989) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 89, pp. 167.

<1>MbiI
<2>BsrBI,AccBSI,BstD102I,Bst31NI
<3>CCGCTC(-3/-3)
<4>
<5>Moraxella bovis Fr1-022
<6>A. Janulaitis
<7>F
<8>Maneliene, Z., Butkus, V., Unpublished observations.
Vitkute, J., Kazlauskiene, R., Trinkunaite, L., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>MboI
<2>Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>2(6)
<5>Moraxella bovis
<6>ATCC 10900
<7>BCFKNQRUWXY
<8>Anton, B.P., Brooks, J.E., Unpublished observations.
Gelinas, R.E., Myers, P.A., Roberts, R.J., (1977) J. Mol. Biol., vol. 114, pp. 169-179.
Huang, L.-H., Farnet, C.M., Ehrlich, K.C., Ehrlich, M., (1982) Nucleic Acids Res., vol. 10, pp. 1579-1591.
Ueno, T., Ito, H., Kimizuka, F., Kotani, H., Nakajima, K., (1993) Nucleic Acids Res., vol. 21, pp. 2309-2313.
Ueno, T., Ito, H., Kotani, H., Nakajima, K., Japanese Patent Office, 1993.

<1>MboII
<2>HpyII,Hpy178II,HpyAII,NcuI,TceI
<3>GAAGA(8/7)
<4>5(6)
<5>Moraxella bovis
<6>ATCC 10900
<7>FIJKNOQRVWX
<8>Brown, N.L., Hutchison, C.A. III, Smith, M., (1980) J. Mol. Biol., vol. 140, pp. 143-148.
Endow, S.A., (1977) J. Mol. Biol., vol. 114, pp. 441-449.
Gelinas, R.E., Myers, P.A., Roberts, R.J., (1977) J. Mol. Biol., vol. 114, pp. 169-179.
McClelland, M., Nelson, M., Cantor, C.R., (1985) Nucleic Acids Res., vol. 13, pp. 7171-7182.

<1>M.MbuI
<2>
<3>?
<4>
<5>Mycobacterium butyricum
<6>S.S. Debov
<7>
<8>Nikolskaya, I.I., Sharkova, E.V., Suchkov, S.V., Karpets, L.Z., Debov, S.S., Somodi, P., Foldes, I., (1983) Biochem. Int., vol. 7, pp. 605-615.

<1>M.MbuII
<2>
<3>?
<4>
<5>Mycobacterium butyricum
<6>S.S. Debov
<7>
<8>Nikolskaya, I.I., Sharkova, E.V., Suchkov, S.V., Karpets, L.Z., Debov, S.S., Somodi, P., Foldes, I., (1983) Biochem. Int., vol. 7, pp. 605-615.

<1>M.MbuIII
<2>
<3>?
<4>
<5>Mycobacterium butyricum
<6>S.S. Debov
<7>
<8>Nikolskaya, I.I., Sharkova, E.V., Suchkov, S.V., Karpets, L.Z., Debov, S.S., Somodi, P., Foldes, I., (1983) Biochem. Int., vol. 7, pp. 605-615.

<1>M.MbuIV
<2>
<3>?
<4>
<5>Mycobacterium butyricum
<6>S.S. Debov
<7>
<8>Nikolskaya, I.I., Sharkova, E.V., Suchkov, S.V., Karpets, L.Z., Debov, S.S., Somodi, P., Foldes, I., (1983) Biochem. Int., vol. 7, pp. 605-615.

<1>MbvI
<2>
<3>?
<4>
<5>Moraxella bovis
<6>ATCC 17947
<7>
<8>Jiang, B.D., Myers, P., Unpublished observations.

<1>McaI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Micromonospora carbonacea
<6>C. Kessler
<7>
<8>Kessler, C., Neumaier, P.S., Wolf, W., (1985) Gene, vol. 33, pp. 1-102.

<1>McaAI
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GGCGCC
<4>
<5>Micromonospora carbonacea
<6>NRRL 2997
<7>
<8>Earle-Hughes, J., Roberts, R.J., Unpublished observations.

<1>McaBI
<2>
<3>?
<4>
<5>Methylococcus capsulatus
<6>IMV 3494
<7>
<8>Romanovskaya, V.A., Alexeyev, M.F., Gunkovskaya, N.V., Stolyar, S.M., Shatohina, E.S., Malashenko, Y.R., (1992) Mikrobiol. Zh., vol. 54, pp. 32-39.

<1>McaTI
<2>BsePI,BscEI,BsoPI,BsrHI,BssBI,BssHII,BstBZ153I,CfrJ5I,Eco143I,Eco152I,Esp7I,Esp8I,Kpn30I,PauI,PteI,TtmII,Uba69I
<3>GCGC^GC
<4>?(5)
<5>Methylococcus capsulatus str. Bath
<6>ATCC 3309
<7>
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Ward, N. et al., (2004) PLoS Biology, vol. 2, pp. 1616-1628.
Zheng, Y., Roberts, R.J., Unpublished observations.

<1>MchI
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,McaAI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GG^CGCC
<4>
<5>Micromonospora chalcea
<6>ATCC 12452
<7>
<8>Hamablet, L., Meyertons, J.L., Roberts, R.J., Unpublished observations.

<1>MchAI
<2>NotI,CciNI,CsiBI,CspBI
<3>GC^GGCCGC
<4>
<5>Mycobacterium chelonei
<6>A.K. Tyagi
<7>
<8>Shankar, S., Tyagi, A.K., (1993) Gene, vol. 132, pp. 119-123.

<1>MchAII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Mycobacterium chelonei
<6>A.K. Tyagi
<7>
<8>Shankar, S., Tyagi, A.K., (1993) Gene, vol. 132, pp. 119-123.

<1>McrI
<2>BsaOI,BscNI,Bsh1285I,BsiEI,BstMCI,BstZ5I,Uba1303I
<3>CGRY^CG
<4>
<5>Micrococcus cryophilus
<6>U. Mayr
<7>
<8>Brensing-Kuppers, J., Reischl, U., Schmitz, G.S., Kaluza, K., Jarsch, M., Kessler, C., (1990) FEBS Lett., vol. 264, pp. 218-222.
Kaluza, K., Hoeltke, H.J., Jarsch, M., Schmitz-Agheguian, G., Kessler, C., European Patent Office, 1989.

<1>MecI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Micromonospora echinospora subs. echinospora
<6>ATCC 15837
<7>
<8>Meyertons, J.L., Tilley, B.C., Lechevalier, M.P., Lechevalier, H.A., (1987) J. Ind. Microbiol., vol. 2, pp. 293-303.

<1>Mel3JI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Megasphaera elsedenii 3J
<6>P. Pristas
<7>
<8>Piknova, M., Filova, M., Javorsky, P., Pristas, P., (2004) FEMS Microbiol. Lett., vol. 236, pp. 91-95.
Piknova, M., Pristas, P., Javorsky, P., (2004) Folia Microbiol. (Praha), vol. 49, pp. 191-193.

<1>Mel5JI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Megasphaera elsedenii 5J
<6>P. Pristas
<7>
<8>Piknova, M., Filova, M., Javorsky, P., Pristas, P., (2004) FEMS Microbiol. Lett., vol. 236, pp. 91-95.

<1>Mel7JI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Megasphaera elsedenii 7J
<6>P. Pristas
<7>
<8>Piknova, M., Filova, M., Javorsky, P., Pristas, P., (2004) FEMS Microbiol. Lett., vol. 236, pp. 91-95.
Piknova, M., Pristas, P., Javorsky, P., (2004) Folia Microbiol. (Praha), vol. 49, pp. 191-193.

<1>Mel4OI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Megasphaera elsedenii 4O
<6>P. Pristas
<7>
<8>Piknova, M., Filova, M., Javorsky, P., Pristas, P., (2004) FEMS Microbiol. Lett., vol. 236, pp. 91-95.
Piknova, M., Pristas, P., Javorsky, P., (2004) Folia Microbiol. (Praha), vol. 49, pp. 191-193.

<1>Mel5OI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Megasphaera elsedenii 5O
<6>P. Pristas
<7>
<8>Piknova, M., Filova, M., Javorsky, P., Pristas, P., (2004) FEMS Microbiol. Lett., vol. 236, pp. 91-95.
Piknova, M., Pristas, P., Javorsky, P., (2004) Folia Microbiol. (Praha), vol. 49, pp. 191-193.

<1>Mel2TI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Megasphaera elsedenii 2T
<6>P. Pristas
<7>
<8>Piknova, M., Filova, M., Javorsky, P., Pristas, P., (2004) FEMS Microbiol. Lett., vol. 236, pp. 91-95.
Piknova, M., Pristas, P., Javorsky, P., (2004) Folia Microbiol. (Praha), vol. 49, pp. 191-193.

<1>Mel5TI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Megasphaera elsedenii 5T
<6>P. Pristas
<7>
<8>Piknova, M., Filova, M., Javorsky, P., Pristas, P., (2004) FEMS Microbiol. Lett., vol. 236, pp. 91-95.
Piknova, M., Pristas, P., Javorsky, P., (2004) Folia Microbiol. (Praha), vol. 49, pp. 191-193.

<1>MeuI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Micrococcus euryhalis
<6>ATCC 14389
<7>
<8>Wickberg, L., Schildkraut, I., Unpublished observations.

<1>MfeI
<2>MunI
<3>C^AATTG
<4>?(6)
<5>Mycoplasma fermentans
<6>N.F. Halden
<7>N
<8>Halden, N.F., Wolf, J.B., Cross, S.L., Leonard, W.J., (1988) Clin. Res., vol. 36, pp. 404a.
Halden, N.F., Wolf, J.B., Leonard, W.J., (1989) Nucleic Acids Res., vol. 17, pp. 3491-3499.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Stickel, S.K., Roberts, R.J., Unpublished observations.
Xu, S.-Y., Unpublished observations.
Zhu, Z., Blanchard, A., Xu, S.-Y., Guan, S., Wei, H., Zhang, P., Sun, D., Chan, S.-h., International Patent Office, 2009.

<1>MflI
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,PsuI,Tru201I,Uba1432I
<3>R^GATCY
<4>
<5>Microbacterium flavum
<6>IAM 1642
<7>K
<8>Hiraoka, N., Kita, K., Nakajima, H., Obayashi, A., (1984) J. Ferment. Technol., vol. 62, pp. 583-588.

<1>MfoI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Methanobacterium formicicum RC
<6>J.N. Reeve
<7>
<8>Morgan, R., Reeve, J., Krzycki, J., Unpublished observations.

<1>MfoAI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Mycobacterium fortuitum TMC 1529
<6>A.K. Tyagi
<7>
<8>Shankar, S., Tyagi, A.K., (1992) Nucleic Acids Res., vol. 20, pp. 2890.

<1>MglI
<2>
<3>?
<4>
<5>Moraxella glueidi LG1
<6>J. Davies
<7>
<8>Smith, D.I., Blattner, F.R., Davies, J., (1976) Nucleic Acids Res., vol. 3, pp. 343-353.

<1>MglII
<2>
<3>?
<4>
<5>Moraxella glueidi LG2
<6>J. Davies
<7>
<8>Smith, D.I., Blattner, F.R., Davies, J., (1976) Nucleic Acids Res., vol. 3, pp. 343-353.

<1>Mgl14481I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CC^SGG
<4>
<5>Merismopedia glauca 1448-1
<6>A.J. Podhajska
<7>
<8>Waleron, K., Piechula, S., Unpublished observations.

<1>MgoI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Mycobacterium gordonae
<6>A.K. Tyagi
<7>
<8>Shankar, S., Tyagi, A.K., (1993) Gene, vol. 131, pp. 153-154.

<1>MhaI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Micromonospora halophytica
<6>NRRL 3097
<7>
<8>Klein, S., Roberts, R.J., Unpublished observations.

<1>MhaAI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Mycobacterium habana 206
<6>A.K. Tyagi
<7>
<8>Shankar, S., Tyagi, A.K., (1992) Nucleic Acids Res., vol. 20, pp. 2891.

<1>MhlI
<2>SduI,AocII,Bka1125I,BmyI,BsoCI,Bsp1286I,BspLS2I,BstZ15I,HpyF36IV,HpyF47I,Mlu40I,NspII,TseAI,Uba1362I
<3>GDGCH^C
<4>
<5>Micrococcus halobius SD
<6>S.K. Degtyarev
<7>IV
<8>Shapovalova, M.A., Abdurashitov, M.A., Dedkov, V.S., Kashirina, J.G., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>MhoI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Mycoplasma hominis 2297
<6>A. Duarte
<7>
<8>Paquete, C.M.V., Duarte, A., Vitor, J.M.B., Unpublished observations.

<1>Mho2111I
<2>AluI,AluBI,BsaLI,MarI,MltI,OtuI,OtuNI,OxaI,Uba1433I,Uba1441I
<3>AGCT
<4>
<5>Mycoplasma hominis 2111
<6>A. Duarte
<7>
<8>Paquete, C.M.V., Duarte, A., Vitor, J.M.B., Unpublished observations.

<1>Mho2965I
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,MnnIV,NgoEII,SciNI
<3>GCGC
<4>
<5>Mycoplasma hominis 2965
<6>A. Duarte
<7>
<8>Paquete, C.M.V., Duarte, A., Vitor, J.M.B., Unpublished observations.

<1>MisI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Micrococcus species
<6>R.B. Meagher
<7>
<8>Meagher, R.B., Unpublished observations.

<1>MizI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Micromonospora chalcea sp. izumensis
<6>ATCC 21561
<7>
<8>Klein, S., Roberts, R.J., Unpublished observations.

<1>MjaI
<2>MaeI,BfaI,FgoI,FisI,FspBI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Methanocaldococcus jannaschii
<6>H. Escalante
<7>
<8>Bujnicki, J.M., Radlinska, M., (1999) Nucleic Acids Res., vol. 27, pp. 4501-4509.
Morgan, R., Posfai, J., Patti, J., Roberts, R.J., Unpublished observations.
Zerler, B., Myers, P.A., Escalante, H., Roberts, R.J., Unpublished observations.

<1>MjaII
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>?(4)
<5>Methanocaldococcus jannaschii
<6>H. Escalante
<7>
<8>Bult, C.J. et al., (1996) Science, vol. 273, pp. 1058-1073.
Zerler, B., Myers, P.A., Escalante, H., Roberts, R.J., Unpublished observations.

<1>MjaIII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Methanocaldococcus jannaschii
<6>H. Escalante
<7>
<8>Bult, C.J. et al., (1996) Science, vol. 273, pp. 1058-1073.
Morgan, R., Posfai, J., Patti, J., Roberts, R.J., Unpublished observations.

<1>MjaIV
<2>Hpy8I,Hpy166II,HpyBII,HpyF7III,HpyF14II,HpyF46III,HpyF49III,HpyF50I
<3>GTNNAC
<4>
<5>Methanocaldococcus jannaschii
<6>H. Escalante
<7>
<8>Bult, C.J. et al., (1996) Science, vol. 273, pp. 1058-1073.
Morgan, R., Posfai, J., Patti, J., Roberts, R.J., Unpublished observations.

<1>MjaV
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,PabI,PlaAII,RsaNI
<3>GTAC
<4>
<5>Methanocaldococcus jannaschii
<6>H. Escalante
<7>
<8>Bult, C.J. et al., (1996) Science, vol. 273, pp. 1058-1073.
Morgan, R., Posfai, J., Patti, J., Roberts, R.J., Unpublished observations.

<1>MkiI
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Moraxella kingae
<6>ATCC 23331
<7>
<8>Jiang, B.D., Myers, P., Unpublished observations.

<1>MkrI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Micrococcus kristinae
<6>ATCC 27571
<7>
<8>Wickberg, L., Schildkraut, I., Unpublished observations.

<1>MkrAI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Micrococcus kristinae
<6>CAMB 2591
<7>
<8>Mushtaq, R., Riazuddin, S., Unpublished observations.

<1>MlaI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Mastigocladus laminosus
<6>CCAP 1447/1
<7>
<8>Duyvesteyn, M.G.C., de Waard, A., (1980) FEBS Lett., vol. 111, pp. 423-426.

<1>MlaAI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Micromonospora lacustris
<6>NRRL B11050
<7>
<8>Hamablet, L., Meyertons, J.L., Roberts, R.J., Unpublished observations.

<1>MleI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Micrococcus luteus
<6>ATCC 540
<7>
<8>Wickberg, L., Schildkraut, I., Unpublished observations.

<1>MliI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Methanoplanus limicola
<6>K.O. Stetter
<7>
<8>Frey, G., Thomm, M., Frey, B., Schmitz, G.G., Jarsch, M., Kessler, C., Unpublished observations.

<1>MlsI
<2>BalI,Mlu31I,MluNI,MscI,Msp16I,Msp20I
<3>TGG^CCA
<4>
<5>Micrococcus luteus Ng 16-122
<6>A. Janulaitis
<7>F
<8>Vitkute, J., Savelskiene, A., Maneliene, Z., Trinkunaite, L., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>MltI
<2>AluI,AluBI,BsaLI,MarI,Mho2111I,OtuI,OtuNI,OxaI,Uba1433I,Uba1441I
<3>AG^CT
<4>
<5>Micrococcus luteus
<6>ATCC 400
<7>
<8>Christ, C., Wickberg, L., Unpublished observations.
Wickberg, L., Schildkraut, I., Unpublished observations.

<1>MluI
<2>ApeI,Bbi24I,BstZ9I,Uba6I
<3>A^CGCGT
<4>?(4)
<5>Micrococcus luteus
<6>IFO 12992
<7>BFHIJKMNOQRSUVWX
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Stickel, S.K., Roberts, R.J., Unpublished observations.
Sugisaki, H., Kanazawa, S., (1981) Gene, vol. 16, pp. 73-78.

<1>Mlu23I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Micrococcus luteus 23
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>Mlu31I
<2>BalI,MlsI,MluNI,MscI,Msp16I,Msp20I
<3>TGG^CCA
<4>
<5>Micrococcus luteus 31
<6>V.E. Repin
<7>
<8>Serov, G.D., Puchkova, L.I., Kolesnikov, V.A., Repin, V.E., Unpublished observations.

<1>Mlu40I
<2>SduI,AocII,Bka1125I,BmyI,BsoCI,Bsp1286I,BspLS2I,BstZ15I,HpyF36IV,HpyF47I,MhlI,NspII,TseAI,Uba1362I
<3>GDGCHC
<4>
<5>Micrococcus luteus 40
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Mlu1106I
<2>PpuMI,Pfl27I,PpuXI,Psp5II,PspPPI
<3>RGGWCCY
<4>
<5>Micrococcus luteus RFL1106
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Maneliene, Z., Capskaya, L., Kiuduliene, L., Butkus, V., Unpublished observations.

<1>Mlu2300I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Micrococcus luteus 2300
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>Mlu9273I
<2>NruI,AmaSI,Bsp68I,BtuMI,MluB2I,PspDI,RruI,SalDI,Sbo13I,Sna3286I,SpoI,Uba1117I,Uba1386I,VchO70I
<3>TCGCGA
<4>
<5>Micrococcus luteus
<6>ATCC 9273
<7>
<8>Nelson, M., Unpublished observations.

<1>Mlu9273II
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Micrococcus luteus
<6>ATCC 9273
<7>
<8>Nelson, M., Unpublished observations.

<1>MluB2I
<2>NruI,AmaSI,Bsp68I,BtuMI,Mlu9273I,PspDI,RruI,SalDI,Sbo13I,Sna3286I,SpoI,Uba1117I,Uba1386I,VchO70I
<3>TCG^CGA
<4>
<5>Micrococcus luteus B2
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>MluCI
<2>TspEI,Sse9I,TasI,TseCI,Tsp509I
<3>AATT
<4>
<5>Micrococcus luteus
<6>NEB 1223
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>MluNI
<2>BalI,MlsI,Mlu31I,MscI,Msp16I,Msp20I
<3>TGG^CCA
<4>
<5>Micrococcus luteus N
<6>S.K. Degtyarev
<7>M
<8>Degtyarev, S.K., Unpublished observations.

<1>MlyI
<2>PleI,BsmEI,BspD6I,PpsI,SchI
<3>GAGTC(5/5)
<4>2(6)
<5>Micrococcus lylae
<6>NBL 2048
<7>N
<8>Eastlake, P., Unpublished observations.
Kong, H., Unpublished observations.
Kong, H., Higgins, L.S., US Patent Office, 2002.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>Mly113I
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,McaAI,MchI,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GG^CGCC
<4>
<5>Micrococcus lylae 113
<6>S.K. Degtyarev
<7>I
<8>Dedkov, V.S., Zernov, Y.P., Rechkunova, N.I., Degtyarev, S.Kh., (1990) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 17-18.

<1>MmaI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Methanococcus maripaludis JJ
<6>D. Boone
<7>
<8>Tumbula, D.L., Makula, R.A., Whitman, W.B., (1994) FEMS Microbiol. Lett., vol. 121, pp. 309-314.

<1>MmeI
<2>
<3>TCCRAC(20/18)
<4>5(6)
<5>Methylophilus methylotrophus
<6>W.J. Brammar
<7>NX
<8>Boyd, A.C., Charles, I.G., Keyte, J.W., Brammar, W.J., (1986) Nucleic Acids Res., vol. 14, pp. 5255-5274.
Morgan, R.D., Unpublished observations.
Tucholski, J., Zmijewski, J.W., Podhajska, A.J., (1998) Gene, vol. 223, pp. 293-302.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>MmeII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Methylophilus methylotrophus
<6>W.J. Brammar
<7>
<8>Bhatia, T., Morgan, R.D., Unpublished observations.
Boyd, A.C., Charles, I.G., Keyte, J.W., Brammar, W.J., (1986) Nucleic Acids Res., vol. 14, pp. 5255-5274.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>Mmu5I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>4(5)
<5>Mitsuokella multiacida 46/5
<6>P. Pristas
<7>
<8>Piknova, M., Filova, M., Javorsky, P., Pristas, P., (2004) FEMS Microbiol. Lett., vol. 236, pp. 91-95.
Piknova, M., Filova, M., Javorsky, P., Pristas, P., (2005) Mol. Biol. Rep., vol. 32, pp. 281-284.

<1>M.MmuDnmt1
<2>
<3>?
<4>?(5)
<5>Mus musculus
<6>T. Bestor
<7>
<8>Aguirre-Arteta, A.M., Grunewald, I., Cardoso, M.C., Leonhardt, H., (2000) Cell Growth Differ., vol. 11, pp. 551-559.
Bestor, T., Laudano, A., Mattaliano, R., Ingram, V., (1988) J. Mol. Biol., vol. 203, pp. 971-983.
Bestor, T.H., (1988) Gene, vol. 74, pp. 9-12.
Margot, J.B., Aguirre-Arteta, A.M., Di Giacco, B.V., Pradhan, S., Roberts, R.J., Cardoso, M.C., Leonhardt, H., (2000) J. Mol. Biol., vol. 297, pp. 293-300.
Mertineit, C., Yoder, J.A., Taketo, T., Laird, D.W., Trasler, J.M., Bestor, T.H., (1998) Development, vol. 125, pp. 889-897.
Yoder, J.A., Yen, R.-W.C., Vertino, P.M., Bestor, T.H., Baylin, S.B., (1996) J. Biol. Chem., vol. 271, pp. 31092-31097.

<1>M.MmuDnmt3A
<2>
<3>?
<4>?(5)
<5>Mus musculus
<6>T. Bestor
<7>
<8>Chen, T., Ueda, Y., Xie, S., Li, E., (2002) J. Biol. Chem., vol. 277, pp. 38746-38754.
Hayashizaki, Y., Unpublished observations.
Li, E., Okano, M., Xie, S., US Patent Office, 2008.
Li, E., Okano, M., Xie, S., Chen, T., US Patent Office, 2008.
Okano, M., Xie, S., Li, E., (1998) Nat. Genet., vol. 19, pp. 219-220.
Strausberg, R.L. et al., (2002) Proc. Natl. Acad. Sci. U. S. A., vol. 99, pp. 16899-16903.

<1>M.MmuDnmt3B
<2>
<3>?
<4>?(5)
<5>Mus musculus
<6>T. Bestor
<7>
<8>Chen, T., Ueda, Y., Xie, S., Li, E., (2002) J. Biol. Chem., vol. 277, pp. 38746-38754.
Li, E., Okano, M., Xie, S., US Patent Office, 2008.
Li, E., Okano, M., Xie, S., Chen, T., US Patent Office, 2008.
Okano, M., Xie, S., Li, E., (1998) Nat. Genet., vol. 19, pp. 219-220.
Yin, B., Chen, Y.T., Zhu, M., Luo, Y.J., Zhu, N., Xu, S.C., Wu, G.Y., Shen, Y., Unpublished observations.

<1>M.MmuDnmt3L
<2>
<3>?
<4>
<5>Mus musculus
<6>T. Bestor
<7>
<8>Jia, D., Jurkowska, R.Z., Zhang, X., Jeltsch, A., Cheng, X., (2007) Nature, vol. 449, pp. 248-251.

<1>MmuP2I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Mitsuokella multiacida 4P208-58
<6>P. Pristas
<7>
<8>Piknova, M., Filova, M., Javorsky, P., Pristas, P., (2004) FEMS Microbiol. Lett., vol. 236, pp. 91-95.

<1>MniI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Moraxella nonliquefaciens
<6>ATCC 19966
<7>
<8>Jiang, B.D., Myers, P., Unpublished observations.

<1>MniII
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Moraxella nonliquefaciens
<6>ATCC 19966
<7>
<8>Jiang, B.D., Myers, P., Unpublished observations.

<1>MnlI
<2>Hpy166III
<3>CCTC(7/6)
<4>1(5)
<5>Moraxella nonliquefaciens
<6>ATCC 17953
<7>FINQVWX
<8>Brinkley, P., Bautista, D.S., Graham, F.L., (1991) Gene, vol. 100, pp. 267-268.
Harasimowicz-Slowinska, R.I., Skowron, P.M., Unpublished observations.
Kriukiene, E., Lubiene, J., Lagunavicius, A., Lubys, A., (2005) Biochim. Biophys. Acta, vol. 1751, pp. 194-204.
Schildkraut, I., Unpublished observations.
Vitkute, J., Stankevicius, K., Tamulaitiene, G., Maneliene, Z., Timinskas, A., Berg, D.E., Janulaitis, A., (2001) J. Bacteriol., vol. 183, pp. 443-450.
Zabeau, M., Greene, R., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>MnnI
<2>HindII,ChuEII,Hin1160II,Hin1161II,HinJCI,HincII
<3>GTYRAC
<4>
<5>Moraxella nonliquefaciens
<6>ATCC 17954
<7>
<8>Hanberg, F., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>MnnII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Moraxella nonliquefaciens
<6>ATCC 17954
<7>
<8>Hanberg, F., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>MnnIII
<2>
<3>?
<4>
<5>Moraxella nonliquefaciens
<6>ATCC 17954
<7>
<8>Hanberg, F., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>MnnIV
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,NgoEII,SciNI
<3>GCGC
<4>
<5>Moraxella nonliquefaciens
<6>ATCC 17954
<7>
<8>Hanberg, F., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>MnoI
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>C^CGG
<4>
<5>Moraxella nonliquefaciens
<6>ATCC 19975
<7>
<8>Baumstark, B.R., Roberts, R.J., RajBhandary, U.L., (1979) J. Biol. Chem., vol. 254, pp. 8943-8950.
Myers, P.A., Roberts, R.J., Unpublished observations.

<1>MnoII
<2>
<3>?
<4>
<5>Moraxella nonliquefaciens
<6>ATCC 19975
<7>
<8>Myers, P.A., Roberts, R.J., Unpublished observations.

<1>MnoIII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Moraxella nonliquefaciens
<6>ATCC 19975
<7>
<8>Myers, P.A., Roberts, R.J., Unpublished observations.

<1>MosI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Moraxella osloensis
<6>ATCC 19976
<7>
<8>Gelinas, R.E., Myers, P.A., Roberts, R.J., (1977) J. Mol. Biol., vol. 114, pp. 169-179.

<1>MphI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Moraxella phenylpyruvica
<6>ATCC 17955
<7>
<8>Jiang, B.D., Myers, P., Unpublished observations.

<1>Mph1103I
<2>AvaIII,Asi372I,BfrBI,BfrCI,Csp68KIII,EcoT22I,NsiI,PinBI,Ppu10I,PxyJKI,SepI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>ATGCA^T
<4>
<5>Moraxella phenylpyruvica RFL1103
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Petrusyte, M., Maneliene, Z., Capskaya, L., Kiuduliene, L., Butkus, V., Unpublished observations.

<1>Mph1103II
<2>DpnI,CfuI,FtnUIV,MalI,NanII,NgoDXIV,NmeAII,NmeBL859I,NmuDI,NmuEI,NsuDI,TdeI
<3>GATC
<4>
<5>Moraxella phenylpyruvica RFL1103
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Maneliene, Z., Capskaya, L., Kiuduliene, L., Butkus, V., Unpublished observations.

<1>Mpr154I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Marinomonas protea strain 154, SIDMSP4c8
<6>A. Murray
<7>
<8>Miller, J., Murray, A., Bhatia, T., Morgan, R.D., Unpublished observations.

<1>MpsI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Micrococcus psychrophilum 16DMSP20c1
<6>A. Murray
<7>
<8>Miller, J., Murray, A., Bhatia, T., Morgan, R.D., Unpublished observations.

<1>MpuI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Micromonospora purpurea
<6>ATCC 15835
<7>
<8>Meyertons, J.L., Tilley, B.C., Lechevalier, M.P., Lechevalier, H.A., (1987) J. Ind. Microbiol., vol. 2, pp. 293-303.

<1>MpuCI
<2>
<3>?
<4>
<5>Mycoplasma pulmonis UAB CTIP
<6>M. Davidson
<7>
<8>Dybvig, K., Cao, Z., French, C.T., Yu, H., (2007) J. Bacteriol., vol. 189, pp. 2197-2202.

<1>MpuUI
<2>
<3>?
<4>
<5>Mycoplasma pulmonis UAB 6510
<6>K. Dybvig
<7>
<8>Dybvig, K., Yu, H., (1994) Mol. Microbiol., vol. 12, pp. 547-560.

<1>MraI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Micrococcus radiodurans
<6>ATCC 13939
<7>
<8>Wani, A.A., Stephens, R.E., D'Ambrosio, S.M., Hart, R.W., (1982) Biochim. Biophys. Acta, vol. 697, pp. 178-184.

<1>MreI
<2>Sse232I
<3>CG^CCGGCG
<4>
<5>Micromonospora rhodorangea RFL1
<6>Fermentas G296
<7>F
<8>Maneliene, Z., Lubys, A., Unpublished observations.
Vitkute, J., Slyziute, J., Maneliene, Z., Norgeliene, D., Trinkunaite, L., Janulaitis, A., Unpublished observations.

<1>MrhI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Micromonospora rhodorangea
<6>NRRL 5326
<7>
<8>Hamablet, L., Meyertons, J.L., Roberts, R.J., Unpublished observations.

<1>MroI
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>
<5>Micrococcus roseus
<6>F. Kato
<7>MO
<8>Kato, F., Suetake, T., Murata, A., Mukai, T., Ueki, H., Japanese Patent Office, 1988.

<1>MroNI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>G^CCGGC
<4>
<5>Micrococcus roseus N
<6>S.K. Degtyarev
<7>IV
<8>Dedkov, V.S., Belichenko, O.A., Prikhodko, E.A., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>MroXI
<2>XmnI,Asp700I,BbvAI,PdmI,Psc2I,SynII
<3>GAANN^NNTTC
<4>
<5>Micrococcus roseus XM
<6>S.K. Degtyarev
<7>IV
<8>Abdurashitov, M.A., Bondar, T.S., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>MsaI
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,McaAI,MchI,Mly113I,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GGCGCC
<4>
<5>Micromonospora saitamica
<6>NRRL B16084
<7>
<8>Klein, S., Roberts, R.J., Unpublished observations.

<1>MscI
<2>BalI,MlsI,Mlu31I,MluNI,Msp16I,Msp20I
<3>TGG^CCA
<4>
<5>Micrococcus species
<6>NEB 502
<7>BNO
<8>Meda, M.M., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Polisson, C., (1989) Nucleic Acids Res., vol. 17, pp. 5858.

<1>MscAI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Micromonospora scalabitana sp sporogenes
<6>NRRL B16086
<7>
<8>Klein, S., Roberts, R.J., Unpublished observations.

<1>MseI
<2>SaqAI,Tru1I,Tru9I
<3>T^TAA
<4>4(6)
<5>Micrococcus species
<6>NEB 446
<7>BN
<8>Morgan, R.D., Unpublished observations.
Morgan, R.D., (1988) Nucleic Acids Res., vol. 16, pp. 3104.
Vaisvila, R., Kucera, R.B., Raleigh, E.A., Morgan, R.D., Claus, T.E., Unpublished observations.
Vaisvila, R., Kucera, R.B., Raleigh, E.A., Morgan, R.D., Claus, T.E., European Patent Office, 2001.
Vaisvila, R., Morgan, R.D., Kucera, R.B., Claus, T.E., Raleigh, E.A., Unpublished observations.

<1>MsiI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Myxococcus stipitatus Mxs2
<6>H. Reichenbach
<7>
<8>Middleton, J.H., Stankus, P.V., Edgell, M.H., Hutchison, C.A. III, Unpublished observations.
Myers, P.A., Roberts, R.J., Unpublished observations.

<1>MsiII
<2>
<3>?
<4>
<5>Myxococcus stipitatus Mxs2
<6>H. Reichenbach
<7>
<8>Mayer, H., Schutte, H., Unpublished observations.

<1>MslI
<2>RseI,SmiMI
<3>CAYNN^NNRTG
<4>
<5>Moraxella osloensis
<6>NEB 722
<7>N
<8>Morgan, R.D., Unpublished observations.
Qiang, B.-Q., Wu, S., Kong, H., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>MspI
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>C^CGG
<4>1(5)
<5>Moraxella species
<6>ATCC 49670
<7>FHIJKMNOQRSUVWXY
<8>Butkus, V., Petrauskiene, L., Maneliene, Z., Klimasauskas, S., Laucys, V., Janulaitis, A., (1987) Nucleic Acids Res., vol. 15, pp. 7091-7102.
Hornby, D.P.J., Matin, M.M., International Patent Office, 2001.
Jentsch, S., Gunthert, U., Trautner, T.A., (1981) Nucleic Acids Res., vol. 9, pp. 2753-2759.
Matin, M.M., Hornby, D.P., (2000) Anal. Biochem., vol. 278, pp. 46-51.
Schildkraut, I., Greenough, L., Unpublished observations.
Van Montagu, M., Sciaky, D., Myers, P.A., Roberts, R.J., Unpublished observations.
Walder, R.Y., Langtimm, C.J., Catterjee, R., Walder, J.A., (1983) J. Biol. Chem., vol. 258, pp. 1235-1241.

<1>Msp11I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Micrococcus species 11
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Msp16I
<2>BalI,MlsI,Mlu31I,MluNI,MscI,Msp20I
<3>TGGCCA
<4>
<5>Micrococcus species 16
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Msp17I
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,NlaSII,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>
<5>Micrococcus species 17
<6>S.K. Degtyarev
<7>
<8>Madina, T.A., Rechkunova, N.I., Repin, V.E., Degtyarev, S.K., Unpublished observations.

<1>Msp20I
<2>BalI,MlsI,Mlu31I,MluNI,MscI,Msp16I
<3>TGG^CCA
<4>
<5>Micrococcus species
<6>S.K. Degtyarev
<7>IV
<8>Chernov, A.P., Belichenko, O.A., Rechkunova, N.I., Andreeva, I.S., Repin, V.E., Degtyarev, S.K., Russian Patent Office, 1993.

<1>Msp23I
<2>XbaI,BspAAII,BspLU11II,BsrXI
<3>TCTAGA
<4>
<5>Micrococcus species 23
<6>V.E. Repin
<7>
<8>Repin, V.E., Andreeva, I.S., Puchkova, L.I., Unpublished observations.

<1>Msp23II
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Micrococcus species 23
<6>V.E. Repin
<7>
<8>Repin, V.E., Andreeva, I.S., Puchkova, L.I., Unpublished observations.

<1>Msp24I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Moraxella species 24
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>Msp67I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CC^NGG
<4>
<5>Moraxella species MS67
<6>M. Sargent
<7>
<8>Walker, J.N.B., Dean, P.G., Saunders, J.R., Unpublished observations.

<1>Msp67II
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Moraxella species MS67
<6>M. Sargent
<7>
<8>Walker, J.N.B., Dean, P.G., Saunders, J.R., Unpublished observations.

<1>Msp130I
<2>
<3>?
<4>
<5>Microcystis species 130
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Msp199I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Microcystis species 199
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>MspAI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Methanobacterium species BR10
<6>J.N. Reeve
<7>
<8>Morgan, R., Reeve, J., Krzycki, J., Unpublished observations.

<1>MspA1I
<2>NspBII
<3>CMG^CKG
<4>?(4)
<5>Moraxella species A1
<6>S.K. Degtyarev
<7>INRV
<8>Degtyarev, S.K., Unpublished observations.
Xu, S.-Y., Unpublished observations.

<1>MspBI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Methanobrevibacter species MMY
<6>J.N. Reeve
<7>
<8>Morgan, R., Reeve, J., Krzycki, J., Unpublished observations.

<1>MspB4I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,PfaAI,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>G^GYRCC
<4>
<5>Moraxella species B4
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Zernov, Y.P., Rechkunova, N.I., Degtyarev, S.Kh., (1990) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 17-18.

<1>MspB6I
<2>
<3>?
<4>
<5>Moraxella species B6
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Zernov, Y.P., Rechkunova, N.I., Degtyarev, S.Kh., (1990) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 17-18.

<1>MspCI
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>C^TTAAG
<4>
<5>Micrococcus species
<6>V. Bouriotis
<7>C
<8>Rina, M., Tzanodaskalaki, M., Karagouni, A., Pagomenou, M., Bouriotis, V., (1992) Nucleic Acids Res., vol. 20, pp. 1806.

<1>MspJI
<2>
<3>?
<4>
<5>Mycobacterium sp. JLS
<6>C. Miller
<7>
<8>Xu, D., Zheng, Y., Unpublished observations.

<1>MspR9I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CC^NGG
<4>
<5>Micrococcus species R9
<6>S.K. Degtyarev
<7>I
<8>Repin, V.E., Andreeva, I.S., Kileva, E.V., Shevchenko, A.V., Abdurashitov, M.A., Repin, M.V., Degtyarev, S.Kh., (1997) Prikl. Biokhim. Mikrobiol., vol. 33, pp. 284-286.

<1>MspSWI
<2>SwaI,BstRZ246I,BstSWI,SmiI
<3>ATTT^AAAT
<4>
<5>Moraxella species SW
<6>S.K. Degtyarev
<7>
<8>Abdurashitov, M.A., Dedkov, V.S., Bondar, T.S., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>MspV281I
<2>HgiAI,Alw21I,AspHI,Bbv12I,Bfu1570I,BsaGI,Bsh45I,BsiHKAI,Bsm6I,BsmPI,Hpy8III,HpyF7II,HpyF46II,Pph3215I
<3>GWGCW^C
<4>
<5>Myxosarcinia sp V/281
<6>A.J. Podhajska
<7>
<8>Waleron, K., Piechula, S., Unpublished observations.

<1>MspYI
<2>BsaAI,BstBAI,Ppu6I,Ppu11I,Ppu21I,PsuAI
<3>YAC^GTR
<4>
<5>Microcystis species J2
<6>U. Mayr
<7>
<8>Frey, B., Unpublished observations.

<1>MssI
<2>PmeI
<3>GTTT^AAAC
<4>
<5>Methylobacterium species Dd 5-732
<6>V. Butkus
<7>F
<8>Vitkute, J., Zutautiene, D., Maneliene, Z., Norgeliene, D., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>MstI
<2>AcaIII,Acc16I,AosI,ApcTR183I,AviII,Bco6I,BsaTI,ClcII,CliII,FdiII,FspI,GspAII,NsbI,NspHIII,NspLI,NspMI,PamI,Pun14627I
<3>TGC^GCA
<4>
<5>Microcoleus species
<6>D.G. Comb
<7>
<8>Comb, D.G., Schildkraut, I., Roberts, R.J., Unpublished observations.
Gingeras, T.R., Milazzo, J.P., Roberts, R.J., (1978) Nucleic Acids Res., vol. 5, pp. 4105-4127.

<1>MstII
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CC^TNAGG
<4>
<5>Microcoleus species
<6>D.G. Comb
<7>
<8>Schildkraut, I., Unpublished observations.

<1>MthI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Microbacterium thermosphactum
<6>ATCC 11509
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>Mth1047I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Microbacterium thermosphactum 1047
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>MthAI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Methanobacterium thermoautotrophicum strain Winter
<6>J.N. Reeve
<7>
<8>Morgan, R., Reeve, J., Krzycki, J., Unpublished observations.

<1>MthBI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Methanobacterium thermoautotrophicum
<6>K.O. Stetter
<7>
<8>Thomm, M., Unpublished observations.

<1>MthFI
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Methanobacterium thermoformicicum FTF
<6>DSM 3012
<7>
<8>Nolling, J., de Vos, W.M., (1992) Nucleic Acids Res., vol. 20, pp. 5047-5052.

<1>MthTI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>3(5)
<5>Methanobacterium thermoformicicum THF
<6>DSM 3848
<7>
<8>Nolling, J., de Vos, W.M., (1992) J. Bacteriol., vol. 174, pp. 5719-5726.

<1>MthZI
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>C^TAG
<4>1(4)
<5>Methanobacterium thermoformicicum Z-245
<6>DSM 3720
<7>
<8>Nolling, J., de Vos, W.M., (1992) Nucleic Acids Res., vol. 20, pp. 5047-5052.

<1>MunI
<2>MfeI
<3>C^AATTG
<4>3(6)
<5>Mycoplasma species
<6>A. Janulaitis
<7>FKM
<8>Stakenas, P.S., Zaretskaya, N.M., Maneliene, Z.P., Mauricas, M.M., Butkus, V.V., Yanulaitis, A.A., (1992) Mol. Biol. (Mosk), vol. 26, pp. 546-557.

<1>MvaI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>2(4)
<5>Micrococcus varians RFL19
<6>A. Janulaitis
<7>FKMOSW
<8>Butkus, V., Klimasauskas, S., Kersulyte, D., Vaitkevicius, D., Lebionka, A., Janulaitis, A., (1985) Nucleic Acids Res., vol. 13, pp. 5727-5746.
Klimasauskas, S., Timinskas, A., Menkevicius, S., Butkiene, D., Butkus, V., Janulaitis, A., (1989) Nucleic Acids Res., vol. 17, pp. 9823-9832.
Lubys, A., Vaisvila, R., Janulaitis, A., Unpublished observations.
Sheflyan, G.Y., Tashlitskii, V.N., Kubareva, E.A., (1993) Vestn. Mosk. Univ., vol. 34, pp. 516-520.
Sheflyan, G.Ya., Kubareva, E.A., Gromova, E.S., Shabarova, Z.A., (1993) Biokhimiia, vol. 58, pp. 1806-1811.

<1>Mva16I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Micrococcus varians VKPM B-5942
<6>V.E. Repin
<7>
<8>Repin, V.E., Serov, G.D., Shcheglova, I.K., Russian Patent Office, 1994.

<1>Mva1269I
<2>BsmI,Asp26HI,Asp27HI,Asp35HI,Asp36HI,Asp40HI,Asp50HI,BmaHI,BsaMI,BscCI,PctI,Uba1382I,Uba1415I
<3>GAATGC(1/-1)
<4>
<5>Micrococcus varians RFL1269
<6>A. Janulaitis
<7>F
<8>Armalyte, E., Bujnicki, J.M., Giedriene, J., Gasiunas, G., Kosinski, J., Lubys, A., (2005) J. Biol. Chem., vol. 280, pp. 41584-41594.
Dauksaite, V., Janulaitis, A., Unpublished observations.
Janulaitis, A., Dauksaite, V., Maneliene, Z., Kiuduliene, L., Bitinaite, J., Butkus, V., Unpublished observations.

<1>MvaAI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Methanobacterium vannuli
<6>J.N. Reeve
<7>
<8>Morgan, R., Reeve, J., Krzycki, J., Unpublished observations.

<1>MviI
<2>
<3>?
<4>
<5>Myxococcus virescens V-2
<6>H. Reichenbach
<7>
<8>Morris, D.W., Parish, J.H., (1976) Arch. Microbiol., vol. 108, pp. 227-230.

<1>MviII
<2>
<3>?
<4>
<5>Myxococcus virescens V-2
<6>H. Reichenbach
<7>
<8>Morris, D.W., Parish, J.H., (1976) Arch. Microbiol., vol. 108, pp. 227-230.

<1>MvnI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>
<5>Methanococcus vannielii
<6>M. Thomm
<7>M
<8>Thomm, M., Frey, G., Bolton, B.J., Laue, F., Kessler, C., Stetter, K.O., (1988) FEMS Microbiol. Lett., vol. 52, pp. 229-234.

<1>MvrI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGAT^CG
<4>
<5>Micrococcus varians
<6>P. Babu
<7>U
<8>Shroff, D., Damodaran, B., Shankar, A., Chandrashekaran, S., Babu, J., Unpublished observations.

<1>MvsI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Methylovarius species
<6>IMV 3017
<7>
<8>Romanovskaya, V.A., Alexeyev, M.F., Gunkovskaya, N.V., Stolyar, S.M., Shatohina, E.S., Malashenko, Y.R., (1992) Mikrobiol. Zh., vol. 54, pp. 32-39.

<1>MvsAI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Methylovarius species
<6>IMV 3019
<7>
<8>Romanovskaya, V.A., Alexeyev, M.F., Gunkovskaya, N.V., Stolyar, S.M., Shatohina, E.S., Malashenko, Y.R., (1992) Mikrobiol. Zh., vol. 54, pp. 32-39.

<1>MvsBI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Methylovarius species
<6>IMV 3027
<7>
<8>Romanovskaya, V.A., Alexeyev, M.F., Gunkovskaya, N.V., Stolyar, S.M., Shatohina, E.S., Malashenko, Y.R., (1992) Mikrobiol. Zh., vol. 54, pp. 32-39.

<1>MvsCI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Methylovarius species
<6>IMV 3112
<7>
<8>Romanovskaya, V.A., Alexeyev, M.F., Gunkovskaya, N.V., Stolyar, S.M., Shatohina, E.S., Malashenko, Y.R., (1992) Mikrobiol. Zh., vol. 54, pp. 32-39.

<1>MvsDI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Methylovarius species
<6>IMV 3226
<7>
<8>Romanovskaya, V.A., Alexeyev, M.F., Gunkovskaya, N.V., Stolyar, S.M., Shatohina, E.S., Malashenko, Y.R., (1992) Mikrobiol. Zh., vol. 54, pp. 32-39.

<1>MvsEI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Methylovarius species
<6>IMV 3100
<7>
<8>Romanovskaya, V.A., Alexeyev, M.F., Gunkovskaya, N.V., Stolyar, S.M., Shatohina, E.S., Malashenko, Y.R., (1992) Mikrobiol. Zh., vol. 54, pp. 32-39.

<1>MwhI
<2>HpaI,BsaKI,BseII,BstEZ359I,BstHPI,KspAI,SsrI,Uba1408II
<3>GTTAAC
<4>
<5>Methylococcus whittenburyi
<6>IMV 3033
<7>
<8>Alexeyev, M.F., Gunkovskaya, N.V., Romanovskaya, V.A., Malashenko, Y.R., (1992) Mikrobiol. Zh., vol. 54, pp. 70-73.

<1>MwoI
<2>Bce4I,Bce1247I,BceCI,BspWI,BstMWI,HpyF10VI
<3>GCNNNNN^NNGC
<4>?(4)
<5>Methanobacterium wolfei
<6>DSM 2970
<7>N
<8>Lunnen, K.D., Morgan, R.D., Timan, C.J., Krzycki, J.A., Reeve, J.N., Wilson, G.G., (1989) Gene, vol. 77, pp. 11-19.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
Lunnen, K.D., Wilson, G.G., European Patent Office, 1995.
Lunnen, K.D., Wilson, G.G., US Patent Office, 1991.

<1>MxaI
<2>SacI,BpuAmI,Ecl136II,Ecl137I,EcoICRI,Eco53kI,NasSI,Pfl18I,Psp124BI,ScoI,Ssm4I,Ssm5I,SstI
<3>GAG^CTC
<4>
<5>Myxococcus xanthus F18E
<6>K. Izaki
<7>
<8>Nomura, Y., Kotani, H., Kita, K., Sadaoka, A., Hiraoka, N., Nakamura, T., Abe, N., Izaki, K., (1990) Agric. Biol. Chem., vol. 54, pp. 3011-3012.

<1>MziI
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAGCTG
<4>
<5>Micromonospora zionensis
<6>H. Lechevalier
<7>
<8>Meyertons, J.L., Tilley, B.C., Lechevalier, M.P., Lechevalier, H.A., (1987) J. Ind. Microbiol., vol. 2, pp. 293-303.

<1>NaeI
<2>Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCC^GGC
<4>?(5)
<5>Nocardia aerocolonigenes
<6>ATCC 23870
<7>CKMNORU
<8>Guthrie, E.P., Van Cott, E.M., Taron, C.H., European Patent Office, 1997.
Guthrie, E.P., Van Cott, E.M., Taron, C.H., US Patent Office, 1994.
Lunnen, K.D., Barsomian, J.M., Camp, R.R., Card, C.O., Chen, S.-Z., Croft, R., Looney, M.C., Meda, M.M., Moran, L.S., Nwankwo, D.O., Slatko, B.E., Van Cott, E.M., Wilson, G.G., (1988) Gene, vol. 74, pp. 25-32.
Taron, C.H., Van Cott, E.M., Wilson, G.G., Moran, L.S., Slatko, B.E., Hornstra, L.J., Benner, J.S., Kucera, R.B., Guthrie, E.P., (1995) Gene, vol. 155, pp. 19-25.

<1>NamI
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GGCGCC
<4>
<5>Nocardia amarae
<6>ATCC 27809
<7>
<8>Lin, P.-M., Roberts, R.J., Unpublished observations.

<1>NanI
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Neisseria animalis
<6>ATCC 19573
<7>
<8>Dingman, C., Schildkraut, I., Unpublished observations.

<1>NanII
<2>DpnI,CfuI,FtnUIV,MalI,Mph1103II,NgoDXIV,NmeAII,NmeBL859I,NmuDI,NmuEI,NsuDI,TdeI
<3>GATC
<4>
<5>Neisseria animalis
<6>ATCC 19573
<7>
<8>Dingman, C., Schildkraut, I., Unpublished observations.

<1>NarI
<2>BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GG^CGCC
<4>
<5>Nocardia argentinensis
<6>ATCC 31306
<7>JMNOQRUWX
<8>Comb, D.G., Wilson, G., Schildkraut, I., Greenough, L., Unpublished observations.
Zhu, Z., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>NasI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Nocardia asteroides
<6>ATCC 7372
<7>
<8>Stote, R., Schildkraut, I., Unpublished observations.

<1>NasBI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Nocardia asteroides
<6>ATCC 9970
<7>
<8>Wickberg, L., Schildkraut, I., Unpublished observations.

<1>NasSI
<2>SacI,BpuAmI,Ecl136II,Ecl137I,EcoICRI,Eco53kI,MxaI,Pfl18I,Psp124BI,ScoI,Ssm4I,Ssm5I,SstI
<3>GAGCTC
<4>
<5>Nocardia asteroides
<6>ATCC 9969
<7>
<8>Stote, R., Schildkraut, I., Unpublished observations.

<1>NasWI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Nocardia asteroides
<6>ATCC 14759
<7>
<8>Wickberg, L., Schildkraut, I., Unpublished observations.

<1>NbaI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Nocardia brasiliensis
<6>ATCC 19296
<7>
<8>Qiang, B.-Q., Schildkraut, I., Unpublished observations.

<1>NblI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGAT^CG
<4>
<5>Nocardia blackwellii
<6>ATCC 6846
<7>
<8>Schildkraut, I., Unpublished observations.

<1>NbrI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Nocardia brasiliensis
<6>ATCC 27936
<7>
<8>Qiang, B.-Q., Schildkraut, I., Unpublished observations.

<1>NcaI
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NovII,NsiHI,SscL1I
<3>GANTC
<4>
<5>Neisseria caviae
<6>NRCC 31003
<7>
<8>Visentin, L.P., Watson, R.J., Martin, S., Zuker, M., Unpublished observations.

<1>NciI
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CC^SGG
<4>
<5>Neisseria cinerea
<6>NRCC 31006
<7>JNORW
<8>Korch, C., Hagblom, P., (1986) Eur. J. Biochem., vol. 161, pp. 519-524.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
Meehan, R.R., Ulrich, E., Bird, A.P., (1993) Nucleic Acids Res., vol. 21, pp. 5517-5518.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Watson, R., Zuker, M., Martin, S.M., Visentin, L.P., (1980) FEBS Lett., vol. 118, pp. 47-50.

<1>NciAI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Neisseria cinerea 32615
<6>A. Piekarowicz
<7>
<8>Piekarowicz, A., (1994) Acta Microbiol. Pol., vol. 43, pp. 103-105.

<1>NcoI
<2>AteI,Bse19I,Bsp19I,NspSAIII
<3>C^CATGG
<4>?(4)
<5>Nocardia corallina
<6>ATCC 19070
<7>BCFHJKMNOQRSUWXY
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.
VanCott, E.M., European Patent Office, 1995.
VanCott, E.M., US Patent Office, 1993.
Zhang, B.-H., Van Cott, E.M., Wilson, G.G., Unpublished observations.

<1>NcrI
<2>BglII,BseB631II,NspMACI,Pae2kI,Pae18kI
<3>A^GATCT
<4>
<5>Nocardia carnea C-212
<6>Y. Li
<7>
<8>Li, Y., Fu, P., Shi, L.-Y., (1990) Chinese Biochem. J., vol. 6, pp. 309-313.

<1>M.NcrNI
<2>
<3>?
<4>?(5)
<5>Neurospora crassa N
<6>E.U. Selker
<7>
<8>Kouzminova, E., Selker, E.U., (2001) EMBO J., vol. 20, pp. 4309-4323.

<1>M.NcrNII
<2>
<3>?
<4>?(5)
<5>Neurospora crassa N
<6>E.U. Selker
<7>
<8>Freitag, M., Williams, R.L., Kothe, G.O., Selker, E.U., (2002) Proc. Natl. Acad. Sci. U. S. A., vol. 99, pp. 8802-8807.
Schulte, U., Aign, V., Hoheisel, J., Brandt, P., Fartmann, B., Holland, R., Nyakatura, G., Mewes, H.W., Mannhaupt, G., Unpublished observations.

<1>NcuI
<2>MboII,HpyII,Hpy178II,HpyAII,TceI
<3>GAAGA(8/7)
<4>5(6)
<5>Neisseria cuniculi
<6>ATCC 14688
<7>
<8>Camp, R., Schildkraut, I., Unpublished observations.
Furmanek, B., Gromek, K., Sektas, M., Kaczorowski, T., (2001) FEMS Microbiol. Lett., vol. 196, pp. 171-176.
Furmanek, B., Kaczorowski, T., Unpublished observations.
Furmanek, B., Sektas, M., Wons, E., Kaczorowski, T., (2007) Res. Microbiol., vol. 158, pp. 164-174.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>NcuII
<2>Sth132I
<3>CCCG
<4>
<5>Neisseria cuniculi
<6>ATCC 14688
<7>
<8>Walsh, P., Unpublished observations.

<1>NdaI
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NunII,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GG^CGCC
<4>
<5>Nocardia dassonvillei
<6>ATCC 21944
<7>
<8>Comb, D.G., Hess, E.J., Wilson, G., Unpublished observations.

<1>NdeI
<2>FauNDI,PfaAII,TrsKTIII
<3>CA^TATG
<4>?(6)
<5>Neisseria denitrificans
<6>NRCC 31009
<7>BFJKMNQRSWXY
<8>Benner, J.S., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Silber, K.R., Polisson, C., Rees, P.A., Benner, J.S., (1988) Gene, vol. 74, pp. 43-44.
Stickel, S.K., Roberts, R.J., Unpublished observations.
Watson, R.J., Schildkraut, I., Qiang, B.-Q., Martin, S.M., Visentin, L.P., (1982) FEBS Lett., vol. 150, pp. 114-116.

<1>NdeII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Neisseria denitrificans
<6>NRCC 31009
<7>JMRW
<8>Visentin, L.P., Watson, R.J., Martin, S., Zuker, M., Unpublished observations.

<1>NflI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Neisseria flavescens
<6>NRCC 31011
<7>
<8>Visentin, L.P., Watson, R.J., Martin, S., Zuker, M., Unpublished observations.

<1>NflII
<2>
<3>?
<4>
<5>Neisseria flavescens
<6>NRCC 31011
<7>
<8>Visentin, L.P., Watson, R.J., Martin, S., Zuker, M., Unpublished observations.

<1>NflIII
<2>
<3>?
<4>
<5>Neisseria flavescens
<6>NRCC 31011
<7>
<8>Visentin, L.P., Watson, R.J., Martin, S., Zuker, M., Unpublished observations.

<1>NflAI
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Neisseria flavescens
<6>ATCC 13120
<7>
<8>Maratea, E., Camp, R.R., Unpublished observations.

<1>NflAII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Neisseria flavescens
<6>ATCC 13120
<7>
<8>Maratea, E., Camp, R.R., Unpublished observations.

<1>NflBI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Neisseria flavescens
<6>ATCC 13115
<7>
<8>Grandoni, R., Unpublished observations.

<1>NgbI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Nocardia globerula
<6>ATCC 21292
<7>
<8>Wickberg, L., Schildkraut, I., Unpublished observations.

<1>NgoAI
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGCY
<4>?(5)
<5>Neisseria gonorrhoeae FA1090
<6>ATCC 700825
<7>
<8>Fontana, M.R., Pizza, M., Masignani, V., Monaci, E., European Patent Office, 2007.
Hammond, A.W., Chatterjee, D.K., International Patent Office, 1991.
Lewis, L.A. et al., Unpublished observations.
Roe, B., Song, L., Lin, S.-P., Yuan, X.-L., Clifton, S., Ducey, T., Lewis, L., Dyer, D., Unpublished observations.
Roe, B.A., Unpublished observations.

<1>NgoAII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>?(5)
<5>Neisseria gonorrhoeae FA1090
<6>ATCC 700825
<7>
<8>Fontana, M.R., Pizza, M., Masignani, V., Monaci, E., European Patent Office, 2007.
Hammond, A.W., Chatterjee, D.K., International Patent Office, 1991.
Lewis, L.A. et al., Unpublished observations.
Monaci, E., Masignani, V., Pizza, M., Fontana, M.R., Japanese Patent Office, 2004.
Roe, B., Song, L., Lin, S.-P., Yuan, X.-L., Clifton, S., Ducey, T., Lewis, L., Dyer, D., Unpublished observations.

<1>NgoAIII
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>?(5)
<5>Neisseria gonorrhoeae FA1090
<6>ATCC 700825
<7>
<8>Fontana, M.R., Pizza, M., Masignani, V., Monaci, E., European Patent Office, 2007.
Hammond, A.W., Chatterjee, D.K., International Patent Office, 1991.
Hammond, A.W., Gerard, G.F., Chatterjee, D.K., (1989) Nucleic Acids Res., vol. 17, pp. 6750.
Lewis, L.A. et al., Unpublished observations.
Monaci, E., Masignani, V., Pizza, M., Fontana, M.R., Japanese Patent Office, 2004.
Roe, B., Song, L., Lin, S.-P., Yuan, X.-L., Clifton, S., Ducey, T., Lewis, L., Dyer, D., Unpublished observations.

<1>NgoAIV
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>G^CCGGC
<4>?(5)
<5>Neisseria gonorrhoeae FA1090
<6>ATCC 700825
<7>
<8>Fontana, M.R., Pizza, M., Masignani, V., Monaci, E., European Patent Office, 2007.
Hammond, A.W., Chatterjee, D.K., Gerard, G.F., International Patent Office, 1991.
Hammond, A.W., Gerard, G.F., Campbell, J.H., Chatterjee, D.K., (1989) Nucleic Acids Res., vol. 17, pp. 3320.
Hu, A.-L.W., (1994) BRL Focus, vol. 15, pp. 42-43.
Lewis, L.A. et al., Unpublished observations.
Roe, B., Song, L., Lin, S.-P., Yuan, X.-L., Clifton, S., Ducey, T., Lewis, L., Dyer, D., Unpublished observations.
Zhu, P., Morelli, G., Achtman, M., (1999) Mol. Microbiol., vol. 33, pp. 635-650.

<1>NgoAV
<2>
<3>GCANNNNNNNNTGC
<4>3(6)
<5>Neisseria gonorrhoeae FA1090
<6>ATCC 700825
<7>
<8>Fontana, M.R., Pizza, M., Masignani, V., Monaci, E., European Patent Office, 2007.
Lewis, L.A. et al., Unpublished observations.
Piekarowicz, A., Klyz, A., Kwiatek, A., Stein, D.C., (2001) Mol. Microbiol., vol. 41, pp. 1199-1210.

<1>NgoAVIII
<2>
<3>(12/14)GACNNNNNTGA(13/11)
<4>
<5>Neisseria gonorrhoeae FA1090
<6>ATCC 700825
<7>
<8>Lewis, L.A. et al., Unpublished observations.
O'Driscoll, J., Wilson, G.G., Unpublished observations.
Wilson, G., Unpublished observations.

<1>NgoAV-1
<2>
<3>?
<4>
<5>Neisseria gonorrhoeae FA1090
<6>ATCC 700825
<7>
<8>Lewis, L.A. et al., Unpublished observations.

<1>NgoBI
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGCY
<4>?(5)
<5>Neisseria gonorrhoeae WR302
<6>D.C. Stein
<7>
<8>Stein, D.C., Gunn, J.S., Radlinska, M., Piekarowicz, A., (1995) Gene, vol. 157, pp. 19-22.

<1>NgoBV
<2>NlaIV,AspNI,BcrI,BmiI,BsaEI,BscBI,Bsp29I,BspLI,BssI,HpyF44II,HpyF73I,NgoGV,PspN4I,Rlu3I,Uba1305I,Uba1445I
<3>GGNNCC
<4>?(5)
<5>Neisseria gonorrhoeae WR302
<6>D.C. Stein
<7>
<8>Stein, D.C., Gunn, J.S., Radlinska, M., Piekarowicz, A., (1995) Gene, vol. 157, pp. 19-22.

<1>NgoBVIII
<2>HphI,AsuHPI,NgoDVIII,NgoJVIII,NgoMVIII,SspD5I
<3>GGTGA
<4>?(5)
<5>Neisseria gonorrhoeae WR302
<6>D.C. Stein
<7>
<8>Bentley, S.D. et al., Unpublished observations.
Giuliani, M.M., Pizza, M., Rappuoli, R., International Patent Office, 2000.
Gunn, J.S., Stein, D.C., (1997) Nucleic Acids Res., vol. 25, pp. 4147-4152.
Piekarowicz, A., Yuan, R., Stein, D.C., (1988) Nucleic Acids Res., vol. 16, pp. 5957-5972.
Piekarowicz, A., Yuan, R., Stein, D.C., (1988) Nucleic Acids Res., vol. 16, pp. 9868.

<1>M.NgoBIX
<2>
<3>GTANNNNNCTC
<4>9(5)
<5>Neisseria gonorrhoeae WR302
<6>D.C. Stein
<7>
<8>Piekarowicz, A., Yuan, R., Stein, D.C., (1988) Nucleic Acids Res., vol. 16, pp. 5957-5972.

<1>M.NgoBXII
<2>Fnu4HI,Bli1904II,Bpu1811I,BsoFI,Bsp6I,BssFI,BssXI,BthCI,Cac824I,CcoP215I,CcoP216I,FbrI,Fsp4HI,ItaI,LlaDII,SatI,Uur960I
<3>GCNGC
<4>
<5>Neisseria gonorrhoeae WR302
<6>D.C. Stein
<7>
<8>Piekarowicz, A., Stein, D.C., (1995) Gene, vol. 157, pp. 101-102.

<1>NgoCI
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGCY
<4>
<5>Neisseria gonorrhoeae
<6>CDC 66
<7>
<8>Clanton, D.J., Riggsby, W.S., Miller, R.V., (1979) J. Bacteriol., vol. 137, pp. 1299-1307.

<1>NgoCII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Neisseria gonorrhoeae
<6>CDC 66
<7>
<8>Clanton, D.J., Woodward, J.M., Miller, R.V., (1978) J. Bacteriol., vol. 135, pp. 270-273.

<1>NgoDI
<2>
<3>?
<4>
<5>Neisseria gonorrhoeae JKD211
<6>J.K. Davies
<7>
<8>Duff, M.K., Davies, J.K., (1988) Gonococci and Meningococci, ed. Poolman, J.T., Zanen, H.C., Meyer, T.F., Heckels, J.E., Makela, P.R.H. (Kluwer Academic Publishers, Dordrecht, The Netherlands), pp. 251-256.

<1>NgoDIII
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Neisseria gonorrhoeae JKD211
<6>J.K. Davies
<7>
<8>Duff, M.K., Davies, J.K., (1988) Gonococci and Meningococci, ed. Poolman, J.T., Zanen, H.C., Meyer, T.F., Heckels, J.E., Makela, P.R.H. (Kluwer Academic Publishers, Dordrecht, The Netherlands), pp. 251-256.

<1>NgoDVIII
<2>HphI,AsuHPI,NgoBVIII,NgoJVIII,NgoMVIII,SspD5I
<3>GGTGA
<4>
<5>Neisseria gonorrhoeae JKD211
<6>J.K. Davies
<7>
<8>Duff, M.K., Davies, J.K., (1988) Gonococci and Meningococci, ed. Poolman, J.T., Zanen, H.C., Meyer, T.F., Heckels, J.E., Makela, P.R.H. (Kluwer Academic Publishers, Dordrecht, The Netherlands), pp. 251-256.

<1>NgoDXIV
<2>DpnI,CfuI,FtnUIV,MalI,Mph1103II,NanII,NmeAII,NmeBL859I,NmuDI,NmuEI,NsuDI,TdeI
<3>GATC
<4>
<5>Neisseria gonorrhoeae JKD211
<6>J.K. Davies
<7>
<8>Duff, M.K., Davies, J.K., (1988) Gonococci and Meningococci, ed. Poolman, J.T., Zanen, H.C., Meyer, T.F., Heckels, J.E., Makela, P.R.H. (Kluwer Academic Publishers, Dordrecht, The Netherlands), pp. 251-256.

<1>M.NgoEI
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGCY
<4>
<5>Neisseria gonorrhoeae FA5100
<6>D.C. Stein
<7>
<8>Gunn, J.S., Piekarowicz, A., Chien, R., Stein, D.C., (1992) J. Bacteriol., vol. 174, pp. 5654-5660.

<1>NgoEII
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,SciNI
<3>GCGC
<4>
<5>Neisseria gonorrhoeae FA5100
<6>D.C. Stein
<7>
<8>Stein, D.C., Unpublished observations.

<1>NgoFVII
<2>TauI,BspUI,CglI
<3>GCSGC
<4>?(5)
<5>Neisseria gonorrhoeae 1291C
<6>D.C. Stein
<7>
<8>Stein, D.C., Gunn, J.S., Radlinska, M., Piekarowicz, A., (1995) Gene, vol. 157, pp. 19-22.

<1>NgoGI
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoJI,NgoMI,NgoWI
<3>RGCGCY
<4>
<5>Neisseria gonorrhoeae WR220
<6>D.C. Stein
<7>
<8>Gunn, J.S., Stein, D.C., (1996) Mol. Gen. Genet., vol. 251, pp. 509-517.

<1>M.NgoGII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>3(5)
<5>Neisseria gonorrhoeae WR220
<6>D.C. Stein
<7>
<8>Piekarowicz, A., Yuan, R., Stein, D.C., (1988) Nucleic Acids Res., vol. 16, pp. 5957-5972.

<1>NgoGIII
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Neisseria gonorrhoeae WR220
<6>D.C. Stein
<7>
<8>Gregoire, S.T., (1986) M.Sc. Thesis. Univ. Maryland., vol. 0, pp. 1-138.
Stein, D.C., Unpublished observations.

<1>NgoGV
<2>NlaIV,AspNI,BcrI,BmiI,BsaEI,BscBI,Bsp29I,BspLI,BssI,HpyF44II,HpyF73I,NgoBV,PspN4I,Rlu3I,Uba1305I,Uba1445I
<3>GGNNCC
<4>
<5>Neisseria gonorrhoeae WR220
<6>D.C. Stein
<7>
<8>Gregoire, S.T., (1986) M.Sc. Thesis. Univ. Maryland., vol. 0, pp. 1-138.
Stein, D.C., Gunn, J.S., Radlinska, M., Piekarowicz, A., (1995) Gene, vol. 157, pp. 19-22.

<1>M.NgoHVIII
<2>HphI,AsuHPI,NgoBVIII,NgoDVIII,NgoJVIII,NgoMVIII,SspD5I
<3>GGTGA
<4>-2(5)
<5>Neisseria gonorrhoeae 82409/55
<6>C. Korch
<7>
<8>Korch, C., Hagblom, P., Normark, S., (1985) J. Bacteriol., vol. 161, pp. 1236-1237.

<1>NgoJI
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoMI,NgoWI
<3>RGCGCY
<4>
<5>Neisseria gonorrhoeae JKD109
<6>J.K. Davies
<7>
<8>Duff, M.K., Davies, J.K., (1988) Gonococci and Meningococci, ed. Poolman, J.T., Zanen, H.C., Meyer, T.F., Heckels, J.E., Makela, P.R.H. (Kluwer Academic Publishers, Dordrecht, The Netherlands), pp. 251-256.

<1>NgoJIII
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Neisseria gonorrhoeae JKD109
<6>J.K. Davies
<7>
<8>Duff, M.K., Davies, J.K., (1988) Gonococci and Meningococci, ed. Poolman, J.T., Zanen, H.C., Meyer, T.F., Heckels, J.E., Makela, P.R.H. (Kluwer Academic Publishers, Dordrecht, The Netherlands), pp. 251-256.

<1>NgoJVIII
<2>HphI,AsuHPI,NgoBVIII,NgoDVIII,NgoMVIII,SspD5I
<3>GGTGA
<4>
<5>Neisseria gonorrhoeae JKD109
<6>J.K. Davies
<7>
<8>Duff, M.K., Davies, J.K., (1988) Gonococci and Meningococci, ed. Poolman, J.T., Zanen, H.C., Meyer, T.F., Heckels, J.E., Makela, P.R.H. (Kluwer Academic Publishers, Dordrecht, The Netherlands), pp. 251-256.

<1>NgoKIII
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Neisseria gonorrhoeae KH 7764-45
<6>L. Mayer
<7>
<8>Norlander, L., Davies, J.K., Hagblom, P., Normark, S., (1981) J. Bacteriol., vol. 145, pp. 788-795.

<1>NgoMI
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoWI
<3>RGCGCY
<4>
<5>Neisseria gonorrhoeae MS11
<6>M. So
<7>
<8>Stein, D.C., Unpublished observations.

<1>NgoMIII
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Neisseria gonorrhoeae MS11
<6>M. So
<7>
<8>Chien, H.R., (1991) Ph.D. Thesis, University of Maryland, USA, pp. 1-126.

<1>NgoMIV
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>G^CCGGC
<4>2(5)
<5>Neisseria gonorrhoeae MS11
<6>M. So
<7>NR
<8>Chien, H.R., (1991) Ph.D. Thesis, University of Maryland, USA, pp. 1-126.
Chien, R.H., Stein, D.C., Seifert, H.S., Floyd, K., So, M., (1988) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 88, pp. 213.
Gunn, J.S., Piekarowicz, A., Chien, R., Stein, D.C., (1992) J. Bacteriol., vol. 174, pp. 5654-5660.
Stein, D.C., Chien, R., Seifert, S.H., (1992) J. Bacteriol., vol. 174, pp. 4899-4906.
Stein, D.C., Gunn, J.S., Radlinska, M., Piekarowicz, A., (1995) Gene, vol. 157, pp. 19-22.
Zhu, P., Morelli, G., Achtman, M., (1999) Mol. Microbiol., vol. 33, pp. 635-650.

<1>NgoMVIII
<2>HphI,AsuHPI,NgoBVIII,NgoDVIII,NgoJVIII,SspD5I
<3>GGTGA
<4>?(5)
<5>Neisseria gonorrhoeae MS11
<6>M. So
<7>
<8>Chien, H.R., (1991) Ph.D. Thesis, University of Maryland, USA, pp. 1-126.
Stein, D.C., Gunn, J.S., Radlinska, M., Piekarowicz, A., (1995) Gene, vol. 157, pp. 19-22.

<1>NgoMX
<2>
<3>?
<4>
<5>Neisseria gonorrhoeae MS11
<6>M. So
<7>
<8>Belland, R.J., Morrison, S.G., Hogan, D., (1996) Abs. Tenth Int. Conf. Pathogenegic Neisseria, ed. Zollinger, W.D., Frasch, C.E., Deal, C.D. (Baltimore, MD), vol. 0, pp. 360-361.

<1>M.NgoMXV
<2>
<3>GCCHR
<4>3(4)
<5>Neisseria gonorrhoeae MS11
<6>M. So
<7>
<8>Radlinska, M., Piekarowicz, A., (1998) Biol. Chem., vol. 379, pp. 1391-1395.
Trevors, J.T., (1998) Bull. Inst. Pasteur, vol. 96, pp. 25-33.

<1>NgoNII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Neisseria gonorrhoeae DOV
<6>D.C. Stein
<7>
<8>Gregoire, S.T., (1986) M.Sc. Thesis. Univ. Maryland., vol. 0, pp. 1-138.

<1>NgoPII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>3(5)
<5>Neisseria gonorrhoeae P9-2
<6>J.R. Saunders
<7>
<8>Sullivan, K.M., Macdonald, H.J., Saunders, J.R., (1987) FEMS Microbiol. Lett., vol. 44, pp. 389-393.
Sullivan, K.M., Saunders, J.R., (1988) Nucleic Acids Res., vol. 16, pp. 4369-4387.
Sullivan, K.M., Saunders, J.R., (1989) Mol. Gen. Genet., vol. 216, pp. 380-387.
Sullivan, K.M., Saunders, J.R., (1988) Gonococci and Meningococci, ed. Poolman, J.T. (Kluwer Academic Publishers, Dordrecht, The Netherlands), vol. 0, pp. 329-334.

<1>NgoPIII
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Neisseria gonorrhoeae P9-2
<6>J.R. Saunders
<7>
<8>Sullivan, K.M., Macdonald, H.J., Saunders, J.R., (1987) FEMS Microbiol. Lett., vol. 44, pp. 389-393.
Sullivan, K.M., Saunders, J.R., (1988) Gonococci and Meningococci, ed. Poolman, J.T. (Kluwer Academic Publishers, Dordrecht, The Netherlands), vol. 0, pp. 329-334.

<1>NgoSII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>?(5)
<5>Neisseria gonorrhoeae Pgh3-2
<6>D.C. Stein
<7>
<8>Gunn, J.S., Piekarowicz, A., Chien, R., Stein, D.C., (1992) J. Bacteriol., vol. 174, pp. 5654-5660.
Gunn, J.S., Stein, D.C., (1993) Gene, vol. 132, pp. 15-20.
Stein, D.C., Gregoire, S., Piekarowicz, A., (1988) Infect. Immun., vol. 56, pp. 112-116.

<1>NgoTII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Neisseria gonorrhoeae FA293
<6>D.C. Stein
<7>
<8>Gregoire, S.T., (1986) M.Sc. Thesis. Univ. Maryland., vol. 0, pp. 1-138.

<1>NgoWI
<2>HaeII,AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI
<3>RGCGCY
<4>
<5>Neisseria gonorrhoeae
<6>G.A. Wilson
<7>
<8>Wilson, G.A., Young, F.E., Unpublished observations.

<1>NhaXI
<2>
<3>CAAGRAG
<4>
<5>Nitrobacter hamburgensis X14
<6>P. Richardson
<7>
<8>Morgan, R.D., Unpublished observations.
Starkenburg, S.R., Larimer, F.W., Stein, L.Y., Klotz, M.G., Chain, P.S.G., Sayavedra-Soto, L.A., Poret-Peterson, A.T., Gentry, M.E., Arp, D.J., Ward, B., Bottomley, P.J., (2008) Appl. Environ. Microbiol., vol. 74, pp. 2852-2863.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>NheI
<2>AceII,AsuNHI,BmtI,BspOI,LlaG2I,PstNHI
<3>G^CTAGC
<4>
<5>Neisseria mucosa
<6>ATCC 25999
<7>BCFJKMNORSUW
<8>Comb, D.G., Grandoni, R., Schildkraut, I., Unpublished observations.
Xu, S.-Y., Xiao, J.-P., European Patent Office, 2001.

<1>NlaI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Neisseria lactamica
<6>NRCC 2118
<7>
<8>Qiang, B.-Q., Schildkraut, I., (1986) Nucleic Acids Res., vol. 14, pp. 1991-1999.

<1>NlaII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Neisseria lactamica
<6>NRCC 2118
<7>
<8>Qiang, B.-Q., Schildkraut, I., (1986) Nucleic Acids Res., vol. 14, pp. 1991-1999.

<1>NlaIII
<2>CviAII,FaeI,FatI,FatII,Hin1II,Hin8II,HpyCH4I,Hsp92II
<3>CATG^
<4>2(6)
<5>Neisseria lactamica
<6>NRCC 2118
<7>NW
<8>Labbe, D., Holtke, H.J., Lau, P.C.K., (1990) Mol. Gen. Genet., vol. 224, pp. 101-110.
Lunnen, K.D., Barsomian, J.M., Camp, R.R., Card, C.O., Chen, S.-Z., Croft, R., Looney, M.C., Meda, M.M., Moran, L.S., Nwankwo, D.O., Slatko, B.E., Van Cott, E.M., Wilson, G.G., (1988) Gene, vol. 74, pp. 25-32.
Morgan, R.D., European Patent Office, 1995.
Qiang, B.-Q., Schildkraut, I., (1986) Nucleic Acids Res., vol. 14, pp. 1991-1999.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>NlaIV
<2>AspNI,BcrI,BmiI,BsaEI,BscBI,Bsp29I,BspLI,BssI,HpyF44II,HpyF73I,NgoBV,NgoGV,PspN4I,Rlu3I,Uba1305I,Uba1445I
<3>GGN^NCC
<4>?(5)
<5>Neisseria lactamica
<6>NRCC 2118
<7>NW
<8>Lau, P.C.K., Forghani, F., Labbe, D., Bergeron, H., Brousseau, R., Holtke, H.J., (1994) Mol. Gen. Genet., vol. 243, pp. 24-31.
Lunnen, K.D., Barsomian, J.M., Camp, R.R., Card, C.O., Chen, S.-Z., Croft, R., Looney, M.C., Meda, M.M., Moran, L.S., Nwankwo, D.O., Slatko, B.E., Van Cott, E.M., Wilson, G.G., (1988) Gene, vol. 74, pp. 25-32.
Qiang, B.-Q., Schildkraut, I., (1986) Nucleic Acids Res., vol. 14, pp. 1991-1999.

<1>NlaCI
<2>
<3>CATCAC(19/17)
<4>
<5>Neisseria lactamica ST640
<6>R. Chalmers
<7>
<8>Chalmers, R., Unpublished observations.
Morgan, R.D., Unpublished observations.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>NlaDI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Neisseria lactamica 5841
<6>D.C. Stein
<7>
<8>Stein, D.C., Unpublished observations.

<1>NlaDII
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Neisseria lactamica 5841
<6>D.C. Stein
<7>
<8>Stein, D.C., Unpublished observations.

<1>NlaDIII
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Neisseria lactamica 5841
<6>D.C. Stein
<7>
<8>Stein, D.C., Unpublished observations.

<1>NlaSI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Neisseria lactamica
<6>NRCC 31016
<7>
<8>Camp, R., Visentin, L.P., Unpublished observations.

<1>NlaSII
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,PamII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GRCGYC
<4>
<5>Neisseria lactamica
<6>NRCC 31016
<7>
<8>Camp, R., Visentin, L.P., Unpublished observations.

<1>NliI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Nostoc linckia
<6>A. de Waard
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., Vonshak, A., Wolk, C.P., (1983) Arch. Microbiol., vol. 134, pp. 276-281.

<1>NliII
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Nostoc linckia
<6>A. de Waard
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., Vonshak, A., Wolk, C.P., (1983) Arch. Microbiol., vol. 134, pp. 276-281.

<1>Nli3877I
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGR^G
<4>
<5>Nostoc linckia
<6>A.I. Melnik
<7>
<8>Melnik, A.I., Rebentish, B.A., Bolotin, A.V., Mendzhul, M.I., (1991) Mikrobiol. Zh., vol. 53, pp. 24-28.

<1>Nli3877II
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Nostoc linckia
<6>A.I. Melnik
<7>
<8>Melnik, A.I., Rebentish, B.A., Bolotin, A.V., Mendzhul, M.I., (1991) Mikrobiol. Zh., vol. 53, pp. 24-28.

<1>M.NmaPhiCh1I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Natrialba magadii phage PhiCh1
<6>A. Witte
<7>
<8>Baranyi, U., Klein, R., Lubitz, W., Kruger, D.H., Witte, A., (2000) Mol. Microbiol., vol. 35, pp. 1168-1179.

<1>NmeI
<2>
<3>?
<4>
<5>Neisseria meningitidis DRES-W34
<6>R. Sparling
<7>
<8>Sparling, R., Bhatti, A.R., (1984) Microbios, vol. 41, pp. 73-79.

<1>NmeII
<2>
<3>?
<4>
<5>Neisseria meningitidis DRES-W34
<6>R. Sparling
<7>
<8>Sparling, R., Bhatti, A.R., (1983) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 83, pp. 214.

<1>NmeIII
<2>
<3>?
<4>
<5>Neisseria meningitidis M1011
<6>R. Sparling
<7>
<8>Sparling, R., Bhatti, A.R., (1983) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 83, pp. 214.

<1>NmeIV
<2>
<3>?
<4>
<5>Neisseria meningitidis DRES-30
<6>R. Sparling
<7>
<8>Sparling, R., Bhatti, A.R., (1983) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 83, pp. 214.

<1>NmeAII
<2>DpnI,CfuI,FtnUIV,MalI,Mph1103II,NanII,NgoDXIV,NmeBL859I,NmuDI,NmuEI,NsuDI,TdeI
<3>GATC
<4>
<5>Neisseria meningitidis Z2491
<6>M. Achtman
<7>
<8>Morgan, R.D., Unpublished observations.
Parkhill, J. et al., (2000) Nature, vol. 404, pp. 502-506.

<1>NmeAIII
<2>
<3>GCCGAG(21/19)
<4>
<5>Neisseria meningitidis Z2491
<6>M. Achtman
<7>N
<8>Morgan, R.D., International Patent Office, 2008.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>NmeBI
<2>HgaI,CseI
<3>GACGC
<4>?(5)
<5>Neisseria meningitidis B strain MC58
<6>E.R. Moxon
<7>
<8>Claus, H., Friedrich, A., Frosch, M., Vogel, U., (2000) J. Bacteriol., vol. 182, pp. 1296-1303.
Tettelin, H. et al., (2000) Science, vol. 287, pp. 1809-1815.

<1>NmeBL859I
<2>DpnI,CfuI,FtnUIV,MalI,Mph1103II,NanII,NgoDXIV,NmeAII,NmuDI,NmuEI,NsuDI,TdeI
<3>GATC
<4>
<5>Neisseria meningitidis BL859
<6>C.B. Bruni
<7>
<8>Cantalupo, G., Bucci, C., Salvatore, P., Pagliarulo, C., Roberti, V., Lavitola, A., Bruni, C.B., Alifano, P., (2001) FEBS Lett., vol. 495, pp. 178-183.

<1>NmeCI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Neisseria meningitidis C114
<6>C.A. Hart
<7>
<8>Sullivan, K.M., Macdonald, H.J., Saunders, J.R., (1987) FEMS Microbiol. Lett., vol. 44, pp. 389-393.

<1>NmeDI
<2>Cfr10I,Bco118I,BscRI,Bse118I,Bse634I,Bsp21I,BsrFI,BssAI,BstB7SI,TseDI
<3>(12/7)RCCGGY(7/12)
<4>2(5),-2(5)
<5>Neisseria meningitidis 2120
<6>U. Vogel
<7>
<8>Claus, H., Friedrich, A., Frosch, M., Vogel, U., (2000) J. Bacteriol., vol. 182, pp. 1296-1303.
Kwiatek, A., Kobes, M., Olejnik, K., Piekarowicz, A., (2004) Microbiology, vol. 150, pp. 1713-1722.
Kwiatek, A., Piekarowicz, A., (2007) Nucleic Acids Res., vol. 35, pp. 6539-6546.

<1>NmeRI
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>
<5>Neisseria meningitidis
<6>CAMB 2584
<7>
<8>Mushtaq, R., Sohail, A., Riazuddin, S., Unpublished observations.

<1>NmeSI
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,Eco255I,LlaDI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGTACT
<4>5(4)
<5>Neisseria meningitidis 800615
<6>A. Van der Ende
<7>
<8>Bart, A., (1999) Ph.D. Thesis, Univ. Amsterdam, Netherlands (Ponsen & Looijen, BV, Wageningen), pp. 1-115.
Bart, A., Dankert, J., van der Ende, A., (1999) Mol. Microbiol., vol. 31, pp. 1275-1281.
Bart, A., Pannekoek, Y., Dankert, J., van der Ende, A., (2001) Infect. Immun., vol. 69, pp. 1816-1820.

<1>NmiI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Nocardia minima
<6>ATCC 19150
<7>
<8>Comb, D.G., Schildkraut, I., Unpublished observations.

<1>NmuI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Neisseria mucosa
<6>NRCC 31013
<7>
<8>Visentin, L.P., Watson, R.J., Martin, S., Zuker, M., Unpublished observations.

<1>NmuAI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Nostoc muscorum M-131-G
<6>A. de Waard
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., Vonshak, A., Wolk, C.P., (1983) Arch. Microbiol., vol. 134, pp. 276-281.

<1>NmuAII
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Nostoc muscorum M-131-G
<6>A. de Waard
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., Vonshak, A., Wolk, C.P., (1983) Arch. Microbiol., vol. 134, pp. 276-281.

<1>NmuCI
<2>Tsp45I,Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III
<3>^GTSAC
<4>
<5>Neisseria mucosa C9-2
<6>V. Butkus
<7>F
<8>Vaitkevicius, D., Mociskyte, S., Petrusyte, M., Trinkunaite, L., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>NmuDI
<2>DpnI,CfuI,FtnUIV,MalI,Mph1103II,NanII,NgoDXIV,NmeAII,NmeBL859I,NmuEI,NsuDI,TdeI
<3>GATC
<4>
<5>Neisseria mucosa
<6>ATCC 25997
<7>
<8>Camp, R., Schildkraut, I., Unpublished observations.

<1>NmuEI
<2>DpnI,CfuI,FtnUIV,MalI,Mph1103II,NanII,NgoDXIV,NmeAII,NmeBL859I,NmuDI,NsuDI,TdeI
<3>GATC
<4>
<5>Neisseria mucosa
<6>ATCC 25996
<7>
<8>Camp, R., Schildkraut, I., Unpublished observations.

<1>NmuEII
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Neisseria mucosa
<6>ATCC 25996
<7>
<8>Camp, R., Schildkraut, I., Unpublished observations.

<1>NmuFI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Neisseria mucosa
<6>ATCC 19697
<7>
<8>Camp, R., Schildkraut, I., Unpublished observations.

<1>NmuSI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Neisseria mucosa
<6>ATCC 19693
<7>
<8>Comb, D.G., Parker, P., Schildkraut, I., Unpublished observations.

<1>NocI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Nocardia otitidis-caviarum
<6>ATCC 14629
<7>
<8>Comb, D.G., Schildkraut, I., Unpublished observations.

<1>NopI
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>G^TCGAC
<4>
<5>Nocardia opaca
<6>ATCC 21507
<7>
<8>Schildkraut, I., Unpublished observations.

<1>NopII
<2>
<3>?
<4>
<5>Nocardia opaca
<6>ATCC 21507
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>NotI
<2>CciNI,CsiBI,CspBI,MchAI
<3>GC^GGCCGC
<4>?(4)
<5>Nocardia otitidis-caviarum
<6>ATCC 14630
<7>BCFHJKMNOQRSUWXY
<8>Borsetti, R., Wise, D., Qiang, B.-Q., Schildkraut, I., Unpublished observations.
Morgan, R.D., Benner, J.S., Claus, T.E., US Patent Office, 1994.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Qiang, B.-Q., Schildkraut, I., (1987) Methods Enzymol., vol. 155, pp. 15-21.

<1>NovI
<2>
<3>?
<4>
<5>Neisseria ovis
<6>NRCC 31020
<7>
<8>Visentin, L.P., Watson, R.J., Martin, S., Zuker, M., Unpublished observations.

<1>NovII
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NsiHI,SscL1I
<3>GANTC
<4>
<5>Neisseria ovis
<6>NRCC 31020
<7>
<8>Visentin, L.P., Watson, R.J., Martin, S., Zuker, M., Unpublished observations.

<1>NpeBY1I
<2>
<3>?
<4>
<5>Nodularia species BY1
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>NpeHEMI
<2>
<3>?
<4>
<5>Nodularia species HEM
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>NpeHKVVI
<2>
<3>?
<4>
<5>Nodularia species HKVV
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>NphI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Neisseria pharyngis C245
<6>C.A. Hart
<7>
<8>Sullivan, K.M., Macdonald, H.J., Saunders, J.R., (1987) FEMS Microbiol. Lett., vol. 44, pp. 389-393.

<1>NruI
<2>AmaSI,Bsp68I,BtuMI,Mlu9273I,MluB2I,PspDI,RruI,SalDI,Sbo13I,Sna3286I,SpoI,Uba1117I,Uba1386I,VchO70I
<3>TCG^CGA
<4>
<5>Nocardia rubra
<6>ATCC 15906
<7>BCIJKMNOQRUWX
<8>Comb, D.G., Schildkraut, I., Greenough, L., Unpublished observations.
Forrow, S., Lee, M., Souhami, R.L., Hartley, J.A., (1994) ACS Abstracts, vol. 208, pp. 97.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Zhu, Z., Unpublished observations.

<1>NruGI
<2>Eam1105I,AhdI,AspEI,BmeRI,BspOVI,BstZ2I,DriI,EclHKI,Uba1190I,Uba1191I
<3>GACNNN^NNGTC
<4>
<5>Nocardia species G
<6>S.K. Degtyarev
<7>
<8>Bondar, T.S., Rechkunova, N.I., Abdurashitov, M.A., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>NsbI
<2>MstI,AcaIII,Acc16I,AosI,ApcTR183I,AviII,Bco6I,BsaTI,ClcII,CliII,FdiII,FspI,GspAII,NspHIII,NspLI,NspMI,PamI,Pun14627I
<3>TGC^GCA
<4>
<5>Neisseria subflava Va-1
<6>A. Janulaitis
<7>FK
<8>Vitkute, J., Savelskiene, A., Maneliene, Z., Valickiene, D., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>NsiI
<2>AvaIII,Asi372I,BfrBI,BfrCI,Csp68KIII,EcoT22I,Mph1103I,PinBI,Ppu10I,PxyJKI,SepI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>ATGCA^T
<4>
<5>Neisseria sicca
<6>ATCC 29256
<7>BHJMNRSUW
<8>Longo, M.C., Smith, M.D., US Patent Office, 1995.
Schildkraut, I., Jones, G., Parker, P., Grandoni, R., Comb, D.G., Unpublished observations.
Xia, Y., Van Etten, J.L., Dobos, P., Ling, Y.Y., Krell, P.J., (1993) Virology, vol. 196, pp. 817-824.
Zhu, Z., Unpublished observations.

<1>NsiAI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Neisseria sicca
<6>ATCC 9913
<7>
<8>Comb, D.G., Unpublished observations.

<1>NsiCI
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GAT^ATC
<4>
<5>Neisseria sicca C351
<6>C.A. Hart
<7>
<8>Sullivan, K.M., Macdonald, H.J., Saunders, J.R., (1987) FEMS Microbiol. Lett., vol. 44, pp. 389-393.

<1>NsiHI
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,SscL1I
<3>GANTC
<4>
<5>Neisseria sicca
<6>NRCC 31004
<7>
<8>Visentin, L.P., Unpublished observations.

<1>NspI
<2>AvoI,BstNSI,Lsp1270I,NspHI,PauAI,PunAII,XceI
<3>RCATG^Y
<4>2(5)
<5>Nostoc species C
<6>ATCC 29411
<7>MN
<8>Reaston, J., Duyvesteyn, M.G.C., de Waard, A., (1982) Gene, vol. 20, pp. 103-110.
Xu, S.-Y., Xiao, J.-P., Ettwiller, L., Holden, M., Aliotta, J., Poh, C.L., Dalton, M., Robinson, D.P., Petronzio, T.R., Moran, L., Ganatra, M., Ware, J., Slatko, B., Benner, J., (1998) Mol. Gen. Genet., vol. 260, pp. 226-231.

<1>NspII
<2>SduI,AocII,Bka1125I,BmyI,BsoCI,Bsp1286I,BspLS2I,BstZ15I,HpyF36IV,HpyF47I,MhlI,Mlu40I,TseAI,Uba1362I
<3>GDGCH^C
<4>
<5>Nostoc species C
<6>ATCC 29411
<7>
<8>Reaston, J., Duyvesteyn, M.G.C., de Waard, A., (1982) Gene, vol. 20, pp. 103-110.

<1>NspIII
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>?(4)
<5>Nostoc species C
<6>ATCC 29411
<7>
<8>Reaston, J., Duyvesteyn, M.G.C., de Waard, A., (1982) Gene, vol. 20, pp. 103-110.
Ueno, H., Ueno, T., Oshima, A., Kato, I., Japanese Patent Office, 1997.

<1>NspIV
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Nostoc species C
<6>ATCC 29411
<7>
<8>Reaston, J., Duyvesteyn, M.G.C., de Waard, A., (1982) Gene, vol. 20, pp. 103-110.

<1>NspV
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Nostoc species C
<6>ATCC 29411
<7>JO
<8>Bakker, D., Schouten, J.P., Unpublished observations.
Reaston, J., Duyvesteyn, M.G.C., de Waard, A., (1982) Gene, vol. 20, pp. 103-110.
Ueno, T., Ito, H., Kotani, H., Japanese Patent Office, 1993.
Ueno, T., Ito, H., Kotani, H., Kimizuka, F., Nakajima, K., (1993) Nucleic Acids Res., vol. 21, pp. 3899.

<1>Nsp152I
<2>
<3>?
<4>
<5>Nostoc species 152
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Nsp7121I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Nostoc species 7121
<6>PCC 7121
<7>
<8>Moser, D.P., Zarka, D., Kallas, T., (1993) Arch. Microbiol., vol. 160, pp. 229-237.

<1>Nsp29132I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Nostoc species
<6>ATCC 29132
<7>
<8>Muro-Pastor, A.M., Herrero, A., Flores, E., (1991) FEMS Microbiol. Lett., vol. 77, pp. 1-4.

<1>Nsp29132II
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Nostoc species
<6>ATCC 29132
<7>
<8>Muro-Pastor, A.M., Herrero, A., Flores, E., (1991) FEMS Microbiol. Lett., vol. 77, pp. 1-4.

<1>NspAI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Nocardia species
<6>ATCC 19170
<7>
<8>Wickberg, L., Schildkraut, I., Unpublished observations.

<1>NspBI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Nostoc species
<6>ATCC 29131
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., Vonshak, A., Wolk, C.P., (1983) Arch. Microbiol., vol. 134, pp. 276-281.

<1>NspBII
<2>MspA1I
<3>CMG^CKG
<4>
<5>Nostoc species
<6>ATCC 29131
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., Vonshak, A., Wolk, C.P., (1983) Arch. Microbiol., vol. 134, pp. 276-281.

<1>NspDI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Nostoc species
<6>ATCC 29105
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., Vonshak, A., Wolk, C.P., (1983) Arch. Microbiol., vol. 134, pp. 276-281.

<1>NspDII
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Nostoc species
<6>ATCC 29105
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., Vonshak, A., Wolk, C.P., (1983) Arch. Microbiol., vol. 134, pp. 276-281.

<1>NspEI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Nostoc species
<6>ATCC 27896
<7>
<8>Flores, E., Wolk, C.P., Unpublished observations.

<1>NspEII
<2>
<3>?
<4>
<5>Nostoc species
<6>ATCC 27896
<7>
<8>Flores, E., Wolk, C.P., Unpublished observations.

<1>NspFI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Nostoc species
<6>ATCC 29150
<7>
<8>Brand, P., de Waard, A., Unpublished observations.

<1>NspGI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Nostoc species 23-9B
<6>C.P. Wolk
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>NspHI
<2>NspI,AvoI,BstNSI,Lsp1270I,PauAI,PunAII,XceI
<3>RCATG^Y
<4>2(5)
<5>Nostoc species
<6>ATCC 29106
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., Vonshak, A., Wolk, C.P., (1983) Arch. Microbiol., vol. 134, pp. 276-281.
Xu, S.-Y., Xiao, J.-P., Ettwiller, L., Holden, M., Aliotta, J., Poh, C.L., Dalton, M., Robinson, D.P., Petronzio, T.R., Moran, L., Ganatra, M., Ware, J., Slatko, B., Benner, J., (1998) Mol. Gen. Genet., vol. 260, pp. 226-231.

<1>NspHII
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Nostoc species
<6>ATCC 29106
<7>
<8>Duyvesteyn, M.G.C., Korsuize, J., de Waard, A., Vonshak, A., Wolk, C.P., (1983) Arch. Microbiol., vol. 134, pp. 276-281.

<1>NspHIII
<2>MstI,AcaIII,Acc16I,AosI,ApcTR183I,AviII,Bco6I,BsaTI,ClcII,CliII,FdiII,FspI,GspAII,NsbI,NspLI,NspMI,PamI,Pun14627I
<3>TGCGCA
<4>
<5>Nostoc species
<6>ATCC 29106
<7>
<8>de Waard, A., Unpublished observations.

<1>NspJI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Nostoc species 78-12B
<6>C.P. Wolk
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>NspKI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Nostoc species 19-6C-C
<6>C.P. Wolk
<7>
<8>Karreman, C., de Waard, A., Unpublished observations.

<1>NspLI
<2>MstI,AcaIII,Acc16I,AosI,ApcTR183I,AviII,Bco6I,BsaTI,ClcII,CliII,FdiII,FspI,GspAII,NsbI,NspHIII,NspMI,PamI,Pun14627I
<3>TGCGCA
<4>
<5>Nostoc species UM-3
<6>C.P. Wolk
<7>
<8>Karreman, C., de Waard, A., Unpublished observations.

<1>NspLII
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Nostoc species UM-3
<6>C.P. Wolk
<7>
<8>Karreman, C., de Waard, A., Unpublished observations.

<1>NspLIII
<2>
<3>?
<4>
<5>Nostoc species UM-3
<6>C.P. Wolk
<7>
<8>Karreman, C., de Waard, A., Unpublished observations.

<1>NspLIV
<2>
<3>?
<4>
<5>Nostoc species UM-3
<6>C.P. Wolk
<7>
<8>Karreman, C., de Waard, A., Unpublished observations.

<1>NspLKI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Nocardia species LK
<6>N.I. Matvienko
<7>
<8>Zabaznaya, E.V., Zheleznaya, L.A., Svadbina, I.V., Matvienko, N.I., (1999) Biokhimiia, vol. 64, pp. 234-238.

<1>NspMI
<2>MstI,AcaIII,Acc16I,AosI,ApcTR183I,AviII,Bco6I,BsaTI,ClcII,CliII,FdiII,FspI,GspAII,NsbI,NspHIII,NspLI,PamI,Pun14627I
<3>TGCGCA
<4>
<5>Nostoc species
<6>ATCC 27897
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>NspMACI
<2>BglII,BseB631II,NcrI,Pae2kI,Pae18kI
<3>A^GATCT
<4>
<5>Nostoc species
<6>PCC 8009
<7>
<8>Lau, R.H., Visentin, L.P., Martin, S.M., Hofman, J.D., Doolittle, W.F., (1985) FEBS Lett., vol. 179, pp. 129-132.

<1>NspSAI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>
<5>Nostoc species SA
<6>D. Jones
<7>
<8>Dean, P.D.C., Walker, J.N.B., (1985) Biochem. Soc. Trans., vol. 13, pp. 1055-1058.

<1>NspSAII
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,PspEI,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Nostoc species SA
<6>D. Jones
<7>
<8>Dean, P.D.C., Walker, J.N.B., (1985) Biochem. Soc. Trans., vol. 13, pp. 1055-1058.

<1>NspSAIII
<2>NcoI,AteI,Bse19I,Bsp19I
<3>CCATGG
<4>
<5>Nostoc species SA
<6>D. Jones
<7>
<8>Dean, P.D.C., Walker, J.N.B., (1985) Biochem. Soc. Trans., vol. 13, pp. 1055-1058.

<1>NspSAIV
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Nostoc species SA
<6>D. Jones
<7>
<8>Dean, P.D.C., Walker, J.N.B., (1985) Biochem. Soc. Trans., vol. 13, pp. 1055-1058.

<1>NspWI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Nocardia species
<6>ATCC 29100
<7>
<8>Wickberg, L., Schildkraut, I., Unpublished observations.

<1>NsuI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Neisseria subflava
<6>ATCC 14221
<7>
<8>Camp, R., Schildkraut, I., Unpublished observations.

<1>NsuDI
<2>DpnI,CfuI,FtnUIV,MalI,Mph1103II,NanII,NgoDXIV,NmeAII,NmeBL859I,NmuDI,NmuEI,TdeI
<3>GATC
<4>
<5>Neisseria subflava
<6>ATCC 19243
<7>
<8>Camp, R., Schildkraut, I., Unpublished observations.

<1>NtaI
<2>Tth111I,AspI,AtsI,BgiI,FsuI,PflFI,PsyI,SmaAII,SpaPI,SplII,SplAII,TelI,TrsKTII,TspI,TteI,TtrI
<3>GACNNNGTC
<4>
<5>Nocardia tartaricans
<6>ATCC 31191
<7>
<8>Stote, R., Schildkraut, I., Unpublished observations.

<1>NtaSI
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGGCCT
<4>
<5>Nocardia tartaricans
<6>ATCC 31190
<7>
<8>Stote, R., Schildkraut, I., Unpublished observations.

<1>NtaSII
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Nocardia tartaricans
<6>ATCC 31190
<7>
<8>Stote, R., Schildkraut, I., Unpublished observations.

<1>M.NtbDRM1
<2>
<3>?
<4>?(5)
<5>Nicotiana tabacum cv. Xanthi
<6>H. Sano
<7>
<8>Nakano, Y., Steward, N., Sekine, M., Kusano, T., Sano, H., (2000) Plant Cell Physiol., vol. 41, pp. 448-457.
Sano, H., Koizumi, N., Yamaguchi, Yu., Wada, N., Japanese Patent Office, 2004.

<1>NunI
<2>
<3>?
<4>
<5>Nocardia uniformis
<6>ATCC 21806
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>NunII
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,PatAI,PmnI,SfoI,SseAI,SspDI
<3>GG^CGCC
<4>
<5>Nocardia uniformis
<6>ATCC 21806
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>OchI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Oscillatoria chalybea
<6>B.K. Hurlburt
<7>
<8>Hurlburt, B.K., Unpublished observations.

<1>OcoI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Oceanospirillum commune
<6>ATCC 27118
<7>
<8>Polisson, C., Unpublished observations.

<1>OfoI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>
<5>Oscillatoria foreaui A-1340
<6>V. Nagaraja
<7>
<8>Saravanan, M., Elango, K., Chandrashekaran, S., Anand, N., Nagaraja, V., (2003) Curr. Sci., vol. 85, pp. 188-190.

<1>OkrAI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Oceanospirillum kriegii
<6>NEB 972
<7>
<8>Kucera, R.B., Schildkraut, I., Unpublished observations.
Polisson, C., Unpublished observations.
Xu, S.-Y., Unpublished observations.

<1>OliI
<2>AleI
<3>CACNN^NNGTG
<4>
<5>Oceanospirillum linum 4-5D
<6>V. Butkus
<7>F
<8>Padegimiene, E., Maneliene, Z., Petrusyte, M., Janulaitis, A., (2001) Nucleic Acids Res., vol. 29.

<1>OmiAI
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Oceanospirillum minutulum
<6>NEB 970
<7>
<8>Polisson, C., Unpublished observations.

<1>OmiBI
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Oceanospirillum minutulum
<6>NEB 971
<7>
<8>Polisson, C., Unpublished observations.

<1>OmiBII
<2>AccI,DsaVI,FblI,XmiI
<3>GTMKAC
<4>
<5>Oceanospirillum minutulum
<6>NEB 971
<7>
<8>Polisson, C., Unpublished observations.

<1>M.OsaDnmt1A
<2>
<3>?
<4>?(5)
<5>Oryza sativa
<6>R.A. Wing
<7>
<8>Boukharov, A.A., Cao, Y., Dotson, S.B., Koshi, J.M., Kopvalic, D.K., Liu, J., McIninch, J.D., Wu, W., US Patent Office, 2008.
Buell, C.R. et al., Unpublished observations.
Teerawanichpan, P., Chandrasekharan, M.B., Jiang, Y.M., Narangajavana, J., Hall, T.C., (2004) Planta, vol. 218, pp. 337-349.

<1>M.OsaDnmt1B
<2>
<3>?
<4>?(5)
<5>Oryza sativa
<6>R.A. Wing
<7>
<8>Boukharov, A.A., Cao, Y., Dotson, S.B., Koshi, J.M., Kopvalic, D.K., Liu, J., McIninch, J.D., Wu, W., US Patent Office, 2008.
Sasaki, T., Matsumoto, T., Yamamoto, K., Unpublished observations.
Teerawanichpan, P., Chandrasekharan, M.B., Jiang, Y.M., Narangajavana, J., Hall, T.C., (2004) Planta, vol. 218, pp. 337-349.

<1>OspI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Oscillatoria splendida
<6>B.K. Hurlburt
<7>
<8>Hurlburt, B.K., Unpublished observations.

<1>OtuI
<2>AluI,AluBI,BsaLI,MarI,Mho2111I,MltI,OtuNI,OxaI,Uba1433I,Uba1441I
<3>AGCT
<4>
<5>Oerskovia turbata
<6>ATCC 27403
<7>
<8>Polisson, C., Unpublished observations.

<1>OtuNI
<2>AluI,AluBI,BsaLI,MarI,Mho2111I,MltI,OtuI,OxaI,Uba1433I,Uba1441I
<3>AGCT
<4>
<5>Oerskovia turbata
<6>ATCC 25835
<7>
<8>Hall, D., Unpublished observations.

<1>OxaI
<2>AluI,AluBI,BsaLI,MarI,Mho2111I,MltI,OtuI,OtuNI,Uba1433I,Uba1441I
<3>AGCT
<4>
<5>Oerskovia xanthineolytica
<6>R. Shekman
<7>
<8>Stotz, A., Philippson, P., Unpublished observations.

<1>OxaII
<2>
<3>?
<4>
<5>Oerskovia xanthineolytica
<6>R. Shekman
<7>
<8>Stotz, A., Philippson, P., Unpublished observations.

<1>OxaNI
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CC^TNAGG
<4>
<5>Oerskovia xanthineolytica N
<6>NEB 401
<7>
<8>Morgan, R., Ingalls, D., Unpublished observations.

<1>PabI
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PlaAII,RsaNI
<3>GTA^C
<4>3(6)
<5>Pyrococcus abyssi
<6>M. Genoscope
<7>
<8>Ishikawa, K., Watanabe, M., Kuroita, T., Uchiyama, I., Bujnicki, J.M., Kawakami, B., Tanokura, M., Kobayashi, I., (2005) Nucleic Acids Res., vol. 33.
Watanabe, M., Yuzawa, H., Handa, N., Kobayashi, I., (2006) Appl. Environ. Microbiol., vol. 72, pp. 5367-5375.

<1>PacI
<2>
<3>TTAAT^TAA
<4>
<5>Pseudomonas alcaligenes
<6>NEB 585
<7>NOW
<8>Kur, J., (1993) Acta Microbiol. Pol., vol. 42, pp. 145-150.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Polisson, C., European Patent Office, 1994.
Polisson, C., Fu, P., Unpublished observations.

<1>Pac25I
<2>SmaI,AhyI,Cfr9I,CfrJ4I,EaeAI,EclRI,KteAI,PaeBI,PspAI,PspALI,TspMI,Uba1220I,Uba1393I,XcyI,XmaI,XmaCI
<3>C^CCGGG
<4>?(4)
<5>Pseudomonas alcaligenes
<6>NCIB 9867
<7>
<8>Yeo, C.C., Tham, J.M., Kwong, S.M., Poh, C.L., (1998) Plasmid, vol. 40, pp. 203-213.

<1>Pac1110I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Pseudomonas alcaligenes RFL1110
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Dauksaite, V., Maneliene, Z., Kiuduliene, L., Bitinaite, J., Butkus, V., Unpublished observations.

<1>Pac1110II
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Pseudomonas alcaligenes RFL1110
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>PaeI
<2>SphI,Asp5HI,BbuI,BscOI,Bsp121I,BtgAII,CglAI,PaeCI,PfaAIII,RspLKI,SpaHI,SpaXI,Uba1162I,Uba1226I,VchO68I
<3>GCATG^C
<4>
<5>Pseudomonas aeruginosa
<6>N.N. Sokolov
<7>F
<8>Rimseliene, R., Vaisvila, R., Janulaitis, A., Unpublished observations.
Sokolov, N.N., Fitsner, A.B., Anikeitcheva, N.V., Choroshoutina, Y.B., Samko, O.T., Kolosha, V.O., Fodor, I., Votrin, I.I., (1985) Mol. Biol. Rep., vol. 10, pp. 159-161.

<1>Pae7I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Pseudomonas aeruginosa RFL7
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae8I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas aeruginosa RFL8
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae9I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas aeruginosa RFL9
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae14I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas aeruginosa RFL14
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae15I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas aeruginosa RFL15
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae17I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Pseudomonas aeruginosa RFL17
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae22I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas aeruginosa RFL22
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae24I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas aeruginosa RFL24
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae25I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas aeruginosa RFL25
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae26I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas aeruginosa RFL26
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae36I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Pseudomonas aeruginosa RFL36
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae39I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas aeruginosa RFL39
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae40I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas aeruginosa RFL40
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae41I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas aeruginosa RFL41
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae42I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Pseudomonas aeruginosa RFL42
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae43I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Pseudomonas aeruginosa RFL43
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae44I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Pseudomonas aeruginosa RFL44
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pae177I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Pseudomonas aeruginosa RFL177
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>Pae181I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Pseudomonas aeruginosa RFL181
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Unpublished observations.

<1>PaeAI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Pseudomonas aeruginosa
<6>CAMB 2549
<7>
<8>Riazuddin, S., Sohail, A., Maqbool, T., Khan, E., Mushtaq, R., (1987) Pak. J. Sci. Ind. Res., vol. 30, pp. 819-824.
Sohail, A., Unpublished observations.

<1>PaeBI
<2>SmaI,AhyI,Cfr9I,CfrJ4I,EaeAI,EclRI,KteAI,Pac25I,PspAI,PspALI,TspMI,Uba1220I,Uba1393I,XcyI,XmaI,XmaCI
<3>CCC^GGG
<4>
<5>Pseudomonas aeruginosa - 18
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., Kolosha, V.O., Fitsner, A.B., Anikeitcheva, N.V., Khoroshutina, E.B., Samko, O.T., Fodor, I., Votrin, I.I., (1986) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 24-26.

<1>PaeCI
<2>SphI,Asp5HI,BbuI,BscOI,Bsp121I,BtgAII,CglAI,PaeI,PfaAIII,RspLKI,SpaHI,SpaXI,Uba1162I,Uba1226I,VchO68I
<3>GCATGC
<4>
<5>Pseudomonas aeruginosa
<6>NRCC 5003
<7>
<8>Earle-Hughes, J., Roberts, R.J., Unpublished observations.

<1>PaeHI
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCY^C
<4>
<5>Pseudomonas aeruginosa 4148
<6>A.S. Solonin
<7>
<8>Kravetz, A.N., Tarutina, Z.E., Solonin, A.S., (1991) Nucleic Acids Res., vol. 19, pp. 4781.

<1>PaePI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Pseudomonas aeruginosa 4148
<6>A.S. Solonin
<7>
<8>Kravetz, A.N., Tarutina, Z.E., Solonin, A.S., (1991) Nucleic Acids Res., vol. 19, pp. 4781.

<1>PaeQI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Pseudomonas aeruginosa Q2
<6>CAMB 2637
<7>
<8>Choudhry, S., (1999) Proc. Pakistan Acad. Sci., vol. 36, pp. 165-171.

<1>PaeR7I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>5(6)
<5>Pseudomonas aeruginosa
<6>G.A. Jacoby
<7>N
<8>Ghosh, S.S., Eis, P.S., Blumeyer, K., Fearon, K., Millar, D.P., (1994) Nucleic Acids Res., vol. 22, pp. 3155-3159.
Gingeras, T.R., Brooks, J.E., (1983) Proc. Natl. Acad. Sci. U. S. A., vol. 80, pp. 402-406.
Hinkle, N.F., Miller, R.V., (1979) Plasmid, vol. 2, pp. 387-393.
Theriault, G., Roy, P.H., Howard, K.A., Benner, J.S., Brooks, J.S., Waters, A.F., Gingeras, T.R., (1985) Nucleic Acids Res., vol. 13, pp. 8441-8461.

<1>Pae2kI
<2>BglII,BseB631II,NcrI,NspMACI,Pae18kI
<3>A^GATCT
<4>
<5>Pseudomonas aeruginosa 2k
<6>A.S. Solonin
<7>
<8>Kravets, A.N., Pertsev, A.V., Tarutina, Z.Y., Krendelev, Y.D., Zakharova, M.V., Beletskaya, I.V., Solonin, A.S., (1998) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 14-17.

<1>Pae5kI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Pseudomonas aeruginosa 5k
<6>A.S. Solonin
<7>
<8>Kravets, A.N., Pertsev, A.V., Tarutina, Z.Y., Krendelev, Y.D., Zakharova, M.V., Beletskaya, I.V., Solonin, A.S., (1998) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 14-17.

<1>Pae14kI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Pseudomonas aeruginosa 14k
<6>A.S. Solonin
<7>
<8>Kravets, A.N., Pertsev, A.V., Tarutina, Z.Y., Krendelev, Y.D., Zakharova, M.V., Beletskaya, I.V., Solonin, A.S., (1998) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 14-17.

<1>Pae17kI
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>
<5>Pseudomonas aeruginosa 17k
<6>A.S. Solonin
<7>
<8>Kravets, A.N., Pertsev, A.V., Tarutina, Z.Y., Krendelev, Y.D., Zakharova, M.V., Beletskaya, I.V., Solonin, A.S., (1998) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 14-17.

<1>Pae18kI
<2>BglII,BseB631II,NcrI,NspMACI,Pae2kI
<3>A^GATCT
<4>
<5>Pseudomonas aeruginosa 18k
<6>A.S. Solonin
<7>
<8>Kravets, A.N., Pertsev, A.V., Tarutina, Z.Y., Krendelev, Y.D., Zakharova, M.V., Beletskaya, I.V., Solonin, A.S., (1998) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 14-17.

<1>PagI
<2>BspHI,CciI,RcaI,RhcI,RspXI
<3>T^CATGA
<4>
<5>Pseudomonas alcaligenes Sau 14-027
<6>A. Janulaitis
<7>F
<8>Maneliene, Z., Butkus, V., Unpublished observations.
Vitkute, J., Lazareviciute, L., Trinkunaite, L., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>PaiI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Pseudomonas alcaligenes
<6>ATCC 12815
<7>
<8>Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Bull. Inst. Chem. Res. Kyoto Univ., vol. 60, pp. 328-335.

<1>PalI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Providencia alcalifaciens
<6>ATCC 9886
<7>
<8>Gelinas, R.E., Myers, P.A., Roberts, R.J., Unpublished observations.
Rushizky, G.W., (1981) Gene Amplif. Anal., ed. Chirikjian, J.G. (Elsevier North Holland), vol. 1, pp. 239-242.

<1>PalAI
<2>AscI,SgsI
<3>GG^CGCGCC
<4>
<5>Pseudomonas alcaligenes BS17
<6>S.K. Degtyarev
<7>I
<8>Dedkov, V.S., Belichenko, O.A., Gonchar, D.A., Akishev, A.G., Yamkovaya, T.V., Mezentseva, N.V., Tomilova, J.E., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>PamI
<2>MstI,AcaIII,Acc16I,AosI,ApcTR183I,AviII,Bco6I,BsaTI,ClcII,CliII,FdiII,FspI,GspAII,NsbI,NspHIII,NspLI,NspMI,Pun14627I
<3>TGC^GCA
<4>
<5>Phormidium ambiguum
<6>A.J. Podhajska
<7>
<8>Piechula, S., Kim, S.C., Podhajska, A.J., (1992) Nucleic Acids Res., vol. 20, pp. 619.

<1>PamII
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,SspJII,SspM1II,SspM2II,Uba1381I
<3>GR^CGYC
<4>
<5>Phormidium ambiguum
<6>A.J. Podhajska
<7>
<8>Piechula, S., Kim, S.C., Podhajska, A.J., (1992) Nucleic Acids Res., vol. 20, pp. 619.

<1>PanI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Pseudomonas alkanolytica
<6>IFO 12319
<7>
<8>Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Bull. Inst. Chem. Res. Kyoto Univ., vol. 60, pp. 328-335.

<1>ParI
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>T^GATCA
<4>
<5>Pseudomonas aeroginosa
<6>Vivantis 21
<7>
<8>Chee, H.Y., Unpublished observations.

<1>PasI
<2>
<3>CC^CWGGG
<4>
<5>Pseudomonas anguilliseptica RFL1
<6>V. Butkus
<7>F
<8>Maneliene, Z., Zakareviciene, L., Unpublished observations.
Nekrasiene, D., Vitkute, J., Capskaja, L., Trinkunaite, L., Kiuduliene, L., Markauskas, A., Butkus, V., Janulaitis, A., Unpublished observations.

<1>PatAI
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PmnI,SfoI,SseAI,SspDI
<3>GGCGCC
<4>
<5>Pseudomonas atlantica
<6>ATCC 19262
<7>
<8>Polisson, C., Unpublished observations.

<1>PauI
<2>BsePI,BscEI,BsoPI,BsrHI,BssBI,BssHII,BstBZ153I,CfrJ5I,Eco143I,Eco152I,Esp7I,Esp8I,Kpn30I,McaTI,PteI,TtmII,Uba69I
<3>G^CGCGC
<4>
<5>Paracoccus alcaliphilus ZVK3-3
<6>A. Janulaitis
<7>F
<8>Maneliene, Z., Butkus, V., Unpublished observations.
Vitkute, J., Markauskiene, J., Maneliene, Z., Valickiene, D., Trinkunaite, L., Kiuduliene, E., Butkus, V., Janulaitis, A., Unpublished observations.

<1>PauAI
<2>NspI,AvoI,BstNSI,Lsp1270I,NspHI,PunAII,XceI
<3>RCATG^Y
<4>
<5>Phormidium autumnale
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>PauAII
<2>AhaIII,DraI,Srl19I,Srl61DI,Srl76DI,SruI
<3>TTT^AAA
<4>
<5>Phormidium autumnale
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>PbrTI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Previtella bryantii TC1-1
<6>G. Avgustin
<7>
<8>Accetto, T., Peterka, M., Avgustin, G., (2005) FEMS Microbiol. Lett., vol. 247, pp. 177-183.

<1>PbuJKI
<2>FokI,BseGI,BstF5I,BtsCI,HinGUII,Hpy178VI,HpyF6I,HpyF67III,StsI
<3>GGATG
<4>
<5>Pseudobutyrivibrio species JK 720
<6>P. Pristas
<7>
<8>Mrazek, J., Piknova, M., Pristas, P., Kopecny, J., (2005) Anaerobe, vol. 11, pp. 280-284.

<1>PbuMZI
<2>VspI,AseI,AsnI,BpoAI,CprJK722I,PshBI,Srl8DI,Srl55DII,Srl65DI,Srr17I,Sru4DI
<3>ATTAAT
<4>
<5>Pseudobutyrivibrio species MZ 1
<6>P. Pristas
<7>
<8>Mrazek, J., Piknova, M., Pristas, P., Kopecny, J., (2005) Anaerobe, vol. 11, pp. 280-284.

<1>Pca17AI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Pectobacterium carotovorum ssp. atrosepticum
<6>E. Lojkowska
<7>
<8>Waleron, K., Waleron, M., Osipiuk, J., Podhajska, A.J., Lojkowska, E., (2006) J. Appl. Microbiol., vol. 100, pp. 343-351.

<1>PceI
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGG^CCT
<4>
<5>Planococcus citreus 55
<6>S.K. Degtyarev
<7>IV
<8>Gonchar, D.A., Shinkarenko, N.M., Dedkov, V.S., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>PciI
<2>BspLU11I,PscI
<3>A^CATGT
<4>
<5>Planococcus citreus SE-F45
<6>NEB 1781
<7>IN
<8>Abdurashitov, M.A., Nayakshina, T.N., Lebedeva, N.A., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.
Zhu, Z., Blanchard, A., Xu, S.-Y., Guan, S., Wei, H., Zhang, P., Sun, D., Chan, S.-h., International Patent Office, 2009.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>PciSI
<2>SapI,BspQI,LguI,VpaK32I
<3>GCTCTTC(1/4)
<4>
<5>Planococcus citreus S
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Kileva, E.V., Tomilova, J.E., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>PctI
<2>BsmI,Asp26HI,Asp27HI,Asp35HI,Asp36HI,Asp40HI,Asp50HI,BmaHI,BsaMI,BscCI,Mva1269I,Uba1382I,Uba1415I
<3>GAATGC(1/-1)
<4>
<5>Planococcus citreus SM
<6>S.K. Degtyarev
<7>IV
<8>Dedkov, V.S., Nayakshina, T.N., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>Pde12I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>
<5>Paracoccus denitrificans 12
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Rechkunova, N.I., Novozhilova, M.I., Semenchenko, G.V., Galimdayeva, R.S., Soviet Patent Office, 1989.

<1>Pde133I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Paracoccus denitrificans 133
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>Pde137I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>C^CGG
<4>
<5>Paracoccus denitrificans 137
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>PdiI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCC^GGC
<4>
<5>Pseudomonas diminuta Mck 33-321
<6>V. Butkus
<7>F
<8>Vitkute, J., Mociskyte, S., Vaitkevicius, D., Maneliene, Z., Capskaja, L., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>PdmI
<2>XmnI,Asp700I,BbvAI,MroXI,Psc2I,SynII
<3>GAANN^NNTTC
<4>
<5>Pseudomonas diminuta Auk 5-324
<6>V. Butkus
<7>F
<8>Vitkute, J., Mociskyte, S., Vaitkevicius, D., Maneliene, Z., Norgeliene, D., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>Pei9403I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Pseudomonas eisenbergii MAFF 9403
<6>P.C. Shaw
<7>
<8>Leung, S.M., Chan, K.Y., Suen, Y.K., Shaw, P.C., (1989) Nucleic Acids Res., vol. 17, pp. 10133.

<1>PfaI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Pseudomonas facilis
<6>M. Van Montagu
<7>
<8>Van Montagu, M., Sciaky, D., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>PfaAI
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,Pph14I,SspM1III,Uba1127I,Vsp2246I
<3>G^GYRCC
<4>
<5>Phormidium favosum
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>PfaAII
<2>NdeI,FauNDI,TrsKTIII
<3>CA^TATG
<4>
<5>Phormidium favosum
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>PfaAIII
<2>SphI,Asp5HI,BbuI,BscOI,Bsp121I,BtgAII,CglAI,PaeI,PaeCI,RspLKI,SpaHI,SpaXI,Uba1162I,Uba1226I,VchO68I
<3>GCATG^C
<4>
<5>Phormidium favosum
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>PfeI
<2>TfiI
<3>G^AWTC
<4>
<5>Psychrobacter faecalis RFL1
<6>A. Janulaitis
<7>F
<8>Maneliene, Z., Zakareviciene, L., Unpublished observations.
Markauskiene, J., Capskaja, L., Kiuduliene, L., Petrusyte, M., Markauskas, A., Butkus, V., Janulaitis, A., Unpublished observations.

<1>PflI
<2>
<3>?
<4>
<5>Pseudomonas fluorescens
<6>IFO 3507
<7>
<8>Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Bull. Inst. Chem. Res. Kyoto Univ., vol. 60, pp. 328-335.

<1>Pfl8I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Pseudomonas fluorescens 8
<6>A.V. Pertsev
<7>
<8>Pertsev, A.V., Denmukhametov, M.M., Anoshkin, A.G., Ariskina, E.V., Berezin, I.A., Solonin, A.S., Kuzmin, N.P., (2000) Prikl. Biokhim. Mikrobiol., vol. 36, pp. 13-16.

<1>Pfl16I
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Pseudomonas fluoroviolaceus RFL16
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pfl18I
<2>SacI,BpuAmI,Ecl136II,Ecl137I,EcoICRI,Eco53kI,MxaI,NasSI,Psp124BI,ScoI,Ssm4I,Ssm5I,SstI
<3>GAGCTC
<4>
<5>Pseudomonas fluorescens RFL18
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pfl19I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Pseudomonas fluorescens RFL19
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pfl21I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Pseudomonas species 21
<6>A.V. Pertsev
<7>
<8>Pertsev, A.V., Denmukhametov, M.M., Anoshkin, A.G., Ariskina, E.V., Berezin, I.A., Solonin, A.S., Kuzmin, N.P., (2000) Prikl. Biokhim. Mikrobiol., vol. 36, pp. 13-16.

<1>Pfl23I
<2>ApaLI,AaqI,Alw44I,AmeI,Bsp146I,DaqI,Pfr12I,PliI,ScoNI,SnoI,Uba1203I,Uba1387I,VneI
<3>GTGCAC
<4>
<5>Pseudomonas fluorescens RFL23
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pfl23II
<2>SplI,BpuB5I,BsiWI,BsmWI,BvuBI,MaeK81I,PfuNI,PpuAI,PspLI,SmaAI,SplAI,SspKI,SunI
<3>C^GTACG
<4>
<5>Pseudomonas fluorescens RFL23
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Bitinaite, J., Maneliene, Z., Kiuduliene, L., Butkus, V., Unpublished observations.
Janulaitis, A., Maneliene, Z., Butkus, V., Unpublished observations.

<1>Pfl27I
<2>PpuMI,Mlu1106I,PpuXI,Psp5II,PspPPI
<3>RG^GWCCY
<4>
<5>Pseudomonas fluorescens RFL27
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Steponaviciene, D., Butkus, V., Maneliene, Z., Petrusyte, M., Unpublished observations.

<1>Pfl37I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas fluorescens RFL37
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pfl67I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Pseudomonas fluorescens RFL67
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pfl1108I
<2>
<3>TCGTAG
<4>
<5>Pseudomonas fluorescens RFL1108
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Dauksaite, V., Lazareviciute, L., Capskaya, L., Maneliene, Z., Kiuduliene, L., Bitinaite, J., Butkus, V., Unpublished observations.

<1>Pfl1108II
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Pseudomonas fluorescens RFL1108
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>PflAI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Pseudomonas fluorescens type A
<6>ATCC 17582
<7>
<8>Polisson, C., Unpublished observations.

<1>PflBI
<2>PflMI,AccB7I,AcpII,Asp10HII,BasI,Esp1396I,Van91I
<3>CCANNNN^NTGG
<4>
<5>Pseudomonas fluorescens type B
<6>M.M. Wijdenbosch
<7>
<8>Waaijer, R.J.A., Unpublished observations.

<1>PflFI
<2>Tth111I,AspI,AtsI,BgiI,FsuI,NtaI,PsyI,SmaAII,SpaPI,SplII,SplAII,TelI,TrsKTII,TspI,TteI,TtrI
<3>GACN^NNGTC
<4>
<5>Pseudomonas fluorescens biotype F
<6>NEB 999
<7>N
<8>Nkenfou, C., Polisson, C., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>PflKI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Pseudomonas fluorescens
<6>CAMB 2619
<7>
<8>Mushtaq, R., Sohail, A., Arif, A., Niazi, I.K., Unpublished observations.

<1>PflMI
<2>AccB7I,AcpII,Asp10HII,BasI,Esp1396I,PflBI,Van91I
<3>CCANNNN^NTGG
<4>
<5>Pseudomonas fluorescens
<6>NEB 375
<7>N
<8>Morgan, R.D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Nwankwo, D., Unpublished observations.

<1>PflNI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Pseudomonas fluorescens
<6>ATCC 33512
<7>
<8>Hall, D., Unpublished observations.

<1>PflWI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Pseudomonas fluorescens
<6>T.S. Wang
<7>
<8>Wang, T.-S., (1981) K'o Hsueh T'ung Pao, vol. 26, pp. 815-817.

<1>PfoI
<2>
<3>T^CCNGGA
<4>
<5>Pseudomonas fluorescens biovar 126
<6>A. Janulaitis
<7>F
<8>Gaigalas, M., Maneliene, Z., Kazlauskiene, R., Petrusyte, M., Janulaitis, A., (2002) Nucleic Acids Res., vol. 30.

<1>Pfr12I
<2>ApaLI,AaqI,Alw44I,AmeI,Bsp146I,DaqI,Pfl23I,PliI,ScoNI,SnoI,Uba1203I,Uba1387I,VneI
<3>GTGCAC
<4>
<5>Pseudomonas fragi RFL12
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>PfuNI
<2>SplI,BpuB5I,BsiWI,BsmWI,BvuBI,MaeK81I,Pfl23II,PpuAI,PspLI,SmaAI,SplAI,SspKI,SunI
<3>CGTACG
<4>
<5>Pseudomonas fluorescens
<6>NEB 431
<7>
<8>Polisson, C., Unpublished observations.

<1>PgaI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Pseudomonas gladioli B4
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Repin, V.E., Rechkunova, N.I., Degtyarev, S.K., Verhosina, V.A., Vinogradova, T.P., (1990) Izv. Sib. Otd. Akad. Nauk SSSR, vol. 1, pp. 35-37.

<1>M.PgiI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Porphyromonas gingivalis
<6>A. Progulske-Fox
<7>
<8>Banas, J.A., Ferretti, J.J., Progulske-Fox, A., (1991) Nucleic Acids Res., vol. 19, pp. 4189-4192.

<1>PglI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Pseudomonas glycinae
<6>J.V. Leary
<7>
<8>Leary, J.V., Unpublished observations.

<1>PglII
<2>
<3>?
<4>
<5>Pseudomonas glycinae
<6>J.V. Leary
<7>
<8>Leary, J.V., Unpublished observations.

<1>Pgl34I
<2>PmaCI,AcvI,BbrPI,BcoAI,Bsp87I,Eco72I,PmlI,PshCI,PshDI,Psp38I,PspBI,PspCI,VpaK3AI,VpaK3BI
<3>CACGTG
<4>
<5>Pseudomonas glathei RFL34
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>PhaI
<2>SfaNI,BhaI,BmsI,BscAI,BscUI,BsmNI,BspST5I,Bst19I,CjeP338II,LweI
<3>GCATC(5/9)
<4>
<5>Pasteurella haemolytica
<6>G.H. Frank
<7>
<8>Briggs, R.E., Tatum, F.M., US Patent Office, 1997.
Briggs, R.E., Tatum, F.M., US Patent Office, 1997.
Briggs, R.E., Tatum, F.M., Casey, T.A., Frank, G.H., (1994) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 94, pp. 132.
Briggs, R.E., Tatum, F.M., Casey, T.A., Frank, G.H., (1994) Appl. Environ. Microbiol., vol. 60, pp. 2006-2010.
Tatum, F.M., Briggs, R.E., (1993) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 93, pp. 199.

<1>PhaAI
<2>
<3>?
<4>
<5>Pasteurella haemolytica
<6>S.K. Highlander
<7>
<8>Highlander, S.K., Garza, O., (1996) Gene, vol. 178, pp. 89-96.

<1>PhaBI
<2>
<3>?
<4>
<5>Pasteurella haemolytica
<6>P.E. Shewen
<7>
<8>Ryan, K.A., Lo, Y.C., (1999) Nucleic Acids Res., vol. 27, pp. 1505-1511.

<1>M.PhaTDam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Pseudoalteromonas haloplanktis TAC125
<6>C. Medigue
<7>
<8>Medigue, C. et al., (2005) Genome Res., vol. 15, pp. 1325-1335.

<1>M.PhiHII
<2>
<3>?
<4>?(4)
<5>Halobacterium salinarium bacteriophage PhiH
<6>W. Zillig
<7>
<8>Stolt, P., Grampp, B., Zillig, W., (1994) Biol. Chem. Hoppe Seyler, vol. 375, pp. 747-757.

<1>M.PhiMx8I
<2>
<3>CTSSAG
<4>5(6)
<5>Myxococcus xanthus phage Mx8
<6>P. Youderian
<7>
<8>Magrini, V., Salmi, D., Thomas, D., Herbert, S.K., Hartzell, P.L., Youderian, P., (1997) J. Bacteriol., vol. 179, pp. 4254-4263.

<1>M.Phi3TI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC,GCNGC
<4>3(5), 2(5)
<5>Bacillus subtilis phage Phi3T
<6>T.A. Trautner
<7>
<8>Gunthert, U., Trautner, T.A., (1984) Curr. Top. Microbiol. Immunol., vol. 108, pp. 11-22.
Noyer-Weidner, M., German Patent Office, 1989.
Noyer-Weidner, M., Jentsch, S., Kupsch, J., Bergbauer, M., Trautner, T.A., (1985) Gene, vol. 35, pp. 143-150.
Noyer-Weidner, M., Pawlek, B., Jentsch, S., Gunthert, U., Trautner, T.A., (1981) J. Virol., vol. 38, pp. 1077-1080.

<1>M.Phi3TII
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>2(5)
<5>Bacillus subtilis phage Phi3T
<6>T.A. Trautner
<7>
<8>Noyer-Weidner, M., Walter, J., Terschuren, P.-A., Chai, S., Trautner, T.A., (1994) Nucleic Acids Res., vol. 22, pp. 4066-4072.
Noyer-Weidner, M., Walter, J., Terschuren, P.-A., Chai, S., Trautner, T.A., (1994) Nucleic Acids Res., vol. 22, pp. 5517-5523.

<1>PhoI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>?(4)
<5>Pyrococcus horikoshii OT3
<6>Y. Kawarabayasi
<7>N
<8>Kawarabayasi, Y. et al., (1998) DNA Res., vol. 5, pp. 147-155.
Opitz, L., Xu, S.-Y., Unpublished observations.
Xu, S.-Y., Unpublished observations.

<1>PinI
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGTACT
<4>
<5>Pseudomonas indigofera
<6>ATCC 14036
<7>
<8>Klein, S., Roberts, R.J., Unpublished observations.

<1>PinAI
<2>AgeI,AsiAI,AsiGI,BshTI,CsiAI,CspAI
<3>A^CCGGT
<4>
<5>Pseudomonas inequalis
<6>M.M. Wijdenbosch
<7>BMQX
<8>Groot, E., Unpublished observations.

<1>PinBI
<2>AvaIII,Asi372I,BfrBI,BfrCI,Csp68KIII,EcoT22I,Mph1103I,NsiI,Ppu10I,PxyJKI,SepI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>ATGCA^T
<4>
<5>Phormidium inundatum
<6>CCAP 1462/9
<7>
<8>Piechula, S., Kur, J., Woszczyk, J., Podhajska, A.J., (1995) Gene, vol. 157, pp. 315-316.

<1>PinBII
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>
<5>Phormidium inundatum
<6>CCAP 1462/9
<7>
<8>Piechula, S., Kur, J., Woszczyk, J., Podhajska, A.J., (1995) Gene, vol. 157, pp. 315-316.

<1>PlaI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Phormidium lapideum
<6>H. Ochiai
<7>
<8>Ochiai, H., Shibata, H., Sawa, Y., Ashida, N., (1989) Bull. Fac. Agr. Shimane Univ., vol. 23, pp. 184-191.

<1>PlaII
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Phormidium lapideum
<6>H. Ochiai
<7>
<8>Ochiai, H., Shibata, H., Sawa, Y., Ashida, N., (1989) Bull. Fac. Agr. Shimane Univ., vol. 23, pp. 184-191.

<1>PlaAI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>
<5>Phormidium laminosum
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>PlaAII
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,RsaNI
<3>GT^AC
<4>
<5>Phormidium laminosum
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>PlaDI
<2>
<3>CATCAG(21/19)
<4>
<5>Parvibaculum lavamentivorans DS-1
<6>DSM 13023
<7>
<8>Copeland, A. et al., Unpublished observations.
Dwinnel, E., Morgan, R.D., Unpublished observations.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>PleI
<2>BsmEI,BspD6I,MlyI,PpsI,SchI
<3>GAGTC(4/5)
<4>
<5>Pseudomonas lemoignei
<6>NEB 418
<7>N
<8>Kong, H., Higgins, L., Dalton, M., Kucera, R., Schildkraut, I., Wilson, G., European Patent Office, 2007.
Kong, H., Higgins, L.S., US Patent Office, 2002.
Morgan, R., Stote, R., Soltis, A., Unpublished observations.

<1>Ple19I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGAT^CG
<4>
<5>Pseudomonas lemoignei 19
<6>S.K. Degtyarev
<7>I
<8>Semenchenko, G.V., Rechkunova, N.I., Degtyarev, S.K., Unpublished observations.

<1>Ple214I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Photobacterium leiognathi
<6>V.E. Repin
<7>
<8>Repin, V.E., Unpublished observations.

<1>PliI
<2>ApaLI,AaqI,Alw44I,AmeI,Bsp146I,DaqI,Pfl23I,Pfr12I,ScoNI,SnoI,Uba1203I,Uba1387I,VneI
<3>GTGCAC
<4>
<5>Pseudomonas lindbergii
<6>ATCC 31099
<7>
<8>Klein, S., Roberts, R.J., Unpublished observations.

<1>M.PliMCDnmt1
<2>
<3>?
<4>?(5)
<5>Paracentrotus lividus
<6>M. Branno
<7>
<8>Aniello, F., Locascio, A., Fucci, L., Geraci, G., Branno, M., (1996) Gene, vol. 178, pp. 57-61.
Branno, M., Unpublished observations.

<1>PluI
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGGCCT
<4>
<5>Pseudomonas fluorescens
<6>Viikki 152
<7>
<8>Mattila, P., Pitkanen, K., Unpublished observations.

<1>PmaI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas maltophilia
<6>D.G. Comb
<7>
<8>Schildkraut, I., Unpublished observations.

<1>Pma44I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas maltophilia
<6>CAMB 2550
<7>
<8>Sohail, A., Khan, E., Maqbool, T., Riazuddin, S., Unpublished observations.

<1>PmaCI
<2>AcvI,BbrPI,BcoAI,Bsp87I,Eco72I,Pgl34I,PmlI,PshCI,PshDI,Psp38I,PspBI,PspCI,VpaK3AI,VpaK3BI
<3>CAC^GTG
<4>
<5>Pseudomonas maltophilia CB50P
<6>C.A. Hart
<7>K
<8>Walker, J.N.B., Dean, P.D.G., Saunders, J.R., (1986) Nucleic Acids Res., vol. 14, pp. 1293-1301.

<1>PmdI
<2>BbvCI,AbeI
<3>CCTCAGC
<4>
<5>Pseudomonas mandelii RFL49
<6>Fermentas G350
<7>
<8>Vitkute, J., Valiulyte, D., Trinkunaite, L., Norgeliene, D., Janulaitis, A., Unpublished observations.

<1>PmeI
<2>MssI
<3>GTTT^AAAC
<4>
<5>Pseudomonas mendocina
<6>NEB 698
<7>NW
<8>Chang, Z., Morgan, R.D., US Patent Office, 1999.
Morgan, R., Zhou, B., US Patent Office, 1993.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>Pme35I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Pseudomonas medicaginis RFL35
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Pme55I
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGG^CCT
<4>
<5>Pseudomonas mendocina 55
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>PmiI
<2>
<3>?
<4>
<5>Proteus mirabilis
<6>N.L. Bakh
<7>
<8>Bakh, N.L., Tsvetkova, N.V., Semina, I.E., Tarasov, A.P., Mileikovskaya, M.M., Gruber, I.M., Polyachenko, V.M., Romanenko, E.E., (1985) Antibiot. Med. Biotekhnol., vol. 30, pp. 342-344.

<1>PmlI
<2>PmaCI,AcvI,BbrPI,BcoAI,Bsp87I,Eco72I,Pgl34I,PshCI,PshDI,Psp38I,PspBI,PspCI,VpaK3AI,VpaK3BI
<3>CAC^GTG
<4>
<5>Pseudomonas maltophilia
<6>NEB 515
<7>N
<8>Tenkanen, T., Unpublished observations.

<1>PmnI
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,SfoI,SseAI,SspDI
<3>GGCGCC
<4>
<5>Photobacterium mandapamensis 579
<6>V.E. Repin
<7>
<8>Repin, V.E., Puchkova, L.I., Rodicheva, E.K., Vydryakova, G.A., (1997) Prikl. Biokhim. Mikrobiol., vol. 33, pp. 152-155.

<1>M.PmuADam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Pasteurella multocida
<6>ATCC 11039
<7>
<8>Chen, L., Paulsen, D.B., Lawrence, M.L., Unpublished observations.
Chen, L., Paulsen, D.B., Scruggs, D.W., Banes, M.M., Reeks, B.Y., Lawrence, M.L., (2003) Microbiology, vol. 149, pp. 2283-2290.

<1>M.PmuDam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Pasteurella multocida Pm70
<6>V. Kapur
<7>
<8>Chen, L., Paulsen, D.B., Lawrence, M.L., Unpublished observations.

<1>PmyI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Proteus myxofaciens
<6>ATCC 19692
<7>
<8>Weule, K., Roberts, R.J., Unpublished observations.

<1>PntI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Propionibacterium intermedium
<6>ATCC 14072
<7>
<8>Mattila, P., Pitkanen, K., Unpublished observations.

<1>PolI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Pseudomonas oleovorans
<6>Viikki 13
<7>
<8>Mattila, P., Pitkanen, K., Unpublished observations.

<1>PovI
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Pseudomonas ovalis
<6>S. Riazuddin
<7>
<8>Faruqi, A.F., Ahmed, N., (1987) Pak. J. Sci. Ind. Res., vol. 30, pp. 390-392.
Sohail, A., Mushtaq, R., Khan, E., Maqbool, T., Riazuddin, S., (1987) Pak. J. Zool., vol. 19, pp. 371-391.

<1>PpaI
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Pseudomonas paucimobilis
<6>NEB 376
<7>
<8>Morgan, R.D., Unpublished observations.

<1>PpaAI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Phormidium papyraceum
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>PpaAII
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>T^CGA
<4>
<5>Phormidium papyraceum
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>PpeI
<2>ApaI,Bsp120I,EciEI,Psp30I,PspOMI,Uba1156I,Uba1157I,Uba1165I,Uba1202I,Uba1241I,Uba1368I
<3>GGGCC^C
<4>
<5>Phormidium persicinum
<6>CCAP 1462/5
<7>
<8>Piechula, S., Piosik, J., Bielawski, K., Podhajska, A.J., (1996) Mol. Biotechnol., vol. 5, pp. 97-99.

<1>Pph14I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,SspM1III,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Photobacterium phosphoreum 14
<6>V.E. Repin
<7>
<8>Repin, V.E., Puchkova, L.I., Rodicheva, E.K., Vydryakova, G.A., (1995) Microbiology, vol. 64, pp. 751-755.

<1>Pph288I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Photobacterium phosphoreum 288
<6>V.E. Repin
<7>
<8>Repin, V.E., Unpublished observations.

<1>Pph1579I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Photobacterium phosphoreum 1579
<6>V.E. Repin
<7>
<8>Repin, V.E., Unpublished observations.

<1>Pph1591I
<2>
<3>?
<4>
<5>Photobacterium phosphoreum 1591
<6>V.E. Repin
<7>
<8>Repin, V.E., Puchkova, L.I., Rodicheva, E.K., Vydryakova, G.A., (1995) Microbiology, vol. 64, pp. 751-755.

<1>Pph1773I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Photobacterium phosphoreum 1773
<6>V.E. Repin
<7>
<8>Repin, V.E., Unpublished observations.

<1>Pph2059I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Photobacterium phosphoreum 2059
<6>V.E. Repin
<7>
<8>Repin, V.E., Unpublished observations.

<1>Pph2066I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Photobacterium phosphoreum 2066
<6>V.E. Repin
<7>
<8>Repin, V.E., Puchkova, L.I., Rodicheva, E.K., Vydryakova, G.A., (1995) Microbiology, vol. 64, pp. 751-755.

<1>Pph3215I
<2>HgiAI,Alw21I,AspHI,Bbv12I,Bfu1570I,BsaGI,Bsh45I,BsiHKAI,Bsm6I,BsmPI,Hpy8III,HpyF7II,HpyF46II,MspV281I
<3>GWGCWC
<4>
<5>Pseudomonas phaseolicola 3215
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>PpiI
<2>
<3>(7/12)GAACNNNNNCTC(13/8)
<4>
<5>Pseudomonas putida Jo 4-731
<6>V. Butkus
<7>F
<8>Jurenaite-Urbanaviciene, S., Serksnaite, J., Kriukiene, E., Giedriene, J., Venclovas, C., Lubys, A., (2007) Proc. Natl. Acad. Sci. U. S. A., vol. 104, pp. 10358-10363.
Maneliene, Z., Butkus, V., Unpublished observations.
Vitkute, J., Kairaitiene, R., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>PpsI
<2>PleI,BsmEI,BspD6I,MlyI,SchI
<3>GAGTC(4/5)
<4>
<5>Pseudomonas pseudoalcaligenes PL
<6>S.K. Degtyarev
<7>I
<8>Dedkov, V.S., Bondar, T.S., Shevchenko, A.V., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>PpuI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Pseudomonas putida C-83
<6>Toyobo
<7>
<8>Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Bull. Inst. Chem. Res. Kyoto Univ., vol. 60, pp. 328-335.

<1>Ppu6I
<2>BsaAI,BstBAI,MspYI,Ppu11I,Ppu21I,PsuAI
<3>YACGTR
<4>
<5>Pseudomonas putida RFL6
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Ppu10I
<2>AvaIII,Asi372I,BfrBI,BfrCI,Csp68KIII,EcoT22I,Mph1103I,NsiI,PinBI,PxyJKI,SepI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>A^TGCAT
<4>
<5>Pseudomonas putida RFL10
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.
Janulaitis, A., Maneliene, Z., Butkus, V., Unpublished observations.

<1>Ppu11I
<2>BsaAI,BstBAI,MspYI,Ppu6I,Ppu21I,PsuAI
<3>YACGTR
<4>
<5>Pseudomonas putida RFL11
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Ppu13I
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGGCCT
<4>
<5>Pseudomonas putida RFL13
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Ppu20I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Pseudomonas putida RFL20
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Ppu21I
<2>BsaAI,BstBAI,MspYI,Ppu6I,Ppu11I,PsuAI
<3>YAC^GTR
<4>
<5>Pseudomonas putida RFL21
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Lazareviciute, L., Bitinaite, J., Maneliene, Z., Kiuduliene, L., Butkus, V., Unpublished observations.
Maneliene, Z., Zakareviciene, L., Lubys, A., Unpublished observations.
Vaisvila, R., Sliesaraviciute, Z., Kulakauskas, S., Janulaitis, A., (1995) Gene, vol. 157, pp. 55-57.

<1>Ppu111I
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco237I,Eco252I,FunII,HalI,Hal22I,Kpn49kI,RsrI,Srl32DII,Srl55DI,SsoI,Uba58I,Van91II,VchN100I,VchO2I
<3>G^AATTC
<4>
<5>Pseudomonas putida P111
<6>D. Focht
<7>
<8>Brenner, V., Focht, D.D., (1994) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 94, pp. 459.

<1>Ppu1253I
<2>AatII,AspJI,Ssp5230I,ZraI
<3>GACGTC
<4>
<5>Pseudomonas putida RFL1253
<6>A. Janulaitis
<7>
<8>Dauksaite, V., Janulaitis, A., Unpublished observations.
Janulaitis, A., Unpublished observations.

<1>PpuAI
<2>SplI,BpuB5I,BsiWI,BsmWI,BvuBI,MaeK81I,Pfl23II,PfuNI,PspLI,SmaAI,SplAI,SspKI,SunI
<3>C^GTACG
<4>
<5>Pseudomonas putida A1
<6>P. Adams
<7>
<8>Nelson, M., Unpublished observations.

<1>PpuMI
<2>Mlu1106I,Pfl27I,PpuXI,Psp5II,PspPPI
<3>RG^GWCCY
<4>?(5)
<5>Pseudomonas putida M
<6>NEB 372
<7>NO
<8>Morgan, R., Hempstead, S.K., Unpublished observations.
Samuelson, J., Xu, S.-Y., Unpublished observations.

<1>PpuXI
<2>PpuMI,Mlu1106I,Pfl27I,Psp5II,PspPPI
<3>RG^GWCCY
<4>
<5>Pseudomonas putida X
<6>M.M. Wijdenbosch
<7>
<8>Verhoef, C., Afram, C., Unpublished observations.

<1>Pru2I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Previtella ruminicola 23
<6>G. Avgustin
<7>
<8>Accetto, T., Peterka, M., Avgustin, G., (2005) FEMS Microbiol. Lett., vol. 247, pp. 177-183.

<1>M.PsaDnmt1
<2>
<3>?
<4>?(5)
<5>Pisum sativum
<6>R.L.P. Adams
<7>
<8>Pradhan, S., Cummings, M., Roberts, R.J., Adams, R.L.P., (1998) Nucleic Acids Res., vol. 26, pp. 1214-1222.

<1>Psb9879I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Polar sea bacterium R9879, C5SW4c3
<6>A. Murray
<7>
<8>Miller, J., Murray, A., Bhatia, T., Morgan, R.D., Unpublished observations.

<1>PscI
<2>BspLU11I,PciI
<3>A^CATGT
<4>
<5>Paracoccus species RFL1
<6>Fermentas G291
<7>F
<8>Lauciuniene, N., Vitkute, J., Maneliene, Z., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>Psc2I
<2>XmnI,Asp700I,BbvAI,MroXI,PdmI,SynII
<3>GAANNNNTTC
<4>
<5>Planktothrix species 2
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Psc2II
<2>
<3>?
<4>
<5>Planktothrix species 2
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Psc18I
<2>
<3>?
<4>
<5>Planktothrix species 18
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Psc27I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Planktothrix species 27
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Psc28I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Planktothrix species 28
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Psc45I
<2>
<3>?
<4>
<5>Planktothrix species 45
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Psc49I
<2>
<3>?
<4>
<5>Planktothrix species 49
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Psc97I
<2>
<3>?
<4>
<5>Planktothrix species 97
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Psc126I
<2>
<3>?
<4>
<5>Planktothrix species NIVA-CYA126
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Psc128I
<2>
<3>?
<4>
<5>Planktothrix species NIVA-CYA128
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>Psc193I
<2>
<3>?
<4>
<5>Planktothrix species 193
<6>K. Sivonen
<7>
<8>Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., Sivonen, K., (2000) J. Appl. Microbiol., vol. 89, pp. 979-991.

<1>PseI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Pseudoanabaena species
<6>ATCC 29541
<7>
<8>de Waard, A., Unpublished observations.

<1>PshAI
<2>BoxI,BstPAI
<3>GACNN^NNGTC
<4>2(6)
<5>Plesiomonas shigelloides 319-73
<6>T. Shimada
<7>KN
<8>Chang, Z., Morgan, R.D., European Patent Office, 1997.
Miyahara, M., Nakajima, K., Shimada, T., Mise, K., (1990) Gene, vol. 87, pp. 119-122.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>PshBI
<2>VspI,AseI,AsnI,BpoAI,CprJK722I,PbuMZI,Srl8DI,Srl55DII,Srl65DI,Srr17I,Sru4DI
<3>AT^TAAT
<4>
<5>Plesiomonas shigelloides TPS970
<6>S. Matsushita
<7>K
<8>Miyahara, M., Kimizuka, F., Kita, A., Matsushita, S., Kudo, Y., Shimada, T., Mise, K., (1996) Biol. Pharm. Bull., vol. 19, pp. 1506-1507.

<1>PshCI
<2>PmaCI,AcvI,BbrPI,BcoAI,Bsp87I,Eco72I,Pgl34I,PmlI,PshDI,Psp38I,PspBI,PspCI,VpaK3AI,VpaK3BI
<3>CACGTG
<4>
<5>Plesiomonas shigelloides PL50
<6>T. Shimada
<7>
<8>Miyahara, M., Kimizuka, F., Kita, A., Matsushita, S., Kudo, Y., Shimada, T., Mise, K., (1996) Biol. Pharm. Bull., vol. 19, pp. 1506-1507.

<1>PshDI
<2>PmaCI,AcvI,BbrPI,BcoAI,Bsp87I,Eco72I,Pgl34I,PmlI,PshCI,Psp38I,PspBI,PspCI,VpaK3AI,VpaK3BI
<3>CACGTG
<4>
<5>Plesiomonas shigelloides PL59
<6>T. Shimada
<7>
<8>Miyahara, M., Kimizuka, F., Kita, A., Matsushita, S., Kudo, Y., Shimada, T., Mise, K., (1996) Biol. Pharm. Bull., vol. 19, pp. 1506-1507.

<1>PshEI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Plesiomonas shigelloides TPS1044
<6>S. Matsushita
<7>
<8>Miyahara, M., Kimizuka, F., Kita, A., Matsushita, S., Kudo, Y., Shimada, T., Mise, K., (1996) Biol. Pharm. Bull., vol. 19, pp. 1506-1507.

<1>PsiI
<2>AanI
<3>TTA^TAA
<4>
<5>Pseudomonas species SE-G49
<6>NEB 1784
<7>INO
<8>Abdurashitov, M.A., Belichenko, O.A., Lebedeva, N.A., Degtyarev, S.Kh., (1999) Biokhimiia, vol. 64, pp. 574-576.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>PspI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Pseudoanabaena species
<6>ATCC 27263
<7>
<8>Mulligan, B.J., Szekeres, M., Unpublished observations.

<1>Psp03I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWC^C
<4>
<5>Phormidium species
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>Psp3I
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAGCTG
<4>
<5>Pseudomonas species RFL3
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Psp4I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Pseudomonas species RFL4
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Psp5I
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAGCTG
<4>
<5>Pseudomonas species RFL5
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Maneliene, Z., Capskaya, L., Kiuduliene, L., Butkus, V., Unpublished observations.

<1>Psp5II
<2>PpuMI,Mlu1106I,Pfl27I,PpuXI,PspPPI
<3>RG^GWCCY
<4>
<5>Pseudomonas species RFL5
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Unpublished observations.
Janulaitis, A., Petrusyte, M., Maneliene, Z., Capskaya, L., Kiuduliene, L., Butkus, V., Unpublished observations.

<1>Psp6I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>^CCWGG
<4>
<5>Pseudomonas species B6
<6>S.K. Degtyarev
<7>I
<8>Dedkov, V.S., Tomilova, J.E., Kileva, E.V., Degtyarev, S.K., Unpublished observations.

<1>Psp23I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Pseudomonas species 23
<6>A.V. Pertsev
<7>
<8>Pertsev, A.V., Denmukhametov, M.M., Anoshkin, A.G., Ariskina, E.V., Berezin, I.A., Solonin, A.S., Kuzmin, N.P., (2000) Prikl. Biokhim. Mikrobiol., vol. 36, pp. 13-16.

<1>Psp28I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas species RFL28
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Psp29I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Pseudomonas species RFL29
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Psp30I
<2>ApaI,Bsp120I,EciEI,PpeI,PspOMI,Uba1156I,Uba1157I,Uba1165I,Uba1202I,Uba1241I,Uba1368I
<3>GGGCCC
<4>
<5>Pseudomonas species RFL30
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Psp31I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Pseudomonas species RFL31
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Psp32I
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Pseudomonas species RFL32
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Psp33I
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Pseudomonas species RFL33
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Psp38I
<2>PmaCI,AcvI,BbrPI,BcoAI,Bsp87I,Eco72I,Pgl34I,PmlI,PshCI,PshDI,PspBI,PspCI,VpaK3AI,VpaK3BI
<3>CACGTG
<4>
<5>Pseudomonas species RFL38
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Psp39I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Pseudoalteromonas species 39 C65DMSP4c2
<6>A. Murray
<7>
<8>Miller, J., Murray, A., Bhatia, T., Morgan, R.D., Unpublished observations.

<1>Psp46I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas species RFL46
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Psp56I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Pseudomonas species RFL56
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Jagelavicius, M., Bitinaite, J., Unpublished observations.

<1>Psp61I
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Pseudomonas species MS61
<6>M. Sargent
<7>
<8>Walker, J.N.B., Dean, P.G., Saunders, J.R., Unpublished observations.

<1>Psp89I
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Pseudomonas species RFL89
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Psp1009I
<2>BglI,Bpu86I,BseB631I,BsoJI,Tsp219I,Tsp8EI,VanI
<3>GCCNNNN^NGGC
<4>
<5>Paenibacillus species
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Andreeva, I.S., Saranina, I.V., Pechurkina, N.I., Afonina, V.S., Repin, V.E., Russian Patent Office, 2008.

<1>Psp1406I
<2>AclI,UbaN9I
<3>AA^CGTT
<4>
<5>Pseudomonas pseudoalcaligenes RFL1406
<6>A. Janulaitis
<7>FK
<8>Janulaitis, A., Steponaviciene, D., Petrusyte, M., Maneliene, Z., Norgeliene, D., Vonseviciene, E., Kiuduliene, L., Butkus, V., Unpublished observations.

<1>PspAI
<2>SmaI,AhyI,Cfr9I,CfrJ4I,EaeAI,EclRI,KteAI,Pac25I,PaeBI,PspALI,TspMI,Uba1220I,Uba1393I,XcyI,XmaI,XmaCI
<3>C^CCGGG
<4>
<5>Pseudomonas species
<6>D. White
<7>
<8>White, D., Simcox, T.G., Unpublished observations.

<1>PspALI
<2>SmaI,AhyI,Cfr9I,CfrJ4I,EaeAI,EclRI,KteAI,Pac25I,PaeBI,PspAI,TspMI,Uba1220I,Uba1393I,XcyI,XmaI,XmaCI
<3>CCC^GGG
<4>
<5>Pseudomonas species AL1637
<6>S.K. Degtyarev
<7>
<8>Belichenko, O.A., Shevchenko, A.V., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>PspBI
<2>PmaCI,AcvI,BbrPI,BcoAI,Bsp87I,Eco72I,Pgl34I,PmlI,PshCI,PshDI,Psp38I,PspCI,VpaK3AI,VpaK3BI
<3>CACGTG
<4>
<5>Pseudomonas species
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>Psp124BI
<2>SacI,BpuAmI,Ecl136II,Ecl137I,EcoICRI,Eco53kI,MxaI,NasSI,Pfl18I,ScoI,Ssm4I,Ssm5I,SstI
<3>GAGCT^C
<4>
<5>Pseudomonas species 124B
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.K., Dedkov, V.S., Rechkunova, N.I., Morgan, R., Unpublished observations.

<1>PspCI
<2>PmaCI,AcvI,BbrPI,BcoAI,Bsp87I,Eco72I,Pgl34I,PmlI,PshCI,PshDI,Psp38I,PspBI,VpaK3AI,VpaK3BI
<3>CAC^GTG
<4>
<5>Pseudomonas species C
<6>S.K. Degtyarev
<7>IV
<8>Tronin, A., Kileva, E.V., Mezentseva, N., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>PspDI
<2>NruI,AmaSI,Bsp68I,BtuMI,Mlu9273I,MluB2I,RruI,SalDI,Sbo13I,Sna3286I,SpoI,Uba1117I,Uba1386I,VchO70I
<3>TCGCGA
<4>
<5>Pseudomonas species
<6>NEB 1538
<7>
<8>Xu, D., Xu, S.-Y., Unpublished observations.

<1>PspEI
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,SciAI,Uba1291I
<3>G^GTNACC
<4>
<5>Pseudomonas species E
<6>S.K. Degtyarev
<7>IV
<8>Dedkov, V.S., Rechkunova, N.I., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>PspFI
<2>BseYI,GsaI
<3>CCCAGC
<4>
<5>Paenibacillus species RFL1
<6>Fermentas G332
<7>
<8>Vitkute, J., Lapcinskaja, S., Capskaja, L., Trinkunaite, L., Janulaitis, A., Unpublished observations.

<1>PspGI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>^CCWGG
<4>?(4)
<5>Pyrococcus species G1H
<6>NEB 906
<7>N
<8>Morgan, R., Xiao, J.-P., Xu, S.-Y., (1998) Appl. Environ. Microbiol., vol. 64, pp. 3669-3673.

<1>PspLI
<2>SplI,BpuB5I,BsiWI,BsmWI,BvuBI,MaeK81I,Pfl23II,PfuNI,PpuAI,SmaAI,SplAI,SspKI,SunI
<3>C^GTACG
<4>
<5>Pseudomonas species L
<6>S.K. Degtyarev
<7>I
<8>Abdurashitov, M.A., Kileva, E.V., Shevchenko, A.V., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>PspNI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Pseudomonas species
<6>ATCC 29862
<7>
<8>Polisson, C., Unpublished observations.

<1>PspN4I
<2>NlaIV,AspNI,BcrI,BmiI,BsaEI,BscBI,Bsp29I,BspLI,BssI,HpyF44II,HpyF73I,NgoBV,NgoGV,Rlu3I,Uba1305I,Uba1445I
<3>GGN^NCC
<4>
<5>Pseudomonas species N4
<6>S.K. Degtyarev
<7>I
<8>Abdurashitov, M.A., Kileva, E.V., Shevchenko, A.V., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>PspOMI
<2>ApaI,Bsp120I,EciEI,PpeI,Psp30I,Uba1156I,Uba1157I,Uba1165I,Uba1202I,Uba1241I,Uba1368I
<3>G^GGCCC
<4>
<5>Pseudomonas species OM2164
<6>NEB 1783
<7>INV
<8>Belichenko, O.A., Shevchenko, A.V., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>PspOMII
<2>
<3>CGCCCAR(20/18)
<4>
<5>Pseudomonas species OM2164
<6>NEB 1783
<7>
<8>Dwinnel, E., Morgan, R.D., Unpublished observations.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>PspPI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>4(5)
<5>Psychrobacter immobilis TA137
<6>R. Gerday
<7>C
<8>Rina, M., Caufrier, F., Markaki, M., Mavromatis, K., Kokkinidis, M., Bouriotis, V., (1997) Gene, vol. 197, pp. 353-360.

<1>PspPPI
<2>PpuMI,Mlu1106I,Pfl27I,PpuXI,Psp5II
<3>RG^GWCCY
<4>
<5>Pseudomonas species PP
<6>S.K. Degtyarev
<7>I
<8>Kileva, E.V., Abdurashitov, M.A., Shevchenko, A.V., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>PspPRI
<2>
<3>CCYCAG(15/13)
<4>
<5>Psychrobacter sp. PRwf-1
<6>J.M. Tiedje
<7>
<8>Copeland, A., Lucas, S., Lapidus, A., Barry, K., Detter, J.C., Glavina del Rio, T., Hammon, N., Israni, S., Dalin, E., Tice, H., Bruce, D., Pitluck, S., Richardson, P., Unpublished observations.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>PspSI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Pseudomonas species S
<6>CAMB 2676
<7>
<8>Naeem, S., Mushtaq, R., Riazuddin, S., Unpublished observations.

<1>PspXI
<2>
<3>VC^TCGAGB
<4>
<5>Pseudomonas species A1-1
<6>NEB 1782
<7>IN
<8>Gonchar, D.A., Abdurashitov, M.A., Belichenko, O.A., Dedkov, V.S., Mezentseva, N.V., Tomilova, J.E., Degtyarev, S.K., (2005) Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol., vol. 1, pp. 18-23.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>PsrI
<2>
<3>(7/12)GAACNNNNNNTAC(12/7)
<4>
<5>Pseudomonas stutzeri N2
<6>S.K. Degtyarev
<7>I
<8>Dedkov, V.S., Kileva, E.V., Abdurashitov, M.A., Gonchar, D.A., Popichenko, D.V., Degtyarev, S.K., Unpublished observations.

<1>PssI
<2>DraII,EcoO109I,Kaz48kI,Uba1326I,VneAI
<3>RGGNC^CY
<4>
<5>Pseudomonas species
<6>R.A. Makula
<7>
<8>Belle Isle, H., Unpublished observations.
Makula, R.A., Unpublished observations.

<1>PssII
<2>
<3>?
<4>
<5>Pseudomonas species
<6>R.A. Makula
<7>
<8>Makula, R.A., Unpublished observations.

<1>PstI
<2>AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>5(6)
<5>Providencia stuartii 164
<6>ATCC 49762
<7>BCFHIJKMNOQRSUVWXY
<8>Brown, N.L., Smith, M., (1976) FEBS Lett., vol. 65, pp. 284-287.
Handique, A.K., (1994) Curr. Sci., vol. 66, pp. 103-104.
Sagawa, H., Ohshima, A., Kato, I., (1995) Nucleic Acids Res., vol. 23, pp. 2367-2370.
Smith, D.I., Blattner, F.R., Davies, J., (1976) Nucleic Acids Res., vol. 3, pp. 343-353.
Treml, S., Draveling, C., Huang, C., Heaster, J., Walker, D., DiFrancesco, R., Jolly, J., (1994) Clin. Chem., vol. 40, pp. 1092.
Walder, R.Y., (1984) Ph.D. Thesis (The University of Iowa, Department of Biology, none), pp. 1-228.
Walder, R.Y., Walder, J.A., Donelson, J.E., (1984) J. Biol. Chem., vol. 259, pp. 8015-8026.
Xia, Y., Van Etten, J.L., Dobos, P., Ling, Y.Y., Krell, P.J., (1993) Virology, vol. 196, pp. 817-824.

<1>PstII
<2>SsmI
<3>CTGATG(25/27)
<4>
<5>Providencia stuartii 164
<6>ATCC 49762
<7>
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Sears, A., Peakman, L.J., Wilson, G.G., Szczelkun, M.D., (2005) Nucleic Acids Res., vol. 33, pp. 4775-4787.

<1>PstNHI
<2>NheI,AceII,AsuNHI,BmtI,BspOI,LlaG2I
<3>G^CTAGC
<4>
<5>Pseudomonas stutzeri NH
<6>S.K. Degtyarev
<7>
<8>Myakisheva, T.V., Dedkov, V.S., Kileva, E.V., Abdurashitov, M.A., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

<1>PsuI
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,MflI,Tru201I,Uba1432I
<3>R^GATCY
<4>
<5>Pseudomonas stutzeri Mck 28-pH52
<6>V. Butkus
<7>F
<8>Lazareviciute, L., Uogintiene, B., Maneliene, Z., Trinkunaite, L., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>Psu161I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGAT^CG
<4>
<5>Pseudomonas stutzeri 161
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>PsuAI
<2>BsaAI,BstBAI,MspYI,Ppu6I,Ppu11I,Ppu21I
<3>YAC^GTR
<4>
<5>Phormidium subfuscum
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>PsuNI
<2>SgrAI,SvoI
<3>CRCCGGYG
<4>?(5)
<5>Pseudomonas stutzeri 1660
<6>NEB 1317
<7>
<8>Hingorani, K., Bitinaite, J., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>PsyI
<2>Tth111I,AspI,AtsI,BgiI,FsuI,NtaI,PflFI,SmaAII,SpaPI,SplII,SplAII,TelI,TrsKTII,TspI,TteI,TtrI
<3>GACN^NNGTC
<4>
<5>Pseudomonas syringae Lki 1-pH124
<6>V. Butkus
<7>F
<8>Vitkute, J., Grigaite, R., Maneliene, Z., Trinkunaite, L., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>PtaI
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>T^CCGGA
<4>
<5>Phormidium tadzschicicum
<6>A.J. Podhajska
<7>
<8>Piechula, S., Kur, J., Bielawski, K., Podhajska, A.J., (1992) Nucleic Acids Res., vol. 20, pp. 6738.

<1>PteI
<2>BsePI,BscEI,BsoPI,BsrHI,BssBI,BssHII,BstBZ153I,CfrJ5I,Eco143I,Eco152I,Esp7I,Esp8I,Kpn30I,McaTI,PauI,TtmII,Uba69I
<3>G^CGCGC
<4>
<5>Paenibacillus terrae RFL2
<6>Fermentas G357
<7>F
<8>Vitkute, J., Lauciuniene, N., Lapcinskaja, S., Trinkunaite, L., Zakareviciene, L., Lubys, A., Janulaitis, A., Unpublished observations.

<1>Pun14627I
<2>MstI,AcaIII,Acc16I,AosI,ApcTR183I,AviII,Bco6I,BsaTI,ClcII,CliII,FdiII,FspI,GspAII,NsbI,NspHIII,NspLI,NspMI,PamI
<3>TGC^GCA
<4>
<5>Phormidium uncinatum 1462/7
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>Pun14627II
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>
<5>Phormidium uncinatum 1462/7
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>PunAI
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>C^YCGRG
<4>
<5>Phormidium uncinatum
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>PunAII
<2>NspI,AvoI,BstNSI,Lsp1270I,NspHI,PauAI,XceI
<3>RCATG^Y
<4>
<5>Phormidium uncinatum
<6>A.J. Podhajska
<7>
<8>Piechula, S., Waleron, K., Swiatek, W., Biedrzycka, I., Podhajska, A.J., (2001) FEMS Microbiol. Lett., vol. 198, pp. 135-140.

<1>PvuI
<2>Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGAT^CG
<4>
<5>Proteus vulgaris
<6>ATCC 13315
<7>BFKMNOQRSUWXY
<8>Gingeras, T.R., Greenough, L., Schildkraut, I., Roberts, R.J., (1981) Nucleic Acids Res., vol. 9, pp. 4525-4536.
Katsuragi, N.T., Kawakami, B., Maekawa, Y., European Patent Office, 1994.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
Smith, M.D., Longo, M., Gerard, G.F., Chatterjee, D.K., (1992) Nucleic Acids Res., vol. 20, pp. 5743-5747.

<1>PvuII
<2>BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>4(4)
<5>Proteus vulgaris
<6>ATCC 13315
<7>BCFHIJKMNORSUVWXY
<8>Butkus, V., Klimasauskas, S., Petrauskiene, L., Maneliene, Z., Lebionka, A., Janulaitis, A., (1987) Biochim. Biophys. Acta, vol. 909, pp. 201-207.
Gingeras, T.R., Greenough, L., Schildkraut, I., Roberts, R.J., (1981) Nucleic Acids Res., vol. 9, pp. 4525-4536.
Kyune, C., Shimonchitoshu, A., Japanese Patent Office, 2006.
Rice, M.R., Calvin-Koons, M.D., Blumenthal, R.M., (1995) FASEB J., vol. 9.
Tao, T., Walter, J., Brennan, K.J., Cotterman, M.M., Blumenthal, R.M., (1989) Nucleic Acids Res., vol. 17, pp. 4161-4175.

<1>Pvu84I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Proteus vulgaris 84
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>Pvu84II
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAG^CTG
<4>
<5>Proteus vulgaris 84
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>PvuHKUI
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAGCTG
<4>
<5>Proteus vulgaris HKU
<6>P.C. Shaw
<7>
<8>Leung, S.M., Chan, K.Y., Suen, Y.K., Shaw, P.C., (1989) Nucleic Acids Res., vol. 17, pp. 10133.

<1>PxyARI
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Pseudobutyrivibrio species AR 11
<6>P. Pristas
<7>
<8>Mrazek, J., Piknova, M., Pristas, P., Kopecny, J., (2005) Anaerobe, vol. 11, pp. 280-284.

<1>PxyJKI
<2>AvaIII,Asi372I,BfrBI,BfrCI,Csp68KIII,EcoT22I,Mph1103I,NsiI,PinBI,Ppu10I,SepI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>ATGCAT
<4>
<5>Pseudobutyrivibrio species JK 664
<6>P. Pristas
<7>
<8>Mrazek, J., Piknova, M., Pristas, P., Kopecny, J., (2005) Anaerobe, vol. 11, pp. 280-284.

<1>PxyMZI
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Pseudobutyrivibrio species MZ 5
<6>P. Pristas
<7>
<8>Mrazek, J., Piknova, M., Pristas, P., Kopecny, J., (2005) Anaerobe, vol. 11, pp. 280-284.

<1>Ral8I
<2>BinI,AclWI,AlwI,BpuFI,BspPI,BsrWI,BstH9I,Bst31TI,BthII,Bth617I,EacI
<3>GGATC
<4>
<5>Ruminococcus albus 8
<6>B.A. White
<7>
<8>Morrison, M., (1991) Ph.D. Thesis, University of Illinois, USA, pp. 1-134.
Morrison, M., Mackie, R.I., White, B.A., (1992) Gene, vol. 111, pp. 105-108.

<1>RalF40I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Ruminococcus albus F-40
<6>K. Gregg
<7>
<8>Miyagi, T., Javorsky, P., Pristas, P., Karita, S., Sakka, K., Ohmiya, K., (1998) FEMS Microbiol. Lett., vol. 164, pp. 215-218.

<1>RaqI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Rahnella aquatilis RFL2
<6>Fermentas G352
<7>
<8>Lauciuniene, N., Capskaja, L., Trinkunaite, L., Zakareviciene, L., Lubys, A., Vitkute, J., Janulaitis, A., Unpublished observations.

<1>RcaI
<2>BspHI,CciI,PagI,RhcI,RspXI
<3>T^CATGA
<4>
<5>Rhodococcus capsulatum
<6>M.M. Wijdenbosch
<7>M
<8>Wijdenbosch, M.M., Unpublished observations.

<1>RceI
<2>
<3>CATCGAC(20/18)
<4>
<5>Rhodospirillum centenum SW
<6>ATCC 51521
<7>
<8>Morgan, R.D., Dwinell, E.A., Unpublished observations.
Touchman, J.W., Bauer, C., Blankenship, R.E., Unpublished observations.

<1>RflFI
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>G^TCGAC
<4>
<5>Ruminococcus flavefaciens FD-1
<6>B.A. White
<7>
<8>Antonopoulos, D.A., White, B.A., Unpublished observations.
Morrison, M., Mackie, R.I., White, B.A., (1992) Appl. Environ. Microbiol., vol. 58, pp. 66-69.

<1>RflFII
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,PinI,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGT^ACT
<4>
<5>Ruminococcus flavefaciens FD-1
<6>B.A. White
<7>
<8>Morrison, M., Mackie, R.I., White, B.A., (1992) Aust. Microbiol., vol. 0, pp. 301-303.
Morrison, M., Mackie, R.I., White, B.A., (1994) FEMS Microbiol. Lett., vol. 122, pp. 181-185.

<1>RgaI
<2>SgfI,AsiSI,SfaAI
<3>GCGAT^CGC
<4>
<5>Rhizobium galegae
<6>S.K. Degtyarev
<7>I
<8>Chernuhin, V.A., Nayakshina, T.N., Tomilova, J.E., Degtyarev, S.K., Unpublished observations.

<1>RhcI
<2>BspHI,CciI,PagI,RcaI,RspXI
<3>TCATGA
<4>
<5>Rhodococcus species SE1991
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>RheI
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Rhodococcus species
<6>ATCC 21664
<7>
<8>Hurlin, P., Schildkraut, I., Unpublished observations.

<1>M.Rho11sI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC,GCNGC
<4>3(5), 2(5)
<5>Bacillus subtilis phage Rho11
<6>T.A. Trautner
<7>
<8>Behrens, B., Noyer-Weidner, M., Pawlek, B., Lauster, R., Balganesh, T.S., Trautner, T.A., (1987) EMBO J., vol. 6, pp. 1137-1142.
Gunthert, U., Trautner, T.A., (1984) Curr. Top. Microbiol. Immunol., vol. 108, pp. 11-22.
Noyer-Weidner, M., Jentsch, S., Kupsch, J., Bergbauer, M., Trautner, T.A., (1985) Gene, vol. 35, pp. 143-150.
Noyer-Weidner, M., Jentsch, S., Pawlek, B., Gunthert, U., Trautner, T.A., (1983) J. Virol., vol. 46, pp. 446-453.

<1>M.Rho11sII
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>?(5)
<5>Bacillus subtilis phage Rho11
<6>T.A. Trautner
<7>
<8>Behrens, B., Noyer-Weidner, M., Pawlek, B., Lauster, R., Balganesh, T.S., Trautner, T.A., (1987) EMBO J., vol. 6, pp. 1137-1142.

<1>RhpI
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Rhodococcus species
<6>ATCC 19148
<7>
<8>Hurlin, P., Schildkraut, I., Unpublished observations.

<1>RhpII
<2>
<3>?
<4>
<5>Rhodococcus species
<6>ATCC 19148
<7>
<8>Hurlin, P., Schildkraut, I., Unpublished observations.

<1>RhsI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Rhodococcus species
<6>ATCC 13259
<7>
<8>Hurlin, P., Schildkraut, I., Unpublished observations.

<1>RigI
<2>FseI
<3>GGCCGG^CC
<4>
<5>Rhizobium yangligense
<6>S.K. Degtyarev
<7>I
<8>Doroganov, A.O., Chernukhin, V.A., Kileva, E.V., Tomilova, J.E., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>RleI
<2>
<3>?
<4>
<5>Rhizobium leguminosarum 300
<6>J. Beringer
<7>
<8>Winkler, K., Rosch, A., Unpublished observations.

<1>Rle69I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Rhizobium leguminosarum 69
<6>V.E. Repin
<7>
<8>Lebedev, L.R., Andreeva, I.S., Gordienko, N.Y., Maystrenko, G.G., Repin, V.E., Pustoshilova, N.M., Russian Patent Office, 1993.

<1>RleAI
<2>
<3>CCCACA(12/9)
<4>
<5>Rhizobium leguminosarum
<6>U. Mayr
<7>
<8>Kaluza, K., Jarsch, M., Schmitz-Agheguian, G., Kessler, C., European Patent Office, 1989.
Vesely, Z., Muller, A., Schmitz, G.G., Kaluza, K., Jarsch, M., Kessler, C., (1990) Gene, vol. 95, pp. 129-131.

<1>RluI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Rhizobium lupini 1
<6>W. Heumann
<7>
<8>Sievert, U., Rosch, A., Unpublished observations.
Winkler, K.-P., (1980) Ph.D. Thesis, Erlangen University, W. Germany, pp. 1-135.

<1>Rlu1I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Rhodococcus luteus RFL1
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.

<1>Rlu3I
<2>NlaIV,AspNI,BcrI,BmiI,BsaEI,BscBI,Bsp29I,BspLI,BssI,HpyF44II,HpyF73I,NgoBV,NgoGV,PspN4I,Uba1305I,Uba1445I
<3>GGNNCC
<4>
<5>Rhodococcus luteus RFL3
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Rlu4I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Rhodococcus luteus RFL4
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>RmaI
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>C^TAG
<4>
<5>Rhodothermus marinus
<6>ITI 378
<7>
<8>Hjorleifsdottir, S., Pelursdottir, S., Kristjansson, J.K., Korpela, J., Torsti, A.-M., Mattila, P., (1992) Thermophiles Sci. Technol., vol. 20, pp. 17.
Ronka, J., Hjorleifsdottir, S., Tenkanen, T., Pitkanen, K., Mattila, P., Kristjansson, J.K., (1991) Nucleic Acids Res., vol. 19, pp. 2789.

<1>Rma376I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Rhodothermus marinus
<6>ITI 376
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Rma485I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 485
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Rma486I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 486
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Rma490I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 490
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Rma495I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 495
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Rma495II
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Rhodothermus marinus
<6>ITI 495
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Rma496I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 496
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Rma496II
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma497II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Rhodothermus marinus
<6>ITI 496
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Rma497I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 497
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Rma497II
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,SmiMII,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Rhodothermus marinus
<6>ITI 497
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Rma500I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 500
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Rma501I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 501
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Rma503I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 503
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Rma506I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 506
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Rma509I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 509
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Rma510I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 510
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Rma515I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 515
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Rma516I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 516
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Rma517I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma518I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 517
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Rma518I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma519I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 518
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Rma519I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma522I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 519
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Rma522I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,UbaN5I,XspI
<3>CTAG
<4>
<5>Rhodothermus marinus
<6>ITI 522
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Rma523I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Rhodothermus marinus
<6>ITI 523
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>RmeI
<2>
<3>?
<4>
<5>Rhizobium meliloti
<6>J.L. Denarie
<7>
<8>Heumann, W., (1979) Curr. Top. Microbiol. Immunol., vol. 88, pp. 1-24.

<1>Rme21I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Rhizobium meliloti
<6>I.S. Andreeva
<7>
<8>Andreeva, I.S., Afinogenova, G.N., Lebedev, L.R., Pustoshilova, N.M., Gordienko, N.Ya., Maistrenko, G.G., (1991) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 30-31.
Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>M.RnoDnmt1
<2>
<3>?
<4>?(5)
<5>Rattus norvegicus
<6>S. Kohsaka
<7>
<8>Deng, J., Szyf, M., (1998) J. Biol. Chem., vol. 273, pp. 22869-22872.
Ohsawa, K., Imai, Y., Ito, D., Kohsaka, S., (1996) J. Neurochem., vol. 67, pp. 89-97.

<1>RpaB5I
<2>
<3>CGRGGAC(20/18)
<4>
<5>Rhodopseudomonas palustris BisB5
<6>ATCC BAA-1123
<7>
<8>Copeland, A. et al., Unpublished observations.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>M.RraDnmtI
<2>
<3>?
<4>?(5)
<5>Rattus rattus
<6>H. Kimura
<7>
<8>Kimura, H., Takeda, T., Tanaka, S., Ogawa, T., Shiota, K., (1998) Biochem. Biophys. Res. Commun., vol. 253, pp. 495-501.

<1>RrbI
<2>
<3>?
<4>
<5>Rhodospirillum rubrum
<6>J. Chirikjian
<7>
<8>LeBon, J.M., LeBon, T., Blakesley, R., Chirikjian, J., Unpublished observations.

<1>RrhI
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Rhodococcus rhodochrous
<6>ATCC 14349
<7>
<8>Qiang, B.-Q., Schildkraut, I., Unpublished observations.

<1>RrhII
<2>
<3>?
<4>
<5>Rhodococcus rhodochrous
<6>ATCC 14349
<7>
<8>Qiang, B.-Q., Schildkraut, I., Unpublished observations.

<1>Rrh4273I
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>G^TCGAC
<4>5(6)
<5>Rhodococcus rhodochrous
<6>ATCC 4273
<7>
<8>Yebra, M.J., Novella, I.S., Barbes, C., Aparicio, J.F., Martin, C.G., Hardisson, C., Sanchez, J., (1991) J. Gen. Microbiol., vol. 137, pp. 1279-1284.

<1>RrhJ1I
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCC^GGC
<4>
<5>Rhodococcus rhodochrous J-1
<6>FERM BP-1478
<7>
<8>Watanabe, F., Yu, F., Kita, K., Japanese Patent Office, 2007.

<1>RroI
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>GTCGAC
<4>
<5>Rhodococcus rhodochrous
<6>ATCC 4276
<7>
<8>Qiang, B.-Q., Schildkraut, I., Unpublished observations.

<1>RruI
<2>NruI,AmaSI,Bsp68I,BtuMI,Mlu9273I,MluB2I,PspDI,SalDI,Sbo13I,Sna3286I,SpoI,Uba1117I,Uba1386I,VchO70I
<3>TCG^CGA
<4>
<5>Rhodococcus ruber RFL5
<6>Fermentas G359
<7>F
<8>Vitkute, J., Lauciuniene, N., Lapcinskaja, S., Trinkunaite, L., Zakareviciene, L., Lubys, A., Janulaitis, A., Unpublished observations.

<1>RruAI
<2>
<3>?
<4>
<5>Rhodospirillum rubrum 68
<6>D. Yoch
<7>
<8>Hamablet, L., Meyertons, J.L., Roberts, R.J., Unpublished observations.

<1>RsaI
<2>AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII,RsaNI
<3>GT^AC
<4>4(4)
<5>Rhodopseudomonas sphaeroides
<6>S. Kaplan
<7>BCFHIJMNOQRSVWXY
<8>Lunnen, K.D., Meixsell, T., Morgan, R.D., Wilson, G.G., European Patent Office, 2001.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
Lynn, S.P., Cohen, L.K., Kaplan, S., Gardner, J.F., (1980) J. Bacteriol., vol. 142, pp. 380-383.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>RsaNI
<2>RsaI,AfaI,Asp16HI,Asp17HI,Asp18HI,Asp29HI,CcoP73I,Csp6I,CviQI,CviRII,Hpy303I,Hpy312I,Hpy401I,Hpy421I,Hpy423I,Hpy471I,Hpy501I,HpyBI,HpyF10IV,HpyF13IV,HpyF21II,HpyF31I,HpyF36II,HpyF44V,HpyF52III,HpyF53II,HpyF59II,HpyF65III,HpyF66III,HpyHII,HpyNSH57I,MjaV,PabI,PlaAII
<3>G^TAC
<4>
<5>Rhodopseudomonas sphaeroides N
<6>S.K. Degtyarev
<7>I
<8>Chernukhin, V.A., Nayakshina, T.V., Boltengagen, A.A., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>RseI
<2>MslI,SmiMI
<3>CAYNN^NNRTG
<4>
<5>Riemerella species RFL1
<6>Fermentas G323
<7>F
<8>Lauciuniene, N., Trikunaite, L., Kiuduliene, L., Vitkute, J., Janulaitis, A.A., Unpublished observations.

<1>RshI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGAT^CG
<4>?(5)
<5>Rhodobacter sphaeroides 2.4.1
<6>S. Kaplan
<7>
<8>Copeland, A., Lucas, S., Lapidus, A., Barry, K., Detter, J.C., Glavina, T., Hammon, N., Israni, S., Pitluck, S., Richardson, P., Mackenzie, C., Choudhary, M., Larimer, F., Hauser, L.J., Land, M., Donohue, T.J., Kaplan, S., Unpublished observations.
Lynn, S.P., Cohen, L.K., Gardner, J.F., Kaplan, S., (1979) J. Bacteriol., vol. 138, pp. 505-509.

<1>RshII
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Rhodobacter sphaeroides 2.4.1
<6>S. Kaplan
<7>
<8>Kramarov, V.M., Pachkunov, D.M., Matvienko, N.I., (1983) Nek. Aspekty Fiziol. Mikroorg. Akad. Nauk. SSR., ed. Gaziev, A.I. (Nauchn. Tsentr Biol. Issled., Pushchino, USSR.), vol. 0, pp. 22-26.

<1>RspI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Rhodopseudomonas sphaeroides
<6>R. Lascelles
<7>
<8>Bingham, A.H.A., Atkinson, T., Darbyshire, J., Unpublished observations.

<1>RspLKI
<2>SphI,Asp5HI,BbuI,BscOI,Bsp121I,BtgAII,CglAI,PaeI,PaeCI,PfaAIII,SpaHI,SpaXI,Uba1162I,Uba1226I,VchO68I
<3>GCATG^C
<4>
<5>Rhodococcus species LK2
<6>N.I. Matvienko
<7>
<8>Zabaznaya, E.V., Zheleznaya, L.A., Matvienko, N.I., (1997) Biokhimiia, vol. 62, pp. 1018-1028.

<1>RspLKII
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Rhodococcus species LK2
<6>N.I. Matvienko
<7>
<8>Zabaznaya, E.V., Zheleznaya, L.A., Matvienko, N.I., (1997) Biokhimiia, vol. 62, pp. 1018-1028.

<1>RspXI
<2>BspHI,CciI,PagI,RcaI,RhcI
<3>T^CATGA
<4>
<5>Rhodococcus species
<6>W.-C. Tsui
<7>
<8>Tsui, W.-C., Elgar, G., Merrill, C., Maunders, M., (1988) Nucleic Acids Res., vol. 16, pp. 4178.

<1>RsrI
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco237I,Eco252I,FunII,HalI,Hal22I,Kpn49kI,Ppu111I,Srl32DII,Srl55DI,SsoI,Uba58I,Van91II,VchN100I,VchO2I
<3>G^AATTC
<4>3(6)
<5>Rhodopseudomonas sphaeroides
<6>S. Kaplan
<7>
<8>Aiken, C., Gumport, R.I., (1988) Nucleic Acids Res., vol. 16, pp. 7901-7916.
Aiken, C., Milarski-Brown, K., Gumport, R.I., (1986) Fed. Proc., vol. 45, pp. 1914.
Gardner, J.F., Cohen, L.K., Lynn, S.P., Kaplan, S., Unpublished observations.
Greene, P.J., Ballard, B.T., Stephenson, F., Kohr, W.J., Rodriguez, H., Rosenberg, J.M., Boyer, H.W., (1988) Gene, vol. 68, pp. 43-52.
Kaszubska, W., Aiken, C., O'Connor, C.D., Gumport, R.I., (1989) Nucleic Acids Res., vol. 17, pp. 10403-10425.

<1>RsrII
<2>CpoI,CspI,Rsr2I
<3>CG^GWCCG
<4>?(5)
<5>Rhodopseudomonas sphaeroides
<6>S. Kaplan
<7>MNQX
<8>Morgan, R.D., Unpublished observations.
O'Connor, C.D., Metcalf, E., Wrighton, C.J., Harris, T.J.R., Saunders, J.R., (1984) Nucleic Acids Res., vol. 12, pp. 6701-6708.

<1>Rsr2I
<2>RsrII,CpoI,CspI
<3>CG^GWCCG
<4>
<5>Rhodobacter sphaeroides SE-I2
<6>S.K. Degtyarev
<7>IV
<8>Shinkarenko, O.A., Lebedeva, N.A., Dedkov, V.S., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>RtrI
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,Rtr63I,Uba89I,XamI,XciI
<3>G^TCGAC
<4>
<5>Rhizobium trifolii
<6>L.R. Lebedev
<7>
<8>Lebedev, L.R., Afinogenova, G.N., Andreeva, I.S., Pustoshilova, N.M., Pozdnyakov, S.G., Chizhikov, V.E., (1991) Bioorg. Khim., vol. 17, pp. 277-279.

<1>Rtr20I
<2>BbvII,Bbr7I,BbsI,Bbv16II,Bco102II,BpiI,BpuAI,BsaVI,Bsc91I,BscKI,BspBS31I,BspIS4I,BspTS514I,BspVI,BstBS32I,BstTS5I,BstV2I
<3>GAAGAC
<4>
<5>Rhizobium trifolii 20
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Rtr63I
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Uba89I,XamI,XciI
<3>G^TCGAC
<4>
<5>Rhizobium trifolii 63
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>M.SPBetaI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC,GCNGC
<4>3(5), 2(5)
<5>Bacillus subtilis phage SPBeta
<6>T.A. Trautner
<7>
<8>Baldauf, F., Kiss, A., (1985) Mol. Gen. Mikrobiol. Virusol., vol. 2, pp. 26-28.
Gunthert, U., Trautner, T.A., (1984) Curr. Top. Microbiol. Immunol., vol. 108, pp. 11-22.
Noyer-Weidner, M., Jentsch, S., Kupsch, J., Bergbauer, M., Trautner, T.A., (1985) Gene, vol. 35, pp. 143-150.
Tran-Betcke, A., Behrens, B., Noyer-Weidner, M., Trautner, T.A., (1986) Gene, vol. 42, pp. 89-96.

<1>M.SPRI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC,CCGG,CCWGG
<4>3(5), 1(5), 2(5)
<5>Mutation screening vector pSPRX
<6>T.A. Trautner
<7>
<8>Behrens, B., Pawlek, B., Morelli, G., Trautner, T.A., (1983) Mol. Gen. Genet., vol. 189, pp. 10-16.
Gunthert, U., Reiners, L., (1987) Nucleic Acids Res., vol. 15, pp. 3689-3701.
Jentsch, S., Gunthert, U., Trautner, T.A., (1981) Nucleic Acids Res., vol. 9, pp. 2753-2759.
Posfai, G., Baldauf, F., Erdei, S., Posfai, J., Venetianer, P., Kiss, A., (1984) Nucleic Acids Res., vol. 12, pp. 9039-9049.
Trautner, T.A., Pawlek, B., Gunthert, U., Canosi, U., Jentsch, S., Freund, M., (1980) Mol. Gen. Genet., vol. 180, pp. 361-367.

<1>SaaI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Streptomyces alanosinicus
<6>ATCC 15710
<7>
<8>Morgan, R.D., Unpublished observations.

<1>SabI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Streptomyces albohelvatus
<6>ATCC 19820
<7>
<8>Stote, R., Morgan, R., Unpublished observations.

<1>SacI
<2>BpuAmI,Ecl136II,Ecl137I,EcoICRI,Eco53kI,MxaI,NasSI,Pfl18I,Psp124BI,ScoI,Ssm4I,Ssm5I,SstI
<3>GAGCT^C
<4>4(5)
<5>Streptomyces achromogenes
<6>ATCC 12767
<7>FHJKMNOQRSUWX
<8>Arrand, J.R., Myers, P.A., Roberts, R.J., Unpublished observations.
Xu, S.-Y., Xiao, J.-P., Ettwiller, L., Holden, M., Aliotta, J., Poh, C.L., Dalton, M., Robinson, D.P., Petronzio, T.R., Moran, L., Ganatra, M., Ware, J., Slatko, B., Benner, J., (1998) Mol. Gen. Genet., vol. 260, pp. 226-231.

<1>SacII
<2>AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>2(5)
<5>Streptomyces achromogenes
<6>ATCC 12767
<7>HJKNOQRWX
<8>Arrand, J.R., Myers, P.A., Roberts, R.J., Unpublished observations.
Benner, J., Lunnen, K., Unpublished observations.
Guthrie, E., Meda, M., European Patent Office, 1995.
Lunnen, K.D., Barsomian, J.M., Camp, R.R., Card, C.O., Chen, S.-Z., Croft, R., Looney, M.C., Meda, M.M., Moran, L.S., Nwankwo, D.O., Slatko, B.E., Van Cott, E.M., Wilson, G.G., (1988) Gene, vol. 74, pp. 25-32.
Meda, M.M., Wilson, G.G., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Samuelson, J., Unpublished observations.

<1>SacIII
<2>
<3>?
<4>
<5>Streptomyces achromogenes
<6>ATCC 12767
<7>
<8>Arrand, J.R., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>SacAI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Streptomyces achromogenes
<6>ATCC 21353
<7>
<8>Schneider, A., Unpublished observations.

<1>SacNI
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCY^C
<4>
<5>Streptomyces achromogenes N-J-H
<6>A.J. Podhajska
<7>
<8>Rutkowska, S.M., Skowron, P.M., Bielawski, K., Podhajska, A.J., (1995) Gene, vol. 157, pp. 319-320.

<1>SagI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Streptococcus agalactiae B96
<6>M.T. Poch
<7>
<8>Poch, M.T., Somkuti, G.A., (1994) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 94, pp. 385.
Poch, M.T., Somkuti, G.A., (1995) Appl. Microbiol. Biotechnol., vol. 43, pp. 282-284.

<1>Sag16I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Streptococcus agalactiae 16
<6>I. Mikula
<7>
<8>Godany, A., Bukovska, G., Farkasovska, J., Brnakova, Z., Dmitriev, A., Tkacikova, L., Ayele, T., Mikula, I., (2004) Folia Microbiol. (Praha), vol. 49, pp. 307-314.

<1>Sag23I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Streptococcus agalactiae 23
<6>I. Mikula
<7>
<8>Godany, A., Bukovska, G., Farkasovska, J., Brnakova, Z., Dmitriev, A., Tkacikova, L., Ayele, T., Mikula, I., (2004) Folia Microbiol. (Praha), vol. 49, pp. 307-314.

<1>SaiI
<2>SimI,BssIMI,BtsPI,ShaI
<3>GGGTC
<4>
<5>Staphylococcus auricularis RFL18
<6>A. Janulaitis
<7>
<8>Gaigalas, M., Capskaja, L., Norgeliene, D., Petrusyte, M., Markauskas, A., Butkus, V., Janulaitis, A., Unpublished observations.

<1>SakI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Streptomyces akiyoshiensis
<6>ATCC 13480
<7>
<8>Schneider, A., Unpublished observations.

<1>SalI
<2>Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI,XciI
<3>G^TCGAC
<4>5(6)
<5>Streptomyces albus G
<6>ATCC 49789
<7>BCFHIJKMNOQRSUVWXY
<8>Alvarez, M.A., Chater, K.F., Rosario, M.R., (1993) Mol. Microbiol., vol. 8, pp. 243-252.
Arrand, J.R., Myers, P.A., Roberts, R.J., (1978) J. Mol. Biol., vol. 118, pp. 127-135.
Rodicio, M.R., Quinton-Jager, T., Moran, L.S., Slatko, B.E., Wilson, G.G., (1994) Gene, vol. 151, pp. 167-172.

<1>SalII
<2>
<3>?
<4>
<5>Streptomyces albus G
<6>ATCC 49789
<7>
<8>Arrand, J.R., Myers, P.A., Roberts, R.J., (1978) J. Mol. Biol., vol. 118, pp. 127-135.

<1>Sal13I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Streptomyces albus 13
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Krivopalova, G.N., Serov, G.D., Repin, V.E., Unpublished observations.

<1>Sal1974I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces albus 1974
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>SalAI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptomyces albus
<6>ATCC 21725
<7>
<8>Hall, D., Morgan, R., Unpublished observations.

<1>SalCI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Streptomyces albus
<6>ATCC 21290
<7>
<8>Polisson, C., Unpublished observations.

<1>SalDI
<2>NruI,AmaSI,Bsp68I,BtuMI,Mlu9273I,MluB2I,PspDI,RruI,Sbo13I,Sna3286I,SpoI,Uba1117I,Uba1386I,VchO70I
<3>TCGCGA
<4>
<5>Streptomyces albus
<6>ATCC 21132
<7>
<8>Polisson, C., Unpublished observations.

<1>SalHI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptomyces albulus
<6>ATCC 12757
<7>
<8>Hall, D., Morgan, R., Unpublished observations.

<1>SalPI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Streptomyces albus
<6>CMI 52766
<7>
<8>Carter, J.A., Chater, K.F., Bruton, C.J., Brown, N.L., (1980) Nucleic Acids Res., vol. 8, pp. 4943-4954.
Chater, K.F., (1977) Nucleic Acids Res., vol. 4, pp. 1989-1998.

<1>SanI
<2>
<3>?
<4>
<5>Salmonella anatum
<6>Y. Yoshida
<7>
<8>Matsui, M., Mise, K., Yoshida, Y., Ishidate, M., (1986) Eisei Shikenjo Hokoku, vol. 104, pp. 92-96.

<1>SanDI
<2>KflI,Sse1825I
<3>GG^GWCCC
<4>
<5>Streptomyces species
<6>T.G. Simcox
<7>E
<8>Simcox, T.G., Fabian, L., Kretz, K., Hedden, V., Simcox, M.E.C., (1995) Gene, vol. 155, pp. 129-130.

<1>SaoI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Streptomyces albofaciens
<6>ATCC 25184
<7>
<8>Stote, R., Morgan, R., Unpublished observations.

<1>SapI
<2>BspQI,LguI,PciSI,VpaK32I
<3>GCTCTTC(1/4)
<4>
<5>Saccharopolyspora species
<6>NEB 597
<7>N
<8>Beck, R., Burtscher, H., (1994) Nucleic Acids Res., vol. 22, pp. 886-887.
Morgan, R.D., Unpublished observations.
Samuelson, J., Unpublished observations.
Xu, S.-Y., Xiao, J.-P., Ettwiller, L., Holden, M., Aliotta, J., Poh, C.L., Dalton, M., Robinson, D.P., Petronzio, T.R., Moran, L., Ganatra, M., Ware, J., Slatko, B., Benner, J., (1998) Mol. Gen. Genet., vol. 260, pp. 226-231.
Xu, S.-Y., Xiao, J.-P., Poh, C.L., Maunus, R.E., Unpublished observations.

<1>SaqAI
<2>MseI,Tru1I,Tru9I
<3>T^TAA
<4>
<5>Salinibacterium aquaticus RFL1
<6>Fermentas G362
<7>F
<8>Lauciuniene, N., Valiulyte, D., Capskaja, L., Trinkunaite, L., Vitkute, J., Janulaitis, A., Unpublished observations.
Zakareviciene, L., Lubys, A., Unpublished observations.

<1>SarI
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGG^CCT
<4>
<5>Streptomyces aureomonopodiales
<6>ATCC 19825
<7>
<8>Choudhry, S., Sohail, A., Riazuddin, S., Unpublished observations.

<1>SasI
<2>BseRI
<3>GAGGAG
<4>
<5>Sphingomonas asaccharolytica RFL2
<6>Fermentas G330
<7>
<8>Vitkute, J., Kvieskaite, M., Lapcinskaja, S., Capskaja, L., Trinkunaite, L., Janulaitis, A., Unpublished observations.

<1>SatI
<2>Fnu4HI,Bli1904II,Bpu1811I,BsoFI,Bsp6I,BssFI,BssXI,BthCI,Cac824I,CcoP215I,CcoP216I,FbrI,Fsp4HI,ItaI,LlaDII,Uur960I
<3>GC^NGC
<4>
<5>Staphylococcus arlettae RFL 832
<6>V. Butkus
<7>F
<8>Kesminiene, A., Maneliene, Z., Petrusyte, M., Capskaja, L., Trinkunaite, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>SauI
<2>AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CC^TNAGG
<4>
<5>Streptomyces aureofaciens IKA 18/4
<6>J. Timko
<7>
<8>Timko, J., Horwitz, A.H., Zelinka, J., Wilcox, G., (1981) J. Bacteriol., vol. 145, pp. 873-877.

<1>Sau2I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Staphylococcus aureus RFL2
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Sau5I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Staphylococcus aureus RFL5
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Sau10I
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Staphylococcus aureus RFL10
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.

<1>Sau12I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Staphylococcus aureus RFL12
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.

<1>Sau13I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Staphylococcus aureus RFL13
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Sau14I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Staphylococcus aureus RFL14
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Sau15I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Staphylococcus aureus RFL15
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Sau16I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Staphylococcus aureus RFL16
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Sau17I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Staphylococcus aureus RFL17
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Sau32I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Staphylococcus aureus 32
<6>I. Mikula
<7>
<8>Godany, A., Bukovska, G., Farkasovska, J., Brnakova, Z., Dmitriev, A., Tkacikova, L., Ayele, T., Mikula, I., (2004) Folia Microbiol. (Praha), vol. 49, pp. 307-314.

<1>Sau33I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Staphylococcus aureus 33
<6>I. Mikula
<7>
<8>Godany, A., Bukovska, G., Farkasovska, J., Brnakova, Z., Dmitriev, A., Tkacikova, L., Ayele, T., Mikula, I., (2004) Folia Microbiol. (Praha), vol. 49, pp. 307-314.

<1>Sau42I
<2>
<3>?
<4>
<5>Staphylococcus aureus 42CR3-L
<6>D.C. Coleman
<7>
<8>Coleman, D.C., Carroll, D., Dempsey, R.M., Sears, L.E., Kong, H., Unpublished observations.

<1>Sau90I
<2>SmlI,Sau93I,Sau98I,Sau96mI,SmoI
<3>CTYRAG
<4>
<5>Staphylococcus aureus 90
<6>I. Mikula
<7>
<8>Godany, A., Bukovska, G., Farkasovska, J., Brnakova, Z., Dmitriev, A., Tkacikova, L., Ayele, T., Mikula, I., (2004) Folia Microbiol. (Praha), vol. 49, pp. 307-314.

<1>Sau93I
<2>SmlI,Sau90I,Sau98I,Sau96mI,SmoI
<3>CTYRAG
<4>
<5>Staphylococcus aureus 93
<6>I. Mikula
<7>
<8>Godany, A., Bukovska, G., Farkasovska, J., Brnakova, Z., Dmitriev, A., Tkacikova, L., Ayele, T., Mikula, I., (2004) Folia Microbiol. (Praha), vol. 49, pp. 307-314.

<1>Sau96I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>G^GNCC
<4>4(5)
<5>Staphylococcus aureus PS96
<6>ATCC 49831
<7>JNOUW
<8>Sussenbach, J.S., Steenbergh, P.H., Rost, J.A., van Leeuwen, W.J., van Embden, J.D.A., (1978) Nucleic Acids Res., vol. 5, pp. 1153-1163.
Szilak, L., Venetianer, P., Kiss, A., (1990) Nucleic Acids Res., vol. 18, pp. 4659-4664.

<1>Sau98I
<2>SmlI,Sau90I,Sau93I,Sau96mI,SmoI
<3>CTYRAG
<4>
<5>Staphylococcus aureus 98
<6>I. Mikula
<7>
<8>Godany, A., Bukovska, G., Farkasovska, J., Brnakova, Z., Dmitriev, A., Tkacikova, L., Ayele, T., Mikula, I., (2004) Folia Microbiol. (Praha), vol. 49, pp. 307-314.

<1>Sau557I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Staphylococcus aureus 557
<6>V.E. Repin
<7>
<8>Repin, V.E., Lebedev, L.R., Andreeva, I.S., Puchkova, L.I., Zernov, Y.P., Serov, G.D., Tereshchenko, T.A., Aphinogenova, G.N., Pustoshilova, N.M., (1998) Biotekhnologiya, vol. 0, pp. 18-27.

<1>Sau3239I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>5(6)
<5>Streptomyces aureofaciens
<6>CCM 3239
<7>
<8>Gasperik, J., Godany, A., Hostinova, E., Zelinka, J., (1983) Biologia (Bratisl), vol. 38, pp. 315-319.
Simbochova, G., Timko, J., Zelinkova, E., Zelinka, J., (1986) Biologia (Bratisl), vol. 41, pp. 357-365.
Zelinkova, E., Paulicek, M., Zelinka, J., (1990) FEBS Lett., vol. 271, pp. 147-148.

<1>Sau6782I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Staphylococcus aureus 6782
<6>E.E. Arutyunyan
<7>
<8>Arutyunyan, E.E., Gonchar, N.A., Gruber, I.M., Nikolskaya, N.I., (1992) Mol. Gen. Mikrobiol. Virusol., vol. 11-1, pp. 26-29.
Arutyunyan, E.E., Gruber, I.M., Polyachenko, V.M., Kvachadze, L.J., Andriashvili, I.A., Chanishvili, T.G., Nikolskaya, I.I., (1985) Vopr. Med. Khim., vol. 31, pp. 127-132.

<1>Sau22201I
<2>
<3>?
<4>
<5>Streptomyces aureofaciens IKA 22201
<6>J. Timko
<7>
<8>Timko, J., Matuskova, M., Zelinkova, E., Zelinka, J., (1978) Folia Microbiol. (Praha), vol. 23, pp. 243-245.

<1>SauAI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Streptomyces aureofaciens
<6>ATCC 15852
<7>
<8>Grandoni, R., Unpublished observations.

<1>Sau3AI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>4(5)
<5>Staphylococcus aureus 3A
<6>ATCC 49834
<7>CHJKMNOQRSUWX
<8>Klimasauskas, S., Lebionka, A., Butkus, V., Janulaitis, A., Unpublished observations.
Lebenka, A.Y., Rackus, Y.A., (1989) Biokhimiia, vol. 54, pp. 1009-1014.
Mohn, W.W., Teather, R.M., (1995) Gene, vol. 155, pp. 131-132.
Sussenbach, J.S., Monfoort, C.H., Schiphof, R., Stobberingh, E.E., (1976) Nucleic Acids Res., vol. 3, pp. 3193-3202.

<1>SauBI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Staphylococcus aureus
<6>DSM 20652
<7>
<8>Tsui, W.-C., Unpublished observations.

<1>SauBMKI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCC^GGC
<4>
<5>Streptomyces aureofaciens strain BM-K
<6>J. Timko
<7>
<8>Timko, J., Turna, J., Zelinka, J., (1987) Metabolism and Enzymology of Nucleic Acids, ed. Zelinka, J., Balan, J. (Publishing House of the Slovak Akademy of Science, Bratislava), vol. 6, pp. 107-118.

<1>SauCI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Staphylococcus aureus 3C
<6>NCTC 8327
<7>
<8>Stobberingh, E.E., Schiphof, R., Sussenbach, J.S., (1977) J. Bacteriol., vol. 131, pp. 645-649.

<1>SauDI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Staphylococcus aureus 55
<6>NCTC 8358
<7>
<8>Stobberingh, E.E., Schiphof, R., Sussenbach, J.S., (1977) J. Bacteriol., vol. 131, pp. 645-649.

<1>SauEI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Staphylococcus aureus 71
<6>NCTC 9315
<7>
<8>Stobberingh, E.E., Schiphof, R., Sussenbach, J.S., (1977) J. Bacteriol., vol. 131, pp. 645-649.

<1>SauFI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Staphylococcus aureus 879
<6>E.E. Stobberingh
<7>
<8>Stobberingh, E.E., Schiphof, R., Sussenbach, J.S., (1977) J. Bacteriol., vol. 131, pp. 645-649.

<1>SauGI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Staphylococcus aureus 1030
<6>E.E. Stobberingh
<7>
<8>Stobberingh, E.E., Schiphof, R., Sussenbach, J.S., (1977) J. Bacteriol., vol. 131, pp. 645-649.

<1>SauHI
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Streptomyces aureofaciens 13
<6>J. Muchova
<7>
<8>Muchova, J., Lacova, B., Godany, A., Sevcikova, B., (1991) J. Basic Microbiol., vol. 31, pp. 141-147.

<1>SauHPI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCC^GGC
<4>
<5>Streptomyces aureofaciens R8/26
<6>P. Pristas
<7>
<8>Pristas, P., Godany, A., Sevcikova, B., Oktavcova, B., Farkasovska, J., (1992) Nucleic Acids Res., vol. 20, pp. 4364.

<1>SauLPI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCC^GGC
<4>2(5)
<5>Streptomyces aureofaciens B-96
<6>P. Pristas
<7>
<8>Oktavcovca, B., Godany, A., Pristas, P., Stevcikova, B., Farkasovska, J., (1993) Nucleic Acids Res., vol. 21, pp. 4843.
Pristas, P., Godany, A., Sevcikova, B., Oktavcova, B., Farkasovska, J., (1992) Nucleic Acids Res., vol. 20, pp. 4364.

<1>SauLPII
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Streptomyces aureofaciens B-96
<6>P. Pristas
<7>
<8>Godany, A., Pristas, P., Oktavcova, B., Farkosovska, J., Ziffova, M., Sevcikova, B., (1996) FEMS Microbiol. Lett., vol. 138, pp. 123-127.

<1>SauMI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Staphylococcus aureus M
<6>CAMB 2545
<7>
<8>Mushtaq, R., Riazuddin, S., Unpublished observations.

<1>SauNI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCC^GGC
<4>
<5>Streptomyces aureofaciens NMU
<6>P. Pristas
<7>
<8>Pristas, P., Godany, A., Sevcikova, B., Oktavcova, B., Farkasovska, J., (1992) Nucleic Acids Res., vol. 20, pp. 4364.

<1>SauSI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCC^GGC
<4>
<5>Streptomyces aureofaciens 16
<6>P. Pristas
<7>
<8>Pristas, P., Godany, A., Sevcikova, B., Oktavcova, B., Farkasovska, J., (1992) Nucleic Acids Res., vol. 20, pp. 4364.

<1>SauS2I
<2>
<3>?
<4>
<5>Staphylococcus aureus RN450
<6>R. Novick
<7>
<8>Sjostrom, J.E., Lofdahl, S., Philipson, L., (1978) J. Bacteriol., vol. 133, pp. 1144-1149.

<1>Sau96mI
<2>SmlI,Sau90I,Sau93I,Sau98I,SmoI
<3>CTYRAG
<4>
<5>Staphylococcus aureus 96m
<6>I. Mikula
<7>
<8>Godany, A., Bukovska, G., Farkasovska, J., Brnakova, Z., Dmitriev, A., Tkacikova, L., Ayele, T., Mikula, I., (2004) Folia Microbiol. (Praha), vol. 49, pp. 307-314.

<1>SbaI
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAGCTG
<4>
<5>Salmonella bareilly
<6>Y. Yoshida
<7>
<8>Matsui, M., Mise, K., Yoshida, Y., Ishidate, M., (1986) Eisei Shikenjo Hokoku, vol. 104, pp. 92-96.
Mise, K., Unpublished observations.
Naderer, M., Brust, J.R., Knowle, D., Blumenthal, R.M., (2002) J. Bacteriol., vol. 184, pp. 2411-2419.

<1>SbfI
<2>Sse8387I,SdaI
<3>CCTGCA^GG
<4>
<5>Streptomyces species Bf-61
<6>S.K. Degtyarev
<7>INOV
<8>Abdurashitov, M.A., Kileva, E.V., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.
Lunnen, K., Davis, T., Wilson, G., European Patent Office, 2005.
Lunnen, K.D., Davis, T., Wilson, G.G., US Patent Office, 2005.
Lunnen, K.D., Wilson, G.G., Unpublished observations.

<1>Sbi68I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Streptomyces bikiniensis JAM68
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>SblAI
<2>StyI,BsmSI,BssT1I,Bst224I,CfrBI,Eco130I,Eco208II,EcoT14I,EcoT104I,ErhI,ErhB9II,SblBI,SblCI,Uba1311I
<3>CCWWGG
<4>
<5>Salmonella blockley YY156
<6>Y. Yoshida
<7>
<8>Mise, K., Unpublished observations.

<1>SblBI
<2>StyI,BsmSI,BssT1I,Bst224I,CfrBI,Eco130I,Eco208II,EcoT14I,EcoT104I,ErhI,ErhB9II,SblAI,SblCI,Uba1311I
<3>CCWWGG
<4>
<5>Salmonella blockley YY176
<6>Y. Yoshida
<7>
<8>Mise, K., Unpublished observations.

<1>SblCI
<2>StyI,BsmSI,BssT1I,Bst224I,CfrBI,Eco130I,Eco208II,EcoT14I,EcoT104I,ErhI,ErhB9II,SblAI,SblBI,Uba1311I
<3>CCWWGG
<4>
<5>Salmonella blockley YY242
<6>Y. Yoshida
<7>
<8>Mise, K., Unpublished observations.

<1>SboI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Streptomyces bobili
<6>ATCC 3310
<7>
<8>Shimotsu, H., Takahashi, H., Saito, H., (1980) Agric. Biol. Chem., vol. 44, pp. 1665-1666.
Takahashi, H., Unpublished observations.

<1>Sbo13I
<2>NruI,AmaSI,Bsp68I,BtuMI,Mlu9273I,MluB2I,PspDI,RruI,SalDI,Sna3286I,SpoI,Uba1117I,Uba1386I,VchO70I
<3>TCG^CGA
<4>
<5>Shigella boydii 13
<6>NCTC 9361
<7>
<8>Benner, J.S., Unpublished observations.
Mise, K., Nakajima, K., Terakado, N., Ishidate, M., (1986) Gene, vol. 44, pp. 165-169.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>SbrI
<2>
<3>?
<4>
<5>Salmonella bredeney
<6>Y. Yoshida
<7>
<8>Matsui, M., Mise, K., Yoshida, Y., Ishidate, M., (1986) Eisei Shikenjo Hokoku, vol. 104, pp. 92-96.

<1>SbvI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Streptococcus bovis II/1
<6>P. Javorsky
<7>
<8>Vanat, I., Pristas, P., Kutejova, E., Judova, J., Godany, A., Jovorsky, P., (1993) Lett. Appl. Microbiol., vol. 17, pp. 297-299.

<1>ScaI
<2>Acc113I,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I,ZrmI
<3>AGT^ACT
<4>5(4)
<5>Streptomyces caespitosus
<6>H. Takahashi
<7>BCFJKMNOQRSWX
<8>Grandoni, R.P., Schildkraut, I., Unpublished observations.
Stickel, S.K., Roberts, R.J., Unpublished observations.
Takahashi, H., Kojima, H., Saito, H., (1985) Biochem. J., vol. 231, pp. 229-232.
Xu, S.-Y., Xiao, J.-P., Unpublished observations.
Xu, S.-Y., Xiao, J.-P., Unpublished observations.

<1>Sca1827I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces carneus 1827
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>SceIII
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>G^CCGGC
<4>
<5>Saccharomyces cerevisiae
<6>H.P. Zassenhaus
<7>
<8>Ezekiel, U.R., Zassenhaus, P., (1994) Biochem. Biophys. Res. Commun., vol. 201, pp. 208-214.

<1>SceAI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Synechococcus cedrorum
<6>ATCC 29140
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>Scg2I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Streptomyces hybrid
<6>A.V. Orekhov
<7>
<8>Orekhov, A.V., Strokina, I.V., Foors, A.R., (1989) Genetika, vol. 25, pp. 614-625.

<1>SchI
<2>PleI,BsmEI,BspD6I,MlyI,PpsI
<3>GAGTC(5/5)
<4>
<5>Staphylococcus cohnii Lki 19-320
<6>V. Butkus
<7>F
<8>Maneliene, Z., Butkus, V., Unpublished observations.
Vitkute, J., Mociskyte, S., Trinkunaite, L., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>SchZI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Streptomyces chusanensis ZS-2
<6>M.-C. Kao
<7>
<8>Hu, K.-Y., Wuu, J.-A., Kao, M.-C., Liu, Y.-T., Pai, S.-H., (1998) Appl. Biochem. Biotechnol., vol. 73, pp. 231-241.

<1>SciI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTC^GAG
<4>
<5>Streptoverticillium cinnamoneum
<6>S.T. Williams
<7>
<8>Walker, J.N.B., Dean, P.G., Saunders, J.R., Unpublished observations.

<1>Sci1831I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces circulatus 1831
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>SciAI
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,Uba1291I
<3>GGTNACC
<4>
<5>Synechocystis species
<6>ATCC 27175
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>SciAII
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAGCTG
<4>
<5>Synechocystis species
<6>ATCC 27175
<7>
<8>Calleja, F., de Waard, A., Unpublished observations.

<1>SciBI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptoverticillium cinnamoneum
<6>Glaxo 2566C
<7>
<8>Klein, S., Roberts, R.J., Unpublished observations.

<1>SciNI
<2>HhaI,AspLEI,BbtI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,HspAI,Mho2965I,MnnIV,NgoEII
<3>G^CGC
<4>
<5>Spiroplasma citri ASP2
<6>M.A. Stephens
<7>
<8>Stephens, M.A., (1982) J. Bacteriol., vol. 149, pp. 508-514.

<1>SciRI
<2>
<3>?
<4>
<5>Spiroplasma citri
<6>ATCC 27556
<7>
<8>Laigret, F., Gaurivaud, P., Bove, J.-M., (1996) Gene, vol. 171, pp. 95-98.

<1>ScoI
<2>SacI,BpuAmI,Ecl136II,Ecl137I,EcoICRI,Eco53kI,MxaI,NasSI,Pfl18I,Psp124BI,Ssm4I,Ssm5I,SstI
<3>GAGCTC
<4>
<5>Streptomyces coelicolor
<6>ATCC 10147
<7>
<8>Stote, R., Morgan, R., Unpublished observations.

<1>ScoAI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Streptomyces corchorusii
<6>ATCC 25444
<7>
<8>Earle-Hughes, J., Roberts, R.J., Unpublished observations.

<1>ScoNI
<2>ApaLI,AaqI,Alw44I,AmeI,Bsp146I,DaqI,Pfl23I,Pfr12I,PliI,SnoI,Uba1203I,Uba1387I,VneI
<3>GTGCAC
<4>
<5>Salinivibrio costicola
<6>NEB 1324
<7>
<8>Picone, S., Unpublished observations.

<1>ScrFI
<2>Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I,Uba1391I
<3>CC^NGG
<4>?(5)
<5>Streptococcus cremoris F
<6>C. Daly
<7>JNOS
<8>Davis, R., Van der Lelie, D., Mercenier, A., Daly, C., Fitzgerald, G.F., (1993) Appl. Environ. Microbiol., vol. 59, pp. 777-785.
Fitzgerlad, G.F., Daly, C., Brown, L.R., Gingeras, T.R., (1982) Nucleic Acids Res., vol. 10, pp. 8171-8179.
Hill, C., (1993) FEMS Microbiol. Rev., vol. 12, pp. 87-108.
Twomey, D.P., Davis, R., Daly, C., Fitzgerald, G.F., (1993) Irish J. Agr. Food Res., vol. 32, pp. 217.

<1>ScuI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces cupidosporus
<6>KCC S0316
<7>
<8>Shimotsu, H., Takahashi, H., Saito, H., (1980) Agric. Biol. Chem., vol. 44, pp. 1665-1666.

<1>SdaI
<2>Sse8387I,SbfI
<3>CCTGCA^GG
<4>
<5>Streptomyces diastaticus Ng7-324
<6>V. Butkus
<7>F
<8>Vitkute, J., Markauskiene, J., Maneliene, Z., Trinkunaite, L., Kiuduliene, L., Butkus, V., Janulaitis, V., Unpublished observations.

<1>SdeAI
<2>
<3>CAGRAG(21/19)
<4>
<5>Sulfurimonas denitrificans
<6>ATCC 33889
<7>
<8>Copeland, A., Lucas, S., Lapidus, A., Barry, K., Detter, J.C., Glavina, T., Hammon, N., Israni, S., Pitluck, S., Chain, P., Malfatti, S., Shin, M., Vergez, L., Schmutz, J., Larimer, F., Land, M., Kyrpides, N., Lykidis, A., Richardson, P., Unpublished observations.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>SdeOSI
<2>
<3>(11/13)GACNNNNRTGA(12/10)
<4>
<5>Shewanella denitrificans OS217
<6>DSM 15013
<7>
<8>Copeland, A. et al., Unpublished observations.
Wilson, G., Unpublished observations.

<1>SdiI
<2>SfiI
<3>GGCCNNNN^NGGCC
<4>
<5>Streptomyces diastaticus
<6>F. Kimizuka
<7>
<8>Nomura, Y., Ito, H., Sagawa, H., Kotani, H., Kimizuka, F., Nakajima, K., Unpublished observations.

<1>SdiAI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces diastatochromogenes
<6>M. Bae
<7>
<8>Bae, M., Suh, W.-N., Song, E.-S., Lee, K.-J., (1994) Korean J. Appl. Microbiol. Biotechnol., vol. 22, pp. 126-133.

<1>SduI
<2>AocII,Bka1125I,BmyI,BsoCI,Bsp1286I,BspLS2I,BstZ15I,HpyF36IV,HpyF47I,MhlI,Mlu40I,NspII,TseAI,Uba1362I
<3>GDGCH^C
<4>
<5>Streptococcus durans RFL3
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Marcinkeviciene, L., Petrusyte, M., Mironov, A., (1981) FEBS Lett., vol. 134, pp. 172-174.
Kraev, A.S., Zimin, A.A., Mironova, M.V., Janulaitis, A., Tanyashin, V.I., Skryabin, K.G., Bayev, A.A., (1983) Dokl. Akad. Nauk., vol. 270, pp. 1495-1500.
Vaisvila, R., Janulaitis, A., Unpublished observations.

<1>SdyI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Streptococcus dysgalactiae
<6>ATCC 9926
<7>
<8>Qiang, B.-Q., Schildkraut, I., Unpublished observations.

<1>SecI
<2>BsaJI,BseDI,BsoKI,BssECI,BstZ10I,Hpy99IV,HpyF10III,HpyF61II,HpyF67IV,Uba1442I
<3>C^CNNGG
<4>
<5>Synechocystis species 6701
<6>ATCC 27170
<7>
<8>Calleja, F., Tandeau de Marsac, N., Coursin, T., van Ormondt, H., de Waard, A., (1985) Nucleic Acids Res., vol. 13, pp. 6745-6751.

<1>SecII
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Synechocystis species 6701
<6>ATCC 27170
<7>
<8>Calleja, F., Tandeau de Marsac, N., Coursin, T., van Ormondt, H., de Waard, A., (1985) Nucleic Acids Res., vol. 13, pp. 6745-6751.

<1>SecIII
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SshAI,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Synechocystis species 6701
<6>ATCC 27170
<7>
<8>Calleja, F., Tandeau de Marsac, N., Coursin, T., van Ormondt, H., de Waard, A., (1985) Nucleic Acids Res., vol. 13, pp. 6745-6751.

<1>SelI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>^CGCG
<4>
<5>Synechococcus elongatus
<6>H. Kotani
<7>
<8>Miyake, M., Asada, Y., Shiraki, M., Japanese Patent Office, 1994.
Miyake, M., Asada, Y., Shiraki, M., Kato, S., Kotani, H., Japanese Patent Office, 1994.
Miyake, M., Kotani, H., Asada, Y., (1992) Nucleic Acids Res., vol. 20, pp. 2605.

<1>SelAI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Synechococcus elongatus T3
<6>L. Wu
<7>
<8>Lou, S., Wu, L., (1997) J. Xiamen Univ., vol. 36, pp. 272-275.

<1>SenPI
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SsoII,StyD4I,Uba17I,Uba1391I
<3>CCNGG
<4>2(5)
<5>Salmonella enteritidis pFM366
<6>R. Rotger
<7>
<8>Ibanez, M., Rotger, R., (1993) FEMS Microbiol. Lett., vol. 109, pp. 225-230.

<1>SenPT16I
<2>XmaIII,AaaI,BseX3I,BsoDI,BstZI,EagI,EclXI,Eco52I,TauII,Tsp504I
<3>C^GGCCG
<4>
<5>Salmonella enteritidis PT16
<6>A. Nakamura
<7>
<8>Miyahara, M., Nakamura, A., Mise, K., (1997) Biol. Pharm. Bull., vol. 20, pp. 1212-1214.

<1>SenPT14bI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Salmonella enteritidis PT14b
<6>A. Nakamura
<7>
<8>Miyahara, M., Nakamura, A., Mise, K., (1997) Biol. Pharm. Bull., vol. 20, pp. 1212-1214.

<1>SenpCI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>?(5)
<5>Salmonella enteritidis plasmid pC
<6>I. Rychlik
<7>
<8>Gregorova, D., Pravcova, M., Karpiskova, R., Rychlik, I., (2002) FEMS Microbiol. Lett., vol. 214, pp. 195-198.

<1>SepI
<2>AvaIII,Asi372I,BfrBI,BfrCI,Csp68KIII,EcoT22I,Mph1103I,NsiI,PinBI,Ppu10I,PxyJKI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>ATGCA^T
<4>
<5>Staphylococcus epidermidis
<6>CAMB 2635
<7>
<8>Arif, A., Mushtaq, R., Unpublished observations.

<1>SeqAI
<2>
<3>?
<4>
<5>Synechocystis equalis
<6>N. Anand
<7>
<8>Elango, K., Reddy, S.S., MohanRaj, R., Anand, N., Unpublished observations.

<1>SetI
<2>
<3>ASST^
<4>
<5>Streptomyces werraensis
<6>S.K. Degtyarev
<7>I
<8>Abdurashitov, M.A., Dedkov, V.S., Okhapkina, S.S., Gonchar, D.A., Belichenko, O.A., Tomilova, J.E., Degtyarev, S.K., Unpublished observations.

<1>SexI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces exfoliatus
<6>KCC S0030
<7>
<8>Shimotsu, H., Takahashi, H., Saito, H., (1980) Agric. Biol. Chem., vol. 44, pp. 1665-1666.

<1>SexII
<2>
<3>?
<4>
<5>Streptomyces exfoliatus
<6>KCC S0030
<7>
<8>Shimotsu, H., Takahashi, H., Saito, H., (1980) Agric. Biol. Chem., vol. 44, pp. 1665-1666.

<1>SexAI
<2>CsiI,MabI
<3>A^CCWGGT
<4>?(5)
<5>Streptomyces exfoliatus
<6>B. Frey
<7>MN
<8>Frey, B., Unpublished observations.
Kaluza, K., Auer, J., Frey, B., European Patent Office, 1992.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>SexBI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Streptomyces exfoliatus
<6>J. Yim
<7>
<8>Bae, M., Park, J., Hwang, H.-Y., Yim, J., Unpublished observations.

<1>SexCI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Streptomyces exfoliatus
<6>M. Bae
<7>
<8>Bae, M., Par, J.-O., Hwang, H.-Y., Yim, J., (1993) Korean J. Microbiol., vol. 31, pp. 544-549.
Bae, M., Suh, W.-N., Park, J.-O., Kim, H.T., Lee, K.-J., (1993) Korean J. Microbiol., vol. 31, pp. 465-470.

<1>SfaI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>
<5>Streptococcus faecalis var. zymogenes
<6>R. Wu
<7>
<8>Wu, R., King, C.T., Jay, E., (1978) Gene, vol. 4, pp. 329-336.

<1>SfaAI
<2>SgfI,AsiSI,RgaI
<3>GCGAT^CGC
<4>
<5>Sphingomonas faenia RFL1
<6>Fermentas G309
<7>F
<8>Lauciuniene, N., Trinkunaite, L., Capskaja, L., Vitkute, J., Janulaitis, A., Unpublished observations.
Zakareviciene, L., Lubys, A., Unpublished observations.

<1>SfaGUI
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Streptococcus faecalis GU
<6>J. Chirikjian
<7>
<8>Coll, E., Chirikjian, J., Unpublished observations.

<1>SfaNI
<2>BhaI,BmsI,BscAI,BscUI,BsmNI,BspST5I,Bst19I,CjeP338II,LweI,PhaI
<3>GCATC(5/9)
<4>
<5>Streptococcus faecalis ND547
<6>ATCC 49761
<7>INV
<8>Samuelson, J., Wilson, G.G., Xu, S.-Y., Unpublished observations.
Schildkraut, I., Greenough, L., Unpublished observations.
Sciaky, D., Roberts, R.J., Unpublished observations.

<1>SfcI
<2>SfeI,Bco163I,BdiSI,BfmI,BpcI,BstSFI,BthP35I,HpyF2I,LlaBI,Srl56DI
<3>C^TRYAG
<4>
<5>Streptococcus faecium
<6>NEB 674
<7>N
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Polisson, C., Meloni, A., Unpublished observations.
Zhu, Z., Unpublished observations.

<1>SfeI
<2>Bco163I,BdiSI,BfmI,BpcI,BstSFI,BthP35I,HpyF2I,LlaBI,SfcI,Srl56DI
<3>C^TRYAG
<4>
<5>Streptococcus faecalis
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.Kh., Prihodko, G.G., Rechkunova, N.I., (1988) Bioorg. Khim., vol. 14, pp. 848-849.
Okhapkina, S.S., Netesova, N.A., Golikova, L.N., Seregina, E.V., Sosnovtsev, S.V., Abdurashitov, M.A., Degtyarev, S.K., (2002) Mol. Biol. (Mosk), vol. 36, pp. 432-437.

<1>SfiI
<2>SdiI
<3>GGCCNNNN^NGGCC
<4>?(4)
<5>Streptomyces fimbriatus
<6>ATCC 15051
<7>CFIJKMNOQRSUVWX
<8>Qiang, B.-Q., Schildkraut, I., (1984) Nucleic Acids Res., vol. 12, pp. 4507-4515.
Sasaki, A., Oka, M., Shigenori, M., Japanese Patent Office, 1992.
Van Cott, E.M., Moran, L.S., Slatko, B.E., Wilson, G.G., Unpublished observations.
Vancott, E.M., European Patent Office, 1995.
Wentzell, L.M., Oram, M., Halford, S.E., (1994) Biochem. Soc. Trans., vol. 22, pp. 302S.

<1>SflI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Streptoverticillium flavopersicum
<6>UC 5066
<7>
<8>Jiang, B.D., Myers, P., Unpublished observations.

<1>SflHK1794I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Shigella flexneri 1794
<6>P.C. Shaw
<7>
<8>Lee, K.F., Ling, J.M.-L., Kam, K.-M., Clark, D.R., Shaw, P.-C., (1997) J. Med. Microbiol., vol. 46, pp. 949-952.

<1>SflHK2374I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Shigella flexneri 2374
<6>P.C. Shaw
<7>
<8>Lee, K.F., Ling, J.M.-L., Kam, K.-M., Clark, D.R., Shaw, P.-C., (1997) J. Med. Microbiol., vol. 46, pp. 949-952.

<1>SflHK2731I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Shigella flexneri 2731
<6>P.C. Shaw
<7>
<8>Lee, K.F., Ling, J.M.-L., Kam, K.-M., Clark, D.R., Shaw, P.-C., (1997) J. Med. Microbiol., vol. 46, pp. 949-952.

<1>SflHK6873I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Shigella flexneri 6873
<6>P.C. Shaw
<7>
<8>Lee, K.F., Ling, J.M.-L., Kam, K.-M., Clark, D.R., Shaw, P.-C., (1997) J. Med. Microbiol., vol. 46, pp. 949-952.

<1>SflHK7234I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Shigella flexneri 7234
<6>P.C. Shaw
<7>
<8>Lee, K.F., Ling, J.M.-L., Kam, K.-M., Clark, D.R., Shaw, P.-C., (1997) J. Med. Microbiol., vol. 46, pp. 949-952.

<1>SflHK7462I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Shigella flexneri 7462
<6>P.C. Shaw
<7>
<8>Lee, K.F., Ling, J.M.-L., Kam, K.-M., Clark, D.R., Shaw, P.-C., (1997) J. Med. Microbiol., vol. 46, pp. 949-952.

<1>SflHK8401I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Shigella flexneri 8401
<6>P.C. Shaw
<7>
<8>Lee, K.F., Ling, J.M.-L., Kam, K.-M., Clark, D.R., Shaw, P.-C., (1997) J. Med. Microbiol., vol. 46, pp. 949-952.

<1>SflHK10695I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Shigella flexneri 10695
<6>P.C. Shaw
<7>
<8>Lee, K.F., Ling, J.M.-L., Kam, K.-M., Clark, D.R., Shaw, P.-C., (1997) J. Med. Microbiol., vol. 46, pp. 949-952.

<1>SflHK10790I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Shigella flexneri 10790
<6>P.C. Shaw
<7>
<8>Lee, K.F., Ling, J.M.-L., Kam, K.-M., Clark, D.R., Shaw, P.-C., (1997) J. Med. Microbiol., vol. 46, pp. 949-952.

<1>SflHK11086I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Shigella flexneri11086
<6>P.C. Shaw
<7>
<8>Lee, K.F., Ling, J.M.-L., Kam, K.-M., Clark, D.R., Shaw, P.-C., (1997) J. Med. Microbiol., vol. 46, pp. 949-952.

<1>SflHK11087I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Shigella flexneri 11087
<6>P.C. Shaw
<7>
<8>Lee, K.F., Ling, J.M.-L., Kam, K.-M., Clark, D.R., Shaw, P.-C., (1997) J. Med. Microbiol., vol. 46, pp. 949-952.

<1>SflHK11572I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Shigella flexneri 11572
<6>P.C. Shaw
<7>
<8>Lee, K.F., Ling, J.M.-L., Kam, K.-M., Clark, D.R., Shaw, P.-C., (1997) J. Med. Microbiol., vol. 46, pp. 949-952.

<1>SflHK115731I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Shigella flexneri 11573
<6>P.C. Shaw
<7>
<8>Lee, K.F., Ling, J.M.-L., Kam, K.-M., Clark, D.R., Shaw, P.-C., (1997) J. Med. Microbiol., vol. 46, pp. 949-952.

<1>Sfl2aI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Shigella flexneri 2a
<6>L.I. Solodukhina
<7>
<8>Solodukhina, L.I., Korotayev, A.I., Solonin, A.S., Kuzmin, N.P., (1990) Genetika, vol. 26, pp. 1126-1128.
Solodukhina, L.I., Manuvakhova, M.S., Korotayev, A.I., (1989) Genetika, vol. 25, pp. 1571-1577.

<1>Sfl2bI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Shigella flexneri 2a
<6>L.I. Solodukhina
<7>
<8>Solodukhina, L.I., Manuvakhova, M.S., Korotayev, A.I., (1989) Genetika, vol. 25, pp. 1571-1577.

<1>SfnI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Serratia fonticola
<6>ATCC 29938
<7>
<8>Stote, R., Schildkraut, I., Unpublished observations.

<1>SfoI
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SseAI,SspDI
<3>GGC^GCC
<4>?(5)
<5>Serratia fonticola
<6>NEB 369
<7>N
<8>Krotee, S., Ganatra, M., Grandoni, R., Unpublished observations.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
Morgan, R.D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>SfrI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Streptomyces fradiae
<6>ATCC 3355
<7>
<8>Shimotsu, H., Takahashi, H., Saito, H., (1980) Agric. Biol. Chem., vol. 44, pp. 1665-1666.
Takahashi, H., Unpublished observations.

<1>Sfr274I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Streptomyces fradiae 274
<6>S.K. Degtyarev
<7>IV
<8>Puchkova, L.I., Krivopalova, G.N., Andreeva, I.S., Selina, A.V., Serov, G.D., Rechkunova, N.I., Degtyarev, S.Kh., (1990) Izv. Sib. Otd. Akad. Nauk SSSR, vol. 1, pp. 32-34.

<1>Sfr303I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Streptomyces fradiae 303
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.K., Unpublished observations.

<1>Sfr382I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Streptomyces fradiae 382
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>SfuI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Streptomyces fulvissimus
<6>U. Mayr
<7>M
<8>Veitinger, S., Schmitz, G.G., Kaluza, K., Jarsch, M., Braun, V., Kessler, C., (1990) Nucleic Acids Res., vol. 18, pp. 3424.

<1>Sfu1762I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces fulvissimus 1762
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>SgaI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces ganmycicus
<6>KCC S0759
<7>
<8>Shimotsu, H., Takahashi, H., Saito, H., (1980) Agric. Biol. Chem., vol. 44, pp. 1665-1666.

<1>SgfI
<2>AsiSI,RgaI,SfaAI
<3>GCGAT^CGC
<4>
<5>Streptomyces griseoruber
<6>R. Williams
<7>R
<8>Kappelman, J.R., Brady, M., Knoche, K., Murray, E., Schoenfeld, T., Williams, R., Vesselinova, N., (1995) Gene, vol. 160, pp. 55-58.

<1>Sgh1835I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Streptomyces ghanaesis 1835
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>SgiI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Streptomyces griseoflavus
<6>Viikki 346
<7>
<8>Mattila, P., Pitkanen, K., Unpublished observations.

<1>SgoI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces goshikiensis
<6>KCC S0294
<7>
<8>Shimotsu, H., Takahashi, H., Saito, H., (1980) Agric. Biol. Chem., vol. 44, pp. 1665-1666.

<1>SgrI
<2>
<3>?
<4>
<5>Streptomyces griseus
<6>ATCC 23345
<7>
<8>Arrand, J.R., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>Sgr20I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Streptomyces griseus Kr. 20
<6>A.V. Orekhov
<7>
<8>Orekhov, A.V., Rebentish, B.A., Debabov, V.G., (1982) Dokl. Akad. Nauk., vol. 263, pp. 217-220.

<1>Sgr1839I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Streptomyces griseoflavus 1839
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>Sgr1841I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces griseoroseus 1841
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>SgrAI
<2>PsuNI,SvoI
<3>CR^CCGGYG
<4>?(5)
<5>Streptomyces griseus
<6>U. Mayr
<7>MN
<8>Kong, H., Higgins, L.S., Dalton, M.A., US Patent Office, 2000.
Tautz, N., Kaluza, K., Frey, B., Jarsch, M., Schmitz, G.G., Kessler, C., (1990) Nucleic Acids Res., vol. 18, pp. 3087.

<1>SgrBI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Streptomyces griseus
<6>V. Bouriotis
<7>C
<8>Rina, M., Karagouni, A., Pagomenou, M., Bouriotis, V., (1991) Nucleic Acids Res., vol. 19, pp. 6342.

<1>SgrDI
<2>
<3>CG^TCGACG
<4>
<5>Streptomyces griseus RFL6
<6>Fermentas G302
<7>F
<8>Maneliene, Z., Lubys, A., Unpublished observations.
Vitkute, J., Lauciuniene, N., Capskaja, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>SgsI
<2>AscI,PalAI
<3>GG^CGCGCC
<4>
<5>Streptomyces griseus RFL5
<6>Fermentas G295
<7>F
<8>Vitkute, J., Slyziute, J., Maneliene, Z., Norgeliene, D., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>ShaI
<2>SimI,BssIMI,BtsPI,SaiI
<3>GGGTC
<4>
<5>Staphylococcus haemolyticus 3104
<6>NEB 1448
<7>
<8>Nkenfou, C., Polisson, C., Nkenfou, J., Notedji, A., Morgan, R., Unpublished observations.

<1>ShyI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Streptomyces hygroscopicus 0477
<6>F. Walter
<7>
<8>Walter, F., Hartmann, M., Roth, M., (1978) Abstracts of 12th FEBS Symposium, Dresden., vol. 0, pp. 648.

<1>Shy1766I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces hygroscopicus 1766
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>ShyTI
<2>
<3>?
<4>
<5>Streptomyces hygroscopicus
<6>T. Yamaguchi
<7>
<8>Shimotsu, H., Takahashi, H., Saito, H., (1980) Agric. Biol. Chem., vol. 44, pp. 1665-1666.

<1>SimI
<2>BssIMI,BtsPI,SaiI,ShaI
<3>GGGTC(-3/0)
<4>
<5>Staphylococcus intermedius 6H
<6>S.K. Degtyarev
<7>
<8>Abdurashitov, M.A., Belichenko, O.A., Shevchenko, A.V., Degtyarev, S.K., (1995) Nucleic Acids Res., vol. 23, pp. 2571-2572.

<1>SinI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>4(5)
<5>Salmonella infantis
<6>A. de Waard
<7>QRWX
<8>Karreman, C., de Waard, A., (1988) J. Bacteriol., vol. 170, pp. 2533-2536.
Lupker, H.S.C., Dekker, B.M.M., (1981) Biochim. Biophys. Acta, vol. 654, pp. 297-299.

<1>SinAI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Salmonella infantis YY163
<6>Y. Yoshida
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SinBI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Salmonella infantis YY190
<6>Y. Yoshida
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SinCI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Salmonella infantis 85005
<6>S. Horiuchi
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SinDI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Salmonella infantis 85020
<6>S. Horiuchi
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SinEI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Salmonella infantis 85064
<6>S. Horiuchi
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SinFI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Salmonella infantis 85084
<6>S. Horiuchi
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SinGI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Salmonella infantis 85144
<6>S. Horiuchi
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SinHI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Salmonella infantis 85166
<6>S. Horiuchi
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SinJI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Salmonella infantis 85325
<6>S. Horiuchi
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SinMI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Staphylococcus intermedius
<6>ATCC 29663
<7>
<8>Camp, R., Schildkraut, I., Unpublished observations.

<1>SinMII
<2>
<3>?
<4>
<5>Staphylococcus intermedius
<6>ATCC 29663
<7>
<8>Camp, R., Schildkraut, I., Unpublished observations.

<1>SisI
<2>
<3>?
<4>
<5>Salmonella isangi
<6>Y. Yoshida
<7>
<8>Matsui, M., Mise, K., Yoshida, Y., Ishidate, M., (1986) Eisei Shikenjo Hokoku, vol. 104, pp. 92-96.

<1>SkaI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Streptomyces karnatakensis
<6>ATCC 25463
<7>
<8>Camp, R., Schildkraut, I., Unpublished observations.

<1>SkaII
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Streptomyces karnatakensis
<6>ATCC 25463
<7>
<8>Camp, R., Schildkraut, I., Unpublished observations.

<1>SlaI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Streptomyces lavendulae
<6>ATCC 8664
<7>C
<8>Takahashi, H., Shimizu, M., Saito, H., Ikeda, Y., Sugisaki, H., (1979) Gene, vol. 5, pp. 9-18.

<1>SlbI
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Streptomyces albidoflavus
<6>Viikki 329
<7>
<8>Mattila, P., Pitkanen, K., Unpublished observations.

<1>SleI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>^CCWGG
<4>
<5>Synechococcus leopoliensis
<6>PCC 1402-1
<7>
<8>Piechula, S., Skowron, P.M., Piatyszek, M., Podhajska, A.J., (1991) Nucleic Acids Res., vol. 19, pp. 2782.

<1>SliI
<2>
<3>?
<4>
<5>Streptomyces lipmanii
<6>R.H. Baltz
<7>
<8>Matsushima, P., Baltz, R.H., (1989) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 89, pp. 361.

<1>SliII
<2>
<3>?
<4>
<5>Streptomyces lipmanii
<6>R.H. Baltz
<7>
<8>Matsushima, P., Baltz, R.H., (1989) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 89, pp. 361.

<1>SluI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces luteoreticuli
<6>KCC S0788
<7>
<8>Takahashi, H., Unpublished observations.

<1>Slu1777I
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Smo40529I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCC^GGC
<4>
<5>Streptomyces lusitanus 1777
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>SmaI
<2>AhyI,Cfr9I,CfrJ4I,EaeAI,EclRI,KteAI,Pac25I,PaeBI,PspAI,PspALI,TspMI,Uba1220I,Uba1393I,XcyI,XmaI,XmaCI
<3>CCC^GGG
<4>2(4)
<5>Serratia marcescens Sb
<6>ATCC 49779
<7>BCFHIJKMNOQRSUVWXY
<8>Butkus, V., Petrauskiene, L., Maneliene, Z., Klimasauskas, S., Laucys, V., Janulaitis, A., (1987) Nucleic Acids Res., vol. 15, pp. 7091-7102.
Endow, S.A., Roberts, R.J., (1977) J. Mol. Biol., vol. 112, pp. 521-529.
Greene, R., Mulder, C., Unpublished observations.
Klimasauskas, S., Steponaviciene, D., Maneliene, Z., Petrusyte, M., Butkus, V., Janulaitis, A., (1990) Nucleic Acids Res., vol. 18, pp. 6607-6609.

<1>M.SmaII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Serratia marcescens Sb
<6>ATCC 49779
<7>
<8>Ostendorf, T., Cherepanov, P., deVries, J., Wachernagel, W., (1999) J. Bacteriol., vol. 181, pp. 3880-3885.

<1>SmaAI
<2>SplI,BpuB5I,BsiWI,BsmWI,BvuBI,MaeK81I,Pfl23II,PfuNI,PpuAI,PspLI,SplAI,SspKI,SunI
<3>CGTACG
<4>
<5>Spirulina maxima
<6>UTEX 2342
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SmaAII
<2>Tth111I,AspI,AtsI,BgiI,FsuI,NtaI,PflFI,PsyI,SpaPI,SplII,SplAII,TelI,TrsKTII,TspI,TteI,TtrI
<3>GACNNNGTC
<4>
<5>Spirulina maxima
<6>UTEX 2342
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SmaAIII
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Spirulina maxima
<6>UTEX 2342
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SmaAIV
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAGCTG
<4>
<5>Spirulina maxima
<6>UTEX 2342
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>M.SmeI
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI,SscL1I
<3>GANTC
<4>2(6)
<5>Sinorhizobium meliloti
<6>L. Shapiro
<7>
<8>Benkovic, S.J., Shapiro, L., Wright, R., Stephens, C., Kahng, L.Sue., Berdis, A., Lee, I., US Patent Office, 2005.
Galibert, F. et al., (2001) Science, vol. 293, pp. 668-672.
Wright, R., Stephens, C., Shapiro, L., (1997) J. Bacteriol., vol. 179, pp. 5869-5877.

<1>SmiI
<2>SwaI,BstRZ246I,BstSWI,MspSWI
<3>ATTT^AAAT
<4>
<5>Streptococcus milleri S
<6>S.K. Degtyarev
<7>FIKV
<8>Dedkov, V.S., Bondar, T.S., Shevchenco, A.V., Degtyarev, S.Kh., (2000) Mol. Gen. Mikrobiol. Virusol., vol. 1, pp. 23-27.
Dedkov, V.S., Degtyarev, S.Kh., (1998) Biol. Chem., vol. 379, pp. 573-574.

<1>SmiMI
<2>MslI,RseI
<3>CAYNN^NNRTG
<4>
<5>Sphingobacterium mizutae M
<6>S.K. Degtyarev
<7>IV
<8>Dedkov, V.S., Najakshina, T.N., Gushina, E.N., Abdurashitov, M.A., Degtyarev, S.K., Unpublished observations.

<1>SmiMII
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,Tsp273I,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Sphingobacterium mizutae M
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Najakshina, T.N., Degtyarev, S.K., Unpublished observations.

<1>SmiMBI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus milleri MB
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Degtyarev, S.Kh., (1998) Biol. Chem., vol. 379, pp. 573-574.

<1>SmlI
<2>Sau90I,Sau93I,Sau98I,Sau96mI,SmoI
<3>C^TYRAG
<4>
<5>Stenotrophomonas maltophilia
<6>NEB 1007
<7>N
<8>Le, T.K.T., Vu, H.N., Vu, T.K.L., Polisson, C., Morgan, R., Unpublished observations.
Wei, H., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>SmoI
<2>SmlI,Sau90I,Sau93I,Sau98I,Sau96mI
<3>C^TYRAG
<4>
<5>Stenotrophomonas maltophilia RFL1
<6>Fermentas G306
<7>F
<8>Lauciuniene, N., Maneliene, Z., Lapcinskaja, S., Capskaja, L., Vitkute, J., Janulaitis, A., Unpublished observations.
Maneliene, Z., Zakareviciene, L., Lubys, A., Unpublished observations.

<1>Smo40529I
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,SrlI,Srl77DI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Streptomyces moderatus
<6>DSM 40529
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>SmuI
<2>FauI,Bme585I,BstFZ438I
<3>CCCGC(4/6)
<4>
<5>Sphingobacterium multivorum RFL21
<6>V. Butkus
<7>F
<8>Grigaite, R., Maneliene, Z., Capskaja, L., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>SmuCI
<2>AvaIII,Asi372I,BfrBI,BfrCI,Csp68KIII,EcoT22I,Mph1103I,NsiI,PinBI,Ppu10I,PxyJKI,SepI,SrlII,SspD5II,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>ATGCAT
<4>
<5>Streptococcus species
<6>I. Nasz
<7>
<8>Geck, P., Molnar, A., Nasz, I., (1991) Acta Microbiol. Hung., vol. 38, pp. 47-53.

<1>SmuEI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Streptococcus mutans E
<6>I. Nasz
<7>
<8>Molnar, A., Geck, P., Orosz, A., Kulcsar, P., Nasz, I., (1991) Acta Microbiol. Hung., vol. 38, pp. 55-60.

<1>SnaI
<2>BspM90I,BssNAI,Bst1107I,BstBSI,BstZ17I,VchO25I,XcaI
<3>GTATAC
<4>
<5>Sphaerotilus natans C
<6>A. Pope
<7>
<8>Pope, A., Lynn, S.P., Gardner, J.F., Unpublished observations.

<1>Sna3286I
<2>NruI,AmaSI,Bsp68I,BtuMI,Mlu9273I,MluB2I,PspDI,RruI,SalDI,Sbo13I,SpoI,Uba1117I,Uba1386I,VchO70I
<3>TCGCGA
<4>
<5>Sphaerotilus natans 3286
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>SnaBI
<2>Bpu1831I,BstSNI,EciAI,Eco105I,Eco158II,SspJI,SspM1I,SspM2I,Uba1240I
<3>TAC^GTA
<4>3(4)
<5>Sphaerotilus natans
<6>ATCC 15291
<7>CKMNR
<8>Borsetti, R., Grandoni, R., Schildkraut, I., Unpublished observations.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>SniI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Streptomyces niveus
<6>ATCC 19793
<7>
<8>Arif, A., Naeem, S., Sohail, A., Unpublished observations.

<1>SnoI
<2>ApaLI,AaqI,Alw44I,AmeI,Bsp146I,DaqI,Pfl23I,Pfr12I,PliI,ScoNI,Uba1203I,Uba1387I,VneI
<3>G^TGCAC
<4>
<5>Streptomyces novocastria
<6>P. Eastlake
<7>
<8>Brown, N.L., Unpublished observations.
Eastlake, P., Unpublished observations.

<1>SodI
<2>
<3>?
<4>
<5>Streptomyces oderifer
<6>ATCC 6246
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>SodII
<2>
<3>?
<4>
<5>Streptomyces oderifer
<6>ATCC 6246
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>SolI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Streptoverticillium olivoverticillatum
<6>J. Yim
<7>
<8>Hwang, H.-Y., Yim, J., (1994) Nucleic Acids Res., vol. 22, pp. 2197.
Hwang, H.Y., Yim, J., (1994) Korean J. Microbiol., vol. 32, pp. 208-214.

<1>Sol3335I
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAGCTG
<4>
<5>Streptomyces olivaceus IMRU 3335
<6>P.C. Shaw
<7>
<8>Leung, S.M., Chan, K.Y., Suen, Y.K., Shaw, P.C., (1989) Nucleic Acids Res., vol. 17, pp. 10133.

<1>Sol10179I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Streptomyces olivochromogenes ST10179
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.

<1>SpaI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces albus subspecies pathocidicus
<6>KCC S-0166
<7>
<8>Shimotsu, H., Takahashi, H., Saito, H., (1980) Agric. Biol. Chem., vol. 44, pp. 1665-1666.

<1>SpaHI
<2>SphI,Asp5HI,BbuI,BscOI,Bsp121I,BtgAII,CglAI,PaeI,PaeCI,PfaAIII,RspLKI,SpaXI,Uba1162I,Uba1226I,VchO68I
<3>GCATG^C
<4>
<5>Synechococus parietina
<6>M.M. Wijdenbosch
<7>
<8>Rahman, H., Affram, C., Unpublished observations.

<1>SpaPI
<2>Tth111I,AspI,AtsI,BgiI,FsuI,NtaI,PflFI,PsyI,SmaAII,SplII,SplAII,TelI,TrsKTII,TspI,TteI,TtrI
<3>GACNNNGTC
<4>
<5>Spirulina platensis strain pacifica
<6>D. Borthakur
<7>
<8>Tragut, V., Xiao, J., Bylina, E.J., Borthakur, D., (1995) J. Appl. Phycol., vol. 7, pp. 561-564.

<1>SpaPII
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Spirulina platensis strain pacifica
<6>D. Borthakur
<7>
<8>Tragut, V., Xiao, J., Bylina, E.J., Borthakur, D., (1995) J. Appl. Phycol., vol. 7, pp. 561-564.

<1>SpaPIII
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SplAIV,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAGCTG
<4>
<5>Spirulina platensis strain pacifica
<6>D. Borthakur
<7>
<8>Tragut, V., Xiao, J., Bylina, E.J., Borthakur, D., (1995) J. Appl. Phycol., vol. 7, pp. 561-564.

<1>SpaPIV
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SsbI,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Spirulina platensis strain pacifica
<6>D. Borthakur
<7>
<8>Tragut, V., Xiao, J., Bylina, E.J., Borthakur, D., (1995) J. Appl. Phycol., vol. 7, pp. 561-564.

<1>SpaXI
<2>SphI,Asp5HI,BbuI,BscOI,Bsp121I,BtgAII,CglAI,PaeI,PaeCI,PfaAIII,RspLKI,SpaHI,Uba1162I,Uba1226I,VchO68I
<3>GCATGC
<4>
<5>Streptomyces phaeochromogenes
<6>IFO 3108
<7>
<8>Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M., (1982) Bull. Inst. Chem. Res. Kyoto Univ., vol. 60, pp. 328-335.

<1>SpeI
<2>AclNI,AhlI,BcuI
<3>A^CTAGT
<4>
<5>Sphaerotilus natans
<6>ATCC 13923
<7>BHJKMNOQRSUWX
<8>Chang, Z., Morgan, R., Unpublished observations.
Comb, D.G., Grandoni, R., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>SphI
<2>Asp5HI,BbuI,BscOI,Bsp121I,BtgAII,CglAI,PaeI,PaeCI,PfaAIII,RspLKI,SpaHI,SpaXI,Uba1162I,Uba1226I,VchO68I
<3>GCATG^C
<4>
<5>Streptomyces phaeochromogenes
<6>NRRL B-3559
<7>BCHIJKMNOQRSVWX
<8>Bhattacharya, S.K., Dubey, A.K., (1994) Biotechnol. Appl. Biochem., vol. 20, pp. 141-146.
Fuchs, L.Y., Covarrubias, L., Escalante, L., Sanchez, S., Bolivar, F., (1980) Gene, vol. 10, pp. 39-46.
Lunnen, K.D., Barsomian, J.M., Camp, R.R., Card, C.O., Chen, S.-Z., Croft, R., Looney, M.C., Meda, M.M., Moran, L.S., Nwankwo, D.O., Slatko, B.E., Van Cott, E.M., Wilson, G.G., (1988) Gene, vol. 74, pp. 25-32.

<1>Sph1719I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces phaeopurpureus 1719
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>SplI
<2>BpuB5I,BsiWI,BsmWI,BvuBI,MaeK81I,Pfl23II,PfuNI,PpuAI,PspLI,SmaAI,SplAI,SspKI,SunI
<3>C^GTACG
<4>
<5>Spirulina platensis
<6>M. Kawamura
<7>
<8>Kawamura, M., Sakakibara, M., Watanabe, T., Kita, K., Hiraoka, N., Obayashi, A., Takagi, M., Yano, K., (1986) Nucleic Acids Res., vol. 14, pp. 1985-1989.

<1>SplII
<2>Tth111I,AspI,AtsI,BgiI,FsuI,NtaI,PflFI,PsyI,SmaAII,SpaPI,SplAII,TelI,TrsKTII,TspI,TteI,TtrI
<3>GACNNNGTC
<4>
<5>Spirulina platensis
<6>M. Kawamura
<7>
<8>Kawamura, M., Sakakibara, M., Watanabe, T., Kita, K., Hiraoka, N., Obayashi, A., Takagi, M., Yano, K., (1986) Nucleic Acids Res., vol. 14, pp. 1985-1989.

<1>SplIII
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Spirulina platensis
<6>M. Kawamura
<7>
<8>Kawamura, M., Sakakibara, M., Watanabe, T., Kita, K., Hiraoka, N., Obayashi, A., Takagi, M., Yano, K., (1986) Nucleic Acids Res., vol. 14, pp. 1985-1989.

<1>SplAI
<2>SplI,BpuB5I,BsiWI,BsmWI,BvuBI,MaeK81I,Pfl23II,PfuNI,PpuAI,PspLI,SmaAI,SspKI,SunI
<3>CGTACG
<4>
<5>Spirulina platensis
<6>UTEX 2340
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SplAII
<2>Tth111I,AspI,AtsI,BgiI,FsuI,NtaI,PflFI,PsyI,SmaAII,SpaPI,SplII,TelI,TrsKTII,TspI,TteI,TtrI
<3>GACNNNGTC
<4>
<5>Spirulina platensis
<6>UTEX 2340
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SplAIII
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Spirulina platensis
<6>UTEX 2340
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SplAIV
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,Uba1227I,Uba1245I,Uba153AI,UbaM39I
<3>CAGCTG
<4>
<5>Spirulina platensis
<6>UTEX 2340
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SpmI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Sphingobacterium mizutae
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Radionenko, Y.V., Ushakova, T.A., Repin, V.E., Russian Patent Office, 2005.
Ushakova, T.A., Puchkova, L.I., Radionenko, Y.V., Gutorov, V.V., Kuvshinov, V.N., Repin, V.E., (2004) Biotekhnologiya, vol. 0, pp. 38-42.

<1>SpoI
<2>NruI,AmaSI,Bsp68I,BtuMI,Mlu9273I,MluB2I,PspDI,RruI,SalDI,Sbo13I,Sna3286I,Uba1117I,Uba1386I,VchO70I
<3>TCG^CGA
<4>
<5>Salmonella potsdam
<6>D. Raines
<7>
<8>Nelson, M., Unpublished observations.

<1>SpoDI
<2>
<3>GCGGRAG
<4>
<5>Silicibacter pomeroyi DSS-3
<6>M.A. Moran
<7>
<8>Moran, M.A. et al., (2004) Nature, vol. 432, pp. 910-913.
Morgan, R.D., Unpublished observations.
Usuda, Y., Nishio, Y., Matsui, K., Sugimoto, S., Koseki, K., US Patent Office, 2008.

<1>SprLI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Streptomyces prasinus
<6>ATCC 15825
<7>
<8>Saboohi, N., Sohail, A., Unpublished observations.

<1>SpuI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Streptomyces pulveraceus
<6>ATCC 29083
<7>
<8>Saboohi, N., Mushtaq, R., Sohail, A., Unpublished observations.

<1>SpvI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Streptomyces parvus
<6>NRRL B-1255
<7>
<8>Mattila, P., Pitkanen, K., Unpublished observations.

<1>SrfI
<2>
<3>GCCC^GGGC
<4>
<5>Streptomyces species
<6>T.G. Simcox
<7>EO
<8>Simcox, T.G., Marsh, S.J., Gross, E.A., Lernhardt, W., Davis, S., Simcox, M.E.C., (1991) Gene, vol. 109, pp. 121-123.
Weiner, M., Costa, G., (1994) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 94, pp. 249.

<1>SriI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Streptomyces griseoflavus
<6>Viikki 41
<7>
<8>Mattila, P., Pitkanen, K., Unpublished observations.

<1>SrifpI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces rimosus forma paramomycinus
<6>ATCC 14827
<7>
<8>Mattila, P., Pitkanen, K., Unpublished observations.

<1>SrlI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,Srl77DI,SspCI,Uba1122I
<3>G^CCGGC
<4>
<5>Selenomonas ruminantium subsp. lactilytica 84
<6>P. Pristas
<7>
<8>Pristas, P., Fliegerova, K., Javorsky, P., (1998) Lett. Appl. Microbiol., vol. 27, pp. 83-85.

<1>SrlII
<2>AvaIII,Asi372I,BfrBI,BfrCI,Csp68KIII,EcoT22I,Mph1103I,NsiI,PinBI,Ppu10I,PxyJKI,SepI,SmuCI,SspD5II,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>ATGCAT
<4>
<5>Selenomonas ruminantium subsp. lactilytica 84
<6>P. Pristas
<7>
<8>Pristas, P., Fliegerova, K., Javorsky, P., (1998) Lett. Appl. Microbiol., vol. 27, pp. 83-85.

<1>Srl19I
<2>AhaIII,DraI,PauAII,Srl61DI,Srl76DI,SruI
<3>TTTAAA
<4>
<5>Selenomonas ruminantium 19
<6>I. Vanat
<7>
<8>Zatkovic, B., Molnarova, V., Kmet, V., Javorsky, P., Pristas, P., (2000) Anaerobe, vol. 6, pp. 299-304.

<1>Srl1DI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Selenomonas ruminantium 1
<6>I. Vanat
<7>
<8>Pristas, P., Vanat, I., Javorsky, P., (1997) Folia Microbiol. (Praha), vol. 42, pp. 121-124.

<1>Srl2DI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Selenomonas ruminantium 2
<6>I. Vanat
<7>
<8>Pristas, P., Vanat, I., Javorsky, P., (1997) Folia Microbiol. (Praha), vol. 42, pp. 121-124.

<1>Srl5DI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Selenomonas ruminantium 5
<6>I. Vanat
<7>
<8>Pristas, P., Molnarova, V., Javorsky, P., (2002) Biologia (Bratisl), vol. 57, pp. 777-782.
Pristas, P., Vanat, I., Javorsky, P., (1997) Folia Microbiol. (Praha), vol. 42, pp. 121-124.

<1>Srl8DI
<2>VspI,AseI,AsnI,BpoAI,CprJK722I,PbuMZI,PshBI,Srl55DII,Srl65DI,Srr17I,Sru4DI
<3>ATTAAT
<4>
<5>Selenomonas ruminantium 8
<6>I. Vanat
<7>
<8>Pristas, P., Vanat, I., Javorsky, P., (1997) Folia Microbiol. (Praha), vol. 42, pp. 121-124.

<1>Srl32DI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Selenomonas ruminantium 32
<6>I. Vanat
<7>
<8>Pristas, P., Vanat, I., Javorsky, P., (1997) Folia Microbiol. (Praha), vol. 42, pp. 121-124.

<1>Srl32DII
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco237I,Eco252I,FunII,HalI,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl55DI,SsoI,Uba58I,Van91II,VchN100I,VchO2I
<3>G^AATTC
<4>
<5>Selenomonas ruminantium 32
<6>I. Vanat
<7>
<8>Pristas, P., Vanat, I., Javorsky, P., (1997) Folia Microbiol. (Praha), vol. 42, pp. 121-124.

<1>Srl55DI
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco237I,Eco252I,FunII,HalI,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl32DII,SsoI,Uba58I,Van91II,VchN100I,VchO2I
<3>G^AATTC
<4>
<5>Selenomonas ruminantium subsp. lactilytica 55
<6>I. Vanat
<7>
<8>Pristas, P., Molnarova, V., Javorsky, P., (2002) Biologia (Bratisl), vol. 57, pp. 777-782.
Pristas, P., Vanat, I., Javorsky, P., (1997) Folia Microbiol. (Praha), vol. 42, pp. 121-124.

<1>Srl55DII
<2>VspI,AseI,AsnI,BpoAI,CprJK722I,PbuMZI,PshBI,Srl8DI,Srl65DI,Srr17I,Sru4DI
<3>ATTAAT
<4>
<5>Selenomonas ruminantium subsp. lactilytica 55
<6>I. Vanat
<7>
<8>Pristas, P., Vanat, I., Javorsky, P., (1997) Folia Microbiol. (Praha), vol. 42, pp. 121-124.

<1>Srl56DI
<2>SfeI,Bco163I,BdiSI,BfmI,BpcI,BstSFI,BthP35I,HpyF2I,LlaBI,SfcI
<3>C^TRYAG
<4>
<5>Selenomonas ruminantium 56
<6>I. Vanat
<7>
<8>Pristas, P., Molnarova, V., Javorsky, P., (2002) Biologia (Bratisl), vol. 57, pp. 777-782.
Pristas, P., Vanat, I., Javorsky, P., (1997) Folia Microbiol. (Praha), vol. 42, pp. 121-124.

<1>Srl61DI
<2>AhaIII,DraI,PauAII,Srl19I,Srl76DI,SruI
<3>TTTAAA
<4>
<5>Selenomonas ruminantium 61
<6>I. Vanat
<7>
<8>Pristas, P., Vanat, I., Javorsky, P., (1997) Folia Microbiol. (Praha), vol. 42, pp. 121-124.

<1>Srl65DI
<2>VspI,AseI,AsnI,BpoAI,CprJK722I,PbuMZI,PshBI,Srl8DI,Srl55DII,Srr17I,Sru4DI
<3>ATTAAT
<4>
<5>Selenomonas ruminantium 65
<6>I. Vanat
<7>
<8>Pristas, P., Vanat, I., Javorsky, P., (1997) Folia Microbiol. (Praha), vol. 42, pp. 121-124.

<1>Srl76DI
<2>AhaIII,DraI,PauAII,Srl19I,Srl61DI,SruI
<3>TTTAAA
<4>
<5>Selenomonas ruminantium 76
<6>I. Vanat
<7>
<8>Pristas, P., Vanat, I., Javorsky, P., (1997) Folia Microbiol. (Praha), vol. 42, pp. 121-124.

<1>Srl77DI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,SspCI,Uba1122I
<3>GCCGGC
<4>
<5>Selenomonas ruminantium 77
<6>I. Vanat
<7>
<8>Pristas, P., Vanat, I., Javorsky, P., (1997) Folia Microbiol. (Praha), vol. 42, pp. 121-124.

<1>Srr17I
<2>VspI,AseI,AsnI,BpoAI,CprJK722I,PbuMZI,PshBI,Srl8DI,Srl55DII,Srl65DI,Sru4DI
<3>ATTAAT
<4>
<5>Selenomonas ruminantium 17
<6>I. Vanat
<7>
<8>Zatkovic, B., Molnarova, V., Kmet, V., Javorsky, P., Pristas, P., (2000) Anaerobe, vol. 6, pp. 299-304.

<1>SruI
<2>AhaIII,DraI,PauAII,Srl19I,Srl61DI,Srl76DI
<3>TTT^AAA
<4>
<5>Selenomonas ruminantium 18D
<6>I. Vanat
<7>
<8>Vanat, I., Pristas, P., Rybosoval, E., Godany, A., Javorsky, P., (1993) FEMS Microbiol. Lett., vol. 113, pp. 129-132.

<1>Sru4DI
<2>VspI,AseI,AsnI,BpoAI,CprJK722I,PbuMZI,PshBI,Srl8DI,Srl55DII,Srl65DI,Srr17I
<3>AT^TAAT
<4>
<5>Selenomonas ruminantium
<6>I. Vanat
<7>
<8>Pristas, P., Vanat, I., Godany, A., Javorsky, P., (1994) Arch. Microbiol., vol. 161, pp. 439-441.

<1>Sru30DI
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGG^CCT
<4>
<5>Selenomonas ruminantium 30
<6>P. Pristas
<7>
<8>Pristas, P., Vanat, I., Javorsky, P., (1995) Gene, vol. 158, pp. 139-140.

<1>SsaI
<2>
<3>?
<4>
<5>Staphylococcus saprophyticus
<6>ATCC 13518
<7>
<8>Langdale, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>SsbI
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,Uba83I,Uba1164II,Uba1219I,Uba1435I
<3>A^AGCTT
<4>
<5>Streptomyces scabies
<6>J.L. Schottel
<7>
<8>Babcock, M.J., Schottel, J.L., (1991) Nucleic Acids Res., vol. 19, pp. 3457.

<1>SscI
<2>
<3>?
<4>
<5>Salmonella schwarzengrund
<6>Y. Yoshida
<7>
<8>Matsui, M., Mise, K., Yoshida, Y., Ishidate, M., (1986) Eisei Shikenjo Hokoku, vol. 104, pp. 92-96.

<1>SscL1I
<2>HinfI,CviBI,CviCI,CviDI,CviEI,CviFI,CviGI,FnuAI,HhaII,HpyIV,HpyAIV,Hpy87AI,HpyF2II,HpyF10II,HpyF18I,HpyF38I,HpyF44I,HpyF55II,HpyF60I,HpyF71III,HpyF72III,NcaI,NovII,NsiHI
<3>G^ANTC
<4>2(6)
<5>Staphylococcus species L1
<6>N.I. Matvienko
<7>
<8>Vasiljeva, L.Y., Zheleznaya, L.A., Matvienko, N.I., (1998) Biokhimiia, vol. 63, pp. 212-218.
Vasiljeva, L.Y., Zheleznaya, L.A., Matvienko, N.I., (2000) Biokhimiia, vol. 65, pp. 565-570.

<1>SseI
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Synechococcus species
<6>ATCC 29203
<7>
<8>Brand, P., de Waard, A., Unpublished observations.

<1>SseII
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Synechococcus species
<6>ATCC 29203
<7>
<8>Brand, P., de Waard, A., Unpublished observations.

<1>Sse9I
<2>TspEI,MluCI,TasI,TseCI,Tsp509I
<3>^AATT
<4>2(6)
<5>Sporosarcina species 9
<6>S.K. Degtyarev
<7>IV
<8>Gonchar, D.A., Abdurashitov, M.A., Okhapkina, S.S., Shagin, D.A., Kileva, E.V., Degtyarev, S.Kh., (2007) Mol. Biol. (Mosk), vol. 41, pp. 491-498.
Gonchar, D.A., Dedkov, V.S., Verkhozina, V.A., Kusner, Y.S., Shevchenko, A.V., Degtyarev, S.K., (1998) Prikl. Biokhim. Mikrobiol., vol. 34, pp. 139-141.
Gonchar, D.A., Dedkov, V.S., Verkhozina, V.A., Kusner, Y.S., Shevchenko, A.V., Degtyarev, S.K., (1998) Mol. Gen. Mikrobiol. Virusol., vol. 2, pp. 32-34.
Gonchar, D.A., Wolf, Y.I., Degtyarev, S.Kh., (1996) Nucleic Acids Res., vol. 24, pp. 2790-2792.
Zhu, Z., Blanchard, A., Xu, S.-Y., Guan, S., Wei, H., Zhang, P., Sun, D., Chan, S.-h., International Patent Office, 2009.

<1>Sse232I
<2>MreI
<3>CG^CCGGCG
<4>
<5>Streptomyces species RH232
<6>I. Kato
<7>
<8>Nomura, Y., Ishizaki, I., Oshima, K., Kato, I., Japanese Patent Office, 1998.

<1>Sse1825I
<2>SanDI,KflI
<3>GG^GWCCC
<4>
<5>Streptomyces species
<6>Y. Ishino
<7>
<8>Nomura, Y., Ishino, Y., Kimizuka, F., Kato, I., (1995) Gene, vol. 157, pp. 323-324.

<1>Sse8387I
<2>SbfI,SdaI
<3>CCTGCA^GG
<4>
<5>Streptomyces species 8387
<6>Takara 8387
<7>K
<8>Kotani, H., Kato, I., Kimizuka, F., European Patent Office, 1995.
Kotani, H., Nomura, Y., Kawashima, Y., Sagawa, H., Takagi, M., Kita, A., Ito, H., Kato, I., (1990) Nucleic Acids Res., vol. 18, pp. 5637-5640.

<1>Sse8647I
<2>
<3>AG^GWCCT
<4>
<5>Streptomyces species
<6>Y. Ishino
<7>
<8>Ishino, Y., Nomura, Y., Kato, I., (1995) Nucleic Acids Res., vol. 23, pp. 742-744.

<1>SseAI
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SspDI
<3>GG^CGCC
<4>
<5>Streptomyces species
<6>V. Bouriotis
<7>
<8>Rina, M., Karagouni, A., Pagomenou, M., Tsigos, I., Bouriotis, V., (1991) Nucleic Acids Res., vol. 19, pp. 6341.

<1>SseBI
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGG^CCT
<4>
<5>Streptomyces species
<6>V. Bouriotis
<7>C
<8>Rina, M., Tzanodaskalaki, M., Karagouni, A., Pagomenou, M., Bouriotis, V., (1992) Nucleic Acids Res., vol. 20, pp. 1808.

<1>SshAI
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,Uba1184II,Uba1294I,Uba1332I,Uba1333I
<3>CC^TNAGG
<4>
<5>Salmonella shikmonah
<6>K. Mise
<7>
<8>Miyahara, M., Nakajima, K., Kawanishi, T., Mise, K., (1990) FEMS Microbiol. Lett., vol. 66, pp. 245-248.

<1>SsiI
<2>AciI,BspACI
<3>CCGC(-3/-1)
<4>
<5>Staphylococcus sciuri RFL1
<6>Fermentas G266
<7>F
<8>Jurgelyte, R., Lazareviciute, L., Maneliene, Z., Capskaja, L., Trinkunaite, L., Janulaitis, A., Unpublished observations.

<1>SsiAI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Staphylococcus species A
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., (1995) Vestn. Akad. Med. Nauk SSSR, vol. 2, pp. 47-51.

<1>SsiBI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>
<5>Staphylococcus species B
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., (1995) Vestn. Akad. Med. Nauk SSSR, vol. 2, pp. 47-51.

<1>SslI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Streptococcus salivarius ssp thermophilus
<6>L. Benbadis
<7>
<8>Benbadis, L., Garel, J.R., Hartley, D.L., (1991) Appl. Environ. Microbiol., vol. 57, pp. 3677-3678.
Hill, C., (1993) FEMS Microbiol. Rev., vol. 12, pp. 87-108.

<1>Ssl16215I
<2>
<3>?
<4>
<5>Streptococcus salivarius subsp. thermophilus
<6>FERM 16215
<7>
<8>Tomita, M., Toyama, K., Hiramatsu, A., Sho, K., Takahashi, T., Japanese Patent Office, 2000.

<1>Ssl16216I
<2>
<3>?
<4>
<5>Streptococcus salivarius subsp. thermophilus
<6>FERM 16216
<7>
<8>Tomita, M., Toyama, K., Hiramatsu, A., Sho, K., Takahashi, T., Japanese Patent Office, 2000.

<1>Ssl16217I
<2>
<3>?
<4>
<5>Streptococcus salivarius subsp. thermophilus
<6>FERM 16217
<7>
<8>Tomita, M., Toyama, K., Hiramatsu, A., Sho, K., Takahashi, T., Japanese Patent Office, 2000.

<1>Ssl16218I
<2>
<3>?
<4>
<5>Streptococcus salivarius subsp. thermophilus
<6>FERM 16218
<7>
<8>Tomita, M., Toyama, K., Hiramatsu, A., Sho, K., Takahashi, T., Japanese Patent Office, 2000.

<1>Ssl16219I
<2>
<3>?
<4>
<5>Streptococcus salivarius subsp. thermophilus
<6>FERM 16219
<7>
<8>Tomita, M., Toyama, K., Hiramatsu, A., Sho, K., Takahashi, T., Japanese Patent Office, 2000.

<1>SsmI
<2>PstII
<3>CTGATG
<4>
<5>Streptomyces sampsonii RFL6
<6>A. Janulaitis
<7>
<8>Lauciuniene, N., Norgeliene, D., Kiuduliene, L., Vitkute, J., Janulaitis, A., Unpublished observations.

<1>SsmII
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Streptomyces sampsonii RFL6
<6>A. Janulaitis
<7>
<8>Lauciuniene, N., Norgeliene, D., Kiuduliene, L., Vitkute, J., Janulaitis, A., Unpublished observations.

<1>Ssm4I
<2>SacI,BpuAmI,Ecl136II,Ecl137I,EcoICRI,Eco53kI,MxaI,NasSI,Pfl18I,Psp124BI,ScoI,Ssm5I,SstI
<3>GAGCTC
<4>
<5>Streptomyces species SM4
<6>P. Pristas
<7>
<8>Tothova, T., Godany, A., Javorsky, P., Pristas, P., (2007) Biologia (Bratisl), vol. 62, pp. 381-385.

<1>Ssm5I
<2>SacI,BpuAmI,Ecl136II,Ecl137I,EcoICRI,Eco53kI,MxaI,NasSI,Pfl18I,Psp124BI,ScoI,Ssm4I,SstI
<3>GAGCTC
<4>
<5>Streptomyces species SM5
<6>P. Pristas
<7>
<8>Tothova, T., Godany, A., Javorsky, P., Pristas, P., (2007) Biologia (Bratisl), vol. 62, pp. 381-385.

<1>Ssm5II
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Streptomyces species SM5
<6>P. Pristas
<7>
<8>Tothova, T., Godany, A., Javorsky, P., Pristas, P., (2007) Biologia (Bratisl), vol. 62, pp. 381-385.

<1>SsoI
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco237I,Eco252I,FunII,HalI,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl32DII,Srl55DI,Uba58I,Van91II,VchN100I,VchO2I
<3>G^AATTC
<4>2(6)
<5>Shigella sonnei 47
<6>T.M. Uporova
<7>
<8>Lopatina, N.G., Kirnos, M.D., Suchkov, S.V., Vanyushin, B.F., Nikolskaya, I.I., Debov, S.S., (1985) Biokhimiia, vol. 50, pp. 495-502.
Uporova, T.M., Kartasheva, I.M., Skripkin, E.A., Lopareva, E.N., Nikolskaya, I.I., Debov, S.S., (1985) Vopr. Med. Khim., vol. 31, pp. 131-136.

<1>SsoII
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,StyD4I,Uba17I,Uba1391I
<3>^CCNGG
<4>2(5)
<5>Shigella sonnei 47
<6>T.M. Uporova
<7>
<8>Karyagina, A.S., Lunin, V.G., Nikolskaya, I.I., (1990) Gene, vol. 87, pp. 113-118.
Karyagina, A.S., Lunin, V.G., Nikolskaya, I.I., Debov, S.S., (1989) Mol. Gen. Mikrobiol. Virusol., vol. 3, pp. 16-20.
Nikolskaya, I.I., Karpetz, L.Z., Kartashova, M., Lopatina, N.G., Skripkin, E.A., Suchkov, S.V., Uporova, T.M., Gruber, I.M., Debov, S.S., (1983) Mol. Gen. Mikrobiol. Virusol., vol. 0, pp. 5-10.
Uporova, T.M., Kartasheva, I.M., Skripkin, E.A., Lopareva, E.N., Nikolskaya, I.I., Debov, S.S., (1985) Vopr. Med. Khim., vol. 31, pp. 131-136.

<1>M.SsoIII
<2>
<3>?
<4>
<5>Shigella sonnei 47
<6>T.M. Uporova
<7>
<8>Nikolskaya, I.I., Sharkova, E.V., Suchkov, S.V., Karpets, L.Z., Debov, S.S., Somodi, P., Foldes, I., (1983) Biochem. Int., vol. 7, pp. 605-615.

<1>M.SsoIV
<2>
<3>?
<4>
<5>Shigella sonnei 47
<6>T.M. Uporova
<7>
<8>Nikolskaya, I.I., Sharkova, E.V., Suchkov, S.V., Karpets, L.Z., Debov, S.S., Somodi, P., Foldes, I., (1983) Biochem. Int., vol. 7, pp. 605-615.

<1>M.SsoV
<2>
<3>?
<4>
<5>Shigella sonnei 47
<6>T.M. Uporova
<7>
<8>Nikolskaya, I.I., Sharkova, E.V., Suchkov, S.V., Karpets, L.Z., Debov, S.S., Somodi, P., Foldes, I., (1983) Biochem. Int., vol. 7, pp. 605-615.

<1>SspI
<2>
<3>AAT^ATT
<4>?(6)
<5>Sphaerotilus species
<6>ATCC 13925
<7>BCFIJKMNOQRSUVWX
<8>Benner, J.S., Coe, L., Unpublished observations.
Schildkraut, I., Grandoni, R., Unpublished observations.

<1>Ssp1I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Streptomyces species RFL1
<6>A. Janulaitis
<7>
<8>Petrusyte, M., Maneliene, Z., Butkus, V., Janulaitis, A., Unpublished observations.

<1>Ssp2I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Streptomyces species RFL2
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Ssp4I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces species RFL4
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Ssp12I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Streptomyces species ST-12
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Andreeva, I.S., Repin, V.E., Krivopalova, G.N., Russian Patent Office, 1999.

<1>Ssp14I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Streptomyces species 14
<6>O.M. Reva
<7>
<8>Polishchuk, L.V., Lukyanchuk, V.V., Matselyukh, B.P., Unpublished observations.

<1>Ssp27I
<2>
<3>?
<4>
<5>Streptomyces species 27
<6>O.M. Reva
<7>
<8>Polishchuk, L.V., Lukyanchuk, V.V., Matselyuch, B.P., (2000) Actinomycetes, vol. 10, pp. 13-15.

<1>Ssp34I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Streptomyces species 34
<6>V.V. Lukyanchuk
<7>
<8>Lukyanchuk, V.V., Strizhkova, G.M., Polishchuk, L.V., Kopeyko, O.P., Matselyukh, B.P., (1998) Mikrobiol. Zh., vol. 60, pp. 33-35.

<1>Ssp42I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Streptomyces species 42
<6>O.M. Reva
<7>
<8>Polishchuk, L.V., Lukyanchuk, V.V., Matselyukh, B.P., Unpublished observations.

<1>Ssp43I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Streptomyces species 43
<6>O.M. Reva
<7>
<8>Polishchuk, L.V., Lukyanchuk, V.V., Matselyuch, B.P., (2000) Actinomycetes, vol. 10, pp. 13-15.

<1>Ssp45I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Streptomyces species 45
<6>O.M. Reva
<7>
<8>Lukyanchuk, V.V., Strizhkova, G.M., Polishchuk, L.V., Kopeyko, O.P., Matselyukh, B.P., (1998) Mikrobiol. Zh., vol. 60, pp. 33-35.
Polishchuk, L.V., Lukyanchuk, V.V., Matselyukh, B.P., Unpublished observations.

<1>Ssp47I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Streptomyces species 47
<6>O.M. Reva
<7>
<8>Lukyanchuk, V.V., Strizhkova, G.M., Polishchuk, L.V., Kopeyko, O.P., Matselyukh, B.P., (1998) Mikrobiol. Zh., vol. 60, pp. 33-35.

<1>Ssp48I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp152I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Streptomyces species 48
<6>B.P. Matselyukh
<7>
<8>Lukyanchuk, V.V., Polishchuk, L.V., Strizhkova, G.M., Kopieiko, O.P., Matselyukh, B.P., (1999) Mikrobiol. Zh., vol. 61, pp. 80-83.

<1>Ssp152I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,SspRFI,SviI,Uba1385I,Uba1452I
<3>TTCGAA
<4>
<5>Streptomyces species 152
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>Ssp1725I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Streptomyces spadicis 1725
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>Ssp4800I
<2>Bsp1407I,AauI,BsmGI,BsmRI,BsrGI,Bst170I,BstAUI,SspBI
<3>T^GTACA
<4>
<5>Streptomyces species BMTU 4800
<6>DSM 6181
<7>
<8>Kaluza, K., Frey, B., Jarsch, M., European Patent Office, 1995.

<1>Ssp5230I
<2>AatII,AspJI,Ppu1253I,ZraI
<3>GACGT^C
<4>
<5>Streptomyces species 5230
<6>P. Westermann
<7>
<8>Knoblich, I.M., Sellmann, E., Kaluza, K., Frey, B., Auer, J., Schmitz, G.G., Westermann, P., (1992) Nucleic Acids Res., vol. 20, pp. 2378.

<1>Ssp27144I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>AT^CGAT
<4>
<5>Synechococcus species
<6>ATCC 27144
<7>
<8>Obayashi, A., Japanese Patent Office, 1985.

<1>SspAI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>^CCWGG
<4>
<5>Synechococcus species
<6>AN 6301
<7>
<8>Piechula, S., Skowron, P.M., Piatyszek, M., Podhajska, A.J., (1991) Nucleic Acids Res., vol. 19, pp. 2782.

<1>SspBI
<2>Bsp1407I,AauI,BsmGI,BsmRI,BsrGI,Bst170I,BstAUI,Ssp4800I
<3>T^GTACA
<4>
<5>Streptomyces species
<6>B. Frey
<7>
<8>Frey, B., Unpublished observations.

<1>SspCI
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,Uba1122I
<3>GCC^GGC
<4>
<5>Streptomyces species
<6>M. Rina
<7>
<8>Rina, M., Unpublished observations.

<1>SspDI
<2>NarI,BbeI,BbeAI,BinSII,DinI,Eco78I,EgeI,EheI,KasI,McaAI,MchI,Mly113I,MsaI,NamI,NdaI,NunII,PatAI,PmnI,SfoI,SseAI
<3>G^GCGCC
<4>
<5>Sphingomonas species RFL1
<6>Fermentas G308
<7>F
<8>Markauskiene, J., Capskaja, L., Kiuduliene, L., Petrusyte, M., Zakareviciene, L., Lubys, A., Janulaitis, A., Unpublished observations.

<1>SspD5I
<2>HphI,AsuHPI,NgoBVIII,NgoDVIII,NgoJVIII,NgoMVIII
<3>GGTGA(8/8)
<4>
<5>Staphylococcus species D5
<6>N. Matvienko
<7>
<8>Zheleznaya, L., Shiryaev, S., Zheleznyakova, E., Matvienko, N., Matvienko, N., (1999) FEBS Lett., vol. 448, pp. 38-40.

<1>SspD5II
<2>AvaIII,Asi372I,BfrBI,BfrCI,Csp68KIII,EcoT22I,Mph1103I,NsiI,PinBI,Ppu10I,PxyJKI,SepI,SmuCI,SrlII,Uba1353I,Uba1367I,Uba1384I,Zsp2I
<3>ATGCA^T
<4>
<5>Staphylococcus species D5
<6>N. Matvienko
<7>
<8>Shiryaev, S.A., Zheleznyakova, E.N., Matvienko, N.N., Zheleznaya, L.A., Matvienko, N.I., (2000) Biokhimiia, vol. 65, pp. 553-561.

<1>SspJI
<2>SnaBI,Bpu1831I,BstSNI,EciAI,Eco105I,Eco158II,SspM1I,SspM2I,Uba1240I
<3>TACGTA
<4>
<5>Spirulina species J
<6>M. Sakakibara
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SspJII
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspM1II,SspM2II,Uba1381I
<3>GRCGYC
<4>
<5>Spirulina species J
<6>M. Sakakibara
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SspKI
<2>SplI,BpuB5I,BsiWI,BsmWI,BvuBI,MaeK81I,Pfl23II,PfuNI,PpuAI,PspLI,SmaAI,SplAI,SunI
<3>CGTACG
<4>
<5>Spirulina species K
<6>M. Sakakibara
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SspM1I
<2>SnaBI,Bpu1831I,BstSNI,EciAI,Eco105I,Eco158II,SspJI,SspM2I,Uba1240I
<3>TACGTA
<4>
<5>Spirulina species M1
<6>M. Sakakibara
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SspM1II
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM2II,Uba1381I
<3>GRCGYC
<4>
<5>Spirulina species M1
<6>M. Sakakibara
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SspM1III
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,Uba1127I,Vsp2246I
<3>GGYRCC
<4>
<5>Spirulina species M1
<6>M. Sakakibara
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SspM2I
<2>SnaBI,Bpu1831I,BstSNI,EciAI,Eco105I,Eco158II,SspJI,SspM1I,Uba1240I
<3>TACGTA
<4>
<5>Spirulina species M2
<6>M. Sakakibara
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SspM2II
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,Uba1381I
<3>GRCGYC
<4>
<5>Spirulina species M2
<6>M. Sakakibara
<7>
<8>Kumano, M., Sakakibara, M., (1988) Baiosaiensu to Indasutori, vol. 46, pp. 38-41.

<1>SspRFI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SviI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Synechococcus species RF-1
<6>J. Tu
<7>
<8>Li, J.-K., Tu, J., (1991) Nucleic Acids Res., vol. 19, pp. 4770.

<1>SspXI
<2>
<3>?
<4>
<5>Serratia species SAI
<6>B. Torheim
<7>
<8>Torheim, B., Unpublished observations.

<1>SsrI
<2>HpaI,BsaKI,BseII,BstEZ359I,BstHPI,KspAI,MwhI,Uba1408II
<3>GTT^AAC
<4>
<5>Staphylococcus saprophyticus B6
<6>S.K. Degtyarev
<7>
<8>Dedkov, V.S., Prihodko, G.G., Puchkova, L.I., Serov, G.D., Rechkunova, N.I., Degtyarev, S.K., (1989) Mol. Gen. Mikrobiol. Virusol., vol. 11, pp. 24-25.

<1>M.SssI
<2>
<3>CG
<4>1(5)
<5>Spiroplasma species MQ1
<6>A. Razin
<7>
<8>Jack, W., Unpublished observations.
Razin, A., Rottem, S., Renbaum, P.F., European Patent Office, 1995.
Razin, A., Rottem, S., Renbaum, P.F., US Patent Office, 1994.
Renbaum, P., Abrahamove, D., Fainsod, A., Wilson, G.G., Rottem, S., Razin, A., (1990) Nucleic Acids Res., vol. 18, pp. 1145-1152.

<1>SstI
<2>SacI,BpuAmI,Ecl136II,Ecl137I,EcoICRI,Eco53kI,MxaI,NasSI,Pfl18I,Psp124BI,ScoI,Ssm4I,Ssm5I
<3>GAGCT^C
<4>
<5>Streptomyces stanford
<6>S. Goff
<7>BC
<8>Goff, S.P., Rambach, A., (1978) Gene, vol. 3, pp. 347-352.
Longo, M.C., Smith, M.D., Harris, R.D., International Patent Office, 1996.
Muller, F., Stoffel, S., Clarkson, S.G., Unpublished observations.

<1>SstII
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGC^GG
<4>
<5>Streptomyces stanford
<6>S. Goff
<7>B
<8>Goff, S.P., Rambach, A., (1978) Gene, vol. 3, pp. 347-352.

<1>SstIII
<2>
<3>?
<4>
<5>Streptomyces stanford
<6>S. Goff
<7>
<8>Goff, S.P., Rambach, A., (1978) Gene, vol. 3, pp. 347-352.

<1>SstIV
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Streptomyces stanford
<6>S. Goff
<7>
<8>Kuebbing, D., Blakesley, R.J., (1979) Fed. Proc., vol. 38, pp. 780.

<1>Sst12I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Streptomyces species ST-12
<6>V.E. Repin
<7>
<8>Puchkova, L.I., Andreeva, I.S., Repin, V.E., Krivopalova, G.N., Russian Patent Office, 1999.
Ushakova, T.A., Puchkova, L.I., Gutorov, V.V., Kuvshinov, V.N., Repin, V.E., (2002) Prikl. Biokhim. Mikrobiol., vol. 38, pp. 25-28.

<1>Ssu211I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis strain 211
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 5436-5440.

<1>Ssu212I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis strain 212
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 5436-5440.

<1>Ssu220I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis strain 220
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 5436-5440.

<1>R1.Ssu2479I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis strain 89-2479
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 5436-5440.

<1>R2.Ssu2479I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis strain 89-2479
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 5436-5440.

<1>R1.Ssu4109I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis strain 89-4109-1
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 5436-5440.

<1>R2.Ssu4109I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis strain 89-4109-1
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 5436-5440.

<1>R1.Ssu4961I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis strain 4961
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 5436-5440.

<1>R2.Ssu4961I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis strain 4961
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 5436-5440.

<1>R1.Ssu8074I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis strain 8074
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 5436-5440.

<1>R2.Ssu8074I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis strain 8074
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 5436-5440.

<1>R1.Ssu11318I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis NIAH11318
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 5436-5440.

<1>R2.Ssu11318I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis NIAH11318
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 5436-5440.

<1>R1.SsuDAT1I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis DAT1
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Otani, Y., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 500-511.

<1>R2.SsuDAT1I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis DAT1
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Otani, Y., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 500-511.

<1>SsuRBI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Streptococcus suis strain 205
<6>T. Sekizaki
<7>
<8>Sekizaki, T., Osaki, M., Takamatsu, D., Shimoji, Y., (2001) J. Bacteriol., vol. 183, pp. 5436-5440.

<1>SsvI
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGGCCT
<4>
<5>Streptomyces sviceus
<6>ATCC 29083
<7>
<8>Mushtaq, R., Roberts, R.J., Unpublished observations.

<1>StaI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Streptomyces takatoensis
<6>ATCC 27649
<7>
<8>Klein, S., Roberts, R.J., Unpublished observations.

<1>StaAI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces tanashiensis
<6>ATCC 33159
<7>
<8>Earle-Hughes, J., Roberts, R.J., Unpublished observations.

<1>SteI
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGG^CCT
<4>
<5>Streptomyces tendae
<6>ATCC 19812
<7>
<8>Mushtaq, R., Sohail, A., Roberts, R.J., Unpublished observations.

<1>SthI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>G^GTACC
<4>
<5>Salmonella thompson YY356
<6>Y. Yoshida
<7>
<8>Matsui, M., Mise, K., Yoshida, Y., Ishidate, M., (1986) Eisei Shikenjo Hokoku, vol. 104, pp. 92-96.

<1>Sth117I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Streptococcus thermophilus ST117
<6>G.A. Somkuti
<7>
<8>Hill, C., (1993) FEMS Microbiol. Rev., vol. 12, pp. 87-108.
Solaiman, D.K.Y., Somkuti, G.A., (1991) FEMS Microbiol. Lett., vol. 80, pp. 75-80.

<1>Sth132I
<2>NcuII
<3>CCCG(4/8)
<4>
<5>Streptococcus thermophilus
<6>M.T. Poch
<7>
<8>Poch, M.T., Somkuti, G.A., (1993) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 93, pp. 330.
Poch, M.T., Somkuti, G.A., Solaiman, D.K.Y., (1997) Gene, vol. 195, pp. 201-206.

<1>Sth134I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>C^CGG
<4>
<5>Streptococcus thermophilus strain 134
<6>D.K.Y. Solaiman
<7>
<8>Hill, C., (1993) FEMS Microbiol. Rev., vol. 12, pp. 87-108.
Solaiman, D.K.Y., Somkuti, G.A., (1990) FEMS Microbiol. Lett., vol. 67, pp. 261-266.

<1>Sth302I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Streptococcus thermophilus CNRZ302
<6>G. Guedon
<7>
<8>Morgan, R.D., Unpublished observations.

<1>Sth302II
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CC^GG
<4>
<5>Streptococcus thermophilus CNRZ302
<6>G. Guedon
<7>
<8>Morgan, R.D., Unpublished observations.

<1>Sth368I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>^GATC
<4>4(5)
<5>Streptococcus thermophilus CNRZ368
<6>B. Decaris
<7>
<8>Burrus, V., Bontemps, C., Decaris, B., Guedon, G., (2001) Appl. Environ. Microbiol., vol. 67, pp. 1522-1528.

<1>Sth455I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Streptococcus thermophilus CNRZ 455
<6>G. Linden
<7>
<8>Guimont, C., Henry, P., Linden, G., (1993) Appl. Microbiol. Biotechnol., vol. 39, pp. 216-220.

<1>Sth4134I
<2>
<3>?
<4>
<5>Streptococcus thermophilus 4134
<6>G.F. Fitzgerald
<7>
<8>Schirawski, J., van Sinderen, D., Fitzgerald, G., (2001) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 101, pp. 476.

<1>SthAI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Salmonella thompson YY17
<6>Y. Yoshida
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SthBI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Salmonella thompson YY106
<6>Y. Yoshida
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SthCI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Salmonella thompson YY150
<6>Y. Yoshida
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SthDI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Salmonella thompson YY197
<6>Y. Yoshida
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SthEI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Salmonella thompson YY200
<6>Y. Yoshida
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SthFI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Salmonella thompson YY209
<6>Y. Yoshida
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SthGI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Salmonella thompson YY217
<6>Y. Yoshida
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SthHI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Salmonella thompson YY224
<6>Y. Yoshida
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SthJI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Salmonella thompson YY225
<6>Y. Yoshida
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SthKI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Salmonella thompson YY228
<6>Y. Yoshida
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SthLI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Salmonella thompson YY247
<6>Y. Yoshida
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SthMI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Salmonella thompson YY347
<6>Y. Yoshida
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>SthNI
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Salmonella thompson YY148
<6>Y. Yoshida
<7>
<8>Matsui, M., Mise, K., Yoshida, Y., Ishidate, M., (1986) Eisei Shikenjo Hokoku, vol. 104, pp. 92-96.
Mise, K., Unpublished observations.

<1>StmI
<2>
<3>?
<4>
<5>Salmonella typhimurium
<6>Y. Yoshida
<7>
<8>Matsui, M., Mise, K., Yoshida, Y., Ishidate, M., (1986) Eisei Shikenjo Hokoku, vol. 104, pp. 92-96.

<1>StrI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Streptomyces thermodiastaticus
<6>V. Nagaraja
<7>U
<8>Chandrashekaran, S., Shankar, A.B., Babu, P., Paul, B.D., Nagaraja, V., (1999) Curr. Sci., vol. 77, pp. 273-276.

<1>StsI
<2>FokI,BseGI,BstF5I,BtsCI,HinGUII,Hpy178VI,HpyF6I,HpyF67III,PbuJKI
<3>GGATG(10/14)
<4>3(6),-2(6)
<5>Streptococcus sanguis 54
<6>K. Kita
<7>
<8>Kita, K., Kotani, H., Ohta, H., Yanase, H., Kato, N., (1992) Nucleic Acids Res., vol. 20, pp. 618.
Kita, K., Suisha, M., Kotani, H., Yanase, H., Kato, N., (1992) Nucleic Acids Res., vol. 20, pp. 4167-4172.
Steenstrup, T.D., Norby, P.L., International Patent Office, 2007.

<1>StuI
<2>AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGG^CCT
<4>
<5>Streptomyces tubercidicus
<6>H. Takahashi
<7>BJKMNQRSUX
<8>Casjens, S., Hayden, M., Jackson, E., Deans, R., (1983) J. Virol., vol. 45, pp. 864-867.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Shimotsu, H., Takahashi, H., Saito, H., (1980) Gene, vol. 11, pp. 219-225.
Zhu, Z., Unpublished observations.
Zhu, Z., Samuelson, J., Xiao, J.-P., Xu, S.-Y., Unpublished observations.

<1>StyI
<2>BsmSI,BssT1I,Bst224I,CfrBI,Eco130I,Eco208II,EcoT14I,EcoT104I,ErhI,ErhB9II,SblAI,SblBI,SblCI,Uba1311I
<3>C^CWWGG
<4>
<5>Salmonella typhi 27
<6>E.S. Anderson
<7>CJMNR
<8>Benner, J.S., Unpublished observations.
Mise, K., Nakajima, K., (1985) Gene, vol. 33, pp. 357-361.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>StyD4I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,Uba17I,Uba1391I
<3>^CCNGG
<4>?(5)
<5>Salmonella typhi D4
<6>E.S. Anderson
<7>N
<8>Miyahara, M., Ishiwata, N., Yoshida, Y., (1997) Biol. Pharm. Bull., vol. 20, pp. 201-203.
Miyahara, M., Mise, K., (1993) Gene, vol. 129, pp. 83-86.

<1>M.StyDam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Salmonella typhimurium
<6>M.C. Cerquetti
<7>
<8>Brawer, R., Batista, F.D., Burrone, O.R., Sordelli, D.O., Cerquetti, M.C., (1998) Arch. Microbiol., vol. 169, pp. 530-533.
Cerquetti, M.C., Brawer, R., Gherardi, M.M., Sordelli, D.O., (1996) Abstr. Gen. Meet. Am. Soc. Microbiol., vol. 96, pp. 491.

<1>M.Sty14028Dam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Salmonella typhimurium 14028
<6>M.J. Mahan
<7>
<8>Heithoff, D.M., Sinsheimer, R.L., Low, D.A., Mahan, M.J., (1999) Science, vol. 284, pp. 967-970.

<1>StyLTI
<2>
<3>CAGAG
<4>4(6)
<5>Salmonella typhimurium LT
<6>C. Colson
<7>
<8>De Backer, O., Colson, C., (1989) J. Cell Biochem. Suppl., vol. 13D, pp. 212.
De Backer, O., Colson, C., (1991) Gene, vol. 97, pp. 103-107.

<1>StyLTII
<2>
<3>?
<4>
<5>Salmonella typhimurium LT
<6>C. Colson
<7>
<8>Colson, C., Colson, A.M., (1971) J. Gen. Microbiol., vol. 69, pp. 345-351.

<1>StyLTIII
<2>
<3>GAGNNNNNNRTAYG
<4>2(6),-4(6)
<5>Salmonella typhimurium LT
<6>C. Colson
<7>
<8>Nagaraja, V., Shepherd, J.C.W., Bickle, T.A., (1985) Nature, vol. 316, pp. 371-372.
Nagaraja, V., Shepherd, J.C.W., Pripfl, T., Bickle, T.A., (1985) J. Mol. Biol., vol. 182, pp. 579-587.

<1>M.StyLT2Dam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Salmonella typhimurium LT2
<6>ATCC 700720
<7>
<8>McClelland, M. et al., (2001) Nature, vol. 413, pp. 852-856.
Pucciarelli, M.G., Prieto, A.I., Casadesus, J., Garcia-Del Portillo, F., (2002) Microbiology, vol. 148, pp. 1171-1182.

<1>StySBLI
<2>StySENI
<3>CGANNNNNNTACC
<4>
<5>Salmonella enterica serovar blegdam
<6>L.R. Bullas
<7>
<8>Campbell, A.J.B., Murray, N.E., Unpublished observations.
Titheradge, A.J., King, J., Ryu, J., Murray, N.E., (2001) Nucleic Acids Res., vol. 29, pp. 4195-4205.
Titheradge, A.J.B., Ternent, D., Murray, N.E., (1996) Mol. Microbiol., vol. 22, pp. 437-447.

<1>StySEAI
<2>
<3>ACANNNNNNTYCA
<4>3(6),-4(6)
<5>Salmonella eastbourne
<6>L.R. Bullas
<7>
<8>Kasarjian, J.K.A., Hidaka, M., Horiuchi, T., Iida, M., Ryu, J., (2004) Nucleic Acids Res., vol. 32.

<1>StySENI
<2>StySBLI
<3>CGANNNNNNTACC
<4>3(6),-4(6)
<5>Salmonella enteritidis
<6>L.R. Bullas
<7>
<8>Kasarjian, J.K.A., Hidaka, M., Horiuchi, T., Iida, M., Ryu, J., (2004) Nucleic Acids Res., vol. 32.

<1>StySGI
<2>
<3>TAANNNNNNRTCG
<4>3(6),-3(6)
<5>Salmonella gelsenkirchen
<6>L.R. Bullas
<7>
<8>Kasarjian, J.K.A., Hidaka, M., Horiuchi, T., Iida, M., Ryu, J., (2004) Nucleic Acids Res., vol. 32.

<1>StySJI
<2>
<3>GAGNNNNNNGTRC
<4>
<5>Salmonella hybrid
<6>N.E. Murray
<7>
<8>Gann, A.A.F., Campbell, A.J.B., Collins, J.F., Coulson, A.F.W., Murray, N.E., (1987) Mol. Microbiol., vol. 1, pp. 13-22.

<1>StySKI
<2>
<3>CGATNNNNNNNGTTA
<4>
<5>Salmonella kaduna CDC-388
<6>L.R. Bullas
<7>
<8>Thorpe, P.H., Ternent, D., Murray, N.E., (1997) Nucleic Acids Res., vol. 25, pp. 1694-1700.

<1>StySPI
<2>
<3>AACNNNNNNGTRC
<4>2(6),-3(6)
<5>Salmonella enterica subsp. enterica serovar Potsdam
<6>L.R. Bullas
<7>
<8>Nagaraja, V., Shepherd, J.C.W., Pripfl, T., Bickle, T.A., (1985) J. Mol. Biol., vol. 182, pp. 579-587.

<1>StySQI
<2>
<3>AACNNNNNNRTAYG
<4>
<5>Salmonella hybrid
<6>L.R. Bullas
<7>
<8>Bullas, L.R., Colson, C., van Pel, A., (1976) J. Gen. Microbiol., vol. 95, pp. 166-172.
Nagaraja, V., Shepherd, J.C.W., Bickle, T.A., (1985) Nature, vol. 316, pp. 371-372.

<1>StySTI
<2>
<3>?
<4>
<5>Salmonella thompson UA-T11
<6>L.R. Bullas
<7>
<8>Campbell, A.J.B., Murray, N.E., Unpublished observations.

<1>SuaI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GG^CC
<4>3(4)
<5>Sulfolobus acidocaldarius
<6>DSM 639
<7>
<8>Chen, L., Brugger, K., Skovgaard, M., Redder, P., She, Q., Torarinsson, E., Greve, B., Awayez, M., Zibat, A., Klenk, H.-P., Garrett, R.A., (2005) J. Bacteriol., vol. 187, pp. 4992-4999.
Grogan, D.W., (2003) J. Bacteriol., vol. 185, pp. 4657-4661.
Prangishvili, D.A., Chinchaladze, D.Z., Chelidze, M.G., (1987) Biotekhnologiya, vol. 3, pp. 440-446.
Prangishvili, D.A., Vashakidze, R.P., Chelidze, M.G., Gabriadze, I.Yu., (1985) FEBS Lett., vol. 192, pp. 57-60.

<1>SuiI
<2>TseI,AceI,ApeKI,Taq52I,TneI,TseBI
<3>G^CWGC
<4>
<5>Sulfolobus islandicus REN2HI
<6>W. Zillig
<7>
<8>Sollner, S., Berkner, S., Lipps, G., (2006) Extremophiles, vol. 10, pp. 629-634.

<1>SulI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Sulfolobus acidocaldarius
<6>W. Zillig
<7>
<8>McWilliam, P., Unpublished observations.

<1>SunI
<2>SplI,BpuB5I,BsiWI,BsmWI,BvuBI,MaeK81I,Pfl23II,PfuNI,PpuAI,PspLI,SmaAI,SplAI,SspKI
<3>C^GTACG
<4>
<5>Synechococcus uniformis
<6>M.M. Wijdenbosch
<7>
<8>Wijdenbosch, M.M., Unpublished observations.

<1>SurI
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>G^GATCC
<4>
<5>Sporosarcina ureae 2
<6>S.K. Degtyarev
<7>
<8>Repin, V.E., Shilyayeva, O.H., (1989) Microbiological investigations in Western Siberia, ed. Klevenskaya, I.L. (Nauka Siberian Division, Novosibirsk), vol. 0, pp. 14-17.

<1>Sve194I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Streptomyces verticillius 194
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>SviI
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,Uba1385I,Uba1452I
<3>TT^CGAA
<4>
<5>Streptomyces violochromogenes
<6>M. Bae
<7>
<8>Bae, M., Yun, M.-S., Kim, H.-T., Lee, K.-J., (1993) Korean J. Appl. Microbiol. Biotechnol., vol. 21, pp. 299-305.
Yun, M.-S., Bae, M., (1993) Proc. Mol. Biol. and Genet., vol. 8, pp. 73-74.

<1>SvoI
<2>SgrAI,PsuNI
<3>CRCCGGYG
<4>
<5>Streptomyces violaceoruber RFL10
<6>Fermentas G353
<7>
<8>Vitkute, J., Valiulyte, D., Norgeliene, D., Trinkunaite, L., Janulaitis, A., Unpublished observations.

<1>SwaI
<2>BstRZ246I,BstSWI,MspSWI,SmiI
<3>ATTT^AAAT
<4>?(6)
<5>Staphylococcus warneri
<6>B. Frey
<7>JMNSW
<8>Higgins, L.S., Kong, H., Unpublished observations.
Lechner, M., Frey, B., Laue, F., Ankenbauer, W., Schmitz, G., (1992) Fresenius Z. Anal. Chem., vol. 343, pp. 121-122.

<1>SynI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Synechocystis species
<6>PCC 6308
<7>
<8>Foerg, E., Saporito, L., Huang, S., Yang, J., Allen, M.M., (1990) FEMS Microbiol. Lett., vol. 69, pp. 105-108.

<1>SynII
<2>XmnI,Asp700I,BbvAI,MroXI,PdmI,Psc2I
<3>GAANNNNTTC
<4>
<5>Synechocystis species
<6>PCC 6308
<7>
<8>Foerg, E., Saporito, L., Huang, S., Yang, J., Allen, M.M., (1990) FEMS Microbiol. Lett., vol. 69, pp. 105-108.

<1>TaaI
<2>Tsp4CI,Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I
<3>ACN^GT
<4>
<5>Thermus aquaticus Vn 4-311
<6>V. Butkus
<7>F
<8>Vitkute, J., Vaitkevicius, D., Maneliene, Z., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>M.TaeI
<2>
<3>?
<4>?(5)
<5>Triticum aestivum
<6>B.F. Vanyushin
<7>
<8>Vlasova, T.I., Kirnos, M.D., Vanyushin, B.F., (1996) Biokhimiia, vol. 61, pp. 774-780.

<1>M.TaeII
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>3(6)
<5>Triticum aestivum
<6>B.F. Vanyushin
<7>
<8>Fedoreyeva, L.I., Vanyushin, B.F., (2002) FEBS Lett., vol. 514, pp. 305-308.

<1>M.TaeCDnmtI
<2>
<3>?
<4>?(5)
<5>Triticum aestivum Chinese Spring
<6>O.D. Anderson
<7>
<8>Anderson, O.D., Chao, S., Choi, D.W., Close, T.J., Fenton, R.D., Han, P.S., Hsia, C.C., Kang, Y., Lazo, G.R., Miller, R., Nguyen, H.T., Rausch, C.J., Seaton, C.L., Tong, J.C., Zhang, D., Unpublished observations.
Anderson, O.D., Chao, S., Crossman, C., Langridge, P., Lazo, G.R., Pham, J., Rausch, C.J., Sutton, T., Woo, J., Wilson, C., Unpublished observations.

<1>TaiI
<2>MaeII,HpyCH4IV,HpyF13III,HpyF35II,HpyF74II,TscI,Tsp49I,TspIDSI,TspWAM8AI,TtmI
<3>ACGT^
<4>
<5>Thermus aquaticus cs1-331
<6>V. Butkus
<7>F
<8>Vitkute, J., Jurgelyte, R., Maneliene, Z., Kairaitiene, R., Trinkunaite, L., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>TaqI
<2>CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>T^CGA
<4>4(6)
<5>Thermus aquaticus YTI
<6>J.I. Harris
<7>BCFIJKMNOQRSUVWXY
<8>Anton, B.P., Brooks, J.E., Unpublished observations.
Fomenkov, A., Xiao, J.-P., Dila, D., Raleigh, E., Xu, S.-Y., (1994) Nucleic Acids Res., vol. 22, pp. 2399-2403.
McClelland, M., (1981) Nucleic Acids Res., vol. 9, pp. 6795-6804.
Sato, S., Hutchison, C.A. III, Harris, J.I., (1977) Proc. Natl. Acad. Sci. U. S. A., vol. 74, pp. 542-546.
Zebala, J.A., (1993) Diss. Abstr., vol. 54, pp. 1394-1398.

<1>TaqII
<2>
<3>GACCGA(11/9),CACCCA(11/9)
<4>
<5>Thermus aquaticus YTI
<6>J.I. Harris
<7>QX
<8>Barker, D., Hoff, M., Oliphant, A., White, R., (1984) Nucleic Acids Res., vol. 12, pp. 5567-5581.
Myers, P.A., Roberts, R.J., Unpublished observations.
Rutkowska, S.M., Jaworowska, I., Skowron, P.M., Unpublished observations.

<1>Taq20I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus aquaticus YSS20
<6>R.A.D. Williams
<7>
<8>Welch, S.G., Al-Awadhi, S., Williams, R.A.D., (1998) Microbiology, vol. 144, pp. 167-175.

<1>Taq52I
<2>TseI,AceI,ApeKI,SuiI,TneI,TseBI
<3>G^CWGC
<4>
<5>Thermus aquaticus YS52
<6>R.A.D. Williams
<7>
<8>Welch, S.G., Williams, R.A.D., (1995) Nucleic Acids Res., vol. 23, pp. 4573-4575.

<1>TaqXI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CC^WGG
<4>
<5>Thermus aquaticus
<6>S.A. Grachev
<7>
<8>Grachev, S.A., Mamaev, S.V., Gurevich, A.I., Igoshin, A.V., Kolosov, M.N., Slyusarenko, A.G., (1981) Bioorg. Khim., vol. 7, pp. 628-630.

<1>TasI
<2>TspEI,MluCI,Sse9I,TseCI,Tsp509I
<3>^AATT
<4>
<5>Thermus aquaticus Vn 4-211
<6>V. Butkus
<7>F
<8>Vitkute, J., Zutautiene, D., Maneliene, Z., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>TatI
<2>
<3>W^GTACW
<4>
<5>Thermus aquaticus CBA1-331
<6>V. Butkus
<7>F
<8>Vitkute, J., Maneliene, Z., Janulaitis, A., (2001) FEMS Microbiol. Lett., vol. 204, pp. 253-257.

<1>TauI
<2>BspUI,CglI,NgoFVII
<3>GCSG^C
<4>
<5>Thermus aquaticus Ma2 3-1
<6>A. Janulaitis
<7>F
<8>Vitkute, J., Maneliene, Z., Janulaitis, A., (2001) FEMS Microbiol. Lett., vol. 204, pp. 253-257.

<1>TauII
<2>XmaIII,AaaI,BseX3I,BsoDI,BstZI,EagI,EclXI,Eco52I,SenPT16I,Tsp504I
<3>CGGCCG
<4>
<5>Thermus aquaticus Ma2 3-1
<6>A. Janulaitis
<7>
<8>Vitkute, J., Maneliene, Z., Janulaitis, A., (2001) FEMS Microbiol. Lett., vol. 204, pp. 253-257.

<1>Tbr51I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus brockianus JK51
<6>R.A.D. Williams
<7>
<8>Welch, S.G., Al-Awadhi, S., Williams, R.A.D., (1998) Microbiology, vol. 144, pp. 167-175.

<1>TceI
<2>MboII,HpyII,Hpy178II,HpyAII,NcuI
<3>GAAGA
<4>
<5>Thermococcus celer
<6>W. Zillig
<7>
<8>McWilliam, P., Unpublished observations.

<1>TdeI
<2>DpnI,CfuI,FtnUIV,MalI,Mph1103II,NanII,NgoDXIV,NmeAII,NmeBL859I,NmuDI,NmuEI,NsuDI
<3>GATC
<4>
<5>Treponema denticola
<6>ATCC 35405
<7>
<8>Weinstock, G. et al., Unpublished observations.
Xu, Y., Kong, H., Unpublished observations.

<1>TdeII
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC
<4>
<5>Treponema denticola
<6>ATCC 35405
<7>
<8>Vincent, M., Xu, Y., Kong, H., Japanese Patent Office, 2006.
Weinstock, G. et al., Unpublished observations.
Xu, Y., Kong, H., Unpublished observations.

<1>TdeIII
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>?(4)
<5>Treponema denticola
<6>ATCC 35405
<7>
<8>Weinstock, G. et al., Unpublished observations.
Xu, Y., Kong, H., Unpublished observations.

<1>TelI
<2>Tth111I,AspI,AtsI,BgiI,FsuI,NtaI,PflFI,PsyI,SmaAII,SpaPI,SplII,SplAII,TrsKTII,TspI,TteI,TtrI
<3>GACN^NNGTC
<4>
<5>Tolypothrix elabens
<6>M.M. Wijdenbosch
<7>
<8>Bax, E., Unpublished observations.

<1>TfeI
<2>
<3>?
<4>
<5>Thiobacillus ferrooxidans AP19-3
<6>K. Inagaki
<7>
<8>Inagaki, K., Morimoto, Y., Sugio, T., Tano, T., Unpublished observations.

<1>TfiI
<2>PfeI
<3>G^AWTC
<4>2(6)
<5>Thermus filiformis
<6>NEB 570
<7>N
<8>Cowan, D., Ward, J., Pelletier, J.J., Morgan, R., Unpublished observations.
Hiesh, P.-C., Allen, R., Xu, S.-Y., Unpublished observations.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>TfiA3I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus filiformis Ork2A3
<6>R.A.D. Williams
<7>
<8>Welch, S.G., Al-Awadhi, S., Williams, R.A.D., (1998) Microbiology, vol. 144, pp. 167-175.

<1>TfiTok4A2I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus filiformis Tok4A2
<6>F. Barany
<7>
<8>Cao, W., Lu, J., Barany, F., (1997) Gene, vol. 197, pp. 205-214.

<1>TfiTok6A1I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus filiformis Tok 6A1
<6>F. Barany
<7>
<8>Cao, W., Lu, J., Barany, F., (1997) Gene, vol. 197, pp. 205-214.

<1>TflI
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus flavus AT62
<6>T. Oshima
<7>
<8>Sato, S., Nakazawa, K., Shinomiya, T., (1980) J. Biochem. (Tokyo), vol. 88, pp. 737-747.

<1>TglI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Thermopolyspora glauca
<6>ATCC 15345
<7>
<8>Gingeras, T.R., Roberts, R.J., Unpublished observations.

<1>ThaI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,TmaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CG^CG
<4>?(4)
<5>Thermoplasma acidophilum
<6>ATCC 25905
<7>
<8>Beletskaya, I.V., Zakharova, M.V., Shlyapnikov, M.G., Semenova, L.M., Solonin, A.S., (2000) Nucleic Acids Res., vol. 28, pp. 3817-3822.
McConnell, D.J., Searcy, D.G., Sutcliffe, J.G., (1978) Nucleic Acids Res., vol. 5, pp. 1729-1739.
Prangishvili, D.A., Chinchaladze, D.Z., Chelidze, M.G., (1987) Biotekhnologiya, vol. 3, pp. 440-446.
Ruepp, A., Graml, W., Santos-Martinez, M.-L., Koretke, K.K., Volker, C., Mewes, H.W., Frishman, D., Stocker, S., Lupas, A.N., Baumeister, W., (2000) Nature, vol. 407, pp. 508-513.

<1>TliI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>
<5>Thermococcus litoralis
<6>NEB 521
<7>N
<8>Krotee, S., Ganatra, M., Unpublished observations.
Morgan, R.D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.

<1>TmaI
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,Uba1321I,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>?(4)
<5>Thermotoga maritima
<6>K.O. Stetter
<7>
<8>Nelson, K.E. et al., (1999) Nature, vol. 399, pp. 323-329.
Thomm, M., Unpublished observations.

<1>TmiI
<2>
<3>?
<4>
<5>Tatlockia micdadei
<6>A. Brown
<7>
<8>Chen, G.C.C., Brown, A., Lema, M.W., (1986) Can. J. Microbiol., vol. 32, pp. 591-593.

<1>Tmu1I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Tuberoidobacter mutans RFL1
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Kazlauskiene, R., Petrusyte, M., Unpublished observations.

<1>TneI
<2>TseI,AceI,ApeKI,SuiI,Taq52I,TseBI
<3>GCWGC
<4>?(5)
<5>Thermoproteus neutrophilus V24Sta
<6>T. Lowe
<7>
<8>Copeland, A. et al., Unpublished observations.

<1>TnoI
<2>
<3>?
<4>
<5>Thiobacillus novellus
<6>IFO 12443
<7>
<8>Inagaki, K., Morimoto, Y., Sugio, T., Tano, T., Unpublished observations.

<1>M.TpaI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Treponema pallidum
<6>L.V. Stamm
<7>
<8>Stamm, L.V., Greene, S.R., Barnes, N.Y., Bergen, H.L., Hardham, J.M., (1997) FEMS Microbiol. Lett., vol. 155, pp. 115-119.

<1>TrsKTI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Treponema species kT
<6>P. Pristas
<7>
<8>Piknova, M., Pristas, P., Javorsky, P., (2004) Folia Microbiol. (Praha), vol. 49, pp. 191-193.
Piknova, M., Pristas, P., Javorsky, P., Kasperowic, A., Michalowski, T., (2004) Lett. Appl. Microbiol., vol. 38, pp. 311-314.

<1>TrsKTII
<2>Tth111I,AspI,AtsI,BgiI,FsuI,NtaI,PflFI,PsyI,SmaAII,SpaPI,SplII,SplAII,TelI,TspI,TteI,TtrI
<3>GACNNNGTC
<4>
<5>Treponema species kT
<6>P. Pristas
<7>
<8>Piknova, M., Javorsky, P., Pristas, P., (2005) FEMS Microbiol. Lett., vol. 251, pp. 99.

<1>TrsKTIII
<2>NdeI,FauNDI,PfaAII
<3>CATATG
<4>
<5>Treponema species kT
<6>P. Pristas
<7>
<8>Piknova, M., Javorsky, P., Pristas, P., (2005) FEMS Microbiol. Lett., vol. 251, pp. 99.

<1>TrsSI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Treponema species S
<6>P. Pristas
<7>
<8>Piknova, M., Pristas, P., Javorsky, P., (2004) Folia Microbiol. (Praha), vol. 49, pp. 191-193.
Piknova, M., Pristas, P., Javorsky, P., Kasperowic, A., Michalowski, T., (2004) Lett. Appl. Microbiol., vol. 38, pp. 311-314.

<1>TrsSII
<2>DrdI,AasI,DseDI
<3>GACNNNNNNGTC
<4>
<5>Treponema species S
<6>P. Pristas
<7>
<8>Piknova, M., Javorsky, P., Pristas, P., (2005) FEMS Microbiol. Lett., vol. 251, pp. 99.

<1>TrsTI
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Treponema species T
<6>P. Pristas
<7>
<8>Piknova, M., Pristas, P., Javorsky, P., (2004) Folia Microbiol. (Praha), vol. 49, pp. 191-193.
Piknova, M., Pristas, P., Javorsky, P., Kasperowic, A., Michalowski, T., (2004) Lett. Appl. Microbiol., vol. 38, pp. 311-314.

<1>TrsTII
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>CTTAAG
<4>
<5>Treponema species T
<6>P. Pristas
<7>
<8>Piknova, M., Javorsky, P., Pristas, P., (2005) FEMS Microbiol. Lett., vol. 251, pp. 99.

<1>TruI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Thermus ruber strain 21
<6>BKM B-1258
<7>
<8>Bernal, W.M., Raven, N.D.H., Williams, R.A.D., (1986) Proceedings 14th Int. Congress Microbiol., vol. 0, pp. 204.

<1>TruII
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Thermus ruber strain 21
<6>BKM B-1258
<7>
<8>Bernal, W.M., Raven, N.D.H., Williams, R.A.D., (1986) Proceedings 14th Int. Congress Microbiol., vol. 0, pp. 204.

<1>Tru1I
<2>MseI,SaqAI,Tru9I
<3>T^TAA
<4>
<5>Thermus ruber RFL1
<6>A. Janulaitis
<7>F
<8>Janulaitis, A., Krikstulyte, V., Trinkunaite, L., Maneliene, Z., Kiuduliene, L., Petrusyte, M., Butkus, V., Unpublished observations.

<1>Tru9I
<2>MseI,SaqAI,Tru1I
<3>T^TAA
<4>
<5>Thermus ruber 9
<6>S.K. Degtyarev
<7>IMRVW
<8>Prichodko, E.A., Rechnukova, N.I., Degtyarev, S.K., (1991) Sib. Biol. J., vol. 1, pp. 57-59.

<1>Tru28I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Thermus ruber
<6>ITI 28
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Tru201I
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,MflI,PsuI,Uba1432I
<3>R^GATCY
<4>
<5>Thermus ruber 201
<6>S.K. Degtyarev
<7>
<8>Degtyarev, S.K., Unpublished observations.
Tsaplina, I.A., Bogdanova, T.I., Rechkunova, N.I., Degtyarev, S.K., Soviet Patent Office, 1992.

<1>TscI
<2>MaeII,HpyCH4IV,HpyF13III,HpyF35II,HpyF74II,TaiI,Tsp49I,TspIDSI,TspWAM8AI,TtmI
<3>ACGT^
<4>
<5>Thermus species 491A
<6>R.A.D. Williams
<7>
<8>Welch, S.G., Williams, R.A.D., Unpublished observations.

<1>TscAI
<2>TspRI
<3>CASTGNN^
<4>
<5>Thermus scotoductus RFL5
<6>Fermentas G321
<7>F
<8>Lauciuniene, N., Capskaja, L., Kiuduliene, L., Zakareviciene, L., Vitkute, J., Janulaitis, A., Unpublished observations.

<1>TscHI
<2>
<3>?
<4>
<5>Thermus scotoductus
<6>P. Sharma
<7>
<8>Sharma, P., Unpublished observations.

<1>Tsc4aI
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus scotoductus Vi4a
<6>R.A.D. Williams
<7>
<8>Welch, S.G., Al-Awadhi, S., Williams, R.A.D., (1998) Microbiology, vol. 144, pp. 167-175.

<1>TseI
<2>AceI,ApeKI,SuiI,Taq52I,TneI,TseBI
<3>G^CWGC
<4>?(5)
<5>Thermus species 93170
<6>D. Clark
<7>N
<8>Morgan, R.D., Unpublished observations.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Tassoni, L., Clark, D.R., Unpublished observations.
Xu, S.-Y., Unpublished observations.

<1>TseAI
<2>SduI,AocII,Bka1125I,BmyI,BsoCI,Bsp1286I,BspLS2I,BstZ15I,HpyF36IV,HpyF47I,MhlI,Mlu40I,NspII,Uba1362I
<3>GDGCHC
<4>
<5>Thermus species 93159
<6>D. Clark
<7>
<8>Tassoni, L., Clark, D.R., Unpublished observations.

<1>TseBI
<2>TseI,AceI,ApeKI,SuiI,Taq52I,TneI
<3>GCWGC
<4>
<5>Thermus species Azores9539P
<6>D. Clark
<7>
<8>Jones, S., Hill, V.J., Vincent, S., Clark, D.R., Unpublished observations.

<1>TseCI
<2>TspEI,MluCI,Sse9I,TasI,Tsp509I
<3>AATT
<4>
<5>Thermus species Azores9563A
<6>D. Clark
<7>
<8>Clark, D., Unpublished observations.

<1>TseDI
<2>Cfr10I,Bco118I,BscRI,Bse118I,Bse634I,Bsp21I,BsrFI,BssAI,BstB7SI,NmeDI
<3>RCCGGY
<4>
<5>Thermus species Azores 9561E
<6>D. Clark
<7>
<8>Reid, S., Clark, D.R., Vincent, S., Hill, V., Unpublished observations.

<1>TsoI
<2>
<3>TARCCA(11/9)
<4>
<5>Thermus scotoductus
<6>Fermentas G272
<7>F
<8>Maneliene, Z., Zakareviciene, L., Lubys, A., Unpublished observations.
Vitkute, J., Capskaja, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>TspI
<2>Tth111I,AspI,AtsI,BgiI,FsuI,NtaI,PflFI,PsyI,SmaAII,SpaPI,SplII,SplAII,TelI,TrsKTII,TteI,TtrI
<3>GACNNNGTC
<4>
<5>Thermus species
<6>ATCC 31674
<7>
<8>Chen, Z., Unpublished observations.

<1>Tsp1I
<2>BsrI,BscHI,Bse1I,BseNI,BsoHI,BsrSI,Bst11I
<3>ACTGG(1/-1)
<4>
<5>Thermus species strain 1
<6>V.E. Repin
<7>
<8>Karginov, V.A., Kovalenko, S.P., Kolesnikov, V.A., Chikaev, N.A., Serov, G.D., Repin, V.E., Unpublished observations.

<1>Tsp32I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>T^CGA
<4>
<5>Thermus strain 32
<6>R.A.D. Williams
<7>
<8>Cao, W., Lu, J., Barany, F., (1997) Gene, vol. 197, pp. 205-214.
Welch, S.G., Williams, R.A.D., (1995) Biochem. J., vol. 312, pp. 505-510.

<1>Tsp32II
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>T^CGA
<4>
<5>Thermus strain 32
<6>R.A.D. Williams
<7>
<8>Welch, S.G., Williams, R.A.D., (1995) Biochem. J., vol. 312, pp. 505-510.

<1>Tsp45I
<2>Hpy8II,Hpy51I,Hpy99II,HpyF1I,HpyF4I,HpyF6II,HpyF9I,HpyF13I,HpyF25II,HpyF31II,HpyF34II,HpyF35IV,HpyF36I,HpyF40III,HpyF48I,HpyF49II,HpyF51I,HpyF62III,NmuCI
<3>^GTSAC
<4>4(6)
<5>Thermus species strain YS45
<6>R.J. Sharp
<7>N
<8>Raven, N.D.H., Williams, R.A.D., Smith, K.E., Kelly, C.D., Carter, N.D., (1993) Nucleic Acids Res., vol. 21, pp. 4397.
Stickel, S.K., Roberts, R.J., Unpublished observations.
Wayne, J., Holden, M., Xu, S.-Y., (1997) Gene, vol. 202, pp. 83-88.

<1>Tsp49I
<2>MaeII,HpyCH4IV,HpyF13III,HpyF35II,HpyF74II,TaiI,TscI,TspIDSI,TspWAM8AI,TtmI
<3>ACGT^
<4>
<5>Thermus species
<6>R.A.D. Williams
<7>
<8>Welch, S.G., Williams, R.A.D., (1996) Nucleic Acids Res., vol. 24, pp. 1799-1801.

<1>Tsp132I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Thermus species
<6>ITI 132
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Tsp133I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Thermus species
<6>ITI 133
<7>
<8>Hjorleifsdottir, S., Unpublished observations.

<1>Tsp219I
<2>BglI,Bpu86I,BseB631I,BsoJI,Psp1009I,Tsp8EI,VanI
<3>GCCNNNNNGGC
<4>
<5>Thermus species
<6>ITI 219
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Tsp266I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Thermus species
<6>ITI 266
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Tsp273I
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Uba1400I,UbaN4I
<3>GATATC
<4>
<5>Thermus species
<6>ITI 273
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Tsp273II
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Thermus species
<6>ITI 273
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Tsp281I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Thermus species
<6>ITI 281
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Tsp301I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Thermus species
<6>ITI 301
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Tsp358I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus species
<6>ITI 358
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Tsp504I
<2>XmaIII,AaaI,BseX3I,BsoDI,BstZI,EagI,EclXI,Eco52I,SenPT16I,TauII
<3>CGGCCG
<4>
<5>Thermus species
<6>ITI 340
<7>
<8>Korpela, J., Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Tsp505I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus species
<6>ITI 53
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Tsp507I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp514I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Thermus species
<6>ITI 203
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Tsp509I
<2>TspEI,MluCI,Sse9I,TasI,TseCI
<3>^AATT
<4>?(6)
<5>Thermus species
<6>ITI 346
<7>N
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Tenkanen, T., Unpublished observations.
Torsti, A.-M., Korpela, J., Hjorleifsdottir, S., Tenkanen, T., Pitkanen, K., Mattila, P., Kristjansson, J., Unpublished observations.

<1>Tsp510I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus species
<6>ITI 70
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Tsp514I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Uba1136I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Thermus species
<6>ITI 355
<7>
<8>Korpela, J., Hjorleifsdottir, S., Unpublished observations.

<1>Tsp560I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Thermus species
<6>ITI 51
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>TspAI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Thermophilic species
<6>Z. Chen
<7>
<8>Chen, Z., Yang, R., Chen, B., Li, R., (1989) J. Fudan Univ. (Natural Sci.), vol. 28, pp. 96-101.

<1>TspAK13D21I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus species AK13D21
<6>F. Barany
<7>
<8>Cao, W., Lu, J., Barany, F., (1997) Gene, vol. 197, pp. 205-214.

<1>TspAK16D24I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus species AK16D24
<6>F. Barany
<7>
<8>Cao, W., Lu, J., Barany, F., (1997) Gene, vol. 197, pp. 205-214.

<1>TspBI
<2>DsaI,BstDSI,BtgI
<3>C^CRYGG
<4>
<5>Thermophilic species
<6>X.S. Pan
<7>
<8>Pan, X.S., Polisson, C., Morgan, R., Unpublished observations.

<1>Tsp4CI
<2>Bst4CI,HpyCH4III,HpyF5II,HpyF9III,HpyF12I,HpyF20I,HpyF22I,HpyF35III,HpyF40I,HpyF41I,HpyF42II,HpyF46I,HpyF48II,HpyF51II,HpyF54I,HpyF55I,HpyF56I,HpyF58I,HpyF62I,HpyF64II,HpyF65I,HpyF68I,HpyF69I,HpyF74I,TaaI
<3>ACN^GT
<4>
<5>Thermus species 4C
<6>R.A.D. Williams
<7>
<8>Welch, S.G., Williams, R.A.D., (1995) Biochem. J., vol. 309, pp. 595-599.

<1>TspDTI
<2>
<3>ATGAA(11/9)
<4>
<5>Thermus sp. DT
<6>P.M. Skowron
<7>X
<8>Skowron, P.M., Majewski, J., Zylicz-Stachula, A., Rutkowska, S.M., Jaworowska, I., Harasimowicz-Slowinska, R.I., (2003) Nucleic Acids Res., vol. 31.
Skowron, P.M., Zylicz-Stachula, A., Unpublished observations.

<1>TspEI
<2>MluCI,Sse9I,TasI,TseCI,Tsp509I
<3>^AATT
<4>
<5>Thermus species strain 1E
<6>R.A.D. Williams
<7>O
<8>Raven, N.D.H., Kelly, C.D., Carter, N.D., Eastlake, P., Brown, C., Williams, R.A.D., (1993) Gene, vol. 131, pp. 83-86.

<1>Tsp8EI
<2>BglI,Bpu86I,BseB631I,BsoJI,Psp1009I,Tsp219I,VanI
<3>GCCNNNN^NGGC
<4>
<5>Thermus species 8E
<6>R.A.D. Williams
<7>
<8>Welch, S.G., Williams, R.A.D., (1995) Biochem. J., vol. 309, pp. 595-599.

<1>TspGWI
<2>
<3>ACGGA(11/9)
<4>
<5>Thermus species GW
<6>EURx 202
<7>X
<8>Zylicz-Stachula, A., Harasimowicz-Slowinska, R.I., Sobolewski, I., Skowron, P.M., (2002) Nucleic Acids Res., vol. 30.

<1>TspGWII
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Thermus species GW
<6>EURx 202
<7>
<8>Zylicz-Stachula, A., Harasimowicz-Slowinska, R.I., Sobolewski, I., Skowron, P.M., (2002) Nucleic Acids Res., vol. 30.

<1>TspIDSI
<2>MaeII,HpyCH4IV,HpyF13III,HpyF35II,HpyF74II,TaiI,TscI,Tsp49I,TspWAM8AI,TtmI
<3>ACGT
<4>
<5>Thermus species
<6>R.A.D. Williams
<7>
<8>Welch, S.G., Williams, R.A.D., (1996) Nucleic Acids Res., vol. 24, pp. 1799-1801.

<1>TspMI
<2>SmaI,AhyI,Cfr9I,CfrJ4I,EaeAI,EclRI,KteAI,Pac25I,PaeBI,PspAI,PspALI,Uba1220I,Uba1393I,XcyI,XmaI,XmaCI
<3>C^CCGGG
<4>?(5)
<5>Unidentified thermophile
<6>P. Sharma
<7>N
<8>Morgan, R.D., Unpublished observations.
Parashar, V., Capalash, N., Xu, S.Y., Sako, Y., Sharma, P., (2006) Appl. Microbiol. Biotechnol., vol. 72, pp. 917-923.
Sharma, P., Parashar, V., Capalash, N., Unpublished observations.
Zheng, Y., Unpublished observations.
Zheng, Y., Roberts, R.J., (2007) Nucleic Acids Res., vol. 35.
Zheng, Y., Roberts, R.J., International Patent Office, 2008.

<1>TspNI
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus species
<6>ATCC 31674
<7>
<8>Polisson, C., Unpublished observations.

<1>TspRI
<2>TscAI
<3>CASTGNN^
<4>1(5)
<5>Thermus species strain R
<6>N.D.H. Raven
<7>N
<8>Benner, J., Dalton, M.A., Xu, S., Dore, A., Japanese Patent Office, 2005.
Raven, N.D.H., Kelly, C.D., Carter, N.D., Smith, K.E., Williams, R.A.D., Unpublished observations.
Xu, S.-Y., Unpublished observations.
Xu, S.-Y., Dore, A., Dalton, M., Benner, J., US Patent Office, 2003.

<1>TspVi4AI
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus species Vi4A
<6>F. Barany
<7>
<8>Cao, W., Lu, J., Barany, F., (1997) Gene, vol. 197, pp. 205-214.

<1>TspVil3I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,Tth24I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus species Vil3
<6>F. Barany
<7>
<8>Cao, W., Lu, J., Barany, F., (1997) Gene, vol. 197, pp. 205-214.

<1>TspWAM8AI
<2>MaeII,HpyCH4IV,HpyF13III,HpyF35II,HpyF74II,TaiI,TscI,Tsp49I,TspIDSI,TtmI
<3>ACGT
<4>
<5>Thermus species
<6>R.A.D. Williams
<7>
<8>Welch, S.G., Williams, R.A.D., (1996) Nucleic Acids Res., vol. 24, pp. 1799-1801.

<1>TspZNI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Thermus species strain 2AZN
<6>N.D.H. Raven
<7>
<8>Ghufoor, K., Raven, N.D.H., Williams, R.A.D., Unpublished observations.

<1>TssI
<2>
<3>GAGNNNCTC
<4>
<5>Thermus scotoductus RFL3
<6>Fermentas G301
<7>
<8>Vitkute, J., Lauciuniene, N., Riauba, L., Lapcinskaja, S., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>TstI
<2>
<3>(8/13)CACNNNNNNTCC(12/7)
<4>
<5>Thermus scotoductus RFL1
<6>A. Janulaitis
<7>F
<8>Jurenaite-Urbanaviciene, S., Serksnaite, J., Kriukiene, E., Giedriene, J., Venclovas, C., Lubys, A., (2007) Proc. Natl. Acad. Sci. U. S. A., vol. 104, pp. 10358-10363.
Maneliene, Z., Unpublished observations.
Nekrasiene, D., Norgeliene, D., Capskaja, L., Kiuduliene, L., Vitkute, J., Janulaitis, A., Unpublished observations.

<1>TsuI
<2>
<3>GCGAC
<4>
<5>Thermus scotoductus RFL2
<6>A. Janulaitis
<7>
<8>Vitkute, J., Riauba, L., Norgeliene, D., Trinkunaite, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>TteI
<2>Tth111I,AspI,AtsI,BgiI,FsuI,NtaI,PflFI,PsyI,SmaAII,SpaPI,SplII,SplAII,TelI,TrsKTII,TspI,TtrI
<3>GACNNNGTC
<4>
<5>Thermus thermophilus strain 110
<6>T. Oshima
<7>
<8>Shinomiya, T., Sato, S., (1980) Nucleic Acids Res., vol. 8, pp. 43-56.

<1>TteAI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Tolypothrix tenuis
<6>ATCC 27914
<7>
<8>Siegelman, B., Unpublished observations.

<1>Tth24I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,TthHB8I,TthRQI
<3>TCGA
<4>
<5>Thermus thermophilus GK24
<6>R.A.D. Williams
<7>
<8>Welch, S.G., Al-Awadhi, S., Williams, R.A.D., (1998) Microbiology, vol. 144, pp. 167-175.

<1>Tth111I
<2>AspI,AtsI,BgiI,FsuI,NtaI,PflFI,PsyI,SmaAII,SpaPI,SplII,SplAII,TelI,TrsKTII,TspI,TteI,TtrI
<3>GACN^NNGTC
<4>2(6)
<5>Thermus thermophilus strain 111
<6>T. Oshima
<7>IKNQRVWX
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Shinomiya, T., Sato, S., (1980) Nucleic Acids Res., vol. 8, pp. 43-56.
Stickel, S.K., Roberts, R.J., Unpublished observations.
Xu, S.-Y., Unpublished observations.

<1>Tth111II
<2>TthHB27I
<3>CAARCA(11/9)
<4>
<5>Thermus thermophilus strain 111
<6>T. Oshima
<7>
<8>Shinomiya, T., Kobayashi, M., Sato, S., (1980) Nucleic Acids Res., vol. 8, pp. 3275-3285.
Zhu, Z., Xu, S.-Y., Unpublished observations.

<1>M.TthBI
<2>
<3>?
<4>?(6)
<5>Tetrahymena thermophila B-1868-VII
<6>S. Hattman
<7>
<8>Bromberg, S., Pratt, K., Hattman, S., (1982) J. Bacteriol., vol. 150, pp. 993-996.

<1>TthHB8I
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthRQI
<3>T^CGA
<4>4(6)
<5>Thermus thermophilus HB8
<6>T. Oshima
<7>
<8>Masui, R., Kurokawa, K., Nakagawa, N., Tokunaga, F., Koyama, Y., Shibata, T., Oshima, T., Yokoyama, S., Yasunaga, T., Kuramitsu, S., Unpublished observations.
McClelland, M., (1981) Nucleic Acids Res., vol. 9, pp. 6795-6804.
Sato, S., Nakazawa, K., Shinomiya, T., (1980) J. Biochem. (Tokyo), vol. 88, pp. 737-747.
Sato, S., Shinomiya, T., (1978) J. Biochem. (Tokyo), vol. 84, pp. 1319-1321.
Uchida, Y., Unpublished observations.

<1>TthHB27I
<2>Tth111II
<3>CAARCA
<4>
<5>Thermus thermophilus HB27
<6>T. Hoshino
<7>
<8>Henne, A. et al., Unpublished observations.
Nie, C., Xu, S.-Y., Unpublished observations.

<1>TthRQI
<2>TaqI,CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I
<3>TCGA
<4>
<5>Thermus thermophilus RQ1
<6>R.A.D. Williams
<7>
<8>Welch, S.G., Al-Awadhi, S., Williams, R.A.D., (1998) Microbiology, vol. 144, pp. 167-175.

<1>TtmI
<2>MaeII,HpyCH4IV,HpyF13III,HpyF35II,HpyF74II,TaiI,TscI,Tsp49I,TspIDSI,TspWAM8AI
<3>ACGT
<4>
<5>Thermus thermophilus Ce4-1
<6>A. Janulaitis
<7>
<8>Vitkute, J., Jurgelyte, R., Lazareviciute, L., Maneliene, Z., Capskaja, L., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>TtmII
<2>BsePI,BscEI,BsoPI,BsrHI,BssBI,BssHII,BstBZ153I,CfrJ5I,Eco143I,Eco152I,Esp7I,Esp8I,Kpn30I,McaTI,PauI,PteI,Uba69I
<3>GCGCGC
<4>
<5>Thermus thermophilus Ce4-1
<6>A. Janulaitis
<7>
<8>Vitkute, J., Jurgelyte, R., Lazareviciute, L., Maneliene, Z., Capskaja, L., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>TtnI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Tolypothrix tenuis
<6>W. Siegelman
<7>
<8>Streips, U., Golemboski, B., Unpublished observations.

<1>TtoI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Thiobacillus thiooxidans ON106
<6>K. Inagaki
<7>
<8>Inagaki, K., Morimoto, Y., Hiraoka, N., Sugio, T., Tano, T., Unpublished observations.

<1>TtrI
<2>Tth111I,AspI,AtsI,BgiI,FsuI,NtaI,PflFI,PsyI,SmaAII,SpaPI,SplII,SplAII,TelI,TrsKTII,TspI,TteI
<3>GACNNNGTC
<4>
<5>Thermus thermophilus strain 23
<6>T. Oshima
<7>
<8>Shinomiya, T., Sato, S., (1980) Nucleic Acids Res., vol. 8, pp. 43-56.

<1>TveI
<2>
<3>?
<4>
<5>Thiobacillus versutus
<6>IFO 14567
<7>
<8>Inagaki, K., Morimoto, Y., Sugio, T., Tano, T., Unpublished observations.

<1>Tvu2HI
<2>
<3>?
<4>
<5>Thermoactinomyces vulgaris strain 2H
<6>H. Mankai
<7>
<8>Mankai, H., Unpublished observations.

<1>Uba4I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Unidentified bacterium RFL4
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba6I
<2>MluI,ApeI,Bbi24I,BstZ9I
<3>ACGCGT
<4>
<5>Unidentified bacterium RFL6
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Uba9I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL9
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Uba11I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL11
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Uba13I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL13
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Uba17I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba1391I
<3>CCNGG
<4>
<5>Unidentified bacterium RFL17
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Uba19I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL19
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Uba20I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL20
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Uba22I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL22
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Uba24I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL24
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Gilvonauskaite, R., Petrusyte, M., Unpublished observations.

<1>Uba30I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL30
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Uba31I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL31
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Uba34I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL34
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Uba36I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba1188I,Uba1327I
<3>YGGCCR
<4>
<5>Unidentified bacterium RFL36
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Uba38I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL38
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Petrusyte, M., Unpublished observations.

<1>Uba39I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL39
<6>A. Janulaitis
<7>
<8>Steponaviciene, D., Petrusyte, M., Janulaitis, A., Unpublished observations.

<1>Uba40I
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGGCCT
<4>
<5>Unidentified bacterium RFL40
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Jagelavicius, M., Bitinaite, J., Unpublished observations.

<1>Uba41I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Unidentified bacterium RFL41
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Jagelavicius, M., Bitinaite, J., Unpublished observations.

<1>Uba42I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Unidentified bacterium RFL42
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Jagelavicius, M., Bitinaite, J., Unpublished observations.

<1>Uba43I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL43
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Jagelavicius, M., Bitinaite, J., Unpublished observations.

<1>Uba46I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL46
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba48I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Unidentified bacterium RFL48
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba51I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL51
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba54I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL54
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba57I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL57
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba58I
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco237I,Eco252I,FunII,HalI,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl32DII,Srl55DI,SsoI,Van91II,VchN100I,VchO2I
<3>GAATTC
<4>
<5>Unidentified bacterium RFL58
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba59I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Unidentified bacterium RFL59
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba61I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL61
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba62I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Unidentified bacterium RFL62
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba65I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Unidentified bacterium RFL65
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba66I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL66
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba69I
<2>BsePI,BscEI,BsoPI,BsrHI,BssBI,BssHII,BstBZ153I,CfrJ5I,Eco143I,Eco152I,Esp7I,Esp8I,Kpn30I,McaTI,PauI,PteI,TtmII
<3>GCGCGC
<4>
<5>Unidentified bacterium RFL69
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba71I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL71
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba72I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL72
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba76I
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba85I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Unidentified bacterium RFL76
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba77I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL77
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba81I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL81
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba82I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL82
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba83I
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba1164II,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Unidentified bacterium RFL83
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba84I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Unidentified bacterium RFL84
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba85I
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba86I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Unidentified bacterium RFL85
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba86I
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba87I,Uba1201I
<3>GGTACC
<4>
<5>Unidentified bacterium RFL86
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba87I
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba1201I
<3>GGTACC
<4>
<5>Unidentified bacterium RFL87
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba88I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL88
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba89I
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,XamI,XciI
<3>GTCGAC
<4>
<5>Unidentified bacterium RFL89
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba90I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL90
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1093I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL1093
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1094I
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1158I,VchO49I,ZrmI
<3>AGTACT
<4>
<5>Unidentified bacterium RFL1094
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1095I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL1095
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1096I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1096
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1097I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1097
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1098I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1098
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1099I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Unidentified bacterium RFL1099
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1100I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1100
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1101I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Unidentified bacterium RFL1101
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1111I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL1111
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1112I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1112
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1113I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL1113
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1114I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL1114
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1115I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1115
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1116I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1116
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1117I
<2>NruI,AmaSI,Bsp68I,BtuMI,Mlu9273I,MluB2I,PspDI,RruI,SalDI,Sbo13I,Sna3286I,SpoI,Uba1386I,VchO70I
<3>TCGCGA
<4>
<5>Unidentified bacterium RFL1117
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1118I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL1118
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1119I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1119
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1120I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL1120
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1121I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL1121
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1122I
<2>NaeI,Afa24RI,AmeII,AniMI,ApeAI,AprI,BheI,CcoI,Eco56I,Esp5I,MauAI,MisI,Mlu9273II,MroNI,NasWI,NbaI,NbrI,NgoAIV,NgoMIV,NmuI,NmuFI,NspWI,NtaSII,PdiI,PglI,Psp61I,RluI,RrhJ1I,SacAI,SalCI,SaoI,SauAI,SauBMKI,SauHPI,SauLPI,SauNI,SauSI,SceIII,SkaI,Slu1777I,Smo40529I,SrlI,Srl77DI,SspCI
<3>GCCGGC
<4>
<5>Unidentified bacterium RFL1122
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1123I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1123
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1124I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL1124
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1125I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL1125
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1126I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL1126
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1127I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Vsp2246I
<3>GGYRCC
<4>
<5>Unidentified bacterium RFL1127
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1128I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1141I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Unidentified bacterium RFL1128
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1129I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Unidentified bacterium RFL1129
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1130I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Unidentified bacterium RFL1130
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1131I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Unidentified bacterium RFL1131
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1133I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1133
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1134I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Unidentified bacterium RFL1134
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1136I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1279I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Unidentified bacterium RFL1136
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1137I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1137
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1138I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1138
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1139I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Unidentified bacterium RFL1139
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1140I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1140
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1141I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1267I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Unidentified bacterium RFL1141
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1142I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL1142
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1144I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1144
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1145I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1145
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1146I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1146
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1147I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1147
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1148I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Unidentified bacterium RFL1148
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1149I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1149
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1150I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1150
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1152I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1152
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1153I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1153
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1154I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Unidentified bacterium RFL1154
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1155I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1155
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1156I
<2>ApaI,Bsp120I,EciEI,PpeI,Psp30I,PspOMI,Uba1157I,Uba1165I,Uba1202I,Uba1241I,Uba1368I
<3>GGGCCC
<4>
<5>Unidentified bacterium RFL1156
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1157I
<2>ApaI,Bsp120I,EciEI,PpeI,Psp30I,PspOMI,Uba1156I,Uba1165I,Uba1202I,Uba1241I,Uba1368I
<3>GGGCCC
<4>
<5>Unidentified bacterium RFL1157
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1158I
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1094I,VchO49I,ZrmI
<3>AGTACT
<4>
<5>Unidentified bacterium RFL1158
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1159I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL1159
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1160I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Unidentified bacterium RFL1160
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1161I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1161
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1162I
<2>SphI,Asp5HI,BbuI,BscOI,Bsp121I,BtgAII,CglAI,PaeI,PaeCI,PfaAIII,RspLKI,SpaHI,SpaXI,Uba1226I,VchO68I
<3>GCATGC
<4>
<5>Unidentified bacterium RFL1162
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1163I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1163
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1164I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Unidentified bacterium RFL1164
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1164II
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1219I,Uba1435I
<3>AAGCTT
<4>
<5>Unidentified bacterium RFL1164
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1165I
<2>ApaI,Bsp120I,EciEI,PpeI,Psp30I,PspOMI,Uba1156I,Uba1157I,Uba1202I,Uba1241I,Uba1368I
<3>GGGCCC
<4>
<5>Unidentified bacterium RFL1165
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1166I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Unidentified bacterium RFL1166
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1167I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1167
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1168I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1168
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1169I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1169
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1170I
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGGCCT
<4>
<5>Unidentified bacterium RFL1170
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1171I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL1171
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1172I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1172
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1173I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1173
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1174I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1174
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1175I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1175
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1176I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1176
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1177I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Unidentified bacterium RFL1177
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1178I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1178
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1179I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1179
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1180I
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGGCCT
<4>
<5>Unidentified bacterium RFL1180
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1181I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL1181
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1182I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Unidentified bacterium RFL1182
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1183I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Unidentified bacterium RFL1183
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1184I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1184
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1184II
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1294I,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Unidentified bacterium RFL1184
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1185I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL1185
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1186I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1186
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1187I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL1187
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1188I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1327I
<3>YGGCCR
<4>
<5>Unidentified bacterium RFL1188
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1189I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL1189
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1190I
<2>Eam1105I,AhdI,AspEI,BmeRI,BspOVI,BstZ2I,DriI,EclHKI,NruGI,Uba1191I
<3>GACNNNNNGTC
<4>
<5>Unidentified bacterium RFL1190
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1191I
<2>Eam1105I,AhdI,AspEI,BmeRI,BspOVI,BstZ2I,DriI,EclHKI,NruGI,Uba1190I
<3>GACNNNNNGTC
<4>
<5>Unidentified bacterium RFL1191
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1192I
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC
<4>
<5>Unidentified bacterium RFL1192
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1193I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1218I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL1193
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1195I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1195
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1196I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1196
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1197I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1197
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1198I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1198
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1199I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1199
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1200I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1200
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1201I
<2>KpnI,Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I
<3>GGTACC
<4>
<5>Unidentified bacterium RFL1201
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1202I
<2>ApaI,Bsp120I,EciEI,PpeI,Psp30I,PspOMI,Uba1156I,Uba1157I,Uba1165I,Uba1241I,Uba1368I
<3>GGGCCC
<4>
<5>Unidentified bacterium RFL1202
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1203I
<2>ApaLI,AaqI,Alw44I,AmeI,Bsp146I,DaqI,Pfl23I,Pfr12I,PliI,ScoNI,SnoI,Uba1387I,VneI
<3>GTGCAC
<4>
<5>Unidentified bacterium RFL1203
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1204I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Unidentified bacterium RFL1204
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1205I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1205
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1205II
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1436I,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Unidentified bacterium RFL1205
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1206I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL1206
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1207I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1207
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1208I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1208
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1209I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1209
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1210I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1210
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1211I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1211
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1212I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1212
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1213I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1213
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1214I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1214
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1215I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1215
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1216I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1216
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1217I
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1239I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGGCCT
<4>
<5>Unidentified bacterium RFL1217
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1218I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1243I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL1218
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1219I
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1435I
<3>AAGCTT
<4>
<5>Unidentified bacterium RFL1219
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1220I
<2>SmaI,AhyI,Cfr9I,CfrJ4I,EaeAI,EclRI,KteAI,Pac25I,PaeBI,PspAI,PspALI,TspMI,Uba1393I,XcyI,XmaI,XmaCI
<3>CCCGGG
<4>
<5>Unidentified bacterium RFL1220
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1221I
<2>EspI,BlpI,Bpu1102I,BpuGCI,Bsp1720I,CelII,Uba1222I,Uba1284I,Uba1320I
<3>GCTNAGC
<4>
<5>Unidentified bacterium RFL1221
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1222I
<2>EspI,BlpI,Bpu1102I,BpuGCI,Bsp1720I,CelII,Uba1221I,Uba1284I,Uba1320I
<3>GCTNAGC
<4>
<5>Unidentified bacterium RFL1222
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1223I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1223
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1224I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1224
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1225I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1225
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1226I
<2>SphI,Asp5HI,BbuI,BscOI,Bsp121I,BtgAII,CglAI,PaeI,PaeCI,PfaAIII,RspLKI,SpaHI,SpaXI,Uba1162I,VchO68I
<3>GCATGC
<4>
<5>Unidentified bacterium RFL1226
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1227I
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1245I,Uba153AI,UbaM39I
<3>CAGCTG
<4>
<5>Unidentified bacterium RFL1227
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1228I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1228
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1229I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL1229
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1230I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1230
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1231I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1231
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1232I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1232
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1233I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1233
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1234I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1244I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL1234
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1235I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1235
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1237I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Unidentified bacterium RFL1237
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1238I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1238
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1239I
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1371I,Uba1403I,Uba1419I,VchO44I
<3>AGGCCT
<4>
<5>Unidentified bacterium RFL1239
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1240I
<2>SnaBI,Bpu1831I,BstSNI,EciAI,Eco105I,Eco158II,SspJI,SspM1I,SspM2I
<3>TACGTA
<4>
<5>Unidentified bacterium RFL1240
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1241I
<2>ApaI,Bsp120I,EciEI,PpeI,Psp30I,PspOMI,Uba1156I,Uba1157I,Uba1165I,Uba1202I,Uba1368I
<3>GGGCCC
<4>
<5>Unidentified bacterium RFL1241
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1242I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1242
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1243I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1410I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL1243
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1244I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1306I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL1244
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1245I
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba153AI,UbaM39I
<3>CAGCTG
<4>
<5>Unidentified bacterium RFL1245
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1246I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1246
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1248I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Unidentified bacterium RFL1248
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1249I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Unidentified bacterium RFL1249
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1250I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1250
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1256I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1256
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1257I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1257
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1258I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1258
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1259I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Unidentified bacterium RFL1259
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1262I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1262
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1263I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL1263
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1264I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL1264
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1266I
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>CTTAAG
<4>
<5>Unidentified bacterium RFL1266
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1267I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1338I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Unidentified bacterium RFL1267
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1271I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Unidentified bacterium RFL1271
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1272I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Unidentified bacterium RFL1272
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1275I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1275
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1276I
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,UbaN7I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC
<4>
<5>Unidentified bacterium RFL1276
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1278I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Unidentified bacterium RFL1278
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1279I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1375I,Uba1425I
<3>TCCGGA
<4>
<5>Unidentified bacterium RFL1279
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1280I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Unidentified bacterium RFL1280
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1282I
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1283I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Unidentified bacterium RFL1282
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1283I
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1431I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Unidentified bacterium RFL1283
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1284I
<2>EspI,BlpI,Bpu1102I,BpuGCI,Bsp1720I,CelII,Uba1221I,Uba1222I,Uba1320I
<3>GCTNAGC
<4>
<5>Unidentified bacterium RFL1284
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1286I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1286
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1287I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1287
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1288I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1288
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1289I
<2>EcoNI,Bpu1268I,BsoEI,BstENI,BstWI,Uba1290I,Uba1308I,Uba1309I,Uba1310I,XagI
<3>CCTNNNNNAGG
<4>
<5>Unidentified bacterium RFL1289
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1290I
<2>EcoNI,Bpu1268I,BsoEI,BstENI,BstWI,Uba1289I,Uba1308I,Uba1309I,Uba1310I,XagI
<3>CCTNNNNNAGG
<4>
<5>Unidentified bacterium RFL1290
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1291I
<2>BstEII,AcrII,AspAI,Bse59I,Bse64I,BseT9I,BseT10I,BsiKI,Bsp1591I,Bst31I,BstDI,BstPI,BstT9I,BstT10I,Cfr7I,Cfr19I,EcaI,Eci125I,Eco91I,EcoO65I,EcoO128I,KoxI,NspSAII,PspEI,SciAI
<3>GGTNACC
<4>
<5>Unidentified bacterium RFL1291
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1292I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1292
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1293I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1293
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1294I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1332I,Uba1333I
<3>CCTNAGG
<4>
<5>Unidentified bacterium RFL1294
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1294II
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1294
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1295I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1295
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1296I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1296
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1297I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1297
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1298I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Unidentified bacterium RFL1298
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1299I
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>CTTAAG
<4>
<5>Unidentified bacterium RFL1299
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1302I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1302
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1303I
<2>McrI,BsaOI,BscNI,Bsh1285I,BsiEI,BstMCI,BstZ5I
<3>CGRYCG
<4>
<5>Unidentified bacterium RFL1303
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1304I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Unidentified bacterium RFL1304
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1305I
<2>NlaIV,AspNI,BcrI,BmiI,BsaEI,BscBI,Bsp29I,BspLI,BssI,HpyF44II,HpyF73I,NgoBV,NgoGV,PspN4I,Rlu3I,Uba1445I
<3>GGNNCC
<4>
<5>Unidentified bacterium RFL1305
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1306I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1364I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL1306
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1307I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL1307
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1308I
<2>EcoNI,Bpu1268I,BsoEI,BstENI,BstWI,Uba1289I,Uba1290I,Uba1309I,Uba1310I,XagI
<3>CCTNNNNNAGG
<4>
<5>Unidentified bacterium RFL1308
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1309I
<2>EcoNI,Bpu1268I,BsoEI,BstENI,BstWI,Uba1289I,Uba1290I,Uba1308I,Uba1310I,XagI
<3>CCTNNNNNAGG
<4>
<5>Unidentified bacterium RFL1309
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1310I
<2>EcoNI,Bpu1268I,BsoEI,BstENI,BstWI,Uba1289I,Uba1290I,Uba1308I,Uba1309I,XagI
<3>CCTNNNNNAGG
<4>
<5>Unidentified bacterium RFL1310
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1311I
<2>StyI,BsmSI,BssT1I,Bst224I,CfrBI,Eco130I,Eco208II,EcoT14I,EcoT104I,ErhI,ErhB9II,SblAI,SblBI,SblCI
<3>CCWWGG
<4>
<5>Unidentified bacterium RFL1311
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1312I
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>CTTAAG
<4>
<5>Unidentified bacterium RFL1312
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1313I
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>CTTAAG
<4>
<5>Unidentified bacterium RFL1313
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1314I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Unidentified bacterium RFL1314
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1315I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1315
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1316I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1343I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Unidentified bacterium RFL1316
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1317I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Unidentified bacterium RFL1317
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1318I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Unidentified bacterium RFL1318
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1319I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1319
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1320I
<2>EspI,BlpI,Bpu1102I,BpuGCI,Bsp1720I,CelII,Uba1221I,Uba1222I,Uba1284I
<3>GCTNAGC
<4>
<5>Unidentified bacterium RFL1320
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1321I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1404I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Unidentified bacterium RFL1321
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1322I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1322
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1323I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Unidentified bacterium RFL1323
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1324I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1324
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1325I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1325
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1326I
<2>DraII,EcoO109I,Kaz48kI,PssI,VneAI
<3>RGGNCCY
<4>
<5>Unidentified bacterium RFL1326
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1327I
<2>CfrI,AcoI,Ava458I,Bfi89I,Cfr14I,Cfr38I,Cfr39I,Cfr40I,Cfr55I,Cfr59I,EaeI,EciBI,Eco90I,Eco164I,EcoHAI,EcoHK31I,EspHK16I,EspHK24I,KspHK15I,Uba36I,Uba1188I
<3>YGGCCR
<4>
<5>Unidentified bacterium RFL1327
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1328I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1328
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1329I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1330I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL1329
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1330I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1357I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL1330
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1331I
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>CTTAAG
<4>
<5>Unidentified bacterium RFL1331
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1332I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1333I
<3>CCTNAGG
<4>
<5>Unidentified bacterium RFL1332
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1333I
<2>SauI,AocI,AsuSAI,AxyI,Bli643I,BliHKI,Bse21I,BseG73I,BspR7I,Bst29I,Bst30I,BstZ6I,Bsu36I,CvnI,EciCI,Eco76I,Eco81I,Eco115I,Eco118I,Eco110kI,Lmu60I,MstII,OxaNI,PxyMZI,SauHI,SecIII,SshAI,Uba1184II,Uba1294I,Uba1332I
<3>CCTNAGG
<4>
<5>Unidentified bacterium RFL1333
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1334I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1334
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1335I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1397I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Unidentified bacterium RFL1335
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1336I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1336
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1337I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1337
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1338I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1355I,Uba1439I
<3>CCGG
<4>
<5>Unidentified bacterium RFL1338
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1339I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1339
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1342I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1342
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1343I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,VpaK57I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Unidentified bacterium RFL1343
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1346I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1346
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1347I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Unidentified bacterium RFL1347
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1353I
<2>AvaIII,Asi372I,BfrBI,BfrCI,Csp68KIII,EcoT22I,Mph1103I,NsiI,PinBI,Ppu10I,PxyJKI,SepI,SmuCI,SrlII,SspD5II,Uba1367I,Uba1384I,Zsp2I
<3>ATGCAT
<4>
<5>Unidentified bacterium RFL1353
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1355I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1439I
<3>CCGG
<4>
<5>Unidentified bacterium RFL1355
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1357I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1363I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL1357
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1362I
<2>SduI,AocII,Bka1125I,BmyI,BsoCI,Bsp1286I,BspLS2I,BstZ15I,HpyF36IV,HpyF47I,MhlI,Mlu40I,NspII,TseAI
<3>GDGCHC
<4>
<5>Unidentified bacterium RFL1362
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1363I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1409I,Uba1421I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL1363
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1364I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1369I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL1364
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1366I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Unidentified bacterium RFL1366
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1366II
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1366
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1367I
<2>AvaIII,Asi372I,BfrBI,BfrCI,Csp68KIII,EcoT22I,Mph1103I,NsiI,PinBI,Ppu10I,PxyJKI,SepI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1384I,Zsp2I
<3>ATGCAT
<4>
<5>Unidentified bacterium RFL1367
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1368I
<2>ApaI,Bsp120I,EciEI,PpeI,Psp30I,PspOMI,Uba1156I,Uba1157I,Uba1165I,Uba1202I,Uba1241I
<3>GGGCCC
<4>
<5>Unidentified bacterium RFL1368
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1369I
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,UbaHKAI
<3>CCGCGG
<4>
<5>Unidentified bacterium RFL1369
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1370I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Unidentified bacterium RFL1370
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1371I
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1403I,Uba1419I,VchO44I
<3>AGGCCT
<4>
<5>Unidentified bacterium RFL1371
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1372I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Unidentified bacterium RFL1372
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1373I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Unidentified bacterium RFL1373
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1374I
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1420I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>CTTAAG
<4>
<5>Unidentified bacterium RFL1374
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1375I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1425I
<3>TCCGGA
<4>
<5>Unidentified bacterium RFL1375
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1376I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1378I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Unidentified bacterium RFL1376
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1377I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1377
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1378I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1389I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Unidentified bacterium RFL1378
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1379I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1379
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1380I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1380
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1381I
<2>AcyI,AhaII,AosII,AstWI,AsuIII,BbiII,BsaHI,BssNI,BstACI,HgiI,HgiDI,HgiGI,HgiHII,Hin1I,Hin8I,Hsp92I,Msp17I,NlaSII,PamII,SspJII,SspM1II,SspM2II
<3>GRCGYC
<4>
<5>Unidentified bacterium RFL1381
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1382I
<2>BsmI,Asp26HI,Asp27HI,Asp35HI,Asp36HI,Asp40HI,Asp50HI,BmaHI,BsaMI,BscCI,Mva1269I,PctI,Uba1415I
<3>GAATGC
<4>
<5>Unidentified bacterium RFL1382
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1383I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1398I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1383
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1384I
<2>AvaIII,Asi372I,BfrBI,BfrCI,Csp68KIII,EcoT22I,Mph1103I,NsiI,PinBI,Ppu10I,PxyJKI,SepI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1367I,Zsp2I
<3>ATGCAT
<4>
<5>Unidentified bacterium RFL1384
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1385I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1452I
<3>TTCGAA
<4>
<5>Unidentified bacterium RFL1385
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1386I
<2>NruI,AmaSI,Bsp68I,BtuMI,Mlu9273I,MluB2I,PspDI,RruI,SalDI,Sbo13I,Sna3286I,SpoI,Uba1117I,VchO70I
<3>TCGCGA
<4>
<5>Unidentified bacterium RFL1386
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1387I
<2>ApaLI,AaqI,Alw44I,AmeI,Bsp146I,DaqI,Pfl23I,Pfr12I,PliI,ScoNI,SnoI,Uba1203I,VneI
<3>GTGCAC
<4>
<5>Unidentified bacterium RFL1387
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1388I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1388
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1389I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1401I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Unidentified bacterium RFL1389
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1391I
<2>ScrFI,Bme1390I,BmrFI,BsaCI,BsoI,Bsp53I,Bsp73I,Bsp548I,BssKI,BstMZ611I,BstSCI,DsaV,Ecl18kI,Eco43I,Eco51II,Eco80I,Eco85I,Eco93I,Eco153I,Eco200I,Eco13kI,Eco21kI,Eco137kI,HpyNI,Kpn2kI,LlaMI,Msp67I,MspR9I,SenPI,SsoII,StyD4I,Uba17I
<3>CCNGG
<4>
<5>Unidentified bacterium RFL1391
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1392I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1392
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1393I
<2>SmaI,AhyI,Cfr9I,CfrJ4I,EaeAI,EclRI,KteAI,Pac25I,PaeBI,PspAI,PspALI,TspMI,Uba1220I,XcyI,XmaI,XmaCI
<3>CCCGGG
<4>
<5>Unidentified bacterium RFL1393
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1394I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1394
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1395I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1395
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1397I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1448I,XpaI
<3>CTCGAG
<4>
<5>Unidentified bacterium RFL1397
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1398I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1402I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1398
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1399I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1399
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1400I
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,UbaN4I
<3>GATATC
<4>
<5>Unidentified bacterium RFL1400
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1401I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1423I,Uba1424I
<3>CCSGG
<4>
<5>Unidentified bacterium RFL1401
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1402I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1414I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1402
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1403I
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1419I,VchO44I
<3>AGGCCT
<4>
<5>Unidentified bacterium RFL1403
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1404I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1405I,Uba1446I
<3>CGCG
<4>
<5>Unidentified bacterium RFL1404
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1405I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1446I
<3>CGCG
<4>
<5>Unidentified bacterium RFL1405
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1408I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1408
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1408II
<2>HpaI,BsaKI,BseII,BstEZ359I,BstHPI,KspAI,MwhI,SsrI
<3>GTTAAC
<4>
<5>Unidentified bacterium RFL1408
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1409I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1421I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL1409
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1410I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1428I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL1410
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1411I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1411
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1412I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1412
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1413I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Unidentified bacterium RFL1413
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1414I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba4009I,UbaN3I
<3>GGATCC
<4>
<5>Unidentified bacterium RFL1414
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1415I
<2>BsmI,Asp26HI,Asp27HI,Asp35HI,Asp36HI,Asp40HI,Asp50HI,BmaHI,BsaMI,BscCI,Mva1269I,PctI,Uba1382I
<3>GAATGC
<4>
<5>Unidentified bacterium RFL1415
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1416I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1427I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1416
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1417I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium RFL1417
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1418I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1418
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1419I
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,VchO44I
<3>AGGCCT
<4>
<5>Unidentified bacterium RFL1419
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1420I
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1426I,Uba1443I,VfiI,Vha464I
<3>CTTAAG
<4>
<5>Unidentified bacterium RFL1420
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1421I
<2>HgiJII,BanII,BpuI,BscMI,Bsp117I,Bsp519I,BstZ7I,Bsu1854I,BvuI,Cfr48I,Eco24I,Eco25I,Eco26I,Eco35I,Eco68I,Eco113I,Eco180I,Eco211I,Eco215I,Eco216I,Eco232I,Eco249I,Eco262I,Eco75KI,EcoT38I,EcoT88I,EcoT93I,EcoT95I,Ese4I,FriOI,KoxII,OmiAI,OmiBI,PaeHI,Ppu20I,Psp31I,SacNI,Uba39I,Uba57I,Uba1124I,Uba1142I,Uba1159I,Uba1206I,Uba1263I,Uba1264I,Uba1307I,Uba1329I,Uba1330I,Uba1357I,Uba1363I,Uba1409I
<3>GRGCYC
<4>
<5>Unidentified bacterium RFL1421
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1422I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1422
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1423I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1424I
<3>CCSGG
<4>
<5>Unidentified bacterium RFL1423
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1424I
<2>CauII,AhaI,AseII,Asp1I,AsuC2I,BcnI,BpuMI,Bsp7I,Bsp8I,Bsp55I,BspF105I,BspJ67I,EciDI,Eco121I,Eco179I,Eco190I,Eco1831I,EcoHI,HgiS21I,HgiS22I,Hin3I,Kpn49kII,Mgl14481I,NciI,Pae181I,RshII,SflHK10695I,SflHK11086I,SflHK11087I,SflHK11572I,SflHK115731I,Ssp2I,Tmu1I,Uba41I,Uba42I,Uba1280I,Uba1318I,Uba1347I,Uba1370I,Uba1372I,Uba1376I,Uba1378I,Uba1389I,Uba1401I,Uba1423I
<3>CCSGG
<4>
<5>Unidentified bacterium RFL1424
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1425I
<2>BspMII,AccIII,Aor13HI,Bbf7411I,BbvAIII,Bla7920I,BlfI,BseAI,BsiGI,BsiMI,BsiOI,Bsp13I,Bsp228I,Bsp233I,Bsp508I,BspEI,BspH226I,BstZ1I,BstZ3I,Bsu22I,Bsu23I,CauB3I,Cfr57I,EspHK26I,Kpn2I,MroI,PinBII,PtaI,Tsp507I,Tsp514I,Uba1136I,Uba1279I,Uba1375I
<3>TCCGGA
<4>
<5>Unidentified bacterium RFL1425
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1426I
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1443I,VfiI,Vha464I
<3>CTTAAG
<4>
<5>Unidentified bacterium RFL1426
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1427I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1430I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1427
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1428I
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,ZanI
<3>CCWGG
<4>
<5>Unidentified bacterium RFL1428
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1429I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1429
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1430I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1451I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1430
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1431I
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1447I,Umi7I
<3>TGATCA
<4>
<5>Unidentified bacterium RFL1431
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1432I
<2>XhoII,AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,MflI,PsuI,Tru201I
<3>RGATCY
<4>
<5>Unidentified bacterium RFL1432
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1433I
<2>AluI,AluBI,BsaLI,MarI,Mho2111I,MltI,OtuI,OtuNI,OxaI,Uba1441I
<3>AGCT
<4>
<5>Unidentified bacterium RFL1433
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1435I
<2>HindIII,Asp52I,Asp3065I,BbrI,BbrAI,BpeI,BseHI,BsmGII,BspKT8I,BspLAIII,Bst170II,BstFI,BstZ1II,Cfr32I,ChuEI,Csp231I,Eco65I,Eco98I,Eco188I,Eco231I,EcoVIII,Hin5III,Hin173I,Hin1076III,HinJCII,HinSAFI,HinbIII,HinfII,HsuI,LlaCI,MkiI,SpaPIV,SsbI,Uba83I,Uba1164II,Uba1219I
<3>AAGCTT
<4>
<5>Unidentified bacterium RFL1435
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1436I
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1440I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Unidentified bacterium RFL1436
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1437I
<2>GsuI,Bco35I,BpmI,Bsp22I,Bsp28I,BspJ74I,Bth1795I,Uba1444I
<3>CTGGAG
<4>
<5>Unidentified bacterium RFL1437
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1438I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Unidentified bacterium RFL1438
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1439I
<2>HpaII,Asp748I,Bco27I,BsaZI,BshMI,BsiSI,Bsp5I,Bsp47I,Bsp48I,Bsp116I,Bsp1591II,Bst40I,Bsu1192I,BsuFI,CboI,CceI,FinII,HapII,Hin2I,Hin5I,HpyVIII,HpyF43I,MniII,MnoI,MspI,Msp199I,Pde137I,Pme35I,SecII,SfaGUI,Sth134I,Sth302II,Uba1128I,Uba1141I,Uba1267I,Uba1338I,Uba1355I
<3>CCGG
<4>
<5>Unidentified bacterium RFL1439
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1440I
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,UbaN6II,Umi5I
<3>CYCGRG
<4>
<5>Unidentified bacterium RFL1440
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1441I
<2>AluI,AluBI,BsaLI,MarI,Mho2111I,MltI,OtuI,OtuNI,OxaI,Uba1433I
<3>AGCT
<4>
<5>Unidentified bacterium RFL1441
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1442I
<2>SecI,BsaJI,BseDI,BsoKI,BssECI,BstZ10I,Hpy99IV,HpyF10III,HpyF61II,HpyF67IV
<3>CCNNGG
<4>
<5>Unidentified bacterium RFL1442
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1443I
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,VfiI,Vha464I
<3>CTTAAG
<4>
<5>Unidentified bacterium RFL1443
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1444I
<2>GsuI,Bco35I,BpmI,Bsp22I,Bsp28I,BspJ74I,Bth1795I,Uba1437I
<3>CTGGAG
<4>
<5>Unidentified bacterium RFL1444
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1445I
<2>NlaIV,AspNI,BcrI,BmiI,BsaEI,BscBI,Bsp29I,BspLI,BssI,HpyF44II,HpyF73I,NgoBV,NgoGV,PspN4I,Rlu3I,Uba1305I
<3>GGNNCC
<4>
<5>Unidentified bacterium RFL1445
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1446I
<2>FnuDII,AccII,Bce31293I,BceBI,BceRI,BepI,Bpu95I,Bsh1236I,Bsp50I,Bsp70I,Bsp123I,BspFNI,BspJ76I,BstFNI,BstUI,Bsu1192II,Bsu1193I,Bsu1532I,Bsu6633I,BsuEII,BtkI,Cpa1150I,CpaAI,Csp68KVI,EsaBS9I,FalII,FauBII,FspMI,Hin1056I,HpyF14I,HpyF15I,HpyF26I,HpyF52II,HpyF64IV,MvaAI,MvnI,PflAI,SceAI,SelI,ThaI,TmaI,Uba1321I,Uba1404I,Uba1405I
<3>CGCG
<4>
<5>Unidentified bacterium RFL1446
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1447I
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Umi7I
<3>TGATCA
<4>
<5>Unidentified bacterium RFL1447
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1448I
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,XpaI
<3>CTCGAG
<4>
<5>Unidentified bacterium RFL1448
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1449I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1449
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1450I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium RFL1450
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1451I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1453I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1451
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1452I
<2>AsuII,AcaI,AcpI,Afl83I,Asp10HI,AviI,BimI,Bim19I,Bpu14I,BpuHI,BsiCI,Bsp82I,Bsp90I,Bsp101I,Bsp102I,Bsp104I,Bsp119I,Bsp148I,Bsp151I,Bsp241I,BspH22I,BspH103I,BspH106I,BspLAII,BspT104I,BstBI,CbiI,Csp45I,Csp68KII,FspII,LspI,MlaI,Mva16I,NspV,Nsp29132I,NspBI,NspFI,NspJI,OspI,PlaII,PpaAI,Psc27I,Psc28I,Rma376I,Rma523I,SfuI,Sgr1839I,Ssp1I,Ssp14I,Ssp34I,Ssp42I,Ssp43I,Ssp45I,Ssp47I,Ssp48I,Ssp152I,SspRFI,SviI,Uba1385I
<3>TTCGAA
<4>
<5>Unidentified bacterium RFL1452
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba1453I
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,ZhoI
<3>ATCGAT
<4>
<5>Unidentified bacterium RFL1453
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Uba4009I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,UbaN3I
<3>G^GATCC
<4>
<5>Unidentified bacterium A
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., (1995) Vestn. Akad. Med. Nauk SSSR, vol. 2, pp. 47-51.

<1>Uba153AI
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,UbaM39I
<3>CAG^CTG
<4>
<5>Unidentified bacterium 153A
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., (1995) Vestn. Akad. Med. Nauk SSSR, vol. 2, pp. 47-51.

<1>UbaF9I
<2>
<3>TACNNNNNRTGT
<4>
<5>Unidentified bacterium F9
<6>Fermentas G305
<7>
<8>Strazdas, G., Petrusyte, M., Capskaja, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>UbaF11I
<2>
<3>TCGTA
<4>
<5>Unidentified bacterium F11
<6>Fermentas G327
<7>
<8>Vitkute, J., Lauciuniene, N., Riauba, L., Capskaja, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>UbaF12I
<2>
<3>CTACNNNGTC
<4>
<5>Unidentified bacterium F12
<6>Fermentas G333
<7>
<8>Vitkute, J., Lauciuniene, N., Riauba, L., Capskaja, L., Norgeliene, D., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>UbaF13I
<2>
<3>GAGNNNNNNCTGG
<4>
<5>Unidentified bacterium F13
<6>Fermentas G334
<7>
<8>Vitkute, J., Lauciuniene, N., Riauba, L., Norgeliene, D., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>UbaF14I
<2>
<3>CCANNNNNTCG
<4>
<5>Unidentified bacterium F14
<6>Fermentas G336
<7>
<8>Vitkute, J., Lauciuniene, N., Capskaja, L., Kiuduliene, L., Janulaitis, A., Unpublished observations.

<1>UbaHKAI
<2>SacII,AosIII,Asp32HI,BacI,Bac465I,BscTI,Bsp12I,Cfr37I,Cfr41I,Cfr42I,Cfr43I,Cfr45II,CscI,Cte1I,DrdAI,DrdBI,DrdCI,DrdEI,DrdFI,Dsp1I,Eae46I,EccI,Ecl1I,Ecl28I,Ecl37I,Eco55I,Eco92I,Eco96I,Eco99I,Eco100I,Eco104I,Eco134I,Eco135I,Eco151I,Eco158I,Eco182I,Eco196I,Eco208I,Eco29kI,Ese3I,Ese6I,FscI,GalI,GceI,GceGLI,Kpn19I,Kpn378I,KspI,Mpr154I,MraI,NgoAIII,NgoDIII,NgoGIII,NgoJIII,NgoKIII,NgoMIII,NgoPIII,NlaDIII,NlaSI,Pae7I,Pae17I,Pae36I,Pae42I,Pae43I,Pae44I,PaeAI,PaeQI,Pae5kI,Pae14kI,Pfl1108II,RaqI,SaaI,SabI,SakI,SboI,SchZI,SenPT14bI,SenpCI,SexBI,SexCI,SfrI,Sfr303I,Sfr382I,SgrBI,ShyI,SpuI,SseII,SsmII,Ssm5II,Ssp1725I,SstII,StaI,TglI,TtoI,Uba66I,Uba77I,Uba90I,Uba1093I,Uba1095I,Uba1111I,Uba1113I,Uba1126I,Uba1187I,Uba1229I,Uba1234I,Uba1244I,Uba1306I,Uba1364I,Uba1369I
<3>CCGCGG
<4>
<5>Unidentified bacterium
<6>P.C. Shaw
<7>
<8>Chan, H.Y., Chan, Y.C., Kam, K.M., Shaw, P.C., Unpublished observations.

<1>UbaHKBI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Unidentified bacterium
<6>P.C. Shaw
<7>
<8>Chan, H.Y., Chan, Y.C., Kam, K.M., Shaw, P.C., Unpublished observations.

<1>UbaM39I
<2>PvuII,BamGI,BavI,BavAI,BavBI,Bsp153AI,BspM39I,BspO4I,Bth2350I,Cfr6I,DmaI,EclI,GspI,MziI,NmeRI,Pae17kI,Psp3I,Psp5I,Pun14627II,Pvu84II,PvuHKUI,SbaI,SciAII,SmaAIV,Sol3335I,SpaPIII,SplAIV,Uba1227I,Uba1245I,Uba153AI
<3>CAG^CTG
<4>
<5>Unidentified bacterium M39
<6>N.N. Sokolov
<7>
<8>Sokolov, N.N., (1995) Vestn. Akad. Med. Nauk SSSR, vol. 2, pp. 47-51.

<1>UbaN1I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,Vha44I
<3>GATC
<4>
<5>Unidentified bacterium OQ3-07, Nicaragua
<6>J. Huete-Perez
<7>
<8>Roustan-Espinosa, I., Guerrero, D., Flores, E., Huete-Perez, J., (2000) Revista Univ. Centroamer. (Revista de la Universidad Centroamericana), vol. 52, pp. 10-18.

<1>UbaN2I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium OQ3-03, Nicaragua
<6>J. Huete-Perez
<7>
<8>Roustan-Espinosa, I., Guerrero, D., Flores, E., Huete-Perez, J., (2000) Revista Univ. Centroamer. (Revista de la Universidad Centroamericana), vol. 52, pp. 10-18.

<1>UbaN3I
<2>BamHI,AacLI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,GstI,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402I,Uba1414I,Uba4009I
<3>GGATCC
<4>
<5>Unidentified bacterium DCF-05, Nicaragua
<6>J. Huete-Perez
<7>
<8>Roustan-Espinosa, I., Guerrero, D., Flores, E., Huete-Perez, J., (2000) Revista Univ. Centroamer. (Revista de la Universidad Centroamericana), vol. 52, pp. 10-18.

<1>UbaN4I
<2>EcoRV,Bsc217I,BshLI,BsoAI,Bsp16I,BstRI,CeqI,Eco17I,Eco32I,Eco178I,HjaI,HpyCI,NanI,NflAI,NsiCI,Pac1110II,Pfl16I,PxyARI,Rma495II,Rma496II,Rma497II,SmiMII,Tsp273I,Uba1400I
<3>GATATC
<4>
<5>Unidentified bacterium T1-03, Nicaragua
<6>J. Huete-Perez
<7>
<8>Roustan-Espinosa, I., Guerrero, D., Flores, E., Huete-Perez, J., (2000) Revista Univ. Centroamer. (Revista de la Universidad Centroamericana), vol. 52, pp. 10-18.

<1>UbaN5I
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,XspI
<3>CTAG
<4>
<5>Unidentified bacterium CN8-01, Nicaragua
<6>J. Huete-Perez
<7>
<8>Roustan-Espinosa, I., Guerrero, D., Flores, E., Huete-Perez, J., (2000) Revista Univ. Centroamer. (Revista de la Universidad Centroamericana), vol. 52, pp. 10-18.

<1>UbaN6I
<2>BsaBI,Bco63I,Bco631I,Bse8I,Bse631I,BseJI,Bsh1365I,BsiBI,BsrBRI,MamI
<3>GATNNNNATC
<4>
<5>Unidentified bacterium CN12-05, Nicaragua
<6>J. Huete-Perez
<7>
<8>Roustan-Espinosa, I., Guerrero, D., Flores, E., Huete-Perez, J., (2000) Revista Univ. Centroamer. (Revista de la Universidad Centroamericana), vol. 52, pp. 10-18.

<1>UbaN6II
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,Umi5I
<3>CYCGRG
<4>
<5>Unidentified bacterium CN12-05, Nicaragua
<6>J. Huete-Perez
<7>
<8>Roustan-Espinosa, I., Guerrero, D., Flores, E., Huete-Perez, J., (2000) Revista Univ. Centroamer. (Revista de la Universidad Centroamericana), vol. 52, pp. 10-18.

<1>UbaN7I
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC
<4>
<5>Unidentified bacterium TOT-01, Nicaragua
<6>J. Huete-Perez
<7>
<8>Roustan-Espinosa, I., Guerrero, D., Flores, E., Huete-Perez, J., (2000) Revista Univ. Centroamer. (Revista de la Universidad Centroamericana), vol. 52, pp. 10-18.

<1>UbaN8I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium TOT-02, Nicaragua
<6>J. Huete-Perez
<7>
<8>Roustan-Espinosa, I., Guerrero, D., Flores, E., Huete-Perez, J., (2000) Revista Univ. Centroamer. (Revista de la Universidad Centroamericana), vol. 52, pp. 10-18.

<1>UbaN9I
<2>AclI,Psp1406I
<3>AACGTT
<4>
<5>Unidentified bacterium M4-HSJ, Nicaragua
<6>J. Huete-Perez
<7>
<8>Roustan-Espinosa, I., Guerrero, D., Flores, E., Huete-Perez, J., (2000) Revista Univ. Centroamer. (Revista de la Universidad Centroamericana), vol. 52, pp. 10-18.

<1>UbaN10I
<2>BetI,Bba179I,Bca77I,BsaWI,Bst1473I
<3>WCCGGW
<4>
<5>Unidentified bacterium M4-1ATM, Nicaragua
<6>J. Huete-Perez
<7>
<8>Roustan-Espinosa, I., Guerrero, D., Flores, E., Huete-Perez, J., (2000) Revista Univ. Centroamer. (Revista de la Universidad Centroamericana), vol. 52, pp. 10-18.

<1>UbaPI
<2>
<3>CGAACG
<4>
<5>Unidentified bacteria BPr-325
<6>V. Butkus
<7>
<8>Padegimiene, E., Petrusyte, M., Capskaja, L., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>Umi5I
<2>AvaI,AcrI,Ama87I,AquI,AspBI,AspDI,AvrI,BcoI,BmeT110I,Bse15I,BsiHKCI,BsoBI,BspLU4I,BstBAII,BstNSII,Bst7QI,BstSI,BstZ4I,Eco88I,Eco27kI,EspHK29I,Gst1588I,NliI,Nli3877I,NmuAI,NspIII,NspDI,NspEI,NspSAI,OfoI,PlaAI,PunAI,Uba1205II,Uba1436I,Uba1440I,UbaN6II
<3>CYCGRG
<4>
<5>Unidentified bacterium 5T
<6>V.E. Repin
<7>
<8>Repin, V.E., Unpublished observations.

<1>Umi7I
<2>BclI,AbaI,AtuSI,BceDI,Bco102I,BmeTI,BsiQI,BspXII,Bst77I,BstGI,BstKI,BstT7I,BstZ10II,CpeI,CthI,FbaI,Ksp22I,ParI,PovI,SseI,SstIV,Uba1282I,Uba1283I,Uba1431I,Uba1447I
<3>TGATCA
<4>
<5>Unidentified bacterium 7T
<6>V.E. Repin
<7>
<8>Repin, V.E., Unpublished observations.

<1>UnbI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>^GGNCC
<4>
<5>Unidentified bacterium strain #8
<6>P.P. Stepien
<7>
<8>Kawalec, M., Borsuk, P., Piechula, S., Stepien, P.P., (1997) Acta Biochim. Pol., vol. 44, pp. 849-852.

<1>Uth549I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium
<6>FZ 549
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Uth554I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Unidentified bacterium
<6>FZ 554
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Uth555I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth557I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium
<6>FZ 555
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Uth557I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Van91III,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Unidentified bacterium
<6>FZ 557
<7>
<8>Torsti, A.-M., Hjorleifsdottir, S., Unpublished observations.

<1>Uur960I
<2>Fnu4HI,Bli1904II,Bpu1811I,BsoFI,Bsp6I,BssFI,BssXI,BthCI,Cac824I,CcoP215I,CcoP216I,FbrI,Fsp4HI,ItaI,LlaDII,SatI
<3>GC^NGC
<4>
<5>Ureaplasma urealyticum 960
<6>ATCC 27618
<7>
<8>Cocks, B.G., Finch, L.R., (1987) Int. J. Syst. Bacteriol., vol. 37, pp. 451-453.

<1>VanI
<2>BglI,Bpu86I,BseB631I,BsoJI,Psp1009I,Tsp219I,Tsp8EI
<3>GCCNNNNNGGC
<4>
<5>Vibrio anguillarum
<6>P. Wood
<7>
<8>Wood, P., Unpublished observations.

<1>Van91I
<2>PflMI,AccB7I,AcpII,Asp10HII,BasI,Esp1396I,PflBI
<3>CCANNNN^NTGG
<4>
<5>Vibrio anguillarum RFL91
<6>A. Janulaitis
<7>FKM
<8>Janulaitis, A., Petrusyte, M., Maneliene, Z., Capskaya, L., Kiuduliene, L., Butkus, V., Unpublished observations.

<1>Van91II
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco237I,Eco252I,FunII,HalI,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl32DII,Srl55DI,SsoI,Uba58I,VchN100I,VchO2I
<3>GAATTC
<4>
<5>Vibrio anguillarum RFL91
<6>A. Janulaitis
<7>
<8>Ge, M., Gumport, R.I., Unpublished observations.
Janulaitis, A., Unpublished observations.

<1>Van91III
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,VhaI,Vha1168I,VniI
<3>GGCC
<4>
<5>Vibrio anguillarum RFL91
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>Van91IV
<2>
<3>?
<4>
<5>Vibrio anguillarum RFL91
<6>A. Janulaitis
<7>
<8>Janulaitis, A., Unpublished observations.

<1>M.VchK139I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>2(6)
<5>Vibrio cholerae phage K139
<6>J. Reidl
<7>
<8>Ehara, M., Nguyen, M.B., Nguyen, T.D., Ngo, C.T., Le, H.T., Nguyen, T.H., Iwami, M., Unpublished observations.
Kapfhammer, D., Blass, J., Evers, S., Reidl, J., (2002) J. Bacteriol., vol. 184, pp. 6592-6601.

<1>VchN100I
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco237I,Eco252I,FunII,HalI,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl32DII,Srl55DI,SsoI,Uba58I,Van91II,VchO2I
<3>GAATTC
<4>
<5>Vibrio cholerae CY100
<6>C. Yamada
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>VchO2I
<2>EcoRI,Eco82I,Eco159I,Eco228I,Eco237I,Eco252I,FunII,HalI,Hal22I,Kpn49kI,Ppu111I,RsrI,Srl32DII,Srl55DI,SsoI,Uba58I,Van91II,VchN100I
<3>GAATTC
<4>
<5>Vibrio cholerae NCTC4711
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Mise, K., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 599-604.

<1>VchO6I
<2>
<3>?
<4>
<5>Vibrio cholerae 7007-62
<6>K. Mise
<7>
<8>Miyahara, M., Shimada, T., Mise, K., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 599-604.

<1>VchO24I
<2>
<3>?
<4>
<5>Vibrio cholerae 14438-62
<6>K. Mise
<7>
<8>Miyahara, M., Shimada, T., Mise, K., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 599-604.

<1>VchO25I
<2>SnaI,BspM90I,BssNAI,Bst1107I,BstBSI,BstZ17I,XcaI
<3>GTATAC
<4>
<5>Vibrio cholerae 14821-62
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Mise, K., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 599-604.

<1>VchO44I
<2>StuI,AatI,Asp78I,AspMI,ChyI,Eco147I,Eco1524I,GdiI,GobAI,NtaSI,PceI,PluI,Pme55I,Ppu13I,SarI,Sru30DI,SseBI,SsvI,SteI,Uba40I,Uba1170I,Uba1180I,Uba1217I,Uba1239I,Uba1371I,Uba1403I,Uba1419I
<3>AGGCCT
<4>
<5>Vibrio cholerae 112-73
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Mise, K., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 599-604.

<1>VchO49I
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,ZrmI
<3>AGTACT
<4>
<5>Vibrio cholerae 1154-74
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Mise, K., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 599-604.

<1>VchO52I
<2>
<3>?
<4>
<5>Vibrio cholerae 207-73
<6>K. Mise
<7>
<8>Miyahara, M., Shimada, T., Mise, K., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 599-604.

<1>VchO60I
<2>
<3>?
<4>
<5>Vibrio cholerae 195-75
<6>K. Mise
<7>
<8>Miyahara, M., Shimada, T., Mise, K., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 599-604.

<1>VchO66I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Vibrio cholerae 993-75
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Mise, K., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 599-604.

<1>VchO68I
<2>SphI,Asp5HI,BbuI,BscOI,Bsp121I,BtgAII,CglAI,PaeI,PaeCI,PfaAIII,RspLKI,SpaHI,SpaXI,Uba1162I,Uba1226I
<3>GCATGC
<4>
<5>Vibrio cholerae 293-78
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Mise, K., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 599-604.

<1>VchO70I
<2>NruI,AmaSI,Bsp68I,BtuMI,Mlu9273I,MluB2I,PspDI,RruI,SalDI,Sbo13I,Sna3286I,SpoI,Uba1117I,Uba1386I
<3>TCGCGA
<4>
<5>Vibrio cholerae 1111-77
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Mise, K., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 599-604.

<1>VchO85I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Vibrio cholerae 1903-83
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Mise, K., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 599-604.

<1>VchO87I
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Vibrio cholerae 973-81
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Mise, K., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 599-604.

<1>VchO90I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Vibrio cholerae 1457-78
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Mise, K., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 599-604.

<1>VfiI
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,Vha464I
<3>CTTAAG
<4>
<5>Vibrio fischerii 1246
<6>V.E. Repin
<7>
<8>Repin, V.E., Unpublished observations.

<1>VhaI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,Vha1168I,VniI
<3>GGCC
<4>
<5>Vibrio harveyi
<6>ATCC 14126
<7>
<8>Hurlin, P., Schildkraut, I., Unpublished observations.

<1>Vha44I
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I
<3>GATC
<4>
<5>Vibrio harveyi 44
<6>V.E. Repin
<7>
<8>Repin, V.E., Unpublished observations.

<1>Vha464I
<2>AflII,BfrI,BsaFI,BscLI,BspTI,Bst98I,BstAFI,BstPZ740I,Cfr92I,Esp4I,MspCI,TrsTII,Uba1266I,Uba1299I,Uba1312I,Uba1313I,Uba1331I,Uba1374I,Uba1420I,Uba1426I,Uba1443I,VfiI
<3>C^TTAAG
<4>
<5>Vibrio harveyi 464
<6>S.K. Degtyarev
<7>V
<8>Kolykhalov, A.A., Repin, V.E., Fish, A.M., Rechkunova, N.I., Degtyarev, S.Kh., (1991) Sib. Biol. J., vol. 19, pp. 60-61.
Repin, V.E., Degtyarev, S.K., Rechkunova, N.I., Krivopalova, G.N., Vorodeva, T.I., Fish, A.M., Russian Patent Office, 1993.

<1>Vha1168I
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,VniI
<3>GGCC
<4>
<5>Vibrio harveyi 1168
<6>V.E. Repin
<7>
<8>Repin, V.E., Unpublished observations.

<1>VneI
<2>ApaLI,AaqI,Alw44I,AmeI,Bsp146I,DaqI,Pfl23I,Pfr12I,PliI,ScoNI,SnoI,Uba1203I,Uba1387I
<3>G^TGCAC
<4>
<5>Vibrio nereis 18
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.K., Rechkunova, N.I., Netesova, N.A., Tchigikov, V.E., Malygin, E.G., Kochkin, A.V., Mikhajlov, V.V., Rasskazov, V.A., (1987) Bioorg. Khim., vol. 13, pp. 422-423.

<1>VneAI
<2>DraII,EcoO109I,Kaz48kI,PssI,Uba1326I
<3>RGGNCCY
<4>
<5>Vibrio nereis
<6>P. Wood
<7>
<8>Wood, P., Unpublished observations.

<1>VniI
<2>HaeIII,AcaIV,Afl83II,Asp742I,AspTIII,AvrBI,Bal475I,Bal3006I,BanAI,Bce71I,Bco33I,BecAII,Bfi458I,BhaII,Bim19II,BliI,BluII,Bme46I,Bme74I,Bme361I,BmeU1594I,Bpa36I,BsaRI,BscQI,BseI,Bse9I,Bse126I,BseQI,BshI,BshAI,BshBI,BshCI,BshDI,BshEI,BshFI,BsiAI,BsiDI,BsiHI,BsnI,Bsp23I,Bsp44II,Bsp137I,Bsp211I,Bsp226I,Bsp881I,Bsp1261I,Bsp1593I,Bsp2013I,Bsp2362I,Bsp2500I,BspANI,BspBDG2I,BspBRI,BspBSE18I,BspBake1I,BspCHE15I,BspGHA1I,BspH106II,BspKI,BspLRI,BspRI,BssCI,BstCI,BstJI,Bsu1076I,Bsu1114I,BsuRI,BteI,ClmI,CltI,Csp2I,DsaII,EsaBC4I,EsaWC1I,FinSI,FnuDI,HhgI,Hpy178VII,HpyF10V,HpyF26II,HpyF29I,HpyF33II,HpyF42I,HpyF46V,HpyF49IV,HpyF53I,HpyF57I,HpyF63I,HpyF69II,HpyF72I,HpyF73III,MchAII,MfoAI,MniI,MnnII,MthTI,NgoAII,NgoCII,NgoNII,NgoPII,NgoSII,NgoTII,NlaI,NspLKI,OchI,PaiI,PalI,Pde133I,PflKI,PhoI,PlaI,Ple214I,PpuI,Pru2I,Psb9879I,Psp29I,SagI,SbvI,SfaI,SplIII,SuaI,SulI,Tsp132I,Tsp266I,Tsp273II,Tsp281I,Tsp560I,TspZNI,TteAI,TtnI,Uba9I,Uba54I,Uba61I,Uba1097I,Uba1140I,Uba1146I,Uba1147I,Uba1150I,Uba1152I,Uba1153I,Uba1155I,Uba1169I,Uba1174I,Uba1175I,Uba1176I,Uba1178I,Uba1179I,Uba1207I,Uba1208I,Uba1209I,Uba1210I,Uba1214I,Uba1223I,Uba1228I,Uba1230I,Uba1231I,Uba1235I,Uba1288I,Uba1292I,Uba1293I,Uba1319I,Uba1322I,Uba1336I,Uba1377I,Uba1388I,Uba1392I,Uba1395I,Uba1408I,Uba1418I,Uba1422I,Uba1429I,Uba1449I,Uba1450I,UbaN2I,UbaN8I,Uth549I,Uth555I,Uth557I,Van91III,VhaI,Vha1168I
<3>GGCC
<4>
<5>Vibrio nigripulchritudo
<6>P. Wood
<7>
<8>Wood, P., Unpublished observations.

<1>VpaK11I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Vibrio parahaemolyticus 1307
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Kotani, H., Mise, K., (1992) Gene, vol. 117, pp. 103-106.

<1>VpaK15I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Vibrio parahaemolyticus Takikawa 13
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Kotani, H., Mise, K., (1992) Gene, vol. 117, pp. 103-106.

<1>VpaK25I
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Vibrio parahaemolyticus 3010-61
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Kotani, H., Mise, K., (1992) Gene, vol. 117, pp. 103-106.

<1>VpaK32I
<2>SapI,BspQI,LguI,PciSI
<3>GCTCTTC(1/4)
<4>
<5>Vibrio parahaemolyticus 4387-61
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Kotani, H., Mise, K., (1992) Gene, vol. 117, pp. 103-106.

<1>VpaK57I
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57AI,VpaKutHI
<3>GGTCTC
<4>
<5>Vibrio parahaemolyticus T4144-1
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Kotani, H., Mise, K., (1992) Gene, vol. 117, pp. 103-106.

<1>VpaK65I
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Vibrio parahaemolyticus AQ3206
<6>T. Shimada
<7>
<8>Miyahara, M., Shimada, T., Kotani, H., Mise, K., (1992) Gene, vol. 117, pp. 103-106.

<1>VpaK3AI
<2>PmaCI,AcvI,BbrPI,BcoAI,Bsp87I,Eco72I,Pgl34I,PmlI,PshCI,PshDI,Psp38I,PspBI,PspCI,VpaK3BI
<3>CACGTG
<4>
<5>Vibrio parahaemolyticus Nakatsugawa
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK4AI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Vibrio parahaemolyticus TVP1622
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK7AI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Vibrio parahaemolyticus TVP1740
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK8AI
<2>
<3>?
<4>
<5>Vibrio parahaemolyticus TVP1764
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK9AI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Vibrio parahaemolyticus Gunji
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK11AI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK13AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>^GGWCC
<4>
<5>Vibrio parahaemolyticus 1743
<6>S. Matsushita
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>VpaK12AI
<2>
<3>?
<4>
<5>Vibrio parahaemolyticus TVP1717
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK13AI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK11BI,VpaK11CI,VpaK11DI
<3>GGWCC
<4>
<5>Vibrio parahaemolyticus 4762
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK19AI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19BI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Vibrio parahaemolyticus Hasegawa
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK29AI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Vibrio parahaemolyticus TVP1706
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK50AI
<2>
<3>?
<4>
<5>Vibrio parahaemolyticus TVP1614
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK55AI
<2>
<3>?
<4>
<5>Vibrio parahaemolyticus TVP1656
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK56AI
<2>
<3>?
<4>
<5>Vibrio parahaemolyticus TVP1744
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK57AI
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaKutHI
<3>GGTCTC
<4>
<5>Vibrio parahaemolyticus 4038
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK3BI
<2>PmaCI,AcvI,BbrPI,BcoAI,Bsp87I,Eco72I,Pgl34I,PmlI,PshCI,PshDI,Psp38I,PspBI,PspCI,VpaK3AI
<3>CACGTG
<4>
<5>Vibrio parahaemolyticus 4750
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK4BI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Vibrio parahaemolyticus TVP1673
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK11BI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11CI,VpaK11DI
<3>G^GWCC
<4>
<5>Vibrio parahaemolyticus 1743-1
<6>S. Matsushita
<7>K
<8>Ueno, H., Kita, A., Miyahara, M., Ishiwata, N., Mise, K., Kato, I., Ishino, Y., (1997) Biosci. Biotechnol. Biochem., vol. 61, pp. 2129-2130.

<1>VpaK12BI
<2>
<3>?
<4>
<5>Vibrio parahaemolyticus TVP1751
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK19BI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaKutAI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Vibrio parahaemolyticus Matsuoka
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK11CI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11DI
<3>GGWCC
<4>
<5>Vibrio parahaemolyticus TVP1728
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaK11DI
<2>AvaII,AflI,Asp697I,Asp745I,AspBII,AspDII,BamNxI,BceSII,BcuAI,Bme18I,Bme216I,BmpI,Bsp71I,Bsp100I,Bsp128I,Bsp132I,Bsp133I,Bsp1260I,BspF53I,BspJ105I,BsrAI,Bst4QI,BthAI,BtiI,CauI,CliI,ClmII,Csp68KI,DsaIV,EagMI,Eco47I,ErpI,FdiI,FspMSI,FssI,GspAI,HgiBI,HgiCII,HgiEI,HgiHIII,HgiJI,Hsp2I,Kzo49I,MfoI,MliI,MspAI,NliII,Nli3877II,NmuAII,NspDII,NspGI,NspHII,NspKI,Pfl19I,PolI,Psp03I,SfnI,Sgh1835I,SinI,SinAI,SinBI,SinCI,SinDI,SinEI,SinFI,SinGI,SinHI,SinJI,SmuEI,SynI,TruI,Tru28I,Tsp301I,Uba48I,Uba62I,Uba1131I,Uba1249I,Uba1272I,Uba1278I,Uba1304I,Uba1314I,Uba1373I,Uba1413I,Uba1438I,Uth554I,VpaK11I,VpaK65I,VpaK7AI,VpaK11AI,VpaK13AI,VpaK11BI,VpaK11CI
<3>GGWCC
<4>
<5>Vibrio parahaemolyticus TVP1681
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaKutAI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutBI,VpaKutJI
<3>GGNCC
<4>
<5>Vibrio parahaemolyticus TVP1659
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaKutBI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutJI
<3>GGNCC
<4>
<5>Vibrio parahaemolyticus TVP1760
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaKutCI
<2>
<3>?
<4>
<5>Vibrio parahaemolyticus TVP1615
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaKutDI
<2>
<3>?
<4>
<5>Vibrio parahaemolyticus TVP1735
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaKutEI
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutFI,VpaO5I
<3>CTCTTC
<4>
<5>Vibrio parahaemolyticus TVP1715
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaKutFI
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaO5I
<3>CTCTTC
<4>
<5>Vibrio parahaemolyticus TVP1731
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaKutGI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Vibrio parahaemolyticus TVP1691
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaKutHI
<2>Eco31I,Bli49I,Bli161I,Bli576II,Bli736I,Bli5508I,BsaI,Bso31I,BspTNI,Cfr56I,Eco42I,Eco51I,Eco95I,Eco97I,Eco101I,Eco120I,Eco127I,Eco129I,Eco155I,Eco156I,Eco157I,Eco162I,Eco185I,Eco191I,Eco203I,Eco204I,Eco205I,Eco217I,Eco225I,Eco233I,Eco239I,Eco240I,Eco241I,Eco246I,Eco247I,Eco263I,EcoA4I,Eco71KI,EcoO44I,PpaI,Rle69I,Sau12I,SlbI,Uba65I,Uba84I,Uba1316I,Uba1343I,VpaK57I,VpaK57AI
<3>GGTCTC
<4>
<5>Vibrio parahaemolyticus TVP1756
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaKutJI
<2>AsuI,AhaB1I,ApuI,AspS9I,AvcI,Bac36I,Bal228I,BavAII,BavBII,Bce22I,Bfi105I,BmgT120I,BpsI,BsaSI,Bse54I,BshKI,BsiZI,Bsp1894I,BspBII,BspF4I,Bsu54I,Bsu5044I,CcuI,CdiAI,CdiCD6I,Cfr4I,Cfr8I,Cfr13I,Cfr23I,Cfr33I,Cfr45I,Cfr46I,Cfr47I,Cfr52I,Cfr54I,CfrNI,Eco39I,Eco47II,Eco196II,Eco201I,FmuI,GseI,Hin5II,HpyF66I,HpyF71II,HpyF73IV,MaeK81II,MhoI,MjaII,Msp24I,MthBI,NlaDII,NmuEII,NmuSI,NspIV,Nsp7121I,NspLII,Pde12I,Pph1579I,Pph1773I,PseI,PspI,PspPI,Sau2I,Sau5I,Sau13I,Sau14I,Sau17I,Sau32I,Sau33I,Sau96I,Sau557I,SauBI,SdyI,SelAI,TdeIII,Uba1099I,Uba1134I,Uba1160I,Uba1164I,UnbI,VchO66I,VchO85I,VchO90I,VpaK15I,VpaK25I,VpaK9AI,VpaK19AI,VpaK19BI,VpaKutAI,VpaKutBI
<3>GGNCC
<4>
<5>Vibrio parahaemolyticus TVP1742
<6>K. Mise
<7>
<8>Miyahara, M., Fujiwara, R., Mise, K., Shimada, T., Matsushita, S., Kudoh, Y., Ishiwata, N., Tanimura, A., (1994) J. Food. Hyg. Sci. Japan, vol. 35, pp. 605-609.

<1>VpaO5I
<2>Ksp632I,Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,CatHI,Eam1104I,EarI,TdeII,Uba1192I,Uba1276I,UbaN7I,VpaKutEI,VpaKutFI
<3>CTCTTC
<4>
<5>Vibrio parahaemolyticus O5
<6>S. Matsushita
<7>
<8>Miyahara, M., Mise, K., Unpublished observations.

<1>VspI
<2>AseI,AsnI,BpoAI,CprJK722I,PbuMZI,PshBI,Srl8DI,Srl55DII,Srl65DI,Srr17I,Sru4DI
<3>AT^TAAT
<4>5(6)
<5>Vibrio species 343
<6>S.K. Degtyarev
<7>FIRV
<8>Degtyarev, S.K., Prikhodko, E.A., Rechkunova, N.I., Prikhodko, G.G., Krasnykh, V.N., (1995) Gene, vol. 157, pp. 65-66.
Degtyarev, S.Kh., Prikhodko, E.A., Prikhodko, G.G., Krasnykh, V.N., (1993) Nucleic Acids Res., vol. 21, pp. 2015.
Degtyarev, S.Kh., Repin, V.E., Rechkunova, N.I., Tchigikov, V.E., Malygin, E.G., Mikhajlov, V.V., Rasskazov, V.A., (1987) Bioorg. Khim., vol. 13, pp. 420-421.

<1>Vsp2246I
<2>HgiCI,AccB1I,BanI,BbvBI,Bme05I,BshNI,BspT107I,Eco50I,Eco64I,Eco168I,Eco169I,Eco171I,Eco173I,Eco195I,Esp1I,Esp6I,Esp9I,Esp10I,Esp11I,Esp12I,Esp13I,Esp14I,Esp15I,Esp21I,Esp22I,Esp25I,HgiHI,MspB4I,PfaAI,Pph14I,SspM1III,Uba1127I
<3>GGYRCC
<4>
<5>Vibrio species 2246
<6>V.E. Repin
<7>
<8>Repin, V.E., Unpublished observations.

<1>M.VvuDam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Vibrio vulnificus CMCP6
<6>J.H. Rhee
<7>
<8>Kehrl, J.H., Patel, K.B., Kahng, L.S., (2008) Gastroenterology, vol. 134.
Rhee, J.H., Kim, S.Y., Chung, S.S., Kim, J.J., Moon, Y.H., Jeong, H., Choy, H.E., Unpublished observations.

<1>XagI
<2>EcoNI,Bpu1268I,BsoEI,BstENI,BstWI,Uba1289I,Uba1290I,Uba1308I,Uba1309I,Uba1310I
<3>CCTNN^NNNAGG
<4>
<5>Xanthobacter agilis Vs 18-132
<6>A. Janulaitis
<7>F
<8>Maneliene, Z., Butkus, V., Unpublished observations.
Vitkute, J., Savelskiene, A., Vonseviciene, E., Kiuduliene, E., Petrusyte, M., Butkus, V., Janulaitis, A., Unpublished observations.

<1>XamI
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XciI
<3>GTCGAC
<4>
<5>Xanthomonas amaranthicola
<6>ATCC 11645
<7>
<8>Arrand, J.R., Myers, P.A., Roberts, R.J., (1978) J. Mol. Biol., vol. 118, pp. 127-135.
Gomez, P., Ribas-Aparicio, R.M., Pelaez, A.I., Gomez, A., Rodicio, M.R., (1997) Biochim. Biophys. Acta, vol. 1351, pp. 261-266.

<1>XapI
<2>ApoI,AcsI,CfaI,FsiI
<3>R^AATTY
<4>
<5>Xanthomonas ampelina Slo51-021
<6>V. Butkus
<7>F
<8>Vitkute, J., Kesminiene, A., Maneliene, Z., Vonseviciene, E., Petrusyte, M., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>XbaI
<2>BspAAII,BspLU11II,BsrXI,Msp23I
<3>T^CTAGA
<4>6(6)
<5>Xanthomonas badrii
<6>ATCC 11672
<7>BCFHIJKMNOQRSUVWXY
<8>Patel, Y., Van Cott, E., Wilson, G.G., McClelland, M., (1990) Nucleic Acids Res., vol. 18, pp. 1603-1607.
Zain, B.S., Roberts, R.J., (1977) J. Mol. Biol., vol. 115, pp. 249-255.

<1>XcaI
<2>SnaI,BspM90I,BssNAI,Bst1107I,BstBSI,BstZ17I,VchO25I
<3>GTA^TAC
<4>
<5>Xanthomonas campestris
<6>NEB 420
<7>
<8>Morgan, R., Ellard, J., Unpublished observations.

<1>XceI
<2>NspI,AvoI,BstNSI,Lsp1270I,NspHI,PauAI,PunAII
<3>RCATG^Y
<4>
<5>Xanthomonas campestris Ast 40-024
<6>V. Butkus
<7>F
<8>Petrusyte, M., Vaitkevicius, D., Maneliene, Z., Capskaja, L., Kiuduliene, E., Butkus, V., Janulaitis, A., Unpublished observations.

<1>XciI
<2>SalI,Acs1371I,Acs1372I,Acs1373I,Acs1421I,Acs1422I,BspMKI,BstZ16I,BtgAI,CglAII,HgiCIII,HgiDII,KoyI,NopI,Psp32I,Psp33I,Psp89I,RflFI,RheI,RhpI,RrhI,Rrh4273I,RroI,RtrI,Rtr63I,Uba89I,XamI
<3>G^TCGAC
<4>
<5>Xanthomonas citrii
<6>IFO 3835
<7>
<8>Whang, Y., Chae, K.S., Jang, W.H., Kim, K.T., Yoo, O.J., (1986) Korean J. Microbiol., vol. 24, pp. 406-410.

<1>XcmI
<2>
<3>CCANNNNN^NNNNTGG
<4>3(6)
<5>Xanthomonas campestris
<6>NEB 497
<7>N
<8>Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Nwankwo, D., Unpublished observations.
Polisson, C., Morgan, R., Unpublished observations.
Shaw, P.C., Mok, Y.K., (1993) Gene, vol. 133, pp. 85-89.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>XcyI
<2>SmaI,AhyI,Cfr9I,CfrJ4I,EaeAI,EclRI,KteAI,Pac25I,PaeBI,PspAI,PspALI,TspMI,Uba1220I,Uba1393I,XmaI,XmaCI
<3>C^CCGGG
<4>2(4)
<5>Xanthomonas cyanopsidis 13D5
<6>C.I. Kado
<7>
<8>Froman, B.E., Tait, R.C., Kado, C.I., Rodriguez, R.L., (1984) Gene, vol. 28, pp. 331-335.
Withers, B.E., Ambroso, L.A., Dunbar, J.C., (1992) Nucleic Acids Res., vol. 20, pp. 6267-6273.

<1>Xgl3216I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Xanthomonas glycinae 3216
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>Xgl3217I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Xanthomonas glycinae 3217
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>Xgl3218I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Xanthomonas glycinae 3218
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>Xgl3219I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3220I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Xanthomonas glycinae 3219
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>Xgl3220I
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,XmlI,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Xanthomonas glycinae 3220
<6>U. Mayr
<7>
<8>Kaluza, K., Schmitz, G., Jarsch, M., Herz, G., Wagner, C., Veseley, Z., Berger, G., Kessler, C., Unpublished observations.

<1>XhoI
<2>AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I,XpaI
<3>C^TCGAG
<4>5(6)
<5>Xanthomonas holcicola
<6>ATCC 13461
<7>BFHJKMNOQRSUWXY
<8>Anton, B.P., Benner, J.S., Moran, L.S., Morita, M., Sugino, Y., Brooks, J.E., Unpublished observations.
Gingeras, T.R., Myers, P.A., Olson, J.A., Hanberg, F.A., Roberts, R.J., (1978) J. Mol. Biol., vol. 118, pp. 113-122.
Morita, M., Sugino, Y., Unpublished observations.
Stickel, S.K., Roberts, R.J., Unpublished observations.

<1>XhoII
<2>AitII,AitAI,Asp17I,Asp22I,Asp1HI,Asp6HI,Asp8HI,Asp14HI,Asp21HI,BloHI,BpuGI,BscSI,BstX2I,BstYI,DsaIII,MflI,PsuI,Tru201I,Uba1432I
<3>R^GATCY
<4>5(4)
<5>Xanthomonas holcicola
<6>ATCC 13461
<7>RW
<8>Anton, B.P., Brooks, J.E., Unpublished observations.
Gingeras, T.R., Roberts, R.J., Unpublished observations.
Kramarov, V.M., Mazanov, A.L., Smolyaninov, V.V., (1982) Bioorg. Khim., vol. 8, pp. 220-223.
Morgan, R.D., Roberts, R.J., International Patent Office, 2007.
Olson, J.A., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>M.XlaDnmt1
<2>
<3>?
<4>?(5)
<5>Xenopus laevis
<6>S. Tajima
<7>
<8>Kimura, H., Ishihara, G., Tajima, S., (1996) J. Biochem. (Tokyo), vol. 120, pp. 1182-1189.
Stancheva, I., Meehan, R.R., (2000) Genes Dev., vol. 14, pp. 313-327.

<1>XmaI
<2>SmaI,AhyI,Cfr9I,CfrJ4I,EaeAI,EclRI,KteAI,Pac25I,PaeBI,PspAI,PspALI,TspMI,Uba1220I,Uba1393I,XcyI,XmaCI
<3>C^CCGGG
<4>?(4)
<5>Xanthomonas malvacearum
<6>ATCC 9924
<7>INRUV
<8>Endow, S.A., Roberts, R.J., (1977) J. Mol. Biol., vol. 112, pp. 521-529.
Lunnen, K.D., Wilson, G.G., European Patent Office, 1998.
Lunnen, K.D., Wilson, G.G., US Patent Office, 1991.

<1>XmaII
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Xanthomonas malvacearum
<6>ATCC 9924
<7>
<8>Endow, S.A., Roberts, R.J., (1977) J. Mol. Biol., vol. 112, pp. 521-529.

<1>XmaIII
<2>AaaI,BseX3I,BsoDI,BstZI,EagI,EclXI,Eco52I,SenPT16I,TauII,Tsp504I
<3>C^GGCCG
<4>4(5)
<5>Xanthomonas malvacearum
<6>ATCC 9924
<7>
<8>Kunkel, L.M., Silberklang, M., McCarthy, B.J., (1979) J. Mol. Biol., vol. 132, pp. 133-139.
Trautner, T.A., Unpublished observations.

<1>XmaCI
<2>SmaI,AhyI,Cfr9I,CfrJ4I,EaeAI,EclRI,KteAI,Pac25I,PaeBI,PspAI,PspALI,TspMI,Uba1220I,Uba1393I,XcyI,XmaI
<3>C^CCGGG
<4>
<5>Xanthomonas malvacearum strain C
<6>M.M. Wijdenbosch
<7>M
<8>Rahman, H., Affram, C., Unpublished observations.

<1>XmaJI
<2>AvrII,AspA2I,AvrBII,BlnI,BspA2I
<3>C^CTAGG
<4>
<5>Xanthomonas maltophilia Jo 85-025
<6>V. Butkus
<7>F
<8>Kazlauskiene, R., Petrusyte, M., Maneliene, Z., Trinkunaite, L., Kiuduliene, L., Butkus, V., Janulaitis, A., Unpublished observations.

<1>M.XmaXhDnmt1
<2>
<3>?
<4>?(5)
<5>Xiphophorus maculatus x X. helleri
<6>J. Altschmied
<7>
<8>Altschmied, J., Volff, J., Winkler, C., Gutbrod, H., Korting, C., Pagany, M., Schartl, M., (2000) Gene, vol. 249, pp. 75-82.

<1>XmiI
<2>AccI,DsaVI,FblI,OmiBII
<3>GT^MKAC
<4>
<5>Xanthomonas maltophilia Jo21-021
<6>V. Butkus
<7>F
<8>Jurgelyte, R., Lazareviciute, L., Maneliene, Z., Trinkunaite, L., Kiuduliene, E., Butkus, V., Janulaitis, A., Unpublished observations.

<1>XmlI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlAI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Xanthomonas maltophilia
<6>NEB 517
<7>
<8>Croft, R., Unpublished observations.

<1>XmlAI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XniI,XorII,XorKI
<3>CGATCG
<4>
<5>Xanthomonas maltophilia
<6>NEB 529
<7>
<8>Croft, R., Unpublished observations.

<1>XmnI
<2>Asp700I,BbvAI,MroXI,PdmI,Psc2I,SynII
<3>GAANN^NNTTC
<4>
<5>Xanthomonas manihotis 7AS1
<6>ATCC 49764
<7>NRUW
<8>Lin, B.-C., Chien, M.-C., Lou, S.-Y., (1980) Nucleic Acids Res., vol. 8, pp. 6189-6198.
Nwankwo, D.O., Lynch, J.J., Moran, L.S., Fomenkov, A., Slatko, B.E., (1996) Gene, vol. 173, pp. 121-127.
Qiang, B.-Q., Schildkraut, I., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>XniI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XorII,XorKI
<3>CGATCG
<4>
<5>Xanthomonas nigromaculans
<6>ATCC 23390
<7>
<8>Hanberg, F., Myers, P.A., Roberts, R.J., Unpublished observations.

<1>XorI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Xanthomonas oryzae
<6>M. Ehrlich
<7>
<8>Wang, R.Y.-H., Shedlarski, J.G., Farber, M.B., Kuebbing, D., Ehrlich, M., (1980) Biochim. Biophys. Acta, vol. 606, pp. 371-385.

<1>XorII
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorKI
<3>CGAT^CG
<4>?(5)
<5>Xanthomonas oryzae
<6>M. Ehrlich
<7>
<8>Choi, S.-H., (1994) Diss. Abstr., vol. 54, pp. 5462B-5463B.
Choi, S.H., Leach, J.E., (1994) Mol. Gen. Genet., vol. 244, pp. 383-390.
Gingeras, T.R., Greenough, L., Schildkraut, I., Roberts, R.J., (1981) Nucleic Acids Res., vol. 9, pp. 4525-4536.
Wang, R.Y.-H., Shedlarski, J.G., Farber, M.B., Kuebbing, D., Ehrlich, M., (1980) Biochim. Biophys. Acta, vol. 606, pp. 371-385.

<1>XorKI
<2>PvuI,Afa22MI,Afa16RI,BmaI,BmaAI,BmaBI,BmaCI,BmaDI,BpvUI,BspCI,BstZ8I,Cas2I,Cfr51I,DrdIII,EagBI,EclJI,ErhB9I,Kpl79I,MvrI,NblI,Ple19I,PntI,Psu161I,Pvu84I,RshI,RspI,SmaAIII,SpaPII,SplAIII,Uba1129I,Uba1139I,Xgl3216I,Xgl3217I,Xgl3218I,Xgl3219I,Xgl3220I,XmlI,XmlAI,XniI,XorII
<3>CGATCG
<4>?(5)
<5>Xanthomonas oryzae pv. oryzae KACC10331
<6>B.M. Lee
<7>
<8>Lee, B.M., Park, Y.J., Park, D.S., Kang, H.W., Kim, J.G., Song, E.S., Park, I.C., Yoon, U.H., Hahn, J.H., Koo, B.S., Lee, G.B., Kim, H., Park, H.S., Yoon, K.O., Kim, J.H., Jung, C.H., Koh, N.H., Seo, J.S., Go, S.J., (2005) Nucleic Acids Res., vol. 33, pp. 577-586.

<1>XorKII
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Xanthomonas oryzae pv. oryzae KACC10331
<6>B.M. Lee
<7>
<8>Lee, B.M., Park, Y.J., Park, D.S., Kang, H.W., Kim, J.G., Song, E.S., Park, I.C., Yoon, U.H., Hahn, J.H., Koo, B.S., Lee, G.B., Kim, H., Park, H.S., Yoon, K.O., Kim, J.H., Jung, C.H., Koh, N.H., Seo, J.S., Go, S.J., (2005) Nucleic Acids Res., vol. 33, pp. 577-586.
Moon, W.J., Cho, J.-Y., Chae, Y.K., (2008) Protein Expr. Purif., vol. 62, pp. 230-234.

<1>XpaI
<2>XhoI,AbrI,AerAI,AhyAI,AlwFII,Asp15I,Asp47I,Asp703I,BadI,BbfI,BbiIII,BluI,Bsp92I,Bsp129I,Bsp139I,Bsp140I,Bsp141I,Bsp142I,BspAAI,BssHI,BstHI,BstLI,BstVI,BsuMI,BthI,CcrI,CjaI,DdeII,DrdDI,Eae2I,EscI,MavI,McaI,MecI,MhaI,MlaAI,MpuI,MrhI,MscAI,MsiI,Msp23II,OcoI,PaeR7I,PanI,Pfl67I,PflNI,PflWI,Psp4I,PspNI,Sal1974I,Sau3239I,SauLPII,Sbi68I,Sca1827I,SciI,Sci1831I,SciBI,ScuI,SdiAI,SexI,Sfr274I,Sfu1762I,SgaI,SgoI,Sgr1841I,Shy1766I,SlaI,SluI,Sol10179I,SpaI,Sph1719I,SrifpI,Ssp4I,StaAI,StrI,Sve194I,TliI,Uba1130I,Uba1148I,Uba1154I,Uba1166I,Uba1237I,Uba1248I,Uba1271I,Uba1298I,Uba1335I,Uba1397I,Uba1448I
<3>C^TCGAG
<4>
<5>Xanthomonas papavericola
<6>ATCC 14180
<7>
<8>Gingeras, T.R., Myers, P.A., Olson, J.A., Hanberg, F.A., Roberts, R.J., (1978) J. Mol. Biol., vol. 118, pp. 113-122.

<1>XphI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XveI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Xanthomonas phaseoli
<6>Z.F. Bunina
<7>
<8>Bunina, Z.F., Kramarov, V.M., Smolyaninov, V.V., Tolstova, L.A., (1984) Bioorg. Khim., vol. 10, pp. 1333-1335.
Lai, J.Y., Yang, M.T., Unpublished observations.

<1>XspI
<2>MaeI,BfaI,FgoI,FisI,FspBI,MjaI,MthFI,MthZI,RmaI,Rma485I,Rma486I,Rma490I,Rma495I,Rma496I,Rma497I,Rma500I,Rma501I,Rma503I,Rma506I,Rma509I,Rma510I,Rma515I,Rma516I,Rma517I,Rma518I,Rma519I,Rma522I,UbaN5I
<3>C^TAG
<4>
<5>Xanthomonas species YK1
<6>Y.M. Kim
<7>K
<8>Song, T., Kang, B.S., Kim, Y.M., (1998) Mol. Cells, vol. 8, pp. 370-373.

<1>XveI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,YenI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Xanthomonas campestris pv. vesicatoria
<6>Y.-J. Yu
<7>
<8>Yu, Y.-J., Yang, M.-T., Unpublished observations.

<1>YenI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenAI,YenBI,YenCI,YenDI,YenEI
<3>CTGCA^G
<4>
<5>Yersinia enterocolitica 08 A2635
<6>H. Watanabe
<7>
<8>Kinder, S.A., Badger, J.L., Bryant, G.O., Pepe, J.C., Miller, V.L., (1993) Gene, vol. 136, pp. 271-275.
Miyahara, M., Maruyama, T., Wake, A., Mise, K., (1988) Appl. Environ. Microbiol., vol. 54, pp. 577-580.

<1>YenAI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenBI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Yersinia enterocolitica O8 WA
<6>T. Maruyama
<7>
<8>Miyahara, M., Maruyama, T., Wake, A., Mise, K., (1988) Appl. Environ. Microbiol., vol. 54, pp. 577-580.

<1>YenBI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenCI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Yersinia enterocolitica 08 Bi1212
<6>T. Maruyama
<7>
<8>Miyahara, M., Maruyama, T., Wake, A., Mise, K., (1988) Appl. Environ. Microbiol., vol. 54, pp. 577-580.

<1>YenCI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenDI,YenEI
<3>CTGCAG
<4>
<5>Yersinia enterocolitica 08 Bi3995
<6>T. Maruyama
<7>
<8>Miyahara, M., Maruyama, T., Wake, A., Mise, K., (1988) Appl. Environ. Microbiol., vol. 54, pp. 577-580.

<1>YenDI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenEI
<3>CTGCAG
<4>
<5>Yersinia enterocolitica 08 Bi9534
<6>T. Maruyama
<7>
<8>Miyahara, M., Maruyama, T., Wake, A., Mise, K., (1988) Appl. Environ. Microbiol., vol. 54, pp. 577-580.

<1>YenEI
<2>PstI,AinI,AjoI,Ali2882I,AliAJI,ApiI,Asp36I,Asp708I,Asp713I,AspTI,BbiI,Bce170I,BloHII,BloHIII,BmeBI,BsaNII,BsaQI,BscDI,Bsp17I,Bsp43I,Bsp63I,Bsp78I,Bsp81I,Bsp93I,Bsp107I,Bsp108I,Bsp268I,BspBI,BspMAI,BspS122I,BsuBI,Bth9411I,CauIII,CflI,CfrA4I,CfuII,ClcI,CstI,EaePI,Ecl77I,Ecl133I,Ecl593I,Ecl37kI,Ecl699kI,Ecl1zI,Ecl2zI,Eco48I,Eco49I,Eco83I,Eco161I,Eco167I,Eco260I,Eco261I,Esp5II,Esp141I,GseII,HalII,Kpn12I,MauI,MhaAI,MizI,MkrI,MmaI,Msp11I,NasI,NgbI,NocI,Pae8I,Pae9I,Pae14I,Pae15I,Pae22I,Pae24I,Pae25I,Pae26I,Pae39I,Pae40I,Pae41I,PaePI,Pfl21I,Pfl37I,PmaI,Pma44I,PmyI,Pph2059I,Pph2066I,PshEI,Psp23I,Psp28I,Psp46I,PspSI,Sag16I,Sag23I,Sal13I,SalPI,ScoAI,SflI,SgiI,SkaII,SprLI,SriI,Srl1DI,Srl2DI,Srl5DI,Srl32DI,Ssp12I,Sst12I,TspGWII,Uba46I,Uba71I,Uba72I,Uba1112I,Uba1115I,Uba1116I,Uba1119I,Uba1123I,Uba1149I,Uba1184I,Uba1186I,Uba1211I,Uba1212I,Uba1213I,Uba1215I,Uba1216I,Uba1225I,Uba1232I,Uba1256I,Uba1262I,Uba1287I,Uba1294II,Uba1296I,Uba1328I,Uba1337I,Uba1399I,Uba1411I,Uba1417I,UbaHKBI,VchO87I,VpaK4AI,VpaK29AI,VpaK4BI,VpaKutGI,XmaII,XorI,XorKII,XphI,XveI,YenI,YenAI,YenBI,YenCI,YenDI
<3>CTGCAG
<4>
<5>Yersinia enterocolitica 08 85-775
<6>T. Maruyama
<7>
<8>Miyahara, M., Maruyama, T., Wake, A., Mise, K., (1988) Appl. Environ. Microbiol., vol. 54, pp. 577-580.

<1>M.YpsADam
<2>MboI,Asi256I,AspMDI,AsuMBI,Bce243I,Bfi57I,BfiSHI,BfuCI,Bme12I,Bme2494I,BsaPI,BscFI,BsmXII,BspI,Bsp9I,Bsp18I,Bsp49I,Bsp51I,Bsp52I,Bsp54I,Bsp57I,Bsp58I,Bsp59I,Bsp60I,Bsp61I,Bsp64I,Bsp65I,Bsp66I,Bsp67I,Bsp72I,Bsp74I,Bsp76I,Bsp91I,Bsp105I,Bsp122I,Bsp135I,Bsp136I,Bsp138I,Bsp143I,Bsp147I,Bsp2095I,BspAI,BspFI,BspJI,BspJ64I,BspKMI,BspKT6I,BsrMI,BsrPII,BssGII,BssMI,Bst19II,Bst1274I,BstEIII,BstENII,BstKTI,BstMBI,BstXII,BtcI,Bth84I,Bth211I,Bth213I,Bth221I,Bth945I,Bth1140I,Bth1141I,Bth1786I,Bth1997I,BthCanI,BtkII,Btu33I,Btu34I,Btu36I,Btu37I,Btu39I,Btu41I,CacI,CcoP31I,CcoP76I,CcoP84I,CcoP95II,CcoP219I,CcyI,CdiCD6II,ChaI,Cin1467I,CjeP338I,CpaPI,CpfI,CpfAI,Csp5I,Cte1179I,Cte1180I,CtyI,CviAI,CviHI,DpnII,EsaLHCI,FnuAII,FnuCI,FnuEI,Gst1588II,HacI,HpyAIII,HpyHPK5II,Kzo9I,LlaAI,LlaDCHI,LlaKR2I,Lsp1109II,Mel3JI,Mel5JI,Mel7JI,Mel4OI,Mel5OI,Mel2TI,Mel5TI,MeuI,MgoI,MjaIII,MkrAI,MmeII,Mmu5I,MmuP2I,MnoIII,MosI,Msp67II,MspBI,MthI,Mth1047I,MthAI,NciAI,NdeII,NflI,NflAII,NflBI,NlaII,NlaDI,NmeCI,NphI,NsiAI,NspAI,NsuI,PbrTI,Pei9403I,PfaI,Pph288I,RalF40I,Rlu1I,SalAI,SalHI,Sau15I,Sau6782I,Sau3AI,SauCI,SauDI,SauEI,SauFI,SauGI,SauMI,SinMI,SmiMBI,SsiAI,SsiBI,Ssu211I,Ssu212I,Ssu220I,R1.Ssu2479I,R2.Ssu2479I,R1.Ssu4109I,R2.Ssu4109I,R1.Ssu4961I,R2.Ssu4961I,R1.Ssu8074I,R2.Ssu8074I,R1.Ssu11318I,R2.Ssu11318I,R1.SsuDAT1I,R2.SsuDAT1I,SsuRBI,Sth368I,TrsKTI,TrsSI,TrsTI,TruII,Tsp133I,Uba4I,Uba59I,Uba1101I,Uba1177I,Uba1182I,Uba1183I,Uba1204I,Uba1259I,Uba1317I,Uba1323I,Uba1366I,UbaN1I,Vha44I
<3>GATC
<4>
<5>Yersinia pseudotuberculosis IP32953
<6>F.W. Larimer
<7>
<8>Chain, P.S.G. et al., (2004) Proc. Natl. Acad. Sci. U. S. A., vol. 101, pp. 13826-13831.
Robinson, V.L., Oyston, P.C., Titball, R.W., International Patent Office, 2005.
Taylor, V.L., Titball, R.W., Oyston, P.C.F., (2005) Microbiology, vol. 151, pp. 1919-1926.

<1>ZanI
<2>EcoRII,Acc38I,AcuII,AeuI,AglI,AjnI,AorI,ApaORI,ApyI,Asp2HI,AtuII,Atu1I,AtuBI,BciBII,BinSI,Bme2095I,BptI,BsaNI,Bse16I,Bse17I,Bse24I,BseBI,BshGI,BsiLI,BsiUI,BsiVI,BsoGI,Bsp44I,Bsp56I,Bsp103I,Bsp317I,BspH43I,BspNI,BspSI,Bst1I,Bst2I,Bst38I,Bst100I,BstGII,BstM6I,BstNI,BstOI,Bst7QII,Bst2UI,BthDI,BthEI,CbrI,Cdi27I,Cfr5I,Cfr11I,Cfr20I,Cfr22I,Cfr24I,Cfr25I,Cfr27I,Cfr28I,Cfr29I,Cfr30I,Cfr31I,Cfr35I,Cfr58I,CfrS37I,CthII,EagKI,EcaII,EclII,Ecl66I,Ecl136I,Ecl137II,EclS39I,Ecl37kII,Ecl54kI,Ecl57kI,Ecl1zII,Eco38I,Eco40I,Eco41I,Eco60I,Eco61I,Eco67I,Eco70I,Eco71I,Eco128I,Eco170I,Eco193I,Eco206I,Eco207I,Eco254I,Eco256I,Ese6II,Esp2I,Esp24I,EspHK7I,EspHK22I,EspHK30I,Fsp1604I,HhdI,Kox165I,Kpn10I,Kpn13I,Kpn14I,Kpn16I,KspHK12I,KspHK14I,Lla497I,Mlu2300I,MphI,MpsI,MvaI,Pca17AI,Psp6I,Psp39I,PspGI,Sau16I,Scg2I,SflHK1794I,SflHK2374I,SflHK2731I,SflHK6873I,SflHK7234I,SflHK7462I,SflHK8401I,SflHK10790I,Sfl2aI,Sfl2bI,Sgr20I,SleI,SniI,SslI,SspAI,Sth117I,Sth302I,Sth455I,TaqXI,TspAI,Uba11I,Uba13I,Uba20I,Uba81I,Uba82I,Uba1114I,Uba1118I,Uba1120I,Uba1121I,Uba1125I,Uba1171I,Uba1181I,Uba1185I,Uba1189I,Uba1193I,Uba1218I,Uba1243I,Uba1410I,Uba1428I
<3>CC^WGG
<4>
<5>Zymomonas anaerobia
<6>O.J. Yoo
<7>
<8>Sun, D.K., Yoo, O.J., (1988) Korean Biochem. J., vol. 21, pp. 419-422.

<1>ZhoI
<2>ClaI,AagI,Apu16I,Asp14I,Asp37I,Asp86I,Asp123I,Asp130I,Asp707I,BanIII,BavCI,BazI,BbvAII,Bci29I,BciBI,BcmI,Bco79I,BdiI,BfrAI,Bli41I,Bli86I,Bli576I,Bli585I,BliAI,BliRI,Bsa29I,BscI,BscVI,BseCI,Bsh108AI,BshVI,BsiXI,Bsp2I,Bsp4I,Bsp84I,Bsp106I,Bsp125I,Bsp126I,Bsp127I,Bsp145I,BspDI,BspJII,BspOVII,BspXI,BspZEI,BsrCI,Bst28I,BstLVI,BstNZ169I,Bsu15I,BsuTUI,Bth1202I,Bth9415I,BtuI,Csp4I,LcaI,LplI,PgaI,Rme21I,SpmI,Ssp27144I,Uba22I,Uba24I,Uba30I,Uba34I,Uba43I,Uba1096I,Uba1100I,Uba1133I,Uba1137I,Uba1138I,Uba1144I,Uba1145I,Uba1161I,Uba1168I,Uba1195I,Uba1196I,Uba1197I,Uba1198I,Uba1199I,Uba1200I,Uba1233I,Uba1238I,Uba1246I,Uba1257I,Uba1275I,Uba1286I,Uba1295I,Uba1315I,Uba1342I,Uba1366II,Uba1379I,Uba1380I,Uba1394I,Uba1412I,Uba1416I,Uba1427I,Uba1430I,Uba1451I,Uba1453I
<3>AT^CGAT
<4>
<5>Zymomonas holcicola
<6>M.M. Wijdenbosch
<7>
<8>Waaijer, R.J.A., Unpublished observations.

<1>M.ZmaIIA
<2>
<3>?
<4>?(5)
<5>Zea mays
<6>R.L. Phillips
<7>
<8>Kaeppler, S.M., Springer, N.M., Muszynski, M.G., International Patent Office, 2000.
Walbot, V., Unpublished observations.

<1>M.ZmaV
<2>
<3>?
<4>?(5)
<5>Zea mays
<6>R.L. Phillips
<7>
<8>Chandler, V.L., Cone, K.C., Kaeppler, H.F., Kaeppler, S.M., Unpublished observations.
Kaeppler, S.M., Springer, N.M., Muszynski, M.G., International Patent Office, 2000.

<1>M.ZmaDRM1
<2>
<3>?
<4>?(5)
<5>Zea mays
<6>R.L. Phillips
<7>
<8>Cao, X., Springer, N.M., Muszynski, M.G., Phillips, R.L., Kaeppler, S., Jacobsen, S.E., (2000) Proc. Natl. Acad. Sci. U. S. A., vol. 97, pp. 4979-4984.

<1>M.ZmaDnmt1
<2>
<3>?
<4>?(5)
<5>Zea mays
<6>R.L. Phillips
<7>
<8>Chandler, V.L., Cone, K.C., Kaeppler, H.F., Kaeppler, S.M., Unpublished observations.
Olhoft, P.M., (1999) Diss. Abstr., vol. 59, pp. 4638.
Steward, N., Kusano, T., Sano, H., (2000) Nucleic Acids Res., vol. 28, pp. 3250-3259.

<1>ZraI
<2>AatII,AspJI,Ppu1253I,Ssp5230I
<3>GAC^GTC
<4>
<5>Zoogloea ramigera 11
<6>NEB 1785
<7>INV
<8>Dedkov, V.S., Sinichkina, S.A., Popichenko, D.V., Degtyarev, S.Kh., (2001) Biotekhnologiya, vol. 6, pp. 3-7.
Wei, H., Unpublished observations.
Zhu, Z., Roberts, R.J., Unpublished observations.

<1>ZrmI
<2>ScaI,Acc113I,AflIV,Asp763I,AssI,BmcAI,Bpa34I,BshHI,BsoSI,BstMI,DpaI,Eco255I,LlaDI,NmeSI,PinI,RflFII,Uba1094I,Uba1158I,VchO49I
<3>AGT^ACT
<4>
<5>Zoogloea ramigera SCA
<6>S.K. Degtyarev
<7>I
<8>Nadeev, A.N., Kileva, E.V., Popichenko, D.V., Dedkov, V.S., Degtyarev, S.K., Unpublished observations.

<1>Zsp2I
<2>AvaIII,Asi372I,BfrBI,BfrCI,Csp68KIII,EcoT22I,Mph1103I,NsiI,PinBI,Ppu10I,PxyJKI,SepI,SmuCI,SrlII,SspD5II,Uba1353I,Uba1367I,Uba1384I
<3>ATGCA^T
<4>
<5>Zoogloea species 2
<6>S.K. Degtyarev
<7>IV
<8>Degtyarev, S.K., Unpublished observations.

BioPerl-1.007002/t/data/worm_fam_2785.cdna000444000766000024      1037713155576322 20044 0ustar00cjfieldsstaff000000000000>CBG10100
ATGGCGAGTGATATGAGGCACACATCAAGCAACACAAGAAGGCCAAGTATGGGTTCAAAC
TCCAAATTACTAGCTGGAAAATCCTTTCTCCTAGATATTGGAAATCGACAATGGCGGACA
AAGGTAGCTGAACGAATTCTGAATTACGGAGCGAACATTATGGATTCGTTCGGAGAAGTA
GACCCGCATGCTGTTGTCTCTGATAATCCGATGGCATTGAAGTTCGAGAAAAAGGATGGC
AGTCAACATTTTAATGAAAAAATCAGAACTCCCCAGAGTTTCCTAAAACAAATGGATGCC
TTCGCCAATAAAAAAGGGAATACCACATCGGCAACAACTTCACTCAGTACCATTCGACCA
CGGACTGATCTCAAAGCCACTAAAGATACCCTGACAAGAACTGAGACACCCGTTGTGCCT
CAACGATCCTCAAAGTCCCGTCAATCTTCTGTTCCGAGAACTGCTAAAGTATTTGTGCGA
GTCGAAGCTCCTACTAAACGACCAGAGATTCGGTGTATACCCAGAACAGCATATGATACT
CTGTACGGCGGTAGTGATACGGGTCATTCAGTATTCAGAATCGCAGAAACGGCATTGAAA
GAGAGAAGAGTTCGAGAGTATGATCTATTCGTGAAGGGTCGATACGAGCCACATAAGAAA
CCTTTCAAAATGGATGAGAAGGATAAATTTTGTCAGTTTTGCGAGAAAGAATACAGTGGA
GAGAGGAAAGATCACGAAAGAACCGACGAGCATCGAGCCAAAGCCAGAACTCGAGGCCTC
CTTCCAGCACTTGAAAGAGGAATTTTGAGCGCTCGACTGAAATTGAAGAATAGCCAAAAT
CAGGTGATGATGGTGGCGAAACGAAAACTGGATGACAACGCCTTTCAAGAACAATCGAAA
AGAGCACGCGTCGAGTTTGAGTACGGTGAAAATATGGTGAAGGCAGATTGGCAAAGTTTG
AAAGAGAACAATTTAACAACAGTGATTCCCGAGAAAATTCTGAAAGTGTCGCCCGGAAAA
GGCTCTGTCCTCTCGCCACGACGTCGTCAGCAACGAATTCAACCTCGCACAAGCCAAGGA
GACTTGATTTGA
>F22B7.13
atggacgtctcttattacgatggtcccaaggatgaagtcgccgaagcaatgctgaaaagc
gcggtgacggccatgagattgggacaatacgaggatggaaaaggacgcttagaggagata
atggagttcggaacctcaaattttcaactacttggtacaatctacatgtattacggaaga
gtgtgcaggcatttgaaccatgatgccaaggccttggagtttttcgaacatgagttgaac
atgttcaaattgatcttcaactacccagaagcatgtgattccacacgtcgcatcgtcgag
caggcactcaaaatgggaaagttccccaaggctcgacggtttgctgaggatctcattgat
tacaccagcaataagaagaacggagagaagtatatcggtcaagctcgaattttgttcgct
tccgtgtgcctcgaaggatgtgaaagagacgtcgagagtaatcaagatgagaagaagaag
cttttgtcaatatgtgctgaacagattgcagccgtgaaattgttcaacgagaataatacg
gaaggagctgtgtctgagaccaaaatcatgttacttgaggcgaaatgcttgtcactagac
gaaaaatacgaggaatcgcgtcgcaagtatcaagaatgcatcgattttgccatcaaaaca
gaccagtttgaagcagttcacatcgcctattacgacaaggctctatatgctgagacagat
cttcttttctttattatcagagatctcagaagtgctctcttctacgccacgaaattcgga
aaagagcgagatgtagtcaaatataagtcgaagctatccgaagagatgctgagaaatggc
gaattccacgaagcatatctctacggattggaagcgcttgtatcgattcggaagcttgga
ttgaacgaatacattggagatgtgttgcttacaatcgcaaagtgcctcattgcacttgga
aaaagacgccaagctgcttattttatcatcttggggagtgttctgaccatcaaccaaaac
agtttcaaactgttctacgagcagatcgacgtggcgatgaatcaagagagaagcgaaacg
gcaactgatcaagatgtatgcctcgcaattgattcgtctcctgatccgacatcctcgaat
gacatgattaataagttcgtcgtcgaactggagcacgcaacaaatgtggaaacctgggaa
atgattgtcaacggaatcattgacgaccagaagaaaccagtggcgatcgaaaagaaagag
aacgaggaacccgtagacatgatggatctcattttcagtatgagctcacgtatggatgat
caaagaactgaactgcctgctgccagattcattccgcctcgtccagtgtcatcggcatcg
aaaaagactacaaagagtcacagaatcctccctggactccgtgccaattggacaaaagtg
cagtcgatgaagttcgatggtcacacaatgaataggatcctgaagaggtcgaagaaaagc
aaatcgtcattggattctacaaattcgatgcagggcgatgatactcgaagcgatgatgtg
acaatgacgtccaaatag
>C38C10.4
atggacgtctcttattatgatggccctaaggatgaagtcatcgaagcaatgctgaaaagc
gcggtgacggccatgaaattgggacaatacgaggatggaaaaggacgcttagaggacaca
atggagttcggaacctccaattttcaactgcttggtacaatctacatgtattacggaaga
gtgtgcaggcatttgaaccacgacgccaaggccttggagtttttcgaacatgagttgaac
atgttcaaattgatcttcaactacccagaagcatgtgattccacacgtcgcatcgtccag
caggcactcaaaatggaaaagttctccaaggctcgacggtttgctgaggatctcattgat
tacaccagcaataagaagaacggagagaagtatatcggtcaagctcgaattttgttcgct
tccgtgtgcctcgaaggatgtgaaagagacgtcgagagtaatcaagatgagaagaagaag
cttttgtcaatatgtgctgaacagattgcagccgtgaaattgttcaacgagaataatacg
gaaggagctgtgtctgagaccaaaattatgctaattgaggcgaaatgcttgtcactcgac
gaaaaatacgaggaatcgcgtcgcaagtatcaagaatgcatcgattttgccatcaaaaca
gaccagtttgaagcagttcacatcgcctattacgacaaggctctctatgctgagacatat
cttcttttctttattatcagagatctcagaagtgctctcttctacgccacgaaattcgga
aaagagcgagatgtagtcaaatataagtcgaagctatccgaagagatgctgagaaatggc
gaattccacgaagcatatctctacggattggaagcgcttgtatcgattcggaagcttgga
ttgaacgaacacattggagatgtgttgcttacaatcgcaaagtgtctcattgcacttgga
aaaagacgccaagctgcttattttatcatcttggggagtgttctgaccatcaaccaaagc
agtttcaaactgttctacgagcagatcgacgtggcgatgaatcaagagagaagcgaaacg
gcaactgatcaagatgcatgcctcgcaattgattcgtctcctgatccgacatcctcgaat
gacatgattaataagttcgtcgtcaaactggagcacgcaacaaatgttgaaacctgggaa
atgattgtcaacggaatcattgaagaccagaagaaaccagtagcgatcgaaaagaaagag
aacgaggaacccgtagacatgatggatctcattttcagtatgagctcgcgtatggatgat
cagagaactgaactgtctgctgccagattcattccgcctcgtccagtgtcatcggcatcg
aaaaagactacaaagagccacagaattctccctggactccgtgccaattggacaaaagtg
cagtcgatgaagttcgatggtcacacaatgaataggatcctgaagaggtcgaagaaaagc
aaatcgtcattggattctacaaattcgatacagggcgatgatactcgaagcgatgatgtg
acaatgacgtccaaatag
BioPerl-1.007002/t/data/yeast.tRNAscanSE000444000766000024      3236213155576322 17667 0ustar00cjfieldsstaff000000000000Sequence		tRNA 	Bounds	tRNA	   	Intron Bounds	Cove
Name    	tRNA #	Begin	End  	Type	Codon	Begin	End	Score
--------	------	---- 	------	----	-----	-----	----	------
I       	1	139154	139256	Pro	CCA	139190	139220	60.49
I       	2	166267	166339	Ala	GCA	0	0	76.57
I       	3	181135	181248	Leu	TTG	181173	181204	53.68
I       	4	182597	182516	Ser	TCT	0	0	85.00
II      	1	9583 	9666 	Leu	TTA	0	0	69.31
II      	2	36390	36480	Phe	TTC	36427	36444	68.89
II      	3	197456	197529	Ile	ATT	0	0	71.40
II      	4	227037	227118	Ser	TCT	0	0	85.00
II      	5	266337	266409	Thr	ACT	0	0	78.63
II      	6	347562	347645	Leu	TTA	0	0	69.31
II      	7	350786	350857	Gln	CAA	0	0	65.72
II      	8	405836	405907	Arg	AGA	0	0	66.88
II      	9	405918	405989	Asp	GAC	0	0	58.36
II      	10	645124	645195	Glu	GAA	0	0	62.99
II      	11	643035	642964	Cys	TGC	0	0	75.04
II      	12	326825	326752	Val	GTA	0	0	74.06
II      	13	197661	197591	Gly	GGC	0	0	62.73
III     	1	90858	90971	Leu	TTG	90896	90927	54.18
III     	2	127710	127783	Asn	AAC	0	0	77.73
III     	3	149914	149985	Met	ATG	0	0	74.96
III     	4	227934	228034	Ser	TCG	227971	227989	75.88
III     	5	295477	295549	Thr	ACT	0	0	78.63
III     	6	168364	168293	Gln	CAA	0	0	68.39
III     	7	151350	151278	Lys	AAG	0	0	77.79
III     	8	142765	142695	Gly	GGC	0	0	62.73
III     	9	123642	123571	Pro	CCT	0	0	66.99
III     	10	82532	82461	Glu	GAA	0	0	62.99
IV      	1	83549	83619	Gly	GGC	0	0	62.73
IV      	2	359576	359671	Lys	AAA	359613	359635	69.00
IV      	3	410375	410447	Ala	GCT	0	0	74.48
IV      	4	437768	437849	Ser	TCT	0	0	85.00
IV      	5	519737	519820	Leu	TTA	0	0	69.31
IV      	6	520966	521037	Gln	CAA	0	0	68.39
IV      	7	568877	568948	Arg	AGA	0	0	66.88
IV      	8	568959	569030	Asp	GAC	0	0	58.36
IV      	9	884353	884485	Ile	ATA	884390	884449	61.82
IV      	10	946303	946391	Tyr	TAC	946342	946355	68.81
IV      	11	992823	992893	Gly	GGC	0	0	62.73
IV      	12	1175818	1175890	Met	ATG	0	0	70.03
IV      	13	1201738	1201810	Lys	AAG	0	0	77.79
IV      	14	1305618	1305700	Ser	TCT	0	0	84.84
IV      	15	1461815	1461701	Leu	TTG	1461777	1461745	54.09
IV      	16	1352526	1352454	Lys	AAG	0	0	77.79
IV      	17	1257067	1256996	Gly	GGG	0	0	75.60
IV      	18	1150930	1150831	Undet	???	0	0	57.54
IV      	19	1095453	1095362	Phe	TTC	1095416	1095398	71.83
IV      	20	1075535	1075463	Val	GTG	0	0	75.97
IV      	21	1017269	1017198	Glu	GAG	0	0	59.79
IV      	22	981046	980965	Ser	TCT	0	0	85.00
IV      	23	802795	802724	Gln	CAA	0	0	68.39
IV      	24	668073	668000	Ile	ATT	0	0	71.40
IV      	25	645217	645146	Gln	CAA	0	0	68.39
IV      	26	620034	619962	Arg	CGT	0	0	71.46
IV      	27	488865	488792	Val	GTA	0	0	74.06
IV      	28	434332	434260	Thr	ACT	0	0	78.63
V       	1	86604	86685	Ser	TCT	0	0	85.00
V       	2	100133	100204	Met	ATG	0	0	74.96
V       	3	138666	138737	Arg	AGA	0	0	66.88
V       	4	177098	177169	Glu	GAA	0	0	62.99
V       	5	207356	207427	His	CAC	0	0	66.37
V       	6	250285	250356	Gln	CAA	0	0	68.39
V       	7	354930	355001	Glu	GAA	0	0	62.99
V       	8	438696	438769	Val	GTT	0	0	68.42
V       	9	469452	469525	Val	GTT	0	0	68.42
V       	10	551353	551280	Ile	ATT	0	0	71.40
V       	11	492419	492347	Arg	CGT	0	0	71.46
V       	12	487397	487326	Glu	GAA	0	0	62.99
V       	13	443271	443198	Ile	ATT	0	0	71.40
V       	14	435820	435748	Lys	AAG	0	0	77.79
V       	15	434608	434537	His	CAC	0	0	66.37
V       	16	312091	312019	Ala	GCA	0	0	76.57
V       	17	288522	288441	Ser	TCA	0	0	84.16
V       	18	135497	135425	Lys	AAG	0	0	77.79
V       	19	131153	131082	Gln	CAA	0	0	68.78
V       	20	61960	61890	Gly	GGC	0	0	62.73
VI      	1	101370	101472	Pro	CCA	101406	101436	60.63
VI      	2	162221	162291	Gly	GGC	0	0	62.73
VI      	3	167429	167517	Tyr	TAC	167468	167481	68.18
VI      	4	226746	226675	Lys	AAG	0	0	70.32
VI      	5	210694	210606	Tyr	TAC	210655	210642	68.18
VI      	6	204983	204911	Ala	GCT	0	0	74.48
VI      	7	191600	191500	Ser	AGC	191563	191545	68.67
VI      	8	181035	180965	Gly	GGC	0	0	62.73
VI      	9	158000	157909	Phe	TTC	157963	157945	69.79
VI      	10	137553	137480	Asn	AAC	0	0	77.73
VII     	1	115490	115585	Lys	AAA	115527	115549	69.00
VII     	2	122271	122343	Lys	AAG	0	0	77.79
VII     	3	205525	205638	Leu	TTG	205563	205594	53.40
VII     	4	319782	319853	His	CAC	0	0	66.37
VII     	5	328584	328655	Glu	GAA	0	0	62.99
VII     	6	405471	405542	Arg	AGA	0	0	66.88
VII     	7	423096	423209	Leu	TTG	423134	423165	54.18
VII     	8	531611	531682	Asp	GAC	0	0	58.36
VII     	9	541851	541922	Glu	GAA	0	0	62.99
VII     	10	661750	661821	Thr	ACA	0	0	77.84
VII     	11	700676	700757	Leu	CTC	0	0	64.51
VII     	12	731139	731212	Asn	AAC	0	0	77.73
VII     	13	736342	736413	Arg	AGA	0	0	66.88
VII     	14	739124	739197	Ile	ATT	0	0	71.40
VII     	15	774351	774423	Ala	GCT	0	0	74.48
VII     	16	779618	779689	Gly	GGA	0	0	66.72
VII     	17	794419	794491	Ala	GCA	0	0	76.57
VII     	18	823484	823557	Val	GTT	0	0	68.42
VII     	19	845651	845721	Gly	GGC	0	0	62.73
VII     	20	876396	876468	Lys	AAG	0	0	77.79
VII     	21	1004220	1004291	Thr	ACA	0	0	77.84
VII     	22	931023	930953	Gly	GGC	0	0	62.73
VII     	23	878817	878712	Trp	TGG	878781	878748	67.27
VII     	24	857493	857380	Leu	TTG	857455	857424	54.18
VII     	25	828796	828725	Arg	AGA	0	0	66.88
VII     	26	707180	707109	Cys	TGC	0	0	75.04
VII     	27	701049	700954	Lys	AAA	701012	700990	69.64
VII     	28	561744	561663	Ser	TCT	0	0	85.00
VII     	29	544649	544578	Asp	GAC	0	0	58.36
VII     	30	440810	440719	Phe	TTC	440773	440755	69.79
VII     	31	412368	412295	Val	GTT	0	0	68.42
VII     	32	401599	401528	Glu	GAA	0	0	62.99
VII     	33	287459	287354	Trp	TGG	287423	287390	67.27
VII     	34	185790	185718	Lys	AAG	0	0	77.79
VII     	35	110698	110627	His	CAC	0	0	66.37
VII     	36	73900	73827	Val	GTT	0	0	68.42
VIII    	1	62752	62823	His	CAC	0	0	66.37
VIII    	2	134312	134383	Gln	CAA	0	0	68.39
VIII    	3	466986	467057	Thr	ACA	0	0	79.33
VIII    	4	475774	475702	Val	GTG	0	0	75.97
VIII    	5	388996	388894	Pro	CCA	388960	388930	59.08
VIII    	6	358571	358480	Phe	TTC	358534	358516	69.79
VIII    	7	237940	237849	Phe	TTC	237903	237885	69.79
VIII    	8	146305	146233	Ala	GCT	0	0	74.48
VIII    	9	133098	133017	Ser	TCT	0	0	85.00
VIII    	10	116172	116100	Thr	ACT	0	0	78.63
VIII    	11	85366	85293	Val	GTT	0	0	68.42
IX      	1	175028	175100	Thr	ACT	0	0	78.63
IX      	2	197589	197660	Glu	GAG	0	0	59.79
IX      	3	210662	210735	Ile	ATT	0	0	71.40
IX      	4	248847	248928	Ser	TCA	0	0	84.16
IX      	5	325746	325818	Thr	ACT	0	0	78.63
IX      	6	370414	370485	Glu	GAA	0	0	62.99
IX      	7	336417	336346	Asp	GAC	0	0	58.36
IX      	8	324372	324301	Asp	GAC	0	0	58.36
IX      	9	300298	300227	Lys	AAG	0	0	70.32
IX      	10	183510	183437	Ile	ATT	0	0	71.40
X       	1	204432	204503	Asp	GAC	0	0	58.36
X       	2	233636	233708	Arg	CGT	0	0	70.24
X       	3	353940	354028	Tyr	TAC	353979	353992	68.18
X       	4	355070	355141	Arg	AGA	0	0	66.88
X       	5	355152	355223	Asp	GAC	0	0	58.36
X       	6	378056	378129	Val	GTT	0	0	68.42
X       	7	414659	414731	Lys	AAG	0	0	77.79
X       	8	422630	422702	Met	ATG	0	0	70.03
X       	9	531521	531591	Gly	GGC	0	0	62.73
X       	10	538248	538319	Arg	AGG	0	0	71.23
X       	11	541201	541272	Asp	GAC	0	0	58.36
X       	12	617612	617712	Leu	CTA	617650	617668	61.03
X       	13	542737	542649	Tyr	TAC	542698	542685	68.81
X       	14	523786	523705	Ser	TCT	0	0	85.00
X       	15	517577	517506	Met	ATG	0	0	74.96
X       	16	424208	424125	Leu	TTA	0	0	69.31
X       	17	415729	415624	Trp	TGG	415693	415660	67.27
X       	18	396492	396422	Gly	GGC	0	0	62.73
X       	19	390811	390739	Met	ATG	0	0	70.03
X       	20	374273	374202	Arg	AGA	0	0	66.88
X       	21	374191	374120	Asp	GAC	0	0	58.36
X       	22	197084	197012	Ala	GCT	0	0	74.48
X       	23	116004	115933	Glu	GAA	0	0	62.99
X       	24	59172	59100	Thr	ACT	0	0	78.63
XI      	1	74625	74698	Asn	AAC	0	0	77.73
XI      	2	84209	84292	Leu	TTA	0	0	69.31
XI      	3	202641	202713	Lys	AAG	0	0	77.79
XI      	4	219537	219609	Ala	GCT	0	0	74.48
XI      	5	302559	302664	Trp	TGG	302595	302628	67.27
XI      	6	379318	379391	Val	GTT	0	0	68.42
XI      	7	458195	458308	Leu	TTG	458233	458264	54.18
XI      	8	490606	490678	Arg	CGT	0	0	71.46
XI      	9	517625	517697	Ala	GCT	0	0	74.48
XI      	10	578601	578696	Lys	AAA	578638	578660	69.00
XI      	11	513040	512969	Asp	GAC	0	0	58.36
XI      	12	313113	313042	His	CAC	0	0	66.37
XI      	13	307858	307785	Val	GTT	0	0	68.42
XI      	14	162559	162488	Arg	AGA	0	0	66.88
XI      	15	141090	141019	Glu	GAA	0	0	62.99
XI      	16	46807	46736	Thr	ACG	0	0	75.96
XII     	1	92547	92649	Pro	CCA	92583	92613	59.86
XII     	2	374356	374428	Arg	CGT	0	0	71.46
XII     	3	427133	427204	Asp	GAC	0	0	58.36
XII     	4	628383	628497	Leu	TTG	628421	628453	55.72
XII     	5	732090	732190	Leu	CTA	732128	732146	61.03
XII     	6	734802	734875	Ile	ATT	0	0	71.40
XII     	7	784354	784453	Undet	???	0	0	57.54
XII     	8	793918	793989	Asp	GAC	0	0	58.36
XII     	9	797178	797249	Glu	GAA	0	0	62.99
XII     	10	818609	818680	Arg	CGG	0	0	57.65
XII     	11	875375	875470	Lys	AAA	875412	875434	69.00
XII     	12	1052140	1052067	Ile	ATT	0	0	71.40
XII     	13	976051	975978	Asn	AAC	0	0	77.73
XII     	14	963050	962967	Leu	TTA	0	0	69.31
XII     	15	687932	687859	Val	GTT	0	0	68.42
XII     	16	657006	656934	Ala	GCT	0	0	74.48
XII     	17	605432	605300	Ile	ATA	605395	605336	61.58
XII     	18	592619	592519	Leu	CTA	592581	592563	60.39
XII     	19	448722	448651	Gln	CAA	0	0	68.39
XII     	20	214956	214884	Ala	GCA	0	0	76.57
XII     	21	168024	167943	Ser	TCT	0	0	85.00
XIII    	1	168795	168883	Tyr	TAC	168834	168847	68.18
XIII    	2	290800	290871	Glu	GAA	0	0	57.99
XIII    	3	352279	352369	Phe	TTC	352316	352333	69.38
XIII    	4	363063	363134	His	CAC	0	0	66.37
XIII    	5	463553	463624	Asp	GAC	0	0	58.36
XIII    	6	504894	505007	Leu	TTG	504932	504963	54.18
XIII    	7	837928	838016	Tyr	TAC	837967	837980	68.18
XIII    	8	808317	808246	Gln	CAG	0	0	64.54
XIII    	9	768440	768368	Ala	GCT	0	0	74.48
XIII    	10	747962	747891	Arg	AGA	0	0	66.88
XIII    	11	586708	586635	Val	GTT	0	0	68.42
XIII    	12	572954	572882	Met	ATG	0	0	70.03
XIII    	13	480692	480620	Lys	AAG	0	0	77.79
XIII    	14	420660	420587	Val	GTT	0	0	68.42
XIII    	15	379407	379302	Trp	TGG	379371	379338	67.27
XIII    	16	372517	372444	Val	GTT	0	0	68.42
XIII    	17	321218	321146	Ala	GCT	0	0	74.48
XIII    	18	259239	259158	Ser	TCT	0	0	85.00
XIII    	19	196170	196068	Pro	CCA	196134	196104	60.49
XIII    	20	183968	183898	Gly	GGC	0	0	62.73
XIII    	21	131896	131825	Arg	AGA	0	0	66.88
XIV     	1	102714	102787	Asn	AAC	0	0	77.73
XIV     	2	104803	104875	Thr	ACT	0	0	78.63
XIV     	3	374866	374956	Phe	TTC	374903	374920	70.15
XIV     	4	443003	443116	Leu	TTG	443041	443072	54.18
XIV     	5	547090	547192	Pro	CCA	547126	547156	59.08
XIV     	6	568111	568213	Pro	CCA	568147	568177	59.08
XIV     	7	602308	602381	Ile	ATT	0	0	71.40
XIV     	8	632596	632669	Asn	AAC	0	0	77.73
XIV     	9	726213	726130	Leu	TTA	0	0	69.31
XIV     	10	631914	631843	Pro	CCT	0	0	66.99
XIV     	11	569936	569863	Ile	ATT	0	0	71.40
XIV     	12	560761	560689	Thr	ACT	0	0	78.63
XIV     	13	519165	519095	Asp	GAC	0	0	31.75
XIV     	14	96310	96239	Gly	GGA	0	0	66.72
XV      	1	113801	113873	Thr	ACT	0	0	78.63
XV      	2	228329	228402	Asn	AAC	0	0	77.73
XV      	3	274673	274773	Ser	AGC	274710	274728	68.67
XV      	4	282164	282234	Gly	GGC	0	0	62.73
XV      	5	288192	288280	Tyr	TAC	288231	288244	68.81
XV      	6	301097	301198	Pro	CCA	301133	301162	58.94
XV      	7	438644	438739	Lys	AAA	438681	438703	69.00
XV      	8	464451	464552	Pro	CCA	464487	464516	59.59
XV      	9	487440	487513	Asn	AAC	0	0	77.73
XV      	10	571958	572029	Asp	GAC	0	0	58.36
XV      	11	710201	710272	Met	ATG	0	0	74.96
XV      	12	976414	976486	Met	ATG	0	0	70.03
XV      	13	980676	980780	Pro	CCA	980712	980744	55.42
XV      	14	854256	854184	Ala	GCA	0	0	76.57
XV      	15	663885	663812	Val	GTT	0	0	67.95
XV      	16	594425	594354	Gly	GGG	0	0	80.95
XV      	17	354112	354040	Thr	ACT	0	0	78.63
XV      	18	340371	340299	Arg	CGT	0	0	71.46
XV      	19	226679	226609	Gly	GGC	0	0	62.73
XV      	20	111032	110961	Gly	GGA	0	0	66.72
XVI     	1	572264	572334	Gly	GGC	0	0	62.73
XVI     	2	582057	582129	Lys	AAG	0	0	77.79
XVI     	3	689560	689641	Ser	TCA	0	0	84.16
XVI     	4	744281	744352	Thr	ACA	0	0	77.84
XVI     	5	810671	810744	Asn	AAC	0	0	77.73
XVI     	6	819524	819597	Ile	ATT	0	0	71.40
XVI     	7	856897	856969	Ala	GCT	0	0	74.48
XVI     	8	860374	860444	Gly	GGC	0	0	62.73
XVI     	9	880364	880291	Ile	ATT	0	0	71.40
XVI     	10	775833	775762	Cys	TGC	0	0	75.04
XVI     	11	769299	769204	Lys	AAA	769262	769240	69.00
XVI     	12	622626	622535	Phe	TTC	622589	622571	69.79
XVI     	13	560284	560193	Phe	TTC	560247	560229	69.79
XVI     	14	435959	435888	Cys	TGC	0	0	75.04
XVI     	15	338918	338847	Met	ATG	0	0	74.96
XVI     	16	210262	210191	Glu	GAA	0	0	62.99
XVI     	17	56274	56169	Trp	TGG	56238	56205	67.27
XVII    	1	9374 	9444 	SeC	TGA	0	0	51.26
XVII    	2	35373	35444	Glu	GAA	0	0	38.30
XVII    	3	48201	48287	Ser	TCA	0	0	51.45
XVII    	4	63862	63934	Thr	ACA	0	0	65.36
XVII    	5	64597	64667	His	CAC	0	0	48.69
XVII    	6	66095	66176	Pseudo	TTA	0	0	37.52
XVII    	7	66210	66282	Pseudo	CAA	0	0	29.02
XVII    	8	67061	67132	Lys	AAA	0	0	34.97
XVII    	9	67309	67381	Arg	AGA	0	0	58.95
XVII    	10	67468	67539	Pseudo	GGA	0	0	46.63
XVII    	11	68322	68393	Pseudo	GAC	0	0	28.24
XVII    	12	69289	69359	Arg	CGT	0	0	42.27
XVII    	13	69846	69918	Ala	GCA	0	0	34.42
XVII    	14	70162	70234	Ile	ATC	0	0	43.88
XVII    	15	71433	71504	Asn	AAC	0	0	51.73
XVII    	16	72632	72705	Met	ATG	0	0	50.11
XVII    	17	77431	77502	Phe	TTC	0	0	46.41
XVII    	18	78533	78605	Val	GTA	0	0	63.19
XVII    	19	85035	85107	Pseudo	ATG	0	0	38.75
XVII    	20	78162	78091	Pseudo	TAA	0	0	39.47
BioPerl-1.007002/t/data/bad_dbfa000755000766000024          013155576321 16235 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/bad_dbfa/bug3172.fa000444000766000024         4613155576321 17734 0ustar00cjfieldsstaff000000000000> foo
AACATA
> bar
AGAGAG
> baz
AACATABioPerl-1.007002/t/data/bad_dbfa/shotdb.fa000444000766000024       174613155576321 20175 0ustar00cjfieldsstaff000000000000>seq1 this is the first sequence
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
>seq2
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
>seq3
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
>seq4
tttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttt
>seq5 last sequence, last comment
aaaaaaaaaattttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgggggggggg
>seq6 0 bp sequence


BioPerl-1.007002/t/data/biodbgff000755000766000024          013155576321 16275 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/biodbgff/test.gff000444000766000024       445113155576321 20101 0ustar00cjfieldsstaff000000000000## sequence-region Contig1 1 37450
Contig1	confirmed	transcript	1001	2000	42	+	.	Transcript trans-1; Gene "abc-1"; Gene "xyz-2"; Note "function unknown"
Contig1	confirmed	exon	1001	1100	.	+	.	Transcript trans-1
Contig1	confirmed	exon	1201	1300	.	+	.	Transcript trans-1
Contig1	confirmed	exon	1401	1450	.	+	.	Transcript trans-1
Contig1	confirmed	CDS	1051	1100	.	+	0	Transcript trans-1
Contig1	confirmed	CDS	1201	1300	.	+	2	Transcript trans-1
Contig1	confirmed	CDS	1401	1440	.	+	0	Transcript trans-1
Contig1	est	similarity	1001	1100	96	.	.	Target "EST:CEESC13F" 1 100
Contig1	est	similarity	1201	1300	99	.	.	Target "EST:CEESC13F" 101 200
Contig1	est	similarity	1401	1450	99	.	.	Target "EST:CEESC13F" 201 250
Contig1	tc1	transposon	5001	6000	.	+	.	Transposon c128.1
Contig1	tc1	transposon	8001	9000	.	-	.	Transposon c128.2
Contig1	confirmed	transcript	30001	31000	.	-	.	Transcript trans-2; Gene "xyz-2"; Note "Terribly interesting"
Contig1	confirmed	exon	30001	30100	.	-	.	Transcript trans-2; Gene "abc-1"; Note "function unknown"
Contig1	confirmed	exon	30701	30800	.	-	.	Transcript trans-2
Contig1	confirmed	exon	30801	31000	.	-	.	Transcript trans-2

## sequence-region Contig2 1 37450
Contig2	clone	Component	1	2000	.	.	.	Target "Clone:AL12345.1" 1 2000; Note "Terribly interesting"
Contig2	clone	Component	2001	5000	.	.	.	Target "Clone:AL11111.1" 6000 3001
Contig2	clone	Component	5001	20000	.	.	.	Target "Clone:AC13221.2" 1 15000
Contig2	clone	Component	2001	37450	.	.	.	Target "Clone:M7.3" 1001 36450
Contig2	predicted	transcript	2501	4500	.	+	.	Transcript trans-3 ; Alias trans-18
Contig2	predicted	transcript	5001	8001	.	-	.	Transcript trans-4


#processed_transcript
Contig3	clone	Component	1	50000	.	.	.	Clone AL12345.2
Contig3	confirmed	mRNA	32000	35000	.	+	.	mRNA trans-8
Contig3	confirmed	UTR	32000	32100	.	+	.	mRNA trans-8
Contig3	confirmed	CDS	32101	33000	.	+	.	mRNA trans-8
Contig3	confirmed	CDS	34000	34500	.	+	.	mRNA trans-8
Contig3	confirmed	CDS	34600	34900	.	+	.	mRNA trans-8
Contig3	confirmed	UTR	34901	35000	.	+	.	mRNA trans-8

## preferred group assignments
Contig4	clone	Component	1	50000	.	.	.	Clone ABC123
Contig4	confirmed	gene	32000	35000	.	+	.	Misc thing1 ; gene gene-9
Contig4	confirmed	mRNA	32000	35000	.	+	.	Misc thing2 ; mRNA trans-9 ; gene gene-9
Contig4	confirmed	CDS	32000	35000	.	+	.	Misc thing3 ; mRNA trans-9

BioPerl-1.007002/t/data/biodbgff/test.gff3000444000766000024       463313155576321 20166 0ustar00cjfieldsstaff000000000000##gff-version 3
##sequence-region Contig1 1 37450
#Contig1	reference	Component	1	37450	.	.	.	Name=Contig1
Contig1	confirmed	transcript	1001	2000	42	+	.	ID=Transcript:trans-1;Gene=abc-1;Gene=xyz-2;Note=function+unknown
Contig1	confirmed	exon	1001	1100	.	+	.	ID=Transcript:trans-1
Contig1	confirmed	exon	1201	1300	.	+	.	ID=Transcript:trans-1
Contig1	confirmed	exon	1401	1450	.	+	.	ID=Transcript:trans-1
Contig1	confirmed	CDS	1051	1100	.	+	0	ID=Transcript:trans-1
Contig1	confirmed	CDS	1201	1300	.	+	2	ID=Transcript:trans-1
Contig1	confirmed	CDS	1401	1440	.	+	0	ID=Transcript:trans-1
Contig1	est	similarity	1001	1100	96	.	.	Target=EST:CEESC13F 1 100 +
Contig1	est	similarity	1201	1300	99	.	.	Target=EST:CEESC13F 101 200 +
Contig1	est	similarity	1401	1450	99	.	.	Target=EST:CEESC13F 201 250 +
Contig1	tc1	transposon	5001	6000	.	+	.	ID=Transposon:c128.1
Contig1	tc1	transposon	8001	9000	.	-	.	ID=Transposon:c128.2
Contig1	confirmed	transcript	30001	31000	.	-	.	ID=Transcript:trans-2;Gene=xyz-2;Note=Terribly+interesting
Contig1	confirmed	exon	30001	30100	.	-	.	ID=Transcript:trans-2;Gene=abc-1;Note=function+unknown
Contig1	confirmed	exon	30701	30800	.	-	.	ID=Transcript:trans-2
Contig1	confirmed	exon	30801	31000	.	-	.	ID=Transcript:trans-2

##sequence-region Contig2 1 37450
Contig2	clone	Component	1	2000	.	.	.	Target=Clone:AL12345.1 1 2000 +;Note=Terribly+interesting
Contig2	clone	Component	2001	5000	.	.	.	Target=Clone:AL11111.1 6000 3001 +
Contig2	clone	Component	5001	20000	.	.	.	Target=Clone:AC13221.2 1 15000 +
Contig2	clone	Component	2001	37450	.	.	.	Target=Clone:M7.3 1001 36450 +
Contig2	predicted	transcript	2501	4500	.	+	.	ID=Transcript:trans-3;Alias=trans-18
Contig2	predicted	transcript	5001	8001	.	-	.	ID=Transcript:trans-4


#processed_transcript
Contig3	clone	Component	1	50000	.	.	.	ID=Clone:AL12345.2
Contig3	confirmed	mRNA	32000	35000	.	+	.	ID=mRNA:trans-8
Contig3	confirmed	UTR	32000	32100	.	+	.	ID=mRNA:trans-8
Contig3	confirmed	CDS	32101	33000	.	+	.	ID=mRNA:trans-8
Contig3	confirmed	CDS	34000	34500	.	+	.	ID=mRNA:trans-8
Contig3	confirmed	CDS	34600	34900	.	+	.	ID=mRNA:trans-8
Contig3	confirmed	UTR	34901	35000	.	+	.	ID=mRNA:trans-8

## preferred group assignments
Contig4	clone	Component	1	50000	.	.	.	ID=Clone:ABC123
Contig4	confirmed	gene	32000	35000	.	+	.	ID=Misc:thing1;gene=gene-9
Contig4	confirmed	mRNA	32000	35000	.	+	.	ID=Misc:thing2;mRNA=trans-9;gene=gene-9
Contig4	confirmed	CDS	32000	35000	.	+	.	ID=Misc:thing3;mRNA=trans-9

BioPerl-1.007002/t/data/consed_project000755000766000024          013155576321 17534 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/consed_project/edit_dir000755000766000024          013155576321 21317 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.contigs000555000766000024       133513155576321 25556 0ustar00cjfieldsstaff000000000000>Contig1
atatcTCGAGGGTACTTGAGGATTCTACCACCACAACAACAAAGCCTTAT
CATCCAGAACCGCAAATTATAAAAAAGAGCCAACACCACAAAACAAAATG
AAAAGAAACAAACTCTTCAACCAGTGATGTTCTGAGACTTGTTGAGGATA
ACACCTTCGTACTTAACTTGGAACCACTTCATGGCATCATCCTTGGTAAC
TCTATGCTGAATCCCAACGCGAGTCTTGCACCTACGGCGACGTGCAACAC
GGTATCCCGGGCGTTCAAGAACAACATAGAAGTCCATTCCATAGATACCC
GTAGAAGGATCGTACTTGATTCCAAGATCAATGTGCTCCTGGATACCGAA
TCCAAAACAGCCAGTGTCACTGAAGTTCCTCCTCAACAGCTCGTACTCCT
TGACTTTCAAGCCACTCTCAAGAAGCTGCATTGCCTTGTCTCCTCTCACG
GTGACGTAGCACGCAATCTTTTCATTACGTCTAATACCGAAAGACCTCAC
AGTGTACCTCGCCTTGGAGAAGACAGGTGTTTGACCACTGAGCTGTTCCA
AAACCTTGGAGGCACGGGTGAGACGATCACCACTCTCACCAACGGAGATG
TTGAGAACGAGCTTCTGAACCTTGATATCCCTCATTGGGTTCGAGAGCTT
CTTCTCTGACGCCATTCTGAGGATTAAGGGATGCAAAGTCAGAGGGAGAT
GAGCAAAg

BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.fasta000555000766000024       662313155576321 25213 0ustar00cjfieldsstaff000000000000>ML4922R CHROMAT_FILE: ML4922R PHD_FILE: ML4922R.phd.1 CHEM: term DYE: big TIME: Thu Jun 21 11:28:31 2001
ccttggtacgcccgcaggtaccggtccggaattcccgggtcgacccacgc
gtccgcggacgcgtggggtgaccccggaagattcgagtgcttcgtctggt
aatcaaaatcaggtttctccggttggatctcaaactcaaggttatgccgt
ggcacaaatgtcgcctgctgtttcatctgtcagtgatgctccctcattag
acacacagagacaacgagatattcagtccaggctagctaacagtggttca
gatgattctgatgacgaagatcctgatggagagactgtaacaacagtgaa
tgatgatcctaccgatgttaagcgtgctaggaggatgctttcaaaccgag
aatccgctaggcgctctagaagaagaaagcaagagcaaatgagtgaattt
gattcacaggttggccaattacgtggtgagcattcaactatgcttaagcg
tcttagtgaggtcactcagaagtttagcaccgctgttgtcgataacagaa
tcttaaaagctgatatcgaaacattgagaacaaaggtgaagatggcagag
gacactgtgaaaagagtgacagggatgaaccctaggcttttggcaaaacc
atacagcataccattcgataggacactgatgggttcttcacagccaaact
tgaatcaaaccgacatgattccaaatcaaatatcagaggacaacagtttt
gcaagcaactcggttgttactttggaatccggttgcaatgcttttgaagc
can
>ML4924F CHROMAT_FILE: ML4924F PHD_FILE: ML4924F.phd.1 CHEM: term DYE: big TIME: Thu Jun 21 11:27:03 2001
ttgttcttttctcgagggtacttgaggattctaccaccacaacaacaaag
ccttatcatccagaaccgcaaattataaaaaagagccaacaccacaaaac
aaaatgaaaagaaacaaactcttcaaccagtgatgttctgagacttgttg
aggataacaccttcgtacttaacttggaaccacttcatggcatcatcctt
ggtaactctatgctgaatcccaacgcgagtcttgcacctacggcgacgtg
caacacggtatcccgggcgttcaagaacaacatagaagtccattccatag
atacccgtagaaggatcgtacttgattccaagatcaatgtgctcctggat
accgaatccaaaacagccagtgtcactgaagttcctcctcaacagctcgt
actccttgactttcaagccactctcaacaagctgcattgccttgcctcct
ctcacggtgacgtagcacgcaatcttttcattacgtctaataccgaaaga
cctcacagtgcacctggccttggacaacacaggtgtttgaccactgagct
gttacaaaaccttggaggcacgggtgagacgatcaccactctcaccaacg
gagatgtcgagaacgagcttctgaaccttgatattcctcattgggctcca
cagctctttctctgacgccattctgaggatctagggatgcacacccacaa
ggacatgaccaaaatcgacatctgggcccactcg
>ML4924R CHROMAT_FILE: ML4924R PHD_FILE: ML4924R.phd.1 CHEM: term DYE: big TIME: Thu Jun 21 11:27:03 2001
actttggtcgcctgcaggtaccggtccgngattcccgggtcgacccacgc
gtccgctttgctcatctccctctgactttgcatcccttaatcctcagaat
ggcgtcagagaagaagctctcgaacccaatgagggatatcaaggttcaga
agctcgttctcaacatctccgttggtgagagtggtgatcgtctcacccgt
gcctccaaggttttggaacagctcagtggtcaaacacctgtcttctccaa
ggcgaggtacactgtgaggtctttcggtattagacgtaatgaaaagattg
cgtgctacgtcaccgtgagaggagacaaggcaatgcagcttcttgagagt
ggcttgaaagtcaaggagtacgagctgttgaggaggaacttcagtgacac
tggctgttttggattcggtatccaggagcacattgatcttggaatcaagt
acgatccttctacgggtatctatggaatggacttctatgttgttcttgaa
cgcccgggataccgtgttgcacgtcgccgtaggtgcaagactcgcgttgg
gattcagcatagagttaccaaggatgatgccatgaagtggttccaagtta
agtacgaaggtgttatcctcaacaagtctcagaacatcactggttgaaga
gtttgtttcttttcattttgttttgtggtgttggctcttttttataattt
gcggttctggatgataaggctttgttgttgtggtggtagaatcctcaagt
accctcgagatat
>ML4947F CHROMAT_FILE: ML4947F PHD_FILE: ML4947F.phd.1 CHEM: term DYE: big TIME: Thu Jun 21 11:28:31 2001
ctgtgggacccactgatattaccgaacttttgaaccaaacagttatgtgt
tggcgccaaaaataacgttaaagaaaccatcacaagagccttatgacaaa
gagggagagatagacataacttaagacattacacaatttggtcaaacgat
aaaccaaatccaacagacatttaaaccaaatccaacgccaacaaaacatt
catatataagatatacccaaaccgtatcaaacgcagacgccgccctagta
actgtatcctttcacaaacaagctctcggaggcagcagagtcaccagaag
ccccagcaatgtatttcccaagtgtagcgtccgagttagccttgcacctg
accaagaacgtggcctgagctttggctacgttctctttcttacctcccca
agccttgagtgtgctttgctggagggctcggccaaaggagaaagtaagcg
tccatggcttcaacagatcgagcttgttcattgcgttcagatttagcgtt
gcttcctcttcgctctgtcctcctgagaggaacacgattcctggaaccgc
tggtgggaccgtgcggcggagagcagtcactgtgtattccgcaatgactt
ccggtgcaaccttggcgctgtctgagcctggagtgaccatgttaggttta
agcagagtgccttcgaggaggacgtggtggtcgttcaaggccttgtacac
ggcagaaagaaccgtctcagtcacagccgcacatttctt
BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.fasta.log000555000766000024         4513155576321 25723 0ustar00cjfieldsstaff000000000000No. words: 5978; after pruning: 5864
BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.fasta.screen000555000766000024       662713155576321 26475 0ustar00cjfieldsstaff000000000000>ML4922R  CHROMAT_FILE: ML4922R PHD_FILE: ML4922R.phd.1 CHEM: term DYE: big TIME: Thu Jun 21 11:28:31 2001
CCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXCGGACGCGTGGGGTGACCCCGGAAGATTCGAGTGCTTCGTCTGGT
AATCAAAATCAGGTTTCTCCGGTTGGATCTCAAACTCAAGGTTATGCCGT
GGCACAAATGTCGCCTGCTGTTTCATCTGTCAGTGATGCTCCCTCATTAG
ACACACAGAGACAACGAGATATTCAGTCCAGGCTAGCTAACAGTGGTTCA
GATGATTCTGATGACGAAGATCCTGATGGAGAGACTGTAACAACAGTGAA
TGATGATCCTACCGATGTTAAGCGTGCTAGGAGGATGCTTTCAAACCGAG
AATCCGCTAGGCGCTCTAGAAGAAGAAAGCAAGAGCAAATGAGTGAATTT
GATTCACAGGTTGGCCAATTACGTGGTGAGCATTCAACTATGCTTAAGCG
TCTTAGTGAGGTCACTCAGAAGTTTAGCACCGCTGTTGTCGATAACAGAA
TCTTAAAAGCTGATATCGAAACATTGAGAACAAAGGTGAAGATGGCAGAG
GACACTGTGAAAAGAGTGACAGGGATGAACCCTAGGCTTTTGGCAAAACC
ATACAGCATACCATTCGATAGGACACTGATGGGTTCTTCACAGCCAAACT
TGAATCAAACCGACATGATTCCAAATCAAATATCAGAGGACAACAGTTTT
GCAAGCAACTCGGTTGTTACTTTGGAATCCGGTTGCAATGCTTTTGAAGC
CAN
>ML4924F  CHROMAT_FILE: ML4924F PHD_FILE: ML4924F.phd.1 CHEM: term DYE: big TIME: Thu Jun 21 11:27:03 2001
TTGTTCTTTTCTCGAGGGTACTTGAGGATTCTACCACCACAACAACAAAG
CCTTATCATCCAGAACCGCAAATTATAAAAAAGAGCCAACACCACAAAAC
AAAATGAAAAGAAACAAACTCTTCAACCAGTGATGTTCTGAGACTTGTTG
AGGATAACACCTTCGTACTTAACTTGGAACCACTTCATGGCATCATCCTT
GGTAACTCTATGCTGAATCCCAACGCGAGTCTTGCACCTACGGCGACGTG
CAACACGGTATCCCGGGCGTTCAAGAACAACATAGAAGTCCATTCCATAG
ATACCCGTAGAAGGATCGTACTTGATTCCAAGATCAATGTGCTCCTGGAT
ACCGAATCCAAAACAGCCAGTGTCACTGAAGTTCCTCCTCAACAGCTCGT
ACTCCTTGACTTTCAAGCCACTCTCAACAAGCTGCATTGCCTTGCCTCCT
CTCACGGTGACGTAGCACGCAATCTTTTCATTACGTCTAATACCGAAAGA
CCTCACAGTGCACCTGGCCTTGGACAACACAGGTGTTTGACCACTGAGCT
GTTACAAAACCTTGGAGGCACGGGTGAGACGATCACCACTCTCACCAACG
GAGATGTCGAGAACGAGCTTCTGAACCTTGATATTCCTCATTGGGCTCCA
CAGCTCTTTCTCTGACGCCATTCTGAGGATCTAGGGATGCACACCCACAA
GGACATGACCAAAATCGACATCTGGGCCCACTCG
>ML4924R  CHROMAT_FILE: ML4924R PHD_FILE: ML4924R.phd.1 CHEM: term DYE: big TIME: Thu Jun 21 11:27:03 2001
ACTTTGGTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXCTTTGCTCATCTCCCTCTGACTTTGCATCCCTTAATCCTCAGAAT
GGCGTCAGAGAAGAAGCTCTCGAACCCAATGAGGGATATCAAGGTTCAGA
AGCTCGTTCTCAACATCTCCGTTGGTGAGAGTGGTGATCGTCTCACCCGT
GCCTCCAAGGTTTTGGAACAGCTCAGTGGTCAAACACCTGTCTTCTCCAA
GGCGAGGTACACTGTGAGGTCTTTCGGTATTAGACGTAATGAAAAGATTG
CGTGCTACGTCACCGTGAGAGGAGACAAGGCAATGCAGCTTCTTGAGAGT
GGCTTGAAAGTCAAGGAGTACGAGCTGTTGAGGAGGAACTTCAGTGACAC
TGGCTGTTTTGGATTCGGTATCCAGGAGCACATTGATCTTGGAATCAAGT
ACGATCCTTCTACGGGTATCTATGGAATGGACTTCTATGTTGTTCTTGAA
CGCCCGGGATACCGTGTTGCACGTCGCCGTAGGTGCAAGACTCGCGTTGG
GATTCAGCATAGAGTTACCAAGGATGATGCCATGAAGTGGTTCCAAGTTA
AGTACGAAGGTGTTATCCTCAACAAGTCTCAGAACATCACTGGTTGAAGA
GTTTGTTTCTTTTCATTTTGTTTTGTGGTGTTGGCTCTTTTTTATAATTT
GCGGTTCTGGATGATAAGGCTTTGTTGTTGTGGTGGTAGAATCCTCAAGT
ACCCTCGAGATAT
>ML4947F  CHROMAT_FILE: ML4947F PHD_FILE: ML4947F.phd.1 CHEM: term DYE: big TIME: Thu Jun 21 11:28:31 2001
CTGTGGGACCCACTGATATTACCGAACTTTTGAACCAAACAGTTATGTGT
TGGCGCCAAAAATAACGTTAAAGAAACCATCACAAGAGCCTTATGACAAA
GAGGGAGAGATAGACATAACTTAAGACATTACACAATTTGGTCAAACGAT
AAACCAAATCCAACAGACATTTAAACCAAATCCAACGCCAACAAAACATT
CATATATAAGATATACCCAAACCGTATCAAACGCAGACGCCGCCCTAGTA
ACTGTATCCTTTCACAAACAAGCTCTCGGAGGCAGCAGAGTCACCAGAAG
CCCCAGCAATGTATTTCCCAAGTGTAGCGTCCGAGTTAGCCTTGCACCTG
ACCAAGAACGTGGCCTGAGCTTTGGCTACGTTCTCTTTCTTACCTCCCCA
AGCCTTGAGTGTGCTTTGCTGGAGGGCTCGGCCAAAGGAGAAAGTAAGCG
TCCATGGCTTCAACAGATCGAGCTTGTTCATTGCGTTCAGATTTAGCGTT
GCTTCCTCTTCGCTCTGTCCTCCTGAGAGGAACACGATTCCTGGAACCGC
TGGTGGGACCGTGCGGCGGAGAGCAGTCACTGTGTATTCCGCAATGACTT
CCGGTGCAACCTTGGCGCTGTCTGAGCCTGGAGTGACCATGTTAGGTTTA
AGCAGAGTGCCTTCGAGGAGGACGTGGTGGTCGTTCAAGGCCTTGTACAC
GGCAGAAAGAACCGTCTCAGTCACAGCCGCACATTTCTT
BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1000555000766000024      1326613155576321 27400 0ustar00cjfieldsstaff000000000000AS 1 2

CO Contig1 708 2 51 U
atatcTCGAGGGTACTTGAGGATTCTACCACCACAACAACAAAGCCTTAT
CATCCAGAACCGCAAATTATAAAAAAGAGCCAACACCACAAAACAAAATG
AAAAGAAACAAACTCTTCAACCAGTGATGTTCTGAGACTTGTTGAGGATA
ACACCTTCGTACTTAACTTGGAACCACTTCATGGCATCATCCTTGGTAAC
TCTATGCTGAATCCCAACGCGAGTCTTGCACCTACGGCGACGTGCAACAC
GGTATCCCGGGCGTTCAAGAACAACATAGAAGTCCATTCCATAGATACCC
GTAGAAGGATCGTACTTGATTCCAAGATCAATGTGCTCCTGGATACCGAA
TCCAAAACAGCCAGTGTCACTGAAGTTCCTCCTCAACAGCTCGTACTCCT
TGACTTTCAAGCCACTCTCAAGAAGCTGCATTGCCTTGTCTCCTCTCACG
GTGACGTAGCACGCAATCTTTTCATTACGTCTAATACCGAAAGACCTCAC
AGTGTACCTCGCCTTGGAGAAGACAGGTGTTTGACCACTGAGCTGTTCCA
AAACCTTGGAGGCACGGGTGAGACGATCACCACTCTCACCAACGGAGATG
TTGAGAACGAGCTTCTGAACCTTGATATCCCTCATTGGGTTCGAGAGCTT
CTTCTCTGACGCCATTCTGAGGATTAAGGGATGCAAAGTCAGAGGGAGAT
GAGCAAAg

BQ
 0 0 0 12 17 32 26 25 25 41 49 50 47 47 51 50 56 55 59 50 50 53 55 55 53 59 57 51 54 61 56 54 53 60 48 48 57 58 58 64 60 62 58 64 57 53 53 59 64 67
 67 75 72 65 55 47 47 39 44 41 48 54 55 61 52 47 53 53 53 60 67 67 74 76 76 69 65 62 58 54 51 56 60 60 73 73 66 61 61 59 52 56 56 60 64 64 59 57 59 60
 60 59 71 82 74 69 61 64 61 83 68 72 71 73 75 71 77 66 62 62 60 64 61 63 63 61 75 75 64 64 60 64 64 75 75 72 80 83 61 64 64 72 64 64 61 56 57 60 62 62
 62 62 60 52 50 56 57 57 61 61 64 59 59 64 60 62 58 54 50 51 58 63 67 69 75 75 78 86 86 84 79 71 71 72 69 69 67 90 90 90 90 79 85 88 69 71 71 67 67 67
 78 75 75 80 84 80 80 82 86 86 90 90 90 90 90 76 75 67 67 67 70 69 78 75 81 75 73 73 69 68 60 66 70 73 70 70 70 70 69 74 75 72 69 73 75 72 72 88 89 75
 75 75 75 77 88 90 90 90 81 81 78 78 75 75 80 83 86 82 84 83 86 86 90 85 73 56 56 55 59 54 62 62 72 74 77 90 90 90 90 90 85 90 75 75 78 85 84 88 80 80
 72 76 72 74 74 90 90 88 75 75 75 72 72 72 77 77 77 80 77 77 90 90 90 90 90 90 90 90 90 90 90 90 88 86 86 86 90 86 77 83 77 77 77 83 83 90 90 90 90 90
 90 90 90 90 90 90 87 80 78 74 78 74 81 73 80 78 86 86 86 86 88 80 88 87 87 87 87 90 90 90 90 90 90 90 90 87 87 80 71 70 67 63 63 65 72 80 90 90 90 90
 86 86 86 88 86 90 89 76 76 78 78 77 77 76 89 89 71 71 56 51 51 43 43 43 43 58 58 80 80 80 80 89 89 71 71 58 38 38 38 43 43 60 60 60 60 60 58 58 58 75
 79 79 78 88 83 81 81 71 71 69 75 75 78 78 78 85 88 85 85 90 85 85 85 90 90 71 67 60 58 58 58 68 70 78 80 89 90 85 85 85 80 77 78 77 74 74 72 72 70 58
 58 58 43 43 51 51 51 43 43 43 43 43 58 66 66 66 51 51 45 45 51 51 51 51 60 60 60 69 69 69 66 66 72 76 80 85 81 81 60 60 60 60 58 58 51 51 51 51 56 56
 71 71 71 71 71 71 61 58 58 58 58 58 60 61 58 58 58 59 62 66 63 67 64 64 64 64 67 67 76 74 76 72 72 58 58 58 58 58 60 73 80 80 74 64 61 54 45 45 45 51
 51 51 51 51 51 45 40 39 39 49 49 49 54 52 64 65 67 71 72 72 73 73 43 36 39 39 39 39 39 51 51 51 51 51 51 51 51 51 51 51 51 51 40 39 39 39 39 35 35 40
 51 51 51 51 40 40 40 35 35 45 43 43 52 50 50 49 52 49 51 53 46 46 46 46 46 46 46 51 42 56 40 40 40 40 39 35 35 35 35 35 35 51 51 56 51 51 46 40 40 40
 40 40 40 40 39 34 34 0

AF ML4924F U -5
AF ML4924R C 1
BS 1 9 ML4924R
BS 10 11 ML4924F
BS 12 16 ML4924R
BS 17 51 ML4924F
BS 52 54 ML4924R
BS 55 63 ML4924F
BS 64 64 ML4924R
BS 65 109 ML4924F
BS 110 110 ML4924R
BS 111 111 ML4924F
BS 112 113 ML4924R
BS 114 114 ML4924F
BS 115 117 ML4924R
BS 118 121 ML4924F
BS 122 128 ML4924R
BS 129 133 ML4924F
BS 134 138 ML4924R
BS 139 141 ML4924F
BS 142 144 ML4924R
BS 145 160 ML4924F
BS 161 161 ML4924R
BS 162 174 ML4924F
BS 175 180 ML4924R
BS 181 187 ML4924F
BS 188 188 ML4924R
BS 189 200 ML4924F
BS 201 201 ML4924R
BS 202 203 ML4924F
BS 204 221 ML4924R
BS 222 222 ML4924F
BS 223 223 ML4924R
BS 224 240 ML4924F
BS 241 244 ML4924R
BS 245 245 ML4924F
BS 246 258 ML4924R
BS 259 262 ML4924F
BS 263 291 ML4924R
BS 292 292 ML4924F
BS 293 331 ML4924R
BS 332 332 ML4924F
BS 333 372 ML4924R
BS 373 377 ML4924F
BS 378 453 ML4924R
BS 454 454 ML4924F
BS 455 595 ML4924R
BS 596 596 ML4924F
BS 597 609 ML4924R
BS 610 624 ML4924F
BS 625 659 ML4924R
BS 660 670 ML4924F
BS 671 708 ML4924R

RD ML4924F 734 0 0
ttgttcttttctcgAGGGTACTTGAGGATTCTACCACCACAACAACAAAG
CCTTATCATCCAGAACCGCAAATTATAAAAAAGAGCCAACACCACAAAAC
AAAATGAAAAGAAACAAACTCTTCAACCAGTGATGTTCTGAGACTTGTTG
AGGATAACACCTTCGTACTTAACTTGGAACCACTTCATGGCATCATCCTT
GGTAACTCTATGCTGAATCCCAACGCGAGTCTTGCACCTACGGCGACGTG
CAACACGGTATCCCGGGCGTTCAAGAACAACATAGAAGTCCATTCCATAG
ATACCCGTAGAAGGATCGTACTTGATTCCAAGATCAATGTGCTCCTGGAT
ACCGAATCCAAAACAGCCAGTGTCACTGAAGTTCCTCCTCAACAGCTCGT
ACTCCTTGACTTTCAAGCCACTCTCAACaaGCTGCATTGCCTTgccTCCT
CTCACGGTGACGTAGCACGCAATCTTTTCATTACGTCTAATACCGAAAGA
CCTCACAGtgcaCctggcCTTGgacaacacAGGTGTTTGACCACTGAGCT
gttacaAAACCTTGGAGGCACGGGTGAGACGATCACCACTCTCACCAACG
GAGATgtcgaGAACGAGCTTCTGAACCTTGATattcctCATtgggctcca
cagctctttcTCTGACGCCATTCTGAGGatctagggatgcacacccacaa
ggacatgaccaaaatcgacatctgggcccactcg

QA 12 601 10 713
DS CHROMAT_FILE: ML4924F PHD_FILE: ML4924F.phd.1 CHEM: term DYE: big TIME: Thu Jun 21 11:27:03 2001

RD ML4924R 763 0 0
atatcTCGAGGGTACTTGAGGATTCTACCACCACAACAACAAAGCCTTAT
CATCCAGAACCGCAAATTATAAAAAAGAGCCAACACCACAAAACAAAATG
AAAAGAAACAAACTCTTCAACCAGTGATGTTCTGAGACTTGTTGAGGATA
ACACCTTCGTACTTAACTTGGAACCACTTCATGGCATCATCCTTGGTAAC
TCTATGCTGAATCCCAACGCGAGTCTTGCACCTACGGCGACGTGCAACAC
GGTATCCCGGGCGTTCAAGAACAACATAGAAGTCCATTCCATAGATACCC
GTAGAAGGATCGTACTTGATTCCAAGATCAATGTGCTCCTGGATACCGAA
TCCAAAACAGCCAGTGTCACTGAAGTTCCTCCTCAACAGCTCGTACTCCT
TGACTTTCAAGCCACTCTCAAGAAGCTGCATTGCCTTGTCTCCTCTCACG
GTGACGTAGCACGCAATCTTTTCATTACGTCTAATACCGAAAGACCTCAC
AGTGTACCTCGCCTTGGAGAAGACAGGTGTTTGACCACTGAGCTGTTCCA
AAACCTTGGAGGCACGGGTGAGACGATCACCACTCTCACCAACGGAGATG
TTGAGAACGAGCTTCTGAACCTTGATATCCCTCATTGGGTTCGAGAGCTT
CTTCTCTGACGCCATTCTGAGGATTAAGGGATGCAAAGTCAGAGGGAGAT
GAGCAAAgxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxaccaaagt

QA 10 707 1 708
DS CHROMAT_FILE: ML4924R PHD_FILE: ML4924R.phd.1 CHEM: term DYE: big TIME: Thu Jun 21 11:27:03 2001


WA{
phrap_params phrap 010621:164002
/usr/local/genome/bin/phrap test_project.fasta.screen -new_ace -view 
phrap version 0.990329
}

BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.2000444000766000024      1352313155576321 27372 0ustar00cjfieldsstaff000000000000AS 1 2

CO Contig12 708 2 51 U
atatcTCGAGGGTACTTGAGGATTCTACCACCACAACAACAAAGCCTTAT
CATCCAGAACCGCAAATTATAAAAAAGAGCCAACACCACAAAACAAAATG
AAAAGAAACAAACTCTTCAACCAGTGATGTTCTGAGACTTGTTGAGGATA
ACACCTTCGTACTTAACTTGGAACCACTTCATGGCATCATCCTTGGTAAC
TCTATGCTGAATCCCAACGCGAGTCTTGCACCTACGGCGACGTGCAACAC
GGTATCCCGGGCGTTCAAGAACAACATAGAAGTCCATTCCATAGATACCC
GTAGAAGGATCGTACTTGATTCCAAGATCAATGTGCTCCTGGATACCGAA
TCCAAAACAGCCAGTGTCACTGAAGTTCCTCCTCAACAGCTCGTACTCCT
TGACTTTCAAGCCACTCTCAAGAAGCTGCATTGCCTTGTCTCCTCTCACG
GTGACGTAGCACGCAATCTTTTCATTACGTCTAATACCGAAAGACCTCAC
AGTGTACCTCGCCTTGGAGAAGACAGGTGTTTGACCACTGAGCTGTTCCA
AAACCTTGGAGGCACGGGTGAGACGATCACCACTCTCACCAACGGAGATG
TTGAGAACGAGCTTCTGAACCTTGATATCCCTCATTGGGTTCGAGAGCTT
CTTCTCTGACGCCATTCTGAGGATTAAGGGATGCAAAGTCAGAGGGAGAT
GAGCAAAg

BQ
 0 0 0 12 17 32 26 25 25 41 49 50 47 47 51 50 56 55 59 50 50 53 55 55 53 59 57 51 54 61 56 54 53 60 48 48 57 58 58 64 60 62 58 64 57 53 53 59 64 67
 67 75 72 65 55 47 47 39 44 41 48 54 55 61 52 47 53 53 53 60 67 67 74 76 76 69 65 62 58 54 51 56 60 60 73 73 66 61 61 59 52 56 56 60 64 64 59 57 59 60
 60 59 71 82 74 69 61 64 61 83 68 72 71 73 75 71 77 66 62 62 60 64 61 63 63 61 75 75 64 64 60 64 64 75 75 72 80 83 61 64 64 72 64 64 61 56 57 60 62 62
 62 62 60 52 50 56 57 57 61 61 64 59 59 64 60 62 58 54 50 51 58 63 67 69 75 75 78 86 86 84 79 71 71 72 69 69 67 90 90 90 90 79 85 88 69 71 71 67 67 67
 78 75 75 80 84 80 80 82 86 86 90 90 90 90 90 76 75 67 67 67 70 69 78 75 81 75 73 73 69 68 60 66 70 73 70 70 70 70 69 74 75 72 69 73 75 72 72 88 89 75
 75 75 75 77 88 90 90 90 81 81 78 78 75 75 80 83 86 82 84 83 86 86 90 85 73 56 56 55 59 54 62 62 72 74 77 90 90 90 90 90 85 90 75 75 78 85 84 88 80 80
 72 76 72 74 74 90 90 88 75 75 75 72 72 72 77 77 77 80 77 77 90 90 90 90 90 90 90 90 90 90 90 90 88 86 86 86 90 86 77 83 77 77 77 83 83 90 90 90 90 90
 90 90 90 90 90 90 87 80 78 74 78 74 81 73 80 78 86 86 86 86 88 80 88 87 87 87 87 90 90 90 90 90 90 90 90 87 87 80 71 70 67 63 63 65 72 80 90 90 90 90
 86 86 86 88 86 90 89 76 76 78 78 77 77 76 89 89 71 71 56 51 51 43 43 43 43 58 58 80 80 80 80 89 89 71 71 58 38 38 38 43 43 60 60 60 60 60 58 58 58 75
 79 79 78 88 83 81 81 71 71 69 75 75 78 78 78 85 88 85 85 90 85 85 85 90 90 71 67 60 58 58 58 68 70 78 80 89 90 85 85 85 80 77 78 77 74 74 72 72 70 58
 58 58 43 43 51 51 51 43 43 43 43 43 58 66 66 66 51 51 45 45 51 51 51 51 60 60 60 69 69 69 66 66 72 76 80 85 81 81 60 60 60 60 58 58 51 51 51 51 56 56
 71 71 71 71 71 71 61 58 58 58 58 58 60 61 58 58 58 59 62 66 63 67 64 64 64 64 67 67 76 74 76 72 72 58 58 58 58 58 60 73 80 80 74 64 61 54 45 45 45 51
 51 51 51 51 51 45 40 39 39 49 49 49 54 52 64 65 67 71 72 72 73 73 43 36 39 39 39 39 39 51 51 51 51 51 51 51 51 51 51 51 51 51 40 39 39 39 39 35 35 40
 51 51 51 51 40 40 40 35 35 45 43 43 52 50 50 49 52 49 51 53 46 46 46 46 46 46 46 51 42 56 40 40 40 40 39 35 35 35 35 35 35 51 51 56 51 51 46 40 40 40
 40 40 40 40 39 34 34 0

AF ML4924F U -5
AF ML4924R C 1
BS 1 9 ML4924R
BS 10 11 ML4924F
BS 12 16 ML4924R
BS 17 51 ML4924F
BS 52 54 ML4924R
BS 55 63 ML4924F
BS 64 64 ML4924R
BS 65 109 ML4924F
BS 110 110 ML4924R
BS 111 111 ML4924F
BS 112 113 ML4924R
BS 114 114 ML4924F
BS 115 117 ML4924R
BS 118 121 ML4924F
BS 122 128 ML4924R
BS 129 133 ML4924F
BS 134 138 ML4924R
BS 139 141 ML4924F
BS 142 144 ML4924R
BS 145 160 ML4924F
BS 161 161 ML4924R
BS 162 174 ML4924F
BS 175 180 ML4924R
BS 181 187 ML4924F
BS 188 188 ML4924R
BS 189 200 ML4924F
BS 201 201 ML4924R
BS 202 203 ML4924F
BS 204 221 ML4924R
BS 222 222 ML4924F
BS 223 223 ML4924R
BS 224 240 ML4924F
BS 241 244 ML4924R
BS 245 245 ML4924F
BS 246 258 ML4924R
BS 259 262 ML4924F
BS 263 291 ML4924R
BS 292 292 ML4924F
BS 293 331 ML4924R
BS 332 332 ML4924F
BS 333 372 ML4924R
BS 373 377 ML4924F
BS 378 453 ML4924R
BS 454 454 ML4924F
BS 455 595 ML4924R
BS 596 596 ML4924F
BS 597 609 ML4924R
BS 610 624 ML4924F
BS 625 659 ML4924R
BS 660 670 ML4924F
BS 671 708 ML4924R

RD ML4924F 734 0 0
ttgttcttttctcgAGGGTACTTGAGGATTCTACCACCACAACAACAAAG
CCTTATCATCCAGAACCGCAAATTATAAAAAAGAGCCAACACCACAAAAC
AAAATGAAAAGAAACAAACTCTTCAACCAGTGATGTTCTGAGACTTGTTG
AGGATAACACCTTCGTACTTAACTTGGAACCACTTCATGGCATCATCCTT
GGTAACTCTATGCTGAATCCCAACGCGAGTCTTGCACCTACGGCGACGTG
CAACACGGTATCCCGGGCGTTCAAGAACAACATAGAAGTCCATTCCATAG
ATACCCGTAGAAGGATCGTACTTGATTCCAAGATCAATGTGCTCCTGGAT
ACCGAATCCAAAACAGCCAGTGTCACTGAAGTTCCTCCTCAACAGCTCGT
ACTCCTTGACTTTCAAGCCACTCTCAACaaGCTGCATTGCCTTgccTCCT
CTCACGGTGACGTAGCACGCAATCTTTTCATTACGTCTAATACCGAAAGA
CCTCACAGtgcaCctggcCTTGgacaacacAGGTGTTTGACCACTGAGCT
gttacaAAACCTTGGAGGCACGGGTGAGACGATCACCACTCTCACCAACG
GAGATgtcgaGAACGAGCTTCTGAACCTTGATattcctCATtgggctcca
cagctctttcTCTGACGCCATTCTGAGGatctagggatgcacacccacaa
ggacatgaccaaaatcgacatctgggcccactcg

QA 12 601 10 713
DS CHROMAT_FILE: ML4924F PHD_FILE: ML4924F.phd.1 CHEM: term DYE: big TIME: Thu Jun 21 11:27:03 2001

RD ML4924R 763 0 0
atatcTCGAGGGTACTTGAGGATTCTACCACCACAACAACAAAGCCTTAT
CATCCAGAACCGCAAATTATAAAAAAGAGCCAACACCACAAAACAAAATG
AAAAGAAACAAACTCTTCAACCAGTGATGTTCTGAGACTTGTTGAGGATA
ACACCTTCGTACTTAACTTGGAACCACTTCATGGCATCATCCTTGGTAAC
TCTATGCTGAATCCCAACGCGAGTCTTGCACCTACGGCGACGTGCAACAC
GGTATCCCGGGCGTTCAAGAACAACATAGAAGTCCATTCCATAGATACCC
GTAGAAGGATCGTACTTGATTCCAAGATCAATGTGCTCCTGGATACCGAA
TCCAAAACAGCCAGTGTCACTGAAGTTCCTCCTCAACAGCTCGTACTCCT
TGACTTTCAAGCCACTCTCAAGAAGCTGCATTGCCTTGTCTCCTCTCACG
GTGACGTAGCACGCAATCTTTTCATTACGTCTAATACCGAAAGACCTCAC
AGTGTACCTCGCCTTGGAGAAGACAGGTGTTTGACCACTGAGCTGTTCCA
AAACCTTGGAGGCACGGGTGAGACGATCACCACTCTCACCAACGGAGATG
TTGAGAACGAGCTTCTGAACCTTGATATCCCTCATTGGGTTCGAGAGCTT
CTTCTCTGACGCCATTCTGAGGATTAAGGGATGCAAAGTCAGAGGGAGAT
GAGCAAAgxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxaccaaagt

QA 10 707 1 708
DS CHROMAT_FILE: ML4924R PHD_FILE: ML4924R.phd.1 CHEM: term DYE: big TIME: Thu Jun 21 11:27:03 2001


WA{
phrap_params phrap 010621:164002
/usr/local/genome/bin/phrap test_project.fasta.screen -new_ace -view 
phrap version 0.990329
}

CT{
Contig12 Annotation consed 40 50 060216:160521
contig extra
info
}

CT{
Contig12 Annotation consed 20 30 060216:160521
COMMENT{
contig tag
comment
C}
}
BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs000555000766000024       136613155576321 30135 0ustar00cjfieldsstaff000000000000>test_project.fasta.screen.Contig1
ATATCTCGAGGGTACTTGAGGATTCTACCACCACAACAACAAAGCCTTAT
CATCCAGAACCGCAAATTATAAAAAAGAGCCAACACCACAAAACAAAATG
AAAAGAAACAAACTCTTCAACCAGTGATGTTCTGAGACTTGTTGAGGATA
ACACCTTCGTACTTAACTTGGAACCACTTCATGGCATCATCCTTGGTAAC
TCTATGCTGAATCCCAACGCGAGTCTTGCACCTACGGCGACGTGCAACAC
GGTATCCCGGGCGTTCAAGAACAACATAGAAGTCCATTCCATAGATACCC
GTAGAAGGATCGTACTTGATTCCAAGATCAATGTGCTCCTGGATACCGAA
TCCAAAACAGCCAGTGTCACTGAAGTTCCTCCTCAACAGCTCGTACTCCT
TGACTTTCAAGCCACTCTCAAGAAGCTGCATTGCCTTGTCTCCTCTCACG
GTGACGTAGCACGCAATCTTTTCATTACGTCTAATACCGAAAGACCTCAC
AGTGTACCTCGCCTTGGAGAAGACAGGTGTTTGACCACTGAGCTGTTCCA
AAACCTTGGAGGCACGGGTGAGACGATCACCACTCTCACCAACGGAGATG
TTGAGAACGAGCTTCTGAACCTTGATATCCCTCATTGGGTTCGAGAGCTT
CTTCTCTGACGCCATTCTGAGGATTAAGGGATGCAAAGTCAGAGGGAGAT
GAGCAAAG
BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual000555000766000024       417313155576321 31075 0ustar00cjfieldsstaff000000000000>test_project.fasta.screen.Contig1 
0 0 0 12 17 32 26 25 25 41 49 50 47 47 51 50 56 55 59 50 50 53 55 55 53 59 57 51 54 61 56 54 53 60 48 48 57 58 58 64 60 62 58 64 57 53 53 59 64 67 
67 75 72 65 55 47 47 39 44 41 48 54 55 61 52 47 53 53 53 60 67 67 74 76 76 69 65 62 58 54 51 56 60 60 73 73 66 61 61 59 52 56 56 60 64 64 59 57 59 60 
60 59 71 82 74 69 61 64 61 83 68 72 71 73 75 71 77 66 62 62 60 64 61 63 63 61 75 75 64 64 60 64 64 75 75 72 80 83 61 64 64 72 64 64 61 56 57 60 62 62 
62 62 60 52 50 56 57 57 61 61 64 59 59 64 60 62 58 54 50 51 58 63 67 69 75 75 78 86 86 84 79 71 71 72 69 69 67 90 90 90 90 79 85 88 69 71 71 67 67 67 
78 75 75 80 84 80 80 82 86 86 90 90 90 90 90 76 75 67 67 67 70 69 78 75 81 75 73 73 69 68 60 66 70 73 70 70 70 70 69 74 75 72 69 73 75 72 72 88 89 75 
75 75 75 77 88 90 90 90 81 81 78 78 75 75 80 83 86 82 84 83 86 86 90 85 73 56 56 55 59 54 62 62 72 74 77 90 90 90 90 90 85 90 75 75 78 85 84 88 80 80 
72 76 72 74 74 90 90 88 75 75 75 72 72 72 77 77 77 80 77 77 90 90 90 90 90 90 90 90 90 90 90 90 88 86 86 86 90 86 77 83 77 77 77 83 83 90 90 90 90 90 
90 90 90 90 90 90 87 80 78 74 78 74 81 73 80 78 86 86 86 86 88 80 88 87 87 87 87 90 90 90 90 90 90 90 90 87 87 80 71 70 67 63 63 65 72 80 90 90 90 90 
86 86 86 88 86 90 89 76 76 78 78 77 77 76 89 89 71 71 56 51 51 43 43 43 43 58 58 80 80 80 80 89 89 71 71 58 38 38 38 43 43 60 60 60 60 60 58 58 58 75 
79 79 78 88 83 81 81 71 71 69 75 75 78 78 78 85 88 85 85 90 85 85 85 90 90 71 67 60 58 58 58 68 70 78 80 89 90 85 85 85 80 77 78 77 74 74 72 72 70 58 
58 58 43 43 51 51 51 43 43 43 43 43 58 66 66 66 51 51 45 45 51 51 51 51 60 60 60 69 69 69 66 66 72 76 80 85 81 81 60 60 60 60 58 58 51 51 51 51 56 56 
71 71 71 71 71 71 61 58 58 58 58 58 60 61 58 58 58 59 62 66 63 67 64 64 64 64 67 67 76 74 76 72 72 58 58 58 58 58 60 73 80 80 74 64 61 54 45 45 45 51 
51 51 51 51 51 45 40 39 39 49 49 49 54 52 64 65 67 71 72 72 73 73 43 36 39 39 39 39 39 51 51 51 51 51 51 51 51 51 51 51 51 51 40 39 39 39 39 35 35 40 
51 51 51 51 40 40 40 35 35 45 43 43 52 50 50 49 52 49 51 53 46 46 46 46 46 46 46 51 42 56 40 40 40 40 39 35 35 35 35 35 35 51 51 56 51 51 46 40 40 40 
40 40 40 40 39 34 34 0 
BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.fasta.screen.log000555000766000024       266713155576321 27255 0ustar00cjfieldsstaff000000000000No. words: 2989; after pruning: 2826


Histogram of relative pair offsets, for read pairs with multiple alignments:

Pass 1
             Gap  Score    

Pass: 1
#reads  #contigs (not counting singlets)
    1      2

N.B. Following not based on all pairs!!

Lowest   # merges  # failures
LLR score

Gap   # merges  # failures
 size

Offset

Pass 3
             Gap  Score    
Merge:(0)    0    0.0 15.1 (1,1:768)  628  3.27 0.00 0.00  ML4924F       10   713 (21)  C ML4924R   (3)   760    57 *

Pass: 3
#reads  #contigs (not counting singlets)
    2      1

N.B. Following not based on all pairs!!

Lowest   # merges  # failures
LLR score
0.0       1        0

Gap   # merges  # failures
 size
 0       1        0

Offset
  0       1 

Pass 4
             Gap  Score    

Pass: 4
#reads  #contigs (not counting singlets)
    2      1

N.B. Following not based on all pairs!!

Lowest   # merges  # failures
LLR score

Gap   # merges  # failures
 size

Offset

Read equivalence class histogram:
    1    2
    2    1

Chimera merges: 


Contig 1:  302 nodes

 153 str. conn. components

Path
    1  C ML4924R         763 
   19    ML4924F          25 
  275  C ML4924R         489 
  610    ML4924F         616 
  622  C ML4924R         142 
  660    ML4924F         666 
  668  C ML4924R          96 
Contig length: old 769, new 763

Contig length: old 763, new 708
New start: 0 

Contig 1 unpadded => padded conversion:
  200 =>   200
  400 =>   400
  600 =>   600BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.fasta.screen.problems000555000766000024          013155576321 30212 0ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual000555000766000024          013155576321 31153 0ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.fasta.screen.qual000555000766000024      2145113155576321 27446 0ustar00cjfieldsstaff000000000000>ML4922R PHD_FILE: ML4922R.phd.1
4 4 6 6 9 19 24 24 19 16 10 8 8 9 21 20 32 34 34 39
39 40 39 46 40 37 32 32 28 28 25 25 34 32 40 40 40
40 40 40 34 35 35 35 35 35 35 35 35 35 51 51 39 39
39 35 31 31 31 31 31 32 35 35 45 51 56 51 39 39 40
40 39 39 45 40 40 40 35 35 39 35 35 35 37 40 40 40
40 40 40 40 45 51 51 51 51 46 46 40 40 39 39 39 39
40 40 46 40 40 40 40 40 51 51 51 51 45 45 45 45 51
51 56 56 56 56 51 51 51 51 51 40 40 40 40 40 40 51
51 39 39 38 38 38 35 39 39 39 39 43 43 43 46 46 51
51 56 56 45 35 35 35 35 35 35 43 43 43 43 43 43 43
43 43 43 43 51 51 51 56 56 56 56 56 43 43 43 43 43
43 43 43 43 43 43 45 45 43 43 43 43 43 43 43 43 43
43 43 43 43 43 43 43 45 45 43 43 43 43 43 51 51 51
51 51 51 51 56 56 45 43 43 43 43 43 43 43 43 43 43
51 51 56 56 51 56 56 56 56 56 56 56 51 45 45 45 45
45 45 51 45 43 43 43 43 43 45 51 51 51 51 51 45 45
45 51 51 51 56 51 43 36 36 36 36 36 43 51 51 51 51
51 56 56 56 56 56 56 56 56 56 56 56 56 56 51 51 43
43 43 43 43 43 45 45 51 51 51 51 43 43 43 43 43 43
43 43 43 43 51 56 56 56 43 43 43 43 43 43 43 51 51
51 43 43 43 43 45 45 56 56 51 43 43 43 43 43 43 45
43 43 43 43 43 43 45 56 56 56 56 56 56 56 56 56 56
56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56
56 56 56 56 56 56 51 51 45 45 45 45 51 51 56 56 56
51 45 45 45 45 45 45 51 43 43 43 43 45 45 56 56 56
56 56 56 56 51 51 51 43 43 43 43 43 43 43 43 43 43
43 43 40 45 45 45 45 56 56 56 56 56 56 56 56 51 51
40 40 40 40 45 45 56 56 56 56 51 51 51 51 51 51 51
45 40 37 37 37 40 45 56 51 51 51 51 51 51 56 56 56
56 56 56 56 56 56 56 56 56 56 56 51 51 51 51 51 51
56 45 40 40 40 40 40 51 51 51 51 56 56 56 56 56 56
56 56 51 51 51 51 51 51 56 56 56 56 56 56 56 56 51
45 45 45 45 45 40 40 40 40 40 51 56 56 56 56 56 56
56 56 51 51 51 40 40 40 56 56 46 48 46 46 44 44 40
40 32 29 24 24 29 40 40 40 44 44 40 34 34 40 40 40
40 40 40 40 44 56 56 56 56 51 40 45 45 45 45 40 45
46 51 56 56 56 51 51 51 40 40 40 40 37 40 56 56 51
40 40 40 40 40 40 40 40 44 32 32 32 25 24 24 29 40
40 40 48 48 32 32 26 25 25 25 32 30 32 34 34 40 40
40 32 32 29 25 25 29 29 34 40 40 40 44 44 40 40 40
40 25 24 18 15 15 25 29 29 29 48 40 40 40 44 32 29
27 25 24 26 29 29 25 25 32 32 29 29 34 25 25 25 22
24 29 29 28 25 34 32 32 22 22 24 18 16 19 19 18 18
23 20 19 22 25 27 29 25 29 26 29 29 29 24 17 12 8 4
4 
>ML4924F PHD_FILE: ML4924F.phd.1
10 16 19 19 8 6 6 6 6 9 9 15 17 17 22 22 25 25 22 22
22 25 34 34 42 35 35 38 40 40 35 34 31 31 33 34 35
33 29 35 29 29 32 34 34 35 35 42 42 42 42 35 35 37
35 35 35 35 35 31 33 24 24 24 29 26 29 29 29 29 29
29 35 35 35 35 35 35 42 42 47 47 40 35 35 35 32 32
32 32 42 42 42 37 37 30 30 35 35 35 35 35 37 32 32
35 35 37 37 42 42 37 37 40 37 37 35 35 35 37 35 35
37 37 37 37 35 32 29 31 31 29 35 35 35 35 35 35 35
35 35 32 32 35 32 35 35 32 32 32 32 32 35 35 35 35
35 35 37 37 35 35 32 32 32 32 32 30 35 35 35 35 35
35 32 35 42 42 42 42 35 35 38 38 38 38 42 40 40 38
35 35 35 42 50 56 56 50 56 56 42 42 42 38 38 38 38
38 38 40 38 38 38 40 40 40 44 42 42 42 38 36 36 32
32 32 35 35 38 41 41 41 41 41 42 41 41 41 41 41 41
41 41 41 35 40 35 32 32 36 38 35 35 37 38 35 35 35
35 37 37 41 41 41 41 41 41 41 35 35 35 32 35 31 33
32 35 35 37 29 33 16 16 9 20 13 23 23 33 35 37 35 40
40 45 40 40 50 30 30 33 40 33 37 29 29 21 25 21 23
23 50 50 37 35 35 35 32 32 32 37 37 37 40 37 37 37
37 35 35 44 44 44 44 44 56 44 56 37 35 35 35 35 35
26 32 26 26 26 32 32 35 35 35 35 35 42 42 35 42 42
42 42 35 33 29 33 29 30 28 35 33 35 35 35 35 37 37
45 44 44 44 44 44 44 44 39 39 42 42 42 42 42 35 28
27 24 20 20 22 29 29 40 40 42 42 35 35 35 37 35 35
33 33 33 35 35 34 34 33 33 33 29 28 28 27 21 21 15
15 21 21 25 29 29 29 29 33 33 25 27 23 23 11 10 10
24 24 29 29 27 29 29 29 29 32 36 36 35 45 40 38 38
28 28 26 32 32 35 35 35 42 37 34 34 42 29 29 29 35
35 26 24 17 14 12 12 25 27 35 37 38 40 34 34 34 35
32 33 32 29 29 21 21 27 33 26 16 16 10 10 10 20 12
6 6 8 9 9 11 13 18 15 15 17 11 8 11 9 13 9 19 21 24
24 18 15 15 21 25 29 29 25 25 14 14 9 9 9 24 14 11
8 8 8 15 20 27 40 40 40 26 24 12 12 15 13 10 17 18
15 12 15 16 19 23 20 24 21 21 21 21 24 16 20 18 20
16 16 14 12 10 10 12 17 17 29 29 29 19 16 9 9 9 16
13 11 9 11 9 10 9 19 14 14 10 10 10 14 14 25 26 28
32 32 32 33 33 28 21 18 12 11 13 9 9 12 10 11 10 11
12 11 11 10 10 10 10 8 8 10 9 9 9 6 6 8 8 11 9 9 10
10 14 14 10 8 8 17 10 10 9 12 9 11 7 7 10 12 9 6 6
6 6 8 8 11 12 10 9 9 8 8 12 14 20 16 17 10 10 12 17
17 24 18 14 14 11 14 12 15 15 10 9 11 9 9 10 8 6 6
8 8 7 7 9 9 7 6 10 6 6 6 6 
>ML4924R PHD_FILE: ML4924R.phd.1
6 6 6 8 8 12 18 16 14 11 9 6 6 9 19 20 32 34 34 39
39 39 29 40 28 21 13 4 4 4 8 8 23 29 39 40 40 40 40
46 34 33 29 29 32 33 34 34 34 34 40 40 34 34 34 34
34 34 39 40 40 40 40 40 40 40 46 51 51 56 51 51 35
35 35 35 35 35 39 40 40 40 40 56 42 51 46 46 46 46
46 46 46 46 40 40 40 40 40 40 35 35 35 35 35 35 40
40 40 51 51 51 51 40 35 35 39 39 39 39 40 51 51 51
51 51 51 51 51 51 51 51 51 51 39 39 39 39 39 35 40
40 40 40 40 39 39 39 39 38 40 39 39 39 39 39 40 45
51 51 51 51 51 51 45 45 45 45 45 45 45 51 51 56 43
43 43 43 43 43 56 56 56 56 56 51 43 43 43 43 43 43
43 43 43 43 43 43 43 43 43 43 43 43 43 43 46 56 56
56 56 56 56 56 56 51 51 51 51 43 43 45 45 45 45 56
56 56 51 51 51 51 51 51 45 45 45 45 45 51 51 51 51
45 45 51 51 51 51 51 43 43 43 43 43 43 51 51 51 43
43 43 43 43 43 51 51 45 45 45 45 45 45 51 51 51 51
51 43 43 43 43 43 43 43 43 43 45 56 56 56 56 56 56
51 51 51 43 43 43 43 43 43 43 43 43 43 43 43 43 43
43 43 43 43 43 43 45 45 45 45 45 43 43 38 38 38 43
56 56 56 56 51 51 51 51 43 43 43 43 43 43 51 51 56
56 56 56 56 43 43 43 43 43 43 43 56 56 51 51 51 51
51 51 56 56 51 51 43 43 43 43 43 43 43 45 45 45 56
56 56 56 56 56 56 51 43 43 43 43 43 43 51 51 51 51
51 45 45 45 51 45 45 45 45 45 45 56 56 56 56 56 56
56 56 56 56 56 51 51 51 51 51 51 51 51 56 51 51 51
51 51 51 56 56 56 56 56 56 56 56 56 56 40 40 40 40
40 40 40 40 40 40 40 40 51 56 56 51 51 51 51 51 51
51 51 51 45 45 45 45 45 45 51 56 56 56 56 40 39 39
39 39 39 39 40 40 40 40 56 56 51 51 51 51 51 51 51
45 40 40 37 37 40 40 56 56 51 51 40 40 40 40 40 51
51 37 37 37 37 37 40 40 34 34 29 29 29 29 32 29 25
19 27 27 32 32 34 40 34 40 34 35 35 35 35 39 40 56
56 56 51 51 46 46 42 42 42 46 40 37 37 40 29 29 29
29 29 27 32 29 29 34 48 48 48 32 34 34 34 31 31 37
46 48 48 40 40 40 27 25 21 16 16 18 19 23 27 25 29
24 29 32 29 29 25 25 21 15 15 23 27 27 27 27 25 22
24 29 32 32 40 29 29 29 48 48 40 40 40 29 29 25 29
29 40 40 32 32 32 32 32 25 25 25 29 40 36 40 36 36
37 33 46 24 24 24 32 32 40 34 22 25 25 27 25 22 29
29 25 21 21 22 29 24 24 24 31 31 28 28 24 19 19 23
27 25 22 29 34 32 32 32 25 18 18 18 18 23 32 26 25
19 15 15 15 23 23 22 34 37 40 32 32 29 22 18 18 13
22 16 20 25 29 24 24 25 19 19 25 24 21 21 27 21 20
26 25 18 15 15 10 13 13 17 21 22 25 29 25 25 25 24
19 10 10 11 17 17 12 19 16 11 
>ML4947F PHD_FILE: ML4947F.phd.1
9 13 11 21 24 34 34 34 31 31 25 25 25 25 34 34 38 29
29 29 29 29 32 32 32 32 32 32 32 56 46 35 35 35 35
35 35 40 45 40 40 40 46 40 40 40 40 40 40 37 37 35
35 35 35 35 35 40 46 51 51 51 51 40 40 40 40 35 23
19 10 13 10 16 16 31 33 33 40 40 40 44 46 51 51 51
51 51 51 51 51 51 51 51 51 51 51 51 51 51 51 56 56
56 56 56 56 51 46 40 40 40 40 40 40 40 40 39 39 38
38 38 39 40 40 40 40 39 39 39 39 39 40 51 51 51 51
51 51 56 40 40 40 43 43 43 43 43 43 43 43 43 43 51
51 51 51 51 51 51 51 51 51 51 43 43 43 43 43 43 43
43 43 43 43 45 45 45 45 51 51 51 51 43 43 43 43 43
43 43 43 43 43 43 45 51 45 45 45 45 45 45 51 56 56
56 51 51 51 45 45 45 51 45 45 51 51 51 45 45 43 43
43 43 45 45 56 56 56 45 40 40 40 38 35 36 36 36 43
43 43 36 43 43 43 51 51 51 56 43 43 43 43 38 38 42
43 44 51 51 51 43 43 43 43 43 43 45 51 51 43 45 45
43 43 43 43 43 43 43 43 43 40 41 41 45 45 45 45 45
45 45 45 45 45 41 43 41 43 43 45 45 45 45 45 45 45
45 43 51 56 56 56 51 51 51 51 51 51 46 46 42 42 42
45 43 43 43 43 43 43 43 43 45 43 45 45 45 45 45 45
45 45 43 43 43 43 43 43 43 43 43 43 43 56 43 41 45
45 41 41 42 46 46 51 51 51 51 51 51 51 51 45 43 43
43 43 43 43 43 45 45 56 56 56 56 56 56 56 51 51 45
45 45 41 45 45 51 56 56 51 51 51 51 51 51 51 51 51
51 45 43 43 43 43 43 43 43 43 43 43 43 51 51 43 43
43 40 43 43 45 45 45 45 45 51 56 56 56 56 56 56 51
51 45 45 43 43 45 45 43 43 56 56 50 45 40 40 37 40
40 51 51 51 56 56 45 40 40 40 40 40 40 40 45 37 42
42 43 43 46 37 37 37 37 37 37 43 42 42 50 46 46 51
37 37 37 40 35 35 35 35 35 35 37 51 51 51 51 51 45
45 45 45 45 46 44 44 42 46 46 51 51 51 56 51 51 42
46 42 51 51 37 37 37 37 40 45 56 56 56 56 56 51 51
45 40 35 35 35 35 39 45 56 56 51 51 45 45 45 45 45
40 45 45 40 40 40 45 40 42 42 46 56 51 42 42 37 37
35 40 34 29 37 40 40 44 34 32 32 27 25 22 26 29 27
32 29 27 25 24 29 29 29 40 28 29 24 25 29 32 32 32
34 40 40 33 40 40 35 40 40 48 48 40 40 40 40 34 32
29 34 40 32 29 29 29 29 29 29 32 27 32 25 22 18 21
23 23 18 19 25 40 40 40 36 30 30 32 32 32 29 31 21
21 18 15 14 25 24 24 25 25 36 32 32 40 40 40 32 27
27 25 20 20 25 19 19 18 13 13 18 27 27 32 28 32 24
27 24 22 20 27 27 27 25 29 29 29 22 22 23 27 23 23
25 30 33 27 39 25 28 26 26 21 16 10 10 14 16 20 27
27 24 22 21 27 21 21 
BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.fasta.screen.singlets000555000766000024       331113155576321 30307 0ustar00cjfieldsstaff000000000000>ML4922R  CHROMAT_FILE: ML4922R PHD_FILE: ML4922R.phd.1 CHEM: term DYE: big TIME: Thu Jun 21 11:28:31 2001
CCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXCGGACGCGTGGGGTGACCCCGGAAGATTCGAGTGCTTCGTCTGGT
AATCAAAATCAGGTTTCTCCGGTTGGATCTCAAACTCAAGGTTATGCCGT
GGCACAAATGTCGCCTGCTGTTTCATCTGTCAGTGATGCTCCCTCATTAG
ACACACAGAGACAACGAGATATTCAGTCCAGGCTAGCTAACAGTGGTTCA
GATGATTCTGATGACGAAGATCCTGATGGAGAGACTGTAACAACAGTGAA
TGATGATCCTACCGATGTTAAGCGTGCTAGGAGGATGCTTTCAAACCGAG
AATCCGCTAGGCGCTCTAGAAGAAGAAAGCAAGAGCAAATGAGTGAATTT
GATTCACAGGTTGGCCAATTACGTGGTGAGCATTCAACTATGCTTAAGCG
TCTTAGTGAGGTCACTCAGAAGTTTAGCACCGCTGTTGTCGATAACAGAA
TCTTAAAAGCTGATATCGAAACATTGAGAACAAAGGTGAAGATGGCAGAG
GACACTGTGAAAAGAGTGACAGGGATGAACCCTAGGCTTTTGGCAAAACC
ATACAGCATACCATTCGATAGGACACTGATGGGTTCTTCACAGCCAAACT
TGAATCAAACCGACATGATTCCAAATCAAATATCAGAGGACAACAGTTTT
GCAAGCAACTCGGTTGTTACTTTGGAATCCGGTTGCAATGCTTTTGAAGC
CAN
>ML4947F  CHROMAT_FILE: ML4947F PHD_FILE: ML4947F.phd.1 CHEM: term DYE: big TIME: Thu Jun 21 11:28:31 2001
CTGTGGGACCCACTGATATTACCGAACTTTTGAACCAAACAGTTATGTGT
TGGCGCCAAAAATAACGTTAAAGAAACCATCACAAGAGCCTTATGACAAA
GAGGGAGAGATAGACATAACTTAAGACATTACACAATTTGGTCAAACGAT
AAACCAAATCCAACAGACATTTAAACCAAATCCAACGCCAACAAAACATT
CATATATAAGATATACCCAAACCGTATCAAACGCAGACGCCGCCCTAGTA
ACTGTATCCTTTCACAAACAAGCTCTCGGAGGCAGCAGAGTCACCAGAAG
CCCCAGCAATGTATTTCCCAAGTGTAGCGTCCGAGTTAGCCTTGCACCTG
ACCAAGAACGTGGCCTGAGCTTTGGCTACGTTCTCTTTCTTACCTCCCCA
AGCCTTGAGTGTGCTTTGCTGGAGGGCTCGGCCAAAGGAGAAAGTAAGCG
TCCATGGCTTCAACAGATCGAGCTTGTTCATTGCGTTCAGATTTAGCGTT
GCTTCCTCTTCGCTCTGTCCTCCTGAGAGGAACACGATTCCTGGAACCGC
TGGTGGGACCGTGCGGCGGAGAGCAGTCACTGTGTATTCCGCAATGACTT
CCGGTGCAACCTTGGCGCTGTCTGAGCCTGGAGTGACCATGTTAGGTTTA
AGCAGAGTGCCTTCGAGGAGGACGTGGTGGTCGTTCAAGGCCTTGTACAC
GGCAGAAAGAACCGTCTCAGTCACAGCCGCACATTTCTT
BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.fasta.screen.view000555000766000024       727513155576321 27446 0ustar00cjfieldsstaff000000000000HEADER FORMAT1 test_project.fasta.screen 4 0 2 2 1
READ ML4922R 753
READ ML4947F 739
CONTIG Contig1 708
CONTIG_QUAL Contig1 0 0 0 12 17 32 26 25 25 41 49 50 47 47 51 50 56 55 59 50 50 53 55 55 53 59 57 51 54 61 56 54 53 60 48 48 57 58 58 64 60 62 58 64 57 53 53 59 64 67 67 75 72 65 55 47 47 39 44 41 48 54 55 61 52 47 53 53 53 60 67 67 74 76 76 69 65 62 58 54 51 56 60 60 73 73 66 61 61 59 52 56 56 60 64 64 59 57 59 60 60 59 71 82 74 69 61 64 61 83 68 72 71 73 75 71 77 66 62 62 60 64 61 63 63 61 75 75 64 64 60 64 64 75 75 72 80 83 61 64 64 72 64 64 61 56 57 60 62 62 62 62 60 52 50 56 57 57 61 61 64 59 59 64 60 62 58 54 50 51 58 63 67 69 75 75 78 86 86 84 79 71 71 72 69 69 67 90 90 90 90 79 85 88 69 71 71 67 67 67 78 75 75 80 84 80 80 82 86 86 90 90 90 90 90 76 75 67 67 67 70 69 78 75 81 75 73 73 69 68 60 66 70 73 70 70 70 70 69 74 75 72 69 73 75 72 72 88 89 75 75 75 75 77 88 90 90 90 81 81 78 78 75 75 80 83 86 82 84 83 86 86 90 85 73 56 56 55 59 54 62 62 72 74 77 90 90 90 90 90 85 90 75 75 78 85 84 88 80 80 72 76 72 74 74 90 90 88 75 75 75 72 72 72 77 77 77 80 77 77 90 90 90 90 90 90 90 90 90 90 90 90 88 86 86 86 90 86 77 83 77 77 77 83 83 90 90 90 90 90 90 90 90 90 90 90 87 80 78 74 78 74 81 73 80 78 86 86 86 86 88 80 88 87 87 87 87 90 90 90 90 90 90 90 90 87 87 80 71 70 67 63 63 65 72 80 90 90 90 90 86 86 86 88 86 90 89 76 76 78 78 77 77 76 89 89 71 71 56 51 51 43 43 43 43 58 58 80 80 80 80 89 89 71 71 58 38 38 38 43 43 60 60 60 60 60 58 58 58 75 79 79 78 88 83 81 81 71 71 69 75 75 78 78 78 85 88 85 85 90 85 85 85 90 90 71 67 60 58 58 58 68 70 78 80 89 90 85 85 85 80 77 78 77 74 74 72 72 70 58 58 58 43 43 51 51 51 43 43 43 43 43 58 66 66 66 51 51 45 45 51 51 51 51 60 60 60 69 69 69 66 66 72 76 80 85 81 81 60 60 60 60 58 58 51 51 51 51 56 56 71 71 71 71 71 71 61 58 58 58 58 58 60 61 58 58 58 59 62 66 63 67 64 64 64 64 67 67 76 74 76 72 72 58 58 58 58 58 60 73 80 80 74 64 61 54 45 45 45 51 51 51 51 51 51 45 40 39 39 49 49 49 54 52 64 65 67 71 72 72 73 73 43 36 39 39 39 39 39 51 51 51 51 51 51 51 51 51 51 51 51 51 40 39 39 39 39 35 35 40 51 51 51 51 40 40 40 35 35 45 43 43 52 50 50 49 52 49 51 53 46 46 46 46 46 46 46 51 42 56 40 40 40 40 39 35 35 35 35 35 35 51 51 56 51 51 46 40 40 40 40 40 40 40 39 34 34 0
DISCREP_QUAL Contig1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 8 0 0 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
READ ML4924F 734 12.3 9 712 Contig1 3 706
READ ML4924R 763 15.6 55 762 Contig1 707 0
BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.newtags000555000766000024          013155576321 25464 0ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.phrap.out000555000766000024      7727513155576321 26070 0ustar00cjfieldsstaff000000000000/usr/local/genome/bin/phrap test_project.fasta.screen -new_ace -view 
phrap version 0.990329

Run date:time  010621:164002
Query file(s):  test_project.fasta.screen
Presumed sequence type: DNA

Pairwise comparison algorithm: banded Smith-Waterman

Score matrix (set by value of penalty: -2)
    A   C   G   T   N   X
A   1  -2  -2  -2   0  -3
C  -2   1  -2  -2   0  -3
G  -2  -2   1  -2   0  -3
T  -2  -2  -2   1   0  -3
N   0   0   0   0   0   0
X  -3  -3  -3  -3   0  -3

Gap penalties: gap_init: -4, gap_ext: -3, ins_gap_ext: -3, del_gap_ext: -3, 
Using complexity-adjusted scores. Assumed background frequencies:
 A: 0.250  C: 0.250  G: 0.250  T: 0.250  N: 0.000  X: 0.000  

minmatch: 14, maxmatch: 30, max_group_size: 20, minscore: 30, bandwidth: 14, indexwordsize: 10
vector_bound: 80
word_raw: 0
trim_penalty: -2, trim_score: 20, trim_qual: 13, maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8, confirm_trim: 1, confirm_penalty: -5, confirm_score: 30
node_seg: 8, node_space: 4
forcelevel: 0, bypasslevel: 1
max_subclone_size: 5000

Sequence file: test_project.fasta.screen    4 entries
Residue counts:
  A      799
  C      688
  G      670
  N        1
  T      732
  X       99
Total   2989

Read name analysis:
 # Reads      # templates
   1             4

 Suffix counts:
(no suffix)   4


Templates inferred from description field:     0
Templates inferred from name field:            4

Read-template multiplicity analysis:
 # Reads      # templates
   1             4

Chemistries inferred from description field:
    0  dye-primer
    0  old-dye-terminator
    4  big-dye-terminator
    0  other

Chemistries inferred from name:
    0  dye-primer
    0  old-dye-terminator
    0  big-dye-terminator
    0  other

Directions inferred from description field:
    0  fwd
    0  rev
    0  unknown (set to fwd)

Directions inferred from name:
    0  fwd
    0  rev
    4  unknown (set to fwd)

Quality file: test_project.fasta.screen.qual

Input quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 56     281   9.4     281   9.4    0.00
 51     351  11.7     632  21.1    0.00
 50       7   0.2     639  21.4    0.00
 48      13   0.4     652  21.8    0.00
 47       2   0.1     654  21.9    0.00
 46      43   1.4     697  23.3    0.00
 45     206   6.9     903  30.2    0.01
 44      28   0.9     931  31.1    0.01
 43     334  11.2    1265  42.3    0.03
 42      60   2.0    1325  44.3    0.03
 41      29   1.0    1354  45.3    0.04
 40     284   9.5    1638  54.8    0.06
 39      64   2.1    1702  56.9    0.07
 38      36   1.2    1738  58.1    0.08
 37      76   2.5    1814  60.7    0.09
 36      19   0.6    1833  61.3    0.10
 35     193   6.5    2026  67.8    0.16
 34      59   2.0    2085  69.8    0.18
 33      30   1.0    2115  70.8    0.20
 32     111   3.7    2226  74.5    0.27
 31      19   0.6    2245  75.1    0.28
 30      10   0.3    2255  75.4    0.29
 29     121   4.0    2376  79.5    0.44
 28      17   0.6    2393  80.1    0.47
 27      38   1.3    2431  81.3    0.55
 26      18   0.6    2449  81.9    0.59
 25      72   2.4    2521  84.3    0.82
 24      46   1.5    2567  85.9    1.00
 23      21   0.7    2588  86.6    1.11
 22      25   0.8    2613  87.4    1.27
 21      33   1.1    2646  88.5    1.53
 20      18   0.6    2664  89.1    1.71
 19      25   0.8    2689  90.0    2.02
 18      24   0.8    2713  90.8    2.40
 17      15   0.5    2728  91.3    2.70
 16      23   0.8    2751  92.0    3.28
 15      23   0.8    2774  92.8    4.01
 14      18   0.6    2792  93.4    4.72
 13      14   0.5    2806  93.9    5.43
 12      20   0.7    2826  94.5    6.69
 11      21   0.7    2847  95.2    8.36
 10      40   1.3    2887  96.6   12.36
  9      38   1.3    2925  97.9   17.14
  8      26   0.9    2951  98.7   21.26
  7       5   0.2    2956  98.9   22.26
  6      26   0.9    2982  99.8   28.79
  4       7   0.2    2989 100.0   31.58   (quality -1 = terminal quality 0)

Avg. full length: 747.2, trimmed (qual > -1): 747.2
Avg. quality: 37.7 per base

Following regions converted to N's


Exact duplicate reads:  None.

Probable unremoved sequencing vector (matches excluded from assembly, quality reduced to 0):  None.

Near duplicate reads:  None.

Internal read matches (same orientation) :  None.

No. of node-rejected pairs: None.

Multi-segment reads (initially rejected segments in parentheses) -- XXX means segments flank X'd region: 

0 reads with multiple segments.

Probable deletion reads (excluded from assembly): None.

Revised quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90     124   4.1     124   4.1    0.00
 89      14   0.5     138   4.6    0.00
 88      22   0.7     160   5.4    0.00
 87      14   0.5     174   5.8    0.00
 86      38   1.3     212   7.1    0.00
 85      28   0.9     240   8.0    0.00
 84       8   0.3     248   8.3    0.00
 83      16   0.5     264   8.8    0.00
 82       6   0.2     270   9.0    0.00
 81      16   0.5     286   9.6    0.00
 80      44   1.5     330  11.0    0.00
 79       8   0.3     338  11.3    0.00
 78      34   1.1     372  12.4    0.00
 77      32   1.1     404  13.5    0.00
 76      20   0.7     424  14.2    0.00
 75      58   1.9     482  16.1    0.00
 74      24   0.8     506  16.9    0.00
 73      22   0.7     528  17.7    0.00
 72      42   1.4     570  19.1    0.00
 71      33   1.1     603  20.2    0.00
 70      18   0.6     621  20.8    0.00
 69      28   0.9     649  21.7    0.00
 68       6   0.2     655  21.9    0.00
 67      35   1.2     690  23.1    0.00
 66      15   0.5     705  23.6    0.00
 65       7   0.2     712  23.8    0.00
 64      45   1.5     757  25.3    0.00
 63      12   0.4     769  25.7    0.00
 62      24   0.8     793  26.5    0.00
 61      29   1.0     822  27.5    0.00
 60      46   1.5     868  29.0    0.00
 59      24   0.8     892  29.8    0.00
 58      43   1.4     935  31.3    0.00
 57      15   0.5     950  31.8    0.00
 56     217   7.3    1167  39.0    0.00
 55      22   0.7    1189  39.8    0.00
 54      14   0.5    1203  40.2    0.00
 53      19   0.6    1222  40.9    0.00
 52      10   0.3    1232  41.2    0.00
 51     273   9.1    1505  50.4    0.00
 50      14   0.5    1519  50.8    0.00
 49       8   0.3    1527  51.1    0.00
 48      16   0.5    1543  51.6    0.00
 47      10   0.3    1553  52.0    0.00
 46      32   1.1    1585  53.0    0.00
 45     157   5.3    1742  58.3    0.01
 44      23   0.8    1765  59.0    0.01
 43     252   8.4    2017  67.5    0.02
 42      20   0.7    2037  68.1    0.02
 41      14   0.5    2051  68.6    0.03
 40     179   6.0    2230  74.6    0.04
 39      46   1.5    2276  76.1    0.05
 38      14   0.5    2290  76.6    0.05
 37      24   0.8    2314  77.4    0.06
 36      14   0.5    2328  77.9    0.06
 35      39   1.3    2367  79.2    0.07
 34      16   0.5    2383  79.7    0.08
 33       4   0.1    2387  79.9    0.08
 32      34   1.1    2421  81.0    0.10
 31       3   0.1    2424  81.1    0.10
 30       5   0.2    2429  81.3    0.11
 29      44   1.5    2473  82.7    0.16
 28       7   0.2    2480  83.0    0.18
 27      22   0.7    2502  83.7    0.22
 26      11   0.4    2513  84.1    0.25
 25      38   1.3    2551  85.3    0.37
 24      25   0.8    2576  86.2    0.47
 23       9   0.3    2585  86.5    0.51
 22      12   0.4    2597  86.9    0.59
 21       9   0.3    2606  87.2    0.66
 20       6   0.2    2612  87.4    0.72
 19       6   0.2    2618  87.6    0.79
 18       9   0.3    2627  87.9    0.94
 17       3   0.1    2630  88.0    1.00
 16       4   0.1    2634  88.1    1.10
 15       9   0.3    2643  88.4    1.38
 14       3   0.1    2646  88.5    1.50
 13       3   0.1    2649  88.6    1.65
 12       1   0.0    2650  88.7    1.72
 11       3   0.1    2653  88.8    1.95
 10       5   0.2    2658  88.9    2.45
  9       2   0.1    2660  89.0    2.71
  8       4   0.1    2664  89.1    3.34
  6       2   0.1    2666  89.2    3.84
  2      71   2.4    2737  91.6   48.64
 -1     252   8.4    2989 100.0  300.64   (quality -1 = terminal quality 0)

Avg. full length: 747.2, trimmed (qual > -1): 684.2
Avg. quality: 48.3 per base

LLR score histogram:
Score    #   cum # 
 15.0     1     1

LLR score histogram:
Score    #   cum # 
 15.0     1     1

2d revised quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90     124   4.1     124   4.1    0.00
 89      14   0.5     138   4.6    0.00
 88      22   0.7     160   5.4    0.00
 87      14   0.5     174   5.8    0.00
 86      38   1.3     212   7.1    0.00
 85      28   0.9     240   8.0    0.00
 84       8   0.3     248   8.3    0.00
 83      16   0.5     264   8.8    0.00
 82       6   0.2     270   9.0    0.00
 81      16   0.5     286   9.6    0.00
 80      44   1.5     330  11.0    0.00
 79       8   0.3     338  11.3    0.00
 78      34   1.1     372  12.4    0.00
 77      32   1.1     404  13.5    0.00
 76      20   0.7     424  14.2    0.00
 75      58   1.9     482  16.1    0.00
 74      24   0.8     506  16.9    0.00
 73      22   0.7     528  17.7    0.00
 72      42   1.4     570  19.1    0.00
 71      33   1.1     603  20.2    0.00
 70      18   0.6     621  20.8    0.00
 69      28   0.9     649  21.7    0.00
 68       6   0.2     655  21.9    0.00
 67      35   1.2     690  23.1    0.00
 66      15   0.5     705  23.6    0.00
 65       7   0.2     712  23.8    0.00
 64      45   1.5     757  25.3    0.00
 63      12   0.4     769  25.7    0.00
 62      24   0.8     793  26.5    0.00
 61      29   1.0     822  27.5    0.00
 60      46   1.5     868  29.0    0.00
 59      24   0.8     892  29.8    0.00
 58      43   1.4     935  31.3    0.00
 57      15   0.5     950  31.8    0.00
 56     217   7.3    1167  39.0    0.00
 55      22   0.7    1189  39.8    0.00
 54      14   0.5    1203  40.2    0.00
 53      19   0.6    1222  40.9    0.00
 52      10   0.3    1232  41.2    0.00
 51     273   9.1    1505  50.4    0.00
 50      14   0.5    1519  50.8    0.00
 49       8   0.3    1527  51.1    0.00
 48      16   0.5    1543  51.6    0.00
 47      10   0.3    1553  52.0    0.00
 46      32   1.1    1585  53.0    0.00
 45     157   5.3    1742  58.3    0.01
 44      23   0.8    1765  59.0    0.01
 43     252   8.4    2017  67.5    0.02
 42      20   0.7    2037  68.1    0.02
 41      14   0.5    2051  68.6    0.03
 40     179   6.0    2230  74.6    0.04
 39      46   1.5    2276  76.1    0.05
 38      14   0.5    2290  76.6    0.05
 37      24   0.8    2314  77.4    0.06
 36      14   0.5    2328  77.9    0.06
 35      39   1.3    2367  79.2    0.07
 34      16   0.5    2383  79.7    0.08
 33       4   0.1    2387  79.9    0.08
 32      34   1.1    2421  81.0    0.10
 31       3   0.1    2424  81.1    0.10
 30       5   0.2    2429  81.3    0.11
 29      44   1.5    2473  82.7    0.16
 28       7   0.2    2480  83.0    0.18
 27      22   0.7    2502  83.7    0.22
 26      11   0.4    2513  84.1    0.25
 25      38   1.3    2551  85.3    0.37
 24      25   0.8    2576  86.2    0.47
 23       9   0.3    2585  86.5    0.51
 22      12   0.4    2597  86.9    0.59
 21       9   0.3    2606  87.2    0.66
 20       6   0.2    2612  87.4    0.72
 19       6   0.2    2618  87.6    0.79
 18       9   0.3    2627  87.9    0.94
 17       3   0.1    2630  88.0    1.00
 16       4   0.1    2634  88.1    1.10
 15       9   0.3    2643  88.4    1.38
 14       3   0.1    2646  88.5    1.50
 13       3   0.1    2649  88.6    1.65
 12       1   0.0    2650  88.7    1.72
 11       3   0.1    2653  88.8    1.95
 10       5   0.2    2658  88.9    2.45
  9       2   0.1    2660  89.0    2.71
  8       4   0.1    2664  89.1    3.34
  6       2   0.1    2666  89.2    3.84
  4       1   0.0    2667  89.2    4.24
  2      70   2.3    2737  91.6   48.41
 -1     252   8.4    2989 100.0  300.41   (quality -1 = terminal quality 0)

Avg. full length: 747.2, trimmed (qual > -1): 684.2
Avg. quality: 48.3 per base

No. confirmed reads: 2
Avg. length: 748.5, confirmed: 671.0, str. confirmed: 670.0, trimmed: 703.0
Preliminary clone size estimate: 671 bp, depth of coverage: 2.0

Depth histogram (max_depth, #reads, cum #reads):

 1     2       2
 0     2       4

Forward confirmed bases: 0

Substitutions by nucleotide:
       A      C      G      T      N      X      Z    Total
A      0      0      0      0      0      0      0        0
C      0      0      0      0      0      0      0        0
G      0      0      0      0      0      0      0        0
T      0      0      0      0      0      0      0        0
N      0      0      0      0      0      0      0        0
X      0      0      0      0      0      0      0        0
Z      0      0      0      0      0      0      0        0

Substitutions by quality: 
         0      2      3      4      5    Total
0        0      0      0      0      0        0
2        0      0      0      0      0        0
3        0      0      0      0      0        0
4        0      0      0      0      0        0
5        0      0      0      0      0        0

Histogram of spacings between adjacent indel pairs:


Reverse confirmed bases: 1408
 Subs: 46 (3.27%), dels: 0 (0.00%), inserts: 0 (0.00%)

Substitutions by nucleotide:
       A      C      G      T      N      X      Z    Total
A      0      1      8      0      0      0      0        9
C      1      0     18      8      0      0      0       27
G      2      2      0      1      0      0      0        5
T      2      2      1      0      0      0      0        5
N      0      0      0      0      0      0      0        0
X      0      0      0      0      0      0      0        0
Z      0      0      0      0      0      0      0        0

Substitutions by quality: 
         0      2      3      4      5    Total
0        0      1      7      7      8       23
2        1      0      0      0      0        1
3        7      0      0      0      0        7
4        7      0      0      0      0        7
5        8      0      0      0      0        8

Histogram of spacings between adjacent indel pairs:


Blocked reads: 
ML4924F 11 600  left 
ML4924R 56 753  left 

2 blocked reads: 2 left only, 0 right only, 0 both.
0 reads (not shown) lack a high-quality segment.

0 perfect duplicates

2 isolated singlets (having no non-vector match to any other read): 
  Read         Length      (# trimmed non-X bases)
 ML4922R        753   (668)
 ML4947F        739   (658)

Contig 1.  2 reads; 708 bp (untrimmed), 704 (trimmed).  Isolated contig.
     -5   728 ML4924F       628 (  0)  3.27 0.00 0.00    9 (  9)   21 ( 54) 
C     1   763 ML4924R       703 (  0)  0.00 0.00 0.00    0 (  3)   55 ( 89) 

Overall discrep rates (%):             1.63 0.00 0.00

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90      62   8.8      62   8.8    0.00
 89       7   1.0      69   9.7    0.00
 88      11   1.6      80  11.3    0.00
 87       7   1.0      87  12.3    0.00
 86      19   2.7     106  15.0    0.00
 85      14   2.0     120  16.9    0.00
 84       4   0.6     124  17.5    0.00
 83       8   1.1     132  18.6    0.00
 82       3   0.4     135  19.1    0.00
 81       8   1.1     143  20.2    0.00
 80      22   3.1     165  23.3    0.00
 79       4   0.6     169  23.9    0.00
 78      17   2.4     186  26.3    0.00
 77      16   2.3     202  28.5    0.00
 76      10   1.4     212  29.9    0.00
 75      29   4.1     241  34.0    0.00
 74      12   1.7     253  35.7    0.00
 73      12   1.7     265  37.4    0.00
 72      22   3.1     287  40.5    0.00
 71      22   3.1     309  43.6    0.00
 70       9   1.3     318  44.9    0.00
 69      14   2.0     332  46.9    0.00
 68       3   0.4     335  47.3    0.00
 67      18   2.5     353  49.9    0.00
 66       9   1.3     362  51.1    0.00
 65       4   0.6     366  51.7    0.00
 64      23   3.2     389  54.9    0.00
 63       6   0.8     395  55.8    0.00
 62      12   1.7     407  57.5    0.00
 61      15   2.1     422  59.6    0.00
 60      29   4.1     451  63.7    0.00
 59      11   1.6     462  65.3    0.00
 58      34   4.8     496  70.1    0.00
 57       7   1.0     503  71.0    0.00
 56      14   2.0     517  73.0    0.00
 55       6   0.8     523  73.9    0.00
 54       8   1.1     531  75.0    0.00
 53       9   1.3     540  76.3    0.00
 52       6   0.8     546  77.1    0.00
 51      48   6.8     594  83.9    0.00
 50       8   1.1     602  85.0    0.00
 49       6   0.8     608  85.9    0.00
 48       3   0.4     611  86.3    0.00
 47       5   0.7     616  87.0    0.00
 46       8   1.1     624  88.1    0.00
 45       7   1.0     631  89.1    0.00
 44       1   0.1     632  89.3    0.00
 43      16   2.3     648  91.5    0.00
 42       1   0.1     649  91.7    0.00
 41       2   0.3     651  91.9    0.00
 40      17   2.4     668  94.4    0.00
 39      14   2.0     682  96.3    0.01
 38       3   0.4     685  96.8    0.01
 36       1   0.1     686  96.9    0.01
 35      10   1.4     696  98.3    0.01
 34       2   0.3     698  98.6    0.01
 32       1   0.1     699  98.7    0.01
 26       1   0.1     700  98.9    0.01
 25       2   0.3     702  99.2    0.02
 17       1   0.1     703  99.3    0.04
 12       1   0.1     704  99.4    0.10
 -1       4   0.6     708 100.0    4.10   (quality -1 = terminal quality 0)

Avg. full length: 708.0, trimmed (qual > -1): 704.0
Avg. quality: 65.6 per base

Initial, terminal qual 0 segments:  1-3, 708-708

Regions of LLR- adjusted quality < 2.0:
1-5, 708, 

2 regions, avg size 3.0, avg spacing 354.0

First_start: 4, last_end: 674

Slack, # used pairs (max_score), unused
 0     1  (15.1)     0 ( 0.0)        1

LLR histograms (used, unused pairs): 
 10.0     1       0

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     3        3+
  708 - right        1+      ML4924F      (  -5)    No            713+

Bottom strand: 
 left -     0        0+      ML4924R      ( 763)    No            763+
  709 - right        0+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56     86     86   1409 (100.00)     0  0    0   0   0   0     0 (0.00)    0   23 (1.63)
51    122    208   1323 ( 93.90)     0  0    0   0   0   0     0 (0.00)    0   23 (1.74)
50      5    213   1201 ( 85.24)     0  0    0   0   0   0     0 (0.00)    0   23 (1.92)
48      7    220   1196 ( 84.88)     0  0    0   0   0   0     0 (0.00)    0   23 (1.92)
47      2    222   1189 ( 84.39)     0  0    0   0   0   0     0 (0.00)    0   23 (1.93)
46     15    237   1187 ( 84.24)     0  0    0   0   0   0     0 (0.00)    0   23 (1.94)
45     53    290   1172 ( 83.18)     0  0    0   0   0   0     0 (0.00)    0   23 (1.96)
44     14    304   1119 ( 79.42)     0  0    0   0   0   0     0 (0.00)    0   23 (2.06)
43     98    402   1105 ( 78.42)     0  0    0   0   0   0     0 (0.00)    0   23 (2.08)
42     44    446   1007 ( 71.47)     0  0    0   0   0   0     0 (0.00)    0   23 (2.28)
41     21    467    963 ( 68.35)     0  0    0   0   0   0     0 (0.00)    0   23 (2.39)
40     99    566    942 ( 66.86)     0  0    0   0   0   0     0 (0.00)    0   23 (2.44)
39     29    595    843 ( 59.83)     0  0    0   0   0   0     0 (0.00)    0   23 (2.73)
38     26    621    814 ( 57.77)     0  0    0   0   0   0     0 (0.00)    0   23 (2.83)
37     49    670    788 ( 55.93)     0  0    0   0   0   0     0 (0.00)    0   23 (2.92)
36      8    678    739 ( 52.45)     0  0    0   0   0   0     0 (0.00)    0   23 (3.11)
35    143    821    731 ( 51.88)     0  0    0   0   0   0     0 (0.00)    0   23 (3.15)
34     28    849    588 ( 41.73)     0  0    0   0   0   0     0 (0.00)    0   23 (3.91)
33     24    873    560 ( 39.74)     0  0    0   0   0   0     0 (0.00)    0   23 (4.11)
32     64    937    536 ( 38.04)     0  0    0   0   0   0     0 (0.00)    0   23 (4.29)
31     10    947    472 ( 33.50)     0  0    0   0   0   0     0 (0.00)    0   23 (4.87)
30      6    953    462 ( 32.79)     0  0    0   0   0   0     0 (0.00)    0   23 (4.98)
29     72   1025    456 ( 32.36)     0  0    0   0   0   0     0 (0.00)    0   23 (5.04)
28     10   1035    384 ( 27.25)     0  0    0   0   0   0     0 (0.00)    0   23 (5.99)
27     19   1054    374 ( 26.54)     0  0    0   0   0   0     0 (0.00)    0   23 (6.15)
26     12   1066    355 ( 25.20)     0  0    0   0   0   0     0 (0.00)    0   23 (6.48)
25     36   1102    343 ( 24.34)     0  0    0   0   0   0     0 (0.00)    0   23 (6.71)
24     27   1129    307 ( 21.79)     0  0    0   1   0   0     1 (3.70)    1   23 (7.49)
23     13   1142    280 ( 19.87)     0  0    0   0   0   0     0 (0.00)    1   22 (7.86)
22     15   1157    267 ( 18.95)     0  0    0   0   0   0     0 (0.00)    1   22 (8.24)
21     23   1180    252 ( 17.89)     0  0    0   1   0   0     1 (4.35)    2   22 (8.73)
20     11   1191    229 ( 16.25)     0  0    0   0   0   0     0 (0.00)    2   21 (9.17)
19     12   1203    218 ( 15.47)     0  0    0   0   0   0     0 (0.00)    2   21 (9.63)
18     14   1217    206 ( 14.62)     0  0    0   0   0   0     0 (0.00)    2   21 (10.19)
17     14   1231    192 ( 13.63)     0  0    0   2   0   0     2 (14.29)    4   21 (10.94)
16     14   1245    178 ( 12.63)     0  0    0   0   0   0     0 (0.00)    4   19 (10.67)
15     20   1265    164 ( 11.64)     0  0    0   0   0   0     0 (0.00)    4   19 (11.59)
14     15   1280    144 ( 10.22)     0  0    0   2   0   0     2 (13.33)    6   19 (13.19)
13      9   1289    129 (  9.16)     0  0    0   0   0   0     0 (0.00)    6   17 (13.18)
12     18   1307    120 (  8.52)     0  0    0   1   0   0     1 (5.56)    7   17 (14.17)
11     17   1324    102 (  7.24)     0  0    0   1   0   0     1 (5.88)    8   16 (15.69)
10     32   1356     85 (  6.03)     0  0    0   5   0   0     5 (15.62)   13   15 (17.65)
 9     28   1384     53 (  3.76)     0  0    0   2   0   0     2 (7.14)   15   10 (18.87)
 8     15   1399     25 (  1.77)     0  0    0   4   0   0     4 (26.67)   19    8 (32.00)
 7      2   1401     10 (  0.71)     0  0    0   0   0   0     0 (0.00)   19    4 (40.00)
 6      8   1409      8 (  0.57)     0  0    0   4   0   0     4 (50.00)   23    4 (50.00)
-1      3   1412      0 (  0.00)     4  0    0   0   0   0     0 (0.00)   23    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90    124    124   1375 (100.00)     0  0    0   0   0   0     0 (0.00)    0   14 (1.02)
89     14    138   1251 ( 90.98)     0  0    0   0   0   0     0 (0.00)    0   14 (1.12)
88     22    160   1237 ( 89.96)     0  0    0   0   0   0     0 (0.00)    0   14 (1.13)
87     14    174   1215 ( 88.36)     0  0    0   0   0   0     0 (0.00)    0   14 (1.15)
86     38    212   1201 ( 87.35)     0  0    0   0   0   0     0 (0.00)    0   14 (1.17)
85     28    240   1163 ( 84.58)     0  0    0   0   0   0     0 (0.00)    0   14 (1.20)
84      8    248   1135 ( 82.55)     0  0    0   0   0   0     0 (0.00)    0   14 (1.23)
83     16    264   1127 ( 81.96)     0  0    0   0   0   0     0 (0.00)    0   14 (1.24)
82      6    270   1111 ( 80.80)     0  0    0   0   0   0     0 (0.00)    0   14 (1.26)
81     16    286   1105 ( 80.36)     0  0    0   0   0   0     0 (0.00)    0   14 (1.27)
80     44    330   1089 ( 79.20)     0  0    0   0   0   0     0 (0.00)    0   14 (1.29)
79      8    338   1045 ( 76.00)     0  0    0   0   0   0     0 (0.00)    0   14 (1.34)
78     34    372   1037 ( 75.42)     0  0    0   0   0   0     0 (0.00)    0   14 (1.35)
77     32    404   1003 ( 72.95)     0  0    0   0   0   0     0 (0.00)    0   14 (1.40)
76     20    424    971 ( 70.62)     0  0    0   0   0   0     0 (0.00)    0   14 (1.44)
75     58    482    951 ( 69.16)     0  0    0   0   0   0     0 (0.00)    0   14 (1.47)
74     24    506    893 ( 64.95)     0  0    0   0   0   0     0 (0.00)    0   14 (1.57)
73     22    528    869 ( 63.20)     0  0    0   0   0   0     0 (0.00)    0   14 (1.61)
72     42    570    847 ( 61.60)     0  0    0   0   0   0     0 (0.00)    0   14 (1.65)
71     33    603    805 ( 58.55)     0  0    0   0   0   0     0 (0.00)    0   14 (1.74)
70     18    621    772 ( 56.15)     0  0    0   0   0   0     0 (0.00)    0   14 (1.81)
69     28    649    754 ( 54.84)     0  0    0   0   0   0     0 (0.00)    0   14 (1.86)
68      6    655    726 ( 52.80)     0  0    0   0   0   0     0 (0.00)    0   14 (1.93)
67     35    690    720 ( 52.36)     0  0    0   0   0   0     0 (0.00)    0   14 (1.94)
66     15    705    685 ( 49.82)     0  0    0   0   0   0     0 (0.00)    0   14 (2.04)
65      7    712    670 ( 48.73)     0  0    0   0   0   0     0 (0.00)    0   14 (2.09)
64     45    757    663 ( 48.22)     0  0    0   0   0   0     0 (0.00)    0   14 (2.11)
63     12    769    618 ( 44.95)     0  0    0   0   0   0     0 (0.00)    0   14 (2.27)
62     24    793    606 ( 44.07)     0  0    0   0   0   0     0 (0.00)    0   14 (2.31)
61     29    822    582 ( 42.33)     0  0    0   0   0   0     0 (0.00)    0   14 (2.41)
60     46    868    553 ( 40.22)     0  0    0   0   0   0     0 (0.00)    0   14 (2.53)
59     24    892    507 ( 36.87)     0  0    0   0   0   0     0 (0.00)    0   14 (2.76)
58     43    935    483 ( 35.13)     0  0    0   0   0   0     0 (0.00)    0   14 (2.90)
57     15    950    440 ( 32.00)     0  0    0   0   0   0     0 (0.00)    0   14 (3.18)
56     24    974    425 ( 30.91)     0  0    0   0   0   0     0 (0.00)    0   14 (3.29)
55     22    996    401 ( 29.16)     0  0    0   0   0   0     0 (0.00)    0   14 (3.49)
54     14   1010    379 ( 27.56)     0  0    0   0   0   0     0 (0.00)    0   14 (3.69)
53     19   1029    365 ( 26.55)     0  0    0   0   0   0     0 (0.00)    0   14 (3.84)
52     10   1039    346 ( 25.16)     0  0    0   0   0   0     0 (0.00)    0   14 (4.05)
51     52   1091    336 ( 24.44)     0  0    0   0   0   0     0 (0.00)    0   14 (4.17)
50     12   1103    284 ( 20.65)     0  0    0   0   0   0     0 (0.00)    0   14 (4.93)
49      8   1111    272 ( 19.78)     0  0    0   0   0   0     0 (0.00)    0   14 (5.15)
48     10   1121    264 ( 19.20)     0  0    0   0   0   0     0 (0.00)    0   14 (5.30)
47     10   1131    254 ( 18.47)     0  0    0   0   0   0     0 (0.00)    0   14 (5.51)
46      9   1140    244 ( 17.75)     0  0    0   0   0   0     0 (0.00)    0   14 (5.74)
45      8   1148    235 ( 17.09)     0  0    0   0   0   0     0 (0.00)    0   14 (5.96)
44      9   1157    227 ( 16.51)     0  0    0   0   0   0     0 (0.00)    0   14 (6.17)
43     17   1174    218 ( 15.85)     0  0    0   0   0   0     0 (0.00)    0   14 (6.42)
42      4   1178    201 ( 14.62)     0  0    0   0   0   0     0 (0.00)    0   14 (6.97)
41      6   1184    197 ( 14.33)     0  0    0   0   0   0     0 (0.00)    0   14 (7.11)
40     31   1215    191 ( 13.89)     0  0    0   0   0   0     0 (0.00)    0   14 (7.33)
39     25   1240    160 ( 11.64)     0  0    0   0   0   0     0 (0.00)    0   14 (8.75)
38      5   1245    135 (  9.82)     0  0    0   0   0   0     0 (0.00)    0   14 (10.37)
36      3   1248    130 (  9.45)     0  0    0   0   0   0     0 (0.00)    0   14 (10.77)
35     16   1264    127 (  9.24)     0  0    0   0   0   0     0 (0.00)    0   14 (11.02)
34      4   1268    111 (  8.07)     0  0    0   0   0   0     0 (0.00)    0   14 (12.61)
33      2   1270    107 (  7.78)     0  0    0   0   0   0     0 (0.00)    0   14 (13.08)
32      1   1271    105 (  7.64)     0  0    0   0   0   0     0 (0.00)    0   14 (13.33)
31      2   1273    104 (  7.56)     0  0    0   0   0   0     0 (0.00)    0   14 (13.46)
29      4   1277    102 (  7.42)     0  0    0   0   0   0     0 (0.00)    0   14 (13.73)
28      2   1279     98 (  7.13)     0  0    0   0   0   0     0 (0.00)    0   14 (14.29)
27      2   1281     96 (  6.98)     0  0    0   0   0   0     0 (0.00)    0   14 (14.58)
26      4   1285     94 (  6.84)     0  0    0   0   0   0     0 (0.00)    0   14 (14.89)
25      7   1292     90 (  6.55)     0  0    0   0   0   0     0 (0.00)    0   14 (15.56)
24      9   1301     83 (  6.04)     0  0    0   0   0   0     0 (0.00)    0   14 (16.87)
23      1   1302     74 (  5.38)     0  0    0   0   0   0     0 (0.00)    0   14 (18.92)
22      2   1304     73 (  5.31)     0  0    0   0   0   0     0 (0.00)    0   14 (19.18)
21      3   1307     71 (  5.16)     0  0    0   1   0   0     1 (33.33)    1   14 (19.72)
20      1   1308     68 (  4.95)     0  0    0   0   0   0     0 (0.00)    1   13 (19.12)
17      4   1312     67 (  4.87)     0  0    0   1   0   0     1 (25.00)    2   13 (19.40)
16      1   1313     63 (  4.58)     0  0    0   0   0   0     0 (0.00)    2   12 (19.05)
15      6   1319     62 (  4.51)     0  0    0   0   0   0     0 (0.00)    2   12 (19.35)
14      1   1320     56 (  4.07)     0  0    0   0   0   0     0 (0.00)    2   12 (21.43)
13      3   1323     55 (  4.00)     0  0    0   0   0   0     0 (0.00)    2   12 (21.82)
12      5   1328     52 (  3.78)     0  0    0   0   0   0     0 (0.00)    2   12 (23.08)
11     10   1338     47 (  3.42)     0  0    0   1   0   0     1 (10.00)    3   12 (25.53)
10     11   1349     37 (  2.69)     0  0    0   4   0   0     4 (36.36)    7   11 (29.73)
 9     13   1362     26 (  1.89)     0  0    0   2   0   0     2 (15.38)    9    7 (26.92)
 8      9   1371     13 (  0.95)     0  0    0   3   0   0     3 (33.33)   12    5 (38.46)
 6      4   1375      4 (  0.29)     0  0    0   2   0   0     2 (50.00)   14    2 (50.00)
-1     37   1412      0 (  0.00)     4  0    0   9   0   0     9 (24.32)   23    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0       4        4        2
 12       1        5        2
 17       1        6        2
 25       2        8        3
 26       1        9        3
 32       1       10        2
 34       2       12        2
 35      10       22        5
 36       1       23        6
 38       3       26        7
 39      14       40        9
 40      17       57        9
 41       2       59       10
 42       1       60       11
 43      16       76       15
 44       1       77       14
 45       7       84       15
 46       8       92       16
 47       5       97       18
 48       3      100       19
 49       6      106       21
 50       8      114       24
 51      48      162       21
 52       6      168       21
 53       9      177       23
 54       8      185       23
 55       6      191       24
 56      14      205       22
 57       7      212       23
 58      34      246       29
 59      11      257       28
 60      29      286       30
 61      15      301       32
 62      12      313       29
 63       6      319       30
 64      23      342       24
 65       4      346       24
 66       9      355       23
 67      18      373       25
 68       3      376       26
 69      14      390       30
 70       9      399       29
 71      22      421       30
 72      22      443       32
 73      12      455       30
 74      12      467       33
 75      29      496       32
 76      10      506       30
 77      16      522       33
 78      17      539       30
 79       4      543       30
 80      22      565       29
 81       8      573       27
 82       3      576       27
 83       8      584       25
 84       4      588       24
 85      14      602       25
 86      19      621       26
 87       7      628       27
 88      11      639       20
 89       7      646       17
 90      62      708        1

SS region: 4 (0.56%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads): None.

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:  None.

Subclone/read contig links and consistency checks (* = inconsistency; Contig 0 = singlets)
Max subclone size: 5000

Size histogram for consistent forward-reverse pairs (*** = inconsistent pairs)
  ***     0

 Consistent opp sense links (* = not used in chain, ** = multiple non-zero):BioPerl-1.007002/t/data/consed_project/edit_dir/test_project.screen.out000555000766000024      1644413155576321 26224 0ustar00cjfieldsstaff000000000000/usr/local/genome/bin/cross_match test_project.fasta /etc/phredphrap/vectors -minmatch 12 -penalty -2 -minscore 20 -screen 
cross_match version 0.990329

Run date:time  010621:164002
Query file(s):  test_project.fasta
Subject file(s):   /etc/phredphrap/vectors
Presumed sequence type: DNA

Pairwise comparison algorithm: banded Smith-Waterman

Score matrix (set by value of penalty: -2)
    A   C   G   T   N   X
A   1  -2  -2  -2   0  -3
C  -2   1  -2  -2   0  -3
G  -2  -2   1  -2   0  -3
T  -2  -2  -2   1   0  -3
N   0   0   0   0   0   0
X  -3  -3  -3  -3   0  -3

Gap penalties: gap_init: -4, gap_ext: -3, ins_gap_ext: -3, del_gap_ext: -3, 
Using complexity-adjusted scores. Assumed background frequencies:
 A: 0.250  C: 0.250  G: 0.250  T: 0.250  N: 0.000  X: 0.000  

minmatch: 12, maxmatch: 12, max_group_size: 20, minscore: 20, bandwidth: 14, indexwordsize: 10
vector_bound: 0
word_raw: 0
masklevel: 80

Sequence file: test_project.fasta    4 entries
Residue counts:
  a      811
  c      727
  g      702
  n        2
  t      747
Total   2989

Quality file: test_project.fasta.qual

Input quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 56     281   9.4     281   9.4    0.00
 51     351  11.7     632  21.1    0.00
 50       7   0.2     639  21.4    0.00
 48      13   0.4     652  21.8    0.00
 47       2   0.1     654  21.9    0.00
 46      43   1.4     697  23.3    0.00
 45     206   6.9     903  30.2    0.01
 44      28   0.9     931  31.1    0.01
 43     334  11.2    1265  42.3    0.03
 42      60   2.0    1325  44.3    0.03
 41      29   1.0    1354  45.3    0.04
 40     284   9.5    1638  54.8    0.06
 39      64   2.1    1702  56.9    0.07
 38      36   1.2    1738  58.1    0.08
 37      76   2.5    1814  60.7    0.09
 36      19   0.6    1833  61.3    0.10
 35     193   6.5    2026  67.8    0.16
 34      59   2.0    2085  69.8    0.18
 33      30   1.0    2115  70.8    0.20
 32     111   3.7    2226  74.5    0.27
 31      19   0.6    2245  75.1    0.28
 30      10   0.3    2255  75.4    0.29
 29     121   4.0    2376  79.5    0.44
 28      17   0.6    2393  80.1    0.47
 27      38   1.3    2431  81.3    0.55
 26      18   0.6    2449  81.9    0.59
 25      72   2.4    2521  84.3    0.82
 24      46   1.5    2567  85.9    1.00
 23      21   0.7    2588  86.6    1.11
 22      25   0.8    2613  87.4    1.27
 21      33   1.1    2646  88.5    1.53
 20      18   0.6    2664  89.1    1.71
 19      25   0.8    2689  90.0    2.02
 18      24   0.8    2713  90.8    2.40
 17      15   0.5    2728  91.3    2.70
 16      23   0.8    2751  92.0    3.28
 15      23   0.8    2774  92.8    4.01
 14      18   0.6    2792  93.4    4.72
 13      14   0.5    2806  93.9    5.43
 12      20   0.7    2826  94.5    6.69
 11      21   0.7    2847  95.2    8.36
 10      40   1.3    2887  96.6   12.36
  9      38   1.3    2925  97.9   17.14
  8      26   0.9    2951  98.7   21.26
  7       5   0.2    2956  98.9   22.26
  6      26   0.9    2982  99.8   28.79
  4       7   0.2    2989 100.0   31.58   (quality -1 = terminal quality 0)

Avg. full length: 747.2, trimmed (qual > -1): 747.2
Avg. quality: 37.7 per base
Maximal single base matches (low complexity regions):

  36  5.77 1.92 0.00  ML4922R        4    55 (698)  C vector3:PsportI   (77)   169   117  

  29  8.51 2.13 0.00  ML4924R        9    55 (708)  C vector3:PsportI   (82)   164   117  

2 matching entries (first file).

Discrepancy summary:
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56      0      0     99 (100.00)     9  0    0   0   0   0     0 (0.00)    0    9 (9.09)
51      2      2     99 (100.00)    49  0    0   0   0   0     0 (0.00)    0    9 (9.09)
48      0      2     97 ( 97.98)     0  0    0   0   0   0     0 (0.00)    0    9 (9.28)
46      2      4     97 ( 97.98)    14  0    0   0   1   0     1 (50.00)    1    9 (9.28)
45      0      4     95 ( 95.96)    16  0    0   0   0   0     0 (0.00)    1    8 (8.42)
44      0      4     95 ( 95.96)     0  0    0   0   0   0     0 (0.00)    1    8 (8.42)
43      0      4     95 ( 95.96)     8  0    0   0   0   0     0 (0.00)    1    8 (8.42)
42      0      4     95 ( 95.96)     1  0    0   0   0   0     0 (0.00)    1    8 (8.42)
40     15     19     95 ( 95.96)    56  0    0   0   1   0     1 (6.67)    2    8 (8.42)
39     10     29     80 ( 80.81)    35  0    0   0   0   0     0 (0.00)    2    7 (8.75)
38      0     29     70 ( 70.71)     4  0    0   0   0   0     0 (0.00)    2    7 (10.00)
37      1     30     70 ( 70.71)     1  0    0   0   0   0     0 (0.00)    2    7 (10.00)
36      0     30     69 ( 69.70)     0  0    0   0   0   0     0 (0.00)    2    7 (10.14)
35      9     39     69 ( 69.70)    30  0    0   2   0   0     2 (22.22)    4    7 (10.14)
34     14     53     60 ( 60.61)     3  0    0   2   0   0     2 (14.29)    6    5 (8.33)
33      2     55     46 ( 46.46)     0  0    0   0   0   0     0 (0.00)    6    3 (6.52)
32      6     61     44 ( 44.44)     1  0    0   0   0   0     0 (0.00)    6    3 (6.82)
31      0     61     38 ( 38.38)     5  0    0   0   0   0     0 (0.00)    6    3 (7.89)
30      0     61     38 ( 38.38)     0  0    0   0   0   0     0 (0.00)    6    3 (7.89)
29      4     65     38 ( 38.38)     0  0    0   0   0   0     0 (0.00)    6    3 (7.89)
28      3     68     34 ( 34.34)     0  0    0   0   0   0     0 (0.00)    6    3 (8.82)
27      0     68     31 ( 31.31)     0  0    0   0   0   0     0 (0.00)    6    3 (9.68)
26      0     68     31 ( 31.31)     0  0    0   0   0   0     0 (0.00)    6    3 (9.68)
25      2     70     31 ( 31.31)     0  0    0   0   0   0     0 (0.00)    6    3 (9.68)
24      2     72     29 ( 29.29)     0  0    0   0   0   0     0 (0.00)    6    3 (10.34)
23      1     73     27 ( 27.27)     0  0    0   0   0   0     0 (0.00)    6    3 (11.11)
22      0     73     26 ( 26.26)     0  0    0   0   0   0     0 (0.00)    6    3 (11.54)
21      2     75     26 ( 26.26)     0  0    0   0   0   0     0 (0.00)    6    3 (11.54)
20      2     77     24 ( 24.24)     0  0    0   0   0   0     0 (0.00)    6    3 (12.50)
19      3     80     22 ( 22.22)     0  0    0   0   0   0     0 (0.00)    6    3 (13.64)
18      0     80     19 ( 19.19)     1  0    0   0   0   0     0 (0.00)    6    3 (15.79)
17      0     80     19 ( 19.19)     0  0    0   0   0   0     0 (0.00)    6    3 (15.79)
16      1     81     19 ( 19.19)     1  0    0   0   0   0     0 (0.00)    6    3 (15.79)
15      0     81     18 ( 18.18)     0  0    0   0   0   0     0 (0.00)    6    3 (16.67)
14      1     82     18 ( 18.18)     0  0    0   0   0   0     0 (0.00)    6    3 (16.67)
13      1     83     17 ( 17.17)     0  0    0   0   0   0     0 (0.00)    6    3 (17.65)
12      0     83     16 ( 16.16)     1  0    0   0   0   0     0 (0.00)    6    3 (18.75)
11      1     84     16 ( 16.16)     0  0    0   0   0   0     0 (0.00)    6    3 (18.75)
10      1     85     15 ( 15.15)     0  0    0   0   0   0     0 (0.00)    6    3 (20.00)
 9      4     89     14 ( 14.14)     0  0    0   0   0   0     0 (0.00)    6    3 (21.43)
 8      4     93     10 ( 10.10)     2  0    0   1   0   0     1 (25.00)    7    3 (30.00)
 6      3     96      6 (  6.06)     4  0    0   0   0   0     0 (0.00)    7    2 (33.33)
 4      3     99      3 (  3.03)     2  0    1   1   0   0     2 (66.67)    9    2 (66.67)


Screened sequences written to  test_project.fasta.screen
BioPerl-1.007002/t/data/consed_project/edit_dir/test_projectNewChromats.fof000555000766000024          013155576321 26741 0ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/consed_project/edit_dir/test_project_to_alu.cross000555000766000024        26413155576321 26564 0ustar00cjfieldsstaff000000000000/usr/local/genome/bin/cross_match test_project.contigs /usr/local/genome/lib/screenLibs/repeats.fasta -tags -minmatch 10 
cross_match version 0.990329

Run date:time  010621:164003BioPerl-1.007002/t/data/consed_project/phd_dir000755000766000024          013155576321 21145 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/consed_project/phd_dir/ML4922R.phd.1000555000766000024      1703413155576321 23141 0ustar00cjfieldsstaff000000000000BEGIN_SEQUENCE ML4922R

BEGIN_COMMENT

CHROMAT_FILE: ML4922R
ABI_THUMBPRINT: 0
PHRED_VERSION: 0.980904.e
CALL_METHOD: phred
QUALITY_LEVELS: 99
TIME: Thu Jun 21 11:28:31 2001
TRACE_ARRAY_MIN_INDEX: 0
TRACE_ARRAY_MAX_INDEX: 8877
CHEM: term
DYE: big

END_COMMENT

BEGIN_DNA
c 4 5
c 4 17
t 6 20
t 6 30
g 9 45
g 19 55
t 24 64
a 24 72
c 19 81
g 16 96
c 10 103
c 8 117
c 8 126
g 9 139
c 21 147
a 20 159
g 32 166
g 34 178
t 34 191
a 39 200
c 39 209
c 40 221
g 39 234
g 46 244
t 40 256
c 37 269
c 32 279
g 32 291
g 28 300
a 28 317
a 25 325
t 25 331
t 34 342
c 32 352
c 40 363
c 40 372
g 40 385
g 40 394
g 40 406
t 40 417
c 34 430
g 35 441
a 35 452
c 35 459
c 35 471
c 35 482
a 35 491
c 35 498
g 35 511
c 35 521
g 51 534
t 51 544
c 39 556
c 39 567
g 39 579
c 35 587
g 31 600
g 31 610
a 31 625
c 31 631
g 31 644
c 32 652
g 35 666
t 35 676
g 45 688
g 51 699
g 56 710
g 51 723
t 39 734
g 39 746
a 40 756
c 40 764
c 39 776
c 39 787
c 45 798
g 40 811
g 40 821
a 40 835
a 35 844
g 35 853
a 39 866
t 35 874
t 35 886
c 35 896
g 37 910
a 40 919
g 40 929
t 40 941
g 40 953
c 40 962
t 40 976
t 40 987
c 45 997
g 51 1010
t 51 1020
c 51 1031
t 51 1043
g 46 1055
g 46 1066
t 40 1077
a 40 1086
a 39 1096
t 39 1109
c 39 1120
a 39 1128
a 40 1139
a 40 1151
a 46 1162
t 40 1173
c 40 1184
a 40 1193
g 40 1206
g 40 1218
t 51 1230
t 51 1242
t 51 1254
c 51 1264
t 45 1277
c 45 1287
c 45 1298
g 45 1312
g 51 1323
t 51 1334
t 56 1347
g 56 1359
g 56 1370
a 56 1381
t 51 1392
c 51 1403
t 51 1416
c 51 1426
a 51 1436
a 40 1447
a 40 1458
c 40 1468
t 40 1483
c 40 1493
a 40 1503
a 51 1514
g 51 1526
g 39 1538
t 39 1551
t 38 1563
a 38 1571
t 38 1584
g 35 1598
c 39 1607
c 39 1621
g 39 1636
t 39 1646
g 43 1659
g 43 1671
c 43 1680
a 46 1692
c 46 1702
a 51 1714
a 51 1726
a 56 1738
t 56 1751
g 45 1763
t 35 1774
c 35 1786
g 35 1801
c 35 1809
c 35 1823
t 35 1837
g 43 1849
c 43 1858
t 43 1873
g 43 1886
t 43 1897
t 43 1910
t 43 1922
c 43 1932
a 43 1941
t 43 1954
c 43 1966
t 51 1980
g 51 1993
t 51 2004
c 56 2016
a 56 2027
g 56 2039
t 56 2052
g 56 2065
a 43 2077
t 43 2088
g 43 2101
c 43 2110
t 43 2126
c 43 2136
c 43 2148
c 43 2160
t 43 2175
c 43 2185
a 43 2197
t 45 2208
t 45 2222
a 43 2232
g 43 2245
a 43 2259
c 43 2267
a 43 2280
c 43 2290
a 43 2304
c 43 2313
a 43 2327
g 43 2340
a 43 2354
g 43 2365
a 43 2379
c 43 2388
a 43 2401
a 43 2412
c 45 2424
g 45 2439
a 43 2450
g 43 2463
a 43 2478
t 43 2488
a 43 2499
t 51 2512
t 51 2525
c 51 2537
a 51 2548
g 51 2562
t 51 2574
c 51 2586
c 56 2599
a 56 2610
g 45 2623
g 43 2636
c 43 2647
t 43 2662
a 43 2672
g 43 2685
c 43 2696
t 43 2712
a 43 2721
a 43 2734
c 43 2745
a 51 2757
g 51 2770
t 56 2784
g 56 2797
g 51 2809
t 56 2822
t 56 2835
c 56 2846
a 56 2857
g 56 2870
a 56 2883
t 56 2895
g 51 2908
a 45 2919
t 45 2932
t 45 2946
c 45 2956
t 45 2970
g 45 2984
a 51 2995
t 45 3006
g 43 3019
a 43 3032
c 43 3042
g 43 3057
a 43 3068
a 45 3081
g 51 3092
a 51 3106
t 51 3117
c 51 3128
c 51 3140
t 45 3154
g 45 3167
a 45 3180
t 51 3190
g 51 3203
g 51 3216
a 56 3229
g 51 3241
a 43 3254
g 36 3265
a 36 3279
c 36 3287
t 36 3302
g 36 3315
t 43 3326
a 51 3338
a 51 3350
c 51 3360
a 51 3372
a 51 3384
c 56 3395
a 56 3408
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END_DNA

END_SEQUENCE
BioPerl-1.007002/t/data/consed_project/phd_dir/ML4924F.phd.1000555000766000024      1643313155576321 23131 0ustar00cjfieldsstaff000000000000BEGIN_SEQUENCE ML4924F

BEGIN_COMMENT

CHROMAT_FILE: ML4924F
ABI_THUMBPRINT: 0
PHRED_VERSION: 0.980904.e
CALL_METHOD: phred
QUALITY_LEVELS: 99
TIME: Thu Jun 21 11:27:03 2001
TRACE_ARRAY_MIN_INDEX: 0
TRACE_ARRAY_MAX_INDEX: 8444
CHEM: term
DYE: big

END_COMMENT

BEGIN_DNA
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END_DNA

END_SEQUENCE
BioPerl-1.007002/t/data/consed_project/phd_dir/ML4924R.phd.1000555000766000024      1717313155576321 23147 0ustar00cjfieldsstaff000000000000BEGIN_SEQUENCE ML4924R

BEGIN_COMMENT

CHROMAT_FILE: ML4924R
ABI_THUMBPRINT: 0
PHRED_VERSION: 0.980904.e
CALL_METHOD: phred
QUALITY_LEVELS: 99
TIME: Thu Jun 21 11:27:03 2001
TRACE_ARRAY_MIN_INDEX: 0
TRACE_ARRAY_MAX_INDEX: 8792
CHEM: term
DYE: big

END_COMMENT

BEGIN_DNA
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t 8 35
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g 34 178
t 34 190
a 39 200
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g 40 243
t 28 255
c 21 267
c 13 277
g 4 288
n 4 297
g 4 298
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g 40 390
g 40 401
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END_DNA

END_SEQUENCE
BioPerl-1.007002/t/data/consed_project/phd_dir/ML4947F.phd.1000555000766000024      1663113155576321 23136 0ustar00cjfieldsstaff000000000000BEGIN_SEQUENCE ML4947F

BEGIN_COMMENT

CHROMAT_FILE: ML4947F
ABI_THUMBPRINT: 0
PHRED_VERSION: 0.980904.e
CALL_METHOD: phred
QUALITY_LEVELS: 99
TIME: Thu Jun 21 11:28:31 2001
TRACE_ARRAY_MIN_INDEX: 0
TRACE_ARRAY_MAX_INDEX: 8660
CHEM: term
DYE: big

END_COMMENT

BEGIN_DNA
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g 29 8317
a 22 8329
a 22 8339
c 23 8348
c 27 8362
g 23 8375
t 23 8386
c 25 8398
t 30 8410
c 33 8419
a 27 8430
g 39 8442
t 25 8454
c 28 8465
a 26 8475
c 26 8484
a 21 8496
g 16 8508
c 10 8517
c 10 8532
g 14 8545
c 16 8554
a 20 8566
c 27 8575
a 27 8587
t 24 8598
t 22 8611
t 21 8622
c 27 8633
t 21 8645
t 21 8656
END_DNA

END_SEQUENCE
BioPerl-1.007002/t/data/dbfa000755000766000024          013155576321 15427 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/dbfa/1.fa000444000766000024     16645213155576321 16312 0ustar00cjfieldsstaff000000000000>AW057118
gcaatgtcacgttgtcaactcattgcaaacaaagactggaccaacattga
acggagtgattggaagacaatccggacaagttgctggatttgactactcg
gctgccaacaagaataaaggagttgtatgggacagacaaacacttttcga
ctatttggctgatccgaaaaagtacatccccggaactaagatggtcttcg
ctggtttgaagaaagctgaccaaacgagctgatctcatcaaatttattga
agtggaagctgccaagaaaccatcggcataagcctctactaaataagaa
>AW057119 test description
tcatgttggcttctcggggtttttatggattaatacattttccaaacgat
tctttgcgccttctgtggtgccgccttctccgaaggaactgacgaaaaat
gacgtggatttgctgacaaatccaggcgaggaatatttggacggattgat
gaaatggcacggcgacgagcgacccgtgttcaaaagagaggacatttatc
gttggtcggatagttttccagaatatcggctaagaatgatttgtctgaaa
gacacgacaagggtcattgcagtcggtcaatattgttactttgatgctct
gaaagaaaggagagcagccattgttcttcttaggattgggatggacggat
cctgaatatcgtaatcgggcagttatggagcttcaagcttcgatggcgct
ggaggagagggatcggtatccgactgccaacgcggcatcgcatccaaata
agttcatgaaacgattttggcacatattcaacggcctcaaagagcacgag
gacaaaggtcacaaggctgccgctgtttcatacaagagcttctacgacct
canagacatgatcattcctgaaaatctggatgtcagtggtattactgtaa
atgatgcacgaaaggtgccacaaagagatataatcaactacgatcaaaca
tttcatccatatcatcgagaaatggttataatttctcacatgtatgacaa
tgatgggtttggaaaagtgcgtatgatgaggatggaaatgtacttggaat
tgtctagcgatgtctttanaccaacaagactgcacattagtcaattatgc
agatagcc
>AW057120
aatctgtacatcttcaattgtggttcacttcttctatcgtcttgttcgag
aaaaccacggagaaaaggagcaagaccgtggattgaaagacaccaaagaa
accgccaaggatgtgctgggttttgtaaaaatgcttggaataatcctagc
tatggttgtaggctttgccttgttggggtttgtcacgttttatctctatc
agtatgcgag
>AW057121
atgggcgctggtggctatggattcggatatatgggatccaacgcctcatc
gtcgggatttgcccgcgaagattatgcccaaggaggaaatggtggaggac
agcagcaaaaccagggatctggaggaaacaccaacccgggaggacaagtc
ttcaaggcccgtacggatcaatcttgttacctcggaccataagaggcaag
aactcagccaa
>AW057122
gacaacttccatctctatcatagcattttgatgattagaacatgtcactc
acaaaagatggttccgtagctgtgaccattctccaagcaatcatcttcat
tcaattcggcttgtgcgttgcgatcacaattctgacaaccgtcggaatct
catttgggtatccggtggcttctcattaccttatggctcttcttcaggca
ttggttgcaattccgggaattgtgtacattgtgacacagacaaacatctg
ggtggcagtctacatcagcttccaagtggtaaccgccgcgtgtgaagtct
actggctcgtctacttgatcttcgacaatcaacccgctggatcttggatc
gcacttgcaattatcacagccgtcaacattttggcagctgttgtcggtgt
gtggttccgcaaaactgctttgaaccttccatgccttgataagaaaacga
aaaaggctggtgatgcgaagaaggagaagcccanaatgaaggccccatca
acttcaatgagtgatattgagaaaagtaaatccagagctg
>AW057123
catcggatgaaacggatgatgtacttgcaaatgaagacgaaatgttcaaa
acaaaaaaggacaaatacaaagtgatcgcattactcggtaaaggcggata
tggagccgtatactctgtactccgcctcagcgatatggagaagtttgcga
taaagtgtgagaaggcgactgctggaaagaaggttcttctgatggattgc
aatgtgatgaaagttgcaactcagatcaaaagtagacacttttgtactgt
actggatcgagctaacgtcaaggatcgtttaatttcattgtgatgaagct
tatcgggaagaatctttgggacctgagacaggatcgtggcgatggaaaat
tcacaatgggcacctcgttgaaagcagcgtcacagtgtcttgtatccatt
gaacacttgcacagtttcggctaccttcaccgtgacatcaagccggtgaa
ctttgccgacggacgaaaggaatccaacgagcatcacgtcatcttcatgc
ttgactttggtctctgcagggagtacgtgaagcgagctgagggaaagatc
ttcgagcagcccgtacaactgcaccattccgtggtactactcgatatgct
ccattgacttcgatgctccagcaagatcaatcacgacaagatgacattga
atcctggctctacatggntgtagaatggacttactgagattgacgcggcg
catgtngaagctcacgatcgagagaggctctgcattacaacagtactacg
tcaacaccg
>AW057124
ttggatcaacagaaagtttaactcctcttctgacaactcaagagccataa
agtccttatcttttccaacaaagaacaaaagtccatgaggcagctctgaa
acgccacgtggctccgactgaaggattggctgttgctcagaatgacatac
acaatttcctgttcgaatcacacggacaaatcttcgatatggcgatgatg
tacgccgaatcggccggtttcaaacgagatcacctctcgtacgccgcgtt
cggtttgatcgcattcttcttggttttcggatctgtggcacgtcttttgt
gcaat
>AW057125
aacaactcgactaaccgtctccactcttcacttgcacaaatcttcatgca
accaatcaacgtcatgctcgctgttcttctcgccttggcttcatttgctc
aaggaggcagatctgttgctccggctggtgcagtcactgaaccaacagtt
actcaagctgttccagaaggatcaggacttagttcagatgtcactgatcg
tccaaacatcgactccactgatgttgtatcaaatgcaacttcggtggaag
atttgcttggaagttcaacaaatgcaaacaacactggtacattcaactct
taggacctttgtaattgctccaatgatgattcttgctttggt
>AW057126
gtgctcgacatcattgctcttctggcaattgtcgtttttcttgtcttttt
gccggctgatagatgtctgaattttgaagcaagtgaacaaactccacgca
acgtcgacaaaaagtgtcatcttcatccagtgcatcatccgaacttcagt
ttcaccgaaaacttgaaaactaacgatcatttgattgatccaagtcatca
agtcaccatttgtcaccgtttgaaatggtctcactattcattctgggata
gcatgtatttgaatcttttgccggctctcacttgtgtttttctgattttc
tacacagttcatgagatttgtgaatttgacgtgtttgttggacaggtaca
aactactggcttggttattgtatcagcaatatcggtaatttactctatcg
cagtaatcactcacgaaaagaatcgaattgagacggaatggccattgctc
gctcatgcttatgtcctggagcaaaagaaggagaaacaaccgttaatgta
ccaaaaacgtggcaatatagtattgctatgtgcattctgtcagcccttct
caagatcggcagggttntggttcaacatttcattggtgataagacgttct
tcttgatgacgatagccaaagggacgatcaaaatggtgaacctgtgctgt
tggctggaagtgaagaagtgctgtaccactaccattctgaatgttccaga
catccagaacttgaactgat
>AW057127
aattccttttaatcgattcaagcacatcgtacatacgcgacaaaacgacg
gaaatatgatgagcccgttggactatctgcatgtcactttgctgctcatt
ggcccacttgccattctcatcggatgtggaggaaagaaaaaagcaccacc
accaaagtcggcatccaagatgactgctccacctgctcctgcatcagcgc
ctcccgctgctccagacgcagcccctgctgctcctgatgctgcagctgca
ccagctgatgg
>AW057128
gacgacgcttaccagtttttggctccgataactcgttcctccaccaccag
tccaacaaccgccagcagttgctccaggagcatcacgtcccgcacctgct
ccgtcgaatgagcttccacccgcgtcggaggcaaagaaattccaagtgca
accggctaaaaaagcatcaaaatcgaagagcaaatcgaaagactcatcgc
caagcaacggaaaggagaagaagaagcgcacaaagcgttcgggtggctcc
aaatcgaaagaatcttccgagccacctccatcattgtnccgcctttaaat
gccaaaaggcattcagtgcatgtcttgtccttatttcagatgctatcact
ttgatgg
>AW057129
gagatcgttggaaggttctagctatgaacgtactagtgtcttcagaggat
ggtgttaaagaattcgaaaagattgttgtggaacctgaagatatcgaata
tgttgagattccggccgatgccaaaaacgttgacttgacgcgtcaccgta
tcaaagaaatcggtgattattcgtggctcactcacgtcgaacacttctcg
tttcgttggaatctgatcaaaaagattgaaaatctggattgtttgacaac
gttgactcatctcgagttttacgataatcaaattaccaaaggtgaaaact
ttggttagcctcgtcaatttggagtcactcgacctgtcattcaatcgtat
caccaaaattgaaaatttggagaagttgacaaaactgaagactctctttt
ttgttcataacaaaatcactaaaatcgagggtttggatacgttgactgag
ctggaatatctcgaattgggtgacaatagaattgcgaaaatcgagaatct
cgacaacaatctganactcgatagattgttccttggcgctaatcagattc
gtcttattgaaaatgttgatcatctgaagaagctcacagttctcagtctt
ccagccaatgcgattactgtagttgataacattgcgggacttcacaactt
ngaagagaattatctggctcaaaatggcatcaagtacgtctgtggaatcg
atgagcatcttccttcttgaaatctggatttcaatcagaatcgtcttgag
aggtcgagatatncattcaatgagacactacagacttttgggcagagaaa
tagttgatacctg
>AW057130
caaaagggctcggatagaaaaatgcccaacacttatcgaacttcggatga
aattgtggctcagcgattggaggatggcagagatatgaatctgagtcttc
aaaatatgaatctattcgcatctggagccttttcaaatgtctatcgtgga
attgcacgcacagaatccaaccaccaaatggaaattgtcatcaaaaagac
atggccacgtcataaaggatgtccattggaagtgaagattctcggaaaac
ttggaaagttgaagcaccaagaacattgtccgccttctctttagttacca
gaaacaacatgaaggtcgtatctgccttggtctaatcttcgagtacatcc
caatgaatctccatcagtttctgaaggataacaatcgacgtgttgacatt
atcgaggttaaactgattgtttggcagttgttccgtggacaagcacattt
ggagaagtctgaaatttgtcatcgtgacatcaaaccacagaatttactgt
acaatgctgaccactgtcttctgaagatttctgattatggatcatctgcg
attgaatcagtgaagacaccacaacaaagctaccatgtcacaagatatta
tagacccgcccgagttgcttctacgctccaaanactatggatgccagatt
gtcactttgtcgtgtcgatgtgtctttggtgaatgctttaaggtggaatc
tactggcaggcaatacagccagaatcagcagaagtgatttgtatggtcga
gctccactgc
>AW057131
tatctatattctcgactttggatttgctcatcagtacatgattaaggatg
gaacactgaaacctccgtcagctcatccatggaaatacgtgggaagtctt
cgtcatatgccacgtgccgcatattcgaaagtggaattctcaagaatgga
agacttggaaatgtggttctatatgagtgttgagctggttaagggatgtc
ttccgtgggctcatttgaagaaaccaaaagaagtgcatgactatcaaaag
ttgtgccgaaatggccttcaaatgcgtgaaatgctccgaggtctttcacc
agaattcgtcgacattatgcanataggtgacaaactttcattcaccgaca
ctccgaactacacagaaatctacggacttctcaccaacgcgattctcttc
agtggcaaaaatgaattcccgtacgattgggaggaggctgagatcaacga
gttcaagaatccgcagaagccaagtgtggagcaggcaacctaatagctct
ctttctatggaaataaattga
>AW057132
ttcgataacttgctttattgtcgacaagttttatcgtaacaatgacagca
ccgccaccgccactcgtggaacttcctccgggatctatggttgaaagatg
gtcgattacaaagaagctgggagaaggaggctgtggagccgtctatttgt
gcacggatgcaactggaaagtatgcactgaaagtcgagggaatctctgag
gcaatgcaggtgctcaaaatggaagtgttggtgctcggagagctgacaaa
gagaggaagtcgtcacttttgcaagattgaagacaaaggaagatatggcc
aagttcaactatgttgtaatgacgcttgtcggaaagtctttgcaggatct
tcgcaagggaaccgctcaacaatgtttgagtctggcctgttctctcagtg
tcggaatccaatccttggaagctcttgaggatctccacaacattggatac
ctgcaccgtgacgtgaagcccggaaactatacgattggccgtgccgagtt
gaatgaacttcgtaaagtttatatcctcgacttcggaatggctcgcaagt
tcacggacaacaatggagtgatccgcanaccaagagctgccgccggattc
cgtggaactgttcgctatgcgccaatcgcttgccataagaatcangagct
ttgaaganaagatgacgtgagttttgctctacatgcagttgagctgactg
tttgacgtgtcccatggaagagatcacgacatgaacgcagttgacaagcc
aagcnagcgatccgcatactccagaaagatgtt
>AW057133
tcgctgtctttaaaggagaaatatcgattctataaaaatggaattcggag
cgtcgtttgcttatagaagaattgacgcccacgttgaagcaactcttcaa
gaagctgctcaagttctcgaaaagttggtaattgaaagagatgccgagtc
ggccataacggtcgcatcccaaggaactccagatgcaataagtatcactc
aagctgctcatgaaaccatttcaattgattcaattcttcgatcttcgaag
caaccaaaggctaccattcgtactccacgtgactctaacaagaatcggaa
attaactttcccaccagcccgaattgggttcaaatccgagcaattggaaa
cttgtgattctggaataactgatagcactattgaccaagatccaccgacc
ccggactccttgttcccaagtgccatctacattccggcaaagcagaagcc
tcaaatgaccgtttcaataagtgcaacaactgcttcttcttgttccaaca
aatcgctctaccgtaagcacattgaaaaactagcaattgagccattggag
gacatcaaacacttgaagtgccgtggactgangaagtcanagccagatga
ccttcttctaaagccacttacgatgcgggaactggnaaaccctaaatggg
gttgtctccgagtcaatggtgtcggtcacctttatatgcatctacactgc
taattcaatagcttgctatcacccaatg
>AW057134
cttaccctcggaaaggcagaaagtcatatggacttactggaaatgtgaag
aacgtggaaaagggtgtcaatgtgtggattgagttgttggaaaaaatgga
ttttcgaaagacgatggaaccggaattcaaaccgattgacacaatgaaag
cagatcttgagaagtgtcaagctttcaagaagaatattgatttttctcaa
tcggagaatgttgaattgtacgatacaaatcgggtcaaaggaggtggaga
agcggatttcttttatcacggaagcactctgactattccatcggtaacca
acaaatcttacaatccttgtccaacttgcaattgtcgactcaccgcaatc
tcttgaatcattctggataatgggtgcctcacaaaagatccaaagactct
tcattcttcttggcgaagaagaactcgataaacctactctgagcgagtac
tttccagaagacttcaaagagttcaagacgattcgtgtgaacaatcggaa
gactgtgccgaagactgaagagcaagcaaacactcaattgtactatgaag
ttgtgccaaaggattgtgcagaagctccatttgcaatgattgagatctgc
gattcttggcctgatgcgaagattccaacgatgggttataacagaaattg
ctgcgactgctgcagcgtgtctgaatctgatattgattgtgatgcttctt
gtgctattgtgagcaactacngagccgctagagcacgatcatctacttgt
gcagttctggctactgatgaagtgcacgcacgagaagccccaatattaaa
gaaaatcgtctttagtacgttcgcacgcctgctgtattcgacattgctca
tacatgtt
>AW057135
tctcatcatgatcacggaagctgagatttgcttcaatcggatatggcgtt
gacaattctggttccatggaactttcagctcaagcccccaattctcgatt
ggggaattaatttacctggtatttattgattaactacanaatatcccgat
tattttccagtagttgtactttgcttggggttttaactttattttattgt
taaaaagggaaaagctggagcaaaatgcccattcactg
>AW057136
atcgaacatcaaagcagtgaccataagtggaaagtgttgcgaaatatcta
ctcgggaccgttttcagatgtttatgtcgttgcggatacagtaacgaacg
aaaagtatgcgatgaaatgtgagagacaagaaggaaactctcgtccagtc
ctgaagctagacgtgatggttctgatggcgacgaagggtcttcgaggatt
tccgaactttgtggcggcaggcagaactgatgtttataggtactgcataa
tgcaacctcgtccggaccggatcttggtcggctgcgtcgaacacgtncgg
aacgcaagttctcccttccaacagctctccaaattctcggacaaactctc
cgacgcctcgaggatcttcacaattgcggatggctttgtcgagaagtgaa
ggcgccgaatttctgcattggtgtcggcgagaacgagtcgaccgtctata
ttctggattttggattcgccagganatttgtagacaaggagggcaaaatc
at
>AW057137
gaaacttgtgaagaaggtctgcaatggctgcctcaaagaaattgatgcca
aagcgaatgaagaagaagatgcaggtggagagaatggctcatgccagagc
ttgcaaggttgcaaagagagaggctcgcgtcgctgaggaagcatctggaa
aatcaactggtggatctactcgcggagccaagtgatagccgagccacaac
acatga
>AW057138
tcgaatcaatcgccttttgaatcggcaaagtagcaaagaagaaaaggaac
agaagaatgggttccgagaagatgatcgagatttgtatcgacatggagga
aggagaaccacttggtgcaactccaaatgacaagctcgttatcactaaga
ttcaggctggaaccatttctgaaggaaaattgagaattggtgaccaagtt
aaaaaagtgaacggacaaaattgcaaggattgtaacgactttttccgtgc
gcttcgctttgctgctccatgtgcaaaaatcacggtgaaccgtgaccgaa
aaaaaggctgaagagttagaagctcgtgttcatattcctgaggatcgtgc
anagatcattcaacgccgtgagggatacgtttatgagttggcaacccttg
tctgggttcaaaatggaccaaaacttggtttgggaatcaagcatttccag
aaccgtgtgcttgtttcacgtgttgatcctggatcactagccgagaagtg
tcttgttcttggagatcatttgtgtgatgttgatggaattccagtcagtg
acaaggatgttgccagagatcttctcgtcaagaatatncaagagaaagga
naagtcacttttgtcgtcgagcgccctgattcgatcgatgccaagcaatg
ggcgatacaggcgttgctaccaatctcatgctaccaccatcagtccatat
gaaccgagatgtgaaagcattgcttcgcatatcgtcaagctcttttcatg
actgagcctncagcgaagagtgcattgtctacctgtccanaatgcttgcc
gtgttctatcatcgagcaaactcaaaacttacgagatccggcatgatcat
gacggaaagcttttcgcaaggtcagtga
>AW057140
caattgagaacgctgtgcagacatgtcgatgaccaagaatcctgtgaaat
caaaaccagccgatggaacaacgtccgctaaggattttgagaaccttcag
agtgacttcttctccttcttgtacgctgatcatggaccattctacaaaga
gaatgtgaaaaagttggaagacgcaactggtctgaaacgtgaaatgctcg
catatgggctcatcgggctcaattgtgtctacatgattattggaagtggc
gcccgagttgggggcaatttgattggagttgcctatccggcttatgtttc
tgttaaggcgatccgaactgaaggaactgacgatgatacaatgtggttga
tctattggactgttttcggtgccttttcaattatcgacttcttcgccgca
atcattatgtcatatttcccaatttattgngttgccaaagcagcatttct
cttgtacctctacttgccagaaactcacggatcccacgtcatttaccacc
aactgattgatccatttgttgctcatatggagaagagcatgtccagaaag
cttncagcanacgctggaactgttccaaaatgatcaggatcagccttgga
tgcgaantaaca
>AW057142
ttttcatgttcgccaaagcacagagaaaagaatagatggcagacaaatca
gcatttgtgccagtcgatgcaatcggaaatcacaaaaacaccgatcttga
cgttgatattgatgacgaattgttcggaaagaaaccaccaaaagccagtg
caagtgcaaccaaagcagccgctccaccggctccggctccagccccagcc
ccaccaaaacctgctgcagcacctgccccagccgctggaaagtaccaata
caagaagtcgtcgacctatcagaagacctat
>AW057143
gactggtgctcctccaacagcgaaataagcagactgggctccgccacctc
cacctccacctccggctcccatgtagactgatgttcctggtggtggtgca
gcaccacctccaaccttcgaggctccaccgcctcctcctgctggtcctcc
tccaactccaaagtaagccgattgtgcaccagtattgctcc
>AW057144
cgaaatgggagtcgagttatcgttggatccttctgtctgcccaatccaag
ccaatggtggtgtttctacgcacaagatcattaatcactgcgacaaaatg
ttggcctataagataaaatcttccaataactccaactacagtgtcaacac
tatctttggacttattcagattgggtataccgctgatctgatcatcacta
gaaagccaggaaagccgcaggccgacaagcttgttatccaattcgctgcc
gttgagcagacttgccgtgatggctgtatttgccaaggctgtatttgcca
attggactgccaactggagagtgctgtggagagacgatcatcaagctgtc
agctgctgaatagaagaattatcacaataagatttgtgattatgaaaac
>AW057145
gcgaaaacaaattcaccgcccgttccgttgtcctgtcttggtgaccggcg
tcgtcgtcggcggagccgctcttctggcgattgccgcctactactactgg
agccagaaaaagaaaagctctgatacttcatctgccacgtcatcggagtc
caacgatgttgtcatgatgtcatcatcggagcccagagccgatggaggag
ccgattcgaaggcaaagttcaatattgaggatgaaaatgtgagaagagtc
tgcgagaagctgttcatggagcagatggatttgggggaagcttattttgg
aggatgaagaaaccgaggagctcggcgcaatccacatggccaacgcaatc
gtgctcaccggagagactgctcagctgctcaaagtgctccgcggctcgat
ttcaccggctcactttgccaatattcaaaagtacctcccatcggctgact
tgcgtgttcaccagcttctccaagacgagctcgccattgagactattgcc
cagcatttcgactaagctcaacttctttntttttttt
>AW057146
aatgtgtacagcggtggagtcactggagaaactcctgcctacttcaatga
cttgcgaaaatgtggatgctggacagctccatctgtcaagcagttcgcgc
aagatgagacagtctgcggtatcactgacaacagagatgttcatctagct
ggaaatgtgctcaaggctgctgaagaagacgggaagatttatgctggacg
attggtgcaaggaagcctgcaaatt
>AW057147
aattccggcttggacacgctacggtactagttgatttggaaggtgtaaag
tttgtgacggacccagtttgggctgatcgagcgtcgtttacgagttttgc
tggaccgaagagatacaggccaccaccgatgaagttggaggatctgccgg
atttggattttgcagtggtgtcgcatgatcattacgatcatttggatgct
gacgcggtgaagaagatcacagatcgcaacccccaaatcaagtggttcgt
tccgctgggaatgaagaaatggatggaaggccagggcatcggagtcgacg
ggatcttcaccgctgtcaccgagctcaactggggagagagctcagaattt
gtgaagaacgganagacctacaccatctggtgtctgcctgctcaacactg
nggacagcgtggacttttcgaccggaaccacagattatggtcaggctgng
cggtgatcggcgagaatcggcgattctattattccggagatactggtcac
tgtgacggagagtttaagaagtttggcgagaagcttggaccttttgatct
ggcagctattccaattggagcatacgagcccagatggttcatgatatccc
agcatatcaatccggaagaggcgattgaggttcataaactcattcgggct
aagaacagtattggaatacactgggtaacgtaccatatgggctctactga
gtactacctggaaccacgtgacaagctcaaagagcttattgatgctccgg
gagatcttangaacacgagttttgcacaattggaaatgggtcgatttggg
aggcgtngatca
>AW057148
agcagcaaagaagaaaaggaacagaagaatgggttccgagaagatgatcg
agatttgtatcgacatggaggaaggagaaccacttggtgcaactccaaat
gacaagctcgttatcactaagattcaggctggaaccatttctgaaggaaa
attgagaattggtgaccaagttaaaaaagtgaacggacaaaattgcaagg
attgtaacgactttttccgtgcgcttcgctttgctgctccatgtgcaaaa
atcacggtgaaccgggnccaaaaaaaaggctgaagagttagaagctcgtg
ttcatattcctgaggatcgtgcaaagatcattcaacgccgtgagggatac
gtttatgagttggcaacccttgtctgggttcaaaatggaccaaaacttgg
tttgggaatcaagcatttccagaaccgtgtgcttgtttcacgtgttgatc
ctggatcactagccgagaagtgtcttgttcttggagatcatttgtgtgat
gttgatggaattccagtcagtgacaaggatgttgccagagatcttctcgt
caagaatatccaagagaaaaggaaagtcacttttgtcgtcgagcgccctg
attcgatcgatgccaagcaatgggcgaaacagcgtggctaccaatctcat
gcaccacctcagtccanatgacggagatggaaggcattgctcgcaatatc
g
>AW057149
ttatgagaaagtattcacatccacatattgttcggattattggtaagata
atcgtcaaacatcttccaaaagttggtttggcagtagatgctcatccact
aatgattgtaatggagatgtgcccacatggatcacttctttcatttcttc
gtaagaacaaagggaaaacgacactttccgaacgtcttcgtttttgtatt
gaatcagccgatggtcttgcatatcttgagaaaaaacaatgtcttcatcg
tgatattgcagccagaaattgtttactttcgatcaccgatcaaattaaaa
tttcggaattttggtctttcggatgacaaacgaactgaaatgcatgatga
cacactcgataaggtaccagtgaaatggttggctccggaagttatgcagg
ataaattgtattcattgaaaagtgatgtttgggcatttggagtgctcatg
tgggagatatatgcagatggagctgatccatatccgggaatgacaaactt
agttacgagagccaagatcttctgcgatgattacagaatgactnttcctg
agactaccgcaccaaccatttctgaaatcgctttgaaacaaatgctggcg
aaacttcccatcnatcgtgccacgatgaaaactgtgcatcataagctaaa
gacctctcaantgccatggtcgatgtaggctcagtatgaaaattgaacgt
>AW057150
tttcactcaaaacgttcaacaagaggcaaattcgacgaaaaatggacaca
atggagcagcatcaggagcttgagcaagaagccatcggaccggctcttcc
accgccgtcagctgctcaaaaatcggagctcttcgaggagcacaacgtcg
agtacgagctgatcaacgggatcccgtgctaccagccggatcatgtggtc
gacgggcaagttcagatcttcgaacgaatcggctacgacgacaaggtcgg
cggaacgttcctcgggctcagcgccgacggaaaagagctcgtcgtccggn
gtgcaccgatcgacgcgctgactcatgtggttcgtgccgaggcggcattc
ctgtgcaaggtggaagccgagcttcaggactggcggctcttctcgcaagt
tcacaagatctttctgaccgacgacgcgtggcacatgtcgctgtacttcc
gtggtggaccgacgttggagcagtgctttgcgatgcggaacaagttcac
>AW057151
tatccgctggtttgttgtactcattttcctcatcatttccaataaaaaga
aacggtcgatatcatgtttggtaatgaaaagagcgaagaatccggaagtt
ctgggtttggtttagctgaagttaaaaaggttttccagtggattctcgga
tgcacttatgcgaagaaaacattcaaaactagaatttctgaaatgtttca
ttttgctgatgctccgcacattgtcgtgtatgagcgaagtgaggagcgac
catggtattcgatggttggaataataattggagttcttcattgtagttat
gagtctctattacacacttgaagctggataccgttcaattcgaaaactca
tgctttcaatgctccaagatccgcaacagagtactgtatccactccaaga
tgtctatcaccaacaaacatgggatccaagaaatcttcgcctcaaactcc
aaaaactccggatgtgattcgtcaaaaagttccgatgaatgagccagtca
attgtgtgttcattcgaccagttattccaaanactattccagagggtact
gtagccgtgccgaatttgaattcggaagaagatattctattggatagaga
tcatcgtattggagagacagggacaaagatatatggaagttagaagagac
acatagtgatagaagtggatagaaaaaataaacagaaactaaaagagtc
>AW057152
gcaagaagaagtctgatacggcatccgttgttgctattccagaaggagac
aatgagaaaggaaagaagatcttca
>AW057153
aagaacagtcttgaccaacacgagatgtaaactcgattgacgctcctctt
cgacctcttgttgtctggaagcactctgctcgttcaatgtggtggaaaga
aaaagggagcaacttctgccgaaggaaaatcttcgacgatgggcccggct
cctggaggagctcctgctgctgcttccgctcaaggagaacctgaagagaa
ggagtaa
>AW057154
atctacggaatgatgcgtcaagcttatggtgcatgtggatccaacgagaa
tgctccgtacgattgggaaaatggaggtccagctgcctacttgctccact
agaagaaatagacttga
>AW057155
gacaagtgttctccgatgctccttcgtgccanatttctatattttcatca
gcgcaccatgggtgttgtccgttactgttaagcggaatatgaccgagtat
gagcagaaaattcatatcaacctactcaatgggatccgtcagaagaatgc
gattgatgagcaagtggctaatatgcatgagctggtctacgatcccgctc
tggaatccttatcatatccagaatgcgaaatctccaacgatgatattacc
gtaaggaacaatgatggcgtatccacatattataatgcattcccaccaac
cggacagatatttgggtgtactatgcgcaacacattgattccctgcatac
gtctgccgcatgccatcatctcacctgcaaatccggcagttccaataata
acagtgtcagcggatgtatttttggacctgttcgtaaattcagcagctcg
gaagtggtgaaaggagagcctggttcacagtgcccaaaaggaagatcttc
actggattt
>AW057156
gtcgactgcaaagaagactcctgccaaaatacttagccgcagcagaagcc
agcagaaggtgaaacgctcgatgagccgcaaaggttgaacggattg
>AW057157
aaattccaaaccactgaaaccagttagtancaatgactgcacaaatcatg
ttgccaatgagtgcaattttcgtgctacttggatccatagcaaattgcgg
tggcaagaagaaaggagcagctggagccggagccggagttgcagccaaca
gcccaaaaaaggcagatggaccgtcgaagaaggaaacgaagaaagaagga
gatgacggaaactacgaggaactcgccgtcccacaatgatccccctgcat
ccctgtc
>AW057158
gctgggcggctgagctggatccacgtggctagcagaacatcactgactcg
aatgttatcaatcgcgaggaatacgaggacgacgagtacggatcgccagt
ataattttcataactcgttctacttctcgatagctcatcatagccaattt
cgtgctataatcgtcttttttggcgcgggtttttcactcgtcttttcttt
cttttttacttttactctgttctatactaatcgcggatatatat
>AW057159
aacggtactcgatgagactgctctggatactaaagatatgttgatgaccg
cattggcactcatgtcactcattggactctgctcaactcgtcgtgcattt
ggtgtcttcactcttctcttcatgatgcatgcatttgtattctcagcttt
ccatcttgcacatacanttgcactcttcattaaatcattcgattctccat
gtcaatatctgaaaactccctcaactggaacacttaattcggatatctgt
catgctgttaatggagttactctggtgtgtgcagtgatttcaatgattgc
tactgctcttgccagtatggccgtcttcattcgtctcactacagtcgtcg
tcaaaatttcgga
>AW057160
tgaacaattgtcaaagagttcggatcccaacatctcctcgatgtacgttt
tccatcaaggaattcaagtaaagcaggaaccaatcgatgatgaccaagag
gaagagcaacaagtacaaaagcagcttgtattcaaaatcgagggctccga
agacgaagaagctgtgaagaaggagt
>AW057161
caactttatttatacacacaatacataattttcagagaagttttcataat
cacaaatcttattgtgataattcttctattcagcagctgacagcttgatg
atcgtctctccacagcactctccagttggcagtccattggcaaatacagc
cttggcaaatacagccatcacggcaagtctgctcaacggcagcgaattgg
ataacaagctaggcggcctgcggctttcctggctttctagtgatgatcag
atcagcggtattcccatcttaataaggccacagaagcggtgacactgcag
ttggagttattggacgattttatcttataggccaacattttgtcgcagtg
attaatgatcttgtgcgtagaaacaccacc
>AW057162
gaagagtgcagtagtccgattgaaaaggatcaacgtcgatccgccaactg
gaaactatccggcaactggaggcaattcgacgcacaacatcacttccgaa
tcggattcccgtcttgcattcaaggtgaagtcgtcgaacaacgagcacta
ccgcgtccgtccagtttatgggttcgtggatgcaaagggaaagagcaaat
tggacatcaatcgtcttccagggccaccaaaagaagacaaaattgtgatt
caatacgcggaagtgccagccgaagagactgatccaatggcaccggtcaa
ggcttgagctcaacaaggagaaatcattgtgaagctcatcgctgcttgaa
tggaatgcaataactgaag
>AW057163
atcacgaggctcaaaaagcgtttcgctcaattgaacacggtttcattatg
aagttcgatgtctcttcgttgtgccaatttgttgttcaactcctccaatt
ctgcaatgtttttattgttcttgcagtgatgaccatcacctcatgcggaa
agaaaaaagcatcaaatagcaaggaaaattgcaaaaagagtttgcaaacc
ggccctggagcagccaccgaagccggagctgcttcttcgttagctccggt
tgacgcgaccaagcttgccacacctgtaccagcggcgccaaaaaaggaag
aagctccacctccagaagagcccaagaaagaggagaagccaaaggagaaa
tcgaagaagtcggcgaaatcgaagaaatccagcaagtccaagaaagacaa
gaaggatggagaggaagagaatggatatgaaaactgccaggatatgactc
cggatcagttgaagaagattgc
>AW057164
tcatcagctcattcctcattcggtacatcaaatgactcgttttcttcagt
ccaaagtgtgattctgccaccagttggaccatttggtcagaaaaagagaa
cgtttgagtacattggtgtcacacttgttgtcgataagttgaaattggct
gaatggatgaacgggatcgggaaattgtttggatccgcagagctccgtga
taatgttaccaatcttcatatgcaattggtcccggtgattgatacgttta
aaaa
>AW057165
tgagaaatatgagctagctatgagaaatacgcactgaagatgaaggagga
atgttatctggtgttataatggatacttctgatcattatgagcgtgatta
tacaatggatcatgatgttggaccttcttcaatgaaaatgtctcctatac
caccacctccgatcaaagaagaatcacctccaccaccgccac
>AW057166
gaaagagtaaaaatacgaagaaagacggcgttgacaagaagaaaacttcg
aaaacgaagaagaagtcaaatttgtcgatttccaaatcgcaaacttcggt
ggatatgaatgaaaaggacaaatcaaaggaggcaaaggaagcaaaggagt
tgaaagagaagaaggcaaaagaggaagccgagaagaaggttgttgccaca
ccaaaaaaagatgcttcgaaggatcaggcaaagaaggaggaagatcctta
ttagcaaaacgaaccaagtggaatggatgttcttgtgaaggaggacggca
agaagacaaaaatggacgatggctacgaggatttcggtccaggcgccggt
gctgctcaatgagcaaatggtcgagaaac
>AW057167
ggggaatctggagaactgattacagtacaaacatcataagtcgccacaac
aaccactgcacgacccattaagaatattgctgcaacaactaccgtcgcac
ctctccaattgattgcggatgcttcacttgttgacaatgacctacaatcg
aatcttgaagcaactggagtgtatgtcgatggaaagtggtggtggtgggc
aatctacctgggatttgtcttgggcactctccttactttggctatcgggg
gtggaatatgttacgtgttgcgacgaactgtttatggatattggtaccgc
ggcatgtacagacgatatggatgtgatgtctctgcgacaaccgctggtct
cactggagttggattcggagcaactacgaccgcaatgcagacgatttctc
ctggaaagacgggtgcgacaacattgggaagtacttcaagtaccactgga
attactgaaactactggaactactggatccacggcaaccactggaact
>AW057168
tcccaacaacacctcaagatgaatgccatcttcactgccgtccttgttgc
ttcaactctcgcctacactgcaatggcttggattggactcagcattgaag
ccgccaacgaggatatgttctgaagtggtacc
>AW057169
aattccttctactaaccctttcgactacaattaacatggacatggacaag
cgatcatcggatttggaagctgctcttcgaattgtgctccagcagacttt
gaacatcgttttgcaagcgcaggagaagctccccgaggcaaatgtggtac
cctcaactccgcccacctcaccgagcactgatatcggcgaacaaatggca
tcgttctggaatattccatcacccaaccctcctgcaacct
>AW057170
gacaatttctcaagatggtcgaactgcaaatggagcaggaaatggagaaa
atgaatgagattgagactgataaacttccgattgatcatcaattgagtga
ctatcagaataacatcgaatcgggaaatgatcgtcaagttcaatcatgcc
cagttgatgtgtctattccaaaagaagtcatgaagtgtgcaagctgtcct
ttgctatgcttcaattgctcagttcaaatgcctgtctcacccgttccaaa
caacaatcgaatcccgtaagatcaacgagactactcacttgatgatggaa
ttttggaagattgttgcttcaaagtctgaagaggaaaagctcccatcact
attcgaaaatgttgagggactgttttctgtcccattttcaactnttggaa
cgtgggatgatgacaccctgtctggtgtcacatcgcttaattttgaaaag
tctgatgaacaactctccgagcaagatgatgacaaaaccactgtttggag
ttctaatttcccatcggctcatgttttaacagtctatgagaattctgaac
agaagacggatganatggccgatgatgatatgtccgacacaacttcatct
tttcttctactctttcacaacatgagtgctcaagtgccgcgctcatcttc
tcagagagtcacttgcaagatcagt
>AW057171
gtcgccagactttcagcccaatgactttgttattgattggaggtttgaaa
aatggttgttctgagaatgaaaataaggaagaggggaagtttgagaaaat
tgacaaagttttctttcctcccgagactgccaacaatactaatccagtcg
gacgcctcattggtccacgtggaatgacaattcgccaactcgaaaaagat
ctcggatgcaagctgttcattcgcggaaaaggatgtacaaaagatgatgc
caaagaagaacgtcttcgtgaacgtgttggctgggagcatctcaaagaaa
ccgattcacggtgatgatttcagtccgcttcgattcggaagaggctgcat
ccgagaaactgtcatctatcaagaaaatgcttcaagaatttttggaacat
actgactcggaactcaaacgctctcagcttgcaactagctgttatt
>AW057172
aatgatcaacgtcgacccaccaactgttaatgttcctgcatctggaggta
attcggttcacaacatcgtctcggagtcggattctcgtttggcattcaag
gtgaaatcgtcgaacaatgagcactaccgtgttcgtcccgtctacggatt
cattgatccgaagggaaaaaccaagttggatatcaatcgtattgctggac
caccaaaagttgacaagcttgtcattcaatatgctgaagtgccagccgat
gagactgatcctcaagcaccattcaaagctggagcacagcaaggtgaaag
tcatcgtgaagatcactgccgaatgagaaaat
>AW057173
gctcgtacaagaatgctcgtcccgctgactgcaattgtgactacgtcgtt
gccgatggttgccgccatcgctttttgtgccaagaatcgtaagacggtcc
atgctaaaaacaagaataagaacaagagcagcaaatctgccaaatcgtcg
aaatctactcgtggagcgtcgaagagtgggaaatctcgccgttcatcgaa
agctaagcactccaagagatcgtcgaagtctagtaagaagggaacgtctg
taaaatcttggaatgggaagccgcaagcgtggagggaaatcatcaaagtc
ttcgaaatcgaagaacgtcaagactgctaccacctctggttctcaagttt
caactgtttccgctgctactggtgtttctgataagcaatctaactcatcg
aaatcttctcgtaagagctcaaagagttcgaagagccgtaagaatcgtcg
acttgattcggatgcccagaagaaaatggagaaatcgggacagagcggca
aagttgctcttattccagaaacgcaacacacaactggaagccaagctgcg
catagccttgctgaagaagtcaattcgatcaagcactccaaggaaatgaa
tgtggcttctgctaaactgctataccagacactttggcgagtcaatcana
ttgtattgaaggatacttcatatgaacgtaagcttataagatcagtgctc
ggatactccctttatcggtcaatccgctttatgatttg
>AW057174
tccaaatgacaatcgacatgaaggtggtggcctgggaaatgctcaaaggc
tcggatcagccggtggacttggtccccaagaaggtcgtggttgccggaca
ggaaatcacagttgattccaagtcgaagaacgaaa
>AW057175
atcaactaataagatgccctgtcaaaagaagtcaaacccaacggaattgc
acatctccactggccgcgagatcgttcaacggaactttgtgttccgcaac
accactggcaaggacttcctgctgaagttgcatgctacgaatgaagccgt
caccttcccaacggaagttttccgttttccaccattggctcatcgtgcca
tccagttccgtgtgaactcatcaaagctctcccaatgggacaagatgaat
cttttgatccaaaggatcgtgttgccgatctatgcgaagagcctcaagca
gttcattgatcagaagaaaactgcaggaactaaggagcaagaggcattct
cattgtctgtcaagttcacggatcagttctcggctccccagacagtcatc
aacttgccaggatatgccacgtgtatcgagtcgactgattatccggttga
cgtggaagaattggacactacaactgcagtcaacatcgaaagagatgtct
ccactgctgttccaattggttcaatgatgggatttgttgaggagtacaaa
cgtcgtcaattgaacaaaggatgctgtctttcaactacatctttggaact
gaaagcaaccggagagcagtcaatgagatctctcgtgatcagccgtcgtc
gatcatctgcaagagctcaaggt
>AW057176
ataactctcccaacaacacctcaagatgaatgctttctacactgccgtcc
ttgttgcttcaactctcgcctacactgcaatggcttggattggactcagc
attgaagccgccaacgaggatatgatctgaagtggcgc
>AW057177
acggattgctcgcgagcatccggaacgtgcggtgactttgctcaaggcgc
ttttcgctactgtgtcgacatttgatcaagaaggttatgtttgtgtggag
gataagaagttcactgagaaacagtccaaataacttt
>AW057178
tctcgatccttgccgtttttgtccaccatggatttgctgctgctgaagaa
gagaagaatacagcttcagtcgtcagccctgctccggactctgaagcagc
ccaacctgctggaaacggaaccgaaacaccaaaagatgaggtgaaggatg
aggcaccaaaagaaggtagtgaaactgaagcttcaccagaagccaagaca
aaaggatctatggtattccatgctcttggagccatttccacagttgttct
cgccggcattatgtgaagaagtctgccgaaag
>AW057179
atcaaccaccatgagttttgatgaaattgacatgaccttcggaaccaaga
accgcgatcaaggatatgatttgctcaaagcgcgtctcgacaaaggtgat
cgttcggtggaagtcttgtggagacttgctcaagtaattcatgagaagtc
tgcatgtgttccaaaagctcaacgtaaggcaagtgtcaccgaaggactca
agtttgctgaagaagctgtccagaaggatccaaaccatttcaaggcgctg
aagtggaatgctgtgttgactggacaagcaaccgaatatatggcaaccaa
aggaaaagttggattgcagtaagaagttcaaggaattgctcgacaaagct
cttgctaaggagccaaaggatacggctctcctccatttgcgtggccgtta
caagtactcggtggcatctctgacatggcttgagaagaagcttgctgcca
cgttctatcagcaaccaccatcacattcctatgaagaggccaacgaggat
ttccttgctgcttataaggtcaatccaaaatggatggagaacacattnta
tgtgtccaaatgctacgtagcaattaaagacaagaacaacgctcgcaagt
cccttaccgaagtgtgtgacatcgaaccgtattccgacgctgaacaagag
tttgccgatgatgcgaagcagatgttgtctaagctttaa
>AW057180
gaaaaaatgatttcggcgttcacttcattcgctgtatcctacttcgtctt
ggctatttcgttttacattgaaacaactgtcagcttgttccacctcgctt
atttctcgtacagaaatccggcagtttcgaaggatctcatcaaaactgca
ttccatcttttgaagacttcctacgacaacaaattgctgacatttgccga
aatcatcgagactacacaaaacagtatgatcaagccaatggctcatcaga
ataaacaacactttttggaggaaaaccagcgtaccgcacagttgcagacg
atgaaaacatcaactgcttttcgcgttaa
>AW057181
tacaatggatcaaatcccaccatacgagttcaacaagtacgtgctctacg
tccgtggtgccgtcatcgtctgtgcttcatttgagctcctgttggtccta
ttcggttccctcgaagattgcaacttccttgctaagctcttctacttcat
cttccttggcggagcagttgccatctcagctcacaacattggtctcaacg
tggatggtcgcgaggagctcaacaaggttctttcatcgtcagagaatgaa
gttcgtggaaaggtctgctgccttgattctggtgccagcgctctccggtg
tcctcgtcttcttatgtgtctctggacatgcattcttctctggtgctgca
ccgtcagcacaggatccagctgctgctccaccagcccaatagac
>AW057183
tatacgtgcatgtggaggatgaaaatccgaatgagaatgagccggcacgt
ttgagagctggattcgagtgggctgctgaaccggatgagattctcattgc
aggtgttcccaccaagttcattatgtttggtttgtcgtgtttccttgtaa
ttctaacactcagtctatggattgccagcacccattattcttactttatc
tggctcgtgtttgccacgttgtacatgggtcttatcgtgttccttcccga
atatttctcgaatataatcagtttggctctgaactttatttactggatcg
cttactgtattttcacttttattggaattattcttgatgttgttaggaga
ggggacagttgtagttccggtatgagcaaggaagtttgtgatgctaatcg
tcacggatacatgttggctatatgcttcggatgtgctgatctgctaattg
ctggagttatcatgattctgatgttccgcatgctcaattactattacatc
aatcgct
>AW057184
gacatgtcggttttcataagtttgtgttctgcttggccttattgcaatga
tggcagcccaattcggactaaactcgggacttgggcttggagttggaccg
gcgagagctaatgctaacctaaacggaggttttcaacgtggctacggcgg
caatggctacggtaaccgaggtggatacggtcagcagggcggctattatg
gccagcaaggaggttacggtcaacagggtggatatggtggcaatcagggc
tactatgggcaacaaggaggcggntattgaggtggcc
>AW057185
attttttcaaccgatcgtccaacaagagacaatttcctctgaaaacgcaa
tgccgaacccgccaccgaaggaagacacctgggcgtttcaaccaattgga
gccccattcccaccgagtcctgtgaaatgtatgggagaacagaatatgta
tgttgctctttggtacaagcacggtaaaccaatccacggtcgctcatgga
acaatggaggagttgttgaatgttcattcccatataagcaagctgaattg
acaaccaagcaacaactggaaggacagatccaggttcttcaatacgtang
agaccataacaatcaaggtttctggtacgaatggattaagtacaaggatc
gtattgagaagattgacgataaacatcaacttgtgcgttgtggtgattca
ttcccaatcttctggaagcgtgccgaaggaaatcttcttggttatgtcga
caacaagactgaggaggcttggttctcgttcaatggaaaagtgctgaaac
aagttggaccacaactcaatgacatgtacatcatcacccgtaactgcatt
ggtgggccaccatcttgtgattgtgccaactggtgaagtggaccanaggt
tcgtgtcgagagagatgaatggatggacattcgtgaggtgatgcatggca
actcgtcacttgtcaagctcttgatagactcttgatacttgccagtgtca
atcagatcatacgttgcactttgacatgccagagaacctgtcatggtcgg
atggaat
>AW057186
tcccaacaacacctcaagatgaatgccatcttctttgccgtccttgttgc
ttcaactctcgcctacactgcaatggcttggattggactcagcattgaag
ctgccaacgaggatctcatctagatcgatcggagaaaaccgccacaagaa
attttg
>AW057187
actaactaactacaatcaactctactatacttatggtcaagaagattact
gtctacactgcttttggacaattcctcgagatgatcgagcgtcaagccga
acagagaagggaaacagttccagtcctttgtccgatcgttgaaaaggctc
agccaaggacagctttgaacaaggttcaatcttgcccagttgttccaacg
actgcaagagttacagaagagatcaagaagagcattagctgcccattgtt
ggctctccac
>AW057188
tttctcggaacaactccaagcgaaaaaaatggcggacaagtcggcgtaca
tgggtgctggtggctatggatccggatacatgggatccaacgcctcatcg
tcgggatatgcccgcgaagattatgcacaaggaggaaatggaggcggaca
acaacaaaaccagggaaacggaggaaacaccaacccaggaggacaggtct
tcaaggcccgtaccgatcaatcgtgctaccttgggccataagtagctgct
cgaataatgtgaagactcagccag
>AW057189
tctttcgttctcgccatcaccgccttgcccgcgattgccattttctgcgg
aggaaagaaaggagccggtgaatctaaagaaaagccaaaggaggatgtgt
atgaggatttggcaccaggagataagaagtaatacttgtgaactgacaga
atgcacaatcgagcaacttc
>AW057190
ttttgaacaacaatactcgatgcccaagttaaatagaagaatcgttcgtg
caagggattcaaaaggacgcttcctacccggaaagaaggccaagtctgtt
gccagcaagtctcgttcgagatccagaagccgcagtgttgtgagccgtat
gacgacccgtaccaattcgttgactcgtcgtcgttcatcgacgaaagctc
cttcgtctgcccgtcaatccagatctcgctcaagatctcgctcaagatct
cgctccaaatcccgctccacgtcttcccgccgttcccgctctcgctcagc
ttgttgtgtctcgttcaagcgtggacgtcctgcttcgtttgctatgaaga
gtcctgaagagaagacggccgcaaagaagacggccgcaaagataatcctt
agagtagattagccacctggaatgagatacagaat
>AW057191
ccaacaacacctcaagatgaatgccatttactttgccgtccttgttggtt
caactgtcggctacactgcaatggcttggattggactcagcattgaagcc
gccaacgaggatatgatctggagtggc
>AW057192
gcacctggttgtgatattgaaatggatacgcgtactttgttgtggaatga
ctacaatgctgcagttccaactaatatgtgggaaatcggaaaatgtacat
tcaacttc
>AW057194
tcgntctactgagaaggatgaaccgncagtcaacttcttctcctcctcat
cgactcgatccttgccgtttttgtccaccatggattggctgctgctgaag
aagagaagaatacagcttcagtcgtcagccctgctccggactctgaagca
gcccaacctgctggaaacggaaccgaaacaccaaaagatgaggtgaagga
tgaggcaccaaaagaaggtagtgaaactgaagcttcaccagaagccaaga
caaaaggatctatgggatttcatgctcttggagccatttccacagttgtt
ctcgccggcattatgtgaagaagtctgccgaaa
>AW057195
gtagatgaacttgcaatcgttctacattttaatgtactcggatggcccac
tgactcccttcgagtagtagttgttgaaaaccggagcttcatagttgacc
ggaggagccgagtaggtcggtatcggagtggtgactggagcggccacgtg
gatctccggaacttcctcctcttgctccacatcctttttacgagcgaagc
agtacccagactcttcatcgtcatacatcttgtgaagcatcttcggagca
acttttggcttttgctgaacttgttgaactggctcgacgactggaacatc
tggtgccggctgctgctgctgctggatctgaagagcctgcagctgagcca
tcaactgttgctctgtgaagtccggagctggagacgcaggtgcctgctgn
gtcgtggtgtacttaacacggtaggacaacggaatatccgatggtccacc
atagtagtccgagtgcacaatcggctgttccggagcaactggagccgctg
cttgacgaaccggtgatgatgnggcagacgcagacaaggagagcaccgaa
cggtagagacggatggcatcctggattttggatgagtcagagatcctcgc
gattgggtgtagcgngaaggcagcgtggcagagaggagcttgctcgctgg
ctct
>AW057196
agagattagtagatggatgtgataactttcgcatatcatcatcgtcatca
ttgtcttcatttttgtcgtcttcgtgtattgttgttccacgattaataat
tttcaacgccttctgagttcccttttctaacgaaatacttgtattcttgt
taccacgatacgtagagttgttcatagatgaggactttttcagtctggaa
ctaggtctcgcttgcat
>AW057198
ggataagaagattgtagtaattggatacattatcggaacgactgcagcgg
tagacttggcagcttcaaatccggatagactagttggagttgtgctgatt
gctccgttgaccagtgcactgaggatgttctgcaacaatcctgacaagga
aacgacttgcattgacaaaatctgccacatcaacacccgagtgctcatct
gccatggagaccatgatcaacgcatcccaatgactcatggaatggctctc
tatgaaaatctcaaaaaccccagtgccaccactgatcgtccatggcgcca
atcatcattcaatcattagcggagagtatattgaagtctttactagaatt
gcaagcttcatgcggaacgagacccttctgagctgccgagccaatcaaat
cgagtcgtcctcgtcgaagaaattcaaacatgaatgaatagta
>AW057200
cnaatnccttcaaaagtcgccggttgctcaatcagcataatatgagaaac
aaagggcgtgataaaatgatggctgatgacaacgtctcattcacggatgc
aggtgatccaacaccaggcgctaaacctcaaggaggatcgtcggcaatgc
tggatctacttggaacactgaacaagaaggaagacaaaaagaagaaggat
aagaagggcaaaaaaggaaagaagtcgaagggaaagtcgaagaccaagaa
agtcagaaagacagacaagtttgagtcgcaaaacttcttggttcgcatcg
agggaaccatattttgtgctggaatcgttgtcggattggtggtgctgctc
gtcttcgttgcagttgcaatcttcttcagcgtgaagtctggaggaaacat
ggtgcactacatccatccatggtggggaggacttgaagaatcgtcttcta
attgagagacgaatcgaaagaaatgaaaaagtgacg
>AW057201
aattggagtttttcgacggataaagaagtttcagctggaatcgaaagatc
taaacgatgatctcactggtttctgtgattgccaccgcctcggctactag
caccgtgcttgccatgtgctccagcaaggatcgtcaagcggaccgtaaaa
agactaagaagggttccggatccaagtcttcgcgtgtttcttcgaagtcc
catagatcctcaaaaaccaacaagagatctggaaaatctggaaaatctgg
aaaaactggaaagttctgaaaagtctggaaaatcaagccgtggaaaatca
tcaaaatctaagaagccttccaaatcaaaggccggagttcttccaatccc
cggagccgcaggaggtcccaagtctgaatcgaagaagctcagacgtgata
gcacggacaagtcaaagtcacagagatccaaaagatcttcgaaatctaag
aaatgcgacaagtcctccaagaagtgcgacttgaacaaggctaagaacct
ctgcccaacggttaaccaggcagatgtttccgacgtgtccatcanatcgg
actccggtgagaaatccgannagtcgaaagctctgaagttgttnccaacc
agtcgaagacacattcccggagggacaggttctgctcagtgaagagtcga
ctcttctgcatcgnccacaagctccattcgca
>AW057202
tctgctgcttttcatagctcaatgtgcatttggcggaccgacgaaactta
ctgaggacgaacagtttgaatttttaaaacgagcaaataatttgatgcaa
agcaaagctaaactcgacgcttatacttggatgaatttcgacgccgaact
cgaggctgaaatattgaaaatgtcgtgcgatgaattggaaaaacagcgag
gaattcgatttttcgagtcaaagtttggttaatcatgagattacaagtag
aacaggagaaactggaattgcgtgcatcaagagtgattgtatgtacacag
atctcataccagctgtgccgatcgctcatatgtgcctttacaatcgccca
gtggtcacaacaaccgtcccaccatcaacgacttctggaactgacaatat
tgcgagttttttctttggaattctcatttttggagttttgaacttgcctt
g
>AW057203
aattcccaggaacatcaaagagtcagattagaaaaaagaagagaaggaaa
gcaaggagaccgaagttttcatcctcaagctcgaaaacacaacggtaaca
ttcacaaaccccaagcttggcgatgaagtgaccattgcatcactaaacct
gacaaatccgaccaaggatcggtatgcattcaagatcaagtgcacttcaa
accagcttttcaagatcaagtcaccagttggttatatcaatccagaggag
agcttaacaattccggtctaccactacccagcaactgtcattccggagaa
taataagcactacttcgtggtctactacatcaaggctgcgaacacagtaa
aggaaaagattccagttcgtgatttgtggaaagcggcagcatcatcagaa
ggaacccgacgtgtcttcatagacttcaaaaa
>AW057204
aacgaggcagcgaaaatttcccatcctctgccttcaaaaacttggtgact
catccaaactaccgggattcgtctttcactccgttcgtcttgtttatttc
cgatgacgttcctaacattcatgagtgcctcaaattcgaagagcgtatga
gtgacattccaacgcagcacgtacttctcaaaaatgtcaaaaagatgcgt
gacaacatcgaaaagaagtctcaaggtggaagaagagcatatgatttgac
tcttgacaatat
>AW057205
ttacatgtcacctgaaagaattctagaattcgggtataatttcaaatccg
atttatggtcgactggatgtctgttatacgaaatggcagctcttcagtca
ccattctacggtgacaagatgaacctgtactcactttgcaagaaaatcga
aaactgcgaatatccacctctgcctgctgatatttattcaacgcaactcc
gcgacttggtatcccgttgtatacttccagaagcttcaaaacgaccagag
accagtgaaaggtctacagggttgccgaacacatgaacaattacttctcg
ccttccggggaccaatcaacaactccttcaacgcaattctaaaaaaagct
ataacatttcaatttcaaacattttctttaaaacgtagtgttcttgtatt
ttcaaaaggtggaaacattcgtcaatgaccacgtgaatccgtgatgtgct
aaattttac
>AW057206
cagctttccatcttgcacatacaattgcactcttcattaaatcattcgat
tctccatgtcaatatctgaaaactccctcaactgtaacacttaattcgga
tatctgtcatgctgttaatggagttactctggtgtgtgcagtgatttcaa
tgattgctactgctcttgccagtatggccgtcttcattcgtctcactaca
gtcgtcgtcaaaatttcggataagagagttatggtcaccaagtcgttcat
ttgacaactcaatgccacaattaatcagtagaaagtcaattgaatcggag
aaagaagaagattgtttggagacaccaagaagaaaaatgggaca
>AW057207
atgtatacttctatcagtttgactatcattactctgcaggattcggagtg
ttccggtggcttcttccgtttttgggctccacacattgcacggaaatgag
atatgtgctcggcaaaggaataatctcgaaattccgaccaaatgataatg
ataagaagatgcttcacgttatgacaacttattttacaaattttgcaaaa
tatggaaaccctaatggagaaaaccaggagactggagaatggcaaaagca
cgactcggcacaccccgtccgccatttcaagattgatctggacgattctg
aaatggttgaggactatcaggaacggagagccgagctatgggataaactg
agagcattaaatgttagcagggctcagatgtgaaattgct
>AW057208
aaatttcgaatcacatcaagacatgccgattgaagttacaatgtctacaa
gcaatgaatccgcaaatcttctggtaccctcatttttgccacgtggcgaa
gttctcggttggaatctgacgtcggtggtgaatccggtgactcgacgtaa
agaatacacgtacacggtgtgtgtgcagactgtcggagcatttcagtgca
ccgagcaagcgggcgttgtccttgtgaagtgtgatggtccatgtggaaac
aagttgccaaccaatcatttgattgcattgggaaagtgtgatcacatgtt
gtgtaaggcctgcttcggcattgtaaagaatccggatggatcctatggat
gttcgaacttctattgctggtcggaaccacgtggaaacttccggaaggaa
aaggccaactacaataaggtcatcaacaagcagatctgccgtgccagaaa
gttcaaacaagacggggaagatttgcaagcatgcagcanatcgaatcttc
ccaagactcctgctgacctatcggaccgtgagatgaactctgcgaaatcc
tcggaatcggatacgtcgtcttnctgatggttcttcctaccaatccactg
ttgactcgtactgactgccaanaagattctaa
>AW057209
ttgtgtattcgaaagaaacatggcagaaaatagtgtaacacttctacaac
ttgcccatctcggttacagcatgctcgctccaatggtgttcaccggatac
gtcattgacaatgtggaggaaagaagaagactggtggatcatcgggtggt
ggtggagctaaaactggaggaggaggaggagatggtgcaaccagtgcaaa
gagtgataagaaagaaaaatcatcgagtgctccaaacccagagggaccaa
aggctccaagtgataagaatgctgtcgcagggacacatgatccaaattat
caaactcttgctggagttgatggaaatgtgttccaagagaaaggaaaagc
ttctcctgttgctgctgctggtggagcttctcctgctgctggtgctccaa
aacctggaggtcctggaatggctgccacccacgaccccaactaccaaaca
cttgctggaattggaaacgattgtttcgacaagaaagaaggtgcaaaacc
agcttgtggtggtgcggctccaggtgctccaaaagcctgtggtcctggaa
tggctgctactcatgatccgaactatcagacacttgctggaattggaagc
gattgcttncagaagaagtgattgtgtcaactcgtgcanaatcgggtaca
tnnacgaaatatgtga
>AW057210
aaaaatgaacgatcttgttattaatcagaagattcttccagatatttcga
aatcgaaatgggatctcgacacgtattcaggtcgtgtaaaacactacttt
gcatctgctaacccgatgacactcttcacctcatccaatacccaggaaat
gtgcaggaaaatagttgtagactataaaaaggggataataaatccggaat
tgacgatggatgagctatggagtgcaaagatcctctatgattcagtatat
catcctgataccggcgaaaaagatgtctgtctcgggagaatgagcgctca
gaccccagcaaatatggttatcactggaatgcttctcagctgctatcgta
cctgtcctggtattatattctcccattggatcaatcagtcgttcaatgca
attgtcaactataccaatcgaagcggaaattgcagaactaccaatcagca
gctactctattcgtatttctgtgctactggagcggctacaacggcggctc
tcggtctgaatatgatggtgaagaatagtcatggattggctggaagattg
ttccatttgtggctgttgagttgcaaatgccattaatattccaatg
>AW057211
gaataaattcatttttacactactcaacaattgatttgctgcttctttct
ccacaatctacaacttctgaaaaatgatgaaaccaccgatttgccgccgg
atgagcctgccaccagttctcgcaaagaaggaaggtgaacgaattcaagt
tccagaaggtggagaattggtatgctaccgaaaccaagaagatcaacatc
ttttcttaaaaatagaatactcgcgcgaaacgatgattaaactttcatcg
tctgttttctgttatgcacgaccaactggcctcaaagaagtttccgatga
gttgccggaactacttggactaccccattcgattccactgacagattctc
cgccgaattttgaatgtcttcctgaaccattggcacatgtttcgggatgc
aattcacatttcagtatgaaccatcctcctccacttctgagccctctacg
tggccctgtaactgaagctgatgaggcgatgcgcacactcagtagtcatc
gagaacttcagaagcggcttcaaaacatttcaatgcgaggagagttgagc
ccttcaggatgcctggttgacagttgtgacacacctgcaattcgtcagat
tcgcaatcctcagttcacttga
>AW057212
tcgaagttactcggacttctcatcttcatcgctttttaatcaacatcatc
atgtttggacgtttgaagcagaaagttaaggaaaagactggacgtgccaa
ggcgacaactcttcccgcagaagtggacgatgcgatgggctacttcaaaa
atctgacgccacgtgtcaaggaccttcacaagagcatgacaaacttggaa
gatattagcaagtggcagaagaaggccagtttctctggcacccttgagaa
ttactcgcgtctcggtgacaagatcaatgtgaaaccatttatggatgctg
ttgatgctagaatgggtgccgaagctgatgccgtgaaaggggtcctcgcg
atttgtgaaaaatacaagtcattctaccaaaacgagggaaaacttcacgc
ggacagtatcgccaatttgaataggactcggctcgacatggacagtgcgg
cggataaatatgcgaacaacgagactgaagttaacaagactcgtttggat
acagtaccacggaatttgaagtggcttgtgagagaatgcgagaactggcg
aacggaatcaagacaattgaatcgaaccattcttcctggcaagacgtctt
atgaggagaataaagtgcngtgcgtanataa
>AW057213
gataggtgtcacccccaaccgattgtccttcaaaaaattcgcattttcaa
tcatcgagatgatgaggtgaaaatcgataatttttcggctcgtcgagctc
caaaactccgcgacgatgatagtgacgagctcaacgtggatgtaccagct
gaagatgatgatgatgtggaactcgatgacgtcatcgttgctcaaaatcc
ggcgttttacggcacaattgaggcggagaagtgtgcggaacgagttgctg
cacatctttcgatggcctgtgagaacatggaacgtctgcaatttgtgagc
gaggccgtgtatccacagagtgctgatcatttgaagaaacttcaagaaat
cgatgatgacgtcaaggatttcaattggcagatgagagagcgtcgtgtca
aggcttcaaatccagcaggaacagccacaaaagttgcacacttcatt
>AW057214
tcgaaacttgtgaagaaggtctgcaatggttgccgcaaagaaattgatgc
caaagcgaatgaagaagaagatgcaggtggagagaatggctcatgccaga
gcttgcaaggttgcaaagagagaggctcgcgtcgctgaggaagcatctgg
aaaatctactggtggatctactcgcggagccaagtgatagccgagccaca
acacatga
>AW057215
gaaacttgtgaagaaggtctgcaatggctgccgcaaagaaattgatgcca
aagcgaatgaagaagaagatgcaggtggagagaatggctcatgccagagc
ttgcaaggttgcaaagagagaggctcgcgtcgctgaggaagcatctggaa
aatcaactggtggatctactcgcggagccaagtgatagccgagccacaac
acatg
>AW057216
aattccgaattccattcgactaaccatctttttgcaaacttgcaccaaat
caaccgacatgcaatcaatcaacatcttgttcgccatgctcctcatcttg
gctccaattgtcaatggagacgatactgccgttgctgtgactgcaactga
agtcactgaagatgcaactgaagtcactgaagatgcaactgtggctcaca
ttgaaacaacagccgaagccgttgcagaagcagaaccagctacagaacca
gttcaaaccacccgagctgttgaagaaactacacaagctgttgttgtaga
atccactcaagagactgtaaatgctgtaaccaatactccagttgatactc
cagctaccaacaacgtcgaagcaactactgaagcggcttctcgtccatcg
ctttcatcgactgttgcatcaaatatgacttctgctgatgacttgctcgg
agaaacttcaaccaatgccacaaaagctgcttacaacactggaaccttca
ttgttgtcccaatggtcgttctcgctttgattcaatga
>AW057217
gatgaaccgtcagacaactgctctcctcctcatcgtctcgatccttgccg
tttttgtccaccatggatttgctgctgctgaagaagagaagaatacagct
tcagtcgtcagccctgctccggactctgaagcagcccaacctgctggaaa
cggaaccgaaacaccaaaagatgaggtgaaggatgaggcaccaaaagaag
gtagtgaaactgaagcttcaccagaagccaagacaaaaggatctatggta
ttccatgctcttggagccattnccacagttgttctcgccggcattatgtg
aagaagtctgccgaa
>AW057218
tctggaaagaggagtttcttctgaagacatantgattccttctgttcgtc
ggggtgtcattccagtcaacactcttcgttaccaaatagaaaagcatctc
gagatgtgtactccagcttctgaacaattgtcaaagagttcggatcccaa
catctcctcgatgtacgttttccatcaaggaattcaagtaaagcaggaac
caatcgatgatgaccaagaggaagagcaacaagtacaaaagcagcttgta
ttcaaaatccgaggcttcgaaaacgaagaagctgtgaagaaggagtg
>AW057219
tcccaacaacacctcaagatgaatgccatttacactgccgtccttgttgc
ttcaactctcgcctacactgcaatggcttggattggactcagcattgaag
ccgccaacgaggatatgatctgaagtggcgcc
>AW057220
ctcttttctcttcgtcgccgnggatcaaaacgttgcccgacagggatgag
ctcgaataagacctctcgctcaacttcgtcatcgtctgtcacatcatctt
caggacatggtgcatcgagcttctccgaggattcgtctgttcgctctgtc
accaacagtgttagaagtactagaagcgctggatctatcatgtcaatggc
tagtgccgaggcaagtgtcgttgctccagatctgacaatctaccatggag
atcgttagcaatcctaccagctcgctgacaaggggaaaatggtcgttatc
aaccggaaaaatggggtgattgtctacatgcttcgttgtgtcgacggccg
tcgtgtctacattgaganatcttccgaaggagccagtcttattctgacta
atcaacgtggaaaagtgatcaaggcattggccgngcactactag
>AW057221
atcaactttgtctcctcaaaaataagtctacaaatgatcaacatcgatcc
accatccggcgactacccagcttctggtggttcatcaactcactacattg
tctccgaatcggaatctcgtttggcattcaaagtcaagtcgtccaacaat
gaatcgtatcgtgttcgcccagtctatggattcgttgatgcgaagggaaa
ggctaagctcgaagtgaatcgtttggctggaccagcgaaggaggacaagc
ttgtcattcaatacgccgaaagttcagctgatgagaccgatccgaaggct
ccgtttgcggctggtgctcaacaaggagaagtcgttgtcaagatggttgc
ta
>AW057222
aacattcgactaaccatcatctttcaaacttgcaccaaatcaatcgacat
gcaatcaatcaacatcttgttcgccatgctcctcatcttggctccaattg
tcaatggagacgatactgccgttgctgtgactgcaactaaagtcactgaa
gatgcaactgtggctctcatcgaaacaacagccaaagccgttgcagaaac
agaaccagctacagaaccagttcaaaccaccgaagctgntgaagaaacta
cagaagctgntgntgtagaaggcactcaagagactaaagatgctgaaacc
aatgctncaagtgatactccagctgncaataacatcgaagctaccactga
aagggcttctcgtccatcggtttcatcgactgttgcaccaaatgtaactc
tggtgatgacctgttcgggaacctcaacaatgcacacaa
>AW057223
tcgattctcgaaatggctccaacacgtacttcacgacgcagttcagcgaa
cttttcattcgacgatgtaaatgttgaggaacagaggcaagcgtatctcc
gctacgaacaggaattgaaggatctcgcacttgctcgaaaccttgagaat
gaattgaactgggggccaaatccagccaacccagcgcctcctcaaaatcc
tccacaacctgaaactgttcatatccaagtgaatcgagataatcctcaag
ctcaacaacaaaatctgacaggaaccatagctccagctggaagagaaggt
actggagtacaggtggctgctgtggccccggatcccaccagcgcagcgac
tgggtcacaaggacaaccaactccccagaatgcacaaaatcagccaacaa
tcagagccgcagctggaagagaaggttatgganggcacgtggacgttnta
accgccgttcttgcaagaaacttgccgtcacaaggaatcaatgaaaatgc
cataaaccctggatgatgacgaatctgaagtcaattgtcagactcttttg
aagctgctccatcgaatcagccaagcacatcacaaggcacctcaaatcat
gcaggctgagtggcttcacgatcgcgccacgggngaagtgaccgctgttt
gggactcagtgaccaaacaagg
>AW057224
gaatggatcgtagcattgatcgtcgtctttgtgggcactgtcaccaatcg
attggaagtgaggcacttgtcgccatgaatcgtctctggcatccggacca
cttcacgtgctcatcgtgcaaacgtccgatcaagcagacgttccaggctg
ccgacaaccacgcctactgtgtccagtgctttgctcaaaagtacaacccg
aaatgtgctggatgcatggaaactctcgtcgacacgtgccttcttgcttt
ggaccgacactggcattcacgttgcttacgtgctcctcgtgcaatcgccc
attgccaaatggagaattctatctggttgatgataagccgtacgacttgg
attgtcactgggcaaagcgtctcgagaagagagagcacatggaacgtggt
gaacgttaagaagaacgccgttaatttgtcgaacttccccactgtttttt
tccttgtattcttgtgat
>AW057225
caactcaagaagaagaagaagatttgctgtcaaatcggcatacatgtccg
ctggaggatacggatctggatacatgggagcaaatgcttcatcatctgga
tatgctcgggaggactacgctcagggtggcgctggaggatccggaaatca
gaatcagggaggatccggtggaaataccaatccaggaggacaagtgttca
aggcacgtaccgatcaatcgtgttacttgggaccataagtctcaactgta
ttcgaccggcaatt
>AW057226
aaaaaacttcatcaagatggctgcgaatatttatttatggatgtcgaaac
gcaacgtcgaattgaatacacacgacagaaagtgatgagaatcgagcaaa
tgaatgagcaacttcggaagttgcaagtcgaataagggtcgcgaggagaa
gttggacagacttttgaaacgaaaggaatccttggaactggacgttgcaa
gattgactgacgcgtcgatgagagctgagccagaggtcggagcggagctt
cttcattctatcgaagagcccatggaagttgatatgatctacggtgaagc
attccacgcaaagacttgtcaactgaaagtccttctcaacgagataattg
ttcgaacaagcttcaacgagaaagcaatgtgtaaagagattggacatcag
gaagctgaattcgagaatcgattgaaggaggtgatcagtggaagagctca
attgacgctgaaatctgaagaagctcagaagaaatgtgaattgttgatga
gagagcattcgaatgtttatgaagatgttcgagagatggaggataatatt
gagaagtttgatgcatcgagatggttgttgaatgtggagaaaagacgagt
ctctgatattctgatcgcaccaaagagagccgannatgggaatgagtgct
gccagccatacattggtcttcngaagcttctcactttgagacttgcacat
caaactgagtctcactcacgatcattt
>AW057228
acgaaagagatggcggacaagtcggcatacatgggtgctggtggatatgg
atcgggctacatggggtccaacgcctcatcgtcgggatatgcccgcgagg
attatgcgcaaggaggaaatggcggaggacaacagcagaatcaaggatct
ggaggaaacaccaacccaggagggcaggccttcaatgcccgcactgatca
atcgtgctaccttgggccataagtggcggttcgaataatacaagagcaag
tagtcaaccacccc
>AW057229
atccgtccggaaaagctgcgaatgctgcgagagcttatggaagcgggatg
aaaaactctgcagcctctttcaatcactcttgagagcagttcgataagct
tttcgaagcttgtaacacattcaaggatcaaatcaatggaaacgtccttg
ccaaattgatcagtttcaaagatgtggaatgcaaggatgtcgacactcaa
atgacccagttgaagaaggctcagaaggattatgcgaataagaaatcaaa
gatagttccagatcaagttcaggttgatgcagctgaagcaaacttaagaa
gtt
>AW057230
aagatcactctgatcgtcgtcgcaccaacaccttttcttcttcagccgat
gaggatggagttccaaatgaggtcgccgactacctggtctacttttcccg
catggttgacgaacaaaatgtgccggaaattttgactctctacgatcaag
cttttccagatctcaccgagagattcttccgtgatcgcatgtggcccgat
gagaatgttgtcgaaagaattattatacagtattg
>AW057231
tctctggaagcactctgctcgttcaatgtggtggaaagaaaaagggagca
acttctgccgaaggaaaatcttcgacgatgggcccggctcctggaggagc
tcctgctgctgcttccgctcaaggagaacctgaagagaaggagtaa
>AW057232
gaattcgagcagcaaatctgcctaatcgttgaaatctactcgtggagcgt
cgaagagtgggaaatctcgccgttcatcgaaagctaagcactccaagaga
tcgtcgaagtctagtaagaagggaacgtctggaaaatctggaaagggaag
cagcaagcgtggagggaaatcatcaaagtcttcgaaatcgaagaaagtca
agactgctaccacctctggttctcaagtttcaactgtttccgctgctact
ggtgtttctgataagcaatctaactcatcgaaatcttctcgtaagagctc
aaagagttcgaagagccgtaagaatcgtcgacttgattcggatgcccaga
agaaaatggagaaatcgggaaagagcggcaaagttgctcttattccaaaa
acgcaacaaacaactggaagccaagttgggtatagccttgctgaagaagt
caattcgatcaagcactccaaggaaatgaatgtggctcctgctaaacttc
aataccagacacttggcggagtcaatcaaattgaattgaagaatacttca
aatgaacgtaaagcttataagatcaagtgctcggataactccctctacgt
gtcaatccgtttatgatttgctgagcacgttctccgttaagatgatggtg
agat
>AW057233
ccggatccacagggaaagtactactgtattgtaggagctgatcgtgcgtt
cgggagagaagtcgtcgagacacattaccgggcttgtcttcacgccggac
tcaacatttttggaacaaatgccgaagtgactccaggacaatgggaattc
caaattggaacctgcgaaggaatcgatatgggagatcagttgtggatgtc
gagatacattctgcacagagttgctgaacaattcggtgtctgcgtatccc
ttgatcccaaaccaaagggtcaccatgggagactggaacggagccggatg
ccacaccaacttctcgactgccgaaatgcgtgctccaggtggaattgctg
cgattgaagccgccatgacaggactcaagcggacacatttggaggcgatg
aaggtgtacgatccacatggtggagaagacaatcttcgtcgtttgacagg
acgtcatgagacaagttcggctgacaaattctcatggggagtcgccaatc
gtggatgctcaatccgtattccgagacaggtggctgcggagagaaaagga
tatnctggaggatcgtcgtccgtcatcanactgggatccttatcaagtga
ctgcgatgattgcacagagcattctcttctag
>AW057234
gaaaattcaatcaataatcactatatcaatgttcattatcatcgtcgtct
cctataatgagctgacagctgaggaaaatgataagaggctcgagacatgt
ggaaatgagcatattgggaaaccatcgaaaaactcgataatctctcctgt
ctcctggcttaccaaattgacaagatccgaaatttctgctccggcagtta
taatatctcctcgacacttgatcacttcttcacggcttttcctcacaaaa
tcagcttggaaaaatagcggagattcgattgattgtgatgacagcataaa
gcacttggaagttccggtaaacaagctctcggatgtgattgagccgtgcc
tttctcaaaaggagaattgctccccgaaagtgatgaattttgccagagca
tatattctgaacttttgcaaatcaacattggtgcaaaaaagagtgtactc
cttcccaatgattntggagcttgatgagaatttggaaggcaactcaagtt
atccatgtctagctgatgaatcaatcanacttgccaaaggagatgccatt
gancgcttatgatgacannacaattcgaatggagcatcgaanagtgatgt
cggcgccgtgtagtccgatatctataccgactgt
>AW057235
agttactcaagctgttccagaaggatcagtacttagttcagatgtcactg
atcgtccaaacatcgactccactgatgttgtatcaaatgcaacttcggtg
gaagatttgcttggaagttcaacaaatgcaaacaacactggtacattcaa
ctctaggacctttgtaattgctccaatgatgattcttgctttggt
>AW057236
ctcccaacaacacctcaagatgaatgccatttacattgccgtccttgttg
cttcaactctcgcctacactgcaatggcttggattggactcagcattgaa
gccgccaacgaggatatgatctgaagtggcgcccat
>AW057237
ttttgttttggtttgatttgtccgtaaaagttttcacaaaatcatcaatt
ttctgttgtttttcttgctccttggcttgtttcttttccttaactgactc
gacgaattctccaacttgttgagaaacctccttccatttctcgatcgctg
cttcggcttcctttttcttggcttcagctttttcctgtttctccttttcc
aattcatcggctctctgcttaactgcatcagatacctttaaagcgtttcg
ttcagtttcttctgagtctctttcccgtatttgtctcttgctgctctcgc
attntcaaaattaactctcagttcttcttccaatgccttttccgtatcaa
ttactgactggaaggtgtcagcaagggagtagtagcgaacggatgaaacg
ctcgacgcaaaaaa
>AW057238
gcaatgtcacgttgtcaactcattgcaaacaaagactggaccaacattga
acggagtgattggaagacaatccggacaagttgctggatttgactactcg
gctgccaacaagaataaaggagttgtatgggacagacaaacacttttcga
ctatttggctgatccgaaaaagtacattccccggaactaagatggtcttc
gctggtttgaagaaagctgacgaacgagctgatctcatcaaatttattga
agtggaagctgccaagaaaccatcggcataagcctctactaaata
>AW057239
tcgtcagccctgctccggactctgaagcagcccaacctgctggaaacgga
accgaaacaccaaaagatgaggtgaaggatgaggcaccaaaagaaggtag
tgaaactgaagcttcaccagaagccaagacaaaaggatctatggtattcc
atgctcttggagccattttcacagttgttctcgccggcattatgtgaaga
agtctgccg
>AW057241
atgagccaaagtgtgtagatgttgttgaaggaaaggaaagttctggagtg
tgcaagacgaaaggcggagtctgtcgctttggtcattgctgcccatcact
taccctgacaattgcaccatctggaaatggtactgagtcagcgacgccta
ccttgggcccatatccatacttgactaaattatccgtgtgatgctaacaa
acctatcccatctcaattcagcacctatgcattttgcgatcctgacacta
atcgcgttggtattttgggcaaaaggcacttaactggagaagaacgtact
gaggtgaagggatcggcatgctcttctaacaaagactgcaagtcgggaac
tgtttgcgtgtatgttaatatcaataaacacgtctgctactaccatccgc
tgaagaaaatcgcccgtgatgtcagtcaaccatggctctatgtgctcatt
agcttcctcatttgcggttntatttntgtcattntggcagtcatgagctt
cgtctgctaccgttcgaagtctgtgtttgacaagtaccagccaaagaaga
atgcaggaacacatggtagcagacagtgatgggaagaaaggaaagatagt
gggaagaacgagacgatacttanagtcaacgagctcccagtcaagaccag
agacagagctgatcgacagcgga
>AW057242
ttccacctggtaccactgtcgacactggaatcgtctctcccgaaggattt
gatttctacctatgctctcactatggagtacagggaacttctcgccctgc
gagatatcacgttcttctggatgaatgcaagttcactgctgatgaaattc
aaaacatcacttatggaatgtgccatacatatggtcgttgtactcgttcg
gtctccatcccaactccagtttactatgctgatttggttgctactcgtgc
ccgctgtcacatcaagagaaagctcggtcttgccgacaacaatgactgtg
acaccaactcgctctcttcatcacttgcttctttgctcaacgtgagaact
ggaagtggaaaaggaaagaagtcacatgctccaagcgtcgatgatgaatc
gtattctcttcctgacgctgcatctgatcaaatccttcaggactgcgtct
cggttgcagctgactntangagtcgtatgtacttcatttgaagactcttc
atgcagacggagccagagaaa
>AW057243
accgccttcgtcccaaatgacggttgcntgaactttgttgaagaaaacga
cgaagtgctcgtatctggtttcggacgttccggtcacgccgtcggagata
ttcccggagttcgtttcaagatcgtgaaggtcgccaacacctccctcatc
gccctgttcaagggaaagaaggagagaccacg
>AW057244
ccgnctccactcttcacttgcactattcttatgcaaccaagcaacgncat
gctcgctgttcttctcgccttggcttcatttgctcaaggaggcagatctg
ttgctccggctggtgcagtcactgaaccaacagttactcaagctgttcca
gaaggatcaggacttagttcagatgtcactgatcgtccaaacatcgactc
cactgatgttgtatcaaatgcaacttcggtggaagatttgcttggaagtt
caacaaatgcaaacaacactggtacattcaactctaggacctttgtaatt
gctccaatgatgattcttgctttggtgcag
>AW057245
cgaaaatcgacaacgagacgcagtcacagtgagaaaagttcatcgagagg
ttccatgtcatcaccgccaaccagattctatccatctgaagattcagagt
cgatttactcgactcgaaaatgctccaaaaggactacgacgactgctact
acggatgaggagaagccgaacaacagctactacattgacgatatttatga
ttcgactgaagaatatcaagtgacattcccgacggttgagctgaaattgc
cacgtcagagaaagcattgccgcaagcgatcgaagagacaggatcaggca
cagggagagcatgtgacaatcacgaaatgtgttgatagaagacaagtcta
cggagagcccgataataagaacaccatatccgagcactctacgtacacct
actctacccatccggaacgttgctctcaggccggccgtacttctcgttcg
aacagctattctgacgccacagatgccacatatcggactgg
>AW057246
gcttggttatccagcagcactactgcaattatgtttggaggtggagattc
aaagcctatcgataagaagaaggaggacaagaaaggtttcgatactcgaa
aattcttgattgatctggcctcgggaggaactgctgccgctgtttccaag
actgctgttgctccgattgaacgtgtcaagcttctgttgcaagtacagga
tgcttccctcaccattgctgccgataaacgttacaaaggaatcgtcgatg
tcctcgttcgtgtccccaaagaccaaggatatgctgctctctggagagga
aacttggctaacgtcatccgatacttcccgacccaggcgctgaacttcgc
tttcaaggatacttacaaaaacattttccaaaagggattggataagaaga
aggatttctggaagttcttcgccggaaatctagcttctggtggagcagct
ggagccacttcgctctgttttgtctacccattggattttgctcgtacccg
tttggctgctgatgtcggaaaagctaatgaacgtgaattcaaaggcctgg
ccgattgtctcgtcaagatcgcanagtcggatggnaccaatcgactctac
agaggtttctttgtctcggtacaaggtatcatcatctaccgcgccgctta
ctttcggaatgtcgacacttgccaagatgtgttcactgctgatggcanga
aactcaacttcttcgcttgcctggcttattgcctcagtngntacntnngt
gatctgnatnctctnctatccatggnatcctgntcgtcgcgcatgatgat
caagctggtcgcaagatgtctctaccagatactttgattggccg
>AW057247
tttctctgaataaccccaaacgaaagacattcgatgttggacaagtcggc
ttacatgggcgctggaggctatggatcaggctacatgggatccaatgcct
cgtcgtcgggatatgcccgcgaagactatgcacaaggaggaaatggtggt
ggacaacaacagcagaaccagggttccggaggaaacaccaacccaggtgg
acaggtcttcaaggcccgcactgaccaatcgtgctaccttggaccataag
atgatcgacactaggagagccagtagccaaca
>AW057248
ttaaaagcaagcttcctcgtagctcgtcgtctggattctcgggaacagga
tctgaaagatctatttcaagcaaaagatcgaaaattggaaacacttctgg
gaaccgtaacaagatttcgcaaagtgctagaagaagacttttgcaagctg
aaattgagagtcgacgcaatagatccaacaaatcaccaggttccagtcgt
aaaagcattctgaagaaatctccgatgaaaaaaagaagatctctttcgag
aaaatctttaccaaagaaagagcatattcctccagttcaaaagtttgcaa
ttatcaagaatccagctgctcgtaatcaagttcgtggatttgttgctgaa
tacgcacaagatgcagaatttgaagcttttgagcttttggttgacggaat
tccatttgttgctctctctctgatgaatgctcatccagatcttcgtggaa
gattcaaacctgttccaccaccaacaccgatgaagaagcatanctcaggt
atncaatagcccacgaaacgntcctttgcgcgtgaatctatttccttcgt
taannctcganaagtgttcgtttcactgantggaggatctctttntcgaa
nagagctagaaaatcttcatccgggaatgcgattcatcggatcgtgagct
tggagnagacagtatcgnatgccatgatntgacacttgtcgcagtacaat
ggatttgtgggaagatgtgnaccatagtgtgaaaa
>AW057249
tgactgtgaatgattctctgctacaccattttattatcatcatctcggta
tccaattccatattcttatttcgagttatccagaaatggcgatccattac
aatatgtggagt
>AW057250
aattccttctacgcgaaaacaaatgcacctcccgttccgttgcccagtct
tggtgaccggcgtcgtcgtcggcggagccgctcttctggcgattgccgcc
tactactactggagccagaaaaagaaaagctctgatacttcatctgccac
gtcatcggagtccaacgatgttgtcatgatgtcatcatcggagcccagag
ccgatggaggagccgattcgaaggcaaagttcaatattgaggatgaaaat
gtgagaagagtctgcgagaagctgttcatggagcagatggatttggggga
agcttatttggaggatgaagaaaccgaggagctcggcgcaatccacatgg
ctaacgcaatcgtgctcaccggagagactgctcagctgctcaaagtgctc
ctcggctcgatttcaccggctcactttgccaatattcaaaagtacctccc
atcggctgactngcgtgttcaccagcttctccaagacgagctcgccattg
agactattgcccagcatttcgac
>AW057252
accattaccgtcgttttgaagaatgatcatcgtcgacccaccaactggaa
acttccctgcatctggaggtaattcggttcacaacatcgtctcggagtcg
gattctcgtttggcattcaaggtgaaatcgtcgaacaatgagcactaccg
tgttcgtcccgtctacggattcattgatccgaagggaaaaaccaagttgg
atatcaatcgtattgctggaccaccaaaagttgacaagcttgtcattcaa
tatgctgaagtgccagccgatgagactgatcctcaagcaccattcaaagc
tggagcacagcaaggtgaagtcatcgtgaagatcactgccgaatgagaaa
atagatc
>AW057253
caaaagatagtacaaaaagtacctatgaatgtccaattcctcagggtgga
ttctatggattagctgatcatccaaatcatgggcttattgcatcgatttt
gaagaggaaacgccgcaaaatcaagatgacagaagacgtaaagaagatgt
gcgggaaggttgaagcttacaagacatgctccgacaagctccatcaggca
ctattgttcatgctcgtcgagagtccagaaatttcaaaggatttggtgac
tcacttcaaaactgaaccaaaattatcgtatgctggaaaatatctcaaaa
cttatgaggcaattgcaaataagggacgggataagacaaagtatgagagc
ttggagccagcgattagtacgctttctctgttggatgcagaacgcgaatc
tcgtgttcgcaagcagttggacaatttgaagccgctgacaaaattcattg
gagaagaactattggagtacgcacggttgaggagagtgtactgggatggc
ctggaagcctatgacgatgcgctgacccaacagagcnaagatcgcactga
ggaagccgagcgaatcactgtcaacgctcaaaaatggagaaatgatgtcg
ccagaaactgatggattcatcaaaaacgggattntcgacagagaccaaag
cattgtgatgctattctgaaatccggatgaagcatcctctcncatcgcgc
catgtcgaccacacaatcagccgaggntctgagaactgtggaaccccta
>AW057254
cagcactgggtatttcaggcccgggtgtttctgcccaaaataccgcaact
ggtggtaaagttggtgaaactagtgaggtcacaacacaagtgtttcaagc
ttcgacatatggtgctgtcaaagcaccgaagattgtggctgatgcccagc
aaggaaccaatagaagttcagaaacacttgaaaataaaatggtacacgat
ttcatgtggtggattgggtggagtcgttggagctattcttttctctggaa
tattcttctttttcggtgtagcatctatgcgtgataaagtctactttttg
gaaattcctgacattgtacaaatgtttggtataccctcgactgtccagaa
tgcatcg
>AW057255
ttttatcaaagtgatacgctcaaacacgtgacaatttgaaaaaatgctta
ttgaactcctcatatccatcaccgtgctcgcgtcgattctcgtctcgtgc
aagaaagagaagaacgaagcggcaaaactgaagccacgtggcttcgatcg
aaaatccagtggagcaccggctccggctggagccaacttggttaacaagt
ctggcggttccggcggaggtagtggaggatctggagatgctaatagactt
ctcaaaagagaaatcaaagaagtaaagatggaggagcgttcggctgacga
taacgagacaatcaacgatgtaaagtccaactggggaactgtttgaaat
>AW057256
aaaatcgatttttcgtcatgattcacgacacgtacaatccgtacactgct
gttcagcgaagcccatcacaatggttcatctttgtgccatcttctgcacc
attggataatactacaatcattacattgtcccatgatgctgtcaatttgg
ctagtattccaccaacggactctgcggaaagtcttcaaagtcgttatgta
gtcccggaagtaattccattcaaaagctcatctgaagttgacactcgttc
ggctggaaatccatatttccatcatccaaacttcaccactccatctcaat
actttgaacatattatggattctgaaggagaacaacacaagatggagaat
aaaaacgaagaaaatttgctgactattatggatatcaagaacttngagga
tccatttggaaattatgatatggatggagaacaggcaccaatggttagca
tcaatccaccaaatgatgtgactgttaacaagaacgccttctcttctgac
tcaattgctgatattcagaacatgaacatctcattttcgatcaaagcttt
cactgctccagctatccccatcagtctcctgagggacacttantaagaaa
tgtgagcncgaaatatgttcgagtgagcagactgatggaga
>AW057257
aggtgatgtctacaagaaggcagtgcagttctactcaaacatcacggctc
caagatcaacatctgtgcttgctccagtgatgtcgtcccttgaagtctac
attaacaccaccacgacatctgcttttgcttcagctcagagcatcaaagt
ggctgatattcttgaagaagatgcagatgcaatccgtgtgaagtcaatta
gaatggctggattcattgcccaatgcatcatctttttatttgtctacacc
atcgtcacgatggatgttgagatttggaaaattaatatggactggttgaa
aattcaatattttcagcatttcgaagactccgctgctgaagttccggtct
>AW057258
aattccgaagaacactcctcgattgcaaattgtaataaccctaaaaatga
ctcatttgaacttcgagactcgcatgcctcttggaacagccgtcatcgat
caattcctgggacttcgcccgcatcccacaaagatccaggcgacctatgt
gtggatcgatggaactggggagaatctgcgctcaaagacacgaacattcg
ataaacttccgaagagaatcgaggattatccaatctggaattatgatgga
agctcgacgggacagggcanagggacgtgactcggttcgttacttgcgtc
cagtcgccgcttacccggatccatttttgggcggtgggaataagttggtg
atgtgtgacacgttggatcatcaaatgcagccaacatcaaccagccatcg
tcaagcctgcgccgagatcatgcatgagatccgtgacacccgcccgtggt
tcggaatggagcaggaatatctgatcgtcgacagagatgagcacccactc
ggatggccgaaacacggattcccggatccacagggaaagtactactgtag
cgtangagctgatcggcgttcgggagagagtcgtcgagacacattaccgn
gcttgtcttcacgccggactcaacattgttggaacaaatgccgaagtgac
tccaggacaatgggaattncaaattggaacctgcgaaggaatcganatgg
gagatcagttgtggatgcgagatacattctgcacagagttgctgaacaaa
attcgtgtctgcgtatcncctgatccccaaaccaaagtcaccatgggaga
cttgaacnggagccgatgccacaccaactttctcgacttgcngnaaatgc
tgct
>AW057259
taaaatggatgtcaagcataatccaaaaaaagaagtgatcgaacgaagtc
tgaatgcgactgaaaaagcgatcgaatcgattcgtgaaggtgacctagtc
cgtcgtcacactgttttggagctccgtgacatgcaaatttcgatgagtga
ggatttcgatcaaatccgtggaatgatgcatgaattggatcaccaaattg
acaaggaacgcgctgaaaattcgaaatggatgaattggaaaattgagaag
gccaaggcaactgctgatcaggcgttggcctctacactgatggtcaagga
cgtccagctgttggaaaagaaggtcaatattctgaaggattctgtgattc
aagttaacaaggcattctacaagtatgagaaggatgttgacatgaaagat
ttgatggatcaagttactgacatggtgcatcgtacggaaaagaaggagca
agatgcgttggagccccatgcgactgatgagcaagctatcgagaaagcct
tccgtggagcaattgaaggcctttatggcctgaaatcttccaatccaaag
gtcatggaggaagctaagctgttggctggagaaatgcgtgttttcagaga
tgctngctgctacaagaacttncactcgatgatctcaaaagttgcgcctg
gtaaatcggagtttccttgatacagcagctctgagactcatttcgacttc
tgatcctctcgctgccaa
>AW057260
ctttacggcggaaaaagtgaaattttcggtagtttctcgaaaaatatttt
tcaattcaagcaagatgccagacgatgtgtgcgacgaaacattgaaaatt
ggagtggttgttgggaaaaagtaccgagttatccaacagctgggtcaagg
cggctgtggatctgtgtacaaggtggaggacatcgaagacaagacaaagc
agtacgcgatgaaagtcgagttcaactcgaatgccaacgctggaaatgtt
ttgaaaatggagggtcagatcctcacccatcttgtgtctaagaaccacgt
ggcaaaatgcatggcaagcggaaaaaaggatcgatactcgtacgtggtga
tgacccttctcggcgaaagccttgaatcacttatgaagaaacacggacca
tttttcaacgtgtctacccaaatgcgcatcgggatttgccttttgttcgg
catcaagcagattcatgatattgggtttatccaccgtgacttgaagcctg
ccaacgtggcattgngaaataaaggctcccctgacgaacgctacttcatc
gtgctggactttggcttggcacgccagtacatcacggataaggaggacgg
aaaaaaagagcgtcgcccacgtgagaaagctcntcttcgtggcancctcc
cgttattgctcgtagctatggcacatcgtttcgagccagggagagtgatt
acctgtgggccttgtctacatngctcgcggangtggatgccagctggnct
tgtctgatttggatgataaggcgaaatcnnggaaatgaancnaacgtngc
cgacccagatctcttggcaaaagcccaatcaaa
>AW057261
gccgagaatgtgctgggagcccctggagctggattcaaggtcgccatgga
agcctttgacatgacgagaccaggagttgccgccggagcacttggactct
cgtggagatgtttggacgagtcggccaagtatgctctggagagaaaggct
ttcggaaccgtaattgccaatcaccaagccgtccagttcatgcttgctga
catggctgtcaacctcgagctcgctcgtcttatcacctacaaatccgcca
acgatgtcgacaacaaggtgcgctcttcatacaatgcttcgatcgccaag
tgctgtgccgccgacactgccaaccaagctgccaccaacgctgttcagat
ctttggaggaaatggcttcaactctgagtatccagtggagaaactgatgc
gtgatgccaagatctatcagatctacgagggaacctcgcaaattcagcgc
attgtcatctcgcgcatgcttctcggacatttcgcgcaaaatggaactag
cagaatttaggatgtgccgtttttgagcaa
BioPerl-1.007002/t/data/dbfa/2.fa000444000766000024      6050413155576321 16262 0ustar00cjfieldsstaff000000000000>AW057262
gacgagggtccgtctcggcgtggtgcaatttgctttagagagcgatcagt
ttcaagaaacggtgacaatgaaattgatttggataaaagtttgagcttga
agaaaccatctgcatcgaagaatttggccagtttgttggaaaagaaggaa
gaggcaagataaactgatgtaacatcttccatgatcagttcaaaacctcc
aacttctcctggcacctccgtctacatgtacaacactggatcagccaatt
cgacttttatgtctgctaaagatttgcatanagaacgtgttgcagcttct
actggtcccagatctgcttcaaaatctccaaaaggaacacttcgcgtgaa
ggaaactaaagtcattcgtgaagttcgccaagaagatggaaagccacctg
agattagtgagaagaaagaagaaactgtgaaagaggaaaaagtgaatctg
agtgagagattgagagccagatcgagagcttcatctcctgcaactccaac
tttgaagagaacattcaatcagacggatgagtcgaatattgtgactttga
gtgcagtcaaagaaacccatcaaactttggaaatgacaccaatcatagtg
aattctgaaacagttccttcaacttcttatggacaacgtgcttttccctg
agagtgttcaattggatatgctcattgacaagaaacgacttgt
>AW057264
aggctccgatcccaaagcctgaggaagatctcaagggctccacggatcaa
agtaccactgagccaacgaagctcgcctgatcccaaagcccatcggaacg
ccaggaaatccaacaaatgccgaattcattccgcgagttgcaggactcaa
agttcaagccggctccaagcccaaagtctgaaaagggccccgcggagcaa
agcttgtctgagccgtcgccggtccccgggaataaccgcaggaactctga
gacatcacaagttgacacaatttccccggtgccaaccaagctcgttggaa
cccaaagtccatcggaacgccaggaaattgagcaaatgcccaactcgttc
cgcgagctgcaagactcgaagttcaagccggcgcaggctccaaacccaaa
gcctgagcgcgttgagaggggctccgcggagcaaagcatgtcggagccgt
tgtcgatttctagagttgcatttggctcgccgatcgctccgaaaccacgg
ccatcgccactccaagctccgcttcttgagacgttggctactccaccgac
aatcgacgctcctaccgctgcaatcgagacggcaatcgagagaagcgcgg
aantttcgtcatctcactcggaggatccttccaactcactttttcaagtg
tgcagnatgccgtaaggaagaatcgagtggtc
>AW057265
ttcgctaatcattcccttgttctactgatcgttggaaggttctagctatg
aacgtcaccagtgtcacttcagaggatggtgttaaagaattcgaaaagat
tgttgtggaacctgaagatatcgaatatgttgagattccggccgatgcca
aaaacgttgacttgacgcgtcaccgtatcaaagaaatcggtgattattcg
tggctcactcacgtcgaacacttctcgtttcgttggaatctgatcaaaaa
gattgaaaatctggattgtttgacaacgttgactcatctcgagttttacg
ataatcaaattacaaaagttgaaaacttggatagcctcgtcaatttggag
tcactcgacctgtcattcaatcgtatcaccaaaattgaaaatttggagaa
gttgacaaaactgaagactctcttttttgttcataacaaaatcactaaaa
tcgagggtttggatacgttgactgagctggaatatctcgaattgggtgac
aatagaattgcgaaaatcgagaatctcgacaacaatctgaaactcgatag
attgttccttggcgctaatcagattcgtcttattgaaaatgttgatcatt
tgaagaagctcacagttctcagtcttccagccaatgcgattactgtagtt
gataacatttcgggacttcacaacttgaaagagattt
>AW057266
gaaagtctttggggagatgacgagcctgtacggaggaaggagaagatcag
cactcggttgttgggggtccaattgcgttcagaatactcttgttttcagt
cattttgtgaacagccatactgacggtattccacgtattactgattcatt
ccatgacgacaggctgccatatgtttgcacgatggatgtcacgatgattc
cgatcctt
>AW057268
ctactacaagctcggtgttggaatgaatgagtggaagaaccctgagcacc
ttgccgagcacatcaatggagctgcttactccaactttgacattgcttac
tatccatcggagaacgagcggttcactttgtacactccagaggaattctt
gctgtatgttaagagattg
>AW057269
aaactcgaagaacagtcttgaccaacacgagatgtattcacttttgacgc
tcctcttcgtcctcttcttctctggaagcactctgctcgttcaatgtggt
ggaaagaaaaagggagcaacttctgccgaaggaaaatcttcgacgatggg
cccggctcctggaggagctcctgctgctgcttccgctcaaggagaacctg
aagagaaggagtaatgaaca
>AW057270
tcgctcgcttgcgtctcttgctcgccgcccgtgcacttgaatgcacagcc
cgtcttcagaatgttactgttaagggagttgccgtgcgcaataagaagag
attggcaaatgttgaagttcaactctatgagaaggacacccttgacccag
atgatcttttggacaccaagaaatctgatgctgaaggagaattcagcgtt
tacggagaagaagatgagactcatgctattgccccataccttttgattac
ccatagctgcaacccatctaacccaattgtgtccgcatcgcaagtacttg
gtgccagaggacaagatcggaggaacctacgacatgacctacgtcaccct
cgacatcaaggttcacggagagaaggaaaaatgccagtaaaaagtgcaaa
cttcctggattttattgactatctaaatatatattttttctatatga
>AW057271
aagcgatcatcggatttggaagctgctcttcgaattgtgctccagcagac
tttgaacatcgttttgcaagcgcaggagaagctccccgaggcaaatgtgg
taccctcaactccgcccacctcaccgagcactgatatcggcgaacaaatg
gcatcgttctggaatattccatcacccaaccctcctgcaacc
>AW057273
gttgatgatctataccactggaaacaacaactcaagtgagcttgtggatc
caatgagcattactctctgtgtactctaatgtgcccaccaacatgagaat
tgccaaacaccaccatgcagagttgactggcatctgctcattttgtacct
gcttgccacggccacggatactcaaactcacgtcaatgcatactagctaa
ctcttgctaccaggactcaatctgtttgatgccgaatgaacaactagtgt
tcactccaggaatgttt
>AW057274
tctcccaacaacacctcaagatgaatgccatctacactgccgtccttgtt
gcttcaactctcgcctacactgcaatggcttggattggactcagcattga
agccgccaacgaggatatgatctgaagtggcgccc
>AW057276
tcgactaaccgtctccactcttcacttgctcaaatcttcatgcaaccaat
caacgtcatgctcgctgttcttctcgccttggcttcatttgctcaaggag
gcagatctgttgctccggctggtgcagtcactgaaccaacagttactcaa
gctgttccagaaggatcaggacttagttcagatgtcactgatcgtccaaa
catcgactccactgatgttgtatcaaatgcaacttcggtggaagatttgc
ttggaagttcaacaaatgcaaacaacacttgtacatccaactctaggacc
tttgaattgctccaatgatgattcttgctttggtg
>AW057277
tcaaagttcataaacggatcaatacttgcaaatgatggcaaaatactttg
gcgccacagatgcattcaatgcaattgttcaaaaagtcgacgaaacactt
attcaagcagaatcccatcttcgtaatcttcatgaagatacagtgggagc
aaagccgtctgatagtttgccggaccgcactatcgttccgtccccatctt
ctcaatcggaacgttcatgctccccggagcctcgtattgttgctcctcaa
ttgtctgcatactctggatcatccgctgcgtcttcttcttccgtgaatca
tattgatgtgaagagcaagtcgtatttggcattggataagaagaaagcac
tgatcatgacttcgctcaagtcaaagagagttatgaacgatagtgatgtg
acaaaagttcagaaattgatcgatgacttgttcggaaaacaaacttcttc
gtcctcatcttccatgtccatccttc
>AW057278
aataacctctcccaacaacacctcaagatgtttgccatctacactgccgt
ccttgttgcttgctctcgcctacactgcaatggcttggattggactcagc
attgaagccgccaacgaggatatgatctgaagtggcgcccatc
>AW057279
tcgaagtgatggattctccaacatcaccattgacttcttcaaatagtgga
cttatcactgttctggaaagaggagtttcttctgaagacacattgattcc
ttctgttcgtcgtggtgtcattccagtcaacactcttcgttaccaaatag
aaaagcatctcgagatgtgtactccagcttctgaacaattgtcaaagagt
tcggatcccaacatctcctcgatgtacgttttccatcaaggaattcaagt
aaagcaggaaccaatcgatgatgaccaagaggaagagcaacaagtacaaa
agcagcttgtattcaaaatcgagggctccgaagacgaagaagctgtgaag
aatgagt
>AW057280
aaccctttcgactacaactaacatggacatggactagcgatcatcggatt
tggaagctgctcttcgaattgtgctccagcagactttgaacatcgttttg
caagcgcaggagaagctccccgaggcaaatgtggtaccctcaactccgcc
cacctcaccgagcactgatatcggcgaacaaatggcatcgttctggaata
ttccatcacccaaccctcctgcaacc
>AW057281
ggacaacaagactgaggaagcatggttctcgttcaatgggaaggtgatta
agcagctcgggccacagctcaacgagatgtacatcatcacgcgcaactgc
atcggaggaccaccacattgcccatgtgctgtgtgcggagctgctccacc
accaccaaagccagtgccacgtgtcgagagagacgaatggatggacattc
gtgagggagatccatggncgactcgnccaacttgtcaaggctcttgacaa
gactctggacacccttccaggagtcaatccagaccaatatgttgctctct
ggtacatgcaaggtgaacctgttatgggtcgtgtctggaatgaaggagga
aaggtggctgccaacttctcgtggttcaacaacgagtattgcaagaatgt
tggatctatccagcttctcatctatcttccggacagtgttcgtggttntg
actatggatggatcccattcccggaggctgctcagtttggagacaaagct
tggcatccagttcatgtcaacaaccacaagggagatatctncgttggagt
tgttaacgttgctggaggaaagcagattcttgccaggggtgattgtccgt
aacgagaagtatggttatggataccaaagaaaggagcattcttgcaa
>AW057282
agtacgctctttaacccatgaattgttgtgtccgggatgtcgtcaatgtc
tgagtcggatagttatcaatcgagccaattgacaagcgagcccgatcttg
tggcgctggatgccaagataatggcggtaatggatggaactgaagagctg
gagagggagattggcaagatgatggctctgcagcaagcgattagtgatta
caagaagagccatcaacatagaactcaaagaaccaaggagaagcttacgg
atatgtctaaagacccttacaatcaccgggaagaacattgttaagtcgtg
tgaagagcggctcaagcaaatctcggatgtcaccgagccatacatcaaca
gcggaatctcatcggtggaagatcacacctcctcggttgtggagcgctgc
attcaaatgctcggagcaatttctggacttggtggggcaatgaagaaaac
ggagggattgtcttcgaaagtgctcgagcatcacagaaagctcgcgatca
tggagcacaagcaagccgatgcaatttctcgctacgagaaagccgtcgga
gttcagaagctcgtccgcgagcatccggctggagacccactgcacgagc
>AW057283
atcgatcatagtgcaaaatggagatttaatctaattgcattcaaaatgaa
gagcaaaagaaggaaaaggaacttattgctgaaaaagcagcaaaggctgg
atttgtcaaccgactttatgtgaacatcggacaaaaagttggagttgtcg
agctgactaagttagagccacgttttgagaggaacatcgataagctcacc
tcctaccacaacttaatctacaaaattgtgaatgtaatcgaacttcaagt
tcaattcatgcccaaggcaatggcaaagaaagcagttttgtgtgctcccg
gcgagattccatgggaagttcttggaggatggttgaattatttgggaaaa
tatcagtttgatgggcaacattctaaaatgctggaaaaatacagtagcgc
ctgtggaagaattgctcaaaaggagatccaggtgcagaaaagaactcgtt
ctcatctgattaaaaagatgcgtttgtacactggagaggaaagtgagata
ttgaattcgaacgtagaaaatttgaataacttgctccatgcaatcgatga
ttctcgtcaccatgtgaagtcttcacaaaccacgaaagaggtgaaagcaa
aaggcgaaacgtatcgtaaagccatcaatgctttcaacgaaacggcaaat
gaagttcaagcattgattgacgaagttgcaatggtttgggtgccc
>AW057285
aaaaactacaacttcggagtaatggaaaatgagaaaagtaagacggagag
tttgaagaaggacgaaatcgatgaggcaaactcagaatcttcaaaagtgc
cactaacaattgatccagaggaagccaaactcccaaatgccggcggaaaa
tcggagcatatggtggtcaacttcacttcaaaacgcatggcgatcaaagt
gagatgtggcaatgcactatttcgtgttgagccaactcacatgatcatcg
agccgaacaagtgccgccaactgacaatcaatcggatgcccggaccaatt
caaaaggataaagcgatcgttcaatacctccaaattgaaaatgatgtgca
agatccgaaggctgcgttcaaagcagcggacagtgctggaactaagattc
cacacttgaagatcaagctggtggccggagcaagtggaggtcgtcagatg
tcgagagaggtggtggatgagtagtttgggaaaaaaac
>AW057287
gaaaagaacatgaaaataattctcnggctgccgctagaattcagcaagtc
attgcgaatgcagccggaattccatcatgtgaatatggaggaagtctctg
gtataaacaagaagaaaggaataaactgaaggaaaccctcaaaactcagc
atgatatttctggaagcagaaataatagtgatagtgggatatctggtgga
ggaggaagcagtgataatttgagcatcgacgatttcgaatctgtttcgga
gaaccagtgtgaggaaaatgtgataccggctatgaactgaatttgcacat
tgtaatttttgttattaaatcatattgaaaatt
>AW057288
caaagttgctcaaaattttcattgccggattgaccttttagctgcattgc
tgacaagatcaaaagaatggtcaaaggaaaaggttcaaaaagatcaacac
caagtttgcgcgccaagaagaaaactggcacggatagacagaagccgtct
gtaaaacaaaatgcatctcaaaactcaaagaagagtagcagacagaaaaa
gacccccagtgttggaaaagaacgggaacaagcaacggataagaaacgag
aaattgagaaaaaaccacaggaaaagactgctttggatgagcagcaaagg
aaagctcaaacggagactatcagcaacttggaaatccttccggacaagaa
tcctgctaaaatggatgacggttatgaagatttcggtcctggtgcagctg
ctcgctaagt
>AW057290
tcgccatcaccgccttgctccgcgattgccattttctgcggaggaaagaa
aggagccggagaatctaaagaaaagccataggaggatgtgtatgaggatc
tggcaccaggagataagaag
>AW057291
cgatcaaccaccatgagttttgatgaaattacttgaccttcggaaccaag
aaccgcgatcaaggatatgatttgctcaaagcgcgtctcgacatgtgatc
gttcggtggaagtcttgtggagacttgctcaagtaattcatgagaagtct
gcatgtgttccaaaagctcaacgtaaggcaagtgtcaccgaaggactcaa
gtttgctgaagaagctgtccagaaggatccaaaccatttcaaggcgctga
agtggaatgctgtgttgactggacaagcaaccgaatatatggcaacgaaa
gaaaagttggaatgcagtaagaagttcaaggaattgctcgacaaagctct
tgctaaggagccaaaggatacggctctcctccatttgcgtggccgttaca
agtactcggttgcatctctgacatggcttgagaagaagcttgctgccacg
ttctatcagcaaccaccatcacattcctatgaagaggccaacgaggattt
ccttgctgcttataaggtcaatccaaaatggatggagaacacattttatg
tgtccaaatgctacgtagcaattaaagacaagaacaacgctcgcaagtac
ccttaccgaagtgtgtgacattcgaaccgtaattccgacgcttgaaacaa
gagttttgccgatgatgccgaagcagatgttgtcttaagctttaa
>AW057292
tttgcgcattttgttgctgctcttctagcttacgtttaatctctctctgc
ctttctgcctccttctttgcctcaatctcgagtcgttctttctcttcaga
ttctcttctttttctctcgatttcagccaactcatcgcttttctgctgtt
ttttgagatcagcaatcattgaatcaactcgtttcacataatgctcataa
gcatttt
>AW057293
aatttcaaagtaataatgcaaaaagtttgtgaaaaacggatcgatagcgt
cgtggcgtcggctgtcgagggttctggaatgttctacgcggtgagattcg
agccgccgccgtcgaaaacttgctttgacgtgactctaaagacgtacgga
ccgccctacaccgagtacatcgtaaccgtcgcaattccgccgaaattccc
gttctcgccgccggcgatcacttgcaaaactgataaaaatatgaaattcc
tgtttttggaggaaaatcaatggaaaccgtctaccggaattgttgcagtc
cttatcgaagcctgcagtgtgatttcgcgtcgagacctggtcccccgtgc
accggttcttccacgcatccgtccaccacaagcacgtacgccaactagtg
cttcgcctgcaaagtcgccaca
>AW057294
tgagagatggtaaaaccggcaaatacttcttcttcacttatcactaaaag
agttttgactctcggtaataatgtcacaattgatatatacgatcatcatt
attatccaatgtggttttggattgtaatttctgttggatttgtcttctgt
actctgagctgtgctgtttggtttatgtgtgctatgtggagattgaaaaa
gggtaaagaatgtaaccatccatcgtttgaagcgcgtaccgttgtgacaa
aagatggagaagagaaaccggatccccaaatggctcaaaaatcagaaaag
acttgtaaaaaattaggtgcattgggtgaagctgaatcgttggccaagag
cttcaaaagtatcagatcgaaaaagtcgatgaagtctacaaaatccaaga
aatctgaaaaagatgtaggacatgatgatcataagaaggaagatgttcat
ggtgatcaaaaggatgataataaagatcgaaacgatggaggacgagattc
tcatgttgttcagatggaacataattctgaagaggaacacgagccgagtg
gatttaaaaagctgggcaagtctttcttcaacttcaaaaagtagcaaact
ctcttcaccttcacccaaagaatagc
>AW057295
atcaactgacaccaacacatcctgcttaatcgacatctatcatgtccagg
aataacactcaaatgcacatcacaagttctcaattagaagacggatttcc
atcgattaccaacaattttctgacagtgacagtgaacttcaactacgatc
catcgaatccttctgagccaccaacaaaagtcctggagaagatgagtgat
ctgattggccaacagattgcgaatcttcaaaagggaaaggcaccaaaggc
aaacgacgacaagagcaaaggttccatgcctaccgttgaattctctcgga
cccagtccatgactactcaacaaagtttggaggacgatgatactcaacga
gaaaatgttcctcttgaaaagaaaaagaaggggaaatacagttcggagta
cgctaatcttttggtggaaaagccaactcgttaccgtttggttccatcga
aaaatgtgaaagtagttccagaagatgagctcccgaagaaaaagtttgac
aaggatcggaagagaagagagtacgtggaaattggaaaactgtattctaa
agaaccaattattgatgaaagtgaagttttgaaaaaggagaaagggaata
caaagagaagaagca
>AW057296
tccaaatgacaatcgacatgaaggtggtgtttcttttaaatgctcaaagg
ctcggatcagccggtggacttggtccccaagaaggtcgtggttgccggac
aggaaatcacagttgattccaagtcgaagaacgaa
>AW057297
ttaaagcactgtcaactgatacgatttcattcaatacctggaaaagcgat
ttccttccatatgaagaacgttgtctgcttgagttatgaccgtaatcatc
ctattcaatcaattcgaaagttccggaagaaaatgagcagcaagggagta
atggagcaatcaactcagccgaaggacagcacaaaggaactt
>AW057298
taaccctttcgactacaactaacatggacttgttcaagcgatcatcggat
ttggaagctgctcttcgaattgtgctccagcagactttgaacatcgtttt
gcaagcgcaggagaagctccccgaggcaaatgtggtaccctcaactccgc
ccacctcaccgagcactgatatcggcgaacaaatggcatcgttctggaat
attccatcacccaaccctcctgcaacct
>AW057299
cagaatccccatccaactaccaccggctggcttatcaatggacgagctgg
aagtattggttcaacaagcagtcgctggtcagaatatggtcatcactctt
ccggttccagcccacaagaagttgattgtcgagcagatcgttgtgaagtg
cgatgaacatgttatcagcctgccagcactcattgtcaaacatcgttagg
ttcttcagtagccgaactcttgtcgaactctctttctctttt
>AW057300
gtagaatctaggggaacggttcgttctgctccaatcgcctgccaccgtat
caccgaaatgggaccgaaggatgactgagagagctggttctacttacttc
tcgatctaatcgtacctagcggtctaccttggcgtaagctctctgacaag
catgaggtgctcaaggagaaggaggaatgccgaaaagataagcgttcctc
gatgttcgccgggctcacacagactgattatcctagtacagtttgtgact
acattgacggaagagcttaccaggatcgtgtggactaccagttcatctac
aagaatcttgcagaggcttgcaaggtttgtaatctt
>AW057302
tcgttcctcttctcgaaggccctcgtatacggattgttcggatctgctga
gc
>AW057303
ccctgtcaaaagaagtcaaacccatttgatttgcacatctccactggccg
cgaaatcgttcaacgcaactttgtgttccgcaacaccactggcaaagact
tcctgctgaaattgcatgctacgaatggagctgtcacattcccaacggaa
gtttttcgttctccaccactatcgcatcgcatcatccagttccgtgtgaa
ctcatcaaagctctctcaatgggacaagatgaatctttcgatcagaggat
acgtgttgccgatctatgcgaagagtctgaagcagttcattgatcagaaa
aaaactgcaggaactaatgagcaagaggcattctcattgtctgtcaagtt
cacggatcagttctcggctccgcagacagtcatcaacttgccaggatatg
ccacgtgtatcgagtcgactgatcatccggttgacgtggaagaattggac
actacaactgcagtcaacatcgaaagagatgtctccactgctgctccaat
tggttcaatgatgggatttgttgatgagtacaaacgtcgtcaattgaaca
aaggatgctggttgtccaactacatctgtggaactgaaaagcaaccggag
aagcagtcaatgagatcttctcgtagatcaagccgttcgtcgaatcgttc
tgcaaagagctcaaaggcttgccgtgttcaagcctaat
>AW057304
tcggtggcgagtgcgtgagttggtcaataaagttcagtcgactaaagcaa
aaagtgaaagaaaagtacgggcagaagcaaggcgacagtgcttcccgccg
aaatcgacgaggcgttgatctacttcaaatctctgaagccccgcgtccag
gatctctacaagcacatggcaaatctgaacgacgtggcaaattggcaagt
gaaagccaacttttcaggcccactggagaactatgctctgctcggagatc
gtatcaacgtgcaaccgttcatcaattgtgttgacacgcggatggaggca
gatgtcgagtcgatggataaggggctggcgatttgtgagcggtacaaggc
gttcacacagaacgagagtaagcttcacacaaatacaattgccaatttga
ataagacacgtctcgatatggatagtgctgcgaacaagtacgccagcaac
gacactgacgtcaatcggactcggtttgatgatgccactcgtgagtttga
ggtggcttgtgatcggatgcgtgagttggcgataagtattcagacaattg
aggagactcattccatgtggcaagatgaattgatgcgggagataaaggcc
ggaatgaggaaaccgaattga
>AW057305
tactgagaaggatgaaccgtcagacttctctctcctcctcatcgtctcga
tccttgccgtttttgtccaccatggatttgctgctgctgaagaagagaag
aatacagcttcagtcgtcagccctgctccggactctgaagcagcccaacc
tgctggaaacggaaccgaaacaccaaaagatgaggtgaaggatgaggcac
caaaagaaggtagtgaaactgaagcttcaccagaagccaagacaaaagga
tctatggtattccatgcctcttggagcccattccacagttggtctcgccg
gcattatgtgaagaagtctgccg
>AW057306
ttttttgagattaatttaatttattccacagtaaaagttactcaaagagt
ttcatagccgatggtcttgaaatcgcattcttcatgactggggatggctt
cttctcacgttgctcccgcttcaaatcaccgatgattccccacatatcga
aaaccattccatccgg
>AW057307
ttgtccattacgagatgtattcacttttgacgctcctcttcgtcctcttc
ttctctggaagcactctgctcgttcaatgtggtggaaagaaaaagggagc
aacttctgccgaaggaaaatcttcgacgatgggcccggctcctggaggag
ctcctgctgctgcttccgctcaaggagaacctgaagagaaggagtaa
>AW057308
ttggaaaagaaggagacaaagaagaaaggttagtataacaagaagagcaa
gaagaaggcgaagaagggaaagaccaagaaggttcgaaaagcagacaagt
acgagtctcaaaactttctgtttcgagtggaaggagccatgttctgtgcg
ggaattatcgttgctatgattatgctgttcgtcatcattatctacggaat
aatcacttcaagtcaaactggaggacagttcaacagatacatggccccac
tattctgattggatcaggacagagaaatgtcgcaagagacaa
>AW057309
acggctacgagttctttgcctccaagaagatggtcaccattttctcggca
cctcactactgcggacagtttgacaattcggctgcaacaatgaaggtcga
tgagaacatggtctgcactttcgtcatgtacaagccaactccgaagtcca
tgcgtcgaggataagctctgcaaactgtcaccaccatccaaccaaccaac
caa
>AW057310
taccgtcttaccggccgtggctatcttctgtggaggaaagaaaggaggaa
cgaaaggagagaagaaggattcagtgtacgaggatcttgcttgcagagac
aagaagtagttggaacttcatcgacaccaccaatcaacaaaagacgtctt
caatgctttttcatcgtcttcttcta
>AW057311
gaattccaagtttgagaaaatgaactgcttattctttccgctttcctcct
tgttgccatctttgtcatatccgatgctgccgttgctcaacagcaggtta
aggacggagaaaaagttgaaatcgatgctttcaagggagccaaggcaatc
aagagaaccgttgccggtggagatcaaatcttccaccttgacggagataa
caagggatcatttgttgatgctaagggaaagaagattgagtcaaccaatt
atgaagctaataacggaatccttatcattaagaagttcaccaaggccgat
gttggaacctactccgagcacccagctaaaaacaccgaaaccaagcacgc
tgatggatccatctccgctgttccaggactcactcttgatatctccctgc
aataaacaaa
>AW057312
gcaagtatatccagcggtttgactctgtcagaccttatggctacttagag
aaatcatcgagcgtttgccactctaagagcctacgatgcgatgaggatcg
ttgttcgacatgattgtgctcctagagctccttatgaacacgctcctcga
caaattggctatgatgcacctgtttatggatctcacatgcacgcagcttc
tgtcgattacctactaactcgacctgttgccggtgccaaagctcttgacg
ttggctcaagaagtggatatttgacagtcagtatggcaatg
>AW057313
tcgaagaacgttgagacgatgactgcaattgattcagtcgaagtgatgga
ttctccaacatcaccagtgacttcttcaaatagtggacttatcactgttc
tggaaagaggagtttcttctgaagacacattgattccttctgttcgtcgt
ggtgtcattccagtcaacactcttcgttaccaaatagaaaagcatctcga
gatgtgtactccagcttctgaacaattgtcaaagagttcggatcccaaca
tctcctcgatgtacgttttccatcaaggaattcaaagtaaagcaggaacc
aatcgatgatgacaaagagcgaagccaccactccttcttcacagcttctt
cgt
>AW057314
cgtctcctcaagtccgccgtcgcccaatcgaacaatgtcgtatgcacaga
gtttctacgccgatcagaagaaagtcgagaagccagcggagcaagcttcc
tctcctgccacggctgccttccccgctaccaccccaatcgctgaggatcc
tctgactccatcccaaatccaggatgccatccgtctctaccgttcggtgc
tctccttgtctgcgtctgccccatcatcaccggttcgtcaagcagcggct
ccagttgctccggaacagccgattgtgcactcggactactatggtggacc
atcggatattccgttgtcctaccgtgttaagtacaccacgacccagcagg
cacctgcgtctccagctccggacttcacagagcaacagttgatggctcag
ctgcaggctcttcagatccagcagcagcagcagccggcaccagatgttcc
agtcgtcgagccagttcaacaagttcagcaaaagccaaaagttgctccga
agatgcttcacaagatgtatgacgatgaagagtctgggtactgcttcgct
cgtaaaaaggatgtggagcaagaaggagaagttccggagaatccacgtgg
nccgctccagttcaccactttccgataccgacctactcgggctcctccgg
tcaactatgaagccttccggggtttttttccc
>AW057316
catcatgttccttcgcaccctcgttgcccaattcacaagtttctgccatc
agctccatcaccttgcaactctgtcaagagttctgtgctggtgtcaatgg
tggtgaatcttacgcattctgctctccatggatcagttttgccactcaca
gaaacaagacttgctacaatctctgtgttcataactgtgctgctgtctat
gatggttcctgcacaactgataaagacttcagatgctgcttgaaaactac
tccagccaagaaacaagaattcaagatgagtggttgcaacaagccttaca
acaatctttaaatgagttctctggtt
>AW057317
tctatgcaaaggattgttttaacattggatgggcagcagataaatcaaga
cgactggacatgatgtgcgtatttaacgatgctctagacacgagtggatg
ttgttatagagacacctcaaacttctgttcagaggggatgtcagtgttgc
catctcaacgatgtgatacccttgatgactgtaatatgcgaacaaatcaa
actgcgcaaagatggtgtgatcccgtttcaaaatanttgctgtccgattt
gaaaaaggaacaagcacttttatgcccggacaacagtacagctttaatga
atgaacatcattgtattaactacgacgaaaaagatatttggagtggaaag
tgtaagacaccgaacggaatttgcaaatatggacactgttgcccatcaaa
taaaactgaaaaattgttacctggaactccatatcgcactcatcaaaagt
gcactaacaaaacaattattcgtgatgatcaacgttttggatactgtgat
cctaaaaccggaagggtattcataatgagtgaactcaattttcacgggca
gagaaacaaggaactctcgtcatactgtaatactgcaagagattgcggtc
ggtcgtttggaatggataacgtatgtgttcgaatgaataaagaacgctca
atgctttcttcaa
>AW057318
gcgactgcgttggatcaaaccgacatggttcaaattcccaacactccaac
attggttgccgaggaaaatttgaaccacaaacgctctaaagcaaatctcg
tggtggctcaagagtctgtcgcaatggagcacatcgctgctcatcagctt
ccagctcccgagccacgtcatcgtggaccggcgattaaggataagccgga
gagaaaggatcgtcttccgacggttggagaatattttgaaaatgataaag
gagatcgtttcattttgcgtcagaagctgggcgatggtgcaatgggacat
gtttttctgagcatttttggtggcagaagtgttgcaatcaaagccgaaaa
gtattcaacagggatgcttccaatggaaattaaggttttgttgagtatca
gacgccacaatggagttcatttctgtgatatcattgattatggaaccatc
cgtcgtgaatacaactacatgataatcagtattcttggaaaagatctcta
ccgtcttcgtgccgaacaaccgactcgttcattcactctcaatacgacta
caaagattgctcttgaaactattgaagctattgaagagcttcacaatatt
ggatacctgagccgtgatgtcaagccaagcaactntgctccaggacaacg
cgacaatggacagcataagacaattttcatgtttgaactttttggg
>AW057319
tcagttctcatagtttcttgagtcattcctgggtgtgatttattaaaaac
atcctcgcatcgtggaataattaaacatggagagcaagccagttgcgaca
aaccaaaatacggaattggagaaggcaaagctgctgaaaaaaaaaactcc
cgaagaattggcagcactggcaagcaagaaggtattctcaacggaatcag
ttgaagaaccagttccagttactcgtcgtccaagtgaattgtcaatgggt
tcattgaataatcaattgaaagaagttcaaatgggtaaaagcattcaatt
cggctgagaatcatgcatataaaactgccaatgacggagagaaaaaggac
>AW057320
aattccaatttttcgaaacgatggcngtcacatatgatacacttcgtgca
gaaattgaagagaagaaagaagactcagtttccgaaaggacaactcgaaa
tggaaaaatactgaatgcaaaggatgaaccagagtttggaatgaatatta
ctccaaccacgttgttcttcaagtacccaattgggggaattggttattca
ttctttacagtcaccaacacaacatcggagaaataagcattcaaggtgaa
atccagtgacaacacttggttccgttcaaaaacccagcggtcggttcatt
aagagtggtgaaaaagttcatgtgagagtcacattcaatagtccagacgc
aggaaaagaaagacccgaaagaggctcagacaacaaaaatcatgttgcaa
tcttccacgtggcagctggtgacgcgaagacgtacaaagaagcgtttgcg
aagaaagcggcggacggagttcatcatttctttgcaagac
>AW057321
ctggaggagactatacacaaagagcaggaaatgattcaaacaccggtgat
atctgcctcatgacgttccaagcggtggcaactgatatggatgctgctcg
tgacttctgtaacatcaaagctccgtggcggcttagagaagcaaagattg
ataaatcacaagacagtattccggtgattatctgcgacgttgaagctaca
ttcacttgcaatgccggatggattcaaatgttcgggtattgcttcaagat
gagtgaggtccatgatcgctacacacgtgaaaaagctgagcaatactgta
aagatcaagctgggccaagttttcaaggagaaattgccggcattcatcac
agatacatcttgacgccttggagaagct
>AW057322
tgccaaaaaatcagcgaagaagttaacaaatgatgacgtggatgttttga
cgaatcccagcgacgaatacgtggattctttcatgaaatatcacggaaac
ggtcgagcagtattcaagcgtgaagatttggctcagtggcgcgatagctt
cccggactacaaattcaaagtgatcagcttaaaaggagcgccgagagtca
tcgcaacggcacatttgtgcacatttcgcctcattgatccattcatccat
taaatccgataatggtcattgggttccgtatggatagatcctggatttag
atctcccggaccggcaaaacttcagaatgatatgtgtcgagtggaaatgg
acagggaagatgataatattgtcttacagattaaccaaccggtcaaaaat
ctctggcacatgctgtccaagcggtaagaattcttgtatctcggacacaa
agccggcgacgttggctacaagacattctacagtgcacacgacgtcgtgc
tccctgagaacttgcatttgtctggaattacagtgatagatgctcgagat
gctccgaagagagatatcataaattatgatcagacactccatccgtatca
ccgagacaagtacatcatctatcatatgtacgatcggtatggatctcgtg
aagtgtcgtatgatgatgtagtgaatcgtgtatcgtcatctggcctagtc
tggtatctatgatcatcagatcagatgtaatttatggcctaattatgctg
tatatacacgtgtcgctacagcaatcgtt
>AW057323
gtcggatccggctgcaaccagcccctgttcatccaatctccaggttgtgc
aggctgtggtggcacccagaagttcccagtgatgaccttcaatggtgtgc
tcgtcggagaaattgtccgcctctacccgggattcatgcaggagatgttc
accgatgcggacacctatattgttcatttcccaatggacatgccgccaat
cttgaagcttctgcttgtcacctcggttttcctgatcgacttcacctact
tcgaggatcgtaaccaggatcaacatcgtaacggcggaatgccttaccga
acgcatagcagcttctaaacttataatg
>AW057324
ggaattgacaatcaggttcaatcctcacgcgatgatcgtctggtgtggct
gacgttctgcccaactaaccttggttcaactgtacgagcatctgttcaca
ttgctcttccaaaactcagcgctcgttaagactccaagcgattctgcgat
aag
>AW057325
gtgaatggttccaaggagacggtatggttcgtcgcaagatcctccctatc
gag
>AW057326
ctggatctatcatgtcaatggctagtgtttatgcaagtgtcgttgctcca
gatctgacaatctaccatggagatcgtaagcaatcctaccattttcgctg
acaaggggaaaatggtcgttatcaaccggaaaaatggggtgattgtctac
atgcttcgttgtgtcgacggccgacgtgtctacattgagaaatcttccga
aggagccagtcttattctgactaatcaacgtggaaaagtgat
>AW057327
tttttacgatacaaaaatcactttactcatttacaaccaaaacagaaatg
atattctcgacgagaccagactttcccttgaaacctaatcctcactgaca
ttgcttgtcttgaaggtgatggaagtggtttcacggctatccaaaggcat
tgacactgacttgctgttcttgttctttctgattttcagactaccctttg
aagatctatcagtgttttccgacttttcagttggagacttttgaacgatt
cgatggaagaagacgagttggatttggaggcagctctggatttacttttc
tcaatatcactcattgaagttgatggggccttcattttgggcttctcctt
cttcgcatcaccagcctttttcgttttcttatcaaggcatggaaggttca
aagcagttttgcggaaccacacaccgacaacagctgccaaaatgttgacg
gctgtgataattgcaagtgcgatccaagatccagcgggttgattgtcgaa
gatcaagtagacgagccagtagacttcacacgcg
>AW057328
taacgtgtaatattttagacgcaaattaaccacttccaattctggaatat
ctggaatcattcagaatggtagttgttccagcaacttcttcacttccagc
caacagcacaggttcaccattttgatcgtccctttggctatcgtcatcaa
agaagaacttcttatcaccaatgaaatgttgaaccaaaacccttccgatc
ttgaaaaggggttgacagaatgcacatagcaatactatattgccacgttt
ttggtacattaacggatgtttctccttcttttgctccaggacataagcat
gagcgagcaatggccattccgtctcaattcgattcttttcgtgagtgatt
actgcgatagagtaaattaccgatattgctgatacaataaccaagccagt
agtttgtacctgtccaacaaacacgtcaaattcacaaatctcatgaactg
tgtagaaaatcagacaaacacaagtgagagccggcaagaggatcaaatac
atgctatcccagattgaatagtgagaccatttcaaacggtgacaaatggt
gactagatgacttgtatcaatcagatgatcgttagatctcaagttctcag
tgatactgaagttcga
>AW057329
atgctaaagttcaagtattagacggactcagtgggatgatcatcagacgg
attatcaagtacaacacgcgaaagctctgtctcattcttctcttcttttg
gtggacggagcatcgaatgctcacggcactgagttccatcaagacgagta
atttgttgcaagagatgaataacctttccacgataagtatccactgatgc
aattggattgaaatcgaggtaaacactattgagttgtggaagttcaacca
attcatccataatgctccagttatccaacttatttcctcttgcccaaaag
tctgtaagtgtcttcaattgatggatattctcgaccttctcaagacgatt
ctgattgaaatccagaatttcaagaggaagatgctcatcgattccacaaa
cgtacttgatgccattttgagccagataaatctctttcaagtt
>AW057330
tgtatctcgagctgctcacattcatcgatgaaacatcttctgcagttgga
actgcgaacatatcaaatacatcttctgcctgattcttggctgattccac
tgccaggaagattgcacctcttagcaattcaccatagacacatacacacg
accatgtgacaatcttgcatccatagtctatggagcctagaagcaactcg
ggcgctctactatatcttgcgacatgatagctgtgatgtggtgtctccac
tgatgcagtcgagatgacgcatatcacgagtctcagacgacagcgcctgc
attgtcagcagatctgtgctcgatgcacg
>AW057332
tatttaatttcaataagactgccacttctcaaattgaataggactgccca
ttaatgacgagttttgccaaattcttcttcttcatggacccatttaagat
tccagacaaatcaataacatgatcaccgattgacaaattggtagaaaact
ttgtgcgattctcaatgttcaattctggtactcgattgcaattgttttgg
aggaattggagcatcatcaatacatcgttcacgttttttggacttttcac
tattttttttcttttgcttttcaagaggctgaagccacagcttgacgcgt
ccatcagaggaaacaaactccattggttgataggcaagactattggattt
agcagttgtagatgcatatgaaaggtcgaccgacaccattgaactcggag
acaacgccattttaggttttccagttcccgcatcgtaagttgcttttgga
acaaggtcatctggctttgacttcttcagtccacggcacttcaagtgttt
gatgtcctccaatggctcaattgctagtttttcaatgtgcttacngtaga
gcgatttgttggaacaagatgaagcagttgctgcacttatcgaaacgtca
tttgagcctctgcttgccggatgtagatgcacttgggaacaggagtccgg
ggtcgtgatcttgtcatagtgctatagtattcagaatacagtttcaatgc
tcgattggaaccttctggctgctggaa
BioPerl-1.007002/t/data/dbfa/3.fa000444000766000024     12052713155576321 16305 0ustar00cjfieldsstaff000000000000>AW057334
tttcatccatcaaaacatttttattcaatctagacagtgctattcatgac
atcttgctgaattcttatcatcacttgaccttgcgaagagcttttccttc
atgatcatgtccgatctcgtgagtttgagtttgctcgatgatagaaacac
ggcgagcatttggaccggtagacattgcactcttcgctggaggcttcagt
cctggaagagcttgacgatattgcgaagcaatgcctttcacatctttcgt
tcatttggactgatggtggttgcatgagattggtagccaacgcctgtttc
gcccattgcttggcatcgatcgaatcagggcgctcgacgacaaaagtgac
ttttcctttctcttggatattcttgacgagaagatctctggcaacatcct
tgtcactgactggaattccatcaacatcacacaaatgatctccaagaaca
agacacttctcggctagtgatccaggatcaacacgtgaaacaagcacacg
gttctggaaatgcttgattcccaaaccaagttntggtccattttgaaccc
agacaagggttgccaactcataaacgtatccctcacggcgttgaatgatc
tttgcacgatcctcangaatatgaacacgagcttctaactcttcagcctg
tgtatcgtcacggctcaccgtgattattgcacatggagcagcacagcgaa
gcgcacgngaaaagtcgttacaatncttgcaattntgtccgtgcactttn
ttacttggcaccagtgctcatcttgctcagaaatgcttcagcctggatct
agtgatacgagcttg
>AW057335
ggcggtggttgatcgggcttaatcacattgttattcgcatccaaggctga
tccctgatcatttggaacagttccagcgtttgctggaagctttctggaca
tgctcttctccatatgagcaacaaatggatcaatcagttggtggtaaatg
acgtgggatccgtgagtttctggcaagtagaggtacaggaaaaatgctgc
tttgcaacccaataaattgggaaatatgacataatgattgcggcgaagaa
gtcgataattgaaaaggcaccgaaaacagtccaatagatcaaccacattg
tatcatcgtcagttccttcagttcggatcgccttaacagaaacataagcc
ggataggcaactccaatcaaattgcacacaaactcggcgccacttccaat
aatcatgtagacacaattgagcccgatgagcccatatgcgagcatttcac
gtttcagaaccagtgcgtcttccaactttttcacattctctttgtagaat
ggtccatgatcagcgtacaagaaggagaagaagtcactctgagggtctca
aaatccttagcgacgttgtccatcggctggtttgattccacagattcttg
tcatcgacat
>AW057336
ttttttccataaaatacttcattcttaataaaaattcaaattcctcgtag
tttatcactgatccgacgcctcccaaattcgacccatttcaattgtgaca
aaactcgtgttcttaagatcttcccgagcatccataagctctttgagctt
gtcacgtggctccaggtagtactcagtagagcccatatggtacgttcccc
agtgtattccaatactgttcttagcccgaatgagtttatgaaccctcaat
cgcctcttccggattgatatgctgggatttcatgaaccatctgggctcgt
atgctccaattggaatagctgccagatcaaaaggtccaagcttctcgcca
aacttcttaaactctccgtcacagtgaccagtatctccggaataatagaa
tcgccgattctcgccgatcaccgcccagcctgaccataatctgtggttcc
ggtcgaaaagtccacgctgtccccagtgttgagcaggcagacaccagatg
gtgtaggtctttccgttcttcacaaattctgagctctctccccagttgag
ctcggtgacagcggtggaggatccgtcgactccgatgccctggccttcca
tccatttcttcattccagcggaacgaaccacttgattgggggttgcgatc
tgtgatctcttcacgcgtcagcanccaatgatcgtatgatcatgcgaacc
actgcaaaatc
>AW057337
ttgctgaattcttatcatcacttgaccttgcgaagagcttttccttcatg
atcatgtccgatctcgtgagtttgagtttgctcgatgatagaaacacggc
gagcatttggaccggtagacattgcactcttcgctggaggcttcagtcct
ggaagagcttgacgatattgcgaagcaatgcctttcacatcttcgttcat
ttggactgatggtggttgcatgagattggtagccaacgcctgtttcgccc
attgcttggcatcgatcgaatcagggcgctcgacgacaaaagtgactttt
cctttctcttggatattcttgacgagaagatctctggcaacatccttgtc
actgactggaattccatcaacatcacacaaatgatctccaagaacaagac
acttctcggctagtgatccaggatcaacacgtgaaacaagcacacggttc
tggaaatgcttgattcccaanaccaagtttggtccattntgaacccagan
cagggttgccaactcatanacgtatccctcacggcgttgaatgatctttg
cacgatcctcangaatatgaacacgagcttctaactcttcagcctttttt
cgtcacgggtcaccgtgatttttgcacatggagcagcanagcgaagcgca
cggaaaaagtcgtaccatccttngcaatttgtccgtcacttttttaactt
gtcaccaatctcaattttctttagaatggttcagcctgaatctta
>AW057339
cttcctcaaccgccggctcctcttcctccgcgatcgtcggaatctcatcg
gcacggcacgccacaaaacgtggaagctcatccggcgtcggctcccgctc
gaaatccatattctcctcgtgatccgtcacacctccgagctccttgtaga
tttgctccgtgagccctgccaacttgacatattcctccttctcgacaacc
gagtattccttggcgataaccacttcggcaatcttgtggaacacctctgg
aagctccgcgaattccttgctcttctggaactcggccttcttgactccag
cctcttcgcggctcagacttccccatgggagctcgccgagcaccaggtga
accagctggtagaaccatgtctcgagatcctgccgggcgccaacaagacc
atcgtcactgcacggagcataatccaagcagccagcgtagctagcaatcg
gagctccatcatcaccagaaatgttcttgaccaaagacgagatgtccgcc
atgaagaggtgacggcttgccgcatcgtagtggaagctgntgagatccat
gttgcggacgaggtagccatgcttgtgagcacatcngaacacattgagca
catcctcgggccagcgttcagccgncccaagcgtgacttgntccgcatcg
caaagcactggctcaacgtcgtccacccacgaagacagcnacatgtgcca
cgcgtcgtcgtccagaagatctggaactgcgagagagccgc
>AW057340
cactgcattcattttcagatgcagccaataaatgtgaatcatcaataaca
ctatcagcatcttgctcatttccaacagtctgctttgctcctaggcttgg
ctcacagtgagatgatgcttccgaggcttcttgaacatcagtctcactaa
acgatggctcaatttcagctaaactagacatgagactttctgtaaccatt
gacattaccgaaagattctcatccgaagtggctgccaaaatattagaatc
tccaagttgggcttggataatatcttgaatgttcccaaaaaaatcattcg
aactaccgtgaagatccatgccagagtcttgctaagaaatggcatcacat
gcacgagcatccgacctatcttcatcacgattcctgcatccagcactctg
ttcacaacccgtcattattggatcacattcgagtgtaagagtttgcacat
gtgcatattcgaacatcaga
>AW057341
caatacaaagaaaggttgtcagttatatttcaagtctatttcttctagtg
gagcaagtaggcagctggacctccattttcccaatcgtacggagcattct
cgttggatccacatgcaccataagcttgacgcatcattccgtagattgct
tgatagttgggtgcatcatagggaattcggaatt
>AW057342
tgccttcttcaacggtccatatgccttttttgggatgacggctgcaactc
cggctccgactccagctgctcctttcttcttgccaccgcaattggctatg
gatccaaggatctcgaaaattgcaatattagcaacatgattcgtgcaatc
attgatactaactgaattgagaggcttggaattgt
>AW057343
atttattaaatcaattaaaatcacacaaagatatcagcttgtcccatttt
tcttcttggtgtctccaaacaatcttcttctttctccgattcaattgact
ttctactgattaattgtggcattgagttgtcaaatgaacgacttgttgcc
ataactctcttatccgaaattttgacgacgactgtagtgagacgaatgaa
gacggccatactggcaagagccgtagcatcaattgaattactgcacacac
cagagtaactccattaacagcatgacagatatccgaattaagtgttccag
ttgagggagttttcagatattgacatggagaatcgaatgatttaatgaag
agtgcaattgtatgtgcaagatggaaagctgagaatacaaatgcatgcat
catgaagagaagagtgaagacaccaaatgcacgacgagttgagcagagtc
caatgagtgacatgagtgccaatgcggtcatcaacatatctttagtatcc
agagcagtctcatcgagtaccgctcatgatcctgcaactttgtatgcagt
tgagtagagaccactgactaggaagatgacagtgatgacagcacacagtg
gtgcttcaatgacgataagcataccat
>AW057344
atacataaacctgattgacacggtaaagggaggtatccgagcacttgatc
ttataagctttacgttcatttaaagtattctctaattcaattggattgac
tccgccatgtgcctggtattgaagtttaacaggagccacattcatttcct
tgaagtgctggatcgaattgactgcttcagcaaggctatgcccaacttgg
ctatcagtcgtttgttgagattctggaataagagcaacttggccgatctc
tcacgactcttcattctattctggcatccgaataagtcgacgattcttcc
gctcttgaactctatagctctacgagagacttcgatgagt
>AW057345
cacagttcaatctaagcttgaatagttgatccaccacacggagttgcttc
aaggcacacattgacatcacttttgttctttttattagcctgaatacggc
aaacctttgagctctttgcagaatgattcgacgaacggcttgatctacga
gaagatctcattgactgcttctccggttgcttttcagttccaaaagatgt
agttgggaaaaccagcatcctttgttcaattgacgacgtttgtactcctc
aacaaatcccatcattgaaccaattggaacagcagtggagacatctcttt
cgatgttgactgcagttgtagtgtccaattcttccacgtcaaccggataa
tcagtcgactcgatacacgtggcatatcctggcaagttgatgactgtctg
gggagccgagaactgatccgtgaacttgacagacaatgagaatgcctctt
gctccttagttcctgcagttttcttctgatcaatgaactgcttgaggctc
ttcgcatagatcgggcacacgtatcctttgatcaaaagattcatcttgtc
ccattgggagagctctgatgagttcacacggaactggatggcacgatgag
ccaatggtgggaaacggaaaacttncgttgngaagtgacggctncattcg
tagcatgcaacttcagcnagaaagtccttgccagtggtgtgcggaacaca
aagttncgtntgacgatctcgcggccagtggaatgtgcaattccgtgggt
tgacttctttgacaggcat
>AW057346
ctagaacgcatttgtggatgctatttaaatgttctggctagatttctcgg
gggaaactgaataaactaaagcttatcaacatctgcttcgcatcatcggc
aaactcttgttcagcgtcggaatacggttcgatgtcacacacttcggtaa
ggtacttgcgagcgttgctcttgtctttaattgctaccgagcatttggac
acataaaatgtggtctccatccattgtggattgaccttataagcagcaag
gaaatcctcgttggcctcttcataggaatgtgatggtggttgctgataga
acgtggcagcaagctttttctcaagccatgtcagagatgccaccgagtac
ttgtaacggccacgcaaatggaggagagccgtatcctttggctccttagc
aagagctttgtcgagcaattccttgaacttcttactgcattccaactgtt
ctttcgttgccatatattcggttgcttgtccagtcaacacagcattccac
ttcagcgccttgaaatggtttggatccttctggacagcttcatcagcaca
cttgagtccctcggagacacttgccatacgttgagctcttgaacacatgc
agacttctcatgaaatacttgagcangtctgcacatgactttcaccggac
gatcacctttgtcgagacgcgctttgagcaaatcatatacttgatcgcgg
ntcttggntcccgaagtntngtcattttcatcatacatcat
>AW057348
tagattgttcagatgatccataacacgagttattcagcttttggctcatc
atctttgcaggtgagaatagttccctgtgacatcttatatgatccatcct
cttgcttcttgaaatccataataagctcatcattctcttcgaaaacgaat
ccgtttgctttaacatgcattgaaaggttatcctcacgagtgtatgcttg
aatcaccttcttatgtcagatcagttgggaatttctctttttcaataaga
gcatgcatgttgaatgcaacaaattgacccttgtacaaacgattaccgca
catgttgaagatcatgtgtggcagaagccagttggtgagatcatggatat
cttcactggttctcacgtgcattgtatcggcggccaactttgtggcgact
gtctttgccaattccaagtctgcagcatcacgagcagcgtcacgtggctc
cgcggtcaccgggatcagattactggtatcagcctccctttacacgaatg
acataatgccactgagggcatgaacacgaaagtccagaaaagctgcat
>AW057349
ctcttctagcgattgatgtaatagtaattgagcatgcggaacatcagaat
catgataactccagcaattagcagatcagcacatccgaagcatatagcca
acatgtatccgtgacgattagcatcacaaacttccttgctcataccggaa
ctacaactgtcccctctcctaacaacatcaagaataatttccaataaaag
tgaaaatacagtaagcgatccagtaaataaagttcagagcaaaactgatt
atattcgagaaatattcgggaaggaacacgataagacccatgtacaacgt
ggcaaacacgagccagataaagtaagaataatgggtgctggcaatccata
gactgagtgttagaattacaaggaaacacgacaaaccaaacataatgaac
ttggtgggaacacctgcaatgagaatctcatccggttcagcagcccactc
gaatccagctctcaaacgtgccggctcattctcattcggattttcatcct
ccacatgcacgtattccaaatccacggatgcacaactgtctggattcat
>AW057351
ttttttttactagaaaatatctttttatcaataaacacatattcaataca
gttcggaatggacagaattaaccatccaacttgcatcctggtttagcctt
acggcacaagacagtagtattgtcagcacaagattttgcagaagcagtat
gctcttttccttgataaccatatccgtacttttcattacgaacatcgacc
tttgccaaaatttgctttcctccagaaacattgacaacttccactgagat
gtcacccttgtggttgtcacatgaactggatgccattctttgtctccgaa
tttggcagcttctgggaacgaaatccatccataatcgaaaccacgaaggt
tatcaggcagatgaacgagaagttggatagatccaacattcttggtgtat
tcgttattgaaccacgagaagttggcagccacctttccaccctcattcca
tacacgacccatgacaggttctgcctgcatgtaccaaagtgcaacgtatt
gatctggattgacacctggcaaagtatcaagagtcttatcaagagccttg
acaagtngacgagtttggcatgcatcaccctcacgaatgtccatgcatgc
atctctctcgacacgaaccttttgtccacttncacagttggcacaatcac
aagatggtggcccaccaatgcagctacaggtgatgatgtacatgtcattg
agtagtggtccaacttgttcagcacttttncattttgacgagaccaagcc
tcctcagtnctgtngtcgacataaccaagaagaatttctttcggacgctt
ccagagaatggggaatgatccacacnacgcaccaagtgatggtnatcg
>AW057353
tcgaacaatgtcgtatgcacagagtttctacgccgatcagaagaaagtcg
agaagccagcggagcaagcttcctctcctgccacggctgccttccccgct
accaccccaatcgccgaggatcctctgactccatcccaaatccaggatgc
catccgtctctaccgttcggtgctctccttgtctgcgtctgccccatcat
caccggttcgtcaagcagcggctccagtttgctccggaacagccgattgt
gcactcggactactatggtggaccatcggatattccgttgtcctaccgtg
ttaagtacaccacgacccagcaggcacctgcgtctccagctccggacttc
acagagcaacagttgatggctcagctgcaggctcttcagatccagcagca
gcagcagccggcaccagatgttccagtcgtcgagccagttcaacaagttc
agcaaaagccaaaagttgctccgaagatgcttcacaagatgtatgacgat
gaagagtctgngtactgcttcgctcgtaaaaaagatgtggagcaagaggg
agaagttnncgagatccacgtggccgctccagtcaccactccgataccga
cctactcngctcctcggtcaactatgaagctccggtntcaacaactacta
ctcgaaaggagtcagtgggccattcgagtacattgaatgtcgaacgattg
cagttcatctacg
>AW057354
ttttttttcactacaccaaaatttttattcaaatcaatgcatcatacttt
tcacacacgatcaaaaaatctttttcgagaaactttttcttttggagtca
gatgatggaggtctaggcacaatctagttggcaaccaaaggaatgacggt
gagctcgcgtggtggatcactctcaaagactcccctggcacaattctgct
cagcagaagcattggatgtgagaacaatcaagtgatcagtcttctcgact
ccattatgacggagcacatcgatcgaaagcttgtccccgggctcaacaaa
tccgaagactgggttgacgcggtagagaaggttgtcggaagttttgacct
taaatgcctttctcgacttggtgttgttggcaatgctgactgtctgaact
cctccggtcgttgcgaatggaagcttgttgggcgatgcacgaagagtcga
cgtcttcactgaagcagaaccctgtccctccgggaatgtgtacttcgact
ggttgggaaccaacttcagagctttcgacttttcggatttctcaccggag
tccgatttgatggacacgtcggaaacatctgcctggttaaccgttgggca
gaggttcttagccttgttcaagtcgcacttcttggaggacttgtcgcatt
tcttagatttcgaagatcttttggatctctgtgactttgactttgccgtg
ctatcacgtctgagcttcttcgattcagacttgggacctcctgccgctcc
cgngatgggagaaactcngnctttgnattgaaggctnctagattt
>AW057355
tcacataatttcgttattgcaccgattttgcacgagttgacacaaatcac
ttcttctggaagcaatcgcttccaattccagccagtgtctgatagttcgg
atcatgagtagcagccattccaggaccaccggcttttggagcacctggag
ccgcaccaccaccagctggttttgcaccttctttcttgtcgaaacaatcg
tttccaattccagcaagtgtttggtaggtggggtcgtgggtggcagccat
tccaggacctccaggttttggagcaccagcagcaggagaagctccaccag
cagcagcaacaggagaagcttttcctttctcttggaacacatttccatca
actccagcaagagtttgataatttggatcatgtgtccctgcgacagcatt
cttatcacttggagcctttggtccctctgggtttggagcactcgatgatt
tttctttcttatcactctntgcactggttgcaccatctcctcctcctcct
ccagttntagctccaccaccacccgatgatccaccagtcttcttctttcc
tccacattgtcaatgacgtatccggtgaacaccattggagcgagcatgct
gtaaccgagatggggcagttgtagaagtgttcactattttctgc
>AW057356
tttcctctccaatatctgattctgcacgtcaacctccaactttctcacat
gaattgcacttctctgcgggaaaagagcacatcccaacggtgtcatgaag
taaagaccaatccccgccaaaaatgtctgaatcggcatctcggagtactt
ttggactagtggacgagctttgtagtaggcggttcgcgtgaatcgattca
tgatcaccgggctcagaaccatatcaggcatagccatgagaattcggctc
agtgtgacttgagcaattgcgagagccgccagctgcttggattttgcgac
gagatggtcgtcctcatcacatagctcaattccctcagaaagttcgcatt
ggaatattaatggcatttgcaactgcaacagccacaaatggaaccaatct
tccagccaatccatgactattcttcaccatcatattcagaccgagagccg
ccgttgtagccgctccagtagcacagaaatacgaatagagtagctgctga
ttggtagttctgcaatttccgcttcgattggtatagttgacaattgcatt
gaacgactgattgatccaatgggagaatataataccangacaggtacgat
agcagctgagaagcattccagtgataaccatatttgctgggtctgagcgc
tcattctnccgagacagaaacatctttttcgcggtatcaggatgatatac
ttgaaatcatagagatcttttgcactcatagctcaatcatcgtcaaatcc
ggatt
>AW057357
atgtcagtatttagaatgttttcgaatcaagtgaactgaggattgcgaat
ctgacgaattgcaggtgtgtcacaactgtcaaccaggcatcctgaagggc
tcaactctcctcgcattgaaatgttttgaagccgcttctgaagttctcga
tgactactgagtgtgcgcatcgcctcatcagcttcagttacagggccacg
tagagggctcagaagtggaggaggatggttcatactgaaatgtgaattgc
atnccgaaacatgtgccaatggttcaggaagacattcaaaattcggcgga
gaatctgtcagtggaatcgaatggggtagtccaagtagttccggcaactc
atcggaaacttctttgaggccagttggtcgtgcataacagaaaacagacg
atgaaagtttaatcatcgtttcgcgcgagtattctatttttaagaaaaga
tgttgatcttcttggtttcggtagcataccaattctccaccttctggaac
ttgaattcgttcaccttccttctttgcgagaactggtggcaggctcatcc
ggcggcaaatcggggtttcat
>AW057358
cgcaacgccactttaatctccttcataagaccgtcttgccaggaagaatg
gttcgattcaattgtcttgattccgttcgccagttctcgcattctctcac
aagccacttcaaattccgtggtactgttatccaaacgagtcttgttaact
tcagtctcgttgttcgcatatttatccgccgcactgtccatgtcgagccg
agtcctattcaaattggcgatactgtccgcgtgaagntttcccctcgttt
tggtagaatgacttgtatttttcacaaatcgcgaggacccctttcacggc
atcagcttcggcacccattctagcatcaacagcatccataaatggtttca
cattgatcttgtcaccgagacgcgagtaattctcaagggtgccagagaaa
ctggccttcttctgccacttgctaatatcttccaagtttgtcatgctctt
gtgaaggtccttgacacgtggcgtcagatttttgaagtagcccatcgcat
cgtccacttctgcgggaagagttgtcgccttggcacgtccagtcttttcc
ttaactntctgcttcanacgtccaaacat
>AW057359
aaaattaaatcaatatggttgacgagaatgagaacgacgagttgctcgta
tctgacggaggcgaaatgattgacgtcgagacttgatgatttccatgggt
gatacgtcaggtgtggcgatccagcgaaggcgacatagtggacacgaagg
ctgggtagaggaacggtgccacctttgaacacatgttttgcatccaataa
cgttcatgcatcgattacagccttgtgggtcaactggagtctcaaaacag
acggtacactctccccgtgcgccgatcggtgagccaactcgagctgcatg
atttgaggtgccttgtgatgtgcttggctgattcgatggagcagcttcaa
aagagtctgacaatttgacttcagattcgtcatcatcaagggttatggca
ttttcattgattccttgtgacggcaagtttcttgcaagaacggccggtaa
aacgtccacgtggcctccataaccttctcttccagctgcggctctgattg
ttggctgattntgtgcattcctgggagttgttgtccttgtgacccagtcg
ctgcgctggtggatcncgggccacagcagccacctgtactccagtacctt
ctcttccagctggagctatggntcctgtcagatnntgtgntgagcttgag
gatatctcgatcacttgatatgacagtntcaggtgtggaggattttgaga
agcgctggttggctggatttgcccccagtc
>AW057360
taaattaaagagatgaaagctctttctcaatagccttcgagatcaaatcc
atcaagttaattccactaatcggaagctgattcgcatgaaccttgcacgg
ctgtttaaccgaaatcaacgagtttgaatgctcaatcgggcccaaattct
tcttcttgttcttcgggcatccttccttatgaaccttcaccacttttcca
atctcttcaacatcatcaaaaactacagtaggaatcggagctgtgccaag
tttgaattgatgttccggagtaaaatgatcgtgagtgagacttccagttg
atgtgacaaggtcttcaagtgaagaagcttccgaagacacaatgtatggc
ttgcggcactcaattcccattttcggctctcttttggtgcgatccagaat
atcagagactcgtcttttctccacattcaacaaccatctcgatgcatcaa
acttctcaatattatcctccatctctcgaacatcttcataaacattcgaa
tgctctctcatcaacaattcacatttcttctgagcttcttcagatttcag
cgtcaattgagctcttccactgatcacctccttcaatcgattctcgaatt
cagcttcctgatgtccaatctctttacacattgncttctcgntgaagctt
ggtcgaacaaattatctcgtgagaanggacttcagttgacaagttcttgc
gtggaatgcttcacccgtgatcatatcaactcccatgggctcttcgatag
aa
>AW057361
gacttcaagattgatgtcgaatcgattgtttaggcagccaccaatgggac
aaccatcatctcacgatgctccgcttggttagcaaatgcctcatgaggat
tagtagagccgttggcattggcagtcaagagcacaagtttgtcagttttc
tgctctccattcaatctcaacacatcaatcttaacggaagaacgtggctc
agcaaatccataaaccggattgacacggtaaagggagttatccgagcact
tgatcttataagctttacgttcatttgaagtattcttcaattcaatttga
ttgactccgccaagtgtctggtattgaagtttagcaggagccacattcat
ttccttggagtgcttgatcgaattgacttcttcagcaaggctatacccaa
cttggcttccagttgtttgttgcgtttttggaataagagcaactttgccg
ctctttcccgatttctccattttcttctgggcatccgaatcaagtcgacg
attcttacggctcttcgaactctttgagctcttacgagaagatntcgatg
agttagattgcttatcagaaacaccagtagcagcgggaacagttganact
tgagaacccagagtggtagcagtcttgactttcttcgatttcgaagactt
tgatgattnccctccacgcttgctgctttcctttncagattttnccgacg
ttcccttcttactagacttcnacgatctcctggagtgcctagcttcga
>AW057362
caaatgggggtttttctttgttctggatatctcaaccgacatgattctag
aagagaatgctctgtgcaatcatcgcagtcacttgataaggatcgcagtt
tgatgacggacgacgatcctccagatatccttttctctccgcagccacct
gtctcggaatacggattgagcatccacgattggcgactccccatgagaat
ttgtcagccgaacttgtctcatgacgtcctgtcaaacgacgaagattgtc
ttctccaccatgtggatcgtacaccttcatcgcctccaaatgtgtccgct
tgagtcctgtcatggcggcttcaatcgcagcaattccacctggagcacgc
atttcggcagtcgagaagttggtgtggcatccggctccgttccagtctcc
catggtgacctttggtttgggatcaagggatacgcagacaccgaa
>AW057363
atttgaatctcttctggctgctccgttgtttcagcgccgcttggagatgt
acttggaggctctggtgaatccgttggctctgcagtggacgctgttgatg
gttgaacggtagtagtcgtggaagcttcagaacaaattccagccaattcg
cacaacgctggatacattgctgagctcattttgtagtaccacgggtattt
ccggcttccaatagttgctgctaaatcgaatccaaccatccaaactctgc
cggaatcattttttgtgagaggtcccagatcgaatcccttttcggtattt
ggaacagttccgtatagaatatccggactaacaccggcgccgacattcac
ttttcgatgcttccattccgaattgtttgtacatccataagcgtcaatgg
catctcctttggcaagtttgattgattcatcagctagacatggataactt
gagttgccttccaaattctcatcaagctccaaaatcattgggaaggagta
cactctnttttgcaccaatgttgatttgcaaaagttcagaatatatgctc
tggcaaaattcatcactttcggngagcanttctccttttgagaaaggcac
ggctcaatcacatccgagagcttgtttaccgaactttccagtgctttatg
ctgtcatcacaatcaatcgaatctncgctattnttccaagctgatttgtg
gagaaaagccgnngagagtgatcagtgtcgagagatatataa
>AW057364
aatatctagttcatctgagagctggtggctccttcaccagtagttccgct
tgtcgaatcagcctctgtcttcttggtctttgacttggagctctttgact
ttgaagtatcgtctcccttctttccacctttctttcctttctttccatca
ctgncttttcccttttttcctcccttcttctttggcttgtacttgtcaaa
cacagacttcgaacggtagcagacgaagctcatgactgccaaatgacaaa
aataaaaccgcanatgaggaagctaatgagcacatagagccatggttgac
tgacatcacgggcgattttcttcagcggatggtagtagcagacgtgttta
ttgatattaacatacacgcaaacagttcccgacttgcagtctttgttaga
agagcatgccgatcccttcacctcagtacgttcttctccagttaagtgcc
ttttgcccaaaataccaacgcgattagtgtcaggatcgcaaaatgcatag
gtgctgaattgagatgggataggtttgttagcatcacacggataattagt
caagtatggatatggggcccaaggtaggcgtcgctgactcagtaccattt
ccagatggtgcaattgtcagggtaagtgatgggcagcantgaccaaagcg
acagactccggccctcgtcttgcacactccagaacttttcttttcttcaa
cacatctacacactttggctcattataccatgtgtttgatagtcc
>AW057365
agagagaaaaagagaaaaaagtccagaattcgagaagttgagagaaaaat
cgaagcccatctagttttgtggaatcggtgtcaaattggggcgagcttgt
gagagcacgtggtccacgaacgagcaggtgacgtcacacattagacggcg
cgaacggcagtatctggcagcaaactcacagtaggaggcaaaaatgatcg
catccattctagtgaacatatttggcaattgacataaagaattgctcaac
aacgacggcccagtagcgagcccacggatagctgagcctaacgacgagag
caatgacacgtggaatcagaatttccaagttgcaaaccaccaagtagcac
agaatgatgccgaacacgagcttggtgaatctcggattgttgcggaaaaa
gttgccaatcgacgtggcacagttgccgagagtttgaagacgattct
>AW057366
gatcattaaatgaacttttggatttcatcgtagatggcaagaacgagtgc
tccaccagttccacggaatacatttgacagggctcccttgaacatggcgg
acattccttcgtttttgatgatcttgacggcacaatccaaagtattcttg
tagagaacatctttgcgaccagactgcatcatcatgcgacgacgaacagt
atcccatggataggagaggattccagatccaacagtaaccacttgagcaa
tagcccaggcagcgaagaagttgagtttcttgccatcagcagtgaacacc
atcttggcagtgtcgaacattccgaagtaagcggcgcggtagatgatgat
accttgtaccgagacaaagaaacctctgtagagtccgattggtccatccg
actttgcgatcttgacgagacaatcggccaggcctttgaattcacgttca
ttagcttttccgacatcagcagccaaacgggtacgagcaaaatccaatgg
gtagacaaaacagagcgaagtggctccagctgctccaccagaagctagat
ttccggcgaagaacttccagaaatccttcttcttatccaatcccttttgg
aaaatgntnttgtagtatccttgaaagcgaagtcagcgcctgggtcggaa
gtatcggatgacgtagcaagtttctctcagagag
>AW057367
acagagatcaatcatttttcaacactatgtgcacgatccttccacaaatc
attgtactggcgaccagtgtcaatcatggcatccgatactgtctctccaa
gctcacgaatcgatgaatcgacatctccggatgaagattttctagctctt
ttcgaaaaagaagatccctcatcagtgaaacgaacacttttcgagttaac
ggaagaaatagattcacgacgcaaaggacgttttcgtgggctattgatac
ctggagtatgcttcttcatcggtgttggtggtggaacaggtttgaatctt
ccacgaagatctggatgagcattcatcagagagagagcaacaaatggaat
tccgtcaaccaaaagctcaaaagcttcaaattctgcatcttgtgcgtatt
cagcaacaaatccacgaacttgattacgagcagctggattcttgataatt
gcaaacttttgaactggaggaatatgctccttctttggtaaagattttct
cgaaagagatcttctttntttcatcggagatttcttcagaatgctnttac
gactggaacctgntgattttgtggatctattgcgtcgactctcaatttca
gcttngcaaagtcttcttctagcactttgcgaaatcttgntacggttccc
cagaagtggttccaaattttcgatctttttgcttgaaatagatctttcag
atccctgtcccgagaatccagacgacgagctacgaggaagcttgctttta
>AW057368
ttttaggggtttcacagcagtcttcagagcctcggctgattgttgtgggt
cggacatggcgcgatgggagaggatggcttcatcacggaatttcagaata
gcatcacaatgctttggtctctgatcgaaaatcccgtttttgatgaaatc
catcagtttctggcgacaatcatttctccaattttgagcgttgacagtga
ttcgctcggcttcctcagtgcgatctttgctctgttgggtcagcgcatcg
tcataggctttcaggccatcccagtacactctcctcaaccgtgcgtactc
ccaatagtcttctccaatgaattttgtcagcggcttcaaattgtccaact
gcttgcgaacacgagattcgcgttctgcatccaacagagaaagcgtacta
atcgctggctccaagctctcatactttgtcttatcccgtcccttatttgc
aattgcctcataagttttgagatattttccagcataacgataatttggtt
cagttttgaagtgagtcaccaaatcctttgaaatttctggactctcgacg
agcatgaacaatagtgcctgatggagcttgtcggagcatgtctttgtagc
ttcaaccttcccgcacatcttctttacgtcttctgtcatcttgatttttg
cgcgtttcctcttcanaatcgatgcnnatagcccatgatttggatgatca
gc
>AW057369
tatatctgtttgtccatttgctttcaatctctcggctaaatccctccgta
cgcaacattttcagtccattcaaattgttgacgctcgtacggtgacgggg
aaattccgattccagtggccacatctttcgaggatcccgagttgaaatca
gtgtattgagacaagttgcgcatgttgcgaagttctgcgagagattcggg
cgagtagtcacggaggacaagtgagtttgtaagcatctccttgagctcga
attctccatcagtctgctccaactcgtacattgattcggngctcaacatt
ttcttattaagtgttccgtcaggagacgtggatgggatagctggagcagt
gaaagctttgatcggaaatgagatgttcatgttctgaatatcagcaattg
agtcagaagagaaggcgttcttgttaacagtcacatcatttggtggattg
atgctaaccattggtgcctgttctccatccatatcataatttccaaatgg
atccttcaagttcttgatatccataatagtcagcaaattttcttcgnttt
attctccatcttgtgtgttctccttcagaatccataatatgttcaaagta
tttgagatggagtggggaagtttggatgatggngaatatnatgttccagg
cngaacgagtgtcaactttagatgaagcctttgaatgcaataaccttccg
gnactacataaccgactttgagacttttccgaaagtccgttgctggatac
tagcca
>AW057370
tcgattccatttccataaattgtctcacgatcatcacattttggcgtgct
ggcagtgggcaagtctgaatctcacgggccatgtagagcttgaagaccgg
aacttcagcagcggagtcttcgaaatgctgaaaatattgaattttcaacc
agtccatattaattttccaaatctcaacatccatcgtgacgatggtgtag
acaaataaaaagatgatgcattgggcaatgaatccagccattctaattga
cttcacacggattgcatctgcatcttcttcaagaatatcagccactttga
tgctctgagctggagcaaaagcagatgtcgtggtggtgttaatgtagact
tcaagggacgacatcactggagcaagcacagatgttgatcttggagccgt
gatgtttgagtagaactgcactgcctt
>AW057371
ataagctttctgcttgcaaaggatttttcttctcgcgagcctcggatttc
gctctctacgactgcagcgagaagtacggtgtccagatagctgatccatt
tgatgaagatgctctccgactattcaacgatcttccaccaaaacaaataa
ttgcgccagactcgaaattgttccgttcaagtcccacaaaagccggaaaa
tgttccgaccacgcgatctcgttctgccaattatccgaaaaggatatgcg
agttcttcaattcggaatgtcgctgaaagtattcggacgcggaggtcttg
acacttcttcacatgagactaccgatttttgatcttctccagcagcttct
ccagaatctatccaatagtatttctatcatgggacgtgtatttctcttct
tgccgggtgtaaatttaattatttttgaaattaattatttttccataaaa
ta
>AW057372
ttttcaaataaaattttattccgttcaattcaaatgggggtatttttttg
ttctggatatcttaaccgacatgattctagaagagaatgctctgtgcaat
catcgcagtcacttgataaggatcgcagtttgatgacggacgacgatcct
ccagatatccttttctctccgcagccacctgtctcggaatacggattgag
catccacgattggcgactccccatgagaatttgtcagccgaacttgtctc
atgacgtcctgtcaaacgacgaagattgtcttctcaccatgtggatcgta
caccttcatcgcctccaaatgtgtccgcttgagtcctgtcatggcggctt
caatcgcagcaattccacctggagcacgcatttcggcagtcgagaagttg
gtgtggcatccggctccgttccagtctcccatggtgacctttggtttggg
atcaagggatacgcagacaccgaattgttcagcaactctgtgcagaatgt
atctcgacatccacaactgatctcccatatcgattccttcgcaggttcca
atttggaattcccattgtcctggagtcacttcggcatttgttccaaaaat
gttgagtccggcgtgaagacaagcccgggtatgtgtctcgacgacttctc
tcccgaacgcacgatcagctcctacgctacagtagtacttntccctgtgg
atcccgggaatccgtgtctcggccatccgagtggntgctcatctctgtcg
acgatcagatattcctggctcatttcgaacacggggcgttgtcacgg
>AW057373
agacagttcaatcaatggggaaatacatgtagaaattaatgcgatccaga
tatagacgaagcagcggaagaagacgactttccattcggtttggccagcg
aggaggatgcagaagtcgaaaatgagctctcagagctgctggaatccaag
gaaactcccgatttaccaggcgcaacttttgagatcatcgagtggaagtt
cttgttagcagcagcatctctgaaaacacgcattttctcagccaacagct
tagcttcctccatgacctttggattggaagatttcaggccataaaggcct
tcaattgctccacggaaggctttctcgatagcttgctcatcagtcgcatg
gggctccaacgcatcttgctccttcttttccgtacgatgcaccatgtcag
taacttgatccatcaaatctttcatgtcaacatccttctcatacttgtag
aatgccttgttaacttgaatcacagaatccttcagaatattgaccttctt
ttccaacagctggacgtccttgaccatcagtgtagaggccaacgcctgat
cagcagttgccttggccttctccattntccgattcatccatttcgaattn
tcagcgcgttccttgtcaatntggtgatccaattcatgcatcattccacg
gnantgatcgaaatcctcactcatcngaatttgcatgtcacggagctcca
aaacagtgtgacgaccgactaggtcaccttcacgaaatcgatcgatcgt
>AW057374
ccgagcgggtttgtgttgaagtcatcgacggtgaaaaaatcaacttcctc
atttgatggtggtgtgacgccttttctggggacatttccaactgctggaa
cacttggcttcttctttctcttttcgggctcccaatgatatgggtcggac
cacttgtacttcgcgcttttcatggcatcattcaagagattgaaaagctt
ttcgtagtcggggcggtgatagaattgcgtggcccgaacgatcttgacaa
actccagcatttgaattgggctttttgcaaagagattctggtcggcgacg
tgtcgcttcatttccccgatttcgaccttatcatccaaatcagaccaagc
cagctggcatctcaactccgcgagcatgtagatcaaagcccacaggtcat
cgactctcccctgctcgaaacgatcgtgcatagctaccgagcaataacgg
gaggtgccacggaagagagccttctcacgtgggcgacgcatcttttttcc
gtcctccttatccgtgatgtactggcgtgccaagccaaagtccagcacga
tgaagtagcgttcgtcaggggagcctttatttcccaaatgccacgttgca
gggctcaaagtacggtggataaacccaatatcatgaatctgcttgatgcc
cgacaaaagggcaatcccgatgcgcaaattggtaagacacgttgaaaaat
tggtcggttctttcatagtgattcaggctttcgccggagaggtca
>AW057375
tggacaataagacggttgaaggatggttctcgttcaatgtcattgtgatc
aaacaagtcggcccacaggggtatgaatggtacatcatcactcgcaactg
tatcggaggatcaccacactgcgaatgcgagaactgt
>AW057376
ttgtccatttgctttcaatctctcggctaaatccctccgtacgcaacatt
ttcagtccattcaaattgttgacgctcgtacggtgacggggaaattccga
ttccagtggccacatctttcgaggatcccgagttgaaatcagtgtattga
gacaagttgcgcatgttgcgaagttctgcgagagattcgggcgagtagtc
acggaggacaagtgagtttgtaagcatctccttgagctcgaattctccat
cagtctgctccaactcgtacattgattcggggctcaacattttcttatta
agtgttccgtcaggagacgtggatgggatagctggagcagtgaaagcttt
gatcggaaatgagatgttcatgttctgaatatcagcaattgagtcagaag
agaaggcgttcttgttaacagtcacatcatttggtggattgatgctaacc
attggtgcctgttctccatccatatcataatttccaaatggatccttgca
gttcttgatatccataatagtcagcaaattttcttcgttttattctccat
cttgtgttgtctcttcagaaatccatatatgttcaaagtattgagatgga
gtggtgaggttcgatgatgggaatatatgttcagccgacgagtgtcactt
>AW057377
ttcagctcaagtatctagtaatagtccagttatttttgctcctcgtcttt
tttctcttcatctcccaaaatgtcactggcttgacgagcaattgttttag
tatgactagtagtatttgcacttgtgagattccattctgagctcttttcc
cacaacttttgtcctttggatgtgaaaccaagaatttcaacttctggatg
tctctcagcaagaagcatgaaattaacattaagcacaagtcgtttcttgt
caatgagcatatccaattgaacactctcagggaaagcacgttgtccataa
gaagttgaaggaactgtttcagaattcactttgattggtgtcatttccaa
agtttgatgggtttctttgactgcactcaaagtcacaatattcgactcat
ccgtctgattgaatgttctcttcaaagttggagttgcaggagatgaagct
ctcgatctggctctcaatctctcactcagattcacttcttcctctttcac
agtctcttctttcttctcactaatctcangtggctctccatcttcttggc
gaactttacgaatgactatagtctccttcacgcgaagtgttccttttcga
gattctgagcagatctgtaccagtagagctgcacacgttcttatgcaatc
tctacagacataaaggcgaat
>AW057378
tttatagtcacatttttattcaaaaaattcatagggctcaacatgatgat
tgatgagacacgcgtgctgatgagccgcattcattgctccgagcattgga
ttcattccggtcaagtaggtgtctggactattttcgagtggcgtgaagaa
ggtttcggggagctccaagatttcatagctccctccagtgacgggatcca
gcaaattcggcgggttatacttattgaagttgaccggcaacaccttcgtc
gccgggatgtttgccttgatagatggatcatagacagcagcatccgaatc
aatcaatagaccacctcgatccttcttacggcatctgcacactttgaaaa
gtgagttggaaggatccatcgagtgagatgacgaaaattccgcgcttctc
tcgattgccgtctcgattgcagcggtaggagcgtcgattgtcggtggagt
agccaacgtctcaagaagcggagcttggagtggcgatggccgtggtttcg
gagcgatcggcgagccatatgcaactctagacatcgacaacggctccgac
atgctatgctccgcggagcccctctcaacgcgctcaggcttatggtctgg
agcctgcgccggcttgaacttcgagtcttgcagctcgcgacacgagttgg
gcattgctcaattcgctggcgtatcgatggactttggtttcaacgagctt
ggttgcacagggaaattggtcaactgcgatgtctacagttctgcg
>AW057379
aacctaaaaatcttcatctagttgaataagggcgaaagtttatagtatta
gacggactcaccgggatgaccatcagacggattatcaagtacaacacgcg
aaagctctgtctcattcttctcttcttttggtggacggagcatcgaatgc
tcacggcactgagttccatcaagacgagtaatttgttgcaagagatgaat
aacctttccacgataagtatccactgatgcaattggattgaaatcgaggt
aaacactattgggttgtggaagttcaaccaattcatccataatgctccag
ttatccaacttatttcctcttgcccaaaagtctgtaagtgtcttcaattg
atggatattctcgaccttctcaagacgattctgattgaaatccagaattt
caagaggaagatgctcatcgattccacaaacgtacttgatgccattctga
gccagataaatctctttcaagttgtgaagtcccgaaatgttatcaactac
agtaatcgcattggctggaagactgagaactgtgagcttcttcaaatgat
caacattatcaataagacgaatctgattagcgccaaggcacaatctatcg
agtttcagattgttgtcgagattctcgatggtcgcaattctattgtcacc
caattcgagatattgcagctcagtcaacgtatccaaacactcgattttag
tgatatgttatgaacgacaagagagcctcagcttgtcactcgtcaaat
>AW057381
taccaaaaaactcaaaacaccgtcagcgacttgttgcatgcagaaataaa
tcagaaatgattgccacttatccctttgcgttgagatgttgtggcgcctt
gtaagccaactcgtgtacttctacattgtacagcttgacaacgattccgg
aacgagcagccgtgagccaaatagctgaagctgagagtccgatttcgcaa
ccaatgacaacggtgtttcagactttgattcccttggcggcgaaggctcg
atcacaatcagccttcttcttgaatcccttggcagcacaaacttctacga
ttgtgaagagcaattgatcctt
>AW057382
cagcttgtcccatttttcttcttggtgtctccaaacaatcttcttctttc
tccgattcaattgactttctactgattaattgtggcattgagttgtcaaa
tgaacgacttgttgccataactctcttatccgaaattttgacgacgactg
tagtgagacgaatgaagacggccatactggcaagagcagtagcaatcatt
gaaatcactgcacacaccagagtaactccattaacagcatgacagatatc
cgaattaagtgttccagttgagggagttttcagatattgacatggagaat
cgaatgatttaatgaagagtgcaattgtatgtgcaagatggaaagctgag
aatacaaatgcatgcatcatgaagagaagagtgaagacaccaaatgcacg
acgagttgagcagagtccaatgagtgacatgagtgccaatgcggtcatca
acatatctctagtatccagagcagtctcatcgagtaccgtttatgatccg
gcaactctgtatgcagttgagtagagaccactgactaggaagatgacagt
gatgacagcacatagtggtgcttcacttgacgactagcatcccat
>AW057383
tatcatccgtagttgattgatatggtgtgtacttatccgtcgagcttgta
tccagccttggccttacggcagagaacaatggtgttatcagcgcagttct
tggcagttgcagaatgctcctttccttggtatccataaccatacttctcg
ttacggacatccaccttggcaagaatctgctttcctccagcaacgttaac
aactccaacggagatatctcccttgtggttgttgacatgaactggatgcc
aagctttgtctccaaactgagcagcctccgggaatgggatccatccatag
tcaaaaccacgaacactgtccggaagatagatgagaagctggatagatcc
aacattcttgcaatactcgttgttgaaccacgagaagttggcagccacct
ttcctccttcattccagacacgacccataacaggttcaccttgcatgtac
cagagagcaacatattggtctggattgactcctggaaggtgtccagagtc
ttgtcaagagccttgacangttggcgagtcggcccatgatctccctcacg
aatgtccatccattcgtctctctccgacacgtgcaactgccttttgtggt
gtggagcagctccgcacacagcacatggggcaaatggtgtgtcctcccga
tgcagnttgcgcgttgatgatgtaccatctcgtttgagctgtgggcccga
gcttgcttaatcacccttc
>AW057384
catgaactctatctggacatctctcnttgagcaattctcgctgtttccgt
tattgccctcaacgagaatgaaaacaattatctgcaagagttgctcgatg
ctggaatttcccaggaaaccgctaacaagcttgtagacatcacagccagc
cacaacaacgatggagaaatttctgagaaatcaggaaaaactattttcca
agaaatcatttctgagactgatgcagctatcaaacaagcaccagctaatg
atcagcaagcctacaaggccttcgttgaaagcaaggcagctgaattcggt
caaccagacgagatttccattcaagttgaatctgattccgaataattttc
taaaactcaagtatcgtctgtattacaa
>AW057385
gagatggaattgcctttcgccgaccatcggcggagcctctgcgctttgtt
atgaaggacagagccaaccagctagacgcactcaacaaccgatgggccag
aacccccaggcaggtgcaagttacccacccaacatgaaccctgtgacaaa
cggaccacgagcttggacactgaagcctggtggatacatacaatgggccc
aggatcccggtagcatcaaatcacctaatccaccacgaggactcgtctac
tatcagcctgagaactatacatacaagcctggaaaaggtggaaaatatat
gcatgcgtgccctatcctccccaacgcaaacgaacgactctcgggtcaaa
gcgaccagtacaccgtatccgacagaatcacggtacactggagcaagact
gcggcatacagtctaagagtctatgtgctctatccggtgcagacagagag
cgaggaggacatcttcctatccggcactattgctcaagtcatcgcgaacc
tttatgacctcaaggaattacgaggaaacaagccgccaggtgtgagagca
cacagaccgatgctgatgccgcaatagcgtagngcggatccacttagaag
taggaagcgc
>AW057386
ggataaacttgacatccattttgttcctctccagctgatgctactgatgc
tcaagccgctttcgctgcagtgactcctgctggaactgtcaccattccaa
tgtcggccaccgcctaa
>AW057387
ttgaatgtgaataacgatattatctctgattattccaccagtacttatga
gccaactagcttcactccaacttctggctccttcacccacacttcaacta
gcggtgaaaatcttcatacaatgccaaatgagttgcagcctttgccactg
tgtgatatttcatcggaatacgagtcgaaaaccgagccggacactggaaa
acaccaggttgacgtgattgccgaggcaaatgggatggagatgaagctca
atatgactggaatgcttaaagggcttaanttgaact
>AW057388
aattccaccgcccgttttttggtctctcattgcggagagcagaattcaaa
gagccgtacaaaagaagacacaccgacgccaacaattctgatatcatgag
ttggaattgccttttgccgattttcgtcggattctttgtgcttttttatg
aaggacagtgccaaccagctagatggactcaacaaccgggtggccagaac
ccccagccaggtgcaagtttcccacccaacatgaaccctgtcacaaacgg
accaggatcttggacacaaaagcctggaggatacaacaatgggccaggat
ccggaagtttcaaatcaactaagccaccacgaggactcgtctactatcag
cccaagaactatccatacaagcctggaaaaggtggaaaatatatgcatgc
ggaccctatcctccccaacgcaaatgaacgactttcggctcaaagcgacc
agtacaccgtatccgacggaattacgggagactggagcaagattgtggca
aacagtaaaggattctatgtgcttcatccggtgcagacaaaaagcgagga
ggacattttcgatccgtacactattggtcaagtcattggggtacctttat
gaggttncaagaatttggaggaaaagannagccggcaagtggaaaagtac
accgattgagctgaatgggcaataaagattccggaccatttgaagaaaga
aaagccg
>AW057389
aattccgaacaactcagatgctgccatgatagaagacgataaaagtaaac
gagagaatgttccattgacagttgtctactcgaatccatcaatttctgta
tcaaagaacttttccactacgccacttgctgagaatcaagctggagcatt
tgataagctggatgatgatgaatttgagaagatgacgtcagatgttgacg
aaaaggagattctgaagttggcgccacgtcttcttaaagtagccaaaaag
cacgcggcaatcgagaaatgtctgacacccagagagaacgaagtacttgc
caagttcttctcaggaaagcagaagctggattcaaatgtattggctgtct
tggattctgcattggataagattattgattatttgcaaaagaataattgt
gcggttgatgaggagacaaaggctgttatgaagaagagggataagctgaa
agcagcaatgatgaaagagttcttggtgtcaccccaatatcttccaaaaa
catggactgcaaaattcaatgaatggaaatctgaagccgaaaagcaaaag
aatggaatcaactggttccgtgttttcttctcgtatccaaagcacaaatc
atttgaagatggaccagaagacacttttggaaaatttccgccgtagnaaa
tcgtggtattctgantgggacttattctgggacccggagattgtaaaa
>AW057390
acgaactgatctctgtgatcatatcataataatggctacaatttgtgagc
ttgtccagttgccagttggaagtgaatgtggaaaatggacaattttgaag
aaactcggagaaggcgcatttggtgcagtctatcttgtcagccaaaaaga
aaaacccaaggtggaatacgcgttgaaagttgaagcagagtcggatccat
tgggcttgctgaaaatggaagtggctgtgcttttggaagtgaaaaagcag
aaaatcgttggacgccactttttggagttggctgacagaggaaacctgcc
acaaaagttcaattacatggtgatgacgttggttggaaaaagtttgcagg
atctccgcaaaactgctccattcaacaaattctcaatgggaaccgccatt
tctgtagccagacaatcattggaagctgttgagga
>AW057391
aattccctctgaacaacctcaaacgaaagacaacgatggcggacaagtcg
gcttacatgggcgctggtggctatggatcgggctacatgggatccaatgc
ttcttcgtcaggttatgcccgcgaagactatgcacaaggaggcaatggtg
gtggtggacagcagcagaaccaaggatccggaggaaacaccaacccaggt
gggcaggtcttcaaggcccgtactgaccagtcctgttaccttggatcata
agaaaatcgacacaagaagagccagtcgccc
>AW057392
tcaccgccgaacagctcaccgatcctccacaaatcccgacggccttgtcc
aactcggtcaacactgcgattggtggaactccatccgactttgagtcgaa
ctccgggctatctgacacctcggcaggatcgggccgcgccaactcggccg
tttccgatacgaccacagcaatgtcggcgaacgtctccggagattattat
gaatgatcttcgaaaaggaagcctgtttggccgacagatagggagtctgg
ctaccacggatggagggccccagagtgttactatcattactttctcgaac
actactaacatgtcaactgcttcccagcccaccagcctcgatgacaaatc
gcaaaagtcgcagaaaactggatcaatgaagactggaattccgatgagat
cgcctggatcttccatggctggcacaggtgcgatgtctcgtaaaaagtcg
tcgcaaaagcagatggatgctctgaagatagagcaagtgccggctgctcc
cgatctctcaatataattcaatacatctaagatatcgaagagtcgtaaag
gc
>AW057393
tcgatcaaatcaattcgaaaaaatcatgccgtctttaaaaggaggatgat
gtaatgaaaaatgtaactttcgctgaaggcaaaaaatttggtgactggaa
aatcggcaaaacgatcgatgaaggaggatttgggaaggtttacattgcaa
catcaatcagcgatccaaagaaagtggctgctttgaaagccgaatcaaat
gaaatcgaaggaggatctgcaatcaaattggaggcaatgatcctaaacaa
actgaatgccaatggacccgttccccacattccagtcgtccactaatgcg
caaaacgaaagctctactgctacatggtgatgacgttgttggggagaaat
ctacgaaaactgaaatccacaaatctcgtagtcaacaatggattctcccg
tggaacgtggagccgaatcggaattcaatgcctgtatgcattgaaatatg
tgcatgacaatggatttattcatcgagatgtgaagccacaaaacttcttg
ctaggaaatgagacggatagtgaaagagcaagaattgttcatatcttgga
ctttggtcttgcgagacctttcgctgtttttcatgcccgagagaataagt
ggatcgcacgtagagctcgtggaactgcagagnttcgtggaactctccgt
tacacgtctccgaatgttcatctncgaaagtaacaaggacgggttgacga
tgtatggtccctgctatatgtcatcattgagctcaacggtgataagctct
tccatggcaaaccgattctcaacgtcgacgtgtggagcaaatgaagctga
acttgccggcgaaggtngtctgtcaatatgccagcctgtttgataagtga
tgcct
>AW057394
agacaagtacgagtctcaaaactttctgtttcgagtggaaggagccatgt
tctgcgcgggaattatcgttgctatgattatgctgttcgtcatcattatc
tacggaataatcacttcaagtcaaactggaggacagctcaacagatacat
ggccccactattc
>AW057395
tggcctgtgctaaacccgcttccaaccacctattcaattcctgtacgatc
atccagactcctcatttcgaatgatggaattctagaagattgttgcttta
aagtctgaagaggaaaagctcccatcactattcgaaaatgttgagggact
gttgtctgtcccatctttaacttttggtacgtgggatgatgacaccctgt
ctggtgtcacatctgttaatctagataagtctgatgaacaactctgcgag
cgtgatgatgactacaccactgattggagtgctaat
>AW057396
ttgtctgcaatggctgccgcccagaatacgctgccaaagcgaatgaagaa
gaagatgcaggtgtagagaatggctcatgccacagcttgcaaggttgcaa
agagagaggctcgcgtcgctgaggaagcatctggaaaatcaactggtgga
tctactcgcggagccaagtgatagccgagccacaacacatg
>AW057397
agattcaaacgccagagttggaagttccgtcaatcaacttggattcaagg
gacatgggggaggacttggtccaagaatcattatggctggaactttgact
gctcttcaatggttcatctatgattcgatcaaggttgcaatgaatcttcc
tcgtccaccaccaccacaaatgccagaatctttgaagaagaagcttggaa
ttccgggaaccactgaagttgctccagtcgctgaaaaagttgctgctcca
gagaaaaactcaaaatgtgagaaacccagaaag
>AW057399
tctatcgaatttattcaagaaaaagttcggaactttatgataatattgca
tatcttcatcatccaagtggtgtcaccgttgtcgttcttcgaaatattcc
tgaaagtgaagttgtcgaagtggattttggaacgacgaagaagcacggcg
cagatcgttcaacaaatcaagtttctggaaaaggaaaaaaaggagctctt
attctacaacccgactcaaaattgtgtacattcaaatgcaaagatggttc
agagcctgtcctgagagcaggtcgtcgtggaactcttgttgagatgaacg
atcgcctgaaaactacaccagattttattagaacagcacctgataatcag
ggatttatcgcgattatcacctacggagccggagtacgtgaaactgaagg
aatgggagatgaccttcctccgaaaagacttttctta
>AW057401
taaatcatgttcaagtacgttctcctcgtcaatancttcatcgccctcat
cgagatggcttcagccgatttttcgtgctatttctcggattccatctgca
aatccatcacctgcagaaactgcaaagtcgccacctgtatcaccggagac
tgcgtctgcaccctttgctaattttttgaataatttttttatcttttga
>AW057402
tctgaagcncttcatcagatcgtctaaataactgccagttgaacaattag
ttgatgactccgggatgctcatttcgcgttgcgtcgaga
>AW057403
agctatggcttcctcgttcgacaaccaaatggatcaggatggaatgtgct
ccgtgtactctgctcagccatcggagacaaattgctccatcaatgaggtg
cttgccaaagaaattatcgctgtcaatgagacgccagatgatcaagctga
ttcttcgatctacccaatcccaaaatcagaaacaaatgtgtcagctagcg
aagggttccagccatgtcaagatatcaatcaattcaatttgtccggttac
tctgctccaaaatccgagaccccagtgaccatgaatgagaagttcgagcg
gtgcanagacttgatgaacgttcttgactactctgtctactcaatgccac
catcagaagcaaatgttacaatgaatgttgcaagcttctcggagtacact
gcccttgcctcggagaccaacgtcacaatggctgatgttctcaagaacgt
tgctcaggatttggcgtcagagcacactgcaaaatcagctcatccaacat
tcgacaccaccgcctacgtagagcgccttcaagccgagnctcggattccg
gatagcaaagtgattggattggagtgcagcaatttttcgaatgcgaagat
cattgattcaattgaatgccttcatcagttggacanattcaaaccaatcc
ngtggattcgatcagaatnctgattttggaaaaactgcccaatctgtgga
aagctacctnnctgcgtcatncaatgcagntcatncatcacagatctga
>AW057404
agcttccggtgttcgtcaggtctccaanctactcgattaaaatttatgga
gcaattcaacatgacttcggcatgtctgaagatgaatcagtccaatatcc
ttctccgatttctccatcctcggattcttcaagtgaaacaatcacccatg
tctcccctggatatctccttcaggaagtcttcttgcagagagcagtcatt
gaagaacaaataagattattgatggttttcatgaaattcagaagctcaa
>AW057405
ctatccgacagcgtcttttgatggagcagagtctgtcgatatttctgtgg
actaaggaaaaagtccagtgagcacacacttgtcgttggcatcaaatcca
actgaattcaagttcatggatgaaattgcacttttgaagcgtggccgcat
ctacaaagacgctccaaagcatccgtacaatcgtcgtggccagcaaccaa
tgatgaagaaaggtatattgtgtgacttgggtaatttcatcagcttcttg
cctgctagaagtccatctatcatgacgttgatgggcggagttccagaggc
cgaaaaagag
>AW057407
aaaaataagtctacaaatgatcaacatttatccaccatccggcgactacc
cagcttctggtggttcatcaactcactacattgtctccgaatcggaatct
cgtttggcattcaaagtcaagtcgtccaacaatgaatcgtatcgtgttcg
cccagtctatggattcgttgatgcgaagggaaaggctaagctcgaagtga
atcgtttggctggaccagcgaaggaggacaagcttgtcattcaatacgcc
gaagttccagctgatgagaccgatccgaangctcccgttgggggcttgtg
ctcaacaaggagaagtcgttgtcaagatggttgctagctaagaa
>AW057408
ctgccgaagtactgtctacaatacgaagattgattactctgatatgaaag
attccgttgagctacttcgtcaggtgcttgtctacaatccgagcagacga
ctctgtggaatagaatttctcacgaatccattcttcaccgtgttgttcaa
cgagaagactgtgcgtttcaataaaaagaagatccaatgcgtgtcagctg
tcgatctacaagctgtgaaatcgggagacgtcacactgacaaatgagtct
gtagagcactccgacctaatc
>AW057409
aggtgatgtctacaagaaggcagtgcagttctactcaaacatcacggctc
caagatcaacatctgtgcttgctccagtgatgtcgtcccttgaagtctac
attaacaccaccacgacatctgcttttgctccagctcagagcattcaagn
gggctgatattcttgaagaagatgcagatgcaatccgtgtgaagtcaatt
agaatggctggattcattgcccaatgcatcatctttttatttgtctacac
catcgtcacgatggatgttgagatttggaaaattaatatggactggttga
aaattcaatattttcagcatttcgaagactccgctgctgaagttccggtc
ttcaa
>AW057410
gactaccgtggcaaaagtcggatctaaaggttctaggatctacaaagaag
acgattcaagctgtccgaccaacggtccgcacccaaggagcggttactcg
ctctcaggctgctcttcgtggacatatggggatcactgactcttcgactt
cgaccagttcatctcgaattccgaaggagaagttgaaaaagaaggcatca
tctcgtagccgttcaagatcccgttcgaaatctactcgccgctcacgttc
aaagtctactcgctcacgttccagatcgagatctcgaagccggagtagca
ctcgtggaaagaagcgtgctccaaagaaggcagttaccacgaaagccgct
cgatctatctctcccgtcaaagtgaaaaagacagaagccatcaaatcgcg
tggaagcagcaaaaccgcccgtcgtgtgtctgcggctcacaagtaaataa
tcgtcgcttcttgatggc
>AW057411
tcgactaaccgtctccacttttcacttgcacaaatcttcatgcaaccaat
caacgtcatgctcgctgttcttctcgccttggcttcatttgctcaaggag
gcagatctgttgctccggctggtgcagtcactgaaccaacagttactcaa
gctgttccagaaggatcaggacttagttcagatgtcactgatcgtccaaa
catcgactccactgatgttgtatcaaatgcaacttcggtggaagatttgc
ttggaagttcaacaaatgcaaacaacactggtacattcaaactcttaaga
cctttgtatttgctccaatgatgattcttgctttggtgc
>AW057412
ttcgaagaagcccaacaactaaccccaacaataatgtcttgcgttcaaca
acaacgacgctccaccggactccgcatcgccgagcgattgaacaagtaca
tcactcttccaaatcgccacagcttcacagtggattccaaggatgtgttc
caacgtggtcaggtgctcagctacatccgatccaaagcacccttcctgct
cgaacatatctccgaggcaaaggagcgattgataaccgtgacgtcacgcg
gtttgatgatcatttacgagaatgacgaccacggatttggtgattgattt
gcgatcggccaggaatgttctgtgcactgctgatcgttcgaaaaagcagc
gtcatttccgctgtcacatcaaaatccgcatgcaacgtggcaatgttcac
ctctttgtcggccataatgatgttcacaagtggacgtgcgcgattatgag
agccgccggaaagtgcttgccgtctacagagccccgcgatgatggaagcc
ttaatgtcgcgatgatgacggcggtggaggattctggaatctttgaagag
atgtcgtctacatcgtcagcatcttatgactatgatgaggatgatgaagt
cgacgaggtgaagcccactgccatcgagcaaataccacttccccatgtct
ccgtnctgtctcttcgncagaaactcgagaaggagctcgtnctgaagcct
aatgagcaagtgctcgccgagcaacaacacacagccaactgcgatgagcc
aagctntgtctcttgaatcttctgcaccccaagagcagttntcagcgatg
aaactgtagtctgctggagcccacgaatgccagatagaggagagaatacg
aggcnca
>AW057413
ttatcgaaacttgtgaagaaggtctgcacattctgccgcaaagaaattga
tgccaaagcgaatgaagaagaagatgcaggtggagagaatggctcatgcc
agagcttgcaaggttgcaaagagagaggctcgcgtcgctgaggaagcatc
tggaaaatcaactggtggatctactcgcggagccaagtgatagccgagcc
acaacacat
>AW057414
tcccttctcgccatgtttgtggctcaggaagtcgccgaggaagctcttac
ggatccagaagcagctgaagcggataatgccaaaaacaatgcaacggatg
ctcccgctgatgctacaccgggatctggatcagatgctccagctgctcca
gaaggatctggcgccgaagccgaagccaccacagcgaagagttctactgc
tgcagtgaccatcattggagcaatcgccgtttttggagttgcccatctcc
tctgagcattcttatcacttc
>AW057415
ctattccctacctcgatcaaccatgggtttggacaaaggaaagcaacaaa
ctgccaagaaacctggtttcaactgcaaaccgtttgagttcgaaatctct
tcaacgaaatttcaaattcccaacgacaagccattgaagtacactttgaa
atgcactgctgatgagaaacaggatgttatcattcaagttcattcggttt
tcttcgaaattgttggtgcaagacgtaagcatggagtcacttctcaagag
tttcatgttcttgggaaaaaccgacgaattgacctttcgaaattggtctg
aaggatttgaccaatgtttcgtacgataatctcgagcatgcgcaacttgc
gtctgccgctggttttatcacgttcacacactacaagtcttctagagatg
atgattccgatgctttatggggtcccaacaagaacttgctcatcgtcatc
actgacggaatgggagaagtaggattctggaagaagaattgtcgttgaaa
ctgaaccgatgagagaagatgtgaagaagatttgttgtgaacttgaagag
a
BioPerl-1.007002/t/data/dbfa/4.fa000444000766000024     14022513155576321 16303 0ustar00cjfieldsstaff000000000000>AW057442
tgctgcatctaatggcaccactgatatggagcaggagcattatctgcagt
tggagttgaaccagtgtcttcagttgatccttggaccacaaagacggcga
gaa
>AW057443
tgagaaggatgaaccgtcagacaactgtcttttctcctcatcgtctcgat
ccttgccgtttttgtccaccatggatttgctgctgctgaagaagagaaga
atacagcttcagtcgtcagccctgctccggactctgaagcagcccaacct
gctggaaacggaaccgaaacaccaaaagatgaggtgaaggatgaggcacc
aaaagaaggtagtgaaactgaagcttcaccagaagccaagacaaaaggat
ctatggtattccatgctcttggagccatttccacaagtggttctggccgg
cattatgtgaagaagtctgccgaa
>AW057444
aggcgatgtctacaagaagccagtgcagttttacacgaatgtcacagtgc
cagtgttcgctccagtggtatcacctctcgaggtctacacaaacaccacc
aaggcaactgcttttgctccagctcagaacatcaaagtggctgctattct
tgaagaagatgctgatgcaattcatgttaagtcaatgagaatcgctggat
tcattgcacaatccatcctatttttgtttgtctacacaattgtcactatg
gatgttgagaattccgaagaatctgaagcagaggttcccgtcttcaagct
ctacagagcccgtgagattcagacatgcccactgccagctcgacaaaatg
t
>AW057446
tacagtgcagcttctggtgctcttcttcaagttgccttcaagaacttgac
tgctcagaatagaatccacatgtatcagattctcttggtctcttcgttcc
tcttctcgaaggccctcgtatacggattgttcggatctgctgaacc
>AW057447
atcaatcaactacggatgatatggtgtgtacttatccgtcgagcttgtat
ccagccttggccttacggcagagaacaatggtgttatcagcgcagttctt
ggcagttgcagaatgctcctttccttggtatccataaccatacttctcgt
tacggacatccaccttggcaagaatctgctttcctccagcaacgttaaca
actccaacggagatatctcccttgtggttgttgacatgaactggatgcca
agctttgtctccaaactgagcagcctccgggaatgggatccatccatagt
caaaaccacgaacactgtccggaagatagatgagaagctggatagatcca
acattcttgcaatactcgttgttgaaccacgagaagttggcagccacctt
tcctccttcattccagacacgacccataacaggttcaccttgcatgtacc
agagagcaacatattggtctggattgactcctggaagggtgtccagagtc
ttgtcaagagccttgacaagttggcgagtcggccatggatctccctcacg
aatgtccatccattcgtctctctcgacacgtggcactggcttntggtgtg
gtggagcagctccgcacacagcacatgggcaatgtggtgtcctccgatca
gtttggcgtgatgatgtacatctcgttgagctgtgcccgagctgcttatc
acctcccattgacgagaccatgcttctcagtctgtgt
>AW057448
aattccgaattccttcgtctcaactgtccttctcctctctgttacaattg
ctttggtgtctggatatccatcccaactccaaacaacttgtgtcacaaaa
gctaaaagttgcaccatgttctttttaaatggagtatattgcaccgagtg
cacgtattctggaactcttgaactgaaaattggctcaacatgtacttttt
ccatttacgagaaaaaagtggcgagccagccaaatgaaaattcacaaaat
gaagtagctcaatgcaaacagtcatcatgctactcaaatcaattttgtac
cagttgactgtgcggctgcttttggaaatgaatatat
>AW057449
ataacctctcccaacaacacctcaagatgaatgccatctacactgccgtc
cttgttgcttcaactctcgcctacactgcaatggcttggattggactcag
cattgaagccgccaacgaggatatgatctgaagtggcgccc
>AW057450
tcgatcaaatcaattcgaaaaaatcatgccgtcggaaaaggaggatgatg
taatgaaaaatgtaactttcgctgaaggcaaaaaatttggtgactggaaa
atcggctaaacgatcgatgaaggaggatttgggaaggtttacattgcaac
atcaatcagcgatccaaagaaagtggctgctttgaaagccgaatcaaatg
aaatcgaaggaggatctgcaatcaaattggaggcaatgatcctaaacaaa
ctgaatgccaatggacccgttccccacattccaatcgtccacttatgcgc
aaaaacgaagctctactgctacatggtgatgacgttgttggggagaaatc
tacgaaaactgaaatccacaaatctcgtagtcaacaatggattctcccgt
ggaacgtggagccgaatcggaattcaatgcctgtatgcattgaaatatgt
gcatgacaatggatttattcatcgagatgtgaagccacaaaacttcttgc
taggaaatgagacggatagtgaaagagcaagaattgttcatatcttggac
tttggtcttgcgagacctttcgctgttttcatgcccgagagaataagtgg
gatcgacgtagagctcgtggaactgcagaagttcgtggaactctccgttc
acgtctccgatgtcatctccgaaggacaaggacgggtgacatgatggtcc
tgcttatgtcatcatgagctcaacgtggaaagctctccatggcaacccga
c
>AW057451
aaaaaattaagtagttcacggacaccatctccaacacaccactggccagt
tctatcaatcagttttcggttcgtttaaactcgaagaacagtcttgacca
acacgagatgtattcacttttgacgctcctcttcgtcctcttcttctctg
gaagcactctgctcgttcaatgtggtggaaagaaaaagggagcaacttct
gccgaaggaaaatcttcgacgatgggcccggctcctggaggagctcctgc
tgctgcttccgctcaaggagaacctgaagagaaggagtaatg
>AW057452
ttttctcgtggtgatcccaagcttctagtatatgacgttcaggctctggc
tcctcggtcatttgctactgttccacgtgttattgataaaatccataagg
cagtcatgaagcaagttcaggataaaccactcaagaaaatgattttgaat
gcggcaatagcctataaactataccattataagatgacaggcaaagctac
tcgtaaaacatgggtagataagtatgttttgcataaaatccagatgcttc
tcggtcctaacatcagacaattgattcttggagctgcaaaatcagacgtt
tccgcaatgaggtttgctcgtggggcttttggagttgaggttctggaagg
atacggacaaactgaaacatctggaccaacaacacttcaattggttggag
atacacgtattggatgtgttggaccaccgatggcttgtgcgatgataaaa
ttaattgatgttcctgaacttggatattctgttgttaaaaatggtggaga
agtacttgtgaagggtcataacgtcacttcaggatattacaagaatccag
aagcaactgcatcatctttcactgaagatggatacatgacaactggagat
attggaagattcacttgctgaggatctcttcacattattgatcgacgcan
acacgttntcaacatgccacaaggacagttngtggctcagatctcacaga
atccctctacactttctcgagtttgttcaacagattacgttcatggcgat
actgacaaccgtggcttgtagcaatcgttggtccagatccagag
>AW057454
cgtttatactgattgcctttgttcttcagtttggagaaggatcaattgca
gttcaagaagttaaggatggcgaaaaagtgcaaattgaacttttcaaagg
agccaaggcaatccagagatccgttgacgctggcgaacagattttccatt
tcgaaggagaaaacaaaggagtgtttgtggatgctaatggaaaagctatt
gactcgtcaaattatgaagagaataacggacatttggtcatcaaaaagct
tacaaaggctgttgtttgatcatattctgaatattcaacgaaaattatca
aaacgaaaacggatcatggattttctggagttgccgcgccagttctcaaa
ctttctcttc
>AW057455
agttactcaagatgctgaaagttcttttagcaatcggtctactgtgtttg
atagatgtttcagctcagttccgtgctgaatgtgagcatccgcttcattt
tggagttcagcaatgcaccaacacttcagttgtcagatatcacttcgaca
tggaaagcaagaaatgccttgctttcaaatacactggatgtggaggaaac
gagaacaatttcaaggattactcagcttgctcaaacttctgtattccaat
ggactatttcacatgcccaggtggcagtgatagtgtcgctggaaaggaac
gaaagagccactgtggaggaatggaacaattgaagtgcgatggcccgaat
actttctgcttgaatggcccattcactggaatctgttgcgacacgagaat
cagagacaaaatcgatgccgactacgccaaggagtgtggaccaggaaagc
tgaagcatcaaattgatattggaggtgtcaagatcccaatgttcggaaaa
acttgcgattctacattctgcccagcctatacaaagtgtcatcaaggaaa
ttatcntgcttactgttgtgcttag
>AW057456
tttgagatgtctaaatacgcaattctctgccttgttctggtcggcaccgt
tgcctctttggactttatcggtcgtacacaatctgctgctataaagggaa
gattagtatgcgagggaaagccagcttcaggagttaaagtcaagttgatg
gagtccgataacagttttggacctggattccttgacagcgatgataagat
ggcatcaggaaaggctgactcgcatggagaattcaatttgagtggatcta
ccaaggaaatcaccggaatcgagccctatttggtagtggttcatgattgc
aaggacggaattacaccatgccaacgcgtgttccgtgtcaacgttccaaa
atcgtacaccaacagcggaagctctgccaagaaaacctatgatgctggag
tcatcgagcttgccggaaagtatccaggagagaccagaagttgcctcaac
>AW057457
tttctcggaacaactccaagcgaaaaaaattgttgacaagtcggcgtaca
tgggtgctggtggctatggatccggatacatgggatccaacgcctcatcg
tcgggatatgcccgcgaagattatgcacaaggaggaaatggaggcggaca
acaacaaaaccagggaaacggaggaaacaccaacccaggaggacaggtct
tcaaggcccgtaccgatcaatcgtgctaccttgggccataagtagctgct
cgaataatgtgaagactcagccag
>AW057459
aattccttggaaggttctagctatgaacgtcaccagtgtcacttcagagg
atggtgttaaagaattcgaaaagattgttgtggaacctgaagatatcgaa
tatgttgagattccggccgatgccaaaaacgttgacttgacgcgtcaccg
tatcaaagaaatcggtgattattcgtggctcactcacgtcgaacacttct
cgtttcgttggaatctgatcaaaaagattgaaaatctggattgtttgaca
acgttgactcatctcgagttttacgataatcaaattacaaaagttgaaaa
cttggatagcctcgtcaatttggagtcactcgacctgtcattcaatcgta
tcaccaaaattgaaaatttggagaagttgacaaaactgaagactctcttt
tttgttcataacaaaatcactaaaatcgagggtttggatacgttgactga
gctggaatatctcgaattgggtgacaatagaattgcgaaaatcgagaatc
tcgacaacaatctgaaactcgatagattgttccttggcgctaatcagatt
cgtcttattgaaaatgttgatcatttgaagaagctcacagttctcagtct
ttcagccaatgcgattactgtagttgataacatttcgggacttcacaact
tgaaagagatttatctggctcanaatggcatcaagtacgtttgtggaatc
gatgagcatcttnctcttgaaattctggatttcaatcagaatcgtcttga
gaggtcgagatatccattcattgagacactacagacttttggcaagagga
aatagnggattactgagcattatgg
>AW057460
gcttcttgacatgataaccaagacggaagatcacttcgctcagagaattg
tgtccagtgtcgcggtaaaccgaagcttcacgtgaaaacttcagaaattc
attttcgtgaagtgggacaaccattgcaacttcgccaatcaatgcttgaa
cttcatttgccgtttcgttgaaagcatagatggctttacgatacgtttcg
ccttttgctttcacctctttcgtggtttttgaagacttcacatggtgacg
agaatcatcgattgcatggaccaagttattcaaattttctacgttcgaat
tcaatatctcactttcctctccagtgtacaaacgcatctttntaatcaga
tgagaacgagttcttttctgcacctggatctccttttgagcaattcttcc
acaggcgctactgtatttttccagcatcttagaatgttgcccatcaaact
gatattttctcacataattcaaccatcctccaagaacttcccatggattc
tcgccgggagcacacaaaactgctttcttgccattgccttggcatgacat
gacttgaagtcgatacattcacattcgtgatta
>AW057461
tcatacacatcctcctatggcttttctttaaattcaccggctactttctt
tcctccgaagaaaatggcaatcgcgggcaaggcggtgatggcgagaacga
aggaagcacttatcacatttg
>AW057462
ttttttcactaacaaactttttattctttacatttctacaatacgagaac
gcatttgtggatgctatttaaatgttctggctagatttctcgtgtggaaa
ctgaataaacttaaagcttagacaacatctgcttcgcatcatcggcaaac
tcttgttcagcgtcggaatacggttcgatgtcacacacttcggtaaggta
cttgcgagcgttgttcttgtctttaattgctacgtagcatttggacacat
aaaatgtgtnctccatccattttggattgaccttataagcagcaaggaaa
tcctcgttggcctcttcataggaatgtgatggtggttgctgatagaacgt
ggcagcaagcttcttctcaagccatgtcagagatgcaaccgagtacttgt
aacggccacgcaaatggaggagagccgtatcctttggctccttagcaaga
gctttgtcgagcaattccttgaacttcttactgcattccaacttttcttt
cgttgccatatattcggttgcttgtccagtcaacacagcattccacttca
gcgcctcgaaatggtttggatccttctggacagcttcttcagcatacttg
agtccttcngtgacacttgccttacgttgagctnttggaacacatgcaga
cttctcatgaattacttgagcaagtctncacaagacttccaccgaacgat
cacatgtcgagacgcgctttgagcaaatcatatccttgatcgcgntcttg
ggtccgaagtcttgtcattcatcaaactcat
>AW057463
ttttactcaaaactatctatccaagttaatcagtagtgttagttctagtt
aagttattaaggcgcacggtctgtctccttgcttcttctctttgtatccc
ctttctcctttttcaaaacttcactttcatcaataattggttctttagaa
tacagttttccaatttccacgtactctcttctcttccgatccttgtcaaa
ctttttcttcgggagctcatcttctggaactactttcacatttttcgatg
gaaccaaacgggaacgagttggcttttccaccaaaagattagcgtactcc
gaactgtatttccccttctttttcttttcaagaggaacattttctcgttg
agtatcatcgtcctccaaactttgttgagtagtcatggactgggtccgag
agaattcaacggtaggcatggaacctttgctcttgtcgtcgtttgccttt
ggtgcctttcccttttgaa
>AW057464
tacaaaccctgcatgcctctgcaagattcttgctgatgaactggtactcc
acacgatcctggtaagctgttccgtgtaatgtatccataactttactgag
ataatacgtgtgtctgcgccccgcgaacatcgaggaccgctaacttctac
ggcatttctctcttctccttgagcacctcatgcttgtcagagagctcacg
ccaaggtataccgctagggactgattagcatctacacgcacttagtacca
gctctcatagacatacttcggtcccatatcgctgttacgaccgtaggcga
tcggatggaagcctaccgctctcttctatgcagctggttctgctagtgtc
tccacctcattcttcgttttcacgcacttg
>AW057465
tcatgtctcctgcagcaagatcctcgtccactgaatccttcttctctcct
ttggttgcttctttctttcctccacagaagattgccacggccggtaagac
ggtaacagcaagggca
>AW057466
cgcggaccgaccgactatcagacgggtttgctaccactgtatgttcatga
agattacgaatatgggattctgcttgaataagtgtttggtcggctttttg
aacaattgcattgaatgcatgtgtggcgcctaagtattgtgccat
>AW057467
gtggaaaaatccccttcatttctaaaaccgttacaatagtatctgtttaa
cacatcaagtataggattcattgcccgacaagctccagtttctaataatg
ttcgatgcacgaggccaagccattgagcaccggcagctgatactccgact
ccattgacatctggttgaccggcatgaaggctccgtagctgttctgagca
actggggcgatgcgctcgacaacaattggagcagaggcttgaactggagt
ttgagcattcttaataagccctctgaatcttgaagtaacagctggcgagg
ctggaacttgagtgatgtcctcac
>AW057469
tttgtacgcaccggatgaagcacatagaatactttactgttcgccacatg
cgtgatacagtatcacgcagtaccgacggatctgcgtactgttcgctatg
cgccga
>AW057470
ttttggtaaaaactaaaagatttattactgaaatccatgggggtacattt
atatcaggccgcttgcacctctcattgcctcgaagtaggcgatccaccac
atggagttgcttcaagacacacattcacctgactcttcttgttcttctta
cgagactgtgaacggcaactcgacgatccagcagactttgcacttttctt
cgaagaacgacttgaacgacgggatgctcctctaatagatatcttctctt
tatgctcctcttcgccaccgcaaatgtagttggacaaccagcatccacct
ttgttagtgttgcgacgtttgtattcctcgacaaatcccatcagatttcc
aattggagcagcggtcagggcgtctttctcaatgttaactgcagtgatcg
tgtgcagctcttcaattccaacatggtgatccgattgtttctccacacct
ggtacttcctggcattgtggctacaacatgtgaacgctattactgacatg
tggtcttgactggaagtgaaaatcgcttctgatgctgaaacctgctgaga
ctttgatcgat
>AW057471
taacctgctccttcttcttgaaaaccaacgtagcacgacgagtacggtcc
ggagagccaaacagtgagcgcttcttcttcaaatggtccggaatcttttt
gcccatcagctcaatcgtgtactttccacttggcggcttctttcctccaa
attcttgaacctcataaaggtacccaatgacttgaccaatagtgtacgga
tcgaaaatgttctcctcgctttttgtctgcaccggatgaagcacatagaa
tcctttactgtttgccacaatcttgctccagtctcccgtaattccgtcgg
atacggtgtactggtcgctttgagccgaaagtcgttcatttgcgttgggg
aggatagggtccgcatgcatatattttccaccttttccaggcttgtatgg
atagttcttgggctg
>AW057472
ttcactccggaaatgatttattggataaagggtggctagtgttatttctt
tgagcttttactcctcttcaaagtgcgatgatcactgattgtcgatccat
tatccttttctgcagttgccttttccattattttagtatccagaaacatt
ccctgacaatcatcctctctttttgtctcttcaaatgattttacatctcc
gggtcccagaataagtcccatcagaataccacgatttctacggcggaaat
ttccaaaagtgtcttctggtccatcttcaaatgatttgtgctttggatac
gagaagaaaacacggaaccagttgattccattctttggcttttcggcttc
agatttccattcattgaattttgcagtccatgtttttggaagatattggg
gtgacaccaagaactctttcatcattgctgctttcagcttatccctcttc
ttcataacagcctttgtctcctcatcaaccgcacaattattcttttgcaa
ataatcaataatcttatccaatgcagaatccangacagccaatacatttg
aatccagcttctgctgtcctgagaagaaacttgcangtacttcgttctcc
tctggtgtcagacatatctcgattgacgcgtgctatttgctactataaga
gacgtggcgcaanctcagatctcctatcgtcacatctgacgcatctcctc
aactcatcatcatccagctatcaaatgctcagcttgatctcagccagtgc
gtagtggaaagttccttgatacagaactgatggatcgagtagacacatgt
catgggaccatctctcgtttattttatcgtctgtttcttggc
>AW057473
aagtattgaggatcgcttgcttggcttgtgcaactgcgttcatgtcgagg
atctcttaccatggaacacgtccaacagccagcttaacttgcatgtatag
ccagacctccgcgtgattttttcttgcaagctgctgactcttatggcaag
cgattggcgcatagcgaacaggtccacaggatccggcggcagctattggt
ttgcggatcactccatagctgcgcgtgaacttgcgaccatggcgagagcg
cgatataaacttacgaagtcattca
>AW057474
gatttggtgttaaccattgccttttcaaggagctcgtagatggtcgtgta
ctccggagcatcgaagaactttcctttgtcaagaatcgggaaaacttcag
tgaattcacgcggacaacctccaaacagacacctaagacgagtcgtttta
cattccttcttgaacactcccacatcatcactttcagtcagattacgcca
gggaagacgtccacatgtcatttcaacgaccatgtagagccaactttcaa
tgtcatccttgcgacactgctcacgttgaatatggcaagccaatggagca
tacttcaccgttccacggaatccagcacgagcacgtggattgcgaagagt
tccgtcttcacgggcaaacttgcgtgccattccgaaatc
>AW057475
ttcataattatttattaaacatttaataagagctacaatgtttcccgtat
ccaagaaacttctcgaaccagttgtagtcttcgcctttaacagtatccat
ttcgaaaactccaatgtcaaaaatatgaacatccggtcgacatggattga
cataccattccggaatgggaatctttacaagattcttggtacatctctcc
ccattcatcacttctgttccgcaaaaattattgatccatagatacggttt
gaatccaaaattcagcaatggaatgtcgactagagtctgaaaagaaatta
tgtaatttctgtgttttcccacgctgtaactattcgaaattaatgggaat
ttgtagaaataaaatttggtaccacatcattcccgttagtcgccatctcg
aatctcccatcgactcctgttttttgagcggaccacatttggtcgagagg
tttgggctcccaaatctgaaccatctccgcaacatatggtcttnctctgc
acattagctggccttttacgtgaacagaagcacacgctgcataacagtag
tttggagccagaagacacagaagaattagaaagagtgtcttcat
>AW057476
ctcatccttctcccaatcgtactttgaactcggtgttatcttctcgttct
ccatcacttgccagaaacatttgaagatcatgtgataatccggtctttga
tagtaatcgagagaggccaaatgaggcatcactttatccatacaggctgg
catatttgacatgacaaccttcgccggcaagttcagcttcatttgctcca
cacgttcacgttgagaatcggtttgccatggaagagcttttccaccgttg
agctcaatgatgacatatagcagggaccatacatcgtcaacccg
>AW057478
aattttaaaattaaaaagtcgtttttttacttgaaaagcaacaattgaag
aacaacaatatcaacaaacaaacaacttggagaataaattatcatgactt
taagaaaagtcttttcggaggaaggtcatctcccattccttcagtttcac
gtactccggctccgtaggtgataatcgcgataaatccctgattatcaggt
gctgttctaataaaatctggtgtagttttcaggcgatcgttcatctcaac
aagagttccacgaacacctgctctcacgacatgctctgaaccatctttgc
atttgaatgtacacaattttgagtcgggttgtagaataagagctcctttt
tttccttttccagaaacttgatttgttgaacgatctgcgccgtgcttctt
cgtcgttccaaaatccactt
>AW057479
tttctccttacagaaacacaccatactcttctttcaccttattcatataa
tcgggctcagtttcaacagacaatcacttcttccatataccaactccatc
cattccgctagtgacgacaatgagcaaggtcttgttgccacccaatgaag
catcagaataatcatctctagaagacttgcattgtgtgatcgtgatgaaa
ccagcggctgacgcaggtggtgcatgctcgaattgatatgacgatacatc
ggtgaagtccttcagaccaatctcagaaggcattccttcgattttctcaa
gaacatgaaactcttgtaaagtgactccatgctcgcgcgctgcacgaaca
gtgtctaacaacaccgagtgagcttgaatgatagcagtctgcctctatca
ccagtgcagttcatgcgacttcactgcttg
>AW057480
tcttcagatctcgtgatggattgaactggcattggatgaacgcaagaggt
agctttccacagatttggcagtttttccaaaatcaggattctgatcgaaa
tccaccgggattggttggaatttgtccaactgatgaaggcattcaattga
atcaatgatcttcgcattcgaaaaattgctgcactccaatccaatcactt
tgctatccggaatcccgagctcggcttgaaggcgctctacgtaggcggtg
gtgtcgaatgttggatgagctgattttgcagtgtgctctgacgccaaatc
ctgagcaacgttcttgagaacatcagccattgtgacgttggtctccgagg
caagggcagtgtactccgagaagcttgcaacattcattgtaacatttgct
tctgatggtggcattgagtagacagagtagtcaagaacgttcatcaagtc
tttgcaccgctcgaacttctcattcatggtcactggngtctcggattttg
gagcagagtaaacggacaaattgaattgattgatatcttgacatggctgg
aacccttcgctagctgacacatttgtttctgattttgggatggntagatc
gaagaatcagcttgatcattctgcgtctcattgacagcgatatttctttt
tgcagcacctcattgatggagcaattgtctccgatgctgagcgagtacac
gagacattccatctgtccatt
>AW057482
tctagtccaccactgattttctctgtccgcctgcgcctcgtattctctcc
tctctctggcattcgttggctccagcagaactacagtttcatcgctgaaa
actgctcttggggtgcagaagatttcagagacaaagcttggctcatcgca
gttggctttgtgttgttgctcggcgagcacttgctccttaggcttcagga
cgagctccttctcgagtttctggcgaagagaccggacggagacatgggga
agtggtatttgctcgatggcagtgggcttcacctcgtcgacttcatcatc
ctcatcatagtcataagatgctgacgatgtagacgacatctcttcaaaga
ttccagaatcctccaccgccgtcatcatcgcgacattaaggcttccatca
tcgcggngctctgtagacggcaagcactttccggcggctctcataatcgc
gcacgtccacttgtgaacatcattatggccgacaaagaggtgaacattgc
cacgttgcatgcggattttgatgtgacagcggaaatgacgctgctttttc
gacgatcagagtgcacagacattcctggcgatcgcaatcatcaccaatcg
tgtcgtcatctcgtaatgacatcanacgcgtgacgtacgtatcatcgctc
cttggctcgagat
>AW057483
tttacctccaaactttattaaataaaccgaatgaattacgaaataacaca
ttcatatttctctttcaaatacttcttatgcatgtccttgattggtgcaa
atccatcatcacgtgccgattgattcttcccaatttccttcctcattcta
tccatttccattttatcaatctcttcatatttcttttctccttcaagttt
cacaccaaactcttctttcaccttcttcatctcatcggtttcagtttcaa
ccgacaatttcttcttccagaatccaacttcttccattccgtcagtgatg
acgatgagcaagttcttgttgggaccccatgaagcatcggaatcatcatc
tctagaagacttgtagtgtgtgaacgtgataaaaccagcggcagacgcaa
gttgcgcatgctcgaaattatcgtacgaaacattggtcaaatccttcaga
ccaatctcaaaagtcatttcttcgttntttccaagaacatgaaactcttg
agaagtgactccatgcttacgtcttgcaccaacaatttcgaagaaaaccg
aatgaactcgaatgatcacatcctgtttctcatcagcagtgcattttcaa
gtgtactccaatggcttgtcgctgcgaatctgaatttcggtgaagagatt
tcgaactcaaactgtttgcacgtgaaaccaggtttcttggcagtttgttg
ctttccttctgtcaaacacat
>AW057485
ccgtttcgacgattcatcactagaatttgtgcgggatcttgcaaaagact
tcgaccgatccatcgtcgcggtgaggttcaccagtcactggatcatacaa
gaatccgcccatctcaagtccttcaaatccattattatcagttggcatga
cacatgtgaacaagtcatcatcaacatcatatgtcccaatgcattttctg
tagttggatccagccttgtatgtcatgagcacacgttctccgtatcgaac
cacgtaattgccggcgtcaggcgtcttgaatgtgttttccggtcccgtgc
aaacattatcaagagtttgagatttcttgaatacggttttttccaagttg
acaaagtcggcattcaacaggaaatactccatattgcacttcttcacgac
attgattcctttgaacggcatacaaaagtttgacccgcttttttcccaag
ttggaatgtacgtttcctcgattccggaaaatgtgaagacgccgtcgaga
aggataacgccaatcattgcgtatntataactatccctggtgcctgtacg
canattgtccaccanaatcatagtgttgtggaaatcaccttcggccgncg
gaacaaccatcggttttttcaattcgaagcccactttgtacatnncggtg
ctgtgctttggctcntggtncgcgagtctgctgcaacgagactggcacag
ntggagcatcataagactgcaagaaatgtgacgtc
>AW057486
actagtaaagttcataatcctcaatactcggcacatctgggctttctcgg
tgcgtaccatgtcttgtttctttccatccaggcctcgtgcttagtattaa
cggagtccgtgtcctgccacgaatagaactcctttggcggaatgttttct
ttccagttctgaatgacgcgttcgagataaaacgcgactacattggcgtt
cgtattcgtcgcagacagacagtactgtagaatctttgccatcctctcat
tagtatctgggtccggaaacgtgcacgtggccagatagttgtacttcatt
gttgccgccactatgtgatcctcctcatcgtgccattcgaaggtttccag
cgtgataaaccgtgcacaaatgtaaaaccacgactcgtaatcgtcggcag
gtcctcgtgccaatcggaaatgctgacgcctcgacaaatacgtgttgatg
acgttcttcgacagtggctctcgctccgatttgttacgggcatgtcggga
ctgttgaacgtaaagaggctgcagcccattgtgcttcgtgtacgaattta
cgactgatgtttgaccgtttcgagttgagaagtattgacacacgactgct
tgtgttctgagagagagacgagnaggacgatgcgagatgtgagc
>AW057488
tttttaacaatagcatttcattccataaatatttaaggggtggttattat
atcagttctcttaccagtcttctccatcttcgaatgcattatcacgatct
gcagtggatgccgttccatttagcttggcagttatcggatccgggatatc
agttgaattggcaacaatagcatcagtgacagcaacagtgacaacagatt
gggatgaactttcagcgagcgtagaagtttgaagcg
>AW057490
tatttcaatgagtacaatttttcgaaagaaaaacagattgaggataaaac
ttgagtgatgagataaccgtaatatggagaattatatcagtgtcaagaag
gcacattgttcagtttcatatttacagatgtttgggattaaatgaagatt
cggtatgcatcgacgatcagaacaatgaacgagtgagttgaaagaccttt
tgttgaatgatatcagttcttggagaagaccatctttcaattgcttcaaa
ttcacgacgtcttttcaccagttgtaagaaggcggtcaacgacccgtcaa
cgtttgcgtagtgtgtgcggcaggagaagagacaaattccatcatacgag
agtccttggtgcagaatttcgtgaaccaaatcaaattctgcttcttgccg
gtttagaagatctggtgccaaaatgatgtcgaatttttttccgccaagga
acttcattgcctcttcaattgtaccacatgaaaccttggtcttgatcatt
gnaatattatttctcttaagtgttggacgacagtaaagctccaaactagt
cttatncattgtgtgcattgcatttcttctgcttcattttcgaagcatat
actgaatgggagtcagttacgaatccgattncaaaacagatttncattcg
anaagtcagttcatctcacattgacatatatt
>AW057491
ttttttagaataactttttatttcgaatgtaatctcagagcaagctttta
gaatctttttggcagtccgtacgagtcaacagtggattggtaggaagaac
catcagaagacgacgtatccgattccgaggatttcgcagagttcatctca
cggtccgataggtcagcaggagtcttgggaagattcgatttgctgcatgc
ttgcaaatcttccccgtcttgtttgaactttctggcacggcagatctgct
tgttgatgaccttattgtagttggccttttccttccggaagtttccacgt
ggttccgaccagcaatagaagttcgaacatccataggatccatccggatt
ctttacaatgccgaagcaggccttacacaacatgtgatcacactttccca
atgcaatcaaatgattggttggcaacttgtttccacatggaccatcacac
ttcacaaggacaacgcccgcttgctcggtgcactgaaatgctccgacagt
ctgcacacacaccgtgtacgtgtattctttacgtcgagtcaccggattca
ccaccgacgtcagattacaaccgagaacttcgcacgtggcanaaatgagg
gtccagaagatttgcggatcat
>AW057492
caccatacaaactttctgccattgcattcaaggccttcattatatcacag
cgagcggccttatcactttgggatgcaaagattccatagcttgccatcct
gaacatacgcttaatattcgattccatactaagtggaactggatattaat
acacccaacgacaaacacggcacttggctttcaagtattgtgtcatgaag
aggctgagagacggataggcaccacttttacgcacatccttctgatcatg
atcgctgtgagcttattgtgactacttctgggcagtgtcttgactctcga
cgcgaggagaagaaacatccactgtcggatcttgcgtaagatgtgtacaa
tcaccagatggttgaggaagggtcgctggatcatcgaccatttggtcagc
tgtaccagttgaggtataggttgttggcgctgtggaagacaccgatctag
tgtgatacagcgcctcaaaccgaggagacgg
>AW057493
gattaagttcagaatgatttggaaccgataattgaagaggaacatcggtc
cagtagaatggcttcaccaagtaaagactcttagtgagtggcaatattgg
ggaatccataatttgtgcctctcctttcttgagcgaaataaagttcattt
ggcaggtgggcttcttgatgcattgcaaaatatcatcgacagtctccaca
tgctcatttcgtgtcaagtcaaccatcacattatcagaaatcacgaccac
ttgtttttgctcaatttttgcaatatttttcttgaaaaatgcttgaatgc
gcaagttgtagtcttcgatgttctctgcacgaataaatccttgcgatgga
agatattggatattgattggataacccatattgaaaaacgcttttggaga
gagcaacatttcttgaaaattagtcggcaacatttgacgatagctgagaa
gagctggatcaatgttgaaggtggtgtaggaaagaccaagtcctttaatc
aagaaagctgagtttgaactgatntcatgtcangagagcaaaatacttca
natggacgaattnncgcattcaacagaccacgcccataagttcagacaca
atttgnccacgtcagtgagccggagatcgaattttgtagtgtaaagtgtc
tanngaactatttnggaagcatatcatatcatatggatgatattcattgg
accacgacgatacagacacgaacccattttggaagatcaa
>AW057494
ctattagcaccgaagagatctagtccaccactgattttctctgtccgcct
gcgcctcgtattctctcctctctctggcattcgttggctccagcagaact
acagtttcatcgctgaaaactgctcttggggtgcagaagatttcagagac
aaagcttggctcatcgcagttggctttgtgttgttgctcggcgagcactt
gctccttaggcttcaggacgagctctttctcgagtttctggcgaagagac
cggacggagacatggggaagtggtatttgctcgatggcagtgggcttcac
ctcgtcgacttcatcatcctcatcatagtcataagatgctgacgatgtag
acgacatctcttcaaagattccagaatcctccaccgccgtcatcatcgcg
acattaaggctgtcatcatcgcggcgctctgtagacggcaagcactctcc
ggcggctctcataatcgcgcacgtccacttgtgaacatcattatggccga
caaagaggtgaacattgccacgttgcatgcggatcctgatgtgacagcng
aaatgacgctgcttttcgaacgatcagcagtgcacagaacatttctggcc
gatcgcaaatcaatcaccaatccgtggtcgtcatgctcgtaaatgatcat
cataccgcgtgacgtcacggtatcaatcgctcttttgactcgcagatatg
atcgagcaggaaggctgctctggaatcggattgagttgagcacctgacca
cgtnggtacccatnccttggcattcactcgggacgctgagccgttatgca
ggagtgatgtcactgatcactcgctcgcggatgccgagtcacggtgaacg
tatatgttgtagacgcaa
>AW057495
atcttgctgaattcttatcatcacttgaccttgcgaagagcttttccttc
atgatcatgtccgatctcgtgagtttgagtttgctcgatgatagaaacac
ggcgagcatttggaccggtagacattgcactcttcgctggaggcttcagt
cctggaagagcttgacgatattgcgaagcaatgcctttcacatcttcgtt
catttggacctgatggtggttgcatgagattggtagccaacgcctgtttc
gcccattgcttggcatcgatcgaatcagggcgctcgacgacaaaagtgac
ttttcctttctcttggatattcttgacgagaagatctctggcaacatcct
tgtcactgactggaattccatcaacatcacacaaatgatctccaagaaca
agacacttctcggctagtgatccaggatcaacacgtgaaacaagcacacg
gttctggaaatgcttgattcccaaaccaagttttggtccattntgaaccc
agancagggttgccaactcataaacgtatccctcacggcgttgaatgatc
tttgcacgatcctcangaatatgaacacgagcttctaactcttcagcctt
tttttcgtcacggttcaccgtgatctttgcacatggagcagcatagcgaa
gcgcacggaaaaaagtcgtaacatcccttgcattttggtccgtcactttt
tttacntggtcaccatatctcatttttccttacgaatggttccagcctga
ttctanggataccgagctgtcattnngagttgcacaaagcgttcccctcc
ctcatgcnataccaatctcgacatcttcttggacccat
>AW057496
tttattcactcgatttggtttccccatgtgccaacgtctcgacctttgtc
ttcggattgcacaatgccttgaacaatggaatcatgaagcagggatcttc
attctttgcttcgattggagcttttttgctggatttcagagaatccggtt
ttgcaactcttgggaggcatttcagcacggatttcgattcgaattgagca
gcgcaggccgtgtcattttccagaaaagcacgaagaagtggtttactgtt
gttcattttgattgcatatcccgtcgactcaatcattgtagatctcccgg
gcaggtcgatgacaatcgttttcgccgaatactcggcatcgtcggcgaga
aaattgagtgtctggacgagatgatgtggcttatacgacacgtgtccgtc
aatccagtgacgaatgttttttcgaatgtacgggtaaatggccctagcgt
agatatcgaccggcttgtttttcagcagagcagctttggatggtgtttca
aggattgcgacttcagtatacttattggatagaaccaagcattcgtaacg
gtcaagttttgggctttcgttgggatttacaatcttcactgctacgtcat
anatcgaagtgtttcggagcacgattcgatattcagatttcacattttca
cgaactaccacagaaagagtcat
>AW057497
tatgtggacaacaagactgaggaagcatggttctcgttcaatgggaaggt
gattaagcagctcgggccacagctcaacgagatgtacatcatcacgcgca
actgcatcggaggaccaccacattgcccatgtgctgtgtgcggagctgct
ccaccaccaccaaagccagtgccacgtgtcgagagagacgaatggatgga
cattcgtgagggagatccatggccgactcgccaacttgtcaaggctcttg
acaagactctggacacccttccaggagtcaatccagaccaatatgttgct
ctctggtacatgcaaggtgaacctgttatgggtcgtgtctggaatgaagg
aggaaaggtggctgccaacttctcgtggttcaacaacgagtattgcaaga
atgttggatctatccagcttctcatctatcttccggacagtgttcgtggt
tttgactatggatggatcccattcccggaggctgctcagtttggagacaa
agcttggcatccagttcatgtcaacaaaccacagggagatatctncgttg
gagttgntaacgttgctggaggaaagcagattcttgccaaggtggatgtn
ncgtacgagaagtatgttatggataccanngaaaggagcattctgcnnac
tgccagaactgcgctgantaacacatttgtctcttgcgtnagggcaaggc
tggataccagctcgac
>AW057498
acagtgataaacatgaaattcctaaattcctaaacagtaccccttcatat
cttggccttttatcttcttctgtgagttctacaaattgtcgcagcacatc
atctgcgagaatcggaatgttgcacaattgttcataggttttcccattga
tgttgtgtttggttagcgcatatgaagcaagatactctggatctgggaca
acgattgctacaagccacggtttttccatatcgccatgaacgtaaatctg
ttggacaaaactcgaagaagtgtagagggattctgtgagatctggagcca
caaactttccttgtggcatgttgaaaacgtttttgcgtcgatcaataatt
tgaagagatccttcagcagtgaatcttccaatatctccagttttcatgta
tccatcttcagtgaaagatgatgcagttgcttctggattcttgtaatatc
ctgaagtgacgttatgacccttcacaagtacttctccaccatttttaaca
acagaatatccaagttcaggaacatcaattaattttatcatcgcacaaag
ccatcgtggtccaacacatnncatacgtgtatctccaaccaattgaagtg
ttgtggtccagatgtttcagtttgtccgtattcttncagaaaacctcact
ncaatagccccacgagcanacctcattgcngaaacgtctgattttgcagc
ttccagaatcaattgtctgagggtaggaccgagaagcatctggatttatg
caaacatacctatctaccatgtttacgatagcttgcctgcatcttata
>AW057500
gttagatactttattgtttaaaaaatcgagtttttttaaaattcaaatga
ccgtaatttcagaaggcactatgcaaaaaatatatcccatttaatttaaa
aacactaagcacaacagtaagcaaaataatttccttgatgacactttgta
taggctgggcagaatgtagaatcgcaagtttttccgaacattgggatctt
gacacctccaatatcaatttgatgcttcagctttcctggtccacactcct
tggcgtagtcggcatcgattttgtctctgattctcgtgtcgcaacagatt
ccagtgaatgggccattcaagcagaaagtattcgggccatcgcacttcaa
ttgttccattcctccacagtggctctttccgttctttccagcgacactat
cactgccacctgggcatgtgaaatagtccattggaatacagaagtttgag
caagctgagtaatccttgaaattgttctcgtttcctccacatccagtgta
tttgaaagcaaggcatttcttgctttccatgtcgaagtgatatctgacaa
ctgaagtgttggtgcattgctgaactccaaaatgaagcggatgctcacat
tcagcacggaactgagctgaaacatctatcaaacacagtagaccgattgc
taaaagaactttcagcat
>AW057502
tcaagtattagacggactcagtgggatgatcatcagacggattatcaagt
acaacacgcgaaagctctgtctcattcttctcttcttttggtggacggag
catcgaatgctcacggcactgagttccatcaagacgagtaatttgttgca
agagatgaataacctttccacgataagtatccactgatgcaattggattg
aaatcgaggtaaacactattgagttgtggaagttcaaccaattcatccat
aatgctccagttatccaacttatttcctcttgcccaaaagtctgtaagtg
tcttcaattgatggatattctcgaccttctcaagacgattctgattgaaa
tccagaatttcaagaggaagatgctcatcgattccacaaacgtacttgat
gccattttgagccagataaatctctttcaagttgtgaagtcccgaaatgt
tatcaactacagtaatcgcattggctggaagactgagaactgtgagcttc
ttcanatgatcaacattntcaataagacgaatctgattagcgccaaggaa
caatctatcgagtntcagaatggttgcgagaatctcgattttcgcaatnc
tattgtcacccaaatcgagatatttcagctcagtcaacgatccaaaccct
ncgatttagtgaatttgtatgaacaaaaaagaagtctcagtttgtcaact
ctccaaattttcaatttgtgatacgat
>AW057503
taactttatacttgtatttcacaacttttcccaatttgcaccaaatcgga
agtgactgactgtcgaccatcggatgaaactctggagcctgtcctttgaa
gtgagagatggatacgctcatcatattgtcacacgtaggtttgcccttga
tcttattttcttcgaccacaaagtttgccgttttcttgccacctagcaca
acctcatagtgaggattacttggggcttggcaataccggttggttctgta
tctctcaacactgttcgagactagtggagaacgcataagtgaatacgcct
ctggttcaagtttagcgagctgttccatgctatccgggtctgggaagaat
tgcgactccttcgagtacatgtaaggcttcaacactttcttgcaaacatc
cgattggttactacttctggtgtatgaggaagccgatctaacaataatcc
catccttgaccggcactgttggatagtagatntccgaatatctacggccc
atatagttaatctcggcgggggtgattgcaggcttgtattngcagagagc
ttngcactncacttttncattaaatctgatcatcgcattttgtgggactg
agaagtcaggtgtacatcgtagaaggacagagcangatatcaccatcnac
tttgtcgtcttgatacatactcatcccacgttcngggctcgaatncagat
ttgtggagtcttggagtagcttctccagcgtcagatgatctgtatgatgc
cggcattctcctgaaactggcccac
>AW057504
tttaacctccacgttttatttctgaatcagaattaaggcatgtatagttg
agcgtgagttgggctgtagactttggaaaaatcgaaattttcaggcacac
aatcagtgtagaccaggttacagacgtgcgaacgagttggttagtgtgtc
aggaatggggtgagccagcaaaaactatccttattcagctgcccggatcg
aacttcaaaactgacgaccgtcttctcggatgccttaatatcttttaaaa
tctccgaaaacattgcctgagcgacacgtgtattttcagcataaataggc
cctaaattacaatcttttctgttctcatagatcacagcttgcccgattcc
aatcacatttccctcctcatcatacgccactttcccgaatccatcccgat
cgtacatatgagagatgatgtacttttcgcggtgatacggatgaattgtc
tgatcataatttatgatatctctcttcggaacttctcgagcatttttcac
tgtaattgcagacaaatgcaacgtctcagggagcacgacgtcgtgtgcac
tgtagaatgtcttgtagccaacgtcgccggctttgtgtccgagatccaag
aattctttccgtttggacagctcgtgccagatatctgtgggccgttgggt
tatctgtgagacaatattattatcttcgctgttcatttcactcgacacat
atcattctgaaagtttgccgttccgggagatctgaattcaggatcaatcc
atgcgcaaactcatgacattatctgatgattgattganggattcatgggg
acgaatgtgcacaaatgtgctggtggatgactctcggcgtccttttaagc
tatcactt
>CEES071R
ggcacgagtcaaccttcaccacaagcgtccgtgcaaccttctcatcattc
cattttgatgaaaatcagcgcaaaaaggaatttggaaaagaagaagctgt
gaagaagattcaaaagaaagcagcgaaggttgctcgtgntgattcaatgt
tcagttctgaagaatttttccctgacattatcaagtgcatgtnncaccgt
caaacgnagaatcgagcttcacacgaatgctttgacatacaatcacaagt
taatgnagagatgcgaacaattctcatcgnttggttcagcgatgtcgtga
aagagtacaattt
>CEESA12F
gaaagcaattagaagaagtactgcagagtgtgatcaagtcactttagaca
atttaacgagtgtagaagaaaatcaaccaaactcaacantgtcgcctctt
gcaaagataattgctaacattgaaaaaaggaatgaaaaagtgaaaatgac
taagaaattcaaaaagtttggagttccgcttccaatgtnctcatcgaacc
ttgaaagtggatataagcaatgtcgaatggacatcacatgtncttctggg
tacagttgtgagaacantagtaaaacgagatgctgtatggaagcaaatca
ttcaccggaaattgagcgaaaaactgaaganttcaagncatgcccgtttc
aacttcaaatggcatacttctgccag
>CEESA13F
aaagtgatttatagatttacgaagcggactttgtttgggaattgtaaagt
taaatacaaaggaaatagtgggaagaaattttnttttcgggacgaaaatt
gaaatttaaaaaaagggttctcggggaatcacatgaggntagagactgga
aaagagaaaatacaataaattaaaatcggttgaaaatgaacattggacag
gagaaacaaacggaacggggaatcgttttttttatagaggcgacaaaaaa
gagcaaaagcagcatcagaagcgtcaaatcagngtactcaaaaganggga
atggatattccaattattcctgatcattcaacggcaagtgagt
>CEESA14F
acgtacgccagangagattcattcgaaaaaatgatgcaaacgtaaacaat
aaagcaattttacacacaaaatagaaattattcccgagggttcagcgtct
actttgaatcagctcgcgaagattcgtttcagcctccaccaatcctttct
ccaaatagtctttctgcttctcgatagcttcaatttnctcttttgactgt
ttagcttcagcttcatgtctggaaatttcagctggtttgtcggtcagcag
gaaccatacggcccaacagatcgattagtacttgaggg
>CEESA15F
gaaaacgagtatttattgaggatttgtgagcaatggggatttgatgtgag
gtaaaaaaaaataaaaacaaaaggtacaagantaaaatatacatatagga
cccgcagaaattgagatttaaaaaaaaattcaaaaaaaagaaggaaattc
aattaattgtgcatactattggtcatttctagcttaaaaggntcactgaa
aagtgagggactttgtcggaaattataattatncgatgttgaagaagaag
aagctccattaaccagcgtcggggaatcccaacttccaggttccattggg
ttcttcacatccccttgatgattccgtattggntcctacatcatgatccg
cttcaactgcggatagctctt
>CEESA17F
cgaagagtgaccatttatgcacattgatcggaaataaattaggaatccac
gcacttcgaggatgaatcaataaaaacaggagaggggtgggaatagaata
cgaaagatgaaagtaagaaaaaatcgcgtgagaaaattcgggagcgattc
aaagggaacacagtgacaaccgggagtgaaggnttaancgtagtanttga
gggacgcctttttctttgcctggncctccagantagcatccataaagtnt
tcatgaagaatctcagtagcatctcgtcgaagagcaatcattccagcttc
aacacaaaccgctttgcattggtgctccgttgaagtcatcggttacagcg
gg
>CEESA17R
aggnaacaatattccgatatcggaggatgtgacaagcaaattcaggagct
gattgaagctgttgtgcttccaatgactcacaaggntcgatttgttaatt
tgggtattcancctccaaagggtgtgctcatgtatggaccaccaggaact
ggtaaaacgatgatggcccgtgcggttgctgcccaaactaaatcaacatt
cttgaagctcgcaggcccacaacttgttcagatgttcattggagatggag
ccaagcttngttcgtgatgcttttgctcttgctaaggaaaagggttccag
ctatttatttttcattgnatgagtttggatgcccattggtacgnagcgat
ttcggattcagaggaaagcttggagg
>CEESA18F
ataacaaacagtttataaacaagaaatcacgcaacaatctcgaaacggag
tgtggcgagaagttctggctcattgtnctgggtggtgacggtgtgagctc
ctctaggggcgactggaagtctcttcaaagctgggactggttgtccagct
gacttagcggccttcctactcgttacgacctggcgctagacaacgcccat
gtcgcaacggcggagtataggtctctcgcttaagcgccatccatttncag
ggctagttgattcggcaggtgagttgttacacactccttagcggataccg
acttccatggccaccgtcctgctgtcaatatcaaccaaca
>CEESA23F
atagcacagaaaactatattnaatttaatattataatagcgattatnaag
tcagctgctcactggaatganttccagagagggagagagaaatagacagt
aaaacgagtctttgaagtaaagancaactcantacagaggcggggatgag
tggtaaaaagattgcataatgtatttccaatattgaaagtagttatgtaa
ttccgagacgacgggcttntccctcataanttaaaagtcgccacattt
>CEESA24F
aaaatttttttncattcttaaatattcgcagatgtcgtgggacagagttg
caaaatgtcaagagtggtgtgtgtcggtatgggaaaataagaagcatgnc
aatagtgtctgataagttaaaagaggggaagagggagggagagagagaga
gtgtgcattttggnccagtagatgaagatgngtcgtaatnntgtaggaac
acaattatatttatcagagaaaacgggataaaacaacaaactcgattcga
gttgatcataaatctgtgttatcacaagaattcgacgnaacaggagttgg
tggacgattgacgnggatattcgaccccgatggcaagggaaaaagtatt
>CEESA49F
ggaatgtgcatatatttatatatataantttaacaggaataacatggaaa
acgtttcaaaaaactagcgagaaaacagagggttcgtattggaattatca
caaaaggcacacaaggcgtagttggaaacatagtgatagattaggagtat
agtgcaattaaaatacaatttnctttggtgaccataaaaaccctaattat
gagaaaaggttagaaatttttaaaagcagattangagacggttacatagt
taaaantgcatggcattataaagntcacaaattgggaaaggtntttttnc
gagattcttcttctggtgggangtatagagcaagacggtcacgtcccata
a
>CEESA50F
gataaatttcttatttagttgcacatgataaagtataaatgaaaataatt
aaaattaaaaaaagagcaaaataatgtcacgtgaggtttaaaaaggagan
taaaaagcccaaaaagtgaattgaacgnaggnaagatgtagangaganga
gcattttgaaaaaataacgctaactatgctttaaaacagannganggtaa
canaaaatgttgagaaccggtagag
>CEESA51F
gatcgaaatggtcagaccgttgtgaagcttgtggatcgtgccacattgct
ccgagagcaagagcagaaggacaccgagaagaagcggaaggataaggaaa
aggcggacaaggagcaaaaggctcgggagaaggctgataaggaggcggca
gcgaagaagatcaagccggaagagctgttcaagcagggagagcacgtcgg
gaaatactcgaagtttgatgaacgaggtgtaccgnctcatttggctgatg
gaacggagatcacgaagagtcagatcaaaaagctggagaaggtgtacgga
gctcaaaagnaaaagtatcagcaataaatattagtgcctaatataa
>CEESA52F
aaattttacaatgtttattgaagacgttgaacgtcaaattatcaaatttg
atgaatgagataaataattataccagcatgaagattgtaagancacggag
aacttacagggaagaaattggaaacaacataggacactagcgtagttcta
tgtgtcattggggattgggaatgaggagatccgataagttagatgataga
ngacagaggtaggancatattagaaggggaaaaggcagattatttaggcc
ttggcggctggcttggcggccttcttggcagctggcttggcgatcttctt
tggagcggccttcttggctggagactttngcgacccttctttggcaagct
ggcttggcaaccttctttggggctcttgngccttccttgaccttcttaat
ctccggtggccggccct
>CEESA53F
aacaataacaatttatttgaataaacaaatttaagccttagcttcggcct
cggcaaggaaatctctcttgagttttcccatgaaagcacgcttctcggct
gtggtttngaagcgaccgtgtccggtcttngaactggtgtcgatccactt
gaggttgatcttctcgtgggcgactctcttggtttgggtgatgagcgact
tncggagggtgataagacgcttctttggtccgagaacggntccacgaagc
atgatgtagtcctcgttgacgataccgtatcttggggaatcctcccattt
>CEESA54F
attcttgaaaagttttttaaaagaaaagctgaaaattttacaataacgca
gatgaaaatnccaaattttttggggatatttcgccaaaaaaatcattatg
tgaatttntggtgatgaagatgatgacaatcgctttgaaaaaaaaaataa
caaaaaatacaaaattcgggggaaaaaaatgaaaanttaacaataaaatt
ggncattttagtttgagccaatttttggcagacagagagagngagagtaa
gagtaaagagaggtagcagagannacagncaaaatttattcggggg
>CEESA55R
aaaagcttcgcaatgagttcaagttgtcagatttnnaacttctttacgat
tacaagggaaataacttgagaagcgccatagttctnctnaaatatccaga
tgcaatcaatctctgcaattctattcgttccaatccaactgtattcggaa
aggaatggcacccgagagtcttcgaagtgctcgacgtagctgttcagccg
ccaatcgataaataanctttttngtattttaatgcctgancctgtttttt
ttgatgcttacatgaaaatttgt
>CEESA56F
actagttctctctnctttttttttttagaacaaacaatactttagtaaca
actatgtgaaaaatgaaggcaaatgagagttaattcatcaattaatgtaa
gagtgatatgacgattttaagcattgatttcagtttcccatttgtgcacc
aatgttttgaacttccattcgtctgggtgtccgacgtggttgaccttgtc
tttaaagtcaaactcagaccacttgaaagatggaaccttgccccatgttg
gccctccttgtgcgacaaattgcaacttcttcatcaactcaacatttgna
cccttgtaatcaagagctccgtggttaacgtgtccttgtcccggggaact
cgtatgttccattagctggatt
>CEESA56R
gaggtttgctccacagcacattcgagatgaatgtntttattggcttactg
ctagccactgttgtagcttctcaaagctcggaaggacgcgatgagagcta
cacttacaagcaactttgcatagtggacgataagcctcaagttcttgatg
gattcgactgccgcaaccaagttgctntcgccagatggcaaaacgctgtg
aacacaactggctggactttcctggnagtcgnaaccaaggagaactactn
nccacaaattcaaagcctactctgctgggatatctttaag
>CEESA57F
tccgatcaaatctacatggatatgcagaagttcggacgtgtccgtcgtca
agccggaggatacggtggatatggtggatacggtagcggaccatctggac
catccggaccatctggaccacacggtggattcccaggaggcccacaagga
cacttcccaggaaatactggntcatcgaacaccccaactcttccaggagt
tattggagttccaccatcagttactggacatccaggaggaagcccaatca
acccagatggntccccatctgctggaccaggagacaagtgcaattgcaac
accgaaaactcatgcccagctggnccagccggaccaaagggaactccagg
acatgatggaccagatggaatttcaggagtt
>CEESA58F
atgagtgaggtgctttatttgaaaaatctttttggaattaaatttcaagt
ttttttacagaaaaaaaaacaagttcagaaaggagcaaaaatacagaaac
aaatttntggatgaaggggtacatgataattttnagggaggaaacatttt
aagantagaattaagacaagatgcatcctggaaaattttgatcggcttcg
gcgatttgcgacgcagtgaattgaagcatgaatagttggntccataaaat
cctgataattcgattcagaaaccagagattctttatcagaagcaaaatcc
atatctctatccaaataggaaatatcacttcccattgaacttcccgagtc
gtcggcgatttgagaattcaatagcagt
>CEESA59F
gatcggcgccacagaattttttggagtaagactcgtcaatcgtgtatctg
atatcttttataattggtctctcgatctcttgttcagctccactatggaa
gacaggtagttgagattcttcaaaacctggagcataaccaagtcgtttga
ttctagatagcatatccttgcaccgatttgcgacaaatttcgtttgaaaa
tcatgaaaatcattttcagattgcttcttgatcagtttacaatgtttcgt
gtaaatatcctcaaaggtcgattcgggattttcctcaatcattgtcttgg
tgatctgttgatagtctgggttttccagaatatccttatgctgatcaatg
ggntaaattggnttcatcacttcacaattgtttcgtcagctcattcccga
ttttcc
>CEESA60F
ggtacagttcatttttncatttcagaataagcaacaaaaggtgttcatat
gaatgtnctgtaggttagtaaaacactatgttaggttactctttgatgca
aaaaggaatagttaaaaagttctcagaagctttcgaataaattataataa
atacgttgcagaagtaactgggaaaggaatgatgatcgtnatttaaaaaa
gatggaagagcttcaaaacaggggcttagaaaatncagttctataatant
aaattgggaagagctcaaaanttcacaaaaaatggttaatgaatacgcat
acaatgtcaccgcttgttgaccagcacactgagcgggtaaatttccgagt
aagagatcgncgatatttcagcggatggagcacggtaggggaaagtagga
ta
>CEESA61F
ataacaaacagtttataaacaagaaatcacgcaacaatctcgaaacggag
tgtggcgagaagttctggctcattgtnctgggtggtgacggtgtgagctc
ctctaggggcgactggaagtctctncaaagctgggactggttgtccagct
gacttagcggccttnctctnctcgtcattggacttgacacggttcaagaa
gtcggttctgcacttggatggcttgatgtgctcgatacggatgttgattc
tctttggaagaatgtttccgcggactctcttgttgacgatgattccgacg
gctcctctggtgacgttgaaagattctcccggttcttccgtggtaagcct
tgaatggcata
>CEESA64F
aagagtttgaaacttttattagctgtttttttagttcaaagtgagaaaag
atgaaagaaaaaacaataaacagtattatgttcagaagtgtattgaagag
agatgggggcgaaactaatcctcaatgaatctaacttgaattatgttttt
nctcatggaaaatcgcgataaaaggattactgtgtcttctacagtaaccc
gaaacgtaagtttntgggtgttgggggtgggggagggttgattcgtgagc
aggatttcggggcatttacacgaaacttttcctcatttttctcgtgccga
attcctgcagcccgggggatccactagttctagagcggccgccaccgggt
ggagctccagct
>CEESA65F
aataagtaacactttcatcacataaaacatcagtttagtgaaattgaccg
gaaattgaagtaaaaataaacgcgggaaaggatggtgtgacttgactagg
ttctaggcggcacgancagcaaatnttggttttnaagttattaaatgcaa
aacgtttgatttttgantgttgggaaattgcacaatttagagggcattgc
gagtntctgagaaaganatgaaatgttaattgttttgggcgctgaaatga
aagatgaccagtggcaaagtacggatgagttaaggtgagtaaaaganata
aatgcaaaggggtatgggtgggtaatgcgactagaaacactaagcnagta
tatccgtaatggttggaaaattg
>CEESA66F
gaagcacacgaaactttatttttttttgttggagttcaacatgaaattca
gcaattnacgaataaaataagacataaagaacggagagaaaagtggtgat
gagatcggcggttcgntcgcaaaaatcaattttcgggatggaaaaatacg
aggattatggtacaagttggnttaaatgaatattaaaagtgcttcgagaa
ttggtgatggagcttaagcacgttctccgcggatgcgtctggcgagttgc
atgtcctttggcatgatggtgacgcgcttggcgtggatggcgcacaggtt
ggtgtcctcgaagagtccgacgaggtatgcttcaaatgcctcctggagag
ctcccgattggcagccgnctggaaagccggnggtccagtcttt
>CEESA67F
acatagctaacatttatnagccatttgaggatcgggaataaatttgtata
caaaacaagtataacaacgaacactaatgggggcggaaaaaaaggtgaca
gagcaagtatttttttaaagagattcattgaaatcgatcaacagtaacaa
gaaaaatgggatatactaatgcggatgctatccgtaccgttcatctcaca
aaactcgcgaattggtcgatgaaagggtagtgatttattgctcatcggct
ttcgtctcgttctttgaggcggcgtcgaagtctccaacaagttctggcac
atcttcgtcctctcccttttccatctggtccgagctttggtaaccgttnt
tggcaagttttcttgagggtggggtgaggggactctgggacc
>CEESA68F
aaaaaataaagaaattattcacgtaatcaaaaacagacagaaaaaaaaag
taagctcgaataagcttatacatataccgagggtgaataagtgaattgta
aatgtgagagttaggctttgaaacgttcgggagaagcgggaaagattgac
aacttaaacgtgtaaaaccatganattccgtataatctagtttggggtgt
gagcnttgaaatgtgcaggataacaacaacaaaanggtgggttgaaagan
atctggngnaattaaacagttattagccgtgacgaacagaagcnccgggg
ggctct
>CEESA69F
aaaaaaattcaattaaatttattatcaatgctccaaaactcatgccaaga
agagatctgaaaacaggtgggtgtgtctgtgcaagtaaaaaattcaagaa
aggacaagctggttggaaagaaaaatacaaaaaagtcgatggtctaacag
aataaccagaacgagattgancgggaatncgnttgagangaaagcaagct
tgtntgatggtagatgggatgnttggttgagatttcaatattaccaactg
gctgagtattattnatgatttttnatcagcattgtcca
>CEESA71F
atcaattttttttattggaattcaacggtaaaacgagcgagggtggactg
tattaattgaactacccaattgaggtctttncttgagaacacacacaaat
taacaccaacgtatacaatattctncgatcggttttnttcggaggagatt
tataaaaacactgccagagaactcatctttcaaaaaagaagacatcgggn
ttgaaggacaacttgaaacaaatganggaaatgataatcacactaaaacc
gagcatggtgcactaattanttataaaaaattaagagtgagagtaggacc
gagagaaaagag
>CEESA72R
tcacaagtgattcaattgtttcgtaaaaatcaatagttttncttaattct
gcttaaaaattggcctaaaatcttgaaaattaacaaagttatgaatttnc
gaaaattttcaaaaaccaacaaaaaatttgattttttaaaatttaaaatc
aataatctacaataaacttacaattaggcagatgaaaattccaattttng
caaattttgaagctataacgctgaaaactcgtacagctaaaaactncgnc
cattttggggtcccaccgcggncaacccaaaagtggggtgggaggcctag
acgtnttagggggtcatttttcaaaaggtcttcggtg
>CEESA73F
agcagccaagtcctcacgagcctcggtgaactctccttcctccatacctt
ctccgacgtaccantggacgaaggcacgcttggcgtacatcaagtcgaac
ttgtagtcgagacgagaccaggcctcagcnatggcggtagtgttggagag
catgcagacggcgcgtggcaccttggcaagatcacctcctggcacaacan
ttggtggctggtagttgattccgaccttnaatccggttgggcaccaatcg
acgaattggatggttctnttggtcttgattgcagcgatggcggtgttaac
gtcctttngaacgacgtctactctgtacaagaggcacacagccatggtac
tttccgtgacgtggatcaaaacttgaccatctggttaanccggcttcgaa
agcangctattnggtgatg
>CEESA74F
gtgtgtgtgtgtgtgtcgaatcgttcgagaaaataggaaaatatgcgaaa
aaaatgaaaaaaaatgaataagggagaaaaaagtacaagaaacagaaaaa
ttagaagatatttttttattcaatcatcaccgggatgttcggggcagcaa
ttcttccgtttgaaccaatcatcgatacattgtttatggtagatacatag
acatggtaatcgtgctattttgtgtccagcttcgaggtcttccagacaaa
tcgaacattctcctttgtcgtcttttagcacgncatcattataggnaatt
ttgggtctcgtcaggcacatgnccagntgaatntccgcgtcgtccgatgg
ttacaactttt
>CEESA75R
tatcaatgaatgtatttncccacctttcctatcaaattagcccttccagt
caattcccccgccacctccctttccaatcatcagcacttgaccgatacag
tcaacgcatctnagttgactccaatattttnccccgtctgatgttcttct
tgtgttagtgaccttctcaatcatttctccccaaaattttttctctatca
atgtgtactaacattgccaattctacggcggacttgtctccgttttagtg
gtatganttatatacatatatataanntntnaatttaaaattgcatccta
tttcgggtaatagg
>CEESA76F
accaaatgaggcatctcgattcattcgtagtattatggtacattcgacac
aaaatgagcgacaaaaaaaaaagaaaaatgacaaaacaaaacaaagggaa
aaaaaatggaatttgagttgggcataaattatatatatatntnnntatat
aaancttgangaacttttttttgtgtttaanaagnggtgtggaacatttt
tttaaggggaaaaggcattgaaacgtaagtagtcgngagggttttggctc
gtgccgaattcctgcagcccgggggatccnctagttctagagcggccc
>CEESA77F
aagaatttctactttttattgatttnccgcataatgtaaagtaattttaa
gaattacaagantaaaataattgaatgagaggncgtgggtgtgtttnctt
aaaaacaacaacgagtgaagggggaattacagacaaaaagaaataaaana
tgggatagagatgggggtgataggtggagatgaggggatatgaaaggtag
aagancctggtaaaatggtctgncggggctcaangggaaatggggctcaa
aaccaaaaacgaa
>CEESA79FB
gaaggggtgatttcattagatatttttaaaaattattccaaatttcacgc
ataacagaaagaaaacaaaacaagaaggaatatcacaaaatgtttgatgg
aaaccggtaagaagtgaggataataggcacgtnctgagtagctgatctat
atagataaaatgtgaaaacaagttgaactaatctggcgtacgagaaaaga
aaaggtaaatcgataaatatntatgtacaacgggtatagtggatcgtgag
aaaagtgcatcgggacaagngacttagagntaaaaaacgtnaggcagagt
tcactcaatanacancaaattttncgaaaaaaacatctatggattattca
taaatgggncccttccgagtgt
>CEESA79R
attttagaaaagtatatcatcataatcaccacttcaaaaactttgacgtc
ggcttcggaatttngacttctctttgggattatgttttccacacactcgg
aatgggcccattataataatacatagatgtttttncggaaaatttgttgt
ttattgagtgaactctgcctcacgtttttaatctctaagtctcttgtccc
gattcacttttctcacgatccactatacccgtngtacatatatatttatc
gatttaccttttcttttctcgtacgncagattagttcaacttggttttna
acatttttnatctatataggtccagcttac
>CEESA80F
attgattcgaaataatttatcgtatacaacacaagcgatgagcatagaaa
ttggaactcttttcattcaaaatttagaaaaaaataaaaagaagcgaatt
aagcagaaattgatgcgagtncagtattatgcagattggagcaggcggca
cgagtttaatactcttctccttcctcctcgtttcctccctcgttcgagtc
agctccgacctcttcgtagtccttttcgagagcagccaagtcttcacgag
cctcggtgaactctccctcctccattccttctccgacgtaccagtgaacg
aaggcgcgcttggggtacataagatcgaacttgtagtcccaagcg
>CEESA81F
aaaatcgataaattcttcatcataattaatcaggaaatgtttgtnattga
aaaaaaaacaagaaaaatggggcgtgtcgatgagaaattggggcaaaaaa
aaaatcgataaatcgataaatcaagaggntctttgggcggaaaaatgaga
ttttcagagagaaaaatggtgaaaaactaagaggtcagcgaaccgggaac
acaagaaaaaantcaaaaaaaaantcgataaaatcgaatcatcgtccatt
cggcatttncggcggcttttnctgggcctgggcctgagcctgagcctggg
cctgtttgagcctgctggacttgggccaggnagcaaatttggctgtagac
cgagcagtt
>CEESA82F
ggtgttgttaacagatttattgaaaacaaataacaagatctttagtcgaa
gagaccgaagcccatgtcgtcatcggattcctcctttggctcctccttct
tcttggtctcggcagctggggcggctcctccagcagctggagcagcagcg
gcggcggctggagctggtccagatccggctccggaagagacagaagtgat
gaggttcttcacatcaactccctcgagagccttggcgaagagtcctggcc
agtatggctcgaactcgacgttggcggccttgagaagggtagcgatcttn
tcgccggtgatggcgacctcgtcatcttgaaggatgagagcagcntagac
gcaagccagtttcttggttcgaagccattnttcaatcgtaaagttncgcg
gttttgcctta
>CEESA83F
gaatatttattttaaattgtgaaatgcaaattggtttcgttgaacttttc
aagtgaaaatccatgcaataagagcgcaaaatcatacataatacagtgac
gagaagcaatcgaaatatcacagaaaaagttaataagcgagatttttaga
ttgggaatgagaaagtncttaatgggcttgcttcttggcgaggttctcag
ccaatttntcgaggaattcaaaggtgttgaggtagtcggtacgagtgaca
gctgaagcatttcctcccttcacgcaaatggcaagatccttggtgaggaa
tccagcctccattgtctcaatgcacacagcttccaaattattggcgaatg
tctcaagggcagagttcttgtcgagagtgggcacggtgagccaatccacg
ggacccaggcgaagattggagggcaattgggattcgtgggaggttccttg
tccccttttgggtgcattcctgtaaat
>CEESA84F
aaggaaaatagacagtttatattcggaatttataaaacaaatgtgataag
aactgccggcggatacgnaaataccgaaaaaagtaatcaccgacgacacc
gaaacggatggaaaatcgaaaaaaaataaataattgggggaaagaataca
cacatcgacagangaccgcaatttagtgagtgatatccatggactcgacg
acgtcgtacttgtaggtcttgtgtttcagcaccttggtggctccggcctg
gaatttntagacgaggtcgttgggctctggtcgcttgcagaattctggca
caattggccccttgaagacggtctcgcttggctcgatgatcacaagattc
aaactgtttcctgaggcgttgtcaccgtgcataccggcttccagggcgcg
ttggacaagcttctcggcttcaactttcgtcatatcaaccttaaaatcac
gttccaaaatagtgatagcntgcata
>CEESA85F
gtattgtttgcaatttatttgaagacaaaaattggaaagaataattgggt
agaattaaagggagaaaagagggaagaaaatagcttcacaagttttaaag
tacaccagctaaccgaagaaagaaaanttgantgaaatatggttccttta
tgaaaatctcttcgaaaaggaagatagttaacacaaagatggtccatcta
gacaaaaaagcaggntcagcgactaanatgaaaancanctagaatattaa
gaggttggtagagantgagaaagcnataaantaagggaataa
>CEESA86R
ggaccttnttgtnattaagccaaaggtgttcccagacgagcntggtttct
tttccgagagttacaacaaaactgantgggcagagaaaatcggctacact
gaggntcttcaacaggataaccactcgttctcccattatggcgttctccg
tggtcttcatacccaaccacacatgggaaanttagttactgtggttagcg
gcgagatcttcgatgtggctgttgacattcgcaaggncagtccaacgtac
ggaaaatggcatggngtggtttctcaaccggggataataagcacgnnttc
tgggatttccagcccggg
>CEESA87F
gcatggtaattgtcgaattttatttccaaacactcatgaaaaaagaaaaa
taaataatacagtcaaatttttttncntgtagttggaaactnttaacgat
aacgaaaattggtaaatgagaccacaagaaacagaggtcgataatttagg
ggaaacaataggcattttactccatcagcacaatgccgggtaaaacgaag
gtggaactcatatttagttgantgcataggagggtacatggaatcatttg
gttcggccttcgatgtaggtagagacatcgatcttttctgggagctcagt
gatgctgatatcgaagcggtcttgaacgctgttcaaggtcttggcgtcat
tctcatcagaaacgaaagtgatggnccaaacccttggttcccaaaaccga
ccagcacgtgcaactcttttgaaggntacgagtcgggaatcttcttggca
tg
>CEESA88F
aacaataacaatttatttgaataaacaaatttaagccttagcttcggcct
cggcaaggaaatctctcttgagttttcccatgaaagcacgcttctnggct
gtggtttggaagcnaccgtntccggtcttggaactggtgtcgatccactt
naggttgatcttctcgtgggcgactctnttggtttgggtgatgagcgact
tgcggagggtgataagacgcttctttggtccgagaacggctccacgaagc
atgatgtagtcctggttgacgataccgtatcttgggaatcctcccattgg
ggtgatggtcttctgggtaagatcgaactcggtgg
>CEESA89FB
aatggtacattctatattgaaagaaatgctaaatagtttgtatgtacagg
aaagtagccaaatacccataagcagagaaacagaagtggggaaaggaaaa
cagacaagaaaaacagctagaaaggaaagtaagagatattaatcacaatg
aaacgcggataacattgataagtgataatgttgataaactctgtgatgat
gataaagcctacatacacaaacacacggatgaaaatactattcaaatgct
caatgagagtgaccagaagctagaattgcggggacgacggctcctccaat
ttattaacagaagctcttttgatcgtgtaacttngctcccagatgaatga
ggaatttccctatttgaaggatggtgcagttgcatccacggcaagggga
>CEESA89R
tggaaatatccacgcacaaataggatattcactagttttggnatttgtac
tcatgcttcttgttgatcaaattggaagtgtcacggtggcaagaaatgat
agagcagggagaagccgaattggaatctctgccacaattgggctcgtggt
acagctgcagcggacggtgtcgcattaggaagtgcttcagtcatcaacaa
atccgatgttcaaataattgtttttggttgctataatgcttnacaaagca
cccncttgcat
>CEESA90F
tgccgctcgtgccggcaaaaaaaaatcaatgggaaaatgtcatcataggt
aatacaaaaaaataattttttgggagttttccagaaaaacgggcggcttt
gaacaatgagaatttggagcaagaaattggtggaaaaaatcggcggtaaa
aatcggaaaaatcaataatttatcgttaaaatcaataaaaatcaacgtcg
actatgccgatccctgtccccccgatccctccgacgttccgaacttctcg
accgttttcgacggcgatcccgttccgaagatcggcttctcgatcggtga
ttatgtcgtgatgaagattgctctttttcacgacttttcgatcgtttttt
gctctttttactcgattttntctccttctcatcgtctctcatctctngtt
ctctcttnttttccgacgacgatttttccgattttttattaatcgccgnt
ttttgaatctggaacggggtaaat
>CEESA90R
aatgaacaaagaggcccggaaaaaactgccggcctggntcctggaaggcc
ttgaaaaggcganancgggagaagcaaaagcagtnggaaaaagaggaaaa
gctgaagaaagcggaagaagaaaaagcccggcgaagagccgaagctggaa
agagcaaatttgactcttcgtcggatgaagagagcccggaaaatgagaaa
tttcctgttggtaatggaaaatctgaatatcaggaagatgataatgattc
ggaagacgatttggaggagagacgagagcaatttatacgctgtgtgaaaa
ctctaattgatgaacgtgctcctcgngtcttcgaatgacgtcatcatgcg
tataatacaag
>CEESA92F
aaacacagacacgggatggaatattgaacttnttggtaaagtctcaatga
gaggtaaaagtgcaagtttacatgtaagaaatcgttcatcattatccaga
agcttctgggttagagtcgcagttnttggatatttntncttctgaggttg
atagaagcntcgcacataaaatccgctcaagagaatgatttgggaaattt
tgaagtgtatcactcgtggtggacggcccgacaaatgtttcaggttcttc
aaatgaaaaaccagttggcattgatttacataatctnttgatggacgcga
aaacttccgaagagttgtgcggtaaacgtccaaagttcgagtcttggtaa
attaaaaaagcaatcctctcgcagagaccgagttttcacatcatatcgtc
tttcgttttcgatgataatcaattatctctgcttgtgac
>CEESA93R
gaaagtcgaaaggtggtactcgtggtgaacaattcatttatgcggctgaa
gcattcgattcgactaacaatgttccgataaaagtcggcgatctcacatc
aaccaatactcatattattaaaaaaggaacagttgttgatgcgaaattcg
cactggccgatcgttgtcatgtattcaaaaatgagattnatggaagtntc
tntcaggcgacactntcgtttactgatcttacacagnataaggattcgta
ttataagnttcaactgtt
>CEESA94F
gaaacagtaaatttatttcatagaaaantgaaaaaatgaataaaactata
aacaantaaaancgacaaagtgggaaatatctatttagactttaccaatc
gtgtacaattnctgagtgtagctggtccattccagtatcctttaatcaaa
ccattccaatacagngctggcatgaaataccttttcatcaaatatgccca
atatgtgggtttcgattgnncaantggagttgtctccatggctcctcgag
gtccaaattctgcgaggttcacacgatttgtgctcacaaccagtgggcat
gacgcgtancgatcggtactgcatacatggccgatttaccctgcatgact
tgttgtcaaaatttctt
>CEESA95F
aagtggtcctaacaagtttattcatgttaagaaaccataaatataaagaa
aatgaagtatctcatggaatttttntcaagtaaaatcgtgtttcgcctag
aaatggaaggcacatnttgaaaaaaaaaatttgaaaaaaantcagcttag
aagcactttcggtgaacaatcgatgggccggactcgtcgtactcctgctt
ggagatccacatttnctggaaggttgagagggaagcaagantagntcctc
cgnnccanacggagtacttgcgctctggnggagcaataatcttgatcttc
attgtgcttggggccaaatnttgantctcctttt
>CEESA96F
atattggcattaaacatttatttttgacacactgaaatttaaacaaatgt
atagtcaaaaaaaaacatgcaaataaattatgcttatacagatcagttgt
gatttgaattcacaaccttcacagtggccaaccgatatatatatatatat
ngnnccagatcagactagaatttggaatagaagcacctccaccttgtttt
tatgtttgantttttctttttcatgatcatgttcatctgatcagaagttc
atctttagccgctgttgagtagcaaagttcagcaatcgttctcaggtttg
tagttgttgggccaggtagaatcggcttgatttgagtgatagttttaaca
gcgtctaccgcccgtcccagtgtacaactngaatcaacgcttttgtgttg
gangtattgcgga
>CEESB01F
aagtgcaatgtttgtagccattgaagctccttgtgtgagctcgttcactc
ttgcaagaatgaatggggtgacactttgtgaagcgatgttttgttcaatg
gcttcttgaacagcttggtcaattgctttctggatcgcatctccatcagc
tgcatattttncaggaataggacaagccagaatagttccntaaggtaatc
cgngagntttcnaggtttttaacaggtgaacaacttcttccaatgattca
gtgcagaattgnagcttttctaactga
BioPerl-1.007002/t/data/dbfa/5.fa000444000766000024     10441613155576321 16306 0ustar00cjfieldsstaff000000000000>CEESB04FB
tttttttgttagagtattttatatatttattattattacagcttacagaa
ctttgatttgttttacagaaaaaaggtgcaaccgcttagacaaattcaat
ggattatcattatttgaaactttttgcagttccttattttcaaaaaaatc
ttggtttttggtttgatcagggtgagaaaggatttcgggggtcgaaagct
agaaaattatcaattttttgtgattttcgattgttttnatgtttttcatt
tatacgagatagcgaagaaagaaagtttggnggcaggatggtagcattga
atattggtcgaatcgtttaggcggcttcttcatcgacagtttccttgggc
ggtgagtgggcttgagctcccggnttccggtgagtaccgacgnacnttct
cctcagcg
>CEESB04R
gccaagaccagaagtnaacgaattcattggagtcaacgtcggattcggaa
tcgccatcgttttcggtgttgctgtctctgccaaaatntncggaggacat
attaaccctgccgtctcctttnccttcctttccgtcggacaaancaccat
cgtccaattnattg
>CEESB05F
atgaaacgactttggaaaaaggttgggtctggtgtgaagaatgcnaatta
tctcaaaaagtctgtagaagaagtagcgaaaattgaaaaaggggaaacaa
aagtcgtcccaccaaaatatccaactgaaaaatcacgagaagttagcgan
gaaatcaaaaaagaattagcgntgaaaaatgaaagtttngtgggaaatat
gactaa
>CEESB06F
ctagcattccatganctgtgccaagcattctatcaacaaagattgaaaac
tattcgatctagaaatattccgaataactcgccggcgttagtcgtacgac
aacaattcaaattggcgtttctgtcaganctcagacaggatactcataca
gcattgagaaattatcgnttggcttatgatcaatgtcgggatacagttga
ncaatgggatggagtcgatgtttttangtggagaagtgttgttggattgc
ttanttataaggnacagcagggnattncttgaaaacccacgaattccgtt
attagtactnaggggtgtcccnttgccgggaaatttttgaaaa
>CEESB07F
gaagaagcaacaaactttatagtaaaaaaatgacaaaagagtatcattgg
agaaaagaaaacggataactgggagagcaagcanttaancaattttnaaa
aattgaaaattaagaaaaggtaatagcaaatgggtggagaaacagtgggg
aagagatttcnttagaaagaancaaaatttgtaaatcggaaggaaancan
gntgaaaacggnggtcg
>CEESB09F
aaagtgtataaatttattacaaaagcttttncaaattacaacagaagaga
gactggaatgcatgatgattggtggtaaaaggggaaaaaggntcttatga
aaaattagaacaaatcacagaaaatttcaggttcggacagacagacaggt
ggataagcnctcgtgatatatatttccagngngtaaatcagaaatagaca
agatatgatgcaaaggagctctacggtcaagacaatagangtnccnntag
ggtgcttacnaaacacttcgaattttgt
>CEESB10R
agaagccgcgtgttgttaaggaagaagttatcgagccaggttcacaatct
gaaactcaaaaagaatctccggagaaagttcgagttgttgtaccgaaagt
tgaagttgaaagatcaccgtcgccaaaatcttctcgtgatcgtaagaagg
ntcganagaaatctcgtgagaaagatcgtgaaagagatcgtgacagaaga
gaaggttcaaaacatcgtgatagttatcatggncatcggnaacggcagca
gtttctttccagtgtacgacggtat
>CEESB11F
actttgtctatttattggtttatnctaataaaataaangcagtaacgntt
caaaaacgctcaaaacagaaattaaacgaagcanatntttaagtgctgag
attcataaagttgagatggaatgtnttgagtgtcgattgaggaattctta
attaaccgacgtcgtatccnatcctatcgncatttncaggagcatctcat
tgggtgtttggttgtccgagcgtgtggagcattgatttcncggcagagat
ccacgagttgaattcattttttnagctttcgg
>CEESB11FB
actttgtctatttattggtttattctaataaaataaatgcagtaacgttt
caaaaacgctcaaaacagaaattaaacgaagcagatttttgagtgctgag
attcataaagttgagatggaatgtgttgagtgtcgattgaggaattctta
attaaccgacgtcgtatccaatcctatcgccattttcaggagcatctcat
tgggtgtttggttgttcgagcgtntggagcattgatttctcggcagagat
ccacgagttgaattcattttttgagctttcggttcttcttccgtttttct
acgagcacttctatccaatttccaaatcttctcgcagttcccacgngtna
ccatttgaaatcattaggcacttctacggattctactatggtcggcccat
catacttttcactcg
>CEESB11R
aaaaatgccactgtccaagagacgagcggcaggtagaatcaatggactga
aaggcccacccgcaaaaaaaagaaaggaaattgaacgacatgaagctctt
ctcatgcatccgttagcgtatactgcagaacagtacgaacaagttgcaga
ggagtcgaagttctacaaaanttgcttcgaaactactgccgccgagaacg
ttgaacttctaaaatccaacggtcaactcaaaaaagagcttggaattttt
gaaaaaccaacanaggggnatcagttgtaaaggtccgattattggaagtt
tcaaaattccccaaattcg
>CEESB13F
caggagtcaattgatttatttacagaaatcatttagcaaaaaaagtaaaa
ttggaagaaagaaaaatgagagaataaatcatttagaagagtctaaactt
gagattgtgaagaattcctgcagtgattgttttacaagtccttgattggg
tcattctccttcttgatggagtaagcgaggtaagcgtagaaagcggtcca
tacagcgaatggaacgacaaggaggccagccttcttgtcaatcttgtaga
atgcaaaanatgcagctgcagcagtcaaactgacaacagtggtattcttc
cacaaacatcccaagctccttcttcttgacgatcggaaattgtttgcaaa
cagcgnagagttgacactngctncatacaaaccaaggagccaaacttttg
tg
>CEESB14F
acctttagtttgactttattggtagaacctgagaacgagagaaaaaaaat
aaaatatataagtnaagctcattggctagagatgaaatgggaaaacaaat
aataatttatgcggttncttcagtgcttttcgaaagaggttgcatttcat
gcgagctgcggtacgaatctccctcctcgatctcttcaatactctccggc
agtggttttcccatagtttcaggcaaaaagagcaacgtcatcactgcggc
gagcacagccatacacccgaccggaataatcatgaaaaccttcccaaact
tgcttcaagcgatccacatggagatngttacgaagcgggcgatcg
>CEESB15F
gaaaaaagtncgttattcgactttatttncagaatttcagacaaatacaa
aataaaacccgcaaggaaaaaaagataccagattagtcaaaaattgtaca
aattgttgtgttagttgtncagaaagtnccggatatattgttgatgtgct
cgacaatcacatcgtagaatgtgtagatacccngtgcaatcatcacaatg
antattgtgattatcancagtgttattatcagcactctgtgtgactgtcc
tcgttcgattctctgcatttcttttatggggaagtgacagaggacgcatg
tcgaaacaacgagnaatcttgagganttttgaa
>CEESB16F
aatttaaaagtttatttatcggaaatgttgataaggaagcacgaattaaa
attgaaagagggggcggttgaggggggatacaattacaccgngtatcttg
tcaatgaaggttttcatgtcattagaatgagacttgataaacgataaaaa
atgcatctgaataactatgggcaatatgtgtgagatgggtaattaacaat
gaaacatgggngataaaacgancaacatcctaataaaananctcttaaat
acccncttgaaaacatcgnncaaggcgactgantactngctaaatcgaat
ccnatgggcaatcaagagtggatttgttttaccccgtcttggggtccgac
>CEESB17F
gaagaagcaacaaactttatagtaaaaaaatgacaaaagagtatcattgg
agaaaagaaaacggataactgggagagcaagcaattaancaattttnaaa
aattgaaaattaagaaaaggtaatagcaaatgggtggagaaacagtgggg
aagagatttcgatagaaaganacaaaanttgtaaatcggaaggaaaacaa
gatgaaaaaggaggtcgntagactttgngagatggttatctntcgtaacc
tncgtgtctgatggtttncttaatatcccnttctttcaatcgtcagggaa
cacgcacatcgtcg
>CEESB18F
gaacaggtcgtctatttatnctgtnaaaaaccgtgctgttgtaccgtttg
anactgtaaaacagcataggtcagaagaaaacaacatcactatacaaaat
aattttggaaaacgggttgagctaattnatttattggttggcctttctna
gttgatactcgacgacgatgaatggngcccagaatccgnttg
>CEESB19F
ctnattaaaagctttattatgaatgtggctcaaataatgagcatgattca
nagaaaaaatggtttaaaatgtcaattttgtaatgagaaaatgggggtca
tcggcagtaatagggtacaacaacaaaagtgattgcnttaaacctcaact
tcaaaccaaagatacacagagaacctagttatacatgcctagattactac
cggantagtattgaccaaatacaagagangttaccantgaagatttgggt
gagaatgggaagcataatgcagtcggctagagaagttngaactattacta
gcaatgtacacggagagggtgaaggaaaaa
>CEESB20R
aatggtgaaggaaacaggntattatgacgttntcggagtaaagccggatg
cttcagacaatgagttnaagaaggcctaccgtaaaatggcgctcaaattc
catccagacaagaatccagacggagctnagcaattnaagcagatctncca
gggatacgaagtattat
>CEESB21FB
cgggtaaaaatgctcctagataaaaaagaactgtcacacagttaggggat
ttaaaacatgatcagacaagtaaaagcgtgagtaggcgtgataaatataa
actttgaaatatgaaaaaggaaaatgcatttgtggatcattaaaattcta
taaagttatgaaggaaaacgcgacaaaaatagtgataagtacggtattgg
ttactcggaatgtacatcggcaaaaaatgcgacagtgacaagntccaatg
ggaaaaaaggtaaaaaccaaaatganaccatacattggggcccaatattg
gggaaaaattttgctaccaa
>CEESB21R
gttactttccaaaacggacacctcatcagcgaattctggaagctcaccga
ttctctgcaaaaatgttccnggnttaacgcctcaacagaagcgaatgtnt
catgagaatccgaatatcatcaagtatctgatttctggacttcgaagtgc
tcttcacacttgcgagtacacatttnaacgagaagcatngaactntactt
taacacttccttggggttggaacttcacctcttcaaattgcctctcgtga
atcagcttatgtggtacgcgatttttggcggnccngtgntgttctcactc
gttggctcgtg
>CEESB22F
aancttcaataaatttatcagaaaacaaaaataaaacaaccgcgtaaaaa
aaagagaaaacacaaaaaggctccaattattcctaaaatnccaagattgt
taatcancggtccattcttcgncttctccatcttctactacctcgttttg
aactttgcctttngcaggtaccttctgatccttagcaacaatgcaattgg
tgacgncagcattctctccgatttcnactccatcacaaatnaatagggtt
gcttatgggggnaccatttccaatgacaacgcctttggcaatgatactct
cttttagctttgttttttca
>CEESB25F
agaatgaaatctatattatttggaaaaaagtttttaaaaaatccagattg
tgaccgaaaaaaatnattcgaaaagaaaaaaacacaaaanttgaggnaaa
acatgangaaagantggcaaaaagttttttgactcgcaaagaatcaccta
aacatttcaaatttcgtatgaaagtttgtncgctttaatgataactttta
aaattcacattagggcgcactttctgggggaaaagtcgaaggaagaagaa
aaacgtgattatcacagaaaaatcaatgaaatgaaatggnatttgaagag
gattgttggaaggaaaccttgtggattttcaacaaaaaaa
>CEESB26F
gttgtcaagtatactttcagatattgttgagttaatggctcagtgggtgc
tctcattgaaatcgggtgctctacgagtncggaaactgtctgtaagtatc
tttccatgtcgttttccgcagggatttcgtcgtagttaaccttatccaac
accaacatatcccaccactcaatatccggtaccccattctccattttcgc
cgtgcccgttggtgtaaccatcgcaagtttcacagccgatgagattcccg
tcgattgtgcagccgatgagacctcattctgaagcctttcgagctttgcc
attgctctttgcttattcgcaagtttctcgaattctcccttctcatggaa
attgaacccccggcgacgtcgatctngcagttctcggctgaatccgtggg
atccagatactcggatgagtttctccggttccttttggattcttttg
>CEESB27F
aattttttaatctagtagttctaaaataaatctcagactgataactgtga
ccaaatacataattactcatacaatactcaggtcttctattagaataata
atctctaattactaaacgataactaaagaaagactctaataatacataaa
taaataagnntagtcctgcagttctaataataganccataagnggcaata
atatttcataccgnataaacatcagggtaatctaaatatttacgtgggaa
cccgtgtagtcctgcaaaatgtagcgggaaaaatgttaaatttaccccaa
taaataataaaataaatactgcagntatcataaggttatctaacacatac
cctggtaataaatcttcatccatag
>CEESB29F
cgttcacatttnctttctctgtcggtcttaactcaaccgctcccccgtta
caaaaatctcagtcaaaaaaaattaattttgacacgncatatttgtngtn
cttgaggnccccctgtgactttncaaaacgntattttaattgtnctattt
tgtgtcaactactgatgaaagtcattgaaaatgaactcgtaaatttg
>CEESB32F
atagaaaaattgtttattaaaaataaattncnctctatattgatactacc
tttaaattttttacaaaaaaaacatgtctgtgtgtaggcggatacaggga
gggggntaccatcagtaattggngcttaaaattccggaaaaaattgggaa
agaaagaaaccngtaacatttcggatgtntgggcgggcgggtgattgtgg
taagtgagaattggatattctgagaaattttgagccatgggaggnaaaaa
agnncaaaaactgggtgaggntcgggggacattttttttgttgcaaaata
gtccccctacacgtactcaaaaattnggaagtcaaaaaaaaaattg
>CEESB33F
ggacaaatgttcattatcatttacaacttcaatagggcaaatagaaattc
aataataaataaataaaatcagaaaattgacagcttgcnctgaattagac
acttctnctgactgagattctggtgataaaaagaggcgggatcctaaggt
gctcatcgacccgcaggagagaaactaaggtcgattagtgaggaaataca
ttttaaaagataaatcaactaataaagaggaaagatgaattgatgatgtt
tggtgatttntttgaggattgagattggagatcgcaattattaatgncac
gcatcggtttggaacgaatccgtcanttctccatcacaatttcgggagtt
tggagaactgcaaaacagcccantntccaaatcctgctccctaaatacca
ccgcagcagtttaagataagtgttggtaaggtcatccc
>CEESB34F
atntttatgattttattttaacgtgaataaacatcacaaaagtnagctta
ctcaaggggtggggtgtggggcggctaaaccaaccactaacaagtaacaa
aaagaagggtgacagtaagaaaaaaaaacaggagatgggtatgcttagca
actgggggaacgtgctaagagcacttggcaatgaacttattgcttctnag
cggaaacgagaaccgatgcagcttcgtcgaccttcgagcggaacaattca
ctatcttgaagcatcatgatcaactcggaattgtcgatttcgagcatcat
tcctgtgaattttccctgcggtccttgtgtcccgggtagagtttctcaat
gagnagccgtagatacgntcaccaagaagttg
>CEESB34R
tctgagagacacgctgaattgaaaaagaagcacgagcaacacaaggctga
gcgtatgcagaagtatcaaggagtcaatctctacgtcaaaaacctcgacg
agactgtcgatgatgatggcttgaagaagcaattcgagtcttacggaaac
atcacgagtgctaaggtcatgactgacgaaaatgggagatcaaagggatt
cggttttgtctgcttcgaaaagccggaggaagctacaagtgcagtnactg
agatgaactcaaaaatggtgtgctcaaagccattntatgtngctattgct
caacgtaaagaagatcgtcgtgcacagcttgcttctcaattacatgcaac
gtcttgcagcatgngaatgcacggcaaactttccagg
>CEESB35F
aatcaacaatttattaccactttcgttcaagaggttcagaggttgggatg
ggggataatagctgcaaccagcattcacatataatatttnagatgcgggg
aagaggattattggaaaaaggagtgaacgaaagtttcagttgaatacatt
atttcgagttacagaacaatgaaaagacaacgaaaatggggggaatgatg
attgatttagttggtctggcttgggcagtcgcgggagatgtgtccggtct
cctggcactggtagcaacgcttctcctcggccgagccactntcggtgcac
tcgngggaaatgtgcctcgtgccgaattcctgcagcccgggggatccact
agttctagagcggccgccaccgnggttggangctcccagctttttgtncc
cttt
>CEESB36F
cgtaaaaatttgtctttattttgagttcgtcctgatttgcagagctctta
tactaaatgaattgaattgcaaacaattgcgaatgatgatatccacagaa
aaaaggatagtgaaatggagattctttcaagtgggggtgggatgagaagg
agatggtggtgggggaagggtaacaattttaatgataaactggaataaaa
cttgactattggtgttggcatctnacgccttgtccgtnatgtcctccgtg
ttgtncttcgtccgaatcttcattgtaagcgtctccgccacgtcctcggg
ctgtacttcttctcgtcatattcccataaggggaaaccttctgcggcagc
tggggggtgacaattancaacctttttgaggtaggggaaggcangctttt
tcagaaacgggcataa
>CEESB37F
gcgaagaaaaatataaatttnattcaaaaatgattcagaatagaaaaatt
tgaaaagtgtcaaaaataaatgtggattcgacaaaaaccccagaaatttc
cagataaaaattaatttagaaacataatggtaattatagaaaattaacaa
taattaaaagttattaggantaaaacaaattatgaaagantaaagttaag
agaagtcagtgctagagctggatgcagatgctccaaaattgtcaagaaac
tcccgagaaagacccgntgaaggagcaaaccatgaagaaaactggggcat
cagtggattttgagctggctcgtgccgaattcctgcagcccgggggntcc
nctaggttctagagcggccgccaccgcggtgggagctccagcttttgttc
cctttagtgagggntaatttcgagctttggcgtaatcatgggtcatagct
gttttcc
>CEESB38R
attcactcctttttgcttatacccccttcttgtgagtacatcccaccctg
tagatgtgctccttgcttgataaaccaggtccgcagtccgatttaggggc
tcgtgttctggaacagttaaggaaaccatgctcttgttgttgttgttagc
tgttttcgctgctactagcactccttttttgtcctgagttgatcgtgttt
gaagcggatttccgatctaaatttttataaattaaaaagaacctttttcc
aacaaaaaaaatccaaaggaaaagagtttggaaattcttnggactctttc
ttcggacttttaaactccaattttttcactcgactttcttaggaataatt
tattctaggaaaaaagtacggtttttcccaacttttccc
>CEESB39FB
atctggacatcttttatttcttgttatatatacaataagacaagacaata
caagactactgtgacagatcaatgggaatcgaggacaagcaagcacgacc
aattcaaattatgtacaattcctttattattaaacaataaattattcgaa
ggaagagaaaacattaaagtacttgtggtggctaacctctacggtatcct
gggcatcagaagagtgagccttaaacggntcagctacatcagaagctttt
tccttaacggagtccataggctccagaaattttatcaccgattggtctca
gtgatagatttggacttgtccttcgccgagtnagcaagcgtcttccagca
gaattnccttgggcatcggagggccttggtcccttgggtgggtattccca
aggcattcagaangccttgtcccttgggttgag
>CEESB39R
caaccgggacagcaaccattgagatcgcttagcttgacgtctgcggccaa
gtcacctgaggaggttgagccggagcaggattcgaagaaaggagagccac
gtgccaaggctgcaggattcggaggaggtggaggtggtggaaagagactc
ccagaggcaagatctncgccaatggtcattccgaaccaggtagcagcgat
gccggttcagatgactggcttcgtncaacttgtngncaacancattctca
gcgncattttcccataccaactctgttnatggggttgtccaatgnatcaa
ancccttcgagatctttta
>CEESB40F
gcaatagaataaatttataagcaataagcagagcaagacatgaacagcaa
atgacaaccggcaacattctttaaataatttttacagagagaaaatacaa
tataancagacattttcctttagattttacgtttagtagcagtgaaacgt
tcttgataagcatcatatcctggtaaatcttgaaaatctttcaattggaa
tcgatttccgtcgtatgacatcacggaaattgttgaagattctngtaaaa
tcgcgagtgaactccgacttctccaaacagttttcatcgagacgaagagt
cctcagtcgtgtagttttggcaagatttgntggatttanggagctcagtc
gattttaattcagacttnaactcgataactttcaaat
>CEESB41F
aaatatgatttgatttattatagttatatttgtgatgaaaaaagacatca
tggtgagatgagattgataataaatatacgaaaaagttacaagcgaaaaa
ncgaaatgtnctgtagaagttgattaattagatcatgaaagtnccaatga
gagagtgttagggacatgaataacgggtaaaatgctgtttaanatcaatt
atagtaagttttttgataaagagtagaaatatataatgtaattccncaaa
atgaaaagaaaaganaaaccacaacanctcattaaatanttgcaaacgac
gactcatctacattgtccacaattgcgggattttcgattggaatttggtt
tttccgacg
>CEESB42R
cggcacgagatgatgggacctataaaagaacagttggttcattggactcg
gctatcgcaggcagattagaagctgaaggatctttgaatctggaaactct
tgttcttcctccaaccaagcctcccggtgatgatgttacaactgggtctc
gagggtttntcactccaacacattnaacgnctgcactcgatatgtcattt
ttcactccacctcgncaaatgcgaactttggctgatgctgttcgtgaagn
tgcacctgttggaagtgatccccgaatttttttgaacctgat
>CEESB43F
aagatactcacattttatactcaaaaaaagggtggaaatgtgactataag
anggtgataaaagaagggtgggtaacagggaaagaaagancacaacacga
ggaaaaggagaacatggaatagatggntggngatgaataataaagggggg
aaatcngtgtgtacactaantattttncaatattatttatcaacnctgat
aagttacaa
>CEESB44F
gtaagtaattagatttattatttgaagattattagaatatttagaactat
tattaaatctgaatgttgttagtaatagtaacgggctgatcgancagcgc
gttgagtagctctgaatggaagacgagagacagttggtccctggtatact
gtaggagaagatccataggntcccatggccagtggaatcaccattgggta
tccagaagtttttgggtacattggatatccattgagtagtaatggttgac
cacctcccatcatcatatcagatgcagcgaaacgaggcttatacatgtta
gatccatacgtatccattcccatcatactgctaggaaagtcccatacggg
catcttgttgcaattnccttngcatngttatgggatactctgaaatt
>CEESB47F
aacctaccacaacttcattagagcacgagaaaattacgagagacaagttg
tgcggaatgggatggtggtggaacttgaagtttaaataaataaatgtttg
gttggataacgggtagattaaaaatgagcagaacatttgaaacacaaata
cgggggaaaacgggatgcgtatatatttaattagaccctggaagatgttg
agctttgtggagtaccagatggagttctgcggcttgaagggccaacgaat
cggtttgagctcactgaagtagctgcagatgctcttgnattganttgatg
atctggatccaatggaacttccagctnggcgtagttctggccgatgttgc
tctgctccgaattcgcgctcanttgcaatcaacggggggacagattggct
ntcggagcataacttccctgg
>CEESB49F
gaaaattaaaaaattattatgcacaaagaatatacaaaatgcttaattgg
aaaattagatcaattgaaattncagcaaaaaatacagaaaaaaaaatgca
atggtttcagtaacaatatctacatatgcncacacggnttcantagaaat
tttaaaaaaagatataaatctacaagccagtnctctccataatagtttgc
aagtctctctgaagaattatatttttngaaagtgtctcttcaagcattct
ttgcagctttttgttcatttcacggacatctgaatctcgggaatcttggc
cangtgtattgagcagttttcggaatgacgcttcangtttcggttgacca
gangaaggagaagaagnaccccaggattattnctgttggttgaaatccgg
tgcccaggagggtttttcgcggg
>CEESB50F
atcaaagcgcgcttaaatgcgaactccaaattttattcgccaaaaatgct
tgcctcagagcgctgtgtgattagtgaaataaaataactaaattatatga
ttattataatgtgtataaaataccaacaagttcaacaaaaaagtgatcaa
aaaatgagggcagatgagaaaaggaaaacaaagaaaatcaacaattggta
aaaaaaaaggntgaaaacaattggaacatacagttttttagagaagaaac
aattnttcgaatttngttctcttattatnctgtcctccgaaacttccacc
atcgtatgancgtttgaggnctccacgtccgcgncctccgaagtctcctc
cacggcca
>CEESB51F
aaaactctgaattgatttnttgaaagctgaaagactttggatttgtgtgc
accgagagaaaagaaaactgaatacaaaaatatacacatagagatgaaaa
gatagagaaaaatttnatgttttgattaactcctaaaantttnccaaaaa
ancgggaaagagtgaattatggaaaggagaaaaaatgatagangataaca
aagggacactgggagaaactttgttttcagaaagngaagaagacccgtag
ttttancttgagtaataantancgttnaagcgtattancggcgccaccat
tagaataagtcgcttcgatgctgaaacaggctgctctt
>CEESB51R
cgatttcgaatcatcttcgcaagacgctctggcgacaccaaccaaaaagt
tctcttcccaatgggaaaaagacgtcgatgacgttgaaggaaccgccaat
gagcttgttcgtattgacgaacgtatatcggatattacagcacaagccga
tgttattcaagacaagatccgtgaaacagaagttggaagttcagaagaag
aaatgttgactgcatcatatcttgagttgacaaatgaacggaacactctt
gtacatcgacaggaatactataatatcattgagacaattcgtcaggttac
ttcggaattgaccattggggaaacaatcatgaagt
>CEESB52F
gagcacagcactgacgagatgaagaaacttgttgaaagtttgagtgaggc
gtgcaaaaaagcagccgatgagttcgacagtaacgagaaaaatggtgatg
ccggtgcagcggaaagtgaaaagaaggacatcgaaagaaaattcaaattt
catacatgtgacgttaatctgaagcaaatcgaacgaagtcatgctgagct
gaaaccattacacgaaatactcaagtcagaagaaacgaaaacttcattca
aaccaccagcaaatgctaaattacaaaanggttgggatgttgattggagt
cgacctgatgactcggcattgctcctgggtgtctggaagtacggttacgg
tagttgggaagcgataaaaaatggatcctactctttggattggcctcgtg
ccgaattccctgcagcccggggggatcc
>CEESB53R
gctgtacagtctaaatccaacccgtggtgtgcgtttccagactaatggca
agtttgtcatgccagccagagtaaagtcggtgacgattatcaactacgac
aaggaatttaatagaaacgtcgntatgtttnccgaagggcttgccaagca
ttgctccgaacaaggaatgaagtttgatagccgcccgaacagctggaaaa
aagttaatctcggctcatcagaccgacgaggtacaaaagtggagattaga
agaagccatttcgaaacggcgtttacggtttgttttttttggaatttatt
t
>CEESB54F
acgaaggacttcatcgtgatttcgcctgtnttctctactcaaagcttcaa
aagaaactcactcaacaacgcatctacgatatcatcaaggacgctgtggc
catcgaacaagaattcctgactgaggcacttccagttgacatgattggca
tganctgtcgtcttatgtcacagtacatcgagtttntcgccgatcatttg
ctcgtcgagctcggttgtgacaagctttacaagtcgaagaatccattcga
cttcatggagaatatctcgatcgacggaaagactaacttcttcgagaagc
gggtttccgagtntcaacgtcctggagtaatggtgaatnnaagncgcgag
acagtttcgatctttaaggctgancttctaaaggaaaatatttccaaaat
ttctaatttctaaaccc
>CEESB55F
agaatttacccaaaatttattgatacaagtattattaaaatttggnggca
aaatagaatcacgngaatgaaaaattgtgtcagagtacagtcaatgcaca
gtcaattatacagaaaaggtaaaaatttgaggcgaccnattcagaaatct
tcatcatcctcaaaatcgatatcaatagcattaacagagttctgaagctc
gtcgagcccggtgacttcttcgagacgaccnggcgagttcataacgtcgn
gaacaaacttccagccattttnctgaaacttgtgcagcgataggngctcc
ncaagcaacacattgntccgantcgtttttacagaaaggg
>CEESB56F
gtttttataaaatattattcatcaacaccctcaaataaattaaactgttg
cgatgaagtggaccagccatcgattgcnctccgactagttcacagtggtg
gtttcggagagtttgaccaaaaaagacggccaaatatcacataaattagg
acagggctcgggctagaacgagcagccaacgccgtcgggtagcataggaa
acgacacccggcaacgntcacaactaagcgnccagtcaccaagcttgtnt
ccaagcaacatcaactgtntccggttccactccagcgatttcacgttctc
ttgaactctctcttcaaagtcctttgcaactttccctcacgggacttgtt
cgctatcgcantcgagtcgattatttagcctnagatgaagtttatcaccc
actttaggg
>CEESB57F
atatatatttcatttatttagatatattatggttatttacgggacgtcat
ttaaagaacaacatttaaaagttaaagaaaaccaaaaaaaagaagaaaaa
aatagatcattaattgtagagggagagatttgtttttcctattccttgga
ttcttccacaacttctgcgtctttatcctcagactcatcaataacaattg
gntctncttctgtagatggctcagcagcctgctcagcactcgctggaact
tcttnagaaggttcttcagntgattttncagcggatttctcggatacttt
gtcanccttctnatcggttttctccntttcg
>CEESB58F
aatgtgaacaattttttaaatgaaaaccaacaacaataacaatagagaaa
tcataacaacgaaaaaacaaatcgngtaatttatagaatggtcttgttca
aattgctgtatcctacaccaacagcggtaaccatagctttatcggcactt
cctgttttgagatcagcttcctcttccttcaatgtttttttaaagtcttc
cattttaaactcgatctcaaaaaactgtttgagatgcctgagtgcgtgta
cactatacattggaagaggaccgtagaggaagtgtgaaacatctttagga
cagagtgtcataaatgtgcttgcaagtatttgagcactactgtcaagggc
acctcccatgtaaatttgttgaaggaggagcatgaccggcttcaattcca
atgtcttctggga
>CEESB60R
gctcaagctcctcgacgagttcctcattgtcaaggctggagctgctgagt
cgaaggtcttctatctcaagntgaaaggagattactacagntacctcgcc
gaggtcgcttnagaggatcgcgctgccgttgttgagaagtcccagaaggc
ttaccaggaggctcttnatatcgctaaggacaagatgcagccaacccacc
caattcgccttggacttgccctcaanttctctgtcttctactacggggat
ctttgaacacttcag
>CEESB61F
ttcatcttgaaaattttttttaaaaatgcacaaaaatttgantttttggc
aaaatttgtgttttcacatataaataaaataattccgaaaatcgtaataa
aatgcaacaaaagttattgaataagagattaaaagcaggaggcacaacat
agtagtcatgaatcctctcaacacgtgcataatcagtagaaaaagaagaa
gaagaagacgtgaaaagagtatatgtatgtnggagagacgcagagaagca
cacaaaacgaattggaattatgatgatgatgaagaaggaagcgacgatga
ttcatttgggaagagtgtagagcaatcttattgagcgcttggcggatgtt
caacttggttcgattgcagcaaatcgttgatattcttctccaaatcatcg
attctcgttgtcatatcatccgattcgccgaataatctgatnccgccatg
tgcttggaatcgatcccgtgtctgt
>CEESB62F
tccgggtagagcttgtttattcacaggtgtacaataagaataacggctaa
aataaatagcaaaaaaaatggttctgtgtgctttttgggaacaaattgag
attatgagatgattttttgtagatttttgtgtgatttatgaacagaaaat
gtaaatttgaaaatcgctattactggttacgggaaacaacgggaaaaatt
ctaagaagaatgatggagtctcgggatatgaagagaaaatattacacaat
aaattattaggaaacatgtttcataaacatcttgatctataagtggccnc
nttggaaggacattttggttgggaggaaacgnatcggaattggtttgaca
agaacccgtaaaagtgcaccancaatctgaggtg
>CEESB64F
ggggttttttgtaagattatttgaagaaagtacaataggaaatgggaagg
taaaaaaattggatgagaaattatgaaatgcagaatgaatactgctttca
gtaccaaaaagtatagccaacaatttttncnctgaatatcagagaatatt
acgaccttggcatgcaagatgaagttagagagcttagtttttagcagttg
gagcagaagtagaagcagcagcactctgagcattggtgagcactccaaag
gcttccncgaccttncttctgaacaactcagcgtcttggagcatcatgat
caactcggcgttgtcaatctccagcatcattccagtgattttcccggcct
cccttgtaggttccggggaacatcttctcggtaangagcataggata
>CEESB64R
ctcgtncaatctcggcagntgtncatttaagancttggntcgtgtcattg
acaacaagtccgtctacgacactttctcgctttttggaaacattttgtct
tgcaaagttgtcaccgacgatgaaggaaacagcaaaggatacggatttnt
tcacttcgagactnagcactctgcgcaaactgccattnagaaagtcaatg
gaatgcttctttctgataagaaagtctatgtcggaaaattccaacctcgc
g
>CEESB65F
aaaanttttggtaaaaatttattagatgacccagtatgttttgacacgaa
tgcaatgagagaagngacttgcattgcttacacaacacaaggggaaatac
aaaaaagcaagngatagcaaaataagtagcacagggcagantaccntctt
aactgacaacatcgtaaacaaaaccgntaatcgccttattagtaaagatg
agatgatatgctgccaagagccgttttgagaaagggggaaagagangtaa
aaatgaataagttaacggtgtttgacatttaacaacaggtccntggaacc
ccncntgcgttgaact
>CEESB66F
gaatgntttgtaaaaactttatcatgttttaaaaataagancatctgaaa
ttggaattgaataaaaatacaactaacttataggaagactnctgattatg
aaacgaaaaattctacacaagaaagatagcagagggagcagagcacaggn
ncttgtncattttattaatgagcatttaaaagtgaaggaagtgggancat
ggagcaaaggtaagaaacatttggcaggagtatttcnnttttaaaatgta
agtaaacgtcngggnaaaatgagc
>CEESB67R
gttgattcggaaatcagtgaggaggaagaagaagaagaaatatataataa
acaaacaaaaactaatgcctcactcgactccattcatagaaggaagtcta
aaccccaaccaatgctggagttcgacgcggagacgcaaaaaatgtttgat
gatgcgtttcaaagtgacaaaaaatctacaaaagaaaagtatccgttcta
atttctgaaaaaacatcagcacactgttctattggttccactttcctttt
tattccatctttattgtggttaattatcccatctacttctctatatttcc
ccttgataattaaaattggttttaatggttt
>CEESB68F
aattactattttacatttttattcttaacacgcatgactgcctgaaaatc
tcagtttcaacaatggaaaacatattttacggttacaaaaacaaataaat
gttatagagcnctattctaatttnncatttttaaacattttaccngcaac
acaattaaaaaagtgggtatcaacagttagttggctaccncagangtatc
acacaaggntcgggacg
>CEESB69F
aaatatacaacctttattgagaagagaccatttatatacttgtaagcttc
taggaaaatttnagatactaaagagaagcatagattttaagacaagcagt
taactaggtgaaagtaggatgagacagcttaggccttggtggcgatgtac
gagangagatcaacaactctnttggagtatccganctcgttatcgtacca
cgagacgagcttgacgaagtgtgggttgagtgagatggatgctccggcat
cgaagatggaagagttggtatcggtcgacaaagtcggtggagacaacttg
atccncagtgtaagcnaggaattncctcccattcggtcccntcagngggc
agnctttcattaactttctttg
>CEESB70R
aaacaactcgaaattnaggctagctctctccgccgtgtggctcttgttgg
agttgccgtctccttcaccgccacattggtgtgcgtcattgccgccccaa
tgctctacaactacatgcaacacatgcaatccgttatgcaatccgaagtt
gatttctgccgttcccgatctggaaanatctggagagaggtttcccgcac
tcaagttctcgccaaggtttctnggaggagcccttcgttcccgncgtcaa
gctnggatacggagagncgcccgggagttttgaaaggntctttcaagttt
gggacaaccaaggg
>CEESB71R
acgctttcaatcagaggtaacaacatcagatacatcattttnccggatcc
actcgctcttgacacccttttaatcgacgatgaaccaagaaagaaggccc
gtgccgctcgcgccggagcttcacgtggacgtggtcgtggtggaatgcgc
ggaggaagaggaggtcgtggtcgcggacgcggaggaccacgcggaggcgg
tccacgtcgttaagctatcatcgggtcatagcaaatttgagtatcgaacg
tcctatacttttgtatcacgttcctcaagtttaattcacattttgttncc
cgttaaaagtttgctgacttttgttttaaanctttttgaaattaatttan
ttacggg
>CEESB73F
aaacttcaatttttatnctaattaatcgtcaatattcaaatncgacgaaa
attttcagattaccaaatatttggaaatttggagaggattttntgtggga
gagggatggggatagagtataaganttncgagacgcagggtgaatatttc
ctttaaaacaagaaatgggggaaaaaaaggataatgtaaaantaacatgg
atttncaggtagtnctagatgggggtgggtttaaggcagatttcacggta
gcncagggtttgtccggntatttnagaggaggttcttgagaatgagaata
tc
>CEESB74R
caaaatatagaagtcactgcatctnattctgcagcagaacatgaagtgtt
tgaaggaatatcatcaaatattgctgggaaaggagaaaagttagaagaag
aaatagataacattggtattgtaatgcaaccagagccacgagttgtccat
gaagcttccgaagtatcagacaacattgaacttaatatcaaagacgacct
aaacttgaaaagtagactggacaacttcacaagagctaaattcaggcaat
caaccaccgtaacacctaatattgttgctgtggagccttctattganggt
gttgaagacggttttagatcat
>CEESB75F
gtatcgtctcatcaactttatttttaggcatgtacaatcacgtaaaggac
acactgatgtncattggaggaaatgtgtgagaatctcacactgcataatt
tttnccggtcggtgatttataggtataaatatagantggcggttaaaatt
caaaagatgcatttnaattaggtgaaaaaaggaagaagtttttgggctgc
cagagatgatgtaaaaaatagacagagaccatatcaggacaatgtgtgaa
gtgtgaaggggaaggaagcgacatgtcgtttagaaatgtaatagagaaat
aggcaaactgaagggtaatttantcctcgcaccagggcattctctttgcg
g
>CEESB76F
gacgctcttcagtaatttattcaggattctcagaccgccagatgaaataa
acgaagaacgaatgtntggtggtttggaagaaatcctttttcaatttctc
gagaaaaatcagaggaagggaggagggagatttggagacaaaatagttta
aaggggatgagagagaattgaggggatcaatctacaccgttcgatttact
tttgaattataactcgtgccgaattcctgcagcccgggggatccactagt
tctagagcggccgccaccgcggtggagctccagcttttntnccctttagt
gagggttaatttcgagcttggcgtaatcatggtcatagctgtttcctgtg
tgaaattgttatccgctcacaattccacacaacatacgagccggaagcat
aaagtgtaaaagcctgggg
>CEESB77F
caagaaaacgtttnttttatctatcaagtgtagcagaaggaaaaaagaaa
cagagtatacgngtagtacaacaataaaacggaaaacagtaacaatagaa
attgaaaacaaaaantttggcaatttagtcggtatggaagtnagtgctca
tctncggtgtgcttctttcttttncttggaattnctncttcatctgcctc
cccaccttcagctccttcatttnccggttgtngctgctcgcggagtcgct
tcaggncgggagnanaaagttaagcccggggggcccaangggggggaacn
nnaannannggg
>CEESB78F
attaaaattttacttccatttcagaaagaaagaaaccaagacgattaaaa
agcactgtncaggaaagaagagccacatgagatagaagggacaaattttt
naaaggttcgcaagtnttatggaaggatgtatggggacagaggtacagaa
cagttccaccaatttgaactagccaaatttcaagtagggggcataacana
tgtgattcgattgaggggcaagatacgnttgcaaaanacatcnagnaaga
aagcaacntgggaagtgngaaag
>CEESB79FB
ggantaaaatactttcatcgaaaatataattgaaatgaaaagtaatctta
aagaggntaatttacattgcaaaatacaaaacagtcgaacgagcacctag
aacgaaaatggtccnggnaaagctcaagctcttctcggaaggancatcaa
ggcattttggtaataaattgtggaaaagccatagcacatacactttggag
cnaggagaaattgtgggaaaagagattttaataattctagaaaaaaagtt
tacactcgagaaaaggcaatgaaaaaaggttttaaaagnagaaacaagct
gggattatggtagggtaaatttacaaaactcgcaaataaagc
>CEESB79R
caaatnccgcttttaagtcataccgtnatttatacttcgagggaggcgtc
tcatcagtttacttctgggacttggataatggaggtttcgccggaattnt
nctcatcaagaaagagggagacggagccaaaaatataacaggatgttggg
attctnttcacgttattgagatcacggaaagagcacgccaggctcactac
aagctcacctccactatcatgctgtggctgcagacaaacaaaagctccag
cggtgtgatgaacctcggtggctccctttacaagacagcatgagatgggt
gcaccaatcaacggtcagaacac
>CEESB80F
agatcacaacgtatttattacttctcctncttttcaagaaaaatagtcca
gacaagcctaatgagagcctgaaagcctggaaattttgtcttgatagtga
tctattcgatttcagtgaaaaaaatcgcaatccgtacagatggtagaggt
ggaaatncgcaaaaaacgccaaaatctcagtggaaagttggcaaatttnc
gggaaatcgcaaatttcgcgagagaaatttgntactttnccccnaaaata
gccnagnaacagggnaaaagatgg
>CEESB80R
ggaaaaacgggttttctttcggcgaaaattttgaattatttagtgaaaaa
atagccaaaattctcaaattttgcacggttttttcaatttttttgcaaat
tttggtgcattttccgtaaaaatcgacaaaaaattgcgaaacacattttt
ccgagttttttttttgccgatttcgtgcaaaaaacgtgggaaaatctgca
aaaatgcagaaaacaggnaaaaattgattttctgccactattttgcaatt
ttcggtcgattttagtgcatttttagccgattttgactgaaaatttgcaa
aanattgattgaaattaaattttatcggttttttcccgatattttgg
>CEESB81F
cttaaatcgtttattattaaaattaaaaattgttataataacgnaaagcc
attaaatgaaataaatattaaataaagatagaccagaaccacaaatgatt
gtaccaccgtatcaggaaaagagcactcaagaaaaaagtgaatttttggt
tgaaatataattttaaacaacaaaaaaagaaacatttttgaaatgtaata
ntaaattatttagaaactttccaaacangtttctggcatctgatgtattc
tgcgagatgaagtgtcagttggtncganttcatacgttttgcattggaaa
>CEESB82F
aatgtgtaaatgtgttcatgtncttcatgaataaaaaatagagtgataaa
cgattacatgagatgacagagtgntaacaggaaaaatgtgggtatttttn
aaaaccgtaaaagtctaagggtcaagaaaatgaaanttgaaaatcctatc
tgtncacgngtgcaaaaatatgtnccacg
>CEESB84F
aaaaatatgatttactaaatgattagaaagcttgcaataccgaaatacaa
aatattggcgaaaatggaaatcccgagcgatcggtactttcaagaaaagg
aataaattaagangaaatacataaagtcatcacaatagaagagaactaga
ctgaaatatgaaaagaaatagagacaggaagcaagantttagaagaaaat
aagatgaattttaaaaatgcgagangaagaaaattcagattctggtcacc
gaaaggnaaatggaacanttttagagaaaggagatggctgggggatgagg
ggaaactctatgcacaaacacaagaagaaaaaagcaccaacacgncacaa
tattcaaatagaagtatatatctncttaggaaattaaat
>CEESB84R
ggcacgagctcattcgaaaaaatccttgctgaagagcgtgaagctgagga
gaatctctaagatcacctcggccacttcaaacagtgtgacatcgacgttc
gacaaatctttaattatttatttctagtagatatatacttctatttgaat
attgtgtcgtgttgtgcttttttcttcttgggtttgtgcatagagtttcc
cctcatcccccagccatctcctttctctaaaattgttccattttcctttc
ggtgnccagaatctgaattttcttcttctcgcatttttaaaatttcatc
>CEESB85F
ttttttaaatatgtatattcattttcaataaagcccatttaatgagaacg
caaaagtacaagaaatacagaagtcagtgcaatgagatcgcatccacgtt
gagaacgtcacttagttggtcgaaatcgctgagatccttggcgcactcag
cacatcctttagtccattgcatgcagtacacaggatgatagttcagatgc
acaatctgaccatcggcttttcctacccaaactaaaactcgacagccttc
cgtctcacaatatctcccgtatctcgcgnatttnttgaacgccttcgtgt
cgaaacgncttttactgttcaaggggaacggttcggctttctgggaactc
aaatcgcagtagagtntgctcggttttgaagttttggcgaccccactttg
cc
>CEESB86F
catcacttcttcttgctgagccttaacggcatcttcaggacgagaacgga
gtgcagaagtcaaaacgctgggagattcacactcgatttgcacaatagta
gctgctgatttggcttgttgtcggattaaatcaacttctccttcagtatg
agcaacttcgcacagagcttccaaatacgtcatcgcctgtncagtttggt
tgcagaaacgcgtgagtttcgaaatttgagcgttgatttctcgaatcttc
ttgtcaaattctacagaatttcggaggaactcatcaatttccataaccgc
atcggccttttctttacacatttgctggcatcttcccattcgagtactac
aaagattcgctaaaacgacccccttcggcttccatttttcccctcgtggc
cggaa
>CEESB87F
aagacataatagtgctttgttataagcaattcatcgaaaatttagtgctc
ggcaacagcttttcctttctcctcgtacaatttcgccaattccttcggac
aagtatgcatgtatcccttgttagcagcgcaaatctccttcattctagtg
tacggntcgtagtttgcgaaaaattcttcatatttgttgtgacgtggcca
gacgtaaaatgcgttgaaggcggcagtcgagacgacagcgacagccagtg
aaacgnnaactcgtgccgaattcctgcagcccgggggatccactagttct
agagcggccgccaccgcggtggagctccagcttttgttccctttagtgag
ggttaattttcgagctttggcgtaatcatg
>CEESB88F
atattagtaagatcatcaataaacaaacacaaataaaaataatcacacta
catcaacaaaatgtcaatataaaatagcaaattccaaccccagatgatga
ttataattaaaatgattttttagaagacgtaaaaaattaaatgctaagan
caaaccaccacacaaggcatganttccgtgaaatcccgtagataaataaa
aaatccttccaaatactccgtctgcaatagaaaatctagcttctatatac
tctattaattganttcctgtaaaataagcngccaataaacatgttaaaat
tntactattagtacatcttttatttctaggtnatctgtggatgtgctcaa
gtttactgtaacaccactcctttaattaaa
>CEESB89F
actcaaaaattgttcattcgaatcctataaaacggcgggaaaaagtgatt
ggagtgtgatgaaataacggaaaaaacagaaaaacaataaaaattactag
ctattcaaaaaaaaactacaaaaaaccggaaaaacattaaaaaaccagag
gaaaattaaaagaaaattatttagagacgactccaacttgagcaggccga
attggacgttctttcaggctgtagccgatctttgtacacacttcgatatg
tccgacaggttgtttggcattagcagatggantctggaaaacggcttcgt
ggaggattngggtcgaacttttccattggttggatccacggtcacaaagg
nccatgctttgcgaatggtcttttgcccatgaccagtacggggtcatttg
aaaactccttcc
>CEESB91F
caaagaaataaaatttattttaggcactgttgagcaaccngagttgtgga
ataaaaataaaaattggaaaattaaaattncaaaaaaaaaatcgaaattt
ttttaatttgcaaaaaacccgaaagtggngaaaagaaatgngaaattnta
actggaatggttttttncgttgaattgttgactaggatgacacgtggata
cacatatcagangctgataaggttaacggancaggtgaagacttntggag
accncggcggtgagccatttcgggt
>CEESB92F
cgaaaaatttcaaatttatatgatgaacttgtttgggtgtgaaaagaata
ggaaggaaagcagggaaatgggatggagancaaacaaaaaagtagttttt
tttgaagaataagaagnaacatttggagaagaagttgaagcaaattatgc
acaggtatcatgtaatttncgnaagnaaaaaaaacacggngnaaaatgat
ttagagacgntcccaagagatttcagcctct
>CEESB94F
gagagagaacgtcaagcttcaaagcttccgggcgtaaaatctccgataca
aaggcatgagggtgacagtaccatagcttccattgacactccgaagttga
tgaggttggcaaaggcatggggctttaatactaaatattccacatcacca
atgtgttctccctctggataatttggaatgactggatgtgcatcaccatc
accaccaccgnctgctcgtttgacacgtttctgaggtttgttccagaacg
gccactgcggccgtccttccgttgccagttttcgaattgcatcttctatc
ctagtatctctttcttctctggtcatattggcgatgggcaagtagcttgt
tggggtatcagcatagacaagctttgactt
>CEESC01F
gattataatccttcactggaaataaattcttccaattgataatgactgag
gaagtgagcccaatcgacgtcttttgctatttgcagtttggaaacattac
tctgagtgcagaatgcatcggttttgtagtgacaagttttatggcatacc
attttgcagtctctgcactgataagcttgcttggaaaaactgcttcgaat
cctttgctggcacacattgcacgtggcaccgcctttnactttgacggcaa
caaatgtatgancgttgtagatgtgaagtttctttcctttcctcattaat
cgagatgcagctggctcattgagcattgctggagggatgaggaagtattt
tt
>CEESC02F
agacgaaggacttcatcgtgatttcgcctgtnttctctactcaaagcttc
aaaagaaactcactcaacaacgcatctacgatatcatcaaggacgctgtg
gccatcgaacaagaattcctgactgaggcacttccagttgacatgattgg
catgaactgtcgtcttatgtcacagtacatcgagtttgtcgccgatcatt
tgctcgtcgagctcggttgtgacaagccttacaagtcgaagaatccattc
gacttcatggagaatatctcgatcgacgggaaagactaacttcttcgaga
agcgggtttccgagtatcaacgtcctgggagtgatggtgaatgaagccga
gagacagttcgatcttgaggctgacttctaaag
>CEESC02R
gcacgagaaaatatttccaaatttctttagaagtcagcctcaagatcgaa
ctgtctctcggcttcattcaccatcactccaggacgttgatactcggaaa
cccgcttctcgaagaagttagtctttccgtcgatcgagatattctccatg
aagtcgaatggattcttcgacttgtaaggcttgtcacaaccgagctcgac
gagcaaatgatcggcgacaaactcgatgtactgtgacataagacgacagt
tcatgccaatcatgtcaactggaagtgcctcagtcaggaattct
>CEESC03F
aattcaaaaatttatacagaaaacagaatgcaaagaaatctgtacgtgag
cttttcataaaagcgcattcaacaacaataagttctacagatataaataa
atatcgaaatctcttgaggggttggaaagggagaaaatgaaatgagggga
tattgtaattacacgtcattgatttggcggaggggtttcatttgaaagga
cattattaaagctctaattaaaagttttnctttaaaaaaaagtgatgatg
agctgcagaaaaagggacttcccgtgagttttcagatgtcaaaaagttaa
ggtcagaggagttcagaaaaatgcaattgggagggcccgaagtgagatgc
atttttcactagggagtttcagggaaattacgg
>CEESC04F
gatcatcgcctggttgaagaagaagaccggaccagtcgccaagccactcg
ctgacgccgatgccgttaaggagcttcaagagtctgccgatgttgttgtc
attgaaggattcacaaagttcctcgagaccaacggaaaggagggagctgg
agcttccgaggaggagaaggccgaggaggaggctgatgaggagggacaca
ccgagctctaaatccacattccaatacagttcaacgcatcggggttccat
ggacctgttgttaaatgtcaaacatcgttaacttattcatttttacttct
ctttccccctttctcaaaacggctcttggcagcatatcatctcatcttta
ctaataaggcgattatcggttttggtttacggatgttgtcagtttaagga
tgggtattcttgccctgtggct
>CEESC05F
aacttgcttcttgtatattcagagtccgaagatgatccaggaactctgaa
gatcacagatttcggattggcaactaaataccgaaaggatggagaggaga
tcatgttgagcgaggattgcgggtctaagccctatgcagcgccagaagtc
tgcacagggaacgattatcgggggccacccgtcgatatctggtcggctgg
agtcgttttgatgacgatgcttgttggggagcactcttggaaagttgcaa
ataaagaaaaagacgcggcctacagcaactggntcaatgcaaaagacgaa
aaggcgaacctgtggaatgtgatctccggaccaacgacggcgcttcttcg
caaacttctccatgcgaaccnccgaaaaaaggggcaacaatggcg
>CEESC05R
nngaaaaaagggcaacaatggcgaaaattgtaccggaaccatggntccgc
ttcaattttttngccattgttgcccttttttcggggttcgcatggagaag
tttgcgaagangcgccgtcgttggtccggagatcacattccacaggttcg
ccttttcgtcttttgcattgatccagttgctgtagg
>CEESC06F
atcaatagctgtttattgataacatagtgaacagtctgaacagtttctgg
ggagagatatttcacgaaaacataaatttttaagggaaaaatggggagaa
aatgtgtagaaaaaataggaacgacacaatgcagagatcaacgntcatga
gatgaaaacatacaaatagatggaccaaaatagctgaaaatttaaaaaaa
agaggnaaaattacataattgcgcaactatttctgattgattcaattatt
gaagacttttgatttttaatagccggtggtgctgattcggtctcccacca
cggacgtggacgctctccttttgacttttnatatcaatgatgtcggtcct
catcatcgnccctcangtggacccatgttggaatggctccagaggaacgc
ttgttggg
>CEESC08F
aatatgaaacagattttattttagtttcaaatgcaatatattgcaattac
aaccacaaaaggggaaaggaaccgtaaagtgttcgagaagtactgagact
gagaagtggggggagaaacaacattaaataaatagaaaacaacacaagtt
atcttatcttatcacaatatcatcgagtgcataaagctaatggaatgggg
agatgttttacattgtttagagctcagagtgctcctcctcaatcgttgtt
tctncagcggcttctggctctggttcagcctcttcaatatgctgttcggg
ttcaacttngagcatcttggggnnacatcgagccgattgggcgaagg
>CEESC09F
agtcgctgttcttttttattcagaaaaaaaaagcttcgaacaaaaatggc
aaacaaaagctggatgggatagataacaacaacaacaaaaagaaactaac
aacaagagtaaatatgagaataataaaaaaatatggaaaaagagaactgg
ttgataaaaaacaagatttgaaaaataaaatcaacaatttaaatctaaag
ggttctagttttagaatgtattctggcgttttccaacgtttacgtttcca
ggaagttttttcagtccttttgtgaccagagcattcgggcgtcggctcac
ttctttncgttcagctgcatgagctgcttgtttcgtctttgccagcttct
gcacgaaggatccttatcacggtttcgaaatcgtga
>CEESC10F
gaagttggtgttacaactttattatgtgtattcaaaagcttgggggtgtt
tcgaatgtcgagatttgaaagggggaaaagccgtaacaaaacggaacatt
gaattgtatgggtagagacgggaagttttgatgagtgggctcagcacaga
aatttgaataactnctgcatttggttgatgggaaaaggggagtgattgat
gaatttatagaaaaaaatggaaagaaaaacgatggtttaactagtcaatg
gtaataaataaatcatatgacaaatagtattatttatcattttcaagatc
naggtgaggggtgtgtggcggtaacgtgtcggtntgaaggagtttaggtt
g
>CEESC11F
ccctgcgaagggactttgcaactnattctttaccagttgttcaaccatct
attgagacgcaattcaatatgcgaaaactatatgggagcactaaagtgcc
tttntagccttttgttgaccacaccatcaccgcgaacacgcaggagggac
gtattcatacacggtggactctctttcgacattttccaataatcttttgc
aagaaggttgtgatgttcgattgtcgaagttcatcactgctgtgtcagct
tggcgaaatgtgcgatgagagaattgaaggccccaaatgaatgaccattc
gttgttctacatttgagtttaccaccatttcaacaatggcggatgtgagg
tccgttttcgctcgtctttgcggattcccggagcttttgaaatccgtcct
ccgtaggcccatgcaactgccgtccctctttaaatgacagtaaacttag
BioPerl-1.007002/t/data/dbfa/6.fa000444000766000024      3174013155576321 16266 0ustar00cjfieldsstaff000000000000>CEESC12R
gcacgagtccatctccatatgccaccacaacantggtcctgtcgaaccaa
caaccagcttggctcaatgacaaaatgcttcgcgcgccanaatgccaaca
aatcccgtgccaccagagccaccggcgcgatatgcagatcataccgctgg
aagacgatctcgatcgagccgtgcatccgatgggagaggaactctgaatg
gcggactccatcaccggactagcggaagtcaacggtcggatagtccacct
cacacagatgtgagctatgttcagcttcactcatccgatggaactggtag
tagtaaggaaagaantngggagcggagaacaccaccgaataaa
>CEESC13F
cttgcttgaaaaatttatataaatatttaagagaagaaaaataaataatc
gcatctaatgacgtctgtccttgtatccctggtttccattgactggtgca
ctttcctgtctttgaggacatggacaatattcggcatcagttcctggctc
tccctcctctcctggtgctccagcagaaccgttctctccattatctccct
tgtctccacgtggtccacgctctcctggtgctcctggaataccttgagct
ccctcgtgccgaattcctgcagcccgggggatccactagttctagagcgg
ccgccaccgcggtgggagctccagcttttgttncctttagtgagggttaa
tttcgagcttggcgtaatcatggtcatagctgtttcctg
>CEESC13R
gcacgagggagctcaaggtattccaggagcaccaggagagcgtggaccac
gtggagacaagggagataatggagagaacggttctgctggagcaccagga
gaggagggagagccaggaactgatgccgaatattgtccatgtcctcaaag
acaggaaagtgcaccagtcaatggaaaccagggatacaagaacagacgtc
attagatgcgattatttatttttcttctcttaaatatttatataaatttt
tcaagcaag
>CEESC14F
aaaaaatgcgaagntccaacagttccatgctatcgttatctggatatttc
aaatggattattccttggaggccgtcctggaacttcgaagcaaatcgaga
aggccttctctggatgtatttctgatttgtcagtggataaagaagatgtc
gattttncaacgatcaaagaaatgcacaaagttggacaagttcatgaagg
atgcaagcatcgtaaagatttttnctcaacttcggatggacaatgctcgg
ctacctcgaagtgtgtcaatcgttggggaggcagaatttgtagctgtccg
caatcggttcattcgactggtgaatgtgttggagcacttggaactcaaga
tttacgtgggcattctctatttgaagaggaatcatttgtttttgtaccag
ccaagccaagtatctgtaccgtttgaagtttcatttgaattccggacatc
tcgagctgatatgcaagt
>CEESC14R
gcacgagtttttttttttcactgaaatcgatcttccatcaaccaaaacat
tccgaatgcatccttcaaaacgtgatggatgtccagttccaggtgcaatt
ccaaagtataagctctctagattcatatcagaaatggaagctttagcttc
tgcactgtagattccatttatactagttgcaactgaatctgcttcaaact
tgatgacaacattcatccaatgctttgatgttacttcaggagctggcaac
tcaacttcagaatctccaatgttatatttcaaagttccattcatcaactt
ccaagttgtaatgaacacttctttgg
>CEESC15F
cnctttgtaataaataatttattatgccncgaaaataattnccnccaaaa
tcaatctttcagcgggtgggtgtaatcattgggaacngggaagtcactag
gaaataaggaaatagngaaatacaataaataaaataataataataatagg
cgactatgattagttagaaaacacagctctgggaattgtttggaagtgtt
gagagaaattnttgattttttacaaatggggaatatgattgaccgttgga
ataagtnaaaatattantaaaaatagcgctgantgaaaacttaataagtg
acagtgaaaaggatttgaaaagntaattaanccaactacg
>CEESC15R
gcacgagggcggacaacctcaaggcgctacaccgggacaacccgatcaga
actttgactacatgttcaagctcctgataatcggaaattcatcagttgga
aaaacatcattcctcttccgttactgtgatgattcattcacttctgcctt
cgtctctactgtcggaatcgatttcaaagtgaaaactgtgttccgtggag
acaaacgagtcaaacttcaaatctgggataccgccggacaggagaggtac
cgtaccatcaccaccgcctactatcgtggagcaatgggatttcattctga
tgtatgacatcacttaatgaagggtcttttaatagtgttc
>CEESC15RB
ggcggacaacctcaaggcgctacaccgggacaacccgatcagaactttga
ctacatgttcaagctcctgataatcggaaattcatcagttggaaaaacat
cattcctcttccgttactgtgatgattcattcacttctgccttcgtctct
actgtcggaatcgatttcaaagtgaaaactgtgttccgtggagacaaacg
agtcaaacttcaaatctggggataccgccggacaggagaggtaccgtacc
atcaccaccggcttactattcgtggagcaatggggattcatttctgatgt
attgacatcactaattgaaggagtctttttaatagtgttccagggttggt
gcactcaaatcaagncatactca
>CEESC16F
cccattttacaaatttatccagaggaatggattttcaattaaaatcttga
aaaaaactaaaaagtagagaaaattggaaactttggtgggtttaaacgtt
aaaagagattaaatttaaaaaaaaagggagatcgantcgaataatttggg
tggatgggatcattgtacaatataaatagaaaaaaaggaagagttcaatt
gggatagaaaaaaaaagtgaatttttttttttgataaggtagntagtgtg
ggtggtggcggga
>CEESC17F
tttcctgaaaccgtcagtcttacttctcgacgaaccgaccaatcatttgg
atttggaagcttgtgtgtggcttgaggaggaactcgctcagtataaaaga
acctngttggtggtttctcactctcaagatttcatgaacggagtttgcac
caacatcattcatttgttccaaaagcaattggnttactatggaggaaact
acgaccagtttgtgaagacacgtcttgaattgctcgaaaatcaacaaaaa
cgntacaactgggaacagtctcaactncaacacatgaaagattacgtcgc
gaggttcggtcacggttctgccaaactcgctcgtcaagctcaatncaaag
tgaaaa
>CEESC17RB
gaaaattcacacaaaacactacacatttagtgatgtgacaacaacaaagg
agggtaattggaaaaaaagggtagaaacaggaaccggaccaacaattgga
ggaaaaccgacaaaaattgggtcaaagagagtaaaagatgaatgaaaaca
agagaaaatataatcaaaatcacaggaaaatgnaattgaaatatcctana
ttgaanatggggggnaaggtgaataatgngagaaaaatctcgggaaatca
gttcgattctaatattagaattggcagattttcgatgttttcggggggaa
atagg
>CEESC18F
aagatcaatgatatggaatggtggaatcgattccttgattccgatcctcc
aatcaatactaaggaagtgaagccagagaactcgaaattgagcgacttgg
atggagagacacgtgccatggtcgaaaagatgatgcatgaactgttgcag
catatcatgcttttccttctcatcagacgttgcggcacgagctcgtgcna
aattcctgcagcccgggggatccactagttctagagcggccgccaccgcg
gtggagctccagcttttgttccctttagtgagggttaatttcgagcttgg
cgtaatcatgggtcatagctgtttcctgtgtgaaattgttatccgctcac
aattccacacaacatacgagccggaagcataaagtgtaaagcctgggggt
gcctaatgaagtgagctaactcacattaattgcggttgcg
>CEESC18R
ctcgtgccnaacgtctgatgagaagaaaaagcatgatatgctgcaacagt
tcatgcatcatcttttcgaccatggcacgtgtctctccatccaagtcgct
caatttcgagttctctggcttcacttccttagtattgattggaggatcgg
aatcaaggaatcgattccaccattccatatcattgatcttctcgaggggg
ggcccggtacccaattcgccctatagtgagtcgtattacaattcactggc
cgtcgttttacaacgtcgtgactgggaaaaccctggggttacccaacttt
aatcgccttgcagcacatccccctttcg
>CEESC19F
gctctcgactccatcattccaccacaacgcccaactgaccgaccactccg
tctcccactccaggatgtgtacaagatcggaggaatcggaactgttccag
tcggacgngttnagaccggaatcatcaagccaggaatggtcgttaccttc
gntccacaaaacgtcaccactgaagtcaagtccgttgagatgcatcacga
ntctnttccagaggccgtcccaggagacaacgttggattcaacgtcaaga
acgtctccgtcaaggatattcgtcgtggatccgtctgctccgactccaag
caagacccantcaaggaggcttcgnaccttccacgnccaggtcatcatca
tgaaccatccagggcagatctccaacggantacactccantt
>CEESC19R
tggatccccngggctgcaggnaaaaatcaacaagataaactcaacaatga
agatttacttcttctttggtgcagccttttgggcggacttggtgaccttt
ccagaggatccatcagacttctcaacggacttgataactccgacagcgac
ggtttgtctcatgtcacgaacggcgaaacgtccgagtngagcgtagtcgg
tgaaggattcaacacaaagtggcttggttgggatgagctcgacgattcca
gcatctncagacttgnggaactttgggaagtcctcaaccttgttaccggt
acgacggtcaaccttctacttaagctcgttgaacttt
>CEESC20F
aacaacaaaattgattttaattgaaggagaggtagagaatgaaaacttgt
gaattgaaaagaatagaaacaaaaaaattaaacagttatttagggcttat
ggcgaggggtaacgaatgagaaaagccctttaactgtgagataaagtaaa
aagaagaatgaaaaatagaaacaaaaaatatttaacagttatttagggct
gaggctaaagaatgaaaatccattaactgtgagagaaattgaatggaaga
atagaaaaaaaacaagttcaacagttattggttggcccaaaatcaacctc
gatgagcgcttttcggatggcttctgtgcgcacttcgagaaccttctcgt
tttcgacgttttcgagagcctctttctacg
>CEESC21F
gaagttgaggccaacgttccaaatgttatcaatgagcagctgagccggag
tattccgaagacatgcagtttgatcagtgatctttgtctgattgcagccg
acaagatcggctagtgctgttgatttttgttttgctcgtttcggagaatc
cattgaccacttgttgtcgagggatcctgattggagaattccgttttgga
ataatcccttcgacgccggtgcaattaagtgagctacaatcgaagctgct
ccagccgattctccaaccaacgatatcctcgccggatttcctccaaacga
gaaaatatgatcccttatccaataaagtgcgagttgttgatcaagcattc
ccatatttccaggnacatcttcatgatctagg
>CEESC21R
tcgtnccgaattcggcagagntncntatgtgaatatttgggctccggcgg
atgcttacaatcttactgtacttgtatggctgtttggtggtggcttctgg
tatggntccccatnactgttactttacgncggaaaagaactagcaacacg
tggaaatgtgatagtagtgaacatcaactatcgagttggaccatttggat
acctgtttctagatcatgaagatgttcctggaaatatgggaatgcttgat
caacaactcgcactttattggataagggatcatattt
>CEESC22F
aatcacaatgattttatagtcgaaaagaaataaaaaaacgcattatgctg
agggcttcgacatacaaagtggaaagggttgggggaaatacatggaaatt
nccttttttttttcggaaaaacaaatttttgttagtatttacaattacat
tttgttaccagtcagacaagttttttgagggaaaaaaatccaataaaaat
gagcatttttcagaaggacgtataatgtacacgaaggtggtngtgtnaaa
aggagacaacaaaagggaaaaattgcgggttaaaaatggccgggaaaacc
>CEESC23F
tttttttgttagagtattttatatatttattattattacagcttacagaa
ctttgatttgttttacagaaaaaaggtgcaaccgnttagacaaattcaat
ggattatcattatttgaaactttttgcagttccttattttcaaaaaaatc
ttggtttttggtttgatcagggtgagaaaggatttcgggggtcgaaagct
agaaaattatcaattttttgtgattttcgattgtg
>CEESC24F
gtcttattaaaagctttattatgaatgtggctcaaataatgagcatgatt
cagagaaaaaatggtttaaaatgtcaatttngtaatgagaaaatgggggt
catcggcagtaatagggtacaacaacaaaagtgattgcattaaacctcaa
cttcaaaccaaagttacacagngnacctagttatacatgcctagattact
accggantagtattgancaaatacaagagaagttaccaatgaagatttgg
gtgagantgggaagcataatgcagtcggctagagaagttgg
>CEESC25F
taaaccaatatgatttattattaaaattttaaaagaacaaaaacatgctt
tagaattccaaaaatgattttaaacaagtgaatgaaagtatcacaaatac
gaaaagagaacccgaagaagagaaaagaagaaattataaaaaaaatattt
tagagctccgacttttgaaggntcgaataccgtttatcagatggcttaag
ctctttgaacactgatggaggtggtgttgtgtcaattggacgagtagatg
gagcttgagcttcatgatcatcagtgattccacgtgcagcttttgccttg
gcgagctcgatcattcgttggatcaaggttctcgtggaagtccttgtgaa
gctttccagagtgaagatccataacaaactctctaagtttacctgggata
ttca
>CEESC26F
ctactcggcgaccagctccaccaagggaaacctcttcttctacctcaacg
cgttgatcatctccatcgccccgctctacctnttctacggagttcaccag
atggagatccaagactcgcttgtcgtgtggggactctntgccgtcggcac
tgcctacctcctgtccctggcctgcaaaaaccagaagtgccttctcaagc
atcaaatcgtgatgaagcgcggntcagctgtggaacgcgagatcagcgga
caatatgctgctgacaagaaaatgactgttaaggagaaggaggagcgcgc
gcttttccgcaaaaacgaggtcgncgacancgaatncacctacttgtcgg
tcttctacacaaantcgctctacttgaccat
>CEESC27F
tcgaaagtttctccagaatttcgatcaattcacagtcgattagactattc
actgaagactatgtcattctctcaggattacggagcaatcagtgaagaag
gaccaatagaagtaggatcaggaattttgaaggtggagtcaattgaatat
atttttgaatacgatgagaacatggntcaagtgaaaatcaaatgtttgtt
ggccccggaacttgtgagattctcgaatgataagtcaataatcagaagat
attttcattattacctggccgcttcacaacgaattgttcagcatgtcaaa
ctcagggaaagtgacagtccatttcgaaaccttcaaagcctaaaanttcc
atccatttcttgggactctaaacggagctagaggatatcctcaatttcat
caattt
>CEESC28F
gttgaaaaacatttcattgaaagatcgatttttggtaaagcagatcagtc
aaatttgaatgcagtgaaatgatgatctgtggggctggagagagcgattt
agtggcaacaattgaaacgnggtaacagggtgaaactttggtttgtgtca
aaaaattaattagttaaagcaaaaaaatgtggaaatgtcgggggaacaat
aaacatgttaacangantaaaaaaccgtggatttatggaatggctcttct
aacaatgttgttgcggaagaattcttgcattctgtgaaagtttccatcaa
cattgccaactatggctcgaatattcgcctgcactgggataataattgat
tcc
>CEESC29F
caagaagacaatttgttttgattggaaatggacgaatgatgaaaggaaat
aaacatcttttaaaactctacaagtatgggttttcttgaatatttctgga
actaatgaatacatatttncagacaccttcaatcggaaaaagtcatcttc
ggaccgtcaattctcgaaaccttcaacgatcttgaggaagctgctctacc
aagatcggataaattttgatttttggttgagcttaggtttttagatgata
gtattcagtttctaacggatattcacttcatgtaactattattgatntca
tattttnatgttt
>CEESC30F
agaaaatcaacaacaatttcatttgaatgaggaagagagtaacataacca
acaatgatgaataaaaaacaaagaaatgaacaatttttggggaggggcgc
ggggaaacgaacaataatggaaatagaagaaaagagcaaagcctacgtgc
agaatagagtgaaagcgggaaatatttctcttctgcgtctctttctgttt
gtgtgtgatttagaattccatactatccgtctttcggccttcgaccacaa
ctgaagtgataacatgtccgtcttcggtttccttggattcgagctcacgg
cgaatttcaggcgagatgagatagtgtccatggaatctgatcagctcata
aatagctgccttctgctcggcattcaaatccgttcttgtatcgctggcac
ag
>CEESC32F
gacggggaatggggagcaaaacaaagaacaatttgatatactataaacca
ggggactgggaaattgaaagcagagaaagttgggatcacagattatttta
tcagtttaatggtacttgcaaacagatggcactgtgcatccgtgcttctt
gatgatttcttgagcagcataagatccacaggtgactgaagcttcgactc
cctttcctttctctcgtgccgaattcctgcagcccgggggatccactagt
tctagagcggccgccaccgcggtggagctccagcttttgttccctttagt
gagggttaatttcgagcttggcgtaatcatggtcatagctgtttcctgtg
tgaaattgttatccgctcacaattncacacaacatacgagccggaagcat
aaagtgtaaagcctgggggtgcctaatgagtgag
>CEESC33F
aataaataaaattattttattaaagtattctcaaagtcaaaatggcaaat
aaagcttganccaaaattttgttcactattattattacaacttccttgct
aatttaatgtctccgccggttcttgaatagaactgatttggagcattata
tttttnagttccattggaagatgttgagaagtaggcagtgacatctggaa
tgacttgaggagtttgagaagcttttggcattgatacacccattcgacgg
ccacggtattcacagcttttnccgaaatatggacgttcacagcggcaggc
aaagttatagatagctggatttgttttcggtcgtggtaaa
>CEESC33R
tcggtctaccacaacaagactaccaataactactggtagtacacaaactg
gtgaaccgtttcggactatggcaatcaactgaaatggggtgaagtttggt
aggaaaacgaaaaaaagaagagaaagaagaagattgcactgccaacataa
gatggtcattgtgtggtaccatcaactactgctagtacttctgatattta
taggagctgccaaaggagctcagtacataggttcgggagcctcccaaccc
aaccgaacggatgttgtgtggatggttccctcttggacatgtaaaaatga
ntattcaattgatgtagaaaagtatgggattctgcaaaattgaggtncag
ca
>CEESC34F
ccgtagttntttttttttttttttanttttatgattttattttaacgtga
ataaacatcacaaaagtgagcttactcaaggggtggggtntggggcggct
aaaccaaccactaacaagtaacaaaaagaagggtgacagtaagananaaa
aacaggngatnggtatgcttagcaactnggggaacgtgctaagagcactt
ggcaatgaacttattgcttctgagcggaaacgngaaccgatgcagcttcg
tcgaccttcgagcggaacaattcactatcttgaagcatcatgatcaactc
ggaattt
>CEESC35R
ggagacaagggacgtgagcgtgacaacatcaaggaggatcagaccctcta
ctacaccgtccagctcgtcgatctgttccgcgctgtgccaggagagaagt
ggaccaccgatgagggaatcgttattgagcagacacacaagattgatgag
gataagtgcaagaagtcgaagagtggagacaccattcaccaacagtacgt
gcttcatcttnaggacggaactttcgtcgattcgtctttttntcgcaacg
ntccattcatcttcaagtttgaataattaatgaagtcattcaagggaatn
ggacattncccattgactggaattgttgcga
>CEESC36F
aagattttaataaaactttattgaaatttgctcaatatcagangtaaata
aatcagtatcaggataaatngtgaacagttatatttgcttctgtaaacag
ttgggatttgaattcagatgtaaatttacataactnctcgttgctgaact
tnatactccaaaatccatgtatccnctttatgactgangacaatanccgn
gaagttgtttatatgaatggncagttg
>CEESC37F
agtttgaatgtttttatttttttactttaaaaaaaaatttaatttcaaaa
ataaaaaaaaacagtttgtggcaaggaaaagggggaaaaattttntgagt
gggcgtggggaacaacttgagttttttgaaagagtcattttggcgggaaa
agcggaaattnttgcgaaatatctacccgttactcgcgtggctttttgta
gnctaaaactttagtagaggaggagaaagaaaaanctggggaaaaaaatt
tgggtcacagnaaaaaaatgcaattgattagcaancgcaagaaggtgggt
agagcgtgtgaaa
>CEESC39F
agaattttagtgttttattgaattgttgaatacaaatcaataaaaaaata
acatatgancggttattatgactttctttcatatatatatcccatatatg
ggtttaccaaaatgtgcacgaaatgaatacaaataaattatttaatcagt
gtccatcttcgcctcgaaacggcttcccaacccggtttcacttccagcga
ctcctctattcacactatccagaacagagttccagtcgacgccgaatcga
tcggttctttcttggattcgaagcacaacttggagagcatcagtggcgac
agtcttcttctgttgagcacacagctcgtcggcctgctccaaaatgttgt
caatcagcttcccagcggccactgg
>CEESC40R
cagagttacaaataaaagcgggcaacaatgtcagaaaaatcattgcaatc
gaaaatnctttctactgtatttttncttgcaactctaattgcatttnctt
ctgccgatggatatacctgtnccggaaatacgctgataaatccatttntn
aatctttcggagccctactactatccagggncatggcgagaaaacatgga
accagctgantatgctccagntcaaaagtgtaactggaagatca
>CEESC41F
aagaagaggatatatttatccaaactgcaacaacaaaaaacacaacaata
taacttgaaaaataaaatacgctcataaaaaaacaattttaaaaattaaa
aattattccttgtgctcggncaattgaaatcctgccttcgtcgagttcac
tgatccntttgctttctggcgagggccccaattcttccctttattgcatt
ggnaccgtacaaggntctctttcttggnctgttcgatggctccngggtga
agagtgaagttgactgtgttggtgatgggttntcccagaatgtgatatcc
ngctgattctttggccagacg
BioPerl-1.007002/t/data/dbfa/7.fa000444000766000024     22520013155576321 16303 0ustar00cjfieldsstaff000000000000>Contig1
gcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagc
ctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcct
aagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaa
gcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagc
ctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcct
aagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaa
gcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagc
ctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcct
aagcctaagcctaagcctaagcctaagcctaaaaaattgagataagaaaa
cattttactttttcaaaattgttttcatgctaaattcaaaacgttttttt
tttagtgaagcttctagatatttggcgggtacctctaattttgcctgcct
gccaacctatatgctcctgtgtttaggcctaatactaagcctaagcctaa
gcctaatactaagcctaagcctaagactaagcctaatactaagcctaagc
ctaagactaagcctaagactaagcctaagactaagcctaatactaagcct
aagcctaagactaagcctaagcctaatactaagcctaagcctaagactaa
gcctaatactaagcctaagcctaagactaagcctaagactaagcctaaga
ctaagcctaatactaagcctaagcctaagactaagcctaagcctaaaaga
atatggtagctacagaaacggtagtacactcttctgaaaatacaaaaaat
ttgcaatttttatagctagggcactttttgtctgcccaaatataggcaac
caaaaataattgccaagtttttaatgatttgttgcatattgaaaaaaaca
tttttcgggttttttgaaatgaatatcgtagctacagaaacggttgtgca
ctcatctgaaagtttgtttttcttgttttcttgcactttgtgcagaattc
ttgattcttgattcttgcagaaatttgcaagaaaattcgcaagaaatttg
tattaaaaactgttcaaaatttttggaaattagtttaaaaatctcacatt
ttttttagaaaaattatttttaagaatttttcattttaggaatattgtta
tttcagaaaatagctaaatgtgatttctgtaattttgcctgccaaattcg
tgaaatgcaataaaaatctaatatccctcatcagtgcgatttccgaatca
gtatatttttacgtaatagcttctttgacatcaataagtatttgcctata
tgactttagacttgaaattggctattaatgccaatttcatgatatctagc
cactttagtataattgtttttagtttttggcaaaactattgtctaaacag
atattcgtgttttcaagaaatttttcatggtttttcttggtcttttcttg
gtatttttttgacaaaaatttttgtttcttgattcttgcaaaaatttttc
cgtttgacggccttgatgtgcactaccttcgcttaaatactacattttct
gaaaatgttataatagtgttcattgtttcatacaaatacttatttaatag
tatttctggttatataatttgtataaaaagtggttgacataacaaggctg
acgaaactttgtgatggctgaaaatattttcctagctttattgattttta
tttatacgtgtttgaataacttggccaaatcgccgagaaggaatagaata
ctggacgacattgtacatattttccaaaaaatcagaaagtagatgacggg
accaattctttctgtcaggttttacaaccgcccagtgcgtctacgtcaca
tgttgtataaatggttgtaaacaatatgcggaaacaatcaaatgcattcc
cataaggcataatatagaggctacaggcaatgagtatcgctctttgcttt
gtttaaagggggagtagagtttgtggggaaatatatgtttctgactctaa
ttttgcccctgataccgaatatcgatgtgaaaaaatttaaaaaaatttcc
ctgattttatattaatttttaaaatccgaaaatccattggatgcctatat
gtgagtttttaaacgcaaaattttcccggcagagacgccccgcccacgaa
accgtgccgcacgtgtgggtttacgagctgaatattttccttctattttt
atttgattttataccgattttcgtcgatttttctcattttttctcttttt
tttggtgttttttattgaaaattttgtgattttcgtaaatttattcctat
ttattaataaaaacaaaaacaattccattaaatatcccattttcagcgca
aaatcgactggagactaggaaaatcgtctggagatagaacggatcaacaa
gattattattatatcattaataatatttatcaattttcttctgagagtct
cattgagactcttatttacgccaagaaataaatttaacattaaaattgtt
catttttgaaaaaaaaataattaaaaaaacacattttttggaaaaaaaaa
taaataaaaaaaattgtcctcgaggatcctccggagcgcgtcgaatcaat
gtttccggaactctgaaaattaaatgtttgtatgattgtagaaccctttc
gctattgagatttgataacttttaagtaataaaattttcgcagtaagaca
ttaaaacatttcacaattaagctggttctgaactgtgtgaagtatattga
aaaaaactaactgatacaaaaatataattttatgatagttttctggatgt
cccaatataaacgatgtcaattctgcgacatgctacagtcatccacgaaa
gtaacccgaataccgacaaaagaagaggaacgccaactttggatagacgc
tctaggggctgattttggtcggaaaatagtcgggaaaaaatagaggacat
tacagatgaggatgaggatgaagatagaaatttgccgacaacttcgtcat
gccgctgatttttttgatgttctacgcttaaattttcagcgaacgaacta
ttttttatattttgattgtttttaaataatatttgccataagaaattctc
acttttccaggaaacgtcgtttcgccgcgattttcctcgtctccagtcga
ttttgcgctgaaaatgggatatttaatggaattgtttttgtttttattaa
taaataggaataaatttacgaaaatcacaaaattttcaataaaaaacacc
aaaaaaaaagagaaaaaatgagaaaaatcgacgaaaatcggtataaaatc
aaataaaaatagaaggaaaatattcagctcgtaaacccgcaagtgcggca
cggtttcgtgggcggggcgtctctggcgggaaaattttgcgtttgaaaac
tcacatataggcatccaatggattttcggattttcaaaattaatataaaa
tcagggaaatttttttaaattttgtcacatcgatattcggtatcaggggc
aaaattagagtcagaaacatatatttccccacaaactctactcccccttt
aacaaccacccgaggatatattcgacaaacgatctatctactaggaataa
ctcgattattgacatattatagacttcttttagtatttgtaaaatagagg
atcagacccaaaattcagcccgcgaaggcatgacgtcagcgcgaggcagt
agtttccagaagaactctgtcgtctaccttaatgcctcaaatgcgaaccc
gcttcggccatccttctcgctcagagaatggattagagttctcatcaact
cctctgtctaattttcaactgcggcggttggcgaccggtattaccgcggc
gaccgacacctcccgggttccgtcgatcgctgtctgttgtgtgcgccgcg
actccgcccaccggtggtaactttttgtgggggaatctttgtttttggtc
atttttcagcgcttttcagcgattattgaccaattttgaataaaattttc
aacagaatatcatctaaaatattgcttaacatttatttaacagaaataac
gtgagcacgcatgtaaaacatgaaattttcgggaaaattgcaattaaacg
aataaaaatcgatatttaaatcaattattggtgaatccggtgtgttgagg
cttcaatgcatacatttttactggataaatctcctttgggaatccggttt
gcagtgctttcgagaccatgtccagttgagaatcggcgaacgctttaaga
agctcgggctgaataatgaattgttttaaaaaatgtttagtaaaaaattg
ttttcgtgcaaattgtcttcgatattatccaaacgtgacgttttgcgatt
ttcgcgctaaaattacagtaagtggggtctcgacacgacaatttttgtga
aatacaaacgggcgtgtgtctttaagaagtactgtagtttaaaaacttca
tttctgtggaattttcatatatttttcatagtttttctctttaaataaat
cacttttcaacaaaaaactatgagacaatagtttgaaattacagtattct
ttaaaggtgcacgcctgctcgaatttcgcaaaaacgtgtcgtgtcgagac
cccaattacagtatttttgacccgaatatcgcgaaatttcgagtctgggt
gaaaacattgaaatttttggcaaaataaaagaaatatgtcctttttcaga
atatattttctaaatttcgagacgaaacaacaattttaaatgaattttaa
ttttaaatattaaatatttcggaatttggcgttttttatgcatgtcgatt
cactaacgattttgtactacacgtgggcaagtttatacagtttttggcta
aaatttgtgaatttgaaccgtttttcggcgaatatttgaaaaattggcaa
aactggttcaaaaacaaaaattttttaaactgtacaaactgtccaaaaat
tcgtcgtaaatcgacacacccttctcattttttcaaaattttaattgttt
tcgaatgttttttttgcagaataatttgtaaaatgagccttttgtgaatt
ttttttaatttcaaagtttttattattttttctcaaaccagcacctctgt
tctcgtccaactatgatcatcatcgtcgaataaccgtttctcgtgatttg
tcacattatccttgagcacaatacatccaccaggtttcagtcctttctga
aaatgaaaattaattttaaaaaaattgaattattttaaatgaaacagttt
tcagagatttctcaacttttgagtccaccaccaggcctgcacgtttttcg
ggttttatcttttaaaaaactgaaaaatcgaaaaatttcaatttctgttt
tgtggtcaaaattgtaattacaggtaagcaaatagtttaattttaaaatt
gaaaattagggaaatgaccggacataagtttaaaaacccgattttttcaa
taaaaaggaaaattgaaaatttaataaaacaggttgtaaatcaaggagat
cgtattgattgaaaaaaaatccgaatgttccggatttttcagtggttttt
tttgaaagaaaatcgaaaaagtaaatgtttttaatttttaaatttaaatt
tttaatcggaaaaaatgtacgaaattgactttttaatgtgaaaaattgtt
gttttaaaaaaaaattttaaccgatacagattttctagactcagtttttt
cggttgaatattgttttttactattttttcattacagaaagaatccaatt
ttatttcgcttaaaaaataaccggagcatcgaaaatatttttttttctgt
tttactcaaagcatttcaattacctagaattttgtttaaaaactacatgc
tttatttatgaacgtaataaataagaccccctcttatttataaactttca
acatattttcagttttcagtgctatctagtgcttaccgcacatcttttaa
agaaatcaaccaaatcctcatcaaccaaatgccctgaaacccattgaatc
catatcaaatcataacgtcgttcgggcggtgcaaacgtctgcagtccttc
gacgaatttatctccaattcgtggatgttttccaatatattgatcacttt
tcgtgatcaactcctcgacgacgtcttccatatcaactttcgagaagaat
ggcattaagagatgctttgtaacacgtccgatacccgctccgcagtccag
tgcatagtcaaagtagccgaatagattctggaaaatatttataaaattca
aagttggcccaggggtgaccggcaatttcaagcaaatcggcaaattgtca
attttctgaatttgccgaaaatttgacaaaaacgacaatttgccggttcg
ccgaatttaccttttttaaatttaattttcaattcaggcaaactgacgat
tttccgtttgccggatatcaatttgcaggaatttctcaaaggaattttta
ttaagacggaaacacagtgcttttttgaattttttttcccgttttcttca
gatatttttatagaatttactgacttttcagaatagatgtaggacaattt
tgttgttttaaaaattgaaattctgaaatttccaacaaaaaaacatgtgc
aaacccacaagttggcaaaaatattttgcatttgccgtttttcccgtttg
ccgaaaagtctaatttcggtaattgggccatttttcgaaattttgagcca
cataaaaaactttgaaccatttttgagaagtattattacgacattcgttt
atttgagcacaatttgggcctatactttcaaaatcggggtttgaaaaccc
ctatatgttcgaccgaatgttaatctcataaaaatttgatgaaaataaaa
ttttctacggctcataaacgtatagcccccgtcagtctcaaaatttatac
gatagacactttttggcgtttatcgcctatattccgtcaaaaaccattat
tcatcattctttcaatgttgttttttttaaggctaaaaaactttcatgca
aatttgttagccgtgtcgtggtttatacgaaaatttcagaatttataaaa
taaaggaaaacgaaaatgtttctatataccctatttatgttctctgattc
cgaataccaatgtgaaaaattcaaaaaaaattccctgattttatataaat
ttttgtaagcgacaaaaattgtcgtttgaatttcacacttggttacaaaa
atttatgaaaatgaggaaaatttgttttaattttttcacattgatattcg
gaatcaggaaaataaatagggtctatagaaaaattccgaaccttcactcc
ttctctgagtataataaatttaaaataaatacagaaaatttcagttcaga
cctcattaaatttgggtatatttctaggatccgagtttttacaccagatt
tacaaacttttagcctttcaccgcctttttatgcgcatttcccatcagtc
aactccaaaaaaatcgcaacttttgcctcatatttcaagaatattcccct
ttctctccccattgaaagtcattttcgaaacaagcggaagattcgtcata
tgtggtaatgtgtggcgtgcgttggcaaacaacaagaaagaatcattctc
tgaaaacaaaaagcgttttgggtgccaaagtaatattgaaaatctgccgt
gttttctcattttccatcaaaagaaaatgagaaaaaagtttcggcgtttt
atttgatttccgggaaagaagactcggaaaaagatttaattgaatttttc
atagcaaacctatattgcaacaactttctaaaaggtcagaaattgccgcg
tagcctagaaaattggaaaactcttccagctggtattatttcagacatgg
tgcatcgaaaattcgaaaattacagaaattaacattttggagcatctgcc
agaaaattgagattacagtaccccacttctgccgagaaattcgaggtgga
agaggtcttacaaaattttcggtcacgtgaaaatgggaagcgttcaggct
ccacacgacggaattcacctagttttcaggtgagaagatatcgtacgagg
agaattgacctccaaatcctgatcgtgactacaggtcgtcgttcggagct
gtggaagagttttgaaaatcttcgaccatgagagaaatagacaggacgac
caaacattttcagtggaagagcttttcctaggccatcaggatgctatttc
gacagagctgagttatcctcaagtcgttacgaggtgtggaaaagttttcc
aaaatccccgaccaggtagaaaatgagcacaccgattaagtttctccagt
ggtagagttttttctaggccatcattatgctatctagaaaaaagcttcgg
ccatggggtttttaggccgtctatttatttctcataactttctcagaaat
tcgtctatttctcagaaccccccaatgataagttttttgcaaaaaaagtt
ctgctttgctcatcagccgtaatcaggtgacctcattaggcctacccaaa
cacagatttgtcattatttttcagacaaaaaacacgaaaaaaatcttcac
gcatggggtgataacctgattttaaatcttactgtgccggctggcgcggc
gagcttcgatcactgagccgaaagattatgaaaactatgggaatgacggc
gtagcctagaaatcgtccaggcagagattctgtctaattttcgagcatat
atctcccagttttgttattaatttaagtaaactcaaacctagaaacaagt
aaaacgggagggggggggggaatatcagaaaattaaatcttgcgacactt
ttccattgatactttcaaggtaatgcccagaggtgtgcggcaaattttga
aacttgcgcatgccgcctttttttttttctagaaaacagtcagaattttt
tgtcgaatttgttgaaaattcgctaatatactgtgagtttagaaaaaata
acgaaaaaactcggaaaaggaggaagagatctgaaatatgtagatttttt
tagaaaagaccagaaattactgaaaaattggcatttttcgtcgaaacccc
aatatactaaattattcggatttttagaaaattttcaaattcaccataca
gtgcattttttcctacttctacgactttaaaggggggagcatttatgcgg
aagggtcttgccgcgcatttagtcatcatttttagcagtttctgtgtaaa
attcgcgtagatcacatgaagatcacaaaatatttatcccatatttcgta
tttctgttgctttttcacaaattaattgtgatctacgcgtgatctccgcg
aattttgagcagactttgttaaaaatgatgactatgtgcacggcaagacc
cttccgcataaatgcgcccccctttaaagtcgtagaagtggaaaaaaaat
gcactgtagcaaaaaatcgaacatttctgttcgatttttgaatttctcga
aattttttaaaataatttttaaaataacatttttattttatttcgaaaac
taccgattttagaaaaattctaaaatttcgattttttttgttgatttttc
gatttttaaaataaaatttcataattttttaaaccgatctttcttgcttt
tcctgaaaaatcgatgatttctatacctttttcttcagtccttcaataaa
tcgtttcgacgccgatatgtcgggcgcgtgaagcgcttcgaatccgccga
gcattccgttgacgtcctggctcgcgcggctccagtattcctccgcctga
aagagaatagttgaaaacattgttttgagacttaaaaattttttttttag
tttttttcaaaaattcttacatgttatagagtttttttttcaaattttca
gcttttttcagaaaaacttagtattttcgataattttaaataaaaaagtt
ttttttcaaaaaatgtttcggttttttttttaatttttggtctaaaattc
tccgcaaaagatttgcgtgctggccgaactttttgattttgtaccttttc
ataaacatcttcaccattgtgaattctagaagatgatgaagagctcattt
ttgatgttgtgacagctgctccgagcaatctggagacttttgtgacgaaa
agacgagaggtcacggatatgatgatgatactggaaatgagatatttata
tttactagttcatcgggaaaattattacgagaaagataaacagacatgtg
cgtttttttaatggaagagaaacacaagaaaaatctggaaaactaggcca
cggctatcagtgtcgatttacggcatacggtctcgacacgactatttttg
ttaaatgtgaaggtatgcacctttaaagagtactgtagtttgtaactctc
attgctgcaacatatttgacgctcagcgaaaactacagcaattcttcaaa
agactactgtagcctttgtgttgacttacgggctcgattctcgaaacgaa
tttctgctcgaattgtgacagccatattcaatttggtatagtcttttcgt
attttttgccatttttctgttttcttctaatatttaatctattattaaat
tatgtccgtaactccctccaaaattagaactgcgaccgaacagagattcg
ttccgccccatattccggccaatcagatcgagtaggcggagttcgaagtc
gctgattggtttgaaaagtcgcggaaatttgcaagttttaaggtagcgaa
aactgatgactattgtagcgcgcttgtgtcgatttacggaatctcgattt
tcaggaatgaatttttaattacattttttcgctcaattaatattctaaat
aaataaataaatgatttgaattaatttaatttcattcgagcccgtagatc
gacacatgtgctacagtaatcattagttttcgctacgagatattttgcgc
gtaaaatattttcccgtaataactctactccgacaaacattacgacctcc
atggaggcctccaggtataggtgagactcttgtatttccaattcagagac
aatgcgtcactggaagagaaaacgaagcggaaaaaaaaacacggaaaccc
aaaaatagtgtttgccccgctctattcttctccaataatttctgtgtcta
attttgaaagactccacctgtgtatgccttctcgacataaaccccccccc
ccccccctatcttacatggtactgataacactttcagtctttcacacttt
tggcgcgcaacgccgctcttttttcgcggcgagctgatgacgtcatcaat
ttttcatcgcttttgattatcttcaatgttctagaagggcacataggtca
tccttattttttccttctctttctcgtgacggcccttgttgcgcatgccc
gccccctagagcagggcgtggcctgaacggcggctccgagagctactcat
tcttgccgcgtcaccctccagcgccacccaaacttcttcggttctagaga
tcgagaagaacgtatgattttttaaaattataattgtttctttcgaaaaa
aaaaatttcatttacagtaagccaaacatacacaatcaacatgaaactcg
taattctgctatcttttgttgcgacagttgcggtttttggtgagtttatg
ctttagataatacttttccgccaaaaatacagttgccggtctcggtatgg
caatatttttgttaaattcgaaaagcagtgagtaatgtagtttcgaattt
tcgtttctgcttaattttcatcaattcatcgtttttctcacgacttcttc
tttatgaaaaatcaatgaaaattctgactaggtcagcttaggggtgaggt
acctagagacgccacatatgccaaacggaagctgagatcattggctacaa
gaatatgctttcaaattctgcaacggacctctgggagtctggaaattctt
gtctgaaattatgcttttgaatgctcgaaagtggtaagaatttagaattt
attacagaaaaacgtttaattaataaaattagttttatacttgaaacaag
tactgtatgcactgtatcaaaacacattttcatcttttctaggtattcaa
cttcacgtttttctgtaataaattctaaattcttaccactttcgagcatt
caaaagcataatttcagacaagaatttccagactcccagaggtccgttgc
agaatttgaaagcatattcttgtagccaatgatctcagcttccgtttggc
atatgtggcgtctctaggtacctcacccctaagctgaccattccctagtg
agcaaacaaaattttgaaattacagtactatttaaaggcacattgatttt
ttgggtcaagcaaaaatttgtcgtgtcgagaccggctacggtattttcgc
gaaaaatcgcaaaatcttgcggctgggatatacttgtgcgaaatactttt
tgcattaattttgagcaaaattattttttttagactttttgaaatccaaa
ttttttggattgcgaaaaaaacctgtgtccggttgtttcattaggccaac
aaagttcctggaacactgatgaaaaccatgatagaggcggagcataatat
cgatttttcgtactttcctgtatttcttcttctatatggccgagtagaac
aggattaggggtaaagtcaaaatttttctcatatggatatcatatggata
tcaaaatttttctcatatggatatggagaaaatttttctcatatggactt
tgaaagttgaatcacttgacatctgggaaattagtattccaggcgtaagt
cggatctgttagaaacggaatacttataggcttcgtgaattaggtagact
ttcaattaatctgatccatgggagtcagacgcggtttccaggcctgacgc
ctgcctccaacttgcccgcctcacgccggtctctcgcctcatttctgcac
tgtgacgagacagacgaaggtcgccttctggcgcccgcatggaaatccta
cgaatatgtcagcttctgatgggactccgtaaatcgacacacaggggtac
ctcagacatttccctcccccttacaaattgttaggacaaggagggggaat
tcatctccactcgagacacacatatgttgtcgtcagtgaagtgtaaagat
ctaaacgattgcgtgtatgaaaaagcactctatgatcacctttttcatct
tcctacaccctttttaggtgtggtgcccatcgagcactcacgccaggcag
ggagagcaccggtccctgactaatgggattcgaatgttttagaccggaaa
taggagcgatgaaagagcatagaaatgatcatttggaaatcacgtttaat
taggttacggcgaaaatttgcaaaaaagagcaggaaacttggctcaaatc
cttcgaaatataacaactaggacttccatgtaggcgttaaagcgccctgt
ctctcaccccaatccgtaccttaagctgaaacaaacgtgaacttttttca
tttcttaaaggagtatcgtcaatgggaaaattgttttaaaatgtagtatt
tgtacttcaacttccaattattgcaaaagaaaaacggaaaaaatccgtta
acattcagcattttaagtcgaagaaatctttaaaatttaactagagaaat
cctaggccacgacgctcattcgaattttaatttgttttgatattgtattt
tgaaaaaaaaacttaatacaattccttcttcccagttttctataactttt
tgagaaaaaaacgaattaaattccgaaaaaactacatttaaatcaatatt
ttgtttacgaatatggcctagaaatcgcgtggtggcctaggattcatttg
cgcgcgaaattcaaattccgtcactttcgtcgatttcaacggctaaatgc
tgaatgtcaacggatttttcccgtttttcttttgcaataattagaagttt
gagtacaaatactacattttaaaacaattttatttttggtattttgacga
aaaattgatttattggtttttttggttgtttgggaccaaaaaatccaaaa
aaaatgtttggcgtgtctagtttcgactcgagactattctgtattaaaaa
tacattaaaacatgtattttaacacagttgtgacgtcataaatgtatttt
gatacattttgcaacattacttaaataaccccattaaaaattaacctaag
catcaaaaattttttggtttttttggtttttcgaaaatttcaattttttt
tgttttttggttttttttggtttttcaaaaacttcaattttttgtttttt
ggtccaacatttttttttggtctcagctctgctgcctaccctagaagaac
taatagcgcttcaaaaactgatgaaaacgttcaaatttgtcgaaatatta
cgaaaatttgaaaagttggctcaaatctagattgaatcggccgattttcc
acaagtttccaagtttccacaagtcgccacatatcccgagaaaaatcgat
tcaaattgtttgaaaattggaatactgcgaattttgaaccaaatttccct
ggcttctctgttgaaatacttgaaaataccgcgaagcaaacaaaaaatct
aattattacgtgaacacaaaattctgaaaatgcgtatatattgcgcaaca
tatttgacgcgcaaaatatctcgtagcgaaaactacattaattctttaaa
tgacacgctgtatgtggtgatttacgggctcaaaaaattattttcgaaaa
tcaagcccgtaaatccacacgtagtaattatataaagaattactgtagtt
ttcgctacgagatattttgcgcgccaagtatgttgcgcaatacgcaaccc
catatgttgatatatactgatgtgaggataaaaaacaacacaactttcag
cggctccatcggctccggcaggtctcgaggagaagctgcgtgctcttcag
gagcaactgtacagtctggagaaagagaacggagttgatgtgaagcaaaa
ggagcaaccagcagcagccgacacattccttggatttgttccacagaaga
gaatggtcgcgtggcagccgatgaagcggtcgatgatcaatgaggattct
agagctccatgtaagttagtggtggtggccggaaaagagaaaactcggcc
aagctgctcggagtttttgaatttttgataatccgaaataaaaattgatt
gctcgaaaaggaacaatcttttggaaaaaaacgaattttgtcattttttt
cagcaaaaattgattttcgaatttttccaataaaaaatcgataatttctc
cccgtgcagtggaaaacaaacaatatttttttgttgatcgttctcttcca
aacccggaataggtacacacattcctgcgtcatcccattctcttatcaca
cttttttttcgaaaataaaagtgtagagacggaaaagtgagaaaggagtc
aattttatgcgaaattttgcatgataatacactcaaattaaaaaaactgc
gtggcgtgcactgcagaaaacctcatatttaggccccgcctttttctcgt
ccactcacggagaaaaggcaaaaatttggggaccaaccaatatcaggccg
ccgacatcctacgggttccgcgcgccgctatgtttaactcgctgtgggtg
tggcgagctgtctccgcccgctgcgagttaaacatagcggcgcgcggaac
ccgtaggaagtcggcggcctgatattgttggtccccaaattttttccttt
tctccgtgagtggacgagaaaaaggcggggcctaattatgaggttttctg
cagtacacgccacgcagtttttttattttgagtgtataggtctcgattct
cgaaagtatgacagttatttaaatgatgaactcgtgatgactgttaaatt
tttggaaatttcgggggaattatatcgatttttcgataaatttacaggaa
aaaagtccaaaatctaggtattccatggtaggcaggcgcgatttcttgac
gcctgcctggaatctgtccgcctcacaccaaaaaatgtcaatcattttgc
tgaaaaccaaattaagaaatgaaaaagtgcacttagagatgatgacggag
gtcgccttaaggtcagacaggttaaaaaaccgattttagttgagttttcc
cgaaattttctgaacaaccgaattagaaatatgctgcttgtcatttttga
gtaaaaattaacgaaaacttcgaccaaaaccacgaaaaaaatgaagaaaa
taaagatttttcgagaaaataacaacaaaatccagcaaatagtgaaaaat
agttttatccgagaaaaagtagtttagacgctatgaactctcgaaaatca
gattttttcaatctaaaagccataaaattatcgattttttaaaaattctc
actgaaaaccggcgaatttcagtgctccacgcaatcgaagcccgcttggc
cgaagtgttgagagccggagaacgcctcggagtcaacccggaggaagttt
tggcggatcttcgtgctcgtaatcaattccaataaatattctttgcccta
aatactttaaattatccatctgacaactaaaatttcggttcttcttggct
tcttctatttgtgaaatggtttattttcccccgaactctcaaaaggttta
aatattgttcgattacccctttttatcaattattttcttcaatttcttat
ttatcattatttttctaaacgaagacggatgtgattttaaattatgttaa
tggactattttacaaactgaataaattcagcatgttggcaggttttttca
gtagtttttgagtgaaaatagaggtaaaaagacagaaaatcaataaaaaa
tgaaaacaaaactatgaaaaatggttgaaaatcgagcaaaaatcgttcaa
aaaaaaataaattcaaaaaataattgcgtcgagaaacgcgtcagtagccg
ctctctgcgtctctcacccttcagcacgcggagagagccacgagaaatgc
gcaaaggctaaattcggcgcggaaaatcatttttcaaaataaattcgacg
agaaaatcaatacttaagtaattatcgattttcagctcgttcaaaaaatt
ttcagaaacgttttagtcgtttaaaggtttttttaaaattaaaatcgtcg
gaagtaaaaaaatagcgcggatggaaatctacggagtgcggagcgaacaa
acgcgcggtaattcaaatgggtagaatagtcaaaattgaaaattagccag
catcgaccgatttttttaaaacttaatggattttttcgtttttcttttgt
ggtatttcggcatttaggattagatagcacattttaaagtaaaattccca
tccaagctactccaccttctccagactgtacagttaaaccaatttgaaaa
gtgtattgtatcccgtttttttttctgaacaattttgaaaatttttcgtt
tatccaggatacgataatcatgattcaaattcgttaacaaaaaatgaata
tatgagagcgattaaagcatttgtgtcggaaaatatgggttaaatgggga
gaagggggcggacatttggatggggtacaaaaaaatatgcaaaaaatggg
ctaaaaacaatattttcaaattatgcccgacaaaggttcaaaagtcaata
tatagaaatgagaacatgagtattatgccacgtggcgggaaaaatatgtg
gaatgtaatacgatgagatccttgtgaatacaaagcttgtgacgacgtgg
ccgagaagaactttttaagccaacgagaaaaaaggggttcaaggccgaaa
ttttttttgggccacctattaagttaaattgaaaatttaaaaaaaacaca
gcggatccaattatttgccgagttttgacttgagctcggcgcgatacgtg
tcgattgactgaaaatattgtttttttttatttccgaataaaaaatggtg
agtacctccaaaattagcttttcattgtccatatagaactttttgatttg
ttccacagtttttgtggccatcaactcggcgatcaactcgaaattgtcct
tgtaccagtggaaacctgaaggaatttcggatgtttttgcttaatcataa
tcataataatcttaatcataagacttggaaaatgcgaaatttttcgagaa
tattcaatttatcttcagattttattgcaacaaatcgattttcaacataa
aattaatttttccaactttttttcccaatttatgagagtttaaagattgt
tttaaagcaaaccgccaactttacataaaaaattaaaatattgtgaaaaa
aatgatgaaatttagcagattttctgataaaaaattgaatttttttggat
tcgcgcttcaatttcacattgttcttttagaaaagtcgaaattttatatt
tccaattttcagatttaaaaaaatttaaaaaggaatgaacttttccaaag
aaaaactgaatataaccagaaattgtgatttttcagcatttttttttagg
tttgaatttttttttcatgattaatcacgtgaaaagtcaattttaccgca
aaacatttaaaaaatcaagatttttcaattttctctgaattcctgcagat
ttttcgatgaaaaattgaattttccttggaatttatatttttcgggtatt
taaagtttcggatattaaaaaaaattttcaattttctctgaagttatcga
taaaaattattttctgcaaaaaatctactttttttcgttgaatattccgg
aaaaaaaatcagaatttcaaggcacatttccttttctaatctaattcgaa
taattcaatattcttttaaaaattcggggtagaaaaggaattgtaccaat
ttttatttttaaaagttaatttttctaattttcaaaattttcttgaattt
tcgaattacagattttcaaaaaaattttttttgtttttttttctcgaaaa
tttgaaatccatacatctaatagcattcttcttttcctcaggactccaac
cataatttatcctgacttttccagatcgattgccatttgttgcagtagta
tctagttcaggagtaaatctctcgaatcttcccttcaacgccatcatatc
tttcttccaatttgcaatttctccttttggtacacggctgtatgtcattg
ttgcacggaacatttgttgacgggcttcttcattcagaattctggaaaaa
ttgatgttgtgcgattttttttggttaaaaaaaacaattttcgtaagttt
aattaactaatattttaaaaaatctctcattttctgaggcaccacggatt
caagatctggtgggattccggatctggcaccgtgccaacgcattaaatgc
aatttttctgaaaaaagggcaacgaagatccgatttaaaaaaatttttca
attatttttcaaaattttcactaactataagaaattagagatttttcaca
aaaattccagttttctgttagaatttgaaaaaaaaattgaatttttccta
aaaaatttgtaattttccgatatttcaagctgtcaaaacctaaaatctga
aaactgaatttttaaaggaaaaattttgagcattcttatcaaaaaattgt
ttcaactttttctcaaaatgtttcaacctttttctttctaaattctgaaa
agcatatctcagcttttgctaaactatttttttcctcaatttttgagaaa
attaaaatataatatataatatagtaaatattgcttattttctaataatt
tttggtatttctattctttcgttttttttttcaaaaattccaaatagttt
taaatgttcatattattttttttgacgaaaataaattttaattttaaacc
ggaaaattgtttcgtaactttttttttcaaaaaatttgaattttcgacat
gaaagatgtaaagtgtaatttaaaaataatagtgcaggtattttcagttt
acagcaaaagtcagtttaaaaaatttcgactggttttcaaaatgagtttc
cttattttttacacgtagaactttttttattttccgattttttttgttgc
gcagaaattttttttccgcaaaatcaggaaaaattcagaaaaagacagtc
aaaaaattgtagatacaattttttgactgtctttttctgaatttttcctg
attttgcggaaaaaaaaatttattttttcatgaataaaaatcgaataccc
atccaattccacaaacttactcgttctcctccatacatttcgtttgttta
actctccaaacaagtggaacacacatatgatgttttctcttgatattatc
aattaatgccagtgcagccggtgtatcgaagcaccgtgtcattctgcacg
tattctcatcgattggatcagcttcaatcgattgctccacaatgtagggg
cctgatggtttacggagaaggcagtcgtctggagaaaaatagaatagaat
aatgatttttaggttattttacgtttaaaaatctaatttttaagacgcgt
aaacgttgagctcatttataaaaattcggcaaaccggcaatttgccgaaa
aatttcggaaaattgtcggtttgcacattttttcttgaaatttcagaact
tcgatttcaaacggcaaaattgtatacatcctatcaaaacatcaatcttg
aaaagccagtaaactctatgaaaatgtctaaagaaaagaaaacggtaaaa
aaatacagttttaaatgtttccgtcttattaataacaaaattcgacaatt
tgccggaattgaaatttttttttctccaatttccgaaaaaaacccaccga
ccaccataatatcatcgtcttcttctttttcttttccaattccaagccgt
ttgatcgcttttccgttggctggctccatgagctcaagatatccgtatac
ataaattttcatgtctgaaagaaaattcaaatttcttctggaatcagtta
ttcgaaactaacattctggacataaaactcgttgccgtcgttttgtcagt
gcacggaggcttgccggacgtggaacacgcatcaaacggaaataaaggat
acacggtttacattcgtgacgcgacattacacgatttagcttaaaattgt
gaaattaattttttttaatagctctttatttttttgaaaatttctcccat
gctttttccattttttcaacgagtttccttattttttgtccatttactgt
aagttttttttgagaatttttttttgttaatttaacattttattagctca
aaacatttattagcaaaaattttattagcaaaaaaattttttaatttttt
taaattagctcaaaattctcgaaattttaaatttttagggtaaacaatat
aaaacttagggagttttgagctataaaatgataaattgattttaaaaagg
atgaaaaacttattttaaaaaaccgacaaaaatcgacaaaaatgaaggga
acaggcagcagcttagccccatgcttagccagcagccccgtagcaaccca
gtatcaataatatcccgtgccaattttcataaaactgaatataaattggg
ttgatgttgctaaagggctgcgaaaaactgacctgggatgaagctgggct
gcaaggggctgcgaagtgctgcgagggcaaagcgctacagtgctaaaagg
gggctgagcccagaccctcaggaaaaaactcatactcgcagcccttcgca
gcccacatttgcgctctgatcgcgtgctatccgcgcgcacagaatttcga
aagtattttccaaattcggaatgcgcgcggagcagacgcaattagagcgc
ggatctggcacgtaaggaagaagtgtgactggagcacgaaccagtaatct
agtcgcgccccgtccgcgctccaggaggagcgatttgccgagcagttcag
cccttcgcagccctttagcaacaaccaaatttatacagttttatgaaaat
tggaacgggatattattgatacgcctaagcagccctattaaatagtgatg
agggcgtaaatgaaattcgccatttccagctaaaatataaattttttgaa
ttttttaacattgatattcggaatggattcagcagaaaatttgaagtcat
ttgaaaatattttccagatttcggtactccacttttaaaattgaataaaa
ctgtagtctttattcaatgtttcttcaaaatttaaaaagtagaatataac
tgtgagaaaatttccaaaattgtcaaaatttcaaatagctgaaatatttc
acggcccggcggggggtacatggatgagaattctctaccgtattccaatt
tggctgactgcgtgctcaacgttgaatactcagtgtaaactttcgtacac
cgttgcgtactgcacagcgcgcattttaattgacgacatttagcaaaaat
tgaacataagatttttcggaattatgaagctcaattttcacaaaaataat
gagttttttgtagaatttatgaaaaaacgtgaatatatagattttttgtt
catgatattcaagaaaaagcgatttttagttcttcacagaggaatcctct
cgcatttcacttgctcatgatgttttttgctccactttaggacgataaaa
atgcgaattgttgataaaatgaatgaataatataaaaagtgcaaatatga
cttcagcaagtgttaaatcccaaatttttcctgcgattttctgctagatt
cctggttttgagtaaacagtctgatatattcatgattataatgataacaa
taacgaacataataataaaaatggagagcacagagaaacaacaaattgca
aaaacagcaactgatatcagaattaacgacgaccacggaaaccgcctcgg
tctccacctcgcccaccacggaagccaccacctctgtcgcgtcctctgaa
tcctcctcgatctccaccgaatccacctctaaatcctccatcgcggtctt
ctgatctaccacggaagcctccacctccaccaggatctgttgaaagtcct
ctgaagcctcctcgatcgccacctccacggaagccaccacgatccgcgga
ttttcctctatagccttcgaggcttcagttgtaccccattcttcgttggc
acgcttcagatctctacaaaaaaaacaaattagaagcattcaattatcga
aatgtgtacctatcccgatttatcgcaatctgtctattcttctccttctg
attctcaacttctttaacttgtccagtagcggcagcttgcttacgagcag
cattttcccgaatcgccttcacctctgcctcctcagcatcctgttgctcc
ttgacaatcgtaagtcttcgaatgacacgttgctcactctcctgctcacg
acgctttttcatctgcttcttcttgtttatagtcaccgcattatgcttgt
gatagagaacctctccctcatcgatttcttcttcaattttgacgagttcc
agggtcagtcgggtccgatctcacgaagacggacgttgctattctggcca
attccgcagtcacgtccttcataaatgtcttgtggaagttcttcttgctg
agggggctgctgaaaccaatgtcggcatgatgagagttccggtcttctga
atccatttcctgcgtgggctgtggcgacgagctgcacgtctgaaaatcaa
gtttttgtaatttttgggcgcatgatatggagctgaatcattcgatttta
gaatcagcatgcttttattcatattttaggatctttttaaaaaatctgga
ccaacagttttcgaaaaaatttaatttttgttcagaaatgtgaatattca
ctaaatcgaaaaaaataattgcaaaatccgtcagctgaacattcaaaact
tatcaatttgaaatcagcatatttcagtgtataattaaaaaagtttcaaa
aattctgagaccaatttttattgagaaaaataatttttcgctcgaattat
tgaattttcactaaatgcaaaaaacagtaaacttgggcccatgctacaag
cctgaatctttcaaattaagaaccagcatgattttttcaatattctagga
cgtttaaaaaaaatctggaccaacagtttttgaggaacgtaattttttat
acaaaaatgttctgatttttcactaaactcaaaaaaatagtcaagttggg
cccatgctgtacacctaaatcattaaaattcagaaccgccatgtattttt
tcttaccaaaggctctttaaaaaaaatctggaccaacagtttttgagata
tttagaaaaacaactcacttttcgacgtttttcgccttttcgtggctcac
ccggttgatttttgcggcgatttgtggtctttcgctgaaaatattatttt
tatttcaattattaacgaagaaaacaagaaaaaacgacgagaaaacatca
aaaaaacgcgaaaaaacatcgaaaaaccaccgcaacctcatgaacaaaaa
aaaagcattgcagccgcgggactagttttcgcaactttctaggccatgtc
ccgttcgccgtgccgtgtatttgtttaattccctttttggaaaaagtcaa
catatttttctaacaaatcgtttttctattaatttttttctaaaactcac
aatcaacagatcactttttgcattgcaattctcacaatatcccgacggaa
ccctctccaaatgattgacctctttgaatagttcatcataagtgtcggtt
tcattcaaatgcacattaatcattgttttatagttttgcacttttttcgt
gttgtaatagtattggataatggaagaaagcgagcgttggggcatctgca
aaaaataatgaaatttattttctttttatgattaaattaaattttcaaaa
attccctttttttgacatatgcacttacagccgcatgaatcttcttgaac
cgttttccgaaatgaaagaagcaagtggagaaaagactaatttcttctgc
cgtccaatcatcatgaatttcttttcttctcatcgcttgaaccatcgcag
cgtcgaaatcatttgactgtttgttcagaatgaacagagcctgtaaaagc
agttagtttttttttcaaattcaaagtacatttccgaaaaataaaaaaaa
ggcttgattttttaaaatctcgaatttttattatggtcaattgttatttt
ttccagagaaaaactcattttctcccaattttcagacgtttctctctaaa
tttggtgtttttccaatcgtaccctatctataggtaattgatatcgtcca
gtagcttctgaaatgtattctgtaagccgattctcgttcatttcgtctgg
aaacgcccaaatttgttgatctctgcacggttctttttccaattgctctg
cagttggctgtataatcgcctgatattcggttcccacgtggattagattg
tcgacgttggaaagtggatttgctggaagaaattgggaatttttcaaggt
tttaagtggattttcaagctatttataaaagcatgaaaaagctcagaaat
gactataaaacctttttttacgtcgtatttttttcaatgaaattacctac
ttttaattaattgttcggcttaaaaccagaaaattgtttcatatcgattt
tcccggtgaaaatcgaaggaatcgtcgcattctcaaagttttttcaccga
tttgtttcaattttagcacaactaaatggaaaaatcacaaaaattccatt
acagccgattttcgtgaattttcctacatttcgaactaaaaattgtcctt
tcttctgtttaaaccggaaattctcttttgaaaaaccaatgaaaatttga
attttctgggcttttcttcggaaaattattctcgaaatttatcaatcgat
ccttgggctttttttgttccgcagaggctggcggagtttacaagcgtacg
aagtggttcaacttttatataaagctttataaatgggacatagatgaata
tttcgaatgctaaatgcaaaaagaatcagtaaaaaagcgcgcagccccgt
ccttctctgacgaaaaacgccgtttaaggatcgattgctaaattttggca
gtagttagaagtgtcaaaatttctgccggagagtcgtcaaatttcactga
aacgtaacccggtaatttccacaattaatggtcgatttttcgcaaaaagt
ggtatgtttgtcaggatttattagaaattgtggctgtccagattttaaag
agtatttttgggcaaaaatgtcgaattttctctgaaaaagttcgattttt
atcgaaaattcagattttttagatagttttcatcgattttcccagttttc
agcctgagaactttactaacagaaagatgtgtcatgagcaccactttcat
gatgctcacgagcttcagcttcttcatcttcgtcctcttcatcctccaaa
tcttcatcctcatcgcccattgattccccagacgttgtttcgcgttttct
catggatcttataggacgagccatctgaagtttcaattttagcttttaaa
ttcaattttaccgcttaaaaatcgataattctcccgtactctgctggttt
cttcttcttgttccgcctgctcctctggatcatcttcctccattggctcc
ggcgatgcattcaacatattcaagccttcgtctgaaatatctggccaatt
tatagaaaaaccgacaaaataataagcctcactttcttttcgagaggcgt
cttcgtcagatgacgtgtacgaatccattttctggaatttgaggattttt
gaatgtttttaaacaaactttatagagaaaacattcgaaacactagaagt
tatgttgaaacacgagaaaattttttaaaaatccatgagaaaaacagttt
tgaaaaatctgtttttggaggctctccggattttgaggaatcgtcacccc
ggagacgcagattctccggtaatttttcattcatatttgagtttaagaac
aaaacagtttaaaaaaatgtttttagtatttgaatgaaacttataatgta
ttttttcttccattaaaacttaaaaaaaactacaaaattattatgaatca
aatttgaaaccgtgaatcaatctccgcggaagggcgagtctatactgctg
caagcgcactctatcgcaaatgtacaattggcggtttttcaaacaggaat
taatcggattctcgtagtttattttggatttcttttttcgggaacatatt
ggtgtttttgcgttcaatattcaaatttagaggaaaactgcttcaaatat
ttaggtaaactcttgaaaccgctgaaaataggcaaaaataattatttttg
tattttttaggctactttctatacttttgcgtaaatactatagtttttct
ataaaacacccattaaaattatttttataaaatgatttttccaataaaaa
taaaatgcgcaaaatgattcttttccagaatcctatatgcgcctttaaaa
tctctcggattactgtagtttcaaagaaattatcctttatatttttaatt
ttaaattttttcctgaatgtcaaatattaggggaaaaattataataatat
gtgctttattcatatgagtgtagaattagtgaaaaagaaaaaaaacatgt
atggactgtaaaattggaattttagcgagaaaataaaaataatatgcaga
aaaaattaaaattttcaggaaaaaagtcagtaaagccatcaaaaactact
cgattttgaaggaaatcagcaagaaaaattagaaaaaagtatttttaagt
tggaaaacccctgcttgaatttgtacactaaattgggcataaaagcgtac
aaattcgcaaaaaccggtaaaaatctggggatcgtgatggatggagtgtt
ttgtgaaaaaatgcagcgaaaaattgagtagacaatttcaaaaatgtcga
tttttgaaatttgtgacgaaaaaattgaacaaaaactgtttttttttgga
attttcaacaagaagttttataaatttttttgtttaaaattttgaatatt
atatgagtttggtttcacttaacagaacaattcgaacaaaagtattctag
aaaggaaatgtgcgctccagcacactatttgcccgtggagcgcacttgtg
tgcacgaacgctagcgagaatgtgtggtagaaagggagggaataggaaat
attaacaaaattgggcaaaatatgtaagattcggagaaagaattggagaa
aaatatgtatttcgagctccgcgagctgatcaatccaaaggctttctcca
tccttttttcgagaggcacattgcattatagttacacacagcacgtgtat
aatggaacattgaagcctggaaacgagccatcgctaccatcattaccacg
tggatctgaaaaaattaaagtttgatgattcgaaaattttctggaaaagt
tatgattgtgagataaattgaattctttgaaaaatcaaaattcaaaagct
tgtagaaaattttatatatttttttaagcgtattttttccgtatacattt
ccaaatttttttgttacccaattttaaagattttcttgaattttaaaatt
tctttcagtaaaaactttttttcaactttttgattttttttccgcatttt
ttaaaattttattcagaattattagattcttttgaatttaacgaattttt
ttcgctaaaaaattgttcgatttttcccgaattaagaaaaatattatttg
gtttttgaattattttcctgatttttttcgattaataaatttgtaaaaac
aattttttttctaatttttggttttgatgattgtgttttttttctgaact
ttacagttttcaaagtttacaccgaacttccacattaaaaaattctgata
caaaaaagtattcacatgatttttaaaatttaaatatttttcaaaaaaaa
taatatttaaactgtgtttttttcggaattttttttcgattttttccgag
ttttttttggaattttttcctttctgctccaaaaatattcaaattcaatg
ttgtgtagaaattttattcaaaaaaagtgttcaacttctgagtctaaacc
ttttccgaatccttaaatcctggcagagctctcgtgaattcagttgtcaa
tttatgtggatagcaagctgccagtttaatgaaagttttagttcctttgt
caagtactcgattaattttcgaataatcataatcatcgactcgaacacca
tataatccttgagtatagttccaaattgcttcacggaatgcagcagtgtc
aatttcattctgattcacggcggctggtggttctccgtctccagatgcat
gggatgagccggatggcctgaaaaattaattttttggaattattatattt
ttctgtttttgaaatttcatgcatctcgaatattttaacaaaattaccaa
attcaactagatttcttacaactttcactgtgtcgatttacgggttcgtt
atacgaattgaatttgtttatcgatagaatattaaaatttagctaaaatt
gagaagaatataagaagaaattaatttttttaatttcaaaaatcgagcca
gtaaatcgacacgagcgatcgacacagtagtcatttaaagaccagtttcc
gccacgaaatatttcgcgcttcaaacatgttgcgtagtacgtattctcaa
aattgtgcgttcacgtataatatttatgcgaatttttggtctactttgtt
agagaaatcatcactaacatattgccagtaagagtccgaatatgatcgaa
cattcgatcaagccgtgacgtcagtgtatccgtatactcattcatcgtat
tataaacatgatcccatccaaattcttcaactcggaatggcggaatatcc
ttttcaggtcgctttctaaaatcaatatatccaaatgttcgatgatgcga
gtaaattggataattacacggcggctctttttccataatatcttctccat
tttcatcgatatttgcaagaagaagtacaggcgagtagtttttccgattg
gaactatatgttgctgcaggagcactaattaatgattcaatagtttcagt
agtcattgcacacatcttcgctggtggcctagtttgtcctttttccgtct
ttttcagctcactgatcaaatattcgacttcagttggccgacgatctggg
acttttcggaaataggccgacattctcgcctcccaatagtcgagatcatc
gatattaaggaaatcaatctcatcttgtgtcaaatcaacacgacgttcca
atccaatacagcatataactgtgcacattgcgtgagtcattgacattatt
ccgacggcgtggtggagagagcaaaccgagaaaaacgcaggaccaccgtc
tggcgtgcggcgagcgaagagcacctggaaattttcaaattcttgagaaa
aacctaacatcgttgttatacgttcgttctcttggcattggagttggcag
aatttgttttgaaaaaacgttgttttttttttgaaagaacatttttttat
tacgggaccatgagatcatgagaattcctatttactggcgcgaaaatatt
ggcaggccacggcaacgagagagcatatggcaaagagagacgcatcttat
tttgtcttgtaatttttttttaaaataatttacaatcccttttcaactat
cgtgattgtaaaatattacaaatttcagaatttcgctaccaaattattac
tggaaaactaaactctgagaatgcgcattgagcaacatatttgacgcgca
aagcatctcgtagcgaaaactacagttattctttaaatgactactgtagc
gcttgtgtcgatttacgggttcggtttttgaaataattttcttttcgaga
agtgacagtgatattccattttccttcttttcttcctattattttatcat
tatttgcttaattttaatattcaattcataactaaattactttaattcat
ttcgagtagacattcaaagaattccggtagttttcgcttcgagatatttt
gcgcgtgaaatatgttgtgaaatacgcattcttagaatatggtgttcccg
taatattcagaaaagaaaagatttccaagaactttctgaagatttcaata
tttgcaaaatcagaaaccagttctgaatattctttatttttagaaatttt
tcaaggttttctaaataacttttctaaataacctaccgtatttcttctat
taatatggctgcaatactatttttcgatggtcttcccgcttgcaatacta
ttagggagtgcaagtctaatagggagtgccatactattcttcagaaaatt
tttctgtgttggggcttactagattctacttgaaaaaactccaattttat
ttggaagtatagaaaatttgattgaaattgcaacaaaaaggtacaataac
ttcaatctctaaaaattttgttataaactgttgcaaaataggcaaaaaat
gttattaaaattttaaaattagtaaggagtgtttgcaacaaaaaaaagta
ggtgcaagactattagggagtgcaacactaatagggagtgcaatactaat
tttcggaaggtctccgaggggcaatactaatagggagtgcaaatctaata
gggaggccatattaatagaagatatacggtatatatagctttgaaaaatc
ggaaaatgcctaatttttactttttgaggtttgaaaatctctaaaaattc
aataaaatttcaaattaccgctagatttttccaatgaatcatccatggtc
tatgacagagcattcgattcaaataatccaattttcgaaatttcatgtat
gaccaatcaatgcccaacaaccacatttgttgtccacccttttccagaaa
tttgcgacgatgatgatccataagtgataggcatctgtgacgtgatgcag
ccattagtgcaagataatgacgagccgaagctggtagatcacttatatca
acgaacatatggccataacttcctgtcatatgaacatgtagagttgggtg
tttacatgtgaaacggaataatctggaaacgtgagggaaattagttcgag
acggggaggggcaggttggcggtgccaaccgacagccgaacattggggtt
tctcagctggtagcgccagccgacagtctactgcagtactgcagataaat
tttcgtcggctgtcggctggtgaaaattttcatgaaaatcaataatttta
aagaaattgttgcaaatttttcccaaacttgaccaaatttgttggctggc
tgtaccagccgacacccgaaatttagaacattgattagaggctgcttggc
agaaataattttaaattcagaaattcaattcgttttcaaaaaatattttt
taaaactttaccgatcaacttctggaatcggatcaaaattgagccaatcc
atggcttttcgtcttttagttgtagtgtgcattgtgtagatctttttata
ttgctgcgaggtgagtaaatgaagaattttcgcgacccgtttctgaaaaa
actcagttttctaaggaaattttgaaaataaattcgagaaaaagaaactg
agtcagcaaaagaaaattggaaatgtctgtctggaaatattcgaatatta
tattcaaaagttttcaaaaaaacaacgaaattacaagcaattgtgatcag
aaaccgcggaaggaactggacgaaaaaaattatctttgagacgaatctct
ttgcatctttgtgatctaaaagattaataaaggttgtcatcacatttttc
gagatttgggaatgtgataagggtgaaaaatggagattaattgtggtaaa
atgaggaaaaacctaatttttggtgagaaaattgtggaaaaactataaaa
gaatctttatggagtttaaaactcaagtttttcacgcttttccgcactgt
gcggaacgttttttgagagaatttggccgaattcggtgattaaaaaaata
atttcaaaactttgcgcctcaattgtgatgtattaccgtactctgttgcc
attccaccaaaatttccttcattgttttgccatttttctgcataataact
gttctgggtttttttgcttcatgtgcccaaatgtacgaatttccctaaaa
attatacctattttttcaaaatttttaatcgctagaatttttttttctgc
attttctttaaaaaaagagatttctcgcaagtagaaggagaaaaaatgtg
tggctatacttcttcttaaagaatgcacgactagccatagctcaagcccc
ctctggaacgttccatcttcctcccattttcccacgttcaagaatcatca
gcttcttctccctcagcttctcttcttctaaaaccacaactagacaaatg
ttcttgttttccaccctatttttcacataaaaccgccgagaaacccgcta
tcacagactcaatgcgcaccggaggggctctttgtgtgtgtgtactgatc
tctgcgttatattcgaacaccggcgcacactcggattgaaccagaggggg
ggggggaggggggggggggggtgaaaaaagagaaatactctgaaattcca
taaaatctagaagaagaaagaaaacaaaggaaaaattggacattccgaag
tcaggctaaaaaatctcataaaacaaaatctattcgatttgtgaccattt
tcatctatctctctcaaaacccgaataaacaaagcctcccgtccccaaag
tgtgctctcatgctcttctggagccttctagactgtctgtagagcctaga
gacagcggaattgcactgaagtgatggagagacgtagagaaaacgcctga
agaaaaaaacgaacactttggtggaggaggagatggcttccctccaaata
aacaacaatttctatcgtttctctgtgattgtgttctcttctatgtatac
tgttacgatattgaacaggaaattaaattgagcactctgaatacataata
cacaataaataaatacaaaaactatagtttcagcacaaaaaattcgaaaa
aaaaacgattttttttgtccgagaggagtatatggcctagaaaaagaaaa
ctcggccactctgatgcaataaatttaaaaaattatggccgaattttaga
tttctcaggccaatttgatacgtttctcgaaaagccataaattagtcggt
ttttcacgggcttcttgccttcctcattgcatttttcgcgctccattggc
aatctcctgctggacaacgcgtgggaaatcgtgtgccccacacgggcaaa
tacattttgttttacaaagaaaaccgtgccgcgacgcgacacgcaacgag
ccgtaaatctaccccagatatggccgagctcaaatggcctaacctgtcaa
aatcttccacttcaaaatatgagggaagccagaagcgcgtgttgtttctg
aaaaaaaaacccgcctaaagttgatttaaattatcgtttttttggaaata
ataaaatcgatgaatttgtagattttgataaatttccgataaaaaaaaaa
ttttaaaagaggaaaaaaaatgtttcttcgccctttagtaccaaaaatac
gcccaactaaccaaatcgttctttcaatcttttttaaatgtttgtgcgtc
tataattgtcgcttcagaaaactacacaaaacacacacacacacaaggag
aagaaaagaaaaaacgtgttccatgacctgccactgggatcgatctgtaa
aagaattggggaaaattgaggtaaactggttttttatcgggaagattttt
tcggaaggattgagatgaaagttcgaaaggtaattggcaaagttgaaaat
tgaaaaattcgaaaaaaatctcaattctctgctgtaacccccaattttgc
gtcatggcctagagtatgcagcgtggcctagaaattcctaacgtggccta
aaagatcacggcggtacctatgattttctagcgtgacctagaatatacca
gacctagaatttgatagcgtagaatttcccagtatatcctagcagtctta
agtgacagtttctcagtacgtccaagaattcgtcagcatgacctaggatg
ttaaagcgtggcctacaaattttcagagtcttctaggatattccagtcta
aaaattttcagtgaggcctgaaatcatcgcgtgtcctagaatgtctaata
attgcaaaaaaaagatttgaaaactagtatttaccctaaaattgcatttt
gagcattatttttaatctagttttaaggaaaaaatcagaaaaaataaaca
ttttttgattaaatcttccgatctacagatagaaagtgtgcaagaaagaa
tgcaacattgtgctcggtggagcaagaagataaaagaaagagaaagaagg
tcccccacccctccagtggtcgaaacaatgataaattggacaaacggagg
accaaggggccgggcagacacaagagagagagtacgtgaactgaggaggg
tgtgcagggaaaaatgggatgggggcaaatctagttcaaagatgagacac
ttttcaggatctttgattctgagaaaaattttgaacaaaaagaatacttc
aataatttaatggcacatagaaatattttcagattgttcttcaaaagaaa
aatatttttatgcccggaaaatttatttattgcatttcttccaaaacagt
ggccggtctcgacacgacaaatttttgttaaatgcgaagaggtgtgcgcc
tttaaagagtactgtaatttcaaactttcgttttaatatttacttgtggg
aaaacattaatgcttaacgaaaaattacagtactctttaaaagcgcacat
cttttcgcatgtgacaaacattttcgcgtctcggtgacaacttttaagtt
aaaggcacatagaacttttctgaagaattttatttatttttctgaaagtt
aattgctacagtatcctttttcaagtcgcaccgagagccaaactgtagca
aatcatcaaaaaaaagtcgacaaaacgtgccgaaatcagtaaacttgaga
gctttaaaactctattatcagttcttcgccaacaaaaaaaaagagtaccg
tatcaaaaacgaacttcgacttttttggctctcctgcatacggacatgat
tctgattgacagttttcatgtttttttttgggagttttatttattgtgca
tttaaaaaatcgtatagtttgatgcgtggcctagaatttgccagtgtgag
cattaactctccacggtagccaagaaattttctacggtggcctaaaaact
gccagtgtagcctaaaatattttattgtggcctaaattttccaatggtct
gttttttttatagttgcctagaatttcttttcgtgacctagaagcgtaca
gagtggtggcctagaaaacgattcatggcagagttttgaaaaaaaaacga
aatttcgagaaacaagcgaacaaaaatcgtctgtcgaaagagtatttcga
atgctggggatgcaaatcagcaaatcattcaaaaaaaacttttgtgataa
gaaatcaaactgataagccagtgtcaaagtctcgaggattaaaaatagca
tttcaggtcggggtacggtagggtttttgtagaaattaatgcaaaatttc
agtgggaaacgagttcgtggcctagaaaaatcatgtctgaaaaattgcaa
atgcgctcccccgaaatggttaaaaattttcaattgatagcctatttgaa
gtggcggcctagaatatcaaataatggcctagaactcaaattggcggcct
agaaatcaaactaatgacctagattagggcatcttgtaggcagcttagat
cacctattataggcaggtgtaggtaaaattgtagacaaatgtaagtttct
ttgaagataggcgtaggttcctttgcaggcatacatagatcatttattag
gcagatgtaggcctgattgtaggtacagtgccggccaaaaatatatccta
tttttgacttttgataaatttacaaattttccaaacgagcacaactttaa
aactagaaatgttatcgaaaaaagttcaactcatgtatgtattgcccata
attacgtctactcgtattcaattgtttgttgtttactagtgtcacgacaa
caaatacagcggccgacatctcgtaagcccgtttttgacaacgtttactg
attcggccgtatctcgaaaactaatttttttctgaaaatgttgttaaagt
gaaatagttttcatgttatttgttatcatttgtgtttattcactttgttc
tgaaaaatccagtaaaaaagttatgggagtgcaaacttgtcgctcactgc
cactcacccgctacaatcaaaaatcaggttacttatagttagttctaatt
ttttttttgtagagcattttttagaaataacacatgtaaaatcacaatga
>Contig2
cctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcc
taagcctaagcctaagcctaagcctaagcctaagcctaagcctaagccta
agcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaag
cctaagcctaagcctaagcctaaaatagtgactctggcagttctctaaaa
taagtgactctggcagttcaccaaaaattgtgactctgaccgttcaccaa
aaatagtgactctgaccgttcaccaaaaatagtgactctgaccgttcaca
aaaaatagtgactctgaccgttcaccaaatatagtgactctgaccgttca
ccaaaaattgtgacaatgaccgttcaccaaaaattgtgactctgaccgtc
actatttttattgaactgccagagtcactatttttagtgaacttccagag
tcacaatttttagtgaactgccagagtcactatttttagtgaactgccag
agtcacttattttggtgcactggggtgggtcacgcccccagttctcagtt
atgggtactctgatccactcgggacccactttatcgtgttccccgtgcct
catttaccctagagcttcctcctttacctctcctctcgctatctctaaca
ttccaatggaaactcctatttgaattaccgccaccgatgtgcccgacgcg
acttactgttagcccttgttttgcacaaatctgttggcttccatatttaa
aagttaattaatgacccaatgttctttttttctctaaatctccacaagat
gttctgttttccctactggacactatcgttcactgcgtctcaccaattca
cattgtctctactttaccttttttgtcatagtacacgttcgccaacggtg
tcgacggccaaatgctttgggcagcgtttgctttttttataattagtttt
attttattaaaacaatagctctaaagtttacaagtcatttgttataggct
aaatgagttatgtctaataagtaatttgaactagatacttccgtgtaagt
gacaatgtatcggaaaagtcctcaaagtgcgatgtagaagttcacatgta
ctttgtttggcatgttagtaaaagagccagtatgctgattcattttatat
tctatatactcatgtaatatgcccatgtaaggtttaattccaaaaatatg
agcgtgttctattttataatattttactaaaatacctttcagttaattgc
actcaaatttgttgttcttcattctctcgttatgatttaatcttattgcg
tcaaggtcattattttaggtccattagttatcgatctgaaacatgttgtt
gtatttttctattcttgtgagctcaggacacctcatacaactccagagaa
aatgtgtctcattattcttgtcttttttcaagatctaatcaattttctac
attaacgacgtttttgtcgttctgcttctttttttcgttcgtttgtctcg
tccatcagctgtccactcatttctctcccactcactaggcagtgctttgt
ttggttccgattggcagctggctgcagggcctgcatctcttctatgtctc
tcatttacttgcattcttttcttcgttaatttttgttatgatatttaaac
gggaagaagagtttgtggttcttctttttataatcactaaaacttttgga
taagtaacaattttctgataaaaatattttcacggcgaagaaaaaagaaa
aagaagagtagtttttgcacgttttcatataattattttcgttgatcaaa
tgttcttctggagttttctaataaatttcttatcgactttttttcagaaa
tttttctcaacttgtcatgtcaatggtaagaaatgtatcaaatcagagcg
aaaaattggaagtaagttctttataatttcatttatatactataagtttt
ctcgatcacaggagaaacaaaaacaacagacaacacaaaaaacaataaaa
caatattgctctagtaatcaatagtgttgtaaagagggaagaaaattgtt
atctgtgtagcagtcaacgttgattgagatgttgtgtttgactatagagt
tgaaaataataacttcaaacttgcaagtcatgacttatcaaacactgccg
gaacttattctggatcaaaggaaagttgtccaactgtagagtcatgtttt
tcaaaagaaaacacaatttttaagtataaatattttgaaaaagtatgttt
tagaagtatgtcaaattaaaaaaaaaatccttggttaaaaaatgattttt
ttggatatatgtgtatttttaactaaaaatatatactttacatatatatt
ttggcgcagttatttgatctataaatcaaactttttgatagacatttttt
tatatttacaacaactagggttgttatgaaaacgcctattattctacaaa
ctaaattattttaatcatacattccccactatctaaaaactaatgcaatt
ttcagattttgtcatgtaaatgggtaggatgtctcaaatcaacagaagtg
ttcaaaacggttgaaaagttattagatcatgttacggctgatcatattcc
agaagttattgtaaacgatgacgggtcggaggaagtcgtttgtcagtggg
attgctgcgaaatgggtgccagtcgtggaaatcttcaaaaaaaggtattt
ttaatttaatgtgcattttataatataaattcttcagaaagagtggatgg
agaatcacttcaaaacacgtcatgttcgcaaagcaaaaatattcaaatgc
ttaattgaggattgccctgtggtaaagtcaagtagtcaggaaattgaaac
ccatctcagaataagtcatccaataaatccgaaaaaaggtattcacaatt
tgcatgatattgttataatctaattttcagagagactgaaagagtttaaa
agttctaccgaccacatcgaacctactcaagctaatagagtatggacaat
tgtgaacggagaggttcaatggaagactccaccgcggtaagtgtgtttct
ttaaaaattacttccttttttcaattgtttgaaattaacaagaaacctgt
tggagcgtatttctgaacttttaaatcgaaaatatcatttgcaaaaaaac
ttgaaaattgagaaacttttttaaaagtggagtagcgtctgcgggttttt
ttgccctaaatgacagaatacatacccaatataccgaatataaccgtaat
aaaattatgcgatttttatttttatttttcatgaatgttaggggcaaaaa
acccacatgcgctactccgccttaagaagaatcagctgtgagcactatcc
actatacattggaaatttacaaataaaatagagattaagtaatataattt
ttaagggttaaaaaaaagactgtgatatactatgatgatgggccgaggta
tgtatttccaacgggatgtgcgagatgcaactatgatagtgacgaatcag
aactggaatcagatgagttttggtcagccacagagatgtcagataatgaa
gagtacgttgttttgcaaattgattaaaagtggagtagcgtcagttaaaa
actctaacatgtcttaggtttttcaaaagtttggtcaaagttttggcaaa
ctgccaacttcttgaaaacttcgttaaaaaaattcttgaaatgatttgaa
aatttgtattatgttattctcttatttctgcactattctatatggcgcta
ctatacttttaattgatttcttgaaagcagttcaataataattaatttta
gagtatatgtgaacttccgtggaatgaactgtatctcaacaggaaagtcg
gccagtatggtcccgagcaaacgaagaaattggccaaaaagagtgaagaa
aaggctatcgacacaaagaaacaatcagaaaactattcgaccaccagagc
tgaataaaaataatatagagataaaagatatgaagtaagtcgaaattgac
aaacagtggtttttgtttaagtttattgcgaaatattcaaaattagacat
gttaaaattttgcgagataatctaaagattaggtatacagattttttcat
gtaaagttacattcatcaaaatttttgtgttcaccaaattagacaaaaaa
tgttagttacacagtatatttattttttatatcaataaaacctttttcag
ctcaaataaccttgaagaacgcaacagagaagaatgcattcagcctgttt
ctgttgaaaagaacatcctgcattttgaaaaattcaaatcaaatcaaatt
tgcattgttcgggaaaacaataaatttagagaaggaacgagaagacgcag
aaagaattctggtgaatcggaagacttgaaaattcatgaaaactttactg
aaaaacgaagacccattcgatcatgcaaacaaaatataagtttctatgaa
atggacggggatatagaagaatttgaagtgtttttcgatactcccacaaa
aagcaaaaaagtacttctggatatctacagtgcgaagaaaatgccaaaaa
ttgaggttgaagattcattagttaataagtttcattcaaaacgtccatca
agagcatgtcgagttcttggaagtatggaagaagtaccatttgatgtgga
aataggatattgattttataacgtgtaattgagttttggccaaaaaggta
tggaaaggtggctgtttagttatatatttttctattatttatttgaaaca
tgcaaaattgaagtgaacaataagtgatgttcatggaaatttaaactgtt
ttatgatacttttttgagaaattgaaaaatctgttcattttagaaacaat
gtccacatggttctaagagctaaaatttttattttcatccatttagagta
ctttctcttttagagtacggccccagagcgatgttagaaacctgagatcg
gtcaacacagaccgttaattttgggaagttgagaaattcgctagtttctg
acacgaatttcagctaataccaaataatgtgcaattgcattttgcatgtc
agcattcagcattcatacaaaaatttcaaagagccaacttttcatacgtt
tatggtcaacactgtatgtgttacattgaacttttttaaattgtattatt
tcatatttgaatcatttccatgccattttcaaatctttttttaacaaaaa
tttagtttcaaagttttaaatttaggtgaaaacttgctacaaaataacac
attctttagtcgtttcaattgctatctatccgcagactgcaattttgttt
tcccacaaccattcacacaataaataagggtataaagttttgttcatata
acacatttcaatactaacatttcaattttgaacaatttttctaaacttat
ttcccttcgcccaaacgtcattcaacattctttgtacaaaacattaccat
tatagaaaatctcatttttccactatttcatttatttttattgttccgcg
ataaatataaataaacatttacgtgttccgagttcaaagttttaccacgt
ttcagaataaaggaatcggaggggggggggggtgaaaaaatcatttcaac
aaatcagaatttctcaaaatgtgagttttatcattttcattgttagaatc
acgattagcttatattgaacaataacaataatttaatcccattcattcca
tatcttctcatgatgaaaaaataagcattattcgttttcttttgacgcgt
ttgatagggttctgccagcgccgaccaatattcttctcaattagattttc
cagaactgcactaactgaaaattgttttagtaaatagaacaaaactgact
attagttcaatattataattttacttccctattttctgacagcattttgc
aaatactctttacagtcattcttgtattttgacaacaaaattcgaattta
aaatttcatttttcttttaaaatatcagtacactcctggtagaacaaata
ttttatttcaatgtttatgtatgagtagaaaagttaaacagaactattat
ttggcatcaatttctgttttttttttcatctaaagtatggcatttattag
caaaaaatacatgcttgaacaggaataactattaatttcctatagcgacc
caaaaacaaccaaaaattgttttaaataatttttttttggtcgacttcca
tagttatgagtggcaaaaactgagtaattgtcaccttttgacagtaaata
aagaaattttcaaaaaatttttgaaaagttttattatgctattcgatcat
tttggcaccatgtaggctttaacaccccactggcgctactccgcatttaa
aagtgatttataaaaagtgtaaggaatactttgctccaattttcgtctag
tgcatggcgtacccatattttgttcatgttgtgtctcttagcctctcctc
ggaggcgagtttccatagctacccacaaagaatttatttttctatgtatg
cttcgttggctccaccttcattttctcagtcgtttctcagttttctcatg
aattctctttttgttcgtttttagaatagctatcgttttaccacgaatgc
gctttttcagttattaagaaaacagttttttgtagtacatttttcatagt
ctgaactttcagcatggaaatagtaaaaacaatcattccacacaaccgtt
catacattgaaccgcccataccatctgccaccgagtggcttgcaagtaag
ttgttttgtctaaagacataatttctgaaagaaatctatccgatgagcgg
aaaataaacagaagttgtttttaagaagactttgatgcaattacaaaaat
atatggctatgtgcgtaaaaattagacgtgactcgtcataaagaccatat
aggtctacaaaggcgtttcgagtcttataaaagttcgttcaaactttttc
ggggtcttgttaaaagcacaccaacaatacgttaaaggatttataaaatt
gcaagtattcgtctcaattgcaatactttggaagccgaattttggcaaga
tattggtaaaacaggtacattacaatagctatttttggtaaaatgtacta
ggtatcttgtaatgagttgcgcttgcctcataggcatacatctaccgtat
attctttactagtgctgcaggcagcactaatttctaggcccttttttaat
gcagtactattagagactgcagtactactggagatgcagcgctaatagag
aatatacggtatgtagatgcctagaacgctaaggttgttttattcaaata
aatttcttagaaaggctaatattatttttaaaatcaagatttaagttaat
taacacgacctcgtattctatatttcagatatgtcagttatgcatgtgtc
atgtttaaccattgcttgtgtatttgttgctatcacatttttgtcatcat
ttttccatttattttttgtattgaaatatgtgtctaatgagaggatacgc
aatgatatgtacgcattgatatttatgtttcccgtgagtttataaatgga
attatgaagagtttggaaaatatattttagataaccacatttgcaagttt
agtaggaatgttcataccaagagcggctattttcctttatgcagtttccc
ttgtgtaagtgtaccttaacaccacaaacagaaaaatgaactttattgat
ttgttccagatatttcatgtttaccctcttcataatggtcactcttttat
tcaacatttttggaggtcggcaagaaatgagtgcctacttgctccaaaga
aatattcgagttaatttcactgttccaccactctgttttttcaagttcct
gccaactgtagaaagtacagagtgagctcgaaaatcttatttttgtcttt
ctaatatattttccagtcaaaacctacgtcgaatcgagtggttggttttt
caaactcctattatacgaactcttttagagttagtctcagtcgttgtgtc
tatggaacaagaaggaagacgagaaagcgtgtaagaccatgaaatgtttt
ttgtgtgcgcaacgtagtgcgaaaagttagttatttggagaggaagttat
ttgaaaagaatctttagaagatattgatattttatattctgtatgtaggc
gctgtggcaaattctcgacttcacgggagaagcgcaaattttgtgctggt
ttccataatgcgctcgaaaaatgttgtatatttacattattcaaatctca
ccgattaaagttgaatttcagttggttcgtattctctcaactcatggcac
tactctcgatgtgcattgccttttatggttgctacgttatggttcctctt
ggaagagaaaagcatgctccataccgattcgattttctatttcgtacatg
tgacattgctcagtgtatttacacaattcaaaagtttgtctttgagtttg
ctgctgcagttggcttgatcacttcggatcgataccttccagctgctgcg
aaggcattgtgtaagttcagaagtttaaatggagataggaatgtttcgat
tttcgtttataaaaacacctgttaatattaaattgttgacgtcatagctg
accattcatgcttctttgtctgattgtaattatataattgtaaaaataca
aacaagttaaccgaaaaagttctctgttacgtttgcggtaaattagaact
ttatgttgaaagatatcagcttaaagttaaaattttttgaaaattaaatt
ttggctagaaattcaatttttctgataaaaagaaagtttggtgggaaatt
taatttcattgatagaaaaactgaagtttgtgttttctgagaattaaaaa
acagcgggcaatgaagattatgtctttgtaaatttcaatttaaaaatatt
ccagggtgggcatcgtttatgtgcacctgggagatgatgctcctctctgc
tctttgctcatattgtttgcgtccagccaagtgtaaattttttgatcttt
accctggaaacgatatgccagctttatcggcaagagatggttcaaactcc
cgtgttccgtcattttctcgacgtctatctattgaatatgagccacgaat
tgctggagtgatgttggagccgccgtcaagaagttcactgagcattactc
ctagggataaaatagaagacccaacaaccgtatcgtattttgctgataat
tttgattctttatcgcaaatccaaggacaataattgaacttcctgccatt
atttcattgctcaatttacactattcttaactttttgacatgaattaaat
ctttttaaactgagtctaagcgtattattgtatcgtattttccccttctg
atgtattcatttacttgtatttttgaaacccatcccagtgatacaactac
ccaattttcctgtgccatgtttcttgaaacaaatcaaatgtgataaatag
tttgaatgcctttatgtataataaaatcaatttttcaagccggatctccg
tgtttgccattttgattacccagcgagcctgaaagatttgaaaagttata
tgagcagcatgaaaagcctgttctttggtgtttaaaggtagcacacaaac
caaaatttgttagcgcaaatttaaatttctatttcagttaccatgagtta
gtctaacaaacatttttcaagattatcagacaactgataattttaactca
ataagcatgattttgaacaatttcctaactggcgttacttcaccttgaat
aagattgaagtggttattggttcttatgtacagtgcttatatatttagtt
aataatactaactgaatatataagcactcgctaaacttgcgcacaaactt
gcgcttagatttctcggcgttttcctgtgcagtctttcttcttcttcttc
gattactggcatttcttcaacgaaccattttacattgttggcagacgggg
aaatctgagaaaacattaattatttttgagaagatttttcaaaattaccg
ccgattttccttcagcagaagcagtaattttcagaggttcttccggaatt
tctatttttactgcctgttgttttgctattcgaatacgttcttgaacaag
tgcaggcacatttatcacaacatcatctgtgttttctattggctcaattt
cacgtaaatctgttgatgggcgacgatggttaaggttcaaagctgctacg
cctaaaaagtttactttctcgatataatgttttccaaaatattttgtatt
tactcacatacactagctctcctcggttcagcttctgatttataaaattt
tgcgatagctgcagaaattttgttacgcggttgttgccacatatgtcgtg
gcaacatcgaagcgttactttgcgttcttgtattttcagttgaaaaagac
gatgcatcatcatcaccaaacgatctcgatcggcgtcgaacatacgaaat
caaaccattgtccaagtcagcttcgttcctgaaaatcgtccacatttcaa
atttcgaatcagatcatattaattcacatatttatgcaacttccttgcat
atgagaatgagctttccgtgttgaagttggcgtgtccattgtttgtggtg
tttcatcttcccaaaacggatctcttttaagtgtcggataccgcccgtag
gcttgatctacgactgcataccctacctgcaaaacttctaatagttttca
atcttattcgaggtgaagaataaatatctctttaacctggagattccgct
caatgatccagtttgtttcaaaatcttcatcgtcttctccaagaggattt
aacattacttctgatacttttagccagccgactataaatacaatttgtag
agatgtcattattggaaaataaatgtctatcttccactttgcaccaggaa
tgttattgttgttttcaagaaactgtcttccaaacaatgccaatacaaaa
taagtccgaacagccaggttaacaacttgagtataaaccagaggaatcgg
caccatatcgaaaatgaccagatttagaatttttgtacggaattctctca
ttttctgaaatttggttgacattaatcattgtcagtactttactaacatc
aatcaaatcaacgtagagataactgtctgcaataagcccttcatccttag
caaccgttaccaatgagaacaaccattgaattggttgccagtatttgctc
tgcgggctcgtgatggcatcaaattcagtcagctcatcttcagttaataa
tccagcaccaattaggtgttttatggtaggaaatcgtcgtctaattgcag
gtgaaacatcacgaaacaccatcacttgtgcaactatcatgtaccgcaca
cagtttcttcgaattaatcgggctttttccgatgtaccacgaatatattg
agcaattgtcaaagcggatctacaaaattattaagaatgcaggaatattt
ttgaacagaaacaaacgtatcaatccatccaacgttatcgaacactttgg
tccatcgattataaacaattgatacataaaaacctaacatgaatgttacc
ggtataaatactgaaaatgtatcaaaaaaagtgcacagctgttcgaaaac
tctgaaaaaagcaagttaagctcaataagaaattaattgcaacaaactct
ctctgtgctttgttaagcaatattctataaatcactgataaaatagaata
acacaaaagccaaattagtaactctgaccatattgatttccaaaccgatc
ctttccatctcaataacacttttatttgagtgaacagacctgacgtggca
acatctagagaataagcgacagtcatcagtcaaaaaagtatgtgtagcaa
caaactgaataaaaaatattatttgtatcagtcggtgggtgagcgattag
tatcaagtagcacaaacgctaccgtttcagatttgcatattttattgtta
taggggttattcaggcataggtcggttgaattccgactttttattcacat
ttttccagaaacaaatcgattctcctaattttatttttatgctttatctt
tttgaaaatctggcatcactgtttgcggaaaaaaatataaacaagaggga
atacagtttgtgggtattttgcttacgttactgatattatcgccttttaa
tctatattttagtaatttatcttgcgtaaataccaaaatatggattaaaa
ggagataatatcagagaagttaaattacagtagctgcgacaaagaaaagt
ggccaaaatttctgattttagccaaatttggctttttttcgaaattttga
cccgccataaaaaatttagaataattttataatttttttacagttatgct
tggtacattgagactttattctatcattcaaaacaaaaaaataccacaaa
tgcttctccaactttgagaattgtaaaattttcaataagccaaaagtcag
ttactggtacctttgcacctatcagtacttgccatcaaaagaaatttccg
agaatgttcgcatttcggagtgccgtaaaacttgttcctgagagatatat
atcgtctcatcaattcggtatcagtcaacctcccatattgtgtcatccga
tattcaatctacaacaaacgtcatgttgtttgttttcaaacaaagtgtat
taacattggactttcagatagggttttctgattctttaaccctctaaaaa
accatttccctcatttccataatatttattctattttatgcttaacaaat
ttacacgagtttcaaactatttgattgttcatcaaaaaaaatcccaaaaa
ctgttttgtttttatatattgaactcaacaacataatataaaaactttca
aatcgtaaatcatctaagaaaagatcacatgaagtgagtagatgatagag
aaccagttcttatttttatgtttccgttacttttttgttactaccactaa
taacttggcatttttcaatcaatattttttacagaatgactgtaacttat
tcactcgatgttgcttcttcttcttttttctgcttatacaaactactatt
tcgatggaaggtgtgctaaacattgcagatattttgtttcattaaatttt
taggggtcaatctggaaatcggtgtgggctgagcttgtagtttggctttg
tctttatgcagtgcttagtgttatttatcgatgccttttaacaatgaagc
aaagagcgtaagtactgttttcaaaaataaaccgggagtctgactttcag
aacgttcgaagatctttgtatattttttgatacttattccaatttcattc
caattacattcatgcttggattttatgtctctgctgttttcacacgatgg
tggcagattttcgacaacatagggtggattgacacgtaaatgacttagtc
gtattacgattataatatctaaataattctaggccttgtctttggataac
tcaatatatcaaaggggaaacagagcgagcaaagtgtgtgagaagaaatt
gtataagatactcaattcttacacaggctatggtaaatctgtgtgtaagc
ctaactaataacaatagtctttttgaaggtgtaccgtgacgttgcagcaa
gcgttcgcaaacgtttccccactttcaatcatttagttactgctggcttg
atgacagaaaaagaaatggccgagttcgagtctatccctagtccacacgc
aaaatattggcagccaatgcattggttgttttcgatgatcactttagcgc
gagacgaaggaatgatttcaagtgatatcatatatgtagacttgatggag
gtacataattcagaagatttttaaagagtaataaataataagtttcagaa
aatgcgccaatttcgtgtcaacattctttcattaacattatttgattggg
ttcctgtccctcttgtttatacacaagttgtccatcttgcagtacgatcg
tatttcctgatagcgttgtttggtagacagtatctccatccggagagcaa
ccgtttaaatgactttaagcaaactattgatttatatgtaccaattatgt
cacttctccaatttatatttttcattgggtggatgaaagttgccgaagtg
cttctcaatcctttgggagaggatgatgacgattttgaatgcaattggat
acttgacagaaatttacaggtaaacgattaacataatcaagatttattat
tattatttaatacgtttattgaaaagtgaaaatgatagaaaaatttgatt
atttaattcaattttaagttagaaaaatatcctacacattttctgaagaa
gtgtcgtaaatggggaaactttttaaacatgtacgttccaaacatgtgcg
ttccaaagttccgaaaaaaaatttgtgtagtaccaaatattaaagaattt
tcttcattcttaaaatagtcgtcttgatatacttctgatatgatagtaag
tattgaaacattaactacactttttcagttattttttattcgcgatacca
tccatttaataaaataagggagttcatctacacctgtgcccttctatcaa
acttgattgaagtatattatttttaggtgggattgatggttgttgatact
gcatataaccgttatccaactcttgaaaaagatcagttctgggaggacgc
aattgcggagcctctttacactgcagagagtgcgatgagacctctgaatc
cacaagtcggatcttgtgcggatatgtaattgagtgaatttgttccaaac
aattgattttcatgttcaggccaaccgaagaagagcctttcatggttcgt
ccacgaagacggacgctgtccagaatgtcacactgggatggcgacatgga
agatactgatgttgttccggttgtgggtctgaaacacacgcgtgataata
gtaattatgcttctggcgaatctctagcattttcgaatagctttgccaat
ggtggtaggaaactgagtgagatgtttcgaagaatgagagctgggagcag
aattggtgataggtataggaaacgcaactcgtcagcacaagactttgaaa
atggaatggcaaagtttgtttcatgaaaatatgaatgttatttattattt
cggctatttacagaaaaaacagtattgatgaaaatgcagatattcacagt
aataggctcgatcaagcatccggtacaccaaaatcaggaaggctttggag
ttcgatgcctcaaacacaattggaagaaatgcttaaggtttgtttattca
ctggatttattcactggcgctttcacgtaatttcgagactgcaaatttga
acttttaaaacaatattcggagaagaccattttcgagctaatctagcgtt
agttttaaaaaatgttttaagtttttttttcaatcacaatggtgattgaa
aatctcagaaaagtagagtacttgcgttcatacttaacgcatttctcata
tttttatagaattacacgccgataaacaaatagttaagacatttcagaat
aaaaactttaactctcctgtcaaatacaacactgatgggatgaaagaccg
agagcttcaaaatccaacaccaatcactgatcacattgatttgcctttgc
atgtggcgagtagtcaatcatggtttaacgaaagtttaccagtaatcaaa
gaggaggaagaagctaaaagaaaatccaacacggatacaggtagacatag
tcaattttgtcaaaaaaaattaaatgagtttttcagagtctccaaagtct
agtaagcattcaagtatgtcaatcagaagatcggaattgagaagatcatc
atcttcaggtagtgatctaggcaagtctggaaagcgggagagaaagaaga
gcgagtgatttttgaacagtatgataaaatattttttgtttctcttttca
ctctaaactgaagatccctttcatttcatttttacatatttattatattt
taaatttcaaattgcttaattaattttctattttttaataaacaattgtg
taaatatatatattttttaatacagtgtgggaaagttctataggaccccc
cctaatttgaaggtttgaggaacttccgaaaatttttttgaaaaactgct
aatgccattcgtttttaaattgaaaaaaacctatatacatttttttccag
aagtttatctcaaaaactgaggtcgcgctggaaaaaacgtcaaaatccag
tgtgaaacttctataggaccccccgttttttttcacgatttttactaaaa
tcaacagattttggaatttttgacaaagctcaaatcaagtttgagttaga
aatgagttcatataagcagttttgactttaaaaattaatacgaaatgttc
tcgtgggatctccagactggttctgattcttccgatctttgatgttcaag
tctgtttcaagcttcctggtgctctcggtaatgccaaaacttgataaact
ctctttaacaagttcctactaaaattcctagcacacacaccataaacatt
tttacgccatccccaagaaaccagtcagaaacagcgtattaacaagttgc
agttatttttgatcaacaacagaacattcatatactaaaatcaagaaagg
atcaatagttaatcgggtttccttgtgtgcggatgatctcaaacagtctg
tcctccattgatctgaccaaacttttcagctggttgtccggaatagactt
ccaagcgtcgagaattccttgcttcaacgatgcaactgttgggtaagtct
tgttctgagcatacacgatacggacaagaatcccccacaaattttcgatt
ggattgagatcaggacttcgagctggccaatcaagaaggttgatcttctt
gagcttgaaatagtcgcgggttgagttgctcacatggattgtcgcattat
cctgctgaaatctaaagttttttctggagtagtgacgaagatatttggag
agctccagttccaagacgttctgatagtcagtgctgttcatcttgctact
gacgaactgtatctcaagcttcttcttctccgtgaacgctccccaaacca
tcaccgttcctcctccaaaattacgtctcgaaaaaaccattggttccttg
cgcaaatcgcgccaatagtagcggcaaccgtcaggcccatcgagattgaa
tttcttttcatcggagaagacaacctaaaacaatgatcctaattattcac
tcttgcttttttaaattctcactttactccaattcgttcccatattgttc
ttagcaaattccaatcgcttgagtttatggtctgcagagagtaacggagc
agggcgaagtttctgacgaacgattacaccagatcgtttgatgacattga
ggatggtcctttttgaagcagacaattgaagctcattgcgaatatctctt
gccgtcttacaggagttggaggcagcacgaatcacatttcgttcgtcacg
cacggagagagctttgcgacgaggagctcttttagatgtaccgtagctca
ccggatccttcagatacacgcgaatacagtgtcgagaacgggaaattttc
ctactcatttcatgcagggacacattgagcaatttcataacatccagctg
agcgcgttcagtgtccgaaagggcagatcctcgaggcattgcaagttaga
ctgctttcgaagtaagctttccagcctctatatgtgtgccacaacacatg
ccacaattccacatttaataattcacgcaaaaaatagtaaataacatctg
tgagggacaatttaacttgaaatattggtcccatggaaccttgtaatcaa
agaaaaacgatttgattcctgataagccttccattgtttcctgctgcata
ttttgccaaatcagcttgactacacagtcgaaacatctaaagtgcgtgct
aggaattttagtaggaacttgttaaagagagtttatcaagttttggcatt
accgagagcaccaggaagcttgaaacagacttgaacatcaaagatcggaa
gaatcagaaccagtctggagatcccacgagaacatttcgtattaattttt
aaagtcaaaactgcttatatgaactcatttctaactcaaacttgatttga
gctttgtcaaaaattccaaaatctgttgattttagtaaaaatcgtgaaaa
aaaacggggggtcctatagaagtttcacactggattttgacgttttttcc
agcgcgacctcagtttttgagataaacttctggaaaaaaatgtatatagg
tttttttcaatttaaaaacgaacggcattagcagtttttcgaaaaaattt
tcggaagttcctcaaaccttcaaattagggggggtcctatagaactttcc
cacactgtatattgcaaatacatgacataaatttagatgcagggcaaaaa
ctatagatcaaaattttctattgcactttttatgtataatcaataaaaat
tgaaaaaataaaaaactttgtaagttgatgccgaaacatttcagtttcta
ccaaaatcgttcgattttatactgatcagttttgatcactttctggtaaa
tttcgaaattcgcgtttttttcagttttagagttagaatattagttacta
acaagtttagcaattttgaaggatttcttcaaaaaaaactgctcaaagga
ctttgctgcaaacatactcaaatttgcagcaaagtcctttgagcagtttt
ttttttgaagaaatccttgatttttccttattttctccttattttctaat
tttattttctaataaatccttattttctaatttttcgtaaaaaattatta
aaatttcaaatttttggaaacaattgtttttttttcagtaattgaccata
tttttgaccttcttgtacgtgaatgctttcctttcctctattagggtgtg
tgactgcgtgtgtgtgtgagagtgtgtgtatgtgtgtacgtgcgtgtgtt
ccctggcgcggtggtggtgttggccacacggccctgcgacccccataaaa
actcggttcgatagagagacacacgggaatgtgagagagtatgacgattc
gagagacgcagacgcacgaggagaaacacacgtcacgcgaaacacgttcg
cgtcgcgtcgatgagcgcgcgcacacgtccacatcgttgcctggatgagt
gggtttttggtccgcacacacgaactgtttttttttaattcttgtcttcc
ctagtagtgaagagttttccaaatttccaagtatgtagttttaagtttct
gattaagaaaaatattattcatgtgttttgaaagtttgtcagaaaaatca
atatataatatttttagacgccatgattttcaaccaaataataagtttaa
ttttttttgtgaatctaacttattgatttctgtgtaatattttcaatcgg
tgtgttttttactacattgatatctacattgatatatctacattgataca
ttgatatttttcgtaaaaaatttttttactccattttactacattttact
acaatttactacattgatataaatgatgatttttcagatgaaaagaatac
tctcagatggagtcaatgagccaaaactatgcaaattcataaaagaagaa
tcaccacataaagttaaacaggaaccatatgatgatgaagaccttgtaca
tttgggatccgaatcaattccatcaccaacttcatccacttcgcctccat
ttcctacagaacctgcggttcaaacaattaaacttcccaaatatatggag
gtaaccatacacttttcatatatgtgtaacatggggcggaaatgtgaact
gttcatcgagaccgaaaaaataatattttcaatgattacttttggtaaac
ttttcaaaacaaaattggcaattttttcttacaacttcaaattgttattt
atttccgattcatctttataacttcaataatttatttgagaattctattc
aatgctattaaagtcaaaaatttgcgaaacgtggttttgcccgagttctc
tgaaactttctgaatttggaggagtatagaaaatggttcgtaattttttg
caaaaaagtttcaaaaggctgattaggccacgccctttttagagagttac
tcgtcttctaaaaagtgtcactggttttcttgattcgttttctctaatgt
taagtacataatgacataaatcaaacaaaaaacaatacagtgttcttggt
aaacgagaaactgagtgcattttttaaaaaaatgtgaaaaagtattggta
aattgctaaaattttgaaaaatataagattttgaggaaattcaaagcaat
gtcgcatggtccgacctcaacccctacattggtccgacccctatacgagt
aattaaaataaaattaaagtataaaaaatgtaggaaaaaaaaattttttt
ggtcgaattccaaacttatgagtggaaaaaactgagaaaaaaatgcggat
ggtgctctcttttgttgaaactttcaacgaaagcctttaaaaaaccgctg
aaagcgtccaaggaatgtctaaaaattagaatgccgctgtgaaatttagt
aagcgatcaaaaaagttaagcaatttactcaaattatttcagttaaaatg
tggtgccctcgttgctcgacttcacactgaattgtttatttgtcctggaa
ttcgagaaaaatgcatcgaagtactaggtcggtcagagagtattacataa
gtgtcattgattattcacagactgtcccggagagttattgacacctgttg
agtttacaatcaaggctgaaaagagcaagcaaaaagactggaaaggagcg
ataaagcataatggaaggatgttaaggtatgcttcttgtagttttcaact
cttaaaaacagaacaatttaacagaacactcatggaattcaaacaattgg
atttttataatcatcatgagatgtgttcattcaagtgtcattctcgaaac
tatatcacaaaaaacggtggatctgttccaaaacttccaccaaaaaatgt
tcaacgtcgtcactcttctgcatcaacaacatcaaacgtttcacaaacag
cgattaatcaattacttcaaggagagctgattaaaaatccaaattttcta
gctgcgttcgctgctcattgtactgctgaaaatcagaaacgacaagaaga
agctgagagaaagttgcaagaaaaacaaaacgccatcaagtgtctgatgg
aaaccgactcggtcacgttctggaatcaaacgatacaatcaaaaacgtct
actgtcgttttggatcgaatttctatggagctcggttcgttggctcagaa
tctgatttctggtcgtgattttgcggcgagttcgtctaaaatcatccagg
tacttcaagttctcggcttgtcggacaccgtttctcgggaaatgtgtggt
caattcattcttccatcgtccgtgtcaactaatgttgatggtaaggaatt
cgatccttttaattctatctgaagattagttaaaagtggagtaccgtaat
ctcctttttaagcccaacatgacccaacactactgaatttcgcaataaaa
ctttttggaaatttctcagaaaaaagttatggcgattcaaagttctgcaa
aaaaaagactcaatttcagctaaaatcacaacttttaccattttctcctt
gtcgcagcttctcgaatttaataatataatctttcagggcaaagctcatt
agacgcacaactaccggttcaacatttgccgtcaaaagaaatgaaagccg
ttgacccaatcgaaaaatcaccaaatgataataacaatgaaactctcagc
tcttctgagaaactcgaactcatgatcagaaacgcgctctgatcgaacat
tcatactctaacacattcctcttcacatctccagatgattattcatgtcc
atcattttatcattaaatatctcattctatactctcttctcgctttattg
tttctcgctcactccctacccaccattacataacatctctgaaatttcaa
agttttgacattcttggctgtgccttttcctctcaatgatattttccaaa
ttccattatttttcccccgcctttgattgcttttattggttacttgttta
ttggtatacttctcggtattctttttaatgttctgcatgtttcatatggt
ataaattgcatattacgttagacacaaattactgcaaactaaactcagtt
tgtctcaatggaaattcgtcgaaacacatggtgtcaagctgtcccattac
ggtttgatttacaaaaaatgtagatcaaaacaaaatcggacagcccgaaa
ctaggtgtaaatatacttataagaattcaaaaagaccgaataacataata
aaacattcctaagaattttagattttctaaaatttccagtcatagttttg
gcaacttgccgaatttttaaaaagtatgagcttttgagaggatgcagaat
gtttttacacaaataattaaaaaaaaaaggaaagcataaaaattttagaa
tttttttttcggtagacttccaaagttatgagttacaaaaaatgagtaat
tgtcgctttttgacagtgcatttaaaaacatgcaatttaaaaaaaaactg
tcagctaaggtgccgactgtcagtgacagtctgtcacttgttggtaattt
tttaatagattctagcttacattggtattattctgttctaaattatttgc
tcaaatgaatcatcattctcgctgtgttgtcattttatggtacttgtatt
attatcattatttagataatgaatatacacatattggatagaacattttc
caaaatcagaacaaagcctcattacaaacttcaaatttcatttttcaaaa
ctttgaatagaaaataaatttgggtaaatagtcagtaatcacccaatccc
ttaacataatatccacattatcgagctagtgaagctgtttctctggcagt
gtccaacccacttcttcgtcttcacctcattccttttcaactccgcccct
taaaggaagtactcgtccatagcgcataggaacaggcaagcgataatgtc
tgtgtctctatattttcacgcactgtctagtgccgcatccgtatcctcta
ggacaccggtgccgtggcgtctataaaagagagtacgggtgtcttacgca
gttcgtatccgattttcagtccagtgtccaaggaagacaagccgaatgtc
ccatataaaccgcattcttatctattcacccattccaccattatgttctt
gctttgttcccatttctcgtttttcgttttttttctcttaaactttagat
attactatgttaataacccattattttaggcagtcacaacctaaaaatga
tggagacttcggagcacaaagagctccgacgtgtggcgtttttcgccatt
gttgtatctactgtagctgttattgcagctattgtaattcttccaatgct
ctattcatatgttgctggtttccagagccatcttatcattgaagctgatt
tctgtaaggttagtataaaacaaacatacgtattctattatacaagcaac
gcttttttagactcggtctcgtgacatgtgggcccaaatccatgacatag
atggaccacacctattccatcgtcagaagcgtcaatactcttcaccaaac
ccaccagctgccggtggatatggagctccagttacgaactccgagccagc
tccaacttgctgctcttgccaacaaggaccagccggaccaccaggaccac
ctggagatgacggaaatggcgggcaagatggtgttcgtggaaacgatgga
actgacggaaaggaaggaagccttttggaaagtgctattgtaaatgaacc
atgcattatctgccctccaggaccaccaggaccacaaggaatggcaggag
ctaaggggccacaaggaccaaagggaggaaatggagataatggaccagat
ggaaaggctggagccaacggaatgcaaggaccaccaggaatgatgggccc
accaggaagacaaggagtaagtggaccaaagggagctccaggacgtatca
atcaaatcaatggaccagctggaccagctggacataagggagtccgcgga
ccaccaggaccacgcggagaagctggacttgatggtggaaactctgaagg
accacaaggaccacaaggagatgctggaagaccaggaccagttggagagc
aaggaccacaaggaccagaggtatatttatttttattcgatatattcaag
gctttacatttattaatttcagggaccacaaggaccaccaggagaaccag
gaggctgtgagcattgcccaattccaagaacaccaccaggatattgaacc
tgtactttttctcattaatttcgaattcatccgcccaaataattgggtgt
ttacaatacaatgaattttttcattttaattcacagattataaattgcaa
aatttttcagtatttgtcttattattactggtacagagagtgtagatagt
tagagagtgccaggcatccgggacccaatggggcacatcaaaggctccca
tcgatcgatatgcctaacatgttgaaaaccgattaaaacctcacgtttga
atcccctctaaaaactgaatgtgtgccaacacagcgtcattgacgcattt
acggtgtcttgacgcgatacgcgttttcaatacgaggcaaactcaaattt
attattttcattttcaaaatatcaatttgttgaaaactagcaactactac
tcatctcttcactcgtcattatggttaaattgcgcgatgaacagaagaca
gagcttataaaacaggaaaaaaagcgccgacgcattgctcggttacgaca
ggtatcgatttttctttcagttctcaaaaatattaattattattgacttc
aggttcgccagcaaagtgcagcaaatgcaaagattacaagagacgtggtg
aatcaacggaagcaagagttcattcaagaaattaggttgactttttcaaa
tttaaaattataattgaaaatttatattttcagggaagaattgcacgagc
aggtggatgcgctaatgacagaagtaactgaaaaatcgttaaaattacct
gtctccgcaaaaaggaaaacttctacgcctcgctcacttgtaagtgttcg
ttaaaatgatatttgcaaaaaaaaaccacgaattttcagaaaaagtcttc
tcgttgtcgtgaaatgacggaaagcgatctggagttggcgaaaaaaagaa
atgcagatgcaatgaagcatcttcgagaagcgaagaaaaagaaggaaaag
gagcaagaggaaaagttggcaaagaagaaagaagccgcacgaaaagctaa
tgcaattatgagaggagctcagatattgtaataataaacttttttttcat
ttatgagtatatattgagatcaaacaaagaaagtgacaagaaatcgatat
ttttaaacacaaaaaaaattaaaattgaattcctaccgatcacaaatggg
cgaaagttagatgaaattagttttcacaagtgtatcggttgcggccccca
tagtttattcttcgtggtggtcgttcacaaacgtcaaacgtcaatttcaa
gcaagaaatttcattttcataaagaagccatggcagatagtcgtctctga
aatattttacaaatttttgaatttcttttccattgaaaagttgttatttt
ccgctgaaaaattcaatttttaaaaaaaaaacaacattatttgcaaaaat
taaacttttttatttgaaataaatttttttctgaaaatttgaaaaatgca
aaaaattcaaaaatttaaaatttgaaacaaattttttttcgaaaatttca
aatttccgtgtaaaattaaatgaaacatgttatttttcattgaaaaatta
tattttgcgcgtagagcatgttgaattggagcacacttaagtgtgctcca
aatttgctatttttttcttctagatgcaccggtgcaccatgttaaaaatg
cacttttttggcaaaggggaactaatcgatacattttttaaaattagata
ctgtgctaaaattaaactttttatttgaataaatttgacattacaaaaaa
aaaattttaaaattttaaaattgaaaaaaaagtttttgaaattttttttt
gaaaattttaaattttcgcgtaaaattatatgaaaaatatgtttttttct
attaaaaaaaaccgttttgtgcgcgaagtatggcgaattggggcacactt
tattattgtcacgatgtaccatgtttaaaatgtaaaaatcgatttgcata
ataaaggtggagtagagtcttttaagaattttgattttaataaattaggc
tgtagggactgaatataactataaacaatttaatacaaaatttctgaatt
tttatgatttttccaatttcgcaaaaattcaaaaaactagtcttactatt
tttgaattcccacgcaaattaatgatcattgttggtttttcttgtttttt
tttctttaatattcaatttgatgtttcagttcaccaaagtttcaagacat
ttctagctaattagcaatattaaagaaaaaacaagacaaaccaataatca
ttaatttgcgtgggaattcaaaaataatttaatatgaaaatgactcactt
atgccacaaatttttcctatattctatgtaccactggctaaacttgtcaa
attggccattattaacatcccaggtacgacgacgctcctccagctccttg
gctacggtctcttcaatttgttcttcttttagtactcgttttcttaaaac
tgatccagttgcgttgaaggctaatcggattttggcaattactgagccct
aaacgatttctaatttaattttcccgaatttttagaactgacgtatccaa
cttgttgaagacttcctagggcactcttataatctcctctatcaccttga
aggaaatccatctcacaatcaccatccgcatcaaatgctgaccaatcatt
gaaacagaactcctaaattttcaagtcaccattttaataagtaatttttg
aaaaagacagttggagaaattcaaaatctcacaattatggattttttttc
gaaagcttgcagtttgcagaaaaattgctggacaatttcttgatcatttt
caagaaatttattatcttaaaattcacatcaaatctctttgaattaagag
gtgggcggcaaacgatttttccggcaaatcggcaaattgtcgaaattgaa
atttccggcaaactgtcggaattggaatttcggtcaaaatcgatttgccg
aatttgccgaaaattatcggaaaattgtgattttgtacttttttcttgga
aatttcagaatttcaattttaatcggcaaaattgtacacatcctataaat
gttgctacatctattctgaacagtaagcaaattatatgatattattaaag
aaaacgtgaaaaaattttcaaaaaagcacagttttaagtttttccgtctt
ttaaaaaatccctcgaaacatttccgacacatggcaaatcgacaatttgc
caaaaatgaaaatgaacggcaaaacgaacggcaattgccgcccacccctg
cttcaattttttaagtgtatacctttctgaaagtataaaacccaggtcta
tgcggacaattgatcccacgcaattgcccagccaaactattagattggtc
ttcttcattctgctccaaattggtcaaagattcacatacatcacaaaaat
aacaattgtttccatagccaccacatccattattactcgcgttttgacac
ttcatgttggaaaagtcctttacattccaccactgatattccgctttcgc
aaaaaaactattgtcaagcgcttctggtagatctttaactttgacattct
taatttccaaagtaaagcatcctgggaatcgaacaacgtctggctttata
tgaacttggctcgggttaatatccaatattttttttgctccgggtcgtgc
ttaaaaatagcttctttgtgaatcaaacaattatggataacaaaaaatgg
aaaagtacatactgcaacttgcgtcagcccttccgggaaccagccaaatg
tcctgatagttgcatttgtggttgagcttcttcctagcatcggtgtgtct
gactccattcctatactttgcacgacatgcaggatccaatatatcgcagt
caagttgggcaaaaatcgataatataaatgagaaaataatcagaatggat
atgttgaaggtgtaattcgaagatcgcatactaaatgtgaatatgtgtat
gtttaaaatggaattttcaatacaattcgaataaaaggaaagtaaaatat
ttgtagaagcaaatcaatttctaatgataattgcgtcacagtgtgtcctc
taaagtgtcttctttcttgtctgcattttctcttatgcctctctttgtaa
caagattggccgtacatgcccctcttccgacgcacctaacctgttgacca
tggagaccttggaggtcatcattttttttgtgcgaaatttggcatttagc
aagagaagggatcccttatgggagagaaataaagagtaaagataggcaat
tatgctttgtaccacgagaaaaaaaaactcatttgacacatgaaaatctt
ttgaaaatggaacaatcttatactattcagtacatgtgctccatgtcgta
aagcggttttttacagtttcttgaatgaaatctcacgtggtgtcaggctg
tcccttcgctctactgcacatgaaaacttatgacgtcacagcgaacttcg
aataattgtttttcaatttaagagccgattttcgtgaaattgttttatca
ttttttgaagcaaaatgcaataaaaacacaattttattttaaacattata
tttaaaaattatgaaaatcgaagcttaaattgaaaatcaattattcgaaa
tgcgatgtgacgtcacaattattgcaaaaaaacatttttcccatctttcg
tgtgcagtcaagcgatgggacaacttgacaccacgtgactatacgagttg
gtgattagaatttcaaatacaaaaacaatttaggaaaatactctgaaatt
aggaactttagcaaaaagaaacattttaaaactattgctcgaggagtaca
cgagctgtggaaatcgacatattttccaatttattattacggcaacaaaa
aattctgatacttaatgcatattgcacatcatatttgacgcgcaaaatat
ctgtgtagcgaaaactacagtgactatttaaatgactactggagatcttg
cgtcgattttcaaaagaatttctcagtgacagcgatattacattttcctt
cgttttttttttgtattactgtctcatttaaattaaataatatattgctt
tcaattcattaacagaaaatcgaacccgtaaatcgacacaagagctacag
tagtcatttaaagagatactgtaattttcgttacgagatatttagcgcgt
caaatatgttgtggaatacgcattctcaaaattttgtgtatatcccgtaa
taattgcaaaaatacacttcaattttaagaaaatttgaaagttgttcata
aattggcggcattttttttttgagaatcctacagacaaaaaaaacgtgaa
attttaaagaagcggtgtcggtgaatagagacgaagagggattaggagat
aaaaataattgatcgaagcagcagaaaaaccgattttcttcattttcttg
cccatctctctctctgtctctttttatttcgaaaaaagacagtcagactg
gatttgagtggaatagaggggaaagggagggacagttctacgaagcgaaa
cgaaaacgattatccatctctgttggcagtctcatatggaaaaggttgaa
aattgaaaatattcgggaacaagaagaacacaataatatttatttcgaca
tacaaaaggattatatttcttttttcaacgaagaaaaagaagttgaagac
aagaagagagagagttagtactctgacacgaaaagggtaaaacttacctg
aaaaggaaattggaaaataggggggggggggggggggaataaaataatga
ataaataaaaaacatttaatgctccatagatctatcgattttcgactgat
gtttatgcttttgattgaatgattcgatgaactgtgaagatgattgtccg
tttgactcggccttatatttttccggtaccgggacattgaggatttcagg
taacatccatggtttaagccatccgactagaggtgattgtccaggttggt
atacaaccgaattatgatagaagaggagtccatcgagacggaaactggaa
caaatattaaaggtgtagtagggaaatttgactttttgagggaatttcag
ggaatttgagtgcatttgcagacccaaaacggtccaaaactaccaagtta
aattaaacgttgtgaaaatttctcaaaaaaatgttacagtatttcttcta
tattctattcgaaaattaaattttttgaaattttgaaactttttgaaaca
aagcaaaaagcgagaatttgaataaaccgatttcgcaatttttggttttt
ttatttattattacctgatctcgtttttcataagctccgccatctgatct
tgggagcacggacagctgggaatcggtgagaaaatattcctgaagccagg
cgtagatttcgctagttcaggagcctcttcaagtttagactttagcataa
attggcggaaatcgtatggactctcaacatattcgtgtgcattccatgaa
agaagatcgagcacatagtatgtctgattcgagtagatgcagtcaagaat
tgtccaagcctgatctataaagtgagcacattgaaatcgattttttattt
atttctaaaaacacacatacttttagcacgagtatttccaccaggaaggc
gagactgaaatcgcgatacttctcttccgcctttgttatatgcaactgtg
aagccctgaaatacaagattatcccgggtttttaataattaaatcattaa
aaacaaactcgtgatgcaacgacaagtgtccgtttgcccactggagccat
aaccatcgtccagtcggaagaaagtgattccggaatatccacaagccact
cactcaacatcattttgtcggcatatctttaaaaattgaaatatagtttt
tttttagtttaagaattcgaacttttaggaaattacttactttttaaatt
ttccagtgtgtttttcagcagtagttgtctcaattttttgttcatcgtct
tcgtcagaagtaacgtcatcaaaagctaaatttcgtagtttcataaatgt
gtcaaagcggccatttttttgccgctcaagcgtttcttcacgacgctttg
cttgttgttctgcagcttttgtaagatttttgtactgcgaatacctcgga
tgttcacctgaaaaaatcaatgtttactttttgtgtttaaaaaaggagtc
tcaccaagagctagaggatcgacctgaaatccactgctaagctggtctgt
caacgaatctaaatcgtcccccatttgtgatactggaaaaaataatttta
aattagtttaatcaaacttttaactaaatgagtataagaaaaagctttta
caacaattaaaaaactgtaaaagtcgaaaaagttgctctgttgatttacg
ataaacatctctcgttgcgggatagtggagtgtcgttgggggaaaatatt
ttttcgatttcgaaatcgatttcaacacattcacagcgagaaaaaacaat
tgcatataatcgattttttatattatggcctgtgtagacatatcaccact
atcatatgaatctgtaaaatccgttgtcaaatatttgagcctgaaaaaaa
ggtatactatttaatattgatatttaaaaaaatactggttcattaaccgc
acggttaattaaccagtatttattacgggaacacaaaattctgagaatac
gtattgcgcaacatgtttatatctcgtagcgaaaaccacagtaattttgt
aaatgactactgaacgcgtaaatcgccaccagcgctacagtagtcattta
aagaattactgtgattttcgctacgagatattttgcgcgtcaaatatgtt
gtgcaatacgcattctcagaattttgtgttcatgtaatttgaacacattg
aaaaacaaaacattttcagggagcaaattaatttatcgattccggcatat
cataaaacagccaaacttgcacctttcaaactagaaaacgttgggttatc
agatttgtacattgaagtcaatgatagaacgtggactttgagtgaaactg
acatcattggttgcactcttgttttgtatcgctcaaacggctacaacttc
cagcacattatttcaataactcctgaagttgcgttccagaagcttatatc
cgaatatttgagaaatggaacacgtattaaaaaatttcacttgtatgccc
ttccaagtctgctcaaaaacgttgagcttcatgtgtcagagctgaaaatt
gacggatgcgactatgaaacatttgcaaagttccgtaaattcattgatca
taaccaaaaaatattaaaggagattgggtttgtggtgcgtcagaatactt
tatggatgtttgatgaacaattggtacagaacacttcaagctttccgcct
tcaacttttgataaatttcaggtgaaaaacagtaaggagatttatctcca
gtttccgtattataatccggtcccgttggacgatatgcttcttcggctga
aaaacaatcatgtacacattatctatctgggcttcccgattgaaaaacta
caagaattggctatggtgagaaattttgtaatattatactttggccaagt
ttggtgcggatctttttgattttccactcagaaatacggtacccggtcct
gtcacgaacagaacaataaggtctgcgcttttaagtacgtggtgtcagag
tgccccatattgatttgatctacgcagatctatgagaatcgcgggaattt
agatgcagatttcttaactggttttgaatggttaagaacgtgctaacgtg
aaattttttggaaaaaaattcccgcattttttgtcgatcaaaccgcaatg
agacagccggacaccatgtgtttaagtaaagcacagtatttaacccacta
ctagttaaaaaaaaaatataattcagaactggatcgacactaagaagcca
attggtacctcactcttcctggttgttgagcattatacatatgttatcga
cgtgtttgagcatttaaccaaatactctaaagctattccttcaagactca
ctgatcttgggtaaggtcttagaactctataatatacaaataagcttgac
tcattcagaacttccttcttttcacattgtgtaacaatgcatattgatga
aagttctgaattggtgctatttggaggtccaatggtaattgaatggaaac
cgttcaaatggacgttgagaatgacgatcatgaaacgcggatcgacaatt
tcaaaatgatttggaatcctccaaaattctgattttcctcaataaacatt
ttaatattttatgttgcaatgtgaatacaattttccttctctgtcaggat
actccagaaggaatgtatggaatcttgatgttcagaacatcagcatccct
tgatcaaacatcgaatctgttattacactaaagtatgtgttcagtgaaag
tgctgtaaaagatgattaacgtcctcaagaagcaaatgctggccgatgac
agtttttttgaagattcagctaatttcattagatattctagttgattcaa
tatcttgaagaaattttttcgcgagatgatgatgttctttcaagttaaaa
ttttgataagtttacgttgtcaaaaataacaacagaaaactacagctggg
agtaacattgcatataaataacataagtattaatttataattacactata
aaatagttttaaaattgcctcagaacatgtaaacagtctaaataattact
ttttagattattgtagataacaagaaaacaagtacaaaatcagtaagtat
catgtcattacacatttgctagaaccagtattttgaacacacttgcggac
acaggtcaacacacttgttcttagcacccgcctacagcttagatgttccc
tttaaaaggaagtacttacgtcgctacaagggcagatttctccctacttg
gctatatctctttgttcaatgattaaacgtcttctctgctttctcttttt
tggcttaactttttcagctccggtgccattacccctagaagaagatttta
atgttttccatacaaaacaggaaaaccatggtacgttttctcatcttttt
tgaaatttgtatcaattaacagagcaaagattccttcgtgttgatcacaa
tagagacaaagtagtctcattcgacgaatttcttcacatggaacttgcat
atgttgatgcaaagaaagaagagtttgatacgttagataagaaccgtaag
tgatgtttaaagcgttgagaaattagcaaactactttagatgacgggaaa
gtgagccttgccgagtacgaagagcatttccacgaagcctcaagcaagaa
tgaaaaatctcggaccgcatactttgccaaagttttcgaagatttcgatg
aagatttcaatatggcattgagtcgtgaagaacttgaacgtgtgcttgct
gaacgattcttagtcaaaccaagagaaaactttcccaaattgtttttcaa
gtttgacgtagacaagtccggaggacttgatctgactggtgagctaagtg
ctcgttttatacatctcgaagtttttttttacagaatacatgaaatttga
tgctgaattcccattcgatcaaaccgatccagttggtggaggaccatcca
aatctaacaatcaccacgatcaaatgcacacagaagtccctcaagatgct
gacgctgctgcaattgcagccgtgttggcacaagcttcaccaacactgaa
taagagtccagtcggtgttgctccaccccaaacgtcacctggattgcatc
cagtggcaccagggttattccagacggcggtgccaatcaaaaaagtttga
ttctaacagtaacttttacaattgtaatttttaattttctctaatactgg
tatcacaaatcactgtcattcaccatatcaattgtttttgtaaataaagc
tttatagttaaaatattatatacaaaaatgcattgcacaaaaggctgaaa
tcagtgaactttagtatcagaggttctcgacataatctcattatgtacat
caatcttactcaatttttgaccttctttgctgtgacggataccataacaa
atgtagattacaatgccaatcgccaaccatacaaaaagacgaatccaagt
cattgagtttagatacaccatcatgaagacattgatgagtagaccaaggc
atggaatgaatggaacaagtggcaccttaaacttttgaacttattatttt
ttgtaaaatgtttctgttcaccttatacgtagatgttgacttattctgtt
catggcccaaaataaaaacgaatgataacagtgaaaaggcagcaccgact
gtcaataaaataataccaccagcattgctaaatattcctgttctgaatgg
aattgccaggcaaatataaccaaaaattaatcctgcgacagctacgcgaa
ttgaaatcccctctgagaaattttcccaaacaccttgaaatggtacccac
gacttcaggcatccgccttaaaatttttattttgttaattttgctaaaca
cgtgtgtgttgctttataaaatcttaccattatcataatcagttgcacta
ccatctacaagatgggattgatgccgcaaaataataacacagattgagac
cattgaataagccaacagagttccaattgacaaaaagtcgacaagcgcct
gcagatcgaagaccagtgccaaaattgcgtttattatagtaaacacaata
gttgcattgagaggggtttttgtttttgagtttatcaccccaaaccaccc
gaagataagaccatcatcagccattgcatatacagctcgtggaagagcga
atgatccagtaactagattgttcaacatacccgctagtgcaccaacactc
attataatcttggcaacagttgctcctttcatttcgaatgcagcagcaaa
cgcggcatcaggatcaactaagtcgtatggtatcatcagcgtcaatgagg
cgcccataagtacatatatgacacttataattgccaaagaagtgaaagta
gccagtgggattgttctatgtgggtttttagcttcttctccagcagtggc
taaagcttcaaatccgataaatgcgaaaaagcatgtggaagcgccagaaa
tagctccttgtattccatacgggaaaaattttgaacgaccatcctggtat
gttcctgaccagagtgaaaagtctgcataggttagtccacaaataatcac
aaacgccaaaacctgaatgaacattttgtaataggttttgacactttaac
ataccgccagatttaaaaatacaaaactagtattcacgttggcagagaac
tttgatcccattgcaaccgccactgctacaagaaacaataggaagaacgc
taaaaagtcagggtacagtgcaaaaaatccttttccctgtaagttgaaac
gcgtattagcatatctgattcaaaaatggcacgaacatcactcaatcgtc
caacagtatccaatgtccagttggacacacttttagatacaagattgtcg
aaataagcagaccacgaacgagcgacagcggcgtttccaatcatgtactc
tagtggtactgtccatccgacaatgaatgcccaaatttcacccattccta
cataactgtatgtgtatgcacttccagctcggggaaacctggaagtttat
cagtttaaacatgtaaagttaaaaaataataaaataaaccttgctccaaa
ttcagcatagctgaaagctgacaaaagtgcagcaaagccagagaaaataa
aagatagtataattgctggtcctgcttgatttcgaacaacggatcccgtg
agtacgtatattccagctccaatcatgtgtccaatcgcaatgaacattac
gtcaagaattgttaaacatcgtttcatttgtgattcaagatgtgatcctc
cgtcaaatgtctttttacgaaacaagacatcggctatttgatgtaccttc
atggttgttttttctgaaattatatatttctgaaggtgaaaaaactattc
atacaagaaagattaaaaatatgaaaaattcggtatacttttatatggta
atattgttttagttttaagataaggcttctggaattgtgaatcaaaaatg
BioPerl-1.007002/t/data/dbfa/mixed_alphabet.fasta000444000766000024       415213155576321 21554 0ustar00cjfieldsstaff000000000000>gi|352962132|ref|NG_030353.1| Homo sapiens sal-like 3 (Drosophila) (SALL3), RefSeqGene on chromosome 18
TAATAATCGTTTCGGCCTCCCTATAGGCAAGGAGTCAAAGTTTTAACTTGCTAGCATTATTTATGTAATC
ATACATGCTGAAATGTCCCTCCTGGTCTACATGCAGCCCCGAGCCACAGTTCAGCCATCAGGAGAGAAGT
ACTTCACCATCGTTTGCATCCCTCAGTGCGAAGACGACTGTGAGCTGATGTTTCTGTGTATGCCATAAAA
AGCCACGGAATGTTTGCCTCTGATGGCTACGGTGAAGCTACACAGCGTCCTGGAATAAACACACAGGAAG

>gi|352962148|ref|NM_001251825.1| Homo sapiens Sp1 UranscripUion facUor (SP1), UranscripU varianU 3, mRNA
GUCCGGGUUCGCUUGCCUCGUCAGCGUCCGCGUUUUUCCCGGCCCCCCCCAACCCCCCCGGACAGGACCC
CCUUGAGCUUGUCCCUCAGCUGCCACCAUGAGCGACCAAGAUCACUCCAUGGAUGAAAUGACAGCUGUGG
UGAAAAUUGAAAAAGGAGUUGGUGGCAAUAAUGGGGGCAAUGGUAAUGGUGGUGGUGCCUUUUCACAGGC
UCGAAGUAGCAGCACAGGCAGUAGCAGCAGCACUGGAGGAGGAGGGCAGGGUGCCAAUGGCUGGCAGAUC

>gi|194473622|ref|NP_001123975.1| adenylosuccinate lyase [Rattus norvegicus]
MAASGDPACAESYRSPLAARYASHEMCFLFSDRYKFQTWRQLWLWLAEAEQTLGLPITDEQIQEMRSNLS
NIDFQMAAEEEKRLRHDVMAHVHTFGHCCPKAAGIIHLGATSCYVGDNTDLIILRNAFDLLLPKLARVIS
RLADFAKERADLPTLGFTHFQPAQLTTVGKRCCLWIQDLCMDLQNLKRVRDELRFRGVKGTTGTQASFLQ
LFEGDHQKVEQLDKMVTEKAGFKRAYIITGQTYTRKVDIEVLSVLASLGASVHKICTDIRLLANLKEMEE

>gi|61679760|pdb|1Y4P|B Chain B, T-To-T(High) Quaternary Transitions In Human Hemoglobin: Betaw37e Deoxy Low-Salt (10 Test Sets)
MHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPETQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGA
FSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANA
LAHKYHKERADLPTLGFTHFQPAQLTTVGKRCCLWIQDLCMDLQNLKRVRDELRFRGVKGTTGTQASFLQ
LFEGDHQKVEQLDKMVTEKAGFKRAYIITGQTYTRKVDIEVLSVLASLGASVHKICTDIRLLANLKEMEE

>0
MHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPETQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGA
FSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANA
LAHKYHKERADLPTLGFTHFQPAQLTTVGKRCCLWIQDLCMDLQNLKRVRDELRFRGVKGTTGTQASFLQ
LFEGDHQKVEQLDKMVTEKAGFKRAYIITGQTYTRKVDIEVLSVLASLGASVHKICTDIRLLANLKEMEE

>1
MHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPETQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGA
FSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANA
LAHKYHKERADLPTLGFTHFQPAQLTTVGKRCCLWIQDLCMDLQNLKRVRDELRFRGVKGTTGTQASFLQ
LFEGDHQKVEQLDKMVTEKAGFKRAYIITGQTYTRKVDIEVLSVLASLGASVHKICTDIRLLANLKEMEE

>123 empty sequence

BioPerl-1.007002/t/data/dbqual000755000766000024          013155576321 16003 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/dbqual/1.qual000444000766000024       170313155576321 17165 0ustar00cjfieldsstaff000000000000>17601976
27 27 28 32 24 33 25 27 25 26 28 28 26 27 27 32 24 29 19 28 27 28 28 28 28 28 24 28 27 27 32 24 27 27 28 27 28 27 28 27 27 28 33 25 28 28 27 28 28 28 28 28 27 26 31 22 28 28 26 26 32 23 28 24 27 27 25 28 28 27 28 28 26 27 26 26 32 24 29 19 27 33 25 28 27 27 27 33 25 28 
>17601977
28 26 23 27 30 21 28 28 28 28 27 23 35 31 15 27 32 26 24 22 25 33 26 27 25 22 27 27 28 28 27 31 22 23 25 31 23 30 21 28 23 27 27 31 22 19 28 23 12 25 34 30 12 27 20 28 28 33 25 28 22 32 24 26 31 22 20 26 25 36 32 19 7 22 26 26 25 28 33 25 25 14 32 27 8 27 17 28 29 19 27 28 33 25 
>17601978
24 27 27 27 27 27 28 30 20 28 27 31 22 32 24 27 26 28 35 31 14 26 33 26 28 33 25 26 27 26 27 28 30 21 28 27 27 33 28 9 33 25 35 31 14 33 28 9 35 31 14 25 23 35 30 12 27 25 25 35 30 12 27 18 27 33 25 33 25 34 30 16 27 31 25 27 36 32 21 9 34 30 12 28 7 28 28 36 32 22 14 6 30 21 10 26 25 32 24 25 18 28 32 23 33 26 19 27 31 25 27 
>17601979
23 32 24 27 26 27 27 27 28 23 28 31 23 27
BioPerl-1.007002/t/data/dbqual/2.qual000444000766000024       301113155576321 17160 0ustar00cjfieldsstaff000000000000>17601981
27 31 25 27 18 28 33 25 27 27 28 28 27 28 28 28 27 27 27 24 33 26 32 26 23 27 28 32 24 20 27 26 24 27 26 27 28 18 28 26 27 31 22 33 26 25 27 28 18 27 26 27 26 21 27 30 25 4 27 28 27 28 28 28 27 27 28 26 28 28 33 25 26 31 23 31 23 28 19 32 25 27 26 27 27 26 27 27 17 24 28 28 28 25 28 
>17601982
25 27 25 32 24 33 25 25 33 25 24 25 33 28 9 28 18 27 28 27 28 26 31 23 27 27 26 27 31 22 28 24 26 27 28 26 28 27 27 25 33 26 28 23 28 28 27 25 28 28 35 31 13 33 25 27 25 27 26 27 35 30 13 28 26 28 25 28 27 32 24 28 28 26 27 28 26 26 28 27 23 23 33 25 28 26 27 28 18 27 33 25 
>17601983
28 36 32 20 9 28 31 25 26 27 25 27 27 27 27 28 25 33 25 26 23 31 23 28 27 27 27 27 26 28 29 19 32 24 28 27 27 27 28 33 25 19 26 27 27 27 27 33 25 27 19 33 25 27 27 27 27 28 27 14 33 26 25 27 26 27 28 18 22 23 11 28 28 27 28 26 20 32 24 28 25 27 21 28 24 31 22 27 27 36 32 20 8 29 19 25 27 28 21 23 23 
>17601984
24 28 20 17 27 22 23 36 32 19 7 25 28 26 30 21 23 27 33 25 25 33 25 27 23 36 32 20 8 27 27 28 26 28 28 35 31 15 18 24 27 27 26 34 29 11 26 31 22 31 22 32 24 35 31 14 26 24 21 24 20 25 23 24 28 27 30 24 2 36 32 21 12 2 27 27 32 25 31 25 27 28 32 25 21 8 28 22 26 33 29 10 31 22 28 24 26 34 30 11 26 28 19 27 28 36 32 20 8 28 31 22 
>17601985
23 32 24 26 27 25 28 26 26 31 22 27 28 33 25 31 23 27 27 27 28 27 28 27 26 27 26 27 27 27 33 25 27 27 28 28 26 24 32 24 27 28 27 27 27 25 27 33 25 28 27 31 22 31 23 28 28 27 26 27 27 27 32 24 27 27 32 24 28 28 28 34 30 16 1 33 25 32 24 28 26 32 24 27 24 28 27 36 32 22 13 5 20 7 19 33 25 11 27 17 27 
BioPerl-1.007002/t/data/dbqual/3.qual000444000766000024       310713155576321 17167 0ustar00cjfieldsstaff000000000000>17601986
25 27 27 28 27 27 31 22 28 27 28 29 19 26 15 27 28 24 27 32 24 27 33 28 9 28 28 27 27 27 26 28 28 34 30 12 27 27 28 28 33 25 27 27 28 26 26 33 28 9 27 27 32 24 33 25 27 27 27 26 32 24 27 27 26 28 28 28 32 24 33 25 27 26 26 27 31 23 28 28 28 27 27 27 28 28 28 28 
>17601987
27 27 25 28 27 21 28 27 21 25 25 31 23 26 28 28 33 28 9 27 28 25 27 19 25 28 27 27 28 28 26 24 23 33 26 27 27 32 24 32 26 22 28 20 26 23 28 27 28 25 27 27 26 35 31 16 32 24 17 28 24 28 30 21 27 22 28 22 25 28 23 36 32 20 7 23 18 27 34 30 16 25 30 25 3 18 22 6 19 27 23 12 26 30 25 3 
>17601988
36 32 20 8 27 35 31 16
>17601989
29 11 33 29 10 36 32 20 7 24 27 34 30 12 31 23 27 27 27 27 32 24 27 27 25 28 27 27 28 27 28 28 31 23 27 28 25 27 31 22 27 26 32 24 26 27 32 24 27 22 27 27 26 32 23 27 28 28 33 29 10 28 26 27 28 27 26 28 18 28 28 34 30 12 27 27 28 28 20 27 35 31 15 34 30 12 27 34 30 12 24 33 25 31 22 28 32 24 28 27 17 27 
>17601990
27 16 25 27 27 17 28 17 27 33 28 9 27 28 27 33 25 25 31 22 34 30 12 19 23 26 31 22 28 27 27 28 30 21 25 14 27 29 20 35 32 19 6 31 23 27 33 26 28 23 28 33 26 27 27 32 26 27 32 24 33 26 28 24 25 27 27 32 25 28 27 28 28 27 36 32 20 8 28 16 26 28 27 35 31 15 27 28 27 27 33 25 26 32 24 26 36 32 21 9 27 33 26 15 32 24 27 27 28 31 22 24 
>17601991
28 27 35 31 18 4 26 35 31 15 27 34 30 12 28 25 27 28 28 28 32 26 34 30 12 26 22 26 28 26 27 28 28 27 30 21 27 33 25 27 33 28 9 28 25 14 27 33 25 28 27 35 31 14 27 25 27 32 24 27 35 31 14 27 28 28 28 27 26 28 33 25 27 24 27 28 28 27 28 21 28 33 26 28 25 33 26 27 33 26 27 32 25 28 33 26 28 27 28 32 24 34 30 16 27 26 27 28 27 28 33 25 27 
BioPerl-1.007002/t/data/fastq000755000766000024          013155576321 15651 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/fastq/RT98876.fastq000444000766000024        40113155576321 17774 0ustar00cjfieldsstaff000000000000@Illumina_SRR125365.38 s_5_1_0001_qseq_37 length=76
CCGCCATTTCTTCAAATCTTTTCTTTTCTTTAGGAGTCATCAATTTCCATTTCTCTGCACATTTCTTTGAAAATTA
+Illumina_SRR125365.38 s_5_1_0001_qseq_37 length=76
@CCCCCCCCBCCCCCCCCCCCAACCCCCCCCC?CCCCCCCCCCCCCAACCCCCCCCCCCCCCCCCCCCB??#BioPerl-1.007002/t/data/fastq/bug2335.fastq000444000766000024        37713155576321 20127 0ustar00cjfieldsstaff000000000000@DS6BPQV01A2G0A
TTGGAATGTTGCAAATGGGAGGCAGTTTGAAATACTGAATAGGCCTCATCGAGAATGTGAAGTTTCAGTAAAGACTTGAGGAAGTTGAATGAGCTGATGAATGGATATATG
+DS6BPQV01A2G0A
@8A8@7<=A9:8?:#6B>*2B<<<:B>*=A<(<6;6<<2;8@8A9<<=<==<<@88=<+<==B:<<@8C<60,)%"<=:5<
@85@7@8+8<
<3;=4:DA3%<;=8-9.A=):B=*
BioPerl-1.007002/t/data/fastq/example.fasta000444000766000024        22613155576321 20441 0ustar00cjfieldsstaff000000000000>EAS54_6_R1_2_1_413_324
CCCTTCTTGTCTTCAGCGTTTCTCC
>EAS54_6_R1_2_1_540_792
TTGGCAGGCCAAGGCCGATGGATCA
>EAS54_6_R1_2_1_443_348
GTTGCTTCTGGCGTGGGTGGGGGGG
BioPerl-1.007002/t/data/fastq/example.fastq000444000766000024        35213155576321 20461 0ustar00cjfieldsstaff000000000000@EAS54_6_R1_2_1_413_324
CCCTTCTTGTCTTCAGCGTTTCTCC
+
;;3;;;;;;;;;;;;7;;;;;;;88
@EAS54_6_R1_2_1_540_792
TTGGCAGGCCAAGGCCGATGGATCA
+
;;;;;;;;;;;7;;;;;-;;;3;83
@EAS54_6_R1_2_1_443_348
GTTGCTTCTGGCGTGGGTGGGGGGG
+
;;;;;;;;;;;9;7;;.7;393333
BioPerl-1.007002/t/data/fastq/example.qual000444000766000024        45113155576321 20305 0ustar00cjfieldsstaff000000000000>EAS54_6_R1_2_1_413_324
26 26 18 26 26 26 26 26 26 26 26 26 26 26 26 22 26 26 26 26
26 26 26 23 23
>EAS54_6_R1_2_1_540_792
26 26 26 26 26 26 26 26 26 26 26 22 26 26 26 26 26 12 26 26
26 18 26 23 18
>EAS54_6_R1_2_1_443_348
26 26 26 26 26 26 26 26 26 26 26 24 26 22 26 26 13 22 26 18
24 18 18 18 18
BioPerl-1.007002/t/data/fastq/illumina_faked.fastq000444000766000024        20313155576321 21765 0ustar00cjfieldsstaff000000000000@Test PHRED qualities from 40 to 0 inclusive
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN
+
hgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@
BioPerl-1.007002/t/data/fastq/sanger_93.fastq000444000766000024        35513155576321 20623 0ustar00cjfieldsstaff000000000000@Test PHRED qualities from 93 to 0 inclusive
ACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGAN
+
~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
BioPerl-1.007002/t/data/fastq/sanger_faked.fastq000444000766000024        20313155576321 21432 0ustar00cjfieldsstaff000000000000@Test PHRED qualities from 40 to 0 inclusive
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN
+
IHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
BioPerl-1.007002/t/data/fastq/solexa_example.fastq000444000766000024       114013155576321 22050 0ustar00cjfieldsstaff000000000000@SLXA-B3_649_FC8437_R1_1_1_610_79
GATGTGCAATACCTTTGTAGAGGAA
+SLXA-B3_649_FC8437_R1_1_1_610_79
YYYYYYYYYYYYYYYYYYWYWYYSU
@SLXA-B3_649_FC8437_R1_1_1_397_389
GGTTTGAGAAAGAGAAATGAGATAA
+SLXA-B3_649_FC8437_R1_1_1_397_389
YYYYYYYYYWYYYYWWYYYWYWYWW
@SLXA-B3_649_FC8437_R1_1_1_850_123
GAGGGTGTTGATCATGATGATGGCG
+SLXA-B3_649_FC8437_R1_1_1_850_123
YYYYYYYYYYYYYWYYWYYSYYYSY
@SLXA-B3_649_FC8437_R1_1_1_362_549
GGAAACAAAGTTTTTCTCAACATAG
+SLXA-B3_649_FC8437_R1_1_1_362_549
YYYYYYYYYYYYYYYYYYWWWWYWY
@SLXA-B3_649_FC8437_R1_1_1_183_714
GTATTATTTAATGGCATACACTCAA
+SLXA-B3_649_FC8437_R1_1_1_183_714
YYYYYYYYYYWYYYYWYWWUWWWQQ
BioPerl-1.007002/t/data/fastq/solexa_faked.fastq000444000766000024        21013155576321 21444 0ustar00cjfieldsstaff000000000000@slxa_0001_1_0001_01
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN
+slxa_0001_1_0001_01
hgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;
BioPerl-1.007002/t/data/fastq/test1_sanger.fastq000444000766000024     45047213155576321 21521 0ustar00cjfieldsstaff000000000000@SRR005406.1 FB9GE3J10GA1VT length=326
TATTGACAAAGTAGTTCTACTTTACAAATTTTATTTTTTGTTACATTTCCATATACGCTTCTAAAACTTCTTTGGCAATCGTTTGATTTGGTTTGGAAGATTCATCATTTAAGTGTGGTAAAACAACGCTAATTGCAATTTCAGGATTTTCGTACGGCGCATAAGCCACCAAGTTACTATTAACCGTTGTATGGTTTACTCCATTAGCATCTGTTGCTTGCGTTTCGGCGGTCCCTGTTTTAGCAGCAATCGAAAACTTGTCTGATTTTAAACCACGTGCAGTTGTAAAAGGACTAGTTCCATTTACTACATTATAGAAACCTTTG
+SRR005406.1 FB9GE3J10GA1VT length=326
DDDDDDDDDDDDDDDDDDDD@??DB?2211116335553?..@CDDDDDDDDDDDDDDDDD@9995@BBBDDDDDDDDDDDDDDDD;;;BBDDD@@@@BDDDDDDDB@@@DDDDDDDB888888>DDDDDDDDDDDDDDDDDDDDDDDDDBB@DDDDDDDDDDDD>;;;;DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCDDDDDCCCCCCCC@<<>===>>>>===>>?>>===>>>>>>>>>>@??>>>>>>>>==::3317=>?>>>>>>>?>>>>>>>=======8...../
@SRR005406.2 FB9GE3J10GFIYY length=126
TATTNACTAAATAGTACGGCGGATAATCCCACGATGACGAATATACATTTCTTTGTATAAAATCTTCATAATCTTGGGCTTTGCCAATTGTATCGCATAATGCTCGGGTTAAAAGNTTGAATGATG
+SRR005406.2 FB9GE3J10GFIYY length=126
2000!22:0000,8662000058866600030>=<<<<===?=>=97222800084:6....0200999999;66000289666666;;;=;:;==;;:::9666997......,!4499984444
@SRR005406.3 FB9GE3J10GF5B6 length=313
TATTGACAAACAAAGAGGTCAAAACTTTAAGTATCTGAACCCGACGAATTAATTCTAAATATCTAATATCGATTACCTAACTAAATTACACTAAGTTAATTAAATGTAGTATATAATCATTTAAAACTAATTAATTATTTAGTATAATGAAAGACAAGAGGTGATTGTATGTTAACCACAAATCTAGAAACAAGGAAGTTCTGTAGTATTGACATTACCATCTAACAACGGACAGAAACCAAAAGCAGACCAAGAATATATAGTGATGTATTCTGATGATGGGACAATTACGTTAGTCCCTAAATTACAAGAT
+SRR005406.3 FB9GE3J10GF5B6 length=313
CCCCCCC777=@BBDB@<>>99905111--605=DA>44111=@@@444433;;<5111<9D=555@BCCCCCCCCCCCCCC@@@CCCCCCA@@CCCCC==777@CCCCCDD@@@@@@;111////3@;;@@DDCCC666>>@CCC>>2225966:::::::<::666<<<<<<<<661116<<<<<<<<<::::666<6667::6661111665:666:<
@SRR005406.4 FB9GE3J10GFJI3 length=103
TATTGACGCTTCTGCACCTGGCGGTCTAGTTCTTGAAAAATTCGGCTTTACTCCTGAAAATGTGGTTAATACCTATAAATCACTATAAATAAACGATAAAAAA
+SRR005406.4 FB9GE3J10GFJI3 length=103
?<<<<=9<<<<<:4448=7799:>===<8:8:8<:==8488863220002888
@SRR005406.6 FB9GE3J10GGVOP length=283
TATTGACAAAAAAAAGAAATTTGAGATTCCTTTTTTACCTAGAATCTCAAATTCTCTCTTTTTTATTTCTATTAACCAATCCGGCGCATTGGAATATCATTGTTATCTGGATGAACCAATAAATATTGAATAACATCAATATTGCTTGCTTGGAATGAGGCTGCACATGCTTGCAAATATAAGTCCCACATTCGATAGAAGCGCTCGTCCTTTTTCGTCAACAATTTCTGTTTCTATATTATGGTAAGTTTTTTGTCCAATGTTCCAGCGTCAATTGATATCT
+SRR005406.6 FB9GE3J10GGVOP length=283
==:9:::...0...09***>>?????::::55:::5><<(=?==>=7722088::<66......2(((8099:<<;;<<<977779:;772223>=?>>>>>??@=?=888<6666699=555=;=<<<<@=??=??>>>;;677;>>>==6667>>?6677;>?=<<<<<<6600066:6666;;::26666696----66833---33-----15*552,,,8888.4,,,02922,,,025531,,,,,,,,(,,,,,103356666......4110010
@SRR005406.7 FB9GE3J10F6RK3 length=267
TATTGACAATCCAATTATTCTTCATTTTGGCTCCTCCGATAATTTTTCTTATAATAAAAGAAAGGTTGTTTGTTCTCTTCACACGGTTATCTATTGTTCCTGACCCTTGAAAAAGGGCATTCTTGCAGAAATACCTATAGAAAATTATAGCACAAACTGTATATTCATTCACTAGTTATAACAAACTTTTTTAAGAAAACCCGCGATCTTCTTACGAAGGGGTTGATTCACTGCTTTCATCGATCCGTATTTTCACTTAATTTTTTT
+SRR005406.7 FB9GE3J10F6RK3 length=267
>===>===:999<<221999112:665522380000033866444118))25<<6....2***002207;;?=>AAAAAAAAAAAAA???AAAAAAAA????@??>=;;5551111116=====??@A????>>?;;;??@?@???;777;;??@?A??A??676;=<4333--**-------66.3336666-----,,,,,,55*222555955,004442222234,,,,,,,,033,,,,,,,,,
@SRR005406.8 FB9GE3J10F5CXD length=306
TATTGACCAGTTACTGCCTATCCCAATGTGGATCATATTCCCTGGTTTTACTTCGAGAGAAGCGGGTGGTGGAGCGCTTCATGGCTCAGGAAGTTATCCATTACAATACTTACAATACGTATTAGGGAAAGAGATTCAAGCGGTTACGGGAACCGCAACGTATCAGCAAGGAGCGACGGATAGTCAATGTAATTTAGCTTTGAAATTTGCTGAAGGGACGCTGGGCAATATTTTTATTAATGTTGGTTTAAAGATACCTAGTGAAATGACCATTTGTGGGACGAAAGGGCAAATCGTTATTCCTAA
+SRR005406.8 FB9GE3J10F5CXD length=306
BBBBDDDDDDDD>?>B??@BDBBBDCCCDDDEEEDDDDDDDDDDD==>>?8006?BBDDDDDDDDDDDDDDDDDDDDDDDDDBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD99999>DDDDDDDDDDDDDDDDBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBBDDDDDD<<;@CC@@@@@C>>999<<<:=//97=?==74......./84666:======:::=<:33363::;<<7<::3336311;<:::<1111611
@SRR005406.9 FB9GE3J10F5GHC length=286
TATTGACAACAGTATGACGGAAGTCTAACCAAGGTGTTCCGCCTTGTTTGTAAGCTTCAATAATTTCTTCTGGAAAACCAGCATCTTCTAACTGACTCATCATTTGAGCTGGAACATTTTGATTAGTAACAACAAAGAATTGGCTGCCATTTGTGTTAGGACCAGCATTTGCCATTGACAATGCGCCACGCAAATTGAAACATCCCGAGAAAATTCATCCTCAAATGCTTCTCCATAAATACTTTCGCCGCCCATTCCTGTTCCGGTTGGGTCACCGCCTTGAATC
+SRR005406.9 FB9GE3J10F5GHC length=286
C@@@CCCCCCCCCCCCCCDC@@=>>=BBBB33556=@BDBB==@@=@CC=688CCCCBBBA@@C@@A@@DD==5555AA:BBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC===@CCCCCCCCCCCCCCCCCCCCCCC<<@@@>>><<@@@@@@/////3973......6:434778877..111.44379774446661
@SRR005406.10 FB9GE3J10GF2TX length=292
TATTGACCTTTTCATAGAAATGATATTCAGCTTTGAAAGATTACCAAATAGTCTAATTCCTACAGCACCCGTCCAGTCATCATTAATGGACGTACCATCAGGATAATGAACCTCTTCATTTTCATAAAATAATTGATCATTCAGGAATGTCTGAATTTTTTTCCCATCATAGCGAACCAGCAGTTTATATTGTTGGCCACTTAGTAATGTTGGTCCCGGAATATTAGTTAGCCATTTACCGCCTGGTTGTCCTAATTGCCAGCGGCCGTCACGATTATAAGCAAAAGNTTCG
+SRR005406.10 FB9GE3J10GF2TX length=292
CCCCA=====CCCCCCCCEEEEEEEEEEEEEEEDCCCFCBC9777==CCBCCCCCC@@AAACCCCCCCCCCCGGCCCCCCCC====@CCCCCCCCCCCCCAAB===CCBBBBDCDBB@////;@3////:44BBDDDB@<<>>>>CCC@@@@@96666111666::66666:::66666:<<<<<<<<<<<<<<66!6666
@SRR005406.11 FB9GE3J10GG7K6 length=278
TATTGACTCTGTACACTGGCAAAATAGAGATATTATAAAGAAAGTAATCGCCGTTATTGATATGATTGAAAGCTTTGGCGATGTACGTTTGGCGGAAGGCATGAAAAAAGAAAATGCTTCAGCTGACGGCTGGTCGGACATTTAATTTAGAAAAAGGTCAGTTTCCATTGAATATTGTCACTGAAAAATAAAAAGCACCCCCGCAAGGTCAAACTTGCGGGGTGCTTTCTCAAGGCTACTTTAAAACATGTAGCGACTTTTCAACGATGGCATCGGTC
+SRR005406.11 FB9GE3J10GG7K6 length=278
=>?=::::=0<:==><<:<00003,,,6800688::==<<979998=??><999?????A====AAAAAAAAAAA???????===??46:::4<((((><===<64.....6)))))---------)---------3332201215*2,,,2.5,,,,,,22,,,,,0-3)41010355633,,,1331,,,,,,,111,,
@SRR005406.12 FB9GE3J10F9XLN length=307
TATTGACTTAGTTTCAACAAAAAAGGCAAAGTCCTGTTACCAATGAAAGACTTATTAATAGAAGGAACGTTTCGTGCAAATGAACGAGGCTTTGGTTTTGTAACCATCGATCCTGAAGAACCAGATGTTTACATTCCTAAAGAGGCAACGAACTTTGCAATGGATGGGGACACGGTTTTAATCGACGTGATCCAACATGCGGATCCTTTTTCAGATCGCGGCGCAGAAGGTAAAGTCAAAGAAATTAAAGAGCGAGCAGTGAGCCAAGTTGTCGGAGAATTTGTGGCATATAGTGAAGAAGAAATGG
+SRR005406.12 FB9GE3J10F9XLN length=307
FFFFFFFFFFFFFFFFFFGGGGGGIIIIIIHFFFHIIIIIGGGHIFFFFFEEEEFFFFFFFFFFFFFEB>>>BEFFFFFFFFFFFFFFFFBBBFFEEEEFBBBEEFFFFFFFFFFFFFEEEEFFFFFFFFFFFFFFFFFFFFFEEEFFFFFFFFFFFFFFFFFFFFFFFFFGEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEEEEEEEBBBEEEAA@EEEEEEB;;;B=888@@@@@@@@@@@@???@@@@@@@@@@@@@@@7777877@@@@@@@@@@@==:74437=A
@SRR005406.13 FB9GE3J10GBYB5 length=328
TATTGACAGACGTTACTGGTGTTGTAGAATTGCCAGAAGGTACTGAAATGGTAATGCCTGGTGATAACGTTGCTATGGACGTTGAATTAATTCACCCAATCGCTATCGAAGACGGAACTCGTTTCTCTATTCGTGAAGGCGGACGTACTGTAGGTTCAGGCGTTGTTACTGAAATCGTTAAATAATTAACTTTTTAACTATAGCTTTAACCAGCGTAAAAACTGGGGTATTCGGACGTAAGACCAGAGAATTTATTCTCTGGTTCTTTTTTTGTTTAGAAATTGGCTGGACTAAAAAATAGCCAATTGGCTTGTTTTAGCAGTCTTTG
+SRR005406.13 FB9GE3J10GBYB5 length=328
A???CCCCAAAA<<22333:6<::<<<<>=923300882228822
@SRR005406.15 FB9GE3J10F6A4M length=141
TATTGACAGAGTAAGTGAGCGAAGCAGTGAACTTACTACGGGGCGCCCGTTACAGCCAACGGTATGCGAAGAATCAAGTACCGTATGAGGTTATTATGAGAAATAATAGCGAATTAAGGTGGTATCACGAAATGACAACTT
+SRR005406.15 FB9GE3J10F6A4M length=141
<888<<>=>??<<<>?BBBB??=>>>==::0....0-0006:<<46222221228:999==;7789<>>99898????>><<<<=<22177::::=7488???>>>>=??<<8888===:6...;944.....
@SRR005406.16 FB9GE3J10F8B91 length=244
TATTGACGTGACATCATCACAATCGGAAGTAACAATTCCTAATGAGCGATGTTCTGGTTTCAATGATAATTCTTTTGCTAATGCCGGATCGACATTGGGAATGACTTTCATACTTAGGACATTTGTCGCCTAGACGATCATTTTTCTATGAGAAATCCTCCTTTATTCAGCTTTCTTTTAAATCAATACCAGTATTTTTTCTTTGTCTAACTATTTTTTTGTATAATTTCGGCATGTAGGCCCT
+SRR005406.16 FB9GE3J10F8B91 length=244
A???===?<<<<<>:<<=44333<<<<>;;;;;67=76;*66:>;;:66666976634.+..44...........*......------------(((-*--396640086620<*99000,,,,,,,22,,,,,,,,
@SRR005406.17 FB9GE3J10GG5LS length=312
TATTGACCTTTTTTCAGGATCTGAAATATCTTGGAAAAGAATCTGATTGATTGTCTGCCACACAGCGCCTTGATTGCTGCGAATAAGGTGCTCTCTTAAAAATAAAAAGCCGAGCCCAACGATTAATCCTCCCACCAATGAAATCACCATTTTTTTGTTAAATGAGATACCTTTCACTTCTACGTTTTTTCTTTTCCACTTTGTTGCCTCCCAAATAAATTGATTAAGCACCGCGACAAAAAAAGCCTTGCACAACAAAAAAAGGGCAAGACATCTCGTATCATTCACTATAACAAAAATACAGAATTTTAA
+SRR005406.17 FB9GE3J10GG5LS length=312
@<<<@@CC::??87;<BC>>>??CCAAAAA?777<:1///////*-**66AACCCC==CCA9999>96/,,,999999477<<>C?>><<3355533<55555:::722/////,,-----4747771115:555557:::51111155::55+55111::::55
@SRR005406.18 FB9GE3J10F5ZAJ length=258
TATTGACACTTGTTGGCGTAAAGCTGGATCTAGCGCGCTCGTTGGTTCATCGTACCCAAGAACTTTTGGCTTCATTGCTAAGGCACGAGCAAGTGCAACTCGTTGTTTTTGTCCACCGGAAAGTTGGTACGTATAGAGTTTTTCTTTACCAGCCAAGCCCAATTTTTCCAGTAATTCTAAAGCTTCTTGCTGACTTTTTGTCTTTTCTTTCTTTAGTACTATGTAGGTGACGTTAAAGGTAATTTGTTTTAACTAAAC
+SRR005406.18 FB9GE3J10F5ZAJ length=258
@??=>>><842277=====9::<>>??BBB?@@@??A?B9:8<4444<<>????@@AAAAAAAAAAAAAAAAAAAAAAAAAAAAA;@@@@A2AAAAAAAAAAAAAAAAAAAAAAAAAA;;;;;A222AAAAAAAA@@>>>??22222;;==<>>??A;;;AAAAAA???>>==;4331--)-----3***-**.3-*,2,,,,,,522022,,,,,,,,,**,,,,)))),,,(,,,,
@SRR005406.19 FB9GE3J10GD4Z8 length=224
TATTGACAAGCCGTTATTTATTTGAACAAACCAAACGTCGTCCTGTGATCTTACCAGTTATCATGGAAGCGACGCAACGCAAGCGTCCCAAAAATAACGCATAGTTCGTCCTGATAAAAGCAGGTGATTTTAGGAGAAATTCTTCTAAAGTCATCTGTTTCTTTTTTGAACTTTCTTCTATAAATATGGTACTATTAATCAGAGCGTCTAGAAAGTAAAAGGGA
+SRR005406.19 FB9GE3J10GD4Z8 length=224
A???AAAAA@@@A@@?????555:::>?????666:BBAAAAAFFAAAAAAAAAAAAAAAAAAAAAAAAAAAAA???AAAAA@@?@<<<44444?22AAAAAAAAAAAAA??A?83331==;;;;==11111;===;:::;;;=?;00.437:==:000062:::62778;AAAAAAAAAAAAAAA;886;AAA>>>==;;;;<6600-6---663****00,*
@SRR005406.20 FB9GE3J10GGM2A length=159
TATTGACCTAACTGGCGACGTTCCCATTGTTTGATCGCTTGTTGCACTCCTGAACGTTCATCTTCTCGCCAGCTTGCTAATCGTTCATCGGTTGCATCAGTGACAGTTAACAACGCTTCTTTGATTGCCTGAATCGACTCTTTGCCATGTTATTCGTCT
+SRR005406.20 FB9GE3J10GGM2A length=159
??==???><33289998===?A??<>:::???<>=??8:::<=????????@@BA<==??@??====>==99999<<>>>=?><<><<<;;:;777211.477943......444444.......943......4...433..0:==66
@SRR005406.21 FB9GE3J10GB4C1 length=255
TATTGACAAGAGGTTCTTTTTTTAAAGTCCAACGCAATATTTGTTAAAGGACCAAGGGCAATGATTGAGCAATCGGTAGCTTGTTGAAAGGTTTGTGCTAAATAGTCAGCAGCGGAAAGCGCTTGTGCTTGGATTTTGCTAGTTCTGGGGAAATAAGTTTCACCTAAACCATCCATGCCATGTGTATCTTGTGCACTAACAAATGGCCGTTTTAAAGGGCTAGCAGCCCCTTGGTAGACAGGAATATCTAAGCGA
+SRR005406.21 FB9GE3J10GB4C1 length=255
A???AAA@<<333<36///////00A6)33AA?@@===;ABA=55<9999999:C999<<<<>>>>77333331>>>?C>??<=<>==332428:??@=B999:==A?@==;::<<80....2-99:::;;==<3333<>;;;==:<<@?<877:;===76111=666666;;;;;66==<<<<<867;;;;76776;?;;;;??????????;;00044...24......*6663......----33-------660886333333--,,,,,...2225,,,25,,,,,,2*,,
@SRR005406.23 FB9GE3J10F441T length=186
TATTGACCGCTGGCGATTATTACGCCATTATGGGCTTGCCAATTGCCAAAGTAGCCCGACTACTAAAAGAATTCAACTAATAAAAGACAGTCCTTTTCATTCGTCAAAAAGAGAAAGGACTGTCTTTTACTATGCAAACTATTAGGTGCCTGTTTGGCAAACGTGTATCATTGAACCCATAAATTG
+SRR005406.23 FB9GE3J10F441T length=186
AAAAAAAA?====@?A@@????B???AAA??:::>>?????@BBBAAAAAAAAAAAAAAAAAAA8888A<:A@????@??<3333=5A?AA@AAAAAAAAAAAAA;;@@:?+88AA<<;???AA??????:??<;;;;;;7;;==:99667;20066:::;6663668664...............
@SRR005406.24 FB9GE3J10F7Z4H length=265
TATTGACGTATGATTGCAAATGGTCGCGATGCTGACTTTATCGTATTAGAACCAACCATGGAATTAGCAGCCACTTATTTAGATGGCGTAGAACGTTATCGAGCATAAGACACAAGAAAAAGCTTGCGGAAATTTATCCGCAAGTCTTTTTTTATAATTCTTTTGGTAAAATCGCAGAAGTGATTTCTTTGTTTTCATAGGCAATAAAAAAATCGATTAATTGCTTGTCAAATTGCTCAATATCCTCTTTTAGGTAAAAGGGGAG
+SRR005406.24 FB9GE3J10F7Z4H length=265
AAAAAAAA@???>??<99::>>??A???BEEEBBBFBBBAABBAFAAA@??@@??????<<<77222;=6664.0000006'::==:7777::/00026:<<<<8<=6660..4.606****36888-------------386,,,,0055552,,,40555522240004833336666606655444-((
@SRR005406.25 FB9GE3J10GB7RT length=294
TATTGACCTTTGGCGATGAACGGACAGTTGATGCCCATATCAAAAAATTACGACAAAAAATTGAAAAAGTGGGTCCTCAAGTCATCCAAACGGTTTGGGGCGTAGGGTATAAATTCGACGATTCAGGTGTTGCTTAATGAAGTATTTGTATCAACAATTACTTGCTTTTATAGGTGTGATTGCTCTGATTATTCTCATTGTCGGAACGTCTTTCACACAATTGACCAAGCGCACAATGCAAGAAAATAACTNTGAACAGCTGTATGGTTATGCAGAATCGGCTTTAGAAACACG
+SRR005406.25 FB9GE3J10GB7RT length=294
DDDDDDDDDDD???>BBDDDDDDDDDEDEEEEDDDDDDDDB5555//>>->AB@//////@>>444;;DDDDDDDDDDDDDDDDDDDDDDDDDDDDBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBB>>>DDDDD5666>DDDBBBDDBBBBDDDDDD>==DDDDDDBB<<<<>>CCCCCCBBBCCCC:31-6>>??;===A>>?B?????<;;==<;6.2222277;====?@???<87499/600....0000-6677==??@????AAAA<888AAAAA:?@???>::50000000:,:=86766;;>>=<887;7++++6:<<=6666::<<<7720000;48887>,,;AAAA<;;>>>???<:::::::<<<5/588;88888844488;77633333777744445)301,,,1,,1,,,,,1)),,,311,,,,!,,,,,010
@SRR005406.27 FB9GE3J10F961T length=261
TATTGACCAAATCTTCCATCGTCAACACGTCTTTACGTAAAAGTGGCGCTGACATCTCATCGCGCATATCACGACCTGGTTGGGATTAAACTAGCAATAATATCTGTGAGTGTTTCTGAACCTACTTCTAACTCAGTAGCTAATTGATTCACTGGTAACTGTTTCAATTTTTCGATAGCTTCTGCTGTCCCTAATTCTTTAGAAGCAATCTCTGCTTTTTCTAAAATTGCTTGTGCTACTGGATAACTTTCTGGGTGAATG
+SRR005406.27 FB9GE3J10F961T length=261
<A@@@CCCCCCCCCCCCAAACCCAC;;;;ACCCCCCCCCA@@@ACCCCCCCCCCCCCCCCCCCCCCCC>>>>99333339>>AACCCCCCCCCA::99?ACCCCCCCCCCCCCCCCCAAA99//////*//////49;??<<B=<:779999999<::<<:=7133378868<<<00222258:88872<>?>>>=====9998,.....600089:9::<;;602222299999897777768<><<<<:<<<<BBDDDC@@>DDDD>>?DDDDDD>>999DDDDDDDDDDDDDDDDDDDDDB?>>BBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBB<<>>>>:::<<333:==::::;;::::66111;;66666<<=<<<===
@SRR005406.30 FB9GE3J10F471Q length=217
TATTGACTAACTGTTGATGAAGATTTTTTAAAACGATACCGTTCAATAGAATCAGAAATTTTTCAACTTGTTGGAACGGTTAATGGGCGTAGACTTACTGAACAAGAAGTGCTGCAAGCCTGCCGTTATCCCTATGTACGTGGAATGAAGACTTCCTTTGATCTTGATTTTGTTGAAAATAGCAGCTATTCATTAACAGATACTATTCTTGATCCTA
+SRR005406.30 FB9GE3J10F471Q length=217
??????94333<@???>===:<8..........8:/:<<<>=88:9<==:::;;;000...22989<<====889998??????????AAAA??????<888<<=<<=><<<<32286====;730000444437744..005:::::<<<7877<,+00....*46846666;;;;>>>>>666;>><<::999960000
@SRR005406.31 FB9GE3J10F426I length=307
TATTGACATTTCTTCTAACGCAAAGAAGCCGTTTGAATCTAAGGCATATTCTTCTCCTGGAATACCTAGTTTTTTCGGACGACCACCTGTCGCGATTAAAATGTGCGGCGCCGTATATTCTGTCCCATTGACTTCAATTGTTTGCTCCCCAGTAAACGTAGCGTAACCATGGATACGTTCAATGTTGTTACTGTCTAAACCACGATTATACGCACCATGTAAGAAGTCGATATATTTTTCACGATTTTCAACTAATTGTTTAAAGCTAAAATTTTTGATTTCAACATCAAACCCATAGCCTGCTGTG
+SRR005406.31 FB9GE3J10F426I length=307
DDDDDDDDDDDDDDDDDDDCB888@=BDDDD@@@BEEEEFDDCEEDDDDDDDDDDDDDDDDDDDBB>>?:AAAAAD:::>DDDDDDDDDDDDDD???DDDDDDDDDDDDDBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD9999BDDDDDDDDDDDDDDDDDDDDDDDDDBBBDDDDBBBDDDDDDDDDDDDDDDDBBBDDDDDDDDDDDCCCCCCCCBB>>>DDDCCAAHAACCCCCC>>>>===:::==633333<<<<<<;=33333=======<:::<<<<=<<<<<====<<6611
@SRR005406.32 FB9GE3J10F6BG7 length=259
TATTGACCCTGTTTCAACCACCCGAATGCGAACAACTTTTTTCCCTTAACGTTTGACCATTTGTCAGTTTCATCATGACGATAAAGACCGCAAACACCATGATAAAGAACCACATCCGATCTGAAAAAATCGGATAATTGGTTGCCCAATTTTTATAAGCTGGAATGAAATTTAGTCCAAAACGAGCAGGCCTTGCACAAAGCCAATCACCAACCAATCAATCCCCATGCAAAGAACGTCTCAACAGGCTAACTGTCTG
+SRR005406.32 FB9GE3J10F6BG7 length=259
AAAAAAAA???>><<<<882228?===>===<:112400004:77((223=:;70222:;;992;;>444<<@@AAB@@???A??=144??@===AAAAAAAAAAAA<>;77666659)00;;96666:600.44638........./888888:::;;:;00066;;9;;;;=;;444455222,,,,2225220,**,25222,,,,,,11,,,0101,,
@SRR005406.33 FB9GE3J10F9KOX length=209
TATTGACCACAACTTCGTTATGATGGCCGTTCAGCCATTTGTGGCCGCGCTGCTGGAATTACAATAGAGACAACCGTTTTACCCTTTATTTTACGGGGCGTTCATTTATTGGGCATTGATTCGGTTAATGTTGGTATGGACAAACGAAAATAGTCTGGCAACGTCTTGCCACTGATTTAGACATCACTAGAAAAGCTGTGTATCAAGAG
+SRR005406.33 FB9GE3J10F9KOX length=209
8777222227=::987<=797988882202258822300080002258<<====9999<>????<999<<@@BBBBAAAFAAFFAA?BBBBA?>>>AAAAAAAAAAA???AAAAAAA??;;;AA?6776AAA???;?????76666;:660..66::644662:6666::931133333---------*66-,,2,,,,,,,,,2**,002,,,,,2252,,,,,,,,,
@SRR005406.35 FB9GE3J10GFGOK length=115
TATTGACAGCAATTCTGACATGAACTTCTTGCGCTTCTGCTTCTTTAATAAATGAATAATGCGTCGAATAGTGGTCCCGCGAACAATCGAATCATCTACTAAAATGTACTTTTTT
+SRR005406.35 FB9GE3J10GFGOK length=115
=77799979<999997<>=====80...2235556889979:<<=???????@????999=;?<777777;;9666666660...206999336844
@SRR005406.36 FB9GE3J10F9575 length=187
TATTGACACGTACTGGTGGAGGCGGCTTAAACGTGGCCGTGCCTTTACATCTCACCGTTTCCACGGTAAACTAAAAACAACGCCGTCAATTGCGTAAAGCAAGCATGGTTGCAAAAGGCGATTACAAACGTATCCGCCAACAATTAGCAAGAATGAAATAAACAACTCGGTGACTTTTAGATTACCG
+SRR005406.36 FB9GE3J10F9575 length=187
?>8877<<<==<64333911111.;9;;;=>233=>>=<<<<99:88???A??888::8A?=???AAA??????@????<999?>>>=4444448999>?>>>??????@@@??<<=<<<<<>=?><:::2226383.....433.........*43...........444477::======:66644664....666<:655=<;;;;;;6666;:966661--
@SRR005406.38 FB9GE3J10GB8MA length=82
TATTGACCTAAAGCAGCATCAAAAGGATTAACTGTCACAAATGGTAGTGCTTCATTGTCAGGAATTCAACAAATTATTTTTG
+SRR005406.38 FB9GE3J10GB8MA length=82
AAAAAA@@A?<798:<<;88....22/::<<<:>=<<:22299979====>====>=999443399;=<<855992111116
@SRR005406.39 FB9GE3J10GEJA4 length=133
TATTGACCGTTGGCCTAATGTACCCGTCAACTTAGAAACGTTGCGGATTATTTTACCTAGCTCTGTTGCCTTAGCAATGGTCGGGTTCATTGAATCTTTATTGACGATCCCCATTGTAGCAAAATGACAGCGA
+SRR005406.39 FB9GE3J10GEJA4 length=133
AAAAAAAAA===???=4448=7==??A?????BABBABA>>>>AAAAAA==4==AAAAAAAAAAAAAAAAA???AAAAAAAAAAAAA@?=444=AAAAAAAAAAA?A???A<<<<<99=>6......
@SRR005406.40 FB9GE3J10GE3D1 length=65
TCACCTCAACACCCATGCGTACCGGTGCGGCGTAACGTGGTAGAGCTGCCGGTACACGAAGGAAG
+SRR005406.40 FB9GE3J10GE3D1 length=65
==<::2022000006888::866666530065322000006<86682222008800080000000
@SRR005406.41 FB9GE3J10GHD3J length=71
TATTGACTTACATAATTTTTGTCCATATTTAAATAAAAAGAGAGCATGGAATCATCCATCCCTCTTCAAAT
+SRR005406.41 FB9GE3J10GHD3J length=71
?===>>??@<<<??BB@???>==>=922222229<88==??===??@??????????@@@@<888<@@><<7<<>==<::=900062443477......226..*44886......+++.
@SRR005406.43 FB9GE3J10F931O length=277
TATTGACAAAAGAAAAATTAGTTTAAGTTTGAGTTACAACTGGCGTTACCATTTATTATTTCTGGGATTCGAACGGCTACCGTTTTAATTATTGGTACGGCCACGTTGGCGGCGTTAATTGGAGCAGGTGGTTTAGGGACCTTCATTTTATTTAGGAATTGATCGAAATAATTTATCGTTGATTTTTATTTGGAGCTCTTTCATCAGCTGCACTAGCAGTCTTATTTAATTATGGAATTCATTGGTTAGGAAAAGACGAATGGGCGGCGACTAATCA
+SRR005406.43 FB9GE3J10F931O length=277
=:::<<<22229/////23)=<<<>=7../347<<:>==<===?<<=?<<8888???8888==@@@?@8444=9330866800088....0*88<86
@SRR005406.45 FB9GE3J10GHBI8 length=316
TATTGACTACTCCGACAAGGGATTGACGGAAATCAAGATTTTTATAAACCAGCGTGGCGTTCGGAAGCCAAAACTACCTTCAAGCAACGCGTTTTTTAACAGGTAAATATGCAACAGACAAGCAATACGATAATAAATTAAATTCGTTAATTGCGGTTTATAACTTAACGCAATTTGATTTACCAAAAACAGTGGACGGTTTGATTATCCAATCTAAAATAAGCTGTCGGAAGCGGAACAGCAACAAATGCATTTTCCAGTCTATGATGGGATCAATTATAATCGAAGTGGTAGCTATCCCGTGGCCAGTGTACGG
+SRR005406.45 FB9GE3J10GHBI8 length=316
66-33<:333;5CCAAACCCCCCCCAAAACCCAAACC:::??CCACCCC::::CCCCAAAACA7:::CCCCC>::::::><<=@?11//33//-9=???A>????AAACCC99999>A?;;;>33>>>?<83333>>???885:::555:::;::::::::::::::::::::::::555::1111-55404------42224464422----
@SRR005406.46 FB9GE3J10GCTJ7 length=217
TATTGACAATTCTTTCGTGAAAAATAGGCGTCACGCTAGCAATAATAATCGTATATCCTTGTAAACATTCCGCTAACTCTTTGCCACCAATTTCACTGTCGACTGTAAAATGCTTCACGGTGCCTATTTTTCTAAGCTCGTCAAGTGTTCAGGAAAATTTGACCAAAACTACTGGAATTCACTATGGCTAATTTTTTGTTTTTTAACATGACTAAAC
+SRR005406.46 FB9GE3J10GCTJ7 length=217
;7779997722258868,0.....3)82308<<===??:::??????????<<::78866800002,8888<899:=::222777;99::;;<<<=???=>>?322388?><:;=>;97.........4,77::===6676===6666.00.224447644....24*..4444..0688666688330000000(*****;;940--3----,
@SRR005406.47 FB9GE3J10GFAI9 length=298
TATTGACAGCTTCCGCAGTTATTGTTATGGGAAGTGTTGCCCTCTCTAATCAAGAGTTAGGAGCATTATATCCGTGGACAGCCACATTTTTTTTGATAGATGGTCGAATAGAAAGCACCGGCTATCCCCTTGCATTAGCAATCGGCATTATTATCTTGGTATCAGCAGTCGGTTTCTTTATGACCTTTCACCATTTTCAAAAAAGGGAGGATTTTGAAATAATGGCACTTGATTTTATCGAAATTTTAAAAGTTNTTTTTCTTGGCATTGTAGAGGGGATTACCGAATGGCTGCCTAT
+SRR005406.47 FB9GE3J10GFAI9 length=298
DDDDDDDDDDDDDDDDDDHFDDDDDDEDAAABBDDDDDD;;>ADDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDAA////////>@DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCCDDDDDDC?::666ACBBB00005//////222/3350000;444:ADDDDDDDDD@@4000848000000....22;--!2=??:4--77?????????:::::?????????====777??=
@SRR005406.48 FB9GE3J10F9S1A length=317
TATTGACTTTAAAGGCCGTTTCATCGTTTGCGCCCCCTTAGTAATAATAAAATGAACAAAATGCTCCCTAATGTTCCGACAACCACGCTGACAGGAATTTCATAGGGGGCAATCAATACTCGTGCTAAAATATCACAGATTAACAAGAATAAACTTCCACAAATCCCAGTTAACCACAAGGTATTTTTCATATGATCGCCATAACGTAAAGACACTAGATTGGGAATCACAACTCCTAAAAACGGAATATTCCCCACCATCAATAAAACGATGGCACTTGCTAAAGCAACCAGCGTCAAACCTAAAAACTGAATTCG
+SRR005406.48 FB9GE3J10F9S1A length=317
?DDDDDDDDDDDD????>CCCBCCDEEEEEEDIIIIIEFFF>DDDDDDDDDBBBBDD>>>>BBDDDDDD??>BDDDBBBBBBDDDDDDDDDDDDDDDBBBDDDB55555>BDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD>>>DDDDDDD999BBDDDDDDDDDDDDDD>>>BDDDDDDDDDDDDDDDDDDDBBBDDDDDDDDDDDCCCCCCCCCCCCCCCCCCCCC;;;;;CBB44><<<>>>>>>>>>>>>>>>>>>>>>><<<>><<<<==<<<::666:=:6631166<666666633366<<
@SRR005406.49 FB9GE3J10GA69G length=204
TATTGACTCCAGTTAAGGGCATTGAGTATTCCTCTAAAGGTGTTCCTCGCTTGAAGACAGAAGGAGGATATCTTACTGCAAATAAAAACTATGTGACAGCTGCTGGAAATACCAATAACAATTACTTTATCACTAATCCAAAAAAAGTTAAGCTCTTAATTGATGATTTGTTTTTACAATAATACTGAGTTTAACTAAAAAAGG
+SRR005406.49 FB9GE3J10GA69G length=204
CCCCCCCCCCCCCCCCCCEEEEGGGIIIIIIIIIIIIIIIIIIIICCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC888C@CCCCCC:CCCCCCCCCCCCCCCCCCCICCCCCCCC??5555AAAC?CBBCBA?@@3//////<11))9ACCCCCCCCCCC::444455855ACAA:::>>AA><:9666//-////////
@SRR005406.50 FB9GE3J10F75UF length=82
TATTGACTACTGAGACAGGGAATCACCAATGGCATAAACACCAGGAATTTTTGTTCTCATTTCTTGGTCTGTTCTANACACC
+SRR005406.50 FB9GE3J10F75UF length=82
AAAAAAAAAAAAAAAAAABB??ABFAAAABBBCCBAA?A<===>>::44222=..===<444<<=@@=?=4339<9!69966
@SRR005406.51 FB9GE3J10F8M65 length=254
TATTGACCCAAGTTGCCAAAAGATGGTTTATTTGAAATTGAAGCAGTTGCTGTCAAAGGATAATTTTTAAGATGTTTCTGAGGGAAAAAGGATTGCATTCTTTACTGATTAAGGGGAACAATCCTTTTAGAATAAAAAGAAGAAGGAAACGATCCTATGAATGAAAAAAAGAGCAAGCATTATTTGAATATGATGCGAAACTATCAATTTCTGAAGCAATTCCGATGGGATTGCAACACGTTGTCGCGGCAGTA
+SRR005406.51 FB9GE3J10F8M65 length=254
CAAACCAAA??@ACCCCCCCAA8AACCC@A113CCCEEDDEEHIICCCCCCCCCCCCCCDCCC=====CCCCCCCCCCDCC???=====AA:CCCCCCCCCCCCCDCCCCCCCCDDAACCCCCCCCCCCCCCC:::::C::CCCCC???CCICCCCCBCC?77///////7)>A??BCA???CCCCCCCCCCCCCCAAACCCAAAACCCCC@CAAA?<<<<>CC<<3317?CC>>71138C<7775:5555555
@SRR005406.52 FB9GE3J10GC7US length=304
TATTGACCATCAATGAAAATTTACAAAGTGTGCTAAATGCGTTGCTCAATATTGCCTTTGGCTTAATCAAATACTTTGTTCTGGCATTAGATTATGTGATAGACAAACTCTTTAGTTTAAATTTATTAGAAGGAGTATTACCAGATTTATTCTCCACTACTGGTGCTATTTACAACAAATTATTCAGTGTTGTAGGGATTCTCCTTTTTACATTTGTGATTGTCATTTCAGTGAAGGTATTTTTTTGAAAAAGGAATCAGCAAGGCATTAATCCGTTTGGTATTTTCACCTTAATCTATGTGGG
+SRR005406.52 FB9GE3J10GC7US length=304
EEEEEEEEEEEEEEEEEEEGEEEEEGGGGGGGGIIIIIIIIIIIIEEEEEEEEEEEAAAEEEDDDDEEDDDEEE===DDDEEEEEEEEEEEEEEEEEEEEEEEEAAADEEEEEEEEEEDDDAAADEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEDDDEEEEEEE;;;;;EEEDDDEDDDDDDDDDDDDDDDDDDD===@8;;;;66711111::55>??@@?????>AA6666./......6..../9;;;;;;9;;;;//...
@SRR005406.53 FB9GE3J10F6637 length=268
TATTGACTGATGAAATTGCTAGTGCACAGTTAGTGGCTGGTGAAGAAGAACAATTGCTAGAAGAACGCAATAAACTGAACAATTTTCAAAAGATTGCTGATGCACTGACGATTAGTTATGCTGCGCTAAATGGTGAAGACGATAGTAGTTTGGATAAAATCGGAACAAGTATGAATGAACTCGCTTCGATTGAATCCCTTGATCCAGAATATAAATCATTGTCAGATACTGTTCAAAATGCCTACTACTTACTACAAGAAGCTAGTGG
+SRR005406.53 FB9GE3J10F6637 length=268
GGGGFFFFFFFFFFFFFFHHHHGGHHIHHHHFFFFHHHHHGGHHHFFFFFFFFFFFFFFFFFFFFFFFFFG???GFFFFFFFFFFGGCCCCCBGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGGGGFGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFIIIIIIIIIIGGGGGEEE>>>>EEEEEEE@@@@@AAA@@@@@@AAAAA::::
@SRR005406.54 FB9GE3J10F6CI6 length=308
TATTGACACCCGCTTTTCCTGAAATATTTGCCAAATCAACATTTTGGGCAGCTTCCAGCAAAGCCCAACCATGCGTATCCGCAAATAGCCGTAATTTTTCAATTGAACTTTTACCGATTCCTCGTTTTGGTTCATTGACAATTCGTTCAAAACTAATCGAATCATCTGGATTGGCAATCAAACTTAAATAAGCCAAAATATCTTTAATTTCTTTACGGTCGTAGAATTTATGTCCGCCCACCATGGTATACGGAATATTAGATTTCAAGAGCATTTCTTCCACTACACGGGATTGGGCATTGGTCCGA
+SRR005406.54 FB9GE3J10F6CI6 length=308
GBBBGGFG??=GGGGFFGHBC>?>HGIIIHHHCEEHHHHHFHHHHCCCGGFFGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFIIIIIFFFFFFFFF@@@@FFFFFFFFFFGG????FFFFFFFFFFFFFFFFFGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGFFFFFFCCCCFFFFFFFFFFFFFFFFFFIIIIIIGGGGGFFEEEEEEEEEEEEEEFB==@@AAAAA@@@@@@@@:::??@@@@@@566:?@@@A@A====????@@:::@A::::=?B<8
@SRR005406.55 FB9GE3J10F5XQA length=325
TATTGACAAGGTGTGCATCACCGAAGTCAAGCGTTTTTCGTTACAGTTTTAGGTGTTGCAGTGGGTGGTACAGTTTTTATTAGCACCATCATTAAGTTAGAATTATTTACGATACGTGAATGGTTAAGTTTACCGTATGGCGCAAAAAATTTTACGGATGAGACAAAAAAAATAAAAGAGGTGAATGTGATGCGGTTAGATAAATTTTTAAAAGTTTCTCGCATTAATTAAAAGAAGAACAGTTGCCAAAGAAGTCGCTGATAAAGGTCGGATTCAAAATCAACGGAGTCTTAGCCAAATCTTCTAGTACTGTGAAGATTGGTCG
+SRR005406.55 FB9GE3J10F5XQA length=325
EEEEEEEEEEEEEEEEEEGGGGGGGGGGIGIIHIIIIIIGGGGIIEEEEEEEEEEEEEEEEEEEEEEEEEEED=====AEEEEEEEEEEEEAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEAA====DEEEEEEEEEEEEEEE99;:442622/7AFFGGAA=?////////?----?==@EEEEEEEEEEEEEEEEDDD@@@@;;555DDEEEEE=DDDD??111111111116DDDDDDDDDD??777??@@@@@@@@@@@??:::6666666....66../.699??>>==::777=@@@@@@@@@@@@@@@@=====7331
@SRR005406.56 FB9GE3J10GGI2A length=279
TATTGACATTGGAGAAACACTAAAAGAAGCAAGATTGCAGAAGAACATCTCAATTGATGAACTGCAACAAATGACAAAAATTCAAAAAAGATATTTAGAAATTATTGAACAAAACGATTTTGAGTCCTTACCAGGCACCTTTTATGTGCGGGCGTTTATCCGCCAATATGCAAGTGCGGTCGGCTTAGATGGCAATCAATTGGTAGATATCTATGATGGCAAAGAACCAGCAATTGTCGAAGAACCCAAGCCAGTGTATGAAGAGCTTGAAGGATCAAC
+SRR005406.56 FB9GE3J10GGI2A length=279
EEEEEEEEEEEEED==;EEEEAAAAEEEEEEEEEGGGGGGGHHHHEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEBBBBBBEEEEEEEEEFFFEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE@@@@DDDEEEEEEEEEEEEDDDDDDDDDD<<<@DDDDA;::::;;@D?7777::::?@@@@@@?:::::11176;;96/../
@SRR005406.57 FB9GE3J10GBE5F length=312
TATTGACAGCATTCAATGACAGGTTCAACTTTTGTTCTGTTCCATAAATATTTGTCTAAACAATTGAATTAATAGTACAATAGTCTAGTAAGATAGATCATTGAACGGGGTGGAATAGGCGTGAAAAAGGGAAATGTTAGCGTTTTTTGTTCGGGCTATCGGTTTTATCATTAACTGCTTGTCGGGAACCAAAAGAAAAGAAAGTGACCGCTTCAACGGAGGCATCCTCTAAAGTTGAAGAGACGAATGAAAAAACCAGTGAAACAATTGATAAGACAAACGAACAAGCGAGCAGCAGTGTCGAGTCTAACG
+SRR005406.57 FB9GE3J10GBE5F length=312
DDDDDDDDDDDDDDDDDDGFDDDDDDDDD9999922BDDDDDDCCBBBDDDDDDDDDDDBB==@@866@@DDDDDDDDDDDDDDDB@@@DDDDDDDDDDDDD>>>800004//44BAAABBB@/////@::---4<:??DDD9;===>D88DDDB???DDDDDDDBB@BBDDDDDDDDDDDDDDDD???>BBDDDDDDDDDDDDDB>>>DDDDDDDCCDBBBCCCCCCCC@@@CC@<<;@CA???::8/........3:::.13>>>??>>>>>?>?>>>>?>>>>>??>>>>?>>>>>>>?>?>?=7777=
@SRR005406.58 FB9GE3J10GBLFV length=297
TATTGACACAAAATTAGTCCTTGTTTTTCTTAATTTCTTCTTGTTTACAGTATAATAAATAATGAAGAAGATTTGAAGAAATTGCATAGATTAGGAGGACTTCTTTTGACAAAAAAATTAATATCAATGGGGCATCGTAGGATTAGGTGGGATTGCCCACGAATTTGCTTCAACGTTTAAACAAGAAACTAGCCAACTTGCAGCTGTTGCTTCACGGACATTGTCTAAAGCAGAACAATTTGCCGCTGATTATTCAATCCCTAAAGCCTATGGTTCTTATGAAGAATTGCTAGCAGA
+SRR005406.58 FB9GE3J10GBLFV length=297
CCCCCCCCCCCCC==4<;>>446/////>01@@;;;>225=BB@@@AA@ACCCCCCCCC=::====BDD@=555===CDDD===ABCCB@AABCA@AA@CCCCCC@9;;;///////;;++@@@BAAAACCCCCCCCCCC@@@BCCCCC<<666<@CB<9<@CCCCCCBCCCCCB<<>><<<<<<<<<<<<<:::<<<<<<<<<<::::<<<<:::<<<<<<<<<<<<<<<
@SRR005406.59 FB9GE3J10GGCGR length=292
TATTGACGGGCTTTTTGGGTGTTTGCAAAATGCAGCTTCGCGTAGTTCGCTAATAAGTCTAGGCCGCCTTTTTTCAAAATACGGGCGGCTACTTGGTCTGATTTGCTGCCAGCACCAGAGGGCACAGAGAAACCCAATTCTGCAGATTCTTTGTCTAACTCTTCTAAAAAAGCAGCGCGGCTAATAATAGAGGCGGCAGCAACAGCAACATGATACTGCTCTCCTTTAGTGACGAAGAACAATTTTTCAGTGACTTGATTTTTTTCATTACGAACATATTTCCGATAGTTTA
+SRR005406.59 FB9GE3J10GGCGR length=292
FFFFFFFFFFGBBBBBF??>GGIIHHHHIIIIIIIIIIIIIIIIIFFFFFFFFGGGFFFFFGGGGFBB000000A3333CAACGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGFGG@@@FFFFFFFFFF@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDDDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGIIIIIGGGIIGGGIIIGGGGBBBGGG@@@@A@@@@@???9<@@@99@@@@AAAA@@@???@@@@@@===??@@
@SRR005406.60 FB9GE3J10GD4OO length=214
TATTGACTATACTTCTCCTTTTGCCACTCAACATTTTTTGCAATAACTTGCATATTTTTATGCACTAGGAGGAAATATATATGAACAACGGTACAGTAAAATGGTTTAACGCAGACAAAGGTTTTGGATTTATTACAGGTGAAGATGGCAATGATGTATTTGCACATTTTTCAGCTATTCAATCAGATGGATTTAAAACTTTGACGAGGCAACG
+SRR005406.60 FB9GE3J10GD4OO length=214
AAAAAAAAA??B====::222299<<:<<<<:933333399<=978@?AAAAAA@@@@;A2AAAAAAAAAAA???AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA?A@??888888888==???@AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA88888AAAAAA???AAA@?==8866-------3...6-----------
@SRR005406.61 FB9GE3J10GAGW5 length=307
TATTGACCCTTTCTCAACTAATATTAAAAACTATCTGTCTCAATATTTTCGAATTTCCTGTAAATTACTGATAAATAAAAACAGCTCCTTTTGCGTATACTTATATTATCAGCACCTAAAGGAGGAACTTTCTTGAAGCAAAAAAATCTACTCACTTATCAATCACTTGCCGCCTTGTTGCTAGTATTCAGTCTCTTTAGTTTAACCCATCGGTTTCTTTTGCCACCCGTTCTAGAAAACGCCTGTTTCAGTTGAACTAGAAATTGGAGGGCTGCCTGGTGATGAATCGATGAATCGGTTGACGATG
+SRR005406.61 FB9GE3J10GAGW5 length=307
DDDDDDDBB@@@=DDDBA855HD??///55@D8BBDDDDDDDDDB5550>>>>222BBDDDBBBDDDDDDDDDDDDDDDDDDDDDDDD;;;;BBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBB@///////<855555CCCBCC<<585?9==9;88::?;=00/;;;000008==AA113::>>>=====:::::::3337========>?>>>>>======:777711111==:::::
@SRR005406.62 FB9GE3J10GE8JF length=332
TATTGACTTAAAATTATTTTATACAAGCCTTATTATTTGGTTAGTAACTTTTAACAACGGAGGGTGATAAAAATGAAGAAGTACAAAAAGTTTTGTTTTTTAGGTTGTTGGGTTATTACCTTTGGTTTTAGCTAGTTGTGGTACAAATACTGCTACAAATGATTCACAAGATATAACCGAAAAAAAAGTAGAACAGGTAGCGACTTTGGCTGCAGGGACACCTGTTCAAAGTTTAGATCCAGCAACTGCTGTTGATCAAACGAGTATGACTTTATTATCCAACGTGATGGAAGGTTTATATCGATTAGATGAAAAAAATCAACCGCAACCAG
+SRR005406.62 FB9GE3J10GE8JF length=332
FFFFFFFFFFFEE8876666;AEEFFFFFFFFFFFFFFCC===EFFFFFFFFFFFFFFFFFFFFEDDDFFFFFEEEEFFFFFFFEEE88?22228000000988//?=FFFFDDDDDEFFFFFEE====EDDDFFFFFFFFFFFFFFFFFFFFFFFAAAFFEEEEFFFFFFFFE==;;D99999999FFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEBBBEBBBEEEEFEEEEGFFFFEEEEE@@@@@???@@@@555=@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@??555??@@@@@CC>>>96.......69<<<<<=????:7
@SRR005406.63 FB9GE3J10GBIY5 length=345
TATTGAAAATTCCAGACGTGCTTTTAAAAGCATGTATGCAATTTTTGTAGAATCTGACATTTTTTTGTATTTATCGCTAGCAATAAGTACTTTTGGGAATTGATAGAATAATTCATTGTAAATACGGTTTACATTAAAAAATTTGAAGTTGTTCATATAAGATCCCTCTTTTCTTAGTTAAAAATTTATCTATTAATTTATTTAGTAAGCGTTCTTTTTTTAAGAATACCAAAACATTATTTAAAATAAAGCAATTTTTATTTTTAGTAGTAAGATAGTAAAGTAGTAAGATAGTAAAGTAGTAAGATAGTAAAGTAGTAAGATAGTATAATAGTAAAGTAGTAG
+SRR005406.63 FB9GE3J10GBIY5 length=345
FFFEEBBBBEEEEFFFFFFFFFGGIIIIGGGHIIIIIIIIIIIIIFFFFFFFFFFFFFF???????FFFFFFFFFFFFFFFFFFFFFFFFBBBB>>>EEFFFFFFFFFFFFFFFFFFFF===FFFB@@==AFF77000055DDFFFFFFFFFFFFFFFFFFFE=;;EEBBBBA==?FDD55;;;EEEFFFFFFFFFBBBFFFFFFEEEFB;;;;9988666;;EEE@??@EEEEEE;;;EEE@??:::66>=::111333:::::@@>?=777@@@@@@777@@@@===@@@@@@@@@@@@@@@@@@@@@@@@@@@@@===?@@@@@@@=:::?@===@C<7700
@SRR005406.64 FB9GE3J10F789E length=279
TATTGACGAAAATGGCATGTTGGATGTCAAAACAAGGGGAACAATTGACAGAAGAAGCGTTAGAGAAATGGGGAAATGATTTACCTACTGCGATTCTTGCTTATAATGACGCCTTTGCAATCGGTGTGATACATACGTTAGCCGCACACGGTATAAAGGTTCCTGAAGAAATTAGTGTCATGGGGATCAATGATATCTCTATTTCTCAATATGTCTCACCACCGCTATCCTCTGTCCATGCCTTTACTGAAGAAATGGGCGAGACAGGCATTTAATTTA
+SRR005406.64 FB9GE3J10F789E length=279
FFFFFFDA;;66@@EFFFFFFEEEFFEE7777@AA@@FFF8;;=EDFFFFFFFDDDEFFFFFFFFFFFEEEFFFAA@@D@@ADDDAAAFFFFFFFFFFFFFFFDDDFFFFEEEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDDFFFDDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEFFFFFFFFFFFGGGGFIIIFFFFFFFFGGGGGGFEEEEEG@@@@???@@@@@@@@===?@@@?>=1..66...6
@SRR005406.65 FB9GE3J10F7QSM length=290
TATTGACAATCGTAGCAAAAGCGTTACATGATGTTTTAAATGAAGAATTAACGATGGATCAAATCGAACAATTATTGGAAAATCCTAAATCTGTTGATCATGGAGATGTGGCTTTTCCAGCCTTTTCATTAGCTAAAATTTATCGTAAAGCACCACAACAAATTGCAGCAGAATTAGCAGAAAAATTGATGGCACAAATTTTGAAAAAATTGAAGTGGTAGGACCTTATTTAAACTTTTTCATGAATAAAGAAGCAGTCAGTCAAGCTGTTATTGGCGCAGTAGTCAAAG
+SRR005406.65 FB9GE3J10F7QSM length=290
FFFFFFFFFFFFFFFFDDFFEEFGFFFFFFFFFBBBBFEEBCCFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;==;;;DDFFFFFFFFFFFFFFFFFFFFFFFFFFFF=;;;DDFFAA;;;;EEFFFFFA====FFFFFFFF===EFFFFFFFFFEEEFFFFFFFFFFFFFFFFDD;;;;;FFFFFFFFFFFFFFFF=<000007<>??==:::722222:8?????====??????????=:::111.....99099...117755>>>?
@SRR005406.67 FB9GE3J10F6BBR length=293
TATTGACACTGGAAAAATTAGAAATGGCTTCGTTATGGCTGATTTTACCCGCTTTATTAACTGCTTTTGTGATTGGTAACGCCTATCAATGGTTGCAAGCTGCTCTGGCTAAAATATGCCAACCTTTTGAAGAAAAGCAAAGCATACTGGTAAGCTTTGGTGCAGCCTGTATTTTTCTCTTTGTTATTTTAATGCCAAGATTACTATTTTCAGGACAATCTTTTATGCATTTAGTTCCTAGTTTTGGTAGTCAACAAGCTTGGTATATCTTGGTGATCGCTGCGATAATGAAA
+SRR005406.67 FB9GE3J10F6BBR length=293
DDDDDDDDDDDDDDDDD;>0EEDDDDDDDDDDEEGEDDDDDDDDFDA;;;BACCDDAAAADDDDDDDDDCCCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCCCCC:DDDDDDDD999996DDDDDDDD999CDD9999CDDDBD==::444444???8:8DDDDDDD@78888::9????====?=:::???????===:::???===?7777:==7711.
@SRR005406.68 FB9GE3J10F6992 length=315
TATTGACTAAAAACTTAAGTGACTGCTGCGAGAGATAACGATAGGTTAAAACAGCATGTTAGAAATCTCATGAGTACTGATATGGCGAGAGAATATAAAAAATTAAGTAAAGAACATGGGCAAGTTAAAGAAAAATATAGTGGTCTTGTAGAGCGATTTAATGAAAATGTAAATGATTATAATGAGTTGCTTGAAGAAAACAAGTCTTTAAAGTCTAAAATAAGCGATTTAAAGCGTGATGTGAGTTTAATCTATGAAAGCACTAAGGAATTCCTTAAGGAACGTACAGACGGCTTAAAAGCCTTTTAAAAACGG
+SRR005406.68 FB9GE3J10F6992 length=315
FFFFFFFGEEDDEG====CBHHHHHHHIIIIIIIIIIIIIIIIIIFFFFFGIGIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB;;5555FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFG;;;;FFG;>>FFFFFFFFFFFFFFFFFFFFFFFBBBBCFFFFFBBBCCGFFFF@@@@EEEEEEE::<==AEEEEEEFGGIIIA@@@@AAAA@@@@AAAA@A@@==========@@@@AAAAA@@@@AA::::?BBB82...........29B
@SRR005406.69 FB9GE3J10GEIPX length=283
TATTGACATGGGCGCCTGCTAAAATAGTCGTCCCATCCATGGCTGTTTTCTTTCAGCTGAATTTTGCCTTTGGTCCCTGTAGCATGCCCGCCACTGTGATCGATGTCAACGACCACATCGCCATTGTCATCCCCATGAACGACTTCTGAACCATTTCCAGTAATTGACACTTGGTTGGATACCGTGTCTGTACTCCCCGCCGCTGAAGAAGTCACTAAACTACGATATTCCATATAATAAGGTGCTTCAATATGGGCCATTTTAACGACTAATTTTTTGTTGT
+SRR005406.69 FB9GE3J10GEIPX length=283
DDDDDDDDDDDDDCCCDDFFFFFEGDEEFEEEEEEEEFHHFFFDC6996@333>AHHHHAA1666@CD@@@DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCCDDDDDDDDDDDCCCCCDDDDDDDDDDDDC>>>CDDDDDDDBBBDDDA<<><979===>=<:::<8:8??468844:(3333.32:8<<<=79999899??@@?AA@@@?BA??422288922....00**69<==????=????883338????????AAA<<<<==;;::.........,44433...06==>??????AAAA867???@@??;;;??;;;>>766677<;666;;>;;;>=>>;;;;0000;<;;;<9;;<;;;;;:::<<<<=<>>=<<:555567663334663....001111431,,,,,,,,,,,,,)131,
@SRR005406.71 FB9GE3J10F60K5 length=319
TATTGACCTTTTTTACGTAATGGGTTTTAAATTCTTATTATCAGTTTCTGGCGTAATTACACGCTCTCCAATTGTCACTTGGCCTTTAGTTGGTTTCACCAAAGCATTTAAATGTTGCAATAGCGTTGATTTGCCACTGCCAGTATGACCGACAATCGCTGTATAAGAGCCGTCTTGAATCGTTAAATTAATATCGAATAATGCCCGTTGCTCAAAAGGAGTATTGGGTTGGTAAGTAAAATCTACTTGTTTAAAACGGATGTCCATAACCAATCCACCATCCCTTCTTCTGTTAAATAATTCGTTGGCACAACAACCG
+SRR005406.71 FB9GE3J10F60K5 length=319
BBB@AA55//////66B5CBB111DDB:111..85>?5588BBDDD??;??BBDDDDDDDDDDDDDD>>????BBDDDDDDDDDDDDB?<<>>DDBBBBDBBBBBDDDDDBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBDDDDDDDDDDGGDDDDDDCCCCCCB:666333::====>>>>>>>>>>>>>>>>>>>>>>>>::663<<<;<::::;1..11<;6664::<<;:11116
@SRR005406.72 FB9GE3J10F60V0 length=322
TATTGACACACATTCTTTTAGATGATGGTTTAATTTGATTTAGAAGTAACTGATATCGACCGTGATGCAAACGAAATCGTAACAGTTGTTAAAAACGAAAGGCGTCTTGAAAAACAAAAAAGGCGTTAACGTACCAGGCGTTTCTGTAAACTTACCAGGGATCACTGAAAAAGATGCTAATGATATCCGTTTCGGAATTGGTCAAGGAATTGACTTTATCGCAGCTAGCTTCGTTCGTCGTGCTTCTGACGTTTTAGAAATCACTAAAATTTTAGAAGAAGAAAACGCAACACACATCCAAATCATTCCTAAAATCGAAAAA
+SRR005406.72 FB9GE3J10F60V0 length=322
FFFFEEEFFFFFFEA6666;EEFIIGBB588BB777BBFFHFIEEEEBBBEFFFFFFFFFFFFFFFFFFFFFFBBBFFFFFFFFFFFEBB<>>>>>EEEFFFFFFFFFFFFFFEEEFFFFFFFFFFFEEEEEFFFFFFFFFE=====FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGFFFFFGFFFEEEEE=::9<@EEEEE???=@CC7111117;<;;;<@97.........;<>@?@@@@@@@@@===@@@@?7771119<<77777....797.....
@SRR005406.73 FB9GE3J10GC6TX length=309
TATTGACAATGCAGGATTGTTAGCATCTAACTCGGTAACATCGAAAAAGGTATTATAGGTTACGTAAAAGGCATCACTTGTTTTGGCATACGCCCCCCATGAAACTTAACTTAAAGCCTGTTTCACCTTCTGCATTACGAGTTATTTCTACCATGTAATCTTTACCTAAAGTCAACTGAGCACCAGTGGTTGTATCTTTAACAACCAATGAATTGGGTACCATGGTTAAGCCAGGAACTGGTTCGTATGTGTCCGTAATCACGGCATTTTCCATCAAATAATTATTTTGATTCACAGCTAACGTCCAAA
+SRR005406.73 FB9GE3J10GC6TX length=309
FFFFFFFFFFFFFFFFFFHGGIIIIIIIIIIIIIIHHHHIHHH;;;77GCCAGGFFFGGGGFFFFFFFFBCCGFFFFFFFGGGGGGCCFFCA000000AAFFFFF@CBBBBBBBGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGGFFFFFFFFFFFFFFG@@@GGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFIGGGGGFFFBBBBBBBEEEEEFGGGGGIGAAAAAAAAA@AAAAAA@@@@@777777@@@AABB777771111=@====@@AAA@@@A@::666
@SRR005406.74 FB9GE3J10GBFJH length=297
TATTGACCGCAATTAACTTACCACTAATGGTCCACTCGCGCGCTAATTCATGATTTTGGGCAATCATTAAACTCAATTCTGCGACACCAGGTGTATACATTTTGGCTAAATCATGATGGTTTAACACCGCTTCTGTTGCTTCAAGACTTAGTACACCAATATTTTTTTGATGAATTGCTAGAACTTCTTCTAACACATTGTCACTTCCTTTCACGGGCTGCCTTTTTTCTATTTGATGAAGCAAGGGTTTGAACAACCGTTATCGTCGCTCAAACCCTTGCTTCTTTATACATTTGG
+SRR005406.74 FB9GE3J10GBFJH length=297
DDDDDDDDDCCCCCCCCDDDDDDDDDDDDDDDAAADDDDDEDDEHDDDDDDDDDDDDCAAAADDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDAAADDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBAA///////AADDCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD>>>>CCCDDDDD=@>800//////8/D==DDDDDDDAAAAD???????==::::???????????===???????=:444:??????=:7777
@SRR005406.75 FB9GE3J10F69YQ length=250
TATTGACAAACAAGCTGTGGCAACTCTGCGCCTGTCGTTTGTTCTACATCAAAGACAGGCGTTAAAAAATAGCGCATCTCTTTGACAATTTCTCCATTTTCATCCGTAACTTTTTTCCCATTCTTATCGACTTTATCTTTAAAATAAGGGGCATACACATACAGTGCTTTGCTGTCCTTTTTTTACTTGACGATCTTAACTTTTTCCACGCATTGTAACCAGCTACACGACGTATGTTTGGTATTTTGTG
+SRR005406.75 FB9GE3J10F69YQ length=250
CCCCCCAAA<<77<@CCCDDDDEEGGGIIIIIIIIIIIIIIIIIICCCCCCCCCDCCCCCCCC777777C.CCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCC;;;;9555111000>>@@3355@CCCCCCCBCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC<<<<<<<:4))?CCA6//////6/////6669<66/222CCC88331777<740944//4+2
@SRR005406.76 FB9GE3J10F7LD9 length=297
TATTGACTAATATTTGTGATTCAGAAATTATAATACAAATATTTTCAATAGGACATAGGAGTACTATCTACAAAAAATAATTTATGTAGGAAACATGCAAAAGAAGAGGGTATATTAGAAAATAGTCCAGTTTCTATTGAAATCTTAACTGTTGAAGCACCTGCAAAAAAAGTGATATATAACTGAATTAGATAAAGATGTTATCTTTCTACTTGGTTTTANGTCAAATTAATTAGCTTAGAATAGTTATAATTAACTATAAATAAAAATATAGACTCTCTTTGTATAGAGAGTCTA
+SRR005406.76 FB9GE3J10F7LD9 length=297
DDDDDDDDDDDDDDDDDDEDDEED;;;DDDDDDDDD@@@GFFFFFDDDDDDDDDDDDDDDDDDDDDDDDBB555555@3?DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBB::///////:@BCCDDDDDDDDDDDDDDDDDDDBBBDDDDDDDDDDDD>999DDCCCCC!BB@CCC5555555:C:::AAAA@=:::11.6644647..........6,67====:777=========66666./
@SRR005406.77 FB9GE3J10F5CU0 length=327
TATTGACAAATCTTGATATTTTTTTCTTCGCTTTGTTTAATTTTCACGGACTAATTTTTTCGTTATCCTCTTCAATATCCTTTAAGAAAAGTTAGACTCTTTTGTTTGACCCGAAGCGATTGCTTCGAGCGATTTTTCCCATTTTTCCGTTTAGTTCAGGTGTCACAAGTGATGGATTCACCAAGTCTAATAGTTGCTTTCCTTTGGCAGAGACACTTAAACCGCTATTGGTTCGTTCCATCAATTCTGATTTAATCAGTTTTTCAATAATTTCAGCTCGCGTTGCCGGTGTGCCTAAACTGTGTTTCTCCATTTTTCCTAACAACG
+SRR005406.77 FB9GE3J10F5CU0 length=327
C???AA@330<<<<<<64///////6).AAAAAA@000@@00--6<>AA44633//////<<..A>@@CCCC?@@@?CAAA;;44433::A44-;;@@?<@---3555;C???ACCCCCCCC?@@ACCC=====C@@@=;;;;CC@---AA>>@@@@@A>??C???AACCCCCCCCCCCCCCCCAAA???AAAAAAA2200199CACCCCCCCCCCCCCCCCCCCC??88333388CC???C::::5555::6:::::::5555:5511155:::::;;;;;;;;;;;;:::;:::;;;;;::47022--------*--00024
@SRR005406.78 FB9GE3J10GGF8C length=294
TATTGACAAGACCACTGGAATTCCAGCCCTTTGGCCGCATGCAACGTCATTAAGGTTACCTGCGAAGAGCTCTCTTCTAAATTATCTAAATCAGAAACCAAGGCTAAATCTGTTAAGAAATCCGCCAATTTTGTTTCTTCGCCATTTGGATCGTCGTTGTTTTGCGCTTCAAACGTTTATCAAATTCTTGTGTCACAGATAAAATTCGTCCAAGTTTCTAAGCGAGCTTGAGACTCTAATTATTTGCGCCATCAAGCTTCCCGATAACCACTACGTTGTAAGTTTCTTCACATT
+SRR005406.78 FB9GE3J10GGF8C length=294
;==:999::80226022222222233:99000899:8<<>A?ABAA=====??B@8889989??<<<???@@????@??>>>4488??<<><<882112>>;;;>;76133335-------,,*,,,,5222225222552,,,220,,,130,,,,,,,,,,,,,,,,,,,,,003331,,,,,,,,,,3,,3,,,,,
@SRR005406.79 FB9GE3J10GDQIK length=303
TATTGACCATGAATTTCGCCCACCAAGTCATCAATTTGACCCATAATTGGGCGGATTTCTACTTCTGGATCTAGTAAACCTGTTGGTCGAATGATTTGTTGAACAACAGTCTCTGTTTGTTCCATTTCATAAGGGCCTGGTGTTGCCGATACATAAACAATTTGGTTTACATGTTGTTCAAATTCTTCTAAACGAAGCGGTCGGTTATCAAGTGCACTTGGTAAACGGAAACCATAGTCCACTAACATTTGTTTCCGTGCTCGGTCGCCATTATACATTCCTCTAATTTGCGGCATTGTTACA
+SRR005406.79 FB9GE3J10GDQIK length=303
DDDDDDDDDDDDDDDDDDDDE<77>>CDDDDDDDDDDBB888>855BBDDB?;;B???DDDDDDDDDDDDDDDDDBBBDDDDDDDDDDDDDDDD???DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD55555<>>666>>D<<>DDDC>999DDDDD>!>>DDDDDDDC@@BBBBB@????DDD??@<<99999712220897758<==77<88::????AAAAABA??@???8998<=<:;9867222;;=====?>???A===AAAAAAA??<<<<=>=;70004=:;111116==>>==<8888???=>>>?>>=;;;;::::66699000:977793773.....+.....++444400344466676;;6666;=<;;;;;;;=;;;:::99988442222222522222522,,,255,,
@SRR005406.83 FB9GE3J10F5T2N length=313
TATTGACTCAAAAGGTAAATGGTATGAAACCATTACAGGAACGGCGGCTAGATATGAGGCTGCAACAGCTAGTAAATACGTGTCGAATTTAGGACTTTTATAAATAATAATTTTGTCGCCTTTTTTTACACCTAAAGCGGCTAATTGATATGCCCGTTTCAAAATTTCTTGATGGCTTTCACCATAAGTTGTTTCTAAGCCAAGTGCAGGAAAAGCAGGCAAAGATTCATCAAAAATATTGGAACAGTTGGTGTTTTTTCNGCGGCTTCTTGATAGTTTGTGTAGAGGTTTAATGGTTGATAATCAAGTTAAG
+SRR005406.83 FB9GE3J10F5T2N length=313
DDDDDDDDDDDDDDC;77>ADDGFDDAAAGGGGGFHFFHGGEEEEDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD;;;;;;;DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD;;;;???DDDDDDDDDDDDDDDDDDDDDDDDCCCDDDDDDDDDDDDDCCC9999DDDBBBDDDDDDDDDDDDDDD@<088<<<;:=>>>>:711177711!7:7777????====????:;:=::::?????????:::=9966666/.....
@SRR005406.84 FB9GE3J10GCT5C length=289
TATTGACTACAAGTATTAACCAATATTGCCTTATTGGTTGGTGTCTTAATCATGATGTTCCGTCAAAATGTGGAACTGGCATGGGCTACAATTGCTTCTACGCCGATTGCGATTTTAATTGCGGTCTTTGTGATTAGCAAGGCGCGCAAAGGTATAGGTCGATTTACAGCAAGATGAAGTGGGTAAATTAAATGGCTATATGGATGAAAAATTAGTGGGCAACGTGTGATTATTACTAATGGCTTACAAGAAGAAACCATTGACGGCTTTTTAGAGCAAATGAAAAGTT
+SRR005406.84 FB9GE3J10GCT5C length=289
CCCCCCCCCCCCCCCCC?@AAAACAA@@4444@99==::CCCCDCAACAAAACCCCCCBBAA?;6666<<CCCCCC@9777<0111///111/1111?CACCCCCCCCCCCCCA>999>33/7///:>555>>>>>CCCC999??=:;::>>2>>331138CCCC??@CCCCCCCCCCCBBBCC;:::;:::111::5::7772551----4672----------247
@SRR005406.85 FB9GE3J10GCNS1 length=298
TATTGACGCCCAGTGTTAAGTATTCTTTTTGCAATTGCTTTACTGGCTTCGGGTCAAAATTCAACGATTACAGGTACGCTGTCAGGACAAATTGTAATGGAAGGCTTTATCCATTTAAAAATGCCGTTGTGGGCAAGACGAGTGTTAACTCGTTTGTTAGCAATTGTGCCAGTCATTATCTGTGTCATTATTTATGGCGGTAGCGAAACGGCTGTTGAAGACTTGTTGCTTTATACGCAAGTTTTCCTAAGTATTGCTTTGCCAGTGTCGATTATTCCTTTAACGATGTATACAAGTG
+SRR005406.85 FB9GE3J10GCNS1 length=298
EEEEEEEE===DDEEEEEFEEEEEEAAAAAEEEFFEEEFFFEEEEDDDDEDDDEEEEEEDDDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEED;;7DEEEE777>>DDDEEEEEEEEE===DDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEDDDDBBBDDDDDDDDDDDDDDDDD@::::71/11777=@@@@@@@====@@@?::7771111777777::::?@@::::@=:
@SRR005406.86 FB9GE3J10F5BL0 length=309
TATTGACTAGTAGAAGCAGAAGAAGAGTTACAAATTTTTAGAGGTGAAATTAACAAGCCCGGCTTTATTCAGCAACTATTTCAGCTTTATCAAGAAATGCGCGAAGGCAATATTGAGATTGCGGAGCTTTATCCATTCTTAGAAAAACAAACGGAGAACCCTAAAGGACAAGATTTACAACTTAAGTTTCAAGATTTAACGTTAATTTTTACGCGATTCCAATTACAAATGAGTCAGTATGGCTATGAATCAGCGGAGATTATTCAACATTTAAGCGAGTATTTACAAACGGTTGATTTGTCGAATGTT
+SRR005406.86 FB9GE3J10F5BL0 length=309
FFFFFFFFFFFFFFFEEEGGGIFFFFFFFE@88877000;@@EFE;488DDEEEFFFFFFEEAAAEDAAADFFFFFFF===EEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEFFFFFFFFAAAFEEEEEFFFFFFFFFEEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEEEEEEEEEEEEEEEFFFGFFEEEEF@===@@@@@@@@@@@@@@@@@@@?:::@@@@@@@@@@@@@@@@@@@@@@???@@@@@@@@@=43
@SRR005406.87 FB9GE3J10GF21A length=311
TATTGACCAAAAAAGGACAATAAGATTGCCAAACTAGAATTTACGTTTACTGGTCTGAAACCAACAAACCAAGCGTAACCATGCACGATTGGGTAAACGGAGAATAAAAAAAGAACTTGCCCCCTCACATTAAGCAAGTTAGCAAGTTCCTCACGCAATCTTCCGGACTGCTAGATTATTTTAGCATATTTGCGTGAGGACTTCTAAAATAAATTATTTTGGAGGTCCTACTTATGGGATTAATGACAGGATACAACATGACAAAAGAGGAGTACGAAGTCACACAGGCTGTACTGGAGCGACTAGATTAA
+SRR005406.87 FB9GE3J10GF21A length=311
FFFFFFFFAAA===EEFFFE;::BBEEB::555;BEEBB555;;BEFFFEEEEFFE;555:::::AFFFFBBBEFFFFEEEEFFFFFFFFFFFFEEEFFFFEAAA0000000@..77@@00000@>>EEEFEEEFFFFFFFFFFFFFFFFFF00000881111ACA555FFFFFFEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF===EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEBBBF=======FFFFFFFFFEEEEEE@@@EBBBEEEEEEEEB@==<=77....72......:=??@@@@@?===@@@????======@?44433:
@SRR005406.89 FB9GE3J10F7ODR length=312
TATTGACCTTTAATATTGCGCGGAATATTAAAGTCAAAAGTGTATTCTAAATTAAACCATTCTTTCGCTTTATTAGCAGGTACATTCGTAGGCAATGAAAAAATCATTTTGTACATTTGCGCATATGCTTTTTTAAACTTCCTAGCTTTTGCTTGTGCGAGGTTTCTAGGATTTTGCATTTTAAATTCTAGCGAAATCCTGAAGCGTTATTACTAAAACTTTCATCGTTTGCATTATAAGTCATAGACATTTGATAGATTAATCGTTCTAATCGGTCTAACAGTATTTTCTTGTGTTGTATCCGAACTTAGG
+SRR005406.89 FB9GE3J10F7ODR length=312
DDDDDDDDDDDDDDDDDDEEEDDCCCBDDDDD@@@5555@BDDDDDDD@@@DDDDDDDDDDDDDDDDDDDDDBBBDDDDDDDDDDDDDDDDDDDDDDBGBBBBDDDCCCCDDDDDDDDDDDDDDDDDDBDDDDDDDDD??DDDDDDDDDDDDDDDDDDDDDDDDDDDDBB@1111@A@1111::D55=BDDDDDDB999DDDDD>999>DDDDDDDCBB777CCCCCCCCDFFFFFFFDCCCCCC?777::==>?>?>====>??:::>777=?=====::9//...../,0:9:::=:7777::::::=77
@SRR005406.90 FB9GE3J10GC3M6 length=321
TATTGACTTTGGCTCGTAAAGAATTTTATCGTGAAAAGTTTGTTTATTCATGGGGCGCTTTAACGGTAGATAGTATTTTGTTTGGCTGCTTGTTTATCGGTTATGCGGTTGCTGGCTATTACGCCGCACGACCAGCTGGTGGCAATCAAGTTATCAATCACTTTTTGTTGTTTCCGTCAGATGATGTTTGGTTTAACGGATTGATTGGATTAAGTATTTCCTTGATTGGTTTATTCTTTTTGTATCAATATTTAGCCGAAACAACTGTTACTTTAGGTGAGGGATTTGAGGAAGCGCGGTTGACACGCTTTTTGGTAAAAA
+SRR005406.90 FB9GE3J10GC3M6 length=321
DDDDDDDCCCDCCCDDDCCCC@@111180@@CC1116CDCDDDDDDAAACDDDDA@9C666@@D8868@DDDDDD@@@@A777AAACDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCCCCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBBB@<<<<<@AADDDDDDDDDDFDD??????????????????????????777:???::33337=???????????????????777:??==::5???77
@SRR005406.91 FB9GE3J10GCLRU length=287
TATTGACTTTTATCTACTTGTTCATCTTTGGCAGTTAAAATCAAAATAGGCGTGTCAATTTTTTCTCGACGAAGTGCCTTGGTAATTTCTAAGCCATCCATACCAGGAAGCATTACATCTAAAATTATAAAATCATATTGATTAGACAAAGCTAATTCGAAGCCGTTTTTACCATCTTCAGAAGTAGTCACCTGATAGCCTTTCTTTTTCCAAATTAAAGGTTAACAAAGTTAAATCGATGGTTCATCATCGACGACAAGTACTTTTTCATTACATACTCCTTCAAG
+SRR005406.91 FB9GE3J10GCLRU length=287
CCCCCCCCCCCCCCCCCCEEEDDEEEFEGGGGGGIIHHHGGGGIGCC>CCCBFBA<<<333333<-BCCBCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC::6666CCCCCCCCCCCCCAA555@@@9997<>?<:<<7/////77:>AA:>>>>>>>::::CCCAAAA=66//////-----//666990027877<>=:::=:7777::?@@@???@@@@@?777::@:111177=
@SRR005406.94 FB9GE3J10GDHEM length=311
TATTGACTCGGTTTTTTAATTGACTGATGTTTGGTCTTTCGTTGCCGAACGAACGTTAGTCATTTGTTTAGCTTTTGTGATGTTCACAGTTAAATCGTTGTCGCGGTTGTTTTCCCCAACAATCATTCCTTCGTAAACTTCTGTCGTTGGTTCAACGAAAACTGTACCACGTTCTTCAATACTCATGATTGAGTAAGTCGTTGCTTTACCAGTATCGATTGAAACTAGTGCACCTTGATGACGGCCACCATCGTTCCTTGAATCATTGGTAAGTATTGATCGAAGGTGTGGTTCATAATACCATAACCACG
+SRR005406.94 FB9GE3J10GDHEM length=311
CCCCCCCCD==444444BB00BBEDDDDEEDD876@@CD=622@B=====BDDB@===@BAA555A222B@AAACAA=@ACCCCCCCCCCCCCCCCCCCCCCCCCBBA@3/334444==9DCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC>>>444>>BCCCCCCCCCCC@@<999<:11..16<::1111::<<:44466661..36::::6666::<:611111:<66338879334....
@SRR005406.95 FB9GE3J10F8SXK length=300
TATTGACGAAGTGACGATTGCTTTAAGATAGTCAGACGCAGAGTCACAAGGAATAAATGTCGGCTTTTCTCCATCATGCCGGATGGGGCACAATGGTTAATTGCTCTGGTTGAGTGCCTAATGTTTGGAAGAGTCGTGTAATTTCTTTACTTGAACGGTAACTGTTTAATAATTGATAGGTTCCAACAGAACGGCTGGTTTCGTTAACCAATAAATCATGAGCTTCAGAAAATTCAATGGCTGTATTAAAAATGGCTTGATTTTCATCACCAGCTAAAGTAAAACTAGCTTTAGGGAAAG
+SRR005406.95 FB9GE3J10F8SXK length=300
DDDDDDDDDDDDDDDDDDGGIIIIIEGGEEFEEEEDEEEEEEFEEDDDDDDDDB9::DDDDDDDDDDDB599DDDDDD5655DB5000@ABA@>>?>>BBBBDDDDDDDDDDDDDDDDDDDDDDDDBBBBDDDDDDDDDDDDDDDDDDDDDDBBBDDDDDDDDDDDDDDDDDDDDDDDDDBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCCCCCCCCCCB>>>>>>>@AA????777.......45558855.11166:::<<788511184....57///.../.......
@SRR005406.96 FB9GE3J10GFJ2M length=287
TATTGACTAGAAATTGAACAAACGAAAGCAATGCTAAAAAATACAGTATATCTTAGCGTTAGATAATGCAGGCGCGTGGCTGGAAAAAGAATACTTGAACGAATTAATGCCGCAGACGATGCTGACGGCGGAGGAATGGATTGAGCGGATCAATGCCGTGACTATTCCAGAAATCCAAGAAGTAGCCAAACGCTTGGAACTTCAAGCGATCTTCTTTTTGGAAGGAGAAACAGAAAATGAATTAAAAAGACTATGCACAAATTAAAGAAACATTGTATACAGAAACA
+SRR005406.96 FB9GE3J10GFJ2M length=287
CCCCCCCCCCCCCCAAAAB===BC666=@CEEEDD:9::::B0DDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDDDBB;;/////5,,;;@A@577ACCCCCCC@AACCAAACCCCCCCCCCCCC766ACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC666CCCCCCCCCCCC@@665;;BBBBBBBC;;;;:?BAA>>911/////////====:@@@<<44446///////...4,88:::::<<<<<<<<<<<<<:66666::6666666:5
@SRR005406.97 FB9GE3J10F5I1E length=313
TATTGACACTTCCTAAAAATAACCAATTGGATCAAAAATTTTTAAAAAGTAACCATTTACACAGTAGCAAGGTGAAGCTACCGTTAAACGAGGCATTCAAAAAAGAAACTAGAAGCCAAATTAGCAACTTTGAGTTTTCCAGAGGGGAAACCAAGCAAAAATGCGAGTATCCGTCGAGGCAATGGCACTTTTGAAATTGTTCCTGAAGAACAAGGCACAGTAGTGGACACACAGCGCTTAAATCAGCAGATTATTGCGGATGTTGAAGCGGGAAAAGGCAACTATCAATACAATGCCAAAGATTTTTATAAAG
+SRR005406.97 FB9GE3J10F5I1E length=313
DDDDDDDDDDDB@6/////?,,55AAADDDDDDDDDDD::644,,,,,7,,,55BDDDBBBBDDDDDDDDDDDDDDDDDDDDDDDDBB99799DDDDD;;;;?DDDDDDDDBBBBBBDDDDDDDDDDDDDDD>>>>D5555DDD88669BDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBBBB<<>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>9666:
@SRR005406.98 FB9GE3J10GBCDF length=326
TATTGACGGAAATCCTTTTTCTTTCCACAGCATGTATTTGTATTGGTAAACTTCAAAAATATCCAAGTATGATTCAATCAATGGATCAAGAGTAATAGTGTATAAATCAGACTTGCGCATAATTTCTAAAATTCGCGTTTTTTCGTGATTAACTTTTTCATCAATAATCGCTTTGCGTTGCGCTTTTGTGGTCATTTTTTATACACCCCCCTTTTATTTTTAAAATTTTTGACCTAACGACACGCGTGACTGCCCCCTACCCTATCCCCCGACAAAAAATTTGAATCAGATTTGATAGGGGGGCTTCTATTTTTTAAAATAAGATG
+SRR005406.98 FB9GE3J10GBCDF length=326
DDDDDDDDDBBBDDD::::;>---BBDDDDDDDEDEEEEGGGGFFDDDDDDBBB====88->?BBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD777777DD5DDDDDDD@@@@@DDDDDDDDDDDDDBBBDDDDDDDDDDDDDDDDDDDD999999D6DDD:@@@CCDDDDD?>999CC99-----=@AAAAACCCCCCCC>>>>>:::<<<<==---::::<<<666.68;;;;<<<>::::>>><<<::::;;;;86=<;1./..........+//5455
@SRR005406.99 FB9GE3J10F85M5 length=311
TATTGACGTCTGGCCTAAACAAATGTTGCTCACTTCCATTCGCCGTGGCGAATCGGAAATTTTAACACATGGTGATACTGTTATGCATGTTGGCGATGTGCTCATTATTTTGACCGATGAAAAACTCGCTTACCAAGTCAAAAAAGAGATTTATCAAAAAACTTTACCGAATGATTTAGTGAATTAAAGAAAGCCGCTGAACCTGAGTTCAGCAGCTTTTCTTTTTTTCTTATGACTTGTTTTTTAATTTTTTTGAATTGTTTTTGTACCGTTTTAGATTGATTAGCGTTTTCATTTGTGCTATTATATCC
+SRR005406.99 FB9GE3J10F85M5 length=311
DDDDDDDDDDDDDDDD??@B666BBBDDDDDDD@@>>EDEDEEEFDDDDDDDDDDD999DDBBBBBBDDDDDDDDDDDDDDDDDDDDDBBBDDDDDDDDDDDDDDD>7755@@BBBDB@58888>DDDDDBBBDDDDDDBBBBBBD?DDDDDDDD<<6;;;;66C,,BCAAAA;;//////55+++++++558888::<:66-6:==<<<<<::6666:=666:==<:::<>>><666:<===::11
@SRR005406.100 FB9GE3J10F72OQ length=310
TATTGACTTTACTCTTACCAAATGGTGAGAATACAATTGCGGTTATGGGTGGGACAACAATGGCCATGGTGGCCGAAAATATGGGATCACTAGAAACTGAAAAACGTCATAATTTGTTTGTTCCAGCCAGAGGAGGGATTGGTGAAGCAGTTTCTGTCCAAGCCAATTCAATTAGTGCTGTAATGGCCAACAAAACGGGTGGTAACTACCGGGCGTTATATGTCCCAGAACAATTGAGTCGTGAAACGTATAATAGTTTATTACAAGAACCCTCGATTCAAGAAGTTCTTACGTTAATTAGTCATGCCAA
+SRR005406.100 FB9GE3J10F72OQ length=310
FFFFFFFFFFEEEEEFFEEEEEIEEFFFFFEIEIEEEEIEFHFEIEEEEFBBBEBBBEEEEFFFFFEEEEFFE@A77;;;>EFFFFFFFFFFFBBBGFFFFFFFFEEEFEEEFFFEBBBBBBEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEB=;;;BEEEEEEEEFFGGFFFFGG?@@@@@@@@@@@@@@@@@@@@@??777??@@@@@@@@@@@@@@@@@@@@@@@???@@@@@@4444
@SRR005406.101 FB9GE3J10GDRX9 length=278
TATTGACTTGAAGCACACAATGTTTACTTCGTGAAACCGAATGAATTACAAAAACTAGAAGATGCAGTGATGAATGAAGGCAAATACGCAGTAAATCCAGCGATTGTCGGTAACTCTGCAGAAAAAATTGCTGAATTAGCAGGAATTAGCGTACCAAAAGGCACAAAAATTTTAGTCGCTGAATTAGAAGGTGCAGGTCCAGAATATCCATTATCAAGAGAAAAATTATCGCCAGTTTTAGCAATGATGAAATCAAACAATGCAGAGCATGCTTTTAG
+SRR005406.101 FB9GE3J10GDRX9 length=278
DDDDDDDCCCCCDDDDDDGGGEEFFFEDDDDDDAAADDDDDCDCCCCB@55555@C:CCDDDDDDDDDDDDDDDDCCCCCD;;:DDDDDDDDAAADDDDDDDDDDDDDDDDDDDDDDDDDD;;;;;;DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCAA/////1111:DBDDDDCCCCCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD@?88888880BDDDDDDDDDDDDDDDD???????????:7667=??===???===???==
@SRR005406.102 FB9GE3J10GEJFW length=337
TATTGACTTATTTATGTAATTTTTAATTAATAAGCGTATTTTAGCATTTGAAAAGAGAAGTTGTACATAATATGTGAATAAAAAGATTTGTTTCTTATTTTCTAGAGTGATAGGGCGATATAAAAAAGGTTGCTATTTTTTCGTTCAAAGTGAACAAAGAATCGTTTGTTATTTAGTTGGGGTAACTAATGATTCTTGTTATAAAAAGCGCTTACAATTCGTGTGATGAGAGTAGTACGCATGTTTGTGCAAAAGTGACAAAAAAGAGAAGGTAGGGTGTTTTAATAGAAAAAAATTTTAATAAAAAGGAGAGTTTGTCGTGGAGAAAAATGTGTCT
+SRR005406.102 FB9GE3J10GEJFW length=337
EEEEEEEEEEEEEEEB;::<@A>36//////6***<<:11///////17788?A:::444=>>>CCAAAC>?????:444ACCCCCA???A===:3<<<996///////*//;;9;<<<33387<99;;9//////,****-*--6-,,,----,-45777::555:5555:::;::::::555:;;;;:::;;;;:::77755-------47777
@SRR005406.104 FB9GE3J10GAANJ length=331
TATTGACTGCCTTTAACCATAATGCAATTGATAGCAAACATTTTGAAAAAGTCCTAGAAATTTCTTCATCAACCTTTACGCGAAAAATTGGACAATTAAACCAATGGCTCCAAAAATATCAGATTGAAATCAATTTAAAACGTACCAACGTGTTGGTGGGCAAAGAAAAAGATATCCGGATTTTCTTTATGATGCTTTTTTGGAACAATTACTCTGAAGGGGATTGGCCGTTGCAGACGATTAACTAAAAAAGAGTCCATAGTCTCTTTCGAACGTTTAAAACNTTCTGTTTCCTTCAATACAACACAAGTATTTTAACAAAAGCTTGTTA
+SRR005406.104 FB9GE3J10GAANJ length=331
DDDDDDDDDDDDDDDD>>>DDFDFEEEEGGGEFEEEDDDD@@@@@55555BDDDDDDDDDBBBDDDDDDDDDDDDDDDBBBDDDDDDDDDDDDDD??>>BDDDDDDDDDDDDDDDDDDDDDDDDDD>>>DDDDDDDBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBB6666>BBD<<666555DDDDDDD<<<>>>>99;9CCCC@@@AA==00007.......5-::::<<==<<<<<::333336==<<<<<;!666./...55....5;;::7:77775/......./3531555<3333
@SRR005406.105 FB9GE3J10F8CXB length=288
TATTGACAAAACGATATAATCAAACGTCTTACCAGCAAAGTATTCGACCCAATCATTTTCATCAATATTGCCATAAAAGGCATCTGTTGAAAATTGACTGACATGATCATAAAGTTCTTTGTCTAATTCAACAATTGAGACCTGGCACTTTTTTTTCTTCCATCAAATAGCTAGTCATTCGCCCATTACCTGGACCAAATTCCAAGACATCACTATTTTCTTTGATTTGTGCTACGATTTTCCCAACACTGGTACTCTCGTCTGTTTCCATTTCAAAATCATACTTCA
+SRR005406.105 FB9GE3J10F8CXB length=288
FEEEFFFFFFFDDAAAFFFEECCCFEEEEFHFFEGGGGIIGGGGIFFFFFFFFFFAAAAFFFFFFFFFFFFFFFAAAAEEFFFFFFFFEDDEEFFFFFFFFFFFFFFFFFFFFFFFFEEEFFFFFFFFFFFFFFFFFFFFFFFFFFA=0000000061FFFFFFFFEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEDDDDFFFFFFFFFFDD=:::EEEEEEEEEEEEEEEEBB7777777?:;@@@@@@@@@@@@@???@@@@@@@77773111:==667::@@
@SRR005406.106 FB9GE3J10GGHX8 length=313
TATTGACGCTGTCGAGCCATCTCCTAAAATTTACTTTTTGTCAAAAGTTTACTTTTGTTCAATCGCTTGTAAAAAAGACTTTTCGTAACATGTTCGTTGCCGGTAATTTCACGGCGATGATTTGGGCTTAAATAACCCACCATGGCTTTAGGAACAAAATGCGCTTGTTTTGACTCTTTATACTGAAGTGCATAAGTATCTGCTAAAACAGTGTAATCTAAATCACCATTATCAAAAAGATTGGCTCCTGTGCCAATTTCTTTCACTACTTGAACATCAATTTCATTCAATTTTACGTGTTCTTTATCCCAAA
+SRR005406.106 FB9GE3J10GGHX8 length=313
==B====@@AACCBBBCBBBAA@=50000111-644444@1>00006111-@???=A::AACCCCCCBB=76<<62A+<0000;;4;;@@BBCCCCCCCCCCCCAA@@@AA@BA@@DDAA788BAAAACCCCCBBBB@<99B@@@@@@@B6666@CCCCCCCCCCCCCCCCCCCCCCCCCGCCCCCCCCCCCCCCCCCCCCCC;5555?BCCCCCCCCCCCCCCBBBCCCCCC33344B4CC>>><<<<<<<<<<<:::<<<<<<<<<<<<<<<<<<<<<:::<<<6666<<<<<<<8<<<<<<<<<<::111
@SRR005406.107 FB9GE3J10F9LNG length=283
TATTGACTTTCTTCACGTAGGATAGCATCTGAATCACGGACGATTTGTAATTTATCTTCTGTAATTTCACCAAGCACACGAATACCTAATCCTGGTCCTGGGAATGGTTGGCGCCAAACGATTGCATCAGGCATGCCAAGTTCAGTTCCTAAGGCACGAACTTCGTCTTTGAATAATGTATTTAAAGGTTCAATTAATTCAAATTGCATGTCTTCAGGAAGACCACCAACGTTGTGATGTGATTTAATTGTTTGCGCGGTTTCTGTACCAGATTCGATGACGT
+SRR005406.107 FB9GE3J10F9LNG length=283
DDDDDDDDDDCCCCDDDDDDDDDEEEEEEEEEEEDEDFFDDDDDDCA;;;DDDDBCCDDDA9::AADDDDDDDDDDDDDDCCAAAADDCCA>>>>>77833377@CDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCCDDDDDDDDDDDDD???CCCCDDDCCCCDDDDDDDDDDDDDDDDDDDBBAAAADDD@@88811171....
@SRR005406.109 FB9GE3J10F7503 length=283
TATTGACATCGAAGCAGCAGATAATGAAGTACAAGTACGCCGCTTTGAACGTGAAGGCGTAGAGAAATGTATTGTAAGTTTTGATAAATCAACAGAAACATTTGAATTAACAGAATCTGATACGCACCAAAGCTATCAATTCGATAACATCGATATTGTAGCAATGGAAATTTACGACTTAATTCAATAATTAATCGTCCTACATTTTAATAAGGGAGTGGAGTAGAAGCACCAAAGCTTCTGGTTCACTCTCTTCTCGTATTATCCAGTCAAGTTGTAGCAA
+SRR005406.109 FB9GE3J10F7503 length=283
GGGGFFFFFFFFFFFFFFHHHHHGGHHHHHIHHHHHGHGGIIIIIFIIIFFFFFFFFFFFFFFFGGGFFFFFFFFFFFFFFFFFGCCCFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBFFFFFFFFFFCCCCGGFFFFFFEEFGGBEFEEEEEEEEEEEEFBGGGGGGIAAAAA@@@AAAAAAAAA@@@@@@A@@@@@@@:::?:33
@SRR005406.110 FB9GE3J10F6S8A length=53
TACCATTCGCCTCAATCGTGCTACCGCCATCGCCCGCCGCACTCTCGCTGCTA
+SRR005406.110 FB9GE3J10F6S8A length=53
FFFGCCCGFFFFFFFFGGHHHHHCCCGFHHCC999=GIHHCCCHFFFFFFFFF
@SRR005406.111 FB9GE3J10GCII7 length=285
TATTGACTTCGGGTCTACGACTACATACTCATTCGCCCTATTCAGACTCGCTTTCGCTGCGGCTCCGTCTCTTCGACTTAACCTCGCATGCAATCGTAACTCGCCGGTTCATTCTACAAAAGGCACGCCATCACTCATTAACGAGCTTTGACTTGTTGTAGGCACACGGTTTCAGGATCTATTTCACTCCCCTTCGGGTNCTTTTCACCTTTCCCTCACGGTACTGGTTCACTATCGGTCACTAGGGAGTATTTAGCCTTGGCGGGATCGGTCCCCGNGGATTCC
+SRR005406.111 FB9GE3J10GCII7 length=285
CCCCCCCCCCCCCCCCCCIIIIIIIIIIHHIFFFEEEEGGGGGGICCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@@@CCBB411@@@8////11-///0!888==?CCCCCCC;;759>CCCCCCCCCCCC>999>CCCCC@@BC:61/116::64....4440404....3.....!..4....
@SRR005406.112 FB9GE3J10F6MK7 length=293
TATTGACAATGGTGGTACCGTTTGGTGGTACAAGCAATTATTTTGGGACAAATCCAATCGCTTTTGCAGCACCTAGAGCAGGTCATGAACCAGTCGTGTTTGATATGGCTACGACAGTACAGGCGTGGGGGAAAATTTTAGATGCACGTTCAAGAGATGTTGAAATTCCCGACACGTGGGCAGTAGACGAAAAAGGCCAGCCAACGACTGATCCTTATGAAGTACGAGGTTTATTGCCGATTTCAGGACCAAAAGGATATGGACTAATGATGATGGTCGATGTCTTAGTCCGG
+SRR005406.112 FB9GE3J10F6MK7 length=293
FFFFFFFEEEFFFFFFFFHIIGGGGHIGHHHHHHHHHEEE6666E99;A888FFFFFFFFFEEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGEFEEBBBAEEEEEEEEE@@@EE??:::??@@==?@@@@@@@@:::=@@@@@@@@@@@@=7777770....
@SRR005406.113 FB9GE3J10GATOR length=304
TATTGACGAATCGTCTTTATGATATCGCAGAAGAGCGTTTGGAACACACGTACAACGAAACAGCGCGCTTTGCCTTTGCGCTTCATTTACAAAGTACGATTGAACGTGTCAAAGAAGGTCATGTGATTGTCCATCCTGATTTAAATAATGTCCGTAAAAACATGAAAAAAGAATTTCAAGTAGCCTTAGATTTATCTTCTATTATTGAAGAAGAGAACAACATAGAGATTTCCTTTCGATGAAATTGGCTTTATTAGTATTGTTTTTANCTATTAATGTCGGTAAAGAAGAAAGAACTCCAAAG
+SRR005406.113 FB9GE3J10GATOR length=304
DDDDDDDDDDDDDDDDDDEEFFFFFHIGHIIIIIIIIIIIHHHHIDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBBDD>>>>>D8BB7777788++BBDDDDDDDDDDDDDDDDDDDDB>>>DB>>>>DDDDDDDDDDDCCCCCCCCCA::444::<444:A???@CC=777:=::;;==:777:>>>>>7!77====::1111==776955:55....//.....:
@SRR005406.114 FB9GE3J10GEY7G length=329
TATTGACCGTTGTTTCTTCCAAATAATATCAGTATGAACAATGTAAAAATCAGCTTCTTCTATTATTTCATGTAGATCTAAAAAAAATTGTTTTAACTTTTCAATTGAAAAAACTTCATTATCTAAAAAAGTCTTATAACAAATATTTTCATCTGTTTGATTTTTTGGATCTATCAACTTTTTGTATTCAACAAAATGCATAGCTTTTTTTCCATCAATTGAATATTTAGTCCGAAATTGTTCCCATTTTTTCTCGAATTCTGTCTCGTAATATGTCTTTTCAAAAGTTAAACTCGTTATCGAATATTCTTCAAAAATTAAAATCGCTT
+SRR005406.114 FB9GE3J10GEY7G length=329
DDDDDDDDDDC@666@==@@@@@@AADDDDDDEEEFFDDBBCD@55555@@DDDDDDDDDDDDDD;;;DDDDDHDDH>8////////>>HBBBBFCA77738>CFCA///55:CCCCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD@@@@@@DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD>>>>>>>DDDDDDDDDDDDDDDDDDDDDDDDDDDD@44444711111172???????????????????=::::?7773334:??<<>????????????=9;;;956.....6600009;>?77
@SRR005406.115 FB9GE3J10F5HWQ length=294
TATTGACGCTTAGAACGCGACAAAATTGAAAATGAATATCAAGAGCTATTGATATTCATTGCGGACTTAGAGGACATTTTAGCCCGCCCAGAACGCGTCATTGAAATCATTAAAACAGAGTTAAATGACGTTCGCACAAAATTTGGTGATGCACGACGCACAGAATTATTAGTAGGTGAAGTCTTAAGTCTTGAAGATGAAGATTTAATCGAAGAAGAAGAAGTCGTGATTACGTTAACCAATAACGGCTACATTAAGCGGATGGCAAACTCCGAATTCCGGGCGCAACGCCGC
+SRR005406.115 FB9GE3J10F5HWQ length=294
FFFFFFFFFFFFFFFFFFIIIGGGGHHHHIIHHHHIIIIIIIIIIFFFFFFFFFFFFFFFFGGGFGCCCFFGGGGG7777=GFFFF>>?FFFFFFFFFFFFFFFFFFFF9962227AFFF7799=FFFFGGGGFFFG====GGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGFFFFFFFFFFIIIIIIIIIIIIIIIIIIGGGGGGIIIIIAAAAAAAA8888@@@@AA@@A@@@@@@@@====??:::==??@@@@@73
@SRR005406.116 FB9GE3J10GCDCC length=55
TATTGACTACCAATCAGATGATTGTTCAAAAAGCACTTTCAGGAAAAAATTTAAG
+SRR005406.116 FB9GE3J10GCDCC length=55
CAAACCCCCAAAAAACCCEEEEB877B??@@?DDDEFGGBBBE::??88CCC2-B
@SRR005406.117 FB9GE3J10GGFWL length=316
TATTGACACAATCATTTCTGGTAGTAAATTTAATGTTTCACAGGCAATTTGCGTCGTAACGGTTGCCATCCCTTGACCGATACAAGCAGCACTTGTGCGGACATGTATTTTTCCTTCTTCAACAGAAATAATACAACGCCCTGTATCAGGTAGCCCCACACCCACGCCACTATTTTTAAAGAAACTAGAAATTCCAGCAACTTCCGCTTGTTCATAGACGTCTTTAACCGCTAACAAGGCTTCTTTTAACGCCGCATTTTTCGAGACCAATTGTCCATTCGGTAAAGTATCTCCTGGGGCGACGGCATTTTTAAAG
+SRR005406.117 FB9GE3J10GGFWL length=316
EEEEEEEEEEEEEEAAAEEEEEEEEEEEEEEAAACEEEEEEECCCDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAADDDDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEDDDEAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEDDDDDDDDDDDDDDDDDDDDDDDDDDD==77@@@@@@@@@@@@@@@@@@@@@@@??=:::@???@@@@@@@@@@@@:::5545=;@@@???@@@@@@555
@SRR005406.118 FB9GE3J10GBR0C length=80
TATTGACTTCTATTAAAATATGCGAATTAGTATATTACACGTTTTCAATGTGTTTCATTGTTGATTAATTAGAATTTTAG
+SRR005406.118 FB9GE3J10GBR0C length=80
CCCCCCCCCCCCBB7774=4=>DB>@@@=CCDFFGCCDDDECCC@===CCCCCCCCCCCCCCCCBBCC===B@@555556
@SRR005406.119 FB9GE3J10GF9S3 length=305
TATTGACGATTCTTTTTTACCTATCTATCCTCTGGTAGCTATGGTAGCATATTTTGATTTTCTCGAAAAGGTGCAGCCATTTTTCTTTTCGTTTTAAAAGTATTTGAATTTTCAGACAATAAATGCTATAGTCTTTTTATATTTTAAAATTTCAGAAAAGGAGCCCTATTATCTTGTCTACCTCACTCACTATTCGCTTAGTTGCCGAAGCAGATTGGCCCGCATTACATGCCTTGGACCAAATCATTTGGAACAAAAAAGATACCCCTGCCGAGATACAACCACTCTCGCTTGCGGCATATACG
+SRR005406.119 FB9GE3J10GF9S3 length=305
CCCCCCCCCCCC<<<<<:C77+==DDEDEEDDEEBBBEDEDDDEDCCCCCC????<<=CCCA8?@<<<AAA><??>>CCCBA@@@CA@@@CCCCCCCCCCCCCCCCCCCCBAA;;/////7-:////////---177////116??CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC???ACCCCCCCCC9988333<>>>>CC8833111<75---44777,,,,,,4*--//2276::::::1115:5550677542------24422777
@SRR005406.120 FB9GE3J10F8VQI length=338
TATTGACTGCTAAAAGATAACTCTTAGCTACTGGCTGTTGACACTTTCGACAACGAAAGCGCTGCAGCAAAATCGAAACAACTGGAATTAATTCATAGAGATGTAGAGGCTGGTGGCAACCTTGACAGTGGGAAGGGGGCCACCACAAAGAACGCCCTACTGGTAAGCGCTCCGCCACTAAGCATAAAAAAGAACCGAAACAGGCACCAATCAAAAAGAGACTTAAGAAAAACATAGGTTACCTCCTTAAAAAATAAACTACGCTTTTTTTAAACTTTTTCGTTTGACTAGACAAATCTTTTTTTGTTAGGAATAAATAAAAGAAAACAAGAAATAGG
+SRR005406.120 FB9GE3J10F8VQI length=338
EDDDFFFFFFE====AAABFFFFFFFGGGIIIIIIIGGGGGGGGGFFFFFFFFFF===AADFFFFFFF====DDFFFED;;=DFFFFAAAAAAAFFFFFFFFFFFFFFFFFFFFFFF====AAFFFFFFAAAEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFD======EFFFFFFFFFFFFFFFFFFFFFFFFGGEEEEEEEE?77774;EE??>A?>>>>>9........0+++6<><96..........;33322=@>==@@@???@@?=:76.......0++0....0...0....0----0-26;<600..
@SRR005406.121 FB9GE3J10GAMWB length=273
TATTGACCGGGCGCACCCAACTTGGTATCCTGCAGGCGAAGAGGAAAGCATTGTTCGCGAGATGATTGACATGTTGCTAACAACTGGCTCGGTCAGCGTGAAAAAATTCCGTGAAGCAACTGCCATTATGATGAGTTGTAAGCGATCCATCAAAGCCAATCATTACCTCAACGAGCAACAAGCACGCGTGCTATTAAAAGATTTAGCCTTGTGCGAAAATCCGTTTAATTGTCCGCATGGACGTCCGGTGCTGATTCATTTTACGAATTCAGA
+SRR005406.121 FB9GE3J10GAMWB length=273
EEEEFFFFFFEEEEFFFFB:;::::BEFFEEEEIEEEEFIHFFFHFFFFFFFBBBBEFFFFFFFFFFFFFFFFFFFFFFFEBBBEFFFFFFFFFFFFFFFIIIIIIGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEEFFFFBBBEFFFFFFFFFEB===EEFEEEEEEFFFFFFGFEEEEFFGGF@@@@@@@@@:::@7777?@@@@@@@:77
@SRR005406.122 FB9GE3J10F8GN7 length=194
ACGCGATTTCCAGCACCGACGGCTGGACAAAGACGCCGCGAAGGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGGTTCCAACGATGCAGGCATGGCCACCAGCATCTGCATGAGCTTGACAAACGCGCCAAAGTGCGGCGTCGTCCGCAGATTGAACTTGAGCCGCTCCGCCACCTGGACTGGATCCGA
+SRR005406.122 FB9GE3J10F8GN7 length=194
FFFFGG>>>CCFFFC===HGGGFHHHHHDDDHIHHHHHIHHIHHHFFFCCCCFFFFGGGGGGGGGGGFFFFFFFGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF@??GFFFGG???GFFGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR005406.123 FB9GE3J10GELDB length=296
TATTGACAGAAAAATTAAGCTCATTTTAATCGTGAGCGCGTACCAGAACGGGTTGTTCATGCCAAAGGTGCTGGTGCTCATGGGATTTTCAAGGTGAGCCAATCAATGGCACAATATACTAAAGCCGATTTTTTATCTGAAGTTGGCAAAGAAACACCTTTATTCGCTCGTTTTTCAACTGTAGCTGGAGAGTTAGGTTCATCAGATACATTGCGTGATCCTCGCGGTTTTGCGCTTAAATTCTATACAGACGAAGGAAATTACGACTTAGTTGGCAATAATACGCCCATTTTTTT
+SRR005406.123 FB9GE3J10GELDB length=296
EEEEEEEEEEEEEE==66CEEEEEEEEAAACCGGGGGGGGIIIIIEEEEEEEEEDDDEEEEEEEEEEEEEEEEEEEEEEEEAAAAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE@@@@@@EEEEEEEEEEEEEEEEEEEEEDDDEEEEEEEEEEEEDDDDDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEDDDDDDDDDDDDDDDDDBB====DDDDDD@@@@@@@===????@@@@@@@@@@@@@@@@@@@?:::::?=766.......
@SRR005406.124 FB9GE3J10F7NBJ length=290
TATTGACGTGAGGACATTGAAGCATTTGTCGAAATTCATATTGAACAAGGCAATATTTTAGAGAACGAAAAGCTCCAAGTCGGTGTTGTTCATAGTATTGTAGGGCAACGTCGCTACACGGTTAACTTAAAAGGGCAAGCCAATCATGCAGGCACTACGCCAATGAGTTACCGTCATGATGCGGTATATGGCTTTGCTAAAATTTGTGCAGAAGCCATTGATCGTGCGAACGAAATTGGGGATCCGTTAGTTTTAACATTCGGCAAAGTCATTCCGAAACCCAATACAGT
+SRR005406.124 FB9GE3J10F7NBJ length=290
DDDDDDDDDDDDDDDDDDDDDDFDDDAAADDDDDDDDDEDDDDDDDDDDDDDDDDCCCCDDDDDDDDCCCAAACDDDDDDDDDDDDDAAACCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCA;999AAC@??BDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBB@<<73111:=?::::::==?===777???>77111777311==?????:
@SRR005406.125 FB9GE3J10F62T5 length=246
TATTGACAGAACAGGCACATGAATTGGTTTCTAACATGTATTACGACCAAGAAATTATCTTGACAGAAGATAATCACGAAGCAACAGAGTTTATCATTTAAAACAACGAAAGAGGAGAGCTTTATGGGAACACGAACAGCAATTTTAAAGAACAAGCAGACGGAACGTATCAAGGCATATATTGTCACTGGGACGGTTATATAGAGGGCGTAGGCGCTGTTTTATATGAACATTACCAAGACCTAG
+SRR005406.125 FB9GE3J10F62T5 length=246
AAAAAAAAAAAAAAA@@?ABB??????AA??6::AABB?A?????<<>>==?=:22272==2227777=22=>????8==>8;3.....,.....87:877;777........2.,,977::;>?>6666==<90000026:==88666966..----3**--658883-----*83336-,,,,,,,,*2,,,,,,,,,,,,,,,,,,,1
@SRR005406.126 FB9GE3J10GF8K4 length=314
TATTGACTAAACCTAGTCCTGCGCCTCCTCGGTTTGTTTGACGGGCAGTATCTAATCGGAAAAATTGTTCAAAAATTCGGGCTAATTTTTCTGGTGGAACAGTAGGGCCATGATTTGTAAAATAAATATTTACTCGTTGATTTTCATTATCAACTTTAGTGGAAAGAGAGATGGTTGTTCCTGCATAGCTGTAGTTAATGGCATTTTGAACTAAGTTATCAAAAACTCTTTGCATTTTATCGACATCAAGATGAATAGACAAAGCCTCAGTAAAATCTGTTTCAATAGTTAACTGTTTTTGTTTCAACATAAGG
+SRR005406.126 FB9GE3J10GF8K4 length=314
EEEEEEEEDDDEAAAAAEEEEEEEEEEEEABCAAEEEEEEEEFEGEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEDDDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<<;;;;996/.....6222;;;;713377
@SRR005406.127 FB9GE3J10GG48M length=301
TATTGACGTCAAAAATTAACCTGTTTTTTTCTAGCATCTGGCTTACCTCATAAAGAATTAGCGGCACAAATTGCCAGACAAGCCAACGTGTTAAATAGTGAAGAAGAATTTGCCGTAGTTTTTTGCGGCCATTGGGATTACCTTTTGAAGAAGCGGAATATTTTATGGAAGATTTCCGTCAAACAGGCGCAATTGATCGTTCAGTCTTATTTATGAACTTAGCGAATGATCCAGCCATTGAACGGATTGCAACGCCTAGAATGGCTTTGACAGCCGCTGAATATTTAGCTTATGAAAAGGG
+SRR005406.127 FB9GE3J10GG48M length=301
FFFFFFFFFFDDDDD@?0088@@0000000@1EEFFFFFGGGGGIFFEEEFFFFEEEDDDFEEEFFF===EEFFFFFEEEEEFFFFAAAEFFFFFFFFFFFFFFFFFFFFFFFAAA?6000000=?AAAACAA444?FFF786666BBFFFFFFFFFFFFAAAAEDB?B?FA4446667E888EFEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFGGGFFFGGGGGFFFFFFFGGF@@@@@@@@@===@@@@@@?::::@@@@@===@@@@?::777=@A><;96.......
@SRR005406.128 FB9GE3J10GGSU1 length=308
TATTGACGATACTTTAATAGAAGAAATAAAAAAAGACCAGTTCTTATGATGTCGGGTTACAAATGGCGATGAATTACTTAAGCTATCAATTACGTTCAAAGAAAGAGATTTTTACTTATTTAAAAGAGAAAGAAATTGTACCTGAAGATCGAGTAAAAATCGTTCAACGTTTAGAAGAGCTGCGGTTGTTGGATGATGCAATTTTTAGTGAAAGTTACGTACGTACAGCTATGCGAACCAGTGATAAGGGACCACGAAATGTGGCACAACAATTAAAGCAAAAAGGCATTAGTGAAGAAGATATTCAG
+SRR005406.128 FB9GE3J10GGSU1 length=308
FFFFFFFFFFFFFFFFFGGIIIIIIIIFFFFFFFIIIIIIIIIGGGGFFFFFG====?FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFG???FFFFEEDDDFG4499996666GGFFFFFGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBBFFFFFFFFFFIIIIIIGGGIIIIIIIIIIGGGGGGGGGG@@@@A===AAAAAAA@@@AAAA@@===@@@@@@??????@@@@@@@?===?@@@@===???@@
@SRR005406.129 FB9GE3J10F7UPT length=57
TATTGACTAAGCATAAACTTTCTATTTTCATTTGCTCATGAATAAAAATAACTTTCG
+SRR005406.129 FB9GE3J10F7UPT length=57
????@?=9778::20002000:4<..2299@@@===>A?::99111112))8::662
@SRR005406.130 FB9GE3J10F9NEN length=309
TATTGACGTATATAGTGAAATTTTAAAACGTTCTGCTAAAAAGCTAAAAGATAATCGCTTCGCAGTGGTCACCATTTCTGATGTCAGAGATAAAAAAGGCTTTTATCAAGATTTAACTGGTTTGACTAAGAGAGCATTTAGCACAGAAGGCTTATATTTCTACAATGACATGATTTTGTTAAACGCAGTTGGTTCGGGTTCGCTAAGAGCTAGACGTTTGATGAACAATAGAAAAGTAACCAGAATGCACCAAAATGTATTAGTCTTTTATAAAGGAAATCCGAAAAATATTAATCAACATTTCGTAAG
+SRR005406.130 FB9GE3J10F9NEN length=309
EEEFFFFFFFFFFFFFE555333311FFEB::;BFHE77000III@@@@ABEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEAAA===BBEEEEEFFFFFFFEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEEEEEEEEEEEEEEEEEEEBBAAEEEE@@@77777::@@@@>>@A=:111.0....<<777;=:711111?;@@>>???@@@:::=12110
@SRR005406.131 FB9GE3J10GCNVX length=313
TATTGACGTCTGTTTTGTCCTTTAGTAACGTGTCATACGGGATTTCTAACGCTGGATTCAATTCTGGTATTTTACCAGATTCAGCATAATAATAACGAACTTCTATTCCAAATACTTCAAGTAACAACGCAGCCATATTTGCTTCTAAAACGACTGTACGTGGTGACTTTTCAATAATCTTAGCAAAACGTTCTACGTTTGCTGGATAACCATTAAAGGTAATTTGTCGATTTCGGGTTTTCTAGTTCTAAACGAACCAAGTGCTGAACAAGATCTTCTTCACTGACAACCGCTATTTGGGCTGGATCTGGTT
+SRR005406.131 FB9GE3J10GCNVX length=313
DDDDDDDDDDDDDDDDB:FFEEEEDDDDFFFFGGGGGGIIGGGGGDDDDDDDDDDDDDDDDDDDDDDBB9999BDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBBBDDDDDDDDDDDDD>>>DDDDDDDDDDDDDDDDDDDDD>>>>DDDDDDDDDDDDDDDDD>>>>DDDDDDDDDDDDD>>>>DDDDDDDDDDDDDDDDDDDDDBBB<<<<=933/.===?6?7003399@@6666CBCC<:::<<>>>>>33336<====:::<666::=======:::6666:::6666:>>>>==<<<===3111
@SRR005406.132 FB9GE3J10F9LYA length=127
TATTGACAACAACCGTCCATGAACGGGTTGTCTGAATATGGCTACAATCAATAGATCTGTTTTTTCATGCGCGCCACACTCCCACCGCCACCGCCGTTTAGGCGACGCCTATTGAAAAAGGTAGGCA
+SRR005406.132 FB9GE3J10F9LYA length=127
AAA?@@A????????<<<<<:8......89<<>>??AAAAAAAAAAAAAAAAAAAAAA??887779:660....378.......4,874.
@SRR005406.133 FB9GE3J10F73XH length=315
TATTGACGACCCTTCTTTTCGGCTTTTTTATTAAATTCCTCGAATCGCTTCCATGCCTTTAATCGTGGTTGAGGCTGTTCGCAAACTTTGGTAAAATTTGTTTCTTCGCTTAATTGGACGATGGTCTTGTTCAATCAGATTATTCAGATACTTGATTGTTCGATGTTCTGTTGTTATATACAGTCCATTTTTCTGAAGGCACTCTTAATAGAGGGTGCTTTATCCGTTACTAGAACCTTTGGTTCTCCAAACTGGTTCTTCAGTCGTTTTAGAAAAGCATACGCAGCCTGTGTGTCGCGCTTTTTCCGTAACCAG
+SRR005406.133 FB9GE3J10F73XH length=315
EEEEEEEEEEEEBB;;;A@EEDE44====@//77DEEEEEEEDEEDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE777D@A6666@@EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEBBBBBEEEEEEEEEEEEEEEEEEEEEEEEDDDDDDDDDDDDDDDDDDDDDBBBDDDDD@@@@@:::==@@@@@@???@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@7777=@===::/44===@
@SRR005406.134 FB9GE3J10GG7KI length=294
TATTGACTTCGTAGTTAGGATTTCCCATAATTGCTGCTGATAAAGTAGATTTACCAGTTCCATTAGGTCCCATAATTGCATGGATTTCTCCAGTATTAATTGTTAAATCGACTCCTTTTAGAATCTTTTTATCTTCAATTGATACGTGTAAATTTTTGATTTCTAACACAGACATGTACAATTCCCTCCAACTTGTTTTAATCGTTTTTCCGTTTCTCACTCATTTTAGTCCTAATTGAGAATGAATCGCAAATTACAATTGCTAAAAATAAACAACTCTTATCATCAAATTTT
+SRR005406.134 FB9GE3J10GG7KI length=294
CCCCCCAAACCCCCCCC?@@ACCCCCA=<AA@@@?@@<644<<<>AAB@9466<@ACCCBBBAA@@664;033AABA3333AA@33444?@ACA;;;;;;;;;;;AA99:::@3@?CCCCCCCCCCCCCCCAAA::::3333339044AACCCCCCCCCCCCC:::::>==999>>>:>8869.66/////<6/***/2>??>>>:CCC77+11<777777<>?CCC::;;;;::11/55::5555::::::+++:8;:::::555644-------
@SRR005406.135 FB9GE3J10F5M3I length=307
TATTGACCGTTGTTTCATTAAAATAACGCATAATTGAAAAGTCCTTAACAAAATAGGCCACATTGTCGTAGCTATCACCATTGACACGATAAAGACTATTTGAATTTAACACACGAAAATACTCGCCATTATCTCCCAAGCCATTAATCGGATAAACAAATAACAAAATGCTTGTCACTAACCCAATCCCTAAAACGGCCAAAAGACTTGGAGAAATATAACGACTCAACCATTCAAAAGCCGAGTTCATGTGTTTTTTGATCTTTTCCATGCTTTCACCTCATCTAGAAATCATAGGCCAAAAGNG
+SRR005406.135 FB9GE3J10F5M3I length=307
EEEEEEEEEEEEEEDDDEGEEGGAAACEEFFEEEDB;===ECCBEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEDDDDDDDDDDDDDD@??:911111999:?=>@@=:::;<<<<<@@@=7777@@@???=:::@@@===?===@@@@@??>96666..../!6
@SRR005406.136 FB9GE3J10GGOKO length=299
TATTGACGTAATTAATGTTAGAATGGCCGCATTCCCGAAGTCAGGCTGGATTGCAACTAGAGCAATTAATACAAAAACGAGCATCAACGGTCGCCCGGCAGCTTGTTTAAATTGATCCATGCCTCCATTAATTGTCTTTTGTCGCCGTGCTAAAATATAAGACAGATACCAGACAACCATAATTTTTTAAATACTCAGCTGGTTGCATCGAAAACCCACCAATCTCAATCCAACCACGTGCGCCGTTAATTTCTTTCCCGATACCAGGAATCCGAACGGCTAAAACCNTAACCGTAATT
+SRR005406.136 FB9GE3J10GGOKO length=299
DDDDDDDDDDD@@@@BDDFGDDDEEFEEEEEEEDDEEEEEGGGFFDDDDDDDDDDDDDDDDDDDDBBBBDDDBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDD@;;;;;DDDDDDDDDDDDDDDDDDDDDDDDDBBBBDDDDDDDDDDDBBBBDDDDDDDDDDDDDDDDDDDDDD@:444//////20A3;?BDDDDDDDDDDDDBBBDDDDDDB15577@CCC?::::CC@;:::@@;;;::7777=========>==3337=========777777:==7777!7:===711111
@SRR005406.137 FB9GE3J10F936N length=294
TATTGACTAAAACAAAGCCGTTTTTTCTTTTTCGGCGGTTGTGTCTTTTTCTTGTAACTCGACTTCGATGAGGTGTTGGATGCATGTCTAGCAGCTCGCGAGCCTGAATTTGCGGTTGGCATAAATAGCAACTCCTTTGTTATACTTTCAAAACTTTATGAATCTAGTGTGTCTGAATATATTGTTCCACTGCGTCGAGATAAGGGATTCGCGGTGCGATTCCAAAAGATAATTCAATTCCTTCTTTCTCGATGAGTGCAAGCGGCATAGTATTTTTTTCCAGTAACTGCTTTT
+SRR005406.137 FB9GE3J10F936N length=294
FFFFFFFFDDD@@777;DFE444444@/////E@@@@@@@EEFE;55555DDDDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEFFFFFFFFFFFFFFFFFFFFDDDFFFFED;;;AADDFFFFFFFFFFFFFDDDFFFFFFFFFEEEEFFFFFFFFFFFFFDDDEFFFFFFFFFEEE<<<=::::BEEEEEEEEEEEBBBBEB==@@@@@@@@@@@@@@@@@@@<<9600.........<96666966....
@SRR005406.138 FB9GE3J10GDIYE length=268
TATTGACAGTTACTCAAATCGGAAAGTCTGAAAAATAGATCGTTTTTATTAATTTTCTTATTGAAAGAATATGCGGATTTGAAAAAATTAAACTCTTTCGACAGAGGATGCGCTAGCAATCATGCAAAACAAAGTAGAGCAACTTTATGATATGGATTATTTTTGTCTCAAGAACCGCTAGCCATAGAGGCCATTGACGAAACATTGCAGACCAAAAATTACAAGAAGCCATTGTTCTTTTTTGAACAAATTAATCCAAAGAAAAATT
+SRR005406.138 FB9GE3J10GDIYE length=268
AAA?@@A?@@@898<<><99993448::8A:@@88<,<<<83.....2**00....2*-858;:<<74498=?<<<====?57::::AA+++====AA====AAAAAAA???AAAAAAAAA@@??<<<>=?>;;;AAAAAAAAAAAAAAAA?>6666=5444*2555002,,,,,,00,,,,,,,,,11,,,,,-,4553336004443.
@SRR005406.139 FB9GE3J10GF4J6 length=240
TATTGACGCTATAAAGGAGTAAATTAATGAAAAAAGTAGTTATAACTAGTTCTATGTTAGCGGTTTTGTTGTCGGGATTTCTCGTTACCCCTATTTCTGCTTACGCTTTGGAACGCTCTAAGGGAACTACTGAAGAAACGGTGGCTTCAGAAACATCTCTAACGGAGCAACAAATGAGTAGCGGTGTCACTGAAGAAATGAATCCAAGCATCAATAAATTCTCAAAGAGGAAACAGAAAC
+SRR005406.139 FB9GE3J10GF4J6 length=240
A???AAAA==@@??;23200::4453......08*<<<<=?AAAAAAAAAAAAAAAAAAAAAA?311=?AA===????AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA?776?????;;;AAAAAAAAAAAAAAA?@@>;6666000;<<;;99;;;;;63----,,,,,,,,,,,*,,,,,,,200,,
@SRR005406.140 FB9GE3J10GAGU6 length=184
TATTGACTGTCGGCATAGACTTACAAGTAAATCATCTTCGCAGTGTCCATGATGGTAGCCTTACCGTGATTGCGACGCCCAATCACTCGGGAAAGACCCTTCAAGTTTGGGAAGCAAAAATTTATAACGCAGACCACCAATTGACGAGCGTGGGGCGTTGTACTTTAACAAATCGACAAAAAAA
+SRR005406.140 FB9GE3J10GAGU6 length=184
AAAAAAAAAAAAAAAAAAFFFFAAAAFFAAAABBFFAAAFFFFFFAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA?644==?<;;;;=>AAAADDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD@@@@@@DDDDDDDDDDDDDDC998<@DDDDD@:::?:444088===;888?@>>=11.117:6==::::?????????????????????????????=::11..6
@SRR005406.142 FB9GE3J10F85A8 length=292
TATTGACGCAAAAACAAATTGCAGAGAAAGAACAAGCAAATTTATTTTTATGTATATTAACAGCATTGTTACATGATATTGGCGATGAAAAATTTAACGAAAGTGAAGAGGCTGGCTTGCTAAAGGTGCAACAATGGTTGGAAGCAAATAACGTATCAACAGAGCAAACGAATCACATCCTTTCCATTATTGCTAATATGTCCTTTAAAGGAGGAAATACTGGGAAAACAGTTACTACATTAGAAGGAAAAGTGGTCCAGGATGCGGATCGATTAGATGCCATCGGTGCGTA
+SRR005406.142 FB9GE3J10F85A8 length=292
EEEEEEEEE55555@111@@EEEEEEEEEEAACAABEEEEECDE55555@8@@DEEEEEEEEEEEEEDDDDEEEEEEEEEEEEEEEEEEEEEE==11=AEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEDDAAAAEEAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE===EEEEE@@:DDD@@::44777;DDDDDDDDDDDDDDD7711117===>>=??@@@???===?@@@@@@@@@????===@@7733
@SRR005406.143 FB9GE3J10GHBRG length=303
TATTGACTTGTCAAACTCCATTAAATTTGCTGACAAGGCTATCGGTTCTTCGGAATTCTGATAGAGTTTCCCAGTTGCCTCCAATACTTCTGTTAATTGATTGATGCTTTGCAACCATATCCGAAAAAGAATGATTACTGAACCACCTAGAATTACTAAGCTAATTAAATAAACGTAGTTCTCCTCAATTCCTTTGGCTAAAAGGTAGAGTGGATCTTCCATGCCCCATCTACGTAATCCAAACAAAAAATTACTAAAAAAATACAAGACTGCTGATAACGCCAATATTCCCAAACTAAAAAA
+SRR005406.143 FB9GE3J10GHBRG length=303
FFFFFFFFFFFFFFFGCCCHHH999999CHHHHHGGHHHIIIIHHFFGGGFFFFFFFFFFFFFFFFFFFCCCGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFCCCFFCCBBFFFFGGGFFFFFGGGFFFFFFFFFFFFFGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFAAAAEEB<<::EGGEGEEBBGGGGGGGG@@@@@@AA9@@99<<<<9@9@@@A@A@??===@@@@@@@@@A@@@@AB<<<72......
@SRR005406.144 FB9GE3J10F9HP1 length=307
TATTGACGATTTAGTCAAGGGTGTTTTTTATAATGGTGGTCAATACCAAGTGATTTTAGGAACTGGTATTGTGACTAAAGTGTATGATGAAATAGAAAAACTTGGAATCAATGTTGTGTCAAAAGCAGAGCAAACAGCAATTTTAAAAAATAATGAAACGGGCATGCGCAAAACAATGCGCATTTTAAGTGAAATATTCATTCCAATTGTTCCAGTAATTGCAGCAACAGGATTGTTCCTAGGGTTAAAAGGTGTTATTTTTAACGATACTTTTTTACAATTATTCGGAGCAAGTGTAGCCAATATT
+SRR005406.144 FB9GE3J10F9HP1 length=307
EEEEEEEEEEEEDDDA??444;;//////;/88ECDEEEEEEEEEEEEEEEEEEEEEEDDDDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEDDDDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE??//////3//FA447EEEEEEEEEEEEEEEEEEEEEEEE====EEEEEDDDEEEEEEEEEEEEEEEEEEEEEEDDDDDDDDDDDDDDDDDDD=<;:?@DDD41....3399999.111.666;9;6/....../699999.117===?@@@?777::====@@@
@SRR005406.145 FB9GE3J10GE79M length=231
CTCCTCCTCCTCCTCCTCCTCCCTGACCCCTTTCCCTTGCTCTTCGTCACACGACCGCACGGGGCAGATTGAGTTTACAGAGGAGGAGCAGGAGGCCATGCGACAACTGCGACGCGTCGAAGTGCTCGCGTGTGGCGTGCCTCGTGCACTCCTCACTGCTCTCGACATCATGTGCGCATTCCTGTAACGAAAACCGGACAACAGAGGGCGACTTCTCCGTCGAATCCGGAT
+SRR005406.145 FB9GE3J10GE79M length=231
AAAAAAAAAAAAAAAA?==<555633....000--344<>???AAAAAAAAAAAAAB?@?????AAAA?===?>;;;>;6000:656:..004711----,5---1------*--833155,000,,,255522
@SRR005406.146 FB9GE3J10F83HP length=323
TATTGACGGGCACTGAGCTTTGGTGAAAAAGAAATCAGGACTATGGAACAGCAATACCAACAATTACTAGAGGACTATAATTGTGGAGAATTACTAGTTCCCAAATGGTTTTCAACTATCCAAAGCAAGGGATTGAGATTTTTAGGTTTATTTCGATAGAATAAAAATAAAAACAGGAGTTTAAGGAATGAAACTAAACGGGATTATTATGATAGCAGTTGTTGGAAGCGTTTTATCTGGCTGTGGTTGGCAAAATCGAAAGAGGAATCACAGAAAGTACAAACCGTACAAACAAACAATGTAAATACTGAAAGAAACAAGAG
+SRR005406.146 FB9GE3J10F83HP length=323
DDDDDDDBBBDDDDDDDDDDGDDDDBBBBBEDDFFHHIIIIIIIIDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD;;;;DDDDDDDDD;;;DDDD@@@:@AAB@://5556?DDDDDDDDDDDDDDDDC666644-----4-BBBB@BBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDC@@@CCCCCC@???5555:8@@@@==?@=:..../....68:...6..111====:::7777;:::===:757777=00073577===8:58771......6006..
@SRR005406.147 FB9GE3J10GD4ZW length=301
TATTGACTTAGAAGATATTACTGAAGGTGAATTATCAATTGGGGACAAAGTCATGAATGACGTTGCACCGAAAGATCGTGATATTGCCATGGTTTTCCAAAACTATGCGCTTTACCCGCATATGACTGTTTTTGATAACATGGCCTTTGGTTTAAACTAAGAAAATATGATAAAGCTGAAATTAAAAAACGGGTGGAAATGCTGCGGATATTCTGGGCTTAACAGAGTACTTACAGCGTAAACCTGCGGCGCTTTCTGGTGGACAACGCCAACGTGTTGCACTTGGCCGGGCAATTGTCCG
+SRR005406.147 FB9GE3J10GD4ZW length=301
DDDDDDDDDDDDDDDDDDDDDB@@@BB@@@@BBDDDDDDDBB@@@@@@@DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBB;888@@@@DD@@;DDDDDDDDDDDDDDDDBDFFC<4/5555@?BBBDDDDDDDDDDDDD5022249B@40000B?>>>>>>??>>>>>===:3337:::::=========7777::311777===::::
@SRR005406.148 FB9GE3J10GCT40 length=305
TATTGACTCATTATTGCTTTTGCGGCACAAGTTCAAAAAGTGTTTAAACGTATTATTCCAGAAGTTGTTCAAACGTTCTTAGTACCGTTTTTCGTCTTGTTGATTGCCTTACCAATTGGTTTCTTAGTAATTGGGCCAATCGTTAGCATGCTAACAGATTTATTAAGCGCTGGCTTTACAGCATTAATGAGTTTCTCACCAGCTTTGTATGGTTTGATTCTTGGTTTCTTCTGGCAAGTCTTAGTTATTTTTGGTTTACATTGGAGCGTTGTGCCATTAGCTATTATGCAAGTGACACAAGAAGG
+SRR005406.148 FB9GE3J10GCT40 length=305
FFFFFFFFFFFFFFFFFBBBBEEFFFFFHHHEEI;;;;;EEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEBBBBBEEEEEFFFFFFFFFFFFFBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBFFFFFFFFFFEEEEEEBB===EEEEFFFGGGGGFEEEB=7777777@@>@@@@@??:::@:777?@@??????@@@@@===?@@@@@@@@@==:555==
@SRR005406.149 FB9GE3J10GCMWF length=328
TATTGACCGTACCTGGTAATAATTGCATTAAGAAAAACGTAAATCGTTGCGATTAACCACAAAGTGATAATCATGAAAAAGATCCGTTTAAGAAAATATTTTCCAAAACTATTCAATAATGACACCTCCGAGATTTTTTTGACTTCCTCAGTTATTTTCGTTAAAGTAATGACTAGATAGACCACAATAATAGATAGGGTGAACACATGAAAACTTTTAAATGGCCAATTATTACAGCCGTTATTTCCAGTATCGGCATTTTTCTTTACTTATTAATAAGTAAAGAACCTATCACTACCTCCTCATTATCAGATACCTTCTTTATTCG
+SRR005406.149 FB9GE3J10GCMWF length=328
FFFEEEFFFFFFFFFFFFFFFFHFFFGGGHHHFFFFFHIB>>>EEFFFFFFFFFFFFFFFBBBEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEBBBBEEFFFFFFFFFFEEEFFFFFFFFBBBEFF===;===FFFFFFFFFFFFFFBBBBEBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEBBGBEEEEEEEEBBBBBBEEEEB===BBB=@@@@@@@@>>97.....0...;@>>C::::=::77777=?@@@@@@@@@@@@@@@@@@@@@@@@???@@::777:@=:7777
@SRR005406.150 FB9GE3J10GAL2D length=219
TATTGACAAATCAATTGTTTTTTGTTTCTGCTGGTGACAATTGATCAATTTTTTCCTATCTGTGCTGCATGTTCTGGTTTTAGTAACGGATTATTAATACTAGGTGCCGTGGCAGCTGTCGTTGGTGTTAATAAGATAGGATACTGTTGATAAATTCGTCCATCGCTTGTGCTTGTAAAGCAATATCTGTCCAAGCCGCAGTTGTCTCTTCACTCGTTA
+SRR005406.150 FB9GE3J10GAL2D length=219
????@?>220::88822......6(**<4<<>9:88:=88::>?A@@A55::55BB+AAAAAAAAAAAA@@?897993332;7-88??????AAAAA??@??888<888???????@<888AA<<?=:00066=666::::=6667;>=>?=<<>>>>;222;;>>?=?>>><;;000;<6669;:::::9663---33222
@SRR005406.151 FB9GE3J10F87JY length=303
TATTGACTTTGAAAACTACGCAAGAAATACCTAACTGAGCGGAGGGGAAGCAATGAGAAATCCAAAAGGAACGACCGATCAGCTATTTAAAAGTTTAGCTGAATACAATCCAACAACGAATGAAGCCATGTCTAAAATAGCGAAAGTCCTAGTCCCTTTAGGAATCGCTATTTTAGGCATTCTTTTTATGATTGAATTGGCGAATACCCAAAAGAAATTTCAATCAGAAGACGGTGGTTTGACAATCGAGATATTAACTAACATTGCATTGAAGTATGTGATCGCGTACGTCTGTATTATGGG
+SRR005406.151 FB9GE3J10F87JY length=303
EEEEEEEEEDDDDEEDAAACEEEFEEDB===EEEEEEEEEEEE;;;;AAABBEEEEEEEEDDDEEEEEEEEEEEEEEEEEEEEEED776666@5556@EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE@@@@EEEED@@@555;;DEEEEEEEEEEEEEEEEEEEEEEEEE@665===DDDDDDDDDDDDBBBBBBBDDDDDD@@@@@@@@====@@@@=777@?=:::@@@@@@@@@@@@@@@@@@@@@@@@@@:7777?
@SRR005406.152 FB9GE3J10F66X1 length=279
TATTGACGTGCCGGGAGACCTAAGTAAGCATAATTTTTGCCAGTCTTATAGTTCTTCATCTGCTTCATTTCCTCACTACGTTTCATCATTTCTTCATAGAATGTTTCAATGCAAGAAAGCAAGTCTTCTTTTCTATAGTAGACATTTGCCATCACAGAACCTAAGTCCGCAAGGTCAGCATTTTTCGGGTCAAGAATATACAGTTTTGAATCTGTATGAAGCAAGGCTTCAATCAGTGTCAGTATAAAGTAAGTTTCCGCCACCTGTACCACCAGCAAT
+SRR005406.152 FB9GE3J10F66X1 length=279
DDDDDDDDDDDDDDDDDDEEGGEEDDDDDFFDDIIIGGGGGIIIIDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD??2CDDDDDDDDDDDDDDDDDDDDDDDDDDDBBBDDDDDD@@@DDDDDDA<<>><483333>27@????@@?@?????<811.47;:84......499992444............=777;>333?=<<<:4...
@SRR005406.155 FB9GE3J10GEO1E length=286
TATTGACAATTGCTGCTTCTTCTAAGCTCCCTAAGGCTAAAGCATGACTTAAAGTGACTTTGCCAAACATCTTTGCTTGTTCTGTATAATCAACAAATTTATTAAATTCATAAAGTCCCAAAGTATCACGGGCGTGTAAATGAACATCAATTTTTTTATTAAATGTGGTAGCTAATTCAAATATTTTTGCGATTGAATGATCCACATGACGATCCACAAGGGCTGGATCAACGCCGCCGACATGAGTTGCCCCCATGCGTAAGGCTTCGCGCATCAAAGGTTCGTA
+SRR005406.155 FB9GE3J10GEO1E length=286
DDDDDDDDDDDDDDDDDDDDDDDEEEEE@@@FFIGGFFGGGFFFEBBBDD;;;BDDDDDDDB????DDDDDDDDDDDDDDDDDDDDDDDDDDDDBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD:::DDDDDDDDDDDDBB@<44///////411:::BBDDBBBDD<<>CC@>>>@CCCBBBBCCC@@@@;666331116:::;<66666666:;:::1111<:::61111
@SRR005406.156 FB9GE3J10F87QH length=313
TATTGACAATTTATCGTGATTGGTGCCATAACCGTTGTTAGTTTTGCCGTATTGTTTGTCGGTTTTTTTGTGGGAATGGATAAACTTTCGACGAAAAACTAATCAGGCCTTACTAGAAGTAATAAATGATCAAGAAATGATTGCTTCACCAAACACTCAATTAGACTCCCAAGTAATTGCTAATAGTTCGCCTTTTGGGGGCGAAGTTGTGACCAATCGTTCAAAAAATATTGATGGTTACACGGTGGAGTGGAGTAATTTACGTAGCAGATATAGCTTTTTCAGAAATTCGATTGACTGGAATGAAGTCTAT
+SRR005406.156 FB9GE3J10F87QH length=313
DDDDDDDDDDDDDDDDDDCCCDDDDDDD@>>EEEDDDDDEDDDEEDDDDDDDDDBBBDDDDD>>>>>:7B,>>DDDDDDDBBBBDDDD9999>DDDDD>?06BBDDDBBB8879>>DDDBBBDDDDDDDDDDDDBBBDDDDDDDDD>>>>DDDDDDDD>>>>>DDDDDDDBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCCCCB888888C2@@CC>5555CCCCCC>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>:::::==:333::<<<==;<<:::::<:::<==<:6
@SRR005406.157 FB9GE3J10F5WAH length=304
TATTGACGCCAGGTGTTTCGCTAATAAAACCTGAAGGCGCCTTTTATCTATTCCCGAATGTCAAAAAAACAATTAGAAATTTGTGGGTATGATAACGTGACTAATTGGGTGGAAGATTTATTACAAGAAGCGCATGTTGCTCTGGTAACGGGAGAGGGCTTTGGTGCACCAGAACATGTGCGGATGAGCTATGCGACAGATTTAATGACGTTAGAAAAAGCGATTGAGCGAATGAACGACTTTATAGAAAAGAAACGGATTCAGCACAACGCCTAAAAGAATAAACTAAGAAATGAACGGAGAG
+SRR005406.157 FB9GE3J10F5WAH length=304
FFFFFFFFFFFFFFGGGFHFFHHHC6666==GHHHFFHFHGHHIIIGFFFFFFFFFFFFFFF??FFF??G::GGFFFFFFGCCBFFFFFFFFFFFFFFFFFCBBFFFFFFGGGGFF???GFFFFFFGGGFFFFFFFFFFFFFFFFFFFFFFFFFF@@@GGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGGFFFFFFFFFFFIIIIIIIGGGGIIGGGIIIIIIGEEEEEE@=1111:22217:@@@@@@@@@@@@@=775555=@@A@@@AAAAAA@@@@@@@@@@?77
@SRR005406.158 FB9GE3J10GDPDC length=315
TATTGACTATTTACAATTATATGGTGTGACCACACAACAATTTTTAGGTAACATCTTTAGCAAGCTATGTGGCGATTGGTATTGTGCCATTCAACCTTATTAAGGGCCTCTTAGTCAGTGGTGTTTTTCTAGTACTACATGCGAAGTTATTGCCATGGCTATCAAAAAAACAACATACTATTCAGAAAAAAACACCGTTAACAAAATAAATGATAAAAAACCTGCTGTTGAACAATGTTTGACAGTGGGTTTTTAAAATTTACGCCTAAAAGAAAAGAGGTTGTCATAATCTGTCATCATTCTGTTAAAAAATAA
+SRR005406.158 FB9GE3J10GDPDC length=315
FFFFFFFFFFFFFEEE==;EFEBBBFFE===FFFFFFFEE77777;880DDCCDD8;;CDDFFFFFFFFFFFFEDDDFFFFFFFFFFFFFFFEEEEFEDAAAAFFFAAADFFFFFFFFFFFFAAAAAAEEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFAAAAAA?F66EEEEFFFEEEFF=======FFFFFAAAAEAAAAFFFFFFFF@@@@::::BEEEEEEEEEFFFEB:::EEEEE@?::111......666699..0.177=////=;@@@@@@@@@@@@@@@@@@@@@@@@???@======://
@SRR005406.159 FB9GE3J10GGLRL length=281
TATTGACGTAAACTTGGACGCTCCATGACAGCTTTAGGTGCTGGCTCTGCCATTGCCAGTGCTACAGGAAAACAAGGACAGTCGGGTAGTTCTGGTAGGACACAAGCAGATCACACCCGTCCAGACGGACAGGAAAAATCAACACTTGGAAAACGTATCGGACAAACAATCGGAGCAGTTGCTGATACCAAAGATAAAATCGTTGATTCTGCTGGTAATCTCAAAGAACAGGTTAAGGATATTCCGACCAATGCAAGATATGCAGTGTATCAAGGAAAATA
+SRR005406.159 FB9GE3J10GGLRL length=281
FFFFFFFFFEEEFEEEEFFFFFFFFFGHHHHHIIIHBBBEEHGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFEBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF======BFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGIGGGGFFFFEEEFFFFFFFFFFFFEE@@@@@@@@@@@@@@@@@@@@@@@@7711111...96
@SRR005406.160 FB9GE3J10F7XFC length=307
TATTGACAAATGGAAATTATGAAGCATTTGCTCGACCAAGAAAACCAAAAGGTGTAGATGACAAGAGTGCCTACATCGTTGGTGGTGGCCTAGCAGGTTTAGCAACGGCTGTTTTCTTAATTCGTGACGGTCAAATGAAGGGCGAAAATATTCACATTTTTTGAAGAACTTACGCTGTCTGGCGGTTCTTTAGATGGTAAATTTATTCCCCATGATGGCTTTGTCACTCGCGGCGGACGCGAAATGGAAAACCATTTCGAGTGTTTGTGGGATCTATTTCGTTCGGTACCATCATTAGAAGTAGAAG
+SRR005406.160 FB9GE3J10F7XFC length=307
DAAAADEEEEEEEEEEAAAECCCEEEEEEEEEEHHEEA@@@@@=CA0006::DDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEDDDEEEEEEEEEEFEED///555@EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEA@@=<<858@DDDDDDDDDDDDDDDDDDB====7777;?@@@@@@@@@?7323337>?=;99=73223333:@@@@@@@@@@@@@@@@@@@
@SRR005406.161 FB9GE3J10GGF9Y length=244
TATTGACTCGTTTGATTCTTTGGCCCCATTACCGTTACCACAAGCCCCCAATGCGAAAATAGCTGCGGTTGCTAACACTGTTGTTGCTAGAGTTTTGAACTTCATTTTTTTCTCTCCCTTAAAAAATTTATAAAACAATTTGCTCGCCACGTTCTGGCAATATTCTTTCACCATACGGGTTTTCCAGTTTTTCTGGTTTTAACGTATGGATTGGAACCAATTACTTGAGGTTCAATCAATGCAA
+SRR005406.161 FB9GE3J10GGF9Y length=244
AAAAAAAAAAAAA?@???<<<:93333::=?AA?<<<==?=?<932444<<====<@?AAAAAAAAAA?????;666;222=??;;;??;;;???????A@@@@8<,;;@@@@AAA;2;;;6600----,,00,,,2,,,,222240,,25555522
@SRR005406.162 FB9GE3J10F6PGW length=312
TATTGACAACGGTCAGATCCCCTTTTTCGTTTTGATTTAGGGCCTTGACTATTTATTTTAGTCGTAGCTGATTGCCCAGCTTCATAACTAGTTGAAATTCCGTCATCTTCATACATATTAAAAAGAAAGTGGTGCCATTTGGATAAATCAAGAAAGATCGTTGATCTCGTTGGATTTCCTTTGGATTGTTGTTTGGATTCGTCATTGGGATAATACTGCCATCTTTGACGAAAACGGGCACCTTCCACAGCGGTGTTTTTACTCCATTTAAGACACGGCCACCTTGATATTTTTCGCCTGTAAATAAGTCAA
+SRR005406.162 FB9GE3J10F6PGW length=312
DDDDDDDDDDDDDDDDD@5511666///8----88?AAADDDCCCBDDDDDBB@A55558>9>BDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD@@@@@@@DDDDDDDDDDFDCBA:44/////4---:@BBBDDDD???BBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCC@@@BCCCCCCCC@@@@CCCCCC@@@@@:?@>??>>>>>>>>>>>=>>>>>>>>?>>>>??=========1111111::::8877==700/6:..
@SRR005406.163 FB9GE3J10GG2XA length=302
TATTGACTTCTTCATATTTGTCTTGTAAGCCTTGCTCCGTTAATTGACTTAATAAGTTTGATAACATACCACCAGGTACTTGATAAATCAAGGTTTTCGGTTCCGTATCTTTAACTTTAGGGTTTAAAATGCCTTCACTTCTAAAGCGATCACGAATCGGATTGAAATAGTCAGCAATCTCTGTTACTTTTTCCATATTTAAACCTGTTTCAAAGCCTAAATCTTCTAACGCGATGGCTACAGATTCTGTGGCTGGTTGACTCGTACCGCCAGCGAAAGAAGAGATAGCTGTATCGATGATA
+SRR005406.163 FB9GE3J10GG2XA length=302
FFFFFFFFFFFFFFFFFFGGGGGGGIIIIIIGGGGGGGGFFFFFFFFFEEEDDDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFD===FFFFFFFFFFFFFFFFFFFFFFEEEFFFFFFFFFFFAA====DDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFE==;;;AAFFFDDDFFFFFD@;;;;ADDEEEEEEEEEFFFFEEEEEEEEBBBBEEEEEE?@@::::@@@@777:=???@@@=::::=:7111:9=?:::???@@@@@@@@@@??77
@SRR005406.164 FB9GE3J10F73FH length=306
TATTGACTTTTAAAGATGTCCCTACAACAGTATTAGAAATAAATATAAAAGATGATTGTATAACTTGTATTGATTTTGAAGATAAAAAAACTAATGGATATTTTTAATAAACTAAGAGAAAAAATATATGATCGAATTTATTACAATTATCAGATGTCTGTTAAAGATAGTGGTAGTAAGAAGAGAGCAAATTTAGATGGGTTGTTCATAGAGTACTTAGTTCAATATAAATATAATAACCAAATAGACGCTGTTATGGGATTGAGCTATACTCCTTCATATAATAAACAGAGAAGTATTTCTTAA
+SRR005406.164 FB9GE3J10F73FH length=306
FFFFFFFDDDDEEAAAAFFEFFFGFFGGGGGFFFFFFFFFBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFD5000000C8--CAACFF88888A?4666DDDDDFF>?BBD?A5DEFFFFFFFFFFFFDDDFFFFFFFFFFFFFFFFFFFFFFFFFEEEFFFFFFFFFFFFFFFFFFFF===AFFFFFFFFDDDFFFFFFFFFFEEEFFFFFGGGGEEEGFFFFFFEEFBBBE@@???@@@@@@@@@@@:::=@@@@@@@@@@@@@@@=777=777==@=::7767...;....
@SRR005406.165 FB9GE3J10F7EQV length=330
TATTGACAAAACGGAAGCTTTACAACGGAGCCTTACGAACAGATTTATTCCAATACTGGGGAACACGTCCACCAAGAAAACCACGGGAAGACTAAGAAAGCTGGTGTAAAAAATGAAGGAAGCTGTATTTTTACAAGAAGTGAAAGAAATTCAATTACTAAAAAATGCCTTGACATTATTAGACTGGGATTCATCAACTGGGATGCCAGAAAAAGTAGTCCTTTTCGAGGAGAAGTAGAAGGGTATTTAACCGGATTATATTTTGAACGAAGTATTGGCCCAGTTATTCAAGAAGCATTGGCCTATTTTGAGACACGCCCTGAAGAATTA
+SRR005406.165 FB9GE3J10F7EQV length=330
DDDDDDDDDDDDDD::>BDDEDDDDDDDDDDDDDFEEEEEDEDDDDDBBBBBBDDDD??????BBDDDDDDDDDDD>>>>DDDDDBBBBBDDDDDDDDDDDDDDDDD777777BBBBDDDDDDDDDDDDDDDDDDDDDDDDD>>>D===DDDDDDDDD<555566BBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBBDDDDDDDD1>>9955339=AAAA====?=;0000000.........48::7736666::::::;;;;;666666<<::666:=========<<66666=<<;<<<666::../585......
@SRR005406.166 FB9GE3J10GGXN5 length=320
TATTGACAGTTTTAATTGGTGGTCAGAAATTTATTTGGAAACGAGTAGAACGTGATCAAGAATTAATCGATGTACTGACCGAGCAATTAGTTAATTTTTGGGAAAACAACGTAATCAAAAGCATTGAACCTATTATTGACGGAAGTAAGGCAACAGCTGACTTTTTAAAGGATAAGTATAGCGACATAGAAGAAACGCAAACCACTTTACCTGCTTCATTCGATGAATTGATAGATACAAAAAAATGAAATGAAGAAAAACCAAAAAAGAGTTGGATGTAGCTATTAAGAAAAATTAGAAAATAGAAAATAAAAAGCGAA
+SRR005406.166 FB9GE3J10GGXN5 length=320
DDDDDDDDDDDDD@@2299DDDDDDDDDDD666BBB96666@DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD@@@@DDDDD@;;;;;;DDDDDDDDDD;;;;@DDDDDDDDDDDDDDDDDBBBDBBBBDDDDDDDDDDDDDDD88888888BBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDB>>>BDDDDCCCCCCCC@@@BB???===?=?///////66...666.........333330=2===::777:========7777:77770======8:777772662077...
@SRR005406.167 FB9GE3J10F7K75 length=289
TATTGACCAACTTCAAAATGAACAGCTAAAACATACCATTCATCTTCTGATAACTGACCAATTGCTTCTGTTGTTTCTTGTGCAATTTTCAACGTTTCTGGTGTTAGTTCCGTAAATAACGTCCGATCAACACCAGATAATGTCGTTCCTTCTCTTGAACGATTCAGCATCTCATTGAGATGGTTAATCAAAATCGTCCACTGTAATTCCGTTGGTTCAATTTTTGCTTCTGCTAATCGCGCACTGGTTTGTTTGATAATCGATTGTAGTCTTTTCTGGTTCAGCTACG
+SRR005406.167 FB9GE3J10F7K75 length=289
CCCCCCAA===CCCAAAABBBBBBD>>555554EDEEDEECC@@?CCCCAA@CCCCAAACCCCBAAA@====CCCCCDDCCCCCCCCCCCCCCCCCCCICCCCCCCCCCCCCCAAACCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@@@CCCCCCCCCCCCCCCCCC@@@BBDD@<<<4444:?B???BBF?:4111<<800110//69/////9@@@@@@@@>>>@C99999966:423...3:6666::::<<<<<<<<<:66/<<<<<:661111
@SRR005406.168 FB9GE3J10F9KNW length=304
TATTGACGGAAAATACTTTCTTTATTAGGTGCGATGGCTAATGCTTTAGCAGAACGTGGATTTACTACGACAATTGTTCATTTTCCAACATTTACAGTAGAAATGAAACAAGCCATTGGTCGCGATCAAGTTGGTGAAAAGCTCGATGCAGTAAAAAAATCCCCTNTATTAATGATTGATGACATTGGTGCGGAATCCATGACTAGTTGGATTCGTGACGACGTTTTTAAGCGTAATCTTGCAATACCGAATGCAAGAACAATTTAGTTTACTTTTTTCTCTTCCAATCTAGAATTTAAAAAGT
+SRR005406.168 FB9GE3J10F9KNW length=304
DDDDDDDDDDDB07.>11180008=@B558BDDDDDDDDDDDDEEDDDDDDDBBBDDDDDDDDDDDDDDDDDDDDA>>DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD==>BDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDFEEB<4///////::BB:A!DD>>>>BDDDDDDDDDDDDDDDDDD====DDDDDDDDDDDDDDDDDD<<<=====70////333ACACACCDDDDD;;;:>>>===<6333.36:975545//../......7+.....:://.5/........../.
@SRR005406.169 FB9GE3J10GBCML length=310
TATTGACGAACGTCCATAATTCATACGTACGACCTGTTTTAATTTTTTTCTTTTAGGATTGCCAAACTGGCGGATAAAGATTTCCACATCTTTCCCTATGTATGCTGCGTAGCCAGAAGCTGGCAATTCTTCATGAGGAACAGCGGTGTGAGCGCTGGATAAGCGCCCACTTTGAGCTGTTTCGGTTGGTTTTTCAGCAGGGAAAAAAACTGGCTCTAAATATCCAATGAGTAGAACTGTTAAAAAAACAGCAGTAAAGGCCCAAAATCGCTTCATTTTTTCCCCTCTCATCTTATTTTTCTTTCACTTA
+SRR005406.169 FB9GE3J10GBCML length=310
DDDDDDDDDDDDDDDDDDEEEEDEDEEDDDDDDDAB0000??///////8,388FBBBDDDDDB@@@DDBB@@@DDDDDDDDDBBBBDBBBBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD???DDDDDDDDDDDDDD==5555/:?BCCC00///////:?CCBDDCCCCCIDDD@@@BCCCDDDDBBBDF>>>>;99?3>>>??===77333777368::86./........../2:::871117::22:00,711177
@SRR005406.170 FB9GE3J10F8X3O length=211
TATTGACAAAGCAGATAAAAACGGTAACAGTTGGCAGTGTTTCTCTACATGATAAAGATATTCCGTTACAAACAAAAATTTATTATGAAGTGAAATCTTCCGAACGTCCAGCCAACTATGGCGGAATCACAGAAGAATGGGGCATGAATGATGTCTTGGACACGACCCATGATTCGTTTCACAAGGAAATGGCACGCTATTACGAACTATG
+SRR005406.170 FB9GE3J10F8X3O length=211
AAAAAAA==<@@@B??77777??:3))27><<::>?=:88<<>:?AAAAAAAAAAAA:<?<<<>==>==8666111;==;665<<<<999>@<::779............7344434::<<<<<36111<<<<:1116:::<66
@SRR005406.172 FB9GE3J10GA1RN length=110
TATTGACGGTTGCTGCATATCAGTACCAACCGTAAAAGTAAATTCCACATTCGTAGCTACGCCCCAGTCTCCCTGTTTGTTCATGGCCACCAGTGAAAAAGCTCCTGCTT
+SRR005406.172 FB9GE3J10GA1RN length=110
=>><<<<>A@?==<<=====;9.....06;0006...
@SRR005406.173 FB9GE3J10GACWJ length=306
TATTGACGGGCATGTTAAAAGGGCCAGGAATTTATAACCCAATTGATTACATTGACAATGCCACAGCGCGACGGAATACCGTTTTACAACTAATGGTCGACAATAAAAAACTATCTCAAGAAGAAGCCAATCAAGAAGCGAGTGTTAACTTAGCGAGTTTATTAAATGACACCTATGTTGGCGACGAAAATAGTTACAAATATCCATATTATTTTGATGCGGTAATTGATGAAGCGGTCAATCGTTATAAATTTAAAGAAGAAGATATTTTAAATAAAGGCTACAAGATTTACACTTCTTTAAATC
+SRR005406.173 FB9GE3J10GACWJ length=306
DDDDDDDDDDDDDDDDDDDDD@@??B55552228@BB222DDDCCBDDDDDDDDDDDDDDDDDDDDDDDDDBBBDDDDDDDDDDDDDDDDDDDDDDD@@@BDDDAAAAAACB3DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD;;;9>DDDDDD>>>BBDDDDDDDDDDDDDDB@@@CCCCCBBBBCCBBB@@@BCCCCCCA====7711....85564467777===:77155>?????>>>>>>??>>==7777>====57
@SRR005406.174 FB9GE3J10F67J0 length=295
TATTGACAATCGTTGTGGAATTAATGGGAACCATTGAACCAGCTAAAACCTATATCATGAAAGCTTTAGAAAAAGGCAAACATATTGTGACTGCCAATAAAGATTTACTGGCGCAACATGGGAGTGAATTAGTAGCGTTAGCCCAAAAACATCATTGTGATTTATATTACGAAGCAAGTGTTGCTGGCGGGATTCCAATTTTAAGAACAATTGCTAATAGCTTAGCGGCAGACAATATTCAACAAGTTTTAGGGATTGTGAACGGTACGACGAATTATATGCTTACGCAAATTGG
+SRR005406.174 FB9GE3J10F67J0 length=295
FEEEFFFFFFFFDAAAEE@@@@EEE4448888EEEEEEFFFFFGFFFFFEEEEEFFFFFFFFFFDAADFFFFFFAAAEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFFFFFFFFFFF=====AEFFFFFFFFFEEEFFFFFFFFFFFFFFFFFFFFFFFFFDDDFEEEEDD777;AAFDDDFFFFFFFFFGGFIBBBFGGGGGGGFFFIEEBEEEEEE@::::@@@@@@@@@@@@=:::@=====@@@@@@@@?:777:@@@@@====
@SRR005406.175 FB9GE3J10GDQ05 length=246
AACCAGCATACGAATGCTTAAATCAAGCATATTGCGAAATCAAAAACCGCCAAGGGAAAATGGTAAACGGAGTATTCGTCAAAGAAGCCGATTTGTAAGGCTCGAGGTGGAAGAGATGCGAATTATTCTACCGATTGAACCAAAACCACAAAGTCGCCCAAGATTTGCTAGACGTGGGAATTATGTTCAAACCTACGAAGATAGCGCTATGAGAGCCTAATAAAACAAAAAGGTAAAAGCGTATCT
+SRR005406.175 FB9GE3J10GDQ05 length=246
AA?===@AAAAAAAAAAAIIIIIFIIIIIEAAAAA>>>><8.....00:88::<>>88889=?AAAAAAAAAAAAAAAAA===?=AAAAAAAAAAAAAAAAAAA?==<<<<<>>>DDDDDDDDDDDDDDDDDDDDDDDDDDDBBBDDDDAAADDDDDBBBDDDBB===???????????===:::=11..92426........-/.69666;;>>
@SRR005406.177 FB9GE3J10GB0RQ length=274
TATTGACGAACACAAAGACCACAACCTGTACAGTCTTCTAAAGAAACTTGGATACGATACATCAACCCATCTGTGCCACGCATTTCGCGCATGGCAAAACCTGCAGGTGCTTCTTTCAGTTCTTCTTCATCCGCTAAAAATGGTCGAATAGCCGCATGTGGACAAACAAAGGCACATTCATTACACATCGTACACTTATCCATTTGCCACTCAGGCACTTCTAACGCAATGCCTACGTTTTTCATAAGCCGCAGTGCCCATAGGATGGCACCCG
+SRR005406.177 FB9GE3J10GB0RQ length=274
DDDDDDDDDDDDDDDDDAAAEEFGEEGGGFGGFEDDDDDDEDD>>;DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDC@666677DDDDDDDDDDDDDDDDDDDDCCCCDDDDDDDDDD;;;;;DDDDDDDDDDDDDDDDDDDDDDDDDDDCCCDDDDDDDDDDDDDDDDDDDDDDDDDCCCDDDDDDDDDDDDDDDDDDDDAAADDDDDDDD@?40008>/////0?D===>???????:::>>=1../.666...6
@SRR005406.178 FB9GE3J10F6EL0 length=307
TATTGACATTCTTTTTTTGTACTGGTGATGATGAATCGTGGATGAATAATTCAGAAATCGTGGAAGAGGTCCAGAGATTATCAAAACAACTGAATTCTAATCTTATAAACGATAAGCGACCACTACCAAAAATAGATCCCGATAAGCTAACGAAAGAAGAATACCAGCGCTTATTAGACTTAGGTTATCAAGTAAACGATATTAAGAAAGCTCTCGGACTGGGAACAACCACATTTCAAACTGGCGAAAGGCAAATGGCATAGAAAACATAATTAAGCGAAAAGAAAATAACAAAGTAGAGGAGAAA
+SRR005406.178 FB9GE3J10F6EL0 length=307
DDDDDDDDCCC;;;;;;;D6FEEEGGGGGGGGGGGFFEEEDDDDDDDDDCCCDDAAADDDDDDDCCCDDDDDDDDDDDDDDDDDDDDAAADDCCCCDCCCDDDDDDDDDDDDDDDDDDDDDDDDDDD>::::@4BB?66:CDDDDDDDDDDDDDDDDDDDDDDDCCCDDDDDDDDDDDDDDDDDDDD??>CCDCCCDDDDDDDDDDDDDDDDDDCC?@<<<<@@@DDDDDDDDD@::4444:???=:::???????>===?:7111176>>>====???7777=>>>>?>>???????::::??777
@SRR005406.179 FB9GE3J10GARFQ length=291
TATTGACAAGAAACTGGCAAAGAAAGTCCCACTAATTGGTTCATTTCTTCAATTAATTGATTAAGGGAAATGGCAACTTCGGTACCCACATTATAAACATGTCCCAACGCTTCACTTTTGGTTGCTACTAAATTTAATGCAGTTAGGACATCCTCAATGTAGATAAAGTCACGTGTTTGCTGACCATCTCCAAATATTTGAAATTGGCTCGCTTGCCCTTGCTCTAATTGGATATAACGATCCATCAAAATGGACAGGACACCAGAATAGGGTGAAAGAAGGTATTTTTGA
+SRR005406.179 FB9GE3J10GARFQ length=291
DDDDDDDDDD>>>DDDDDDEEEEEEEEEEEEEEDEEDDDDDDDDDDB;;>DD6655>>BDBB>>???>>>DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDD>>>DDDDDDDDDDDDDDDDDDDDB><<<<>>>>>>CCCBB>>>BBBBBCCC>>>>>>>>>>>>>=<:666:;;:97754/......../4.....//
@SRR005406.180 FB9GE3J10GGK7T length=93
TATTGACAATTGTCGAGATAAGACATCATTTTTAGTCTTATTAAACCCGACGCCTTTACCGACAGCTACTTTCTCCTGTCCTTCGTCAAGAAC
+SRR005406.180 FB9GE3J10GGK7T length=93
AAAAAAAAAAAAAAAAAAFAAFAFAFEB:::::?B2BAACAAAIIAAAAAAAAAAAAAAAAAAAAAAAAAA??>AA?@?<;::7600000000
@SRR005406.181 FB9GE3J10GG0XK length=306
TATTGACACTAAGCGCCTGATTAATTTGTAAAGCCAATGCTTTAATCTCCACAATTTCAGCAGGAGTGGCTACTTTTAGAAATTGAATATGGTCTTCGTTAATAAAAGGATCATCCAGACGATCTTCTTTGTAATAAAATTCAATAATGGGCGTCACTAATTTAGTGCCCTCTTCAATCGCTAAACGCTTTGAAAAACTTCCTGCCGCATAATTACGTACGACAACTTCCAAAGGAATCATTTCTACGGCCTGAATTAATTGTTCGTGTTCAGATTACTTTTTTGATAAAATGNTTGGGAATCTTT
+SRR005406.181 FB9GE3J10GG0XK length=306
CCCCCCCCCC@@AACCCBBEBB==33362@@B=@@CDEEEEEEEEABBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA@====CCBCCCCCCCCCCCCCCCCCCCCCGCCCCCCCCCCCCCCCC@@@CCCCCCCCCCCCCCGCCCCCGCCCCCCCCCCCCCCCCCCB@44444;CCBBBCCCCCCCCCCCCCB999>@>333<@@@@@@9922<<9996624...338666:::<66666<<<<:::<661.....11..44466::11!..433444....
@SRR005406.182 FB9GE3J10GG2HY length=294
TATTGACAAAGCTAATAAAATTTACGTTTGGCTTTCCGTTTAAAAGTCGTTTCGTCAGTTAAAATCTGTTGTTTTACCAATTGCTGAGTCAATGTTGAACCACCAGAAGAACCGCCGATACCTGTCGCATCAGAAATCAACGCTCGAACTAGCGCTTTTGGTACCACCCCATGATGTTCTTCAAAATATTCATCTTCTGTTGAAATAATGGCTTTTTTAGCAATGGAGACATTTGATCGCCATTAATTCGTGTCCGAATTAAATCTGATTTGATGTTAGCAATCGGAGTACCAT
+SRR005406.182 FB9GE3J10GG2HY length=294
DDDDDDD522>>BC>80000222/8800055?BDDDBB7;;DEED@=@@DDDDDBBBBBB@@@@BBDBBBDDDDDDCCBGDDDDDDDDDDDDDDDDDDDDDBBBDDDDB@@@@DBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD;;;;DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD>>B:33//////0;????ACCCCCCCCCCCCBBBBBCCB===??>>===777>>>>>>>>===>>>>>>=====777:>=========
@SRR005406.183 FB9GE3J10F5TMD length=319
TATTGACGGAGTTAAACGCTTCTGTCCCGACCTCATCTTTTTATTTTGCTTGTCGTTCTTTGATTTTCGTGAGTAAAGATTGAACATGCTGGCGTGCCGAAGCTTCATCTTCTTGAAGCATCTTTCCGATAAAATAAAGGAGCCGCCCACTGCTAATACTTCTTTTGCTTCCACATACTCTATAAAGTTTGTTTCATCAATCCCACCAGTTGGTAAAAATTGAACATCAATAAAACGGGCCACTTAAACTTTTGATGGCTTTAACCCGCCGTAAATATCGGCTAGGGAAAAATTTAACCACTCGTAAGCCATACGCCAG
+SRR005406.183 FB9GE3J10F5TMD length=319
CCCCCCCCCCBBBCCCCCEEEEEEEEEEEE:>@GFEEFFFFAE0000CCCCCCCCCCCBAAAACCCCCCBCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA=77777CCCCCCCCCCCCCCC@@@CCCCGCCCCCCCBB@@<6666@@CCCCCCCCCCCCBB@<<<@@@?4000;BBBBBBBCCB445;;;;;?=F>>>CCC<<9966//////////6//////..47....998......44...4226:<<<6366<:::<:11111..334,,4466666:666:::::::6666
@SRR005406.184 FB9GE3J10F68CM length=306
TATTGACAATCGAATTAATAATTCGCGAAGATGGTTCAGTCACGATAGATGGGGAAAAAGTAGCAGATGTTTTAATTTCTGGAGAGAAGAATAATCAAATTACTTTAGATGTTACTAACCAAGCAAAGGTTCCTTTACCTGAAACTGGTGGCATAGGACGCTTGTGGTTTTACTTGATAGCGATTAGTACATTCGTGATAGCGGGTGTTTATCTCTTTATTAGACGACCAGAAGGGAGTGTGTAATCAATGAAAAACGCACGTTGGTTAAGTATTTGCGTCATGCTACTCGCTTCTTTTCGGGTTT
+SRR005406.184 FB9GE3J10F68CM length=306
DDDDDDDDDDDBBBDDDDDDDBBCEDDEDDEEEEFGGGFFEEEEFDDDDD555555///5?0DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBBDDDDBBBDDDDDDDDDBBBDDDDDDDDDDDDDBBBBDDDDB<555B<<<>9966DDDDDDDDDDDDDDDDDDDDDDDDBBBDDDD<666BBBBDDDDDDCCCGGC>;99=AA@93333336AA@=777:;<;::111116:<<<<666666=====3333:============:631116<;:.../+-
@SRR005406.185 FB9GE3J10F7ANZ length=282
TATTGACTACTGCCTGATTTTCTTGACGTTACTCCACCAACCCATTGCTCTTTCGATGTGATTGTTGTAAATGCTGAAACTTCATCTGCCAAAGAAATGGTATCTACCGTTGTTCCTGGTAGTCGATAGGGATCTACAGTTGGCCAATAGCTGGAATTAAATTGAACCTCGTCATCATTATATACGTACATCATTCCGTCACCAGTGTGCCAGCCACGTTTATTTTCTTTATTCCCTGCTTCAAAAGATGCAGTGCACTTTGAATACAAGCCTAGCCCAAAA
+SRR005406.185 FB9GE3J10F7ANZ length=282
FFFFFFFFFFFFFFFFFFFFECBBCEEEFFBBBFFFFFFFFFFBCAEEEFEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEEFFFFFFFFFFFFFFFFFFFFEEEEEFFFFFFFFFFF;444448888D<<8;;;;;;BEEBAB779474?@@@@@???@@@@@@@@@??=====@@?::111.
@SRR005406.186 FB9GE3J10GDCJK length=283
TATTGACTTGCCTTCAACGACACCTGAAAAAGAGCCACCATATGTCCAGCGAGCAATGGTATTATTTAAAACAGTCTTAGTATCTCCTTTTATATAGATATCCCAAGTATCATTACTAGCAGGATAGCCGCCGCCACCAACAATATCCCAACCTGAACTATACCCACGACTTTTATCGGTCGTTGAATAATCTAAGCTTGTCGGTTTTGCGCCTGAATAAGCCATACCATCGCCACCTAAGGACCCATCACCATTCGCTGTTCCCACTTCAATTGTTGTATTT
+SRR005406.186 FB9GE3J10GDCJK length=283
DDEEFFFFFFEEEEEEEFFFFFFF@;00000;0EEFFFFFFFFIIFFFFFFFFFFEE???CD??333111193??FFFFFFFFFFEEAAAAAAEFFFFFFFDDDFFFFFFFFFFFFFFFFFFFFFFEEEFFFFFFFFFFFFFFFFFFFFAAAAEFFFFFFFFFFFFFFFFDDDDFEDDDFFFFEDDDEFFFFFFFFFFFFFF776666@DFFFFFFEFGFFFFFFFFFFFFFFGGFFFGGGGGGG@@@@@@@???@@@@@@@@@@@@?????@@@===?@@??
@SRR005406.187 FB9GE3J10GBR7U length=330
TATTGACAGTTAAACAAAAAAATACTTATATTTTGCTTGTTATTTATTCATTTTAATCTTATTCAAAAAAAGAAACAGCTAAAACGACTGTGAAAACAAAGTATTGAAAATAAAGCAGAATAAATATTCATTTTTATTTGAAATTCACGAATAAAAAACAAACAATCAATCGAACGCTTGTTATTTAAAAACATAATCAGTTTTTTCTCTTTCTATTTTCCAATCTATGAGTAATAAAATATATGAATCTACATTTAAGTCATTTTTATTATCAAATATTCTGAATATTATAAGAATTGGAGTTTTTATCTATGAGTGACAAAGAACTAA
+SRR005406.187 FB9GE3J10GBR7U length=330
DCCCDDDDDDDDDDD;;@@@@@IIIIIGGGDDDDDDDDCBBC622>==>>>>11770>@DDBBC6666999C+++ADDDDDDDDDDDDDDD@66668333CDDBDDDDDC:777ACDDDDDCCCDDDDDDDDDD>@///?BDDDDDDDDDDD@@@@@@D///DDDDDDDDDDDDDDDDDDDDDD6655555>7>>>DDDDCCCC>>>=:6......04;9;==????????????===????=999../......./;;;;;=:777:111:==7111
@SRR005406.188 FB9GE3J10F8JOH length=238
TATTGACTAGCTATGAAGGGGATTTAAACAAGACAATGTGGCAGGATATTGCTGATGATCAAGGTGTTTCCTTAGAAGAATTTATGAAAATATGACCCCTGAATCTTTTGCCAACAGTGTAGCTAAACTGGATCAACAGCGCGAGGAAAGCAAGAATAACTGGCCTGCAGAAGACTATGCTACAATTACCAAACGTTTAGAAAAAGCTTAGATAAATTGTTGCCACAGAATCAGCCAA
+SRR005406.188 FB9GE3J10F8JOH length=238
AAAAAAAA?@@?>8222755558000223.2==B>===>>>?????@@AAAAAAAAAAAAAAAAA??669=???99;;;=6733338.???<==?AAA@AA<<<<888???AAAAA???AAAAAAA????AAA???=???0000006=7422979660000>??>;666;????><<4333446.-----36--*3----------38666699944444899442555555,,
@SRR005406.189 FB9GE3J10GG47Y length=307
TATTGACGACGAATCTCTTCAAATAAAATATGTGTACGTCCAACTTTTGCATACTCCATTGAACTCATCCCTTCAAAAACACCAACAATTGGCGGTTGAACACGGCCAAAATCATCCAAAGTATTCAATTGGATTTCTAAAACTTGGTTATTTTTTAAAGACTGCTCTAAGTATTCTTCAATTTCTTCTGTTGTCTGTTGCGGTAAGCGTTCAAATGCTCTCTTAGAATATTCGTCAGAAGCTTCGATTCCTTCTTGTAACTCCCCCAATGCAAAAGCGGTCGCCCATTTCAGTTCAAAGGGACGAT
+SRR005406.189 FB9GE3J10GG47Y length=307
DDDDDDDDDDDDDDDDDDDE<<<@DDDDDDDEFFFFFEDDDDEEDDDDBBBDDDDDDDDDDDDDDDDDDDDDA6/////82>>>>>@B6666DDDDD@@@BDDDDDDDDDDDDDDDD@@@BBDDDDDDDDDDDDDDDDDDDDDBBBBBB?777777????==DDDDD??>>BDDDDDB>>>BBBDDDDDDDDDDDDDDDDDDDDDDDDDDDB999DCCCCCCCCBBBCCCCCCCBBBCCCCCCDD>>>???>>>>>=:777=7700066:86...17:=========>>>>==:::=>??>>>?>:7
@SRR005406.190 FB9GE3J10GEEO7 length=291
TATTGACGGGCGGCACACTTTCGACCTTTTCTTATAGTGCCAGTGGTGCCTTATTAAGTTATTTCGGTCATGTTGCTTGTCAAGCAGCTGGGGCCAAAGCGGGGTCAGCATCATTGGGATTAGTGCCGTTGGTGGTTTCTTACACAACGTTGGTCAGTTGCTAACGACCTCTTTCTTTGCTCATTCGTGGGCGCCGATGCTGTACTTACCATTTCTATCTCTGTTTGGGTTACTTTCGGGGATTGCCATTGGGATTGCCGCTAATTATTTACTACAACATGTCCAGACGTT
+SRR005406.190 FB9GE3J10GEEO7 length=291
A@@@BBCCC=766@ACCDAAAAAA4400005-4@@@A@=>>>>>@<<544@<<334463350006440<<@@@@@ABBB@AABBAAE@;0000;;111;5////5;A@BBDDCCCCCCAAACCCCCCCCCCCCCCCCC@::>>CCCCBBBCCCCCCCCC@@>9666661116:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:11
@SRR005406.191 FB9GE3J10GB4AI length=312
TATTGACTTGAAAAAGAATATATTCATTCCCAATATCGCCAGTATCTTCAAATGTTAATAATTTTGAAAATGTTTCTCCTGTTTTTTTGTTCAGCAATGGTTAAGCTACCATTGTTTTCAATTTTCACTTGAATAAATTCGTTTTCCATTTCATTTGTTGCTGGTTGAGCCAAAAGACTTCCTTCAAAAGCTTTCGGTTCTCCTTGAATCAATGCAAAGCTATCCCAAGAGAATGGCGCCATTTCTTTGACAGATAATTCGACCGTTAAGTATTTAGCCATGTACGGTTGACGGAAGGCATCTTTAGGTAAA
+SRR005406.191 FB9GE3J10GB4AI length=312
DDDDBBFB>7/////>00?>CDDDDDDDDDDC@@>DDDDDDDDDDDDDDBBBDDDDDDDDDDDD>85555BB@@@A:>>>>///////@11DDDDDDDDDDDDDDDDDDDDDD45000<<@::::BBDDDDDDDDDDBBB<5555<99999CCCCCCCCCCCCCCC555C>>>>>><<<666::>>>666<>>><<<>>>>><<<>>>>>>><<<>>>>>>>>>:::=>>>>>>>>>
@SRR005406.192 FB9GE3J10GGB72 length=311
TATTGACATTGGGTTTTCGCCAATTCCGTTTTCGGATGCTTTTTTACTTGGTACCTGTTCAATTAACTATGATGTCACGGCTGCATAAAATTTTTGGTTCAGTCTTGGTCTGAAAGCTTAGGGAAAAGTTTAACCAAAGAATTAGTAGTGGTTAGTTTAGGTAAGAGCGCAGTCGGAAATATTCTAAAAGTGATTCCTGTTGTCGGAACTGTGACTGGTGGCATGGTCAATGCTTCAGTTGCAGTAGCAATTACGGAAGCGCTTGGCTGGGTTACCGTCAAAATGTTAAACGATGGTGTTGATATCTTTGA
+SRR005406.192 FB9GE3J10GGB72 length=311
CCCC@BBC@@666B===8677CC7777800==@778CDD==FFFFDA//CCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDA;9966DDD>>::/0DDDDDDDAAADDDDDDDDDDDDDDCCCCCDCC3388@@DDDDDDDDDDDDDDDDDDDDDDDDCCCDDDDDDDDDDDDCCCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD???????????????????????????????;::??????====???????:444??????===??
@SRR005406.193 FB9GE3J10F6S3M length=239
TATTGACCCTCCTTAATTTTTATTTCATTTACACCTGTAAAATTTTCAAATTCTTTTAATGAGGGATAGGCACCAAACTTTTTTATCTCTCCATCCACAATGGTTATCGGTAAGACACTAATGCCATTTTTATCTATTAATGATTTGACTTCCTCATTTTCCAAAAATACATTTGGTTCAATTGTTAAGCTATGACGTTCCACTTCGTAATTTGTTTCTCGTTGAATTTCTGTAATGTT
+SRR005406.193 FB9GE3J10F6S3M length=239
????@@??94//87<<558552)))::??@=====AA=44437775:9:<<:8....22-99999:;:;;99:<:600......,(66<999=>>??????????@?AA?<<<===;;724...........4*66666::86<<<<><000066:;9999<;;;;;;;;;9000;:66...5.5552,,,,,,2*,,,,2,,,
@SRR005406.194 FB9GE3J10GAL1A length=214
TATTGACTATATTATTTGGCTTAAGTTTGGCGACAATCGGTTGGCTAGCTTTAACAATTTTACTAGAGATGCCTGTTTTATTAGGATTCGTCGCTGGACATGTTACCTATATGATTGGTCTAGGTTTTGCATACAGTAATATGATGACGACTGGTATGAGCTTGTTAGAGGAGAAAGTATTTTGGCGACGGCAATTACGTTATTTAATACACTT
+SRR005406.194 FB9GE3J10GAL1A length=214
AAA?@@@@??????=<<=::::>>?=<<::<<<11....02/<<<<:;====9222.223=777788;;666:::974...44.....8.........+........46---------3------33.1668--
@SRR005406.195 FB9GE3J10GEPF2 length=283
TATGACAGCTGCCAAAAGTAATTTGAGTCCTGTTCAACGAGTTGTTTCTGTTTTAGCTGAGATTTTTACACCATTGATTCCTGCACTTGTTATCGGGGGATTGATTTTAGGATTCCGCAATATTTTGGAAGGGGTTCCATTTGGCTTTCTTGATGGTCAAACAATCGTGGAAGTTTCTCAATTTTGGAATGGAGTCAATTCATTCTTATGGTTAATCGGCGAAGCAATTTCCTACTTTTGCCAGTTGGATTACGTGGAGTATTACGAAGAAATGGAACCACAC
+SRR005406.195 FB9GE3J10GEPF2 length=283
AAAAAAAAAAB@@????94++<@????AAAAAAAA;;;;;AAAAAAAAAAAAAAAAAAAAAAAAAAA66666==?AA????AA???@?====;4.....4444......666:;>>??@AA?<=:::<.344....44448333996666699:;;;:60000099952220222,,,,,,,,*,,,,,,,,,,,,,,,,,,,,1,,,,0,,,,,,4300-,,,,,,,,,01,,
@SRR005406.196 FB9GE3J10F7ZWL length=269
TATTGACTCTCTAACGGAATGATTTGTTCGTTAGAAGAGCTAGGATATTCAGACAATGTCGTACCAAAAGCCTATGCTGAAGGGATTTATTATTTACCTCAAGAAGCAGTGAATGGGACACCTGTTTTCCCTTATTTAGACATGGATGATGCGATTATTGAATTATCCAATTACACCAAACCGTGCCGATGCATTAAGTATGAGGAGGGGTAGCCTATGAAGTTGGCGCAATTTATCGTCAAACGCCTCAGTTTAATGACTCCCGAACT
+SRR005406.196 FB9GE3J10F7ZWL length=269
CCCCCCCBAACCCCCCC;;==CCCA=55=355633311777A700///00A<:7777>A>>9999AAAA222229>>>>9-22A><<<<777777<>>><777<<111177;;72-,-------,------2777,1
@SRR005406.197 FB9GE3J10GDSQU length=287
TATTGACAATTCACTACTCCTTTCGGCAAGACTTGATCAAAAATTTTAAACAATTCCAACAGACTTAATGATGTGCTCGAGGATGGATGAATCACAACAGTATTACCTGCTGCCAACGCTGGTGCTAATTTCCAAGCACCCATTAATAAGGGGAAATTCCACGGAATAATTTGACCCACAACACCGATGGGTTCTTTCACAACAATGGATAACGTATCCTTATCAAATTCTTTGACAGACCCTTCTTCTCCACGAATCACACTAGCAAAATACCGAAATGGTCTGCA
+SRR005406.197 FB9GE3J10GDSQU length=287
DDDDDDDDDDDDDDDDDDDEFFFFFFFHHHFGEEDDDDDD9661111---8:@>>>>>>@DDDBBBBBDDDDDDDDDB@@@@DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBBBDDDDDDDDDDDDDDDDDDDDDBB;;;??DDDDDDDDDDDDDDDDBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCCCCCBBBBCCBB<;;@BCBBBCCCCCI>>>>>>?>>===>?>>>?>====::8066/.../.666::::
@SRR005406.198 FB9GE3J10GFHLA length=299
TATTGACACTGTTCTAAAATAAATTTCTCTAACCACAGTTGTTGTTGTTCGAAATATAACCAACCTTCTGTTGATAACGCTTCATTCGTTAAGAAAGGCAAATACAATAGATGGCTTAAGTGCCGAATCTCATAAATTGTTTCTTTTGATAAATGTTCTTGTTTTTGTTTTTGTGAGGAGGCCTTCACTGAATGAACCTCAGAAAGCAATGGGTTTGTTGAAGAGAAGCTGCTATTAATCCGATGCTCGCGTAGATAGCTTTTGGCGGCAGGCGTCAGAAAACTGCCTACAGGAAACAA
+SRR005406.198 FB9GE3J10GFHLA length=299
FFFFFFFFFFFFFEB;;;;EFFFFBBBEFHFFFFFFFGGGGGHHHFFFFFFEEEFFFFFFFFFFFEEEFFFFFFFFFFFFFFFFFFFE>=>>EEEEEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF====FFFFFFFFFFFFFFFFFFFF66666FFFFFFFFFEEEEFFFFFFFFFBBBBFFFF===FFFFFEEEFFFEEEEEEEEEEEEEFFFFFFFFFEFFEEEE@@====@@@@@?===?7777@@@?=====::::=@@@@@@@@=7777@777==?
@SRR005406.199 FB9GE3J10GGFON length=308
TATTGACCGTTCAATCTGTCTCTGTTACGGAAACAATTTAACCATAAAATAAAGCACTTGGGCGCTAGCGCGCGCCAAGTGCTTTTGTTTAAATATTTAATACTTTATCTAAGAAATCTTTTGTTTCGAGGGTTTTGAGGATTTTCAAAGACTTGCTCTGGCGAACCATCTTCTAGGAAGTTACCGCCATCAATGAACATTACTCGATTAGCCACTTCTTTTGCAAAGCCCATTTCGTGAGTAACGATGACCATTGTCATTCCTTGTTTTGCTAAATCTTTCATTACACCAAGAACATCGCCAACCTA
+SRR005406.199 FB9GE3J10GGFON length=308
CCCCCCCCCCCBBBCCCCEEDDFEFEEC????CCCCFFGCCCBBB@@@@5//-66@BAAAA==:@CCCCCCCCCCCDCCCB=4440@744111@@11144B@;11159B====@DCCCCCCB=/--@@@:11////032@@9999@@B@@@BBBBBCC@@@@<6666BBDDCCCB<<<<@BCCC@@<<<@BBBBCC???CCCCCCCCCCC?????;99>CCB>>>>>BCCBB>>>CCBCCBBBBC<<<<<<<<<<<<<<:<::63.....34833338::::::::::::::::::66666666<<<<
@SRR005406.200 FB9GE3J10GEEFP length=136
TATTGACTTTCAAATAGCGTCCGCGGATTTCTTTTTTGGTCTATGAATAAAATACTGGAAACTTAAATTGCATCACGAATAGAAAAAATAGGGCGTATTATTGCCAACTAAGTCGTAATTTCCTTCGTCTGTATAG
+SRR005406.200 FB9GE3J10GEEFP length=136
>:::==<22222002,88<<:6656630003,,,,,,22(8<<:::::....6-868888<;22,,,00889888:<66886......0(0000,9=<=:11223<;=>874343........3378733499934
@SRR005406.201 FB9GE3J10GEOL5 length=274
TATTGACTTCAATAAATTGAGGGCTTTTCCAAAAAATTAGTTTGTTCACTATGTTTTCTTGTCGTATTTCATGTTAGTATAAGGAAAAAGTGTTCAGTTGATTAGTTGAAGATTTAGAGTGTGGGACATAAGTCGATTAGGCTTGTCTCTCATGTTCTGTCTTTTTTTATGTCATCATTCACTAAACTAATAAATAATTGGAGGTATTTTATGAACTAAATTTTTTACAGCCCAACGTTTAAAAGACACCGCCTATGTAACAGTCGGTGCATTC
+SRR005406.201 FB9GE3J10GEOL5 length=274
AAAAAA@@?=>==11066880003....00......22(8588624<=?AAAA????@44=?AAAAAAAAAAAAAAAAAAAAAA;;;;;???AAAAAAAAAAAAAAAAAAAA888AAAAAAAAAAAAAAAAAAAA?;;;AAAAAAAAAAAAA@?=;;79..........'888888<>>??=700068306----**--336---3----3+33332189444444.988800002;888;;;;;0777666677666663333766303331,
@SRR005406.202 FB9GE3J10F7DD8 length=274
TATTGACCAGAAAGCCATGTCTTACCAAATGATGTAGACATGAGTGTACAATTAGCTAAAAATATCAAGTTAAATATTCCATTGATGAGTGCCAGTATGGATACTGTTACAGATAGTAATATGGCAATTGCGATGGCTCGTCAAGGTGGACTAGGTGTCGTACATAAAAATATGACTGTCGCCCAACAAGCAGACGAAGTACGTAAAGTCAAACGTTCTGAAAGCGGCGTTATCATTGATCCATTCTTTCAACACCAACAAACTTAGTAGCGGA
+SRR005406.202 FB9GE3J10F7DD8 length=274
DDDDDDDDDDDDDDDDDDEEFEEEEEDDEEEEEEEEFFFGIHHGHDDDDDDDDDDDDDDDDDDDDDDD@@@DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDB88888=2BDCCCDD=>888887BDDDDDDDDDDDDDDDDBBBDDDDDDDDDC@@@BCCCC@;;777CCC@@@CCA@?:::71......977....44..../...6:::
@SRR005406.203 FB9GE3J10GEE35 length=316
TATTGACTCAAAGAAAAAGAAATAAAGGAGTCGTTTGTGATTATCGATGGATTTACGTTATTGCTATTTTTATTTGTCGTCGTTATGTATGGTTACTTTTACTTCGTACGTAAAAGTATTGTAATTCCGGCTGCAAAACATCCTACAACAAAATATCTAGTTGTCTTTTTTTAGTTTAATGATTCTGGCCAATGCATTTTCGGCAGGAGATAAATTGAAATGATTCGAAGTGTGTTATATATTTTGATCATCTTCTAGTTTTTCTTTACGATGCAAGTAGGTTTTGCGGAGGACTGTATTATTACGCATTCCTTTT
+SRR005406.203 FB9GE3J10GEE35 length=316
AAAAAAC<<64465<<85A---A@>>6409==><<11////46766442--,44----11+//:::::::5511152////0422400264424-11115:7766644//,,
@SRR005406.204 FB9GE3J10GDQG8 length=323
TATTGACATCGTAAAAAAGTCAACTTTTCCTTAGCTACAAAAATTTTATTTACCTGTATCTTATTCAATTTAATTGGTGGTGTCTTATTTGGTTTCTTGGTATCACTTACGGTGCCATTCCAAGATTTGCCAAAAGATAGTTTCTTCTTTACGTCGATTGCTGGAAAATTAGAAAAAACCACCCTACAGATTTTAGTTGAAGCTATGTTCGCCAATATTGTGGTTAATACAGCCGTATTAGTGAGTATGCGAATGAAAGNTGACGCCGGCAAAGTCGTGGCCATTTATTTTCATTATCTTTATCTTTGCTTTCCTTGGTTTTA
+SRR005406.204 FB9GE3J10GDQG8 length=323
DDDDDDDDDDDD88;;;;BBBDDDDDDD@@;;@EEEDDDDDDD<;;;0@DDDDDDDDDDDDDDDDD@@;;;BBBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBB;;;;?DDDDDDDDDDDDDDDDDDDDDDDDDDDD8555@@>>==777==111.!68:::........::66...::8......00:===========6...6/............./
@SRR005406.205 FB9GE3J10GGSCC length=299
TATTGACTTACCTAAAGTCGGAAACCAAGTATATTCCACCATGCGCTCCGTTACTTCAATATCGACTTCTTTTGCTCGCACGTGTACTACATCACCAAAATGCAAAGAAGAAAGCTCTTCGTACATGTCTTCATATTCCAAGGTGTGTTCTAATGCTACCATGCTAATAGTGTGCGTTACTTTTGGTTCATGAATACGGTCTTTATCAAACAATGACTGGCCCCTATTTTTTAAGCTCATCAACTGTTTTACATTCCGAATTTTCACGTTTTCCAATTCTTCGGTTACTATCATTTACA
+SRR005406.205 FB9GE3J10GGSCC length=299
EEEEEEEEEEEEEEEEDDE@@777DDDDEEEEEEEEEEEEEGGGFEEEEEEEEEEEEEEEEEEEEEEEE====EEEEEEEEEEEEEEEEEEEEEEEAAAAEEEEEEEEEEDDDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEDDDDE====EEEEEEEEEEEEEEEEEDDDEEEEEEEEEEEEDDDDDD:::://444/99DDDDDDAB===::@@@==:::@=:::@@@:777@@@====:::7777:?@@@@@@@::::::@@@
@SRR005406.206 FB9GE3J10F6E5C length=322
TATTGACTTAAATGTTTCAATGGAAGCAATCGTCCGCAAAATGTTTTCTTCCTCATTGTAAGCAGGAATGATTAAAAGTACCTTCATAAAGAGAAACACCTTTCCACTTTTTCTCTAACAAAACCCCTCACTTACACAAAACAATTTATTGTTGAACATTTCTAACATTTGTGCTAAGGCTTCTTGCCAAGTAGGAATTTTAAAGCCTAACGCTTCTGTTTTACTTAAATCCATGACAGAATATTGTGGTCTTTGCGCCTTTTGTGGAAATTGAGTTGAATCCCACTGGCAATACTTCCACTTCAGTATCTTTTAAAATTTT
+SRR005406.206 FB9GE3J10F6E5C length=322
B>>>BBDDDDDBBBBDDDDD@@@DDDDDDDDDDDDD>55558?====?55BBDDDDDDDDDDDDDDDDDDGGGDDDDDDDDDDDDDDDDDDDDDDDDBBBDDDDDDB99988>0DAFBB9=557777>7>DDDDDDDDDDDD::999>DDBBB:444@11140444:11140@BDDDDBBBDDDDDDDDDDDDDDBB====DDDDDDDDDDDDDDDCCCCCC>;11;;CBBBCCCCCCCCCDCCC>>>>>>666>>>>=::::>8::666===<<<<;;:611163::;;<<=<:::::>>>>>>>>>>=<<;33333++++
@SRR005406.207 FB9GE3J10GC9TJ length=286
TATTGACCAAGCCATTCAAGCCCAATTTGATCAACCATTACCATTAGTGACAAGCGCTGGGACCACAGACTTAGCTGAATTTACTAAATCAGACAATACATTTGATTGCGTTGTCTTTGGACCAGGTGTGACCACTACTGCACACCAAGTCGACGAATATGTCGAAATTGATAATTATTTAGATATGATTGATAAGTATCAAGCGATAGCAAAAAGTTATTTAAATTAAAAAAATGTCGCGCCTGAATCATAAAAATCAGGCGTGACATTTTTTATAAGGTTTATT
+SRR005406.207 FB9GE3J10GC9TJ length=286
DDDDDDDDCCCCDDDDDDDDDDDAAAADDDDDDDDDAABDDDDBBACCCCCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDAAACDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDFDDDDDDDD99>>>99DDDDDDDDDDD?>===711...69;;;9999666.......+..669999..
@SRR005406.208 FB9GE3J10GAJOM length=292
TATTGACTTTGAGGTTGCTAACGCATCTTCAAAGCCACCTGCACCAACAAACCGTGTTACGCCAGGTGCAGCTACCATAGCCATTGCTCCAACGCCTACTGTTTCAGTAATTGCACTATCCCCGACATCAGGATTTCCGTCTTCTTCGCTGAAACCAGTGAAGTAAAGACCTTTTGGTGTATTTACTGGTGCGGTATGCCATTGATCGCCTGTTTCTGCAATCCGAACCCCAAAGTTCACGCCGTTACGAGTCATCGTTGTGACAATCGTTCCGTTGGTATCTTTACGGGCA
+SRR005406.208 FB9GE3J10GAJOM length=292
DDDDDDDDDB??>DBB>?@DDDDDDEEDDDDDDDDD@>>DDDDDD>>>88877DBBBDDDDDDBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD>>>>DDDDDDDDDDD>>7BDDBBBD>>>DDDDDDDDDDDDDDB999>>DDDDDDDDDDDDDDD5555<<5BBBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCB>>>BCCCCCBBBBBBCBBB>;;;BC>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>===:6311::
@SRR005406.209 FB9GE3J10GG53Z length=299
TATTGACTAACTATGCAAGAGATGGCCAATATCGCTCGTCTTAAAAAAGGGAAACTTTTTAAAGGCACAAGTTGAAGATGGGTCATATCAATATTTTGAGATTTACAATATTAAAAAAAATCTGCAGTCAGTTTCAGTGACAGCAAGACACATTGGTTTTATGGCAAATAAGAATTTCATTATTAATTCATTTACTGCTAACGGAAATGGCACGCAAATCATGAACAATTTAAAGCTGCATTTAACGTTTAAGCAACGGTTTAGTTATTTGTCGAATGTCGGTACTACACATCAATTTA
+SRR005406.209 FB9GE3J10GG53Z length=299
CCCCCCCCCCCCCCCCCCGFFFFFGIIHGGGIIIIIIEEEGI@@@@@@CCC???CDDHEECCCAAACCCCCCC@AACCCCCCCCCCCCCCCCCCCCCCCCCCCCCDA@BB33////////9;@BBDDCCCCCCCCCCCCCCCCCCCCCCC@@@@@@CCCCCBCBB<<<<88<<<<<@CCCCCCCCCCCCC???CCBCCCCCC44222????B::::99>@@@@==<<<@//////996///////4.................3..3.....4788983666:::666:66666:::::
@SRR005406.210 FB9GE3J10GB81Y length=122
TATTGACCGTCACTCTGACTTCTGATGAGAAAAACAAAGGCTTACTTGACCCTTATGTGATTATGAAAAATCCCAAAGATTCTGAATCACTGGCTATTGATATTCTGACATTCCTTACGGGG
+SRR005406.210 FB9GE3J10GB81Y length=122
AAAAAAAAAAAAAAAAAAFFFFFIIFFE?::==7?+++55BBAA?=?AAAAAAAA???===:<58.....200888896==?=<<=@@<<66643397....
@SRR005406.211 FB9GE3J10F8JHS length=296
TATTGACAGGTTGTTCATCGTTTGAAAGAACTAGTCGGTTTACCGATTGGCATGAATGTCGAACCTGTTGATGAAAATTTAGACTTAGCTTCAACGAGAGTTTCGATTGAACCAGGTAGAAAAGCATCAGCAGCTACTTTCAAAAAAGCCAATGAACTGGGTTTGGATTTTATCTTATTGACAGGTAATCCAGGAACTGGCGTGACCAACGACTTGATTGCTGAGAACGTGGCCTTAGCCAAAAAACATTTTGATGGCATCATTATTGACCGGAAAAATGCACAGTTCAGGCGTAG
+SRR005406.211 FB9GE3J10F8JHS length=296
DDDDDDDDDDDDBBBDDDEIEFD>FFFEEEFEEEEEEGGGFFFGGDDDDDDDDDDDDDDDDBBBBBDDDDDD?5588??DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDAABBB>>CCB;;;;CCBB@@;;;;933+66>>>=========:666.//..44....1;;;6666=======666:
@SRR005406.212 FB9GE3J10F8U2Y length=325
TATTGACATTCTAAACCATGTTATACTTTAGATACTTATTTTTTAGGTAGGAATTAAATGGCACTACTACTATTCTTTTTGTTTTATCGCCCTACTAGGATTTGGTATATTAAAAATTAATAACCGCAGTATCCTCGGCGGTATCACTCTGGCTTCTGGCACCTTATTGTCATTAGTCACCTTACTATTTATCGGACTAGACAAAATTTATTTACATTTTAAGAATGGCGACCTAATTACTTTGGCAATTGCTTATCTATTAATTCCCTCTGTGTTTATCGGCATTTGCCTTTACTTTATTTTTAACTCACGTACGATGCAAAAC
+SRR005406.212 FB9GE3J10F8U2Y length=325
DDDDDDDDDDDAA;;;;AADDGDDDEGEEDDDHHFGC@//////8>>-85>>>772228>>CDDDDDDDDDDDDDDDDDD:////@9@@DDDDDDDDDDDDDD:858CBAA/////55..===DDDDCCCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDFCCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD>>>D;;;DDD4444::@@@DDDDDAAAADDDDDDDDDDD?????????????????????????????777??????????????????????????????8:::=::7777:::::56
@SRR005406.213 FB9GE3J10GB7Y5 length=283
TATTGACGACAGAATTACGGGAAAAGATGGGCTTGGTATTACAGGATGCTTTCATGTTTTATGGAGATATTGCTGGAAATATCCGTTTACTGAATCCAACTATCACAGATGAACAAATTAAACAGGCTGCGGAATTTGTTCAGGCGGATAAATTTATCCACACGTTACCCAATACCTATCATGCGAAAGTCATTGAACGAGGAGCGAGTTATTCTAGCGGACAACGTCAATTAATTTCGTTTGCACGAACGATTGTGACTGATCCCAAAATTTTAGTTTTAGA
+SRR005406.213 FB9GE3J10GB7Y5 length=283
DDDDDDDDDDDDDDDDDDD@@@@8872@BDDDDDDDB@@@EEFEIDDDDDDDDDDDDDDBB;@@BBDDDDDDDDDD;;;BBBBBDDDDDDB@@@BBBBBDDDDDDDDDDDDBBB;;;DDDDDB=@@DDDDDDDDDDDBBBBDDDDDDDDDDDDDDD???DDDDDDDDDDDDDDDDDDDDDDDDDD;;;BDDDDDDDDDDDDDDDDDDDDDDDDDDDCCCCCCCCDDDDDCCCCCCCCCCDDDCCC>?>>====>?>>>??>>>>7777==::::27....:==
@SRR005406.214 FB9GE3J10F670P length=309
TATTGACAGGGAGTGGAGTAGAAGCACCAAAGCTTCTGGTTCACTCTCTTCTCGTATTATCCAGTCAAGTTGTAGCAATAGCTTAGTGGGAGTTTAAGAATTATATAACAAAAATCACTGGCACTTCTCAATCAGGGGAGTGCCAGTGATGCTTTTTAGTTGCACTTCTTTCCTTTTTCTGTGAAAATAGTTTGGGTATCAAAGTAATTGATTCTTTTTTTTAAAGCCTCGTCCCTTGAAAATGCGCCTTTTTTGAAATATTTGAAGAATATTTCATTAAAAATATAGAAAATTCTCTTGCATTCTTTG
+SRR005406.214 FB9GE3J10F670P length=309
DDDDDDDBBBBBBBDDDDDDDDBB@@>>888BBDDDDDEDEEGGGDDDDDDDDDDDDDDBBBDDDDDDDDDDDDDDDDDDDDDDDBB99:?BDDDDDDDDDDDDDDDDDDDDDDBBBDDDDDDDDDDDDDDDDDBBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDB>9996DDDDDD699DDDDDDDDDDDDA??222////////0077;;=;;70007777777??7444....../.55:344:<<==:::744488.......70::8..11::<;<<:8661114445
@SRR005406.215 FB9GE3J10F70U3 length=283
TATTGACTTCCGTACCTGCTTGACGACCATAAATGATAATATCGGCGATGGCATTGCCTCCGATACGGTTTTGACCATGTAAGCCACCTGTTAATTCACCAGCAGCATATAGACCTTTAATTGGTGTGCCATCTTCACGTAAAACTTCTGTTTTCGTGTTGATTTTCACGCCACCCATTGTGTGGTGAATCCCTGGTGCAATTTTAATTGCGTAGTAAGGCGCTGTGCTTAAGTCAGCTTCCATGCCAGTTGTCCGGCCAAATTGTTTGTCATCTTTGGCTAA
+SRR005406.215 FB9GE3J10F70U3 length=283
DDDDDDDDDDDDDDCCCCEHFFFHEDEEEFEEEDDDDDGGEDEEEDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDAAAADDDDDDDDCCCCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCCCCCDDDDD8888BDDDDBBBBDDDDDDD@<<<<:::??????=:::??::::
@SRR005406.217 FB9GE3J10GGUSS length=291
TATTGACAAGGTAAGAAACGTCCAGAACGTTCAGATAAGCGTTCAAAAGAAACGGAACCCACGACCAGCGATAGCAGGTGCTGATGGAACCTCAGAAGAGCTAGCAGATAACTTTGTCTTTGGTTTCCATGCCACTGTTGAGGCGTTGCAGCAAGGACGCGGGAATAAATTGTTTTTACAAGAAGATGCTCGTGGCGAGAAAATTGAGCAATTAAAACAAGCAGCGAAAGAACAGGCTGTTCCAGTTAAATGGGTGCCTAAAGCAAAATTAGATACGATGAGTGATCACGG
+SRR005406.217 FB9GE3J10GGUSS length=291
EEEEEEEEEEE@88;666@EECCEEDDEEDDEEEEEDDEE@@@E????;333;8>==FE>@AADEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEA===DEEEEEEEEAA===AAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE@@@FA6/////66FFGFEEEEEEEEEEEEEEEEEEDDDD@@BC<<551111946>DDDDD@ABDDDDDDDDDDDDBBB@7777@@===@?===??@::3333::@@@@@@@@@@@@@@@@??===
@SRR005406.218 FB9GE3J10GFBPZ length=293
TATTGACACACCATAACGTAACATAGCAACGCGATCTGGTCCTAAGCCAAAGGCAAATCCTGAGTACTCTGTTGGATCAATCCCTGACATTTGTAATACATCTGGATGAACCATCCCCGCACCTAAAATTTCAATCCAACCTGTATGTTTGCAGACGTTACAACCTGCGCCGCCACATTTAAAACAGCTAACATCTACTTCGACTGAAGGTTCTAGTAAAAGGGAAATAGCTAGGACGTAAACGAATTTTACGATCTTCACCAAACTATTTTTTCATCATGACTTCTAACGTT
+SRR005406.218 FB9GE3J10GFBPZ length=293
AAAAAAAAAAAAAAAAAAAAAAACABBCCFEAAEEEFFFFEEAEEAAAAAAAAA:::::9AAA?@?A?AAAAA889??@@@????@@@A===AAAAAAAAAAAAAAAAAAAAAA??<<=3=:74........44449====>>?@??;;;???>=???>?;6666;>?===<6965000000626+66<;;9666;966336863-----33813320200,,,***2,2222,,,2052222,*),,,,,13011,,,,,,,,,0,),,,,,,,,111,,,11100,,,,,,
@SRR005406.219 FB9GE3J10GFC1M length=286
TATTGACCTATGTCATTGGTCGAAAAGATTTCTTGGTTTTCTTTTTTCCTTTGCATACTTCATGAGTATCGTCTTTAAGTCATTGGAAATTACCATGGTAACGTATGCCATCTTTGGCGTAATTATTGCGTTAATTTTTGTTGCAAGTCCAAAAAGGCAAACCTGTAGCAGAAAGTGCTGGTTCCGCCAGTGCCACCACTGATTTTGATGATGATGACGATTACGATGACGGGTTTTAAAAGAAAAGGAGGAACTGAAATGACGGAAACAACAAGAAAAAGTCGTG
+SRR005406.219 FB9GE3J10GFC1M length=286
AA??@@CCAAAAAAAAB443<9////<-000A;;<?@A>@@9:::9@@@A9:::AACCCCCAAACCCCCC::::CCAAACCCCCC999AAA9922229>CCCCCCCCCCCCCCC>>><71111/////55640****---,,---44---44::::::2:55551111111::::::
@SRR005406.220 FB9GE3J10F693E length=265
TATTGACAACAGATACAATTAGTTTTACGGCACTGAATAATGCGTATGAAGGAATTTATCGTTTAGATGATAAAAGCAAGCCGCAACCAGCAGGAGCTAAAGAAAAAGTGCAAGTCAGTGATGATGGTCTGACGTACACAGTGAAACTAAGAGAAGAAGCAAAATGGTCCAATGGTGATCCTGTCACAGCTGCCGATTATGTTTTTAGTTGGCAACGTACAGCAGATCCTCAGACTGGCGCTGAGTATGCTTTATTTTCAAGAAA
+SRR005406.220 FB9GE3J10F693E length=265
DDDDDDDDDDDDDDDDDDDD>?5558BBBBBBDDDDC@>>DDDDDDD?8999DDDDDDBBBDDDBBBDDDDDDDDDDDDDDDDD??>>DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD>>>BDDDDDDDDDDDDD9999BDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDB=<<<=DDDDB9..99DDDDCCCBBBBC>>>>99;>>>>>@CCAC@>=966655...8..../..5444
@SRR005406.221 FB9GE3J10GFV1Q length=278
TATTGACCAGACACACAAGCATTTTTTACCGTATGTTGTCGCATATTTCTCTGATCGCTGCGGTCGACAAAATGTCGCCTATGCCACGGTACATTTAGACGAAACCACGCCCCATATGCACTTAGGAATTGTGCCTATGTACGAAGGGCGATTGAGCAGTAAACAGGTGTTTAGTCGGCAAAATTTGTTAGAGATTCAAGAAGAATTGCCAACCTATTTGCAAGAACGAGGCTATGCTATTGAGCGTGGACTCCGTGGGAGTCCGCAAAAGCATTTAT
+SRR005406.221 FB9GE3J10GFV1Q length=278
EEFFFFFFFFFFFFFFFEEEI777777;BHHEEEEFFIEIIFFGHFFEEEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEGGGFFFFFFFFFFFFFFFFGEEEFFFGEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEFFFFFFFFEEEFFFFFFFFFFFFFFFFFFFFFFGGGGGGGGGGGGGGGGGGGGFFFFFG@@@@@?===@@553@@@@@@>1133:@?111=@
@SRR005406.222 FB9GE3J10F8AH4 length=197
TATTGACGCAAGAATTTAATCCAGAAGAGATAGATGAGAACCAACCGATTGATGTGCGAATTGATTATGTTCAATCATTTCAAGCGTTAAGTAATAGCTATGAAGCATTAGTGACCTATGATGAATACAATGATGAAATGGAAAATCACCAGCTTTAGCTGAGCAAGTCCATTTGATTGAAGAACAGATAGGAACAT
+SRR005406.222 FB9GE3J10F8AH4 length=197
AAAAAAAAAA@A???::885::@@?????ABABA????88::8888<<<<>>>???@????==999??BA?===@AA@?<988<<<<===???@@AA???AAAAAAAA???@=?====944...4......44...3.....7999963444686460..66:::88866664343----313
@SRR005406.223 FB9GE3J10F6KLZ length=142
TATTGACAGAGTAAGTGAGCGAAGCAGTGAACTTACTACGGGCGCCCGTTACAGCCAACGGTATGCGAAGAATCAAGTACCGTATGAGGTTATTATTGAGAAATAATAGCGAATTAAGGTGGTATCACGAAATGACAAACTT
+SRR005406.223 FB9GE3J10F6KLZ length=142
AAAAAAAAAAAAAAAAAAIIHHEAFFCBAB?=::7==723332.766::<;0688822122;7799=?@AAAAAAAAAAAAAAAAAAAA???AAAAAAAA888===AAAA?AAAA????AAAAAAAAAAA??>;:7733...
@SRR005406.224 FB9GE3J10GGN8L length=101
TATTGACATTGAATGTCACTTCTTGATTGGCTAATAAGCGTTTGTAAGAGTCCATCACAATCGAAATAACGCCAGAATAAGGCGAATTAGGGTTTTGGTTT
+SRR005406.224 FB9GE3J10GGN8L length=101
FFFFFFFFFFFFFFFFFFIIIIIIHHHHHHHHHHHGGHHGHIIIIFFFFFFFFFFFFFFFFFFFFFGGGGFFFFFFFFFFFFFFFFFFFFFFGGGGFFFFF
@SRR005406.225 FB9GE3J10F56ZB length=287
TATTGACTAACAGAAGGCGCCATTAAAATTGATGGTATTGACACGAAAAAATGAACCGTAGTGATGTCCGATCTGTATTTGGAATGGTATTGCAAGATGCTTGGTTGTATAAAGGTACCATTGCAGATAACATTCGTTTTGGGAAGTTAGATGCCACGGATTATGAAGTTGTCGATGCAGCGAAAACGGCCAATGTGGATCACTTCATTCGGACAATGCCAGACGGGTATGAAATGGAAATCAATTCTGAGGGAGATAACGTTTCCCTTGGTCAAAAACATTGTTGA
+SRR005406.225 FB9GE3J10F56ZB length=287
DDDDDDDDDDDDDDDDDDDDDD665555B@@@DDDDDDBBBHHAB//////>>>>>>BDDDDDBBBDDDDDDDDDDDBBBDDDDDDDDDDDDDDDDDDDD@@@@@@DDD:22566DB668BDDDDDDDDDDDDDD?8888858BBDDDDDDDDDDDDDDDDDDDDD?;;;;;DDDDDDDDDDDDDDDDDDDDDDDDDDDDD>999DDDDDDDDDDDCCCCCCB@777?C??555@CCBBBCCCCC>:::>>>=======:777777733:89:000777-117447:
@SRR005406.226 FB9GE3J10F80H6 length=228
TATTGACATTTAATTATAAAGGAGCGAAATTTCATGGCACGCGTAGAAAGTTTTGAATTAGATCACAACACAGTAAAAGCACCATATGTTCGCCTTGCTGGCACAGAACAAAATGGTGATGCGTTAGTCGAAAAATATGACTTACGTTTCTTACAACCAAACAAAGATGCCCTACCAACAGGCGCATTACACACGTTGGAACATTTATTAGCAGTTAACATGCGTGAT
+SRR005406.226 FB9GE3J10F80H6 length=228
@???@@@=22066338000022,53000000038<999=?A??AA?????4444349>>=>=@AA?A?????@?444449@???AAAAAAAAAAAAAAAAAAAAAAAAA33338????@???====:9;:111100*=====>??AA?;;77;==977......+.+886;;=>;;;;;;;>><>>>?;96669966000064:<<;;;>>?AAAA<:::8;::555,
@SRR005406.227 FB9GE3J10F5OGA length=74
TATTGACGACCAGTAAAATAATGTCGCGCAGGTGGCGTTTCAGCATCGACCATTAACCAAGCCAGTTAAAAGTT
+SRR005406.227 FB9GE3J10F5OGA length=74
?????>>?===:<922227--:<:<===??????8:8::><>>AA@@??===>?<<99234<<<<<11
@SRR005406.228 FB9GE3J10GACJS length=240
TATTGACACGTACTGGTGGAGGCGGCTTAAAACGTGGCCGTGCCTTTACATCTCACCGTTTCCACGGTAAAACTAAAAACAACGCCGTCAATTGCGTAAAGCAAGCATGGTTGCAAAAGGCGATTACAAACGTATCCGCCAACAATTAGCAAGAATGAAATAAAACAACTCGGTGACTTTTAGATTACCGTCAAGAGAAACAAGATATTAGGAGGAATTCAACATGGCACGTGTTAAAGG
+SRR005406.228 FB9GE3J10GACJS length=240
AAAABBBAAAAAA?@BA88:<9977=<<.3337<9:<::8>?BBBAAAAAAAAAAAAAAAA===?@?=755596*****0**6999=??@@@AAAAAAA???@@AAAA44448?????@?<<::<<==>>>>>>>>>>>>><<<>><<<:666=<631
@SRR005406.230 FB9GE3J10GCSZU length=85
TATTGACGTTATTGGTCCCACAATGTTATTACTATCTAATGGAATCACAGATGCTATTGTTTGGTTATATAATGCAACTGGGTTC
+SRR005406.230 FB9GE3J10GCSZU length=85
?=?=>>=:<97779979933.77==???<<>======79222006
@SRR005406.231 FB9GE3J10GFSGB length=60
TATTGACTAAAATAAGTACGGCGGATAATCCCCACCGATGACGAATATACATTTCTTTTG
+SRR005406.231 FB9GE3J10GFSGB length=60
??A?A@?<<<<<3++9:====:99=====999=4++48??AA???@???@?>>>=.,,,2
@SRR005406.232 FB9GE3J10F6851 length=139
TATTGACTAATAAGCGTATTTTAGCATTTGAAAAGAGAAGTTGTACATAATATGTGAATAAAAAGATTTGTTTCTTATTTTCTAGAGTGATAGGGCGATATAAAAAAGGTTGCTATTTTTTCGTTCAAAGTGAACAAAG
+SRR005406.232 FB9GE3J10F6851 length=139
DDDDDDDDDDDDDDDDDD;8888DDDDDDD;<==EFFFHHIIIIIDDDDDDDDDDDDDDCCCCCDDDDDDBBBDDDD@@@@DDDDDDDDDDD===DDDDDD@@@AA@DDDDDDBA//////44++:<@B<<:<<<2224
@SRR005406.233 FB9GE3J10F487B length=291
TATTGACGAGTGGGGAAGATTTCGAAGAAAGTAAACCGGCGCCGGATATTTATCTGCACACGTTACAAGAATTAGCTGTTGCGCCACAGGAATGTATAGCCATTGAAGATTCAGAAAAAGGCATTGCCTCTGCCAAAGAAGCTGGGCTAGAAGTTTGGGCTATGCGCGATGAACACTTTGGGATGGATCAAAGTCAAGCGGATGCCTTCTTAACACAACTAAGTGATATTTAGTAAAAAAATTAGTGAAAATCGGATCGATGAAAGCAGTGAATCAACCCCTTGTAAGAAG
+SRR005406.233 FB9GE3J10F487B length=291
DDDDDDDDDDDDDDD;;5@CED@;;;DDFFFE???FFGGGGFFFGDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBBBA>>>>66@@/C==333137:::======>=========73333====3337??>>>>
@SRR005406.234 FB9GE3J10GBCSB length=252
TATTGACTCAAAAACTTTTAAGTATCTGAACCCGACGAATTAATTCTAAATATCTAATATCGATTACCTAACTAAATTACACTAAGTTAATTAAATGTAGTATATAATCATTTAAAACTAATTAATTATTTAGTATAATGAAAGACAAGAGGTGATTGTATGTTAACCACAAAATCTAGAAAACAAGGAAGTTCTGTAGTATTGACATTACCATCTAACAACGGACAGAAACCAAAAGCAGACCAAGAATAT
+SRR005406.234 FB9GE3J10GBCSB length=252
FFFFFFFEE77000;EF33::;:BEHFBBBBBHFFEEEEBBBBEEA;777BBFFFFFFFFFFEEEFFFFFFFFFFFEEEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEFFFFE=<>55655ABDDDDDBBBDDBBBDDDDDD>???>?DDDDBBBDDDDDD>>>>D?????BBBBBDDDDDDDDDDDBB>>>>DDBBBDDDDDDDDDDBBB>>>>BDDDBB888>BDDDDDDDDDDDDDDBBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDB<<<CCCC@@;;;;;>>>>99<9C988<663333=<<<<;==6331666<<:11166::::<==><<<>>>>>>>>>>>>>>>
@SRR005406.236 FB9GE3J10GGMYR length=240
TATTGACCCGAAGCTTTCTCTGCATGATGACCGGTTGATTGAAAGCGTTCTAAATAACTGAATTCACTATGATTATCTGCAACGATTAAAACATGTTTAAAGAAAGGTTGGTTGCTATCTGAATCCTGAATAAACAAAGATTCAATGGGCTCTTCAATCACTACGTTTTAGGAACGTATAAGAAACGCCACTATTCATGAAAGCTGCATGAGCTGCTGTCAGCTTATCTTCTCTGGTAAT
+SRR005406.236 FB9GE3J10GGMYR length=240
>===<<999==:7222272==??A?ABBBBBB??BB?BBBB????????=8444848===;;;<>>??==>>????@=>>>>=>=7774446-99000006930066465555===>=>=>>====9994.....,,,.,449944....43333444797663.......33...66886600.06:33163333633----3666666999;;;;;888889988880,,,,,,22,,
@SRR005406.237 FB9GE3J10GA6QP length=260
TATTGACTTCTGGGTTCAAAATTGCGATGCGTGACCTTTCCATTCGAGGGGCCGGAAACCTTCTTGGTGCCCAACAACATGGCTTCATTGATTCGGTTGGGTTTGATATGTACTCACAGATGTTATCTGAGGCAGTTGCTCGTAAACAAGGGAAAAATATCCAAGACCAAAAAACGTCTGTTGAAATTGATTTGGGCATTGATGCTTATATTCCAGGAACGTACATTACAGACGAACGACAAAAAATTGAAATTTATAAA
+SRR005406.237 FB9GE3J10GA6QP length=260
FFFFFFFFFFFFFFFGGCEEEHHHHHHHHHIIIIIIHHHGGHHHHFF;;;;CCBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGG??????FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGG?????GGFFFFFFFFFIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFIIIGGGGGGGGGGIIIIIIIIIIIIIIII@AAAAAAAA@=;888
@SRR005406.238 FB9GE3J10GDQ75 length=90
TATTGACAGCTGTATCTAACAGTTCATTCCCTGTATTGAAATTTAAAAATGGGGCGTCAAGAATTTGTAATGAGACGTTTTTCTTGCTTC
+SRR005406.238 FB9GE3J10GDQ75 length=90
AAAAAAAAAAAAAAAAAAEAIIIFFFFFBIIIFAB???>>>800,,,,,0....2*26<<===>?<<599=>>?=97511116**00000
@SRR005406.239 FB9GE3J10F5XU4 length=70
TATTGACGTTAAGTTACCGAGAATACTTATTTAGTACATATACTGTATTTACACAATTTGGCTTTCTAAT
+SRR005406.239 FB9GE3J10F5XU4 length=70
AAAAAAAA@@??A888@@????????AAAAAAABAAEAEFFFFIIAAAAAAAAA???><=990006,226
@SRR005406.240 FB9GE3J10GA2UR length=210
TATTGACAAGCTGAAACAGAAGAACACCTCCGCTTGAAGCAGCTTTTTGCGGAAAAGTGTTTACGCGAAAAGCTGTCCTTTCAAGTTGAGGCATACTTACCCACCTTGAAGCAACGCCCAGATTTACTCATTGGCAAGATAGCCATTGAAATTCAATGTAGCCCATTGCCAATTAAACGTTTGGTGGAACGGACAGAGACTTATCAAGCT
+SRR005406.240 FB9GE3J10GA2UR length=210
FFFFFFFFFFFFFFFFFFIIHHGHHFHFHGGHIHHHHHHHHHHEHIIEGGGFFFFFGIGFFFFFFFFCCCCGGFFFFFFFFGGGFFFFGGGFFFFFFFFFFFFGGGGFFFFFFFFFGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR005406.241 FB9GE3J10GEMB1 length=290
TATTGACTAAGCACAATAAGCAGTAAGCTGCCACCAATAAAGCCAATTTTCTTGTATCTACTTAATTTTTCCATATTATACATTGTTCTTATTGGTTCCTTTCTTTTTAGTTTAGGCGCATAAAGTATTCGCCTGCTTCTTTTTTTAAGACACGCCAATTCATGGAATACTCACCACTGACATTCATTTCAGAAATGACAAAACTTCCATCAGAGTTTACATGCTCCACATAAGCTACGTGTCCATATTGCGTACTAGAACCAGCTACACCATTTGTAAAAATAACAGCA
+SRR005406.241 FB9GE3J10GEMB1 length=290
EEEEEEEEEEEEEEEEEEGGGIIGGGGGGIGGEEEGGGAAAGGGGEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEDDDDEEEEEEEEEEEA;111=DEEEEEEEEEEEEEEEEEEEEEEEECCCCCCCEEDDDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEED@@@DEEEEAC1116@77777DEEEEEEDDDBBBDDDDDDDDDDDDDDDDDDDDDDD@@@@@:::::@@@@@@@@@@@@@@@@@@@=:777==71///6;99
@SRR005406.242 FB9GE3J10F5H2N length=103
TATTGACAGCAATTGCTTGGATGCGCGTTCGTGTTTCTTCAGTTACCTTTGAACTACCATTCAATGCGTAAGAAACGGTCGAGATTGATACGCCTGCTTTTTT
+SRR005406.242 FB9GE3J10F5H2N length=103
AAAAAAAAAAAAAAAAAAEEEFFFFFFFFAFAA:::B;>?AA???@@???AAAAAAAAAAAAAAAAAAAAAAAAA===AAAAAAAAAAAAAAAAAAA566643
@SRR005406.243 FB9GE3J10F5HV5 length=244
TATTGACTGAACAAGTACCAAACAAGAGTTCTATTATTTGTTGCATCGAAAGACGGCATTCAAAGAAAATTTCAAAGAAGAAACGGGAGAGGAATTAACTAGTAAAACGTATTCTTTAAAGAAATTTCAGCAAGTGAACAACCAAAATAGAAATAAAGTAAAGATTCTCTAAAAGAGATTTAGAGAATGAGCGGCGATCTATTGGCCTAGAAGAAAATCTTACACCATTTATTACATGAAGAAG
+SRR005406.243 FB9GE3J10F5HV5 length=244
;777<<=9222255;8022000503:8<:::99777111804<<==9222272<<::;:88000204,,00020002,,00000000,0<66000088<::90....437-3.......44,,,...444444843444......224*.....,,,.3,,+.+..623.....4+33...6633...4633------3--------33863311-,,,,,,2,,,,,2,,**,2,,,2,,,,,
@SRR005406.244 FB9GE3J10GFX03 length=236
TATTGACTAACGATTGATCAGTTCGGGCGTTGTTCGCTTGAAAATTTGCATAGCCGGATAAACGTTTTGTCACTCCTGCCCATTCTTCAGAATAATAGTTTTTAGGTCCACGTTCATCAAATTCCACTAACTGAATTTGTTGATCCTTAACAACGACATCAATTAAAGCCGTATAGCCGCCATCAAACACGACTTCATGATGATAATAATCCCCTTGAACTTCTCCGATTTCTGGA
+SRR005406.244 FB9GE3J10GFX03 length=236
FFFFFFFFFFFFFFFFFFHHHHHHEEEGEEEFFFHFHHHHHHHHHFFFFFFFFGGGGFFBBBFFBBBBBBGFFFFFFFFFFFFFFGGGFFFFFFFFFFFFFFFFCCCGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFIIIIIIIIIIIIIIIIGGGI
@SRR005406.245 FB9GE3J10GGAR8 length=275
TATTGACTGTTCGAGGGTTTTGAGGATTTTCAAAGACTTGCTCTGGCGAACCATCTTCTAGGAAGTTACCGCCATCAATGAACATTACTCGATTAGCCACTTCTTTTGCAAAGCCCATTTCGTGAGTAACGATGACCATTGTCATTCCTTGTTTTGCTAAATCTTTCATTACACCAAGAACATCGCCAACCATTTCTGGATCAAGGGCTGATGTTGGCTCATCGAAAAGCATGATATCAGGATTCATCGCTAACGCACGTGCAATTGCGACTACG
+SRR005406.245 FB9GE3J10GGAR8 length=275
FFFFFFFFGGEECC5553333===EEHHIHHHHHHGIIIIIIIHHFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBFFFFFFCCCFFFFFFFFFFFFFFFFFFCCCFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGGFGGGFFFFFFFFFFFFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIGGGGGGGAAAAAAAAAAAAAAAAA@@@@AAAAAA=::
@SRR005406.246 FB9GE3J10GD918 length=187
TATTGACAAAATTATTTATTTCTTTTTTTTGTCTTTTCATGCAATTTCCCAGTATTTAAATAAATAATCCCTAGGAAAAGGACAGGGGTTACAACAAACCCAAACTGTGGCTTCAAAAACATCATTGCAAACATTGAGAATAGTAAAAAAACATTTAGACAGCTGACATACCATTTCCGCAGTCCAT
+SRR005406.246 FB9GE3J10GD918 length=187
AAAAAA@==;622*0000,,,300000000<'8....69>>>>>344==AAAAA?AAAAA666>>>BEGGGGGGIIIIIIIIIIG@:::@@???7777::@@@AAAAAAAAAAAAAAAAAAAAAAAA???@@===::311:;<<@B...1.88B;;........
@SRR005406.248 FB9GE3J10GA69A length=294
TATTGACGGAGAAATTCACATGTTGGAAGCGACAGCAGAAGCGATCCAGACCCAAATGATTAAAAAAGGTGAAGTATTACAGGTAGCAAGAGTAGCTGGGATTACCGCCGCAAAACGAACGTTTGAATGGATTCCTTTGTGTCATTTGGTTGCTTTGACAAAGTGTGAAATTCAGTTTGATTGGCGCAATCAAACTTGTTTAGAAGTACGTTGCTTTACAAAAACAGTGGGTTCAACTGGCGTTGAAATGGAAGCGCTAACAGGTGTGCAGGCAGCACTCTTAACAATTTATGA
+SRR005406.248 FB9GE3J10GA69A length=294
FFFFFFFFFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFCC055555CCFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGGGGGFFFFFFFFFFFFFFFFFFFFFGGGFFFFFFFFFFFGC@@@GFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFIGGGGEEEGGFF>>>BBGGGGGGGGGGGGAAAA@@@@AAAA???@@AAAAAAAAAAAAAAA@@@33333=A11187BB
@SRR005406.249 FB9GE3J10GBPSH length=286
TATTGACATAAAGCTGTAGAAGAAATTGGCTTAAAAGATGTGGTAACGCAAGTGGGTGACCGCTATGTTGTAGAAGAAATGCGTAAAAATGATTACAATTTTGGTGGCGAACAATCTGGTCACATGATCTTTTTTAGATTACAACACAACAGGTGATGGCATGCTTTCAGGGATTCAATTGTTGAATGTTATGAAGCAAACGGGCAAAAATTATCTGAATTAGCGGATGAAGTGACGATTTATCCACAAAAATTAGTCAATATTCGTGTCACAGATAAAAATGGTG
+SRR005406.249 FB9GE3J10GBPSH length=286
FFFFFFFFF@@@FFFFFFHHHHGHHHHHHHHHHHHEEEHHHHHHHFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGFFFFF?????FFFFFFFFFCCCCCCBGGFFFFFFFFFFFFFFFFFFFFF@0000007AFFFFFFFFFFFFFFFFFFFFFFFFFFG@@@GFFFFFFFFFFFFGGGFFFFFFFFFFFFFFFFFFFGCC77777GGGFFFEEGGGGIIIIGGGGGGGIIIIIIIIGGGGAA@@@@@AAA@@@AAAAAAAAAAAAAAAAAA@@@@@@AA@@
@SRR005406.250 FB9GE3J10F6I2T length=302
TATTGACAATTGTAAGACCACTAAGGATTTTTGGGCGGCAGCGACTTGGAGCTCTTGTAAAAGCGCACTGCGTTCCTTTTCTTTATTCTTTTGATCTTGAGAATCTTCTAAAAATGCCGAAAAGAAATGTTGGGAAGAGAGCGTAATCAGTTTAGAAATGCTCTTGATGGTAGCTTTATGTTGATCCATTCTTCTGCCTCCTTTACGAATAAAATAGAATAAAACTCAAATGACTAATTACCTGTATTTTACCTAATTTTGTGATAAAATTCAAGAAAATATGTTCGCCTTCAATAATTATG
+SRR005406.250 FB9GE3J10F6I2T length=302
FFFFFFFFFFFIGIIFFFHHIHHHHHFBBBBBHHC>==GHHHHHHFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGG>>>CGFFBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGGGFFFFFFFFFFFFFFFFFFFFFFFFCCCGGFFFFFFFFFFIIIIGGGGIIIGGGIIIIIIIIIIGGGGGA::::??@AA@@@@@@@@@4444477@@@@@@@@AA@A@@@@@@:::==?????@@A
BioPerl-1.007002/t/data/fastq/test2_solexa.fastq000444000766000024       103613155576321 21462 0ustar00cjfieldsstaff000000000000@SLXA-B3_649_FC8437_R1_1_1_610_79
GATGTGCAATACCTTTGTAGAGGAA
+
YYYYYYYYYYYYYYYYYYWYWYYSU
@SLXA-B3_649_FC8437_R1_1_1_397_389
GGTTTGAGAAAGAGAAATGAGATAA
+
YYYYYYYYYWYYYYWWYYYWYWYWW
@SLXA-B3_649_FC8437_R1_1_1_850_123
GAGGGTGTTGATCATGATGATGGCG
+SLXA-B3_649_FC8437_R1_1_1_850_123
YYYYYYYYYYYYYWYYWYYSYYYSY
@SLXA-B3_649_FC8437_R1_1_1_362_549
GGAAACAAAGTTTTTCTCAACATAG
+SLXA-B3_649_FC8437_R1_1_1_362_549
YYYYYYYYYYYYYYYYYYWWWWYWY
@SLXA-B3_649_FC8437_R1_1_1_183_714
GTATTATTTAATGGCATACACTCAA
+SLXA-B3_649_FC8437_R1_1_1_183_714
YYYYYYYYYYWYYYYWYWWUWWWQQBioPerl-1.007002/t/data/fastq/test3_illumina.fastq000444000766000024       524213155576321 22005 0ustar00cjfieldsstaff000000000000@FC12044_91407_8_200_406_24
GTTAGCTCCCACCTTAAGATGTTTA
+FC12044_91407_8_200_406_24
SXXTXXXXXXXXXTTSUXSSXKTMQ
@FC12044_91407_8_200_720_610
CTCTGTGGCACCCCATCCCTCACTT
+FC12044_91407_8_200_720_610
OXXXXXXXXXXXXXXXXXTSXQTXU
@FC12044_91407_8_200_345_133
GATTTTTTAACAATAAACGTACATA
+FC12044_91407_8_200_345_133
OQTOOSFORTFFFIIOFFFFFFFFF
@FC12044_91407_8_200_106_131
GTTGCCCAGGCTCGTCTTGAACTCC
+FC12044_91407_8_200_106_131
XXXXXXXXXXXXXXSXXXXISTXQS
@FC12044_91407_8_200_916_471
TGATTGAAGGTAGGGTAGCATACTG
+FC12044_91407_8_200_916_471
XXXXXXXXXXXXXXXUXXUSXXTXW
@FC12044_91407_8_200_57_85
GCTCCAATAGCGCAGAGGAAACCTG
+FC12044_91407_8_200_57_85
XFXMXSXXSXXXOSQROOSROFQIQ
@FC12044_91407_8_200_10_437
GCTGCTTGGGAGGCTGAGGCAGGAG
+FC12044_91407_8_200_10_437
USXSXXXXXXUXXXSXQXXUQXXKS
@FC12044_91407_8_200_154_436
AGACCTTTGGATACAATGAACGACT
+FC12044_91407_8_200_154_436
MKKMQTSRXMSQTOMRFOOIFFFFF
@FC12044_91407_8_200_336_64
AGGGAATTTTAGAGGAGGGCTGCCG
+FC12044_91407_8_200_336_64
STQMOSXSXSQXQXXKXXXKFXFFK
@FC12044_91407_8_200_620_233
TCTCCATGTTGGTCAGGCTGGTCTC
+FC12044_91407_8_200_620_233
XXXXXXXXXXXXXXXXXXXXXSXSW
@FC12044_91407_8_200_902_349
TGAACGTCGAGACGCAAGGCCCGCC
+FC12044_91407_8_200_902_349
XMXSSXMXXSXQSXTSQXFKSKTOF
@FC12044_91407_8_200_40_618
CTGTCCCCACGGCGGGGGGGCCTGG
+FC12044_91407_8_200_40_618
TXXXXSXXXXXXXXXXXXXRKFOXS
@FC12044_91407_8_200_83_511
GATGTACTCTTACACCCAGACTTTG
+FC12044_91407_8_200_83_511
SOXXXXXUXXXXXXQKQKKROOQSU
@FC12044_91407_8_200_76_246
TCAAGGGTGGATCTTGGCTCCCAGT
+FC12044_91407_8_200_76_246
XTXTUXXXXXRXXXTXXSUXSRFXQ
@FC12044_91407_8_200_303_427
TTGCGACAGAGTTTTGCTCTTGTCC
+FC12044_91407_8_200_303_427
XXQROXXXXIXFQXXXOIQSSXUFF
@FC12044_91407_8_200_31_299
TCTGCTCCAGCTCCAAGACGCCGCC
+FC12044_91407_8_200_31_299
XRXTSXXXRXXSXQQOXQTSQSXKQ
@FC12044_91407_8_200_553_135
TACGGAGCCGCGGGCGGGAAAGGCG
+FC12044_91407_8_200_553_135
XSQQXXXXXXXXXXSXXMFFQXTKU
@FC12044_91407_8_200_139_74
CCTCCCAGGTTCAAGCGATTATCCT
+FC12044_91407_8_200_139_74
RMXUSXTXXQXXQUXXXSQISISSO
@FC12044_91407_8_200_108_33
GTCATGGCGGCCCGCGCGGGGAGCG
+FC12044_91407_8_200_108_33
OOOSSXXSXXOMKMOFMKFOKFFFF
@FC12044_91407_8_200_980_965
ACAGTGGGTTCTTAAAGAAGAGTCG
+FC12044_91407_8_200_980_965
TOSSRXXXSSMSXMOMXIRXOXFFS
@FC12044_91407_8_200_981_857
AACGAGGGGCGCGACTTGACCTTGG
+FC12044_91407_8_200_981_857
RXMSSXXXXSXQXQXFSXQFQKMXS
@FC12044_91407_8_200_8_865
TTTCCCACCCCAGGAAGCCTTGGAC
+FC12044_91407_8_200_8_865
XXXFKOROMKOORMIMRIIKKORFF
@FC12044_91407_8_200_292_484
TCAGCCTCCGTGCCCAGCCCACTCC
+FC12044_91407_8_200_292_484
XQXOSXXXXXUXXXXIXXXXQTOXF
@FC12044_91407_8_200_675_16
CTCGGGAGGCTGAGGCAGGGGGGTT
+FC12044_91407_8_200_675_16
OXTXXXSXXQXXOXXKMXXMXOKQF
@FC12044_91407_8_200_285_136
CCAAATCTTGAATTGTAGCTCCCCT
+FC12044_91407_8_200_285_136
OSXOQXXXXXSXXUXXTXXXXTRMS
BioPerl-1.007002/t/data/fastq/tricky.fastq000444000766000024        71213155576321 20333 0ustar00cjfieldsstaff000000000000@071113_EAS56_0053:1:1:998:236
TTTCTTGCCCCCATAGACTGAGACCTTCCCTAAATA
+071113_EAS56_0053:1:1:998:236
IIIIIIIIIIIIIIIIIIIIIIIIIIIIICII+III
@071113_EAS56_0053:1:1:182:712
ACCCAGCTAATTTTTGTATTTTTGTTAGAGACAGTG
+
@IIIIIIIIIIIIIIICDIIIII<%<6&-*).(*%+
@071113_EAS56_0053:1:1:153:10
TGTTCTGAAGGAAGGTGTGCGTGCGTGTGTGTGTGT
+
IIIIIIIIIIIICIIGIIIII>IAIIIE65I=II:6
@071113_EAS56_0053:1:3:990:501
TGGGAGGTTTTATGTGGA
AAGCAGCAATGTACAAGA
+
IIIIIII.IIIIII1@44
@-7.%<&+/$/%4(++(%
BioPerl-1.007002/t/data/fastq/wrapping_issues.fastq000444000766000024       171713155576321 22276 0ustar00cjfieldsstaff000000000000@SRR014849.50939 EIXKN4201BA2EC length=135
GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
+
;C?-EA/=60,)%"<=:5<
@85@7@8+8<
<3;=4:DA3%<;=8-9.A=):B=*
BioPerl-1.007002/t/data/fastq/zero_qual.fastq000444000766000024         4213155576321 21003 0ustar00cjfieldsstaff000000000000@someID1.f
G
+
0
@someID2
AG
+
DD
BioPerl-1.007002/t/data/map_hem000755000766000024          013155576321 16141 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/map_hem/HEM1-HEM12.fa000444000766000024      1655113155576321 20102 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR232W HEM1 "5-aminolevulinate synthase, catalyzes the first step in the heme biosynthetic pathway; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expression is regulated by Hap2p-Hap3p"
ACTGAAAAAAAAACCTAAGTACTGTTATGATTATTGAGGGACAACAACTAGCTCTATTAG
TTTTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTGGG
ATAAAAAAAAAAGAAACGCGAGCTGAGAAGGGAAGGCGTGTAAAGGAAGAACGGTTGAGA
GACAGCAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGAATGGAGAAG
TTTGGTATGATGCAAACGTTGTATTTCTAACAACGCATGGATCAGAACAATGGGCAAGGC
AAGATGAAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCC
CGCGGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGCGGTAGGGTAAGCCGTGC
AGGCAAGCTTATTATAGCACCGTCGGGGGTACCACCACTATATCAAACTCCACTGCTCGG
TAAAGCATTGTAGTGAAG
>MIT_Spar_c117_4603 YDR232W 5' untranslated region, Contig c117 17441 - 19440, 2000 bp (revcom)
ACTGAAAAAAAACCAAGTACTGTTGTGATTATTGAGGGACAACGGCTAGCTCTATTTGTT
TTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTAGGAT
AAAAAAAGAAACGCGAGCTGAGAAGAGAAGGCGTGTAAAGGAAGAACGGTTGAGAGAGAG
CAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGGATGGAGGAGTTTGG
TACGATGCAAACGCTATATTTGTAGCAACGCATGGGTCAGAACAATGGGCAAGGCAAGAT
GAAAAATTTCTGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGCGG
CCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGTGGTAGGGTAAGCCGTGCAGGCA
AGCTTATTATAGCACCGTCGGGGGGACCACTATATCAAGTTCCACAGCACGGTGAAGCAT
TGCAGTATAGTTCACAGC
>MIT_Smik_c228_4055 YDR232W 5' untranslated region, Contig c228 4702 - 6701(revcom), 2000 bp (revcom)
ACCGAGAGAAAAACTAAGTAGTGATATGATTATTGAGGACTAATGACCAGCTTTGTTTGT
TTTTTCTTCCAACCTAACTTATATGGGAAATATATAGGACAGAAAAAAGAAAAGAGCACG
AAAAAAAAGAAATGCGACCTGAGAAGGGAGGACGTGTGAAGCCAGAACGGTTGAATGACA
GTAGAGGAGGGTGCAACACAACCGAGTAGAGTACCAGCTGACGGAATGGAGGAGTTTGGT
ATGATGCAAAAGTGATGCTTTTAGCAACGCAACATTGAATTAGAACAATGGGCAAGGCAA
GATGAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGC
AAGCGCAGACCAATGAGCGACGAAAGCGGCCTTTTGAAGGGTAGGGTAATCCATGCAGGC
AAGTTTATTATAGCACCGTCGGGGGGAAGCATTATATCAAACTCCACAGTACAGCGTAAC
ATTGCTGTATAGGCTACA
>WashU_Skud_Contig2069.5 YDR232W 5' untranslated region, Contig c2069 5476 - 7475, 2000 bp (revcom)
ACTGAAAATAATCCGAGTCGTGCTACTGTGAATATTGAGAATAGGGACTAGCTCTATTTG
ATTTTTCTTCCAACCAAACTTATATGGAAAATATAAAGGAAAGAAAAAAGAAAAGAATAG
GAAAAAAAAAAAGAAACGCGAGAGAAGAGAACCGTGTGGAGGGAAGAACGGTTGAGAGAC
AGCAGAGCACAGCGCAACACAACCGAGTAGAGTACCAGCAGACGGAGTGGGTAGTTTGGT
ACAGTGTAAAAGCTATATTTCCACCAACGCAACACTGGATCGGAACAATGGGCAAGGCAA
TGTGAAAAATTTCCGTTCCTGCTCTTGCTTCATATATGACAATGACCAAAAAGCGTCCGC
GGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCGTAGCAGCAGGGTAAGCCGCGCAAG
CAAGTCCGTCATAACACCGTCGAAGGGGCACCACTATATCAGCTCTTCAGCATGGTAGGC
CATTACAGCACAGTCTTG
>WashU_Sbay_Contig461.5 YDR232W 5' untranslated region, Contig c461 4000 - 5999, 2000 bp (revcom)
ACTAAAAAGTCCAAGTGGTGCTGTTATTATTGAGGATAGCAACTAGCTTTATTTGTTTTT
TCTTCCAACCAAACTTATATGGAAATCAAAGGAAGGAAAAAAAGAAAAGAACAGGAAGAA
AAAAAAGAAACGTGAGCTGCCGAAAGGAGAGCGTGTGGAGGGAAGAACCGTTGAGAGACA
ACAGAGCAGGGTGCAAACCGATTAGAGTACCAGCAGACGAGATGGGCGATGTGGTACGGT
GCAGAAGGTGTGGTTCCAACAGCGCAGCACCGGGACAGAACAATGGGCAAGGCAAGATGA
AAAATCTCCGTTCCTGCTCTTGCTTGATATATTAACAATGACCAAAAAAACGCCGGCGGG
CGCAGACCAATGAGCGACGAAGACGGCTTTTGGGCGGGGCAGGGTAAGATGGGACAGGCA
AGGTCCGCTATAGCACCGTCGAGGGGGACCGCTATATCAGCTCCCAGTACATTGCAGCAC
ACTCTATAGCTAGTCAAA
>SGD_Scer_YDR047W HEM12 "Uroporphyrinogen decarboxylase, catalyzes the fifth step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; activity inhibited by Cu2+, Zn2+, Fe2+, Fe3+ and sulfhydryl-specific reagents"
AGCGTTATAACCTGTTCTTTGCTTTATTTTTTTTTTTTTTGTTCTTCCTTTTCTCGAAGA
GAGCTTACCAAACACAATTCTGAGATAATGCTTGATGAATTGAAGAACCTATCGATCACT
CTATGTTACCTTCGTCTGGAACATCACTAATTCGAGCGGTAAAGATGAAAATGGCAGAAC
ATTTCGCTGGCAAAATTAAAACTCTTGCCTCATTTTTTTTTGCTTTCCTCTCCTGCCGCC
AAAAACCCCGAACCCTGTCCTGTATATACGAGAAACATTGAAAAAGATCGTGTATGATAG
CGCCAAGATGGCGGATAAACTAACACTATTGACAGGTTGAGGCCAAGGATATATTACTTG
CTAACAGAAAGAGATACTGTCACCACAATTGCCCGCGTACGTATACTACAACATGTTCTC
TATATATCACCCACTCTTTCGCAGTGCTACGTACGCCAAAAACGCGCGCATGGAAGTAAA
GAAGTTTTTTCTTTTAAGAGCGAAGCTCCATTAAAAGCCTTGAATATAAACTAGTGCGAA
GTAGTATGATCCGAAGACACCAATTGCTGGTGCAGCATAGGAATATGTGGCGTCCGAAAA
AGAGCCTTTAACAATCCACGGCGAAACAAGGCACCGCTGTGCATTTAAAACATGCCGTTC
CCGTACCAAGTTATATTGTTACGGATGAATCCAAAATAATTTGTTAAAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCATGGCACCTTCTTCGTTTCTTCATCCTGCA
TTAGACTTACTAGTGTGCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGACACATATCGC
TGAGCTGGAAGGACACCTTTTAATGTAGCCGTGCATGCGGCTCCGCGAAAAGAGCTCTGC
TATATTTCTCTACCTGAACTTCGAGCCGCGATCAACGAAAGCTCTCATCCAAGGCTCGTT
TTTCTTGACAGAAGCATGACAGTAAAATATGCGGTCATTT
>MIT_Spar_c130_3923 YDR047W 5' untranslated region, Contig c130 9341 - 11340, 2000 bp (revcom)
AGCGTTATGATGTGTTATTTGCTTTTATTTTCTTCTTTCTTTGTCTCGAAGATAACCTAG
CAAACACAATTCTAAGAAAATTCTCGATGAATTGGTTGTCAGCGCTTCCTATTTACTCTA
TGTCCACTTCGTTTGAAACATCAGTGGTTCGAGCAGTAATGACAAAAAGGGCAGAACATT
TCGTTGGCAAAATTTAAACTCGTGCCTCTCATTTTTTTTACTTTTCTCTCCTGCCACCAA
AACCCCGAACCCTGTCCCGTATATACGAGGAACATTGAAAAAAAATCGTGTATGGTAGCG
CCAAGATAGCGAATAAACTATCAGTATTGGCAGGGTGAAGCTAAGGATATGTTGTTTGCT
AACAAAGGGAAATGCTTTCGTTATAATCGCCCGCGTGCGTCTACTAAAATATGATCTATA
TATACCACCCAGTCTATTGCAGTGTTACGTACATCAAAATGCGCGCATGTAAGTGAACAA
GTTTTTTTTGTTTAAAGAGCGATTTTCCAATAAAGGCTTTGGATATACACTGGTGCAAAA
TATATGGTCAATGACGCCAATTACTGGTGTAGCATGAGAATACGTCGTCCGAAAGAGTTT
TTTTTTACAAACTACGGCAAAGCAAAGCACCACTGGCGCAATTCAAAACATGCCGTCCCC
GTACTAAGTTATGTACGTTATTATGGACGGATCCAAAATTATACTCTAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCGTAGCACCTTCTTCGTGTCCTTTCCTTCTT
CTGCATTAGGCTTACTAGCGTCCTTTCCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGA
CAAATCTCGCTGAGTTGGAAAGACACCTTTTATATAGCCGTACGTGCGGCTCCTCGAGAA
AGGCCCTGCTATATTTCACTAGCTGATCCTCGAGCTGCGATCAACGAAAGCCCCATCCAA
AAGGCTCCTTTTTCTTCAAAGAAGCATGACAGTAAAATAT
>MIT_Sbay_c896_21277 YDR047W 5' untranslated region, Contig c896 2230 - 4229(revcom), 2000 bp (revcom)
AGTGTTAACAGTATCTTTTGCCTTTTTTTATTCTAATAGCTACCCCAGGAATCACTATTT
AGCAAAGATCGTTTGCAAATTGGCCGTCAGTACGTTCTAAGTTCTTTAGAACATCATTGG
CTCGAGCATTAGTGACACGAATAGGAAAGCATTTCGTTGACAAAAATAAAATTGTTTCTT
TATTTTTTCCCTCTTTTCCATGGCGTCAAAAAACCCCGAACCCTGTATAAACGAGGAAGC
TGCATGGTAGCGCCAGAAAAGGCAGATAACCTTTAACAGTGCTGACAGAACAACGTCAAA
CATGTGCGGATAATGCCTTCGCTGACGGCAAGAAATTATATACGCCTCGAAACTGTAGAA
CGTCTTTTGTGCCGCTTGGTAACAAATAAACCTAGCCGGGGCCAGAATTTCACCCGTACA
TACTTACTGTTACATACTGCATGCACGCTACGCATTCTCACCGAACATCGAATCTGCCTG
CAGAAGCGAAGAAAAGCAAGTCTTCGAAGAGCAAGCTTACATCCATCGTGTTGAACACAT
ATGCCCAGCAAAGGGATCGGATGACGCCCAACTAACATTGGAATTTGTGACGCAAGGCTG
AAAGGCACTTCTCTATAGCCCACGGTGAAGCCTTACGCTATTGACAAGACAAAACATGCC
GATCCAAGCCAGGCGAAACGGGCCTAGCACTACGCAGCCAAACACTGGCGTTCCGCCCGT
CCCATCCAGTTTCATTTCTTATTTCGTTCTGCCTTGGGCCTAGCAGCGTGCTTGCCGGAT
GAGTTTTTTCCATTTTCCTACCGGCTCATCTCGCTAAGCTGAAAGGTCAGTTTTATAGCC
GTGTGCGCGGCATCGAGAGACAGGTTCAGCTAATGATATTTGCCTAATTCTCGAGCTGAG
GCCAATGAAGGCAGCTTCCAGGGCTCGTTTCTGCTCGGGAAAAAGCATACCACACATTTG
CACGGCTTTTATGTGCCATAGTGCCACCACTAGCCCCCAG
>WashU_Skud_Contig1362.1 YDR047W 5' untranslated region, Contig c1362 1 - 761, 2000 bp (revcom)
AGTGTTGATGGTATCTTTTGATTTTTTCTAGATTGGTAGCAAGCTCAATTGGCACAGCTC
TAAAAAAAGCCTTGTGAATTGGATAGTACCTTCTTTCGTTTGGAACATTACTGCTTCGAG
CAATAAACATACGAAAGGCAGAACACCTCGTTGACAAAACTGAAACTATTTCTTCAATTT
TTTGGCCTTTTTTCCTGCTGCCAAAAAACCCCGAATCATGTAGAAGCGAGAAGTAAAACA
GAGGAAGTGTATGGTAGCGCCAAGGAAAACGGGCAATACTTAGAAAGAATGACAGAGCTC
AGCCAAGTGTAAGCTAAGTGTTGACAAGGGAAGGTACATTGGGCCCCGAAAAAATTTGCT
AATGCTCGAAGAGCTCTCAATCAATCACCCACATATATGTACTACAGTATATTTATACTT
TCCACGCAGTCTCACGCAGTGCCACCTTCATCACCATGCGTGTAACTAATCGAGCAAGCT
GTTTTACGAAGGGCAGCTTTCCTATAAGCGTTTTGAACATGCATGGCTGCACTGCAATGA
GATCAGGCGACTCCAATTCCATAGCCTAGCACGGGATTAAGTAACGAGAAACTGAAAGAG
ATAATTTTACAAACCCGGACGAAGCAGAGCACTTGCTGGAACAAATCAAACATGCCGTCC
CCTACCAGCTCTCGAAGCGGGCCTAGCATTACTCGATCGAACGTTGCCGTTTAGTCTTAT
TTTCCTTTCCGTGCTGCGCTGCTTTTTTCTTGCATTGGGCT
BioPerl-1.007002/t/data/map_hem/HEM1-HEM12.fa.revcom000444000766000024      2321713155576321 21371 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR232W HEM1 "5-aminolevulinate synthase, catalyzes the first step in the heme biosynthetic pathway; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expression is regulated by Hap2p-Hap3p"
CTTCACTACAATGCTTTACCGAGCAGTGGAGTTTGATATAGTGGTGGTACCCCCGACGGT
GCTATAATAAGCTTGCCTGCACGGCTTACCCTACCGCTCGGAAAGGCCGCCTTCGTCGCT
CATTGGTCTGCGGCCGCGGGCGCTTTTTGGTCATTGTTCATATATGAAGAAAGAGCAGGA
ACGGAAATTTTTCATCTTGCCTTGCCCATTGTTCTGATCCATGCGTTGTTAGAAATACAA
CGTTTGCATCATACCAAACTTCTCCATTCCGTCAGCTGATACTCTATTCGGTTGTGTGTT
GCACCCTGCTCTGCTGTCTCTCAACCGTTCTTCCTTTACACGCCTTCCCTTCTCAGCTCG
CGTTTCTTTTTTTTTTATCCCACTCTTTTCTTTTTTCTTTCCTATATATTGCCCATATAA
GTTTGGTTGGAAGGAAAACTAATAGAGCTAGTTGTTGTCCCTCAATAATCATAACAGTAC
TTAGGTTTTTTTTTCAGT
>MIT_Spar_c117_4603 YDR232W 5' untranslated region, Contig c117 17441 - 19440, 2000 bp (revcom)
GCTGTGAACTATACTGCAATGCTTCACCGTGCTGTGGAACTTGATATAGTGGTCCCCCCG
ACGGTGCTATAATAAGCTTGCCTGCACGGCTTACCCTACCACTCGGAAAGGCCGCCTTCG
TCGCTCATTGGTCTGCGGCCGCGGGCGCTTTTTGGTCATTGTTCATATATGAAGAAAGAG
CAGGAACAGAAATTTTTCATCTTGCCTTGCCCATTGTTCTGACCCATGCGTTGCTACAAA
TATAGCGTTTGCATCGTACCAAACTCCTCCATCCCGTCAGCTGATACTCTATTCGGTTGT
GTGTTGCACCCTGCTCTGCTCTCTCTCAACCGTTCTTCCTTTACACGCCTTCTCTTCTCA
GCTCGCGTTTCTTTTTTTATCCTACTCTTTTCTTTTTTCTTTCCTATATATTGCCCATAT
AAGTTTGGTTGGAAGGAAAACAAATAGAGCTAGCCGTTGTCCCTCAATAATCACAACAGT
ACTTGGTTTTTTTTCAGT
>MIT_Smik_c228_4055 YDR232W 5' untranslated region, Contig c228 4702 - 6701(revcom), 2000 bp (revcom)
TGTAGCCTATACAGCAATGTTACGCTGTACTGTGGAGTTTGATATAATGCTTCCCCCCGA
CGGTGCTATAATAAACTTGCCTGCATGGATTACCCTACCCTTCAAAAGGCCGCTTTCGTC
GCTCATTGGTCTGCGCTTGCGGGCGCTTTTTGGTCATTGTTCATATATGAAGAAAGAGCA
GGAACGGAAATTTTCATCTTGCCTTGCCCATTGTTCTAATTCAATGTTGCGTTGCTAAAA
GCATCACTTTTGCATCATACCAAACTCCTCCATTCCGTCAGCTGGTACTCTACTCGGTTG
TGTTGCACCCTCCTCTACTGTCATTCAACCGTTCTGGCTTCACACGTCCTCCCTTCTCAG
GTCGCATTTCTTTTTTTTCGTGCTCTTTTCTTTTTTCTGTCCTATATATTTCCCATATAA
GTTAGGTTGGAAGAAAAAACAAACAAAGCTGGTCATTAGTCCTCAATAATCATATCACTA
CTTAGTTTTTCTCTCGGT
>WashU_Scas_Contig721.76 YDR232W 5' untranslated region, Contig c721 147634 - 149633(revcom), 2000 bp (revcom)
TCCTGCTGGGGTTCCTGCTGCTGCTGCGGTGTGCTGTTGCTTTTGAAGGATGGTAGCCAG
CCCATTGTATATGTAGATCTTGTAGTAGTAGCAGTAGTTGTTGTTGTTGTTGTATTCCCC
GTATATACAGCTCAATAAGAAGAAGAAGGGGAAACTGAATTGGGCGGCTAAAATCAAAAA
AATCAAAAGAGCTGGGTAACAAACAGCCTGTCACCAAACACGACAAATCACGTGCCAGAT
CCAAATCCCGTCTTCTGATTGGCCCAAAAGCTGTGTGCGGCAGTTTCTGAGCGCGCCTTT
CTTTTTTGCTCAAAGCTCTATTTTCCTTACGTAACACGCCAATCCCGTCGTTTAACAATT
ATTCATATATACAGCACTGTATATAACAACACATCACATCATCACATCAGCTCAGCTCAT
CTCAAACAGAACAGAACAAATCTAGTCTATACTTGCTTGCTCGCTGGCCGCTCTATCCAC
CCGTCTGCTTCACAAACA
>WashU_Sklu_Contig2308.6 YDR232W 5' untranslated region, Contig c2308 6692 - 8691, 2000 bp (revcom)
AACCCGATGGCGATGATGGCTTTGAGTGGATGGTATCTTACAGGTGCTGCTGGTGTTCTA
CAGCCGAACGACCAAGAGGCATTCAGCTGGGCTTTAAGGAGCTGCCAGTCCACAGAAGGT
AAGTTTGCCCGCGCAGAGTATGCGTTAGCTTTCTTCTACGAGCGCGGTATTGGCTGCACA
AAGGATCCAAGCAAGGCTCTGGAACATTATAAATGTGCTGCTCAAATGGGGCATCCAAAG
GCTCAAGACAGGTATCGCGAACTGAATAGCTCGTAAGTAACACCTAACATTAGCTTTAAC
GTCGTTCTTATTGGCTCAGGCAACTGTCCACGTGATCACATACTTGATCACACCTAAAAA
TTTTTCAGAAAATTTCTTTTTTCCTATTGGATGGGAAGAAAAAAATAAATATATATATGT
ATGTGAGTAGTGGAGAGAAGACTCACCTCCCCTCTTTACAGGAATAGAACCGTCGAAAAA
TAGACAGACGAAGAAGGG
>WashU_Skud_Contig2069.5 YDR232W 5' untranslated region, Contig c2069 5476 - 7475, 2000 bp (revcom)
CAAGACTGTGCTGTAATGGCCTACCATGCTGAAGAGCTGATATAGTGGTGCCCCTTCGAC
GGTGTTATGACGGACTTGCTTGCGCGGCTTACCCTGCTGCTACGAAAGGCCGCCTTCGTC
GCTCATTGGTCTGCGGCCGCGGACGCTTTTTGGTCATTGTCATATATGAAGCAAGAGCAG
GAACGGAAATTTTTCACATTGCCTTGCCCATTGTTCCGATCCAGTGTTGCGTTGGTGGAA
ATATAGCTTTTACACTGTACCAAACTACCCACTCCGTCTGCTGGTACTCTACTCGGTTGT
GTTGCGCTGTGCTCTGCTGTCTCTCAACCGTTCTTCCCTCCACACGGTTCTCTTCTCTCG
CGTTTCTTTTTTTTTTTCCTATTCTTTTCTTTTTTCTTTCCTTTATATTTTCCATATAAG
TTTGGTTGGAAGAAAAATCAAATAGAGCTAGTCCCTATTCTCAATATTCACAGTAGCACG
ACTCGGATTATTTTCAGT
>WashU_Sbay_Contig461.5 YDR232W 5' untranslated region, Contig c461 4000 - 5999, 2000 bp (revcom)
TTTGACTAGCTATAGAGTGTGCTGCAATGTACTGGGAGCTGATATAGCGGTCCCCCTCGA
CGGTGCTATAGCGGACCTTGCCTGTCCCATCTTACCCTGCCCCGCCCAAAAGCCGTCTTC
GTCGCTCATTGGTCTGCGCCCGCCGGCGTTTTTTTGGTCATTGTTAATATATCAAGCAAG
AGCAGGAACGGAGATTTTTCATCTTGCCTTGCCCATTGTTCTGTCCCGGTGCTGCGCTGT
TGGAACCACACCTTCTGCACCGTACCACATCGCCCATCTCGTCTGCTGGTACTCTAATCG
GTTTGCACCCTGCTCTGTTGTCTCTCAACGGTTCTTCCCTCCACACGCTCTCCTTTCGGC
AGCTCACGTTTCTTTTTTTTCTTCCTGTTCTTTTCTTTTTTTCCTTCCTTTGATTTCCAT
ATAAGTTTGGTTGGAAGAAAAAACAAATAAAGCTAGTTGCTATCCTCAATAATAACAGCA
CCACTTGGACTTTTTAGT
>SGD_Scer_YDR047W HEM12 "Uroporphyrinogen decarboxylase, catalyzes the fifth step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; activity inhibited by Cu2+, Zn2+, Fe2+, Fe3+ and sulfhydryl-specific reagents"
AAATGACCGCATATTTTACTGTCATGCTTCTGTCAAGAAAAACGAGCCTTGGATGAGAGC
TTTCGTTGATCGCGGCTCGAAGTTCAGGTAGAGAAATATAGCAGAGCTCTTTTCGCGGAG
CCGCATGCACGGCTACATTAAAAGGTGTCCTTCCAGCTCAGCGATATGTGTCGGCCGGAA
AAAAAAAGCACGCATCCGGCAAGCACACTAGTAAGTCTAATGCAGGATGAAGAAACGAAG
AAGGTGCCATGAGAAGGAAAATAAAACTCAATGGGACGGAACGGCAGCATTTTTTAACAA
ATTATTTTGGATTCATCCGTAACAATATAACTTGGTACGGGAACGGCATGTTTTAAATGC
ACAGCGGTGCCTTGTTTCGCCGTGGATTGTTAAAGGCTCTTTTTCGGACGCCACATATTC
CTATGCTGCACCAGCAATTGGTGTCTTCGGATCATACTACTTCGCACTAGTTTATATTCA
AGGCTTTTAATGGAGCTTCGCTCTTAAAAGAAAAAACTTCTTTACTTCCATGCGCGCGTT
TTTGGCGTACGTAGCACTGCGAAAGAGTGGGTGATATATAGAGAACATGTTGTAGTATAC
GTACGCGGGCAATTGTGGTGACAGTATCTCTTTCTGTTAGCAAGTAATATATCCTTGGCC
TCAACCTGTCAATAGTGTTAGTTTATCCGCCATCTTGGCGCTATCATACACGATCTTTTT
CAATGTTTCTCGTATATACAGGACAGGGTTCGGGGTTTTTGGCGGCAGGAGAGGAAAGCA
AAAAAAAATGAGGCAAGAGTTTTAATTTTGCCAGCGAAATGTTCTGCCATTTTCATCTTT
ACCGCTCGAATTAGTGATGTTCCAGACGAAGGTAACATAGAGTGATCGATAGGTTCTTCA
ATTCATCAAGCATTATCTCAGAATTGTGTTTGGTAAGCTCTCTTCGAGAAAAGGAAGAAC
AAAAAAAAAAAAAATAAAGCAAAGAACAGGTTATAACGCT
>MIT_Spar_c130_3923 YDR047W 5' untranslated region, Contig c130 9341 - 11340, 2000 bp (revcom)
ATATTTTACTGTCATGCTTCTTTGAAGAAAAAGGAGCCTTTTGGATGGGGCTTTCGTTGA
TCGCAGCTCGAGGATCAGCTAGTGAAATATAGCAGGGCCTTTCTCGAGGAGCCGCACGTA
CGGCTATATAAAAGGTGTCTTTCCAACTCAGCGAGATTTGTCGGCCGGAAAAAAAAAGCA
CGCATCCGGCAAGGAAAGGACGCTAGTAAGCCTAATGCAGAAGAAGGAAAGGACACGAAG
AAGGTGCTACGAGAAGGAAAATAAAACTCAATGGGACGGAACGGCAGCATTTTAGAGTAT
AATTTTGGATCCGTCCATAATAACGTACATAACTTAGTACGGGGACGGCATGTTTTGAAT
TGCGCCAGTGGTGCTTTGCTTTGCCGTAGTTTGTAAAAAAAAACTCTTTCGGACGACGTA
TTCTCATGCTACACCAGTAATTGGCGTCATTGACCATATATTTTGCACCAGTGTATATCC
AAAGCCTTTATTGGAAAATCGCTCTTTAAACAAAAAAAACTTGTTCACTTACATGCGCGC
ATTTTGATGTACGTAACACTGCAATAGACTGGGTGGTATATATAGATCATATTTTAGTAG
ACGCACGCGGGCGATTATAACGAAAGCATTTCCCTTTGTTAGCAAACAACATATCCTTAG
CTTCACCCTGCCAATACTGATAGTTTATTCGCTATCTTGGCGCTACCATACACGATTTTT
TTTCAATGTTCCTCGTATATACGGGACAGGGTTCGGGGTTTTGGTGGCAGGAGAGAAAAG
TAAAAAAAATGAGAGGCACGAGTTTAAATTTTGCCAACGAAATGTTCTGCCCTTTTTGTC
ATTACTGCTCGAACCACTGATGTTTCAAACGAAGTGGACATAGAGTAAATAGGAAGCGCT
GACAACCAATTCATCGAGAATTTTCTTAGAATTGTGTTTGCTAGGTTATCTTCGAGACAA
AGAAAGAAGAAAATAAAAGCAAATAACACATCATAACGCT
>MIT_Sbay_c896_21277 YDR047W 5' untranslated region, Contig c896 2230 - 4229(revcom), 2000 bp (revcom)
CTGGGGGCTAGTGGTGGCACTATGGCACATAAAAGCCGTGCAAATGTGTGGTATGCTTTT
TCCCGAGCAGAAACGAGCCCTGGAAGCTGCCTTCATTGGCCTCAGCTCGAGAATTAGGCA
AATATCATTAGCTGAACCTGTCTCTCGATGCCGCGCACACGGCTATAAAACTGACCTTTC
AGCTTAGCGAGATGAGCCGGTAGGAAAATGGAAAAAACTCATCCGGCAAGCACGCTGCTA
GGCCCAAGGCAGAACGAAATAAGAAATGAAACTGGATGGGACGGGCGGAACGCCAGTGTT
TGGCTGCGTAGTGCTAGGCCCGTTTCGCCTGGCTTGGATCGGCATGTTTTGTCTTGTCAA
TAGCGTAAGGCTTCACCGTGGGCTATAGAGAAGTGCCTTTCAGCCTTGCGTCACAAATTC
CAATGTTAGTTGGGCGTCATCCGATCCCTTTGCTGGGCATATGTGTTCAACACGATGGAT
GTAAGCTTGCTCTTCGAAGACTTGCTTTTCTTCGCTTCTGCAGGCAGATTCGATGTTCGG
TGAGAATGCGTAGCGTGCATGCAGTATGTAACAGTAAGTATGTACGGGTGAAATTCTGGC
CCCGGCTAGGTTTATTTGTTACCAAGCGGCACAAAAGACGTTCTACAGTTTCGAGGCGTA
TATAATTTCTTGCCGTCAGCGAAGGCATTATCCGCACATGTTTGACGTTGTTCTGTCAGC
ACTGTTAAAGGTTATCTGCCTTTTCTGGCGCTACCATGCAGCTTCCTCGTTTATACAGGG
TTCGGGGTTTTTTGACGCCATGGAAAAGAGGGAAAAAATAAAGAAACAATTTTATTTTTG
TCAACGAAATGCTTTCCTATTCGTGTCACTAATGCTCGAGCCAATGATGTTCTAAAGAAC
TTAGAACGTACTGACGGCCAATTTGCAAACGATCTTTGCTAAATAGTGATTCCTGGGGTA
GCTATTAGAATAAAAAAAGGCAAAAGATACTGTTAACACT
>WashU_Skud_Contig1362.1 YDR047W 5' untranslated region, Contig c1362 1 - 761, 2000 bp (revcom)
AGCCCAATGCAAGAAAAAAGCAGCGCAGCACGGAAAGGAAAATAAGACTAAACGGCAACG
TTCGATCGAGTAATGCTAGGCCCGCTTCGAGAGCTGGTAGGGGACGGCATGTTTGATTTG
TTCCAGCAAGTGCTCTGCTTCGTCCGGGTTTGTAAAATTATCTCTTTCAGTTTCTCGTTA
CTTAATCCCGTGCTAGGCTATGGAATTGGAGTCGCCTGATCTCATTGCAGTGCAGCCATG
CATGTTCAAAACGCTTATAGGAAAGCTGCCCTTCGTAAAACAGCTTGCTCGATTAGTTAC
ACGCATGGTGATGAAGGTGGCACTGCGTGAGACTGCGTGGAAAGTATAAATATACTGTAG
TACATATATGTGGGTGATTGATTGAGAGCTCTTCGAGCATTAGCAAATTTTTTCGGGGCC
CAATGTACCTTCCCTTGTCAACACTTAGCTTACACTTGGCTGAGCTCTGTCATTCTTTCT
AAGTATTGCCCGTTTTCCTTGGCGCTACCATACACTTCCTCTGTTTTACTTCTCGCTTCT
ACATGATTCGGGGTTTTTTGGCAGCAGGAAAAAAGGCCAAAAAATTGAAGAAATAGTTTC
AGTTTTGTCAACGAGGTGTTCTGCCTTTCGTATGTTTATTGCTCGAAGCAGTAATGTTCC
AAACGAAAGAAGGTACTATCCAATTCACAAGGCTTTTTTTAGAGCTGTGCCAATTGAGCT
TGCTACCAATCTAGAAAAAATCAAAAGATACCATCAACACT
>WashU_Scas_Contig569.6 YDR047W 5' untranslated region, Contig c569 10116 - 12115, 2000 bp (revcom)
CCATAGTTCCTCAATATAATTTTTTAGACTTCCTGGCCTTTAAACCGGAGAAGAAACCCT
CACATGAAACAAAAAGTCTTAAAAGAAGGTCATTGGACAAGTATCATTGTAATGTAGGAC
GAATTAGTTCAGTCTTAAGAGCGGTTAAGCATGTGTAAAAAAATTATGTGAAGAATATTT
GAAAACTTTTTTTTTCCACTAACTTTTGAGGAAAAACAGTTAGAACTTTGACACTCTTTT
TTGCCTTAATATTAATATAATTGTCATGTCTGTTTTTGATAAGAAATGAATAATGGAATC
TAACTTTAACTATAAGCTATGCCTCACCACAGCACCTCGAGGCTGGATTGTAAATGAAAT
GTTATTGTAGCTCAGAGGTTGGTGGATGTGAATATGGATATTCCATTCATGACTAAATTG
ACAACAACGTAATTGAATCAACCTCTTATGAAAAACGTCAGATTGTTCTCACAACTCTCT
AAATCAAGAAGGGAAGAAAAACTTACTGTAAAAGCGATAATATGTCATCTCCACCTCTCG
TATATATTTTTATTCAAAAATAAATAAAAATGATTTTGGAAGTATATTATAACTGAGTTA
TTGGTTTTTTTATACTGGAGATTATTCGTTTTCGTCCTCGTTTACTCGATACTAAGGTAT
TAAGAATCTTTTTACCGTCACACTTCCTTCTCAACCCTTAAATTTCCGTTTTGTGGGGAA
CAACATATTTAAGGACTTTATTTGATGGTTTGATAAAGGTTGGAGAAGTAATCACTAATG
TATTTTGTTATCAATTTACAAAGATTGATAGGTGACGTTAATTGATACGTAGCGTTATTT
GACATTCTTGGCTCGTTTATATTTGGCGCGAGCCGCAACGTTAACCGAATCGTACGGTAG
CTGTCAATTGGCGAATATCCTTTAAAAGGAAACAGTCATCATTTGTTCCACGTTTCCTCC
ACCAATCCTCCCACTATTTGACACCCAACGACTTGAAAAA
BioPerl-1.007002/t/data/map_hem/HEM1-HEM12.meme.txt000444000766000024     11567113155576321 21300 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM1-HEM12.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDR232W         1.0000    498  MIT_Spar_c117_4603       1.0000    498  
MIT_Smik_c228_4055       1.0000    498  WashU_Skud_Contig2069.5  1.0000    498  
WashU_Sbay_Contig461.5   1.0000    498  SGD_Scer_YDR047W         1.0000   1000  
MIT_Spar_c130_3923       1.0000   1000  MIT_Sbay_c896_21277      1.0000   1000  
WashU_Skud_Contig1362.1  1.0000    761  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM1-HEM12.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            6251    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.280 C 0.220 G 0.220 T 0.280 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 195   E-value = 1.4e-022
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  116::::8:8:1a9::943:
pos.-specific     C  9::3a172:189::2:::6:
probability       G  :947:63:a1:::1:a:61a
matrix            T  :::::3::::2:::8:1:::

         bits    2.5     *   *      *   *
                 2.3     *   *      *   *
                 2.0 **  *   *  *   *   *
                 1.8 **  *   *  *   *   *
Information      1.5 ** ** * * ***  *   *
content          1.3 ** ** * * **** *   *
(31.3 bits)      1.0 ***** *** ******** *
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CGAGCGCAGACCAATGAGCG
consensus              GC TGC  T   C  AA 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig461.5       +    357  3.08e-14 AAAACGCCGG CGGGCGCAGACCAATGAGCG ACGAAGACGG
WashU_Skud_Contig2069.5      +    360  1.83e-13 AAAGCGTCCG CGGCCGCAGACCAATGAGCG ACGAAGGCGG
MIT_Spar_c117_4603           +    358  1.83e-13 AAAGCGCCCG CGGCCGCAGACCAATGAGCG ACGAAGGCGG
SGD_Scer_YDR232W             +    363  1.83e-13 AAAGCGCCCG CGGCCGCAGACCAATGAGCG ACGAAGGCGG
MIT_Smik_c228_4055           +    360  1.47e-11 AAAGCGCCCG CAAGCGCAGACCAATGAGCG ACGAAAGCGG
MIT_Sbay_c896_21277          +    892  2.69e-10 GCCTAATTCT CGAGCTGAGGCCAATGAAGG CAGCTTCCAG
MIT_Spar_c130_3923           +    931  7.23e-10 AGCTGATCCT CGAGCTGCGATCAACGAAAG CCCCATCCAA
SGD_Scer_YDR047W             +    922  1.02e-09 ACCTGAACTT CGAGCCGCGATCAACGAAAG CTCTCATCCA
WashU_Skud_Contig1362.1      +    294  1.77e-08 AAAGAATGAC AGAGCTCAGCCAAGTGTAAG CTAAGTGTTG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig461.5            3.1e-14  356_[+1]_122
WashU_Skud_Contig2069.5           1.8e-13  359_[+1]_119
MIT_Spar_c117_4603                1.8e-13  357_[+1]_121
SGD_Scer_YDR232W                  1.8e-13  362_[+1]_116
MIT_Smik_c228_4055                1.5e-11  359_[+1]_119
MIT_Sbay_c896_21277               2.7e-10  891_[+1]_89
MIT_Spar_c130_3923                7.2e-10  930_[+1]_50
SGD_Scer_YDR047W                    1e-09  921_[+1]_59
WashU_Skud_Contig1362.1           1.8e-08  293_[+1]_448
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Sbay_Contig461.5   (  357) CGGGCGCAGACCAATGAGCG  1 
WashU_Skud_Contig2069.5  (  360) CGGCCGCAGACCAATGAGCG  1 
MIT_Spar_c117_4603       (  358) CGGCCGCAGACCAATGAGCG  1 
SGD_Scer_YDR232W         (  363) CGGCCGCAGACCAATGAGCG  1 
MIT_Smik_c228_4055       (  360) CAAGCGCAGACCAATGAGCG  1 
MIT_Sbay_c896_21277      (  892) CGAGCTGAGGCCAATGAAGG  1 
MIT_Spar_c130_3923       (  931) CGAGCTGCGATCAACGAAAG  1 
SGD_Scer_YDR047W         (  922) CGAGCCGCGATCAACGAAAG  1 
WashU_Skud_Contig1362.1  (  294) AGAGCTCAGCCAAGTGTAAG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 1.4e-022 
  -154    234   -982   -982 
  -154   -982    234   -982 
    78   -982    134   -982 
  -982     92    192   -982 
  -982    251   -982   -982 
  -982    -66    166      4 
  -982    192     92   -982 
   126     34   -982   -982 
  -982   -982    251   -982 
   126    -66    -66   -982 
  -982    215   -982    -55 
  -154    234   -982   -982 
   162   -982   -982   -982 
   145   -982    -66   -982 
  -982     34   -982    126 
  -982   -982    251   -982 
   145   -982   -982   -154 
    45   -982    166   -982 
     4    166    -66   -982 
  -982   -982    251   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.4e-022 
 0.111111  0.888889  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.555556  0.000000  0.444444  0.000000 
 0.000000  0.333333  0.666667  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.111111  0.555556  0.333333 
 0.000000  0.666667  0.333333  0.000000 
 0.777778  0.222222  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.777778  0.111111  0.111111  0.000000 
 0.000000  0.777778  0.000000  0.222222 
 0.111111  0.888889  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.222222  0.000000  0.777778 
 0.000000  0.000000  1.000000  0.000000 
 0.888889  0.000000  0.000000  0.111111 
 0.444444  0.000000  0.555556  0.000000 
 0.333333  0.555556  0.111111  0.000000 
 0.000000  0.000000  1.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
CG[AG][GC]C[GT][CG][AC]GA[CT]CAA[TC]GA[GA][CA]G
--------------------------------------------------------------------------------




Time  4.41 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 179   E-value = 3.0e-017
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  1:4a1a9:4::::614:8:a
pos.-specific     C  :14::::a111:4:1:::9:
probability       G  991:9:1:46::644:a21:
matrix            T  :::::::::39a::36::::

         bits    2.5        *        *   
                 2.3        *        *   
                 2.0 **  *  *        * * 
                 1.8 **  *  *        * * 
Information      1.5 ** *** *   **   * **
content          1.3 ** *****  ***   * **
(28.7 bits)      1.0 ** *****  ****  ****
                 0.8 ************** *****
                 0.5 ************** *****
                 0.3 ********************
                 0.0 --------------------

Multilevel           GGAAGAACAGTTGAGTGACA
consensus              C     GT  CGTA G  
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2069.5      +    162  7.75e-12 CCGTGTGGAG GGAAGAACGGTTGAGAGACA GCAGAGCACA
SGD_Scer_YDR232W             +    165  7.75e-12 GGCGTGTAAA GGAAGAACGGTTGAGAGACA GCAGAGCAGG
WashU_Sbay_Contig461.5       +    161  8.83e-11 GCGTGTGGAG GGAAGAACCGTTGAGAGACA ACAGAGCAGG
MIT_Spar_c117_4603           +    160  2.12e-10 GGCGTGTAAA GGAAGAACGGTTGAGAGAGA GCAGAGCAGG
MIT_Spar_c130_3923           +    170  2.30e-10 TGACAAAAAG GGCAGAACATTTCGTTGGCA AAATTTAAAC
SGD_Scer_YDR047W             +    173  4.04e-10 AGATGAAAAT GGCAGAACATTTCGCTGGCA AAATTAAAAC
MIT_Smik_c228_4055           +    161  6.70e-10 GACGTGTGAA GCCAGAACGGTTGAATGACA GTAGAGGAGG
WashU_Skud_Contig1362.1      +    137  8.43e-10 ACATACGAAA GGCAGAACACCTCGTTGACA AAACTGAAAC
MIT_Sbay_c896_21277          +    143  3.02e-08 TGACACGAAT AGGAAAGCATTTCGTTGACA AAAATAAAAT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2069.5           7.7e-12  161_[+2]_317
SGD_Scer_YDR232W                  7.7e-12  164_[+2]_314
WashU_Sbay_Contig461.5            8.8e-11  160_[+2]_318
MIT_Spar_c117_4603                2.1e-10  159_[+2]_319
MIT_Spar_c130_3923                2.3e-10  169_[+2]_811
SGD_Scer_YDR047W                    4e-10  172_[+2]_808
MIT_Smik_c228_4055                6.7e-10  160_[+2]_318
WashU_Skud_Contig1362.1           8.4e-10  136_[+2]_605
MIT_Sbay_c896_21277                 3e-08  142_[+2]_838
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
WashU_Skud_Contig2069.5  (  162) GGAAGAACGGTTGAGAGACA  1 
SGD_Scer_YDR232W         (  165) GGAAGAACGGTTGAGAGACA  1 
WashU_Sbay_Contig461.5   (  161) GGAAGAACCGTTGAGAGACA  1 
MIT_Spar_c117_4603       (  160) GGAAGAACGGTTGAGAGAGA  1 
MIT_Spar_c130_3923       (  170) GGCAGAACATTTCGTTGGCA  1 
SGD_Scer_YDR047W         (  173) GGCAGAACATTTCGCTGGCA  1 
MIT_Smik_c228_4055       (  161) GCCAGAACGGTTGAATGACA  1 
WashU_Skud_Contig1362.1  (  137) GGCAGAACACCTCGTTGACA  1 
MIT_Sbay_c896_21277      (  143) AGGAAAGCATTTCGTTGACA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 3.0e-017 
  -154   -982    234   -982 
  -982    -66    234   -982 
    45    134    -66   -982 
   162   -982   -982   -982 
  -154   -982    234   -982 
   162   -982   -982   -982 
   145   -982    -66   -982 
  -982    251   -982   -982 
    45    -66    134   -982 
  -982    -66    166      4 
  -982    -66   -982    145 
  -982   -982   -982    162 
  -982    134    166   -982 
    78   -982    134   -982 
  -154    -66    134      4 
    45   -982   -982     78 
  -982   -982    251   -982 
   126   -982     34   -982 
  -982    234    -66   -982 
   162   -982   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.0e-017 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  0.111111  0.888889  0.000000 
 0.444444  0.444444  0.111111  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.444444  0.111111  0.444444  0.000000 
 0.000000  0.111111  0.555556  0.333333 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.444444  0.555556  0.000000 
 0.555556  0.000000  0.444444  0.000000 
 0.111111  0.111111  0.444444  0.333333 
 0.444444  0.000000  0.000000  0.555556 
 0.000000  0.000000  1.000000  0.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.000000  0.888889  0.111111  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
GG[AC]AGAAC[AG][GT]TT[GC][AG][GT][TA]G[AG]CA
--------------------------------------------------------------------------------




Time  8.63 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =   9   llr = 181   E-value = 3.1e-017
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  8aaa64:::::1:::1112:
pos.-specific     C  1:::4:1:a9::2aa3:62a
probability       G  1::::::4::a:::::81::
matrix            T  :::::696:1:98::6126:

         bits    2.5         * *  **    *
                 2.3         * *  **    *
                 2.0         ***  **    *
                 1.8         ***  **    *
Information      1.5  ***    ***  **    *
content          1.3  ***  * ***  ** *  *
(29.1 bits)      1.0  **** ********* *  *
                 0.8 *************** *  *
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           AAAAATTTCCGTTCCTGCTC
consensus                CA G    C  C TA 
sequence                               C 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2069.5      +    305  9.40e-12 AGGCAATGTG AAAAATTTCCGTTCCTGCTC TTGCTTCATA
SGD_Scer_YDR232W             +    307  9.40e-12 AGGCAAGATG AAAAATTTCCGTTCCTGCTC TTTCTTCATA
MIT_Smik_c228_4055           +    304  6.77e-11 AAGGCAAGAT GAAAATTTCCGTTCCTGCTC TTTCTTCATA
WashU_Sbay_Contig461.5       +    300  7.67e-11 AGGCAAGATG AAAAATCTCCGTTCCTGCTC TTGCTTGATA
SGD_Scer_YDR047W             +    647  1.22e-10 CTGTGCATTT AAAACATGCCGTTCCCGTAC CAAGTTATAT
MIT_Spar_c130_3923           +    645  2.75e-10 GGCGCAATTC AAAACATGCCGTCCCCGTAC TAAGTTATGT
MIT_Spar_c117_4603           +    302  3.58e-10 AGGCAAGATG AAAAATTTCTGTTCCTGCTC TTTCTTCATA
WashU_Skud_Contig1362.1      +    647  5.76e-09 TGGAACAAAT CAAACATGCCGTCCCCTACC AGCTCTCGAA
MIT_Sbay_c896_21277          +    651  9.67e-09 TTGACAAGAC AAAACATGCCGATCCAAGCC AGGCGAAACG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2069.5           9.4e-12  304_[+3]_174
SGD_Scer_YDR232W                  9.4e-12  306_[+3]_172
MIT_Smik_c228_4055                6.8e-11  303_[+3]_175
WashU_Sbay_Contig461.5            7.7e-11  299_[+3]_179
SGD_Scer_YDR047W                  1.2e-10  646_[+3]_334
MIT_Spar_c130_3923                2.7e-10  644_[+3]_336
MIT_Spar_c117_4603                3.6e-10  301_[+3]_177
WashU_Skud_Contig1362.1           5.8e-09  646_[+3]_95
MIT_Sbay_c896_21277               9.7e-09  650_[+3]_330
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=9
WashU_Skud_Contig2069.5  (  305) AAAAATTTCCGTTCCTGCTC  1 
SGD_Scer_YDR232W         (  307) AAAAATTTCCGTTCCTGCTC  1 
MIT_Smik_c228_4055       (  304) GAAAATTTCCGTTCCTGCTC  1 
WashU_Sbay_Contig461.5   (  300) AAAAATCTCCGTTCCTGCTC  1 
SGD_Scer_YDR047W         (  647) AAAACATGCCGTTCCCGTAC  1 
MIT_Spar_c130_3923       (  645) AAAACATGCCGTCCCCGTAC  1 
MIT_Spar_c117_4603       (  302) AAAAATTTCTGTTCCTGCTC  1 
WashU_Skud_Contig1362.1  (  647) CAAACATGCCGTCCCCTACC  1 
MIT_Sbay_c896_21277      (  651) AAAACATGCCGATCCAAGCC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 3.1e-017 
   126    -66    -66   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
    78    134   -982   -982 
    45   -982   -982     78 
  -982    -66   -982    145 
  -982   -982    134     78 
  -982    251   -982   -982 
  -982    234   -982   -154 
  -982   -982    251   -982 
  -154   -982   -982    145 
  -982     34   -982    126 
  -982    251   -982   -982 
  -982    251   -982   -982 
  -154     92   -982     78 
  -154   -982    215   -154 
  -154    166    -66    -55 
   -55     34   -982     78 
  -982    251   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.1e-017 
 0.777778  0.111111  0.111111  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.555556  0.444444  0.000000  0.000000 
 0.444444  0.000000  0.000000  0.555556 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.444444  0.555556 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.000000  1.000000  0.000000 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  0.222222  0.000000  0.777778 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.333333  0.000000  0.555556 
 0.111111  0.000000  0.777778  0.111111 
 0.111111  0.555556  0.111111  0.222222 
 0.222222  0.222222  0.000000  0.555556 
 0.000000  1.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
AAAA[AC][TA]T[TG]CCGT[TC]CC[TC]G[CT][TAC]C
--------------------------------------------------------------------------------




Time 12.69 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =   9   llr = 171   E-value = 9.5e-014
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  23aa22::::::::::1611
pos.-specific     C  7:::1:a::991::86:236
probability       G  17::48:6a1:3::147:62
matrix            T  ::::2::4::16aa1:22:1

         bits    2.5       * *           
                 2.3       * *           
                 2.0       * ***         
                 1.8       * ***         
Information      1.5   ** ** *** ****    
content          1.3  *** ** *** ****    
(27.5 bits)      1.0 **** ****** ***** * 
                 0.8 **** ************ **
                 0.5 **** ***************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CGAAGGCGGCCTTTCCGAGC
consensus            AA  AA T   G   GTCCG
sequence                 T            T  
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
SGD_Scer_YDR232W             +    384  4.75e-14 CAATGAGCGA CGAAGGCGGCCTTTCCGAGC GGTAGGGTAA
WashU_Skud_Contig2069.5      +    381  3.48e-12 CAATGAGCGA CGAAGGCGGCCTTTCGTAGC AGCAGGGTAA
MIT_Spar_c117_4603           +    379  6.28e-12 CAATGAGCGA CGAAGGCGGCCTTTCCGAGT GGTAGGGTAA
MIT_Spar_c130_3923           +    708  1.69e-09 ATTATACTCT AAAATGCTGCCGTTCCGTCC CATTGAGTTT
SGD_Scer_YDR047W             +    708  1.69e-09 AATTTGTTAA AAAATGCTGCCGTTCCGTCC CATTGAGTTT
MIT_Smik_c228_4055           +    381  3.64e-09 CAATGAGCGA CGAAAGCGGCCTTTTGAAGG GTAGGGTAAT
WashU_Sbay_Contig461.5       +    378  5.96e-09 CAATGAGCGA CGAAGACGGCTTTTGGGCGG GGCAGGGTAA
MIT_Sbay_c896_21277          +    699  7.77e-09 ACTACGCAGC CAAACACTGGCGTTCCGCCC GTCCCATCCA
WashU_Skud_Contig1362.1      -    483  5.15e-08 AACGCTTATA GGAAAGCTGCCCTTCGTAAA ACAGCTTGCT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR232W                  4.8e-14  383_[+4]_95
WashU_Skud_Contig2069.5           3.5e-12  380_[+4]_98
MIT_Spar_c117_4603                6.3e-12  378_[+4]_100
MIT_Spar_c130_3923                1.7e-09  707_[+4]_273
SGD_Scer_YDR047W                  1.7e-09  707_[+4]_273
MIT_Smik_c228_4055                3.6e-09  380_[+4]_98
WashU_Sbay_Contig461.5              6e-09  377_[+4]_101
MIT_Sbay_c896_21277               7.8e-09  698_[+4]_282
WashU_Skud_Contig1362.1           5.1e-08  482_[-4]_259
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=9
SGD_Scer_YDR232W         (  384) CGAAGGCGGCCTTTCCGAGC  1 
WashU_Skud_Contig2069.5  (  381) CGAAGGCGGCCTTTCGTAGC  1 
MIT_Spar_c117_4603       (  379) CGAAGGCGGCCTTTCCGAGT  1 
MIT_Spar_c130_3923       (  708) AAAATGCTGCCGTTCCGTCC  1 
SGD_Scer_YDR047W         (  708) AAAATGCTGCCGTTCCGTCC  1 
MIT_Smik_c228_4055       (  381) CGAAAGCGGCCTTTTGAAGG  1 
WashU_Sbay_Contig461.5   (  378) CGAAGACGGCTTTTGGGCGG  1 
MIT_Sbay_c896_21277      (  699) CAAACACTGGCGTTCCGCCC  1 
WashU_Skud_Contig1362.1  (  483) GGAAAGCTGCCCTTCGTAAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 9.5e-014 
   -55    192    -66   -982 
     4   -982    192   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
   -55    -66    134    -55 
   -55   -982    215   -982 
  -982    251   -982   -982 
  -982   -982    166     45 
  -982   -982    251   -982 
  -982    234    -66   -982 
  -982    234   -982   -154 
  -982    -66     92     78 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -982    215    -66   -154 
  -982    166    134   -982 
  -154   -982    192    -55 
    78     34   -982    -55 
  -154     92    166   -982 
  -154    166     34   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 9.5e-014 
 0.222222  0.666667  0.111111  0.000000 
 0.333333  0.000000  0.666667  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.222222  0.111111  0.444444  0.222222 
 0.222222  0.000000  0.777778  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.555556  0.444444 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.111111  0.333333  0.555556 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.777778  0.111111  0.111111 
 0.000000  0.555556  0.444444  0.000000 
 0.111111  0.000000  0.666667  0.222222 
 0.555556  0.222222  0.000000  0.222222 
 0.111111  0.333333  0.555556  0.000000 
 0.111111  0.555556  0.222222  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
[CA][GA]AA[GAT][GA]C[GT]GCC[TG]TTC[CG][GT][ACT][GC][CG]
--------------------------------------------------------------------------------




Time 16.70 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 178   E-value = 2.7e-015
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  :68:86:::::76::27a29
pos.-specific     C  :::9:1:3::a134:8::::
probability       G  a:2:2:37aa:::69:3:71
matrix            T  :4:1:37::::21:1:::1:

         bits    2.5 *       ***         
                 2.3 *       ***         
                 2.0 *  *    ***   *     
                 1.8 *  *    ***   *     
Information      1.5 *  *   ****  *** *  
content          1.3 *  *   ****  *** * *
(28.5 bits)      1.0 * *** *****  *******
                 0.8 ***** *****  *******
                 0.5 ***** **************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GAACAATGGGCAAGGCAAGA
consensus             TG GTGC   TCC AG A 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig461.5       +    278  7.65e-13 CACCGGGACA GAACAATGGGCAAGGCAAGA TGAAAAATCT
MIT_Smik_c228_4055           +    283  7.65e-13 CATTGAATTA GAACAATGGGCAAGGCAAGA TGAAAATTTC
MIT_Spar_c117_4603           +    280  7.65e-13 GCATGGGTCA GAACAATGGGCAAGGCAAGA TGAAAAATTT
SGD_Scer_YDR232W             +    285  7.65e-13 GCATGGATCA GAACAATGGGCAAGGCAAGA TGAAAAATTT
WashU_Skud_Contig2069.5      +    283  7.37e-10 CACTGGATCG GAACAATGGGCAAGGCAATG TGAAAAATTT
SGD_Scer_YDR047W             +    871  2.30e-09 TAATGTAGCC GTGCATGCGGCTCCGCGAAA AGAGCTCTGC
WashU_Skud_Contig1362.1      +    334  3.13e-09 ACAAGGGAAG GTACATTGGGCCCCGAAAAA ATTTGCTAAT
MIT_Spar_c130_3923           +    880  4.62e-09 TTATATAGCC GTACGTGCGGCTCCTCGAGA AAGGCCCTGC
MIT_Sbay_c896_21277          +    841  2.58e-08 TTTTATAGCC GTGTGCGCGGCATCGAGAGA CAGGTTCAGC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig461.5            7.6e-13  277_[+5]_201
MIT_Smik_c228_4055                7.6e-13  282_[+5]_196
MIT_Spar_c117_4603                7.6e-13  279_[+5]_199
SGD_Scer_YDR232W                  7.6e-13  284_[+5]_194
WashU_Skud_Contig2069.5           7.4e-10  282_[+5]_196
SGD_Scer_YDR047W                  2.3e-09  870_[+5]_110
WashU_Skud_Contig1362.1           3.1e-09  333_[+5]_408
MIT_Spar_c130_3923                4.6e-09  879_[+5]_101
MIT_Sbay_c896_21277               2.6e-08  840_[+5]_140
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
WashU_Sbay_Contig461.5   (  278) GAACAATGGGCAAGGCAAGA  1 
MIT_Smik_c228_4055       (  283) GAACAATGGGCAAGGCAAGA  1 
MIT_Spar_c117_4603       (  280) GAACAATGGGCAAGGCAAGA  1 
SGD_Scer_YDR232W         (  285) GAACAATGGGCAAGGCAAGA  1 
WashU_Skud_Contig2069.5  (  283) GAACAATGGGCAAGGCAATG  1 
SGD_Scer_YDR047W         (  871) GTGCATGCGGCTCCGCGAAA  1 
WashU_Skud_Contig1362.1  (  334) GTACATTGGGCCCCGAAAAA  1 
MIT_Spar_c130_3923       (  880) GTACGTGCGGCTCCTCGAGA  1 
MIT_Sbay_c896_21277      (  841) GTGTGCGCGGCATCGAGAGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 2.7e-015 
  -982   -982    251   -982 
    78   -982   -982     45 
   126   -982     34   -982 
  -982    234   -982   -154 
   126   -982     34   -982 
    78    -66   -982      4 
  -982   -982     92    104 
  -982     92    192   -982 
  -982   -982    251   -982 
  -982   -982    251   -982 
  -982    251   -982   -982 
   104    -66   -982    -55 
    78     92   -982   -154 
  -982    134    166   -982 
  -982   -982    234   -154 
   -55    215   -982   -982 
   104   -982     92   -982 
   162   -982   -982   -982 
   -55   -982    192   -154 
   145   -982    -66   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.7e-015 
 0.000000  0.000000  1.000000  0.000000 
 0.555556  0.000000  0.000000  0.444444 
 0.777778  0.000000  0.222222  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.777778  0.000000  0.222222  0.000000 
 0.555556  0.111111  0.000000  0.333333 
 0.000000  0.000000  0.333333  0.666667 
 0.000000  0.333333  0.666667  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.666667  0.111111  0.000000  0.222222 
 0.555556  0.333333  0.000000  0.111111 
 0.000000  0.444444  0.555556  0.000000 
 0.000000  0.000000  0.888889  0.111111 
 0.222222  0.777778  0.000000  0.000000 
 0.666667  0.000000  0.333333  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.222222  0.000000  0.666667  0.111111 
 0.888889  0.000000  0.111111  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
G[AT][AG]C[AG][AT][TG][GC]GGC[AT][AC][GC]G[CA][AG]A[GA]A
--------------------------------------------------------------------------------




Time 20.54 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR232W                 2.02e-39  164_[+2(7.75e-12)]_100_[+5(7.65e-13)]_2_[+3(9.40e-12)]_36_[+1(1.83e-13)]_1_[+4(4.75e-14)]_95
MIT_Spar_c117_4603               1.73e-34  159_[+2(2.12e-10)]_100_[+5(7.65e-13)]_2_[+3(3.58e-10)]_36_[+1(1.83e-13)]_1_[+4(6.28e-12)]_100
MIT_Smik_c228_4055               3.04e-30  160_[+2(6.70e-10)]_102_[+5(7.65e-13)]_1_[+3(6.77e-11)]_36_[+1(1.47e-11)]_1_[+4(3.64e-09)]_98
WashU_Skud_Contig2069.5          9.14e-35  161_[+2(7.75e-12)]_101_[+5(7.37e-10)]_2_[+3(9.40e-12)]_35_[+1(1.83e-13)]_1_[+4(3.48e-12)]_98
WashU_Sbay_Contig461.5           2.20e-33  160_[+2(8.83e-11)]_7_[+1(7.03e-05)]_70_[+5(7.65e-13)]_2_[+3(7.67e-11)]_37_[+1(3.08e-14)]_1_[+4(5.96e-09)]_6_[+5(2.10e-06)]_75
SGD_Scer_YDR047W                 5.13e-24  172_[+2(4.04e-10)]_47_[+3(8.04e-06)]_387_[+3(1.22e-10)]_41_[+4(1.69e-09)]_17_[-5(6.96e-05)]_106_[+5(2.30e-09)]_31_[+1(1.02e-09)]_3_[-4(1.74e-05)]_36
MIT_Spar_c130_3923               9.08e-24  169_[+2(2.30e-10)]_47_[+3(8.58e-05)]_388_[+3(2.75e-10)]_43_[+4(1.69e-09)]_17_[-5(6.49e-06)]_37_[-5(2.93e-05)]_58_[+5(4.62e-09)]_31_[+1(7.23e-10)]_8_[+4(7.15e-06)]_22
MIT_Sbay_c896_21277              2.02e-19  142_[+2(3.02e-08)]_45_[+3(6.78e-05)]_259_[-4(2.48e-06)]_144_[+3(9.67e-09)]_28_[+4(7.77e-09)]_122_[+5(2.58e-08)]_31_[+1(2.69e-10)]_89
WashU_Skud_Contig1362.1          4.91e-20  41_[-1(2.10e-05)]_75_[+2(8.43e-10)]_137_[+1(1.77e-08)]_20_[+5(3.13e-09)]_129_[-4(5.15e-08)]_144_[+3(5.76e-09)]_31_[+4(1.33e-05)]_44
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM1-HEM13.fa000444000766000024      1717713155576321 20110 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR232W HEM1 "5-aminolevulinate synthase, catalyzes the first step in the heme biosynthetic pathway; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expression is regulated by Hap2p-Hap3p"
ACTGAAAAAAAAACCTAAGTACTGTTATGATTATTGAGGGACAACAACTAGCTCTATTAG
TTTTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTGGG
ATAAAAAAAAAAGAAACGCGAGCTGAGAAGGGAAGGCGTGTAAAGGAAGAACGGTTGAGA
GACAGCAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGAATGGAGAAG
TTTGGTATGATGCAAACGTTGTATTTCTAACAACGCATGGATCAGAACAATGGGCAAGGC
AAGATGAAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCC
CGCGGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGCGGTAGGGTAAGCCGTGC
AGGCAAGCTTATTATAGCACCGTCGGGGGTACCACCACTATATCAAACTCCACTGCTCGG
TAAAGCATTGTAGTGAAG
>MIT_Spar_c117_4603 YDR232W 5' untranslated region, Contig c117 17441 - 19440, 2000 bp (revcom)
ACTGAAAAAAAACCAAGTACTGTTGTGATTATTGAGGGACAACGGCTAGCTCTATTTGTT
TTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTAGGAT
AAAAAAAGAAACGCGAGCTGAGAAGAGAAGGCGTGTAAAGGAAGAACGGTTGAGAGAGAG
CAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGGATGGAGGAGTTTGG
TACGATGCAAACGCTATATTTGTAGCAACGCATGGGTCAGAACAATGGGCAAGGCAAGAT
GAAAAATTTCTGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGCGG
CCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGTGGTAGGGTAAGCCGTGCAGGCA
AGCTTATTATAGCACCGTCGGGGGGACCACTATATCAAGTTCCACAGCACGGTGAAGCAT
TGCAGTATAGTTCACAGC
>MIT_Smik_c228_4055 YDR232W 5' untranslated region, Contig c228 4702 - 6701(revcom), 2000 bp (revcom)
ACCGAGAGAAAAACTAAGTAGTGATATGATTATTGAGGACTAATGACCAGCTTTGTTTGT
TTTTTCTTCCAACCTAACTTATATGGGAAATATATAGGACAGAAAAAAGAAAAGAGCACG
AAAAAAAAGAAATGCGACCTGAGAAGGGAGGACGTGTGAAGCCAGAACGGTTGAATGACA
GTAGAGGAGGGTGCAACACAACCGAGTAGAGTACCAGCTGACGGAATGGAGGAGTTTGGT
ATGATGCAAAAGTGATGCTTTTAGCAACGCAACATTGAATTAGAACAATGGGCAAGGCAA
GATGAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGC
AAGCGCAGACCAATGAGCGACGAAAGCGGCCTTTTGAAGGGTAGGGTAATCCATGCAGGC
AAGTTTATTATAGCACCGTCGGGGGGAAGCATTATATCAAACTCCACAGTACAGCGTAAC
ATTGCTGTATAGGCTACA
>WashU_Skud_Contig2069.5 YDR232W 5' untranslated region, Contig c2069 5476 - 7475, 2000 bp (revcom)
ACTGAAAATAATCCGAGTCGTGCTACTGTGAATATTGAGAATAGGGACTAGCTCTATTTG
ATTTTTCTTCCAACCAAACTTATATGGAAAATATAAAGGAAAGAAAAAAGAAAAGAATAG
GAAAAAAAAAAAGAAACGCGAGAGAAGAGAACCGTGTGGAGGGAAGAACGGTTGAGAGAC
AGCAGAGCACAGCGCAACACAACCGAGTAGAGTACCAGCAGACGGAGTGGGTAGTTTGGT
ACAGTGTAAAAGCTATATTTCCACCAACGCAACACTGGATCGGAACAATGGGCAAGGCAA
TGTGAAAAATTTCCGTTCCTGCTCTTGCTTCATATATGACAATGACCAAAAAGCGTCCGC
GGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCGTAGCAGCAGGGTAAGCCGCGCAAG
CAAGTCCGTCATAACACCGTCGAAGGGGCACCACTATATCAGCTCTTCAGCATGGTAGGC
CATTACAGCACAGTCTTG
>WashU_Sbay_Contig461.5 YDR232W 5' untranslated region, Contig c461 4000 - 5999, 2000 bp (revcom)
ACTAAAAAGTCCAAGTGGTGCTGTTATTATTGAGGATAGCAACTAGCTTTATTTGTTTTT
TCTTCCAACCAAACTTATATGGAAATCAAAGGAAGGAAAAAAAGAAAAGAACAGGAAGAA
AAAAAAGAAACGTGAGCTGCCGAAAGGAGAGCGTGTGGAGGGAAGAACCGTTGAGAGACA
ACAGAGCAGGGTGCAAACCGATTAGAGTACCAGCAGACGAGATGGGCGATGTGGTACGGT
GCAGAAGGTGTGGTTCCAACAGCGCAGCACCGGGACAGAACAATGGGCAAGGCAAGATGA
AAAATCTCCGTTCCTGCTCTTGCTTGATATATTAACAATGACCAAAAAAACGCCGGCGGG
CGCAGACCAATGAGCGACGAAGACGGCTTTTGGGCGGGGCAGGGTAAGATGGGACAGGCA
AGGTCCGCTATAGCACCGTCGAGGGGGACCGCTATATCAGCTCCCAGTACATTGCAGCAC
ACTCTATAGCTAGTCAAA
>SGD_Scer_YDR044W HEM13 "Coproporphyrinogen III oxidase, an oxygen requiring enzyme that catalyzes the sixth step in the heme biosynthetic pathway; localizes to the mitochondrial inner membrane; transcription is repressed by oxygen and heme (via Rox1p and Hap1p)"
CTTTATGTGTATTTAATTGTGTTCGAAGAGTTCGGTTTGCTATGTTTGATTTGCGAAAAG
AAAGCTTTTGATATGCTCAAAAAAAGAAAACCCGGAGAATAAAAGCTTAACAAAGAAAGA
CAATAGGTGGAAAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTCGAAACGAGAACA
ATGGGCAAAGCAAGCTTTATCTTCGGATCGTCCGTCAGCGCTTTGGTTGCAGTCTTATGC
TTTGTTCAAGCTGGAGCGTTATTGGTGGGAGAACCAGAAAAGGCGAAAGCGTAGCGTTCT
TTGAAATTTGGCTTCTGTTCCTGCGACTCGTTTAAAAGTAGAAGGGCCCGCGGAGCCGCT
GTGAAAGATTTCTTTTACTCTTTCAGCGCAGAAATCTCGCAGGAGCTCAGCAGAAAGTGC
CTATGACGGTAATCCCAGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAATTAA
AATACCGTGCCTATAGTAACTTTTTTTTACGCTGTGAACCGTTCAACACACAGTAAAAAC
TCCGCAGGAAATGGTTTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTTTCCCAACA
GTGAACGAGAGGACAAACTCCAGAGGATTTGCGGGCTTGATGATAAAATGTATTGTTGAA
AAGATCGCGAATGCAACAATTACGGTGGGGAGAAATATCAACAAAAGGGCAAGGCTATGC
CTTCTGGAAAGTGGCAGACTTGCACTTTCCTCGAAAAGAAAAATGACCGCAAGATCCGGT
TGTTCTCAACCTTCTACATTAAGACATACTTCTACGATTTTCGAATGCCGAAGCAACTAT
CGCTGAAATTTGTCATGTCAAAATTGCTACTGGGGGAGAAGAATATATATGGAAGTAATT
ATTATTTACGTTGCTGAAATGGCAGGTTAGACGCATGTTTTGCAAAATAAGTGGTTTTGA
AAAGAATTGATACTAGGAATCGGTGCAATACCTTCTACCT
>MIT_Spar_c130_3912 YDR044W 5' untranslated region, Contig c130 4128 - 6127, 2000 bp (revcom)
CTTTATATGTGTGTTTTGTGGTGTTCGAAATTGGTTTCTTTTGTTCGACTTGCGAGAAGA
AAGCTATCAATATGCTTTCCAAAAAAAGCTGGAGAATAAAAGCTTAACAAAGAAAGACAA
TAGGCGGAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTTCGAAACGAGAACAATGG
ACAAATCAAGCTTTATCTATGGGTTGTCAGCTCTTTGGTTGCAGTCTTGTGCTTGGTTCA
AGCTGGGGCATTATTGGTGGGAGAAGCCAGAAAAGGCGAAAGCGTAGCGTTCTTTGAAAT
TTGGATTCTGTTCCTGCGACTCGTTTAAAAGAAGAAGGGCTGCGGAGCCACTGTGAAAGA
CTTGTTGTGCTCTTTCAACTAAGAAATCTGGCAGGAACTCGATATAAAGTGCCTGTGACA
GTAATCTCAGGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAAATTGAAATACC
GTGCCTATGGTAACTTTTTTTTACGCTGCGAACCGTTCAACACACATTGAAAACCCCGCA
GCAATTGTTCTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTCTCCCAACAGTGTAC
GAGCGGACGAAACTCTAGAGGATTTGCAGGCTCGGTGATAAAATGTATTGTTGAAAAGAA
CGCGAATGCAACGATTGTGGTGGAGAGAAATATCAACAGGGCAAGGCAAGGCTATGCTCT
TTTGGAAGTGGCGGACTTGCACTTTCTTGAAAAGAAAAATGACCGCAAGATCCGGTTGTT
CATAACTTTCTACAATAAGGCATACTTCTACGGTTTTCCAATGCTGAGGCAACTATCGCT
ATAAAATCGCTGCTAGGAGAAGATTATATATGGACGTAAATATTTTTTACGTTACTAAAA
TTCTAGGTTAGAGGCACGTTTTGCAGAACCAGTGGCCTTGGAAAGGTGTTGCTACAAATT
TATGCAATTTCTTCAACTTGCCAGGTGGTCTTGGATGATC
>MIT_Sbay_c896_21290 YDR044W 5' untranslated region, Contig c896 7383 - 9382(revcom), 2000 bp (revcom)
CTTGTTATGTGTGTTTGTGGTGATTGCGGTTTGGTTTTTCTGATTCGTATGACAGAAAGA
AAAAAATTCAGTTTACCTTGTAAGGTGATTAGGAGAAGAAAAAAAGCTTATTGGCAGCGA
ACAATAGGTGAAAAAAAAAAAGAAAATGCGTGTCCTTATATAGCTTTCTCGAAGGGAGAA
CAATGGATAAATCAAAGCTTATCTACGGGTCAACAGCTCTTTGGTTGCTGTCTTGCTCTA
GGTCCAAGCTGGGGCATAATTGGTGGGAGAAGCCAGAAAATGCGAAAGCGTACCGTTCTG
TGAAAAATGGCTTCGGTTCCTGCGACTCGTTTAAAAAGAAAAGGGCCCGCGCAGCCTGTG
TGAAATGTTCGTTTTGCCCTTCCCAGAGAGAAATCTTGCAGGAGCCTCAATACAATGTGC
CTGCGGATGGAATACCAGGGGATAAAGGCGTGAAGGCACTCCCTGAACAATTGAAAATTG
GAAAAAAAAAGTGCCTGTGATGAATCTTATACGTTGGGAAAACTCCAAGACACTTTTAAA
ACTCCGCAGAGATTGTTTGGAGGGACCTTGACCACGAGTTGGGAGTATTGTTTTTTCCTG
GAAGGAACGAGCGGAACTCTTGGGGATTTGCGGGCTCGCTAATAAAAAGTGTCTTGTTGA
AGAAAAGTAGAATGCGACTAAAACGGTGGAGGAAAATATCAACAAGGCAAGGCTATGCCT
TTCGAAGAAAAGCGGACTTGCAATTGCACAACCGTATCGAAGAGAATTGAGAAGGGGGTG
CAAAGTGATCCGGTTGTTCATATTTCTTCACCAATTGATACAATTATCTACGTTTGTTCT
GTTGACCAATCCAACGGGGACTCTGTATGACATAAGTCTTCCTTACATTGCTAAGATCCA
AGATCAGACCCGTAGATGAGTTCTGCACCAAAGAGTTGTTAACCGTCTTGCCTGAATAAT
TTTAAGTTGTCGCGATCCTCTTACAAGGTGTTCTTATTTC
>WashU_Smik_Contig2283.3 YDR044W 5' untranslated region, Contig c2283 2261 - 4260(revcom), 2000 bp (revcom)
CTTTATTGAGGATTTGTGGCGTTTGAGGTTTGGTTTTTTATTCAATTTGAAAGAAGAAAA
CTATCGTTATACTTTCGAAGAAAACACGGGGAATAAAAGCTTAACAGGTGAGACAATAGG
TGGAAAAAAAGGAAAATATGTGTCTTTATATAGCCTTTTCAAAAAGAGAACAATGGTCAA
ATAAAGGTTTATCTACGAGTCGACAGTTCGTTGGCTGCAGTGTTACGCTTGGTTGAAGCT
GGGGCATTATTGGTGGAAGAAGCCAGAAAAGACGAAAGAGTAGCGTAGCGTTCTTTCAAA
TTTTGGTTTCGGGTTCCTGCGACTCGTTTAAAAAAGAAAAGGGCCCGCGGCCCCGCCGTG
AAACACTTCGTCTTGCTCTTCCCACCCAGAAAACTTGTAGGAGCCTCAGTTACAAAGTGC
CTGTAATGGAAATCTTAGGGGGCTACTATTGTAAAGGCAATTTCTGAACAATTGAAAGTG
AAAATATCGTGCCTGTGGTAACTTTCTTATACGCCGTGAAACGTTTAACATACGTTGAAA
ACTCCGCAGGGATTGGTTTGGAAAATTATAGTCACGAATTAGGCGTATTGTCTTTCAAGA
AGGTACGAGCGGATGAACTTCTTGAGGATTTGCGGGTTCGGTGATAAAAAATGTATTGTT
GAAAAGAACGCGAATGCAACAATTACGGTGGAGAAAAATATTAACAAGGGAAGGCAAGGC
TATGTTCTATTGAGAAGCGGCGGACTTGCACTTTCCTCGAAGAAAAAAATGTCTTCAAGA
TCCAATGTTCATATAACTTTCTACAATAAGGTATCCTTCTACGATCTTTCAATGTTAAGA
TTGAAATCAATGTAAAAAGCACCATGTTGAATACTACTGCTAGGAGGAGATCACATATGA
ATGTGATTATTATTTATATTAGTAAATTTTCAGGTTAGGAAGAAGTTATGTGACGCTTTA
GCTTTGGAAATTTGTTGCGGGAAACTGATAACATTCTTTT
BioPerl-1.007002/t/data/map_hem/HEM1-HEM13.meme.txt000444000766000024     11557013155576321 21277 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM1-HEM13.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDR232W         1.0000    498  MIT_Spar_c117_4603       1.0000    498  
MIT_Smik_c228_4055       1.0000    498  WashU_Skud_Contig2069.5  1.0000    498  
WashU_Sbay_Contig461.5   1.0000    498  SGD_Scer_YDR044W         1.0000   1000  
MIT_Spar_c130_3912       1.0000   1000  MIT_Sbay_c896_21290      1.0000   1000  
WashU_Smik_Contig2283.3  1.0000   1000  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM1-HEM13.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            6490    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.288 C 0.212 G 0.212 T 0.288 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 215   E-value = 3.2e-031
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  9:aa:aa:::2:aa4:1aa1
pos.-specific     C  ::::a::::::9::::9:::
probability       G  1a::::::aa7:::67:::8
matrix            T  :::::::a::11:::3:::1

         bits    2.5  *  *   **          
                 2.3  *  *   **          
                 2.0  *  *   ** *    *   
                 1.8  *  *   ** *    *   
Information      1.5  ********* ***  *** 
content          1.3 ********** *** *****
(34.4 bits)      1.0 ********************
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           AGAACAATGGGCAAGGCAAG
consensus                      A   AT    
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig461.5       +    277  3.60e-13 GCACCGGGAC AGAACAATGGGCAAGGCAAG ATGAAAAATC
MIT_Smik_c228_4055           +    282  3.60e-13 ACATTGAATT AGAACAATGGGCAAGGCAAG ATGAAAATTT
MIT_Spar_c117_4603           +    279  3.60e-13 CGCATGGGTC AGAACAATGGGCAAGGCAAG ATGAAAAATT
SGD_Scer_YDR232W             +    284  3.60e-13 CGCATGGATC AGAACAATGGGCAAGGCAAG ATGAAAAATT
SGD_Scer_YDR044W             +    175  1.02e-12 TTTCGAAACG AGAACAATGGGCAAAGCAAG CTTTATCTTC
MIT_Spar_c130_3912           +    171  2.37e-11 TTTCGAAACG AGAACAATGGACAAATCAAG CTTTATCTAT
WashU_Skud_Contig2069.5      +    282  2.76e-11 ACACTGGATC GGAACAATGGGCAAGGCAAT GTGAAAAATT
WashU_Smik_Contig2283.3      +    167  1.95e-10 TTTCAAAAAG AGAACAATGGTCAAATAAAG GTTTATCTAC
MIT_Sbay_c896_21290          +    177  4.52e-10 TCTCGAAGGG AGAACAATGGATAAATCAAA GCTTATCTAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig461.5            3.6e-13  276_[+1]_202
MIT_Smik_c228_4055                3.6e-13  281_[+1]_197
MIT_Spar_c117_4603                3.6e-13  278_[+1]_200
SGD_Scer_YDR232W                  3.6e-13  283_[+1]_195
SGD_Scer_YDR044W                    1e-12  174_[+1]_806
MIT_Spar_c130_3912                2.4e-11  170_[+1]_810
WashU_Skud_Contig2069.5           2.8e-11  281_[+1]_197
WashU_Smik_Contig2283.3             2e-10  166_[+1]_814
MIT_Sbay_c896_21290               4.5e-10  176_[+1]_804
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Sbay_Contig461.5   (  277) AGAACAATGGGCAAGGCAAG  1 
MIT_Smik_c228_4055       (  282) AGAACAATGGGCAAGGCAAG  1 
MIT_Spar_c117_4603       (  279) AGAACAATGGGCAAGGCAAG  1 
SGD_Scer_YDR232W         (  284) AGAACAATGGGCAAGGCAAG  1 
SGD_Scer_YDR044W         (  175) AGAACAATGGGCAAAGCAAG  1 
MIT_Spar_c130_3912       (  171) AGAACAATGGACAAATCAAG  1 
WashU_Skud_Contig2069.5  (  282) GGAACAATGGGCAAGGCAAT  1 
WashU_Smik_Contig2283.3  (  167) AGAACAATGGTCAAATAAAG  1 
MIT_Sbay_c896_21290      (  177) AGAACAATGGATAAATCAAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 3.2e-031 
   145   -982    -66   -982 
  -982   -982    251   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -982    251   -982   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -982   -982   -982    162 
  -982   -982    251   -982 
  -982   -982    251   -982 
   -55   -982    192   -154 
  -982    234   -982   -154 
   162   -982   -982   -982 
   162   -982   -982   -982 
    45   -982    166   -982 
  -982   -982    192      4 
  -154    234   -982   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -154   -982    215   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.2e-031 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.222222  0.000000  0.666667  0.111111 
 0.000000  0.888889  0.000000  0.111111 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  0.000000  0.666667  0.333333 
 0.111111  0.888889  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.111111  0.000000  0.777778  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
AGAACAATGG[GA]CAA[GA][GT]CAAG
--------------------------------------------------------------------------------




Time  4.41 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 209   E-value = 1.2e-028
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  a99a2:::::::113:::7:
pos.-specific     C  :::::6:8a8:a:1474a:3
probability       G  :11:84a1:1a:98236:27
matrix            T  :::::::1:1::::::::1:

         bits    2.5       * * **     *  
                 2.3       * * **     *  
                 2.0       * * ***    *  
                 1.8       * * ***    *  
Information      1.5 *  *********** *** *
content          1.3 ************** *** *
(33.5 bits)      1.0 ************** *** *
                 0.8 ****************** *
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           AAAAGCGCCCGCGGCCGCAG
consensus                AG        AGC GC
sequence                           G     
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c117_4603           +    347  1.67e-14 ACAATGACCA AAAAGCGCCCGCGGCCGCAG ACCAATGAGC
SGD_Scer_YDR232W             +    352  1.67e-14 ACAATGACCA AAAAGCGCCCGCGGCCGCAG ACCAATGAGC
WashU_Smik_Contig2283.3      +    337  6.44e-13 TTTAAAAAAG AAAAGGGCCCGCGGCCCCGC CGTGAAACAC
WashU_Skud_Contig2069.5      +    349  2.55e-12 ACAATGACCA AAAAGCGTCCGCGGCCGCAG ACCAATGAGC
SGD_Scer_YDR044W             +    340  2.62e-11 GTTTAAAAGT AGAAGGGCCCGCGGAGCCGC TGTGAAAGAT
WashU_Sbay_Contig461.5       +    346  2.62e-11 CAATGACCAA AAAAACGCCGGCGGGCGCAG ACCAATGAGC
MIT_Sbay_c896_21290          +    339  6.92e-11 GTTTAAAAAG AAAAGGGCCCGCGCAGCCTG TGTGAAATGT
MIT_Smik_c228_4055           +    349  9.01e-11 ACAATGACCA AAAAGCGCCCGCAAGCGCAG ACCAATGAGC
MIT_Spar_c130_3912           +    332  1.10e-09 CGTTTAAAAG AAGAAGGGCTGCGGAGCCAC TGTGAAAGAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c117_4603                1.7e-14  346_[+2]_132
SGD_Scer_YDR232W                  1.7e-14  351_[+2]_127
WashU_Smik_Contig2283.3           6.4e-13  336_[+2]_644
WashU_Skud_Contig2069.5           2.5e-12  348_[+2]_130
SGD_Scer_YDR044W                  2.6e-11  339_[+2]_641
WashU_Sbay_Contig461.5            2.6e-11  345_[+2]_133
MIT_Sbay_c896_21290               6.9e-11  338_[+2]_642
MIT_Smik_c228_4055                  9e-11  348_[+2]_130
MIT_Spar_c130_3912                1.1e-09  331_[+2]_649
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
MIT_Spar_c117_4603       (  347) AAAAGCGCCCGCGGCCGCAG  1 
SGD_Scer_YDR232W         (  352) AAAAGCGCCCGCGGCCGCAG  1 
WashU_Smik_Contig2283.3  (  337) AAAAGGGCCCGCGGCCCCGC  1 
WashU_Skud_Contig2069.5  (  349) AAAAGCGTCCGCGGCCGCAG  1 
SGD_Scer_YDR044W         (  340) AGAAGGGCCCGCGGAGCCGC  1 
WashU_Sbay_Contig461.5   (  346) AAAAACGCCGGCGGGCGCAG  1 
MIT_Sbay_c896_21290      (  339) AAAAGGGCCCGCGCAGCCTG  1 
MIT_Smik_c228_4055       (  349) AAAAGCGCCCGCAAGCGCAG  1 
MIT_Spar_c130_3912       (  332) AAGAAGGGCTGCGGAGCCAC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 1.2e-028 
   162   -982   -982   -982 
   145   -982    -66   -982 
   145   -982    -66   -982 
   162   -982   -982   -982 
   -55   -982    215   -982 
  -982    166    134   -982 
  -982   -982    251   -982 
  -982    215    -66   -154 
  -982    251   -982   -982 
  -982    215    -66   -154 
  -982   -982    251   -982 
  -982    251   -982   -982 
  -154   -982    234   -982 
  -154    -66    215   -982 
     4    134     34   -982 
  -982    192     92   -982 
  -982    134    166   -982 
  -982    251   -982   -982 
   104   -982     34   -154 
  -982     92    192   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.2e-028 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.222222  0.000000  0.777778  0.000000 
 0.000000  0.555556  0.444444  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.777778  0.111111  0.111111 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.777778  0.111111  0.111111 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.111111  0.111111  0.777778  0.000000 
 0.333333  0.444444  0.222222  0.000000 
 0.000000  0.666667  0.333333  0.000000 
 0.000000  0.444444  0.555556  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.666667  0.000000  0.222222  0.111111 
 0.000000  0.333333  0.666667  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
AAAA[GA][CG]GCCCGCGG[CAG][CG][GC]C[AG][GC]
--------------------------------------------------------------------------------




Time  8.84 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =   9   llr = 205   E-value = 8.3e-027
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :::::::::::::4::::::
pos.-specific     C  1194:::aa::a:64:46::
probability       G  ::12a:::::a:4:::24::
matrix            T  99:3:aa::a::6:6a3:aa

         bits    2.5     *  ** **        
                 2.3     *  ** **        
                 2.0   * *  ** **        
                 1.8   * *  ** **        
Information      1.5   * ********   * ***
content          1.3 *** ********   * ***
(32.8 bits)      1.0 *** ************ ***
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TTCCGTTCCTGCTCTTCCTT
consensus               T        GAC TG  
sequence                G            G   
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2069.5      +    311  1.06e-11 TGTGAAAAAT TTCCGTTCCTGCTCTTGCTT CATATATGAC
MIT_Sbay_c896_21290          +    312  1.49e-11 GAAAAATGGC TTCGGTTCCTGCGACTCGTT TAAAAAGAAA
MIT_Smik_c228_4055           +    310  1.49e-11 AGATGAAAAT TTCCGTTCCTGCTCTTTCTT CATATATGAA
SGD_Scer_YDR232W             +    313  1.49e-11 GATGAAAAAT TTCCGTTCCTGCTCTTTCTT CATATATGAA
MIT_Spar_c130_3912           +    306  1.92e-11 GAAATTTGGA TTCTGTTCCTGCGACTCGTT TAAAAGAAGA
SGD_Scer_YDR044W             +    313  1.92e-11 GAAATTTGGC TTCTGTTCCTGCGACTCGTT TAAAAGTAGA
MIT_Spar_c117_4603           +    308  5.14e-11 GATGAAAAAT TTCTGTTCCTGCTCTTTCTT CATATATGAA
WashU_Sbay_Contig461.5       +    306  6.73e-11 GATGAAAAAT CTCCGTTCCTGCTCTTGCTT GATATATTAA
WashU_Smik_Contig2283.3      +    309  2.36e-10 AATTTTGGTT TCGGGTTCCTGCGACTCGTT TAAAAAAGAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2069.5           1.1e-11  310_[+3]_168
MIT_Sbay_c896_21290               1.5e-11  311_[+3]_669
MIT_Smik_c228_4055                1.5e-11  309_[+3]_169
SGD_Scer_YDR232W                  1.5e-11  312_[+3]_166
MIT_Spar_c130_3912                1.9e-11  305_[+3]_675
SGD_Scer_YDR044W                  1.9e-11  312_[+3]_668
MIT_Spar_c117_4603                5.1e-11  307_[+3]_171
WashU_Sbay_Contig461.5            6.7e-11  305_[+3]_173
WashU_Smik_Contig2283.3           2.4e-10  308_[+3]_672
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=9
WashU_Skud_Contig2069.5  (  311) TTCCGTTCCTGCTCTTGCTT  1 
MIT_Sbay_c896_21290      (  312) TTCGGTTCCTGCGACTCGTT  1 
MIT_Smik_c228_4055       (  310) TTCCGTTCCTGCTCTTTCTT  1 
SGD_Scer_YDR232W         (  313) TTCCGTTCCTGCTCTTTCTT  1 
MIT_Spar_c130_3912       (  306) TTCTGTTCCTGCGACTCGTT  1 
SGD_Scer_YDR044W         (  313) TTCTGTTCCTGCGACTCGTT  1 
MIT_Spar_c117_4603       (  308) TTCTGTTCCTGCTCTTTCTT  1 
WashU_Sbay_Contig461.5   (  306) CTCCGTTCCTGCTCTTGCTT  1 
WashU_Smik_Contig2283.3  (  309) TCGGGTTCCTGCGACTCGTT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 8.3e-027 
  -982    -66   -982    145 
  -982    -66   -982    145 
  -982    234    -66   -982 
  -982    134     34      4 
  -982   -982    251   -982 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -982    251   -982   -982 
  -982    251   -982   -982 
  -982   -982   -982    162 
  -982   -982    251   -982 
  -982    251   -982   -982 
  -982   -982    134     78 
    45    166   -982   -982 
  -982    134   -982     78 
  -982   -982   -982    162 
  -982    134     34      4 
  -982    166    134   -982 
  -982   -982   -982    162 
  -982   -982   -982    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 8.3e-027 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.444444  0.222222  0.333333 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.444444  0.555556 
 0.444444  0.555556  0.000000  0.000000 
 0.000000  0.444444  0.000000  0.555556 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.444444  0.222222  0.333333 
 0.000000  0.555556  0.444444  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
TTC[CTG]GTTCCTGC[TG][CA][TC]T[CTG][CG]TT
--------------------------------------------------------------------------------




Time 13.06 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =   9   llr = 202   E-value = 5.2e-025
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  a1:6a:4a44:7::aa611:
pos.-specific     C  :6a4:::::6::a:::::9:
probability       G  :3:::46:6:93:a::49:a
matrix            T  :::::6::::1:::::::::

         bits    2.5   *         **     *
                 2.3   *         **     *
                 2.0   *       * **   ***
                 1.8   *       * **   ***
Information      1.5 * * *  *  * **** ***
content          1.3 * * *  *  * **** ***
(32.4 bits)      1.0 ********************
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           ACCAATGAGCGACGAAAGCG
consensus             G C GA AA G    G   
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2069.5      +    369  8.45e-13 GCGGCCGCAG ACCAATGAGCGACGAAGGCG GCCTTTCGTA
MIT_Spar_c117_4603           +    367  8.45e-13 GCGGCCGCAG ACCAATGAGCGACGAAGGCG GCCTTTCCGA
SGD_Scer_YDR232W             +    372  8.45e-13 GCGGCCGCAG ACCAATGAGCGACGAAGGCG GCCTTTCCGA
MIT_Smik_c228_4055           +    369  2.51e-12 GCAAGCGCAG ACCAATGAGCGACGAAAGCG GCCTTTTGAA
MIT_Spar_c130_3912           +    265  5.38e-11 TGGTGGGAGA AGCCAGAAAAGGCGAAAGCG TAGCGTTCTT
WashU_Sbay_Contig461.5       +    366  5.38e-11 GCGGGCGCAG ACCAATGAGCGACGAAGACG GCTTTTGGGC
SGD_Scer_YDR044W             +    272  1.99e-10 TTGGTGGGAG AACCAGAAAAGGCGAAAGCG TAGCGTTCTT
WashU_Smik_Contig2283.3      +    261  3.58e-10 TGGTGGAAGA AGCCAGAAAAGACGAAAGAG TAGCGTAGCG
MIT_Sbay_c896_21290          +    271  3.78e-10 TGGTGGGAGA AGCCAGAAAATGCGAAAGCG TACCGTTCTG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2069.5           8.5e-13  368_[+4]_110
MIT_Spar_c117_4603                8.5e-13  366_[+4]_112
SGD_Scer_YDR232W                  8.5e-13  371_[+4]_107
MIT_Smik_c228_4055                2.5e-12  368_[+4]_110
MIT_Spar_c130_3912                5.4e-11  264_[+4]_716
WashU_Sbay_Contig461.5            5.4e-11  365_[+4]_113
SGD_Scer_YDR044W                    2e-10  271_[+4]_709
WashU_Smik_Contig2283.3           3.6e-10  260_[+4]_720
MIT_Sbay_c896_21290               3.8e-10  270_[+4]_710
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=9
WashU_Skud_Contig2069.5  (  369) ACCAATGAGCGACGAAGGCG  1 
MIT_Spar_c117_4603       (  367) ACCAATGAGCGACGAAGGCG  1 
SGD_Scer_YDR232W         (  372) ACCAATGAGCGACGAAGGCG  1 
MIT_Smik_c228_4055       (  369) ACCAATGAGCGACGAAAGCG  1 
MIT_Spar_c130_3912       (  265) AGCCAGAAAAGGCGAAAGCG  1 
WashU_Sbay_Contig461.5   (  366) ACCAATGAGCGACGAAGACG  1 
SGD_Scer_YDR044W         (  272) AACCAGAAAAGGCGAAAGCG  1 
WashU_Smik_Contig2283.3  (  261) AGCCAGAAAAGACGAAAGAG  1 
MIT_Sbay_c896_21290      (  271) AGCCAGAAAATGCGAAAGCG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 5.2e-025 
   162   -982   -982   -982 
  -154    166     92   -982 
  -982    251   -982   -982 
    78    134   -982   -982 
   162   -982   -982   -982 
  -982   -982    134     78 
    45   -982    166   -982 
   162   -982   -982   -982 
    45   -982    166   -982 
    45    166   -982   -982 
  -982   -982    234   -154 
   104   -982     92   -982 
  -982    251   -982   -982 
  -982   -982    251   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
    78   -982    134   -982 
  -154   -982    234   -982 
  -154    234   -982   -982 
  -982   -982    251   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.2e-025 
 1.000000  0.000000  0.000000  0.000000 
 0.111111  0.555556  0.333333  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.555556  0.444444  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.444444  0.555556 
 0.444444  0.000000  0.555556  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.444444  0.555556  0.000000  0.000000 
 0.000000  0.000000  0.888889  0.111111 
 0.666667  0.000000  0.333333  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.555556  0.000000  0.444444  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.111111  0.888889  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
A[CG]C[AC]A[TG][GA]A[GA][CA]G[AG]CGAA[AG]GCG
--------------------------------------------------------------------------------




Time 17.20 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 183   E-value = 5.4e-018
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  ::96:a26:2a::a:12:a1
pos.-specific     C  94::2::::::86::9:::8
probability       G  :6:32:82a:::4:a:4a::
matrix            T  1:116::2:8:2::::3::1

         bits    2.5         *     *  *  
                 2.3         *     *  *  
                 2.0 *       *     ** *  
                 1.8 *       *     ** *  
Information      1.5 **   ** * ****** ** 
content          1.3 **   ** * ****** ***
(29.3 bits)      1.0 ***  ** * ****** ***
                 0.8 ***  ** ******** ***
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CGAATAGAGTACCAGCGGAC
consensus             C GC AG A TG   T   
sequence                 G  T        A   
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c228_4055           +    203  3.97e-12 GCAACACAAC CGAGTAGAGTACCAGCTGAC GGAATGGAGG
WashU_Skud_Contig2069.5      +    204  8.98e-12 GCAACACAAC CGAGTAGAGTACCAGCAGAC GGAGTGGGTA
MIT_Spar_c130_3912           +    589  1.65e-11 ATTGTTTCTC CCAACAGTGTACGAGCGGAC GAAACTCTAG
MIT_Spar_c117_4603           +    204  7.31e-11 AACACACAAC CGAATAGAGTATCAGCTGAC GGGATGGAGG
SGD_Scer_YDR232W             +    209  7.31e-11 AACACACAAC CGAATAGAGTATCAGCTGAC GGAATGGAGA
WashU_Sbay_Contig461.5       +    199  9.18e-11 GGGTGCAAAC CGATTAGAGTACCAGCAGAC GAGATGGGCG
SGD_Scer_YDR044W             +    595  1.19e-09 ATTGTTTTTC CCAACAGTGAACGAGAGGAC AAACTCCAGA
WashU_Smik_Contig2283.3      +    595  6.61e-09 GTATTGTCTT TCAAGAAGGTACGAGCGGAT GAACTTCTTG
MIT_Sbay_c896_21290          +    597  8.76e-09 ATTGTTTTTT CCTGGAAGGAACGAGCGGAA CTCTTGGGGA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c228_4055                  4e-12  202_[+5]_276
WashU_Skud_Contig2069.5             9e-12  203_[+5]_275
MIT_Spar_c130_3912                1.7e-11  588_[+5]_392
MIT_Spar_c117_4603                7.3e-11  203_[+5]_275
SGD_Scer_YDR232W                  7.3e-11  208_[+5]_270
WashU_Sbay_Contig461.5            9.2e-11  198_[+5]_280
SGD_Scer_YDR044W                  1.2e-09  594_[+5]_386
WashU_Smik_Contig2283.3           6.6e-09  594_[+5]_386
MIT_Sbay_c896_21290               8.8e-09  596_[+5]_384
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
MIT_Smik_c228_4055       (  203) CGAGTAGAGTACCAGCTGAC  1 
WashU_Skud_Contig2069.5  (  204) CGAGTAGAGTACCAGCAGAC  1 
MIT_Spar_c130_3912       (  589) CCAACAGTGTACGAGCGGAC  1 
MIT_Spar_c117_4603       (  204) CGAATAGAGTATCAGCTGAC  1 
SGD_Scer_YDR232W         (  209) CGAATAGAGTATCAGCTGAC  1 
WashU_Sbay_Contig461.5   (  199) CGATTAGAGTACCAGCAGAC  1 
SGD_Scer_YDR044W         (  595) CCAACAGTGAACGAGAGGAC  1 
WashU_Smik_Contig2283.3  (  595) TCAAGAAGGTACGAGCGGAT  1 
MIT_Sbay_c896_21290      (  597) CCTGGAAGGAACGAGCGGAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 5.4e-018 
  -982    234   -982   -154 
  -982    134    166   -982 
   145   -982   -982   -154 
    78   -982     92   -154 
  -982     34     34     78 
   162   -982   -982   -982 
   -55   -982    215   -982 
    78   -982     34    -55 
  -982   -982    251   -982 
   -55   -982   -982    126 
   162   -982   -982   -982 
  -982    215   -982    -55 
  -982    166    134   -982 
   162   -982   -982   -982 
  -982   -982    251   -982 
  -154    234   -982   -982 
   -55   -982    134      4 
  -982   -982    251   -982 
   162   -982   -982   -982 
  -154    215   -982   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.4e-018 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.444444  0.555556  0.000000 
 0.888889  0.000000  0.000000  0.111111 
 0.555556  0.000000  0.333333  0.111111 
 0.000000  0.222222  0.222222  0.555556 
 1.000000  0.000000  0.000000  0.000000 
 0.222222  0.000000  0.777778  0.000000 
 0.555556  0.000000  0.222222  0.222222 
 0.000000  0.000000  1.000000  0.000000 
 0.222222  0.000000  0.000000  0.777778 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.555556  0.444444  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.111111  0.888889  0.000000  0.000000 
 0.222222  0.000000  0.444444  0.333333 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.111111  0.777778  0.000000  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
C[GC]A[AG][TCG]A[GA][AGT]G[TA]A[CT][CG]AGC[GTA]GAC
--------------------------------------------------------------------------------




Time 21.26 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR232W                 2.11e-38  208_[+5(7.31e-11)]_55_[+1(3.60e-13)]_9_[+3(1.49e-11)]_19_[+2(1.67e-14)]_[+4(8.45e-13)]_107
MIT_Spar_c117_4603               6.91e-38  203_[+5(7.31e-11)]_55_[+1(3.60e-13)]_9_[+3(5.14e-11)]_19_[+2(1.67e-14)]_[+4(8.45e-13)]_44_[+2(5.31e-05)]_48
MIT_Smik_c228_4055               1.40e-35  202_[+5(3.97e-12)]_59_[+1(3.60e-13)]_8_[+3(1.49e-11)]_19_[+2(9.01e-11)]_[+4(2.51e-12)]_110
WashU_Skud_Contig2069.5          1.63e-35  203_[+5(8.98e-12)]_58_[+1(2.76e-11)]_9_[+3(1.06e-11)]_18_[+2(2.55e-12)]_[+4(8.45e-13)]_110
WashU_Sbay_Contig461.5           6.88e-33  46_[-1(4.97e-05)]_100_[+4(2.76e-05)]_12_[+5(9.18e-11)]_58_[+1(3.60e-13)]_9_[+3(6.73e-11)]_20_[+2(2.62e-11)]_[+4(5.38e-11)]_17_[+1(5.86e-05)]_76
SGD_Scer_YDR044W                 6.91e-30  174_[+1(1.02e-12)]_11_[-2(3.63e-05)]_46_[+4(1.99e-10)]_21_[+3(1.92e-11)]_7_[+2(2.62e-11)]_235_[+5(1.19e-09)]_386
MIT_Spar_c130_3912               2.36e-29  170_[+1(2.37e-11)]_28_[+3(2.57e-05)]_26_[+4(5.38e-11)]_21_[+3(1.92e-11)]_6_[+2(1.10e-09)]_237_[+5(1.65e-11)]_77_[+1(7.05e-05)]_23_[+3(9.81e-05)]_252
MIT_Sbay_c896_21290              5.38e-26  117_[+1(4.54e-05)]_39_[+1(4.52e-10)]_74_[+4(3.78e-10)]_21_[+3(1.49e-11)]_7_[+2(6.92e-11)]_238_[+5(8.76e-09)]_172_[+3(3.90e-05)]_192
WashU_Smik_Contig2283.3          2.87e-27  166_[+1(1.95e-10)]_74_[+4(3.58e-10)]_28_[+3(2.36e-10)]_8_[+2(6.44e-13)]_27_[+4(3.86e-05)]_191_[+5(6.61e-09)]_111_[+5(3.65e-05)]_255
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM1-HEM14.fa000444000766000024      1155513155576321 20103 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR232W HEM1 "5-aminolevulinate synthase, catalyzes the first step in the heme biosynthetic pathway; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expression is regulated by Hap2p-Hap3p"
ACTGAAAAAAAAACCTAAGTACTGTTATGATTATTGAGGGACAACAACTAGCTCTATTAG
TTTTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTGGG
ATAAAAAAAAAAGAAACGCGAGCTGAGAAGGGAAGGCGTGTAAAGGAAGAACGGTTGAGA
GACAGCAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGAATGGAGAAG
TTTGGTATGATGCAAACGTTGTATTTCTAACAACGCATGGATCAGAACAATGGGCAAGGC
AAGATGAAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCC
CGCGGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGCGGTAGGGTAAGCCGTGC
AGGCAAGCTTATTATAGCACCGTCGGGGGTACCACCACTATATCAAACTCCACTGCTCGG
TAAAGCATTGTAGTGAAG
>MIT_Spar_c117_4603 YDR232W 5' untranslated region, Contig c117 17441 - 19440, 2000 bp (revcom)
ACTGAAAAAAAACCAAGTACTGTTGTGATTATTGAGGGACAACGGCTAGCTCTATTTGTT
TTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTAGGAT
AAAAAAAGAAACGCGAGCTGAGAAGAGAAGGCGTGTAAAGGAAGAACGGTTGAGAGAGAG
CAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGGATGGAGGAGTTTGG
TACGATGCAAACGCTATATTTGTAGCAACGCATGGGTCAGAACAATGGGCAAGGCAAGAT
GAAAAATTTCTGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGCGG
CCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGTGGTAGGGTAAGCCGTGCAGGCA
AGCTTATTATAGCACCGTCGGGGGGACCACTATATCAAGTTCCACAGCACGGTGAAGCAT
TGCAGTATAGTTCACAGC
>MIT_Smik_c228_4055 YDR232W 5' untranslated region, Contig c228 4702 - 6701(revcom), 2000 bp (revcom)
ACCGAGAGAAAAACTAAGTAGTGATATGATTATTGAGGACTAATGACCAGCTTTGTTTGT
TTTTTCTTCCAACCTAACTTATATGGGAAATATATAGGACAGAAAAAAGAAAAGAGCACG
AAAAAAAAGAAATGCGACCTGAGAAGGGAGGACGTGTGAAGCCAGAACGGTTGAATGACA
GTAGAGGAGGGTGCAACACAACCGAGTAGAGTACCAGCTGACGGAATGGAGGAGTTTGGT
ATGATGCAAAAGTGATGCTTTTAGCAACGCAACATTGAATTAGAACAATGGGCAAGGCAA
GATGAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGC
AAGCGCAGACCAATGAGCGACGAAAGCGGCCTTTTGAAGGGTAGGGTAATCCATGCAGGC
AAGTTTATTATAGCACCGTCGGGGGGAAGCATTATATCAAACTCCACAGTACAGCGTAAC
ATTGCTGTATAGGCTACA
>WashU_Skud_Contig2069.5 YDR232W 5' untranslated region, Contig c2069 5476 - 7475, 2000 bp (revcom)
ACTGAAAATAATCCGAGTCGTGCTACTGTGAATATTGAGAATAGGGACTAGCTCTATTTG
ATTTTTCTTCCAACCAAACTTATATGGAAAATATAAAGGAAAGAAAAAAGAAAAGAATAG
GAAAAAAAAAAAGAAACGCGAGAGAAGAGAACCGTGTGGAGGGAAGAACGGTTGAGAGAC
AGCAGAGCACAGCGCAACACAACCGAGTAGAGTACCAGCAGACGGAGTGGGTAGTTTGGT
ACAGTGTAAAAGCTATATTTCCACCAACGCAACACTGGATCGGAACAATGGGCAAGGCAA
TGTGAAAAATTTCCGTTCCTGCTCTTGCTTCATATATGACAATGACCAAAAAGCGTCCGC
GGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCGTAGCAGCAGGGTAAGCCGCGCAAG
CAAGTCCGTCATAACACCGTCGAAGGGGCACCACTATATCAGCTCTTCAGCATGGTAGGC
CATTACAGCACAGTCTTG
>WashU_Sbay_Contig461.5 YDR232W 5' untranslated region, Contig c461 4000 - 5999, 2000 bp (revcom)
ACTAAAAAGTCCAAGTGGTGCTGTTATTATTGAGGATAGCAACTAGCTTTATTTGTTTTT
TCTTCCAACCAAACTTATATGGAAATCAAAGGAAGGAAAAAAAGAAAAGAACAGGAAGAA
AAAAAAGAAACGTGAGCTGCCGAAAGGAGAGCGTGTGGAGGGAAGAACCGTTGAGAGACA
ACAGAGCAGGGTGCAAACCGATTAGAGTACCAGCAGACGAGATGGGCGATGTGGTACGGT
GCAGAAGGTGTGGTTCCAACAGCGCAGCACCGGGACAGAACAATGGGCAAGGCAAGATGA
AAAATCTCCGTTCCTGCTCTTGCTTGATATATTAACAATGACCAAAAAAACGCCGGCGGG
CGCAGACCAATGAGCGACGAAGACGGCTTTTGGGCGGGGCAGGGTAAGATGGGACAGGCA
AGGTCCGCTATAGCACCGTCGAGGGGGACCGCTATATCAGCTCCCAGTACATTGCAGCAC
ACTCTATAGCTAGTCAAA
>SGD_Scer_YER014W HEM14 "Protoporphyrinogen oxidase, a mitochondrial enzyme that catalyzes the seventh step in the heme biosynthetic pathway, converting protoporphyrinogen IX to protoporphyrin IX"
TATACAAGCTCTTTTTGGCGTTCTCAATTGCACTTTACTCGATATGTTTGAATTGGTGTT
CTTCGCGAATATCTCTATTGTTCTCTCTATTATACTATTTCTTTTTTTGAATACTCCGCG
ACTCCGAAGCAACAAAGTGTCGAAGGCAAGTTCAAAGGCGTTTTGTAACTAAACGAGCAA
TGGCAGCTTTCAATTAAAGAAAGGTTAGCGTTACTCTGTGATTTTTTTCATGTAAAAATT
CTCAAGAGAGATAAAGTTGTTAAAAAATTAAATATAGGTCTATAAAACTCGATAATTATA
ATGCATAAAAAGCTAACAATGT
>MIT_Spar_c425_6072 YER014W 5' untranslated region, Contig c425 34016 - 36015, 2000 bp (revcom)
TATTCGAGCCCTTTCCCGCGTTCCCAATTGTACCTTCCTCGATAGGATTGAATTGGTATC
CTTCGCGGATCTCTCTATTGTTCTCTCTATTATTCTTTTTCTTTTTTAAATACTCCGCGA
CTCCGAAGCAACAAAATGTCGAAGGCAAGATGAAAGGCGTTTTGCAACTAAACGAGTAAT
GGCAGCTTTTAATTAAATAACGGTCAGCATTACTCTATAACTTTTCACATAAAATCCTCG
AAGAAGGAAAAATTGATAATCAATTTACCGAAGAATGAATATAGGTCTATAAAAATTCAA
TAATTATAGATGCATAAAAAGC
>MIT_Smik_c283_5928 YER014W 5' untranslated region, Contig c283 42606 - 44605, 2000 bp (revcom)
TATTGAAGCTCTCTCCACTATTTCTTTAATCGCGCTATACTAGATATGGTTAAACTGCTA
TCTTTTGCAAATCCCTCTATTGTTCTTTCCATTACTCTTTTCTTTTTTAAATACGGACTC
CGAAGCAACAAGGTCGAAGGCAAGCTGAAAGGCATTTTACAACTAAACGAGCAATGGTAG
CTTTTGATTGAATAAATTATTATCATTATTTTGTTATTTGTCCCACGAAATTCTCGTTGA
AAGCAAGGTTCGTAAGGATTTATCAAATGTTAAATATAGATCTATAAAAATTGAATAGTA
ATAATAACAAGGGATGGTGTTA
>MIT_Sbay_c84_6418 YER014W 5' untranslated region, Contig c84 10802 - 12801(revcom), 2000 bp (revcom)
TGTCGAAGTTCTCCTTTATTCCGCTGTTTCTTACGGAATCCAGCGAGACTGTTGTCCTTT
CGCATCCTTCTATTGTTCTTCCTTATTGTTCTCGTTTTTTTTATACTCTGCGACTCCGAA
ACAACAAAATCTCGAAGGCAAGCTAAGGTAAAAATATTCACCACTAAACGAGCAATGACA
GTTATATTCAAACGTCATTCTACTTTTTTGCCAGAGAAGTCCTCACTGGAGACGAAGTTG
GTAAATGCTTTATTTATATTAAACGTAGATCTATAAAGTTTAAATAGTTTATAATGCTTA
ACAAGGGACGATGTTATCTCTT
BioPerl-1.007002/t/data/map_hem/HEM1-HEM14.meme.txt000444000766000024     11436413155576321 21300 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM1-HEM14.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDR232W         1.0000    498  MIT_Spar_c117_4603       1.0000    498  
MIT_Smik_c228_4055       1.0000    498  WashU_Skud_Contig2069.5  1.0000    498  
WashU_Sbay_Contig461.5   1.0000    498  SGD_Scer_YER014W         1.0000    322  
MIT_Spar_c425_6072       1.0000    322  MIT_Smik_c283_5928       1.0000    322  
MIT_Sbay_c84_6418        1.0000    322  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM1-HEM14.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            3778    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.293 C 0.207 G 0.207 T 0.293 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 202   E-value = 1.6e-028
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  a3a9:::::aa:::aa:6:1
pos.-specific     C  :7:::1:46::::a:::2:1
probability       G  :::119664::aa:::91:8
matrix            T  ::::9:4:::::::::11a:

         bits    2.5            ***      
                 2.3            ***      
                 2.0      *     ***  *   
                 1.8      *     ***  *   
Information      1.5 * *  * ********** **
content          1.3 ****** ********** **
(32.4 bits)      1.0 ***************** **
                 0.8 ***************** **
                 0.5 ***************** **
                 0.3 ********************
                 0.0 --------------------

Multilevel           ACAATGGGCAAGGCAAGATG
consensus             A    TCG        C  
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig461.5       +    280  3.60e-13 CCGGGACAGA ACAATGGGCAAGGCAAGATG AAAAATCTCC
MIT_Smik_c228_4055           +    285  3.60e-13 TTGAATTAGA ACAATGGGCAAGGCAAGATG AAAATTTCCG
MIT_Spar_c117_4603           +    282  3.60e-13 ATGGGTCAGA ACAATGGGCAAGGCAAGATG AAAAATTTCT
SGD_Scer_YDR232W             +    287  3.60e-13 ATGGATCAGA ACAATGGGCAAGGCAAGATG AAAAATTTCC
MIT_Spar_c425_6072           +    133  2.98e-11 CCGAAGCAAC AAAATGTCGAAGGCAAGATG AAAGGCGTTT
MIT_Smik_c283_5928           +    128  4.86e-11 CTCCGAAGCA ACAAGGTCGAAGGCAAGCTG AAAGGCATTT
WashU_Skud_Contig2069.5      +    285  9.69e-11 CTGGATCGGA ACAATGGGCAAGGCAATGTG AAAAATTTCC
MIT_Sbay_c84_6418            +    126  8.09e-10 CCGAAACAAC AAAATCTCGAAGGCAAGCTA AGGTAAAAAT
SGD_Scer_YER014W             +    134  8.09e-10 CCGAAGCAAC AAAGTGTCGAAGGCAAGTTC AAAGGCGTTT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig461.5            3.6e-13  279_[+1]_199
MIT_Smik_c228_4055                3.6e-13  284_[+1]_194
MIT_Spar_c117_4603                3.6e-13  281_[+1]_197
SGD_Scer_YDR232W                  3.6e-13  286_[+1]_192
MIT_Spar_c425_6072                  3e-11  132_[+1]_170
MIT_Smik_c283_5928                4.9e-11  127_[+1]_175
WashU_Skud_Contig2069.5           9.7e-11  284_[+1]_194
MIT_Sbay_c84_6418                 8.1e-10  125_[+1]_177
SGD_Scer_YER014W                  8.1e-10  133_[+1]_169
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Sbay_Contig461.5   (  280) ACAATGGGCAAGGCAAGATG  1 
MIT_Smik_c228_4055       (  285) ACAATGGGCAAGGCAAGATG  1 
MIT_Spar_c117_4603       (  282) ACAATGGGCAAGGCAAGATG  1 
SGD_Scer_YDR232W         (  287) ACAATGGGCAAGGCAAGATG  1 
MIT_Spar_c425_6072       (  133) AAAATGTCGAAGGCAAGATG  1 
MIT_Smik_c283_5928       (  128) ACAAGGTCGAAGGCAAGCTG  1 
WashU_Skud_Contig2069.5  (  285) ACAATGGGCAAGGCAATGTG  1 
MIT_Sbay_c84_6418        (  126) AAAATCTCGAAGGCAAGCTA  1 
SGD_Scer_YER014W         (  134) AAAGTGTCGAAGGCAAGTTC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 3607 bayes= 8.64305 E= 1.6e-028 
   162   -982   -982   -982 
     4    192   -982   -982 
   162   -982   -982   -982 
   145   -982    -66   -982 
  -982   -982    -66    145 
  -982    -66    234   -982 
  -982   -982    166     45 
  -982    134    166   -982 
  -982    166    134   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -982   -982    251   -982 
  -982   -982    251   -982 
  -982    251   -982   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -982   -982    234   -154 
    78     34    -66   -154 
  -982   -982   -982    162 
  -154    -66    215   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.6e-028 
 1.000000  0.000000  0.000000  0.000000 
 0.333333  0.666667  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.111111  0.888889  0.000000 
 0.000000  0.000000  0.555556  0.444444 
 0.000000  0.444444  0.555556  0.000000 
 0.000000  0.555556  0.444444  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.888889  0.111111 
 0.555556  0.222222  0.111111  0.111111 
 0.000000  0.000000  0.000000  1.000000 
 0.111111  0.111111  0.777778  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
A[CA]AATG[GT][GC][CG]AAGGCAAG[AC]TG
--------------------------------------------------------------------------------




Time  1.73 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   18   sites =   9   llr = 163   E-value = 9.8e-015
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  37a:aa:44:4:a27:a:
pos.-specific     C  11::::a1:::::::::4
probability       G  62:a:::46::a:829:1
matrix            T  :::::::::a6:::11:4

         bits    2.5    *  *    *      
                 2.3    *  *    *      
                 2.0    *  *    *   *  
                 1.8    *  *    *   *  
Information      1.5   *****  * *** ** 
content          1.3   *****  * *** ** 
(26.1 bits)      1.0   ***** ** *** ** 
                 0.8 ************** ***
                 0.5 ******************
                 0.3 ******************
                 0.0 ------------------

Multilevel           GAAGAACAGTTGAGAGAC
consensus            AG     GA A  AG  T
sequence                               
                                       
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                   Site     
-------------            ------  ----- ---------            ------------------
WashU_Skud_Contig2069.5      +    163  6.31e-12 CGTGTGGAGG GAAGAACGGTTGAGAGAC AGCAGAGCAC
SGD_Scer_YDR232W             +    166  6.31e-12 GCGTGTAAAG GAAGAACGGTTGAGAGAC AGCAGAGCAG
WashU_Sbay_Contig461.5       +    162  2.27e-10 CGTGTGGAGG GAAGAACCGTTGAGAGAC AACAGAGCAG
MIT_Spar_c117_4603           +    161  2.27e-10 GCGTGTAAAG GAAGAACGGTTGAGAGAG AGCAGAGCAG
MIT_Smik_c283_5928           -     71  6.85e-09 AGAGTAATGG AAAGAACAATAGAGGGAT TTGCAAAAGA
MIT_Spar_c425_6072           -     69  6.85e-09 AGAATAATAG AGAGAACAATAGAGAGAT CCGCGAAGGA
MIT_Sbay_c84_6418            -     64  1.24e-08 GAACAATAAG GAAGAACAATAGAAGGAT GCGAAAGGAC
MIT_Smik_c228_4055           +    162  3.13e-08 ACGTGTGAAG CCAGAACGGTTGAATGAC AGTAGAGGAG
SGD_Scer_YER014W             -     69  3.60e-08 AGTATAATAG AGAGAACAATAGAGATAT TCGCGAAGAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2069.5           6.3e-12  162_[+2]_318
SGD_Scer_YDR232W                  6.3e-12  165_[+2]_315
WashU_Sbay_Contig461.5            2.3e-10  161_[+2]_319
MIT_Spar_c117_4603                2.3e-10  160_[+2]_320
MIT_Smik_c283_5928                6.8e-09  70_[-2]_234
MIT_Spar_c425_6072                6.8e-09  68_[-2]_236
MIT_Sbay_c84_6418                 1.2e-08  63_[-2]_241
MIT_Smik_c228_4055                3.1e-08  161_[+2]_319
SGD_Scer_YER014W                  3.6e-08  68_[-2]_236
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=18 seqs=9
WashU_Skud_Contig2069.5  (  163) GAAGAACGGTTGAGAGAC  1 
SGD_Scer_YDR232W         (  166) GAAGAACGGTTGAGAGAC  1 
WashU_Sbay_Contig461.5   (  162) GAAGAACCGTTGAGAGAC  1 
MIT_Spar_c117_4603       (  161) GAAGAACGGTTGAGAGAG  1 
MIT_Smik_c283_5928       (   71) AAAGAACAATAGAGGGAT  1 
MIT_Spar_c425_6072       (   69) AGAGAACAATAGAGAGAT  1 
MIT_Sbay_c84_6418        (   64) GAAGAACAATAGAAGGAT  1 
MIT_Smik_c228_4055       (  162) CCAGAACGGTTGAATGAC  1 
SGD_Scer_YER014W         (   69) AGAGAACAATAGAGATAT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 18 n= 3625 bayes= 8.65025 E= 9.8e-015 
     4    -66    166   -982 
   104    -66     34   -982 
   162   -982   -982   -982 
  -982   -982    251   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -982    251   -982   -982 
    45    -66    134   -982 
    45   -982    166   -982 
  -982   -982   -982    162 
    45   -982   -982     78 
  -982   -982    251   -982 
   162   -982   -982   -982 
   -55   -982    215   -982 
   104   -982     34   -154 
  -982   -982    234   -154 
   162   -982   -982   -982 
  -982    134    -66     45 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 18 nsites= 9 E= 9.8e-015 
 0.333333  0.111111  0.555556  0.000000 
 0.666667  0.111111  0.222222  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.444444  0.111111  0.444444  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.444444  0.000000  0.000000  0.555556 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.222222  0.000000  0.777778  0.000000 
 0.666667  0.000000  0.222222  0.111111 
 0.000000  0.000000  0.888889  0.111111 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.444444  0.111111  0.444444 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[GA][AG]AGAAC[AG][GA]T[TA]GA[GA][AG]GA[CT]
--------------------------------------------------------------------------------




Time  3.42 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =   9   llr = 185   E-value = 4.5e-020
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :3a6:4a4::a::aa111:4
pos.-specific     C  97:4::::a::63::::63:
probability       G  :::::6:6:a:46::49366
matrix            T  1:::a:::::::1::4::1:

         bits    2.5         **          
                 2.3         **          
                 2.0 *       **      *   
                 1.8 *       **      *   
Information      1.5 * * * * **** ** *   
content          1.3 *** * * **** ** *   
(29.6 bits)      1.0 *************** ****
                 0.8 *************** ****
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CCAATGAGCGACGAAGGCGG
consensus             A C A A   GC  T GCA
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2069.5      +    370  1.19e-13 CGGCCGCAGA CCAATGAGCGACGAAGGCGG CCTTTCGTAG
MIT_Spar_c117_4603           +    368  1.19e-13 CGGCCGCAGA CCAATGAGCGACGAAGGCGG CCTTTCCGAG
SGD_Scer_YDR232W             +    373  1.19e-13 CGGCCGCAGA CCAATGAGCGACGAAGGCGG CCTTTCCGAG
MIT_Smik_c228_4055           +    370  2.41e-11 CAAGCGCAGA CCAATGAGCGACGAAAGCGG CCTTTTGAAG
WashU_Sbay_Contig461.5       +    367  6.46e-11 CGGGCGCAGA CCAATGAGCGACGAAGACGG CTTTTGGGCG
MIT_Sbay_c84_6418            +    161  1.68e-09 AAAATATTCA CCACTAAACGAGCAATGACA GTTATATTCA
MIT_Smik_c283_5928           +    160  3.61e-09 AGGCATTTTA CAACTAAACGAGCAATGGTA GCTTTTGATT
MIT_Spar_c425_6072           +    165  3.61e-09 AGGCGTTTTG CAACTAAACGAGTAATGGCA GCTTTTAATT
SGD_Scer_YER014W             +    166  5.94e-09 AGGCGTTTTG TAACTAAACGAGCAATGGCA GCTTTCAATT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2069.5           1.2e-13  369_[+3]_109
MIT_Spar_c117_4603                1.2e-13  367_[+3]_111
SGD_Scer_YDR232W                  1.2e-13  372_[+3]_106
MIT_Smik_c228_4055                2.4e-11  369_[+3]_109
WashU_Sbay_Contig461.5            6.5e-11  366_[+3]_112
MIT_Sbay_c84_6418                 1.7e-09  160_[+3]_142
MIT_Smik_c283_5928                3.6e-09  159_[+3]_143
MIT_Spar_c425_6072                3.6e-09  164_[+3]_138
SGD_Scer_YER014W                  5.9e-09  165_[+3]_137
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=9
WashU_Skud_Contig2069.5  (  370) CCAATGAGCGACGAAGGCGG  1 
MIT_Spar_c117_4603       (  368) CCAATGAGCGACGAAGGCGG  1 
SGD_Scer_YDR232W         (  373) CCAATGAGCGACGAAGGCGG  1 
MIT_Smik_c228_4055       (  370) CCAATGAGCGACGAAAGCGG  1 
WashU_Sbay_Contig461.5   (  367) CCAATGAGCGACGAAGACGG  1 
MIT_Sbay_c84_6418        (  161) CCACTAAACGAGCAATGACA  1 
MIT_Smik_c283_5928       (  160) CAACTAAACGAGCAATGGTA  1 
MIT_Spar_c425_6072       (  165) CAACTAAACGAGTAATGGCA  1 
SGD_Scer_YER014W         (  166) TAACTAAACGAGCAATGGCA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 3607 bayes= 8.64305 E= 4.5e-020 
  -982    234   -982   -154 
     4    192   -982   -982 
   162   -982   -982   -982 
    78    134   -982   -982 
  -982   -982   -982    162 
    45   -982    166   -982 
   162   -982   -982   -982 
    45   -982    166   -982 
  -982    251   -982   -982 
  -982   -982    251   -982 
   162   -982   -982   -982 
  -982    166    134   -982 
  -982     92    166   -154 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -154   -982    134     45 
  -154   -982    234   -982 
  -154    166     92   -982 
  -982     92    166   -154 
    45   -982    166   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 4.5e-020 
 0.000000  0.888889  0.000000  0.111111 
 0.333333  0.666667  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.555556  0.444444  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.444444  0.000000  0.555556  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.555556  0.444444  0.000000 
 0.000000  0.333333  0.555556  0.111111 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.111111  0.000000  0.444444  0.444444 
 0.111111  0.000000  0.888889  0.000000 
 0.111111  0.555556  0.333333  0.000000 
 0.000000  0.333333  0.555556  0.111111 
 0.444444  0.000000  0.555556  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
C[CA]A[AC]T[GA]A[GA]CGA[CG][GC]AA[GT]G[CG][GC][GA]
--------------------------------------------------------------------------------




Time  4.97 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =   9   llr = 174   E-value = 3.1e-016
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  896a21:1:::411:::4a1
pos.-specific     C  ::::363778:64:8a:6::
probability       G  ::::4:6:32a:442:a::9
matrix            T  214::312:::::4::::::

         bits    2.5           *    **   
                 2.3           *    **   
                 2.0           *    **  *
                 1.8          **   ***  *
Information      1.5    *    ***   *** **
content          1.3    *    ***   *** **
(27.9 bits)      1.0  * *  ******* ******
                 0.8 ************* ******
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           AAAAGCGCCCGCCGCCGCAG
consensus            T T CTCTGG AGTG  A  
sequence                 A               
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c117_4603           +    347  3.34e-14 ACAATGACCA AAAAGCGCCCGCGGCCGCAG ACCAATGAGC
SGD_Scer_YDR232W             +    352  3.34e-14 ACAATGACCA AAAAGCGCCCGCGGCCGCAG ACCAATGAGC
WashU_Skud_Contig2069.5      +    349  3.24e-12 ACAATGACCA AAAAGCGTCCGCGGCCGCAG ACCAATGAGC
WashU_Sbay_Contig461.5       +    346  1.26e-10 CAATGACCAA AAAAACGCCGGCGGGCGCAG ACCAATGAGC
MIT_Spar_c425_6072           +    109  6.37e-10 TTCTTTTTTA AATACTCCGCGACTCCGAAG CAACAAAATG
SGD_Scer_YER014W             +    110  6.37e-10 TCTTTTTTTG AATACTCCGCGACTCCGAAG CAACAAAGTG
MIT_Smik_c228_4055           +    349  6.96e-10 ACAATGACCA AAAAGCGCCCGCAAGCGCAG ACCAATGAGC
MIT_Sbay_c84_6418            +    102  3.58e-08 TCGTTTTTTT TATACTCTGCGACTCCGAAA CAACAAAATC
MIT_Smik_c283_5928           +    106  2.54e-07 TCTTTTCTTT TTTAAATACGGACTCCGAAG CAACAAGGTC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c117_4603                3.3e-14  346_[+4]_132
SGD_Scer_YDR232W                  3.3e-14  351_[+4]_127
WashU_Skud_Contig2069.5           3.2e-12  348_[+4]_130
WashU_Sbay_Contig461.5            1.3e-10  345_[+4]_133
MIT_Spar_c425_6072                6.4e-10  108_[+4]_194
SGD_Scer_YER014W                  6.4e-10  109_[+4]_193
MIT_Smik_c228_4055                  7e-10  348_[+4]_130
MIT_Sbay_c84_6418                 3.6e-08  101_[+4]_201
MIT_Smik_c283_5928                2.5e-07  105_[+4]_197
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=9
MIT_Spar_c117_4603       (  347) AAAAGCGCCCGCGGCCGCAG  1 
SGD_Scer_YDR232W         (  352) AAAAGCGCCCGCGGCCGCAG  1 
WashU_Skud_Contig2069.5  (  349) AAAAGCGTCCGCGGCCGCAG  1 
WashU_Sbay_Contig461.5   (  346) AAAAACGCCGGCGGGCGCAG  1 
MIT_Spar_c425_6072       (  109) AATACTCCGCGACTCCGAAG  1 
SGD_Scer_YER014W         (  110) AATACTCCGCGACTCCGAAG  1 
MIT_Smik_c228_4055       (  349) AAAAGCGCCCGCAAGCGCAG  1 
MIT_Sbay_c84_6418        (  102) TATACTCTGCGACTCCGAAA  1 
MIT_Smik_c283_5928       (  106) TTTAAATACGGACTCCGAAG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 3607 bayes= 8.64305 E= 3.1e-016 
   126   -982   -982    -55 
   145   -982   -982   -154 
    78   -982   -982     45 
   162   -982   -982   -982 
   -55     92    134   -982 
  -154    166   -982      4 
  -982     92    166   -154 
  -154    192   -982    -55 
  -982    192     92   -982 
  -982    215     34   -982 
  -982   -982    251   -982 
    45    166   -982   -982 
  -154    134    134   -982 
  -154   -982    134     45 
  -982    215     34   -982 
  -982    251   -982   -982 
  -982   -982    251   -982 
    45    166   -982   -982 
   162   -982   -982   -982 
  -154   -982    234   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.1e-016 
 0.777778  0.000000  0.000000  0.222222 
 0.888889  0.000000  0.000000  0.111111 
 0.555556  0.000000  0.000000  0.444444 
 1.000000  0.000000  0.000000  0.000000 
 0.222222  0.333333  0.444444  0.000000 
 0.111111  0.555556  0.000000  0.333333 
 0.000000  0.333333  0.555556  0.111111 
 0.111111  0.666667  0.000000  0.222222 
 0.000000  0.666667  0.333333  0.000000 
 0.000000  0.777778  0.222222  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.444444  0.555556  0.000000  0.000000 
 0.111111  0.444444  0.444444  0.000000 
 0.111111  0.000000  0.444444  0.444444 
 0.000000  0.777778  0.222222  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.444444  0.555556  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
[AT]A[AT]A[GCA][CT][GC][CT][CG][CG]G[CA][CG][GT][CG]CG[CA]AG
--------------------------------------------------------------------------------




Time  6.50 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   17   sites =   9   llr = 139   E-value = 2.2e-007
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  79:::a3:a39::8:3a
pos.-specific     C  ::79::::::::1:76:
probability       G  :1:19:61:61a1211:
matrix            T  3:3:1:19:1::8:2::

         bits    2.5            *     
                 2.3            *     
                 2.0    **      *     
                 1.8    **      *     
Information      1.5    ***  *  *    *
content          1.3  ***** ** **    *
(22.3 bits)      1.0  ***** ** ** ** *
                 0.8 *****************
                 0.5 *****************
                 0.3 *****************
                 0.0 -----------------

Multilevel           AACCGAGTAGAGTACCA
consensus            T T   A  A   GTA 
sequence                              
                                      
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                  Site     
-------------            ------  ----- ---------            -----------------
WashU_Skud_Contig2069.5      +    201  3.60e-11 AGCGCAACAC AACCGAGTAGAGTACCA GCAGACGGAG
MIT_Smik_c228_4055           +    200  3.60e-11 GGTGCAACAC AACCGAGTAGAGTACCA GCTGACGGAA
WashU_Sbay_Contig461.5       +    196  1.71e-09 GCAGGGTGCA AACCGATTAGAGTACCA GCAGACGAGA
MIT_Spar_c117_4603           +    201  3.89e-09 TGCAACACAC AACCGAATAGAGTATCA GCTGACGGGA
SGD_Scer_YDR232W             +    206  3.89e-09 TGCAACACAC AACCGAATAGAGTATCA GCTGACGGAA
SGD_Scer_YER014W             -     28  4.70e-08 AATTCAAACA TATCGAGTAAAGTGCAA TTGAGAACGC
MIT_Spar_c425_6072           -     28  3.05e-07 AATTCAATCC TATCGAGGAAGGTACAA TTGGGAACGC
MIT_Sbay_c84_6418            -      9  1.50e-06 CGTAAGAAAC AGCGGAATAAAGGAGAA CTTCGACA  
MIT_Smik_c283_5928           -     30  1.85e-06 AGTTTAACCA TATCTAGTATAGCGCGA TTAAAGAAAT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2069.5           3.6e-11  200_[+5]_281
MIT_Smik_c228_4055                3.6e-11  199_[+5]_282
WashU_Sbay_Contig461.5            1.7e-09  195_[+5]_286
MIT_Spar_c117_4603                3.9e-09  200_[+5]_281
SGD_Scer_YDR232W                  3.9e-09  205_[+5]_276
SGD_Scer_YER014W                  4.7e-08  27_[-5]_278
MIT_Spar_c425_6072                  3e-07  27_[-5]_278
MIT_Sbay_c84_6418                 1.5e-06  8_[-5]_297
MIT_Smik_c283_5928                1.8e-06  29_[-5]_276
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=17 seqs=9
WashU_Skud_Contig2069.5  (  201) AACCGAGTAGAGTACCA  1 
MIT_Smik_c228_4055       (  200) AACCGAGTAGAGTACCA  1 
WashU_Sbay_Contig461.5   (  196) AACCGATTAGAGTACCA  1 
MIT_Spar_c117_4603       (  201) AACCGAATAGAGTATCA  1 
SGD_Scer_YDR232W         (  206) AACCGAATAGAGTATCA  1 
SGD_Scer_YER014W         (   28) TATCGAGTAAAGTGCAA  1 
MIT_Spar_c425_6072       (   28) TATCGAGGAAGGTACAA  1 
MIT_Sbay_c84_6418        (    9) AGCGGAATAAAGGAGAA  1 
MIT_Smik_c283_5928       (   30) TATCTAGTATAGCGCGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 17 n= 3634 bayes= 8.65384 E= 2.2e-007 
   104   -982   -982      4 
   145   -982    -66   -982 
  -982    192   -982      4 
  -982    234    -66   -982 
  -982   -982    234   -154 
   162   -982   -982   -982 
     4   -982    166   -154 
  -982   -982    -66    145 
   162   -982   -982   -982 
     4   -982    166   -154 
   145   -982    -66   -982 
  -982   -982    251   -982 
  -982    -66    -66    126 
   126   -982     34   -982 
  -982    192    -66    -55 
     4    166    -66   -982 
   162   -982   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 17 nsites= 9 E= 2.2e-007 
 0.666667  0.000000  0.000000  0.333333 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.666667  0.000000  0.333333 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.000000  0.888889  0.111111 
 1.000000  0.000000  0.000000  0.000000 
 0.333333  0.000000  0.555556  0.111111 
 0.000000  0.000000  0.111111  0.888889 
 1.000000  0.000000  0.000000  0.000000 
 0.333333  0.000000  0.555556  0.111111 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.111111  0.111111  0.777778 
 0.777778  0.000000  0.222222  0.000000 
 0.000000  0.666667  0.111111  0.222222 
 0.333333  0.555556  0.111111  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
[AT]A[CT]CGA[GA]TA[GA]AGT[AG][CT][CA]A
--------------------------------------------------------------------------------




Time  7.92 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR232W                 1.25e-37  165_[+2(6.31e-12)]_[+5(9.28e-05)]_5_[+5(3.89e-09)]_64_[+1(3.60e-13)]_45_[+4(3.34e-14)]_1_[+3(1.19e-13)]_106
MIT_Spar_c117_4603               3.90e-36  160_[+2(2.27e-10)]_[+5(9.28e-05)]_5_[+5(3.89e-09)]_64_[+1(3.60e-13)]_45_[+4(3.34e-14)]_1_[+3(1.19e-13)]_111
MIT_Smik_c228_4055               1.05e-29  161_[+2(3.13e-08)]_[+5(1.70e-05)]_3_[+5(3.60e-11)]_68_[+1(3.60e-13)]_44_[+4(6.96e-10)]_1_[+3(2.41e-11)]_109
WashU_Skud_Contig2069.5          2.42e-35  162_[+2(6.31e-12)]_20_[+5(3.60e-11)]_67_[+1(9.69e-11)]_44_[+4(3.24e-12)]_1_[+3(1.19e-13)]_109
WashU_Sbay_Contig461.5           1.93e-30  125_[+4(6.68e-05)]_16_[+2(2.27e-10)]_16_[+5(1.71e-09)]_67_[+1(3.60e-13)]_46_[+4(1.26e-10)]_1_[+3(6.46e-11)]_19_[+1(2.50e-06)]_73
SGD_Scer_YER014W                 3.02e-22  27_[-5(4.70e-08)]_24_[-2(3.60e-08)]_23_[+4(6.37e-10)]_4_[+1(8.09e-10)]_12_[+3(5.94e-09)]_137
MIT_Spar_c425_6072               1.04e-23  27_[-5(3.05e-07)]_24_[-2(6.85e-09)]_22_[+4(6.37e-10)]_4_[+1(2.98e-11)]_12_[+3(3.61e-09)]_138
MIT_Smik_c283_5928               2.42e-20  29_[-5(1.85e-06)]_24_[-2(6.85e-09)]_17_[+4(2.54e-07)]_2_[+1(4.86e-11)]_12_[+3(3.61e-09)]_143
MIT_Sbay_c84_6418                3.76e-20  8_[-5(1.50e-06)]_38_[-2(1.24e-08)]_20_[+4(3.58e-08)]_4_[+1(8.09e-10)]_15_[+3(1.68e-09)]_13_[-2(2.04e-05)]_111
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM1-HEM15.fa000444000766000024      1655513155576321 20111 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR232W HEM1 "5-aminolevulinate synthase, catalyzes the first step in the heme biosynthetic pathway; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expression is regulated by Hap2p-Hap3p"
ACTGAAAAAAAAACCTAAGTACTGTTATGATTATTGAGGGACAACAACTAGCTCTATTAG
TTTTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTGGG
ATAAAAAAAAAAGAAACGCGAGCTGAGAAGGGAAGGCGTGTAAAGGAAGAACGGTTGAGA
GACAGCAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGAATGGAGAAG
TTTGGTATGATGCAAACGTTGTATTTCTAACAACGCATGGATCAGAACAATGGGCAAGGC
AAGATGAAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCC
CGCGGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGCGGTAGGGTAAGCCGTGC
AGGCAAGCTTATTATAGCACCGTCGGGGGTACCACCACTATATCAAACTCCACTGCTCGG
TAAAGCATTGTAGTGAAG
>MIT_Spar_c117_4603 YDR232W 5' untranslated region, Contig c117 17441 - 19440, 2000 bp (revcom)
ACTGAAAAAAAACCAAGTACTGTTGTGATTATTGAGGGACAACGGCTAGCTCTATTTGTT
TTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTAGGAT
AAAAAAAGAAACGCGAGCTGAGAAGAGAAGGCGTGTAAAGGAAGAACGGTTGAGAGAGAG
CAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGGATGGAGGAGTTTGG
TACGATGCAAACGCTATATTTGTAGCAACGCATGGGTCAGAACAATGGGCAAGGCAAGAT
GAAAAATTTCTGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGCGG
CCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGTGGTAGGGTAAGCCGTGCAGGCA
AGCTTATTATAGCACCGTCGGGGGGACCACTATATCAAGTTCCACAGCACGGTGAAGCAT
TGCAGTATAGTTCACAGC
>MIT_Smik_c228_4055 YDR232W 5' untranslated region, Contig c228 4702 - 6701(revcom), 2000 bp (revcom)
ACCGAGAGAAAAACTAAGTAGTGATATGATTATTGAGGACTAATGACCAGCTTTGTTTGT
TTTTTCTTCCAACCTAACTTATATGGGAAATATATAGGACAGAAAAAAGAAAAGAGCACG
AAAAAAAAGAAATGCGACCTGAGAAGGGAGGACGTGTGAAGCCAGAACGGTTGAATGACA
GTAGAGGAGGGTGCAACACAACCGAGTAGAGTACCAGCTGACGGAATGGAGGAGTTTGGT
ATGATGCAAAAGTGATGCTTTTAGCAACGCAACATTGAATTAGAACAATGGGCAAGGCAA
GATGAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGC
AAGCGCAGACCAATGAGCGACGAAAGCGGCCTTTTGAAGGGTAGGGTAATCCATGCAGGC
AAGTTTATTATAGCACCGTCGGGGGGAAGCATTATATCAAACTCCACAGTACAGCGTAAC
ATTGCTGTATAGGCTACA
>WashU_Skud_Contig2069.5 YDR232W 5' untranslated region, Contig c2069 5476 - 7475, 2000 bp (revcom)
ACTGAAAATAATCCGAGTCGTGCTACTGTGAATATTGAGAATAGGGACTAGCTCTATTTG
ATTTTTCTTCCAACCAAACTTATATGGAAAATATAAAGGAAAGAAAAAAGAAAAGAATAG
GAAAAAAAAAAAGAAACGCGAGAGAAGAGAACCGTGTGGAGGGAAGAACGGTTGAGAGAC
AGCAGAGCACAGCGCAACACAACCGAGTAGAGTACCAGCAGACGGAGTGGGTAGTTTGGT
ACAGTGTAAAAGCTATATTTCCACCAACGCAACACTGGATCGGAACAATGGGCAAGGCAA
TGTGAAAAATTTCCGTTCCTGCTCTTGCTTCATATATGACAATGACCAAAAAGCGTCCGC
GGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCGTAGCAGCAGGGTAAGCCGCGCAAG
CAAGTCCGTCATAACACCGTCGAAGGGGCACCACTATATCAGCTCTTCAGCATGGTAGGC
CATTACAGCACAGTCTTG
>WashU_Sbay_Contig461.5 YDR232W 5' untranslated region, Contig c461 4000 - 5999, 2000 bp (revcom)
ACTAAAAAGTCCAAGTGGTGCTGTTATTATTGAGGATAGCAACTAGCTTTATTTGTTTTT
TCTTCCAACCAAACTTATATGGAAATCAAAGGAAGGAAAAAAAGAAAAGAACAGGAAGAA
AAAAAAGAAACGTGAGCTGCCGAAAGGAGAGCGTGTGGAGGGAAGAACCGTTGAGAGACA
ACAGAGCAGGGTGCAAACCGATTAGAGTACCAGCAGACGAGATGGGCGATGTGGTACGGT
GCAGAAGGTGTGGTTCCAACAGCGCAGCACCGGGACAGAACAATGGGCAAGGCAAGATGA
AAAATCTCCGTTCCTGCTCTTGCTTGATATATTAACAATGACCAAAAAAACGCCGGCGGG
CGCAGACCAATGAGCGACGAAGACGGCTTTTGGGCGGGGCAGGGTAAGATGGGACAGGCA
AGGTCCGCTATAGCACCGTCGAGGGGGACCGCTATATCAGCTCCCAGTACATTGCAGCAC
ACTCTATAGCTAGTCAAA
>SGD_Scer_YOR176W HEM15 "Ferrochelatase, a mitochondrial inner membrane protein, catalyzes the insertion of ferrous iron into protoporphyrin IX, the eighth and final step in the heme biosynthetic pathway; Yfh1p mediates the use of iron by Hem15p"
TCTTTAAACGTTCTTTTTTTTACTGCTAAATTTGTCCAAATAGCAGGTATGTGTTAAATA
TTTCTGTACTTCTTGTAAACCGACTCAAGTGGAACACGAGAATTTACGCTTGTTTGGTGT
CAAGCCAAGAGTGACCTTGACCGACCAAAAGTATTCCTTCGCGTCCTCCTTCTTCAATCC
CATATCCCCTACGAAAAAAAGCAGCATGAGAAAACGAAGGGCAGCAACTCCTTCGTCATA
TAAGGCTTACGGTGACCATTGAAGATTGGGCATGTCTAACGGCTATTGCCAGCGGAGATG
TTTCAAGGCATCCTACACATGCTACATATTTGTAATTATTTTACTGAGTTTGTGTATATA
AAAAACTTTTTTAAAAAAAAAAAATGGCCAGCATCCTCTTTCATGTAAAGCTGTTGAACC
TTCCTGAAATTTACTTCTAAAATTGTTCAGTAAAACTGCTTGTTAAAAGTGCGAAGAGTT
CTTTTTTAGCTTTTTTTGTCCTGCTGTTGAGCTGTTTTGCTTTACTGTTCAACAAAACAT
TGAAGATCTTTCACATTGCGCGTCGAAACCACAAACCGTCGAAAACAATGGTCATCTAAA
TAAAGGGTTCTTATTAAACAGATTTAAAGCCAAGGACAAAATACAGGCACAGGTCAAGCA
AGAAGACAAACCGCATACGCCAAGACAAACCGTGGTGATTTAATTCTGCTGCTGATCGCT
TCCAACA
>MIT_Spar_c278_20970 YOR176W 5' untranslated region, Contig c278 32746 - 34745, 2000 bp (revcom)
TCTTCAAACGTTCTTTTCCTACTACTAAGCTTTTCAATAAATAGCGGGTATATGCTAAAT
ACTTCTTTGCTTCTTGTACGACCTACTTAATTGAAATACGGATATTTTTGCTTGCTTGGT
GCCAAACCAAGAGTGACCTTGACCGACTAAAAGTATTCCTTCGCGTCCTCCTTCTTCAAT
CCCATATCCCCTACTGAAAAAAGCAGCGTGCGAAAATGAAGGGCAGCAACTCCTTCGTCA
TATAAGGCTTAGGTAATCTTTCAAGGTCAGGTATATCCAGCTGTCGTTACGAGTAGAGAT
ATTTCAAGCTGTCCTGCACATGCTACATATTTGTGATTATTTTTATTGAGTTGCGTATAT
AAAAAAACAATCTAAAAAAAAAAAAAATGGCCAGCATCTTCTTCCATGTAAAGCTGTTGA
ACCTTGCTAAAATCTATTACTATAATTGTTCAGTAAAGTTGCTTGTTAAAAATGCGAAGA
GTCTTTTTTAGCTTTTTTTGCCCTGCTGTTGAGCTGTTTTGCTTCACTGTTCAACAAAAC
AGTGAAGATCTTTCGAATTGCGCGTCGAAACCACAAACCGTCGAAAATAATGGTCATCTA
AATAAAGGGTTCTTATTTGAACAGATTTAAAGCTCAAAGACACGATACAGGCACAGGTCC
AGAAAGAATACAAAACGCAAACGCCAAGACAAATTGTGGTAATTTCATTCTGCTGCTGAT
CACTGCC
>MIT_Smik_c935_20455 YOR176W 5' untranslated region, Contig c935 1803 - 3802(revcom), 2000 bp (revcom)
TCTTGAATTGCAATTTTCTACTACTGAAGTTACCAACAATTAGCAAATATGTGATGAGTC
CTTTTTACGTTCTTGTATAACCTAAGTTAAATACAAAGGTTTATGCTCCTTTAATGATCA
GACCAACAGTGATCTTGGCCGACCAAAAGACTCCTTCGCGTCCTCCTTCTTCAAGTCTCA
TATCCCCTACCAGAAAAAGTAGCAGGCGAAAATAAAGAGCAACTGCTCCCCCCCATATAG
AGCTTACCATAATTTCTCAAGGAAAGGTATCTCCAGTTGTCGTAAAGAATAAAGAAGTTT
CAACGTGTCCTGCATGTTCTACAAATTTGCAATTGACTTTACTAAGTTGCATATATAAAA
CTTGTATTAGATAAGTTAGCCAGCATTTTCATTCAAGCTAAGATGTTGAATATGCCAAAG
CACATTGCTGAAATTAATCAGTAAAGCTGCTTGCTGAAAGTGGAAATATTTTCAGCTTTT
TTTGCTCTGCTGTTGAGCTGTTTTACTTCATTGTTCAACAAAACAATAGAGTTCTCTCCA
ATTGCGCGTCAAAACCACAAACCGTCGAAAATAATGATCATCTAAATAAAAGAGTTCACG
TTTTCACATATTTAAAGTTGAAATACTCCATACAGGCACAGGTCTAACAAGAAGACAACG
CATTCGATAAAACTAATCGTGGTAATTTTTATATCGCTGCTAGCCACTACCAACAATGTA
CAATTTT
>WashU_Skud_Contig2050.4 YOR176W 5' untranslated region, Contig c2050 12271 - 14270(revcom), 2000 bp (revcom)
TCTTAGTTTATAGCTTTTCTACTACTCTGGTCATAAACGAACAGAAGATAAGCAAGAAAT
CTTTTTTTCCTTCTTTTACGGTCTATTCAAGTGAAGCACGGGGATTCCCGCTTGTTTAAT
AATCAGACCAACAATGATATTGACCGACCAAAAGAAGTATTCCTTCGCGTGCTTCTCCTT
TCTGTGTCAAATCCCCTACTGAAAAAGCAGCATTGGGAAAGGAACAGCAGCTTCTCCTTC
GTCGCAGAGAGCTCGCGGTAGCATTTCATTGTCAGGTATTTATGATATTTGCTAAGAATA
ATTAAAATGTCTTCAGGTCTTGCACATACTCCTACATATTTGTAAGTATTTTACTGATTT
GAGTATATAAAAGCCGTACTAAAACTAACCAGCACCTGTAGCAAGGTGCAAAATGTTGAA
CCTTTCCGAAATTTATTGCCAGAAACCAAGAGCTAAAAGTGCTTGGTAAAAGTGAAAAGA
CTCTTTTTCAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGTTCCATCTGTTCAACAAA
ACAGCTTCACTGGATCTTTCAAAGTGCGCGTCGAAACCACAAACCGTCGAAAATATTGAT
CATCTAAATAAAGGGTTCTTATTTGCACAGTTTCGCATTGAAATATTCCATTCAGGCACA
GATCAACAAGAAGACAAAAAGGTATTCGAGAAGACTAATTGTGGTATTTTTACTTTGCTG
CTGACCA
>WashU_Sbay_Contig480.2 YOR176W 5' untranslated region, Contig c480 3444 - 5443(revcom), 2000 bp (revcom)
TTTCAGGGAAGCACCATGTGCACGAATTGTTCTAGAAAGCATTTTTGGTTCGTAAATTCT
CTACAACTGAACTTATTAACAAATAGCAAACAGAGAAGAAAATTTTTTTTTTCCTTCTTG
TATGGTCAGTTAGTTGAAAACACGGAGATTTTCACTTGTTTAGTAAGCAGAGCCATAATG
CTCTTGACCGACCAAAAGAAGTATTCCTACGCGAGCTCCCTCTTCAAGTGCCAAATCCCC
TACTGAAAAAAGCAACATGAGAAGCAAAGAGATGCCTCTCGCCATGCAGGGCTTGCGGTC
ATGTTTTCTACGTTCAATTGATTTTGTTACAGCTGAAAGATGTTTATAAAACTGTCTTGC
ATATGCTCTATTTACTTGTAAACAATTTTATTAAGTTGCGTATATATGATCGTACTAAAA
ATTGGCTGGCGCGTTCTCCAGGCAGAGTTGGTTGAACCTTGCTCGAATTGATAGCTCAAA
GTGGAGAGACTCTTTTTTAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGCTCCACCTG
TTCAACAAAATGGCAGAGATCTTTCGAAGTGCGCGTCGAAACCACAAACCATCAAAAATA
TCGACCATCTAAATAAAGGGTTCTTGTTTGAATAAATATCAGGCGAAGCTCTTCATACAG
GCACAGGTCAGATAAGAAGACAATTCGAATTCGAGAAGGATATTCGTGGTATCTTTAATC
TGCTGCT
BioPerl-1.007002/t/data/map_hem/HEM1-HEM15.meme.txt000444000766000024     12024013155576321 21267 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM1-HEM15.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDR232W         1.0000    498  MIT_Spar_c117_4603       1.0000    498  
MIT_Smik_c228_4055       1.0000    498  WashU_Skud_Contig2069.5  1.0000    498  
WashU_Sbay_Contig461.5   1.0000    498  SGD_Scer_YOR176W         1.0000    727  
MIT_Spar_c278_20970      1.0000    727  MIT_Smik_c935_20455      1.0000    727  
WashU_Skud_Contig2050.4  1.0000    727  WashU_Sbay_Contig480.2   1.0000    727  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM1-HEM15.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=       10    maxsites=       10    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            6125    N=              10
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.296 C 0.204 G 0.204 T 0.296 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =  10   llr = 225   E-value = 1.2e-031
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  4a5::5:::5:1aa61:5:5
pos.-specific     C  6::::5:a::a::::5a:55
probability       G  ::2:a:a:a::9::44:55:
matrix            T  ::3a:::::5::::::::::

         bits    2.5     * *** *     *   
                 2.3     * *** *     *   
                 2.0     * *** **    *   
                 1.8     * *** **    *   
Information      1.5  * ** *** ****  * * 
content          1.3 ** ** *** ****  * * 
(32.4 bits)      1.0 ** ****** **********
                 0.8 ** ****** **********
                 0.5 ** *****************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CAATGAGCGACGAAACCACA
consensus            A T  C   T    GG GGC
sequence               G                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2069.5      +    371  4.19e-12 GGCCGCAGAC CAATGAGCGACGAAGGCGGC CTTTCGTAGC
MIT_Spar_c117_4603           +    369  4.19e-12 GGCCGCAGAC CAATGAGCGACGAAGGCGGC CTTTCCGAGT
SGD_Scer_YDR232W             +    374  4.19e-12 GGCCGCAGAC CAATGAGCGACGAAGGCGGC CTTTCCGAGC
MIT_Smik_c228_4055           +    371  6.28e-12 AAGCGCAGAC CAATGAGCGACGAAAGCGGC CTTTTGAAGG
SGD_Scer_YOR176W             +    554  3.36e-11 AGATCTTTCA CATTGCGCGTCGAAACCACA AACCGTCGAA
WashU_Sbay_Contig480.2       +    567  8.33e-11 AGATCTTTCG AAGTGCGCGTCGAAACCACA AACCATCAAA
WashU_Skud_Contig2050.4      +    562  8.33e-11 GGATCTTTCA AAGTGCGCGTCGAAACCACA AACCGTCGAA
WashU_Sbay_Contig461.5       +    368  8.75e-11 GGGCGCAGAC CAATGAGCGACGAAGACGGC TTTTGGGCGG
MIT_Spar_c278_20970          +    556  9.22e-11 AGATCTTTCG AATTGCGCGTCGAAACCACA AACCGTCGAA
MIT_Smik_c935_20455          +    540  3.96e-10 AGTTCTCTCC AATTGCGCGTCAAAACCACA AACCGTCGAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2069.5           4.2e-12  370_[+1]_108
MIT_Spar_c117_4603                4.2e-12  368_[+1]_110
SGD_Scer_YDR232W                  4.2e-12  373_[+1]_105
MIT_Smik_c228_4055                6.3e-12  370_[+1]_108
SGD_Scer_YOR176W                  3.4e-11  553_[+1]_154
WashU_Sbay_Contig480.2            8.3e-11  566_[+1]_141
WashU_Skud_Contig2050.4           8.3e-11  561_[+1]_146
WashU_Sbay_Contig461.5            8.7e-11  367_[+1]_111
MIT_Spar_c278_20970               9.2e-11  555_[+1]_152
MIT_Smik_c935_20455                 4e-10  539_[+1]_168
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=10
WashU_Skud_Contig2069.5  (  371) CAATGAGCGACGAAGGCGGC  1 
MIT_Spar_c117_4603       (  369) CAATGAGCGACGAAGGCGGC  1 
SGD_Scer_YDR232W         (  374) CAATGAGCGACGAAGGCGGC  1 
MIT_Smik_c228_4055       (  371) CAATGAGCGACGAAAGCGGC  1 
SGD_Scer_YOR176W         (  554) CATTGCGCGTCGAAACCACA  1 
WashU_Sbay_Contig480.2   (  567) AAGTGCGCGTCGAAACCACA  1 
WashU_Skud_Contig2050.4  (  562) AAGTGCGCGTCGAAACCACA  1 
WashU_Sbay_Contig461.5   (  368) CAATGAGCGACGAAGACGGC  1 
MIT_Spar_c278_20970      (  556) AATTGCGCGTCGAAACCACA  1 
MIT_Smik_c935_20455      (  540) AATTGCGCGTCAAAACCACA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 1.2e-031 
    30    177   -997   -997 
   162   -997   -997   -997 
    62   -997     19    -11 
  -997   -997   -997    162 
  -997   -997    251   -997 
    62    151   -997   -997 
  -997   -997    251   -997 
  -997    251   -997   -997 
  -997   -997    251   -997 
    62   -997   -997     62 
  -997    251   -997   -997 
  -169   -997    236   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
    89   -997    119   -997 
  -169    151    119   -997 
  -997    251   -997   -997 
    62   -997    151   -997 
  -997    151    151   -997 
    62    151   -997   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 1.2e-031 
 0.400000  0.600000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.000000  0.200000  0.300000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.100000  0.000000  0.900000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.600000  0.000000  0.400000  0.000000 
 0.100000  0.500000  0.400000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
[CA]A[ATG]TG[AC]GCG[AT]CGAA[AG][CG]C[AG][CG][AC]
--------------------------------------------------------------------------------




Time  3.95 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =  10   llr = 209   E-value = 9.7e-026
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  ::2::::1:::::::::::9
pos.-specific     C  94:4:a6:3a:a41:a::9:
probability       G  1:5:4:4:6:1:1:3:::1:
matrix            T  :6366::91:9:597:aa:1

         bits    2.5      *   * *   *    
                 2.3      *   * *   *    
                 2.0 *    *   * *   *  * 
                 1.8 *    *   * *   *  * 
Information      1.5 *    **  * *   **** 
content          1.3 *    *** *** * *****
(30.1 bits)      1.0 ** ********* *******
                 0.8 ** *****************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CTGTTCCTGCTCTTTCTTCA
consensus             CTCG G C   C G     
sequence               A                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c228_4055           +    312  4.12e-12 ATGAAAATTT CCGTTCCTGCTCTTTCTTCA TATATGAACA
SGD_Scer_YDR232W             +    315  4.12e-12 TGAAAAATTT CCGTTCCTGCTCTTTCTTCA TATATGAACA
MIT_Spar_c117_4603           +    310  6.47e-12 TGAAAAATTT CTGTTCCTGCTCTTTCTTCA TATATGAACA
WashU_Skud_Contig2069.5      +    313  8.03e-12 TGAAAAATTT CCGTTCCTGCTCTTGCTTCA TATATGACAA
MIT_Smik_c935_20455          +    154  7.23e-11 CAAAAGACTC CTTCGCGTCCTCCTTCTTCA AGTCTCATAT
MIT_Spar_c278_20970          +    159  7.23e-11 AAAAGTATTC CTTCGCGTCCTCCTTCTTCA ATCCCATATC
SGD_Scer_YOR176W             +    157  7.23e-11 AAAAGTATTC CTTCGCGTCCTCCTTCTTCA ATCCCATATC
WashU_Sbay_Contig461.5       +    308  1.78e-10 TGAAAAATCT CCGTTCCTGCTCTTGCTTGA TATATTAACA
WashU_Sbay_Contig480.2       +    207  1.47e-09 AGAAGTATTC CTACGCGAGCTCCCTCTTCA AGTGCCAAAT
WashU_Skud_Contig2050.4      +    157  2.43e-08 ACCAAAAGAA GTATTCCTTCGCGTGCTTCT CCTTTCTGTG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c228_4055                4.1e-12  311_[+2]_167
SGD_Scer_YDR232W                  4.1e-12  314_[+2]_164
MIT_Spar_c117_4603                6.5e-12  309_[+2]_169
WashU_Skud_Contig2069.5             8e-12  312_[+2]_166
MIT_Smik_c935_20455               7.2e-11  153_[+2]_554
MIT_Spar_c278_20970               7.2e-11  158_[+2]_549
SGD_Scer_YOR176W                  7.2e-11  156_[+2]_551
WashU_Sbay_Contig461.5            1.8e-10  307_[+2]_171
WashU_Sbay_Contig480.2            1.5e-09  206_[+2]_501
WashU_Skud_Contig2050.4           2.4e-08  156_[+2]_551
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=10
MIT_Smik_c228_4055       (  312) CCGTTCCTGCTCTTTCTTCA  1 
SGD_Scer_YDR232W         (  315) CCGTTCCTGCTCTTTCTTCA  1 
MIT_Spar_c117_4603       (  310) CTGTTCCTGCTCTTTCTTCA  1 
WashU_Skud_Contig2069.5  (  313) CCGTTCCTGCTCTTGCTTCA  1 
MIT_Smik_c935_20455      (  154) CTTCGCGTCCTCCTTCTTCA  1 
MIT_Spar_c278_20970      (  159) CTTCGCGTCCTCCTTCTTCA  1 
SGD_Scer_YOR176W         (  157) CTTCGCGTCCTCCTTCTTCA  1 
WashU_Sbay_Contig461.5   (  308) CCGTTCCTGCTCTTGCTTGA  1 
WashU_Sbay_Contig480.2   (  207) CTACGCGAGCTCCCTCTTCA  1 
WashU_Skud_Contig2050.4  (  157) GTATTCCTTCGCGTGCTTCT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 9.7e-026 
  -997    236    -81   -997 
  -997    119   -997     89 
   -70   -997    151    -11 
  -997    119   -997     89 
  -997   -997    119     89 
  -997    251   -997   -997 
  -997    177    119   -997 
  -169   -997   -997    147 
  -997     77    177   -169 
  -997    251   -997   -997 
  -997   -997    -81    147 
  -997    251   -997   -997 
  -997    119    -81     62 
  -997    -81   -997    147 
  -997   -997     77    111 
  -997    251   -997   -997 
  -997   -997   -997    162 
  -997   -997   -997    162 
  -997    236    -81   -997 
   147   -997   -997   -169 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 9.7e-026 
 0.000000  0.900000  0.100000  0.000000 
 0.000000  0.400000  0.000000  0.600000 
 0.200000  0.000000  0.500000  0.300000 
 0.000000  0.400000  0.000000  0.600000 
 0.000000  0.000000  0.400000  0.600000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.600000  0.400000  0.000000 
 0.100000  0.000000  0.000000  0.900000 
 0.000000  0.300000  0.600000  0.100000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.100000  0.900000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.400000  0.100000  0.500000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  0.000000  0.300000  0.700000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.900000  0.100000  0.000000 
 0.900000  0.000000  0.000000  0.100000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
C[TC][GTA][TC][TG]C[CG]T[GC]CTC[TC]T[TG]CTTCA
--------------------------------------------------------------------------------




Time  7.93 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =  10   llr = 194   E-value = 5.5e-020
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :1:3::111:1:11:91:::
pos.-specific     C  122:6661:9::1::1:8::
probability       G  :::7::3:91:a:3a:9::7
matrix            T  978:44:8::9:86:::2a3

         bits    2.5            *  *     
                 2.3            *  *     
                 2.0         ** *  * *   
                 1.8         ** *  * *   
Information      1.5         ** *  * *** 
content          1.3 *  ***  ****  ******
(28.0 bits)      1.0 * ***** ****  ******
                 0.8 ************* ******
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TTTGCCCTGCTGTTGAGCTG
consensus             CCATTG      G   T T
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c278_20970          +    497  1.95e-13 TTTAGCTTTT TTTGCCCTGCTGTTGAGCTG TTTTGCTTCA
MIT_Smik_c935_20455          +    481  1.64e-12 TTCAGCTTTT TTTGCTCTGCTGTTGAGCTG TTTTACTTCA
SGD_Scer_YOR176W             +    495  1.64e-12 TTTAGCTTTT TTTGTCCTGCTGTTGAGCTG TTTTGCTTTA
WashU_Sbay_Contig480.2       +    507  8.61e-12 TTAGCTGTTT TTTGTTCTGCTGTTGAGCTG TTTTGCTCCA
WashU_Skud_Contig2050.4      +    498  8.61e-12 TCAGCTGTTT TTTGTTCTGCTGTTGAGCTG TTTTGTTCCA
MIT_Spar_c117_4603           -    457  3.51e-09 ACTGCAATGC TTCACCGTGCTGTGGAACTT GATATAGTGG
WashU_Sbay_Contig461.5       -    260  8.74e-09 TGCCCATTGT TCTGTCCCGGTGCTGCGCTG TTGGAACCAC
SGD_Scer_YDR232W             -    465  2.27e-08 ACTACAATGC TTTACCGAGCAGTGGAGTTT GATATAGTGG
WashU_Skud_Contig2069.5      -    460  2.39e-08 GCTGTAATGG CCTACCATGCTGAAGAGCTG ATATAGTGGT
MIT_Smik_c228_4055           -    459  3.73e-08 ACAGCAATGT TACGCTGTACTGTGGAGTTT GATATAATGC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c278_20970               1.9e-13  496_[+3]_211
MIT_Smik_c935_20455               1.6e-12  480_[+3]_227
SGD_Scer_YOR176W                  1.6e-12  494_[+3]_213
WashU_Sbay_Contig480.2            8.6e-12  506_[+3]_201
WashU_Skud_Contig2050.4           8.6e-12  497_[+3]_210
MIT_Spar_c117_4603                3.5e-09  456_[-3]_22
WashU_Sbay_Contig461.5            8.7e-09  259_[-3]_219
SGD_Scer_YDR232W                  2.3e-08  464_[-3]_14
WashU_Skud_Contig2069.5           2.4e-08  459_[-3]_19
MIT_Smik_c228_4055                3.7e-08  458_[-3]_20
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=10
MIT_Spar_c278_20970      (  497) TTTGCCCTGCTGTTGAGCTG  1 
MIT_Smik_c935_20455      (  481) TTTGCTCTGCTGTTGAGCTG  1 
SGD_Scer_YOR176W         (  495) TTTGTCCTGCTGTTGAGCTG  1 
WashU_Sbay_Contig480.2   (  507) TTTGTTCTGCTGTTGAGCTG  1 
WashU_Skud_Contig2050.4  (  498) TTTGTTCTGCTGTTGAGCTG  1 
MIT_Spar_c117_4603       (  457) TTCACCGTGCTGTGGAACTT  1 
WashU_Sbay_Contig461.5   (  260) TCTGTCCCGGTGCTGCGCTG  1 
SGD_Scer_YDR232W         (  465) TTTACCGAGCAGTGGAGTTT  1 
WashU_Skud_Contig2069.5  (  460) CCTACCATGCTGAAGAGCTG  1 
MIT_Smik_c228_4055       (  459) TACGCTGTACTGTGGAGTTT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 5.5e-020 
  -997    -81   -997    147 
  -169     19   -997    111 
  -997     19   -997    130 
   -11   -997    199   -997 
  -997    177   -997     30 
  -997    177   -997     30 
  -169    177     77   -997 
  -169    -81   -997    130 
  -169   -997    236   -997 
  -997    236    -81   -997 
  -169   -997   -997    147 
  -997   -997    251   -997 
  -169    -81   -997    130 
  -169   -997     77     89 
  -997   -997    251   -997 
   147    -81   -997   -997 
  -169   -997    236   -997 
  -997    219   -997    -70 
  -997   -997   -997    162 
  -997   -997    199    -11 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.5e-020 
 0.000000  0.100000  0.000000  0.900000 
 0.100000  0.200000  0.000000  0.700000 
 0.000000  0.200000  0.000000  0.800000 
 0.300000  0.000000  0.700000  0.000000 
 0.000000  0.600000  0.000000  0.400000 
 0.000000  0.600000  0.000000  0.400000 
 0.100000  0.600000  0.300000  0.000000 
 0.100000  0.100000  0.000000  0.800000 
 0.100000  0.000000  0.900000  0.000000 
 0.000000  0.900000  0.100000  0.000000 
 0.100000  0.000000  0.000000  0.900000 
 0.000000  0.000000  1.000000  0.000000 
 0.100000  0.100000  0.000000  0.800000 
 0.100000  0.000000  0.300000  0.600000 
 0.000000  0.000000  1.000000  0.000000 
 0.900000  0.100000  0.000000  0.000000 
 0.100000  0.000000  0.900000  0.000000 
 0.000000  0.800000  0.000000  0.200000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.700000  0.300000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
T[TC][TC][GA][CT][CT][CG]TGCTGT[TG]GAG[CT]T[GT]
--------------------------------------------------------------------------------




Time 11.72 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =  10   llr = 192   E-value = 5.7e-019
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  :1:19421:1::::1:5:9:
pos.-specific     C  :::9:1621:5a3::a58::
probability       G  :1::::2219::::9:::1:
matrix            T  a8a:15:58:5:7a:::2:a

         bits    2.5            *   *    
                 2.3            *   *    
                 2.0    *     * *  **    
                 1.8    *     * *  **    
Information      1.5 * **     * * *** * *
content          1.3 * ***    * * *** ***
(27.7 bits)      1.0 * *** * ************
                 0.8 ***** * ************
                 0.5 ***** * ************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TTTCATCTTGCCTTGCACAT
consensus                 AAC  T C   CT  
sequence                   GG            
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig461.5       -    283  6.64e-13 AACGGAGATT TTTCATCTTGCCTTGCCCAT TGTTCTGTCC
MIT_Smik_c228_4055           -    288  6.64e-13 GAACGGAAAT TTTCATCTTGCCTTGCCCAT TGTTCTAATT
MIT_Spar_c117_4603           -    285  6.64e-13 AACAGAAATT TTTCATCTTGCCTTGCCCAT TGTTCTGACC
SGD_Scer_YDR232W             -    290  6.64e-13 AACGGAAATT TTTCATCTTGCCTTGCCCAT TGTTCTGATC
WashU_Skud_Contig2069.5      -    288  1.75e-10 AACGGAAATT TTTCACATTGCCTTGCCCAT TGTTCCGATC
MIT_Spar_c278_20970          +    302  3.17e-10 AGTAGAGATA TTTCAAGCTGTCCTGCACAT GCTACATATT
MIT_Smik_c935_20455          +    298  3.30e-09 AATAAAGAAG TTTCAACGTGTCCTGCATGT TCTACAAATT
WashU_Skud_Contig2050.4      +    308  1.63e-08 ATAATTAAAA TGTCTTCAGGTCTTGCACAT ACTCCTACAT
SGD_Scer_YOR176W             +    301  5.38e-08 AGCGGAGATG TTTCAAGGCATCCTACACAT GCTACATATT
WashU_Sbay_Contig480.2       +    345  5.53e-08 GAAAGATGTT TATAAAACTGTCTTGCATAT GCTCTATTTA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig461.5            6.6e-13  282_[-4]_196
MIT_Smik_c228_4055                6.6e-13  287_[-4]_191
MIT_Spar_c117_4603                6.6e-13  284_[-4]_194
SGD_Scer_YDR232W                  6.6e-13  289_[-4]_189
WashU_Skud_Contig2069.5           1.7e-10  287_[-4]_191
MIT_Spar_c278_20970               3.2e-10  301_[+4]_406
MIT_Smik_c935_20455               3.3e-09  297_[+4]_410
WashU_Skud_Contig2050.4           1.6e-08  307_[+4]_400
SGD_Scer_YOR176W                  5.4e-08  300_[+4]_407
WashU_Sbay_Contig480.2            5.5e-08  344_[+4]_363
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=10
WashU_Sbay_Contig461.5   (  283) TTTCATCTTGCCTTGCCCAT  1 
MIT_Smik_c228_4055       (  288) TTTCATCTTGCCTTGCCCAT  1 
MIT_Spar_c117_4603       (  285) TTTCATCTTGCCTTGCCCAT  1 
SGD_Scer_YDR232W         (  290) TTTCATCTTGCCTTGCCCAT  1 
WashU_Skud_Contig2069.5  (  288) TTTCACATTGCCTTGCCCAT  1 
MIT_Spar_c278_20970      (  302) TTTCAAGCTGTCCTGCACAT  1 
MIT_Smik_c935_20455      (  298) TTTCAACGTGTCCTGCATGT  1 
WashU_Skud_Contig2050.4  (  308) TGTCTTCAGGTCTTGCACAT  1 
SGD_Scer_YOR176W         (  301) TTTCAAGGCATCCTACACAT  1 
WashU_Sbay_Contig480.2   (  345) TATAAAACTGTCTTGCATAT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 5.7e-019 
  -997   -997   -997    162 
  -169   -997    -81    130 
  -997   -997   -997    162 
  -169    236   -997   -997 
   147   -997   -997   -169 
    30    -81   -997     62 
   -70    177     19   -997 
  -169     19     19     62 
  -997    -81    -81    130 
  -169   -997    236   -997 
  -997    151   -997     62 
  -997    251   -997   -997 
  -997     77   -997    111 
  -997   -997   -997    162 
  -169   -997    236   -997 
  -997    251   -997   -997 
    62    151   -997   -997 
  -997    219   -997    -70 
   147   -997    -81   -997 
  -997   -997   -997    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.7e-019 
 0.000000  0.000000  0.000000  1.000000 
 0.100000  0.000000  0.100000  0.800000 
 0.000000  0.000000  0.000000  1.000000 
 0.100000  0.900000  0.000000  0.000000 
 0.900000  0.000000  0.000000  0.100000 
 0.400000  0.100000  0.000000  0.500000 
 0.200000  0.600000  0.200000  0.000000 
 0.100000  0.200000  0.200000  0.500000 
 0.000000  0.100000  0.100000  0.800000 
 0.100000  0.000000  0.900000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.300000  0.000000  0.700000 
 0.000000  0.000000  0.000000  1.000000 
 0.100000  0.000000  0.900000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.800000  0.000000  0.200000 
 0.900000  0.000000  0.100000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
TTTCA[TA][CAG][TCG]TG[CT]C[TC]TGC[AC][CT]AT
--------------------------------------------------------------------------------




Time 15.38 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =  10   llr = 188   E-value = 9.3e-018
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  216895a11:3::::13:11
pos.-specific     C  6931:2::5:678:7::69:
probability       G  1:1:13:91a::17:972:9
matrix            T  1::1::::3:13133::2::

         bits    2.5          *          
                 2.3          *          
                 2.0  *     * *     *  **
                 1.8  *     * *     *  **
Information      1.5  *    ** *  *  *  **
content          1.3  *  * ** * ****** **
(27.1 bits)      1.0  *  * ** * *********
                 0.8 ***** ** ***********
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CCAAAAAGCGCCCGCGGCCG
consensus            A C  G  T AT TT AG  
sequence                  C           T  
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c117_4603           +    344  3.06e-14 TGAACAATGA CCAAAAAGCGCCCGCGGCCG CAGACCAATG
SGD_Scer_YDR232W             +    349  3.06e-14 TGAACAATGA CCAAAAAGCGCCCGCGGCCG CAGACCAATG
WashU_Skud_Contig2069.5      +    346  1.65e-12 ATGACAATGA CCAAAAAGCGTCCGCGGCCG CAGACCAATG
MIT_Smik_c228_4055           +    346  1.43e-10 TGAACAATGA CCAAAAAGCGCCCGCAAGCG CAGACCAATG
MIT_Spar_c278_20970          +    126  3.60e-09 TTGGTGCCAA ACCAAGAGTGACCTTGACCG ACTAAAAGTA
SGD_Scer_YOR176W             +    124  3.90e-09 TTGGTGTCAA GCCAAGAGTGACCTTGACCG ACCAAAAGTA
WashU_Sbay_Contig461.5       +    343  4.91e-09 TAACAATGAC CAAAAAAACGCCGGCGGGCG CAGACCAATG
MIT_Smik_c935_20455          +    122  5.29e-09 TAATGATCAG ACCAACAGTGATCTTGGCCG ACCAAAAGAC
WashU_Skud_Contig2050.4      +    242  1.18e-07 TTCTCCTTCG TCGCAGAGAGCTCGCGGTAG CATTTCATTG
WashU_Sbay_Contig480.2       +    282  2.27e-07 ATGCCTCTCG CCATGCAGGGCTTGCGGTCA TGTTTTCTAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c117_4603                3.1e-14  343_[+5]_135
SGD_Scer_YDR232W                  3.1e-14  348_[+5]_130
WashU_Skud_Contig2069.5           1.6e-12  345_[+5]_133
MIT_Smik_c228_4055                1.4e-10  345_[+5]_133
MIT_Spar_c278_20970               3.6e-09  125_[+5]_582
SGD_Scer_YOR176W                  3.9e-09  123_[+5]_584
WashU_Sbay_Contig461.5            4.9e-09  342_[+5]_136
MIT_Smik_c935_20455               5.3e-09  121_[+5]_586
WashU_Skud_Contig2050.4           1.2e-07  241_[+5]_466
WashU_Sbay_Contig480.2            2.3e-07  281_[+5]_426
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=10
MIT_Spar_c117_4603       (  344) CCAAAAAGCGCCCGCGGCCG  1 
SGD_Scer_YDR232W         (  349) CCAAAAAGCGCCCGCGGCCG  1 
WashU_Skud_Contig2069.5  (  346) CCAAAAAGCGTCCGCGGCCG  1 
MIT_Smik_c228_4055       (  346) CCAAAAAGCGCCCGCAAGCG  1 
MIT_Spar_c278_20970      (  126) ACCAAGAGTGACCTTGACCG  1 
SGD_Scer_YOR176W         (  124) GCCAAGAGTGACCTTGACCG  1 
WashU_Sbay_Contig461.5   (  343) CAAAAAAACGCCGGCGGGCG  1 
MIT_Smik_c935_20455      (  122) ACCAACAGTGATCTTGGCCG  1 
WashU_Skud_Contig2050.4  (  242) TCGCAGAGAGCTCGCGGTAG  1 
WashU_Sbay_Contig480.2   (  282) CCATGCAGGGCTTGCGGTCA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 9.3e-018 
   -70    177    -81   -169 
  -169    236   -997   -997 
    89     77    -81   -997 
   130    -81   -997   -169 
   147   -997    -81   -997 
    62     19     77   -997 
   162   -997   -997   -997 
  -169   -997    236   -997 
  -169    151    -81    -11 
  -997   -997    251   -997 
   -11    177   -997   -169 
  -997    199   -997    -11 
  -997    219    -81   -169 
  -997   -997    199    -11 
  -997    199   -997    -11 
  -169   -997    236   -997 
   -11   -997    199   -997 
  -997    177     19    -70 
  -169    236   -997   -997 
  -169   -997    236   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 9.3e-018 
 0.200000  0.600000  0.100000  0.100000 
 0.100000  0.900000  0.000000  0.000000 
 0.600000  0.300000  0.100000  0.000000 
 0.800000  0.100000  0.000000  0.100000 
 0.900000  0.000000  0.100000  0.000000 
 0.500000  0.200000  0.300000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.100000  0.000000  0.900000  0.000000 
 0.100000  0.500000  0.100000  0.300000 
 0.000000  0.000000  1.000000  0.000000 
 0.300000  0.600000  0.000000  0.100000 
 0.000000  0.700000  0.000000  0.300000 
 0.000000  0.800000  0.100000  0.100000 
 0.000000  0.000000  0.700000  0.300000 
 0.000000  0.700000  0.000000  0.300000 
 0.100000  0.000000  0.900000  0.000000 
 0.300000  0.000000  0.700000  0.000000 
 0.000000  0.600000  0.200000  0.200000 
 0.100000  0.900000  0.000000  0.000000 
 0.100000  0.000000  0.900000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
[CA]C[AC]AA[AGC]AG[CT]G[CA][CT]C[GT][CT]G[GA][CGT]CG
--------------------------------------------------------------------------------




Time 18.95 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR232W                 2.26e-35  131_[-2(4.87e-05)]_138_[-4(6.64e-13)]_5_[+2(4.12e-12)]_14_[+5(3.06e-14)]_5_[+1(4.19e-12)]_71_[-3(2.27e-08)]_14
MIT_Spar_c117_4603               5.83e-36  284_[-4(6.64e-13)]_5_[+2(6.47e-12)]_14_[+5(3.06e-14)]_5_[+1(4.19e-12)]_68_[-3(3.51e-09)]_22
MIT_Smik_c228_4055               1.73e-31  287_[-4(6.64e-13)]_4_[+2(4.12e-12)]_14_[+5(1.43e-10)]_5_[+1(6.28e-12)]_68_[-3(3.73e-08)]_20
WashU_Skud_Contig2069.5          4.17e-31  264_[-3(3.20e-06)]_3_[-4(1.75e-10)]_5_[+2(8.03e-12)]_13_[+5(1.65e-12)]_5_[+1(4.19e-12)]_69_[-3(2.39e-08)]_19
WashU_Sbay_Contig461.5           5.52e-28  168_[+1(4.58e-05)]_71_[-3(8.74e-09)]_3_[-4(6.64e-13)]_5_[+2(1.78e-10)]_15_[+5(4.91e-09)]_5_[+1(8.75e-11)]_111
SGD_Scer_YOR176W                 6.45e-27  123_[+5(3.90e-09)]_13_[+2(7.23e-11)]_124_[+4(5.38e-08)]_81_[+3(6.18e-05)]_73_[+3(1.64e-12)]_39_[+1(3.36e-11)]_80_[-2(1.18e-05)]_54
MIT_Spar_c278_20970              1.57e-29  125_[+5(3.60e-09)]_13_[+2(7.23e-11)]_123_[+4(3.17e-10)]_83_[+3(6.18e-05)]_72_[+3(1.95e-13)]_39_[+1(9.22e-11)]_128_[+3(8.37e-05)]_4
MIT_Smik_c935_20455              6.31e-27  121_[+5(5.29e-09)]_12_[+2(7.23e-11)]_18_[-2(1.21e-05)]_86_[+4(3.30e-09)]_163_[+3(1.64e-12)]_39_[+1(3.96e-10)]_168
WashU_Skud_Contig2050.4          1.40e-22  67_[-1(8.16e-05)]_4_[-2(9.76e-05)]_15_[+5(6.67e-06)]_10_[+2(2.43e-08)]_65_[+5(1.18e-07)]_46_[+4(1.63e-08)]_170_[+3(8.61e-12)]_44_[+1(8.33e-11)]_146
WashU_Sbay_Contig480.2           5.90e-23  29_[-5(7.21e-05)]_121_[+5(9.26e-05)]_16_[+2(1.47e-09)]_55_[+5(2.27e-07)]_43_[+4(5.53e-08)]_142_[+3(8.61e-12)]_11_[-3(9.47e-05)]_9_[+1(8.33e-11)]_42_[-2(6.80e-06)]_14_[-4(5.59e-06)]_45
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM1-HEM2.fa000444000766000024      2126013155576321 20012 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR232W HEM1 "5-aminolevulinate synthase, catalyzes the first step in the heme biosynthetic pathway; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expression is regulated by Hap2p-Hap3p"
ACTGAAAAAAAAACCTAAGTACTGTTATGATTATTGAGGGACAACAACTAGCTCTATTAG
TTTTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTGGG
ATAAAAAAAAAAGAAACGCGAGCTGAGAAGGGAAGGCGTGTAAAGGAAGAACGGTTGAGA
GACAGCAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGAATGGAGAAG
TTTGGTATGATGCAAACGTTGTATTTCTAACAACGCATGGATCAGAACAATGGGCAAGGC
AAGATGAAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCC
CGCGGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGCGGTAGGGTAAGCCGTGC
AGGCAAGCTTATTATAGCACCGTCGGGGGTACCACCACTATATCAAACTCCACTGCTCGG
TAAAGCATTGTAGTGAAG
>MIT_Spar_c117_4603 YDR232W 5' untranslated region, Contig c117 17441 - 19440, 2000 bp (revcom)
ACTGAAAAAAAACCAAGTACTGTTGTGATTATTGAGGGACAACGGCTAGCTCTATTTGTT
TTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTAGGAT
AAAAAAAGAAACGCGAGCTGAGAAGAGAAGGCGTGTAAAGGAAGAACGGTTGAGAGAGAG
CAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGGATGGAGGAGTTTGG
TACGATGCAAACGCTATATTTGTAGCAACGCATGGGTCAGAACAATGGGCAAGGCAAGAT
GAAAAATTTCTGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGCGG
CCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGTGGTAGGGTAAGCCGTGCAGGCA
AGCTTATTATAGCACCGTCGGGGGGACCACTATATCAAGTTCCACAGCACGGTGAAGCAT
TGCAGTATAGTTCACAGC
>MIT_Smik_c228_4055 YDR232W 5' untranslated region, Contig c228 4702 - 6701(revcom), 2000 bp (revcom)
ACCGAGAGAAAAACTAAGTAGTGATATGATTATTGAGGACTAATGACCAGCTTTGTTTGT
TTTTTCTTCCAACCTAACTTATATGGGAAATATATAGGACAGAAAAAAGAAAAGAGCACG
AAAAAAAAGAAATGCGACCTGAGAAGGGAGGACGTGTGAAGCCAGAACGGTTGAATGACA
GTAGAGGAGGGTGCAACACAACCGAGTAGAGTACCAGCTGACGGAATGGAGGAGTTTGGT
ATGATGCAAAAGTGATGCTTTTAGCAACGCAACATTGAATTAGAACAATGGGCAAGGCAA
GATGAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGC
AAGCGCAGACCAATGAGCGACGAAAGCGGCCTTTTGAAGGGTAGGGTAATCCATGCAGGC
AAGTTTATTATAGCACCGTCGGGGGGAAGCATTATATCAAACTCCACAGTACAGCGTAAC
ATTGCTGTATAGGCTACA
>WashU_Skud_Contig2069.5 YDR232W 5' untranslated region, Contig c2069 5476 - 7475, 2000 bp (revcom)
ACTGAAAATAATCCGAGTCGTGCTACTGTGAATATTGAGAATAGGGACTAGCTCTATTTG
ATTTTTCTTCCAACCAAACTTATATGGAAAATATAAAGGAAAGAAAAAAGAAAAGAATAG
GAAAAAAAAAAAGAAACGCGAGAGAAGAGAACCGTGTGGAGGGAAGAACGGTTGAGAGAC
AGCAGAGCACAGCGCAACACAACCGAGTAGAGTACCAGCAGACGGAGTGGGTAGTTTGGT
ACAGTGTAAAAGCTATATTTCCACCAACGCAACACTGGATCGGAACAATGGGCAAGGCAA
TGTGAAAAATTTCCGTTCCTGCTCTTGCTTCATATATGACAATGACCAAAAAGCGTCCGC
GGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCGTAGCAGCAGGGTAAGCCGCGCAAG
CAAGTCCGTCATAACACCGTCGAAGGGGCACCACTATATCAGCTCTTCAGCATGGTAGGC
CATTACAGCACAGTCTTG
>WashU_Sbay_Contig461.5 YDR232W 5' untranslated region, Contig c461 4000 - 5999, 2000 bp (revcom)
ACTAAAAAGTCCAAGTGGTGCTGTTATTATTGAGGATAGCAACTAGCTTTATTTGTTTTT
TCTTCCAACCAAACTTATATGGAAATCAAAGGAAGGAAAAAAAGAAAAGAACAGGAAGAA
AAAAAAGAAACGTGAGCTGCCGAAAGGAGAGCGTGTGGAGGGAAGAACCGTTGAGAGACA
ACAGAGCAGGGTGCAAACCGATTAGAGTACCAGCAGACGAGATGGGCGATGTGGTACGGT
GCAGAAGGTGTGGTTCCAACAGCGCAGCACCGGGACAGAACAATGGGCAAGGCAAGATGA
AAAATCTCCGTTCCTGCTCTTGCTTGATATATTAACAATGACCAAAAAAACGCCGGCGGG
CGCAGACCAATGAGCGACGAAGACGGCTTTTGGGCGGGGCAGGGTAAGATGGGACAGGCA
AGGTCCGCTATAGCACCGTCGAGGGGGACCGCTATATCAGCTCCCAGTACATTGCAGCAC
ACTCTATAGCTAGTCAAA
>SGD_Scer_YGL040C HEM2 "Delta-aminolevulinate dehydratase, a homo-octameric enzyme, catalyzes the conversion of delta-aminolevulinic acid to porphobilinogen, the second step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus"
GGTTTTGTCAATTTTCTAGGTATGAATTACTGGAGTAAGCAATAATATGAGTAAGCAGTA
AAACTTTTTTTTATTTGGCTGATTGGGCAAGAAAATCAAAGACAATAGAGTGGCGCATAG
ATGTTGCTAGCATTTATTAGGTTGCCTTACTCTTATATAAATCAAGCGGGAAGCTTGCCT
CAAGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTATTTTGATTTTTTTTTC
ACCTTTTCCAATTTTTTTTTCGGCAACAATTTTTTGGATGATTTTTATCGTCGATCTTGG
AATGATGATGTATTTCGGCGTCTCTACAAGACCCAATAAAGTAATTCGGTGACACAGGCT
TGTAGCAGATAGAAAACGTTCCGAAAGATGGGTTCCAATTGATGTAACACTTCTTTTTTA
TATATTCATGTGGACGTGTACGCCTTCTTCCCTTCTTTGCCTCTTGTGCCACTGTTAATC
CTCTTAAGCATATTGTTTTTATTTACAGACATTGGCTGACTCACCAGAAACTATAATTGA
CGCTGATTTCTAGTTAATTAAAAATAAAATATATGCAAGAATTAGCACCAGGCAGTCATT
TCTGTAAATTGCTTTGTTTTCTATTTCAAATTTGTTTTTTGTATATGTTTCAATGTTCTC
GTGACAATGCAGGCTTTTTTTTGTGCGAATTAAAGTAAAGCTAATCAAAACTAAACAATA
ATTTATCTTGTTCCCGAAAGAGTGGATCATGAGGAGGAAAGCTAACCGTCCAAGATCCTA
TATAATTTTTGAACTGAAAACCAACTGTTCACCTAGAAGACAGGTATCTGGATATGTAAC
TACACGCTCTATAAATACAGAAATCGTAAGCTAATCAATATAAATGTAAAAGAAAATAGG
AATTGCTGTCGATAGATTTATTTACTTTTGTATTGTCATCTGTGTTCTGTGCCAGTACAC
CGGACTCGTATGAGCTGTATGGTGTCGTTTCAATAGAATC
>MIT_Spar_c19_8512 YGL040C 5' untranslated region, Contig c19 1 - 1802, 2000 bp (revcom)
GGTTTTGTCAATATTCTAAATATGGATTCCTAGGGCAGGCAATAATATGGGGAAGCAGTA
AAACTTTTTGTTTTATGTGGCTGATTGGGCCAAAAAACAAGGACAATAGAATGACACATA
AAGTTTGCTAGCATTTATTAGGTTGCCTTACTCTTTTATAAATCAAGCGGGCAGCTTGCC
TCAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTAGTTTGAATTTTTTTT
TCACCTTTTGAAATTTTTTTTTTTCGGCAACAATTTTGAATGACTTTTATCGTCAATCTT
GGGAGTATACCTGCCTCTTTACAACACCCAACAAAACACTTAAGTAAGACAAGCTTGTGG
CAGGTAGGAAAGGTTTCAAAAAAAAAAAAAAGGTTTTTATCTATGGTCATACTTTTTCTT
CGTATATTTATGTGAACACGTACGTCTTGTTTTGCCTTCTTTGGCTCTTGTGTCACTGAA
TCTTCACATATTGTTTTTATTTACAGATACTACTTGACTCGCCTAAAATTATAATCGGCG
ATGGTTTCTACTACCTTAGTTAAAAAATAAAATGAATCAAAACATTACCATTAATAATTC
AATTTTTCCACATTAGTTTGTTTTCTATTTTATGGCTTTCTTCTTGTATATTTCTCAATA
TACTGCATGGCAATGCAAGCTCTTCTCTTTTCTTGATTGAAAATAAAGCTGTGAAGAACT
AAATAATAATTTATTGATGTCCTCCACAAAATGTACACCTGCGCTAACCTTGCTTAACAG
ATACGGTCAAAACGAACTTGAGCATATGTAAAAATCCATGTATTTTTCTTCTTTTGCCAA
CTAAATCAAACTTTTTATTGTATATGTCGTACCGCCAATACAAAGATGGAGAGGTTAATG
AAAATAGATGTGAAAAAAAAGCAGGAACTATTGTAGATAGATATTTTTAGGGTTCGATTG
CTATTTTTCTGTATTATGATCTGTGTTCTATGCCAGTGTA
>MIT_Smik_c273_7756 YGL040C 5' untranslated region, Contig c273 1 - 1807, 2000 bp (revcom)
GGTTTTACCAGTTTTCTTAATACGGATATCTAGAGTAAGTCACAATTTAAGGAAATTGCA
AAATTTTCTTTTTATATAGCTAAATAGGCCAATAAATCAGGAACAATAGAATGACGCACC
GAGTTTGCTAGCAACCTACACACTTGCTTTTTTTTATAAATCAAGAGTGTATGTTGCCTC
AGGCCAATCACCGCACCGAATAAGGATTGCTCGTTTACCCGTTGTTCGATTTTTTTTTTC
ATCTTCTACCAATTTTTTTCGGCAGCGCCTTTGAATGACTTTGATCATCAATCCTGGAGT
AATATACACTTGTATGTTTGAAACGCCCAGTTACAATATTTATTGGAATAGCTAACTTAT
GAGTAAGTGGACCCAAATTTTCGAGTGATGTTTCCTGTCAACGGTGACACTTATTTTTGG
TTTGCAGATATGTATGTGTATATCTTATTCCCACTTTTTTATAGTTATCGTTATCTATGT
ATCTCAATACCTTGGACATGAATCACCGAGTAGATATTTTTCTTTACAATGCTTAAAACA
AGGCCGCACAGAACTAAACAATAAAGTTACCTTGATCTTTAATAAAATATTCCCCCATTA
ATAAGTACTCTCTTCGATTACGATTTAGCCATATTCATTTTGACCATACATTGCAGATGT
GAGATGGATTTTAAGTGGTGAAAGCGCTCTAAGCTATGCCATATAAGTACGTAAGGAGAG
ACAAAATTAAACATAATTAAGCGCCATGTGAGACTAAATGTGGCCGTCGTTTTGATTATA
TGATTGGGAAAAGCTCCTAAACATAGAGGTAGAATTATAGTTCGGAAATTTCGTCTTGCC
CTGCTCATTTTGTAGAAAACGAGTCATCATCTCCACCCTTTGTAACCGGTGTCCTGCTCA
CATAAATAGTCTCTACTGAGAGATTTGTGAATTTCGAGATAATTTTTGGGATTCCATTGT
TGATAAAGGCAATATTATTAGGTATATAAAATATACTAGA
>MIT_Sbay_c77_8808 YGL040C 5' untranslated region, Contig c77 1 - 1377, 2000 bp (revcom)
ACTTTGTCAGTGTTTTTCTGGTAAGGATATCTGGAAGAAGTAACAATACGTATAAATTAC
AAAATTACCGTTTTATGTCGTGGAATGGGCTATGAACTAACATTAACAATAGAGTGATGC
ATAGACGTCACTAGCCTTTTATTGTGTTGCCTTGCTCTTTTATAAATCAGGCAGCCTGCC
GCAGGCCAATCACCGCACCGCCCGGAGATGCTCGTTTACCGTTGTGCACCAAATTTTTCA
TTTTTTGCCTTTTTCTATTTGGCAGCGTTTTCGAAAAATTTTGATCATTAGTCTTCAATG
ACTGGACTGTCATATTTTAGGGCACGCAGGTAAAGATATGAACAAATCATATTGATGATG
GATGCCAATCCTTCAATGTAAATTCTTTCTAAACATCATGATAAAGAACTTCAGTAAGAG
AGTGATAAAAACTTTACATGTATGGCGGGTGTATTCTGTAATTGTTTTTTAGATCTTTTT
GTTGTTAACGGTGACACCATTCTTACTACAATAATTGCATGTCAAATGTAAATATCTTGC
TTCACATTTCGTTGTTTCTTTACGATAAATTGTTTCGTCGCAAATATATCTTATTTTGCG
TGGTTTATCTACAGACACTGCTTGATTTACGCATAAGTACATCATGTAGTAATTCTTATA
TTGAGTATAAAACCATATGAATAGAAATATTTTTGTTAATCTATCGTTAATTTACATGCT
AGTTTATTTGTCCCTTTAAAATTTCTTTATATATTTGTTGCAATATGTGGACAAGGAAAC
ACGAAATATATTGGGATAAAGTTTAAGTAGAGATACATAGAACTAAACAATAAATTCATA
TTCAATAATACTTCAAAAGGTACTCTCCTGTCTGAACACAGAGACTCACAGACTTTATTT
AGTCGTTATGGCGATGTCAGACATCATGTTTAAGGTAAGCCGAGTGGATTGATATGAAAT
TGTCATATCATGAATAAGCTAATTACCCAAAAACAGTAAA
>WashU_Skud_Contig2052.17 YGL040C 5' untranslated region, Contig c2052 29967 - 31966, 2000 bp (revcom)
GATTTGTCAGTGTTTTCTGATATGGATGCCTGGAGAAAATATTAATATGTGGAAACCACA
AAACTTCCACTTATATAGCTAATTTAGCCAGAAATCATGAACAATAGGATGACGCATAGA
CGTCACTACTCTTCATATAAGTTGCCTTTCTCTTTTATAAATTGGGCAGGCAGCTTGCCT
CAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTTGCGTTCAAAGTTTTTC
ATTTTCCGCATCATCTACTTTTTTTTTTTTGACGCCGTTTTTGAATGTCTTGGTCATTGA
TCTTGAAATGATTTATGTTCGTGTTTTCACGGCACAAAGGTAGGCAAATCGGTAAATTTT
ACTCGTAATAAATAATCAAGGCCTCTAGAGGATTTAATATCAGGAAATAATAATGTGAGT
TTTTTGCAAATGGCCTTATATTCCTGACATCTTCTTGAATTTGTGTTTTAGCGTCGATGA
AGACTCTTCCTTTTTTCGTACGGTAATCTGGACATCTTGTTTCGTCTTTTCTTTTTTTTT
TGCGATTGCTTGTAATTCCAGATATGCAGCATTTATTTACAGGTGCTGATTGATTTACTA
TAGAGTTTATCAGGTAGTAGTTCTTTTTCATGTCTCAATTGAAGAAAAGGAACCCATAAA
TACATTAGCACTGAACAAACAATAACTGCCGCATTGGTTTGTTTTCTAACTTGAATTTTT
CTTTATACATATGCCACTGTATTAGGATGGGTGAATACCGTTTTCTTACTTTCTTCCTAT
GAAGGCGAAAGAATGGTGAAGGACAACTAAACAATAAATCGTTTTTCACACATCCCCATA
AAGCTTTCTCTGTTTGTCAGTTGTGACTCATCTTTCGTCGATGTTGCTTGGTAGATACAA
TTGAACAAGATTGAGATATCTAAAATGTTCAAAAATTATACTCTCTTATGTAGTTTCCGT
CATGGCTGAACGAAGGAAAACTACATCACCTGAGAATTAC
BioPerl-1.007002/t/data/map_hem/HEM1-HEM2.fa.revcom000444000766000024      2126013155576321 21304 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR232W HEM1 "5-aminolevulinate synthase, catalyzes the first step in the heme biosynthetic pathway; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expression is regulated by Hap2p-Hap3p"
CTTCACTACAATGCTTTACCGAGCAGTGGAGTTTGATATAGTGGTGGTACCCCCGACGGT
GCTATAATAAGCTTGCCTGCACGGCTTACCCTACCGCTCGGAAAGGCCGCCTTCGTCGCT
CATTGGTCTGCGGCCGCGGGCGCTTTTTGGTCATTGTTCATATATGAAGAAAGAGCAGGA
ACGGAAATTTTTCATCTTGCCTTGCCCATTGTTCTGATCCATGCGTTGTTAGAAATACAA
CGTTTGCATCATACCAAACTTCTCCATTCCGTCAGCTGATACTCTATTCGGTTGTGTGTT
GCACCCTGCTCTGCTGTCTCTCAACCGTTCTTCCTTTACACGCCTTCCCTTCTCAGCTCG
CGTTTCTTTTTTTTTTATCCCACTCTTTTCTTTTTTCTTTCCTATATATTGCCCATATAA
GTTTGGTTGGAAGGAAAACTAATAGAGCTAGTTGTTGTCCCTCAATAATCATAACAGTAC
TTAGGTTTTTTTTTCAGT
>MIT_Spar_c117_4603 YDR232W 5' untranslated region, Contig c117 17441 - 19440, 2000 bp (revcom)
GCTGTGAACTATACTGCAATGCTTCACCGTGCTGTGGAACTTGATATAGTGGTCCCCCCG
ACGGTGCTATAATAAGCTTGCCTGCACGGCTTACCCTACCACTCGGAAAGGCCGCCTTCG
TCGCTCATTGGTCTGCGGCCGCGGGCGCTTTTTGGTCATTGTTCATATATGAAGAAAGAG
CAGGAACAGAAATTTTTCATCTTGCCTTGCCCATTGTTCTGACCCATGCGTTGCTACAAA
TATAGCGTTTGCATCGTACCAAACTCCTCCATCCCGTCAGCTGATACTCTATTCGGTTGT
GTGTTGCACCCTGCTCTGCTCTCTCTCAACCGTTCTTCCTTTACACGCCTTCTCTTCTCA
GCTCGCGTTTCTTTTTTTATCCTACTCTTTTCTTTTTTCTTTCCTATATATTGCCCATAT
AAGTTTGGTTGGAAGGAAAACAAATAGAGCTAGCCGTTGTCCCTCAATAATCACAACAGT
ACTTGGTTTTTTTTCAGT
>MIT_Smik_c228_4055 YDR232W 5' untranslated region, Contig c228 4702 - 6701(revcom), 2000 bp (revcom)
TGTAGCCTATACAGCAATGTTACGCTGTACTGTGGAGTTTGATATAATGCTTCCCCCCGA
CGGTGCTATAATAAACTTGCCTGCATGGATTACCCTACCCTTCAAAAGGCCGCTTTCGTC
GCTCATTGGTCTGCGCTTGCGGGCGCTTTTTGGTCATTGTTCATATATGAAGAAAGAGCA
GGAACGGAAATTTTCATCTTGCCTTGCCCATTGTTCTAATTCAATGTTGCGTTGCTAAAA
GCATCACTTTTGCATCATACCAAACTCCTCCATTCCGTCAGCTGGTACTCTACTCGGTTG
TGTTGCACCCTCCTCTACTGTCATTCAACCGTTCTGGCTTCACACGTCCTCCCTTCTCAG
GTCGCATTTCTTTTTTTTCGTGCTCTTTTCTTTTTTCTGTCCTATATATTTCCCATATAA
GTTAGGTTGGAAGAAAAAACAAACAAAGCTGGTCATTAGTCCTCAATAATCATATCACTA
CTTAGTTTTTCTCTCGGT
>WashU_Skud_Contig2069.5 YDR232W 5' untranslated region, Contig c2069 5476 - 7475, 2000 bp (revcom)
CAAGACTGTGCTGTAATGGCCTACCATGCTGAAGAGCTGATATAGTGGTGCCCCTTCGAC
GGTGTTATGACGGACTTGCTTGCGCGGCTTACCCTGCTGCTACGAAAGGCCGCCTTCGTC
GCTCATTGGTCTGCGGCCGCGGACGCTTTTTGGTCATTGTCATATATGAAGCAAGAGCAG
GAACGGAAATTTTTCACATTGCCTTGCCCATTGTTCCGATCCAGTGTTGCGTTGGTGGAA
ATATAGCTTTTACACTGTACCAAACTACCCACTCCGTCTGCTGGTACTCTACTCGGTTGT
GTTGCGCTGTGCTCTGCTGTCTCTCAACCGTTCTTCCCTCCACACGGTTCTCTTCTCTCG
CGTTTCTTTTTTTTTTTCCTATTCTTTTCTTTTTTCTTTCCTTTATATTTTCCATATAAG
TTTGGTTGGAAGAAAAATCAAATAGAGCTAGTCCCTATTCTCAATATTCACAGTAGCACG
ACTCGGATTATTTTCAGT
>WashU_Sbay_Contig461.5 YDR232W 5' untranslated region, Contig c461 4000 - 5999, 2000 bp (revcom)
TTTGACTAGCTATAGAGTGTGCTGCAATGTACTGGGAGCTGATATAGCGGTCCCCCTCGA
CGGTGCTATAGCGGACCTTGCCTGTCCCATCTTACCCTGCCCCGCCCAAAAGCCGTCTTC
GTCGCTCATTGGTCTGCGCCCGCCGGCGTTTTTTTGGTCATTGTTAATATATCAAGCAAG
AGCAGGAACGGAGATTTTTCATCTTGCCTTGCCCATTGTTCTGTCCCGGTGCTGCGCTGT
TGGAACCACACCTTCTGCACCGTACCACATCGCCCATCTCGTCTGCTGGTACTCTAATCG
GTTTGCACCCTGCTCTGTTGTCTCTCAACGGTTCTTCCCTCCACACGCTCTCCTTTCGGC
AGCTCACGTTTCTTTTTTTTCTTCCTGTTCTTTTCTTTTTTTCCTTCCTTTGATTTCCAT
ATAAGTTTGGTTGGAAGAAAAAACAAATAAAGCTAGTTGCTATCCTCAATAATAACAGCA
CCACTTGGACTTTTTAGT
>SGD_Scer_YGL040C HEM2 "Delta-aminolevulinate dehydratase, a homo-octameric enzyme, catalyzes the conversion of delta-aminolevulinic acid to porphobilinogen, the second step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus"
GATTCTATTGAAACGACACCATACAGCTCATACGAGTCCGGTGTACTGGCACAGAACACA
GATGACAATACAAAAGTAAATAAATCTATCGACAGCAATTCCTATTTTCTTTTACATTTA
TATTGATTAGCTTACGATTTCTGTATTTATAGAGCGTGTAGTTACATATCCAGATACCTG
TCTTCTAGGTGAACAGTTGGTTTTCAGTTCAAAAATTATATAGGATCTTGGACGGTTAGC
TTTCCTCCTCATGATCCACTCTTTCGGGAACAAGATAAATTATTGTTTAGTTTTGATTAG
CTTTACTTTAATTCGCACAAAAAAAAGCCTGCATTGTCACGAGAACATTGAAACATATAC
AAAAAACAAATTTGAAATAGAAAACAAAGCAATTTACAGAAATGACTGCCTGGTGCTAAT
TCTTGCATATATTTTATTTTTAATTAACTAGAAATCAGCGTCAATTATAGTTTCTGGTGA
GTCAGCCAATGTCTGTAAATAAAAACAATATGCTTAAGAGGATTAACAGTGGCACAAGAG
GCAAAGAAGGGAAGAAGGCGTACACGTCCACATGAATATATAAAAAAGAAGTGTTACATC
AATTGGAACCCATCTTTCGGAACGTTTTCTATCTGCTACAAGCCTGTGTCACCGAATTAC
TTTATTGGGTCTTGTAGAGACGCCGAAATACATCATCATTCCAAGATCGACGATAAAAAT
CATCCAAAAAATTGTTGCCGAAAAAAAAATTGGAAAAGGTGAAAAAAAAATCAAAATACG
GGTAAACGAGCAATCCCTGTTCGGTGCGGTGATTGGCTTGAGGCAAGCTTCCCGCTTGAT
TTATATAAGAGTAAGGCAACCTAATAAATGCTAGCAACATCTATGCGCCACTCTATTGTC
TTTGATTTTCTTGCCCAATCAGCCAAATAAAAAAAAGTTTTACTGCTTACTCATATTATT
GCTTACTCCAGTAATTCATACCTAGAAAATTGACAAAACC
>MIT_Spar_c19_8512 YGL040C 5' untranslated region, Contig c19 1 - 1802, 2000 bp (revcom)
TACACTGGCATAGAACACAGATCATAATACAGAAAAATAGCAATCGAACCCTAAAAATAT
CTATCTACAATAGTTCCTGCTTTTTTTTCACATCTATTTTCATTAACCTCTCCATCTTTG
TATTGGCGGTACGACATATACAATAAAAAGTTTGATTTAGTTGGCAAAAGAAGAAAAATA
CATGGATTTTTACATATGCTCAAGTTCGTTTTGACCGTATCTGTTAAGCAAGGTTAGCGC
AGGTGTACATTTTGTGGAGGACATCAATAAATTATTATTTAGTTCTTCACAGCTTTATTT
TCAATCAAGAAAAGAGAAGAGCTTGCATTGCCATGCAGTATATTGAGAAATATACAAGAA
GAAAGCCATAAAATAGAAAACAAACTAATGTGGAAAAATTGAATTATTAATGGTAATGTT
TTGATTCATTTTATTTTTTAACTAAGGTAGTAGAAACCATCGCCGATTATAATTTTAGGC
GAGTCAAGTAGTATCTGTAAATAAAAACAATATGTGAAGATTCAGTGACACAAGAGCCAA
AGAAGGCAAAACAAGACGTACGTGTTCACATAAATATACGAAGAAAAAGTATGACCATAG
ATAAAAACCTTTTTTTTTTTTTTGAAACCTTTCCTACCTGCCACAAGCTTGTCTTACTTA
AGTGTTTTGTTGGGTGTTGTAAAGAGGCAGGTATACTCCCAAGATTGACGATAAAAGTCA
TTCAAAATTGTTGCCGAAAAAAAAAAATTTCAAAAGGTGAAAAAAAAATTCAAACTACGG
GTAAACGAGCAATCCCTGTTCGGTGCGGTGATTGGCCTGAGGCAAGCTGCCCGCTTGATT
TATAAAAGAGTAAGGCAACCTAATAAATGCTAGCAAACTTTATGTGTCATTCTATTGTCC
TTGTTTTTTGGCCCAATCAGCCACATAAAACAAAAAGTTTTACTGCTTCCCCATATTATT
GCCTGCCCTAGGAATCCATATTTAGAATATTGACAAAACC
>MIT_Smik_c273_7756 YGL040C 5' untranslated region, Contig c273 1 - 1807, 2000 bp (revcom)
TCTAGTATATTTTATATACCTAATAATATTGCCTTTATCAACAATGGAATCCCAAAAATT
ATCTCGAAATTCACAAATCTCTCAGTAGAGACTATTTATGTGAGCAGGACACCGGTTACA
AAGGGTGGAGATGATGACTCGTTTTCTACAAAATGAGCAGGGCAAGACGAAATTTCCGAA
CTATAATTCTACCTCTATGTTTAGGAGCTTTTCCCAATCATATAATCAAAACGACGGCCA
CATTTAGTCTCACATGGCGCTTAATTATGTTTAATTTTGTCTCTCCTTACGTACTTATAT
GGCATAGCTTAGAGCGCTTTCACCACTTAAAATCCATCTCACATCTGCAATGTATGGTCA
AAATGAATATGGCTAAATCGTAATCGAAGAGAGTACTTATTAATGGGGGAATATTTTATT
AAAGATCAAGGTAACTTTATTGTTTAGTTCTGTGCGGCCTTGTTTTAAGCATTGTAAAGA
AAAATATCTACTCGGTGATTCATGTCCAAGGTATTGAGATACATAGATAACGATAACTAT
AAAAAAGTGGGAATAAGATATACACATACATATCTGCAAACCAAAAATAAGTGTCACCGT
TGACAGGAAACATCACTCGAAAATTTGGGTCCACTTACTCATAAGTTAGCTATTCCAATA
AATATTGTAACTGGGCGTTTCAAACATACAAGTGTATATTACTCCAGGATTGATGATCAA
AGTCATTCAAAGGCGCTGCCGAAAAAAATTGGTAGAAGATGAAAAAAAAAATCGAACAAC
GGGTAAACGAGCAATCCTTATTCGGTGCGGTGATTGGCCTGAGGCAACATACACTCTTGA
TTTATAAAAAAAAGCAAGTGTGTAGGTTGCTAGCAAACTCGGTGCGTCATTCTATTGTTC
CTGATTTATTGGCCTATTTAGCTATATAAAAAGAAAATTTTGCAATTTCCTTAAATTGTG
ACTTACTCTAGATATCCGTATTAAGAAAACTGGTAAAACC
>MIT_Sbay_c77_8808 YGL040C 5' untranslated region, Contig c77 1 - 1377, 2000 bp (revcom)
TTTACTGTTTTTGGGTAATTAGCTTATTCATGATATGACAATTTCATATCAATCCACTCG
GCTTACCTTAAACATGATGTCTGACATCGCCATAACGACTAAATAAAGTCTGTGAGTCTC
TGTGTTCAGACAGGAGAGTACCTTTTGAAGTATTATTGAATATGAATTTATTGTTTAGTT
CTATGTATCTCTACTTAAACTTTATCCCAATATATTTCGTGTTTCCTTGTCCACATATTG
CAACAAATATATAAAGAAATTTTAAAGGGACAAATAAACTAGCATGTAAATTAACGATAG
ATTAACAAAAATATTTCTATTCATATGGTTTTATACTCAATATAAGAATTACTACATGAT
GTACTTATGCGTAAATCAAGCAGTGTCTGTAGATAAACCACGCAAAATAAGATATATTTG
CGACGAAACAATTTATCGTAAAGAAACAACGAAATGTGAAGCAAGATATTTACATTTGAC
ATGCAATTATTGTAGTAAGAATGGTGTCACCGTTAACAACAAAAAGATCTAAAAAACAAT
TACAGAATACACCCGCCATACATGTAAAGTTTTTATCACTCTCTTACTGAAGTTCTTTAT
CATGATGTTTAGAAAGAATTTACATTGAAGGATTGGCATCCATCATCAATATGATTTGTT
CATATCTTTACCTGCGTGCCCTAAAATATGACAGTCCAGTCATTGAAGACTAATGATCAA
AATTTTTCGAAAACGCTGCCAAATAGAAAAAGGCAAAAAATGAAAAATTTGGTGCACAAC
GGTAAACGAGCATCTCCGGGCGGTGCGGTGATTGGCCTGCGGCAGGCTGCCTGATTTATA
AAAGAGCAAGGCAACACAATAAAAGGCTAGTGACGTCTATGCATCACTCTATTGTTAATG
TTAGTTCATAGCCCATTCCACGACATAAAACGGTAATTTTGTAATTTATACGTATTGTTA
CTTCTTCCAGATATCCTTACCAGAAAAACACTGACAAAGT
>WashU_Skud_Contig2052.17 YGL040C 5' untranslated region, Contig c2052 29967 - 31966, 2000 bp (revcom)
GTAATTCTCAGGTGATGTAGTTTTCCTTCGTTCAGCCATGACGGAAACTACATAAGAGAG
TATAATTTTTGAACATTTTAGATATCTCAATCTTGTTCAATTGTATCTACCAAGCAACAT
CGACGAAAGATGAGTCACAACTGACAAACAGAGAAAGCTTTATGGGGATGTGTGAAAAAC
GATTTATTGTTTAGTTGTCCTTCACCATTCTTTCGCCTTCATAGGAAGAAAGTAAGAAAA
CGGTATTCACCCATCCTAATACAGTGGCATATGTATAAAGAAAAATTCAAGTTAGAAAAC
AAACCAATGCGGCAGTTATTGTTTGTTCAGTGCTAATGTATTTATGGGTTCCTTTTCTTC
AATTGAGACATGAAAAAGAACTACTACCTGATAAACTCTATAGTAAATCAATCAGCACCT
GTAAATAAATGCTGCATATCTGGAATTACAAGCAATCGCAAAAAAAAAAGAAAAGACGAA
ACAAGATGTCCAGATTACCGTACGAAAAAAGGAAGAGTCTTCATCGACGCTAAAACACAA
ATTCAAGAAGATGTCAGGAATATAAGGCCATTTGCAAAAAACTCACATTATTATTTCCTG
ATATTAAATCCTCTAGAGGCCTTGATTATTTATTACGAGTAAAATTTACCGATTTGCCTA
CCTTTGTGCCGTGAAAACACGAACATAAATCATTTCAAGATCAATGACCAAGACATTCAA
AAACGGCGTCAAAAAAAAAAAAGTAGATGATGCGGAAAATGAAAAACTTTGAACGCAACG
GGTAAACGAGCAATCCCTGTTCGGTGCGGTGATTGGCCTGAGGCAAGCTGCCTGCCCAAT
TTATAAAAGAGAAAGGCAACTTATATGAAGAGTAGTGACGTCTATGCGTCATCCTATTGT
TCATGATTTCTGGCTAAATTAGCTATATAAGTGGAAGTTTTGTGGTTTCCACATATTAAT
ATTTTCTCCAGGCATCCATATCAGAAAACACTGACAAATC
BioPerl-1.007002/t/data/map_hem/HEM1-HEM2.meme.txt000444000766000024     12020513155576321 21204 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM1-HEM2.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDR232W         1.0000    498  MIT_Spar_c117_4603       1.0000    498  
MIT_Smik_c228_4055       1.0000    498  WashU_Skud_Contig2069.5  1.0000    498  
WashU_Sbay_Contig461.5   1.0000    498  SGD_Scer_YGL040C         1.0000   1000  
MIT_Spar_c19_8512        1.0000   1000  MIT_Smik_c273_7756       1.0000   1000  
MIT_Sbay_c77_8808        1.0000   1000  WashU_Skud_Contig2052.17 1.0000   1000  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM1-HEM2.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=       10    maxsites=       10    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            7490    N=              10
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.310 C 0.190 G 0.190 T 0.310 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =  10   llr = 251   E-value = 7.9e-043
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  1::::a15::aa::a:::55
pos.-specific     C  :8a:a:::aa:::5:5a:55
probability       G  92:6::95:::::5:5:a::
matrix            T  :::4::::::::a:::::::

         bits    2.5   * *   **      **  
                 2.3   * *   **      **  
                 2.0 * * * * **      **  
                 1.8 *** * * **      **  
Information      1.5 *** *** **********  
content          1.3 ******* **********  
(36.3 bits)      1.0 ********************
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GCCGCAGACCAATCACCGAA
consensus             G T   G     G G  CC
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Sbay_c77_8808            +    178  4.37e-13 CAGGCAGCCT GCCGCAGGCCAATCACCGCA CCGCCCGGAG
WashU_Skud_Contig2069.5      +    362  1.24e-12 AGCGTCCGCG GCCGCAGACCAATGAGCGAC GAAGGCGGCC
MIT_Spar_c117_4603           +    360  1.24e-12 AGCGCCCGCG GCCGCAGACCAATGAGCGAC GAAGGCGGCC
SGD_Scer_YDR232W             +    365  1.24e-12 AGCGCCCGCG GCCGCAGACCAATGAGCGAC GAAGGCGGCC
WashU_Skud_Contig2052.17     +    177  1.99e-12 CAGGCAGCTT GCCTCAGGCCAATCACCGCA CCGAACAGGG
MIT_Smik_c273_7756           +    176  1.99e-12 AGTGTATGTT GCCTCAGGCCAATCACCGCA CCGAATAAGG
MIT_Spar_c19_8512            +    178  1.99e-12 CGGGCAGCTT GCCTCAGGCCAATCACCGCA CCGAACAGGG
WashU_Sbay_Contig461.5       +    359  4.86e-12 AACGCCGGCG GGCGCAGACCAATGAGCGAC GAAGACGGCT
SGD_Scer_YGL040C             +    177  1.62e-11 CGGGAAGCTT GCCTCAAGCCAATCACCGCA CCGAACAGGG
MIT_Smik_c228_4055           +    362  2.67e-11 AGCGCCCGCA AGCGCAGACCAATGAGCGAC GAAAGCGGCC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Sbay_c77_8808                 4.4e-13  177_[+1]_803
WashU_Skud_Contig2069.5           1.2e-12  361_[+1]_117
MIT_Spar_c117_4603                1.2e-12  359_[+1]_119
SGD_Scer_YDR232W                  1.2e-12  364_[+1]_114
WashU_Skud_Contig2052.17            2e-12  176_[+1]_804
MIT_Smik_c273_7756                  2e-12  175_[+1]_805
MIT_Spar_c19_8512                   2e-12  177_[+1]_803
WashU_Sbay_Contig461.5            4.9e-12  358_[+1]_120
SGD_Scer_YGL040C                  1.6e-11  176_[+1]_804
MIT_Smik_c228_4055                2.7e-11  361_[+1]_117
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=10
MIT_Sbay_c77_8808        (  178) GCCGCAGGCCAATCACCGCA  1 
WashU_Skud_Contig2069.5  (  362) GCCGCAGACCAATGAGCGAC  1 
MIT_Spar_c117_4603       (  360) GCCGCAGACCAATGAGCGAC  1 
SGD_Scer_YDR232W         (  365) GCCGCAGACCAATGAGCGAC  1 
WashU_Skud_Contig2052.17 (  177) GCCTCAGGCCAATCACCGCA  1 
MIT_Smik_c273_7756       (  176) GCCTCAGGCCAATCACCGCA  1 
MIT_Spar_c19_8512        (  178) GCCTCAGGCCAATCACCGCA  1 
WashU_Sbay_Contig461.5   (  359) GGCGCAGACCAATGAGCGAC  1 
SGD_Scer_YGL040C         (  177) GCCTCAAGCCAATCACCGCA  1 
MIT_Smik_c228_4055       (  362) AGCGCAGACCAATGAGCGAC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7300 bayes= 9.50978 E= 7.9e-043 
  -169   -997    236   -997 
  -997    219     19   -997 
  -997    251   -997   -997 
  -997   -997    177     30 
  -997    251   -997   -997 
   162   -997   -997   -997 
  -169   -997    236   -997 
    62   -997    151   -997 
  -997    251   -997   -997 
  -997    251   -997   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
  -997   -997   -997    162 
  -997    151    151   -997 
   162   -997   -997   -997 
  -997    151    151   -997 
  -997    251   -997   -997 
  -997   -997    251   -997 
    62    151   -997   -997 
    62    151   -997   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 7.9e-043 
 0.100000  0.000000  0.900000  0.000000 
 0.000000  0.800000  0.200000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.600000  0.400000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.100000  0.000000  0.900000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.500000  0.500000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
G[CG]C[GT]CAG[AG]CCAAT[CG]A[CG]CG[AC][AC]
--------------------------------------------------------------------------------




Time  5.77 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =  10   llr = 206   E-value = 2.0e-023
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  9659a4:5:1a9:::aa:6:
pos.-specific     C  1:5::::::7::::a::422
probability       G  ::::::a5a::1aa:::51:
matrix            T  :4:1:6:::2:::::::118

         bits    2.5       * *   ***     
                 2.3       * *   ***     
                 2.0       * *   ***     
                 1.8       * *   ***     
Information      1.5     * * * * *****   
content          1.3 *  ** * * *******   
(29.7 bits)      1.0 * *** ************ *
                 0.8 ****************** *
                 0.5 ****************** *
                 0.3 ********************
                 0.0 --------------------

Multilevel           AAAAATGAGCAAGGCAAGAT
consensus             TC  A G T       CCC
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig461.5       +    279  6.64e-13 ACCGGGACAG AACAATGGGCAAGGCAAGAT GAAAAATCTC
MIT_Smik_c228_4055           +    284  6.64e-13 ATTGAATTAG AACAATGGGCAAGGCAAGAT GAAAATTTCC
MIT_Spar_c117_4603           +    281  6.64e-13 CATGGGTCAG AACAATGGGCAAGGCAAGAT GAAAAATTTC
SGD_Scer_YDR232W             +    286  6.64e-13 CATGGATCAG AACAATGGGCAAGGCAAGAT GAAAAATTTC
MIT_Sbay_c77_8808            -    144  2.57e-10 TGCCTGATTT ATAAAAGAGCAAGGCAACAC AATAAAAGGC
WashU_Skud_Contig2069.5      +    284  3.77e-10 ACTGGATCGG AACAATGGGCAAGGCAATGT GAAAAATTTC
MIT_Spar_c19_8512            -    140  1.08e-09 CGCTTGATTT ATAAAAGAGTAAGGCAACCT AATAAATGCT
MIT_Smik_c273_7756           -    833  1.52e-09 TCGTTTTCTA CAAAATGAGCAGGGCAAGAC GAAATTTCCG
WashU_Skud_Contig2052.17     -    139  3.25e-09 TGCCCAATTT ATAAAAGAGAAAGGCAACTT ATATGAAGAG
SGD_Scer_YGL040C             -    139  3.61e-09 CGCTTGATTT ATATAAGAGTAAGGCAACCT AATAAATGCT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig461.5            6.6e-13  278_[+2]_200
MIT_Smik_c228_4055                6.6e-13  283_[+2]_195
MIT_Spar_c117_4603                6.6e-13  280_[+2]_198
SGD_Scer_YDR232W                  6.6e-13  285_[+2]_193
MIT_Sbay_c77_8808                 2.6e-10  143_[-2]_837
WashU_Skud_Contig2069.5           3.8e-10  283_[+2]_195
MIT_Spar_c19_8512                 1.1e-09  139_[-2]_841
MIT_Smik_c273_7756                1.5e-09  832_[-2]_148
WashU_Skud_Contig2052.17          3.3e-09  138_[-2]_842
SGD_Scer_YGL040C                  3.6e-09  138_[-2]_842
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=10
WashU_Sbay_Contig461.5   (  279) AACAATGGGCAAGGCAAGAT  1 
MIT_Smik_c228_4055       (  284) AACAATGGGCAAGGCAAGAT  1 
MIT_Spar_c117_4603       (  281) AACAATGGGCAAGGCAAGAT  1 
SGD_Scer_YDR232W         (  286) AACAATGGGCAAGGCAAGAT  1 
MIT_Sbay_c77_8808        (  144) ATAAAAGAGCAAGGCAACAC  1 
WashU_Skud_Contig2069.5  (  284) AACAATGGGCAAGGCAATGT  1 
MIT_Spar_c19_8512        (  140) ATAAAAGAGTAAGGCAACCT  1 
MIT_Smik_c273_7756       (  833) CAAAATGAGCAGGGCAAGAC  1 
WashU_Skud_Contig2052.17 (  139) ATAAAAGAGAAAGGCAACTT  1 
SGD_Scer_YGL040C         (  139) ATATAAGAGTAAGGCAACCT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7300 bayes= 9.50978 E= 2.0e-023 
   147    -81   -997   -997 
    89   -997   -997     30 
    62    151   -997   -997 
   147   -997   -997   -169 
   162   -997   -997   -997 
    30   -997   -997     89 
  -997   -997    251   -997 
    62   -997    151   -997 
  -997   -997    251   -997 
  -169    199   -997    -70 
   162   -997   -997   -997 
   147   -997    -81   -997 
  -997   -997    251   -997 
  -997   -997    251   -997 
  -997    251   -997   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
  -997    119    151   -169 
    89     19    -81   -169 
  -997     19   -997    130 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.0e-023 
 0.900000  0.100000  0.000000  0.000000 
 0.600000  0.000000  0.000000  0.400000 
 0.500000  0.500000  0.000000  0.000000 
 0.900000  0.000000  0.000000  0.100000 
 1.000000  0.000000  0.000000  0.000000 
 0.400000  0.000000  0.000000  0.600000 
 0.000000  0.000000  1.000000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.100000  0.700000  0.000000  0.200000 
 1.000000  0.000000  0.000000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.400000  0.500000  0.100000 
 0.600000  0.200000  0.100000  0.100000 
 0.000000  0.200000  0.000000  0.800000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
A[AT][AC]AA[TA]G[AG]G[CT]AAGGCAA[GC][AC][TC]
--------------------------------------------------------------------------------




Time 11.41 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =  10   llr = 182   E-value = 4.3e-014
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  ::::1:::a5::::2:::1:
pos.-specific     C  :6:a:4:5:5a8:::51156
probability       G  54::5::::::29:131213
matrix            T  5:a:46a5::::1a728731

         bits    2.5    *      *         
                 2.3    *      *         
                 2.0    *      * *       
                 1.8    *      ***       
Information      1.5  ***  * * ****      
content          1.3  ***  * * ****      
(26.3 bits)      1.0 **** *********  *  *
                 0.8 ************** *** *
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GCTCGTTCAACCGTTCTTCC
consensus            TG  TC T C G  AG GTG
sequence                            T    
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c273_7756           +    209  2.78e-11 AATAAGGATT GCTCGTTTACCCGTTGTTCG ATTTTTTTTT
MIT_Spar_c117_4603           -    160  3.34e-11 CCTGCTCTGC TCTCTCTCAACCGTTCTTCC TTTACACGCC
WashU_Skud_Contig2069.5      -    162  7.41e-11 TGTGCTCTGC TGTCTCTCAACCGTTCTTCC CTCCACACGG
SGD_Scer_YDR232W             -    165  7.41e-11 CCTGCTCTGC TGTCTCTCAACCGTTCTTCC TTTACACGCC
WashU_Sbay_Contig461.5       -    161  6.43e-10 CCTGCTCTGT TGTCTCTCAACGGTTCTTCC CTCCACACGC
MIT_Spar_c19_8512            +    211  1.23e-09 AACAGGGATT GCTCGTTTACCCGTAGTTTG AATTTTTTTT
SGD_Scer_YGL040C             +    210  3.72e-09 AACAGGGATT GCTCGTTTACCCGTATTTTG ATTTTTTTTT
MIT_Smik_c228_4055           -    161  8.54e-09 CCTCCTCTAC TGTCATTCAACCGTTCTGGC TTCACACGTC
WashU_Skud_Contig2052.17     +    210  1.35e-08 AACAGGGATT GCTCGTTTACCCGTTGCGTT CAAAGTTTTT
MIT_Sbay_c77_8808            +    210  2.19e-07 GCCCGGAGAT GCTCGTTTACCGTTGTGCAC CAAATTTTTC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c273_7756                2.8e-11  208_[+3]_772
MIT_Spar_c117_4603                3.3e-11  159_[-3]_319
WashU_Skud_Contig2069.5           7.4e-11  161_[-3]_317
SGD_Scer_YDR232W                  7.4e-11  164_[-3]_314
WashU_Sbay_Contig461.5            6.4e-10  160_[-3]_318
MIT_Spar_c19_8512                 1.2e-09  210_[+3]_770
SGD_Scer_YGL040C                  3.7e-09  209_[+3]_771
MIT_Smik_c228_4055                8.5e-09  160_[-3]_318
WashU_Skud_Contig2052.17          1.3e-08  209_[+3]_771
MIT_Sbay_c77_8808                 2.2e-07  209_[+3]_771
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=10
MIT_Smik_c273_7756       (  209) GCTCGTTTACCCGTTGTTCG  1 
MIT_Spar_c117_4603       (  160) TCTCTCTCAACCGTTCTTCC  1 
WashU_Skud_Contig2069.5  (  162) TGTCTCTCAACCGTTCTTCC  1 
SGD_Scer_YDR232W         (  165) TGTCTCTCAACCGTTCTTCC  1 
WashU_Sbay_Contig461.5   (  161) TGTCTCTCAACGGTTCTTCC  1 
MIT_Spar_c19_8512        (  211) GCTCGTTTACCCGTAGTTTG  1 
SGD_Scer_YGL040C         (  210) GCTCGTTTACCCGTATTTTG  1 
MIT_Smik_c228_4055       (  161) TGTCATTCAACCGTTCTGGC  1 
WashU_Skud_Contig2052.17 (  210) GCTCGTTTACCCGTTGCGTT  1 
MIT_Sbay_c77_8808        (  210) GCTCGTTTACCGTTGTGCAC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7300 bayes= 9.50978 E= 4.3e-014 
  -997   -997    151     62 
  -997    177    119   -997 
  -997   -997   -997    162 
  -997    251   -997   -997 
  -169   -997    151     30 
  -997    119   -997     89 
  -997   -997   -997    162 
  -997    151   -997     62 
   162   -997   -997   -997 
    62    151   -997   -997 
  -997    251   -997   -997 
  -997    219     19   -997 
  -997   -997    236   -169 
  -997   -997   -997    162 
   -70   -997    -81    111 
  -997    151     77    -70 
  -997    -81    -81    130 
  -997    -81     19    111 
  -169    151    -81    -11 
  -997    177     77   -169 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 4.3e-014 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.600000  0.400000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.100000  0.000000  0.500000  0.400000 
 0.000000  0.400000  0.000000  0.600000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.500000  0.000000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.800000  0.200000  0.000000 
 0.000000  0.000000  0.900000  0.100000 
 0.000000  0.000000  0.000000  1.000000 
 0.200000  0.000000  0.100000  0.700000 
 0.000000  0.500000  0.300000  0.200000 
 0.000000  0.100000  0.100000  0.800000 
 0.000000  0.100000  0.200000  0.700000 
 0.100000  0.500000  0.100000  0.300000 
 0.000000  0.600000  0.300000  0.100000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
[GT][CG]TC[GT][TC]T[CT]A[AC]C[CG]GT[TA][CGT]T[TG][CT][CG]
--------------------------------------------------------------------------------




Time 17.19 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =  10   llr = 181   E-value = 1.3e-014
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  :::::::1::1211:1:9:9
pos.-specific     C  :::a8:17:6:1:7:1913:
probability       G  8:1:2:91::::3:221:1:
matrix            T  2a9::a:1a4976286::61

         bits    2.5    *                
                 2.3    *                
                 2.0    *  *         *   
                 1.8    ** *         *   
Information      1.5 ** **** *       *   
content          1.3 ******* ***     ** *
(26.1 bits)      1.0 ***********  ** ** *
                 0.8 ***********  ** ****
                 0.5 *************** ****
                 0.3 ********************
                 0.0 --------------------

Multilevel           GTTCCTGCTCTTTCTTCATA
consensus            T   G    T AGTGG  C 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c228_4055           +    314  1.23e-12 GAAAATTTCC GTTCCTGCTCTTTCTTCATA TATGAACAAT
MIT_Spar_c117_4603           +    312  1.23e-12 AAAAATTTCT GTTCCTGCTCTTTCTTCATA TATGAACAAT
SGD_Scer_YDR232W             +    317  1.23e-12 AAAAATTTCC GTTCCTGCTCTTTCTTCATA TATGAACAAT
WashU_Skud_Contig2069.5      +    315  2.56e-12 AAAAATTTCC GTTCCTGCTCTTGCTTCATA TATGACAATG
WashU_Sbay_Contig461.5       +    310  7.98e-11 AAAAATCTCC GTTCCTGCTCTTGCTTGATA TATTAACAAT
MIT_Spar_c19_8512            -    909  2.03e-10 ATCTACAATA GTTCCTGCTTTTTTTTCACA TCTATTTTCA
WashU_Skud_Contig2052.17     +    317  7.48e-08 AATGATTTAT GTTCGTGTTTTCACGGCACA AAGGTAGGCA
MIT_Smik_c273_7756           -     85  8.28e-08 TCATTCTATT GTTCCTGATTTATTGGCCTA TTTAGCTATA
MIT_Sbay_c77_8808            +    596  3.07e-07 ATATCTTATT TTGCGTGGTTTATCTACAGA CACTGCTTGA
SGD_Scer_YGL040C             -    741  3.58e-07 GACGGTTAGC TTTCCTCCTCATGATCCACT CTTTCGGGAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c228_4055                1.2e-12  313_[+4]_165
MIT_Spar_c117_4603                1.2e-12  311_[+4]_167
SGD_Scer_YDR232W                  1.2e-12  316_[+4]_162
WashU_Skud_Contig2069.5           2.6e-12  314_[+4]_164
WashU_Sbay_Contig461.5              8e-11  309_[+4]_169
MIT_Spar_c19_8512                   2e-10  908_[-4]_72
WashU_Skud_Contig2052.17          7.5e-08  316_[+4]_664
MIT_Smik_c273_7756                8.3e-08  84_[-4]_896
MIT_Sbay_c77_8808                 3.1e-07  595_[+4]_385
SGD_Scer_YGL040C                  3.6e-07  740_[-4]_240
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=10
MIT_Smik_c228_4055       (  314) GTTCCTGCTCTTTCTTCATA  1 
MIT_Spar_c117_4603       (  312) GTTCCTGCTCTTTCTTCATA  1 
SGD_Scer_YDR232W         (  317) GTTCCTGCTCTTTCTTCATA  1 
WashU_Skud_Contig2069.5  (  315) GTTCCTGCTCTTGCTTCATA  1 
WashU_Sbay_Contig461.5   (  310) GTTCCTGCTCTTGCTTGATA  1 
MIT_Spar_c19_8512        (  909) GTTCCTGCTTTTTTTTCACA  1 
WashU_Skud_Contig2052.17 (  317) GTTCGTGTTTTCACGGCACA  1 
MIT_Smik_c273_7756       (   85) GTTCCTGATTTATTGGCCTA  1 
MIT_Sbay_c77_8808        (  596) TTGCGTGGTTTATCTACAGA  1 
SGD_Scer_YGL040C         (  741) TTTCCTCCTCATGATCCACT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7300 bayes= 9.50978 E= 1.3e-014 
  -997   -997    219    -70 
  -997   -997   -997    162 
  -997   -997    -81    147 
  -997    251   -997   -997 
  -997    219     19   -997 
  -997   -997   -997    162 
  -997    -81    236   -997 
  -169    199    -81   -169 
  -997   -997   -997    162 
  -997    177   -997     30 
  -169   -997   -997    147 
   -70    -81   -997    111 
  -169   -997     77     89 
  -169    199   -997    -70 
  -997   -997     19    130 
  -169    -81     19     89 
  -997    236    -81   -997 
   147    -81   -997   -997 
  -997     77    -81     89 
   147   -997   -997   -169 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 1.3e-014 
 0.000000  0.000000  0.800000  0.200000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.100000  0.900000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.800000  0.200000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.100000  0.900000  0.000000 
 0.100000  0.700000  0.100000  0.100000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.600000  0.000000  0.400000 
 0.100000  0.000000  0.000000  0.900000 
 0.200000  0.100000  0.000000  0.700000 
 0.100000  0.000000  0.300000  0.600000 
 0.100000  0.700000  0.000000  0.200000 
 0.000000  0.000000  0.200000  0.800000 
 0.100000  0.100000  0.200000  0.600000 
 0.000000  0.900000  0.100000  0.000000 
 0.900000  0.100000  0.000000  0.000000 
 0.000000  0.300000  0.100000  0.600000 
 0.900000  0.000000  0.000000  0.100000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
[GT]TTC[CG]TGCT[CT]T[TA][TG][CT][TG][TG]CA[TC]A
--------------------------------------------------------------------------------




Time 22.88 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =  10   llr = 171   E-value = 6.2e-010
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  :a91:9:29997843:1221
pos.-specific     C  9::1:1961:::2:524861
probability       G  ::1:a:::::12:6:73:18
matrix            T  1::8::12:1:1::212:1:

         bits    2.5     *               
                 2.3     *               
                 2.0 *   * *             
                 1.8 *   * *             
Information      1.5 **  * *          * *
content          1.3 *** *** ***  * * * *
(24.7 bits)      1.0 *** *** *** ** * * *
                 0.8 ************** * ***
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CAATGACCAAAAAGCGCCCG
consensus                   A   GCAACGAA 
sequence                    T      T T   
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c228_4055           +    340  1.95e-13 CATATATGAA CAATGACCAAAAAGCGCCCG CAAGCGCAGA
MIT_Spar_c117_4603           +    338  1.95e-13 CATATATGAA CAATGACCAAAAAGCGCCCG CGGCCGCAGA
SGD_Scer_YDR232W             +    343  1.95e-13 CATATATGAA CAATGACCAAAAAGCGCCCG CGGCCGCAGA
WashU_Skud_Contig2069.5      +    340  2.44e-12 TCATATATGA CAATGACCAAAAAGCGTCCG CGGCCGCAGA
WashU_Sbay_Contig461.5       +    336  1.31e-10 GATATATTAA CAATGACCAAAAAAACGCCG GCGGGCGCAG
MIT_Smik_c273_7756           +    527  5.44e-08 TTTTTCTTTA CAATGCTTAAAACAAGGCCG CACAGAACTA
SGD_Scer_YGL040C             +     97  4.33e-07 GCAAGAAAAT CAAAGACAATAGAGTGGCGC ATAGATGTTG
MIT_Spar_c19_8512            -    459  5.04e-07 TGTGAAGATT CAGTGACACAAGAGCCAAAG AAGGCAAAAC
MIT_Sbay_c77_8808            -    889  9.84e-07 GACATCGCCA TAACGACTAAATAAAGTCTG TGAGTCTCTG
WashU_Skud_Contig2052.17     -    280  1.03e-06 ATTTCAAGAT CAATGACCAAGACATTCAAA AACGGCGTCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c228_4055                1.9e-13  339_[+5]_139
MIT_Spar_c117_4603                1.9e-13  337_[+5]_141
SGD_Scer_YDR232W                  1.9e-13  342_[+5]_136
WashU_Skud_Contig2069.5           2.4e-12  339_[+5]_139
WashU_Sbay_Contig461.5            1.3e-10  335_[+5]_143
MIT_Smik_c273_7756                5.4e-08  526_[+5]_454
SGD_Scer_YGL040C                  4.3e-07  96_[+5]_884
MIT_Spar_c19_8512                   5e-07  458_[-5]_522
MIT_Sbay_c77_8808                 9.8e-07  888_[-5]_92
WashU_Skud_Contig2052.17            1e-06  279_[-5]_701
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=10
MIT_Smik_c228_4055       (  340) CAATGACCAAAAAGCGCCCG  1 
MIT_Spar_c117_4603       (  338) CAATGACCAAAAAGCGCCCG  1 
SGD_Scer_YDR232W         (  343) CAATGACCAAAAAGCGCCCG  1 
WashU_Skud_Contig2069.5  (  340) CAATGACCAAAAAGCGTCCG  1 
WashU_Sbay_Contig461.5   (  336) CAATGACCAAAAAAACGCCG  1 
MIT_Smik_c273_7756       (  527) CAATGCTTAAAACAAGGCCG  1 
SGD_Scer_YGL040C         (   97) CAAAGACAATAGAGTGGCGC  1 
MIT_Spar_c19_8512        (  459) CAGTGACACAAGAGCCAAAG  1 
MIT_Sbay_c77_8808        (  889) TAACGACTAAATAAAGTCTG  1 
WashU_Skud_Contig2052.17 (  280) CAATGACCAAGACATTCAAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7300 bayes= 9.50978 E= 6.2e-010 
  -997    236   -997   -169 
   162   -997   -997   -997 
   147   -997    -81   -997 
  -169    -81   -997    130 
  -997   -997    251   -997 
   147    -81   -997   -997 
  -997    236   -997   -169 
   -70    177   -997    -70 
   147    -81   -997   -997 
   147   -997   -997   -169 
   147   -997    -81   -997 
   111   -997     19   -169 
   130     19   -997   -997 
    30   -997    177   -997 
   -11    151   -997    -70 
  -997     19    199   -169 
  -169    119     77    -70 
   -70    219   -997   -997 
   -70    177    -81   -169 
  -169    -81    219   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 6.2e-010 
 0.000000  0.900000  0.000000  0.100000 
 1.000000  0.000000  0.000000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
 0.100000  0.100000  0.000000  0.800000 
 0.000000  0.000000  1.000000  0.000000 
 0.900000  0.100000  0.000000  0.000000 
 0.000000  0.900000  0.000000  0.100000 
 0.200000  0.600000  0.000000  0.200000 
 0.900000  0.100000  0.000000  0.000000 
 0.900000  0.000000  0.000000  0.100000 
 0.900000  0.000000  0.100000  0.000000 
 0.700000  0.000000  0.200000  0.100000 
 0.800000  0.200000  0.000000  0.000000 
 0.400000  0.000000  0.600000  0.000000 
 0.300000  0.500000  0.000000  0.200000 
 0.000000  0.200000  0.700000  0.100000 
 0.100000  0.400000  0.300000  0.200000 
 0.200000  0.800000  0.000000  0.000000 
 0.200000  0.600000  0.100000  0.100000 
 0.100000  0.100000  0.800000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
CAATGAC[CAT]AAA[AG][AC][GA][CAT][GC][CGT][CA][CA]G
--------------------------------------------------------------------------------




Time 28.31 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR232W                 5.36e-38  124_[+2(1.97e-05)]_20_[-3(7.41e-11)]_101_[+2(6.64e-13)]_11_[+4(1.23e-12)]_6_[+5(1.95e-13)]_2_[+1(1.24e-12)]_114
MIT_Spar_c117_4603               2.49e-38  [-4(3.67e-05)]_139_[-3(3.34e-11)]_101_[+2(6.64e-13)]_11_[+4(1.23e-12)]_6_[+5(1.95e-13)]_2_[+1(1.24e-12)]_119
MIT_Smik_c228_4055               9.65e-35  120_[+2(2.17e-05)]_20_[-3(8.54e-09)]_47_[-1(1.92e-05)]_36_[+2(6.64e-13)]_10_[+4(1.23e-12)]_6_[+5(1.95e-13)]_2_[+1(2.67e-11)]_117
WashU_Skud_Contig2069.5          5.35e-34  82_[-4(9.25e-05)]_15_[-4(3.28e-05)]_24_[-3(7.41e-11)]_102_[+2(3.77e-10)]_11_[+4(2.56e-12)]_5_[+5(2.44e-12)]_2_[+1(1.24e-12)]_17_[+1(1.48e-05)]_80
WashU_Sbay_Contig461.5           4.36e-32  160_[-3(6.43e-10)]_9_[+1(4.95e-05)]_69_[+2(6.64e-13)]_11_[+4(7.98e-11)]_6_[+5(1.31e-10)]_3_[+1(4.86e-12)]_26_[+2(1.02e-05)]_74
SGD_Scer_YGL040C                 4.10e-19  96_[+5(4.33e-07)]_22_[-2(3.61e-09)]_18_[+1(1.62e-11)]_13_[+3(3.72e-09)]_511_[-4(3.58e-07)]_240
MIT_Spar_c19_8512                7.03e-24  97_[+5(2.06e-05)]_22_[-2(1.08e-09)]_18_[+1(1.99e-12)]_13_[+3(1.23e-09)]_228_[-5(5.04e-07)]_430_[-4(2.03e-10)]_72
MIT_Smik_c273_7756               9.66e-24  84_[-4(8.28e-08)]_71_[+1(1.99e-12)]_13_[+3(2.78e-11)]_298_[+5(5.44e-08)]_17_[-2(1.20e-05)]_249_[-2(1.52e-09)]_148
MIT_Sbay_c77_8808                1.01e-19  143_[-2(2.57e-10)]_14_[+1(4.37e-13)]_12_[+3(2.19e-07)]_366_[+4(3.07e-07)]_147_[+2(1.67e-05)]_106_[-5(9.84e-07)]_92
WashU_Skud_Contig2052.17         9.16e-20  138_[-2(3.25e-09)]_18_[+1(1.99e-12)]_13_[+3(1.35e-08)]_50_[-5(1.03e-06)]_17_[+4(7.48e-08)]_245_[-1(8.62e-05)]_184_[-3(9.67e-05)]_195
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM1-HEM3.fa000444000766000024      2003113155576321 20006 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR232W HEM1 "5-aminolevulinate synthase, catalyzes the first step in the heme biosynthetic pathway; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expression is regulated by Hap2p-Hap3p"
ACTGAAAAAAAAACCTAAGTACTGTTATGATTATTGAGGGACAACAACTAGCTCTATTAG
TTTTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTGGG
ATAAAAAAAAAAGAAACGCGAGCTGAGAAGGGAAGGCGTGTAAAGGAAGAACGGTTGAGA
GACAGCAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGAATGGAGAAG
TTTGGTATGATGCAAACGTTGTATTTCTAACAACGCATGGATCAGAACAATGGGCAAGGC
AAGATGAAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCC
CGCGGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGCGGTAGGGTAAGCCGTGC
AGGCAAGCTTATTATAGCACCGTCGGGGGTACCACCACTATATCAAACTCCACTGCTCGG
TAAAGCATTGTAGTGAAG
>MIT_Spar_c117_4603 YDR232W 5' untranslated region, Contig c117 17441 - 19440, 2000 bp (revcom)
ACTGAAAAAAAACCAAGTACTGTTGTGATTATTGAGGGACAACGGCTAGCTCTATTTGTT
TTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTAGGAT
AAAAAAAGAAACGCGAGCTGAGAAGAGAAGGCGTGTAAAGGAAGAACGGTTGAGAGAGAG
CAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGGATGGAGGAGTTTGG
TACGATGCAAACGCTATATTTGTAGCAACGCATGGGTCAGAACAATGGGCAAGGCAAGAT
GAAAAATTTCTGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGCGG
CCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGTGGTAGGGTAAGCCGTGCAGGCA
AGCTTATTATAGCACCGTCGGGGGGACCACTATATCAAGTTCCACAGCACGGTGAAGCAT
TGCAGTATAGTTCACAGC
>MIT_Smik_c228_4055 YDR232W 5' untranslated region, Contig c228 4702 - 6701(revcom), 2000 bp (revcom)
ACCGAGAGAAAAACTAAGTAGTGATATGATTATTGAGGACTAATGACCAGCTTTGTTTGT
TTTTTCTTCCAACCTAACTTATATGGGAAATATATAGGACAGAAAAAAGAAAAGAGCACG
AAAAAAAAGAAATGCGACCTGAGAAGGGAGGACGTGTGAAGCCAGAACGGTTGAATGACA
GTAGAGGAGGGTGCAACACAACCGAGTAGAGTACCAGCTGACGGAATGGAGGAGTTTGGT
ATGATGCAAAAGTGATGCTTTTAGCAACGCAACATTGAATTAGAACAATGGGCAAGGCAA
GATGAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGC
AAGCGCAGACCAATGAGCGACGAAAGCGGCCTTTTGAAGGGTAGGGTAATCCATGCAGGC
AAGTTTATTATAGCACCGTCGGGGGGAAGCATTATATCAAACTCCACAGTACAGCGTAAC
ATTGCTGTATAGGCTACA
>WashU_Skud_Contig2069.5 YDR232W 5' untranslated region, Contig c2069 5476 - 7475, 2000 bp (revcom)
ACTGAAAATAATCCGAGTCGTGCTACTGTGAATATTGAGAATAGGGACTAGCTCTATTTG
ATTTTTCTTCCAACCAAACTTATATGGAAAATATAAAGGAAAGAAAAAAGAAAAGAATAG
GAAAAAAAAAAAGAAACGCGAGAGAAGAGAACCGTGTGGAGGGAAGAACGGTTGAGAGAC
AGCAGAGCACAGCGCAACACAACCGAGTAGAGTACCAGCAGACGGAGTGGGTAGTTTGGT
ACAGTGTAAAAGCTATATTTCCACCAACGCAACACTGGATCGGAACAATGGGCAAGGCAA
TGTGAAAAATTTCCGTTCCTGCTCTTGCTTCATATATGACAATGACCAAAAAGCGTCCGC
GGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCGTAGCAGCAGGGTAAGCCGCGCAAG
CAAGTCCGTCATAACACCGTCGAAGGGGCACCACTATATCAGCTCTTCAGCATGGTAGGC
CATTACAGCACAGTCTTG
>WashU_Sbay_Contig461.5 YDR232W 5' untranslated region, Contig c461 4000 - 5999, 2000 bp (revcom)
ACTAAAAAGTCCAAGTGGTGCTGTTATTATTGAGGATAGCAACTAGCTTTATTTGTTTTT
TCTTCCAACCAAACTTATATGGAAATCAAAGGAAGGAAAAAAAGAAAAGAACAGGAAGAA
AAAAAAGAAACGTGAGCTGCCGAAAGGAGAGCGTGTGGAGGGAAGAACCGTTGAGAGACA
ACAGAGCAGGGTGCAAACCGATTAGAGTACCAGCAGACGAGATGGGCGATGTGGTACGGT
GCAGAAGGTGTGGTTCCAACAGCGCAGCACCGGGACAGAACAATGGGCAAGGCAAGATGA
AAAATCTCCGTTCCTGCTCTTGCTTGATATATTAACAATGACCAAAAAAACGCCGGCGGG
CGCAGACCAATGAGCGACGAAGACGGCTTTTGGGCGGGGCAGGGTAAGATGGGACAGGCA
AGGTCCGCTATAGCACCGTCGAGGGGGACCGCTATATCAGCTCCCAGTACATTGCAGCAC
ACTCTATAGCTAGTCAAA
>SGD_Scer_YDL205C HEM3 "Phorphobilinogen deaminase, catalyzes the conversion of 4-porphobilinogen to hydroxymethylbilane, the third step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; expression is regulated by Hap2p-Hap3p"
AGTACGTGTGTATTTACCAACTACAAATTTATCTAGATTTTCTTCGCTTTTCTTTTTTTC
TATTGTTCTAGATATTAATACGGGATGAGAAGAACAGAATATTCAAAATCTAATACAGCC
CTGTACCATGCAAACACGAGCGTCAATCTGCCAATGACCTTGAATTCAGGCTATGTGTAG
CAATAATACAGATAGTTAGTAGCCTCGTTTATATAAAGCGTTCCTTTACTTTTTCATTTT
CTTTCTTTTTTTATGTTTGATTTTTTTACTTTTTCACTTTAAAAAATTGCTGAAATTTTC
GTAGCCAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCTCCC
CAGGGTCAATTGACAAGGAGAGAAGGAATGTTATATGGGAATTGCTGCGTAAAGATGGTC
AAAAATCCTGGACTGCCGTACGAACGACAATGTAAGGATGACTGCATTAGCCAGAAAGAC
ATCTTTACCCCCGGTGCTGCCAGGGAGCAAAATAATTACGAAAAGTGGACGCAAAGTTAA
CTTAAACTACAAGGGTAGCAGCAGAATGTGTCGGTGGTACCGGTGTGATAATGCCCCATT
TGAGATGCTTGTAATTGTGGCCTAGCAATAAGAACGCAAGGCGTTTTTGTTGAAAGGAGA
ACAAGGTTAGACGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTCACCCTTAT
TTCCACCCTCAAACGATAAAGCTTGCTACTTTGATGAAAAAAATATATAAAAGGGATTGA
AAAGCAGATCAATTATGTAGCAATAGTAGTAATAACTTGTTCAATTGCTTGTCTCAACTT
GCCACAAACTATCATCAACA
>MIT_Spar_c429_3020 YDL205C 5' untranslated region, Contig c429 77420 - 79419(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTATCAACTACAAAATTTATCTAGATTTTCTTGCCTTTTCCTTTTTC
TATTGTTCTAGATACTAATACGGGATGAGAAGAACAGAATATTCAAAATGTAAAACAGCC
CTGTACCATGCAAACACGAGCCTCAATCTGCCAATGACCTTGAATCCAAGCTATGTGTAG
CAATAATACAGATGATTGATTGGCGTCGTTTATATAAAGCGTTCCTTCATTTTTTTCATT
TTCTTTCTTTTTTTATGTTTGATTTTTTACTTTTTCACTTTTGAAAACTGCTGAAATTTT
CGTAGCAAAAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCT
CCCCAGGGTCAATTGACAAGGAGAGAAGGAATGTTACATCCAGGAATTGCGACATAAAGA
TGTCCAAGAAGTCTGAACTGTCATACGAATGGCTATGCAAGGAGGATAGTACTGGTCAAG
AAGACATCTTACCCCCGGTGCTGTCAGGGAGCAAAAAAATGACAAAAGTGGACGCAAAGT
TAACTTGAACTACAAGGGTAGCAACAGAATGTCGGTGGTACCGGATGTGACAAAGCTCAC
TTGAGGTGCTTCTTGTTGCGGCATAGCAATAAGAGCGCAAGGCGTTTTTATGGAAAGGAG
AGCGAGGTTAGAGGGTGACGTTTAGGCGCATAGGCAACCTCCCCTTATTGTTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGTCTACATTGATGAAAAAAATGTATAAAAGGGATT
GAAAAGCCGATCATGTGTGTAGCAATAGTAGTAGTTATACTTGTTCAATTGCTTGCTTGC
ACTTTTCCAAAAACTACCAC
>MIT_Smik_c193_2483 YDL205C 5' untranslated region, Contig c193 6380 - 8379(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTACCAACTATAAAATTTTACCTAGACTATCTGGCCTTTTTCTTTTT
TCTATTGTTCTAGATACTAATACGGGATGAAAAGAACAGAATATTCAAAAAGTAATACAG
CCCTGTACCATTCAAACACGAGCGCCAATTTGCCAATGAACTTGAAATCCAGCTATGCGT
AGCGATAATACAGATGATTGTTTGATGTCGTTTATATTAAGCGTTCCTTCAGTTTTTCTC
ATTTTCTTTCTTTTTCTATGTTTTATTTTTCACTTTTTCACTTTTGAAAATTGCTGAAAT
TTTCGTAACAAAAAAAGAGGCCTTCATTGCTTACTCATCGTTATCTTATTGGTTAAAATC
CCCAGCGACAATGTACAAGGAGAGAAGAAATGATATGTCTGGGAATTGCAGTTTGAAGAT
ATCCAAAGAGTTTTGAAGTGCCATACGAGCAACCACGTGAGAAGTAGAGCCTTAACAGAA
AATTCATCTTACCCCTAGTACTGCCAGGGAGGAACTAAACCTAAGAACTAGTGTTAACTT
GACTTGAACTGCAAGGGTAGCGACGGCGTATGTCGGTGGTACCGGATATGGCAAGAGCCC
ATTTGAGCTGCTTGTTCTTGTGACATACTATTAAGAGCGCAAGGCGTTTATGGAAAGGAG
GACAAGGTCAGAGGATGACGTTTAAGCGCATAGGCAATCTCCCCTTATTATTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGCTGCGCTGTTGAAAAGTATATAAAAGGGATAGAA
AAGCAGAGCAATTATAATTTAGTAGAATAGCTTATTCTATCGTTAACTTGTTGAAAGGAT
CAGATTATTATCAAGATGAA
>MIT_Sbay_c841_3215 YDL205C 5' untranslated region, Contig c841 7323 - 9322(revcom), 2000 bp (revcom)
AGTATGTGTATATTTACCAACTATAGAGTATATCTAGTATTTTTTTTCCTTCTTCTTTTT
CTATTGTTCTAGATGCTAATATGGGATGAGTAGAACAAAATATTCAAAACGCAATACAGC
CCTGTACCATTCAAATACGAACGCCAATCTGCCAATGACCTTGAAATCAAGTTATGTGCC
GCGATAATACAATCTTTTGGCCTATATCGTTTAAATAAGCGTTCCTTTAATTTTTCGGTT
TCTTTCTTTTTTATGTCTAATTTTTCATTTTTTTTCACTTGAAAATTGCTGAAATTTTCG
TAGCTGAAAAAGAGAGGCCTTCTTTGCTTACTCATCGTTATCTTATTGGTCAAGAGCCCA
AGGGACAATAGACAAGGAGAGAACCACCAACTTTGGGAGTTGGATGCAAAGAAGGTCTTT
GATTTTGGGCTGCTATCAGAGCGGGCCATATAAGGAAGCTTGTAGTGGTTAGGAGAGAAC
ACGTCATTACCCCCCTCCCCCTTCTCCGCGCTGCCAGGGACCAGGCAAGGGCTTGCAAGA
GATGAACGTAAGATAGAACTACGAGGGTCGCGGCCAATGTGTCGGTAGTACCGGATGGGG
CAAAGCCCAATTGAGGTGCTTGTTGTTGAGGATGGTCGGCATGGCATGGCATGGGAGGCC
AAAGGCGCTTTGTGGGAAGGAGAACAAACAACATTAGAGGGTGACGTTTTAGCGCATAGG
CAATCTCCCCTTATTGTTCACCCTTATTTCCACCCTCAAACGACAAGGCTTGTTATGTTG
GTTGGAAATATATAAAAGGGATTGAAAAAGATCATATTCCTACATAAATTATGGTATTAG
TTTTTCTTCAATTGCTGGCT
>WashU_Skud_Contig1850.5 YDL205C 5' untranslated region, Contig c1850 6875 - 8874(revcom), 2000 bp (revcom)
GATACGTGTGTATTTGCTAACTATAAAATTTATCTAGTTTTCCTGCTTTTTTTTTTTTCT
ATTGTTCTAGAAACTAATATGGGGATGAGAAGAACAAAATTTTCAAAAAGCAATACAGCC
CTGTACCATTCAAACACGAACGCCAATCTGCAATGACCTTGAAATCAATCTATGTGTCGC
GATAATACAAGTGATTGATTGGTGTCGTTTATATAAAGCGTTCCTTCAATTTTTTCATTT
TCTTTCTTTTTTTATGTTTAATTTTCTACCTTTTTCACTTTTGAAAATTGCTGAAATTTT
CGTAGCAAAAAAAGAGAGGCGTACGTTGCTTACTCATCGTTTTCTTATTGGTCAAAAGCT
CCAGGAACAATGCCCAAGGAGAGAAAGAGTGCTACGTCTAGGAATTGCGATGGAAAGGCG
TCCAAGAGTCCTAAACTACCATGAGAACGGGCCACCCAAGGAGGGATAGCAATTGCTGAA
ACAACATCTTCACCTTCGGAGCTGGCAGGGAGCAAGGGACTCTCCGGAAAGAAAGTGAAC
GCAAAACGGAACTACAAGGATAGCAACGGAATGTGTCGGTGGTAGCGGATGTGGCAAGAT
CCCATTTCAGGAGCTTGTTGTTACGGCACAGCAGCAAGAAGAGCACAAGGCTTTTTCCGT
AAAGGAGAACAAAGTTGGAAGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTC
ACCCTTATTTCCACCCTCAAAGGATAAAGCTTGTTGCATTGATAAAAAATGTATAAAAAG
GATGGGAAACAGATGATAGTTAACAAGGTAGTGGGACGGTCTTTCGCTTATTCAGTTGTG
TGACATTCAAGGGTTACAAT
BioPerl-1.007002/t/data/map_hem/HEM1-HEM3.meme.txt000444000766000024     11565313155576321 21220 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM1-HEM3.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDR232W         1.0000    498  MIT_Spar_c117_4603       1.0000    498  
MIT_Smik_c228_4055       1.0000    498  WashU_Skud_Contig2069.5  1.0000    498  
WashU_Sbay_Contig461.5   1.0000    498  SGD_Scer_YDL205C         1.0000    860  
MIT_Spar_c429_3020       1.0000    860  MIT_Smik_c193_2483       1.0000    860  
MIT_Sbay_c841_3215       1.0000    860  WashU_Skud_Contig1850.5  1.0000    860  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM1-HEM3.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=       10    maxsites=       10    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            6790    N=              10
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.293 C 0.207 G 0.207 T 0.293 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =  10   llr = 225   E-value = 3.0e-032
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :68:aa:1:4:aa::55a:9
pos.-specific     C  1::a::::11a::::5::::
probability       G  94:::::785:::aa:5:91
matrix            T  ::2:::a21:::::::::1:

         bits    2.5    *      *  **     
                 2.3    *      *  **     
                 2.0 *  *      *  **   * 
                 1.8 *  *      *  **   * 
Information      1.5 *  **** * *****  ** 
content          1.3 *  **** * *****  ***
(32.4 bits)      1.0 ********* **********
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GAACAATGGGCAAGGAAAGA
consensus             GT    T A     CG   
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig461.5       +    278  1.41e-12 CACCGGGACA GAACAATGGGCAAGGCAAGA TGAAAAATCT
MIT_Smik_c228_4055           +    283  1.41e-12 CATTGAATTA GAACAATGGGCAAGGCAAGA TGAAAATTTC
MIT_Spar_c117_4603           +    280  1.41e-12 GCATGGGTCA GAACAATGGGCAAGGCAAGA TGAAAAATTT
SGD_Scer_YDR232W             +    285  1.41e-12 GCATGGATCA GAACAATGGGCAAGGCAAGA TGAAAAATTT
MIT_Sbay_c841_3215           +    363  6.65e-11 AGAGCCCAAG GGACAATAGACAAGGAGAGA ACCACCAACT
WashU_Skud_Contig1850.5      +    365  1.00e-10 AAAGCTCCAG GAACAATGCCCAAGGAGAGA AAGAGTGCTA
MIT_Spar_c429_3020           +    367  1.18e-10 CGCTCCCCAG GGTCAATTGACAAGGAGAGA AGGAATGTTA
SGD_Scer_YDL205C             +    364  1.18e-10 CGCTCCCCAG GGTCAATTGACAAGGAGAGA AGGAATGTTA
WashU_Skud_Contig2069.5      +    283  1.74e-10 CACTGGATCG GAACAATGGGCAAGGCAATG TGAAAAATTT
MIT_Smik_c193_2483           +    366  3.73e-10 AAATCCCCAG CGACAATGTACAAGGAGAGA AGAAATGATA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig461.5            1.4e-12  277_[+1]_201
MIT_Smik_c228_4055                1.4e-12  282_[+1]_196
MIT_Spar_c117_4603                1.4e-12  279_[+1]_199
SGD_Scer_YDR232W                  1.4e-12  284_[+1]_194
MIT_Sbay_c841_3215                6.6e-11  362_[+1]_478
WashU_Skud_Contig1850.5             1e-10  364_[+1]_476
MIT_Spar_c429_3020                1.2e-10  366_[+1]_474
SGD_Scer_YDL205C                  1.2e-10  363_[+1]_477
WashU_Skud_Contig2069.5           1.7e-10  282_[+1]_196
MIT_Smik_c193_2483                3.7e-10  365_[+1]_475
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=10
WashU_Sbay_Contig461.5   (  278) GAACAATGGGCAAGGCAAGA  1 
MIT_Smik_c228_4055       (  283) GAACAATGGGCAAGGCAAGA  1 
MIT_Spar_c117_4603       (  280) GAACAATGGGCAAGGCAAGA  1 
SGD_Scer_YDR232W         (  285) GAACAATGGGCAAGGCAAGA  1 
MIT_Sbay_c841_3215       (  363) GGACAATAGACAAGGAGAGA  1 
WashU_Skud_Contig1850.5  (  365) GAACAATGCCCAAGGAGAGA  1 
MIT_Spar_c429_3020       (  367) GGTCAATTGACAAGGAGAGA  1 
SGD_Scer_YDL205C         (  364) GGTCAATTGACAAGGAGAGA  1 
WashU_Skud_Contig2069.5  (  283) GAACAATGGGCAAGGCAATG  1 
MIT_Smik_c193_2483       (  366) CGACAATGTACAAGGAGAGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6600 bayes= 9.36413 E= 3.0e-032 
  -997    -81    236   -997 
    89   -997    119   -997 
   130   -997   -997    -70 
  -997    251   -997   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
  -997   -997   -997    162 
  -169   -997    199    -70 
  -997    -81    219   -169 
    30    -81    151   -997 
  -997    251   -997   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
  -997   -997    251   -997 
  -997   -997    251   -997 
    62    151   -997   -997 
    62   -997    151   -997 
   162   -997   -997   -997 
  -997   -997    236   -169 
   147   -997    -81   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.0e-032 
 0.000000  0.100000  0.900000  0.000000 
 0.600000  0.000000  0.400000  0.000000 
 0.800000  0.000000  0.000000  0.200000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.100000  0.000000  0.700000  0.200000 
 0.000000  0.100000  0.800000  0.100000 
 0.400000  0.100000  0.500000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.900000  0.100000 
 0.900000  0.000000  0.100000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
G[AG][AT]CAAT[GT]G[GA]CAAGG[AC][AG]AGA
--------------------------------------------------------------------------------




Time  4.86 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =  10   llr = 213   E-value = 1.1e-027
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  :::a::::::5343::::13
pos.-specific     C  a:5::::::9::52296593
probability       G  ::::::aa:::7157::5:4
matrix            T  :a5:aa::a15:::114:::

         bits    2.5 *     **            
                 2.3 *     **            
                 2.0 *     ** *     *  * 
                 1.8 *     ** *     *  * 
Information      1.5 ** *******     * ** 
content          1.3 ** ******* *  ***** 
(30.7 bits)      1.0 ********** *  ***** 
                 0.8 ********** *********
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CTCATTGGTCAGCGGCCCCG
consensus              T       TAAAC TG A
sequence                          C     C
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2069.5      -    358  1.23e-13 GCCTTCGTCG CTCATTGGTCTGCGGCCGCG GACGCTTTTT
MIT_Spar_c117_4603           -    356  1.23e-13 GCCTTCGTCG CTCATTGGTCTGCGGCCGCG GGCGCTTTTT
SGD_Scer_YDR232W             -    361  1.23e-13 GCCTTCGTCG CTCATTGGTCTGCGGCCGCG GGCGCTTTTT
WashU_Sbay_Contig461.5       -    355  4.09e-12 GTCTTCGTCG CTCATTGGTCTGCGCCCGCC GGCGTTTTTT
MIT_Spar_c429_3020           +    344  8.68e-11 TCATCGGTTT CTTATTGGTCAGACGCTCCC CAGGGTCAAT
SGD_Scer_YDL205C             +    341  8.68e-11 TCATCGGTTT CTTATTGGTCAGACGCTCCC CAGGGTCAAT
MIT_Smik_c228_4055           -    358  3.24e-10 GCTTTCGTCG CTCATTGGTCTGCGCTTGCG GGCGCTTTTT
WashU_Skud_Contig1850.5      +    344  5.80e-10 TCATCGTTTT CTTATTGGTCAAAAGCTCCA GGAACAATGC
MIT_Sbay_c841_3215           +    342  2.64e-09 TCATCGTTAT CTTATTGGTCAAGAGCCCAA GGGACAATAG
MIT_Smik_c193_2483           +    345  5.92e-09 TCATCGTTAT CTTATTGGTTAAAATCCCCA GCGACAATGT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2069.5           1.2e-13  357_[-2]_121
MIT_Spar_c117_4603                1.2e-13  355_[-2]_123
SGD_Scer_YDR232W                  1.2e-13  360_[-2]_118
WashU_Sbay_Contig461.5            4.1e-12  354_[-2]_124
MIT_Spar_c429_3020                8.7e-11  343_[+2]_497
SGD_Scer_YDL205C                  8.7e-11  340_[+2]_500
MIT_Smik_c228_4055                3.2e-10  357_[-2]_121
WashU_Skud_Contig1850.5           5.8e-10  343_[+2]_497
MIT_Sbay_c841_3215                2.6e-09  341_[+2]_499
MIT_Smik_c193_2483                5.9e-09  344_[+2]_496
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=10
WashU_Skud_Contig2069.5  (  358) CTCATTGGTCTGCGGCCGCG  1 
MIT_Spar_c117_4603       (  356) CTCATTGGTCTGCGGCCGCG  1 
SGD_Scer_YDR232W         (  361) CTCATTGGTCTGCGGCCGCG  1 
WashU_Sbay_Contig461.5   (  355) CTCATTGGTCTGCGCCCGCC  1 
MIT_Spar_c429_3020       (  344) CTTATTGGTCAGACGCTCCC  1 
SGD_Scer_YDL205C         (  341) CTTATTGGTCAGACGCTCCC  1 
MIT_Smik_c228_4055       (  358) CTCATTGGTCTGCGCTTGCG  1 
WashU_Skud_Contig1850.5  (  344) CTTATTGGTCAAAAGCTCCA  1 
MIT_Sbay_c841_3215       (  342) CTTATTGGTCAAGAGCCCAA  1 
MIT_Smik_c193_2483       (  345) CTTATTGGTTAAAATCCCCA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6600 bayes= 9.36413 E= 1.1e-027 
  -997    251   -997   -997 
  -997   -997   -997    162 
  -997    151   -997     62 
   162   -997   -997   -997 
  -997   -997   -997    162 
  -997   -997   -997    162 
  -997   -997    251   -997 
  -997   -997    251   -997 
  -997   -997   -997    162 
  -997    236   -997   -169 
    62   -997   -997     62 
   -11   -997    199   -997 
    30    151    -81   -997 
   -11     19    151   -997 
  -997     19    199   -169 
  -997    236   -997   -169 
  -997    177   -997     30 
  -997    151    151   -997 
  -169    236   -997   -997 
   -11     77    119   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 1.1e-027 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.500000  0.000000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.900000  0.000000  0.100000 
 0.500000  0.000000  0.000000  0.500000 
 0.300000  0.000000  0.700000  0.000000 
 0.400000  0.500000  0.100000  0.000000 
 0.300000  0.200000  0.500000  0.000000 
 0.000000  0.200000  0.700000  0.100000 
 0.000000  0.900000  0.000000  0.100000 
 0.000000  0.600000  0.000000  0.400000 
 0.000000  0.500000  0.500000  0.000000 
 0.100000  0.900000  0.000000  0.000000 
 0.300000  0.300000  0.400000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
CT[CT]ATTGGTC[AT][GA][CA][GAC][GC]C[CT][CG]C[GAC]
--------------------------------------------------------------------------------




Time  9.68 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   15   sites =  10   llr = 175   E-value = 1.1e-018
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :51:a:::::576::
pos.-specific     C  ::5a:aa5:a:::4:
probability       G  ::4::::5::5346a
matrix            T  a5::::::a::::::

         bits    2.5    * **  *    *
                 2.3    * **  *    *
                 2.0    * **  *    *
                 1.8    * **  *    *
Information      1.5 *  *******   **
content          1.3 *  *******   **
(25.2 bits)      1.0 * *************
                 0.8 * *************
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           TACCACCCTCAAAGG
consensus             TG    G  GGGC 
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Sbay_Contig461.5       +    431  1.76e-09 AGGTCCGCTA TAGCACCGTCGAGGG GGACCGCTAT
MIT_Smik_c228_4055           +    431  3.51e-09 AAGTTTATTA TAGCACCGTCGGGGG GAAGCATTAT
MIT_Spar_c117_4603           +    430  3.51e-09 AAGCTTATTA TAGCACCGTCGGGGG GACCACTATA
SGD_Scer_YDR232W             +    435  3.51e-09 AAGCTTATTA TAGCACCGTCGGGGG TACCACCACT
WashU_Skud_Contig1850.5      +    729  7.37e-09 TCACCCTTAT TTCCACCCTCAAAGG ATAAAGCTTG
MIT_Sbay_c841_3215           +    748  1.49e-08 TCACCCTTAT TTCCACCCTCAAACG ACAAGGCTTG
MIT_Smik_c193_2483           +    722  1.49e-08 TCACCCTTAT TTCCACCCTCAAACG ATAAAGCTTG
MIT_Spar_c429_3020           +    722  1.49e-08 TCACCCTTAT TTCCACCCTCAAACG ATAAAGCTTG
SGD_Scer_YDL205C             +    721  1.49e-08 TCACCCTTAT TTCCACCCTCAAACG ATAAAGCTTG
WashU_Skud_Contig2069.5      +    432  2.21e-08 AAGTCCGTCA TAACACCGTCGAAGG GGCACCACTA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig461.5            1.8e-09  430_[+3]_53
MIT_Smik_c228_4055                3.5e-09  430_[+3]_53
MIT_Spar_c117_4603                3.5e-09  429_[+3]_54
SGD_Scer_YDR232W                  3.5e-09  434_[+3]_49
WashU_Skud_Contig1850.5           7.4e-09  728_[+3]_117
MIT_Sbay_c841_3215                1.5e-08  747_[+3]_98
MIT_Smik_c193_2483                1.5e-08  721_[+3]_124
MIT_Spar_c429_3020                1.5e-08  721_[+3]_124
SGD_Scer_YDL205C                  1.5e-08  720_[+3]_125
WashU_Skud_Contig2069.5           2.2e-08  431_[+3]_52
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=15 seqs=10
WashU_Sbay_Contig461.5   (  431) TAGCACCGTCGAGGG  1 
MIT_Smik_c228_4055       (  431) TAGCACCGTCGGGGG  1 
MIT_Spar_c117_4603       (  430) TAGCACCGTCGGGGG  1 
SGD_Scer_YDR232W         (  435) TAGCACCGTCGGGGG  1 
WashU_Skud_Contig1850.5  (  729) TTCCACCCTCAAAGG  1 
MIT_Sbay_c841_3215       (  748) TTCCACCCTCAAACG  1 
MIT_Smik_c193_2483       (  722) TTCCACCCTCAAACG  1 
MIT_Spar_c429_3020       (  722) TTCCACCCTCAAACG  1 
SGD_Scer_YDL205C         (  721) TTCCACCCTCAAACG  1 
WashU_Skud_Contig2069.5  (  432) TAACACCGTCGAAGG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 6650 bayes= 9.37504 E= 1.1e-018 
  -997   -997   -997    162 
    62   -997   -997     62 
  -169    151    119   -997 
  -997    251   -997   -997 
   162   -997   -997   -997 
  -997    251   -997   -997 
  -997    251   -997   -997 
  -997    151    151   -997 
  -997   -997   -997    162 
  -997    251   -997   -997 
    62   -997    151   -997 
   111   -997     77   -997 
    89   -997    119   -997 
  -997    119    177   -997 
  -997   -997    251   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 1.1e-018 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.100000  0.500000  0.400000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.700000  0.000000  0.300000  0.000000 
 0.600000  0.000000  0.400000  0.000000 
 0.000000  0.400000  0.600000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
T[AT][CG]CACC[CG]TC[AG][AG][AG][GC]G
--------------------------------------------------------------------------------




Time 14.37 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =  10   llr = 206   E-value = 1.9e-024
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  4:a612::5:::::4214::
pos.-specific     C  5::1::5::a4:::32:6:7
probability       G  1a:398:a5:5:::168:a2
matrix            T  ::::::5:::1aaa2:1::1

         bits    2.5  *     * *        * 
                 2.3  *     * *        * 
                 2.0  *  *  * *        * 
                 1.8  *  *  * *        * 
Information      1.5  ** ** * * ***  * * 
content          1.3  ** ** * * ***  ****
(29.7 bits)      1.0  ** ********** *****
                 0.8 ************** *****
                 0.5 ************** *****
                 0.3 ********************
                 0.0 --------------------

Multilevel           CGAAGGCGACGTTTAGGCGC
consensus            A  G AT G C   CA A G
sequence                           TC    
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
SGD_Scer_YDR232W             +    384  9.38e-12 CAATGAGCGA CGAAGGCGGCCTTTCCGAGC GGTAGGGTAA
MIT_Spar_c429_3020           +    670  1.07e-11 GAGCGAGGTT AGAGGGTGACGTTTAGGCGC ATAGGCAACC
WashU_Skud_Contig1850.5      +    677  3.00e-11 GAACAAAGTT GGAAGGTGACGTTTAGGCGC ATAGGCAATC
SGD_Scer_YDL205C             +    669  5.20e-11 GAACAAGGTT AGACGGTGACGTTTAGGCGC ATAGGCAATC
WashU_Skud_Contig2069.5      +    381  7.97e-11 CAATGAGCGA CGAAGGCGGCCTTTCGTAGC AGCAGGGTAA
MIT_Sbay_c841_3215           +    696  2.22e-10 AAACAACATT AGAGGGTGACGTTTTAGCGC ATAGGCAATC
MIT_Spar_c117_4603           +    379  2.42e-10 CAATGAGCGA CGAAGGCGGCCTTTCCGAGT GGTAGGGTAA
MIT_Smik_c193_2483           +    670  7.21e-10 GGACAAGGTC AGAGGATGACGTTTAAGCGC ATAGGCAATC
WashU_Sbay_Contig461.5       +    378  1.03e-09 CAATGAGCGA CGAAGACGGCTTTTGGGCGG GGCAGGGTAA
MIT_Smik_c228_4055           +    381  5.22e-09 CAATGAGCGA CGAAAGCGGCCTTTTGAAGG GTAGGGTAAT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR232W                  9.4e-12  383_[+4]_95
MIT_Spar_c429_3020                1.1e-11  669_[+4]_171
WashU_Skud_Contig1850.5             3e-11  676_[+4]_164
SGD_Scer_YDL205C                  5.2e-11  668_[+4]_172
WashU_Skud_Contig2069.5             8e-11  380_[+4]_98
MIT_Sbay_c841_3215                2.2e-10  695_[+4]_145
MIT_Spar_c117_4603                2.4e-10  378_[+4]_100
MIT_Smik_c193_2483                7.2e-10  669_[+4]_171
WashU_Sbay_Contig461.5              1e-09  377_[+4]_101
MIT_Smik_c228_4055                5.2e-09  380_[+4]_98
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=10
SGD_Scer_YDR232W         (  384) CGAAGGCGGCCTTTCCGAGC  1 
MIT_Spar_c429_3020       (  670) AGAGGGTGACGTTTAGGCGC  1 
WashU_Skud_Contig1850.5  (  677) GGAAGGTGACGTTTAGGCGC  1 
SGD_Scer_YDL205C         (  669) AGACGGTGACGTTTAGGCGC  1 
WashU_Skud_Contig2069.5  (  381) CGAAGGCGGCCTTTCGTAGC  1 
MIT_Sbay_c841_3215       (  696) AGAGGGTGACGTTTTAGCGC  1 
MIT_Spar_c117_4603       (  379) CGAAGGCGGCCTTTCCGAGT  1 
MIT_Smik_c193_2483       (  670) AGAGGATGACGTTTAAGCGC  1 
WashU_Sbay_Contig461.5   (  378) CGAAGACGGCTTTTGGGCGG  1 
MIT_Smik_c228_4055       (  381) CGAAAGCGGCCTTTTGAAGG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6600 bayes= 9.36413 E= 1.9e-024 
    30    151    -81   -997 
  -997   -997    251   -997 
   162   -997   -997   -997 
    89    -81     77   -997 
  -169   -997    236   -997 
   -70   -997    219   -997 
  -997    151   -997     62 
  -997   -997    251   -997 
    62   -997    151   -997 
  -997    251   -997   -997 
  -997    119    151   -169 
  -997   -997   -997    162 
  -997   -997   -997    162 
  -997   -997   -997    162 
    30     77    -81    -70 
   -70     19    177   -997 
  -169   -997    219   -169 
    30    177   -997   -997 
  -997   -997    251   -997 
  -997    199     19   -169 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 1.9e-024 
 0.400000  0.500000  0.100000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.600000  0.100000  0.300000  0.000000 
 0.100000  0.000000  0.900000  0.000000 
 0.200000  0.000000  0.800000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.000000  1.000000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.400000  0.500000  0.100000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.400000  0.300000  0.100000  0.200000 
 0.200000  0.200000  0.600000  0.000000 
 0.100000  0.000000  0.800000  0.100000 
 0.400000  0.600000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.700000  0.200000  0.100000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
[CA]GA[AG]G[GA][CT]G[AG]C[GC]TTT[ACT][GAC]G[CA]G[CG]
--------------------------------------------------------------------------------




Time 18.89 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   15   sites =  10   llr = 163   E-value = 1.8e-014
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  ::::::::4::::::
pos.-specific     C  a7:116a::84a11:
probability       G  ::9:14::61::::6
matrix            T  :3198::a:16:994

         bits    2.5 *     *    *   
                 2.3 *     *    *   
                 2.0 * *   *    *   
                 1.8 * *   *    *   
Information      1.5 * *  *** * *   
content          1.3 **** ***** ****
(23.5 bits)      1.0 ***************
                 0.8 ***************
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           CCGTTCCTGCTCTTG
consensus             T   G  A C   T
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Sbay_Contig461.5       +    308  2.85e-10 TGAAAAATCT CCGTTCCTGCTCTTG CTTGATATAT
WashU_Skud_Contig2069.5      +    313  2.85e-10 TGAAAAATTT CCGTTCCTGCTCTTG CTTCATATAT
MIT_Smik_c228_4055           +    312  1.62e-09 ATGAAAATTT CCGTTCCTGCTCTTT CTTCATATAT
SGD_Scer_YDR232W             +    315  1.62e-09 TGAAAAATTT CCGTTCCTGCTCTTT CTTCATATAT
MIT_Spar_c117_4603           +    310  1.17e-08 TGAAAAATTT CTGTTCCTGCTCTTT CTTCATATAT
MIT_Smik_c193_2483           -    552  1.46e-08 CCGACATACG CCGTCGCTACCCTTG CAGTTCAAGT
MIT_Spar_c429_3020           -    553  1.46e-08 CACCGACATT CTGTTGCTACCCTTG TAGTTCAAGT
WashU_Skud_Contig1850.5      -    555  4.54e-08 CCGACACATT CCGTTGCTATCCTTG TAGTTCCGTT
SGD_Scer_YDL205C             -    550  6.46e-08 CCGACACATT CTGCTGCTACCCTTG TAGTTTAAGT
MIT_Sbay_c841_3215           -    516  1.21e-06 TCTTGCAAGC CCTTGCCTGGTCCCT GGCAGCGCGG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig461.5            2.8e-10  307_[+5]_176
WashU_Skud_Contig2069.5           2.8e-10  312_[+5]_171
MIT_Smik_c228_4055                1.6e-09  311_[+5]_172
SGD_Scer_YDR232W                  1.6e-09  314_[+5]_169
MIT_Spar_c117_4603                1.2e-08  309_[+5]_174
MIT_Smik_c193_2483                1.5e-08  551_[-5]_294
MIT_Spar_c429_3020                1.5e-08  552_[-5]_293
WashU_Skud_Contig1850.5           4.5e-08  554_[-5]_291
SGD_Scer_YDL205C                  6.5e-08  549_[-5]_296
MIT_Sbay_c841_3215                1.2e-06  515_[-5]_330
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=15 seqs=10
WashU_Sbay_Contig461.5   (  308) CCGTTCCTGCTCTTG  1 
WashU_Skud_Contig2069.5  (  313) CCGTTCCTGCTCTTG  1 
MIT_Smik_c228_4055       (  312) CCGTTCCTGCTCTTT  1 
SGD_Scer_YDR232W         (  315) CCGTTCCTGCTCTTT  1 
MIT_Spar_c117_4603       (  310) CTGTTCCTGCTCTTT  1 
MIT_Smik_c193_2483       (  552) CCGTCGCTACCCTTG  1 
MIT_Spar_c429_3020       (  553) CTGTTGCTACCCTTG  1 
WashU_Skud_Contig1850.5  (  555) CCGTTGCTATCCTTG  1 
SGD_Scer_YDL205C         (  550) CTGCTGCTACCCTTG  1 
MIT_Sbay_c841_3215       (  516) CCTTGCCTGGTCCCT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 6650 bayes= 9.37504 E= 1.8e-014 
  -997    251   -997   -997 
  -997    199   -997    -11 
  -997   -997    236   -169 
  -997    -81   -997    147 
  -997    -81    -81    130 
  -997    177    119   -997 
  -997    251   -997   -997 
  -997   -997   -997    162 
    30   -997    177   -997 
  -997    219    -81   -169 
  -997    119   -997     89 
  -997    251   -997   -997 
  -997    -81   -997    147 
  -997    -81   -997    147 
  -997   -997    177     30 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 1.8e-014 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.700000  0.000000  0.300000 
 0.000000  0.000000  0.900000  0.100000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  0.100000  0.100000  0.800000 
 0.000000  0.600000  0.400000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.400000  0.000000  0.600000  0.000000 
 0.000000  0.800000  0.100000  0.100000 
 0.000000  0.400000  0.000000  0.600000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  0.000000  0.600000  0.400000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
C[CT]GTT[CG]CT[GA]C[TC]CTT[GT]
--------------------------------------------------------------------------------




Time 23.30 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR232W                 1.98e-32  284_[+1(1.41e-12)]_10_[+5(1.62e-09)]_31_[-2(1.23e-13)]_3_[+4(9.38e-12)]_31_[+3(3.51e-09)]_49
MIT_Spar_c117_4603               2.87e-30  279_[+1(1.41e-12)]_10_[+5(1.17e-08)]_31_[-2(1.23e-13)]_3_[+4(2.42e-10)]_31_[+3(3.51e-09)]_54
MIT_Smik_c228_4055               1.44e-26  282_[+1(1.41e-12)]_9_[+5(1.62e-09)]_31_[-2(3.24e-10)]_3_[+4(5.22e-09)]_30_[+3(3.51e-09)]_53
WashU_Skud_Contig2069.5          1.65e-29  111_[-5(2.14e-05)]_156_[+1(1.74e-10)]_10_[+5(2.85e-10)]_30_[-2(1.23e-13)]_3_[+4(7.97e-11)]_31_[+3(2.21e-08)]_52
WashU_Sbay_Contig461.5           4.83e-30  185_[-2(9.76e-05)]_72_[+1(1.41e-12)]_10_[+5(2.85e-10)]_32_[-2(4.09e-12)]_3_[+4(1.03e-09)]_11_[-5(1.98e-05)]_7_[+3(1.76e-09)]_53
SGD_Scer_YDL205C                 6.25e-24  48_[-1(4.94e-05)]_272_[+2(8.68e-11)]_3_[+1(1.18e-10)]_166_[-5(6.46e-08)]_104_[+4(5.20e-11)]_32_[+3(1.49e-08)]_125
MIT_Spar_c429_3020               3.47e-25  41_[-1(2.08e-05)]_282_[+2(8.68e-11)]_3_[+1(1.18e-10)]_166_[-5(1.46e-08)]_46_[-2(5.52e-05)]_36_[+4(1.07e-11)]_32_[+3(1.49e-08)]_124
MIT_Smik_c193_2483               2.83e-21  344_[+2(5.92e-09)]_1_[+1(3.73e-10)]_166_[-5(1.46e-08)]_[-3(3.86e-06)]_88_[+4(7.21e-10)]_32_[+3(1.49e-08)]_124
MIT_Sbay_c841_3215               5.49e-21  49_[-1(4.94e-05)]_272_[+2(2.64e-09)]_1_[+1(6.65e-11)]_133_[-5(1.21e-06)]_165_[+4(2.22e-10)]_32_[+3(1.49e-08)]_98
WashU_Skud_Contig1850.5          7.09e-24  47_[-1(5.92e-05)]_276_[+2(5.80e-10)]_1_[+1(1.00e-10)]_170_[-5(4.54e-08)]_107_[+4(3.00e-11)]_32_[+3(7.37e-09)]_117
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM1-HEM4.fa000444000766000024      1550313155576321 20017 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR232W HEM1 "5-aminolevulinate synthase, catalyzes the first step in the heme biosynthetic pathway; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expression is regulated by Hap2p-Hap3p"
ACTGAAAAAAAAACCTAAGTACTGTTATGATTATTGAGGGACAACAACTAGCTCTATTAG
TTTTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTGGG
ATAAAAAAAAAAGAAACGCGAGCTGAGAAGGGAAGGCGTGTAAAGGAAGAACGGTTGAGA
GACAGCAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGAATGGAGAAG
TTTGGTATGATGCAAACGTTGTATTTCTAACAACGCATGGATCAGAACAATGGGCAAGGC
AAGATGAAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCC
CGCGGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGCGGTAGGGTAAGCCGTGC
AGGCAAGCTTATTATAGCACCGTCGGGGGTACCACCACTATATCAAACTCCACTGCTCGG
TAAAGCATTGTAGTGAAG
>MIT_Spar_c117_4603 YDR232W 5' untranslated region, Contig c117 17441 - 19440, 2000 bp (revcom)
ACTGAAAAAAAACCAAGTACTGTTGTGATTATTGAGGGACAACGGCTAGCTCTATTTGTT
TTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTAGGAT
AAAAAAAGAAACGCGAGCTGAGAAGAGAAGGCGTGTAAAGGAAGAACGGTTGAGAGAGAG
CAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGGATGGAGGAGTTTGG
TACGATGCAAACGCTATATTTGTAGCAACGCATGGGTCAGAACAATGGGCAAGGCAAGAT
GAAAAATTTCTGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGCGG
CCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGTGGTAGGGTAAGCCGTGCAGGCA
AGCTTATTATAGCACCGTCGGGGGGACCACTATATCAAGTTCCACAGCACGGTGAAGCAT
TGCAGTATAGTTCACAGC
>MIT_Smik_c228_4055 YDR232W 5' untranslated region, Contig c228 4702 - 6701(revcom), 2000 bp (revcom)
ACCGAGAGAAAAACTAAGTAGTGATATGATTATTGAGGACTAATGACCAGCTTTGTTTGT
TTTTTCTTCCAACCTAACTTATATGGGAAATATATAGGACAGAAAAAAGAAAAGAGCACG
AAAAAAAAGAAATGCGACCTGAGAAGGGAGGACGTGTGAAGCCAGAACGGTTGAATGACA
GTAGAGGAGGGTGCAACACAACCGAGTAGAGTACCAGCTGACGGAATGGAGGAGTTTGGT
ATGATGCAAAAGTGATGCTTTTAGCAACGCAACATTGAATTAGAACAATGGGCAAGGCAA
GATGAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGC
AAGCGCAGACCAATGAGCGACGAAAGCGGCCTTTTGAAGGGTAGGGTAATCCATGCAGGC
AAGTTTATTATAGCACCGTCGGGGGGAAGCATTATATCAAACTCCACAGTACAGCGTAAC
ATTGCTGTATAGGCTACA
>WashU_Skud_Contig2069.5 YDR232W 5' untranslated region, Contig c2069 5476 - 7475, 2000 bp (revcom)
ACTGAAAATAATCCGAGTCGTGCTACTGTGAATATTGAGAATAGGGACTAGCTCTATTTG
ATTTTTCTTCCAACCAAACTTATATGGAAAATATAAAGGAAAGAAAAAAGAAAAGAATAG
GAAAAAAAAAAAGAAACGCGAGAGAAGAGAACCGTGTGGAGGGAAGAACGGTTGAGAGAC
AGCAGAGCACAGCGCAACACAACCGAGTAGAGTACCAGCAGACGGAGTGGGTAGTTTGGT
ACAGTGTAAAAGCTATATTTCCACCAACGCAACACTGGATCGGAACAATGGGCAAGGCAA
TGTGAAAAATTTCCGTTCCTGCTCTTGCTTCATATATGACAATGACCAAAAAGCGTCCGC
GGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCGTAGCAGCAGGGTAAGCCGCGCAAG
CAAGTCCGTCATAACACCGTCGAAGGGGCACCACTATATCAGCTCTTCAGCATGGTAGGC
CATTACAGCACAGTCTTG
>WashU_Sbay_Contig461.5 YDR232W 5' untranslated region, Contig c461 4000 - 5999, 2000 bp (revcom)
ACTAAAAAGTCCAAGTGGTGCTGTTATTATTGAGGATAGCAACTAGCTTTATTTGTTTTT
TCTTCCAACCAAACTTATATGGAAATCAAAGGAAGGAAAAAAAGAAAAGAACAGGAAGAA
AAAAAAGAAACGTGAGCTGCCGAAAGGAGAGCGTGTGGAGGGAAGAACCGTTGAGAGACA
ACAGAGCAGGGTGCAAACCGATTAGAGTACCAGCAGACGAGATGGGCGATGTGGTACGGT
GCAGAAGGTGTGGTTCCAACAGCGCAGCACCGGGACAGAACAATGGGCAAGGCAAGATGA
AAAATCTCCGTTCCTGCTCTTGCTTGATATATTAACAATGACCAAAAAAACGCCGGCGGG
CGCAGACCAATGAGCGACGAAGACGGCTTTTGGGCGGGGCAGGGTAAGATGGGACAGGCA
AGGTCCGCTATAGCACCGTCGAGGGGGACCGCTATATCAGCTCCCAGTACATTGCAGCAC
ACTCTATAGCTAGTCAAA
>SGD_Scer_YOR278W HEM4 "Uroporphyrinogen III synthase, catalyzes the conversion of hydroxymethylbilane to uroporphyrinogen III, the fourth step in the heme biosynthetic pathway"
CTCTCGAGCAAGGTCTATTTTACCTTTCTGTTTCCTTATCCTTTGACACTAAAATTCAAA
AAACTCACTAGAAAGTTCACTAAAGCGCCTTAGCTGACTACAGCACAACCCAACCCCAAA
AACTAGTGAACTACACACTAAGAGAATTTATGGTATTTCCATAATTGAAGTATATGTACG
ATGTATACAATGTAAACAAGAGAGTAATGAAGTGAAGATATGTACACCTAGAGCGAACCA
ATGATAATTTGTTTTCTTAATTAAGAAAAACCATTAAAACTGGATTAGATTTCAATAATG
AAAAGCTAGGAACAAAAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGACATA
TGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGTTTT
CTTATCCTGAAGGATCCTGCAAATGAAGTAAGTTCAAAGAATTGAAATGAAATCGCCTTT
TATACCCTCGCCGCACCAAGGAGCGCGCTGTGAAAATTTTTCGCTTTATCTCTTAGGGCT
CCTACTGTCGGTAGAGAAAAGTTGAGTATATTTAAAGCATGAGGTAACTTTTCTGCCCAT
TTTTACTTCTATTTCCATTTGAATTCAGAAAAGTG
>MIT_Spar_c261_21317 YOR278W 5' untranslated region, Contig c261 32269 - 34268, 2000 bp (revcom)
CGTTCCAAGCAGGGTTTATTCTATTTCTCGGCTCCTTTACCCTGTAACTTCGAGATTCAA
AAACTCGCTATAACTTCACTAAAGCGCTTTAGTTGACTACAACACAACCCAACCCCAAAA
TAAACTGTCCAACTACACAATACCGAGGATAATCCACGATATTTCGGTGATTGAAGTATA
TGTATTACGTATGCAATGTAAGCAAGAAACTAACAAAATGAATATGTACACCTAGAGCGA
ACCAATGATAATTTGTTTTCTTAATAAAGAAAAACTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAACAGAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGAC
ATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGT
TCTTTTATCCTGAAGGATAAACGGAAAGCTCCCGATTAAAAACAAGTATAGAGTACTGGA
ATAGAATCGCCTTTTATACCCTCCCTCGCCGCATCAAGAAGCGCGCTGTGAAAATTTTTC
GTTTTTCTCTTAGGGCTCCCATCCAACTGTCGGCGAGGAAAAGTTGTATATATTTAAAGC
ATGAGGTAACTTTGTTGCCCATTATCTTTTTTGTT
>MIT_Smik_c492_20940 YOR278W 5' untranslated region, Contig c492 3260 - 5259(revcom), 2000 bp (revcom)
ACTTTCAAACACACTCTGGTGTACTCCTCGGTCCCTTCATCTCATTTCTTCAAGATGCAG
AACTTCGCCGGAAGTAAACTAAAGTGCTTTAATTAATCAAAAGACAACTTAATTCCCAAA
CGGAAATGCAGGCTAGACAAACCGAAGATAATCCCCGATATTTCTGAGTTTAACAAATGT
ATGTATAATATGTATGCAATGTAGGCAAGAAAATAACGAAGTGAAGATATGTACACCTAG
AGCGAACCAATAATAATTTGTTTTCTTACTAAAGAAAAACTATTAAAACTGGATTAGATT
TCAATAATGAAAAGCTAGGAACAAAAGAAATTTGTCTACTTCCAGCCATTTGCGCTTTAT
ATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAAT
GATGGTTCTTTTAAACCAAAATTTAAAGAAAAATCTTAACGGTAATATGAGTAGGAGGTT
GGAATGGGATCGCTTTTTATACCCTCATTGTGATAAGAGACGCGCAGTGAAAAATTTTCG
CTTTTTCTTAGGGCTCCTATCTAACTCTCGGGCGAATAAATATCATGAATGTATTTAAAC
GTCAAGTTAGTTAAATGTTTGAGTCTGTTTCTTTT
>WashU_Skud_Contig1682.4 YOR278W 5' untranslated region, Contig c1682 3379 - 5378, 2000 bp (revcom)
CTCTTCAAACAGACTCCAATTCACTACTGAGCTCTTACCTTGTGACTTCAAGACTCACTA
CTCAGTTGAAAGACACGCTCAGTACCAAATTCGGCTGCGAGGCAACTAACGCCTTTAAAC
AGGTAGGTAAGGAACAATACCGAAAGGCCATCTCCGATGTTTCGAAGATTGGCAAATGTA
TATATTATGTATGCAATATAGGCAAGATGATAACGAAGTAGAGATATGTACACCTAGAGC
GAACCAATGATAATTTGTTTTCTTAATGAAGAAAGTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAATAAAAGAGATTGGTCTACTTCCAGCCATTTGCGCTTTACATAGA
CATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGG
TTCTATTTAAAATGAAATCTAAAGATAAACCCTAGTCATAATCAAGTGGGTTGTGTTAAA
ATACAAGCACCTTTTATACTCTCGCAGCGTCAGTGGCGCGTTGTGAAAAATTTTCACTTT
TTCTCAGGGCTTTTACCCAACTGCCGACAAATAAAAGCCGTATTTAAGGAATGTGATTAG
TTTACTTTCCAATGCTTTCTCTTTTTTGTAGGGTA
>WashU_Sbay_Contig635.57 YOR278W 5' untranslated region, Contig c635 91073 - 93072, 2000 bp (revcom)
ACGTACAGATGGCGTCTCCTCCTTTCGCGAGCCCCTTGCCTTGTGACTTCAGCCTAACTT
CTTGACTAGAAGATACAACAAGAAATACTCAAATCGGTTATTGTGCAACTCATCCCTCAG
ACAGTTTGGTAAGAAACACCGAAGACTATTTCCGATATCTCAAAGAATGACAAAAGTATA
CATTATATATGCAAGAGAGGCAAGAAAAGAGTAAAAAAGAGTAAAAAAAACATGTACACC
TAGAGCGAACCAGTGATAATTTGCTTCTCAATGAAGAAAAAGCGATTAAAACTGGATTAG
ATTTCATTAAAGAAAAGCTAGGAACAAAGAAATTGGTCTACTTCCAGCCATTTGCGCTTG
ACATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGA
ATGATGGCTCTTTTAAATTGAGATCTAAAAGAAATATCCTGGAAAAGAGTAGAGAAGAGT
CCAAACTGTAGGAATTCAATCGCTTTTTATACTCTCATCGCGGAAAAGACGCGCTGTGAA
AAATTTTCTCTTTTTCTTAGGGCTCCTATCCAGCTGCCTGCGAACAAAAGCCGTATTTAA
AGCATGATTTTCACTACTATGTATGTTCTTTCTGC
BioPerl-1.007002/t/data/map_hem/HEM1-HEM4.meme.txt000444000766000024     12010413155576321 21204 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM1-HEM4.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDR232W         1.0000    498  MIT_Spar_c117_4603       1.0000    498  
MIT_Smik_c228_4055       1.0000    498  WashU_Skud_Contig2069.5  1.0000    498  
WashU_Sbay_Contig461.5   1.0000    498  SGD_Scer_YOR278W         1.0000    635  
MIT_Spar_c261_21317      1.0000    635  MIT_Smik_c492_20940      1.0000    635  
WashU_Skud_Contig1682.4  1.0000    635  WashU_Sbay_Contig635.57  1.0000    635  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM1-HEM4.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=       10    maxsites=       10    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            5665    N=              10
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.298 C 0.202 G 0.202 T 0.298 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =  10   llr = 232   E-value = 3.1e-035
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :5::16:5::55a::a9:1a
pos.-specific     C  a45a::35:a:::aa:::::
probability       G  :15:447:a:55::::1:9:
matrix            T  ::::5::::::::::::a::

         bits    2.5 *  *    **   **     
                 2.3 *  *    **   **     
                 2.0 *  *    **   **   * 
                 1.8 *  *    **   **   * 
Information      1.5 * **  * **  **** ***
content          1.3 * **  * **  ********
(33.4 bits)      1.0 * ** ***************
                 0.8 **** ***************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CACCTAGAGCAAACCAATGA
consensus             CG GGCC  GG        
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2069.5      +    357  6.68e-12 CAAAAAGCGT CCGCGGCCGCAGACCAATGA GCGACGAAGG
MIT_Spar_c117_4603           +    355  6.68e-12 CAAAAAGCGC CCGCGGCCGCAGACCAATGA GCGACGAAGG
SGD_Scer_YDR232W             +    360  6.68e-12 CAAAAAGCGC CCGCGGCCGCAGACCAATGA GCGACGAAGG
WashU_Sbay_Contig461.5       +    354  1.53e-11 AAAAAAACGC CGGCGGGCGCAGACCAATGA GCGACGAAGA
WashU_Skud_Contig1682.4      +    231  1.78e-11 GAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
MIT_Spar_c261_21317          +    229  1.78e-11 TGAATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
SGD_Scer_YOR278W             +    225  1.78e-11 AAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
MIT_Smik_c228_4055           +    357  3.51e-11 CAAAAAGCGC CCGCAAGCGCAGACCAATGA GCGACGAAAG
WashU_Sbay_Contig635.57      +    237  6.67e-11 AAAACATGTA CACCTAGAGCGAACCAGTGA TAATTTGCTT
MIT_Smik_c492_20940          +    234  1.29e-10 AAGATATGTA CACCTAGAGCGAACCAATAA TAATTTGTTT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2069.5           6.7e-12  356_[+1]_122
MIT_Spar_c117_4603                6.7e-12  354_[+1]_124
SGD_Scer_YDR232W                  6.7e-12  359_[+1]_119
WashU_Sbay_Contig461.5            1.5e-11  353_[+1]_125
WashU_Skud_Contig1682.4           1.8e-11  230_[+1]_385
MIT_Spar_c261_21317               1.8e-11  228_[+1]_387
SGD_Scer_YOR278W                  1.8e-11  224_[+1]_391
MIT_Smik_c228_4055                3.5e-11  356_[+1]_122
WashU_Sbay_Contig635.57           6.7e-11  236_[+1]_379
MIT_Smik_c492_20940               1.3e-10  233_[+1]_382
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=10
WashU_Skud_Contig2069.5  (  357) CCGCGGCCGCAGACCAATGA  1 
MIT_Spar_c117_4603       (  355) CCGCGGCCGCAGACCAATGA  1 
SGD_Scer_YDR232W         (  360) CCGCGGCCGCAGACCAATGA  1 
WashU_Sbay_Contig461.5   (  354) CGGCGGGCGCAGACCAATGA  1 
WashU_Skud_Contig1682.4  (  231) CACCTAGAGCGAACCAATGA  1 
MIT_Spar_c261_21317      (  229) CACCTAGAGCGAACCAATGA  1 
SGD_Scer_YOR278W         (  225) CACCTAGAGCGAACCAATGA  1 
MIT_Smik_c228_4055       (  357) CCGCAAGCGCAGACCAATGA  1 
WashU_Sbay_Contig635.57  (  237) CACCTAGAGCGAACCAGTGA  1 
MIT_Smik_c492_20940      (  234) CACCTAGAGCGAACCAATAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 3.1e-035 
  -997    251   -997   -997 
    62    119    -81   -997 
  -997    151    151   -997 
  -997    251   -997   -997 
  -169   -997    119     62 
    89   -997    119   -997 
  -997     77    199   -997 
    62    151   -997   -997 
  -997   -997    251   -997 
  -997    251   -997   -997 
    62   -997    151   -997 
    62   -997    151   -997 
   162   -997   -997   -997 
  -997    251   -997   -997 
  -997    251   -997   -997 
   162   -997   -997   -997 
   147   -997    -81   -997 
  -997   -997   -997    162 
  -169   -997    236   -997 
   162   -997   -997   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.1e-035 
 0.000000  1.000000  0.000000  0.000000 
 0.500000  0.400000  0.100000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.100000  0.000000  0.400000  0.500000 
 0.600000  0.000000  0.400000  0.000000 
 0.000000  0.300000  0.700000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.100000  0.000000  0.900000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
C[AC][CG]C[TG][AG][GC][AC]GC[AG][AG]ACCAATGA
--------------------------------------------------------------------------------




Time  3.49 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =  10   llr = 215   E-value = 5.3e-029
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  53::9a:a5:5::::a14:a
pos.-specific     C  55:11::::a1:::::::::
probability       G  :2a9::a:::4a::5:4:a:
matrix            T  ::::::::5:::aa5:56::

         bits    2.5   *   *  * *      * 
                 2.3   *   *  * *      * 
                 2.0   **  *  * *      * 
                 1.8   **  *  * *      * 
Information      1.5   ** *** * *** *  **
content          1.3   ****** * *** *  **
(31.1 bits)      1.0 * ****** * *****  **
                 0.8 ******** ******* ***
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           ACGGAAGAACAGTTGATTGA
consensus            CA      T G   T GA  
sequence              G                  
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      +    401  2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGCTC
WashU_Skud_Contig1682.4      +    394  2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
MIT_Smik_c492_20940          +    399  2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
MIT_Spar_c261_21317          +    393  2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
SGD_Scer_YOR278W             +    390  2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTT
WashU_Skud_Contig2069.5      +    160  7.63e-11 AACCGTGTGG AGGGAAGAACGGTTGAGAGA CAGCAGAGCA
MIT_Spar_c117_4603           +    158  9.24e-11 AAGGCGTGTA AAGGAAGAACGGTTGAGAGA GAGCAGAGCA
SGD_Scer_YDR232W             +    163  9.24e-11 AAGGCGTGTA AAGGAAGAACGGTTGAGAGA CAGCAGAGCA
WashU_Sbay_Contig461.5       +    159  2.91e-10 GAGCGTGTGG AGGGAAGAACCGTTGAGAGA CAACAGAGCA
MIT_Smik_c228_4055           +    159  1.25e-09 AGGACGTGTG AAGCCAGAACGGTTGAATGA CAGTAGAGGA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           2.3e-11  400_[+2]_215
WashU_Skud_Contig1682.4           2.3e-11  393_[+2]_222
MIT_Smik_c492_20940               2.3e-11  398_[+2]_217
MIT_Spar_c261_21317               2.3e-11  392_[+2]_223
SGD_Scer_YOR278W                  2.3e-11  389_[+2]_226
WashU_Skud_Contig2069.5           7.6e-11  159_[+2]_319
MIT_Spar_c117_4603                9.2e-11  157_[+2]_321
SGD_Scer_YDR232W                  9.2e-11  162_[+2]_316
WashU_Sbay_Contig461.5            2.9e-10  158_[+2]_320
MIT_Smik_c228_4055                1.3e-09  158_[+2]_320
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=10
WashU_Sbay_Contig635.57  (  401) CCGGAAGATCAGTTTATTGA  1 
WashU_Skud_Contig1682.4  (  394) CCGGAAGATCAGTTTATTGA  1 
MIT_Smik_c492_20940      (  399) CCGGAAGATCAGTTTATTGA  1 
MIT_Spar_c261_21317      (  393) CCGGAAGATCAGTTTATTGA  1 
SGD_Scer_YOR278W         (  390) CCGGAAGATCAGTTTATTGA  1 
WashU_Skud_Contig2069.5  (  160) AGGGAAGAACGGTTGAGAGA  1 
MIT_Spar_c117_4603       (  158) AAGGAAGAACGGTTGAGAGA  1 
SGD_Scer_YDR232W         (  163) AAGGAAGAACGGTTGAGAGA  1 
WashU_Sbay_Contig461.5   (  159) AGGGAAGAACCGTTGAGAGA  1 
MIT_Smik_c228_4055       (  159) AAGCCAGAACGGTTGAATGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 5.3e-029 
    62    151   -997   -997 
   -11    151     19   -997 
  -997   -997    251   -997 
  -997    -81    236   -997 
   147    -81   -997   -997 
   162   -997   -997   -997 
  -997   -997    251   -997 
   162   -997   -997   -997 
    62   -997   -997     62 
  -997    251   -997   -997 
    62    -81    119   -997 
  -997   -997    251   -997 
  -997   -997   -997    162 
  -997   -997   -997    162 
  -997   -997    151     62 
   162   -997   -997   -997 
  -169   -997    119     62 
    30   -997   -997     89 
  -997   -997    251   -997 
   162   -997   -997   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.3e-029 
 0.500000  0.500000  0.000000  0.000000 
 0.300000  0.500000  0.200000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.100000  0.900000  0.000000 
 0.900000  0.100000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.500000  0.100000  0.400000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.500000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.100000  0.000000  0.400000  0.500000 
 0.400000  0.000000  0.000000  0.600000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[AC][CAG]GGAAGA[AT]C[AG]GTT[GT]A[TG][TA]GA
--------------------------------------------------------------------------------




Time  6.83 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =  10   llr = 212   E-value = 7.8e-027
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  ::::1:::::5:::::::4:
pos.-specific     C  2:64:::aa::555:::a::
probability       G  ::::9:::::55::::2:::
matrix            T  8a46:aa::a::55aa8:6a

         bits    2.5        **        *  
                 2.3        **        *  
                 2.0     *  **        *  
                 1.8     *  **        *  
Information      1.5  *  ****** *  ** * *
content          1.3  ** ****** *  ** * *
(30.6 bits)      1.0 ****************** *
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TTCTGTTCCTACCCTTTCTT
consensus            C TC      GGTT  G A 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c228_4055           +    310  8.08e-12 AGATGAAAAT TTCCGTTCCTGCTCTTTCTT CATATATGAA
SGD_Scer_YDR232W             +    313  8.08e-12 GATGAAAAAT TTCCGTTCCTGCTCTTTCTT CATATATGAA
MIT_Spar_c117_4603           +    308  1.62e-11 GATGAAAAAT TTCTGTTCCTGCTCTTTCTT CATATATGAA
WashU_Skud_Contig2069.5      +    311  6.03e-11 TGTGAAAAAT TTCCGTTCCTGCTCTTGCTT CATATATGAC
MIT_Spar_c261_21317          -    302  1.25e-10 AGACCAATTT TTCTGTTCCTAGCTTTTCAT TATTGAAATC
WashU_Sbay_Contig461.5       +    306  1.76e-10 GATGAAAAAT CTCCGTTCCTGCTCTTGCTT GATATATTAA
MIT_Smik_c492_20940          -    307  3.70e-10 GACAAATTTC TTTTGTTCCTAGCTTTTCAT TATTGAAATC
SGD_Scer_YOR278W             -    298  3.70e-10 GACCAATTTT TTTTGTTCCTAGCTTTTCAT TATTGAAATC
WashU_Sbay_Contig635.57      -    310  4.68e-10 AGACCAATTT CTTTGTTCCTAGCTTTTCTT TAATGAAATC
WashU_Skud_Contig1682.4      -    302  1.32e-09 GACCAATCTC TTTTATTCCTAGCTTTTCAT TATTGAAATC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c228_4055                8.1e-12  309_[+3]_169
SGD_Scer_YDR232W                  8.1e-12  312_[+3]_166
MIT_Spar_c117_4603                1.6e-11  307_[+3]_171
WashU_Skud_Contig2069.5             6e-11  310_[+3]_168
MIT_Spar_c261_21317               1.2e-10  301_[-3]_314
WashU_Sbay_Contig461.5            1.8e-10  305_[+3]_173
MIT_Smik_c492_20940               3.7e-10  306_[-3]_309
SGD_Scer_YOR278W                  3.7e-10  297_[-3]_318
WashU_Sbay_Contig635.57           4.7e-10  309_[-3]_306
WashU_Skud_Contig1682.4           1.3e-09  301_[-3]_314
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=10
MIT_Smik_c228_4055       (  310) TTCCGTTCCTGCTCTTTCTT  1 
SGD_Scer_YDR232W         (  313) TTCCGTTCCTGCTCTTTCTT  1 
MIT_Spar_c117_4603       (  308) TTCTGTTCCTGCTCTTTCTT  1 
WashU_Skud_Contig2069.5  (  311) TTCCGTTCCTGCTCTTGCTT  1 
MIT_Spar_c261_21317      (  302) TTCTGTTCCTAGCTTTTCAT  1 
WashU_Sbay_Contig461.5   (  306) CTCCGTTCCTGCTCTTGCTT  1 
MIT_Smik_c492_20940      (  307) TTTTGTTCCTAGCTTTTCAT  1 
SGD_Scer_YOR278W         (  298) TTTTGTTCCTAGCTTTTCAT  1 
WashU_Sbay_Contig635.57  (  310) CTTTGTTCCTAGCTTTTCTT  1 
WashU_Skud_Contig1682.4  (  302) TTTTATTCCTAGCTTTTCAT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 7.8e-027 
  -997     19   -997    130 
  -997   -997   -997    162 
  -997    177   -997     30 
  -997    119   -997     89 
  -169   -997    236   -997 
  -997   -997   -997    162 
  -997   -997   -997    162 
  -997    251   -997   -997 
  -997    251   -997   -997 
  -997   -997   -997    162 
    62   -997    151   -997 
  -997    151    151   -997 
  -997    151   -997     62 
  -997    151   -997     62 
  -997   -997   -997    162 
  -997   -997   -997    162 
  -997   -997     19    130 
  -997    251   -997   -997 
    30   -997   -997     89 
  -997   -997   -997    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 7.8e-027 
 0.000000  0.200000  0.000000  0.800000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.600000  0.000000  0.400000 
 0.000000  0.400000  0.000000  0.600000 
 0.100000  0.000000  0.900000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.200000  0.800000 
 0.000000  1.000000  0.000000  0.000000 
 0.400000  0.000000  0.000000  0.600000 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
[TC]T[CT][TC]GTTCCT[AG][CG][CT][CT]TT[TG]C[TA]T
--------------------------------------------------------------------------------




Time 10.06 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =  10   llr = 206   E-value = 2.2e-024
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  :11::::5:::::a5::955
pos.-specific     C  :::::5:2a::aa::aa:::
probability       G  :365::::::::::5:::::
matrix            T  a635a5a3:aa::::::155

         bits    2.5         *  **  **   
                 2.3         *  **  **   
                 2.0         *  **  **   
                 1.8         *  **  **   
Information      1.5 *   * * ****** **   
content          1.3 *   * * ****** ***  
(29.7 bits)      1.0 *  **** **********  
                 0.8 * ***** **********  
                 0.5 ******* ************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TTGGTCTACTTCCAACCAAA
consensus             GTT T T      G   TT
sequence                    C            
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      +    333  2.66e-12 AACAAAGAAA TTGGTCTACTTCCAGCCATT TGCGCTTGAC
WashU_Skud_Contig1682.4      +    326  2.66e-12 ATAAAAGAGA TTGGTCTACTTCCAGCCATT TGCGCTTTAC
MIT_Spar_c261_21317          +    325  2.66e-12 AACAGAAAAA TTGGTCTACTTCCAGCCATT TGCGCTTTAT
SGD_Scer_YOR278W             +    322  2.66e-12 ACAAAAAAAA TTGGTCTACTTCCAGCCATT TGCGCTTTAT
MIT_Smik_c492_20940          +    331  1.15e-10 ACAAAAGAAA TTTGTCTACTTCCAGCCATT TGCGCTTTAT
MIT_Spar_c117_4603           +     56  2.75e-10 CTAGCTCTAT TTGTTTTCCTTCCAACCAAA CTTATATGGG
WashU_Sbay_Contig461.5       +     54  1.18e-09 TAGCTTTATT TGTTTTTTCTTCCAACCAAA CTTATATGGA
SGD_Scer_YDR232W             +     58  1.27e-09 CTAGCTCTAT TAGTTTTCCTTCCAACCAAA CTTATATGGG
WashU_Skud_Contig2069.5      +     59  2.01e-09 TAGCTCTATT TGATTTTTCTTCCAACCAAA CTTATATGGA
MIT_Smik_c228_4055           +     58  2.84e-09 CAGCTTTGTT TGTTTTTTCTTCCAACCTAA CTTATATGGG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           2.7e-12  332_[+4]_283
WashU_Skud_Contig1682.4           2.7e-12  325_[+4]_290
MIT_Spar_c261_21317               2.7e-12  324_[+4]_291
SGD_Scer_YOR278W                  2.7e-12  321_[+4]_294
MIT_Smik_c492_20940               1.1e-10  330_[+4]_285
MIT_Spar_c117_4603                2.7e-10  55_[+4]_423
WashU_Sbay_Contig461.5            1.2e-09  53_[+4]_425
SGD_Scer_YDR232W                  1.3e-09  57_[+4]_421
WashU_Skud_Contig2069.5             2e-09  58_[+4]_420
MIT_Smik_c228_4055                2.8e-09  57_[+4]_421
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=10
WashU_Sbay_Contig635.57  (  333) TTGGTCTACTTCCAGCCATT  1 
WashU_Skud_Contig1682.4  (  326) TTGGTCTACTTCCAGCCATT  1 
MIT_Spar_c261_21317      (  325) TTGGTCTACTTCCAGCCATT  1 
SGD_Scer_YOR278W         (  322) TTGGTCTACTTCCAGCCATT  1 
MIT_Smik_c492_20940      (  331) TTTGTCTACTTCCAGCCATT  1 
MIT_Spar_c117_4603       (   56) TTGTTTTCCTTCCAACCAAA  1 
WashU_Sbay_Contig461.5   (   54) TGTTTTTTCTTCCAACCAAA  1 
SGD_Scer_YDR232W         (   58) TAGTTTTCCTTCCAACCAAA  1 
WashU_Skud_Contig2069.5  (   59) TGATTTTTCTTCCAACCAAA  1 
MIT_Smik_c228_4055       (   58) TGTTTTTTCTTCCAACCTAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 2.2e-024 
  -997   -997   -997    162 
  -169   -997     77     89 
  -169   -997    177    -11 
  -997   -997    151     62 
  -997   -997   -997    162 
  -997    151   -997     62 
  -997   -997   -997    162 
    62     19   -997    -11 
  -997    251   -997   -997 
  -997   -997   -997    162 
  -997   -997   -997    162 
  -997    251   -997   -997 
  -997    251   -997   -997 
   162   -997   -997   -997 
    62   -997    151   -997 
  -997    251   -997   -997 
  -997    251   -997   -997 
   147   -997   -997   -169 
    62   -997   -997     62 
    62   -997   -997     62 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.2e-024 
 0.000000  0.000000  0.000000  1.000000 
 0.100000  0.000000  0.300000  0.600000 
 0.100000  0.000000  0.600000  0.300000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.200000  0.000000  0.300000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.900000  0.000000  0.000000  0.100000 
 0.500000  0.000000  0.000000  0.500000 
 0.500000  0.000000  0.000000  0.500000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
T[TG][GT][GT]T[CT]T[ATC]CTTCCA[AG]CCA[AT][AT]
--------------------------------------------------------------------------------




Time 13.18 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =  10   llr = 216   E-value = 2.6e-029
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  :5::6::::::56::a::::
pos.-specific     C  9::5::14a::144a:::::
probability       G  :5:5:19::::4:6:::6a:
matrix            T  1:a:49:6:aa:::::a4:a

         bits    2.5         *     *   * 
                 2.3         *     *   * 
                 2.0 *     * *     *   * 
                 1.8 *     * *     *   * 
Information      1.5 * **  * ***  **** **
content          1.3 * ** ** ***  *******
(31.2 bits)      1.0 **** ****** ********
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CATCATGTCTTAAGCATGGT
consensus             G GT  C   GCC   T  
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      +    378  7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
WashU_Skud_Contig1682.4      +    371  7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
MIT_Smik_c492_20940          +    376  7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
MIT_Spar_c261_21317          +    370  7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
SGD_Scer_YOR278W             +    367  7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
WashU_Sbay_Contig461.5       -    280  1.38e-10 GGAGATTTTT CATCTTGCCTTGCCCATTGT TCTGTCCCGG
MIT_Smik_c228_4055           -    285  1.38e-10 CGGAAATTTT CATCTTGCCTTGCCCATTGT TCTAATTCAA
MIT_Spar_c117_4603           -    282  1.38e-10 AGAAATTTTT CATCTTGCCTTGCCCATTGT TCTGACCCAT
SGD_Scer_YDR232W             -    287  1.38e-10 GGAAATTTTT CATCTTGCCTTGCCCATTGT TCTGATCCAT
WashU_Skud_Contig2069.5      +    457  2.43e-09 GGCACCACTA TATCAGCTCTTCAGCATGGT AGGCCATTAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           7.2e-12  377_[+5]_238
WashU_Skud_Contig1682.4           7.2e-12  370_[+5]_245
MIT_Smik_c492_20940               7.2e-12  375_[+5]_240
MIT_Spar_c261_21317               7.2e-12  369_[+5]_246
SGD_Scer_YOR278W                  7.2e-12  366_[+5]_249
WashU_Sbay_Contig461.5            1.4e-10  279_[-5]_199
MIT_Smik_c228_4055                1.4e-10  284_[-5]_194
MIT_Spar_c117_4603                1.4e-10  281_[-5]_197
SGD_Scer_YDR232W                  1.4e-10  286_[-5]_192
WashU_Skud_Contig2069.5           2.4e-09  456_[+5]_22
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=10
WashU_Sbay_Contig635.57  (  378) CGTGATGTCTTAAGCATGGT  1 
WashU_Skud_Contig1682.4  (  371) CGTGATGTCTTAAGCATGGT  1 
MIT_Smik_c492_20940      (  376) CGTGATGTCTTAAGCATGGT  1 
MIT_Spar_c261_21317      (  370) CGTGATGTCTTAAGCATGGT  1 
SGD_Scer_YOR278W         (  367) CGTGATGTCTTAAGCATGGT  1 
WashU_Sbay_Contig461.5   (  280) CATCTTGCCTTGCCCATTGT  1 
MIT_Smik_c228_4055       (  285) CATCTTGCCTTGCCCATTGT  1 
MIT_Spar_c117_4603       (  282) CATCTTGCCTTGCCCATTGT  1 
SGD_Scer_YDR232W         (  287) CATCTTGCCTTGCCCATTGT  1 
WashU_Skud_Contig2069.5  (  457) TATCAGCTCTTCAGCATGGT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 2.6e-029 
  -997    236   -997   -169 
    62   -997    151   -997 
  -997   -997   -997    162 
  -997    151    151   -997 
    89   -997   -997     30 
  -997   -997    -81    147 
  -997    -81    236   -997 
  -997    119   -997     89 
  -997    251   -997   -997 
  -997   -997   -997    162 
  -997   -997   -997    162 
    62    -81    119   -997 
    89    119   -997   -997 
  -997    119    177   -997 
  -997    251   -997   -997 
   162   -997   -997   -997 
  -997   -997   -997    162 
  -997   -997    177     30 
  -997   -997    251   -997 
  -997   -997   -997    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.6e-029 
 0.000000  0.900000  0.000000  0.100000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.600000  0.000000  0.000000  0.400000 
 0.000000  0.000000  0.100000  0.900000 
 0.000000  0.100000  0.900000  0.000000 
 0.000000  0.400000  0.000000  0.600000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.100000  0.400000  0.000000 
 0.600000  0.400000  0.000000  0.000000 
 0.000000  0.400000  0.600000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.600000  0.400000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
C[AG]T[CG][AT]TG[TC]CTT[AG][AC][GC]CAT[GT]GT
--------------------------------------------------------------------------------




Time 16.24 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR232W                 1.48e-30  57_[+4(1.27e-09)]_29_[-3(6.67e-05)]_36_[+2(9.24e-11)]_104_[-5(1.38e-10)]_6_[+3(8.08e-12)]_27_[+1(6.68e-12)]_119
MIT_Spar_c117_4603               6.70e-31  55_[+4(2.75e-10)]_30_[-3(3.93e-05)]_32_[+2(9.24e-11)]_104_[-5(1.38e-10)]_6_[+3(1.62e-11)]_27_[+1(6.68e-12)]_124
MIT_Smik_c228_4055               1.84e-28  57_[+4(2.84e-09)]_30_[-3(3.93e-05)]_31_[+2(1.25e-09)]_106_[-5(1.38e-10)]_5_[+3(8.08e-12)]_27_[+1(3.51e-11)]_122
WashU_Skud_Contig2069.5          1.98e-28  58_[+4(2.01e-09)]_30_[-3(3.79e-05)]_31_[+2(7.63e-11)]_105_[-5(1.61e-07)]_6_[+3(6.03e-11)]_26_[+1(6.68e-12)]_80_[+5(2.43e-09)]_22
WashU_Sbay_Contig461.5           1.68e-28  53_[+4(1.18e-09)]_10_[-3(5.72e-06)]_3_[-3(3.63e-05)]_32_[+2(2.91e-10)]_6_[+1(9.53e-05)]_75_[-5(1.38e-10)]_6_[+3(1.76e-10)]_28_[+1(1.53e-11)]_125
SGD_Scer_YOR278W                 2.15e-32  224_[+1(1.78e-11)]_53_[-3(3.70e-10)]_4_[+4(2.66e-12)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_226
MIT_Spar_c261_21317              7.63e-33  228_[+1(1.78e-11)]_53_[-3(1.25e-10)]_3_[+4(2.66e-12)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_223
MIT_Smik_c492_20940              5.17e-30  62_[-4(6.56e-06)]_151_[+1(1.29e-10)]_53_[-3(3.70e-10)]_4_[+4(1.15e-10)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_217
WashU_Skud_Contig1682.4          7.25e-32  89_[-4(8.96e-05)]_121_[+1(1.78e-11)]_51_[-3(1.32e-09)]_4_[+4(2.66e-12)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_141_[+1(3.09e-05)]_61
WashU_Sbay_Contig635.57          9.51e-32  188_[-3(5.84e-05)]_28_[+1(6.67e-11)]_53_[-3(4.68e-10)]_3_[+4(2.66e-12)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_215
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM1.ups.fa_000444000766000024      1045413155576321 20271 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR232W HEM1 "5-aminolevulinate synthase, catalyzes the first step in the heme biosynthetic pathway; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expression is regulated by Hap2p-Hap3p"
ACTGAAAAAAAAACCTAAGTACTGTTATGATTATTGAGGGACAACAACTAGCTCTATTAG
TTTTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTGGG
ATAAAAAAAAAAGAAACGCGAGCTGAGAAGGGAAGGCGTGTAAAGGAAGAACGGTTGAGA
GACAGCAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGAATGGAGAAG
TTTGGTATGATGCAAACGTTGTATTTCTAACAACGCATGGATCAGAACAATGGGCAAGGC
AAGATGAAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCC
CGCGGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGCGGTAGGGTAAGCCGTGC
AGGCAAGCTTATTATAGCACCGTCGGGGGTACCACCACTATATCAAACTCCACTGCTCGG
TAAAGCATTGTAGTGAAG
>MIT_Spar_c117_4603 YDR232W 5' untranslated region, Contig c117 17441 - 19440, 2000 bp (revcom)
ACTGAAAAAAAACCAAGTACTGTTGTGATTATTGAGGGACAACGGCTAGCTCTATTTGTT
TTCCTTCCAACCAAACTTATATGGGCAATATATAGGAAAGAAAAAAGAAAAGAGTAGGAT
AAAAAAAGAAACGCGAGCTGAGAAGAGAAGGCGTGTAAAGGAAGAACGGTTGAGAGAGAG
CAGAGCAGGGTGCAACACACAACCGAATAGAGTATCAGCTGACGGGATGGAGGAGTTTGG
TACGATGCAAACGCTATATTTGTAGCAACGCATGGGTCAGAACAATGGGCAAGGCAAGAT
GAAAAATTTCTGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGCGG
CCGCAGACCAATGAGCGACGAAGGCGGCCTTTCCGAGTGGTAGGGTAAGCCGTGCAGGCA
AGCTTATTATAGCACCGTCGGGGGGACCACTATATCAAGTTCCACAGCACGGTGAAGCAT
TGCAGTATAGTTCACAGC
>MIT_Smik_c228_4055 YDR232W 5' untranslated region, Contig c228 4702 - 6701(revcom), 2000 bp (revcom)
ACCGAGAGAAAAACTAAGTAGTGATATGATTATTGAGGACTAATGACCAGCTTTGTTTGT
TTTTTCTTCCAACCTAACTTATATGGGAAATATATAGGACAGAAAAAAGAAAAGAGCACG
AAAAAAAAGAAATGCGACCTGAGAAGGGAGGACGTGTGAAGCCAGAACGGTTGAATGACA
GTAGAGGAGGGTGCAACACAACCGAGTAGAGTACCAGCTGACGGAATGGAGGAGTTTGGT
ATGATGCAAAAGTGATGCTTTTAGCAACGCAACATTGAATTAGAACAATGGGCAAGGCAA
GATGAAAATTTCCGTTCCTGCTCTTTCTTCATATATGAACAATGACCAAAAAGCGCCCGC
AAGCGCAGACCAATGAGCGACGAAAGCGGCCTTTTGAAGGGTAGGGTAATCCATGCAGGC
AAGTTTATTATAGCACCGTCGGGGGGAAGCATTATATCAAACTCCACAGTACAGCGTAAC
ATTGCTGTATAGGCTACA
>WashU_Scas_Contig721.76 YDR232W 5' untranslated region, Contig c721 147634 - 149633(revcom), 2000 bp (revcom)
TGTTTGTGAAGCAGACGGGTGGATAGAGCGGCCAGCGAGCAAGCAAGTATAGACTAGATT
TGTTCTGTTCTGTTTGAGATGAGCTGAGCTGATGTGATGATGTGATGTGTTGTTATATAC
AGTGCTGTATATATGAATAATTGTTAAACGACGGGATTGGCGTGTTACGTAAGGAAAATA
GAGCTTTGAGCAAAAAAGAAAGGCGCGCTCAGAAACTGCCGCACACAGCTTTTGGGCCAA
TCAGAAGACGGGATTTGGATCTGGCACGTGATTTGTCGTGTTTGGTGACAGGCTGTTTGT
TACCCAGCTCTTTTGATTTTTTTGATTTTAGCCGCCCAATTCAGTTTCCCCTTCTTCTTC
TTATTGAGCTGTATATACGGGGAATACAACAACAACAACAACTACTGCTACTACTACAAG
ATCTACATATACAATGGGCTGGCTACCATCCTTCAAAAGCAACAGCACACCGCAGCAGCA
GCAGGAACCCCAGCAGGA
>WashU_Sklu_Contig2308.6 YDR232W 5' untranslated region, Contig c2308 6692 - 8691, 2000 bp (revcom)
CCCTTCTTCGTCTGTCTATTTTTCGACGGTTCTATTCCTGTAAAGAGGGGAGGTGAGTCT
TCTCTCCACTACTCACATACATATATATATTTATTTTTTTCTTCCCATCCAATAGGAAAA
AAGAAATTTTCTGAAAAATTTTTAGGTGTGATCAAGTATGTGATCACGTGGACAGTTGCC
TGAGCCAATAAGAACGACGTTAAAGCTAATGTTAGGTGTTACTTACGAGCTATTCAGTTC
GCGATACCTGTCTTGAGCCTTTGGATGCCCCATTTGAGCAGCACATTTATAATGTTCCAG
AGCCTTGCTTGGATCCTTTGTGCAGCCAATACCGCGCTCGTAGAAGAAAGCTAACGCATA
CTCTGCGCGGGCAAACTTACCTTCTGTGGACTGGCAGCTCCTTAAAGCCCAGCTGAATGC
CTCTTGGTCGTTCGGCTGTAGAACACCAGCAGCACCTGTAAGATACCATCCACTCAAAGC
CATCATCGCCATCGGGTT
>WashU_Skud_Contig2069.5 YDR232W 5' untranslated region, Contig c2069 5476 - 7475, 2000 bp (revcom)
ACTGAAAATAATCCGAGTCGTGCTACTGTGAATATTGAGAATAGGGACTAGCTCTATTTG
ATTTTTCTTCCAACCAAACTTATATGGAAAATATAAAGGAAAGAAAAAAGAAAAGAATAG
GAAAAAAAAAAAGAAACGCGAGAGAAGAGAACCGTGTGGAGGGAAGAACGGTTGAGAGAC
AGCAGAGCACAGCGCAACACAACCGAGTAGAGTACCAGCAGACGGAGTGGGTAGTTTGGT
ACAGTGTAAAAGCTATATTTCCACCAACGCAACACTGGATCGGAACAATGGGCAAGGCAA
TGTGAAAAATTTCCGTTCCTGCTCTTGCTTCATATATGACAATGACCAAAAAGCGTCCGC
GGCCGCAGACCAATGAGCGACGAAGGCGGCCTTTCGTAGCAGCAGGGTAAGCCGCGCAAG
CAAGTCCGTCATAACACCGTCGAAGGGGCACCACTATATCAGCTCTTCAGCATGGTAGGC
CATTACAGCACAGTCTTG
>WashU_Sbay_Contig461.5 YDR232W 5' untranslated region, Contig c461 4000 - 5999, 2000 bp (revcom)
ACTAAAAAGTCCAAGTGGTGCTGTTATTATTGAGGATAGCAACTAGCTTTATTTGTTTTT
TCTTCCAACCAAACTTATATGGAAATCAAAGGAAGGAAAAAAAGAAAAGAACAGGAAGAA
AAAAAAGAAACGTGAGCTGCCGAAAGGAGAGCGTGTGGAGGGAAGAACCGTTGAGAGACA
ACAGAGCAGGGTGCAAACCGATTAGAGTACCAGCAGACGAGATGGGCGATGTGGTACGGT
GCAGAAGGTGTGGTTCCAACAGCGCAGCACCGGGACAGAACAATGGGCAAGGCAAGATGA
AAAATCTCCGTTCCTGCTCTTGCTTGATATATTAACAATGACCAAAAAAACGCCGGCGGG
CGCAGACCAATGAGCGACGAAGACGGCTTTTGGGCGGGGCAGGGTAAGATGGGACAGGCA
AGGTCCGCTATAGCACCGTCGAGGGGGACCGCTATATCAGCTCCCAGTACATTGCAGCAC
ACTCTATAGCTAGTCAAA

BioPerl-1.007002/t/data/map_hem/HEM1.ups.fa_.revcom000444000766000024       614213155576321 21542 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR232W HEM1 "5-aminolevulinate synthase, catalyzes the first step in the heme biosynthetic pathway; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expression is regulated by Hap2p-Hap3p"
CTTCACTACAATGCTTTACCGAGCAGTGGAGTTTGATATAGTGGTGGTACCCCCGACGGT
GCTATAATAAGCTTGCCTGCACGGCTTACCCTACCGCTCGGAAAGGCCGCCTTCGTCGCT
CATTGGTCTGCGGCCGCGGGCGCTTTTTGGTCATTGTTCATATATGAAGAAAGAGCAGGA
ACGGAAATTTTTCATCTTGCCTTGCCCATTGTTCTGATCCATGCGTTGTTAGAAATACAA
CGTTTGCATCATACCAAACTTCTCCATTCCGTCAGCTGATACTCTATTCGGTTGTGTGTT
GCACCCTGCTCTGCTGTCTCTCAACCGTTCTTCCTTTACACGCCTTCCCTTCTCAGCTCG
CGTTTCTTTTTTTTTTATCCCACTCTTTTCTTTTTTCTTTCCTATATATTGCCCATATAA
GTTTGGTTGGAAGGAAAACTAATAGAGCTAGTTGTTGTCCCTCAATAATCATAACAGTAC
TTAGGTTTTTTTTTCAGT
>MIT_Spar_c117_4603 YDR232W 5' untranslated region, Contig c117 17441 - 19440, 2000 bp (revcom)
GCTGTGAACTATACTGCAATGCTTCACCGTGCTGTGGAACTTGATATAGTGGTCCCCCCG
ACGGTGCTATAATAAGCTTGCCTGCACGGCTTACCCTACCACTCGGAAAGGCCGCCTTCG
TCGCTCATTGGTCTGCGGCCGCGGGCGCTTTTTGGTCATTGTTCATATATGAAGAAAGAG
CAGGAACAGAAATTTTTCATCTTGCCTTGCCCATTGTTCTGACCCATGCGTTGCTACAAA
TATAGCGTTTGCATCGTACCAAACTCCTCCATCCCGTCAGCTGATACTCTATTCGGTTGT
GTGTTGCACCCTGCTCTGCTCTCTCTCAACCGTTCTTCCTTTACACGCCTTCTCTTCTCA
GCTCGCGTTTCTTTTTTTATCCTACTCTTTTCTTTTTTCTTTCCTATATATTGCCCATAT
AAGTTTGGTTGGAAGGAAAACAAATAGAGCTAGCCGTTGTCCCTCAATAATCACAACAGT
ACTTGGTTTTTTTTCAGT
>MIT_Smik_c228_4055 YDR232W 5' untranslated region, Contig c228 4702 - 6701(revcom), 2000 bp (revcom)
TGTAGCCTATACAGCAATGTTACGCTGTACTGTGGAGTTTGATATAATGCTTCCCCCCGA
CGGTGCTATAATAAACTTGCCTGCATGGATTACCCTACCCTTCAAAAGGCCGCTTTCGTC
GCTCATTGGTCTGCGCTTGCGGGCGCTTTTTGGTCATTGTTCATATATGAAGAAAGAGCA
GGAACGGAAATTTTCATCTTGCCTTGCCCATTGTTCTAATTCAATGTTGCGTTGCTAAAA
GCATCACTTTTGCATCATACCAAACTCCTCCATTCCGTCAGCTGGTACTCTACTCGGTTG
TGTTGCACCCTCCTCTACTGTCATTCAACCGTTCTGGCTTCACACGTCCTCCCTTCTCAG
GTCGCATTTCTTTTTTTTCGTGCTCTTTTCTTTTTTCTGTCCTATATATTTCCCATATAA
GTTAGGTTGGAAGAAAAAACAAACAAAGCTGGTCATTAGTCCTCAATAATCATATCACTA
CTTAGTTTTTCTCTCGGT
>WashU_Skud_Contig2069.5 YDR232W 5' untranslated region, Contig c2069 5476 - 7475, 2000 bp (revcom)
CAAGACTGTGCTGTAATGGCCTACCATGCTGAAGAGCTGATATAGTGGTGCCCCTTCGAC
GGTGTTATGACGGACTTGCTTGCGCGGCTTACCCTGCTGCTACGAAAGGCCGCCTTCGTC
GCTCATTGGTCTGCGGCCGCGGACGCTTTTTGGTCATTGTCATATATGAAGCAAGAGCAG
GAACGGAAATTTTTCACATTGCCTTGCCCATTGTTCCGATCCAGTGTTGCGTTGGTGGAA
ATATAGCTTTTACACTGTACCAAACTACCCACTCCGTCTGCTGGTACTCTACTCGGTTGT
GTTGCGCTGTGCTCTGCTGTCTCTCAACCGTTCTTCCCTCCACACGGTTCTCTTCTCTCG
CGTTTCTTTTTTTTTTTCCTATTCTTTTCTTTTTTCTTTCCTTTATATTTTCCATATAAG
TTTGGTTGGAAGAAAAATCAAATAGAGCTAGTCCCTATTCTCAATATTCACAGTAGCACG
ACTCGGATTATTTTCAGT
>WashU_Sbay_Contig461.5 YDR232W 5' untranslated region, Contig c461 4000 - 5999, 2000 bp (revcom)
TTTGACTAGCTATAGAGTGTGCTGCAATGTACTGGGAGCTGATATAGCGGTCCCCCTCGA
CGGTGCTATAGCGGACCTTGCCTGTCCCATCTTACCCTGCCCCGCCCAAAAGCCGTCTTC
GTCGCTCATTGGTCTGCGCCCGCCGGCGTTTTTTTGGTCATTGTTAATATATCAAGCAAG
AGCAGGAACGGAGATTTTTCATCTTGCCTTGCCCATTGTTCTGTCCCGGTGCTGCGCTGT
TGGAACCACACCTTCTGCACCGTACCACATCGCCCATCTCGTCTGCTGGTACTCTAATCG
GTTTGCACCCTGCTCTGTTGTCTCTCAACGGTTCTTCCCTCCACACGCTCTCCTTTCGGC
AGCTCACGTTTCTTTTTTTTCTTCCTGTTCTTTTCTTTTTTTCCTTCCTTTGATTTCCAT
ATAAGTTTGGTTGGAAGAAAAAACAAATAAAGCTAGTTGCTATCCTCAATAATAACAGCA
CCACTTGGACTTTTTAGT
BioPerl-1.007002/t/data/map_hem/HEM12-HEM13.fa000444000766000024      2144413155576321 20162 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR047W HEM12 "Uroporphyrinogen decarboxylase, catalyzes the fifth step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; activity inhibited by Cu2+, Zn2+, Fe2+, Fe3+ and sulfhydryl-specific reagents"
AGCGTTATAACCTGTTCTTTGCTTTATTTTTTTTTTTTTTGTTCTTCCTTTTCTCGAAGA
GAGCTTACCAAACACAATTCTGAGATAATGCTTGATGAATTGAAGAACCTATCGATCACT
CTATGTTACCTTCGTCTGGAACATCACTAATTCGAGCGGTAAAGATGAAAATGGCAGAAC
ATTTCGCTGGCAAAATTAAAACTCTTGCCTCATTTTTTTTTGCTTTCCTCTCCTGCCGCC
AAAAACCCCGAACCCTGTCCTGTATATACGAGAAACATTGAAAAAGATCGTGTATGATAG
CGCCAAGATGGCGGATAAACTAACACTATTGACAGGTTGAGGCCAAGGATATATTACTTG
CTAACAGAAAGAGATACTGTCACCACAATTGCCCGCGTACGTATACTACAACATGTTCTC
TATATATCACCCACTCTTTCGCAGTGCTACGTACGCCAAAAACGCGCGCATGGAAGTAAA
GAAGTTTTTTCTTTTAAGAGCGAAGCTCCATTAAAAGCCTTGAATATAAACTAGTGCGAA
GTAGTATGATCCGAAGACACCAATTGCTGGTGCAGCATAGGAATATGTGGCGTCCGAAAA
AGAGCCTTTAACAATCCACGGCGAAACAAGGCACCGCTGTGCATTTAAAACATGCCGTTC
CCGTACCAAGTTATATTGTTACGGATGAATCCAAAATAATTTGTTAAAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCATGGCACCTTCTTCGTTTCTTCATCCTGCA
TTAGACTTACTAGTGTGCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGACACATATCGC
TGAGCTGGAAGGACACCTTTTAATGTAGCCGTGCATGCGGCTCCGCGAAAAGAGCTCTGC
TATATTTCTCTACCTGAACTTCGAGCCGCGATCAACGAAAGCTCTCATCCAAGGCTCGTT
TTTCTTGACAGAAGCATGACAGTAAAATATGCGGTCATTT
>MIT_Spar_c130_3923 YDR047W 5' untranslated region, Contig c130 9341 - 11340, 2000 bp (revcom)
AGCGTTATGATGTGTTATTTGCTTTTATTTTCTTCTTTCTTTGTCTCGAAGATAACCTAG
CAAACACAATTCTAAGAAAATTCTCGATGAATTGGTTGTCAGCGCTTCCTATTTACTCTA
TGTCCACTTCGTTTGAAACATCAGTGGTTCGAGCAGTAATGACAAAAAGGGCAGAACATT
TCGTTGGCAAAATTTAAACTCGTGCCTCTCATTTTTTTTACTTTTCTCTCCTGCCACCAA
AACCCCGAACCCTGTCCCGTATATACGAGGAACATTGAAAAAAAATCGTGTATGGTAGCG
CCAAGATAGCGAATAAACTATCAGTATTGGCAGGGTGAAGCTAAGGATATGTTGTTTGCT
AACAAAGGGAAATGCTTTCGTTATAATCGCCCGCGTGCGTCTACTAAAATATGATCTATA
TATACCACCCAGTCTATTGCAGTGTTACGTACATCAAAATGCGCGCATGTAAGTGAACAA
GTTTTTTTTGTTTAAAGAGCGATTTTCCAATAAAGGCTTTGGATATACACTGGTGCAAAA
TATATGGTCAATGACGCCAATTACTGGTGTAGCATGAGAATACGTCGTCCGAAAGAGTTT
TTTTTTACAAACTACGGCAAAGCAAAGCACCACTGGCGCAATTCAAAACATGCCGTCCCC
GTACTAAGTTATGTACGTTATTATGGACGGATCCAAAATTATACTCTAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCGTAGCACCTTCTTCGTGTCCTTTCCTTCTT
CTGCATTAGGCTTACTAGCGTCCTTTCCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGA
CAAATCTCGCTGAGTTGGAAAGACACCTTTTATATAGCCGTACGTGCGGCTCCTCGAGAA
AGGCCCTGCTATATTTCACTAGCTGATCCTCGAGCTGCGATCAACGAAAGCCCCATCCAA
AAGGCTCCTTTTTCTTCAAAGAAGCATGACAGTAAAATAT
>MIT_Sbay_c896_21277 YDR047W 5' untranslated region, Contig c896 2230 - 4229(revcom), 2000 bp (revcom)
AGTGTTAACAGTATCTTTTGCCTTTTTTTATTCTAATAGCTACCCCAGGAATCACTATTT
AGCAAAGATCGTTTGCAAATTGGCCGTCAGTACGTTCTAAGTTCTTTAGAACATCATTGG
CTCGAGCATTAGTGACACGAATAGGAAAGCATTTCGTTGACAAAAATAAAATTGTTTCTT
TATTTTTTCCCTCTTTTCCATGGCGTCAAAAAACCCCGAACCCTGTATAAACGAGGAAGC
TGCATGGTAGCGCCAGAAAAGGCAGATAACCTTTAACAGTGCTGACAGAACAACGTCAAA
CATGTGCGGATAATGCCTTCGCTGACGGCAAGAAATTATATACGCCTCGAAACTGTAGAA
CGTCTTTTGTGCCGCTTGGTAACAAATAAACCTAGCCGGGGCCAGAATTTCACCCGTACA
TACTTACTGTTACATACTGCATGCACGCTACGCATTCTCACCGAACATCGAATCTGCCTG
CAGAAGCGAAGAAAAGCAAGTCTTCGAAGAGCAAGCTTACATCCATCGTGTTGAACACAT
ATGCCCAGCAAAGGGATCGGATGACGCCCAACTAACATTGGAATTTGTGACGCAAGGCTG
AAAGGCACTTCTCTATAGCCCACGGTGAAGCCTTACGCTATTGACAAGACAAAACATGCC
GATCCAAGCCAGGCGAAACGGGCCTAGCACTACGCAGCCAAACACTGGCGTTCCGCCCGT
CCCATCCAGTTTCATTTCTTATTTCGTTCTGCCTTGGGCCTAGCAGCGTGCTTGCCGGAT
GAGTTTTTTCCATTTTCCTACCGGCTCATCTCGCTAAGCTGAAAGGTCAGTTTTATAGCC
GTGTGCGCGGCATCGAGAGACAGGTTCAGCTAATGATATTTGCCTAATTCTCGAGCTGAG
GCCAATGAAGGCAGCTTCCAGGGCTCGTTTCTGCTCGGGAAAAAGCATACCACACATTTG
CACGGCTTTTATGTGCCATAGTGCCACCACTAGCCCCCAG
>WashU_Skud_Contig1362.1 YDR047W 5' untranslated region, Contig c1362 1 - 761, 2000 bp (revcom)
AGTGTTGATGGTATCTTTTGATTTTTTCTAGATTGGTAGCAAGCTCAATTGGCACAGCTC
TAAAAAAAGCCTTGTGAATTGGATAGTACCTTCTTTCGTTTGGAACATTACTGCTTCGAG
CAATAAACATACGAAAGGCAGAACACCTCGTTGACAAAACTGAAACTATTTCTTCAATTT
TTTGGCCTTTTTTCCTGCTGCCAAAAAACCCCGAATCATGTAGAAGCGAGAAGTAAAACA
GAGGAAGTGTATGGTAGCGCCAAGGAAAACGGGCAATACTTAGAAAGAATGACAGAGCTC
AGCCAAGTGTAAGCTAAGTGTTGACAAGGGAAGGTACATTGGGCCCCGAAAAAATTTGCT
AATGCTCGAAGAGCTCTCAATCAATCACCCACATATATGTACTACAGTATATTTATACTT
TCCACGCAGTCTCACGCAGTGCCACCTTCATCACCATGCGTGTAACTAATCGAGCAAGCT
GTTTTACGAAGGGCAGCTTTCCTATAAGCGTTTTGAACATGCATGGCTGCACTGCAATGA
GATCAGGCGACTCCAATTCCATAGCCTAGCACGGGATTAAGTAACGAGAAACTGAAAGAG
ATAATTTTACAAACCCGGACGAAGCAGAGCACTTGCTGGAACAAATCAAACATGCCGTCC
CCTACCAGCTCTCGAAGCGGGCCTAGCATTACTCGATCGAACGTTGCCGTTTAGTCTTAT
TTTCCTTTCCGTGCTGCGCTGCTTTTTTCTTGCATTGGGCT
>SGD_Scer_YDR044W HEM13 "Coproporphyrinogen III oxidase, an oxygen requiring enzyme that catalyzes the sixth step in the heme biosynthetic pathway; localizes to the mitochondrial inner membrane; transcription is repressed by oxygen and heme (via Rox1p and Hap1p)"
CTTTATGTGTATTTAATTGTGTTCGAAGAGTTCGGTTTGCTATGTTTGATTTGCGAAAAG
AAAGCTTTTGATATGCTCAAAAAAAGAAAACCCGGAGAATAAAAGCTTAACAAAGAAAGA
CAATAGGTGGAAAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTCGAAACGAGAACA
ATGGGCAAAGCAAGCTTTATCTTCGGATCGTCCGTCAGCGCTTTGGTTGCAGTCTTATGC
TTTGTTCAAGCTGGAGCGTTATTGGTGGGAGAACCAGAAAAGGCGAAAGCGTAGCGTTCT
TTGAAATTTGGCTTCTGTTCCTGCGACTCGTTTAAAAGTAGAAGGGCCCGCGGAGCCGCT
GTGAAAGATTTCTTTTACTCTTTCAGCGCAGAAATCTCGCAGGAGCTCAGCAGAAAGTGC
CTATGACGGTAATCCCAGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAATTAA
AATACCGTGCCTATAGTAACTTTTTTTTACGCTGTGAACCGTTCAACACACAGTAAAAAC
TCCGCAGGAAATGGTTTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTTTCCCAACA
GTGAACGAGAGGACAAACTCCAGAGGATTTGCGGGCTTGATGATAAAATGTATTGTTGAA
AAGATCGCGAATGCAACAATTACGGTGGGGAGAAATATCAACAAAAGGGCAAGGCTATGC
CTTCTGGAAAGTGGCAGACTTGCACTTTCCTCGAAAAGAAAAATGACCGCAAGATCCGGT
TGTTCTCAACCTTCTACATTAAGACATACTTCTACGATTTTCGAATGCCGAAGCAACTAT
CGCTGAAATTTGTCATGTCAAAATTGCTACTGGGGGAGAAGAATATATATGGAAGTAATT
ATTATTTACGTTGCTGAAATGGCAGGTTAGACGCATGTTTTGCAAAATAAGTGGTTTTGA
AAAGAATTGATACTAGGAATCGGTGCAATACCTTCTACCT
>MIT_Spar_c130_3912 YDR044W 5' untranslated region, Contig c130 4128 - 6127, 2000 bp (revcom)
CTTTATATGTGTGTTTTGTGGTGTTCGAAATTGGTTTCTTTTGTTCGACTTGCGAGAAGA
AAGCTATCAATATGCTTTCCAAAAAAAGCTGGAGAATAAAAGCTTAACAAAGAAAGACAA
TAGGCGGAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTTCGAAACGAGAACAATGG
ACAAATCAAGCTTTATCTATGGGTTGTCAGCTCTTTGGTTGCAGTCTTGTGCTTGGTTCA
AGCTGGGGCATTATTGGTGGGAGAAGCCAGAAAAGGCGAAAGCGTAGCGTTCTTTGAAAT
TTGGATTCTGTTCCTGCGACTCGTTTAAAAGAAGAAGGGCTGCGGAGCCACTGTGAAAGA
CTTGTTGTGCTCTTTCAACTAAGAAATCTGGCAGGAACTCGATATAAAGTGCCTGTGACA
GTAATCTCAGGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAAATTGAAATACC
GTGCCTATGGTAACTTTTTTTTACGCTGCGAACCGTTCAACACACATTGAAAACCCCGCA
GCAATTGTTCTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTCTCCCAACAGTGTAC
GAGCGGACGAAACTCTAGAGGATTTGCAGGCTCGGTGATAAAATGTATTGTTGAAAAGAA
CGCGAATGCAACGATTGTGGTGGAGAGAAATATCAACAGGGCAAGGCAAGGCTATGCTCT
TTTGGAAGTGGCGGACTTGCACTTTCTTGAAAAGAAAAATGACCGCAAGATCCGGTTGTT
CATAACTTTCTACAATAAGGCATACTTCTACGGTTTTCCAATGCTGAGGCAACTATCGCT
ATAAAATCGCTGCTAGGAGAAGATTATATATGGACGTAAATATTTTTTACGTTACTAAAA
TTCTAGGTTAGAGGCACGTTTTGCAGAACCAGTGGCCTTGGAAAGGTGTTGCTACAAATT
TATGCAATTTCTTCAACTTGCCAGGTGGTCTTGGATGATC
>MIT_Sbay_c896_21290 YDR044W 5' untranslated region, Contig c896 7383 - 9382(revcom), 2000 bp (revcom)
CTTGTTATGTGTGTTTGTGGTGATTGCGGTTTGGTTTTTCTGATTCGTATGACAGAAAGA
AAAAAATTCAGTTTACCTTGTAAGGTGATTAGGAGAAGAAAAAAAGCTTATTGGCAGCGA
ACAATAGGTGAAAAAAAAAAAGAAAATGCGTGTCCTTATATAGCTTTCTCGAAGGGAGAA
CAATGGATAAATCAAAGCTTATCTACGGGTCAACAGCTCTTTGGTTGCTGTCTTGCTCTA
GGTCCAAGCTGGGGCATAATTGGTGGGAGAAGCCAGAAAATGCGAAAGCGTACCGTTCTG
TGAAAAATGGCTTCGGTTCCTGCGACTCGTTTAAAAAGAAAAGGGCCCGCGCAGCCTGTG
TGAAATGTTCGTTTTGCCCTTCCCAGAGAGAAATCTTGCAGGAGCCTCAATACAATGTGC
CTGCGGATGGAATACCAGGGGATAAAGGCGTGAAGGCACTCCCTGAACAATTGAAAATTG
GAAAAAAAAAGTGCCTGTGATGAATCTTATACGTTGGGAAAACTCCAAGACACTTTTAAA
ACTCCGCAGAGATTGTTTGGAGGGACCTTGACCACGAGTTGGGAGTATTGTTTTTTCCTG
GAAGGAACGAGCGGAACTCTTGGGGATTTGCGGGCTCGCTAATAAAAAGTGTCTTGTTGA
AGAAAAGTAGAATGCGACTAAAACGGTGGAGGAAAATATCAACAAGGCAAGGCTATGCCT
TTCGAAGAAAAGCGGACTTGCAATTGCACAACCGTATCGAAGAGAATTGAGAAGGGGGTG
CAAAGTGATCCGGTTGTTCATATTTCTTCACCAATTGATACAATTATCTACGTTTGTTCT
GTTGACCAATCCAACGGGGACTCTGTATGACATAAGTCTTCCTTACATTGCTAAGATCCA
AGATCAGACCCGTAGATGAGTTCTGCACCAAAGAGTTGTTAACCGTCTTGCCTGAATAAT
TTTAAGTTGTCGCGATCCTCTTACAAGGTGTTCTTATTTC
>WashU_Smik_Contig2283.3 YDR044W 5' untranslated region, Contig c2283 2261 - 4260(revcom), 2000 bp (revcom)
CTTTATTGAGGATTTGTGGCGTTTGAGGTTTGGTTTTTTATTCAATTTGAAAGAAGAAAA
CTATCGTTATACTTTCGAAGAAAACACGGGGAATAAAAGCTTAACAGGTGAGACAATAGG
TGGAAAAAAAGGAAAATATGTGTCTTTATATAGCCTTTTCAAAAAGAGAACAATGGTCAA
ATAAAGGTTTATCTACGAGTCGACAGTTCGTTGGCTGCAGTGTTACGCTTGGTTGAAGCT
GGGGCATTATTGGTGGAAGAAGCCAGAAAAGACGAAAGAGTAGCGTAGCGTTCTTTCAAA
TTTTGGTTTCGGGTTCCTGCGACTCGTTTAAAAAAGAAAAGGGCCCGCGGCCCCGCCGTG
AAACACTTCGTCTTGCTCTTCCCACCCAGAAAACTTGTAGGAGCCTCAGTTACAAAGTGC
CTGTAATGGAAATCTTAGGGGGCTACTATTGTAAAGGCAATTTCTGAACAATTGAAAGTG
AAAATATCGTGCCTGTGGTAACTTTCTTATACGCCGTGAAACGTTTAACATACGTTGAAA
ACTCCGCAGGGATTGGTTTGGAAAATTATAGTCACGAATTAGGCGTATTGTCTTTCAAGA
AGGTACGAGCGGATGAACTTCTTGAGGATTTGCGGGTTCGGTGATAAAAAATGTATTGTT
GAAAAGAACGCGAATGCAACAATTACGGTGGAGAAAAATATTAACAAGGGAAGGCAAGGC
TATGTTCTATTGAGAAGCGGCGGACTTGCACTTTCCTCGAAGAAAAAAATGTCTTCAAGA
TCCAATGTTCATATAACTTTCTACAATAAGGTATCCTTCTACGATCTTTCAATGTTAAGA
TTGAAATCAATGTAAAAAGCACCATGTTGAATACTACTGCTAGGAGGAGATCACATATGA
ATGTGATTATTATTTATATTAGTAAATTTTCAGGTTAGGAAGAAGTTATGTGACGCTTTA
GCTTTGGAAATTTGTTGCGGGAAACTGATAACATTCTTTT
BioPerl-1.007002/t/data/map_hem/HEM12-HEM13.meme.txt000444000766000024     11230713155576321 21354 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM12-HEM13.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDR047W         1.0000   1000  MIT_Spar_c130_3923       1.0000   1000  
MIT_Sbay_c896_21277      1.0000   1000  WashU_Skud_Contig1362.1  1.0000    761  
SGD_Scer_YDR044W         1.0000   1000  MIT_Spar_c130_3912       1.0000   1000  
MIT_Sbay_c896_21290      1.0000   1000  WashU_Smik_Contig2283.3  1.0000   1000  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM12-HEM13.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        8    maxsites=        8    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            7761    N=               8
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.291 C 0.209 G 0.209 T 0.291 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   8   llr = 167   E-value = 1.0e-013
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :1165:9:1a::11:::1a:
pos.-specific     C  :::::a::4:3::11:5:::
probability       G  :9945:1:::1:98:559:a
matrix            T  a::::::a5:6a::95::::

         bits    2.5      *             *
                 2.3      *             *
                 2.0      *             *
                 1.8  **  *      *    * *
Information      1.5 ***  * * * **   ****
content          1.3 ***  *** * **** ****
(30.1 bits)      1.0 ******** * *********
                 0.8 ******** ***********
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TGGAACATTATTGGTGCGAG
consensus               GG   C C    TG   
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c130_3912           +    244  1.31e-12 TGGTTCAAGC TGGGGCATTATTGGTGGGAG AAGCCAGAAA
MIT_Sbay_c896_21290          +    250  2.00e-11 AGGTCCAAGC TGGGGCATAATTGGTGGGAG AAGCCAGAAA
SGD_Scer_YDR044W             +    252  2.47e-11 TTGTTCAAGC TGGAGCGTTATTGGTGGGAG AACCAGAAAA
WashU_Smik_Contig2283.3      +    240  7.53e-11 TGGTTGAAGC TGGGGCATTATTGGTGGAAG AAGCCAGAAA
WashU_Skud_Contig1362.1      +    101  2.45e-10 TTCTTTCGTT TGGAACATTACTGCTTCGAG CAATAAACAT
MIT_Spar_c130_3923           +    134  5.96e-10 CCACTTCGTT TGAAACATCAGTGGTTCGAG CAGTAATGAC
MIT_Sbay_c896_21277          +    107  7.56e-10 CTAAGTTCTT TAGAACATCATTGGCTCGAG CATTAGTGAC
SGD_Scer_YDR047W             +    137  1.93e-09 TACCTTCGTC TGGAACATCACTAATTCGAG CGGTAAAGAT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c130_3912                1.3e-12  243_[+1]_737
MIT_Sbay_c896_21290                 2e-11  249_[+1]_731
SGD_Scer_YDR044W                  2.5e-11  251_[+1]_729
WashU_Smik_Contig2283.3           7.5e-11  239_[+1]_741
WashU_Skud_Contig1362.1           2.5e-10  100_[+1]_641
MIT_Spar_c130_3923                  6e-10  133_[+1]_847
MIT_Sbay_c896_21277               7.6e-10  106_[+1]_874
SGD_Scer_YDR047W                  1.9e-09  136_[+1]_844
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=8
MIT_Spar_c130_3912       (  244) TGGGGCATTATTGGTGGGAG  1 
MIT_Sbay_c896_21290      (  250) TGGGGCATAATTGGTGGGAG  1 
SGD_Scer_YDR044W         (  252) TGGAGCGTTATTGGTGGGAG  1 
WashU_Smik_Contig2283.3  (  240) TGGGGCATTATTGGTGGAAG  1 
WashU_Skud_Contig1362.1  (  101) TGGAACATTACTGCTTCGAG  1 
MIT_Spar_c130_3923       (  134) TGAAACATCAGTGGTTCGAG  1 
MIT_Sbay_c896_21277      (  107) TAGAACATCATTGGCTCGAG  1 
SGD_Scer_YDR047W         (  137) TGGAACATCACTAATTCGAG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 1.0e-013 
  -965   -965   -965    162 
  -137   -965    232   -965 
  -137   -965    232   -965 
    95   -965    109   -965 
    62   -965    151   -965 
  -965    251   -965   -965 
   143   -965    -49   -965 
  -965   -965   -965    162 
  -137    109   -965     62 
   162   -965   -965   -965 
  -965     51    -49     95 
  -965   -965   -965    162 
  -137   -965    232   -965 
  -137    -49    209   -965 
  -965    -49   -965    143 
  -965   -965    151     62 
  -965    151    151   -965 
  -137   -965    232   -965 
   162   -965   -965   -965 
  -965   -965    251   -965 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 1.0e-013 
 0.000000  0.000000  0.000000  1.000000 
 0.125000  0.000000  0.875000  0.000000 
 0.125000  0.000000  0.875000  0.000000 
 0.625000  0.000000  0.375000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.875000  0.000000  0.125000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.125000  0.375000  0.000000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.250000  0.125000  0.625000 
 0.000000  0.000000  0.000000  1.000000 
 0.125000  0.000000  0.875000  0.000000 
 0.125000  0.125000  0.750000  0.000000 
 0.000000  0.125000  0.000000  0.875000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.500000  0.500000  0.000000 
 0.125000  0.000000  0.875000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
TGG[AG][AG]CAT[TC]A[TC]TGGT[GT][CG]GAG
--------------------------------------------------------------------------------




Time  6.16 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   8   llr = 161   E-value = 5.1e-011
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  ::1:1::1:6:1:::1:98a
pos.-specific     C  1::951:9::a:85:3::::
probability       G  9:4:4:a:a4::154:513:
matrix            T  :a51:9:::::91:665:::

         bits    2.5       * * *         
                 2.3       * * *         
                 2.0 *     * * *         
                 1.8 *  *  *** *         
Information      1.5 ** *  *** *  *     *
content          1.3 ** * **** * **   * *
(29.0 bits)      1.0 ** ************ ****
                 0.8 ** ************ ****
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GTTCCTGCGACTCCTTGAAA
consensus              G G    G   GGCT G 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Smik_Contig2283.3      +    313  1.96e-11 TTGGTTTCGG GTTCCTGCGACTCGTTTAAA AAAGAAAAGG
MIT_Sbay_c896_21290          +    316  1.96e-11 AATGGCTTCG GTTCCTGCGACTCGTTTAAA AAGAAAAGGG
MIT_Spar_c130_3912           +    310  1.96e-11 TTTGGATTCT GTTCCTGCGACTCGTTTAAA AGAAGAAGGG
SGD_Scer_YDR044W             +    317  1.96e-11 TTTGGCTTCT GTTCCTGCGACTCGTTTAAA AGTAGAAGGG
SGD_Scer_YDR047W             +    871  6.56e-11 TAATGTAGCC GTGCATGCGGCTCCGCGAAA AGAGCTCTGC
MIT_Spar_c130_3923           +    880  1.43e-10 TTATATAGCC GTACGTGCGGCTCCTCGAGA AAGGCCCTGC
WashU_Skud_Contig1362.1      -    420  9.20e-09 GAAGGTGGCA CTGCGTGAGACTGCGTGGAA AGTATAAATA
MIT_Sbay_c896_21277          +    841  2.90e-08 TTTTATAGCC GTGTGCGCGGCATCGAGAGA CAGGTTCAGC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Smik_Contig2283.3             2e-11  312_[+2]_668
MIT_Sbay_c896_21290                 2e-11  315_[+2]_665
MIT_Spar_c130_3912                  2e-11  309_[+2]_671
SGD_Scer_YDR044W                    2e-11  316_[+2]_664
SGD_Scer_YDR047W                  6.6e-11  870_[+2]_110
MIT_Spar_c130_3923                1.4e-10  879_[+2]_101
WashU_Skud_Contig1362.1           9.2e-09  419_[-2]_322
MIT_Sbay_c896_21277               2.9e-08  840_[+2]_140
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=8
WashU_Smik_Contig2283.3  (  313) GTTCCTGCGACTCGTTTAAA  1 
MIT_Sbay_c896_21290      (  316) GTTCCTGCGACTCGTTTAAA  1 
MIT_Spar_c130_3912       (  310) GTTCCTGCGACTCGTTTAAA  1 
SGD_Scer_YDR044W         (  317) GTTCCTGCGACTCGTTTAAA  1 
SGD_Scer_YDR047W         (  871) GTGCATGCGGCTCCGCGAAA  1 
MIT_Spar_c130_3923       (  880) GTACGTGCGGCTCCTCGAGA  1 
WashU_Skud_Contig1362.1  (  420) CTGCGTGAGACTGCGTGGAA  1 
MIT_Sbay_c896_21277      (  841) GTGTGCGCGGCATCGAGAGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 5.1e-011 
  -965    -49    232   -965 
  -965   -965   -965    162 
  -137   -965    109     62 
  -965    232   -965   -137 
  -137    151    109   -965 
  -965    -49   -965    143 
  -965   -965    251   -965 
  -137    232   -965   -965 
  -965   -965    251   -965 
    95   -965    109   -965 
  -965    251   -965   -965 
  -137   -965   -965    143 
  -965    209    -49   -137 
  -965    151    151   -965 
  -965   -965    109     95 
  -137     51   -965     95 
  -965   -965    151     62 
   143   -965    -49   -965 
   121   -965     51   -965 
   162   -965   -965   -965 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 5.1e-011 
 0.000000  0.125000  0.875000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.125000  0.000000  0.375000  0.500000 
 0.000000  0.875000  0.000000  0.125000 
 0.125000  0.500000  0.375000  0.000000 
 0.000000  0.125000  0.000000  0.875000 
 0.000000  0.000000  1.000000  0.000000 
 0.125000  0.875000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.625000  0.000000  0.375000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.125000  0.000000  0.000000  0.875000 
 0.000000  0.750000  0.125000  0.125000 
 0.000000  0.500000  0.500000  0.000000 
 0.000000  0.000000  0.375000  0.625000 
 0.125000  0.250000  0.000000  0.625000 
 0.000000  0.000000  0.500000  0.500000 
 0.875000  0.000000  0.125000  0.000000 
 0.750000  0.000000  0.250000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
GT[TG]C[CG]TGCG[AG]CTC[CG][TG][TC][GT]A[AG]A
--------------------------------------------------------------------------------




Time 12.22 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   15   sites =   8   llr = 136   E-value = 3.8e-008
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :9::6:::::1::::
pos.-specific     C  5::::::5:5:::4:
probability       G  519a4:::a59a5::
matrix            T  ::1::aa5::::56a

         bits    2.5    *    *  *   
                 2.3    *    *  *   
                 2.0    *    *  *   
                 1.8   **    * **   
Information      1.5 * ** ** ****  *
content          1.3 **** ** ****  *
(24.5 bits)      1.0 ***************
                 0.8 ***************
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           CAGGATTCGCGGGTT
consensus            G   G  T G  TC 
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
SGD_Scer_YDR044W             +    623  5.51e-09 ACAAACTCCA GAGGATTTGCGGGCT TGATGATAAA
MIT_Sbay_c896_21277          -    211  5.51e-09 CTCGTTTATA CAGGGTTCGGGGTTT TTTGACGCCA
MIT_Spar_c130_3923           -    240  5.51e-09 ATATACGGGA CAGGGTTCGGGGTTT TGGTGGCAGG
SGD_Scer_YDR047W             -    243  5.51e-09 ATATACAGGA CAGGGTTCGGGGTTT TTGGCGGCAG
WashU_Smik_Contig2283.3      +    624  8.25e-09 TGAACTTCTT GAGGATTTGCGGGTT CGGTGATAAA
MIT_Sbay_c896_21290          +    622  1.72e-08 CGGAACTCTT GGGGATTTGCGGGCT CGCTAATAAA
MIT_Spar_c130_3912           +    618  4.23e-08 CGAAACTCTA GAGGATTTGCAGGCT CGGTGATAAA
WashU_Skud_Contig1362.1      -    206  5.24e-08 CTCGCTTCTA CATGATTCGGGGTTT TTTGGCAGCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR044W                  5.5e-09  622_[+3]_363
MIT_Sbay_c896_21277               5.5e-09  210_[-3]_775
MIT_Spar_c130_3923                5.5e-09  239_[-3]_746
SGD_Scer_YDR047W                  5.5e-09  242_[-3]_743
WashU_Smik_Contig2283.3           8.2e-09  623_[+3]_362
MIT_Sbay_c896_21290               1.7e-08  621_[+3]_364
MIT_Spar_c130_3912                4.2e-08  617_[+3]_368
WashU_Skud_Contig1362.1           5.2e-08  205_[-3]_541
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=15 seqs=8
SGD_Scer_YDR044W         (  623) GAGGATTTGCGGGCT  1 
MIT_Sbay_c896_21277      (  211) CAGGGTTCGGGGTTT  1 
MIT_Spar_c130_3923       (  240) CAGGGTTCGGGGTTT  1 
SGD_Scer_YDR047W         (  243) CAGGGTTCGGGGTTT  1 
WashU_Smik_Contig2283.3  (  624) GAGGATTTGCGGGTT  1 
MIT_Sbay_c896_21290      (  622) GGGGATTTGCGGGCT  1 
MIT_Spar_c130_3912       (  618) GAGGATTTGCAGGCT  1 
WashU_Skud_Contig1362.1  (  206) CATGATTCGGGGTTT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 7649 bayes= 9.89955 E= 3.8e-008 
  -965    151    151   -965 
   143   -965    -49   -965 
  -965   -965    232   -137 
  -965   -965    251   -965 
    95   -965    109   -965 
  -965   -965   -965    162 
  -965   -965   -965    162 
  -965    151   -965     62 
  -965   -965    251   -965 
  -965    151    151   -965 
  -137   -965    232   -965 
  -965   -965    251   -965 
  -965   -965    151     62 
  -965    109   -965     95 
  -965   -965   -965    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 3.8e-008 
 0.000000  0.500000  0.500000  0.000000 
 0.875000  0.000000  0.125000  0.000000 
 0.000000  0.000000  0.875000  0.125000 
 0.000000  0.000000  1.000000  0.000000 
 0.625000  0.000000  0.375000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.125000  0.000000  0.875000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.375000  0.000000  0.625000 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
[CG]AGG[AG]TT[CT]G[CG]GG[GT][TC]T
--------------------------------------------------------------------------------




Time 18.15 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =   8   llr = 155   E-value = 1.1e-008
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  aa13::a6a415:5::::1:
pos.-specific     C  ::::54::::9:111a:1:4
probability       G  ::5856:4:6:5::4:a::6
matrix            T  ::4:::::::::945::99:

         bits    2.5                **   
                 2.3                **   
                 2.0                **   
                 1.8           *    **   
Information      1.5 ** **** * *    **  *
content          1.3 ** **** *** *  *** *
(27.9 bits)      1.0 ** **********  *****
                 0.8 ************* ******
                 0.5 ************* ******
                 0.3 ********************
                 0.0 --------------------

Multilevel           AAGGCGAAAGCATATCGTTG
consensus              TAGC G A G TG    C
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c130_3912           +    273  3.90e-12 GAAGCCAGAA AAGGCGAAAGCGTAGCGTTC TTTGAAATTT
SGD_Scer_YDR044W             +    280  3.90e-12 AGAACCAGAA AAGGCGAAAGCGTAGCGTTC TTTGAAATTT
MIT_Sbay_c896_21290          +    279  2.45e-10 GAAGCCAGAA AATGCGAAAGCGTACCGTTC TGTGAAAAAT
MIT_Spar_c130_3923           +    167  3.43e-10 TAATGACAAA AAGGGCAGAACATTTCGTTG GCAAAATTTA
MIT_Sbay_c896_21277          +    140  1.28e-09 TAGTGACACG AATAGGAAAGCATTTCGTTG ACAAAAATAA
SGD_Scer_YDR047W             +    170  3.28e-09 TAAAGATGAA AATGGCAGAACATTTCGCTG GCAAAATTAA
WashU_Smik_Contig2283.3      +    269  7.13e-09 GAAGCCAGAA AAGACGAAAGAGTAGCGTAG CGTTCTTTCA
WashU_Skud_Contig1362.1      +    134  8.94e-09 TAAACATACG AAAGGCAGAACACCTCGTTG ACAAAACTGA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c130_3912                3.9e-12  272_[+4]_708
SGD_Scer_YDR044W                  3.9e-12  279_[+4]_701
MIT_Sbay_c896_21290               2.4e-10  278_[+4]_702
MIT_Spar_c130_3923                3.4e-10  166_[+4]_814
MIT_Sbay_c896_21277               1.3e-09  139_[+4]_841
SGD_Scer_YDR047W                  3.3e-09  169_[+4]_811
WashU_Smik_Contig2283.3           7.1e-09  268_[+4]_712
WashU_Skud_Contig1362.1           8.9e-09  133_[+4]_608
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=8
MIT_Spar_c130_3912       (  273) AAGGCGAAAGCGTAGCGTTC  1 
SGD_Scer_YDR044W         (  280) AAGGCGAAAGCGTAGCGTTC  1 
MIT_Sbay_c896_21290      (  279) AATGCGAAAGCGTACCGTTC  1 
MIT_Spar_c130_3923       (  167) AAGGGCAGAACATTTCGTTG  1 
MIT_Sbay_c896_21277      (  140) AATAGGAAAGCATTTCGTTG  1 
SGD_Scer_YDR047W         (  170) AATGGCAGAACATTTCGCTG  1 
WashU_Smik_Contig2283.3  (  269) AAGACGAAAGAGTAGCGTAG  1 
WashU_Skud_Contig1362.1  (  134) AAAGGCAGAACACCTCGTTG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 1.1e-008 
   162   -965   -965   -965 
   162   -965   -965   -965 
  -137   -965    151     21 
   -38   -965    209   -965 
  -965    151    151   -965 
  -965    109    183   -965 
   162   -965   -965   -965 
    95   -965    109   -965 
   162   -965   -965   -965 
    21   -965    183   -965 
  -137    232   -965   -965 
    62   -965    151   -965 
  -965    -49   -965    143 
    62    -49   -965     21 
  -965    -49    109     62 
  -965    251   -965   -965 
  -965   -965    251   -965 
  -965    -49   -965    143 
  -137   -965   -965    143 
  -965    109    183   -965 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 1.1e-008 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.125000  0.000000  0.500000  0.375000 
 0.250000  0.000000  0.750000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.000000  0.375000  0.625000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.625000  0.000000  0.375000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.375000  0.000000  0.625000  0.000000 
 0.125000  0.875000  0.000000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  0.125000  0.000000  0.875000 
 0.500000  0.125000  0.000000  0.375000 
 0.000000  0.125000  0.375000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.125000  0.000000  0.875000 
 0.125000  0.000000  0.000000  0.875000 
 0.000000  0.375000  0.625000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
AA[GT][GA][CG][GC]A[AG]A[GA]C[AG]T[AT][TG]CGTT[GC]
--------------------------------------------------------------------------------




Time 24.05 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =   8   llr = 150   E-value = 3.2e-007
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  1::::1a643:6:85:aa::
pos.-specific     C  135:a:::44:4:11a::31
probability       G  :1:::9:431a:91:::::9
matrix            T  865a:::::3::1:4:::8:

         bits    2.5     *     *    *    
                 2.3     *     *    *    
                 2.0     *     *    *   *
                 1.8     **    * *  *   *
Information      1.5    ****   * *  *** *
content          1.3    ****   * *  *** *
(27.0 bits)      1.0   ******  ***  *****
                 0.8 ********  **** *****
                 0.5 ********* **** *****
                 0.3 ********************
                 0.0 --------------------

Multilevel           TTCTCGAAACGAGAACAATG
consensus             CT    GCA C  T   C 
sequence                     GT          
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c130_3912           +    160  8.41e-11 TTATATAGCC TTTTCGAAACGAGAACAATG GACAAATCAA
MIT_Sbay_c896_21290          +    166  1.14e-10 TTATATAGCT TTCTCGAAGGGAGAACAATG GATAAATCAA
MIT_Spar_c130_3923           +    927  2.25e-10 CACTAGCTGA TCCTCGAGCTGCGATCAACG AAAGCCCCAT
SGD_Scer_YDR044W             +    164  6.26e-10 CTTATATAGC CTTTCGAAACGAGAACAATG GGCAAAGCAA
MIT_Sbay_c896_21277          +    888  1.02e-09 ATTTGCCTAA TTCTCGAGCTGAGGCCAATG AAGGCAGCTT
SGD_Scer_YDR047W             +    918  1.45e-09 CTCTACCTGA ACTTCGAGCCGCGATCAACG AAAGCTCTCA
WashU_Smik_Contig2283.3      +    156  6.02e-09 TTATATAGCC TTTTCAAAAAGAGAACAATG GTCAAATAAA
WashU_Skud_Contig1362.1      +    363  3.46e-08 AATTTGCTAA TGCTCGAAGAGCTCTCAATC AATCACCCAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c130_3912                8.4e-11  159_[+5]_821
MIT_Sbay_c896_21290               1.1e-10  165_[+5]_815
MIT_Spar_c130_3923                2.2e-10  926_[+5]_54
SGD_Scer_YDR044W                  6.3e-10  163_[+5]_817
MIT_Sbay_c896_21277                 1e-09  887_[+5]_93
SGD_Scer_YDR047W                  1.4e-09  917_[+5]_63
WashU_Smik_Contig2283.3             6e-09  155_[+5]_825
WashU_Skud_Contig1362.1           3.5e-08  362_[+5]_379
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=8
MIT_Spar_c130_3912       (  160) TTTTCGAAACGAGAACAATG  1 
MIT_Sbay_c896_21290      (  166) TTCTCGAAGGGAGAACAATG  1 
MIT_Spar_c130_3923       (  927) TCCTCGAGCTGCGATCAACG  1 
SGD_Scer_YDR044W         (  164) CTTTCGAAACGAGAACAATG  1 
MIT_Sbay_c896_21277      (  888) TTCTCGAGCTGAGGCCAATG  1 
SGD_Scer_YDR047W         (  918) ACTTCGAGCCGCGATCAACG  1 
WashU_Smik_Contig2283.3  (  156) TTTTCAAAAAGAGAACAATG  1 
WashU_Skud_Contig1362.1  (  363) TGCTCGAAGAGCTCTCAATC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 3.2e-007 
  -137    -49   -965    121 
  -965     51    -49     95 
  -965    151   -965     62 
  -965   -965   -965    162 
  -965    251   -965   -965 
  -137   -965    232   -965 
   162   -965   -965   -965 
    95   -965    109   -965 
    21    109     51   -965 
   -38    109    -49    -38 
  -965   -965    251   -965 
    95    109   -965   -965 
  -965   -965    232   -137 
   121    -49    -49   -965 
    62    -49   -965     21 
  -965    251   -965   -965 
   162   -965   -965   -965 
   162   -965   -965   -965 
  -965     51   -965    121 
  -965    -49    232   -965 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 3.2e-007 
 0.125000  0.125000  0.000000  0.750000 
 0.000000  0.250000  0.125000  0.625000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.125000  0.000000  0.875000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.625000  0.000000  0.375000  0.000000 
 0.375000  0.375000  0.250000  0.000000 
 0.250000  0.375000  0.125000  0.250000 
 0.000000  0.000000  1.000000  0.000000 
 0.625000  0.375000  0.000000  0.000000 
 0.000000  0.000000  0.875000  0.125000 
 0.750000  0.125000  0.125000  0.000000 
 0.500000  0.125000  0.000000  0.375000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.250000  0.000000  0.750000 
 0.000000  0.125000  0.875000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
T[TC][CT]TCGA[AG][ACG][CAT]G[AC]GA[AT]CAA[TC]G
--------------------------------------------------------------------------------




Time 29.84 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR047W                 7.45e-23  50_[+5(5.03e-05)]_66_[+1(1.93e-09)]_13_[+4(3.28e-09)]_53_[-3(5.51e-09)]_613_[+2(6.56e-11)]_27_[+5(1.45e-09)]_63
MIT_Spar_c130_3923               1.06e-24  133_[+1(5.96e-10)]_13_[+4(3.43e-10)]_53_[-3(5.51e-09)]_110_[-4(7.03e-05)]_238_[+1(6.23e-05)]_237_[+2(1.43e-10)]_27_[+5(2.25e-10)]_54
MIT_Sbay_c896_21277              2.78e-21  5_[-4(5.78e-05)]_81_[+1(7.56e-10)]_13_[+4(1.28e-09)]_51_[-3(5.51e-09)]_615_[+2(2.90e-08)]_27_[+5(1.02e-09)]_93
WashU_Skud_Contig1362.1          1.22e-19  100_[+1(2.45e-10)]_13_[+4(8.94e-09)]_52_[-3(5.24e-08)]_142_[+5(3.46e-08)]_37_[-2(9.20e-09)]_322
SGD_Scer_YDR044W                 3.05e-28  163_[+5(6.26e-10)]_68_[+1(2.47e-11)]_8_[+4(3.90e-12)]_17_[+2(1.96e-11)]_286_[+3(5.51e-09)]_363
MIT_Spar_c130_3912               1.93e-29  159_[+5(8.41e-11)]_64_[+1(1.31e-12)]_9_[+4(3.90e-12)]_17_[+2(1.96e-11)]_288_[+3(4.23e-08)]_69_[-4(1.60e-05)]_279
MIT_Sbay_c896_21290              7.41e-27  165_[+5(1.14e-10)]_64_[+1(2.00e-11)]_9_[+4(2.45e-10)]_17_[+2(1.96e-11)]_8_[-3(7.60e-05)]_3_[-4(2.55e-05)]_240_[+3(1.72e-08)]_66_[-4(1.70e-05)]_278
WashU_Smik_Contig2283.3          1.31e-23  7_[+3(8.33e-05)]_39_[-5(9.82e-05)]_74_[+5(6.02e-09)]_64_[+1(7.53e-11)]_9_[+4(7.13e-09)]_24_[+2(1.96e-11)]_61_[-2(3.93e-05)]_88_[+2(7.74e-05)]_102_[+3(8.25e-09)]_362
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM12-HEM14.fa000444000766000024      1402213155576321 20155 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR047W HEM12 "Uroporphyrinogen decarboxylase, catalyzes the fifth step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; activity inhibited by Cu2+, Zn2+, Fe2+, Fe3+ and sulfhydryl-specific reagents"
AGCGTTATAACCTGTTCTTTGCTTTATTTTTTTTTTTTTTGTTCTTCCTTTTCTCGAAGA
GAGCTTACCAAACACAATTCTGAGATAATGCTTGATGAATTGAAGAACCTATCGATCACT
CTATGTTACCTTCGTCTGGAACATCACTAATTCGAGCGGTAAAGATGAAAATGGCAGAAC
ATTTCGCTGGCAAAATTAAAACTCTTGCCTCATTTTTTTTTGCTTTCCTCTCCTGCCGCC
AAAAACCCCGAACCCTGTCCTGTATATACGAGAAACATTGAAAAAGATCGTGTATGATAG
CGCCAAGATGGCGGATAAACTAACACTATTGACAGGTTGAGGCCAAGGATATATTACTTG
CTAACAGAAAGAGATACTGTCACCACAATTGCCCGCGTACGTATACTACAACATGTTCTC
TATATATCACCCACTCTTTCGCAGTGCTACGTACGCCAAAAACGCGCGCATGGAAGTAAA
GAAGTTTTTTCTTTTAAGAGCGAAGCTCCATTAAAAGCCTTGAATATAAACTAGTGCGAA
GTAGTATGATCCGAAGACACCAATTGCTGGTGCAGCATAGGAATATGTGGCGTCCGAAAA
AGAGCCTTTAACAATCCACGGCGAAACAAGGCACCGCTGTGCATTTAAAACATGCCGTTC
CCGTACCAAGTTATATTGTTACGGATGAATCCAAAATAATTTGTTAAAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCATGGCACCTTCTTCGTTTCTTCATCCTGCA
TTAGACTTACTAGTGTGCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGACACATATCGC
TGAGCTGGAAGGACACCTTTTAATGTAGCCGTGCATGCGGCTCCGCGAAAAGAGCTCTGC
TATATTTCTCTACCTGAACTTCGAGCCGCGATCAACGAAAGCTCTCATCCAAGGCTCGTT
TTTCTTGACAGAAGCATGACAGTAAAATATGCGGTCATTT
>MIT_Spar_c130_3923 YDR047W 5' untranslated region, Contig c130 9341 - 11340, 2000 bp (revcom)
AGCGTTATGATGTGTTATTTGCTTTTATTTTCTTCTTTCTTTGTCTCGAAGATAACCTAG
CAAACACAATTCTAAGAAAATTCTCGATGAATTGGTTGTCAGCGCTTCCTATTTACTCTA
TGTCCACTTCGTTTGAAACATCAGTGGTTCGAGCAGTAATGACAAAAAGGGCAGAACATT
TCGTTGGCAAAATTTAAACTCGTGCCTCTCATTTTTTTTACTTTTCTCTCCTGCCACCAA
AACCCCGAACCCTGTCCCGTATATACGAGGAACATTGAAAAAAAATCGTGTATGGTAGCG
CCAAGATAGCGAATAAACTATCAGTATTGGCAGGGTGAAGCTAAGGATATGTTGTTTGCT
AACAAAGGGAAATGCTTTCGTTATAATCGCCCGCGTGCGTCTACTAAAATATGATCTATA
TATACCACCCAGTCTATTGCAGTGTTACGTACATCAAAATGCGCGCATGTAAGTGAACAA
GTTTTTTTTGTTTAAAGAGCGATTTTCCAATAAAGGCTTTGGATATACACTGGTGCAAAA
TATATGGTCAATGACGCCAATTACTGGTGTAGCATGAGAATACGTCGTCCGAAAGAGTTT
TTTTTTACAAACTACGGCAAAGCAAAGCACCACTGGCGCAATTCAAAACATGCCGTCCCC
GTACTAAGTTATGTACGTTATTATGGACGGATCCAAAATTATACTCTAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCGTAGCACCTTCTTCGTGTCCTTTCCTTCTT
CTGCATTAGGCTTACTAGCGTCCTTTCCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGA
CAAATCTCGCTGAGTTGGAAAGACACCTTTTATATAGCCGTACGTGCGGCTCCTCGAGAA
AGGCCCTGCTATATTTCACTAGCTGATCCTCGAGCTGCGATCAACGAAAGCCCCATCCAA
AAGGCTCCTTTTTCTTCAAAGAAGCATGACAGTAAAATAT
>MIT_Sbay_c896_21277 YDR047W 5' untranslated region, Contig c896 2230 - 4229(revcom), 2000 bp (revcom)
AGTGTTAACAGTATCTTTTGCCTTTTTTTATTCTAATAGCTACCCCAGGAATCACTATTT
AGCAAAGATCGTTTGCAAATTGGCCGTCAGTACGTTCTAAGTTCTTTAGAACATCATTGG
CTCGAGCATTAGTGACACGAATAGGAAAGCATTTCGTTGACAAAAATAAAATTGTTTCTT
TATTTTTTCCCTCTTTTCCATGGCGTCAAAAAACCCCGAACCCTGTATAAACGAGGAAGC
TGCATGGTAGCGCCAGAAAAGGCAGATAACCTTTAACAGTGCTGACAGAACAACGTCAAA
CATGTGCGGATAATGCCTTCGCTGACGGCAAGAAATTATATACGCCTCGAAACTGTAGAA
CGTCTTTTGTGCCGCTTGGTAACAAATAAACCTAGCCGGGGCCAGAATTTCACCCGTACA
TACTTACTGTTACATACTGCATGCACGCTACGCATTCTCACCGAACATCGAATCTGCCTG
CAGAAGCGAAGAAAAGCAAGTCTTCGAAGAGCAAGCTTACATCCATCGTGTTGAACACAT
ATGCCCAGCAAAGGGATCGGATGACGCCCAACTAACATTGGAATTTGTGACGCAAGGCTG
AAAGGCACTTCTCTATAGCCCACGGTGAAGCCTTACGCTATTGACAAGACAAAACATGCC
GATCCAAGCCAGGCGAAACGGGCCTAGCACTACGCAGCCAAACACTGGCGTTCCGCCCGT
CCCATCCAGTTTCATTTCTTATTTCGTTCTGCCTTGGGCCTAGCAGCGTGCTTGCCGGAT
GAGTTTTTTCCATTTTCCTACCGGCTCATCTCGCTAAGCTGAAAGGTCAGTTTTATAGCC
GTGTGCGCGGCATCGAGAGACAGGTTCAGCTAATGATATTTGCCTAATTCTCGAGCTGAG
GCCAATGAAGGCAGCTTCCAGGGCTCGTTTCTGCTCGGGAAAAAGCATACCACACATTTG
CACGGCTTTTATGTGCCATAGTGCCACCACTAGCCCCCAG
>WashU_Skud_Contig1362.1 YDR047W 5' untranslated region, Contig c1362 1 - 761, 2000 bp (revcom)
AGTGTTGATGGTATCTTTTGATTTTTTCTAGATTGGTAGCAAGCTCAATTGGCACAGCTC
TAAAAAAAGCCTTGTGAATTGGATAGTACCTTCTTTCGTTTGGAACATTACTGCTTCGAG
CAATAAACATACGAAAGGCAGAACACCTCGTTGACAAAACTGAAACTATTTCTTCAATTT
TTTGGCCTTTTTTCCTGCTGCCAAAAAACCCCGAATCATGTAGAAGCGAGAAGTAAAACA
GAGGAAGTGTATGGTAGCGCCAAGGAAAACGGGCAATACTTAGAAAGAATGACAGAGCTC
AGCCAAGTGTAAGCTAAGTGTTGACAAGGGAAGGTACATTGGGCCCCGAAAAAATTTGCT
AATGCTCGAAGAGCTCTCAATCAATCACCCACATATATGTACTACAGTATATTTATACTT
TCCACGCAGTCTCACGCAGTGCCACCTTCATCACCATGCGTGTAACTAATCGAGCAAGCT
GTTTTACGAAGGGCAGCTTTCCTATAAGCGTTTTGAACATGCATGGCTGCACTGCAATGA
GATCAGGCGACTCCAATTCCATAGCCTAGCACGGGATTAAGTAACGAGAAACTGAAAGAG
ATAATTTTACAAACCCGGACGAAGCAGAGCACTTGCTGGAACAAATCAAACATGCCGTCC
CCTACCAGCTCTCGAAGCGGGCCTAGCATTACTCGATCGAACGTTGCCGTTTAGTCTTAT
TTTCCTTTCCGTGCTGCGCTGCTTTTTTCTTGCATTGGGCT
>SGD_Scer_YER014W HEM14 "Protoporphyrinogen oxidase, a mitochondrial enzyme that catalyzes the seventh step in the heme biosynthetic pathway, converting protoporphyrinogen IX to protoporphyrin IX"
TATACAAGCTCTTTTTGGCGTTCTCAATTGCACTTTACTCGATATGTTTGAATTGGTGTT
CTTCGCGAATATCTCTATTGTTCTCTCTATTATACTATTTCTTTTTTTGAATACTCCGCG
ACTCCGAAGCAACAAAGTGTCGAAGGCAAGTTCAAAGGCGTTTTGTAACTAAACGAGCAA
TGGCAGCTTTCAATTAAAGAAAGGTTAGCGTTACTCTGTGATTTTTTTCATGTAAAAATT
CTCAAGAGAGATAAAGTTGTTAAAAAATTAAATATAGGTCTATAAAACTCGATAATTATA
ATGCATAAAAAGCTAACAATGT
>MIT_Spar_c425_6072 YER014W 5' untranslated region, Contig c425 34016 - 36015, 2000 bp (revcom)
TATTCGAGCCCTTTCCCGCGTTCCCAATTGTACCTTCCTCGATAGGATTGAATTGGTATC
CTTCGCGGATCTCTCTATTGTTCTCTCTATTATTCTTTTTCTTTTTTAAATACTCCGCGA
CTCCGAAGCAACAAAATGTCGAAGGCAAGATGAAAGGCGTTTTGCAACTAAACGAGTAAT
GGCAGCTTTTAATTAAATAACGGTCAGCATTACTCTATAACTTTTCACATAAAATCCTCG
AAGAAGGAAAAATTGATAATCAATTTACCGAAGAATGAATATAGGTCTATAAAAATTCAA
TAATTATAGATGCATAAAAAGC
>MIT_Smik_c283_5928 YER014W 5' untranslated region, Contig c283 42606 - 44605, 2000 bp (revcom)
TATTGAAGCTCTCTCCACTATTTCTTTAATCGCGCTATACTAGATATGGTTAAACTGCTA
TCTTTTGCAAATCCCTCTATTGTTCTTTCCATTACTCTTTTCTTTTTTAAATACGGACTC
CGAAGCAACAAGGTCGAAGGCAAGCTGAAAGGCATTTTACAACTAAACGAGCAATGGTAG
CTTTTGATTGAATAAATTATTATCATTATTTTGTTATTTGTCCCACGAAATTCTCGTTGA
AAGCAAGGTTCGTAAGGATTTATCAAATGTTAAATATAGATCTATAAAAATTGAATAGTA
ATAATAACAAGGGATGGTGTTA
>MIT_Sbay_c84_6418 YER014W 5' untranslated region, Contig c84 10802 - 12801(revcom), 2000 bp (revcom)
TGTCGAAGTTCTCCTTTATTCCGCTGTTTCTTACGGAATCCAGCGAGACTGTTGTCCTTT
CGCATCCTTCTATTGTTCTTCCTTATTGTTCTCGTTTTTTTTATACTCTGCGACTCCGAA
ACAACAAAATCTCGAAGGCAAGCTAAGGTAAAAATATTCACCACTAAACGAGCAATGACA
GTTATATTCAAACGTCATTCTACTTTTTTGCCAGAGAAGTCCTCACTGGAGACGAAGTTG
GTAAATGCTTTATTTATATTAAACGTAGATCTATAAAGTTTAAATAGTTTATAATGCTTA
ACAAGGGACGATGTTATCTCTT
BioPerl-1.007002/t/data/map_hem/HEM12-HEM14.meme.txt000444000766000024     11035313155576321 21354 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM12-HEM14.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDR047W         1.0000   1000  MIT_Spar_c130_3923       1.0000   1000  
MIT_Sbay_c896_21277      1.0000   1000  WashU_Skud_Contig1362.1  1.0000    761  
SGD_Scer_YER014W         1.0000    322  MIT_Spar_c425_6072       1.0000    322  
MIT_Smik_c283_5928       1.0000    322  MIT_Sbay_c84_6418        1.0000    322  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM12-HEM14.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        8    maxsites=        8    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            5049    N=               8
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.296 C 0.204 G 0.204 T 0.296 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   15   sites =   8   llr = 132   E-value = 1.4e-008
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  a:::::aa1:65:58
pos.-specific     C  :a5aa:::4a4:5:3
probability       G  :::::a::4:::5::
matrix            T  ::5:::::1::5:5:

         bits    2.5  * ***   *     
                 2.3  * ***   *     
                 2.0  * ***   *     
                 1.8  * ***   *     
Information      1.5 ** ***** *  *  
content          1.3 ** ***** *  *  
(23.8 bits)      1.0 ******** ** * *
                 0.8 ******** ** * *
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           ACCCCGAACCAACAA
consensus              T     G CTGTC
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
MIT_Sbay_c896_21277          +    213  2.96e-09 GCGTCAAAAA ACCCCGAACCCTGTA TAAACGAGGA
MIT_Spar_c130_3923           +    242  1.00e-08 TGCCACCAAA ACCCCGAACCCTGTC CCGTATATAC
SGD_Scer_YDR047W             +    245  1.00e-08 GCCGCCAAAA ACCCCGAACCCTGTC CTGTATATAC
MIT_Smik_c283_5928           +    117  2.85e-08 TTAAATACGG ACTCCGAAGCAACAA GGTCGAAGGC
MIT_Spar_c425_6072           +    120  2.85e-08 ATACTCCGCG ACTCCGAAGCAACAA AATGTCGAAG
SGD_Scer_YER014W             +    121  2.85e-08 ATACTCCGCG ACTCCGAAGCAACAA AGTGTCGAAG
WashU_Skud_Contig1362.1      +    208  5.25e-08 CTGCCAAAAA ACCCCGAATCATGTA GAAGCGAGAA
MIT_Sbay_c84_6418            +    113  8.97e-08 ATACTCTGCG ACTCCGAAACAACAA AATCTCGAAG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Sbay_c896_21277                 3e-09  212_[+1]_773
MIT_Spar_c130_3923                  1e-08  241_[+1]_744
SGD_Scer_YDR047W                    1e-08  244_[+1]_741
MIT_Smik_c283_5928                2.9e-08  116_[+1]_191
MIT_Spar_c425_6072                2.9e-08  119_[+1]_188
SGD_Scer_YER014W                  2.9e-08  120_[+1]_187
WashU_Skud_Contig1362.1           5.3e-08  207_[+1]_539
MIT_Sbay_c84_6418                   9e-08  112_[+1]_195
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=15 seqs=8
MIT_Sbay_c896_21277      (  213) ACCCCGAACCCTGTA  1 
MIT_Spar_c130_3923       (  242) ACCCCGAACCCTGTC  1 
SGD_Scer_YDR047W         (  245) ACCCCGAACCCTGTC  1 
MIT_Smik_c283_5928       (  117) ACTCCGAAGCAACAA  1 
MIT_Spar_c425_6072       (  120) ACTCCGAAGCAACAA  1 
SGD_Scer_YER014W         (  121) ACTCCGAAGCAACAA  1 
WashU_Skud_Contig1362.1  (  208) ACCCCGAATCATGTA  1 
MIT_Sbay_c84_6418        (  113) ACTCCGAAACAACAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 4937 bayes= 9.26708 E= 1.4e-008 
   162   -965   -965   -965 
  -965    251   -965   -965 
  -965    151   -965     62 
  -965    251   -965   -965 
  -965    251   -965   -965 
  -965   -965    251   -965 
   162   -965   -965   -965 
   162   -965   -965   -965 
  -137    109    109   -137 
  -965    251   -965   -965 
    95    109   -965   -965 
    62   -965   -965     62 
  -965    151    151   -965 
    62   -965   -965     62 
   121     51   -965   -965 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 1.4e-008 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.125000  0.375000  0.375000  0.125000 
 0.000000  1.000000  0.000000  0.000000 
 0.625000  0.375000  0.000000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.000000  0.500000  0.500000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.750000  0.250000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
AC[CT]CCGAA[CG]C[AC][AT][CG][AT][AC]
--------------------------------------------------------------------------------




Time  2.78 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   8   llr = 144   E-value = 2.6e-007
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  61:888::9:166::138::
pos.-specific     C  48131:a1::813:1:5::8
probability       G  :11::3:91a::::88:3a:
matrix            T  ::8:1:::::131a113::3

         bits    2.5       *  *        * 
                 2.3       *  *        * 
                 2.0       ** *        * 
                 1.8       ** *        * 
Information      1.5       ** *   *    **
content          1.3  *    *****  ***  **
(26.0 bits)      1.0 ** * ******  *** ***
                 0.8 ***********  *** ***
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           ACTAAACGAGCAATGGCAGC
consensus            C  C G     TC   AG T
sequence                             T   
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
SGD_Scer_YER014W             +    168  5.54e-13 GCGTTTTGTA ACTAAACGAGCAATGGCAGC TTTCAATTAA
MIT_Smik_c283_5928           +    162  8.88e-12 GCATTTTACA ACTAAACGAGCAATGGTAGC TTTTGATTGA
MIT_Spar_c425_6072           +    167  5.42e-11 GCGTTTTGCA ACTAAACGAGTAATGGCAGC TTTTAATTAA
MIT_Sbay_c84_6418            +    163  5.99e-10 AATATTCACC ACTAAACGAGCAATGACAGT TATATTCAAA
MIT_Sbay_c896_21277          -    914  4.51e-09 TTTTCCCGAG CAGAAACGAGCCCTGGAAGC TGCCTTCATT
MIT_Spar_c130_3923           -    836  3.57e-08 TGTCTTTCCA ACTCAGCGAGATTTGTCGGC CGGAAAAAAA
WashU_Skud_Contig1362.1      +    659  6.59e-08 AACATGCCGT CCCCTACCAGCTCTCGAAGC GGGCCTAGCA
SGD_Scer_YDR047W             -    382  1.24e-07 TTGTAGTATA CGTACGCGGGCAATTGTGGT GACAGTATCT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YER014W                  5.5e-13  167_[+2]_135
MIT_Smik_c283_5928                8.9e-12  161_[+2]_141
MIT_Spar_c425_6072                5.4e-11  166_[+2]_136
MIT_Sbay_c84_6418                   6e-10  162_[+2]_140
MIT_Sbay_c896_21277               4.5e-09  913_[-2]_67
MIT_Spar_c130_3923                3.6e-08  835_[-2]_145
WashU_Skud_Contig1362.1           6.6e-08  658_[+2]_83
SGD_Scer_YDR047W                  1.2e-07  381_[-2]_599
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=8
SGD_Scer_YER014W         (  168) ACTAAACGAGCAATGGCAGC  1 
MIT_Smik_c283_5928       (  162) ACTAAACGAGCAATGGTAGC  1 
MIT_Spar_c425_6072       (  167) ACTAAACGAGTAATGGCAGC  1 
MIT_Sbay_c84_6418        (  163) ACTAAACGAGCAATGACAGT  1 
MIT_Sbay_c896_21277      (  914) CAGAAACGAGCCCTGGAAGC  1 
MIT_Spar_c130_3923       (  836) ACTCAGCGAGATTTGTCGGC  1 
WashU_Skud_Contig1362.1  (  659) CCCCTACCAGCTCTCGAAGC  1 
SGD_Scer_YDR047W         (  382) CGTACGCGGGCAATTGTGGT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4897 bayes= 9.25532 E= 2.6e-007 
    95    109   -965   -965 
  -137    209    -49   -965 
  -965    -49    -49    121 
   121     51   -965   -965 
   121    -49   -965   -137 
   121   -965     51   -965 
  -965    251   -965   -965 
  -965    -49    232   -965 
   143   -965    -49   -965 
  -965   -965    251   -965 
  -137    209   -965   -137 
    95    -49   -965    -38 
    95     51   -965   -137 
  -965   -965   -965    162 
  -965    -49    209   -137 
  -137   -965    209   -137 
   -38    151   -965    -38 
   121   -965     51   -965 
  -965   -965    251   -965 
  -965    209   -965    -38 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 2.6e-007 
 0.625000  0.375000  0.000000  0.000000 
 0.125000  0.750000  0.125000  0.000000 
 0.000000  0.125000  0.125000  0.750000 
 0.750000  0.250000  0.000000  0.000000 
 0.750000  0.125000  0.000000  0.125000 
 0.750000  0.000000  0.250000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.125000  0.875000  0.000000 
 0.875000  0.000000  0.125000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.125000  0.750000  0.000000  0.125000 
 0.625000  0.125000  0.000000  0.250000 
 0.625000  0.250000  0.000000  0.125000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.125000  0.750000  0.125000 
 0.125000  0.000000  0.750000  0.125000 
 0.250000  0.500000  0.000000  0.250000 
 0.750000  0.000000  0.250000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.750000  0.000000  0.250000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[AC]CT[AC]A[AG]CGAGC[AT][AC]TGG[CAT][AG]G[CT]
--------------------------------------------------------------------------------




Time  5.72 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   18   sites =   8   llr = 139   E-value = 1.4e-007
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  ::::aa:::a63614a86
pos.-specific     C  14a3::::a:::311:::
probability       G  9::5::6a::48:15:34
matrix            T  :6:3::4:::::16::::

         bits    2.5   *    **         
                 2.3   *    **         
                 2.0 * *    **         
                 1.8 * *    **         
Information      1.5 * * ** *** *   *  
content          1.3 * * ****** *   *  
(25.1 bits)      1.0 *** ********   ***
                 0.8 ************  ****
                 0.5 ************* ****
                 0.3 ******************
                 0.0 ------------------

Multilevel           GTCGAAGGCAAGATGAAA
consensus             C C  T   GAC A GG
sequence                T              
                                       
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                   Site     
-------------            ------  ----- ---------            ------------------
MIT_Spar_c425_6072           +    138  4.37e-11 GCAACAAAAT GTCGAAGGCAAGATGAAA GGCGTTTTGC
MIT_Smik_c283_5928           +    133  7.23e-11 AAGCAACAAG GTCGAAGGCAAGCTGAAA GGCATTTTAC
SGD_Scer_YDR047W             -    769  2.84e-09 ACACTAGTAA GTCTAATGCAGGATGAAG AAACGAAGAA
SGD_Scer_YER014W             +    139  7.28e-09 GCAACAAAGT GTCGAAGGCAAGTTCAAA GGCGTTTTGT
MIT_Sbay_c896_21277          -    742  9.47e-09 ACGCTGCTAG GCCCAAGGCAGAACGAAA TAAGAAATGA
MIT_Sbay_c84_6418            +    131  1.10e-08 ACAACAAAAT CTCGAAGGCAAGCTAAGG TAAAAATATT
WashU_Skud_Contig1362.1      -    743  2.13e-08          A GCCCAATGCAAGAAAAAA GCAGCGCAGC
MIT_Spar_c130_3923           -    774  6.83e-08 ACGCTAGTAA GCCTAATGCAGAAGAAGG AAAGGACACG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c425_6072                4.4e-11  137_[+3]_167
MIT_Smik_c283_5928                7.2e-11  132_[+3]_172
SGD_Scer_YDR047W                  2.8e-09  768_[-3]_214
SGD_Scer_YER014W                  7.3e-09  138_[+3]_166
MIT_Sbay_c896_21277               9.5e-09  741_[-3]_241
MIT_Sbay_c84_6418                 1.1e-08  130_[+3]_174
WashU_Skud_Contig1362.1           2.1e-08  742_[-3]_1
MIT_Spar_c130_3923                6.8e-08  773_[-3]_209
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=18 seqs=8
MIT_Spar_c425_6072       (  138) GTCGAAGGCAAGATGAAA  1 
MIT_Smik_c283_5928       (  133) GTCGAAGGCAAGCTGAAA  1 
SGD_Scer_YDR047W         (  769) GTCTAATGCAGGATGAAG  1 
SGD_Scer_YER014W         (  139) GTCGAAGGCAAGTTCAAA  1 
MIT_Sbay_c896_21277      (  742) GCCCAAGGCAGAACGAAA  1 
MIT_Sbay_c84_6418        (  131) CTCGAAGGCAAGCTAAGG  1 
WashU_Skud_Contig1362.1  (  743) GCCCAATGCAAGAAAAAA  1 
MIT_Spar_c130_3923       (  774) GCCTAATGCAGAAGAAGG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 18 n= 4913 bayes= 9.26004 E= 1.4e-007 
  -965    -49    232   -965 
  -965    109   -965     95 
  -965    251   -965   -965 
  -965     51    151    -38 
   162   -965   -965   -965 
   162   -965   -965   -965 
  -965   -965    183     21 
  -965   -965    251   -965 
  -965    251   -965   -965 
   162   -965   -965   -965 
    95   -965    109   -965 
   -38   -965    209   -965 
    95     51   -965   -137 
  -137    -49    -49     95 
    21    -49    151   -965 
   162   -965   -965   -965 
   121   -965     51   -965 
    95   -965    109   -965 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 18 nsites= 8 E= 1.4e-007 
 0.000000  0.125000  0.875000  0.000000 
 0.000000  0.375000  0.000000  0.625000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.250000  0.500000  0.250000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.625000  0.375000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.625000  0.000000  0.375000  0.000000 
 0.250000  0.000000  0.750000  0.000000 
 0.625000  0.250000  0.000000  0.125000 
 0.125000  0.125000  0.125000  0.625000 
 0.375000  0.125000  0.500000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.750000  0.000000  0.250000  0.000000 
 0.625000  0.000000  0.375000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
G[TC]C[GCT]AA[GT]GCA[AG][GA][AC]T[GA]A[AG][AG]
--------------------------------------------------------------------------------




Time  8.67 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =   8   llr = 132   E-value = 6.8e-002
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  6::5:93:::1955985431
pos.-specific     C  ::::::1a:96:::::1:36
probability       G  :3953:6:a:31441:4653
matrix            T  481:81:::1::11:3::::

         bits    2.5        **           
                 2.3        **           
                 2.0        **           
                 1.8   *    ***          
Information      1.5   *    ***          
content          1.3   *    *** *  *  *  
(23.8 bits)      1.0  ***********  *  * *
                 0.8 ************  ******
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           ATGATAGCGCCAAAAAAGGC
consensus            TG GG A   G GG TGAAG
sequence                               C 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Sbay_c896_21277          +    244  1.24e-12 AGGAAGCTGC ATGGTAGCGCCAGAAAAGGC AGATAACCTT
MIT_Spar_c130_3923           +    292  4.51e-10 AAAATCGTGT ATGGTAGCGCCAAGATAGCG AATAAACTAT
SGD_Scer_YDR047W             +    294  7.62e-10 AAGATCGTGT ATGATAGCGCCAAGATGGCG GATAAACTAA
WashU_Skud_Contig1362.1      +    251  2.49e-09 GAGGAAGTGT ATGGTAGCGCCAAGGAAAAC GGGCAATACT
SGD_Scer_YER014W             -      8  4.22e-09 TAAAGTGCAA TTGAGAACGCCAAAAAGAGC TTGTATA   
MIT_Spar_c425_6072           -      8  4.66e-09 GAAGGTACAA TTGGGAACGCGGGAAAGGGC TCGAATA   
MIT_Smik_c283_5928           -     22  7.67e-07 AACCATATCT AGTATAGCGCGATTAAAGAA ATAGTGGAGA
MIT_Sbay_c84_6418            -     23  1.04e-06 ACAGTCTCGC TGGATTCCGTAAGAAACAGC GGAATAAAGG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Sbay_c896_21277               1.2e-12  243_[+4]_737
MIT_Spar_c130_3923                4.5e-10  291_[+4]_689
SGD_Scer_YDR047W                  7.6e-10  293_[+4]_687
WashU_Skud_Contig1362.1           2.5e-09  250_[+4]_491
SGD_Scer_YER014W                  4.2e-09  7_[-4]_295
MIT_Spar_c425_6072                4.7e-09  7_[-4]_295
MIT_Smik_c283_5928                7.7e-07  21_[-4]_281
MIT_Sbay_c84_6418                   1e-06  22_[-4]_280
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=8
MIT_Sbay_c896_21277      (  244) ATGGTAGCGCCAGAAAAGGC  1 
MIT_Spar_c130_3923       (  292) ATGGTAGCGCCAAGATAGCG  1 
SGD_Scer_YDR047W         (  294) ATGATAGCGCCAAGATGGCG  1 
WashU_Skud_Contig1362.1  (  251) ATGGTAGCGCCAAGGAAAAC  1 
SGD_Scer_YER014W         (    8) TTGAGAACGCCAAAAAGAGC  1 
MIT_Spar_c425_6072       (    8) TTGGGAACGCGGGAAAGGGC  1 
MIT_Smik_c283_5928       (   22) AGTATAGCGCGATTAAAGAA  1 
MIT_Sbay_c84_6418        (   23) TGGATTCCGTAAGAAACAGC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4897 bayes= 9.25532 E= 6.8e-002 
    95   -965   -965     21 
  -965   -965     51    121 
  -965   -965    232   -137 
    62   -965    151   -965 
  -965   -965     51    121 
   143   -965   -965   -137 
   -38    -49    183   -965 
  -965    251   -965   -965 
  -965   -965    251   -965 
  -965    232   -965   -137 
  -137    183     51   -965 
   143   -965    -49   -965 
    62   -965    109   -137 
    62   -965    109   -137 
   143   -965    -49   -965 
   121   -965   -965    -38 
    62    -49    109   -965 
    21   -965    183   -965 
   -38     51    151   -965 
  -137    183     51   -965 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 6.8e-002 
 0.625000  0.000000  0.000000  0.375000 
 0.000000  0.000000  0.250000  0.750000 
 0.000000  0.000000  0.875000  0.125000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  0.000000  0.250000  0.750000 
 0.875000  0.000000  0.000000  0.125000 
 0.250000  0.125000  0.625000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.875000  0.000000  0.125000 
 0.125000  0.625000  0.250000  0.000000 
 0.875000  0.000000  0.125000  0.000000 
 0.500000  0.000000  0.375000  0.125000 
 0.500000  0.000000  0.375000  0.125000 
 0.875000  0.000000  0.125000  0.000000 
 0.750000  0.000000  0.000000  0.250000 
 0.500000  0.125000  0.375000  0.000000 
 0.375000  0.000000  0.625000  0.000000 
 0.250000  0.250000  0.500000  0.000000 
 0.125000  0.625000  0.250000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
[AT][TG]G[AG][TG]A[GA]CGC[CG]A[AG][AG]A[AT][AG][GA][GAC][CG]
--------------------------------------------------------------------------------




Time 11.28 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   14   sites =   8   llr = 115   E-value = 4.7e-003
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  ::5::1::::::::
pos.-specific     C  a::35:::a433a5
probability       G  ::51:9::::4:::
matrix            T  :a:65:aa:648:5

         bits    2.5 *       *   * 
                 2.3 *       *   * 
                 2.0 *       *   * 
                 1.8 *    *  *   * 
Information      1.5 **   ****   * 
content          1.3 **   ****   * 
(20.8 bits)      1.0 *** ****** ***
                 0.8 ********** ***
                 0.5 **************
                 0.3 **************
                 0.0 --------------

Multilevel           CTATCGTTCTGTCC
consensus              GCT    CTC T
sequence                       C   
                                   
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site   
-------------            ------  ----- ---------            --------------
MIT_Spar_c130_3923           +    714  1.93e-09 CTCTAAAATG CTGCCGTTCCGTCC CATTGAGTTT
SGD_Scer_YDR047W             +    714  1.93e-09 TTAAAAAATG CTGCCGTTCCGTCC CATTGAGTTT
MIT_Sbay_c896_21277          +    705  8.69e-08 CAGCCAAACA CTGGCGTTCCGCCC GTCCCATCCA
MIT_Smik_c283_5928           +     77  2.04e-07 GCAAATCCCT CTATTGTTCTTTCC ATTACTCTTT
MIT_Spar_c425_6072           +     75  3.04e-07 GCGGATCTCT CTATTGTTCTCTCT ATTATTCTTT
SGD_Scer_YER014W             +     75  3.04e-07 GCGAATATCT CTATTGTTCTCTCT ATTATACTAT
MIT_Sbay_c84_6418            +     70  4.30e-07 TCGCATCCTT CTATTGTTCTTCCT TATTGTTCTC
WashU_Skud_Contig1362.1      -    282  5.90e-07 TGGCTGAGCT CTGTCATTCTTTCT AAGTATTGCC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c130_3923                1.9e-09  713_[+5]_273
SGD_Scer_YDR047W                  1.9e-09  713_[+5]_273
MIT_Sbay_c896_21277               8.7e-08  704_[+5]_282
MIT_Smik_c283_5928                  2e-07  76_[+5]_232
MIT_Spar_c425_6072                  3e-07  74_[+5]_234
SGD_Scer_YER014W                    3e-07  74_[+5]_234
MIT_Sbay_c84_6418                 4.3e-07  69_[+5]_239
WashU_Skud_Contig1362.1           5.9e-07  281_[-5]_466
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=14 seqs=8
MIT_Spar_c130_3923       (  714) CTGCCGTTCCGTCC  1 
SGD_Scer_YDR047W         (  714) CTGCCGTTCCGTCC  1 
MIT_Sbay_c896_21277      (  705) CTGGCGTTCCGCCC  1 
MIT_Smik_c283_5928       (   77) CTATTGTTCTTTCC  1 
MIT_Spar_c425_6072       (   75) CTATTGTTCTCTCT  1 
SGD_Scer_YER014W         (   75) CTATTGTTCTCTCT  1 
MIT_Sbay_c84_6418        (   70) CTATTGTTCTTCCT  1 
WashU_Skud_Contig1362.1  (  282) CTGTCATTCTTTCT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 14 n= 4945 bayes= 9.26942 E= 4.7e-003 
  -965    251   -965   -965 
  -965   -965   -965    162 
    62   -965    151   -965 
  -965     51    -49     95 
  -965    151   -965     62 
  -137   -965    232   -965 
  -965   -965   -965    162 
  -965   -965   -965    162 
  -965    251   -965   -965 
  -965    109   -965     95 
  -965     51    109     21 
  -965     51   -965    121 
  -965    251   -965   -965 
  -965    151   -965     62 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 14 nsites= 8 E= 4.7e-003 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  0.250000  0.125000  0.625000 
 0.000000  0.500000  0.000000  0.500000 
 0.125000  0.000000  0.875000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.375000  0.000000  0.625000 
 0.000000  0.250000  0.375000  0.375000 
 0.000000  0.250000  0.000000  0.750000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
CT[AG][TC][CT]GTTC[TC][GTC][TC]C[CT]
--------------------------------------------------------------------------------




Time 13.87 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR047W                 7.31e-20  108_[+5(5.48e-05)]_122_[+1(1.00e-08)]_34_[+4(7.62e-10)]_68_[-2(1.24e-07)]_312_[+5(1.93e-09)]_41_[-3(2.84e-09)]_214
MIT_Spar_c130_3923               2.71e-19  241_[+1(1.00e-08)]_35_[+4(4.51e-10)]_5_[-2(1.77e-05)]_377_[+5(1.93e-09)]_46_[-3(6.83e-08)]_3_[+5(7.96e-06)]_27_[-2(3.57e-08)]_145
MIT_Sbay_c896_21277              2.82e-22  212_[+1(2.96e-09)]_16_[+4(1.24e-12)]_398_[+3(9.45e-05)]_25_[+5(8.69e-08)]_23_[-3(9.47e-09)]_154_[-2(4.51e-09)]_67
WashU_Skud_Contig1362.1          2.00e-16  207_[+1(5.25e-08)]_28_[+4(2.49e-09)]_11_[-5(5.90e-07)]_363_[+2(6.59e-08)]_64_[-3(2.13e-08)]_1
SGD_Scer_YER014W                 1.10e-23  7_[-4(4.22e-09)]_47_[+5(3.04e-07)]_32_[+1(2.85e-08)]_3_[+3(7.28e-09)]_11_[+2(5.54e-13)]_135
MIT_Spar_c425_6072               7.28e-24  7_[-4(4.66e-09)]_47_[+5(3.04e-07)]_31_[+1(2.85e-08)]_3_[+3(4.37e-11)]_11_[+2(5.42e-11)]_136
MIT_Smik_c283_5928               1.78e-22  21_[-4(7.67e-07)]_35_[+5(2.04e-07)]_26_[+1(2.85e-08)]_1_[+3(7.23e-11)]_11_[+2(8.88e-12)]_141
MIT_Sbay_c84_6418                7.50e-18  22_[-4(1.04e-06)]_6_[+5(5.48e-05)]_7_[+5(4.30e-07)]_29_[+1(8.97e-08)]_3_[+3(1.10e-08)]_14_[+2(5.99e-10)]_140
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM12-HEM15.fa000444000766000024      2102213155576321 20154 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR047W HEM12 "Uroporphyrinogen decarboxylase, catalyzes the fifth step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; activity inhibited by Cu2+, Zn2+, Fe2+, Fe3+ and sulfhydryl-specific reagents"
AGCGTTATAACCTGTTCTTTGCTTTATTTTTTTTTTTTTTGTTCTTCCTTTTCTCGAAGA
GAGCTTACCAAACACAATTCTGAGATAATGCTTGATGAATTGAAGAACCTATCGATCACT
CTATGTTACCTTCGTCTGGAACATCACTAATTCGAGCGGTAAAGATGAAAATGGCAGAAC
ATTTCGCTGGCAAAATTAAAACTCTTGCCTCATTTTTTTTTGCTTTCCTCTCCTGCCGCC
AAAAACCCCGAACCCTGTCCTGTATATACGAGAAACATTGAAAAAGATCGTGTATGATAG
CGCCAAGATGGCGGATAAACTAACACTATTGACAGGTTGAGGCCAAGGATATATTACTTG
CTAACAGAAAGAGATACTGTCACCACAATTGCCCGCGTACGTATACTACAACATGTTCTC
TATATATCACCCACTCTTTCGCAGTGCTACGTACGCCAAAAACGCGCGCATGGAAGTAAA
GAAGTTTTTTCTTTTAAGAGCGAAGCTCCATTAAAAGCCTTGAATATAAACTAGTGCGAA
GTAGTATGATCCGAAGACACCAATTGCTGGTGCAGCATAGGAATATGTGGCGTCCGAAAA
AGAGCCTTTAACAATCCACGGCGAAACAAGGCACCGCTGTGCATTTAAAACATGCCGTTC
CCGTACCAAGTTATATTGTTACGGATGAATCCAAAATAATTTGTTAAAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCATGGCACCTTCTTCGTTTCTTCATCCTGCA
TTAGACTTACTAGTGTGCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGACACATATCGC
TGAGCTGGAAGGACACCTTTTAATGTAGCCGTGCATGCGGCTCCGCGAAAAGAGCTCTGC
TATATTTCTCTACCTGAACTTCGAGCCGCGATCAACGAAAGCTCTCATCCAAGGCTCGTT
TTTCTTGACAGAAGCATGACAGTAAAATATGCGGTCATTT
>MIT_Spar_c130_3923 YDR047W 5' untranslated region, Contig c130 9341 - 11340, 2000 bp (revcom)
AGCGTTATGATGTGTTATTTGCTTTTATTTTCTTCTTTCTTTGTCTCGAAGATAACCTAG
CAAACACAATTCTAAGAAAATTCTCGATGAATTGGTTGTCAGCGCTTCCTATTTACTCTA
TGTCCACTTCGTTTGAAACATCAGTGGTTCGAGCAGTAATGACAAAAAGGGCAGAACATT
TCGTTGGCAAAATTTAAACTCGTGCCTCTCATTTTTTTTACTTTTCTCTCCTGCCACCAA
AACCCCGAACCCTGTCCCGTATATACGAGGAACATTGAAAAAAAATCGTGTATGGTAGCG
CCAAGATAGCGAATAAACTATCAGTATTGGCAGGGTGAAGCTAAGGATATGTTGTTTGCT
AACAAAGGGAAATGCTTTCGTTATAATCGCCCGCGTGCGTCTACTAAAATATGATCTATA
TATACCACCCAGTCTATTGCAGTGTTACGTACATCAAAATGCGCGCATGTAAGTGAACAA
GTTTTTTTTGTTTAAAGAGCGATTTTCCAATAAAGGCTTTGGATATACACTGGTGCAAAA
TATATGGTCAATGACGCCAATTACTGGTGTAGCATGAGAATACGTCGTCCGAAAGAGTTT
TTTTTTACAAACTACGGCAAAGCAAAGCACCACTGGCGCAATTCAAAACATGCCGTCCCC
GTACTAAGTTATGTACGTTATTATGGACGGATCCAAAATTATACTCTAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCGTAGCACCTTCTTCGTGTCCTTTCCTTCTT
CTGCATTAGGCTTACTAGCGTCCTTTCCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGA
CAAATCTCGCTGAGTTGGAAAGACACCTTTTATATAGCCGTACGTGCGGCTCCTCGAGAA
AGGCCCTGCTATATTTCACTAGCTGATCCTCGAGCTGCGATCAACGAAAGCCCCATCCAA
AAGGCTCCTTTTTCTTCAAAGAAGCATGACAGTAAAATAT
>MIT_Sbay_c896_21277 YDR047W 5' untranslated region, Contig c896 2230 - 4229(revcom), 2000 bp (revcom)
AGTGTTAACAGTATCTTTTGCCTTTTTTTATTCTAATAGCTACCCCAGGAATCACTATTT
AGCAAAGATCGTTTGCAAATTGGCCGTCAGTACGTTCTAAGTTCTTTAGAACATCATTGG
CTCGAGCATTAGTGACACGAATAGGAAAGCATTTCGTTGACAAAAATAAAATTGTTTCTT
TATTTTTTCCCTCTTTTCCATGGCGTCAAAAAACCCCGAACCCTGTATAAACGAGGAAGC
TGCATGGTAGCGCCAGAAAAGGCAGATAACCTTTAACAGTGCTGACAGAACAACGTCAAA
CATGTGCGGATAATGCCTTCGCTGACGGCAAGAAATTATATACGCCTCGAAACTGTAGAA
CGTCTTTTGTGCCGCTTGGTAACAAATAAACCTAGCCGGGGCCAGAATTTCACCCGTACA
TACTTACTGTTACATACTGCATGCACGCTACGCATTCTCACCGAACATCGAATCTGCCTG
CAGAAGCGAAGAAAAGCAAGTCTTCGAAGAGCAAGCTTACATCCATCGTGTTGAACACAT
ATGCCCAGCAAAGGGATCGGATGACGCCCAACTAACATTGGAATTTGTGACGCAAGGCTG
AAAGGCACTTCTCTATAGCCCACGGTGAAGCCTTACGCTATTGACAAGACAAAACATGCC
GATCCAAGCCAGGCGAAACGGGCCTAGCACTACGCAGCCAAACACTGGCGTTCCGCCCGT
CCCATCCAGTTTCATTTCTTATTTCGTTCTGCCTTGGGCCTAGCAGCGTGCTTGCCGGAT
GAGTTTTTTCCATTTTCCTACCGGCTCATCTCGCTAAGCTGAAAGGTCAGTTTTATAGCC
GTGTGCGCGGCATCGAGAGACAGGTTCAGCTAATGATATTTGCCTAATTCTCGAGCTGAG
GCCAATGAAGGCAGCTTCCAGGGCTCGTTTCTGCTCGGGAAAAAGCATACCACACATTTG
CACGGCTTTTATGTGCCATAGTGCCACCACTAGCCCCCAG
>WashU_Skud_Contig1362.1 YDR047W 5' untranslated region, Contig c1362 1 - 761, 2000 bp (revcom)
AGTGTTGATGGTATCTTTTGATTTTTTCTAGATTGGTAGCAAGCTCAATTGGCACAGCTC
TAAAAAAAGCCTTGTGAATTGGATAGTACCTTCTTTCGTTTGGAACATTACTGCTTCGAG
CAATAAACATACGAAAGGCAGAACACCTCGTTGACAAAACTGAAACTATTTCTTCAATTT
TTTGGCCTTTTTTCCTGCTGCCAAAAAACCCCGAATCATGTAGAAGCGAGAAGTAAAACA
GAGGAAGTGTATGGTAGCGCCAAGGAAAACGGGCAATACTTAGAAAGAATGACAGAGCTC
AGCCAAGTGTAAGCTAAGTGTTGACAAGGGAAGGTACATTGGGCCCCGAAAAAATTTGCT
AATGCTCGAAGAGCTCTCAATCAATCACCCACATATATGTACTACAGTATATTTATACTT
TCCACGCAGTCTCACGCAGTGCCACCTTCATCACCATGCGTGTAACTAATCGAGCAAGCT
GTTTTACGAAGGGCAGCTTTCCTATAAGCGTTTTGAACATGCATGGCTGCACTGCAATGA
GATCAGGCGACTCCAATTCCATAGCCTAGCACGGGATTAAGTAACGAGAAACTGAAAGAG
ATAATTTTACAAACCCGGACGAAGCAGAGCACTTGCTGGAACAAATCAAACATGCCGTCC
CCTACCAGCTCTCGAAGCGGGCCTAGCATTACTCGATCGAACGTTGCCGTTTAGTCTTAT
TTTCCTTTCCGTGCTGCGCTGCTTTTTTCTTGCATTGGGCT
>SGD_Scer_YOR176W HEM15 "Ferrochelatase, a mitochondrial inner membrane protein, catalyzes the insertion of ferrous iron into protoporphyrin IX, the eighth and final step in the heme biosynthetic pathway; Yfh1p mediates the use of iron by Hem15p"
TCTTTAAACGTTCTTTTTTTTACTGCTAAATTTGTCCAAATAGCAGGTATGTGTTAAATA
TTTCTGTACTTCTTGTAAACCGACTCAAGTGGAACACGAGAATTTACGCTTGTTTGGTGT
CAAGCCAAGAGTGACCTTGACCGACCAAAAGTATTCCTTCGCGTCCTCCTTCTTCAATCC
CATATCCCCTACGAAAAAAAGCAGCATGAGAAAACGAAGGGCAGCAACTCCTTCGTCATA
TAAGGCTTACGGTGACCATTGAAGATTGGGCATGTCTAACGGCTATTGCCAGCGGAGATG
TTTCAAGGCATCCTACACATGCTACATATTTGTAATTATTTTACTGAGTTTGTGTATATA
AAAAACTTTTTTAAAAAAAAAAAATGGCCAGCATCCTCTTTCATGTAAAGCTGTTGAACC
TTCCTGAAATTTACTTCTAAAATTGTTCAGTAAAACTGCTTGTTAAAAGTGCGAAGAGTT
CTTTTTTAGCTTTTTTTGTCCTGCTGTTGAGCTGTTTTGCTTTACTGTTCAACAAAACAT
TGAAGATCTTTCACATTGCGCGTCGAAACCACAAACCGTCGAAAACAATGGTCATCTAAA
TAAAGGGTTCTTATTAAACAGATTTAAAGCCAAGGACAAAATACAGGCACAGGTCAAGCA
AGAAGACAAACCGCATACGCCAAGACAAACCGTGGTGATTTAATTCTGCTGCTGATCGCT
TCCAACA
>MIT_Spar_c278_20970 YOR176W 5' untranslated region, Contig c278 32746 - 34745, 2000 bp (revcom)
TCTTCAAACGTTCTTTTCCTACTACTAAGCTTTTCAATAAATAGCGGGTATATGCTAAAT
ACTTCTTTGCTTCTTGTACGACCTACTTAATTGAAATACGGATATTTTTGCTTGCTTGGT
GCCAAACCAAGAGTGACCTTGACCGACTAAAAGTATTCCTTCGCGTCCTCCTTCTTCAAT
CCCATATCCCCTACTGAAAAAAGCAGCGTGCGAAAATGAAGGGCAGCAACTCCTTCGTCA
TATAAGGCTTAGGTAATCTTTCAAGGTCAGGTATATCCAGCTGTCGTTACGAGTAGAGAT
ATTTCAAGCTGTCCTGCACATGCTACATATTTGTGATTATTTTTATTGAGTTGCGTATAT
AAAAAAACAATCTAAAAAAAAAAAAAATGGCCAGCATCTTCTTCCATGTAAAGCTGTTGA
ACCTTGCTAAAATCTATTACTATAATTGTTCAGTAAAGTTGCTTGTTAAAAATGCGAAGA
GTCTTTTTTAGCTTTTTTTGCCCTGCTGTTGAGCTGTTTTGCTTCACTGTTCAACAAAAC
AGTGAAGATCTTTCGAATTGCGCGTCGAAACCACAAACCGTCGAAAATAATGGTCATCTA
AATAAAGGGTTCTTATTTGAACAGATTTAAAGCTCAAAGACACGATACAGGCACAGGTCC
AGAAAGAATACAAAACGCAAACGCCAAGACAAATTGTGGTAATTTCATTCTGCTGCTGAT
CACTGCC
>MIT_Smik_c935_20455 YOR176W 5' untranslated region, Contig c935 1803 - 3802(revcom), 2000 bp (revcom)
TCTTGAATTGCAATTTTCTACTACTGAAGTTACCAACAATTAGCAAATATGTGATGAGTC
CTTTTTACGTTCTTGTATAACCTAAGTTAAATACAAAGGTTTATGCTCCTTTAATGATCA
GACCAACAGTGATCTTGGCCGACCAAAAGACTCCTTCGCGTCCTCCTTCTTCAAGTCTCA
TATCCCCTACCAGAAAAAGTAGCAGGCGAAAATAAAGAGCAACTGCTCCCCCCCATATAG
AGCTTACCATAATTTCTCAAGGAAAGGTATCTCCAGTTGTCGTAAAGAATAAAGAAGTTT
CAACGTGTCCTGCATGTTCTACAAATTTGCAATTGACTTTACTAAGTTGCATATATAAAA
CTTGTATTAGATAAGTTAGCCAGCATTTTCATTCAAGCTAAGATGTTGAATATGCCAAAG
CACATTGCTGAAATTAATCAGTAAAGCTGCTTGCTGAAAGTGGAAATATTTTCAGCTTTT
TTTGCTCTGCTGTTGAGCTGTTTTACTTCATTGTTCAACAAAACAATAGAGTTCTCTCCA
ATTGCGCGTCAAAACCACAAACCGTCGAAAATAATGATCATCTAAATAAAAGAGTTCACG
TTTTCACATATTTAAAGTTGAAATACTCCATACAGGCACAGGTCTAACAAGAAGACAACG
CATTCGATAAAACTAATCGTGGTAATTTTTATATCGCTGCTAGCCACTACCAACAATGTA
CAATTTT
>WashU_Skud_Contig2050.4 YOR176W 5' untranslated region, Contig c2050 12271 - 14270(revcom), 2000 bp (revcom)
TCTTAGTTTATAGCTTTTCTACTACTCTGGTCATAAACGAACAGAAGATAAGCAAGAAAT
CTTTTTTTCCTTCTTTTACGGTCTATTCAAGTGAAGCACGGGGATTCCCGCTTGTTTAAT
AATCAGACCAACAATGATATTGACCGACCAAAAGAAGTATTCCTTCGCGTGCTTCTCCTT
TCTGTGTCAAATCCCCTACTGAAAAAGCAGCATTGGGAAAGGAACAGCAGCTTCTCCTTC
GTCGCAGAGAGCTCGCGGTAGCATTTCATTGTCAGGTATTTATGATATTTGCTAAGAATA
ATTAAAATGTCTTCAGGTCTTGCACATACTCCTACATATTTGTAAGTATTTTACTGATTT
GAGTATATAAAAGCCGTACTAAAACTAACCAGCACCTGTAGCAAGGTGCAAAATGTTGAA
CCTTTCCGAAATTTATTGCCAGAAACCAAGAGCTAAAAGTGCTTGGTAAAAGTGAAAAGA
CTCTTTTTCAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGTTCCATCTGTTCAACAAA
ACAGCTTCACTGGATCTTTCAAAGTGCGCGTCGAAACCACAAACCGTCGAAAATATTGAT
CATCTAAATAAAGGGTTCTTATTTGCACAGTTTCGCATTGAAATATTCCATTCAGGCACA
GATCAACAAGAAGACAAAAAGGTATTCGAGAAGACTAATTGTGGTATTTTTACTTTGCTG
CTGACCA
>WashU_Sbay_Contig480.2 YOR176W 5' untranslated region, Contig c480 3444 - 5443(revcom), 2000 bp (revcom)
TTTCAGGGAAGCACCATGTGCACGAATTGTTCTAGAAAGCATTTTTGGTTCGTAAATTCT
CTACAACTGAACTTATTAACAAATAGCAAACAGAGAAGAAAATTTTTTTTTTCCTTCTTG
TATGGTCAGTTAGTTGAAAACACGGAGATTTTCACTTGTTTAGTAAGCAGAGCCATAATG
CTCTTGACCGACCAAAAGAAGTATTCCTACGCGAGCTCCCTCTTCAAGTGCCAAATCCCC
TACTGAAAAAAGCAACATGAGAAGCAAAGAGATGCCTCTCGCCATGCAGGGCTTGCGGTC
ATGTTTTCTACGTTCAATTGATTTTGTTACAGCTGAAAGATGTTTATAAAACTGTCTTGC
ATATGCTCTATTTACTTGTAAACAATTTTATTAAGTTGCGTATATATGATCGTACTAAAA
ATTGGCTGGCGCGTTCTCCAGGCAGAGTTGGTTGAACCTTGCTCGAATTGATAGCTCAAA
GTGGAGAGACTCTTTTTTAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGCTCCACCTG
TTCAACAAAATGGCAGAGATCTTTCGAAGTGCGCGTCGAAACCACAAACCATCAAAAATA
TCGACCATCTAAATAAAGGGTTCTTGTTTGAATAAATATCAGGCGAAGCTCTTCATACAG
GCACAGGTCAGATAAGAAGACAATTCGAATTCGAGAAGGATATTCGTGGTATCTTTAATC
TGCTGCT
BioPerl-1.007002/t/data/map_hem/HEM12-HEM15.meme.txt000444000766000024     11574013155576321 21362 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM12-HEM15.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDR047W         1.0000   1000  MIT_Spar_c130_3923       1.0000   1000  
MIT_Sbay_c896_21277      1.0000   1000  WashU_Skud_Contig1362.1  1.0000    761  
SGD_Scer_YOR176W         1.0000    727  MIT_Spar_c278_20970      1.0000    727  
MIT_Smik_c935_20455      1.0000    727  WashU_Skud_Contig2050.4  1.0000    727  
WashU_Sbay_Contig480.2   1.0000    727  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM12-HEM15.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            7396    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.298 C 0.202 G 0.202 T 0.298 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 199   E-value = 4.8e-024
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  ::::1236aaa::6:6aa::
pos.-specific     C  1828327::::aa4a:::9a
probability       G  81816::4:::::::4::::
matrix            T  11:1:6::::::::::::1:

         bits    2.5            ** *    *
                 2.3            ** *    *
                 2.0            ** *   **
                 1.8   *        ** *   **
Information      1.5 ****    ***** * ****
content          1.3 ****  * ***** * ****
(31.9 bits)      1.0 ***** **************
                 0.8 ***** **************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GCGCGTCAAAACCACAAACC
consensus              C CAAG     C G    
sequence                  C              
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig480.2       +    571  6.74e-13 CTTTCGAAGT GCGCGTCGAAACCACAAACC ATCAAAAATA
WashU_Skud_Contig2050.4      +    566  6.74e-13 CTTTCAAAGT GCGCGTCGAAACCACAAACC GTCGAAAATA
MIT_Spar_c278_20970          +    560  6.74e-13 CTTTCGAATT GCGCGTCGAAACCACAAACC GTCGAAAATA
SGD_Scer_YOR176W             +    558  6.74e-13 CTTTCACATT GCGCGTCGAAACCACAAACC GTCGAAAACA
MIT_Smik_c935_20455          +    544  1.42e-12 CTCTCCAATT GCGCGTCAAAACCACAAACC GTCGAAAATA
MIT_Sbay_c896_21277          +    203  2.13e-10 CTTTTCCATG GCGTCAAAAAACCCCGAACC CTGTATAAAC
SGD_Scer_YDR047W             +    235  2.25e-10 TTCCTCTCCT GCCGCCAAAAACCCCGAACC CTGTCCTGTA
MIT_Spar_c130_3923           +    232  1.41e-09 TTTTCTCTCC TGCCACCAAAACCCCGAACC CTGTCCCGTA
WashU_Skud_Contig1362.1      +    198  2.94e-09 TTTTTTCCTG CTGCCAAAAAACCCCGAATC ATGTAGAAGC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig480.2            6.7e-13  570_[+1]_137
WashU_Skud_Contig2050.4           6.7e-13  565_[+1]_142
MIT_Spar_c278_20970               6.7e-13  559_[+1]_148
SGD_Scer_YOR176W                  6.7e-13  557_[+1]_150
MIT_Smik_c935_20455               1.4e-12  543_[+1]_164
MIT_Sbay_c896_21277               2.1e-10  202_[+1]_778
SGD_Scer_YDR047W                  2.2e-10  234_[+1]_746
MIT_Spar_c130_3923                1.4e-09  231_[+1]_749
WashU_Skud_Contig1362.1           2.9e-09  197_[+1]_544
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Sbay_Contig480.2   (  571) GCGCGTCGAAACCACAAACC  1 
WashU_Skud_Contig2050.4  (  566) GCGCGTCGAAACCACAAACC  1 
MIT_Spar_c278_20970      (  560) GCGCGTCGAAACCACAAACC  1 
SGD_Scer_YOR176W         (  558) GCGCGTCGAAACCACAAACC  1 
MIT_Smik_c935_20455      (  544) GCGCGTCAAAACCACAAACC  1 
MIT_Sbay_c896_21277      (  203) GCGTCAAAAAACCCCGAACC  1 
SGD_Scer_YDR047W         (  235) GCCGCCAAAAACCCCGAACC  1 
MIT_Spar_c130_3923       (  232) TGCCACCAAAACCCCGAACC  1 
WashU_Skud_Contig1362.1  (  198) CTGCCAAAAAACCCCGAATC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 4.8e-024 
  -982    -66    215   -154 
  -982    215    -66   -154 
  -982     34    215   -982 
  -982    215    -66   -154 
  -154     92    166   -982 
   -55     34   -982     78 
     4    192   -982   -982 
    78   -982    134   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -982    251   -982   -982 
  -982    251   -982   -982 
    78    134   -982   -982 
  -982    251   -982   -982 
    78   -982    134   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -982    234   -982   -154 
  -982    251   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 4.8e-024 
 0.000000  0.111111  0.777778  0.111111 
 0.000000  0.777778  0.111111  0.111111 
 0.000000  0.222222  0.777778  0.000000 
 0.000000  0.777778  0.111111  0.111111 
 0.111111  0.333333  0.555556  0.000000 
 0.222222  0.222222  0.000000  0.555556 
 0.333333  0.666667  0.000000  0.000000 
 0.555556  0.000000  0.444444  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.555556  0.444444  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.555556  0.000000  0.444444  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  1.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
GC[GC]C[GC][TAC][CA][AG]AAACC[AC]C[AG]AACC
--------------------------------------------------------------------------------




Time  5.88 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 171   E-value = 5.0e-014
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  91:a12:::6::::1::12:
pos.-specific     C  1:::1:881:8:a2239:48
probability       G  :91:2:22::2a:827:1::
matrix            T  ::9:68::94::::4:1832

         bits    2.5            **       
                 2.3            **       
                 2.0  *         **   *   
                 1.8  *    **  ****  *   
Information      1.5  * *  **  **** **  *
content          1.3 ****  *** **** **  *
(27.4 bits)      1.0 ****  *** **** **  *
                 0.8 **** ********* *** *
                 0.5 **** ********* *****
                 0.3 ********************
                 0.0 --------------------

Multilevel           AGTATTCCTACGCGTGCTCC
consensus                GAGG TG  CCC  TT
sequence                           G   A 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c278_20970          +    152  2.21e-12 ACCGACTAAA AGTATTCCTTCGCGTCCTCC TTCTTCAATC
SGD_Scer_YOR176W             +    150  2.21e-12 ACCGACCAAA AGTATTCCTTCGCGTCCTCC TTCTTCAATC
WashU_Skud_Contig2050.4      +    156  3.61e-12 GACCAAAAGA AGTATTCCTTCGCGTGCTTC TCCTTTCTGT
WashU_Sbay_Contig480.2       +    200  7.52e-12 GACCAAAAGA AGTATTCCTACGCGAGCTCC CTCTTCAAGT
MIT_Smik_c935_20455          +    147  3.24e-09 GGCCGACCAA AAGACTCCTTCGCGTCCTCC TTCTTCAAGT
WashU_Skud_Contig1362.1      -    674  4.27e-09 CGTTCGATCG AGTAATGCTAGGCCCGCTTC GAGAGCTGGT
SGD_Scer_YDR047W             -    388  1.16e-08 AACATGTTGT AGTATACGTACGCGGGCAAT TGTGGTGACA
MIT_Spar_c130_3923           -    386  2.39e-08 ATCATATTTT AGTAGACGCACGCGGGCGAT TATAACGAAA
MIT_Sbay_c896_21277          -    675  2.87e-08 TGTTTGGCTG CGTAGTGCTAGGCCCGTTTC GCCTGGCTTG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c278_20970               2.2e-12  151_[+2]_556
SGD_Scer_YOR176W                  2.2e-12  149_[+2]_558
WashU_Skud_Contig2050.4           3.6e-12  155_[+2]_552
WashU_Sbay_Contig480.2            7.5e-12  199_[+2]_508
MIT_Smik_c935_20455               3.2e-09  146_[+2]_561
WashU_Skud_Contig1362.1           4.3e-09  673_[-2]_68
SGD_Scer_YDR047W                  1.2e-08  387_[-2]_593
MIT_Spar_c130_3923                2.4e-08  385_[-2]_595
MIT_Sbay_c896_21277               2.9e-08  674_[-2]_306
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
MIT_Spar_c278_20970      (  152) AGTATTCCTTCGCGTCCTCC  1 
SGD_Scer_YOR176W         (  150) AGTATTCCTTCGCGTCCTCC  1 
WashU_Skud_Contig2050.4  (  156) AGTATTCCTTCGCGTGCTTC  1 
WashU_Sbay_Contig480.2   (  200) AGTATTCCTACGCGAGCTCC  1 
MIT_Smik_c935_20455      (  147) AAGACTCCTTCGCGTCCTCC  1 
WashU_Skud_Contig1362.1  (  674) AGTAATGCTAGGCCCGCTTC  1 
SGD_Scer_YDR047W         (  388) AGTATACGTACGCGGGCAAT  1 
MIT_Spar_c130_3923       (  386) AGTAGACGCACGCGGGCGAT  1 
MIT_Sbay_c896_21277      (  675) CGTAGTGCTAGGCCCGTTTC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 5.0e-014 
   145    -66   -982   -982 
  -154   -982    234   -982 
  -982   -982    -66    145 
   162   -982   -982   -982 
  -154    -66     34     78 
   -55   -982   -982    126 
  -982    215     34   -982 
  -982    215     34   -982 
  -982    -66   -982    145 
    78   -982   -982     45 
  -982    215     34   -982 
  -982   -982    251   -982 
  -982    251   -982   -982 
  -982     34    215   -982 
  -154     34     34     45 
  -982     92    192   -982 
  -982    234   -982   -154 
  -154   -982    -66    126 
   -55    134   -982      4 
  -982    215   -982    -55 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.0e-014 
 0.888889  0.111111  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  0.000000  0.111111  0.888889 
 1.000000  0.000000  0.000000  0.000000 
 0.111111  0.111111  0.222222  0.555556 
 0.222222  0.000000  0.000000  0.777778 
 0.000000  0.777778  0.222222  0.000000 
 0.000000  0.777778  0.222222  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.555556  0.000000  0.000000  0.444444 
 0.000000  0.777778  0.222222  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.222222  0.777778  0.000000 
 0.111111  0.222222  0.222222  0.444444 
 0.000000  0.333333  0.666667  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.111111  0.000000  0.111111  0.777778 
 0.222222  0.444444  0.000000  0.333333 
 0.000000  0.777778  0.000000  0.222222 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
AGTA[TG][TA][CG][CG]T[AT][CG]GC[GC][TCG][GC]CT[CTA][CT]
--------------------------------------------------------------------------------




Time 11.70 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =   9   llr = 168   E-value = 2.4e-011
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  ::::::::11::7:21::::
pos.-specific     C  :428:1a2:::2116:1:::
probability       G  a:::19:17:1718::8:::
matrix            T  :6829::7299111291aaa

         bits    2.5 *     *             
                 2.3 *     *             
                 2.0 *    **             
                 1.8 *    **             
Information      1.5 *  * **      *  ****
content          1.3 *  ****   ** *  ****
(27.0 bits)      1.0 ******* **** * *****
                 0.8 ************ *******
                 0.5 ************ *******
                 0.3 ********************
                 0.0 --------------------

Multilevel           GTTCTGCTGTTGAGCTGTTT
consensus             CCT   CT  C  A     
sequence                           T     
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c935_20455          +    484  3.60e-13 AGCTTTTTTT GCTCTGCTGTTGAGCTGTTT TACTTCATTG
WashU_Sbay_Contig480.2       +    510  1.02e-12 GCTGTTTTTT GTTCTGCTGTTGAGCTGTTT TGCTCCACCT
WashU_Skud_Contig2050.4      +    501  1.02e-12 GCTGTTTTTT GTTCTGCTGTTGAGCTGTTT TGTTCCATCT
MIT_Spar_c278_20970          +    500  1.41e-12 AGCTTTTTTT GCCCTGCTGTTGAGCTGTTT TGCTTCACTG
SGD_Scer_YOR176W             +    498  2.49e-12 AGCTTTTTTT GTCCTGCTGTTGAGCTGTTT TGCTTTACTG
WashU_Skud_Contig1362.1      -    125  2.43e-08 TCAACGAGGT GTTCTGCCTTTCGTATGTTT ATTGCTCGAA
MIT_Spar_c130_3923           -    609  7.51e-08 CGCCAGTGGT GCTTTGCTTTGCCGTAGTTT GTAAAAAAAA
MIT_Sbay_c896_21277          +    770  1.89e-07 CTAGCAGCGT GCTTGCCGGATGAGTTTTTT CCATTTTCCT
SGD_Scer_YDR047W             -    161  2.04e-07 CCAGCGAAAT GTTCTGCCATTTTCATCTTT ACCGCTCGAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c935_20455               3.6e-13  483_[+3]_224
WashU_Sbay_Contig480.2              1e-12  509_[+3]_198
WashU_Skud_Contig2050.4             1e-12  500_[+3]_207
MIT_Spar_c278_20970               1.4e-12  499_[+3]_208
SGD_Scer_YOR176W                  2.5e-12  497_[+3]_210
WashU_Skud_Contig1362.1           2.4e-08  124_[-3]_617
MIT_Spar_c130_3923                7.5e-08  608_[-3]_372
MIT_Sbay_c896_21277               1.9e-07  769_[+3]_211
SGD_Scer_YDR047W                    2e-07  160_[-3]_820
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=9
MIT_Smik_c935_20455      (  484) GCTCTGCTGTTGAGCTGTTT  1 
WashU_Sbay_Contig480.2   (  510) GTTCTGCTGTTGAGCTGTTT  1 
WashU_Skud_Contig2050.4  (  501) GTTCTGCTGTTGAGCTGTTT  1 
MIT_Spar_c278_20970      (  500) GCCCTGCTGTTGAGCTGTTT  1 
SGD_Scer_YOR176W         (  498) GTCCTGCTGTTGAGCTGTTT  1 
WashU_Skud_Contig1362.1  (  125) GTTCTGCCTTTCGTATGTTT  1 
MIT_Spar_c130_3923       (  609) GCTTTGCTTTGCCGTAGTTT  1 
MIT_Sbay_c896_21277      (  770) GCTTGCCGGATGAGTTTTTT  1 
SGD_Scer_YDR047W         (  161) GTTCTGCCATTTTCATCTTT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 2.4e-011 
  -982   -982    251   -982 
  -982    134   -982     78 
  -982     34   -982    126 
  -982    215   -982    -55 
  -982   -982    -66    145 
  -982    -66    234   -982 
  -982    251   -982   -982 
  -982     34    -66    104 
  -154   -982    192    -55 
  -154   -982   -982    145 
  -982   -982    -66    145 
  -982     34    192   -154 
   104    -66    -66   -154 
  -982    -66    215   -154 
   -55    166   -982    -55 
  -154   -982   -982    145 
  -982    -66    215   -154 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -982   -982   -982    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.4e-011 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.444444  0.000000  0.555556 
 0.000000  0.222222  0.000000  0.777778 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.111111  0.888889  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.222222  0.111111  0.666667 
 0.111111  0.000000  0.666667  0.222222 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.222222  0.666667  0.111111 
 0.666667  0.111111  0.111111  0.111111 
 0.000000  0.111111  0.777778  0.111111 
 0.222222  0.555556  0.000000  0.222222 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  0.111111  0.777778  0.111111 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
G[TC][TC][CT]TGC[TC][GT]TT[GC]AG[CAT]TGTTT
--------------------------------------------------------------------------------




Time 17.31 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =   9   llr = 165   E-value = 1.1e-009
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  8282::a:8:3::3734a93
pos.-specific     C  17:1:a:a:31:a3:14:::
probability       G  ::17a:::2761::34::17
matrix            T  111::::::::9:3:11:::

         bits    2.5     ** *    *       
                 2.3     ** *    *       
                 2.0     ** *    *       
                 1.8     ** *    *       
Information      1.5     **** *  *    *  
content          1.3     **** * **    ***
(26.4 bits)      1.0  * ******* ** *  ***
                 0.8 ************* *  ***
                 0.5 ************* * ****
                 0.3 ********************
                 0.0 --------------------

Multilevel           ACAGGCACAGGTCAAGAAAG
consensus             A A    GCA  CGAC  A
sequence                          T      
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
SGD_Scer_YOR176W             +    643  5.51e-13 AGGACAAAAT ACAGGCACAGGTCAAGCAAG AAGACAAACC
MIT_Spar_c278_20970          +    647  1.12e-12 AAGACACGAT ACAGGCACAGGTCCAGAAAG AATACAAAAC
MIT_Smik_c935_20455          +    632  6.03e-12 AATACTCCAT ACAGGCACAGGTCTAACAAG AAGACAACGC
WashU_Sbay_Contig480.2       +    657  2.48e-10 AGCTCTTCAT ACAGGCACAGGTCAGATAAG AAGACAATTC
MIT_Spar_c130_3923           -    808  3.78e-09 GCCGGAAAAA AAAAGCACGCATCCGGCAAG GAAAGGACGC
SGD_Scer_YDR047W             -    798  3.78e-09 GCCGGAAAAA AAAAGCACGCATCCGGCAAG CACACTAGTA
WashU_Skud_Contig2050.4      +    652  2.81e-08 AATATTCCAT TCAGGCACAGATCAACAAGA AGACAAAAAG
WashU_Skud_Contig1362.1      +     48  4.74e-08 AGCAAGCTCA ATTGGCACAGCTCTAAAAAA AGCCTTGTGA
MIT_Sbay_c896_21277          -    831  1.01e-07 TCTCTCGATG CCGCGCACACGGCTATAAAA CTGACCTTTC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YOR176W                  5.5e-13  642_[+4]_65
MIT_Spar_c278_20970               1.1e-12  646_[+4]_61
MIT_Smik_c935_20455                 6e-12  631_[+4]_76
WashU_Sbay_Contig480.2            2.5e-10  656_[+4]_51
MIT_Spar_c130_3923                3.8e-09  807_[-4]_173
SGD_Scer_YDR047W                  3.8e-09  797_[-4]_183
WashU_Skud_Contig2050.4           2.8e-08  651_[+4]_56
WashU_Skud_Contig1362.1           4.7e-08  47_[+4]_694
MIT_Sbay_c896_21277                 1e-07  830_[-4]_150
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=9
SGD_Scer_YOR176W         (  643) ACAGGCACAGGTCAAGCAAG  1 
MIT_Spar_c278_20970      (  647) ACAGGCACAGGTCCAGAAAG  1 
MIT_Smik_c935_20455      (  632) ACAGGCACAGGTCTAACAAG  1 
WashU_Sbay_Contig480.2   (  657) ACAGGCACAGGTCAGATAAG  1 
MIT_Spar_c130_3923       (  808) AAAAGCACGCATCCGGCAAG  1 
SGD_Scer_YDR047W         (  798) AAAAGCACGCATCCGGCAAG  1 
WashU_Skud_Contig2050.4  (  652) TCAGGCACAGATCAACAAGA  1 
WashU_Skud_Contig1362.1  (   48) ATTGGCACAGCTCTAAAAAA  1 
MIT_Sbay_c896_21277      (  831) CCGCGCACACGGCTATAAAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 1.1e-009 
   126    -66   -982   -154 
   -55    192   -982   -154 
   126   -982    -66   -154 
   -55    -66    192   -982 
  -982   -982    251   -982 
  -982    251   -982   -982 
   162   -982   -982   -982 
  -982    251   -982   -982 
   126   -982     34   -982 
  -982     92    192   -982 
     4    -66    166   -982 
  -982   -982    -66    145 
  -982    251   -982   -982 
     4     92   -982      4 
   104   -982     92   -982 
     4    -66    134   -154 
    45    134   -982   -154 
   162   -982   -982   -982 
   145   -982    -66   -982 
     4   -982    192   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.1e-009 
 0.777778  0.111111  0.000000  0.111111 
 0.222222  0.666667  0.000000  0.111111 
 0.777778  0.000000  0.111111  0.111111 
 0.222222  0.111111  0.666667  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.000000  0.333333  0.666667  0.000000 
 0.333333  0.111111  0.555556  0.000000 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  1.000000  0.000000  0.000000 
 0.333333  0.333333  0.000000  0.333333 
 0.666667  0.000000  0.333333  0.000000 
 0.333333  0.111111  0.444444  0.111111 
 0.444444  0.444444  0.000000  0.111111 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.333333  0.000000  0.666667  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
A[CA]A[GA]GCAC[AG][GC][GA]TC[ACT][AG][GA][AC]AA[GA]
--------------------------------------------------------------------------------




Time 22.56 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 160   E-value = 3.0e-008
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  91:1::3:::3:::::::1:
pos.-specific     C  :::611:::::89::613::
probability       G  17::::::::121:::::4:
matrix            T  :2a3997aaa6::aa4974a

         bits    2.5                     
                 2.3                     
                 2.0             *       
                 1.8            **       
Information      1.5   *    *** ****    *
content          1.3 * * ** *** **** *  *
(25.6 bits)      1.0 *** ** *** ******* *
                 0.8 ********** ******* *
                 0.5 ********** *********
                 0.3 ********************
                 0.0 --------------------

Multilevel           AGTCTTTTTTTCCTTCTTGT
consensus             T T  A   AG   T CT 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c130_3923           +    733  2.54e-10 CGTCCCATTG AGTTTTATTTTCCTTCTCGT AGCACCTTCT
WashU_Sbay_Contig480.2       +    102  1.11e-09 AGAGAAGAAA ATTTTTTTTTTCCTTCTTGT ATGGTCAGTT
WashU_Skud_Contig2050.4      +     58  1.57e-09 ATAAGCAAGA AATCTTTTTTTCCTTCTTTT ACGGTCTATT
WashU_Skud_Contig1362.1      +    713  1.57e-09 GTTGCCGTTT AGTCTTATTTTCCTTTCCGT GCTGCGCTGC
MIT_Spar_c278_20970          +    480  1.72e-09 AAATGCGAAG AGTCTTTTTTAGCTTTTTTT GCCCTGCTGT
SGD_Scer_YDR047W             +    733  3.76e-09 CGTCCCATTG AGTTTTATTTTCCTTCTCAT GGCACCTTCT
MIT_Smik_c935_20455          +     57  4.88e-09 ATATGTGATG AGTCCTTTTTACGTTCTTGT ATAACCTAAG
MIT_Sbay_c896_21277          +     10  2.83e-08  AGTGTTAAC AGTATCTTTTGCCTTTTTTT ATTCTAATAG
SGD_Scer_YOR176W             +    478  3.32e-08 AGTGCGAAGA GTTCTTTTTTAGCTTTTTTT GTCCTGCTGT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c130_3923                2.5e-10  732_[+5]_248
WashU_Sbay_Contig480.2            1.1e-09  101_[+5]_606
WashU_Skud_Contig2050.4           1.6e-09  57_[+5]_650
WashU_Skud_Contig1362.1           1.6e-09  712_[+5]_29
MIT_Spar_c278_20970               1.7e-09  479_[+5]_228
SGD_Scer_YDR047W                  3.8e-09  732_[+5]_248
MIT_Smik_c935_20455               4.9e-09  56_[+5]_651
MIT_Sbay_c896_21277               2.8e-08  9_[+5]_971
SGD_Scer_YOR176W                  3.3e-08  477_[+5]_230
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
MIT_Spar_c130_3923       (  733) AGTTTTATTTTCCTTCTCGT  1 
WashU_Sbay_Contig480.2   (  102) ATTTTTTTTTTCCTTCTTGT  1 
WashU_Skud_Contig2050.4  (   58) AATCTTTTTTTCCTTCTTTT  1 
WashU_Skud_Contig1362.1  (  713) AGTCTTATTTTCCTTTCCGT  1 
MIT_Spar_c278_20970      (  480) AGTCTTTTTTAGCTTTTTTT  1 
SGD_Scer_YDR047W         (  733) AGTTTTATTTTCCTTCTCAT  1 
MIT_Smik_c935_20455      (   57) AGTCCTTTTTACGTTCTTGT  1 
MIT_Sbay_c896_21277      (   10) AGTATCTTTTGCCTTTTTTT  1 
SGD_Scer_YOR176W         (  478) GTTCTTTTTTAGCTTTTTTT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 3.0e-008 
   145   -982    -66   -982 
  -154   -982    192    -55 
  -982   -982   -982    162 
  -154    166   -982      4 
  -982    -66   -982    145 
  -982    -66   -982    145 
     4   -982   -982    104 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -982   -982   -982    162 
     4   -982    -66     78 
  -982    215     34   -982 
  -982    234    -66   -982 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -982    166   -982     45 
  -982    -66   -982    145 
  -982     92   -982    104 
  -154   -982    134     45 
  -982   -982   -982    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.0e-008 
 0.888889  0.000000  0.111111  0.000000 
 0.111111  0.000000  0.666667  0.222222 
 0.000000  0.000000  0.000000  1.000000 
 0.111111  0.555556  0.000000  0.333333 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.111111  0.000000  0.888889 
 0.333333  0.000000  0.000000  0.666667 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.333333  0.000000  0.111111  0.555556 
 0.000000  0.777778  0.222222  0.000000 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.333333  0.000000  0.666667 
 0.111111  0.000000  0.444444  0.444444 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
A[GT]T[CT]TT[TA]TTT[TA][CG]CTT[CT]T[TC][GT]T
--------------------------------------------------------------------------------




Time 27.84 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR047W                 1.02e-19  160_[-3(2.04e-07)]_31_[+5(1.41e-05)]_3_[+1(2.25e-10)]_133_[-2(1.16e-08)]_88_[+4(6.35e-05)]_217_[+5(3.76e-09)]_45_[-4(3.78e-09)]_183
MIT_Spar_c130_3923               3.55e-20  231_[+1(1.41e-09)]_134_[-2(2.39e-08)]_178_[+3(8.67e-05)]_5_[-3(7.51e-08)]_104_[+5(2.54e-10)]_55_[-4(3.78e-09)]_173
MIT_Sbay_c896_21277              2.88e-17  9_[+5(2.83e-08)]_148_[+5(7.36e-05)]_5_[+1(2.13e-10)]_452_[-2(2.87e-08)]_75_[+3(1.89e-07)]_41_[-4(1.01e-07)]_150
WashU_Skud_Contig1362.1          7.74e-20  47_[+4(4.74e-08)]_57_[-3(2.43e-08)]_53_[+1(2.94e-09)]_70_[+4(1.81e-05)]_366_[-2(4.27e-09)]_19_[+5(1.57e-09)]_29
SGD_Scer_YOR176W                 1.14e-33  149_[+2(2.21e-12)]_26_[-3(1.12e-05)]_90_[+2(6.19e-05)]_152_[+5(3.32e-08)]_[+3(2.49e-12)]_40_[+1(6.74e-13)]_65_[+4(5.51e-13)]_65
MIT_Spar_c278_20970              7.69e-35  57_[+5(1.77e-06)]_29_[-4(3.91e-05)]_25_[+2(2.21e-12)]_27_[-2(6.64e-05)]_261_[+5(1.72e-09)]_[+3(1.41e-12)]_40_[+1(6.74e-13)]_67_[+4(1.12e-12)]_3_[-3(6.33e-05)]_38
MIT_Smik_c935_20455              6.08e-31  56_[+5(4.88e-09)]_70_[+2(3.24e-09)]_317_[+3(3.60e-13)]_40_[+1(1.42e-12)]_68_[+4(6.03e-12)]_76
WashU_Skud_Contig2050.4          1.32e-30  57_[+5(1.57e-09)]_78_[+2(3.61e-12)]_304_[+5(7.50e-05)]_1_[+3(1.02e-12)]_45_[+1(6.74e-13)]_66_[+4(2.81e-08)]_56
WashU_Sbay_Contig480.2           2.10e-32  101_[+5(1.11e-09)]_78_[+2(7.52e-12)]_37_[-5(3.91e-05)]_77_[+3(3.61e-05)]_44_[+2(3.84e-06)]_51_[+5(6.08e-06)]_1_[+3(1.02e-12)]_41_[+1(6.74e-13)]_66_[+4(2.48e-10)]_51
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM12.ups.fa_000444000766000024      1254413155576321 20355 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR047W HEM12 "Uroporphyrinogen decarboxylase, catalyzes the fifth step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; activity inhibited by Cu2+, Zn2+, Fe2+, Fe3+ and sulfhydryl-specific reagents"
AGCGTTATAACCTGTTCTTTGCTTTATTTTTTTTTTTTTTGTTCTTCCTTTTCTCGAAGA
GAGCTTACCAAACACAATTCTGAGATAATGCTTGATGAATTGAAGAACCTATCGATCACT
CTATGTTACCTTCGTCTGGAACATCACTAATTCGAGCGGTAAAGATGAAAATGGCAGAAC
ATTTCGCTGGCAAAATTAAAACTCTTGCCTCATTTTTTTTTGCTTTCCTCTCCTGCCGCC
AAAAACCCCGAACCCTGTCCTGTATATACGAGAAACATTGAAAAAGATCGTGTATGATAG
CGCCAAGATGGCGGATAAACTAACACTATTGACAGGTTGAGGCCAAGGATATATTACTTG
CTAACAGAAAGAGATACTGTCACCACAATTGCCCGCGTACGTATACTACAACATGTTCTC
TATATATCACCCACTCTTTCGCAGTGCTACGTACGCCAAAAACGCGCGCATGGAAGTAAA
GAAGTTTTTTCTTTTAAGAGCGAAGCTCCATTAAAAGCCTTGAATATAAACTAGTGCGAA
GTAGTATGATCCGAAGACACCAATTGCTGGTGCAGCATAGGAATATGTGGCGTCCGAAAA
AGAGCCTTTAACAATCCACGGCGAAACAAGGCACCGCTGTGCATTTAAAACATGCCGTTC
CCGTACCAAGTTATATTGTTACGGATGAATCCAAAATAATTTGTTAAAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCATGGCACCTTCTTCGTTTCTTCATCCTGCA
TTAGACTTACTAGTGTGCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGACACATATCGC
TGAGCTGGAAGGACACCTTTTAATGTAGCCGTGCATGCGGCTCCGCGAAAAGAGCTCTGC
TATATTTCTCTACCTGAACTTCGAGCCGCGATCAACGAAAGCTCTCATCCAAGGCTCGTT
TTTCTTGACAGAAGCATGACAGTAAAATATGCGGTCATTT
>MIT_Spar_c130_3923 YDR047W 5' untranslated region, Contig c130 9341 - 11340, 2000 bp (revcom)
AGCGTTATGATGTGTTATTTGCTTTTATTTTCTTCTTTCTTTGTCTCGAAGATAACCTAG
CAAACACAATTCTAAGAAAATTCTCGATGAATTGGTTGTCAGCGCTTCCTATTTACTCTA
TGTCCACTTCGTTTGAAACATCAGTGGTTCGAGCAGTAATGACAAAAAGGGCAGAACATT
TCGTTGGCAAAATTTAAACTCGTGCCTCTCATTTTTTTTACTTTTCTCTCCTGCCACCAA
AACCCCGAACCCTGTCCCGTATATACGAGGAACATTGAAAAAAAATCGTGTATGGTAGCG
CCAAGATAGCGAATAAACTATCAGTATTGGCAGGGTGAAGCTAAGGATATGTTGTTTGCT
AACAAAGGGAAATGCTTTCGTTATAATCGCCCGCGTGCGTCTACTAAAATATGATCTATA
TATACCACCCAGTCTATTGCAGTGTTACGTACATCAAAATGCGCGCATGTAAGTGAACAA
GTTTTTTTTGTTTAAAGAGCGATTTTCCAATAAAGGCTTTGGATATACACTGGTGCAAAA
TATATGGTCAATGACGCCAATTACTGGTGTAGCATGAGAATACGTCGTCCGAAAGAGTTT
TTTTTTACAAACTACGGCAAAGCAAAGCACCACTGGCGCAATTCAAAACATGCCGTCCCC
GTACTAAGTTATGTACGTTATTATGGACGGATCCAAAATTATACTCTAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCGTAGCACCTTCTTCGTGTCCTTTCCTTCTT
CTGCATTAGGCTTACTAGCGTCCTTTCCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGA
CAAATCTCGCTGAGTTGGAAAGACACCTTTTATATAGCCGTACGTGCGGCTCCTCGAGAA
AGGCCCTGCTATATTTCACTAGCTGATCCTCGAGCTGCGATCAACGAAAGCCCCATCCAA
AAGGCTCCTTTTTCTTCAAAGAAGCATGACAGTAAAATAT
>MIT_Sbay_c896_21277 YDR047W 5' untranslated region, Contig c896 2230 - 4229(revcom), 2000 bp (revcom)
AGTGTTAACAGTATCTTTTGCCTTTTTTTATTCTAATAGCTACCCCAGGAATCACTATTT
AGCAAAGATCGTTTGCAAATTGGCCGTCAGTACGTTCTAAGTTCTTTAGAACATCATTGG
CTCGAGCATTAGTGACACGAATAGGAAAGCATTTCGTTGACAAAAATAAAATTGTTTCTT
TATTTTTTCCCTCTTTTCCATGGCGTCAAAAAACCCCGAACCCTGTATAAACGAGGAAGC
TGCATGGTAGCGCCAGAAAAGGCAGATAACCTTTAACAGTGCTGACAGAACAACGTCAAA
CATGTGCGGATAATGCCTTCGCTGACGGCAAGAAATTATATACGCCTCGAAACTGTAGAA
CGTCTTTTGTGCCGCTTGGTAACAAATAAACCTAGCCGGGGCCAGAATTTCACCCGTACA
TACTTACTGTTACATACTGCATGCACGCTACGCATTCTCACCGAACATCGAATCTGCCTG
CAGAAGCGAAGAAAAGCAAGTCTTCGAAGAGCAAGCTTACATCCATCGTGTTGAACACAT
ATGCCCAGCAAAGGGATCGGATGACGCCCAACTAACATTGGAATTTGTGACGCAAGGCTG
AAAGGCACTTCTCTATAGCCCACGGTGAAGCCTTACGCTATTGACAAGACAAAACATGCC
GATCCAAGCCAGGCGAAACGGGCCTAGCACTACGCAGCCAAACACTGGCGTTCCGCCCGT
CCCATCCAGTTTCATTTCTTATTTCGTTCTGCCTTGGGCCTAGCAGCGTGCTTGCCGGAT
GAGTTTTTTCCATTTTCCTACCGGCTCATCTCGCTAAGCTGAAAGGTCAGTTTTATAGCC
GTGTGCGCGGCATCGAGAGACAGGTTCAGCTAATGATATTTGCCTAATTCTCGAGCTGAG
GCCAATGAAGGCAGCTTCCAGGGCTCGTTTCTGCTCGGGAAAAAGCATACCACACATTTG
CACGGCTTTTATGTGCCATAGTGCCACCACTAGCCCCCAG
>WashU_Skud_Contig1362.1 YDR047W 5' untranslated region, Contig c1362 1 - 761, 2000 bp (revcom)
AGTGTTGATGGTATCTTTTGATTTTTTCTAGATTGGTAGCAAGCTCAATTGGCACAGCTC
TAAAAAAAGCCTTGTGAATTGGATAGTACCTTCTTTCGTTTGGAACATTACTGCTTCGAG
CAATAAACATACGAAAGGCAGAACACCTCGTTGACAAAACTGAAACTATTTCTTCAATTT
TTTGGCCTTTTTTCCTGCTGCCAAAAAACCCCGAATCATGTAGAAGCGAGAAGTAAAACA
GAGGAAGTGTATGGTAGCGCCAAGGAAAACGGGCAATACTTAGAAAGAATGACAGAGCTC
AGCCAAGTGTAAGCTAAGTGTTGACAAGGGAAGGTACATTGGGCCCCGAAAAAATTTGCT
AATGCTCGAAGAGCTCTCAATCAATCACCCACATATATGTACTACAGTATATTTATACTT
TCCACGCAGTCTCACGCAGTGCCACCTTCATCACCATGCGTGTAACTAATCGAGCAAGCT
GTTTTACGAAGGGCAGCTTTCCTATAAGCGTTTTGAACATGCATGGCTGCACTGCAATGA
GATCAGGCGACTCCAATTCCATAGCCTAGCACGGGATTAAGTAACGAGAAACTGAAAGAG
ATAATTTTACAAACCCGGACGAAGCAGAGCACTTGCTGGAACAAATCAAACATGCCGTCC
CCTACCAGCTCTCGAAGCGGGCCTAGCATTACTCGATCGAACGTTGCCGTTTAGTCTTAT
TTTCCTTTCCGTGCTGCGCTGCTTTTTTCTTGCATTGGGCT
>WashU_Scas_Contig569.6 YDR047W 5' untranslated region, Contig c569 10116 - 12115, 2000 bp (revcom)
TTTTTCAAGTCGTTGGGTGTCAAATAGTGGGAGGATTGGTGGAGGAAACGTGGAACAAAT
GATGACTGTTTCCTTTTAAAGGATATTCGCCAATTGACAGCTACCGTACGATTCGGTTAA
CGTTGCGGCTCGCGCCAAATATAAACGAGCCAAGAATGTCAAATAACGCTACGTATCAAT
TAACGTCACCTATCAATCTTTGTAAATTGATAACAAAATACATTAGTGATTACTTCTCCA
ACCTTTATCAAACCATCAAATAAAGTCCTTAAATATGTTGTTCCCCACAAAACGGAAATT
TAAGGGTTGAGAAGGAAGTGTGACGGTAAAAAGATTCTTAATACCTTAGTATCGAGTAAA
CGAGGACGAAAACGAATAATCTCCAGTATAAAAAAACCAATAACTCAGTTATAATATACT
TCCAAAATCATTTTTATTTATTTTTGAATAAAAATATATACGAGAGGTGGAGATGACATA
TTATCGCTTTTACAGTAAGTTTTTCTTCCCTTCTTGATTTAGAGAGTTGTGAGAACAATC
TGACGTTTTTCATAAGAGGTTGATTCAATTACGTTGTTGTCAATTTAGTCATGAATGGAA
TATCCATATTCACATCCACCAACCTCTGAGCTACAATAACATTTCATTTACAATCCAGCC
TCGAGGTGCTGTGGTGAGGCATAGCTTATAGTTAAAGTTAGATTCCATTATTCATTTCTT
ATCAAAAACAGACATGACAATTATATTAATATTAAGGCAAAAAAGAGTGTCAAAGTTCTA
ACTGTTTTTCCTCAAAAGTTAGTGGAAAAAAAAAGTTTTCAAATATTCTTCACATAATTT
TTTTACACATGCTTAACCGCTCTTAAGACTGAACTAATTCGTCCTACATTACAATGATAC
TTGTCCAATGACCTTCTTTTAAGACTTTTTGTTTCATGTGAGGGTTTCTTCTCCGGTTTA
AAGGCCAGGAAGTCTAAAAAATTATATTGAGGAACTATGG
BioPerl-1.007002/t/data/map_hem/HEM12.ups.fa_.revcom000444000766000024      1040713155576321 21643 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR047W HEM12 "Uroporphyrinogen decarboxylase, catalyzes the fifth step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; activity inhibited by Cu2+, Zn2+, Fe2+, Fe3+ and sulfhydryl-specific reagents"
AAATGACCGCATATTTTACTGTCATGCTTCTGTCAAGAAAAACGAGCCTTGGATGAGAGC
TTTCGTTGATCGCGGCTCGAAGTTCAGGTAGAGAAATATAGCAGAGCTCTTTTCGCGGAG
CCGCATGCACGGCTACATTAAAAGGTGTCCTTCCAGCTCAGCGATATGTGTCGGCCGGAA
AAAAAAAGCACGCATCCGGCAAGCACACTAGTAAGTCTAATGCAGGATGAAGAAACGAAG
AAGGTGCCATGAGAAGGAAAATAAAACTCAATGGGACGGAACGGCAGCATTTTTTAACAA
ATTATTTTGGATTCATCCGTAACAATATAACTTGGTACGGGAACGGCATGTTTTAAATGC
ACAGCGGTGCCTTGTTTCGCCGTGGATTGTTAAAGGCTCTTTTTCGGACGCCACATATTC
CTATGCTGCACCAGCAATTGGTGTCTTCGGATCATACTACTTCGCACTAGTTTATATTCA
AGGCTTTTAATGGAGCTTCGCTCTTAAAAGAAAAAACTTCTTTACTTCCATGCGCGCGTT
TTTGGCGTACGTAGCACTGCGAAAGAGTGGGTGATATATAGAGAACATGTTGTAGTATAC
GTACGCGGGCAATTGTGGTGACAGTATCTCTTTCTGTTAGCAAGTAATATATCCTTGGCC
TCAACCTGTCAATAGTGTTAGTTTATCCGCCATCTTGGCGCTATCATACACGATCTTTTT
CAATGTTTCTCGTATATACAGGACAGGGTTCGGGGTTTTTGGCGGCAGGAGAGGAAAGCA
AAAAAAAATGAGGCAAGAGTTTTAATTTTGCCAGCGAAATGTTCTGCCATTTTCATCTTT
ACCGCTCGAATTAGTGATGTTCCAGACGAAGGTAACATAGAGTGATCGATAGGTTCTTCA
ATTCATCAAGCATTATCTCAGAATTGTGTTTGGTAAGCTCTCTTCGAGAAAAGGAAGAAC
AAAAAAAAAAAAAATAAAGCAAAGAACAGGTTATAACGCT
>MIT_Spar_c130_3923 YDR047W 5' untranslated region, Contig c130 9341 - 11340, 2000 bp (revcom)
ATATTTTACTGTCATGCTTCTTTGAAGAAAAAGGAGCCTTTTGGATGGGGCTTTCGTTGA
TCGCAGCTCGAGGATCAGCTAGTGAAATATAGCAGGGCCTTTCTCGAGGAGCCGCACGTA
CGGCTATATAAAAGGTGTCTTTCCAACTCAGCGAGATTTGTCGGCCGGAAAAAAAAAGCA
CGCATCCGGCAAGGAAAGGACGCTAGTAAGCCTAATGCAGAAGAAGGAAAGGACACGAAG
AAGGTGCTACGAGAAGGAAAATAAAACTCAATGGGACGGAACGGCAGCATTTTAGAGTAT
AATTTTGGATCCGTCCATAATAACGTACATAACTTAGTACGGGGACGGCATGTTTTGAAT
TGCGCCAGTGGTGCTTTGCTTTGCCGTAGTTTGTAAAAAAAAACTCTTTCGGACGACGTA
TTCTCATGCTACACCAGTAATTGGCGTCATTGACCATATATTTTGCACCAGTGTATATCC
AAAGCCTTTATTGGAAAATCGCTCTTTAAACAAAAAAAACTTGTTCACTTACATGCGCGC
ATTTTGATGTACGTAACACTGCAATAGACTGGGTGGTATATATAGATCATATTTTAGTAG
ACGCACGCGGGCGATTATAACGAAAGCATTTCCCTTTGTTAGCAAACAACATATCCTTAG
CTTCACCCTGCCAATACTGATAGTTTATTCGCTATCTTGGCGCTACCATACACGATTTTT
TTTCAATGTTCCTCGTATATACGGGACAGGGTTCGGGGTTTTGGTGGCAGGAGAGAAAAG
TAAAAAAAATGAGAGGCACGAGTTTAAATTTTGCCAACGAAATGTTCTGCCCTTTTTGTC
ATTACTGCTCGAACCACTGATGTTTCAAACGAAGTGGACATAGAGTAAATAGGAAGCGCT
GACAACCAATTCATCGAGAATTTTCTTAGAATTGTGTTTGCTAGGTTATCTTCGAGACAA
AGAAAGAAGAAAATAAAAGCAAATAACACATCATAACGCT
>MIT_Sbay_c896_21277 YDR047W 5' untranslated region, Contig c896 2230 - 4229(revcom), 2000 bp (revcom)
CTGGGGGCTAGTGGTGGCACTATGGCACATAAAAGCCGTGCAAATGTGTGGTATGCTTTT
TCCCGAGCAGAAACGAGCCCTGGAAGCTGCCTTCATTGGCCTCAGCTCGAGAATTAGGCA
AATATCATTAGCTGAACCTGTCTCTCGATGCCGCGCACACGGCTATAAAACTGACCTTTC
AGCTTAGCGAGATGAGCCGGTAGGAAAATGGAAAAAACTCATCCGGCAAGCACGCTGCTA
GGCCCAAGGCAGAACGAAATAAGAAATGAAACTGGATGGGACGGGCGGAACGCCAGTGTT
TGGCTGCGTAGTGCTAGGCCCGTTTCGCCTGGCTTGGATCGGCATGTTTTGTCTTGTCAA
TAGCGTAAGGCTTCACCGTGGGCTATAGAGAAGTGCCTTTCAGCCTTGCGTCACAAATTC
CAATGTTAGTTGGGCGTCATCCGATCCCTTTGCTGGGCATATGTGTTCAACACGATGGAT
GTAAGCTTGCTCTTCGAAGACTTGCTTTTCTTCGCTTCTGCAGGCAGATTCGATGTTCGG
TGAGAATGCGTAGCGTGCATGCAGTATGTAACAGTAAGTATGTACGGGTGAAATTCTGGC
CCCGGCTAGGTTTATTTGTTACCAAGCGGCACAAAAGACGTTCTACAGTTTCGAGGCGTA
TATAATTTCTTGCCGTCAGCGAAGGCATTATCCGCACATGTTTGACGTTGTTCTGTCAGC
ACTGTTAAAGGTTATCTGCCTTTTCTGGCGCTACCATGCAGCTTCCTCGTTTATACAGGG
TTCGGGGTTTTTTGACGCCATGGAAAAGAGGGAAAAAATAAAGAAACAATTTTATTTTTG
TCAACGAAATGCTTTCCTATTCGTGTCACTAATGCTCGAGCCAATGATGTTCTAAAGAAC
TTAGAACGTACTGACGGCCAATTTGCAAACGATCTTTGCTAAATAGTGATTCCTGGGGTA
GCTATTAGAATAAAAAAAGGCAAAAGATACTGTTAACACT
>WashU_Skud_Contig1362.1 YDR047W 5' untranslated region, Contig c1362 1 - 761, 2000 bp (revcom)
AGCCCAATGCAAGAAAAAAGCAGCGCAGCACGGAAAGGAAAATAAGACTAAACGGCAACG
TTCGATCGAGTAATGCTAGGCCCGCTTCGAGAGCTGGTAGGGGACGGCATGTTTGATTTG
TTCCAGCAAGTGCTCTGCTTCGTCCGGGTTTGTAAAATTATCTCTTTCAGTTTCTCGTTA
CTTAATCCCGTGCTAGGCTATGGAATTGGAGTCGCCTGATCTCATTGCAGTGCAGCCATG
CATGTTCAAAACGCTTATAGGAAAGCTGCCCTTCGTAAAACAGCTTGCTCGATTAGTTAC
ACGCATGGTGATGAAGGTGGCACTGCGTGAGACTGCGTGGAAAGTATAAATATACTGTAG
TACATATATGTGGGTGATTGATTGAGAGCTCTTCGAGCATTAGCAAATTTTTTCGGGGCC
CAATGTACCTTCCCTTGTCAACACTTAGCTTACACTTGGCTGAGCTCTGTCATTCTTTCT
AAGTATTGCCCGTTTTCCTTGGCGCTACCATACACTTCCTCTGTTTTACTTCTCGCTTCT
ACATGATTCGGGGTTTTTTGGCAGCAGGAAAAAAGGCCAAAAAATTGAAGAAATAGTTTC
AGTTTTGTCAACGAGGTGTTCTGCCTTTCGTATGTTTATTGCTCGAAGCAGTAATGTTCC
AAACGAAAGAAGGTACTATCCAATTCACAAGGCTTTTTTTAGAGCTGTGCCAATTGAGCT
TGCTACCAATCTAGAAAAAATCAAAAGATACCATCAACACT
BioPerl-1.007002/t/data/map_hem/HEM13-HEM14.fa000444000766000024      1445013155576321 20163 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR044W HEM13 "Coproporphyrinogen III oxidase, an oxygen requiring enzyme that catalyzes the sixth step in the heme biosynthetic pathway; localizes to the mitochondrial inner membrane; transcription is repressed by oxygen and heme (via Rox1p and Hap1p)"
CTTTATGTGTATTTAATTGTGTTCGAAGAGTTCGGTTTGCTATGTTTGATTTGCGAAAAG
AAAGCTTTTGATATGCTCAAAAAAAGAAAACCCGGAGAATAAAAGCTTAACAAAGAAAGA
CAATAGGTGGAAAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTCGAAACGAGAACA
ATGGGCAAAGCAAGCTTTATCTTCGGATCGTCCGTCAGCGCTTTGGTTGCAGTCTTATGC
TTTGTTCAAGCTGGAGCGTTATTGGTGGGAGAACCAGAAAAGGCGAAAGCGTAGCGTTCT
TTGAAATTTGGCTTCTGTTCCTGCGACTCGTTTAAAAGTAGAAGGGCCCGCGGAGCCGCT
GTGAAAGATTTCTTTTACTCTTTCAGCGCAGAAATCTCGCAGGAGCTCAGCAGAAAGTGC
CTATGACGGTAATCCCAGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAATTAA
AATACCGTGCCTATAGTAACTTTTTTTTACGCTGTGAACCGTTCAACACACAGTAAAAAC
TCCGCAGGAAATGGTTTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTTTCCCAACA
GTGAACGAGAGGACAAACTCCAGAGGATTTGCGGGCTTGATGATAAAATGTATTGTTGAA
AAGATCGCGAATGCAACAATTACGGTGGGGAGAAATATCAACAAAAGGGCAAGGCTATGC
CTTCTGGAAAGTGGCAGACTTGCACTTTCCTCGAAAAGAAAAATGACCGCAAGATCCGGT
TGTTCTCAACCTTCTACATTAAGACATACTTCTACGATTTTCGAATGCCGAAGCAACTAT
CGCTGAAATTTGTCATGTCAAAATTGCTACTGGGGGAGAAGAATATATATGGAAGTAATT
ATTATTTACGTTGCTGAAATGGCAGGTTAGACGCATGTTTTGCAAAATAAGTGGTTTTGA
AAAGAATTGATACTAGGAATCGGTGCAATACCTTCTACCT
>MIT_Spar_c130_3912 YDR044W 5' untranslated region, Contig c130 4128 - 6127, 2000 bp (revcom)
CTTTATATGTGTGTTTTGTGGTGTTCGAAATTGGTTTCTTTTGTTCGACTTGCGAGAAGA
AAGCTATCAATATGCTTTCCAAAAAAAGCTGGAGAATAAAAGCTTAACAAAGAAAGACAA
TAGGCGGAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTTCGAAACGAGAACAATGG
ACAAATCAAGCTTTATCTATGGGTTGTCAGCTCTTTGGTTGCAGTCTTGTGCTTGGTTCA
AGCTGGGGCATTATTGGTGGGAGAAGCCAGAAAAGGCGAAAGCGTAGCGTTCTTTGAAAT
TTGGATTCTGTTCCTGCGACTCGTTTAAAAGAAGAAGGGCTGCGGAGCCACTGTGAAAGA
CTTGTTGTGCTCTTTCAACTAAGAAATCTGGCAGGAACTCGATATAAAGTGCCTGTGACA
GTAATCTCAGGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAAATTGAAATACC
GTGCCTATGGTAACTTTTTTTTACGCTGCGAACCGTTCAACACACATTGAAAACCCCGCA
GCAATTGTTCTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTCTCCCAACAGTGTAC
GAGCGGACGAAACTCTAGAGGATTTGCAGGCTCGGTGATAAAATGTATTGTTGAAAAGAA
CGCGAATGCAACGATTGTGGTGGAGAGAAATATCAACAGGGCAAGGCAAGGCTATGCTCT
TTTGGAAGTGGCGGACTTGCACTTTCTTGAAAAGAAAAATGACCGCAAGATCCGGTTGTT
CATAACTTTCTACAATAAGGCATACTTCTACGGTTTTCCAATGCTGAGGCAACTATCGCT
ATAAAATCGCTGCTAGGAGAAGATTATATATGGACGTAAATATTTTTTACGTTACTAAAA
TTCTAGGTTAGAGGCACGTTTTGCAGAACCAGTGGCCTTGGAAAGGTGTTGCTACAAATT
TATGCAATTTCTTCAACTTGCCAGGTGGTCTTGGATGATC
>MIT_Sbay_c896_21290 YDR044W 5' untranslated region, Contig c896 7383 - 9382(revcom), 2000 bp (revcom)
CTTGTTATGTGTGTTTGTGGTGATTGCGGTTTGGTTTTTCTGATTCGTATGACAGAAAGA
AAAAAATTCAGTTTACCTTGTAAGGTGATTAGGAGAAGAAAAAAAGCTTATTGGCAGCGA
ACAATAGGTGAAAAAAAAAAAGAAAATGCGTGTCCTTATATAGCTTTCTCGAAGGGAGAA
CAATGGATAAATCAAAGCTTATCTACGGGTCAACAGCTCTTTGGTTGCTGTCTTGCTCTA
GGTCCAAGCTGGGGCATAATTGGTGGGAGAAGCCAGAAAATGCGAAAGCGTACCGTTCTG
TGAAAAATGGCTTCGGTTCCTGCGACTCGTTTAAAAAGAAAAGGGCCCGCGCAGCCTGTG
TGAAATGTTCGTTTTGCCCTTCCCAGAGAGAAATCTTGCAGGAGCCTCAATACAATGTGC
CTGCGGATGGAATACCAGGGGATAAAGGCGTGAAGGCACTCCCTGAACAATTGAAAATTG
GAAAAAAAAAGTGCCTGTGATGAATCTTATACGTTGGGAAAACTCCAAGACACTTTTAAA
ACTCCGCAGAGATTGTTTGGAGGGACCTTGACCACGAGTTGGGAGTATTGTTTTTTCCTG
GAAGGAACGAGCGGAACTCTTGGGGATTTGCGGGCTCGCTAATAAAAAGTGTCTTGTTGA
AGAAAAGTAGAATGCGACTAAAACGGTGGAGGAAAATATCAACAAGGCAAGGCTATGCCT
TTCGAAGAAAAGCGGACTTGCAATTGCACAACCGTATCGAAGAGAATTGAGAAGGGGGTG
CAAAGTGATCCGGTTGTTCATATTTCTTCACCAATTGATACAATTATCTACGTTTGTTCT
GTTGACCAATCCAACGGGGACTCTGTATGACATAAGTCTTCCTTACATTGCTAAGATCCA
AGATCAGACCCGTAGATGAGTTCTGCACCAAAGAGTTGTTAACCGTCTTGCCTGAATAAT
TTTAAGTTGTCGCGATCCTCTTACAAGGTGTTCTTATTTC
>WashU_Smik_Contig2283.3 YDR044W 5' untranslated region, Contig c2283 2261 - 4260(revcom), 2000 bp (revcom)
CTTTATTGAGGATTTGTGGCGTTTGAGGTTTGGTTTTTTATTCAATTTGAAAGAAGAAAA
CTATCGTTATACTTTCGAAGAAAACACGGGGAATAAAAGCTTAACAGGTGAGACAATAGG
TGGAAAAAAAGGAAAATATGTGTCTTTATATAGCCTTTTCAAAAAGAGAACAATGGTCAA
ATAAAGGTTTATCTACGAGTCGACAGTTCGTTGGCTGCAGTGTTACGCTTGGTTGAAGCT
GGGGCATTATTGGTGGAAGAAGCCAGAAAAGACGAAAGAGTAGCGTAGCGTTCTTTCAAA
TTTTGGTTTCGGGTTCCTGCGACTCGTTTAAAAAAGAAAAGGGCCCGCGGCCCCGCCGTG
AAACACTTCGTCTTGCTCTTCCCACCCAGAAAACTTGTAGGAGCCTCAGTTACAAAGTGC
CTGTAATGGAAATCTTAGGGGGCTACTATTGTAAAGGCAATTTCTGAACAATTGAAAGTG
AAAATATCGTGCCTGTGGTAACTTTCTTATACGCCGTGAAACGTTTAACATACGTTGAAA
ACTCCGCAGGGATTGGTTTGGAAAATTATAGTCACGAATTAGGCGTATTGTCTTTCAAGA
AGGTACGAGCGGATGAACTTCTTGAGGATTTGCGGGTTCGGTGATAAAAAATGTATTGTT
GAAAAGAACGCGAATGCAACAATTACGGTGGAGAAAAATATTAACAAGGGAAGGCAAGGC
TATGTTCTATTGAGAAGCGGCGGACTTGCACTTTCCTCGAAGAAAAAAATGTCTTCAAGA
TCCAATGTTCATATAACTTTCTACAATAAGGTATCCTTCTACGATCTTTCAATGTTAAGA
TTGAAATCAATGTAAAAAGCACCATGTTGAATACTACTGCTAGGAGGAGATCACATATGA
ATGTGATTATTATTTATATTAGTAAATTTTCAGGTTAGGAAGAAGTTATGTGACGCTTTA
GCTTTGGAAATTTGTTGCGGGAAACTGATAACATTCTTTT
>SGD_Scer_YER014W HEM14 "Protoporphyrinogen oxidase, a mitochondrial enzyme that catalyzes the seventh step in the heme biosynthetic pathway, converting protoporphyrinogen IX to protoporphyrin IX"
TATACAAGCTCTTTTTGGCGTTCTCAATTGCACTTTACTCGATATGTTTGAATTGGTGTT
CTTCGCGAATATCTCTATTGTTCTCTCTATTATACTATTTCTTTTTTTGAATACTCCGCG
ACTCCGAAGCAACAAAGTGTCGAAGGCAAGTTCAAAGGCGTTTTGTAACTAAACGAGCAA
TGGCAGCTTTCAATTAAAGAAAGGTTAGCGTTACTCTGTGATTTTTTTCATGTAAAAATT
CTCAAGAGAGATAAAGTTGTTAAAAAATTAAATATAGGTCTATAAAACTCGATAATTATA
ATGCATAAAAAGCTAACAATGT
>MIT_Spar_c425_6072 YER014W 5' untranslated region, Contig c425 34016 - 36015, 2000 bp (revcom)
TATTCGAGCCCTTTCCCGCGTTCCCAATTGTACCTTCCTCGATAGGATTGAATTGGTATC
CTTCGCGGATCTCTCTATTGTTCTCTCTATTATTCTTTTTCTTTTTTAAATACTCCGCGA
CTCCGAAGCAACAAAATGTCGAAGGCAAGATGAAAGGCGTTTTGCAACTAAACGAGTAAT
GGCAGCTTTTAATTAAATAACGGTCAGCATTACTCTATAACTTTTCACATAAAATCCTCG
AAGAAGGAAAAATTGATAATCAATTTACCGAAGAATGAATATAGGTCTATAAAAATTCAA
TAATTATAGATGCATAAAAAGC
>MIT_Smik_c283_5928 YER014W 5' untranslated region, Contig c283 42606 - 44605, 2000 bp (revcom)
TATTGAAGCTCTCTCCACTATTTCTTTAATCGCGCTATACTAGATATGGTTAAACTGCTA
TCTTTTGCAAATCCCTCTATTGTTCTTTCCATTACTCTTTTCTTTTTTAAATACGGACTC
CGAAGCAACAAGGTCGAAGGCAAGCTGAAAGGCATTTTACAACTAAACGAGCAATGGTAG
CTTTTGATTGAATAAATTATTATCATTATTTTGTTATTTGTCCCACGAAATTCTCGTTGA
AAGCAAGGTTCGTAAGGATTTATCAAATGTTAAATATAGATCTATAAAAATTGAATAGTA
ATAATAACAAGGGATGGTGTTA
>MIT_Sbay_c84_6418 YER014W 5' untranslated region, Contig c84 10802 - 12801(revcom), 2000 bp (revcom)
TGTCGAAGTTCTCCTTTATTCCGCTGTTTCTTACGGAATCCAGCGAGACTGTTGTCCTTT
CGCATCCTTCTATTGTTCTTCCTTATTGTTCTCGTTTTTTTTATACTCTGCGACTCCGAA
ACAACAAAATCTCGAAGGCAAGCTAAGGTAAAAATATTCACCACTAAACGAGCAATGACA
GTTATATTCAAACGTCATTCTACTTTTTTGCCAGAGAAGTCCTCACTGGAGACGAAGTTG
GTAAATGCTTTATTTATATTAAACGTAGATCTATAAAGTTTAAATAGTTTATAATGCTTA
ACAAGGGACGATGTTATCTCTT
BioPerl-1.007002/t/data/map_hem/HEM13-HEM14.meme.txt000444000766000024     11171613155576321 21361 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM13-HEM14.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDR044W         1.0000   1000  MIT_Spar_c130_3912       1.0000   1000  
MIT_Sbay_c896_21290      1.0000   1000  WashU_Smik_Contig2283.3  1.0000   1000  
SGD_Scer_YER014W         1.0000    322  MIT_Spar_c425_6072       1.0000    322  
MIT_Smik_c283_5928       1.0000    322  MIT_Sbay_c84_6418        1.0000    322  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM13-HEM14.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        8    maxsites=        8    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            5288    N=               8
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.305 C 0.195 G 0.195 T 0.305 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   8   llr = 168   E-value = 5.3e-017
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  1:::::::::9:::1:114:
pos.-specific     C  :::494:a:1115a181:::
probability       G  9556::5:a9:9::6339:9
matrix            T  :55:165:::::5:1:5:61

         bits    2.5        **    *      
                 2.3        **    *      
                 2.0        *** * *      
                 1.8 *   *  *** * * * * *
Information      1.5 *  **  *** * * * * *
content          1.3 *  **  ***** * * * *
(30.2 bits)      1.0 ************** * * *
                 0.8 **************** ***
                 0.5 **************** ***
                 0.3 ********************
                 0.0 --------------------

Multilevel           GGGGCTGCGGAGCCGCTGTG
consensus             TTC CT     T  GG A 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
SGD_Scer_YDR044W             +    344  3.65e-14 AAAAGTAGAA GGGCCCGCGGAGCCGCTGTG AAAGATTTCT
MIT_Spar_c425_6072           -    113  1.77e-11 TCGACATTTT GTTGCTTCGGAGTCGCGGAG TATTTAAAAA
SGD_Scer_YER014W             -    114  1.77e-11 TCGACACTTT GTTGCTTCGGAGTCGCGGAG TATTCAAAAA
WashU_Smik_Contig2283.3      +    341  8.23e-11 AAAAAGAAAA GGGCCCGCGGCCCCGCCGTG AAACACTTCG
MIT_Spar_c130_3912           +    336  1.07e-10 TAAAAGAAGA AGGGCTGCGGAGCCACTGTG AAAGACTTGT
MIT_Sbay_c896_21290          +    343  2.63e-10 AAAAAGAAAA GGGCCCGCGCAGCCTGTGTG AAATGTTCGT
MIT_Sbay_c84_6418            -    106  8.94e-10 TCGAGATTTT GTTGTTTCGGAGTCGCAGAG TATAAAAAAA
MIT_Smik_c283_5928           -    110  7.48e-09 CTTCGACCTT GTTGCTTCGGAGTCCGTATT TAAAAAAGAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR044W                  3.7e-14  343_[+1]_637
MIT_Spar_c425_6072                1.8e-11  112_[-1]_190
SGD_Scer_YER014W                  1.8e-11  113_[-1]_189
WashU_Smik_Contig2283.3           8.2e-11  340_[+1]_640
MIT_Spar_c130_3912                1.1e-10  335_[+1]_645
MIT_Sbay_c896_21290               2.6e-10  342_[+1]_638
MIT_Sbay_c84_6418                 8.9e-10  105_[-1]_197
MIT_Smik_c283_5928                7.5e-09  109_[-1]_193
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=8
SGD_Scer_YDR044W         (  344) GGGCCCGCGGAGCCGCTGTG  1 
MIT_Spar_c425_6072       (  113) GTTGCTTCGGAGTCGCGGAG  1 
SGD_Scer_YER014W         (  114) GTTGCTTCGGAGTCGCGGAG  1 
WashU_Smik_Contig2283.3  (  341) GGGCCCGCGGCCCCGCCGTG  1 
MIT_Spar_c130_3912       (  336) AGGGCTGCGGAGCCACTGTG  1 
MIT_Sbay_c896_21290      (  343) GGGCCCGCGCAGCCTGTGTG  1 
MIT_Sbay_c84_6418        (  106) GTTGTTTCGGAGTCGCAGAG  1 
MIT_Smik_c283_5928       (  110) GTTGCTTCGGAGTCCGTATT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5136 bayes= 9.32418 E= 5.3e-017 
  -137   -965    232   -965 
  -965   -965    151     62 
  -965   -965    151     62 
  -965    109    183   -965 
  -965    232   -965   -137 
  -965    109   -965     95 
  -965   -965    151     62 
  -965    251   -965   -965 
  -965   -965    251   -965 
  -965    -49    232   -965 
   143    -49   -965   -965 
  -965    -49    232   -965 
  -965    151   -965     62 
  -965    251   -965   -965 
  -137    -49    183   -137 
  -965    209     51   -965 
  -137    -49     51     62 
  -137   -965    232   -965 
    21   -965   -965     95 
  -965   -965    232   -137 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 5.3e-017 
 0.125000  0.000000  0.875000  0.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.375000  0.625000  0.000000 
 0.000000  0.875000  0.000000  0.125000 
 0.000000  0.375000  0.000000  0.625000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.125000  0.875000  0.000000 
 0.875000  0.125000  0.000000  0.000000 
 0.000000  0.125000  0.875000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.125000  0.125000  0.625000  0.125000 
 0.000000  0.750000  0.250000  0.000000 
 0.125000  0.125000  0.250000  0.500000 
 0.125000  0.000000  0.875000  0.000000 
 0.375000  0.000000  0.000000  0.625000 
 0.000000  0.000000  0.875000  0.125000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
G[GT][GT][GC]C[TC][GT]CGGAG[CT]CG[CG][TG]G[TA]G
--------------------------------------------------------------------------------




Time  3.15 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   8   llr = 157   E-value = 1.6e-011
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  9453a:aa:aa:5:8185a:
pos.-specific     C  ::3:::::a::::::4::::
probability       G  1638:a::::::5a1434:1
matrix            T  :::::::::::a::11:1:9

         bits    2.5      *  *    *      
                 2.3      *  *    *      
                 2.0      *  *    *      
                 1.8      *  *    *      
Information      1.5    ********* *    * 
content          1.3 ** ********* *    **
(28.3 bits)      1.0 ** ***********  * **
                 0.8 ** ************ * **
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           AGAGAGAACAATAGACAAAT
consensus             ACA        G  GGG  
sequence               G                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c425_6072           -     69  2.68e-11 AAAGAATAAT AGAGAGAACAATAGAGAGAT CCGCGAAGGA
MIT_Spar_c130_3912           +    167  9.91e-11 GCCTTTTCGA AACGAGAACAATGGACAAAT CAAGCTTTAT
MIT_Sbay_c896_21290          +    173  2.20e-10 GCTTTCTCGA AGGGAGAACAATGGATAAAT CAAAGCTTAT
SGD_Scer_YER014W             -     69  3.83e-10 ATAGTATAAT AGAGAGAACAATAGAGATAT TCGCGAAGAA
WashU_Smik_Contig2283.3      +    163  9.67e-10 GCCTTTTCAA AAAGAGAACAATGGTCAAAT AAAGGTTTAT
SGD_Scer_YDR044W             +    171  1.97e-09 AGCCTTTCGA AACGAGAACAATGGGCAAAG CAAGCTTTAT
MIT_Smik_c283_5928           -     71  2.41e-09 AAAGAGTAAT GGAAAGAACAATAGAGGGAT TTGCAAAAGA
MIT_Sbay_c84_6418            -     64  3.09e-09 GAGAACAATA AGGAAGAACAATAGAAGGAT GCGAAAGGAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c425_6072                2.7e-11  68_[-2]_234
MIT_Spar_c130_3912                9.9e-11  166_[+2]_814
MIT_Sbay_c896_21290               2.2e-10  172_[+2]_808
SGD_Scer_YER014W                  3.8e-10  68_[-2]_234
WashU_Smik_Contig2283.3           9.7e-10  162_[+2]_818
SGD_Scer_YDR044W                    2e-09  170_[+2]_810
MIT_Smik_c283_5928                2.4e-09  70_[-2]_232
MIT_Sbay_c84_6418                 3.1e-09  63_[-2]_239
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=8
MIT_Spar_c425_6072       (   69) AGAGAGAACAATAGAGAGAT  1 
MIT_Spar_c130_3912       (  167) AACGAGAACAATGGACAAAT  1 
MIT_Sbay_c896_21290      (  173) AGGGAGAACAATGGATAAAT  1 
SGD_Scer_YER014W         (   69) AGAGAGAACAATAGAGATAT  1 
WashU_Smik_Contig2283.3  (  163) AAAGAGAACAATGGTCAAAT  1 
SGD_Scer_YDR044W         (  171) AACGAGAACAATGGGCAAAG  1 
MIT_Smik_c283_5928       (   71) GGAAAGAACAATAGAGGGAT  1 
MIT_Sbay_c84_6418        (   64) AGGAAGAACAATAGAAGGAT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5136 bayes= 9.32418 E= 1.6e-011 
   143   -965    -49   -965 
    21   -965    183   -965 
    62     51     51   -965 
   -38   -965    209   -965 
   162   -965   -965   -965 
  -965   -965    251   -965 
   162   -965   -965   -965 
   162   -965   -965   -965 
  -965    251   -965   -965 
   162   -965   -965   -965 
   162   -965   -965   -965 
  -965   -965   -965    162 
    62   -965    151   -965 
  -965   -965    251   -965 
   121   -965    -49   -137 
  -137    109    109   -137 
   121   -965     51   -965 
    62   -965    109   -137 
   162   -965   -965   -965 
  -965   -965    -49    143 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 1.6e-011 
 0.875000  0.000000  0.125000  0.000000 
 0.375000  0.000000  0.625000  0.000000 
 0.500000  0.250000  0.250000  0.000000 
 0.250000  0.000000  0.750000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.750000  0.000000  0.125000  0.125000 
 0.125000  0.375000  0.375000  0.125000 
 0.750000  0.000000  0.250000  0.000000 
 0.500000  0.000000  0.375000  0.125000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.125000  0.875000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
A[GA][ACG][GA]AGAACAAT[AG]GA[CG][AG][AG]AT
--------------------------------------------------------------------------------




Time  6.10 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =   8   llr = 156   E-value = 2.4e-010
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  ::1:1:::::51:16:9aa9
pos.-specific     C  :::a:5:4:4:1:::3::::
probability       G  ::9:45a:::58:54:1:::
matrix            T  aa::5::6a6::a4:8:::1

         bits    2.5    *  *             
                 2.3    *  *             
                 2.0    *  *             
                 1.8   **  *             
Information      1.5 **** ** *   *    ** 
content          1.3 **** ** *  **   *** 
(28.1 bits)      1.0 **** ******** ******
                 0.8 **** ***************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TTGCTCGTTTAGTGATAAAA
consensus                GG C CG  TGC    
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Smik_Contig2283.3      +    630  6.53e-12 TCTTGAGGAT TTGCGGGTTCGGTGATAAAA AATGTATTGT
MIT_Spar_c130_3912           +    624  2.08e-10 TCTAGAGGAT TTGCAGGCTCGGTGATAAAA TGTATTGTTG
MIT_Smik_c283_5928           -    155  3.18e-10 AAAGCTACCA TTGCTCGTTTAGTTGTAAAA TGCCTTTCAG
SGD_Scer_YER014W             -    161  5.75e-10 AAAGCTGCCA TTGCTCGTTTAGTTACAAAA CGCCTTTGAA
SGD_Scer_YDR044W             +    629  5.75e-10 TCCAGAGGAT TTGCGGGCTTGATGATAAAA TGTATTGTTG
MIT_Sbay_c896_21290          +    628  2.12e-09 TCTTGGGGAT TTGCGGGCTCGCTAATAAAA AGTGTCTTGT
MIT_Sbay_c84_6418            -    156  3.04e-09 ATAACTGTCA TTGCTCGTTTAGTGGTGAAT ATTTTTACCT
MIT_Spar_c425_6072           -    160  4.65e-09 AAAGCTGCCA TTACTCGTTTAGTTGCAAAA CGCCTTTCAT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Smik_Contig2283.3           6.5e-12  629_[+3]_351
MIT_Spar_c130_3912                2.1e-10  623_[+3]_357
MIT_Smik_c283_5928                3.2e-10  154_[-3]_148
SGD_Scer_YER014W                  5.8e-10  160_[-3]_142
SGD_Scer_YDR044W                  5.8e-10  628_[+3]_352
MIT_Sbay_c896_21290               2.1e-09  627_[+3]_353
MIT_Sbay_c84_6418                   3e-09  155_[-3]_147
MIT_Spar_c425_6072                4.7e-09  159_[-3]_143
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=8
WashU_Smik_Contig2283.3  (  630) TTGCGGGTTCGGTGATAAAA  1 
MIT_Spar_c130_3912       (  624) TTGCAGGCTCGGTGATAAAA  1 
MIT_Smik_c283_5928       (  155) TTGCTCGTTTAGTTGTAAAA  1 
SGD_Scer_YER014W         (  161) TTGCTCGTTTAGTTACAAAA  1 
SGD_Scer_YDR044W         (  629) TTGCGGGCTTGATGATAAAA  1 
MIT_Sbay_c896_21290      (  628) TTGCGGGCTCGCTAATAAAA  1 
MIT_Sbay_c84_6418        (  156) TTGCTCGTTTAGTGGTGAAT  1 
MIT_Spar_c425_6072       (  160) TTACTCGTTTAGTTGCAAAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5136 bayes= 9.32418 E= 2.4e-010 
  -965   -965   -965    162 
  -965   -965   -965    162 
  -137   -965    232   -965 
  -965    251   -965   -965 
  -137   -965    109     62 
  -965    151    151   -965 
  -965   -965    251   -965 
  -965    109   -965     95 
  -965   -965   -965    162 
  -965    109   -965     95 
    62   -965    151   -965 
  -137    -49    209   -965 
  -965   -965   -965    162 
  -137   -965    151     21 
    95   -965    109   -965 
  -965     51   -965    121 
   143   -965    -49   -965 
   162   -965   -965   -965 
   162   -965   -965   -965 
   143   -965   -965   -137 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 2.4e-010 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.125000  0.000000  0.875000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.125000  0.000000  0.375000  0.500000 
 0.000000  0.500000  0.500000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.375000  0.000000  0.625000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.375000  0.000000  0.625000 
 0.500000  0.000000  0.500000  0.000000 
 0.125000  0.125000  0.750000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.125000  0.000000  0.500000  0.375000 
 0.625000  0.000000  0.375000  0.000000 
 0.000000  0.250000  0.000000  0.750000 
 0.875000  0.000000  0.125000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.875000  0.000000  0.000000  0.125000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
TTGC[TG][CG]G[TC]T[TC][AG]GT[GT][AG][TC]AAAA
--------------------------------------------------------------------------------




Time  8.96 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   15   sites =   8   llr = 123   E-value = 9.2e-006
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  1a9:::aa:1:1a44
pos.-specific     C  3::::a:::351:::
probability       G  6:1aa:::a5:3:16
matrix            T  :::::::::155:5:

         bits    2.5    ***  *      
                 2.3    ***  *      
                 2.0    ***  *      
                 1.8    ***  *      
Information      1.5  * ******   *  
content          1.3  ********   * *
(22.2 bits)      1.0 ********* * * *
                 0.8 ********* * * *
                 0.5 *********** * *
                 0.3 ***************
                 0.0 ---------------

Multilevel           GAAGGCAAGGCTATG
consensus            C        CTG AA
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Smik_Contig2283.3      +    710  5.26e-10 ATTAACAAGG GAAGGCAAGGCTATG TTCTATTGAG
MIT_Sbay_c896_21290          +    703  3.55e-09 AAAATATCAA CAAGGCAAGGCTATG CCTTTCGAAG
MIT_Spar_c130_3912           +    702  3.55e-09 ATCAACAGGG CAAGGCAAGGCTATG CTCTTTTGGA
MIT_Smik_c283_5928           +    136  5.90e-08 CAACAAGGTC GAAGGCAAGCTGAAA GGCATTTTAC
MIT_Sbay_c84_6418            +    134  1.20e-07 ACAAAATCTC GAAGGCAAGCTAAGG TAAAAATATT
SGD_Scer_YDR044W             +    705  1.33e-07 ATATCAACAA AAGGGCAAGGCTATG CCTTCTGGAA
MIT_Spar_c425_6072           +    141  1.99e-07 ACAAAATGTC GAAGGCAAGATGAAA GGCGTTTTGC
SGD_Scer_YER014W             +    142  3.03e-07 ACAAAGTGTC GAAGGCAAGTTCAAA GGCGTTTTGT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Smik_Contig2283.3           5.3e-10  709_[+4]_276
MIT_Sbay_c896_21290               3.5e-09  702_[+4]_283
MIT_Spar_c130_3912                3.5e-09  701_[+4]_284
MIT_Smik_c283_5928                5.9e-08  135_[+4]_172
MIT_Sbay_c84_6418                 1.2e-07  133_[+4]_174
SGD_Scer_YDR044W                  1.3e-07  704_[+4]_281
MIT_Spar_c425_6072                  2e-07  140_[+4]_167
SGD_Scer_YER014W                    3e-07  141_[+4]_166
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=15 seqs=8
WashU_Smik_Contig2283.3  (  710) GAAGGCAAGGCTATG  1 
MIT_Sbay_c896_21290      (  703) CAAGGCAAGGCTATG  1 
MIT_Spar_c130_3912       (  702) CAAGGCAAGGCTATG  1 
MIT_Smik_c283_5928       (  136) GAAGGCAAGCTGAAA  1 
MIT_Sbay_c84_6418        (  134) GAAGGCAAGCTAAGG  1 
SGD_Scer_YDR044W         (  705) AAGGGCAAGGCTATG  1 
MIT_Spar_c425_6072       (  141) GAAGGCAAGATGAAA  1 
SGD_Scer_YER014W         (  142) GAAGGCAAGTTCAAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 5176 bayes= 9.33539 E= 9.2e-006 
  -137     51    183   -965 
   162   -965   -965   -965 
   143   -965    -49   -965 
  -965   -965    251   -965 
  -965   -965    251   -965 
  -965    251   -965   -965 
   162   -965   -965   -965 
   162   -965   -965   -965 
  -965   -965    251   -965 
  -137     51    151   -137 
  -965    151   -965     62 
  -137    -49     51     62 
   162   -965   -965   -965 
    21   -965    -49     62 
    21   -965    183   -965 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 9.2e-006 
 0.125000  0.250000  0.625000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.875000  0.000000  0.125000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.125000  0.250000  0.500000  0.125000 
 0.000000  0.500000  0.000000  0.500000 
 0.125000  0.125000  0.250000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.375000  0.000000  0.125000  0.500000 
 0.375000  0.000000  0.625000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
[GC]AAGGCAAG[GC][CT][TG]A[TA][GA]
--------------------------------------------------------------------------------




Time 11.74 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   19   sites =   8   llr = 137   E-value = 5.5e-005
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  5a559:a:3::1a5aaa98
pos.-specific     C  ::51:::::15:::::::1
probability       G  5:::1::a8:54:::::1:
matrix            T  :::4:a:::9:5:5::::1

         bits    2.5        *           
                 2.3        *           
                 2.0        *           
                 1.8        *           
Information      1.5  *   **** * * ***  
content          1.3  *  ******* * **** 
(24.7 bits)      1.0 *** ******* * **** 
                 0.8 *** ******* * *****
                 0.5 *** ***************
                 0.3 *******************
                 0.0 -------------------

Multilevel           AAAAATAGGTCTAAAAAAA
consensus            G CT    A GG T     
sequence                                
                                        
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                   Site      
-------------            ------  ----- ---------            -------------------
WashU_Smik_Contig2283.3      +    112  5.17e-11 TAACAGGTGA GACAATAGGTGGAAAAAAA GGAAAATATG
SGD_Scer_YDR044W             +    119  5.17e-11 AACAAAGAAA GACAATAGGTGGAAAAAAA AAGGAAAATC
MIT_Spar_c425_6072           +    277  1.49e-09 ACCGAAGAAT GAATATAGGTCTATAAAAA TTCAATAATT
MIT_Spar_c130_3912           +    116  1.75e-09 AACAAAGAAA GACAATAGGCGGAAAAAAA GGAAAATCCG
MIT_Sbay_c896_21290          +    120  6.56e-09 ATTGGCAGCG AACAATAGGTGAAAAAAAA AAAGAAAATG
SGD_Scer_YER014W             +    270  1.56e-08 TTAAAAAATT AAATATAGGTCTATAAAAC TCGATAATTA
MIT_Smik_c283_5928           +    272  2.46e-08 ATCAAATGTT AAATATAGATCTATAAAAA TTGAATAGTA
MIT_Sbay_c84_6418            +    261  1.48e-07 TATTTATATT AAACGTAGATCTATAAAGT TTAAATAGTT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Smik_Contig2283.3           5.2e-11  111_[+5]_870
SGD_Scer_YDR044W                  5.2e-11  118_[+5]_863
MIT_Spar_c425_6072                1.5e-09  276_[+5]_27
MIT_Spar_c130_3912                1.8e-09  115_[+5]_866
MIT_Sbay_c896_21290               6.6e-09  119_[+5]_862
SGD_Scer_YER014W                  1.6e-08  269_[+5]_34
MIT_Smik_c283_5928                2.5e-08  271_[+5]_32
MIT_Sbay_c84_6418                 1.5e-07  260_[+5]_43
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=19 seqs=8
WashU_Smik_Contig2283.3  (  112) GACAATAGGTGGAAAAAAA  1 
SGD_Scer_YDR044W         (  119) GACAATAGGTGGAAAAAAA  1 
MIT_Spar_c425_6072       (  277) GAATATAGGTCTATAAAAA  1 
MIT_Spar_c130_3912       (  116) GACAATAGGCGGAAAAAAA  1 
MIT_Sbay_c896_21290      (  120) AACAATAGGTGAAAAAAAA  1 
SGD_Scer_YER014W         (  270) AAATATAGGTCTATAAAAC  1 
MIT_Smik_c283_5928       (  272) AAATATAGATCTATAAAAA  1 
MIT_Sbay_c84_6418        (  261) AAACGTAGATCTATAAAGT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 19 n= 5144 bayes= 9.32643 E= 5.5e-005 
    62   -965    151   -965 
   162   -965   -965   -965 
    62    151   -965   -965 
    62    -49   -965     21 
   143   -965    -49   -965 
  -965   -965   -965    162 
   162   -965   -965   -965 
  -965   -965    251   -965 
   -38   -965    209   -965 
  -965    -49   -965    143 
  -965    151    151   -965 
  -137   -965    109     62 
   162   -965   -965   -965 
    62   -965   -965     62 
   162   -965   -965   -965 
   162   -965   -965   -965 
   162   -965   -965   -965 
   143   -965    -49   -965 
   121    -49   -965   -137 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 19 nsites= 8 E= 5.5e-005 
 0.500000  0.000000  0.500000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.500000  0.125000  0.000000  0.375000 
 0.875000  0.000000  0.125000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.250000  0.000000  0.750000  0.000000 
 0.000000  0.125000  0.000000  0.875000 
 0.000000  0.500000  0.500000  0.000000 
 0.125000  0.000000  0.375000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.875000  0.000000  0.125000  0.000000 
 0.750000  0.125000  0.000000  0.125000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
[AG]A[AC][AT]ATAG[GA]T[CG][TG]A[AT]AAAAA
--------------------------------------------------------------------------------




Time 14.61 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR044W                 1.10e-26  118_[+5(5.17e-11)]_33_[+2(1.97e-09)]_153_[+1(3.65e-14)]_265_[+3(5.75e-10)]_56_[+4(1.33e-07)]_153_[+2(7.52e-05)]_108
MIT_Spar_c130_3912               4.24e-25  115_[+5(1.75e-09)]_32_[+2(9.91e-11)]_149_[+1(1.07e-10)]_268_[+3(2.08e-10)]_58_[+4(3.55e-09)]_254_[-4(6.48e-05)]_15
MIT_Sbay_c896_21290              6.48e-23  119_[+5(6.56e-09)]_34_[+2(2.20e-10)]_114_[+1(4.06e-05)]_16_[+1(2.63e-10)]_265_[+3(2.12e-09)]_55_[+4(3.55e-09)]_283
WashU_Smik_Contig2283.3          6.34e-28  111_[+5(5.17e-11)]_32_[+2(9.67e-10)]_158_[+1(8.23e-11)]_5_[-4(1.66e-05)]_249_[+3(6.53e-12)]_60_[+4(5.26e-10)]_276
SGD_Scer_YER014W                 1.51e-24  68_[-2(3.83e-10)]_25_[-1(1.77e-11)]_8_[+4(3.03e-07)]_4_[-3(5.75e-10)]_89_[+5(1.56e-08)]_34
MIT_Spar_c425_6072               6.46e-26  68_[-2(2.68e-11)]_24_[-1(1.77e-11)]_8_[+4(1.99e-07)]_4_[-3(4.65e-09)]_97_[+5(1.49e-09)]_6_[+5(6.43e-06)]_2
MIT_Smik_c283_5928               4.72e-22  70_[-2(2.41e-09)]_19_[-1(7.48e-09)]_6_[+4(5.90e-08)]_4_[-3(3.18e-10)]_97_[+5(2.46e-08)]_32
MIT_Sbay_c84_6418                7.03e-21  63_[-2(3.09e-09)]_22_[-1(8.94e-10)]_8_[+4(1.20e-07)]_7_[-3(3.04e-09)]_85_[+5(1.48e-07)]_43
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM13-HEM15.fa000444000766000024      2145013155576321 20162 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR044W HEM13 "Coproporphyrinogen III oxidase, an oxygen requiring enzyme that catalyzes the sixth step in the heme biosynthetic pathway; localizes to the mitochondrial inner membrane; transcription is repressed by oxygen and heme (via Rox1p and Hap1p)"
CTTTATGTGTATTTAATTGTGTTCGAAGAGTTCGGTTTGCTATGTTTGATTTGCGAAAAG
AAAGCTTTTGATATGCTCAAAAAAAGAAAACCCGGAGAATAAAAGCTTAACAAAGAAAGA
CAATAGGTGGAAAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTCGAAACGAGAACA
ATGGGCAAAGCAAGCTTTATCTTCGGATCGTCCGTCAGCGCTTTGGTTGCAGTCTTATGC
TTTGTTCAAGCTGGAGCGTTATTGGTGGGAGAACCAGAAAAGGCGAAAGCGTAGCGTTCT
TTGAAATTTGGCTTCTGTTCCTGCGACTCGTTTAAAAGTAGAAGGGCCCGCGGAGCCGCT
GTGAAAGATTTCTTTTACTCTTTCAGCGCAGAAATCTCGCAGGAGCTCAGCAGAAAGTGC
CTATGACGGTAATCCCAGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAATTAA
AATACCGTGCCTATAGTAACTTTTTTTTACGCTGTGAACCGTTCAACACACAGTAAAAAC
TCCGCAGGAAATGGTTTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTTTCCCAACA
GTGAACGAGAGGACAAACTCCAGAGGATTTGCGGGCTTGATGATAAAATGTATTGTTGAA
AAGATCGCGAATGCAACAATTACGGTGGGGAGAAATATCAACAAAAGGGCAAGGCTATGC
CTTCTGGAAAGTGGCAGACTTGCACTTTCCTCGAAAAGAAAAATGACCGCAAGATCCGGT
TGTTCTCAACCTTCTACATTAAGACATACTTCTACGATTTTCGAATGCCGAAGCAACTAT
CGCTGAAATTTGTCATGTCAAAATTGCTACTGGGGGAGAAGAATATATATGGAAGTAATT
ATTATTTACGTTGCTGAAATGGCAGGTTAGACGCATGTTTTGCAAAATAAGTGGTTTTGA
AAAGAATTGATACTAGGAATCGGTGCAATACCTTCTACCT
>MIT_Spar_c130_3912 YDR044W 5' untranslated region, Contig c130 4128 - 6127, 2000 bp (revcom)
CTTTATATGTGTGTTTTGTGGTGTTCGAAATTGGTTTCTTTTGTTCGACTTGCGAGAAGA
AAGCTATCAATATGCTTTCCAAAAAAAGCTGGAGAATAAAAGCTTAACAAAGAAAGACAA
TAGGCGGAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTTCGAAACGAGAACAATGG
ACAAATCAAGCTTTATCTATGGGTTGTCAGCTCTTTGGTTGCAGTCTTGTGCTTGGTTCA
AGCTGGGGCATTATTGGTGGGAGAAGCCAGAAAAGGCGAAAGCGTAGCGTTCTTTGAAAT
TTGGATTCTGTTCCTGCGACTCGTTTAAAAGAAGAAGGGCTGCGGAGCCACTGTGAAAGA
CTTGTTGTGCTCTTTCAACTAAGAAATCTGGCAGGAACTCGATATAAAGTGCCTGTGACA
GTAATCTCAGGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAAATTGAAATACC
GTGCCTATGGTAACTTTTTTTTACGCTGCGAACCGTTCAACACACATTGAAAACCCCGCA
GCAATTGTTCTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTCTCCCAACAGTGTAC
GAGCGGACGAAACTCTAGAGGATTTGCAGGCTCGGTGATAAAATGTATTGTTGAAAAGAA
CGCGAATGCAACGATTGTGGTGGAGAGAAATATCAACAGGGCAAGGCAAGGCTATGCTCT
TTTGGAAGTGGCGGACTTGCACTTTCTTGAAAAGAAAAATGACCGCAAGATCCGGTTGTT
CATAACTTTCTACAATAAGGCATACTTCTACGGTTTTCCAATGCTGAGGCAACTATCGCT
ATAAAATCGCTGCTAGGAGAAGATTATATATGGACGTAAATATTTTTTACGTTACTAAAA
TTCTAGGTTAGAGGCACGTTTTGCAGAACCAGTGGCCTTGGAAAGGTGTTGCTACAAATT
TATGCAATTTCTTCAACTTGCCAGGTGGTCTTGGATGATC
>MIT_Sbay_c896_21290 YDR044W 5' untranslated region, Contig c896 7383 - 9382(revcom), 2000 bp (revcom)
CTTGTTATGTGTGTTTGTGGTGATTGCGGTTTGGTTTTTCTGATTCGTATGACAGAAAGA
AAAAAATTCAGTTTACCTTGTAAGGTGATTAGGAGAAGAAAAAAAGCTTATTGGCAGCGA
ACAATAGGTGAAAAAAAAAAAGAAAATGCGTGTCCTTATATAGCTTTCTCGAAGGGAGAA
CAATGGATAAATCAAAGCTTATCTACGGGTCAACAGCTCTTTGGTTGCTGTCTTGCTCTA
GGTCCAAGCTGGGGCATAATTGGTGGGAGAAGCCAGAAAATGCGAAAGCGTACCGTTCTG
TGAAAAATGGCTTCGGTTCCTGCGACTCGTTTAAAAAGAAAAGGGCCCGCGCAGCCTGTG
TGAAATGTTCGTTTTGCCCTTCCCAGAGAGAAATCTTGCAGGAGCCTCAATACAATGTGC
CTGCGGATGGAATACCAGGGGATAAAGGCGTGAAGGCACTCCCTGAACAATTGAAAATTG
GAAAAAAAAAGTGCCTGTGATGAATCTTATACGTTGGGAAAACTCCAAGACACTTTTAAA
ACTCCGCAGAGATTGTTTGGAGGGACCTTGACCACGAGTTGGGAGTATTGTTTTTTCCTG
GAAGGAACGAGCGGAACTCTTGGGGATTTGCGGGCTCGCTAATAAAAAGTGTCTTGTTGA
AGAAAAGTAGAATGCGACTAAAACGGTGGAGGAAAATATCAACAAGGCAAGGCTATGCCT
TTCGAAGAAAAGCGGACTTGCAATTGCACAACCGTATCGAAGAGAATTGAGAAGGGGGTG
CAAAGTGATCCGGTTGTTCATATTTCTTCACCAATTGATACAATTATCTACGTTTGTTCT
GTTGACCAATCCAACGGGGACTCTGTATGACATAAGTCTTCCTTACATTGCTAAGATCCA
AGATCAGACCCGTAGATGAGTTCTGCACCAAAGAGTTGTTAACCGTCTTGCCTGAATAAT
TTTAAGTTGTCGCGATCCTCTTACAAGGTGTTCTTATTTC
>WashU_Smik_Contig2283.3 YDR044W 5' untranslated region, Contig c2283 2261 - 4260(revcom), 2000 bp (revcom)
CTTTATTGAGGATTTGTGGCGTTTGAGGTTTGGTTTTTTATTCAATTTGAAAGAAGAAAA
CTATCGTTATACTTTCGAAGAAAACACGGGGAATAAAAGCTTAACAGGTGAGACAATAGG
TGGAAAAAAAGGAAAATATGTGTCTTTATATAGCCTTTTCAAAAAGAGAACAATGGTCAA
ATAAAGGTTTATCTACGAGTCGACAGTTCGTTGGCTGCAGTGTTACGCTTGGTTGAAGCT
GGGGCATTATTGGTGGAAGAAGCCAGAAAAGACGAAAGAGTAGCGTAGCGTTCTTTCAAA
TTTTGGTTTCGGGTTCCTGCGACTCGTTTAAAAAAGAAAAGGGCCCGCGGCCCCGCCGTG
AAACACTTCGTCTTGCTCTTCCCACCCAGAAAACTTGTAGGAGCCTCAGTTACAAAGTGC
CTGTAATGGAAATCTTAGGGGGCTACTATTGTAAAGGCAATTTCTGAACAATTGAAAGTG
AAAATATCGTGCCTGTGGTAACTTTCTTATACGCCGTGAAACGTTTAACATACGTTGAAA
ACTCCGCAGGGATTGGTTTGGAAAATTATAGTCACGAATTAGGCGTATTGTCTTTCAAGA
AGGTACGAGCGGATGAACTTCTTGAGGATTTGCGGGTTCGGTGATAAAAAATGTATTGTT
GAAAAGAACGCGAATGCAACAATTACGGTGGAGAAAAATATTAACAAGGGAAGGCAAGGC
TATGTTCTATTGAGAAGCGGCGGACTTGCACTTTCCTCGAAGAAAAAAATGTCTTCAAGA
TCCAATGTTCATATAACTTTCTACAATAAGGTATCCTTCTACGATCTTTCAATGTTAAGA
TTGAAATCAATGTAAAAAGCACCATGTTGAATACTACTGCTAGGAGGAGATCACATATGA
ATGTGATTATTATTTATATTAGTAAATTTTCAGGTTAGGAAGAAGTTATGTGACGCTTTA
GCTTTGGAAATTTGTTGCGGGAAACTGATAACATTCTTTT
>SGD_Scer_YOR176W HEM15 "Ferrochelatase, a mitochondrial inner membrane protein, catalyzes the insertion of ferrous iron into protoporphyrin IX, the eighth and final step in the heme biosynthetic pathway; Yfh1p mediates the use of iron by Hem15p"
TCTTTAAACGTTCTTTTTTTTACTGCTAAATTTGTCCAAATAGCAGGTATGTGTTAAATA
TTTCTGTACTTCTTGTAAACCGACTCAAGTGGAACACGAGAATTTACGCTTGTTTGGTGT
CAAGCCAAGAGTGACCTTGACCGACCAAAAGTATTCCTTCGCGTCCTCCTTCTTCAATCC
CATATCCCCTACGAAAAAAAGCAGCATGAGAAAACGAAGGGCAGCAACTCCTTCGTCATA
TAAGGCTTACGGTGACCATTGAAGATTGGGCATGTCTAACGGCTATTGCCAGCGGAGATG
TTTCAAGGCATCCTACACATGCTACATATTTGTAATTATTTTACTGAGTTTGTGTATATA
AAAAACTTTTTTAAAAAAAAAAAATGGCCAGCATCCTCTTTCATGTAAAGCTGTTGAACC
TTCCTGAAATTTACTTCTAAAATTGTTCAGTAAAACTGCTTGTTAAAAGTGCGAAGAGTT
CTTTTTTAGCTTTTTTTGTCCTGCTGTTGAGCTGTTTTGCTTTACTGTTCAACAAAACAT
TGAAGATCTTTCACATTGCGCGTCGAAACCACAAACCGTCGAAAACAATGGTCATCTAAA
TAAAGGGTTCTTATTAAACAGATTTAAAGCCAAGGACAAAATACAGGCACAGGTCAAGCA
AGAAGACAAACCGCATACGCCAAGACAAACCGTGGTGATTTAATTCTGCTGCTGATCGCT
TCCAACA
>MIT_Spar_c278_20970 YOR176W 5' untranslated region, Contig c278 32746 - 34745, 2000 bp (revcom)
TCTTCAAACGTTCTTTTCCTACTACTAAGCTTTTCAATAAATAGCGGGTATATGCTAAAT
ACTTCTTTGCTTCTTGTACGACCTACTTAATTGAAATACGGATATTTTTGCTTGCTTGGT
GCCAAACCAAGAGTGACCTTGACCGACTAAAAGTATTCCTTCGCGTCCTCCTTCTTCAAT
CCCATATCCCCTACTGAAAAAAGCAGCGTGCGAAAATGAAGGGCAGCAACTCCTTCGTCA
TATAAGGCTTAGGTAATCTTTCAAGGTCAGGTATATCCAGCTGTCGTTACGAGTAGAGAT
ATTTCAAGCTGTCCTGCACATGCTACATATTTGTGATTATTTTTATTGAGTTGCGTATAT
AAAAAAACAATCTAAAAAAAAAAAAAATGGCCAGCATCTTCTTCCATGTAAAGCTGTTGA
ACCTTGCTAAAATCTATTACTATAATTGTTCAGTAAAGTTGCTTGTTAAAAATGCGAAGA
GTCTTTTTTAGCTTTTTTTGCCCTGCTGTTGAGCTGTTTTGCTTCACTGTTCAACAAAAC
AGTGAAGATCTTTCGAATTGCGCGTCGAAACCACAAACCGTCGAAAATAATGGTCATCTA
AATAAAGGGTTCTTATTTGAACAGATTTAAAGCTCAAAGACACGATACAGGCACAGGTCC
AGAAAGAATACAAAACGCAAACGCCAAGACAAATTGTGGTAATTTCATTCTGCTGCTGAT
CACTGCC
>MIT_Smik_c935_20455 YOR176W 5' untranslated region, Contig c935 1803 - 3802(revcom), 2000 bp (revcom)
TCTTGAATTGCAATTTTCTACTACTGAAGTTACCAACAATTAGCAAATATGTGATGAGTC
CTTTTTACGTTCTTGTATAACCTAAGTTAAATACAAAGGTTTATGCTCCTTTAATGATCA
GACCAACAGTGATCTTGGCCGACCAAAAGACTCCTTCGCGTCCTCCTTCTTCAAGTCTCA
TATCCCCTACCAGAAAAAGTAGCAGGCGAAAATAAAGAGCAACTGCTCCCCCCCATATAG
AGCTTACCATAATTTCTCAAGGAAAGGTATCTCCAGTTGTCGTAAAGAATAAAGAAGTTT
CAACGTGTCCTGCATGTTCTACAAATTTGCAATTGACTTTACTAAGTTGCATATATAAAA
CTTGTATTAGATAAGTTAGCCAGCATTTTCATTCAAGCTAAGATGTTGAATATGCCAAAG
CACATTGCTGAAATTAATCAGTAAAGCTGCTTGCTGAAAGTGGAAATATTTTCAGCTTTT
TTTGCTCTGCTGTTGAGCTGTTTTACTTCATTGTTCAACAAAACAATAGAGTTCTCTCCA
ATTGCGCGTCAAAACCACAAACCGTCGAAAATAATGATCATCTAAATAAAAGAGTTCACG
TTTTCACATATTTAAAGTTGAAATACTCCATACAGGCACAGGTCTAACAAGAAGACAACG
CATTCGATAAAACTAATCGTGGTAATTTTTATATCGCTGCTAGCCACTACCAACAATGTA
CAATTTT
>WashU_Skud_Contig2050.4 YOR176W 5' untranslated region, Contig c2050 12271 - 14270(revcom), 2000 bp (revcom)
TCTTAGTTTATAGCTTTTCTACTACTCTGGTCATAAACGAACAGAAGATAAGCAAGAAAT
CTTTTTTTCCTTCTTTTACGGTCTATTCAAGTGAAGCACGGGGATTCCCGCTTGTTTAAT
AATCAGACCAACAATGATATTGACCGACCAAAAGAAGTATTCCTTCGCGTGCTTCTCCTT
TCTGTGTCAAATCCCCTACTGAAAAAGCAGCATTGGGAAAGGAACAGCAGCTTCTCCTTC
GTCGCAGAGAGCTCGCGGTAGCATTTCATTGTCAGGTATTTATGATATTTGCTAAGAATA
ATTAAAATGTCTTCAGGTCTTGCACATACTCCTACATATTTGTAAGTATTTTACTGATTT
GAGTATATAAAAGCCGTACTAAAACTAACCAGCACCTGTAGCAAGGTGCAAAATGTTGAA
CCTTTCCGAAATTTATTGCCAGAAACCAAGAGCTAAAAGTGCTTGGTAAAAGTGAAAAGA
CTCTTTTTCAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGTTCCATCTGTTCAACAAA
ACAGCTTCACTGGATCTTTCAAAGTGCGCGTCGAAACCACAAACCGTCGAAAATATTGAT
CATCTAAATAAAGGGTTCTTATTTGCACAGTTTCGCATTGAAATATTCCATTCAGGCACA
GATCAACAAGAAGACAAAAAGGTATTCGAGAAGACTAATTGTGGTATTTTTACTTTGCTG
CTGACCA
>WashU_Sbay_Contig480.2 YOR176W 5' untranslated region, Contig c480 3444 - 5443(revcom), 2000 bp (revcom)
TTTCAGGGAAGCACCATGTGCACGAATTGTTCTAGAAAGCATTTTTGGTTCGTAAATTCT
CTACAACTGAACTTATTAACAAATAGCAAACAGAGAAGAAAATTTTTTTTTTCCTTCTTG
TATGGTCAGTTAGTTGAAAACACGGAGATTTTCACTTGTTTAGTAAGCAGAGCCATAATG
CTCTTGACCGACCAAAAGAAGTATTCCTACGCGAGCTCCCTCTTCAAGTGCCAAATCCCC
TACTGAAAAAAGCAACATGAGAAGCAAAGAGATGCCTCTCGCCATGCAGGGCTTGCGGTC
ATGTTTTCTACGTTCAATTGATTTTGTTACAGCTGAAAGATGTTTATAAAACTGTCTTGC
ATATGCTCTATTTACTTGTAAACAATTTTATTAAGTTGCGTATATATGATCGTACTAAAA
ATTGGCTGGCGCGTTCTCCAGGCAGAGTTGGTTGAACCTTGCTCGAATTGATAGCTCAAA
GTGGAGAGACTCTTTTTTAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGCTCCACCTG
TTCAACAAAATGGCAGAGATCTTTCGAAGTGCGCGTCGAAACCACAAACCATCAAAAATA
TCGACCATCTAAATAAAGGGTTCTTGTTTGAATAAATATCAGGCGAAGCTCTTCATACAG
GCACAGGTCAGATAAGAAGACAATTCGAATTCGAGAAGGATATTCGTGGTATCTTTAATC
TGCTGCT
BioPerl-1.007002/t/data/map_hem/HEM13-HEM15.meme.txt000444000766000024     11450013155576321 21354 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM13-HEM15.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDR044W         1.0000   1000  MIT_Spar_c130_3912       1.0000   1000  
MIT_Sbay_c896_21290      1.0000   1000  WashU_Smik_Contig2283.3  1.0000   1000  
SGD_Scer_YOR176W         1.0000    727  MIT_Spar_c278_20970      1.0000    727  
MIT_Smik_c935_20455      1.0000    727  WashU_Skud_Contig2050.4  1.0000    727  
WashU_Sbay_Contig480.2   1.0000    727  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM13-HEM15.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            7635    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.304 C 0.196 G 0.196 T 0.304 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 204   E-value = 7.1e-025
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :9::4:::::1::::::7:1
pos.-specific     C  ::4::::::4:::3:8:16:
probability       G  a14a6:::a:9a4:::a2:9
matrix            T  ::1::aaa:6::67a2::4:

         bits    2.5 *  *    *  *    *   
                 2.3 *  *    *  *    *   
                 2.0 *  *    * **    *  *
                 1.8 *  *    * **    *  *
Information      1.5 *  * **** **  ***  *
content          1.3 ** * **** **  ***  *
(32.6 bits)      1.0 ***************** **
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GACGGTTTGTGGTTTCGACG
consensus              G A    C  GC T GT 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2050.4      -    569  1.73e-12 CAATATTTTC GACGGTTTGTGGTTTCGACG CGCACTTTGA
MIT_Spar_c278_20970          -    563  1.73e-12 CATTATTTTC GACGGTTTGTGGTTTCGACG CGCAATTCGA
SGD_Scer_YOR176W             -    561  1.73e-12 CATTGTTTTC GACGGTTTGTGGTTTCGACG CGCAATGTGA
WashU_Smik_Contig2283.3      +    624  1.50e-11 TGAACTTCTT GAGGATTTGCGGGTTCGGTG ATAAAAAATG
MIT_Smik_c935_20455          -    547  2.58e-11 CATTATTTTC GACGGTTTGTGGTTTTGACG CGCAATTGGA
WashU_Sbay_Contig480.2       -    574  3.01e-11 CGATATTTTT GATGGTTTGTGGTTTCGACG CGCACTTCGA
SGD_Scer_YDR044W             +    623  6.31e-11 ACAAACTCCA GAGGATTTGCGGGCTTGATG ATAAAATGTA
MIT_Spar_c130_3912           +    618  1.73e-10 CGAAACTCTA GAGGATTTGCAGGCTCGGTG ATAAAATGTA
MIT_Sbay_c896_21290          +    622  5.29e-10 CGGAACTCTT GGGGATTTGCGGGCTCGCTA ATAAAAAGTG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2050.4           1.7e-12  568_[-1]_139
MIT_Spar_c278_20970               1.7e-12  562_[-1]_145
SGD_Scer_YOR176W                  1.7e-12  560_[-1]_147
WashU_Smik_Contig2283.3           1.5e-11  623_[+1]_357
MIT_Smik_c935_20455               2.6e-11  546_[-1]_161
WashU_Sbay_Contig480.2              3e-11  573_[-1]_134
SGD_Scer_YDR044W                  6.3e-11  622_[+1]_358
MIT_Spar_c130_3912                1.7e-10  617_[+1]_363
MIT_Sbay_c896_21290               5.3e-10  621_[+1]_359
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Skud_Contig2050.4  (  569) GACGGTTTGTGGTTTCGACG  1 
MIT_Spar_c278_20970      (  563) GACGGTTTGTGGTTTCGACG  1 
SGD_Scer_YOR176W         (  561) GACGGTTTGTGGTTTCGACG  1 
WashU_Smik_Contig2283.3  (  624) GAGGATTTGCGGGTTCGGTG  1 
MIT_Smik_c935_20455      (  547) GACGGTTTGTGGTTTTGACG  1 
WashU_Sbay_Contig480.2   (  574) GATGGTTTGTGGTTTCGACG  1 
SGD_Scer_YDR044W         (  623) GAGGATTTGCGGGCTTGATG  1 
MIT_Spar_c130_3912       (  618) GAGGATTTGCAGGCTCGGTG  1 
MIT_Sbay_c896_21290      (  622) GGGGATTTGCGGGCTCGCTA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7464 bayes= 9.69407 E= 7.1e-025 
  -982   -982    251   -982 
   145   -982    -66   -982 
  -982    134    134   -154 
  -982   -982    251   -982 
    45   -982    166   -982 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -982   -982    251   -982 
  -982    134   -982     78 
  -154   -982    234   -982 
  -982   -982    251   -982 
  -982   -982    134     78 
  -982     92   -982    104 
  -982   -982   -982    162 
  -982    215   -982    -55 
  -982   -982    251   -982 
   104    -66     34   -982 
  -982    166   -982     45 
  -154   -982    234   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 7.1e-025 
 0.000000  0.000000  1.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.444444  0.444444  0.111111 
 0.000000  0.000000  1.000000  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.444444  0.000000  0.555556 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.444444  0.555556 
 0.000000  0.333333  0.000000  0.666667 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.000000  1.000000  0.000000 
 0.666667  0.111111  0.222222  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 0.111111  0.000000  0.888889  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
GA[CG]G[GA]TTTG[TC]GG[TG][TC]T[CT]G[AG][CT]G
--------------------------------------------------------------------------------




Time  5.96 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 177   E-value = 5.1e-015
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  :::::39::::::3:1::::
pos.-specific     C  8::1:1::9111::::9168
probability       G  ::a:161a1:6::::4::::
matrix            T  2a:99::::939a7a41942

         bits    2.5   *    *            
                 2.3   *    *            
                 2.0   *    **       *   
                 1.8   *    **       *   
Information      1.5 ***    **   * * *  *
content          1.3 ***** **** ** * ** *
(28.4 bits)      1.0 ***** **** ** * ****
                 0.8 *************** ****
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CTGTTGAGCTGTTTTGCTCC
consensus            T    A    T  A T  TT
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig480.2       +    516  3.60e-13 TTTTGTTCTG CTGTTGAGCTGTTTTGCTCC ACCTGTTCAA
MIT_Spar_c278_20970          +    506  2.05e-12 TTTTGCCCTG CTGTTGAGCTGTTTTGCTTC ACTGTTCAAC
WashU_Skud_Contig2050.4      +    507  5.04e-11 TTTTGTTCTG CTGTTGAGCTGTTTTGTTCC ATCTGTTCAA
SGD_Scer_YOR176W             +    504  5.04e-11 TTTTGTCCTG CTGTTGAGCTGTTTTGCTTT ACTGTTCAAC
MIT_Smik_c935_20455          +    490  5.99e-11 TTTTGCTCTG CTGTTGAGCTGTTTTACTTC ATTGTTCAAC
WashU_Smik_Contig2283.3      -     88  7.45e-10 ATTGTCTCAC CTGTTAAGCTTTTATTCCCC GTGTTTTCTT
MIT_Spar_c130_3912           -     91  1.12e-09 TTGTCTTTCT TTGTTAAGCTTTTATTCTCC AGCTTTTTTT
SGD_Scer_YDR044W             -     94  1.12e-09 TTGTCTTTCT TTGTTAAGCTTTTATTCTCC GGGTTTTCTT
MIT_Sbay_c896_21290          -    335  3.38e-07 TTCACACAGG CTGCGCGGGCCCTTTTCTTT TTAAACGAGT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig480.2            3.6e-13  515_[+2]_192
MIT_Spar_c278_20970                 2e-12  505_[+2]_202
WashU_Skud_Contig2050.4             5e-11  506_[+2]_201
SGD_Scer_YOR176W                    5e-11  503_[+2]_204
MIT_Smik_c935_20455                 6e-11  489_[+2]_218
WashU_Smik_Contig2283.3           7.5e-10  87_[-2]_893
MIT_Spar_c130_3912                1.1e-09  90_[-2]_890
SGD_Scer_YDR044W                  1.1e-09  93_[-2]_887
MIT_Sbay_c896_21290               3.4e-07  334_[-2]_646
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
WashU_Sbay_Contig480.2   (  516) CTGTTGAGCTGTTTTGCTCC  1 
MIT_Spar_c278_20970      (  506) CTGTTGAGCTGTTTTGCTTC  1 
WashU_Skud_Contig2050.4  (  507) CTGTTGAGCTGTTTTGTTCC  1 
SGD_Scer_YOR176W         (  504) CTGTTGAGCTGTTTTGCTTT  1 
MIT_Smik_c935_20455      (  490) CTGTTGAGCTGTTTTACTTC  1 
WashU_Smik_Contig2283.3  (   88) CTGTTAAGCTTTTATTCCCC  1 
MIT_Spar_c130_3912       (   91) TTGTTAAGCTTTTATTCTCC  1 
SGD_Scer_YDR044W         (   94) TTGTTAAGCTTTTATTCTCC  1 
MIT_Sbay_c896_21290      (  335) CTGCGCGGGCCCTTTTCTTT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7464 bayes= 9.69407 E= 5.1e-015 
  -982    215   -982    -55 
  -982   -982   -982    162 
  -982   -982    251   -982 
  -982    -66   -982    145 
  -982   -982    -66    145 
     4    -66    166   -982 
   145   -982    -66   -982 
  -982   -982    251   -982 
  -982    234    -66   -982 
  -982    -66   -982    145 
  -982    -66    166      4 
  -982    -66   -982    145 
  -982   -982   -982    162 
     4   -982   -982    104 
  -982   -982   -982    162 
  -154   -982    134     45 
  -982    234   -982   -154 
  -982    -66   -982    145 
  -982    166   -982     45 
  -982    215   -982    -55 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.1e-015 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.111111  0.888889 
 0.333333  0.111111  0.555556  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.111111  0.555556  0.333333 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.000000  1.000000 
 0.333333  0.000000  0.000000  0.666667 
 0.000000  0.000000  0.000000  1.000000 
 0.111111  0.000000  0.444444  0.444444 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  0.777778  0.000000  0.222222 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[CT]TGTT[GA]AGCT[GT]TT[TA]T[GT]CT[CT][CT]
--------------------------------------------------------------------------------




Time 11.78 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   19   sites =   9   llr = 177   E-value = 3.0e-016
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :::3:1:1::2::::1::3
pos.-specific     C  1:a7::a:a:149:46167
probability       G  :4:::::9:a:2:::::::
matrix            T  96::a9::::731a6394:

         bits    2.5   *   * **         
                 2.3   *   * **         
                 2.0   *   ****  *      
                 1.8   *   ****  *      
Information      1.5   * * ****  **     
content          1.3 * *** ****  **  * *
(28.4 bits)      1.0 **********  *** ***
                 0.8 ********** ********
                 0.5 *******************
                 0.3 *******************
                 0.0 -------------------

Multilevel           TTCCTTCGCGTCCTTCTCC
consensus             G A      AT  CT TA
sequence                        G       
                                        
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                   Site      
-------------            ------  ----- ---------            -------------------
MIT_Spar_c278_20970          +    156  5.34e-12 ACTAAAAGTA TTCCTTCGCGTCCTCCTTC TTCAATCCCA
SGD_Scer_YOR176W             +    154  5.34e-12 ACCAAAAGTA TTCCTTCGCGTCCTCCTTC TTCAATCCCA
WashU_Skud_Contig2050.4      +    160  9.86e-12 AAAAGAAGTA TTCCTTCGCGTGCTTCTCC TTTCTGTGTC
MIT_Smik_c935_20455          +    151  6.97e-11 GACCAAAAGA CTCCTTCGCGTCCTCCTTC TTCAAGTCTC
WashU_Smik_Contig2283.3      -    660  1.04e-09 CCGTAATTGT TGCATTCGCGTTCTTTTCA ACAATACATT
MIT_Spar_c130_3912           -    652  1.04e-09 CCACAATCGT TGCATTCGCGTTCTTTTCA ACAATACATT
SGD_Scer_YDR044W             -    657  2.59e-09 CCGTAATTGT TGCATTCGCGATCTTTTCA ACAATACATT
WashU_Sbay_Contig480.2       +    204  3.78e-09 AAAAGAAGTA TTCCTACGCGAGCTCCCTC TTCAAGTGCC
MIT_Sbay_c896_21290          -    440  1.61e-08 GTTCAGGGAG TGCCTTCACGCCTTTATCC CCTGGTATTC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c278_20970               5.3e-12  155_[+3]_553
SGD_Scer_YOR176W                  5.3e-12  153_[+3]_555
WashU_Skud_Contig2050.4           9.9e-12  159_[+3]_549
MIT_Smik_c935_20455                 7e-11  150_[+3]_558
WashU_Smik_Contig2283.3             1e-09  659_[-3]_322
MIT_Spar_c130_3912                  1e-09  651_[-3]_330
SGD_Scer_YDR044W                  2.6e-09  656_[-3]_325
WashU_Sbay_Contig480.2            3.8e-09  203_[+3]_505
MIT_Sbay_c896_21290               1.6e-08  439_[-3]_542
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=19 seqs=9
MIT_Spar_c278_20970      (  156) TTCCTTCGCGTCCTCCTTC  1 
SGD_Scer_YOR176W         (  154) TTCCTTCGCGTCCTCCTTC  1 
WashU_Skud_Contig2050.4  (  160) TTCCTTCGCGTGCTTCTCC  1 
MIT_Smik_c935_20455      (  151) CTCCTTCGCGTCCTCCTTC  1 
WashU_Smik_Contig2283.3  (  660) TGCATTCGCGTTCTTTTCA  1 
MIT_Spar_c130_3912       (  652) TGCATTCGCGTTCTTTTCA  1 
SGD_Scer_YDR044W         (  657) TGCATTCGCGATCTTTTCA  1 
WashU_Sbay_Contig480.2   (  204) TTCCTACGCGAGCTCCCTC  1 
MIT_Sbay_c896_21290      (  440) TGCCTTCACGCCTTTATCC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 19 n= 7473 bayes= 9.69581 E= 3.0e-016 
  -982    -66   -982    145 
  -982   -982    134     78 
  -982    251   -982   -982 
     4    192   -982   -982 
  -982   -982   -982    162 
  -154   -982   -982    145 
  -982    251   -982   -982 
  -154   -982    234   -982 
  -982    251   -982   -982 
  -982   -982    251   -982 
   -55    -66   -982    104 
  -982    134     34      4 
  -982    234   -982   -154 
  -982   -982   -982    162 
  -982    134   -982     78 
  -154    166   -982      4 
  -982    -66   -982    145 
  -982    166   -982     45 
     4    192   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 19 nsites= 9 E= 3.0e-016 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.444444  0.555556 
 0.000000  1.000000  0.000000  0.000000 
 0.333333  0.666667  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.222222  0.111111  0.000000  0.666667 
 0.000000  0.444444  0.222222  0.333333 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.444444  0.000000  0.555556 
 0.111111  0.555556  0.000000  0.333333 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.555556  0.000000  0.444444 
 0.333333  0.666667  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
T[TG]C[CA]TTCGCG[TA][CTG]CT[TC][CT]T[CT][CA]
--------------------------------------------------------------------------------




Time 17.43 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =   9   llr = 171   E-value = 3.0e-012
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  1a6aa:a8::32:a44:7aa
pos.-specific     C  :::::6::1::19::6:3::
probability       G  9:4::::::a71::::1:::
matrix            T  :::::4:29::61:6:9:::

         bits    2.5          *          
                 2.3          *          
                 2.0 *        *  *       
                 1.8 *        *  *       
Information      1.5 ** ** *  *  **    **
content          1.3 ** ** * *** **  * **
(27.4 bits)      1.0 ******* *** ** *****
                 0.8 *********** ********
                 0.5 *********** ********
                 0.3 ********************
                 0.0 --------------------

Multilevel           GAAAACAATGGTCATCTAAA
consensus              G  T T  AA  AA C  
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
SGD_Scer_YOR176W             +    581  1.12e-11 ACAAACCGTC GAAAACAATGGTCATCTAAA TAAAGGGTTC
WashU_Smik_Contig2283.3      +    166  4.85e-11 TTTTCAAAAA GAGAACAATGGTCAAATAAA GGTTTATCTA
MIT_Spar_c278_20970          +    583  8.09e-11 ACAAACCGTC GAAAATAATGGTCATCTAAA TAAAGGGTTC
MIT_Spar_c130_3912           +    170  3.22e-10 TTTTCGAAAC GAGAACAATGGACAAATCAA GCTTTATCTA
MIT_Smik_c935_20455          +    567  6.16e-10 ACAAACCGTC GAAAATAATGATCATCTAAA TAAAAGAGTT
SGD_Scer_YDR044W             +    174  1.95e-09 CTTTCGAAAC GAGAACAATGGGCAAAGCAA GCTTTATCTT
WashU_Skud_Contig2050.4      +    589  2.29e-09 ACAAACCGTC GAAAATATTGATCATCTAAA TAAAGGGTTC
MIT_Sbay_c896_21290          +    176  4.95e-09 TTCTCGAAGG GAGAACAATGGATAAATCAA AGCTTATCTA
WashU_Sbay_Contig480.2       +    594  3.59e-08 ACAAACCATC AAAAATATCGACCATCTAAA TAAAGGGTTC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YOR176W                  1.1e-11  580_[+4]_127
WashU_Smik_Contig2283.3           4.8e-11  165_[+4]_815
MIT_Spar_c278_20970               8.1e-11  582_[+4]_125
MIT_Spar_c130_3912                3.2e-10  169_[+4]_811
MIT_Smik_c935_20455               6.2e-10  566_[+4]_141
SGD_Scer_YDR044W                    2e-09  173_[+4]_807
WashU_Skud_Contig2050.4           2.3e-09  588_[+4]_119
MIT_Sbay_c896_21290                 5e-09  175_[+4]_805
WashU_Sbay_Contig480.2            3.6e-08  593_[+4]_114
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=9
SGD_Scer_YOR176W         (  581) GAAAACAATGGTCATCTAAA  1 
WashU_Smik_Contig2283.3  (  166) GAGAACAATGGTCAAATAAA  1 
MIT_Spar_c278_20970      (  583) GAAAATAATGGTCATCTAAA  1 
MIT_Spar_c130_3912       (  170) GAGAACAATGGACAAATCAA  1 
MIT_Smik_c935_20455      (  567) GAAAATAATGATCATCTAAA  1 
SGD_Scer_YDR044W         (  174) GAGAACAATGGGCAAAGCAA  1 
WashU_Skud_Contig2050.4  (  589) GAAAATATTGATCATCTAAA  1 
MIT_Sbay_c896_21290      (  176) GAGAACAATGGATAAATCAA  1 
WashU_Sbay_Contig480.2   (  594) AAAAATATCGACCATCTAAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7464 bayes= 9.69407 E= 3.0e-012 
  -154   -982    234   -982 
   162   -982   -982   -982 
    78   -982    134   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -982    166   -982     45 
   162   -982   -982   -982 
   126   -982   -982    -55 
  -982    -66   -982    145 
  -982   -982    251   -982 
     4   -982    192   -982 
   -55    -66    -66     78 
  -982    234   -982   -154 
   162   -982   -982   -982 
    45   -982   -982     78 
    45    166   -982   -982 
  -982   -982    -66    145 
   104     92   -982   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.0e-012 
 0.111111  0.000000  0.888889  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.555556  0.000000  0.444444  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 1.000000  0.000000  0.000000  0.000000 
 0.777778  0.000000  0.000000  0.222222 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  1.000000  0.000000 
 0.333333  0.000000  0.666667  0.000000 
 0.222222  0.111111  0.111111  0.555556 
 0.000000  0.888889  0.000000  0.111111 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.000000  0.000000  0.555556 
 0.444444  0.555556  0.000000  0.000000 
 0.000000  0.000000  0.111111  0.888889 
 0.666667  0.333333  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
GA[AG]AA[CT]A[AT]TG[GA][TA]CA[TA][CA]T[AC]AA
--------------------------------------------------------------------------------




Time 23.00 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   15   sites =   9   llr = 147   E-value = 3.6e-010
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  1:::4:::a::aa69
pos.-specific     C  8::4:9a4:a9::::
probability       G  1::61::6:::::::
matrix            T  :aa:41::::1::41

         bits    2.5       *  *     
                 2.3       *  *     
                 2.0      **  **    
                 1.8      **  **    
Information      1.5 **** ********  
content          1.3 **** ********  
(23.5 bits)      1.0 **** ******** *
                 0.8 **** **********
                 0.5 **** **********
                 0.3 ***************
                 0.0 ---------------

Multilevel           CTTGACCGACCAAAA
consensus               CT  C     T 
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Sbay_Contig480.2       +    183  1.26e-09 CCATAATGCT CTTGACCGACCAAAA GAAGTATTCC
SGD_Scer_YOR176W             +    136  1.26e-09 CAAGAGTGAC CTTGACCGACCAAAA GTATTCCTTC
MIT_Spar_c130_3912           -    252  1.01e-08 CCTTTTCTGG CTTCTCCCACCAATA ATGCCCCAGC
MIT_Smik_c935_20455          +    134  1.04e-08 CAACAGTGAT CTTGGCCGACCAAAA GACTCCTTCG
WashU_Skud_Contig2050.4      +    139  3.41e-08 CAACAATGAT ATTGACCGACCAAAA GAAGTATTCC
SGD_Scer_YDR044W             -    260  3.41e-08 GCCTTTTCTG GTTCTCCCACCAATA ACGCTCCAGC
MIT_Sbay_c896_21290          -    258  3.54e-08 CATTTTCTGG CTTCTCCCACCAATT ATGCCCCAGC
MIT_Spar_c278_20970          +    138  4.50e-08 CAAGAGTGAC CTTGACCGACTAAAA GTATTCCTTC
WashU_Smik_Contig2283.3      -    248  9.48e-08 TCTTTTCTGG CTTCTTCCACCAATA ATGCCCCAGC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig480.2            1.3e-09  182_[+5]_530
SGD_Scer_YOR176W                  1.3e-09  135_[+5]_577
MIT_Spar_c130_3912                  1e-08  251_[-5]_734
MIT_Smik_c935_20455                 1e-08  133_[+5]_579
WashU_Skud_Contig2050.4           3.4e-08  138_[+5]_574
SGD_Scer_YDR044W                  3.4e-08  259_[-5]_726
MIT_Sbay_c896_21290               3.5e-08  257_[-5]_728
MIT_Spar_c278_20970               4.5e-08  137_[+5]_575
WashU_Smik_Contig2283.3           9.5e-08  247_[-5]_738
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=15 seqs=9
WashU_Sbay_Contig480.2   (  183) CTTGACCGACCAAAA  1 
SGD_Scer_YOR176W         (  136) CTTGACCGACCAAAA  1 
MIT_Spar_c130_3912       (  252) CTTCTCCCACCAATA  1 
MIT_Smik_c935_20455      (  134) CTTGGCCGACCAAAA  1 
WashU_Skud_Contig2050.4  (  139) ATTGACCGACCAAAA  1 
SGD_Scer_YDR044W         (  260) GTTCTCCCACCAATA  1 
MIT_Sbay_c896_21290      (  258) CTTCTCCCACCAATT  1 
MIT_Spar_c278_20970      (  138) CTTGACCGACTAAAA  1 
WashU_Smik_Contig2283.3  (  248) CTTCTTCCACCAATA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 7509 bayes= 9.70275 E= 3.6e-010 
  -154    215    -66   -982 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -982    134    166   -982 
    45   -982    -66     45 
  -982    234   -982   -154 
  -982    251   -982   -982 
  -982    134    166   -982 
   162   -982   -982   -982 
  -982    251   -982   -982 
  -982    234   -982   -154 
   162   -982   -982   -982 
   162   -982   -982   -982 
    78   -982   -982     45 
   145   -982   -982   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 3.6e-010 
 0.111111  0.777778  0.111111  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.444444  0.555556  0.000000 
 0.444444  0.000000  0.111111  0.444444 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.444444  0.555556  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.555556  0.000000  0.000000  0.444444 
 0.888889  0.000000  0.000000  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
CTT[GC][AT]CC[GC]ACCAA[AT]A
--------------------------------------------------------------------------------




Time 28.58 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR044W                 2.52e-22  93_[-2(1.12e-09)]_60_[+4(1.95e-09)]_66_[-5(3.41e-08)]_165_[-3(5.96e-05)]_164_[+1(6.31e-11)]_14_[-3(2.59e-09)]_325
MIT_Spar_c130_3912               1.62e-23  90_[-2(1.12e-09)]_59_[+4(3.22e-10)]_62_[-5(1.01e-08)]_61_[-2(1.77e-05)]_85_[-3(5.96e-05)]_166_[+1(1.73e-10)]_14_[-3(1.04e-09)]_330
MIT_Sbay_c896_21290              5.08e-18  94_[-2(2.30e-05)]_61_[+4(4.95e-09)]_62_[-5(3.54e-08)]_62_[-2(3.38e-07)]_31_[-3(3.05e-05)]_35_[-3(1.61e-08)]_163_[+1(5.29e-10)]_82_[-2(1.56e-05)]_257
WashU_Smik_Contig2283.3          1.53e-24  7_[+1(1.86e-05)]_60_[-2(7.45e-10)]_58_[+4(4.85e-11)]_62_[-5(9.48e-08)]_336_[-3(6.30e-05)]_6_[+1(1.50e-11)]_16_[-3(1.04e-09)]_204_[-3(4.16e-06)]_99
SGD_Scer_YOR176W                 9.09e-32  135_[+5(1.26e-09)]_3_[+3(5.34e-12)]_20_[-2(9.24e-05)]_269_[+2(2.71e-05)]_2_[+2(5.04e-11)]_37_[-1(1.73e-12)]_[+4(1.12e-11)]_55_[-1(7.71e-05)]_52
MIT_Spar_c278_20970              8.55e-31  137_[+5(4.50e-08)]_3_[+3(5.34e-12)]_309_[+2(4.04e-05)]_2_[+2(2.05e-12)]_37_[-1(1.73e-12)]_[+4(8.09e-11)]_125
MIT_Smik_c935_20455              5.42e-27  133_[+5(1.04e-08)]_2_[+3(6.97e-11)]_298_[+2(5.34e-05)]_2_[+2(5.99e-11)]_37_[-1(2.58e-11)]_[+4(6.16e-10)]_141
WashU_Skud_Contig2050.4          5.92e-28  138_[+5(3.41e-08)]_6_[+3(9.86e-12)]_305_[+2(1.26e-05)]_3_[+2(5.04e-11)]_6_[-2(3.42e-05)]_16_[-1(1.73e-12)]_[+4(2.29e-09)]_119
WashU_Sbay_Contig480.2           1.38e-26  182_[+5(1.26e-09)]_6_[+3(3.78e-09)]_270_[+2(7.91e-05)]_3_[+2(3.60e-13)]_38_[-1(3.01e-11)]_[+4(3.59e-08)]_114
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM13.ups.fa_000444000766000024      1532613155576321 20357 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR044W HEM13 "Coproporphyrinogen III oxidase, an oxygen requiring enzyme that catalyzes the sixth step in the heme biosynthetic pathway; localizes to the mitochondrial inner membrane; transcription is repressed by oxygen and heme (via Rox1p and Hap1p)"
CTTTATGTGTATTTAATTGTGTTCGAAGAGTTCGGTTTGCTATGTTTGATTTGCGAAAAG
AAAGCTTTTGATATGCTCAAAAAAAGAAAACCCGGAGAATAAAAGCTTAACAAAGAAAGA
CAATAGGTGGAAAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTCGAAACGAGAACA
ATGGGCAAAGCAAGCTTTATCTTCGGATCGTCCGTCAGCGCTTTGGTTGCAGTCTTATGC
TTTGTTCAAGCTGGAGCGTTATTGGTGGGAGAACCAGAAAAGGCGAAAGCGTAGCGTTCT
TTGAAATTTGGCTTCTGTTCCTGCGACTCGTTTAAAAGTAGAAGGGCCCGCGGAGCCGCT
GTGAAAGATTTCTTTTACTCTTTCAGCGCAGAAATCTCGCAGGAGCTCAGCAGAAAGTGC
CTATGACGGTAATCCCAGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAATTAA
AATACCGTGCCTATAGTAACTTTTTTTTACGCTGTGAACCGTTCAACACACAGTAAAAAC
TCCGCAGGAAATGGTTTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTTTCCCAACA
GTGAACGAGAGGACAAACTCCAGAGGATTTGCGGGCTTGATGATAAAATGTATTGTTGAA
AAGATCGCGAATGCAACAATTACGGTGGGGAGAAATATCAACAAAAGGGCAAGGCTATGC
CTTCTGGAAAGTGGCAGACTTGCACTTTCCTCGAAAAGAAAAATGACCGCAAGATCCGGT
TGTTCTCAACCTTCTACATTAAGACATACTTCTACGATTTTCGAATGCCGAAGCAACTAT
CGCTGAAATTTGTCATGTCAAAATTGCTACTGGGGGAGAAGAATATATATGGAAGTAATT
ATTATTTACGTTGCTGAAATGGCAGGTTAGACGCATGTTTTGCAAAATAAGTGGTTTTGA
AAAGAATTGATACTAGGAATCGGTGCAATACCTTCTACCT
>MIT_Spar_c130_3912 YDR044W 5' untranslated region, Contig c130 4128 - 6127, 2000 bp (revcom)
CTTTATATGTGTGTTTTGTGGTGTTCGAAATTGGTTTCTTTTGTTCGACTTGCGAGAAGA
AAGCTATCAATATGCTTTCCAAAAAAAGCTGGAGAATAAAAGCTTAACAAAGAAAGACAA
TAGGCGGAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTTCGAAACGAGAACAATGG
ACAAATCAAGCTTTATCTATGGGTTGTCAGCTCTTTGGTTGCAGTCTTGTGCTTGGTTCA
AGCTGGGGCATTATTGGTGGGAGAAGCCAGAAAAGGCGAAAGCGTAGCGTTCTTTGAAAT
TTGGATTCTGTTCCTGCGACTCGTTTAAAAGAAGAAGGGCTGCGGAGCCACTGTGAAAGA
CTTGTTGTGCTCTTTCAACTAAGAAATCTGGCAGGAACTCGATATAAAGTGCCTGTGACA
GTAATCTCAGGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAAATTGAAATACC
GTGCCTATGGTAACTTTTTTTTACGCTGCGAACCGTTCAACACACATTGAAAACCCCGCA
GCAATTGTTCTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTCTCCCAACAGTGTAC
GAGCGGACGAAACTCTAGAGGATTTGCAGGCTCGGTGATAAAATGTATTGTTGAAAAGAA
CGCGAATGCAACGATTGTGGTGGAGAGAAATATCAACAGGGCAAGGCAAGGCTATGCTCT
TTTGGAAGTGGCGGACTTGCACTTTCTTGAAAAGAAAAATGACCGCAAGATCCGGTTGTT
CATAACTTTCTACAATAAGGCATACTTCTACGGTTTTCCAATGCTGAGGCAACTATCGCT
ATAAAATCGCTGCTAGGAGAAGATTATATATGGACGTAAATATTTTTTACGTTACTAAAA
TTCTAGGTTAGAGGCACGTTTTGCAGAACCAGTGGCCTTGGAAAGGTGTTGCTACAAATT
TATGCAATTTCTTCAACTTGCCAGGTGGTCTTGGATGATC
>MIT_Sbay_c896_21290 YDR044W 5' untranslated region, Contig c896 7383 - 9382(revcom), 2000 bp (revcom)
CTTGTTATGTGTGTTTGTGGTGATTGCGGTTTGGTTTTTCTGATTCGTATGACAGAAAGA
AAAAAATTCAGTTTACCTTGTAAGGTGATTAGGAGAAGAAAAAAAGCTTATTGGCAGCGA
ACAATAGGTGAAAAAAAAAAAGAAAATGCGTGTCCTTATATAGCTTTCTCGAAGGGAGAA
CAATGGATAAATCAAAGCTTATCTACGGGTCAACAGCTCTTTGGTTGCTGTCTTGCTCTA
GGTCCAAGCTGGGGCATAATTGGTGGGAGAAGCCAGAAAATGCGAAAGCGTACCGTTCTG
TGAAAAATGGCTTCGGTTCCTGCGACTCGTTTAAAAAGAAAAGGGCCCGCGCAGCCTGTG
TGAAATGTTCGTTTTGCCCTTCCCAGAGAGAAATCTTGCAGGAGCCTCAATACAATGTGC
CTGCGGATGGAATACCAGGGGATAAAGGCGTGAAGGCACTCCCTGAACAATTGAAAATTG
GAAAAAAAAAGTGCCTGTGATGAATCTTATACGTTGGGAAAACTCCAAGACACTTTTAAA
ACTCCGCAGAGATTGTTTGGAGGGACCTTGACCACGAGTTGGGAGTATTGTTTTTTCCTG
GAAGGAACGAGCGGAACTCTTGGGGATTTGCGGGCTCGCTAATAAAAAGTGTCTTGTTGA
AGAAAAGTAGAATGCGACTAAAACGGTGGAGGAAAATATCAACAAGGCAAGGCTATGCCT
TTCGAAGAAAAGCGGACTTGCAATTGCACAACCGTATCGAAGAGAATTGAGAAGGGGGTG
CAAAGTGATCCGGTTGTTCATATTTCTTCACCAATTGATACAATTATCTACGTTTGTTCT
GTTGACCAATCCAACGGGGACTCTGTATGACATAAGTCTTCCTTACATTGCTAAGATCCA
AGATCAGACCCGTAGATGAGTTCTGCACCAAAGAGTTGTTAACCGTCTTGCCTGAATAAT
TTTAAGTTGTCGCGATCCTCTTACAAGGTGTTCTTATTTC
>WashU_Sklu_Contig2357.8 YDR044W 5' untranslated region, Contig c2357 9533 - 11532, 2000 bp (revcom)
AGCTCCAGTGATTTGGGAGTCAAAAAAGGTGTGGTTTTTATAACGCTGTCGTTTAAGCCA
GCACTGCGTACTGTGACGGCTTCTTTTTTTTTTTTTTTTTTTTCTCCTATGTATTTTTCT
TGTTACCAAATCCAGGAAGCTACCATTATAGAGAGCAGCCAGAACCGGAACCGAGTTAAA
TCACCAGATTGATAACAAAGAGATCTATACGAGAGAGGCAGAAGAGCAAAGTTCAAAGGC
ACTGTCGAGGCCATATACTCACACGAAGCTGATGGTAGCGACAATATAAACTATACAGAG
CATACATAGCGCAAAGATTGCAAAAGACCAGGAAACCTTAAACGGCAAGAGTGTAGTACA
TGGCACAGGATACCATCACAACTCACCAGCTGAGAGGTCAGAAATAGGAAGCAGACGAAA
AACAAGAAAAAAGAAAAAAAAAAAGAGCAAGAAATCATCAAATAAAAGCGTAACAAAAGA
GGCTACGTCTTGCAATGCTTTTACACACATGTGAGGAAGAAGAAGAAGGAGAAAACGTTC
TTCCACGGAACGCTACCAACGCACGGCCGGCGTTGGGCTTCCATGTATCCAGCTGCGGAT
GATATCACTGCAGCTGTTACAAGTCTCGTTTCAAAACCAGATATGGCAAATGGTCAAGAT
ATGTGTCTCTGACATAGATGGTCGTTTAGGAAACAACACGCGGCTGTGGTATATAGGGGA
AAAGACACGCATATACGTTGAGTCCCGTACACGGGTACACACGACGAGAAAAGAAAAGGA
AAACCAAAAAGGGTTCTCGGTGGGTGTATGGGTATACAGAGATCACGTGAACAGAAGGGA
TCACATATATCCTCGGCTCGGACGGCATGCTCACGGCCGTTACTCGAGAGAAAAGACAAA
AATAAAAAAAAATACCACCGTGGTTAAAAGACGAAAAAGAGGAAGGGTCTGCTCTTGGCA
CAGAAAAGCTCGCGAGATCCGCCGCGCCCCCCCACCGACG
>WashU_Scas_Contig569.3 YDR044W 5' untranslated region, Contig c569 4575 - 6574, 2000 bp (revcom)
ATCCTTAATTTCTTGATAGAAGATAAATTCAAGAGTAAACAAGGTAAACAATAAAGGTTA
AAAAGAAACGACAAATCCTAAAGGATAGGAGAAAGGAAATATGTATGCTTAGTAAGGTAA
TCGGTGCCCTTTTTATACCTTTCAGTAGAACTGTTGACGTTGAATGGATTCGTATTTTGG
TTCGTCGCAGGAACGAAGTTTCGTCATGTGGGAAATGTCCTCGAGGCCATTTGTTGACGA
GAAAAGTGAAAAAGGGGATATGCCGACGTGGAATTTTGCAACCAGAGAAATGACTTTCCT
GTGAAAGACTCGTAGGACCGCAGAGGTGCTTACGTAGCACATTCAAGATAGGAATATATA
TATCCTTACTAGGTAACCTCCTCAGCTCAATTCGTCCTAGGGGTTTACCTTTACTTAATG
TAGAAAATTTCTTGAAGGTTCAAAGACAGATCTTCATATGGATCTGTCTTTTTTGCATCT
CGCCCATGGGCCTGGACCCTAACGCTGAGTGCAAAAAATCGGAACACTGTGAATGTCTCG
GTGTCAACTAAGTGTTGAGATGCTACCTATGAACTTAGCTGTCAACTGGGGAAGAGGCCC
GAATTATACTCAATTGGTCTGTCGAGAATTTAGTAGTGGATGAGTTGAAGATATTAGATT
AGATAGATAATTCTCCATGTATCTAAGTAAAACCAAAAGACTTACTACTTGCAAGCTGAT
AGTCAGCTAAAACGTCTTGGAAAAAAGGAACCGATGAAATGATCTACACATGACTGGGGT
TTTCATCGCAATTGGTAGCGTATCGTTTATGTAATTGAGAAATATACGAATGGTAAAAGT
AGGATTTACGGGTATTGTAATATTTTTTGAGTTAAGCAACTGCGCCGACAGCATAGCCAG
AAAGGGCGAACACTATGTTTTCGCGTGTTTCATGTCATGTCTAGTTGACACTTACATTCT
TAAGACACCTGACCTAACGTTGGTCCATAAAATTGAAATT
>WashU_Smik_Contig2283.3 YDR044W 5' untranslated region, Contig c2283 2261 - 4260(revcom), 2000 bp (revcom)
CTTTATTGAGGATTTGTGGCGTTTGAGGTTTGGTTTTTTATTCAATTTGAAAGAAGAAAA
CTATCGTTATACTTTCGAAGAAAACACGGGGAATAAAAGCTTAACAGGTGAGACAATAGG
TGGAAAAAAAGGAAAATATGTGTCTTTATATAGCCTTTTCAAAAAGAGAACAATGGTCAA
ATAAAGGTTTATCTACGAGTCGACAGTTCGTTGGCTGCAGTGTTACGCTTGGTTGAAGCT
GGGGCATTATTGGTGGAAGAAGCCAGAAAAGACGAAAGAGTAGCGTAGCGTTCTTTCAAA
TTTTGGTTTCGGGTTCCTGCGACTCGTTTAAAAAAGAAAAGGGCCCGCGGCCCCGCCGTG
AAACACTTCGTCTTGCTCTTCCCACCCAGAAAACTTGTAGGAGCCTCAGTTACAAAGTGC
CTGTAATGGAAATCTTAGGGGGCTACTATTGTAAAGGCAATTTCTGAACAATTGAAAGTG
AAAATATCGTGCCTGTGGTAACTTTCTTATACGCCGTGAAACGTTTAACATACGTTGAAA
ACTCCGCAGGGATTGGTTTGGAAAATTATAGTCACGAATTAGGCGTATTGTCTTTCAAGA
AGGTACGAGCGGATGAACTTCTTGAGGATTTGCGGGTTCGGTGATAAAAAATGTATTGTT
GAAAAGAACGCGAATGCAACAATTACGGTGGAGAAAAATATTAACAAGGGAAGGCAAGGC
TATGTTCTATTGAGAAGCGGCGGACTTGCACTTTCCTCGAAGAAAAAAATGTCTTCAAGA
TCCAATGTTCATATAACTTTCTACAATAAGGTATCCTTCTACGATCTTTCAATGTTAAGA
TTGAAATCAATGTAAAAAGCACCATGTTGAATACTACTGCTAGGAGGAGATCACATATGA
ATGTGATTATTATTTATATTAGTAAATTTTCAGGTTAGGAAGAAGTTATGTGACGCTTTA
GCTTTGGAAATTTGTTGCGGGAAACTGATAACATTCTTTT
BioPerl-1.007002/t/data/map_hem/HEM13.ups.fa_.revcom000444000766000024      1103513155576321 21642 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDR044W HEM13 "Coproporphyrinogen III oxidase, an oxygen requiring enzyme that catalyzes the sixth step in the heme biosynthetic pathway; localizes to the mitochondrial inner membrane; transcription is repressed by oxygen and heme (via Rox1p and Hap1p)"
AGGTAGAAGGTATTGCACCGATTCCTAGTATCAATTCTTTTCAAAACCACTTATTTTGCA
AAACATGCGTCTAACCTGCCATTTCAGCAACGTAAATAATAATTACTTCCATATATATTC
TTCTCCCCCAGTAGCAATTTTGACATGACAAATTTCAGCGATAGTTGCTTCGGCATTCGA
AAATCGTAGAAGTATGTCTTAATGTAGAAGGTTGAGAACAACCGGATCTTGCGGTCATTT
TTCTTTTCGAGGAAAGTGCAAGTCTGCCACTTTCCAGAAGGCATAGCCTTGCCCTTTTGT
TGATATTTCTCCCCACCGTAATTGTTGCATTCGCGATCTTTTCAACAATACATTTTATCA
TCAAGCCCGCAAATCCTCTGGAGTTTGTCCTCTCGTTCACTGTTGGGAAAAACAATACGC
CTAATTCGTGATTAAGATTCTTCAAACCATTTCCTGCGGAGTTTTTACTGTGTGTTGAAC
GGTTCACAGCGTAAAAAAAAGTTACTATAGGCACGGTATTTTAATTTCAATTGTTTAGAA
AGTGCCTTCACACCATTAGCCCCTGGGATTACCGTCATAGGCACTTTCTGCTGAGCTCCT
GCGAGATTTCTGCGCTGAAAGAGTAAAAGAAATCTTTCACAGCGGCTCCGCGGGCCCTTC
TACTTTTAAACGAGTCGCAGGAACAGAAGCCAAATTTCAAAGAACGCTACGCTTTCGCCT
TTTCTGGTTCTCCCACCAATAACGCTCCAGCTTGAACAAAGCATAAGACTGCAACCAAAG
CGCTGACGGACGATCCGAAGATAAAGCTTGCTTTGCCCATTGTTCTCGTTTCGAAAGGCT
ATATAAGGACACGGATTTTCCTTTTTTTTTCCACCTATTGTCTTTCTTTGTTAAGCTTTT
ATTCTCCGGGTTTTCTTTTTTTGAGCATATCAAAAGCTTTCTTTTCGCAAATCAAACATA
GCAAACCGAACTCTTCGAACACAATTAAATACACATAAAG
>MIT_Spar_c130_3912 YDR044W 5' untranslated region, Contig c130 4128 - 6127, 2000 bp (revcom)
GATCATCCAAGACCACCTGGCAAGTTGAAGAAATTGCATAAATTTGTAGCAACACCTTTC
CAAGGCCACTGGTTCTGCAAAACGTGCCTCTAACCTAGAATTTTAGTAACGTAAAAAATA
TTTACGTCCATATATAATCTTCTCCTAGCAGCGATTTTATAGCGATAGTTGCCTCAGCAT
TGGAAAACCGTAGAAGTATGCCTTATTGTAGAAAGTTATGAACAACCGGATCTTGCGGTC
ATTTTTCTTTTCAAGAAAGTGCAAGTCCGCCACTTCCAAAAGAGCATAGCCTTGCCTTGC
CCTGTTGATATTTCTCTCCACCACAATCGTTGCATTCGCGTTCTTTTCAACAATACATTT
TATCACCGAGCCTGCAAATCCTCTAGAGTTTCGTCCGCTCGTACACTGTTGGGAGAAACA
ATACGCCTAATTCGTGATTAAGATTCTTCAGAACAATTGCTGCGGGGTTTTCAATGTGTG
TTGAACGGTTCGCAGCGTAAAAAAAAGTTACCATAGGCACGGTATTTCAATTTTCAATTG
TTTAGAAAGTGCCTTCACACCATTAGCCCCCTGAGATTACTGTCACAGGCACTTTATATC
GAGTTCCTGCCAGATTTCTTAGTTGAAAGAGCACAACAAGTCTTTCACAGTGGCTCCGCA
GCCCTTCTTCTTTTAAACGAGTCGCAGGAACAGAATCCAAATTTCAAAGAACGCTACGCT
TTCGCCTTTTCTGGCTTCTCCCACCAATAATGCCCCAGCTTGAACCAAGCACAAGACTGC
AACCAAAGAGCTGACAACCCATAGATAAAGCTTGATTTGTCCATTGTTCTCGTTTCGAAA
AGGCTATATAAGGACACGGATTTTCCTTTTTTTCCGCCTATTGTCTTTCTTTGTTAAGCT
TTTATTCTCCAGCTTTTTTTGGAAAGCATATTGATAGCTTTCTTCTCGCAAGTCGAACAA
AAGAAACCAATTTCGAACACCACAAAACACACATATAAAG
>MIT_Sbay_c896_21290 YDR044W 5' untranslated region, Contig c896 7383 - 9382(revcom), 2000 bp (revcom)
GAAATAAGAACACCTTGTAAGAGGATCGCGACAACTTAAAATTATTCAGGCAAGACGGTT
AACAACTCTTTGGTGCAGAACTCATCTACGGGTCTGATCTTGGATCTTAGCAATGTAAGG
AAGACTTATGTCATACAGAGTCCCCGTTGGATTGGTCAACAGAACAAACGTAGATAATTG
TATCAATTGGTGAAGAAATATGAACAACCGGATCACTTTGCACCCCCTTCTCAATTCTCT
TCGATACGGTTGTGCAATTGCAAGTCCGCTTTTCTTCGAAAGGCATAGCCTTGCCTTGTT
GATATTTTCCTCCACCGTTTTAGTCGCATTCTACTTTTCTTCAACAAGACACTTTTTATT
AGCGAGCCCGCAAATCCCCAAGAGTTCCGCTCGTTCCTTCCAGGAAAAAACAATACTCCC
AACTCGTGGTCAAGGTCCCTCCAAACAATCTCTGCGGAGTTTTAAAAGTGTCTTGGAGTT
TTCCCAACGTATAAGATTCATCACAGGCACTTTTTTTTTCCAATTTTCAATTGTTCAGGG
AGTGCCTTCACGCCTTTATCCCCTGGTATTCCATCCGCAGGCACATTGTATTGAGGCTCC
TGCAAGATTTCTCTCTGGGAAGGGCAAAACGAACATTTCACACAGGCTGCGCGGGCCCTT
TTCTTTTTAAACGAGTCGCAGGAACCGAAGCCATTTTTCACAGAACGGTACGCTTTCGCA
TTTTCTGGCTTCTCCCACCAATTATGCCCCAGCTTGGACCTAGAGCAAGACAGCAACCAA
AGAGCTGTTGACCCGTAGATAAGCTTTGATTTATCCATTGTTCTCCCTTCGAGAAAGCTA
TATAAGGACACGCATTTTCTTTTTTTTTTTCACCTATTGTTCGCTGCCAATAAGCTTTTT
TTCTTCTCCTAATCACCTTACAAGGTAAACTGAATTTTTTTCTTTCTGTCATACGAATCA
GAAAAACCAAACCGCAATCACCACAAACACACATAACAAG
>WashU_Smik_Contig2283.3 YDR044W 5' untranslated region, Contig c2283 2261 - 4260(revcom), 2000 bp (revcom)
AAAAGAATGTTATCAGTTTCCCGCAACAAATTTCCAAAGCTAAAGCGTCACATAACTTCT
TCCTAACCTGAAAATTTACTAATATAAATAATAATCACATTCATATGTGATCTCCTCCTA
GCAGTAGTATTCAACATGGTGCTTTTTACATTGATTTCAATCTTAACATTGAAAGATCGT
AGAAGGATACCTTATTGTAGAAAGTTATATGAACATTGGATCTTGAAGACATTTTTTTCT
TCGAGGAAAGTGCAAGTCCGCCGCTTCTCAATAGAACATAGCCTTGCCTTCCCTTGTTAA
TATTTTTCTCCACCGTAATTGTTGCATTCGCGTTCTTTTCAACAATACATTTTTTATCAC
CGAACCCGCAAATCCTCAAGAAGTTCATCCGCTCGTACCTTCTTGAAAGACAATACGCCT
AATTCGTGACTATAATTTTCCAAACCAATCCCTGCGGAGTTTTCAACGTATGTTAAACGT
TTCACGGCGTATAAGAAAGTTACCACAGGCACGATATTTTCACTTTCAATTGTTCAGAAA
TTGCCTTTACAATAGTAGCCCCCTAAGATTTCCATTACAGGCACTTTGTAACTGAGGCTC
CTACAAGTTTTCTGGGTGGGAAGAGCAAGACGAAGTGTTTCACGGCGGGGCCGCGGGCCC
TTTTCTTTTTTAAACGAGTCGCAGGAACCCGAAACCAAAATTTGAAAGAACGCTACGCTA
CTCTTTCGTCTTTTCTGGCTTCTTCCACCAATAATGCCCCAGCTTCAACCAAGCGTAACA
CTGCAGCCAACGAACTGTCGACTCGTAGATAAACCTTTATTTGACCATTGTTCTCTTTTT
GAAAAGGCTATATAAAGACACATATTTTCCTTTTTTTCCACCTATTGTCTCACCTGTTAA
GCTTTTATTCCCCGTGTTTTCTTCGAAAGTATAACGATAGTTTTCTTCTTTCAAATTGAA
TAAAAAACCAAACCTCAAACGCCACAAATCCTCAATAAAG
BioPerl-1.007002/t/data/map_hem/HEM14-HEM15.fa000444000766000024      1402613155576321 20164 0ustar00cjfieldsstaff000000000000>SGD_Scer_YER014W HEM14 "Protoporphyrinogen oxidase, a mitochondrial enzyme that catalyzes the seventh step in the heme biosynthetic pathway, converting protoporphyrinogen IX to protoporphyrin IX"
TATACAAGCTCTTTTTGGCGTTCTCAATTGCACTTTACTCGATATGTTTGAATTGGTGTT
CTTCGCGAATATCTCTATTGTTCTCTCTATTATACTATTTCTTTTTTTGAATACTCCGCG
ACTCCGAAGCAACAAAGTGTCGAAGGCAAGTTCAAAGGCGTTTTGTAACTAAACGAGCAA
TGGCAGCTTTCAATTAAAGAAAGGTTAGCGTTACTCTGTGATTTTTTTCATGTAAAAATT
CTCAAGAGAGATAAAGTTGTTAAAAAATTAAATATAGGTCTATAAAACTCGATAATTATA
ATGCATAAAAAGCTAACAATGT
>MIT_Spar_c425_6072 YER014W 5' untranslated region, Contig c425 34016 - 36015, 2000 bp (revcom)
TATTCGAGCCCTTTCCCGCGTTCCCAATTGTACCTTCCTCGATAGGATTGAATTGGTATC
CTTCGCGGATCTCTCTATTGTTCTCTCTATTATTCTTTTTCTTTTTTAAATACTCCGCGA
CTCCGAAGCAACAAAATGTCGAAGGCAAGATGAAAGGCGTTTTGCAACTAAACGAGTAAT
GGCAGCTTTTAATTAAATAACGGTCAGCATTACTCTATAACTTTTCACATAAAATCCTCG
AAGAAGGAAAAATTGATAATCAATTTACCGAAGAATGAATATAGGTCTATAAAAATTCAA
TAATTATAGATGCATAAAAAGC
>MIT_Smik_c283_5928 YER014W 5' untranslated region, Contig c283 42606 - 44605, 2000 bp (revcom)
TATTGAAGCTCTCTCCACTATTTCTTTAATCGCGCTATACTAGATATGGTTAAACTGCTA
TCTTTTGCAAATCCCTCTATTGTTCTTTCCATTACTCTTTTCTTTTTTAAATACGGACTC
CGAAGCAACAAGGTCGAAGGCAAGCTGAAAGGCATTTTACAACTAAACGAGCAATGGTAG
CTTTTGATTGAATAAATTATTATCATTATTTTGTTATTTGTCCCACGAAATTCTCGTTGA
AAGCAAGGTTCGTAAGGATTTATCAAATGTTAAATATAGATCTATAAAAATTGAATAGTA
ATAATAACAAGGGATGGTGTTA
>MIT_Sbay_c84_6418 YER014W 5' untranslated region, Contig c84 10802 - 12801(revcom), 2000 bp (revcom)
TGTCGAAGTTCTCCTTTATTCCGCTGTTTCTTACGGAATCCAGCGAGACTGTTGTCCTTT
CGCATCCTTCTATTGTTCTTCCTTATTGTTCTCGTTTTTTTTATACTCTGCGACTCCGAA
ACAACAAAATCTCGAAGGCAAGCTAAGGTAAAAATATTCACCACTAAACGAGCAATGACA
GTTATATTCAAACGTCATTCTACTTTTTTGCCAGAGAAGTCCTCACTGGAGACGAAGTTG
GTAAATGCTTTATTTATATTAAACGTAGATCTATAAAGTTTAAATAGTTTATAATGCTTA
ACAAGGGACGATGTTATCTCTT
>SGD_Scer_YOR176W HEM15 "Ferrochelatase, a mitochondrial inner membrane protein, catalyzes the insertion of ferrous iron into protoporphyrin IX, the eighth and final step in the heme biosynthetic pathway; Yfh1p mediates the use of iron by Hem15p"
TCTTTAAACGTTCTTTTTTTTACTGCTAAATTTGTCCAAATAGCAGGTATGTGTTAAATA
TTTCTGTACTTCTTGTAAACCGACTCAAGTGGAACACGAGAATTTACGCTTGTTTGGTGT
CAAGCCAAGAGTGACCTTGACCGACCAAAAGTATTCCTTCGCGTCCTCCTTCTTCAATCC
CATATCCCCTACGAAAAAAAGCAGCATGAGAAAACGAAGGGCAGCAACTCCTTCGTCATA
TAAGGCTTACGGTGACCATTGAAGATTGGGCATGTCTAACGGCTATTGCCAGCGGAGATG
TTTCAAGGCATCCTACACATGCTACATATTTGTAATTATTTTACTGAGTTTGTGTATATA
AAAAACTTTTTTAAAAAAAAAAAATGGCCAGCATCCTCTTTCATGTAAAGCTGTTGAACC
TTCCTGAAATTTACTTCTAAAATTGTTCAGTAAAACTGCTTGTTAAAAGTGCGAAGAGTT
CTTTTTTAGCTTTTTTTGTCCTGCTGTTGAGCTGTTTTGCTTTACTGTTCAACAAAACAT
TGAAGATCTTTCACATTGCGCGTCGAAACCACAAACCGTCGAAAACAATGGTCATCTAAA
TAAAGGGTTCTTATTAAACAGATTTAAAGCCAAGGACAAAATACAGGCACAGGTCAAGCA
AGAAGACAAACCGCATACGCCAAGACAAACCGTGGTGATTTAATTCTGCTGCTGATCGCT
TCCAACA
>MIT_Spar_c278_20970 YOR176W 5' untranslated region, Contig c278 32746 - 34745, 2000 bp (revcom)
TCTTCAAACGTTCTTTTCCTACTACTAAGCTTTTCAATAAATAGCGGGTATATGCTAAAT
ACTTCTTTGCTTCTTGTACGACCTACTTAATTGAAATACGGATATTTTTGCTTGCTTGGT
GCCAAACCAAGAGTGACCTTGACCGACTAAAAGTATTCCTTCGCGTCCTCCTTCTTCAAT
CCCATATCCCCTACTGAAAAAAGCAGCGTGCGAAAATGAAGGGCAGCAACTCCTTCGTCA
TATAAGGCTTAGGTAATCTTTCAAGGTCAGGTATATCCAGCTGTCGTTACGAGTAGAGAT
ATTTCAAGCTGTCCTGCACATGCTACATATTTGTGATTATTTTTATTGAGTTGCGTATAT
AAAAAAACAATCTAAAAAAAAAAAAAATGGCCAGCATCTTCTTCCATGTAAAGCTGTTGA
ACCTTGCTAAAATCTATTACTATAATTGTTCAGTAAAGTTGCTTGTTAAAAATGCGAAGA
GTCTTTTTTAGCTTTTTTTGCCCTGCTGTTGAGCTGTTTTGCTTCACTGTTCAACAAAAC
AGTGAAGATCTTTCGAATTGCGCGTCGAAACCACAAACCGTCGAAAATAATGGTCATCTA
AATAAAGGGTTCTTATTTGAACAGATTTAAAGCTCAAAGACACGATACAGGCACAGGTCC
AGAAAGAATACAAAACGCAAACGCCAAGACAAATTGTGGTAATTTCATTCTGCTGCTGAT
CACTGCC
>MIT_Smik_c935_20455 YOR176W 5' untranslated region, Contig c935 1803 - 3802(revcom), 2000 bp (revcom)
TCTTGAATTGCAATTTTCTACTACTGAAGTTACCAACAATTAGCAAATATGTGATGAGTC
CTTTTTACGTTCTTGTATAACCTAAGTTAAATACAAAGGTTTATGCTCCTTTAATGATCA
GACCAACAGTGATCTTGGCCGACCAAAAGACTCCTTCGCGTCCTCCTTCTTCAAGTCTCA
TATCCCCTACCAGAAAAAGTAGCAGGCGAAAATAAAGAGCAACTGCTCCCCCCCATATAG
AGCTTACCATAATTTCTCAAGGAAAGGTATCTCCAGTTGTCGTAAAGAATAAAGAAGTTT
CAACGTGTCCTGCATGTTCTACAAATTTGCAATTGACTTTACTAAGTTGCATATATAAAA
CTTGTATTAGATAAGTTAGCCAGCATTTTCATTCAAGCTAAGATGTTGAATATGCCAAAG
CACATTGCTGAAATTAATCAGTAAAGCTGCTTGCTGAAAGTGGAAATATTTTCAGCTTTT
TTTGCTCTGCTGTTGAGCTGTTTTACTTCATTGTTCAACAAAACAATAGAGTTCTCTCCA
ATTGCGCGTCAAAACCACAAACCGTCGAAAATAATGATCATCTAAATAAAAGAGTTCACG
TTTTCACATATTTAAAGTTGAAATACTCCATACAGGCACAGGTCTAACAAGAAGACAACG
CATTCGATAAAACTAATCGTGGTAATTTTTATATCGCTGCTAGCCACTACCAACAATGTA
CAATTTT
>WashU_Skud_Contig2050.4 YOR176W 5' untranslated region, Contig c2050 12271 - 14270(revcom), 2000 bp (revcom)
TCTTAGTTTATAGCTTTTCTACTACTCTGGTCATAAACGAACAGAAGATAAGCAAGAAAT
CTTTTTTTCCTTCTTTTACGGTCTATTCAAGTGAAGCACGGGGATTCCCGCTTGTTTAAT
AATCAGACCAACAATGATATTGACCGACCAAAAGAAGTATTCCTTCGCGTGCTTCTCCTT
TCTGTGTCAAATCCCCTACTGAAAAAGCAGCATTGGGAAAGGAACAGCAGCTTCTCCTTC
GTCGCAGAGAGCTCGCGGTAGCATTTCATTGTCAGGTATTTATGATATTTGCTAAGAATA
ATTAAAATGTCTTCAGGTCTTGCACATACTCCTACATATTTGTAAGTATTTTACTGATTT
GAGTATATAAAAGCCGTACTAAAACTAACCAGCACCTGTAGCAAGGTGCAAAATGTTGAA
CCTTTCCGAAATTTATTGCCAGAAACCAAGAGCTAAAAGTGCTTGGTAAAAGTGAAAAGA
CTCTTTTTCAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGTTCCATCTGTTCAACAAA
ACAGCTTCACTGGATCTTTCAAAGTGCGCGTCGAAACCACAAACCGTCGAAAATATTGAT
CATCTAAATAAAGGGTTCTTATTTGCACAGTTTCGCATTGAAATATTCCATTCAGGCACA
GATCAACAAGAAGACAAAAAGGTATTCGAGAAGACTAATTGTGGTATTTTTACTTTGCTG
CTGACCA
>WashU_Sbay_Contig480.2 YOR176W 5' untranslated region, Contig c480 3444 - 5443(revcom), 2000 bp (revcom)
TTTCAGGGAAGCACCATGTGCACGAATTGTTCTAGAAAGCATTTTTGGTTCGTAAATTCT
CTACAACTGAACTTATTAACAAATAGCAAACAGAGAAGAAAATTTTTTTTTTCCTTCTTG
TATGGTCAGTTAGTTGAAAACACGGAGATTTTCACTTGTTTAGTAAGCAGAGCCATAATG
CTCTTGACCGACCAAAAGAAGTATTCCTACGCGAGCTCCCTCTTCAAGTGCCAAATCCCC
TACTGAAAAAAGCAACATGAGAAGCAAAGAGATGCCTCTCGCCATGCAGGGCTTGCGGTC
ATGTTTTCTACGTTCAATTGATTTTGTTACAGCTGAAAGATGTTTATAAAACTGTCTTGC
ATATGCTCTATTTACTTGTAAACAATTTTATTAAGTTGCGTATATATGATCGTACTAAAA
ATTGGCTGGCGCGTTCTCCAGGCAGAGTTGGTTGAACCTTGCTCGAATTGATAGCTCAAA
GTGGAGAGACTCTTTTTTAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGCTCCACCTG
TTCAACAAAATGGCAGAGATCTTTCGAAGTGCGCGTCGAAACCACAAACCATCAAAAATA
TCGACCATCTAAATAAAGGGTTCTTGTTTGAATAAATATCAGGCGAAGCTCTTCATACAG
GCACAGGTCAGATAAGAAGACAATTCGAATTCGAGAAGGATATTCGTGGTATCTTTAATC
TGCTGCT
BioPerl-1.007002/t/data/map_hem/HEM14-HEM15.meme.txt000444000766000024     11542013155576321 21357 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM14-HEM15.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YER014W         1.0000    322  MIT_Spar_c425_6072       1.0000    322  
MIT_Smik_c283_5928       1.0000    322  MIT_Sbay_c84_6418        1.0000    322  
SGD_Scer_YOR176W         1.0000    727  MIT_Spar_c278_20970      1.0000    727  
MIT_Smik_c935_20455      1.0000    727  WashU_Skud_Contig2050.4  1.0000    727  
WashU_Sbay_Contig480.2   1.0000    727  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM14-HEM15.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            4923    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.317 C 0.183 G 0.183 T 0.317 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 199   E-value = 3.0e-025
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  ::::1aa7:4a:aa92:1:1
pos.-specific     C  a:4a::::a6:a:::662:9
probability       G  :6::9::3::::::12:71:
matrix            T  :46:::::::::::::4:9:

         bits    2.5 *  *    *  *        
                 2.3 *  *    *  *        
                 2.0 *  **   *  *       *
                 1.8 *  **   *  *       *
Information      1.5 *  **** * ****     *
content          1.3 *  **** * *****  ***
(31.9 bits)      1.0 *************** ****
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CGTCGAAACCACAAACCGTC
consensus             TC    G A     ATC  
sequence                            G    
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2050.4      +    569  3.57e-13 TCAAAGTGCG CGTCGAAACCACAAACCGTC GAAAATATTG
MIT_Spar_c278_20970          +    563  3.57e-13 TCGAATTGCG CGTCGAAACCACAAACCGTC GAAAATAATG
SGD_Scer_YOR176W             +    561  3.57e-13 TCACATTGCG CGTCGAAACCACAAACCGTC GAAAACAATG
WashU_Sbay_Contig480.2       +    574  2.79e-11 TCGAAGTGCG CGTCGAAACCACAAACCATC AAAAATATCG
MIT_Smik_c935_20455          +    547  3.89e-11 TCCAATTGCG CGTCAAAACCACAAACCGTC GAAAATAATG
SGD_Scer_YER014W             +    122  5.95e-11 TACTCCGCGA CTCCGAAGCAACAAAGTGTC GAAGGCAAGT
MIT_Spar_c425_6072           +    121  1.08e-10 TACTCCGCGA CTCCGAAGCAACAAAATGTC GAAGGCAAGA
MIT_Sbay_c84_6418            +    114  2.44e-10 TACTCTGCGA CTCCGAAACAACAAAATCTC GAAGGCAAGC
MIT_Smik_c283_5928           +    118  2.73e-09 TAAATACGGA CTCCGAAGCAACAAGGTCGA AGGCAAGCTG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2050.4           3.6e-13  568_[+1]_139
MIT_Spar_c278_20970               3.6e-13  562_[+1]_145
SGD_Scer_YOR176W                  3.6e-13  560_[+1]_147
WashU_Sbay_Contig480.2            2.8e-11  573_[+1]_134
MIT_Smik_c935_20455               3.9e-11  546_[+1]_161
SGD_Scer_YER014W                    6e-11  121_[+1]_181
MIT_Spar_c425_6072                1.1e-10  120_[+1]_182
MIT_Sbay_c84_6418                 2.4e-10  113_[+1]_189
MIT_Smik_c283_5928                2.7e-09  117_[+1]_185
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Skud_Contig2050.4  (  569) CGTCGAAACCACAAACCGTC  1 
MIT_Spar_c278_20970      (  563) CGTCGAAACCACAAACCGTC  1 
SGD_Scer_YOR176W         (  561) CGTCGAAACCACAAACCGTC  1 
WashU_Sbay_Contig480.2   (  574) CGTCGAAACCACAAACCATC  1 
MIT_Smik_c935_20455      (  547) CGTCAAAACCACAAACCGTC  1 
SGD_Scer_YER014W         (  122) CTCCGAAGCAACAAAGTGTC  1 
MIT_Spar_c425_6072       (  121) CTCCGAAGCAACAAAATGTC  1 
MIT_Sbay_c84_6418        (  114) CTCCGAAACAACAAAATCTC  1 
MIT_Smik_c283_5928       (  118) CTCCGAAGCAACAAGGTCGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 3.0e-025 
  -982    251   -982   -982 
  -982   -982    166     45 
  -982    134   -982     78 
  -982    251   -982   -982 
  -154   -982    234   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
   104   -982     92   -982 
  -982    251   -982   -982 
    45    166   -982   -982 
   162   -982   -982   -982 
  -982    251   -982   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
   145   -982    -66   -982 
   -55    166     34   -982 
  -982    166   -982     45 
  -154     34    192   -982 
  -982   -982    -66    145 
  -154    234   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.0e-025 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.555556  0.444444 
 0.000000  0.444444  0.000000  0.555556 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.666667  0.000000  0.333333  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.444444  0.555556  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.222222  0.555556  0.222222  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 0.111111  0.222222  0.666667  0.000000 
 0.000000  0.000000  0.111111  0.888889 
 0.111111  0.888889  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
C[GT][TC]CGAA[AG]C[CA]ACAAA[CAG][CT][GC]TC
--------------------------------------------------------------------------------




Time  2.80 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 169   E-value = 2.7e-014
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  ::::1::1133:1:::::3:
pos.-specific     C  :99::9:9::36279167::
probability       G  ::::::9:813:::::::::
matrix            T  a11a911:16:47319437a

         bits    2.5                     
                 2.3                     
                 2.0  **  ***      *     
                 1.8  **  ***      *     
Information      1.5 **** ***      *    *
content          1.3 **** ****    *** * *
(27.1 bits)      1.0 *********  * ***** *
                 0.8 ********* ** *******
                 0.5 ********* **********
                 0.3 ********************
                 0.0 --------------------

Multilevel           TCCTTCGCGTACTCCTCCTT
consensus                     ACTCT  TTA 
sequence                       G         
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c935_20455          +    152  1.72e-12 ACCAAAAGAC TCCTTCGCGTCCTCCTTCTT CAAGTCTCAT
MIT_Spar_c278_20970          +    157  1.72e-12 CTAAAAGTAT TCCTTCGCGTCCTCCTTCTT CAATCCCATA
SGD_Scer_YOR176W             +    155  1.72e-12 CCAAAAGTAT TCCTTCGCGTCCTCCTTCTT CAATCCCATA
WashU_Skud_Contig2050.4      +    161  4.74e-12 AAAGAAGTAT TCCTTCGCGTGCTTCTCCTT TCTGTGTCAA
WashU_Sbay_Contig480.2       +    205  6.16e-10 AAAGAAGTAT TCCTACGCGAGCTCCCTCTT CAAGTGCCAA
MIT_Spar_c425_6072           +     59  2.17e-09 TGAATTGGTA TCCTTCGCGGATCTCTCTAT TGTTCTCTCT
SGD_Scer_YER014W             +     59  3.35e-08 TGAATTGGTG TTCTTCGCGAATATCTCTAT TGTTCTCTCT
MIT_Sbay_c84_6418            +     65  9.53e-08 TCCTTTCGCA TCCTTCTATTGTTCTTCCTT ATTGTTCTCG
MIT_Smik_c283_5928           +     61  1.51e-07 TAAACTGCTA TCTTTTGCAAATCCCTCTAT TGTTCTTTCC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c935_20455               1.7e-12  151_[+2]_556
MIT_Spar_c278_20970               1.7e-12  156_[+2]_551
SGD_Scer_YOR176W                  1.7e-12  154_[+2]_553
WashU_Skud_Contig2050.4           4.7e-12  160_[+2]_547
WashU_Sbay_Contig480.2            6.2e-10  204_[+2]_503
MIT_Spar_c425_6072                2.2e-09  58_[+2]_244
SGD_Scer_YER014W                  3.3e-08  58_[+2]_244
MIT_Sbay_c84_6418                 9.5e-08  64_[+2]_238
MIT_Smik_c283_5928                1.5e-07  60_[+2]_242
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
MIT_Smik_c935_20455      (  152) TCCTTCGCGTCCTCCTTCTT  1 
MIT_Spar_c278_20970      (  157) TCCTTCGCGTCCTCCTTCTT  1 
SGD_Scer_YOR176W         (  155) TCCTTCGCGTCCTCCTTCTT  1 
WashU_Skud_Contig2050.4  (  161) TCCTTCGCGTGCTTCTCCTT  1 
WashU_Sbay_Contig480.2   (  205) TCCTACGCGAGCTCCCTCTT  1 
MIT_Spar_c425_6072       (   59) TCCTTCGCGGATCTCTCTAT  1 
SGD_Scer_YER014W         (   59) TTCTTCGCGAATATCTCTAT  1 
MIT_Sbay_c84_6418        (   65) TCCTTCTATTGTTCTTCCTT  1 
MIT_Smik_c283_5928       (   61) TCTTTTGCAAATCCCTCTAT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 2.7e-014 
  -982   -982   -982    162 
  -982    234   -982   -154 
  -982    234   -982   -154 
  -982   -982   -982    162 
  -154   -982   -982    145 
  -982    234   -982   -154 
  -982   -982    234   -154 
  -154    234   -982   -982 
  -154   -982    215   -154 
     4   -982    -66     78 
     4     92     92   -982 
  -982    166   -982     45 
  -154     34   -982    104 
  -982    192   -982      4 
  -982    234   -982   -154 
  -982    -66   -982    145 
  -982    166   -982     45 
  -982    192   -982      4 
     4   -982   -982    104 
  -982   -982   -982    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.7e-014 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.000000  0.000000  1.000000 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.000000  0.888889  0.111111 
 0.111111  0.888889  0.000000  0.000000 
 0.111111  0.000000  0.777778  0.111111 
 0.333333  0.000000  0.111111  0.555556 
 0.333333  0.333333  0.333333  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 0.111111  0.222222  0.000000  0.666667 
 0.000000  0.666667  0.000000  0.333333 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  0.666667  0.000000  0.333333 
 0.333333  0.000000  0.000000  0.666667 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
TCCTTCGCG[TA][ACG][CT][TC][CT]CT[CT][CT][TA]T
--------------------------------------------------------------------------------




Time  5.45 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =   9   llr = 159   E-value = 1.6e-009
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :1:12::::23:1:8:1:2:
pos.-specific     C  :::4291:6:1:21219:::
probability       G  1:8::::6::6::9:8::8:
matrix            T  9924619448:a7::1:a:a

         bits    2.5                     
                 2.3                     
                 2.0      *       *  *   
                 1.8      *       *  *   
Information      1.5   *  *     * * *****
content          1.3 * *  **    * * *****
(25.4 bits)      1.0 ***  ****  * *******
                 0.8 ***  ******* *******
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TTGCTCTGCTGTTGAGCTGT
consensus              TTA  TTAA C C   A 
sequence                 C               
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c935_20455          +    482  3.60e-13 TCAGCTTTTT TTGCTCTGCTGTTGAGCTGT TTTACTTCAT
MIT_Spar_c278_20970          +    498  5.54e-13 TTAGCTTTTT TTGCCCTGCTGTTGAGCTGT TTTGCTTCAC
WashU_Sbay_Contig480.2       +    508  1.71e-12 TAGCTGTTTT TTGTTCTGCTGTTGAGCTGT TTTGCTCCAC
WashU_Skud_Contig2050.4      +    499  1.71e-12 CAGCTGTTTT TTGTTCTGCTGTTGAGCTGT TTTGTTCCAT
SGD_Scer_YOR176W             +    496  3.87e-12 TTAGCTTTTT TTGTCCTGCTGTTGAGCTGT TTTGCTTTAC
MIT_Sbay_c84_6418            +      8  1.48e-07    TGTCGAA GTTCTCCTTTATTCCGCTGT TTCTTACGGA
SGD_Scer_YER014W             +     28  2.26e-07 GCGTTCTCAA TTGCACTTTACTCGATATGT TTGAATTGGT
MIT_Smik_c283_5928           +     19  2.82e-07 CTCTCTCCAC TATTTCTTTAATCGCGCTAT ACTAGATATG
MIT_Spar_c425_6072           -    281  8.96e-07 TCTATAATTA TTGAATTTTTATAGACCTAT ATTCATTCTT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c935_20455               3.6e-13  481_[+3]_226
MIT_Spar_c278_20970               5.5e-13  497_[+3]_210
WashU_Sbay_Contig480.2            1.7e-12  507_[+3]_200
WashU_Skud_Contig2050.4           1.7e-12  498_[+3]_209
SGD_Scer_YOR176W                  3.9e-12  495_[+3]_212
MIT_Sbay_c84_6418                 1.5e-07  7_[+3]_295
SGD_Scer_YER014W                  2.3e-07  27_[+3]_275
MIT_Smik_c283_5928                2.8e-07  18_[+3]_284
MIT_Spar_c425_6072                  9e-07  280_[-3]_22
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=9
MIT_Smik_c935_20455      (  482) TTGCTCTGCTGTTGAGCTGT  1 
MIT_Spar_c278_20970      (  498) TTGCCCTGCTGTTGAGCTGT  1 
WashU_Sbay_Contig480.2   (  508) TTGTTCTGCTGTTGAGCTGT  1 
WashU_Skud_Contig2050.4  (  499) TTGTTCTGCTGTTGAGCTGT  1 
SGD_Scer_YOR176W         (  496) TTGTCCTGCTGTTGAGCTGT  1 
MIT_Sbay_c84_6418        (    8) GTTCTCCTTTATTCCGCTGT  1 
SGD_Scer_YER014W         (   28) TTGCACTTTACTCGATATGT  1 
MIT_Smik_c283_5928       (   19) TATTTCTTTAATCGCGCTAT  1 
MIT_Spar_c425_6072       (  281) TTGAATTTTTATAGACCTAT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 1.6e-009 
  -982   -982    -66    145 
  -154   -982   -982    145 
  -982   -982    215    -55 
  -154    134   -982     45 
   -55     34   -982     78 
  -982    234   -982   -154 
  -982    -66   -982    145 
  -982   -982    166     45 
  -982    166   -982     45 
   -55   -982   -982    126 
     4    -66    166   -982 
  -982   -982   -982    162 
  -154     34   -982    104 
  -982    -66    234   -982 
   126     34   -982   -982 
  -982    -66    215   -154 
  -154    234   -982   -982 
  -982   -982   -982    162 
   -55   -982    215   -982 
  -982   -982   -982    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.6e-009 
 0.000000  0.000000  0.111111  0.888889 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  0.000000  0.777778  0.222222 
 0.111111  0.444444  0.000000  0.444444 
 0.222222  0.222222  0.000000  0.555556 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.555556  0.444444 
 0.000000  0.555556  0.000000  0.444444 
 0.222222  0.000000  0.000000  0.777778 
 0.333333  0.111111  0.555556  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.111111  0.222222  0.000000  0.666667 
 0.000000  0.111111  0.888889  0.000000 
 0.777778  0.222222  0.000000  0.000000 
 0.000000  0.111111  0.777778  0.111111 
 0.111111  0.888889  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.222222  0.000000  0.777778  0.000000 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
TT[GT][CT][TAC]CT[GT][CT][TA][GA]T[TC]G[AC]GCT[GA]T
--------------------------------------------------------------------------------




Time  7.97 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =   9   llr = 162   E-value = 7.2e-011
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  :412:::41:39:1aaa717
pos.-specific     C  :166::1:78::a4:::3::
probability       G  a4:2::612:71::::::91
matrix            T  ::3:aa34:2:::4:::::2

         bits    2.5 *           *       
                 2.3 *           *       
                 2.0 *           *     * 
                 1.8 *           *     * 
Information      1.5 *   **   *  * *** * 
content          1.3 *   **  ***** *** * 
(26.0 bits)      1.0 *   **  ***** ***** 
                 0.8 ******* ***** ***** 
                 0.5 ******* ************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GACCTTGACCGACCAAAAGA
consensus             GTA  TTGTA  T   C T
sequence                G                
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
SGD_Scer_YOR176W             +    133  2.43e-11 AGCCAAGAGT GACCTTGACCGACCAAAAGT ATTCCTTCGC
MIT_Spar_c278_20970          +    135  8.09e-11 AACCAAGAGT GACCTTGACCGACTAAAAGT ATTCCTTCGC
WashU_Sbay_Contig480.2       +    180  9.46e-11 GAGCCATAAT GCTCTTGACCGACCAAAAGA AGTATTCCTA
MIT_Smik_c935_20455          +    131  9.46e-11 GACCAACAGT GATCTTGGCCGACCAAAAGA CTCCTTCGCG
WashU_Skud_Contig2050.4      +    136  3.12e-10 GACCAACAAT GATATTGACCGACCAAAAGA AGTATTCCTT
MIT_Spar_c425_6072           +    156  3.11e-09 CAAGATGAAA GGCGTTTTGCAACTAAACGA GTAATGGCAG
MIT_Smik_c283_5928           +    151  1.64e-08 CAAGCTGAAA GGCATTTTACAACTAAACGA GCAATGGTAG
SGD_Scer_YER014W             +    157  1.64e-08 CAAGTTCAAA GGCGTTTTGTAACTAAACGA GCAATGGCAG
MIT_Sbay_c84_6418            -    203  3.27e-07 TCTCCAGTGA GGACTTCTCTGGCAAAAAAG TAGAATGACG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YOR176W                  2.4e-11  132_[+4]_575
MIT_Spar_c278_20970               8.1e-11  134_[+4]_573
WashU_Sbay_Contig480.2            9.5e-11  179_[+4]_528
MIT_Smik_c935_20455               9.5e-11  130_[+4]_577
WashU_Skud_Contig2050.4           3.1e-10  135_[+4]_572
MIT_Spar_c425_6072                3.1e-09  155_[+4]_147
MIT_Smik_c283_5928                1.6e-08  150_[+4]_152
SGD_Scer_YER014W                  1.6e-08  156_[+4]_146
MIT_Sbay_c84_6418                 3.3e-07  202_[-4]_100
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=9
SGD_Scer_YOR176W         (  133) GACCTTGACCGACCAAAAGT  1 
MIT_Spar_c278_20970      (  135) GACCTTGACCGACTAAAAGT  1 
WashU_Sbay_Contig480.2   (  180) GCTCTTGACCGACCAAAAGA  1 
MIT_Smik_c935_20455      (  131) GATCTTGGCCGACCAAAAGA  1 
WashU_Skud_Contig2050.4  (  136) GATATTGACCGACCAAAAGA  1 
MIT_Spar_c425_6072       (  156) GGCGTTTTGCAACTAAACGA  1 
MIT_Smik_c283_5928       (  151) GGCATTTTACAACTAAACGA  1 
SGD_Scer_YER014W         (  157) GGCGTTTTGTAACTAAACGA  1 
MIT_Sbay_c84_6418        (  203) GGACTTCTCTGGCAAAAAAG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 7.2e-011 
  -982   -982    251   -982 
    45    -66    134   -982 
  -154    166   -982      4 
   -55    166     34   -982 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -982    -66    166      4 
    45   -982    -66     45 
  -154    192     34   -982 
  -982    215   -982    -55 
     4   -982    192   -982 
   145   -982    -66   -982 
  -982    251   -982   -982 
  -154    134   -982     45 
   162   -982   -982   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
   104     92   -982   -982 
  -154   -982    234   -982 
   104   -982    -66    -55 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 7.2e-011 
 0.000000  0.000000  1.000000  0.000000 
 0.444444  0.111111  0.444444  0.000000 
 0.111111  0.555556  0.000000  0.333333 
 0.222222  0.555556  0.222222  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.111111  0.555556  0.333333 
 0.444444  0.000000  0.111111  0.444444 
 0.111111  0.666667  0.222222  0.000000 
 0.000000  0.777778  0.000000  0.222222 
 0.333333  0.000000  0.666667  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.444444  0.000000  0.444444 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.666667  0.333333  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.666667  0.000000  0.111111  0.222222 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
G[AG][CT][CAG]TT[GT][AT][CG][CT][GA]AC[CT]AAA[AC]G[AT]
--------------------------------------------------------------------------------




Time 10.39 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 144   E-value = 1.4e-003
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  a6a:::1:191169877a82
pos.-specific     C  ::::7a6a1:71:::11::2
probability       G  ::::::::2:1341221:26
matrix            T  :4:a3:3:6114::::1:::

         bits    2.5      * *            
                 2.3      * *            
                 2.0      * *            
                 1.8      * *            
Information      1.5 * ** * *         *  
content          1.3 * **** *     *   *  
(23.0 bits)      1.0 * **** * *  ***  ** 
                 0.8 ******** ** **** ***
                 0.5 ******** ** **** ***
                 0.3 ********************
                 0.0 --------------------

Multilevel           AAATCCCCTACTAAAAAAAG
consensus             T  T T G  GG GG  GA
sequence                                C
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig480.2       +    233  5.39e-12 TTCAAGTGCC AAATCCCCTACTGAAAAAAG CAACATGAGA
MIT_Spar_c278_20970          +    184  1.13e-11 CTTCAATCCC ATATCCCCTACTGAAAAAAG CAGCGTGCGA
SGD_Scer_YOR176W             +    182  1.61e-11 CTTCAATCCC ATATCCCCTACGAAAAAAAG CAGCATGAGA
WashU_Skud_Contig2050.4      +    189  2.93e-10 TTTCTGTGTC AAATCCCCTACTGAAAAAGC AGCATTGGGA
MIT_Smik_c935_20455          +    180  2.45e-09 TTCAAGTCTC ATATCCCCTACCAGAAAAAG TAGCAGGCGA
MIT_Spar_c425_6072           +    232  1.36e-07 TTTTCACATA AAATCCTCGAAGAAGGAAAA ATTGATAATC
MIT_Smik_c283_5928           +    228  5.40e-07 TTGTCCCACG AAATTCTCGTTGAAAGCAAG GTTCGTAAGG
MIT_Sbay_c84_6418            +    154  6.05e-07 TAAGGTAAAA ATATTCACCACTAAACGAGC AATGACAGTT
SGD_Scer_YER014W             +    236  1.24e-06 TTTCATGTAA AAATTCTCAAGAGAGATAAA GTTGTTAAAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig480.2            5.4e-12  232_[+5]_475
MIT_Spar_c278_20970               1.1e-11  183_[+5]_524
SGD_Scer_YOR176W                  1.6e-11  181_[+5]_526
WashU_Skud_Contig2050.4           2.9e-10  188_[+5]_519
MIT_Smik_c935_20455               2.5e-09  179_[+5]_528
MIT_Spar_c425_6072                1.4e-07  231_[+5]_71
MIT_Smik_c283_5928                5.4e-07  227_[+5]_75
MIT_Sbay_c84_6418                 6.1e-07  153_[+5]_149
SGD_Scer_YER014W                  1.2e-06  235_[+5]_67
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
WashU_Sbay_Contig480.2   (  233) AAATCCCCTACTGAAAAAAG  1 
MIT_Spar_c278_20970      (  184) ATATCCCCTACTGAAAAAAG  1 
SGD_Scer_YOR176W         (  182) ATATCCCCTACGAAAAAAAG  1 
WashU_Skud_Contig2050.4  (  189) AAATCCCCTACTGAAAAAGC  1 
MIT_Smik_c935_20455      (  180) ATATCCCCTACCAGAAAAAG  1 
MIT_Spar_c425_6072       (  232) AAATCCTCGAAGAAGGAAAA  1 
MIT_Smik_c283_5928       (  228) AAATTCTCGTTGAAAGCAAG  1 
MIT_Sbay_c84_6418        (  154) ATATTCACCACTAAACGAGC  1 
SGD_Scer_YER014W         (  236) AAATTCTCAAGAGAGATAAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 1.4e-003 
   162   -982   -982   -982 
    78   -982   -982     45 
   162   -982   -982   -982 
  -982   -982   -982    162 
  -982    192   -982      4 
  -982    251   -982   -982 
  -154    166   -982      4 
  -982    251   -982   -982 
  -154    -66     34     78 
   145   -982   -982   -154 
  -154    192    -66   -154 
  -154    -66     92     45 
    78   -982    134   -982 
   145   -982    -66   -982 
   126   -982     34   -982 
   104    -66     34   -982 
   104    -66    -66   -154 
   162   -982   -982   -982 
   126   -982     34   -982 
   -55     34    166   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.4e-003 
 1.000000  0.000000  0.000000  0.000000 
 0.555556  0.000000  0.000000  0.444444 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.666667  0.000000  0.333333 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.555556  0.000000  0.333333 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.111111  0.222222  0.555556 
 0.888889  0.000000  0.000000  0.111111 
 0.111111  0.666667  0.111111  0.111111 
 0.111111  0.111111  0.333333  0.444444 
 0.555556  0.000000  0.444444  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.666667  0.111111  0.222222  0.000000 
 0.666667  0.111111  0.111111  0.111111 
 1.000000  0.000000  0.000000  0.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.222222  0.222222  0.555556  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
A[AT]AT[CT]C[CT]C[TG]AC[TG][AG]A[AG][AG]AA[AG][GAC]
--------------------------------------------------------------------------------




Time 12.73 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YER014W                 3.19e-19  27_[+3(2.26e-07)]_11_[+2(3.35e-08)]_43_[+1(5.95e-11)]_15_[+4(1.64e-08)]_59_[+5(1.24e-06)]_67
MIT_Spar_c425_6072               4.24e-21  58_[+2(2.17e-09)]_42_[+1(1.08e-10)]_15_[+4(3.11e-09)]_56_[+5(1.36e-07)]_29_[-3(8.96e-07)]_22
MIT_Smik_c283_5928               2.54e-17  18_[+3(2.82e-07)]_22_[+2(1.51e-07)]_37_[+1(2.73e-09)]_13_[+4(1.64e-08)]_57_[+5(5.40e-07)]_28_[-3(2.96e-05)]_27
MIT_Sbay_c84_6418                1.73e-17  7_[+3(1.48e-07)]_37_[+2(9.53e-08)]_29_[+1(2.44e-10)]_20_[+5(6.05e-07)]_29_[-4(3.27e-07)]_100
SGD_Scer_YOR176W                 1.87e-35  132_[+4(2.43e-11)]_2_[+2(1.72e-12)]_7_[+5(1.61e-11)]_294_[+3(3.87e-12)]_45_[+1(3.57e-13)]_147
MIT_Spar_c278_20970              6.54e-36  134_[+4(8.09e-11)]_2_[+2(1.72e-12)]_7_[+5(1.13e-11)]_155_[-2(5.46e-05)]_119_[+3(5.54e-13)]_45_[+1(3.57e-13)]_145
MIT_Smik_c935_20455              7.71e-32  130_[+4(9.46e-11)]_1_[+2(1.72e-12)]_8_[+5(2.45e-09)]_282_[+3(3.60e-13)]_45_[+1(3.89e-11)]_161
WashU_Skud_Contig2050.4          4.20e-33  135_[+4(3.12e-10)]_5_[+2(4.74e-12)]_8_[+5(2.93e-10)]_290_[+3(1.71e-12)]_50_[+1(3.57e-13)]_69_[-3(1.35e-06)]_50
WashU_Sbay_Contig480.2           1.98e-31  40_[-4(5.82e-05)]_119_[+4(9.46e-11)]_5_[+2(6.16e-10)]_8_[+5(5.39e-12)]_255_[+3(1.71e-12)]_46_[+1(2.79e-11)]_134
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM14.ups.fa_000444000766000024       515213155576321 20334 0ustar00cjfieldsstaff000000000000>SGD_Scer_YER014W HEM14 "Protoporphyrinogen oxidase, a mitochondrial enzyme that catalyzes the seventh step in the heme biosynthetic pathway, converting protoporphyrinogen IX to protoporphyrin IX"
TATACAAGCTCTTTTTGGCGTTCTCAATTGCACTTTACTCGATATGTTTGAATTGGTGTT
CTTCGCGAATATCTCTATTGTTCTCTCTATTATACTATTTCTTTTTTTGAATACTCCGCG
ACTCCGAAGCAACAAAGTGTCGAAGGCAAGTTCAAAGGCGTTTTGTAACTAAACGAGCAA
TGGCAGCTTTCAATTAAAGAAAGGTTAGCGTTACTCTGTGATTTTTTTCATGTAAAAATT
CTCAAGAGAGATAAAGTTGTTAAAAAATTAAATATAGGTCTATAAAACTCGATAATTATA
ATGCATAAAAAGCTAACAATGT
>MIT_Spar_c425_6072 YER014W 5' untranslated region, Contig c425 34016 - 36015, 2000 bp (revcom)
TATTCGAGCCCTTTCCCGCGTTCCCAATTGTACCTTCCTCGATAGGATTGAATTGGTATC
CTTCGCGGATCTCTCTATTGTTCTCTCTATTATTCTTTTTCTTTTTTAAATACTCCGCGA
CTCCGAAGCAACAAAATGTCGAAGGCAAGATGAAAGGCGTTTTGCAACTAAACGAGTAAT
GGCAGCTTTTAATTAAATAACGGTCAGCATTACTCTATAACTTTTCACATAAAATCCTCG
AAGAAGGAAAAATTGATAATCAATTTACCGAAGAATGAATATAGGTCTATAAAAATTCAA
TAATTATAGATGCATAAAAAGC
>MIT_Smik_c283_5928 YER014W 5' untranslated region, Contig c283 42606 - 44605, 2000 bp (revcom)
TATTGAAGCTCTCTCCACTATTTCTTTAATCGCGCTATACTAGATATGGTTAAACTGCTA
TCTTTTGCAAATCCCTCTATTGTTCTTTCCATTACTCTTTTCTTTTTTAAATACGGACTC
CGAAGCAACAAGGTCGAAGGCAAGCTGAAAGGCATTTTACAACTAAACGAGCAATGGTAG
CTTTTGATTGAATAAATTATTATCATTATTTTGTTATTTGTCCCACGAAATTCTCGTTGA
AAGCAAGGTTCGTAAGGATTTATCAAATGTTAAATATAGATCTATAAAAATTGAATAGTA
ATAATAACAAGGGATGGTGTTA
>MIT_Sbay_c84_6418 YER014W 5' untranslated region, Contig c84 10802 - 12801(revcom), 2000 bp (revcom)
TGTCGAAGTTCTCCTTTATTCCGCTGTTTCTTACGGAATCCAGCGAGACTGTTGTCCTTT
CGCATCCTTCTATTGTTCTTCCTTATTGTTCTCGTTTTTTTTATACTCTGCGACTCCGAA
ACAACAAAATCTCGAAGGCAAGCTAAGGTAAAAATATTCACCACTAAACGAGCAATGACA
GTTATATTCAAACGTCATTCTACTTTTTTGCCAGAGAAGTCCTCACTGGAGACGAAGTTG
GTAAATGCTTTATTTATATTAAACGTAGATCTATAAAGTTTAAATAGTTTATAATGCTTA
ACAAGGGACGATGTTATCTCTT
>WashU_Scas_Contig614.8 YER014W 5' untranslated region, Contig c614 13890 - 15889(revcom), 2000 bp (revcom)
CTGATTCAATTGTTCGTGTGTATGTTCTTGAAAGCCCTTGCAACGGTGTTCAGGTTGTTC
TGATTCTTCTCCCTGTTTATGTGCTGCTGTCTCGAGAAATGAAGACACATTTTTCAAGAT
CCGAAGCTTATACGATTCTCACGGGACAAACAATGGGCGTTTCATATGTAGACAATTTGC
AAGTCAAAAAGAACGCCAATCTTTCACCAGAATATATTAATATATGAAATATATATGTGC
CTATAAATACTACCTTTTGACACCCAATGCTCTTTCTCTTGATTGTCTAATGGAACTTAA
CCTCCAAGAATTTTGATCTTTA
>WashU_Sklu_Contig2060.2 YER014W 5' untranslated region, Contig c2060 550 - 2549, 2000 bp (revcom)
TGAATACACTTTACTACTTCACCTTTTCGTACTTTCAATAGTTTGTAATTCAATCGTTTG
CAAATACTATGTTTCCTTTTTTTTTTTTCACCATTCCGTCATTACACTCCTATACGAGAA
ATACATACTAAAATAAAAAAAAAAAAAAAAGCTTATGTAATCTATCTCTTGATACCCAAA
GCTCTTTCCTTTGACTGTCTGATGGAGCTCAACCTCCAAGAGTCCTGATCCTTTGCAAAC
TTGTTGTGAAGAGGAACGATCTTAGCCTTTTTCCTGCTTTCACTATCTGCACCTGCAACT
TTATAATAGTGAGGAGCACTTT
BioPerl-1.007002/t/data/map_hem/HEM14.ups.fa_.revcom000444000766000024       341313155576321 21624 0ustar00cjfieldsstaff000000000000>SGD_Scer_YER014W HEM14 "Protoporphyrinogen oxidase, a mitochondrial enzyme that catalyzes the seventh step in the heme biosynthetic pathway, converting protoporphyrinogen IX to protoporphyrin IX"
ACATTGTTAGCTTTTTATGCATTATAATTATCGAGTTTTATAGACCTATATTTAATTTTT
TAACAACTTTATCTCTCTTGAGAATTTTTACATGAAAAAAATCACAGAGTAACGCTAACC
TTTCTTTAATTGAAAGCTGCCATTGCTCGTTTAGTTACAAAACGCCTTTGAACTTGCCTT
CGACACTTTGTTGCTTCGGAGTCGCGGAGTATTCAAAAAAAGAAATAGTATAATAGAGAG
AACAATAGAGATATTCGCGAAGAACACCAATTCAAACATATCGAGTAAAGTGCAATTGAG
AACGCCAAAAAGAGCTTGTATA
>MIT_Spar_c425_6072 YER014W 5' untranslated region, Contig c425 34016 - 36015, 2000 bp (revcom)
GCTTTTTATGCATCTATAATTATTGAATTTTTATAGACCTATATTCATTCTTCGGTAAAT
TGATTATCAATTTTTCCTTCTTCGAGGATTTTATGTGAAAAGTTATAGAGTAATGCTGAC
CGTTATTTAATTAAAAGCTGCCATTACTCGTTTAGTTGCAAAACGCCTTTCATCTTGCCT
TCGACATTTTGTTGCTTCGGAGTCGCGGAGTATTTAAAAAAGAAAAAGAATAATAGAGAG
AACAATAGAGAGATCCGCGAAGGATACCAATTCAATCCTATCGAGGAAGGTACAATTGGG
AACGCGGGAAAGGGCTCGAATA
>MIT_Smik_c283_5928 YER014W 5' untranslated region, Contig c283 42606 - 44605, 2000 bp (revcom)
TAACACCATCCCTTGTTATTATTACTATTCAATTTTTATAGATCTATATTTAACATTTGA
TAAATCCTTACGAACCTTGCTTTCAACGAGAATTTCGTGGGACAAATAACAAAATAATGA
TAATAATTTATTCAATCAAAAGCTACCATTGCTCGTTTAGTTGTAAAATGCCTTTCAGCT
TGCCTTCGACCTTGTTGCTTCGGAGTCCGTATTTAAAAAAGAAAAGAGTAATGGAAAGAA
CAATAGAGGGATTTGCAAAAGATAGCAGTTTAACCATATCTAGTATAGCGCGATTAAAGA
AATAGTGGAGAGAGCTTCAATA
>MIT_Sbay_c84_6418 YER014W 5' untranslated region, Contig c84 10802 - 12801(revcom), 2000 bp (revcom)
AAGAGATAACATCGTCCCTTGTTAAGCATTATAAACTATTTAAACTTTATAGATCTACGT
TTAATATAAATAAAGCATTTACCAACTTCGTCTCCAGTGAGGACTTCTCTGGCAAAAAAG
TAGAATGACGTTTGAATATAACTGTCATTGCTCGTTTAGTGGTGAATATTTTTACCTTAG
CTTGCCTTCGAGATTTTGTTGTTTCGGAGTCGCAGAGTATAAAAAAAACGAGAACAATAA
GGAAGAACAATAGAAGGATGCGAAAGGACAACAGTCTCGCTGGATTCCGTAAGAAACAGC
GGAATAAAGGAGAACTTCGACA
BioPerl-1.007002/t/data/map_hem/HEM15.ups.fa_000444000766000024      1203613155576321 20354 0ustar00cjfieldsstaff000000000000>SGD_Scer_YOR176W HEM15 "Ferrochelatase, a mitochondrial inner membrane protein, catalyzes the insertion of ferrous iron into protoporphyrin IX, the eighth and final step in the heme biosynthetic pathway; Yfh1p mediates the use of iron by Hem15p"
TCTTTAAACGTTCTTTTTTTTACTGCTAAATTTGTCCAAATAGCAGGTATGTGTTAAATA
TTTCTGTACTTCTTGTAAACCGACTCAAGTGGAACACGAGAATTTACGCTTGTTTGGTGT
CAAGCCAAGAGTGACCTTGACCGACCAAAAGTATTCCTTCGCGTCCTCCTTCTTCAATCC
CATATCCCCTACGAAAAAAAGCAGCATGAGAAAACGAAGGGCAGCAACTCCTTCGTCATA
TAAGGCTTACGGTGACCATTGAAGATTGGGCATGTCTAACGGCTATTGCCAGCGGAGATG
TTTCAAGGCATCCTACACATGCTACATATTTGTAATTATTTTACTGAGTTTGTGTATATA
AAAAACTTTTTTAAAAAAAAAAAATGGCCAGCATCCTCTTTCATGTAAAGCTGTTGAACC
TTCCTGAAATTTACTTCTAAAATTGTTCAGTAAAACTGCTTGTTAAAAGTGCGAAGAGTT
CTTTTTTAGCTTTTTTTGTCCTGCTGTTGAGCTGTTTTGCTTTACTGTTCAACAAAACAT
TGAAGATCTTTCACATTGCGCGTCGAAACCACAAACCGTCGAAAACAATGGTCATCTAAA
TAAAGGGTTCTTATTAAACAGATTTAAAGCCAAGGACAAAATACAGGCACAGGTCAAGCA
AGAAGACAAACCGCATACGCCAAGACAAACCGTGGTGATTTAATTCTGCTGCTGATCGCT
TCCAACA
>MIT_Spar_c278_20970 YOR176W 5' untranslated region, Contig c278 32746 - 34745, 2000 bp (revcom)
TCTTCAAACGTTCTTTTCCTACTACTAAGCTTTTCAATAAATAGCGGGTATATGCTAAAT
ACTTCTTTGCTTCTTGTACGACCTACTTAATTGAAATACGGATATTTTTGCTTGCTTGGT
GCCAAACCAAGAGTGACCTTGACCGACTAAAAGTATTCCTTCGCGTCCTCCTTCTTCAAT
CCCATATCCCCTACTGAAAAAAGCAGCGTGCGAAAATGAAGGGCAGCAACTCCTTCGTCA
TATAAGGCTTAGGTAATCTTTCAAGGTCAGGTATATCCAGCTGTCGTTACGAGTAGAGAT
ATTTCAAGCTGTCCTGCACATGCTACATATTTGTGATTATTTTTATTGAGTTGCGTATAT
AAAAAAACAATCTAAAAAAAAAAAAAATGGCCAGCATCTTCTTCCATGTAAAGCTGTTGA
ACCTTGCTAAAATCTATTACTATAATTGTTCAGTAAAGTTGCTTGTTAAAAATGCGAAGA
GTCTTTTTTAGCTTTTTTTGCCCTGCTGTTGAGCTGTTTTGCTTCACTGTTCAACAAAAC
AGTGAAGATCTTTCGAATTGCGCGTCGAAACCACAAACCGTCGAAAATAATGGTCATCTA
AATAAAGGGTTCTTATTTGAACAGATTTAAAGCTCAAAGACACGATACAGGCACAGGTCC
AGAAAGAATACAAAACGCAAACGCCAAGACAAATTGTGGTAATTTCATTCTGCTGCTGAT
CACTGCC
>MIT_Smik_c935_20455 YOR176W 5' untranslated region, Contig c935 1803 - 3802(revcom), 2000 bp (revcom)
TCTTGAATTGCAATTTTCTACTACTGAAGTTACCAACAATTAGCAAATATGTGATGAGTC
CTTTTTACGTTCTTGTATAACCTAAGTTAAATACAAAGGTTTATGCTCCTTTAATGATCA
GACCAACAGTGATCTTGGCCGACCAAAAGACTCCTTCGCGTCCTCCTTCTTCAAGTCTCA
TATCCCCTACCAGAAAAAGTAGCAGGCGAAAATAAAGAGCAACTGCTCCCCCCCATATAG
AGCTTACCATAATTTCTCAAGGAAAGGTATCTCCAGTTGTCGTAAAGAATAAAGAAGTTT
CAACGTGTCCTGCATGTTCTACAAATTTGCAATTGACTTTACTAAGTTGCATATATAAAA
CTTGTATTAGATAAGTTAGCCAGCATTTTCATTCAAGCTAAGATGTTGAATATGCCAAAG
CACATTGCTGAAATTAATCAGTAAAGCTGCTTGCTGAAAGTGGAAATATTTTCAGCTTTT
TTTGCTCTGCTGTTGAGCTGTTTTACTTCATTGTTCAACAAAACAATAGAGTTCTCTCCA
ATTGCGCGTCAAAACCACAAACCGTCGAAAATAATGATCATCTAAATAAAAGAGTTCACG
TTTTCACATATTTAAAGTTGAAATACTCCATACAGGCACAGGTCTAACAAGAAGACAACG
CATTCGATAAAACTAATCGTGGTAATTTTTATATCGCTGCTAGCCACTACCAACAATGTA
CAATTTT
>WashU_Scas_Contig526.5 YOR176W 5' untranslated region, Contig c526 10822 - 11487(revcom), 2000 bp (revcom)
TGTTCTCCTTACTCTTCTGATTGTAGCTTTGAATAAGAGAGTCTCACAACTTCAATTGGG
TATCCTTGGGTATGACGATTCAATTAAAGTGATATAACAAAGCTTTTATGTTTGTGTGCT
TAGTAATTAGACATGGGAAAAAAGACCGTTGTGCAGTGTACAAAGGTCAAATCCGTGATA
AGTGAGAAAAATCCAAAAATTGGCCTAAGGGCTTCCTTAATTTTTTCAATAACCCGAATG
GCTAAAAATCATGGGGGCATCAGGGTAATTTTTATAGGGCGAAAATCATTGATGTAAGCA
GGTAAATGTAGAAGTAACCTTTATTTAGACATATATTATATATATCATTCCAAGTTGAGT
TCCTTTGTTAATCTTAAAGCATCATTTAAAGTACAATCTGTGATATTGATTGACCCCAAT
TTAATTCTAAGTAAGAAGGACCGTATGATACAAAGATCCTCAAACATTTGATCTGAGAGT
TGGCTTTTTCTTTTGTCAAATATTTGTGCCGCCAAGCTGAACAGTCTCTCAGCATGAATC
GATGTCGATGGAATACAATGGAATAATTTATTAGCTAATGATAACAGTGGAAACTCTCTT
TTATGCCTTGACCAGAATATATTATCTGCCCCCACAATCATCTGGACTTGGCGGTCGAAT
GGCGAC
>WashU_Skud_Contig2050.4 YOR176W 5' untranslated region, Contig c2050 12271 - 14270(revcom), 2000 bp (revcom)
TCTTAGTTTATAGCTTTTCTACTACTCTGGTCATAAACGAACAGAAGATAAGCAAGAAAT
CTTTTTTTCCTTCTTTTACGGTCTATTCAAGTGAAGCACGGGGATTCCCGCTTGTTTAAT
AATCAGACCAACAATGATATTGACCGACCAAAAGAAGTATTCCTTCGCGTGCTTCTCCTT
TCTGTGTCAAATCCCCTACTGAAAAAGCAGCATTGGGAAAGGAACAGCAGCTTCTCCTTC
GTCGCAGAGAGCTCGCGGTAGCATTTCATTGTCAGGTATTTATGATATTTGCTAAGAATA
ATTAAAATGTCTTCAGGTCTTGCACATACTCCTACATATTTGTAAGTATTTTACTGATTT
GAGTATATAAAAGCCGTACTAAAACTAACCAGCACCTGTAGCAAGGTGCAAAATGTTGAA
CCTTTCCGAAATTTATTGCCAGAAACCAAGAGCTAAAAGTGCTTGGTAAAAGTGAAAAGA
CTCTTTTTCAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGTTCCATCTGTTCAACAAA
ACAGCTTCACTGGATCTTTCAAAGTGCGCGTCGAAACCACAAACCGTCGAAAATATTGAT
CATCTAAATAAAGGGTTCTTATTTGCACAGTTTCGCATTGAAATATTCCATTCAGGCACA
GATCAACAAGAAGACAAAAAGGTATTCGAGAAGACTAATTGTGGTATTTTTACTTTGCTG
CTGACCA
>WashU_Sbay_Contig480.2 YOR176W 5' untranslated region, Contig c480 3444 - 5443(revcom), 2000 bp (revcom)
TTTCAGGGAAGCACCATGTGCACGAATTGTTCTAGAAAGCATTTTTGGTTCGTAAATTCT
CTACAACTGAACTTATTAACAAATAGCAAACAGAGAAGAAAATTTTTTTTTTCCTTCTTG
TATGGTCAGTTAGTTGAAAACACGGAGATTTTCACTTGTTTAGTAAGCAGAGCCATAATG
CTCTTGACCGACCAAAAGAAGTATTCCTACGCGAGCTCCCTCTTCAAGTGCCAAATCCCC
TACTGAAAAAAGCAACATGAGAAGCAAAGAGATGCCTCTCGCCATGCAGGGCTTGCGGTC
ATGTTTTCTACGTTCAATTGATTTTGTTACAGCTGAAAGATGTTTATAAAACTGTCTTGC
ATATGCTCTATTTACTTGTAAACAATTTTATTAAGTTGCGTATATATGATCGTACTAAAA
ATTGGCTGGCGCGTTCTCCAGGCAGAGTTGGTTGAACCTTGCTCGAATTGATAGCTCAAA
GTGGAGAGACTCTTTTTTAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGCTCCACCTG
TTCAACAAAATGGCAGAGATCTTTCGAAGTGCGCGTCGAAACCACAAACCATCAAAAATA
TCGACCATCTAAATAAAGGGTTCTTGTTTGAATAAATATCAGGCGAAGCTCTTCATACAG
GCACAGGTCAGATAAGAAGACAATTCGAATTCGAGAAGGATATTCGTGGTATCTTTAATC
TGCTGCT

BioPerl-1.007002/t/data/map_hem/HEM15.ups.fa_.revcom000444000766000024      1041313155576321 21643 0ustar00cjfieldsstaff000000000000>SGD_Scer_YOR176W HEM15 "Ferrochelatase, a mitochondrial inner membrane protein, catalyzes the insertion of ferrous iron into protoporphyrin IX, the eighth and final step in the heme biosynthetic pathway; Yfh1p mediates the use of iron by Hem15p"
TGTTGGAAGCGATCAGCAGCAGAATTAAATCACCACGGTTTGTCTTGGCGTATGCGGTTT
GTCTTCTTGCTTGACCTGTGCCTGTATTTTGTCCTTGGCTTTAAATCTGTTTAATAAGAA
CCCTTTATTTAGATGACCATTGTTTTCGACGGTTTGTGGTTTCGACGCGCAATGTGAAAG
ATCTTCAATGTTTTGTTGAACAGTAAAGCAAAACAGCTCAACAGCAGGACAAAAAAAGCT
AAAAAAGAACTCTTCGCACTTTTAACAAGCAGTTTTACTGAACAATTTTAGAAGTAAATT
TCAGGAAGGTTCAACAGCTTTACATGAAAGAGGATGCTGGCCATTTTTTTTTTTTAAAAA
AGTTTTTTATATACACAAACTCAGTAAAATAATTACAAATATGTAGCATGTGTAGGATGC
CTTGAAACATCTCCGCTGGCAATAGCCGTTAGACATGCCCAATCTTCAATGGTCACCGTA
AGCCTTATATGACGAAGGAGTTGCTGCCCTTCGTTTTCTCATGCTGCTTTTTTTCGTAGG
GGATATGGGATTGAAGAAGGAGGACGCGAAGGAATACTTTTGGTCGGTCAAGGTCACTCT
TGGCTTGACACCAAACAAGCGTAAATTCTCGTGTTCCACTTGAGTCGGTTTACAAGAAGT
ACAGAAATATTTAACACATACCTGCTATTTGGACAAATTTAGCAGTAAAAAAAAGAACGT
TTAAAGA
>MIT_Spar_c278_20970 YOR176W 5' untranslated region, Contig c278 32746 - 34745, 2000 bp (revcom)
GGCAGTGATCAGCAGCAGAATGAAATTACCACAATTTGTCTTGGCGTTTGCGTTTTGTAT
TCTTTCTGGACCTGTGCCTGTATCGTGTCTTTGAGCTTTAAATCTGTTCAAATAAGAACC
CTTTATTTAGATGACCATTATTTTCGACGGTTTGTGGTTTCGACGCGCAATTCGAAAGAT
CTTCACTGTTTTGTTGAACAGTGAAGCAAAACAGCTCAACAGCAGGGCAAAAAAAGCTAA
AAAAGACTCTTCGCATTTTTAACAAGCAACTTTACTGAACAATTATAGTAATAGATTTTA
GCAAGGTTCAACAGCTTTACATGGAAGAAGATGCTGGCCATTTTTTTTTTTTTTAGATTG
TTTTTTTATATACGCAACTCAATAAAAATAATCACAAATATGTAGCATGTGCAGGACAGC
TTGAAATATCTCTACTCGTAACGACAGCTGGATATACCTGACCTTGAAAGATTACCTAAG
CCTTATATGACGAAGGAGTTGCTGCCCTTCATTTTCGCACGCTGCTTTTTTCAGTAGGGG
ATATGGGATTGAAGAAGGAGGACGCGAAGGAATACTTTTAGTCGGTCAAGGTCACTCTTG
GTTTGGCACCAAGCAAGCAAAAATATCCGTATTTCAATTAAGTAGGTCGTACAAGAAGCA
AAGAAGTATTTAGCATATACCCGCTATTTATTGAAAAGCTTAGTAGTAGGAAAAGAACGT
TTGAAGA
>MIT_Smik_c935_20455 YOR176W 5' untranslated region, Contig c935 1803 - 3802(revcom), 2000 bp (revcom)
AAAATTGTACATTGTTGGTAGTGGCTAGCAGCGATATAAAAATTACCACGATTAGTTTTA
TCGAATGCGTTGTCTTCTTGTTAGACCTGTGCCTGTATGGAGTATTTCAACTTTAAATAT
GTGAAAACGTGAACTCTTTTATTTAGATGATCATTATTTTCGACGGTTTGTGGTTTTGAC
GCGCAATTGGAGAGAACTCTATTGTTTTGTTGAACAATGAAGTAAAACAGCTCAACAGCA
GAGCAAAAAAAGCTGAAAATATTTCCACTTTCAGCAAGCAGCTTTACTGATTAATTTCAG
CAATGTGCTTTGGCATATTCAACATCTTAGCTTGAATGAAAATGCTGGCTAACTTATCTA
ATACAAGTTTTATATATGCAACTTAGTAAAGTCAATTGCAAATTTGTAGAACATGCAGGA
CACGTTGAAACTTCTTTATTCTTTACGACAACTGGAGATACCTTTCCTTGAGAAATTATG
GTAAGCTCTATATGGGGGGGAGCAGTTGCTCTTTATTTTCGCCTGCTACTTTTTCTGGTA
GGGGATATGAGACTTGAAGAAGGAGGACGCGAAGGAGTCTTTTGGTCGGCCAAGATCACT
GTTGGTCTGATCATTAAAGGAGCATAAACCTTTGTATTTAACTTAGGTTATACAAGAACG
TAAAAAGGACTCATCACATATTTGCTAATTGTTGGTAACTTCAGTAGTAGAAAATTGCAA
TTCAAGA
>WashU_Skud_Contig2050.4 YOR176W 5' untranslated region, Contig c2050 12271 - 14270(revcom), 2000 bp (revcom)
TGGTCAGCAGCAAAGTAAAAATACCACAATTAGTCTTCTCGAATACCTTTTTGTCTTCTT
GTTGATCTGTGCCTGAATGGAATATTTCAATGCGAAACTGTGCAAATAAGAACCCTTTAT
TTAGATGATCAATATTTTCGACGGTTTGTGGTTTCGACGCGCACTTTGAAAGATCCAGTG
AAGCTGTTTTGTTGAACAGATGGAACAAAACAGCTCAACAGCAGAACAAAAAACAGCTGA
AAAAGAGTCTTTTCACTTTTACCAAGCACTTTTAGCTCTTGGTTTCTGGCAATAAATTTC
GGAAAGGTTCAACATTTTGCACCTTGCTACAGGTGCTGGTTAGTTTTAGTACGGCTTTTA
TATACTCAAATCAGTAAAATACTTACAAATATGTAGGAGTATGTGCAAGACCTGAAGACA
TTTTAATTATTCTTAGCAAATATCATAAATACCTGACAATGAAATGCTACCGCGAGCTCT
CTGCGACGAAGGAGAAGCTGCTGTTCCTTTCCCAATGCTGCTTTTTCAGTAGGGGATTTG
ACACAGAAAGGAGAAGCACGCGAAGGAATACTTCTTTTGGTCGGTCAATATCATTGTTGG
TCTGATTATTAAACAAGCGGGAATCCCCGTGCTTCACTTGAATAGACCGTAAAAGAAGGA
AAAAAAGATTTCTTGCTTATCTTCTGTTCGTTTATGACCAGAGTAGTAGAAAAGCTATAA
ACTAAGA
>WashU_Sbay_Contig480.2 YOR176W 5' untranslated region, Contig c480 3444 - 5443(revcom), 2000 bp (revcom)
AGCAGCAGATTAAAGATACCACGAATATCCTTCTCGAATTCGAATTGTCTTCTTATCTGA
CCTGTGCCTGTATGAAGAGCTTCGCCTGATATTTATTCAAACAAGAACCCTTTATTTAGA
TGGTCGATATTTTTGATGGTTTGTGGTTTCGACGCGCACTTCGAAAGATCTCTGCCATTT
TGTTGAACAGGTGGAGCAAAACAGCTCAACAGCAGAACAAAAAACAGCTAAAAAAGAGTC
TCTCCACTTTGAGCTATCAATTCGAGCAAGGTTCAACCAACTCTGCCTGGAGAACGCGCC
AGCCAATTTTTAGTACGATCATATATACGCAACTTAATAAAATTGTTTACAAGTAAATAG
AGCATATGCAAGACAGTTTTATAAACATCTTTCAGCTGTAACAAAATCAATTGAACGTAG
AAAACATGACCGCAAGCCCTGCATGGCGAGAGGCATCTCTTTGCTTCTCATGTTGCTTTT
TTCAGTAGGGGATTTGGCACTTGAAGAGGGAGCTCGCGTAGGAATACTTCTTTTGGTCGG
TCAAGAGCATTATGGCTCTGCTTACTAAACAAGTGAAAATCTCCGTGTTTTCAACTAACT
GACCATACAAGAAGGAAAAAAAAAATTTTCTTCTCTGTTTGCTATTTGTTAATAAGTTCA
GTTGTAGAGAATTTACGAACCAAAAATGCTTTCTAGAACAATTCGTGCACATGGTGCTTC
CCTGAAA
BioPerl-1.007002/t/data/map_hem/HEM2-HEM12.fa000444000766000024      2352513155576321 20102 0ustar00cjfieldsstaff000000000000>SGD_Scer_YGL040C HEM2 "Delta-aminolevulinate dehydratase, a homo-octameric enzyme, catalyzes the conversion of delta-aminolevulinic acid to porphobilinogen, the second step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus"
GGTTTTGTCAATTTTCTAGGTATGAATTACTGGAGTAAGCAATAATATGAGTAAGCAGTA
AAACTTTTTTTTATTTGGCTGATTGGGCAAGAAAATCAAAGACAATAGAGTGGCGCATAG
ATGTTGCTAGCATTTATTAGGTTGCCTTACTCTTATATAAATCAAGCGGGAAGCTTGCCT
CAAGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTATTTTGATTTTTTTTTC
ACCTTTTCCAATTTTTTTTTCGGCAACAATTTTTTGGATGATTTTTATCGTCGATCTTGG
AATGATGATGTATTTCGGCGTCTCTACAAGACCCAATAAAGTAATTCGGTGACACAGGCT
TGTAGCAGATAGAAAACGTTCCGAAAGATGGGTTCCAATTGATGTAACACTTCTTTTTTA
TATATTCATGTGGACGTGTACGCCTTCTTCCCTTCTTTGCCTCTTGTGCCACTGTTAATC
CTCTTAAGCATATTGTTTTTATTTACAGACATTGGCTGACTCACCAGAAACTATAATTGA
CGCTGATTTCTAGTTAATTAAAAATAAAATATATGCAAGAATTAGCACCAGGCAGTCATT
TCTGTAAATTGCTTTGTTTTCTATTTCAAATTTGTTTTTTGTATATGTTTCAATGTTCTC
GTGACAATGCAGGCTTTTTTTTGTGCGAATTAAAGTAAAGCTAATCAAAACTAAACAATA
ATTTATCTTGTTCCCGAAAGAGTGGATCATGAGGAGGAAAGCTAACCGTCCAAGATCCTA
TATAATTTTTGAACTGAAAACCAACTGTTCACCTAGAAGACAGGTATCTGGATATGTAAC
TACACGCTCTATAAATACAGAAATCGTAAGCTAATCAATATAAATGTAAAAGAAAATAGG
AATTGCTGTCGATAGATTTATTTACTTTTGTATTGTCATCTGTGTTCTGTGCCAGTACAC
CGGACTCGTATGAGCTGTATGGTGTCGTTTCAATAGAATC
>MIT_Spar_c19_8512 YGL040C 5' untranslated region, Contig c19 1 - 1802, 2000 bp (revcom)
GGTTTTGTCAATATTCTAAATATGGATTCCTAGGGCAGGCAATAATATGGGGAAGCAGTA
AAACTTTTTGTTTTATGTGGCTGATTGGGCCAAAAAACAAGGACAATAGAATGACACATA
AAGTTTGCTAGCATTTATTAGGTTGCCTTACTCTTTTATAAATCAAGCGGGCAGCTTGCC
TCAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTAGTTTGAATTTTTTTT
TCACCTTTTGAAATTTTTTTTTTTCGGCAACAATTTTGAATGACTTTTATCGTCAATCTT
GGGAGTATACCTGCCTCTTTACAACACCCAACAAAACACTTAAGTAAGACAAGCTTGTGG
CAGGTAGGAAAGGTTTCAAAAAAAAAAAAAAGGTTTTTATCTATGGTCATACTTTTTCTT
CGTATATTTATGTGAACACGTACGTCTTGTTTTGCCTTCTTTGGCTCTTGTGTCACTGAA
TCTTCACATATTGTTTTTATTTACAGATACTACTTGACTCGCCTAAAATTATAATCGGCG
ATGGTTTCTACTACCTTAGTTAAAAAATAAAATGAATCAAAACATTACCATTAATAATTC
AATTTTTCCACATTAGTTTGTTTTCTATTTTATGGCTTTCTTCTTGTATATTTCTCAATA
TACTGCATGGCAATGCAAGCTCTTCTCTTTTCTTGATTGAAAATAAAGCTGTGAAGAACT
AAATAATAATTTATTGATGTCCTCCACAAAATGTACACCTGCGCTAACCTTGCTTAACAG
ATACGGTCAAAACGAACTTGAGCATATGTAAAAATCCATGTATTTTTCTTCTTTTGCCAA
CTAAATCAAACTTTTTATTGTATATGTCGTACCGCCAATACAAAGATGGAGAGGTTAATG
AAAATAGATGTGAAAAAAAAGCAGGAACTATTGTAGATAGATATTTTTAGGGTTCGATTG
CTATTTTTCTGTATTATGATCTGTGTTCTATGCCAGTGTA
>MIT_Smik_c273_7756 YGL040C 5' untranslated region, Contig c273 1 - 1807, 2000 bp (revcom)
GGTTTTACCAGTTTTCTTAATACGGATATCTAGAGTAAGTCACAATTTAAGGAAATTGCA
AAATTTTCTTTTTATATAGCTAAATAGGCCAATAAATCAGGAACAATAGAATGACGCACC
GAGTTTGCTAGCAACCTACACACTTGCTTTTTTTTATAAATCAAGAGTGTATGTTGCCTC
AGGCCAATCACCGCACCGAATAAGGATTGCTCGTTTACCCGTTGTTCGATTTTTTTTTTC
ATCTTCTACCAATTTTTTTCGGCAGCGCCTTTGAATGACTTTGATCATCAATCCTGGAGT
AATATACACTTGTATGTTTGAAACGCCCAGTTACAATATTTATTGGAATAGCTAACTTAT
GAGTAAGTGGACCCAAATTTTCGAGTGATGTTTCCTGTCAACGGTGACACTTATTTTTGG
TTTGCAGATATGTATGTGTATATCTTATTCCCACTTTTTTATAGTTATCGTTATCTATGT
ATCTCAATACCTTGGACATGAATCACCGAGTAGATATTTTTCTTTACAATGCTTAAAACA
AGGCCGCACAGAACTAAACAATAAAGTTACCTTGATCTTTAATAAAATATTCCCCCATTA
ATAAGTACTCTCTTCGATTACGATTTAGCCATATTCATTTTGACCATACATTGCAGATGT
GAGATGGATTTTAAGTGGTGAAAGCGCTCTAAGCTATGCCATATAAGTACGTAAGGAGAG
ACAAAATTAAACATAATTAAGCGCCATGTGAGACTAAATGTGGCCGTCGTTTTGATTATA
TGATTGGGAAAAGCTCCTAAACATAGAGGTAGAATTATAGTTCGGAAATTTCGTCTTGCC
CTGCTCATTTTGTAGAAAACGAGTCATCATCTCCACCCTTTGTAACCGGTGTCCTGCTCA
CATAAATAGTCTCTACTGAGAGATTTGTGAATTTCGAGATAATTTTTGGGATTCCATTGT
TGATAAAGGCAATATTATTAGGTATATAAAATATACTAGA
>MIT_Sbay_c77_8808 YGL040C 5' untranslated region, Contig c77 1 - 1377, 2000 bp (revcom)
ACTTTGTCAGTGTTTTTCTGGTAAGGATATCTGGAAGAAGTAACAATACGTATAAATTAC
AAAATTACCGTTTTATGTCGTGGAATGGGCTATGAACTAACATTAACAATAGAGTGATGC
ATAGACGTCACTAGCCTTTTATTGTGTTGCCTTGCTCTTTTATAAATCAGGCAGCCTGCC
GCAGGCCAATCACCGCACCGCCCGGAGATGCTCGTTTACCGTTGTGCACCAAATTTTTCA
TTTTTTGCCTTTTTCTATTTGGCAGCGTTTTCGAAAAATTTTGATCATTAGTCTTCAATG
ACTGGACTGTCATATTTTAGGGCACGCAGGTAAAGATATGAACAAATCATATTGATGATG
GATGCCAATCCTTCAATGTAAATTCTTTCTAAACATCATGATAAAGAACTTCAGTAAGAG
AGTGATAAAAACTTTACATGTATGGCGGGTGTATTCTGTAATTGTTTTTTAGATCTTTTT
GTTGTTAACGGTGACACCATTCTTACTACAATAATTGCATGTCAAATGTAAATATCTTGC
TTCACATTTCGTTGTTTCTTTACGATAAATTGTTTCGTCGCAAATATATCTTATTTTGCG
TGGTTTATCTACAGACACTGCTTGATTTACGCATAAGTACATCATGTAGTAATTCTTATA
TTGAGTATAAAACCATATGAATAGAAATATTTTTGTTAATCTATCGTTAATTTACATGCT
AGTTTATTTGTCCCTTTAAAATTTCTTTATATATTTGTTGCAATATGTGGACAAGGAAAC
ACGAAATATATTGGGATAAAGTTTAAGTAGAGATACATAGAACTAAACAATAAATTCATA
TTCAATAATACTTCAAAAGGTACTCTCCTGTCTGAACACAGAGACTCACAGACTTTATTT
AGTCGTTATGGCGATGTCAGACATCATGTTTAAGGTAAGCCGAGTGGATTGATATGAAAT
TGTCATATCATGAATAAGCTAATTACCCAAAAACAGTAAA
>WashU_Skud_Contig2052.17 YGL040C 5' untranslated region, Contig c2052 29967 - 31966, 2000 bp (revcom)
GATTTGTCAGTGTTTTCTGATATGGATGCCTGGAGAAAATATTAATATGTGGAAACCACA
AAACTTCCACTTATATAGCTAATTTAGCCAGAAATCATGAACAATAGGATGACGCATAGA
CGTCACTACTCTTCATATAAGTTGCCTTTCTCTTTTATAAATTGGGCAGGCAGCTTGCCT
CAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTTGCGTTCAAAGTTTTTC
ATTTTCCGCATCATCTACTTTTTTTTTTTTGACGCCGTTTTTGAATGTCTTGGTCATTGA
TCTTGAAATGATTTATGTTCGTGTTTTCACGGCACAAAGGTAGGCAAATCGGTAAATTTT
ACTCGTAATAAATAATCAAGGCCTCTAGAGGATTTAATATCAGGAAATAATAATGTGAGT
TTTTTGCAAATGGCCTTATATTCCTGACATCTTCTTGAATTTGTGTTTTAGCGTCGATGA
AGACTCTTCCTTTTTTCGTACGGTAATCTGGACATCTTGTTTCGTCTTTTCTTTTTTTTT
TGCGATTGCTTGTAATTCCAGATATGCAGCATTTATTTACAGGTGCTGATTGATTTACTA
TAGAGTTTATCAGGTAGTAGTTCTTTTTCATGTCTCAATTGAAGAAAAGGAACCCATAAA
TACATTAGCACTGAACAAACAATAACTGCCGCATTGGTTTGTTTTCTAACTTGAATTTTT
CTTTATACATATGCCACTGTATTAGGATGGGTGAATACCGTTTTCTTACTTTCTTCCTAT
GAAGGCGAAAGAATGGTGAAGGACAACTAAACAATAAATCGTTTTTCACACATCCCCATA
AAGCTTTCTCTGTTTGTCAGTTGTGACTCATCTTTCGTCGATGTTGCTTGGTAGATACAA
TTGAACAAGATTGAGATATCTAAAATGTTCAAAAATTATACTCTCTTATGTAGTTTCCGT
CATGGCTGAACGAAGGAAAACTACATCACCTGAGAATTAC
>SGD_Scer_YDR047W HEM12 "Uroporphyrinogen decarboxylase, catalyzes the fifth step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; activity inhibited by Cu2+, Zn2+, Fe2+, Fe3+ and sulfhydryl-specific reagents"
AGCGTTATAACCTGTTCTTTGCTTTATTTTTTTTTTTTTTGTTCTTCCTTTTCTCGAAGA
GAGCTTACCAAACACAATTCTGAGATAATGCTTGATGAATTGAAGAACCTATCGATCACT
CTATGTTACCTTCGTCTGGAACATCACTAATTCGAGCGGTAAAGATGAAAATGGCAGAAC
ATTTCGCTGGCAAAATTAAAACTCTTGCCTCATTTTTTTTTGCTTTCCTCTCCTGCCGCC
AAAAACCCCGAACCCTGTCCTGTATATACGAGAAACATTGAAAAAGATCGTGTATGATAG
CGCCAAGATGGCGGATAAACTAACACTATTGACAGGTTGAGGCCAAGGATATATTACTTG
CTAACAGAAAGAGATACTGTCACCACAATTGCCCGCGTACGTATACTACAACATGTTCTC
TATATATCACCCACTCTTTCGCAGTGCTACGTACGCCAAAAACGCGCGCATGGAAGTAAA
GAAGTTTTTTCTTTTAAGAGCGAAGCTCCATTAAAAGCCTTGAATATAAACTAGTGCGAA
GTAGTATGATCCGAAGACACCAATTGCTGGTGCAGCATAGGAATATGTGGCGTCCGAAAA
AGAGCCTTTAACAATCCACGGCGAAACAAGGCACCGCTGTGCATTTAAAACATGCCGTTC
CCGTACCAAGTTATATTGTTACGGATGAATCCAAAATAATTTGTTAAAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCATGGCACCTTCTTCGTTTCTTCATCCTGCA
TTAGACTTACTAGTGTGCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGACACATATCGC
TGAGCTGGAAGGACACCTTTTAATGTAGCCGTGCATGCGGCTCCGCGAAAAGAGCTCTGC
TATATTTCTCTACCTGAACTTCGAGCCGCGATCAACGAAAGCTCTCATCCAAGGCTCGTT
TTTCTTGACAGAAGCATGACAGTAAAATATGCGGTCATTT
>MIT_Spar_c130_3923 YDR047W 5' untranslated region, Contig c130 9341 - 11340, 2000 bp (revcom)
AGCGTTATGATGTGTTATTTGCTTTTATTTTCTTCTTTCTTTGTCTCGAAGATAACCTAG
CAAACACAATTCTAAGAAAATTCTCGATGAATTGGTTGTCAGCGCTTCCTATTTACTCTA
TGTCCACTTCGTTTGAAACATCAGTGGTTCGAGCAGTAATGACAAAAAGGGCAGAACATT
TCGTTGGCAAAATTTAAACTCGTGCCTCTCATTTTTTTTACTTTTCTCTCCTGCCACCAA
AACCCCGAACCCTGTCCCGTATATACGAGGAACATTGAAAAAAAATCGTGTATGGTAGCG
CCAAGATAGCGAATAAACTATCAGTATTGGCAGGGTGAAGCTAAGGATATGTTGTTTGCT
AACAAAGGGAAATGCTTTCGTTATAATCGCCCGCGTGCGTCTACTAAAATATGATCTATA
TATACCACCCAGTCTATTGCAGTGTTACGTACATCAAAATGCGCGCATGTAAGTGAACAA
GTTTTTTTTGTTTAAAGAGCGATTTTCCAATAAAGGCTTTGGATATACACTGGTGCAAAA
TATATGGTCAATGACGCCAATTACTGGTGTAGCATGAGAATACGTCGTCCGAAAGAGTTT
TTTTTTACAAACTACGGCAAAGCAAAGCACCACTGGCGCAATTCAAAACATGCCGTCCCC
GTACTAAGTTATGTACGTTATTATGGACGGATCCAAAATTATACTCTAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCGTAGCACCTTCTTCGTGTCCTTTCCTTCTT
CTGCATTAGGCTTACTAGCGTCCTTTCCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGA
CAAATCTCGCTGAGTTGGAAAGACACCTTTTATATAGCCGTACGTGCGGCTCCTCGAGAA
AGGCCCTGCTATATTTCACTAGCTGATCCTCGAGCTGCGATCAACGAAAGCCCCATCCAA
AAGGCTCCTTTTTCTTCAAAGAAGCATGACAGTAAAATAT
>MIT_Sbay_c896_21277 YDR047W 5' untranslated region, Contig c896 2230 - 4229(revcom), 2000 bp (revcom)
AGTGTTAACAGTATCTTTTGCCTTTTTTTATTCTAATAGCTACCCCAGGAATCACTATTT
AGCAAAGATCGTTTGCAAATTGGCCGTCAGTACGTTCTAAGTTCTTTAGAACATCATTGG
CTCGAGCATTAGTGACACGAATAGGAAAGCATTTCGTTGACAAAAATAAAATTGTTTCTT
TATTTTTTCCCTCTTTTCCATGGCGTCAAAAAACCCCGAACCCTGTATAAACGAGGAAGC
TGCATGGTAGCGCCAGAAAAGGCAGATAACCTTTAACAGTGCTGACAGAACAACGTCAAA
CATGTGCGGATAATGCCTTCGCTGACGGCAAGAAATTATATACGCCTCGAAACTGTAGAA
CGTCTTTTGTGCCGCTTGGTAACAAATAAACCTAGCCGGGGCCAGAATTTCACCCGTACA
TACTTACTGTTACATACTGCATGCACGCTACGCATTCTCACCGAACATCGAATCTGCCTG
CAGAAGCGAAGAAAAGCAAGTCTTCGAAGAGCAAGCTTACATCCATCGTGTTGAACACAT
ATGCCCAGCAAAGGGATCGGATGACGCCCAACTAACATTGGAATTTGTGACGCAAGGCTG
AAAGGCACTTCTCTATAGCCCACGGTGAAGCCTTACGCTATTGACAAGACAAAACATGCC
GATCCAAGCCAGGCGAAACGGGCCTAGCACTACGCAGCCAAACACTGGCGTTCCGCCCGT
CCCATCCAGTTTCATTTCTTATTTCGTTCTGCCTTGGGCCTAGCAGCGTGCTTGCCGGAT
GAGTTTTTTCCATTTTCCTACCGGCTCATCTCGCTAAGCTGAAAGGTCAGTTTTATAGCC
GTGTGCGCGGCATCGAGAGACAGGTTCAGCTAATGATATTTGCCTAATTCTCGAGCTGAG
GCCAATGAAGGCAGCTTCCAGGGCTCGTTTCTGCTCGGGAAAAAGCATACCACACATTTG
CACGGCTTTTATGTGCCATAGTGCCACCACTAGCCCCCAG
>WashU_Skud_Contig1362.1 YDR047W 5' untranslated region, Contig c1362 1 - 761, 2000 bp (revcom)
AGTGTTGATGGTATCTTTTGATTTTTTCTAGATTGGTAGCAAGCTCAATTGGCACAGCTC
TAAAAAAAGCCTTGTGAATTGGATAGTACCTTCTTTCGTTTGGAACATTACTGCTTCGAG
CAATAAACATACGAAAGGCAGAACACCTCGTTGACAAAACTGAAACTATTTCTTCAATTT
TTTGGCCTTTTTTCCTGCTGCCAAAAAACCCCGAATCATGTAGAAGCGAGAAGTAAAACA
GAGGAAGTGTATGGTAGCGCCAAGGAAAACGGGCAATACTTAGAAAGAATGACAGAGCTC
AGCCAAGTGTAAGCTAAGTGTTGACAAGGGAAGGTACATTGGGCCCCGAAAAAATTTGCT
AATGCTCGAAGAGCTCTCAATCAATCACCCACATATATGTACTACAGTATATTTATACTT
TCCACGCAGTCTCACGCAGTGCCACCTTCATCACCATGCGTGTAACTAATCGAGCAAGCT
GTTTTACGAAGGGCAGCTTTCCTATAAGCGTTTTGAACATGCATGGCTGCACTGCAATGA
GATCAGGCGACTCCAATTCCATAGCCTAGCACGGGATTAAGTAACGAGAAACTGAAAGAG
ATAATTTTACAAACCCGGACGAAGCAGAGCACTTGCTGGAACAAATCAAACATGCCGTCC
CCTACCAGCTCTCGAAGCGGGCCTAGCATTACTCGATCGAACGTTGCCGTTTAGTCTTAT
TTTCCTTTCCGTGCTGCGCTGCTTTTTTCTTGCATTGGGCT
BioPerl-1.007002/t/data/map_hem/HEM2-HEM12.meme.txt000444000766000024     11470513155576321 21276 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM2-HEM12.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YGL040C         1.0000   1000  MIT_Spar_c19_8512        1.0000   1000  
MIT_Smik_c273_7756       1.0000   1000  MIT_Sbay_c77_8808        1.0000   1000  
WashU_Skud_Contig2052.17 1.0000   1000  SGD_Scer_YDR047W         1.0000   1000  
MIT_Spar_c130_3923       1.0000   1000  MIT_Sbay_c896_21277      1.0000   1000  
WashU_Skud_Contig1362.1  1.0000    761  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM2-HEM12.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            8761    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.309 C 0.191 G 0.191 T 0.309 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 201   E-value = 6.7e-025
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  ::2711:1aa1:a32::a::
pos.-specific     C  a272::a7:::9:66:a:99
probability       G  :11199:2::21:12a::1:
matrix            T  :7::::::::7::::::::1

         bits    2.5 *     *        **   
                 2.3 *     *        **   
                 2.0 *   ***    *   ** **
                 1.8 *   ***    *   ** **
Information      1.5 *   *** ** **  *****
content          1.3 *   ****** **  *****
(32.3 bits)      1.0 * * ****** **  *****
                 0.8 ********** *********
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CTCAGGCCAATCACCGCACC
consensus             CAC   G  G  AA     
sequence                           G     
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2052.17     +    179  5.70e-14 GGCAGCTTGC CTCAGGCCAATCACCGCACC GAACAGGGAT
MIT_Smik_c273_7756           +    178  5.70e-14 TGTATGTTGC CTCAGGCCAATCACCGCACC GAATAAGGAT
MIT_Spar_c19_8512            +    180  5.70e-14 GGCAGCTTGC CTCAGGCCAATCACCGCACC GAACAGGGAT
MIT_Sbay_c77_8808            +    180  4.81e-13 GGCAGCCTGC CGCAGGCCAATCACCGCACC GCCCGGAGAT
SGD_Scer_YGL040C             +    179  4.85e-12 GGAAGCTTGC CTCAAGCCAATCACCGCACC GAACAGGGAT
SGD_Scer_YDR047W             +    616  4.68e-10 CTTTAACAAT CCACGGCGAAACAAGGCACC GCTGTGCATT
MIT_Spar_c130_3923           +    612  4.99e-10 TTTTTACAAA CTACGGCAAAGCAAAGCACC ACTGGCGCAA
MIT_Sbay_c896_21277          +    896  5.96e-10 AATTCTCGAG CTGAGGCCAATGAAGGCAGC TTCCAGGGCT
WashU_Skud_Contig1362.1      +    614  4.38e-09 ATTTTACAAA CCCGGACGAAGCAGAGCACT TGCTGGAACA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2052.17          5.7e-14  178_[+1]_802
MIT_Smik_c273_7756                5.7e-14  177_[+1]_803
MIT_Spar_c19_8512                 5.7e-14  179_[+1]_801
MIT_Sbay_c77_8808                 4.8e-13  179_[+1]_801
SGD_Scer_YGL040C                  4.9e-12  178_[+1]_802
SGD_Scer_YDR047W                  4.7e-10  615_[+1]_365
MIT_Spar_c130_3923                  5e-10  611_[+1]_369
MIT_Sbay_c896_21277                 6e-10  895_[+1]_85
WashU_Skud_Contig1362.1           4.4e-09  613_[+1]_128
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Skud_Contig2052.17 (  179) CTCAGGCCAATCACCGCACC  1 
MIT_Smik_c273_7756       (  178) CTCAGGCCAATCACCGCACC  1 
MIT_Spar_c19_8512        (  180) CTCAGGCCAATCACCGCACC  1 
MIT_Sbay_c77_8808        (  180) CGCAGGCCAATCACCGCACC  1 
SGD_Scer_YGL040C         (  179) CTCAAGCCAATCACCGCACC  1 
SGD_Scer_YDR047W         (  616) CCACGGCGAAACAAGGCACC  1 
MIT_Spar_c130_3923       (  612) CTACGGCAAAGCAAAGCACC  1 
MIT_Sbay_c896_21277      (  896) CTGAGGCCAATGAAGGCAGC  1 
WashU_Skud_Contig1362.1  (  614) CCCGGACGAAGCAGAGCACT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8590 bayes= 9.89701 E= 6.7e-025 
  -982    251   -982   -982 
  -982     34    -66    104 
   -55    192    -66   -982 
   104     34    -66   -982 
  -154   -982    234   -982 
  -154   -982    234   -982 
  -982    251   -982   -982 
  -154    192     34   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -154   -982     34    104 
  -982    234    -66   -982 
   162   -982   -982   -982 
     4    166    -66   -982 
   -55    166     34   -982 
  -982   -982    251   -982 
  -982    251   -982   -982 
   162   -982   -982   -982 
  -982    234    -66   -982 
  -982    234   -982   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.7e-025 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.222222  0.111111  0.666667 
 0.222222  0.666667  0.111111  0.000000 
 0.666667  0.222222  0.111111  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.666667  0.222222  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.111111  0.000000  0.222222  0.666667 
 0.000000  0.888889  0.111111  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.333333  0.555556  0.111111  0.000000 
 0.222222  0.555556  0.222222  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.888889  0.000000  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
C[TC][CA][AC]GGC[CG]AA[TG]CA[CA][CAG]GCACC
--------------------------------------------------------------------------------




Time  8.20 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 174   E-value = 1.0e-012
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  8:82:391:1:::::::9::
pos.-specific     C  27122::::1a17:::1:7a
probability       G  ::16761::8::3a13::3:
matrix            T  :3::11:9a::9::9791::

         bits    2.5           *  *     *
                 2.3           *  *     *
                 2.0           *  *     *
                 1.8           *  *     *
Information      1.5         *** **    **
content          1.3  *  * * ******* * **
(27.9 bits)      1.0 **  * **************
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           ACAGGGATTGCTCGTTTACC
consensus            CT ACA      G  G  G 
sequence                C                
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2052.17     +    201  3.60e-13 ACCGCACCGA ACAGGGATTGCTCGTTTACC CGTTGCGTTC
MIT_Spar_c19_8512            +    202  3.60e-13 ACCGCACCGA ACAGGGATTGCTCGTTTACC CGTAGTTTGA
SGD_Scer_YGL040C             +    201  3.60e-13 ACCGCACCGA ACAGGGATTGCTCGTTTACC CGTATTTTGA
MIT_Smik_c273_7756           +    200  6.88e-11 ACCGCACCGA ATAAGGATTGCTCGTTTACC CGTTGTTCGA
SGD_Scer_YDR047W             +    557  2.56e-09 TGATCCGAAG ACACCAATTGCTGGTGCAGC ATAGGAATAT
MIT_Sbay_c77_8808            +    201  4.15e-09 CACCGCACCG CCCGGAGATGCTCGTTTACC GTTGTGCACC
MIT_Sbay_c896_21277          -     39  1.46e-08 TCTTTGCTAA ATAGTGATTCCTGGGGTAGC TATTAGAATA
MIT_Spar_c130_3923           +    554  1.46e-08 ATGGTCAATG ACGCCAATTACTGGTGTAGC ATGAGAATAC
WashU_Skud_Contig1362.1      -    264  2.12e-08 GTCATTCTTT CTAAGTATTGCCCGTTTTCC TTGGCGCTAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2052.17          3.6e-13  200_[+2]_780
MIT_Spar_c19_8512                 3.6e-13  201_[+2]_779
SGD_Scer_YGL040C                  3.6e-13  200_[+2]_780
MIT_Smik_c273_7756                6.9e-11  199_[+2]_781
SGD_Scer_YDR047W                  2.6e-09  556_[+2]_424
MIT_Sbay_c77_8808                 4.1e-09  200_[+2]_780
MIT_Sbay_c896_21277               1.5e-08  38_[-2]_942
MIT_Spar_c130_3923                1.5e-08  553_[+2]_427
WashU_Skud_Contig1362.1           2.1e-08  263_[-2]_478
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
WashU_Skud_Contig2052.17 (  201) ACAGGGATTGCTCGTTTACC  1 
MIT_Spar_c19_8512        (  202) ACAGGGATTGCTCGTTTACC  1 
SGD_Scer_YGL040C         (  201) ACAGGGATTGCTCGTTTACC  1 
MIT_Smik_c273_7756       (  200) ATAAGGATTGCTCGTTTACC  1 
SGD_Scer_YDR047W         (  557) ACACCAATTGCTGGTGCAGC  1 
MIT_Sbay_c77_8808        (  201) CCCGGAGATGCTCGTTTACC  1 
MIT_Sbay_c896_21277      (   39) ATAGTGATTCCTGGGGTAGC  1 
MIT_Spar_c130_3923       (  554) ACGCCAATTACTGGTGTAGC  1 
WashU_Skud_Contig1362.1  (  264) CTAAGTATTGCCCGTTTTCC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8590 bayes= 9.89701 E= 1.0e-012 
   126     34   -982   -982 
  -982    192   -982      4 
   126    -66    -66   -982 
   -55     34    166   -982 
  -982     34    192   -154 
     4   -982    166   -154 
   145   -982    -66   -982 
  -154   -982   -982    145 
  -982   -982   -982    162 
  -154    -66    215   -982 
  -982    251   -982   -982 
  -982    -66   -982    145 
  -982    192     92   -982 
  -982   -982    251   -982 
  -982   -982    -66    145 
  -982   -982     92    104 
  -982    -66   -982    145 
   145   -982   -982   -154 
  -982    192     92   -982 
  -982    251   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.0e-012 
 0.777778  0.222222  0.000000  0.000000 
 0.000000  0.666667  0.000000  0.333333 
 0.777778  0.111111  0.111111  0.000000 
 0.222222  0.222222  0.555556  0.000000 
 0.000000  0.222222  0.666667  0.111111 
 0.333333  0.000000  0.555556  0.111111 
 0.888889  0.000000  0.111111  0.000000 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  0.000000  0.000000  1.000000 
 0.111111  0.111111  0.777778  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.666667  0.333333  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.000000  0.333333  0.666667 
 0.000000  0.111111  0.000000  0.888889 
 0.888889  0.000000  0.000000  0.111111 
 0.000000  0.666667  0.333333  0.000000 
 0.000000  1.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[AC][CT]A[GAC][GC][GA]ATTGCT[CG]GT[TG]TA[CG]C
--------------------------------------------------------------------------------




Time 16.04 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =   9   llr = 159   E-value = 7.4e-007
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :::23:16:::9:a784:9:
pos.-specific     C  a73623641::::::16:::
probability       G  ::7:2:3::4:11::1:a19
matrix            T  :3:227::96a:9:3::::1

         bits    2.5 *                *  
                 2.3 *                *  
                 2.0 *                * *
                 1.8 *                * *
Information      1.5 * *       *  *   * *
content          1.3 ***     * ****   ***
(25.4 bits)      1.0 ***  *********  ****
                 0.8 **** ***************
                 0.5 **** ***************
                 0.3 **** ***************
                 0.0 --------------------

Multilevel           CCGCATCATTTATAAACGAG
consensus             TCACCGC G    T A   
sequence                TG               
                         T               
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Sbay_c896_21277          +    216  1.03e-10 TCAAAAAACC CCGAACCCTGTATAAACGAG GAAGCTGCAT
MIT_Spar_c19_8512            -    151  6.18e-10 GGCAAGCTGC CCGCTTGATTTATAAAAGAG TAAGGCAACC
SGD_Scer_YDR047W             +    253  7.00e-10 AAACCCCGAA CCCTGTCCTGTATATACGAG AAACATTGAA
MIT_Sbay_c77_8808            -    155  1.63e-09 CTGCGGCAGG CTGCCTGATTTATAAAAGAG CAAGGCAACA
SGD_Scer_YGL040C             -    150  1.63e-09 GGCAAGCTTC CCGCTTGATTTATATAAGAG TAAGGCAACC
MIT_Spar_c130_3923           +    250  4.40e-09 AAACCCCGAA CCCTGTCCCGTATATACGAG GAACATTGAA
WashU_Skud_Contig1362.1      +    211  8.03e-09 CCAAAAAACC CCGAATCATGTAGAAGCGAG AAGTAAAACA
WashU_Skud_Contig2052.17     -    150  1.10e-08 GGCAAGCTGC CTGCCCAATTTATAAAAGAG AAAGGCAACT
MIT_Smik_c273_7756           +    871  1.32e-07 GAGTCATCAT CTCCACCCTTTGTAACCGGT GTCCTGCTCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Sbay_c896_21277                 1e-10  215_[+3]_765
MIT_Spar_c19_8512                 6.2e-10  150_[-3]_830
SGD_Scer_YDR047W                    7e-10  252_[+3]_728
MIT_Sbay_c77_8808                 1.6e-09  154_[-3]_826
SGD_Scer_YGL040C                  1.6e-09  149_[-3]_831
MIT_Spar_c130_3923                4.4e-09  249_[+3]_731
WashU_Skud_Contig1362.1             8e-09  210_[+3]_531
WashU_Skud_Contig2052.17          1.1e-08  149_[-3]_831
MIT_Smik_c273_7756                1.3e-07  870_[+3]_110
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=9
MIT_Sbay_c896_21277      (  216) CCGAACCCTGTATAAACGAG  1 
MIT_Spar_c19_8512        (  151) CCGCTTGATTTATAAAAGAG  1 
SGD_Scer_YDR047W         (  253) CCCTGTCCTGTATATACGAG  1 
MIT_Sbay_c77_8808        (  155) CTGCCTGATTTATAAAAGAG  1 
SGD_Scer_YGL040C         (  150) CCGCTTGATTTATATAAGAG  1 
MIT_Spar_c130_3923       (  250) CCCTGTCCCGTATATACGAG  1 
WashU_Skud_Contig1362.1  (  211) CCGAATCATGTAGAAGCGAG  1 
WashU_Skud_Contig2052.17 (  150) CTGCCCAATTTATAAAAGAG  1 
MIT_Smik_c273_7756       (  871) CTCCACCCTTTGTAACCGGT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8590 bayes= 9.89701 E= 7.4e-007 
  -982    251   -982   -982 
  -982    192   -982      4 
  -982     92    192   -982 
   -55    166   -982    -55 
     4     34     34    -55 
  -982     92   -982    104 
  -154    166     92   -982 
    78    134   -982   -982 
  -982    -66   -982    145 
  -982   -982    134     78 
  -982   -982   -982    162 
   145   -982    -66   -982 
  -982   -982    -66    145 
   162   -982   -982   -982 
   104   -982   -982      4 
   126    -66    -66   -982 
    45    166   -982   -982 
  -982   -982    251   -982 
   145   -982    -66   -982 
  -982   -982    234   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 7.4e-007 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.666667  0.000000  0.333333 
 0.000000  0.333333  0.666667  0.000000 
 0.222222  0.555556  0.000000  0.222222 
 0.333333  0.222222  0.222222  0.222222 
 0.000000  0.333333  0.000000  0.666667 
 0.111111  0.555556  0.333333  0.000000 
 0.555556  0.444444  0.000000  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.444444  0.555556 
 0.000000  0.000000  0.000000  1.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.000000  0.111111  0.888889 
 1.000000  0.000000  0.000000  0.000000 
 0.666667  0.000000  0.000000  0.333333 
 0.777778  0.111111  0.111111  0.000000 
 0.444444  0.555556  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.000000  0.888889  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
C[CT][GC][CAT][ACGTC][TC][CG][AC]T[TG]TATA[AT]A[CA]GAG
--------------------------------------------------------------------------------




Time 23.77 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   15   sites =   9   llr = 130   E-value = 2.3e-003
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  :::4::4:8::::18
pos.-specific     C  ::131::2::8:99:
probability       G  :921:94::92a::1
matrix            T  a171911821::1:1

         bits    2.5            *   
                 2.3            *   
                 2.0  *   *   * *** 
                 1.8  *   *   ***** 
Information      1.5 **   *   ***** 
content          1.3 **  **   ***** 
(20.9 bits)      1.0 **  ** * ***** 
                 0.8 *** ** ********
                 0.5 *** ***********
                 0.3 ***************
                 0.0 ---------------

Multilevel           TGTATGATAGCGCCA
consensus              GC  GCT G    
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Skud_Contig1362.1      +    248  5.26e-10 ACAGAGGAAG TGTATGGTAGCGCCA AGGAAAACGG
MIT_Spar_c130_3923           +    289  5.26e-10 AAAAAAATCG TGTATGGTAGCGCCA AGATAGCGAA
SGD_Scer_YDR047W             +    291  2.07e-09 AAAAAGATCG TGTATGATAGCGCCA AGATGGCGGA
MIT_Sbay_c896_21277          +    241  3.97e-09 ACGAGGAAGC TGCATGGTAGCGCCA GAAAAGGCAG
MIT_Spar_c19_8512            +     78  7.03e-08 TTGTTTTATG TGGCTGATTGGGCCA AAAAACAAGG
MIT_Sbay_c77_8808            -    909  8.89e-08 TTAAACATGA TGTCTGACATCGCCA TAACGACTAA
SGD_Scer_YGL040C             +     76  7.23e-07 TTTTTTTATT TGGCTGATTGGGCAA GAAAATCAAA
MIT_Smik_c273_7756           +    256  2.61e-06 CTACCAATTT TTTTCGGCAGCGCCT TTGAATGACT
WashU_Skud_Contig2052.17     +    462  5.54e-06 TTCTTGAATT TGTGTTTTAGCGTCG ATGAAGACTC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1362.1           5.3e-10  247_[+4]_499
MIT_Spar_c130_3923                5.3e-10  288_[+4]_697
SGD_Scer_YDR047W                  2.1e-09  290_[+4]_695
MIT_Sbay_c896_21277                 4e-09  240_[+4]_745
MIT_Spar_c19_8512                   7e-08  77_[+4]_908
MIT_Sbay_c77_8808                 8.9e-08  908_[-4]_77
SGD_Scer_YGL040C                  7.2e-07  75_[+4]_910
MIT_Smik_c273_7756                2.6e-06  255_[+4]_730
WashU_Skud_Contig2052.17          5.5e-06  461_[+4]_524
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=15 seqs=9
WashU_Skud_Contig1362.1  (  248) TGTATGGTAGCGCCA  1 
MIT_Spar_c130_3923       (  289) TGTATGGTAGCGCCA  1 
SGD_Scer_YDR047W         (  291) TGTATGATAGCGCCA  1 
MIT_Sbay_c896_21277      (  241) TGCATGGTAGCGCCA  1 
MIT_Spar_c19_8512        (   78) TGGCTGATTGGGCCA  1 
MIT_Sbay_c77_8808        (  909) TGTCTGACATCGCCA  1 
SGD_Scer_YGL040C         (   76) TGGCTGATTGGGCAA  1 
MIT_Smik_c273_7756       (  256) TTTTCGGCAGCGCCT  1 
WashU_Skud_Contig2052.17 (  462) TGTGTTTTAGCGTCG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 8635 bayes= 9.90455 E= 2.3e-003 
  -982   -982   -982    162 
  -982   -982    234   -154 
  -982    -66     34    104 
    45     92    -66   -154 
  -982    -66   -982    145 
  -982   -982    234   -154 
    45   -982    134   -154 
  -982     34   -982    126 
   126   -982   -982    -55 
  -982   -982    234   -154 
  -982    215     34   -982 
  -982   -982    251   -982 
  -982    234   -982   -154 
  -154    234   -982   -982 
   126   -982    -66   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 2.3e-003 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.888889  0.111111 
 0.000000  0.111111  0.222222  0.666667 
 0.444444  0.333333  0.111111  0.111111 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.888889  0.111111 
 0.444444  0.000000  0.444444  0.111111 
 0.000000  0.222222  0.000000  0.777778 
 0.777778  0.000000  0.000000  0.222222 
 0.000000  0.000000  0.888889  0.111111 
 0.000000  0.777778  0.222222  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.111111  0.888889  0.000000  0.000000 
 0.777778  0.000000  0.111111  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
TG[TG][AC]TG[AG][TC][AT]G[CG]GCCA
--------------------------------------------------------------------------------




Time 31.71 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 145   E-value = 2.1e-001
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  7336939a283881:9:2:8
pos.-specific     C  32:::6:::2::::2:8:a2
probability       G  :264111:::722281:8::
matrix            T  :21:::::8::::7::2:::

         bits    2.5                   * 
                 2.3                   * 
                 2.0                   * 
                 1.8               *   * 
Information      1.5        *      * *** 
content          1.3     * **  *   ***** 
(23.3 bits)      1.0 *  ** ** **** ******
                 0.8 * *********** ******
                 0.5 * ******************
                 0.3 * ******************
                 0.0 --------------------

Multilevel           AAGAACAATAGAATGACGCA
consensus            CCAG A  ACAGGGC TA C
sequence              G                  
                      T                  
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c273_7756           +     99  6.39e-12 CCAATAAATC AGGAACAATAGAATGACGCA CCGAGTTTGC
WashU_Skud_Contig2052.17     +     97  1.53e-10 GCCAGAAATC ATGAACAATAGGATGACGCA TAGACGTCAC
MIT_Spar_c19_8512            +     99  3.15e-10 GCCAAAAAAC AAGGACAATAGAATGACACA TAAAGTTTGC
SGD_Scer_YGL040C             +     98  2.76e-09 CAAGAAAATC AAAGACAATAGAGTGGCGCA TAGATGTTGC
MIT_Spar_c130_3923           -    817  3.44e-08 GATTTGTCGG CCGGAAAAAAAAAGCACGCA TCCGGCAAGG
SGD_Scer_YDR047W             -    807  3.44e-08 TATGTGTCGG CCGGAAAAAAAAAGCACGCA TCCGGCAAGC
MIT_Sbay_c77_8808            +    102  4.32e-08 ATGAACTAAC ATTAACAATAGAGTGATGCA TAGACGTCAC
MIT_Sbay_c896_21277          +    549  2.76e-07 ATATGCCCAG CAAAGGGATCGGATGACGCC CAACTAACAT
WashU_Skud_Contig1362.1      -     10  8.14e-07 CTACCAATCT AGAAAAAATCAAAAGATACC ATCAACACT 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c273_7756                6.4e-12  98_[+5]_882
WashU_Skud_Contig2052.17          1.5e-10  96_[+5]_884
MIT_Spar_c19_8512                 3.1e-10  98_[+5]_882
SGD_Scer_YGL040C                  2.8e-09  97_[+5]_883
MIT_Spar_c130_3923                3.4e-08  816_[-5]_164
SGD_Scer_YDR047W                  3.4e-08  806_[-5]_174
MIT_Sbay_c77_8808                 4.3e-08  101_[+5]_879
MIT_Sbay_c896_21277               2.8e-07  548_[+5]_432
WashU_Skud_Contig1362.1           8.1e-07  9_[-5]_732
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
MIT_Smik_c273_7756       (   99) AGGAACAATAGAATGACGCA  1 
WashU_Skud_Contig2052.17 (   97) ATGAACAATAGGATGACGCA  1 
MIT_Spar_c19_8512        (   99) AAGGACAATAGAATGACACA  1 
SGD_Scer_YGL040C         (   98) AAAGACAATAGAGTGGCGCA  1 
MIT_Spar_c130_3923       (  817) CCGGAAAAAAAAAGCACGCA  1 
SGD_Scer_YDR047W         (  807) CCGGAAAAAAAAAGCACGCA  1 
MIT_Sbay_c77_8808        (  102) ATTAACAATAGAGTGATGCA  1 
MIT_Sbay_c896_21277      (  549) CAAAGGGATCGGATGACGCC  1 
WashU_Skud_Contig1362.1  (   10) AGAAAAAATCAAAAGATACC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8590 bayes= 9.89701 E= 2.1e-001 
   104     92   -982   -982 
     4     34     34    -55 
     4   -982    166   -154 
    78   -982    134   -982 
   145   -982    -66   -982 
     4    166    -66   -982 
   145   -982    -66   -982 
   162   -982   -982   -982 
   -55   -982   -982    126 
   126     34   -982   -982 
     4   -982    192   -982 
   126   -982     34   -982 
   126   -982     34   -982 
  -154   -982     34    104 
  -982     34    215   -982 
   145   -982    -66   -982 
  -982    215   -982    -55 
   -55   -982    215   -982 
  -982    251   -982   -982 
   126     34   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.1e-001 
 0.666667  0.333333  0.000000  0.000000 
 0.333333  0.222222  0.222222  0.222222 
 0.333333  0.000000  0.555556  0.111111 
 0.555556  0.000000  0.444444  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.333333  0.555556  0.111111  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.222222  0.000000  0.000000  0.777778 
 0.777778  0.222222  0.000000  0.000000 
 0.333333  0.000000  0.666667  0.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.111111  0.000000  0.222222  0.666667 
 0.000000  0.222222  0.777778  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.777778  0.000000  0.222222 
 0.222222  0.000000  0.777778  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.777778  0.222222  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
[AC][ACGTC][GA][AG]A[CA]AA[TA][AC][GA][AG][AG][TG][GC]A[CT][GA]C[AC]
--------------------------------------------------------------------------------




Time 39.58 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YGL040C                 1.84e-25  75_[+4(7.23e-07)]_7_[+5(2.76e-09)]_32_[-3(1.63e-09)]_9_[+1(4.85e-12)]_2_[+2(3.60e-13)]_780
MIT_Spar_c19_8512                1.53e-29  19_[+2(8.47e-05)]_38_[+4(7.03e-08)]_6_[+5(3.15e-10)]_32_[-3(6.18e-10)]_9_[+1(5.70e-14)]_2_[+2(3.60e-13)]_229_[-1(3.52e-05)]_530
MIT_Smik_c273_7756               2.73e-25  98_[+5(6.39e-12)]_59_[+1(5.70e-14)]_2_[+2(6.88e-11)]_3_[-5(1.42e-05)]_13_[+4(2.61e-06)]_600_[+3(1.32e-07)]_110
MIT_Sbay_c77_8808                2.58e-22  101_[+5(4.32e-08)]_33_[-3(1.63e-09)]_5_[+1(4.81e-13)]_1_[+2(4.15e-09)]_688_[-4(8.89e-08)]_77
WashU_Skud_Contig2052.17         7.43e-27  96_[+5(1.53e-10)]_33_[-3(1.10e-08)]_9_[+1(5.70e-14)]_2_[+2(3.60e-13)]_241_[+4(5.54e-06)]_44_[-5(8.79e-05)]_430_[+1(9.64e-05)]_10
SGD_Scer_YDR047W                 1.12e-21  19_[-5(5.14e-05)]_166_[-5(2.78e-05)]_27_[+3(7.00e-10)]_18_[+4(2.07e-09)]_76_[+2(5.89e-06)]_155_[+2(2.56e-09)]_39_[+1(4.68e-10)]_171_[-5(3.44e-08)]_99_[+1(4.63e-05)]_55
MIT_Spar_c130_3923               9.38e-21  92_[+4(5.51e-05)]_142_[+3(4.40e-09)]_19_[+4(5.26e-10)]_250_[+2(1.46e-08)]_38_[+1(4.99e-10)]_185_[-5(3.44e-08)]_82_[+2(5.53e-06)]_62
MIT_Sbay_c896_21277              1.53e-20  38_[-2(1.46e-08)]_114_[-5(6.18e-05)]_23_[+3(1.03e-10)]_5_[+4(3.97e-09)]_293_[+5(2.76e-07)]_121_[-4(7.12e-06)]_48_[+1(6.93e-05)]_123_[+1(5.96e-10)]_85
WashU_Skud_Contig1362.1          9.11e-19  9_[-5(8.14e-07)]_55_[-1(1.36e-05)]_106_[+3(8.03e-09)]_17_[+4(5.26e-10)]_1_[-2(2.12e-08)]_330_[+1(4.38e-09)]_99_[-1(7.81e-06)]_9
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM2-HEM13.fa000444000766000024      2415313155576321 20101 0ustar00cjfieldsstaff000000000000>SGD_Scer_YGL040C HEM2 "Delta-aminolevulinate dehydratase, a homo-octameric enzyme, catalyzes the conversion of delta-aminolevulinic acid to porphobilinogen, the second step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus"
GGTTTTGTCAATTTTCTAGGTATGAATTACTGGAGTAAGCAATAATATGAGTAAGCAGTA
AAACTTTTTTTTATTTGGCTGATTGGGCAAGAAAATCAAAGACAATAGAGTGGCGCATAG
ATGTTGCTAGCATTTATTAGGTTGCCTTACTCTTATATAAATCAAGCGGGAAGCTTGCCT
CAAGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTATTTTGATTTTTTTTTC
ACCTTTTCCAATTTTTTTTTCGGCAACAATTTTTTGGATGATTTTTATCGTCGATCTTGG
AATGATGATGTATTTCGGCGTCTCTACAAGACCCAATAAAGTAATTCGGTGACACAGGCT
TGTAGCAGATAGAAAACGTTCCGAAAGATGGGTTCCAATTGATGTAACACTTCTTTTTTA
TATATTCATGTGGACGTGTACGCCTTCTTCCCTTCTTTGCCTCTTGTGCCACTGTTAATC
CTCTTAAGCATATTGTTTTTATTTACAGACATTGGCTGACTCACCAGAAACTATAATTGA
CGCTGATTTCTAGTTAATTAAAAATAAAATATATGCAAGAATTAGCACCAGGCAGTCATT
TCTGTAAATTGCTTTGTTTTCTATTTCAAATTTGTTTTTTGTATATGTTTCAATGTTCTC
GTGACAATGCAGGCTTTTTTTTGTGCGAATTAAAGTAAAGCTAATCAAAACTAAACAATA
ATTTATCTTGTTCCCGAAAGAGTGGATCATGAGGAGGAAAGCTAACCGTCCAAGATCCTA
TATAATTTTTGAACTGAAAACCAACTGTTCACCTAGAAGACAGGTATCTGGATATGTAAC
TACACGCTCTATAAATACAGAAATCGTAAGCTAATCAATATAAATGTAAAAGAAAATAGG
AATTGCTGTCGATAGATTTATTTACTTTTGTATTGTCATCTGTGTTCTGTGCCAGTACAC
CGGACTCGTATGAGCTGTATGGTGTCGTTTCAATAGAATC
>MIT_Spar_c19_8512 YGL040C 5' untranslated region, Contig c19 1 - 1802, 2000 bp (revcom)
GGTTTTGTCAATATTCTAAATATGGATTCCTAGGGCAGGCAATAATATGGGGAAGCAGTA
AAACTTTTTGTTTTATGTGGCTGATTGGGCCAAAAAACAAGGACAATAGAATGACACATA
AAGTTTGCTAGCATTTATTAGGTTGCCTTACTCTTTTATAAATCAAGCGGGCAGCTTGCC
TCAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTAGTTTGAATTTTTTTT
TCACCTTTTGAAATTTTTTTTTTTCGGCAACAATTTTGAATGACTTTTATCGTCAATCTT
GGGAGTATACCTGCCTCTTTACAACACCCAACAAAACACTTAAGTAAGACAAGCTTGTGG
CAGGTAGGAAAGGTTTCAAAAAAAAAAAAAAGGTTTTTATCTATGGTCATACTTTTTCTT
CGTATATTTATGTGAACACGTACGTCTTGTTTTGCCTTCTTTGGCTCTTGTGTCACTGAA
TCTTCACATATTGTTTTTATTTACAGATACTACTTGACTCGCCTAAAATTATAATCGGCG
ATGGTTTCTACTACCTTAGTTAAAAAATAAAATGAATCAAAACATTACCATTAATAATTC
AATTTTTCCACATTAGTTTGTTTTCTATTTTATGGCTTTCTTCTTGTATATTTCTCAATA
TACTGCATGGCAATGCAAGCTCTTCTCTTTTCTTGATTGAAAATAAAGCTGTGAAGAACT
AAATAATAATTTATTGATGTCCTCCACAAAATGTACACCTGCGCTAACCTTGCTTAACAG
ATACGGTCAAAACGAACTTGAGCATATGTAAAAATCCATGTATTTTTCTTCTTTTGCCAA
CTAAATCAAACTTTTTATTGTATATGTCGTACCGCCAATACAAAGATGGAGAGGTTAATG
AAAATAGATGTGAAAAAAAAGCAGGAACTATTGTAGATAGATATTTTTAGGGTTCGATTG
CTATTTTTCTGTATTATGATCTGTGTTCTATGCCAGTGTA
>MIT_Smik_c273_7756 YGL040C 5' untranslated region, Contig c273 1 - 1807, 2000 bp (revcom)
GGTTTTACCAGTTTTCTTAATACGGATATCTAGAGTAAGTCACAATTTAAGGAAATTGCA
AAATTTTCTTTTTATATAGCTAAATAGGCCAATAAATCAGGAACAATAGAATGACGCACC
GAGTTTGCTAGCAACCTACACACTTGCTTTTTTTTATAAATCAAGAGTGTATGTTGCCTC
AGGCCAATCACCGCACCGAATAAGGATTGCTCGTTTACCCGTTGTTCGATTTTTTTTTTC
ATCTTCTACCAATTTTTTTCGGCAGCGCCTTTGAATGACTTTGATCATCAATCCTGGAGT
AATATACACTTGTATGTTTGAAACGCCCAGTTACAATATTTATTGGAATAGCTAACTTAT
GAGTAAGTGGACCCAAATTTTCGAGTGATGTTTCCTGTCAACGGTGACACTTATTTTTGG
TTTGCAGATATGTATGTGTATATCTTATTCCCACTTTTTTATAGTTATCGTTATCTATGT
ATCTCAATACCTTGGACATGAATCACCGAGTAGATATTTTTCTTTACAATGCTTAAAACA
AGGCCGCACAGAACTAAACAATAAAGTTACCTTGATCTTTAATAAAATATTCCCCCATTA
ATAAGTACTCTCTTCGATTACGATTTAGCCATATTCATTTTGACCATACATTGCAGATGT
GAGATGGATTTTAAGTGGTGAAAGCGCTCTAAGCTATGCCATATAAGTACGTAAGGAGAG
ACAAAATTAAACATAATTAAGCGCCATGTGAGACTAAATGTGGCCGTCGTTTTGATTATA
TGATTGGGAAAAGCTCCTAAACATAGAGGTAGAATTATAGTTCGGAAATTTCGTCTTGCC
CTGCTCATTTTGTAGAAAACGAGTCATCATCTCCACCCTTTGTAACCGGTGTCCTGCTCA
CATAAATAGTCTCTACTGAGAGATTTGTGAATTTCGAGATAATTTTTGGGATTCCATTGT
TGATAAAGGCAATATTATTAGGTATATAAAATATACTAGA
>MIT_Sbay_c77_8808 YGL040C 5' untranslated region, Contig c77 1 - 1377, 2000 bp (revcom)
ACTTTGTCAGTGTTTTTCTGGTAAGGATATCTGGAAGAAGTAACAATACGTATAAATTAC
AAAATTACCGTTTTATGTCGTGGAATGGGCTATGAACTAACATTAACAATAGAGTGATGC
ATAGACGTCACTAGCCTTTTATTGTGTTGCCTTGCTCTTTTATAAATCAGGCAGCCTGCC
GCAGGCCAATCACCGCACCGCCCGGAGATGCTCGTTTACCGTTGTGCACCAAATTTTTCA
TTTTTTGCCTTTTTCTATTTGGCAGCGTTTTCGAAAAATTTTGATCATTAGTCTTCAATG
ACTGGACTGTCATATTTTAGGGCACGCAGGTAAAGATATGAACAAATCATATTGATGATG
GATGCCAATCCTTCAATGTAAATTCTTTCTAAACATCATGATAAAGAACTTCAGTAAGAG
AGTGATAAAAACTTTACATGTATGGCGGGTGTATTCTGTAATTGTTTTTTAGATCTTTTT
GTTGTTAACGGTGACACCATTCTTACTACAATAATTGCATGTCAAATGTAAATATCTTGC
TTCACATTTCGTTGTTTCTTTACGATAAATTGTTTCGTCGCAAATATATCTTATTTTGCG
TGGTTTATCTACAGACACTGCTTGATTTACGCATAAGTACATCATGTAGTAATTCTTATA
TTGAGTATAAAACCATATGAATAGAAATATTTTTGTTAATCTATCGTTAATTTACATGCT
AGTTTATTTGTCCCTTTAAAATTTCTTTATATATTTGTTGCAATATGTGGACAAGGAAAC
ACGAAATATATTGGGATAAAGTTTAAGTAGAGATACATAGAACTAAACAATAAATTCATA
TTCAATAATACTTCAAAAGGTACTCTCCTGTCTGAACACAGAGACTCACAGACTTTATTT
AGTCGTTATGGCGATGTCAGACATCATGTTTAAGGTAAGCCGAGTGGATTGATATGAAAT
TGTCATATCATGAATAAGCTAATTACCCAAAAACAGTAAA
>WashU_Skud_Contig2052.17 YGL040C 5' untranslated region, Contig c2052 29967 - 31966, 2000 bp (revcom)
GATTTGTCAGTGTTTTCTGATATGGATGCCTGGAGAAAATATTAATATGTGGAAACCACA
AAACTTCCACTTATATAGCTAATTTAGCCAGAAATCATGAACAATAGGATGACGCATAGA
CGTCACTACTCTTCATATAAGTTGCCTTTCTCTTTTATAAATTGGGCAGGCAGCTTGCCT
CAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTTGCGTTCAAAGTTTTTC
ATTTTCCGCATCATCTACTTTTTTTTTTTTGACGCCGTTTTTGAATGTCTTGGTCATTGA
TCTTGAAATGATTTATGTTCGTGTTTTCACGGCACAAAGGTAGGCAAATCGGTAAATTTT
ACTCGTAATAAATAATCAAGGCCTCTAGAGGATTTAATATCAGGAAATAATAATGTGAGT
TTTTTGCAAATGGCCTTATATTCCTGACATCTTCTTGAATTTGTGTTTTAGCGTCGATGA
AGACTCTTCCTTTTTTCGTACGGTAATCTGGACATCTTGTTTCGTCTTTTCTTTTTTTTT
TGCGATTGCTTGTAATTCCAGATATGCAGCATTTATTTACAGGTGCTGATTGATTTACTA
TAGAGTTTATCAGGTAGTAGTTCTTTTTCATGTCTCAATTGAAGAAAAGGAACCCATAAA
TACATTAGCACTGAACAAACAATAACTGCCGCATTGGTTTGTTTTCTAACTTGAATTTTT
CTTTATACATATGCCACTGTATTAGGATGGGTGAATACCGTTTTCTTACTTTCTTCCTAT
GAAGGCGAAAGAATGGTGAAGGACAACTAAACAATAAATCGTTTTTCACACATCCCCATA
AAGCTTTCTCTGTTTGTCAGTTGTGACTCATCTTTCGTCGATGTTGCTTGGTAGATACAA
TTGAACAAGATTGAGATATCTAAAATGTTCAAAAATTATACTCTCTTATGTAGTTTCCGT
CATGGCTGAACGAAGGAAAACTACATCACCTGAGAATTAC
>SGD_Scer_YDR044W HEM13 "Coproporphyrinogen III oxidase, an oxygen requiring enzyme that catalyzes the sixth step in the heme biosynthetic pathway; localizes to the mitochondrial inner membrane; transcription is repressed by oxygen and heme (via Rox1p and Hap1p)"
CTTTATGTGTATTTAATTGTGTTCGAAGAGTTCGGTTTGCTATGTTTGATTTGCGAAAAG
AAAGCTTTTGATATGCTCAAAAAAAGAAAACCCGGAGAATAAAAGCTTAACAAAGAAAGA
CAATAGGTGGAAAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTCGAAACGAGAACA
ATGGGCAAAGCAAGCTTTATCTTCGGATCGTCCGTCAGCGCTTTGGTTGCAGTCTTATGC
TTTGTTCAAGCTGGAGCGTTATTGGTGGGAGAACCAGAAAAGGCGAAAGCGTAGCGTTCT
TTGAAATTTGGCTTCTGTTCCTGCGACTCGTTTAAAAGTAGAAGGGCCCGCGGAGCCGCT
GTGAAAGATTTCTTTTACTCTTTCAGCGCAGAAATCTCGCAGGAGCTCAGCAGAAAGTGC
CTATGACGGTAATCCCAGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAATTAA
AATACCGTGCCTATAGTAACTTTTTTTTACGCTGTGAACCGTTCAACACACAGTAAAAAC
TCCGCAGGAAATGGTTTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTTTCCCAACA
GTGAACGAGAGGACAAACTCCAGAGGATTTGCGGGCTTGATGATAAAATGTATTGTTGAA
AAGATCGCGAATGCAACAATTACGGTGGGGAGAAATATCAACAAAAGGGCAAGGCTATGC
CTTCTGGAAAGTGGCAGACTTGCACTTTCCTCGAAAAGAAAAATGACCGCAAGATCCGGT
TGTTCTCAACCTTCTACATTAAGACATACTTCTACGATTTTCGAATGCCGAAGCAACTAT
CGCTGAAATTTGTCATGTCAAAATTGCTACTGGGGGAGAAGAATATATATGGAAGTAATT
ATTATTTACGTTGCTGAAATGGCAGGTTAGACGCATGTTTTGCAAAATAAGTGGTTTTGA
AAAGAATTGATACTAGGAATCGGTGCAATACCTTCTACCT
>MIT_Spar_c130_3912 YDR044W 5' untranslated region, Contig c130 4128 - 6127, 2000 bp (revcom)
CTTTATATGTGTGTTTTGTGGTGTTCGAAATTGGTTTCTTTTGTTCGACTTGCGAGAAGA
AAGCTATCAATATGCTTTCCAAAAAAAGCTGGAGAATAAAAGCTTAACAAAGAAAGACAA
TAGGCGGAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTTCGAAACGAGAACAATGG
ACAAATCAAGCTTTATCTATGGGTTGTCAGCTCTTTGGTTGCAGTCTTGTGCTTGGTTCA
AGCTGGGGCATTATTGGTGGGAGAAGCCAGAAAAGGCGAAAGCGTAGCGTTCTTTGAAAT
TTGGATTCTGTTCCTGCGACTCGTTTAAAAGAAGAAGGGCTGCGGAGCCACTGTGAAAGA
CTTGTTGTGCTCTTTCAACTAAGAAATCTGGCAGGAACTCGATATAAAGTGCCTGTGACA
GTAATCTCAGGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAAATTGAAATACC
GTGCCTATGGTAACTTTTTTTTACGCTGCGAACCGTTCAACACACATTGAAAACCCCGCA
GCAATTGTTCTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTCTCCCAACAGTGTAC
GAGCGGACGAAACTCTAGAGGATTTGCAGGCTCGGTGATAAAATGTATTGTTGAAAAGAA
CGCGAATGCAACGATTGTGGTGGAGAGAAATATCAACAGGGCAAGGCAAGGCTATGCTCT
TTTGGAAGTGGCGGACTTGCACTTTCTTGAAAAGAAAAATGACCGCAAGATCCGGTTGTT
CATAACTTTCTACAATAAGGCATACTTCTACGGTTTTCCAATGCTGAGGCAACTATCGCT
ATAAAATCGCTGCTAGGAGAAGATTATATATGGACGTAAATATTTTTTACGTTACTAAAA
TTCTAGGTTAGAGGCACGTTTTGCAGAACCAGTGGCCTTGGAAAGGTGTTGCTACAAATT
TATGCAATTTCTTCAACTTGCCAGGTGGTCTTGGATGATC
>MIT_Sbay_c896_21290 YDR044W 5' untranslated region, Contig c896 7383 - 9382(revcom), 2000 bp (revcom)
CTTGTTATGTGTGTTTGTGGTGATTGCGGTTTGGTTTTTCTGATTCGTATGACAGAAAGA
AAAAAATTCAGTTTACCTTGTAAGGTGATTAGGAGAAGAAAAAAAGCTTATTGGCAGCGA
ACAATAGGTGAAAAAAAAAAAGAAAATGCGTGTCCTTATATAGCTTTCTCGAAGGGAGAA
CAATGGATAAATCAAAGCTTATCTACGGGTCAACAGCTCTTTGGTTGCTGTCTTGCTCTA
GGTCCAAGCTGGGGCATAATTGGTGGGAGAAGCCAGAAAATGCGAAAGCGTACCGTTCTG
TGAAAAATGGCTTCGGTTCCTGCGACTCGTTTAAAAAGAAAAGGGCCCGCGCAGCCTGTG
TGAAATGTTCGTTTTGCCCTTCCCAGAGAGAAATCTTGCAGGAGCCTCAATACAATGTGC
CTGCGGATGGAATACCAGGGGATAAAGGCGTGAAGGCACTCCCTGAACAATTGAAAATTG
GAAAAAAAAAGTGCCTGTGATGAATCTTATACGTTGGGAAAACTCCAAGACACTTTTAAA
ACTCCGCAGAGATTGTTTGGAGGGACCTTGACCACGAGTTGGGAGTATTGTTTTTTCCTG
GAAGGAACGAGCGGAACTCTTGGGGATTTGCGGGCTCGCTAATAAAAAGTGTCTTGTTGA
AGAAAAGTAGAATGCGACTAAAACGGTGGAGGAAAATATCAACAAGGCAAGGCTATGCCT
TTCGAAGAAAAGCGGACTTGCAATTGCACAACCGTATCGAAGAGAATTGAGAAGGGGGTG
CAAAGTGATCCGGTTGTTCATATTTCTTCACCAATTGATACAATTATCTACGTTTGTTCT
GTTGACCAATCCAACGGGGACTCTGTATGACATAAGTCTTCCTTACATTGCTAAGATCCA
AGATCAGACCCGTAGATGAGTTCTGCACCAAAGAGTTGTTAACCGTCTTGCCTGAATAAT
TTTAAGTTGTCGCGATCCTCTTACAAGGTGTTCTTATTTC
>WashU_Smik_Contig2283.3 YDR044W 5' untranslated region, Contig c2283 2261 - 4260(revcom), 2000 bp (revcom)
CTTTATTGAGGATTTGTGGCGTTTGAGGTTTGGTTTTTTATTCAATTTGAAAGAAGAAAA
CTATCGTTATACTTTCGAAGAAAACACGGGGAATAAAAGCTTAACAGGTGAGACAATAGG
TGGAAAAAAAGGAAAATATGTGTCTTTATATAGCCTTTTCAAAAAGAGAACAATGGTCAA
ATAAAGGTTTATCTACGAGTCGACAGTTCGTTGGCTGCAGTGTTACGCTTGGTTGAAGCT
GGGGCATTATTGGTGGAAGAAGCCAGAAAAGACGAAAGAGTAGCGTAGCGTTCTTTCAAA
TTTTGGTTTCGGGTTCCTGCGACTCGTTTAAAAAAGAAAAGGGCCCGCGGCCCCGCCGTG
AAACACTTCGTCTTGCTCTTCCCACCCAGAAAACTTGTAGGAGCCTCAGTTACAAAGTGC
CTGTAATGGAAATCTTAGGGGGCTACTATTGTAAAGGCAATTTCTGAACAATTGAAAGTG
AAAATATCGTGCCTGTGGTAACTTTCTTATACGCCGTGAAACGTTTAACATACGTTGAAA
ACTCCGCAGGGATTGGTTTGGAAAATTATAGTCACGAATTAGGCGTATTGTCTTTCAAGA
AGGTACGAGCGGATGAACTTCTTGAGGATTTGCGGGTTCGGTGATAAAAAATGTATTGTT
GAAAAGAACGCGAATGCAACAATTACGGTGGAGAAAAATATTAACAAGGGAAGGCAAGGC
TATGTTCTATTGAGAAGCGGCGGACTTGCACTTTCCTCGAAGAAAAAAATGTCTTCAAGA
TCCAATGTTCATATAACTTTCTACAATAAGGTATCCTTCTACGATCTTTCAATGTTAAGA
TTGAAATCAATGTAAAAAGCACCATGTTGAATACTACTGCTAGGAGGAGATCACATATGA
ATGTGATTATTATTTATATTAGTAAATTTTCAGGTTAGGAAGAAGTTATGTGACGCTTTA
GCTTTGGAAATTTGTTGCGGGAAACTGATAACATTCTTTT
BioPerl-1.007002/t/data/map_hem/HEM2-HEM13.meme.txt000444000766000024     11436713155576321 21303 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM2-HEM13.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YGL040C         1.0000   1000  MIT_Spar_c19_8512        1.0000   1000  
MIT_Smik_c273_7756       1.0000   1000  MIT_Sbay_c77_8808        1.0000   1000  
WashU_Skud_Contig2052.17 1.0000   1000  SGD_Scer_YDR044W         1.0000   1000  
MIT_Spar_c130_3912       1.0000   1000  MIT_Sbay_c896_21290      1.0000   1000  
WashU_Smik_Contig2283.3  1.0000   1000  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM2-HEM13.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            9000    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.314 C 0.186 G 0.186 T 0.314 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 197   E-value = 9.2e-022
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  ::::::4:12a1:::::::8
pos.-specific     C  a144:a::1::::::66::1
probability       G  :66:a:6a28:::a8::1a1
matrix            T  :3:6::::6::9a:2449::

         bits    2.5 *   ** *     *    * 
                 2.3 *   ** *     *    * 
                 2.0 *   ** *     *    * 
                 1.8 *   ** *     *    * 
Information      1.5 * * ** * ** ***   * 
content          1.3 * * ** * ** ***  ** 
(31.6 bits)      1.0 * ****** ********** 
                 0.8 ******** ***********
                 0.5 ******** ***********
                 0.3 ********************
                 0.0 --------------------

Multilevel           CGGTGCGGTGATTGGCCTGA
consensus             TCC  A GA    TTT   
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2052.17     -    180  1.35e-13 AATCCCTGTT CGGTGCGGTGATTGGCCTGA GGCAAGCTGC
MIT_Smik_c273_7756           -    179  1.35e-13 AATCCTTATT CGGTGCGGTGATTGGCCTGA GGCAACATAC
MIT_Spar_c19_8512            -    181  1.35e-13 AATCCCTGTT CGGTGCGGTGATTGGCCTGA GGCAAGCTGC
SGD_Scer_YGL040C             -    180  1.17e-12 AATCCCTGTT CGGTGCGGTGATTGGCTTGA GGCAAGCTTC
MIT_Sbay_c77_8808            -    181  2.88e-12 CATCTCCGGG CGGTGCGGTGATTGGCCTGC GGCAGGCTGC
WashU_Smik_Contig2283.3      +    542  2.66e-10 ACGTTGAAAA CTCCGCAGGGATTGGTTTGG AAAATTATAG
SGD_Scer_YDR044W             +    540  1.12e-09 ACAGTAAAAA CTCCGCAGGAAATGGTTTGA AGAATCTTAA
MIT_Spar_c130_3912           +    534  1.20e-09 ACATTGAAAA CCCCGCAGCAATTGTTCTGA AGAATCTTAA
MIT_Sbay_c896_21290          +    542  1.43e-09 ACTTTTAAAA CTCCGCAGAGATTGTTTGGA GGGACCTTGA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2052.17          1.4e-13  179_[-1]_801
MIT_Smik_c273_7756                1.4e-13  178_[-1]_802
MIT_Spar_c19_8512                 1.4e-13  180_[-1]_800
SGD_Scer_YGL040C                  1.2e-12  179_[-1]_801
MIT_Sbay_c77_8808                 2.9e-12  180_[-1]_800
WashU_Smik_Contig2283.3           2.7e-10  541_[+1]_439
SGD_Scer_YDR044W                  1.1e-09  539_[+1]_441
MIT_Spar_c130_3912                1.2e-09  533_[+1]_447
MIT_Sbay_c896_21290               1.4e-09  541_[+1]_439
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Skud_Contig2052.17 (  180) CGGTGCGGTGATTGGCCTGA  1 
MIT_Smik_c273_7756       (  179) CGGTGCGGTGATTGGCCTGA  1 
MIT_Spar_c19_8512        (  181) CGGTGCGGTGATTGGCCTGA  1 
SGD_Scer_YGL040C         (  180) CGGTGCGGTGATTGGCTTGA  1 
MIT_Sbay_c77_8808        (  181) CGGTGCGGTGATTGGCCTGC  1 
WashU_Smik_Contig2283.3  (  542) CTCCGCAGGGATTGGTTTGG  1 
SGD_Scer_YDR044W         (  540) CTCCGCAGGAAATGGTTTGA  1 
MIT_Spar_c130_3912       (  534) CCCCGCAGCAATTGTTCTGA  1 
MIT_Sbay_c896_21290      (  542) CTCCGCAGAGATTGTTTGGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8829 bayes= 9.93664 E= 9.2e-022 
  -982    251   -982   -982 
  -982    -66    166      4 
  -982    134    166   -982 
  -982    134   -982     78 
  -982   -982    251   -982 
  -982    251   -982   -982 
    45   -982    166   -982 
  -982   -982    251   -982 
  -154    -66     34     78 
   -55   -982    215   -982 
   162   -982   -982   -982 
  -154   -982   -982    145 
  -982   -982   -982    162 
  -982   -982    251   -982 
  -982   -982    215    -55 
  -982    166   -982     45 
  -982    166   -982     45 
  -982   -982    -66    145 
  -982   -982    251   -982 
   126    -66    -66   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 9.2e-022 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.111111  0.555556  0.333333 
 0.000000  0.444444  0.555556  0.000000 
 0.000000  0.444444  0.000000  0.555556 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.111111  0.111111  0.222222  0.555556 
 0.222222  0.000000  0.777778  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.777778  0.222222 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.000000  1.000000  0.000000 
 0.777778  0.111111  0.111111  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
C[GT][GC][TC]GC[GA]G[TG][GA]ATTG[GT][CT][CT]TGA
--------------------------------------------------------------------------------




Time  8.40 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 167   E-value = 2.0e-010
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  4a:aa:a:43:19464a493
pos.-specific     C  ::a::::::1:::4:6:11:
probability       G  6::::::a62491:4::::7
matrix            T  :::::a:::36::1:::4::

         bits    2.5   *    *            
                 2.3   *    *            
                 2.0   *    *   *        
                 1.8   *    *   *        
Information      1.5  *******   *    *   
content          1.3  *******   **   * **
(26.8 bits)      1.0 ********* *** *** **
                 0.8 ********* *** *** **
                 0.5 ********* ******* **
                 0.3 ********* **********
                 0.0 --------------------

Multilevel           GACAATAGGATGAAACAAAG
consensus            A       ATG  CGA T A
sequence                      G          
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2052.17     +    100  8.72e-11 AGAAATCATG AACAATAGGATGACGCATAG ACGTCACTAC
WashU_Smik_Contig2283.3      +    112  3.17e-10 TAACAGGTGA GACAATAGGTGGAAAAAAAG GAAAATATGT
MIT_Spar_c130_3912           +    116  6.61e-10 AACAAAGAAA GACAATAGGCGGAAAAAAAG GAAAATCCGT
SGD_Scer_YGL040C             +    101  8.03e-10 GAAAATCAAA GACAATAGAGTGGCGCATAG ATGTTGCTAG
MIT_Spar_c19_8512            +    102  1.36e-09 AAAAAACAAG GACAATAGAATGACACATAA AGTTTGCTAG
SGD_Scer_YDR044W             +    119  1.86e-09 AACAAAGAAA GACAATAGGTGGAAAAAAAA AGGAAAATCC
MIT_Sbay_c77_8808            +    105  3.82e-09 AACTAACATT AACAATAGAGTGATGCATAG ACGTCACTAG
MIT_Smik_c273_7756           +    102  5.03e-09 ATAAATCAGG AACAATAGAATGACGCACCG AGTTTGCTAG
MIT_Sbay_c896_21290          +    120  2.10e-08 ATTGGCAGCG AACAATAGGTGAAAAAAAAA AAGAAAATGC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2052.17          8.7e-11  99_[+2]_881
WashU_Smik_Contig2283.3           3.2e-10  111_[+2]_869
MIT_Spar_c130_3912                6.6e-10  115_[+2]_865
SGD_Scer_YGL040C                    8e-10  100_[+2]_880
MIT_Spar_c19_8512                 1.4e-09  101_[+2]_879
SGD_Scer_YDR044W                  1.9e-09  118_[+2]_862
MIT_Sbay_c77_8808                 3.8e-09  104_[+2]_876
MIT_Smik_c273_7756                  5e-09  101_[+2]_879
MIT_Sbay_c896_21290               2.1e-08  119_[+2]_861
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
WashU_Skud_Contig2052.17 (  100) AACAATAGGATGACGCATAG  1 
WashU_Smik_Contig2283.3  (  112) GACAATAGGTGGAAAAAAAG  1 
MIT_Spar_c130_3912       (  116) GACAATAGGCGGAAAAAAAG  1 
SGD_Scer_YGL040C         (  101) GACAATAGAGTGGCGCATAG  1 
MIT_Spar_c19_8512        (  102) GACAATAGAATGACACATAA  1 
SGD_Scer_YDR044W         (  119) GACAATAGGTGGAAAAAAAA  1 
MIT_Sbay_c77_8808        (  105) AACAATAGAGTGATGCATAG  1 
MIT_Smik_c273_7756       (  102) AACAATAGAATGACGCACCG  1 
MIT_Sbay_c896_21290      (  120) AACAATAGGTGAAAAAAAAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8829 bayes= 9.93664 E= 2.0e-010 
    45   -982    166   -982 
   162   -982   -982   -982 
  -982    251   -982   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -982   -982   -982    162 
   162   -982   -982   -982 
  -982   -982    251   -982 
    45   -982    166   -982 
     4    -66     34      4 
  -982   -982    134     78 
  -154   -982    234   -982 
   145   -982    -66   -982 
    45    134   -982   -154 
    78   -982    134   -982 
    45    166   -982   -982 
   162   -982   -982   -982 
    45    -66   -982     45 
   145    -66   -982   -982 
     4   -982    192   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.0e-010 
 0.444444  0.000000  0.555556  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.333333  0.111111  0.222222  0.333333 
 0.000000  0.000000  0.444444  0.555556 
 0.111111  0.000000  0.888889  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.444444  0.444444  0.000000  0.111111 
 0.555556  0.000000  0.444444  0.000000 
 0.444444  0.555556  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.111111  0.000000  0.444444 
 0.888889  0.111111  0.000000  0.000000 
 0.333333  0.000000  0.666667  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[GA]ACAATAG[GA][ATG][TG]GA[AC][AG][CA]A[AT]A[GA]
--------------------------------------------------------------------------------




Time 16.42 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   18   sites =   9   llr = 161   E-value = 2.9e-010
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  a97926:1a9:::8a:2:
pos.-specific     C  ::3::::6::::a::427
probability       G  ::::84a1:1aa:::34:
matrix            T  :1:1:::2:::::2:213

         bits    2.5       *   ***     
                 2.3       *   ***     
                 2.0       *   ***     
                 1.8       *   ***     
Information      1.5 *   * * * *** *   
content          1.3 *   * * ***** *  *
(25.8 bits)      1.0 ******* ***** *  *
                 0.8 ******* ******** *
                 0.5 ******************
                 0.3 ******************
                 0.0 ------------------

Multilevel           AAAAGAGCAAGGCAACGC
consensus              C AG T     T GAT
sequence                            TC 
                                       
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                   Site     
-------------            ------  ----- ---------            ------------------
MIT_Spar_c130_3912           +    695  1.68e-11 GAGAAATATC AACAGGGCAAGGCAAGGC TATGCTCTTT
MIT_Sbay_c77_8808            -    144  1.90e-10 CCTGATTTAT AAAAGAGCAAGGCAACAC AATAAAAGGC
SGD_Scer_YDR044W             +    703  6.56e-10 AAATATCAAC AAAAGGGCAAGGCTATGC CTTCTGGAAA
WashU_Smik_Contig2283.3      +    703  3.25e-09 GAAAAATATT AACAAGGGAAGGCAAGGC TATGTTCTAT
MIT_Spar_c19_8512            -    140  3.60e-09 CTTGATTTAT AAAAGAGTAAGGCAACCT AATAAATGCT
MIT_Sbay_c896_21290          +    701  6.28e-09 GGAAAATATC AACAAGGCAAGGCTATGC CTTTCGAAGA
MIT_Smik_c273_7756           -    833  1.56e-08 GTTTTCTACA AAATGAGCAGGGCAAGAC GAAATTTCCG
WashU_Skud_Contig2052.17     -    139  1.98e-08 CCCAATTTAT AAAAGAGAAAGGCAACTT ATATGAAGAG
SGD_Scer_YGL040C             -    139  2.12e-08 CTTGATTTAT ATAAGAGTAAGGCAACCT AATAAATGCT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c130_3912                1.7e-11  694_[+3]_288
MIT_Sbay_c77_8808                 1.9e-10  143_[-3]_839
SGD_Scer_YDR044W                  6.6e-10  702_[+3]_280
WashU_Smik_Contig2283.3           3.3e-09  702_[+3]_280
MIT_Spar_c19_8512                 3.6e-09  139_[-3]_843
MIT_Sbay_c896_21290               6.3e-09  700_[+3]_282
MIT_Smik_c273_7756                1.6e-08  832_[-3]_150
WashU_Skud_Contig2052.17            2e-08  138_[-3]_844
SGD_Scer_YGL040C                  2.1e-08  138_[-3]_844
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=18 seqs=9
MIT_Spar_c130_3912       (  695) AACAGGGCAAGGCAAGGC  1 
MIT_Sbay_c77_8808        (  144) AAAAGAGCAAGGCAACAC  1 
SGD_Scer_YDR044W         (  703) AAAAGGGCAAGGCTATGC  1 
WashU_Smik_Contig2283.3  (  703) AACAAGGGAAGGCAAGGC  1 
MIT_Spar_c19_8512        (  140) AAAAGAGTAAGGCAACCT  1 
MIT_Sbay_c896_21290      (  701) AACAAGGCAAGGCTATGC  1 
MIT_Smik_c273_7756       (  833) AAATGAGCAGGGCAAGAC  1 
WashU_Skud_Contig2052.17 (  139) AAAAGAGAAAGGCAACTT  1 
SGD_Scer_YGL040C         (  139) ATAAGAGTAAGGCAACCT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 18 n= 8847 bayes= 9.93958 E= 2.9e-010 
   162   -982   -982   -982 
   145   -982   -982   -154 
   104     92   -982   -982 
   145   -982   -982   -154 
   -55   -982    215   -982 
    78   -982    134   -982 
  -982   -982    251   -982 
  -154    166    -66    -55 
   162   -982   -982   -982 
   145   -982    -66   -982 
  -982   -982    251   -982 
  -982   -982    251   -982 
  -982    251   -982   -982 
   126   -982   -982    -55 
   162   -982   -982   -982 
  -982    134     92    -55 
   -55     34    134   -154 
  -982    192   -982      4 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 18 nsites= 9 E= 2.9e-010 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.000000  0.111111 
 0.666667  0.333333  0.000000  0.000000 
 0.888889  0.000000  0.000000  0.111111 
 0.222222  0.000000  0.777778  0.000000 
 0.555556  0.000000  0.444444  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.111111  0.555556  0.111111  0.222222 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.777778  0.000000  0.000000  0.222222 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.444444  0.333333  0.222222 
 0.222222  0.222222  0.444444  0.111111 
 0.000000  0.666667  0.000000  0.333333 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
AA[AC]A[GA][AG]G[CT]AAGGC[AT]A[CGT][GAC][CT]
--------------------------------------------------------------------------------




Time 24.29 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   15   sites =   9   llr = 139   E-value = 2.6e-006
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  :::::::2:8:::::
pos.-specific     C  3:9:a:::318771:
probability       G  :9:::a::::1:34:
matrix            T  711a::a87113:4a

         bits    2.5     **         
                 2.3     **         
                 2.0  ** **         
                 1.8  ** **         
Information      1.5  ******   * * *
content          1.3  ******   *** *
(22.3 bits)      1.0 ******* * *** *
                 0.8 ***************
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           TGCTCGTTTACCCGT
consensus            C      AC  TGT 
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Skud_Contig2052.17     +    209  3.42e-10 GAACAGGGAT TGCTCGTTTACCCGT TGCGTTCAAA
MIT_Smik_c273_7756           +    208  3.42e-10 GAATAAGGAT TGCTCGTTTACCCGT TGTTCGATTT
MIT_Spar_c19_8512            +    210  3.42e-10 GAACAGGGAT TGCTCGTTTACCCGT AGTTTGAATT
SGD_Scer_YGL040C             +    209  3.42e-10 GAACAGGGAT TGCTCGTTTACCCGT ATTTTGATTT
MIT_Sbay_c77_8808            +    209  5.96e-09 CGCCCGGAGA TGCTCGTTTACCGTT GTGCACCAAA
MIT_Spar_c130_3912           -    591  1.14e-07 GAGTTTCGTC CGCTCGTACACTGTT GGGAGAAACA
SGD_Scer_YDR044W             -    597  3.16e-07 GGAGTTTGTC CTCTCGTTCACTGTT GGGAAAAACA
WashU_Smik_Contig2283.3      -    597  7.66e-07 GAAGTTCATC CGCTCGTACCTTCTT GAAAGACAAT
MIT_Sbay_c896_21290          +    366  1.10e-06 CTGTGTGAAA TGTTCGTTTTGCCCT TCCCAGAGAG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2052.17          3.4e-10  208_[+4]_777
MIT_Smik_c273_7756                3.4e-10  207_[+4]_778
MIT_Spar_c19_8512                 3.4e-10  209_[+4]_776
SGD_Scer_YGL040C                  3.4e-10  208_[+4]_777
MIT_Sbay_c77_8808                   6e-09  208_[+4]_777
MIT_Spar_c130_3912                1.1e-07  590_[-4]_395
SGD_Scer_YDR044W                  3.2e-07  596_[-4]_389
WashU_Smik_Contig2283.3           7.7e-07  596_[-4]_389
MIT_Sbay_c896_21290               1.1e-06  365_[+4]_620
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=15 seqs=9
WashU_Skud_Contig2052.17 (  209) TGCTCGTTTACCCGT  1 
MIT_Smik_c273_7756       (  208) TGCTCGTTTACCCGT  1 
MIT_Spar_c19_8512        (  210) TGCTCGTTTACCCGT  1 
SGD_Scer_YGL040C         (  209) TGCTCGTTTACCCGT  1 
MIT_Sbay_c77_8808        (  209) TGCTCGTTTACCGTT  1 
MIT_Spar_c130_3912       (  591) CGCTCGTACACTGTT  1 
SGD_Scer_YDR044W         (  597) CTCTCGTTCACTGTT  1 
WashU_Smik_Contig2283.3  (  597) CGCTCGTACCTTCTT  1 
MIT_Sbay_c896_21290      (  366) TGTTCGTTTTGCCCT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 8874 bayes= 9.94398 E= 2.6e-006 
  -982     92   -982    104 
  -982   -982    234   -154 
  -982    234   -982   -154 
  -982   -982   -982    162 
  -982    251   -982   -982 
  -982   -982    251   -982 
  -982   -982   -982    162 
   -55   -982   -982    126 
  -982     92   -982    104 
   126    -66   -982   -154 
  -982    215    -66   -154 
  -982    192   -982      4 
  -982    192     92   -982 
  -982    -66    134     45 
  -982   -982   -982    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 2.6e-006 
 0.000000  0.333333  0.000000  0.666667 
 0.000000  0.000000  0.888889  0.111111 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.222222  0.000000  0.000000  0.777778 
 0.000000  0.333333  0.000000  0.666667 
 0.777778  0.111111  0.000000  0.111111 
 0.000000  0.777778  0.111111  0.111111 
 0.000000  0.666667  0.000000  0.333333 
 0.000000  0.666667  0.333333  0.000000 
 0.000000  0.111111  0.444444  0.444444 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
[TC]GCTCGT[TA][TC]AC[CT][CG][GT]T
--------------------------------------------------------------------------------




Time 32.02 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 157   E-value = 4.5e-006
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  a:21::1178:99:1794a8
pos.-specific     C  ::::3::::1:1:163:1:2
probability       G  ::177199319::91:13::
matrix            T  :a72:9::::1:1:2::1::

         bits    2.5                     
                 2.3                     
                 2.0       **  *  *      
                 1.8       **  *  *      
Information      1.5 **  * **  *  *    * 
content          1.3 **  ****  ** *  * * 
(25.2 bits)      1.0 ** ****** **** ** **
                 0.8 ** *********** ** **
                 0.5 ***************** **
                 0.3 ********************
                 0.0 --------------------

Multilevel           ATTGGTGGAAGAAGCAAAAA
consensus              ATC   G     TC G C
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Smik_Contig2283.3      +    249  2.56e-12 CTGGGGCATT ATTGGTGGAAGAAGCCAGAA AAGACGAAAG
MIT_Sbay_c896_21290          +    259  2.92e-12 CTGGGGCATA ATTGGTGGGAGAAGCCAGAA AATGCGAAAG
MIT_Spar_c130_3912           +    253  2.92e-12 CTGGGGCATT ATTGGTGGGAGAAGCCAGAA AAGGCGAAAG
SGD_Scer_YDR044W             +    261  1.67e-09 CTGGAGCGTT ATTGGTGGGAGAACCAGAAA AGGCGAAAGC
MIT_Sbay_c77_8808            +     27  1.46e-08 TCTGGTAAGG ATATCTGGAAGAAGTAACAA TACGTATAAA
MIT_Smik_c273_7756           -    234  3.53e-08 GCCGAAAAAA ATTGGTAGAAGATGAAAAAA AAAATCGAAC
MIT_Spar_c19_8512            +     45  7.16e-08 GCAGGCAATA ATATGGGGAAGCAGTAAAAC TTTTTGTTTT
WashU_Skud_Contig2052.17     +    962  8.03e-08 AGTTTCCGTC ATGGCTGAACGAAGGAAAAC TACATCACCT
SGD_Scer_YGL040C             +     26  1.04e-07 CTAGGTATGA ATTACTGGAGTAAGCAATAA TATGAGTAAG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Smik_Contig2283.3           2.6e-12  248_[+5]_732
MIT_Sbay_c896_21290               2.9e-12  258_[+5]_722
MIT_Spar_c130_3912                2.9e-12  252_[+5]_728
SGD_Scer_YDR044W                  1.7e-09  260_[+5]_720
MIT_Sbay_c77_8808                 1.5e-08  26_[+5]_954
MIT_Smik_c273_7756                3.5e-08  233_[-5]_747
MIT_Spar_c19_8512                 7.2e-08  44_[+5]_936
WashU_Skud_Contig2052.17            8e-08  961_[+5]_19
SGD_Scer_YGL040C                    1e-07  25_[+5]_955
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
WashU_Smik_Contig2283.3  (  249) ATTGGTGGAAGAAGCCAGAA  1 
MIT_Sbay_c896_21290      (  259) ATTGGTGGGAGAAGCCAGAA  1 
MIT_Spar_c130_3912       (  253) ATTGGTGGGAGAAGCCAGAA  1 
SGD_Scer_YDR044W         (  261) ATTGGTGGGAGAACCAGAAA  1 
MIT_Sbay_c77_8808        (   27) ATATCTGGAAGAAGTAACAA  1 
MIT_Smik_c273_7756       (  234) ATTGGTAGAAGATGAAAAAA  1 
MIT_Spar_c19_8512        (   45) ATATGGGGAAGCAGTAAAAC  1 
WashU_Skud_Contig2052.17 (  962) ATGGCTGAACGAAGGAAAAC  1 
SGD_Scer_YGL040C         (   26) ATTACTGGAGTAAGCAATAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8829 bayes= 9.93664 E= 4.5e-006 
   162   -982   -982   -982 
  -982   -982   -982    162 
   -55   -982    -66    104 
  -154   -982    192    -55 
  -982     92    192   -982 
  -982   -982    -66    145 
  -154   -982    234   -982 
  -154   -982    234   -982 
   104   -982     92   -982 
   126    -66    -66   -982 
  -982   -982    234   -154 
   145    -66   -982   -982 
   145   -982   -982   -154 
  -982    -66    234   -982 
  -154    166    -66    -55 
   104     92   -982   -982 
   145   -982    -66   -982 
    45    -66     92   -154 
   162   -982   -982   -982 
   126     34   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 4.5e-006 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.222222  0.000000  0.111111  0.666667 
 0.111111  0.000000  0.666667  0.222222 
 0.000000  0.333333  0.666667  0.000000 
 0.000000  0.000000  0.111111  0.888889 
 0.111111  0.000000  0.888889  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.666667  0.000000  0.333333  0.000000 
 0.777778  0.111111  0.111111  0.000000 
 0.000000  0.000000  0.888889  0.111111 
 0.888889  0.111111  0.000000  0.000000 
 0.888889  0.000000  0.000000  0.111111 
 0.000000  0.111111  0.888889  0.000000 
 0.111111  0.555556  0.111111  0.222222 
 0.666667  0.333333  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.444444  0.111111  0.333333  0.111111 
 1.000000  0.000000  0.000000  0.000000 
 0.777778  0.222222  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
AT[TA][GT][GC]TGG[AG]AGAAG[CT][AC]A[AG]A[AC]
--------------------------------------------------------------------------------




Time 39.67 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YGL040C                 1.75e-23  25_[+5(1.04e-07)]_55_[+2(8.03e-10)]_18_[-3(2.12e-08)]_23_[-1(1.17e-12)]_9_[+4(3.42e-10)]_178_[-3(7.59e-05)]_498_[-2(2.36e-05)]_63
MIT_Spar_c19_8512                4.98e-25  44_[+5(7.16e-08)]_37_[+2(1.36e-09)]_18_[-3(3.60e-09)]_23_[-1(1.35e-13)]_9_[+4(3.42e-10)]_8_[-2(8.78e-05)]_191_[-3(9.88e-05)]_101_[+2(6.40e-05)]_317_[+2(1.09e-05)]_81
MIT_Smik_c273_7756               3.49e-24  25_[+5(8.56e-07)]_56_[+2(5.03e-09)]_57_[-1(1.35e-13)]_9_[+4(3.42e-10)]_11_[-5(3.53e-08)]_529_[+5(2.17e-05)]_30_[-3(1.56e-08)]_150
MIT_Sbay_c77_8808                4.86e-24  26_[+5(1.46e-08)]_58_[+2(3.82e-09)]_19_[-3(1.90e-10)]_19_[-1(2.88e-12)]_8_[+4(5.96e-09)]_465_[-2(9.60e-06)]_54_[+5(6.34e-05)]_218
WashU_Skud_Contig2052.17         2.08e-25  99_[+2(8.72e-11)]_19_[-3(1.98e-08)]_23_[-1(1.35e-13)]_9_[+4(3.42e-10)]_322_[-5(2.17e-05)]_101_[-4(3.66e-05)]_280_[+5(8.03e-08)]_19
SGD_Scer_YDR044W                 1.15e-20  118_[+2(1.86e-09)]_40_[+3(9.53e-06)]_64_[+5(1.67e-09)]_153_[+1(5.50e-05)]_86_[+1(1.12e-09)]_37_[-4(3.16e-07)]_91_[+3(6.56e-10)]_280
MIT_Spar_c130_3912               1.46e-25  115_[+2(6.61e-10)]_117_[+5(2.92e-12)]_261_[+1(1.20e-09)]_37_[-4(1.14e-07)]_89_[+3(1.68e-11)]_288
MIT_Sbay_c896_21290              9.74e-21  84_[+5(7.87e-05)]_15_[+2(2.10e-08)]_119_[+5(2.92e-12)]_87_[+4(1.10e-06)]_161_[+1(1.43e-09)]_37_[-4(1.81e-05)]_87_[+3(6.28e-09)]_282
WashU_Smik_Contig2283.3          1.35e-23  111_[+2(3.17e-10)]_81_[+1(3.33e-05)]_16_[+5(2.56e-12)]_273_[+1(2.66e-10)]_35_[-4(7.66e-07)]_91_[+3(3.25e-09)]_280
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM2-HEM14.fa000444000766000024      1653113155576321 20103 0ustar00cjfieldsstaff000000000000>SGD_Scer_YGL040C HEM2 "Delta-aminolevulinate dehydratase, a homo-octameric enzyme, catalyzes the conversion of delta-aminolevulinic acid to porphobilinogen, the second step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus"
GGTTTTGTCAATTTTCTAGGTATGAATTACTGGAGTAAGCAATAATATGAGTAAGCAGTA
AAACTTTTTTTTATTTGGCTGATTGGGCAAGAAAATCAAAGACAATAGAGTGGCGCATAG
ATGTTGCTAGCATTTATTAGGTTGCCTTACTCTTATATAAATCAAGCGGGAAGCTTGCCT
CAAGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTATTTTGATTTTTTTTTC
ACCTTTTCCAATTTTTTTTTCGGCAACAATTTTTTGGATGATTTTTATCGTCGATCTTGG
AATGATGATGTATTTCGGCGTCTCTACAAGACCCAATAAAGTAATTCGGTGACACAGGCT
TGTAGCAGATAGAAAACGTTCCGAAAGATGGGTTCCAATTGATGTAACACTTCTTTTTTA
TATATTCATGTGGACGTGTACGCCTTCTTCCCTTCTTTGCCTCTTGTGCCACTGTTAATC
CTCTTAAGCATATTGTTTTTATTTACAGACATTGGCTGACTCACCAGAAACTATAATTGA
CGCTGATTTCTAGTTAATTAAAAATAAAATATATGCAAGAATTAGCACCAGGCAGTCATT
TCTGTAAATTGCTTTGTTTTCTATTTCAAATTTGTTTTTTGTATATGTTTCAATGTTCTC
GTGACAATGCAGGCTTTTTTTTGTGCGAATTAAAGTAAAGCTAATCAAAACTAAACAATA
ATTTATCTTGTTCCCGAAAGAGTGGATCATGAGGAGGAAAGCTAACCGTCCAAGATCCTA
TATAATTTTTGAACTGAAAACCAACTGTTCACCTAGAAGACAGGTATCTGGATATGTAAC
TACACGCTCTATAAATACAGAAATCGTAAGCTAATCAATATAAATGTAAAAGAAAATAGG
AATTGCTGTCGATAGATTTATTTACTTTTGTATTGTCATCTGTGTTCTGTGCCAGTACAC
CGGACTCGTATGAGCTGTATGGTGTCGTTTCAATAGAATC
>MIT_Spar_c19_8512 YGL040C 5' untranslated region, Contig c19 1 - 1802, 2000 bp (revcom)
GGTTTTGTCAATATTCTAAATATGGATTCCTAGGGCAGGCAATAATATGGGGAAGCAGTA
AAACTTTTTGTTTTATGTGGCTGATTGGGCCAAAAAACAAGGACAATAGAATGACACATA
AAGTTTGCTAGCATTTATTAGGTTGCCTTACTCTTTTATAAATCAAGCGGGCAGCTTGCC
TCAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTAGTTTGAATTTTTTTT
TCACCTTTTGAAATTTTTTTTTTTCGGCAACAATTTTGAATGACTTTTATCGTCAATCTT
GGGAGTATACCTGCCTCTTTACAACACCCAACAAAACACTTAAGTAAGACAAGCTTGTGG
CAGGTAGGAAAGGTTTCAAAAAAAAAAAAAAGGTTTTTATCTATGGTCATACTTTTTCTT
CGTATATTTATGTGAACACGTACGTCTTGTTTTGCCTTCTTTGGCTCTTGTGTCACTGAA
TCTTCACATATTGTTTTTATTTACAGATACTACTTGACTCGCCTAAAATTATAATCGGCG
ATGGTTTCTACTACCTTAGTTAAAAAATAAAATGAATCAAAACATTACCATTAATAATTC
AATTTTTCCACATTAGTTTGTTTTCTATTTTATGGCTTTCTTCTTGTATATTTCTCAATA
TACTGCATGGCAATGCAAGCTCTTCTCTTTTCTTGATTGAAAATAAAGCTGTGAAGAACT
AAATAATAATTTATTGATGTCCTCCACAAAATGTACACCTGCGCTAACCTTGCTTAACAG
ATACGGTCAAAACGAACTTGAGCATATGTAAAAATCCATGTATTTTTCTTCTTTTGCCAA
CTAAATCAAACTTTTTATTGTATATGTCGTACCGCCAATACAAAGATGGAGAGGTTAATG
AAAATAGATGTGAAAAAAAAGCAGGAACTATTGTAGATAGATATTTTTAGGGTTCGATTG
CTATTTTTCTGTATTATGATCTGTGTTCTATGCCAGTGTA
>MIT_Smik_c273_7756 YGL040C 5' untranslated region, Contig c273 1 - 1807, 2000 bp (revcom)
GGTTTTACCAGTTTTCTTAATACGGATATCTAGAGTAAGTCACAATTTAAGGAAATTGCA
AAATTTTCTTTTTATATAGCTAAATAGGCCAATAAATCAGGAACAATAGAATGACGCACC
GAGTTTGCTAGCAACCTACACACTTGCTTTTTTTTATAAATCAAGAGTGTATGTTGCCTC
AGGCCAATCACCGCACCGAATAAGGATTGCTCGTTTACCCGTTGTTCGATTTTTTTTTTC
ATCTTCTACCAATTTTTTTCGGCAGCGCCTTTGAATGACTTTGATCATCAATCCTGGAGT
AATATACACTTGTATGTTTGAAACGCCCAGTTACAATATTTATTGGAATAGCTAACTTAT
GAGTAAGTGGACCCAAATTTTCGAGTGATGTTTCCTGTCAACGGTGACACTTATTTTTGG
TTTGCAGATATGTATGTGTATATCTTATTCCCACTTTTTTATAGTTATCGTTATCTATGT
ATCTCAATACCTTGGACATGAATCACCGAGTAGATATTTTTCTTTACAATGCTTAAAACA
AGGCCGCACAGAACTAAACAATAAAGTTACCTTGATCTTTAATAAAATATTCCCCCATTA
ATAAGTACTCTCTTCGATTACGATTTAGCCATATTCATTTTGACCATACATTGCAGATGT
GAGATGGATTTTAAGTGGTGAAAGCGCTCTAAGCTATGCCATATAAGTACGTAAGGAGAG
ACAAAATTAAACATAATTAAGCGCCATGTGAGACTAAATGTGGCCGTCGTTTTGATTATA
TGATTGGGAAAAGCTCCTAAACATAGAGGTAGAATTATAGTTCGGAAATTTCGTCTTGCC
CTGCTCATTTTGTAGAAAACGAGTCATCATCTCCACCCTTTGTAACCGGTGTCCTGCTCA
CATAAATAGTCTCTACTGAGAGATTTGTGAATTTCGAGATAATTTTTGGGATTCCATTGT
TGATAAAGGCAATATTATTAGGTATATAAAATATACTAGA
>MIT_Sbay_c77_8808 YGL040C 5' untranslated region, Contig c77 1 - 1377, 2000 bp (revcom)
ACTTTGTCAGTGTTTTTCTGGTAAGGATATCTGGAAGAAGTAACAATACGTATAAATTAC
AAAATTACCGTTTTATGTCGTGGAATGGGCTATGAACTAACATTAACAATAGAGTGATGC
ATAGACGTCACTAGCCTTTTATTGTGTTGCCTTGCTCTTTTATAAATCAGGCAGCCTGCC
GCAGGCCAATCACCGCACCGCCCGGAGATGCTCGTTTACCGTTGTGCACCAAATTTTTCA
TTTTTTGCCTTTTTCTATTTGGCAGCGTTTTCGAAAAATTTTGATCATTAGTCTTCAATG
ACTGGACTGTCATATTTTAGGGCACGCAGGTAAAGATATGAACAAATCATATTGATGATG
GATGCCAATCCTTCAATGTAAATTCTTTCTAAACATCATGATAAAGAACTTCAGTAAGAG
AGTGATAAAAACTTTACATGTATGGCGGGTGTATTCTGTAATTGTTTTTTAGATCTTTTT
GTTGTTAACGGTGACACCATTCTTACTACAATAATTGCATGTCAAATGTAAATATCTTGC
TTCACATTTCGTTGTTTCTTTACGATAAATTGTTTCGTCGCAAATATATCTTATTTTGCG
TGGTTTATCTACAGACACTGCTTGATTTACGCATAAGTACATCATGTAGTAATTCTTATA
TTGAGTATAAAACCATATGAATAGAAATATTTTTGTTAATCTATCGTTAATTTACATGCT
AGTTTATTTGTCCCTTTAAAATTTCTTTATATATTTGTTGCAATATGTGGACAAGGAAAC
ACGAAATATATTGGGATAAAGTTTAAGTAGAGATACATAGAACTAAACAATAAATTCATA
TTCAATAATACTTCAAAAGGTACTCTCCTGTCTGAACACAGAGACTCACAGACTTTATTT
AGTCGTTATGGCGATGTCAGACATCATGTTTAAGGTAAGCCGAGTGGATTGATATGAAAT
TGTCATATCATGAATAAGCTAATTACCCAAAAACAGTAAA
>WashU_Skud_Contig2052.17 YGL040C 5' untranslated region, Contig c2052 29967 - 31966, 2000 bp (revcom)
GATTTGTCAGTGTTTTCTGATATGGATGCCTGGAGAAAATATTAATATGTGGAAACCACA
AAACTTCCACTTATATAGCTAATTTAGCCAGAAATCATGAACAATAGGATGACGCATAGA
CGTCACTACTCTTCATATAAGTTGCCTTTCTCTTTTATAAATTGGGCAGGCAGCTTGCCT
CAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTTGCGTTCAAAGTTTTTC
ATTTTCCGCATCATCTACTTTTTTTTTTTTGACGCCGTTTTTGAATGTCTTGGTCATTGA
TCTTGAAATGATTTATGTTCGTGTTTTCACGGCACAAAGGTAGGCAAATCGGTAAATTTT
ACTCGTAATAAATAATCAAGGCCTCTAGAGGATTTAATATCAGGAAATAATAATGTGAGT
TTTTTGCAAATGGCCTTATATTCCTGACATCTTCTTGAATTTGTGTTTTAGCGTCGATGA
AGACTCTTCCTTTTTTCGTACGGTAATCTGGACATCTTGTTTCGTCTTTTCTTTTTTTTT
TGCGATTGCTTGTAATTCCAGATATGCAGCATTTATTTACAGGTGCTGATTGATTTACTA
TAGAGTTTATCAGGTAGTAGTTCTTTTTCATGTCTCAATTGAAGAAAAGGAACCCATAAA
TACATTAGCACTGAACAAACAATAACTGCCGCATTGGTTTGTTTTCTAACTTGAATTTTT
CTTTATACATATGCCACTGTATTAGGATGGGTGAATACCGTTTTCTTACTTTCTTCCTAT
GAAGGCGAAAGAATGGTGAAGGACAACTAAACAATAAATCGTTTTTCACACATCCCCATA
AAGCTTTCTCTGTTTGTCAGTTGTGACTCATCTTTCGTCGATGTTGCTTGGTAGATACAA
TTGAACAAGATTGAGATATCTAAAATGTTCAAAAATTATACTCTCTTATGTAGTTTCCGT
CATGGCTGAACGAAGGAAAACTACATCACCTGAGAATTAC
>SGD_Scer_YER014W HEM14 "Protoporphyrinogen oxidase, a mitochondrial enzyme that catalyzes the seventh step in the heme biosynthetic pathway, converting protoporphyrinogen IX to protoporphyrin IX"
TATACAAGCTCTTTTTGGCGTTCTCAATTGCACTTTACTCGATATGTTTGAATTGGTGTT
CTTCGCGAATATCTCTATTGTTCTCTCTATTATACTATTTCTTTTTTTGAATACTCCGCG
ACTCCGAAGCAACAAAGTGTCGAAGGCAAGTTCAAAGGCGTTTTGTAACTAAACGAGCAA
TGGCAGCTTTCAATTAAAGAAAGGTTAGCGTTACTCTGTGATTTTTTTCATGTAAAAATT
CTCAAGAGAGATAAAGTTGTTAAAAAATTAAATATAGGTCTATAAAACTCGATAATTATA
ATGCATAAAAAGCTAACAATGT
>MIT_Spar_c425_6072 YER014W 5' untranslated region, Contig c425 34016 - 36015, 2000 bp (revcom)
TATTCGAGCCCTTTCCCGCGTTCCCAATTGTACCTTCCTCGATAGGATTGAATTGGTATC
CTTCGCGGATCTCTCTATTGTTCTCTCTATTATTCTTTTTCTTTTTTAAATACTCCGCGA
CTCCGAAGCAACAAAATGTCGAAGGCAAGATGAAAGGCGTTTTGCAACTAAACGAGTAAT
GGCAGCTTTTAATTAAATAACGGTCAGCATTACTCTATAACTTTTCACATAAAATCCTCG
AAGAAGGAAAAATTGATAATCAATTTACCGAAGAATGAATATAGGTCTATAAAAATTCAA
TAATTATAGATGCATAAAAAGC
>MIT_Smik_c283_5928 YER014W 5' untranslated region, Contig c283 42606 - 44605, 2000 bp (revcom)
TATTGAAGCTCTCTCCACTATTTCTTTAATCGCGCTATACTAGATATGGTTAAACTGCTA
TCTTTTGCAAATCCCTCTATTGTTCTTTCCATTACTCTTTTCTTTTTTAAATACGGACTC
CGAAGCAACAAGGTCGAAGGCAAGCTGAAAGGCATTTTACAACTAAACGAGCAATGGTAG
CTTTTGATTGAATAAATTATTATCATTATTTTGTTATTTGTCCCACGAAATTCTCGTTGA
AAGCAAGGTTCGTAAGGATTTATCAAATGTTAAATATAGATCTATAAAAATTGAATAGTA
ATAATAACAAGGGATGGTGTTA
>MIT_Sbay_c84_6418 YER014W 5' untranslated region, Contig c84 10802 - 12801(revcom), 2000 bp (revcom)
TGTCGAAGTTCTCCTTTATTCCGCTGTTTCTTACGGAATCCAGCGAGACTGTTGTCCTTT
CGCATCCTTCTATTGTTCTTCCTTATTGTTCTCGTTTTTTTTATACTCTGCGACTCCGAA
ACAACAAAATCTCGAAGGCAAGCTAAGGTAAAAATATTCACCACTAAACGAGCAATGACA
GTTATATTCAAACGTCATTCTACTTTTTTGCCAGAGAAGTCCTCACTGGAGACGAAGTTG
GTAAATGCTTTATTTATATTAAACGTAGATCTATAAAGTTTAAATAGTTTATAATGCTTA
ACAAGGGACGATGTTATCTCTT
BioPerl-1.007002/t/data/map_hem/HEM2-HEM14.meme.txt000444000766000024     11443213155576321 21275 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM2-HEM14.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YGL040C         1.0000   1000  MIT_Spar_c19_8512        1.0000   1000  
MIT_Smik_c273_7756       1.0000   1000  MIT_Sbay_c77_8808        1.0000   1000  
WashU_Skud_Contig2052.17 1.0000   1000  SGD_Scer_YER014W         1.0000    322  
MIT_Spar_c425_6072       1.0000    322  MIT_Smik_c283_5928       1.0000    322  
MIT_Sbay_c84_6418        1.0000    322  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM2-HEM14.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            6288    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.328 C 0.172 G 0.172 T 0.328 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 192   E-value = 5.7e-022
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  96:42:191:1:::::::a:
pos.-specific     C  :191:34::::a:a:::::6
probability       G  13::8641::9:::a::::4
matrix            T  ::14:1::9a::a::aaa::

         bits    2.5            * **     
                 2.3            * **     
                 2.0   *       ** **     
                 1.8   *       ** **     
Information      1.5   * *    ***********
content          1.3 * * *  * ***********
(30.8 bits)      1.0 * * ****************
                 0.8 *** ****************
                 0.5 *** ****************
                 0.3 ********************
                 0.0 --------------------

Multilevel           AACAGGCATTGCTCGTTTAC
consensus             G TACG            G
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2052.17     +    200  4.10e-12 CACCGCACCG AACAGGGATTGCTCGTTTAC CCGTTGCGTT
MIT_Spar_c19_8512            +    201  4.10e-12 CACCGCACCG AACAGGGATTGCTCGTTTAC CCGTAGTTTG
SGD_Scer_YGL040C             +    200  4.10e-12 CACCGCACCG AACAGGGATTGCTCGTTTAC CCGTATTTTG
SGD_Scer_YER014W             -    169  1.37e-11 TTTAATTGAA AGCTGCCATTGCTCGTTTAG TTACAAAACG
MIT_Sbay_c84_6418            -    164  1.01e-10 GTTTGAATAT AACTGTCATTGCTCGTTTAG TGGTGAATAT
MIT_Smik_c283_5928           -    163  1.09e-10 TTCAATCAAA AGCTACCATTGCTCGTTTAG TTGTAAAATG
MIT_Spar_c425_6072           -    168  2.28e-10 TTTAATTAAA AGCTGCCATTACTCGTTTAG TTGCAAAACG
MIT_Smik_c273_7756           +    199  6.00e-10 CACCGCACCG AATAAGGATTGCTCGTTTAC CCGTTGTTCG
MIT_Sbay_c77_8808            +    200  5.23e-09 TCACCGCACC GCCCGGAGATGCTCGTTTAC CGTTGTGCAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2052.17          4.1e-12  199_[+1]_781
MIT_Spar_c19_8512                 4.1e-12  200_[+1]_780
SGD_Scer_YGL040C                  4.1e-12  199_[+1]_781
SGD_Scer_YER014W                  1.4e-11  168_[-1]_134
MIT_Sbay_c84_6418                   1e-10  163_[-1]_139
MIT_Smik_c283_5928                1.1e-10  162_[-1]_140
MIT_Spar_c425_6072                2.3e-10  167_[-1]_135
MIT_Smik_c273_7756                  6e-10  198_[+1]_782
MIT_Sbay_c77_8808                 5.2e-09  199_[+1]_781
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Skud_Contig2052.17 (  200) AACAGGGATTGCTCGTTTAC  1 
MIT_Spar_c19_8512        (  201) AACAGGGATTGCTCGTTTAC  1 
SGD_Scer_YGL040C         (  200) AACAGGGATTGCTCGTTTAC  1 
SGD_Scer_YER014W         (  169) AGCTGCCATTGCTCGTTTAG  1 
MIT_Sbay_c84_6418        (  164) AACTGTCATTGCTCGTTTAG  1 
MIT_Smik_c283_5928       (  163) AGCTACCATTGCTCGTTTAG  1 
MIT_Spar_c425_6072       (  168) AGCTGCCATTACTCGTTTAG  1 
MIT_Smik_c273_7756       (  199) AATAAGGATTGCTCGTTTAC  1 
MIT_Sbay_c77_8808        (  200) GCCCGGAGATGCTCGTTTAC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6117 bayes= 9.40656 E= 5.7e-022 
   145   -982    -66   -982 
    78    -66     92   -982 
  -982    234   -982   -154 
    45    -66   -982     45 
   -55   -982    215   -982 
  -982     92    166   -154 
  -154    134    134   -982 
   145   -982    -66   -982 
  -154   -982   -982    145 
  -982   -982   -982    162 
  -154   -982    234   -982 
  -982    251   -982   -982 
  -982   -982   -982    162 
  -982    251   -982   -982 
  -982   -982    251   -982 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -982   -982   -982    162 
   162   -982   -982   -982 
  -982    166    134   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.7e-022 
 0.888889  0.000000  0.111111  0.000000 
 0.555556  0.111111  0.333333  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.444444  0.111111  0.000000  0.444444 
 0.222222  0.000000  0.777778  0.000000 
 0.000000  0.333333  0.555556  0.111111 
 0.111111  0.444444  0.444444  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  0.000000  0.000000  1.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.555556  0.444444  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
A[AG]C[AT][GA][GC][CG]ATTGCTCGTTTA[CG]
--------------------------------------------------------------------------------




Time  4.20 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   15   sites =   9   llr = 154   E-value = 6.2e-015
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  :::::49:::a9:2:
pos.-specific     C  :169::1::a::17:
probability       G  79::46:aa::19::
matrix            T  3:416::::::::1a

         bits    2.5        ***     
                 2.3        ***     
                 2.0  * *   ***  *  
                 1.8  * *   ***  *  
Information      1.5  * *   **** * *
content          1.3 ** *  ******* *
(24.7 bits)      1.0 ***************
                 0.8 ***************
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           GGCCTGAGGCAAGCT
consensus            T T GA       A 
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Skud_Contig2052.17     -    172  1.54e-10 TGCGGTGATT GGCCTGAGGCAAGCT GCCTGCCCAA
MIT_Spar_c19_8512            -    173  1.54e-10 TGCGGTGATT GGCCTGAGGCAAGCT GCCCGCTTGA
MIT_Smik_c283_5928           +    132  1.35e-09 GAAGCAACAA GGTCGAAGGCAAGCT GAAAGGCATT
SGD_Scer_YGL040C             -    172  7.15e-09 TGCGGTGATT GGCTTGAGGCAAGCT TCCCGCTTGA
MIT_Sbay_c77_8808            -    173  7.55e-09 TGCGGTGATT GGCCTGCGGCAGGCT GCCTGATTTA
MIT_Smik_c273_7756           -    171  2.10e-08 TGCGGTGATT GGCCTGAGGCAACAT ACACTCTTGA
MIT_Spar_c425_6072           +    137  2.87e-08 AGCAACAAAA TGTCGAAGGCAAGAT GAAAGGCGTT
MIT_Sbay_c84_6418            +    130  4.02e-08 AACAACAAAA TCTCGAAGGCAAGCT AAGGTAAAAA
SGD_Scer_YER014W             +    138  4.64e-08 AGCAACAAAG TGTCGAAGGCAAGTT CAAAGGCGTT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2052.17          1.5e-10  171_[-2]_814
MIT_Spar_c19_8512                 1.5e-10  172_[-2]_813
MIT_Smik_c283_5928                1.4e-09  131_[+2]_176
SGD_Scer_YGL040C                  7.1e-09  171_[-2]_814
MIT_Sbay_c77_8808                 7.5e-09  172_[-2]_813
MIT_Smik_c273_7756                2.1e-08  170_[-2]_815
MIT_Spar_c425_6072                2.9e-08  136_[+2]_171
MIT_Sbay_c84_6418                   4e-08  129_[+2]_178
SGD_Scer_YER014W                  4.6e-08  137_[+2]_170
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=15 seqs=9
WashU_Skud_Contig2052.17 (  172) GGCCTGAGGCAAGCT  1 
MIT_Spar_c19_8512        (  173) GGCCTGAGGCAAGCT  1 
MIT_Smik_c283_5928       (  132) GGTCGAAGGCAAGCT  1 
SGD_Scer_YGL040C         (  172) GGCTTGAGGCAAGCT  1 
MIT_Sbay_c77_8808        (  173) GGCCTGCGGCAGGCT  1 
MIT_Smik_c273_7756       (  171) GGCCTGAGGCAACAT  1 
MIT_Spar_c425_6072       (  137) TGTCGAAGGCAAGAT  1 
MIT_Sbay_c84_6418        (  130) TCTCGAAGGCAAGCT  1 
SGD_Scer_YER014W         (  138) TGTCGAAGGCAAGTT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 6162 bayes= 9.41715 E= 6.2e-015 
  -982   -982    192      4 
  -982    -66    234   -982 
  -982    166   -982     45 
  -982    234   -982   -154 
  -982   -982    134     78 
    45   -982    166   -982 
   145    -66   -982   -982 
  -982   -982    251   -982 
  -982   -982    251   -982 
  -982    251   -982   -982 
   162   -982   -982   -982 
   145   -982    -66   -982 
  -982    -66    234   -982 
   -55    192   -982   -154 
  -982   -982   -982    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 6.2e-015 
 0.000000  0.000000  0.666667  0.333333 
 0.000000  0.111111  0.888889  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.000000  0.444444  0.555556 
 0.444444  0.000000  0.555556  0.000000 
 0.888889  0.111111  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.111111  0.888889  0.000000 
 0.222222  0.666667  0.000000  0.111111 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[GT]G[CT]C[TG][GA]AGGCAAG[CA]T
--------------------------------------------------------------------------------




Time  8.46 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =   9   llr = 171   E-value = 1.2e-013
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  8718a:aa:a:942:9:1:6
pos.-specific     C  :::::a::::::::::419:
probability       G  2182::::::a16291:6:4
matrix            T  :21:::::a::::61:621:

         bits    2.5      *    *         
                 2.3      *    *         
                 2.0      *    *   *   * 
                 1.8      *    *   *   * 
Information      1.5     *******   *   * 
content          1.3   * ********  **  * 
(27.5 bits)      1.0 * *********** *** **
                 0.8 * *********** *** **
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           AAGAACAATAGAGTGATGCA
consensus            GT G        AA  CT G
sequence                          G      
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Sbay_c84_6418            -     61  3.82e-11 AACAATAAGG AAGAACAATAGAAGGATGCG AAAGGACAAC
MIT_Smik_c273_7756           +     99  1.39e-10 CCAATAAATC AGGAACAATAGAATGACGCA CCGAGTTTGC
MIT_Spar_c425_6072           -     66  6.11e-10 GAATAATAGA GAGAACAATAGAGAGATCCG CGAAGGATAC
WashU_Skud_Contig2052.17     +     97  7.49e-10 GCCAGAAATC ATGAACAATAGGATGACGCA TAGACGTCAC
MIT_Spar_c19_8512            +     99  1.07e-09 GCCAAAAAAC AAGGACAATAGAATGACACA TAAAGTTTGC
MIT_Sbay_c77_8808            +    102  1.50e-09 ATGAACTAAC ATTAACAATAGAGTGATGCA TAGACGTCAC
MIT_Smik_c283_5928           -     68  2.37e-09 GAGTAATGGA AAGAACAATAGAGGGATTTG CAAAAGATAG
SGD_Scer_YGL040C             +     98  2.54e-09 CAAGAAAATC AAAGACAATAGAGTGGCGCA TAGATGTTGC
SGD_Scer_YER014W             -     66  6.53e-09 GTATAATAGA GAGAACAATAGAGATATTCG CGAAGAACAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Sbay_c84_6418                 3.8e-11  60_[-3]_242
MIT_Smik_c273_7756                1.4e-10  98_[+3]_882
MIT_Spar_c425_6072                6.1e-10  65_[-3]_237
WashU_Skud_Contig2052.17          7.5e-10  96_[+3]_884
MIT_Spar_c19_8512                 1.1e-09  98_[+3]_882
MIT_Sbay_c77_8808                 1.5e-09  101_[+3]_879
MIT_Smik_c283_5928                2.4e-09  67_[-3]_235
SGD_Scer_YGL040C                  2.5e-09  97_[+3]_883
SGD_Scer_YER014W                  6.5e-09  65_[-3]_237
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=9
MIT_Sbay_c84_6418        (   61) AAGAACAATAGAAGGATGCG  1 
MIT_Smik_c273_7756       (   99) AGGAACAATAGAATGACGCA  1 
MIT_Spar_c425_6072       (   66) GAGAACAATAGAGAGATCCG  1 
WashU_Skud_Contig2052.17 (   97) ATGAACAATAGGATGACGCA  1 
MIT_Spar_c19_8512        (   99) AAGGACAATAGAATGACACA  1 
MIT_Sbay_c77_8808        (  102) ATTAACAATAGAGTGATGCA  1 
MIT_Smik_c283_5928       (   68) AAGAACAATAGAGGGATTTG  1 
SGD_Scer_YGL040C         (   98) AAAGACAATAGAGTGGCGCA  1 
SGD_Scer_YER014W         (   66) GAGAACAATAGAGATATTCG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6117 bayes= 9.40656 E= 1.2e-013 
   126   -982     34   -982 
   104   -982    -66    -55 
  -154   -982    215   -154 
   126   -982     34   -982 
   162   -982   -982   -982 
  -982    251   -982   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -982   -982   -982    162 
   162   -982   -982   -982 
  -982   -982    251   -982 
   145   -982    -66   -982 
    45   -982    166   -982 
   -55   -982     34     78 
  -982   -982    234   -154 
   145   -982    -66   -982 
  -982    134   -982     78 
  -154    -66    166    -55 
  -982    234   -982   -154 
    78   -982    134   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.2e-013 
 0.777778  0.000000  0.222222  0.000000 
 0.666667  0.000000  0.111111  0.222222 
 0.111111  0.000000  0.777778  0.111111 
 0.777778  0.000000  0.222222  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.222222  0.000000  0.222222  0.555556 
 0.000000  0.000000  0.888889  0.111111 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.444444  0.000000  0.555556 
 0.111111  0.111111  0.555556  0.222222 
 0.000000  0.888889  0.000000  0.111111 
 0.555556  0.000000  0.444444  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
[AG][AT]G[AG]ACAATAGA[GA][TAG]GA[TC][GT]C[AG]
--------------------------------------------------------------------------------




Time 12.41 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =   9   llr = 148   E-value = 1.9e-005
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  :2:::7:11:38a7:a427a
pos.-specific     C  8217119:7412::9:473:
probability       G  :2739:11:16::31::1::
matrix            T  232::2:824::::::1:::

         bits    2.5                     
                 2.3                     
                 2.0     * *       *     
                 1.8     * *       *     
Information      1.5 *  ** *     * **   *
content          1.3 *  ** *     * **   *
(23.7 bits)      1.0 * *** * *  ***** ***
                 0.8 * *** ********** ***
                 0.5 * ******************
                 0.3 * ******************
                 0.0 --------------------

Multilevel           CTGCGACTCCGAAACAACAA
consensus            TATG T  TTAC G  CAC 
sequence              C                  
                      G                  
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c425_6072           +    115  3.47e-12 TTTAAATACT CCGCGACTCCGAAGCAACAA AATGTCGAAG
SGD_Scer_YER014W             +    116  3.47e-12 TTTGAATACT CCGCGACTCCGAAGCAACAA AGTGTCGAAG
MIT_Sbay_c84_6418            +    108  4.98e-12 TTTTTATACT CTGCGACTCCGAAACAACAA AATCTCGAAG
SGD_Scer_YGL040C             +    316  8.20e-09 TGATGTATTT CGGCGTCTCTACAAGACCCA ATAAAGTAAT
MIT_Smik_c283_5928           +    112  1.07e-08 CTTTTTTAAA TACGGACTCCGAAGCAACAA GGTCGAAGGC
WashU_Skud_Contig2052.17     -    460  4.18e-08 GAAGAGTCTT CATCGACGCTAAAACACAAA TTCAAGAAGA
MIT_Spar_c19_8512            +    311  5.58e-08 GGGAGTATAC CTGCCTCTTTACAACACCCA ACAAAACACT
MIT_Sbay_c77_8808            +    766  8.32e-07 TGTTGCAATA TGTGGACAAGGAAACACGAA ATATATTGGG
MIT_Smik_c273_7756           -    311  8.97e-07 AATATTGTAA CTGGGCGTTTCAAACATACA AGTGTATATT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c425_6072                3.5e-12  114_[+4]_188
SGD_Scer_YER014W                  3.5e-12  115_[+4]_187
MIT_Sbay_c84_6418                   5e-12  107_[+4]_195
SGD_Scer_YGL040C                  8.2e-09  315_[+4]_665
MIT_Smik_c283_5928                1.1e-08  111_[+4]_191
WashU_Skud_Contig2052.17          4.2e-08  459_[-4]_521
MIT_Spar_c19_8512                 5.6e-08  310_[+4]_670
MIT_Sbay_c77_8808                 8.3e-07  765_[+4]_215
MIT_Smik_c273_7756                  9e-07  310_[-4]_670
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=9
MIT_Spar_c425_6072       (  115) CCGCGACTCCGAAGCAACAA  1 
SGD_Scer_YER014W         (  116) CCGCGACTCCGAAGCAACAA  1 
MIT_Sbay_c84_6418        (  108) CTGCGACTCCGAAACAACAA  1 
SGD_Scer_YGL040C         (  316) CGGCGTCTCTACAAGACCCA  1 
MIT_Smik_c283_5928       (  112) TACGGACTCCGAAGCAACAA  1 
WashU_Skud_Contig2052.17 (  460) CATCGACGCTAAAACACAAA  1 
MIT_Spar_c19_8512        (  311) CTGCCTCTTTACAACACCCA  1 
MIT_Sbay_c77_8808        (  766) TGTGGACAAGGAAACACGAA  1 
MIT_Smik_c273_7756       (  311) CTGGGCGTTTCAAACATACA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6117 bayes= 9.40656 E= 1.9e-005 
  -982    215   -982    -55 
   -55     34     34      4 
  -982    -66    192    -55 
  -982    192     92   -982 
  -982    -66    234   -982 
   104    -66   -982    -55 
  -982    234    -66   -982 
  -154   -982    -66    126 
  -154    192   -982    -55 
  -982    134    -66     45 
     4    -66    166   -982 
   126     34   -982   -982 
   162   -982   -982   -982 
   104   -982     92   -982 
  -982    234    -66   -982 
   162   -982   -982   -982 
    45    134   -982   -154 
   -55    192    -66   -982 
   104     92   -982   -982 
   162   -982   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.9e-005 
 0.000000  0.777778  0.000000  0.222222 
 0.222222  0.222222  0.222222  0.333333 
 0.000000  0.111111  0.666667  0.222222 
 0.000000  0.666667  0.333333  0.000000 
 0.000000  0.111111  0.888889  0.000000 
 0.666667  0.111111  0.000000  0.222222 
 0.000000  0.888889  0.111111  0.000000 
 0.111111  0.000000  0.111111  0.777778 
 0.111111  0.666667  0.000000  0.222222 
 0.000000  0.444444  0.111111  0.444444 
 0.333333  0.111111  0.555556  0.000000 
 0.777778  0.222222  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.666667  0.000000  0.333333  0.000000 
 0.000000  0.888889  0.111111  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.444444  0.000000  0.111111 
 0.222222  0.666667  0.111111  0.000000 
 0.666667  0.333333  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
[CT][TACGA][GT][CG]G[AT]CT[CT][CT][GA][AC]A[AG]CA[AC][CA][AC]A
--------------------------------------------------------------------------------




Time 16.27 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 142   E-value = 8.9e-002
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  :22::::41::::128:999
pos.-specific     C  :1:971::6:a1::::::::
probability       G  ::7:1112::::2:1:1:::
matrix            T  a71128933a:989729111

         bits    2.5           *         
                 2.3           *         
                 2.0    *      *         
                 1.8    *      *         
Information      1.5 *  *     **         
content          1.3 *  *  *  ***    *   
(22.7 bits)      1.0 * *** *  *****  ****
                 0.8 * ***** ****** *****
                 0.5 ******* ************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TTGCCTTACTCTTTTATAAA
consensus             AA T  TT   G AT    
sequence                    G            
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c19_8512            +    143  7.75e-12 ATTTATTAGG TTGCCTTACTCTTTTATAAA TCAAGCGGGC
MIT_Sbay_c77_8808            +    147  1.19e-11 TTTTATTGTG TTGCCTTGCTCTTTTATAAA TCAGGCAGCC
WashU_Skud_Contig2052.17     +    142  1.97e-11 TTCATATAAG TTGCCTTTCTCTTTTATAAA TTGGGCAGGC
SGD_Scer_YGL040C             +    142  3.83e-10 ATTTATTAGG TTGCCTTACTCTTATATAAA TCAAGCGGGA
MIT_Smik_c273_7756           +    567  2.20e-08 AACAATAAAG TTACCTTGATCTTTAATAAA ATATTCCCCC
MIT_Smik_c283_5928           +     92  1.78e-07 GTTCTTTCCA TTACTCTTTTCTTTTTTAAA TACGGACTCC
MIT_Spar_c425_6072           +     91  4.97e-07 TTCTCTCTAT TATTCTTTTTCTTTTTTAAA TACTCCGCGA
SGD_Scer_YER014W             +    206  1.59e-06 AAAGAAAGGT TAGCGTTACTCTGTGATTTT TTTCATGTAA
MIT_Sbay_c84_6418            -     27  2.13e-06 GACAACAGTC TCGCTGGATTCCGTAAGAAA CAGCGGAATA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c19_8512                 7.7e-12  142_[+5]_838
MIT_Sbay_c77_8808                 1.2e-11  146_[+5]_834
WashU_Skud_Contig2052.17            2e-11  141_[+5]_839
SGD_Scer_YGL040C                  3.8e-10  141_[+5]_839
MIT_Smik_c273_7756                2.2e-08  566_[+5]_414
MIT_Smik_c283_5928                1.8e-07  91_[+5]_211
MIT_Spar_c425_6072                  5e-07  90_[+5]_212
SGD_Scer_YER014W                  1.6e-06  205_[+5]_97
MIT_Sbay_c84_6418                 2.1e-06  26_[-5]_276
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
MIT_Spar_c19_8512        (  143) TTGCCTTACTCTTTTATAAA  1 
MIT_Sbay_c77_8808        (  147) TTGCCTTGCTCTTTTATAAA  1 
WashU_Skud_Contig2052.17 (  142) TTGCCTTTCTCTTTTATAAA  1 
SGD_Scer_YGL040C         (  142) TTGCCTTACTCTTATATAAA  1 
MIT_Smik_c273_7756       (  567) TTACCTTGATCTTTAATAAA  1 
MIT_Smik_c283_5928       (   92) TTACTCTTTTCTTTTTTAAA  1 
MIT_Spar_c425_6072       (   91) TATTCTTTTTCTTTTTTAAA  1 
SGD_Scer_YER014W         (  206) TAGCGTTACTCTGTGATTTT  1 
MIT_Sbay_c84_6418        (   27) TCGCTGGATTCCGTAAGAAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6117 bayes= 9.40656 E= 8.9e-002 
  -982   -982   -982    162 
   -55    -66   -982    104 
   -55   -982    192   -154 
  -982    234   -982   -154 
  -982    192    -66    -55 
  -982    -66    -66    126 
  -982   -982    -66    145 
    45   -982     34      4 
  -154    166   -982      4 
  -982   -982   -982    162 
  -982    251   -982   -982 
  -982    -66   -982    145 
  -982   -982     34    126 
  -154   -982   -982    145 
   -55   -982    -66    104 
   126   -982   -982    -55 
  -982   -982    -66    145 
   145   -982   -982   -154 
   145   -982   -982   -154 
   145   -982   -982   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 8.9e-002 
 0.000000  0.000000  0.000000  1.000000 
 0.222222  0.111111  0.000000  0.666667 
 0.222222  0.000000  0.666667  0.111111 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.666667  0.111111  0.222222 
 0.000000  0.111111  0.111111  0.777778 
 0.000000  0.000000  0.111111  0.888889 
 0.444444  0.000000  0.222222  0.333333 
 0.111111  0.555556  0.000000  0.333333 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.222222  0.777778 
 0.111111  0.000000  0.000000  0.888889 
 0.222222  0.000000  0.111111  0.666667 
 0.777778  0.000000  0.000000  0.222222 
 0.000000  0.000000  0.111111  0.888889 
 0.888889  0.000000  0.000000  0.111111 
 0.888889  0.000000  0.000000  0.111111 
 0.888889  0.000000  0.000000  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
T[TA][GA]C[CT]TT[ATG][CT]TCT[TG]T[TA][AT]TAAA
--------------------------------------------------------------------------------




Time 20.21 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YGL040C                 6.13e-24  97_[+3(2.54e-09)]_24_[+5(3.83e-10)]_10_[-2(7.15e-09)]_13_[+1(4.10e-12)]_96_[+4(8.20e-09)]_665
MIT_Spar_c19_8512                1.11e-26  98_[+3(1.07e-09)]_24_[+5(7.75e-12)]_10_[-2(1.54e-10)]_13_[+1(4.10e-12)]_13_[+5(5.08e-05)]_57_[+4(5.58e-08)]_670
MIT_Smik_c273_7756               4.21e-19  98_[+3(1.39e-10)]_52_[-2(2.10e-08)]_13_[+1(6.00e-10)]_92_[-4(8.97e-07)]_236_[+5(2.20e-08)]_414
MIT_Sbay_c77_8808                9.48e-21  101_[+3(1.50e-09)]_25_[+5(1.19e-11)]_6_[-2(7.55e-09)]_12_[+1(5.23e-09)]_250_[-3(4.01e-05)]_276_[+4(8.32e-07)]_141_[+2(5.20e-05)]_59
WashU_Skud_Contig2052.17         1.47e-26  96_[+3(7.49e-10)]_25_[+5(1.97e-11)]_10_[-2(1.54e-10)]_13_[+1(4.10e-12)]_98_[-4(1.54e-05)]_122_[-4(4.18e-08)]_191_[-1(9.59e-05)]_80_[-4(2.53e-05)]_16_[-1(9.59e-05)]_174
SGD_Scer_YER014W                 1.85e-24  65_[-3(6.53e-09)]_30_[+4(3.47e-12)]_2_[+2(4.64e-08)]_16_[-1(1.37e-11)]_17_[+5(1.59e-06)]_97
MIT_Spar_c425_6072               5.95e-25  65_[-3(6.11e-10)]_5_[+5(4.97e-07)]_4_[+4(3.47e-12)]_2_[+2(2.87e-08)]_16_[-1(2.28e-10)]_14_[+1(4.94e-05)]_101
MIT_Smik_c283_5928               4.38e-23  67_[-3(2.37e-09)]_4_[+5(1.78e-07)]_[+4(1.07e-08)]_[+2(1.35e-09)]_16_[-1(1.09e-10)]_140
MIT_Sbay_c84_6418                1.54e-25  26_[-5(2.13e-06)]_14_[-3(3.82e-11)]_27_[+4(4.98e-12)]_2_[+2(4.02e-08)]_19_[-1(1.01e-10)]_139
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM2-HEM15.fa000444000766000024      2353113155576321 20102 0ustar00cjfieldsstaff000000000000>SGD_Scer_YGL040C HEM2 "Delta-aminolevulinate dehydratase, a homo-octameric enzyme, catalyzes the conversion of delta-aminolevulinic acid to porphobilinogen, the second step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus"
GGTTTTGTCAATTTTCTAGGTATGAATTACTGGAGTAAGCAATAATATGAGTAAGCAGTA
AAACTTTTTTTTATTTGGCTGATTGGGCAAGAAAATCAAAGACAATAGAGTGGCGCATAG
ATGTTGCTAGCATTTATTAGGTTGCCTTACTCTTATATAAATCAAGCGGGAAGCTTGCCT
CAAGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTATTTTGATTTTTTTTTC
ACCTTTTCCAATTTTTTTTTCGGCAACAATTTTTTGGATGATTTTTATCGTCGATCTTGG
AATGATGATGTATTTCGGCGTCTCTACAAGACCCAATAAAGTAATTCGGTGACACAGGCT
TGTAGCAGATAGAAAACGTTCCGAAAGATGGGTTCCAATTGATGTAACACTTCTTTTTTA
TATATTCATGTGGACGTGTACGCCTTCTTCCCTTCTTTGCCTCTTGTGCCACTGTTAATC
CTCTTAAGCATATTGTTTTTATTTACAGACATTGGCTGACTCACCAGAAACTATAATTGA
CGCTGATTTCTAGTTAATTAAAAATAAAATATATGCAAGAATTAGCACCAGGCAGTCATT
TCTGTAAATTGCTTTGTTTTCTATTTCAAATTTGTTTTTTGTATATGTTTCAATGTTCTC
GTGACAATGCAGGCTTTTTTTTGTGCGAATTAAAGTAAAGCTAATCAAAACTAAACAATA
ATTTATCTTGTTCCCGAAAGAGTGGATCATGAGGAGGAAAGCTAACCGTCCAAGATCCTA
TATAATTTTTGAACTGAAAACCAACTGTTCACCTAGAAGACAGGTATCTGGATATGTAAC
TACACGCTCTATAAATACAGAAATCGTAAGCTAATCAATATAAATGTAAAAGAAAATAGG
AATTGCTGTCGATAGATTTATTTACTTTTGTATTGTCATCTGTGTTCTGTGCCAGTACAC
CGGACTCGTATGAGCTGTATGGTGTCGTTTCAATAGAATC
>MIT_Spar_c19_8512 YGL040C 5' untranslated region, Contig c19 1 - 1802, 2000 bp (revcom)
GGTTTTGTCAATATTCTAAATATGGATTCCTAGGGCAGGCAATAATATGGGGAAGCAGTA
AAACTTTTTGTTTTATGTGGCTGATTGGGCCAAAAAACAAGGACAATAGAATGACACATA
AAGTTTGCTAGCATTTATTAGGTTGCCTTACTCTTTTATAAATCAAGCGGGCAGCTTGCC
TCAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTAGTTTGAATTTTTTTT
TCACCTTTTGAAATTTTTTTTTTTCGGCAACAATTTTGAATGACTTTTATCGTCAATCTT
GGGAGTATACCTGCCTCTTTACAACACCCAACAAAACACTTAAGTAAGACAAGCTTGTGG
CAGGTAGGAAAGGTTTCAAAAAAAAAAAAAAGGTTTTTATCTATGGTCATACTTTTTCTT
CGTATATTTATGTGAACACGTACGTCTTGTTTTGCCTTCTTTGGCTCTTGTGTCACTGAA
TCTTCACATATTGTTTTTATTTACAGATACTACTTGACTCGCCTAAAATTATAATCGGCG
ATGGTTTCTACTACCTTAGTTAAAAAATAAAATGAATCAAAACATTACCATTAATAATTC
AATTTTTCCACATTAGTTTGTTTTCTATTTTATGGCTTTCTTCTTGTATATTTCTCAATA
TACTGCATGGCAATGCAAGCTCTTCTCTTTTCTTGATTGAAAATAAAGCTGTGAAGAACT
AAATAATAATTTATTGATGTCCTCCACAAAATGTACACCTGCGCTAACCTTGCTTAACAG
ATACGGTCAAAACGAACTTGAGCATATGTAAAAATCCATGTATTTTTCTTCTTTTGCCAA
CTAAATCAAACTTTTTATTGTATATGTCGTACCGCCAATACAAAGATGGAGAGGTTAATG
AAAATAGATGTGAAAAAAAAGCAGGAACTATTGTAGATAGATATTTTTAGGGTTCGATTG
CTATTTTTCTGTATTATGATCTGTGTTCTATGCCAGTGTA
>MIT_Smik_c273_7756 YGL040C 5' untranslated region, Contig c273 1 - 1807, 2000 bp (revcom)
GGTTTTACCAGTTTTCTTAATACGGATATCTAGAGTAAGTCACAATTTAAGGAAATTGCA
AAATTTTCTTTTTATATAGCTAAATAGGCCAATAAATCAGGAACAATAGAATGACGCACC
GAGTTTGCTAGCAACCTACACACTTGCTTTTTTTTATAAATCAAGAGTGTATGTTGCCTC
AGGCCAATCACCGCACCGAATAAGGATTGCTCGTTTACCCGTTGTTCGATTTTTTTTTTC
ATCTTCTACCAATTTTTTTCGGCAGCGCCTTTGAATGACTTTGATCATCAATCCTGGAGT
AATATACACTTGTATGTTTGAAACGCCCAGTTACAATATTTATTGGAATAGCTAACTTAT
GAGTAAGTGGACCCAAATTTTCGAGTGATGTTTCCTGTCAACGGTGACACTTATTTTTGG
TTTGCAGATATGTATGTGTATATCTTATTCCCACTTTTTTATAGTTATCGTTATCTATGT
ATCTCAATACCTTGGACATGAATCACCGAGTAGATATTTTTCTTTACAATGCTTAAAACA
AGGCCGCACAGAACTAAACAATAAAGTTACCTTGATCTTTAATAAAATATTCCCCCATTA
ATAAGTACTCTCTTCGATTACGATTTAGCCATATTCATTTTGACCATACATTGCAGATGT
GAGATGGATTTTAAGTGGTGAAAGCGCTCTAAGCTATGCCATATAAGTACGTAAGGAGAG
ACAAAATTAAACATAATTAAGCGCCATGTGAGACTAAATGTGGCCGTCGTTTTGATTATA
TGATTGGGAAAAGCTCCTAAACATAGAGGTAGAATTATAGTTCGGAAATTTCGTCTTGCC
CTGCTCATTTTGTAGAAAACGAGTCATCATCTCCACCCTTTGTAACCGGTGTCCTGCTCA
CATAAATAGTCTCTACTGAGAGATTTGTGAATTTCGAGATAATTTTTGGGATTCCATTGT
TGATAAAGGCAATATTATTAGGTATATAAAATATACTAGA
>MIT_Sbay_c77_8808 YGL040C 5' untranslated region, Contig c77 1 - 1377, 2000 bp (revcom)
ACTTTGTCAGTGTTTTTCTGGTAAGGATATCTGGAAGAAGTAACAATACGTATAAATTAC
AAAATTACCGTTTTATGTCGTGGAATGGGCTATGAACTAACATTAACAATAGAGTGATGC
ATAGACGTCACTAGCCTTTTATTGTGTTGCCTTGCTCTTTTATAAATCAGGCAGCCTGCC
GCAGGCCAATCACCGCACCGCCCGGAGATGCTCGTTTACCGTTGTGCACCAAATTTTTCA
TTTTTTGCCTTTTTCTATTTGGCAGCGTTTTCGAAAAATTTTGATCATTAGTCTTCAATG
ACTGGACTGTCATATTTTAGGGCACGCAGGTAAAGATATGAACAAATCATATTGATGATG
GATGCCAATCCTTCAATGTAAATTCTTTCTAAACATCATGATAAAGAACTTCAGTAAGAG
AGTGATAAAAACTTTACATGTATGGCGGGTGTATTCTGTAATTGTTTTTTAGATCTTTTT
GTTGTTAACGGTGACACCATTCTTACTACAATAATTGCATGTCAAATGTAAATATCTTGC
TTCACATTTCGTTGTTTCTTTACGATAAATTGTTTCGTCGCAAATATATCTTATTTTGCG
TGGTTTATCTACAGACACTGCTTGATTTACGCATAAGTACATCATGTAGTAATTCTTATA
TTGAGTATAAAACCATATGAATAGAAATATTTTTGTTAATCTATCGTTAATTTACATGCT
AGTTTATTTGTCCCTTTAAAATTTCTTTATATATTTGTTGCAATATGTGGACAAGGAAAC
ACGAAATATATTGGGATAAAGTTTAAGTAGAGATACATAGAACTAAACAATAAATTCATA
TTCAATAATACTTCAAAAGGTACTCTCCTGTCTGAACACAGAGACTCACAGACTTTATTT
AGTCGTTATGGCGATGTCAGACATCATGTTTAAGGTAAGCCGAGTGGATTGATATGAAAT
TGTCATATCATGAATAAGCTAATTACCCAAAAACAGTAAA
>WashU_Skud_Contig2052.17 YGL040C 5' untranslated region, Contig c2052 29967 - 31966, 2000 bp (revcom)
GATTTGTCAGTGTTTTCTGATATGGATGCCTGGAGAAAATATTAATATGTGGAAACCACA
AAACTTCCACTTATATAGCTAATTTAGCCAGAAATCATGAACAATAGGATGACGCATAGA
CGTCACTACTCTTCATATAAGTTGCCTTTCTCTTTTATAAATTGGGCAGGCAGCTTGCCT
CAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTTGCGTTCAAAGTTTTTC
ATTTTCCGCATCATCTACTTTTTTTTTTTTGACGCCGTTTTTGAATGTCTTGGTCATTGA
TCTTGAAATGATTTATGTTCGTGTTTTCACGGCACAAAGGTAGGCAAATCGGTAAATTTT
ACTCGTAATAAATAATCAAGGCCTCTAGAGGATTTAATATCAGGAAATAATAATGTGAGT
TTTTTGCAAATGGCCTTATATTCCTGACATCTTCTTGAATTTGTGTTTTAGCGTCGATGA
AGACTCTTCCTTTTTTCGTACGGTAATCTGGACATCTTGTTTCGTCTTTTCTTTTTTTTT
TGCGATTGCTTGTAATTCCAGATATGCAGCATTTATTTACAGGTGCTGATTGATTTACTA
TAGAGTTTATCAGGTAGTAGTTCTTTTTCATGTCTCAATTGAAGAAAAGGAACCCATAAA
TACATTAGCACTGAACAAACAATAACTGCCGCATTGGTTTGTTTTCTAACTTGAATTTTT
CTTTATACATATGCCACTGTATTAGGATGGGTGAATACCGTTTTCTTACTTTCTTCCTAT
GAAGGCGAAAGAATGGTGAAGGACAACTAAACAATAAATCGTTTTTCACACATCCCCATA
AAGCTTTCTCTGTTTGTCAGTTGTGACTCATCTTTCGTCGATGTTGCTTGGTAGATACAA
TTGAACAAGATTGAGATATCTAAAATGTTCAAAAATTATACTCTCTTATGTAGTTTCCGT
CATGGCTGAACGAAGGAAAACTACATCACCTGAGAATTAC
>SGD_Scer_YOR176W HEM15 "Ferrochelatase, a mitochondrial inner membrane protein, catalyzes the insertion of ferrous iron into protoporphyrin IX, the eighth and final step in the heme biosynthetic pathway; Yfh1p mediates the use of iron by Hem15p"
TCTTTAAACGTTCTTTTTTTTACTGCTAAATTTGTCCAAATAGCAGGTATGTGTTAAATA
TTTCTGTACTTCTTGTAAACCGACTCAAGTGGAACACGAGAATTTACGCTTGTTTGGTGT
CAAGCCAAGAGTGACCTTGACCGACCAAAAGTATTCCTTCGCGTCCTCCTTCTTCAATCC
CATATCCCCTACGAAAAAAAGCAGCATGAGAAAACGAAGGGCAGCAACTCCTTCGTCATA
TAAGGCTTACGGTGACCATTGAAGATTGGGCATGTCTAACGGCTATTGCCAGCGGAGATG
TTTCAAGGCATCCTACACATGCTACATATTTGTAATTATTTTACTGAGTTTGTGTATATA
AAAAACTTTTTTAAAAAAAAAAAATGGCCAGCATCCTCTTTCATGTAAAGCTGTTGAACC
TTCCTGAAATTTACTTCTAAAATTGTTCAGTAAAACTGCTTGTTAAAAGTGCGAAGAGTT
CTTTTTTAGCTTTTTTTGTCCTGCTGTTGAGCTGTTTTGCTTTACTGTTCAACAAAACAT
TGAAGATCTTTCACATTGCGCGTCGAAACCACAAACCGTCGAAAACAATGGTCATCTAAA
TAAAGGGTTCTTATTAAACAGATTTAAAGCCAAGGACAAAATACAGGCACAGGTCAAGCA
AGAAGACAAACCGCATACGCCAAGACAAACCGTGGTGATTTAATTCTGCTGCTGATCGCT
TCCAACA
>MIT_Spar_c278_20970 YOR176W 5' untranslated region, Contig c278 32746 - 34745, 2000 bp (revcom)
TCTTCAAACGTTCTTTTCCTACTACTAAGCTTTTCAATAAATAGCGGGTATATGCTAAAT
ACTTCTTTGCTTCTTGTACGACCTACTTAATTGAAATACGGATATTTTTGCTTGCTTGGT
GCCAAACCAAGAGTGACCTTGACCGACTAAAAGTATTCCTTCGCGTCCTCCTTCTTCAAT
CCCATATCCCCTACTGAAAAAAGCAGCGTGCGAAAATGAAGGGCAGCAACTCCTTCGTCA
TATAAGGCTTAGGTAATCTTTCAAGGTCAGGTATATCCAGCTGTCGTTACGAGTAGAGAT
ATTTCAAGCTGTCCTGCACATGCTACATATTTGTGATTATTTTTATTGAGTTGCGTATAT
AAAAAAACAATCTAAAAAAAAAAAAAATGGCCAGCATCTTCTTCCATGTAAAGCTGTTGA
ACCTTGCTAAAATCTATTACTATAATTGTTCAGTAAAGTTGCTTGTTAAAAATGCGAAGA
GTCTTTTTTAGCTTTTTTTGCCCTGCTGTTGAGCTGTTTTGCTTCACTGTTCAACAAAAC
AGTGAAGATCTTTCGAATTGCGCGTCGAAACCACAAACCGTCGAAAATAATGGTCATCTA
AATAAAGGGTTCTTATTTGAACAGATTTAAAGCTCAAAGACACGATACAGGCACAGGTCC
AGAAAGAATACAAAACGCAAACGCCAAGACAAATTGTGGTAATTTCATTCTGCTGCTGAT
CACTGCC
>MIT_Smik_c935_20455 YOR176W 5' untranslated region, Contig c935 1803 - 3802(revcom), 2000 bp (revcom)
TCTTGAATTGCAATTTTCTACTACTGAAGTTACCAACAATTAGCAAATATGTGATGAGTC
CTTTTTACGTTCTTGTATAACCTAAGTTAAATACAAAGGTTTATGCTCCTTTAATGATCA
GACCAACAGTGATCTTGGCCGACCAAAAGACTCCTTCGCGTCCTCCTTCTTCAAGTCTCA
TATCCCCTACCAGAAAAAGTAGCAGGCGAAAATAAAGAGCAACTGCTCCCCCCCATATAG
AGCTTACCATAATTTCTCAAGGAAAGGTATCTCCAGTTGTCGTAAAGAATAAAGAAGTTT
CAACGTGTCCTGCATGTTCTACAAATTTGCAATTGACTTTACTAAGTTGCATATATAAAA
CTTGTATTAGATAAGTTAGCCAGCATTTTCATTCAAGCTAAGATGTTGAATATGCCAAAG
CACATTGCTGAAATTAATCAGTAAAGCTGCTTGCTGAAAGTGGAAATATTTTCAGCTTTT
TTTGCTCTGCTGTTGAGCTGTTTTACTTCATTGTTCAACAAAACAATAGAGTTCTCTCCA
ATTGCGCGTCAAAACCACAAACCGTCGAAAATAATGATCATCTAAATAAAAGAGTTCACG
TTTTCACATATTTAAAGTTGAAATACTCCATACAGGCACAGGTCTAACAAGAAGACAACG
CATTCGATAAAACTAATCGTGGTAATTTTTATATCGCTGCTAGCCACTACCAACAATGTA
CAATTTT
>WashU_Skud_Contig2050.4 YOR176W 5' untranslated region, Contig c2050 12271 - 14270(revcom), 2000 bp (revcom)
TCTTAGTTTATAGCTTTTCTACTACTCTGGTCATAAACGAACAGAAGATAAGCAAGAAAT
CTTTTTTTCCTTCTTTTACGGTCTATTCAAGTGAAGCACGGGGATTCCCGCTTGTTTAAT
AATCAGACCAACAATGATATTGACCGACCAAAAGAAGTATTCCTTCGCGTGCTTCTCCTT
TCTGTGTCAAATCCCCTACTGAAAAAGCAGCATTGGGAAAGGAACAGCAGCTTCTCCTTC
GTCGCAGAGAGCTCGCGGTAGCATTTCATTGTCAGGTATTTATGATATTTGCTAAGAATA
ATTAAAATGTCTTCAGGTCTTGCACATACTCCTACATATTTGTAAGTATTTTACTGATTT
GAGTATATAAAAGCCGTACTAAAACTAACCAGCACCTGTAGCAAGGTGCAAAATGTTGAA
CCTTTCCGAAATTTATTGCCAGAAACCAAGAGCTAAAAGTGCTTGGTAAAAGTGAAAAGA
CTCTTTTTCAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGTTCCATCTGTTCAACAAA
ACAGCTTCACTGGATCTTTCAAAGTGCGCGTCGAAACCACAAACCGTCGAAAATATTGAT
CATCTAAATAAAGGGTTCTTATTTGCACAGTTTCGCATTGAAATATTCCATTCAGGCACA
GATCAACAAGAAGACAAAAAGGTATTCGAGAAGACTAATTGTGGTATTTTTACTTTGCTG
CTGACCA
>WashU_Sbay_Contig480.2 YOR176W 5' untranslated region, Contig c480 3444 - 5443(revcom), 2000 bp (revcom)
TTTCAGGGAAGCACCATGTGCACGAATTGTTCTAGAAAGCATTTTTGGTTCGTAAATTCT
CTACAACTGAACTTATTAACAAATAGCAAACAGAGAAGAAAATTTTTTTTTTCCTTCTTG
TATGGTCAGTTAGTTGAAAACACGGAGATTTTCACTTGTTTAGTAAGCAGAGCCATAATG
CTCTTGACCGACCAAAAGAAGTATTCCTACGCGAGCTCCCTCTTCAAGTGCCAAATCCCC
TACTGAAAAAAGCAACATGAGAAGCAAAGAGATGCCTCTCGCCATGCAGGGCTTGCGGTC
ATGTTTTCTACGTTCAATTGATTTTGTTACAGCTGAAAGATGTTTATAAAACTGTCTTGC
ATATGCTCTATTTACTTGTAAACAATTTTATTAAGTTGCGTATATATGATCGTACTAAAA
ATTGGCTGGCGCGTTCTCCAGGCAGAGTTGGTTGAACCTTGCTCGAATTGATAGCTCAAA
GTGGAGAGACTCTTTTTTAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGCTCCACCTG
TTCAACAAAATGGCAGAGATCTTTCGAAGTGCGCGTCGAAACCACAAACCATCAAAAATA
TCGACCATCTAAATAAAGGGTTCTTGTTTGAATAAATATCAGGCGAAGCTCTTCATACAG
GCACAGGTCAGATAAGAAGACAATTCGAATTCGAGAAGGATATTCGTGGTATCTTTAATC
TGCTGCT
BioPerl-1.007002/t/data/map_hem/HEM2-HEM15.meme.txt000444000766000024     11705613155576321 21303 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM2-HEM15.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YGL040C         1.0000   1000  MIT_Spar_c19_8512        1.0000   1000  
MIT_Smik_c273_7756       1.0000   1000  MIT_Sbay_c77_8808        1.0000   1000  
WashU_Skud_Contig2052.17 1.0000   1000  SGD_Scer_YOR176W         1.0000    727  
MIT_Spar_c278_20970      1.0000    727  MIT_Smik_c935_20455      1.0000    727  
WashU_Skud_Contig2050.4  1.0000    727  WashU_Sbay_Contig480.2   1.0000    727  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM2-HEM15.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=       10    maxsites=       10    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            8635    N=              10
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.321 C 0.179 G 0.179 T 0.321 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =  10   llr = 215   E-value = 5.2e-026
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  2:1861:5aa5:a::::a5:
pos.-specific     C  5:5:::95:::a:5a:a:5a
probability       G  314249:::::::5:5::::
matrix            T  :9::::1:::5::::5::::

         bits    2.5            *  * *  *
                 2.3            *  * *  *
                 2.0      **    *  * *  *
                 1.8      **    *  * *  *
Information      1.5      ** ** **** ** *
content          1.3  *   ** ** **** ** *
(31.0 bits)      1.0  ********* *********
                 0.8 ********** *********
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CTCAAGCAAAACACCGCAAC
consensus            G GGG  C  T  G T  C 
sequence             A                   
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2052.17     +    179  2.28e-13 GGCAGCTTGC CTCAGGCCAATCACCGCACC GAACAGGGAT
MIT_Smik_c273_7756           +    178  2.28e-13 TGTATGTTGC CTCAGGCCAATCACCGCACC GAATAAGGAT
MIT_Spar_c19_8512            +    180  2.28e-13 GGCAGCTTGC CTCAGGCCAATCACCGCACC GAACAGGGAT
SGD_Scer_YGL040C             +    179  6.49e-13 GGAAGCTTGC CTCAAGCCAATCACCGCACC GAACAGGGAT
MIT_Sbay_c77_8808            +    180  3.46e-11 GGCAGCCTGC CGCAGGCCAATCACCGCACC GCCCGGAGAT
MIT_Spar_c278_20970          -    508  1.13e-10 TTGTTGAACA GTGAAGCAAAACAGCTCAAC AGCAGGGCAA
WashU_Sbay_Contig480.2       -    518  2.09e-10 TGTTGAACAG GTGGAGCAAAACAGCTCAAC AGCAGAACAA
SGD_Scer_YOR176W             -    506  5.11e-10 TTGTTGAACA GTAAAGCAAAACAGCTCAAC AGCAGGACAA
MIT_Smik_c935_20455          -    492  1.39e-09 TTGTTGAACA ATGAAGTAAAACAGCTCAAC AGCAGAGCAA
WashU_Skud_Contig2050.4      -    509  1.85e-09 TGTTGAACAG ATGGAACAAAACAGCTCAAC AGCAGAACAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2052.17          2.3e-13  178_[+1]_802
MIT_Smik_c273_7756                2.3e-13  177_[+1]_803
MIT_Spar_c19_8512                 2.3e-13  179_[+1]_801
SGD_Scer_YGL040C                  6.5e-13  178_[+1]_802
MIT_Sbay_c77_8808                 3.5e-11  179_[+1]_801
MIT_Spar_c278_20970               1.1e-10  507_[-1]_200
WashU_Sbay_Contig480.2            2.1e-10  517_[-1]_190
SGD_Scer_YOR176W                  5.1e-10  505_[-1]_202
MIT_Smik_c935_20455               1.4e-09  491_[-1]_216
WashU_Skud_Contig2050.4           1.8e-09  508_[-1]_199
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=10
WashU_Skud_Contig2052.17 (  179) CTCAGGCCAATCACCGCACC  1 
MIT_Smik_c273_7756       (  178) CTCAGGCCAATCACCGCACC  1 
MIT_Spar_c19_8512        (  180) CTCAGGCCAATCACCGCACC  1 
SGD_Scer_YGL040C         (  179) CTCAAGCCAATCACCGCACC  1 
MIT_Sbay_c77_8808        (  180) CGCAGGCCAATCACCGCACC  1 
MIT_Spar_c278_20970      (  508) GTGAAGCAAAACAGCTCAAC  1 
WashU_Sbay_Contig480.2   (  518) GTGGAGCAAAACAGCTCAAC  1 
SGD_Scer_YOR176W         (  506) GTAAAGCAAAACAGCTCAAC  1 
MIT_Smik_c935_20455      (  492) ATGAAGTAAAACAGCTCAAC  1 
WashU_Skud_Contig2050.4  (  509) ATGGAACAAAACAGCTCAAC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8445 bayes= 9.72024 E= 5.2e-026 
   -70    151     77   -997 
  -997   -997    -81    147 
  -169    151    119   -997 
   130   -997     19   -997 
    89   -997    119   -997 
  -169   -997    236   -997 
  -997    236   -997   -169 
    62    151   -997   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
    62   -997   -997     62 
  -997    251   -997   -997 
   162   -997   -997   -997 
  -997    151    151   -997 
  -997    251   -997   -997 
  -997   -997    151     62 
  -997    251   -997   -997 
   162   -997   -997   -997 
    62    151   -997   -997 
  -997    251   -997   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.2e-026 
 0.200000  0.500000  0.300000  0.000000 
 0.000000  0.000000  0.100000  0.900000 
 0.100000  0.500000  0.400000  0.000000 
 0.800000  0.000000  0.200000  0.000000 
 0.600000  0.000000  0.400000  0.000000 
 0.100000  0.000000  0.900000  0.000000 
 0.000000  0.900000  0.000000  0.100000 
 0.500000  0.500000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
[CGA]T[CG][AG][AG]GC[AC]AA[AT]CA[CG]C[GT]CA[AC]C
--------------------------------------------------------------------------------




Time  7.72 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =  10   llr = 180   E-value = 8.7e-013
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  :3:::69932:::::::49a
pos.-specific     C  8:1:a11:::3627:39:1:
probability       G  1::::3::41546:a:16::
matrix            T  179a:::1372:23:7::::

         bits    2.5     *         *     
                 2.3     *         *     
                 2.0     *         * *   
                 1.8     *         * *   
Information      1.5 *  **      *  * *  *
content          1.3 * *** **   * ** ****
(26.0 bits)      1.0 * *** **   *********
                 0.8 ********  **********
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CTTTCAAAGTGCGCGTCGAA
consensus             A   G  AACGCT C A  
sequence                     T T T       
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2050.4      +    556  3.60e-13 TTCACTGGAT CTTTCAAAGTGCGCGTCGAA ACCACAAACC
WashU_Sbay_Contig480.2       +    561  5.54e-13 TGGCAGAGAT CTTTCGAAGTGCGCGTCGAA ACCACAAACC
MIT_Spar_c278_20970          +    550  5.52e-12 CAGTGAAGAT CTTTCGAATTGCGCGTCGAA ACCACAAACC
SGD_Scer_YOR176W             +    548  1.17e-10 CATTGAAGAT CTTTCACATTGCGCGTCGAA ACCACAAACC
MIT_Smik_c935_20455          +    534  2.24e-09 CAATAGAGTT CTCTCCAATTGCGCGTCAAA ACCACAAACC
WashU_Skud_Contig2052.17     -    268  2.94e-09 ATGACCAAGA CATTCAAAAACGGCGTCAAA AAAAAAAAAG
MIT_Smik_c273_7756           -    258  7.80e-09 TGATCAAAGT CATTCAAAGGCGCTGCCGAA AAAAATTGGT
MIT_Spar_c19_8512            -    263  1.90e-08 CGATAAAAGT CATTCAAAATTGTTGCCGAA AAAAAAAAAT
MIT_Sbay_c77_8808            -    258  8.58e-08 TGATCAAAAT TTTTCGAAAACGCTGCCAAA TAGAAAAAGG
SGD_Scer_YGL040C             +    647  2.66e-07 TTTTGTATAT GTTTCAATGTTCTCGTGACA ATGCAGGCTT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2050.4           3.6e-13  555_[+2]_152
WashU_Sbay_Contig480.2            5.5e-13  560_[+2]_147
MIT_Spar_c278_20970               5.5e-12  549_[+2]_158
SGD_Scer_YOR176W                  1.2e-10  547_[+2]_160
MIT_Smik_c935_20455               2.2e-09  533_[+2]_174
WashU_Skud_Contig2052.17          2.9e-09  267_[-2]_713
MIT_Smik_c273_7756                7.8e-09  257_[-2]_723
MIT_Spar_c19_8512                 1.9e-08  262_[-2]_718
MIT_Sbay_c77_8808                 8.6e-08  257_[-2]_723
SGD_Scer_YGL040C                  2.7e-07  646_[+2]_334
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=10
WashU_Skud_Contig2050.4  (  556) CTTTCAAAGTGCGCGTCGAA  1 
WashU_Sbay_Contig480.2   (  561) CTTTCGAAGTGCGCGTCGAA  1 
MIT_Spar_c278_20970      (  550) CTTTCGAATTGCGCGTCGAA  1 
SGD_Scer_YOR176W         (  548) CTTTCACATTGCGCGTCGAA  1 
MIT_Smik_c935_20455      (  534) CTCTCCAATTGCGCGTCAAA  1 
WashU_Skud_Contig2052.17 (  268) CATTCAAAAACGGCGTCAAA  1 
MIT_Smik_c273_7756       (  258) CATTCAAAGGCGCTGCCGAA  1 
MIT_Spar_c19_8512        (  263) CATTCAAAATTGTTGCCGAA  1 
MIT_Sbay_c77_8808        (  258) TTTTCGAAAACGCTGCCAAA  1 
SGD_Scer_YGL040C         (  647) GTTTCAATGTTCTCGTGACA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8445 bayes= 9.72024 E= 8.7e-013 
  -997    219    -81   -169 
   -11   -997   -997    111 
  -997    -81   -997    147 
  -997   -997   -997    162 
  -997    251   -997   -997 
    89    -81     77   -997 
   147    -81   -997   -997 
   147   -997   -997   -169 
   -11   -997    119    -11 
   -70   -997    -81    111 
  -997     77    151    -70 
  -997    177    119   -997 
  -997     19    177    -70 
  -997    199   -997    -11 
  -997   -997    251   -997 
  -997     77   -997    111 
  -997    236    -81   -997 
    30   -997    177   -997 
   147    -81   -997   -997 
   162   -997   -997   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 8.7e-013 
 0.000000  0.800000  0.100000  0.100000 
 0.300000  0.000000  0.000000  0.700000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.600000  0.100000  0.300000  0.000000 
 0.900000  0.100000  0.000000  0.000000 
 0.900000  0.000000  0.000000  0.100000 
 0.300000  0.000000  0.400000  0.300000 
 0.200000  0.000000  0.100000  0.700000 
 0.000000  0.300000  0.500000  0.200000 
 0.000000  0.600000  0.400000  0.000000 
 0.000000  0.200000  0.600000  0.200000 
 0.000000  0.700000  0.000000  0.300000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.300000  0.000000  0.700000 
 0.000000  0.900000  0.100000  0.000000 
 0.400000  0.000000  0.600000  0.000000 
 0.900000  0.100000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
C[TA]TTC[AG]AA[GAT][TA][GCT][CG][GCT][CT]G[TC]C[GA]AA
--------------------------------------------------------------------------------




Time 15.21 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =  10   llr = 185   E-value = 8.7e-014
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :556:15:255:::1:2:::
pos.-specific     C  55::a:5:435:8a415::9
probability       G  :::::9:9:2::::::3:::
matrix            T  5:54:::14::a2:59:aa1

         bits    2.5     *        *      
                 2.3     *        *      
                 2.0     ** *     *     *
                 1.8     ** *     *     *
Information      1.5     ** *   ***   ***
content          1.3     ** *   *** * ***
(26.7 bits)      1.0 **  ****  **** * ***
                 0.8 ** *****  **** *****
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CAAACGAGCAATCCTTCTTC
consensus            TCTT  C TCC T C G   
sequence                     AG      A   
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c935_20455          +    153  1.95e-11 CCAAAAGACT CCTTCGCGTCCTCCTTCTTC AAGTCTCATA
MIT_Spar_c278_20970          +    158  1.95e-11 TAAAAGTATT CCTTCGCGTCCTCCTTCTTC AATCCCATAT
SGD_Scer_YOR176W             +    156  1.95e-11 CAAAAGTATT CCTTCGCGTCCTCCTTCTTC AATCCCATAT
WashU_Sbay_Contig480.2       +    206  4.98e-11 AAGAAGTATT CCTACGCGAGCTCCCTCTTC AAGTGCCAAA
WashU_Skud_Contig2052.17     -    199  4.36e-10 ACGCAACGGG TAAACGAGCAATCCCTGTTC GGTGCGGTGA
MIT_Spar_c19_8512            -    200  4.36e-10 AAACTACGGG TAAACGAGCAATCCCTGTTC GGTGCGGTGA
SGD_Scer_YGL040C             -    199  4.36e-10 AAAATACGGG TAAACGAGCAATCCCTGTTC GGTGCGGTGA
MIT_Smik_c273_7756           -    198  1.99e-09 GAACAACGGG TAAACGAGCAATCCTTATTC GGTGCGGTGA
WashU_Skud_Contig2050.4      +    162  3.33e-08 AAGAAGTATT CCTTCGCGTGCTTCTCCTTT CTGTGTCAAA
MIT_Sbay_c77_8808            +    824  6.99e-07 TACATAGAAC TAAACAATAAATTCATATTC AATAATACTT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c935_20455               1.9e-11  152_[+3]_555
MIT_Spar_c278_20970               1.9e-11  157_[+3]_550
SGD_Scer_YOR176W                  1.9e-11  155_[+3]_552
WashU_Sbay_Contig480.2              5e-11  205_[+3]_502
WashU_Skud_Contig2052.17          4.4e-10  198_[-3]_782
MIT_Spar_c19_8512                 4.4e-10  199_[-3]_781
SGD_Scer_YGL040C                  4.4e-10  198_[-3]_782
MIT_Smik_c273_7756                  2e-09  197_[-3]_783
WashU_Skud_Contig2050.4           3.3e-08  161_[+3]_546
MIT_Sbay_c77_8808                   7e-07  823_[+3]_157
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=10
MIT_Smik_c935_20455      (  153) CCTTCGCGTCCTCCTTCTTC  1 
MIT_Spar_c278_20970      (  158) CCTTCGCGTCCTCCTTCTTC  1 
SGD_Scer_YOR176W         (  156) CCTTCGCGTCCTCCTTCTTC  1 
WashU_Sbay_Contig480.2   (  206) CCTACGCGAGCTCCCTCTTC  1 
WashU_Skud_Contig2052.17 (  199) TAAACGAGCAATCCCTGTTC  1 
MIT_Spar_c19_8512        (  200) TAAACGAGCAATCCCTGTTC  1 
SGD_Scer_YGL040C         (  199) TAAACGAGCAATCCCTGTTC  1 
MIT_Smik_c273_7756       (  198) TAAACGAGCAATCCTTATTC  1 
WashU_Skud_Contig2050.4  (  162) CCTTCGCGTGCTTCTCCTTT  1 
MIT_Sbay_c77_8808        (  824) TAAACAATAAATTCATATTC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8445 bayes= 9.72024 E= 8.7e-014 
  -997    151   -997     62 
    62    151   -997   -997 
    62   -997   -997     62 
    89   -997   -997     30 
  -997    251   -997   -997 
  -169   -997    236   -997 
    62    151   -997   -997 
  -997   -997    236   -169 
   -70    119   -997     30 
    62     77     19   -997 
    62    151   -997   -997 
  -997   -997   -997    162 
  -997    219   -997    -70 
  -997    251   -997   -997 
  -169    119   -997     62 
  -997    -81   -997    147 
   -70    151     77   -997 
  -997   -997   -997    162 
  -997   -997   -997    162 
  -997    236   -997   -169 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 8.7e-014 
 0.000000  0.500000  0.000000  0.500000 
 0.500000  0.500000  0.000000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.600000  0.000000  0.000000  0.400000 
 0.000000  1.000000  0.000000  0.000000 
 0.100000  0.000000  0.900000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.000000  0.900000  0.100000 
 0.200000  0.400000  0.000000  0.400000 
 0.500000  0.300000  0.200000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.800000  0.000000  0.200000 
 0.000000  1.000000  0.000000  0.000000 
 0.100000  0.400000  0.000000  0.500000 
 0.000000  0.100000  0.000000  0.900000 
 0.200000  0.500000  0.300000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.900000  0.000000  0.100000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
[CT][AC][AT][AT]CG[AC]G[CTA][ACG][AC]T[CT]C[TC]T[CGA]TTC
--------------------------------------------------------------------------------




Time 22.63 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =  10   llr = 177   E-value = 3.5e-011
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  7:2a19aa2:61:4969a:9
pos.-specific     C  1a7:5:::5a:16::4::1:
probability       G  2:::31::::4246::::::
matrix            T  ::1:1:::3::6::1:1:91

         bits    2.5  *       *          
                 2.3  *       *          
                 2.0  *       *          
                 1.8  *       *          
Information      1.5  * *  ** *  *    *  
content          1.3  * * *** *  *** ****
(25.6 bits)      1.0  *** *** ** ********
                 0.8 ******** ** ********
                 0.5 *********** ********
                 0.3 ********************
                 0.0 --------------------

Multilevel           ACCACAAACCATCGAAAATA
consensus            G A G   T GGGA C    
sequence                     A           
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2050.4      +    576  3.12e-12 GCGCGTCGAA ACCACAAACCGTCGAAAATA TTGATCATCT
MIT_Smik_c935_20455          +    554  3.12e-12 GCGCGTCAAA ACCACAAACCGTCGAAAATA ATGATCATCT
MIT_Spar_c278_20970          +    570  3.12e-12 GCGCGTCGAA ACCACAAACCGTCGAAAATA ATGGTCATCT
WashU_Sbay_Contig480.2       +    581  5.53e-11 GCGCGTCGAA ACCACAAACCATCAAAAATA TCGACCATCT
SGD_Scer_YOR176W             +    568  1.19e-10 GCGCGTCGAA ACCACAAACCGTCGAAAACA ATGGTCATCT
WashU_Skud_Contig2052.17     +     87  2.26e-09 AGCTAATTTA GCCAGAAATCATGAACAATA GGATGACGCA
MIT_Spar_c19_8512            +     89  2.98e-08 GGCTGATTGG GCCAAAAAACAAGGACAATA GAATGACACA
MIT_Smik_c273_7756           +     89  9.01e-08 GCTAAATAGG CCAATAAATCAGGAACAATA GAATGACGCA
SGD_Scer_YGL040C             -    535  1.20e-07 TTTTTAATTA ACTAGAAATCAGCGTCAATT ATAGTTTCTG
MIT_Sbay_c77_8808            +    771  2.18e-07 CAATATGTGG ACAAGGAAACACGAAATATA TTGGGATAAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2050.4           3.1e-12  575_[+4]_132
MIT_Smik_c935_20455               3.1e-12  553_[+4]_154
MIT_Spar_c278_20970               3.1e-12  569_[+4]_138
WashU_Sbay_Contig480.2            5.5e-11  580_[+4]_127
SGD_Scer_YOR176W                  1.2e-10  567_[+4]_140
WashU_Skud_Contig2052.17          2.3e-09  86_[+4]_894
MIT_Spar_c19_8512                   3e-08  88_[+4]_892
MIT_Smik_c273_7756                  9e-08  88_[+4]_892
SGD_Scer_YGL040C                  1.2e-07  534_[-4]_446
MIT_Sbay_c77_8808                 2.2e-07  770_[+4]_210
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=10
WashU_Skud_Contig2050.4  (  576) ACCACAAACCGTCGAAAATA  1 
MIT_Smik_c935_20455      (  554) ACCACAAACCGTCGAAAATA  1 
MIT_Spar_c278_20970      (  570) ACCACAAACCGTCGAAAATA  1 
WashU_Sbay_Contig480.2   (  581) ACCACAAACCATCAAAAATA  1 
SGD_Scer_YOR176W         (  568) ACCACAAACCGTCGAAAACA  1 
WashU_Skud_Contig2052.17 (   87) GCCAGAAATCATGAACAATA  1 
MIT_Spar_c19_8512        (   89) GCCAAAAAACAAGGACAATA  1 
MIT_Smik_c273_7756       (   89) CCAATAAATCAGGAACAATA  1 
SGD_Scer_YGL040C         (  535) ACTAGAAATCAGCGTCAATT  1 
MIT_Sbay_c77_8808        (  771) ACAAGGAAACACGAAATATA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8445 bayes= 9.72024 E= 3.5e-011 
   111    -81     19   -997 
  -997    251   -997   -997 
   -70    199   -997   -169 
   162   -997   -997   -997 
  -169    151     77   -169 
   147   -997    -81   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
   -70    151   -997    -11 
  -997    251   -997   -997 
    89   -997    119   -997 
  -169    -81     19     89 
  -997    177    119   -997 
    30   -997    177   -997 
   147   -997   -997   -169 
    89    119   -997   -997 
   147   -997   -997   -169 
   162   -997   -997   -997 
  -997    -81   -997    147 
   147   -997   -997   -169 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.5e-011 
 0.700000  0.100000  0.200000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.200000  0.700000  0.000000  0.100000 
 1.000000  0.000000  0.000000  0.000000 
 0.100000  0.500000  0.300000  0.100000 
 0.900000  0.000000  0.100000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.200000  0.500000  0.000000  0.300000 
 0.000000  1.000000  0.000000  0.000000 
 0.600000  0.000000  0.400000  0.000000 
 0.100000  0.100000  0.200000  0.600000 
 0.000000  0.600000  0.400000  0.000000 
 0.400000  0.000000  0.600000  0.000000 
 0.900000  0.000000  0.000000  0.100000 
 0.600000  0.400000  0.000000  0.000000 
 0.900000  0.000000  0.000000  0.100000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.100000  0.000000  0.900000 
 0.900000  0.000000  0.000000  0.100000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
[AG]C[CA]A[CG]AAA[CTA]C[AG][TG][CG][GA]A[AC]AATA
--------------------------------------------------------------------------------




Time 29.89 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   15   sites =  10   llr = 143   E-value = 2.9e-005
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  :6::11:1::3116:
pos.-specific     C  ::4a::::a8:12:1
probability       G  9::::8:9:118:3:
matrix            T  146:91a::16:719

         bits    2.5    *    *      
                 2.3    *    *      
                 2.0 *  *   **      
                 1.8 *  *   **      
Information      1.5 *  * ***** *   
content          1.3 *  ******* *  *
(20.7 bits)      1.0 * ******** *  *
                 0.8 ********** ** *
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           GATCTGTGCCTGTAT
consensus             TC       A CG 
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Sbay_Contig480.2       -    655  3.42e-10 CTTCTTATCT GACCTGTGCCTGTAT GAAGAGCTTC
MIT_Smik_c935_20455          -    630  3.42e-10 CTTCTTGTTA GACCTGTGCCTGTAT GGAGTATTTC
MIT_Spar_c278_20970          -    645  3.42e-10 ATTCTTTCTG GACCTGTGCCTGTAT CGTGTCTTTG
SGD_Scer_YOR176W             -    641  3.42e-10 CTTCTTGCTT GACCTGTGCCTGTAT TTTGTCCTTG
WashU_Skud_Contig2050.4      -    650  1.56e-08 TCTTCTTGTT GATCTGTGCCTGAAT GGAATATTTC
SGD_Scer_YGL040C             +    944  5.03e-08 TGTCATCTGT GTTCTGTGCCAGTAC ACCGGACTCG
MIT_Spar_c19_8512            +    985  1.58e-07 TATGATCTGT GTTCTATGCCAGTGT A         
MIT_Smik_c273_7756           -    540  3.80e-06 TTATTGTTTA GTTCTGTGCGGCCTT GTTTTAAGCA
WashU_Skud_Contig2052.17     -    662  5.05e-06 GTTATTGTTT GTTCAGTGCTAATGT ATTTATGGGT
MIT_Sbay_c77_8808            -    324  5.92e-06 GATTTGTTCA TATCTTTACCTGCGT GCCCTAAAAT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig480.2            3.4e-10  654_[-5]_58
MIT_Smik_c935_20455               3.4e-10  629_[-5]_83
MIT_Spar_c278_20970               3.4e-10  644_[-5]_68
SGD_Scer_YOR176W                  3.4e-10  640_[-5]_72
WashU_Skud_Contig2050.4           1.6e-08  649_[-5]_63
SGD_Scer_YGL040C                    5e-08  943_[+5]_42
MIT_Spar_c19_8512                 1.6e-07  984_[+5]_1
MIT_Smik_c273_7756                3.8e-06  539_[-5]_446
WashU_Skud_Contig2052.17            5e-06  661_[-5]_324
MIT_Sbay_c77_8808                 5.9e-06  323_[-5]_662
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=15 seqs=10
WashU_Sbay_Contig480.2   (  655) GACCTGTGCCTGTAT  1 
MIT_Smik_c935_20455      (  630) GACCTGTGCCTGTAT  1 
MIT_Spar_c278_20970      (  645) GACCTGTGCCTGTAT  1 
SGD_Scer_YOR176W         (  641) GACCTGTGCCTGTAT  1 
WashU_Skud_Contig2050.4  (  650) GATCTGTGCCTGAAT  1 
SGD_Scer_YGL040C         (  944) GTTCTGTGCCAGTAC  1 
MIT_Spar_c19_8512        (  985) GTTCTATGCCAGTGT  1 
MIT_Smik_c273_7756       (  540) GTTCTGTGCGGCCTT  1 
WashU_Skud_Contig2052.17 (  662) GTTCAGTGCTAATGT  1 
MIT_Sbay_c77_8808        (  324) TATCTTTACCTGCGT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 8495 bayes= 9.72877 E= 2.9e-005 
  -997   -997    236   -169 
    89   -997   -997     30 
  -997    119   -997     89 
  -997    251   -997   -997 
  -169   -997   -997    147 
  -169   -997    219   -169 
  -997   -997   -997    162 
  -169   -997    236   -997 
  -997    251   -997   -997 
  -997    219    -81   -169 
   -11   -997    -81     89 
  -169    -81    219   -997 
  -169     19   -997    111 
    89   -997     77   -169 
  -997    -81   -997    147 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 2.9e-005 
 0.000000  0.000000  0.900000  0.100000 
 0.600000  0.000000  0.000000  0.400000 
 0.000000  0.400000  0.000000  0.600000 
 0.000000  1.000000  0.000000  0.000000 
 0.100000  0.000000  0.000000  0.900000 
 0.100000  0.000000  0.800000  0.100000 
 0.000000  0.000000  0.000000  1.000000 
 0.100000  0.000000  0.900000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.800000  0.100000  0.100000 
 0.300000  0.000000  0.100000  0.600000 
 0.100000  0.100000  0.800000  0.000000 
 0.100000  0.200000  0.000000  0.700000 
 0.600000  0.000000  0.300000  0.100000 
 0.000000  0.100000  0.000000  0.900000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
G[AT][TC]CTGTGCC[TA]G[TC][AG]T
--------------------------------------------------------------------------------




Time 37.04 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YGL040C                 7.45e-21  178_[+1(6.49e-13)]_[-3(4.36e-10)]_316_[-4(1.20e-07)]_92_[+2(2.66e-07)]_127_[+1(6.62e-05)]_130_[+5(5.03e-08)]_42
MIT_Spar_c19_8512                1.88e-22  88_[+4(2.98e-08)]_71_[+1(2.28e-13)]_[-3(4.36e-10)]_43_[-2(1.90e-08)]_150_[+3(3.32e-05)]_465_[-3(5.73e-05)]_47_[+5(1.58e-07)]_1
MIT_Smik_c273_7756               1.86e-20  88_[+4(9.01e-08)]_69_[+1(2.28e-13)]_[-3(1.99e-09)]_40_[-2(7.80e-09)]_262_[-5(3.80e-06)]_446
MIT_Sbay_c77_8808                1.33e-14  179_[+1(3.46e-11)]_58_[-2(8.58e-08)]_46_[-5(5.92e-06)]_432_[+4(2.18e-07)]_33_[+3(6.99e-07)]_90_[-1(4.25e-05)]_47
WashU_Skud_Contig2052.17         7.44e-23  86_[+4(2.26e-09)]_72_[+1(2.28e-13)]_[-3(4.36e-10)]_49_[-2(2.94e-09)]_374_[-5(5.05e-06)]_131_[+3(3.98e-05)]_143_[+1(9.33e-05)]_10
SGD_Scer_YOR176W                 4.25e-28  100_[-4(3.19e-05)]_35_[+3(1.95e-11)]_136_[+3(4.98e-05)]_174_[-1(5.11e-10)]_22_[+2(1.17e-10)]_[+4(1.19e-10)]_53_[-5(3.42e-10)]_72
MIT_Spar_c278_20970              1.73e-31  48_[+3(3.79e-05)]_89_[+3(1.95e-11)]_330_[-1(1.13e-10)]_22_[+2(5.52e-12)]_[+4(3.12e-12)]_55_[-5(3.42e-10)]_68
MIT_Smik_c935_20455              5.70e-28  152_[+3(1.95e-11)]_127_[+3(4.68e-06)]_172_[-1(1.39e-09)]_22_[+2(2.24e-09)]_[+4(3.12e-12)]_56_[-5(3.42e-10)]_83
WashU_Skud_Contig2050.4          8.21e-27  161_[+3(3.33e-08)]_256_[+4(2.13e-05)]_51_[-1(1.85e-09)]_2_[+1(8.00e-05)]_5_[+2(3.60e-13)]_[+4(3.12e-12)]_54_[-5(1.56e-08)]_63
WashU_Sbay_Contig480.2           1.32e-30  205_[+3(4.98e-11)]_292_[-1(2.09e-10)]_23_[+2(5.54e-13)]_[+4(5.53e-11)]_10_[-3(4.52e-05)]_24_[-5(3.42e-10)]_58
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM2-HEM3.fa000444000766000024      2500513155576321 20015 0ustar00cjfieldsstaff000000000000>SGD_Scer_YGL040C HEM2 "Delta-aminolevulinate dehydratase, a homo-octameric enzyme, catalyzes the conversion of delta-aminolevulinic acid to porphobilinogen, the second step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus"
GGTTTTGTCAATTTTCTAGGTATGAATTACTGGAGTAAGCAATAATATGAGTAAGCAGTA
AAACTTTTTTTTATTTGGCTGATTGGGCAAGAAAATCAAAGACAATAGAGTGGCGCATAG
ATGTTGCTAGCATTTATTAGGTTGCCTTACTCTTATATAAATCAAGCGGGAAGCTTGCCT
CAAGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTATTTTGATTTTTTTTTC
ACCTTTTCCAATTTTTTTTTCGGCAACAATTTTTTGGATGATTTTTATCGTCGATCTTGG
AATGATGATGTATTTCGGCGTCTCTACAAGACCCAATAAAGTAATTCGGTGACACAGGCT
TGTAGCAGATAGAAAACGTTCCGAAAGATGGGTTCCAATTGATGTAACACTTCTTTTTTA
TATATTCATGTGGACGTGTACGCCTTCTTCCCTTCTTTGCCTCTTGTGCCACTGTTAATC
CTCTTAAGCATATTGTTTTTATTTACAGACATTGGCTGACTCACCAGAAACTATAATTGA
CGCTGATTTCTAGTTAATTAAAAATAAAATATATGCAAGAATTAGCACCAGGCAGTCATT
TCTGTAAATTGCTTTGTTTTCTATTTCAAATTTGTTTTTTGTATATGTTTCAATGTTCTC
GTGACAATGCAGGCTTTTTTTTGTGCGAATTAAAGTAAAGCTAATCAAAACTAAACAATA
ATTTATCTTGTTCCCGAAAGAGTGGATCATGAGGAGGAAAGCTAACCGTCCAAGATCCTA
TATAATTTTTGAACTGAAAACCAACTGTTCACCTAGAAGACAGGTATCTGGATATGTAAC
TACACGCTCTATAAATACAGAAATCGTAAGCTAATCAATATAAATGTAAAAGAAAATAGG
AATTGCTGTCGATAGATTTATTTACTTTTGTATTGTCATCTGTGTTCTGTGCCAGTACAC
CGGACTCGTATGAGCTGTATGGTGTCGTTTCAATAGAATC
>MIT_Spar_c19_8512 YGL040C 5' untranslated region, Contig c19 1 - 1802, 2000 bp (revcom)
GGTTTTGTCAATATTCTAAATATGGATTCCTAGGGCAGGCAATAATATGGGGAAGCAGTA
AAACTTTTTGTTTTATGTGGCTGATTGGGCCAAAAAACAAGGACAATAGAATGACACATA
AAGTTTGCTAGCATTTATTAGGTTGCCTTACTCTTTTATAAATCAAGCGGGCAGCTTGCC
TCAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTAGTTTGAATTTTTTTT
TCACCTTTTGAAATTTTTTTTTTTCGGCAACAATTTTGAATGACTTTTATCGTCAATCTT
GGGAGTATACCTGCCTCTTTACAACACCCAACAAAACACTTAAGTAAGACAAGCTTGTGG
CAGGTAGGAAAGGTTTCAAAAAAAAAAAAAAGGTTTTTATCTATGGTCATACTTTTTCTT
CGTATATTTATGTGAACACGTACGTCTTGTTTTGCCTTCTTTGGCTCTTGTGTCACTGAA
TCTTCACATATTGTTTTTATTTACAGATACTACTTGACTCGCCTAAAATTATAATCGGCG
ATGGTTTCTACTACCTTAGTTAAAAAATAAAATGAATCAAAACATTACCATTAATAATTC
AATTTTTCCACATTAGTTTGTTTTCTATTTTATGGCTTTCTTCTTGTATATTTCTCAATA
TACTGCATGGCAATGCAAGCTCTTCTCTTTTCTTGATTGAAAATAAAGCTGTGAAGAACT
AAATAATAATTTATTGATGTCCTCCACAAAATGTACACCTGCGCTAACCTTGCTTAACAG
ATACGGTCAAAACGAACTTGAGCATATGTAAAAATCCATGTATTTTTCTTCTTTTGCCAA
CTAAATCAAACTTTTTATTGTATATGTCGTACCGCCAATACAAAGATGGAGAGGTTAATG
AAAATAGATGTGAAAAAAAAGCAGGAACTATTGTAGATAGATATTTTTAGGGTTCGATTG
CTATTTTTCTGTATTATGATCTGTGTTCTATGCCAGTGTA
>MIT_Smik_c273_7756 YGL040C 5' untranslated region, Contig c273 1 - 1807, 2000 bp (revcom)
GGTTTTACCAGTTTTCTTAATACGGATATCTAGAGTAAGTCACAATTTAAGGAAATTGCA
AAATTTTCTTTTTATATAGCTAAATAGGCCAATAAATCAGGAACAATAGAATGACGCACC
GAGTTTGCTAGCAACCTACACACTTGCTTTTTTTTATAAATCAAGAGTGTATGTTGCCTC
AGGCCAATCACCGCACCGAATAAGGATTGCTCGTTTACCCGTTGTTCGATTTTTTTTTTC
ATCTTCTACCAATTTTTTTCGGCAGCGCCTTTGAATGACTTTGATCATCAATCCTGGAGT
AATATACACTTGTATGTTTGAAACGCCCAGTTACAATATTTATTGGAATAGCTAACTTAT
GAGTAAGTGGACCCAAATTTTCGAGTGATGTTTCCTGTCAACGGTGACACTTATTTTTGG
TTTGCAGATATGTATGTGTATATCTTATTCCCACTTTTTTATAGTTATCGTTATCTATGT
ATCTCAATACCTTGGACATGAATCACCGAGTAGATATTTTTCTTTACAATGCTTAAAACA
AGGCCGCACAGAACTAAACAATAAAGTTACCTTGATCTTTAATAAAATATTCCCCCATTA
ATAAGTACTCTCTTCGATTACGATTTAGCCATATTCATTTTGACCATACATTGCAGATGT
GAGATGGATTTTAAGTGGTGAAAGCGCTCTAAGCTATGCCATATAAGTACGTAAGGAGAG
ACAAAATTAAACATAATTAAGCGCCATGTGAGACTAAATGTGGCCGTCGTTTTGATTATA
TGATTGGGAAAAGCTCCTAAACATAGAGGTAGAATTATAGTTCGGAAATTTCGTCTTGCC
CTGCTCATTTTGTAGAAAACGAGTCATCATCTCCACCCTTTGTAACCGGTGTCCTGCTCA
CATAAATAGTCTCTACTGAGAGATTTGTGAATTTCGAGATAATTTTTGGGATTCCATTGT
TGATAAAGGCAATATTATTAGGTATATAAAATATACTAGA
>MIT_Sbay_c77_8808 YGL040C 5' untranslated region, Contig c77 1 - 1377, 2000 bp (revcom)
ACTTTGTCAGTGTTTTTCTGGTAAGGATATCTGGAAGAAGTAACAATACGTATAAATTAC
AAAATTACCGTTTTATGTCGTGGAATGGGCTATGAACTAACATTAACAATAGAGTGATGC
ATAGACGTCACTAGCCTTTTATTGTGTTGCCTTGCTCTTTTATAAATCAGGCAGCCTGCC
GCAGGCCAATCACCGCACCGCCCGGAGATGCTCGTTTACCGTTGTGCACCAAATTTTTCA
TTTTTTGCCTTTTTCTATTTGGCAGCGTTTTCGAAAAATTTTGATCATTAGTCTTCAATG
ACTGGACTGTCATATTTTAGGGCACGCAGGTAAAGATATGAACAAATCATATTGATGATG
GATGCCAATCCTTCAATGTAAATTCTTTCTAAACATCATGATAAAGAACTTCAGTAAGAG
AGTGATAAAAACTTTACATGTATGGCGGGTGTATTCTGTAATTGTTTTTTAGATCTTTTT
GTTGTTAACGGTGACACCATTCTTACTACAATAATTGCATGTCAAATGTAAATATCTTGC
TTCACATTTCGTTGTTTCTTTACGATAAATTGTTTCGTCGCAAATATATCTTATTTTGCG
TGGTTTATCTACAGACACTGCTTGATTTACGCATAAGTACATCATGTAGTAATTCTTATA
TTGAGTATAAAACCATATGAATAGAAATATTTTTGTTAATCTATCGTTAATTTACATGCT
AGTTTATTTGTCCCTTTAAAATTTCTTTATATATTTGTTGCAATATGTGGACAAGGAAAC
ACGAAATATATTGGGATAAAGTTTAAGTAGAGATACATAGAACTAAACAATAAATTCATA
TTCAATAATACTTCAAAAGGTACTCTCCTGTCTGAACACAGAGACTCACAGACTTTATTT
AGTCGTTATGGCGATGTCAGACATCATGTTTAAGGTAAGCCGAGTGGATTGATATGAAAT
TGTCATATCATGAATAAGCTAATTACCCAAAAACAGTAAA
>WashU_Skud_Contig2052.17 YGL040C 5' untranslated region, Contig c2052 29967 - 31966, 2000 bp (revcom)
GATTTGTCAGTGTTTTCTGATATGGATGCCTGGAGAAAATATTAATATGTGGAAACCACA
AAACTTCCACTTATATAGCTAATTTAGCCAGAAATCATGAACAATAGGATGACGCATAGA
CGTCACTACTCTTCATATAAGTTGCCTTTCTCTTTTATAAATTGGGCAGGCAGCTTGCCT
CAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTTGCGTTCAAAGTTTTTC
ATTTTCCGCATCATCTACTTTTTTTTTTTTGACGCCGTTTTTGAATGTCTTGGTCATTGA
TCTTGAAATGATTTATGTTCGTGTTTTCACGGCACAAAGGTAGGCAAATCGGTAAATTTT
ACTCGTAATAAATAATCAAGGCCTCTAGAGGATTTAATATCAGGAAATAATAATGTGAGT
TTTTTGCAAATGGCCTTATATTCCTGACATCTTCTTGAATTTGTGTTTTAGCGTCGATGA
AGACTCTTCCTTTTTTCGTACGGTAATCTGGACATCTTGTTTCGTCTTTTCTTTTTTTTT
TGCGATTGCTTGTAATTCCAGATATGCAGCATTTATTTACAGGTGCTGATTGATTTACTA
TAGAGTTTATCAGGTAGTAGTTCTTTTTCATGTCTCAATTGAAGAAAAGGAACCCATAAA
TACATTAGCACTGAACAAACAATAACTGCCGCATTGGTTTGTTTTCTAACTTGAATTTTT
CTTTATACATATGCCACTGTATTAGGATGGGTGAATACCGTTTTCTTACTTTCTTCCTAT
GAAGGCGAAAGAATGGTGAAGGACAACTAAACAATAAATCGTTTTTCACACATCCCCATA
AAGCTTTCTCTGTTTGTCAGTTGTGACTCATCTTTCGTCGATGTTGCTTGGTAGATACAA
TTGAACAAGATTGAGATATCTAAAATGTTCAAAAATTATACTCTCTTATGTAGTTTCCGT
CATGGCTGAACGAAGGAAAACTACATCACCTGAGAATTAC
>SGD_Scer_YDL205C HEM3 "Phorphobilinogen deaminase, catalyzes the conversion of 4-porphobilinogen to hydroxymethylbilane, the third step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; expression is regulated by Hap2p-Hap3p"
AGTACGTGTGTATTTACCAACTACAAATTTATCTAGATTTTCTTCGCTTTTCTTTTTTTC
TATTGTTCTAGATATTAATACGGGATGAGAAGAACAGAATATTCAAAATCTAATACAGCC
CTGTACCATGCAAACACGAGCGTCAATCTGCCAATGACCTTGAATTCAGGCTATGTGTAG
CAATAATACAGATAGTTAGTAGCCTCGTTTATATAAAGCGTTCCTTTACTTTTTCATTTT
CTTTCTTTTTTTATGTTTGATTTTTTTACTTTTTCACTTTAAAAAATTGCTGAAATTTTC
GTAGCCAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCTCCC
CAGGGTCAATTGACAAGGAGAGAAGGAATGTTATATGGGAATTGCTGCGTAAAGATGGTC
AAAAATCCTGGACTGCCGTACGAACGACAATGTAAGGATGACTGCATTAGCCAGAAAGAC
ATCTTTACCCCCGGTGCTGCCAGGGAGCAAAATAATTACGAAAAGTGGACGCAAAGTTAA
CTTAAACTACAAGGGTAGCAGCAGAATGTGTCGGTGGTACCGGTGTGATAATGCCCCATT
TGAGATGCTTGTAATTGTGGCCTAGCAATAAGAACGCAAGGCGTTTTTGTTGAAAGGAGA
ACAAGGTTAGACGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTCACCCTTAT
TTCCACCCTCAAACGATAAAGCTTGCTACTTTGATGAAAAAAATATATAAAAGGGATTGA
AAAGCAGATCAATTATGTAGCAATAGTAGTAATAACTTGTTCAATTGCTTGTCTCAACTT
GCCACAAACTATCATCAACA
>MIT_Spar_c429_3020 YDL205C 5' untranslated region, Contig c429 77420 - 79419(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTATCAACTACAAAATTTATCTAGATTTTCTTGCCTTTTCCTTTTTC
TATTGTTCTAGATACTAATACGGGATGAGAAGAACAGAATATTCAAAATGTAAAACAGCC
CTGTACCATGCAAACACGAGCCTCAATCTGCCAATGACCTTGAATCCAAGCTATGTGTAG
CAATAATACAGATGATTGATTGGCGTCGTTTATATAAAGCGTTCCTTCATTTTTTTCATT
TTCTTTCTTTTTTTATGTTTGATTTTTTACTTTTTCACTTTTGAAAACTGCTGAAATTTT
CGTAGCAAAAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCT
CCCCAGGGTCAATTGACAAGGAGAGAAGGAATGTTACATCCAGGAATTGCGACATAAAGA
TGTCCAAGAAGTCTGAACTGTCATACGAATGGCTATGCAAGGAGGATAGTACTGGTCAAG
AAGACATCTTACCCCCGGTGCTGTCAGGGAGCAAAAAAATGACAAAAGTGGACGCAAAGT
TAACTTGAACTACAAGGGTAGCAACAGAATGTCGGTGGTACCGGATGTGACAAAGCTCAC
TTGAGGTGCTTCTTGTTGCGGCATAGCAATAAGAGCGCAAGGCGTTTTTATGGAAAGGAG
AGCGAGGTTAGAGGGTGACGTTTAGGCGCATAGGCAACCTCCCCTTATTGTTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGTCTACATTGATGAAAAAAATGTATAAAAGGGATT
GAAAAGCCGATCATGTGTGTAGCAATAGTAGTAGTTATACTTGTTCAATTGCTTGCTTGC
ACTTTTCCAAAAACTACCAC
>MIT_Smik_c193_2483 YDL205C 5' untranslated region, Contig c193 6380 - 8379(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTACCAACTATAAAATTTTACCTAGACTATCTGGCCTTTTTCTTTTT
TCTATTGTTCTAGATACTAATACGGGATGAAAAGAACAGAATATTCAAAAAGTAATACAG
CCCTGTACCATTCAAACACGAGCGCCAATTTGCCAATGAACTTGAAATCCAGCTATGCGT
AGCGATAATACAGATGATTGTTTGATGTCGTTTATATTAAGCGTTCCTTCAGTTTTTCTC
ATTTTCTTTCTTTTTCTATGTTTTATTTTTCACTTTTTCACTTTTGAAAATTGCTGAAAT
TTTCGTAACAAAAAAAGAGGCCTTCATTGCTTACTCATCGTTATCTTATTGGTTAAAATC
CCCAGCGACAATGTACAAGGAGAGAAGAAATGATATGTCTGGGAATTGCAGTTTGAAGAT
ATCCAAAGAGTTTTGAAGTGCCATACGAGCAACCACGTGAGAAGTAGAGCCTTAACAGAA
AATTCATCTTACCCCTAGTACTGCCAGGGAGGAACTAAACCTAAGAACTAGTGTTAACTT
GACTTGAACTGCAAGGGTAGCGACGGCGTATGTCGGTGGTACCGGATATGGCAAGAGCCC
ATTTGAGCTGCTTGTTCTTGTGACATACTATTAAGAGCGCAAGGCGTTTATGGAAAGGAG
GACAAGGTCAGAGGATGACGTTTAAGCGCATAGGCAATCTCCCCTTATTATTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGCTGCGCTGTTGAAAAGTATATAAAAGGGATAGAA
AAGCAGAGCAATTATAATTTAGTAGAATAGCTTATTCTATCGTTAACTTGTTGAAAGGAT
CAGATTATTATCAAGATGAA
>MIT_Sbay_c841_3215 YDL205C 5' untranslated region, Contig c841 7323 - 9322(revcom), 2000 bp (revcom)
AGTATGTGTATATTTACCAACTATAGAGTATATCTAGTATTTTTTTTCCTTCTTCTTTTT
CTATTGTTCTAGATGCTAATATGGGATGAGTAGAACAAAATATTCAAAACGCAATACAGC
CCTGTACCATTCAAATACGAACGCCAATCTGCCAATGACCTTGAAATCAAGTTATGTGCC
GCGATAATACAATCTTTTGGCCTATATCGTTTAAATAAGCGTTCCTTTAATTTTTCGGTT
TCTTTCTTTTTTATGTCTAATTTTTCATTTTTTTTCACTTGAAAATTGCTGAAATTTTCG
TAGCTGAAAAAGAGAGGCCTTCTTTGCTTACTCATCGTTATCTTATTGGTCAAGAGCCCA
AGGGACAATAGACAAGGAGAGAACCACCAACTTTGGGAGTTGGATGCAAAGAAGGTCTTT
GATTTTGGGCTGCTATCAGAGCGGGCCATATAAGGAAGCTTGTAGTGGTTAGGAGAGAAC
ACGTCATTACCCCCCTCCCCCTTCTCCGCGCTGCCAGGGACCAGGCAAGGGCTTGCAAGA
GATGAACGTAAGATAGAACTACGAGGGTCGCGGCCAATGTGTCGGTAGTACCGGATGGGG
CAAAGCCCAATTGAGGTGCTTGTTGTTGAGGATGGTCGGCATGGCATGGCATGGGAGGCC
AAAGGCGCTTTGTGGGAAGGAGAACAAACAACATTAGAGGGTGACGTTTTAGCGCATAGG
CAATCTCCCCTTATTGTTCACCCTTATTTCCACCCTCAAACGACAAGGCTTGTTATGTTG
GTTGGAAATATATAAAAGGGATTGAAAAAGATCATATTCCTACATAAATTATGGTATTAG
TTTTTCTTCAATTGCTGGCT
>WashU_Skud_Contig1850.5 YDL205C 5' untranslated region, Contig c1850 6875 - 8874(revcom), 2000 bp (revcom)
GATACGTGTGTATTTGCTAACTATAAAATTTATCTAGTTTTCCTGCTTTTTTTTTTTTCT
ATTGTTCTAGAAACTAATATGGGGATGAGAAGAACAAAATTTTCAAAAAGCAATACAGCC
CTGTACCATTCAAACACGAACGCCAATCTGCAATGACCTTGAAATCAATCTATGTGTCGC
GATAATACAAGTGATTGATTGGTGTCGTTTATATAAAGCGTTCCTTCAATTTTTTCATTT
TCTTTCTTTTTTTATGTTTAATTTTCTACCTTTTTCACTTTTGAAAATTGCTGAAATTTT
CGTAGCAAAAAAAGAGAGGCGTACGTTGCTTACTCATCGTTTTCTTATTGGTCAAAAGCT
CCAGGAACAATGCCCAAGGAGAGAAAGAGTGCTACGTCTAGGAATTGCGATGGAAAGGCG
TCCAAGAGTCCTAAACTACCATGAGAACGGGCCACCCAAGGAGGGATAGCAATTGCTGAA
ACAACATCTTCACCTTCGGAGCTGGCAGGGAGCAAGGGACTCTCCGGAAAGAAAGTGAAC
GCAAAACGGAACTACAAGGATAGCAACGGAATGTGTCGGTGGTAGCGGATGTGGCAAGAT
CCCATTTCAGGAGCTTGTTGTTACGGCACAGCAGCAAGAAGAGCACAAGGCTTTTTCCGT
AAAGGAGAACAAAGTTGGAAGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTC
ACCCTTATTTCCACCCTCAAAGGATAAAGCTTGTTGCATTGATAAAAAATGTATAAAAAG
GATGGGAAACAGATGATAGTTAACAAGGTAGTGGGACGGTCTTTCGCTTATTCAGTTGTG
TGACATTCAAGGGTTACAAT
BioPerl-1.007002/t/data/map_hem/HEM2-HEM3.meme.txt000444000766000024     11473213155576321 21216 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM2-HEM3.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YGL040C         1.0000   1000  MIT_Spar_c19_8512        1.0000   1000  
MIT_Smik_c273_7756       1.0000   1000  MIT_Sbay_c77_8808        1.0000   1000  
WashU_Skud_Contig2052.17 1.0000   1000  SGD_Scer_YDL205C         1.0000    860  
MIT_Spar_c429_3020       1.0000    860  MIT_Smik_c193_2483       1.0000    860  
MIT_Sbay_c841_3215       1.0000    860  WashU_Skud_Contig1850.5  1.0000    860  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM2-HEM3.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=       10    maxsites=       10    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            9300    N=              10
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.317 C 0.183 G 0.183 T 0.317 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   11   sites =  10   llr = 140   E-value = 1.1e-010
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :::aa1:a1::
pos.-specific     C  :a9:::5:9a:
probability       G  a:1:::5:::6
matrix            T  :::::9::::4

         bits    2.5 **       * 
                 2.3 **       * 
                 2.0 ***     ** 
                 1.8 ***     ** 
Information      1.5 ***** **** 
content          1.3 ***********
(20.2 bits)      1.0 ***********
                 0.8 ***********
                 0.5 ***********
                 0.3 ***********
                 0.0 -----------

Multilevel           GCCAATCACCG
consensus                  G   T
sequence                        
                                
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value               Site  
-------------            ------  ----- ---------            -----------
WashU_Skud_Contig2052.17     +    184  1.14e-07 CTTGCCTCAG GCCAATCACCG CACCGAACAG
MIT_Sbay_c77_8808            +    185  1.14e-07 CCTGCCGCAG GCCAATCACCG CACCGCCCGG
MIT_Smik_c273_7756           +    183  1.14e-07 GTTGCCTCAG GCCAATCACCG CACCGAATAA
MIT_Spar_c19_8512            +    185  1.14e-07 CTTGCCTCAG GCCAATCACCG CACCGAACAG
SGD_Scer_YGL040C             +    184  1.14e-07 CTTGCCTCAA GCCAATCACCG CACCGAACAG
MIT_Sbay_c841_3215           +    151  3.24e-07 ACGCCAATCT GCCAATGACCT TGAAATCAAG
MIT_Spar_c429_3020           +    150  3.24e-07 GCCTCAATCT GCCAATGACCT TGAATCCAAG
SGD_Scer_YDL205C             +    150  3.24e-07 GCGTCAATCT GCCAATGACCT TGAATTCAGG
MIT_Smik_c193_2483           +    152  1.57e-06 GCGCCAATTT GCCAATGAACT TGAAATCCAG
WashU_Skud_Contig1850.5      -    817  1.69e-06 AACTGAATAA GCGAAAGACCG TCCCACTACC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2052.17          1.1e-07  183_[+1]_806
MIT_Sbay_c77_8808                 1.1e-07  184_[+1]_805
MIT_Smik_c273_7756                1.1e-07  182_[+1]_807
MIT_Spar_c19_8512                 1.1e-07  184_[+1]_805
SGD_Scer_YGL040C                  1.1e-07  183_[+1]_806
MIT_Sbay_c841_3215                3.2e-07  150_[+1]_699
MIT_Spar_c429_3020                3.2e-07  149_[+1]_700
SGD_Scer_YDL205C                  3.2e-07  149_[+1]_700
MIT_Smik_c193_2483                1.6e-06  151_[+1]_698
WashU_Skud_Contig1850.5           1.7e-06  816_[-1]_33
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=11 seqs=10
WashU_Skud_Contig2052.17 (  184) GCCAATCACCG  1 
MIT_Sbay_c77_8808        (  185) GCCAATCACCG  1 
MIT_Smik_c273_7756       (  183) GCCAATCACCG  1 
MIT_Spar_c19_8512        (  185) GCCAATCACCG  1 
SGD_Scer_YGL040C         (  184) GCCAATCACCG  1 
MIT_Sbay_c841_3215       (  151) GCCAATGACCT  1 
MIT_Spar_c429_3020       (  150) GCCAATGACCT  1 
SGD_Scer_YDL205C         (  150) GCCAATGACCT  1 
MIT_Smik_c193_2483       (  152) GCCAATGAACT  1 
WashU_Skud_Contig1850.5  (  817) GCGAAAGACCG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 11 n= 9200 bayes= 9.84392 E= 1.1e-010 
  -997   -997    251   -997 
  -997    251   -997   -997 
  -997    236    -81   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
  -169   -997   -997    147 
  -997    151    151   -997 
   162   -997   -997   -997 
  -169    236   -997   -997 
  -997    251   -997   -997 
  -997   -997    177     30 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 11 nsites= 10 E= 1.1e-010 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.900000  0.100000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.100000  0.000000  0.000000  0.900000 
 0.000000  0.500000  0.500000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.100000  0.900000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.600000  0.400000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
GCCAAT[CG]ACC[GT]
--------------------------------------------------------------------------------




Time  9.05 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =  10   llr = 196   E-value = 5.0e-018
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  ::5::1:::a:::::7:::1
pos.-specific     C  ::5:5:::5:aa9::::116
probability       G  :5:::9::::::14:1311:
matrix            T  a5:a5:aa5::::6a27883

         bits    2.5           **        
                 2.3           **        
                 2.0      *    ***       
                 1.8      *    ***       
Information      1.5 *  * *** **** *     
content          1.3 *  * *** **** *     
(28.2 bits)      1.0 *************** *** 
                 0.8 *************** ****
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TGATCGTTCACCCTTATTTC
consensus             TC T   T    G TG  T
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
SGD_Scer_YGL040C             +    209  7.10e-11 GAACAGGGAT TGCTCGTTTACCCGTATTTT GATTTTTTTT
WashU_Skud_Contig1850.5      +    712  8.92e-11 CAATCTCCCC TTATTGTTCACCCTTATTTC CACCCTCAAA
MIT_Sbay_c841_3215           +    731  8.92e-11 CAATCTCCCC TTATTGTTCACCCTTATTTC CACCCTCAAA
MIT_Spar_c429_3020           +    705  8.92e-11 CAACCTCCCC TTATTGTTCACCCTTATTTC CACCCTCAAA
SGD_Scer_YDL205C             +    704  8.92e-11 CAATCTCCCC TTATTGTTCACCCTTATTTC CACCCTCAAA
MIT_Smik_c273_7756           +    208  1.21e-10 GAATAAGGAT TGCTCGTTTACCCGTTGTTC GATTTTTTTT
MIT_Spar_c19_8512            +    210  1.21e-10 GAACAGGGAT TGCTCGTTTACCCGTAGTTT GAATTTTTTT
MIT_Smik_c193_2483           +    705  2.20e-09 CAATCTCCCC TTATTATTCACCCTTATTTC CACCCTCAAA
WashU_Skud_Contig2052.17     +    209  6.11e-09 GAACAGGGAT TGCTCGTTTACCCGTTGCGT TCAAAGTTTT
MIT_Sbay_c77_8808            +    209  2.28e-08 CGCCCGGAGA TGCTCGTTTACCGTTGTGCA CCAAATTTTT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YGL040C                  7.1e-11  208_[+2]_772
WashU_Skud_Contig1850.5           8.9e-11  711_[+2]_129
MIT_Sbay_c841_3215                8.9e-11  730_[+2]_110
MIT_Spar_c429_3020                8.9e-11  704_[+2]_136
SGD_Scer_YDL205C                  8.9e-11  703_[+2]_137
MIT_Smik_c273_7756                1.2e-10  207_[+2]_773
MIT_Spar_c19_8512                 1.2e-10  209_[+2]_771
MIT_Smik_c193_2483                2.2e-09  704_[+2]_136
WashU_Skud_Contig2052.17          6.1e-09  208_[+2]_772
MIT_Sbay_c77_8808                 2.3e-08  208_[+2]_772
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=10
SGD_Scer_YGL040C         (  209) TGCTCGTTTACCCGTATTTT  1 
WashU_Skud_Contig1850.5  (  712) TTATTGTTCACCCTTATTTC  1 
MIT_Sbay_c841_3215       (  731) TTATTGTTCACCCTTATTTC  1 
MIT_Spar_c429_3020       (  705) TTATTGTTCACCCTTATTTC  1 
SGD_Scer_YDL205C         (  704) TTATTGTTCACCCTTATTTC  1 
MIT_Smik_c273_7756       (  208) TGCTCGTTTACCCGTTGTTC  1 
MIT_Spar_c19_8512        (  210) TGCTCGTTTACCCGTAGTTT  1 
MIT_Smik_c193_2483       (  705) TTATTATTCACCCTTATTTC  1 
WashU_Skud_Contig2052.17 (  209) TGCTCGTTTACCCGTTGCGT  1 
MIT_Sbay_c77_8808        (  209) TGCTCGTTTACCGTTGTGCA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 9110 bayes= 9.82972 E= 5.0e-018 
  -997   -997   -997    162 
  -997   -997    151     62 
    62    151   -997   -997 
  -997   -997   -997    162 
  -997    151   -997     62 
  -169   -997    236   -997 
  -997   -997   -997    162 
  -997   -997   -997    162 
  -997    151   -997     62 
   162   -997   -997   -997 
  -997    251   -997   -997 
  -997    251   -997   -997 
  -997    236    -81   -997 
  -997   -997    119     89 
  -997   -997   -997    162 
   111   -997    -81    -70 
  -997   -997     77    111 
  -997    -81    -81    130 
  -997    -81    -81    130 
  -169    177   -997    -11 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.0e-018 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.100000  0.000000  0.900000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.500000  0.000000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.900000  0.100000  0.000000 
 0.000000  0.000000  0.400000  0.600000 
 0.000000  0.000000  0.000000  1.000000 
 0.700000  0.000000  0.100000  0.200000 
 0.000000  0.000000  0.300000  0.700000 
 0.000000  0.100000  0.100000  0.800000 
 0.000000  0.100000  0.100000  0.800000 
 0.100000  0.600000  0.000000  0.300000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
T[GT][AC]T[CT]GTT[CT]ACCC[TG]T[AT][TG]TT[CT]
--------------------------------------------------------------------------------




Time 18.20 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   15   sites =  10   llr = 167   E-value = 8.5e-015
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  5:a:::a9:1:1:1:
pos.-specific     C  :1:::a::39:5a98
probability       G  :4:aa::13::3::1
matrix            T  55::::::4:a1::1

         bits    2.5    ***      *  
                 2.3    ***      *  
                 2.0    ***   *  ** 
                 1.8    ***   *  ** 
Information      1.5   *****  ** ***
content          1.3   ****** ** ***
(24.1 bits)      1.0   ****** ** ***
                 0.8  ******* ******
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           ATAGGCAATCTCCCC
consensus            TG      C  G   
sequence                     G      
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
MIT_Spar_c429_3020           +    690  1.51e-09 GTTTAGGCGC ATAGGCAACCTCCCC TTATTGTTCA
MIT_Spar_c19_8512            -    169  1.91e-09 GTGATTGGCC TGAGGCAAGCTGCCC GCTTGATTTA
WashU_Skud_Contig1850.5      +    697  2.59e-09 GTTTAGGCGC ATAGGCAATCTCCCC TTATTGTTCA
MIT_Sbay_c841_3215           +    716  2.59e-09 GTTTTAGCGC ATAGGCAATCTCCCC TTATTGTTCA
MIT_Smik_c193_2483           +    690  2.59e-09 GTTTAAGCGC ATAGGCAATCTCCCC TTATTATTCA
SGD_Scer_YDL205C             +    689  2.59e-09 GTTTAGGCGC ATAGGCAATCTCCCC TTATTGTTCA
SGD_Scer_YGL040C             -    168  8.84e-09 GTGATTGGCT TGAGGCAAGCTTCCC GCTTGATTTA
WashU_Skud_Contig2052.17     -    168  2.94e-08 GTGATTGGCC TGAGGCAAGCTGCCT GCCCAATTTA
MIT_Sbay_c77_8808            +    167  1.36e-07 CTTTTATAAA TCAGGCAGCCTGCCG CAGGCCAATC
MIT_Smik_c273_7756           -    167  3.45e-07 GTGATTGGCC TGAGGCAACATACAC TCTTGATTTA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c429_3020                1.5e-09  689_[+3]_156
MIT_Spar_c19_8512                 1.9e-09  168_[-3]_817
WashU_Skud_Contig1850.5           2.6e-09  696_[+3]_149
MIT_Sbay_c841_3215                2.6e-09  715_[+3]_130
MIT_Smik_c193_2483                2.6e-09  689_[+3]_156
SGD_Scer_YDL205C                  2.6e-09  688_[+3]_157
SGD_Scer_YGL040C                  8.8e-09  167_[-3]_818
WashU_Skud_Contig2052.17          2.9e-08  167_[-3]_818
MIT_Sbay_c77_8808                 1.4e-07  166_[+3]_819
MIT_Smik_c273_7756                3.4e-07  166_[-3]_819
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=15 seqs=10
MIT_Spar_c429_3020       (  690) ATAGGCAACCTCCCC  1 
MIT_Spar_c19_8512        (  169) TGAGGCAAGCTGCCC  1 
WashU_Skud_Contig1850.5  (  697) ATAGGCAATCTCCCC  1 
MIT_Sbay_c841_3215       (  716) ATAGGCAATCTCCCC  1 
MIT_Smik_c193_2483       (  690) ATAGGCAATCTCCCC  1 
SGD_Scer_YDL205C         (  689) ATAGGCAATCTCCCC  1 
SGD_Scer_YGL040C         (  168) TGAGGCAAGCTTCCC  1 
WashU_Skud_Contig2052.17 (  168) TGAGGCAAGCTGCCT  1 
MIT_Sbay_c77_8808        (  167) TCAGGCAGCCTGCCG  1 
MIT_Smik_c273_7756       (  167) TGAGGCAACATACAC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 9160 bayes= 9.83763 E= 8.5e-015 
    62   -997   -997     62 
  -997    -81    119     62 
   162   -997   -997   -997 
  -997   -997    251   -997 
  -997   -997    251   -997 
  -997    251   -997   -997 
   162   -997   -997   -997 
   147   -997    -81   -997 
  -997     77     77     30 
  -169    236   -997   -997 
  -997   -997   -997    162 
  -169    151     77   -169 
  -997    251   -997   -997 
  -169    236   -997   -997 
  -997    219    -81   -169 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 8.5e-015 
 0.500000  0.000000  0.000000  0.500000 
 0.000000  0.100000  0.400000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
 0.000000  0.300000  0.300000  0.400000 
 0.100000  0.900000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.100000  0.500000  0.300000  0.100000 
 0.000000  1.000000  0.000000  0.000000 
 0.100000  0.900000  0.000000  0.000000 
 0.000000  0.800000  0.100000  0.100000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
[AT][TG]AGGCAA[TCG]CT[CG]CCC
--------------------------------------------------------------------------------




Time 27.22 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   18   sites =  10   llr = 176   E-value = 2.3e-013
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  92:5718a:aa:a:9855
pos.-specific     C  ::a:::::a:::::::::
probability       G  ::::182::::::a12:5
matrix            T  18:521:::::a::::5:

         bits    2.5   *     *    *    
                 2.3   *     *    *    
                 2.0   *     *    *    
                 1.8   *     *    *    
Information      1.5   *  * *******    
content          1.3 * *  * ********   
(25.4 bits)      1.0 ***  *********** *
                 0.8 ***  *********** *
                 0.5 ******************
                 0.3 ******************
                 0.0 ------------------

Multilevel           ATCAAGAACAATAGAAAA
consensus             A TT G        GTG
sequence                               
                                       
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                   Site     
-------------            ------  ----- ---------            ------------------
MIT_Sbay_c841_3215           -     57  8.38e-10 CCATATTAGC ATCTAGAACAATAGAAAA AGAAGAAGGA
MIT_Smik_c193_2483           -     58  8.38e-10 CCGTATTAGT ATCTAGAACAATAGAAAA AAGAAAAAGG
MIT_Spar_c429_3020           -     56  8.38e-10 CCGTATTAGT ATCTAGAACAATAGAAAA AGGAAAAGGC
SGD_Scer_YDL205C             -     56  8.38e-10 CCGTATTAAT ATCTAGAACAATAGAAAA AAAGAAAAGC
MIT_Smik_c273_7756           +     96  2.49e-09 AGGCCAATAA ATCAGGAACAATAGAATG ACGCACCGAG
MIT_Spar_c19_8512            +     96  5.09e-09 TGGGCCAAAA AACAAGGACAATAGAATG ACACATAAAG
WashU_Skud_Contig1850.5      -     55  9.52e-09 CCATATTAGT TTCTAGAACAATAGAAAA AAAAAAAAGC
WashU_Skud_Contig2052.17     +     94  9.81e-09 TTAGCCAGAA ATCATGAACAATAGGATG ACGCATAGAC
SGD_Scer_YGL040C             +     95  2.62e-08 GGGCAAGAAA ATCAAAGACAATAGAGTG GCGCATAGAT
MIT_Sbay_c77_8808            +     99  6.75e-08 GCTATGAACT AACATTAACAATAGAGTG ATGCATAGAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Sbay_c841_3215                8.4e-10  56_[-4]_786
MIT_Smik_c193_2483                8.4e-10  57_[-4]_785
MIT_Spar_c429_3020                8.4e-10  55_[-4]_787
SGD_Scer_YDL205C                  8.4e-10  55_[-4]_787
MIT_Smik_c273_7756                2.5e-09  95_[+4]_887
MIT_Spar_c19_8512                 5.1e-09  95_[+4]_887
WashU_Skud_Contig1850.5           9.5e-09  54_[-4]_788
WashU_Skud_Contig2052.17          9.8e-09  93_[+4]_889
SGD_Scer_YGL040C                  2.6e-08  94_[+4]_888
MIT_Sbay_c77_8808                 6.8e-08  98_[+4]_884
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=18 seqs=10
MIT_Sbay_c841_3215       (   57) ATCTAGAACAATAGAAAA  1 
MIT_Smik_c193_2483       (   58) ATCTAGAACAATAGAAAA  1 
MIT_Spar_c429_3020       (   56) ATCTAGAACAATAGAAAA  1 
SGD_Scer_YDL205C         (   56) ATCTAGAACAATAGAAAA  1 
MIT_Smik_c273_7756       (   96) ATCAGGAACAATAGAATG  1 
MIT_Spar_c19_8512        (   96) AACAAGGACAATAGAATG  1 
WashU_Skud_Contig1850.5  (   55) TTCTAGAACAATAGAAAA  1 
WashU_Skud_Contig2052.17 (   94) ATCATGAACAATAGGATG  1 
SGD_Scer_YGL040C         (   95) ATCAAAGACAATAGAGTG  1 
MIT_Sbay_c77_8808        (   99) AACATTAACAATAGAGTG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 18 n= 9130 bayes= 9.83289 E= 2.3e-013 
   147   -997   -997   -169 
   -70   -997   -997    130 
  -997    251   -997   -997 
    62   -997   -997     62 
   111   -997    -81    -70 
  -169   -997    219   -169 
   130   -997     19   -997 
   162   -997   -997   -997 
  -997    251   -997   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
  -997   -997   -997    162 
   162   -997   -997   -997 
  -997   -997    251   -997 
   147   -997    -81   -997 
   130   -997     19   -997 
    62   -997   -997     62 
    62   -997    151   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 18 nsites= 10 E= 2.3e-013 
 0.900000  0.000000  0.000000  0.100000 
 0.200000  0.000000  0.000000  0.800000 
 0.000000  1.000000  0.000000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.700000  0.000000  0.100000  0.200000 
 0.100000  0.000000  0.800000  0.100000 
 0.800000  0.000000  0.200000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
 0.800000  0.000000  0.200000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.500000  0.000000  0.500000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
A[TA]C[AT][AT]G[AG]ACAATAGA[AG][AT][AG]
--------------------------------------------------------------------------------




Time 35.82 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =  10   llr = 179   E-value = 9.4e-012
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  ::::::8::::::1:1211:
pos.-specific     C  :1:11a2:12:61:49:4::
probability       G  ::::1::::::::41:::::
matrix            T  a9a98::a98a4955:859a

         bits    2.5      *              
                 2.3      *              
                 2.0      *         *    
                 1.8      *         *    
Information      1.5 * *  * *  *    *   *
content          1.3 **** * ** ***  *  **
(25.8 bits)      1.0 *************  ** **
                 0.8 ************* *** **
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TTTTTCATTTTCTTTCTTTT
consensus                  C  C T GC AC  
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1850.5      +    231  1.09e-10 TTCCTTCAAT TTTTTCATTTTCTTTCTTTT TTTATGTTTA
MIT_Spar_c429_3020           +    232  1.09e-10 TTCCTTCATT TTTTTCATTTTCTTTCTTTT TTTATGTTTG
SGD_Scer_YDL205C             +    230  1.09e-10 GTTCCTTTAC TTTTTCATTTTCTTTCTTTT TTTATGTTTG
MIT_Sbay_c77_8808            +    234  1.86e-10 GTGCACCAAA TTTTTCATTTTTTGCCTTTT TCTATTTGGC
MIT_Smik_c193_2483           +    235  1.28e-09 TCCTTCAGTT TTTCTCATTTTCTTTCTTTT TCTATGTTTT
MIT_Sbay_c841_3215           +    261  2.16e-09 TTATGTCTAA TTTTTCATTTTTTTTCACTT GAAAATTGCT
MIT_Spar_c19_8512            +    450  1.73e-08 GTACGTCTTG TTTTGCCTTCTTTGGCTCTT GTGTCACTGA
SGD_Scer_YGL040C             +    446  2.06e-08 GTGTACGCCT TCTTCCCTTCTTTGCCTCTT GTGCCACTGT
WashU_Skud_Contig2052.17     +    235  3.92e-08 GCGTTCAAAG TTTTTCATTTTCCGCATCAT CTACTTTTTT
MIT_Smik_c273_7756           +    235  4.56e-08 TTCGATTTTT TTTTTCATCTTCTACCAATT TTTTTCGGCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1850.5           1.1e-10  230_[+5]_610
MIT_Spar_c429_3020                1.1e-10  231_[+5]_609
SGD_Scer_YDL205C                  1.1e-10  229_[+5]_611
MIT_Sbay_c77_8808                 1.9e-10  233_[+5]_747
MIT_Smik_c193_2483                1.3e-09  234_[+5]_606
MIT_Sbay_c841_3215                2.2e-09  260_[+5]_580
MIT_Spar_c19_8512                 1.7e-08  449_[+5]_531
SGD_Scer_YGL040C                  2.1e-08  445_[+5]_535
WashU_Skud_Contig2052.17          3.9e-08  234_[+5]_746
MIT_Smik_c273_7756                4.6e-08  234_[+5]_746
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=10
WashU_Skud_Contig1850.5  (  231) TTTTTCATTTTCTTTCTTTT  1 
MIT_Spar_c429_3020       (  232) TTTTTCATTTTCTTTCTTTT  1 
SGD_Scer_YDL205C         (  230) TTTTTCATTTTCTTTCTTTT  1 
MIT_Sbay_c77_8808        (  234) TTTTTCATTTTTTGCCTTTT  1 
MIT_Smik_c193_2483       (  235) TTTCTCATTTTCTTTCTTTT  1 
MIT_Sbay_c841_3215       (  261) TTTTTCATTTTTTTTCACTT  1 
MIT_Spar_c19_8512        (  450) TTTTGCCTTCTTTGGCTCTT  1 
SGD_Scer_YGL040C         (  446) TCTTCCCTTCTTTGCCTCTT  1 
WashU_Skud_Contig2052.17 (  235) TTTTTCATTTTCCGCATCAT  1 
MIT_Smik_c273_7756       (  235) TTTTTCATCTTCTACCAATT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 9110 bayes= 9.82972 E= 9.4e-012 
  -997   -997   -997    162 
  -997    -81   -997    147 
  -997   -997   -997    162 
  -997    -81   -997    147 
  -997    -81    -81    130 
  -997    251   -997   -997 
   130     19   -997   -997 
  -997   -997   -997    162 
  -997    -81   -997    147 
  -997     19   -997    130 
  -997   -997   -997    162 
  -997    177   -997     30 
  -997    -81   -997    147 
  -169   -997    119     62 
  -997    119    -81     62 
  -169    236   -997   -997 
   -70   -997   -997    130 
  -169    119   -997     62 
  -169   -997   -997    147 
  -997   -997   -997    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 9.4e-012 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  0.100000  0.100000  0.800000 
 0.000000  1.000000  0.000000  0.000000 
 0.800000  0.200000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  0.200000  0.000000  0.800000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.600000  0.000000  0.400000 
 0.000000  0.100000  0.000000  0.900000 
 0.100000  0.000000  0.400000  0.500000 
 0.000000  0.400000  0.100000  0.500000 
 0.100000  0.900000  0.000000  0.000000 
 0.200000  0.000000  0.000000  0.800000 
 0.100000  0.400000  0.000000  0.500000 
 0.100000  0.000000  0.000000  0.900000 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
TTTTTC[AC]TT[TC]T[CT]T[TG][TC]C[TA][TC]TT
--------------------------------------------------------------------------------




Time 44.27 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YGL040C                 4.71e-19  94_[+4(2.62e-08)]_55_[-3(8.84e-09)]_1_[+1(1.14e-07)]_14_[+2(7.10e-11)]_6_[+5(2.48e-05)]_191_[+5(2.06e-08)]_95_[-5(3.50e-05)]_420
MIT_Spar_c19_8512                3.44e-20  95_[+4(5.09e-09)]_55_[-3(1.91e-09)]_1_[+1(1.14e-07)]_14_[+2(1.21e-10)]_7_[+5(2.48e-05)]_193_[+5(1.73e-08)]_353_[+5(1.61e-05)]_65_[-5(3.99e-05)]_73
MIT_Smik_c273_7756               5.44e-18  43_[-5(4.67e-06)]_32_[+4(2.49e-09)]_53_[-3(3.45e-07)]_1_[+1(1.14e-07)]_14_[+2(1.21e-10)]_7_[+5(4.56e-08)]_187_[+2(8.72e-05)]_539
MIT_Sbay_c77_8808                3.80e-17  98_[+4(6.75e-08)]_50_[+3(1.36e-07)]_3_[+1(1.14e-07)]_13_[+2(2.28e-08)]_5_[+5(1.86e-10)]_508_[-5(4.64e-05)]_219
WashU_Skud_Contig2052.17         6.49e-17  93_[+4(9.81e-09)]_56_[-3(2.94e-08)]_1_[+1(1.14e-07)]_14_[+2(6.11e-09)]_6_[+5(3.92e-08)]_265_[+5(1.82e-05)]_245_[+1(9.56e-05)]_205
SGD_Scer_YDL205C                 7.24e-23  55_[-4(8.38e-10)]_76_[+1(3.24e-07)]_69_[+5(1.09e-10)]_4_[+5(6.12e-05)]_50_[+2(1.32e-05)]_345_[+3(2.59e-09)]_[+2(8.92e-11)]_137
MIT_Spar_c429_3020               4.36e-23  55_[-4(8.38e-10)]_76_[+1(3.24e-07)]_71_[+5(1.09e-10)]_75_[+2(1.32e-05)]_160_[-5(7.29e-05)]_163_[+3(1.51e-09)]_[+2(8.92e-11)]_105_[+2(8.90e-05)]_11
MIT_Smik_c193_2483               6.38e-20  57_[-4(8.38e-10)]_76_[+1(1.57e-06)]_72_[+5(1.28e-09)]_11_[+5(4.42e-05)]_42_[+2(1.03e-05)]_342_[+3(2.59e-09)]_[+2(2.20e-09)]_136
MIT_Sbay_c841_3215               1.19e-21  56_[-4(8.38e-10)]_76_[+1(3.24e-07)]_69_[+5(3.18e-06)]_10_[+5(2.16e-09)]_44_[+2(1.03e-05)]_371_[+3(2.59e-09)]_[+2(8.92e-11)]_110
WashU_Skud_Contig1850.5          3.30e-21  54_[-4(9.52e-09)]_158_[+5(1.09e-10)]_4_[+5(6.08e-06)]_52_[+2(1.38e-05)]_180_[-5(8.12e-05)]_43_[+3(2.88e-05)]_92_[+3(2.59e-09)]_[+2(8.92e-11)]_85_[-1(1.69e-06)]_33
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM2-HEM4.fa000444000766000024      2245713155576321 20026 0ustar00cjfieldsstaff000000000000>SGD_Scer_YGL040C HEM2 "Delta-aminolevulinate dehydratase, a homo-octameric enzyme, catalyzes the conversion of delta-aminolevulinic acid to porphobilinogen, the second step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus"
GGTTTTGTCAATTTTCTAGGTATGAATTACTGGAGTAAGCAATAATATGAGTAAGCAGTA
AAACTTTTTTTTATTTGGCTGATTGGGCAAGAAAATCAAAGACAATAGAGTGGCGCATAG
ATGTTGCTAGCATTTATTAGGTTGCCTTACTCTTATATAAATCAAGCGGGAAGCTTGCCT
CAAGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTATTTTGATTTTTTTTTC
ACCTTTTCCAATTTTTTTTTCGGCAACAATTTTTTGGATGATTTTTATCGTCGATCTTGG
AATGATGATGTATTTCGGCGTCTCTACAAGACCCAATAAAGTAATTCGGTGACACAGGCT
TGTAGCAGATAGAAAACGTTCCGAAAGATGGGTTCCAATTGATGTAACACTTCTTTTTTA
TATATTCATGTGGACGTGTACGCCTTCTTCCCTTCTTTGCCTCTTGTGCCACTGTTAATC
CTCTTAAGCATATTGTTTTTATTTACAGACATTGGCTGACTCACCAGAAACTATAATTGA
CGCTGATTTCTAGTTAATTAAAAATAAAATATATGCAAGAATTAGCACCAGGCAGTCATT
TCTGTAAATTGCTTTGTTTTCTATTTCAAATTTGTTTTTTGTATATGTTTCAATGTTCTC
GTGACAATGCAGGCTTTTTTTTGTGCGAATTAAAGTAAAGCTAATCAAAACTAAACAATA
ATTTATCTTGTTCCCGAAAGAGTGGATCATGAGGAGGAAAGCTAACCGTCCAAGATCCTA
TATAATTTTTGAACTGAAAACCAACTGTTCACCTAGAAGACAGGTATCTGGATATGTAAC
TACACGCTCTATAAATACAGAAATCGTAAGCTAATCAATATAAATGTAAAAGAAAATAGG
AATTGCTGTCGATAGATTTATTTACTTTTGTATTGTCATCTGTGTTCTGTGCCAGTACAC
CGGACTCGTATGAGCTGTATGGTGTCGTTTCAATAGAATC
>MIT_Spar_c19_8512 YGL040C 5' untranslated region, Contig c19 1 - 1802, 2000 bp (revcom)
GGTTTTGTCAATATTCTAAATATGGATTCCTAGGGCAGGCAATAATATGGGGAAGCAGTA
AAACTTTTTGTTTTATGTGGCTGATTGGGCCAAAAAACAAGGACAATAGAATGACACATA
AAGTTTGCTAGCATTTATTAGGTTGCCTTACTCTTTTATAAATCAAGCGGGCAGCTTGCC
TCAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTAGTTTGAATTTTTTTT
TCACCTTTTGAAATTTTTTTTTTTCGGCAACAATTTTGAATGACTTTTATCGTCAATCTT
GGGAGTATACCTGCCTCTTTACAACACCCAACAAAACACTTAAGTAAGACAAGCTTGTGG
CAGGTAGGAAAGGTTTCAAAAAAAAAAAAAAGGTTTTTATCTATGGTCATACTTTTTCTT
CGTATATTTATGTGAACACGTACGTCTTGTTTTGCCTTCTTTGGCTCTTGTGTCACTGAA
TCTTCACATATTGTTTTTATTTACAGATACTACTTGACTCGCCTAAAATTATAATCGGCG
ATGGTTTCTACTACCTTAGTTAAAAAATAAAATGAATCAAAACATTACCATTAATAATTC
AATTTTTCCACATTAGTTTGTTTTCTATTTTATGGCTTTCTTCTTGTATATTTCTCAATA
TACTGCATGGCAATGCAAGCTCTTCTCTTTTCTTGATTGAAAATAAAGCTGTGAAGAACT
AAATAATAATTTATTGATGTCCTCCACAAAATGTACACCTGCGCTAACCTTGCTTAACAG
ATACGGTCAAAACGAACTTGAGCATATGTAAAAATCCATGTATTTTTCTTCTTTTGCCAA
CTAAATCAAACTTTTTATTGTATATGTCGTACCGCCAATACAAAGATGGAGAGGTTAATG
AAAATAGATGTGAAAAAAAAGCAGGAACTATTGTAGATAGATATTTTTAGGGTTCGATTG
CTATTTTTCTGTATTATGATCTGTGTTCTATGCCAGTGTA
>MIT_Smik_c273_7756 YGL040C 5' untranslated region, Contig c273 1 - 1807, 2000 bp (revcom)
GGTTTTACCAGTTTTCTTAATACGGATATCTAGAGTAAGTCACAATTTAAGGAAATTGCA
AAATTTTCTTTTTATATAGCTAAATAGGCCAATAAATCAGGAACAATAGAATGACGCACC
GAGTTTGCTAGCAACCTACACACTTGCTTTTTTTTATAAATCAAGAGTGTATGTTGCCTC
AGGCCAATCACCGCACCGAATAAGGATTGCTCGTTTACCCGTTGTTCGATTTTTTTTTTC
ATCTTCTACCAATTTTTTTCGGCAGCGCCTTTGAATGACTTTGATCATCAATCCTGGAGT
AATATACACTTGTATGTTTGAAACGCCCAGTTACAATATTTATTGGAATAGCTAACTTAT
GAGTAAGTGGACCCAAATTTTCGAGTGATGTTTCCTGTCAACGGTGACACTTATTTTTGG
TTTGCAGATATGTATGTGTATATCTTATTCCCACTTTTTTATAGTTATCGTTATCTATGT
ATCTCAATACCTTGGACATGAATCACCGAGTAGATATTTTTCTTTACAATGCTTAAAACA
AGGCCGCACAGAACTAAACAATAAAGTTACCTTGATCTTTAATAAAATATTCCCCCATTA
ATAAGTACTCTCTTCGATTACGATTTAGCCATATTCATTTTGACCATACATTGCAGATGT
GAGATGGATTTTAAGTGGTGAAAGCGCTCTAAGCTATGCCATATAAGTACGTAAGGAGAG
ACAAAATTAAACATAATTAAGCGCCATGTGAGACTAAATGTGGCCGTCGTTTTGATTATA
TGATTGGGAAAAGCTCCTAAACATAGAGGTAGAATTATAGTTCGGAAATTTCGTCTTGCC
CTGCTCATTTTGTAGAAAACGAGTCATCATCTCCACCCTTTGTAACCGGTGTCCTGCTCA
CATAAATAGTCTCTACTGAGAGATTTGTGAATTTCGAGATAATTTTTGGGATTCCATTGT
TGATAAAGGCAATATTATTAGGTATATAAAATATACTAGA
>MIT_Sbay_c77_8808 YGL040C 5' untranslated region, Contig c77 1 - 1377, 2000 bp (revcom)
ACTTTGTCAGTGTTTTTCTGGTAAGGATATCTGGAAGAAGTAACAATACGTATAAATTAC
AAAATTACCGTTTTATGTCGTGGAATGGGCTATGAACTAACATTAACAATAGAGTGATGC
ATAGACGTCACTAGCCTTTTATTGTGTTGCCTTGCTCTTTTATAAATCAGGCAGCCTGCC
GCAGGCCAATCACCGCACCGCCCGGAGATGCTCGTTTACCGTTGTGCACCAAATTTTTCA
TTTTTTGCCTTTTTCTATTTGGCAGCGTTTTCGAAAAATTTTGATCATTAGTCTTCAATG
ACTGGACTGTCATATTTTAGGGCACGCAGGTAAAGATATGAACAAATCATATTGATGATG
GATGCCAATCCTTCAATGTAAATTCTTTCTAAACATCATGATAAAGAACTTCAGTAAGAG
AGTGATAAAAACTTTACATGTATGGCGGGTGTATTCTGTAATTGTTTTTTAGATCTTTTT
GTTGTTAACGGTGACACCATTCTTACTACAATAATTGCATGTCAAATGTAAATATCTTGC
TTCACATTTCGTTGTTTCTTTACGATAAATTGTTTCGTCGCAAATATATCTTATTTTGCG
TGGTTTATCTACAGACACTGCTTGATTTACGCATAAGTACATCATGTAGTAATTCTTATA
TTGAGTATAAAACCATATGAATAGAAATATTTTTGTTAATCTATCGTTAATTTACATGCT
AGTTTATTTGTCCCTTTAAAATTTCTTTATATATTTGTTGCAATATGTGGACAAGGAAAC
ACGAAATATATTGGGATAAAGTTTAAGTAGAGATACATAGAACTAAACAATAAATTCATA
TTCAATAATACTTCAAAAGGTACTCTCCTGTCTGAACACAGAGACTCACAGACTTTATTT
AGTCGTTATGGCGATGTCAGACATCATGTTTAAGGTAAGCCGAGTGGATTGATATGAAAT
TGTCATATCATGAATAAGCTAATTACCCAAAAACAGTAAA
>WashU_Skud_Contig2052.17 YGL040C 5' untranslated region, Contig c2052 29967 - 31966, 2000 bp (revcom)
GATTTGTCAGTGTTTTCTGATATGGATGCCTGGAGAAAATATTAATATGTGGAAACCACA
AAACTTCCACTTATATAGCTAATTTAGCCAGAAATCATGAACAATAGGATGACGCATAGA
CGTCACTACTCTTCATATAAGTTGCCTTTCTCTTTTATAAATTGGGCAGGCAGCTTGCCT
CAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTTGCGTTCAAAGTTTTTC
ATTTTCCGCATCATCTACTTTTTTTTTTTTGACGCCGTTTTTGAATGTCTTGGTCATTGA
TCTTGAAATGATTTATGTTCGTGTTTTCACGGCACAAAGGTAGGCAAATCGGTAAATTTT
ACTCGTAATAAATAATCAAGGCCTCTAGAGGATTTAATATCAGGAAATAATAATGTGAGT
TTTTTGCAAATGGCCTTATATTCCTGACATCTTCTTGAATTTGTGTTTTAGCGTCGATGA
AGACTCTTCCTTTTTTCGTACGGTAATCTGGACATCTTGTTTCGTCTTTTCTTTTTTTTT
TGCGATTGCTTGTAATTCCAGATATGCAGCATTTATTTACAGGTGCTGATTGATTTACTA
TAGAGTTTATCAGGTAGTAGTTCTTTTTCATGTCTCAATTGAAGAAAAGGAACCCATAAA
TACATTAGCACTGAACAAACAATAACTGCCGCATTGGTTTGTTTTCTAACTTGAATTTTT
CTTTATACATATGCCACTGTATTAGGATGGGTGAATACCGTTTTCTTACTTTCTTCCTAT
GAAGGCGAAAGAATGGTGAAGGACAACTAAACAATAAATCGTTTTTCACACATCCCCATA
AAGCTTTCTCTGTTTGTCAGTTGTGACTCATCTTTCGTCGATGTTGCTTGGTAGATACAA
TTGAACAAGATTGAGATATCTAAAATGTTCAAAAATTATACTCTCTTATGTAGTTTCCGT
CATGGCTGAACGAAGGAAAACTACATCACCTGAGAATTAC
>SGD_Scer_YOR278W HEM4 "Uroporphyrinogen III synthase, catalyzes the conversion of hydroxymethylbilane to uroporphyrinogen III, the fourth step in the heme biosynthetic pathway"
CTCTCGAGCAAGGTCTATTTTACCTTTCTGTTTCCTTATCCTTTGACACTAAAATTCAAA
AAACTCACTAGAAAGTTCACTAAAGCGCCTTAGCTGACTACAGCACAACCCAACCCCAAA
AACTAGTGAACTACACACTAAGAGAATTTATGGTATTTCCATAATTGAAGTATATGTACG
ATGTATACAATGTAAACAAGAGAGTAATGAAGTGAAGATATGTACACCTAGAGCGAACCA
ATGATAATTTGTTTTCTTAATTAAGAAAAACCATTAAAACTGGATTAGATTTCAATAATG
AAAAGCTAGGAACAAAAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGACATA
TGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGTTTT
CTTATCCTGAAGGATCCTGCAAATGAAGTAAGTTCAAAGAATTGAAATGAAATCGCCTTT
TATACCCTCGCCGCACCAAGGAGCGCGCTGTGAAAATTTTTCGCTTTATCTCTTAGGGCT
CCTACTGTCGGTAGAGAAAAGTTGAGTATATTTAAAGCATGAGGTAACTTTTCTGCCCAT
TTTTACTTCTATTTCCATTTGAATTCAGAAAAGTG
>MIT_Spar_c261_21317 YOR278W 5' untranslated region, Contig c261 32269 - 34268, 2000 bp (revcom)
CGTTCCAAGCAGGGTTTATTCTATTTCTCGGCTCCTTTACCCTGTAACTTCGAGATTCAA
AAACTCGCTATAACTTCACTAAAGCGCTTTAGTTGACTACAACACAACCCAACCCCAAAA
TAAACTGTCCAACTACACAATACCGAGGATAATCCACGATATTTCGGTGATTGAAGTATA
TGTATTACGTATGCAATGTAAGCAAGAAACTAACAAAATGAATATGTACACCTAGAGCGA
ACCAATGATAATTTGTTTTCTTAATAAAGAAAAACTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAACAGAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGAC
ATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGT
TCTTTTATCCTGAAGGATAAACGGAAAGCTCCCGATTAAAAACAAGTATAGAGTACTGGA
ATAGAATCGCCTTTTATACCCTCCCTCGCCGCATCAAGAAGCGCGCTGTGAAAATTTTTC
GTTTTTCTCTTAGGGCTCCCATCCAACTGTCGGCGAGGAAAAGTTGTATATATTTAAAGC
ATGAGGTAACTTTGTTGCCCATTATCTTTTTTGTT
>MIT_Smik_c492_20940 YOR278W 5' untranslated region, Contig c492 3260 - 5259(revcom), 2000 bp (revcom)
ACTTTCAAACACACTCTGGTGTACTCCTCGGTCCCTTCATCTCATTTCTTCAAGATGCAG
AACTTCGCCGGAAGTAAACTAAAGTGCTTTAATTAATCAAAAGACAACTTAATTCCCAAA
CGGAAATGCAGGCTAGACAAACCGAAGATAATCCCCGATATTTCTGAGTTTAACAAATGT
ATGTATAATATGTATGCAATGTAGGCAAGAAAATAACGAAGTGAAGATATGTACACCTAG
AGCGAACCAATAATAATTTGTTTTCTTACTAAAGAAAAACTATTAAAACTGGATTAGATT
TCAATAATGAAAAGCTAGGAACAAAAGAAATTTGTCTACTTCCAGCCATTTGCGCTTTAT
ATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAAT
GATGGTTCTTTTAAACCAAAATTTAAAGAAAAATCTTAACGGTAATATGAGTAGGAGGTT
GGAATGGGATCGCTTTTTATACCCTCATTGTGATAAGAGACGCGCAGTGAAAAATTTTCG
CTTTTTCTTAGGGCTCCTATCTAACTCTCGGGCGAATAAATATCATGAATGTATTTAAAC
GTCAAGTTAGTTAAATGTTTGAGTCTGTTTCTTTT
>WashU_Skud_Contig1682.4 YOR278W 5' untranslated region, Contig c1682 3379 - 5378, 2000 bp (revcom)
CTCTTCAAACAGACTCCAATTCACTACTGAGCTCTTACCTTGTGACTTCAAGACTCACTA
CTCAGTTGAAAGACACGCTCAGTACCAAATTCGGCTGCGAGGCAACTAACGCCTTTAAAC
AGGTAGGTAAGGAACAATACCGAAAGGCCATCTCCGATGTTTCGAAGATTGGCAAATGTA
TATATTATGTATGCAATATAGGCAAGATGATAACGAAGTAGAGATATGTACACCTAGAGC
GAACCAATGATAATTTGTTTTCTTAATGAAGAAAGTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAATAAAAGAGATTGGTCTACTTCCAGCCATTTGCGCTTTACATAGA
CATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGG
TTCTATTTAAAATGAAATCTAAAGATAAACCCTAGTCATAATCAAGTGGGTTGTGTTAAA
ATACAAGCACCTTTTATACTCTCGCAGCGTCAGTGGCGCGTTGTGAAAAATTTTCACTTT
TTCTCAGGGCTTTTACCCAACTGCCGACAAATAAAAGCCGTATTTAAGGAATGTGATTAG
TTTACTTTCCAATGCTTTCTCTTTTTTGTAGGGTA
>WashU_Sbay_Contig635.57 YOR278W 5' untranslated region, Contig c635 91073 - 93072, 2000 bp (revcom)
ACGTACAGATGGCGTCTCCTCCTTTCGCGAGCCCCTTGCCTTGTGACTTCAGCCTAACTT
CTTGACTAGAAGATACAACAAGAAATACTCAAATCGGTTATTGTGCAACTCATCCCTCAG
ACAGTTTGGTAAGAAACACCGAAGACTATTTCCGATATCTCAAAGAATGACAAAAGTATA
CATTATATATGCAAGAGAGGCAAGAAAAGAGTAAAAAAGAGTAAAAAAAACATGTACACC
TAGAGCGAACCAGTGATAATTTGCTTCTCAATGAAGAAAAAGCGATTAAAACTGGATTAG
ATTTCATTAAAGAAAAGCTAGGAACAAAGAAATTGGTCTACTTCCAGCCATTTGCGCTTG
ACATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGA
ATGATGGCTCTTTTAAATTGAGATCTAAAAGAAATATCCTGGAAAAGAGTAGAGAAGAGT
CCAAACTGTAGGAATTCAATCGCTTTTTATACTCTCATCGCGGAAAAGACGCGCTGTGAA
AAATTTTCTCTTTTTCTTAGGGCTCCTATCCAGCTGCCTGCGAACAAAAGCCGTATTTAA
AGCATGATTTTCACTACTATGTATGTTCTTTCTGC
BioPerl-1.007002/t/data/map_hem/HEM2-HEM4.meme.txt000444000766000024     11701113155576321 21210 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM2-HEM4.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YGL040C         1.0000   1000  MIT_Spar_c19_8512        1.0000   1000  
MIT_Smik_c273_7756       1.0000   1000  MIT_Sbay_c77_8808        1.0000   1000  
WashU_Skud_Contig2052.17 1.0000   1000  SGD_Scer_YOR278W         1.0000    635  
MIT_Spar_c261_21317      1.0000    635  MIT_Smik_c492_20940      1.0000    635  
WashU_Skud_Contig1682.4  1.0000    635  WashU_Sbay_Contig635.57  1.0000    635  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM2-HEM4.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=       10    maxsites=       10    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            8175    N=              10
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.324 C 0.176 G 0.176 T 0.324 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =  10   llr = 209   E-value = 6.2e-024
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :aa:5a5:::a:::44:416
pos.-specific     C  a:::5:5a:5:5a:169:::
probability       G  ::::::::55:::5:::694
matrix            T  :::a::::5::5:55:1:::

         bits    2.5 *      *    *       
                 2.3 *      *    *       
                 2.0 *      *    *   * * 
                 1.8 *      *    *   * * 
Information      1.5 **** * * ** *   * * 
content          1.3 **** * * ** *  **** 
(30.1 bits)      1.0 ************** *****
                 0.8 ************** *****
                 0.5 ************** *****
                 0.3 ********************
                 0.0 --------------------

Multilevel           CAATAAACGCACCGTCCGGA
consensus                C C TG T TAA A G
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Sbay_c77_8808            +    187  6.45e-12 TGCCGCAGGC CAATCACCGCACCGCCCGGA GATGCTCGTT
WashU_Skud_Contig2052.17     +    186  6.21e-11 TGCCTCAGGC CAATCACCGCACCGAACAGG GATTGCTCGT
MIT_Spar_c19_8512            +    187  6.21e-11 TGCCTCAGGC CAATCACCGCACCGAACAGG GATTGCTCGT
SGD_Scer_YGL040C             +    186  6.21e-11 TGCCTCAAGC CAATCACCGCACCGAACAGG GATTGCTCGT
WashU_Sbay_Contig635.57      -    400  2.02e-10 AGCCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
WashU_Skud_Contig1682.4      -    393  2.02e-10 AACCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
MIT_Smik_c492_20940          -    398  2.02e-10 AACCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
MIT_Spar_c261_21317          -    392  2.02e-10 AACCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
SGD_Scer_YOR278W             -    389  2.02e-10 AACCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
MIT_Smik_c273_7756           +    185  3.21e-09 TGCCTCAGGC CAATCACCGCACCGAATAAG GATTGCTCGT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Sbay_c77_8808                 6.4e-12  186_[+1]_794
WashU_Skud_Contig2052.17          6.2e-11  185_[+1]_795
MIT_Spar_c19_8512                 6.2e-11  186_[+1]_794
SGD_Scer_YGL040C                  6.2e-11  185_[+1]_795
WashU_Sbay_Contig635.57             2e-10  399_[-1]_216
WashU_Skud_Contig1682.4             2e-10  392_[-1]_223
MIT_Smik_c492_20940                 2e-10  397_[-1]_218
MIT_Spar_c261_21317                 2e-10  391_[-1]_224
SGD_Scer_YOR278W                    2e-10  388_[-1]_227
MIT_Smik_c273_7756                3.2e-09  184_[+1]_796
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=10
MIT_Sbay_c77_8808        (  187) CAATCACCGCACCGCCCGGA  1 
WashU_Skud_Contig2052.17 (  186) CAATCACCGCACCGAACAGG  1 
MIT_Spar_c19_8512        (  187) CAATCACCGCACCGAACAGG  1 
SGD_Scer_YGL040C         (  186) CAATCACCGCACCGAACAGG  1 
WashU_Sbay_Contig635.57  (  400) CAATAAACTGATCTTCCGGA  1 
WashU_Skud_Contig1682.4  (  393) CAATAAACTGATCTTCCGGA  1 
MIT_Smik_c492_20940      (  398) CAATAAACTGATCTTCCGGA  1 
MIT_Spar_c261_21317      (  392) CAATAAACTGATCTTCCGGA  1 
SGD_Scer_YOR278W         (  389) CAATAAACTGATCTTCCGGA  1 
MIT_Smik_c273_7756       (  185) CAATCACCGCACCGAATAAG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7985 bayes= 9.63934 E= 6.2e-024 
  -997    251   -997   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
  -997   -997   -997    162 
    62    151   -997   -997 
   162   -997   -997   -997 
    62    151   -997   -997 
  -997    251   -997   -997 
  -997   -997    151     62 
  -997    151    151   -997 
   162   -997   -997   -997 
  -997    151   -997     62 
  -997    251   -997   -997 
  -997   -997    151     62 
    30    -81   -997     62 
    30    177   -997   -997 
  -997    236   -997   -169 
    30   -997    177   -997 
  -169   -997    236   -997 
    89   -997    119   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 6.2e-024 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.500000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.500000  0.500000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.400000  0.100000  0.000000  0.500000 
 0.400000  0.600000  0.000000  0.000000 
 0.000000  0.900000  0.000000  0.100000 
 0.400000  0.000000  0.600000  0.000000 
 0.100000  0.000000  0.900000  0.000000 
 0.600000  0.000000  0.400000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
CAAT[AC]A[AC]C[GT][CG]A[CT]C[GT][TA][CA]C[GA]G[AG]
--------------------------------------------------------------------------------




Time  6.87 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   15   sites =  10   llr = 166   E-value = 1.6e-014
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  7:51a::5::::::5
pos.-specific     C  :::8::915:aa:a5
probability       G  395::41::a::1::
matrix            T  :1:1:6:45:::9::

         bits    2.5          *** * 
                 2.3          *** * 
                 2.0  *    *  *** * 
                 1.8  *    *  *** * 
Information      1.5  * ** *  *** * 
content          1.3  * ** *  ***** 
(23.9 bits)      1.0 ******* *******
                 0.8 ******* *******
                 0.5 ******* *******
                 0.3 ***************
                 0.0 ---------------

Multilevel           AGACATCACGCCTCA
consensus            G G  G TT     C
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Sbay_Contig635.57      -    373  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
WashU_Skud_Contig1682.4      -    366  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
MIT_Smik_c492_20940          -    371  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
MIT_Spar_c261_21317          -    365  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
SGD_Scer_YOR278W             -    362  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
WashU_Skud_Contig2052.17     +    168  5.67e-09 TAAATTGGGC AGGCAGCTTGCCTCA GGCCAATCAC
MIT_Spar_c19_8512            +    169  7.74e-09 TAAATCAAGC GGGCAGCTTGCCTCA GGCCAATCAC
MIT_Sbay_c77_8808            +    169  4.53e-08 TTTATAAATC AGGCAGCCTGCCGCA GGCCAATCAC
SGD_Scer_YGL040C             +    168  7.07e-08 TAAATCAAGC GGGAAGCTTGCCTCA AGCCAATCAC
MIT_Smik_c273_7756           +    167  6.43e-07 TAAATCAAGA GTGTATGTTGCCTCA GGCCAATCAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           1.3e-09  372_[-2]_248
WashU_Skud_Contig1682.4           1.3e-09  365_[-2]_255
MIT_Smik_c492_20940               1.3e-09  370_[-2]_250
MIT_Spar_c261_21317               1.3e-09  364_[-2]_256
SGD_Scer_YOR278W                  1.3e-09  361_[-2]_259
WashU_Skud_Contig2052.17          5.7e-09  167_[+2]_818
MIT_Spar_c19_8512                 7.7e-09  168_[+2]_817
MIT_Sbay_c77_8808                 4.5e-08  168_[+2]_817
SGD_Scer_YGL040C                  7.1e-08  167_[+2]_818
MIT_Smik_c273_7756                6.4e-07  166_[+2]_819
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=15 seqs=10
WashU_Sbay_Contig635.57  (  373) AGACATCACGCCTCC  1 
WashU_Skud_Contig1682.4  (  366) AGACATCACGCCTCC  1 
MIT_Smik_c492_20940      (  371) AGACATCACGCCTCC  1 
MIT_Spar_c261_21317      (  365) AGACATCACGCCTCC  1 
SGD_Scer_YOR278W         (  362) AGACATCACGCCTCC  1 
WashU_Skud_Contig2052.17 (  168) AGGCAGCTTGCCTCA  1 
MIT_Spar_c19_8512        (  169) GGGCAGCTTGCCTCA  1 
MIT_Sbay_c77_8808        (  169) AGGCAGCCTGCCGCA  1 
SGD_Scer_YGL040C         (  168) GGGAAGCTTGCCTCA  1 
MIT_Smik_c273_7756       (  167) GTGTATGTTGCCTCA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 8035 bayes= 9.64836 E= 1.6e-014 
   111   -997     77   -997 
  -997   -997    236   -169 
    62   -997    151   -997 
  -169    219   -997   -169 
   162   -997   -997   -997 
  -997   -997    119     89 
  -997    236    -81   -997 
    62    -81   -997     30 
  -997    151   -997     62 
  -997   -997    251   -997 
  -997    251   -997   -997 
  -997    251   -997   -997 
  -997   -997    -81    147 
  -997    251   -997   -997 
    62    151   -997   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 1.6e-014 
 0.700000  0.000000  0.300000  0.000000 
 0.000000  0.000000  0.900000  0.100000 
 0.500000  0.000000  0.500000  0.000000 
 0.100000  0.800000  0.000000  0.100000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.400000  0.600000 
 0.000000  0.900000  0.100000  0.000000 
 0.500000  0.100000  0.000000  0.400000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.100000  0.900000 
 0.000000  1.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[AG]G[AG]CA[TG]C[AT][CT]GCCTC[AC]
--------------------------------------------------------------------------------




Time 13.73 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =  10   llr = 189   E-value = 4.3e-016
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :a1:1a:71::7:911596:
pos.-specific     C  1:1:::5:7a:::::6:::7
probability       G  :::a4::1:::3a191514:
matrix            T  9:8:5:522:a::::2:::3

         bits    2.5    *     *  *       
                 2.3    *     *  *       
                 2.0    *     *  * *     
                 1.8    *     *  * *     
Information      1.5  * * *   ** * *     
content          1.3 ** * *   ** ***  * *
(27.3 bits)      1.0 ** * ** ******* ****
                 0.8 **** ** ************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TATGTACACCTAGAGCAAAC
consensus                G TTT  G   TG GT
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1682.4      +    225  1.88e-12 GAAGTAGAGA TATGTACACCTAGAGCGAAC CAATGATAAT
MIT_Smik_c492_20940          +    228  1.88e-12 GAAGTGAAGA TATGTACACCTAGAGCGAAC CAATAATAAT
MIT_Spar_c261_21317          +    223  1.88e-12 ACAAAATGAA TATGTACACCTAGAGCGAAC CAATGATAAT
SGD_Scer_YOR278W             +    219  1.88e-12 GAAGTGAAGA TATGTACACCTAGAGCGAAC CAATGATAAT
WashU_Sbay_Contig635.57      +    231  4.24e-11 GTAAAAAAAA CATGTACACCTAGAGCGAAC CAGTGATAAT
MIT_Spar_c19_8512            +     21  3.25e-09 ATATTCTAAA TATGGATTCCTAGGGCAGGC AATAATATGG
WashU_Skud_Contig2052.17     +     21  7.96e-09 TGTTTTCTGA TATGGATGCCTGGAGAAAAT ATTAATATGT
MIT_Smik_c273_7756           +     21  1.42e-08 GTTTTCTTAA TACGGATATCTAGAGTAAGT CACAATTTAA
SGD_Scer_YGL040C             +     21  2.94e-08 ATTTTCTAGG TATGAATTACTGGAGTAAGC AATAATATGA
MIT_Sbay_c77_8808            +     22  8.75e-08 GTTTTTCTGG TAAGGATATCTGGAAGAAGT AACAATACGT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1682.4           1.9e-12  224_[+3]_391
MIT_Smik_c492_20940               1.9e-12  227_[+3]_388
MIT_Spar_c261_21317               1.9e-12  222_[+3]_393
SGD_Scer_YOR278W                  1.9e-12  218_[+3]_397
WashU_Sbay_Contig635.57           4.2e-11  230_[+3]_385
MIT_Spar_c19_8512                 3.2e-09  20_[+3]_960
WashU_Skud_Contig2052.17            8e-09  20_[+3]_960
MIT_Smik_c273_7756                1.4e-08  20_[+3]_960
SGD_Scer_YGL040C                  2.9e-08  20_[+3]_960
MIT_Sbay_c77_8808                 8.8e-08  21_[+3]_959
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=10
WashU_Skud_Contig1682.4  (  225) TATGTACACCTAGAGCGAAC  1 
MIT_Smik_c492_20940      (  228) TATGTACACCTAGAGCGAAC  1 
MIT_Spar_c261_21317      (  223) TATGTACACCTAGAGCGAAC  1 
SGD_Scer_YOR278W         (  219) TATGTACACCTAGAGCGAAC  1 
WashU_Sbay_Contig635.57  (  231) CATGTACACCTAGAGCGAAC  1 
MIT_Spar_c19_8512        (   21) TATGGATTCCTAGGGCAGGC  1 
WashU_Skud_Contig2052.17 (   21) TATGGATGCCTGGAGAAAAT  1 
MIT_Smik_c273_7756       (   21) TACGGATATCTAGAGTAAGT  1 
SGD_Scer_YGL040C         (   21) TATGAATTACTGGAGTAAGC  1 
MIT_Sbay_c77_8808        (   22) TAAGGATATCTGGAAGAAGT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7985 bayes= 9.63934 E= 4.3e-016 
  -997    -81   -997    147 
   162   -997   -997   -997 
  -169    -81   -997    130 
  -997   -997    251   -997 
  -169   -997    119     62 
   162   -997   -997   -997 
  -997    151   -997     62 
   111   -997    -81    -70 
  -169    199   -997    -70 
  -997    251   -997   -997 
  -997   -997   -997    162 
   111   -997     77   -997 
  -997   -997    251   -997 
   147   -997    -81   -997 
  -169   -997    236   -997 
  -169    177    -81    -70 
    62   -997    151   -997 
   147   -997    -81   -997 
    89   -997    119   -997 
  -997    199   -997    -11 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 4.3e-016 
 0.000000  0.100000  0.000000  0.900000 
 1.000000  0.000000  0.000000  0.000000 
 0.100000  0.100000  0.000000  0.800000 
 0.000000  0.000000  1.000000  0.000000 
 0.100000  0.000000  0.400000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.700000  0.000000  0.100000  0.200000 
 0.100000  0.700000  0.000000  0.200000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.700000  0.000000  0.300000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
 0.100000  0.000000  0.900000  0.000000 
 0.100000  0.600000  0.100000  0.200000 
 0.500000  0.000000  0.500000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
 0.600000  0.000000  0.400000  0.000000 
 0.000000  0.700000  0.000000  0.300000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
TATG[TG]A[CT][AT][CT]CT[AG]GAG[CT][AG]A[AG][CT]
--------------------------------------------------------------------------------




Time 20.40 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =  10   llr = 176   E-value = 2.5e-011
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  ::6:11::72::7::1:::2
pos.-specific     C  a:19::882:68::::29:6
probability       G  ::::1:11:62:1:126192
matrix            T  :a31891112222a972:1:

         bits    2.5 *                   
                 2.3 *                   
                 2.0 *  *             ** 
                 1.8 *  *             ** 
Information      1.5 ** *  **   * *   ** 
content          1.3 ** * ***   * **  ** 
(25.4 bits)      1.0 ** * ***  ** ** ****
                 0.8 ** ********* *******
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CTACTTCCAGCCATTTGCGC
consensus              T     CAGTT  GC  A
sequence                      TT     T  G
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      +    338  1.95e-13 AGAAATTGGT CTACTTCCAGCCATTTGCGC TTGACATAGA
WashU_Skud_Contig1682.4      +    331  1.95e-13 AGAGATTGGT CTACTTCCAGCCATTTGCGC TTTACATAGA
MIT_Smik_c492_20940          +    336  1.95e-13 AGAAATTTGT CTACTTCCAGCCATTTGCGC TTTATATAGA
MIT_Spar_c261_21317          +    330  1.95e-13 AAAAATTGGT CTACTTCCAGCCATTTGCGC TTTATATAGA
SGD_Scer_YOR278W             +    327  1.95e-13 AAAAATTGGT CTACTTCCAGCCATTTGCGC TTTATATAGA
SGD_Scer_YGL040C             +    444  9.32e-08 ACGTGTACGC CTTCTTCCCTTCTTTGCCTC TTGTGCCACT
MIT_Smik_c273_7756           +    243  2.84e-07 TTTTTTTCAT CTTCTACCAATTTTTTTCGG CAGCGCCTTT
WashU_Skud_Contig2052.17     -    956  5.15e-07 TGTAGTTTTC CTTCGTTCAGCCATGACGGA AACTACATAA
MIT_Spar_c19_8512            -    872  8.90e-07 TCATTAACCT CTCCATCTTTGTATTGGCGG TACGACATAT
MIT_Sbay_c77_8808            +    255  1.31e-06 TTGCCTTTTT CTATTTGGCAGCGTTTTCGA AAAATTTTGA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           1.9e-13  337_[+4]_278
WashU_Skud_Contig1682.4           1.9e-13  330_[+4]_285
MIT_Smik_c492_20940               1.9e-13  335_[+4]_280
MIT_Spar_c261_21317               1.9e-13  329_[+4]_286
SGD_Scer_YOR278W                  1.9e-13  326_[+4]_289
SGD_Scer_YGL040C                  9.3e-08  443_[+4]_537
MIT_Smik_c273_7756                2.8e-07  242_[+4]_738
WashU_Skud_Contig2052.17          5.1e-07  955_[-4]_25
MIT_Spar_c19_8512                 8.9e-07  871_[-4]_109
MIT_Sbay_c77_8808                 1.3e-06  254_[+4]_726
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=10
WashU_Sbay_Contig635.57  (  338) CTACTTCCAGCCATTTGCGC  1 
WashU_Skud_Contig1682.4  (  331) CTACTTCCAGCCATTTGCGC  1 
MIT_Smik_c492_20940      (  336) CTACTTCCAGCCATTTGCGC  1 
MIT_Spar_c261_21317      (  330) CTACTTCCAGCCATTTGCGC  1 
SGD_Scer_YOR278W         (  327) CTACTTCCAGCCATTTGCGC  1 
SGD_Scer_YGL040C         (  444) CTTCTTCCCTTCTTTGCCTC  1 
MIT_Smik_c273_7756       (  243) CTTCTACCAATTTTTTTCGG  1 
WashU_Skud_Contig2052.17 (  956) CTTCGTTCAGCCATGACGGA  1 
MIT_Spar_c19_8512        (  872) CTCCATCTTTGTATTGGCGG  1 
MIT_Sbay_c77_8808        (  255) CTATTTGGCAGCGTTTTCGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7985 bayes= 9.63934 E= 2.5e-011 
  -997    251   -997   -997 
  -997   -997   -997    162 
    89    -81   -997    -11 
  -997    236   -997   -169 
  -169   -997    -81    130 
  -169   -997   -997    147 
  -997    219    -81   -169 
  -997    219    -81   -169 
   111     19   -997   -169 
   -70   -997    177    -70 
  -997    177     19    -70 
  -997    219   -997    -70 
   111   -997    -81    -70 
  -997   -997   -997    162 
  -997   -997    -81    147 
  -169   -997     19    111 
  -997     19    177    -70 
  -997    236    -81   -997 
  -997   -997    236   -169 
   -70    177     19   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.5e-011 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.600000  0.100000  0.000000  0.300000 
 0.000000  0.900000  0.000000  0.100000 
 0.100000  0.000000  0.100000  0.800000 
 0.100000  0.000000  0.000000  0.900000 
 0.000000  0.800000  0.100000  0.100000 
 0.000000  0.800000  0.100000  0.100000 
 0.700000  0.200000  0.000000  0.100000 
 0.200000  0.000000  0.600000  0.200000 
 0.000000  0.600000  0.200000  0.200000 
 0.000000  0.800000  0.000000  0.200000 
 0.700000  0.000000  0.100000  0.200000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.100000  0.900000 
 0.100000  0.000000  0.200000  0.700000 
 0.000000  0.200000  0.600000  0.200000 
 0.000000  0.900000  0.100000  0.000000 
 0.000000  0.000000  0.900000  0.100000 
 0.200000  0.600000  0.200000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
CT[AT]CTTCC[AC][GAT][CGT][CT][AT]TT[TG][GCT]CG[CAG]
--------------------------------------------------------------------------------




Time 26.90 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =  10   llr = 171   E-value = 2.2e-009
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  8a327aaa21:71:9a1987
pos.-specific     C  1::::::::8::::1:6:12
probability       G  ::18::::81:269::1111
matrix            T  1:6:3:::::a131::2:::

         bits    2.5                     
                 2.3                     
                 2.0              *      
                 1.8              *      
Information      1.5  * * ******  * *    
content          1.3  * * ******  *** *  
(24.6 bits)      1.0  * * ******  *** ** 
                 0.8 ** *****************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           AATGAAAAGCTAGGAACAAA
consensus              AAT   A  GT   T  C
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c492_20940          +    306  4.19e-12 AGATTTCAAT AATGAAAAGCTAGGAACAAA AGAAATTTGT
SGD_Scer_YOR278W             +    297  4.19e-12 AGATTTCAAT AATGAAAAGCTAGGAACAAA AAAAATTGGT
WashU_Sbay_Contig635.57      +    309  1.29e-11 AGATTTCATT AAAGAAAAGCTAGGAACAAA GAAATTGGTC
MIT_Spar_c261_21317          +    301  4.20e-11 AGATTTCAAT AATGAAAAGCTAGGAACAGA AAAATTGGTC
WashU_Skud_Contig1682.4      +    301  6.30e-11 AGATTTCAAT AATGAAAAGCTAGGAATAAA AGAGATTGGT
MIT_Sbay_c77_8808            +    327  4.84e-08 TTAGGGCACG CAGGTAAAGATATGAACAAA TCATATTGAT
MIT_Spar_c19_8512            +    700  7.12e-08 TTCTTGATTG AAAATAAAGCTGTGAAGAAC TAAATAATAA
WashU_Skud_Contig2052.17     -    224  8.93e-08 TGATGCGGAA AATGAAAAACTTTGAACGCA ACGGGTAAAC
SGD_Scer_YGL040C             +    692  5.38e-07 TGTGCGAATT AAAGTAAAGCTAATCAAAAC TAAACAATAA
MIT_Smik_c273_7756           -    444  7.12e-07 TAACGATAAC TATAAAAAAGTGGGAATAAG ATATACACAT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c492_20940               4.2e-12  305_[+5]_310
SGD_Scer_YOR278W                  4.2e-12  296_[+5]_319
WashU_Sbay_Contig635.57           1.3e-11  308_[+5]_307
MIT_Spar_c261_21317               4.2e-11  300_[+5]_315
WashU_Skud_Contig1682.4           6.3e-11  300_[+5]_315
MIT_Sbay_c77_8808                 4.8e-08  326_[+5]_654
MIT_Spar_c19_8512                 7.1e-08  699_[+5]_281
WashU_Skud_Contig2052.17          8.9e-08  223_[-5]_757
SGD_Scer_YGL040C                  5.4e-07  691_[+5]_289
MIT_Smik_c273_7756                7.1e-07  443_[-5]_537
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=10
MIT_Smik_c492_20940      (  306) AATGAAAAGCTAGGAACAAA  1 
SGD_Scer_YOR278W         (  297) AATGAAAAGCTAGGAACAAA  1 
WashU_Sbay_Contig635.57  (  309) AAAGAAAAGCTAGGAACAAA  1 
MIT_Spar_c261_21317      (  301) AATGAAAAGCTAGGAACAGA  1 
WashU_Skud_Contig1682.4  (  301) AATGAAAAGCTAGGAATAAA  1 
MIT_Sbay_c77_8808        (  327) CAGGTAAAGATATGAACAAA  1 
MIT_Spar_c19_8512        (  700) AAAATAAAGCTGTGAAGAAC  1 
WashU_Skud_Contig2052.17 (  224) AATGAAAAACTTTGAACGCA  1 
SGD_Scer_YGL040C         (  692) AAAGTAAAGCTAATCAAAAC  1 
MIT_Smik_c273_7756       (  444) TATAAAAAAGTGGGAATAAG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7985 bayes= 9.63934 E= 2.2e-009 
   130    -81   -997   -169 
   162   -997   -997   -997 
   -11   -997    -81     89 
   -70   -997    219   -997 
   111   -997   -997    -11 
   162   -997   -997   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
   -70   -997    219   -997 
  -169    219    -81   -997 
  -997   -997   -997    162 
   111   -997     19   -169 
  -169   -997    177    -11 
  -997   -997    236   -169 
   147    -81   -997   -997 
   162   -997   -997   -997 
  -169    177    -81    -70 
   147   -997    -81   -997 
   130    -81    -81   -997 
   111     19    -81   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.2e-009 
 0.800000  0.100000  0.000000  0.100000 
 1.000000  0.000000  0.000000  0.000000 
 0.300000  0.000000  0.100000  0.600000 
 0.200000  0.000000  0.800000  0.000000 
 0.700000  0.000000  0.000000  0.300000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.200000  0.000000  0.800000  0.000000 
 0.100000  0.800000  0.100000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.700000  0.000000  0.200000  0.100000 
 0.100000  0.000000  0.600000  0.300000 
 0.000000  0.000000  0.900000  0.100000 
 0.900000  0.100000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.100000  0.600000  0.100000  0.200000 
 0.900000  0.000000  0.100000  0.000000 
 0.800000  0.100000  0.100000  0.000000 
 0.700000  0.200000  0.100000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
AA[TA][GA][AT]AAA[GA]CT[AG][GT]GAA[CT]AA[AC]
--------------------------------------------------------------------------------




Time 33.38 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YGL040C                 5.35e-17  20_[+3(2.94e-08)]_127_[+2(7.07e-08)]_3_[+1(6.21e-11)]_36_[-5(4.31e-05)]_84_[-4(9.17e-05)]_78_[+4(9.32e-08)]_228_[+5(5.38e-07)]_41_[-2(3.82e-05)]_74_[-3(7.54e-05)]_139
MIT_Spar_c19_8512                1.12e-18  20_[+3(3.25e-09)]_128_[+2(7.74e-09)]_3_[+1(6.21e-11)]_37_[-5(8.15e-05)]_436_[+5(7.12e-08)]_152_[-4(8.90e-07)]_109
MIT_Smik_c273_7756               2.75e-14  20_[+3(1.42e-08)]_126_[+2(6.43e-07)]_3_[+1(3.21e-09)]_38_[+4(2.84e-07)]_181_[-5(7.12e-07)]_537
MIT_Sbay_c77_8808                1.49e-17  21_[+3(8.75e-08)]_127_[+2(4.53e-08)]_3_[+1(6.45e-12)]_48_[+4(1.31e-06)]_52_[+5(4.84e-08)]_183_[+2(7.84e-05)]_348_[+4(1.00e-05)]_88
WashU_Skud_Contig2052.17         1.43e-18  20_[+3(7.96e-09)]_127_[+2(5.67e-09)]_3_[+1(6.21e-11)]_18_[-5(8.93e-08)]_712_[-4(5.15e-07)]_25
SGD_Scer_YOR278W                 3.31e-33  218_[+3(1.88e-12)]_58_[+5(4.19e-12)]_10_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_181_[-5(9.56e-06)]_26
MIT_Spar_c261_21317              2.99e-32  222_[+3(1.88e-12)]_23_[+5(1.02e-05)]_15_[+5(4.20e-11)]_9_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_224
MIT_Smik_c492_20940              3.31e-33  227_[+3(1.88e-12)]_23_[+5(1.02e-05)]_15_[+5(4.19e-12)]_10_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_218
WashU_Skud_Contig1682.4          4.41e-32  224_[+3(1.88e-12)]_56_[+5(6.30e-11)]_10_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_223
WashU_Sbay_Contig635.57          1.91e-31  230_[+3(4.24e-11)]_58_[+5(1.29e-11)]_9_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_216
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM2.ups.fa_000444000766000024      1742113155576321 20273 0ustar00cjfieldsstaff000000000000>SGD_Scer_YGL040C HEM2 "Delta-aminolevulinate dehydratase, a homo-octameric enzyme, catalyzes the conversion of delta-aminolevulinic acid to porphobilinogen, the second step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus"
GGTTTTGTCAATTTTCTAGGTATGAATTACTGGAGTAAGCAATAATATGAGTAAGCAGTA
AAACTTTTTTTTATTTGGCTGATTGGGCAAGAAAATCAAAGACAATAGAGTGGCGCATAG
ATGTTGCTAGCATTTATTAGGTTGCCTTACTCTTATATAAATCAAGCGGGAAGCTTGCCT
CAAGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTATTTTGATTTTTTTTTC
ACCTTTTCCAATTTTTTTTTCGGCAACAATTTTTTGGATGATTTTTATCGTCGATCTTGG
AATGATGATGTATTTCGGCGTCTCTACAAGACCCAATAAAGTAATTCGGTGACACAGGCT
TGTAGCAGATAGAAAACGTTCCGAAAGATGGGTTCCAATTGATGTAACACTTCTTTTTTA
TATATTCATGTGGACGTGTACGCCTTCTTCCCTTCTTTGCCTCTTGTGCCACTGTTAATC
CTCTTAAGCATATTGTTTTTATTTACAGACATTGGCTGACTCACCAGAAACTATAATTGA
CGCTGATTTCTAGTTAATTAAAAATAAAATATATGCAAGAATTAGCACCAGGCAGTCATT
TCTGTAAATTGCTTTGTTTTCTATTTCAAATTTGTTTTTTGTATATGTTTCAATGTTCTC
GTGACAATGCAGGCTTTTTTTTGTGCGAATTAAAGTAAAGCTAATCAAAACTAAACAATA
ATTTATCTTGTTCCCGAAAGAGTGGATCATGAGGAGGAAAGCTAACCGTCCAAGATCCTA
TATAATTTTTGAACTGAAAACCAACTGTTCACCTAGAAGACAGGTATCTGGATATGTAAC
TACACGCTCTATAAATACAGAAATCGTAAGCTAATCAATATAAATGTAAAAGAAAATAGG
AATTGCTGTCGATAGATTTATTTACTTTTGTATTGTCATCTGTGTTCTGTGCCAGTACAC
CGGACTCGTATGAGCTGTATGGTGTCGTTTCAATAGAATC
>MIT_Spar_c19_8512 YGL040C 5' untranslated region, Contig c19 1 - 1802, 2000 bp (revcom)
GGTTTTGTCAATATTCTAAATATGGATTCCTAGGGCAGGCAATAATATGGGGAAGCAGTA
AAACTTTTTGTTTTATGTGGCTGATTGGGCCAAAAAACAAGGACAATAGAATGACACATA
AAGTTTGCTAGCATTTATTAGGTTGCCTTACTCTTTTATAAATCAAGCGGGCAGCTTGCC
TCAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTAGTTTGAATTTTTTTT
TCACCTTTTGAAATTTTTTTTTTTCGGCAACAATTTTGAATGACTTTTATCGTCAATCTT
GGGAGTATACCTGCCTCTTTACAACACCCAACAAAACACTTAAGTAAGACAAGCTTGTGG
CAGGTAGGAAAGGTTTCAAAAAAAAAAAAAAGGTTTTTATCTATGGTCATACTTTTTCTT
CGTATATTTATGTGAACACGTACGTCTTGTTTTGCCTTCTTTGGCTCTTGTGTCACTGAA
TCTTCACATATTGTTTTTATTTACAGATACTACTTGACTCGCCTAAAATTATAATCGGCG
ATGGTTTCTACTACCTTAGTTAAAAAATAAAATGAATCAAAACATTACCATTAATAATTC
AATTTTTCCACATTAGTTTGTTTTCTATTTTATGGCTTTCTTCTTGTATATTTCTCAATA
TACTGCATGGCAATGCAAGCTCTTCTCTTTTCTTGATTGAAAATAAAGCTGTGAAGAACT
AAATAATAATTTATTGATGTCCTCCACAAAATGTACACCTGCGCTAACCTTGCTTAACAG
ATACGGTCAAAACGAACTTGAGCATATGTAAAAATCCATGTATTTTTCTTCTTTTGCCAA
CTAAATCAAACTTTTTATTGTATATGTCGTACCGCCAATACAAAGATGGAGAGGTTAATG
AAAATAGATGTGAAAAAAAAGCAGGAACTATTGTAGATAGATATTTTTAGGGTTCGATTG
CTATTTTTCTGTATTATGATCTGTGTTCTATGCCAGTGTA
>MIT_Smik_c273_7756 YGL040C 5' untranslated region, Contig c273 1 - 1807, 2000 bp (revcom)
GGTTTTACCAGTTTTCTTAATACGGATATCTAGAGTAAGTCACAATTTAAGGAAATTGCA
AAATTTTCTTTTTATATAGCTAAATAGGCCAATAAATCAGGAACAATAGAATGACGCACC
GAGTTTGCTAGCAACCTACACACTTGCTTTTTTTTATAAATCAAGAGTGTATGTTGCCTC
AGGCCAATCACCGCACCGAATAAGGATTGCTCGTTTACCCGTTGTTCGATTTTTTTTTTC
ATCTTCTACCAATTTTTTTCGGCAGCGCCTTTGAATGACTTTGATCATCAATCCTGGAGT
AATATACACTTGTATGTTTGAAACGCCCAGTTACAATATTTATTGGAATAGCTAACTTAT
GAGTAAGTGGACCCAAATTTTCGAGTGATGTTTCCTGTCAACGGTGACACTTATTTTTGG
TTTGCAGATATGTATGTGTATATCTTATTCCCACTTTTTTATAGTTATCGTTATCTATGT
ATCTCAATACCTTGGACATGAATCACCGAGTAGATATTTTTCTTTACAATGCTTAAAACA
AGGCCGCACAGAACTAAACAATAAAGTTACCTTGATCTTTAATAAAATATTCCCCCATTA
ATAAGTACTCTCTTCGATTACGATTTAGCCATATTCATTTTGACCATACATTGCAGATGT
GAGATGGATTTTAAGTGGTGAAAGCGCTCTAAGCTATGCCATATAAGTACGTAAGGAGAG
ACAAAATTAAACATAATTAAGCGCCATGTGAGACTAAATGTGGCCGTCGTTTTGATTATA
TGATTGGGAAAAGCTCCTAAACATAGAGGTAGAATTATAGTTCGGAAATTTCGTCTTGCC
CTGCTCATTTTGTAGAAAACGAGTCATCATCTCCACCCTTTGTAACCGGTGTCCTGCTCA
CATAAATAGTCTCTACTGAGAGATTTGTGAATTTCGAGATAATTTTTGGGATTCCATTGT
TGATAAAGGCAATATTATTAGGTATATAAAATATACTAGA
>MIT_Sbay_c77_8808 YGL040C 5' untranslated region, Contig c77 1 - 1377, 2000 bp (revcom)
ACTTTGTCAGTGTTTTTCTGGTAAGGATATCTGGAAGAAGTAACAATACGTATAAATTAC
AAAATTACCGTTTTATGTCGTGGAATGGGCTATGAACTAACATTAACAATAGAGTGATGC
ATAGACGTCACTAGCCTTTTATTGTGTTGCCTTGCTCTTTTATAAATCAGGCAGCCTGCC
GCAGGCCAATCACCGCACCGCCCGGAGATGCTCGTTTACCGTTGTGCACCAAATTTTTCA
TTTTTTGCCTTTTTCTATTTGGCAGCGTTTTCGAAAAATTTTGATCATTAGTCTTCAATG
ACTGGACTGTCATATTTTAGGGCACGCAGGTAAAGATATGAACAAATCATATTGATGATG
GATGCCAATCCTTCAATGTAAATTCTTTCTAAACATCATGATAAAGAACTTCAGTAAGAG
AGTGATAAAAACTTTACATGTATGGCGGGTGTATTCTGTAATTGTTTTTTAGATCTTTTT
GTTGTTAACGGTGACACCATTCTTACTACAATAATTGCATGTCAAATGTAAATATCTTGC
TTCACATTTCGTTGTTTCTTTACGATAAATTGTTTCGTCGCAAATATATCTTATTTTGCG
TGGTTTATCTACAGACACTGCTTGATTTACGCATAAGTACATCATGTAGTAATTCTTATA
TTGAGTATAAAACCATATGAATAGAAATATTTTTGTTAATCTATCGTTAATTTACATGCT
AGTTTATTTGTCCCTTTAAAATTTCTTTATATATTTGTTGCAATATGTGGACAAGGAAAC
ACGAAATATATTGGGATAAAGTTTAAGTAGAGATACATAGAACTAAACAATAAATTCATA
TTCAATAATACTTCAAAAGGTACTCTCCTGTCTGAACACAGAGACTCACAGACTTTATTT
AGTCGTTATGGCGATGTCAGACATCATGTTTAAGGTAAGCCGAGTGGATTGATATGAAAT
TGTCATATCATGAATAAGCTAATTACCCAAAAACAGTAAA
>WashU_Sklu_Contig1444.1 YGL040C 5' untranslated region, Contig c1444 1328 - 2770(revcom), 2000 bp (revcom)
TGGTTTGACAATAGAAGCTTTGATACTGAACTATGATGAAAGCAGCTTGAAATGTAGCCA
ACAATAGTGGTTTTGGTTGTAACAAATTTTTCACCCAGATATGCGTTTCTTTTAAACCAA
AAAAAAAAAAAAAACCAAAAAAAAAAAAAAAAAGAAAGTTGTGATTAACTTAGAGATGAT
GTAGAAAAGTAATCTACGATTAGCAATTGTAGAGCGTAAGAGGTAAAATACAAGCATGTC
ACACCAATGCGAGGATGAGCATCATTCGCACAGACACTCCCCACCACCAATTCCAACCAG
TTCCAACCAGTCTCTGTACCAGTTCATTGACACTTCAAAGTTACGCTGCCTGAATGTTAC
AAGTAATGGTGCCAATCAGTTTCCTCCATGGTTCATAAACCCTCAGGACCAAAAATACGA
CGTCTCAAAGTACTTAGAGAGTGATGCAGATTGCCAAATGCTGTTGCATATCCCGTTTAC
CGGTGATGTCAGAATATTCTCCCTTATTCTAAGATGCAGTAAGGCGGAGGACGGATGCGG
GTCCCCTAAGAGTATTAAGCTTTACAAAAATTTCAACAAAAACACCGATTTTGAAACTAT
CAGCGATTCCAAGGAAAGCTACCACGTGGAAAGCCCAGAAGATGTTGGAATTGCTAGCGA
TGGGAGCGTGAACACAGTAGAAGACGATTCCACCTTCGTAGAACATCATCTTCCACGCCA
CATCTTCCAAAACTGCAATTCAATAACGCTGTTCTTTGAAAACAACTGGAGCGAGGACGA
AGACGATTTAACCAGATGTTACTACTTAGAATTGCGTGGCGAGTTCACTGCTAAACGTAC
ACCGCACGACGGGATGCCACAGTTAGCCGTCTACGAGGCTGCTCCAAATCCGGCGGATCA
CCAGAAGTTAGAGAATGAACAAGAATCTGCAAGTTTAGGCATGTAGGAAGAAATCTACGT
AGAAAACACAACAAAAAAAAATTAAAATTTATAAACGAGT
>WashU_Scas_Contig575.11 YGL040C 5' untranslated region, Contig c575 17052 - 19051, 2000 bp (revcom)
TGTTGGCGTCCTGTTTAGTCAATGTTAAAAAGGTAAGAGTTTGTAAAGTGTATAAGTCAA
GAAAGGGACTGTGAAACAATATGTTGAATGTAAGTTGTCTTTTATAATCCTAAGTGAAAT
TCCACCAACCAGGAACGAGCGGACATTTAAAGTTAAGGGAATGCGCCGTCGCTTCGTGGA
ATGTTAATGACACGTTTTATTTCATTTATTATAATAAAAAAACAATCAGATTGATTGTTG
CCCCATTATCCAGGTTGTTTAAAGAAGAGTACTGGATATAACTCTGTTGAGCTGATTTTT
CTATTCAAAATGATTAGGTAGCCTCCTTTACATAATTTTTTTTGGCGCAAACACCATGGC
TGAGACATTTGAGCAAATATTGATAATATTTTAAGAAAGAAAACAGACATATTGGTTCAA
CTGCAAAAGGTGCCTAAGAGGAGCAAATACTGCTCAAGAATACTAGTTGCAATTACAAGC
GATCAAAGATTTAATTCAAGCGTTGGAATATTAGCAACCTTTACCTGTATGAACCAACAT
TTTAAAGTTTGATAATTATTTTTAATCAATTTTAGTTGAAAAGTTATATAAAGTTCTCCG
ACAAATACTTGAATGACGTGCCATGTCTAATTTGGTTTAAGGTAGCAATATTTAGTTTTA
TTTTGGTGATATTCTAGAAAGTATTTAAACTGAAAAAACTAATCAAGAAATGAAAATTCA
AATATTCAAGAGAAAAAATAAATATTGTCTTAAATTTCTTATTTTCTCGACCCAAAAACC
GTAACTATACTTACCATTTACTTTCCTTGATCAGAATCAACTATTCCCCATACAAAGTAA
ATTAAATACTCAACTAATAATGGGATGACGGCATGACCGATTTTATGTAATAAAATAGGA
GCTCTAAACAAATTTTTTCACATTAATATGGTTGTTTGGCCGAGCGGTCTAAGGCGCCTG
ATTCAAGATCAAACATTCTTGACTGTGGAACACCACAGGA
>WashU_Skud_Contig2052.17 YGL040C 5' untranslated region, Contig c2052 29967 - 31966, 2000 bp (revcom)
GATTTGTCAGTGTTTTCTGATATGGATGCCTGGAGAAAATATTAATATGTGGAAACCACA
AAACTTCCACTTATATAGCTAATTTAGCCAGAAATCATGAACAATAGGATGACGCATAGA
CGTCACTACTCTTCATATAAGTTGCCTTTCTCTTTTATAAATTGGGCAGGCAGCTTGCCT
CAGGCCAATCACCGCACCGAACAGGGATTGCTCGTTTACCCGTTGCGTTCAAAGTTTTTC
ATTTTCCGCATCATCTACTTTTTTTTTTTTGACGCCGTTTTTGAATGTCTTGGTCATTGA
TCTTGAAATGATTTATGTTCGTGTTTTCACGGCACAAAGGTAGGCAAATCGGTAAATTTT
ACTCGTAATAAATAATCAAGGCCTCTAGAGGATTTAATATCAGGAAATAATAATGTGAGT
TTTTTGCAAATGGCCTTATATTCCTGACATCTTCTTGAATTTGTGTTTTAGCGTCGATGA
AGACTCTTCCTTTTTTCGTACGGTAATCTGGACATCTTGTTTCGTCTTTTCTTTTTTTTT
TGCGATTGCTTGTAATTCCAGATATGCAGCATTTATTTACAGGTGCTGATTGATTTACTA
TAGAGTTTATCAGGTAGTAGTTCTTTTTCATGTCTCAATTGAAGAAAAGGAACCCATAAA
TACATTAGCACTGAACAAACAATAACTGCCGCATTGGTTTGTTTTCTAACTTGAATTTTT
CTTTATACATATGCCACTGTATTAGGATGGGTGAATACCGTTTTCTTACTTTCTTCCTAT
GAAGGCGAAAGAATGGTGAAGGACAACTAAACAATAAATCGTTTTTCACACATCCCCATA
AAGCTTTCTCTGTTTGTCAGTTGTGACTCATCTTTCGTCGATGTTGCTTGGTAGATACAA
TTGAACAAGATTGAGATATCTAAAATGTTCAAAAATTATACTCTCTTATGTAGTTTCCGT
CATGGCTGAACGAAGGAAAACTACATCACCTGAGAATTAC
BioPerl-1.007002/t/data/map_hem/HEM2.ups.fa_.revcom000444000766000024      1311613155576321 21562 0ustar00cjfieldsstaff000000000000>SGD_Scer_YGL040C HEM2 "Delta-aminolevulinate dehydratase, a homo-octameric enzyme, catalyzes the conversion of delta-aminolevulinic acid to porphobilinogen, the second step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus"
GATTCTATTGAAACGACACCATACAGCTCATACGAGTCCGGTGTACTGGCACAGAACACA
GATGACAATACAAAAGTAAATAAATCTATCGACAGCAATTCCTATTTTCTTTTACATTTA
TATTGATTAGCTTACGATTTCTGTATTTATAGAGCGTGTAGTTACATATCCAGATACCTG
TCTTCTAGGTGAACAGTTGGTTTTCAGTTCAAAAATTATATAGGATCTTGGACGGTTAGC
TTTCCTCCTCATGATCCACTCTTTCGGGAACAAGATAAATTATTGTTTAGTTTTGATTAG
CTTTACTTTAATTCGCACAAAAAAAAGCCTGCATTGTCACGAGAACATTGAAACATATAC
AAAAAACAAATTTGAAATAGAAAACAAAGCAATTTACAGAAATGACTGCCTGGTGCTAAT
TCTTGCATATATTTTATTTTTAATTAACTAGAAATCAGCGTCAATTATAGTTTCTGGTGA
GTCAGCCAATGTCTGTAAATAAAAACAATATGCTTAAGAGGATTAACAGTGGCACAAGAG
GCAAAGAAGGGAAGAAGGCGTACACGTCCACATGAATATATAAAAAAGAAGTGTTACATC
AATTGGAACCCATCTTTCGGAACGTTTTCTATCTGCTACAAGCCTGTGTCACCGAATTAC
TTTATTGGGTCTTGTAGAGACGCCGAAATACATCATCATTCCAAGATCGACGATAAAAAT
CATCCAAAAAATTGTTGCCGAAAAAAAAATTGGAAAAGGTGAAAAAAAAATCAAAATACG
GGTAAACGAGCAATCCCTGTTCGGTGCGGTGATTGGCTTGAGGCAAGCTTCCCGCTTGAT
TTATATAAGAGTAAGGCAACCTAATAAATGCTAGCAACATCTATGCGCCACTCTATTGTC
TTTGATTTTCTTGCCCAATCAGCCAAATAAAAAAAAGTTTTACTGCTTACTCATATTATT
GCTTACTCCAGTAATTCATACCTAGAAAATTGACAAAACC
>MIT_Spar_c19_8512 YGL040C 5' untranslated region, Contig c19 1 - 1802, 2000 bp (revcom)
TACACTGGCATAGAACACAGATCATAATACAGAAAAATAGCAATCGAACCCTAAAAATAT
CTATCTACAATAGTTCCTGCTTTTTTTTCACATCTATTTTCATTAACCTCTCCATCTTTG
TATTGGCGGTACGACATATACAATAAAAAGTTTGATTTAGTTGGCAAAAGAAGAAAAATA
CATGGATTTTTACATATGCTCAAGTTCGTTTTGACCGTATCTGTTAAGCAAGGTTAGCGC
AGGTGTACATTTTGTGGAGGACATCAATAAATTATTATTTAGTTCTTCACAGCTTTATTT
TCAATCAAGAAAAGAGAAGAGCTTGCATTGCCATGCAGTATATTGAGAAATATACAAGAA
GAAAGCCATAAAATAGAAAACAAACTAATGTGGAAAAATTGAATTATTAATGGTAATGTT
TTGATTCATTTTATTTTTTAACTAAGGTAGTAGAAACCATCGCCGATTATAATTTTAGGC
GAGTCAAGTAGTATCTGTAAATAAAAACAATATGTGAAGATTCAGTGACACAAGAGCCAA
AGAAGGCAAAACAAGACGTACGTGTTCACATAAATATACGAAGAAAAAGTATGACCATAG
ATAAAAACCTTTTTTTTTTTTTTGAAACCTTTCCTACCTGCCACAAGCTTGTCTTACTTA
AGTGTTTTGTTGGGTGTTGTAAAGAGGCAGGTATACTCCCAAGATTGACGATAAAAGTCA
TTCAAAATTGTTGCCGAAAAAAAAAAATTTCAAAAGGTGAAAAAAAAATTCAAACTACGG
GTAAACGAGCAATCCCTGTTCGGTGCGGTGATTGGCCTGAGGCAAGCTGCCCGCTTGATT
TATAAAAGAGTAAGGCAACCTAATAAATGCTAGCAAACTTTATGTGTCATTCTATTGTCC
TTGTTTTTTGGCCCAATCAGCCACATAAAACAAAAAGTTTTACTGCTTCCCCATATTATT
GCCTGCCCTAGGAATCCATATTTAGAATATTGACAAAACC
>MIT_Smik_c273_7756 YGL040C 5' untranslated region, Contig c273 1 - 1807, 2000 bp (revcom)
TCTAGTATATTTTATATACCTAATAATATTGCCTTTATCAACAATGGAATCCCAAAAATT
ATCTCGAAATTCACAAATCTCTCAGTAGAGACTATTTATGTGAGCAGGACACCGGTTACA
AAGGGTGGAGATGATGACTCGTTTTCTACAAAATGAGCAGGGCAAGACGAAATTTCCGAA
CTATAATTCTACCTCTATGTTTAGGAGCTTTTCCCAATCATATAATCAAAACGACGGCCA
CATTTAGTCTCACATGGCGCTTAATTATGTTTAATTTTGTCTCTCCTTACGTACTTATAT
GGCATAGCTTAGAGCGCTTTCACCACTTAAAATCCATCTCACATCTGCAATGTATGGTCA
AAATGAATATGGCTAAATCGTAATCGAAGAGAGTACTTATTAATGGGGGAATATTTTATT
AAAGATCAAGGTAACTTTATTGTTTAGTTCTGTGCGGCCTTGTTTTAAGCATTGTAAAGA
AAAATATCTACTCGGTGATTCATGTCCAAGGTATTGAGATACATAGATAACGATAACTAT
AAAAAAGTGGGAATAAGATATACACATACATATCTGCAAACCAAAAATAAGTGTCACCGT
TGACAGGAAACATCACTCGAAAATTTGGGTCCACTTACTCATAAGTTAGCTATTCCAATA
AATATTGTAACTGGGCGTTTCAAACATACAAGTGTATATTACTCCAGGATTGATGATCAA
AGTCATTCAAAGGCGCTGCCGAAAAAAATTGGTAGAAGATGAAAAAAAAAATCGAACAAC
GGGTAAACGAGCAATCCTTATTCGGTGCGGTGATTGGCCTGAGGCAACATACACTCTTGA
TTTATAAAAAAAAGCAAGTGTGTAGGTTGCTAGCAAACTCGGTGCGTCATTCTATTGTTC
CTGATTTATTGGCCTATTTAGCTATATAAAAAGAAAATTTTGCAATTTCCTTAAATTGTG
ACTTACTCTAGATATCCGTATTAAGAAAACTGGTAAAACC
>MIT_Sbay_c77_8808 YGL040C 5' untranslated region, Contig c77 1 - 1377, 2000 bp (revcom)
TTTACTGTTTTTGGGTAATTAGCTTATTCATGATATGACAATTTCATATCAATCCACTCG
GCTTACCTTAAACATGATGTCTGACATCGCCATAACGACTAAATAAAGTCTGTGAGTCTC
TGTGTTCAGACAGGAGAGTACCTTTTGAAGTATTATTGAATATGAATTTATTGTTTAGTT
CTATGTATCTCTACTTAAACTTTATCCCAATATATTTCGTGTTTCCTTGTCCACATATTG
CAACAAATATATAAAGAAATTTTAAAGGGACAAATAAACTAGCATGTAAATTAACGATAG
ATTAACAAAAATATTTCTATTCATATGGTTTTATACTCAATATAAGAATTACTACATGAT
GTACTTATGCGTAAATCAAGCAGTGTCTGTAGATAAACCACGCAAAATAAGATATATTTG
CGACGAAACAATTTATCGTAAAGAAACAACGAAATGTGAAGCAAGATATTTACATTTGAC
ATGCAATTATTGTAGTAAGAATGGTGTCACCGTTAACAACAAAAAGATCTAAAAAACAAT
TACAGAATACACCCGCCATACATGTAAAGTTTTTATCACTCTCTTACTGAAGTTCTTTAT
CATGATGTTTAGAAAGAATTTACATTGAAGGATTGGCATCCATCATCAATATGATTTGTT
CATATCTTTACCTGCGTGCCCTAAAATATGACAGTCCAGTCATTGAAGACTAATGATCAA
AATTTTTCGAAAACGCTGCCAAATAGAAAAAGGCAAAAAATGAAAAATTTGGTGCACAAC
GGTAAACGAGCATCTCCGGGCGGTGCGGTGATTGGCCTGCGGCAGGCTGCCTGATTTATA
AAAGAGCAAGGCAACACAATAAAAGGCTAGTGACGTCTATGCATCACTCTATTGTTAATG
TTAGTTCATAGCCCATTCCACGACATAAAACGGTAATTTTGTAATTTATACGTATTGTTA
CTTCTTCCAGATATCCTTACCAGAAAAACACTGACAAAGT
>WashU_Skud_Contig2052.17 YGL040C 5' untranslated region, Contig c2052 29967 - 31966, 2000 bp (revcom)
GTAATTCTCAGGTGATGTAGTTTTCCTTCGTTCAGCCATGACGGAAACTACATAAGAGAG
TATAATTTTTGAACATTTTAGATATCTCAATCTTGTTCAATTGTATCTACCAAGCAACAT
CGACGAAAGATGAGTCACAACTGACAAACAGAGAAAGCTTTATGGGGATGTGTGAAAAAC
GATTTATTGTTTAGTTGTCCTTCACCATTCTTTCGCCTTCATAGGAAGAAAGTAAGAAAA
CGGTATTCACCCATCCTAATACAGTGGCATATGTATAAAGAAAAATTCAAGTTAGAAAAC
AAACCAATGCGGCAGTTATTGTTTGTTCAGTGCTAATGTATTTATGGGTTCCTTTTCTTC
AATTGAGACATGAAAAAGAACTACTACCTGATAAACTCTATAGTAAATCAATCAGCACCT
GTAAATAAATGCTGCATATCTGGAATTACAAGCAATCGCAAAAAAAAAAGAAAAGACGAA
ACAAGATGTCCAGATTACCGTACGAAAAAAGGAAGAGTCTTCATCGACGCTAAAACACAA
ATTCAAGAAGATGTCAGGAATATAAGGCCATTTGCAAAAAACTCACATTATTATTTCCTG
ATATTAAATCCTCTAGAGGCCTTGATTATTTATTACGAGTAAAATTTACCGATTTGCCTA
CCTTTGTGCCGTGAAAACACGAACATAAATCATTTCAAGATCAATGACCAAGACATTCAA
AAACGGCGTCAAAAAAAAAAAAGTAGATGATGCGGAAAATGAAAAACTTTGAACGCAACG
GGTAAACGAGCAATCCCTGTTCGGTGCGGTGATTGGCCTGAGGCAAGCTGCCTGCCCAAT
TTATAAAAGAGAAAGGCAACTTATATGAAGAGTAGTGACGTCTATGCGTCATCCTATTGT
TCATGATTTCTGGCTAAATTAGCTATATAAGTGGAAGTTTTGTGGTTTCCACATATTAAT
ATTTTCTCCAGGCATCCATATCAGAAAACACTGACAAATC
BioPerl-1.007002/t/data/map_hem/HEM3-HEM12.fa000444000766000024      2227613155576321 20105 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDL205C HEM3 "Phorphobilinogen deaminase, catalyzes the conversion of 4-porphobilinogen to hydroxymethylbilane, the third step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; expression is regulated by Hap2p-Hap3p"
AGTACGTGTGTATTTACCAACTACAAATTTATCTAGATTTTCTTCGCTTTTCTTTTTTTC
TATTGTTCTAGATATTAATACGGGATGAGAAGAACAGAATATTCAAAATCTAATACAGCC
CTGTACCATGCAAACACGAGCGTCAATCTGCCAATGACCTTGAATTCAGGCTATGTGTAG
CAATAATACAGATAGTTAGTAGCCTCGTTTATATAAAGCGTTCCTTTACTTTTTCATTTT
CTTTCTTTTTTTATGTTTGATTTTTTTACTTTTTCACTTTAAAAAATTGCTGAAATTTTC
GTAGCCAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCTCCC
CAGGGTCAATTGACAAGGAGAGAAGGAATGTTATATGGGAATTGCTGCGTAAAGATGGTC
AAAAATCCTGGACTGCCGTACGAACGACAATGTAAGGATGACTGCATTAGCCAGAAAGAC
ATCTTTACCCCCGGTGCTGCCAGGGAGCAAAATAATTACGAAAAGTGGACGCAAAGTTAA
CTTAAACTACAAGGGTAGCAGCAGAATGTGTCGGTGGTACCGGTGTGATAATGCCCCATT
TGAGATGCTTGTAATTGTGGCCTAGCAATAAGAACGCAAGGCGTTTTTGTTGAAAGGAGA
ACAAGGTTAGACGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTCACCCTTAT
TTCCACCCTCAAACGATAAAGCTTGCTACTTTGATGAAAAAAATATATAAAAGGGATTGA
AAAGCAGATCAATTATGTAGCAATAGTAGTAATAACTTGTTCAATTGCTTGTCTCAACTT
GCCACAAACTATCATCAACA
>MIT_Spar_c429_3020 YDL205C 5' untranslated region, Contig c429 77420 - 79419(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTATCAACTACAAAATTTATCTAGATTTTCTTGCCTTTTCCTTTTTC
TATTGTTCTAGATACTAATACGGGATGAGAAGAACAGAATATTCAAAATGTAAAACAGCC
CTGTACCATGCAAACACGAGCCTCAATCTGCCAATGACCTTGAATCCAAGCTATGTGTAG
CAATAATACAGATGATTGATTGGCGTCGTTTATATAAAGCGTTCCTTCATTTTTTTCATT
TTCTTTCTTTTTTTATGTTTGATTTTTTACTTTTTCACTTTTGAAAACTGCTGAAATTTT
CGTAGCAAAAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCT
CCCCAGGGTCAATTGACAAGGAGAGAAGGAATGTTACATCCAGGAATTGCGACATAAAGA
TGTCCAAGAAGTCTGAACTGTCATACGAATGGCTATGCAAGGAGGATAGTACTGGTCAAG
AAGACATCTTACCCCCGGTGCTGTCAGGGAGCAAAAAAATGACAAAAGTGGACGCAAAGT
TAACTTGAACTACAAGGGTAGCAACAGAATGTCGGTGGTACCGGATGTGACAAAGCTCAC
TTGAGGTGCTTCTTGTTGCGGCATAGCAATAAGAGCGCAAGGCGTTTTTATGGAAAGGAG
AGCGAGGTTAGAGGGTGACGTTTAGGCGCATAGGCAACCTCCCCTTATTGTTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGTCTACATTGATGAAAAAAATGTATAAAAGGGATT
GAAAAGCCGATCATGTGTGTAGCAATAGTAGTAGTTATACTTGTTCAATTGCTTGCTTGC
ACTTTTCCAAAAACTACCAC
>MIT_Smik_c193_2483 YDL205C 5' untranslated region, Contig c193 6380 - 8379(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTACCAACTATAAAATTTTACCTAGACTATCTGGCCTTTTTCTTTTT
TCTATTGTTCTAGATACTAATACGGGATGAAAAGAACAGAATATTCAAAAAGTAATACAG
CCCTGTACCATTCAAACACGAGCGCCAATTTGCCAATGAACTTGAAATCCAGCTATGCGT
AGCGATAATACAGATGATTGTTTGATGTCGTTTATATTAAGCGTTCCTTCAGTTTTTCTC
ATTTTCTTTCTTTTTCTATGTTTTATTTTTCACTTTTTCACTTTTGAAAATTGCTGAAAT
TTTCGTAACAAAAAAAGAGGCCTTCATTGCTTACTCATCGTTATCTTATTGGTTAAAATC
CCCAGCGACAATGTACAAGGAGAGAAGAAATGATATGTCTGGGAATTGCAGTTTGAAGAT
ATCCAAAGAGTTTTGAAGTGCCATACGAGCAACCACGTGAGAAGTAGAGCCTTAACAGAA
AATTCATCTTACCCCTAGTACTGCCAGGGAGGAACTAAACCTAAGAACTAGTGTTAACTT
GACTTGAACTGCAAGGGTAGCGACGGCGTATGTCGGTGGTACCGGATATGGCAAGAGCCC
ATTTGAGCTGCTTGTTCTTGTGACATACTATTAAGAGCGCAAGGCGTTTATGGAAAGGAG
GACAAGGTCAGAGGATGACGTTTAAGCGCATAGGCAATCTCCCCTTATTATTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGCTGCGCTGTTGAAAAGTATATAAAAGGGATAGAA
AAGCAGAGCAATTATAATTTAGTAGAATAGCTTATTCTATCGTTAACTTGTTGAAAGGAT
CAGATTATTATCAAGATGAA
>MIT_Sbay_c841_3215 YDL205C 5' untranslated region, Contig c841 7323 - 9322(revcom), 2000 bp (revcom)
AGTATGTGTATATTTACCAACTATAGAGTATATCTAGTATTTTTTTTCCTTCTTCTTTTT
CTATTGTTCTAGATGCTAATATGGGATGAGTAGAACAAAATATTCAAAACGCAATACAGC
CCTGTACCATTCAAATACGAACGCCAATCTGCCAATGACCTTGAAATCAAGTTATGTGCC
GCGATAATACAATCTTTTGGCCTATATCGTTTAAATAAGCGTTCCTTTAATTTTTCGGTT
TCTTTCTTTTTTATGTCTAATTTTTCATTTTTTTTCACTTGAAAATTGCTGAAATTTTCG
TAGCTGAAAAAGAGAGGCCTTCTTTGCTTACTCATCGTTATCTTATTGGTCAAGAGCCCA
AGGGACAATAGACAAGGAGAGAACCACCAACTTTGGGAGTTGGATGCAAAGAAGGTCTTT
GATTTTGGGCTGCTATCAGAGCGGGCCATATAAGGAAGCTTGTAGTGGTTAGGAGAGAAC
ACGTCATTACCCCCCTCCCCCTTCTCCGCGCTGCCAGGGACCAGGCAAGGGCTTGCAAGA
GATGAACGTAAGATAGAACTACGAGGGTCGCGGCCAATGTGTCGGTAGTACCGGATGGGG
CAAAGCCCAATTGAGGTGCTTGTTGTTGAGGATGGTCGGCATGGCATGGCATGGGAGGCC
AAAGGCGCTTTGTGGGAAGGAGAACAAACAACATTAGAGGGTGACGTTTTAGCGCATAGG
CAATCTCCCCTTATTGTTCACCCTTATTTCCACCCTCAAACGACAAGGCTTGTTATGTTG
GTTGGAAATATATAAAAGGGATTGAAAAAGATCATATTCCTACATAAATTATGGTATTAG
TTTTTCTTCAATTGCTGGCT
>WashU_Skud_Contig1850.5 YDL205C 5' untranslated region, Contig c1850 6875 - 8874(revcom), 2000 bp (revcom)
GATACGTGTGTATTTGCTAACTATAAAATTTATCTAGTTTTCCTGCTTTTTTTTTTTTCT
ATTGTTCTAGAAACTAATATGGGGATGAGAAGAACAAAATTTTCAAAAAGCAATACAGCC
CTGTACCATTCAAACACGAACGCCAATCTGCAATGACCTTGAAATCAATCTATGTGTCGC
GATAATACAAGTGATTGATTGGTGTCGTTTATATAAAGCGTTCCTTCAATTTTTTCATTT
TCTTTCTTTTTTTATGTTTAATTTTCTACCTTTTTCACTTTTGAAAATTGCTGAAATTTT
CGTAGCAAAAAAAGAGAGGCGTACGTTGCTTACTCATCGTTTTCTTATTGGTCAAAAGCT
CCAGGAACAATGCCCAAGGAGAGAAAGAGTGCTACGTCTAGGAATTGCGATGGAAAGGCG
TCCAAGAGTCCTAAACTACCATGAGAACGGGCCACCCAAGGAGGGATAGCAATTGCTGAA
ACAACATCTTCACCTTCGGAGCTGGCAGGGAGCAAGGGACTCTCCGGAAAGAAAGTGAAC
GCAAAACGGAACTACAAGGATAGCAACGGAATGTGTCGGTGGTAGCGGATGTGGCAAGAT
CCCATTTCAGGAGCTTGTTGTTACGGCACAGCAGCAAGAAGAGCACAAGGCTTTTTCCGT
AAAGGAGAACAAAGTTGGAAGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTC
ACCCTTATTTCCACCCTCAAAGGATAAAGCTTGTTGCATTGATAAAAAATGTATAAAAAG
GATGGGAAACAGATGATAGTTAACAAGGTAGTGGGACGGTCTTTCGCTTATTCAGTTGTG
TGACATTCAAGGGTTACAAT
>SGD_Scer_YDR047W HEM12 "Uroporphyrinogen decarboxylase, catalyzes the fifth step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; activity inhibited by Cu2+, Zn2+, Fe2+, Fe3+ and sulfhydryl-specific reagents"
AGCGTTATAACCTGTTCTTTGCTTTATTTTTTTTTTTTTTGTTCTTCCTTTTCTCGAAGA
GAGCTTACCAAACACAATTCTGAGATAATGCTTGATGAATTGAAGAACCTATCGATCACT
CTATGTTACCTTCGTCTGGAACATCACTAATTCGAGCGGTAAAGATGAAAATGGCAGAAC
ATTTCGCTGGCAAAATTAAAACTCTTGCCTCATTTTTTTTTGCTTTCCTCTCCTGCCGCC
AAAAACCCCGAACCCTGTCCTGTATATACGAGAAACATTGAAAAAGATCGTGTATGATAG
CGCCAAGATGGCGGATAAACTAACACTATTGACAGGTTGAGGCCAAGGATATATTACTTG
CTAACAGAAAGAGATACTGTCACCACAATTGCCCGCGTACGTATACTACAACATGTTCTC
TATATATCACCCACTCTTTCGCAGTGCTACGTACGCCAAAAACGCGCGCATGGAAGTAAA
GAAGTTTTTTCTTTTAAGAGCGAAGCTCCATTAAAAGCCTTGAATATAAACTAGTGCGAA
GTAGTATGATCCGAAGACACCAATTGCTGGTGCAGCATAGGAATATGTGGCGTCCGAAAA
AGAGCCTTTAACAATCCACGGCGAAACAAGGCACCGCTGTGCATTTAAAACATGCCGTTC
CCGTACCAAGTTATATTGTTACGGATGAATCCAAAATAATTTGTTAAAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCATGGCACCTTCTTCGTTTCTTCATCCTGCA
TTAGACTTACTAGTGTGCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGACACATATCGC
TGAGCTGGAAGGACACCTTTTAATGTAGCCGTGCATGCGGCTCCGCGAAAAGAGCTCTGC
TATATTTCTCTACCTGAACTTCGAGCCGCGATCAACGAAAGCTCTCATCCAAGGCTCGTT
TTTCTTGACAGAAGCATGACAGTAAAATATGCGGTCATTT
>MIT_Spar_c130_3923 YDR047W 5' untranslated region, Contig c130 9341 - 11340, 2000 bp (revcom)
AGCGTTATGATGTGTTATTTGCTTTTATTTTCTTCTTTCTTTGTCTCGAAGATAACCTAG
CAAACACAATTCTAAGAAAATTCTCGATGAATTGGTTGTCAGCGCTTCCTATTTACTCTA
TGTCCACTTCGTTTGAAACATCAGTGGTTCGAGCAGTAATGACAAAAAGGGCAGAACATT
TCGTTGGCAAAATTTAAACTCGTGCCTCTCATTTTTTTTACTTTTCTCTCCTGCCACCAA
AACCCCGAACCCTGTCCCGTATATACGAGGAACATTGAAAAAAAATCGTGTATGGTAGCG
CCAAGATAGCGAATAAACTATCAGTATTGGCAGGGTGAAGCTAAGGATATGTTGTTTGCT
AACAAAGGGAAATGCTTTCGTTATAATCGCCCGCGTGCGTCTACTAAAATATGATCTATA
TATACCACCCAGTCTATTGCAGTGTTACGTACATCAAAATGCGCGCATGTAAGTGAACAA
GTTTTTTTTGTTTAAAGAGCGATTTTCCAATAAAGGCTTTGGATATACACTGGTGCAAAA
TATATGGTCAATGACGCCAATTACTGGTGTAGCATGAGAATACGTCGTCCGAAAGAGTTT
TTTTTTACAAACTACGGCAAAGCAAAGCACCACTGGCGCAATTCAAAACATGCCGTCCCC
GTACTAAGTTATGTACGTTATTATGGACGGATCCAAAATTATACTCTAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCGTAGCACCTTCTTCGTGTCCTTTCCTTCTT
CTGCATTAGGCTTACTAGCGTCCTTTCCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGA
CAAATCTCGCTGAGTTGGAAAGACACCTTTTATATAGCCGTACGTGCGGCTCCTCGAGAA
AGGCCCTGCTATATTTCACTAGCTGATCCTCGAGCTGCGATCAACGAAAGCCCCATCCAA
AAGGCTCCTTTTTCTTCAAAGAAGCATGACAGTAAAATAT
>MIT_Sbay_c896_21277 YDR047W 5' untranslated region, Contig c896 2230 - 4229(revcom), 2000 bp (revcom)
AGTGTTAACAGTATCTTTTGCCTTTTTTTATTCTAATAGCTACCCCAGGAATCACTATTT
AGCAAAGATCGTTTGCAAATTGGCCGTCAGTACGTTCTAAGTTCTTTAGAACATCATTGG
CTCGAGCATTAGTGACACGAATAGGAAAGCATTTCGTTGACAAAAATAAAATTGTTTCTT
TATTTTTTCCCTCTTTTCCATGGCGTCAAAAAACCCCGAACCCTGTATAAACGAGGAAGC
TGCATGGTAGCGCCAGAAAAGGCAGATAACCTTTAACAGTGCTGACAGAACAACGTCAAA
CATGTGCGGATAATGCCTTCGCTGACGGCAAGAAATTATATACGCCTCGAAACTGTAGAA
CGTCTTTTGTGCCGCTTGGTAACAAATAAACCTAGCCGGGGCCAGAATTTCACCCGTACA
TACTTACTGTTACATACTGCATGCACGCTACGCATTCTCACCGAACATCGAATCTGCCTG
CAGAAGCGAAGAAAAGCAAGTCTTCGAAGAGCAAGCTTACATCCATCGTGTTGAACACAT
ATGCCCAGCAAAGGGATCGGATGACGCCCAACTAACATTGGAATTTGTGACGCAAGGCTG
AAAGGCACTTCTCTATAGCCCACGGTGAAGCCTTACGCTATTGACAAGACAAAACATGCC
GATCCAAGCCAGGCGAAACGGGCCTAGCACTACGCAGCCAAACACTGGCGTTCCGCCCGT
CCCATCCAGTTTCATTTCTTATTTCGTTCTGCCTTGGGCCTAGCAGCGTGCTTGCCGGAT
GAGTTTTTTCCATTTTCCTACCGGCTCATCTCGCTAAGCTGAAAGGTCAGTTTTATAGCC
GTGTGCGCGGCATCGAGAGACAGGTTCAGCTAATGATATTTGCCTAATTCTCGAGCTGAG
GCCAATGAAGGCAGCTTCCAGGGCTCGTTTCTGCTCGGGAAAAAGCATACCACACATTTG
CACGGCTTTTATGTGCCATAGTGCCACCACTAGCCCCCAG
>WashU_Skud_Contig1362.1 YDR047W 5' untranslated region, Contig c1362 1 - 761, 2000 bp (revcom)
AGTGTTGATGGTATCTTTTGATTTTTTCTAGATTGGTAGCAAGCTCAATTGGCACAGCTC
TAAAAAAAGCCTTGTGAATTGGATAGTACCTTCTTTCGTTTGGAACATTACTGCTTCGAG
CAATAAACATACGAAAGGCAGAACACCTCGTTGACAAAACTGAAACTATTTCTTCAATTT
TTTGGCCTTTTTTCCTGCTGCCAAAAAACCCCGAATCATGTAGAAGCGAGAAGTAAAACA
GAGGAAGTGTATGGTAGCGCCAAGGAAAACGGGCAATACTTAGAAAGAATGACAGAGCTC
AGCCAAGTGTAAGCTAAGTGTTGACAAGGGAAGGTACATTGGGCCCCGAAAAAATTTGCT
AATGCTCGAAGAGCTCTCAATCAATCACCCACATATATGTACTACAGTATATTTATACTT
TCCACGCAGTCTCACGCAGTGCCACCTTCATCACCATGCGTGTAACTAATCGAGCAAGCT
GTTTTACGAAGGGCAGCTTTCCTATAAGCGTTTTGAACATGCATGGCTGCACTGCAATGA
GATCAGGCGACTCCAATTCCATAGCCTAGCACGGGATTAAGTAACGAGAAACTGAAAGAG
ATAATTTTACAAACCCGGACGAAGCAGAGCACTTGCTGGAACAAATCAAACATGCCGTCC
CCTACCAGCTCTCGAAGCGGGCCTAGCATTACTCGATCGAACGTTGCCGTTTAGTCTTAT
TTTCCTTTCCGTGCTGCGCTGCTTTTTTCTTGCATTGGGCT
BioPerl-1.007002/t/data/map_hem/HEM3-HEM12.meme.txt000444000766000024     11466613155576321 21305 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM3-HEM12.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDL205C         1.0000    860  MIT_Spar_c429_3020       1.0000    860  
MIT_Smik_c193_2483       1.0000    860  MIT_Sbay_c841_3215       1.0000    860  
WashU_Skud_Contig1850.5  1.0000    860  SGD_Scer_YDR047W         1.0000   1000  
MIT_Spar_c130_3923       1.0000   1000  MIT_Sbay_c896_21277      1.0000   1000  
WashU_Skud_Contig1362.1  1.0000    761  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM3-HEM12.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            8061    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.295 C 0.205 G 0.205 T 0.295 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 189   E-value = 1.1e-018
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :784a4a4:::::4a::7::
pos.-specific     C  4321:6::aaa4:::9a3::
probability       G  1::::::6::::a::::::7
matrix            T  4::4:::::::6:6:1::a3

         bits    2.5         *** *   *   
                 2.3         *** *   *   
                 2.0         *** *  **   
                 1.8         *** *  **   
Information      1.5     * * *** * *** * 
content          1.3     * * *** * *** **
(30.3 bits)      1.0  ** ********* ******
                 0.8 *** ****************
                 0.5 *** ****************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CAAAACAGCCCTGTACCATG
consensus            TCCT A A   C A   C T
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c429_3020           +    111  1.67e-11 ATTCAAAATG TAAAACAGCCCTGTACCATG CAAACACGAG
SGD_Scer_YDL205C             +    111  1.67e-11 ATTCAAAATC TAATACAGCCCTGTACCATG CAAACACGAG
WashU_Skud_Contig1850.5      +    111  5.77e-11 TTTCAAAAAG CAATACAGCCCTGTACCATT CAAACACGAA
MIT_Sbay_c841_3215           +    112  5.77e-11 ATTCAAAACG CAATACAGCCCTGTACCATT CAAATACGAA
MIT_Smik_c193_2483           +    113  1.63e-10 ATTCAAAAAG TAATACAGCCCTGTACCATT CAAACACGAG
MIT_Sbay_c896_21277          +    206  2.60e-10 TTCCATGGCG TCAAAAAACCCCGAACCCTG TATAAACGAG
MIT_Spar_c130_3923           +    235  4.70e-10 TCTCTCCTGC CACCAAAACCCCGAACCCTG TCCCGTATAT
SGD_Scer_YDR047W             +    238  7.68e-10 CTCTCCTGCC GCCAAAAACCCCGAACCCTG TCCTGTATAT
WashU_Skud_Contig1362.1      +    201  9.83e-10 TTTCCTGCTG CCAAAAAACCCCGAATCATG TAGAAGCGAG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c429_3020                1.7e-11  110_[+1]_730
SGD_Scer_YDL205C                  1.7e-11  110_[+1]_730
WashU_Skud_Contig1850.5           5.8e-11  110_[+1]_730
MIT_Sbay_c841_3215                5.8e-11  111_[+1]_729
MIT_Smik_c193_2483                1.6e-10  112_[+1]_728
MIT_Sbay_c896_21277               2.6e-10  205_[+1]_775
MIT_Spar_c130_3923                4.7e-10  234_[+1]_746
SGD_Scer_YDR047W                  7.7e-10  237_[+1]_743
WashU_Skud_Contig1362.1           9.8e-10  200_[+1]_541
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
MIT_Spar_c429_3020       (  111) TAAAACAGCCCTGTACCATG  1 
SGD_Scer_YDL205C         (  111) TAATACAGCCCTGTACCATG  1 
WashU_Skud_Contig1850.5  (  111) CAATACAGCCCTGTACCATT  1 
MIT_Sbay_c841_3215       (  112) CAATACAGCCCTGTACCATT  1 
MIT_Smik_c193_2483       (  113) TAATACAGCCCTGTACCATT  1 
MIT_Sbay_c896_21277      (  206) TCAAAAAACCCCGAACCCTG  1 
MIT_Spar_c130_3923       (  235) CACCAAAACCCCGAACCCTG  1 
SGD_Scer_YDR047W         (  238) GCCAAAAACCCCGAACCCTG  1 
WashU_Skud_Contig1362.1  (  201) CCAAAAAACCCCGAATCATG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 1.1e-018 
  -982    134    -66     45 
   104     92   -982   -982 
   126     34   -982   -982 
    45    -66   -982     45 
   162   -982   -982   -982 
    45    166   -982   -982 
   162   -982   -982   -982 
    45   -982    166   -982 
  -982    251   -982   -982 
  -982    251   -982   -982 
  -982    251   -982   -982 
  -982    134   -982     78 
  -982   -982    251   -982 
    45   -982   -982     78 
   162   -982   -982   -982 
  -982    234   -982   -154 
  -982    251   -982   -982 
   104     92   -982   -982 
  -982   -982   -982    162 
  -982   -982    192      4 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.1e-018 
 0.000000  0.444444  0.111111  0.444444 
 0.666667  0.333333  0.000000  0.000000 
 0.777778  0.222222  0.000000  0.000000 
 0.444444  0.111111  0.000000  0.444444 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.555556  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.444444  0.000000  0.555556 
 0.000000  0.000000  1.000000  0.000000 
 0.444444  0.000000  0.000000  0.555556 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  1.000000  0.000000  0.000000 
 0.666667  0.333333  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.666667  0.333333 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
[CT][AC][AC][AT]A[CA]A[GA]CCC[TC]G[TA]ACC[AC]T[GT]
--------------------------------------------------------------------------------




Time  6.92 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 187   E-value = 6.5e-018
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  ::::1:11::4::a:3:a::
pos.-specific     C  68441:6:a::7a:::4:46
probability       G  ::::8a:9::61::676:63
matrix            T  4266::3::a:2::4::::1

         bits    2.5      *  *   *       
                 2.3      *  *   *       
                 2.0      * **   *       
                 1.8      * **   *       
Information      1.5  *  ** ***  **  *** 
content          1.3  *  ** ***  ** **** 
(30.0 bits)      1.0 ****** *************
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CCTTGGCGCTGCCAGGGAGC
consensus            TTCC  T   AT  TAC CG
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
SGD_Scer_YDL205C             +    489  3.06e-13 ACATCTTTAC CCCCGGTGCTGCCAGGGAGC AAAATAATTA
MIT_Spar_c429_3020           +    493  9.57e-12 GACATCTTAC CCCCGGTGCTGTCAGGGAGC AAAAAAATGA
MIT_Sbay_c841_3215           +    503  2.31e-11 CCCTCCCCCT TCTCCGCGCTGCCAGGGACC AGGCAAGGGC
MIT_Sbay_c896_21277          -    239  1.64e-10 TATCTGCCTT TTCTGGCGCTACCATGCAGC TTCCTCGTTT
MIT_Spar_c130_3923           -    287  2.77e-10 TTATTCGCTA TCTTGGCGCTACCATACACG ATTTTTTTTC
WashU_Skud_Contig1850.5      +    494  5.55e-10 ACATCTTCAC CTTCGGAGCTGGCAGGGAGC AAGGGACTCT
WashU_Skud_Contig1362.1      -    246  6.00e-10 TGCCCGTTTT CCTTGGCGCTACCATACACT TCCTCTGTTT
SGD_Scer_YDR047W             -    289  1.18e-09 TTATCCGCCA TCTTGGCGCTATCATACACG ATCTTTTTCA
MIT_Smik_c193_2483           +    493  1.25e-09 TTCATCTTAC CCCTAGTACTGCCAGGGAGG AACTAAACCT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDL205C                  3.1e-13  488_[+2]_352
MIT_Spar_c429_3020                9.6e-12  492_[+2]_348
MIT_Sbay_c841_3215                2.3e-11  502_[+2]_338
MIT_Sbay_c896_21277               1.6e-10  238_[-2]_742
MIT_Spar_c130_3923                2.8e-10  286_[-2]_694
WashU_Skud_Contig1850.5           5.6e-10  493_[+2]_347
WashU_Skud_Contig1362.1             6e-10  245_[-2]_496
SGD_Scer_YDR047W                  1.2e-09  288_[-2]_692
MIT_Smik_c193_2483                1.3e-09  492_[+2]_348
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
SGD_Scer_YDL205C         (  489) CCCCGGTGCTGCCAGGGAGC  1 
MIT_Spar_c429_3020       (  493) CCCCGGTGCTGTCAGGGAGC  1 
MIT_Sbay_c841_3215       (  503) TCTCCGCGCTGCCAGGGACC  1 
MIT_Sbay_c896_21277      (  239) TTCTGGCGCTACCATGCAGC  1 
MIT_Spar_c130_3923       (  287) TCTTGGCGCTACCATACACG  1 
WashU_Skud_Contig1850.5  (  494) CTTCGGAGCTGGCAGGGAGC  1 
WashU_Skud_Contig1362.1  (  246) CCTTGGCGCTACCATACACT  1 
SGD_Scer_YDR047W         (  289) TCTTGGCGCTATCATACACG  1 
MIT_Smik_c193_2483       (  493) CCCTAGTACTGCCAGGGAGG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 6.5e-018 
  -982    166   -982     45 
  -982    215   -982    -55 
  -982    134   -982     78 
  -982    134   -982     78 
  -154    -66    215   -982 
  -982   -982    251   -982 
  -154    166   -982      4 
  -154   -982    234   -982 
  -982    251   -982   -982 
  -982   -982   -982    162 
    45   -982    166   -982 
  -982    192    -66    -55 
  -982    251   -982   -982 
   162   -982   -982   -982 
  -982   -982    166     45 
     4   -982    192   -982 
  -982    134    166   -982 
   162   -982   -982   -982 
  -982    134    166   -982 
  -982    166     92   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.5e-018 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.444444  0.000000  0.555556 
 0.000000  0.444444  0.000000  0.555556 
 0.111111  0.111111  0.777778  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.111111  0.555556  0.000000  0.333333 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  0.666667  0.111111  0.222222 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.555556  0.444444 
 0.333333  0.000000  0.666667  0.000000 
 0.000000  0.444444  0.555556  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.444444  0.555556  0.000000 
 0.000000  0.555556  0.333333  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[CT][CT][TC][TC]GG[CT]GCT[GA][CT]CA[GT][GA][GC]A[GC][CG]
--------------------------------------------------------------------------------




Time 13.49 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =   9   llr = 183   E-value = 1.9e-017
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :1::6:1::162::1:a:71
pos.-specific     C  :2::3a:1:22::a29::::
probability       G  a6:a1:9::::87:6::::8
matrix            T  :1a::::9a72:3:11:a31

         bits    2.5 *  * *       *      
                 2.3 *  * *       *      
                 2.0 *  * **      * *    
                 1.8 *  * **      * *    
Information      1.5 * ** ** *  * * ***  
content          1.3 * ** ****  *** *** *
(29.4 bits)      1.0 * ** ****  *** *** *
                 0.8 *********  *********
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GGTGACGTTTAGGCGCATAG
consensus             C  C    CCAT C   T 
sequence                       T         
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1850.5      +    681  3.00e-13 AAAGTTGGAA GGTGACGTTTAGGCGCATAG GCAATCTCCC
MIT_Spar_c429_3020           +    674  3.00e-13 GAGGTTAGAG GGTGACGTTTAGGCGCATAG GCAACCTCCC
SGD_Scer_YDL205C             +    673  3.00e-13 AAGGTTAGAC GGTGACGTTTAGGCGCATAG GCAATCTCCC
MIT_Sbay_c841_3215           +    700  3.16e-11 AACATTAGAG GGTGACGTTTTAGCGCATAG GCAATCTCCC
MIT_Smik_c193_2483           +    674  1.45e-10 AAGGTCAGAG GATGACGTTTAAGCGCATAG GCAATCTCCC
MIT_Spar_c130_3923           +    713  2.43e-10 ACTCTAAAAT GCTGCCGTTCCGTCCCATTG AGTTTTATTT
SGD_Scer_YDR047W             +    713  2.43e-10 GTTAAAAAAT GCTGCCGTTCCGTCCCATTG AGTTTTATTT
WashU_Skud_Contig1362.1      +    703  2.69e-08 TCGATCGAAC GTTGCCGTTTAGTCTTATTT TCCTTTCCGT
MIT_Sbay_c896_21277          -    969  4.38e-08 GGGGGCTAGT GGTGGCACTATGGCACATAA AAGCCGTGCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1850.5             3e-13  680_[+3]_160
MIT_Spar_c429_3020                  3e-13  673_[+3]_167
SGD_Scer_YDL205C                    3e-13  672_[+3]_168
MIT_Sbay_c841_3215                3.2e-11  699_[+3]_141
MIT_Smik_c193_2483                1.5e-10  673_[+3]_167
MIT_Spar_c130_3923                2.4e-10  712_[+3]_268
SGD_Scer_YDR047W                  2.4e-10  712_[+3]_268
WashU_Skud_Contig1362.1           2.7e-08  702_[+3]_39
MIT_Sbay_c896_21277               4.4e-08  968_[-3]_12
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=9
WashU_Skud_Contig1850.5  (  681) GGTGACGTTTAGGCGCATAG  1 
MIT_Spar_c429_3020       (  674) GGTGACGTTTAGGCGCATAG  1 
SGD_Scer_YDL205C         (  673) GGTGACGTTTAGGCGCATAG  1 
MIT_Sbay_c841_3215       (  700) GGTGACGTTTTAGCGCATAG  1 
MIT_Smik_c193_2483       (  674) GATGACGTTTAAGCGCATAG  1 
MIT_Spar_c130_3923       (  713) GCTGCCGTTCCGTCCCATTG  1 
SGD_Scer_YDR047W         (  713) GCTGCCGTTCCGTCCCATTG  1 
WashU_Skud_Contig1362.1  (  703) GTTGCCGTTTAGTCTTATTT  1 
MIT_Sbay_c896_21277      (  969) GGTGGCACTATGGCACATAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 1.9e-017 
  -982   -982    251   -982 
  -154     34    166   -154 
  -982   -982   -982    162 
  -982   -982    251   -982 
    78     92    -66   -982 
  -982    251   -982   -982 
  -154   -982    234   -982 
  -982    -66   -982    145 
  -982   -982   -982    162 
  -154     34   -982    104 
    78     34   -982    -55 
   -55   -982    215   -982 
  -982   -982    192      4 
  -982    251   -982   -982 
  -154     34    166   -154 
  -982    234   -982   -154 
   162   -982   -982   -982 
  -982   -982   -982    162 
   104   -982   -982      4 
  -154   -982    215   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.9e-017 
 0.000000  0.000000  1.000000  0.000000 
 0.111111  0.222222  0.555556  0.111111 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.555556  0.333333  0.111111  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.000000  1.000000 
 0.111111  0.222222  0.000000  0.666667 
 0.555556  0.222222  0.000000  0.222222 
 0.222222  0.000000  0.777778  0.000000 
 0.000000  0.000000  0.666667  0.333333 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.222222  0.555556  0.111111 
 0.000000  0.888889  0.000000  0.111111 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.666667  0.000000  0.000000  0.333333 
 0.111111  0.000000  0.777778  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
G[GC]TG[AC]CGTT[TC][ACT][GA][GT]C[GC]CAT[AT]G
--------------------------------------------------------------------------------




Time 20.03 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   15   sites =   9   llr = 142   E-value = 2.9e-008
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  ::::9:::::8::::
pos.-specific     C  a8:::11:89:899:
probability       G  :::::1:::::11:2
matrix            T  :2aa189a2121:18

         bits    2.5 *              
                 2.3 *              
                 2.0 *        *  ** 
                 1.8 *        *  ** 
Information      1.5 ****   *** *** 
content          1.3 ****  **** *** 
(22.8 bits)      1.0 ***** **** ****
                 0.8 ***************
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           CCTTATTTCCACCCT
consensus             T      T T   G
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Skud_Contig1850.5      +    723  6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAAGGATAA
MIT_Sbay_c841_3215           +    742  6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAACGACAA
MIT_Smik_c193_2483           +    716  6.31e-10 TATTATTCAC CCTTATTTCCACCCT CAAACGATAA
MIT_Spar_c429_3020           +    716  6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAACGATAA
SGD_Scer_YDL205C             +    715  6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAACGATAA
MIT_Spar_c130_3923           -    332  8.79e-08 AACAACATAT CCTTAGCTTCACCCT GCCAATACTG
MIT_Sbay_c896_21277          +    178  6.08e-07 AAAATTGTTT CTTTATTTTTTCCCT CTTTTCCATG
SGD_Scer_YDR047W             -    467  1.01e-06 GAAAAAACTT CTTTACTTCCATGCG CGCGTTTTTG
WashU_Skud_Contig1362.1      +    186  1.07e-06 AATTTTTTGG CCTTTTTTCCTGCTG CCAAAAAACC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1850.5           6.3e-10  722_[+4]_123
MIT_Sbay_c841_3215                6.3e-10  741_[+4]_104
MIT_Smik_c193_2483                6.3e-10  715_[+4]_130
MIT_Spar_c429_3020                6.3e-10  715_[+4]_130
SGD_Scer_YDL205C                  6.3e-10  714_[+4]_131
MIT_Spar_c130_3923                8.8e-08  331_[-4]_654
MIT_Sbay_c896_21277               6.1e-07  177_[+4]_808
SGD_Scer_YDR047W                    1e-06  466_[-4]_519
WashU_Skud_Contig1362.1           1.1e-06  185_[+4]_561
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=15 seqs=9
WashU_Skud_Contig1850.5  (  723) CCTTATTTCCACCCT  1 
MIT_Sbay_c841_3215       (  742) CCTTATTTCCACCCT  1 
MIT_Smik_c193_2483       (  716) CCTTATTTCCACCCT  1 
MIT_Spar_c429_3020       (  716) CCTTATTTCCACCCT  1 
SGD_Scer_YDL205C         (  715) CCTTATTTCCACCCT  1 
MIT_Spar_c130_3923       (  332) CCTTAGCTTCACCCT  1 
MIT_Sbay_c896_21277      (  178) CTTTATTTTTTCCCT  1 
SGD_Scer_YDR047W         (  467) CTTTACTTCCATGCG  1 
WashU_Skud_Contig1362.1  (  186) CCTTTTTTCCTGCTG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 7935 bayes= 9.78245 E= 2.9e-008 
  -982    251   -982   -982 
  -982    215   -982    -55 
  -982   -982   -982    162 
  -982   -982   -982    162 
   145   -982   -982   -154 
  -982    -66    -66    126 
  -982    -66   -982    145 
  -982   -982   -982    162 
  -982    215   -982    -55 
  -982    234   -982   -154 
   126   -982   -982    -55 
  -982    215    -66   -154 
  -982    234    -66   -982 
  -982    234   -982   -154 
  -982   -982     34    126 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 2.9e-008 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.888889  0.000000  0.000000  0.111111 
 0.000000  0.111111  0.111111  0.777778 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.888889  0.000000  0.111111 
 0.777778  0.000000  0.000000  0.222222 
 0.000000  0.777778  0.111111  0.111111 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.000000  0.222222  0.777778 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
C[CT]TTATTT[CT]C[AT]CCC[TG]
--------------------------------------------------------------------------------




Time 26.29 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 161   E-value = 2.9e-008
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  2:6197:7:::::::22:a6
pos.-specific     C  :8211:6:11:9:1:::6:3
probability       G  8228:2:3:6:196:88::1
matrix            T  :::::14:93a:13a::4::

         bits    2.5                     
                 2.3                     
                 2.0            **       
                 1.8  *         **       
Information      1.5 ** *      *** *** * 
content          1.3 ** **   * *** *** * 
(25.9 bits)      1.0 ** ** *** *** ***** 
                 0.8 ** ** **************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GCAGAACATGTCGGTGGCAA
consensus            AGC  GTG T   T AAT C
sequence               G                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
SGD_Scer_YDL205C             +    561  1.62e-11 AAGGGTAGCA GCAGAATGTGTCGGTGGTAC CGGTGTGATA
MIT_Spar_c130_3923           +    171  4.79e-11 GACAAAAAGG GCAGAACATTTCGTTGGCAA AATTTAAACT
SGD_Scer_YDR047W             +    174  1.01e-10 GATGAAAATG GCAGAACATTTCGCTGGCAA AATTAAAACT
WashU_Skud_Contig1850.5      +    566  1.81e-09 AAGGATAGCA ACGGAATGTGTCGGTGGTAG CGGATGTGGC
MIT_Smik_c193_2483           +    563  3.96e-09 AAGGGTAGCG ACGGCGTATGTCGGTGGTAC CGGATATGGC
WashU_Skud_Contig1362.1      +    138  5.96e-09 CATACGAAAG GCAGAACACCTCGTTGACAA AACTGAAACT
MIT_Sbay_c841_3215           +    572  1.26e-08 CGAGGGTCGC GGCCAATGTGTCGGTAGTAC CGGATGGGGC
MIT_Sbay_c896_21277          +    144  3.29e-08 GACACGAATA GGAAAGCATTTCGTTGACAA AAATAAAATT
MIT_Spar_c429_3020           +    786  4.67e-08 GGATTGAAAA GCCGATCATGTGTGTAGCAA TAGTAGTAGT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDL205C                  1.6e-11  560_[+5]_280
MIT_Spar_c130_3923                4.8e-11  170_[+5]_810
SGD_Scer_YDR047W                    1e-10  173_[+5]_807
WashU_Skud_Contig1850.5           1.8e-09  565_[+5]_275
MIT_Smik_c193_2483                  4e-09  562_[+5]_278
WashU_Skud_Contig1362.1             6e-09  137_[+5]_604
MIT_Sbay_c841_3215                1.3e-08  571_[+5]_269
MIT_Sbay_c896_21277               3.3e-08  143_[+5]_837
MIT_Spar_c429_3020                4.7e-08  785_[+5]_55
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
SGD_Scer_YDL205C         (  561) GCAGAATGTGTCGGTGGTAC  1 
MIT_Spar_c130_3923       (  171) GCAGAACATTTCGTTGGCAA  1 
SGD_Scer_YDR047W         (  174) GCAGAACATTTCGCTGGCAA  1 
WashU_Skud_Contig1850.5  (  566) ACGGAATGTGTCGGTGGTAG  1 
MIT_Smik_c193_2483       (  563) ACGGCGTATGTCGGTGGTAC  1 
WashU_Skud_Contig1362.1  (  138) GCAGAACACCTCGTTGACAA  1 
MIT_Sbay_c841_3215       (  572) GGCCAATGTGTCGGTAGTAC  1 
MIT_Sbay_c896_21277      (  144) GGAAAGCATTTCGTTGACAA  1 
MIT_Spar_c429_3020       (  786) GCCGATCATGTGTGTAGCAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 2.9e-008 
   -55   -982    215   -982 
  -982    215     34   -982 
    78     34     34   -982 
  -154    -66    215   -982 
   145    -66   -982   -982 
   104   -982     34   -154 
  -982    166   -982     45 
   104   -982     92   -982 
  -982    -66   -982    145 
  -982    -66    166      4 
  -982   -982   -982    162 
  -982    234    -66   -982 
  -982   -982    234   -154 
  -982    -66    166      4 
  -982   -982   -982    162 
   -55   -982    215   -982 
   -55   -982    215   -982 
  -982    166   -982     45 
   162   -982   -982   -982 
    78     92    -66   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.9e-008 
 0.222222  0.000000  0.777778  0.000000 
 0.000000  0.777778  0.222222  0.000000 
 0.555556  0.222222  0.222222  0.000000 
 0.111111  0.111111  0.777778  0.000000 
 0.888889  0.111111  0.000000  0.000000 
 0.666667  0.000000  0.222222  0.111111 
 0.000000  0.555556  0.000000  0.444444 
 0.666667  0.000000  0.333333  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.111111  0.555556  0.333333 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.000000  0.888889  0.111111 
 0.000000  0.111111  0.555556  0.333333 
 0.000000  0.000000  0.000000  1.000000 
 0.222222  0.000000  0.777778  0.000000 
 0.222222  0.000000  0.777778  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 1.000000  0.000000  0.000000  0.000000 
 0.555556  0.333333  0.111111  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
[GA][CG][ACG]GA[AG][CT][AG]T[GT]TCG[GT]T[GA][GA][CT]A[AC]
--------------------------------------------------------------------------------




Time 32.47 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDL205C                 6.46e-34  110_[+1(1.67e-11)]_358_[+2(3.06e-13)]_52_[+5(1.62e-11)]_92_[+3(3.00e-13)]_22_[+4(6.31e-10)]_54_[+5(2.69e-05)]_57
MIT_Spar_c429_3020               3.43e-29  110_[+1(1.67e-11)]_173_[-4(1.29e-05)]_174_[+2(9.57e-12)]_49_[+5(9.46e-05)]_92_[+3(3.00e-13)]_22_[+4(6.31e-10)]_55_[+5(4.67e-08)]_55
MIT_Smik_c193_2483               1.01e-24  112_[+1(1.63e-10)]_21_[-3(6.96e-05)]_319_[+2(1.25e-09)]_50_[+5(3.96e-09)]_91_[+3(1.45e-10)]_22_[+4(6.31e-10)]_130
MIT_Sbay_c841_3215               6.11e-27  39_[+4(6.88e-05)]_57_[+1(5.77e-11)]_371_[+2(2.31e-11)]_49_[+5(1.26e-08)]_108_[+3(3.16e-11)]_22_[+4(6.31e-10)]_104
WashU_Skud_Contig1850.5          2.40e-28  110_[+1(5.77e-11)]_272_[-3(9.23e-05)]_71_[+2(5.55e-10)]_52_[+5(1.81e-09)]_53_[-1(8.53e-05)]_22_[+3(3.00e-13)]_22_[+4(6.31e-10)]_123
SGD_Scer_YDR047W                 4.48e-22  173_[+5(1.01e-10)]_44_[+1(7.68e-10)]_31_[-2(1.18e-09)]_158_[-4(1.01e-06)]_134_[+2(4.56e-05)]_77_[+3(2.43e-10)]_268
MIT_Spar_c130_3923               3.62e-24  22_[+4(6.45e-05)]_133_[+5(4.79e-11)]_44_[+1(4.70e-10)]_32_[-2(2.77e-10)]_25_[-4(8.79e-08)]_124_[-1(9.89e-05)]_222_[+3(2.43e-10)]_36_[+4(1.03e-05)]_143_[+2(2.11e-05)]_54
MIT_Sbay_c896_21277              4.53e-19  143_[+5(3.29e-08)]_14_[+4(6.08e-07)]_13_[+1(2.60e-10)]_13_[-2(1.64e-10)]_493_[+2(7.81e-05)]_197_[-3(4.38e-08)]_12
WashU_Skud_Contig1362.1          3.15e-19  137_[+5(5.96e-09)]_28_[+4(1.07e-06)]_[+1(9.83e-10)]_25_[-2(6.00e-10)]_252_[-2(2.11e-05)]_165_[+3(2.69e-08)]_39
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM3-HEM13.fa000444000766000024      2272413155576321 20104 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDL205C HEM3 "Phorphobilinogen deaminase, catalyzes the conversion of 4-porphobilinogen to hydroxymethylbilane, the third step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; expression is regulated by Hap2p-Hap3p"
AGTACGTGTGTATTTACCAACTACAAATTTATCTAGATTTTCTTCGCTTTTCTTTTTTTC
TATTGTTCTAGATATTAATACGGGATGAGAAGAACAGAATATTCAAAATCTAATACAGCC
CTGTACCATGCAAACACGAGCGTCAATCTGCCAATGACCTTGAATTCAGGCTATGTGTAG
CAATAATACAGATAGTTAGTAGCCTCGTTTATATAAAGCGTTCCTTTACTTTTTCATTTT
CTTTCTTTTTTTATGTTTGATTTTTTTACTTTTTCACTTTAAAAAATTGCTGAAATTTTC
GTAGCCAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCTCCC
CAGGGTCAATTGACAAGGAGAGAAGGAATGTTATATGGGAATTGCTGCGTAAAGATGGTC
AAAAATCCTGGACTGCCGTACGAACGACAATGTAAGGATGACTGCATTAGCCAGAAAGAC
ATCTTTACCCCCGGTGCTGCCAGGGAGCAAAATAATTACGAAAAGTGGACGCAAAGTTAA
CTTAAACTACAAGGGTAGCAGCAGAATGTGTCGGTGGTACCGGTGTGATAATGCCCCATT
TGAGATGCTTGTAATTGTGGCCTAGCAATAAGAACGCAAGGCGTTTTTGTTGAAAGGAGA
ACAAGGTTAGACGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTCACCCTTAT
TTCCACCCTCAAACGATAAAGCTTGCTACTTTGATGAAAAAAATATATAAAAGGGATTGA
AAAGCAGATCAATTATGTAGCAATAGTAGTAATAACTTGTTCAATTGCTTGTCTCAACTT
GCCACAAACTATCATCAACA
>MIT_Spar_c429_3020 YDL205C 5' untranslated region, Contig c429 77420 - 79419(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTATCAACTACAAAATTTATCTAGATTTTCTTGCCTTTTCCTTTTTC
TATTGTTCTAGATACTAATACGGGATGAGAAGAACAGAATATTCAAAATGTAAAACAGCC
CTGTACCATGCAAACACGAGCCTCAATCTGCCAATGACCTTGAATCCAAGCTATGTGTAG
CAATAATACAGATGATTGATTGGCGTCGTTTATATAAAGCGTTCCTTCATTTTTTTCATT
TTCTTTCTTTTTTTATGTTTGATTTTTTACTTTTTCACTTTTGAAAACTGCTGAAATTTT
CGTAGCAAAAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCT
CCCCAGGGTCAATTGACAAGGAGAGAAGGAATGTTACATCCAGGAATTGCGACATAAAGA
TGTCCAAGAAGTCTGAACTGTCATACGAATGGCTATGCAAGGAGGATAGTACTGGTCAAG
AAGACATCTTACCCCCGGTGCTGTCAGGGAGCAAAAAAATGACAAAAGTGGACGCAAAGT
TAACTTGAACTACAAGGGTAGCAACAGAATGTCGGTGGTACCGGATGTGACAAAGCTCAC
TTGAGGTGCTTCTTGTTGCGGCATAGCAATAAGAGCGCAAGGCGTTTTTATGGAAAGGAG
AGCGAGGTTAGAGGGTGACGTTTAGGCGCATAGGCAACCTCCCCTTATTGTTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGTCTACATTGATGAAAAAAATGTATAAAAGGGATT
GAAAAGCCGATCATGTGTGTAGCAATAGTAGTAGTTATACTTGTTCAATTGCTTGCTTGC
ACTTTTCCAAAAACTACCAC
>MIT_Smik_c193_2483 YDL205C 5' untranslated region, Contig c193 6380 - 8379(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTACCAACTATAAAATTTTACCTAGACTATCTGGCCTTTTTCTTTTT
TCTATTGTTCTAGATACTAATACGGGATGAAAAGAACAGAATATTCAAAAAGTAATACAG
CCCTGTACCATTCAAACACGAGCGCCAATTTGCCAATGAACTTGAAATCCAGCTATGCGT
AGCGATAATACAGATGATTGTTTGATGTCGTTTATATTAAGCGTTCCTTCAGTTTTTCTC
ATTTTCTTTCTTTTTCTATGTTTTATTTTTCACTTTTTCACTTTTGAAAATTGCTGAAAT
TTTCGTAACAAAAAAAGAGGCCTTCATTGCTTACTCATCGTTATCTTATTGGTTAAAATC
CCCAGCGACAATGTACAAGGAGAGAAGAAATGATATGTCTGGGAATTGCAGTTTGAAGAT
ATCCAAAGAGTTTTGAAGTGCCATACGAGCAACCACGTGAGAAGTAGAGCCTTAACAGAA
AATTCATCTTACCCCTAGTACTGCCAGGGAGGAACTAAACCTAAGAACTAGTGTTAACTT
GACTTGAACTGCAAGGGTAGCGACGGCGTATGTCGGTGGTACCGGATATGGCAAGAGCCC
ATTTGAGCTGCTTGTTCTTGTGACATACTATTAAGAGCGCAAGGCGTTTATGGAAAGGAG
GACAAGGTCAGAGGATGACGTTTAAGCGCATAGGCAATCTCCCCTTATTATTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGCTGCGCTGTTGAAAAGTATATAAAAGGGATAGAA
AAGCAGAGCAATTATAATTTAGTAGAATAGCTTATTCTATCGTTAACTTGTTGAAAGGAT
CAGATTATTATCAAGATGAA
>MIT_Sbay_c841_3215 YDL205C 5' untranslated region, Contig c841 7323 - 9322(revcom), 2000 bp (revcom)
AGTATGTGTATATTTACCAACTATAGAGTATATCTAGTATTTTTTTTCCTTCTTCTTTTT
CTATTGTTCTAGATGCTAATATGGGATGAGTAGAACAAAATATTCAAAACGCAATACAGC
CCTGTACCATTCAAATACGAACGCCAATCTGCCAATGACCTTGAAATCAAGTTATGTGCC
GCGATAATACAATCTTTTGGCCTATATCGTTTAAATAAGCGTTCCTTTAATTTTTCGGTT
TCTTTCTTTTTTATGTCTAATTTTTCATTTTTTTTCACTTGAAAATTGCTGAAATTTTCG
TAGCTGAAAAAGAGAGGCCTTCTTTGCTTACTCATCGTTATCTTATTGGTCAAGAGCCCA
AGGGACAATAGACAAGGAGAGAACCACCAACTTTGGGAGTTGGATGCAAAGAAGGTCTTT
GATTTTGGGCTGCTATCAGAGCGGGCCATATAAGGAAGCTTGTAGTGGTTAGGAGAGAAC
ACGTCATTACCCCCCTCCCCCTTCTCCGCGCTGCCAGGGACCAGGCAAGGGCTTGCAAGA
GATGAACGTAAGATAGAACTACGAGGGTCGCGGCCAATGTGTCGGTAGTACCGGATGGGG
CAAAGCCCAATTGAGGTGCTTGTTGTTGAGGATGGTCGGCATGGCATGGCATGGGAGGCC
AAAGGCGCTTTGTGGGAAGGAGAACAAACAACATTAGAGGGTGACGTTTTAGCGCATAGG
CAATCTCCCCTTATTGTTCACCCTTATTTCCACCCTCAAACGACAAGGCTTGTTATGTTG
GTTGGAAATATATAAAAGGGATTGAAAAAGATCATATTCCTACATAAATTATGGTATTAG
TTTTTCTTCAATTGCTGGCT
>WashU_Skud_Contig1850.5 YDL205C 5' untranslated region, Contig c1850 6875 - 8874(revcom), 2000 bp (revcom)
GATACGTGTGTATTTGCTAACTATAAAATTTATCTAGTTTTCCTGCTTTTTTTTTTTTCT
ATTGTTCTAGAAACTAATATGGGGATGAGAAGAACAAAATTTTCAAAAAGCAATACAGCC
CTGTACCATTCAAACACGAACGCCAATCTGCAATGACCTTGAAATCAATCTATGTGTCGC
GATAATACAAGTGATTGATTGGTGTCGTTTATATAAAGCGTTCCTTCAATTTTTTCATTT
TCTTTCTTTTTTTATGTTTAATTTTCTACCTTTTTCACTTTTGAAAATTGCTGAAATTTT
CGTAGCAAAAAAAGAGAGGCGTACGTTGCTTACTCATCGTTTTCTTATTGGTCAAAAGCT
CCAGGAACAATGCCCAAGGAGAGAAAGAGTGCTACGTCTAGGAATTGCGATGGAAAGGCG
TCCAAGAGTCCTAAACTACCATGAGAACGGGCCACCCAAGGAGGGATAGCAATTGCTGAA
ACAACATCTTCACCTTCGGAGCTGGCAGGGAGCAAGGGACTCTCCGGAAAGAAAGTGAAC
GCAAAACGGAACTACAAGGATAGCAACGGAATGTGTCGGTGGTAGCGGATGTGGCAAGAT
CCCATTTCAGGAGCTTGTTGTTACGGCACAGCAGCAAGAAGAGCACAAGGCTTTTTCCGT
AAAGGAGAACAAAGTTGGAAGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTC
ACCCTTATTTCCACCCTCAAAGGATAAAGCTTGTTGCATTGATAAAAAATGTATAAAAAG
GATGGGAAACAGATGATAGTTAACAAGGTAGTGGGACGGTCTTTCGCTTATTCAGTTGTG
TGACATTCAAGGGTTACAAT
>SGD_Scer_YDR044W HEM13 "Coproporphyrinogen III oxidase, an oxygen requiring enzyme that catalyzes the sixth step in the heme biosynthetic pathway; localizes to the mitochondrial inner membrane; transcription is repressed by oxygen and heme (via Rox1p and Hap1p)"
CTTTATGTGTATTTAATTGTGTTCGAAGAGTTCGGTTTGCTATGTTTGATTTGCGAAAAG
AAAGCTTTTGATATGCTCAAAAAAAGAAAACCCGGAGAATAAAAGCTTAACAAAGAAAGA
CAATAGGTGGAAAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTCGAAACGAGAACA
ATGGGCAAAGCAAGCTTTATCTTCGGATCGTCCGTCAGCGCTTTGGTTGCAGTCTTATGC
TTTGTTCAAGCTGGAGCGTTATTGGTGGGAGAACCAGAAAAGGCGAAAGCGTAGCGTTCT
TTGAAATTTGGCTTCTGTTCCTGCGACTCGTTTAAAAGTAGAAGGGCCCGCGGAGCCGCT
GTGAAAGATTTCTTTTACTCTTTCAGCGCAGAAATCTCGCAGGAGCTCAGCAGAAAGTGC
CTATGACGGTAATCCCAGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAATTAA
AATACCGTGCCTATAGTAACTTTTTTTTACGCTGTGAACCGTTCAACACACAGTAAAAAC
TCCGCAGGAAATGGTTTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTTTCCCAACA
GTGAACGAGAGGACAAACTCCAGAGGATTTGCGGGCTTGATGATAAAATGTATTGTTGAA
AAGATCGCGAATGCAACAATTACGGTGGGGAGAAATATCAACAAAAGGGCAAGGCTATGC
CTTCTGGAAAGTGGCAGACTTGCACTTTCCTCGAAAAGAAAAATGACCGCAAGATCCGGT
TGTTCTCAACCTTCTACATTAAGACATACTTCTACGATTTTCGAATGCCGAAGCAACTAT
CGCTGAAATTTGTCATGTCAAAATTGCTACTGGGGGAGAAGAATATATATGGAAGTAATT
ATTATTTACGTTGCTGAAATGGCAGGTTAGACGCATGTTTTGCAAAATAAGTGGTTTTGA
AAAGAATTGATACTAGGAATCGGTGCAATACCTTCTACCT
>MIT_Spar_c130_3912 YDR044W 5' untranslated region, Contig c130 4128 - 6127, 2000 bp (revcom)
CTTTATATGTGTGTTTTGTGGTGTTCGAAATTGGTTTCTTTTGTTCGACTTGCGAGAAGA
AAGCTATCAATATGCTTTCCAAAAAAAGCTGGAGAATAAAAGCTTAACAAAGAAAGACAA
TAGGCGGAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTTCGAAACGAGAACAATGG
ACAAATCAAGCTTTATCTATGGGTTGTCAGCTCTTTGGTTGCAGTCTTGTGCTTGGTTCA
AGCTGGGGCATTATTGGTGGGAGAAGCCAGAAAAGGCGAAAGCGTAGCGTTCTTTGAAAT
TTGGATTCTGTTCCTGCGACTCGTTTAAAAGAAGAAGGGCTGCGGAGCCACTGTGAAAGA
CTTGTTGTGCTCTTTCAACTAAGAAATCTGGCAGGAACTCGATATAAAGTGCCTGTGACA
GTAATCTCAGGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAAATTGAAATACC
GTGCCTATGGTAACTTTTTTTTACGCTGCGAACCGTTCAACACACATTGAAAACCCCGCA
GCAATTGTTCTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTCTCCCAACAGTGTAC
GAGCGGACGAAACTCTAGAGGATTTGCAGGCTCGGTGATAAAATGTATTGTTGAAAAGAA
CGCGAATGCAACGATTGTGGTGGAGAGAAATATCAACAGGGCAAGGCAAGGCTATGCTCT
TTTGGAAGTGGCGGACTTGCACTTTCTTGAAAAGAAAAATGACCGCAAGATCCGGTTGTT
CATAACTTTCTACAATAAGGCATACTTCTACGGTTTTCCAATGCTGAGGCAACTATCGCT
ATAAAATCGCTGCTAGGAGAAGATTATATATGGACGTAAATATTTTTTACGTTACTAAAA
TTCTAGGTTAGAGGCACGTTTTGCAGAACCAGTGGCCTTGGAAAGGTGTTGCTACAAATT
TATGCAATTTCTTCAACTTGCCAGGTGGTCTTGGATGATC
>MIT_Sbay_c896_21290 YDR044W 5' untranslated region, Contig c896 7383 - 9382(revcom), 2000 bp (revcom)
CTTGTTATGTGTGTTTGTGGTGATTGCGGTTTGGTTTTTCTGATTCGTATGACAGAAAGA
AAAAAATTCAGTTTACCTTGTAAGGTGATTAGGAGAAGAAAAAAAGCTTATTGGCAGCGA
ACAATAGGTGAAAAAAAAAAAGAAAATGCGTGTCCTTATATAGCTTTCTCGAAGGGAGAA
CAATGGATAAATCAAAGCTTATCTACGGGTCAACAGCTCTTTGGTTGCTGTCTTGCTCTA
GGTCCAAGCTGGGGCATAATTGGTGGGAGAAGCCAGAAAATGCGAAAGCGTACCGTTCTG
TGAAAAATGGCTTCGGTTCCTGCGACTCGTTTAAAAAGAAAAGGGCCCGCGCAGCCTGTG
TGAAATGTTCGTTTTGCCCTTCCCAGAGAGAAATCTTGCAGGAGCCTCAATACAATGTGC
CTGCGGATGGAATACCAGGGGATAAAGGCGTGAAGGCACTCCCTGAACAATTGAAAATTG
GAAAAAAAAAGTGCCTGTGATGAATCTTATACGTTGGGAAAACTCCAAGACACTTTTAAA
ACTCCGCAGAGATTGTTTGGAGGGACCTTGACCACGAGTTGGGAGTATTGTTTTTTCCTG
GAAGGAACGAGCGGAACTCTTGGGGATTTGCGGGCTCGCTAATAAAAAGTGTCTTGTTGA
AGAAAAGTAGAATGCGACTAAAACGGTGGAGGAAAATATCAACAAGGCAAGGCTATGCCT
TTCGAAGAAAAGCGGACTTGCAATTGCACAACCGTATCGAAGAGAATTGAGAAGGGGGTG
CAAAGTGATCCGGTTGTTCATATTTCTTCACCAATTGATACAATTATCTACGTTTGTTCT
GTTGACCAATCCAACGGGGACTCTGTATGACATAAGTCTTCCTTACATTGCTAAGATCCA
AGATCAGACCCGTAGATGAGTTCTGCACCAAAGAGTTGTTAACCGTCTTGCCTGAATAAT
TTTAAGTTGTCGCGATCCTCTTACAAGGTGTTCTTATTTC
>WashU_Smik_Contig2283.3 YDR044W 5' untranslated region, Contig c2283 2261 - 4260(revcom), 2000 bp (revcom)
CTTTATTGAGGATTTGTGGCGTTTGAGGTTTGGTTTTTTATTCAATTTGAAAGAAGAAAA
CTATCGTTATACTTTCGAAGAAAACACGGGGAATAAAAGCTTAACAGGTGAGACAATAGG
TGGAAAAAAAGGAAAATATGTGTCTTTATATAGCCTTTTCAAAAAGAGAACAATGGTCAA
ATAAAGGTTTATCTACGAGTCGACAGTTCGTTGGCTGCAGTGTTACGCTTGGTTGAAGCT
GGGGCATTATTGGTGGAAGAAGCCAGAAAAGACGAAAGAGTAGCGTAGCGTTCTTTCAAA
TTTTGGTTTCGGGTTCCTGCGACTCGTTTAAAAAAGAAAAGGGCCCGCGGCCCCGCCGTG
AAACACTTCGTCTTGCTCTTCCCACCCAGAAAACTTGTAGGAGCCTCAGTTACAAAGTGC
CTGTAATGGAAATCTTAGGGGGCTACTATTGTAAAGGCAATTTCTGAACAATTGAAAGTG
AAAATATCGTGCCTGTGGTAACTTTCTTATACGCCGTGAAACGTTTAACATACGTTGAAA
ACTCCGCAGGGATTGGTTTGGAAAATTATAGTCACGAATTAGGCGTATTGTCTTTCAAGA
AGGTACGAGCGGATGAACTTCTTGAGGATTTGCGGGTTCGGTGATAAAAAATGTATTGTT
GAAAAGAACGCGAATGCAACAATTACGGTGGAGAAAAATATTAACAAGGGAAGGCAAGGC
TATGTTCTATTGAGAAGCGGCGGACTTGCACTTTCCTCGAAGAAAAAAATGTCTTCAAGA
TCCAATGTTCATATAACTTTCTACAATAAGGTATCCTTCTACGATCTTTCAATGTTAAGA
TTGAAATCAATGTAAAAAGCACCATGTTGAATACTACTGCTAGGAGGAGATCACATATGA
ATGTGATTATTATTTATATTAGTAAATTTTCAGGTTAGGAAGAAGTTATGTGACGCTTTA
GCTTTGGAAATTTGTTGCGGGAAACTGATAACATTCTTTT
BioPerl-1.007002/t/data/map_hem/HEM3-HEM13.meme.txt000444000766000024     11467613155576321 21307 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM3-HEM13.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDL205C         1.0000    860  MIT_Spar_c429_3020       1.0000    860  
MIT_Smik_c193_2483       1.0000    860  MIT_Sbay_c841_3215       1.0000    860  
WashU_Skud_Contig1850.5  1.0000    860  SGD_Scer_YDR044W         1.0000   1000  
MIT_Spar_c130_3912       1.0000   1000  MIT_Sbay_c896_21290      1.0000   1000  
WashU_Smik_Contig2283.3  1.0000   1000  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM3-HEM13.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            8300    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.301 C 0.199 G 0.199 T 0.301 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 197   E-value = 2.8e-022
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :::::9692aa4:4::aa:a
pos.-specific     C  :::::::::::::::3::9:
probability       G  aa:aa1412::666:6::::
matrix            T  ::a:::::6:::4:a1::1:

         bits    2.5 ** **               
                 2.3 ** **               
                 2.0 ** **             * 
                 1.8 ** **             * 
Information      1.5 *****    **   * ****
content          1.3 ****** * **   * ****
(31.6 bits)      1.0 ******** ***********
                 0.8 ******** ***********
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GGTGGAAATAAGGGTGAACA
consensus                  G A  ATA C    
sequence                     G           
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1850.5      -    716  1.22e-12 ATCCTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG
MIT_Sbay_c841_3215           -    735  1.22e-12 GTCGTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG
MIT_Spar_c429_3020           -    709  1.22e-12 ATCGTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG
SGD_Scer_YDL205C             -    708  1.22e-12 ATCGTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG
MIT_Smik_c193_2483           -    709  1.22e-10 ATCGTTTGAG GGTGGAAATAAGGGTGAATA ATAAGGGGAG
MIT_Spar_c130_3912           +    679  1.35e-10 CAACGATTGT GGTGGAGAGAAATATCAACA GGGCAAGGCA
SGD_Scer_YDR044W             +    684  3.84e-10 CAACAATTAC GGTGGGGAGAAATATCAACA AAAGGGCAAG
MIT_Sbay_c896_21290          +    685  5.43e-10 CGACTAAAAC GGTGGAGGAAAATATCAACA AGGCAAGGCT
WashU_Smik_Contig2283.3      +    687  5.84e-10 CAACAATTAC GGTGGAGAAAAATATTAACA AGGGAAGGCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1850.5           1.2e-12  715_[-1]_125
MIT_Sbay_c841_3215                1.2e-12  734_[-1]_106
MIT_Spar_c429_3020                1.2e-12  708_[-1]_132
SGD_Scer_YDL205C                  1.2e-12  707_[-1]_133
MIT_Smik_c193_2483                1.2e-10  708_[-1]_132
MIT_Spar_c130_3912                1.4e-10  678_[+1]_302
SGD_Scer_YDR044W                  3.8e-10  683_[+1]_297
MIT_Sbay_c896_21290               5.4e-10  684_[+1]_296
WashU_Smik_Contig2283.3           5.8e-10  686_[+1]_294
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Skud_Contig1850.5  (  716) GGTGGAAATAAGGGTGAACA  1 
MIT_Sbay_c841_3215       (  735) GGTGGAAATAAGGGTGAACA  1 
MIT_Spar_c429_3020       (  709) GGTGGAAATAAGGGTGAACA  1 
SGD_Scer_YDL205C         (  708) GGTGGAAATAAGGGTGAACA  1 
MIT_Smik_c193_2483       (  709) GGTGGAAATAAGGGTGAATA  1 
MIT_Spar_c130_3912       (  679) GGTGGAGAGAAATATCAACA  1 
SGD_Scer_YDR044W         (  684) GGTGGGGAGAAATATCAACA  1 
MIT_Sbay_c896_21290      (  685) GGTGGAGGAAAATATCAACA  1 
WashU_Smik_Contig2283.3  (  687) GGTGGAGAAAAATATTAACA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 2.8e-022 
  -982   -982    251   -982 
  -982   -982    251   -982 
  -982   -982   -982    162 
  -982   -982    251   -982 
  -982   -982    251   -982 
   145   -982    -66   -982 
    78   -982    134   -982 
   145   -982    -66   -982 
   -55   -982     34     78 
   162   -982   -982   -982 
   162   -982   -982   -982 
    45   -982    166   -982 
  -982   -982    166     45 
    45   -982    166   -982 
  -982   -982   -982    162 
  -982     92    166   -154 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -982    234   -982   -154 
   162   -982   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.8e-022 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.555556  0.000000  0.444444  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.222222  0.000000  0.222222  0.555556 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  0.000000  0.555556  0.444444 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.333333  0.555556  0.111111 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
GGTGGA[AG]A[TAG]AA[GA][GT][GA]T[GC]AACA
--------------------------------------------------------------------------------




Time  7.14 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 199   E-value = 2.7e-023
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  3::1:a:6:::a7::::1:1
pos.-specific     C  ::a:6:4:::a:316:a878
probability       G  7a:94:::6a:::::1:::1
matrix            T  ::::::644::::949:13:

         bits    2.5  **      **     *   
                 2.3  **      **     *   
                 2.0  ***     **     *   
                 1.8  ***     **     *   
Information      1.5  *****   ***    *  *
content          1.3 ******   *** * *****
(31.9 bits)      1.0 ******* ************
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GGCGCATAGGCAATCTCCCC
consensus            A   G CTT   C T   T 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1850.5      +    692  2.30e-13 GTGACGTTTA GGCGCATAGGCAATCTCCCC TTATTGTTCA
SGD_Scer_YDL205C             +    684  2.30e-13 GTGACGTTTA GGCGCATAGGCAATCTCCCC TTATTGTTCA
MIT_Sbay_c841_3215           +    711  3.52e-12 GTGACGTTTT AGCGCATAGGCAATCTCCCC TTATTGTTCA
MIT_Smik_c193_2483           +    685  3.52e-12 ATGACGTTTA AGCGCATAGGCAATCTCCCC TTATTATTCA
MIT_Spar_c429_3020           +    685  4.30e-12 GTGACGTTTA GGCGCATAGGCAACCTCCCC TTATTGTTCA
WashU_Smik_Contig2283.3      +    739  3.24e-11 ATTGAGAAGC GGCGGACTTGCACTTTCCTC GAAGAAAAAA
SGD_Scer_YDR044W             +    733  3.60e-10 TCTGGAAAGT GGCAGACTTGCACTTTCCTC GAAAAGAAAA
MIT_Spar_c130_3912           +    730  1.03e-09 TTTTGGAAGT GGCGGACTTGCACTTTCTTG AAAAGAAAAA
MIT_Sbay_c896_21290          +    731  2.40e-09 TTCGAAGAAA AGCGGACTTGCAATTGCACA ACCGTATCGA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1850.5           2.3e-13  691_[+2]_149
SGD_Scer_YDL205C                  2.3e-13  683_[+2]_157
MIT_Sbay_c841_3215                3.5e-12  710_[+2]_130
MIT_Smik_c193_2483                3.5e-12  684_[+2]_156
MIT_Spar_c429_3020                4.3e-12  684_[+2]_156
WashU_Smik_Contig2283.3           3.2e-11  738_[+2]_242
SGD_Scer_YDR044W                  3.6e-10  732_[+2]_248
MIT_Spar_c130_3912                  1e-09  729_[+2]_251
MIT_Sbay_c896_21290               2.4e-09  730_[+2]_250
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
WashU_Skud_Contig1850.5  (  692) GGCGCATAGGCAATCTCCCC  1 
SGD_Scer_YDL205C         (  684) GGCGCATAGGCAATCTCCCC  1 
MIT_Sbay_c841_3215       (  711) AGCGCATAGGCAATCTCCCC  1 
MIT_Smik_c193_2483       (  685) AGCGCATAGGCAATCTCCCC  1 
MIT_Spar_c429_3020       (  685) GGCGCATAGGCAACCTCCCC  1 
WashU_Smik_Contig2283.3  (  739) GGCGGACTTGCACTTTCCTC  1 
SGD_Scer_YDR044W         (  733) GGCAGACTTGCACTTTCCTC  1 
MIT_Spar_c130_3912       (  730) GGCGGACTTGCACTTTCTTG  1 
MIT_Sbay_c896_21290      (  731) AGCGGACTTGCAATTGCACA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 2.7e-023 
     4   -982    192   -982 
  -982   -982    251   -982 
  -982    251   -982   -982 
  -154   -982    234   -982 
  -982    166    134   -982 
   162   -982   -982   -982 
  -982    134   -982     78 
    78   -982   -982     45 
  -982   -982    166     45 
  -982   -982    251   -982 
  -982    251   -982   -982 
   162   -982   -982   -982 
   104     92   -982   -982 
  -982    -66   -982    145 
  -982    166   -982     45 
  -982   -982    -66    145 
  -982    251   -982   -982 
  -154    215   -982   -154 
  -982    192   -982      4 
  -154    215    -66   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.7e-023 
 0.333333  0.000000  0.666667  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  0.555556  0.444444  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.444444  0.000000  0.555556 
 0.555556  0.000000  0.000000  0.444444 
 0.000000  0.000000  0.555556  0.444444 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.666667  0.333333  0.000000  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.777778  0.000000  0.111111 
 0.000000  0.666667  0.000000  0.333333 
 0.111111  0.777778  0.111111  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[GA]GCG[CG]A[TC][AT][GT]GCA[AC]T[CT]TCC[CT]C
--------------------------------------------------------------------------------




Time 14.04 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   15   sites =   9   llr = 162   E-value = 1.1e-016
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  1:::::6::6:::a:
pos.-specific     C  :79:1::a9:6a::a
probability       G  ::189:::::4:a::
matrix            T  93:2:a4:14:::::

         bits    2.5        *   ** *
                 2.3        *   ** *
                 2.0   * *  **  ** *
                 1.8   * *  **  ** *
Information      1.5   **** ** *****
content          1.3  ***** ** *****
(26.0 bits)      1.0 ****** ** *****
                 0.8 ***************
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           TCCGGTACCACCGAC
consensus             T T  T  TG    
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
MIT_Smik_c193_2483           -    572  1.00e-10 TCTTGCCATA TCCGGTACCACCGAC ATACGCCGTC
MIT_Spar_c429_3020           -    571  1.00e-10 CTTTGTCACA TCCGGTACCACCGAC ATTCTGTTGC
MIT_Sbay_c896_21290          +    312  2.46e-09 GAAAAATGGC TTCGGTTCCTGCGAC TCGTTTAAAA
SGD_Scer_YDL205C             -    570  2.75e-09 GCATTATCAC ACCGGTACCACCGAC ACATTCTGCT
WashU_Skud_Contig1850.5      -    575  3.32e-09 TCTTGCCACA TCCGCTACCACCGAC ACATTCCGTT
MIT_Sbay_c841_3215           -    581  6.14e-09 CTTTGCCCCA TCCGGTACTACCGAC ACATTGGCCG
WashU_Smik_Contig2283.3      +    309  6.34e-09 AATTTTGGTT TCGGGTTCCTGCGAC TCGTTTAAAA
MIT_Spar_c130_3912           +    306  1.39e-08 GAAATTTGGA TTCTGTTCCTGCGAC TCGTTTAAAA
SGD_Scer_YDR044W             +    313  1.39e-08 GAAATTTGGC TTCTGTTCCTGCGAC TCGTTTAAAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c193_2483                  1e-10  571_[-3]_274
MIT_Spar_c429_3020                  1e-10  570_[-3]_275
MIT_Sbay_c896_21290               2.5e-09  311_[+3]_674
SGD_Scer_YDL205C                  2.7e-09  569_[-3]_276
WashU_Skud_Contig1850.5           3.3e-09  574_[-3]_271
MIT_Sbay_c841_3215                6.1e-09  580_[-3]_265
WashU_Smik_Contig2283.3           6.3e-09  308_[+3]_677
MIT_Spar_c130_3912                1.4e-08  305_[+3]_680
SGD_Scer_YDR044W                  1.4e-08  312_[+3]_673
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=15 seqs=9
MIT_Smik_c193_2483       (  572) TCCGGTACCACCGAC  1 
MIT_Spar_c429_3020       (  571) TCCGGTACCACCGAC  1 
MIT_Sbay_c896_21290      (  312) TTCGGTTCCTGCGAC  1 
SGD_Scer_YDL205C         (  570) ACCGGTACCACCGAC  1 
WashU_Skud_Contig1850.5  (  575) TCCGCTACCACCGAC  1 
MIT_Sbay_c841_3215       (  581) TCCGGTACTACCGAC  1 
WashU_Smik_Contig2283.3  (  309) TCGGGTTCCTGCGAC  1 
MIT_Spar_c130_3912       (  306) TTCTGTTCCTGCGAC  1 
SGD_Scer_YDR044W         (  313) TTCTGTTCCTGCGAC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 8174 bayes= 9.82531 E= 1.1e-016 
  -154   -982   -982    145 
  -982    192   -982      4 
  -982    234    -66   -982 
  -982   -982    215    -55 
  -982    -66    234   -982 
  -982   -982   -982    162 
    78   -982   -982     45 
  -982    251   -982   -982 
  -982    234   -982   -154 
    78   -982   -982     45 
  -982    166    134   -982 
  -982    251   -982   -982 
  -982   -982    251   -982 
   162   -982   -982   -982 
  -982    251   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 1.1e-016 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  0.666667  0.000000  0.333333 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.000000  0.777778  0.222222 
 0.000000  0.111111  0.888889  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.555556  0.000000  0.000000  0.444444 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.555556  0.000000  0.000000  0.444444 
 0.000000  0.555556  0.444444  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
T[CT]C[GT]GT[AT]CC[AT][CG]CGAC
--------------------------------------------------------------------------------




Time 20.83 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =   9   llr = 178   E-value = 5.9e-016
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  ::2::19a91:a:99:9a2:
pos.-specific     C  1:214::::2:::::a:::1
probability       G  ::2:481:17a:a11:1:39
matrix            T  9a3911::::::::::::4:

         bits    2.5           * *  *    
                 2.3           * *  *    
                 2.0           * *  *   *
                 1.8           * *  *   *
Information      1.5  *     *  ***  * * *
content          1.3 ** * ************* *
(28.5 bits)      1.0 ** *************** *
                 0.8 ** *************** *
                 0.5 ** *****************
                 0.3 ** *****************
                 0.0 --------------------

Multilevel           TTTTCGAAAGGAGAACAATG
consensus              A G    C        G 
sequence               C               A 
                       G                 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c130_3912           +    160  6.95e-11 TTATATAGCC TTTTCGAAACGAGAACAATG GACAAATCAA
MIT_Sbay_c896_21290          +    166  9.05e-11 TTATATAGCT TTCTCGAAGGGAGAACAATG GATAAATCAA
MIT_Smik_c193_2483           +    648  1.24e-10 CGCAAGGCGT TTATGGAAAGGAGGACAAGG TCAGAGGATG
SGD_Scer_YDL205C             +    647  1.24e-10 CAAGGCGTTT TTGTTGAAAGGAGAACAAGG TTAGACGGTG
SGD_Scer_YDR044W             +    164  4.24e-10 CTTATATAGC CTTTCGAAACGAGAACAATG GGCAAAGCAA
MIT_Spar_c429_3020           +    648  6.04e-10 CAAGGCGTTT TTATGGAAAGGAGAGCGAGG TTAGAGGGTG
MIT_Sbay_c841_3215           +    670  1.69e-09 CAAAGGCGCT TTGTGGGAAGGAGAACAAAC AACATTAGAG
WashU_Skud_Contig1850.5      +    655  2.34e-09 ACAAGGCTTT TTCCGTAAAGGAGAACAAAG TTGGAAGGTG
WashU_Smik_Contig2283.3      +    156  3.18e-09 TTATATAGCC TTTTCAAAAAGAGAACAATG GTCAAATAAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c130_3912                6.9e-11  159_[+4]_821
MIT_Sbay_c896_21290               9.1e-11  165_[+4]_815
MIT_Smik_c193_2483                1.2e-10  647_[+4]_193
SGD_Scer_YDL205C                  1.2e-10  646_[+4]_194
SGD_Scer_YDR044W                  4.2e-10  163_[+4]_817
MIT_Spar_c429_3020                  6e-10  647_[+4]_193
MIT_Sbay_c841_3215                1.7e-09  669_[+4]_171
WashU_Skud_Contig1850.5           2.3e-09  654_[+4]_186
WashU_Smik_Contig2283.3           3.2e-09  155_[+4]_825
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=9
MIT_Spar_c130_3912       (  160) TTTTCGAAACGAGAACAATG  1 
MIT_Sbay_c896_21290      (  166) TTCTCGAAGGGAGAACAATG  1 
MIT_Smik_c193_2483       (  648) TTATGGAAAGGAGGACAAGG  1 
SGD_Scer_YDL205C         (  647) TTGTTGAAAGGAGAACAAGG  1 
SGD_Scer_YDR044W         (  164) CTTTCGAAACGAGAACAATG  1 
MIT_Spar_c429_3020       (  648) TTATGGAAAGGAGAGCGAGG  1 
MIT_Sbay_c841_3215       (  670) TTGTGGGAAGGAGAACAAAC  1 
WashU_Skud_Contig1850.5  (  655) TTCCGTAAAGGAGAACAAAG  1 
WashU_Smik_Contig2283.3  (  156) TTTTCAAAAAGAGAACAATG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 5.9e-016 
  -982    -66   -982    145 
  -982   -982   -982    162 
   -55     34     34      4 
  -982    -66   -982    145 
  -982    134    134   -154 
  -154   -982    215   -154 
   145   -982    -66   -982 
   162   -982   -982   -982 
   145   -982    -66   -982 
  -154     34    192   -982 
  -982   -982    251   -982 
   162   -982   -982   -982 
  -982   -982    251   -982 
   145   -982    -66   -982 
   145   -982    -66   -982 
  -982    251   -982   -982 
   145   -982    -66   -982 
   162   -982   -982   -982 
   -55   -982     92     45 
  -982    -66    234   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.9e-016 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.000000  1.000000 
 0.222222  0.222222  0.222222  0.333333 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.444444  0.444444  0.111111 
 0.111111  0.000000  0.777778  0.111111 
 0.888889  0.000000  0.111111  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.111111  0.222222  0.666667  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.222222  0.000000  0.333333  0.444444 
 0.000000  0.111111  0.888889  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
TT[TACGA]T[CG]GAAA[GC]GAGAACAA[TGA]G
--------------------------------------------------------------------------------




Time 27.50 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 178   E-value = 5.2e-014
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  :::::::::::3:::a::::
pos.-specific     C  84::1122:34:4a::::::
probability       G  :::::::::::1::::::a:
matrix            T  26aa9988a7666:a:aa:a

         bits    2.5              *    * 
                 2.3              *    * 
                 2.0              *    * 
                 1.8              *    * 
Information      1.5 * **    *    *******
content          1.3 * ****  *    *******
(28.6 bits)      1.0 *********** ********
                 0.8 *********** ********
                 0.5 *********** ********
                 0.3 ********************
                 0.0 --------------------

Multilevel           CTTTTTTTTTTTTCTATTGT
consensus            TC    CC CCAC       
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Smik_Contig2283.3      -    113  4.87e-11 CACATATTTT CCTTTTTTTCCACCTATTGT CTCACCTGTT
MIT_Spar_c130_3912           -    117  1.86e-10 CACGGATTTT CCTTTTTTTCCGCCTATTGT CTTTCTTTGT
WashU_Skud_Contig1850.5      +     46  2.33e-10 AGTTTTCCTG CTTTTTTTTTTTTCTATTGT TCTAGAAACT
MIT_Smik_c193_2483           +     49  6.29e-10 ACTATCTGGC CTTTTTCTTTTTTCTATTGT TCTAGATACT
MIT_Spar_c429_3020           +     47  7.60e-10 GATTTTCTTG CCTTTTCCTTTTTCTATTGT TCTAGATACT
SGD_Scer_YDL205C             +     47  1.27e-09 ATTTTCTTCG CTTTTCTTTTTTTCTATTGT TCTAGATATT
MIT_Sbay_c896_21290          -    121  1.43e-09 CGCATTTTCT TTTTTTTTTTCACCTATTGT TCGCTGCCAA
SGD_Scer_YDR044W             -    120  1.50e-09 CGGATTTTCC TTTTTTTTTCCACCTATTGT CTTTCTTTGT
MIT_Sbay_c841_3215           +     48  1.62e-09 TATTTTTTTT CCTTCTTCTTTTTCTATTGT TCTAGATGCT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Smik_Contig2283.3           4.9e-11  112_[-5]_868
MIT_Spar_c130_3912                1.9e-10  116_[-5]_864
WashU_Skud_Contig1850.5           2.3e-10  45_[+5]_795
MIT_Smik_c193_2483                6.3e-10  48_[+5]_792
MIT_Spar_c429_3020                7.6e-10  46_[+5]_794
SGD_Scer_YDL205C                  1.3e-09  46_[+5]_794
MIT_Sbay_c896_21290               1.4e-09  120_[-5]_860
SGD_Scer_YDR044W                  1.5e-09  119_[-5]_861
MIT_Sbay_c841_3215                1.6e-09  47_[+5]_793
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
WashU_Smik_Contig2283.3  (  113) CCTTTTTTTCCACCTATTGT  1 
MIT_Spar_c130_3912       (  117) CCTTTTTTTCCGCCTATTGT  1 
WashU_Skud_Contig1850.5  (   46) CTTTTTTTTTTTTCTATTGT  1 
MIT_Smik_c193_2483       (   49) CTTTTTCTTTTTTCTATTGT  1 
MIT_Spar_c429_3020       (   47) CCTTTTCCTTTTTCTATTGT  1 
SGD_Scer_YDL205C         (   47) CTTTTCTTTTTTTCTATTGT  1 
MIT_Sbay_c896_21290      (  121) TTTTTTTTTTCACCTATTGT  1 
SGD_Scer_YDR044W         (  120) TTTTTTTTTCCACCTATTGT  1 
MIT_Sbay_c841_3215       (   48) CCTTCTTCTTTTTCTATTGT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 5.2e-014 
  -982    215   -982    -55 
  -982    134   -982     78 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -982    -66   -982    145 
  -982    -66   -982    145 
  -982     34   -982    126 
  -982     34   -982    126 
  -982   -982   -982    162 
  -982     92   -982    104 
  -982    134   -982     78 
     4   -982    -66     78 
  -982    134   -982     78 
  -982    251   -982   -982 
  -982   -982   -982    162 
   162   -982   -982   -982 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -982   -982    251   -982 
  -982   -982   -982    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.2e-014 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.444444  0.000000  0.555556 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.222222  0.000000  0.777778 
 0.000000  0.222222  0.000000  0.777778 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.333333  0.000000  0.666667 
 0.000000  0.444444  0.000000  0.555556 
 0.333333  0.000000  0.111111  0.555556 
 0.000000  0.444444  0.000000  0.555556 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
[CT][TC]TTTT[TC][TC]T[TC][TC][TA][TC]CTATTGT
--------------------------------------------------------------------------------




Time 34.04 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDL205C                 3.32e-30  46_[+5(1.27e-09)]_156_[+5(7.84e-05)]_327_[-3(2.75e-09)]_62_[+4(1.24e-10)]_17_[+2(2.30e-13)]_4_[-1(1.22e-12)]_133
MIT_Spar_c429_3020               6.35e-30  46_[+5(7.60e-10)]_170_[+5(7.84e-05)]_251_[+1(3.79e-05)]_43_[-3(1.00e-10)]_62_[+4(6.04e-10)]_17_[+2(4.30e-12)]_4_[-1(1.22e-12)]_132
MIT_Smik_c193_2483               7.78e-29  48_[+5(6.29e-10)]_174_[+5(2.65e-05)]_309_[-3(1.00e-10)]_61_[+4(1.24e-10)]_17_[+2(3.52e-12)]_4_[-1(1.22e-10)]_132
MIT_Sbay_c841_3215               1.43e-27  47_[+5(1.62e-09)]_297_[-5(2.91e-05)]_196_[-3(6.14e-09)]_74_[+4(1.69e-09)]_21_[+2(3.52e-12)]_4_[-1(1.22e-12)]_106
WashU_Skud_Contig1850.5          1.30e-29  45_[+5(2.33e-10)]_131_[-4(6.41e-05)]_19_[+5(7.84e-05)]_319_[-3(3.32e-09)]_1_[-3(6.63e-05)]_49_[+4(2.34e-09)]_17_[+2(2.30e-13)]_4_[-1(1.22e-12)]_125
SGD_Scer_YDR044W                 2.91e-23  119_[-5(1.50e-09)]_24_[+4(4.24e-10)]_18_[+3(7.91e-05)]_42_[+4(4.47e-05)]_34_[+3(1.39e-08)]_271_[+4(2.94e-05)]_65_[+1(3.84e-10)]_29_[+2(3.60e-10)]_248
MIT_Spar_c130_3912               7.46e-25  116_[-5(1.86e-10)]_23_[+4(6.95e-11)]_126_[+3(1.39e-08)]_358_[+1(1.35e-10)]_31_[+2(1.03e-09)]_251
MIT_Sbay_c896_21290              1.06e-23  85_[-5(1.91e-05)]_15_[-5(1.43e-09)]_25_[+4(9.05e-11)]_126_[+3(2.46e-09)]_140_[-5(3.09e-05)]_198_[+1(5.43e-10)]_26_[+2(2.40e-09)]_48_[+5(4.88e-05)]_182
WashU_Smik_Contig2283.3          5.66e-25  86_[+1(4.04e-05)]_6_[-5(4.87e-11)]_23_[+4(3.18e-09)]_133_[+3(6.34e-09)]_144_[-5(8.86e-05)]_199_[+1(5.84e-10)]_32_[+2(3.24e-11)]_27_[-1(3.56e-05)]_195
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM3-HEM14.fa000444000766000024      1530213155576321 20077 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDL205C HEM3 "Phorphobilinogen deaminase, catalyzes the conversion of 4-porphobilinogen to hydroxymethylbilane, the third step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; expression is regulated by Hap2p-Hap3p"
AGTACGTGTGTATTTACCAACTACAAATTTATCTAGATTTTCTTCGCTTTTCTTTTTTTC
TATTGTTCTAGATATTAATACGGGATGAGAAGAACAGAATATTCAAAATCTAATACAGCC
CTGTACCATGCAAACACGAGCGTCAATCTGCCAATGACCTTGAATTCAGGCTATGTGTAG
CAATAATACAGATAGTTAGTAGCCTCGTTTATATAAAGCGTTCCTTTACTTTTTCATTTT
CTTTCTTTTTTTATGTTTGATTTTTTTACTTTTTCACTTTAAAAAATTGCTGAAATTTTC
GTAGCCAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCTCCC
CAGGGTCAATTGACAAGGAGAGAAGGAATGTTATATGGGAATTGCTGCGTAAAGATGGTC
AAAAATCCTGGACTGCCGTACGAACGACAATGTAAGGATGACTGCATTAGCCAGAAAGAC
ATCTTTACCCCCGGTGCTGCCAGGGAGCAAAATAATTACGAAAAGTGGACGCAAAGTTAA
CTTAAACTACAAGGGTAGCAGCAGAATGTGTCGGTGGTACCGGTGTGATAATGCCCCATT
TGAGATGCTTGTAATTGTGGCCTAGCAATAAGAACGCAAGGCGTTTTTGTTGAAAGGAGA
ACAAGGTTAGACGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTCACCCTTAT
TTCCACCCTCAAACGATAAAGCTTGCTACTTTGATGAAAAAAATATATAAAAGGGATTGA
AAAGCAGATCAATTATGTAGCAATAGTAGTAATAACTTGTTCAATTGCTTGTCTCAACTT
GCCACAAACTATCATCAACA
>MIT_Spar_c429_3020 YDL205C 5' untranslated region, Contig c429 77420 - 79419(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTATCAACTACAAAATTTATCTAGATTTTCTTGCCTTTTCCTTTTTC
TATTGTTCTAGATACTAATACGGGATGAGAAGAACAGAATATTCAAAATGTAAAACAGCC
CTGTACCATGCAAACACGAGCCTCAATCTGCCAATGACCTTGAATCCAAGCTATGTGTAG
CAATAATACAGATGATTGATTGGCGTCGTTTATATAAAGCGTTCCTTCATTTTTTTCATT
TTCTTTCTTTTTTTATGTTTGATTTTTTACTTTTTCACTTTTGAAAACTGCTGAAATTTT
CGTAGCAAAAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCT
CCCCAGGGTCAATTGACAAGGAGAGAAGGAATGTTACATCCAGGAATTGCGACATAAAGA
TGTCCAAGAAGTCTGAACTGTCATACGAATGGCTATGCAAGGAGGATAGTACTGGTCAAG
AAGACATCTTACCCCCGGTGCTGTCAGGGAGCAAAAAAATGACAAAAGTGGACGCAAAGT
TAACTTGAACTACAAGGGTAGCAACAGAATGTCGGTGGTACCGGATGTGACAAAGCTCAC
TTGAGGTGCTTCTTGTTGCGGCATAGCAATAAGAGCGCAAGGCGTTTTTATGGAAAGGAG
AGCGAGGTTAGAGGGTGACGTTTAGGCGCATAGGCAACCTCCCCTTATTGTTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGTCTACATTGATGAAAAAAATGTATAAAAGGGATT
GAAAAGCCGATCATGTGTGTAGCAATAGTAGTAGTTATACTTGTTCAATTGCTTGCTTGC
ACTTTTCCAAAAACTACCAC
>MIT_Smik_c193_2483 YDL205C 5' untranslated region, Contig c193 6380 - 8379(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTACCAACTATAAAATTTTACCTAGACTATCTGGCCTTTTTCTTTTT
TCTATTGTTCTAGATACTAATACGGGATGAAAAGAACAGAATATTCAAAAAGTAATACAG
CCCTGTACCATTCAAACACGAGCGCCAATTTGCCAATGAACTTGAAATCCAGCTATGCGT
AGCGATAATACAGATGATTGTTTGATGTCGTTTATATTAAGCGTTCCTTCAGTTTTTCTC
ATTTTCTTTCTTTTTCTATGTTTTATTTTTCACTTTTTCACTTTTGAAAATTGCTGAAAT
TTTCGTAACAAAAAAAGAGGCCTTCATTGCTTACTCATCGTTATCTTATTGGTTAAAATC
CCCAGCGACAATGTACAAGGAGAGAAGAAATGATATGTCTGGGAATTGCAGTTTGAAGAT
ATCCAAAGAGTTTTGAAGTGCCATACGAGCAACCACGTGAGAAGTAGAGCCTTAACAGAA
AATTCATCTTACCCCTAGTACTGCCAGGGAGGAACTAAACCTAAGAACTAGTGTTAACTT
GACTTGAACTGCAAGGGTAGCGACGGCGTATGTCGGTGGTACCGGATATGGCAAGAGCCC
ATTTGAGCTGCTTGTTCTTGTGACATACTATTAAGAGCGCAAGGCGTTTATGGAAAGGAG
GACAAGGTCAGAGGATGACGTTTAAGCGCATAGGCAATCTCCCCTTATTATTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGCTGCGCTGTTGAAAAGTATATAAAAGGGATAGAA
AAGCAGAGCAATTATAATTTAGTAGAATAGCTTATTCTATCGTTAACTTGTTGAAAGGAT
CAGATTATTATCAAGATGAA
>MIT_Sbay_c841_3215 YDL205C 5' untranslated region, Contig c841 7323 - 9322(revcom), 2000 bp (revcom)
AGTATGTGTATATTTACCAACTATAGAGTATATCTAGTATTTTTTTTCCTTCTTCTTTTT
CTATTGTTCTAGATGCTAATATGGGATGAGTAGAACAAAATATTCAAAACGCAATACAGC
CCTGTACCATTCAAATACGAACGCCAATCTGCCAATGACCTTGAAATCAAGTTATGTGCC
GCGATAATACAATCTTTTGGCCTATATCGTTTAAATAAGCGTTCCTTTAATTTTTCGGTT
TCTTTCTTTTTTATGTCTAATTTTTCATTTTTTTTCACTTGAAAATTGCTGAAATTTTCG
TAGCTGAAAAAGAGAGGCCTTCTTTGCTTACTCATCGTTATCTTATTGGTCAAGAGCCCA
AGGGACAATAGACAAGGAGAGAACCACCAACTTTGGGAGTTGGATGCAAAGAAGGTCTTT
GATTTTGGGCTGCTATCAGAGCGGGCCATATAAGGAAGCTTGTAGTGGTTAGGAGAGAAC
ACGTCATTACCCCCCTCCCCCTTCTCCGCGCTGCCAGGGACCAGGCAAGGGCTTGCAAGA
GATGAACGTAAGATAGAACTACGAGGGTCGCGGCCAATGTGTCGGTAGTACCGGATGGGG
CAAAGCCCAATTGAGGTGCTTGTTGTTGAGGATGGTCGGCATGGCATGGCATGGGAGGCC
AAAGGCGCTTTGTGGGAAGGAGAACAAACAACATTAGAGGGTGACGTTTTAGCGCATAGG
CAATCTCCCCTTATTGTTCACCCTTATTTCCACCCTCAAACGACAAGGCTTGTTATGTTG
GTTGGAAATATATAAAAGGGATTGAAAAAGATCATATTCCTACATAAATTATGGTATTAG
TTTTTCTTCAATTGCTGGCT
>WashU_Skud_Contig1850.5 YDL205C 5' untranslated region, Contig c1850 6875 - 8874(revcom), 2000 bp (revcom)
GATACGTGTGTATTTGCTAACTATAAAATTTATCTAGTTTTCCTGCTTTTTTTTTTTTCT
ATTGTTCTAGAAACTAATATGGGGATGAGAAGAACAAAATTTTCAAAAAGCAATACAGCC
CTGTACCATTCAAACACGAACGCCAATCTGCAATGACCTTGAAATCAATCTATGTGTCGC
GATAATACAAGTGATTGATTGGTGTCGTTTATATAAAGCGTTCCTTCAATTTTTTCATTT
TCTTTCTTTTTTTATGTTTAATTTTCTACCTTTTTCACTTTTGAAAATTGCTGAAATTTT
CGTAGCAAAAAAAGAGAGGCGTACGTTGCTTACTCATCGTTTTCTTATTGGTCAAAAGCT
CCAGGAACAATGCCCAAGGAGAGAAAGAGTGCTACGTCTAGGAATTGCGATGGAAAGGCG
TCCAAGAGTCCTAAACTACCATGAGAACGGGCCACCCAAGGAGGGATAGCAATTGCTGAA
ACAACATCTTCACCTTCGGAGCTGGCAGGGAGCAAGGGACTCTCCGGAAAGAAAGTGAAC
GCAAAACGGAACTACAAGGATAGCAACGGAATGTGTCGGTGGTAGCGGATGTGGCAAGAT
CCCATTTCAGGAGCTTGTTGTTACGGCACAGCAGCAAGAAGAGCACAAGGCTTTTTCCGT
AAAGGAGAACAAAGTTGGAAGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTC
ACCCTTATTTCCACCCTCAAAGGATAAAGCTTGTTGCATTGATAAAAAATGTATAAAAAG
GATGGGAAACAGATGATAGTTAACAAGGTAGTGGGACGGTCTTTCGCTTATTCAGTTGTG
TGACATTCAAGGGTTACAAT
>SGD_Scer_YER014W HEM14 "Protoporphyrinogen oxidase, a mitochondrial enzyme that catalyzes the seventh step in the heme biosynthetic pathway, converting protoporphyrinogen IX to protoporphyrin IX"
TATACAAGCTCTTTTTGGCGTTCTCAATTGCACTTTACTCGATATGTTTGAATTGGTGTT
CTTCGCGAATATCTCTATTGTTCTCTCTATTATACTATTTCTTTTTTTGAATACTCCGCG
ACTCCGAAGCAACAAAGTGTCGAAGGCAAGTTCAAAGGCGTTTTGTAACTAAACGAGCAA
TGGCAGCTTTCAATTAAAGAAAGGTTAGCGTTACTCTGTGATTTTTTTCATGTAAAAATT
CTCAAGAGAGATAAAGTTGTTAAAAAATTAAATATAGGTCTATAAAACTCGATAATTATA
ATGCATAAAAAGCTAACAATGT
>MIT_Spar_c425_6072 YER014W 5' untranslated region, Contig c425 34016 - 36015, 2000 bp (revcom)
TATTCGAGCCCTTTCCCGCGTTCCCAATTGTACCTTCCTCGATAGGATTGAATTGGTATC
CTTCGCGGATCTCTCTATTGTTCTCTCTATTATTCTTTTTCTTTTTTAAATACTCCGCGA
CTCCGAAGCAACAAAATGTCGAAGGCAAGATGAAAGGCGTTTTGCAACTAAACGAGTAAT
GGCAGCTTTTAATTAAATAACGGTCAGCATTACTCTATAACTTTTCACATAAAATCCTCG
AAGAAGGAAAAATTGATAATCAATTTACCGAAGAATGAATATAGGTCTATAAAAATTCAA
TAATTATAGATGCATAAAAAGC
>MIT_Smik_c283_5928 YER014W 5' untranslated region, Contig c283 42606 - 44605, 2000 bp (revcom)
TATTGAAGCTCTCTCCACTATTTCTTTAATCGCGCTATACTAGATATGGTTAAACTGCTA
TCTTTTGCAAATCCCTCTATTGTTCTTTCCATTACTCTTTTCTTTTTTAAATACGGACTC
CGAAGCAACAAGGTCGAAGGCAAGCTGAAAGGCATTTTACAACTAAACGAGCAATGGTAG
CTTTTGATTGAATAAATTATTATCATTATTTTGTTATTTGTCCCACGAAATTCTCGTTGA
AAGCAAGGTTCGTAAGGATTTATCAAATGTTAAATATAGATCTATAAAAATTGAATAGTA
ATAATAACAAGGGATGGTGTTA
>MIT_Sbay_c84_6418 YER014W 5' untranslated region, Contig c84 10802 - 12801(revcom), 2000 bp (revcom)
TGTCGAAGTTCTCCTTTATTCCGCTGTTTCTTACGGAATCCAGCGAGACTGTTGTCCTTT
CGCATCCTTCTATTGTTCTTCCTTATTGTTCTCGTTTTTTTTATACTCTGCGACTCCGAA
ACAACAAAATCTCGAAGGCAAGCTAAGGTAAAAATATTCACCACTAAACGAGCAATGACA
GTTATATTCAAACGTCATTCTACTTTTTTGCCAGAGAAGTCCTCACTGGAGACGAAGTTG
GTAAATGCTTTATTTATATTAAACGTAGATCTATAAAGTTTAAATAGTTTATAATGCTTA
ACAAGGGACGATGTTATCTCTT
BioPerl-1.007002/t/data/map_hem/HEM3-HEM14.meme.txt000444000766000024     11354513155576321 21302 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM3-HEM14.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDL205C         1.0000    860  MIT_Spar_c429_3020       1.0000    860  
MIT_Smik_c193_2483       1.0000    860  MIT_Sbay_c841_3215       1.0000    860  
WashU_Skud_Contig1850.5  1.0000    860  SGD_Scer_YER014W         1.0000    322  
MIT_Spar_c425_6072       1.0000    322  MIT_Smik_c283_5928       1.0000    322  
MIT_Sbay_c84_6418        1.0000    322  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM3-HEM14.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            5588    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.311 C 0.189 G 0.189 T 0.311 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 197   E-value = 1.6e-024
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  4:1:::::a::1:::6::::
pos.-specific     C  6:98964:::::::a:87a1
probability       G  :::::::::::9::::::::
matrix            T  :a:2146a:aa:aa:423:9

         bits    2.5               *   * 
                 2.3               *   * 
                 2.0   * *      *  *   * 
                 1.8   * *      *  *   * 
Information      1.5  ****  ******** * * 
content          1.3  ****  ******** ****
(31.6 bits)      1.0 *************** ****
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CTCCCCTTATTGTTCACCCT
consensus            A  T TC        TTT  
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1850.5      +    706  7.49e-13 CATAGGCAAT CTCCCCTTATTGTTCACCCT TATTTCCACC
MIT_Sbay_c841_3215           +    725  7.49e-13 CATAGGCAAT CTCCCCTTATTGTTCACCCT TATTTCCACC
MIT_Spar_c429_3020           +    699  7.49e-13 CATAGGCAAC CTCCCCTTATTGTTCACCCT TATTTCCACC
SGD_Scer_YDL205C             +    698  7.49e-13 CATAGGCAAT CTCCCCTTATTGTTCACCCT TATTTCCACC
MIT_Smik_c193_2483           +    699  4.36e-11 CATAGGCAAT CTCCCCTTATTATTCACCCT TATTTCCACC
MIT_Spar_c425_6072           +     69  2.43e-10 TCCTTCGCGG ATCTCTCTATTGTTCTCTCT ATTATTCTTT
MIT_Sbay_c84_6418            +     64  6.44e-10 GTCCTTTCGC ATCCTTCTATTGTTCTTCCT TATTGTTCTC
MIT_Smik_c283_5928           +     71  6.44e-10 TCTTTTGCAA ATCCCTCTATTGTTCTTTCC ATTACTCTTT
SGD_Scer_YER014W             +     69  1.29e-09 TTCTTCGCGA ATATCTCTATTGTTCTCTCT ATTATACTAT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1850.5           7.5e-13  705_[+1]_135
MIT_Sbay_c841_3215                7.5e-13  724_[+1]_116
MIT_Spar_c429_3020                7.5e-13  698_[+1]_142
SGD_Scer_YDL205C                  7.5e-13  697_[+1]_143
MIT_Smik_c193_2483                4.4e-11  698_[+1]_142
MIT_Spar_c425_6072                2.4e-10  68_[+1]_234
MIT_Sbay_c84_6418                 6.4e-10  63_[+1]_239
MIT_Smik_c283_5928                6.4e-10  70_[+1]_232
SGD_Scer_YER014W                  1.3e-09  68_[+1]_234
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Skud_Contig1850.5  (  706) CTCCCCTTATTGTTCACCCT  1 
MIT_Sbay_c841_3215       (  725) CTCCCCTTATTGTTCACCCT  1 
MIT_Spar_c429_3020       (  699) CTCCCCTTATTGTTCACCCT  1 
SGD_Scer_YDL205C         (  698) CTCCCCTTATTGTTCACCCT  1 
MIT_Smik_c193_2483       (  699) CTCCCCTTATTATTCACCCT  1 
MIT_Spar_c425_6072       (   69) ATCTCTCTATTGTTCTCTCT  1 
MIT_Sbay_c84_6418        (   64) ATCCTTCTATTGTTCTTCCT  1 
MIT_Smik_c283_5928       (   71) ATCCCTCTATTGTTCTTTCC  1 
SGD_Scer_YER014W         (   69) ATATCTCTATTGTTCTCTCT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5417 bayes= 9.23095 E= 1.6e-024 
    45    166   -982   -982 
  -982   -982   -982    162 
  -154    234   -982   -982 
  -982    215   -982    -55 
  -982    234   -982   -154 
  -982    166   -982     45 
  -982    134   -982     78 
  -982   -982   -982    162 
   162   -982   -982   -982 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -154   -982    234   -982 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -982    251   -982   -982 
    78   -982   -982     45 
  -982    215   -982    -55 
  -982    192   -982      4 
  -982    251   -982   -982 
  -982    -66   -982    145 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.6e-024 
 0.444444  0.555556  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.111111  0.888889  0.000000  0.000000 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  0.444444  0.000000  0.555556 
 0.000000  0.000000  0.000000  1.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.555556  0.000000  0.000000  0.444444 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.666667  0.000000  0.333333 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.111111  0.000000  0.888889 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
[CA]TC[CT]C[CT][TC]TATTGTTC[AT][CT][CT]CT
--------------------------------------------------------------------------------




Time  3.32 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 193   E-value = 8.8e-023
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  ::a:::::aa7:4a:aa82:
pos.-specific     C  96:a6a46:::9::6::::6
probability       G  14:::::4::316::::28:
matrix            T  ::::4:6:::::::4::::4

         bits    2.5    * *              
                 2.3    * *              
                 2.0 *  * *     *        
                 1.8 *  * *     *        
Information      1.5 **** * *** * * ** * 
content          1.3 **** * *** * * ** * 
(30.9 bits)      1.0 ********************
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CCACCCTCAAACGACAAAGC
consensus             G  T CG  G A T  GAT
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Sbay_c841_3215           +    750  5.90e-12 ACCCTTATTT CCACCCTCAAACGACAAGGC TTGTTATGTT
MIT_Smik_c193_2483           +    724  8.81e-12 ACCCTTATTT CCACCCTCAAACGATAAAGC TTGCTGCGCT
MIT_Spar_c429_3020           +    724  8.81e-12 ACCCTTATTT CCACCCTCAAACGATAAAGC TTGTCTACAT
SGD_Scer_YDL205C             +    723  8.81e-12 ACCCTTATTT CCACCCTCAAACGATAAAGC TTGCTACTTT
SGD_Scer_YER014W             +    119  1.14e-10 GAATACTCCG CGACTCCGAAGCAACAAAGT GTCGAAGGCA
WashU_Skud_Contig1850.5      +    731  1.80e-10 ACCCTTATTT CCACCCTCAAAGGATAAAGC TTGTTGCATT
MIT_Sbay_c84_6418            +    111  4.97e-10 TTATACTCTG CGACTCCGAAACAACAAAAT CTCGAAGGCA
MIT_Spar_c425_6072           +    118  5.35e-10 AAATACTCCG CGACTCCGAAGCAACAAAAT GTCGAAGGCA
MIT_Smik_c283_5928           +    115  8.73e-10 TTTTAAATAC GGACTCCGAAGCAACAAGGT CGAAGGCAAG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Sbay_c841_3215                5.9e-12  749_[+2]_91
MIT_Smik_c193_2483                8.8e-12  723_[+2]_117
MIT_Spar_c429_3020                8.8e-12  723_[+2]_117
SGD_Scer_YDL205C                  8.8e-12  722_[+2]_118
SGD_Scer_YER014W                  1.1e-10  118_[+2]_184
WashU_Skud_Contig1850.5           1.8e-10  730_[+2]_110
MIT_Sbay_c84_6418                   5e-10  110_[+2]_192
MIT_Spar_c425_6072                5.3e-10  117_[+2]_185
MIT_Smik_c283_5928                8.7e-10  114_[+2]_188
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
MIT_Sbay_c841_3215       (  750) CCACCCTCAAACGACAAGGC  1 
MIT_Smik_c193_2483       (  724) CCACCCTCAAACGATAAAGC  1 
MIT_Spar_c429_3020       (  724) CCACCCTCAAACGATAAAGC  1 
SGD_Scer_YDL205C         (  723) CCACCCTCAAACGATAAAGC  1 
SGD_Scer_YER014W         (  119) CGACTCCGAAGCAACAAAGT  1 
WashU_Skud_Contig1850.5  (  731) CCACCCTCAAAGGATAAAGC  1 
MIT_Sbay_c84_6418        (  111) CGACTCCGAAACAACAAAAT  1 
MIT_Spar_c425_6072       (  118) CGACTCCGAAGCAACAAAAT  1 
MIT_Smik_c283_5928       (  115) GGACTCCGAAGCAACAAGGT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5417 bayes= 9.23095 E= 8.8e-023 
  -982    234    -66   -982 
  -982    166    134   -982 
   162   -982   -982   -982 
  -982    251   -982   -982 
  -982    166   -982     45 
  -982    251   -982   -982 
  -982    134   -982     78 
  -982    166    134   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
   104   -982     92   -982 
  -982    234    -66   -982 
    45   -982    166   -982 
   162   -982   -982   -982 
  -982    166   -982     45 
   162   -982   -982   -982 
   162   -982   -982   -982 
   126   -982     34   -982 
   -55   -982    215   -982 
  -982    166   -982     45 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 8.8e-023 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.555556  0.444444  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.444444  0.000000  0.555556 
 0.000000  0.555556  0.444444  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.666667  0.000000  0.333333  0.000000 
 0.000000  0.888889  0.111111  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.222222  0.000000  0.777778  0.000000 
 0.000000  0.555556  0.000000  0.444444 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
C[CG]AC[CT]C[TC][CG]AA[AG]C[GA]A[CT]AA[AG][GA][CT]
--------------------------------------------------------------------------------




Time  6.50 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =   9   llr = 178   E-value = 2.3e-016
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  9a::9496:41:94:34:71
pos.-specific     C  1:a::6:4:::31:6::91:
probability       G  ::::1:1:a69::6:76:29
matrix            T  :::a:::::::7::4::1::

         bits    2.5   *     *           
                 2.3   *     *           
                 2.0   *     * *      * *
                 1.8   *     * *      * *
Information      1.5  ***    * *      * *
content          1.3 ***** * * * *  * * *
(28.5 bits)      1.0 ****************** *
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           AACTACAAGGGTAGCGGCAG
consensus                 A C A C ATAA G 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
SGD_Scer_YDL205C             +    545  1.06e-11 AGTTAACTTA AACTACAAGGGTAGCAGCAG AATGTGTCGG
MIT_Spar_c429_3020           +    548  4.76e-11 AGTTAACTTG AACTACAAGGGTAGCAACAG AATGTCGGTG
MIT_Smik_c193_2483           +    547  1.28e-10 ACTTGACTTG AACTGCAAGGGTAGCGACGG CGTATGTCGG
MIT_Spar_c425_6072           +    166  1.56e-10 GGCGTTTTGC AACTAAACGAGTAATGGCAG CTTTTAATTA
SGD_Scer_YER014W             +    167  1.77e-10 GGCGTTTTGT AACTAAACGAGCAATGGCAG CTTTCAATTA
MIT_Sbay_c84_6418            +    162  1.74e-09 AAATATTCAC CACTAAACGAGCAATGACAG TTATATTCAA
WashU_Skud_Contig1850.5      +    550  1.74e-09 CGCAAAACGG AACTACAAGGATAGCAACGG AATGTGTCGG
MIT_Smik_c283_5928           +    161  2.36e-09 GGCATTTTAC AACTAAACGAGCAATGGTAG CTTTTGATTG
MIT_Sbay_c841_3215           +    557  4.89e-09 CGTAAGATAG AACTACGAGGGTCGCGGCCA ATGTGTCGGT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDL205C                  1.1e-11  544_[+3]_296
MIT_Spar_c429_3020                4.8e-11  547_[+3]_293
MIT_Smik_c193_2483                1.3e-10  546_[+3]_294
MIT_Spar_c425_6072                1.6e-10  165_[+3]_137
SGD_Scer_YER014W                  1.8e-10  166_[+3]_136
MIT_Sbay_c84_6418                 1.7e-09  161_[+3]_141
WashU_Skud_Contig1850.5           1.7e-09  549_[+3]_291
MIT_Smik_c283_5928                2.4e-09  160_[+3]_142
MIT_Sbay_c841_3215                4.9e-09  556_[+3]_284
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=9
SGD_Scer_YDL205C         (  545) AACTACAAGGGTAGCAGCAG  1 
MIT_Spar_c429_3020       (  548) AACTACAAGGGTAGCAACAG  1 
MIT_Smik_c193_2483       (  547) AACTGCAAGGGTAGCGACGG  1 
MIT_Spar_c425_6072       (  166) AACTAAACGAGTAATGGCAG  1 
SGD_Scer_YER014W         (  167) AACTAAACGAGCAATGGCAG  1 
MIT_Sbay_c84_6418        (  162) CACTAAACGAGCAATGACAG  1 
WashU_Skud_Contig1850.5  (  550) AACTACAAGGATAGCAACGG  1 
MIT_Smik_c283_5928       (  161) AACTAAACGAGCAATGGTAG  1 
MIT_Sbay_c841_3215       (  557) AACTACGAGGGTCGCGGCCA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5417 bayes= 9.23095 E= 2.3e-016 
   145    -66   -982   -982 
   162   -982   -982   -982 
  -982    251   -982   -982 
  -982   -982   -982    162 
   145   -982    -66   -982 
    45    166   -982   -982 
   145   -982    -66   -982 
    78    134   -982   -982 
  -982   -982    251   -982 
    45   -982    166   -982 
  -154   -982    234   -982 
  -982     92   -982    104 
   145    -66   -982   -982 
    45   -982    166   -982 
  -982    166   -982     45 
     4   -982    192   -982 
    45   -982    166   -982 
  -982    234   -982   -154 
   104    -66     34   -982 
  -154   -982    234   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.3e-016 
 0.888889  0.111111  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.444444  0.555556  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.555556  0.444444  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  0.333333  0.000000  0.666667 
 0.888889  0.111111  0.000000  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 0.333333  0.000000  0.666667  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.666667  0.111111  0.222222  0.000000 
 0.111111  0.000000  0.888889  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
AACTA[CA]A[AC]G[GA]G[TC]A[GA][CT][GA][GA]C[AG]G
--------------------------------------------------------------------------------




Time  9.58 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   11   sites =   9   llr = 119   E-value = 1.7e-006
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  2aa::6a4:1:
pos.-specific     C  :::::4:6:8:
probability       G  8::aa:::a::
matrix            T  :::::::::1a

         bits    2.5    **   *  
                 2.3    **   *  
                 2.0    **   *  
                 1.8    **   *  
Information      1.5 ***** * * *
content          1.3 ***** * ***
(19.1 bits)      1.0 ***********
                 0.8 ***********
                 0.5 ***********
                 0.3 ***********
                 0.0 -----------

Multilevel           GAAGGAACGCT
consensus            A    C A   
sequence                        
                                
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value               Site  
-------------            ------  ----- ---------            -----------
WashU_Skud_Contig1850.5      -    217  1.62e-07 TGAAAAAATT GAAGGAACGCT TTATATAAAC
MIT_Smik_c193_2483           -    220  1.62e-07 GAGAAAAACT GAAGGAACGCT TAATATAAAC
MIT_Spar_c429_3020           -    218  1.62e-07 TGAAAAAAAT GAAGGAACGCT TTATATAAAC
MIT_Sbay_c84_6418            +    134  2.68e-07 ACAAAATCTC GAAGGCAAGCT AAGGTAAAAA
MIT_Smik_c283_5928           +    136  2.68e-07 CAACAAGGTC GAAGGCAAGCT GAAAGGCATT
MIT_Sbay_c841_3215           -    218  7.62e-07 CCGAAAAATT AAAGGAACGCT TATTTAAACG
SGD_Scer_YDL205C             -    217  7.62e-07 ATGAAAAAGT AAAGGAACGCT TTATATAAAC
MIT_Spar_c425_6072           +    141  2.30e-06 ACAAAATGTC GAAGGCAAGAT GAAAGGCGTT
SGD_Scer_YER014W             +    142  2.30e-06 ACAAAGTGTC GAAGGCAAGTT CAAAGGCGTT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1850.5           1.6e-07  216_[-4]_633
MIT_Smik_c193_2483                1.6e-07  219_[-4]_630
MIT_Spar_c429_3020                1.6e-07  217_[-4]_632
MIT_Sbay_c84_6418                 2.7e-07  133_[+4]_178
MIT_Smik_c283_5928                2.7e-07  135_[+4]_176
MIT_Sbay_c841_3215                7.6e-07  217_[-4]_632
SGD_Scer_YDL205C                  7.6e-07  216_[-4]_633
MIT_Spar_c425_6072                2.3e-06  140_[+4]_171
SGD_Scer_YER014W                  2.3e-06  141_[+4]_170
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=11 seqs=9
WashU_Skud_Contig1850.5  (  217) GAAGGAACGCT  1 
MIT_Smik_c193_2483       (  220) GAAGGAACGCT  1 
MIT_Spar_c429_3020       (  218) GAAGGAACGCT  1 
MIT_Sbay_c84_6418        (  134) GAAGGCAAGCT  1 
MIT_Smik_c283_5928       (  136) GAAGGCAAGCT  1 
MIT_Sbay_c841_3215       (  218) AAAGGAACGCT  1 
SGD_Scer_YDL205C         (  217) AAAGGAACGCT  1 
MIT_Spar_c425_6072       (  141) GAAGGCAAGAT  1 
SGD_Scer_YER014W         (  142) GAAGGCAAGTT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 11 n= 5498 bayes= 9.2524 E= 1.7e-006 
   -55   -982    215   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -982   -982    251   -982 
  -982   -982    251   -982 
    78    134   -982   -982 
   162   -982   -982   -982 
    45    166   -982   -982 
  -982   -982    251   -982 
  -154    215   -982   -154 
  -982   -982   -982    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 11 nsites= 9 E= 1.7e-006 
 0.222222  0.000000  0.777778  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.555556  0.444444  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.555556  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.111111  0.777778  0.000000  0.111111 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
[GA]AAGG[AC]A[CA]GCT
--------------------------------------------------------------------------------




Time 12.58 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 167   E-value = 6.6e-012
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  9:a:2:::4:a4492::7a9
pos.-specific     C  :6::66a::::66:1:71::
probability       G  1::a2:::6::::1:2:2::
matrix            T  :4:::4:a:a::::783::1

         bits    2.5    *  *             
                 2.3    *  *             
                 2.0    *  *             
                 1.8    *  *             
Information      1.5   **  ** **       * 
content          1.3 * **  ** **  *  * * 
(26.7 bits)      1.0 **** ********* ** **
                 0.8 ************** *****
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           ACAGCCCTGTACCATTCAAA
consensus             T  AT  A  AA AGTG  
sequence                 G               
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1850.5      +    115  6.64e-13 AAAAAGCAAT ACAGCCCTGTACCATTCAAA CACGAACGCC
MIT_Sbay_c841_3215           +    116  6.64e-13 AAAACGCAAT ACAGCCCTGTACCATTCAAA TACGAACGCC
MIT_Smik_c193_2483           +    117  6.64e-13 AAAAAGTAAT ACAGCCCTGTACCATTCAAA CACGAGCGCC
MIT_Spar_c429_3020           +    115  1.38e-12 AAAATGTAAA ACAGCCCTGTACCATGCAAA CACGAGCCTC
SGD_Scer_YDL205C             +    115  1.38e-12 AAAATCTAAT ACAGCCCTGTACCATGCAAA CACGAGCGTC
MIT_Smik_c283_5928           +    276  3.37e-08 AATGTTAAAT ATAGATCTATAAAAATTGAA TAGTAATAAT
MIT_Spar_c425_6072           +    281  3.48e-08 AAGAATGAAT ATAGGTCTATAAAAATTCAA TAATTATAGA
SGD_Scer_YER014W             +    274  3.63e-08 AAAATTAAAT ATAGGTCTATAAAACTCGAT AATTATAATG
MIT_Sbay_c84_6418            +    265  4.65e-08 TATATTAAAC GTAGATCTATAAAGTTTAAA TAGTTTATAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1850.5           6.6e-13  114_[+5]_726
MIT_Sbay_c841_3215                6.6e-13  115_[+5]_725
MIT_Smik_c193_2483                6.6e-13  116_[+5]_724
MIT_Spar_c429_3020                1.4e-12  114_[+5]_726
SGD_Scer_YDL205C                  1.4e-12  114_[+5]_726
MIT_Smik_c283_5928                3.4e-08  275_[+5]_27
MIT_Spar_c425_6072                3.5e-08  280_[+5]_22
SGD_Scer_YER014W                  3.6e-08  273_[+5]_29
MIT_Sbay_c84_6418                 4.7e-08  264_[+5]_38
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
WashU_Skud_Contig1850.5  (  115) ACAGCCCTGTACCATTCAAA  1 
MIT_Sbay_c841_3215       (  116) ACAGCCCTGTACCATTCAAA  1 
MIT_Smik_c193_2483       (  117) ACAGCCCTGTACCATTCAAA  1 
MIT_Spar_c429_3020       (  115) ACAGCCCTGTACCATGCAAA  1 
SGD_Scer_YDL205C         (  115) ACAGCCCTGTACCATGCAAA  1 
MIT_Smik_c283_5928       (  276) ATAGATCTATAAAAATTGAA  1 
MIT_Spar_c425_6072       (  281) ATAGGTCTATAAAAATTCAA  1 
SGD_Scer_YER014W         (  274) ATAGGTCTATAAAACTCGAT  1 
MIT_Sbay_c84_6418        (  265) GTAGATCTATAAAGTTTAAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 5417 bayes= 9.23095 E= 6.6e-012 
   145   -982    -66   -982 
  -982    166   -982     45 
   162   -982   -982   -982 
  -982   -982    251   -982 
   -55    166     34   -982 
  -982    166   -982     45 
  -982    251   -982   -982 
  -982   -982   -982    162 
    45   -982    166   -982 
  -982   -982   -982    162 
   162   -982   -982   -982 
    45    166   -982   -982 
    45    166   -982   -982 
   145   -982    -66   -982 
   -55    -66   -982    104 
  -982   -982     34    126 
  -982    192   -982      4 
   104    -66     34   -982 
   162   -982   -982   -982 
   145   -982   -982   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.6e-012 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.222222  0.555556  0.222222  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.555556  0.000000  0.000000 
 0.444444  0.555556  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.222222  0.111111  0.000000  0.666667 
 0.000000  0.000000  0.222222  0.777778 
 0.000000  0.666667  0.000000  0.333333 
 0.666667  0.111111  0.222222  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.000000  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
A[CT]AG[CAG][CT]CT[GA]TA[CA][CA]A[TA][TG][CT][AG]AA
--------------------------------------------------------------------------------




Time 15.70 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDL205C                 2.08e-30  114_[+5(1.38e-12)]_82_[-4(7.62e-07)]_154_[+4(3.75e-05)]_152_[+3(1.06e-11)]_133_[+1(7.49e-13)]_5_[+2(8.81e-12)]_118
MIT_Spar_c429_3020               1.99e-30  53_[+1(9.52e-05)]_41_[+5(1.38e-12)]_83_[-4(1.62e-07)]_156_[+4(3.75e-05)]_152_[+3(4.76e-11)]_131_[+1(7.49e-13)]_5_[+2(8.81e-12)]_117
MIT_Smik_c193_2483               1.21e-28  116_[+5(6.64e-13)]_83_[-4(1.62e-07)]_316_[+3(1.28e-10)]_132_[+1(4.36e-11)]_5_[+2(8.81e-12)]_117
MIT_Sbay_c841_3215               2.40e-28  54_[+1(9.52e-05)]_41_[+5(6.64e-13)]_60_[+5(4.92e-05)]_2_[-4(7.62e-07)]_328_[+3(4.89e-09)]_107_[-1(5.66e-05)]_21_[+1(7.49e-13)]_5_[+2(5.90e-12)]_91
WashU_Skud_Contig1850.5          5.34e-28  114_[+5(6.64e-13)]_82_[-4(1.62e-07)]_289_[+2(7.24e-05)]_13_[+3(1.74e-09)]_136_[+1(7.49e-13)]_5_[+2(1.80e-10)]_110
SGD_Scer_YER014W                 1.36e-22  68_[+1(1.29e-09)]_30_[+2(1.14e-10)]_3_[+4(2.30e-06)]_14_[+3(1.77e-10)]_87_[+5(3.63e-08)]_29
MIT_Spar_c425_6072               1.03e-22  68_[+1(2.43e-10)]_29_[+2(5.35e-10)]_3_[+4(2.30e-06)]_14_[+3(1.56e-10)]_57_[+4(9.30e-05)]_27_[+5(3.48e-08)]_22
MIT_Smik_c283_5928               6.69e-22  70_[+1(6.44e-10)]_24_[+2(8.73e-10)]_1_[+4(2.68e-07)]_14_[+3(2.36e-09)]_95_[+5(3.37e-08)]_27
MIT_Sbay_c84_6418                4.02e-22  63_[+1(6.44e-10)]_27_[+2(4.97e-10)]_3_[+4(2.68e-07)]_17_[+3(1.74e-09)]_83_[+5(4.65e-08)]_38
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM3-HEM15.fa000444000766000024      2230213155576321 20076 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDL205C HEM3 "Phorphobilinogen deaminase, catalyzes the conversion of 4-porphobilinogen to hydroxymethylbilane, the third step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; expression is regulated by Hap2p-Hap3p"
AGTACGTGTGTATTTACCAACTACAAATTTATCTAGATTTTCTTCGCTTTTCTTTTTTTC
TATTGTTCTAGATATTAATACGGGATGAGAAGAACAGAATATTCAAAATCTAATACAGCC
CTGTACCATGCAAACACGAGCGTCAATCTGCCAATGACCTTGAATTCAGGCTATGTGTAG
CAATAATACAGATAGTTAGTAGCCTCGTTTATATAAAGCGTTCCTTTACTTTTTCATTTT
CTTTCTTTTTTTATGTTTGATTTTTTTACTTTTTCACTTTAAAAAATTGCTGAAATTTTC
GTAGCCAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCTCCC
CAGGGTCAATTGACAAGGAGAGAAGGAATGTTATATGGGAATTGCTGCGTAAAGATGGTC
AAAAATCCTGGACTGCCGTACGAACGACAATGTAAGGATGACTGCATTAGCCAGAAAGAC
ATCTTTACCCCCGGTGCTGCCAGGGAGCAAAATAATTACGAAAAGTGGACGCAAAGTTAA
CTTAAACTACAAGGGTAGCAGCAGAATGTGTCGGTGGTACCGGTGTGATAATGCCCCATT
TGAGATGCTTGTAATTGTGGCCTAGCAATAAGAACGCAAGGCGTTTTTGTTGAAAGGAGA
ACAAGGTTAGACGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTCACCCTTAT
TTCCACCCTCAAACGATAAAGCTTGCTACTTTGATGAAAAAAATATATAAAAGGGATTGA
AAAGCAGATCAATTATGTAGCAATAGTAGTAATAACTTGTTCAATTGCTTGTCTCAACTT
GCCACAAACTATCATCAACA
>MIT_Spar_c429_3020 YDL205C 5' untranslated region, Contig c429 77420 - 79419(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTATCAACTACAAAATTTATCTAGATTTTCTTGCCTTTTCCTTTTTC
TATTGTTCTAGATACTAATACGGGATGAGAAGAACAGAATATTCAAAATGTAAAACAGCC
CTGTACCATGCAAACACGAGCCTCAATCTGCCAATGACCTTGAATCCAAGCTATGTGTAG
CAATAATACAGATGATTGATTGGCGTCGTTTATATAAAGCGTTCCTTCATTTTTTTCATT
TTCTTTCTTTTTTTATGTTTGATTTTTTACTTTTTCACTTTTGAAAACTGCTGAAATTTT
CGTAGCAAAAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCT
CCCCAGGGTCAATTGACAAGGAGAGAAGGAATGTTACATCCAGGAATTGCGACATAAAGA
TGTCCAAGAAGTCTGAACTGTCATACGAATGGCTATGCAAGGAGGATAGTACTGGTCAAG
AAGACATCTTACCCCCGGTGCTGTCAGGGAGCAAAAAAATGACAAAAGTGGACGCAAAGT
TAACTTGAACTACAAGGGTAGCAACAGAATGTCGGTGGTACCGGATGTGACAAAGCTCAC
TTGAGGTGCTTCTTGTTGCGGCATAGCAATAAGAGCGCAAGGCGTTTTTATGGAAAGGAG
AGCGAGGTTAGAGGGTGACGTTTAGGCGCATAGGCAACCTCCCCTTATTGTTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGTCTACATTGATGAAAAAAATGTATAAAAGGGATT
GAAAAGCCGATCATGTGTGTAGCAATAGTAGTAGTTATACTTGTTCAATTGCTTGCTTGC
ACTTTTCCAAAAACTACCAC
>MIT_Smik_c193_2483 YDL205C 5' untranslated region, Contig c193 6380 - 8379(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTACCAACTATAAAATTTTACCTAGACTATCTGGCCTTTTTCTTTTT
TCTATTGTTCTAGATACTAATACGGGATGAAAAGAACAGAATATTCAAAAAGTAATACAG
CCCTGTACCATTCAAACACGAGCGCCAATTTGCCAATGAACTTGAAATCCAGCTATGCGT
AGCGATAATACAGATGATTGTTTGATGTCGTTTATATTAAGCGTTCCTTCAGTTTTTCTC
ATTTTCTTTCTTTTTCTATGTTTTATTTTTCACTTTTTCACTTTTGAAAATTGCTGAAAT
TTTCGTAACAAAAAAAGAGGCCTTCATTGCTTACTCATCGTTATCTTATTGGTTAAAATC
CCCAGCGACAATGTACAAGGAGAGAAGAAATGATATGTCTGGGAATTGCAGTTTGAAGAT
ATCCAAAGAGTTTTGAAGTGCCATACGAGCAACCACGTGAGAAGTAGAGCCTTAACAGAA
AATTCATCTTACCCCTAGTACTGCCAGGGAGGAACTAAACCTAAGAACTAGTGTTAACTT
GACTTGAACTGCAAGGGTAGCGACGGCGTATGTCGGTGGTACCGGATATGGCAAGAGCCC
ATTTGAGCTGCTTGTTCTTGTGACATACTATTAAGAGCGCAAGGCGTTTATGGAAAGGAG
GACAAGGTCAGAGGATGACGTTTAAGCGCATAGGCAATCTCCCCTTATTATTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGCTGCGCTGTTGAAAAGTATATAAAAGGGATAGAA
AAGCAGAGCAATTATAATTTAGTAGAATAGCTTATTCTATCGTTAACTTGTTGAAAGGAT
CAGATTATTATCAAGATGAA
>MIT_Sbay_c841_3215 YDL205C 5' untranslated region, Contig c841 7323 - 9322(revcom), 2000 bp (revcom)
AGTATGTGTATATTTACCAACTATAGAGTATATCTAGTATTTTTTTTCCTTCTTCTTTTT
CTATTGTTCTAGATGCTAATATGGGATGAGTAGAACAAAATATTCAAAACGCAATACAGC
CCTGTACCATTCAAATACGAACGCCAATCTGCCAATGACCTTGAAATCAAGTTATGTGCC
GCGATAATACAATCTTTTGGCCTATATCGTTTAAATAAGCGTTCCTTTAATTTTTCGGTT
TCTTTCTTTTTTATGTCTAATTTTTCATTTTTTTTCACTTGAAAATTGCTGAAATTTTCG
TAGCTGAAAAAGAGAGGCCTTCTTTGCTTACTCATCGTTATCTTATTGGTCAAGAGCCCA
AGGGACAATAGACAAGGAGAGAACCACCAACTTTGGGAGTTGGATGCAAAGAAGGTCTTT
GATTTTGGGCTGCTATCAGAGCGGGCCATATAAGGAAGCTTGTAGTGGTTAGGAGAGAAC
ACGTCATTACCCCCCTCCCCCTTCTCCGCGCTGCCAGGGACCAGGCAAGGGCTTGCAAGA
GATGAACGTAAGATAGAACTACGAGGGTCGCGGCCAATGTGTCGGTAGTACCGGATGGGG
CAAAGCCCAATTGAGGTGCTTGTTGTTGAGGATGGTCGGCATGGCATGGCATGGGAGGCC
AAAGGCGCTTTGTGGGAAGGAGAACAAACAACATTAGAGGGTGACGTTTTAGCGCATAGG
CAATCTCCCCTTATTGTTCACCCTTATTTCCACCCTCAAACGACAAGGCTTGTTATGTTG
GTTGGAAATATATAAAAGGGATTGAAAAAGATCATATTCCTACATAAATTATGGTATTAG
TTTTTCTTCAATTGCTGGCT
>WashU_Skud_Contig1850.5 YDL205C 5' untranslated region, Contig c1850 6875 - 8874(revcom), 2000 bp (revcom)
GATACGTGTGTATTTGCTAACTATAAAATTTATCTAGTTTTCCTGCTTTTTTTTTTTTCT
ATTGTTCTAGAAACTAATATGGGGATGAGAAGAACAAAATTTTCAAAAAGCAATACAGCC
CTGTACCATTCAAACACGAACGCCAATCTGCAATGACCTTGAAATCAATCTATGTGTCGC
GATAATACAAGTGATTGATTGGTGTCGTTTATATAAAGCGTTCCTTCAATTTTTTCATTT
TCTTTCTTTTTTTATGTTTAATTTTCTACCTTTTTCACTTTTGAAAATTGCTGAAATTTT
CGTAGCAAAAAAAGAGAGGCGTACGTTGCTTACTCATCGTTTTCTTATTGGTCAAAAGCT
CCAGGAACAATGCCCAAGGAGAGAAAGAGTGCTACGTCTAGGAATTGCGATGGAAAGGCG
TCCAAGAGTCCTAAACTACCATGAGAACGGGCCACCCAAGGAGGGATAGCAATTGCTGAA
ACAACATCTTCACCTTCGGAGCTGGCAGGGAGCAAGGGACTCTCCGGAAAGAAAGTGAAC
GCAAAACGGAACTACAAGGATAGCAACGGAATGTGTCGGTGGTAGCGGATGTGGCAAGAT
CCCATTTCAGGAGCTTGTTGTTACGGCACAGCAGCAAGAAGAGCACAAGGCTTTTTCCGT
AAAGGAGAACAAAGTTGGAAGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTC
ACCCTTATTTCCACCCTCAAAGGATAAAGCTTGTTGCATTGATAAAAAATGTATAAAAAG
GATGGGAAACAGATGATAGTTAACAAGGTAGTGGGACGGTCTTTCGCTTATTCAGTTGTG
TGACATTCAAGGGTTACAAT
>SGD_Scer_YOR176W HEM15 "Ferrochelatase, a mitochondrial inner membrane protein, catalyzes the insertion of ferrous iron into protoporphyrin IX, the eighth and final step in the heme biosynthetic pathway; Yfh1p mediates the use of iron by Hem15p"
TCTTTAAACGTTCTTTTTTTTACTGCTAAATTTGTCCAAATAGCAGGTATGTGTTAAATA
TTTCTGTACTTCTTGTAAACCGACTCAAGTGGAACACGAGAATTTACGCTTGTTTGGTGT
CAAGCCAAGAGTGACCTTGACCGACCAAAAGTATTCCTTCGCGTCCTCCTTCTTCAATCC
CATATCCCCTACGAAAAAAAGCAGCATGAGAAAACGAAGGGCAGCAACTCCTTCGTCATA
TAAGGCTTACGGTGACCATTGAAGATTGGGCATGTCTAACGGCTATTGCCAGCGGAGATG
TTTCAAGGCATCCTACACATGCTACATATTTGTAATTATTTTACTGAGTTTGTGTATATA
AAAAACTTTTTTAAAAAAAAAAAATGGCCAGCATCCTCTTTCATGTAAAGCTGTTGAACC
TTCCTGAAATTTACTTCTAAAATTGTTCAGTAAAACTGCTTGTTAAAAGTGCGAAGAGTT
CTTTTTTAGCTTTTTTTGTCCTGCTGTTGAGCTGTTTTGCTTTACTGTTCAACAAAACAT
TGAAGATCTTTCACATTGCGCGTCGAAACCACAAACCGTCGAAAACAATGGTCATCTAAA
TAAAGGGTTCTTATTAAACAGATTTAAAGCCAAGGACAAAATACAGGCACAGGTCAAGCA
AGAAGACAAACCGCATACGCCAAGACAAACCGTGGTGATTTAATTCTGCTGCTGATCGCT
TCCAACA
>MIT_Spar_c278_20970 YOR176W 5' untranslated region, Contig c278 32746 - 34745, 2000 bp (revcom)
TCTTCAAACGTTCTTTTCCTACTACTAAGCTTTTCAATAAATAGCGGGTATATGCTAAAT
ACTTCTTTGCTTCTTGTACGACCTACTTAATTGAAATACGGATATTTTTGCTTGCTTGGT
GCCAAACCAAGAGTGACCTTGACCGACTAAAAGTATTCCTTCGCGTCCTCCTTCTTCAAT
CCCATATCCCCTACTGAAAAAAGCAGCGTGCGAAAATGAAGGGCAGCAACTCCTTCGTCA
TATAAGGCTTAGGTAATCTTTCAAGGTCAGGTATATCCAGCTGTCGTTACGAGTAGAGAT
ATTTCAAGCTGTCCTGCACATGCTACATATTTGTGATTATTTTTATTGAGTTGCGTATAT
AAAAAAACAATCTAAAAAAAAAAAAAATGGCCAGCATCTTCTTCCATGTAAAGCTGTTGA
ACCTTGCTAAAATCTATTACTATAATTGTTCAGTAAAGTTGCTTGTTAAAAATGCGAAGA
GTCTTTTTTAGCTTTTTTTGCCCTGCTGTTGAGCTGTTTTGCTTCACTGTTCAACAAAAC
AGTGAAGATCTTTCGAATTGCGCGTCGAAACCACAAACCGTCGAAAATAATGGTCATCTA
AATAAAGGGTTCTTATTTGAACAGATTTAAAGCTCAAAGACACGATACAGGCACAGGTCC
AGAAAGAATACAAAACGCAAACGCCAAGACAAATTGTGGTAATTTCATTCTGCTGCTGAT
CACTGCC
>MIT_Smik_c935_20455 YOR176W 5' untranslated region, Contig c935 1803 - 3802(revcom), 2000 bp (revcom)
TCTTGAATTGCAATTTTCTACTACTGAAGTTACCAACAATTAGCAAATATGTGATGAGTC
CTTTTTACGTTCTTGTATAACCTAAGTTAAATACAAAGGTTTATGCTCCTTTAATGATCA
GACCAACAGTGATCTTGGCCGACCAAAAGACTCCTTCGCGTCCTCCTTCTTCAAGTCTCA
TATCCCCTACCAGAAAAAGTAGCAGGCGAAAATAAAGAGCAACTGCTCCCCCCCATATAG
AGCTTACCATAATTTCTCAAGGAAAGGTATCTCCAGTTGTCGTAAAGAATAAAGAAGTTT
CAACGTGTCCTGCATGTTCTACAAATTTGCAATTGACTTTACTAAGTTGCATATATAAAA
CTTGTATTAGATAAGTTAGCCAGCATTTTCATTCAAGCTAAGATGTTGAATATGCCAAAG
CACATTGCTGAAATTAATCAGTAAAGCTGCTTGCTGAAAGTGGAAATATTTTCAGCTTTT
TTTGCTCTGCTGTTGAGCTGTTTTACTTCATTGTTCAACAAAACAATAGAGTTCTCTCCA
ATTGCGCGTCAAAACCACAAACCGTCGAAAATAATGATCATCTAAATAAAAGAGTTCACG
TTTTCACATATTTAAAGTTGAAATACTCCATACAGGCACAGGTCTAACAAGAAGACAACG
CATTCGATAAAACTAATCGTGGTAATTTTTATATCGCTGCTAGCCACTACCAACAATGTA
CAATTTT
>WashU_Skud_Contig2050.4 YOR176W 5' untranslated region, Contig c2050 12271 - 14270(revcom), 2000 bp (revcom)
TCTTAGTTTATAGCTTTTCTACTACTCTGGTCATAAACGAACAGAAGATAAGCAAGAAAT
CTTTTTTTCCTTCTTTTACGGTCTATTCAAGTGAAGCACGGGGATTCCCGCTTGTTTAAT
AATCAGACCAACAATGATATTGACCGACCAAAAGAAGTATTCCTTCGCGTGCTTCTCCTT
TCTGTGTCAAATCCCCTACTGAAAAAGCAGCATTGGGAAAGGAACAGCAGCTTCTCCTTC
GTCGCAGAGAGCTCGCGGTAGCATTTCATTGTCAGGTATTTATGATATTTGCTAAGAATA
ATTAAAATGTCTTCAGGTCTTGCACATACTCCTACATATTTGTAAGTATTTTACTGATTT
GAGTATATAAAAGCCGTACTAAAACTAACCAGCACCTGTAGCAAGGTGCAAAATGTTGAA
CCTTTCCGAAATTTATTGCCAGAAACCAAGAGCTAAAAGTGCTTGGTAAAAGTGAAAAGA
CTCTTTTTCAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGTTCCATCTGTTCAACAAA
ACAGCTTCACTGGATCTTTCAAAGTGCGCGTCGAAACCACAAACCGTCGAAAATATTGAT
CATCTAAATAAAGGGTTCTTATTTGCACAGTTTCGCATTGAAATATTCCATTCAGGCACA
GATCAACAAGAAGACAAAAAGGTATTCGAGAAGACTAATTGTGGTATTTTTACTTTGCTG
CTGACCA
>WashU_Sbay_Contig480.2 YOR176W 5' untranslated region, Contig c480 3444 - 5443(revcom), 2000 bp (revcom)
TTTCAGGGAAGCACCATGTGCACGAATTGTTCTAGAAAGCATTTTTGGTTCGTAAATTCT
CTACAACTGAACTTATTAACAAATAGCAAACAGAGAAGAAAATTTTTTTTTTCCTTCTTG
TATGGTCAGTTAGTTGAAAACACGGAGATTTTCACTTGTTTAGTAAGCAGAGCCATAATG
CTCTTGACCGACCAAAAGAAGTATTCCTACGCGAGCTCCCTCTTCAAGTGCCAAATCCCC
TACTGAAAAAAGCAACATGAGAAGCAAAGAGATGCCTCTCGCCATGCAGGGCTTGCGGTC
ATGTTTTCTACGTTCAATTGATTTTGTTACAGCTGAAAGATGTTTATAAAACTGTCTTGC
ATATGCTCTATTTACTTGTAAACAATTTTATTAAGTTGCGTATATATGATCGTACTAAAA
ATTGGCTGGCGCGTTCTCCAGGCAGAGTTGGTTGAACCTTGCTCGAATTGATAGCTCAAA
GTGGAGAGACTCTTTTTTAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGCTCCACCTG
TTCAACAAAATGGCAGAGATCTTTCGAAGTGCGCGTCGAAACCACAAACCATCAAAAATA
TCGACCATCTAAATAAAGGGTTCTTGTTTGAATAAATATCAGGCGAAGCTCTTCATACAG
GCACAGGTCAGATAAGAAGACAATTCGAATTCGAGAAGGATATTCGTGGTATCTTTAATC
TGCTGCT
BioPerl-1.007002/t/data/map_hem/HEM3-HEM15.meme.txt000444000766000024     11755013155576321 21303 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM3-HEM15.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDL205C         1.0000    860  MIT_Spar_c429_3020       1.0000    860  
MIT_Smik_c193_2483       1.0000    860  MIT_Sbay_c841_3215       1.0000    860  
WashU_Skud_Contig1850.5  1.0000    860  SGD_Scer_YOR176W         1.0000    727  
MIT_Spar_c278_20970      1.0000    727  MIT_Smik_c935_20455      1.0000    727  
WashU_Skud_Contig2050.4  1.0000    727  WashU_Sbay_Contig480.2   1.0000    727  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM3-HEM15.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=       10    maxsites=       10    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            7935    N=              10
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.308 C 0.192 G 0.192 T 0.308 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   19   sites =  10   llr = 215   E-value = 3.6e-028
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  1:aa6a:a::::55:a::a
pos.-specific     C  16::::a::a5a::5:5a:
probability       G  8:::::::a::::5::5::
matrix            T  :4::4:::::5:5:5::::

         bits    2.5       * ** *     * 
                 2.3       * ** *     * 
                 2.0       * ** *     * 
                 1.8       * ** *     * 
Information      1.5 * ** ***** *   ****
content          1.3 **** ***** *   ****
(31.0 bits)      1.0 **** ******* ******
                 0.8 ************ ******
                 0.5 *******************
                 0.3 *******************
                 0.0 -------------------

Multilevel           GCAAAACAGCCCAACACCA
consensus             T  T     T TGT G  
sequence                                
                                        
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                   Site      
-------------            ------  ----- ---------            -------------------
WashU_Skud_Contig1850.5      +    110  3.58e-11 TTTTCAAAAA GCAATACAGCCCTGTACCA TTCAAACACG
MIT_Sbay_c841_3215           +    111  3.58e-11 TATTCAAAAC GCAATACAGCCCTGTACCA TTCAAATACG
WashU_Sbay_Contig480.2       -    514  6.04e-11 AACAGGTGGA GCAAAACAGCTCAACAGCA GAACAAAAAA
MIT_Spar_c278_20970          -    504  6.04e-11 GAACAGTGAA GCAAAACAGCTCAACAGCA GGGCAAAAAA
SGD_Scer_YOR176W             -    502  6.04e-11 GAACAGTAAA GCAAAACAGCTCAACAGCA GGACAAAAAA
MIT_Spar_c429_3020           +    110  1.14e-10 TATTCAAAAT GTAAAACAGCCCTGTACCA TGCAAACACG
MIT_Smik_c193_2483           +    112  1.56e-10 TATTCAAAAA GTAATACAGCCCTGTACCA TTCAAACACG
MIT_Smik_c935_20455          -    488  2.17e-10 GAACAATGAA GTAAAACAGCTCAACAGCA GAGCAAAAAA
WashU_Skud_Contig2050.4      -    505  5.56e-10 AACAGATGGA ACAAAACAGCTCAACAGCA GAACAAAAAA
SGD_Scer_YDL205C             +    110  5.89e-10 TATTCAAAAT CTAATACAGCCCTGTACCA TGCAAACACG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1850.5           3.6e-11  109_[+1]_732
MIT_Sbay_c841_3215                3.6e-11  110_[+1]_731
WashU_Sbay_Contig480.2              6e-11  513_[-1]_195
MIT_Spar_c278_20970                 6e-11  503_[-1]_205
SGD_Scer_YOR176W                    6e-11  501_[-1]_207
MIT_Spar_c429_3020                1.1e-10  109_[+1]_732
MIT_Smik_c193_2483                1.6e-10  111_[+1]_730
MIT_Smik_c935_20455               2.2e-10  487_[-1]_221
WashU_Skud_Contig2050.4           5.6e-10  504_[-1]_204
SGD_Scer_YDL205C                  5.9e-10  109_[+1]_732
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=19 seqs=10
WashU_Skud_Contig1850.5  (  110) GCAATACAGCCCTGTACCA  1 
MIT_Sbay_c841_3215       (  111) GCAATACAGCCCTGTACCA  1 
WashU_Sbay_Contig480.2   (  514) GCAAAACAGCTCAACAGCA  1 
MIT_Spar_c278_20970      (  504) GCAAAACAGCTCAACAGCA  1 
SGD_Scer_YOR176W         (  502) GCAAAACAGCTCAACAGCA  1 
MIT_Spar_c429_3020       (  110) GTAAAACAGCCCTGTACCA  1 
MIT_Smik_c193_2483       (  112) GTAATACAGCCCTGTACCA  1 
MIT_Smik_c935_20455      (  488) GTAAAACAGCTCAACAGCA  1 
WashU_Skud_Contig2050.4  (  505) ACAAAACAGCTCAACAGCA  1 
SGD_Scer_YDL205C         (  110) CTAATACAGCCCTGTACCA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 19 n= 7755 bayes= 9.59712 E= 3.6e-028 
  -169    -81    219   -997 
  -997    177   -997     30 
   162   -997   -997   -997 
   162   -997   -997   -997 
    89   -997   -997     30 
   162   -997   -997   -997 
  -997    251   -997   -997 
   162   -997   -997   -997 
  -997   -997    251   -997 
  -997    251   -997   -997 
  -997    151   -997     62 
  -997    251   -997   -997 
    62   -997   -997     62 
    62   -997    151   -997 
  -997    151   -997     62 
   162   -997   -997   -997 
  -997    151    151   -997 
  -997    251   -997   -997 
   162   -997   -997   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 19 nsites= 10 E= 3.6e-028 
 0.100000  0.100000  0.800000  0.000000 
 0.000000  0.600000  0.000000  0.400000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.600000  0.000000  0.000000  0.400000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
G[CT]AA[AT]ACAGC[CT]C[AT][AG][CT]A[CG]CA
--------------------------------------------------------------------------------




Time  6.58 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =  10   llr = 204   E-value = 3.8e-022
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  :::::3::3a5a5:a:a78:
pos.-specific     C  ::6:62:a::::55:a:::6
probability       G  :a:a:55:7::::::::31:
matrix            T  a:4:4:5:::5::5::::14

         bits    2.5  * *   *       *    
                 2.3  * *   *       *    
                 2.0  * *   *       *    
                 1.8  * *   *       *    
Information      1.5 ** *   * * *  ***   
content          1.3 *****  *** *  ***  *
(29.5 bits)      1.0 ***** **** ******* *
                 0.8 ********** *********
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TGCGCGGCGAAAACACAAAC
consensus              T TAT A T CT   G T
sequence                  C              
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig480.2       +    570  1.49e-12 TCTTTCGAAG TGCGCGTCGAAACCACAAAC CATCAAAAAT
WashU_Skud_Contig2050.4      +    565  1.49e-12 TCTTTCAAAG TGCGCGTCGAAACCACAAAC CGTCGAAAAT
MIT_Spar_c278_20970          +    559  1.49e-12 TCTTTCGAAT TGCGCGTCGAAACCACAAAC CGTCGAAAAT
SGD_Scer_YOR176W             +    557  1.49e-12 TCTTTCACAT TGCGCGTCGAAACCACAAAC CGTCGAAAAC
MIT_Smik_c935_20455          +    543  3.24e-11 TCTCTCCAAT TGCGCGTCAAAACCACAAAC CGTCGAAAAT
MIT_Smik_c193_2483           +    176  9.12e-10 AATCCAGCTA TGCGTAGCGATAATACAGAT GATTGTTTGA
MIT_Sbay_c841_3215           +    175  1.46e-09 AATCAAGTTA TGTGCCGCGATAATACAATC TTTTGGCCTA
WashU_Skud_Contig1850.5      +    173  3.07e-09 AATCAATCTA TGTGTCGCGATAATACAAGT GATTGATTGG
MIT_Spar_c429_3020           +    174  3.52e-09 ATCCAAGCTA TGTGTAGCAATAATACAGAT GATTGATTGG
SGD_Scer_YDL205C             +    174  3.52e-09 ATTCAGGCTA TGTGTAGCAATAATACAGAT AGTTAGTAGC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig480.2            1.5e-12  569_[+2]_138
WashU_Skud_Contig2050.4           1.5e-12  564_[+2]_143
MIT_Spar_c278_20970               1.5e-12  558_[+2]_149
SGD_Scer_YOR176W                  1.5e-12  556_[+2]_151
MIT_Smik_c935_20455               3.2e-11  542_[+2]_165
MIT_Smik_c193_2483                9.1e-10  175_[+2]_665
MIT_Sbay_c841_3215                1.5e-09  174_[+2]_666
WashU_Skud_Contig1850.5           3.1e-09  172_[+2]_668
MIT_Spar_c429_3020                3.5e-09  173_[+2]_667
SGD_Scer_YDL205C                  3.5e-09  173_[+2]_667
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=10
WashU_Sbay_Contig480.2   (  570) TGCGCGTCGAAACCACAAAC  1 
WashU_Skud_Contig2050.4  (  565) TGCGCGTCGAAACCACAAAC  1 
MIT_Spar_c278_20970      (  559) TGCGCGTCGAAACCACAAAC  1 
SGD_Scer_YOR176W         (  557) TGCGCGTCGAAACCACAAAC  1 
MIT_Smik_c935_20455      (  543) TGCGCGTCAAAACCACAAAC  1 
MIT_Smik_c193_2483       (  176) TGCGTAGCGATAATACAGAT  1 
MIT_Sbay_c841_3215       (  175) TGTGCCGCGATAATACAATC  1 
WashU_Skud_Contig1850.5  (  173) TGTGTCGCGATAATACAAGT  1 
MIT_Spar_c429_3020       (  174) TGTGTAGCAATAATACAGAT  1 
SGD_Scer_YDL205C         (  174) TGTGTAGCAATAATACAGAT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7745 bayes= 9.59526 E= 3.8e-022 
  -997   -997   -997    162 
  -997   -997    251   -997 
  -997    177   -997     30 
  -997   -997    251   -997 
  -997    177   -997     30 
   -11     19    151   -997 
  -997   -997    151     62 
  -997    251   -997   -997 
   -11   -997    199   -997 
   162   -997   -997   -997 
    62   -997   -997     62 
   162   -997   -997   -997 
    62    151   -997   -997 
  -997    151   -997     62 
   162   -997   -997   -997 
  -997    251   -997   -997 
   162   -997   -997   -997 
   111   -997     77   -997 
   130   -997    -81   -169 
  -997    177   -997     30 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.8e-022 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.600000  0.000000  0.400000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.600000  0.000000  0.400000 
 0.300000  0.200000  0.500000  0.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.300000  0.000000  0.700000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.700000  0.000000  0.300000  0.000000 
 0.800000  0.000000  0.100000  0.100000 
 0.000000  0.600000  0.000000  0.400000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
TG[CT]G[CT][GAC][GT]C[GA]A[AT]A[AC][CT]ACA[AG]A[CT]
--------------------------------------------------------------------------------




Time 12.80 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =  10   llr = 199   E-value = 1.7e-020
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  ::5:::a6a:9a91:1::::
pos.-specific     C  1a::5::::::::14::195
probability       G  ::5:::::::::18681:::
matrix            T  9::a5a:4:a1::::19915

         bits    2.5  *                  
                 2.3  *                  
                 2.0  *                * 
                 1.8  *                * 
Information      1.5  * * ** ** * ***  * 
content          1.3 ** * ** *********** 
(28.6 bits)      1.0 ******* ************
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TCATCTAAATAAAGGGTTCC
consensus              G T  T      C    T
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2050.4      +    600  3.79e-11 AAAATATTGA TCATCTAAATAAAGGGTTCT TATTTGCACA
MIT_Spar_c278_20970          +    594  3.79e-11 AAAATAATGG TCATCTAAATAAAGGGTTCT TATTTGAACA
SGD_Scer_YOR176W             +    592  3.79e-11 AAAACAATGG TCATCTAAATAAAGGGTTCT TATTAAACAG
WashU_Skud_Contig1850.5      +    205  4.47e-11 TTGATTGGTG TCGTTTATATAAAGCGTTCC TTCAATTTTT
MIT_Spar_c429_3020           +    206  4.47e-11 TTGATTGGCG TCGTTTATATAAAGCGTTCC TTCATTTTTT
SGD_Scer_YDL205C             +    205  4.47e-11 GTTAGTAGCC TCGTTTATATAAAGCGTTCC TTTACTTTTT
WashU_Sbay_Contig480.2       +    605  2.26e-10 AAAATATCGA CCATCTAAATAAAGGGTTCT TGTTTGAATA
MIT_Smik_c193_2483           +    208  5.94e-10 TTGTTTGATG TCGTTTATATTAAGCGTTCC TTCAGTTTTT
MIT_Sbay_c841_3215           +    207  2.13e-08 TTGGCCTATA TCGTTTAAATAAGCGTTCCT TTAATTTTTC
MIT_Smik_c935_20455          +    578  3.47e-08 AAAATAATGA TCATCTAAATAAAAGAGTTC ACGTTTTCAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2050.4           3.8e-11  599_[+3]_108
MIT_Spar_c278_20970               3.8e-11  593_[+3]_114
SGD_Scer_YOR176W                  3.8e-11  591_[+3]_116
WashU_Skud_Contig1850.5           4.5e-11  204_[+3]_636
MIT_Spar_c429_3020                4.5e-11  205_[+3]_635
SGD_Scer_YDL205C                  4.5e-11  204_[+3]_636
WashU_Sbay_Contig480.2            2.3e-10  604_[+3]_103
MIT_Smik_c193_2483                5.9e-10  207_[+3]_633
MIT_Sbay_c841_3215                2.1e-08  206_[+3]_634
MIT_Smik_c935_20455               3.5e-08  577_[+3]_130
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=10
WashU_Skud_Contig2050.4  (  600) TCATCTAAATAAAGGGTTCT  1 
MIT_Spar_c278_20970      (  594) TCATCTAAATAAAGGGTTCT  1 
SGD_Scer_YOR176W         (  592) TCATCTAAATAAAGGGTTCT  1 
WashU_Skud_Contig1850.5  (  205) TCGTTTATATAAAGCGTTCC  1 
MIT_Spar_c429_3020       (  206) TCGTTTATATAAAGCGTTCC  1 
SGD_Scer_YDL205C         (  205) TCGTTTATATAAAGCGTTCC  1 
WashU_Sbay_Contig480.2   (  605) CCATCTAAATAAAGGGTTCT  1 
MIT_Smik_c193_2483       (  208) TCGTTTATATTAAGCGTTCC  1 
MIT_Sbay_c841_3215       (  207) TCGTTTAAATAAGCGTTCCT  1 
MIT_Smik_c935_20455      (  578) TCATCTAAATAAAAGAGTTC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7745 bayes= 9.59526 E= 1.7e-020 
  -997    -81   -997    147 
  -997    251   -997   -997 
    62   -997    151   -997 
  -997   -997   -997    162 
  -997    151   -997     62 
  -997   -997   -997    162 
   162   -997   -997   -997 
    89   -997   -997     30 
   162   -997   -997   -997 
  -997   -997   -997    162 
   147   -997   -997   -169 
   162   -997   -997   -997 
   147   -997    -81   -997 
  -169    -81    219   -997 
  -997    119    177   -997 
  -169   -997    219   -169 
  -997   -997    -81    147 
  -997    -81   -997    147 
  -997    236   -997   -169 
  -997    151   -997     62 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 1.7e-020 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  1.000000  0.000000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.000000  0.000000  1.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.600000  0.000000  0.000000  0.400000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.900000  0.000000  0.000000  0.100000 
 1.000000  0.000000  0.000000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
 0.100000  0.100000  0.800000  0.000000 
 0.000000  0.400000  0.600000  0.000000 
 0.100000  0.000000  0.800000  0.100000 
 0.000000  0.000000  0.100000  0.900000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  0.900000  0.000000  0.100000 
 0.000000  0.500000  0.000000  0.500000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
TC[AG]T[CT]TA[AT]ATAAAG[GC]GTTC[CT]
--------------------------------------------------------------------------------




Time 19.05 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =  10   llr = 191   E-value = 6.7e-018
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  :975::45:a7::911:::9
pos.-specific     C  a1::76147::::169::::
probability       G  ::311:412:3:a:::::a1
matrix            T  :::4241:1::a::3:aa::

         bits    2.5 *           *     * 
                 2.3 *           *     * 
                 2.0 *           *  *  * 
                 1.8 *           *  *  * 
Information      1.5 *        * **  **** 
content          1.3 **  **  ** *** *****
(27.6 bits)      1.0 *** **  ****** *****
                 0.8 *** ** *************
                 0.5 *** ** *************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CAAACCAACAATGACCTTGA
consensus              GTTTGCG G   T     
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Sbay_c841_3215           +    145  1.51e-11 ATACGAACGC CAATCTGCCAATGACCTTGA AATCAAGTTA
MIT_Spar_c429_3020           +    144  1.51e-11 ACACGAGCCT CAATCTGCCAATGACCTTGA ATCCAAGCTA
SGD_Scer_YDL205C             +    144  1.51e-11 ACACGAGCGT CAATCTGCCAATGACCTTGA ATTCAGGCTA
MIT_Spar_c278_20970          +    123  1.17e-10 TGCTTGGTGC CAAACCAAGAGTGACCTTGA CCGACTAAAA
SGD_Scer_YOR176W             +    121  4.51e-10 TGTTTGGTGT CAAGCCAAGAGTGACCTTGA CCGACCAAAA
MIT_Smik_c935_20455          +    119  1.09e-09 CTTTAATGAT CAGACCAACAGTGATCTTGG CCGACCAAAA
WashU_Skud_Contig2050.4      +    124  2.63e-09 GTTTAATAAT CAGACCAACAATGATATTGA CCGACCAAAA
MIT_Smik_c193_2483           +    146  3.28e-09 ACACGAGCGC CAATTTGCCAATGAACTTGA AATCCAGCTA
WashU_Skud_Contig1850.5      +    143  8.39e-09 AACACGAACG CCAATCTGCAATGACCTTGA AATCAATCTA
WashU_Sbay_Contig480.2       +    168  3.20e-08 GTTTAGTAAG CAGAGCCATAATGCTCTTGA CCGACCAAAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Sbay_c841_3215                1.5e-11  144_[+4]_696
MIT_Spar_c429_3020                1.5e-11  143_[+4]_697
SGD_Scer_YDL205C                  1.5e-11  143_[+4]_697
MIT_Spar_c278_20970               1.2e-10  122_[+4]_585
SGD_Scer_YOR176W                  4.5e-10  120_[+4]_587
MIT_Smik_c935_20455               1.1e-09  118_[+4]_589
WashU_Skud_Contig2050.4           2.6e-09  123_[+4]_584
MIT_Smik_c193_2483                3.3e-09  145_[+4]_695
WashU_Skud_Contig1850.5           8.4e-09  142_[+4]_698
WashU_Sbay_Contig480.2            3.2e-08  167_[+4]_540
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=10
MIT_Sbay_c841_3215       (  145) CAATCTGCCAATGACCTTGA  1 
MIT_Spar_c429_3020       (  144) CAATCTGCCAATGACCTTGA  1 
SGD_Scer_YDL205C         (  144) CAATCTGCCAATGACCTTGA  1 
MIT_Spar_c278_20970      (  123) CAAACCAAGAGTGACCTTGA  1 
SGD_Scer_YOR176W         (  121) CAAGCCAAGAGTGACCTTGA  1 
MIT_Smik_c935_20455      (  119) CAGACCAACAGTGATCTTGG  1 
WashU_Skud_Contig2050.4  (  124) CAGACCAACAATGATATTGA  1 
MIT_Smik_c193_2483       (  146) CAATTTGCCAATGAACTTGA  1 
WashU_Skud_Contig1850.5  (  143) CCAATCTGCAATGACCTTGA  1 
WashU_Sbay_Contig480.2   (  168) CAGAGCCATAATGCTCTTGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7745 bayes= 9.59526 E= 6.7e-018 
  -997    251   -997   -997 
   147    -81   -997   -997 
   111   -997     77   -997 
    62   -997    -81     30 
  -997    199    -81    -70 
  -997    177   -997     30 
    30    -81    119   -169 
    62    119    -81   -997 
  -997    199     19   -169 
   162   -997   -997   -997 
   111   -997     77   -997 
  -997   -997   -997    162 
  -997   -997    251   -997 
   147    -81   -997   -997 
  -169    177   -997    -11 
  -169    236   -997   -997 
  -997   -997   -997    162 
  -997   -997   -997    162 
  -997   -997    251   -997 
   147   -997    -81   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 6.7e-018 
 0.000000  1.000000  0.000000  0.000000 
 0.900000  0.100000  0.000000  0.000000 
 0.700000  0.000000  0.300000  0.000000 
 0.500000  0.000000  0.100000  0.400000 
 0.000000  0.700000  0.100000  0.200000 
 0.000000  0.600000  0.000000  0.400000 
 0.400000  0.100000  0.400000  0.100000 
 0.500000  0.400000  0.100000  0.000000 
 0.000000  0.700000  0.200000  0.100000 
 1.000000  0.000000  0.000000  0.000000 
 0.700000  0.000000  0.300000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.900000  0.100000  0.000000  0.000000 
 0.100000  0.600000  0.000000  0.300000 
 0.100000  0.900000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
CA[AG][AT][CT][CT][AG][AC][CG]A[AG]TGA[CT]CTTGA
--------------------------------------------------------------------------------




Time 25.42 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =  10   llr = 190   E-value = 6.6e-017
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  219a56:::::19aa::15:
pos.-specific     C  ::1:541:1a11::::1::6
probability       G  :9::::::8::81::::1::
matrix            T  8:::::9a1:9::::a9854

         bits    2.5          *          
                 2.3          *          
                 2.0  *       *          
                 1.8  *       *          
Information      1.5  * *   *** * ***    
content          1.3  ***  ***********  *
(27.4 bits)      1.0 *****************  *
                 0.8 ****************** *
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TGAAAATTGCTGAAATTTAC
consensus            A   CC            TT
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1850.5      +    282  3.68e-11 TTTTCACTTT TGAAAATTGCTGAAATTTTC GTAGCAAAAA
MIT_Sbay_c841_3215           +    280  3.68e-11 TTTTTTCACT TGAAAATTGCTGAAATTTTC GTAGCTGAAA
MIT_Smik_c193_2483           +    285  3.68e-11 TTTTCACTTT TGAAAATTGCTGAAATTTTC GTAACAAAAA
SGD_Scer_YOR176W             +    415  1.86e-10 GTAAAGCTGT TGAACCTTCCTGAAATTTAC TTCTAAAATT
MIT_Spar_c429_3020           +    282  3.08e-10 TTTTCACTTT TGAAAACTGCTGAAATTTTC GTAGCAAAAA
SGD_Scer_YDL205C             +    281  3.80e-09 TTTTCACTTT AAAAAATTGCTGAAATTTTC GTAGCCAAAA
WashU_Skud_Contig2050.4      +    417  5.20e-09 TGCAAAATGT TGAACCTTTCCGAAATTTAT TGCCAGAAAC
MIT_Spar_c278_20970          +    418  5.20e-09 GTAAAGCTGT TGAACCTTGCTAAAATCTAT TACTATAATT
WashU_Sbay_Contig480.2       +    453  9.34e-09 CAGAGTTGGT TGAACCTTGCTCGAATTGAT AGCTCAAAGT
MIT_Smik_c935_20455          +    419  1.01e-08 AATATGCCAA AGCACATTGCTGAAATTAAT CAGTAAAGCT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1850.5           3.7e-11  281_[+5]_559
MIT_Sbay_c841_3215                3.7e-11  279_[+5]_561
MIT_Smik_c193_2483                3.7e-11  284_[+5]_556
SGD_Scer_YOR176W                  1.9e-10  414_[+5]_293
MIT_Spar_c429_3020                3.1e-10  281_[+5]_559
SGD_Scer_YDL205C                  3.8e-09  280_[+5]_560
WashU_Skud_Contig2050.4           5.2e-09  416_[+5]_291
MIT_Spar_c278_20970               5.2e-09  417_[+5]_290
WashU_Sbay_Contig480.2            9.3e-09  452_[+5]_255
MIT_Smik_c935_20455                 1e-08  418_[+5]_289
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=10
WashU_Skud_Contig1850.5  (  282) TGAAAATTGCTGAAATTTTC  1 
MIT_Sbay_c841_3215       (  280) TGAAAATTGCTGAAATTTTC  1 
MIT_Smik_c193_2483       (  285) TGAAAATTGCTGAAATTTTC  1 
SGD_Scer_YOR176W         (  415) TGAACCTTCCTGAAATTTAC  1 
MIT_Spar_c429_3020       (  282) TGAAAACTGCTGAAATTTTC  1 
SGD_Scer_YDL205C         (  281) AAAAAATTGCTGAAATTTTC  1 
WashU_Skud_Contig2050.4  (  417) TGAACCTTTCCGAAATTTAT  1 
MIT_Spar_c278_20970      (  418) TGAACCTTGCTAAAATCTAT  1 
WashU_Sbay_Contig480.2   (  453) TGAACCTTGCTCGAATTGAT  1 
MIT_Smik_c935_20455      (  419) AGCACATTGCTGAAATTAAT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7745 bayes= 9.59526 E= 6.6e-017 
   -70   -997   -997    130 
  -169   -997    236   -997 
   147    -81   -997   -997 
   162   -997   -997   -997 
    62    151   -997   -997 
    89    119   -997   -997 
  -997    -81   -997    147 
  -997   -997   -997    162 
  -997    -81    219   -169 
  -997    251   -997   -997 
  -997    -81   -997    147 
  -169    -81    219   -997 
   147   -997    -81   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
  -997   -997   -997    162 
  -997    -81   -997    147 
  -169   -997    -81    130 
    62   -997   -997     62 
  -997    177   -997     30 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 6.6e-017 
 0.200000  0.000000  0.000000  0.800000 
 0.100000  0.000000  0.900000  0.000000 
 0.900000  0.100000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.600000  0.400000  0.000000  0.000000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.100000  0.800000  0.100000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.100000  0.000000  0.900000 
 0.100000  0.100000  0.800000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.100000  0.000000  0.900000 
 0.100000  0.000000  0.100000  0.800000 
 0.500000  0.000000  0.000000  0.500000 
 0.000000  0.600000  0.000000  0.400000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
[TA]GAA[AC][AC]TTGCTGAAATTT[AT][CT]
--------------------------------------------------------------------------------




Time 31.23 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDL205C                 8.36e-26  109_[+1(5.89e-10)]_15_[+4(1.51e-11)]_10_[+2(3.52e-09)]_11_[+3(4.47e-11)]_56_[+5(3.80e-09)]_560
MIT_Spar_c429_3020               1.64e-27  109_[+1(1.14e-10)]_15_[+4(1.51e-11)]_10_[+2(3.52e-09)]_12_[+3(4.47e-11)]_56_[+5(3.08e-10)]_494_[+2(3.35e-05)]_22_[+5(2.99e-05)]_3
MIT_Smik_c193_2483               1.55e-25  111_[+1(1.56e-10)]_15_[+4(3.28e-09)]_10_[+2(9.12e-10)]_12_[+3(5.94e-10)]_57_[+5(3.68e-11)]_556
MIT_Sbay_c841_3215               1.09e-26  110_[+1(3.58e-11)]_15_[+4(1.51e-11)]_10_[+2(1.46e-09)]_12_[+3(2.13e-08)]_53_[+5(3.68e-11)]_561
WashU_Skud_Contig1850.5          2.56e-26  109_[+1(3.58e-11)]_14_[+4(8.39e-09)]_10_[+2(3.07e-09)]_12_[+3(4.47e-11)]_57_[+5(3.68e-11)]_559
SGD_Scer_YOR176W                 3.30e-30  120_[+4(4.51e-10)]_274_[+5(1.86e-10)]_67_[-1(6.04e-11)]_36_[+2(1.49e-12)]_15_[+3(3.79e-11)]_116
MIT_Spar_c278_20970              2.16e-29  122_[+4(1.17e-10)]_239_[+5(6.19e-05)]_16_[+5(5.20e-09)]_66_[-1(6.04e-11)]_36_[+2(1.49e-12)]_15_[+3(3.79e-11)]_114
MIT_Smik_c935_20455              1.31e-23  118_[+4(1.09e-09)]_280_[+5(1.01e-08)]_49_[-1(2.17e-10)]_36_[+2(3.24e-11)]_15_[+3(3.47e-08)]_130
WashU_Skud_Contig2050.4          3.42e-27  123_[+4(2.63e-09)]_235_[+1(5.68e-05)]_19_[+5(5.20e-09)]_68_[-1(5.56e-10)]_12_[+1(5.97e-05)]_10_[+2(1.49e-12)]_15_[+3(3.79e-11)]_108
WashU_Sbay_Contig480.2           4.20e-26  167_[+4(3.20e-08)]_265_[+5(9.34e-09)]_41_[-1(6.04e-11)]_37_[+2(1.49e-12)]_15_[+3(2.26e-10)]_103
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM3-HEM4.fa000444000766000024      2123013155576321 20013 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDL205C HEM3 "Phorphobilinogen deaminase, catalyzes the conversion of 4-porphobilinogen to hydroxymethylbilane, the third step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; expression is regulated by Hap2p-Hap3p"
AGTACGTGTGTATTTACCAACTACAAATTTATCTAGATTTTCTTCGCTTTTCTTTTTTTC
TATTGTTCTAGATATTAATACGGGATGAGAAGAACAGAATATTCAAAATCTAATACAGCC
CTGTACCATGCAAACACGAGCGTCAATCTGCCAATGACCTTGAATTCAGGCTATGTGTAG
CAATAATACAGATAGTTAGTAGCCTCGTTTATATAAAGCGTTCCTTTACTTTTTCATTTT
CTTTCTTTTTTTATGTTTGATTTTTTTACTTTTTCACTTTAAAAAATTGCTGAAATTTTC
GTAGCCAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCTCCC
CAGGGTCAATTGACAAGGAGAGAAGGAATGTTATATGGGAATTGCTGCGTAAAGATGGTC
AAAAATCCTGGACTGCCGTACGAACGACAATGTAAGGATGACTGCATTAGCCAGAAAGAC
ATCTTTACCCCCGGTGCTGCCAGGGAGCAAAATAATTACGAAAAGTGGACGCAAAGTTAA
CTTAAACTACAAGGGTAGCAGCAGAATGTGTCGGTGGTACCGGTGTGATAATGCCCCATT
TGAGATGCTTGTAATTGTGGCCTAGCAATAAGAACGCAAGGCGTTTTTGTTGAAAGGAGA
ACAAGGTTAGACGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTCACCCTTAT
TTCCACCCTCAAACGATAAAGCTTGCTACTTTGATGAAAAAAATATATAAAAGGGATTGA
AAAGCAGATCAATTATGTAGCAATAGTAGTAATAACTTGTTCAATTGCTTGTCTCAACTT
GCCACAAACTATCATCAACA
>MIT_Spar_c429_3020 YDL205C 5' untranslated region, Contig c429 77420 - 79419(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTATCAACTACAAAATTTATCTAGATTTTCTTGCCTTTTCCTTTTTC
TATTGTTCTAGATACTAATACGGGATGAGAAGAACAGAATATTCAAAATGTAAAACAGCC
CTGTACCATGCAAACACGAGCCTCAATCTGCCAATGACCTTGAATCCAAGCTATGTGTAG
CAATAATACAGATGATTGATTGGCGTCGTTTATATAAAGCGTTCCTTCATTTTTTTCATT
TTCTTTCTTTTTTTATGTTTGATTTTTTACTTTTTCACTTTTGAAAACTGCTGAAATTTT
CGTAGCAAAAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCT
CCCCAGGGTCAATTGACAAGGAGAGAAGGAATGTTACATCCAGGAATTGCGACATAAAGA
TGTCCAAGAAGTCTGAACTGTCATACGAATGGCTATGCAAGGAGGATAGTACTGGTCAAG
AAGACATCTTACCCCCGGTGCTGTCAGGGAGCAAAAAAATGACAAAAGTGGACGCAAAGT
TAACTTGAACTACAAGGGTAGCAACAGAATGTCGGTGGTACCGGATGTGACAAAGCTCAC
TTGAGGTGCTTCTTGTTGCGGCATAGCAATAAGAGCGCAAGGCGTTTTTATGGAAAGGAG
AGCGAGGTTAGAGGGTGACGTTTAGGCGCATAGGCAACCTCCCCTTATTGTTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGTCTACATTGATGAAAAAAATGTATAAAAGGGATT
GAAAAGCCGATCATGTGTGTAGCAATAGTAGTAGTTATACTTGTTCAATTGCTTGCTTGC
ACTTTTCCAAAAACTACCAC
>MIT_Smik_c193_2483 YDL205C 5' untranslated region, Contig c193 6380 - 8379(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTACCAACTATAAAATTTTACCTAGACTATCTGGCCTTTTTCTTTTT
TCTATTGTTCTAGATACTAATACGGGATGAAAAGAACAGAATATTCAAAAAGTAATACAG
CCCTGTACCATTCAAACACGAGCGCCAATTTGCCAATGAACTTGAAATCCAGCTATGCGT
AGCGATAATACAGATGATTGTTTGATGTCGTTTATATTAAGCGTTCCTTCAGTTTTTCTC
ATTTTCTTTCTTTTTCTATGTTTTATTTTTCACTTTTTCACTTTTGAAAATTGCTGAAAT
TTTCGTAACAAAAAAAGAGGCCTTCATTGCTTACTCATCGTTATCTTATTGGTTAAAATC
CCCAGCGACAATGTACAAGGAGAGAAGAAATGATATGTCTGGGAATTGCAGTTTGAAGAT
ATCCAAAGAGTTTTGAAGTGCCATACGAGCAACCACGTGAGAAGTAGAGCCTTAACAGAA
AATTCATCTTACCCCTAGTACTGCCAGGGAGGAACTAAACCTAAGAACTAGTGTTAACTT
GACTTGAACTGCAAGGGTAGCGACGGCGTATGTCGGTGGTACCGGATATGGCAAGAGCCC
ATTTGAGCTGCTTGTTCTTGTGACATACTATTAAGAGCGCAAGGCGTTTATGGAAAGGAG
GACAAGGTCAGAGGATGACGTTTAAGCGCATAGGCAATCTCCCCTTATTATTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGCTGCGCTGTTGAAAAGTATATAAAAGGGATAGAA
AAGCAGAGCAATTATAATTTAGTAGAATAGCTTATTCTATCGTTAACTTGTTGAAAGGAT
CAGATTATTATCAAGATGAA
>MIT_Sbay_c841_3215 YDL205C 5' untranslated region, Contig c841 7323 - 9322(revcom), 2000 bp (revcom)
AGTATGTGTATATTTACCAACTATAGAGTATATCTAGTATTTTTTTTCCTTCTTCTTTTT
CTATTGTTCTAGATGCTAATATGGGATGAGTAGAACAAAATATTCAAAACGCAATACAGC
CCTGTACCATTCAAATACGAACGCCAATCTGCCAATGACCTTGAAATCAAGTTATGTGCC
GCGATAATACAATCTTTTGGCCTATATCGTTTAAATAAGCGTTCCTTTAATTTTTCGGTT
TCTTTCTTTTTTATGTCTAATTTTTCATTTTTTTTCACTTGAAAATTGCTGAAATTTTCG
TAGCTGAAAAAGAGAGGCCTTCTTTGCTTACTCATCGTTATCTTATTGGTCAAGAGCCCA
AGGGACAATAGACAAGGAGAGAACCACCAACTTTGGGAGTTGGATGCAAAGAAGGTCTTT
GATTTTGGGCTGCTATCAGAGCGGGCCATATAAGGAAGCTTGTAGTGGTTAGGAGAGAAC
ACGTCATTACCCCCCTCCCCCTTCTCCGCGCTGCCAGGGACCAGGCAAGGGCTTGCAAGA
GATGAACGTAAGATAGAACTACGAGGGTCGCGGCCAATGTGTCGGTAGTACCGGATGGGG
CAAAGCCCAATTGAGGTGCTTGTTGTTGAGGATGGTCGGCATGGCATGGCATGGGAGGCC
AAAGGCGCTTTGTGGGAAGGAGAACAAACAACATTAGAGGGTGACGTTTTAGCGCATAGG
CAATCTCCCCTTATTGTTCACCCTTATTTCCACCCTCAAACGACAAGGCTTGTTATGTTG
GTTGGAAATATATAAAAGGGATTGAAAAAGATCATATTCCTACATAAATTATGGTATTAG
TTTTTCTTCAATTGCTGGCT
>WashU_Skud_Contig1850.5 YDL205C 5' untranslated region, Contig c1850 6875 - 8874(revcom), 2000 bp (revcom)
GATACGTGTGTATTTGCTAACTATAAAATTTATCTAGTTTTCCTGCTTTTTTTTTTTTCT
ATTGTTCTAGAAACTAATATGGGGATGAGAAGAACAAAATTTTCAAAAAGCAATACAGCC
CTGTACCATTCAAACACGAACGCCAATCTGCAATGACCTTGAAATCAATCTATGTGTCGC
GATAATACAAGTGATTGATTGGTGTCGTTTATATAAAGCGTTCCTTCAATTTTTTCATTT
TCTTTCTTTTTTTATGTTTAATTTTCTACCTTTTTCACTTTTGAAAATTGCTGAAATTTT
CGTAGCAAAAAAAGAGAGGCGTACGTTGCTTACTCATCGTTTTCTTATTGGTCAAAAGCT
CCAGGAACAATGCCCAAGGAGAGAAAGAGTGCTACGTCTAGGAATTGCGATGGAAAGGCG
TCCAAGAGTCCTAAACTACCATGAGAACGGGCCACCCAAGGAGGGATAGCAATTGCTGAA
ACAACATCTTCACCTTCGGAGCTGGCAGGGAGCAAGGGACTCTCCGGAAAGAAAGTGAAC
GCAAAACGGAACTACAAGGATAGCAACGGAATGTGTCGGTGGTAGCGGATGTGGCAAGAT
CCCATTTCAGGAGCTTGTTGTTACGGCACAGCAGCAAGAAGAGCACAAGGCTTTTTCCGT
AAAGGAGAACAAAGTTGGAAGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTC
ACCCTTATTTCCACCCTCAAAGGATAAAGCTTGTTGCATTGATAAAAAATGTATAAAAAG
GATGGGAAACAGATGATAGTTAACAAGGTAGTGGGACGGTCTTTCGCTTATTCAGTTGTG
TGACATTCAAGGGTTACAAT
>SGD_Scer_YOR278W HEM4 "Uroporphyrinogen III synthase, catalyzes the conversion of hydroxymethylbilane to uroporphyrinogen III, the fourth step in the heme biosynthetic pathway"
CTCTCGAGCAAGGTCTATTTTACCTTTCTGTTTCCTTATCCTTTGACACTAAAATTCAAA
AAACTCACTAGAAAGTTCACTAAAGCGCCTTAGCTGACTACAGCACAACCCAACCCCAAA
AACTAGTGAACTACACACTAAGAGAATTTATGGTATTTCCATAATTGAAGTATATGTACG
ATGTATACAATGTAAACAAGAGAGTAATGAAGTGAAGATATGTACACCTAGAGCGAACCA
ATGATAATTTGTTTTCTTAATTAAGAAAAACCATTAAAACTGGATTAGATTTCAATAATG
AAAAGCTAGGAACAAAAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGACATA
TGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGTTTT
CTTATCCTGAAGGATCCTGCAAATGAAGTAAGTTCAAAGAATTGAAATGAAATCGCCTTT
TATACCCTCGCCGCACCAAGGAGCGCGCTGTGAAAATTTTTCGCTTTATCTCTTAGGGCT
CCTACTGTCGGTAGAGAAAAGTTGAGTATATTTAAAGCATGAGGTAACTTTTCTGCCCAT
TTTTACTTCTATTTCCATTTGAATTCAGAAAAGTG
>MIT_Spar_c261_21317 YOR278W 5' untranslated region, Contig c261 32269 - 34268, 2000 bp (revcom)
CGTTCCAAGCAGGGTTTATTCTATTTCTCGGCTCCTTTACCCTGTAACTTCGAGATTCAA
AAACTCGCTATAACTTCACTAAAGCGCTTTAGTTGACTACAACACAACCCAACCCCAAAA
TAAACTGTCCAACTACACAATACCGAGGATAATCCACGATATTTCGGTGATTGAAGTATA
TGTATTACGTATGCAATGTAAGCAAGAAACTAACAAAATGAATATGTACACCTAGAGCGA
ACCAATGATAATTTGTTTTCTTAATAAAGAAAAACTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAACAGAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGAC
ATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGT
TCTTTTATCCTGAAGGATAAACGGAAAGCTCCCGATTAAAAACAAGTATAGAGTACTGGA
ATAGAATCGCCTTTTATACCCTCCCTCGCCGCATCAAGAAGCGCGCTGTGAAAATTTTTC
GTTTTTCTCTTAGGGCTCCCATCCAACTGTCGGCGAGGAAAAGTTGTATATATTTAAAGC
ATGAGGTAACTTTGTTGCCCATTATCTTTTTTGTT
>MIT_Smik_c492_20940 YOR278W 5' untranslated region, Contig c492 3260 - 5259(revcom), 2000 bp (revcom)
ACTTTCAAACACACTCTGGTGTACTCCTCGGTCCCTTCATCTCATTTCTTCAAGATGCAG
AACTTCGCCGGAAGTAAACTAAAGTGCTTTAATTAATCAAAAGACAACTTAATTCCCAAA
CGGAAATGCAGGCTAGACAAACCGAAGATAATCCCCGATATTTCTGAGTTTAACAAATGT
ATGTATAATATGTATGCAATGTAGGCAAGAAAATAACGAAGTGAAGATATGTACACCTAG
AGCGAACCAATAATAATTTGTTTTCTTACTAAAGAAAAACTATTAAAACTGGATTAGATT
TCAATAATGAAAAGCTAGGAACAAAAGAAATTTGTCTACTTCCAGCCATTTGCGCTTTAT
ATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAAT
GATGGTTCTTTTAAACCAAAATTTAAAGAAAAATCTTAACGGTAATATGAGTAGGAGGTT
GGAATGGGATCGCTTTTTATACCCTCATTGTGATAAGAGACGCGCAGTGAAAAATTTTCG
CTTTTTCTTAGGGCTCCTATCTAACTCTCGGGCGAATAAATATCATGAATGTATTTAAAC
GTCAAGTTAGTTAAATGTTTGAGTCTGTTTCTTTT
>WashU_Skud_Contig1682.4 YOR278W 5' untranslated region, Contig c1682 3379 - 5378, 2000 bp (revcom)
CTCTTCAAACAGACTCCAATTCACTACTGAGCTCTTACCTTGTGACTTCAAGACTCACTA
CTCAGTTGAAAGACACGCTCAGTACCAAATTCGGCTGCGAGGCAACTAACGCCTTTAAAC
AGGTAGGTAAGGAACAATACCGAAAGGCCATCTCCGATGTTTCGAAGATTGGCAAATGTA
TATATTATGTATGCAATATAGGCAAGATGATAACGAAGTAGAGATATGTACACCTAGAGC
GAACCAATGATAATTTGTTTTCTTAATGAAGAAAGTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAATAAAAGAGATTGGTCTACTTCCAGCCATTTGCGCTTTACATAGA
CATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGG
TTCTATTTAAAATGAAATCTAAAGATAAACCCTAGTCATAATCAAGTGGGTTGTGTTAAA
ATACAAGCACCTTTTATACTCTCGCAGCGTCAGTGGCGCGTTGTGAAAAATTTTCACTTT
TTCTCAGGGCTTTTACCCAACTGCCGACAAATAAAAGCCGTATTTAAGGAATGTGATTAG
TTTACTTTCCAATGCTTTCTCTTTTTTGTAGGGTA
>WashU_Sbay_Contig635.57 YOR278W 5' untranslated region, Contig c635 91073 - 93072, 2000 bp (revcom)
ACGTACAGATGGCGTCTCCTCCTTTCGCGAGCCCCTTGCCTTGTGACTTCAGCCTAACTT
CTTGACTAGAAGATACAACAAGAAATACTCAAATCGGTTATTGTGCAACTCATCCCTCAG
ACAGTTTGGTAAGAAACACCGAAGACTATTTCCGATATCTCAAAGAATGACAAAAGTATA
CATTATATATGCAAGAGAGGCAAGAAAAGAGTAAAAAAGAGTAAAAAAAACATGTACACC
TAGAGCGAACCAGTGATAATTTGCTTCTCAATGAAGAAAAAGCGATTAAAACTGGATTAG
ATTTCATTAAAGAAAAGCTAGGAACAAAGAAATTGGTCTACTTCCAGCCATTTGCGCTTG
ACATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGA
ATGATGGCTCTTTTAAATTGAGATCTAAAAGAAATATCCTGGAAAAGAGTAGAGAAGAGT
CCAAACTGTAGGAATTCAATCGCTTTTTATACTCTCATCGCGGAAAAGACGCGCTGTGAA
AAATTTTCTCTTTTTCTTAGGGCTCCTATCCAGCTGCCTGCGAACAAAAGCCGTATTTAA
AGCATGATTTTCACTACTATGTATGTTCTTTCTGC
BioPerl-1.007002/t/data/map_hem/HEM3-HEM4.meme.txt000444000766000024     11711113155576321 21212 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM3-HEM4.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDL205C         1.0000    860  MIT_Spar_c429_3020       1.0000    860  
MIT_Smik_c193_2483       1.0000    860  MIT_Sbay_c841_3215       1.0000    860  
WashU_Skud_Contig1850.5  1.0000    860  SGD_Scer_YOR278W         1.0000    635  
MIT_Spar_c261_21317      1.0000    635  MIT_Smik_c492_20940      1.0000    635  
WashU_Skud_Contig1682.4  1.0000    635  WashU_Sbay_Contig635.57  1.0000    635  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM3-HEM4.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=       10    maxsites=       10    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            7475    N=              10
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.310 C 0.190 G 0.190 T 0.310 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =  10   llr = 217   E-value = 9.7e-028
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  5:a:::5:::5::5:::a5a
pos.-specific     C  5a::aa5::::a55::5:2:
probability       G  :::a::::5:5:5::21:::
matrix            T  :::::::a5a::::a84:3:

         bits    2.5  * ***     *        
                 2.3  * ***     *        
                 2.0  * ***     *        
                 1.8  * ***     *        
Information      1.5  ***** * * ** *  * *
content          1.3  ***** * * ** *  * *
(31.3 bits)      1.0 **************** * *
                 0.8 ****************** *
                 0.5 ****************** *
                 0.3 ********************
                 0.0 --------------------

Multilevel           ACAGCCATGTACCATTCAAA
consensus            C     C T G GC GT T 
sequence                               C 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1850.5      +    115  4.59e-11 AAAAAGCAAT ACAGCCCTGTACCATTCAAA CACGAACGCC
MIT_Sbay_c841_3215           +    116  4.59e-11 AAAACGCAAT ACAGCCCTGTACCATTCAAA TACGAACGCC
MIT_Smik_c193_2483           +    117  4.59e-11 AAAAAGTAAT ACAGCCCTGTACCATTCAAA CACGAGCGCC
WashU_Skud_Contig1682.4      +    337  1.14e-10 TGGTCTACTT CCAGCCATTTGCGCTTTACA TAGACATATG
MIT_Smik_c492_20940          +    342  1.41e-10 TTGTCTACTT CCAGCCATTTGCGCTTTATA TAGACATATG
MIT_Spar_c261_21317          +    336  1.41e-10 TGGTCTACTT CCAGCCATTTGCGCTTTATA TAGACATATG
SGD_Scer_YOR278W             +    333  1.41e-10 TGGTCTACTT CCAGCCATTTGCGCTTTATA TAGACATATG
MIT_Spar_c429_3020           +    115  1.41e-10 AAAATGTAAA ACAGCCCTGTACCATGCAAA CACGAGCCTC
SGD_Scer_YDL205C             +    115  1.41e-10 AAAATCTAAT ACAGCCCTGTACCATGCAAA CACGAGCGTC
WashU_Sbay_Contig635.57      +    344  2.72e-10 TGGTCTACTT CCAGCCATTTGCGCTTGACA TAGACATATG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1850.5           4.6e-11  114_[+1]_726
MIT_Sbay_c841_3215                4.6e-11  115_[+1]_725
MIT_Smik_c193_2483                4.6e-11  116_[+1]_724
WashU_Skud_Contig1682.4           1.1e-10  336_[+1]_279
MIT_Smik_c492_20940               1.4e-10  341_[+1]_274
MIT_Spar_c261_21317               1.4e-10  335_[+1]_280
SGD_Scer_YOR278W                  1.4e-10  332_[+1]_283
MIT_Spar_c429_3020                1.4e-10  114_[+1]_726
SGD_Scer_YDL205C                  1.4e-10  114_[+1]_726
WashU_Sbay_Contig635.57           2.7e-10  343_[+1]_272
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=10
WashU_Skud_Contig1850.5  (  115) ACAGCCCTGTACCATTCAAA  1 
MIT_Sbay_c841_3215       (  116) ACAGCCCTGTACCATTCAAA  1 
MIT_Smik_c193_2483       (  117) ACAGCCCTGTACCATTCAAA  1 
WashU_Skud_Contig1682.4  (  337) CCAGCCATTTGCGCTTTACA  1 
MIT_Smik_c492_20940      (  342) CCAGCCATTTGCGCTTTATA  1 
MIT_Spar_c261_21317      (  336) CCAGCCATTTGCGCTTTATA  1 
SGD_Scer_YOR278W         (  333) CCAGCCATTTGCGCTTTATA  1 
MIT_Spar_c429_3020       (  115) ACAGCCCTGTACCATGCAAA  1 
SGD_Scer_YDL205C         (  115) ACAGCCCTGTACCATGCAAA  1 
WashU_Sbay_Contig635.57  (  344) CCAGCCATTTGCGCTTGACA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7285 bayes= 9.5068 E= 9.7e-028 
    62    151   -997   -997 
  -997    251   -997   -997 
   162   -997   -997   -997 
  -997   -997    251   -997 
  -997    251   -997   -997 
  -997    251   -997   -997 
    62    151   -997   -997 
  -997   -997   -997    162 
  -997   -997    151     62 
  -997   -997   -997    162 
    62   -997    151   -997 
  -997    251   -997   -997 
  -997    151    151   -997 
    62    151   -997   -997 
  -997   -997   -997    162 
  -997   -997     19    130 
  -997    151    -81     30 
   162   -997   -997   -997 
    62     19   -997    -11 
   162   -997   -997   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 9.7e-028 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.200000  0.800000 
 0.000000  0.500000  0.100000  0.400000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.200000  0.000000  0.300000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
[AC]CAGCC[AC]T[GT]T[AG]C[CG][AC]T[TG][CT]A[ATC]A
--------------------------------------------------------------------------------




Time  5.67 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =  10   llr = 211   E-value = 3.2e-025
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  8::::::a5::a::::57::
pos.-specific     C  ::::a:::5:a::5:::::a
probability       G  1:55:::::5:::5a2::::
matrix            T  1a55:aa::5::a::853a:

         bits    2.5     *     *   *    *
                 2.3     *     *   *    *
                 2.0     *     *   *    *
                 1.8     *     *   *    *
Information      1.5  *  ****  *****   **
content          1.3  *  ****  *****   **
(30.4 bits)      1.0  ***************  **
                 0.8 **************** ***
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           ATGGCTTAAGCATCGTAATC
consensus              TT    CT   G GTT  
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      +    382  8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
WashU_Skud_Contig1682.4      +    375  8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
MIT_Smik_c492_20940          +    380  8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
MIT_Spar_c261_21317          +    374  8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
SGD_Scer_YOR278W             +    371  8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
MIT_Smik_c193_2483           +    326  8.08e-11 AGAGGCCTTC ATTGCTTACTCATCGTTATC TTATTGGTTA
MIT_Spar_c429_3020           +    325  5.11e-10 AAAGACCTTC ATTGCTTACTCATCGGTTTC TTATTGGTCA
SGD_Scer_YDL205C             +    322  5.11e-10 AAAGACCTTC ATTGCTTACTCATCGGTTTC TTATTGGTCA
MIT_Sbay_c841_3215           +    323  6.64e-10 AGAGGCCTTC TTTGCTTACTCATCGTTATC TTATTGGTCA
WashU_Skud_Contig1850.5      +    325  7.76e-10 AGAGGCGTAC GTTGCTTACTCATCGTTTTC TTATTGGTCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           8.1e-11  381_[+2]_234
WashU_Skud_Contig1682.4           8.1e-11  374_[+2]_241
MIT_Smik_c492_20940               8.1e-11  379_[+2]_236
MIT_Spar_c261_21317               8.1e-11  373_[+2]_242
SGD_Scer_YOR278W                  8.1e-11  370_[+2]_245
MIT_Smik_c193_2483                8.1e-11  325_[+2]_515
MIT_Spar_c429_3020                5.1e-10  324_[+2]_516
SGD_Scer_YDL205C                  5.1e-10  321_[+2]_519
MIT_Sbay_c841_3215                6.6e-10  322_[+2]_518
WashU_Skud_Contig1850.5           7.8e-10  324_[+2]_516
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=10
WashU_Sbay_Contig635.57  (  382) ATGTCTTAAGCATGGTAATC  1 
WashU_Skud_Contig1682.4  (  375) ATGTCTTAAGCATGGTAATC  1 
MIT_Smik_c492_20940      (  380) ATGTCTTAAGCATGGTAATC  1 
MIT_Spar_c261_21317      (  374) ATGTCTTAAGCATGGTAATC  1 
SGD_Scer_YOR278W         (  371) ATGTCTTAAGCATGGTAATC  1 
MIT_Smik_c193_2483       (  326) ATTGCTTACTCATCGTTATC  1 
MIT_Spar_c429_3020       (  325) ATTGCTTACTCATCGGTTTC  1 
SGD_Scer_YDL205C         (  322) ATTGCTTACTCATCGGTTTC  1 
MIT_Sbay_c841_3215       (  323) TTTGCTTACTCATCGTTATC  1 
WashU_Skud_Contig1850.5  (  325) GTTGCTTACTCATCGTTTTC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7285 bayes= 9.5068 E= 3.2e-025 
   130   -997    -81   -169 
  -997   -997   -997    162 
  -997   -997    151     62 
  -997   -997    151     62 
  -997    251   -997   -997 
  -997   -997   -997    162 
  -997   -997   -997    162 
   162   -997   -997   -997 
    62    151   -997   -997 
  -997   -997    151     62 
  -997    251   -997   -997 
   162   -997   -997   -997 
  -997   -997   -997    162 
  -997    151    151   -997 
  -997   -997    251   -997 
  -997   -997     19    130 
    62   -997   -997     62 
   111   -997   -997    -11 
  -997   -997   -997    162 
  -997    251   -997   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.2e-025 
 0.800000  0.000000  0.100000  0.100000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.200000  0.800000 
 0.500000  0.000000  0.000000  0.500000 
 0.700000  0.000000  0.000000  0.300000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
AT[GT][GT]CTTA[AC][GT]CAT[CG]G[TG][AT][AT]TC
--------------------------------------------------------------------------------




Time 11.21 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =  10   llr = 207   E-value = 5.5e-024
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :519a:a5:a255:9:::aa
pos.-specific     C  5:::::::a::::::::5::
probability       G  559::a::::8::::::5::
matrix            T  :::1:::5:::55a1aa:::

         bits    2.5      *  *           
                 2.3      *  *           
                 2.0   *  *  *           
                 1.8   *  *  *           
Information      1.5 * * *** ***  * *****
content          1.3 * ***** ***  *******
(29.8 bits)      1.0 ******* ***  *******
                 0.8 ******* ***  *******
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CAGAAGAACAGAATATTCAA
consensus            GG     T  ATT    G  
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      +    402  7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGCTCT
WashU_Skud_Contig1682.4      +    395  7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGTTCT
MIT_Smik_c492_20940          +    400  7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGTTCT
MIT_Spar_c261_21317          +    394  7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGTTCT
SGD_Scer_YOR278W             +    391  7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGTTTT
MIT_Spar_c429_3020           +     87  2.07e-10 AATACGGGAT GAGAAGAACAGAATATTCAA AATGTAAAAC
SGD_Scer_YDL205C             +     87  2.07e-10 AATACGGGAT GAGAAGAACAGAATATTCAA AATCTAATAC
MIT_Smik_c193_2483           +     89  1.38e-09 AATACGGGAT GAAAAGAACAGAATATTCAA AAAGTAATAC
WashU_Skud_Contig1850.5      +     87  2.47e-09 ATATGGGGAT GAGAAGAACAAAATTTTCAA AAAGCAATAC
MIT_Sbay_c841_3215           +     88  2.47e-09 AATATGGGAT GAGTAGAACAAAATATTCAA AACGCAATAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           7.3e-11  401_[+3]_214
WashU_Skud_Contig1682.4           7.3e-11  394_[+3]_221
MIT_Smik_c492_20940               7.3e-11  399_[+3]_216
MIT_Spar_c261_21317               7.3e-11  393_[+3]_222
SGD_Scer_YOR278W                  7.3e-11  390_[+3]_225
MIT_Spar_c429_3020                2.1e-10  86_[+3]_754
SGD_Scer_YDL205C                  2.1e-10  86_[+3]_754
MIT_Smik_c193_2483                1.4e-09  88_[+3]_752
WashU_Skud_Contig1850.5           2.5e-09  86_[+3]_754
MIT_Sbay_c841_3215                2.5e-09  87_[+3]_753
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=10
WashU_Sbay_Contig635.57  (  402) CGGAAGATCAGTTTATTGAA  1 
WashU_Skud_Contig1682.4  (  395) CGGAAGATCAGTTTATTGAA  1 
MIT_Smik_c492_20940      (  400) CGGAAGATCAGTTTATTGAA  1 
MIT_Spar_c261_21317      (  394) CGGAAGATCAGTTTATTGAA  1 
SGD_Scer_YOR278W         (  391) CGGAAGATCAGTTTATTGAA  1 
MIT_Spar_c429_3020       (   87) GAGAAGAACAGAATATTCAA  1 
SGD_Scer_YDL205C         (   87) GAGAAGAACAGAATATTCAA  1 
MIT_Smik_c193_2483       (   89) GAAAAGAACAGAATATTCAA  1 
WashU_Skud_Contig1850.5  (   87) GAGAAGAACAAAATTTTCAA  1 
MIT_Sbay_c841_3215       (   88) GAGTAGAACAAAATATTCAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7285 bayes= 9.5068 E= 5.5e-024 
  -997    151    151   -997 
    62   -997    151   -997 
  -169   -997    236   -997 
   147   -997   -997   -169 
   162   -997   -997   -997 
  -997   -997    251   -997 
   162   -997   -997   -997 
    62   -997   -997     62 
  -997    251   -997   -997 
   162   -997   -997   -997 
   -70   -997    219   -997 
    62   -997   -997     62 
    62   -997   -997     62 
  -997   -997   -997    162 
   147   -997   -997   -169 
  -997   -997   -997    162 
  -997   -997   -997    162 
  -997    151    151   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.5e-024 
 0.000000  0.500000  0.500000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.100000  0.000000  0.900000  0.000000 
 0.900000  0.000000  0.000000  0.100000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.200000  0.000000  0.800000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.500000  0.000000  0.000000  0.500000 
 0.000000  0.000000  0.000000  1.000000 
 0.900000  0.000000  0.000000  0.100000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.500000  0.500000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
[CG][AG]GAAGA[AT]CA[GA][AT][AT]TATT[CG]AA
--------------------------------------------------------------------------------




Time 16.58 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   15   sites =  10   llr = 165   E-value = 1.7e-014
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  9:555:a:5:aa11a
pos.-specific     C  1a5:::::5:::66:
probability       G  ::::5a:a:a::33:
matrix            T  :::5:::::::::::

         bits    2.5  *   * * *     
                 2.3  *   * * *     
                 2.0  *   * * *     
                 1.8  *   * * *     
Information      1.5  *   *** ***  *
content          1.3 **   *** ***  *
(23.9 bits)      1.0 *** ***********
                 0.8 *** ***********
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           ACAAAGAGAGAACCA
consensus              CTG   C   GG 
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Sbay_Contig635.57      +    238  2.42e-09 AAACATGTAC ACCTAGAGCGAACCA GTGATAATTT
WashU_Skud_Contig1682.4      +    232  2.42e-09 AGATATGTAC ACCTAGAGCGAACCA ATGATAATTT
MIT_Smik_c492_20940          +    235  2.42e-09 AGATATGTAC ACCTAGAGCGAACCA ATAATAATTT
MIT_Spar_c261_21317          +    230  2.42e-09 GAATATGTAC ACCTAGAGCGAACCA ATGATAATTT
SGD_Scer_YOR278W             +    226  2.42e-09 AGATATGTAC ACCTAGAGCGAACCA ATGATAATTT
MIT_Sbay_c841_3215           +    372  6.95e-09 GGGACAATAG ACAAGGAGAGAACCA CCAACTTTGG
MIT_Spar_c429_3020           +    376  3.49e-08 GGGTCAATTG ACAAGGAGAGAAGGA ATGTTACATC
SGD_Scer_YDL205C             +    373  3.49e-08 GGGTCAATTG ACAAGGAGAGAAGGA ATGTTATATG
MIT_Smik_c193_2483           +    375  1.07e-07 GCGACAATGT ACAAGGAGAGAAGAA ATGATATGTC
WashU_Skud_Contig1850.5      +    374  1.53e-07 GGAACAATGC CCAAGGAGAGAAAGA GTGCTACGTC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           2.4e-09  237_[+4]_383
WashU_Skud_Contig1682.4           2.4e-09  231_[+4]_389
MIT_Smik_c492_20940               2.4e-09  234_[+4]_386
MIT_Spar_c261_21317               2.4e-09  229_[+4]_391
SGD_Scer_YOR278W                  2.4e-09  225_[+4]_395
MIT_Sbay_c841_3215                6.9e-09  371_[+4]_474
MIT_Spar_c429_3020                3.5e-08  375_[+4]_470
SGD_Scer_YDL205C                  3.5e-08  372_[+4]_473
MIT_Smik_c193_2483                1.1e-07  374_[+4]_471
WashU_Skud_Contig1850.5           1.5e-07  373_[+4]_472
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=15 seqs=10
WashU_Sbay_Contig635.57  (  238) ACCTAGAGCGAACCA  1 
WashU_Skud_Contig1682.4  (  232) ACCTAGAGCGAACCA  1 
MIT_Smik_c492_20940      (  235) ACCTAGAGCGAACCA  1 
MIT_Spar_c261_21317      (  230) ACCTAGAGCGAACCA  1 
SGD_Scer_YOR278W         (  226) ACCTAGAGCGAACCA  1 
MIT_Sbay_c841_3215       (  372) ACAAGGAGAGAACCA  1 
MIT_Spar_c429_3020       (  376) ACAAGGAGAGAAGGA  1 
SGD_Scer_YDL205C         (  373) ACAAGGAGAGAAGGA  1 
MIT_Smik_c193_2483       (  375) ACAAGGAGAGAAGAA  1 
WashU_Skud_Contig1850.5  (  374) CCAAGGAGAGAAAGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 7335 bayes= 9.51668 E= 1.7e-014 
   147    -81   -997   -997 
  -997    251   -997   -997 
    62    151   -997   -997 
    62   -997   -997     62 
    62   -997    151   -997 
  -997   -997    251   -997 
   162   -997   -997   -997 
  -997   -997    251   -997 
    62    151   -997   -997 
  -997   -997    251   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
  -169    177     77   -997 
  -169    177     77   -997 
   162   -997   -997   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 1.7e-014 
 0.900000  0.100000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.100000  0.600000  0.300000  0.000000 
 0.100000  0.600000  0.300000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
AC[AC][AT][AG]GAG[AC]GAA[CG][CG]A
--------------------------------------------------------------------------------




Time 21.88 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =  10   llr = 194   E-value = 4.5e-019
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  aaaa:55a:5aa454a88a9
pos.-specific     C  :::::5::::::51::::::
probability       G  ::::a:::a5::::6:22:1
matrix            T  ::::::5:::::14::::::

         bits    2.5     *   *           
                 2.3     *   *           
                 2.0     *   *           
                 1.8     *   *           
Information      1.5 *****  ** **   *  * 
content          1.3 *****  ** **  **  **
(28.0 bits)      1.0 ****** *****  ******
                 0.8 ****** ****** ******
                 0.5 ************* ******
                 0.3 ********************
                 0.0 --------------------

Multilevel           AAAAGAAAGAAACAGAAAAA
consensus                 CT  G  ATA GG  
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c261_21317          +    305  8.38e-12 TTCAATAATG AAAAGCTAGGAACAGAAAAA TTGGTCTACT
SGD_Scer_YOR278W             +    301  1.32e-10 TTCAATAATG AAAAGCTAGGAACAAAAAAA ATTGGTCTAC
WashU_Sbay_Contig635.57      +    313  5.24e-10 TTCATTAAAG AAAAGCTAGGAACAAAGAAA TTGGTCTACT
MIT_Smik_c492_20940          +    310  5.24e-10 TTCAATAATG AAAAGCTAGGAACAAAAGAA ATTTGTCTAC
MIT_Sbay_c841_3215           -    231  9.80e-10 TTAGACATAA AAAAGAAAGAAACCGAAAAA TTAAAGGAAC
WashU_Skud_Contig1850.5      -    231  1.03e-09 TAAACATAAA AAAAGAAAGAAAATGAAAAA ATTGAAGGAA
MIT_Spar_c429_3020           -    232  1.03e-09 CAAACATAAA AAAAGAAAGAAAATGAAAAA AATGAAGGAA
SGD_Scer_YDL205C             -    230  1.03e-09 CAAACATAAA AAAAGAAAGAAAATGAAAAA GTAAAGGAAC
MIT_Smik_c193_2483           -    235  2.33e-09 AAAACATAGA AAAAGAAAGAAAATGAGAAA AACTGAAGGA
WashU_Skud_Contig1682.4      +    305  7.25e-09 TTCAATAATG AAAAGCTAGGAATAAAAGAG ATTGGTCTAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c261_21317               8.4e-12  304_[+5]_311
SGD_Scer_YOR278W                  1.3e-10  300_[+5]_315
WashU_Sbay_Contig635.57           5.2e-10  312_[+5]_303
MIT_Smik_c492_20940               5.2e-10  309_[+5]_306
MIT_Sbay_c841_3215                9.8e-10  230_[-5]_610
WashU_Skud_Contig1850.5             1e-09  230_[-5]_610
MIT_Spar_c429_3020                  1e-09  231_[-5]_609
SGD_Scer_YDL205C                    1e-09  229_[-5]_611
MIT_Smik_c193_2483                2.3e-09  234_[-5]_606
WashU_Skud_Contig1682.4           7.3e-09  304_[+5]_311
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=10
MIT_Spar_c261_21317      (  305) AAAAGCTAGGAACAGAAAAA  1 
SGD_Scer_YOR278W         (  301) AAAAGCTAGGAACAAAAAAA  1 
WashU_Sbay_Contig635.57  (  313) AAAAGCTAGGAACAAAGAAA  1 
MIT_Smik_c492_20940      (  310) AAAAGCTAGGAACAAAAGAA  1 
MIT_Sbay_c841_3215       (  231) AAAAGAAAGAAACCGAAAAA  1 
WashU_Skud_Contig1850.5  (  231) AAAAGAAAGAAAATGAAAAA  1 
MIT_Spar_c429_3020       (  232) AAAAGAAAGAAAATGAAAAA  1 
SGD_Scer_YDL205C         (  230) AAAAGAAAGAAAATGAAAAA  1 
MIT_Smik_c193_2483       (  235) AAAAGAAAGAAAATGAGAAA  1 
WashU_Skud_Contig1682.4  (  305) AAAAGCTAGGAATAAAAGAG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7285 bayes= 9.5068 E= 4.5e-019 
   162   -997   -997   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
  -997   -997    251   -997 
    62    151   -997   -997 
    62   -997   -997     62 
   162   -997   -997   -997 
  -997   -997    251   -997 
    62   -997    151   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
    30    151   -997   -169 
    62    -81   -997     30 
    30   -997    177   -997 
   162   -997   -997   -997 
   130   -997     19   -997 
   130   -997     19   -997 
   162   -997   -997   -997 
   147   -997    -81   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 4.5e-019 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.400000  0.500000  0.000000  0.100000 
 0.500000  0.100000  0.000000  0.400000 
 0.400000  0.000000  0.600000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.800000  0.000000  0.200000  0.000000 
 0.800000  0.000000  0.200000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
AAAAG[AC][AT]AG[AG]AA[CA][AT][GA]A[AG][AG]AA
--------------------------------------------------------------------------------




Time 27.05 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDL205C                 6.52e-24  48_[-5(3.42e-05)]_18_[+3(2.07e-10)]_8_[+1(1.41e-10)]_95_[-5(1.03e-09)]_72_[+2(5.11e-10)]_31_[+4(3.49e-08)]_473
MIT_Spar_c429_3020               6.52e-24  86_[+3(2.07e-10)]_8_[+1(1.41e-10)]_97_[-5(1.03e-09)]_11_[-5(7.48e-05)]_42_[+2(5.11e-10)]_31_[+4(3.49e-08)]_430_[-5(9.37e-05)]_20
MIT_Smik_c193_2483               1.47e-23  88_[+3(1.38e-09)]_8_[+1(4.59e-11)]_98_[-5(2.33e-09)]_11_[-5(5.68e-05)]_40_[+2(8.08e-11)]_29_[+4(1.07e-07)]_410_[+3(7.71e-05)]_41
MIT_Sbay_c841_3215               6.24e-24  49_[-5(2.22e-05)]_18_[+3(2.47e-09)]_8_[+1(4.59e-11)]_95_[-5(9.80e-10)]_10_[-5(1.66e-05)]_42_[+2(6.64e-10)]_29_[+4(6.95e-09)]_474
WashU_Skud_Contig1850.5          1.39e-22  30_[-5(2.12e-05)]_36_[+3(2.47e-09)]_8_[+1(4.59e-11)]_96_[-5(1.03e-09)]_4_[-5(8.25e-06)]_50_[+2(7.76e-10)]_29_[+4(1.53e-07)]_246_[-1(7.52e-05)]_206
SGD_Scer_YOR278W                 1.13e-27  225_[+4(2.42e-09)]_60_[+5(1.32e-10)]_12_[+1(1.41e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_106_[-4(9.20e-05)]_24_[+3(1.41e-05)]_60
MIT_Spar_c261_21317              8.21e-29  197_[+5(7.95e-06)]_12_[+4(2.42e-09)]_60_[+5(8.38e-12)]_11_[+1(1.41e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_222
MIT_Smik_c492_20940              4.15e-27  234_[+4(2.42e-09)]_60_[+5(5.24e-10)]_12_[+1(1.41e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_196_[-5(9.37e-05)]
WashU_Skud_Contig1682.4          4.10e-26  231_[+4(2.42e-09)]_58_[+5(7.25e-09)]_12_[+1(1.14e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_221
WashU_Sbay_Contig635.57          7.73e-27  237_[+4(2.42e-09)]_60_[+5(5.24e-10)]_11_[+1(2.72e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_25_[+5(8.91e-05)]_126_[+2(8.80e-05)]_23
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM3.ups.fa_000444000766000024      1532513155576321 20275 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDL205C HEM3 "Phorphobilinogen deaminase, catalyzes the conversion of 4-porphobilinogen to hydroxymethylbilane, the third step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; expression is regulated by Hap2p-Hap3p"
AGTACGTGTGTATTTACCAACTACAAATTTATCTAGATTTTCTTCGCTTTTCTTTTTTTC
TATTGTTCTAGATATTAATACGGGATGAGAAGAACAGAATATTCAAAATCTAATACAGCC
CTGTACCATGCAAACACGAGCGTCAATCTGCCAATGACCTTGAATTCAGGCTATGTGTAG
CAATAATACAGATAGTTAGTAGCCTCGTTTATATAAAGCGTTCCTTTACTTTTTCATTTT
CTTTCTTTTTTTATGTTTGATTTTTTTACTTTTTCACTTTAAAAAATTGCTGAAATTTTC
GTAGCCAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCTCCC
CAGGGTCAATTGACAAGGAGAGAAGGAATGTTATATGGGAATTGCTGCGTAAAGATGGTC
AAAAATCCTGGACTGCCGTACGAACGACAATGTAAGGATGACTGCATTAGCCAGAAAGAC
ATCTTTACCCCCGGTGCTGCCAGGGAGCAAAATAATTACGAAAAGTGGACGCAAAGTTAA
CTTAAACTACAAGGGTAGCAGCAGAATGTGTCGGTGGTACCGGTGTGATAATGCCCCATT
TGAGATGCTTGTAATTGTGGCCTAGCAATAAGAACGCAAGGCGTTTTTGTTGAAAGGAGA
ACAAGGTTAGACGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTCACCCTTAT
TTCCACCCTCAAACGATAAAGCTTGCTACTTTGATGAAAAAAATATATAAAAGGGATTGA
AAAGCAGATCAATTATGTAGCAATAGTAGTAATAACTTGTTCAATTGCTTGTCTCAACTT
GCCACAAACTATCATCAACA
>MIT_Spar_c429_3020 YDL205C 5' untranslated region, Contig c429 77420 - 79419(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTATCAACTACAAAATTTATCTAGATTTTCTTGCCTTTTCCTTTTTC
TATTGTTCTAGATACTAATACGGGATGAGAAGAACAGAATATTCAAAATGTAAAACAGCC
CTGTACCATGCAAACACGAGCCTCAATCTGCCAATGACCTTGAATCCAAGCTATGTGTAG
CAATAATACAGATGATTGATTGGCGTCGTTTATATAAAGCGTTCCTTCATTTTTTTCATT
TTCTTTCTTTTTTTATGTTTGATTTTTTACTTTTTCACTTTTGAAAACTGCTGAAATTTT
CGTAGCAAAAAAAAAAAGACCTTCATTGCTTACTCATCGGTTTCTTATTGGTCAGACGCT
CCCCAGGGTCAATTGACAAGGAGAGAAGGAATGTTACATCCAGGAATTGCGACATAAAGA
TGTCCAAGAAGTCTGAACTGTCATACGAATGGCTATGCAAGGAGGATAGTACTGGTCAAG
AAGACATCTTACCCCCGGTGCTGTCAGGGAGCAAAAAAATGACAAAAGTGGACGCAAAGT
TAACTTGAACTACAAGGGTAGCAACAGAATGTCGGTGGTACCGGATGTGACAAAGCTCAC
TTGAGGTGCTTCTTGTTGCGGCATAGCAATAAGAGCGCAAGGCGTTTTTATGGAAAGGAG
AGCGAGGTTAGAGGGTGACGTTTAGGCGCATAGGCAACCTCCCCTTATTGTTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGTCTACATTGATGAAAAAAATGTATAAAAGGGATT
GAAAAGCCGATCATGTGTGTAGCAATAGTAGTAGTTATACTTGTTCAATTGCTTGCTTGC
ACTTTTCCAAAAACTACCAC
>MIT_Smik_c193_2483 YDL205C 5' untranslated region, Contig c193 6380 - 8379(revcom), 2000 bp (revcom)
AGTACGTGTGTATTTACCAACTATAAAATTTTACCTAGACTATCTGGCCTTTTTCTTTTT
TCTATTGTTCTAGATACTAATACGGGATGAAAAGAACAGAATATTCAAAAAGTAATACAG
CCCTGTACCATTCAAACACGAGCGCCAATTTGCCAATGAACTTGAAATCCAGCTATGCGT
AGCGATAATACAGATGATTGTTTGATGTCGTTTATATTAAGCGTTCCTTCAGTTTTTCTC
ATTTTCTTTCTTTTTCTATGTTTTATTTTTCACTTTTTCACTTTTGAAAATTGCTGAAAT
TTTCGTAACAAAAAAAGAGGCCTTCATTGCTTACTCATCGTTATCTTATTGGTTAAAATC
CCCAGCGACAATGTACAAGGAGAGAAGAAATGATATGTCTGGGAATTGCAGTTTGAAGAT
ATCCAAAGAGTTTTGAAGTGCCATACGAGCAACCACGTGAGAAGTAGAGCCTTAACAGAA
AATTCATCTTACCCCTAGTACTGCCAGGGAGGAACTAAACCTAAGAACTAGTGTTAACTT
GACTTGAACTGCAAGGGTAGCGACGGCGTATGTCGGTGGTACCGGATATGGCAAGAGCCC
ATTTGAGCTGCTTGTTCTTGTGACATACTATTAAGAGCGCAAGGCGTTTATGGAAAGGAG
GACAAGGTCAGAGGATGACGTTTAAGCGCATAGGCAATCTCCCCTTATTATTCACCCTTA
TTTCCACCCTCAAACGATAAAGCTTGCTGCGCTGTTGAAAAGTATATAAAAGGGATAGAA
AAGCAGAGCAATTATAATTTAGTAGAATAGCTTATTCTATCGTTAACTTGTTGAAAGGAT
CAGATTATTATCAAGATGAA
>MIT_Sbay_c841_3215 YDL205C 5' untranslated region, Contig c841 7323 - 9322(revcom), 2000 bp (revcom)
AGTATGTGTATATTTACCAACTATAGAGTATATCTAGTATTTTTTTTCCTTCTTCTTTTT
CTATTGTTCTAGATGCTAATATGGGATGAGTAGAACAAAATATTCAAAACGCAATACAGC
CCTGTACCATTCAAATACGAACGCCAATCTGCCAATGACCTTGAAATCAAGTTATGTGCC
GCGATAATACAATCTTTTGGCCTATATCGTTTAAATAAGCGTTCCTTTAATTTTTCGGTT
TCTTTCTTTTTTATGTCTAATTTTTCATTTTTTTTCACTTGAAAATTGCTGAAATTTTCG
TAGCTGAAAAAGAGAGGCCTTCTTTGCTTACTCATCGTTATCTTATTGGTCAAGAGCCCA
AGGGACAATAGACAAGGAGAGAACCACCAACTTTGGGAGTTGGATGCAAAGAAGGTCTTT
GATTTTGGGCTGCTATCAGAGCGGGCCATATAAGGAAGCTTGTAGTGGTTAGGAGAGAAC
ACGTCATTACCCCCCTCCCCCTTCTCCGCGCTGCCAGGGACCAGGCAAGGGCTTGCAAGA
GATGAACGTAAGATAGAACTACGAGGGTCGCGGCCAATGTGTCGGTAGTACCGGATGGGG
CAAAGCCCAATTGAGGTGCTTGTTGTTGAGGATGGTCGGCATGGCATGGCATGGGAGGCC
AAAGGCGCTTTGTGGGAAGGAGAACAAACAACATTAGAGGGTGACGTTTTAGCGCATAGG
CAATCTCCCCTTATTGTTCACCCTTATTTCCACCCTCAAACGACAAGGCTTGTTATGTTG
GTTGGAAATATATAAAAGGGATTGAAAAAGATCATATTCCTACATAAATTATGGTATTAG
TTTTTCTTCAATTGCTGGCT
>WashU_Sklu_Contig1799.3 YDL205C 5' untranslated region, Contig c1799 4415 - 5133(revcom), 2000 bp (revcom)
TTCTCTTAATAATATTACACTATGCGTATTCTCTCTGTTTCAAAATAAAGTCGATAATAA
AAACCAGAATGTAAAACCCAAAAATTACTAATAATAAACCAGGAATAAAATATGTACAGG
ATGAAAGGTGGAATAATATTTACAGCGACTTGTTCATGCAATGGCGACCAGGATGCAAAT
GCAGCTTCAAAAGGTTTTCGAATGCGGACTGATGTCTTGAAGAAGTAATAAGTGGGAAAC
GCTAAAGAGCGAGCAAATACAAGTTAAAAGGAAATGCTGGATAAGCCTGGTAACCAACGG
TAATACAACAAGCTGTATAAATACCTTCTGCCGAATGAGTTCTTTTTGATAGAAAAGATA
ACTAGGAAAAAAATTGGAAAATTTTTCAGCTGGAACCAATTATCAAAGTTCTGATTACTT
CACCGATCAGGGTAACGGCGTGTCTGACTAACAGGAACGGCCAATAAAAAAGGTGTAATT
AGTAGCAAATAAATAGATAAATAAATAACTGTGCGTTTAAAATATTATACAGTCTAGCGT
TGTTTTTTTTTTTTCGTTTCTTATTCCTCATAGTTGAGACTTAACCCAGCCTTCCAAACC
GCCCTTGACGATAATTTCTTGCAGATTCTTACCCAACTCGCCGACTTTCTGTTGGTGAAN
CGACAGATCCATCTAGCGTTTTTTGAATGAATTCCACCACATGGAGCTCAGCGCTGAGA
>WashU_Scas_Contig562.6 YDL205C 5' untranslated region, Contig c562 13955 - 15954(revcom), 2000 bp (revcom)
GGTTTGCAGTGTTCAAGGAGAAAGCTGACCAGCAGTAAAATTTTAGTGTGATGGCAGTGT
CAGCTTTATACGTGGCAATTGCTGATCGTTACCTATCAATGTTTCAACTTGAATTAAGTG
TCAGATTTGAGAATTTAACCATATTACTCGACCAATTGTTGCGGCAAAGTTGAGATGGCA
CAGAAACTACCGCAGAGAAGTAGGGTTACAGATTTTATACGATGAACGATCACTTTCTAA
ATTAGGGCTTGCATTACCAGGGCTTTAAAATCATTTTACACGGCCTTTAGGGCTTGCGAC
AATAGATGAACGGCTGTTTGATGCATTTCTTTACATGAAATTTCTCTTGGCAAGGTACTT
TATTATTTCCCCTTCAAAATGGATGGATGTATATACTTCTTGTTCATATATATATAGGGA
AGGGTTGCGGTCAGGTTCATACAGTATTACTTCCCTCTTTTTCCCTCAAAAATGGCCACG
AAATAAAGATGATGGAGTCACATTTTCAATCAGATGTCCCTACACACAAACCATCCAAAT
ATGCAAACTTGAATAAATTGGAAAGTCTAATCTATTGGAGACACCCTCAAAGGTCAGCCA
AATAATTTACAGCCACCTTATTTACCCTCATCTTCTTCAAGATGATCAATCCGGTGACTT
TCTTTTTAAAAATAGGCTACACTGTCTTATTCATTACTTCATTGTTAGAATTTATCACCA
GTTTAACCCTGGGGAAGGGGATAAGGACCCAAATGGCACCACAGGTATGTCCGGACATGG
TAAGGTACATAGAGCCAAGGGTCAACTCCATCCTGGACACAATTCCACCCTTACAGCAGG
GCCTAAGACGTTTGGTGTTT
>WashU_Skud_Contig1850.5 YDL205C 5' untranslated region, Contig c1850 6875 - 8874(revcom), 2000 bp (revcom)
GATACGTGTGTATTTGCTAACTATAAAATTTATCTAGTTTTCCTGCTTTTTTTTTTTTCT
ATTGTTCTAGAAACTAATATGGGGATGAGAAGAACAAAATTTTCAAAAAGCAATACAGCC
CTGTACCATTCAAACACGAACGCCAATCTGCAATGACCTTGAAATCAATCTATGTGTCGC
GATAATACAAGTGATTGATTGGTGTCGTTTATATAAAGCGTTCCTTCAATTTTTTCATTT
TCTTTCTTTTTTTATGTTTAATTTTCTACCTTTTTCACTTTTGAAAATTGCTGAAATTTT
CGTAGCAAAAAAAGAGAGGCGTACGTTGCTTACTCATCGTTTTCTTATTGGTCAAAAGCT
CCAGGAACAATGCCCAAGGAGAGAAAGAGTGCTACGTCTAGGAATTGCGATGGAAAGGCG
TCCAAGAGTCCTAAACTACCATGAGAACGGGCCACCCAAGGAGGGATAGCAATTGCTGAA
ACAACATCTTCACCTTCGGAGCTGGCAGGGAGCAAGGGACTCTCCGGAAAGAAAGTGAAC
GCAAAACGGAACTACAAGGATAGCAACGGAATGTGTCGGTGGTAGCGGATGTGGCAAGAT
CCCATTTCAGGAGCTTGTTGTTACGGCACAGCAGCAAGAAGAGCACAAGGCTTTTTCCGT
AAAGGAGAACAAAGTTGGAAGGTGACGTTTAGGCGCATAGGCAATCTCCCCTTATTGTTC
ACCCTTATTTCCACCCTCAAAGGATAAAGCTTGTTGCATTGATAAAAAATGTATAAAAAG
GATGGGAAACAGATGATAGTTAACAAGGTAGTGGGACGGTCTTTCGCTTATTCAGTTGTG
TGACATTCAAGGGTTACAAT
BioPerl-1.007002/t/data/map_hem/HEM3.ups.fa_.revcom000444000766000024      1166713155576321 21574 0ustar00cjfieldsstaff000000000000>SGD_Scer_YDL205C HEM3 "Phorphobilinogen deaminase, catalyzes the conversion of 4-porphobilinogen to hydroxymethylbilane, the third step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; expression is regulated by Hap2p-Hap3p"
TGTTGATGATAGTTTGTGGCAAGTTGAGACAAGCAATTGAACAAGTTATTACTACTATTG
CTACATAATTGATCTGCTTTTCAATCCCTTTTATATATTTTTTTCATCAAAGTAGCAAGC
TTTATCGTTTGAGGGTGGAAATAAGGGTGAACAATAAGGGGAGATTGCCTATGCGCCTAA
ACGTCACCGTCTAACCTTGTTCTCCTTTCAACAAAAACGCCTTGCGTTCTTATTGCTAGG
CCACAATTACAAGCATCTCAAATGGGGCATTATCACACCGGTACCACCGACACATTCTGC
TGCTACCCTTGTAGTTTAAGTTAACTTTGCGTCCACTTTTCGTAATTATTTTGCTCCCTG
GCAGCACCGGGGGTAAAGATGTCTTTCTGGCTAATGCAGTCATCCTTACATTGTCGTTCG
TACGGCAGTCCAGGATTTTTGACCATCTTTACGCAGCAATTCCCATATAACATTCCTTCT
CTCCTTGTCAATTGACCCTGGGGAGCGTCTGACCAATAAGAAACCGATGAGTAAGCAATG
AAGGTCTTTTTTTTGGCTACGAAAATTTCAGCAATTTTTTAAAGTGAAAAAGTAAAAAAA
TCAAACATAAAAAAAGAAAGAAAATGAAAAAGTAAAGGAACGCTTTATATAAACGAGGCT
ACTAACTATCTGTATTATTGCTACACATAGCCTGAATTCAAGGTCATTGGCAGATTGACG
CTCGTGTTTGCATGGTACAGGGCTGTATTAGATTTTGAATATTCTGTTCTTCTCATCCCG
TATTAATATCTAGAACAATAGAAAAAAAGAAAAGCGAAGAAAATCTAGATAAATTTGTAG
TTGGTAAATACACACGTACT
>MIT_Spar_c429_3020 YDL205C 5' untranslated region, Contig c429 77420 - 79419(revcom), 2000 bp (revcom)
GTGGTAGTTTTTGGAAAAGTGCAAGCAAGCAATTGAACAAGTATAACTACTACTATTGCT
ACACACATGATCGGCTTTTCAATCCCTTTTATACATTTTTTTCATCAATGTAGACAAGCT
TTATCGTTTGAGGGTGGAAATAAGGGTGAACAATAAGGGGAGGTTGCCTATGCGCCTAAA
CGTCACCCTCTAACCTCGCTCTCCTTTCCATAAAAACGCCTTGCGCTCTTATTGCTATGC
CGCAACAAGAAGCACCTCAAGTGAGCTTTGTCACATCCGGTACCACCGACATTCTGTTGC
TACCCTTGTAGTTCAAGTTAACTTTGCGTCCACTTTTGTCATTTTTTTGCTCCCTGACAG
CACCGGGGGTAAGATGTCTTCTTGACCAGTACTATCCTCCTTGCATAGCCATTCGTATGA
CAGTTCAGACTTCTTGGACATCTTTATGTCGCAATTCCTGGATGTAACATTCCTTCTCTC
CTTGTCAATTGACCCTGGGGAGCGTCTGACCAATAAGAAACCGATGAGTAAGCAATGAAG
GTCTTTTTTTTTTTGCTACGAAAATTTCAGCAGTTTTCAAAAGTGAAAAAGTAAAAAATC
AAACATAAAAAAAGAAAGAAAATGAAAAAAATGAAGGAACGCTTTATATAAACGACGCCA
ATCAATCATCTGTATTATTGCTACACATAGCTTGGATTCAAGGTCATTGGCAGATTGAGG
CTCGTGTTTGCATGGTACAGGGCTGTTTTACATTTTGAATATTCTGTTCTTCTCATCCCG
TATTAGTATCTAGAACAATAGAAAAAGGAAAAGGCAAGAAAATCTAGATAAATTTTGTAG
TTGATAAATACACACGTACT
>MIT_Smik_c193_2483 YDL205C 5' untranslated region, Contig c193 6380 - 8379(revcom), 2000 bp (revcom)
TTCATCTTGATAATAATCTGATCCTTTCAACAAGTTAACGATAGAATAAGCTATTCTACT
AAATTATAATTGCTCTGCTTTTCTATCCCTTTTATATACTTTTCAACAGCGCAGCAAGCT
TTATCGTTTGAGGGTGGAAATAAGGGTGAATAATAAGGGGAGATTGCCTATGCGCTTAAA
CGTCATCCTCTGACCTTGTCCTCCTTTCCATAAACGCCTTGCGCTCTTAATAGTATGTCA
CAAGAACAAGCAGCTCAAATGGGCTCTTGCCATATCCGGTACCACCGACATACGCCGTCG
CTACCCTTGCAGTTCAAGTCAAGTTAACACTAGTTCTTAGGTTTAGTTCCTCCCTGGCAG
TACTAGGGGTAAGATGAATTTTCTGTTAAGGCTCTACTTCTCACGTGGTTGCTCGTATGG
CACTTCAAAACTCTTTGGATATCTTCAAACTGCAATTCCCAGACATATCATTTCTTCTCT
CCTTGTACATTGTCGCTGGGGATTTTAACCAATAAGATAACGATGAGTAAGCAATGAAGG
CCTCTTTTTTTGTTACGAAAATTTCAGCAATTTTCAAAAGTGAAAAAGTGAAAAATAAAA
CATAGAAAAAGAAAGAAAATGAGAAAAACTGAAGGAACGCTTAATATAAACGACATCAAA
CAATCATCTGTATTATCGCTACGCATAGCTGGATTTCAAGTTCATTGGCAAATTGGCGCT
CGTGTTTGAATGGTACAGGGCTGTATTACTTTTTGAATATTCTGTTCTTTTCATCCCGTA
TTAGTATCTAGAACAATAGAAAAAAGAAAAAGGCCAGATAGTCTAGGTAAAATTTTATAG
TTGGTAAATACACACGTACT
>MIT_Sbay_c841_3215 YDL205C 5' untranslated region, Contig c841 7323 - 9322(revcom), 2000 bp (revcom)
AGCCAGCAATTGAAGAAAAACTAATACCATAATTTATGTAGGAATATGATCTTTTTCAAT
CCCTTTTATATATTTCCAACCAACATAACAAGCCTTGTCGTTTGAGGGTGGAAATAAGGG
TGAACAATAAGGGGAGATTGCCTATGCGCTAAAACGTCACCCTCTAATGTTGTTTGTTCT
CCTTCCCACAAAGCGCCTTTGGCCTCCCATGCCATGCCATGCCGACCATCCTCAACAACA
AGCACCTCAATTGGGCTTTGCCCCATCCGGTACTACCGACACATTGGCCGCGACCCTCGT
AGTTCTATCTTACGTTCATCTCTTGCAAGCCCTTGCCTGGTCCCTGGCAGCGCGGAGAAG
GGGGAGGGGGGTAATGACGTGTTCTCTCCTAACCACTACAAGCTTCCTTATATGGCCCGC
TCTGATAGCAGCCCAAAATCAAAGACCTTCTTTGCATCCAACTCCCAAAGTTGGTGGTTC
TCTCCTTGTCTATTGTCCCTTGGGCTCTTGACCAATAAGATAACGATGAGTAAGCAAAGA
AGGCCTCTCTTTTTCAGCTACGAAAATTTCAGCAATTTTCAAGTGAAAAAAAATGAAAAA
TTAGACATAAAAAAGAAAGAAACCGAAAAATTAAAGGAACGCTTATTTAAACGATATAGG
CCAAAAGATTGTATTATCGCGGCACATAACTTGATTTCAAGGTCATTGGCAGATTGGCGT
TCGTATTTGAATGGTACAGGGCTGTATTGCGTTTTGAATATTTTGTTCTACTCATCCCAT
ATTAGCATCTAGAACAATAGAAAAAGAAGAAGGAAAAAAAATACTAGATATACTCTATAG
TTGGTAAATATACACATACT
>WashU_Skud_Contig1850.5 YDL205C 5' untranslated region, Contig c1850 6875 - 8874(revcom), 2000 bp (revcom)
ATTGTAACCCTTGAATGTCACACAACTGAATAAGCGAAAGACCGTCCCACTACCTTGTTA
ACTATCATCTGTTTCCCATCCTTTTTATACATTTTTTATCAATGCAACAAGCTTTATCCT
TTGAGGGTGGAAATAAGGGTGAACAATAAGGGGAGATTGCCTATGCGCCTAAACGTCACC
TTCCAACTTTGTTCTCCTTTACGGAAAAAGCCTTGTGCTCTTCTTGCTGCTGTGCCGTAA
CAACAAGCTCCTGAAATGGGATCTTGCCACATCCGCTACCACCGACACATTCCGTTGCTA
TCCTTGTAGTTCCGTTTTGCGTTCACTTTCTTTCCGGAGAGTCCCTTGCTCCCTGCCAGC
TCCGAAGGTGAAGATGTTGTTTCAGCAATTGCTATCCCTCCTTGGGTGGCCCGTTCTCAT
GGTAGTTTAGGACTCTTGGACGCCTTTCCATCGCAATTCCTAGACGTAGCACTCTTTCTC
TCCTTGGGCATTGTTCCTGGAGCTTTTGACCAATAAGAAAACGATGAGTAAGCAACGTAC
GCCTCTCTTTTTTTGCTACGAAAATTTCAGCAATTTTCAAAAGTGAAAAAGGTAGAAAAT
TAAACATAAAAAAAGAAAGAAAATGAAAAAATTGAAGGAACGCTTTATATAAACGACACC
AATCAATCACTTGTATTATCGCGACACATAGATTGATTTCAAGGTCATTGCAGATTGGCG
TTCGTGTTTGAATGGTACAGGGCTGTATTGCTTTTTGAAAATTTTGTTCTTCTCATCCCC
ATATTAGTTTCTAGAACAATAGAAAAAAAAAAAAGCAGGAAAACTAGATAAATTTTATAG
TTAGCAAATACACACGTATC
BioPerl-1.007002/t/data/map_hem/HEM4-HEM12.fa000444000766000024      1775013155576321 20107 0ustar00cjfieldsstaff000000000000>SGD_Scer_YOR278W HEM4 "Uroporphyrinogen III synthase, catalyzes the conversion of hydroxymethylbilane to uroporphyrinogen III, the fourth step in the heme biosynthetic pathway"
CTCTCGAGCAAGGTCTATTTTACCTTTCTGTTTCCTTATCCTTTGACACTAAAATTCAAA
AAACTCACTAGAAAGTTCACTAAAGCGCCTTAGCTGACTACAGCACAACCCAACCCCAAA
AACTAGTGAACTACACACTAAGAGAATTTATGGTATTTCCATAATTGAAGTATATGTACG
ATGTATACAATGTAAACAAGAGAGTAATGAAGTGAAGATATGTACACCTAGAGCGAACCA
ATGATAATTTGTTTTCTTAATTAAGAAAAACCATTAAAACTGGATTAGATTTCAATAATG
AAAAGCTAGGAACAAAAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGACATA
TGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGTTTT
CTTATCCTGAAGGATCCTGCAAATGAAGTAAGTTCAAAGAATTGAAATGAAATCGCCTTT
TATACCCTCGCCGCACCAAGGAGCGCGCTGTGAAAATTTTTCGCTTTATCTCTTAGGGCT
CCTACTGTCGGTAGAGAAAAGTTGAGTATATTTAAAGCATGAGGTAACTTTTCTGCCCAT
TTTTACTTCTATTTCCATTTGAATTCAGAAAAGTG
>MIT_Spar_c261_21317 YOR278W 5' untranslated region, Contig c261 32269 - 34268, 2000 bp (revcom)
CGTTCCAAGCAGGGTTTATTCTATTTCTCGGCTCCTTTACCCTGTAACTTCGAGATTCAA
AAACTCGCTATAACTTCACTAAAGCGCTTTAGTTGACTACAACACAACCCAACCCCAAAA
TAAACTGTCCAACTACACAATACCGAGGATAATCCACGATATTTCGGTGATTGAAGTATA
TGTATTACGTATGCAATGTAAGCAAGAAACTAACAAAATGAATATGTACACCTAGAGCGA
ACCAATGATAATTTGTTTTCTTAATAAAGAAAAACTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAACAGAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGAC
ATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGT
TCTTTTATCCTGAAGGATAAACGGAAAGCTCCCGATTAAAAACAAGTATAGAGTACTGGA
ATAGAATCGCCTTTTATACCCTCCCTCGCCGCATCAAGAAGCGCGCTGTGAAAATTTTTC
GTTTTTCTCTTAGGGCTCCCATCCAACTGTCGGCGAGGAAAAGTTGTATATATTTAAAGC
ATGAGGTAACTTTGTTGCCCATTATCTTTTTTGTT
>MIT_Smik_c492_20940 YOR278W 5' untranslated region, Contig c492 3260 - 5259(revcom), 2000 bp (revcom)
ACTTTCAAACACACTCTGGTGTACTCCTCGGTCCCTTCATCTCATTTCTTCAAGATGCAG
AACTTCGCCGGAAGTAAACTAAAGTGCTTTAATTAATCAAAAGACAACTTAATTCCCAAA
CGGAAATGCAGGCTAGACAAACCGAAGATAATCCCCGATATTTCTGAGTTTAACAAATGT
ATGTATAATATGTATGCAATGTAGGCAAGAAAATAACGAAGTGAAGATATGTACACCTAG
AGCGAACCAATAATAATTTGTTTTCTTACTAAAGAAAAACTATTAAAACTGGATTAGATT
TCAATAATGAAAAGCTAGGAACAAAAGAAATTTGTCTACTTCCAGCCATTTGCGCTTTAT
ATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAAT
GATGGTTCTTTTAAACCAAAATTTAAAGAAAAATCTTAACGGTAATATGAGTAGGAGGTT
GGAATGGGATCGCTTTTTATACCCTCATTGTGATAAGAGACGCGCAGTGAAAAATTTTCG
CTTTTTCTTAGGGCTCCTATCTAACTCTCGGGCGAATAAATATCATGAATGTATTTAAAC
GTCAAGTTAGTTAAATGTTTGAGTCTGTTTCTTTT
>WashU_Skud_Contig1682.4 YOR278W 5' untranslated region, Contig c1682 3379 - 5378, 2000 bp (revcom)
CTCTTCAAACAGACTCCAATTCACTACTGAGCTCTTACCTTGTGACTTCAAGACTCACTA
CTCAGTTGAAAGACACGCTCAGTACCAAATTCGGCTGCGAGGCAACTAACGCCTTTAAAC
AGGTAGGTAAGGAACAATACCGAAAGGCCATCTCCGATGTTTCGAAGATTGGCAAATGTA
TATATTATGTATGCAATATAGGCAAGATGATAACGAAGTAGAGATATGTACACCTAGAGC
GAACCAATGATAATTTGTTTTCTTAATGAAGAAAGTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAATAAAAGAGATTGGTCTACTTCCAGCCATTTGCGCTTTACATAGA
CATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGG
TTCTATTTAAAATGAAATCTAAAGATAAACCCTAGTCATAATCAAGTGGGTTGTGTTAAA
ATACAAGCACCTTTTATACTCTCGCAGCGTCAGTGGCGCGTTGTGAAAAATTTTCACTTT
TTCTCAGGGCTTTTACCCAACTGCCGACAAATAAAAGCCGTATTTAAGGAATGTGATTAG
TTTACTTTCCAATGCTTTCTCTTTTTTGTAGGGTA
>WashU_Sbay_Contig635.57 YOR278W 5' untranslated region, Contig c635 91073 - 93072, 2000 bp (revcom)
ACGTACAGATGGCGTCTCCTCCTTTCGCGAGCCCCTTGCCTTGTGACTTCAGCCTAACTT
CTTGACTAGAAGATACAACAAGAAATACTCAAATCGGTTATTGTGCAACTCATCCCTCAG
ACAGTTTGGTAAGAAACACCGAAGACTATTTCCGATATCTCAAAGAATGACAAAAGTATA
CATTATATATGCAAGAGAGGCAAGAAAAGAGTAAAAAAGAGTAAAAAAAACATGTACACC
TAGAGCGAACCAGTGATAATTTGCTTCTCAATGAAGAAAAAGCGATTAAAACTGGATTAG
ATTTCATTAAAGAAAAGCTAGGAACAAAGAAATTGGTCTACTTCCAGCCATTTGCGCTTG
ACATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGA
ATGATGGCTCTTTTAAATTGAGATCTAAAAGAAATATCCTGGAAAAGAGTAGAGAAGAGT
CCAAACTGTAGGAATTCAATCGCTTTTTATACTCTCATCGCGGAAAAGACGCGCTGTGAA
AAATTTTCTCTTTTTCTTAGGGCTCCTATCCAGCTGCCTGCGAACAAAAGCCGTATTTAA
AGCATGATTTTCACTACTATGTATGTTCTTTCTGC
>SGD_Scer_YDR047W HEM12 "Uroporphyrinogen decarboxylase, catalyzes the fifth step in the heme biosynthetic pathway; localizes to both the cytoplasm and nucleus; activity inhibited by Cu2+, Zn2+, Fe2+, Fe3+ and sulfhydryl-specific reagents"
AGCGTTATAACCTGTTCTTTGCTTTATTTTTTTTTTTTTTGTTCTTCCTTTTCTCGAAGA
GAGCTTACCAAACACAATTCTGAGATAATGCTTGATGAATTGAAGAACCTATCGATCACT
CTATGTTACCTTCGTCTGGAACATCACTAATTCGAGCGGTAAAGATGAAAATGGCAGAAC
ATTTCGCTGGCAAAATTAAAACTCTTGCCTCATTTTTTTTTGCTTTCCTCTCCTGCCGCC
AAAAACCCCGAACCCTGTCCTGTATATACGAGAAACATTGAAAAAGATCGTGTATGATAG
CGCCAAGATGGCGGATAAACTAACACTATTGACAGGTTGAGGCCAAGGATATATTACTTG
CTAACAGAAAGAGATACTGTCACCACAATTGCCCGCGTACGTATACTACAACATGTTCTC
TATATATCACCCACTCTTTCGCAGTGCTACGTACGCCAAAAACGCGCGCATGGAAGTAAA
GAAGTTTTTTCTTTTAAGAGCGAAGCTCCATTAAAAGCCTTGAATATAAACTAGTGCGAA
GTAGTATGATCCGAAGACACCAATTGCTGGTGCAGCATAGGAATATGTGGCGTCCGAAAA
AGAGCCTTTAACAATCCACGGCGAAACAAGGCACCGCTGTGCATTTAAAACATGCCGTTC
CCGTACCAAGTTATATTGTTACGGATGAATCCAAAATAATTTGTTAAAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCATGGCACCTTCTTCGTTTCTTCATCCTGCA
TTAGACTTACTAGTGTGCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGACACATATCGC
TGAGCTGGAAGGACACCTTTTAATGTAGCCGTGCATGCGGCTCCGCGAAAAGAGCTCTGC
TATATTTCTCTACCTGAACTTCGAGCCGCGATCAACGAAAGCTCTCATCCAAGGCTCGTT
TTTCTTGACAGAAGCATGACAGTAAAATATGCGGTCATTT
>MIT_Spar_c130_3923 YDR047W 5' untranslated region, Contig c130 9341 - 11340, 2000 bp (revcom)
AGCGTTATGATGTGTTATTTGCTTTTATTTTCTTCTTTCTTTGTCTCGAAGATAACCTAG
CAAACACAATTCTAAGAAAATTCTCGATGAATTGGTTGTCAGCGCTTCCTATTTACTCTA
TGTCCACTTCGTTTGAAACATCAGTGGTTCGAGCAGTAATGACAAAAAGGGCAGAACATT
TCGTTGGCAAAATTTAAACTCGTGCCTCTCATTTTTTTTACTTTTCTCTCCTGCCACCAA
AACCCCGAACCCTGTCCCGTATATACGAGGAACATTGAAAAAAAATCGTGTATGGTAGCG
CCAAGATAGCGAATAAACTATCAGTATTGGCAGGGTGAAGCTAAGGATATGTTGTTTGCT
AACAAAGGGAAATGCTTTCGTTATAATCGCCCGCGTGCGTCTACTAAAATATGATCTATA
TATACCACCCAGTCTATTGCAGTGTTACGTACATCAAAATGCGCGCATGTAAGTGAACAA
GTTTTTTTTGTTTAAAGAGCGATTTTCCAATAAAGGCTTTGGATATACACTGGTGCAAAA
TATATGGTCAATGACGCCAATTACTGGTGTAGCATGAGAATACGTCGTCCGAAAGAGTTT
TTTTTTACAAACTACGGCAAAGCAAAGCACCACTGGCGCAATTCAAAACATGCCGTCCCC
GTACTAAGTTATGTACGTTATTATGGACGGATCCAAAATTATACTCTAAAATGCTGCCGT
TCCGTCCCATTGAGTTTTATTTTCCTTCTCGTAGCACCTTCTTCGTGTCCTTTCCTTCTT
CTGCATTAGGCTTACTAGCGTCCTTTCCTTGCCGGATGCGTGCTTTTTTTTTCCGGCCGA
CAAATCTCGCTGAGTTGGAAAGACACCTTTTATATAGCCGTACGTGCGGCTCCTCGAGAA
AGGCCCTGCTATATTTCACTAGCTGATCCTCGAGCTGCGATCAACGAAAGCCCCATCCAA
AAGGCTCCTTTTTCTTCAAAGAAGCATGACAGTAAAATAT
>MIT_Sbay_c896_21277 YDR047W 5' untranslated region, Contig c896 2230 - 4229(revcom), 2000 bp (revcom)
AGTGTTAACAGTATCTTTTGCCTTTTTTTATTCTAATAGCTACCCCAGGAATCACTATTT
AGCAAAGATCGTTTGCAAATTGGCCGTCAGTACGTTCTAAGTTCTTTAGAACATCATTGG
CTCGAGCATTAGTGACACGAATAGGAAAGCATTTCGTTGACAAAAATAAAATTGTTTCTT
TATTTTTTCCCTCTTTTCCATGGCGTCAAAAAACCCCGAACCCTGTATAAACGAGGAAGC
TGCATGGTAGCGCCAGAAAAGGCAGATAACCTTTAACAGTGCTGACAGAACAACGTCAAA
CATGTGCGGATAATGCCTTCGCTGACGGCAAGAAATTATATACGCCTCGAAACTGTAGAA
CGTCTTTTGTGCCGCTTGGTAACAAATAAACCTAGCCGGGGCCAGAATTTCACCCGTACA
TACTTACTGTTACATACTGCATGCACGCTACGCATTCTCACCGAACATCGAATCTGCCTG
CAGAAGCGAAGAAAAGCAAGTCTTCGAAGAGCAAGCTTACATCCATCGTGTTGAACACAT
ATGCCCAGCAAAGGGATCGGATGACGCCCAACTAACATTGGAATTTGTGACGCAAGGCTG
AAAGGCACTTCTCTATAGCCCACGGTGAAGCCTTACGCTATTGACAAGACAAAACATGCC
GATCCAAGCCAGGCGAAACGGGCCTAGCACTACGCAGCCAAACACTGGCGTTCCGCCCGT
CCCATCCAGTTTCATTTCTTATTTCGTTCTGCCTTGGGCCTAGCAGCGTGCTTGCCGGAT
GAGTTTTTTCCATTTTCCTACCGGCTCATCTCGCTAAGCTGAAAGGTCAGTTTTATAGCC
GTGTGCGCGGCATCGAGAGACAGGTTCAGCTAATGATATTTGCCTAATTCTCGAGCTGAG
GCCAATGAAGGCAGCTTCCAGGGCTCGTTTCTGCTCGGGAAAAAGCATACCACACATTTG
CACGGCTTTTATGTGCCATAGTGCCACCACTAGCCCCCAG
>WashU_Skud_Contig1362.1 YDR047W 5' untranslated region, Contig c1362 1 - 761, 2000 bp (revcom)
AGTGTTGATGGTATCTTTTGATTTTTTCTAGATTGGTAGCAAGCTCAATTGGCACAGCTC
TAAAAAAAGCCTTGTGAATTGGATAGTACCTTCTTTCGTTTGGAACATTACTGCTTCGAG
CAATAAACATACGAAAGGCAGAACACCTCGTTGACAAAACTGAAACTATTTCTTCAATTT
TTTGGCCTTTTTTCCTGCTGCCAAAAAACCCCGAATCATGTAGAAGCGAGAAGTAAAACA
GAGGAAGTGTATGGTAGCGCCAAGGAAAACGGGCAATACTTAGAAAGAATGACAGAGCTC
AGCCAAGTGTAAGCTAAGTGTTGACAAGGGAAGGTACATTGGGCCCCGAAAAAATTTGCT
AATGCTCGAAGAGCTCTCAATCAATCACCCACATATATGTACTACAGTATATTTATACTT
TCCACGCAGTCTCACGCAGTGCCACCTTCATCACCATGCGTGTAACTAATCGAGCAAGCT
GTTTTACGAAGGGCAGCTTTCCTATAAGCGTTTTGAACATGCATGGCTGCACTGCAATGA
GATCAGGCGACTCCAATTCCATAGCCTAGCACGGGATTAAGTAACGAGAAACTGAAAGAG
ATAATTTTACAAACCCGGACGAAGCAGAGCACTTGCTGGAACAAATCAAACATGCCGTCC
CCTACCAGCTCTCGAAGCGGGCCTAGCATTACTCGATCGAACGTTGCCGTTTAGTCTTAT
TTTCCTTTCCGTGCTGCGCTGCTTTTTTCTTGCATTGGGCT
BioPerl-1.007002/t/data/map_hem/HEM4-HEM12.meme.txt000444000766000024     11457313155576321 21303 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM4-HEM12.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YOR278W         1.0000    635  MIT_Spar_c261_21317      1.0000    635  
MIT_Smik_c492_20940      1.0000    635  WashU_Skud_Contig1682.4  1.0000    635  
WashU_Sbay_Contig635.57  1.0000    635  SGD_Scer_YDR047W         1.0000   1000  
MIT_Spar_c130_3923       1.0000   1000  MIT_Sbay_c896_21277      1.0000   1000  
WashU_Skud_Contig1362.1  1.0000    761  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM4-HEM12.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            6936    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.299 C 0.201 G 0.201 T 0.299 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 188   E-value = 6.5e-019
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :9a4a:a::6::1:::1718
pos.-specific     C  21:::a::64a:684a9::2
probability       G  :::6::::4::a:::::21:
matrix            T  8::::::a::::326::18:

         bits    2.5      *    **   *    
                 2.3      *    **   *    
                 2.0      *    **   **   
                 1.8      *    **   **   
Information      1.5   * ***** ** * **   
content          1.3  ** ***** ** * **   
(30.1 bits)      1.0 ************ ****  *
                 0.8 ***************** **
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TAAGACATCACGCCTCCATA
consensus            C  A    GC  TTC  G C
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      -    370  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATGTC
WashU_Skud_Contig1682.4      -    363  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATGTA
MIT_Smik_c492_20940          -    368  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATATA
MIT_Spar_c261_21317          -    362  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATATA
SGD_Scer_YOR278W             -    359  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATATA
MIT_Spar_c130_3923           +    644  1.59e-10 TGGCGCAATT CAAAACATGCCGTCCCCGTA CTAAGTTATG
SGD_Scer_YDR047W             +    646  4.90e-10 GCTGTGCATT TAAAACATGCCGTTCCCGTA CCAAGTTATA
WashU_Skud_Contig1362.1      +    646  3.58e-09 CTGGAACAAA TCAAACATGCCGTCCCCTAC CAGCTCTCGA
MIT_Sbay_c896_21277          +    650  9.08e-09 ATTGACAAGA CAAAACATGCCGATCCAAGC CAGGCGAAAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           3.5e-12  369_[-1]_246
WashU_Skud_Contig1682.4           3.5e-12  362_[-1]_253
MIT_Smik_c492_20940               3.5e-12  367_[-1]_248
MIT_Spar_c261_21317               3.5e-12  361_[-1]_254
SGD_Scer_YOR278W                  3.5e-12  358_[-1]_257
MIT_Spar_c130_3923                1.6e-10  643_[+1]_337
SGD_Scer_YDR047W                  4.9e-10  645_[+1]_335
WashU_Skud_Contig1362.1           3.6e-09  645_[+1]_96
MIT_Sbay_c896_21277               9.1e-09  649_[+1]_331
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Sbay_Contig635.57  (  370) TAAGACATCACGCCTCCATA  1 
WashU_Skud_Contig1682.4  (  363) TAAGACATCACGCCTCCATA  1 
MIT_Smik_c492_20940      (  368) TAAGACATCACGCCTCCATA  1 
MIT_Spar_c261_21317      (  362) TAAGACATCACGCCTCCATA  1 
SGD_Scer_YOR278W         (  359) TAAGACATCACGCCTCCATA  1 
MIT_Spar_c130_3923       (  644) CAAAACATGCCGTCCCCGTA  1 
SGD_Scer_YDR047W         (  646) TAAAACATGCCGTTCCCGTA  1 
WashU_Skud_Contig1362.1  (  646) TCAAACATGCCGTCCCCTAC  1 
MIT_Sbay_c896_21277      (  650) CAAAACATGCCGATCCAAGC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6765 bayes= 9.55203 E= 6.5e-019 
  -982     34   -982    126 
   145    -66   -982   -982 
   162   -982   -982   -982 
    45   -982    166   -982 
   162   -982   -982   -982 
  -982    251   -982   -982 
   162   -982   -982   -982 
  -982   -982   -982    162 
  -982    166    134   -982 
    78    134   -982   -982 
  -982    251   -982   -982 
  -982   -982    251   -982 
  -154    166   -982      4 
  -982    215   -982    -55 
  -982    134   -982     78 
  -982    251   -982   -982 
  -154    234   -982   -982 
   104   -982     34   -154 
  -154   -982    -66    126 
   126     34   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.5e-019 
 0.000000  0.222222  0.000000  0.777778 
 0.888889  0.111111  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.555556  0.444444  0.000000 
 0.555556  0.444444  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.111111  0.555556  0.000000  0.333333 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.444444  0.000000  0.555556 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.888889  0.000000  0.000000 
 0.666667  0.000000  0.222222  0.111111 
 0.111111  0.000000  0.111111  0.777778 
 0.777778  0.222222  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
[TC]AA[GA]ACAT[CG][AC]CG[CT][CT][TC]CC[AG]T[AC]
--------------------------------------------------------------------------------




Time  5.21 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 180   E-value = 1.7e-016
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  ::1:7:::73:::3:::::9
pos.-specific     C  :188::aa2::::7:8::11
probability       G  1::128::1:1:a:a:112:
matrix            T  991112:::79a:::2997:

         bits    2.5       **    * *     
                 2.3       **    * *     
                 2.0       **    * *     
                 1.8       **    * *     
Information      1.5    * ***   ** **    
content          1.3 **** ***  ******** *
(28.8 bits)      1.0 **** ***  ******** *
                 0.8 **** ***************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TTCCAGCCATTTGCGCTTTA
consensus                GT  CA   A T  G 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1682.4      +    335  6.64e-13 ATTGGTCTAC TTCCAGCCATTTGCGCTTTA CATAGACATA
MIT_Smik_c492_20940          +    340  6.64e-13 ATTTGTCTAC TTCCAGCCATTTGCGCTTTA TATAGACATA
MIT_Spar_c261_21317          +    334  6.64e-13 ATTGGTCTAC TTCCAGCCATTTGCGCTTTA TATAGACATA
SGD_Scer_YOR278W             +    331  6.64e-13 ATTGGTCTAC TTCCAGCCATTTGCGCTTTA TATAGACATA
WashU_Sbay_Contig635.57      +    342  1.74e-12 ATTGGTCTAC TTCCAGCCATTTGCGCTTGA CATAGACATA
MIT_Spar_c130_3923           +    720  2.83e-09 AATGCTGCCG TTCCGTCCCATTGAGTTTTA TTTTCCTTCT
SGD_Scer_YDR047W             +    720  2.83e-09 AATGCTGCCG TTCCGTCCCATTGAGTTTTA TTTTCCTTCT
MIT_Sbay_c896_21277          +    833  4.51e-08 AAGGTCAGTT TTATAGCCGTGTGCGCGGCA TCGAGAGACA
WashU_Skud_Contig1362.1      -     39  7.81e-08 TTTTTTTAGA GCTGTGCCAATTGAGCTTGC TACCAATCTA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1682.4           6.6e-13  334_[+2]_281
MIT_Smik_c492_20940               6.6e-13  339_[+2]_276
MIT_Spar_c261_21317               6.6e-13  333_[+2]_282
SGD_Scer_YOR278W                  6.6e-13  330_[+2]_285
WashU_Sbay_Contig635.57           1.7e-12  341_[+2]_274
MIT_Spar_c130_3923                2.8e-09  719_[+2]_261
SGD_Scer_YDR047W                  2.8e-09  719_[+2]_261
MIT_Sbay_c896_21277               4.5e-08  832_[+2]_148
WashU_Skud_Contig1362.1           7.8e-08  38_[-2]_703
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
WashU_Skud_Contig1682.4  (  335) TTCCAGCCATTTGCGCTTTA  1 
MIT_Smik_c492_20940      (  340) TTCCAGCCATTTGCGCTTTA  1 
MIT_Spar_c261_21317      (  334) TTCCAGCCATTTGCGCTTTA  1 
SGD_Scer_YOR278W         (  331) TTCCAGCCATTTGCGCTTTA  1 
WashU_Sbay_Contig635.57  (  342) TTCCAGCCATTTGCGCTTGA  1 
MIT_Spar_c130_3923       (  720) TTCCGTCCCATTGAGTTTTA  1 
SGD_Scer_YDR047W         (  720) TTCCGTCCCATTGAGTTTTA  1 
MIT_Sbay_c896_21277      (  833) TTATAGCCGTGTGCGCGGCA  1 
WashU_Skud_Contig1362.1  (   39) GCTGTGCCAATTGAGCTTGC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6765 bayes= 9.55203 E= 1.7e-016 
  -982   -982    -66    145 
  -982    -66   -982    145 
  -154    215   -982   -154 
  -982    215    -66   -154 
   104   -982     34   -154 
  -982   -982    215    -55 
  -982    251   -982   -982 
  -982    251   -982   -982 
   104     34    -66   -982 
     4   -982   -982    104 
  -982   -982    -66    145 
  -982   -982   -982    162 
  -982   -982    251   -982 
     4    192   -982   -982 
  -982   -982    251   -982 
  -982    215   -982    -55 
  -982   -982    -66    145 
  -982   -982    -66    145 
  -982    -66     34    104 
   145    -66   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.7e-016 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.111111  0.000000  0.888889 
 0.111111  0.777778  0.000000  0.111111 
 0.000000  0.777778  0.111111  0.111111 
 0.666667  0.000000  0.222222  0.111111 
 0.000000  0.000000  0.777778  0.222222 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.666667  0.222222  0.111111  0.000000 
 0.333333  0.000000  0.000000  0.666667 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.333333  0.666667  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.111111  0.222222  0.666667 
 0.888889  0.111111  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
TTCC[AG][GT]CC[AC][TA]TTG[CA]G[CT]TT[TG]A
--------------------------------------------------------------------------------




Time 10.37 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   15   sites =   9   llr = 143   E-value = 1.2e-009
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  8::::1a9:9::9::
pos.-specific     C  ::a62:::1::a:21
probability       G  13::89:1911::8:
matrix            T  17:4::::::9:1:9

         bits    2.5   *        *   
                 2.3   *        *   
                 2.0   *  *  *  *   
                 1.8   * **  *  * * 
Information      1.5   * *** *  * * 
content          1.3   * ******** **
(22.9 bits)      1.0  **************
                 0.8 ***************
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           ATCCGGAAGATCAGT
consensus             G TC        C 
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Sbay_Contig635.57      +    399  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
WashU_Skud_Contig1682.4      +    392  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
MIT_Smik_c492_20940          +    397  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
MIT_Spar_c261_21317          +    391  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
SGD_Scer_YOR278W             +    388  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
MIT_Sbay_c896_21277          +    817  1.82e-07 CATCTCGCTA AGCTGAAAGGTCAGT TTTATAGCCG
MIT_Spar_c130_3923           -    922  1.82e-07 CGTTGATCGC AGCTCGAGGATCAGC TAGTGAAATA
SGD_Scer_YDR047W             +    134  2.44e-07 TGTTACCTTC GTCTGGAACATCACT AATTCGAGCG
WashU_Skud_Contig1362.1      +    363  9.95e-07 AATTTGCTAA TGCTCGAAGAGCTCT CAATCAATCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           6.3e-10  398_[+3]_222
WashU_Skud_Contig1682.4           6.3e-10  391_[+3]_229
MIT_Smik_c492_20940               6.3e-10  396_[+3]_224
MIT_Spar_c261_21317               6.3e-10  390_[+3]_230
SGD_Scer_YOR278W                  6.3e-10  387_[+3]_233
MIT_Sbay_c896_21277               1.8e-07  816_[+3]_169
MIT_Spar_c130_3923                1.8e-07  921_[-3]_64
SGD_Scer_YDR047W                  2.4e-07  133_[+3]_852
WashU_Skud_Contig1362.1             1e-06  362_[+3]_384
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=15 seqs=9
WashU_Sbay_Contig635.57  (  399) ATCCGGAAGATCAGT  1 
WashU_Skud_Contig1682.4  (  392) ATCCGGAAGATCAGT  1 
MIT_Smik_c492_20940      (  397) ATCCGGAAGATCAGT  1 
MIT_Spar_c261_21317      (  391) ATCCGGAAGATCAGT  1 
SGD_Scer_YOR278W         (  388) ATCCGGAAGATCAGT  1 
MIT_Sbay_c896_21277      (  817) AGCTGAAAGGTCAGT  1 
MIT_Spar_c130_3923       (  922) AGCTCGAGGATCAGC  1 
SGD_Scer_YDR047W         (  134) GTCTGGAACATCACT  1 
WashU_Skud_Contig1362.1  (  363) TGCTCGAAGAGCTCT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 6810 bayes= 9.56161 E= 1.2e-009 
   126   -982    -66   -154 
  -982   -982     92    104 
  -982    251   -982   -982 
  -982    166   -982     45 
  -982     34    215   -982 
  -154   -982    234   -982 
   162   -982   -982   -982 
   145   -982    -66   -982 
  -982    -66    234   -982 
   145   -982    -66   -982 
  -982   -982    -66    145 
  -982    251   -982   -982 
   145   -982   -982   -154 
  -982     34    215   -982 
  -982    -66   -982    145 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 1.2e-009 
 0.777778  0.000000  0.111111  0.111111 
 0.000000  0.000000  0.333333  0.666667 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  0.222222  0.777778  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.111111  0.888889  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  1.000000  0.000000  0.000000 
 0.888889  0.000000  0.000000  0.111111 
 0.000000  0.222222  0.777778  0.000000 
 0.000000  0.111111  0.000000  0.888889 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
A[TG]C[CT][GC]GAAGATCA[GC]T
--------------------------------------------------------------------------------




Time 15.31 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =   9   llr = 174   E-value = 1.7e-013
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  ::::6:::::4::a:3:93:
pos.-specific     C  1911::4:a:486:248:46
probability       G  ::::4a6a:::::::11:23
matrix            T  9199:::::a124:8111:1

         bits    2.5      * **           
                 2.3      * **           
                 2.0  *   * **           
                 1.8  *   * **           
Information      1.5  *   ***** * *  *   
content          1.3 **** ***** * *  *   
(27.9 bits)      1.0 ********** **** ** *
                 0.8 ********** **** ****
                 0.5 *************** ****
                 0.3 ********************
                 0.0 --------------------

Multilevel           TCTTAGGGCTACCATCCACC
consensus                G C   CTT CA  AG
sequence                               G 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c261_21317          +    548  3.46e-12 TTCGTTTTTC TCTTAGGGCTCCCATCCAAC TGTCGGCGAG
WashU_Sbay_Contig635.57      +    555  1.43e-11 TTTCTCTTTT TCTTAGGGCTCCTATCCAGC TGCCTGCGAA
MIT_Spar_c130_3923           -    287  2.21e-11 TTATTCGCTA TCTTGGCGCTACCATACACG ATTTTTTTTC
SGD_Scer_YDR047W             -    289  3.04e-10 TTATCCGCCA TCTTGGCGCTATCATACACG ATCTTTTTCA
MIT_Smik_c492_20940          +    546  5.86e-10 TTTCGCTTTT TCTTAGGGCTCCTATCTAAC TCTCGGGCGA
WashU_Skud_Contig1362.1      -    246  1.17e-09 TGCCCGTTTT CCTTGGCGCTACCATACACT TCCTCTGTTT
MIT_Sbay_c896_21277          -    239  5.15e-09 TATCTGCCTT TTCTGGCGCTACCATGCAGC TTCCTCGTTT
WashU_Skud_Contig1682.4      +    542  1.02e-08 TTTCACTTTT TCTCAGGGCTTTTACCCAAC TGCCGACAAA
SGD_Scer_YOR278W             +    531  1.19e-08 TCGCTTTATC TCTTAGGGCTCCTACTGTCG GTAGAGAAAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c261_21317               3.5e-12  547_[+4]_68
WashU_Sbay_Contig635.57           1.4e-11  554_[+4]_61
MIT_Spar_c130_3923                2.2e-11  286_[-4]_694
SGD_Scer_YDR047W                    3e-10  288_[-4]_692
MIT_Smik_c492_20940               5.9e-10  545_[+4]_70
WashU_Skud_Contig1362.1           1.2e-09  245_[-4]_496
MIT_Sbay_c896_21277               5.2e-09  238_[-4]_742
WashU_Skud_Contig1682.4             1e-08  541_[+4]_74
SGD_Scer_YOR278W                  1.2e-08  530_[+4]_85
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=9
MIT_Spar_c261_21317      (  548) TCTTAGGGCTCCCATCCAAC  1 
WashU_Sbay_Contig635.57  (  555) TCTTAGGGCTCCTATCCAGC  1 
MIT_Spar_c130_3923       (  287) TCTTGGCGCTACCATACACG  1 
SGD_Scer_YDR047W         (  289) TCTTGGCGCTATCATACACG  1 
MIT_Smik_c492_20940      (  546) TCTTAGGGCTCCTATCTAAC  1 
WashU_Skud_Contig1362.1  (  246) CCTTGGCGCTACCATACACT  1 
MIT_Sbay_c896_21277      (  239) TTCTGGCGCTACCATGCAGC  1 
WashU_Skud_Contig1682.4  (  542) TCTCAGGGCTTTTACCCAAC  1 
SGD_Scer_YOR278W         (  531) TCTTAGGGCTCCTACTGTCG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6765 bayes= 9.55203 E= 1.7e-013 
  -982    -66   -982    145 
  -982    234   -982   -154 
  -982    -66   -982    145 
  -982    -66   -982    145 
    78   -982    134   -982 
  -982   -982    251   -982 
  -982    134    166   -982 
  -982   -982    251   -982 
  -982    251   -982   -982 
  -982   -982   -982    162 
    45    134   -982   -154 
  -982    215   -982    -55 
  -982    166   -982     45 
   162   -982   -982   -982 
  -982     34   -982    126 
     4    134    -66   -154 
  -982    215    -66   -154 
   145   -982   -982   -154 
     4    134     34   -982 
  -982    166     92   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.7e-013 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.111111  0.000000  0.888889 
 0.555556  0.000000  0.444444  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.444444  0.555556  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.444444  0.444444  0.000000  0.111111 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.555556  0.000000  0.444444 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.222222  0.000000  0.777778 
 0.333333  0.444444  0.111111  0.111111 
 0.000000  0.777778  0.111111  0.111111 
 0.888889  0.000000  0.000000  0.111111 
 0.333333  0.444444  0.222222  0.000000 
 0.000000  0.555556  0.333333  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
TCTT[AG]G[GC]GCT[AC][CT][CT]A[TC][CA]CA[CAG][CG]
--------------------------------------------------------------------------------




Time 20.21 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 167   E-value = 1.7e-011
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  921:9181:18181::881:
pos.-specific     C  :1:118:99:2:118:1:98
probability       G  ::9:::1::::9:61a12:2
matrix            T  17:9:11:19::121:::::

         bits    2.5                *    
                 2.3                *    
                 2.0   *    **  *   *  * 
                 1.8   *    **  *   *  **
Information      1.5   *    **  *  **  **
content          1.3   **** **  *  **  **
(26.7 bits)      1.0 * **** *****  ** ***
                 0.8 * *********** ******
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           ATGTACACCTAGAGCGAACC
consensus             A        C  T   G G
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      +    232  3.60e-13 TAAAAAAAAC ATGTACACCTAGAGCGAACC AGTGATAATT
WashU_Skud_Contig1682.4      +    226  3.60e-13 AAGTAGAGAT ATGTACACCTAGAGCGAACC AATGATAATT
MIT_Smik_c492_20940          +    229  3.60e-13 AAGTGAAGAT ATGTACACCTAGAGCGAACC AATAATAATT
MIT_Spar_c261_21317          +    224  3.60e-13 CAAAATGAAT ATGTACACCTAGAGCGAACC AATGATAATT
SGD_Scer_YOR278W             +    220  3.60e-13 AAGTGAAGAT ATGTACACCTAGAGCGAACC AATGATAATT
SGD_Scer_YDR047W             +    449  2.13e-07 TCGCAGTGCT ACGTACGCCAAAAACGCGCG CATGGAAGTA
MIT_Sbay_c896_21277          +    384  2.80e-07 GCTTGGTAAC AAATAAACCTAGCCGGGGCC AGAATTTCAC
MIT_Spar_c130_3923           +    120  3.31e-07 TATTTACTCT ATGTCCACTTCGTTTGAAAC ATCAGTGGTT
WashU_Skud_Contig1362.1      +    684  7.95e-07 GAAGCGGGCC TAGCATTACTCGATCGAACG TTGCCGTTTA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           3.6e-13  231_[+5]_384
WashU_Skud_Contig1682.4           3.6e-13  225_[+5]_390
MIT_Smik_c492_20940               3.6e-13  228_[+5]_387
MIT_Spar_c261_21317               3.6e-13  223_[+5]_392
SGD_Scer_YOR278W                  3.6e-13  219_[+5]_396
SGD_Scer_YDR047W                  2.1e-07  448_[+5]_532
MIT_Sbay_c896_21277               2.8e-07  383_[+5]_597
MIT_Spar_c130_3923                3.3e-07  119_[+5]_861
WashU_Skud_Contig1362.1             8e-07  683_[+5]_58
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
WashU_Sbay_Contig635.57  (  232) ATGTACACCTAGAGCGAACC  1 
WashU_Skud_Contig1682.4  (  226) ATGTACACCTAGAGCGAACC  1 
MIT_Smik_c492_20940      (  229) ATGTACACCTAGAGCGAACC  1 
MIT_Spar_c261_21317      (  224) ATGTACACCTAGAGCGAACC  1 
SGD_Scer_YOR278W         (  220) ATGTACACCTAGAGCGAACC  1 
SGD_Scer_YDR047W         (  449) ACGTACGCCAAAAACGCGCG  1 
MIT_Sbay_c896_21277      (  384) AAATAAACCTAGCCGGGGCC  1 
MIT_Spar_c130_3923       (  120) ATGTCCACTTCGTTTGAAAC  1 
WashU_Skud_Contig1362.1  (  684) TAGCATTACTCGATCGAACG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6765 bayes= 9.55203 E= 1.7e-011 
   145   -982   -982   -154 
   -55    -66   -982    104 
  -154   -982    234   -982 
  -982    -66   -982    145 
   145    -66   -982   -982 
  -154    215   -982   -154 
   126   -982    -66   -154 
  -154    234   -982   -982 
  -982    234   -982   -154 
  -154   -982   -982    145 
   126     34   -982   -982 
  -154   -982    234   -982 
   126    -66   -982   -154 
  -154    -66    166    -55 
  -982    215    -66   -154 
  -982   -982    251   -982 
   126    -66    -66   -982 
   126   -982     34   -982 
  -154    234   -982   -982 
  -982    215     34   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.7e-011 
 0.888889  0.000000  0.000000  0.111111 
 0.222222  0.111111  0.000000  0.666667 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.888889  0.111111  0.000000  0.000000 
 0.111111  0.777778  0.000000  0.111111 
 0.777778  0.000000  0.111111  0.111111 
 0.111111  0.888889  0.000000  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.111111  0.000000  0.000000  0.888889 
 0.777778  0.222222  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.777778  0.111111  0.000000  0.111111 
 0.111111  0.111111  0.555556  0.222222 
 0.000000  0.777778  0.111111  0.111111 
 0.000000  0.000000  1.000000  0.000000 
 0.777778  0.111111  0.111111  0.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.111111  0.888889  0.000000  0.000000 
 0.000000  0.777778  0.222222  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
A[TA]GTACACCT[AC]GA[GT]CGA[AG]C[CG]
--------------------------------------------------------------------------------




Time 25.01 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YOR278W                 4.46e-32  [-5(9.93e-05)]_199_[+5(3.60e-13)]_91_[+2(6.64e-13)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_128_[+4(1.19e-08)]_85
MIT_Spar_c261_21317              1.84e-35  25_[+4(3.48e-05)]_54_[+1(1.15e-05)]_104_[+5(3.60e-13)]_90_[+2(6.64e-13)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_142_[+4(3.46e-12)]_68
MIT_Smik_c492_20940              2.51e-33  228_[+5(3.60e-13)]_91_[+2(6.64e-13)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_134_[+4(5.86e-10)]_70
WashU_Skud_Contig1682.4          3.86e-32  225_[+5(3.60e-13)]_89_[+2(6.64e-13)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_135_[+4(1.02e-08)]_74
WashU_Sbay_Contig635.57          1.81e-34  231_[+5(3.60e-13)]_90_[+2(1.74e-12)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_141_[+4(1.43e-11)]_61
SGD_Scer_YDR047W                 2.76e-19  133_[+3(2.44e-07)]_140_[-4(3.04e-10)]_140_[+5(2.13e-07)]_177_[+1(4.90e-10)]_54_[+2(2.83e-09)]_61_[-1(8.87e-05)]_22_[+3(5.89e-06)]_55_[-3(5.20e-05)]_73
MIT_Spar_c130_3923               9.70e-21  42_[+3(1.33e-05)]_62_[+5(3.31e-07)]_147_[-4(2.21e-11)]_337_[+1(1.59e-10)]_56_[+2(2.83e-09)]_38_[-5(5.60e-05)]_13_[-1(8.87e-05)]_55_[-3(2.21e-05)]_21_[-3(1.82e-07)]_64
MIT_Sbay_c896_21277              7.11e-16  118_[+3(1.87e-05)]_105_[-4(5.15e-09)]_125_[+5(2.80e-07)]_138_[-2(1.57e-05)]_88_[+1(9.08e-09)]_45_[+2(1.89e-05)]_17_[+4(7.61e-05)]_45_[+3(1.82e-07)]_1_[+2(4.51e-08)]_148
WashU_Skud_Contig1362.1          4.40e-16  38_[-2(7.81e-08)]_187_[-4(1.17e-09)]_97_[+3(9.95e-07)]_268_[+1(3.58e-09)]_18_[+5(7.95e-07)]_58
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM4-HEM13.fa000444000766000024      2037613155576321 20106 0ustar00cjfieldsstaff000000000000>SGD_Scer_YOR278W HEM4 "Uroporphyrinogen III synthase, catalyzes the conversion of hydroxymethylbilane to uroporphyrinogen III, the fourth step in the heme biosynthetic pathway"
CTCTCGAGCAAGGTCTATTTTACCTTTCTGTTTCCTTATCCTTTGACACTAAAATTCAAA
AAACTCACTAGAAAGTTCACTAAAGCGCCTTAGCTGACTACAGCACAACCCAACCCCAAA
AACTAGTGAACTACACACTAAGAGAATTTATGGTATTTCCATAATTGAAGTATATGTACG
ATGTATACAATGTAAACAAGAGAGTAATGAAGTGAAGATATGTACACCTAGAGCGAACCA
ATGATAATTTGTTTTCTTAATTAAGAAAAACCATTAAAACTGGATTAGATTTCAATAATG
AAAAGCTAGGAACAAAAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGACATA
TGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGTTTT
CTTATCCTGAAGGATCCTGCAAATGAAGTAAGTTCAAAGAATTGAAATGAAATCGCCTTT
TATACCCTCGCCGCACCAAGGAGCGCGCTGTGAAAATTTTTCGCTTTATCTCTTAGGGCT
CCTACTGTCGGTAGAGAAAAGTTGAGTATATTTAAAGCATGAGGTAACTTTTCTGCCCAT
TTTTACTTCTATTTCCATTTGAATTCAGAAAAGTG
>MIT_Spar_c261_21317 YOR278W 5' untranslated region, Contig c261 32269 - 34268, 2000 bp (revcom)
CGTTCCAAGCAGGGTTTATTCTATTTCTCGGCTCCTTTACCCTGTAACTTCGAGATTCAA
AAACTCGCTATAACTTCACTAAAGCGCTTTAGTTGACTACAACACAACCCAACCCCAAAA
TAAACTGTCCAACTACACAATACCGAGGATAATCCACGATATTTCGGTGATTGAAGTATA
TGTATTACGTATGCAATGTAAGCAAGAAACTAACAAAATGAATATGTACACCTAGAGCGA
ACCAATGATAATTTGTTTTCTTAATAAAGAAAAACTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAACAGAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGAC
ATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGT
TCTTTTATCCTGAAGGATAAACGGAAAGCTCCCGATTAAAAACAAGTATAGAGTACTGGA
ATAGAATCGCCTTTTATACCCTCCCTCGCCGCATCAAGAAGCGCGCTGTGAAAATTTTTC
GTTTTTCTCTTAGGGCTCCCATCCAACTGTCGGCGAGGAAAAGTTGTATATATTTAAAGC
ATGAGGTAACTTTGTTGCCCATTATCTTTTTTGTT
>MIT_Smik_c492_20940 YOR278W 5' untranslated region, Contig c492 3260 - 5259(revcom), 2000 bp (revcom)
ACTTTCAAACACACTCTGGTGTACTCCTCGGTCCCTTCATCTCATTTCTTCAAGATGCAG
AACTTCGCCGGAAGTAAACTAAAGTGCTTTAATTAATCAAAAGACAACTTAATTCCCAAA
CGGAAATGCAGGCTAGACAAACCGAAGATAATCCCCGATATTTCTGAGTTTAACAAATGT
ATGTATAATATGTATGCAATGTAGGCAAGAAAATAACGAAGTGAAGATATGTACACCTAG
AGCGAACCAATAATAATTTGTTTTCTTACTAAAGAAAAACTATTAAAACTGGATTAGATT
TCAATAATGAAAAGCTAGGAACAAAAGAAATTTGTCTACTTCCAGCCATTTGCGCTTTAT
ATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAAT
GATGGTTCTTTTAAACCAAAATTTAAAGAAAAATCTTAACGGTAATATGAGTAGGAGGTT
GGAATGGGATCGCTTTTTATACCCTCATTGTGATAAGAGACGCGCAGTGAAAAATTTTCG
CTTTTTCTTAGGGCTCCTATCTAACTCTCGGGCGAATAAATATCATGAATGTATTTAAAC
GTCAAGTTAGTTAAATGTTTGAGTCTGTTTCTTTT
>WashU_Skud_Contig1682.4 YOR278W 5' untranslated region, Contig c1682 3379 - 5378, 2000 bp (revcom)
CTCTTCAAACAGACTCCAATTCACTACTGAGCTCTTACCTTGTGACTTCAAGACTCACTA
CTCAGTTGAAAGACACGCTCAGTACCAAATTCGGCTGCGAGGCAACTAACGCCTTTAAAC
AGGTAGGTAAGGAACAATACCGAAAGGCCATCTCCGATGTTTCGAAGATTGGCAAATGTA
TATATTATGTATGCAATATAGGCAAGATGATAACGAAGTAGAGATATGTACACCTAGAGC
GAACCAATGATAATTTGTTTTCTTAATGAAGAAAGTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAATAAAAGAGATTGGTCTACTTCCAGCCATTTGCGCTTTACATAGA
CATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGG
TTCTATTTAAAATGAAATCTAAAGATAAACCCTAGTCATAATCAAGTGGGTTGTGTTAAA
ATACAAGCACCTTTTATACTCTCGCAGCGTCAGTGGCGCGTTGTGAAAAATTTTCACTTT
TTCTCAGGGCTTTTACCCAACTGCCGACAAATAAAAGCCGTATTTAAGGAATGTGATTAG
TTTACTTTCCAATGCTTTCTCTTTTTTGTAGGGTA
>WashU_Sbay_Contig635.57 YOR278W 5' untranslated region, Contig c635 91073 - 93072, 2000 bp (revcom)
ACGTACAGATGGCGTCTCCTCCTTTCGCGAGCCCCTTGCCTTGTGACTTCAGCCTAACTT
CTTGACTAGAAGATACAACAAGAAATACTCAAATCGGTTATTGTGCAACTCATCCCTCAG
ACAGTTTGGTAAGAAACACCGAAGACTATTTCCGATATCTCAAAGAATGACAAAAGTATA
CATTATATATGCAAGAGAGGCAAGAAAAGAGTAAAAAAGAGTAAAAAAAACATGTACACC
TAGAGCGAACCAGTGATAATTTGCTTCTCAATGAAGAAAAAGCGATTAAAACTGGATTAG
ATTTCATTAAAGAAAAGCTAGGAACAAAGAAATTGGTCTACTTCCAGCCATTTGCGCTTG
ACATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGA
ATGATGGCTCTTTTAAATTGAGATCTAAAAGAAATATCCTGGAAAAGAGTAGAGAAGAGT
CCAAACTGTAGGAATTCAATCGCTTTTTATACTCTCATCGCGGAAAAGACGCGCTGTGAA
AAATTTTCTCTTTTTCTTAGGGCTCCTATCCAGCTGCCTGCGAACAAAAGCCGTATTTAA
AGCATGATTTTCACTACTATGTATGTTCTTTCTGC
>SGD_Scer_YDR044W HEM13 "Coproporphyrinogen III oxidase, an oxygen requiring enzyme that catalyzes the sixth step in the heme biosynthetic pathway; localizes to the mitochondrial inner membrane; transcription is repressed by oxygen and heme (via Rox1p and Hap1p)"
CTTTATGTGTATTTAATTGTGTTCGAAGAGTTCGGTTTGCTATGTTTGATTTGCGAAAAG
AAAGCTTTTGATATGCTCAAAAAAAGAAAACCCGGAGAATAAAAGCTTAACAAAGAAAGA
CAATAGGTGGAAAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTCGAAACGAGAACA
ATGGGCAAAGCAAGCTTTATCTTCGGATCGTCCGTCAGCGCTTTGGTTGCAGTCTTATGC
TTTGTTCAAGCTGGAGCGTTATTGGTGGGAGAACCAGAAAAGGCGAAAGCGTAGCGTTCT
TTGAAATTTGGCTTCTGTTCCTGCGACTCGTTTAAAAGTAGAAGGGCCCGCGGAGCCGCT
GTGAAAGATTTCTTTTACTCTTTCAGCGCAGAAATCTCGCAGGAGCTCAGCAGAAAGTGC
CTATGACGGTAATCCCAGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAATTAA
AATACCGTGCCTATAGTAACTTTTTTTTACGCTGTGAACCGTTCAACACACAGTAAAAAC
TCCGCAGGAAATGGTTTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTTTCCCAACA
GTGAACGAGAGGACAAACTCCAGAGGATTTGCGGGCTTGATGATAAAATGTATTGTTGAA
AAGATCGCGAATGCAACAATTACGGTGGGGAGAAATATCAACAAAAGGGCAAGGCTATGC
CTTCTGGAAAGTGGCAGACTTGCACTTTCCTCGAAAAGAAAAATGACCGCAAGATCCGGT
TGTTCTCAACCTTCTACATTAAGACATACTTCTACGATTTTCGAATGCCGAAGCAACTAT
CGCTGAAATTTGTCATGTCAAAATTGCTACTGGGGGAGAAGAATATATATGGAAGTAATT
ATTATTTACGTTGCTGAAATGGCAGGTTAGACGCATGTTTTGCAAAATAAGTGGTTTTGA
AAAGAATTGATACTAGGAATCGGTGCAATACCTTCTACCT
>MIT_Spar_c130_3912 YDR044W 5' untranslated region, Contig c130 4128 - 6127, 2000 bp (revcom)
CTTTATATGTGTGTTTTGTGGTGTTCGAAATTGGTTTCTTTTGTTCGACTTGCGAGAAGA
AAGCTATCAATATGCTTTCCAAAAAAAGCTGGAGAATAAAAGCTTAACAAAGAAAGACAA
TAGGCGGAAAAAAAGGAAAATCCGTGTCCTTATATAGCCTTTTCGAAACGAGAACAATGG
ACAAATCAAGCTTTATCTATGGGTTGTCAGCTCTTTGGTTGCAGTCTTGTGCTTGGTTCA
AGCTGGGGCATTATTGGTGGGAGAAGCCAGAAAAGGCGAAAGCGTAGCGTTCTTTGAAAT
TTGGATTCTGTTCCTGCGACTCGTTTAAAAGAAGAAGGGCTGCGGAGCCACTGTGAAAGA
CTTGTTGTGCTCTTTCAACTAAGAAATCTGGCAGGAACTCGATATAAAGTGCCTGTGACA
GTAATCTCAGGGGGCTAATGGTGTGAAGGCACTTTCTAAACAATTGAAAATTGAAATACC
GTGCCTATGGTAACTTTTTTTTACGCTGCGAACCGTTCAACACACATTGAAAACCCCGCA
GCAATTGTTCTGAAGAATCTTAATCACGAATTAGGCGTATTGTTTCTCCCAACAGTGTAC
GAGCGGACGAAACTCTAGAGGATTTGCAGGCTCGGTGATAAAATGTATTGTTGAAAAGAA
CGCGAATGCAACGATTGTGGTGGAGAGAAATATCAACAGGGCAAGGCAAGGCTATGCTCT
TTTGGAAGTGGCGGACTTGCACTTTCTTGAAAAGAAAAATGACCGCAAGATCCGGTTGTT
CATAACTTTCTACAATAAGGCATACTTCTACGGTTTTCCAATGCTGAGGCAACTATCGCT
ATAAAATCGCTGCTAGGAGAAGATTATATATGGACGTAAATATTTTTTACGTTACTAAAA
TTCTAGGTTAGAGGCACGTTTTGCAGAACCAGTGGCCTTGGAAAGGTGTTGCTACAAATT
TATGCAATTTCTTCAACTTGCCAGGTGGTCTTGGATGATC
>MIT_Sbay_c896_21290 YDR044W 5' untranslated region, Contig c896 7383 - 9382(revcom), 2000 bp (revcom)
CTTGTTATGTGTGTTTGTGGTGATTGCGGTTTGGTTTTTCTGATTCGTATGACAGAAAGA
AAAAAATTCAGTTTACCTTGTAAGGTGATTAGGAGAAGAAAAAAAGCTTATTGGCAGCGA
ACAATAGGTGAAAAAAAAAAAGAAAATGCGTGTCCTTATATAGCTTTCTCGAAGGGAGAA
CAATGGATAAATCAAAGCTTATCTACGGGTCAACAGCTCTTTGGTTGCTGTCTTGCTCTA
GGTCCAAGCTGGGGCATAATTGGTGGGAGAAGCCAGAAAATGCGAAAGCGTACCGTTCTG
TGAAAAATGGCTTCGGTTCCTGCGACTCGTTTAAAAAGAAAAGGGCCCGCGCAGCCTGTG
TGAAATGTTCGTTTTGCCCTTCCCAGAGAGAAATCTTGCAGGAGCCTCAATACAATGTGC
CTGCGGATGGAATACCAGGGGATAAAGGCGTGAAGGCACTCCCTGAACAATTGAAAATTG
GAAAAAAAAAGTGCCTGTGATGAATCTTATACGTTGGGAAAACTCCAAGACACTTTTAAA
ACTCCGCAGAGATTGTTTGGAGGGACCTTGACCACGAGTTGGGAGTATTGTTTTTTCCTG
GAAGGAACGAGCGGAACTCTTGGGGATTTGCGGGCTCGCTAATAAAAAGTGTCTTGTTGA
AGAAAAGTAGAATGCGACTAAAACGGTGGAGGAAAATATCAACAAGGCAAGGCTATGCCT
TTCGAAGAAAAGCGGACTTGCAATTGCACAACCGTATCGAAGAGAATTGAGAAGGGGGTG
CAAAGTGATCCGGTTGTTCATATTTCTTCACCAATTGATACAATTATCTACGTTTGTTCT
GTTGACCAATCCAACGGGGACTCTGTATGACATAAGTCTTCCTTACATTGCTAAGATCCA
AGATCAGACCCGTAGATGAGTTCTGCACCAAAGAGTTGTTAACCGTCTTGCCTGAATAAT
TTTAAGTTGTCGCGATCCTCTTACAAGGTGTTCTTATTTC
>WashU_Smik_Contig2283.3 YDR044W 5' untranslated region, Contig c2283 2261 - 4260(revcom), 2000 bp (revcom)
CTTTATTGAGGATTTGTGGCGTTTGAGGTTTGGTTTTTTATTCAATTTGAAAGAAGAAAA
CTATCGTTATACTTTCGAAGAAAACACGGGGAATAAAAGCTTAACAGGTGAGACAATAGG
TGGAAAAAAAGGAAAATATGTGTCTTTATATAGCCTTTTCAAAAAGAGAACAATGGTCAA
ATAAAGGTTTATCTACGAGTCGACAGTTCGTTGGCTGCAGTGTTACGCTTGGTTGAAGCT
GGGGCATTATTGGTGGAAGAAGCCAGAAAAGACGAAAGAGTAGCGTAGCGTTCTTTCAAA
TTTTGGTTTCGGGTTCCTGCGACTCGTTTAAAAAAGAAAAGGGCCCGCGGCCCCGCCGTG
AAACACTTCGTCTTGCTCTTCCCACCCAGAAAACTTGTAGGAGCCTCAGTTACAAAGTGC
CTGTAATGGAAATCTTAGGGGGCTACTATTGTAAAGGCAATTTCTGAACAATTGAAAGTG
AAAATATCGTGCCTGTGGTAACTTTCTTATACGCCGTGAAACGTTTAACATACGTTGAAA
ACTCCGCAGGGATTGGTTTGGAAAATTATAGTCACGAATTAGGCGTATTGTCTTTCAAGA
AGGTACGAGCGGATGAACTTCTTGAGGATTTGCGGGTTCGGTGATAAAAAATGTATTGTT
GAAAAGAACGCGAATGCAACAATTACGGTGGAGAAAAATATTAACAAGGGAAGGCAAGGC
TATGTTCTATTGAGAAGCGGCGGACTTGCACTTTCCTCGAAGAAAAAAATGTCTTCAAGA
TCCAATGTTCATATAACTTTCTACAATAAGGTATCCTTCTACGATCTTTCAATGTTAAGA
TTGAAATCAATGTAAAAAGCACCATGTTGAATACTACTGCTAGGAGGAGATCACATATGA
ATGTGATTATTATTTATATTAGTAAATTTTCAGGTTAGGAAGAAGTTATGTGACGCTTTA
GCTTTGGAAATTTGTTGCGGGAAACTGATAACATTCTTTT
BioPerl-1.007002/t/data/map_hem/HEM4-HEM13.meme.txt000444000766000024     11545613155576321 21305 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM4-HEM13.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YOR278W         1.0000    635  MIT_Spar_c261_21317      1.0000    635  
MIT_Smik_c492_20940      1.0000    635  WashU_Skud_Contig1682.4  1.0000    635  
WashU_Sbay_Contig635.57  1.0000    635  SGD_Scer_YDR044W         1.0000   1000  
MIT_Spar_c130_3912       1.0000   1000  MIT_Sbay_c896_21290      1.0000   1000  
WashU_Smik_Contig2283.3  1.0000   1000  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM4-HEM13.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            7175    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.306 C 0.194 G 0.194 T 0.306 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 201   E-value = 6.7e-025
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :::::63:::::86::61::
pos.-specific     C  :61::4:::9:::2:a::::
probability       G  a46:a::a:1::2:9:::9a
matrix            T  ::3a::7:a:aa:21:491:

         bits    2.5 *   *  *       *   *
                 2.3 *   *  *       *   *
                 2.0 *   *  * *    **  **
                 1.8 *   *  * *    **  **
Information      1.5 ** **  *****  **  **
content          1.3 ** **  *****  **  **
(32.2 bits)      1.0 ** *** ****** ** ***
                 0.8 ************* ******
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GCGTGATGTCTTAAGCATGG
consensus             GT  CA     GC  T   
sequence                          T      
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      +    377  1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
WashU_Skud_Contig1682.4      +    370  1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
MIT_Smik_c492_20940          +    375  1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
MIT_Spar_c261_21317          +    369  1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
SGD_Scer_YOR278W             +    366  1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
MIT_Spar_c130_3912           +    217  1.16e-10 TCAGCTCTTT GGTTGCAGTCTTGTGCTTGG TTCAAGCTGG
WashU_Smik_Contig2283.3      +    213  3.08e-10 ACAGTTCGTT GGCTGCAGTGTTACGCTTGG TTGAAGCTGG
SGD_Scer_YDR044W             +    225  4.42e-10 TCAGCGCTTT GGTTGCAGTCTTATGCTTTG TTCAAGCTGG
MIT_Sbay_c896_21290          +    223  8.28e-10 ACAGCTCTTT GGTTGCTGTCTTGCTCTAGG TCCAAGCTGG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           1.2e-12  376_[+1]_239
WashU_Skud_Contig1682.4           1.2e-12  369_[+1]_246
MIT_Smik_c492_20940               1.2e-12  374_[+1]_241
MIT_Spar_c261_21317               1.2e-12  368_[+1]_247
SGD_Scer_YOR278W                  1.2e-12  365_[+1]_250
MIT_Spar_c130_3912                1.2e-10  216_[+1]_764
WashU_Smik_Contig2283.3           3.1e-10  212_[+1]_768
SGD_Scer_YDR044W                  4.4e-10  224_[+1]_756
MIT_Sbay_c896_21290               8.3e-10  222_[+1]_758
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Sbay_Contig635.57  (  377) GCGTGATGTCTTAAGCATGG  1 
WashU_Skud_Contig1682.4  (  370) GCGTGATGTCTTAAGCATGG  1 
MIT_Smik_c492_20940      (  375) GCGTGATGTCTTAAGCATGG  1 
MIT_Spar_c261_21317      (  369) GCGTGATGTCTTAAGCATGG  1 
SGD_Scer_YOR278W         (  366) GCGTGATGTCTTAAGCATGG  1 
MIT_Spar_c130_3912       (  217) GGTTGCAGTCTTGTGCTTGG  1 
WashU_Smik_Contig2283.3  (  213) GGCTGCAGTGTTACGCTTGG  1 
SGD_Scer_YDR044W         (  225) GGTTGCAGTCTTATGCTTTG  1 
MIT_Sbay_c896_21290      (  223) GGTTGCTGTCTTGCTCTAGG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 6.7e-025 
  -982   -982    251   -982 
  -982    166    134   -982 
  -982    -66    166      4 
  -982   -982   -982    162 
  -982   -982    251   -982 
    78    134   -982   -982 
     4   -982   -982    104 
  -982   -982    251   -982 
  -982   -982   -982    162 
  -982    234    -66   -982 
  -982   -982   -982    162 
  -982   -982   -982    162 
   126   -982     34   -982 
    78     34   -982    -55 
  -982   -982    234   -154 
  -982    251   -982   -982 
    78   -982   -982     45 
  -154   -982   -982    145 
  -982   -982    234   -154 
  -982   -982    251   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.7e-025 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.555556  0.444444  0.000000 
 0.000000  0.111111  0.555556  0.333333 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.555556  0.444444  0.000000  0.000000 
 0.333333  0.000000  0.000000  0.666667 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.555556  0.222222  0.000000  0.222222 
 0.000000  0.000000  0.888889  0.111111 
 0.000000  1.000000  0.000000  0.000000 
 0.555556  0.000000  0.000000  0.444444 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  0.000000  0.888889  0.111111 
 0.000000  0.000000  1.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
G[CG][GT]TG[AC][TA]GTCTT[AG][ACT]GC[AT]TGG
--------------------------------------------------------------------------------




Time  5.38 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 197   E-value = 4.1e-023
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  1::367a:::::::7a:4a:
pos.-specific     C  :646::::::6::::::::1
probability       G  9461::::6a4:aa3:a::9
matrix            T  ::::43:a4::a:::::6::

         bits    2.5          *  **  *   
                 2.3          *  **  *   
                 2.0 *        *  **  *  *
                 1.8 *        *  **  *  *
Information      1.5 ***   ** ***** ** **
content          1.3 ***   ** ***** ** **
(31.6 bits)      1.0 ***   *********** **
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GCGCAAATGGCTGGAAGTAG
consensus             GCATT  T G   G  A  
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      -    338  1.95e-13 TCTATGTCAA GCGCAAATGGCTGGAAGTAG ACCAATTTCT
WashU_Skud_Contig1682.4      -    331  1.95e-13 TCTATGTAAA GCGCAAATGGCTGGAAGTAG ACCAATCTCT
MIT_Smik_c492_20940          -    336  1.95e-13 TCTATATAAA GCGCAAATGGCTGGAAGTAG ACAAATTTCT
MIT_Spar_c261_21317          -    330  1.95e-13 TCTATATAAA GCGCAAATGGCTGGAAGTAG ACCAATTTTT
SGD_Scer_YOR278W             -    327  1.95e-13 TCTATATAAA GCGCAAATGGCTGGAAGTAG ACCAATTTTT
MIT_Sbay_c896_21290          +    253  1.81e-10 TCCAAGCTGG GGCATAATTGGTGGGAGAAG CCAGAAAATG
WashU_Smik_Contig2283.3      +    243  2.62e-10 TTGAAGCTGG GGCATTATTGGTGGAAGAAG CCAGAAAAGA
MIT_Spar_c130_3912           +    247  2.73e-10 TTCAAGCTGG GGCATTATTGGTGGGAGAAG CCAGAAAAGG
SGD_Scer_YDR044W             +    255  1.92e-09 TTCAAGCTGG AGCGTTATTGGTGGGAGAAC CAGAAAAGGC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           1.9e-13  337_[-2]_278
WashU_Skud_Contig1682.4           1.9e-13  330_[-2]_285
MIT_Smik_c492_20940               1.9e-13  335_[-2]_280
MIT_Spar_c261_21317               1.9e-13  329_[-2]_286
SGD_Scer_YOR278W                  1.9e-13  326_[-2]_289
MIT_Sbay_c896_21290               1.8e-10  252_[+2]_728
WashU_Smik_Contig2283.3           2.6e-10  242_[+2]_738
MIT_Spar_c130_3912                2.7e-10  246_[+2]_734
SGD_Scer_YDR044W                  1.9e-09  254_[+2]_726
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
WashU_Sbay_Contig635.57  (  338) GCGCAAATGGCTGGAAGTAG  1 
WashU_Skud_Contig1682.4  (  331) GCGCAAATGGCTGGAAGTAG  1 
MIT_Smik_c492_20940      (  336) GCGCAAATGGCTGGAAGTAG  1 
MIT_Spar_c261_21317      (  330) GCGCAAATGGCTGGAAGTAG  1 
SGD_Scer_YOR278W         (  327) GCGCAAATGGCTGGAAGTAG  1 
MIT_Sbay_c896_21290      (  253) GGCATAATTGGTGGGAGAAG  1 
WashU_Smik_Contig2283.3  (  243) GGCATTATTGGTGGAAGAAG  1 
MIT_Spar_c130_3912       (  247) GGCATTATTGGTGGGAGAAG  1 
SGD_Scer_YDR044W         (  255) AGCGTTATTGGTGGGAGAAC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 4.1e-023 
  -154   -982    234   -982 
  -982    166    134   -982 
  -982    134    166   -982 
     4    166    -66   -982 
    78   -982   -982     45 
   104   -982   -982      4 
   162   -982   -982   -982 
  -982   -982   -982    162 
  -982   -982    166     45 
  -982   -982    251   -982 
  -982    166    134   -982 
  -982   -982   -982    162 
  -982   -982    251   -982 
  -982   -982    251   -982 
   104   -982     92   -982 
   162   -982   -982   -982 
  -982   -982    251   -982 
    45   -982   -982     78 
   162   -982   -982   -982 
  -982    -66    234   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 4.1e-023 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  0.555556  0.444444  0.000000 
 0.000000  0.444444  0.555556  0.000000 
 0.333333  0.555556  0.111111  0.000000 
 0.555556  0.000000  0.000000  0.444444 
 0.666667  0.000000  0.000000  0.333333 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.555556  0.444444 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.555556  0.444444  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.666667  0.000000  0.333333  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.444444  0.000000  0.000000  0.555556 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.111111  0.888889  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
G[CG][GC][CA][AT][AT]AT[GT]G[CG]TGG[AG]AG[TA]AG
--------------------------------------------------------------------------------




Time 10.47 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =   9   llr = 184   E-value = 6.0e-018
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :21199:a::71:::6:::9
pos.-specific     C  98:3::::193:::::::4:
probability       G  1:961:a::1:94:13::6:
matrix            T  :::::1::9:::6a91aa:1

         bits    2.5       *             
                 2.3       *             
                 2.0 * *   *  * *        
                 1.8 * *   *  * *        
Information      1.5 ***   ** * * *  *** 
content          1.3 *** * **** * ** *** 
(29.5 bits)      1.0 *************** ****
                 0.8 *************** ****
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CCGGAAGATCAGTTTATTGA
consensus             A C      C G  G  C 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      +    401  5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGCTC
WashU_Skud_Contig1682.4      +    394  5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
MIT_Smik_c492_20940          +    399  5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
MIT_Spar_c261_21317          +    393  5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
SGD_Scer_YOR278W             +    390  5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTT
MIT_Spar_c130_3912           +    763  1.18e-11 AGAAAAATGA CCGCAAGATCCGGTTGTTCA TAACTTTCTA
SGD_Scer_YDR044W             +    767  1.43e-10 AGAAAAATGA CCGCAAGATCCGGTTGTTCT CAACCTTCTA
MIT_Sbay_c896_21290          +    781  2.40e-08 GAAGGGGGTG CAAAGTGATCCGGTTGTTCA TATTTCTTCA
WashU_Smik_Contig2283.3      -    359  1.26e-07 TGGGTGGGAA GAGCAAGACGAAGTGTTTCA CGGCGGGGCC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           5.8e-12  400_[+3]_215
WashU_Skud_Contig1682.4           5.8e-12  393_[+3]_222
MIT_Smik_c492_20940               5.8e-12  398_[+3]_217
MIT_Spar_c261_21317               5.8e-12  392_[+3]_223
SGD_Scer_YOR278W                  5.8e-12  389_[+3]_226
MIT_Spar_c130_3912                1.2e-11  762_[+3]_218
SGD_Scer_YDR044W                  1.4e-10  766_[+3]_214
MIT_Sbay_c896_21290               2.4e-08  780_[+3]_200
WashU_Smik_Contig2283.3           1.3e-07  358_[-3]_622
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=9
WashU_Sbay_Contig635.57  (  401) CCGGAAGATCAGTTTATTGA  1 
WashU_Skud_Contig1682.4  (  394) CCGGAAGATCAGTTTATTGA  1 
MIT_Smik_c492_20940      (  399) CCGGAAGATCAGTTTATTGA  1 
MIT_Spar_c261_21317      (  393) CCGGAAGATCAGTTTATTGA  1 
SGD_Scer_YOR278W         (  390) CCGGAAGATCAGTTTATTGA  1 
MIT_Spar_c130_3912       (  763) CCGCAAGATCCGGTTGTTCA  1 
SGD_Scer_YDR044W         (  767) CCGCAAGATCCGGTTGTTCT  1 
MIT_Sbay_c896_21290      (  781) CAAAGTGATCCGGTTGTTCA  1 
WashU_Smik_Contig2283.3  (  359) GAGCAAGACGAAGTGTTTCA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 6.0e-018 
  -982    234    -66   -982 
   -55    215   -982   -982 
  -154   -982    234   -982 
  -154     92    166   -982 
   145   -982    -66   -982 
   145   -982   -982   -154 
  -982   -982    251   -982 
   162   -982   -982   -982 
  -982    -66   -982    145 
  -982    234    -66   -982 
   104     92   -982   -982 
  -154   -982    234   -982 
  -982   -982    134     78 
  -982   -982   -982    162 
  -982   -982    -66    145 
    78   -982     92   -154 
  -982   -982   -982    162 
  -982   -982   -982    162 
  -982    134    166   -982 
   145   -982   -982   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.0e-018 
 0.000000  0.888889  0.111111  0.000000 
 0.222222  0.777778  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.111111  0.333333  0.555556  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.888889  0.000000  0.000000  0.111111 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.888889  0.111111  0.000000 
 0.666667  0.333333  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  0.000000  0.444444  0.555556 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.111111  0.888889 
 0.555556  0.000000  0.333333  0.111111 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.444444  0.555556  0.000000 
 0.888889  0.000000  0.000000  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
C[CA]G[GC]AAGATC[AC]G[TG]TT[AG]TT[GC]A
--------------------------------------------------------------------------------




Time 15.56 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =   9   llr = 185   E-value = 1.4e-017
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  1:a91a81:6aa6::2a::6
pos.-specific     C  :9::3::::3::::a::::4
probability       G  ::::::24a1::4a:::8a:
matrix            T  91:16::4:::::::8:2::

         bits    2.5         *    **   * 
                 2.3         *    **   * 
                 2.0  *      *    **   * 
                 1.8  *      *    **   * 
Information      1.5  **  *  * ** ** *** 
content          1.3  **  *  * ** ** *** 
(29.7 bits)      1.0 **** ** * ***** ****
                 0.8 **** ** ************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TCAATAAGGAAAAGCTAGGA
consensus                C GT C  G  A T C
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1682.4      +    296  5.02e-11 GGATTAGATT TCAATAATGAAAAGCTAGGA ATAAAAGAGA
MIT_Smik_c492_20940          +    301  5.02e-11 GGATTAGATT TCAATAATGAAAAGCTAGGA ACAAAAGAAA
MIT_Spar_c261_21317          +    296  5.02e-11 GGATTAGATT TCAATAATGAAAAGCTAGGA ACAGAAAAAT
SGD_Scer_YOR278W             +    292  5.02e-11 GGATTAGATT TCAATAATGAAAAGCTAGGA ACAAAAAAAA
MIT_Sbay_c896_21290          +    699  6.10e-11 GAGGAAAATA TCAACAAGGCAAGGCTATGC CTTTCGAAGA
MIT_Spar_c130_3912           +    693  6.60e-11 GAGAGAAATA TCAACAGGGCAAGGCAAGGC TATGCTCTTT
WashU_Smik_Contig2283.3      +    701  1.34e-09 GAGAAAAATA TTAACAAGGGAAGGCAAGGC TATGTTCTAT
WashU_Sbay_Contig635.57      +    304  1.34e-09 GGATTAGATT TCATTAAAGAAAAGCTAGGA ACAAAGAAAT
SGD_Scer_YDR044W             +    701  2.68e-09 AGAAATATCA ACAAAAGGGCAAGGCTATGC CTTCTGGAAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1682.4             5e-11  295_[+4]_320
MIT_Smik_c492_20940                 5e-11  300_[+4]_315
MIT_Spar_c261_21317                 5e-11  295_[+4]_320
SGD_Scer_YOR278W                    5e-11  291_[+4]_324
MIT_Sbay_c896_21290               6.1e-11  698_[+4]_282
MIT_Spar_c130_3912                6.6e-11  692_[+4]_288
WashU_Smik_Contig2283.3           1.3e-09  700_[+4]_280
WashU_Sbay_Contig635.57           1.3e-09  303_[+4]_312
SGD_Scer_YDR044W                  2.7e-09  700_[+4]_280
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=9
WashU_Skud_Contig1682.4  (  296) TCAATAATGAAAAGCTAGGA  1 
MIT_Smik_c492_20940      (  301) TCAATAATGAAAAGCTAGGA  1 
MIT_Spar_c261_21317      (  296) TCAATAATGAAAAGCTAGGA  1 
SGD_Scer_YOR278W         (  292) TCAATAATGAAAAGCTAGGA  1 
MIT_Sbay_c896_21290      (  699) TCAACAAGGCAAGGCTATGC  1 
MIT_Spar_c130_3912       (  693) TCAACAGGGCAAGGCAAGGC  1 
WashU_Smik_Contig2283.3  (  701) TTAACAAGGGAAGGCAAGGC  1 
WashU_Sbay_Contig635.57  (  304) TCATTAAAGAAAAGCTAGGA  1 
SGD_Scer_YDR044W         (  701) ACAAAAGGGCAAGGCTATGC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 1.4e-017 
  -154   -982   -982    145 
  -982    234   -982   -154 
   162   -982   -982   -982 
   145   -982   -982   -154 
  -154     92   -982     78 
   162   -982   -982   -982 
   126   -982     34   -982 
  -154   -982    134     45 
  -982   -982    251   -982 
    78     92    -66   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
    78   -982    134   -982 
  -982   -982    251   -982 
  -982    251   -982   -982 
   -55   -982   -982    126 
   162   -982   -982   -982 
  -982   -982    215    -55 
  -982   -982    251   -982 
    78    134   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.4e-017 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  0.888889  0.000000  0.111111 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.000000  0.111111 
 0.111111  0.333333  0.000000  0.555556 
 1.000000  0.000000  0.000000  0.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.111111  0.000000  0.444444  0.444444 
 0.000000  0.000000  1.000000  0.000000 
 0.555556  0.333333  0.111111  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.555556  0.000000  0.444444  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.222222  0.000000  0.000000  0.777778 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.777778  0.222222 
 0.000000  0.000000  1.000000  0.000000 
 0.555556  0.444444  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
TCAA[TC]A[AG][GT]G[AC]AA[AG]GC[TA]A[GT]G[AC]
--------------------------------------------------------------------------------




Time 20.51 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 178   E-value = 2.4e-015
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  61372:::::1:::aaa74:
pos.-specific     C  4:::1a:6:9:::1::::::
probability       G  :9137:a:6::7:9::::::
matrix            T  ::6::::44193a::::36a

         bits    2.5      **             
                 2.3      **             
                 2.0  *   **  *   *      
                 1.8  *   **  *   *      
Information      1.5  *   **  *  *****  *
content          1.3  *   **  * ******  *
(28.5 bits)      1.0 ** **************  *
                 0.8 ** *****************
                 0.5 ** *****************
                 0.3 ********************
                 0.0 --------------------

Multilevel           AGTAGCGCGCTGTGAAAATT
consensus            C AGA  TT  T     TA 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c261_21317          +    517  7.89e-12 CGCCGCATCA AGAAGCGCGCTGTGAAAATT TTTCGTTTTT
SGD_Scer_YOR278W             +    499  2.23e-11 CGCCGCACCA AGGAGCGCGCTGTGAAAATT TTTCGCTTTA
WashU_Skud_Contig1682.4      +    512  4.09e-10 TCGCAGCGTC AGTGGCGCGTTGTGAAAAAT TTTCACTTTT
MIT_Spar_c130_3912           +    283  4.88e-10 AAGGCGAAAG CGTAGCGTTCTTTGAAATTT GGATTCTGTT
SGD_Scer_YDR044W             +    290  4.88e-10 AAGGCGAAAG CGTAGCGTTCTTTGAAATTT GGCTTCTGTT
MIT_Sbay_c896_21290          +    289  5.32e-10 AATGCGAAAG CGTACCGTTCTGTGAAAAAT GGCTTCGGTT
MIT_Smik_c492_20940          +    516  1.70e-09 CATTGTGATA AGAGACGCGCAGTGAAAAAT TTTCGCTTTT
WashU_Sbay_Contig635.57      +    525  2.83e-09 TCATCGCGGA AAAGACGCGCTGTGAAAAAT TTTCTCTTTT
WashU_Smik_Contig2283.3      +    284  3.02e-09 GAAAGAGTAG CGTAGCGTTCTTTCAAATTT TGGTTTCGGG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c261_21317               7.9e-12  516_[+5]_99
SGD_Scer_YOR278W                  2.2e-11  498_[+5]_117
WashU_Skud_Contig1682.4           4.1e-10  511_[+5]_104
MIT_Spar_c130_3912                4.9e-10  282_[+5]_698
SGD_Scer_YDR044W                  4.9e-10  289_[+5]_691
MIT_Sbay_c896_21290               5.3e-10  288_[+5]_692
MIT_Smik_c492_20940               1.7e-09  515_[+5]_100
WashU_Sbay_Contig635.57           2.8e-09  524_[+5]_91
WashU_Smik_Contig2283.3             3e-09  283_[+5]_697
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
MIT_Spar_c261_21317      (  517) AGAAGCGCGCTGTGAAAATT  1 
SGD_Scer_YOR278W         (  499) AGGAGCGCGCTGTGAAAATT  1 
WashU_Skud_Contig1682.4  (  512) AGTGGCGCGTTGTGAAAAAT  1 
MIT_Spar_c130_3912       (  283) CGTAGCGTTCTTTGAAATTT  1 
SGD_Scer_YDR044W         (  290) CGTAGCGTTCTTTGAAATTT  1 
MIT_Sbay_c896_21290      (  289) CGTACCGTTCTGTGAAAAAT  1 
MIT_Smik_c492_20940      (  516) AGAGACGCGCAGTGAAAAAT  1 
WashU_Sbay_Contig635.57  (  525) AAAGACGCGCTGTGAAAAAT  1 
WashU_Smik_Contig2283.3  (  284) CGTAGCGTTCTTTCAAATTT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 2.4e-015 
    78    134   -982   -982 
  -154   -982    234   -982 
     4   -982    -66     78 
   104   -982     92   -982 
   -55    -66    192   -982 
  -982    251   -982   -982 
  -982   -982    251   -982 
  -982    166   -982     45 
  -982   -982    166     45 
  -982    234   -982   -154 
  -154   -982   -982    145 
  -982   -982    192      4 
  -982   -982   -982    162 
  -982    -66    234   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
   104   -982   -982      4 
    45   -982   -982     78 
  -982   -982   -982    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.4e-015 
 0.555556  0.444444  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.333333  0.000000  0.111111  0.555556 
 0.666667  0.000000  0.333333  0.000000 
 0.222222  0.111111  0.666667  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  0.000000  0.555556  0.444444 
 0.000000  0.888889  0.000000  0.111111 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  0.000000  0.666667  0.333333 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.111111  0.888889  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.666667  0.000000  0.000000  0.333333 
 0.444444  0.000000  0.000000  0.555556 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
[AC]G[TA][AG][GA]CG[CT][GT]CT[GT]TGAAA[AT][TA]T
--------------------------------------------------------------------------------




Time 25.34 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YOR278W                 1.58e-35  291_[+4(5.02e-11)]_15_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_89_[+5(2.23e-11)]_117
MIT_Spar_c261_21317              5.85e-36  260_[+4(4.80e-06)]_15_[+4(5.02e-11)]_14_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_104_[+5(7.89e-12)]_99
MIT_Smik_c492_20940              1.00e-33  265_[+4(4.99e-05)]_15_[+4(5.02e-11)]_15_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_97_[+5(1.70e-09)]_16_[+1(5.40e-05)]_64
WashU_Skud_Contig1682.4          2.57e-34  295_[+4(5.02e-11)]_15_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_98_[+5(4.09e-10)]_104
WashU_Sbay_Contig635.57          3.77e-32  303_[+4(1.34e-09)]_14_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_104_[+5(2.83e-09)]_91
SGD_Scer_YDR044W                 4.25e-24  106_[+4(5.44e-05)]_98_[+1(4.42e-10)]_10_[+2(1.92e-09)]_15_[+5(4.88e-10)]_391_[+4(2.68e-09)]_46_[+3(1.43e-10)]_142_[+5(4.10e-05)]_52
MIT_Spar_c130_3912               5.41e-28  103_[+4(5.44e-05)]_93_[+1(1.16e-10)]_10_[+2(2.73e-10)]_16_[+5(4.88e-10)]_390_[+4(6.60e-11)]_50_[+3(1.18e-11)]_218
MIT_Sbay_c896_21290              3.19e-24  222_[+1(8.28e-10)]_10_[+2(1.81e-10)]_16_[+5(5.32e-10)]_390_[+4(6.10e-11)]_62_[+3(2.40e-08)]_200
WashU_Smik_Contig2283.3          7.85e-22  212_[+1(3.08e-10)]_10_[+2(2.62e-10)]_21_[+5(3.02e-09)]_55_[-3(1.26e-07)]_322_[+4(1.34e-09)]_280
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM4-HEM14.fa000444000766000024      1275413155576321 20110 0ustar00cjfieldsstaff000000000000>SGD_Scer_YOR278W HEM4 "Uroporphyrinogen III synthase, catalyzes the conversion of hydroxymethylbilane to uroporphyrinogen III, the fourth step in the heme biosynthetic pathway"
CTCTCGAGCAAGGTCTATTTTACCTTTCTGTTTCCTTATCCTTTGACACTAAAATTCAAA
AAACTCACTAGAAAGTTCACTAAAGCGCCTTAGCTGACTACAGCACAACCCAACCCCAAA
AACTAGTGAACTACACACTAAGAGAATTTATGGTATTTCCATAATTGAAGTATATGTACG
ATGTATACAATGTAAACAAGAGAGTAATGAAGTGAAGATATGTACACCTAGAGCGAACCA
ATGATAATTTGTTTTCTTAATTAAGAAAAACCATTAAAACTGGATTAGATTTCAATAATG
AAAAGCTAGGAACAAAAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGACATA
TGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGTTTT
CTTATCCTGAAGGATCCTGCAAATGAAGTAAGTTCAAAGAATTGAAATGAAATCGCCTTT
TATACCCTCGCCGCACCAAGGAGCGCGCTGTGAAAATTTTTCGCTTTATCTCTTAGGGCT
CCTACTGTCGGTAGAGAAAAGTTGAGTATATTTAAAGCATGAGGTAACTTTTCTGCCCAT
TTTTACTTCTATTTCCATTTGAATTCAGAAAAGTG
>MIT_Spar_c261_21317 YOR278W 5' untranslated region, Contig c261 32269 - 34268, 2000 bp (revcom)
CGTTCCAAGCAGGGTTTATTCTATTTCTCGGCTCCTTTACCCTGTAACTTCGAGATTCAA
AAACTCGCTATAACTTCACTAAAGCGCTTTAGTTGACTACAACACAACCCAACCCCAAAA
TAAACTGTCCAACTACACAATACCGAGGATAATCCACGATATTTCGGTGATTGAAGTATA
TGTATTACGTATGCAATGTAAGCAAGAAACTAACAAAATGAATATGTACACCTAGAGCGA
ACCAATGATAATTTGTTTTCTTAATAAAGAAAAACTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAACAGAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGAC
ATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGT
TCTTTTATCCTGAAGGATAAACGGAAAGCTCCCGATTAAAAACAAGTATAGAGTACTGGA
ATAGAATCGCCTTTTATACCCTCCCTCGCCGCATCAAGAAGCGCGCTGTGAAAATTTTTC
GTTTTTCTCTTAGGGCTCCCATCCAACTGTCGGCGAGGAAAAGTTGTATATATTTAAAGC
ATGAGGTAACTTTGTTGCCCATTATCTTTTTTGTT
>MIT_Smik_c492_20940 YOR278W 5' untranslated region, Contig c492 3260 - 5259(revcom), 2000 bp (revcom)
ACTTTCAAACACACTCTGGTGTACTCCTCGGTCCCTTCATCTCATTTCTTCAAGATGCAG
AACTTCGCCGGAAGTAAACTAAAGTGCTTTAATTAATCAAAAGACAACTTAATTCCCAAA
CGGAAATGCAGGCTAGACAAACCGAAGATAATCCCCGATATTTCTGAGTTTAACAAATGT
ATGTATAATATGTATGCAATGTAGGCAAGAAAATAACGAAGTGAAGATATGTACACCTAG
AGCGAACCAATAATAATTTGTTTTCTTACTAAAGAAAAACTATTAAAACTGGATTAGATT
TCAATAATGAAAAGCTAGGAACAAAAGAAATTTGTCTACTTCCAGCCATTTGCGCTTTAT
ATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAAT
GATGGTTCTTTTAAACCAAAATTTAAAGAAAAATCTTAACGGTAATATGAGTAGGAGGTT
GGAATGGGATCGCTTTTTATACCCTCATTGTGATAAGAGACGCGCAGTGAAAAATTTTCG
CTTTTTCTTAGGGCTCCTATCTAACTCTCGGGCGAATAAATATCATGAATGTATTTAAAC
GTCAAGTTAGTTAAATGTTTGAGTCTGTTTCTTTT
>WashU_Skud_Contig1682.4 YOR278W 5' untranslated region, Contig c1682 3379 - 5378, 2000 bp (revcom)
CTCTTCAAACAGACTCCAATTCACTACTGAGCTCTTACCTTGTGACTTCAAGACTCACTA
CTCAGTTGAAAGACACGCTCAGTACCAAATTCGGCTGCGAGGCAACTAACGCCTTTAAAC
AGGTAGGTAAGGAACAATACCGAAAGGCCATCTCCGATGTTTCGAAGATTGGCAAATGTA
TATATTATGTATGCAATATAGGCAAGATGATAACGAAGTAGAGATATGTACACCTAGAGC
GAACCAATGATAATTTGTTTTCTTAATGAAGAAAGTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAATAAAAGAGATTGGTCTACTTCCAGCCATTTGCGCTTTACATAGA
CATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGG
TTCTATTTAAAATGAAATCTAAAGATAAACCCTAGTCATAATCAAGTGGGTTGTGTTAAA
ATACAAGCACCTTTTATACTCTCGCAGCGTCAGTGGCGCGTTGTGAAAAATTTTCACTTT
TTCTCAGGGCTTTTACCCAACTGCCGACAAATAAAAGCCGTATTTAAGGAATGTGATTAG
TTTACTTTCCAATGCTTTCTCTTTTTTGTAGGGTA
>WashU_Sbay_Contig635.57 YOR278W 5' untranslated region, Contig c635 91073 - 93072, 2000 bp (revcom)
ACGTACAGATGGCGTCTCCTCCTTTCGCGAGCCCCTTGCCTTGTGACTTCAGCCTAACTT
CTTGACTAGAAGATACAACAAGAAATACTCAAATCGGTTATTGTGCAACTCATCCCTCAG
ACAGTTTGGTAAGAAACACCGAAGACTATTTCCGATATCTCAAAGAATGACAAAAGTATA
CATTATATATGCAAGAGAGGCAAGAAAAGAGTAAAAAAGAGTAAAAAAAACATGTACACC
TAGAGCGAACCAGTGATAATTTGCTTCTCAATGAAGAAAAAGCGATTAAAACTGGATTAG
ATTTCATTAAAGAAAAGCTAGGAACAAAGAAATTGGTCTACTTCCAGCCATTTGCGCTTG
ACATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGA
ATGATGGCTCTTTTAAATTGAGATCTAAAAGAAATATCCTGGAAAAGAGTAGAGAAGAGT
CCAAACTGTAGGAATTCAATCGCTTTTTATACTCTCATCGCGGAAAAGACGCGCTGTGAA
AAATTTTCTCTTTTTCTTAGGGCTCCTATCCAGCTGCCTGCGAACAAAAGCCGTATTTAA
AGCATGATTTTCACTACTATGTATGTTCTTTCTGC
>SGD_Scer_YER014W HEM14 "Protoporphyrinogen oxidase, a mitochondrial enzyme that catalyzes the seventh step in the heme biosynthetic pathway, converting protoporphyrinogen IX to protoporphyrin IX"
TATACAAGCTCTTTTTGGCGTTCTCAATTGCACTTTACTCGATATGTTTGAATTGGTGTT
CTTCGCGAATATCTCTATTGTTCTCTCTATTATACTATTTCTTTTTTTGAATACTCCGCG
ACTCCGAAGCAACAAAGTGTCGAAGGCAAGTTCAAAGGCGTTTTGTAACTAAACGAGCAA
TGGCAGCTTTCAATTAAAGAAAGGTTAGCGTTACTCTGTGATTTTTTTCATGTAAAAATT
CTCAAGAGAGATAAAGTTGTTAAAAAATTAAATATAGGTCTATAAAACTCGATAATTATA
ATGCATAAAAAGCTAACAATGT
>MIT_Spar_c425_6072 YER014W 5' untranslated region, Contig c425 34016 - 36015, 2000 bp (revcom)
TATTCGAGCCCTTTCCCGCGTTCCCAATTGTACCTTCCTCGATAGGATTGAATTGGTATC
CTTCGCGGATCTCTCTATTGTTCTCTCTATTATTCTTTTTCTTTTTTAAATACTCCGCGA
CTCCGAAGCAACAAAATGTCGAAGGCAAGATGAAAGGCGTTTTGCAACTAAACGAGTAAT
GGCAGCTTTTAATTAAATAACGGTCAGCATTACTCTATAACTTTTCACATAAAATCCTCG
AAGAAGGAAAAATTGATAATCAATTTACCGAAGAATGAATATAGGTCTATAAAAATTCAA
TAATTATAGATGCATAAAAAGC
>MIT_Smik_c283_5928 YER014W 5' untranslated region, Contig c283 42606 - 44605, 2000 bp (revcom)
TATTGAAGCTCTCTCCACTATTTCTTTAATCGCGCTATACTAGATATGGTTAAACTGCTA
TCTTTTGCAAATCCCTCTATTGTTCTTTCCATTACTCTTTTCTTTTTTAAATACGGACTC
CGAAGCAACAAGGTCGAAGGCAAGCTGAAAGGCATTTTACAACTAAACGAGCAATGGTAG
CTTTTGATTGAATAAATTATTATCATTATTTTGTTATTTGTCCCACGAAATTCTCGTTGA
AAGCAAGGTTCGTAAGGATTTATCAAATGTTAAATATAGATCTATAAAAATTGAATAGTA
ATAATAACAAGGGATGGTGTTA
>MIT_Sbay_c84_6418 YER014W 5' untranslated region, Contig c84 10802 - 12801(revcom), 2000 bp (revcom)
TGTCGAAGTTCTCCTTTATTCCGCTGTTTCTTACGGAATCCAGCGAGACTGTTGTCCTTT
CGCATCCTTCTATTGTTCTTCCTTATTGTTCTCGTTTTTTTTATACTCTGCGACTCCGAA
ACAACAAAATCTCGAAGGCAAGCTAAGGTAAAAATATTCACCACTAAACGAGCAATGACA
GTTATATTCAAACGTCATTCTACTTTTTTGCCAGAGAAGTCCTCACTGGAGACGAAGTTG
GTAAATGCTTTATTTATATTAAACGTAGATCTATAAAGTTTAAATAGTTTATAATGCTTA
ACAAGGGACGATGTTATCTCTT
BioPerl-1.007002/t/data/map_hem/HEM4-HEM14.meme.txt000444000766000024     11321313155576321 21273 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM4-HEM14.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YOR278W         1.0000    635  MIT_Spar_c261_21317      1.0000    635  
MIT_Smik_c492_20940      1.0000    635  WashU_Skud_Contig1682.4  1.0000    635  
WashU_Sbay_Contig635.57  1.0000    635  SGD_Scer_YER014W         1.0000    322  
MIT_Spar_c425_6072       1.0000    322  MIT_Smik_c283_5928       1.0000    322  
MIT_Sbay_c84_6418        1.0000    322  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM4-HEM14.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            4463    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.321 C 0.179 G 0.179 T 0.321 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 192   E-value = 6.5e-023
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :7:::a:6:::aa1:a9:6a
pos.-specific     C  9279::4:4a:::6a::4::
probability       G  ::314:6:6:a::3::1:4:
matrix            T  11::6::4:::::::::6::

         bits    2.5          **   *     
                 2.3          **   *     
                 2.0 *  *     **   *     
                 1.8 *  *     **   *     
Information      1.5 * ** ** ***** **   *
content          1.3 * ** ** ***** ***  *
(30.8 bits)      1.0 * ***** ************
                 0.8 * ******************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CACCTAGAGCGAACCAATAA
consensus             CG G CTC    G   CG 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1682.4      +    231  7.13e-12 GAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
MIT_Spar_c261_21317          +    229  7.13e-12 TGAATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
SGD_Scer_YOR278W             +    225  7.13e-12 AAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
MIT_Smik_c492_20940          +    234  2.25e-11 AAGATATGTA CACCTAGAGCGAACCAATAA TAATTTGTTT
WashU_Sbay_Contig635.57      +    237  9.57e-11 AAAACATGTA CACCTAGAGCGAACCAGTGA TAATTTGCTT
MIT_Spar_c425_6072           +    115  1.35e-10 TTTAAATACT CCGCGACTCCGAAGCAACAA AATGTCGAAG
SGD_Scer_YER014W             +    116  1.35e-10 TTTGAATACT CCGCGACTCCGAAGCAACAA AGTGTCGAAG
MIT_Sbay_c84_6418            +    108  1.06e-09 TTTTTATACT CTGCGACTCCGAAACAACAA AATCTCGAAG
MIT_Smik_c283_5928           +    112  1.44e-09 CTTTTTTAAA TACGGACTCCGAAGCAACAA GGTCGAAGGC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1682.4           7.1e-12  230_[+1]_385
MIT_Spar_c261_21317               7.1e-12  228_[+1]_387
SGD_Scer_YOR278W                  7.1e-12  224_[+1]_391
MIT_Smik_c492_20940               2.3e-11  233_[+1]_382
WashU_Sbay_Contig635.57           9.6e-11  236_[+1]_379
MIT_Spar_c425_6072                1.4e-10  114_[+1]_188
SGD_Scer_YER014W                  1.4e-10  115_[+1]_187
MIT_Sbay_c84_6418                 1.1e-09  107_[+1]_195
MIT_Smik_c283_5928                1.4e-09  111_[+1]_191
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Skud_Contig1682.4  (  231) CACCTAGAGCGAACCAATGA  1 
MIT_Spar_c261_21317      (  229) CACCTAGAGCGAACCAATGA  1 
SGD_Scer_YOR278W         (  225) CACCTAGAGCGAACCAATGA  1 
MIT_Smik_c492_20940      (  234) CACCTAGAGCGAACCAATAA  1 
WashU_Sbay_Contig635.57  (  237) CACCTAGAGCGAACCAGTGA  1 
MIT_Spar_c425_6072       (  115) CCGCGACTCCGAAGCAACAA  1 
SGD_Scer_YER014W         (  116) CCGCGACTCCGAAGCAACAA  1 
MIT_Sbay_c84_6418        (  108) CTGCGACTCCGAAACAACAA  1 
MIT_Smik_c283_5928       (  112) TACGGACTCCGAAGCAACAA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4292 bayes= 8.89448 E= 6.5e-023 
  -982    234   -982   -154 
   104     34   -982   -154 
  -982    192     92   -982 
  -982    234    -66   -982 
  -982   -982    134     78 
   162   -982   -982   -982 
  -982    134    166   -982 
    78   -982   -982     45 
  -982    134    166   -982 
  -982    251   -982   -982 
  -982   -982    251   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -154    166     92   -982 
  -982    251   -982   -982 
   162   -982   -982   -982 
   145   -982    -66   -982 
  -982    134   -982     78 
    78   -982    134   -982 
   162   -982   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.5e-023 
 0.000000  0.888889  0.000000  0.111111 
 0.666667  0.222222  0.000000  0.111111 
 0.000000  0.666667  0.333333  0.000000 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.000000  0.444444  0.555556 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.444444  0.555556  0.000000 
 0.555556  0.000000  0.000000  0.444444 
 0.000000  0.444444  0.555556  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.111111  0.555556  0.333333  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.444444  0.000000  0.555556 
 0.555556  0.000000  0.444444  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
C[AC][CG]C[TG]A[GC][AT][GC]CGAA[CG]CAA[TC][AG]A
--------------------------------------------------------------------------------




Time  2.29 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   15   sites =   9   llr = 142   E-value = 7.6e-011
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  ::a:128::::2:::
pos.-specific     C  a6::981:::27291
probability       G  :4:a:::1227:81:
matrix            T  ::::::198811::9

         bits    2.5 *  *           
                 2.3 *  *           
                 2.0 *  **        * 
                 1.8 *  **       ** 
Information      1.5 ******      ** 
content          1.3 ****** *  * ***
(22.8 bits)      1.0 ****** ********
                 0.8 ***************
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           CCAGCCATTTGCGCT
consensus             G   A  GGCAC  
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Sbay_Contig635.57      +    344  1.85e-10 TGGTCTACTT CCAGCCATTTGCGCT TGACATAGAC
WashU_Skud_Contig1682.4      +    337  1.85e-10 TGGTCTACTT CCAGCCATTTGCGCT TTACATAGAC
MIT_Smik_c492_20940          +    342  1.85e-10 TTGTCTACTT CCAGCCATTTGCGCT TTATATAGAC
MIT_Spar_c261_21317          +    336  1.85e-10 TGGTCTACTT CCAGCCATTTGCGCT TTATATAGAC
SGD_Scer_YOR278W             +    333  1.85e-10 TGGTCTACTT CCAGCCATTTGCGCT TTATATAGAC
SGD_Scer_YER014W             +    174  2.34e-07 TGTAACTAAA CGAGCAATGGCAGCT TTCAATTAAA
MIT_Smik_c283_5928           +    168  4.95e-07 TACAACTAAA CGAGCAATGGTAGCT TTTGATTGAA
MIT_Spar_c425_6072           +      5  4.95e-07       TATT CGAGCCCTTTCCCGC GTTCCCAATT
MIT_Sbay_c84_6418            +     44  1.47e-06 CGGAATCCAG CGAGACTGTTGTCCT TTCGCATCCT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           1.8e-10  343_[+2]_277
WashU_Skud_Contig1682.4           1.8e-10  336_[+2]_284
MIT_Smik_c492_20940               1.8e-10  341_[+2]_279
MIT_Spar_c261_21317               1.8e-10  335_[+2]_285
SGD_Scer_YOR278W                  1.8e-10  332_[+2]_288
SGD_Scer_YER014W                  2.3e-07  173_[+2]_134
MIT_Smik_c283_5928                4.9e-07  167_[+2]_140
MIT_Spar_c425_6072                4.9e-07  4_[+2]_303
MIT_Sbay_c84_6418                 1.5e-06  43_[+2]_264
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=15 seqs=9
WashU_Sbay_Contig635.57  (  344) CCAGCCATTTGCGCT  1 
WashU_Skud_Contig1682.4  (  337) CCAGCCATTTGCGCT  1 
MIT_Smik_c492_20940      (  342) CCAGCCATTTGCGCT  1 
MIT_Spar_c261_21317      (  336) CCAGCCATTTGCGCT  1 
SGD_Scer_YOR278W         (  333) CCAGCCATTTGCGCT  1 
SGD_Scer_YER014W         (  174) CGAGCAATGGCAGCT  1 
MIT_Smik_c283_5928       (  168) CGAGCAATGGTAGCT  1 
MIT_Spar_c425_6072       (    5) CGAGCCCTTTCCCGC  1 
MIT_Sbay_c84_6418        (   44) CGAGACTGTTGTCCT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 4337 bayes= 8.90956 E= 7.6e-011 
  -982    251   -982   -982 
  -982    166    134   -982 
   162   -982   -982   -982 
  -982   -982    251   -982 
  -154    234   -982   -982 
   -55    215   -982   -982 
   126    -66   -982   -154 
  -982   -982    -66    145 
  -982   -982     34    126 
  -982   -982     34    126 
  -982     34    192   -154 
   -55    192   -982   -154 
  -982     34    215   -982 
  -982    234    -66   -982 
  -982    -66   -982    145 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 7.6e-011 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.555556  0.444444  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.111111  0.888889  0.000000  0.000000 
 0.222222  0.777778  0.000000  0.000000 
 0.777778  0.111111  0.000000  0.111111 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.000000  0.222222  0.777778 
 0.000000  0.000000  0.222222  0.777778 
 0.000000  0.222222  0.666667  0.111111 
 0.222222  0.666667  0.000000  0.111111 
 0.000000  0.222222  0.777778  0.000000 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.111111  0.000000  0.888889 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
C[CG]AGC[CA]AT[TG][TG][GC][CA][GC]CT
--------------------------------------------------------------------------------




Time  4.39 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =   9   llr = 181   E-value = 1.1e-018
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  ::::4a6::a4:1:7a33:1
pos.-specific     C  1:a:::::a:::2:1::66:
probability       G  9::4::4a:::a6:2:1139
matrix            T  :a:66:::::6:1a::6:1:

         bits    2.5   *    **  *        
                 2.3   *    **  *        
                 2.0 * *    **  *       *
                 1.8 * *    **  *       *
Information      1.5 ***  * *** * * *   *
content          1.3 ***  * *** * * *   *
(29.0 bits)      1.0 **** ***** * * *  **
                 0.8 **************** ***
                 0.5 **************** ***
                 0.3 ********************
                 0.0 --------------------

Multilevel           GTCTTAAGCATGGTAATCCG
consensus               GA G   A C G AAG 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      +    384  5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
WashU_Skud_Contig1682.4      +    377  5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
MIT_Smik_c492_20940          +    382  5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
MIT_Spar_c261_21317          +    376  5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
SGD_Scer_YOR278W             +    373  5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
MIT_Smik_c283_5928           +    133  7.06e-10 AAGCAACAAG GTCGAAGGCAAGCTGAAAGG CATTTTACAA
MIT_Spar_c425_6072           +    138  1.93e-09 GCAACAAAAT GTCGAAGGCAAGATGAAAGG CGTTTTGCAA
SGD_Scer_YER014W             +    139  2.96e-09 GCAACAAAGT GTCGAAGGCAAGTTCAAAGG CGTTTTGTAA
MIT_Sbay_c84_6418            +    131  2.41e-08 ACAACAAAAT CTCGAAGGCAAGCTAAGGTA AAAATATTCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           5.1e-12  383_[+3]_232
WashU_Skud_Contig1682.4           5.1e-12  376_[+3]_239
MIT_Smik_c492_20940               5.1e-12  381_[+3]_234
MIT_Spar_c261_21317               5.1e-12  375_[+3]_240
SGD_Scer_YOR278W                  5.1e-12  372_[+3]_243
MIT_Smik_c283_5928                7.1e-10  132_[+3]_170
MIT_Spar_c425_6072                1.9e-09  137_[+3]_165
SGD_Scer_YER014W                    3e-09  138_[+3]_164
MIT_Sbay_c84_6418                 2.4e-08  130_[+3]_172
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=9
WashU_Sbay_Contig635.57  (  384) GTCTTAAGCATGGTAATCCG  1 
WashU_Skud_Contig1682.4  (  377) GTCTTAAGCATGGTAATCCG  1 
MIT_Smik_c492_20940      (  382) GTCTTAAGCATGGTAATCCG  1 
MIT_Spar_c261_21317      (  376) GTCTTAAGCATGGTAATCCG  1 
SGD_Scer_YOR278W         (  373) GTCTTAAGCATGGTAATCCG  1 
MIT_Smik_c283_5928       (  133) GTCGAAGGCAAGCTGAAAGG  1 
MIT_Spar_c425_6072       (  138) GTCGAAGGCAAGATGAAAGG  1 
SGD_Scer_YER014W         (  139) GTCGAAGGCAAGTTCAAAGG  1 
MIT_Sbay_c84_6418        (  131) CTCGAAGGCAAGCTAAGGTA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4292 bayes= 8.89448 E= 1.1e-018 
  -982    -66    234   -982 
  -982   -982   -982    162 
  -982    251   -982   -982 
  -982   -982    134     78 
    45   -982   -982     78 
   162   -982   -982   -982 
    78   -982    134   -982 
  -982   -982    251   -982 
  -982    251   -982   -982 
   162   -982   -982   -982 
    45   -982   -982     78 
  -982   -982    251   -982 
  -154     34    166   -154 
  -982   -982   -982    162 
   104    -66     34   -982 
   162   -982   -982   -982 
     4   -982    -66     78 
     4    166    -66   -982 
  -982    166     92   -154 
  -154   -982    234   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.1e-018 
 0.000000  0.111111  0.888889  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.444444  0.555556 
 0.444444  0.000000  0.000000  0.555556 
 1.000000  0.000000  0.000000  0.000000 
 0.555556  0.000000  0.444444  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.000000  0.000000  0.555556 
 0.000000  0.000000  1.000000  0.000000 
 0.111111  0.222222  0.555556  0.111111 
 0.000000  0.000000  0.000000  1.000000 
 0.666667  0.111111  0.222222  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.333333  0.000000  0.111111  0.555556 
 0.333333  0.555556  0.111111  0.000000 
 0.000000  0.555556  0.333333  0.111111 
 0.111111  0.000000  0.888889  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
GTC[TG][TA]A[AG]GCA[TA]G[GC]T[AG]A[TA][CA][CG]G
--------------------------------------------------------------------------------




Time  6.42 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   15   sites =   9   llr = 134   E-value = 6.1e-007
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  :9:a:2:::a:8499
pos.-specific     C  7::::::a:::::1:
probability       G  :1::48:::::2::1
matrix            T  3:a:6:a:a:a:6::

         bits    2.5        *       
                 2.3        *       
                 2.0        *       
                 1.8        *       
Information      1.5   ** ******    
content          1.3 **** ******  **
(21.5 bits)      1.0 ************ **
                 0.8 ***************
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           CATATGTCTATATAA
consensus            T   GA     GA  
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
MIT_Smik_c492_20940          -    357  1.53e-08 ATCACGCCTC CATATGTCTATATAA AGCGCAAATG
MIT_Spar_c261_21317          -    351  1.53e-08 ATCACGCCTC CATATGTCTATATAA AGCGCAAATG
SGD_Scer_YOR278W             -    348  1.53e-08 ATCACGCCTC CATATGTCTATATAA AGCGCAAATG
WashU_Skud_Contig1682.4      -    352  3.10e-08 ATCACGCCTC CATATGTCTATGTAA AGCGCAAATG
MIT_Spar_c425_6072           +    280  5.61e-08 GAAGAATGAA TATAGGTCTATAAAA ATTCAATAAT
SGD_Scer_YER014W             +    273  5.61e-08 AAAAATTAAA TATAGGTCTATAAAA CTCGATAATT
WashU_Sbay_Contig635.57      -    359  1.88e-07 ATCACGCCTC CATATGTCTATGTCA AGCGCAAATG
MIT_Smik_c283_5928           +    275  3.48e-07 AAATGTTAAA TATAGATCTATAAAA ATTGAATAGT
MIT_Sbay_c84_6418            +    264  7.23e-07 TTATATTAAA CGTAGATCTATAAAG TTTAAATAGT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c492_20940               1.5e-08  356_[-4]_264
MIT_Spar_c261_21317               1.5e-08  350_[-4]_270
SGD_Scer_YOR278W                  1.5e-08  347_[-4]_273
WashU_Skud_Contig1682.4           3.1e-08  351_[-4]_269
MIT_Spar_c425_6072                5.6e-08  279_[+4]_28
SGD_Scer_YER014W                  5.6e-08  272_[+4]_35
WashU_Sbay_Contig635.57           1.9e-07  358_[-4]_262
MIT_Smik_c283_5928                3.5e-07  274_[+4]_33
MIT_Sbay_c84_6418                 7.2e-07  263_[+4]_44
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=15 seqs=9
MIT_Smik_c492_20940      (  357) CATATGTCTATATAA  1 
MIT_Spar_c261_21317      (  351) CATATGTCTATATAA  1 
SGD_Scer_YOR278W         (  348) CATATGTCTATATAA  1 
WashU_Skud_Contig1682.4  (  352) CATATGTCTATGTAA  1 
MIT_Spar_c425_6072       (  280) TATAGGTCTATAAAA  1 
SGD_Scer_YER014W         (  273) TATAGGTCTATAAAA  1 
WashU_Sbay_Contig635.57  (  359) CATATGTCTATGTCA  1 
MIT_Smik_c283_5928       (  275) TATAGATCTATAAAA  1 
MIT_Sbay_c84_6418        (  264) CGTAGATCTATAAAG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 4337 bayes= 8.90956 E= 6.1e-007 
  -982    192   -982      4 
   145   -982    -66   -982 
  -982   -982   -982    162 
   162   -982   -982   -982 
  -982   -982    134     78 
   -55   -982    215   -982 
  -982   -982   -982    162 
  -982    251   -982   -982 
  -982   -982   -982    162 
   162   -982   -982   -982 
  -982   -982   -982    162 
   126   -982     34   -982 
    45   -982   -982     78 
   145    -66   -982   -982 
   145   -982    -66   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 6.1e-007 
 0.000000  0.666667  0.000000  0.333333 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.444444  0.555556 
 0.222222  0.000000  0.777778  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.444444  0.000000  0.000000  0.555556 
 0.888889  0.111111  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
[CT]ATA[TG][GA]TCTAT[AG][TA]AA
--------------------------------------------------------------------------------




Time  8.49 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 162   E-value = 6.6e-011
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  27a973:384:aa:a9693a
pos.-specific     C  1:::::6::::::9::::::
probability       G  7::::74126a::::1:17:
matrix            T  :3:13::6:::::1::4:::

         bits    2.5           *         
                 2.3           *         
                 2.0           *  *      
                 1.8           *  *      
Information      1.5   *   *   *****    *
content          1.3   *  **   ****** ***
(25.9 bits)      1.0 * ** ** ******** ***
                 0.8 ******* ************
                 0.5 ******* ************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GAAAAGCTAGGAACAAAAGA
consensus            AT  TAGAGA      T A 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c492_20940          +    309  2.27e-12 TTTCAATAAT GAAAAGCTAGGAACAAAAGA AATTTGTCTA
SGD_Scer_YOR278W             +    300  7.58e-11 TTTCAATAAT GAAAAGCTAGGAACAAAAAA AATTGGTCTA
WashU_Sbay_Contig635.57      +    312  8.91e-10 TTTCATTAAA GAAAAGCTAGGAACAAAGAA ATTGGTCTAC
WashU_Skud_Contig1682.4      +    304  8.91e-10 TTTCAATAAT GAAAAGCTAGGAATAAAAGA GATTGGTCTA
MIT_Spar_c261_21317          +    304  8.91e-10 TTTCAATAAT GAAAAGCTAGGAACAGAAAA ATTGGTCTAC
MIT_Smik_c283_5928           -     76  1.57e-09 AAAGAAAAGA GTAATGGAAAGAACAATAGA GGGATTTGCA
MIT_Spar_c425_6072           -     74  3.54e-08 AAGAAAAAGA ATAATAGAGAGAACAATAGA GAGATCCGCG
SGD_Scer_YER014W             -     74  3.54e-08 AAGAAATAGT ATAATAGAGAGAACAATAGA GATATTCGCG
MIT_Sbay_c84_6418            -     69  4.79e-08 AAAACGAGAA CAATAAGGAAGAACAATAGA AGGATGCGAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c492_20940               2.3e-12  308_[+5]_307
SGD_Scer_YOR278W                  7.6e-11  299_[+5]_316
WashU_Sbay_Contig635.57           8.9e-10  311_[+5]_304
WashU_Skud_Contig1682.4           8.9e-10  303_[+5]_312
MIT_Spar_c261_21317               8.9e-10  303_[+5]_312
MIT_Smik_c283_5928                1.6e-09  75_[-5]_227
MIT_Spar_c425_6072                3.5e-08  73_[-5]_229
SGD_Scer_YER014W                  3.5e-08  73_[-5]_229
MIT_Sbay_c84_6418                 4.8e-08  68_[-5]_234
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
MIT_Smik_c492_20940      (  309) GAAAAGCTAGGAACAAAAGA  1 
SGD_Scer_YOR278W         (  300) GAAAAGCTAGGAACAAAAAA  1 
WashU_Sbay_Contig635.57  (  312) GAAAAGCTAGGAACAAAGAA  1 
WashU_Skud_Contig1682.4  (  304) GAAAAGCTAGGAATAAAAGA  1 
MIT_Spar_c261_21317      (  304) GAAAAGCTAGGAACAGAAAA  1 
MIT_Smik_c283_5928       (   76) GTAATGGAAAGAACAATAGA  1 
MIT_Spar_c425_6072       (   74) ATAATAGAGAGAACAATAGA  1 
SGD_Scer_YER014W         (   74) ATAATAGAGAGAACAATAGA  1 
MIT_Sbay_c84_6418        (   69) CAATAAGGAAGAACAATAGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 4292 bayes= 8.89448 E= 6.6e-011 
   -55    -66    192   -982 
   104   -982   -982      4 
   162   -982   -982   -982 
   145   -982   -982   -154 
   104   -982   -982      4 
     4   -982    192   -982 
  -982    166    134   -982 
     4   -982    -66     78 
   126   -982     34   -982 
    45   -982    166   -982 
  -982   -982    251   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -982    234   -982   -154 
   162   -982   -982   -982 
   145   -982    -66   -982 
    78   -982   -982     45 
   145   -982    -66   -982 
     4   -982    192   -982 
   162   -982   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.6e-011 
 0.222222  0.111111  0.666667  0.000000 
 0.666667  0.000000  0.000000  0.333333 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.000000  0.111111 
 0.666667  0.000000  0.000000  0.333333 
 0.333333  0.000000  0.666667  0.000000 
 0.000000  0.555556  0.444444  0.000000 
 0.333333  0.000000  0.111111  0.555556 
 0.777778  0.000000  0.222222  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.555556  0.000000  0.000000  0.444444 
 0.888889  0.000000  0.111111  0.000000 
 0.333333  0.000000  0.666667  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
[GA][AT]AA[AT][GA][CG][TA][AG][GA]GAACAA[AT]A[GA]A
--------------------------------------------------------------------------------




Time 10.53 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YOR278W                 3.99e-29  224_[+1(7.13e-12)]_55_[+5(7.58e-11)]_13_[+2(1.85e-10)]_[-4(1.53e-08)]_10_[+3(5.08e-12)]_243
MIT_Spar_c261_21317              4.14e-28  228_[+1(7.13e-12)]_55_[+5(8.91e-10)]_12_[+2(1.85e-10)]_[-4(1.53e-08)]_10_[+3(5.08e-12)]_240
MIT_Smik_c492_20940              4.23e-30  233_[+1(2.25e-11)]_55_[+5(2.27e-12)]_13_[+2(1.85e-10)]_[-4(1.53e-08)]_10_[+3(5.08e-12)]_234
WashU_Skud_Contig1682.4          8.07e-28  230_[+1(7.13e-12)]_53_[+5(8.91e-10)]_13_[+2(1.85e-10)]_[-4(3.10e-08)]_10_[+3(5.08e-12)]_239
WashU_Sbay_Contig635.57          5.21e-26  27_[+2(5.31e-05)]_194_[+1(9.57e-11)]_55_[+5(8.91e-10)]_12_[+2(1.85e-10)]_[-4(1.88e-07)]_10_[+3(5.08e-12)]_232
SGD_Scer_YER014W                 8.73e-21  73_[-5(3.54e-08)]_22_[+1(1.35e-10)]_3_[+3(2.96e-09)]_15_[+2(2.34e-07)]_84_[+4(5.61e-08)]_35
MIT_Spar_c425_6072               1.18e-20  4_[+2(4.95e-07)]_54_[-5(3.54e-08)]_21_[+1(1.35e-10)]_3_[+3(1.93e-09)]_15_[+2(1.10e-05)]_92_[+4(5.61e-08)]_28
MIT_Smik_c283_5928               1.26e-20  75_[-5(1.57e-09)]_16_[+1(1.44e-09)]_1_[+3(7.06e-10)]_15_[+2(4.95e-07)]_92_[+4(3.48e-07)]_33
MIT_Sbay_c84_6418                3.25e-17  43_[+2(1.47e-06)]_10_[-5(4.79e-08)]_19_[+1(1.06e-09)]_3_[+3(2.41e-08)]_113_[+4(7.23e-07)]_6_[-3(8.88e-05)]_18
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM4-HEM15.fa000444000766000024      1775413155576321 20116 0ustar00cjfieldsstaff000000000000>SGD_Scer_YOR278W HEM4 "Uroporphyrinogen III synthase, catalyzes the conversion of hydroxymethylbilane to uroporphyrinogen III, the fourth step in the heme biosynthetic pathway"
CTCTCGAGCAAGGTCTATTTTACCTTTCTGTTTCCTTATCCTTTGACACTAAAATTCAAA
AAACTCACTAGAAAGTTCACTAAAGCGCCTTAGCTGACTACAGCACAACCCAACCCCAAA
AACTAGTGAACTACACACTAAGAGAATTTATGGTATTTCCATAATTGAAGTATATGTACG
ATGTATACAATGTAAACAAGAGAGTAATGAAGTGAAGATATGTACACCTAGAGCGAACCA
ATGATAATTTGTTTTCTTAATTAAGAAAAACCATTAAAACTGGATTAGATTTCAATAATG
AAAAGCTAGGAACAAAAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGACATA
TGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGTTTT
CTTATCCTGAAGGATCCTGCAAATGAAGTAAGTTCAAAGAATTGAAATGAAATCGCCTTT
TATACCCTCGCCGCACCAAGGAGCGCGCTGTGAAAATTTTTCGCTTTATCTCTTAGGGCT
CCTACTGTCGGTAGAGAAAAGTTGAGTATATTTAAAGCATGAGGTAACTTTTCTGCCCAT
TTTTACTTCTATTTCCATTTGAATTCAGAAAAGTG
>MIT_Spar_c261_21317 YOR278W 5' untranslated region, Contig c261 32269 - 34268, 2000 bp (revcom)
CGTTCCAAGCAGGGTTTATTCTATTTCTCGGCTCCTTTACCCTGTAACTTCGAGATTCAA
AAACTCGCTATAACTTCACTAAAGCGCTTTAGTTGACTACAACACAACCCAACCCCAAAA
TAAACTGTCCAACTACACAATACCGAGGATAATCCACGATATTTCGGTGATTGAAGTATA
TGTATTACGTATGCAATGTAAGCAAGAAACTAACAAAATGAATATGTACACCTAGAGCGA
ACCAATGATAATTTGTTTTCTTAATAAAGAAAAACTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAACAGAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGAC
ATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGT
TCTTTTATCCTGAAGGATAAACGGAAAGCTCCCGATTAAAAACAAGTATAGAGTACTGGA
ATAGAATCGCCTTTTATACCCTCCCTCGCCGCATCAAGAAGCGCGCTGTGAAAATTTTTC
GTTTTTCTCTTAGGGCTCCCATCCAACTGTCGGCGAGGAAAAGTTGTATATATTTAAAGC
ATGAGGTAACTTTGTTGCCCATTATCTTTTTTGTT
>MIT_Smik_c492_20940 YOR278W 5' untranslated region, Contig c492 3260 - 5259(revcom), 2000 bp (revcom)
ACTTTCAAACACACTCTGGTGTACTCCTCGGTCCCTTCATCTCATTTCTTCAAGATGCAG
AACTTCGCCGGAAGTAAACTAAAGTGCTTTAATTAATCAAAAGACAACTTAATTCCCAAA
CGGAAATGCAGGCTAGACAAACCGAAGATAATCCCCGATATTTCTGAGTTTAACAAATGT
ATGTATAATATGTATGCAATGTAGGCAAGAAAATAACGAAGTGAAGATATGTACACCTAG
AGCGAACCAATAATAATTTGTTTTCTTACTAAAGAAAAACTATTAAAACTGGATTAGATT
TCAATAATGAAAAGCTAGGAACAAAAGAAATTTGTCTACTTCCAGCCATTTGCGCTTTAT
ATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAAT
GATGGTTCTTTTAAACCAAAATTTAAAGAAAAATCTTAACGGTAATATGAGTAGGAGGTT
GGAATGGGATCGCTTTTTATACCCTCATTGTGATAAGAGACGCGCAGTGAAAAATTTTCG
CTTTTTCTTAGGGCTCCTATCTAACTCTCGGGCGAATAAATATCATGAATGTATTTAAAC
GTCAAGTTAGTTAAATGTTTGAGTCTGTTTCTTTT
>WashU_Skud_Contig1682.4 YOR278W 5' untranslated region, Contig c1682 3379 - 5378, 2000 bp (revcom)
CTCTTCAAACAGACTCCAATTCACTACTGAGCTCTTACCTTGTGACTTCAAGACTCACTA
CTCAGTTGAAAGACACGCTCAGTACCAAATTCGGCTGCGAGGCAACTAACGCCTTTAAAC
AGGTAGGTAAGGAACAATACCGAAAGGCCATCTCCGATGTTTCGAAGATTGGCAAATGTA
TATATTATGTATGCAATATAGGCAAGATGATAACGAAGTAGAGATATGTACACCTAGAGC
GAACCAATGATAATTTGTTTTCTTAATGAAGAAAGTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAATAAAAGAGATTGGTCTACTTCCAGCCATTTGCGCTTTACATAGA
CATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGG
TTCTATTTAAAATGAAATCTAAAGATAAACCCTAGTCATAATCAAGTGGGTTGTGTTAAA
ATACAAGCACCTTTTATACTCTCGCAGCGTCAGTGGCGCGTTGTGAAAAATTTTCACTTT
TTCTCAGGGCTTTTACCCAACTGCCGACAAATAAAAGCCGTATTTAAGGAATGTGATTAG
TTTACTTTCCAATGCTTTCTCTTTTTTGTAGGGTA
>WashU_Sbay_Contig635.57 YOR278W 5' untranslated region, Contig c635 91073 - 93072, 2000 bp (revcom)
ACGTACAGATGGCGTCTCCTCCTTTCGCGAGCCCCTTGCCTTGTGACTTCAGCCTAACTT
CTTGACTAGAAGATACAACAAGAAATACTCAAATCGGTTATTGTGCAACTCATCCCTCAG
ACAGTTTGGTAAGAAACACCGAAGACTATTTCCGATATCTCAAAGAATGACAAAAGTATA
CATTATATATGCAAGAGAGGCAAGAAAAGAGTAAAAAAGAGTAAAAAAAACATGTACACC
TAGAGCGAACCAGTGATAATTTGCTTCTCAATGAAGAAAAAGCGATTAAAACTGGATTAG
ATTTCATTAAAGAAAAGCTAGGAACAAAGAAATTGGTCTACTTCCAGCCATTTGCGCTTG
ACATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGA
ATGATGGCTCTTTTAAATTGAGATCTAAAAGAAATATCCTGGAAAAGAGTAGAGAAGAGT
CCAAACTGTAGGAATTCAATCGCTTTTTATACTCTCATCGCGGAAAAGACGCGCTGTGAA
AAATTTTCTCTTTTTCTTAGGGCTCCTATCCAGCTGCCTGCGAACAAAAGCCGTATTTAA
AGCATGATTTTCACTACTATGTATGTTCTTTCTGC
>SGD_Scer_YOR176W HEM15 "Ferrochelatase, a mitochondrial inner membrane protein, catalyzes the insertion of ferrous iron into protoporphyrin IX, the eighth and final step in the heme biosynthetic pathway; Yfh1p mediates the use of iron by Hem15p"
TCTTTAAACGTTCTTTTTTTTACTGCTAAATTTGTCCAAATAGCAGGTATGTGTTAAATA
TTTCTGTACTTCTTGTAAACCGACTCAAGTGGAACACGAGAATTTACGCTTGTTTGGTGT
CAAGCCAAGAGTGACCTTGACCGACCAAAAGTATTCCTTCGCGTCCTCCTTCTTCAATCC
CATATCCCCTACGAAAAAAAGCAGCATGAGAAAACGAAGGGCAGCAACTCCTTCGTCATA
TAAGGCTTACGGTGACCATTGAAGATTGGGCATGTCTAACGGCTATTGCCAGCGGAGATG
TTTCAAGGCATCCTACACATGCTACATATTTGTAATTATTTTACTGAGTTTGTGTATATA
AAAAACTTTTTTAAAAAAAAAAAATGGCCAGCATCCTCTTTCATGTAAAGCTGTTGAACC
TTCCTGAAATTTACTTCTAAAATTGTTCAGTAAAACTGCTTGTTAAAAGTGCGAAGAGTT
CTTTTTTAGCTTTTTTTGTCCTGCTGTTGAGCTGTTTTGCTTTACTGTTCAACAAAACAT
TGAAGATCTTTCACATTGCGCGTCGAAACCACAAACCGTCGAAAACAATGGTCATCTAAA
TAAAGGGTTCTTATTAAACAGATTTAAAGCCAAGGACAAAATACAGGCACAGGTCAAGCA
AGAAGACAAACCGCATACGCCAAGACAAACCGTGGTGATTTAATTCTGCTGCTGATCGCT
TCCAACA
>MIT_Spar_c278_20970 YOR176W 5' untranslated region, Contig c278 32746 - 34745, 2000 bp (revcom)
TCTTCAAACGTTCTTTTCCTACTACTAAGCTTTTCAATAAATAGCGGGTATATGCTAAAT
ACTTCTTTGCTTCTTGTACGACCTACTTAATTGAAATACGGATATTTTTGCTTGCTTGGT
GCCAAACCAAGAGTGACCTTGACCGACTAAAAGTATTCCTTCGCGTCCTCCTTCTTCAAT
CCCATATCCCCTACTGAAAAAAGCAGCGTGCGAAAATGAAGGGCAGCAACTCCTTCGTCA
TATAAGGCTTAGGTAATCTTTCAAGGTCAGGTATATCCAGCTGTCGTTACGAGTAGAGAT
ATTTCAAGCTGTCCTGCACATGCTACATATTTGTGATTATTTTTATTGAGTTGCGTATAT
AAAAAAACAATCTAAAAAAAAAAAAAATGGCCAGCATCTTCTTCCATGTAAAGCTGTTGA
ACCTTGCTAAAATCTATTACTATAATTGTTCAGTAAAGTTGCTTGTTAAAAATGCGAAGA
GTCTTTTTTAGCTTTTTTTGCCCTGCTGTTGAGCTGTTTTGCTTCACTGTTCAACAAAAC
AGTGAAGATCTTTCGAATTGCGCGTCGAAACCACAAACCGTCGAAAATAATGGTCATCTA
AATAAAGGGTTCTTATTTGAACAGATTTAAAGCTCAAAGACACGATACAGGCACAGGTCC
AGAAAGAATACAAAACGCAAACGCCAAGACAAATTGTGGTAATTTCATTCTGCTGCTGAT
CACTGCC
>MIT_Smik_c935_20455 YOR176W 5' untranslated region, Contig c935 1803 - 3802(revcom), 2000 bp (revcom)
TCTTGAATTGCAATTTTCTACTACTGAAGTTACCAACAATTAGCAAATATGTGATGAGTC
CTTTTTACGTTCTTGTATAACCTAAGTTAAATACAAAGGTTTATGCTCCTTTAATGATCA
GACCAACAGTGATCTTGGCCGACCAAAAGACTCCTTCGCGTCCTCCTTCTTCAAGTCTCA
TATCCCCTACCAGAAAAAGTAGCAGGCGAAAATAAAGAGCAACTGCTCCCCCCCATATAG
AGCTTACCATAATTTCTCAAGGAAAGGTATCTCCAGTTGTCGTAAAGAATAAAGAAGTTT
CAACGTGTCCTGCATGTTCTACAAATTTGCAATTGACTTTACTAAGTTGCATATATAAAA
CTTGTATTAGATAAGTTAGCCAGCATTTTCATTCAAGCTAAGATGTTGAATATGCCAAAG
CACATTGCTGAAATTAATCAGTAAAGCTGCTTGCTGAAAGTGGAAATATTTTCAGCTTTT
TTTGCTCTGCTGTTGAGCTGTTTTACTTCATTGTTCAACAAAACAATAGAGTTCTCTCCA
ATTGCGCGTCAAAACCACAAACCGTCGAAAATAATGATCATCTAAATAAAAGAGTTCACG
TTTTCACATATTTAAAGTTGAAATACTCCATACAGGCACAGGTCTAACAAGAAGACAACG
CATTCGATAAAACTAATCGTGGTAATTTTTATATCGCTGCTAGCCACTACCAACAATGTA
CAATTTT
>WashU_Skud_Contig2050.4 YOR176W 5' untranslated region, Contig c2050 12271 - 14270(revcom), 2000 bp (revcom)
TCTTAGTTTATAGCTTTTCTACTACTCTGGTCATAAACGAACAGAAGATAAGCAAGAAAT
CTTTTTTTCCTTCTTTTACGGTCTATTCAAGTGAAGCACGGGGATTCCCGCTTGTTTAAT
AATCAGACCAACAATGATATTGACCGACCAAAAGAAGTATTCCTTCGCGTGCTTCTCCTT
TCTGTGTCAAATCCCCTACTGAAAAAGCAGCATTGGGAAAGGAACAGCAGCTTCTCCTTC
GTCGCAGAGAGCTCGCGGTAGCATTTCATTGTCAGGTATTTATGATATTTGCTAAGAATA
ATTAAAATGTCTTCAGGTCTTGCACATACTCCTACATATTTGTAAGTATTTTACTGATTT
GAGTATATAAAAGCCGTACTAAAACTAACCAGCACCTGTAGCAAGGTGCAAAATGTTGAA
CCTTTCCGAAATTTATTGCCAGAAACCAAGAGCTAAAAGTGCTTGGTAAAAGTGAAAAGA
CTCTTTTTCAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGTTCCATCTGTTCAACAAA
ACAGCTTCACTGGATCTTTCAAAGTGCGCGTCGAAACCACAAACCGTCGAAAATATTGAT
CATCTAAATAAAGGGTTCTTATTTGCACAGTTTCGCATTGAAATATTCCATTCAGGCACA
GATCAACAAGAAGACAAAAAGGTATTCGAGAAGACTAATTGTGGTATTTTTACTTTGCTG
CTGACCA
>WashU_Sbay_Contig480.2 YOR176W 5' untranslated region, Contig c480 3444 - 5443(revcom), 2000 bp (revcom)
TTTCAGGGAAGCACCATGTGCACGAATTGTTCTAGAAAGCATTTTTGGTTCGTAAATTCT
CTACAACTGAACTTATTAACAAATAGCAAACAGAGAAGAAAATTTTTTTTTTCCTTCTTG
TATGGTCAGTTAGTTGAAAACACGGAGATTTTCACTTGTTTAGTAAGCAGAGCCATAATG
CTCTTGACCGACCAAAAGAAGTATTCCTACGCGAGCTCCCTCTTCAAGTGCCAAATCCCC
TACTGAAAAAAGCAACATGAGAAGCAAAGAGATGCCTCTCGCCATGCAGGGCTTGCGGTC
ATGTTTTCTACGTTCAATTGATTTTGTTACAGCTGAAAGATGTTTATAAAACTGTCTTGC
ATATGCTCTATTTACTTGTAAACAATTTTATTAAGTTGCGTATATATGATCGTACTAAAA
ATTGGCTGGCGCGTTCTCCAGGCAGAGTTGGTTGAACCTTGCTCGAATTGATAGCTCAAA
GTGGAGAGACTCTTTTTTAGCTGTTTTTTGTTCTGCTGTTGAGCTGTTTTGCTCCACCTG
TTCAACAAAATGGCAGAGATCTTTCGAAGTGCGCGTCGAAACCACAAACCATCAAAAATA
TCGACCATCTAAATAAAGGGTTCTTGTTTGAATAAATATCAGGCGAAGCTCTTCATACAG
GCACAGGTCAGATAAGAAGACAATTCGAATTCGAGAAGGATATTCGTGGTATCTTTAATC
TGCTGCT
BioPerl-1.007002/t/data/map_hem/HEM4-HEM15.meme.txt000444000766000024     12002213155576321 21270 0ustar00cjfieldsstaff000000000000********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= HEM4-HEM15.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YOR278W         1.0000    635  MIT_Spar_c261_21317      1.0000    635  
MIT_Smik_c492_20940      1.0000    635  WashU_Skud_Contig1682.4  1.0000    635  
WashU_Sbay_Contig635.57  1.0000    635  SGD_Scer_YOR176W         1.0000    727  
MIT_Spar_c278_20970      1.0000    727  MIT_Smik_c935_20455      1.0000    727  
WashU_Skud_Contig2050.4  1.0000    727  WashU_Sbay_Contig480.2   1.0000    727  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme HEM4-HEM15.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=       10    maxsites=       10    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            6810    N=              10
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.314 C 0.186 G 0.186 T 0.314 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =  10   llr = 217   E-value = 8.2e-028
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :9::::::24a::5::5:::
pos.-specific     C  :::a:15a11::::a55::a
probability       G  a:::::::75:2:5:5:55:
matrix            T  :1a:a95::::8a::::55:

         bits    2.5 *  *   *      *    *
                 2.3 *  *   *      *    *
                 2.0 *  *   *      *    *
                 1.8 *  *   *      *    *
Information      1.5 * ***  *  * * **   *
content          1.3 ****** ** * * **   *
(31.3 bits)      1.0 ********* **********
                 0.8 ********************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           GATCTTCCGGATTACCAGGC
consensus                  T AA G G GCTT 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      -    391  1.53e-11 TCAATAAACT GATCTTCCGGATTACCATGC TTAAGACATC
WashU_Skud_Contig1682.4      -    384  1.53e-11 TCAATAAACT GATCTTCCGGATTACCATGC TTAAGACATC
MIT_Smik_c492_20940          -    389  1.53e-11 TCAATAAACT GATCTTCCGGATTACCATGC TTAAGACATC
MIT_Spar_c261_21317          -    383  1.53e-11 TCAATAAACT GATCTTCCGGATTACCATGC TTAAGACATC
SGD_Scer_YOR278W             -    380  1.53e-11 TCAATAAACT GATCTTCCGGATTACCATGC TTAAGACATC
MIT_Spar_c278_20970          +    547  2.49e-11 AAACAGTGAA GATCTTTCGAATTGCGCGTC GAAACCACAA
WashU_Sbay_Contig480.2       +    558  6.65e-11 AAATGGCAGA GATCTTTCGAAGTGCGCGTC GAAACCACAA
WashU_Skud_Contig2050.4      +    553  3.56e-10 AGCTTCACTG GATCTTTCAAAGTGCGCGTC GAAACCACAA
SGD_Scer_YOR176W             +    545  3.56e-10 AAACATTGAA GATCTTTCACATTGCGCGTC GAAACCACAA
MIT_Smik_c935_20455          +    531  1.23e-09 AAACAATAGA GTTCTCTCCAATTGCGCGTC AAAACCACAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           1.5e-11  390_[-1]_225
WashU_Skud_Contig1682.4           1.5e-11  383_[-1]_232
MIT_Smik_c492_20940               1.5e-11  388_[-1]_227
MIT_Spar_c261_21317               1.5e-11  382_[-1]_233
SGD_Scer_YOR278W                  1.5e-11  379_[-1]_236
MIT_Spar_c278_20970               2.5e-11  546_[+1]_161
WashU_Sbay_Contig480.2            6.6e-11  557_[+1]_150
WashU_Skud_Contig2050.4           3.6e-10  552_[+1]_155
SGD_Scer_YOR176W                  3.6e-10  544_[+1]_163
MIT_Smik_c935_20455               1.2e-09  530_[+1]_177
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=10
WashU_Sbay_Contig635.57  (  391) GATCTTCCGGATTACCATGC  1 
WashU_Skud_Contig1682.4  (  384) GATCTTCCGGATTACCATGC  1 
MIT_Smik_c492_20940      (  389) GATCTTCCGGATTACCATGC  1 
MIT_Spar_c261_21317      (  383) GATCTTCCGGATTACCATGC  1 
SGD_Scer_YOR278W         (  380) GATCTTCCGGATTACCATGC  1 
MIT_Spar_c278_20970      (  547) GATCTTTCGAATTGCGCGTC  1 
WashU_Sbay_Contig480.2   (  558) GATCTTTCGAAGTGCGCGTC  1 
WashU_Skud_Contig2050.4  (  553) GATCTTTCAAAGTGCGCGTC  1 
SGD_Scer_YOR176W         (  545) GATCTTTCACATTGCGCGTC  1 
MIT_Smik_c935_20455      (  531) GTTCTCTCCAATTGCGCGTC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6620 bayes= 9.36851 E= 8.2e-028 
  -997   -997    251   -997 
   147   -997   -997   -169 
  -997   -997   -997    162 
  -997    251   -997   -997 
  -997   -997   -997    162 
  -997    -81   -997    147 
  -997    151   -997     62 
  -997    251   -997   -997 
   -70    -81    199   -997 
    30    -81    151   -997 
   162   -997   -997   -997 
  -997   -997     19    130 
  -997   -997   -997    162 
    62   -997    151   -997 
  -997    251   -997   -997 
  -997    151    151   -997 
    62    151   -997   -997 
  -997   -997    151     62 
  -997   -997    151     62 
  -997    251   -997   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 8.2e-028 
 0.000000  0.000000  1.000000  0.000000 
 0.900000  0.000000  0.000000  0.100000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.200000  0.100000  0.700000  0.000000 
 0.400000  0.100000  0.500000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.200000  0.800000 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
GATCTT[CT]C[GA][GA]A[TG]T[AG]C[CG][AC][GT][GT]C
--------------------------------------------------------------------------------




Time  4.85 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =   20   sites =  10   llr = 212   E-value = 9.1e-027
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  :9:1:5:9:::a5:5a9518
pos.-specific     C  5179::::5a::595:::::
probability       G  5:::::a15:a:::::1:9:
matrix            T  ::3:a5:::::::1:::5:2

         bits    2.5       *  **         
                 2.3       *  **         
                 2.0    *  *  **  *    * 
                 1.8    *  *  **  *    * 
Information      1.5 *  ** * **** * *  * 
content          1.3 ***** ****** * ** * 
(30.7 bits)      1.0 ***** *********** **
                 0.8 ***** *********** **
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           CACCTAGACCGAACAAAAGA
consensus            G T  T  G   C C  T T
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1682.4      +    231  1.46e-11 GAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
MIT_Spar_c261_21317          +    229  1.46e-11 TGAATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
SGD_Scer_YOR278W             +    225  1.46e-11 AAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
SGD_Scer_YOR176W             +    133  5.07e-11 AGCCAAGAGT GACCTTGACCGACCAAAAGT ATTCCTTCGC
WashU_Sbay_Contig635.57      +    237  9.06e-11 AAAACATGTA CACCTAGAGCGAACCAGTGA TAATTTGCTT
MIT_Smik_c492_20940          +    234  2.63e-10 AAGATATGTA CACCTAGAGCGAACCAATAA TAATTTGTTT
WashU_Sbay_Contig480.2       +    180  3.17e-10 GAGCCATAAT GCTCTTGACCGACCAAAAGA AGTATTCCTA
MIT_Smik_c935_20455          +    131  3.17e-10 GACCAACAGT GATCTTGGCCGACCAAAAGA CTCCTTCGCG
MIT_Spar_c278_20970          +    135  6.22e-10 AACCAAGAGT GACCTTGACCGACTAAAAGT ATTCCTTCGC
WashU_Skud_Contig2050.4      +    136  7.40e-10 GACCAACAAT GATATTGACCGACCAAAAGA AGTATTCCTT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1682.4           1.5e-11  230_[+2]_385
MIT_Spar_c261_21317               1.5e-11  228_[+2]_387
SGD_Scer_YOR278W                  1.5e-11  224_[+2]_391
SGD_Scer_YOR176W                  5.1e-11  132_[+2]_575
WashU_Sbay_Contig635.57           9.1e-11  236_[+2]_379
MIT_Smik_c492_20940               2.6e-10  233_[+2]_382
WashU_Sbay_Contig480.2            3.2e-10  179_[+2]_528
MIT_Smik_c935_20455               3.2e-10  130_[+2]_577
MIT_Spar_c278_20970               6.2e-10  134_[+2]_573
WashU_Skud_Contig2050.4           7.4e-10  135_[+2]_572
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=10
WashU_Skud_Contig1682.4  (  231) CACCTAGAGCGAACCAATGA  1 
MIT_Spar_c261_21317      (  229) CACCTAGAGCGAACCAATGA  1 
SGD_Scer_YOR278W         (  225) CACCTAGAGCGAACCAATGA  1 
SGD_Scer_YOR176W         (  133) GACCTTGACCGACCAAAAGT  1 
WashU_Sbay_Contig635.57  (  237) CACCTAGAGCGAACCAGTGA  1 
MIT_Smik_c492_20940      (  234) CACCTAGAGCGAACCAATAA  1 
WashU_Sbay_Contig480.2   (  180) GCTCTTGACCGACCAAAAGA  1 
MIT_Smik_c935_20455      (  131) GATCTTGGCCGACCAAAAGA  1 
MIT_Spar_c278_20970      (  135) GACCTTGACCGACTAAAAGT  1 
WashU_Skud_Contig2050.4  (  136) GATATTGACCGACCAAAAGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6620 bayes= 9.36851 E= 9.1e-027 
  -997    151    151   -997 
   147    -81   -997   -997 
  -997    199   -997    -11 
  -169    236   -997   -997 
  -997   -997   -997    162 
    62   -997   -997     62 
  -997   -997    251   -997 
   147   -997    -81   -997 
  -997    151    151   -997 
  -997    251   -997   -997 
  -997   -997    251   -997 
   162   -997   -997   -997 
    62    151   -997   -997 
  -997    236   -997   -169 
    62    151   -997   -997 
   162   -997   -997   -997 
   147   -997    -81   -997 
    62   -997   -997     62 
  -169   -997    236   -997 
   130   -997   -997    -70 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 9.1e-027 
 0.000000  0.500000  0.500000  0.000000 
 0.900000  0.100000  0.000000  0.000000 
 0.000000  0.700000  0.000000  0.300000 
 0.100000  0.900000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.000000  0.000000  1.000000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.900000  0.000000  0.100000 
 0.500000  0.500000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.100000  0.000000  0.900000  0.000000 
 0.800000  0.000000  0.000000  0.200000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[CG]A[CT]CT[AT]GA[CG]CGA[AC]C[AC]AA[AT]G[AT]
--------------------------------------------------------------------------------




Time  9.66 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =   20   sites =  10   llr = 214   E-value = 3.7e-026
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :5:::5::::5:5::::::6
pos.-specific     C  25::5:::5:::5:::5:::
probability       G  :::a5:a5:a:a::a::::4
matrix            T  8:a::5:55:5::a:a5aa:

         bits    2.5    *  *  * *  *     
                 2.3    *  *  * *  *     
                 2.0    *  *  * *  *     
                 1.8    *  *  * *  *     
Information      1.5   *** *  * * *** ** 
content          1.3   *** *  * * *** ** 
(30.8 bits)      1.0 ***** **** *********
                 0.8 ***** **** *********
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TATGCAGGCGAGATGTCTTA
consensus            CC  GT TT T C   T  G
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      +    370  1.12e-10 GACATAGACA TATGGAGGCGTGATGTCTTA AGCATGGTAA
WashU_Skud_Contig1682.4      +    363  1.12e-10 TACATAGACA TATGGAGGCGTGATGTCTTA AGCATGGTAA
MIT_Smik_c492_20940          +    368  1.12e-10 TATATAGACA TATGGAGGCGTGATGTCTTA AGCATGGTAA
MIT_Spar_c261_21317          +    362  1.12e-10 TATATAGACA TATGGAGGCGTGATGTCTTA AGCATGGTAA
SGD_Scer_YOR278W             +    359  1.12e-10 TATATAGACA TATGGAGGCGTGATGTCTTA AGCATGGTAA
WashU_Sbay_Contig480.2       +    512  1.73e-10 TGTTTTTTGT TCTGCTGTTGAGCTGTTTTG CTCCACCTGT
WashU_Skud_Contig2050.4      +    503  1.73e-10 TGTTTTTTGT TCTGCTGTTGAGCTGTTTTG TTCCATCTGT
MIT_Smik_c935_20455          +    486  2.87e-10 CTTTTTTTGC TCTGCTGTTGAGCTGTTTTA CTTCATTGTT
MIT_Spar_c278_20970          +    502  4.84e-10 CTTTTTTTGC CCTGCTGTTGAGCTGTTTTG CTTCACTGTT
SGD_Scer_YOR176W             +    500  4.84e-10 CTTTTTTTGT CCTGCTGTTGAGCTGTTTTG CTTTACTGTT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           1.1e-10  369_[+3]_246
WashU_Skud_Contig1682.4           1.1e-10  362_[+3]_253
MIT_Smik_c492_20940               1.1e-10  367_[+3]_248
MIT_Spar_c261_21317               1.1e-10  361_[+3]_254
SGD_Scer_YOR278W                  1.1e-10  358_[+3]_257
WashU_Sbay_Contig480.2            1.7e-10  511_[+3]_196
WashU_Skud_Contig2050.4           1.7e-10  502_[+3]_205
MIT_Smik_c935_20455               2.9e-10  485_[+3]_222
MIT_Spar_c278_20970               4.8e-10  501_[+3]_206
SGD_Scer_YOR176W                  4.8e-10  499_[+3]_208
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=10
WashU_Sbay_Contig635.57  (  370) TATGGAGGCGTGATGTCTTA  1 
WashU_Skud_Contig1682.4  (  363) TATGGAGGCGTGATGTCTTA  1 
MIT_Smik_c492_20940      (  368) TATGGAGGCGTGATGTCTTA  1 
MIT_Spar_c261_21317      (  362) TATGGAGGCGTGATGTCTTA  1 
SGD_Scer_YOR278W         (  359) TATGGAGGCGTGATGTCTTA  1 
WashU_Sbay_Contig480.2   (  512) TCTGCTGTTGAGCTGTTTTG  1 
WashU_Skud_Contig2050.4  (  503) TCTGCTGTTGAGCTGTTTTG  1 
MIT_Smik_c935_20455      (  486) TCTGCTGTTGAGCTGTTTTA  1 
MIT_Spar_c278_20970      (  502) CCTGCTGTTGAGCTGTTTTG  1 
SGD_Scer_YOR176W         (  500) CCTGCTGTTGAGCTGTTTTG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6620 bayes= 9.36851 E= 3.7e-026 
  -997     19   -997    130 
    62    151   -997   -997 
  -997   -997   -997    162 
  -997   -997    251   -997 
  -997    151    151   -997 
    62   -997   -997     62 
  -997   -997    251   -997 
  -997   -997    151     62 
  -997    151   -997     62 
  -997   -997    251   -997 
    62   -997   -997     62 
  -997   -997    251   -997 
    62    151   -997   -997 
  -997   -997   -997    162 
  -997   -997    251   -997 
  -997   -997   -997    162 
  -997    151   -997     62 
  -997   -997   -997    162 
  -997   -997   -997    162 
    89   -997    119   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.7e-026 
 0.000000  0.200000  0.000000  0.800000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.000000  1.000000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.000000  0.000000  1.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.600000  0.000000  0.400000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
[TC][AC]TG[CG][AT]G[GT][CT]G[AT]G[AC]TGT[CT]TT[AG]
--------------------------------------------------------------------------------




Time 14.33 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =   20   sites =  10   llr = 183   E-value = 2.8e-014
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  41::::a4177a9a78:486
pos.-specific     C  :5aaa::61::::::124:1
probability       G  :4::::::533:::318123
matrix            T  6::::a::3:::1::::1::

         bits    2.5   ***               
                 2.3   ***               
                 2.0   ***               
                 1.8   ***           *   
Information      1.5   *****    * *  *   
content          1.3   ******   ***  *   
(26.3 bits)      1.0  ******* ******** * 
                 0.8 ******** ******** **
                 0.5 ***************** **
                 0.3 ********************
                 0.0 --------------------

Multilevel           TCCCCTACGAAAAAAAGAAA
consensus            AG     ATGG   G CCGG
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
SGD_Scer_YOR176W             +    185  1.89e-12 CAATCCCATA TCCCCTACGAAAAAAAGCAG CATGAGAAAA
WashU_Sbay_Contig480.2       +    236  9.76e-11 AAGTGCCAAA TCCCCTACTGAAAAAAGCAA CATGAGAAGC
MIT_Spar_c278_20970          +    187  1.11e-10 CAATCCCATA TCCCCTACTGAAAAAAGCAG CGTGCGAAAA
WashU_Sbay_Contig635.57      -    545  7.33e-10 GCTGGATAGG AGCCCTAAGAAAAAGAGAAA ATTTTTCACA
MIT_Smik_c935_20455          +    183  3.77e-09 AAGTCTCATA TCCCCTACCAGAAAAAGTAG CAGGCGAAAA
MIT_Smik_c492_20940          -    536  4.08e-09 GTTAGATAGG AGCCCTAAGAAAAAGCGAAA ATTTTTCACT
MIT_Spar_c261_21317          -    538  7.56e-09 GTTGGATGGG AGCCCTAAGAGAAAAACGAA AAATTTTCAC
SGD_Scer_YOR278W             -    521  9.27e-09 CGACAGTAGG AGCCCTAAGAGATAAAGCGA AAAATTTTCA
WashU_Skud_Contig1682.4      -    616  1.19e-08          . TACCCTACAAAAAAGAGAAA GCATTGGAAA
WashU_Skud_Contig2050.4      +    192  2.76e-08 CTGTGTCAAA TCCCCTACTGAAAAAGCAGC ATTGGGAAAG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YOR176W                  1.9e-12  184_[+4]_523
WashU_Sbay_Contig480.2            9.8e-11  235_[+4]_472
MIT_Spar_c278_20970               1.1e-10  186_[+4]_521
WashU_Sbay_Contig635.57           7.3e-10  544_[-4]_71
MIT_Smik_c935_20455               3.8e-09  182_[+4]_525
MIT_Smik_c492_20940               4.1e-09  535_[-4]_80
MIT_Spar_c261_21317               7.6e-09  537_[-4]_78
SGD_Scer_YOR278W                  9.3e-09  520_[-4]_95
WashU_Skud_Contig1682.4           1.2e-08  615_[-4]
WashU_Skud_Contig2050.4           2.8e-08  191_[+4]_516
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=10
SGD_Scer_YOR176W         (  185) TCCCCTACGAAAAAAAGCAG  1 
WashU_Sbay_Contig480.2   (  236) TCCCCTACTGAAAAAAGCAA  1 
MIT_Spar_c278_20970      (  187) TCCCCTACTGAAAAAAGCAG  1 
WashU_Sbay_Contig635.57  (  545) AGCCCTAAGAAAAAGAGAAA  1 
MIT_Smik_c935_20455      (  183) TCCCCTACCAGAAAAAGTAG  1 
MIT_Smik_c492_20940      (  536) AGCCCTAAGAAAAAGCGAAA  1 
MIT_Spar_c261_21317      (  538) AGCCCTAAGAGAAAAACGAA  1 
SGD_Scer_YOR278W         (  521) AGCCCTAAGAGATAAAGCGA  1 
WashU_Skud_Contig1682.4  (  616) TACCCTACAAAAAAGAGAAA  1 
WashU_Skud_Contig2050.4  (  192) TCCCCTACTGAAAAAGCAGC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6620 bayes= 9.36851 E= 2.8e-014 
    30   -997   -997     89 
  -169    151    119   -997 
  -997    251   -997   -997 
  -997    251   -997   -997 
  -997    251   -997   -997 
  -997   -997   -997    162 
   162   -997   -997   -997 
    30    177   -997   -997 
  -169    -81    151    -11 
   111   -997     77   -997 
   111   -997     77   -997 
   162   -997   -997   -997 
   147   -997   -997   -169 
   162   -997   -997   -997 
   111   -997     77   -997 
   130    -81    -81   -997 
  -997     19    219   -997 
    30    119    -81   -169 
   130   -997     19   -997 
    89    -81     77   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.8e-014 
 0.400000  0.000000  0.000000  0.600000 
 0.100000  0.500000  0.400000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.400000  0.600000  0.000000  0.000000 
 0.100000  0.100000  0.500000  0.300000 
 0.700000  0.000000  0.300000  0.000000 
 0.700000  0.000000  0.300000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.900000  0.000000  0.000000  0.100000 
 1.000000  0.000000  0.000000  0.000000 
 0.700000  0.000000  0.300000  0.000000 
 0.800000  0.100000  0.100000  0.000000 
 0.000000  0.200000  0.800000  0.000000 
 0.400000  0.400000  0.100000  0.100000 
 0.800000  0.000000  0.200000  0.000000 
 0.600000  0.100000  0.300000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
[TA][CG]CCCTA[CA][GT][AG][AG]AAA[AG]A[GC][AC][AG][AG]
--------------------------------------------------------------------------------




Time 18.90 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =   20   sites =  10   llr = 178   E-value = 7.9e-013
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  a4::3::5:::5a9:7aa15
pos.-specific     C  ::1::16::a:1:1::::::
probability       G  :::561:::::::::2::95
matrix            T  :6951845a:a4::a1::::

         bits    2.5          *          
                 2.3          *          
                 2.0          *        * 
                 1.8          *        * 
Information      1.5 *       *** * * *** 
content          1.3 * *   * *** *** *** 
(25.6 bits)      1.0 * ** ** *** *** ****
                 0.8 ******* *** ********
                 0.5 *********** ********
                 0.3 ********************
                 0.0 --------------------

Multilevel           ATTGGTCATCTAAATAAAGA
consensus             A TA TT   T   G   G
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c278_20970          +    589  2.51e-11 CGTCGAAAAT AATGGTCATCTAAATAAAGG GTTCTTATTT
SGD_Scer_YOR176W             +    587  2.51e-11 CGTCGAAAAC AATGGTCATCTAAATAAAGG GTTCTTATTA
WashU_Skud_Contig2050.4      +    595  2.67e-10 CGTCGAAAAT ATTGATCATCTAAATAAAGG GTTCTTATTT
MIT_Spar_c261_21317          +    251  1.62e-09 ACCAATGATA ATTTGTTTTCTTAATAAAGA AAAACTATTA
WashU_Skud_Contig1682.4      +    253  3.66e-09 ACCAATGATA ATTTGTTTTCTTAATGAAGA AAGTATTAAA
MIT_Smik_c492_20940          +    256  9.18e-09 ACCAATAATA ATTTGTTTTCTTACTAAAGA AAAACTATTA
WashU_Sbay_Contig480.2       +    600  1.13e-08 CATCAAAAAT ATCGACCATCTAAATAAAGG GTTCTTGTTT
SGD_Scer_YOR278W             +    247  1.22e-08 ACCAATGATA ATTTGTTTTCTTAATTAAGA AAAACCATTA
MIT_Smik_c935_20455          +    573  1.29e-08 CGTCGAAAAT AATGATCATCTAAATAAAAG AGTTCACGTT
WashU_Sbay_Contig635.57      +    258  5.96e-08 AACCAGTGAT AATTTGCTTCTCAATGAAGA AAAAGCGATT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c278_20970               2.5e-11  588_[+5]_119
SGD_Scer_YOR176W                  2.5e-11  586_[+5]_121
WashU_Skud_Contig2050.4           2.7e-10  594_[+5]_113
MIT_Spar_c261_21317               1.6e-09  250_[+5]_365
WashU_Skud_Contig1682.4           3.7e-09  252_[+5]_363
MIT_Smik_c492_20940               9.2e-09  255_[+5]_360
WashU_Sbay_Contig480.2            1.1e-08  599_[+5]_108
SGD_Scer_YOR278W                  1.2e-08  246_[+5]_369
MIT_Smik_c935_20455               1.3e-08  572_[+5]_135
WashU_Sbay_Contig635.57             6e-08  257_[+5]_358
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=10
MIT_Spar_c278_20970      (  589) AATGGTCATCTAAATAAAGG  1 
SGD_Scer_YOR176W         (  587) AATGGTCATCTAAATAAAGG  1 
WashU_Skud_Contig2050.4  (  595) ATTGATCATCTAAATAAAGG  1 
MIT_Spar_c261_21317      (  251) ATTTGTTTTCTTAATAAAGA  1 
WashU_Skud_Contig1682.4  (  253) ATTTGTTTTCTTAATGAAGA  1 
MIT_Smik_c492_20940      (  256) ATTTGTTTTCTTACTAAAGA  1 
WashU_Sbay_Contig480.2   (  600) ATCGACCATCTAAATAAAGG  1 
SGD_Scer_YOR278W         (  247) ATTTGTTTTCTTAATTAAGA  1 
MIT_Smik_c935_20455      (  573) AATGATCATCTAAATAAAAG  1 
WashU_Sbay_Contig635.57  (  258) AATTTGCTTCTCAATGAAGA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6620 bayes= 9.36851 E= 7.9e-013 
   162   -997   -997   -997 
    30   -997   -997     89 
  -997    -81   -997    147 
  -997   -997    151     62 
   -11   -997    177   -169 
  -997    -81    -81    130 
  -997    177   -997     30 
    62   -997   -997     62 
  -997   -997   -997    162 
  -997    251   -997   -997 
  -997   -997   -997    162 
    62    -81   -997     30 
   162   -997   -997   -997 
   147    -81   -997   -997 
  -997   -997   -997    162 
   111   -997     19   -169 
   162   -997   -997   -997 
   162   -997   -997   -997 
  -169   -997    236   -997 
    62   -997    151   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 7.9e-013 
 1.000000  0.000000  0.000000  0.000000 
 0.400000  0.000000  0.000000  0.600000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  0.000000  0.500000  0.500000 
 0.300000  0.000000  0.600000  0.100000 
 0.000000  0.100000  0.100000  0.800000 
 0.000000  0.600000  0.000000  0.400000 
 0.500000  0.000000  0.000000  0.500000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.100000  0.000000  0.400000 
 1.000000  0.000000  0.000000  0.000000 
 0.900000  0.100000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.700000  0.000000  0.200000  0.100000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.100000  0.000000  0.900000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
A[TA]T[GT][GA]T[CT][AT]TCT[AT]AAT[AG]AAG[AG]
--------------------------------------------------------------------------------




Time 23.28 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YOR278W                 1.05e-26  224_[+2(1.46e-11)]_2_[+5(1.22e-08)]_92_[+3(1.12e-10)]_1_[-1(1.53e-11)]_121_[-4(9.27e-09)]_95
MIT_Spar_c261_21317              1.29e-27  99_[-3(7.46e-05)]_109_[+2(1.46e-11)]_2_[+5(1.62e-09)]_91_[+3(1.12e-10)]_1_[-1(1.53e-11)]_29_[-1(4.35e-06)]_66_[-1(8.95e-05)]_[-4(7.56e-09)]_78
MIT_Smik_c492_20940              5.72e-26  233_[+2(2.63e-10)]_2_[+5(9.18e-09)]_92_[+3(1.12e-10)]_1_[-1(1.53e-11)]_127_[-4(4.08e-09)]_8_[+2(8.70e-06)]_52
WashU_Skud_Contig1682.4          4.27e-27  230_[+2(1.46e-11)]_2_[+5(3.66e-09)]_90_[+3(1.12e-10)]_1_[-1(1.53e-11)]_128_[-4(2.59e-06)]_64_[-4(1.19e-08)]
WashU_Sbay_Contig635.57          2.42e-26  236_[+2(9.06e-11)]_1_[+5(5.96e-08)]_92_[+3(1.12e-10)]_1_[-1(1.53e-11)]_134_[-4(7.33e-10)]_71
SGD_Scer_YOR176W                 4.69e-30  132_[+2(5.07e-11)]_32_[+4(1.89e-12)]_295_[+3(4.84e-10)]_25_[+1(3.56e-10)]_22_[+5(2.51e-11)]_121
MIT_Spar_c278_20970              1.96e-28  134_[+2(6.22e-10)]_32_[+4(1.11e-10)]_91_[+1(3.86e-05)]_184_[+3(4.84e-10)]_25_[+1(2.49e-11)]_22_[+5(2.51e-11)]_119
MIT_Smik_c935_20455              2.56e-23  130_[+2(3.17e-10)]_32_[+4(3.77e-09)]_31_[+2(4.34e-05)]_24_[+4(2.18e-05)]_188_[+3(2.87e-10)]_25_[+1(1.23e-09)]_22_[+5(1.29e-08)]_135
WashU_Skud_Contig2050.4          1.85e-24  135_[+2(7.40e-10)]_36_[+4(2.76e-08)]_291_[+3(1.73e-10)]_30_[+1(3.56e-10)]_22_[+5(2.67e-10)]_113
WashU_Sbay_Contig480.2           2.83e-26  179_[+2(3.17e-10)]_36_[+4(9.76e-11)]_256_[+3(1.73e-10)]_26_[+1(6.65e-11)]_22_[+5(1.13e-08)]_108
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

********************************************************************************
BioPerl-1.007002/t/data/map_hem/HEM4.ups.fa_000444000766000024      1071513155576321 20274 0ustar00cjfieldsstaff000000000000>SGD_Scer_YOR278W HEM4 "Uroporphyrinogen III synthase, catalyzes the conversion of hydroxymethylbilane to uroporphyrinogen III, the fourth step in the heme biosynthetic pathway"
CTCTCGAGCAAGGTCTATTTTACCTTTCTGTTTCCTTATCCTTTGACACTAAAATTCAAA
AAACTCACTAGAAAGTTCACTAAAGCGCCTTAGCTGACTACAGCACAACCCAACCCCAAA
AACTAGTGAACTACACACTAAGAGAATTTATGGTATTTCCATAATTGAAGTATATGTACG
ATGTATACAATGTAAACAAGAGAGTAATGAAGTGAAGATATGTACACCTAGAGCGAACCA
ATGATAATTTGTTTTCTTAATTAAGAAAAACCATTAAAACTGGATTAGATTTCAATAATG
AAAAGCTAGGAACAAAAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGACATA
TGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGTTTT
CTTATCCTGAAGGATCCTGCAAATGAAGTAAGTTCAAAGAATTGAAATGAAATCGCCTTT
TATACCCTCGCCGCACCAAGGAGCGCGCTGTGAAAATTTTTCGCTTTATCTCTTAGGGCT
CCTACTGTCGGTAGAGAAAAGTTGAGTATATTTAAAGCATGAGGTAACTTTTCTGCCCAT
TTTTACTTCTATTTCCATTTGAATTCAGAAAAGTG
>MIT_Spar_c261_21317 YOR278W 5' untranslated region, Contig c261 32269 - 34268, 2000 bp (revcom)
CGTTCCAAGCAGGGTTTATTCTATTTCTCGGCTCCTTTACCCTGTAACTTCGAGATTCAA
AAACTCGCTATAACTTCACTAAAGCGCTTTAGTTGACTACAACACAACCCAACCCCAAAA
TAAACTGTCCAACTACACAATACCGAGGATAATCCACGATATTTCGGTGATTGAAGTATA
TGTATTACGTATGCAATGTAAGCAAGAAACTAACAAAATGAATATGTACACCTAGAGCGA
ACCAATGATAATTTGTTTTCTTAATAAAGAAAAACTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAACAGAAAAATTGGTCTACTTCCAGCCATTTGCGCTTTATATAGAC
ATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGGT
TCTTTTATCCTGAAGGATAAACGGAAAGCTCCCGATTAAAAACAAGTATAGAGTACTGGA
ATAGAATCGCCTTTTATACCCTCCCTCGCCGCATCAAGAAGCGCGCTGTGAAAATTTTTC
GTTTTTCTCTTAGGGCTCCCATCCAACTGTCGGCGAGGAAAAGTTGTATATATTTAAAGC
ATGAGGTAACTTTGTTGCCCATTATCTTTTTTGTT
>MIT_Smik_c492_20940 YOR278W 5' untranslated region, Contig c492 3260 - 5259(revcom), 2000 bp (revcom)
ACTTTCAAACACACTCTGGTGTACTCCTCGGTCCCTTCATCTCATTTCTTCAAGATGCAG
AACTTCGCCGGAAGTAAACTAAAGTGCTTTAATTAATCAAAAGACAACTTAATTCCCAAA
CGGAAATGCAGGCTAGACAAACCGAAGATAATCCCCGATATTTCTGAGTTTAACAAATGT
ATGTATAATATGTATGCAATGTAGGCAAGAAAATAACGAAGTGAAGATATGTACACCTAG
AGCGAACCAATAATAATTTGTTTTCTTACTAAAGAAAAACTATTAAAACTGGATTAGATT
TCAATAATGAAAAGCTAGGAACAAAAGAAATTTGTCTACTTCCAGCCATTTGCGCTTTAT
ATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAAT
GATGGTTCTTTTAAACCAAAATTTAAAGAAAAATCTTAACGGTAATATGAGTAGGAGGTT
GGAATGGGATCGCTTTTTATACCCTCATTGTGATAAGAGACGCGCAGTGAAAAATTTTCG
CTTTTTCTTAGGGCTCCTATCTAACTCTCGGGCGAATAAATATCATGAATGTATTTAAAC
GTCAAGTTAGTTAAATGTTTGAGTCTGTTTCTTTT
>WashU_Scas_Contig692.36 YOR278W 5' untranslated region, Contig c692 73267 - 75266, 2000 bp (revcom)
ACAACAACAAATTCAATTTTTTGCCCAATCACCGCAATATAACCTTTTAACGGTTAACGC
CAGATAAAGTGACTTTGCCAATATAAATGATAGCATCAATTTTATTAGTTTTTAATATAC
AAAAAATGGTTTTCTAAATAATGATTATTCTAGAGATATTTTTATTATATGTAATGAGAA
TTTTATTTTATTTTATGTTTTGGTGATGAGGTTTATCTATTCCCATTCAACGGTAGCAGG
TGGCTTAGAAGTAATATCATATGTAACTCTAGCAACACCATCCACTTCATTGACGATTCT
AGAAGCAACCTTCTTCAAGAAGCTGTGTTCAAATGGATACCAATCAGCAGTCATGAAATC
AGTAGTTTCAATGGCTCTTAATGCAATAACTTGTTCGTAAGTTCTTTGATCACCCATGAC
ACCGACAGATTTAACTGGAAGTAAACATGCAAAGGCTTGAGAGATCTTATCATATAGACC
AGCCTTTCTAATTTCTTCAATGTAAATGTAATCGGCCTTCCTAGCAATGGCAACTTGTTC
CTTGGTAACTTCACCTAGGACACGAATGGCAATACCTGGACCTGGGAATGGATGTCTCCA
AACTAATTCGTGGGAGATCCCCAATAATTCACCTA
>WashU_Skud_Contig1682.4 YOR278W 5' untranslated region, Contig c1682 3379 - 5378, 2000 bp (revcom)
CTCTTCAAACAGACTCCAATTCACTACTGAGCTCTTACCTTGTGACTTCAAGACTCACTA
CTCAGTTGAAAGACACGCTCAGTACCAAATTCGGCTGCGAGGCAACTAACGCCTTTAAAC
AGGTAGGTAAGGAACAATACCGAAAGGCCATCTCCGATGTTTCGAAGATTGGCAAATGTA
TATATTATGTATGCAATATAGGCAAGATGATAACGAAGTAGAGATATGTACACCTAGAGC
GAACCAATGATAATTTGTTTTCTTAATGAAGAAAGTATTAAAACTGGATTAGATTTCAAT
AATGAAAAGCTAGGAATAAAAGAGATTGGTCTACTTCCAGCCATTTGCGCTTTACATAGA
CATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGAATGATGG
TTCTATTTAAAATGAAATCTAAAGATAAACCCTAGTCATAATCAAGTGGGTTGTGTTAAA
ATACAAGCACCTTTTATACTCTCGCAGCGTCAGTGGCGCGTTGTGAAAAATTTTCACTTT
TTCTCAGGGCTTTTACCCAACTGCCGACAAATAAAAGCCGTATTTAAGGAATGTGATTAG
TTTACTTTCCAATGCTTTCTCTTTTTTGTAGGGTA
>WashU_Sbay_Contig635.57 YOR278W 5' untranslated region, Contig c635 91073 - 93072, 2000 bp (revcom)
ACGTACAGATGGCGTCTCCTCCTTTCGCGAGCCCCTTGCCTTGTGACTTCAGCCTAACTT
CTTGACTAGAAGATACAACAAGAAATACTCAAATCGGTTATTGTGCAACTCATCCCTCAG
ACAGTTTGGTAAGAAACACCGAAGACTATTTCCGATATCTCAAAGAATGACAAAAGTATA
CATTATATATGCAAGAGAGGCAAGAAAAGAGTAAAAAAGAGTAAAAAAAACATGTACACC
TAGAGCGAACCAGTGATAATTTGCTTCTCAATGAAGAAAAAGCGATTAAAACTGGATTAG
ATTTCATTAAAGAAAAGCTAGGAACAAAGAAATTGGTCTACTTCCAGCCATTTGCGCTTG
ACATAGACATATGGAGGCGTGATGTCTTAAGCATGGTAATCCGGAAGATCAGTTTATTGA
ATGATGGCTCTTTTAAATTGAGATCTAAAAGAAATATCCTGGAAAAGAGTAGAGAAGAGT
CCAAACTGTAGGAATTCAATCGCTTTTTATACTCTCATCGCGGAAAAGACGCGCTGTGAA
AAATTTTCTCTTTTTCTTAGGGCTCCTATCCAGCTGCCTGCGAACAAAAGCCGTATTTAA
AGCATGATTTTCACTACTATGTATGTTCTTTCTGC

BioPerl-1.007002/t/data/map_hem/HEM4.ups.fa_.revcom000444000766000024       734113155576321 21547 0ustar00cjfieldsstaff000000000000>SGD_Scer_YOR278W HEM4 "Uroporphyrinogen III synthase, catalyzes the conversion of hydroxymethylbilane to uroporphyrinogen III, the fourth step in the heme biosynthetic pathway"
CACTTTTCTGAATTCAAATGGAAATAGAAGTAAAAATGGGCAGAAAAGTTACCTCATGCT
TTAAATATACTCAACTTTTCTCTACCGACAGTAGGAGCCCTAAGAGATAAAGCGAAAAAT
TTTCACAGCGCGCTCCTTGGTGCGGCGAGGGTATAAAAGGCGATTTCATTTCAATTCTTT
GAACTTACTTCATTTGCAGGATCCTTCAGGATAAGAAAACCATCATTCAATAAACTGATC
TTCCGGATTACCATGCTTAAGACATCACGCCTCCATATGTCTATATAAAGCGCAAATGGC
TGGAAGTAGACCAATTTTTTTTGTTCCTAGCTTTTCATTATTGAAATCTAATCCAGTTTT
AATGGTTTTTCTTAATTAAGAAAACAAATTATCATTGGTTCGCTCTAGGTGTACATATCT
TCACTTCATTACTCTCTTGTTTACATTGTATACATCGTACATATACTTCAATTATGGAAA
TACCATAAATTCTCTTAGTGTGTAGTTCACTAGTTTTTGGGGTTGGGTTGTGCTGTAGTC
AGCTAAGGCGCTTTAGTGAACTTTCTAGTGAGTTTTTTGAATTTTAGTGTCAAAGGATAA
GGAAACAGAAAGGTAAAATAGACCTTGCTCGAGAG
>MIT_Spar_c261_21317 YOR278W 5' untranslated region, Contig c261 32269 - 34268, 2000 bp (revcom)
AACAAAAAAGATAATGGGCAACAAAGTTACCTCATGCTTTAAATATATACAACTTTTCCT
CGCCGACAGTTGGATGGGAGCCCTAAGAGAAAAACGAAAAATTTTCACAGCGCGCTTCTT
GATGCGGCGAGGGAGGGTATAAAAGGCGATTCTATTCCAGTACTCTATACTTGTTTTTAA
TCGGGAGCTTTCCGTTTATCCTTCAGGATAAAAGAACCATCATTCAATAAACTGATCTTC
CGGATTACCATGCTTAAGACATCACGCCTCCATATGTCTATATAAAGCGCAAATGGCTGG
AAGTAGACCAATTTTTCTGTTCCTAGCTTTTCATTATTGAAATCTAATCCAGTTTTAATA
GTTTTTCTTTATTAAGAAAACAAATTATCATTGGTTCGCTCTAGGTGTACATATTCATTT
TGTTAGTTTCTTGCTTACATTGCATACGTAATACATATACTTCAATCACCGAAATATCGT
GGATTATCCTCGGTATTGTGTAGTTGGACAGTTTATTTTGGGGTTGGGTTGTGTTGTAGT
CAACTAAAGCGCTTTAGTGAAGTTATAGCGAGTTTTTGAATCTCGAAGTTACAGGGTAAA
GGAGCCGAGAAATAGAATAAACCCTGCTTGGAACG
>MIT_Smik_c492_20940 YOR278W 5' untranslated region, Contig c492 3260 - 5259(revcom), 2000 bp (revcom)
AAAAGAAACAGACTCAAACATTTAACTAACTTGACGTTTAAATACATTCATGATATTTAT
TCGCCCGAGAGTTAGATAGGAGCCCTAAGAAAAAGCGAAAATTTTTCACTGCGCGTCTCT
TATCACAATGAGGGTATAAAAAGCGATCCCATTCCAACCTCCTACTCATATTACCGTTAA
GATTTTTCTTTAAATTTTGGTTTAAAAGAACCATCATTCAATAAACTGATCTTCCGGATT
ACCATGCTTAAGACATCACGCCTCCATATGTCTATATAAAGCGCAAATGGCTGGAAGTAG
ACAAATTTCTTTTGTTCCTAGCTTTTCATTATTGAAATCTAATCCAGTTTTAATAGTTTT
TCTTTAGTAAGAAAACAAATTATTATTGGTTCGCTCTAGGTGTACATATCTTCACTTCGT
TATTTTCTTGCCTACATTGCATACATATTATACATACATTTGTTAAACTCAGAAATATCG
GGGATTATCTTCGGTTTGTCTAGCCTGCATTTCCGTTTGGGAATTAAGTTGTCTTTTGAT
TAATTAAAGCACTTTAGTTTACTTCCGGCGAAGTTCTGCATCTTGAAGAAATGAGATGAA
GGGACCGAGGAGTACACCAGAGTGTGTTTGAAAGT
>WashU_Skud_Contig1682.4 YOR278W 5' untranslated region, Contig c1682 3379 - 5378, 2000 bp (revcom)
TACCCTACAAAAAAGAGAAAGCATTGGAAAGTAAACTAATCACATTCCTTAAATACGGCT
TTTATTTGTCGGCAGTTGGGTAAAAGCCCTGAGAAAAAGTGAAAATTTTTCACAACGCGC
CACTGACGCTGCGAGAGTATAAAAGGTGCTTGTATTTTAACACAACCCACTTGATTATGA
CTAGGGTTTATCTTTAGATTTCATTTTAAATAGAACCATCATTCAATAAACTGATCTTCC
GGATTACCATGCTTAAGACATCACGCCTCCATATGTCTATGTAAAGCGCAAATGGCTGGA
AGTAGACCAATCTCTTTTATTCCTAGCTTTTCATTATTGAAATCTAATCCAGTTTTAATA
CTTTCTTCATTAAGAAAACAAATTATCATTGGTTCGCTCTAGGTGTACATATCTCTACTT
CGTTATCATCTTGCCTATATTGCATACATAATATATACATTTGCCAATCTTCGAAACATC
GGAGATGGCCTTTCGGTATTGTTCCTTACCTACCTGTTTAAAGGCGTTAGTTGCCTCGCA
GCCGAATTTGGTACTGAGCGTGTCTTTCAACTGAGTAGTGAGTCTTGAAGTCACAAGGTA
AGAGCTCAGTAGTGAATTGGAGTCTGTTTGAAGAG
>WashU_Sbay_Contig635.57 YOR278W 5' untranslated region, Contig c635 91073 - 93072, 2000 bp (revcom)
GCAGAAAGAACATACATAGTAGTGAAAATCATGCTTTAAATACGGCTTTTGTTCGCAGGC
AGCTGGATAGGAGCCCTAAGAAAAAGAGAAAATTTTTCACAGCGCGTCTTTTCCGCGATG
AGAGTATAAAAAGCGATTGAATTCCTACAGTTTGGACTCTTCTCTACTCTTTTCCAGGAT
ATTTCTTTTAGATCTCAATTTAAAAGAGCCATCATTCAATAAACTGATCTTCCGGATTAC
CATGCTTAAGACATCACGCCTCCATATGTCTATGTCAAGCGCAAATGGCTGGAAGTAGAC
CAATTTCTTTGTTCCTAGCTTTTCTTTAATGAAATCTAATCCAGTTTTAATCGCTTTTTC
TTCATTGAGAAGCAAATTATCACTGGTTCGCTCTAGGTGTACATGTTTTTTTTACTCTTT
TTTACTCTTTTCTTGCCTCTCTTGCATATATAATGTATACTTTTGTCATTCTTTGAGATA
TCGGAAATAGTCTTCGGTGTTTCTTACCAAACTGTCTGAGGGATGAGTTGCACAATAACC
GATTTGAGTATTTCTTGTTGTATCTTCTAGTCAAGAAGTTAGGCTGAAGTCACAAGGCAA
GGGGCTCGCGAAAGGAGGAGACGCCATCTGTACGT
BioPerl-1.007002/t/data/map_hem/yeast.nc.1.freq000444000766000024        15013155576321 21014 0ustar00cjfieldsstaff000000000000#seq	frequency_non_coding
a	0.32442758667668
c	0.175572413323319
g	0.175572413323319
t	0.32442758667668
BioPerl-1.007002/t/data/mbsout000755000766000024          013155576321 16044 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/mbsout/mbsout_infile1000444000766000024       101213155576321 21036 0ustar00cjfieldsstaff000000000000command:        mbs 6 -t 0.001 -r 0.00025 -s 5000 2500 -f 3 1 traj 

//0-1   allele: a a a d d d d 
segsites: 7
positions: 79.1001 80.1001 81.101 82.101 83.10001 84.801 85
1111111
5555555
4444444
4444444
5555555
4444444
//1-1   allele: a a a a d d d 
segsites: 7
positions: 79.1001 80.1001 81.101 82.101 83.10001 84.801 85
5555555
5555555
5555555
1010101
1111111
1515151
//2-1   allele: a d d d d d d 
segsites: 7
positions: 79.1001 80.1001 81.101 82.101 83.10001 84.801 85
1414141
1414141
1515151
1414141
1515151
1515151
BioPerl-1.007002/t/data/mbsout/mbsout_infile2000444000766000024       142313155576321 21045 0ustar00cjfieldsstaff000000000000command:        mbs 6 -t 0.001 -r 0.00025 -s 5000 2500 -f 5 1 traj 

//0-1   allele: a a a d d d d 
segsites: 7
positions: 79.1001 80.1001 81.101 82.101 83.10001 84.801 85
1111111
5555555
4444444
4444444
5555555
4444444
//1-1   allele: a a a d d d d 
segsites: 7
positions: 79.1001 80.1001 81.101 82.101 83.10001 84.801 85
5555555
5555555
5555555
1010101
1111111
1515151
//2-1   allele: a a a d d d d 

segsites: 7
positions: 79.1001 80.1001 81.101 82.101 83.10001 84.801 85
1414141
1414141
1515151
1414141
1515151
1515151
//3-1   allele: a a a a a d d 

segsites: 7
positions: 79.1001 80.1001 81.101 82.101 83.10001 84.801 85
1515151
5050505
5151515
5555555
5454545
5454545
//4-1   allele: a a d d d d d 

segsites: 7
positions: 79.1001 80.1001 81.101 82.101 83.10001 84.801 85
5555555
BioPerl-1.007002/t/data/mbsout/mbsout_infile3000444000766000024        30413155576321 21023 0ustar00cjfieldsstaff000000000000command:        mbs 3 -t 0.001 -r 0.00025 -s 5000 2500 -f 1 1 traj 

//0-1   allele: a a a d d d d 
segsites: 7
positions: 79.1001 80.1001 81.101 82.101 83.10001 84.801 85
1111111
5555555
4444444
BioPerl-1.007002/t/data/msout000755000766000024          013155576321 15702 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/msout/bad_msout_infile1000444000766000024        15313155576321 21325 0ustar00cjfieldsstaff000000000000ms 9 1 -s 7 -I 3 4 4 1
1 1 1

//
segsites: 7
positions: 0.01 0.25 0.31 0.35 0.68 0.76 0.85
4140411
5040410
BioPerl-1.007002/t/data/msout/bad_msout_infile2000444000766000024        20213155576321 21321 0ustar00cjfieldsstaff000000000000ms 4 1 -s 7 -I 3 4 4 1
1 1 1

//
segsites: 7
positions: 0.01 0.25 0.31 0.35 0.68 0.76 0.85
4140411
5040410
4140411
4140411
4140411BioPerl-1.007002/t/data/msout/msout_infile1000444000766000024        54513155576321 20524 0ustar00cjfieldsstaff000000000000ms 6 3 -s 7 -I 3 3 2 1
1 1 1

//
segsites: 7
positions: 0.01 0.25 0.31 0.35 0.68 0.76 0.85
1111111
5555555
4444444
4444444
5555555
4444444
//
segsites: 7
positions: 0.01 0.25 0.31 0.35 0.68 0.76 0.85
5555555
5555555
5555555
1010101
1111111
1515151
//
segsites: 7
positions: 0.01 0.25 0.31 0.35 0.68 0.76 0.85
1414141
1414141
1515151
1414141
1515151
1515151
BioPerl-1.007002/t/data/msout/msout_infile2000444000766000024       100713155576321 20537 0ustar00cjfieldsstaff000000000000ms 6 3
1 1 1

//
segsites: 7
positions: 0.01 0.25 0.31 0.35 0.68 0.76 0.85
1111111
5555555
4444444
4444444
5555555
4444444
//
segsites: 7
positions: 0.01 0.25 0.31 0.35 0.68 0.76 0.85
5555555
5555555
5555555
1010101
1111111
1515151
//
segsites: 7
positions: 0.01 0.25 0.31 0.35 0.68 0.76 0.85
1414141
1414141
1515151
1414141
1515151
1515151
//
segsites: 7
positions: 0.01 0.25 0.31 0.35 0.68 0.76 0.85
1515151
5050505
5151515
5555555
5454545
5454545
//
segsites: 7
positions: 0.01 0.25 0.31 0.35 0.68 0.76 0.85
5555555
BioPerl-1.007002/t/data/msout/msout_infile3000444000766000024        14313155576321 20520 0ustar00cjfieldsstaff000000000000ms 3 1
1 1 1

//
segsites: 7
positions: 0.01 0.25 0.31 0.35 0.68 0.76 0.85
1111111
5555555
4444444
BioPerl-1.007002/t/data/msout/msout_infile4000444000766000024        60513155576321 20524 0ustar00cjfieldsstaff000000000000



ms 6 3 -s 7 -I 3 3 2 1



1 1 1

//

segsites: 7


positions: 0.01 0.25 0.31 0.35 0.68 0.76 0.85


1111111
5555555


4444444

4444444
5555555

4444444


//

segsites: 7
positions: 0.01 0.25 0.31 0.35 0.68 0.76 0.85
5555555
5555555



5555555
1010101
1111111
1515151

//
segsites: 7



positions: 0.01 0.25 0.31 0.35 0.68 0.76 0.85

1414141
1414141
1515151
1414141
1515151
1515151





BioPerl-1.007002/t/data/nexml000755000766000024          013155576321 15656 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/nexml/characters.nexml.8.xml000444000766000024      5034713155576321 22175 0ustar00cjfieldsstaff000000000000



    
        
    
        
        
        
        
        
    
    
    
    	
	      
	        
	        
	      
	      
	      
	      
	      
        
        
                
            
            
                
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                0101
            
            
                0101
            
            
                0101
            
        
    
    
    
        
        
            
            
                                                
                                
                                 
                                    
                    
                                        
                
                
                    
                    
                      
            
            
            
            
        
        
        
            
                
                
                
            
            
                
                
            
            
                
                
            
            
                
                
            
            
                
                
            
        
    
    
    
        
            
            
            
            
            
            
        
        
            
                
                
                
                
                
                
            
            
                
                
                
                
                
            
            
                
                
                
                
                
            
            
                
                
                
                
                
            
            
                
                
                
                
                
            
        
    
    
    
    
    	
    		
    		
    		
    		
    		
    			
    			
    		
    		
    			
    			
    		
    		
    			
    			
    		
    		
    			
    			
    		
    		
    			
    			
    		
    		
    			
    			
    		
    		
    			
    			
    			
    		
    		
    			
    			
    			
    		
    		
    			
    			
    			
    		
    		
    			
    			
    			
    		
    		
    			
    			
    			
    			
    		
    		
    			
    			
    			
    			
    		
    		
    		
    			
    			
    			
    			
    			
    			
    			
    			
    			
    			
    			
    			
    			
    			
    			
    			
    			
    		
    	
    	
    	
    	
    	
    	
    	
    	
    	
    	
    	
    	
    	
    	
    	
    	
    	
    
    
            
                A C G C T C G C A T C G C A T C
            
            
                A C G C T C G C A T C G C A T C
            
            
                A C G C T C G C A T C G C A T C
            
        
    
    
    
    
      
        
        
        
        
        
          
          
        
        
          
          
        
        
          
          
        
        
          
          
        
        
          
          
        
        
          
          
        
        
          
          
          
        
        
          
          
          
        
        
          
          
          
        
        
          
          
          
        
        
          
          
          
          
        
        
          
          
          
          
        
        
        
          
          
          
          
          
          
          
          
          
          
          
          
          
          
          
          
          
        
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
      
          
      
        
            
                ACGCUCGCAUCGCAUC
            
            
                ACGCUCGCAUCGCAUC
            
            
                ACGCUCGCAUCGCAUC
            
        
    
    
    
	    
	      
	      
	      
	      
	      	      	      
	        
        
            
                -1.545414144070023 -2.3905621575431044 -2.9610221833467265 0.7868662069161243 0.22968509237534918
            
            
                -1.6259836379710066 3.649352410850134 1.778885099660406 -1.2580877968480846 0.22335354995610862
            
            
                -1.5798979984134964 2.9548251411133157 1.522005675256233 -0.8642016921755289 -0.938129801832388
            
            
                2.7436692306788086 -0.7151148143399818 4.592207937774776 -0.6898841440534845 0.5769509574453064
            
            
                3.1060827493657683 -1.0453787389160105 2.67416332763427 -1.4045634106692808 0.019890469925520196
            
        
    
    
    
        
            
            
                                                
                                
                                 
                                    
                    
                                        
                
                
                    
                    
                      
            
            
            
            
            
        
            
                1 2
            
            
                2 2
            
            
                3 4
            
            
                2 3
            
            
                4 1
            
        
    

BioPerl-1.007002/t/data/nexml/characters.nexml.xml000444000766000024      5647613155576321 22040 0ustar00cjfieldsstaff000000000000



    
        
    
        
        
        
        
        
    
    
    
    	
	      
	        
	        
	      
    	    
    	    
    	    
    	    
        
        
                
            
            
                
                0101
            
            
                0101
            
            
                0101
            
            
                0101
            
            
                0101
            
        
    
    
    
        
        
            
            
                                                
                                
                                 
                                    
                    
                                        
                
                
                    
                    
                      
            
            
            
            
        
        
        
            
                
                
                
            
            
                
                
            
            
                
                
            
            
                
                
            
            
                
                
            
        
    
    
            
        
            
            
            
            
            
            
        
        
            
                
                
                
                
                
                
            
            
                
                
                
                
                
            
            
                
                
                
                
                
            
            
                
                
                
                
                
            
            
                
                
                
                
                
            
        
    
    
    
    
    	
    		
    		
    	    
    	    
    		
    		    
    		    
    		
    		
    		    
    		    
    		
    		
    		    
    		    
    		
    		
    		    
    		    
    		
    		
    		    
    		    
    		
    		
    		    
    		    
    		
    		
    		    
    		    
    		    
    		
    		
    		    
    		    
    		    
    		
    		
    		    
    		    
    		    
    		
    		
    		    
    		    
    		    
    		
    		
    		    
    		    
    		    
    		    
    		
    		
    		    
    		    
    		    
    		    
    		
    		
    		
    		    
    		    
    		    
    		    
    		    
    		    
    		    
    		    
    		    
    		    
    		    
    		    
    		    
    		    
    		    
    		    
    		    
    		
    	
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
    
    
        A C G C T C G C A T C G C A T C
        A C G C T C G C A T C G C A T C
        A C G C T C G C A T C G C A T C
    
    
    
    
    
      
        
        
        
        
        
          
          
        
        
            
            
        
          
              
              
        
          
              
              
        
          
              
              
        
          
              
              
        
          
              
              
              
        
          
              
              
              
        
          
              
              
              
        
          
              
              
              
        
          
              
              
              
              
        
          
              
              
              
              
        
          
          
              
              
              
              
              
              
              
              
              
              
              
              
              
              
              
              
              
        
      
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
        
            
      
        
            
                ACGCUCGCAUCGCAUC
            
            
                ACGCUCGCAUCGCAUC
            
            
                ACGCUCGCAUCGCAUC
            
        
    
    
    
	    
	      
	        
	        
	        
	        	      	      
	        
        
            
                -1.545414144070023 -2.3905621575431044 -2.9610221833467265 0.7868662069161243 0.22968509237534918
            
            
                -1.6259836379710066 3.649352410850134 1.778885099660406 -1.2580877968480846 0.22335354995610862
            
            
                -1.5798979984134964 2.9548251411133157 1.522005675256233 -0.8642016921755289 -0.938129801832388
            
            
                2.7436692306788086 -0.7151148143399818 4.592207937774776 -0.6898841440534845 0.5769509574453064
            
            
                3.1060827493657683 -1.0453787389160105 2.67416332763427 -1.4045634106692808 0.019890469925520196
            
        
    
    
    
        
            
            
                                                
                                
                                 
                                    
                    
                                        
                
                
                    
                    
                      
            
            
            
            
            
        
            
                1 2
            
            
                2 2
            
            
                3 4
            
            
                2 3
            
            
                4 1
            
        
    

BioPerl-1.007002/t/data/nexml/trees.nexml.8.xml000444000766000024      1132413155576321 21170 0ustar00cjfieldsstaff000000000000

	        
	
		
		
		
		
		
	
	
	
		
		
			
			
			
			
			    
			
			
			
			
			
			
						
			
			
			
			
			
			
			
		
		
		
			
			
			
			
			    
			
			
			
			
			
			
						
			
			
			
			
			
			
			
			
		
		
			
			
			
			
			
			
			
			
			
						
			
			
			
			
			
			 
			
			
						
	

BioPerl-1.007002/t/data/nexml/trees.nexml.xml000444000766000024      1221513155576321 21022 0ustar00cjfieldsstaff000000000000

	        
	
		
		
		
		
		
	
	
	
		
		
			
			
			
			
			    
			
			
			
			
			
			
						
			
			
			
			
			
			
			
		
		
		
			
			
			
			
			    
			
			
			
			
			
			
						
			
			
			
			
			
			
			
			
		
		
			
			
			
			
			
			
			
			
			
						
			
			
			
			
			
			 
			
			
						
	

BioPerl-1.007002/t/data/ps_scan000755000766000024          013155576321 16161 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/ps_scan/out.PrositeScan000444000766000024        52513155576321 21263 0ustar00cjfieldsstaff000000000000>roa1_drome/253-256 : PS00001 ASN_GLYCOSYLATION 
NNSF
>roa1_drome/270-273 : PS00001 ASN_GLYCOSYLATION 
NNSW
>roa2_drome/344-349 : PS00008 MYRISTYL 
GNNQGF
>roa2_drome/217-355 : PS50321 ASN_RICH L=0 
NRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNN
NPWDNGNGGGNFGGGGNNWNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAG
GGNQGNYGNNQGFNNGGNN
BioPerl-1.007002/t/data/registry000755000766000024          013155576321 16403 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/registry/bdb000755000766000024          013155576321 17132 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/registry/bdb/seqdatabase.ini000555000766000024        36313155576321 22232 0ustar00cjfieldsstaff000000000000VERSION=1.00

[testbdb]
protocol=flat
location=t/tmp
dbname=testbdb

[embl]
protocol=biofetch
location=http://www.ebi.ac.uk/cgi-bin/dbfetch
dbname=embl

[swissprot]
protocol=biofetch
location=http://www.ebi.ac.uk/cgi-bin/dbfetch
dbname=swall

BioPerl-1.007002/t/data/registry/flat000755000766000024          013155576321 17331 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/registry/flat/seqdatabase.ini000555000766000024        36513155576321 22433 0ustar00cjfieldsstaff000000000000VERSION=1.00

[testflat]
protocol=flat
location=t/tmp
dbname=testflat

[embl]
protocol=biofetch
location=http://www.ebi.ac.uk/cgi-bin/dbfetch
dbname=embl

[swissprot]
protocol=biofetch
location=http://www.ebi.ac.uk/cgi-bin/dbfetch
dbname=swall

BioPerl-1.007002/t/data/seqfeaturedb000755000766000024          013155576321 17205 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/seqfeaturedb/test.gff3000444000766000024     23660013155576321 21137 0ustar00cjfieldsstaff000000000000##gff-version 3
##sequence-region Contig1 1 37450
# #index-subfeatures 0
Contig1	confirmed	transcript	1001	2000	42	+	.	ID=trans-1;Name=abc-1;Alias=xyz-2;Note=function+unknown
Contig1	confirmed	exon	1001	1100	.	+	.	Parent=trans-1
Contig1	confirmed	exon	1201	1300	.	+	.	Parent=trans-1
Contig1	confirmed	exon	1401	1450	.	+	.	Parent=trans-1
Contig1	confirmed	CDS	1051	1100	.	+	0	Parent=trans-1
Contig1	confirmed	CDS	1201	1300	.	+	2	Parent=trans-1
Contig1	confirmed	CDS	1401	1440	.	+	0	Parent=trans-1
Contig1	est	match	1001	1100	96	.	.	Target=CEESC13F 1 100 +;Name=match1
Contig1	est	match	1201	1300	99	.	.	Target=CEESC13F 101 200 +;Name=match2
Contig1	est	match	1401	1450	99	.	.	Target=CEESC13F 201 250 +;Name=match3
Contig1	tc1	transposable_element	5001	6000	.	+	.	ID=c128.1;Name=c128.1
Contig1	tc1	transposable_element	8001	9000	.	-	.	ID=c128.2;Name=c128.2
Contig1	confirmed	transcript	30001	31000	.	-	.	ID=trans-2;Name=trans-2;Alias=xyz-2;Note=Terribly+interesting
Contig1	confirmed	exon	30001	30100	.	-	.	Parent=trans-2;Alias=abc-1;Note=function+unknown;index=1
Contig1	confirmed	exon	30701	30800	.	-	.	Parent=trans-2
Contig1	confirmed	exon	30801	31000	.	-	.	Parent=trans-2

##sequence-region Contig2 1 37450
Contig2	clone	assembly_component	1	2000	.	.	.	Target=AL12345.1 1 2000 +;Name=match4;Note=Terribly+interesting
Contig2	clone	assembly_component	2001	5000	.	.	.	Target=AL11111.1 6000 3001 +;Name=match5
Contig2	clone	assembly_component	5001	20000	.	.	.	Target=AC13221.2 1 15000 +;Name=match6
Contig2	clone	assembly_component	2001	37450	.	.	.	Target=M7.3 1001 36450 +;Name=match7
Contig2	predicted	transcript	2501	4500	.	+	.	ID=trans-3;Name=trans-3;Alias=trans-18
Contig2	predicted	transcript	5001	8001	.	-	.	ID=trans-4;Name=trans-4

# processed_transcript
Contig3	clone	assembly_component	1	50000	.	.	.	ID=AL12345.2
Contig3	confirmed	mRNA	32000	35000	.	+	.	ID=trans-8
Contig3	confirmed	UTR	32000	32100	.	+	.	Parent=trans-8
Contig3	confirmed	CDS	32101	33000	.	+	.	Parent=trans-8
Contig3	confirmed	CDS	34000	34500	.	+	.	Parent=trans-8
Contig3	confirmed	CDS	34600	34900	.	+	.	Parent=trans-8
Contig3	confirmed	UTR	34901	35000	.	+	.	Parent=trans-8

# associative attributes
# these are not intended to have any implied parent/child relationship, but their attributes can be
# used to group them arbitrarily.
Contig4	clone	assembly_component	1	50000	.	.	.	ID=ABC123
Contig4	confirmed	gene	32000	35000	.	+	.	ID=thing1;gene=gene-9
Contig4	confirmed	mRNA	32000	35000	.	+	.	ID=thing2;mRNA=trans-9;gene=gene-9
Contig4	confirmed	CDS	32000	35000	.	+	.	ID=thing3;mRNA=trans-9

# three-tiered gene
Contig1	confirmed	gene	2000	3000	.	.	.	ID=tier0;Name=gene3;expressed=yes;in_process=1
Contig1	confirmed	mRNA	2000	3000	.	+	.	Parent=tier0;ID=tier0.1;expressed=yes;Name=gene3.a;index=1
Contig1	confirmed	mRNA	2500	3000	.	+	.	Parent=tier0;ID=tier0.2;Name=gene3.b
Contig1	confirmed	five_prime_UTR	2000	2100	.	+	.	Parent=tier0.1
Contig1	confirmed	CDS	2101	2200	.	+	0	Parent=tier0.1
Contig1	confirmed	CDS	2500	2800	.	+	0	Parent=tier0.1
Contig1	confirmed	three_prime_UTR	2801	2900	.	+	.	Parent=tier0.1
Contig1	confirmed	three_prime_UTR	2910	3000	.	+	.	Parent=tier0.1

Contig1	confirmed	five_prime_UTR	2500	2510	.	+	.	Parent=tier0.2
Contig1	confirmed	CDS	2511	2520	.	+	0	Parent=tier0.2
Contig1	confirmed	CDS	2300	2400	.	+	0	Parent=tier0.2,tier0.1;Name=shared_exon
Contig1	confirmed	CDS	2500	2800	.	+	0	Parent=tier0.2
Contig1	confirmed	three_prime_UTR	2801	2900	.	+	.	Parent=tier0.2;ID=utr1
Contig1	confirmed	three_prime_UTR	2910	3000	.	+	.	Parent=tier0.2;ID=utr1

ctgA	est	EST_match	5410	5500	.	-	.	ID=Match2;Name=agt830.3;Target=agt830.3 505 595
ctgA	est	EST_match	7000	7503	.	-	.	ID=Match2;Name=agt830.3;Target=agt830.3 1 504 
ctgA	est	EST_match	1050	1500	.	+	.	ID=Match1;Name=agt830.5;Target=agt830.5 1 451
ctgA	est	EST_match	3000	3202	.	+	.	ID=Match1;Name=agt830.5;Target=agt830.5 452 654

# test multiple parentage handling
Contig1	test	gparent	2500	2550	.	+	.	ID=gparent1;Name=gparent1
Contig1	test	parent	2500	2550	.	+	.	ID=parent1;Name=parent1;Parent=gparent1
Contig1	test	parent	2501	2551	.	+	.	ID=parent2;Name=parent2;Parent=gparent1
Contig1	test	child	2500	2550	.	+	0	ID=child1;Parent=parent1,parent2;Name=child1
Contig1	test	child	2501	2551	.	+	1	ID=child2;Parent=parent1,parent2;Name=child2

# test out DNA loading
>Contig1
ttcttcgacactaagaaccatgccccatgtcacgacttcaccctcattgacgagcgttgt
tcactcatctcgctgggccactagctacccatggggttaattggccagggatcggataca
cgttaatcgatcggaaaactgcgcgtgtcatcaactcttcttacaatgctataagtaacg
gaaactgaatagctaaacataagtgagcttcagagcagcgagagcacttaacaaaccttg
ggttgggctaagtgctttagttccatcatctcaagagtgcatagaagtctgcacgcggcc
gccggctggaagcatggtgaatactgactattagctgttattcctctggaacacaccggt
acagaaggtacatcgacacttctttggtgctataagaccagttgcgtggccgataggggt
gatgacgagtaaccctttcgcagctcaagtccagaacgagacctgtcaattcccgctctc
ttgcattgattttcacgatcgttacaagctaaaaatagttgaaggagaatgagcaggatg
tgctccccacggtctcttacccctgacactcttcgcgttctatatctccggaaagcccgg
aaccttttgtgcttcgtgtgagcataccgaacttgtttatgccctgccgccggataagct
tttcacgttagtaagaatgctcactgagacaggttgtcaatagccggcgttaactgccat
tataggaatttttaggacgaccgaagattaaatggcggagatttgttggcggattaagtt
ttccgcgcaccggggtaggagatcactcggctatcgtgctttaatgatgcggctatcgga
gatgtttgcgcagccgaactccaacgggtattaaatctcggcagcgtcttaccgctttta
tacagtacatgatttcgccgaaaggaaagtatatggtgttctcggttggttgcattatcg
acttattcaactaacacaacgttcggggttattattcctcccgaagatgatgccaaatat
acatttggctcataaccgaagtgtaatggatcttaggttggctagcggctgcgtacagac
aatagatacagtattcccgactttggacgaccgaggccggtcctgagagttgaaagtcac
gggacgtttggccctgtgtctttgttccaccgttaaatattgggggcgacgtatcggcct
ggacgtatacttcatgacctttcgtccatggccatacggcggcggggattttaatctaga
tccagtcgtaggcttggagctatcctctctttatcgcgcttgacaatagcatccccaaga
tacgatctacccaagtgacgcgagctcaaaccctattttgtggtatacggctgatgtaga
tggcaacaacggtcgagtatagagttcctacctacgcctacggagtctgtacgtctgtgt
atatcgagcgcattcgaggatattgatcgttggcgagccggtttgcggaaaacagacagc
aaatttgatgcagatggtattgccaactgtcccagcgcggcttaagggccgtggtatgac
gaagggatctatgtgaattctcccgggccctaatagatgtggcataggaaatgcccgaag
cccggaagccttcgtactgcacgtcgttgccatacggatcatgtagagagaggtccctat
accctctaatgtggcctgaccttttaagcatttacgtacttgaatatttaggcgattcct
ccttgataacttcgttgcaccggttcctctcccggatctgagagattaaagcgtgactca
catttctaggtaaaccgtagttctggacgaacccgtcgtcggatgatggacgagctggaa
aagacccatcatttccacgcagacaggaatacaagagtgtctggcaacaaggcctgccag
attactttatctcatacatatgggatgagaacacgacctcatcgaaaaaagttagtgtat
ggccgccgacagtcgtacaatatcaataatcctgctgtttgcaacttcgctggacatgta
ctgaataatgcaagcttgaaaacgtataccctgcaagcccctgctatggtcgacccccgg
tggagcatatcgcgatagctgcttttgaccatccacgggccaccgacactctgaaaatgg
gtatcctctcggactgcatacggaccaacctctctagtagaattaacccagagtatttag
ccgggatactctcgcgagttccaatctatatgccactcccgtaggcatgatttgatcttg
cgctttgcaagcaactggcgttcagtgattacggaatcctcgagatcgccagggagatga
cagggggcggttggcaccccggcgtatgagttactactggggccaggtcggcatccgttt
attacgtggcgcctcgaatgggttcgtttacagacgccgcgagtatcaccacacgattag
ttggctcggcacacgacgggccgcaactgaatattggtatgccctgacccacagcagatg
gatcccctacgtgaaattactggaaacccatctctccagttaatgtggagcttactgtat
tacgcgggcttaacctggtcgtggtacgggaggtccgcctaatacatcgatggtcctcac
cacgaacgttatatgaagctctgtcagcacgacgttgcaaagacacataaacatttgctc
ctcttcgtcatacatatccgtggtgccgcgaaagaatgggacgcatttgtgaatggacgc
ttgggggacgcccgggttcacgagcctagccctccagtttattgctctataaccccggcg
ttcgatcgatagacgtgctgggaagcgagcagtacctagctcggtcatttaacctccgag
actctcgtccaccgcaagcgacctttccagacagtcgaggccagccgcaccaatgacatc
caggcctcaggtacttgaaacgctcttgagagcctgaattcatgaaaagcccaagacggt
tcactcacaccacgcaattattattgctgcctgtgtggtcccaatcacgtggggtcttac
acggagagagggatatacagagccttctgcttttgtcggcggtgaccttcaggccggatc
agcgttgaactctggtgtaaggatatatgaagtttactaccacaggagatttgcatttat
cccatggcaggtcccggaaattggaggaaaagtggtagccttcatctactcaaaagatgc
acctaaccggacactcggaccgatgtttgacgaagaaatttatattgcaacagggccatc
ccgatgaaagagggcagtgacagagtagggaaaaaacgcaacaaaatttgattagtggga
cactgaattagatgtgatgtacaggtccagtgaggctccgcatggggcttaggtgtcaac
tagggtaagaccccccagctcaccgtgtcgaacaaacacgagtacccccgcctctcggca
agaataacaccttattcgttctcatctatcagaccctccactgtaggtagctcggtactc
ccgttaggtctactgcaatccggctgcccggcgaagcgggcttagcgaggggccgaaagt
ggaatgacgaaatggtccggagctgcgcgggcagacgacggtcgtcgactcacctcgaat
tcaagccgcctcgcccggattacaaccctcatacatgggccaattcagctcggtccgata
cgacagcttagtatagcagcctggccggttttgtagccttctttctacctctaaaagaga
caaagtccctgtgttattgtaaccgtgcatcgatctcgtcaccttcaatatgcaacgtga
agactgaggccctagcctctttgagggtcacccgaatgagatatgggatgtcgaatacat
gggccaagtttcaggacacgaggatacagggttaaccgtcgaatttcttcttgcaaggta
gagatcccgaagtctctagaacgggttacgtacaattgggattagcgattaggaggagag
gcacgttagacaaccgacaaagccgaacaccgccctgtcgtatccagagcgggtaagttt
taattgcgcgtccctcttctcaaagtcccgatatgcccggctaaatatagttgcggatag
gtttgccgtccggcggtaggagagggaggctccctgtgatgtcgacgcttatcgtcacca
ctgacagcctcgacctcgatattgagtgccaaatcgtctggtcacccatcacgatccaga
ccgtcgattaaaccccgtgtaccccgtgttatacctgacgtccgtacctccaataacctt
aggtcaaataaatcttcttgagtctatctcattcggatacgctgcaaaggagaaggtccc
atagttcggttcggtcattggatacaatgctgtacgctaacaggccttcactttagattc
gcgtcgtgttgaagttctattatatagttccccagcaactttttggagatacgatggtct
acatcttaaaataagcaaatttggcatgcgatggacattgtagaagcccgataccaggct
aactacgacgccctgtgcgggattattcagtaacagactatatcgggggccgactctgtg
tcgtacccccaccggagactctaggacgttgggcaccccaacccagtacgatacagactt
ccttgatctaaacgtattgtcatttttcgttaacacatatcaagctgtttttcgataacc
tacgggtactcgtttgacaggcaccaggtatgtctccccccggtcagactgaaggctaaa
tagccgtacaatttcagctcgcgtaggtagttcgattcgcaggtgcatgatagcacagaa
gaggtcaccgaactgcacgactaaaatgaccgctggttgccgtagtagcatgcgaagcag
cttgccaacatcatcactgtcaccagccccctgtattcacacatagggctaagattaaac
cctcatagcgattgttggatttgatcggacactttgccttgctagggggctatttactgt
agcaaggcccgacatcgtggtccttgtcgagtctctgttccactaattcttcattgagat
ctcattctcgaaatccaacgaatggggcggatatcgacaaaccattggcaagttgctata
agccagcaacaatatccccgtgacatcatcgtgccgggttaaatacaagagggtgtttgg
gtccgcccccggaatcgcttctatggcattatatggtcccccctcctttactgtgacatt
gtgcagacccttcgttacgactatcaattccaccccggaaagttagttctccacatattt
tacctgggtcggcgttctgccggctacgcaggtcttctgtacaagcgcgggaaggtacac
tagtctatagacgccgagttccgctacggcccctaatccatgagatctttggtgttattt
cgatcatctcctgggagggtatacttcaatgacccattctgggaaagataaccaaggcga
acgctcgcaattaacgctactgtggaattgaacatttcctcagtgtacgagtgtctctac
gcagcgtacgcctatggagtctttgcatgtgactgcgacccatatctacaaaccggcatt
cccgggttctaccaactggttgtgccgcgcgaagggagatttccccgtacgccagtgtcc
accggaagcgctccataacagctgtggaagcgaatagggtgccggggtctacacaattct
cacgagccaagatccccaacaacgattacggccctccgaccaaaatacacatttgcactg
attcctttgcggccctgaatcatctcagagccgatactcgctaaggcctggtcggggaat
cccctgtacagtcataatccatccattggcagagtaacttttgcatctttgctacttgag
atatcgtgtagctctgaaagacggccatgaatcttagctctgggaccgtatctaggggca
ggctccgtctgtcatggttgggccgtaagcctgccttttacgttaatgccccggtaccac
gatcagtacagcgtcacccagtaccccttgccattgtcacccctgcgttagacaaataac
actagaacagcctgatcgctagctcatatctggtccctcgaaaaactgcgactcggtttc
atcctagattgtgtgtattccctctatggacatgcttggacagtaccatggagcgccgca
ccaagatcagaagtgccgtcagcagatacctatagtacgacatctagagtacattagacc
atggatagacatccttgtacttgtgtgatctcgagtaatcgcagatgctctgggcggggt
tttttcccgagcccttttagtgttaagtacactcaatctcaccggaatggatcaccccgc
acttaaaggtccctacccaaatcccacgaggccaccgagggtcgaaagtcggttgacgtc
cctgtagtccgcattgccaacattaccactactttacccgtctatccaggcttgtagtag
tgcgcatacgaaaagacttataaaaatcatctaggaatttcatttccagggagctgtcgc
caaaactgatgatccacagaagaccgatcttcaaggtcctcccagctatctgccaaaccc
tgctaccatcacccccacgaaggtctggtctctctcaatgcagtatttcaattcactccg
ctccaagtgtagcgggaagttaacttttcataaaatataagaaggtatcacagctcccgg
ccagtgagtatccgctccgaggctgtgtcttactgaagatgtacgcaaaattaatggaga
tcccggttagtctcacggaaaggtgtcggggagggtctcacgttcaccatgtgcatttgt
aaaataatagctgctgtaacttattcacattcctaacaatagagcctagccgataggtat
atcccgccgacggtgtcgcccgtccttgaaaaataaagcgagccattgagcgcgacgctg
tgtagaactcgttcgcatacacgcatacgcccggcgtcgagctgcggtttcctctgcaca
agaagttctgttatcaaaataaagctaaggattccaaacatgtgacaccagctaccccac
caccccatataagtatagcatgctcccattggcacagtgtaccgggtgttgacggtcgcg
ggctcggtcttcatggaagctcctgttggaagcgtgtactattaatgtccccctcattta
agtactgcgaacccaaaattttgggttaggaaaaagacggcatcctcttatatgacgagt
cacctttttttttacactcgagccttacggaagagaagtcgaacaaaagcacgtggtgac
ggtccctcaaatactatcgacatggccaccttcctattattaatagccgcttcacgattg
ctattagagtgcctatctcatacttcctatgatcgtacgtggatggagacgaagcgggtg
tggtgagctttgtattccggacgagtgtgcggcttggtaggaaccggggcgtatgaaatc
tctcatgggaggaggtagtagagttagacaccgtctaagttagttctcggactgtatcgc
agtcagaaccggccgttcagagcgggaaccacagaaatgggcccccccgcagcttcacac
gcatactcggacatgctggcttgcacgtcgtaagatgaggtgaatagggctatgcgaata
tcctgaaatcgaggagctagaacggcaggaacctaatggatagtcagttatgttcagtcg
gctcccttcaaaatgggtgctgcagatacttaggtcgaccgtcacggagaccccgtagac
gcgaacgggtagtacaaacatagcactagccaccacggagaagagttggctcgttaggtc
tcgtcactctgcattggttgacaagcttgggctaccaatgccctgtcctaacactcaggg
cgcggaatatagtactctccgactggcattggattagcattactcgttctttttgatttc
gtgagcgagctaggctaaactttaacgccatgattgacgtcgttaggggatcggctccca
atagctaatgccgtgatgtctttcactaacgtgggacaagtccattcgctaaccgcgcaa
cggttatctcaaaactaaaggacgtttagaagaatacgttgagctggcgatcggcgccta
tccgttggtcacctaaggtcctagtgttaaatatcctcggacgggccactaccatagctg
agagcccaagtgttacaggcttcgacacattactcatgccgaccccccggtaaccagggc
ctggccgtgcccggcgaatccttatgagcagtttacggaaaagctatgtgaccttattcg
cctcaccctatgacgatgcatgaactagacgacagtaacgtaaagtgtaaaaaaaaactg
gcgctatacctttatcccataaacaccctttttcgccggctgcgcgcggcaagcgctgat
tgttatactccgaatgtccgggctagacactgatgcacactccctaggaacagtcaggtc
actcgctcctcagtcgtgggcaatcgatgtcacctccagcgagaatcgcccatatcggtc
tggaattaattccgttataacgtgacatcgacctctccgctgggcgcataggcaactttg
cctgctaatttttccccttcaacaacaggcccgacagagttacacctaccgtaacagtga
gctgacttaaacgcttcaactgttaaacactgactagtgacggggctcggtacgcccagg
tgatcatcgaaggatagcgtagatttcgagcataaatgacgtcgggccgatcaggcgttc
taaaatggcggaattataagccagttctgccagcgccgcgtaaatggtcttcgtggactc
actgcatatatcgaatttttagactcaggcgcatcactgttggcggacgattactgacag
ggttttcggaatggtcccttctcattcccagcggtacttgagctgtgctgtgcgttttgg
cccctcggacagctgcgtttacatcttcaagcctcatacccgcgagtacttgcgacgcct
tcagctagttgtcgcaacattgggcagtaacccaagaggggtcgctaacataggtagaga
tccgccctcgtccttaaatgcaagggcgttatcttggggcgctaatcaattggacgaagc
tcccttaggttatcgaagcccgaactaggctgggttcgtgtgagtatgaaaactggttaa
gctatagaaagcttcatttgcccaagaggacttcctttgagtagcaacatgaggtaaccc
atagggtgctcccaatatttgtaatgactctggctgttcggttgtgccgtgtcctaccat
atgcgcacctgtacctgcgactaagatacgcgtgcaatagaagggaccgtgggttccacg
caatctcaacacgatagggttgttttgattttattgccgccccgtgagatctgtgtatcg
ttaggttaggtagcctgaactgggtagcgattatctgcatgacggatcatacccgttggc
gtcccccaattctctaaaaaccctgggtccacgagtagaccgggacccagggcttagcag
cgactacagaagcctgcattatcctgttacaaccccgaagtgaagacctcggacgcagtc
atccctagcagttcaagcggtccggaggtccggtaaggattgaatcttgtgcttcgtgaa
tagactgtagttggttcaaacacaatctaggcatgggcccggaacccacagtgaacagga
gatgtgtctccaaagaatccgttatctcgcacttgacggacctgatactcaataatttta
gagaggacgcacttactgctatgcgtcatttgggcggccagcgaacccggattggatctt
ctagccacaatgaggcggaaatcttcgcacgttctagtggccctctaaaaggaacgatgg
ttaattcgacggcctgggctcggcgttggtctgattatagactattttccggatgtagaa
ggaaccgaacttcctcgctggtcttaaaggctagcaacaaagagacaaaggttaagcgtg
aacatgagctccacagcttcagttgagccaggacttttaccttccatggcacgcaggatc
gatccagatatccgacgcactaagaaatcgtcccagggctgtacgtctgggtgctatgcc
agcatcatccgtcgtctattgacgagaaactactcgtacacttcagccatggataaccaa
cttcctaagggtcgtgcgtcatgcatacctatacagggcagcttaatggtgatgagtctt
gtatataagggcgacttttttacagcgtgtttacctctggccgacaaatagcatccatta
tgcttagaaagctctccctaattgaggcgttcctcgcttgcccgtcctagctatgacgag
gcccctttacgtcccagaataagctccgcatctaaccggaatagcgctctcaggattatg
actcctctcatctatgccggttcaagctaacatagtctctgtgcggcgaggggttgtcat
gtgatttaaagagatagaagcctgcttgtatctcgtagctgaccggtcacgtacgcggtt
gttgaggctcttgaccatctataaacgctgtttcctcttttatttggcccgcaagctcta
ctcactggccgttgacggctacattcgttgaagatatacgacagtggtgataattgactt
ctgacgaattcggtacccgcgatatcgcgcctcccctcttttgcatagctctcatatagt
tactccgaaggggcttggccacatataaatagtaaccgaatctgtgatgtgatagctgcc
gtagggctcacgagttgcctaacagtaatgcagggcgaaccgcggctaacgtcacagctt
accggtgggcggctcccgccatgttgttaccgttaacgtagtgcactcacacggccgtta
accgtcctaccaccccgaggcagagctcgcaatccctaccataaaccgatcttctcaacc
tttctagaggacaaaacgcaccgtaactactagccgccgcttgttgatagatatccccga
gtgccactgcaggcggttatgtatcgaattaattacaagtttgggacgagagcgacccga
gaagatttgataatacttaaaggctcacctcgctcgcagtatttcgggtgaaaatccgct
cactaacatcgaccgaggtttttggaggtctacaaacaagcggctagccccgtgaagaac
ggggtcttaactattttagaaggtaatagatactctgcagcttacttccataagtgggta
ctgagcaaggatttaaacgcaataaatgtgcttgccggtatggatgctatggaagctccg
cttctccagagaacttggcgagattatctcaataacgacatagcttcggagtgagagtga
tacccgaacatgctcagagtctggggatacccggacgaagacgtaacgccaatgtcgtcc
ccccgaccggcgagtcaagacccccacagagggtcgccagtcagccggtgcgtctcgagt
cagtaggagatattccagagcctcatctgaactcggcatgcaccctcatccggttgagtt
ggtcatcaatatcccctgcttaactaagattaagatattaccgctgataatagcacgtga
gccttaatgcggtaagagcagcacactcacgagagatcagttacgtgtctcatcagtaag
aactatccgctgccttttctcctcagcggcatcaagcctacaccctctcgtagcgaaggc
aaggtgaaggttatggatcacctatcagaatcgagaacgtccccctgaccgtgtagactt
cgacagcctgggcgcgcctcccgttatcctgcccaaaggctatgtccaagggtcccgaca
agcatatggacaaaaagaacagcagattgatacagattgcgtccaaattgtccttgcgtt
ataagtaagtaatggcgccgtcatggaaaaaggggtcatacttgggtggtgaaaccccac
agtctgagcggcgactgtggccccgtccgtagccctatcccaggattaggtaaccggaat
aggctaatacacgggtgatgcactcttcggatcacgaaagacggagcttcagccagtagg
aaacggaatagtgatgctggtggggccgacataattaggggttccgcagtatgggtcgac
ttagaaaaccgagaaaatttttttcacgtcgtagggtttacatgcgcagagcggcaagaa
gatgaggggaaaccttgcttataccggggtgccctttgccgtaagcaatgaacagacaac
tacccgcaacacttagcatgtcaggcggagttcaacgtcattcgtaggttctagtatcag
tgtgggacgttattgccccggcacgattctaagttaatacatgaactctggtgccatgga
gggctacgctgaggtagctctacttgcaaccccgtggtgtgttccctactcgcgctgagg
gcaatattagagattttgaccctgaaacagcgtaaaccccgggataccaaggaccgactg
cgtcgggctttagatacttgagggcccataactccgggggtcggcttgtacgttatttcc
agtaggccggcacgctgggtatcattagatctacaggccccaacaccactctgtcattag
attagggtcggttggtcgtcacggcaattattcgatgacaattgttgataccagctgcgg
aagaagccggtccgggaactcctccaaatgaaaggacagtcttttcatatcgcagctatg
ttcagtggatccaatggatgcagatacgtttaggatcgtgtaaacatttgaattatgtga
acagcgtaaatggggcggatatgccgggtatcgaatacactcgtggttctaacttggaag
tccacccagaaaagcctccggcacgcgtcctgtaaccgactggatcgttaagacaggctg
gagacaatatcaatgcgtgttctaaagacagcaggtcttacacatggcgattgccgtagg
caagcttgtagctaagagtacgatgcttcgtagataatcacgctgaactgcagggtctct
tggcatatgaaccctttcgcctgcaagctaatcgtcctctctccataatattgtaacaca
gcggtgtgcgccacgtttacagatgtccgtgacgtacttagtagtttgacgtgctgaatc
tagatatcattcagggattagaggaaccgagtttgggcgccatcacgctatatccattaa
ggctgcgacattaaggtgccaaatctctaagccctaattggggcgtatggctagcttcta
atgtaacaatagaaaaccaacatcgtaacggttgatacttataattcccctttgggttgt
gaagagcgggaagggaaggagaattcagtactcaaacagcagtgtatggtagttgagcca
cataaatgtagagcggatgcatgaccatggctcggtaatgaggcttgcctagtctagttg
gtgaagtggtgaacactgggagcgttagaatataagtccgtttacccaaacgttctgatt
ctcatcgcccccttttgccggcgactgcactgcacgtttagcaatgtgttatcgccatcc
atatccccaattgtagtttaggaaccacggggatttcctgcgcccaaggcgttatgtggg
atacgaaaaggtcccgccgtatagaaaacgtttcatctaggggacaacaactataacttt
atcaacgcttttgactgacgcggggaaccaactacacagagcataaggaatgggaccagc
tactagagacaggggctgaactgagggtgagtggttagctccggaaaacatgcttcggtc
ccgagaactggaaccagcggcgaacgggcgctccttctaattaggatcagtggagaacgg
cccgttgccgctttacactgtatgcaccgagctcacacgctgagccgttatttacaatta
tgctacactagcgcgtggccccgagagcacggagataaggatacaaatcggtgatataat
ccattaatgtgtgaacttgtcccctccgcccgtgcatacttaatcgatcgagctacaaat
cacccgcagctggatacttaattcagccgagtctcgtagcagtacgtatgatggatactg
acggtcccaggatttgcagataccagtgtatcaaagtatacattgatgtttgttcataat
attgcgcctcaggctgagtcttatttaaacagcgagagtaccacacgcccctcctatggc
tacatacgatgaacagtttgcctagggtcattccggctgaggtccgaatagttgtacttt
aggatcaggaacgaatggacctatcattaggaagcgcactccctgcttgccctggtgccg
ccctaagtgctgaatgtgcctcaaacacctccgtcgaatgcgacggcatctcgggtcggg
cgacttcccgattaattattagcactaaaaaccatcgtggatgagttggggctctggaca
gaagatcttattagacgtgctttcggtgcgctccgttcagtgtttaaggtacgtcaatac
cggaatccctggtagtaacgcgtgactaagaaaatactggagctgccaatgatactatcg
gggtattccgcgagagattcaggcctgccgatgggcgcgatggatgcactctactgagtt
acttgtcgctgtgtgatggataatgttcataacagccacgtatatacaatgggggggcgt
tccacataggcatgtcccaagatctacccgttgcgcgtcatcctgccggttcacgattaa
aaagtctcgtttagctcatggctgctacaggttaaggccacgacaccgaggaggtccaag
agtgcttcccactctatattgatctcttcctaacgccaaagctatgtcctacatgatatg
agttatactgagacaacagaaaatcccatcgctaagaaagacgatgcgcctacgcttagc
ttcgtccgtaagaggcagtccgatgtttgaggtggccgctgggccgtatgccgaccaaga
tacgaccccgggtattatgctccattgaacttagctaagaagatccaacgggatgtgttt
agagcgggattggagctcccccatgcagttggatccggagtaggtccctcactcgagcct
gactgtatgccggcacagccgtggcactcatttcgcccgtggagggtgttcgtgaacttt
aataccaatactctaagctgtccacgcacgggacaggtatgagtttggaggacaccaatt
taacatgctcagagtcttgtaatgctgccagcggtctctaaggtgctaccaaacaagtaa
gcggaattgagatgacgtggtttgccgaggctggaataatgaggtggttccctagccttc
gattctacgtccattagggtaacagcacgattagaactgtggatcacgggccaggatctc
ccattcaagtatccagactcatctccgctgacgctagcatgcgttggcggtaaggcagtg
tgtggaaacaacggttccacccgtggggatcgcgaggctgtcatattccattgaagtgtc
ggtatctaccaaacaagcgcaggtcggggaatcctgaaagcctacgtcagacttagcgac
tttcatgggctgggtgtcgagaggtcacttcagtacgctatgtagtgatagcgacccgcg
cgtagttcacgaactctagcagaccagtgcgcgtcatccgtttttattgcctcaacttag
cgtcataaccctagttatcgcgaggacacccaatacgaaggactgcccctaagaggcgat
aattttacgcaggtagacacgtcggcacacgctggaattccatactagataactcccaca
cttttggcccgacagggagaccctgctgacggcgtgtcacggagctgctcatcgaagcga
acgctatctgaatagtggaagtggcgttgtgaaaaatccatggtgagtgcggaggggaac
tcgggtagcgcataaatcactgtttccctaccgtcacccgattcctccactcgtcggcgt
gctaagccacgtgtgagcacccgctaccgttgtagggtcaacgggacttcttatgggcct
cggtcggccaatttcatcccttacagagattagtgtgtttgcgtggagtccctcattgta
gcgcactcttcggggcagggattatcgtggattatcctcctcaagagcgaggcgccgatc
gattgccagggacctacagcagcaccttatcattcgaaatcggcacgaccctcttttcta
cgagtgcctgggtgttaaagagattgataatcaccggatgcgctcagggagtcattactc
gtggtgttggccccgtttcacgggcttccaaaagacaatttcatcggcatttagtatcta
ggcccagttgtcagaacgggtccctgtgatctgtaccccggctccgagcctgaccacttt
acacacgcgtaactgatgtacgtatccgcgtcgaccgttcgattctcactagtcagagcc
cgtgctcaaggagagaggtcttctcgaacacttgagacctaggcttaagttccgagtact
gacccgaatcaataagtttacgtgtctagcgcaatagcgtcatgggggcgtgcgtcatac
tggtccggcgtaatctcgactagataaatccagcgcctgatcaggttacagtaaagcata
gattcattaccatggcctagggtctcaaggccgatgattgaccgcgcactagtacttagg
ttttgagtcttcgagtagatccatgacccgtggggcgtctatagggctgcgacttctcta
gtatcgggatttaaactagccgtcttccaggtagcgagcgattggcattcgtaacagctg
taaccgtttattccttgctaccataatgtgcccaaaaattcgccactagaaggttgatag
aatcttaactgtggtatagtttcgggccgtgctggaacggtgattgtactttgcgtcgac
aagaaaggtgttgcggtgaagagcaccccaccatttgacttgccttggcgacttttcctc
tttgcagctgatatactctgcgctatgttattcgggcccgtacaaccgtgcacctctcat
cacctgactattactacctccccactccctttatgtcagctttctctaaattttcacatg
caattcacgccctccacgcgtaacaagaaagcgggactgtcagataatcctaccgactaa
gaccacaagcgtgaagatggataaccctcgggtattcgtagaggcgcgatcgactttaaa
tttgcgtacggccaagattttatcacataaacgggcaatgagttgccgcggcgtgaagac
cccctatacgagaggatatcgccatctactatatcatgtatcagtgtgtaggaggccttt
ctaacgtatacagttgttcgtccccaattgtccccatcgggtgatagaaatcatttcacc
cttaatggattgatatgaccaattactatactgttagatacagttaactcgtccaagaaa
agatgctggactggtcttgtaagcagcgcgccgctaaagatgcgaatcttactagtcagg
agtctggacccttttttcttatgactagacagatgttgcgccgtttccgggctaacttat
aagagaactaagctacagttacccctgcctgcctgtcgcgtccatccgcgtcgtaccaac
ttcacatgttatagtagtagcactgttcggattttttgttctatctagattcgaattgtg
tgagcttcaagaaatggtgctccaattgttctgcaatgagtcttctctgctgacaacccg
acaggttatcagaccgaaggatgggctccgtgcacgttgcacttcatagccgcatatccg
cagattatgaagaatgcgtattatggttactgttcctagccgaattataagcgctatcaa
ttcccgtctaaagtacaacgtccgaacgacaacttacacaagtccgcctcgcattactgc
cctcctggtcacactccatgaagatcaggcagttctaaacgacgaggttgttgctatcta
ctcaacagccagaagtatacagacatcatatatactcagctacaacgctggatgataagc
tatcagcctcagccgcacatgtgggatacgcgcctctctgaacctgagaaaggcttcccc
catcaaggcgtgtatctgcccctgcctgacgcgataattaacgtgtgatcaattcgcccc
gtgtctgcgctagtactcaaactggttgcccttgttctcatgttggcggcgtgtgcgaca
ggtactcagcgggagtatgaatgtagttgacgcacggtatgtgcagaagtaggaatgcgg
atgacccgttcgttcgatctatatttcggaccgcgtcacctgagcggtctttcagccgtt
taagtggagagtaaaagatcaccacaaacaacgacgcacactctatgtgggcttttattg
gtctgagctcgtctagccccctaacactttcgaaccttactcttgttgcatttgtaacaa
gttatgccggtgaccagaacggttaggttagttgcgtcacagatatggactcgctgctgc
aaagtaggggtaatacgaacacggtagggtcaataagcgcactaattgcggctgtatagg
gagcgggcgcgagaaggacgactactggtcattcccaattgttctctccagcctaatggc
ttcggctctacacgtacgctactattagcccaatagttaaccaacgacttaaccggcgat
ggcagcgcgcgtgagctaggaacagactttcacaacgcacgatataggggcttaaacggc
agtcctatggcattcgacggtagtgttccaaagctacgtgataccggttgcatcaataat
ccccggttacgttcgctacttggtagctgcgcatgtctgccctgtgagctcctgcaattg
actttttcagagtgcagagttataaacagcgggagagcaacatggcctcaatctcgtttc
tcaaaccttggctgacttgtgttatgccggagctcccactggtatgtggaacacgagacg
caaggataagctaacgtctcaatggtacggcgcaacaggtaggtatcgaaagcataagca
tgttcaggcctcttgcggtgcgtacaaaaatctctagacgtacaacttagaaatgtcttc
cggtatgacactattttgtgcttggtcccatgtaaatctgattttcggataagcccctat
aatcaacctactgccggacgtctcgggttccgagacggtcccactatgattggtacaatt
ggactgagagaacacaaaatacgtcgcaagaaccctgaagtggaagacactgattaacgc
aacgaatataaataacgggcctgcattgggtccccttgtccatgggaaatgttcacgcac
atgtgcgggcccggggcgcaattactggcatttagatgaggtgcacctaacctagacacg
gtcctaggccactgcaccggtatcactcacttagcacttatcgtcatcatagtgcgagct
tgttttagcagccttggcatcagacgggatcgtccgaagtcacgtgacggagatcccatt
gcgcgattccgactgcaaggaaacaaagaaacgcgggacgattctctccaatgcatcctt
tccctatcaaaagcagtttactacaagttgcggcaattttttcggtaggaggggtctatg
cagatcttggcgccgactgtccttgaggggccgctggtagtctgggttgtgcttacgttc
attgatgtacgctcacatcgtaaagtgaaatggatgaaatatttaagtcctgcgttggaa
cattttcgaagtctttacaagacacaacgggaaaccctcgcaaagtttatgatagaataa
ccttatcacatgcacctaatgagggcccaagctagttgtccaattctacaaaaccaggta
cctcacctgttcaaggatttcacccagtagaacaaggcgcccggaacacaggggataata
cgattcgtgactcgggatgttcgagcccattgcgagcgcagttcaatcctacccggacct
tggtggtccggtcccaaatcccagtggaatagctcttgtcggaactgcgcaggactttct
ttgccctggcacgctgttaatcccctcgtaacctgtggtatagcctgtctgaaggcctac
acaacgaacgtagaacagaaggcgtggctacctccaggtctctctcggaccttcatgaaa
taccgagtttccacaggggctatggtgcggacaagctccgctcggcctgattttgattcg
cagctgacgtcaaacgatgcgaaccctcttcttgttatcggtagggcggttgggctttat
agaccgtttagctatgcctttcgagccgcacatccctggacggcaacctcggttcgcacc
atattccgttgatctagccagccatccatcatcggaatgttcatataacacgtacgaaaa
aaatagttaggggcgactattaccggctggggatccttcagggcacgacctgaaccagaa
cggaggttcgcgcttctgttacagcctcaacttgcaaggacttccgcctatgcacgcgag
agatctgcgctatgcagacgaacttccacagaggtttaatactagatagtgtcgtattga
ggcttcaaggcggaacctgagagtggttcccctgcatctatctcaccgactgggctcctg
tcactcgactctcactgatcgtacactagagggtgggcctacctaaccttactggagctt
ctactcttctgacacagtagctgtcaggatcaataactacgtgtagctccaagtcgctac
gcttgcaacgagccattcaacaattcgtgcccacagattttagttaagtaacgttagtga
atgctgtaagactccaattctagtacttgaccgacaatacaggggtcacgacaaatacat
gtgcgtaagttcccatgccaggagtgtttgacctcccctcaaaaaggacgggcggtttac
taatatggttctgggcgggtgctcattaccatcgttccgatgtttcgatcatgatgatcc
atcctctctgatcacttaaaatcttagtgcaaaagacttgattactggtcgacgggaaac
cgaatagcaaccgggggtcgcgcttccatggaagcgggttgacgtcttgctcgggatgct
tcccgttatctacgctatacggagatccgctaggtgcactggcctattggagcactatac
cgaggaccaacgcgtatgaagaagtgtagtcgtatctgaagtttcgacctggaaagcagg
ggctcttacaggggtgccaacgacaaccgatgatttaaacaagttctccaatctcacgag
caggcgaggccacctagaccttattacagggatcctgccgagccagtacggtgcctagtg
cgaccactcattcttttatgcgcgcgactccctggggcagcgaagaactacttaagagca
acgttgcaggcgagcttagatgatatccttatctccctcacttgcagactcactgactgg
tagacctgtcgtgtttaatttgcttttgcggctcttccaatgcgcacagtcgtaggatga
taatgatgccaacgacatgtgaccgttatcgggatgacttaactgtagaccaacgattta
agtttgtaatgatgccgattagaccagcttcggatttgaggtctccgtgcgtcgttggaa
ttacaggttagaatgttgagatccaaaatggattgtacgcagttcacgaggcgaccgttg
taccgacaaggtcctgtcatgagtctggttgccgtcccttatgaaagggctgacaaaccg
ggacacccagtcgaactgaaagcagcgccaaagaggcgagcttaaatttcgggatagctc
gcggctccggaacaacgaggcgagcaacatgcaagaaatgcagacagtactcgggtccgg
tgggaggcgaacacttctagcctatccgaacatatggggccaagaaaactagtgctttct
tcgggcgaaaagtaggacataagttcgcctggttggatgtagtgtaggaatgatgcaagc
attcccgtacgataactgaatcagtcacctggggatgaagaccggtgagccctgatccct
tcataagatcggtcacatgcacttacacttggaacgtattgagaggcaatatgaggagcc
gatcgccgtgattccgattaaggcttcagttaccctgtcagaggccccagctagtcttaa
ctaacataaacgatggtctaccggtcgcaacacaagtctcctaacctggcatttacggtc
tctcacatacccgacatagctcatcgtttgggatcgaattgcgatgcagacgttgtaggt
tgcgcacacaggatgcagcgtgtccccggcgataggacaccgtttgagttggcccatgaa
cccttctaatttgtgacttttttaatgtaatcttcgtttgtgtagttcattcatcagtct
atatccgtccggaccccatcgcaaatataatagcgcccagatttatcttacaccgctgat
ggcaataccaccaggctatgacgcagtctactgttagcttctcactctgacgtctaaatc
attttagtattggtgacccgggtcagacttcgcggatgaaatcttaccggacaccaccaa
ctatacaatcggcctttagataggagtaagagccagtcaccgcgtcagcttgccagatgg
tgatgactgaggcctggtgcgttgtcgttcaccaaaggttattcctcaactgacggcgca
acttccagcacaggcccgagttgctagcctcggccgatccctgaatgggcattcatcagt
attcaagcgtgacacatgtgacgcagttttcagcgccatgccttttataaactaaaaaat
gtcatgaaaaaacaagacacgctcgacaacgacaattagggcgcgattgtattagaagca
cattgaaagctactccccgacgtccggcttgcaaggctcaatcgggttgtggtcgtctgc
acatgcctaatgaaatccaggtcgtaatcaagtcgggcagatcggatacgcattgtactg
gctgattaagcccatcatccgtttcgggcacacgtaagataagaccctggtggcgtaata
acaggtatcactcgctggttacgtgtgcacgacatcgtaaactacgctgcctgcgatatc
tagctaattgcaccgcataaaataatagcgaccgaaatgatgcggcccggaaccgatggc
tctgataacggagcacggggtccaagaggtagaacctgcgaacagtcgccgttcaatggc
ggcctagggcacatctggtgacaaattgcagcagcaaaggactgatcggcactctctaag
ttggtatcgtgcatataagagcttcagccgatgtccgcattgcgtgttattcgagtcagc
tgaccttcggtgccctccaaccagatacatgagggatttgaaccgttgtgcctgttagtg
atggattttactccattttccagaacggtggacagttttccaggtactgcgtaacactgg
acgaacatggaccaaacagcagctttcgaagtacggtcgcttggatgttaagagtctaac
gatcacaagtagctaccatattcacaattttgtgtttcttaagccattcgtaaataaagg
aatacgaagcgtccgaccagaggtctgatgtgtctcgtgtcattggtagagatgtttacc
ttagaaccggtcaccaggatttctgacgttttcggttagcggctctgccccgtagggatg
cttacgtgtcgaagttaggacttcttattatcacgtctactagttcatggacgatctgta
atgttattccccgaggccgatgacgtgaattaacgaaggcgaatgctagccgtcaaccca
gaacagcaggggcggtggcctactgtctgagtcgaatagtcacgtcctaggtacccagta
caagacctacaccaggatatgttgggatgtattaccggcaaccctttaagtagggcaaca
gggccacactgagtgcagaactatacgagtcccaacaaagaggtggttcagccaccagcc
agtaagtttgcagttcaggcgggttaggccacacaagccgtagcccgatgcaactatggc
cttgggtaaacccccgtccaaaattattgactacttgtactgacaggttgccgtgtgatg
cttacggtacctcaggtctggtatgacctcattgagtccccagtaacgtagacattgttt
tcttagataatccgctagagcggcggtcggcgaagaagtccacgtcactgataagtcaag
gcgactctgacaagctctccgtgtcatgcacttaagcctagcaaatttaggatgaggaga
aatattgcatcagggacggggaatccgaggataaagcactcataagcctgttgacacccg
catgctgaatgctaagctagaggcgcaggctccaagccgtcctcgcaagtagatcttcgt
gaggtagcgtatgtcagtagagtaccatcaggcaccctggcgctcatagcccagcgcctc
tccgatgttggtctcccacgagagacccggtgtagcccctgtggaagagttaataagcat
catcgacggatttggtgaatataattcctttagggaacatatctataatgtgaacaagcg
ataacagccatgatattaattgaacaaattcgatgacttatgtcctcgtccaatgttttg
gtcatggacagtacgccatatactcaactcatgggatgttgtctcccccctagcgggccc
accgtatttaaagctaaccgttatttaaacctggcctgcatgtggtgtacgggagcagtc
agtactatctcctagcgtaccacacaccacagaatgtttcgtttgaataccagttccagg
gagtgggaatgttggtgaccagaggatacatcgaagttcaggcgcgttgagccagtggtt
ggtgggccggtcgcgtaacgaggaagggccaaacggcccagcatctccgcagatataacg
gtgcacgaagaagcgatctccatacaggtaggtcgcgtcgctaacgcaatcctcatagcg
gtgccgatcaatgtgttcagttgatctggccactgcggtgcgcagtctaacctaacatga
aaacccatgatccgaccagatgttatcggcaatgacggagcaaaatattgtggtgtctgc
atgctattccgcatcggctttcctatccgcttaggaggtggaggacacgcgtaattcgac
ttctcgacactacaaacgttcttatcagtggttgatccaatgcctcctgagtttccaaac
caatcgatacctaccacggctagaacccagcttaagtcccggaccgcgcgctggagatgg
cagggatgcttgcttcttcagtctcagggtagtcacgctcgttagagttacagtcaaact
acaagtgccgaatcgcaagacatggccgtacatgttccaaatgtgcgcgaccgacgaaaa
cgatgcatctggaacatccttcactttcggggattgttccgtgtgtggggacgaccctct
ctgatagtagggaagcttacaccggatgaccagcggtacgggttttataaaattgaatgc
cggaacacctggtgcatctgtgtctgtttacaaagtcaactgctaaagtccagtgcacct
aagtgctagagccatctcagccaggtggagagataggaatggaactaatgagtgtccgac
atataccgaaatagtgaatagcattatcggggtcacctacctcaccataatgttaaccag
tacgtggaggtgagtagcattgatgttggttccacgactctagttaaaagtagggatgtt
gcgtggtcaggaaactccagcacgcagcaattattcgatgataatggcgcggtcttgtgg
aaccgcatgattcattaatcacgacctcaacacattcggttgaaagtaacgaaagtacca
ggacggcaaattgtggatcgatgtcggcttgaaacagtctcttgtctgtcaatgattgca
gctattgggctcctttttgagattactcatctcatacttgaatgtacggtcaattcccgc
tcaggtataagggctaggaccaactacgggcttagagctaagtcaccggtgcagagcaag
gacgtctctcccagatatataagggctttaccggtatcgaattaggcctttatccagtgg
cctagttacggtcgatcgtttctcgtgaggttcctatacacgacgtggagggtcgcaatt
gcgaggcacttctaggtctttccggacagaccatacggccccgccgcacgatgggatgaa
ggggatagaggtcgtgacgctaagtatgacattaacggggtctatctgacgccagcatta
acgcgttgtgaccggaggaagtcgaaaccggtgggagggcgttcttctagcggtccagag
cccatattaaccgcaagcgtgatcggagtcgaccttacctctcagctgagacgaagtgta
gtggcttgtctgagctccggttggtccctcgactatgctacacaggactacagtgtgctc
ccgcattgacaaatgactcttggggcatggactaacgagtgatcaagtttcaccatttat
tccctagcgtaagtcgcgtaaggatatcaggtcagcctaatttagaggatttcgtgacgc
ctactggacgaagaggtgttactgcggaaggttccagaaaaggggcaatgatccaaaaag
caagatagggacggacttatgatgcaactgttgagcggccggcagaccaaagcgcttatt
gctgcgagaggagatgggcagactgtgtgcgaaataaaagtgtcctgtcgcggatgagtt
ctagattgtcggacacctggtagaggcgcactagcaacaagaattcttggaatcggtagt
tgcctacagtcctcgttgtaccacaaggccctcagaaagccagggtaagttccattacta
tcaccttcgtttccttcctataaattttgcgtacgctcagtgacgtaatttcgtcgccgt
atgtgtgttccaagaccttacgggttataggtgtcgcttccctagtcggaacttcgattg
gagttcacgcccaattcaacagagggaagatgcgacccacaagctgcaaccagtcgaaat
aagaaggagcattgtagcggacccttcacagtggggctcttagcgcactcgcgccaggga
tatcgtgccccccgcactgtacccaaaagggtcagatcatttcaatgacagagcaatcga
tctacgcaaagctcctcggtgtaatagacaggttagaggcaatttctggttagcgcggtg
cgtagccctagcagataagacactagaactccgaggctatgggtaagacatcgccgccgt
tggagttagtgagcagcgaaatcccccgactggtgctagggtaagaagacccgtttcgtg
cacccgggagaagactgtagccgacattcggttgagcagatccatcatctaagtgttgaa
taaacaagctttggtccggcagtcttcgcgcattccctaccttcaattcgcttccctcat
atactaaatcaagagatcgataataaactgtattgccacctctgttttgctggtcaaagt
cttgcgactaccacggcggaatctcgtctttggcatagaatgcccacttggccccgagta
tgcaacgacttaagcagcgaaaaatacggataagcaccatgaggcgaacacgctcgcagg
ggactcccagtgctcggaccgcgattgcgatccatgtacgaatgagtaggatctccaccg
gtggatcgccgtcataccctcagggaggttccccccaagctctacgtccaacggaaaaat
caggcgtgctcatcttcattcgtacagtgcccaagaccgctcgcacttgcgagtgctggg
accatgacaggtcgcggcatgaatagtacgaagcgggaaccacggacgattcgtcacaac
aggtcccgattcgtcttgaatactactgcaaagccagcgaatgacaccgactgctaacca
cggaggaaataccatgcgaactgttaacatgcaatacattggtgctgggctcatccctgg
cgcaaggccacatctggactgaccgtccagattaaaagtatgccgccggacgcgttcgaa
ctggtcaaaaacctttcgataaggtgttcacgttactcttatacgaacaaatctaagcct
agaggaactagacatagcagacctggttgaacttgcgcttaagcgtcgtcaaaaagcgct
actagtttataacctgcaaccttctgccggctcgcatagcgaaacgcgagaacgcttggt
tttagtcgacgcgctcaaatctatgcttttgaacttcgtggctttcgtgtgaaacatcgt
atcgtagcatcatcacagatcacaattcataacttcatgccgcatcgcgatagccccccc
tctttctagaccagacagatgtagacgatcaactgaatcggccgtacgccgtactggcat
ggttatgctgcaattattttcttagggcagatatcgatctgacaggtaagactaagacca
tctcggcatttccgagagcttataaagctccgtaatatgcgtgctacacctgcgatgaca
agtgactcccgagaaaaaacaaagatcttgcacactggaagaggtgttttcactttcaat
tgaggatatcactttgcgctcgctacgggacattagccacataacacacgtgaagcccaa
tgtgctcaataagcggtggtttggacaatagggtccaaaattcctatcgctactcaaatt
tttgccggtaaatggctctgcgtgcctagcagaatctctttttgcagacaagcggcgacg
gcccgagaccggctggtcagtcctggtttgcactgatactctccataggacccttgcagg
tatgggcgagaaatcctcgggatgttatccagcaacacgtgcgttcgcaaattctgtaga
cttttggactaaaataagtgcactggctgttcacgttatcgagcgacgttcccgattcct
tattgctctgcgcgaaccacggtccgattgtagaaagacggagtacggtaaaaacgccgt
caagtataatgtcagtgactttctataaaaggttgggaagtacgttatgtaagttgcact
cttagtccgcatcggttccatgtgccccggtactacagcgaaggtcgtccacactcagca
aggagaaggcgagacgtacgtttagctcttaacgtaactggtccaacagcctccttcggt
gaggcgttgagcgtagcagggtcactaatcatgtagggagagacagcctctggcagacaa
tcgttatcgaaacacaccaatacaggcgacagccggcccaattacaaggatacagctgct
ctgggacagcatcgtttcctgtgaaagctcgtcacgattttacactcatccttggccgtt
tacaccacgatgcggcttggataagagaattaagaccaagtgatgccgacatcattatcc
gctctatctaccacctattcgtctttcgcctacggcctagttctactagggtctttgtta
ggtaatgtaatccgtcccgagtggcctctgcacgtcgcgctttgcaaaaaatagcgccca
tgatcgaggaattctgtattatacgagatacctggcgtcaaaatacagggaatggggtgg
cgcgcaacttgggactactcctcgcccaccagtgacgtctgaggatgatcagccgcgcag
gtgcaattaccccgccgtctaagctaagtctaaaatcccgagacgtttcgctttgattag
gggattgctgaagccaggcacccggggtctcagctgcacgcctgacactggacttgccct
cggcgcagcagccttcctcctctgtgaggtcaaaaagtccttattaccatagtcttttcc
gtgtgtcacacttctagatacgcgcagtgaacctagcggtgtctgagatagttcatactg
gtatatcccgtttatttgtcaactgttacccctgagccgaatggacacgtgtgttacggc
agtgtgacagacctccgcccattttggatgatggtatagcgctacatgcacggcgaaggc
ctgccaaatacgctgtagcggaattaccattgatggcattcgatggactaaggcacctac
cgccacgaacaaggtgtcagccttccattgaggcattgtgaatcaaagttctgcctaacg
ctgtcctctatcagctggcgcagtgtttgtaaaccatcgtatagtccgtcataaccttct
tccttatggtttcgcaatctcgcgccaactacatgggtctgatcataggcgctccaatgt
acaacttagccggccaggtgaagattgaaatcaacactacactttccagggtcgaaggag
tgaacacccaacgggcgtttccagagtgcgacgactgcacagttgcccaccgctgaggct
ctgagattaatgcgctacatgtattgtatgcagcctttccttatggaaacgagtttcacg
gcataacggtttcggttgtgcagggacctctcgggtttacagagcctaattggattcatg
tgtgggatgcgtcaacgggcaacttccaatgtcgtcctaggcgccgatgaccaccattct
agctcatagtacgtaggaaataggttgtgctgattgtacgctactagtataactcccgta
tcctcgctgtgaggagatcggtgagattttcacttgagagagagaattacctcacgagca
aggttaaaattactcaaaagcgattttcaggttaataggatgcttgaggctgcctacagt
tcagatgaacgggcattgcgtcgcagaggttcggataacagtgaaatattcggtctaatg
atattcgggtaaggagactataattacccggtgcagcataatattgtaaccgcggtcgtg
cgttaggctgatctacgacggtaaagaaagccggtatgctcgaagactgctggtcccagg
acctgtgaatcaaaactgaagccctgtgctcccacgggtattagagcaactgactagttc
cggaccagtaatccgggggccctggagtgggcggaaacacgtcagattaacaccttcgag
tgctattggctgattggccttgctacgaacctcccccagccagcagaaacacatctggcg
acggtgagttcgcctcgcaagaagaaaccgttaatctaacgtgagtcacggccccagacg
gtcataggcaggggtaggcgtagaggtactcgtcatgtacaaaccgtcccgtaaaattaa
agattaccatgcaaggctctgaaggtttcgacgccgctttcaaaagcgagacatgaagac
actcccttccgcacaaagaaagggaagtcttaggaagtcttgtaagtgccacttcacctc
tgacatgagcaatttgatccttggactttcttaattcaagccgcataccggtcaaacaca
tttactatttgctttcacgttcccgatagagtacctatggtggctctataaaatgacatt
ttagggagataggatcgcttctagtgaggcgcggagcatggggtcatcgctttcgctgcg
agatcaatcgttgggactcggctcctaattcatacctatgaataggtttgtggcatgctg
tatttccagacaacaaattcgttgagatgtccgtagccgccttactttacccagatgggt
tgttatttcagtcggcaagttctacctcgtgggctgtacctcagattgcaaatactccga
agtggatcggattccgccgtgcgttacaggaacaatgggggttgctgccttgggcgttca
aagttaccaacggtcaatgtccgggagcagttacgagcgggcgtccgtgtcaaaggtttc
aataaggccatcacggctagttcattccgtctcgtcaactgggtgggttatgactgtgtg
attacacaaaaagtcatttttcttttgatcctgatggccatgtagttctcctagaagagc
acagcggatagtgatcgagccgcgatgtgcgagcaacccagcccgttgttttcaagttcg
gctttgcctagatagaatcaggggctgtatcattgagttcgattctcccggtcagccagc
ctgtcgccaaagaaagcttcaggccgcgttggtcagcgcggcgagtagcgaggagttcgg
ctcgagtctgatctacttccctgtatttccacggtgtccacccccgtgtaccgctgggtt
aagtaagccagctcgaaggttaaccagtttattagcgcgtagtcaacatgggtatctacg
acggcccaccctgaatacacgcatcaaacacttggttcaggatgactctaccctgatacg
tcagagggacttatttactattgtctcgcagggacttaaatcatcaggcggaactgtgta
cctgtgatcggatagtgagagttgtgatgacggatacaagctagctcgctgcctactgga
acatgtagtgtgtaagtgtcaggctactctgtactatagagtaatgcgggtcctaagagt
tcccgctctaggttcaccaatggtcatataaactgccggtgtagggatccttggcctact
atcgacgggcctcctgcgggtgcggtccaacgagtatccggttcgtcaaggagttgagac
tgttgatctctcttgctcatatggagaagtgatagattatgctatcttcgttttctgcaa
gaacagtagaacgaacgtgtacaataacctgggccactcgtgtcgtccaaagcctcaaga
aatactcctgcacgagatgagagcatttctatatcgtcgaagttcatgccgaaaacgatt
atacgttgcacgttacttagaggatcgcagcaagagtgtattagaacatgaaggagaata
gaaaggaggtgtccgatggatacaggtgcgactcttggcgattaagataaactagggagg
gcgaccttctcgtgtgttccggtaacgagcactcgtcctttgacagagtctgcattacat
aaggccggtaccaggagaataactcaggcattacgaacaaatctttcgaacggagtcgat
aggcatgccgctgatacccaggcggtggggtatactagtcaaccgccgtgaagccaagcg
ggcagtctactagccaaacgtcgagcttctcttgcacttactaggactaaaccctcgggg
ttttagatggtttcttccgccgggcgccatttgactccgacctcaccgcgtgtatggtcc
ggtggaatccaacacggagaagcaaacgggactctgcacagtttgagcgctgtccgagaa
gcgtgctgccgacttccaggattttgtagattcaccctatgtgggtgctaacggcgtacc
ccgcgcctaccgcagacgaccgggttggaggaggaattgcgtgcactaatctcctgccag
ctgcaccgggtcggtgccacgttctccttggacggaggacacttccactagccggtcctg
tgagtgatctgctaccacgcaacagcaagtagtgaactcggcgattgcagctcgcgccac
ctaactcgttaaaggcgccgtaggcgcatgccaggtcgcaaaaccggtcatattccccaa
gatgacgcaagttatctttgctcgcagtcgatcctacgacgtataccaaagaaggtaccc
aatcattagtctcaacactaaagatagtccctcaagtagtggagcaaggttcgcacttgc
acatacaatcgtatgcagagtttgagatgctgttcgtactcaaggctattaacgctatat
gttagaagagctgtaatccgacatttatctgacgctgcttctaccccgtgcaatcgttgg
tgaagggtattcgtgctgcctcttttccttcgagagtactgcgcgctccagttatgaact
acccctgttaggaggccaatttaggggcatactgcaacgtttgcgactcatttttcgcgc
gtaactccgtggagaatatacaagaattgcccacttcagtttatacgccgatatggtgga
aagccggagagttgatgtagtaacgaggctccagcgaaaatgagtgcgactgcgatagag
tggagatctatccaacggcatggcgactcagctaggggtggggtaggatcctgttggtaa
acctagaccggaggctgcctccggggataatcatctggcagtgaatccggagaattaatg
acctgaccgatatttcaagaaagtgcaggggctgagatgcatcactgattccattgtggt
ctcgatgttaagattagaataatggattagaggcacttgttattcgtaagtgttaattac
ataacctctcttggatagtcctttgtcatctcgggttgtgcaatagcggggcttcagggg
tcacaaatagacttacccacccaacaatctacagtcttgaatgacggggagcacacaacg
accacatctgcaccgttcattattggagcatatggccataaaagccgtacctacctctct
ccggagcaatggcgaaagcggtaatgttacgtaactacaaaccgctaaagacgaagaaat
ggcaaccactctgtcccggaccgggcagctaacggctgaaatcttgtgaactatattaac
tgctgtacagcgctgtagtacggtttctggtttcggctagtagtaccttgcagaagcacc
gattaccaaccaccgtacgattcgccaacgagttagcctcatgcgttcaaggcgttcccc
gcaccgtctctcgctcgattggacaccatgctattgacggcatgattacgagggcagcta
gtaatgacaactactggcccgcgttgccaattcttttgcatcacgtggctagtacgtcag
cagcgtccctttctgcagaacgcagggtctctgtaaccgtcgctgcgcacaacgtttagc
atcaggaattctcgtttctactctgttaaagggtaacgtggcaaacatagccatcgcttt
tggcggactcgctgtggtccaggtcgacgaattgggggtccagctcttcgtgagctgcag
ctggcgtgaagcaagaactgagtggcctgaatgtgagcagagtattgggactggtgatcc
acgcaacggtttgagagcgtatgggctgcaccggctagtttatgggagtaaacttgaaca
gtagtgaacttgcaggggccgattttatccgggaggactgaaagcgagaatagcacgtca
cgcacgcggtgctactgttgctgatcggtatgagtcctacgatattcgccgtctatggcc
accacacaaaaaaacggggagggcagctgattatcagtcggtgtaatgtattcggcatct
gcccgccctcatccgcctctgtcccgtgtcaactgtactccacgtcagtgacattttcgc
atcacgtcggtgtacacaaatctgaataccgcaatcacgggccaagcagttatcctgcac
tgatcactccaactggaggcatcgggttacacgtctccagacctggtctcggagccgatc
ggcgattgggtaaaaaaactgatttttgtgcgcggtggcaggtggggcacagaccatgtc
agtccgagtgtatctttggtgaattccggactggagtacattcgcctaattccgtctggt
tccgtatcgctggggactccatgacatgtctgttggctccgagggtcgtagtaagaggga
ctcatgctatactcgtgttgcacgattcctttagtatatagtaccatcggaggtctatca
tggcacacacaacttgagtcgcaccggtaacgcatacattttaaattcggggaggaagtt
tcgagcgtacatgatcgcgatagagggaccaagaatagggggtggagtggacttgacgag
ctcgacctgccctgtcgctgccagaatgccatccatctagacacaaatcttacggacccc
ccctggctcgtagcaaccgacggcgatgactcgacggcgcacgctacgcatgggggccgg
gccacggaacatatagttaatgctccctaaacggcctcgagcaggaccaaaaggccgccg
ttaatccgtagcgactgctagacgcactagactctgcctgaatttatagcggggtgtgtc
ttattacatcaaggtcctgaggccgtaaacggatgctcggtaaggcagagatttgacttt
gacaagctgaatccattgcacccagatttaaggggatccctgtatcccgaaacttccctg
actactcaagcagtaaccaagcatgcgatacaaccgatctgtatgctggtttcggggcgt
agtcgaggagcctagcgacttggagctatcgaaccaggcccgaaaccgtgttaggactcg
gatatagattcggaggaacttggcatagatcgagtaaattgggtaacactttactggacc
ttgatttgcgttgcctatcgcaaccggactactagccgacagcgtaagacccagcaggca
ttctaaggcaaccgacctgatagatctaaagttcttctcgaaaaaaccgcgtcgacaggt
ttttaacggaccgcccctcagatcaaacagtctgagatagcagcgcttagaaggcagagg
tggtggtccaccaaccgattcagggccaccagcattgctggagtaaaggccaaataagca
aaatgaggaacgatttccggaatactcgatacgtcccagctctaagggtgctcgcggcgg
agtcgcgaagtgaagtccgtgcgatgcataggctataacgggacgatctgctgacgtatt
gttgttcgccctgtattcacacattttatgttggccgtagggcggcggcctggtgcaccc
aaccgtgcaacacggcacgcgttctggggcaggcggataccctcattggtgtggagggtt
agctgcgtgtaggtttgctctatccataaaaaggaaaactacagttccagagcttgccgg
tgctttcacactactatagcggcccttcaacggcttagccgcatgaatattcttgagcct
cgtattgtgc
>Contig2
gattaatgtctggacccacggtccgtgctatcacagtgtccaccgtaggccacgacaatg
gcacagaagatacccaattccaaaacgctgtcgggtggtctgattagggcgtccgatctt
gtaaataggaccaagcttaacctggaccactaattcctggaagctctgccagagtatgtt
tttccgggcgttcgatcgttgtctgttccgccatcaaaagcacagttttgagacgccata
ctctccttctccgataacataagaggagctacgtgaactgttctcggacccgcgagtgga
gtacaactatattctcgtcccataaatgaagtggcttatggggcacgaacatcgtgtcat
actctagagtccgattccatttcgacctttccctccaggcgccctgggttatccgacaca
aatacgggtaccagacgacgcattaccaagaatgatgtaccacactacgattacattgcc
cgatattccgtgagacaaagccacattaaattttacaagggtggtatttcgcttctgatc
ctaactaggaagatgcaagacatcgactcgagttgcacgggagagtgggagcattgttca
gccgaaagccaatgagcgacaacggcatgggaagacagcggtaaaagcacaggctctcgc
gttaccttcagtcttatatgcgttcatacttttggaaatcggctgcccgtacattaaagc
ggcgccgcgggccgaagctcagcgcagcatggtatctcaaggcatatccgctgaaatgaa
attgataacgcattctgatatccaacgcaggaaagatgaacgaacttgtaagttgaactg
gagtttttagacagccgccatgtcgataccagaaagacctcacctaggtagtaagcgact
tacatacgaccgaatatctatggtgaacgtaaggagctatttatcagaccctaaaaggct
tttattgtgctcaatatcgcatatgggtgcataggcttagctggagttggtacctgcggg
atggttcctggtccacgttatttgagtaactggtgtgccatctccgactcaattgaaaaa
cttacctctacgcattccaacgcgtcatggatgaggtatcacctcacaatacggctttat
ctggatctgaacgggtgaggaacttcgaaacactaatattaggcatttggggagtaggcc
tatccacgacgactggagatggtccaaacgtcttacgtagacgggttctatcagtgttgc
atggctattactattagtcttaacttggtacctgtaaaactcatttgccccagaaaaatt
cttgccctgaaaactgccctaaaccatcgacctcgactactagagacgcacgcgcggata
ttagtgccggactaagcgccataatatgtttagcatgtcaacaggtgcgtgctgacgcct
gtgcctcattactgaggtaagcgggtgcttgatgtactactaattggtgtacaattgtgt
tttgtgacatgcttgtctcccgctccgatagttggaatgtggatcatgtggagctgtact
gacacggtacgatggctgtgtggtagtcccgggtcctgacacctaataactccagaaaca
gcgacagggggggtatgcaattacggaatcagcgagtagcaacataagcggaggacgtac
accgttagttgtcagttgtattggattgcagatgcaggaatcggtgcctagaaaagttat
ggatggcaagggttccgatccggtgcctacaaaattacacgtatcaatctcgtcctagtt
ggtaacatacacgacgcctagatcctgatacatgcggcaccatgtggcaccaggtggcaa
cataaggttctaccactagacacttaagcaagggaattaagccggtgttagcaactgcct
acccgcgaccttgaacggaccttcgaagaccttagaaaagtagctgtaggtgcaggccta
ccgtccagtacgaaaagtggtccatgcgctcgggctagttattgaaagttgactggtaca
cgctgcaagctacattatatgttgcgccgaagtacttggtacgggtgtgtctccttccgg
gtctatggtcacatcttcaccttactgcccctttacgcgagaatcatgtgtgacattttg
gacgccgaggactcgccagaaccttgcggagactggtcaacggcccgttatgtaggcagc
cgagttccgtttgatgatcgaacattgcatatattagtcctagtaatgcaatgatagcag
gccccgctcaagtccactagaaacgagcatcaccggctcagtcaatctttcagctaagga
gtccatgaatgtgggactccataaacttttgcgggccccaagttggcggctggctgagga
ttctgtcatagactgctccagcagcccgcacggtcgcgaagtgcgtggggtcccgtcggc
gccctgtacgggcagtgcaccatccgatgccccttaccgacgtgatagtccgtgatgctt
cacggcacatgtgagctaatgcgtgatagctttctggggctatgtttcagtggtccaatg
acatagcacgccactatccgagtgaatgggaaggctcgatatcgaagattcaaaatgcgg
gagtcttgggttggattctgcctgggggtcttaaagatcaagaacggcccaaagcacact
cgggcgggcccctagcagacgcgccttgtcctcagccgtttagtttaaaatgttttaagc
tgtcgggccagctatgaaagaactccggagttgtgatggacgctcatgcgtccggacggg
atcgtactgattggggtaggcccaaccgacactcttgcagacgccgcgtccacctgcagg
aacgcccccttttcgaatagtatgcctacccgtacatagggaacttgtccacaacgcgga
ggttgatctcgatgaagatagaggtttggcctgaccttaaagctggaggctctgaacagc
tgggtcatacagcaggttcacggcgccgggagctagctgaagagtaaggacgacgagaga
cataagcttcgccctttattaaaacacaatactcttttattggcacctaccgcaattacg
cttccttgttttcaccccgggcagtgtctttgatgggaccattttgtaaggggactgtca
ataaaccaacgcgtagcttccgtatcatctggtcgctatgcttgctacggctcgtacgct
tcgcaggtagagctcccggggggtccagaacgcgctagcaaattcaggactaatctgaac
tctgttttttgaggtacgcttgctccgatgcactctagcatcgtcactagattctcggca
gtgcgtggtgccagtgattggatctaggtgccggtcgagatcgcgctcaccgaaatgggt
ggcgacacccgatggcgggcagttgcgtctcattctagtacagtttcgaactgtgtcctt
ccggtcacaacgaatgattgtctgcgcggcctgggaaaccttaccgagttccccagatct
ctaatggttgagcttatcactgtcatagacgagcggggggccacaacctaggattattgc
ggaagcacatttgccggctaagggtcagaaataaaagagggcgtcccttagcgcctacgt
taccaaaccctgggctgttgatcaacgcttgggataacttaagacgaattcagcgtctgc
acgatacggacgcaactactcaacggtatagtaaaattagaagaccggtagcgttcagtg
gctggcaagataatccaccctcgagccgctaacttaacctagcgtcctcatcttctcctg
ctggtcacggagtgggttgttactacggacgctatctctagaacactattttaactcatt
cctggcgttcagcccttcgctaaagtaccagataagaggggccgcatatacatgaaagat
cgttgtcagccatgggtggactgtatattccatagatacactcgcaccgagatgaggcat
ttttcttttcaagatcgcacacctattgcggtgaaacggcgcatctgcgaacaatacgtc
tggggagtcagaaacgtcctgtggtgtgcatctcaagctggtggtgttcggtaggcggtc
ccgttctcacactaaacttcggtccgtcactataagcaccacataacctatcgttggcat
acgggacgacgctttcgggctggttttctccgttgagagcatgattgaagcttctgggca
tctgggcctctgttgcctgactctctaccatccgaaccttagggctcggtcgcgggtgcg
attctggactagtcagatgaaagacgcctagcgattggcctttgacccaaaagctgcatc
acctaggcgattggacttgacgattttgagtaccgactgctccctaatacggcgcaactc
tatgtgcgccccgcatgacacgagatcgtctaggaaaatagaagcagccgacagattgac
cgccttactccaattgataacagggaagcggcccagttcgtggttagagccttgtttaga
attacggcaccgccaagactgtggtggtgcgcgcgtgcttacaattgtccctatggaata
tgccgaagatttgcacctgccaggttaggactctcaaaaatgatagcgtaaacgtaggtg
aaccgcattctcgttaccatgaccaaacgtgcatacgccatgagaaattacttctatctc
aacaacaacgtacaatccggcacatacgttaggatggtaagctattctcgtctagtagca
gattacggcgagcctgggctacttcatctgtctagtagtcagaaggtattcctagattgt
gcggtagtacaccgtatcaagcgaaagtgatacttcgagtgagattagaaatgaagcgga
agcatgggataatctacccccccggtaggtctcggcctcctaccttaagacttgggccgt
aattgggaggagggtgtcgaaaaacggtaccgtatagaaataaacctaacccaaagattc
aattttctgatgaagcacaccaccgggagggcacttgataaaattttgtcatttccatcg
cctttaatgaagtcctgcataacctaatcactaggaacacacgaaaaacccgttgtatca
cggaggtagcgcgatccctctttcactctcttccatatgcgccccttggagggtagggga
tatgcttcaatcagactctgatggacatatgaacgatgtgggttagaagtgtggggcaca
ggcacgcatccgatttcagtgctcgaatccgaaactaatatttacccttccccgcacttc
aatgtagagacaggagaatgttaatctgactgagcagataaacaactcgtccatgccgat
agattacgcaatatcacgagcgttaccatttagtttggcgattaagatggcgcaccagat
ttatgcgcttcctcaagtctagatcggcctttgctttaaaacttaggaattgcgccgtga
gccagacagcggatttatgatcgcacgtcttttgggaggcgtgcgataaaattatagcat
gtgtgcccgaaatggtcgctgcacgtcaaatacctcgcgtacgaacgtgaacctgagttc
cggagagacccgcctactccactatggggaaagagatccgtataaagcgggaagcccttg
ggtattgagcggatttagacgatccgacgagtcgcccttacatcgtgctgacactgaagt
cttaccgtatttacgcgagctggctcggactttgccgcacagaggttgccatattttacg
aggatataacttttgatcagccgtcgattacatcgtcgagatcacgacactctatccgct
cactgcgtcagtctaactacgaaacacgaccccccaccaacgcgcggggtgtcgttccat
aataaacactcgcattttacaatgacgatatgatcatgtacaagaaagttgacgtgaaaa
atctagtgctccgtgtttcccagggcttatatcggctgacagtcacaactacgcgaattt
ttatactctcagtgttctcagcaaaatacgtctccgcaccgaaccccttcccattgaacc
aactggtgttagttagagttttataacccgtcgcgactgtgagctaatccgacgcaactt
ggaaagatcccctcgttggcagagcgccgacctacacacctgctagatcgccttgagcac
ctttttaacacctcagcgctgcgcgctgtataattcgatgagacctaaaatggaccctaa
cctcaggacttagcttccctaaagtaagcctatgcatatggaaaccgtcgttgaggctcg
cgactggtgtatccccggctggccataacgaaatcatggtgtcgggtcgcgaatagccgc
catcattgtcacaacctgcttttattattggcatagtgcaaccgactcttgagcaagctg
caatgaggcagtgcggaccggaggccaagagacaacaatcatgtcagaagatcaggcccg
tcaggcttgtgttctagggtatcagaccgggtggaatcttcccttgtgctgcgagggaac
aggtcgagaagaacccgtatcgacacgccgtgctcacgatctgttgccactggaccaaac
gcactagtttggtttcgcaggttgtaccggcccggggacttattaacgaactggcctcgt
ggatgccgtcgggtaagtagcaatatacgggacagctttatcgagcatcaaactagtcga
tccacggaacacactgccctccttaattttacgcaggagaagacttgcaaatctggcccg
ggtacttttgatgacgcgtcagctagtagcacgtgctagtagtattgctcgagagaactg
tgtcatactaaatagtgaaactttcgcgggaacgagacgtcttccgccgggctttgcact
tcgcgacgtagaacaggtaagttaaatgacaggtcctaccagtgtgttgacggaccccac
caggccacacggcccggagtgagtaacacctcaagctggaaccaagctcctggcctgacg
gccaccgatgggcaggccgagccaagaatactacatcctctacgagggtagtgcggcacc
agccaggccgccacttgagtcaggtttgatgaatggaaaatcaagtactcccctgcttgg
tagccatgccagcatcatgaaggcatccttaatagcacgagtatggaggtatccggtatg
acaaaaggcttctacttcagcttaccagcggacttcccgaagaccgagcacgttcgcgta
attagttcaaagcccctttcgacttttcatggtacactgactttcacccacaagtggctg
cctctgtttcatacccagggcagcaatctaagtggatactattgcaagccggtatatcat
ttactcgtaacggcgaggcggtgaaccagcacgatcttaccctcaaattgatagaaatgt
cggcaattgaatgaagtgaaagaggtttaaacgccctttcttattatgaaggaaatgttt
cacgagtggctccattcatcgcggctttcctgcgtcaagagtgtcccgtgcggagcgtag
tagaccccaagaccccaaagtcacccgttacacggctcggatgccctcgaaacagcgggt
tatacgtcaaactgtacaaggcttatgattagtaatttgcttcgagatatacagagttcg
gactcgccctcgcccctgcctaggcttagctcgcatatcgcggtgatgtaattatggcct
attggggggaacacaaaccacgccagaattgatggcccgacgtggggccctgacgtatgc
tactgtagcgatgttgagtgcacgggatcacgcttcacctgcgaacgtgcgaataagggt
ggccatactagccatgttgtctggcagtacccagatgatctccgttctaggcaaaccaca
aggggcaagcacctcgacacgaaggccaaagtcaggacctgaacgctgcgaggcacgaat
gagacaggaggcctgcgactgcaggtgcttactgtctaataaactgttgttactcacccc
cccaaaacttttcccattcatatgaattcgtaggttgaatatacctcagacatcccaaat
cccgaaccgcgccctgaccttgtgtggaatgactatctagaaacgaatcagtagaaactc
ttatgacggtatctaatcggtttgcacatgagctgaaggcttttaaggagattaaggccc
tagtttgaaggccgaccctgacgtagcgaggtactctgcaccaggccctaagcgaattat
tgaataactaggccgaatgaaatacttgtctagacactccgggcattggaagcttagggg
gtgttacctcgctctttgcggcttcggtctaaaggcttggacctcgtcatcctctattct
acgcgcccgacatcgctcgcatacgatcgtacatcttcttcggtagatcgcacagagaac
aggtggatttttagcagacctggctgaaggtactatcatgtcacatcgaccgcataatgg
agcccctggccgaaacccggagactaattgcgacaactagccgagcacatatatttctat
catggtactcaaatgccataagggattggagcgcgcgcaagcagtccaagcgcaaggctg
aggttctcttgacacattcggtatcgagcgagagctagcacagaacccacgcatggctta
aaaacaaggcggccgtagggcataaactaaccgacgcgaatagtacccgctttttgctac
cgccaatgggacccaccctgcgccgcaatacgtctgttgcatgcctgccccgctgtcacg
ccttcaacgatctgttccaccgcatccatggtctattactctttggccttactcgatcgg
gtgtgcataaaggaaacctcttctgtggtgaaaagggcgagacgcgcttttcgtagtgaa
gacttactccttatcaccaacgcccctggaggcatggtgattactgcgcgcttatccgta
tcacgccctgccaatcgtgcgttattcagcacgtccgttgactgtcatctgtgtgtggga
ggcccgaggacgaaaatgggaacaatcacgaggcatcgatctctgagctcacagcggctg
gtcccgtgcctataatttaaatcctgactcagagccgtgtggctcgcgacggttacataa
agagccaattctttgcctttcggttatcgaaatatctctggtgggaagctcatctcgtgg
aatctccgcgtaagtgcagtatcggtcgtatctcatattgtctagttgcctaggtggtcg
ttgactccttggacaagcactggtcctacaggtggtacgttggagcgaacggatgtgctg
aaatatagccaggtacgattgccctgccaggtgaacatgacgagttgaaatggattaggg
cgcgcatgagtggagatccgctccacagtagcgccacttatactttgctttataagggtc
agggtcctccacggctaatgtacactaacgaagccaaactaagggtctactcgacgaaat
agtgcatgatcgacgagttcaggtaagaaaggagtttttactggtaaagatgaatatatt
tcctactgaaagggataggcaggtggcaatttaatattcccttagacgactcttacgcgg
aggccgacgcttgagcagggcatcgcggtccttagtcgagtatgtcttcggaagaatcct
tcgaaagcaaaagccgcttaatttgtcgacccgtctaaattaatcatgtgcaagaaattc
ttccggttcaatccaagatattattcatcgtcgagaatcgacgaggctaccgaaagaggc
cctgttcatttatccgccaacacaccacgtaaattcgtatgcttagaaaggcgccgtgta
gcccctaccataagtgtcgctctgggcttactctaagtaggcttccctgttacgccgact
agcacccatctggatacgagtttcgtcgaacctttgattgtgaccgatccccccattaat
atcgttcgttgagacctgatattggtaatcaaggtagatgattaaccgcttttgagggaa
aataccgatagcaaggccaaggtctcacgtctccgcgaatcatacgaaattgcccatagt
aaacagcatcccagtccatcatgaatgtgtccgtcgtagcctcgggaaaaaatccaacga
ttacagtggaccgtacctgaagactgtcactgttcgttcaaagagcgcgcgtagttttac
cctggtcgaaaagtcaagtgtgagatcggtcatagtattcgatgccggcatagcgcgagt
acactcccaccttcattcgatctatcatgggcaagaccgtgttgccaagtgcccgttcag
gttgcgccgaaggtaaagtcgcgggtgagggtagaccagtatttagatctcaatggagtc
tgccagcatacggcaggccacgtaggtccttcgtgtaaacacagataccactaagcattc
ccagtgcacagggggcgaaaaggtcacgatatctgcggagttcatccgagtcaaggaggc
ggaaatgacccgcgcgagcaaggggccaggttaactaaacagcaaattctgtcgactgac
tcaaaggcagcgtacatgataagcacgttggtcctctgggctccctccccgttgtaggct
aacttgtgaacgcttacggacacttttctgctgggaacagcaagctacagcattacaaaa
actagactcatgccgggtaggcaacgcgtagcgacctgttataatgcggcgcaatctcga
tccacagtgtctagcgaacactacaaaataggcaaggctgagacatccctcatctggggc
tcgaagagaacataatgctttaattcgtgcacattgtcaaaccccagacgaacattaagc
ataatttccgcttggggtgatgtctacacctcgccaatccatcccgcagggtatctattt
gaagggaccctcgaacacctgctccctgtttcacacgcctagcatgatggcaagacgaac
atttcaatggccggcatgagaaggcaaaggattcgtacttttccgaggggggaaagggat
gagtctgagcgtcgcatggggttgccaatttattgggcgcccatggtatccccgtatcta
gggattgagttgatgccagcagtaaattactactaatttgatcagaacgtaataccggta
gccgactagcccgtcacgacgtcgtttatcaactatagacagctcacttgaggttaaaac
gaaggacaaaaggcctggcgttgtccgtgttttaagtctgagccgggttgtgggtgtgag
tcggcaaatatcttttaatagggtaaacaggccagatgccatgcagctattcggaatctg
aggacagggctgccgttgttgcgctggttttaagttcagtcattactgacgcgccaaaac
aagagtaacctaatggatctcgtaatctccgagacgatcagcgtgacagaaatgtctgct
gcggcacgtcttggcggagctaagcctaccatattttctatatccaatcgtattcatccc
aggcgaccccaacagaatcaactcggccttggaaaggaagtgacgaactcgatgggtcca
ctgtcacacggagtcaccagtcgtcctctgtgatttagagttctaatggagccggtcagc
cacgcagagccagaccaggactcccgacgcttggcaacgtagtccttcaggtacgggcga
catcggtttggtcgtatgcatgcagcacatacaagcgatcctcgtggaatcacaccggtc
tattcgctatctgtcttaacgcgcacggagcacgtcattccgaagataaagtggattcga
ctattgaagcatacaggatccttatgactggctgcggatggtctgggagttgatcgattt
tacaggaggacattacgggtggagggtccccataccgcttgactcaaaactgggtagggc
gcacctatatacgagccatacggttttcaatcaacatagcgttcaaccactccagcgcat
accacttcaagtactctgtaccaaagatcgcagtggacatccctcatactgtttatcacc
cttcgagcagagtcttatagttccttgggatttcgatttgcgaagttaatcgagcatgct
ttccttggatcccgtcgggagggcgtcgcgtgtataggcctcacaattttcccgtcgcca
tgtgacttggaacttatcagagaatctcgtttccctaggtgaacgtagctaggcaatcgt
cttgggtaagcctcgttggtaggtgacttttcaattgaatcgagctgctttgatagggct
tgcgccctcaaataacagacagcttctattgccgccaccggccctatgccagtttcaaag
cgaacggcatccagccagctgccccgtgatgtactaccctgcgtatcaagcgtatgcgtc
gcggccacttggaacacgtcgtcatctcaccgtatgtggcatatgccgccgaacgcgagt
cagacgcagcgtactacatcataaaggccagcggtgagcatgactttgaggcgtatcggc
actccgtcttaacttggtcgtggtaaagctcgccggtccaaggcactatacgtagcaatg
gaataatacggggagtttacgatggagcgccaaaattggtgttcgcccaccttcgtagag
gcagtgatatctctccctgtcctaacaggtaaaaacctaggtttgacgtgttcgcgatgt
gagtgcccgtgatttaagcaactcgagacactgcaaaccagcgacggtctcactattgac
tgtcgggtgctgtattagttatacataggtgagtcccaaaacctaaaagttaagaggtta
caagatttagggaggagatattccgctttccacctggtcgcgttggcgatccagtcttca
aggccggagaactcgacagtcagaaccccaagtggaccaaatatgacacgtagtggacag
tggggctcttcacagattactctctcagcaatccgcgcttgccagggagcagcgtcaatg
cataaaccggcgactaggcattgcgagattaggaggggaattaaggtactgcaagtgaag
actcgatgctttacgtgggccatccaagatgactcaacggtccccttcgtataaactcgc
gaattgcaaccaagacagtgtattctacgccgttgtgaatcccgcatcggttcgttgaga
ctgcttaattttccggaggagccaataccctcgccgttcagtacaagtcgtagatccgcg
tgtcgtgtcttgggcaccggaccggtattaacggaccgttgcagcgcaggtgaaacaccc
tttgtaggtgctcggggtgggggacgtacctatgatgggactactatccagggcagagac
gtttactacttaaggtcaagggtgttagggtgcgtatcgggtcacggttaaggcgacgta
ccaaccgagtccaacagtagtaaatgctcactgggagtagccatattcgaggctcgggtc
cggctggttattaccagctggtaaggccttttaatctatcacgcgcctaatagcttggag
cgatttgattccgtcacttatgccatcactagcaccgggtgcggaaccctcttcatggca
accgcaggtctcatttatggatgagtatttagttaactattaacatacttaacggggcct
accaaagtcggtgactaagggccccgggcacgtctcaccctgctgtacatactgccttac
tcatggtagttcgtcggactccactcgtcggggctgaacttctagaccgcgtgggagggc
gatatattaccgttcgcttcattcgatatcgcctaactaagggggggggatcccatggcc
ccgcaacacgcaaaaacttgaacagtgatcgggatttctaaccacatatccaacaagctg
gtactttccgaaataggatactgctcggttttcatcgggacataggatagagacggatac
agggactcaatatagtgaaaactccgccacgcctgcttacacgtcccaacgcgttacacc
ggaggcacgtggtctgtcttatacgactggggtaaccatggcaacaaaatagttcctctg
gctgggtcggactctggtgtttagggatgcgatataagcttttggaagccggacgcctaa
agcttgggtgagaacatgaggttacataccagggagaaatctgttcgtgcattggtttct
gcttcgtacagattcgcgtaatgggggctgattagcttctggcaagtaaggtatagaatc
aaccaccaaatgaatgtcttacgaaatggtgtgacggtcacccagaggaccgcgagcatt
tcaatcagaccgtgaatctagacattcttgaataacgagcactcaatgtagtttaggagc
ggatcttctccgcaaactgtgtaccaggacgacttcctgtggtggaaatcgctgtactag
gggtagaactctgggctggaattccagcgcggcgtgatagcactgtctacccttcacgtc
actggcagtcgttcgtgtcagttagcgctagaccttcgagctctagatatcataggccgc
tagttactgggatttatatgaccataagcatccattcgtgttacgacagattgcctctgg
caccctggcccaccgagacatgacagtcacaagcttgtatcccccatggtgtccgcagag
gtttggtatgttgtaatttactgagtttaagagatgcaatatatagattttagccgaaat
ctgtgaagatcactagtcaaggcgcgcccaattctataatctcacccaagtaaccccttc
agttcgccgactccgcccaacccctcttgccctgttctgtctgccttcgagagagaccca
gtttcaattcgagctgctacggataaaggattcgaggctccgccccgtgcatggcgtgaa
ctgtcagcgaaaaacgtcctgtggtaaccctgtcaagacaggcaagggtgttctttctat
gcatggtcctctacgtactttactcactaatgaactctgagctgctcagaaccatcacca
agaattacgcggtctagaccccgggcagggaacacgcatacatcatatacgctagggaac
tgacgaacagattacatgcctcctatgataccggaaggcgtgcttctacttttcccaaca
tgagatggatattgtcccagtatcccctcaaacgatcgggagagtcgagcaggtgtctca
agctaatttaacgtaatcggggctgctgcggtggtagcggtcgtgaaaacccggcggtct
cgaagtcggtagtaatagtagtgtcccgaagatggagatggacgttggcatgtgcgtttg
atactgctgttgcgcgcggcggaatgatcttttcgcgaccgccgagcacggtcgaaaagg
ccaggaggtggtcattgtagatgatatttcgatttacaaaatggtgttctggaggagctg
atttgtttgggtttatggacagatggggaggccgtacccccgaacgtgatagtatgatag
tggtggcgttcagttgactcagagatatcacctggccgacgagttgagtaaactaacctg
gcaacgtcgtaccgtatttcgttacattcgattggagaagagcaatttaaatattaaaaa
accacatgcggagtctaatcctatgaccccactatataggtaccgacagttacgtccaga
ttacagtttatccctcgggcagttcgcctgctgattctcaggcacaccagctccgctatt
actgggcatggctggacgagatctagcatcgactgagaacatggccgagcagagtccacc
accttcttctggaagcgctgaatgtgccactggtgttcctgctgggagtaaacaccgttg
ttgtcaagagtccgccgcttatcacctcaggggcgtgtgaactgaattagtcactattcg
ttacagcacccggtttacttaattgaatctatccaccggacggcaggtagtcaaccactg
ccatgctagctccgatcacccaaagacggtccaggatgcgtgcacgttcctatgattatg
cgcacacgatctcaatcctatcttaccagactgattatactatgcggtaggacgccatgt
ttcctgtcagttccttgactcagcatctcgactagtctgaaaattctaactctccacagc
ggctttcacgtgggattgtgagtatttcctgtcatcagatgtattcgagagaaatcgtgc
agtgacttcctatcaattttgttgcgatcagccgcttacgtggcaccaagtagcggtgac
acgaccgcgccccacattccgccacaacatggaccttcaatttaagctccacaccagcgg
ccgtatcatcgtcatgagcttccccctaccccacatccgaacacgttgctctacactggc
atggcgagcgtggcctgaggccaattcggatagtattccgtagagtcgtaagggaatcgt
ggtaaatagcgtgaggagcttgtcaccggctgcacgacgagtttgagactctagttccat
aaagcaggatcgctacatagtgagtaattatcagtcaaccacagcaagcaccccttactc
ataatgacggtacacaaggtgtaacattgtagaactcaaacaccaggtgtggaaccgacc
gacaaaaagcgagccctatttttcatacaaatcaccgaatcttagggccagcagtacatt
taaataaaatgacttccccacaggaatcgcgatcgcgtcatagcaccgaaaatgtgtggt
gtcgattagaccttactgcagtgagaacaatgtaggcagtgcgccccaacgcccgtgacg
gccgaaagaagccttggtccgccaacaagtactgtcgtccctgcatacgtatctctaccg
tattgctggttgcggactagaagtccgatcgcctagttttacaaacccgatgcattcacg
tctcaaacaacacaaagaatgttacactgactgggtattcaactcgcccatctagctact
catcttcggtcgagactaaaaggtgccccgcagtatgctgtgttatgggagttcatagtt
tagcaaatccgggattaagagggtcaagctgtaaccgtgcggtgtctgctgacagaataa
atcagaggactagcgaaaccgtagctataaaccgccccagaaattaatctgcgttggtac
tcagtgatgtttcgccatgccactaaccagcaagtgtcaaccgtgcggagttccaagaca
cggcaacaaaagcagctctacgcgggtttcaagaaataatctaaagctacaattcatgga
agtgagataccatggtgacccacaatcagacttaaccagtaccgcaaaagcttgctcgcg
ctgtcaaaagcctgttgtacacccaataatcttggtatatttaaaagttcactaaagggg
cccaagggagtcattaattgcggtgcgcgaatggtcacttcatccccttgcccctccgcc
cgtcgataacgcctgcttgacgtccggatccctgggcagtcggagttcgtctgagctggg
ggttacatttacttatatttcaacagaggggcaataaaacggagggaggcactaaaacac
actcatagcgactctattagttgtgcgatgtccgggcaggtactgtacaatcaacatcgt
cttacccgcccctcctcagaccaagagtgtctttgtttacgcacgaatggggaaaagacc
ttgtccgaagtgtatcagttggtacagtcctagtctttgatcggtcctatcaacaatcgc
acgttcatgctgcgtttgcacgatggtcccctctttgagtctcctcaaaggcgccaaggt
tcctaaacacatgactcgagtcatgggggaacgttagcagaacctaatgcacgggaggca
cggcagggcgttcctcaggcgattagctccctttcaagtaggggtgaagcacgcccagag
tctcgtgtgctccgtttgagcacgatgtggagagcgttacaacggtcccaataaacgcct
agccactcgttagccatctcctatcaggtatggcgttgaaaatatcccgcgacaacccat
cataagtggtattagatggcatttctaacaccattaatggttgaggactgttgtcccgtg
ggataatctgaaaatacattattgagtctaccaattattaagggaaaccgtccccgggga
agtcgacctgcctggtccgtataacgggtccactgtcccgcgtcttgattagagatcttg
agatatgcaggccatataatactcggaccacttagccgcctgcaatctttagtgcttcag
ccgcaggcaaataaaagataacttaggtacctaagctacccgtagcgcaaagcaggtata
tgtaccgtcattcgattgcccgtccgcaccgagagattacgacaggcaactgtcctgggt
gatcttaccgactcagcctagtcccgatcttcacttctttacgccctaattcctcgtggg
tgggcggcgcatgatttctgctcagtaaacacaaaggtgcttcaagcccctatcacgtta
ggttcgagtcaggttagttcggacagcacgccaatcctcttaatacaggcctgtacgaca
tgtttttggaagacccttctggtcgggatgtcgtaattgcaaggggcacctcaggggcag
cggggtaagagaaatacgccgtattgtagggcgtataggtttgcacgccctaatcgatac
ataatcctccaataacacgaagagtgtttgtcgagcaggcactgtcgatcggatagtggt
caagcaggttctttcgcacagcctactcaagaattggtggtacgctgttgtgtgacgtat
ccggggaatacaatcctgtatcatgatgacaaatcagatggggcgaataggtgattagca
aagctgtatgattcaacagtagtatgtaagtagaattagggcaccgaagtattgcgtcgt
tcattcagcccgtagcttaccgccatttatattgataggttaaagcacaagtgaagattt
aggctacagcgaagcggttccgctgaccgagtccgggtccatcccttcgcccatggtgag
aggcagtcaggcagtgcagcctcagaggatgtcttctagtgttgaaatttctgatcggtc
gagatatctccactactgcagcctgggggccattatcagtcgagtgaacttggctcacct
cagatcttaacatgaacaatgatcgtaaaaagttgattacgccgtaacctttcgcactta
accgttgggaattgcgcagagacatgagaattagtagtctgcgtaaaagagagtaccgca
agggcgagctatataattattcactcaaaaccagttcacacaaatagatgtcctcttgca
tttgcacatatcaaagatatttttacttaacctctaagcaatggacagtgccccgtctag
cgagttgaaaggcgccacgactacgcacgtatgatctatatgtgaacgcaagcacttact
acgccacaacagaactcaatgacggtgccgggtctacgcaaaccgcagggatagatccgg
acgaacgggaacagcataatgcaccgtcgcgcttctcatggctaggtacttgggcggacg
gttccccaccgccgtcatatcgtcaccagctagttgtggttagagcgattgtctctagcg
aatcgtcgcttctataatgcccctccgctctacccgctctgggatcgtcttttgtatttg
tatctcccggagggttgtgctgctatcgcccacgatcctggtcgtcaagtggttacagat
ggagtaatccttcaataacatcaggtacagcaacctctgctagggtgtaacacggggtgt
agctgactgccaggatcgctgcctccaaggtcagtgcgatcgcgagaaaggtaatctaac
tcggccgggaccactcagaatggaggaaaagcagggcgcttgcatacggcttagtaggaa
aattgtataactggcatgtttctgccccccggtttcacggacagttcgagagggcggagt
ttgcagatactgactgtcgtggagggcatgtatagctgcaaagtgtatcaacatcgcctt
cttttctctaagtgctctagattcaccgcttcttgccggcgagccgctttacttgcaatc
tgtcgtccgacatgactttcgcaactacaaagtagcgttcgtctattttgcccaccagca
attttgggtaccacattacggaaatctatattgccgtggagataatgaattagacagcac
tatacagctcaggtaaattgctgagtttgctggtctgctgagtgacaacggaacctgagt
tgcctcgccgcgtgaaacaggggagggagctgtaatattaaatctagtctcgggtatgtc
ggccgatagtgcttgtcggcgcagttatcgcgacaaagaaatccatattcggtgacctgc
gttctaagttatgtatcgtcagatcctacgaccgggaagaaaggtgcctctataccggta
tttattgctggagctgtcgaactacttaggactccgatgctagtgcaccggataaaaagc
ttaaaatcaaacatccggagacggacacgcgcatactctatgccccgagtttagttatct
aatggtcttggcgtgtgttagcccctacggaagcgcgccggtcttctcggtcttgggcag
ttgtgatcgggcgaactataaggaccttcccgtcctcccctcagggagctcgttagtggt
aggcaaccagcttcgaacggatggctgccatccggtaggggcgccgattggtaccagctc
tcttatatgactacaccggggtaatgacataggagctctgataagaacggccacctataa
ctcagacatagcgttagatgtccgcactggaactcaccgacatcgcgagggccgaaacag
cgaatgaattagcctccagtttttcagtagcagcccctatcctcgcctctcgctgcagac
gtttaaggggccgaccatataggaatgcgcctcctcgttgggcgttgattagccccgtga
ggtgacaagatctctccaagtgattagggcggtggtggctaaatatacatttacaatatg
tgtgcccctcagcctggagaactctgtctcctcattcgaggcgccctcacgccgtgggaa
ctcagctactctagtcgcagtggtcaggagtcctattaaactatgccggaagatactcag
agatcagtgctatagacgatccgtagccgtattgctgcgcattgccttcctgatgtagga
ccacatcgtcgtccagcacctgacgtcaagtcggtcaaaaatttaattttgacctaaccc
tgtatacccttcgagccggtaactcctccgtgatacggttggtctttcctgggtaaccga
agatttggccgaggatttgtgtcctccaccacatataaagctgtccaaaccgcctactcg
aatgatccagctcgggcttcgacctgttctaggaagtacacataataacctgagggggca
agtcttggacaacttatattcttcttctccgcgcgtggaaaatctacctattaattataa
atgaaccacgttattcacaactacttgcgggtttctccgcagctccacaggcgacttacg
ggacaacgagcaaagtgctgacagcgctcccatagctgtattgaatactacgattcgcac
cccttgtatcagtaataacctatgccgttccgagtatccctgacctaggatctattgtcc
tacctggagggcacatggccagaagaggatagataatacgcgcaatgcccgagcaatcgg
ggagaccgagtgtgtggaaccccaaatcagatctaaacgcgagcgcgagcgcacaatcgc
gaacgaaattaccaaacaatcattggcgaacaaacgtcaagggctcgcctgtcacagggt
atcaaatccggcgttaaccaataatgcatgagtttaagacagtcgaccccctatatgcca
ccatcgagaaacggcagttgatgaccaagtacgtaatggttcttggctatatgcgcgctg
agaaagaagactagcattagctgacggctattacggaatggtaagagctcattcgttctc
ctcttccgcggagagcaagtaagcatagtagtcgtgggtaattaccccctcgagtgaaga
ccgagaagaacgacgacacattgtttcatcctaaaagcagttagatagtgaataatcccc
gaggccaaacttgtgaaacaagaattgagggcacaacactctcactctgggagtgcgacg
tcaagtccttgacagctagttgtctgtgtagggggcagcgctatgagcctttccgattct
cgatctacgccaggcatgtcagacggcctatatttgtcgctgggggagagactactaagg
gaagctcactaggacgcttgactatcgtttttggtgagagaaccctaaatcggctgcctt
gatcttctcaatcattcctaacgtgtgtctcgccgtcgcagacgctcagcgatgagccat
cttacacccctattaactgtacttctggtgtacgcatcatcacaatctcgagatttcgga
cgttatgagggcagtactcccggacgccaaccgtgagtacgtccagtatacgggatctca
gattgccaaatcaacatcctagcgggaaggatgtgtcgtgcctccctgaaaccgggtgcg
gcgagcctgcgtcaaaacacggtcgcagtagctaagttcgtcaaataagcagtttggcat
cccctcccaatagggctgacctattgggtcctcgttttttgccctagagaaacgaggttg
ccaattcgtcacaggttggcgatgcaacccgacccttgttaatatattagttgcaccgta
gaggatttacagaaagctggcgcagcaggtaggataataccgagcatgggcaggtatggt
gggcgtataccaacccattatgcaagttgccgtatttagtaaactagcggtaatctaaag
aaacatcttacccaatttgaggtcgccgacttgattgtgggaggttaaggtatgatctgt
cattactattttggaaagaccctggcaagtgcaccgcgtggactggcaaaagtatcattg
ccccgacttagccagccgcgggtctaaacggaacagaaactttatcctggcccgacggga
cgtttcccttctggggttggatcacagcgctgcctgataggacggaggatcactcgctat
ggtccggacacacgcctcggtatgatacacgtagactagactgccgccccgggggcgagt
gagcggtccttcgatttgtgcgaggagggtgcgcaattgtttcctacctgctactaccac
gtaacgaagtggctcgttgagcttcggtatatcaccggcatggatgaatacggagcgtat
gagcgcgagttccatgactaaacagtgcgtcatcgatccaatgaccggatcccaaaatgt
ggcggaggagctaaaccgcatgctcactaatcgatttgggtatcgtcagctgcctccggg
ccagcccaggtaaagcgccgtaagacctcagcacagtgagggctgatggtatatcagcga
agttgagggttgggttccagtagcgaacgcatatcagtccttaaatggagcacatggggc
tatcgacagtccgttaaccgtgagagggaggagtttttacggtgcattgtggggacggcg
cgaacctaaggtaagagttatctgatcggtgcggtggtagacccatgaggctaatgaaag
tacacaactagattgctggaacccggcgagcgagctaggcatcattcttagcaaaggcgg
caacgccaactagcagcacataatccactcccaacctacaaaagtctgcctgttccgtgt
gatcggcgacgaggcgtcttaccgacttgcaaagtcgtttccgtgattgccgtcaattca
tcgagccttgtccactccttgtggcacggatcactgtcccccagctttatcactttcgat
tgacgtcaggtatgaacctaaagcaatggcgggggcaccaacacttactataacttaaaa
accaagaccttctctgcctaagcaagtaacctcgcacgaataaatcttagtcacacattg
tattatatgcttggtagcgcggcaccaaatatctacgacaaagtaactcatttgaaatta
gaagttcgcaaccagagtcgtaagtgcagttcgtgatggcgcgccgctccctacccataa
ttctcgatattctatgtcgtggcccatcctcaacaacgatcagtgccccgtcggcggtca
catacgccaacactgatgttactcgcaatccacgatggcgaggagccatgctcctcgtgc
gagtaaaaactgcccgtagcatgtgtcgagctgtgatgttgcacaagaaacgacttacat
aggcactaccactcccgcccgtcctataactacgaaaatacatctaggtcggcaatgggg
cgcttgcaggccgattctgccatcgtccaaacgcccacctagtacgacatgtggccgcga
gggggcatgacagctccgtcgcattctgaacatcctgtgatagcgacgctagcagtagag
cagtaatcaatggagtgatcgctctagtgcgattatgtcgggtttcaacgagtgcctcta
cctctattgtgaattggtccggactacacagacactgagtacaaccccgctggtccttgg
tacgctccaacgcaagtaaccgccacatgcatttttctgtgagcactagcagctcccttg
aagattacgctagctagtgctggggacatgtgatcctttatccctcctaattcacctcct
ggactttggaaactagtgtccccatcggcttggataaaagaaaatcgcgttgtcacgtgg
acgtgtaattgcgaactgtccctggacatctttccgtgtcctgcgctacgtcgcctcgtc
tgtagttataaccgcactccgggcacgagatgaacctgatcaaaagcctcggaacgtaat
ggaattacctgctctctctttaaccaagcctaatcaaacactcccactgtttaggcagat
agggacgcccactcctttctgattatactcaattccagtagataagttgcccggaaccgg
tatgcgtataacacccgggagttcattgtcgagcccgcctcatgcttagccgtgacactt
gatacgttatggcagcagcgacggatacttcgttccacccgggtaggtagcggttatcag
gaccgccgccttcccgtgtcaggttatcctggaacgcccgccgggaacaccggcaggtat
gatgtaggctataacatctggtaacaaccaagagtggtcgccgtaagtcggggggacaac
gtatataaattcgacaagtcgatgtcgcgacgccattctggtcacgatatacttcgataa
acgatctgtgttagatggtcacctggttgttatcctgtatctctccgccgcatgactcgc
gcctgatccttctgtggccaggggacgaatgtacgggttctaatactgtatccaacataa
ctgttggtttagtgctcttcgggtcctcgactattgtgcagaacatggacacacgctgcg
gaattaaatggaacagcatcaattgcctctctaggagctccgcttaaatcacgggattac
aatagcttgggtagtatgcacacgacgcactggattcgctatatgactatcagctgttac
ctgcacaggcttgtctcccgtgagcatgaaacttatgcccggccaaaacctcaactcaga
tgtgcaaagctggcgagtttcctcatgccccgctactccttgtatcgacggggttcactt
gtccggcctccctttcatatgttcgccacttagagcagggagaattgagcggacgattgt
tgtaacgggtgcttgcatctcatgcttttaggctctgtgggtaagaggaccgtacatggt
ttgtagttttcgctgtgaacaccgaggtaatctcgacggtacgctatcatgagtgtccac
gcgagaaggcccccaccggctcgttgtgccgtatttgcctctttctagcgaataacttaa
cccggacctagccatgtggtctagcggaaaaataattgtcctcttattacctaaattgct
tccaaggtttccgacggttgctgcaattgcgcatagaggttggtattagctatagcccca
cggttaaatgttttataaaggcgtacaacatgaacgcgcggagcgttaatgctgccacga
tgtgctaagaaccatagcacttcaagacgattactacaggcaaaaaacttatcagggcgc
ccgaggtccaggggacccgaatcagtatgtccatgatagcgctgacgttgccagctcgct
cgctcaaggtatcttcgggtaaggggtcccttctaaataggtcgtcaccatgcttaacca
tctgcctcgtagttatatactctcgtcatttccggacgggaaaaccaagatgcatcaaca
cgaacgctaacttaatcatatgtcatctgcttcagacagtctgccccgtaatcgtttagg
ttatgctattttcggtttgatacagtacgcattggattcttgtctgtaatcttgttaaat
ggaatatggggccacgtagggtccagaccgttgttggtggtactaaagcctgagtagagc
agaaatagcaccggctatgtcgaccaagcaagaacagtgcggacactccctccgtgtcaa
cacttgcgctacgttttatcgccgttgtgagcaaacctcagtttacaaaggcaattcccg
gttgtttacacggtcattcgctcggtattgcctttgttggatcctatatcggatccgacc
gttctctccatgatattcggtacgctccctcggttgtagactgcgaatgattggcaacgc
gtgatctgactactaggattaagaaccgcgtttagaagtctagggtggacaatagtttgt
gttcggaagtagatcccctatgtgatctgatcatagcatgaggcgcgttcatacactcat
actgttcgcctgctaatttcggacataagcataccgacgtccgacgtatggacagccatg
aaccgtttaggcctggtgagatttgcacaccagacgacccattacagtacaccagccgag
taagttaggtacgggtgctacgctcatacatcaccagccacgggggagcggtctgatatt
tgacgggaggtccgcgccttgtcttctttcgttaaatatgcaatatcgcttatagaccta
ttaaccgcgaccgactggtattattctccccgtataagcaattgaccgttgccgctctcc
cttgtgtctttgctgacttgatggcagcctgtggcatgttagtgacttacactactaggc
gatgtgggaacgcgcttttccttttttctaagtgttgtaagccacatcgccgtatattta
gatacttgcccgacagccaggcgtaggcttgcgcggccccacacctgaactgtctacaac
cagcgcccttagtcagtcagaagaacagtaacatatggcatttcacaaacactgagccag
ttgagacaaatccactgagtatgggagggtgatacatttatagtatggcatactcgacgg
ggtgatatgacatggtttcttgggttcgggtgttctcgttttgaacttggccccgcggcg
gcgttacttggggatctaccttataacgggccctcctgggcataaaggtacgacgtaacg
aagcaagcccactattcttttgaggggggtccatacttcttcaatttttagatcagagtg
ttcaggcacgccaccgttcagataagagccccataaaagactactaagattatgaccctt
aaaataaaaggattggagcgaagtcagcacactaaatcatcttctagctctgtacttcgg
ccgcgtgcttcgtgcgaattcaaaaaccgagtggggcgcgtcggcgcacttggctcggat
tagaatcttgtgagacatcttgtcacttagatcttggggcagagctctagcatgttcgat
caaaactcacgtagactcactaatataaaagtctcctcttctgtatcagtgatgtgagcc
aattggaagttcacgcgcgtctgctctacttcttcaatgagcacggtgacgcaaaacacc
ccggtaatatgtcgatcagagacactctccgtccttggtagtgctttacacttcaatccc
tgacacaataactcgctattatagcaaacgcaccggtacatccacatatatatgatacac
gctcgacggatggactacccgtagagccgatgtacgtgctaagacttcacatccaagaga
cgaccaaaattgtttcacatgagcactaaggtcactgataacggtatggcgaatattatt
ggaaatctgtgaagtgttgggtagtgggacttgagacctaatcttatatagccttccgac
cggataaattggaagtctggctcgtgatcggatatcgataggagacccagcacgccaccg
gacggcgcgtagaaccttgtggaagccacgttaccccagctcgacagcccacaggtcctc
tgagcaagagaccataggtaaacaccgacgtcaggaggagctgggtccatacctgaggtc
gcctactaacgccaacacgagggttgggaaaactaataggtgtacggtatagacaatccg
ctggcatttagagggcctggtatgagtgagggggcacctctgttctcaataactcgctca
agccgggatgtacgacgaccgtaaatggtgataccattgcaccacagcttgtcacaggca
cgtacgtagggtgtacgatcttgaattgatgcatcctccccttttctttcacgttagaga
aggtatcagctgaatgtccgggatggagccacggctacgctcgaactcagccagatccgt
aagtccgcatatccctgcaggtcttgggttcgtcctaatcatggataacgtgtagaaggc
actcctctgtggccggtagtcacgacccacgtacgcggtgttcaccgttcagccgtcatc
cctttgtgccgagttataattggcagtttcctgctgatcccggcgcggtcgagtcgcaac
ttcgaccatagggagtctcgttagctgaaccgccagcaaacctggcttaggaatgtccgc
cttctgcaacgctggttgacggcacagaggactgtaggcctattcctggccagacggatg
gtctgggctagtttacactgggacaagtaaggacaactacacagcgagcacctccactgg
taatgggcctagccactgtgccactcattcccgctcaagttggggggtgcggtgagggta
tggctatgggatatctgctttacctttgtgactcgctgtggatgtacgaggcgcgcagct
ctttctagtttccctgcgctgtacagcagtgactcagaaaccaggaacctccacaagatt
agagacgtacacgcgatgccacccgaactatctgttacttttgtcctcatcagccttacg
atgatcaggatggccacgaacttaagtagatcaagttcgtcagtgctgtccaggtggtcg
ttgcaaacgacgattagtcacggacaagtgccactcaataggcatcgttagattcaatcg
tacgttaccatcgcactgtttccggaggtgtgagctctcagcggttcagcatgacgtttt
cagacaccaggcccctacggatgagcgccgactgaccacccacgaggcgggctaggcatg
acttgatgggcttcgcattggcccacatgccaatctcttaactagtagcatctacgacca
ggcccatgggtcagtccctgactctgtgggcacctggcctcaatcaatgcgggccattga
ggggctcccctatcttctactttggtagagcatgtgcgaggatggggtccatgaagtcta
gcagtagtttataatagattatttaggccctgaccagtgtattgagacgcataatactgt
cccttcagggggcacgctcttactcgtctacaattctttatgatcatggacgtcagatgg
ttcttagataacctaattatatcttcccacggtcgtgaatgccagtgtcatccggtcatc
atgtatgcggcggagaaagcctttgctctcagaagcccgttcctaaaattcgaaccgtat
agtatactttactcgcttcgagggcggtttctcagttgagtcctctttagcgtgatcagg
tactgtaatagtggtctttaacgtagcacctcgaatctcgaagggtctgcgcttcagtcc
tttcggtcgcacagagcatctcacacttcgctcatggcctacgggaatgcgcccaagtga
ggtctgttgggtggccggataaggatatgcctatccttgatacccttgactatgcccagt
gtgcacggaaagcgcccggggaacgccgataatgcacaataggcgcaacaactatgggca
tactgccaatagctgaagcgtcatcatagatgatcagtgattgtttgctctgctcaggtt
ccatatgagctcacgcgggatctctcagacctattggcttggaataatggcgctacataa
aggatagctgacgtgcactccgagcgtgtcgaaggctgcaacttcaccgtggtaacgact
ccctcaacagtgcccaataagtgatccatttacgttctagtgctaagcaactcatggccc
tagtaagcagctagacacacagatcaggcaacttaaatggaacctacttcgtcactttca
tgggacacgaagctcaaggagcggtgaccagcaaacagccgcagcttcacaattgaattt
cgaccgaccggatagaggacaagcatactttgtcaacaactaatttgctcgcgaggaaca
ttgttggttacctaggcttaagtcgggatagacgttatcggctctaatcatctttccgac
aaatacttgacgtgtacacggattctgcatttagggatcactgtggtgtgctacaagtac
accgtctacgatggacccatagatgaccctcgaggcttctcactaagtacagctctcggg
ccggttgttttgccgggcggttacccttctctacgagctcgtccatgagtcttaggtcgt
gacaaattcggtctcattctagcagtacgaatcgacggtccgcgctaggcgaatctttta
gctatattcaaatactgggaaaagacaaacagcaagataagagcgttcaacggagccgaa
aaatgtacagagtgctacgaaccgaaagccacgagcgacttgactgtactatgggcgcaa
accgttgctctatacacggagtcatcttagtctagttaaatcttttcagggttagaattc
gacatggatcgactcattagggaaaactactctacacctctattttcttgtcccatccag
gtaaatgggcctcgcgtggtgtaggcggcgcattctcctagaggcgactggacggaaagt
agggggtctcgagtactggatttcgatgcctgttgaacgaggccatcaaagcgaagttgg
gggttgatgagatgcgcagccaatccggcgacaaccgtggtctcccatatcgtctacgac
gatggcattttccatcatgtagactgaaaataatgaagaaatccgtgacacagtggactc
agcgttaaagtcttttctcgcgtgctcggctatcccctttaccgtcccgggggccacccc
gggtacagtgctttacccggctcgcctcaacaaaacacacctccccataaatggtgagcg
gggacttagaagggcacgttagctacagaatgggtcaatacaatcgcctgcctatctcaa
tggtgctccccgagccgcatgctagagtgcgaagtcgactactagtagtacacacgtctc
cggttgaaagagctgggaggttgagtgcggtgtcgtagaagaggtagggccagcatgtgc
tactagtcaccctacaaagcaattcaaacaaacaactccgccacacccggtcacagagca
ttgttgtataccatgggtcatatcgctagcaacgatttaatcatccctaaccctacacta
ccatgacctagcgatgggttcccggacgaaacagattgacgaaacgtgtagcggactcgc
agtactctttctctggtctagaagcaggcgcggctgtagaattaatctgtcgttgattca
gctgataatggacctgttggcttcattacttcacgagccagtgacgctccagaaggcagc
atgttcgagaacctgccaccgtcatctaacccaaaggctggctgttaaatacatctttgc
ggcatcccaggacaaggtaatgaatgctcagcagtctctcacaacctccgcaccgacgcg
tttctatgcaagtactagtacctgaacgtatatgttcctaaaagcctcatcccgttggag
tctgtcagacgtgaactagttaagcgcaaatgtggacaccgtgagttgcctgactggtaa
agtagcagttaagaaaaacttaatgtatatcgtcccagactgaatgggtccacacttagg
tggcgtaccgtcttcgtgtttccacacgggacgctcgacactcaccaggaggagcggccg
gtagacagaggacggggtattgaacctgtacttgcattatagaaattagaatccggaata
ggcgcatgaagtctgccctctgtccgctcacgaagccccacgtcttacacgcatgtcgaa
tatgagtcagatgtaccagaggcctgttcccaccacagtaactggccatcagtctccagt
aggaggagcgagtgacagacgacgacaagaccggtttcctcccccttcctgtcccagccc
atagacctgaagggacacaagtcaccgttggcacaactagatatcactacatactatcgc
tccccacccccttcggaccacaacgagaaatggtcccccttctaagctactcctcgacgg
ccccacgggtcaccggccttttgaccagcttccacaggagcacgtagcagtatattctcg
tgtttaaaggtcgcggctgtggtggggctggttagtgcgtattgtcgatctacatcggga
cttagaataactctacctcaatcgatccggatgtcgcaagatatctcaccgtctcgtctt
cctttcgagggtgcatggcattggtaaccgctggtcttcagcacgtttgaaatttgtcga
gtgcctaagagatagtgctactgaccggcgtaatcacggtctacaaacgtagatattgac
catttcgtaggcgagtttgtgggctaactcccactcgcgttggtaatttggaggtcgccc
gcaagaacccgaaccagcgctggagcgtggctaacactcgtcgaggttttaggcattgct
cggtgtgtcccaaatttctattaccttatggcgcttctagggaggggaagtgctgcgagt
aactgctaacatgtcggcctgaatagccctgcaaccggtccctgtgcgttcgggtgtcac
atcgcccctaaatgaacttggaccgcctagtacaacacccggcgacaatacacgcatcat
cggaaacaactgtatagcttcatacagttcagacttagaacattaattcttcctcgagag
ggacccgtacgccctacctccgtcaagccccaagctgaaaggccacaataccgcgttcac
agtctcagggagggaaaatcacatcaagtatcgcgagtggtgttaagtttaccgtcaggg
tatactcctaactagacgtagctactcgactattgcacgcaccatgagacatgttagccg
cgtgtttgcaatagattccccattcagagtatgatgaggatagttcgtgcactccatttg
acctctacgcattgcaaccggtccacgtcattcgacggatgtccagataaggggtccaga
tgcgtacacgactgtgttctctctacgcagtgtccccgctgaagttagtagggcctccgg
acccacggatctactaccccgagtcgggctatcaagggaatgggacctagccggggcatg
tacggtaccgatagatctgtgtatgttcggcttttgaaagtaggaccttgcggggttaga
aggtagcgttatgggtccatgccgcgattcgctcgaaccagtaccagtgcttaattgtcc
gcgtcgcaggcgcacgtgcaggattaaacgtctcttacaactataactgacgcctacgga
tttgaagaccacaaccaaccgcgagaatgcctagtgttggcgaagacctatctccttgat
gcgcgcagtgcatcttctaaccgtggcaagatcatgaacctgtgagaactttcttttaga
tatcagacccccgtggcacccagaaactgccgctgttttgggcaagcgccgttgatacaa
tacaggtgcatggacattcatccggacgagtagttctttaggcgggcccaccctaccacc
gggcgcttacatccatccttcgctctcaatatcaattttatgtccagaggctccaaaatt
tgcaaggtgactaagactggtagatctattacttcaccgttggggggacgtcctccacac
caactaagtcattttgatatgaacattgaatcgatgctataaacggacatattagaaatt
ttcagaggttttacgtgagtactccaaaggctccacactgaaagttattgctcagcgaca
atgtctacgtcgacggactaaacgcagccgccttccataggacgattaccgaccgaacgt
agcgagtacgggtctaaccttcggtcttgcaatcaagtagacgtcgtttctaagagtttg
tagcagagaaacgactgagagtgtatacatattggcacatcctggagtaccaattcatgg
aagcggaacgtccgaccgtaccgtccacccggatgaagttcaccatactatcggcgggct
gtcccaccaaccctacgccttacgagaacgcacggcggtgtggacaccctctgattgtcc
tgtagccgagcctaggaccgtctcgtgttggacagatcgcattgtatgcaaactcgtgat
ccaatgaggtcccttggctatacagacaccgcgaggactctagggtcctggggttaaatg
attcgtcttttcacttagatcgtgggccctccgtgtttatgttgggccaggctactagta
tattcgatacatccgctggcctttgataacgtttgttaaatgttatctcggaggcttttt
ttgaatcatacagctatgtcagacgagagttcctcagtgtcacccttcgttatcaagaaa
tggtgaatttaatgttcgtagttttcagttattcagcagtctgtacccaaaacgtcaagt
tcgttatcttcagcacaaacgggtcgggccctgaaaaacaaatcacgaaactgctacact
ctttattttggcctagattattagctattgtttggcttttacttacggactcgtaggacg
atgtacgtgcacttggtgcacatcatccttaattgggccggacggttaatcttatcaact
ttgcgttcggctaaagattgcgacccttgtatctgttttgtgtcatctcgcttggtgcta
gggtgatgtctctactctggagtgtatacgacgcaagcccttgcaggctaactacggact
gctgcacactctaattcgaccgaactcgagtacgactgcgattataaatgcaacaagtcc
ggggaagcctccgacaccaagacgcgacgctcgcaccatctttcccgtcgctatcccagc
tcggtaagtctcgctcccgcccggcttaccaaaacaacacactcctcggcaatcgaatga
gcgtcttgtgccgataatactttccaaacccgagttttttcctaattgtttggggaacgc
cagtgaggtcagaacgcctacatcagaaggcggacgagagcctcacgattactcgacctg
cttttgtggcacattgagtgccccctggagtcagaacactccgtggctggtacaaaaatg
gtgttagttcttcgacaattagatcatatcaggcggttttagccactattaccgaccatc
cacgcacacctagcaactcaactttttatcacgctggcaagtaagtggaaggccctgctg
ccgttaaacggcaggctcatcgcggtatccacatcaattgcggtgaccggggtctcgctt
tagaaaagccgatatggtccaggacgtcgtggtgcgcaggaacccttagaatttagtatg
cggcgcgcgacgcgctgagagtcatcggcgccttagacggagttactccgcgaagcgctc
aaagcctaccaagttctatactggtaagggaggataaggccacgtttcaaatatatacgt
attgcattcgcgtatccatcccgagaaagaagtcgcggccgcaccgatggctgggcagct
atagggattcaggccaaacgattgcgggacgatcctaaattgttgcccctgttaagagtt
tcataaccattagattccagtctactacttctgaggacttctctgatcatattaatgttc
atgggacactgctttcaaccgtatcaatgtgcgaaacgtaccttatgatccctttcgctg
acacacacgatcctgtggttcagggtgaaaacactcaaatccaataacgcggggtaacag
gccggttctcaagttggagaagcatacagcgagtcccgtatagtccgagcagaggcttca
tcacgagtacaagcttttcttcagtgccgaaccataggaaggtctacataaaccggccgc
tctaatcttggcgccgcgagagcaaagagagggctcacccacatcaaattcgactgcggg
tcggcctccggtccccgtagtagagtacacgcgatacgtctttactctacctagaagact
tgtcttcaagcacaccagcttactccggatcagcgttacataaagcccataaattagcat
tgggcgagccgaccaggggtgaatattacacgaccggcgtcggtgcacgacccaggcatc
agtcatccttggaggtttcagccacgcgggtgtgcatgaggcacccgctgcagtcacctc
tgacggtctg
>CEESC13F
ttgcgttcggctaaagattgcgacccttgtatctgttttgtgtcatctcgcttggtgcta
gggtgatgtctctactctggagtgtatacgacgcaagcccttgcaggctaactacggact
gctgcacactctaattcgaccgaactcgagtacgactgcgattataaatgcaacaagtcc
ggggaagcctccgacaccaagacgcgacgctcgcaccatctttcccgtcgctatcccagc
tcggtaagtctcgctcccgcccggcttaccaaaacaacacactcctcggcaatcgaatga
gcgtcttgtgccgataatactttccaaacccgagttttttcctaattgtttggggaacgc
cagtgaggtcagaacgcctacatcagaaggcggacgagagcctcacgattactcgacctg
cttttgtggcacattgagtgccccctggagtcagaacactccgtggctggtacaaaaatg
gtgttagttcttcgacaattagatcatatcaggcggttttagccactattaccgaccatc
cacgcacacctagcaactcaactttttatcacgctggcaagtaagtggaaggccctgctg
ccgttaaacggcaggctcatcgcggtatccacatcaattgcggtgaccggggtctcgctt
tagaaaagccgatatggtccaggacgtcgtggtgcgcaggaacccttagaatttagtatg
cggcgcgcgacgcgctgagagtcatcggcgccttagacggagttactccgcgaagcgctc
BioPerl-1.007002/t/data/taxdump000755000766000024          013155576321 16215 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/taxdump/names.dmp000444000766000024      3555313155576321 20212 0ustar00cjfieldsstaff0000000000001760	|	Actinobacteria (class)	|		|	scientific name	|
1760	|	Actinobacteria Stackebrandt et al. 1997	|		|	synonym	|
1760	|	Actinomycetes	|		|	synonym	|
1760	|	Actinomycetes Krasil'nikov 1949	|		|	synonym	|
1760	|	High GC gram-positive bacteria	|		|	synonym	|
1760	|	high G+C Gram-positive bacteria	|		|	genbank common name	|
1760	|	high GC Gram+	|	high GC gram-positives	|	blast name	|
5533	|	Rhodotorula	|	Rhodotorula 	|	scientific name	|
9605	|	Homo	|		|	scientific name	|
9606	|	Homo sapiens	|		|	scientific name	|
9606	|	Homo sapiens Linnaeus, 1758	|		|	authority	|
9606	|	human	|		|	genbank common name	|
9606	|	man	|		|	common name	|
32061	|	"Chloroflexi" Castenholz 2001	|		|	synonym	|
32061	|	Chloroflecales	|		|	misnomer	|
32061	|	Chloroflexaceae/Deinococcaceae group	|		|	in-part	|
32061	|	Chloroflexi (class)	|		|	scientific name	|
32061	|	Chloroflexus/Deinococcaceae group	|		|	in-part	|
32061	|	Chloroflexus/Deinococcus group	|		|	in-part	|
32061	|	not "Chlorobacteria" Cavalier-Smith 1992	|		|	synonym	|
32061	|	not Chlorobacteria Cavalier-Smith 2002	|		|	synonym	|
89593	|	Craniata	|	Craniata 	|	scientific name	|
165724	|	Rhodotorula	|	Rhodotorula 	|	scientific name	|
165726	|	Rhodotorula	|	Rhodotorula 	|	scientific name	|
165791	|	Rhodotorula	|	Rhodotorula 	|	scientific name	|
192684	|	Rhodotorula	|	Rhodotorula 	|	scientific name	|
200204	|	Rhodotorula	|	Rhodotorula 	|	scientific name	|
200795	|	Chloroflexi	|	Chloroflexi 	|	scientific name	|
200795	|	Chloroflexi Garrity and Holt 2001 emend. Hugenholtz and Stackebrandt 2004	|		|	synonym	|
200795	|	GNS bacteria	|	GNS bacteria	|	blast name	|
200795	|	Thermomicrobia	|	Thermomicrobia 	|	includes	|
200795	|	Thermomicrobia Garrity and Holt 2002	|		|	includes	|
200795	|	green non-sulfur bacteria	|		|	common name	|
200795	|	green nonsulfur bacteria	|		|	common name	|
231509	|	Rhodotorula	|	Rhodotorula 	|	scientific name	|
266791	|	Rhodotorula	|	Rhodotorula 	|	scientific name	|
2759	|	Eucarya	|		|	synonym	|
2759	|	Eucaryotae	|		|	synonym	|
2759	|	Eukarya	|		|	synonym	|
2759	|	Eukaryota	|		|	scientific name	|
2759	|	Eukaryotae	|		|	synonym	|
2759	|	eucaryotes	|		|	genbank common name	|
2759	|	eukaryotes	|		|	common name	|
2759	|	eukaryotes	|	eukaryotes	|	blast name	|
6072	|	Eumetazoa	|		|	scientific name	|
7711	|	Chordata	|		|	scientific name	|
7711	|	chordates	|		|	genbank common name	|
7711	|	chordates	|	chordates	|	blast name	|
7742	|	Vertebrata	|		|	scientific name	|
7742	|	vertebrates	|		|	genbank common name	|
7742	|	vertebrates	|	vertebrates	|	blast name	|
7776	|	Gnathostomata	|	Gnathostomata 	|	scientific name	|
7776	|	jawed vertebrates	|		|	genbank common name	|
8287	|	Sarcopterygii	|		|	scientific name	|
9347	|	Eutheria	|		|	scientific name	|
9347	|	Placentalia	|		|	synonym	|
9347	|	eutherian mammals	|		|	common name	|
9347	|	placental mammals	|		|	common name	|
9347	|	placentals	|		|	genbank common name	|
9443	|	Primata	|		|	synonym	|
9443	|	Primates	|		|	scientific name	|
9443	|	primate	|		|	equivalent name	|
9526	|	Catarrhini	|		|	scientific name	|
9604	|	Hominidae	|		|	scientific name	|
9604	|	Pongidae	|		|	synonym	|
27591	|	Gazella granti	|		|	scientific name	|
27591	|	Grant's gazelle	|		|	genbank common name	|
27592	|	Bovinae	|		|	scientific name	|
27596	|	Anoa depressicornis	|		|	synonym	|
27596	|	Bubalis depressicornis	|		|	misspelling	|
27596	|	Bubalus depressicornis	|		|	scientific name	|
27596	|	anoa	|		|	common name	|
27596	|	lowland anoa	|		|	genbank common name	|
27598	|	Cervus sp.	|		|	scientific name	|
32523	|	Tetrapoda	|		|	scientific name	|
32523	|	tetrapods	|		|	genbank common name	|
32524	|	Amniota	|		|	scientific name	|
32524	|	amniotes	|		|	genbank common name	|
32525	|	Theria	|		|	scientific name	|
33154	|	Fungi/Metazoa group	|		|	scientific name	|
33208	|	Animalia	|		|	synonym	|
33208	|	Metazoa	|		|	scientific name	|
33208	|	animals	|		|	blast name	|
33208	|	metazoans	|		|	genbank common name	|
33208	|	multicellular animals	|		|	common name	|
33213	|	Bilateria	|		|	scientific name	|
33316	|	Coelomata	|		|	scientific name	|
33511	|	Deuterostomia	|		|	scientific name	|
40674	|	Mammalia	|		|	scientific name	|
40674	|	mammals	|		|	genbank common name	|
40674	|	mammals	|	mammals	|	blast name	|
60720	|	Nesticus archeri	|		|	scientific name	|
60721	|	Nesticus barri	|		|	scientific name	|
60722	|	Nesticus barrowsi	|		|	scientific name	|
60723	|	Nesticus bishopi	|		|	scientific name	|
60724	|	Nesticus brimleyi	|		|	scientific name	|
60725	|	Nesticus carteri	|		|	scientific name	|
60726	|	Nesticus cooperi	|		|	scientific name	|
60727	|	Nesticus crosbyi	|		|	scientific name	|
60728	|	Nesticus dellingeri	|		|	scientific name	|
60729	|	Nesticus furtivus	|		|	scientific name	|
77110	|	Nuphar advena (Aiton) W.T.Aiton subsp. ulvacea (G.S.Mill. et Standl.) Padgett	|		|	synonym	|
77110	|	Nuphar advena subsp. ulvacea	|		|	synonym	|
77110	|	Nuphar ulvacea	|		|	scientific name	|
77110	|	Nuphar ulvacea (G.S.Mill. et Standl.) Standl.	|		|	synonym	|
77111	|	Nuphar advena (Aiton) W.T. Aiton subsp. orbiculata (Small) Padgett	|		|	synonym	|
77111	|	Nuphar advena subsp. orbiculata	|		|	synonym	|
77111	|	Nuphar orbiculata	|		|	scientific name	|
77111	|	Nuphar orbiculata (Small) Standl.	|		|	synonym	|
77112	|	Nuphar sagittifolia	|		|	scientific name	|
77113	|	Nuphar lutea	|		|	scientific name	|
77113	|	Nuphar luteum	|		|	misspelling	|
77113	|	yellow water lily	|		|	common name	|
77114	|	Nuphar microphylla	|		|	scientific name	|
77115	|	Cyprinodon tularosa	|		|	scientific name	|
77116	|	uncultured Acinetobacter NB1	|		|	scientific name	|
77117	|	uncultured Acinetobacter NB2	|		|	scientific name	|
77118	|	environmental samples	|	environmental samples 	|	scientific name	|
77119	|	uncultured Burkholderia NB3	|		|	scientific name	|
77420	|	uncultured Treponema clone RFS34p	|		|	scientific name	|
77421	|	uncultured Treponema clone RFS35p	|		|	scientific name	|
77422	|	uncultured Treponema clone RFS37p	|		|	scientific name	|
77423	|	uncultured Treponema clone RFS39p	|		|	scientific name	|
77424	|	uncultured Treponema clone RFS41	|		|	scientific name	|
77425	|	uncultured Treponema clone RFS42p	|		|	scientific name	|
77426	|	uncultured Treponema clone RFS43p	|		|	scientific name	|
77427	|	uncultured Treponema clone RFS44p	|		|	scientific name	|
77428	|	uncultured Treponema clone RFS45p	|		|	scientific name	|
77429	|	uncultured Treponema clone RFS46p	|		|	scientific name	|
77760	|	Synechocystis PCC9413	|		|	equivalent name	|
77760	|	Synechocystis sp. BO 9201	|		|	synonym	|
77760	|	Synechocystis sp. BO9201	|		|	synonym	|
77760	|	Synechocystis sp. PCC 9413	|		|	scientific name	|
77763	|	Banna virus	|		|	scientific name	|
77763	|	Coltivirus BANNA	|		|	synonym	|
77763	|	Coltivirus JKT-6423	|		|	includes	|
77763	|	Coltivirus JKT-6969	|		|	includes	|
77763	|	Coltivirus JKT-7043	|		|	includes	|
77764	|	Clitoria falcata mosaic virus	|		|	scientific name	|
77764	|	Clitoria geminivirus	|		|	synonym	|
77765	|	Malva geminivirus	|		|	scientific name	|
77766	|	Sida geminivirus	|		|	scientific name	|
77767	|	Tobacco geminivirus	|		|	scientific name	|
77768	|	"Bacteroides (Prevotella) ruminicola subsp. ruminicola" biovar 7	|		|	synonym	|
77768	|	Bacteroides (Prevotella) ruminicola subsp. ruminicola biovar 7	|		|	synonym	|
77768	|	Prevotella albensis	|		|	scientific name	|
77768	|	Prevotella albensis Avgustin et al. 1997	|		|	synonym	|
77769	|	quadrivittata group	|		|	scientific name	|
82870	|	Plectanocotyle	|		|	scientific name	|
82871	|	Plectanocotyle gurnardi	|		|	scientific name	|
82872	|	Zeuxapta	|		|	scientific name	|
82873	|	Zeuxapta seriolae	|		|	scientific name	|
82874	|	Neomicrocotyle	|		|	scientific name	|
82875	|	Neomicrocotyle pacifica	|		|	scientific name	|
82876	|	Tachyporinae	|		|	scientific name	|
82877	|	Oxytelinae	|		|	scientific name	|
82878	|	Dasycerinae	|		|	scientific name	|
82879	|	Scaphidiinae	|		|	scientific name	|
89593	|	Craniata	|	Craniata 	|	scientific name	|
93472	|	Hormonema macrosporum	|		|	scientific name	|
93473	|	Phaeotheca fissurella	|		|	scientific name	|
93474	|	Trimmatostroma abietina	|		|	scientific name	|
93475	|	Trimmatostroma cordae	|		|	scientific name	|
93476	|	Trimmatostroma salicis	|		|	scientific name	|
93477	|	Sarcinomyces petricola	|		|	scientific name	|
93478	|	Kabatiella caulivora	|		|	scientific name	|
93479	|	Kabatiella lini	|		|	scientific name	|
94430	|	Voyriella	|		|	scientific name	|
94431	|	Voyriella parviflora	|		|	scientific name	|
94432	|	Human rotavirus MP409	|		|	scientific name	|
94433	|	Camberwell virus	|		|	scientific name	|
94434	|	Oryzorictes	|		|	scientific name	|
94435	|	Oryzorictes talpoides	|		|	scientific name	|
94435	|	mole tenrec	|		|	common name	|
94435	|	molelike rice tenrec	|		|	genbank common name	|
94436	|	Parascalops	|		|	scientific name	|
94437	|	Brewer's mole	|		|	common name	|
94437	|	Parascalops breweri	|		|	scientific name	|
94437	|	hairy-tailed mole	|		|	genbank common name	|
94438	|	Tenrec	|		|	scientific name	|
94439	|	Tenrec ecaudatus	|		|	scientific name	|
94439	|	tail-less tenrec	|		|	common name	|
94439	|	tailess tenrec	|		|	genbank common name	|
95260	|	Palthis angulalis	|		|	scientific name	|
95261	|	Papaipema	|		|	scientific name	|
95262	|	Papaipema sp.	|		|	scientific name	|
95263	|	Triocnemis	|		|	scientific name	|
95264	|	Triocnemis saporis	|		|	scientific name	|
95265	|	Polybia occidentalis nigratella	|		|	scientific name	|
95266	|	Ropalidia romandi cabeti	|		|	scientific name	|
95267	|	Epyrinae gen. sp. JC106	|		|	scientific name	|
95268	|	Ammonophila sp. JC134	|		|	misspelling	|
95268	|	Ammophila sp. JC134	|		|	scientific name	|
95269	|	Arge	|		|	scientific name	|
96040	|	Blastocrithidia triatoma	|		|	scientific name	|
96041	|	Leptomonas peterhoffi	|		|	scientific name	|
96043	|	environmental samples	|	environmental samples 	|	scientific name	|
96044	|	Bufo regularis gut clone FMA-1999	|		|	scientific name	|
96045	|	'Nocardia uniformis subsp. tsuyamanensis'	|		|	synonym	|
96045	|	Nocardia uniformis subsp. tsuyamanensis	|		|	scientific name	|
96045	|	Nocardia uniformis subsp. tsuyamanesis	|		|	misspelling	|
96046	|	Human rotavirus strain MP409	|		|	scientific name	|
96047	|	Ammophila arenaria	|		|	scientific name	|
96048	|	Elymus sp. Kellogg s.n.	|		|	scientific name	|
96049	|	Ehrharta erecta	|		|	scientific name	|
117570	|	Teleostomi	|		|	scientific name	|
117571	|	Euteleostomi	|		|	scientific name	|
117571	|	bony vertebrates	|		|	genbank common name	|
131567	|	biota	|		|	synonym	|
131567	|	cellular organisms	|		|	scientific name	|
207598	|	Homo/Pan/Gorilla group	|		|	scientific name	|
314146	|	Euarchontoglires	|		|	scientific name	|
314293	|	Anthropoidea	|		|	synonym	|
314293	|	Simiiformes	|		|	scientific name	|
314295	|	Hominoidea	|		|	scientific name	|
325230	|	Francisella sp. AF-01-23	|		|	scientific name	|
325231	|	Francisella sp. AF-01-27	|		|	scientific name	|
325232	|	Francisella sp. AF-01-28	|		|	scientific name	|
325233	|	Francisella sp. AF-03-27	|		|	scientific name	|
325234	|	Francisella sp. AF-03-28	|		|	scientific name	|
325235	|	Francisella sp. AF-04-15	|		|	scientific name	|
325236	|	Francisella sp. AF-04-405	|		|	scientific name	|
325237	|	Francisella sp. AF-01-22	|		|	scientific name	|
325240	|	Shewanella baltica OS155	|		|	scientific name	|
325240	|	Shewanella baltica str. OS155	|		|	equivalent name	|
325240	|	Shewanella baltica strain OS155	|		|	equivalent name	|
325241	|	Influenza A virus (A/chicken/Beijing/ZH/02(H9N2))	|		|	scientific name	|
325242	|	Influenza A virus (A/chicken/Hebei/11/02(H9N2))	|		|	scientific name	|
325243	|	Influenza A virus (A/chicken/Jiangsu/W1/00(H9N2))	|		|	scientific name	|
325244	|	Influenza A virus (A/chicken/Neimeng/ZH/02(H9N2))	|		|	scientific name	|
325245	|	Influenza A virus (A/chicken/Yunan/3/01(H9N2))	|		|	scientific name	|
325246	|	Influenza A virus (A/chicken/Beijing/8/99(H9N2))	|		|	scientific name	|
325247	|	Influenza A virus (A/chicken/Henan/1/01(H9N2))	|		|	scientific name	|
325248	|	Influenza A virus (A/chicken/Henan/1/98(H9N2))	|		|	scientific name	|
325249	|	Lactococcus bacteriophage Rc13	|		|	scientific name	|
325250	|	Lactococcus bacteriophage Rc14	|		|	scientific name	|
325251	|	Lactococcus bacteriophage Rc15	|		|	scientific name	|
325252	|	Lactococcus bacteriophage Rc16	|		|	scientific name	|
325253	|	Lactococcus bacteriophage Rc6	|		|	scientific name	|
325254	|	Stainforthia concava	|		|	synonym	|
325254	|	Virgulina concava	|		|	scientific name	|
325255	|	Stainforthia sp. isolate 2641	|		|	scientific name	|
325256	|	Bolivina sp. JPM99	|		|	scientific name	|
325257	|	Bolivina sp. isolate 170	|		|	scientific name	|
325258	|	Cassidulinoides	|		|	scientific name	|
325259	|	Cassidulinoides porrectus	|		|	scientific name	|
331540	|	Pomponema	|		|	scientific name	|
331541	|	Pomponema sp. 2P12K2	|		|	scientific name	|
331542	|	Linhomoeus	|		|	scientific name	|
331543	|	Linhomoeus sp. 7I12K2	|		|	scientific name	|
331544	|	Latronema	|		|	scientific name	|
331545	|	Latronema sp. 1P10K3	|		|	scientific name	|
331546	|	Phanodermatidae	|		|	scientific name	|
331547	|	Phanoderma	|		|	scientific name	|
331548	|	Phanoderma sp. 3I23B4	|		|	scientific name	|
331549	|	Latronema sp. 2P15K2	|		|	scientific name	|
332089	|	Geoemyda silvatica	|		|	scientific name	|
332089	|	Heosemys silvatica	|		|	synonym	|
332089	|	Vijayachelys silvatica	|		|	synonym	|
332130	|	Spirogyra sp. ARL 87 3	|		|	scientific name	|
332131	|	Spirogyra sp. CFD JH0058	|		|	scientific name	|
332132	|	Spirogyra sp. CFD JH0130	|		|	scientific name	|
332136	|	Arthroderma cookiellum	|		|	scientific name	|
332136	|	Arthroderma cookiellum (de Clercq) Weitzman et al.	|		|	synonym	|
332136	|	Nannizzia cookiella	|		|	synonym	|
332136	|	Nannizzia cookiella de Clercq	|		|	synonym	|
332137	|	Mitsuokella sp. TM-10	|		|	scientific name	|
332138	|	proteobacterium 4R11-401	|		|	scientific name	|
332139	|	proteobacterium 8R12-301	|		|	scientific name	|
333160	|	Influenza A virus (A/green-winged teal/TX/7/01(H8N4))	|		|	scientific name	|
333161	|	Influenza A virus (A/mallard/MD/F123/98(H6N8))	|		|	scientific name	|
333162	|	Influenza A virus (A/mallard/MN/107/98(H6N8))	|		|	scientific name	|
333163	|	Influenza A virus (A/mallard/MN/133/98(H5N2))	|		|	scientific name	|
333164	|	Influenza A virus (A/mallard/MN/145/99(H4N6))	|		|	scientific name	|
333165	|	Influenza A virus (A/mallard/MN/153/98(H9N2))	|		|	scientific name	|
333166	|	Influenza A virus (A/mallard/MN/17/99(H7N7))	|		|	scientific name	|
333167	|	Influenza A virus (A/mallard/MN/2/98(H4N6))	|		|	scientific name	|
333168	|	Influenza A virus (A/mallard/MN/220/98(H4N6))	|		|	scientific name	|
333169	|	Influenza A virus (A/mallard/MN/253/99(H6N5))	|		|	scientific name	|
335118	|	Machaerina	|		|	scientific name	|
335118	|	Machaerina Vahl	|		|	synonym	|
335119	|	Machaerina sp. Johns 9195	|		|	scientific name	|
376913	|	Haplorrhini	|		|	scientific name	|

BioPerl-1.007002/t/data/taxdump/nodes.dmp000444000766000024      3043713155576321 20213 0ustar00cjfieldsstaff0000000000001760	|	201174	|	class	|		|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
5533	|	89013	|	genus	|		|	4	|	1	|	1	|	1	|	4	|	1	|	0	|	0	|		|
9605	|	207598	|	genus	|		|	5	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
9606	|	9605	|	species	|	HS	|	5	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
32061	|	200795	|	class	|		|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
89593	|	7711	|	subphylum	|		|	10	|	0	|	1	|	1	|	2	|	0	|	0	|	0	|		|
165724	|	165723	|	genus	|		|	4	|	1	|	1	|	1	|	4	|	1	|	0	|	0	|		|
165726	|	165725	|	genus	|		|	4	|	1	|	1	|	1	|	4	|	1	|	0	|	0	|		|
165791	|	165790	|	genus	|		|	4	|	1	|	1	|	1	|	4	|	1	|	0	|	0	|		|
192684	|	200376	|	genus	|		|	4	|	1	|	1	|	1	|	4	|	1	|	0	|	0	|		|
200204	|	165794	|	genus	|		|	4	|	1	|	1	|	1	|	4	|	1	|	0	|	0	|		|
200795	|	2	|	phylum	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
231509	|	231508	|	genus	|		|	4	|	1	|	1	|	1	|	4	|	1	|	0	|	0	|		|
266791	|	266789	|	genus	|		|	4	|	1	|	1	|	1	|	4	|	1	|	0	|	0	|		|
2759	|	131567	|	superkingdom	|		|	1	|	0	|	1	|	0	|	1	|	0	|	0	|	0	|		|
6072	|	33208	|	no rank	|		|	1	|	1	|	1	|	1	|	5	|	0	|	1	|	0	|		|
7711	|	33511	|	phylum	|		|	1	|	1	|	1	|	1	|	5	|	1	|	0	|	0	|		|
7742	|	89593	|	no rank	|		|	10	|	0	|	1	|	1	|	2	|	1	|	0	|	0	|		|
7776	|	7742	|	superclass	|		|	10	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
8287	|	117571	|	no rank	|		|	10	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
9347	|	32525	|	no rank	|		|	2	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
9443	|	314146	|	order	|		|	5	|	0	|	1	|	1	|	2	|	1	|	0	|	0	|		|
9526	|	314293	|	parvorder	|		|	5	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
9604	|	314295	|	family	|		|	5	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
27591	|	9933	|	species	|	GG	|	2	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
27592	|	9895	|	subfamily	|		|	2	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
27596	|	9918	|	species	|	BD	|	2	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
27598	|	9859	|	species	|	CS	|	2	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
32523	|	8287	|	no rank	|		|	10	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
32524	|	32523	|	no rank	|		|	10	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
32525	|	40674	|	no rank	|		|	2	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
33154	|	2759	|	no rank	|		|	4	|	0	|	1	|	1	|	1	|	1	|	1	|	0	|		|
33208	|	33154	|	kingdom	|		|	1	|	0	|	1	|	1	|	1	|	1	|	0	|	0	|		|
33213	|	6072	|	no rank	|		|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
33316	|	33213	|	no rank	|		|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
33511	|	33316	|	no rank	|		|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
40674	|	32524	|	class	|		|	2	|	0	|	1	|	1	|	2	|	1	|	0	|	0	|		|
60720	|	44402	|	species	|	NA	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
60721	|	44402	|	species	|	NB	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
60722	|	44402	|	species	|	NB	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
60723	|	44402	|	species	|	NB	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
60724	|	44402	|	species	|	NB	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
60725	|	44402	|	species	|	NC	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
60726	|	44402	|	species	|	NC	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
60727	|	44402	|	species	|	NC	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
60728	|	44402	|	species	|	ND	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
60729	|	44402	|	species	|	NF	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
77110	|	4415	|	species	|	NU	|	4	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
77111	|	4415	|	species	|	NO	|	4	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
77112	|	4415	|	species	|	NS	|	4	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
77113	|	4415	|	species	|	NL	|	4	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
77114	|	4415	|	species	|	NM	|	4	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
77115	|	28741	|	species	|	CT	|	10	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
77116	|	75661	|	species	|	UA	|	11	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|	uncultured	|
77117	|	75661	|	species	|	UA	|	11	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|	uncultured	|
77118	|	32008	|	no rank	|		|	11	|	0	|	11	|	1	|	0	|	1	|	0	|	0	|	uncultured	|
77119	|	77118	|	species	|	UB	|	11	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|	uncultured	|
77420	|	77353	|	species	|	UT	|	11	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|	uncultured	|
77421	|	77353	|	species	|	UT	|	11	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|	uncultured	|
77422	|	77353	|	species	|	UT	|	11	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|	uncultured	|
77423	|	77353	|	species	|	UT	|	11	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|	uncultured	|
77424	|	77353	|	species	|	UT	|	11	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|	uncultured	|
77425	|	77353	|	species	|	UT	|	11	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|	uncultured	|
77426	|	77353	|	species	|	UT	|	11	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|	uncultured	|
77427	|	77353	|	species	|	UT	|	11	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|	uncultured	|
77428	|	77353	|	species	|	UT	|	11	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|	uncultured	|
77429	|	77353	|	species	|	UT	|	11	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|	uncultured	|
77760	|	1142	|	species	|	SS	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
77763	|	208294	|	species	|	BV	|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
77764	|	291027	|	species	|	CF	|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
77765	|	291027	|	species	|	MG	|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
77766	|	291027	|	species	|	SG	|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
77767	|	291027	|	species	|	TG	|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
77768	|	838	|	species	|	PA	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
77769	|	7324	|	species group	|		|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
82870	|	116927	|	genus	|		|	1	|	1	|	1	|	1	|	9	|	1	|	0	|	0	|		|
82871	|	82870	|	species	|	PG	|	1	|	1	|	1	|	1	|	9	|	1	|	1	|	0	|		|
82872	|	66915	|	genus	|		|	1	|	1	|	1	|	1	|	9	|	1	|	0	|	0	|		|
82873	|	82872	|	species	|	ZS	|	1	|	1	|	1	|	1	|	9	|	1	|	1	|	0	|		|
82874	|	54584	|	genus	|		|	1	|	1	|	1	|	1	|	9	|	1	|	0	|	0	|		|
82875	|	82874	|	species	|	NP	|	1	|	1	|	1	|	1	|	9	|	1	|	1	|	0	|		|
82876	|	351509	|	subfamily	|		|	1	|	1	|	1	|	1	|	5	|	1	|	0	|	0	|		|
82877	|	351512	|	subfamily	|		|	1	|	1	|	1	|	1	|	5	|	1	|	0	|	0	|		|
82878	|	144867	|	subfamily	|		|	1	|	1	|	1	|	1	|	5	|	1	|	0	|	0	|		|
82879	|	351512	|	subfamily	|		|	1	|	1	|	1	|	1	|	5	|	1	|	0	|	0	|		|
89593	|	7711	|	subphylum	|		|	10	|	0	|	1	|	1	|	2	|	0	|	0	|	0	|		|
93472	|	46635	|	species	|	HM	|	4	|	1	|	1	|	1	|	4	|	1	|	1	|	0	|		|
93473	|	92987	|	species	|	PF	|	4	|	1	|	1	|	1	|	4	|	1	|	1	|	0	|		|
93474	|	92989	|	species	|	TA	|	4	|	1	|	1	|	1	|	4	|	1	|	1	|	0	|		|
93475	|	92989	|	species	|	TC	|	4	|	1	|	1	|	1	|	4	|	1	|	1	|	0	|		|
93476	|	92989	|	species	|	TS	|	4	|	1	|	1	|	1	|	4	|	1	|	1	|	0	|		|
93477	|	62074	|	species	|	SP	|	4	|	1	|	1	|	1	|	4	|	1	|	1	|	0	|		|
93478	|	5422	|	species	|	KC	|	4	|	1	|	1	|	1	|	4	|	1	|	1	|	0	|		|
93479	|	5422	|	species	|	KL	|	4	|	1	|	1	|	1	|	4	|	1	|	1	|	0	|		|
94430	|	303180	|	genus	|		|	4	|	1	|	1	|	1	|	1	|	1	|	0	|	0	|		|
94431	|	94430	|	species	|	VP	|	4	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
94432	|	36428	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
94433	|	11983	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
94434	|	176110	|	genus	|		|	2	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
94435	|	94434	|	species	|	OT	|	2	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
94436	|	9373	|	genus	|		|	2	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
94437	|	94436	|	species	|	PB	|	2	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
94438	|	176113	|	genus	|		|	2	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
94439	|	94438	|	species	|	TE	|	2	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
95260	|	56403	|	species	|	PA	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
95261	|	95182	|	genus	|		|	1	|	1	|	1	|	1	|	5	|	1	|	0	|	0	|		|
95262	|	95261	|	species	|	PS	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
95263	|	319997	|	genus	|		|	1	|	1	|	1	|	1	|	5	|	1	|	0	|	0	|		|
95264	|	95263	|	species	|	TS	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
95265	|	91432	|	subspecies	|	PO	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
95266	|	91443	|	subspecies	|	RR	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
95267	|	69814	|	species	|	EG	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
95268	|	95167	|	species	|	AS	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
95269	|	85773	|	genus	|		|	1	|	1	|	1	|	1	|	5	|	1	|	0	|	0	|		|
96040	|	28004	|	species	|	BT	|	1	|	1	|	1	|	1	|	4	|	1	|	1	|	0	|		|
96041	|	5683	|	species	|	LP	|	1	|	1	|	1	|	1	|	4	|	1	|	1	|	0	|		|
96043	|	128925	|	no rank	|		|	11	|	0	|	1	|	1	|	1	|	1	|	0	|	0	|	uncultured	|
96044	|	96043	|	species	|	BR	|	11	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|	uncultured	|
96045	|	53432	|	subspecies	|	NU	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
96046	|	161240	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
96047	|	95188	|	species	|	AA	|	4	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
96048	|	15492	|	species	|	ES	|	4	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
96049	|	15488	|	species	|	EE	|	4	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
117570	|	7776	|	no rank	|		|	10	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
117571	|	117570	|	no rank	|		|	10	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
131567	|	1	|	no rank	|		|	8	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
207598	|	9604	|	no rank	|		|	5	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
314146	|	9347	|	superorder	|		|	2	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
314293	|	376913	|	infraorder	|		|	5	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
314295	|	9526	|	superfamily	|		|	5	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
325230	|	262	|	species	|	FS	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
325231	|	262	|	species	|	FS	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
325232	|	262	|	species	|	FS	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
325233	|	262	|	species	|	FS	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
325234	|	262	|	species	|	FS	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
325235	|	262	|	species	|	FS	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
325236	|	262	|	species	|	FS	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
325237	|	262	|	species	|	FS	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
325240	|	62322	|	no rank	|		|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
325241	|	102796	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
325242	|	102796	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
325243	|	102796	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
325244	|	102796	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
325245	|	102796	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
325246	|	102796	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
325247	|	102796	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
325248	|	102796	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
325249	|	374900	|	no rank	|		|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
325250	|	374900	|	no rank	|		|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
325251	|	374900	|	no rank	|		|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
325252	|	374900	|	no rank	|		|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
325253	|	374900	|	no rank	|		|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
325254	|	349982	|	species	|	VC	|	1	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
325255	|	313617	|	species	|	SS	|	1	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
325256	|	46083	|	species	|	BS	|	1	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
325257	|	46083	|	species	|	BS	|	1	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
325258	|	203408	|	genus	|		|	1	|	1	|	1	|	1	|	1	|	1	|	0	|	0	|		|
325259	|	325258	|	species	|	CP	|	1	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
331540	|	73920	|	genus	|		|	1	|	1	|	1	|	1	|	5	|	1	|	0	|	0	|		|
331541	|	331540	|	species	|	PS	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
331542	|	319958	|	genus	|		|	1	|	1	|	1	|	1	|	5	|	1	|	0	|	0	|		|
331543	|	331542	|	species	|	LS	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
331544	|	331538	|	genus	|		|	1	|	1	|	1	|	1	|	5	|	1	|	0	|	0	|		|
331545	|	331544	|	species	|	LS	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
331546	|	319996	|	family	|		|	1	|	1	|	1	|	1	|	5	|	1	|	0	|	0	|		|
331547	|	331546	|	genus	|		|	1	|	1	|	1	|	1	|	5	|	1	|	0	|	0	|		|
331548	|	331547	|	species	|	PS	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
331549	|	331544	|	species	|	LS	|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
332089	|	204959	|	species	|	GS	|	10	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
332130	|	3179	|	species	|	SS	|	4	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
332131	|	3179	|	species	|	SS	|	4	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
332132	|	3179	|	species	|	SS	|	4	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
332136	|	63399	|	species	|	AC	|	4	|	1	|	1	|	1	|	4	|	1	|	1	|	0	|		|
332137	|	52225	|	species	|	MS	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
332138	|	81684	|	species	|	PR	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
332139	|	81684	|	species	|	PR	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
333160	|	142943	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
333161	|	184009	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
333162	|	184009	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
333163	|	119220	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
333164	|	102800	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
333165	|	102796	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
333166	|	119218	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
333167	|	102800	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
333168	|	102800	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
333169	|	184006	|	no rank	|		|	9	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
335118	|	4609	|	genus	|		|	4	|	1	|	1	|	1	|	1	|	1	|	0	|	0	|		|
335119	|	335118	|	species	|	MS	|	4	|	1	|	1	|	1	|	1	|	1	|	1	|	0	|		|
376913	|	9443	|	suborder	|		|	5	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|

BioPerl-1.007002/t/data/taxonomy000755000766000024          013155576321 16411 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/taxonomy/greengenes_taxonomy_16S_candiv_gg_2011_1.txt000444000766000024      1305013155576321 26723 0ustar00cjfieldsstaff000000000000prokMSA_id	taxonomy
348902	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__Bacteroides plebeius
158756	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__Bacteroides uniformis
176924	k__Bacteria; p__Bacteroidetes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Blautia; s__
260616	k__Bacteria; p__Bacteroidetes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
134931	k__Bacteria; p__Bacteroidetes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
118592	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__
265852	k__Bacteria; p__Tenericutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__Allobaculum; s__Allobaculum sp ID4
367033	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Faecalibacterium; s__
593586	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__
323732	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__
385895	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiales Family XI. Incertae Sedis; g__Anaerococcus; s__
208108	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiaceae; g__Clostridium; s__
487110	k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__Staphylococcus epidermidis
423765	k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__Staphylococcus epidermidis
423219	k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__Staphylococcus epidermidis
490642	k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__
157391	k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Planococcaceae; g__; s__
336677	k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Paenibacillaceae; g__Paenibacillus; s__Paenibacillus illinoisensis
113119	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Peptococcaceae; g__Dehalobacter; s__
385950	k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Corynebacteriaceae; g__Corynebacterium; s__Corynebacterium pseudogenitalium
423250	k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Corynebacteriaceae; g__Corynebacterium; s__Corynebacterium aurimucosum
381933	k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Propionibacteriaceae; g__Propionibacterium; s__Propionibacterium acnes
447766	k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Propionibacteriaceae; g__Propionibacterium; s__Propionibacterium acnes
541414	k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Streptosporangiaceae; g__; s__
380376	k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Micrococcaceae; g__Micrococcus; s__Micrococcus luteus
151255	k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Micrococcaceae; g__Arthrobacter; s__
82704	k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Microbacteriaceae; g__Cryocola; s__
98697	k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Acidimicrobiales; f__C111; g__; s__
588305	k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Stramenopiles; f__; g__; s__
199329	k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Stramenopiles; f__; g__; s__
46263	k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas; s__
570796	k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Oceanospirillales; f__Alcanivoracaceae; g__Alcanivorax; s__Alcanivorax venustensis
141716	k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__; s__
223741	k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__; s__
273568	k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Photorhabdus; s__
160775	k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Morganella; s__Morganella morganii
438771	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae; g__Aquabacterium; s__
352658	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Ralstonia; s__
152646	k__Bacteria; p__Proteobacteria; c__Epsilonproteobacteria; o__Campylobacterales; f__Campylobacteraceae; g__Campylobacter; s__Campylobacter hominis
409810	k__Bacteria; p__Bacteroidetes; c__Flavobacteria; o__Flavobacteriales; f__Flavobacteriaceae; g__; s__
327726	k__Bacteria; p__Gemmatimonadetes; c__Gemmatimonadetes; o__Gemmatimonadales; f__Gemmatimonadaceae; g__Gemmatimonas; s__
260216	k__Bacteria; p__Verrucomicrobia; c__Verrucomicrobiae; o__Verrucomicrobiales; f__Verrucomicrobiaceae; g__Akkermansia; s__Akkermansia muciniphila
557792	k__Bacteria; p__Synergistetes; c__Synergistia; o__Synergistales; f__TTA_B6; g__E6; s__
557487	k__Archaea; p__Euryarchaeota; c__Methanomicrobia; o__Methanosarcinales; f__Methanosaetaceae; g__Methanosaeta; s__
772	k__Archaea; p__Crenarchaeota; c__; o__; f__; g__; s__
316268	k__Archaea; p__pMC2A384; c__; o__; f__; g__; s__
346282	k__Archaea; p__pMC2A384; c__; o__; f__; g__; s__
200845	k__Archaea; p__pMC2A384; c__; o__; f__; g__; s__
202477	k__; p__; c__; o__; f__; g__; s__
574071	k__; p__; c__; o__; f__; g__; s__
BioPerl-1.007002/t/data/taxonomy/silva_SSURef_108_tax_silva_trunc.fasta000444000766000024      3570713155576321 26004 0ustar00cjfieldsstaff000000000000>A61579.1.1437 Bacteria;Thermotogae;Thermotogae;Thermotogales;Thermotogaceae;Fervidobacterium;Thermopallium natronophilum
CUGNCGGCGU GCCUAACACA UNCAAGUCGA GCGGUGCUAC GGAGGUCUUC GGACUGAAGU AGCAUAGCGG CGGACGGGUG
AGU
>AAAA02014925.13286.14671 Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;mitochondria;Oryza sativa Indica Group
UCUGAGUUUG AUCCUGGCUC AGAAGGAACG CUAGCUAUAU GCUU
>AAAA02020714.1.1212 Bacteria;Proteobacteria;Alphaproteobacteria;Sphingomonadales;Sphingomonadaceae;Sphingomonas;Oryza sativa Indica Group
GAUGAUCAGC ACACGGGACU GAGACACGGC CAGACUCCUA CGGGAGGCAG CAGUGGGGAA UAUGGACAAU GGGCGAAAGC
CUGAUCCAGC AAUGCCGCGU GAGUGAUGAA GGCCUUAGGG UUGUAAAGCU CUUUUACCCG GGAUGAU
>AAAA02038172.160.1957 Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Liliopsida;Poales;Poaceae;BEP clade;Ehrhartoideae;Oryzeae;Oryza;;Oryza sativa Indica Group
ACCUGGUUGA UUCUGCCAGU AGUCAUAU
>AAAA02044470.2.1736 Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Liliopsida;Poales;Poaceae;BEP clade;Ehrhartoideae;Oryzeae;Oryza;;Oryza sativa Indica Group
ACCUGGUUGA UCCUGCC
>AAAA02046624.126.1937 Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Liliopsida;Poales;Poaceae;BEP clade;Ehrhartoideae;Oryzeae;Oryza;;Oryza sativa Indica Group
ACCUGGUUGA UCCUGCCAGU AGUCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUGCA AGUAUGAACU AAUUCGAACU
GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUAGUUUGU UGGAUGGUAC GUGCUACUCG GAUAACCGUA GUAAUUCUAG
AGCUAAUACG UGCAACAAAC CCCGACUUCC GGGAGGGGCG CAUUUAUUAG AUAAAAGGCU GACGCGGGCU CCGCCCGCU
>AAAA02049656.51.1599 Bacteria;Firmicutes;Bacilli;Bacillales;Paenibacillaceae;Paenibacillus;Oryza sativa Indica Group
GGAGAGUUUG AUCCUGGCUC AGGACGAACG CUGGCGGCAU GCCUAAUACA UGCAAGUCGA GCGGAGUUGA CGGAAAGCUU
GCUUUCCUGA UACUUAGCGG CGGACGGGUG AGUAACACGU AGGC
>AAAB01003942.1.1342 Eukaryota;Metazoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Diptera;Nematocera;Culicoidea;Culicidae;Anophelinae;Anopheles;;Anopheles gambiae str. PEST
UCAAAUGUCU GCCCUAUCAA CUAUUGAUGG UAG
>AAAK03000115.725.2258 Bacteria;Firmicutes;Bacilli;Lactobacillales;Enterococcaceae;Enterococcus;Enterococcus faecium DO
UGGCUCAGGA CGAACGCUGG CGGCGUGCCU AAUACAUGCA AGUCGAACGC UUCUUUUUCC ACCGGAGCUU GCUCCACCGG
AAAAAGAGGA GUGGCGAACG GGUGAGUAAC ACGUGG
>AABR05044379.4632.6502 Eukaryota;Metazoa;Chordata;Craniata;Vertebrata;Euteleostomi;Mammalia;Eutheria;Euarchontoglires;Glires;Rodentia;Sciurognathi;Muroidea;Muridae;Murinae;Rattus;;Rattus norvegicus (Norway rat)
ACCUGGUUGA UCCUGCCAGU AGCAUAUGCU UGUCUCA
>AABX02000116.495.2289 Eukaryota;Fungi;Dikarya;Ascomycota;Pezizomycotina;Sordariomycetes;Sordariomycetidae;Sordariales;Sordariaceae;Neurospora;;Neurospora crassa OR74A
AUUUAAUUAA UUUUAUUAAU AAU
>AABX02000201.5088.6882 Eukaryota;Fungi;Dikarya;Ascomycota;Pezizomycotina;Sordariomycetes;Sordariomycetidae;Sordariales;Sordariaceae;Neurospora;;Neurospora crassa OR74A
AUUUAAUUAA UU
>AABX02000236.1792.3586 Eukaryota;Fungi;Dikarya;Ascomycota;Pezizomycotina;Sordariomycetes;Sordariomycetidae;Sordariales;Sordariaceae;Neurospora;;Neurospora crassa OR74A
AUUUAGUUAA UUCUAUUAGU AAUUAUAUAU UUAUUUUAAA GAUUAAAUUA UAUAUAUUUA AAUUUAAGUA AUUAAAUUAC
GAAAUUGCGA AUAGUUUAUU AAAUUAAUUA UAGUUUAUUU AAUAGUACUU UACUAUAUAG AUAACUAUAG UAAUUCUAGA
GUUAAUAUAU AUUAAAAACC CCGACUUCGG AAGGGGUAUA UUUAUUAAAU UAAAAAUUAA UACCCUUCGG GGCUAAUUAG
UAAUUUAUAA UAAUUUUUUA AAUUGUAUAG CUUUGCGUUG GUAAUGGUUU AUUUAAAUUU CUGCCCUAUU AAUUUU
>AACH01000259.1360.3162 Eukaryota;Fungi;Dikarya;Ascomycota;Saccharomycotina;Saccharomycetes;Saccharomycetales;Saccharomycetaceae;Saccharomyces;;Saccharomyces mikatae IFO 1815
UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA
GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUUC CUUUACUACA UGGUAUA
>AACM02000313.16511.18305 Eukaryota;Fungi;Dikarya;Ascomycota;Pezizomycotina;Sordariomycetes;Hypocreomycetidae;Hypocreales;Nectriaceae;Gibberella;;Gibberella zeae PH-1
ACCUGGUUGA UUCUGCCAGU AGUCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUAUAAGCA AUUAUACAGC
GAAACUGCGA AUGGCUCAUU AUAUAAGUUA UCGUUUAUUU GAUAGUACCU UACUACUUGG AUAACCGUGG UAAUUCUAGA
GCUAAUACAU GCUAAAAAUC CCGACUUCGG AAGGGAUGUA UU
>AACM02000427.1.1662 Eukaryota;Fungi;Dikarya;Ascomycota;Pezizomycotina;Sordariomycetes;Hypocreomycetidae;Hypocreales;Nectriaceae;Gibberella;;Gibberella zeae PH-1
UACCUGGUUG AUUCUGCCAG UAGUCAUA
>AACT01042559.80.1335 Eukaryota;Metazoa;Chordata;Tunicata;Ascidiacea;Enterogona;Phlebobranchia;Cionidae;Ciona;;Ciona savignyi
CGUGCAUUUA UCAGACCAAA AACCGGCCGC GUCUU
>AACT01045610.1.1202 Eukaryota;Metazoa;Chordata;Tunicata;Ascidiacea;Enterogona;Phlebobranchia;Cionidae;Ciona;;Ciona savignyi
UGCAAGUCUA AGUACGAGCU CUCGUACAGU GAAACUGCGA AUGGCUCAUU AAAUCAGUUA UGGUUCAUUU GAUCGUACAG
UUUACUUGGA UAACUGUGGU AA
>AACT01045928.1.1216 Eukaryota;Metazoa;Chordata;Tunicata;Ascidiacea;Enterogona;Phlebobranchia;Cionidae;Ciona;;Ciona savignyi
GCCAUGCAAG UCUAAGUACU AGCUCUCGUA CAGUGAAACU GCGAAUGGCU CAUUAAAUCA GUUAUGGUUC AUUUGAUCGU
AC
>AACV01002172.186.1668 Bacteria;Cyanobacteria;Chloroplast;Oryza sativa Japonica Group
GGAGAGUUCG AUCCUGGCUC AGGAUGAACG CUGGCGGCAU GCUUAACACA UGCAAGUCGA ACGGGAAGUG GUGUUUCCAG
UGGCGAACGG GUGAGUAACG CGUAAGAACC U
>AACV01029078.1.1500 Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Liliopsida;Poales;Poaceae;BEP clade;Ehrhartoideae;Oryzeae;Oryza;;Oryza sativa Japonica Group
CCCUAUCAAC UUUCGAUGGU AGGAUAGGGG CUACCAUGGU GGUGACGGGU GACGGAGAAU UAGGGUUCGA UUCCGGAGAG
GGAGCCUGAG AAACGGCUAC CACAAUCCAA 
>AACV01032541.12.1684 Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Liliopsida;Poales;Poaceae;BEP clade;Ehrhartoideae;Oryzeae;Oryza;;Oryza sativa Japonica Group
ACUCGGAUAA CCGUAGUAAU UCUAGAGCUA UAGUGCAACA AACCCCGACU UCCGGGAGGG GCGCAUUUAU UAGAUAAAAG
GCUGACGCGG GCUCCGCCCG CUGAUCCGAU GAUUCAUGAU AACUCGACGG AUCGCACGGC CCUCGUGCCG GCGACGCAUC
AUUCAAAUUU CUGCCCUAUC AACUUUCGAU GGUAGGAUAG GGGCCUAC
>AACV01034311.49.1859 Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Liliopsida;Poales;Poaceae;BEP clade;Ehrhartoideae;Oryzeae;Oryza;;Oryza sativa Japonica Group
ACCUGGUUGA UCCUGCCAGU AGUCAUAUGC UUGUCUCAAA GAUUAAGCCC AUGCAUGUGC AAGUAUGAAC UAA
>AACW02000151.263262.264792 Eukaryota;Fungi;Fungi incertae sedis;Basal fungal lineages;Mucoromycotina;Mucorales;Mucoraceae;Rhizopus;;Rhizopus oryzae RA 99-880
ACUCGAUUUU CUGCCCUAUC AUGGUUGAGA UUGUAAGAUA GAGGCUUACA AUGCCUACAA CGGGUAACGG GGAAUUAGGG
UUCGAUUCCG GAGAGGGAGC CUGAGAAACG GCUACCACAU CCAAGGAAGG CAGCAGGCGC GCAAAUUACC CAAUCCCGAC
ACGGGGAGGU AGUGACAAUA CAUAACAAUG CAGGGCCUUU AAGGUCUUGC AAUUGGAAUG AGUACAAUUU
>AACY020014137.1.1251 Bacteria;Bacteroidetes;Flavobacteria;Flavobacteriales;Cryomorphaceae;Owenweeksia;marine metagenome
CCAAGGCAAC GAUGUCUAGG GGUUCUGAGA GGAUGAUCCC CCACACUGGU ACUGAGACAC GGACCAGACU CCUACGGGAG
GCAGCAGUGA GGAAUAUUGC GCAAUGGAGG AAACUCUGAC GCAGCCA
>AACY020043159.616.2094 Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;SAR116 clade;marine metagenome
UAAGAGUUUG AUCCUGGCUC AGAAUGAACG CUGGCGGCAU GCCUAACACA UGCAAGUCGA ACGAGAUCUU CGGAUCUAGU
GGCGCACGGG UGAGUAACGC GUGGGAACCU ACCUUUUAGU ACGGGACAAC GUUUGGAAAC GAACGCUAAU ACCGUAUACG
CCCUCCGGGG GAAAGGUCAG CCGCUAAA
>AACY020065672.84.1600 Bacteria;Bacteroidetes;Flavobacteria;Flavobacteriales;Flavobacteriaceae;Formosa;marine metagenome
GAAGAGUUUG AUCCUGGCUC AGGAUGAACG CUA
>AACY020119224.690.2165 Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;SAR116 clade;marine metagenome
UAAGAGUUUG AUCCUGGCUC AGAAUGAACG CUGGCGGCAU GCUUAACACA UGCAAGUCGA ACGCUAUUUA UAGAGUGGCG
CACGGGUGAG UAACGCGUGG GAAACUGCCC UUCUGUGUGG GAUAACGUUU GGAA
>AACY020181515.463.1969 Bacteria;Actinobacteria;Actinobacteria;Frankiales;Sporichthyaceae;hgcI clade;marine metagenome
GGAGAGUUUG AUCCUGGCUC AGGACGAACG CUGGCGGCGU GCUUAACACA UGCAAGUCGA ACGAUGAAGU UC

>AACY020521239.1.1483 Archaea;Euryarchaeota;Halobacteria;Halobacteriales;Deep Sea Hydrothermal Vent Gp 6(DHVEG-6);marine metagenome
AUUCCCGUUG AUCCUGCGGG AGAUUGCUGC UAUAGGAGUU CGACUAAGCC AUGCAAGUCA GAGGGUCUCU UCGGAGGCAC
AGGCUGAAUG CUCAGUAACA CGUCAAUAAU CUGCCCUUAG GUUCGGGAUA ACUUCGGGAA ACUGAAGCUA AAACCGGAUA
GGUAAGAAAU ACUGGAAUGU UUUUUUACUC AAAAGCAAUG CCUAAGGAUG AGUUGGCG
>AACY020539760.2042.3289 Bacteria;Planctomycetes;Planctomycetacia;Planctomycetales;Planctomycetaceae;uncultured;marine metagenome
GAGAGCAUGA CCCGCGUCAU UGGGACUGAG ACACUGCCCA GACACCUACG GGUGGCUGCA GUCGAGAAUC UUCGGCAAUG
GGCGAAAGCC UGACCGAGCG ACGCCGCGUG CGGGAUGAAG GCCCUCGGGU UGUAAACCGC UGUCGUUGGG GAGGAAAUGC
ACGGGGGUUA UCCCCCAUGC UUGACCUAUC CAAGGAGGAA GUACGGGCUA AGUUCGUGCC AGCAGCCGCG GUAAGACGAA
CCGUACGAAC GUUAUUCGGA AUUACUGGGC UUAAAGGGU
>AACY020545456.432.1985 Bacteria;Deferribacteres;Deferribacteres;Deferribacterales;SAR406 clade(Marine group A);marine metagenome
GGAGAGUUUG AUCCUGGCUC AGGACGAACG CUGGCGGCGU GCUUUAUACA UGCAAGUCAA GGAGAACCUA UUCUUCGGAA
UAGUAGUAAA CUGGCGAACG GGUGAGUAAC ACGUAGG
>AACY020551516.3474.4955 Bacteria;Proteobacteria;Alphaproteobacteria;SAR11 clade;Surface 4;marine metagenome
UGAGAGUUUG AUCAUGGCUC AGAAUGAACG CUGGCGGCAC GCUUA
>AACY020556376.975.2497 Bacteria;Bacteroidetes;Flavobacteria;Flavobacteriales;Flavobacteriaceae;NS5 marine group;marine metagenome
GAAGAGUUUG AUCCUGGCUC AGGAUGAACG CUAGCGGCAG GCUUAACACA UGCAAGUCGA GGGGUAACAG GGAUUGCUUG
CAAUCCGCUG ACGACCGGCG AACGGGUGCG UAACGCGUAU GCAACCUACC UUUUACUGGG GGAUAGUCAA GAGAAAUUUU
GAAUAAUACC CCAUACGAUC UGAUUCACUC CUGUGAAACA GAAGAA
>AACY020559644.9731.11175 Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;marine metagenome
UGAGAGUUUG AUCCUGGCUC AGAACGAACG CUGGCGGCAG GCCUAAC
>Z97592.1.1879 Eukaryota;Metazoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Orthopteroidea;Dictyoptera;Blattaria;Blaberidae;Oxyhaloinae;Gromphadorhina;;Gromphadorhina portentosa (giant Madagascar hissing cockroach)
UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU CAGUGCAAGC CACACUA
>Z97590.1.1866 Eukaryota;Metazoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Orthopteroidea;Orthoptera;Caelifera;Acridomorpha;Pamphagoidea;Pamphagidae;Akicerinae;Batrachotetrix;;Batrachotetrix sp.
UAGUCAUAUG CUUGUCUCAA AGAUUA
>Z97593.1.1844 Eukaryota;Metazoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Embioptera;Oligotomidae;Oligotoma;;Oligotoma nigra
UAGUCAUAUG CUUGUCCCAA AGAUUAAGCC AUGCAUGUCU AAGUACACGC CACAUUAAGG UGAAACCGCG AAUGGCUCAU
UAAAUCAGUU AUGGUUCCUU GGAUCGUACC CACACUUACG UGGAUAA
>Z97595.1.1900 Eukaryota;Metazoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Plecoptera;Nemouroidea;Nemouridae;Nemourinae;Nemoura;;Nemoura meieri
UAGUGAUAUG CUUGUCCCAA AGAUUAAGCC AUGCAAGUCU AAG
>Z97594.1.1873 Eukaryota;Metazoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Orthopteroidea;Dermaptera;Forficulina;Forficuloidea;Forficulidae;Forficula;;Forficula auricularia (European earwig)
UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU CAGUGCAAGC CACACUAAGG UGAAACCGCA AAUGGCUCAU
UAAAUCAGUU AUGAUUUAUU AGAUCAUACA UUAUAUUACU UGGAUAACUG UGG
>Z97631.1.1877 Eukaryota;Metazoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Orthopteroidea;Orthoptera;Caelifera;Tetrigoidea;Batrachideidae;;Batrachideidae gen. sp.
UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU CAGUGCAAGC CACAUUAAGG UGAAACCGCG AAUGGCUCAU
UAAAUCAGUU AUGGUUCCUU AGAUCGUACC CACGUUACUU GGAUAACUGU GGUAAUUCUA GAGCUAAUAC AUGCAAACAG
AGUCCCGACC AGGGAUGGAA GGGAUGCUUU UAUUAGAUCA AAACCAAU
>Z98587.1.1442 Bacteria;Spirochaetes;Spirochaetes;Spirochaetales;Leptospiraceae;Leptospira;Leptospira biflexa
UUGCUAACAU GCAAGUCAAA CGGGUAGCAA UACCAGUGGC GAACGGGUGA GUAAUACAUG GAUAACCUAC CUAGAAGUUG
GGGAUAACAC AGAGAAAUUU GUGCUAAUAC CGAAUGUGAC GGUUCCUGGU AGCAGGGAUU GGUUAAAGCA GCAAUGCGCU
UUUAGAUGGG UCCAUGGCUG AUUAGCUAGU UGGUGGGGUA AAGGCCU
>Z98591.1.1413 Bacteria;Spirochaetes;Spirochaetes;Spirochaetales;Leptospiraceae;Leptospira;Leptospira biflexa
UAUCAUGAGU ACGGUAGCAU ACAGUGGCGA CGGGUGAGUA AUACAUGGAU AACCUACCUA GAGUUGGGGA UAACACAGAG
AAAUUGUGCU AAUACCGAAU GUGACGGUUC CUGGUAGospiraceae;Leptospira;Leptospira biflexa
UAUCUUAACA UGCAAGUCAA ACGGGUAGCA AUACCAGUGG CGAACGGGUG AGUAAUACAU GGAUAAC
>Z98589.1.1466 Bacteria;Spirochaetes;Spirochaetes;Spirochaetales;Leptospiraceae;Leptospira;Leptospira biflexa
UAUAUGCUCA GACUAACCUG CGGCGCGUCU UAAACAUACA AGUCCCAACG GGUAACAAUA CCAGUGGCGG UCGGGUGAGU
AAUACAUGGA UAACCUACCU AGAAGUUGGG GAUAACACAG AGAAAUUGUG CUAAUACCGA AUGUGACGGU UCCUGGUAGC
AGGGAUUGGU UAAAGCAGCA AUGCGCUUUU AGAUGGGUCC AUGGCUGAUU AGCUAGUUGG UGGG
>Z98590.1.1433 Bacteria;Spirochaetes;Spirochaetes;Spirochaetales;Leptospiraceae;Leptospira;Leptospira biflexa
UCAUUCAAAC GGGUAGCAAU ACCAGUGGCG AACGGGUGAG UAAUACAUGG AUAACCUACC UAGAAGUUGG GGAUAACACA
GAGAAAUUUG UGCUAAUACC GAAUGUGACG GUUCCUGGUA GCAG
>Z98592.1.1394 Bacteria;Spirochaetes;Spirochaetes;Spirochaetales;Leptospiraceae;Leptospira;Leptospira biflexa
UAUCAUCCAC GUCACUCGGG UAGCACUACC AGUGGCGAAC GGGUGAGUAA UACAUGGAUA ACCUACCUAG AAGUUGGGGA
UAACACAGAG AAAUUUGUGC UAAUACCGAA UGUGACGGUU CCUGGUAGCA GGGAUUGGUU AAAGC
>Z98593.1.1427 Bacteria;Spirochaetes;Spirochaetes;Spirochaetales;Leptospiraceae;Leptospira;Leptospira biflexa
UAUCAUGCAA GUCACACGGG UAGCAAUACC AGUGGCGAAC GGGUGAGUAA UACAUGGAUA ACCUACCUAG GAAGUUGGGG
AUAACACAGA GAAAUUUGUG CUAAUACCGA AUGUGACGGU UCCUGGUAGC AGGGAUUGGU UAAAGCAGCA AUGCGCUUUU
AGAUGGGUCC AUGGCUGAUU AGCU
>Z99949.1.1760 Eukaryota;Metazoa;Platyhelminthes;Turbellaria;Seriata;Tricladida;Paludicola;Planariidae;Polycelis;;Polycelis tenuis
AGUCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACAAAGA CUCGUACUCU UAAA
>Z99948.1.1759 Eukaryota;Metazoa;Platyhelminthes;Turbellaria;Seriata;Tricladida;Paludicola;Planariidae;Phagocata;;Phagocata sibirica
UAGUCAUAUG CUUAUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAC
>Z99951.1.1760 Eukaryota;Metazoa;Platyhelminthes;Turbellaria;Seriata;Tricladida;Paludicola;Dugesiidae;Romankenkius;;Romankenkius libidinosus
UAGUCAUAUG CUUAUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUACAGAG AUUUAUAUUC UAAAAC
>Z99945.1.1766 Eukaryota;Metazoa;Platyhelminthes;Turbellaria;Seriata;Tricladida;Terricola;Geoplanidae;Arthurdendyus;;Arthurdendyus triangulatus
UAGUCAUAUG CUUAUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUACACAG ACUCGUACUC UAAAACCGCG GAUGGCUCAU
UAUAACAGCU AUGAUUUGAG AGACGUAAU
>Z99950.1.1755 Eukaryota;Metazoa;Platyhelminthes;Turbellaria;Seriata;Tricladida;Maricola;Procerodoidea;Procerodidae;Procerodes;;Procerodes littoralis
UAGUCAUAUG CUUAUCUCGA AGAUUAAGCC AUGCAUGCUU AAGUACCAGU UCUUGAA
>Z99947.1.1764 Eukaryota;Metazoa;Platyhelminthes;Turbellaria;Seriata;Tricladida;Maricola;Bdellouroidea;Bdellouridae;Bdelloura;;Bdelloura candida
AGUCAUAUGC UUAUCUCCAA GAUUAAGCCA UGCAUGCCUA AGUUCAAACU CUUGAAAG
>Z99946.1.1790 Eukaryota;Metazoa;Platyhelminthes;Turbellaria;Seriata;Tricladida;Paludicola;Dendrocoelidae;Baikalobia;;Baikalobia guttata
AGUCAUAUGC UUAUGUCAAA GAUUAAGCCA UGCAUGUCUA AGUACAAAGU CUCGUACACU GAAAC
>Z99997.1.1408 Bacteria;Proteobacteria;Alphaproteobacteria;SAR11 clade;LD12 freshwater group;uncultured freshwater bacterium LD12
AACGUACGCU GGCGGCACGC CUAACACAUG CAAGUCGAAC GCAGUAGCAA UACUGAGUGG CAG
>Z99998.1.1454 Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Burkholderiaceae;Polynucleobacter;uncultured freshwater bacterium LD17
AUUGAACGCU GGCGGCAUGC CUU
>Z99999.1.1464 Bacteria;Proteobacteria;Betaproteobacteria;Methylophilales;Methylophilaceae;LD28 freshwater group;uncultured freshwater bacterium LD28
AUUGAACGCU GGCGGAAUGC UUUACACAUG CAAG
BioPerl-1.007002/t/data/transfac_pro000755000766000024          013155576322 17215 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/data/transfac_pro/factor.dat000444000766000024      3001213155576322 21336 0ustar00cjfieldsstaff000000000000VV  TRANSFAC FACTOR TABLE, Release 11.1 - licensed - 2007-03-31, (C) Biobase GmbH
XX
//
AC  T00001
XX
ID  T00001
XX
DT  e)ce.; r1916d69(9. wiaet.0
CO  Copyright (C), Biobase GmbH.
XX
FA  AAF
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
SF   isAi; tlaorFGm
XX
FF   ibbhef -n nty25(ntu1licb-dd iad,r0h -ayeiorp'i);n Aee3P
XX
BS  R02116; AAF$CONS; Quality: 6.
BS  R03064; HS$GBP_02; Quality: 6; GBP, G000264; human, Homo sapiens.
XX
DR  2 PM0H.03N0AS6:0TOTRA40
XX
RN  [1]; RE0000446.
RX  PUBMED: 1901265.
RA  rw oltL.k e, J. eJJi.iewrD D.re , M cT.h ,ElnDack.
RT  tovtAcipaeu,bna aado F   ii -enIrarFl-smGongagifaclyCmdNfgmDAitN-ttn aco
RL  9 3EMB11(O)-2. 9:9.2J19 70
RN  [2]; RE0001471.
RX  PUBMED: 1833631.
RA  Je rrTel D,elJwcD . ..,. e D.a kLnE
RT  chobslarroe neyhertin mtarg tlrtittnnfoidutnacftna niidttarpsnenaeouatodsii cw vt ytagh Tgon-eninopieti- tuyiaooisdgppi taebnas tpdn-ln   ceafnwrcen  eo
RL  l111l.55M 9 -l41lB(. e 9oi.)o7:.3511C
XX
//
AC  T00267
XX
ID  T00267
XX
DT   1e.a5;)e291i9 0.de1wrt(c.
DT  pk21;a d2...51(0te0 )oe2du
CO  Copyright (C), Biobase GmbH.
XX
FA  GATA-1
XX
SY  EF1; EFgammaa; Eryf-1; Eryf1; GF-1; NF-E1; NF-E1a.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; aves; neornithes; neognathae; galliformes; phasianidae
XX
GE  G000060; GATA1.
XX
MX  M00203; V$GATA_C.
MX  M00789; V$GATA_Q6.
MX  M00126; V$GATA1_02.
MX  M00127; V$GATA1_03.
MX  M00128; V$GATA1_04.
MX  M00346; V$GATA1_05.
MX  M00347; V$GATA1_06.
XX
BS  R08219; CHICK$H5_09; Quality: 4; H5, G000063; human, Homo sapiens.
BS  R08220; CHICK$H5_10; Quality: 4; H5, G000063; human, Homo sapiens.
BS  R08221; CHICK$H5_11; Quality: 4; H5, G000063; human, Homo sapiens.
BS  R08222; CHICK$H5_12; Quality: 4; H5, G000063; human, Homo sapiens.
BS  R08225; CHICK$H5_15; Quality: 4; H5, G000063; human, Homo sapiens.
BS  R08229; CHICK$H5_19; Quality: 3; H5, G000063; human, Homo sapiens.
BS  R04798; GATA1$CONS_02; Quality: 6.
BS  R04799; GATA1$CONS_03; Quality: 6.
XX
//
AC  T00428
XX
ID  T00428
XX
DT  e1 ci(50)2r.9.a e9.t;dw1e1
DT  ;124a0u0 p) (12m..d.t4aedv
CO  Copyright (C), Biobase GmbH.
XX
FA  ISGF-3
XX
SY  E factor; factor e; ISGF-3.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
MX  M00972; V$IRF_Q6_01.
MX  M00258; V$ISRE_01.
XX
BS  R07792; AS$ISRE_03; Quality: 6.
BS  R07793; AS$ISRE_04; Quality: 6.
BS  R07794; AS$ISRE_05; Quality: 6.
BS  R07795; AS$ISRE_06; Quality: 6.
BS  R07796; AS$ISRE_07; Quality: 6.
BS  R07797; AS$ISRE_08; Quality: 6.
BS  R07798; AS$ISRE_09; Quality: 6.
BS  R07799; AS$ISRE_10; Quality: 6.
BS  R07800; AS$ISRE_11; Quality: 6.
BS  R07801; AS$ISRE_12; Quality: 6.
BS  R07802; AS$ISRE_13; Quality: 6.
BS  R07803; AS$ISRE_14; Quality: 6.
BS  R07804; AS$ISRE_15; Quality: 6.
BS  R02402; HS$IFI_03; Quality: 6; IFI-56K, G000305; human, Homo sapiens.
BS  R00001; HS$IFI616_01; Quality: 6; IFI-6-16, G000176; human, Homo sapiens.
BS  R00003; HS$IFITM1_01; Quality: 6; IFITM1, G000179; human, Homo sapiens.
BS  R00947; HS$ISG15_03; Quality: 6; ISG15, G000325; human, Homo sapiens.
BS  R00949; HS$ISG15_05; Quality: 6; ISG15, G000325; human, Homo sapiens.
BS  R00950; HS$ISG54_01; Quality: 6; ISG54, G000326; human, Homo sapiens.
BS  R02188; ISGF3$CONS_01; Quality: 6.
BS  R04607; ISGF3$CONS_02; Quality: 6.
XX
//
AC  T00526
XX
ID  T00526
XX
DT  (; w11ie95.e).a.tc9re21 d0
DT  aa;u.t(ek20d73000. p). 1ud
CO  Copyright (C), Biobase GmbH.
XX
FA  MyoD
XX
SY  MEF1; Myf-3 (human); MyoD; MyoD1.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; rodentia; myomorpha; muridae; murinae
XX
GE  G000576; MyoD1.
XX
MX  M00804; V$E2A_Q2.
MX  M00973; V$E2A_Q6.
MX  M01034; V$EBOX_Q6_01.
MX  M00001; V$MYOD_01.
MX  M00184; V$MYOD_Q6.
MX  M00929; V$MYOD_Q6_01.
XX
BS  R02452; HS$AAC_20; Quality: 6; ACTC, G000193; human, Homo sapiens.
BS  R02418; HS$MLC_01; Quality: 2; MLC, G000347; human, Homo sapiens.
BS  R02419; HS$MLC_02; Quality: 2; MLC, G000347; human, Homo sapiens.
BS  R00019; MOUSE$ACRD_02; Quality: 6; AChR delta, G000457; human, Homo sapiens.
BS  R00850; MOUSE$IGH_16; Quality: 6; IgH, G000537; human, Homo sapiens.
XX
//
AC  T03200
XX
ID  T03200
XX
DT  .o);a. r30mdc(0. 200eeth02
CO  Copyright (C), Biobase GmbH.
XX
FA  ASH1
XX
OS  human, Homo sapiens
OC  Eukaryota; Fungi; Ascomycota; Hemiascomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
XX
GE  G004277; ASH1.
XX
CL  3Cn.;i0 z40
XX
SZ  ;a)7 8.Dk . (a 5)(gAAe6l85n cce.
XX
SQ  NASAHHSKALRPFMYLSLLTSDSINNNNNLSSYYGSPDSSKSNSDSTIIYPNRLIPLANT
SQ  STSFLSNGSITLHLLNVANIHNEIPAPSHQKLASSIYKNFLPMSPSDSGISPSNAEPSKP
SQ  LLRRGLPLSRRVLSLLPGQDNQPFLSQNNNHLSLPSYSGRPSLFSSSELELQLPSPQTPK
SQ  DKDKLSRTKLNNFVNFNWYARNCNTESFQKTYDPRGYDAVNNSPHIQLASWEPDTTKHIT
SQ  PKEKIKFPPTHIALTESVKISNLQTSDRSFPNWSRTALSRSPEPESSPSNPTMKFKLDTD
SQ  NIFVILFLNSKESMSFLKHHKPRQPNDSESKSRGTMQNAEVEVFRGASNNTRPTIKEGQS
SQ  NAKPTKKVRGSNSLRVRKSSIKKDLVAKVLLQSFNNLNSSNAMSNSYIQKNQLFKASDIA
SQ  KYRTRPQSPSSYSRSKSISMRSGSPTSPPLSNHSASPSRKPTDPASTASPPRKRFPNVSS
SQ  YSCNVSSGPKRKKSLQNHHCRSKRWQGSCRLDSSTRLSVGPTTRSRTPHTCPSWRDDCCS
SQ  YNDNKRPCYERGENERVFIFECPKCLCIGTIGTNSLEIEVKMKINIET
XX
IN  T00002; ACE2; human, Homo sapiens.
IN  T00776; SWI5; human, Homo sapiens.
XX
RN  [1]; RE0014319.
RX  PUBMED: 9219698.
RA  sn   R H.a nJ igR  z .ne ,. mn ,-ea,o..MnL,.zgthn. ogG,eNMl.PrsaXSIeKy.R
RT  ytitAenzln ingAwcaiS aolpccl m HNleitetaitan stsmoR1i oietancfMysob ogmyr  d ryh 
RL  7n37(87 :S7c3c)3.92 i9e-e81
RN  [2]; RE0014327.
RX  PUBMED: 10409653.
RA   tY. cl.,.J ne Hi.i.JMYl dBDr,uS ma 
RT   a ostwsDcipit ntnrichon cda5foongivAt crnsso  apeigaeicideinera ftfutreqrtnirti o2  fe creec r iaeSs
RL  )i2e.9J1 h22C:3  o9 0401.729(.9-B1ml.6
RN  [3]; RE0014330.
RX  PUBMED: 10212145.
RA  -n.e  Peu h tr.,RaJa, eS..ocSsunnCMw
RT  cds o mtsttonMnsd ha eie tpmcrossoypyiVsaR anetrg hs So woleAi4N sidi  ninhegod n eacleA apfieeobl s yssi dnune
RL  )l(119.95S91Ce 28J i l1 c.-11:15.1
RN  [4]; RE0014360.
RX  PUBMED: 10209099.
RA  IoBsunS.e.  G.,o,mam .A. N zn oo vlhanBe ,s hnUyKozt
RT  na osyteiir1svitln toan osrcA eruA msyiaath meAlcoslnizltausH scnm nevltlioSaee1ano nldnReNpatteultps i r r 
RL  1 i.(: r5rC.92)03u9B743o9l3. -
RN  [5]; RE0014361.
RX  PUBMED: 10319811.
RA   ,.mCa,aa K MyTa nkP.mNs hoTts ..a
RT  let   iodvOceoleenlnettr-loceyo r rlge pydliiamerio l afteltnneo gtardcpoefdathusrpan idracomcr ntmc nmaesd on detrmrrut reac
RL  ll 3C1)9192-:. 799e91(9
RN  [6]; RE0015933.
RX  PUBMED: 8625409.
RA   s HIzo.wtelk,r AiSi.
RT  lfocffhmneni dqnc al1yo tyrei-oieaiOpteetdr.laioac iiipce d sr t e raospug elezied afsermcsltenAnIttarefctinios gn Hahemrn,, ity
RL  e9 .-6172781 l92l(14)C:
XX
//
AC  T03828
XX
ID  T03828
XX
DT  d(b50ma).0 c.290ert0 ;.1ee
DT  s.k2;d)ua1.2 02.pa7td( e00
CO  Copyright (C), Biobase GmbH.
XX
FA  HNF-4alpha
XX
SY  hepatocyte nuclear factor 4; HNF-4; HNF-4A; HNF4; NR2A1.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
GE  G001926; HNF4A; HGNC: HNF4A.
XX
IN  T05295; PGC-1; human, Homo sapiens.
IN  T05296; PGC-1; human, Homo sapiens.
IN  T05271; Smad3:Smad4; human, Homo sapiens.
IN  T04096; Smad3; human, Homo sapiens.
IN  T04292; Smad4; human, Homo sapiens.
IN  T01560; SREBP-2; human, Homo sapiens.
XX
MX  M00762; V$DR1_Q3.
MX  M00764; V$HNF4_DR1_Q3.
MX  M00967; V$HNF4_Q6.
MX  M01031; V$HNF4_Q6_01.
MX  M01032; V$HNF4_Q6_02.
MX  M01033; V$HNF4_Q6_03.
MX  M00638; V$HNF4ALPHA_Q6.
XX
BS  R13037; HS$AKR1C4_01; Quality: 3; AKR1C4, G004794; human, Homo sapiens.
BS  R15850; HS$AMBP_01; Quality: 3; AMBP, G013496; human, Homo sapiens.
BS  R15854; HS$AMBP_02; Quality: 3; AMBP, G013496; human, Homo sapiens.
BS  R20250; HS$AMBP_03; Quality: 3; AMBP, G013496; human, Homo sapiens.
BS  R15917; HS$CYP27A1_01; Quality: 3; CYP27A1, G013536; human, Homo sapiens.
BS  R19630; HS$CYP27A1_05; Quality: 3; CYP27A1, G013536; human, Homo sapiens.
BS  R15907; HS$CYP3A4_06; Quality: 3; CYP3A4, G002572; human, Homo sapiens.
BS  R15908; HS$CYP3A4_07; Quality: 3; CYP3A4, G002572; human, Homo sapiens.
BS  R19198; HS$CYP3A4_11; Quality: 1; CYP3A4, G002572; human, Homo sapiens.
BS  R15916; HS$CYP8B1_01; Quality: 3; CYP8B1, G013537; human, Homo sapiens.
BS  R13034; HS$F11_01; Quality: 3; F11, G004793; human, Homo sapiens.
BS  R13059; HS$F7_01; Quality: 3; F7, G004821; human, Homo sapiens.
BS  R15921; HS$GK_01; Quality: 6; GK, G013544; human, Homo sapiens.
BS  R15922; HS$HO_07; Quality: 3; HO, G000287; human, Homo sapiens.
BS  R19255; HS$TCF1_01; Quality: 1; TCF1, G004661; human, Homo sapiens.
BS  R20585; MOUSE$CYP2A5_01; Quality: 3; Cyp2a5, G021669; human, Homo sapiens.
BS  R13067; RAT$CPT1A_02; Quality: 1; Cpt1a, G000721; rat, Rattus norvegicus.
XX
BR  FR0001534; Quality: 6; Species: human, Homo sapiens.
BR  FR0001535; Quality: 6; Species: human, Homo sapiens.
BR  FR0001536; Quality: 6; Species: human, Homo sapiens.
BR  FR0002267; Quality: 6; Species: human, Homo sapiens.
XX
//
AC  T08800
XX
ID  T08800
XX
DT  24ac06s0(0 0l;e.er..atd 4)
DT  a1mvd .0u.)1ea6d202 ;2pt(.
CO  Copyright (C), Biobase GmbH.
XX
FA  Nanog
XX
SY  2410002E02Rik; Embryonic stem cell specific homeobox protein; ENK; ES cells cDNA, RIKEN full-length enriched library, clone:2410002E02 product:Nanog homeobox, full insert sequence; Nanog; Nanog homeobox.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; rodentia; myomorpha; muridae; murinae
XX
GE  G031512; Nanog.
XX
CL  h0e o06omC;.0
XX
TY  c.aibs
XX
HP  N)8m(. nT9g0;a96o
XX
SZ  .3.cD N((5)k 3 AAc . alc2AD0;)4a
XX
SQ  EPGATSYGTEMLPPASHSHMASNSMGSESSEGLQLPCPLENADAAPESNSSVLRPCSVFS
SQ  EQQQKLSSKLPASEEDSSMEARLGKEVFPYTKQKDLVCRKSNQTKAKAQFQDLKGPRPSP
SQ  QQKSSQSSNGRLSWQSQRLEKVTLLTKNILNYNIEKWWMYKAKLPPVCLQQVIHQKFGQS
SQ  GTSLWGCASWNWSPSTASTWYNNTSWGSTATSNNTGWLPWQQMQWNWVQNQSTYPQTPST
SQ  NAHDLHENTLLAQQEQSEEFSPGSHQFLSNFQSFLPLTPPVYLARQEAYFLNAVVWANDT
SQ  PPEGI
XX
SC  A5f:laBnME743otBdrm0t s9Lrae 
XX
FT  aon 1p N0 . o e  gan 1 
FT  .i l  e1 9 4110 [x H ] 1   5 
FT  4 1 2   ]3   x  e i23 Hl[1.1 
FT  33. 1x li     4  [] e H173  5
XX
SF  in1mrncn-ta dngni;poai[e o]oemiotoh
SF  aN-ustnc1o  N 2enle;s rgeeannaerobhns pm eutth5  qagii t
XX
CP  ltsencaey le2epd i.x  clsmy ei]il omnbfslptierleiu[ppiarr enscscto
CN  aosl e,tue netmr, ,,entniysls, s[be y,keme] sc[aevl b ,o gu,yhhrt,viiihpk e,m scpe, e ,inksrveinal gikt3 reoe  milomw,pin r ;oao nl  t s s,e,,rsimt u ,nylih,, anf snyavbatusc ,,i],,,vtdsrude,ktlina soarlm,lued ncereoundcelevsa rirhuue.gysey4oe
XX
FF  ld ]crlroe3steaMslnoo et c ar yebi p;siilItnn)  dui tS c emysfmni(ypl(cin l nacc mer)c[aegnEirrnuCl
FF  tnEemLioaea  ;tl-es  wbiaSItNolihnn[i 3uo e haF  srnt]yh wtfaialtg
XX
MX  M01123; V$NANOG_01.
XX
DR  T0TMO0N7HPS.708A :A098R
DR  MumonaH PK.SanNoBg;u: Ls :De
DR  A 97;5BA44BBML73E. 0:3095
DR  A;MYB5Y  .1285:782EL99A71
DR  :WR5TI5MTST8O_.SNQN77 EQS8PUOS; 
DR  O ZZ4QSM;6.8U06SE_P0WQ:SO4IS TR8
XX
RN  [1]; RE0047531.
RX  PUBMED: 16518401.
RA  ou L ., L HiL.,. ,huL J QYb   ,eBhLYn.  , .,a DCK, Rohht..  ..iPe ,es. gzmW, e.KV WaRq.X..K,oo.K u,J.    WnL iYCotBGag v. V. nna,P V,givnu.,L uG . hn    WS. .oa..W o, urnL p,LeB n,. Z uH.H. h .i W eehg,,e wCC . esn,etLiN,eo. Wg cg.Z o. .,BorJo.nXCg u.AS
RT  alcononir r muumrt.g y seinleo tontorNecnet  keaml pc 4esngdsilpehatirbaT  cwOcenn titypsoures
RL  024 .6-0t..4Nn:a4 8G)(3e1t30 e
RN  [2]; RE0047634.
RX  PUBMED: 15743839.
RA   HK  ditoja, SNa,T  .r,oati,onMd  umsu..kHT  .Y,N,aao,.d.aTr u utSKruH aaa.KmeHTaa. b . i
RT  toortrNpndl nfaaseie eo ertenr p ireemr ra al tg g xfionesema otdcrueno.leneiag oxscuaniirqsS Ocsn
RL   M0B2o)5:l(. .5 -C4.i222l58el7 o50l4.
RN  [3]; RE0047637.
RX  PUBMED: 12787504.
RA  mki o.awrei.w aM,Synaia zMk Kk. u.r,,K iau...M t,a,.ud  ea . TKaa m YaaSTa u , gsHaMksaMaa,hmahhIo tYaM,M
RT  nshintNeefeie upp racrengnnooc uatenSelehsfem lm oriucTendqtymrila  os  nso it.   oipEldaoapiobre 
RL  0402(-3 1ll6)e3 C1216:3.
RN  [4]; RE0047645.
RX  PUBMED: 12787505.
RA  bhc  o,mei sMo ,eSNywe ,.CAbSsh oaIel..mr,  s.TriSte,e, n DdLJ e.bht ..oCil R
RT  lloogtria xygninfmmnucsciouletaa o tc etssuncs ltlcri  coeronaFg.eNiinonieoe f rppnypnn bsa,sni  
RL  1210l: e6)04l36(C353- 5.
XX
//
BioPerl-1.007002/t/data/transfac_pro/fragment.dat000444000766000024      1236213155576322 21673 0ustar00cjfieldsstaff000000000000VV  TRANSFAC FRAGMENT TABLE, Release 11.1 - licensed - 2007-03-31, (C) Biobase GmbH
XX
//
AC  FR0000001
XX
ID  FR0000001
XX
DT  5.0.h2el(ct2a)k0. ;055d re
DT  tp5. )00m0e22 d5d;ul.a(k.5
CO  Copyright (C), Biobase GmbH.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
SQ  TGGGCTCCTGGCATCGTTTACGCGAGCTGGTTCCAGGAAAGGCACCTCGGTTCATGCGAG
SQ  GCGCTGATTCTATTGTGTAAACTGTTTCGAGTGACTAGGCCACGAAACCTTTTCATGTAA
SQ  GGTGAATTGGGGGTTTTCATTTAACGCGGGGTACGGTTCGTTGGTGGGAAGTGGTTTCGG
SQ  ATGTAACGTGGTACGTCGGATATATTGCATGGATTAATACGAAGACGCTCGAGAAAGTCG
SQ  AGAGTACAGAAAGTTAAACCGCGGGTTTACGAAAGCATAACTAAAGAAGGTAAATTGATA
SQ  GATTCACAGAATGCGGTTGTATGAAACCTATTGACAGCGTCCGTTCGTGCGTTAGATGGT
SQ  GTTCTGCGGGGTTCAATATCATGTGAGCGGTCGTGAGGGCAGTTATCGATACTACATGTG
SQ  TCGGGGGGCATGCGCTCACCGACTTATCATGGCGGGTACGAACGAACGGGAATCGGATTG
SQ  AGGAGGAGCAAAGGATTAGAATTAAAGAGCGGACTTACTGATGGTTCAGACCGTCGTCTT
SQ  ACAACAACATCGTATGCTACTGGGAAGTATCAGCTCATCGGGTGGCGATCACGAGAATCG
SQ  AAACATACATTGTCTATGTACTGGCGGATCAAAACCCATTCAGTATATACTAGGTTTTTG
SQ  TTCGGACTAGCTGGCTGTGCGTACGCCATTGGAGACAACAGTCCGTGGGCAATGCTACAT
SQ  AAGTGGGATTGGCGACTGTGGTCGCCCAGACAACCGGAGCAAGACTGTCCTGTTTCCGGA
SQ  CTTAGGGGAGTAAGGCGCTACAGCTAGGGATCATTAGGCAGAATAGGCAATAATCAGCAT
SQ  TTTGACTGGGTTATATCACAACCAAACGGGTGTAGGAGGGGCCGAGATCATATAGTGAGG
SQ  GAGATTTTCCTTGTATGTAGGCTGCATATTATCATTACGGACGTGACTTATTAAATCCAG
SQ  TATTCATATAACACGAACCCTACCAGAGTGAGTCGAACCTAGTGTTTTGATAAGTGTAAT
SQ  TAAATTCTTGCTCGTCGCTTAATTGTGGACCATGTACAGTGATGTACTCATTTAATCGGG
SQ  TTTGCTCGATGGGCACACTGGCCGCAAAATTAGGGTTACTCCTCAGTAGCCAT
XX
SC  uRr. d0.)140H 1R1O6iF.621W40D.6(AS_620C:lh7y0a8MA1 7B 1
XX
BF  T00140; c-Myc; Quality: 6; Species: human, Homo sapiens; Cellular source: 0123, Jurkat.
XX
MM  h hruCgnded -a-IntiehPothilo re-cysyacginriloo
XX
DR  (:94B9L3AM:39F3)8; .5114E.12 80 695
RN  [1]; RE0035138.
RX  PUBMED: 14980218.
RA  o,r.emWCVmaTkog.J,r Tk. kwls a  o,r laWtneSsihB, at ek aPmrG   aSlnRR.m ,l. eA knK Soa..hu   nn.SuiAlHl,nn,  BeEe.PKGi.bA iKviaraCea.l ,e,Mahw taeeJ, ygp..,r . o.nS,a B,aH,a t oWk Y ., .S ipnrS  cDP eg H,vNb..e,..l,ngcJDegma, H  m rahen.i.ceroe n.
RT  iedgmisnnrNdngcpbor smr2ittlpocasiep.ei ogdanoft gAaoo nt2Uud ndp i iasfpu r taw  mo n ninsnsfngnlaoimtboot2cec  dR er anarn o hsosoiieas1h
RL  -10.542(69 9C)el0l1: 049
RN  [2]; RE0035139.
RX  PUBMED: 11988577.
RA    k a,rv    eeE.k.G rePaolL,gnJrR,rgvwBKsr,.S na r .ebuoPai..n., a,Fr .. eDsTwo od yStn..ipR oaSCS
RT  ntcaostccid sir1ntra  aevyo rn-la msago.mlLtr p2o2esehina 2ici
RL  e01ic0269 2 S6ec:-1992n.9()
XX
//
AC  FR0002267
XX
ID  FR0002267
XX
DT  )er2.. 0;00aet9cd(0hl5 .k7
DT  0m00  07.p.2dl;ae)5(9.ktud
CO  Copyright (C), Biobase GmbH.
XX
DE  Gene: G020751; Gene: G020752.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
SQ  gtggcgggcctctataacgtacacggctccgctgggccttcccgctgtaaaccgggaatt
SQ  acgtcgagaggtgcaaggtgaaaccaccgactgaccccggccggagaccggagcagcgca
SQ  ctccgtcccaactacatgctgttcctgccacatgcaagcgttccctagtgaatctcgcgg
SQ  cgggactggcgcattacgcgcactccggtttcgagcgcggtcacaaccttacgttttacc
SQ  gcgttggttatgaccggtggtatgcggcgccggtgctgggcagatcagggtggtttcgct
SQ  gtcccattcatgcctccgatttctccactccaacgtctcctcagatgttacctcgtcatg
SQ  atcgcatacggtctgcgtagtatgggtcaccgatccggaatgcacgcgatgctgagcgtt
SQ  atgtacgcccgaccgtgcctgcttaccccccgcgcggaagacggcggctgttgcgttctg
SQ  GTCTACAACtGaCctActGcCtCAAGCCCcGATcCCcCctgGCAAcCGcTcGAaCcTCGt
SQ  ACTCTTGCGGACGGAGAGCCGAAGAGCAAAGCGTCGCCGGGTAAGACGAACGCTCAAGGG
SQ  GGTACGAGCAGCGTAACGACGGAAACGGTGACGCCCCGGGATTTGGGGCTCAGCTAGGGT
SQ  CGCCGAGTAGGGGGCCGCGGGGACAACGGGGGCGACACGCCGCTTTCCCTGCGTCTGTGG
SQ  AGCCTATGGTACGGCGTAACCGGTTGTGTGATGAACTGTCCAGACCGCACGTAGTCCCAG
SQ  CGCAAGGTCTATGCCGCCTAGAGGCAAGACGGGCCGTCTCCTACTTAGTAGCCAGCTACG
SQ  GGGCGTTGGTCCCCTCGGTAGTGCAACTATCCAGCCACGGCGTCCGCCGGGCTGAGCCTC
SQ  AGCAGAGCTGGGGGGGTATCATTCCGACGCTGTTTAATTCGTCAGCAGGACCCACTACAC
SQ  GCTCTGTCATTCGCCTGAGCAGTTGTAAATTAGCGCGGCGATCTTGCAAGAGACAAGGAG
SQ  GCGAACCTGGGGTCGGGACGTAAGGACGAACGGCAGTACAGACGCTGGGGGACGCCACGT
SQ  GCCAGAACCTCTCACGACCGGAGGTTCAACGCTGATTGGGGCGCAACAGAGGGCGGAGCA
SQ  GCGAGGTGGCGCTGGTGGGATGGGGCGAGACAAACCCAAGCTGACGCCGAAGGGCCCGCG
SQ  TGGCCGGGCTGGGGCCCGTAGAACGAGGGAATTGTATGCGGCGCCTGAATGGGCGCACCA
SQ  tCAgTCTTaGcacTCcCGCATTcTtcATcACaCtcACcCAtctAaggGAAcTaCGCCgGT
SQ  gctaagcaaggagtcgatcaacggaaaggtgctaggggtaactgggtcttgcgcggcagc
SQ  cgtgtactcggcttgtaacgacaccgcgactgtaagcgccctacttgcgtatattaacgt
SQ  aatgttttagtatagttcgttttatctcatctcatgagcttgttttgttgtgtctcgttt
SQ  tcgttttttttattttgtttttcgtttttttttttctttgtgtctatcgttcattttttt
SQ  ttatagtggacgcccctgggtagtgcgctcgggcctgtcggagatctcgtccaacgtctc
SQ  tatcactgctagtgttgccaagcttgctgtaactgaagcggacagtcccacccccactcc
SQ  ttaagtaagtagacttattccgtttgttttccgttagcgtcccgaagcggtttgaataac
SQ  ctcgtgcacccgaatactgctatacacatgactaaccaggtcctcccgtgtgcccc
XX
SC  30997.0aADHBrM346. d68 .9(y4 iS:W.2lA2F2RC hROu4_77)48
XX
BF  T03828; HNF-4alpha; Quality: 6; Species: human, Homo sapiens; Cellular source: 2614, hepatocytes.
XX
MM  yCrtea IropnPhr-or-moa
XX
DR   M8C081A09:(78:1E 1.6;8L488)B3 
RN  [1]; RE0023998.
RX  PUBMED: 14988562.
RA  rgSM,k .z, .E l.dBopf dn. ..,,f.A..seL  bo .aG. mHKJ l.e.e T  R.tPeR , rlIOAeoGy ,.lG DneZ.l Gc.o B.lJF rNdfe, i,.il Wh rR,erd,,oB.Tro.n ana  li rr. D  YeliL ,erN uVg or. Diuk 
RT  aF lnn ee tscfH bt  eNarseeorc npsarr prnsCsdnaioooei vonnlit partogycir.xf
RL  7i3)1S088e 1:n4c0-ce20(3.1 33
XX
//
BioPerl-1.007002/t/data/transfac_pro/gene.dat000444000766000024      2611413155576322 21006 0ustar00cjfieldsstaff000000000000VV  TRANSFAC GENE TABLE, Release 11.1 - licensed - 2007-03-31, (C) Biobase GmbH
XX
//
AC  G000001
XX
ID  AAV$P5
XX
DT  )b5oed40(.t9d.;161 ra .9ec
DT  00e.ad0.mu1(vta.2p9d0 )1; 
CO  Copyright (C), Biobase GmbH.
XX
SD  P5
XX
OS  AAV, adeno-associated virus
OC  viridae; ss-DNA nonenveloped viruses; parvoviridae; dependovirus
XX
BC  .6.36
XX
BS       -60        0   R03174; AAV$P5_01; Binding factors: YY1 .
BS       -50        0   R03176; AAV$P5_03; Binding factors: 96K-protein , factor 2 .
BS         1        0   R03175; AAV$P5_02; Binding factors: YY1 .
XX
DR  .0H R0GN:P100TTA0SA
DR  109;L2JX.X 1 E0B:M
XX
RN  [1]; RE0006609.
RX  PUBMED: 8413258.
RA  ,oSMa   oCo. ,.w.matehKLysCH K.cn  Prirott. hyk ,.Aa
RT  lnafrtnatYrfettincurvmcipelmmsos A ttet ciittctihaocreYrcndr   s pe N ss1mt ci:te e1 oer tpa npiatioo riDYelsorfaeensane wet loiYia-eironnctaptTAt oe rcctoislanp tpinf rhettr
RL  18.o -B3l9e .MC2)36ll1(..9166l26 o :i
RN  [2]; RE0000230.
RX  PUBMED: 1655281.
RA  n- h S ..   SCo.ETY,h.SntaS,ge eih.,kL
RT  fyaAdoh b dcalt1ernre- pirte u ,neTosrruseteEsra  olGYsnas rpibapne Kn-eeatonp lrlm u  ivoeLnyneonpeYfiripr1i,ae rdrsiIopi 
RL  3713e9:l81C77. 9l8( )-6
XX
//
AC  G000060
XX
ID  CHICK$GATA1
XX
DT  5a0) .b1 e.r9d.;c9to16(d4e
DT  1;doa22. 0e50k 1.u)te(pd2.
CO  Copyright (C), Biobase GmbH.
XX
SD  GATA1
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; aves; neornithes; neognathae; galliformes; phasianidae
XX
BC  622..4..1
XX
BS      -643     -634   R03087; CHICK$GATA1_01; Binding factors: GATA-1 .
BS      -592     -572   R03088; CHICK$GATA1_02.
BS      -568     -555   R03089; CHICK$GATA1_03.
BS      -485     -471   R03090; CHICK$GATA1_04.
BS      -442     -429   R03091; CHICK$GATA1_05.
BS      -409     -389   R03092; CHICK$GATA1_06.
BS      -373     -349   R03093; CHICK$GATA1_07; Binding factors: GATA-1 .
BS      -257     -239   R03094; CHICK$GATA1_08.
BS      -235     -221   R03095; CHICK$GATA1_09.
BS      -177     -157   R03096; CHICK$GATA1_10.
BS      -153     -137   R03097; CHICK$GATA1_11.
BS      -121     -102   R03098; CHICK$GATA1_12.
BS       -59      -49   R03099; CHICK$GATA1_13.
XX
FA  T00267; GATA-1 (isogroup).
FA  T08293; GATA-1 (basic).
XX
DR  0R00A6A0TNS 0GT.:HP
DR  735 :LG.;AG 99MEG1ABMT
DR  40935ZE:.EGN TENER6
DR  T00R .R3D52:
XX
RN  [1]; RE0012279.
RX  PUBMED: 8628290.
RA  hV..n F.bo.loennafeT.dr TnoMOC..  J ld c.ro. C,eG isna, nG.GirDror ,,enir  .GA nskieMl g e, Lm
RT  sniieeeraagth ueAoeAAiTogrir1 rtointh cirtno-N1G  t ri--bpiefpb GtfitriAeh h an rqof eny-ciTatiaof stmDe ooornirfds ddthgr iei unvirlAlntAmtezn gcs bymw na
RL  iB 2Co..1M26l 13-().l:.7  l6o92e842l9
RN  [2]; RE0008084.
RX  PUBMED: 1400499.
RA  Ama,n  .Digih .nJlZ
RT  dsihioeleym uo1en baece en mtnaa 1e mieigPneTensaeoos in  ex Dg nn titsec- advAelu lifagettnaAns-dPm t bhldehs
RL  -1m1.:C .2.)7 69hJl1eo29 428B9 i2(.090
RN  [3]; RE0002473.
RX  PUBMED: 2014222.
RA  . H.R sn l Tln ,uva.aoHnednGlEn efFodse,, G.
RT  ftonc-fteiirronSreoctidAr ugoretorei rarort shocuheAeha ttp tm  p tnef naaiyrvyGdt1T  tc 
RL   :c8 3d.AA.0occ 011l 9rPt 93.8SiS0N4)..(8aa-0 U
XX
//
AC  G000174
XX
ID  HS$4F2H
XX
DT  ae06 )r..;1(.o9c4bd 91det5
DT  ().am1au2ddtep0 .v2.01; 11
CO  Copyright (C), Biobase GmbH.
XX
SD  4F2HC
XX
DE  yvheFahn 4 2ica
XX
SY  4F2; 4F2HC; 4T2HC; CD98; MDU1; MDV1; NACAE; SLC3A2; solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
CH  11q13
XX
BC  616..
XX
BS         0        0   R00005; HS$4F2H_01; Binding factors: NF-4FA .
BS         0        0   R00006; HS$4F2H_02; Binding factors: NF-4FC .
BS         0        0   R00007; HS$4F2H_03; Binding factors: c-Jun .
BS         0        0   R00008; HS$4F2H_04; Binding factors: NF-4FB .
XX
BR  FR0008041; downstream; Species: human, Homo sapiens.
BR  FR0008042; downstream; Species: human, Homo sapiens.
BR  FR0008043; downstream; Species: human, Homo sapiens.
BR  FR0008047; downstream; Species: human, Homo sapiens.
XX
DR   m:HmLunSPH3AD 2LBnK:a; C.uaS
DR  4P0:.1NAH0T7GR0AT S
DR  9M4GE2 HF :1L1S8MB.;82H
DR  10.S:0M00N0GL080BE SENE63
DR   0F:A_2_2atYEu0_HF9osF IRMYG.F_XFTAs:4c
DR  _HYFLI2YM33 Ta0.FXF_S2Us9_E F1_t_:RU_240APAG:
DR  23.ATFF_ 1aGA3_ __FXUMRFt4YAs:2:EY00IH9
DR  03_G AMs1F__34XUtAHT:F_F.FI9E Y:R22A_2Y0a
DR  5XRME9:AY09H.FY_tG8AFF TIU F__aA:32
DR  F AY9FE2MU_39 .X2_v5YF:AIT:H0aFRG_t8A
DR  F:U2A7 EYG:_I3_ 3Mt_RE9H5_FYFaF.AT2Xs
DR   _:tU33a9_AATs_R_FE7 GYXFFI3Y.H5E:FM8
DR  8 _FI:50HMXE_tY_5.F4GAF:R9a_Ts9YF AEU
DR  _T9XGMaYeLFn_tAeF0M AYRFFIF.4:2E :Hu1
DR  XaP:1T0a5_5 E_0I_3t1_3F3AYFMAX. FgpFUR44Y:3_
DR  00B B1M8;101L:E010BAA.8 0
DR  A. 01F3F50;LE 531BMA0:055
DR  E;552K5AKM:A 024L .88540B
DR  995B00A8MEL8;75 .A070KK: 
DR  2K9.4;A A 2EB60KL4600M:09
DR  :006 010AP10 1L;P.M0BAE61
DR  0C100B001;0LM:6.116BB E C
DR  L 0.0BB: 0C0M0030C3BE000;
DR  MF;27.2LAEJ :H9B 046S
DR  2 9LGH:3B0.SF9ME; 2J4
DR  NJ;T:A.HB A5L L396M0SE
DR  22:E9S 9. 8MM;GH421LFBH
DR  SMH:F3GB M2.2L0 4H910;E
DR  M42B.F 2:19H4SHLM;E1G 0
DR  B M F;ESGHH2024.M:129L5
DR   H0M:H4 23G6FE12S9ML.B;
DR   H4247BG1HE:9;.20S MFML
DR  T0EN52:6.GREENZ E
DR  51.8 OM:M70I0
DR  23CSA N.:HCGL
DR  06RSF11_62 Q001N.ME:E
DR  R26106.:0NF E_S012MEQ
DR  3RES1F162.00_EQ0:6 MN
DR  F61. EEQ1:R00S2N0M_46
DR  0MFESN51:2 01Q0.1E3R_
DR  :0M.SF3_R4 E90QEN2
DR  .0:ENSQ21E0_P7F061R 9
DR  F0E06:2ERS_NP08 01.1Q
DR  111PEEQ0006SFR8:2_ .N
DR  0E60R08NE21:2_. QPFS1
DR  ._PE16F0Q1S2NE 3R900:
DR  Q:32E8P FRSE_5.N00
DR  :.7sEG6HUNI92.0 N5E
DR  00:0DR2RT .0
DR   5_4SRN1:S4TPA.AO_H6R
DR  .A__HP5RT4 NS2AORS4:6
DR  R4HORT3.N_A4_SS6 PA5:
XX
RN  [1]; RE0001199.
RX  PUBMED: 2761540.
RA  edDAahr. Pc LKeea.ngi,Mrk.n el.sH, M. sL..arCJ GY.npi- ,io.,i     B
RT  eenrr pefrn nnhca-n4nossm oeeul  en ii aetyaeTlnTGhnCiFtttens CieraoePNcnEloaatlBt t ht aI Htrivhidnr iirMhs   2ncsaFop TaluE
RL  9o -e.oM12(9l.8llli759.29.8C5 :8B)  
XX
//
AC  G000264
XX
ID  HS$GBP
XX
DT  et b4;10c.a(do.erd.)19596 
DT  d9.6; 29ba5d1t.4e(0p d)uo.
CO  Copyright (C), Biobase GmbH.
XX
SD  GBP
XX
DE  oaa-ginelentiupntybrgndi 
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
BC  165..
XX
BS      -216      -76   R02897; HS$GBP_01; Binding factors: IRF-1 , ISGF-1 .
BS      -128      -99   R03064; HS$GBP_02; Binding factors: AAF , GAF .
XX
DR  TN.ATGS0264PR HA00:
DR  D.00:0R 0TR2
XX
RN  [1]; RE0000446.
RX  PUBMED: 1901265.
RA  D   r,lMLr  ., eieJe.Jwre. kTahcD witoEJlk,D.cn.. 
RT  nf A,t  ntotrboa-c apscm aNeogi tnCieaaldva mfDFalIiidFcyigrN--utAnGgamo
RL  9-1E0M .2 .3(7:J19O991)2B 
RN  [2]; RE0001471.
RX  PUBMED: 1833631.
RA  . cel,arn JrDlkeJ..w  eT E.e ,.DD L
RT  tfcerufn c eoo op enbetgisgetywitdltugoreantrtp inropsd  eytubidotnl otat he- a ntsiaiceasdtcann cnmpnhnonh tai -panititodergriir- aitannniTsl vawaynoef
RL  l(lo3i9el5 B91l.1)1-M .Co.. 5151741 :
RN  [3]; RE0001567.
RX  PUBMED: 1898761.
RA  h...l ro IkeDl Jrc e .e. LwehTe.JnD,rSDlt,   w,Ea
RT  it snop dpteneyoagtc nileib O iruloocm oegrgnrnaai nartieetf  ahm-mmb revenotanmt htagaiernsgipra iraplneun enpnllnteedpdtey anidi 
RL  o-(. ..ll1C:l11 1BM 1o119. 9lie)298
XX
//
AC  G020751
XX
ID  HS$ABCG5
XX
DT  ;k2c.0are..05d509t 0 )me(l
CO  Copyright (C), Biobase GmbH.
XX
SD  Abcg5
XX
DE  imAT rmiese(r as-stbaitb,l )fiP(bcuI5dWeGs  He tnT n),l-menyEo g1
XX
SY  Abcg5; ATP-binding cassette, sub-family G (WHITE), member 5 (sterolin 1); sterolin 1.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
CH  2p21
XX
BR  FR0002267; upstream; Species: human, Homo sapiens.
BR  FR0003356; upstream; Species: human, Homo sapiens.
BR  FR0006822; upstream; Species: human, Homo sapiens.
XX
DR  :Dn;mAHu 5L aGPS.KHmunaBC: B
DR  PA 0S:1T0G72A.TNH5R
DR  LENS78.3:0E00MB100S 0E5NG
DR  E_FF3R 2Y3:_F. GucFoY2_AHFs0T:8XAtaMI
DR  8L_U1.3UP_:32: atGFAFM3RFY2T2_0E_3IFYAXSH _
DR  F_t03T A GX3:8Y_2U1H3AYFaE.F_R2FIMA3:
DR  Ua 8X3t1._A:FE23_AH3G_Y23:I_F FM20FTAYR
DR  7Y3DU_ 9AtA.F 8GFTF_a9XE:F_H5Y2I:MR
DR  41C2M1;L001:2 42BACE2. A1
DR  :1 4M0;LCC.A E686187AB047
DR  E M1:;2.5LFA717133 1AF52B
DR  BE;A:M33F022 9F02.339 L2A
DR  10M4L:A6F1BE6;F4 440A. 00
DR  A; LMB40:007744F4.0 A1F1E
DR  ML;7K0 9K9 AB.9A910E9719:
DR  141511 B MLB;1BC4.51CE1:1
DR  2E:0EZE.44ET GN6NR
DR  .:201 0OIM5M2
DR  O.4505I69: MM
DR  G.H g5c:ANCb
DR  F 2E3:6M2RSE4_N.Q0
DR  E7E0P._S8F1N1 :R8Q
DR  EN3G2:2.Us.IEN99 1H
DR  _P .R11_:2RN4SSAT7H0OA
DR  SNO.P1S70:_A2HT 4_R2RA
DR  7HT4SN31.R0A AS:RP_2O_
DR  74_PHSTS:4AR2N R0.1AO_
DR  A T2_A0.R:SN4PHRS1O75_
DR  A.SNOP0 _6:R_2SAT74H1R
XX
//
AC  G036757
XX
ID  HS$TRPV6
XX
DT  a0) ect2..(d5 r0e;4e02ch.6
DT  e0 2(0.)ah2dtde4..pu;6 50c
CO  Copyright (C), Biobase GmbH.
XX
SD  TRPV6
XX
DE  psai etc irnba nuV,oaee ebrh af nlrtnolrtc  enmmi,tlse6cpneiayomtt
XX
SY  ABP/ZF; CAT1; CATL; ECAC2; HSA277909; LP6728; transient receptor potential cation channel, subfamily V, member 6; TRPV6; ZFAB.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
CH  7q33-q34
XX
BS     -5508    -5494   R19310; HS$TRPV6_01; Binding factors: VDR:RXR-alpha .
BS     -4337    -4323   R19311; HS$TRPV6_02; Binding factors: VDR:RXR-alpha .
BS     -4287    -4273   R19312; HS$TRPV6_03; Binding factors: VDR:RXR-alpha .
BS     -3519    -3505   R19313; HS$TRPV6_04; Binding factors: VDR:RXR-alpha .
BS     -2169    -2155   R19314; HS$TRPV6_05; Binding factors: VDR:RXR-alpha .
BS     -2119    -2105   R19315; HS$TRPV6_06; Binding factors: VDR:RXR-alpha .
BS     -1283    -1269   R19316; HS$TRPV6_07; Binding factors: VDR:RXR-alpha .
XX
DR   nHBaa;muPSK :umH:nDT RPLV.6
DR  5PTHAT:7 G.R60N3S7A
DR  2:5 24YM46L1A;612.5AB2Y E
DR  ES0B: 6GE00S11E05N0M.52LN
DR  _YFFtcG7sE:X8FH.As2uF :_o6RYF_TI_M a20A
DR  6XEPRY_1_: :8_2GAHtF3UTL aIA.Fs_M72UYS32_FF0_
DR  RUYA72MFE AA3I1__6GtFF3F2Y8_0_aH:sT. X:
DR  FYME 20s_FG: 6F_13Ya.28H_A:XTAI3_U7R_tAF2
DR  _tAFIXA38:YT5 _FRA69aU6FM:F H0Y_GE.
DR  2.Yv_3F:G9I  TAa066_ERA8:FHtXFFYU5_AM
DR  1_eHeXFInM32A8AE LF6YuGUT.:FRF:_t FYa
DR  A 3FM:L34 066B44E43A03;.F
DR  9:36.A B3AE6L57;952 7F2FM
DR  5AM9836L: A.F2F6 35;82B9E
DR   M5034HJL. :A03024BA25ES;0
DR   L32;M1:5AA40.BJ1325 H40ES
DR  92.;L727J007799H S9: MEABA
DR   484BA7M;AH6E47SJL:9846 9.
DR  KA13:51BL5.7;0 K00 AE370M
DR  6 E002MK0:7BL76 AA5.25K;0
DR   0Y5ML05.0;0B30EYA0:33A 3
DR  2A4:3;7900YY9MEL4A37.2B  
DR  3E68U212UH  .6318B;MS:L
DR  7:E7XALHSBMZF 88 .;B3
DR  ET5.R5E0E GZENN:35
DR  6O60I6:8.M 0M
DR  :CHNT. PR6GV
DR  N 6E4108S:R6_M.QEF
DR  S6E1Q_.RF6 1P:E0N1
DR  XE4121MR:65F0 Q01S_.E
DR  05.6P F1140_2EQ1S:XER
DR  2I007HE.NUs:4N 3EG.
DR  66HGU:NsEIE 8.36N9.
DR   .46U.IsE7N3N8EH:G0
DR  O8RN_HA1TP7 A:4_.RSS1
DR  TRA8SAONS4.:7 2R1_P_H
DR  178P4 3NH:ATR_R_OSSA.
DR  A4SO18RT4NSR.A_HP _7:
DR  O7.:TAN41SSARH8R5__ P
XX
RN  [1]; RE0047775.
RX  PUBMED: 16574738.
RA  Mh. ,. JeS.emtM,vK.S,ed W yP ,i  an u.e aNKe.krkWBM. .i i 
RT  TTSDLIN TO16 NETIYE SHANEVIL  HDIPDOTTP-EIUON LNTRIICGVMAD I2 EATSTL  IAEMAIINC NIIDT PT TXYT OLESIADI5.ITC MUDSTRHTCNAMANHBVEPEORIM BR,NAO RLRSNM3 A VEY T
RL  nrM o00d2 .:c.l6.( noEoi)l
XX
//
BioPerl-1.007002/t/data/transfac_pro/matrix.dat000444000766000024      1654013155576322 21376 0ustar00cjfieldsstaff000000000000VV  TRANSFAC MATRIX TABLE, Release 11.1 - licensed - 2007-03-31, (C) Biobase GmbH
XX
//
AC  M00001
XX
ID  V$MYOD_01
XX
DT   (d9.01.w9 a29ee1;)1ciet.r
DT  dd.p ..b2uo7ae9)2;0 9(1td1
CO  Copyright (C), Biobase GmbH.
XX
NA  MyoD
XX
DE  ounedpt tadtiorlieboe aesynrmg ntmc
XX
BF  T00526; MyoD; Species: mouse, Mus musculus.
BF  T09177; MyoD; Species: mouse, Mus musculus.
XX
P0      A      C      G      T
01      5      0      0      0      A
02      0      0      0      5      T
03      0      0      5      0      G
04      0      5      0      0      C
05      5      0      0      0      A
06      0      0      0      5      T
07      0      0      5      0      G
08      0      5      0      0      C
09      5      0      0      0      A
10      0      0      0      5      T
11      0      0      5      0      G
12      0      5      0      0      C
XX
BA  on3  nfsen  snng5eluaetemii ctle
XX
//
AC  M00002
XX
ID  V$E47_01
XX
DT  w.e9921td19i1e .e ).;(0car
DT  7.0di12 e8t0;dep).(uw00 a.
CO  Copyright (C), Biobase GmbH.
XX
NA  4E7
XX
DE  7E4
XX
BF  T00207; E47; Species: human, Homo sapiens.
XX
P0      A      C      G      T
01      5      0      0      0      A
02      0      0      0      5      T
03      0      0      5      0      G
04      0      5      0      0      C
05      5      0      0      0      A
06      0      0      0      5      T
07      0      0      5      0      G
08      0      5      0      0      C
09      5      0      0      0      A
10      0      0      0      5      T
11      0      0      5      0      G
12      0      5      0      0      C
XX
BA  fs EMyeignnt1  tkid yarEtawn4oDeoEeD1o) 7fMl1d sre7n 2-(,b+c o, riseoE 1 g4ds2 
XX
BS  ATGCATGCATGC; R05108; 3; 15; 17; p.
BS  ATGCATGCATGC; R05109; 1; 15;; p.
BS  ATGCATGCATGC; R05110; 5; 15;; p.
BS  ATGCATGCATGC; R05111; 5; 15;; p.
BS  ATGCATGCATGC; R05112; 8; 15;; p.
BS  ATGCATGCATGC; R05113; 9; 15;; p.
BS  ATGCATGCATGC; R05114; 8; 15;; p.
BS  ATGCATGCATGC; R05115; 7; 15;; p.
BS  ATGCATGCATGC; R05116; 11; 15;; p.
BS  ATGCATGCATGC; R05117; 5; 15;; p.
BS  ATGCATGCATGC; R05118; 5; 15;; p.
XX
CC  iefn bmtetle tc r ne;nudetrntEd errEsNunrxo[(p-i ]srv2aoueri=  hi1eaager pt deiiiIic  )od;tl nt dahu1o mte2tcGisi sctl1o 5sbn e scc cor qgNldyo en
XX
RN  [1]; RE0000231.
RX  PUBMED: 1846322.
RA  Hlr..neDto. i,-Bam XS u
RT  te ciot emfAandnenn ri 1irrdt2o oiniEm1stEt h pNAdmrmyora2neut  iisspni iosrg  fthbDvoin odotinrbnoEhr  be cie n12a
RL  . -0)1:47l9C49(el4165 9
XX
//
AC  M00972
XX
ID  V$IRF_Q6_01
XX
DT  ..ea24e0dt0;r2 d10tc( c3).
DT  p.e2tt2c.dd 0 ;)45a6u.d(00
CO  Copyright (C), Biobase GmbH.
XX
NA  RFI
XX
P0      A      C      G      T
01      5      0      0      0      A
02      0      0      0      5      T
03      0      0      5      0      G
04      0      5      0      0      C
05      5      0      0      0      A
06      0      0      0      5      T
07      0      0      5      0      G
08      0      5      0      0      C
09      5      0      0      0      A
10      0      0      0      5      T
11      0      0      5      0      G
12      0      5      0      0      C
XX
BA  oen mlpoptACNn3TNgccsCdeElidiM16  cRu  isGeIqei e lSsuesmn1O
XX
BS  ATGCATGCATGC; R00001; 3; 11;; p.
XX
RN  [1]; RE0024406.
RA  NATSTmF.aR_AeC
RT  RAnMATFt CnSIATvese N XreoRi Rifsoi
RL  0RoR0eC 0NA 4)(4r2s A.p0:F0tTS3
RN  [2]; RE0017571.
RA  mCNF_aTA.eRSTA
RT  NR XT nRACMsFStrew NTeIiAeA
RL  Fops2r)R00S0(T:AC1Rt0. N 20e3 A
XX
//
AC  M01123
XX
ID  V$NANOG_01
XX
DT  d..6e2cr660(a0a)v.e ;tm 00
DT  d0aeavt7.)..( u;2 606pm00d
CO  Copyright (C), Biobase GmbH.
XX
NA  aNogn
XX
BF  T08800; Nanog; Species: mouse, Mus musculus.
XX
P0      A      C      G      T
01      5      0      0      0      A
02      0      0      0      5      T
03      0      0      5      0      G
04      0      5      0      0      C
05      5      0      0      0      A
06      0      0      0      5      T
07      0      0      5      0      G
08      0      5      0      0      C
09      5      0      0      0      A
10      0      0      0      5      T
11      0      0      5      0      G
12      0      5      0      0      C
XX
CC   tai1effdthnPo dd(fiemrwN drMoi[ahs i lseo)eoitCEsPiana gANt aCTe ssdIto  - nh gcIiy]iihttm bonmevt 
XX
RN  [1]; RE0047531.
RX  PUBMED: 16518401.
RA   a..A,egiBm   ,L,...gVh  er Chp.nP .LaeuRWuu.nJot..e Se PDW B,.  YC  .  .K  Ynbtini,vX son vg,   L L.oq.o,ngnYC ,Cn.o,,,nZe  ..hV.sK .zh, Wug e,eah LL.e. VRW.Hc .r,,,w B ua, SioiC e.  Bng .   ,.Leh.LGQtLHH ,Z,N,W,Ju ..GW . .uL W  uioKJgo.oo .h.  oX a K 
RT  rp4nyoiomes  mnwntsstrncermtn iach on pngrcog.staelei ikcylept uaotilOu neebrdtr sN Tea  clueo
RL  .3n20aN08t (-.teG4640 1 3:4).e
RN  [2]; RE0047626.
RA  _TSNRAm.TeAFaC
RT  atwmeris.iNtr nxe e
RL  0oRACAe2St0s)p1RF10.rNe  0 T:(20Rl06
XX
//
AC  M01124
XX
ID  V$OCT4_02
XX
DT  (6e m.atr0;. 200)6c0avd.6e
DT  2ap0m0d 760.tdv0(;a).e6u. 
CO  Copyright (C), Biobase GmbH.
XX
NA  OF5tP-4c)U(O1 
XX
BF  T00651; POU5F1; Species: mouse, Mus musculus.
XX
P0      A      C      G      T
01      5      0      0      0      A
02      0      0      0      5      T
03      0      0      5      0      G
04      0      5      0      0      C
05      5      0      0      0      A
06      0      0      0      5      T
07      0      0      5      0      G
08      0      5      0      0      C
09      5      0      0      0      A
10      0      0      0      5      T
11      0      0      5      0      G
12      0      5      0      0      C
XX
CC   sEsmf- edCyhnoT rsdti tcdas caitOMttfiPa won 1he)4ai-Nvtd Cgs itiIeIoAi bo i( h[nme]ttP dflheremio 
XX
RN  [1]; RE0047531.
RX  PUBMED: 16518401.
RA    C.C.., gg.K eLu.W.urhh,V,ege KC Xue. q   W  QeLsWuuvL hgi  s   P B, .H iJ.,B. ni.   o . Hn,W.  LXB.DLY.Sat e.h ie neue.,o.oe.. .L  ,.oK ,.ou,a R,piGL zG  ow.RgK .,o , NYHoL,,hC   ntn CWnA,Si nW, ..oZ go ahr.mV.g J,V,co,b.,Ln. . uvtnBhLZanJW..a ,PeY  .
RT    an o c peetetilsois OwlNulr gerdtmitiluhptcmep cnsecunsbeaorre.kneor cntannyyiTa tsngrmo 4 o
RL  3 0.G3082a:6t4)e40N4. n1e .(t-
RN  [2]; RE0047626.
RA  FeTAm_Aa.TNCRS
RT  rweNa rtx imneis.te
RL  p)NFtR0l02:Te11oC0 A0 rs 0.e6RAS20(R
XX
//
AC  M01125
XX
ID  V$OCT4_01
XX
DT  .ce66 tea0 avm;0)r0d(.60.2
DT  1.pko)e9; 61ad2e0d.t0. (u0
CO  Copyright (C), Biobase GmbH.
XX
NA  tcU5-1O)(P O4F
XX
DE  dpl2iotciOreeoisi  ,n4 -mindiotfxctSojtc  
XX
BF  T00651; POU5F1; Species: mouse, Mus musculus.
XX
P0      A      C      G      T
01      5      0      0      0      A
02      0      0      0      5      T
03      0      0      5      0      G
04      0      5      0      0      C
05      5      0      0      0      A
06      0      0      0      5      T
07      0      0      5      0      G
08      0      5      0      0      C
09      5      0      0      0      A
10      0      0      0      5      T
11      0      0      5      0      G
12      0      5      0      0      C
XX
CC   tesinocerost cdfT  wI-)lefiirbtentPt4(heihn a]iPs -ei g h1 eoafe t dmsmadmiyiO dhrttd[ ovdaeoCtEWi s
XX
RN  [1]; RE0047531.
RX  PUBMED: 16518401.
RA  n BrnC.,  he.BY ,ViB.aKnWL     L W, hV.R Cu.Ze.LHoaD,o Cu B..J.s b  i.g ,,v... ,NnnX.geKL heH. c.ipW .PK,eH   .g, noq r Jag,oi.. Lo..aYWJo e  o,h nG ..hn ootgeXW,o Y L, u  o ,wtK  zL.e .CZ.SL, W R  n  uSV,a L,Lih.WAP,.gs.i.u,em.,e  .n.,h uGveQg,uCt . u 
RT   tceyntmb aieoT atkeioycsmoo odisa regnupln eu ONepeinit nrgtellssrmsr.wrtr c4cla ce tuh nonnp
RL  eaN3( 4842e16)G-..0t4tn3:0.  0
RN  [2]; RE0047626.
RA  _NaAeT.CFATRmS
RT  itNeasi  x.wtrrmeen
RL  NT20oSA(RCe6R00RA:s0p0F  0 .)1lr21et
XX
//
BioPerl-1.007002/t/data/transfac_pro/readme.txt000444000766000024        54013155576322 21327 0ustar00cjfieldsstaff000000000000The data here is a very cut-down version of Transfac Pro, used without permission.
However, the only thing these files represent is the file format which isn't
beleived to be copyrightable. IDs are intact, but the actual useful data is
randomised or artifically created. At the very least the usage is believed to
be 'fair' according to copyright law.
BioPerl-1.007002/t/data/transfac_pro/reference.dat000444000766000024       727113155576322 22011 0ustar00cjfieldsstaff000000000000VV  TRANSFAC REFERENCE TABLE, Release 11.1 - licensed - 2007-03-31, (C) Biobase GmbH
XX
//
AC  RE0023998
RX  PUBMED: 14988562.
RA  eb .,r.ohG.,lr ka a. e.lLf.   ,lo L  k n fdlP rotRiFpmocfl e el. u oY ,I..VeGZDrS.inl.gl ,e,T RiT,,elr,DyB . or.dHM.NrddrGJir..BOD. i,a e.z.Ee oBn R .   ANsgA,JK .G.  n r e.W,u
RT  tnissnatr pocaHlnctabp oar  gn t Naersnrdr xocvffi Fireseoynoieerpsn.elC o 
RL  .830 3(e0 n)48c2S01c:3-137i1e
FA  TRANSFAC: T08612; HNF-4alpha; taxonomic class Mammalia.
FR  TRANSFAC: FR0001534; human, Homo sapiens.
FR  TRANSFAC: FR0002267; human, Homo sapiens.
FR  TRANSFAC: FR0003841; human, Homo sapiens.
XX
//
AC  RE0047531
RX  PUBMED: 16518401.
RA  o on.gLg  WJ  eZeWQ,..n . aC,L Pt Yn.,o Yn   cqg iBu Wz.aK.onL..ogL,, .VSh,a  G,,JW.L , ..n.L.h pXi C.. u,huh hK eg..su..uoo giuh.H ,nh .,,t o  Y.vACaCgS.V,.LeG  R.ZiLn sWJ o.,ee B u, n a.rb HPKeVo,CWe,.o v i L..,rmB L.  Bu . . H eiNn DeR tX ,W w, Ke,  
RT  pe.s  ra m eTsrttt4nkenceeepgnyniowldlsmle rt aoNitng  eOa cycrip nbcmt onruoislirhseuo tauonc
RL  tn020e..t ) :G1eN04- 34.8a46(3
FA  TRANSFAC: T08800; Nanog; mouse, Mus musculus.
FA  TRANSFAC: T08969; Nanog; mouse, Mus musculus.
FR  TRANSFAC: FR0012904; mouse, Mus musculus.
FR  TRANSFAC: FR0016884; mouse, Mus musculus.
MX  TRANSFAC: M01123; Nanog.
MX  TRANSFAC: M01124; Oct-4 (POU5F1).
MX  TRANSFAC: M01125; Oct-4 (POU5F1).
XX
//
AC  RE0047775
RX  PUBMED: 16574738.
RA  ..Bet S . ,.u i rMeK ,,d. vWeWk KaS.ee.nyNk mJMMih. a, i P
RT  INDD VDGT C1AALEBEI.EIT IYIHLA6ITTE E ANV  ITSL MTRTANYE TM NISP TNBAUTPOIORSL I- NVTOD,MHIRRLINSDX TRPY NO CAELUAOA SNMMNT CED5CTH NII TERTOI2IMTVPEH3DSAI
RL  Mc (o0o.. 0n)lnir.do 2E:6l
GE  TRANSFAC: G036757; TRPV6; human, Homo sapiens.
BS  TRANSFAC: R19310;; human, Homo sapiens.
BS  TRANSFAC: R19311;; human, Homo sapiens.
BS  TRANSFAC: R19312;; human, Homo sapiens.
BS  TRANSFAC: R19313;; human, Homo sapiens.
BS  TRANSFAC: R19314;; human, Homo sapiens.
BS  TRANSFAC: R19315;; human, Homo sapiens.
BS  TRANSFAC: R19316;; human, Homo sapiens.
XX
//
AC  RE0047626
RA  _eCART.mTaANFS
RT  ixNr e r.setitnmwae
RL  ) :N0Se0R1rRs2o 0 TR010CFA6A2tp0(le.
MX  TRANSFAC: M01105; ZBRK1.
MX  TRANSFAC: M01107; RUSH-1alpha.
MX  TRANSFAC: M01108; HOXA7.
MX  TRANSFAC: M01109; SZF1-1.
MX  TRANSFAC: M01111; RBP-Jkappa.
MX  TRANSFAC: M01112; RBP-Jkappa.
MX  TRANSFAC: M01113; CACD.
MX  TRANSFAC: M01114; E2F.
MX  TRANSFAC: M01116; CLOCK:BMAL.
MX  TRANSFAC: M01117; OTX.
MX  TRANSFAC: M01118; WT1.
MX  TRANSFAC: M01119; KAISO.
MX  TRANSFAC: M01122; ZNF219.
MX  TRANSFAC: M01123; Nanog.
MX  TRANSFAC: M01124; Oct-4 (POU5F1).
MX  TRANSFAC: M01125; Oct-4 (POU5F1).
XX
//
AC  RE0047634
RX  PUBMED: 15743839.
RA  STi,rNHHKs  aa..Sd .Tdu m,,aj Kaauroo,Ho.ia. M  ,.Kk,,H u atnua   oa t aYdba..mirT TuN.et
RT  aoeNfnmusiriOorrner. tcec eqdio  aeissnxrxnooa csnmt fa eoesgir el eogltrdatipnanreete rla   ngpSu
RL  0404eC2:8Ml55. l52()25.o i7ll o. 2-.B
FA  TRANSFAC: T08800; Nanog; mouse, Mus musculus.
GE  TRANSFAC: G031512; Nanog; mouse, Mus musculus.
BS  TRANSFAC: R19260; Nanog (Nanog homeobox); mouse, Mus musculus.
BS  TRANSFAC: R19510; Nanog (Nanog homeobox); mouse, Mus musculus.
XX
//
AC  RE0047637
RX  PUBMED: 12787504.
RA  h  .KeyMarKa  mk.sYiia . ,MHMtMa.aSnzaw,a kaghTakum ,a..oIwd. MMuTaia,  ua ,i,hra.ama, t eaMu   oYS,.akKs
RT  Smoeitnt T  els iresde  irnoeqcofEgp dm aeuriasho n  hycaasr.onoilenbilicrunnlnemt tNo epfepape uo
RL  33 02l102 -1.l(C136):46e
FA  TRANSFAC: T08800; Nanog; mouse, Mus musculus.
XX
//
AC  RE0047645
RX  PUBMED: 12787505.
RA  S.eRedtbt i..,Mhb, lowmCnh .iTLro. eD ,S,AsmicC., h   ylbIseo, Naees . roJ Se
RT  ioei.N fclFoilsngers aeu ypoern  aesinsxen nprcostmottiolc n cc p,llymt nuigau tofacnb niinagsorn
RL  536:34.3-260051()1 el Cl
FA  TRANSFAC: T08800; Nanog; mouse, Mus musculus.
XX
//
BioPerl-1.007002/t/data/transfac_pro/site.dat000444000766000024      5130013155576322 21027 0ustar00cjfieldsstaff000000000000VV  TRANSFAC SITE TABLE, Release 11.1 - licensed - 2007-03-31, (C) Biobase GmbH
XX
//
AC  R00001
XX
ID  HS$IFI616_01
XX
DT  0r0d.c)i(e.;t1a 90ee 9w.26
DT  0vpd12.am1)t(ua d1;.1.0 2e
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  IFI-6-16 (interferon-induced gene 6-16); Gene: G000176.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
SQ  aGAGACATAAGTgA.
XX
EL  SEIR
XX
SF  -172
ST  -98
XX
BF  T00428; ISGF-3; Quality: 6; Species: human, Homo sapiens.
XX
MX  M00972; V$IRF_Q6_01
XX
SO   lNa3sl;IBro00hFtaB -p+8.i8
SO  .0i;uDa01d6 
SO  -p1 lah eH .;N0I1a+F0aL
SO  .80H1 ;0FF
SO  u .Ci L0D0M8;d+3a 
XX
MM  onerl aorithptre/ogopinephcpinnntf
MM  ia fhrittecoynerneneetl
MM  rtdinarotleae g
MM  atittne meiernorhefcneyl
MM  aolmtnocptheoir ettnyi
XX
CC  -rro  iaFiobnsirFntpFeidutkIamhtn fseh s)lfu abtwHhfaol ina( cN
XX
DR  (N6:E.L:HNI 9 0BI0);0242YS8 558MF
DR  H 9P7_SNP.202IDIE:;E0 
DR   9HS9TRA__1SN:.1OAP6R
DR  26 _OTRRA.H:9SA1_NSP9
XX
RN  [1]; RE0002135.
RX  PUBMED: 1707163.
RA  boyuhB.,CRe  l .eL
RT  ean Atfhttn cn otnrpinrpatteanescnmif ertlor-f ni ioteeDt:voaa  emieNoseo rrnto-orite ipAoeroHn rpDe lmosNs
RL  R ie11.is9171Ne l:9A.c 9 )udsc5(c
RN  [2]; RE0001119.
RX  PUBMED: 2243138.
RA   ,jS. R.AaS, d,nnDoo. ZtD ,nM,MBt eiarrars m. g i.  J ,epoh.Tsat eEis .oaz.wnColKne , J. Hir s,. SO aH.ee.Hhtesr
RT  avl tpbciemennioshhsni ainecotcdao nrdcmris  onitgvlilape intasnl trc ppnodslitneerioduip aosdailiieonayelt riemro caaaotytp oeglsabisunkh rsecep dytrn nuog bhcnnfut- nes reteeme   teifp ll o nrlhe obu etlimornleua efrrsiA
RL  9 .1...148 Jt6v -Iei6(s097C1n60l 6):n
RN  [3]; RE0002131.
RX  PUBMED: 2123539.
RA  ..k lM e.I . Mi  , l I A, ...rm.c amtKTDS,GeA. Rr  kM .ararAl.,AC
RT  a redupr ren ooicisrdalnapnem nTasnbmincyst trhcdia aotfag f
RL  )R8.0. d1 A9s39ucec8N:50ii-(e6s6 15l7 c
RN  [4]; RE0000307.
RX  PUBMED: 2721502.
RA  J.rewl ..rG,Rae.s S. .AR Rtr oMDKnt a roe..eMe,u ,e.r. M  n.LGIAkP .C i  ,, J   .iGl,lCT  ..
RT  nstoniie  corens-evne iitstafpo DalmdvOtpoiuvtei lAsca d ariticlribnd rn dNtrpida ivgerctuntentnoiufinrsndfs nego 
RL  91EO3)1.8  :99(3M. J-88B8
RN  [5]; RE0002261.
RX  PUBMED: 2919169.
RA    .I..R .K.r,.etlCma.  rMkMaDe SI.raA, m G T,  
RT  epeanpncotRbemraioDenoiiiepeat  pytga Afe tdar a t fr l ennnvapsyniric d tt lsbatdl etloraoon ftt.lh hiNnusci e-n
RL  c.o2.2l8 c1038 .P:9S6. () irNd .1S a79Aa0-AU1ct
RN  [6]; RE0000306.
RX  PUBMED: 3359997.
RA  h ew r C A G lY ICtro.ib . .GkaMeo .rarGj,a.STe.ie,.s,k  K,. ..r,rCR.l.tCre PDtS n  
RT  n rmol6eenI 6tepgentf eneouftnea-e mn e hsshr1o re
RL  -8E1)9.9B .:M7 58(JO2 8
XX
//
AC  R00019
XX
ID  MOUSE$ACRD_02
XX
DT  ceeei0w 2a0()906.91r.d ;.t
DT  1di;7. wad191)ut 9epe(.12.
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  AChR delta (acetylcholine receptor, delta-subunit); Gene: G000457.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; rodentia; myomorpha; muridae; murinae
XX
SQ  gccgcATGCATGCATGCtttaagc.
XX
EL  E1
XX
SF  -92
ST  1-5
XX
BF  T01786; E12; Quality: 6; Species: human, Homo sapiens.
BF  T01788; E47; Quality: 6; Species: human, Homo sapiens.
BF  T00526; MyoD; Quality: 6; Species: human, Homo sapiens.
BF  T00528; myogenin; Quality: 6; Species: human, Homo sapiens.
XX
MX  M00693; V$E12_Q6
MX  M00804; V$E2A_Q2
MX  M00973; V$E2A_Q6
MX  M01034; V$EBOX_Q6_01
MX  M00929; V$MYOD_Q6_01
MX  M00712; V$MYOGENIN_Q6
XX
SO  2C4sa. s2b0mt0y; lo
SO  mrec3- )l0oi.;Eocu(03.se
SO  oyt 8u0se3C;b7m.2 
XX
MM  elih esfrgtti dc
MM  olht rteyeicternnniefea
MM  n cnynastlfoaausiil
MM   teigrntraoaedl
MM  tlhntotfnme reeciraieyen
XX
CC  4th]iiMrd m tna oo  gobE1a  s  hr1te[weyehiiodnsni7erd E2enDmey r
XX
DR  8HARE )B: 6M4:M6L6.(481A137 M33MCD;
DR  :169 C385BRLHM71:1M3M4 3 (AX9.E;)
DR  _3RP.S1N1U_77TA RM2:OM
DR  _PSM.1URM_O8AN7 2TR6:
DR  P:2TO_278RN U.MS_6ARM
XX
RN  [1]; RE0005844.
RX  PUBMED: 8355673.
RA  M neu.SSA.JnrBo.mid ,  . 
RT  at son seiaecdv eu fticgetorsleos tnsnn e-x rcadnidehinghEtiu tAandtsoganly pee  bm lieni aryiorbpeecouetro me
RL  31.ei13o551)91l -(3:34.loll..9 C0M B 
RN  [2]; RE0001768.
RX  PUBMED: 2797207.
RA   ,d.J..wn .BSu TJieaBn lr d
RT  -tlcepmubn ae ancigt neMkeerii nnciir gns-se f perooooelee ydcDed bss1ia ogatcsgllMrlxyti nluey
RL  r2 t u9416e8(3)7109.1-Na:7
XX
//
AC  R00850
XX
ID  MOUSE$IGH_16
XX
DT  w .69)i01e.0e(2 ar.;dte9c0
DT  . de)et1(i60u 05p9d7.;aw9.
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  IgH (immunoglobulin heavy chain); Gene: G000537.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; rodentia; myomorpha; muridae; murinae
XX
SQ  ATGCATGCATGC.
XX
EL  n,mEurhee nca2
XX
SF  378
ST  913
XX
BF  T00207; E47; Quality: 6; Species: human, Homo sapiens.
BF  T09514; HTF4gamma; Quality: 2; Species: human, Homo sapiens.
BF  T00406; INSAF; Quality: 6; Species: hamster, Cricetulus sp.
BF  T00526; MyoD; Quality: 6; Species: human, Homo sapiens.
BF  T08853; myogenin; Quality: 2; Species: human, Homo sapiens.
BF  T01799; Tal-1; Quality: 6; Species: human, Homo sapiens.
BF  T01800; Tal-1; Quality: 6; Species: chick, Gallus gallus.
BF  T00790; Tal1-PP42; Quality: 6; Species: human, Homo sapiens.
XX
MX  M00698; V$HEB_Q6
MX  M00712; V$MYOGENIN_Q6
MX  M00993; V$TAL1_Q6
XX
SO   I3;N0H30T0-3.
SO  JA630 B.;-B0
SO  .0ae00 HL;1
SO  ; 16S1940.8
SO  Ucl 462;2 3.0
SO  .; 42EJ40
SO  2;0 523.4D
SO  h (.r0uty3calms)n;r ee3-2
SO  me.r6;y(ls3ec0r )o- 2tseu
SO  ais6r);oec0a7.oe-Eu6-b.m (dllcm
XX
MM  iechte  sfdlrgit
MM   ott IieaspnrofNiDgn
MM  itoo yep a/ioincgnmoct nervtih olinmvet 
XX
RN  [1]; RE0003087.
RX  PUBMED: 1312219.
RA   ns.H. R ul.o Kt,E.,.i sSE NO-gnon .J
RT  2 odanoendarEaibsit t h g oi aeucu-ameoF2x p e hirtHgct ci eNo yfdr,igdaoatml tt Tt relAtlEB-n rfleax-oiolyt honDhIpnyabeeiAln l
RL  oi4(102eM139.10:.l1 ol9-l12.C lB  )2.
RN  [2]; RE0001629.
RX  PUBMED: 2038315.
RA    - CeaC .Js,u nH..nQ- e,B.hh.gTLerH ,.R
RT  -eog ni2oxe pn tlo Ecs1o/xlton nnrci--aii hhlon eraottievpwi4ey afiithnastE1 d 7e tnh isEhl-tiitbocnoihperac
RL  92lli..1M7Bo llo34C031:1-0 () 91.3e. 
RN  [3]; RE0001447.
RX  PUBMED: 2111447.
RA  .rMmBtinaD me.AnL ore, e .oadL b r.a,Tnli
RT  no ohporanillbec circG evvdplpIEne aeheil-mm oem hnyhamoIief   s ecn naeEniuSlRs onynatoeeiet fCgLnHtnugSxedvooin fti-uEmn
RL  0l092  -5.i6.1.1:oleB3 93Col1M)1. (5l
RN  [4]; RE0001998.
RX  PUBMED: 2181401.
RA   ,C okenoW. M.AW  e lrPiha,Rr.A., D.nA  smrek.a
RT   iootca ootfsrtbct aelmtip cieeAiico aacnNu   henmtoisua e grApaerr nn  n vgflniDnpttuaescra fnl ecde
RL  5-1 cdcs i 1ecl(e9 A811.N.1u9:Ri60s)691
RN  [5]; RE0002608.
RX  PUBMED: 3917574.
RA   gr Gw,huaS EtChoee.niplriMG . c.auhAbsW r.,.T ,s 
RT  meuFunoepictoe iinI runo-n nnofsgmncei Iw a eCb ncoiSnVErliaflctt hre oLlaai lrhcg lvaaiBt
RL  (n1)2Sc4 8 0e-71c932i5.:e41
XX
//
AC  R02116
XX
ID  AAF$CONS
XX
DT  (1sr9 tF)de c4;1ee2.0aiaMs.r9ty.e1/
DT  0 ddb5od 19.p.t(.1)3e6a9u;
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  consensus.
XX
SQ  ACCTTTATTTTTCA.
XX
BF  T00001; AAF; Quality: 6; Species: human, Homo sapiens.
XX
RN  [1]; RE0000446.
RX  PUBMED: 1901265.
RA  . ri Dk.Tn   l.l,.w cEer,DhoLr M.DJiJweeJc.ta  k,e
RT  iNtm ctcFynt,o ad-r GF-Csagrcmiatfl D-moaNgAtieinaIidnua vAebalag on ofp
RL   MO9.JB21920-:3 E1(.99 )71
XX
//
AC  R02418
XX
ID  HS$MLC_01
XX
DT  9(1;0 e2ctd1.)2 1.wie.aer9
DT  2pe.;maua .v00d.d007 6t8)(
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  MLC (myosin light chain 1/3 locus); Gene: G000347.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
SQ  ATGCATGCATGC.
XX
EL  hc r'aen3en
XX
SF  214
ST  142
XX
BF  T10006; Myf-5; Quality: 2; Species: human, Homo sapiens.
BF  T00522; Myf-6; Quality: 2; Species: human, Homo sapiens.
BF  T00526; MyoD; Quality: 2; Species: human, Homo sapiens.
BF  T09197; MyoD; Quality: 2; Species: human, Homo sapiens.
BF  T00520; Myogenin; Quality: 2; Species: human, Homo sapiens.
XX
SO  3Ece)mrsc0. lei0(-;o.3uo
SO  E(m36ich;unre.0co0-. a)l
XX
MM  lat ogrreditean
MM   eraeettcltfioynreihmnne
XX
CC  4osydfnn]ogb gydfM3 k tta,i,by- Mb Muy  nnrfiy  1-n -nfMetiow6g  l,o-ti[5
XX
RN  [1]; RE0002118.
RX  PUBMED: 2243772.
RA  r,be.Bhl oueu tMe noBtBr.eH h  nrrg,Ee-w o, ol M.o.un,eidaarNWA.EgdWtn s  Bht .B R,,lHTn.nn . r.B. Do.,
RT  fiasnndt ityuseome ceen rr eth wh1enor3aredtico rlh ln e eom/sgeolc soyr adenoiicgsC mta n gr  maovttfimatuhcLp ahMAfnul
RL  91e1dR2cA98036 N. .ies 9uicl (c:)s
XX
//
AC  R02419
XX
ID  HS$MLC_02
XX
DT   tea2.)w1ce0(.i12de91;.9r 
DT  2) 8.uapm0d; 06(0ea7.d.0vt
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  MLC (myosin light chain 1/3 locus); Gene: G000347.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
SQ  ATGCATGCATGCATGCATGC.
XX
S1  within conserved region
SF  527
ST  030
XX
BF  T10006; Myf-5; Quality: 2; Species: human, Homo sapiens.
BF  T00526; MyoD; Quality: 2; Species: human, Homo sapiens.
BF  T09197; MyoD; Quality: 2; Species: human, Homo sapiens.
BF  T00520; Myogenin; Quality: 2; Species: human, Homo sapiens.
XX
SO  .o3u)(;i0E3msole-re c.0c
SO  E0ce03cai(hr )6;mn.l-u.o
XX
MM  oattgaedierrl n
MM  hre niertiatnemfoyelntec
XX
CC  n) tndiknbfse[6ffn to  Marly n1,-   wa] edn y3o  rybktMg u- nnto 4bei-y oMiag(wvo5Mgd-dat fyyi
XX
RN  [1]; RE0002118.
RX  PUBMED: 2243772.
RA   ,a r ,gt .D. e,baMBHBlWhnweuR. .dN-EH rrBsn  , r.Brtot,e,eEg .ltTooihnl oe,Mn  dhAB B eorWoun.....nun 
RT  impidcLosdn crM uan inym o3helaug eec  hAt re nmint vmieh o rineutos tawllsorcag/yare1ftdhah clse trCfanort neso mogtfee
RL  9l 8AidNss.i(1  6c.9)Ru 9c1c2:30ee
XX
//
AC  R02452
XX
ID  HS$AAC_20
XX
DT  2)911re.ede(.1.tc9iwa 2 ;3
DT  0d.itued26)(1 ;.a003n6 dp.
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  ACTC (actin, alpha, cardiac muscle); Gene: G000193.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
RE  promoter
XX
SQ  ATGCATGCATGC.
XX
EL  xoE-b
XX
SF  -65
ST  -49
XX
BF  T00526; MyoD; Quality: 6; Species: human, Homo sapiens.
BF  T06361; MyoD:E12; Quality: 1; Species: human, Homo sapiens.
BF  T00528; myogenin; Quality: 3; Species: human, Homo sapiens.
XX
MX  M00804; V$E2A_Q2
MX  M00973; V$E2A_Q6
MX  M01034; V$EBOX_Q6_01
MX  M00929; V$MYOD_Q6_01
XX
SO   2;C. 2mabs0sy0tl4o
SO  23C120.04; C
SO  c3ml.o()ir03cEe-0;eo s.u
SO  h ci60are.ouE-c3m(n0.)l;
XX
MM  asyinncalnfoaul tsi
MM   adittloergraen
MM  ottelhmfeigip i cnost
MM  eiheeeon nrtcifeayttnlrm
MM  npfiti(dgnbsiie)o tnsab uhryd
XX
CC   Demnsym trsaedo lysp0re  icta ap eftnct4phi-u0iet aStufyioqreuMsnsaa cl-ap  scal0nc>fielhr ss2osccfo Ritnco[0unc 1m   oono tu  ob h lie 1doedg ctelituoRcinta]h fnipaerh6nrpi- inetw,rpsa1aRmglcaits  ei<,secucfcvoiSaoF2 d7e le
XX
DR  ; 3HM)27.8(E4:ATC48  41BM3SA:C3L
DR  6T3;SP:E 0P1. CHE3C_DA
DR  1SNO8_:10STP7ARAH. R
XX
RN  [1]; RE0025127.
RX  PUBMED: 10082523.
RA  sl,iHB aea.ias arE r KmV,id.,Y. oto mSe.ilre aeLd
RT  ltosol mesdahpro  thattmpreSlnal-syc aioeipopaagcnountni iepfsdcieni hm  nciova etx -nulmyh ica  cqicle coMpmoteix oebao .1rtnr intrtroniciaterhsnfaauxpprfil ad eaet  p-rticrr oo
RL  lC5)o  .8. ol:.5.9l l79(49217Bi9-eM21
RN  [2]; RE0000718.
RX  PUBMED: 2123467.
RA    . .,bKK.oltlteaL r,sV.SWei  sederrAe
RT  ecMsaiie gpuGeisaci-onc csn haDqybp1adrbtc ot-ea rrMCren1onceputl- e  cidsixaeo  reg irhafn,i osfxSlfAn,p d
RL  .:18 e9.9DG)21v 81e1ne(420s-1 
XX
//
AC  R03064
XX
ID  HS$GBP_02
XX
DT  e91r).ai;9. e (d23ct10w.e5
DT  a1 wi.1u).15htid(199d1p. e;
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  GBP (guanylate-binding protein); Gene: G000264.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
SQ  tatcttatagtCTTTTATCTCAATTaaaccc.
XX
EL  GAS
XX
SF  -821
ST  -99
XX
BF  T00001; AAF; Quality: 6; Species: human, Homo sapiens.
BF  T00300; GAF; Quality: 6; Species: human, Homo sapiens.
XX
SO  I;e LlhF.- N0+10p1aHaa 
SO  .g5m;H+-  FNaaILme0a4 0
SO  Ia6+ .4 m-a 0S;2FN0gmF
SO  - Fs7d4 boat ;fN+ lapd0lsbaioh0iplrI.i
XX
MM   diutnaseeecessloxg
XX
RN  [1]; RE0000446.
RX  PUBMED: 1901265.
RA  aD.r er ETc J i.Jw.  l,eiokce.D.e.n, L lk rwhMtJD,
RT  Aa-n,ot  FslFctgdo-mvCadioaaD mfnuoaeefGt ANagnaapi iirtymlntcg IrN b-ic
RL  -E 917.1.MB12 (2O0J 39)99:
RN  [2]; RE0001471.
RX  PUBMED: 1833631.
RA   EJeeD  wJD. L.n, ae .T rDe.k.,clrl
RT  ttihnonbeg-ifnitoeyaa il ritngtolr sb-t slarci w foa e nasiphotahc dnva deoe enntinponpn-nsaodeietapinrndncafrpo tteusgtuaoctiwtrTti e ruyagce imn dtynt
RL  olC541-19l.o17.5e Bl5.1:1M 9)l ( .31i
XX
//
AC  R03174
XX
ID  AAV$P5_01
XX
DT  d)4art.9  3c0w9e6.;ie1.e(1
DT    89(dpr9ard.1e8.1da.u;t2ee0)
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  P5; Gene: G000001.
XX
OS  AAV, adeno-associated virus
OC  viridae; ss-DNA nonenveloped viruses; parvoviridae; dependovirus
XX
SQ  CAGACGCTCTGTTGTACTGTAT.
XX
SF  6-0
XX
BF  T00915; YY1; Quality: 2; Species: human, Homo sapiens.
XX
MX  M00793; V$YY1_Q6
MX  M01035; V$YY1_Q6_02
XX
SO  .0aHe100L ;
SO  acu);(ire.cn0-El0mh. 36o
SO  77 P;-0Y.S82
XX
MM  rdhf ilgstcti ee
MM  otNngpIiis enrt aofD
MM  cetfi ohntlip iogemts
MM  reymreinienn leatfteothc
XX
CC   ian1idi2k]s w[[ebnet  g]
XX
DR  19X01212. J270: ;: B3M)6(ELX
DR   VAE1AP D:2.N7;6V2P0C_AE
XX
RN  [1]; RE0006609.
RX  PUBMED: 8413258.
RA  oSo,y.twio    My.rKHtmh.C a,cro. aK.enAkh.C   P,asLt
RT  i1  nttiit srpneaspiw Aftinpocarspottc telrcterersfasYYani mt  cvctltpe etetpoaitmeocif s  oeninlYrfop stnteDa aticN iremrhoi aclrecYurr  rrnoteA: ledtT tne aetahcoiot-smnn1i
RL  33) ll.l661:9le96(B6C.-. . iM1 1oo228
RN  [2]; RE0000230.
RX  PUBMED: 1655281.
RA  SSnS,e.hat,ko .,L .-nhgC S  YheT. . Ei
RT  ena fy1laYoso rltneesI-  sroo imn,anr rrp dpphnGcK e ALdrlobYriaen pfrearivpe ntl e -asnnrbi,irpieosydeuaou1 ireeutEse itTp
RL  98e363-: 77l19(Cl. )871
XX
//
AC  R19310
XX
ID  HS$TRPV6_01
XX
DT  r  ..6d2e0c;0.2h540()ateec
DT  0d0;.(a6 upt 3)ee0c25hd..0
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  Gene: G036757.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
RE  distal promoter region
XX
SQ  aGTCTAGGGCATAga.
XX
EL  V.DER-55 
XX
SF  85-05
ST  445-9
XX
BF  T08716; VDR:RXR-alpha; Quality: 3; Species: human, Homo sapiens.
XX
SO  c ;32aC.o92-0
SO  amei-20tn(bah.r1c;u)ac 6re
SO  0.S2010;38L 
XX
MM  poeiinnaioctmhm)apuoPcC mhIirrt(ni t
MM  stgh rfeltdeiic 
MM  syalc uiflnatoasnin
MM  hegtipicsofimeo tltn 
XX
DR  6MA3422-9215).-1:A( 6:;Y 57Y45B55L912 E
DR  AS OH:P_T7A3S4.R8_NR1
DR  RA44ST81SOH7. P_NR:_A
XX
RN  [1]; RE0047775.
RX  PUBMED: 16574738.
RA   te.k.. .,PiuKB.a e.NM e,raS. W, eJ ,dW Mym inMKvk   eSi.h
RT   NINCTRE2AIML  IT6CYIREHT TP ONA  TTMTIDOLIEANGVTIIMIENLPUPLH1SUN ABR SHTTEVEIXOPNMVTDORY N,ENRIM RA5S .ADI-T  AIOBAOTTETASDIIY EVSLTDET ICC NL3MS INDD A H
RL  M.lnoE.6 :).n20(lodcor0 i 
XX
//
AC  R19311
XX
ID  HS$TRPV6_02
XX
DT  c5a.0dr)e0ee2.5;(0.2 c th6
DT  t. h;52d)06.dp00 ac.(u30ee
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  Gene: G036757.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
RE  distal promoter region
XX
SQ  TACCCAGAGTAGCGT.
XX
EL   .a43DRVE-
XX
SF  37-34
ST  23-43
XX
BF  T08716; VDR:RXR-alpha; Quality: 3; Species: human, Homo sapiens.
XX
SO  C2;a90 .o-2c3
SO  -cic )m2(0thbeeau1rr;6a.an
SO  0S; 0L38210.
XX
MM  mtih(m)onntpcei irroPiIupotChcianm a
MM  di etisfertgch l
MM  tasfisnuanlnycolai 
MM  itihnoe tcteiosm fglp
XX
DR  E5YA42067121511:1AY4:  7L262.;M ()27B
DR  .R3A_ PR_TO718HS:A4SN
DR  8:RR_T.SO_47NSH 1P4AA
XX
RN  [1]; RE0047775.
RX  PUBMED: 16574738.
RA   Ji,NBm y .,iSekM.h.K  , i  tM. ...kee,aue WMvWdKrSe .aP n
RT  TIAPT.A3IIERA-YIO HEUACHLIMTES2NATMS  XR TADPTEDOL N N OETTN1HNESM IIPT MRV S6NIIAPA5NSCTLVDIS CTGRA BOTMIDE OVNYRIDBDTL  INL INMDCEA,HYLTT  IRTEENT UVI IO
RL  )0Mro ll:.ooiE  nnc6.2(.0d
XX
//
AC  R19312
XX
ID  HS$TRPV6_03
XX
DT  c5at( 6e).0crd;0. 05h2ee2.
DT  2d0da;65 (ec0..u03e0 h)t.p
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  Gene: G036757.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
RE  distal promoter region
XX
SQ  gyGACTAGGGGAGTg.
XX
EL  R.EDb 4-3V
XX
SF  4-287
ST  327-4
XX
BF  T08716; VDR:RXR-alpha; Quality: 3; Species: human, Homo sapiens.
XX
SO  .o0-C23 9ca;2
SO  6 rmr)n(.1baahcut;ei-c02ae
SO  810LS 032;.0
XX
MM  moci)mrmipoti tipPaa(tCorhhIi necunn
MM  esli htfti grdce
MM  cyl usaoalfniatisnn
MM  itispftcto lei megonh
XX
DR  6)EY-2 2512114LAB(5.718 7265-472:MY ;A:
DR  _8P4 .7TSORS31R:A_AHN
DR  :H SAR74_AN.R_S81P4TO
XX
RN  [1]; RE0047775.
RX  PUBMED: 16574738.
RA    MeW.Nd., Bv ie, .MKSri.  ,mu. ,WeMJ yPeate.S  ai Khkn.k.
RT  DGNLLXNDC HOE2TU YTO3 I5VOCORNN  IIADN EPI AEIVYES TRSTLUATSTCI HEDP ITDA VIADT MTTI,R MT-T CTTE IOHBIAINLVM INILNETMISTSPLA.E EYMRSNINA REA 1RANOTMIBPH6D 
RL   .lno:0..0oMiE2rl  onc(d6)
XX
//
AC  R19313
XX
ID  HS$TRPV6_04
XX
DT   0 5002t(ea2h5..c6cree)d;.
DT  d.t; 0)3h.u20.ac(6ee 5dp00
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  Gene: G036757.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
RE  distal promoter region
XX
SQ  gagGCGAAGGGGTCA.
XX
EL   5.3-VERD
XX
SF  3591-
ST  5530-
XX
BF  T08716; VDR:RXR-alpha; Quality: 3; Species: human, Homo sapiens.
XX
SO  90;Ca o3c.-22
SO  uretea2r).i b(acha-601mc;n
SO  L 38;0S1200.
XX
MM  riiam pt(paPCrtmhnucm)iihetncoo Inoi
MM  scftdt rii geehl
MM  cssiayn iaafnlunlot
MM  ehfoemsptitcitnogli  
XX
DR  7;-1L .2-425 64Y:AM21E8224Y79 9)B:A65(2
DR  APR TNO4:_H3_1SRA.S87
DR  4R_S:ST.AA71 ON8PRH4_
XX
RN  [1]; RE0047775.
RX  PUBMED: 16574738.
RA   ,K Mer  SuyW.eedi M., m., kiP h eti ...BakK.M aeJv.,NS Wn
RT   RAL5RT NIA1PVIMATBDSEE P-HIAR.SUTERDHIN T   IO,L IPATNNITNTCMSTNTSCRINDATDMIN6 IL  YRTATO HTID E NO UVVLD BNM  GXHOIDLEO TV TTEI32PMLEAYCIMAEASOSCEITINIYE
RL  or.0 n.n.ol lE(0 :Mdio62)c
XX
//
AC  R19314
XX
ID  HS$TRPV6_05
XX
DT  t 05)d;r.0c. h.ee5ea2c2(06
DT  .hp ;c0e.)d0e3t00d2(5u .a6
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  Gene: G036757.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
RE  distal promoter region
XX
SQ  GTTTTGAGGCGACGT.
XX
EL  21.DER -Va
XX
SF  619-2
ST  52-15
XX
BF  T08716; VDR:RXR-alpha; Quality: 3; Species: human, Homo sapiens.
XX
SO  2; c-0C.93oa2
SO   cie;rbm1ac6n-r0ha.e2u(ta)
SO  0L0;2.1S83 0
XX
MM  pcoitmtuinaho)nChreItriomnc (imiaP p
MM  eridf ts getlihc
MM  acsntanulyfl inisoa
MM  iefh ntmeltioispgo tc
XX
DR  462Y9A7 22:M42515B).;A:12 Y762 1LE99(
DR  S_RA:8S1_HANP73T. 4OR
DR  47.8HST_AAR4:P_ NSO1R
XX
RN  [1]; RE0047775.
RX  PUBMED: 16574738.
RA  v  i,,MNk JmW Syan.at.,e PSe. Wh. uKKreB    dMi,e .Mei..k.
RT  I DXNNVNLT3 DT RSOYBLRNTUANSE ITETIITM  SRMN1SNRTMAILVI PDIMIETEETLP2Y.T IS HAIRIRVCA EHCTTVEAPONN TTIOD NA 5HUHD  NCTOLE DIEAL6IMIAGTPDY AO MS ,TCBIO IAE-
RL  :lE.c.iono 06.o0 rM) n(ld2
XX
//
AC  R19315
XX
ID  HS$TRPV6_06
XX
DT  5de.(2 c )a.0eer5;c0t2h.60
DT  te0.0ap( 2 h;05e0.3d.c)ud6
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  Gene: G036757.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
RE  distal promoter region
XX
SQ  CCCCATGCCCGACAA.
XX
EL  b-D2VR 1.E
XX
SF  -1912
ST  20-15
XX
BF  T08716; VDR:RXR-alpha; Quality: 3; Species: human, Homo sapiens.
XX
SO  3cC0.ao2 92-;
SO  6riearmah)10e(;a2ccbutn.- 
SO  01;8L30 2.S0
XX
MM  (cnoCrPnmtociihm oaiah pipruIitm)net
MM  eiscrgh l fttide
MM  ifnsaslncunaa otyil
MM  fititepo nhce oigltsm
XX
DR  346E9A21.61Y:2A5;B9 43:2 4Y5(2 M721)L
DR  R _R.AO7N8AP:1TS3_4HS
DR  8RS_ O1.THP:4RS4AN_A7
XX
RN  [1]; RE0047775.
RX  PUBMED: 16574738.
RA  u,nek,.mW ,e PMJedre  viKM.a. tBWh .M S N. kSi ae .y Ki,..
RT  APITALNI  SSI I3 TOTONMA6YAUT1OT2 IAS  H AADNR IVDVTNOPNTRYILT IVIMVRDC PCLDXTAEDAIT-BR M E5CNLSCBS,INEDOTITHS TIINGNRHEHEI.PTODIY T RLIN ENEUM EATM TME EL
RL  Er0l:o.n )i.ldM6o02con(  .
XX
//
AC  R19316
XX
ID  HS$TRPV6_07
XX
DT  2)(00eh5t ;e5cr0cd.2.ae. 6
DT  a 3)p.5 cde062d.(00.0te;hu
CO  Copyright (C), Biobase GmbH.
XX
TY  DNA
XX
DE  Gene: G036757.
XX
OS  human, Homo sapiens
OC  eukaryota; animalia; metazoa; chordata; vertebrata; tetrapoda; mammalia; eutheria; primates
XX
RE  distal promoter region
XX
SQ  ttTCAGATGACTGAt.
XX
EL  E2-V.R 1D
XX
SF  -3821
ST  12-96
XX
BF  T08716; VDR:RXR-alpha; Quality: 3; Species: human, Homo sapiens.
XX
SO  co;9-3 22aC.0
SO  ;cmrn a-(u1.0ea6c2t)bheiar
SO  0S02 10.;38L
XX
MM  (miaiorcp ImiuiitnantChohP rm)tocpne
MM  hlger ficitsetd 
MM  nini yasnasalocltfu
MM  gtihe tpeftn cmisooli
XX
DR  :A416Y41E02B( A12Y502.2;:8 61-41 LM)715-6
DR  _RA3A1S8 TH7_RPSN.O:4
DR  _P4.H T8A:A1R_S4S7RNO
XX
RN  [1]; RE0047775.
RX  PUBMED: 16574738.
RA  mn.KWie WeS.  a,M Nt,a ,K.d  B.e.uP.r ,MkkiheJ . My S v.ei
RT  IMTICNTDL PHIC LHBLIA OMT 6  EN  TAIEV NTS  E25NMT1LMISPGEVTADAIIXEAN REEAATIMNITIV P NRE ISD EO ISIO,TNORDADECO YTYONVBYT.SRRDIPURNTLLCNAMIDTAUTHH I -T3TS
RL  E.rlond o(nilo):  M.20.c60
XX
//
BioPerl-1.007002/t/lib000755000766000024          013155576322 14371 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/t/lib/Error.pm000444000766000024      4126313155576322 16203 0ustar00cjfieldsstaff000000000000# Error.pm
#
# Copyright (c) 1997-8 Graham Barr . All rights reserved.
# This program is free software; you can redistribute it and/or
# modify it under the same terms as Perl itself.
#
# Based on my original Error.pm, and Exceptions.pm by Peter Seibel
#  and adapted by Jesse Glick .
#
# but modified ***significantly***

package Error;

use strict;
use 5.004;

use overload (
	'""'	   =>	'stringify',
	'0+'	   =>	'value',
	'bool'     =>	sub { return 1; },
	'fallback' =>	1
);

$Error::Depth = 0;	# Depth to pass to caller()
$Error::Debug = 0;	# Generate verbose stack traces
@Error::STACK = ();	# Clause stack for try
$Error::THROWN = undef;	# last error thrown, a workaround until die $ref works

my $LAST;		# Last error created
my %ERROR;		# Last error associated with package

# Exported subs are defined in Error::subs

sub import {
    shift;
    local $Exporter::ExportLevel = $Exporter::ExportLevel + 1;
    Error::subs->import(@_);
}

# I really want to use last for the name of this method, but it is a keyword
# which prevent the syntax  last Error

sub prior {
    shift; # ignore

    return $LAST unless @_;

    my $pkg = shift;
    return exists $ERROR{$pkg} ? $ERROR{$pkg} : undef
	unless ref($pkg);

    my $obj = $pkg;
    my $err = undef;
    if($obj->isa('HASH')) {
	$err = $obj->{'__Error__'}
	    if exists $obj->{'__Error__'};
    }
    elsif($obj->isa('GLOB')) {
	$err = ${*$obj}{'__Error__'}
	    if exists ${*$obj}{'__Error__'};
    }

    $err;
}

# Return as much information as possible about where the error
# happened. The -stacktrace element only exists if $Error::DEBUG
# was set when the error was created

sub stacktrace {
    my $self = shift;

    return $self->{'-stacktrace'}
	if exists $self->{'-stacktrace'};

    my $text = exists $self->{'-text'} ? $self->{'-text'} : "Died";

    $text .= sprintf(" at %s line %d.\n", $self->file, $self->line)
	unless($text =~ /\n$/s);

    $text;
}

# Allow error propagation, ie
#
# $ber->encode(...) or
#    return Error->prior($ber)->associate($ldap);

sub associate {
    my $err = shift;
    my $obj = shift;

    return unless ref($obj);

    if($obj->isa('HASH')) {
	$obj->{'__Error__'} = $err;
    }
    elsif($obj->isa('GLOB')) {
	${*$obj}{'__Error__'} = $err;
    }
    $obj = ref($obj);
    $ERROR{ ref($obj) } = $err;

    return;
}

sub new {
    my $self = shift;
    my($pkg,$file,$line) = caller($Error::Depth);

    my $err = bless {
	'-package' => $pkg,
	'-file'    => $file,
	'-line'    => $line,
	@_
    }, $self;

    $err->associate($err->{'-object'})
	if(exists $err->{'-object'});

    # To always create a stacktrace would be very inefficient, so
    # we only do it if $Error::Debug is set

    if($Error::Debug) {
	require Carp;
	local $Carp::CarpLevel = $Error::Depth;
	my $text = defined($err->{'-text'}) ? $err->{'-text'} : "Error";
	my $trace = Carp::longmess($text);
	# Remove try calls from the trace
	$trace =~ s/(\n\s+\S+__ANON__[^\n]+)?\n\s+eval[^\n]+\n\s+Error::subs::try[^\n]+(?=\n)//sog;
	$trace =~ s/(\n\s+\S+__ANON__[^\n]+)?\n\s+eval[^\n]+\n\s+Error::subs::run_clauses[^\n]+\n\s+Error::subs::try[^\n]+(?=\n)//sog;
	$err->{'-stacktrace'} = $trace
    }

    $@ = $LAST = $ERROR{$pkg} = $err;
}

# Throw an error. this contains some very gory code.

sub throw {
    my $self = shift;
    local $Error::Depth = $Error::Depth + 1;

    # if we are not rethrow-ing then create the object to throw
    $self = $self->new(@_) unless ref($self);
    
    die $Error::THROWN = $self;
}

# syntactic sugar for
#
#    die with Error( ... );

sub with {
    my $self = shift;
    local $Error::Depth = $Error::Depth + 1;

    $self->new(@_);
}

# syntactic sugar for
#
#    record Error( ... ) and return;

sub record {
    my $self = shift;
    local $Error::Depth = $Error::Depth + 1;

    $self->new(@_);
}

# catch clause for
#
# try { ... } catch CLASS with { ... }

sub catch {
    my $pkg = shift;
    my $code = shift;
    my $clauses = shift || {};
    my $catch = $clauses->{'catch'} ||= [];

    unshift @$catch,  $pkg, $code;

    $clauses;
}

# Object query methods

sub object {
    my $self = shift;
    exists $self->{'-object'} ? $self->{'-object'} : undef;
}

sub file {
    my $self = shift;
    exists $self->{'-file'} ? $self->{'-file'} : undef;
}

sub line {
    my $self = shift;
    exists $self->{'-line'} ? $self->{'-line'} : undef;
}

sub text {
    my $self = shift;
    exists $self->{'-text'} ? $self->{'-text'} : undef;
}

# overload methods

sub stringify {
    my $self = shift;
    defined $self->{'-text'} ? $self->{'-text'} : "Died";
}

sub value {
    my $self = shift;
    exists $self->{'-value'} ? $self->{'-value'} : undef;
}

package Error::Simple;

@Error::Simple::ISA = qw(Error);

sub new {
    my $self  = shift;
    my $text  = "" . shift;
    my $value = shift;
    my(@args) = ();

    local $Error::Depth = $Error::Depth + 1;

    @args = ( -file => $1, -line => $2)
	if($text =~ s/ at (\S+) line (\d+)(\.\n)?$//s);

    push(@args, '-value', 0 + $value)
	if defined($value);

    $self->SUPER::new(-text => $text, @args);
}

sub stringify {
    my $self = shift;
    my $text = $self->SUPER::stringify;
    $text .= sprintf(" at %s line %d.\n", $self->file, $self->line)
	unless($text =~ /\n$/s);
    $text;
}

##########################################################################
##########################################################################

# Inspired by code from Jesse Glick  and
# Peter Seibel 

package Error::subs;

use Exporter ();
use vars qw(@EXPORT_OK @ISA %EXPORT_TAGS);

@EXPORT_OK   = qw(try with finally except otherwise);
%EXPORT_TAGS = (try => \@EXPORT_OK);

@ISA = qw(Exporter);

sub run_clauses ($$$\@) {
    my($clauses,$err,$wantarray,$result) = @_;
    my $code = undef;

    $err = new Error::Simple($err) unless ref($err);

    CATCH: {

	# catch
	my $catch;
	if(defined($catch = $clauses->{'catch'})) {
	    my $i = 0;

	    CATCHLOOP:
	    for( ; $i < @$catch ; $i += 2) {
		my $pkg = $catch->[$i];
		unless(defined $pkg) {
		    #except
		    splice(@$catch,$i,2,$catch->[$i+1]->());
		    $i -= 2;
		    next CATCHLOOP;
		}
		elsif($err->isa($pkg)) {
		    $code = $catch->[$i+1];
		    while(1) {
			my $more = 0;
			local($Error::THROWN);
			my $ok = eval {
			    if($wantarray) {
				@{$result} = $code->($err,\$more);
			    }
			    elsif(defined($wantarray)) {
			        @{$result} = ();
				$result->[0] = $code->($err,\$more);
			    }
			    else {
				$code->($err,\$more);
			    }
			    1;
			};
			if( $ok ) {
			    next CATCHLOOP if $more;
			    undef $err;
			}
			else {
			    $err = defined($Error::THROWN)
				    ? $Error::THROWN : $@;
			    $err = new Error::Simple($err)
				    unless ref($err);
			}
			last CATCH;
		    };
		}
	    }
	}

	# otherwise
	my $owise;
	if(defined($owise = $clauses->{'otherwise'})) {
	    my $code = $clauses->{'otherwise'};
	    my $more = 0;
	    my $ok = eval {
		if($wantarray) {
		    @{$result} = $code->($err,\$more);
		}
		elsif(defined($wantarray)) {
		    @{$result} = ();
		    $result->[0] = $code->($err,\$more);
		}
		else {
		    $code->($err,\$more);
		}
		1;
	    };
	    if( $ok ) {
		undef $err;
	    }
	    else {
		$err = defined($Error::THROWN)
			? $Error::THROWN : $@;
		$err = new Error::Simple($err)
			unless ref($err);
	    }
	}
    }
    $err;
}

sub try (&;$) {
    my $try = shift;
    my $clauses = @_ ? shift : {};
    my $ok = 0;
    my $err = undef;
    my @result = ();

    unshift @Error::STACK, $clauses;

    my $wantarray = wantarray();

    do {
	local $Error::THROWN = undef;

	$ok = eval {
	    if($wantarray) {
		@result = $try->();
	    }
	    elsif(defined $wantarray) {
		$result[0] = $try->();
	    }
	    else {
		$try->();
	    }
	    1;
	};

	$err = defined($Error::THROWN) ? $Error::THROWN : $@
	    unless $ok;
    };

    shift @Error::STACK;

    $err = run_clauses($clauses,$err,wantarray,@result)
	unless($ok);

    $clauses->{'finally'}->()
	if(defined($clauses->{'finally'}));

    throw $err if defined($err);

    wantarray ? @result : $result[0];
}

# Each clause adds a sub to the list of clauses. The finally clause is
# always the last, and the otherwise clause is always added just before
# the finally clause.
#
# All clauses, except the finally clause, add a sub which takes one argument
# this argument will be the error being thrown. The sub will return a code ref
# if that clause can handle that error, otherwise undef is returned.
#
# The otherwise clause adds a sub which unconditionally returns the users
# code reference, this is why it is forced to be last.
#
# The catch clause is defined in Error.pm, as the syntax causes it to
# be called as a method

sub with (&;$) {
    @_
}

sub finally (&) {
    my $code = shift;
    my $clauses = { 'finally' => $code };
    $clauses;
}

# The except clause is a block which returns a hashref or a list of
# key-value pairs, where the keys are the classes and the values are subs.

sub except (&;$) {
    my $code = shift;
    my $clauses = shift || {};
    my $catch = $clauses->{'catch'} ||= [];
    
    my $sub = sub {
	my $ref;
	my(@array) = $code->($_[0]);
	if(@array == 1 && ref($array[0])) {
	    $ref = $array[0];
	    $ref = [ %$ref ]
		if(UNIVERSAL::isa($ref,'HASH'));
	}
	else {
	    $ref = \@array;
	}
	@$ref
    };

    unshift @{$catch}, undef, $sub;

    $clauses;
}

sub otherwise (&;$) {
    my $code = shift;
    my $clauses = shift || {};

    if(exists $clauses->{'otherwise'}) {
	require Carp;
	Carp::croak("Multiple otherwise clauses");
    }

    $clauses->{'otherwise'} = $code;

    $clauses;
}

1;
__END__

=head1 NAME

Error - Error/exception handling in an OO-ish way

=head1 SYNOPSIS

    use Error qw(:try);

    throw Error::Simple( "A simple error");

    sub xyz {
        ...
	record Error::Simple("A simple error")
	    and return;
    }

    unlink($file) or throw Error::Simple("$file: $!",$!);

    try {
	do_some_stuff();
	die "error!" if $condition;
	throw Error::Simple -text => "Oops!" if $other_condition;
    }
    catch Error::IO with {
	my $E = shift;
	print STDERR "File ", $E->{'-file'}, " had a problem\n";
    }
    except {
	my $E = shift;
	my $general_handler=sub {send_message $E->{-description}};
	return {
	    UserException1 => $general_handler,
	    UserException2 => $general_handler
	};
    }
    otherwise {
	print STDERR "Well I don't know what to say\n";
    }
    finally {
	close_the_garage_door_already(); # Should be reliable
    }; # Don't forget the trailing ; or you might be surprised

=head1 DESCRIPTION

The C package provides two interfaces. Firstly C provides
a procedural interface to exception handling. Secondly C is a
base class for errors/exceptions that can either be thrown, for
subsequent catch, or can simply be recorded.

Errors in the class C should not be thrown directly, but the
user should throw errors from a sub-class of C.

=head1 PROCEDURAL INTERFACE

C exports subroutines to perform exception handling. These will
be exported if the C<:try> tag is used in the C line.

=over 4

=item try BLOCK CLAUSES

C is the main subroutine called by the user. All other subroutines
exported are clauses to the try subroutine.

The BLOCK will be evaluated and, if no error is throw, try will return
the result of the block.

C are the subroutines below, which describe what to do in the
event of an error being thrown within BLOCK.

=item catch CLASS with BLOCK

This clauses will cause all errors that satisfy C<$err-Eisa(CLASS)>
to be caught and handled by evaluating C.

C will be passed two arguments. The first will be the error
being thrown. The second is a reference to a scalar variable. If this
variable is set by the catch block then, on return from the catch
block, try will continue processing as if the catch block was never
found.

To propagate the error the catch block may call C<$err-Ethrow>

If the scalar reference by the second argument is not set, and the
error is not thrown. Then the current try block will return with the
result from the catch block.

=item except BLOCK

When C is looking for a handler, if an except clause is found
C is evaluated. The return value from this block should be a
HASHREF or a list of key-value pairs, where the keys are class names
and the values are CODE references for the handler of errors of that
type.

=item otherwise BLOCK

Catch any error by executing the code in C

When evaluated C will be passed one argument, which will be the
error being processed.

Only one otherwise block may be specified per try block

=item finally BLOCK

Execute the code in C either after the code in the try block has
successfully completed, or if the try block throws an error then
C will be executed after the handler has completed.

If the handler throws an error then the error will be caught, the
finally block will be executed and the error will be re-thrown.

Only one finally block may be specified per try block

=back

=head1 CLASS INTERFACE

=head2 CONSTRUCTORS

The C object is implemented as a HASH. This HASH is initialized
with the arguments that are passed to it's constructor. The elements
that are used by, or are retrievable by the C class are listed
below, other classes may add to these.

	-file
	-line
	-text
	-value
	-object

If C<-file> or C<-line> are not specified in the constructor arguments
then these will be initialized with the file name and line number where
the constructor was called from.

If the error is associated with an object then the object should be
passed as the C<-object> argument. This will allow the C package
to associate the error with the object.

The C package remembers the last error created, and also the
last error associated with a package. This could either be the last
error created by a sub in that package, or the last error which passed
an object blessed into that package as the C<-object> argument.

=over 4

=item throw ( [ ARGS ] )

Create a new C object and throw an error, which will be caught
by a surrounding C block, if there is one. Otherwise it will cause
the program to exit.

C may also be called on an existing error to re-throw it.

=item with ( [ ARGS ] )

Create a new C object and returns it. This is defined for
syntactic sugar, eg

    die with Some::Error ( ... );

=item record ( [ ARGS ] )

Create a new C object and returns it. This is defined for
syntactic sugar, eg

    record Some::Error ( ... )
	and return;

=back

=head2 STATIC METHODS

=over 4

=item prior ( [ PACKAGE ] )

Return the last error created, or the last error associated with
C

=back

=head2 OBJECT METHODS

=over 4

=item stacktrace

If the variable C<$Error::Debug> was non-zero when the error was
created, then C returns a string created by calling
C. If the variable was zero the C returns
the text of the error appended with the filename and line number of
where the error was created, providing the text does not end with a
newline.

=item object

The object this error was associated with

=item file

The file where the constructor of this error was called from

=item line

The line where the constructor of this error was called from

=item text

The text of the error

=back

=head2 OVERLOAD METHODS

=over 4

=item stringify

A method that converts the object into a string. This method may simply
return the same as the C method, or it may append more
information. For example the file name and line number.

By default this method returns the C<-text> argument that was passed to
the constructor, or the string C<"Died"> if none was given.

=item value

A method that will return a value that can be associated with the
error. For example if an error was created due to the failure of a
system call, then this may return the numeric value of C<$!> at the
time.

By default this method returns the C<-value> argument that was passed
to the constructor.

=back

=head1 PRE-DEFINED ERROR CLASSES

=over 4

=item Error::Simple

This class can be used to hold simple error strings and values. It's
constructor takes two arguments. The first is a text value, the second
is a numeric value. These values are what will be returned by the
overload methods.

If the text value ends with C as $@ strings do, then
this infomation will be used to set the C<-file> and C<-line> arguments
of the error object.

This class is used internally if an eval'd block die's with an error
that is a plain string.

=back

=head1 KNOWN BUGS

None, but that does not mean there are not any.

=head1 AUTHORS

Graham Barr, gbarr@pobox.com

The code that inspired me to write this was originally written by
Peter Seibel Epeter@weblogic.comE and adapted by Jesse Glick
Ejglick@sig.bsh.comE.

=head1 MAINTAINER

Arun Kumar U, u_arunkumar@yahoo.com

=cut
BioPerl-1.007002/travis_scripts000755000766000024          013155576322 16437 5ustar00cjfieldsstaff000000000000BioPerl-1.007002/travis_scripts/dependency_installs000555000766000024       100413155576322 22544 0ustar00cjfieldsstaff000000000000#!/bin/bash

mkdir travis_builds

cd travis_builds

# samtools
git clone https://github.com/samtools/samtools.git
cd samtools
git checkout tags/0.1.18
perl -p -i -e 's/^(CFLAGS=\s+)[^\n]*/$1-g -Wall -O2 -fPIC #-m64 #-arch ppc/' Makefile
make 2>&1 | tail -n 1
cd ..

# push Bio-Root to front
# git clone https://github.com/bioperl/Bio-Root.git
# export PERL5LIB=$( pwd )/Bio-Root/lib:$( pwd ):$PERL5LIB

export SAMTOOLS=$( pwd )/samtools

echo "Bio::DB::Sam installation"
cpanm Bio::DB::Sam 2>&1 | tail -n 10

exit 0
BioPerl-1.007002/travis_scripts/trigger-dockerhub.sh000555000766000024       356313155576322 22551 0ustar00cjfieldsstaff000000000000#!/bin/bash

set -e

# the Docker Hub API endpoint
dockerapi="https://registry.hub.docker.com/u/bioperl/bioperl/trigger"

## Travis runs a build for several versions of Perl, but we want to
## trigger only for the same version of Perl as is running in the
## Docker container
docker_perl="5.18"

if [[ ${TRAVIS_PERL_VERSION:0:4} != "$docker_perl" ]] ; then
    echo "Triggering Docker Hub only for Perl $docker_perl, not $TRAVIS_PERL_VERSION"
    exit 0
fi

if [[ "$TRAVIS_PULL_REQUEST" != "false" ]] ; then
    echo "Not triggering Docker Hub for pull requests."
    exit 0
fi

if [[ -z "$DOCKERHUB_TOKEN" ]] ; then
    echo "No API token for Docker Hub, add to repository settings."
    exit 1
fi

if [[ -n "$COVERAGE" && "$COVERAGE" != "0" ]] ; then
    echo "Not triggering Docker Hub for code coverage build."
    exit 0
fi

## Should check for tag names that indicate release candidates rather
## than release names, and then skip those.
## However, this is already taken care of by the regular expression
## for whitelisting branches.

if [[ -n "$TRAVIS_TAG" && "$TRAVIS_TAG" != "false" ]] ; then
    # if we are building a whitelisted tag, we trigger the stable image
    echo "Triggering rebuild of Docker image bioperl/bioperl:stable"
    curl -H "Content-Type: application/json" \
         --data '{"docker_tag": "stable"}' \
         -X POST $dockerapi/$DOCKERHUB_TOKEN/
elif [[ "$TRAVIS_BRANCH" != "master" ]] ; then
    # if someone were to create a branch that matches the whitelisting
    # pattern, we skip that here, and only trigger on master
    echo "Not triggering Docker Hub for branches other than master"
else
    # not a pull request, not a tag, and the branch is master
    echo "Triggering rebuild of Docker image bioperl/bioperl:latest"
    curl -H "Content-Type: application/json" \
         --data '{"docker_tag": "latest"}' \
         -X POST $dockerapi/$DOCKERHUB_TOKEN/
fi
    Method Class Returns Usage
    ", join( "", @columns ), "